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


DroAna_CAF1_left   G---AACCAGACACGTGCGTGAAAACTCCGGAAAA--CCAGGGGAGGGGGGACAAAAAAAAAAACGGAA--AGGAAAAACGGAAAACGAACGAAAAACGTTTGT-AAACTCCAATGATTT
DroEre_CAF1_left   C---GTGCGTGAAAAACGCTCAGATGCAGATGTTG--TTGATGT-GATGTTATAAAGACCACGATCGAAAGAGGAAAAACGGATAGCGGACGAAAAGCGTTTGT-A-ACTCCAATGATTT
DroMel_CAF1_left   A---GGCACGTGCGTGAAA-AACGCTCAGATGCAG--ATGTTGTTGATGTTATAAAGACCACGATCGAAAGAGGAAAAACGGAAAACGAACGAAAAGCGTTTGT-A-ACTCCAATGATTT
DroSec_CAF1_left   GCCAGGCACGTGCGTGAAA-AACGCTCAGATGCAG--ATGTT---GATGTTATAAAGACCACGATCGAGTGAGGAAAAACCGAAAACGAACGAAAAGCGTTTGT-A-ACTCCAATGATTT
DroSim_CAF1_left   A---GGCACGTGCGTGAAA-AACGCTCAGATGCAG--ATGTTGTTGATGTTATAAAGACCACGATCGAATGAGGAAAAACGGAAAACGAACGAAAAGCGTTTGT-A-ACTCCAATGATTT
DroWil_CAF1_left   A---TATAAGAGTGAAAAA-TGTGTGCCCTCCCTTCCCCTTCGC-GTTGTCGCGCCCGCC-CTCATCTTCGTCTACCCTGATGATTTGTTTTTTTTTCATACAT-T-TTTTTGATGATTT
DroYak_CAF1_left   A---TGTTGTTGTTGTAGTTGTTGTTGATATGTTG--TTGTTGC-TTTATAAAGACCACGATCATCGAAAGAGGAAAAACGGAAAGCGAACGAAAAGCGTTTGT-A-ACTCCAATGATTT
DroVir_CAF1_left   A---TAAAAGTGCTACTTC-TCGCTGCCCACCGTC--TCCTACCCCTCGCA-AGATGCCAACC--CGCACCC-CCCCCCCCCCCCCGCGCGCTCTTTGTGTGTCGT-CTATCTCTGATTT

DroAna_CAF1_left   GACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTTTTTATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATACCACATTCCACATTCCGATGTATTTTTTTTTTTCTAC
DroEre_CAF1_left   GACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTTTTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATACCACATTCCACATTCCGATGGTCGATTTTTGTTGCTT
DroMel_CAF1_left   GACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTTTTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATACCACATTCCACATTCCGATGGTCGATTTTTGTTGTTT
DroSec_CAF1_left   GACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTTTTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATACCACATTCCACATTCCGATGGTCGATTTTTGTTGTTT
DroSim_CAF1_left   GACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTTTTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATACCACATTCCACATTCCGATGGTCGATTTTTGTTGTTT
DroWil_CAF1_left   GACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTTTTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATACCACAGAAAAAAA-AAGAAGAAAAAAAAATAACGATC
DroYak_CAF1_left   GACTACGAAACCGGTTTTCGATTTGGTTTGACTGTTTTTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATACCACATTCCACATTCCGATGGTCGATTTTGTTGTTGT
DroVir_CAF1_left   GACTACGAAACCGGTTTTCGATTTGGTTTGACTGTATTTCATACAAGTGAGATCATTTTGAAAGCTGATTTTGTCAATGAATACCACATTCCACATTCCAATG--------GTTTTT-GT

DroAna_CAF1_left   ---GTTTTTGGTTTTTTGTGTGCCTACACACA-GCCATATAGCGATATCGTGTAACAAAGCTTTGAACTAAT
DroEre_CAF1_left   ---GCTGTGCCTACACAGATATAGCGATATCGTGTAACAAAGCTTTGAACTAATGCCGACCGATC-CAAGTC
DroMel_CAF1_left   ---GGTGTGCCTACACAGATATAGCGATATCGTGTAACAAAGCTTTGAACTTATGCCGACCGATC-CCAGTC
DroSec_CAF1_left   ---GGTGTGCCTACACAGATATAGCGATATCGTGTAACAAAGCTTTGAACTTATGCCGACCGATC-CAAGTC
DroSim_CAF1_left   ---GGTGTGCCTACACAGATATAGCGATATCGTGTAACAAAGCTTTGAACTTATGCCGACAGATC-CAAGTC
DroWil_CAF1_left   ATCATCTTGC-CACATTCCGATGGCTCTGGCTCCTAACGAGATATCGTGTAACAAAGCTTTGAAC--TAATG
DroYak_CAF1_left   ---TGTTGTTGCTCGCTGTGCTATACTGTGCTGTGCCTACACAGATATAGCGATATCGTGTAACA-AAGCTT
DroVir_CAF1_left   ----GTGC-CCTGCACAC---AAGCACA--CGCTC-ACACA------CACACACGCTG--C------TAGAG