AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ifhlA_mjan_opreg_100.orf -g0.314 -x5 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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0443 43 conserved hypothetical protein #2 MJ0444 265 conserved hypothetical protein #3 MJ0516 113 carbon monoxide dehydrogenase, hydrogenase subunit CooL (cooL) #4 MJ0520 192 NADH-ubiquinone oxidoreductase, subunit 1 #5 MJ0676 108 hydrogenase expression/formation protein (hypE) #6 MJ0995 57 VAR1 protein isolog #7 MJ1027 125 formate hydrogenlyase, subunit 5 #8 MJ1309 37 carbon monoxide dehydrogenase, hydrogenase anchor subunit CooM (cooM) #9 MJ1310 83 conserved hypothetical protein #10 MJ1363 300 formate hydrogenlyase, subunit 7 Motif number 1 TATTTCTAATTTTTATTTTATATGGTTTTTAT 1 22 1 TTTATTATTT 0.893921 -22 ACTCTTTAAGAGTTTTCATGTAACTTTCTTAAAGTT 2 10 0 ATTTTTAATT 0.980859 -256 CCTCACCCAGATTTTTATTTTAATATTT 4 2 0 ATTTTTAATT 0.973969 -191 TTTTCGTTCAACTTTTTCTAAAAGTTTCGTTTATAGT 4 62 0 ATTTTTAATT 0.980859 -131 ATTTGAATTTTACTTCATTTTTTTAATTTTGT 5 6 1 ATTTTTATTT 0.980138 -103 TCATTTTTTTAATTTTGTTTTAAAATTTTATTGAAAG 5 25 1 ATTTTTAATT 0.658827 -84 AATACTTAAATATTTTGATATATTTTTTACAATCTTT 5 58 0 TTTTTTATTT 0.94721 -51 TCACTCTTTAACTTTTATTGAATACTTAAATATTTTG 5 78 0 ATTTTTATTT 0.980694 -31 ACATTAAAATACTTTTTATAAAATATTTTAACTATTA 6 24 1 ATTTTTAATT 0.979217 -34 TATCATTATTAATTATGATAAATTATCTATTCATTAC 7 57 1 ATTATTATTC 0.903066 -69 TTCTATTTAACTTTCTCTAAAAGATTGGAGGGAGAA 8 10 1 ATTTCTAATT 0.866684 -28 ATGAGTTTGTTTTTATTTTGTATGTTTTAGGGTTCGA 10 21 0 TTTATTATTT 0.893921 -280 AAAAAGTATTACTAATTTTTCAATTTTAAAGTTTTAT 10 72 0 ATAATTAATT 0.673121 -229 AATTAGTAATACTTTTTATTAATTTTCCAATACCAAA 10 92 1 ATTTTTATTC 0.952486 -209 GCATAATAGATTTTTTAATTTAATTTCTTGCTTCTTG 10 193 0 TTTTTTAATC 0.875293 -108 AGCATAATCTATTTATATTTTATACATCACTATTTGT 10 249 1 ATTATTATAT 0.672643 -52 * **** * ** ** Masking position 9 Map Score: 21.8591 Number of sites scoring better than the average of aligned sites = 544 Number in coding regions = 358 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 2 ATTAGAAATAAGAATTCTAAT 1 2 0 AGAATTCTAA 0.880358 -42 AAACTCTTTAAGAGTTTTCATGTAACTTTC 2 19 0 AGAGTTTTCA 0.982583 -247 AAACTCTTAAAGAGTTTTCATAGCCCGAAG 2 32 1 AGAGTTTTCA 0.982583 -234 GTATATCCACAGAACTTTCACAGCTTTATA 2 129 1 AGAACTTTCA 0.974551 -137 CTATTGGCACAGAACTTTCACAGGAAAGTA 2 209 0 AGAACTTTCA 0.974551 -57 GAAAACTCTAAGAGTTTTCGTTCAACTTTT 4 83 0 AGAGTTTTCG 0.906438 -110 GAAAACTCTTAGAGTTTTCATAGCTGGAAA 4 94 1 AGAGTTTTCA 0.982583 -99 ATCTTTCAATAAAATTTTAAAACAAAATTA 5 34 0 AAAATTTTAA 0.904418 -75 TTTTATAAAAAGTATTTTAATGTCTTTGGT 6 17 0 AGTATTTTAA 0.905694 -41 CTTTTTATAAAATATTTTAACTATTATTAT 6 35 1 AATATTTTAA 0.679492 -23 