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


DroAna_CAF1_left   ACAC-CTACT--ATGACGCATTGTTGGGCTTATATTATAAAT-TTTATA--ATCTAATTATAGTCTCTGCTCTCTCTAGACCT-CCTCG-CATCTGGAATT-CAGACATTCTACCG-ATT
DroEre_CAF1_left   GCTATAAATG--CATAGCTTTCGTTTATCTC---GGAAGTAT-TCTAATATTTGT-CTTTTCGATTAGGTCAGCAAACGAAAA-GTTCCGATAGTAACTAT-CAGTGATTGTACAA-AGG
DroMel_CAF1_left   TAAATGTTCT--TCTATGACTCAGCTATCGTTTATCTTGCAA-GTATTC--TATT-TTTTTCGATAAGATCAGCAAACGAAGA-GTTCCGAGGGTAAATAT-TAGG-ATTTTACGA-AAT
DroSec_CAF1_left   AAAT-GTTTT--TCTATGACTCAGCTATCGTTTATCTTGCAA-GTATTC--TATTTTTTTTCGATAAGATCAGCAAACGAAGA-GTTCCAATGGTAAATAT-TAGG-TATTTACGA-AAT
DroSim_CAF1_left   AAT--GTTTT--TCTATGACTCAGCTATCGTTTATCTTGCAA-AGATTCTATTTT-TTTTTCGATAAGTTCAGCAAACGAAGA-GTTCCGATGGTAAATAT-TAGG-ACTTTACGA-AAT
DroYak_CAF1_left   TTAT-GACTC--ATAGCCAGCGTTTATTTGGGAAGTAATGTAATAACAT--TTG--TGTTTTGATAAGATCAGCAAACTAAGA-GTTCCGAAGGTAAATAT-TTGT-GAT-TGTACCAAA
DroPer_CAF1_left   GGCT-CTATCGGGCGCGGGGCCTATGA-AATA---GAACCAA-ATCCAAA-ATAA-CTCTTCCCTTTTTTCCGGAATCTATAAGGAGCAGATGACACAAAATAACA-ACTTGACGG-CGG
DroPse_CAF1_left   CCAA-ATCCA--AAATAGCCAATGAGTCATCG---TTTGCAA-TTGGAAACTCTT-CAAGTCCCTTTTTTCCGGAATCTATAAGGAGCAGATGACACAAAATAACA-ATTTGACGG-CGG

DroAna_CAF1_left   GGATTCCATGTCCTCGATAGTATAGTGGTTAGTATCCCCGCCTGTCACGCGGGAGACCGGGGTTCAATTCCCCGTCGGGGAGGTT-AATTTTTTTTTA---ATT--CGTA---TAAGAAT
DroEre_CAF1_left   CAGTACCAAGTCCTCGATAGTTTAGTGGTTAGTATCCCCGCCTGTCACGCGGGAGACCGGGGTTCAATTCCCCGTCGGGGAGACGCGAGCGATTCGTATT---T-----T---TTTCTCT
DroMel_CAF1_left   TGATGCCAAGTCCTCGATAGTATAGTGGTTAGTATCCCCGCCTGTCACGCGGGAGACCGGGGTTCAATTCCCCGTCGGGGAGACGTGAGAGATTCGTTTAATTTTTTGTTG--TTCCTCT
DroSec_CAF1_left   TTGTCTCAAGTCCTCGATAGTATAGTGGTTAGTATCCCCGCCTGTCACGCGGGAGACCGGGGTTCAATTCCCCGTCGGGGAGACGTGAGAGATTCGTTTTATTTTTTGTGTTTTTCCTCT
DroSim_CAF1_left   TTGTGCCAAGTCCTCGATAGTATAGTGGTTAGTATCCCCGCCTGTCACGCGGGAGACCGGGGTTCAATTCCCCGTCGGGGAGACGCGAGAGGATCGTTTTATTTTTTGTG---TTCCTCT
DroYak_CAF1_left   GTACACCAAGTCCTCGATAGTATAGTGGTTAGTATCCCCGCCTGTCACGCGGGAGACCGGGGTTCAATTCCCCGTCGGGGAGATGCGAGTGAATCGTA--TTTATTTGTT----------
DroPer_CAF1_left   GAGAACCACATCCTCGATAGTATAGTGGTTAGTATCCCCGCCTGTCACGCGGGAGACCGGGGTTCAATTCCCCGTCGGGGAGATTCCAATTTGTTTTAT--T-------T---TTCTTCA
DroPse_CAF1_left   GAGAACCACATCCTCGATAGTATAGTGGTTAGTATCCCCGCCTGTCACGCGGGAGACCGGGGTTCAATTCCCCGTCGGGGAGATTCCAATTAGTTTTAT--T-------T---TTCTTCA

DroAna_CAF1_left   TTCAG-------------AGGCTTTAATATTGTCTTTAAGGAAATTAACATAATTTTGAAAGTTTTGCGGTAGGAGAAAA-CGATGCTC-CAATGAAGTTAAACATTTCTATTTGAATTT
DroEre_CAF1_left   CTCAGAAT-----ATGTTT-GCTTATTTATTGTATCTAAAAAAATTTACATAATTTTGAAAGTTTTAAAAGGCTT--TAAGACAGACGCTCGATAAAATCAAACATTTCTATTTGGAATT
DroMel_CAF1_left   CTTAGAATCTTTTTTGTTTTGCTTATTTATTGCTGCTAAAAACATTAACATAATTTTGAAAGTTTTAAAATGCCATATAAGCCAGACGCTCAATAAAATCAAACATTTCTATTTGGAATT
DroSec_CAF1_left   CTTAGAATCT-TTATGTTTGGCTTATTTATTGCTGCTAAAAACATTAACATAATTTTGAAAGTTTTAAAATGCTATATAAGCCAGACGCTCAATAAAATCAAACATTTCTATTTGGAATT
DroSim_CAF1_left   CTTAGAATCT-TTATGTTTGGCTTATTTATTGCTGATAAAAACATTAACATAATTTTGAAAGTTTTAAAATGCTATATAAGCCAGACGCTCAATAAAATCAAACATTTCTATTTGGAATT
DroYak_CAF1_left   --TTTCCTCT-TTTTGTTTTGCTTATTTATTGCTTCTAAAAACATTTACATAATTTTGAAAGTTTTAAAATGCTA--AAGGCCTGACGCTCAATAAAATCAAACATTTCTATTTGGAATT
DroPer_CAF1_left   GAGAATTTAA-TTTT-----G-TGAGATTTGCATATTTTTGAAAGTTTCTAGTAGTAGAAACCGG-ATAA--CCAA-------TCAAGCTGAACATTTCTATTCGAAT--GTTTTAAAAT
DroPse_CAF1_left   GAGAATTTAA-TTTT-----G-TGAGATTTGCATATTTTTGAAAGTTTCTAGTAGTAGAAACCGG-ATAA--CCAA-------TCAAGCTGAACATTTCTATTCGAAT--GTTTTAAAAT

DroAna_CAF1_left   CTGGACAGTCGG
DroEre_CAF1_left   TTTGGCAATGTT
DroMel_CAF1_left   TTTCGC--GGAG
DroSec_CAF1_left   TTTCGC--GAAG
DroSim_CAF1_left   TTTCGC--GAAG
DroYak_CAF1_left   TTTGGCAAAGTT
DroPer_CAF1_left   TAGCTCTCATTT
DroPse_CAF1_left   TAGCTCTCATTT