AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -ifhlA_pyro_opreg_300.orf -g0.419 -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 = 0.419 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 PH0879 300 367aa long hypothetical hydrogenase expression/formation protein hypD #2 PH1353 66 679aa long hypothetical formate dehydrogenase #3 PH1354 28 196aa long hypothetical protein #4 PH1427 209 167aa long hypothetical protein #5 PH1428 259 121aa long hypothetical protein #6 PHS039 52 64aa long hypothetical protein #7 PH1429 288 147aa long hypothetical protein #8 PH1433 59 118aa long hypothetical protein #9 PH1437 45 427aa long hypothetical NADH-ubiquinone oxidoreductase subunit #10 PH1439 300 321aa long hypothetical NADH-ubiquinone oxidoreductase subunit #11 PH1454 265 241aa long hypothetical protein #12 PH1455 247 120aa long hypothetical protein #13 PH1456 82 174aa long hypothetical phaE product #14 PH1581 75 139aa long hypothetical protein Motif number 1 CTTGACCTTCTAACCGATGTAAGAGCTGGTGATTAC 1 170 1 TACGGAGAGC 0.957212 -131 ATAGAAAAACTCGACGAGGAAAAAGCTAAGGAAATA 1 230 1 TCCGGAAAGC 0.985488 -71 TGCTTTTAAATATTCACTAAAAGAGCTAC 4 4 0 TACAAAGAGC 0.769436 -206 CAATTGTGTATCACCAAAACCAAAGATATTAAACCA 4 50 1 TCCAAAAAGA 0.647453 -160 TTTTTCTTCTTCAGAGAGAAGATAGCGTAGAAATCT 4 135 0 TCAGAATAGC 0.811442 -75 TATGCTGTATTCCTCATTGGAATAGCCGGATTGATA 5 31 1 TCCAGATAGC 0.990803 -229 GAGAGGGCAATTTACATTGACATAGCGATAGTTTAT 5 175 1 TTCAGATAGC 0.913504 -85 TTTTATGTAGTAATCATCGGTATAGCGATATCTTTT 7 115 0 TACAGATAGC 0.977174 -174 GCAACGGTTTTATTCACGGCAATAGCCGGAGCTGTA 7 232 1 TACAGATAGC 0.977174 -57 CTAGCCGATGTCGTCGTTGCAATAGCCTCTATAGAT 10 106 1 TCCGGATAGC 0.99242 -195 ACCGATAGGGTAGCCGTAGTGAAAGAAGGCAAGAAG 10 157 1 TACGGAAAGA 0.830284 -144 AAGAAGATTATCCTAACCGAAAAAGATCTGCTAAAA 10 187 1 TCAAGAAAGA 0.647452 -114 GTTTATTTAGTCTTAATAGCGATAGCAACGCTACTT 12 22 1 TCAAGATAGC 0.951293 -226 GTACTATCCTTCGCCGGGGTTATAGCATTTGCAAGG 12 205 1 TCCGGATAGC 0.99242 -43 ** ** * ***** Masking position 12 Map Score: 17.4923 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 173 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 CTGAGAAAACTTCCTCCCAAGCTTCAAGTATT 1 262 0 TTCTCCCAGC 0.915986 -39 TCACTCACCTCCAAGGGCTGAGAAAAC 1 284 0 CACTCCAAGG 0.971967 -17 CATAGCTAAGTATCTCCAGGGGGGATTGAC 5 240 1 TACTCCAGGG 0.936536 -20 CCAATTCATAATCCTCCTAGGGATCATACTCA 6 20 1 ATCTCCTAGG 0.906726 -33 ATAATATTTGCTGCTCTTATGGTTGCTCTTAG 7 40 1 CTCTCTTAGG 0.861996 -249 AAAACCGTTGCTTCTCCAATGGTATCGTAACC 7 211 0 CTCTCCAAGG 0.988642 -78 TCCTCTCCCTCCTCCAGGGCCTTAGAAGAG 7 269 0 CTCTCCAGGC 0.955891 -20 AGGTCATCCCTATCTCCTGAGGAGGGGAGGTA 9 23 1 TACTCCTGGG 0.936537 -23 CTAATGCATCCTACTCCCGCGGGAGTGGGATC 10 268 0 CTCTCCCGGG 0.993784 -33 GATTTGCTAGCTGCTACCGTGGGAATGGCCGC 11 85 1 CTCTACCGGG 0.91984 -181 CCGCTCAGGGCCGCTCCTATGGCCGCTTCCGT 11 175 0 CCCTCCTAGG 0.953126 -91 TTTTAATAAATTTCACCCATGGTTAAGGACTT 13 51 0 TTCACCCAGG 0.854565 -32 ** ****** ** Masking position 4 Map Score: 12.7494 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 334 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 AGTTGATTTTGGAGGTGTGAAAAGGGAGGT 1 136 1 GGAGGTGTGA 0.927127 -165 GTGTGAAAAGGGAGGTTAGACTTGACCTTC 1 150 1 GGAGGTTAGA 0.916112 -151 CTCAGCCCTTGGAGGTGAGTGA 1 289 1 GGAGGTGAGT 0.936424 -12 CAATGGTTGAGGAGGTTTGGAG 4 198 1 GGAGGTTTGG 0.932252 -12 GTATCTCCAGGGGGGATTGAC 5 249 1 GGGGGATTGA 0.812567 -11 GGCCCTGGAGGAGGGAGAGGA 7 278 1 GAGGGAGAGG 0.966704 -11 TATCTCCTGAGGAGGGGAGGTAA 9 33 1 GGAGGGGAGG 0.976936 -13 GGAAGAAGGGTAGGGATGGTCCCG 10 5 1 GAAGGGTAGG 0.883975 -296 CCGTCAGATGGAAGATGAGGGAACCAACTT 10 32 1 GAAGATGAGG 0.810744 -269 TCCTACTCCCGCGGGAGTGGGATCCCCTTT 10 262 0 GCGGGAGTGG 0.830927 -39 GGATGCATTAGGGGGTGAGGAT 10 289 1 GGGGGTGAGG 0.98705 -12 TGAAAGCGAGGAGGAAGAGAAACCTGGTTG 11 246 1 GAGGAAGAGA 0.574401 -20 TAACCCCGGCGAAGGATAGTACTGCATATA 12 197 0 GAAGGATAGT 0.690353 -51 ********** Masking position 4 Map Score: 13.2692 Number of sites scoring better than the average of aligned sites = 737 Number in coding regions = 668 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 4 TTCTTGAAATTAAAGGAAACATCGGGATAGTTG 1 108 1 TAAGGAACTC 0.884911 -193 CTCAGACTAATCCTGGGACCTACAACCTCTGAT 5 73 1 TCCGGACCAC 0.937389 -187 TTGAGGGTATCCAGGGCAACTACCCTATCAGAG 5 99 0 CCAGGAACAC 0.98411 -161 AGCAAGAGCATAATGGCAACGACTAGTGTGTTG 5 129 0 TAAGGAACAC 0.936808 -131 GTAACTATGTTCATTCCACCCACGTCTTCGAGT 7 156 0 TCATCACCAC 0.749462 -133 ATCTTCCATCTGACGGGACCATCCCTACCCTTC 10 15 0 TGAGGACCTC 0.932329 -286 AGATGGAAGATGAGGGAACCAACTTTTCCCAAC 10 37 1 TGAGGACCAC 0.96372 -264 TCTATAGAGGCTATTGCAACGACGACATCGGCT 10 108 0 CTATGAACAC 0.690477 -193 GCCGCTTCCGTCATTGCAACGTCGGGGGCCTGA 11 153 0 TCATGAACTC 0.92644 -113 TACAGGGTCTTCAGGGGACCCACTACCGTAGAT 12 64 1 TCAGGACCAC 0.988664 -184 GTCATTATATCCACGGCAACTAGTCTATCTACG 12 90 0 CCAGGAACAG 0.868187 -158 ACTGCATATACCAATGCAACGTCAAGGAAGATC 12 174 0 CCATGAACTC 0.911979 -74 *** ** *** ** Masking position 8 Map Score: 8.46376 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 171 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 