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


DroPer_CAF1_left   TT-----TCAATTTTTACCCATCCATTGTTGAATTATGCTCTTCAATACGTACTTATGTTATT------GTTTTTTTTTACATTTCCAGTTTGAACCATTGATGCATGGA-TTGT----G
DroPse_CAF1_left   TT-----AAATTT-TTACCCATCCATTGTTGAATTATGCTCTTCAATACGTATTTATGTTATT------GTTTTTTTTTACATTTCCAGTTTGAACCATTGATGCATGGAATTGT----G
DroEre_CAF1_left   AG-----CTGACAAAATATCGCTATT---TGCGATAGCT-----AAACACTAGCCAT-TGTTT-AATATCCATAT---TATTTTTCCTTCTAGGTAATACCTGACATCTG-GCATCGATT
DroMel_CAF1_left   AG-----CTGACAACATAACGCATTT---CGTTATAGTT-----GATAAATCGACAT-TTGTTTTAAATCCACATTGTTATTTTTCCTTTTAGGTAATACCTGACATCTG-GCTT----T
DroSec_CAF1_left   AG-----CTGACAAAATAACTAATTT---CGTTATAGTT-----AATATATCGCCAT-TTGTTTTAAATCCACATTGTTATTTTTCCTTTTAGGTAATACCTGACATCTG-GCTT----T
DroSim_CAF1_left   AG-----CTGACAAAATAACTCGTTT---CGTTATTGTT-----AATAAATCGCCAT-TTGTTTTAAATCCACATTGTTGTTATTCCTTTTAGGTAATACCTGTCATCTG-GCCT----T
DroYak_CAF1_left   AATTCAGCTGACATAAACTCGTCATT---CGTGAAAGCT-----AAACACTCGACATTTGTTT-AATATCCACTT---TATCGTTTCTTCTAGGC--TACCTGGCTTTAG-GCTT----T

DroPer_CAF1_left   GCATGGCCCTCTTGTGAGCTAATGGTACGTAATA-TTTAATTTGTTGACCCTCCGCTGATTC-CATTTCATGACGAATACCTTGACAAGCATATACCTGAATGTTTATGTCGAATACACA
DroPse_CAF1_left   GCATGGCCCTCTTGTGAGCTAATGGTACGTAATA-TTTAATTTGTTGACCCTCCACTGATTC-CCTTTCATGACGAATACCTTGACAAGCATATACCTGAATGTTTATGTCGAATACACA
DroEre_CAF1_left   GTGA-TTCTGCTAAACTATGGTGGTA-AGTATT---TTTTAAATTCTTGCAAGATTA-TCAT-TTTTTCTTGAAGAAAACCTAGACAAGCATATAGCTGAATTTCTCTGTCGAAAACTCA
DroMel_CAF1_left   GTGA-TTCAGCTGAACTTTTGTGGTA-AGTATTT-GCTTTAAATTTTTGCCAGCTTA-TCAT-TTTTTCTTGATGAAAACCTAGACAAGCATATAGCTGAATTTCTCTGTCGACAACTCA
DroSec_CAF1_left   GTGA-TTCAGCTGAACTTTTGTGGTA-AGTATTT-GTTTTTAATTCTTGCCAGCTTA-TCATTTTTTTCTTGATGAAAACCTAGACAAGCATATAGCTGAATTTCTCTGTCGACATCTCA
DroSim_CAF1_left   GTGA-TTCAGCTGAACTTTTGTGGTA-AGTATTT-GTTTTTAATTCTCGCCAGCTTA-TCAT-TTTTTCTTGATGAAAACCTAGACAAGCATATAGCTGAATTTCTCTGTCGACAACTCA
DroYak_CAF1_left   GTGA-ATCAACTGAACTTTGT-GGTA-AGTATTTTTTTTTTATTTCGTGCCAGGTTA-TCAT-TTTTTCTTGATGAAAACCTAGGCAAGCATATAGCTGAATTTCTCTGTCGATAACACA

DroPer_CAF1_left   CTTGACTGATCCCCAAGCACACCCATCCACC-CCCTCCGCTCAATGTGATTCATTCGCAATCAGTAACTGATTCGTATCTT-ATCCTTT-TATTGTAGCCAGTGGCAGAATTCTGGAGAA
DroPse_CAF1_left   CTTGACTGATCCCCAAGCACACCCACCCACC-CCCTCCGCTCAATGTGATTCATTCGCAATCAGTAACTGATTCGTATCTT-ATCCTTT-TATTGCAGCCAGAGGCAGAATTCTGGAGAA
DroEre_CAF1_left   TGTGACTGAT---CAGTCACATTTATTTCTATCAATGTGATTAAACCTTAA-GAACACAACCTAATTTCTATGTTACCTTT---TTGCAGGT-ATCATACGGATTGTGAAGATCGATCAC
DroMel_CAF1_left   CGCGACTGATC--AAGTCATATTTATTTCCATCAATGTGATTAACCATTTA-ATACTGAAACTAATTTCCATCTTATCTGT-TCTTGCAGGT-ATCGTGCGAATTGCAAAGATCGACCAA
DroSec_CAF1_left   CGCGACTGAT---AAGTCACATTTATTTCCATCAATGTGATTAACCCTTTA-GTACTGAAACTAATTTACATTTTATCTAT-TCTTGCAGGT-ATATTGCGAAGATCGAACAAAGCCATT
DroSim_CAF1_left   CGCGACTGAT---AAGTCACATTTATTTCCATCAAAGTGATTAAGCCTTTA-AAACTGAAACTAATTTACATCTTATCTTTTTCTTGCAGGT-ATCATGCGAATTGCCAAGATCGACCAA
DroYak_CAF1_left   CGTGACTGAT---CAGTCACATTTATTTTCGTCAATATTATTAAACCTTAA-ATACAGAAACTAATTTCTATCTTATCTGT-TCTTGCAGGT-ATCATGCGGATTGCGAAGATCAAACAC

DroPer_CAF1_left   C-ATCGAC-TGA
DroPse_CAF1_left   A-AACTAA-ACT
DroEre_CAF1_left   CAAACGACAACA
DroMel_CAF1_left   C-GCCATT-TCA
DroSec_CAF1_left   T-CACTCC-AAA
DroSim_CAF1_left   C-G-CCAT-TTC
DroYak_CAF1_left   C-TCACTC-TGA