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


DroAna_CAF1_left   A-AAAA---ACATCGAAACTGGTTCGT-TGCATTATAAATTTAAATTTCCCTTTTG-TGGTTATTTTTAG-AAAATGTGTGCTATCGGTCGCTCA-ATTGGGCTA-TTTCGCCACGACAA
DroEre_CAF1_left   A-CAAA-AGACAT-TAAACAAGTTTTC-TGCATTGGAAATTAAAATACCACTATCT-AGTCTATTTTAAG-CTTGGGCCGGCGATT-TTCTCTCG-TTTGGGCTA-TTTGGCCATTCTGA
DroMel_CAF1_left   C-AAAA--GACATTTAAACAAGTTATA-TGCATTGCAAATTACAATTTCACTATCG-TGTGTATTTCAAG-CTTTGGGCAACAATT-TTCCCTCG-TTTGGGCTA-TTTGGCCGTCCCCA
DroMoj_CAF1_left   C-ATGT--TTTTTATAAGCCCGAAACT-GGTTAGATGCATAATAAATAGATTATTTGGGTCTTTTTTGAC-TATTTG-ATGAATCA-GTTACTTA-TAAAGGCTA-CTAGGCGATCGTCA
DroPer_CAF1_left   C-AAAA--GATACCGAAACTGGTT-GG-TGCATAACAAATTAAGATTTCAATTTTT--GGCTATTTTTAGATTTTGGCTAGCAATT-GGTTGTTGAAGTCGACTA-TTGGGACGCCCAAA
DroPse_CAF1_left   C-AAAA--GATACCGAAACTGGTT-GG-TGCATAACAAATTGAGATTTCACTTTTT--GGCTATTTTTAGATTTTTGCTAGCAATT-GGTTGTTGAAGTCGACTA-TTGGGACGCCTCAA
DroSec_CAF1_left   C-AAAA--GACATTTAAACAAGTTATA-TGCATTGCTAATTACAATTTCACTATCG-TGTCTATTTTATG-ATTTGGTCAACAATT-TTCCCTTG-TTTGGGCTA-TTTTGCCGCCCGAA
DroSim_CAF1_left   C-AAAA--GACATTTAAACAAGTTATA-TGCATTGCTAATTACAATTTCACTATCG-TGTCTATTTTAAG-ATTTGGTCAACAATT-TTCCCTTG-TTTGGGCTA-TTTGGCCGCCCGAA
DroWil_CAF1_left   T-GGTT--GATTGCATAATTTATT-GC-TGACTTTCACTTTTGGCCATGAATAACT-ATTTATAGACTTT-AAAACGATCGTTTCC-ATAACTTA-TAAAGGCCAATTCGGCTGTCGGAA
DroYak_CAF1_left   ACGAAA--GAAATTTAAACAAGTTACC-TGCATTGGAAATTAAAAT-TCACTATCT-GGTCTATTTTTAG-CTATGGCCAGCGGTT-TTTCCTCA-TTTGGGCTA-TTTGGCGGTCCTAA
DroVir_CAF1_left   C-ACGCATTTTTAAGAAACTAAAACTGGTTGAATGCATACTAAATAGATATTTTCG-ATTTGTGGGCTAT-TTTTGA-TAGC--CT-GAAGATTA-TAAGCACTA-CCTGGCGATCATAA

