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


DroAna_CAF1_left   CGCAGCTCAGGAACATCGTCGGGCGATGGAATGTATCTTTAAGACTATACTTCACAGGATCATTTCTGTAGTCAGTCTTCACATACTTTCACATTAGATGAAAGCTAAGCACACCCGCGT
DroEre_CAF1_left   CGTAGCGCACCAAGATCCACAGGTTGGGCAGCGAAAAGTTAAGACTATACTTCACAGGATCATTTCTGTAGTCAGTCTTCACATACTTTCACACTAGATGAAAGCTGAGTGCACCCGCGT
DroGri_CAF1_left   GGTGAGGCGACTAGAGCTCATTGTTGGGCGTTATAAAATTAAGACTATACTTCACAGGATCATTTCTGTAGTCAGTCTTCACTTACTTTCACACTATCTGAAAGCACTTCACACCCGCGT
DroMel_CAF1_left   CGCAGCGCACCAAGATCCACAGGTTGGGCAGCAAAAACTTAAGACTATACTTCACAGGATCATTTCTGTAGTCAGTCTTCACATACTTTCACACTAGCTGAAAGCCAAGTGCACCCGCGT
DroMoj_CAF1_left   AGCGCAGCGTATAGAGCGCTTCGGTGAGCGTTGAAAATTTAAGACTATACTTCACAGGATCATTTCTGTAGTCAGTCTTCACTTACTTTCACACAAAATGAAAGCACACCATACCCACGC
DroPer_CAF1_left   CGCGGCGGGTGAAGATCCACAGGTCGTGGCTGTAAAAGTTAAGACTATACTTCACAGGATCATTTCTGTAGTCAGTCTTCACTTACTTTCGCACAAATTGAAAGCCAAACACACCCGCGT
DroPse_CAF1_left   CGCGGCGGGTCAAGATCCACAGGTCGTGGCTGTAAAAGTTAAGACTATACTTCACAGGATCATTTCTGTAGTCAGTCTTCACTTACTTTCGCACAAATTGAAAGCCAAACACACCCGCGT
DroSec_CAF1_left   GACAGCGCACCAAGATCCACAGGTTGGGCGGCGAACAGTTAAGACTATACTTCACAGGATCATTTCTGTAGTCAGTCTTCACATACTTTCACACTAGCTGAAAGCCAAGTGCACCCGCGT
DroSim_CAF1_left   GACAGCGCACCAAGATCCACAGGTTGGGCAGCGAATAGTTAAGACTATACTTCACAGGATCATTTCTGTAGTCAGTCTTCACATACTTTCACACTAGCTGAAAGCCAAGTGCACCCGCGT
DroVir_CAF1_left   TGAGTGGCGTATAGAGCATTTTGGTGGGCATTGAAAAATTAAGACTATACTTCACAGGATCATTTCTGTAGTCAGTCTTCACTTACTTTCACACTTTCTGAAAGCAAGTCACACCCGCGT
DroYak_CAF1_left   TGCTGCGCACCAAGATCCACAGGTTGGACAGCGAATAGTTAAGACTATACTTCACAGGATCATTTCTGTAGTCAGTCTTCACATACTTTCACACTAGCTGAAAGCCAAGCGCACCCGCGT
DroWil_CAF1_left   CGATCAGCACCAAGGGGCCATTGACGGGCGTTGAAAATTTAAGACTATACTTCACAGGATCATTTCTGTAGTCAGTCTTCACTTACTTTCACATTGAAAGAAAGCCACATACACCCGCGT

DroAna_CAF1_left   TGATGAGGTGAATCGTTCTATTCGGCAGCGTGAGGATTTGTCCAGCGGCCTTTGTG-GTGTGGCGCTTCGGTGTCCGCATCCTCC--GGGTCGTCGGGCTTCGATGATCGCTCGGTA-AC
