AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_bsub_reg_100.orf -o00860_bsub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yacL 115 similar to hypothetical proteins #2 gltX 90 glutamyl-tRNA synthetase #3 nasF 60 uroporphyrin-III C-methyltransferase #4 nasE 31 assimilatory nitrite reductase (subunit) #5 nasD 121 assimilatory nitrite reductase (subunit) #6 gsaB 263 glutamate-1-semialdehyde aminotransferase #7 hemE 121 uroporphyrinogen III decarboxylase #8 hemH 71 ferrochelatase #9 proB 300 gamma-glutamyl kinase #10 cysH 300 phosphoadenosine phosphosulfate #11 ylnB 48 similar to sulfate adenylyltransferase #12 ylnD 98 similar to uroporphyrin-III C-methyltransferase #13 hemL 29 glutamate-1-semialdehyde 2,1-aminotransferase #14 hemC 32 porphobilinogen deaminase (hydroxymethylbilane synthase) #15 hemA 163 glutamyl-tRNA reductase Motif number 1 ACTATCATTGAGGAGGAATGGAC 4 19 1 AGGAGGAATG 0.93869 -13 GCCGTATGAAAGGTGGAAATCAG 7 109 1 AGGTGGAAAT 0.936926 -13 TTGGAGTCCTAGGGGGAAAACCTAGGCGCA 9 147 1 AGGGGGAAAA 0.946311 -154 CTGATTCATAAGGACGAAATGGGTTTCCGT 9 235 0 AGGACGAAAT 0.914772 -66 CTTATGAATCAGGATGAAATGGGTTTTTTT 9 253 1 AGGATGAAAT 0.878668 -48 AGAAGAGCCGCGGAGGAGAATAA 9 288 1 CGGAGGAGAA 0.921181 -13 ACTTTCAATCCGGCGGAAAGAAAGACAGGA 10 161 0 CGGCGGAAAG 0.98372 -140 AAAAGACAACCGGCAGAAAGCTACTGTTTG 10 254 1 CGGCAGAAAG 0.840744 -47 TGTCTCCGAAAGGAGGAAAGAAGAA 10 286 1 AGGAGGAAAG 0.992492 -15 TAAGTTAACTAGGAGGAGATGGATATT 11 32 1 AGGAGGAGAT 0.966361 -17 TCGAATAGATCGGGGGAAATACG 12 86 1 CGGGGGAAAT 0.974287 -13 AAGCAGATTCGGGAGGAAAGAA 14 21 1 GGGAGGAAAG 0.972306 -12 ********** Masking position 7 Map Score: 15.0532 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 352 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 2 TTCTACCACCAAATAGACCCGGCATCAAAACA 2 13 0 AAAAGACCGG 0.983423 -78 GACCACTAGAAAAGTGATCCGGTCTTTTGA 3 9 0 AAATGACCGG 0.972205 -52 CAGATGATCCGCTCCTTATCAA 5 110 0 CAGTGACCGC 0.979325 -12 CGCTTAATAAAAAAACATCCGGAGGTAACGTA 6 11 0 AAAACACCGG 0.933938 -253 TGCAACAGGAGAACCGCCGCCGACTGC 6 247 0 CAGAGACCGC 0.987705 -17 GACAGAGAGCAAAATGAACCGCTGAAACATTT 9 88 1 AAATGACCGC 0.97659 -213 TTTTTTATTGTAGAAGAGCCGCGGAGGAGAAT 9 277 1 TAGAGACCGC 0.952876 -24 TTTCCCATGTAATGTGATTCGCGGCTGCTGAT 10 225 0 AATTGATCGC 0.718259 -76 TTACATGGGAAAAGACAACCGGCAGAAAGCTA 10 245 1 AAAACACCGG 0.933938 -56 CGAGTTCTTCCAGAAGATTCGCTGTGATGATG 12 57 0 CAGAGATCGC 0.952153 -42 ACGATGTCCCAAGCAGATTCGGGAGGAAAGAA 14 11 1 AAGAGATCGG 0.959074 -22 *** *** **** Masking position 7 Map Score: 14.8322 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 383 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 TTTCGGTTAAAACCTTATGAATACGGGTAT 1 9 1 AAAACTATGA 0.892271 -107 GGCCTCAGGCAAAAATGTATGAATCTATTCTA 2 40 0 AAAAATATGA 0.955714 -51 TGACAAAAACTATCATTGAGGAGGA 4 4 1 CAAAATATCA 