# Supplementary Table summarizing all loci mentioned in the paper.
#
# Best viewed in a (very) wide-screen text editor.  This is a whitespace
# delimited file. Lines beginning with # are comments; anything after
# // on a data line is a comment; ignore blank lines.
#
# Fields:
#  1. Locus name.    "Distinct" loci are called "OncXX"; other loci in the same "quasiallelic" group are called "OncXX.y".
#  2. Start coord.   
#  3. End coord.     If start > end, locus is on Crick strand.
#  4. Source contig. A sequence name in the WGS+pilot dataset, all.fa. 
#  5. Stage.         Highest stage the contig reached in the screen: 0-5. 0=incomplete contigs in WGS+pilot; 1-5 = Stage1..Stage5 datasets.
#  6. Locus type.    Semi-controlled classification vocabulary: U2_snRNA or C/D_snoRNA, for example.
#  7. Length.        Length of the locus in nt.
#  8. Experiments.   N = size, expression confirmed on Northern;  R = size, expression, ends confirmed by overlapping 5',3' RACE-PCRs. N,R=both .=neither.
#  9. Self BLAST.    Closest related locus, other than the unique locus defining each quasiallelic group: <% id>|<coverage in nt>|<name>
# 10. Stylonychia.   Homologous BLASTN alignment in Stylonychia shotgun dataset. <E-value>|<% id>|<coverage in nt>|<name>
# 11. Upstream.      BLASTN of 100nt upstream back to WGS+pilot; used to cluster quasiallelic groups
# 12. Downstream.    BLASTN of 100nt downstream back to WGS+pilot; used to cluster quasiallelic groups
# 13. BLASTX/NR      For subset of Stage>=1, Rfam-detected contigs in Table1: X=contig has BLASTX hit in NR protein db
# 14. BLASTN/Sty     For subset of Stage>=1, Rfam-detected contigs in Table1: N=contig has another BLASTN hit in Sty, other than the ncRNA locus itself
# 15. Nanogf         For subset of Stage>=1, Rfam-detected contigs in Table1: G=contig classified as coding by the nanoclassifier.
#
# Although the OncXX numbering goes to Onc154, the numbers are not all
# used (there are not 154 distinct loci in this file). The assignment
# of "distinct loci" is subjective, and we rearranged it late in our
# analysis when we realized there's a pretty clear pattern of up to
# four "alleles" per quasiallelic group - suggesting that the
# macronuclear genome is tetraploid. This converted many loci from
# "distinct" to "quasialleles", and these are noted in comments (so we
# can backtrack in our notebooks).
#
# Also, the OncXX numbers aren't consecutive in this file. OncXX
# numbers were assigned as we discovered new loci, whereas this file
# is arranged into sensible sections: tRNAs, rRNAs, miscRNAs, snRNAs,
# snoRNAs, and finally the "novel" candidates identified by the
# nanogenefinder screen.
#
# Cross-references such as [xref SRE:0122-oxy-snRNAs] refer to
# personal electronic notebook pages; copies are available upon
# request.
#
# Perl scripts we used for producing, formatting, processing this file
# (a "tbl" file) are available upon request.
#
# SRE, Wed Mar 24 09:05:20 2010

################################################################
## tRNAs
##
## All identified by Rfam RF00005 model, E<=0.001, in Stage1 dataset.
## We did not include tRNAs in WGS+pilot data. tRNA data was only used
## for Table1, where we studied only the Stage1 dataset. Also, there
## appear to be many bacterial tRNA genes in the incomplete contigs,
## which would have been difficult to distinguish.
##
Onc1      377   449  Contig19117.1    4  tRNA(Asn,GTT)  73nt  .  Rfam:RF00005:1e-13  100%|73|Onc2   5e-26|97%|73|contig49842   100%|100|Contig74674.2    100%|100|Contig74674.2    .  .  .  
Onc1.2    324   396  Contig74674.2    4  tRNA(Asn,GTT)  73nt  .  Rfam:RF00005:1e-13  100%|73|Onc1   5e-26|97%|73|contig49842   100%|100|Contig19117.1    100%|100|Contig19117.1    .  .  .  

Onc2      701   629  Contig76935.2    1  tRNA(Asn,GTT)  73nt  .  Rfam:RF00005:1e-13  100%|73|Onc1   5e-26|97%|73|contig49842   -                         -                         .  .  G  
		                     
Onc3      259   188  Contig200270     4  tRNA(Lys,TTT)  72nt  N  Rfam:RF00005:4e-14  87%|72|Onc7    2e-27|100%|72|contig05384  98%|100|Contig53310.1     100%|100|Contig53310.1    .  .  .  
Onc3.2    265   194  Contig40129.1    4  tRNA(Lys,TTT)  72nt  n  Rfam:RF00005:4e-14  100%|72|Onc3   2e-27|100%|72|contig05384  99%|100|Contig53310.1     100%|100|Contig200270     .  .  G   // was Onc4
Onc3.3    257   186  Contig53310.1    4  tRNA(Lys,TTT)  72nt  n  Rfam:RF00005:4e-14  100%|72|Onc3   2e-27|100%|72|contig05384  99%|100|Contig40129.1     100%|100|Contig200270     .  .  G   // was Onc5
		                     
Onc53     176   248  OXAO-aab15f07    4  tRNA(Lys,CTT)  73nt  N  Rfam:RF00005:5e-13  100%|73|Onc8   5e-26|97%|73|contig51700   100%|100|Contig35865.1    100%|100|Contig35865.1    .  .  G  
Onc53.2   229   301  Contig35865.1    1  tRNA(Lys,CTT)  73nt  n  Rfam:RF00005:5e-13  100%|73|Onc53  5e-26|97%|73|contig51700   100%|100|OXAO-aab15f07    100%|100|OXAO-aab15f07    .  .  G   // was Onc6
Onc53.3  1184  1112  OXAO-aab17e12    1  tRNA(Lys,CTT)  73nt  n  Rfam:RF00005:5e-13  100%|73|Onc53  5e-26|97%|73|contig51700   97%|100|OXAO-aab15f07     96%|100|OXAO-aab15f07     .  .  G   // was Onc54

Onc7      381   453  Contig38385.1    1  tRNA(Lys,CTT)  73nt  n  Rfam:RF00005:5e-13  100%|73|Onc8   5e-26|97%|73|contig51700   100%|100|Contig91659      100%|100|Contig91659      .  .  G   // 100%id to Onc53, so Onc53 Northern crosses
Onc7.2    188   260  Contig91659      1  tRNA(Lys,CTT)  73nt  n  Rfam:RF00005:5e-13  100%|73|Onc7   5e-26|97%|73|contig51700   100%|100|Contig38385.1    100%|100|Contig38385.1    .  .  G  

Onc8      607   535  Contig42095.1    1  tRNA(Lys,CTT)  73nt  n  Rfam:RF00005:5e-13  100%|73|Onc7   5e-26|97%|73|contig51700   100%|100|UGC1O0003_C05_F  100%|100|UGC1O0003_C05_F  .  .  G   // 100%id to Onc53, so Onc53 Northern crosses
Onc8.2    197   269  UGC1O0003_C05_F  1  tRNA(Lys,CTT)  73nt  n  Rfam:RF00005:5e-13  100%|73|Onc8   5e-26|97%|73|contig51700   100%|100|Contig42095.1    100%|100|Contig42095.1    .  .  G   // was Onc55

Onc9      451   524  Contig201758     4  tRNA(Val,AAC)  74nt  .  Rfam:RF00005:8e-12  77%|59|Onc58   2e-21|92%|74|contig53388   99%|100|OXAC-aaa03e08     100%|100|OXAC-aaa03e08    .  .  .  
Onc9.2    619   546  OXAC-aaa03e08    4  tRNA(Val,AAC)  74nt  .  Rfam:RF00005:8e-12  100%|74|Onc9   2e-21|92%|74|contig53388   99%|100|Contig201758      100%|100|Contig201758     .  .  .   // was Onc10
		                     
Onc11     266   194  Contig82806.1    1  tRNA(Val,TAC)  73nt  .  Rfam:RF00005:9e-14  82%|58|Onc28   8e-27|98%|73|contig04864   -                         -                         X  N  G  
		                     
Onc12    2257  2185  Contig75612.1    1  tRNA(Val,CAC)  73nt  .  Rfam:RF00005:7e-11  77%|57|Onc31   5e-28|100%|73|contig51933  89%|100|Contig81063.2     96%|100|Contig81063.2     X  N  G  
Onc12.2  2259  2187  Contig81063.2    1  tRNA(Val,CAC)  73nt  .  Rfam:RF00005:7e-11  100%|73|Onc12  5e-28|100%|73|contig51933  89%|100|Contig75612.1     96%|100|Contig75612.1     X  N  G  
		                     
Onc13     433   363  Contig202880     4  tRNA(Gln,CTG)  71nt  .  Rfam:RF00005:3e-13  84%|62|Onc39   5e-26|98%|71|contig05180   100%|100|Contig76779.1    100%|100|Contig76779.1    .  .  .  
Onc13.2   423   353  Contig76779.1    4  tRNA(Gln,CTG)  71nt  .  Rfam:RF00005:3e-13  100%|71|Onc13  5e-26|98%|71|contig05180   100%|100|Contig202880     100%|100|Contig202880     .  .  .  
Onc13.3   492   422  Contig82969.1    4  tRNA(Gln,CTG)  71nt  .  Rfam:RF00005:3e-13  100%|71|Onc13  5e-26|98%|71|contig05180   98%|100|Contig202880      96%|100|Contig202880      .  .  .  
		                     
Onc14     248   177  Contig78714.1    1  tRNA(Gln,TTG)  72nt  .  Rfam:RF00005:3e-14  -              3e-25|97%|72|contig53736   99%|100|Contig79809.1     99%|100|Contig79809.1     X  N  G  
Onc14.2   302   231  Contig79809.1    1  tRNA(Gln,TTG)  72nt  .  Rfam:RF00005:3e-14  100%|72|Onc14  3e-25|97%|72|contig53736   99%|100|Contig78714.1     99%|100|Contig78714.1     X  N  G  
		                     
Onc15    1064  1134  Contig42065.1    1  tRNA(Gln,CTA)  71nt  .  Rfam:RF00005:3e-12  81%|69|Onc39   5e-27|100%|71|contig41303  95%|100|Contig50398.1     98%|100|Contig50398.1     .  .  G  
Onc15.2  1064  1134  Contig50398.1    1  tRNA(Gln,CTA)  71nt  .  Rfam:RF00005:5e-12  98%|71|Onc15   5e-26|98%|71|contig41303   95%|100|Contig42065.1     98%|100|Contig42065.1     .  .  G  
		                    
Onc39     243   172  OXAD-aaa02e11    4  tRNA(Gln,TTA)  72nt  .  Rfam:RF00005:3e-14  81%|70|Onc15   2e-26|98%|72|contig00104   100%|100|OXAD-aaa04h06    100%|100|OXAD-aaa04h06    .  .  .  
Onc39.2   243   172  OXAD-aaa04h06    4  tRNA(Gln,TTA)  72nt  .  Rfam:RF00005:3e-14  100%|72|Onc39  2e-26|98%|72|contig00104   100%|100|OXAD-aaa02e11    100%|100|OXAD-aaa02e11    .  .  .  
 
