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


DroAna_CAF1_left   ATTCAAAATATTCATTTCAGATAT--AGTTTTAAGGGAGAT-ACTTAGGGTTTTTCAAAAA-ATA------AG-AATATTTTTAAAAATATATATTT-----ATGGATCAACATTTTTGT
DroEre_CAF1_left   TTTTATTTTGTGCT---T--TTAATATTAATGG--ATTTTGCAAC-TATCTAAAATGGAAATTAA------GTTTTAAGAT-CTGT--CATCTCTAAAAATAATATTACCACAATTCTAG
DroYak_CAF1_left   AGGATAATAC-------TTTTGTG--CTTTTAAATAATTTG-ATTTTGCAAATATCTTAAATCGA------AA-TTAAATTTTAAGATCTGCTCTAA-----AAATAATATTACCGCAAT
DroMel_CAF1_left   ATACTACTTCTGTATT-CGTTAT--AATAATGGATT---------CTGCAAATATCTGCATGTTAAATTATATTTTCAGAT-AATT--CATCT--ATAAATAATATTACCGGAAATCTTA
DroSec_CAF1_left   AAATACAGGTTTTAGT-TGTTCA--GGGTAATACTC---------CAGAAAACGTCTACATTTTGAATTATATTTTCAGAC-CTTA--CATCT--ATAAATAATATTACCGAAATTCTTG
DroSim_CAF1_left   AAATACAGGTTTTAGT-TGTTCA--GGGTAGTACTC---------CAGAAAACATCTACATTTTGAATTATATTTTCAGAC-ATTA--CATCT--ATAAATAATATTACCGAAATTCTTG

DroAna_CAF1_left   GATCTAAATGGATGCGACATGAT---CACAAGTCCCATATTGTCTAGTGGTTAGGATATCCGGCTCTCACCCGGAAGGCCCGGGTTCGATTCCCGGTATGGGAAACTTTTTTGCTAGAGT
DroEre_CAF1_left   GACATG-----TTTTCGATGTTGCATTCCAAGTCCCATATTGTCTAGTGGTTAGGATATCCGGCTCTCACCCGGAAGGCCCGGGTTCAATTCCCGGTATGGGAAATATGGC---TGTCAA
DroYak_CAF1_left   TCTTGGACGTGTTCTCGAAATTGCATCCCAAGTCCCATATTGTCTAGTGGTTAGGATATCCGGCTCTCACCCGGAAGGCCCGGGTTCAATTCCCGGTATGGGAAATATGGC---TGTAAA
DroMel_CAF1_left   AAA-----ATGTTTTTGATACTGCATCCCAAGTCCCATATTGTCTAGTGGTTAGGATATCCGGCTCTCACCCGGAAGGCCCGGGTTCAATTCCCGGTATGGGAAATATGGCTACAAGTAT
DroSec_CAF1_left   AAA-----CTGTTTTTGATTCTGCATCCCAAGTCCCATATTGTCTAGTGGTTAGGATATCCGGCTCTCACCCGGAAGGCCCGGGTTCAATTCCCGGTATGGGAAATATGGCTACAAATAT
DroSim_CAF1_left   AAA-----CTGTTTTTGATTCTGCATCCCAAGTCCCATATTGTCTAGTGGTTAGGATATCCGGCTCTCACCCGGAAGGCCCGGGTTCAATTCCCGGTATGGGAAATATGGCTACAAATAT

DroAna_CAF1_left   TATTAGTTCCAGCTTTAATTAATCGCTATGTTGCGAGATTCTTATAGCTTTTCATTACCTTTTT-GGACCACCTACAAACTGGG---TAGCCAAA-ATTTCG-TTCC--GTATGCTGTTC
DroEre_CAF1_left   GTT------TTTTTTT--TA-------TTTTGAAAACTTTCACGAGTAAGAAAAAGAAATAACT-TGCATTTATTACCTCTTTG---CTTGCATCAGTTATTATGACCCTGTTTGACGTT
DroYak_CAF1_left   GTT-----TTTTTTACATGTACACACATTTTGAATACTTTCACGAACAAGGAAATAAACTAACT-TGCATTTATTACTTATTTG---CTTGTAGT-TATAGT-TTAT--AGCTTATTGTT
DroMel_CAF1_left   T----TTTCCATA--CACAATTACATATTTTGAAAAAACTCACGACATAGGAAAATATCTAACT-AGACCACCAAG-AATTTGGCAGCTTCAAAA--ATTTG-GACG--TTGACTGTGTT
DroSec_CAF1_left   TTT--TTTCCATA--CACCATTGCACATTTTGAAAAAACTCACGAATAAGGAAAATATCCAAATTGGG--TTTATT-TTTCCTGCAGCTTTATTT--CATCA-TGCC--CTGATTAATGT
DroSim_CAF1_left   TTT--TTTTCATA--CACCATTGCACATTTTGAAAAAACTCACGACTAAGGAAAATAT-------GGG--TTTATT-TTTTCTGCAGCTCTATTT--CATTA-TGCC--CTGATTAATGT

DroAna_CAF1_left   TAAATCTCCGAAATCTCGGCCCG------ACA
DroEre_CAF1_left   GAGACCACCAGCGAATTGG-----------GC
DroYak_CAF1_left   TAGACCACCAACGAATTAGGCAG-------CT
DroMel_CAF1_left   CTAAATCT-AAATCTCTGAAAT-------CTC
DroSec_CAF1_left   TAGACCAGCAAATAAATCGGGAG-------CT
DroSim_CAF1_left   TAGATCAGCAAAGAATTCGGGAGCTTCGAAAA