0.909306 -28 AAAAGTTCTAAAAATTTTATGAAAAAT 5 6 0 AAAATTATGA 0.842633 -116 TAAAATGTAACAAAATATACGAAAAGTTCTAA 5 27 0 CAAAATACGA 0.776208 -95 CTACGCTGGAAAAAACATTTGATAAGGAGCGG 5 92 1 AAAAATTTGA 0.949045 -30 TCTTGCATACAAAATCAATTGAACTTCACAAT 6 161 1 AAAATATTGA 0.485604 -103 ATTAAGATACCAAAAGATATGC 8 1 0 CAAAATATGC 0.776208 -71 TGATCTGATACAAACATTTTGACAGGATATCA 8 32 0 CAAACTTTGA 0.879305 -40 CATAATATAAAAAAATCATTGAGCGTTGAAGA 9 32 1 AAAAAATTGA 0.79187 -269 TTTCATGCGGCAAAATGTTTCAGCGGTTCATT 9 100 0 CAAAATTTCA 0.896415 -201 CTACAAATCTAAAAACTTATCAAGAGCGGCTG 10 31 1 AAAAATATCA 0.907742 -270 CTCTTAAAATAAAAAACTTTCAATCCGGCGGA 10 174 0 AAAAATTTCA 0.894654 -127 ***** ***** Masking position 4 Map Score: 8.22063 Number of sites scoring better than the average of aligned sites = 484 Number in coding regions = 395 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 4 GTTAAAACCTTATGAATACGGGTATATTAAT 1 16 1 TTGAATACGG 0.909055 -100 CTTGTTTTGATGCCGGGTCTATTTGG 2 6 1 TTGATGCCGG 0.988827 -85 CTCAGCTGAATCTGAAGCCCGAAGCCATTGT 6 72 1 TTGAAGCCCG 0.988661 -192 ATTTCGTCCTTATGAATCAGGATGAAATGGG 9 245 1 TTGAATCAGG 0.92049 -56 GGACTGGACCTATGAAGCCCGGCAACCTGCA 10 65 1 TTGAAGCCCG 0.98867 -236 AATAAAAAACTTTCAATCCGGCGGAAAGAAA 10 168 0 TTCAATCCGG 0.936768 -133 TCCCATGTAATGTGATTCGCGGCTGCTGATA 10 224 0 TTGATTCGCG 0.868075 -77 TGCGTTCTTCTCAGATGCCGGAATGCAAGCG 12 22 1 TAGATGCCGG 0.940685 -77 * ********* Masking position 5 Map Score: 6.23636 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 367 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 TAAAATGTTAAAAAAGGAGGTGGGGGT 1 99 1 AAAAAGGAGG 0.93708 -17 GGCCTCAGGCAAAAATGTATGAATCTATTC 2 42 0 AAAAATGTAT 0.589659 -49 ATACATGACATGAAAGGAAGTATTTGAAA 2 72 1 TGAAAGGAAG 0.915627 -19 CGTCACTGTAAAAAATGAAGGACCACTAGA 3 31 0 AAAAATGAAG 0.869003 -30 GTAGCACAGCAAAAAGGAATATTTAAGATA 5 66 0 AAAAAGGAAT 0.869003 -56 ATGCTACAATAGAAAGGACGCATGGAGATA 6 117 1 AGAAAGGACG 0.951092 -147 CAAATGGTATAGAAATGTAGCTCAAAGTTC 7 30 0 AGAAATGTAG 0.881495 -92 GGTTGCCGTATGAAAGGTGGAAATCAG 7 105 1 TGAAAGGTGG 0.840706 -17 TCTCTGTCACAGAAAGGTCTGCTTACTAAT 9 66 0 AGAAAGGTCT 0.808139 -235 CTACTTCCAGCAAAATGAATTCCATTTTGA 10 110 1 CAAAATGAAT 0.543657 -191 TGTTTGTCTCCGAAAGGAGGAAAGAAGAA 10 282 1 CGAAAGGAGG 0.932642 -19 ********** Masking position 5 Map Score: 5.19467 Number of sites scoring better than the average of aligned sites = 1099 Number in coding regions = 710 Number in noncoding regions = 389 Number of orfs with sites within 600 bp upstream = 451 Fraction of orfs with sites within 600 bp upstream = 0.0724382 Motif number 6 CGGGCTGTTTACACCGCCGACAATGTGCTG 6 202 0 ACACCGCCGA 0.949873 -62 AACAGGAGAACCGCCGCCGACTGCTTTATA 6 241 0 CCGCCGCCGA 0.994649 -23 TTATTCTCCTCCGCGGCTCTTCTACAA 9 284 0 CCTCCGCGGC 0.977865 -17 AGGTCCAGTCCCTCAGCCGCTCTTGATAAG 10 46 0 CCTCAGCCGC 0.989992 -255 