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


DroAna_CAF1_left   TATT-TTC-AGTCAAA--TATTA--TTTATTGTTT-AGAGAAAAGTTTAGAGA-GATG-AGGTGT-CTATATTG-TATCCTATATTGTATCCGGA-ACGCAGGTTCGCAGGAACGTAGAT
DroEre_CAF1_left   TCTCATCAGTTTTTGC--CAAAT--GTTCAAAGCT-TGAGGAATTTGTGCAAT-CAC---AATCT-GTCGAAGC-AAAATATTTCTATTTCATGT-ACTGGCAAACCACTGAACGCAGAT
DroGri_CAF1_left   AAAG-TTA-ATTAATT--TTGAT--GTGAGTGGAA-ATATAAAATGCATATAT-ATAT-TTAGCA-CAAGCTGA-AAAAATACACATCATTTCAA-AAATATTAGTTGCATAAAGTTGAA
DroMel_CAF1_left   CTC-ATCAGTTTTTCC--CAAAT--GTTCAAAGCT-TGAGGAATTTGTGCAAT-CAGA--AGTCT-GTTGACGG-AAAATATTTCTGTTTCATGT-CCTGGCAAACCACTGAACGTAGAT
DroMoj_CAF1_left   CAAT-TTA-AACTACA--ATAAG--TTCATATAAGACAACTCCATATAGCACA-CAGT-AA-AGG-TAACTCTC-TCTCTCGATTGGATCTTTGG-AAATTCTTCATTCTCAACGTTGAA
DroPer_CAF1_left   ATAT-ACTTTACTCTC--CTGAATCTGAGATATTC-TCTCCAACTTTTCGTAA-CATT-AATAAT---GTGTACACTT-TTTTTTTATATT-TCGAAAC-TGAAGTCCTGGATCGTTGAT
DroPse_CAF1_left   CATAAACTTTACTCTC--CTGAATCTGAGATATTC-TATCAAACTTTTCGTAA-CATT-AATAAT---GTGTACACTT-TT-TTTTATATT-TCGAAAC-TGAAGTCCTGGATCGGTGAT
DroSec_CAF1_left   TCA--TCAGTTTTTCC--CAAAT--GTTCAAAGCT-TGAGGAATTTGTGCAAT-CAGA-AAGTCT-GTTGAAGG-AAAATATTTCTGTTTCATGT-CCTGGCAAACCACTGAACGTAGAT
DroSim_CAF1_left   TCA--TCAGTTTTTCC--CAAAT--GTTCAAAGCT-TGAGGAATTTGTGCAAT-CAGA-AAGTCT-GTTGAAGG-AAAATATTTCTGTTTCATGT-CCTGGCAAACCACTGAACGTAGAT
DroVir_CAF1_left   AAAT-T-ATTCTTTAA--TATAT--TTTAATATT--TTAATATTGCTCAAAAAATGA--AATGATATAAAACAC-TTTATTATTAAATGAATCTC-TTTTTTTTTAAGAATTAAGTTGAG
DroYak_CAF1_left   CTC-ATCAGTTTTTCC--CAAAT--GCTCAAAGCT-TGAGGAATTTGTGCAAT-CACA--AGTCT-GTGGAAGG-AAAGCATTTCTATTTCATGT-CCTGGCACACCACTGAATGTAGAT
DroWil_CAF1_left   AGAA-C-GTTGAAACCGGGATTA--GAATAAGGAA-ACTACAAAATACTTGAT-GGTATATCAAT-CCATATT--GTTTTTTGTCTAAAAT-TTTATAT-GAA-ATTTTATATTGTTGAT

