# STOCKHOLM 1.0

# Alignment of all Arisong RNAs detected in four species:
#   Oxytricha trifallax     (15)
#   Stylonychia lemnae       (8)
#   Paramecium tetraurelia   (8)
#   Nyctotherus ovalis       (1)
#  
# The Oxytricha loci are named "OncXX"; for genome assembly coords and
# other information, see Oxy_ncRNAs.list in the supplementary
# material.
#
# The other loci result from Infernal 1.0.2 searches using a model
# built from the alignment of the 15 Oxytricha RNAs. The model only
# includes the structurally conserved 3' end of the Onc RNAs, so only
# homology to this region is detected in these searches; that is,
# these RNAs are expected to extend further 5', as the Oxytricha RNAs
# do.


Onc91                          ..........................................................acucuccaacaguaaccaauacuuUCGAGGUCUUAAGCCAGUGUAACUGGUUGCGGGUGAGGGACCU.AUUC-GGGAUCCUGAACCCGUUC
Onc91.2                        ..........................................................acucuccaacaguaaccaauacuuUCGAGGUCUUAAGCCAGUGUAACUGGUUGCGGGUGAGGGACCU.AUUC-GGGAUCCUGAACCCGUUC
Onc92                          ...............................................................aagauaaagugaaaauccuUCCAGGUCUUAAGCCAGUGUAACUGGCUGCGGGGGAGGGACCU.AUUC-GGGAUCCCGAACCCGUUC
Onc92.2                        ...............................................................aagauaaagugaaaauccuUCCAGGUCUUAAGCCAGUGUAACUGGCUGCGGGGGAGGGACCU.AUUC-GGGAUCCCGAACCCGUUC
Onc92.3                        ...............................................................aagauaaagugaaaauccuUCCAGGUCUUAAGCCAGUGUAACUGGCUGCGGGGGAGGGACCU.AUUC-GGGAUCCCGAACCCGUUC
Onc94                          ................................................aaccuuucuugaaaaaaguuucaauuuucguuaaUCCU-AACUUCAGA-GGUCCGGCC-UCUGCGGCU--UGGGGAC.ACAAAGUU-CCUG--AGCCGUUC
Onc95                          ........................................................aacucuuacaaaaacguucguguuaaUCCUAAACUUCAGA-GGUAUGGCC-UCUGCGGGG--UGUUUCC.ACAAAGGA-AAUG--UCCCGUUC
Onc95.2                        ........................................................aacucuuacaaaaacguucguguuaaUCCUAAACUUCAGA-GGUAUGGCC-UCUGCGGGG--UGUUUCC.ACAAAGGA-AAUG--UCCCGUUC
Onc95.3                        ........................................................aacucuuacaaaaacguucguguuaaUCCUAAACUUCAGA-GGUAUGGCC-UCUGCGGGG--UGUUUCC.ACAAAGGA-AAUG--UCCCGUUC
Onc96                          gauuauuguuugcauuccguaguugaacuaggccccccaaagggucuuuagugaggcugcggggugcugacgaaguuuuuaaUUCU-UUUUUCAGC-AGUCCGGCU-GCUGCGGGG--AUGGGCC.AUAUUGGU-UUGU--CUCCGUUC
Onc155                         .............................................................acgcccacuaaguaacaaauuUCCAAGUUUUAGGCCAGUUUAACUGGUCGCGGGGA-AUGGGCCuUUUCUGGU-CACUGAACCCGUUU
Onc155.2                       .............................................................acgcccacuaaguaacaaauuUCCAAGUUUUAGGCCAGUUUAACUGGUCGCGGGGA-AUGGGCCuUUUCUGGU-CACUGAACCCGUUU
Onc155.3                       .............................................................acgcccacuaaguaacaaauuUCCAAGUUUUAGGCCAGUUUAACUGGUCGCGGGGA-AUGGGCCuUUUCUGGU-CACUGAACCCGUUU
Onc156                         .......gaugaccgucuucguuuuggucuugugggaagguaaaacuuuucgcagguccaggauggaaacaaaaguuuuuaaUUCU-UUUUUCAGC-AGUUCGGCU-GCUGCGGGG--AUGGGCC.AUAUUGGC-UUGU--CUCCGUUC
Onc156.2                       .......gaugaccgucuucguuuuggucuugugggaagguaaaacuuuucgcagguccaggauggaaacaaaaguuuuuaaUUCU-CUUUUCAGC-AGUUCGGCU-GCUGCGGGG--AUGGGCC.AUAUUGGC-UUGU--CUCCGUUC