Onc16     419   490  Contig35667.1    4  tRNA(Gly,TCC)  72nt  n  Rfam:RF00005:2e-13  100%|72|Onc17  5e-26|100%|69|contig08324  100%|100|OXAE-aad39c12    100%|100|OXAE-aad39c12    .  .  .  // 100% id to Onc17, so Onc17 Northern crosses.
Onc16.2   232   303  OXAE-aad39c12    4  tRNA(Gly,TCC)  72nt  n  Rfam:RF00005:2e-13  100%|72|Onc16  5e-26|100%|69|contig08324  100%|100|UGC1O0005_L02_F  100%|100|UGC1O0005_L02_F  .  .  .  
Onc16.3   224   295  UGC1O0005_L02_F  4  tRNA(Gly,TCC)  72nt  n  Rfam:RF00005:2e-13  100%|72|Onc16  5e-26|100%|69|contig08324  100%|100|OXAE-aad39c12    100%|100|OXAE-aad39c12    .  .  .  

Onc17     458   529  Contig72578.1    4  tRNA(Gly,TCC)  72nt  N  Rfam:RF00005:2e-13  100%|72|Onc16  5e-26|100%|69|contig08324  100%|100|Contig72585.2    100%|100|Contig72585.2    .  .  .  
Onc17.2   442   513  Contig72585.2    4  tRNA(Gly,TCC)  72nt  n  Rfam:RF00005:2e-13  100%|72|Onc17  5e-26|100%|69|contig08324  100%|100|Contig72578.1    100%|100|Contig72578.1    .  .  .  
Onc17.3   375   446  Contig72592.3    4  tRNA(Gly,TCC)  72nt  n  Rfam:RF00005:2e-13  100%|72|Onc17  5e-26|100%|69|contig08324  100%|100|Contig72585.2    100%|100|Contig72585.2    .  .  .  
		                     
Onc18     617   547  Contig38449.1    4  tRNA(Gly,GCC)  71nt  .  Rfam:RF00005:4e-12  95%|23|Onc58   7e-25|97%|71|contig04084   97%|100|OXAO-aaa61c10     97%|100|Contig93074       .  .  .  
Onc18.2   388   458  OXAO-aaa61c10    4  tRNA(Gly,GCC)  71nt  .  Rfam:RF00005:4e-12  100%|71|Onc18  7e-25|97%|71|contig04084   100%|100|Contig93074      96%|97|Contig93074        .  .  .   // was Onc19
Onc18.3   196   126  Contig93074      1  tRNA(Gly,GCC)  71nt  .  Rfam:RF00005:4e-12  100%|71|Onc18  7e-25|97%|71|contig04084   100%|100|OXAO-aaa61c10    97%|100|Contig38449.1     .  .  G   // was Onc19.2
		                     
Onc20     367   439  Contig41931.1    4  tRNA(Thr,AGT)  73nt  .  Rfam:RF00005:1e-11  77%|72|Onc2    9e-26|97%|73|contig06216   -                         -                         .  .  .  
		                     
Onc21     206   135  OXAB-aaa03d02    1  tRNA(Thr,TGT)  72nt  .  Rfam:RF00005:5e-14  78%|70|Onc3    3e-25|97%|72|contig52602   85%|99|Contig36821.1      100%|100|Contig36821.1    X  N  G  
Onc21.2   989  1060  Contig36821.1    1  tRNA(Thr,TGT)  72nt  .  Rfam:RF00005:5e-14  100%|50|Onc21  1e-19|96%|60|contig52602   92%|95|OXAB-aaa03d02      97%|92|OXAB-aaa03d02      X  N  G   // was Onc22
		                     
Onc23     230   159  Contig42299.1    4  tRNA(Met,CAT)  72nt  .  Rfam:RF00005:5e-10  -              2e-27|100%|72|contig07836  97%|100|OXAO-aab16f12     100%|99|OXAO-aab16f12     .  .  .  
Onc23.2   216   145  OXAO-aab16f12    4  tRNA(Met,CAT)  72nt  .  Rfam:RF00005:5e-10  100%|72|Onc23  2e-27|100%|72|contig07836  97%|100|Contig42299.1     100%|99|Contig42299.1     .  .  .  
Onc23.3   233   162  Contig42454.1    4  tRNA(Met,CAT)  72nt  .  Rfam:RF00005:5e-10  100%|72|Onc23  2e-27|100%|72|contig07836  97%|100|OXAO-aab16f12     97%|100|OXAO-aab16f12     .  .  .  
		                     
Onc24     221   293  Contig78307.1    1  tRNA(Met,CAT)  73nt  .  Rfam:RF00005:4e-12  78%|54|Onc36   9e-26|97%|73|contig03923   -                         -                         X  N  G  
		                     
Onc25     192   120  Contig44069.1    4  tRNA(Ala,AGC)  73nt  .  Rfam:RF00005:1e-09  100%|73|Onc26  5e-26|97%|73|contig51118   99%|100|OXAE-aae01d07     97%|100|Contig44272.1     .  .  .  
Onc25.2   737   809  Contig44272.1    4  tRNA(Ala,AGC)  73nt  .  Rfam:RF00005:1e-09  100%|73|Onc25  5e-26|97%|73|contig51118   100%|100|OXAE-aae01d07    97%|100|Contig44069.1     .  .  .  
Onc25.3   176   104  OXAE-aae01d07    4  tRNA(Ala,AGC)  73nt  .  Rfam:RF00005:1e-09  100%|73|Onc25  5e-26|97%|73|contig51118   100%|100|Contig44272.1    97%|100|Contig44272.1     .  .  .  
Onc25.4   724   796  OXAC-aaa08h01    4  tRNA(Ala,AGC)  73nt  .  Rfam:RF00005:1e-09  100%|73|Onc25  5e-26|97%|73|contig51118   97%|100|Contig44069.1     96%|100|Contig44272.1     .  .  .  
		                     
Onc26     185   113  Contig202071     1  tRNA(Ala,AGC)  73nt  .  Rfam:RF00005:1e-09  100%|73|Onc25  5e-26|97%|73|contig51118   93%|100|Contig7063.1      96%|90|Contig7063.1       .  .  G  
Onc26.2  2253  2181  Contig7063.1     1  tRNA(Ala,AGC)  73nt  .  Rfam:RF00005:1e-09  100%|73|Onc26  5e-26|97%|73|contig51118   93%|100|Contig202071      96%|90|Contig202071       X  N  G   // was Onc27
		                     
Onc28     210   281  Contig83003.1    1  tRNA(Ala,TGC)  72nt  .  Rfam:RF00005:5e-13  94%|72|Onc29   2e-27|100%|72|contig00029  98%|100|Contig83010.2     93%|100|Contig83010.2     X  N  G  
Onc28.2   252   323  Contig83010.2    1  tRNA(Ala,TGC)  72nt  .  Rfam:RF00005:5e-13  100%|72|Onc28  2e-27|100%|72|contig00029  98%|100|Contig83003.1     93%|100|Contig83003.1     X  N  G  
		                     
Onc29    1032   961  Contig56335.1    1  tRNA(Ala,CGC)  72nt  .  Rfam:RF00005:8e-13  94%|72|Onc28   4e-23|94%|72|contig00029   91%|98|Contig57947.1      95%|100|Contig57947.1     X  N  G  
Onc29.2   193   264  Contig57947.1    1  tRNA(Ala,CGC)  72nt  .  Rfam:RF00005:8e-13  100%|72|Onc29  4e-23|94%|72|contig00029   91%|99|Contig56335.1      95%|100|Contig56335.1     X  N  G   // was Onc30
		                     
Onc31     655   727  Contig50209.1    4  tRNA(Pro,TGG)  73nt  .  Rfam:RF00005:2e-09  85%|69|Onc34   7e-28|100%|73|contig00434  93%|100|OXAO-aab17f04     94%|90|OXAO-aab17f04      .  .  .  
Onc31.2   183   111  OXAO-aab17f04    4  tRNA(Pro,TGG)  73nt  .  Rfam:RF00005:2e-09  100%|73|Onc31  7e-28|100%|73|contig00434  93%|100|Contig50209.1     94%|90|Contig50209.1      .  .  .   // was Onc32
Onc31.3   183   111  OXAD-aaa08e07    4  tRNA(Pro,TGG)  73nt  .  Rfam:RF00005:2e-09  100%|73|Onc31  7e-28|100%|73|contig00434  94%|35|OXAO-aab17f04      84%|31|Contig36615.1      .  .  .   // was Onc33

Onc34    1363  1434  Contig63474.1    4  tRNA(Pro,AGG)  72nt  .  Rfam:RF00005:2e-09  88%|72|Onc35   3e-25|97%|72|contig11019   -                         -                         .  .  .  
		                     
Onc35    3309  3238  Contig53709.1    1  tRNA(Pro,CGG)  72nt  .  Rfam:RF00005:4e-11  88%|72|Onc34   3e-25|97%|72|contig05046   -                         -                         X  N  G  
		                     
Onc36     662   590  Contig67238.1    4  tRNA(Phe,GAA)  73nt  .  Rfam:RF00005:6e-12  78%|54|Onc24   4e-27|98%|73|contig50888   -                         -                         .  .  G  
		                     
Onc37     234   162  Contig71359.1    4  tRNA(Arg,TCT)  73nt  N  Rfam:RF00005:2e-12  71%|61|Onc38   6e-28|100%|73|contig53118  98%|100|Contig79483.1     100%|100|Contig79483.1    .  .  .  
Onc37.2   226   154  Contig79483.1    4  tRNA(Arg,TCT)  73nt  n  Rfam:RF00005:2e-12  100%|73|Onc37  6e-28|100%|73|contig53118  99%|100|OXAD-aaa04e08     100%|100|Contig71359.1    .  .  G  
Onc37.3   815   887  Contig77349.1    4  tRNA(Arg,TCT)  73nt  n  Rfam:RF00005:2e-12  100%|73|Onc37  6e-28|100%|73|contig53118  100%|100|OXAD-aaa04e08    99%|100|Contig79483.1     .  .  .  
Onc37.4   211   139  OXAD-aaa04e08    4  tRNA(Arg,TCT)  73nt  n  Rfam:RF00005:2e-12  100%|73|Onc37  6e-28|100%|73|contig53118  100%|100|Contig77349.1    98%|100|Contig77349.1     .  .  .  
		                     
