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


DroEre_CAF1_left   GGGGCTA-TACTTTCT-AATAATAAACAACTCATCTACATATGTCCGTGTAATCAGCTTACTCCATTTAAAATCCT-AAGAACTCCCTACTAATATTATT------ATGTTTAA-TTTTT
DroMel_CAF1_left   ATCTATA-TACATATAGATATACTGATCTGATACTGAT-ATATACTGATCTATATCCATATACTCCTTATAAACCT-AAGAACGCTCTACTTATTTTATTTTGTTCAAATTGTAATGGCT
DroPse_CAF1_left   GGCAGGTTAATTTCCT-TGCGACCATTCAATT--------TGCTCCAGCA-GCGATCAAACACAAAAAAAAAACAATAAAAACGTATATATGAACATATATATTTGTTAAGGCTGAAACT
DroSec_CAF1_left   TTTGGGG-TTGTTACT-TCCCTGGAAATTTAAACAATTCATCTACTCAGTACTCAGGCTACTCCATTTACTAACCT-AAGAACGCTCTACTAATTTTATATTGTTTAAATTGTAATTGTT
DroSim_CAF1_left   TTGTTCC-CTGTAAAT-TTAAACAATTCATCTACCTATGTATATCCATGTACTCAGGCTAATCCATTTACTAACCT-AAGAATGCTCCACTAATTTTATGTTGCTTAAATTGTAATTGTT
DroYak_CAF1_left   ACGGTTT-TGGGGGCT-AGTAACAAAAAACTCATCTGCATATATCCGTGTAATCAGCTCACCCCATTTAAAACCCT-AAGAACTCTCTTCTAATTTTATGTTGCCTAAATTTTA-GTTCT
DroPer_CAF1_left   GCAGGTT-AATTTCCT-TGCGACCATTCAATTTGCTCCAGCAGCGATCAAACACAAAAAAAAAAACAATAAAA------ACGTATA-TATGAACATACATATTTGTTAAGGGCTGAAACT

DroEre_CAF1_left   TA----TCGTTGTATGGAGCTGTTGATTA-AATTTTGGCACCCGCAGAACCACAGAATAA--TAAAATCAACTGTGAATTCTCCCAGTGCCAAGACTCAAAGTCAGCTATGGT-------
DroMel_CAF1_left   TAGAAATCGTTGTACAAAGCCGGTTTTTA-AGTTTTGGCACCCGCAGAACCACAGAATAA--TAAAGTCAACTGTGAATTCTCCCAGTGCCAAGACTCAAAGTCAGCAAATTGAAGAGCT
DroPse_CAF1_left   TTTCAGCTGCTGTTTCGAGCCGAACATTC-GATTTTGGCACCCGCAGAACCACAGAATATATGGAAACCAACTGTGAATTCTCCCAGTGCCAAGAGCCAATGCCAGCAATAACGATCGCC
DroSec_CAF1_left   TAGAAATCGTTGTATAAAGCCGGTTTTTA-AGTTTTGGCACCCGCAGAACCACAGAATAA--TCAAGTCAACTGTGAATTCTCCCAGTGCCAAGACTCAAAGTCAGCAAATTGAAGAGCT
DroSim_CAF1_left   AAGAATTTGTTGTATAAAGCCGGTTTTTA-AGTTTTGGCACCCGCAGAACCACAGAATAA--TCAAGTCAACTGTGAATTCTCCCAGTGCCAAGACTCAAAGTCAGCAAATTGAAGAGCT
DroYak_CAF1_left   TAGAAATCGTTGTATAGAGCCGTTGATTA-AATTTTGGCACCCGCAGAACCACAGAATAA--TAAAGTCAACTGTGAATTCTCCCAGTGCCAAGACTCAAAGTCAGCAGATTGAAGAGCT
DroPer_CAF1_left   TTTCAGCTGCTGTTTCGAGCCGAACATTCGATTTTGGGCACCCGCAGAACCACAGAATATATGAAAACCAACTGTGAATTCTCCCAGTGCCAAGAGCCAATGCCAGCAATAACGATCGCC

