CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left CGCT-G-GAATGTCA-GTGTTGTA--AAGCGGCGACTTGAGC-AAC-GCGCAGAAG--CTTTCC-CTGCTTTCCAATCGGCAT-TAGTC-GGCACATTGACGAAGCACGTTAACAAGCAG DroGri_CAF1_left CGTT-A-TCGTAACA-TTTTACGT--GATTCAGTAGTTAC-G-CTC-TGTTAAGAC--AACATA-TGCTCGTCAACAGTAGCAGAAGTG-GGCACATTGCTGTAGACAACCAACAAGCAG DroMel_CAF1_left TTAT-T-TCACTTTT-GATTTTTC--CATATTTCAAATTT-C-GCT-GTTAAATCG--GTTACA-GTTTCTCTACACCTAAGCTAACAC-TGGATTTGACATCACTAGTTGCAAGAGCAG DroMoj_CAF1_left GGTT-T--TCTGTTACCGTAACAGTACGTTATTTGATG---A-AAA-TGTTAATAC--AACACA-AATGCTT-TAACAGTGATACAAATAGTCACATTGCAATGCTTCAGACAGAAGCAG DroPer_CAF1_left GTAT-T--AACATAA-TGTTATGTTAACATATCTATGT---T-ATT-TAGTAATTT--TATTGT-GGGTTTCTTTTTTATGCGGAAAATAGGCATTTTGCGCCACCCCATCAACAAGCAG DroPse_CAF1_left AGTATT--AACATAA-TGTTATGTTAACATATCTATGT---T-ATT-TAGTAATTT--TATTGT-AGGTTTCTTTTTTATGCGGAAAATAGGCATTTTGCGCCA-CCCATCAACAAGCAG DroSec_CAF1_left ATTT-CTGCACATTT-CAAATTTCG-CTGTTAAATCGG---T-TAG-CGGTTTTAC--TTTACA-GTTTCTCTACACCTAAGCTAACACTGGTTTT-TACATCACTCGCTGCAAGAGCAG DroSim_CAF1_left ATTT-CTGCACATTT-CAAATTTCG-CTGTTAAATCGG---T-AAG-CAGTTTTAC--TTTACA-GTTTCTCTACACCTAAGCTAACACTGGTTTT-TACATCACTCGTTGCAAGAGCAG DroVir_CAF1_left TGTT-A-GAATAACA-TTAC-GTG--ATTCGATAAAATTA-CCCTCTGTTAAGT-T--AACATACGTGCTTCAACAGTTGCAC-AAGTT-GGCATATTGCTGTGCTGTAGTCACAAGCAG DroYak_CAF1_left T--A-CAGCATATTT-TAAAGTTTG-CTGTTAACTTGG---C-TAT-GGGTTATACATTTTACA-TTTTCTTTACATCTAAGCTAACACTGGTTTT-GACTTCATTCGTAGCAAGAGCAG DroEre_CAF1_left ATTT-TCGCACTTTT-AAAATTTTT-CCATTAAATTGG---T-TAT-CGGCTTTAT--TTTACA-GTTTCTCTACATCTAAGCTAACATTGGTTTT-GACTTCACTCGCTGCAAGAGCAG DroAna_CAF1_left TCGTGGCCGAGCGGTTAAGGCGTCTGACTAGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGACTGCGAAGTTGTTCTAAT--T-TTTTATTATTT---TTTTTTATTT- DroGri_CAF1_left CCGTGGCCGAGCGGTTAAGGCGTCTGACTAGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGGCTGCGAAATG-GAA--AA--TTTATT--TTTTT---TATTTTGTATT DroMel_CAF1_left TCGTGGCCGAGCGGTTAAGGCGTCTGACTAGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGACTGCGATGAC-AAG--AG--T-TACT--TTTTT---GTTTTTAACTT DroMoj_CAF1_left CCGTGGCCGAGCGGTTAAGGCGTCTGACTAGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGGCTGCGAGAGA-TTTGAAT--T-CATTTTTTTTT---TTTTTTTTAA- DroPer_CAF1_left CCGTGGCCGAGCGGTTAAGGCGTCTGACTAGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGGCTGCGTTTCG-TCGGATG--T-TTTTCATTCCT---TTTTTTTTTT- DroPse_CAF1_left