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


DroAna_CAF1_left   AT-----TTT---TTTGTG-----AAAAAGCGACCATACCGACAATCGCCATTCAATTTTAAAAT-TCTGATGCTAAAAATCACTTAC--A---ATTTGA--TGAATTGATTCTTCGTTG
DroEre_CAF1_left   CTTTGAAAAA---GAGACC-----ATACCGACATTCGCCATTCAATTTTAAAACTGCAGTGCCT--ATAACACTTACTCTGCATTTG-------T--TGT--TGATTTGTAGTTGCGTCG
DroGri_CAF1_left   CA-----ATC---GCCATT-----T-AATTTTAAAATACTGGCTGGGTT-TGACTGCAACACACACAAAACACTGCAAAACACTGCAAAAT---TC-ACC--ATTTTATATTCTTTTCTT
DroMel_CAF1_left   AA-----A-----GAGACC-----ATACCGACATTCGCCATTCAATTTTAAAACTGGAGTGCCCA-ATATCACTTACTCTTGATTTTTTGA---TTTAAT--TGATTTGAAGTTGCGACG
DroMoj_CAF1_left   TA-----ATT---TTAAAATTTTATAATTTTCGAACAC-----TGGAAATGAAACACTGAAAGT--GAAACACTGATAGTGAAACACTGGA---AC-TGA--AACACTCCTCCTTTGTGC
DroPer_CAF1_left   GGT--AAAAA---GCGACC-----AAACCGACAATCGCCATTTAATTTTAAAATTTGTCTTCTT---T--TTCTGCGACACACACACTTTA---TC-GCC--ATTCTTGTACACTTGTTG
DroPse_CAF1_left   GGT--AAAAA---GCGACC-----AAACCGACAATCGCCATTTAATTTTAAAATTTGTCTTCTT---T--TTCTGCGACACACACACTTTA---TC-GCC--ATTCTTGTACACTTGTTG
DroSec_CAF1_left   AA-----AAA---GAGACC-----ATACCGACATTCGCCATTCAATTTTAAAACTGGAGTGCCCA-ATATAACTTACTCTTGATTTTTTGA---T--TGT--TGATTTGTAGTTGCGACG
DroSim_CAF1_left   AA-----AAA---GAGACC-----ATACCGACATTCGCCATTCAATTTTAAAACTGGAGTGCCCA-ATATCACTTACTCTTGCTTTTTGGA---T--TGT--TGATTTGAAGTAGCGACG
DroWil_CAF1_left   TTG-GAAAAA---GAGACT-----ATACCGACAATCGCCATTCAATTTTA---AAAGTAATTTCA-ATTGCATAGTCACTCACTAAGTTTG---GTTGGC--TAACTTTTTGGGTTGATA
DroYak_CAF1_left   AA-----A-----GAGACC-----ATACCGACATTCGCCATTCAATTTTAAAACTGGAGTGCCT--ATAACACTTACTCTTCTCTTTTGCATTAC--TGT--TGATTTGTAGCTGCGTCG
DroVir_CAF1_left   AT-----TTAATTTTAAAA-----TACTGGAATATTGG-----AATTGAAACACTGGAATACTGG-AACACTGTCACACTGAAACACTGGA--AT--ATCTGAGCTGCGT-TATTTTCTC

