AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00100_mjan_reg_100.orf -o00100_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MJ0703.1 125 M. jannaschii predicted coding region MJ0703.1 #2 MJ0704 95 M. jannaschii predicted coding region MJ0704 #3 MJ0861 131 conserved hypothetical protein #4 MJ1081 130 conserved hypothetical protein #5 MJ1083 69 iron-sulfur flavoprotein (isf) #6 MJ1084 88 shikimate 5-dehydrogenase (aroE) #7 MJ1085 25 M. jannaschii predicted coding region MJ1085 Motif number 1 CAATCTAATGAAAAAATAAACACTACTTTT 1 35 1 AAAAAATAAA 0.976963 -91 AAAAATAATAAAATAGTTCTAT 1 114 0 AAATAATAAA 0.976964 -12 TTAAAAAAATTATTATAACTACA 2 4 1 AAAAAATTAT 0.828573 -92 AGAAAAGCATAAGCAATTAAGAGAATAGAT 2 72 0 AAGCAATTAA 0.781931 -24 ACATCTAAGATAAAAATAAAAATCATAAAT 3 37 0 TAAAAATAAA 0.901655 -95 AATTTATTTAAAATAATTAAATATTTATAA 3 76 1 AAATAATTAA 0.971576 -56 AAATATTTATAAACATTAAAATTATAAAAA 3 94 1 AAACATTAAA 0.940558 -38 TTAAAATTATAAAAAATTAAAGGATGTGAG 3 109 1 AAAAAATTAA 0.971518 -23 GTTCTAAATTATTAAATTATAACTA 4 6 1 AAATTATTAA 0.946008 -125 TATTAAATTATAACTATAAATTATAACTAT 4 20 1 TAACTATAAA 0.814657 -111 ATTAAATTTTAAATATTAAACTTGAATAGT 4 45 0 AAATATTAAA 0.944195 -86 TTTAATATTTAAAATTTAATTAAGGTCTTA 4 55 1 AAAATTTAAT 0.55122 -76 AAAACATATCAAAAATTTAATTGGGTATTG 4 98 1 AAAAATTTAA 0.93157 -33 GAAAAACTATTAAAACCTATTTC 5 4 1 AAACTATTAA 0.942482 -66 AAGAGAAGGTAAAAAATAAATATCAAATAA 6 23 0 AAAAAATAAA 0.976963 -66 TAAAAATTGTAAATTACAAAGAGAAGGTAA 6 41 0 AAATTACAAA 0.709164 -48 TTACAATTTTTAATTATAAAAACTAATTTA 6 59 1 TAATTATAAA 0.82456 -30 AAATATTTAATAAATTTAAT 7 1 1 AAATATTTAA 0.931679 -25 ********** Masking position 2 Map Score: 28.7231 Number of sites scoring better than the average of aligned sites = 2676 Number in coding regions = 1900 Number in noncoding regions = 776 Number of orfs with sites within 600 bp upstream = 518 Fraction of orfs with sites within 600 bp upstream = 0.0831995 Motif number 2 ATCTAATGAAAAAATAAACACTACTTTTTA 1 37 1 AAAATAAACA 0.781036 -89 AAAAATAATAAAATAGTTCTATAC 1 112 0 ATAATAAAAT 0.882448 -14 TATTGTAGTTATAATAATTTTTTTAA 2 7 0 ATAATAATTT 0.471976 -89 AGATATCCATTTATTAAAATCTCCTACAAA 2 46 0 TTATTAAAAT 0.863448 -50 ATCTAAGATAAAAATAAAAATCATAAATGG 3 35 0 AAAATAAAAA 0.862776 -97 TTAATTATTTTAAATAAATTTACAGCCTAA 3 66 0 TAAATAAATT 0.93408 -66 TTATTTAAAATAATTAAATATTTATAAACA 3 79 1 TAATTAAATA 0.890341 -53 ATATTTATAAACATTAAAATTATAAAAAAT 3 96 1 ACATTAAAAT 0.840378 -36 GTTCTAAATTATTAAATTATAACTATAA 4 9 1 TTATTAAATT 0.906352 -122 TAAATTTTAAATATTAAACTTGAATAGTTA 4 43 0 ATATTAAACT 0.840378 -88 GATAAGACCTTAATTAAATTTTAAATATTA 4 57 0 TAATTAAATT 0.931438 -74 CCGCAATACCCAATTAAATTTTTGATATGT 4 101 0 CAATTAAATT 0.823638 -30 TATTTCTGATAAAATACATTAGGTCAGAAT 5 28 1 AAAATACATT 0.814767 -42 GAGAAGGTAAAAAATAAATATCAAATAACA 6 21 0 AAAATAAATA 0.911056 -68 TAAAAATTGTAAATTACAAAGAGAAGGTAA 6 41 0 AAATTACAAA 0.631034 -48 TTAGTTTTTATAATTAAAAATTGTAAATTA 6 55 0 TAATTAAAAA 0.841204 -34 ATTATCACATTAAATTAGTTTTTATA 