CCGTGGCCGAGCGGTTAAGGCGTCTGACTAGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGGCTGCGTTCCG-TTGGATG--T-TTTT-TTTCCG---T-TTTTTTTT- DroSec_CAF1_left TCGTGGCCGAGCGGTTAAGGCGTCTGACTAGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGACTGCGATGAC-AAG--AG--T-TTCT--TTTTT---TTAACTTTTA- DroSim_CAF1_left TCGTGGCCGAGCGGTTAAGGCGTCTGACTAGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGACTGCGATGAC-AAG--AG--T-TTCT--TTTTT---TTTAATTTTT- DroVir_CAF1_left CCGTGGCCGAGCGGTTAAGGCGTCTGACTAGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGGCTGCGA--AA-CAA--GGTGT-TT----CTTTT---TTTTTTATTTT DroYak_CAF1_left TCGTGGCCGAGCGGTTAAGGCGTCTGACTAGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGACTGCGGTGAA-TTA--AG--T-TTCT--TTTTT---TTTTTAATTT- DroEre_CAF1_left TCGTGGCCGAGCGGTTAAGGCGTCTGACTAGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGACTGCGATGAA-TTG--AG--T-TTCT--TTTTTTTCTTTTTCTCTA- DroAna_CAF1_left ----TTATTTT--C-TGATGATTAAAAAATTA--TTCTTA--GGTATTAAACTTTATCAGG---TC----ACTTAAAATTTA--TAATTAA--AATTTTAAAAA-AAGTTAGGGACCA DroGri_CAF1_left TGTTAAAAACTTTT-TACTTAAATATTTAA----C------ATTTCTTTTATCA---TTGC---A-----GCCACT--CGACA-AAAATCAGCATAT-GTGGAG-GTGGC---ACACG DroMel_CAF1_left TTTGCCCAAAA--G-AACAATTTTAAGGTT----A------TTAATTTGATCCTTTTTCAT---A-----ATGTTT-CAAAGA-ATGTTGTGCT-AG-ATTTGTGTGTTT---GCTTT DroMoj_CAF1_left ----ATAAATT--TGTATTTGATGCAACAC----ATTAT-TTATTATTACTTTTATAATAA---TA----ATAATAATTT--------ATATTTGTA--TACTAACTGCA---ATAAT DroPer_CAF1_left ----AATATTT--C-ATTAAAAATATACTGAAGATTTGA-TTTAATTAAAATTTATTAAGA---TA----TCAAAATTTACA--AAACTGTGTCGGA--CAGGTTTCTCG---GCAGC DroPse_CAF1_left ----AATATTT--C-ATTAAAAATATACTGAAGATTTGA-TTTAATTAAAATTTATTAAGA---TA----TCAAAATTTACA--AAACTGTGTCGGA--CAGGTTTCTCG---GCAGC DroSec_CAF1_left -------AAGA--A-AAGAAAATTTAAAAGTT--TATTA-ATTTTTTTTATGTATTCAGAA---A-----ATTGT--GCTAGATTTG-TTTTTTCGC-TTTTGCAAGCGT---AA-AC DroSim_CAF1_left -------AAAG--AAAAGAAAAT-TTAAAGTT--TATTAATTTTTTCTTTTTTTTATGTAT---TC----AAAAA--ATTGTGCTAG-ATTTGTTTT-TTCG-C-TTTTG---CAAGC DroVir_CAF1_left TGTATAAGATA--T-TGTTTTGTCTATATT----A------ATATTGATTGTTTTATTTTTTATT-----TTTTGC-AATATG-CATATTATTAAAT-CATTTA--AAAC---TATTA DroYak_CAF1_left -------TCCT--TAAAAATTAT-TTATTTTC--TAATA-TTTATTTTTTTCCTTTTTCTA---TG----TATTA--GGAAAATTTG-TTTGCTAGA-TTTTTTATTCTA---GCTTT DroEre_CAF1_left ----AAGAAAC--A-TTTATGTTTTAAAAATTGTGTTTT----------TTTCTATCTTAATGTATAAAGAAAACT--------TTTGTTAGATTT--CTGTTTTTGCTT---TCGTA