Onc38    6108  6180  Contig45919.1    1  tRNA(Arg,CCT)  73nt  .  Rfam:RF00005:6e-13  71%|61|Onc37   7e-28|100%|73|contig53580  -                         -                         X  N  G  
		                     
Onc40     284   213  Contig50373.1    1  tRNA(Cys,GCA)  72nt  .  Rfam:RF00005:1e-13  80%|54|Onc21   5e-20|90%|72|contig53660   98%|100|Contig79368.1     99%|100|Contig79368.1     .  .  G  
Onc40.2   292   221  Contig79368.1    1  tRNA(Cys,GCA)  72nt  .  Rfam:RF00005:1e-13  100%|72|Onc40  5e-20|90%|72|contig53660   98%|100|Contig50373.1     99%|100|Contig50373.1     .  N  G  
		                     
Onc41     204   132  OXAE-aaa18e02    4  tRNA(Ile,AAT)  73nt  .  Rfam:RF00005:2e-13  78%|63|Onc21   5e-28|100%|73|contig50916  100%|100|OXAD-aaa01f07    90%|100|OXAD-aaa01f07     .  .  G  
Onc41.2   616   688  OXAD-aaa01f07    1  tRNA(Ile,AAT)  73nt  .  Rfam:RF00005:2e-13  100%|73|Onc41  5e-28|100%|73|contig50916  100%|100|OXAD-aaa07f12    99%|100|UGC1O0003_P04_R   .  .  G  
Onc41.3   186   114  OXAD-aaa07f12    1  tRNA(Ile,AAT)  73nt  .  Rfam:RF00005:2e-13  100%|73|Onc41  5e-28|100%|73|contig50916  100%|100|OXAD-aaa01f07    97%|93|UGC1O0003_P04_R    .  .  G  
Onc41.4   228   156  UGC1O0003_P04_R  4  tRNA(Ile,AAT)  73nt  .  Rfam:RF00005:2e-13  100%|73|Onc41  5e-28|100%|73|contig50916  96%|100|OXAD-aaa01f07     99%|100|OXAD-aaa01f07     .  .  .   // was Onc42
		                     
Onc43    3333  3405  Contig2009.1     1  tRNA(Ile,TAT)  73nt  .  Rfam:RF00005:6e-14  87%|24|Onc11   7e-28|100%|73|contig04572  -                         -                         X  N  G  
		                     
Onc44     246   167  OXAE-aad49e12    4  tRNA(Leu,AAG)  80nt  .  Rfam:RF00005:4e-11  92%|80|Onc48   3e-31|100%|80|contig05181  98%|100|UGC1O0002_B18_R   98%|100|UGC1O0002_B18_R   .  .  .  
Onc44.2   255   176  UGC1O0002_B18_R  4  tRNA(Leu,AAG)  80nt  .  Rfam:RF00005:4e-11  100%|80|Onc44  3e-31|100%|80|contig05181  98%|100|OXAE-aad49e12     98%|100|OXAE-aad49e12     .  .  .   // was Onc45
		                     
Onc46     231   148  OXAE-aad58g07    1  tRNA(Leu,CAA)  84nt  .  Rfam:RF00005:5e-11  79%|72|Onc44   8e-29|95%|84|contig49729   92%|100|OXAD-aaa01e03     87%|88|OXAD-aaa01e03      .  .  G  
Onc46.2   921  1004  OXAD-aaa01e03    1  tRNA(Leu,CAA)  84nt  .  Rfam:RF00005:5e-11  100%|84|Onc46  8e-29|95%|84|contig49729   92%|100|OXAE-aad58g07     87%|88|OXAE-aad58g07      .  .  G   // was Onc47
		                     
Onc48    2804  2725  Contig81525.1    1  tRNA(Leu,CAG)  80nt  .  Rfam:RF00005:1e-11  92%|80|Onc44   6e-27|95%|80|contig00254   -                         -                         X  N  G  
		                     
Onc49    2298  2215  Contig41162.1    1  tRNA(Leu,TAA)  84nt  .  Rfam:RF00005:4e-10  -              8e-29|95%|84|contig04717   97%|100|Contig60633.1     98%|100|Contig60633.1     X  N  G  
Onc49.2  1911  1828  Contig60633.1    1  tRNA(Leu,TAA)  84nt  .  Rfam:RF00005:4e-10  100%|84|Onc49  8e-29|95%|84|contig04717   97%|100|Contig41162.1     98%|100|Contig41162.1     X  N  G  
		                     
Onc50     207   122  OXAO-aaa58g12    4  tRNA(Tyr,GTA)  86nt  .  Rfam:RF00005:1e-09  91%|23|Onc20   2e-23|88%|86|contig36076   100%|100|Contig66860.1    94%|84|Contig66860.1      .  .  .  
Onc50.2   201   116  UGC1O0001_O16_R  4  tRNA(Tyr,GTA)  86nt  .  Rfam:RF00005:1e-09  100%|86|Onc50  2e-23|88%|86|contig36076   97%|100|OXAO-aaa58g12     98%|100|Contig66860.1     .  .  .   // was Onc51
Onc50.3   246   161  Contig66860.1    1  tRNA(Tyr,GTA)  86nt  .  Rfam:RF00005:1e-09  100%|86|Onc50  2e-23|88%|86|contig36076   100%|100|OXAO-aaa58g12    98%|100|UGC1O0001_O16_R   X  N  G   // was Onc52
		                     
Onc56     180   252  OXAO-aab16e01    4  tRNA(Glu,TTC)  73nt  .  Rfam:RF00005:3e-10  100%|73|Onc57  7e-28|100%|73|contig53698  99%|100|OXAO-aab16g01     100%|100|OXAO-aab16d08    .  .  G  
Onc56.2   806   733  OXAO-aab16g01    1  tRNA(Glu,TTC)  74nt  .  Rfam:RF00005:4e-10  98%|74|Onc56   1e-26|98%|74|contig53698   99%|100|OXAO-aab16e01     100%|100|OXAO-aab16d08    .  .  G  

Onc57     307   379  Contig42902.1    1  tRNA(Glu,TTC)  73nt  .  Rfam:RF00005:3e-10  100%|73|Onc56  7e-28|100%|73|contig53698  97%|100|Contig47833.1     93%|97|Contig47833.1      X  N  G  
Onc57.2   207   279  Contig47833.1    1  tRNA(Glu,TTC)  73nt  .  Rfam:RF00005:3e-10  100%|73|Onc57  7e-28|100%|73|contig53698  97%|100|Contig42902.1     93%|96|Contig42902.1      X  N  G  
Onc57.3   256   328  Contig61332.1    1  tRNA(Glu,TTC)  73nt  .  Rfam:RF00005:3e-10  100%|73|Onc57  7e-28|100%|73|contig53698  96%|100|Contig47833.1     91%|100|Contig42902.1     X  N  G  
		                     
Onc58     204   132  OXAE-aaa06f08    1  tRNA(Glu,CTC)  73nt  .  Rfam:RF00005:5e-12  100%|73|Onc60  8e-26|97%|73|contig00331   96%|100|UGC1O0002_B22_R   91%|100|UGC1O0002_B22_R   .  N  G  
Onc58.2   211   139  UGC1O0002_B22_R  1  tRNA(Glu,CTC)  73nt  .  Rfam:RF00005:5e-12  100%|73|Onc58  8e-26|97%|73|contig00331   96%|100|OXAE-aaa06f08     91%|100|OXAE-aaa06f08     .  N  G   // was Onc59
		                     
Onc60     174   246  Contig44957.1    1  tRNA(Glu,CTC)  73nt  .  Rfam:RF00005:5e-12  100%|73|Onc58  8e-26|97%|73|contig00331   -                         -                         .  N  G  
		                     
Onc61     199   128  OXAE-aaf79d05    4  tRNA(Asp,GTC)  72nt  .  Rfam:RF00005:2e-12  100%|72|Onc63  2e-27|100%|72|contig51238  100%|100|OXAO-aab15d01    93%|99|OXAO-aab15d01      .  N  .  
Onc61.2   499   570  OXAO-aab15d01    4  tRNA(Asp,GTC)  72nt  .  Rfam:RF00005:2e-12  100%|72|Onc61  2e-27|100%|72|contig51238  100%|100|OXAE-aaf79d05    93%|98|OXAE-aaf79d05      .  N  .   // was Onc62
		                     
Onc63     276   205  Contig52579.1    1  tRNA(Asp,GTC)  72nt  .  Rfam:RF00005:2e-12  100%|72|Onc61  2e-27|100%|72|contig51238  97%|98|Contig74115.1      98%|100|Contig74115.1     X  N  G  
Onc63.2   220   149  Contig74115.1    1  tRNA(Asp,GTC)  72nt  .  Rfam:RF00005:2e-12  100%|72|Onc63  2e-27|100%|72|contig51238  97%|98|Contig52579.1      98%|100|Contig52579.1     X  N  G   // was Onc64
		                     
Onc65    1082  1011  OXAE-aaa29d04    1  tRNA(His,GTG)  72nt  .  Rfam:RF00005:3e-11  100%|72|Onc67  2e-25|97%|72|contig04726   100%|100|Contig51714.1    100%|100|Contig51714.1    X  N  G  
Onc65.2  2271  2200  Contig51714.1    1  tRNA(His,GTG)  72nt  .  Rfam:RF00005:3e-11  100%|72|Onc65  2e-25|97%|72|contig04726   100%|100|OXAE-aaa29d04    100%|100|OXAE-aaa29d04    X  N  G  
Onc65.3  2253  2182  Contig73221.2    1  tRNA(His,GTG)  72nt  .  Rfam:RF00005:3e-11  100%|72|Onc65  2e-25|97%|72|contig04726   86%|98|OXAE-aaa29d04      98%|100|OXAE-aaa29d04     X  N  G   // was Onc66

Onc67    1214  1143  Contig37344.1    1  tRNA(His,GTG)  72nt  .  Rfam:RF00005:3e-11  100%|72|Onc65  2e-25|97%|72|contig04726   -                         -                         .  .  G  
		                     
