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


DroAna_CAF1_left   ACAGG-TTTTTATTTTTAA----T------TAA---TTGGGTGTCGAATTGAAATGGCCTACTGACTTGAAATA--T---------GAAATTAGTTAATTTTCCGT-T------------
DroMel_CAF1_left   ATC---CATCCATGTTCG----CATATGCTTTAAGCCTAATTAGTTAATTA---------AAAGATATCCGATA------------GTCGAGAGT-CTCGACA--ATTGATTTTCTCT--
DroSec_CAF1_left   TTA-----TCCATGTTCA----CATCAGCTTTAAACCTAGTTAGTTAAGTA---------AAGGATACGTGATA------------GTCGAGAGT-CTCGACACAATAGGTT---TCCTC
DroSim_CAF1_left   GTAAT-TATCCATGTTCG----CATCAGCTTTAAACCTAATTAGTTAAGTA---------AAGGATACGTGATA------------GTCGAGAGT-CTCGACACAATATGTT---TCC--
DroYak_CAF1_left   TACATACATACATACATGTGAAAATCTGAATTAAACATGATTAGATGAGTA---------ACGGGTATCTGATA------------GTCGATAGT-GTCGACA--ATGAGTT---CTTG-
DroPer_CAF1_left   TTTTA-CTCCTTGATCG------ATCACTATGAAAC--AACAAGTATCTTA---------GGGTTTGTCGGAAAAGAATGGGCATCTATGTATGTATATATAT--CTG------------
DroPse_CAF1_left   TTTTA-CTCCTTGATCG------ATCACTATGAAAC--AACAAGTATCTTA---------GGGTTTGTCGGAAAAGAATGGGCATCTATGTATGTATATATAT--CTG------------

DroAna_CAF1_left   -AATACCCAATCGCCCGAATGACAAAAAAAAGA-AACGCGACCAAAATAATGAAATGCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAG
DroMel_CAF1_left   -GGTAATCAATTAACTATTAA-------AATTTGAATATTTACTACAAAATATTGGTCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAG
DroSec_CAF1_left   CGGTAATGAATTAACTATTAA-------AATTT-AATATTTAATACAAAATATTGATCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAG
DroSim_CAF1_left   -GGTAT-CATTTAACTATTAA-------AATTT-AATATTTAATACAAAATATTGATCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAG
DroYak_CAF1_left   ----TC-TATTAATTATTAAA-------ATTTG-AATATTTAAAGCAAAATATTGATCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAG
DroPer_CAF1_left   --TTTA-TTATTCACCTATTG-------CTTCA-AAAGATAGACCAAAAATAAATGTCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAG
DroPse_CAF1_left   --TTTA-TTATTCACCTATTG-------CTTCA-AAAGATAGACCAAAAATAAATGTCGCCCAACGTGGGGCTCGAACCCACGACCCTGAGATTAAGAGTCTCATGCTCTACCGACTGAG

DroAna_CAF1_left   CTAGCCGGGCATGTGGGCGTATCCGATCGGTATCAGAACCGG--AAGGTGTTCCC-----AATAG-ACCCGTGA-TATAGTTTCGGTCGTA---ATACTATAAAC-ACTACTTGCTCCCA
DroMel_CAF1_left   CTAGCCGGGCAGGTAAATGAATTTGCTGTCTGCCAAAACTCCGGAAAATATATGGGGT-AAATGG-GGTTATGAACTTGACATTCGTCT-A---ATATTTAGTTT-AGAAAAACAGTC-A
DroSec_CAF1_left   CTAGCCGGGCAGGTAACCGAATTTGGTGTCTGTGAAAAGTTGGGAAAATATATCA-----AATGG-GGTTATGAACTAGATCTTCGTCT-A---GTATTTAGTTT-AGAAAAACTATCGT
DroSim_CAF1_left   CTAGCCGGGCAGGTAACCGAATTTGGTGTCTGTGAAAAGTTCGGAAAATATATCA-----AATGG-GGTTATGAACTAGATCTTCGTCT-A---GTATTTAGTTT-AGAAAAACTATCGT
DroYak_CAF1_left   CTAGCCGGGCAGGTAAACGAATCCGCTGACTGTCAAAACTCGCGAAAATATATCAAAT-GGTTAT-AAACAGATTCGTTCTCTTAGATC------------GTTCTCTTAGAACTGTTCG
DroPer_CAF1_left   CTAGCCGGGCATGTGGGCCAATCGAATGCGATCCGTATCCGGCCAACACCTGCCAGGGCTGATGTCGATCTCAGT--CGTGATTCCACC-TCGTTCCACTGCGCC-ATAATATAAATATA
DroPse_CAF1_left   CTAGCCGGGCATGTGGGCCAATCGAATGCGATCCGTATCCGGCCAACACCTGCCAGGGCTGATGTCGATCTCAGT--CGTGATTCCACC-TCGTTCCACTGCGCC-ATGATATAAATATA

DroAna_CAF1_left   TACCAACTACATC--AA-G-TTGAACGCCCTTT--TCTT
DroMel_CAF1_left   CGCGAATTTTTAA--TC----GAACATACTT-A--TTTT
DroSec_CAF1_left   AGCTAAAATCAGT--AT-G-AAAACTGTCACGC--GAAT
DroSim_CAF1_left   ATCTAAAATCAGT--AT-G-AAAACTGTCACGC--GACT
DroYak_CAF1_left   TTTAATATTTAGTTTAT-AAATAATAATAATAG--TTTA
DroPer_CAF1_left   GGGCATCGTTCGA--AATG-GTTTCGACAACGCCTTTTG
DroPse_CAF1_left   GGGCATCGTTCGA--AATG-GTTTCGACAACGCCTTTTG