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


DroAna_CAF1_left   T---TCC-CATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAGCCTAGATTTCCATAATCCGAGTGCCAAGTGTCGAAAGCATCC-TG-----CCTCCTGCATCCTCC--
DroMel_CAF1_left   A---GAA-TTTTTCACATATCACAGTTGCT-GTTTCTTTTAGATAGCTCTTTTGTAAACA-GCCTAGATCCGAATGCGAGTATCCGA---GTGCCTTG-----C---GTGAATCC-TG--
DroPse_CAF1_left   C---T-------TTACATATCACAGTTGCT-GTTTCTTTTAGATAGCTCTTTTGTAAGCA-GCCTAGATCGGGGGCGATTCGAGTGA---GTGA-ATCCCTTTC---TGTGATGG-TGCG
DroSec_CAF1_left   T---GAT-TTTTTCACATATCACAGTTGCT-GTTTCTTTTAGATAGCTCTTTTGTAAGCA-GCCTAGATCCGAATGCGACTATCCGA---GTGCCTTG-----C---GTGAATCC-TG--
DroSim_CAF1_left   T---GCA-TTTTTCACATATCACAGTTGCT-GTTTCTTTTAGATAGCTCTTTTGTAAGCA-GCCTAGATCCGAATGCGACTATCCGA---GTGCCTTG-----C---GTGAATCC-TG--
DroWil_CAF1_left   TATTCAAATCTTTGACATATCACAGTTGCT-GTTTCTTTTAGATAGCTCTTTTGTAAGCA-GCCTAAAGT-GAC--TGAGTGCCCGA---GTGCCT-G-----A---GTGAATTT-TG--
DroYak_CAF1_left   A---GAA-TTTTTCACATATCACAGTTGCT-GTTTCTTTTAGATAGCTCTTTTGTAAGCA-GCCTAGTTCCGAATGCGAATATCCGA---GTGCCTAG-----C---GTGTATCC-TG--
DroPer_CAF1_left   A---TAT-CACAGTT-GCTGTTTCTTTTAG-ATAGCTCTTTTGTAAGCAGCCTAGATCGG-G-GGCGATTCGAGTGAGTGAATCCCT---TTCCGGTT-----C---TGTGATGG-TGCG

DroAna_CAF1_left   -----TTCCCCAGGGTCC-TCCGGTTTCAATTTGTGGGATACACACGGTTCAGTTGTGTCACTTT-TGCGAGCATCACTGGGCTTTGTTTATCTCATAAGACTGAAATTTGTTCAACTT-
DroMel_CAF1_left   -----GATGAAAAGGTCC-TTCGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACT--TCAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCAACAGG
DroPse_CAF1_left   TGTGAAACGTGTGCCTCT-TTTGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACATT--TCGAGCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCAACTG-
DroSec_CAF1_left   -----TATGAAAAGGTCC-TTCGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACT--TCAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCAACAGG
DroSim_CAF1_left   -----TATGAAAAGGTCC-TTCGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCACACT--TTAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTATTCAACAGG
DroWil_CAF1_left   -----AATCAATTGTGCCAGACGGTTTCAATTTATGGGATACACCAAGTTCAGTTTTGTCGCATTCCACGAGCATCACTGGGCTTTGTTTATCTCATAGAGGAGAAATGAATACAACTT-
DroYak_CAF1_left   -----GATGAAAAGGTCC-TCCGGTTTCAGTTTATGGGATACACACAGTTCAGTTTTGTCGCACT--ACAAGCATCACTGGGCTTTGTTTATCTCATGAGAGCGAAATTTGTTCAACAG-
DroPer_CAF1_left   TGCGAAACGTGTGCCTCT-TTTGGTTTCAATTTATGGGATGCACCAAGTTCAGTTTTGTCACATT--TCGAGCATCACTGGGCTTTGTTTATCTCATAAGAGCGAAATTGATTCAACTG-

DroAna_CAF1_left   ------TACAT--------TCGATTGGATT-ATCTAATT-GGATTATTTAA-ATTAAATATGTAACGTGCCTAA-A-------A----TT-TACATA---GG
DroMel_CAF1_left   AAACCTTAAATCATAC-CAATATATAAAAAAATCTGTAT-ATAAAACATTT-GAATTTCTTGGATCAAGTTTTT-AAGCTT--AATCAGAAAA---GTAAGT
DroPse_CAF1_left   TTTCGGGTACTCAAAACCATAGCCTCAATGGAAGCTGCT-GAATCGCTCTT-CATAAGTATGCAACGTTATCCG-ATATAT--TAATAGT-ATATCTT--TT
DroSec_CAF1_left   GAACCTTAAATCCTAC-CTATATCTCAAAAAATCTGTTC-ATAAAACATTT-GAATTTCTTCGATCAATTTTTA-AGCTTTATCAG---AAAAGTAAG--TA
DroSim_CAF1_left   GAACCTTAAATCCTAC-CTATATCTAAAAAAATCTGTTG-GTAAAAAATTG-GAATTTTGTCGATCGATTTAAA-AAAAAAAGAAAAAGAAAA---GT--AA
DroWil_CAF1_left   ACTGGGCTGGACA-GG-CAGGATTTGAAATCCTTGGGTA-AATCGACCACCGCCATGTGATCATGTGGTCGCTTTGGTCCC--GAAATGC-TGCTAAC--AA
DroYak_CAF1_left   AAACCTTAAATCACTA-ATCTGTTTATGAGAAATACCACAAGATTGGAACA-TCTTTGATCAACTCTTAGGCTT-CATCAG--AACACGT-AAGTAAG--TA
DroPer_CAF1_left   TTTCGGTTACTCAAAT-CCATAGCCGTAATATGATATCC-GTCTCTGTA-C-GATGCAGACGGTTATCAGGGAA-CTCAATGGAAGCTGCTG-AATCG--CT