DroEre_CAF1_left   TGATGAGTTGAATCGTTCTATTCGGCAGCGTGAGGATTTGTCCAGTGTCCTTTT-G-GT-----GCTT-CGC------ATCTTTC--GGGACGCAGGGCTTCGATGATCGCTCGGTAGAA
DroGri_CAF1_left   TGATGAGGTGAATCGTTTTATTCGGCAGCGTGAGGTTTTGCGTGATGCCCTTT--G-CGGTATGACTTCGGTCAT--CCGTGTTG--TGGGCGTGGCGCTTCGATGATCGCTCGGTA-AC
DroMel_CAF1_left   TGATGAGTTGAATCGTTCTATTCGGCAGCGTGAGGATTTGCCCAGTGTTCTTTGTG-GT-----GCCT-CGC------ATCGTTC--GGGACGCAGGGCTTCGATGATCGCTCGGTAGAA
DroMoj_CAF1_left   TGATGAGATGAATCGGTTTATTCGGTAGCGTGAGGATTTGCGTTATGCCCTTTACGTTG----TGACTTGTTG-----CACGTATGATGGGTGTAGCGCTTCGATGATCGCTCGGTC-AC
DroPer_CAF1_left   TGATGAGTTAAATCGTCCTATTCGGCAGCGTGAGGTTTTGCCCAGCGCCCTTTCTG-GTGCGGCACTTCGGTGTCCGTGTCGTTC--GGGGCGCAGAGCTTCGATGATCGCTCGGTA-AA
DroPse_CAF1_left   TGATGAGTTAAATCGTCCTATTCGGCAGCGTGAGGTTTTGCCCAGCGCCCTTTCTG-GTGCGGCACTTCGGTGTCCGTGTCGTTC--GGGGCGCAGAGCTTCGATGATCGCTCGGTA-AA
DroSec_CAF1_left   TGATGAGTTGAATCGTTCTATTCGGCAGCGTGAGGATTTGCCCAGTGTCCTTGTTG-GT-----GCCT-CGC------ATCGTTC--GGGACGCAGGGCTTCGATGATCGCTCGGTAGAA
DroSim_CAF1_left   TGATGAGTTGAATCGTTCTATTCGGCAGCGTGAGGATTTGCCCAGTGTCCTTTTTG-GT-----GCCT-CGC------ATCGTTC--GGGACGCAGGGCTTCGATGATCGCTCGGTAGAA
DroVir_CAF1_left   TGATGAGATGAATCGTTTTATTCGGCAGCGTGAGGATTTGCGTGATGCCCTT--TG-CGATGTGATTT-TATCAC--TCGTTTTG--TGGGCGTGGCGCTTCGATGATCGCTCGGTA-AC
DroYak_CAF1_left   TGATGAGTTGAATCGTTCTATTCGGCAGCGTGAGGATTTGTCCAGTGTCCTTTGTG-GT-----GCTT-CGC------ACTGTTC--GGGATGCAGGGCTTCGATGATCGCTCGGTAACC
DroWil_CAF1_left   TGATGAGTTGGATCGTTCTATTCGGCAGCGTGAGGTATTTCGCAGTGCCCTCTT-----------------------------TG--GGGGCGCAGCGTTTCGATGATCGCTCGGTA-AA

DroAna_CAF1_left   ACGAATAGAGCGAATTCTGAGTGGTGCTCCTTTTTCTTGAATAA-ATTTGAAAT-CGTAACTATAGAAGAAA-CTATATATACTC----TTTGAT-C-GCA-AAA-T--GCTGT-GTGGC
DroEre_CAF1_left   ACGGATAGAGCGAATTCTGAGTGGTGCCCCCTTTTTTGCAAATC-AATTTAAAA-TCAAATTCAATTATTTAAGTATT---GCTT----AGTTAT-TAGTATTTTATATTTCGT-GAAGT
