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


DroMel_CAF1_left   G-----------TGTGTA-----------------------------------------TTAGAA-TATG------GT----GTA-TCTAT-------CAGAGACTGGGGGCAAAC--A-
DroMoj_CAF1_left   C-----------GAGA-TGACGAAGACCTGCAATCAAAATGCGAAATT-ATAACGC-CG---CTTA-CTCAAA-TAGCAGAGACACAGCAT--TT-ACAGTGTGGCCAGTC-AA----AT
DroSim_CAF1_left   N-----------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNCTG-TGGTGGATTCGTGTAT-TAGAATATGCTGTCTAT-------CAGAGACTGG-GACAATC--A-
DroVir_CAF1_left   T-----------TTAAATCAAATACATTTGGAGCGCGCATTTAACAGC-GAATCTG-CA---GTGT-GACCAG-CTATGATCAAACGCAAA--ATCCCTGCTTTTCTTTTA-ATGTGCGT
DroWil_CAF1_left   A-----------CCAA-TCGGACGCGATGAGATGACGAAAACCTAACA-AAAGATT-GTAA-ATTA-GCTCTT-TGCTTGA---CTACAAG--T--GTATTAAGTCTTCAA-AAATTGAG
DroYak_CAF1_left   G-----------ATCTGCGGGA---GAAGTGT--------T--------GAATTAGAATATGCTC------GATTTG-TC----AGGGGAT-------G-GGGAAAGG---CAATC--C-
DroAna_CAF1_left   CACGGCACGCTGGCCAATGGGACGCGACGAGATGACGAAGACCT--AAAAGGG------GAGAATGGGT-TAG-TTTCTTTCCGAAAATGGGATATAAAGTATCACTC------TT--C-
DroPer_CAF1_left   G-----------GCCGATGGGACGCGACGAGATGACGAAGACCT--GT-CGAA------TGAAAGGACAAAAT-TAGTTATCTGCATTTTACTGCGACCGTGGAACCC------TG--G-
DroPse_CAF1_left   G-----------GCCGATGGGACGCGACGAGATGACGAAGACCT--GT-CGAA------TGAAAGGACAAAAT-TAGTTATCTGCATTTTACTGCGACAGTGAAACCC------TG--G-

DroMel_CAF1_left   CTCCGAGGC---GTTGA---GGCGTGGCTGG-----TCAGCAGTGAAG-TTGAAATCATTGAATTTCATACCCGAAAGATTAGTA-AT-AAACTCA-----TCACGCTAGCCA-CGCCGC
DroMoj_CAF1_left   GT---ATGT---ATGCT-G-TGTTTG-GGCG---TATCAGTTGAAAAG-TTGAAATCATTGAATTTCATACCCGAAAGATTAGAT-AA--ATCTCA-----TCATGTGCACCA-AACGCA
DroSim_CAF1_left   CTCCGAGGC---GTTGA---GGCGTGGCTGG-----TCAGCAGTGAAG-TTGAAATCATTGAATTTCATACCCGAAAGATTAGTA-AT-AAACTCA-----TCACGCTAGCCA-CGCCGC
DroVir_CAF1_left   GCG--TTGT---GTGTGTC-GCGTGGCGGCG---TGTCAGTTGTGAAG-TTGAAATCATTGCATTTCATACCCGAAAGATTAGAT-AG--GAATCA-----TCATGTGCACCT-ACGCGA
DroWil_CAF1_left   TTG--AGGA---TTTAGGTTTGGCA-TCATA---AATCAGTAGTAAAGAGTGAAATCATTAAATTTCATACCCGAAAGATTAGTG-TA-AAACTCA-----TCATGTATGACACGCCG--
DroYak_CAF1_left   CTCCGAGGC---AGTGA---GGCGTGGCTGG-----TCAGCAGTGAAG-TTGAAATCATTGAATTTCATACCCGAAAGATTAGTG-AT-AAACTCA-----TCACGTTGGCCA-CGCCGC
DroAna_CAF1_left   CAT-----AGTGAGGCT---T----GGCT-----GGTCAGCGGTGAAA-GTGAAATCATTGCATTTCATACCCGAAAGATTAAAAGAATCATCACGTGCAGCCACGCCTTCAG--AAGGA
DroPer_CAF1_left   CTTT---TCTGTGGGCT---TGTGAGGCGTGGCATATCAGCT-TTAAG-TTGAAATCATTGCATTTCATACCCGAAAGATACAAA-AATCATCATATG-AACCACGGGGTCGG--TCCTC
DroPse_CAF1_left   CTTT---TCTGTGGGCT---TGTGAGGCGTGGCATATCAGCT-TTAAG-TTGAAATCATTGCATTTCATACCCGAAAGATAAAAA-AATCATCATATG-AACCACGGGGTCGG--TCCTC

DroMel_CAF1_left   ACTG--GTA-TGC--CAT---GGAATTCTGCACTTGTACTCACGTCCGAGGGGTTA-TC-GATGGC-CACGATGGCGCGGGCCGCCAGCTGCAGCTTCTCCCAGGTCT--------TG-C
DroMoj_CAF1_left   ACAA--GCA-TAC--CATCG----ATAAGC----AAATACATATGTATAA--TTCA-TTTG-TTACTCACATCGGATGCATTCTCAATGGCCACAATGGCGCGTGCAGCCAAAACCAG-T
DroSim_CAF1_left   ACTT--TGA-TGC--AAT---GGAA-TCTGCACTTGTACTCACGTCCGAAGGGTTA-TC-GATGGC-CACGATGGCGCGGGCCGCCAGCTGCAGCTTCTCCCAGGTCT--------TGCC
DroVir_CAF1_left   GCCC--ACA-CAT--CAACGGAGTATTTGCTTT-AATGAAAAGCGTATAA--TTCG-CTTTGCGACTTACATCGGAGGCGTTCTCAATGGCCACGATGGCGCGGGCAG--------CG-A
DroWil_CAF1_left   --CC--TCA-CCC--TCTCAACCATACTTTTTGCTAATACAAATATTAAG--CAGTTTC-TATAACTTACATCTGAGGCGTTCTCAATGGCCACAATGGCGCGAGCAG--------CC-A
DroYak_CAF1_left   ACTC--AAAGAGC--CCT---GCAATTCTGCACTTGTACTTACGTCCGAGGGGTTA-TC-GATGGC-CACGATGGCGCGGGCCGCCAGCTGCAGCTTCTCCCAGGTCT--------T--G
DroAna_CAF1_left   TCGAGTTCA--GAGACCA---CAT-GGGAGG-GTATA-CTCACATCAGAAGCGTTG-TC-GATGGC-CACGATGGCACGGGCAGCAAGCTGCAGCTTCTCCC-----------------A
DroPer_CAF1_left   ACAAAAGCA--GA-ATAT---AGA-GCTAGGCGCACAACTTACATCTGAGGCGTTC-TC-AATGGC-CACGATGGCGCGAGCGGCCAGCTGGAGCTTCTCC------------------C
DroPse_CAF1_left   ACAAAAGCA--GA-ATAT---AGA-GCTAGGCGCACAACTTACATCTGAGGCGTTC-TC-AATGGC-CACGATGGCGCGAGCGGCCAGCTGGAGCTTCTCC------------------C