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


DroEre_CAF1_left   AACAGCCC--GCCTAAA----CTTTT--TTCTTTTAGAGAAGT-AGTTCTGTAACTTTCAGATGATCAGTCTT-ATACTCCCGTGGGTAG-AGGG-AAATTGGAAGATCCACCTGA-ATA
DroMel_CAF1_left   CT--ACTT------TTAGGTGAGAAAACCACTACATGATTG-G-GGTGCTATAACTTTTAAATAGCTAGTCTT-ATACTCCCGAAAGTAT-TACGAAAATGTGAAGATCCACCTAA-ATA
DroSec_CAF1_left   CA--GCTTCTAGTTGTAGGTGAGAAAACCACTATATCATTG-G-GGTGCTATAACTTTTAGATAGCTAGTCTT-------TCGAAAGTAT-TTCGAAAATTTGAAGATACACCTGA-ATA
DroSim_CAF1_left   CA--GCTTCTACTTTTAGGTGAGAAAACCACTATATCATTG-G-GGTGCTATAACTTTCAGATAGCTAGTCTT-------CCGAAAGTAT-TTCGAAAATTGAAAGATCCACCTAA-ATA
DroWil_CAF1_left   AC-TACTT--TG---------AGA-ATCGCTGATCTTATTC-G-----CAATCTTCCAG--ATTTTGGTACAA-ATCATCAAAAATGTAT-CACTTTGTCA--TTGAAAGTTAGTTTTTA
DroYak_CAF1_left   CA--ACCC--GCCTATA----CTTTTTCTTCTTCCAGAGAAAT-AGGACTTTAACTTTCAGATAGCCAGTCTT-ATACTTCCGAGAATAT-TGAG-ATATGGGAAGATCCACCTGA-ATA
DroAna_CAF1_left   C---TTTACT------C----CGATC--TTTATAAAAAGTTTCAA-TG---AAAACCTTT--ACAATACTCACCCATTTCTTGTCAAACCTTTCATT----------AAAGAATA--ATC
DroPer_CAF1_left   TC--TTCATAT---TTA----CGAGT--AATGAACCATTTTCATGGCGCTAATGGCGTGA--TTTTTCGTCTGCTTACGCAAAATTGATCCCTCGCA----------TGATTTTAG-AAG
DroPse_CAF1_left   TC--TTCATAT---TTA----CGAGT--AATGAACCATTTTCATGGCGCTAATGGCGTGA--TTTTTCGTCTGCTTACGCAAAATTGATCCCTCGCA----------TGATTTTAG-AAG

DroEre_CAF1_left   CTCACCAGAAAATGACCTCCCCT--TA-AGACGCATCGCG--GTACCAGACTTGAAAATCGTCCGATGAATGCTAAACAAATTTCTCACACACCTGAAATTTTGCTCAACCGGAT-CGTA
DroMel_CAF1_left   TTTACCAGAAAATGATCTCCATT--TA-AGCCGATTCACT--TTACCAAACTGGAAAATTCTCCGATGAATGCTAAACACATTTCTCACACACCTGAAATTTTGCTCAACCGGAT-CGTT
DroSec_CAF1_left   CTCACCGGAA-ATG---AT------------------------CACCAGTCTGATAAATCCTCCGATGAATGCTAAACACATTTCTCACACACCTGAAATTTTGCTCAACCGGAT-CGTT
DroSim_CAF1_left   CTCACCGGAA-ATGATCTCCATT--CA-AGCCCCATCACT--TTACCAGACTGGAAAATCCTCCGATGAATGCTAAACACATTTCTCACACACCTGAAATTTTGCTCAACCGGAT-CGTT
DroWil_CAF1_left   T--ATATTTGAATTTTCA-CAAT--AT-T---TGATCACT-----TCGTTTGGGGTATTCCAACGATGTTACCGTCACAAATTTCTCACACACCTGAAATTTTGCTCAACCGGAAATGAT
DroYak_CAF1_left   CTCACCAGATAAGGATCTCCACC--CA-AGCCGCATTGCT--TTACCAACTTTGCAAATCCTCCGATGAATGCTAAACAAATTTCTCACACACCTGAAATTTTGCTCAACCGGAT-CGAA
DroAna_CAF1_left   TTTGAAATTTTCATACCAGGACTCAAAGAT-CTC--GATTGTATTCC-----AAACTATCTTTTGAAGATTGCTTAACAAATTTCTCACACACCTGAAATTTTGCTCAACCGGAT-TCTG
DroPer_CAF1_left   TTCCCTAATGACTCACCGCCAAAGACAGAGTTTCAATCCC--GATTCCG-ACTGCTGATGGAGTGAAGATTGCTTAACAAATTTCTCACACACCTGAAATTTTGCTCAACCGGGA-TGAA
DroPse_CAF1_left   TCCCCTAATGACTCACCGCCAAAGACAGAGTTTCAATCCC--GATTCCG-ACTGCTGATGGAGTGAAGATTGCTTAACAAATTTCTCACACACCTGAAATTTTGCTCAACCGGGA-TGAA