Onc68    2162  2082  Contig47137.1    1  tRNA(Ser,AGA)  81nt  .  Rfam:RF00005:5e-12  89%|75|Onc70   1e-31|100%|81|contig05316  96%|100|Contig76987.1     97%|100|Contig76987.1     X  N  G  
Onc68.2  2155  2075  Contig76987.1    1  tRNA(Ser,AGA)  81nt  .  Rfam:RF00005:5e-12  100%|81|Onc68  1e-31|100%|81|contig05316  96%|100|Contig47137.1     97%|100|Contig47137.1     X  N  G  
		                     
Onc69    2304  2386  Contig74257.1    1  tRNA(Ser,GCT)  83nt  .  Rfam:RF00005:3e-11  76%|83|Onc68   1e-32|100%|83|contig06989  100%|100|Contig84423.1    90%|100|Contig84423.1     X  N  G  
Onc69.2  2293  2375  Contig84423.1    1  tRNA(Ser,GCT)  83nt  .  Rfam:RF00005:3e-11  100%|83|Onc69  1e-32|100%|83|contig06989  100%|100|Contig74257.1    90%|100|Contig74257.1     X  N  G  
		                     
Onc70     312   393  Contig35394.1    1  tRNA(Ser,TGA)  82nt  .  Rfam:RF00005:2e-10  89%|76|Onc68   4e-31|98%|82|contig49785   96%|100|Contig37182.1     85%|100|Contig37182.1     .  .  G  
Onc70.2  1744  1663  Contig37182.1    1  tRNA(Ser,TGA)  82nt  .  Rfam:RF00005:2e-10  100%|82|Onc70  4e-31|98%|82|contig49785   96%|100|Contig35394.1     85%|100|Contig35394.1     .  .  G   // was Onc71
		                     
Onc72     244   316  Contig41301.1    1  tRNA(Trp,CCA)  73nt  .  Rfam:RF00005:8e-12  -              4e-28|100%|73|contig50873  96%|100|Contig85126.1     98%|100|Contig85126.1     X  N  G  
Onc72.2   240   312  Contig85126.1    1  tRNA(Trp,CCA)  73nt  .  Rfam:RF00005:8e-12  100%|73|Onc72  4e-28|100%|73|contig50873  96%|100|Contig41301.1     98%|100|Contig41301.1     X  N  G   // was Onc73
		                     
Onc74     192   262  Contig72432.1    1  tRNA(Undet)    71nt  .  Rfam:RF00005:1e-06  90%|71|Onc63   2e-19|90%|71|contig51238   -                         -                         X  N  G  

################################################################
# rRNAs
#
# As with tRNAs and for the same reasons, rRNAs are only annotated
# for the Stage1 dataset of complete nanochromosomes, not the entire
# WGS+pilot dataset.
#
# comparative analysis: [xref sre:0222-more-homologs]
#

## 5S rRNA
Onc75      441   323  Contig350.1      4  5S_rRNA    119nt   .  Rfam:RF00001:3e-23  .               2e-43|94%|119|contig07472   100%|100|OXAO-aab14b11  100%|100|UGC1O0003_F04_R  .  .  .   // polIIIterm
Onc75.2    462   580  Contig73674.2    4  5S_rRNA    119nt   .  Rfam:RF00001:3e-23  100%|119|Onc75  2e-43|94%|119|contig07472   100%|100|OXAO-aab14b11  100%|100|UGC1O0003_F04_R  .  .  .   // was Onc75.1
Onc75.3    427   309  UGC1O0003_F04_R  4  5S_rRNA    119nt   .  Rfam:RF00001:3e-23  100%|119|Onc75  2e-43|94%|119|contig07472   99%|100|OXAO-aab14b11   100%|100|Contig73674.2    .  .  .   // was Onc75.2
Onc75.4    429   311  Contig45583.1    4  5S_rRNA    119nt   .  Rfam:RF00001:3e-23  100%|119|Onc75  2e-43|94%|119|contig07472   100%|100|OXAO-aab14b11  100%|100|Contig56473.2    .  .  .   // was Onc76.1
Onc75.5    670   552  Contig45590.2    4  5S_rRNA    119nt   .  Rfam:RF00001:3e-23  100%|119|Onc75  2e-43|94%|119|contig07472   100%|100|OXAO-aab14b11  100%|100|Contig45583.1    .  .  .   // was Onc76.1
Onc75.6    438   320  Contig56466.1    4  5S_rRNA    119nt   .  Rfam:RF00001:3e-23  100%|119|Onc75  2e-43|94%|119|contig07472   100%|100|OXAO-aab14b11  100%|100|Contig45583.1    .  .  .   // was Onc76.1
Onc75.7    660   542  Contig56473.2    4  5S_rRNA    119nt   .  Rfam:RF00001:3e-23  100%|119|Onc75  2e-43|94%|119|contig07472   100%|100|OXAO-aab14b11  100%|100|Contig45583.1    .  .  .   // was Onc76.1
Onc75.8    458   576  Contig37908.2    4  5S_rRNA    119nt   .  Rfam:RF00001:3e-23  100%|119|Onc75  2e-43|94%|119|contig07472   100%|100|OXAO-aab14b11  100%|100|OXAO-aaa59b10    .  .  .   // was Onc76.2
Onc75.9    216   334  Contig46616.1    4  5S_rRNA    119nt   .  Rfam:RF00001:3e-23  100%|119|Onc75  2e-43|94%|119|contig07472   100%|100|OXAO-aab14b11  100%|100|OXAO-aaa59b10    .  .  .   // was Onc76.2
Onc75.10   660   542  Contig79253.2    4  5S_rRNA    119nt   .  Rfam:RF00001:3e-23  100%|119|Onc75  2e-43|94%|119|contig07472   100%|100|OXAO-aab14b11  100%|100|OXAO-aaa59b10    .  .  .   // was Onc76.2
Onc75.11   449   567  Contig44402.1    4  5S_rRNA    119nt   .  Rfam:RF00001:3e-23  100%|119|Onc75  2e-43|94%|119|contig07472   100%|100|OXAO-aab14b11  100%|100|OXAO-aaa59b10    .  .  .   // was Onc76.3
Onc75.12   199   317  OXAO-aab14b11    4  5S_rRNA    119nt   .  Rfam:RF00001:3e-23  100%|119|Onc75  2e-43|94%|119|contig07472   100%|100|Contig44402.1  100%|100|OXAO-aaa59b10    .  .  .   // was Onc76.4
Onc75.13   411   293  OXAO-aaa59b10    4  5S_rRNA    119nt   .  Rfam:RF00001:1e-22  99%|119|Onc75   3e-42|94%|119|contig07472   93%|98|OXAO-aab14b11    100%|100|OXAO-aab14b11    .  .  .   // was Onc76.5

## canonical rDNA repeat
##
Onc113    3652  3804  rDNA             2  5.8S_rRNA  153nt   .  Rfam:RF00002:6e-40  .               4e-58|95%|153|contig00036   .                       .                         .  .  .  
Onc152    1750  3521  rDNA             2  SSU_rRNA   1772nt  .  gb:FJ545743.1       .               0e+00|98%|1772|contig00036  .                       .                         .  .  .  
Onc153    4008  7392  rDNA             2  LSU_rRNA   3385nt  .  gb:FJ545743.1       .               0e+00|96%|3383|contig00036  .                       .                         .  .  .  


################################################################
# Miscellaneous ncRNAs 
# Detected by Rfam9.1/Infernal searches against WGS+pilot dataset
# 
# comparative analysis of SRP, MRP:  [xref sre:0221-candidate-alignments]
# comparative of RNaseP, telomerase: [xref sre:0222-more-homologs]
#
Onc81     2567  2850  Contig82592.1    1  SRP_euk_arch                284nt  .    Rfam:RF00017:1e-36  .                  1e-101|92%|277|contig06227  100%|100|Contig56789.1    97%|100|Contig56789.1     X  N  G   // PSE; possible polIIIterm
Onc81.2    557   274  Contig56789.1    0  SRP_euk_arch                284nt  .    Rfam:RF00017:1e-36  100%|284|Onc81     1e-101|92%|277|contig06227  100%|100|Contig82592.1    97%|100|Contig82592.1     .  .  .  

Onc82     1118   790  OXAO-aaa59f01    1  RNase_MRP                   329nt  .    Rfam:RF00030:4e-32  .                  6e-59|93%|33|contig22299    100%|100|Contig84242.1    96%|100|Contig84242.1     .  .  G   
Onc82.2   1141   812  Contig77949.2    0  RNase_MRP                   330nt  .    Rfam:RF00030:4e-32  99%|330|Onc82      6e-59|93%|33|contig22299    99%|100|Contig77942.1     99%|100|Contig77942.1     .  .  .  
Onc82.3   1181   853  Contig77942.1    0  RNase_MRP                   329nt  .    Rfam:RF00030:4e-32  99%|329|Onc82      6e-59|93%|33|contig22299    99%|100|Contig77949.2     99%|100|Contig84242.1     .  .  .  
Onc82.4    143   471  Contig84242.1    0  RNase_MRP                   329nt  .    Rfam:RF00030:4e-32  100%|329|Onc82     6e-59|93%|33|contig22299    100%|100|OXAO-aaa59f01    99%|100|Contig77942.1     .  .  .  

Onc149     573   246  Contig62031.2    0  RNaseP_nuc                  328nt  .    Rfam:RF00009:3e-27  .                  8e-44|87%|158|contig29216   98%|99|Contig39152.2      99%|100|Contig62024.1     .  .  .   // PSE
Onc149.2   270   597  Contig39152.2    0  RNaseP_nuc                  328nt  .    Rfam:RF00009:2e-26  99%|328|Onc149     8e-44|87%|158|contig29216   98%|99|Contig62031.2      98%|100|Contig62024.1     .  .  .   
Onc149.3   582   255  Contig62024.1    0  RNaseP_nuc                  328nt  .    Rfam:RF00009:3e-19  98%|327|Onc149     6e-39|84%|157|contig29216   96%|100|Contig62031.2     99%|100|Contig62031.2     .  .  .   