TCTTAAAAATAAAACTTTAAAATTGAAAAA 10 64 1 AAAACTTTAA 0.841013 -237 TGCTTTATTGAGAATTTTAATATGCATAAT 10 223 0 AGAATTTTAA 0.977201 -78 ********** Masking position 1 Map Score: 18.1819 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 198 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 TCATGTAACTTTCTTAAAGTT 2 1 0 TTTTAAAGTT 0.757044 -265 TAGCTTCGGGCTATGAAAACTCTTTAAGAGT 2 34 0 CTTGAAAACT 0.926822 -232 TATTATAAAGCTGTGAAAGTTCTGTGGATAT 2 131 0 CTTGAAAGTT 0.963292 -135 GGATACTTTCCTGTGAAAGTTCTGTGCCAAT 2 206 1 CTTGAAAGTT 0.963292 -60 GAAGCAATGCCTCTTAAAATTTATTGGGAGG 3 86 1 CTTTAAAATT 0.97137 -28 TGCTTTCCAGCTATGAAAACTCTAAGAGTTT 4 96 0 CTTGAAAACT 0.926822 -97 TTTTAATTTTGTTTTAAAATTTTATTGAAAG 5 31 1 GTTTAAAATT 0.799463 -78 AATCTCACTCTTTAACTTTTATTGAATA 5 91 0 CTTTTAACTT 0.807576 -18 TTCTATTTAACTTTCTCTAAAAG 8 3 1 CTTTTAACTT 0.808468 -35 ATTTAACTTTCTCTAAAAGATTGGAGGGAGA 8 15 1 CTTAAAAGAT 0.641184 -23 TGTTTATATACTGTTAAACCTAATCTGTCAT 9 61 1 CTTTAAACCT 0.931392 -23 CTCATAAATTCTCTTAAAAATAAAACTTTAA 10 53 1 CTTTAAAAAT 0.915026 -248 TAATTTTTCAATTTTAAAGTTTTATTTTTAA 10 66 0 ATTTAAAGTT 0.879975 -235 CCTACTTATAATCTTAAAAATCCGAAAGATT 10 138 1 ATTTAAAAAT 0.549204 -163 TCTATTATGCATATTAAAATTCTCAATAAAG 10 220 1 ATTTAAAATT 0.871517 -81 ** ******** Masking position 7 Map Score: 15.0925 Number of sites scoring better than the average of aligned sites = 586 Number in coding regions = 493 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 4 TGATGAAACCGAAGCGTAGCTTCGGGCTAT 2 51 0 GAAGCGTAGC 0.987688 -215 TTTACACCTCCGAGCGTAGCAAGGAGGTGT 2 87 0 CGAGCGTAGC 0.981813 -179 GTGCCAATAGGGGGCGAAGCCCCCTATGGA 2 229 1 GGGGCGAAGC 0.989548 -37 GTATCCCAATAGGGCGAAGCCCTATGGTTT 3 33 0 AGGGCGAAGC 0.962724 -81 CTTCTTTGCAGAAGCAATGCATCCTGGGTA 3 60 0 GAAGCAATGC 0.90523 -54 TAAATTTTAAGAGGCATTGCTTCTTTGCAG 3 79 0 GAGGCATTGC 0.938084 -35 AATTTATTGGGAGGAATAGCC 3 103 1 GAGGAATAGC 0.826444 -11 TCATAGCTGGAAAGCATAGCTCTCCATTTC 4 111 1 AAAGCATAGC 0.932082 -82 TTTACACTTCCGAGCGAAGCGAGGAGGTGT 4 152 0 CGAGCGAAGC 0.973597 -41 TTGCTTCTTGTGAGCATAGCGAACAGGTTT 10 173 0 TGAGCATAGC 0.925435 -128 ********** Masking position 10 Map Score: 14.0218 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 41 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 TCATCAAAGCTAACACCTCCTTGCTACGCT 2 75 1 TAACACCTCC 0.994811 -191 CAAATTTAATTTACACCTCCGAGCGTAGCA 2 96 0 TTACACCTCC 0.994811 -170 CATCAAAAACTAACACCTCCTCGCTTCGCT 4 140 1 TAACACCTCC 0.994811 -53 AGTTGTAAATTTACACTTCCGAGCGAAGCG 4 161 0 TTACACTTCC 0.979698 -32 ********** Masking position 5 Map Score: 7.07498 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 1 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 AAAAACCATATAAAATAAAAATTAGAAATA 1 22 0 TAAAATAAAA 