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


DroAna_CAF1_left   CAGGTC-G-TGGGTTTATT-TTAGTTTTTAATCT-CAA-G-C-AACCCAAAT-TC-CAG-CC-ACTAGTTATAAG---GAAATATATATCCCACCCAAATACGTTGT----TTT--GTAT
DroEre_CAF1_left   CACGTT-CTTGGGTTTA-T-TT-TAATTGTTGAT-CAT-C-A-GCCCAGATT-TT-AAA-ATTCCTT-TAT-TTCAAATCCGCCTAAGAACCTTTCTAA-GCGTTGT----GTT--GTGT
DroGri_CAF1_left   TGAACT-G-AAGTCTAA-C-TA-AT-TATGACAG-ATA-TTCACAACATTTA-AT-TTT-TGCACAT-TTAAGTAATGTTCGTTTGAAAACCATTTCTT-ACACAGC-----TT--GTGT
DroMel_CAF1_left   TTTATT-T-TAATTTTA-A-AT-TATCAGCAACC-CAG-A-T-TTTTAAATT-CC-TTA-CGATTGA-CTTTTTTCATTTTGCCTTAGAACCTTTTTTG-GCGCTGT----GCT--TTGT
DroMoj_CAF1_left   TTTTTT-T-TTTTGTAA-A-TT-TAATT-GTGTG-CAA-A-C-TTCCTTAATATA-CAT-TTTGAAA-ATAATCC--C-TTGAAAATAAACAAAAACTCGTTCCAGA----ATCTGAAAT
DroPer_CAF1_left   TAATTT-C-TTAACGAT-C-GA-CAGAACGAACC-CAG-T-T-TCCACAATCGTT-CAA-AATACCA-ATGTTCT--GTTAATTGTGTCGCATTCTTAGGGCCTTGG----CTT--GTGT
DroPse_CAF1_left   TCATTT-C-TTAACGAT-C-GA-CAGAACGAACC-CAG-T-T-TCCACAATCGTT-CAA-AATACCA-ATGTTCT--GTTAATTGTGTCGCATTCTTAGGGCCTTGG----CTT--GTGT
DroSec_CAF1_left   TTTATT-T-TAATTTTA-A-AT-TATCAACAACC-CAG-A-T-TTTAAAATT-CC-TTA-AGATCAA-ATTTTTTCACTTTACCTTAGAACCTTTTTAG-GCGTTGT----GTT--CTGT
DroSim_CAF1_left   TTTATT-T-TAATTTTA-A-AT-TATCAACAACC-CAG-A-T-TTTAAAATT-CC-TTA-AGATCAA-ATTTTTTCACTTTACCTTAGAACCTTTTTAA-GCGTTGT----TTT--CTCT
DroWil_CAF1_left   GTTAAC-G-TAAATTTC-CGAA-TAATTTCAAAT-TA--T-A-TTTAAAATA-TT-ATA-CAAAATG-CCAAATGTCGGATACTTGCACACATTTTAAA-GCGTTTG----CTT--GAAC
DroYak_CAF1_left   TGGGCT-TATTTTAATT-T-GT-AATCATCAGCC-CAG-A-T-TTTAAAATT-CC-TTA-AGATCGA-ATT-ATTCAGTTTGGCTAAGAACCTTTTTAA-GGTTTGC----GTT--CTGT
DroVir_CAF1_left   GTTTAAAC-ATATTGTT-T-TG-CAATATCTCCCACAATA-T-ACATATAAA-TAATACGAAAACTT-TCAAATACATACAAACAAGTTCCAATTCTTT-TTAGTATATTATCT--TAGA