Onc150     419   234  Contig41445.1    0  Telomerase_cil              186nt  .    Rfam:RF00025:3e-14  .                  1e-04|84%|44|contig02980    .                         .                         .  .  .   // PSE,polIIIt

################################################################
## Spliceosomal snRNAs
## Detected by Infernal/Rfam9.1 searches in WGS+pilot dataset
## In some cases (U4atac) subthreshold hits were manually analyzed and accepted.
## 
## For alignments and conserved features: [xref sre:0122-oxy-snRNAs]
## For analysis of U4atac/U6atac:         [xref sre:0318-U4atac]
## 
Onc120    1860  1698  Contig51351.1    0  U1_snRNA                    163nt  .    Rfam:RF00003:7e-24  .                  6e-57|92%|163|contig03734   98%|100|Contig206433      91%|100|Contig75046.1     .  .  .  // PSE,TATA,3box
Onc120.2   149   311  Contig75046.1    0  U1_snRNA                    163nt  .    Rfam:RF00003:7e-24  100%|163|Onc120    6e-57|92%|163|contig03734   98%|100|Contig206433      91%|99|Contig51351.1      .  .  .  
Onc120.3   223   386  Contig206433     0  U1_snRNA                    164nt  .    Rfam:RF00003:7e-24  99%|163|Onc120     2e-57|92%|164|contig03734   98%|100|Contig75046.1     .                         .  .  .  

Onc121     979   790  Contig36667.2    0  U2_snRNA                    190nt  .    Rfam:RF00004:4e-42  89%|190|Onc77      2e-31|100%|82|contig22213   95%|100|Contig58942.2     98%|100|Contig58942.2     .  .  .  // PSE,TATA,3box
Onc121.2   627   438  Contig58942.2    0  U2_snRNA                    190nt  .    Rfam:RF00004:4e-42  100%|190|Onc121    2e-31|100%|82|contig22213   95%|100|Contig36667.2     98%|100|Contig36667.2     .  .  .  // was:Onc122

Onc77      465   654  Contig57619.1    4  U2_snRNA                    190nt  N    Rfam:RF00004:2e-37  92%|190|Onc123     8e-24|92%|81|contig22213    100%|100|OXAO-aab15a03    100%|100|Contig71215.1    .  .  .  // PSE,TATA,3box
Onc77.2    558   369  Contig71215.1    4  U2_snRNA                    190nt  n    Rfam:RF00004:2e-37  100%|190|Onc77     8e-24|92%|81|contig22213    100%|100|OXAO-aab15a03    100%|100|Contig57619.1    .  .  .  
Onc77.3    675   486  Contig72791.1    4  U2_snRNA                    190nt  n    Rfam:RF00004:2e-37  100%|190|Onc77     8e-24|92%|81|contig22213    100%|100|OXAO-aab15a03    100%|100|OXAO-aab15a03    .  .  .  
Onc77.4    163   352  OXAO-aab15a03    4  U2_snRNA                    190nt  n    Rfam:RF00004:2e-37  100%|190|Onc77     8e-24|92%|81|contig22213    100%|100|Contig71215.1    100%|100|Contig72791.1    .  .  .  

Onc123     527   721  Contig201159     0  U2_snRNA                    195nt  .    Rfam:RF00004:2e-34  92%|195|Onc77      6e-25|93%|81|contig22213    100%|100|Contig201160     100%|100|Contig201160     .  .  .  // PSE,TATA,3box
Onc123.2   195   389  Contig201160     0  U2_snRNA                    195nt  .    Rfam:RF00004:2e-34  100%|195|Onc123    6e-25|93%|81|contig22213    100%|100|Contig201159     100%|100|Contig201159     .  .  .  

Onc125     393   265  Contig51899.1    0  U4_snRNA                    129nt  .    Rfam:RF00015:1e-20  .                  .                           100%|100|Contig71125.2    85%|100|Contig54249.2     .  .  .  // PSE,TATA,3box;  no Sty homolog found
Onc125.2  3763  3891  Contig71125.2    0  U4_snRNA                    129nt  .    Rfam:RF00015:1e-20  100%|129|Onc125    .                           100%|100|Contig51899.1    93%|100|Contig54249.2     .  .  .  
Onc125.3   530   658  Contig54249.2    0  U4_snRNA                    129nt  .    Rfam:RF00015:1e-20  100%|129|Onc125    .                           99%|100|Contig51899.1     93%|100|Contig71125.2     .  .  .  // was:Onc126
                                      
Onc127     649   537  Contig44339.2    0  U5_snRNA                    113nt  .    Rfam:RF00020:3e-12  .                  2e-39|93%|113|contig19741   76%|76|Contig36667.2      91%|37|Contig51899.1      .  .  .  // PSE,TATA,3box
                                      
Onc128     485   382  Contig70576.1    0  U6_snRNA                    104nt  .    Rfam:RF00026:5e-29  .                  6e-44|100%|104|contig44922  79%|52|Contig27349.1      .                         .  .  .  // PSE,TATA,polIIIterm

Onc151    1312  1247  Contig200992     0  U4atac_snRNA                66nt   .    Rfam:RF00618:3e-3   .                  5e-13|85%|64|contig39911    96%|100|Contig76036.2     99%|100|Contig71676.2     .  .  .   // PSE,TATA; weak hit supported by manual analysis of Sty conservation and U6atac base pairing.
Onc151.2   764   829  Contig42569.2    0  U4atac_snRNA                66nt   .    Rfam:RF00618:2e-3   98%|66|Onc151      5e-13|85%|64|contig39911    96%|100|Contig76036.2     96%|100|Contig71676.2     .  .  .  
Onc151.3  1676  1741  Contig76036.2    0  U4atac_snRNA                66nt   .    Rfam:RF00618:3e-3   100%|66|Onc151     5e-13|85%|64|contig39911    96%|100|Contig42569.2     100%|100|Contig71676.2    .  .  .  
Onc151.4   630   565  Contig71676.2    0  U4atac_snRNA                66nt   .    Rfam:RF00618:3e-3   100%|66|Onc151     5e-13|85%|64|contig39911    .                         100%|100|Contig76036.2    .  .  .  

Onc114     171   273  Contig73994.1    1  U6atac_snRNA                103nt  .    Rfam:RF00619:8e-06  .                  3e-31|90%|103|contig04908   84%|100|Contig74999.1     94%|100|Contig74999.1     .  N  G   // PSE,TATA,polIIIterm
Onc114.2  2568  2466  Contig74999.1    1  U6atac_snRNA                103nt  .    Rfam:RF00619:8e-06  100%|103|Onc114    3e-31|90%|103|contig04908   88%|100|Contig60127.1     95%|100|Contig60127.1     .  N  G   // was:Onc115
Onc114.3   168   270  Contig60127.1    0  U6atac_snRNA                103nt  .    Rfam:RF00619:8e-06  100%|103|Onc114    3e-31|90%|103|contig04908   88%|100|Contig74999.1     95%|100|Contig74999.1     .  .  .   // was:Onc129


################################################################
## Small nucleolar RNAs (snoRNAs), by various methods enumerated below.
##
## 1. Detected by Infernal/Rfam9.1 searches against WGS+pilot:
##    (Note that for Table 1, E-values are slightly better because those searches were
##    done against the smaller Stage1 dataset. snoMe28S-Cm2645 passes E<=1e-3 threshold
##    in that experiment.)
##
## In every case below, the weak Infernal hit has been corroborated by
## manual analysis of Stylonychia conservation pattern
## [xref:SRE,0126-oxy-snoRNAs].  Two other weak hits were declared
## probable false positives based on this analysis: sR1 hit at
## Contig82752.1/411-357 and snoR64a hit at Contig1085.1/2109-2032.
##
## For U3 comparative analysis:  [xref sre:0122-oxy-snRNAs]
##
Onc124    2618  2387  Contig66111.1    0  U3_snoRNA                   232nt  .    Rfam:RF00012:1e-18  .                  2e-88|96%|217|contig52687   99%|100|Contig68732.1     100%|100|Contig68732.1    .  .  .  // PSE,TATA,3box
Onc124.2  3175  2944  Contig68732.1    0  U3_snoRNA                   232nt  .    Rfam:RF00012:1e-18  100%|232|Onc124    2e-88|96%|217|contig52687   99%|100|Contig66111.1     100%|100|Contig66111.1    .  .  .  

Onc78     1134  1206  Contig9982.1     4  C/D_snoRNA|U18              73nt   N    Rfam:RF01159:2e-05  .                  1e-18|91%|68|contig05557    91%|100|Contig36677.1     100%|100|Contig36677.1    .  .  G   // snoscan predicts target site: LSU681; 5'SS upstream, probably intronic
Onc78.2    144   216  OXAE-aae58h12    4  C/D_snoRNA|U18              73nt   n    Rfam:RF01159:2e-05  100%|73|Onc78      1e-18|91%|68|contig05557    98%|91|OXAO-aab15a01      100%|100|Contig36684.2    .  .  .   // was:Onc79
Onc78.3    181   109  OXAO-aab15a01    1  C/D_snoRNA|U18              73nt   n    Rfam:RF01159:2e-05  100%|73|Onc78      1e-18|91%|68|contig05557    100%|100|UGC1O0005_I02_R  99%|100|OXAE-aae58h12     .  .  .   // was:Onc80
Onc78.4    209   137  Contig36677.1    0  C/D_snoRNA|U18              73nt   n    Rfam:RF01159:2e-05  100%|73|Onc78      1e-18|91%|68|contig05557    92%|99|Contig9982.1       100%|100|Contig9982.1     .  .  .   // was:Onc80.2
Onc78.5    242   170  Contig36684.2    0  C/D_snoRNA|U18              73nt   n    Rfam:RF01159:2e-05  100%|73|Onc78      1e-18|91%|68|contig05557    100%|100|OXAO-aab15a01    100%|100|OXAE-aae58h12    .  .  .   // was:Onc80.3
Onc78.6    197   125  UGC1O0005_I02_R  0  C/D_snoRNA|U18              73nt   n    Rfam:RF01159:2e-05  100%|73|Onc78      1e-18|91%|68|contig05557    100%|100|OXAO-aab15a01    99%|100|OXAE-aae58h12     .  .  .   // was:Onc80.4

Onc83      325   240  OXAO-aaa59f01    1  C/D_snoRNA|snoZ196          86nt   N    Rfam:RF00134:3e-06  .                  1e-17|85%|80|contig22299    100%|100|Contig84242.1    100%|100|Contig84242.1    .  .  G   // snoscan predicts target site: LSU834
Onc83.2    381   296  Contig77942.1    0  C/D_snoRNA|snoZ196          86nt   n    Rfam:RF00134:3e-06  100%|86|Onc83      1e-17|85%|80|contig22299    97%|100|OXAO-aaa59f01     97%|100|OXAO-aaa59f01     .  .  .  
Onc83.3    340   255  Contig77949.2    0  C/D_snoRNA|snoZ196          86nt   n    Rfam:RF00134:3e-06  100%|86|Onc83      1e-17|85%|80|contig22299    95%|100|Contig77942.1     96%|100|OXAO-aaa59f01     .  .  .  
Onc83.4    943  1028  Contig84242.1    0  C/D_snoRNA|snoZ196          86nt   n    Rfam:RF00134:3e-06  100%|86|Onc83      1e-17|85%|80|contig22299    100%|100|OXAO-aaa59f01    100%|100|OXAO-aaa59f01    .  .  .  