0.808769 -22 TCGGTTTCATCAAAGCTAACACCTCCTTGC 2 69 1 CAAAGCTAAC 0.583606 -197 AAATATTAAAATAAAAATCTGGGTGA 4 7 1 TAAAATAAAA 0.808769 -186 CCATTTCATCAAAAACTAACACCTCCTCGC 4 134 1 AAAAACTAAC 0.877845 -59 AATAAAATTTTAAAACAAAATTAAAAAAAT 5 27 0 TAAAACAAAA 0.942245 -82 AGTATTCAATAAAAGTTAAAGAGTGAGATT 5 89 1 AAAAGTTAAA 0.600638 -20 ATAACTTTATTAAAACAAAACTATATAAAA 7 15 1 TAAAACAAAA 0.942245 -111 AAAAGCTATTAAAAACATAAATATTAAT 9 9 0 AAAAACATAA 0.846891 -75 TTAGCAACCAAAAAGCTAAAAGCTATTAAA 9 26 0 AAAAGCTAAA 0.852976 -58 TTTCGAACCCTAAAACATACAAAATAAAAA 10 19 1 TAAAACATAC 0.81283 -282 CATACAAAATAAAAACAAACTCATAAATTC 10 34 1 AAAAACAAAC 0.945026 -267 AAATTCTCTTAAAAATAAAACTTTAAAATT 10 58 1 AAAAATAAAA 0.830495 -243 TTCCAATACCAAAATCAAACAACCTACTTA 10 116 1 AAAATCAAAC 0.707503 -185 AAATTCTCAATAAAGCATAATCTATTTATA 10 236 1 TAAAGCATAA 0.778061 -65 ********** Masking position 4 Map Score: 14.0686 Number of sites scoring better than the average of aligned sites = 976 Number in coding regions = 818 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 7 CTAAATAACCTTTTCTTTCCATAGG 2 251 0 ATAACTTTTC 0.841633 -15 TATCAAAATATTTAAGTATTCAATAAAAGTT 5 75 1 TTTAGTATTC 0.624309 -34 AATCTCACTCTTTAACTTTTATTGAATACTT 5 88 0 TTTACTTTTA 0.69239 -21 AATATTTTATAAAAAGTATTTTAATGTCTTT 6 20 0 AAAAGTATTT 0.642155 -38 TATAAAATATTTTAACTATTATTATAAG 6 40 1 TTTACTATTA 0.84361 -18 GATAATTAGCTTAACCTTTTATATAGTTTTG 7 30 0 TTAACTTTTA 0.813602 -96 ATTATGATAAATTATCTATTCATTACCTTAG 7 68 1 ATTACTATTC 0.867514 -58 TAGTGAGTCATATACCTATTATCATGTTTAT 7 96 1 TATACTATTA 0.825941 -30 CCAAAAAGCTAAAAGCTATTAAAAACATAAA 9 18 0 AAAACTATTA 0.931262 -66 AAAAACTATTTCGAACCCTAA 10 1 1 AAAACTATTT 0.83015 -300 TTTTTCAATTTTAAAGTTTTATTTTTAAGAG 10 63 0 TTAAGTTTTA 0.5809 -238 GAAAATTAATAAAAAGTATTACTAATTTTTC 10 88 0 AAAAGTATTA 0.8115 -213 AAAGATTTCTAAAACCTGTTCGCTATGCTCA 10 162 1 AAAACTGTTC 0.678047 -139 ATTAAATTAAAAAATCTATTATGCATATTAA 10 206 1 AAAACTATTA 0.931262 -95 TCAATAAAGCATAATCTATTTATATTTTATA 10 242 1 ATAACTATTT 0.860245 -59 **** ****** Masking position 4 Map Score: 9.70616 Number of sites scoring better than the average of aligned sites = 817 Number in coding regions = 648 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 8 GCTTTGATGAAACCGAAGCGTAGCTTCGGGCTA 2 52 0 ACAAGCGTAG 0.925452 -214 TTAATTTACACCTCCGAGCGTAGCAAGGAGGTG 2 88 0 CCGAGCGTAG 0.994033 -178 TTCTGTGCCAATAGGGGGCGAAGCCCCCTATGG 2 225 1 AGGGGCGAAG 0.959204 -41 CTGGGTATCCCAATAGGGCGAAGCCCTATGGTT 3 34 0 CTGGGCGAAG 0.955941 -80 GTTTTCATAGCTGGAAAGCATAGCTCTCCATTT 4 107 1 CGAAGCATAG 0.925452 -86 TAAATTTACACTTCCGAGCGAAGCGAGGAGGTG 4 153 0 CCGAGCGAAG 0.992065 -40 TTTCTTGCTTCTTGTGAGCATAGCGAACAGGTT 10 174 0 CGGAGCATAG 0.978496 -127 * * ******** Masking position 