CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA


DroPer_CAF1_left   TAC-AT-ATGAAA-GTCTTTCAAC--ATCATTCTGGAGAAC--GGATAG--ACTAAATCAATTTTGA-TTGTACT-CTAACTCTACTCT--ATTGCCAATGGTTCGATATTTATTATTTA
DroPse_CAF1_left   TTT-CA-ACAGCA-TTCTGGAGTA--CGGATAAGCCATCGG--CCCGGC--CCCACACTCAACCAAC-TAGCTTA-ATTTCCTATTTCT--ATTTGCACTGCTCTGATATTTATTATTTA
DroAna_CAF1_left   TAC-GTGATATTT-GCTACGCCAA-T-CGTGCACATAGGT---TCTGTAACGCAATTA-AC-GGTTATCTGGTAT-TATGGCA-ATTAT--AATAAGTTAAATTTCATATTTATTATTTA
DroEre_CAF1_left   ATT-TG-CAATTT---TTCAAATCAATAAAGGCCACAAAT---CTTTTG--GGTATTTTTTTTGAAT-TCTTTTC-CGGATTT-TAGGACGTTATTTTCAAAATTCAAATTAATTATCAA
DroMel_CAF1_left   AAC-AA-ACACAA---AGTGCGCAAGAATTTGCCATAATTCGATATCAA--CTATA-TTCC-GCGTTGTTCATAA-CATTTTG-CTATT--TCCTTAATAGTTTGAATATTTATTATAAA
DroSec_CAF1_left   AAA-AA-TCAAAA-TCAACGGGACAACAGATTGCTGTCAA---TTCAAT--ACAAAACTACATTTGA-ATCGTTC-ATAACAT-TTTGT--TTTTATTTTTAGTTTAAATTTATTATAAA
DroSim_CAF1_left   CAC-AA-CAAATT-G-CTTGTCAA-TTCAATCCCAAACTA---CATTTAGAGCTGTTC-AT-AACACTTTGTTTA-TATTTTACAGTTT--TACTATTTTTAGCTTAGATTTATTATGAA
DroWil_CAF1_left   TGG-CA-TATGTA-TGTGTGTGTG--GTTTGGTTAAATGCTA-ATCTTT--TCCCATTTCT-AAACTAATGATAGTAAGAAAA-CTGTT--GTTAGGTTATATTTAGATTTATTAATTAA
DroYak_CAF1_left   ACACAA-ACAGCAAGGATATTGATTTTTTAAAGAATATTT---CCCTTA--TATGGAAA-T-TATTA-AAAGTTA-CTAATTT-CTTTT--TAGGTTTTATTTTTTAAATTTATTATTAA

DroPer_CAF1_left   TGTCGGGACGGCGCGAACGCCATTCCCGGCTACCAAAAATTACACGCACGAGTTATTCACATTAGGAATAATCGCAGAGGTCAACTCAGCCGC-AGTGCAATGGCCAAGCCTCACTCCGG
DroPse_CAF1_left   TGTCGGGACGGCGCGAACGCCATTCCCGGCTACCAAAAATTACACGCACGAGTTATTCACATTAGGAATAATCGCAGAGGTCAACTCAGCCGA-AGTGCAATGGCCAAGCCTCACTCCGG
DroAna_CAF1_left   TGTCGGGACGGCGCGAACGCCATTCCCGGCTACCAAAAATTACACGCACGAGTTATTCACATTAGGAATAATCGCAGAGGTCAACTCAGCCGA-GGTGCAATGGCCAAGCCTCACTCCGG
DroEre_CAF1_left   TGTCGGGACGGCGCGAACGCCATTCCCGGCTACCAAAAATTACACGCACGAGTTATTCACATTAGGAATAATCGCAGAGGTCAACTCAGCCGA-GGTGCAATGGCCAAGCCTCACTCCGG
DroMel_CAF1_left   TGTCGGGACGGCGCGAACGCCATTCCCGGCTACCAAAAATTACACGCACGAGTTATTCACATTAGGAATAATCGCAGAGGTCAACTCAGCCGA-GGTGCAATGGCCAAGCCTCACTCCGG
DroSec_CAF1_left   TGTCGGGACGGCGCGAACGCCATTCCCGGCTACCAAAAATTACACGCACGAGTTATTCACATTAGGAATAATCGCAGAGGTCAACTCAGCCGA-GGTGCAATGGCCAAGCCTCACTCCGG
DroSim_CAF1_left   TGTCGGGACGGCGCGAACGCCATTCCCGGCTACCAAAAATTACACGCACGAGTTATTCACATTAGGAATAATCGCAGAGGTCAACTCAGCCGA-GGTGCAATGGCCAAGCCTCACTCCGG
DroWil_CAF1_left   GGTCGGGACGGCGCGAACGCCATTCCCGGCTACCAAAAATTACACGCACGAGTTATTCACATTAGGAATAATCGCAGAGGTCAACTCAGCCGAATGTGCAATGGCCAAGCCTCACTCCGG
DroYak_CAF1_left   TGTCGGGACGGCGCGAACGCCATTCCCGGCTACCAAAAATTACACGCACGAGTTATTCACATTAGGAATAATCGCAGAGGTCAACTCAGCCGA-GGTGCAATGGCCAAGCCTCACTCCGG

