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


DroPer_CAF1_left   -TTTCGCAACTTCGC-TCTGCTTGTGCTCTCTGCTGTCGGTATGCTGTCGGC-TCTTGTGT---TCTTGT-ATCGCTTAAGCGCCGTCGCTCGCGAGTTCTCGGGTGGCTGAGTTGTTAG
DroPse_CAF1_left   -TTTCGCAACTTCGC-TCTGCTTGTGCTCTCTGCTGTCGGTATTCTGTCGGC-TCTTGTGT---TCTTGT-ATCGCTTAAGCGCTGTCGCTCGCGAGTTCTCGGGTAGCTGAGTTGTTAG
DroAna_CAF1_left   -TAGCGCAGTCGCTC-TTTGGGAACACACTCG----CAAGTTCTCTTTATTTCGCACGCTTCGCTCTTAT-GCTGCTTTAGCGCACGTCCATGCATGTGCCCGGGTAGCTCAGTCGGTAG
DroEre_CAF1_left   AAGAGAGT-A--CAG---AACGGCAGAGCGCCAGAACAGTTCTCTTGATTTTGGCGAGC-TTACTCTTATTCCGTTTTTCGCGACCCTGTTTCCATGTGCCCGGGTAGCTCAGTCGGTAG
DroGri_CAF1_left   -ACACACTCACACAC-GCAGTGACGCTCAGCG----AGAGCAAAGTGCGCTCTTTTCGCTTACTTGTTAG-TCAGCCACAGCGCCTCAGCATGCAAGTGCCCGGGTAGCTCAGTCGGTAG
DroMel_CAF1_left   -AGAGAGT-A--CAG---AATGGCAGAGCGCCAGAATTGTTCTCTTGATTTTGGCAAGCTTTGCTCTTATTGCATTTTTCGCGAGCCTGTTGCCATCTGCCCGGGTAGCTCAGTCGGTAG
DroMoj_CAF1_left   -ACGCACACTCACAC-AGAACTGCTGCTCTCC----TGAGCAAAGTGCGCTCTCGCAGGTTTGCTCTTAA-ACAGCCACGGTGCCTCAATTCGCAAGTGCCCGGGTAGCTCAGTCGGTAG
DroSim_CAF1_left   -GA-GAGT-A--CAG--GAATGGCAGAGCGCCAGAATTGTTCTCTTGATTTTGGCGAGCTTTGCTATTATTGCACTTGTCGCGAGCCTGTTGCCATGTGCCCGGGTAGCTCAGTCGGTAG
DroVir_CAF1_left   -CGTGAAT-ACTCAGAACAACCTCGTGGCGCTGAGAGCGAA-GTGCGCTCTTTTGGT---TTACTCTTAAG-CAGTCACAGCGCCTCGTTCTGCAAGTGCCCGGGTAGCTCAGTCGGTAG
DroYak_CAF1_left   -AGAAAGT-A--CAG---AATGGCAGAGCGCCAGAACTGTTCTCTTGATTTTGGCGATGTTTGCTCTTATTTCGTTTTTCGCGACCCTGTTGCCATGTGCCCGGGTAGCTCAGTCGGTAG

