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


DroAna_CAF1_left   TTAGTAA-GAAA-----T-TCA-AAAATGTGAATATTAATAT-TAAA-AGG-------GAAAATAAGGAATAGTTTGAAAGT-AATGTCATTGT-TTTTAAATTAAACAAT-TACATTGA
DroEre_CAF1_left   ATCAAAT-GTATTGCT-A-TTT-GTATCCAAAT-----GTATTGCAT-TGA-ATAATTGTGACATTT-TAAATAAA-AACTA-AGTTACTAGCC-T-GT--TTG-AAGGAT-TAAACTGA
DroMoj_CAF1_left   GATCACT-TCGCAATC-A-GCG-TTAATAA-------AGCAGTGCATATTA-ATTACAA-AGCAGTGCAAATAAA---TTGTTTTTGTTCAC---TTGA--CAT-AACTAA-CGCATTTT
DroPer_CAF1_left   CAATCAA-TTATTTGA-A-TTT-GCAAACGAAT-----CG-A-CAAT-GAA-ATTTTTCTGTAATTTCTAAATTGC-AACCG-TAATAGAAGTC-CCAG--TTG-AACAAT-TGCTTTGA
DroPse_CAF1_left   AATCAAT-TATTTGA--A-TTT-GCAAACAAAT-----TCGA-CAAT-GAA-ATTTTTCTGCAATTTCTAAATTGC-ATCCG-TAATAGAAGTC-CCAG--TTG-AACAAT-TGCTTTGA
DroVir_CAF1_left   TCACAAG-CCAG--------CA-AGCAGTATAATATTTGTTC-TTCA-TTC-------AAAAAAGTGTCACTTTTTGTATGG-AGATTTGGGGC-ACTTGGCATAAGTAAAGCAATTTGC
DroYak_CAF1_left   CAACTTCGGCTACCGAAATTAC-CGAGCGT-------TTAAAAGTATTGAA-TAATTGT-GACATTTAAATCAAA---ATTATATTAGTAAC---CTGT--TTG-AAGGAT-TAGACTGA
DroGri_CAF1_left   CGGTCAA-TTATTTTA-C-ACG-TCTTGCA-------AGCAG-TC-G-AAAAACAATGTTTTATCATTCAAG-AAA-GCAAT-TTCTT-TTC-GCTTGG--TAC-AAGTAA-AGCATTTT
DroMel_CAF1_left   CAATTGG-GAATTGGA-A-AGGACTTGAAC-------AATTG-TTTT-GTC-AATTTCGAATTTGAACTTTTTTGG-ACTAA-GTTTC-AAGTGGGAAA--TAT-AACAAT-TACTCTGA
DroSec_CAF1_left   TCAGAAA-ACCAAATA-T-ATTGCAAGTCT-------ACCGA-AATA-ATT-GAGTATTGGAAAGTACTTTTTTGG-ACAAT-TATGT-TATTCGCACG--TTC-AACAAT-TACTCTGA
DroSim_CAF1_left   TCAGAAA-ACCAAATA-T-ATTGCAAGTCT-------ACCGA-AATA-GTT-GAGTATTGGAAAGTACTTTTTTGG-ACAAT-TATGT-TATTCGCACG--TTC-AAGAAT-TACTCTGA

DroAna_CAF1_left   AATGCCCAT--TATCCTATGGGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCAG-TCTGGA--C---TGGTTAGTTTTTTT
DroEre_CAF1_left   TATTCTTGCGGTTCT---ATGGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCAT-GATCAG--G---GAAAATTCTTTTTA
DroMoj_CAF1_left   CCCCAACTCGTTCTC---ATGGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCAG-TACAAC--A---ATTGGATAAT----
DroPer_CAF1_left   ACAGCTGACAATTTC---AAGGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCAT-TAAATT--C---GAGGCCACTTTTGT
DroPse_CAF1_left   ACAGCCGACAATTTC---AAGGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCAT-TAAATT--C---GAGCCCACTTTTGT
DroVir_CAF1_left   ACAACCCGT--TTTC---ATGGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCAT-ATTAAAATCTAGCTATTGGATATTTT
DroYak_CAF1_left   TATTTATGTGCTTCT---ATGGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCAA-GATAAG--G---AGAAGTTATTTTGT
DroGri_CAF1_left   TCTTAAATCGTTTTC---ATGGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCAGTTTGGAA------TTCTACTTCTTTTT
DroMel_CAF1_left   TAATAATGCGGTTCT---ATGGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCAT-GTTCAG------GAGATATTGTTCTT
DroSec_CAF1_left   TAATAGCGGGGTTCC---ATGGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCAT-TATCGG------GAGGTTTTTTTTAC
DroSim_CAF1_left   TAATAATGGGGTTCT---ATGGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCAT-TATCGG------GAGGTTTTTTTTAC