GACACATTAGCTTCACCATTAAGAAGTGCT 1 60 0 CTTCACCATT 0.918353 -241 CAAGTATTTCCTTAGCTTTTTCCTCGTCGA 1 240 0 CTTAGCTTTT 0.657387 -61 AGGAAGTTTTCTCAGCCCTTGGAGGTGAGT 1 279 1 CTCAGCCCTT 0.81503 -22 TCCAAACCTCCTCAACCATTGGTTTAAAAC 4 189 0 CTCAACCATT 0.83958 -21 ACACACTAGTCGTTGCCATTATGCTCTTGC 5 131 1 CGTTGCCATT 0.791461 -129 CCTGGAGATACTTAGCTATGATCAGTGTCC 5 230 0 CTTAGCTATG 0.888979 -30 AAAGAGCTTTGGCATTTCTCTCATTG 7 7 1 CTTTGGCATT 0.827664 -282 CTTCCAATCCCTTCGCTATTGTGAACAAGT 10 68 0 CTTCGCTATT 0.918343 -233 ATCGGTACAGCTTAGGCATGGATCTATAGA 10 133 0 CTTAGGCATG 0.891493 -168 CTGTCTTCATCTTCGCCATTAAAAGGACGT 11 209 1 CTTCGCCATT 0.978452 -57 AGAATAAGTCCTTAACCATGGGTGAAATTT 13 46 1 CTTAACCATG 0.895181 -37 ********** Masking position 9 Map Score: 5.2711 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 322 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 TTTTAGACATTTTTAAAACCAAAAGTTTTCAAC 1 18 0 TTTAAAAAAA 0.95947 -283 CAGGAAAGGTTCTTGAAATTAAAGGAAACATCG 1 99 1 TTTGAAAAAA 0.86362 -202 ATAAATGTTAAAAATAAAAATATTATTC 2 49 0 TTTAAAAAAA 0.959748 -18 AAAGCTTAGAATTGAAAATAAAAGTGTTCAACC 4 88 0 ATGAAAAAAA 0.741915 -122 CTATCTTCTCTCTGAAGAAGAAAAAATAAGGAA 4 146 1 TTGAAGAAAA 0.90085 -64 TTGCTATCGCTATTAAGACTAAATAAACATTAA 12 17 0 TTTAAGAAAA 0.931041 -231 GGGTGAAATTTATTAAAAGGAAAAATCC 13 65 1 TTTAAAAAAA 0.959749 -18 TATATTATAGTTTAAAAATGAAAGGGATTACAT 14 29 0 TTAAAAAAAA 0.854621 -47 * ****** *** Masking position 6 Map Score: 1.75756 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 27 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 GTGTTGAGGGTATCCAGGGCAACTACCCTA 5 105 0 TATCCAGGGC 0.986578 -155 TAGCTAAGTATCTCCAGGGGGGATTGAC 5 242 1 TCTCCAGGGG 0.984627 -18 TCTTTTCCAATCTTCACCGCCTAGACCAAA 7 91 0 TCTTCACCGC 0.914952 -198 GCAACGGTTTTATTCACGGCAATAGCCGGA 7 232 1 TATTCACGGC 0.964406 -57 TCCTCTCCCTCCTCCAGGGCCTTAGAAGAG 7 269 0 CCTCCAGGGC 0.979036 -20 ATGTACAGGGTCTTCAGGGGACCCACTACC 12 61 1 TCTTCAGGGG 0.968765 -187 GTCGTCATTATATCCACGGCAACTAGTCTA 12 96 0 TATCCACGGC 0.982444 -152 ********** Masking position 6 Map Score: 7.99842 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 94 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 CCAGCTCTTACATCGGTTAGAAGGTCAAGT 1 169 0 CATCGGTTAG 0.881501 -132 TCAGAGAGAAGATAGCGTAGAAATCTTAAA 4 131 0 GATAGCGTAG 0.950912 -79 TACAACCTCTGATAGGGTAGTTGCCCTGGA 5 93 1 GATAGGGTAG 0.985551 -167 GCAACGACGACATCGGCTAGTTGATTTCCT 10 96 0 CATCGGCTAG 0.953031 -205 AAGCTGTACCGATAGGGTAGCCGTAGTGAA 10 150 1 GATAGGGTAG 0.985551 -151 