DroPer_CAF1_left   AGGAACACGCCTTGGTGATCACGGTTAACCTCTACGCCAGGTAAGTATGCTTTTCTCCGCTCGACAGCAGGGTTTCCTTGCCCCTGTGGCTAGAACTGGTTGGGAATTATAAGGCTT
DroPse_CAF1_left   AGGAACACGCCTTGGTGATCACGGTTAACCTCTACGCCAGGTAAGTATGCTTTCCTCCGCTCGACAGCAGGGTTTCCTTGACACCGAGGCTAGAACTGGTTGGGAATTATAAGGCCC
DroAna_CAF1_left   AGGAAC-CGCCTTCGTGATCACGGTTAACCTCTACGCCAGGTAAGTATGCTTTATTCCGCTGAACAAAAGGGTTTCCACTAAAGTGCTGCTAGAATCAGTTGAGAATTATAACGGTC
DroEre_CAF1_left   AGGAAC-CGCCTTCGTGATCACGGTTAACCTCTACGCCAGGTAAGTATGCTTTTGGCTGCTCGGCAGCAGGGTCTCCATGCCACAGCAGCTAGAACCAGTTGGGAATTGCAACGAGC
DroMel_CAF1_left   AGGAAC-CGCCTTCGTGATCACGGTTAACCTCTACGCCAGGTAAGTATGCTTTTCGATGCTCGGCAGCAGGGTTTCCATGGCTGAGCAGCTAAAACCAGTTGGGAATTGCAACGAAC
DroSec_CAF1_left   AGGAAC-CGCCTTCGTGATCACGGTTAACCTCTACGCCAGGTAAGTATGCTTTTCGCTGCTCGGCAGCAGGGCTTCCATGACTGAGCGGCTAAAACCAGTTGGGAATTGCAACGAAC
DroSim_CAF1_left   AGGAAC-CGCCTTCGTGATCACGGTTAACCTCTACGCCAGGTAAGTATGCTTATCGCTGCTCGGCAGCAAGGTTTCCATGCCTAAGCGGCTAAAACCAGTTGGGAATTGCAACGAAC
DroWil_CAF1_left   AGGAAC-CGCCTTCGTGATCACGGTTAACCTCTACGCCAGGTAAGTATGCTTTTCTCCGCTCAGGATAAGGGTTACCATGCCTGAGTTGCTAGAACTGTTTGGGAATTGTAAAGAGA
DroYak_CAF1_left   AGGAAC-CGCCTTCGTGATCACGGTTAACCTCTACGCCAGGTAAGTATGCTTTTCGCTGCTCGGCAGCAGGGTTTCCATGCCAGAGCGGCCAGAACCAGTTGGGAATTGTAACGAAC