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


DroAna_CAF1_left   TGTTCTT------------GGTTTTCTTTAA---ATATATTTTAAAT--ATTTAAAA-ACGCCAACA--AAACATA-AATAAATAATAAAGTAAAAACTTTTAAAGCATATTTGGCCAAA
DroMel_CAF1_left   TTAAGCCTAATT---------AGTT-AAGTA-AAGGATATGTGATAG--TCGAGAGT-CTCGACATA--ATGGGTT-TCCTCTGG--TAATCAATTAACTATTAAAATTTG---TATATT
DroSec_CAF1_left   TTAAACCTAATTAGTTAAGTAATGG-ATATGTTGATAGTAGAGAGTT--TCGACACA-ATGGGTTT-----------CC-TCTGG--TAATCAATTAATTATTAAAATTTG---ATATTT
DroSim_CAF1_left   AATT--------AGTTAAGTAATGG-ATATG-TGATAGTCGAGAGTC--TCGACACA-ATGGGTTTC--CAATTAA-TCAATGGG--TAATCAATTAATTATTAAAATTTG---ATATTT
DroYak_CAF1_left   AAAT-CTGAATTAA-------A----CATGA-TTAGATGAGTAACGGGTATCTGATAGTCGATAGTG--TCGA-CAATG-AGTTA--TTGTCTAATAATTATTAAAATTTG-A-ATATTT
DroEre_CAF1_left   TCAAGACTTC-TAT-------C----CATTT-ATAAATTAGGATAAA-TTGAATTGCTAAAT-AGGAAGCTCG--A-AAATTGTT--TTTTATTA-T--TTATTCATTTGG---AA----
DroPer_CAF1_left   AGGTTATTCA-TTC-------G----AAATT-GATTGAGCCCGACAT-TAGGTCAATTGGAA-TTTTATTTCC--A-TTTTAAGT--AAAATATA-GTTTTACGCAACAGA---AAAATG
DroPse_CAF1_left   AGGTTATTCA-TTC-------G----AAATT-GATTGAGCCCGACAT-TAGGTCAATTGGAA-TTTTATTTCC--A-TTTTAAGT--AAAATATA-GTTTTACGCAACAGA---AAAATG

DroAna_CAF1_left   AATAAAAAATT-GTAAGTCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAGCTAGCCGGGCTGTTGAAATTAGGGCAGCAAAGTTCTCAA
DroMel_CAF1_left   TACTACAAAAT-ATTGGTCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAGCTAGCCGGGCAGGTAAACAAA-ATTGCCGTCTGTCAAAA
DroSec_CAF1_left   AATACAAAATA-TTTGGTCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAGCTAGCCGGGCAGGTAAACGGA-TATGCTGTCTGTCAAAA
DroSim_CAF1_left   AATACAAAATA-TTTGGTCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAGCTAGCCGGGCAGGTAAACGGA-TATGCTGTCTGTCAAAA
DroYak_CAF1_left   AGAGTAAAATATATTGATCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAGCTAGCCGGGCATGTGAATTTG-GTCGCTGGCTGTCAAAA
DroEre_CAF1_left   --TTAAAAAAA-ATGCATCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAGCTAGCCGGGCAGGTAAACGAA-TTCGCTGTCTGTCAAAA
DroPer_CAF1_left   ACAAAAGAAAA-AAACGTCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAGCTAGCCGGGCATGTAATTTAG-GCCA---AAACATATA-
DroPse_CAF1_left   ACAAAAGAAAA-AAACGTCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAGCTAGCCGGGCATGTAATTTAG-GCCA---AAACATATA-

DroAna_CAF1_left   AGCAAGTTAACAG-TTCCACATA--AT-T-----ATGTTATTCTAAAAATAGATA--GAC-TATTTAAATGTGT---TTAGAACTATTTCTATT-TTTATAAAAATATATCTAATCATTA
DroMel_CAF1_left   CTCGGGAAAA-TATATCAAATGGGGTT-AGGAACTATAGACATGCGT-CTAGTAT--TTTGTTT-AGAAATGAA---AAACAAGATAGA--ATTCTAAAGT--CGTGTTC-----CCTGA
DroSec_CAF1_left   CTCGGGAAAA-TATATCAGATA---CT-A-----GATAGATGTCCGT-CTAGTAT--TTTCTTT-AGAAATTAA---AGAGAGAATGCTATAGTCGAGATCCCCGACTATC-AGAATTCC
DroSim_CAF1_left   CTCGGGAAAA-TATATCAGATA---CT-A-----GATAGATGTCCGT-CTAGTAT--TTTCTTT-AGAAATTAA---AGAGAGAATGCTATAGTCGAGATCCCCGACTATC-AGAATTCC
DroYak_CAF1_left   CGATCTAAAA-CTGAATAAATT---TAGA-----ATTAAACCTATAA-AATAAGT--TTATGAA-AGTATTG-G---TTCTACAACATATAAAACATTTTCAGTCAAAAAC-AAGAGAGA
DroEre_CAF1_left   CTCGGGAAAA-TATTATATCAATTGGT-T-----ATAAACAGAT----TCGTTCTACGAGA----TCTTCGCCTAGTATTTAGTCAATAAATTGAAAA--CTAGATCAATA-TCAAAACT
DroPer_CAF1_left   --TCCACAAG-GAATATTCGATATAGT-A-----TATAGTATAT----CCATTTC--TATA----A-ATAGTCT---TTCGAAACAAAATTTTCCGAG--C-AGAATTTTC-C---TAGG
DroPse_CAF1_left   --TCCACAAG-GAATATTCGATATAGT-A-----TATAGTATAT----CCATTTC--TATA----A-ATATCCA-T-TTCTATACAAAATTTTCCGAG--C-AGAATTTTC-C---TAGG

DroAna_CAF1_left   GGCCTA
DroMel_CAF1_left   CTATCA
DroSec_CAF1_left   GTTACT
DroSim_CAF1_left   GCTACT
DroYak_CAF1_left   ACGCTA
DroEre_CAF1_left   GGCACG
DroPer_CAF1_left   ATGGTA
DroPse_CAF1_left   ATGG-T