Onc84     1953  2040  Contig147.1      1  C/D_snoRNA|snoR38           88nt   N    Rfam:RF00213:3e-05  .                  2e-19|90%|73|contig06317    98%|100|Contig90551       99%|100|Contig81698.2     X  N  G   // intronic 
Onc84.2   1948  2035  Contig90550      0  C/D_snoRNA|snoR38           88nt   n    Rfam:RF00213:5e-05  100%|88|Onc84.3    2e-18|89%|73|contig06317    99%|100|Contig90551       100%|100|Contig81698.2    .  .  .  
Onc84.3    599   686  Contig90551      0  C/D_snoRNA|snoR38           88nt   n    Rfam:RF00213:5e-05  100%|88|Onc84.2    2e-18|89%|73|contig06317    100%|97|Contig90550       100%|100|Contig81698.2    .  .  .  
Onc84.4   1915  2002  Contig81691.1    0  C/D_snoRNA|snoR38           88nt   n    Rfam:RF00213:5e-05  100%|88|Onc84.2    2e-18|89%|73|contig06317    100%|100|Contig81698.2    100%|100|Contig81698.2    .  .  .  
Onc84.5    523   610  Contig81698.2    0  C/D_snoRNA|snoR38           88nt   n    Rfam:RF00213:5e-05  100%|88|Onc84.2    2e-18|89%|73|contig06317    100%|100|Contig81691.1    100%|100|Contig90551      .  .  .  

Onc116     665   587  Contig60671.1    1  C/D_snoRNA|snoMe28S-Cm2645  79nt   .    Rfam:RF00530:2e-3   .                  2e-05|75%|74|contig37977    96%|100|Contig74184.1     93%|99|Contig74184.1      .  .  G  
Onc116.2  1056  1134  Contig74810.1    1  C/D_snoRNA|snoMe28S-Cm2645  79nt   .    Rfam:RF00530:2e-3   100%|79|Onc116     2e-05|75%|74|contig37977    97%|100|Contig74184.1     94%|100|Contig60671.1     .  .  G   // was: Onc117
Onc116.3   698   620  Contig74184.1    0  C/D_snoRNA|snoMe28S-Cm2645  79nt   .    Rfam:RF00530:2e-3   100%|79|Onc116     2e-05|75%|74|contig37977    97%|100|Contig74810.1     93%|99|Contig60671.1      .  .  .   // was: Onc117.2

Onc108     688   609  Contig83501.3    0  C/D_snoRNA|SNORD36          80nt   N    Rfam:RF00049:4e-3   .                  1e-14|83%|72|contig05272    .                         .                         .  .  .   // array, probably intronic

Onc109    1777  1691  Contig201200     0  C/D_snoRNA|SNORD24          87nt   N    Rfam:RF00069:2e-04  .                  3e-14|82%|76|contig02205    96%|100|Contig1162.2      99%|100|Contig1162.2      .  .  .   // array, probably intronic
			                 
## 2. snoRNAs detected by snoscan screen:
##    Again, each of these is corroborated by manual analysis of Sty conservation.
##    Coords are approximate predictions.
##
Onc110    1389  1318  Contig76679.1    1  C/D_snoRNA                  72nt   N    snoscan             .                  1e-13|87%|61|contig53224    94%|100|Contig77473.1     96%|100|Contig46873.1     .  .  .   // intronic
Onc110.2  1054  1123  Contig46873.1    1  C/D_snoRNA                  70nt   n    snoscan             98%|69|Onc110      5e-14|86%|64|contig53224    97%|100|Contig77473.1     96%|100|Contig76679.1     .  .  .  
Onc110.3  1658  1589  Contig77473.1    0  C/D_snoRNA                  70nt   n    snoscan             98%|70|Onc110      1e-13|87%|61|contig53224    96%|99|Contig46873.1      96%|100|Contig76679.1     .  .  .  

Onc111    4173  4099  Contig70178.1    1  C/D_snoRNA                  75nt   N    snoscan             .                  3e-13|84%|71|contig04860    92%|100|Contig546.2       87%|100|Contig546.2       .  .  .   // intronic
Onc111.2   116   190  Contig546.2      0  C/D_snoRNA                  75nt   n    snoscan             100%|75|Onc111     3e-13|84%|71|contig04860    92%|100|Contig70178.1     87%|100|Contig70178.1     .  .  .  

Onc112    1164  1066  Contig80897.1    1  C/D_snoRNA                  99nt   N    snoscan             .                  3e-30|91%|96|contig07528    100%|100|Contig51398.1    97%|100|Contig51398.1     .  .  .   // intronic
Onc112.2  2005  2103  Contig51398.1    0  C/D_snoRNA                  99nt   n    snoscan             100%|99|Onc112     3e-30|91%|96|contig07528    100%|100|Contig80897.1    97%|100|Contig80897.1     .  .  .  
Onc112.3  2403  2501  Contig66429.1    0  C/D_snoRNA                  99nt   n    snoscan             100%|99|Onc112     3e-30|91%|96|contig07528    99%|100|Contig51398.1     97%|100|Contig80897.1     .  .  .  


# 3. snoRNAs detected in arrays with other id'ed snoRNAs
#    Ends are approximate, based on Stylonychia conservation,
#    and thus probably conservative (real RNA may extend a few more nt).
#
# for comparative analysis: [xref sre:0126-oxy-snoRNAs]
#
Onc130    3208  3126  Contig201200     0  C/D_snoRNA|snR77            83nt   .    array:Onc109        .                  2e-24|91%|83|contig02205    100%|100|Contig201201     100%|100|Contig201201     .  .  .   // probably intronic;  snR77 homology was recognized later (Rfam:RF01181:2e-07)
Onc131    2866  2794  Contig201200     0  C/D_snoRNA                  73nt   .    array:Onc109        .                  1e-17|89%|73|contig02205    97%|100|Contig19537.1     100%|100|Contig19537.1    .  .  .   // probably intronic
Onc132    2494  2410  Contig201200     0  C/D_snoRNA                  85nt   .    array:Onc109        .                  2e-24|90%|85|contig02205    96%|100|Contig19537.1     100%|100|Contig1162.2     .  .  .   // probably intronic
Onc133    2249  2124  Contig201200     0  C/D_snoRNA                  126nt  .    array:Onc109        .                  6e-23|78%|126|contig02205   99%|100|Contig1162.2      96%|100|Contig1162.2      .  .  .   // probably intronic
Onc134    1930  1871  Contig201200     0  C/D_snoRNA                  60nt   .    array:Onc109        .                  6e-12|86%|59|contig02205    94%|100|Contig1162.2      96%|100|Contig1162.2      .  .  .   // probably intronic
Onc135    1541  1474  Contig201200     0  C/D_snoRNA                  68nt   .    array:Onc109        .                  9e-08|78%|68|contig02205    99%|100|Contig1162.2      91%|99|Contig1162.2       .  .  .   // probably intronic
Onc136    1362  1301  Contig201200     0  C/D_snoRNA                  62nt   .    array:Onc109        .                  6e-08|81%|62|contig02205    90%|100|Contig1162.2      89%|48|Contig46059.1      .  .  .   // probably intronic
Onc137    1225  1136  Contig201200     0  C/D_snoRNA                  90nt   .    array:Onc109        .                  8e-04|71%|87|contig02205    .                         99%|100|Contig1162.1      .  .  .   // probably intronic
Onc138     962   878  Contig201200     0  C/D_snoRNA                  85nt   .    array:Onc109        .                  5e-10|91%|34|contig02205    98%|100|Contig46059.1     97%|99|Contig1162.1       .  .  .   // probably intronic
Onc139     689   615  Contig201200     0  C/D_snoRNA                  75nt   .    array:Onc109        .                  4e-19|88%|75|contig02205    98%|100|Contig46059.1     99%|100|Contig46059.1     .  .  .   // probably intronic
Onc140     416   332  Contig201200     0  C/D_snoRNA                  85nt   .    array:Onc109        .                  2e-26|94%|85|contig02205    99%|100|Contig46059.1     96%|98|Contig1162.1       .  .  .   // probably intronic

Onc141    1263  1180  Contig83501.3    0  C/D_snoRNA                  84nt   .    array:Onc108        .                  4e-08|78%|84|contig25192    .                         .                         .  .  .   // probably intronic
Onc142     923   830  Contig83501.3    0  C/D_snoRNA                  94nt   .    array:Onc108        .                  9e-14|87%|64|contig25192    .                         .                         .  .  .   // probably intronic
Onc143     342   428  Contig83501.3    0  C/D_snoRNA                  87nt   .    array:Onc108        .                  6e-14|79%|87|contig05272    .                         .                         .  .  .   // probably intronic

Onc144     754   836  Contig4340.2     5  H/ACA_snoRNA                83nt   .    array:Onc86         .                  8e-13|95%|22|contig11292    .                         .                         .  .  .   // bounds uncertain; conservation pattern odd; probably targets SSU1295; human ACA15 modifies homologous human position

Onc130.2  1885  1803  Contig1162.2     0  C/D_snoRNA|snR77            83nt   .    array               100%|83|Onc130.3   2e-23|91%|81|contig02205    100%|100|Contig201201     98%|100|Contig201201      .  .  .  
Onc131.2  1547  1475  Contig1162.2     0  C/D_snoRNA                  73nt   .    array               100%|73|Onc131.3   3e-18|90%|72|contig02205    97%|100|Contig19537.1     100%|100|Contig19537.1    .  .  .  
Onc132.2  1176  1092  Contig1162.2     0  C/D_snoRNA                  85nt   .    array               100%|85|Onc132     2e-24|90%|85|contig02205    97%|100|Contig19537.1     100%|100|Contig201200     .  .  .  
Onc133.2   931   806  Contig1162.2     0  C/D_snoRNA                  126nt  .    array               100%|126|Onc133    6e-23|78%|126|contig02205   99%|100|Contig19537.1     96%|100|Contig201200      .  .  .  
Onc134.2   612   553  Contig1162.2     0  C/D_snoRNA                  60nt   .    array               98%|59|Onc134      1e-11|85%|59|contig02205    94%|100|Contig201200      96%|100|Contig201200      .  .  .  
Onc109.2   459   373  Contig1162.2     0  C/D_snoRNA                  87nt   .    array               98%|87|Onc109      2e-15|84%|76|contig02205    96%|100|Contig201200      99%|100|Contig201200      .  .  .  
Onc135.2   224   158  Contig1162.2     0  C/D_snoRNA                  67nt   .    array               98%|67|Onc135      1e-07|90%|40|contig02205    99%|100|Contig201200      90%|100|Contig201200      .  .  .  

