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Gal10

Gal4. TBP. GAL4. GAL4. GAL4. GAL4. MIG1. MIG1. TBP. Factor footprint. Conservation island. Gal10. Gal1. GAL10. Scer TTATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATATACA

palila
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Gal10

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  1. Gal4 TBP GAL4 GAL4 GAL4 GAL4 MIG1 MIG1 TBP Factor footprint Conservation island Gal10 Gal1 GAL10 Scer TTATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATATACA Spar CTATGTTGATCTTTTCAGAATTTTT-CACTATATTAAGATGGGTGCAAAGAAGTGTGATTATTATATTACATCGCTTTCCTATCATACACA Smik GTATATTGAATTTTTCAGTTTTTTTTCACTATCTTCAAGGTTATGTAAAAAA-TGTCAAGATAATATTACATTTCGTTACTATCATACACA Sbay TTTTTTTGATTTCTTTAGTTTTCTTTCTTTAACTTCAAAATTATAAAAGAAAGTGTAGTCACATCATGCTATCT-GTCACTATCACATATA * * **** * * * ** ** * * ** ** ** * * * ** ** * * * ** * * * Scer TATCCATATCTAATCTTACTTATATGTTGT-GGAAAT-GTAAAGAGCCCCATTATCTTAGCCTAAAAAAACC--TTCTCTTTGGAACTTTCAGTAATACG Spar TATCCATATCTAGTCTTACTTATATGTTGT-GAGAGT-GTTGATAACCCCAGTATCTTAACCCAAGAAAGCC--TT-TCTATGAAACTTGAACTG-TACG Smik TACCGATGTCTAGTCTTACTTATATGTTAC-GGGAATTGTTGGTAATCCCAGTCTCCCAGATCAAAAAAGGT--CTTTCTATGGAGCTTTG-CTA-TATG Sbay TAGATATTTCTGATCTTTCTTATATATTATAGAGAGATGCCAATAAACGTGCTACCTCGAACAAAAGAAGGGGATTTTCTGTAGGGCTTTCCCTATTTTG ** ** *** **** ******* ** * * * * * * * ** ** * *** * *** * * * Scer CTTAACTGCTCATTGC-----TATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCCTCCGACGGAAGACTCTCCTCCGTGCGTCCTCGTCT Spar CTAAACTGCTCATTGC-----AATATTGAAGTACGGATCAGAAGCCGCCGAGCGGACGACAGCCCTCCGACGGAATATTCCCCTCCGTGCGTCGCCGTCT Smik TTTAGCTGTTCAAG--------ATATTGAAATACGGATGAGAAGCCGCCGAACGGACGACAATTCCCCGACGGAACATTCTCCTCCGCGCGGCGTCCTCT Sbay TCTTATTGTCCATTACTTCGCAATGTTGAAATACGGATCAGAAGCTGCCGACCGGATGACAGTACTCCGGCGGAAAACTGTCCTCCGTGCGAAGTCGTCT ** ** ** ***** ******* ****** ***** *** **** * *** ***** * * ****** *** * *** Scer TCACCGG-TCGCGTTCCTGAAACGCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGATTCTACAA-----TACTAGCTTTT--ATGGTTATGAA Spar TCGTCGGGTTGTGTCCCTTAA-CATCGATGTACCTCGCGCCGCCCTGCTCCGAACAATAAGGATTCTACAAGAAA-TACTTGTTTTTTTATGGTTATGAC Smik ACGTTGG-TCGCGTCCCTGAA-CATAGGTACGGCTCGCACCACCGTGGTCCGAACTATAATACTGGCATAAAGAGGTACTAATTTCT--ACGGTGATGCC Sbay GTG-CGGATCACGTCCCTGAT-TACTGAAGCGTCTCGCCCCGCCATACCCCGAACAATGCAAATGCAAGAACAAA-TGCCTGTAGTG--GCAGTTATGGT ** * ** *** * * ***** ** * * ****** ** * * ** * * ** *** Scer GAGGA-AAAATTGGCAGTAA----CCTGGCCCCACAAACCTT-CAAATTAACGAATCAAATTAACAACCATA-GGATGATAATGCGA------TTAG--T Spar AGGAACAAAATAAGCAGCCC----ACTGACCCCATATACCTTTCAAACTATTGAATCAAATTGGCCAGCATA-TGGTAATAGTACAG------TTAG--G Smik CAACGCAAAATAAACAGTCC----CCCGGCCCCACATACCTT-CAAATCGATGCGTAAAACTGGCTAGCATA-GAATTTTGGTAGCAA-AATATTAG--G Sbay GAACGTGAAATGACAATTCCTTGCCCCT-CCCCAATATACTTTGTTCCGTGTACAGCACACTGGATAGAACAATGATGGGGTTGCGGTCAAGCCTACTCG **** * * ***** *** * * * * * * * * ** Scer TTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCG--ATGATTTTT-GATCTATTAACAGATATATAAATGGAAAAGCTGCATAACCAC-----TT Spar GTTTT--TCTTATTCCTGAGACAATTCATCCGCAAAAAATAATGGTTTTT-GGTCTATTAGCAAACATATAAATGCAAAAGTTGCATAGCCAC-----TT Smik TTCTCA--CCTTTCTCTGTGATAATTCATCACCGAAATG--ATGGTTTA--GGACTATTAGCAAACATATAAATGCAAAAGTCGCAGAGATCA-----AT Sbay TTTTCCGTTTTACTTCTGTAGTGGCTCAT--GCAGAAAGTAATGGTTTTCTGTTCCTTTTGCAAACATATAAATATGAAAGTAAGATCGCCTCAATTGTA * * * *** * ** * * *** *** * * ** ** * ******** **** * Scer TAACTAATACTTTCAACATTTTCAGT--TTGTATTACTT-CTTATTCAAAT----GTCATAAAAGTATCAACA-AAAAATTGTTAATATACCTCTATACT Spar TAAATAC-ATTTGCTCCTCCAAGATT--TTTAATTTCGT-TTTGTTTTATT----GTCATGGAAATATTAACA-ACAAGTAGTTAATATACATCTATACT Smik TCATTCC-ATTCGAACCTTTGAGACTAATTATATTTAGTACTAGTTTTCTTTGGAGTTATAGAAATACCAAAA-AAAAATAGTCAGTATCTATACATACA Sbay TAGTTTTTCTTTATTCCGTTTGTACTTCTTAGATTTGTTATTTCCGGTTTTACTTTGTCTCCAATTATCAAAACATCAATAACAAGTATTCAACATTTGT * * * * * * ** *** * * * * ** ** ** * * * * * *** * Scer TTAA-CGTCAAGGA---GAAAAAACTATA Spar TTAT-CGTCAAGGAAA-GAACAAACTATA Smik TCGTTCATCAAGAA----AAAAAACTA.. Sbay TTATCCCAAAAAAACAACAACAACATATA * * ** * ** ** ** GAL1