DroAna_CAF1_left   TCG-AACTCTGCC-AGTCGATGTTCATCTGGTTCCATAGTGTAGCGGTTATCACGTCTGCTTTACACGCAGAAGGTCTCCGGTTCGATCCCGGATGGAACCAGGTTGATGA-GTAACTTT
DroEre_CAF1_left   TTG-AGTCTTGTC-ATTCGGTTGGCATCTGGTTCCATAGTGTAGCGGTTATCACGTCTGCTTTACACGCAGAAGGTCTCCGGTTCGATCCCGGATGGAACCAGCAGGAAAGTAGCTTTTT
DroGri_CAF1_left   TGT-AGCTTAGAC-ACTCGGCGCTCAATTGGTTCCATAGTGTAGCGGTTATCACGTCTGCTTTACACGCAGAAGGTCTCCGGTTCGATCCCGGATGGAACCATGTGGATTA-CTTTTTGT
DroMel_CAF1_left   TTG-CGTTGTGTC-AAGCGATTGGCATCTGGTTCCATAGTGTAGCGGTTATCACGTCTGCTTTACACGCAGAAGGTCTCCGGTTCGATCCCGGATGGAACCAGGAGGAAGT-AACTTTTT
DroMoj_CAF1_left   TAT-CAAATAAGC-AAACGTTTTGCAACTGGTTCCATAGTGTAGCGGTTATCACGTCTGCTTTACACGCAAAAGGTCTCCGGTTCGATCCCGGATGGAACCATGTGGGTTT-TTTTTTTT
DroPer_CAF1_left   AGG-AGTTCTGAA-ATGCAGACATCAGCTGGTTCCATAGTGTAGCGGTTATCACGTCTGCTTTACACGCAGAAGGTCTCCGGTTCGATCCCGGATGGAACCAGAAGGAAAT-TAACTTTT
DroPse_CAF1_left   AGG-AGTTCTGAA-ATGCAGACGTCAGCTGGTTCCATAGTGTAGCGGTTATCACGTCTGCTTTACACGCAGAAGGTCTCCGGTTCGATCCCGGATGGAACCAGAAGGAAAT-TAACTTTT
DroSec_CAF1_left   TTG-AGATTTGTC-ACACGAATGGTATCTGGTTCCATAGTGTAGCGGTTATCACGTCTGCTTTACACGCAGAAGGTCTCCGGTTCGATCCCGGATGGAACCAGGAGGAAAT-AACTTTTT
DroSim_CAF1_left   TTG-AGATTTGTC-AAACGAATGGCATCTGGTTCCATAGTGTAGCGGTTATCACGTCTGCTTTACACGCAGAAGGTCTCCGGTTCGATCCCGGATGGAACCAGGAGGAAAT-AGCTTTTT
DroWil_CAF1_left   AGA-GACTTTGTCGCTGCGGCTTTCAACTGGTTCCATAGTGTAGCGGTTATCACGTCTGCTTTACACGCAGAAGGTCTCCGGTTCGATCCCGGATGGAACCAGGATTCTGG-TTGAGTCA
DroYak_CAF1_left   TTG-AGTTTTGTC-ATTCAAATGTCATCTGGTTCCATAGTGTAGCGGTTATCACGTCTGCTTTACACGCAGAAGGTCTCCGGTTCGATCCCGGATGGAACCAGCAGGAAAGTAACTTTTT
DroVir_CAF1_left   TGCAGGTATAGAC-AGACGGTGCTCAACTGGTTCCATAGTGTAGCGGTTATCACGTCTGCTTTACACGCAGAAGGTCTCCGGTTCGATCCCGGATGGAACCAAGTGGCTTT-ACTTTTGG

DroAna_CAF1_left   TT-TGAGTTTCTTTTTTAATATTT-AGTAATAATTTTATTTAATTTTTTAATATT-TTTATTTAGTAAAGTTTTTTT-TACCAC-GAAAGATT
DroEre_CAF1_left   T-TTTCTAATTACTTTTGCGCCTA-ATAATTTTTT-TTTAAATCCTTTCATTATA-AAAGTTCACAAAGAAAATCGG-TAAGAT-ATTATTTC
DroGri_CAF1_left   C-AAATATATTTTACAAAATTAAT-TTGTTATATGGCTAATATATTTTGAATGTT-TATGACATTTTGAATAATGTG-ATTCGC-TAAGTTTC
DroMel_CAF1_left   T-TTATTTTTATTTTTTTAAACGC-TTACTAAGTGGAGTTTTAGCAAACAAAAGT-ATATAATATGTTATATATAAT-TCTTTC-GTGTTCAT
DroMoj_CAF1_left   AAATTTTCATTCTTTTT-TTTTTCTATTGTAATTTATAAA--A-GAAATTCCAAT-AGTTTTTTTAAATATTCAGAAAATATATTAATAGATA
DroPer_CAF1_left   TCCACAATTATTTTTCA-TCCCATACCCCTTTTGTGGTAC--AAATTTTTTAATTGAAAAGTCGTTTGAAAGTTGTC-ATTTTC-ATTTTATT
DroPse_CAF1_left   TCCACAATTATTTTAAA-TTATTATTATTTTAAATTAAGA--TTAATTTATATTC-ATTTTATTAAATTAATTTGTATACAGAA-TGCACAGA
DroSec_CAF1_left   TTTATTTCTTTTGATTTTTTTAAA-CGTTTAAAAATGGATC-TTTAGCAAACAAA-AGTATATAATATGTTATATAT-AATTCT-TTCGTTCA
DroSim_CAF1_left   T-CATTTCTTTTGATNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNN-NNNNNN-NNNNNNNN
DroWil_CAF1_left   ATTTTTTGTTTTTTTTT-TCAGTCTGTTTTTATTTTTTTT-TAAAGTCTGGTGAA-AGTTATGATATTACAAACCAT-ACAGTG-CGAGTGTA
DroYak_CAF1_left   T-CTATGTGTTATTTTTTTTTTAT-TTAGAACGTTTTGTGG-CAAACAGAATTAA-TAAATAATATTTCAAAGTGTA-CAAAGA-AAATCGGT
DroVir_CAF1_left   AAAAAATCTATTTTTAT-ATGCTTTAGGATAATTGAATAGA-ATATGTTGTCATT-AAAATAGTTAGTTTCTAATAT-TATGAA-ACATGTGC