Onc130.3   224   306  Contig19537.1    0  C/D_snoRNA|snR77            83nt   .    array               100%|83|Onc130.2   2e-23|91%|81|contig02205    100%|100|Contig201201     100%|100|Contig201201     .  .  .  
Onc131.3   562   634  Contig19537.1    0  C/D_snoRNA                  73nt   .    array               100%|73|Onc131.2   3e-18|90%|72|contig02205    97%|100|Contig1162.2      100%|100|Contig1162.2     .  .  .  
Onc132.3   933  1017  Contig19537.1    0  C/D_snoRNA                  85nt   .    array               100%|85|Onc132     2e-24|90%|85|contig02205    97%|100|Contig1162.2      99%|100|Contig201200      .  .  .  
Onc133.3  1178  1303  Contig19537.1    0  C/D_snoRNA                  126nt  .    array               100%|126|Onc133    6e-23|78%|126|contig02205   99%|100|Contig1162.2      .                         .  .  .  

Onc130.4   442   360  Contig201201     0  C/D_snoRNA|snR77            83nt   .    array               100%|83|Onc130.2   2e-23|91%|81|contig02205    100%|100|Contig19537.1    100%|100|Contig19537.1    .  .  .  
Onc131.4   103    31  Contig201201     0  C/D_snoRNA                  73nt   .    array               100%|73|Onc131.2   3e-18|90%|72|contig02205    96%|100|Contig201200      .                         .  .  .  

Onc137.2  1209  1129  Contig1162.1     0  C/D_snoRNA                  81nt   .    array               95%|81|Onc137      .                           .                         100%|100|Contig46059.1    .  .  .  
Onc138.2   954   871  Contig1162.1     0  C/D_snoRNA                  84nt   .    array               100%|84|Onc138.3   3e-11|91%|34|contig02205    97%|100|Contig201200      97%|99|Contig46059.1      .  .  .  
Onc139.2   682   608  Contig1162.1     0  C/D_snoRNA                  75nt   .    array               100%|75|Onc139     4e-19|88%|75|contig02205    99%|100|Contig46059.1     98%|100|Contig46059.1     .  .  .  
Onc140.2   409   325  Contig1162.1     0  C/D_snoRNA                  85nt   .    array               100%|85|Onc140     2e-26|94%|85|contig02205    99%|100|Contig46059.1     98%|100|Contig46059.1     .  .  .  

Onc137.3  1218  1130  Contig46059.1    0  C/D_snoRNA                  89nt   .    array               92%|89|Onc137      .                           .                         100%|100|Contig1162.1     .  .  .  
Onc138.3   954   871  Contig46059.1    0  C/D_snoRNA                  84nt   .    array               100%|84|Onc138.2   3e-11|91%|34|contig02205    98%|100|Contig201200      97%|99|Contig1162.1       .  .  .  
Onc139.3   682   608  Contig46059.1    0  C/D_snoRNA                  75nt   .    array               100%|75|Onc139     4e-19|88%|75|contig02205    99%|100|Contig1162.1      99%|100|Contig201200      .  .  .  
Onc140.3   409   325  Contig46059.1    0  C/D_snoRNA                  85nt   .    array               100%|85|Onc140     2e-26|94%|85|contig02205    99%|100|Contig1162.1      98%|100|Contig1162.1      .  .  .  


# 4. snoRNAs detected by 3box screen: [xref sre:0227-3box-screen]
#    Coords are approximate, based on manual analysis and Stylonychia conservation (where available).
#
# for H/ACA target site predictions:                  [xref sre:0302-haca-targets]
# Onc154 upgraded to a locus despite no Sty coverage: [xref sre:0302-haca-targets]
# 
Onc145     492   562  Contig6909.1     1  C/D_snoRNA                  71nt   -    3box_screen         .                  3e-18|90%|70|contig00889    .                         73%|67|Contig27482.1      .  .  .   // 3box; negative on Northern, but independently predicted by SJ with snoscan and SRE with 3box screen

Onc146    1972  1887  Contig47518.1    1  C/D_snoRNA                  86nt   .    3box_screen         .                  6e-19|84%|86|contig00548    95%|99|Contig42170.1      96%|98|Contig42170.1      .  .  .   // 3box; 3box is not conserved in Sty
Onc146.2  1037  1122  Contig92891      0  C/D_snoRNA                  86nt   .    3box_screen         100%|86|Onc146     6e-19|84%|86|contig00548    100%|86|Contig47518.1     100%|100|Contig92893      .  .  .  
Onc146.3  1965  1880  Contig42170.1    0  C/D_snoRNA                  86nt   .    3box_screen         100%|86|Onc146     6e-19|84%|86|contig00548    .                         96%|98|Contig47518.1      .  .  .  
Onc146.4   167   252  Contig92893      0  C/D_snoRNA                  86nt   .    3box_screen         100%|86|Onc146     6e-19|84%|86|contig00548    98%|88|Contig92891        100%|100|Contig92891      .  .  .  

Onc147    3094  2955  Contig48640.1    0  H/ACA_snoRNA                140nt  .    3box_screen         .                  3e-32|84%|138|contig02723   84%|100|Contig61584.1     91%|98|Contig8120.2       .  .  .   // 3box; 3box is not conserved in Sty; targets LSU2256; possible homolog U19/snR191
Onc147.2   709   570  Contig61584.1    0  H/ACA_snoRNA                140nt  .    3box_screen         100%|140|Onc147.3  4e-31|83%|138|contig02723   100%|100|Contig74386.1    100%|100|Contig74386.1    .  .  .  
Onc147.3   999  1138  Contig8120.2     0  H/ACA_snoRNA                140nt  .    3box_screen         100%|140|Onc147.2  4e-31|83%|138|contig02723   97%|100|Contig61584.1     98%|95|Contig61584.1      .  .  .  
Onc147.4  1003  1142  Contig74386.1    0  H/ACA_snoRNA                140nt  .    3box_screen         100%|140|Onc147.2  4e-31|83%|138|contig02723   100%|100|Contig61584.1    100%|100|Contig61584.1    .  .  .  

Onc148    2280  2223  Contig79173.1    1  C/D_snoRNA                  58nt   .    3box_screen         .                  3e-10|93%|30|contig31817    99%|100|Contig36772.1     95%|100|Contig36772.1     .  .  .   // 3box; 3box is not conserved in Sty
Onc148.2   163   220  Contig36772.1    0  C/D_snoRNA                  58nt   .    3box_screen         100%|58|Onc148     3e-10|93%|30|contig31817    99%|100|Contig79173.1     95%|100|Contig79173.1     .  .  .  

Onc154     674   545  Contig50244.2    3  H/ACA_snoRNA                130nt  .    3box_screen         .                  .                           100%|100|Contig50237.1    100%|100|Contig50237.1    .  .  .   // 3box; predicted LSU2859 target; conserved pseudoU in yeast,human
Onc154.2   706   577  Contig47714.1    3  H/ACA_snoRNA                130nt  .    3box_screen         100%|130|Onc154    .                           99%|100|Contig7084.1      86%|100|Contig50237.1     .  .  .  
Onc154.3   330   459  Contig7084.1     3  H/ACA_snoRNA                130nt  .    3box_screen         100%|130|Onc154    .                           99%|100|Contig47714.1     96%|100|Contig50237.1     .  .  .  
Onc154.4   515   386  Contig50237.1    3  H/ACA_snoRNA                130nt  .    3box_screen         100%|130|Onc154    .                           100%|100|Contig50244.2    100%|100|Contig50244.2    .  .  .  


################################################################
# ncRNA candidates identified in the nanochromosome screen
#
# The candidates fall in three groups, after subsequent
# computational and experimental analysis:
#   - ncRNAs we recognize (C/D snoRNAs, H/ACA snoRNAs)
#   - loci that are clearly ncRNAs, which we don't recognize
#   - loci that we have not experimentally observed as RNAs,
#     and which we have low confidence in aft
#

# Candidates that appear to be snoRNAs.
# Also includes close homologs found on incomplete contigs in 
# the WGS+pilot dataset.
# 
# for comparative analysis:   [xref sre:0126-oxy-snoRNAs] 
# for Onc90 comparative:      [xref sre:0221-candidate-alignments]
# for Onc90 H/ACA assignment: [xref sre:0224-paramecium]
# for Onc90 U17/snR30 assign: [xref sre:0226-onc90]
#
Onc85      395   317  Contig93299      5  C/D_snoRNA|SNORD96          79nt   N    nano_screen         .                  3e-18|87%|74|contig52826    97%|98|Contig76610.1      95%|100|Contig76610.1     .  .  .   // detectable by snoscan (target site: LSU832)
Onc85.2    393   315  Contig76610.1    0  C/D_snoRNA|SNORD96          79nt   n    nano_screen         98%|79|Onc85       3e-19|89%|74|contig52826    97%|98|Contig93299        95%|100|Contig93299       .  .  .  

Onc86      360   431  Contig4340.2     5  C/D_snoRNA                  72nt   N/R  nano_screen         .                  6e-17|88%|69|contig11292    .                         75%|65|Contig21805.1      .  .  .   // array,intronic; detectable by snoscan (target site: SSU8 or LSU1242)    
		                     
Onc87      418   496  Contig23611.1    5  C/D_snoRNA                  79nt   N/R  nano_screen         100%|79|Onc88      2e-13|82%|73|contig52882    97%|100|Contig63555.1     97%|100|OXAC-aaa05b11     .  .  .   // detectable by snoscan (target site: LSU678)     
Onc87.2    772   850  Contig80821.1    4  C/D_snoRNA                  79nt   n/r  nano_screen         100%|79|Onc87      2e-13|82%|73|contig52882    100%|100|OXAE-aaa21b05    100%|100|OXAE-aaa21b05    .  .  .   
Onc87.3    407   485  OXAC-aaa05b11    4  C/D_snoRNA                  79nt   n/r  nano_screen         100%|79|Onc87      2e-13|82%|73|contig52882    100%|100|OXAE-aaa21b05    100%|100|OXAE-aaa21b05    .  .  .   
Onc87.4    515   437  OXAE-aaa21b05    4  C/D_snoRNA                  79nt   n/r  nano_screen         100%|79|Onc87      2e-13|82%|73|contig52882    100%|100|OXAC-aaa05b11    100%|100|OXAC-aaa05b11    .  .  .   
Onc87.5    419   497  Contig47479.1    4  C/D_snoRNA                  79nt   n/r  nano_screen         100%|79|Onc87      2e-13|82%|73|contig52882    94%|95|OXAE-aaa21b05      97%|100|OXAC-aaa05b11     .  .  .   
Onc87.6    530   452  Contig63555.1    4  C/D_snoRNA                  79nt   n/r  nano_screen         100%|79|Onc87      2e-13|82%|73|contig52882    97%|100|Contig23611.1     97%|100|Contig23611.1     .  .  .   // was Onc88 
		                     