  2. ancestral mutation deletion G G G G G G G G G G G C C C C C C C C C A A A A A A A A A A A A A A T T T T T T T T T T T T T T insertion derived sequence sequence

  3. G G G G G G G C C C C C C A A A A A A A A A T T T T T T T T T T T offset: +1 S1 A C G T C A T C A S2 offset: -2 S1 A C G T C A T C A S2 S1 S2

  4. G G G C C C C A A A A A T T T T T S1 S1 A A C C G G T T C C A A T T C C A A S2 S2 T T A A G G T T G G T T C C A A A G T T C A LCSS S1 S2

  5. Rabbits per generation Leaves per height Romanesque spirals Nautilus size Coneflower spirals Leaf ordering

  6. A G T - - A A G C Initialization: • Top left: 0 • M(i,0)=M(i-1,0) - 2 • M(0,j)=M(0,j-1) - 2 Update Rule: M(i,j)=max{ } Termination: 0 -2 -4 -6 gap gap -2 -4 -6 -8

  7. A G T - - A -1 -1 A -1 G -1 C Initialization: • Top left: 0 • M(i,0)=M(i-1,0) - 2 • M(0,j)=M(0,j-1) - 2 Update Rule: M(i,j)=max{ • M(i-1 , j ) - 2 • M( i , j-1) - 2 • M(i-1 , j-1) -1 • M(i-1 , j-1)+1} Termination: • Bottom right 0 -2 -4 -6 1 gap gap -2 1 -3 -5 1 -4 -1 0 -4 gap 1 gap mismatch -6 -5 0 -1 match -8 -7 -2 -1

  8. x1 ………………………… xM y1 ………………………… yN k(N)

  9. A G T - - A A G -1 C 0 -2 -4 -6 1 Traceback frombottom right -2 1 -3 -5 1 Final alignment: -4 -1 0 -4 A – G TA A G C 1 -6 -5 0 -1 OR – A G T A A G C -8 -7 -2 -1

  10. k* N-k* M/2 M/2

  11. Human Mouse x y x y x+y Human Mouse Human Mouse

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