12 Map Score: 3.37321 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 8 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 TCCATATCAATAAGGATACTTTCCTGTGAAA 2 193 1 TAAGGATATT 0.899159 -73 TGGGTGAGGATATGGATACTTCACTGATAGG 4 30 1 TATGGATATT 0.866257 -163 TTTAAAATTTTATTGAAAGATTGTAAAAAAT 5 43 1 TATTGAAAAT 0.746587 -66 TACTTAAATATTTTGATATATTTTTTACAAT 5 62 0 TTTTGATAAT 0.807219 -47 CTTATAATAATAGTTAAAATATTTT 6 43 0 TAATAATATT 0.669659 -15 TCATAATTAATAATGATAATTAGCTTAACCT 7 44 0 TAATGATATT 0.962576 -82 TCATTATTAATTATGATAAATTATCTATTCA 7 59 1 TTATGATAAT 0.852166 -67 TAATGACAGATTAGGTTTAAC 9 73 0 TAATGACAAT 0.917097 -11 GATTATGCTTTATTGAGAATTTTAATATGCA 10 227 0 TATTGAGATT 0.813658 -74 AAGCATAATCTATTTATATTTTATACATCAC 10 248 1 TATTTATATT 0.595557 -53 TCATTATCATTAATGACAAATAGTGATGTAT 10 270 0 TAATGACAAT 0.917073 -31 TCATTAATGATAATGATAAATTACTG 10 285 1 TAATGATAAT 0.962584 -16 ******** ** Masking position 6 Map Score: 8.68545 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 293 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 10 AGGAAAGTATCCTTATTGATATGGACGCCTA 2 187 0 CCTTATTGAA 0.973575 -79 GGGCTTCGCCCCCTATTGGCACAGAACTTTC 2 220 0 CCCTATTGGA 0.984395 -46 GGGCGAAGCCCCCTATGGAAAGAAAAGGTTA 2 240 1 CCCTATGGAA 0.980844 -26 TAGGGCGAAGCCCTATGGTTTCTGAATAATT 3 23 0 CCCTATGGTT 0.871307 -91 TAGGGCTTCGCCCTATTGGGATACCCAGGAT 3 39 1 CCCTATTGGA 0.98439 -75 CTATTCATTACCTTAGTGAGTCATATACCTA 7 83 1 CCTTAGTGAT 0.831412 -43 ATAGATTATGCTTTATTGAGAATTTTAATAT 10 230 0 CTTTATTGAA 0.826953 -71 ********* * Masking position 5 Map Score: 3.63974 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 44 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 11 TTCTTATTTCTAATTTTTATTTTATATGGT 1 18 1 TAATTTTTAT 0.959767 -26 GAATTTTACTTCATTTTTTTAATTTTGTTT 5 15 1 TCATTTTTTT 0.786542 -94 TCTCACTCTTTAACTTTTATTGAATACTTA 5 87 0 TAACTTTTAT 0.847876 -22 AAAAGTATTTTAATGTCTTTGGTGATAAC 6 10 0 TAATGTCTTT 0.633212 -48 GACATTAAAATACTTTTTATAAAATATTTT 6 23 1 TACTTTTTAT 0.921014 -35 ATACCTATTATCATGTTTATAATTGTTGG 7 107 1 TCATGTTTAT 0.919545 -19 ATTAATATTTATGTTTTTAATA 9 3 1 TAATATTTAT 0.85476 -81 GTTGCTAACGTAATGTTTATATACTGTTAA 9 48 1 TAATGTTTAT 0.958986 -36 AAATTAGTAATACTTTTTATTAATTTTCCA 10 91 1 TACTTTTTAT 0.921014 -210 ********** Masking position 6 Map Score: 6.24283 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 191 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 12 ********** No masking Map Score: 9.53751e-15 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 13 ********** No masking Map Score: 9.53751e-15 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 14 ********** No masking Map Score: 9.53751e-15 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