ATCTGTATATCAGCAGCCGCGAATCACATT 10 217 1 CAGCAGCCGC 0.971828 -84 TCTGAGAAGAACGCAGCAGATCATAT 12 7 0 ACGCAGCAGA 0.90178 -92 ********** Masking position 6 Map Score: 3.43589 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 541 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 TTTTTTAACATTTTAATTTCACAAAGTCTTATG 1 81 0 TTTTATTACA 0.810033 -35 CAAATGTTTTTTCCAGCGTAGCACAGCAAAAAG 5 80 0 TTCCACTGCA 0.927644 -42 CATGCGTCCTTTCTATTGTAGCATGCTTCCGAA 6 108 0 TTCTATTGCA 0.963374 -156 TATAGGAGGTTTTTATTCTTGCATACAAAATCA 6 145 1 TTTTATTGCA 0.960921 -119 TCGGCGGCGGTTCTCCTGTTGCA 6 251 1 TTCTCTTGCA 0.931054 -13 GACAAGTGTCTTTTTTCTTTGCATAATATAAAA 9 11 1 TTTTTCTGCA 0.734703 -290 AAATGGGTTTTTTTATTGTAGAAGAGCCGCGGA 9 269 1 TTTTATTGAA 0.791166 -32 GCAAAATGAATTCCATTTTGAAAGATAAGGGCT 10 119 1 TTCCATTAAA 0.496834 -182 CTGAAGCTTTTTCTAATATAGCATAAGAATTTT 15 29 1 TTCTATTGCA 0.963374 -135 TTTATAATCATTCTAACATAGAACTCATTATTT 15 108 0 TTCTACTGAA 0.660016 -56 ***** * * *** Masking position 9 Map Score: 5.36707 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 205 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 8 CTTGTTTTGATGCCGGGTCTATTTGGT 2 8 1 TGATGCCGGG 0.767633 -83 TGTCATGTATGGCCTCAGGCAAAAATGTAT 2 52 0 GGCCTCAGGC 0.965765 -39 CAAGAACAATGGCTTCGGGCTTCAGATTCA 6 78 0 GGCTTCGGGC 0.946653 -186 GTTCTTGTTCGGAAGCATGCTACAATAGAA 6 101 1 GGAAGCATGC 0.819436 -163 ACAATAGAAAGGACGCATGGAGATATAGGA 6 122 1 GGACGCATGG 0.894585 -142 AGGTTCGGCAGGTTTCATGCGGCAAAATGT 9 114 0 GGTTTCATGC 0.896369 -187 AAACTATGCAGGTTGCCGGGCTTCATAGGT 10 72 0 GGTTGCCGGG 0.94753 -229 GAAAGATAAGGGCTGCATGCTGTTCCTGTC 10 138 1 GGCTGCATGC 0.866271 -163 GTTCTCGCTTGCATTCCGGCATCTGAGAAG 12 28 0 GCATTCCGGC 0.798357 -71 TATTAGAAAAAGCTTCAGGGAAAAGAAGCA 15 17 0 AGCTTCAGGG 0.799341 -147 ********** Masking position 6 Map Score: 2.57573 Number of sites scoring better than the average of aligned sites = 1378 Number in coding regions = 1269 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 9 CGAATATCAGAATAAACAAAAACCAACATT 1 44 0 AATAAACAAA 0.900568 -72 GGATACGCTTAATAAAAAAACATCCGGAGG 6 18 0 AATAAAAAAA 0.961195 -246 TTCTTTGCATAATATAAAAAAATCATTGAG 9 25 1 AATATAAAAA 0.929951 -276 GCTCTTCTACAATAAAAAAACCCATTTCAT 9 266 0 AATAAAAAAA 0.961195 -35 ATTTACTACAAATCTAAAAACTTATCAAGA 10 26 1 AATCTAAAAA 0.829184 -275 TACCTCTTAAAATAAAAAACTTTCAATCCG 10 179 0 AATAAAAAAC 0.900568 -122 ********** Masking position 6 Map Score: 2.7714 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 175 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 10 ********** No masking Map Score: 5.31729e-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 11 ********** No masking Map Score: 5.31729e-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 12 ********** No masking Map Score: 5.31729e-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