6 73 0 ACATTAAATT 0.895342 -16 AAATATTTAATAAATTTAATAGAGG 7 7 1 TTAATAAATT 0.896879 -19 ********** Masking position 5 Map Score: 21.0841 Number of sites scoring better than the average of aligned sites = 2249 Number in coding regions = 1480 Number in noncoding regions = 769 Number of orfs with sites within 600 bp upstream = 521 Fraction of orfs with sites within 600 bp upstream = 0.0836813 Motif number 3 ACCATCTTTTAAATATGTTTCTGTAAAAAG 1 60 0 AAATATGTTT 0.761405 -66 AAAAATAATAAAATAGTTCTATACCTCAAC 1 106 0 AAATAGTTCT 0.928294 -20 GCAATTAAGAGAATAGATATCCATTTATTA 2 60 0 GAATAGATAT 0.888764 -36 TAATTATTTTAAATAAATTTACAGCCTAAC 3 65 0 AAATAAATTT 0.711194 -67 TAAAATAATTAAATATTTATAAACATTAAA 3 84 1 AAATATTTAT 0.916608 -48 TATTAAACTTGAATAGTTATAATTTATAGT 4 32 0 GAATAGTTAT 0.938459 -99 AAATAGGTTTTAATAGTTTTTC 5 3 0 TAATAGTTTT 0.847788 -67 ATTTTATCAGAAATAGGTTTTAATAGTTTT 5 13 0 AAATAGGTTT 0.948248 -57 AGAAGGTAAAAAATAAATATCAAATAACAC 6 20 0 AAATAAATAT 0.806048 -69 TATCACATTAAATTAGTTTTTATAATTAAA 6 67 0 AATTAGTTTT 0.818294 -22 AAATATTTAATAAATTTAAT 7 1 1 AAATATTTAA 0.595851 -25 ********** Masking position 5 Map Score: 9.03771 Number of sites scoring better than the average of aligned sites = 847 Number in coding regions = 608 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 227 Fraction of orfs with sites within 600 bp upstream = 0.03646 Motif number 4 TGAATTCATCAACTGATAGAACTTTA 1 7 0 AACTGATAGA 0.824655 -119 ACAGAAACATATTTAAAAGATGGTGTTATA 1 66 1 ATTTAAAAGA 0.930089 -60 AAGCATAAGCAATTAAGAGAATAGATATCC 2 68 0 AATTAAGAGA 0.944837 -28 ACAGCCTAACATCTAAGATAAAAATAAAAA 3 45 0 ATCTAAGATA 0.881879 -87 CTGTAAATTTATTTAAAATAATTAAATATT 3 71 1 ATTTAAAATA 0.752656 -61 AAATTAAAGGATGTGAGAGA 3 122 1 ATGTGAGAGA 0.969692 -10 TTATGTCCATAGGTGAGAGAGT 5 58 1 AGGTGAGAGA 0.921251 -12 TATTTAATAAATTTAATAGAGG 7 14 1 ATTTAATAGA 0.93009 -12 ********** Masking position 6 Map Score: 4.54773 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 682 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 5 GATTTTAATAAATGGATATCTATTCTCTTA 2 55 1 AATGGATATC 0.803569 -41 AAAATCATAAATGGGATAACAGTATTAACA 3 19 0 ATGGGATAAC 0.945575 -113 TATAGTTATAATTTAATAATTTAGAAC 4 8 0 ATTTAATAAT 0.702404 -123 TTTTGATTTGATGTGATAAGACCTTAATTA 4 71 0 ATGTGATAAG 0.935319 -60 CCAATTAAATTTTTGATATGTTTTTGATTT 4 92 0 TTTTGATATG 0.772978 -39 CAAAAATTTAATTGGGTATTGCGGATATAA 4 107 1 ATTGGGTATT 0.833906 -24 GATTTTATATCCGCAATACCC 4 120 0 ATTTTATATC 0.778413 -11 CTTTTGTGTTATTTGATATTTATTTTTTAC 6 15 1 ATTTGATATT 0.963013 -74 AACTAATTTAATGTGATAAT 6 79 1 ATGTGATAAT 0.945773 -10 ********** Masking position 7 Map Score: 2.32599 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 468 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 ********** No masking Map Score: 1.5372e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: 1.5372e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: 1.5372e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0