Onc89      550   418  Contig204907     5  H/ACA_snoRNA                133nt  N/R  nano_screen         .                  3e-24|80%|124|contig33479   98%|100|Contig204908      100%|100|Contig204908     .  .  .   // 3box; detectable by sno-GPS (in relatively low score); predicted to modify LSU2517, but homologous position is C in human, and not pseudouridylated in yeast
Onc89.2    280   148  Contig63528.1    0  H/ACA_snoRNA                133nt  n/r  nano_screen         100%|133|Onc89     3e-24|80%|124|contig33479   84%|97|Contig204907       95%|100|Contig204907      .  .  .  
Onc89.3    301   169  Contig204908     0  H/ACA_snoRNA                133nt  n/r  nano_screen         100%|133|Onc89     3e-24|80%|124|contig33479   98%|100|Contig204907      100%|100|Contig204907     .  .  .  
Onc89.4    281   149  Contig60002.1    0  H/ACA_snoRNA                133nt  n/r  nano_screen         99%|133|Onc89      3e-24|80%|124|contig33479   93%|99|Contig204908       95%|100|Contig204907      .  .  .  
Onc89.5    550   682  Contig42459.2    0  H/ACA_snoRNA                133nt  n/r  nano_screen         96%|133|Onc89      3e-23|80%|124|contig33479   96%|100|Contig204907      94%|98|Contig204907       .  .  .  

Onc90      485   241  UGC1O0002_K14_R  5  H/ACA_snoRNA|U17|snR30      245nt  N/R  nano_screen         .                  3e-53|84%|151|contig08123   100%|100|Contig49311.1    100%|100|Contig49311.1    .  .  .   // 3box; has IH1,IH2 extra stems; conserves U17 non-guide interaction w/ SSU rRNA
Onc90.2    527   283  Contig49311.1    0  H/ACA_snoRNA                245nt  n/r  nano_screen         100%|245|Onc90     3e-53|84%|151|contig08123   100%|100|UGC1O0002_K14_R  100%|100|UGC1O0002_K14_R  .  .  .  
Onc90.3    607   363  Contig68403.1    0  H/ACA_snoRNA                245nt  n/r  nano_screen         100%|245|Onc90     3e-53|84%|151|contig08123   98%|100|UGC1O0002_K14_R   96%|100|UGC1O0002_K14_R   .  .  .  
Onc90.4   3492  3736  Contig53912.1    0  H/ACA_snoRNA                245nt  n/r  nano_screen         100%|245|Onc90     3e-53|84%|151|contig08123   98%|100|Contig68403.1     96%|100|UGC1O0002_K14_R   .  .  .  
	                     
# Candidates which appear to be novel RNAs.
# All in one homologous family that we call "arisong" loci which was named as "classII".
# The name is historical; "class I" loci were the Onc90 quasiallelic group,
# which we subsequently recognized as an H/ACA.
# 
# Also includes close homologs found on incomplete contigs in 
# the WGS+pilot dataset.
#
# for comparative analysis:  [xref sre:0221-candidate-alignments]
# for Onc155,Onc156:         [xref sre:0405-oxy-classII]
#
Onc91      165   253  Contig63727.1    5  arisong                     89nt   N/R  nano_screen          91%|72|Onc92      3e-25|90%|89|contig07687    100%|100|Contig71315.1    100%|100|Contig71315.1    .  .  .   // PSE,3box
Onc91.2    752   664  Contig71315.1    4  arisong                     89nt   n/r  nano_screen         100%|89|Onc91      3e-25|90%|89|contig07687    100%|100|Contig63727.1    100%|100|Contig63727.1    .  .  .   
		                     
Onc92      693   610  Contig36242.1    4  arisong                     84nt   .    nano_screen          91%|71|Onc91      3e-19|92%|66|contig07687    98%|100|OXAO-aab16b04     99%|100|OXAO-aab16b04     .  .  .   // PSE,TATA,3box
Onc92.2    534   451  OXAO-aab16b04    4  arisong                     84nt   .    nano_screen         100%|84|Onc92      3e-19|92%|66|contig07687    100%|100|Contig65300.1    100%|100|Contig65300.1    .  .  .   // was Onc93
Onc92.3    543   460  Contig65300.1    0  arisong                     84nt   .    nano_screen         100%|84|Onc92      3e-19|92%|66|contig07687    100%|100|OXAO-aab16b04    100%|100|OXAO-aab16b04    .  .  .  
		                     
Onc94      761   670  Contig13832.1    5  arisong                     92nt   N/R  nano_screen         76%|63|Onc95       5e-07|94%|36|contig38690    .                         .                         .  .  .   // PSE,TATA,3box
		                     
Onc95      580   496  Contig44542.1    4  arisong                     85nt   R    nano_screen         76%|64|Onc94       7e-03|75%|64|contig38690    99%|100|OXAD-aaa04a12     100%|100|OXAD-aaa04a12    .  .  .   // PSE,TATA,3box
Onc95.2    132   216  OXAD-aaa04a12    4  arisong                     85nt   r    nano_screen         100%|85|Onc95      7e-03|75%|64|contig38690    99%|100|Contig44542.1     100%|100|Contig44542.1    .  .  .   
Onc95.3    531   447  Contig57964.1    0  arisong                     85nt   r    nano_screen         100%|85|Onc95      7e-03|75%|64|contig38690    98%|100|Contig44542.1     99%|100|OXAD-aaa04a12     .  .  .  
	                     
Onc96      285   146  OXAO-aab17f07    4  arisong                     140nt  R    nano_screen         .                  .                           .                         .                         .  .  .   // PSE,TATA,3box; whole nano passed Sty conservation test because 3box is highly conserved, but locus itself is diverged below BLASTN radar

Onc155     343   428  Contig48963.1    1  arisong                     86nt   .    nano_screen         78%|75|Onc91       9e-09|82%|61|contig07687    96%|100|Contig53488.1     95%|100|Contig53488.1     .  .  .   // PSE,3box
Onc155.2   255   340  Contig65636.1    0  arisong                     86nt   .    nano_screen         100%|86|Onc155     9e-09|82%|61|contig07687    100%|100|Contig48963.1    92%|96|Contig38772.1      .  .  . 
Onc155.3   209   294  Contig38772.1    0  arisong                     86nt   .    nano_screen         100%|86|Onc155     9e-09|82%|61|contig07687    100%|100|Contig48963.1    90%|100|Contig65636.1     .  .  .

Onc156    1587  1719  Contig203665     1  arisong                    133nt   .    nano_screen         97%|68|Onc96       .                           94%|100|Contig203666      99%|100|Contig203666      .  .  .   // PSE,TATA,3box
Onc156.2  628    760  Contig203666     0  arisong                    133nt   .    nano_screen         99%|133|Onc156     .                           94%|100|Contig203665      99%|100|Contig203665      .  .  .

# Candidates for which we detected no small RNA transcripts on Northern.
# Coords are rough, the bounds of the conserved region we considered as a candidate.
# This group does not include homologous alleles in WGS+pilot; didn't bother.
#
# Upon further analysis:   [xref sre:0220-candidate-alignments]
#   5/10 appear to be fragments of other nanos, containing either conserved coding or promoter fragment
#   1/10 appears to be a coding region, by multiple alignment analysis; missed by BLASTX and nanogf
#   4/10 are not identifiable; two of these look like possible ncRNAs, but we lack experimental confirmation of the transcripts.
#
Onc97      371   499  Contig91146      5  ?                           129nt  -    nano_screen         .                  4e-16|77%|129|contig26647   100%|99|Contig91145       100%|100|Contig91145      .  .  .  // AT-rich conservation; may be a promoter?
			               
Onc98      444   554  Contig63260.1    5  ?                           111nt  -    nano_screen         .                  4e-17|76%|111|contig24047   .                         .                         .  .  .  // possible ncRNA. reasonable conservation; not obvious what it is
			               
Onc99       18   123  OXAE-aae57g05    5  ?                           106nt  -    nano_screen         .                  1e-13|75%|106|contig06705   .                         .                         .  .  .  // fragment of another coding nano, containing conserved promoter for proteosome subunit alpha
			               
Onc100     281   396  Contig40627.1    5  ?                           116nt  -    nano_screen         .                  4e-12|75%|116|contig07615   97%|100|Contig65897.1     100%|100|Contig30261.1    .  .  .  // one small patch of conservation.
Onc100.2   325   440  Contig65897.1    4  ?                           116nt  -    nano_screen         100%|116|Onc100    4e-12|75%|116|contig07615   97%|100|Contig40627.1     100%|100|Contig30261.1    .  .  .  
			               
Onc102      21    94  OXAE-aae64g09    5  ?                           74nt   -    nano_screen         .                  1e-10|78%|74|contig07628    .                         .                         .  .  .  // coding fragment, malate dehydrogenase
			               
Onc103     657   717  Contig47258.1    5  ?                           61nt   -    nano_screen         .                  1e-11|83%|61|contig22660    91%|100|Contig63235.2     91%|87|Contig63235.2      .  .  .  // coding fragment, phosphate transporter
			               
Onc104    1447  1675  Contig64625.1    5  ?                           229nt  -    nano_screen         .                  8e-11|68%|151|contig15825   .                         .                         .  .  .  // coding fragment, by multiple alignment analysis; ciliate-specific protein
			               
Onc105     489   553  Contig63601.1    5  ?                           65nt   -    nano_screen         .                  1e-09|87%|49|contig02580    99%|100|Contig69957.1     100%|100|Contig69957.1    .  .  .  // rearranged contig containing two coding fragments
Onc105.2   241   279  Contig69957.1    4  ?                           39nt   -    nano_screen         .                  9e-10|94%|39|contig06648    100%|100|Contig63601.1    99%|100|Contig63601.1     .  .  .  
			               
Onc106     480   554  Contig54011.1    5  ?                           75nt   -    nano_screen         .                  5e-08|74%|75|contig40131    .                         .                         .  .  .  // possible ncRNA. reasonable conservation; almost H/ACA-like
			               
Onc107      40   130  OXAE-aaa57c10    5  ?                           91nt   -    nano_screen         .                  3e-06|72%|91|contig05126    .                         .                         .  .  .  // fragment of a nano, containing a conserved promoter