DroAna_CAF1_left   CGATTGGCAAACAAAAAAGAACAGCCACTGTGATATAAATGATGCGAAT------AACTACATCAGCAGCGACCGTTCCCTTCTTTTTGAACAATTTTCAATTTCTGTCCACCAACGTGA
DroEre_CAF1_left   CGATTGGCAAACAAAAAAGAACAGCCACTGTGATATAAATTGTGAGAGTTT--CGAACTACATCATCAGCCACCGTTCCCTTCTTTTTGAACAATTTTCAATTTTCG--CACCAAGGTGA
DroGri_CAF1_left   TCATTGATAAACAAAAAAGAACAGCCACTGTGATATAAAATATTTGAATCA--TGAACTACATCAGCAGCGAGCGTTCTCTTCCTTTTAAACAATTTATGAGTGGAG-TTAACAAAAAAA
DroMel_CAF1_left   CGATTGCCAAACAAAAAAGAACAGCCACTGTGATATAAATTGTGAGAGTTT--CAAACTACATCATCAGCAACCGTTCCCTTCTTTTTGTACAATTTTCAATTTTCG--CACTGAGGTGA
DroMoj_CAF1_left   AAATTGTTAAACAAAAAAGAACAGCCACTGTGATATAAAGATTAAATGAAT--TCGACTACATCAACAGCGAACGTTCTCTTCTCTTTAAGCAATTTACGGC-CACG--ATTTGAAACTG
DroPer_CAF1_left   CGATTGGCAAACAAAAAAGAACAGCCACTGTGATATAAATTGTGCGAAACT--TGAACTACATCAGCAGCAACCGTTCCCTTCTTTTTGAACAATTTTCAATTTG----GTGAATGCGC-
DroPse_CAF1_left   CGATTGGCAAACAAAAAAGAACAGCCACTGTGATATAAATTGTGCAAAACT--TGAACTACATCAGCAGCAACCGTTCCCTTCTTTTTGAACAATTTTCAATTTG----GCGAATGCGC-
DroSec_CAF1_left   CGATTGCCAAACAAAAAAGAACAGCCACTGTGATATAAATTGTGAGAGTTT--CGAACTACATCATCAGCAACCGTTCCCTTCTTTTTGTACAATTTTCAATTTTCG--CACTGAGGTGA
DroSim_CAF1_left   CGATTGCCAAACAAAAAAGAACAGCCACTGTGATATAAATTGTGAGAGTTT--CGAACTACATCATCAGCAACCGTTCCCTTCTTTTTGTACAATTTTCAATTTTCG--CACTGAGGTGA
DroVir_CAF1_left   AAATTGCTAAACAAAAAAGAACAGCCACTGTGATATAAAGAGTACAAAGGT--C-GACTACATCAACAGCGAACGTTCTCTTCCTTTTAAACAATTGACGAGCG-TC--ATTAAAGTGAA
DroYak_CAF1_left   CGATTGCCAAATAAAAAAGAACAGCCACTGTGATATAAATTGAGAGAGTTT--CGAACTACATCATCAGCAACCGTTCCCTTCTTTTTGAACAATTTTCAATTTTCG--CACTGAGGTGA
DroWil_CAF1_left   TGATTGTTAAACAAAAAAGAACAGCCACTGTGATATATTGTTAAACAAAATGGTATACTACATCAACAGCAACCGTTCCCTTCTTTTTAAACAAAAAATGA---------AAGAAAACGG

DroAna_CAF1_left   CACAAATGCGTGCC-ACAAATGAC-AAATCGGTGAACT-----TGTCGGTGCAGCCAAAA-AGAACAGCCACTGTGATATAGGT--------GAT--TTTTTTTTT
DroEre_CAF1_left   CACAAATGCGTGCC-ACAAATGAC-AAATCGCTGGAAT-----TGGCCGTGCAACCAAAA-AGAACAGCCACTGTGATATAGGA--------GTTTTCAATAATAT
DroGri_CAF1_left   AACACACGTAAAAT-AAAATAGAA-TAAAACACTGACA-----AATCGTTGCAAATGGCG-ATG-CAACCAAAAAGAACA--GC--------CACTGTGATATAGT
DroMel_CAF1_left   CACAAATGCGTGCC-ACAAATGAC-AAATCGTTGGAAT-----TGGCCGTGCAACCAAAA-AGAACAGCCACTGTGATATAGTA--------GTTTTTCAATAATA
DroMoj_CAF1_left   AACAA-ATCACATACTTAAGATAA-CACTATTCAAGAT-----TTATTTCACAGACAAAT-TGTTGGCTATTTGCGATGCAACC--------A-AAAAGAACAGCC
DroPer_CAF1_left   ------G--GCGGC-GGAGATGAC-AAATCGTTGGACT-----TGGCCGTGCAACCAAAA-AGAACAGCCACTGTGATATAGAAATGTCAAAGATGGGTGGATAAT
DroPse_CAF1_left   ------G--GCGGC-GGAGATGAC-AAATCGTTGGACT-----TGGCCGTGCAACCAAAA-AGAACAGCCACTGTGATATAGAAATGTCAAAGATGGGTGGATAAT
DroSec_CAF1_left   CACAAATGCGTGCC-ACAAATGAC-AAATCGTTGGAAT-----TGGCCGTGCAACCAAAA-AGAACAGCCACTGTGATATAGGA--------GTTTTTCAATAATA
DroSim_CAF1_left   CACAAATGCGTGCC-ACAAATGAC-AAATCGTTGGAAT-----TGGCCGTGCAACCAAAA-AGAACAGCCACTGTGATATAGGA--------GTTTTTCAATAATA
DroVir_CAF1_left   CAAATT-G-----C-ACAAGTTAGTTAATAATAAAAGTACTTTCGGCTGACAAATTGTTGTGGATTGCGATGCAACCAAA--AA--------GAACAGCCACTGTG
DroYak_CAF1_left   CAAAAATGCGGGCC-ACAAATGAC-AAATCGTTGGAAT-----TGGCCGTGCAACCAAAA-AGAACAGCCACTGTGATATAGAA--------GTTTCTCAATAATA
DroWil_CAF1_left   TAAAACAGAGAAAT-CTAAAAATA-AAGTTGTTGAAAA-----TGATCGTAAAACCAAAA-AGAACAGCCACTGTGATATAG-----------AAAATC--ATTTT