CACTACCGTAGATAGACTAGTTGCCGTGGA 12 84 1 GATAGACTAG 0.899729 -164 ********** Masking position 3 Map Score: 2.99671 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 25 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 AAGGGTTTTTTAAAGCTTAGAATTGAAAAT 4 102 0 TAAAGCTTAG 0.883331 -108 CAATGAGGAATACAGCATAGAGAAACATCG 5 20 0 TACAGCATAG 0.965034 -240 TTAGAAGAGCTACAGCTCCGGCTATTGCCG 7 248 0 TACAGCTCCG 0.97876 -41 ACCCTATCGGTACAGCTTAGGCATGGATCT 10 138 0 TACAGCTTAG 0.975328 -163 CGAAGATGAAGACAGCACCGCTCAGGGCCG 11 194 0 GACAGCACCG 0.935438 -72 ********** Masking position 4 Map Score: 0.277295 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 21 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 10 TTAAAAATGTCTAAAAATATTGGTAAGCACT 1 35 1 CTAAAATATT 0.660055 -266 AATGTTAAAAATAAAAATATTATTCGCAAGT 2 43 0 ATAAAATATT 0.863206 -24 TAGTGAATATTTAAAAGCATTTTGGGGCACA 4 21 1 TTAAAACATT 0.731927 -189 AGAATTGAAAATAAAAGTGTTCAACCTTTGG 4 83 0 ATAAAATGTT 0.925361 -127 CGTAGAAATCTTAAAAGGGTTTTTTAAAGCT 4 115 0 TTAAAAGGTT 0.666789 -95 ATTGCCGTGAATAAAACCGTTGCTTCTCCAA 7 224 0 ATAAAACGTT 0.910923 -65 TGTGTTGAAGATATAATTGTTCTCCTAATGA 11 22 1 ATATAATGTT 0.894384 -244 AGTATTGCGGATATAATCATTAGGAGAACAA 11 38 0 ATATAACATT 0.78047 -228 GGACTTATTCTTATAAATGTTTACCTTTGTC 13 26 0 TTATAATGTT 0.816248 -57 AAACTATAATATATAAATCTTGTCAGGTGAT 14 49 1 ATATAATCTT 0.660055 -27 ****** **** Masking position 6 Map Score: 0.340717 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 85 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 11 CTAAAAATATTGGTAAGCACTTCTTAATGGTGAA 1 45 1 TGTGCATTCT 0.886945 -256 TTGAACACTTTTATTTTCAATTCTAAGCTTTAAA 4 90 1 TTTTCATTCT 0.740074 -120 CCCAGGATTAGTCTGAGCAATACTATCAATCCGG 5 56 0 GTTGCATACT 0.983126 -204 CATAGCGATAGTTTATGCACTTCTCAGTTACATA 5 195 1 GTTGCATTCT 0.989398 -65 AAAGAGCTTTGGCATTTCTCTCATTGATG 7 6 1 GCTGCATTCT 0.966397 -283 TGAATTGAAAGTTTTAGCAGATCTTTTTCGGTTA 10 200 0 GTTGCAATCT 0.943646 -101 CCTAATGATTATATCCGCAATACTTTCCGTTGAA 11 45 1 ATTGCATACT 0.90011 -221 CGTTGCATTGGTATATGCAGTACTATCCTTCGCC 12 186 1 GTTGCATACT 0.983101 -62 ** * *** **** Masking position 9 Map Score: 3.65101 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 43 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 ********** No masking Map Score: -7.238e-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 13 ********** No masking Map Score: -7.238e-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 14 ********** No masking Map Score: -7.238e-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