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


DroAna_CAF1_left   AATTACCTTTTATAATTCTCAACTTGTTTAAGCAACCA-TTGACAGGAGTAGTAGGCTATTTGGTGTTAAAGGTCACTCTGGTTTCTCTTCAATTGTCGAATAAATCTTTCGCCTTTTAC
DroMel_CAF1_left   TTACAATCATTATGATTCCCAACATGTTCAAGCTCGTT-CTAAATGATCGGGCTGATACTTTTCGTTGTAAATTTACTCTGGTTTCTCTTCAATTGTCGAATAAATCTTTCGCCTTTTAC
DroMoj_CAF1_left   GCTTCTAAGTTAGAATTCCCAAGGAGTTCAAGCATGTC-CTAGAGTACATCGGGGTTGGTTTTCACAGTTTCTTTACTCTGGCTTCTCTTCAGTTGTCGAATAAATCTTTCGCCTTTTAC
DroPer_CAF1_left   TAGTGTTTCCTTTAATTCCCAACTAGTTCTGGCGACTC-TTATTCAAGGTAGGGTGTGTTTGTTATGGCAAAATTACTCTGGCTTCTCTTCAATTGTCGAATAAATCTTTCGCCTTTTAC
DroPse_CAF1_left   TAGTATTTCCATTAATTCCCAACTAGTTCTGGCGACTC-TTATTTAAGGTAGGGTGTGTTTGTTATGGCAAAATTACTCTGGCTTCTCTTCAATTGTCGAATAAATCTTTCGCCTTTTAC
DroSec_CAF1_left   TTACAAACATTATGATTCCCAACATGTTCAAGCTCGTT-CCAAATGGTAGGGCAGATACGTTTCGATGTAAAGTTACTCTGGTTTCTCTTCAATTGTCGAATAAATCTTTCGCCTTTTAC
DroSim_CAF1_left   TTACAAATATTATGATTCCCAACACGTTCAAGCTCGTT-CTAAATGGTAGGGTAAATACTTTTCGATGTTAAGTTACTCTGGTTTCTCTTCAATTGTCGAATAAATCTTTCGCCTTTTAC
DroVir_CAF1_left   CTTGTGTGTTCGAATT-CCCAAACAGTTAAAGCTGGGTTGGAGTGTAGATGAGGGTTGGTTGCTCTTCAAAATCTACTCTGGTTTCTCTTCAGTTGTCGAATAAATCTTTCGCCTTTTAC

DroAna_CAF1_left   TAAAGATTTCCGTGGAGAGGAGCACTCTAATGAGTCTATACT-AATT-TTTTG-TAGGGCCTAGCATGACTTCTTGCCGGGCCCGATAAA-TAATAAATTTTAATCTATCA-------TA
DroMel_CAF1_left   TAAAGATTTCCGTGGAGAGGAACACTCTAATGAGTCTAAAAT-AATC-TTTT-GTAGTGCCCGGCGACTTCGGTAGCTGGGCCA--TAAG-GAATTCATTGTAAA-GTTTT-------TT
DroMoj_CAF1_left   TAAAGATTTCCGTGGAGAGGAGCACTCTAATGAGTCTAAATTGAATT-TTTTGATTGTGTCTGACGGCGTTTGCTGTCAGGCCA--TAAA-GAATACATCGGAATCACTCT-------TA
DroPer_CAF1_left   TAAAGATTTCCGTGGAGAGGGGCACTCTAATGAGTCTAAACTGAATTTTTTCG-TAGTTCCTGGCGACTTCGGTTGCCGGGACA--ATCAAGAATGAATGCCAAAATCGAATGGGGCTTT
DroPse_CAF1_left   TAAAGATTTCCGTGGAGAGGGGCACTCTAATGAGTCTAAACTGAATTTTTTCA-TAGTTCCTGGCGACTTCGGTTGCCGGGACA--ATCAAGAATGAATGCCAAAATCGAATGGGGCTTT
DroSec_CAF1_left   TAAAGATTTCCGTGGAGAGGAACACTCTAATGAGTCTAAAATAATTT-TTTTG-TAGTGCCCGGCGACTTTTGTAGCTGGGCCA--TAAG-GAATTCATTGTAAGGTTTTT-------T-
DroSim_CAF1_left   TAAAGATTTCCGTGGAGAGGAACACTCTAATGAGTCTAAAATAATTT-TTTTG-TAGTGCCCGGCGACTTCGGTAGCTGGGCCA--TAAT-GAATTCATTATAAGGTTTTT-------G-
DroVir_CAF1_left   TAAAGATTTCCGTGGAGAGGAACACTCTAATGAGTCTAA-TGAAATT-TTTTG-CAGTGCCTGGCCGCGTTTGTTGCCAGGCCA--TAAT-TAATATGTTCAAGTAAATCA-------TT

DroAna_CAF1_left   AGTTCTTA-----GTTTACAAATGTGTCGTAACATGACGTATTTGTACTTGGCC-AAAGTTGAACCTCTGT-TGGCGCTA-AGTATGCCATA-AATCTTAT----TATTATATTGCTGCC
DroMel_CAF1_left   GCTTATTA-TTATAAGGTCTGGTGGTCATATACATGGACTACTCTAC----TAA-GGTTACCAGAAGAGTG-ATGAAAT--TTTA----CTC-GAATCGAGTTTGTACCGT-AGA-CGG-
DroMoj_CAF1_left   GTGTTATAGTTACAAAATTTTCTTTTCATTAGGAATCAC-GACATTC----TGG-GTCTAGGTATGATGCA-CTTTAGAA-AATA----CTA-TATCCTGATATTTTGCATTTATCTGC-
DroPer_CAF1_left   TTGAT--------TT-----CAGCCAACTTTGTTAGTTGTTTGTTAGCAATTTC-ATGTTATGGGCATAAA-CAAACAAA-TAGAGGC-TAACCAGACCGGA---CTCTGGGGGGCA---
DroPse_CAF1_left   TTGAT--------TT-----CAGCCAACTTTGTTAGTTGTTTGTTAGCAATTTC-ATGTTATGGGCATAAA-CAAACAAATTAGAGGC-TAACCAGACTGGA---CTCTGGGGGGCA---
DroSec_CAF1_left   --TTAATA-TTATAAAATCTGGTGGTCATATGGAGTGATGAAATTTT----ACTCGTACCGTAGAC--GGC-GCTAAAT--GTGC----CAT-AAATCAGCT---TATTATATTGCAGT-
DroSim_CAF1_left   -TTTATTA-TTATAAAATCTGGTGGTCATATGGAGTGATGAAATTTT----ACTCGTACCGTAGAC-GGGC-GCTAAAT--GTGC----CAT-AAATCAGCT---TATTATATTGCAGT-
DroVir_CAF1_left   GGAAATAT-GT------GGGTGACTATGTAAATTATTTAATTGCTTACAGTTAC-AGTTTAGAAAGCA-CTGATTTCTT--ATGG----CTG-CTATCTTCT---CTAATTAG--TTG--

DroAna_CAF1_left   TATT-T-ATT
DroMel_CAF1_left   -----C-GCT
DroMoj_CAF1_left   TGCT-C-TAA
DroPer_CAF1_left   A-TAGT-GAG
DroPse_CAF1_left   A-TAGT-G-A
DroSec_CAF1_left   ---C-AATAT
DroSim_CAF1_left   ---C-A-ATT
DroVir_CAF1_left   ---G-T-GGT