DroAna_CAF1_left   AATCAAGCGGCTCAATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCGGATT--AATTTTT-TT-GTATTTATT-TAT-TTAA-A-A
DroEre_CAF1_left   AATTAATAGGCTCAATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCGATTT--ATTTCTT-TT-GCTTCTTTA-TTC-TTAA-T-T
DroMel_CAF1_left   AACTAAGAGGCTCAATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCAGTAT--ATAATTT-TT-GGTATTTAA-TTC-TTAA--AA
DroMoj_CAF1_left   ACGCAAGAGGCTCAATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCGCAA----ATTTTT-TT-TCATTTTAT-TGA-ATTA--AA
DroPer_CAF1_left   ATGGAAGAGGCTCAATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCGGATC--TATTTTT-GT-TCGGCTTCC-TGAATTT--TAG
DroPse_CAF1_left   ATGGAAGAGGCTCAATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCGGATT--TATTTTT-GT-TCGGCTTCC-CGGATTTT-AGG
DroSec_CAF1_left   AACTAAGAGGCTCAATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCAGCTA--TACAATTTTT-GGTATTTAA-TTC-TTAA-AAT
DroSim_CAF1_left   AACTAAGAGGCTCAATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCAGCTA--TACAATT-TTTGG-TATTTAATTC-TTAA-AAT
DroWil_CAF1_left   CTCGAAGAGGCTCAATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCGGCAA--TATATTT-TT-TTGTTTCACTTTA-TCAA-TAA
DroYak_CAF1_left   AATTAAGAGGCTCAATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCGACTT--TTTTATT-TT-ACTTCTTAA-TTC-TCAA-TTT
DroVir_CAF1_left   ATGCATGAGGCTCAATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCGACGAACTTTTTA--TTATTT-GTTTT-AAA-TTTTAATA

DroAna_CAF1_left   AGTAAACTAT-TATTTTGTTATTTAGAAAAATTCAGTTT---TCTAC----TTA-TA-GATTTATTGAAAAATTATTCAAACAT-TTTTA--AA-CGCCGCAT
DroEre_CAF1_left   T-ACTACTTT-TCAATTAAAAATAACTATCATTCTTGAC---TCCGT----TAT-CT-TATTCTTCCATGGCGTCTTCTTTCAT-TTAATTCTA-TAAAATAC
DroMel_CAF1_left   TTTTGTTCAAGGAACTT-----GTTAAATTGAATATAAT---TTGTATATTTTT-GA-ACAGAGAATAGCTTTTAGAATAGCGT-TTATTCTT--GACTCTGT
DroMoj_CAF1_left   AATATTTTAT-TATGCA---CTT-AATATAAATTATTATCTTGGGACT---TGAACT--ATCTTTGTAAAATGATTAAG--CAT-ATAGATTAT-AATTCGGT
DroPer_CAF1_left   AGTAGTGCTA-TACCCA---TACAAAGAGTATCTTTACT---TTTAAAAAGCGT-TT-GCGACACATATGTATAATATGATATA-TATAAAATG-TATAATTC
DroPse_CAF1_left   AGTAGTGCTA-TACCCA---TACAAAGAGTATCTTTACT---TTTAAAAAGCGC-TT-GCGACACACAAAATATTTAA-AGTAT-AATGGCAGT-CCTTCCTT
DroSec_CAF1_left   TTTGTTCCAG-GAATTT-----GTTAATTTTAATATAAT---TTCATTTA-TTTTTC--AACAGAGAATAGCTTTTATTCTTGA-CTCTGTTAT-CCTATTCT
DroSim_CAF1_left   TTTGTTTCAG-GAATTT-----GTTAAATTTAATATAAT---TTGACTT--ATT-TT-TCAACAGAGAATAGGTTTTTGT-TCTTGACTCTGTTATCTTATTC
DroWil_CAF1_left   ACAATTTAAC-TGCGTT-----GACAATAAGGAAACATG---TTTTTGAA-AATCAC-G-CTGTAGCAAAGTTATAAAACTATT-GTGTTTTAC-CCAAGAAA
DroYak_CAF1_left   ACTTTATTTC-CACAGA-----AAATATTTGAATATCTT---ATTTTTCC-CTTGCT--TTTTCTGTAAGTTAATTTTGTAAAA-AAATGTCTT-GTATGAAA
DroVir_CAF1_left   AGAG--AAAT--TTTGT-----TCACAGTAGTGAGTGTT---ATCTCCCA-TAATCTAATGCCATCTA---TTAACAATCTCTG-TATACTCAG-TAAACATG