DroEre_CAF1_left   ------TTGAATCGCCAGTGGCTAAGCGGAGATCACCTGAGATCGCTTACCTTTGGATAGT-TTCTC-CAAATCTGACAGTTGTAAAGCACTTTTCAGGTTGATCCTTTCCGGTTTCTGG
DroMel_CAF1_left   ACAGCTCTGGATCGCT-------------GGATCACCTGAGATCGCTTACCTTTAGATAGT-TTCTC-CAAATCTGGCAGTTGTC-AGCACTTTTCAGGTTGATCCTTTTCGGCTTTTGG
DroPse_CAF1_left   GTAGTCGTTGTCTCAAACTA----------AGCTAAACTAAGCTAAACACTTTTCCTAAGC-CTAAGCGAAGACCATCATCTATG-GGCTTACCTCTGGAGGATCTTTCGTTTCGAATGA
DroSec_CAF1_left   AGCGCTCTGGATCGCCAGTTTAAAAGCGAAGATCACCTAGGATCGCTTACCTTTAGGTAGT-TTCTC-CAAATCTGGCAGTTGTC-AGCACTTTTCAGGTTGCTCCTTTTCGGTTTCTGA
DroSim_CAF1_left   AGAGCTCTGGATCGCCAGTTTAAAAGCGAAGATCACCTAGGATCGCTTACCTTTAGATAGT-TTCTC-CAAATCTGGCAGTTGTC-AGCACTTTTCAGGTTGATCCTTTTCGGTTTCTGA
DroYak_CAF1_left   ATCGTTCTGGATCCTCAGTTTCTAAGCGGGGATCACCTGAGATCGCTTACCTTTAGATAGT-TTCTC-CAAATCTGAGAGTTGTTGAGCACTTTTAAGGTTGATCCTTTTCGGTTTCTGG
DroPer_CAF1_left   GTAGTCGTTGTCTCA----AACTAAGCTAAACTAAGCTAA--ACACTTTTCC-T-AGCCTATCGAAG-ACCATCATCTATGGGCT-TACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

DroEre_CAF1_left   T-CGCGTTTC-ATCACTTTTTGGCAAGTCAGTGAGTAATT-TGGCTCTGAAGATTGTTTTTCGCATTGGTCTTCACTGGTTCACACA--TGCTGCAGCTGCAAGGACATGCTAATCC
DroMel_CAF1_left   C-CGTGTTTC-TTCACTTTTTGGCAAGCTAGTGAGTAATT-TGGTTCTGAAGATTGTATTTTTCAGTGGTCTTCACTGGTTCACACTGCAGCTGCAGCTGCAAGGACATGCTAA--T
DroPse_CAF1_left   TGTGTCTGTG-TTCCCTTTTGGCCACAGGATGGATGAATAATTTGTTCTATCTCTGGTCTCTGCACTACTGGCTTGTGGCTACCA-G--TTCTCATGCTGCAGCCGCAAGGACATGT
DroSec_CAF1_left   C-CGTGTTTT-TTCACTTTTTGGCAAGCTAGTGAGTATTT-TGATTCTGAAGATTGTATTTTGCAGTGGTCTTCACTGGTTCACACA--TGCTGCAGCTGCAAGGACATGCTAATCC
DroSim_CAF1_left   C-CGTGTTTTTTTCACTTTTTGGCAAGCTAGTGAGTAATT-TGGTTCTGAAGATTGTATTTTGCAGTGGTCTTCACTGGTTCACACA--TGCTGCAGCTGCAAGGACATGCTAATCC
DroYak_CAF1_left   C-CGTGTTGC-TTCACTTTTTGGCAAGTCAGTGAGTAATT-TGGTTCTGAAGATTGTATTTCGCATTGGTGTTCACTGGTTCACACA--TGCTGCAGCTGCAAGGACATGCTAATCC
DroPer_CAF1_left   N-NNNNNNNN-NNN-NNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTCTGCACTACTGGCTTGTGGCT--ACCAGTCTCATGC--TGCA