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


DroGri_CAF1_left   TCG--TATCT-ATCTATCT-TAGGTAA-ATAATGCATG-A--CAAAAGCAT-CTGCA-AGATGCAGAAATTATGTATAAAAATTTGTCGA---A-ATATCTATTTTTGCATGAGCGGCTC
DroMoj_CAF1_left   AAA--TAATGCACGCTATT-TTAAATA-AAT-TAT-TCACGCTAAGATC-A-ACTTG-AGTTGCAATA---AAAC-AATTAAAATTTT-GTTAAATTTACCTTCCGATCGTAAGCGGCTC
DroPer_CAF1_left   CGC--GACGA-ATGTATCC-GTTAGTT-GGATGCA-AATAGTTGATTGCAT-CTTTG-AGATACAATTGG-AAGCTGA-AAAACTCAAAA---T-GCACCGATTGTATCATGTGCGGCTC
DroPse_CAF1_left   CGC--GACGA-ATGTATCC-GTTAGTT-GGATGCA-AATGGTTGATTGCAT-CTTTG-AGATAAAATTGG-AAGCTGA-AAAACTCAAAA---T-GCACCGATTGTATCATGTGCGGCTC
DroVir_CAF1_left   TAT--ATATATATAAAATA-AATTATG-CAT-GCC-AGATGTATCCAAA-AGTTGAT-TGAAGCGATT---AAAAATA-TAAAATATGTTTAAAACTT--GCTTTGATCATGTGCGGCTC
DroWil_CAF1_left   AGT--TAAAAGTTGTATCT-ACAAGATAGCT-GAC-CTTGT-AATTTTA-A-AATTG-ATATACAATTTCATGATTTA-TATTTTATAAAT----ATTTCCCTCGTTTCAAGAGAGGCTC
DroYak_CAF1_left   AAT--ATGCA-TGTCGAAA-TTGTATC-TTTGGAT-GTGCAAAGCAGACGT-AAATT-CATCATTGCTTT-AAGCTTA-AGAAACCAAAA---A-TTTAACCTGTTATCATAGGCGGCTC
DroEre_CAF1_left   AATATGCATG-TCGGAAATGTATCTTT-AG--GTG-TGCAGAGGCAGGCAT-AAATTCCTCATCA-CATT-AAGCTTA-AAAAGCCAAAA---A-TTTAACCCGTTATCA-TGGCGGCTC
DroMel_CAF1_left   TAT--GCATG-TCGGAAATGTATCTTC-AG--ATG-GGCTGAAGCCGATAT-AAATGTATCATCAGATTT-TAGCTTA-AAAAGCCAAAA---A-TTGTAGCCGTTATCTTAAGAGGCTC
DroSec_CAF1_left   TAT--GCATG-TCGGAAATGTATCTTC-AG--ATG-GGCTGAAACAGATAT-AAATTTTTAATCAGTTTT-AAGCTTA-AATAGCCAAAA---A-TTGTGGCCGTTATCTTAAGCGGCTC
DroSim_CAF1_left   TAT--GCATG-TCGGAAATGTATCTTC-AG--ATG-GGCTGAAACAGGTAT-AAATTTATAATCAGTTTT-AAGCTTA-AATAGCCAAAA---A-TTGTAGCCGTTATCTTAAGCGGCTC