DroEre_CAF1_left   -GGCCATAA-TGGCAACGGTTCAGCAAGATACAGGCGCGAATGAAATATGCCGCC-AAAGGACTCG--TGTTCAGCAAGGAC-AAATGAATCA--CCAA-GTAGGTATC--ACTAGCACT
DroMel_CAF1_left   -GGCCATAA-TGGCAGCGGTTCAGCAAGATACAGGCGCGAATGAAATGTGTTGCC-AAAGGACTTTG-GTGTCAACGAGGACGAAATGAATCA--CCAT-GT----A-----CCACCACT
DroSec_CAF1_left   -GGCCATGA-TGGCAGCGGTTCAGCAAGATACAGGCGCGAATGAAATGTGCCGCC-AAAGGACTTGG-TTGTCAGCCAGGACGAAATGAATCA--CCAT-TTAAGTAGCA-AGTAACACT
DroSim_CAF1_left   -GGCCATGA-TGGCAGCGGTTCAGCAAGATACAGGCGCGAATGAAATGTGCCGCC-AAAGGACTTAA-GTGTCAGCCAGGACGAAATTAATCA--CCAT-TTAAGTATCA-TCTAACACT
DroWil_CAF1_left   -GATCACAATTGGTAACGGTTCAGCAAGATACAGGCGCGAATGAAATATGCCGGCCAAATGTTAATT-TTGATTGGAACCAT-GAAGGATACA--CAGG-GACACAGACACACCCACACA
DroYak_CAF1_left   -GACCATAA-TTGTAACGGTTCAGCAAGATACAGGCGCGAATGAAATATGCCGCC-AAAGGACTTG--GACACAACCAGGAC-AAATGAATCA--CCAA-GTAGATATG--ACTAGCACT
DroAna_CAF1_left   -TGCCATAT-CGGTAACGGTTCAGCAAGATACAGGCGCGAATGAAATATGCCGCT-TGAAAGGATTCACTTAAATCCAGAATCTATG-CTTCACTAGCACTAAATATTTTGGGTATTACC
DroPer_CAF1_left   AGACCATTA-TGGCTACGGTTCAGCAAGATACAGGCGCGAATGAAATATGCCAGC-ACACGGTAGGATGTCAAGGAAAATCTCTAAG-CACCA-GAGCT-TGAAGGGACACTTGGATATG
DroPse_CAF1_left   AGACCATTA-TGGCTACGGTTCAGCAAGATACAGGCGCGAATGAAATATGCCAGC-ACACGGTAGGATGTCAAGGAAAATCTCCAAG-CACCA-GAGCT-TGAAGGGACACTTGGATATG

DroEre_CAF1_left   GAAACAGCGAGT-GCCACTGGAACCGGGACCGCAACTTTTCCT-GGCCACGCTCG----G
DroMel_CAF1_left   GAATCAGCACTTGGTCACTGAAACCGGGACCGCAACTTTTCCT-GGCCACGCTCGGATTC
DroSec_CAF1_left   GAATCAACACTTGGTCATTGGAACCGGGACCGCAACTTTTCCT-GGCCACG--------C
DroSim_CAF1_left   GAATCAGCACTTGGTCACTGGAACCGGGACCGCAACTTTTCCC-GGCCACG--------C
DroWil_CAF1_left   CAAGGTAGAAACTAGAATTGGAACCGTAACCGCAACTATTCCG-GACAACGTT-----TG
DroYak_CAF1_left   GGAACTGCGTGT-GGCACTGGAACCGGGACCGCAACTTTTCCT-GGCCACGCTCG----G
DroAna_CAF1_left   GTAAC--------CGCAACTTTTCCTGACCACGCTCGGACTCGAACTGATGGCCA---AA
DroPer_CAF1_left   GAAGT--------AGAACCGCGACCGCAACCGCAACTATTCCT-GGCAACGCTCG---AA
DroPse_CAF1_left   GAAGT--------AGAACCGCGACCGCAACCGCAACTATTCCT-GGCAACGCTCG---AA