Stl|contig07687/132-196        ..................................................................................UCGAAGUCUUAAGCCAGUGUAACUGGUUGCGGGCGAGGGACCU.AUUC-GGGAUUCCGAACCCGUUC
Stl|contig07687/646-710        ..................................................................................UAGAAGUCUUAAGCCAGUUUAACUGGUUGCGGGUGAUGGACCU.AUUC-GGGAUCCUGACCCCGUUC
Stl|contig29728/235-171        ..................................................................................UCCCAGUUCUAUGCCAGUUUAACUGGUAGCGAGGGAGGGACCU.AUUC-GGGCUCCCGAACUCGUUC
Stl|contig09855/859-923        ..................................................................................UCGAAGUGUUAAGCCAGUUUAACUGGUUGCGGGAAGAGAACCU.AUUC-GGGAUUCUUGCCCCGUUC
Stl|contig37331/136-200        ..................................................................................UAGCAGUUCUUAACCAGUUUAACUGGUUGCGGAUGAGGGACCU.AUUC-GGGAUCCUGACUCCGUUC
Stl|contig15263/138-192        ..................................................................................UUCU-AAUUUCAGA-GGUCCGGCC-UCUGCGGAG--GAUAUCC.-UAA-GG--UAUC--UUCCGUUC
Stl|contig38690/136-190        ..................................................................................UUCU-AAUUUCAGA-GGUCCGGCC-UCUGCGGAG--GAUAUCC.-UAA-GG--UAUC--UUCCGUUC
Stl|contig05146/1257-1203      ..................................................................................UUCU-AUUUUCAGA-UGUUCAGCA-UCUGCGGGU..CCUU-UC.CUAA-GA--GGGG..AUCCGUUC
Pat|scaffold_63/404588-404525  ..................................................................................UCCA-AGUUUAAACCAAUAUAAUUGGUUGUGGGGGAGAGUCCU.AUUCCGG-AACUCGAGCCCAUUU
Pat|scaffold_149/135969-136032 ..................................................................................UCCA-AGUUUAAACCUAUUUAAUAGGUUGCGGGCGAGGCUCCU.AUUCCGG-AAGCUAAGCUCGUUC
Pat|scaffold_58/125078-125141  ..................................................................................UCCA-AGUUUAAACCUAUUUAAUAGGUUGCGGGCAAGGCUCCU.AUUCCGG-AAGCUGAGCUCGUUC
Pat|scaffold_58/139292-139229  ..................................................................................UCCA-AGUUUAAACCUAUUUAAUAGGUUGCGGGCAAGGCUCCU.AUUCCGG-AAGCUGAGCUCGUUC
Pat|scaffold_127/137631-137568 ..................................................................................UCCA-AGUUUAAACCUAUUUAAUAGGUUGCGGGCAAGGCUCCU.AUUCCGG-AAGCUAAGCUCGUUC
Pat|scaffold_149/137102-137165 ..................................................................................UCCA-AGUUUAAACCUAUUUAAUAGGUUGCGGGCAAGGCUCCU.AUUCCGG-AAGCUAAGCUCGUUC
Pat|scaffold_63/404799-404862  ..................................................................................UCCA-AGUUUAAACCAAUAUAAUUGGCUGUGGGAGAGAGUCCU.AUUCCGG-AACUCGAACCCAUUU
Pat|scaffold_56/155470-155407  ..................................................................................UCCA-AGUUUAAACCUAUUUAAUAGGUUGCGGGCGAGGCUCCU.AUUCCGG-AAGCUGAGCUCGUUU
Nyo|AM890213/167-230           ..................................................................................UCCU-AGCAUCGGCUAGUAUAACUAGUCGCGGGUGGAGGACCU.AUUCCGG-AUCCAAAGCCCGUUU
#=GC SS_cons                   ..................................................................................:::::::::::<<<<<<<___>>>>>>><<<<<<--<<<<<<<._____>>>->>>>-->>>>>>::
#=GC RF                        ..................................................................................UCCuaaUuUUcAGCCaGuuuGgCuGGCUGCGGgggAagggcCC.AUAauGGgAcccuGAccCCGUUC
//