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


DroAna_CAF1_left   AACAACCTAAAAAAACTAAA-TTGAAAATAAATTAAATATAG-TT-AAA-----GCAAAATAAAATAA-AATTTAAAAAATAA-GATTTAATCAATGAAAAAATTAAAA-AT-AAATACA
DroGri_CAF1_left   TTATTTAA--TGTACCTTGAGCACTTTGCGT-TTTAAATTTTAAA-AA------ACG-GGCAATGCAA-AGTAGGCAGCTTTTATAATTTTTAT-TTGAAAACTAC-AA-AA-AATGTAC
DroMel_CAF1_left   GTTCTAACTTTTTG-GAACTTCGTAAAATAT-TTTTTAAATAAAT-ATA-----TTT-AAATTTTTTTAAGCAAAACATAATT-TAAAAAAATATAGTTGATAACAAAA-AT-TATTATC
DroMoj_CAF1_left   CAAATTTCAAATTA-TAAGTGTTAAAACATC-AGTAAAAATTATT-GTT-----ACATTTAAAAACAA-AAATATTAGTATAA-AAATAAAATATATAAAAAGTAAAAA-TT-TAATCCC
DroSec_CAF1_left   TTTTAAATTTTTTC-TAAACA--AAACATAA-TTAAAAAATAAAGTTGA-----TAA-CAAAAAATTGATATCAAA-A-TATT-TTTATATATATGTACGAGAAAAAAA-AA-AAACA-T
DroSim_CAF1_left   NNNNNNNNNNNNNN-NNNNNNNNNNNNNNNN-NNNNNNNNNNNNN-NNN-----NNN-NNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNAAA-AT-TATTCCC
DroYak_CAF1_left   TTTTTTAAACTTAA-TATATATAATTACTTT-AAAATTATTATAA-TTTATACAGAA-AAAACTATTTTTT----TTTAACAT-ATACATAATTGATAAAAAAAAAAAAGTAGGTTA-CC

DroAna_CAF1_left   ACT-TGGAGATGCGGGGTATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCGATGTACATGGTTGTACCAAATGCCC-TACTTGGTACTAGGC-
DroGri_CAF1_left   TTT-TGGAGATGCGGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCATTGAAACTGTTGTTATCCATTGAGC---GTTTTATCAGTCG-
DroMel_CAF1_left   AAT-TGGAGATGCGGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCGTCAGAAACTGTTGTGTCAAAGTACC-AAAATAGC-CAGCGT-
DroMoj_CAF1_left   AATTTGGAGATGCGGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCGTTGACCAAGTTGGGAACAGC-TGA--GCATTTTGTGAAACA-
DroSec_CAF1_left   CCT-TGGAGATGCGGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCGACGCAAATACCTGTGTCAAAATACC-TAAATAGG-CAGCGT-
DroSim_CAF1_left   AAT-TGGAGATGCGGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCGTTGCTAACGCTTGTGTCAAAATACC-TAAATACG-CAGGGT-
DroYak_CAF1_left   GAC-TGGAGATGCTGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCGTTGCAGAAAGTTGTGTCTAAATAGGCAGCATTGCT-G-TTTC

DroAna_CAF1_left   -CTTTGCAATTTGCTTTG--ATTTTGGCCAATTCAT----------TTTCAGATGGCCAACAAAATGTTTT-TTCTTTC-GCCC-CA-GATATTT-G-C-TTTTAG---CCTT
DroGri_CAF1_left   -GCTTGCGATTTG--TTGACATTGAA-----GAAAA----------ACCCGAGGCGACTGGAAGAGTCAATATCTATGTGAGTA-AATGAAATACCAAATTTTAATT--AATT
DroMel_CAF1_left   AGA-T---GTTCA--AAATCACTTCT-----TTTGGT-CAACTCATTTGGTAATTGAAAACATAAGTT--------GTTTTTTG-GTCGTAATTTCTGGTTTCAGCCTTGAAT
DroMoj_CAF1_left   -GCTTGCGATTTG--TTG--AATTTGTCTTGAGCAA----------AATTAAAGCGCTTTATAAAATCTTT-TTAAAACAAAAA-TT-TTCAAACAATATTACTTA---TCTT
DroSec_CAF1_left   AGC-T---GTTCA--AATTTATTTCT-----TTTGGT-CAATTCATTTGGTGATTGCCCACATAACTT--------GTTTTTTG-GTCGTAAGTTCTGGTTTCAGCCTTGAAT
DroSim_CAF1_left   AGC-T---GTTCA--AATTTATTTCT-----TTTGGT-CAATTCATTTGGTGATTGCCCACATAACTT--------GTTTCTTG-GTCGTAAGTTCATGTTTCAGCCTTGAAT
DroYak_CAF1_left   TTTTGGACACTTC------ATTTGAT-----G-ATTGGCCACATAACTTG-TTTCTTGGTC-----G---------TGATATCTGGT-TTTAGCCTTGAGTAC--TTGAAAAT