DroPer_CAF1_left   AGCATTGGACTGTTAACCCAAAAGGATCCAGGGTTCAAGTCCCTGCTGGGGCGATTCCAACTCCTTTTTCTTTT-----TT-ATTTCGTTT-TAAAAT--A-TTTTAATAATTATTTTTC
DroPse_CAF1_left   AGCATTGGACTTTTAACCCAAAAGGATCCAGGGTTCGAGTCCCTGTTGGGGCGATTCCAACTCCTTTTTCTTTT-----TT-ATTTCGCTT-TAAAAT--A-TTTTAATAATTATTTTTC
DroAna_CAF1_left   AGCATTGGACTTTTAATCCAAGG--GTCCAGGGTTCAAGTCCCTGCTCGGGCGAGCCAACTTTTTTTGCTTTAT-----TT-TTTATTATT-TAATTT--T-TTAGCAAATTATTTTAAA
DroEre_CAF1_left   AGCATTGGACTTTTAATCCAAGG--GTCCAGGGTTCAAGTCCCTGCTCGGGCGATCTGC-TTTTTTACTTTTT-----AAT-TCCACAACT-TTTTTTAGC-GCAGACTAATT-------
DroGri_CAF1_left   AGCATTGGACTTTTAATCCAAGG--GTCCAGGGTTCAAGTCCCTGCTCGGGCGAGCCAAACTTTTTTTTTAAAT-----TT-TCTCTTCCAGTTTTAT--T-TCAAAATATTTATTCGTA
DroMel_CAF1_left   AGCATTGGACTTTTAATCCAAGG--GTCCAGGGTTCAAGTCCCTGCTCGGGCGAAACATCAT-TTTTTTCCACT---------TTTTAACT-TTTTTCAGC-GCAGACTAATT-------
DroMoj_CAF1_left   AGCATTGGACTTTTAATCCAAGG--GTCCAGGGTTCAAGTCCCTGCTCGGGCGAGCCAACTTTTTTTAATTTTT-----TT-TTTATTATT-TAATTCTTT-TCAGTTCTTTATGTTTTA
DroSim_CAF1_left   AGCATTGGACTTTTAATCCAAGG--GTCCAGGGTTCAAGTCCCTGCTCGGGCGAAAAATCTT-TTTGTTCACTT-TTTAACTTCCATAACT-TTTTTCAGC-GCAGACTAATT-------
DroVir_CAF1_left   AGCATTGGACTTTTAATCCAAGG--GTCCAGGGTTCAAGTCCCTGCTCGGGCGAGCCATTTTTTTATGTTTTAGTTTTTATTTTAATATTT-TTTTTATTTATTATATATTTT-------
DroYak_CAF1_left   AGCATTGGACTTTTAATCCAAGG--GTCCAGGGTTCAAGTCCCTGCTCGGGCGATCCATTTTTTATACTTTTT-----AAT-TCCATAACA-TTTTTCAGC-ACAGACTAATT-------

DroPer_CAF1_left   CATAC--ATTCTTCTCAT-TTTTTATTCTGTCTTTTTAGT-TT--TTTTGTAG--AGT----GTGG-GAA-AGAGCCT---------GGA-G
DroPse_CAF1_left   CATAC--ATTCTTCTCAT-TTTTTATTTTCTCTTTTTAGT-TT--TTTTGTAG--AGT----GTGG-GAA-AGAGCCT---------GGA-G
DroAna_CAF1_left   CATAT--TTC-CCTTTTTTTTATAAATATTTTTCATTCAT-TC-AGGGTGTGTGGGAA----AGAGCTGGAGGCT--T---------TGG-T
DroEre_CAF1_left   CATTT--TTA-TAAATAA-TTTCCATTCGTGTGGGAAAGA-GC-TGGAGGCTGTGATT-----CAT-TCATAAAAATG---------TGCAT
DroGri_CAF1_left   TATTTTAGAA-TTTTGGTGCGTGTGGGAAACTGCTGGCGGCGCAAAATTTCATTAATAAAATCCAAGAAAAAAGAATC---------TGC-A
DroMel_CAF1_left   CATTT--TTA-TAAATAT-TTTTCATTCGTGTGGGAAAGA-GC-TGGAGGCTGTGATT-----CAT-TCATAAAAATGTGCATGTGCAAC-A
DroMoj_CAF1_left   TATTT--AA------TGCGTGTGTGGGAAAGTGCCAGCGG-CCAAGATTTCAGTTC----ATTCATAAAATAAATGCA---------TGC-A
DroSim_CAF1_left   CATTT--TTA-TAAATAT-TTTTCATTCGTGTGGGAAAGA-GC-TGGAGGCTGTGATT-----CAT-TCATAAAAATG---------TGC-A
DroVir_CAF1_left   TGTCT--TGG-TTTTGTG-TGTGGGAAAATGCCTGCGGGC-AT-TGGAATTTCAT-TC-----ATA-AAATAAATGCA---------CGC-A
DroYak_CAF1_left   CATTT--TTA-TAAATATTTTTTCATTCGTGTGGGAAAGT-GC-TGGAGGCTGTGATT-----CAT-TCATAAAAATG---------TGC-A