DroGri_CAF1_left   ACGAATAGAACGAATTCTGAGTGGTGTACAAAACCTTTTTAAAT-AATCAATTTGAACCTAATATTTTAAGT---GGA--AGTAG----TTAAGTAGCTGTCGG-----ACTCT-TCAGT
DroMel_CAF1_left   ACGGATAGAGCGAATTCTGAGTGGTGCCCCCTTTTATGCAAATA-AATTTAAAT-ATGTTTGTGAGTCTATA-GGTGT--CAAGG----TCAAAC-CAAGTCACTCTGACAAGA-TATTT
DroMoj_CAF1_left   ACGAATAAAACGAATTCTGAGTGGTTCTCAAACTTTTTAACGAATAAATTTAAT-AGTAGAGTAAGAGTTAA-GTATA--CTTGG----GTA-AA-AGCAGCTCATTGAGGTGA-ACCGG
DroPer_CAF1_left   ACGGATAGAACGAATTCTGAGTGGTGTACCTTTTTTAACAATAC-ATTTGACAA-ATTAAATCTTACTCATA-GTTTC--CACCC----AAC-TCTTTAGATTCTGAGTTGAGG-GTTGG
DroPse_CAF1_left   ACGGATAGAACGAATTCTGAGTGGTGTACCCTTTTTAACAATAC-ATTTGACAA-ATTAAATCTTGCTCATA-GTTTC--CCGCCCCCAAAC-TCTTTAGATTCTGAGTT-----GAGGG
DroSec_CAF1_left   ACGGATAGAGCGAATTCTGAGTGGTGCCCCCTTTTATGCAAATC-AATTTAAAC-ATCTATGCAAGTGCTGA-GAAAA--CAGTA----TTT-TT-AAAGTCATTAGGAATCGT-TCAGT
DroSim_CAF1_left   ACGGATAGAGCGAATTCTGAGTGGTGCCCCCTTTTATGCAAATC-AATTTAAAC-AGAGAGAGAAAAGAGTATTTTTA--AAATC----ATTAGG-AATTG-----TTCAGTTC-CTTCT
DroVir_CAF1_left   ACGAATAGAACGAATTCTGAGTGGTGTACCATCCTTTTAATGAA-TCAATTTAA-AGTTA-AAAACTATTGC-GTAGATAAATAG----CTAAAC-A-GTT-AGC-A--GTTGTTTAAAT
DroYak_CAF1_left   ACGGATAGAGCGAATTCTGAGTGGTGCTCTCTTTTATGCAAATC-AATTTCAAA-ATTTTCGGTTGTG-AGA-GATTT--TTAAA----TCT-GGTAGCTATAATCTAGATTTA-AGTAC
DroWil_CAF1_left   ACGAGTAGAACGAATTCTGAGTGGTGTATCTACACTTTTTTATT-AATCAATTTCAATTAAAAGAAAATATT-TTAAA--ATATT----GCA-A--GAGGTTATTGAGGATTGA-CAGCT

DroAna_CAF1_left   AAC-ATT-----GT-GTCTCAAC
DroEre_CAF1_left   ----TGG-----AT-TTCTGTCG
DroGri_CAF1_left   CTGATTT---T-CG-CTAGTAAA
DroMel_CAF1_left   ----GCA-----GA-GGATGTGT
DroMoj_CAF1_left   ----CTC-----AC-TCGCTCTT
DroPer_CAF1_left   ----AAA-----AT-GCTCAAAA
DroPse_CAF1_left   ----TTG-----GA-AAATGCTC
DroSec_CAF1_left   ----TCC-----TTCTTAAATTA
DroSim_CAF1_left   ----TAAATTATCC-TGA-TGTG
DroVir_CAF1_left   TAT-GTT-----AA-ATGCGAAC
DroYak_CAF1_left   ----ATA---G-TA-TGTTGTAT
DroWil_CAF1_left   --T-TAT-----AC-AAGTACGT