DroAna_CAF1_left   AGATGGCCAAGATCCTGAGACACACTTTGCCCAGTGATGGATA-T-ATTTT-TG---------GTGCATAACTGCACAAAATGCGTCCCAAGATCGTAGCCAGTTGGGG-GCT-CACA-G
DroEre_CAF1_left   AAGTGGCCAGGATCTTGAGACACACTTTGCCCAGTGATGTG-A-G----AT-AG---------AAACATAACTGCACAAGATGCATCCCAGGATCAGGACCTT-GGTGG-GTT-CACA-A
DroGri_CAF1_left   TACTTGCCACAATTTTGAGACACACTTTGCCCAGTGATGGT-TTT-ACAAGAGT---------CAACATTACTGTACAGAATGCATCCCAAAAGCAGAGCTAT-GAAAA--TTTGGCA-A
DroMel_CAF1_left   ATGTGGCCAGGATCTTGAGACACACTTTGCCCAGTGATGTG-A-G----AT-TG---------AAACATAACTGCACAAGATGCATCCCAGGATCGGGACCTT-AGGTG-GCT-CACA-A
DroMoj_CAF1_left   TAGTTGCCCCAATTTTGAGACACACTTTGCCCAGTGATGGG-T-TTCCAAT-CG---------TTAGACATCTGCACAAAATGCATCCCAAAAGTAGAGCTGC-GAGAG--TT-CCGT-T
DroPer_CAF1_left   GCGGGGCTGCAATCCTGAGACACACTTTGCCCAGTGATGAGGATG-ATCAC-GT---------AGACATAACTGCACAAAATGCATCCCAGGATCGTTGCCTC-GGTAT-CGT-CGTTCA
DroPse_CAF1_left   GCGGGGCTGCAATCCTGAGACACACTTTGCCCAGTGATGAGGATG-ATCAC-GT---------AGACATAACTGCACAAAATGCATCCCAGGATCGTTGCCTC-GGTAT-CGT-CGTTCA
DroSec_CAF1_left   ATGTGGCCAGGATCTTGAGACACACTTTGCCCAGTGATGTG-A-G----AT-TG---------AAACATAACTGCACAAGATGCATCCCAGGATCGGGACCTT-TGGTG-ATT-CACA-A
DroSim_CAF1_left   ATGTGGCCAGGATCTTGAGACACACTTTGCCCAGTGATGTG-A-G----AT-TG---------GAACATAACTGCACAAGATGCATCCCAGGATCGGGACCTT-TGGTG-GTT-CACA-A
DroWil_CAF1_left   TGGTTACCAAAATTATGAGACACACTTTGCCCAGTGATGAG-A-G----AA-TTATCACATGAAGACATAACTGCACAAAATGCATCCCAAAATCATGGTCTA-AATTCGATTACTCT-C
DroYak_CAF1_left   AAGTGGCCAAGATCTTGAGACACACTTTGCCCAGTGATGTG-A-G----AT-GG---------AAACATGACTGCACAAGATGCATCCCAGGATCAGGACCTT-TGATG-GTT-CACA-C
DroVir_CAF1_left   TGGTAGCCACAATTTTGAGACACACTTTGCCCAGTGATGGG-T-TTTGGAG-GC---------AGACATAACCGCACAAAATGCATCCCAAAAGCAGAGCTAT-GAGAT--TC-TGGT-A

DroAna_CAF1_left   ATGTCT---GGACGGCTTTTTTATAGATTATAGGACAAA-CTTTA-CCCAGTGCT-GCTAGGAAA-T-TGGCAAAACCGAACAAGGTTTGTCGTATAAT-GA-TCTTC
DroEre_CAF1_left   TTGGCT---GGTCGTCGTTTCGG--GATTATAGGACAAA-CTTTA-CCCAGTGCTGGCTAGGAAA-T-TGGCAAAACCGAACAAGGTTTGTCGTATAATTGC-TGTTC
DroGri_CAF1_left   GTATTT---TTA-TATACATCTT--TTAGCTGATCCATT-TCGAT-TATACGACAAACTTCACCCAG-T-GATGATGCACAGAAACAAAGTTGTCAAAACTG-AACAA
DroMel_CAF1_left   TTAGCT---GGTCGTCGTTTCGG--GATTATAGGACAAA-CTTTA-CCCAGTGCTGGCTTGGAAA-T-TGGCAAAACCGAACAAGGTTTGTCGTATAATTGC-TATTC
DroMoj_CAF1_left   GAATTGACTGGACTTTTTCCTTG--CTGTTTCGTTTCGA-TTATA-CGACAAACTTC----ACCC-A-GTGATGCGCACAACATAGAACCCGGCAAAACTGAACAAAG
DroPer_CAF1_left   CAATGT---GCGCTGAGACGCTC--GCTGATCGCTTACTGTGGGATTATAAGACAAACTTCACCC-A-GTGCTGCAAGCAAGTTGGCAAAACTGAACAAAGTTTATCG
DroPse_CAF1_left   CAATGT---GCGCTGAGACGCTC--GCTGATCGCTTACTGTGGGATTATAAGACAAACTTCACCC-A-GTGCTGCAAGCAAGTTGGCAAAACTGAACAAAGTTTATCG
DroSec_CAF1_left   TTAGCT---GGTCGTCGTTTCGG--GATTATAGGACAAA-CTTTA-CCCAGTGCTGGCTTGGAAA-T-TGGCAAAACCGAACAAGGTTTGTCGTATAATTGC-TGTTC
DroSim_CAF1_left   TTAGCT---GGTCGTCGTTTCGG--GATTATAGGACAAA-CTTTA-CCCAGTGCTGGCTTGGAAA-T-TGGCAAAACCGAACAAGGTTTGTCGTATAATTGC-TGTTC
DroWil_CAF1_left   CTTTTT---TTTTAACACTCCAA--TTGTATTTTGATTG-TAGTT-TAAAGATTATAAGACAAAC-T-TCACCCAGTGATGCTAAGGA--ATTTTCTT-GATTTTTTG
DroYak_CAF1_left   TTGGCTGCTGGTCGTCGTTTCGG--GATTATAGGACAAA-CTTTA-CCCAGTGCTGGCTAGGAAA-T-TGGCAAAACAGAACAAGGTTTGTCGTATAATTG----CTG
DroVir_CAF1_left   TTTTTA----TTTAATAATATTG--TTTTATTTTTATTT-TTTTT-TGCTGTTCTTTTTGCGATT-ATACGACAAACTTCACCCAGTGATGCGCACAAAAAG-AGCCT