DroGri_CAF1_left   AATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCGTA--TCTCCAATTTTTTTTGT-GCTCT--CT-CAATGTA-AA--TAA-T-AA
DroMoj_CAF1_left   AATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCGTT--GTGCATTCTTTTACTTATTTCTTATTTGTTAC-TT-T--TTTTTTCAA
DroPer_CAF1_left   AATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCTTA--ACTCAACTTTTTACTCA-TTCCA--ACGGCCA-TG-CC--CAC---AG
DroPse_CAF1_left   AATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCTTA--ACTCAACTTTTTACTCA-TTCCA--ACGGCCA-TG-CC--CAC---AG
DroVir_CAF1_left   AATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCTTA--TATTTTTTTCTTTAA---CTTTTTGCCGCATC-CG-C--CCAA-A-AG
DroWil_CAF1_left   AATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCTGTCTAATTTTTTTTGCTTT---CTGTTGTGAACATT-TC-ATTTTTA-T-TT
DroYak_CAF1_left   AATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCATT--TTCAC-ATTTTGGCTCT-CTTTTTCCCTCGCT-AG-GA--TTC-T-AG
DroEre_CAF1_left   AATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCAGT--TTA-AAATTTTTGCTCT-CTTTTTCCTCCCAA-ACGGA--TAC-T-AA
DroMel_CAF1_left   AATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCTTG--TTTAAAATTTTTGCTCT-CTTTTTCCACCCTA-AA-GA--TTC-T-AA
DroSec_CAF1_left   AATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCTTG--TTTAAAATTTTTGCTCT-CTTTTTCCACCCTA-AG-GA--TTC-C-AA
DroSim_CAF1_left   AATGGTCTAGGGGTATGATTCTCGCTTTGGGTGCGAGAGGTCCCGGGTTCAAATCCCGGTTGAGCCCTTG--TTTAAAATTTTTGCTGT-CTTTTTCCACCTTA-AG-GA--TTC-C-AA

DroGri_CAF1_left   TAAT-TTTATACAGGCG---TTGACAA--TGTG-------A----------CTTTATTGCCTATACAATAGATAAAAATTCAATTCAG-GATTTGCTACCATGC---CCTC
DroMoj_CAF1_left   ATGT-AAATAATAATTCTATACA-GGC--GCTG-------TGACAATGTGACTTTATTGCCCATACAATAGATAAAAATTCAATTCAG-GATTTTGTCGCAAAC---ACAG
DroPer_CAF1_left   TCA--CAACCACAATCC---ACA-TTC--CGCC-------ATATCCTCCATCCTCCTAGCCATGCCTAG-AG--------AAATT-TT-AA-GAGTAAACAATA---ATCA
DroPse_CAF1_left   TCA--CAACCACAATCC---ACA-TTC--CGCC-------ATATC-------CTCCTAGCCATGCCTAG-AGAAATT--TTAAGAGTA-AA-CAATAATCATTT---TATA
DroVir_CAF1_left   TAAA-TAATAATAATTTTATACA-GAC--GCAC-------TGACAATGTATCTTTATTGCCTATACAATAGATAAAAATTCAATTCAG-GATTTT-------------GTT
DroWil_CAF1_left   GGGTAAATAATAATCATTTTATA-CTG--GATG-------TGACAATGTGACTTTATTGCCAATACAATAGATAAAAATTCAATTCAG-GA--------------------
DroYak_CAF1_left   GGAG-AAAATATAGGCC---GCGATGA--AGGG-------GGAGT-------AAGAGTAAACAATAATT-TTATACA--TGCTGTGAC-AA-TG-TGACTTTAT---TGCC
DroEre_CAF1_left   GGAG-AAAATATAGGCC---GTGATGG--TGGG-------GGAGTAGG-----------AGTAAACAATAATCATTTTATACATGCTGTGA-CA--ATGTGACT---TTAT
DroMel_CAF1_left   GGAG-AAAATATAGGCC---CTGATGGTGTTAGAAAGGGGGGGGGGGG-----------AGTAAGGGGAGTAAACAATAATCATTT-TATA-CA---TGC---------TG
DroSec_CAF1_left   GGAG-AAAATATAGGCC---CTGCTGTAGG-GG-------GGAGTAGG-----------AGTAAACAATAATCATTTTATACATGCTGTGA-CA--ATGTGACT---TTAT
DroSim_CAF1_left   -----AAAATATAGGCC---CTGATGTAGGGGG-------GGAGTAGG-----------AGTAAACAATAATCATTTTATACATGCTGTGA-CA--ATGTGACTTTATTGC