DroAna_CAF1_left   CATCCTTTT-TT-A-C--ACTTTT-----CGTTATAT-TTTGGAACTCACCGATTCAGACTGCTAACTGTCCGAACGCCACGACGTCCCTCGATGATGGAG-AG--------------CG
DroEre_CAF1_left   AAT-----C-CT-T-TTTTACTT-TCAAGGTG-AAGGG-ATGGAGCTCACCTATTTAAGCTGCTGACGGTGCGAACACCTCGTCGTCCCTCGATAATCGAA-ATAG------------TT
DroMoj_CAF1_left   TTTGTTT-T-TT-T-TTTCTACA-TTAT-TTTG---A-TGTTTAGCTTACCGATTTAAGCTGCTGACAGATCGCACGCCCCGTCGTCCTTCAATTATGGAA-ATCGTTA---------CA
DroPer_CAF1_left   GTCGTTTTT-TT-A-TACAGTTT-TTATAACT-GAAGACTTATAACTTACCGGTTTAAGCTACTGACAGTTCGCACACCACGGCGTCCCTCGATTATCG--------------------A
DroPse_CAF1_left   GTCGTTTTT-TA-A-TACATT----------------TTTTATAACTTACCGGTTTAAGCTACTGACAGTTCGCACACCACGACGTCCCTCGATGATCGATATGTT-CACAAT-----GT
DroVir_CAF1_left   TACCCATTG-GA-A-T--GCTTTTTTAATAGTTTTTT-TAATGCTCTTACCGATTTAAACCGCTGATAGCTCGGATGCCACGACGTCCTTCGATAATGGAA-AT--------------A-
DroYak_CAF1_left   TTTAAAT-T-CT-T-TTTTGCTT-TGAA-GTTAATAG-GATGGAGCTTACCTATTTAAGCTGCTTACGGTGCGAACACCTCGTCGTCCTTCGATGATCGAA-A----------------T
DroGri_CAF1_left   TATTTTTGA-AT---AA-CTT---------------T-TTGCTCACTCACCGATTTAAACTGCTGATGGGACGAACACCCCGACGTCCTTCGATAATGGAT-ATGGTGACATTATGTCCC
DroMel_CAF1_left   TTTTTACTTTGAATGTG-TAG---------------G-GGTGGGACTCACCTATTTAAGCTGCTAATGGTGCGAACACCTCGTCTTCCCTCGATGATCGAA-ATAGTTACATT-----AT
DroSec_CAF1_left   TTTTGAATG-GT---AA-GGG---------------A-TGGGGGACTCACCTATTTAAGCTGCTAACGGTGCGAACACCTCGTCTTCCCTCGATGATCGAA-ATAGTTACAT-------T
DroSim_CAF1_left   TTTTGAATG-GT---AA-GGG---------------A-TGGGGGACTCACCTATTTAAGCTGCTAACGGTGCGAACACCTCGTCTTCCCTCAATGATCGAA-ATAGTTACAT-------T

DroAna_CAF1_left   T
DroEre_CAF1_left   A
DroMoj_CAF1_left   T
DroPer_CAF1_left   T
DroPse_CAF1_left   A
DroVir_CAF1_left   G
DroYak_CAF1_left   A
DroGri_CAF1_left   T
DroMel_CAF1_left   A
DroSec_CAF1_left   A
DroSim_CAF1_left   A