AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_bsub_reg_300.orf -o00860_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/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 ctsR 300 transcriptional regulator #2 sms 91 DNA repair protein homolog #3 yacL 115 similar to hypothetical proteins #4 gltX 90 glutamyl-tRNA synthetase #5 nasF 60 uroporphyrin-III C-methyltransferase #6 nasE 31 assimilatory nitrite reductase (subunit) #7 nasD 121 assimilatory nitrite reductase (subunit) #8 nasB 179 assimilatory nitrate reductase (electron transfer subunit) #9 gsaB 263 glutamate-1-semialdehyde aminotransferase #10 pbpF 121 penicillin-binding protein 1A #11 hemE 121 uroporphyrinogen III decarboxylase #12 hemH 71 ferrochelatase #13 proB 300 gamma-glutamyl kinase #14 cysH 300 phosphoadenosine phosphosulfate #15 ylnB 48 similar to sulfate adenylyltransferase #16 ylnD 98 similar to uroporphyrin-III C-methyltransferase #17 hemL 29 glutamate-1-semialdehyde 2,1-aminotransferase #18 hemC 32 porphobilinogen deaminase (hydroxymethylbilane synthase) #19 hemA 163 glutamyl-tRNA reductase Motif number 1 GGCGTCCTACTCTCACAGGGGGAAACCCCCGACTA 1 29 0 TTAGGGGAAA 0.987793 -272 TATAGAAGACGGAAATGAGGCATAC 2 1 1 TTAGAGGAAA 0.821446 -91 ACAAAAACTATCATTGAGGAGGAATGGAC 6 13 1 TAAGGGGAAT 0.933824 -19 TGACATAATTTTTAATAGGAGAAAACTTACGAGCT 8 134 1 TTAGGGAAAA 0.853605 -46 TACAGCACATTGTCGGCGGTGTAAACAGCCCGTCT 9 200 1 TTCGGGTAAA 0.891637 -64 ATGGTTGCCGTATGAAAGGTGGAAATCAG 11 103 1 TTAGGGGAAA 0.98785 -19 ATCAGATCATTAAAGAGGGTGTAAACA 12 55 1 TAGGGGTAAA 0.891784 -17 CCTGCCTTGGAGTCCTAGGGGGAAAACCTAGGCGC 13 141 1 ATAGGGGAAA 0.956233 -160 TTCGTCCTTATGAATCAGGATGAAATGGGTTTTTT 13 247 1 TAAGGTGAAA 0.821446 -54 TAAAAAACTTTCAATCCGGCGGAAAGAAAGACAGG 14 162 0 TACGGGGAAA 0.97847 -139 TTTGTTTGTCTCCGAAAGGAGGAAAGAAGAA 14 280 1 TCAGGGGAAA 0.955744 -21 ATTTTATAAGTTAACTAGGAGGAGATGGATATT 15 26 1 TAAGGGGAGA 0.916861 -23 AAGAACTCGAATAGATCGGGGGAAATACG 16 80 1 AACGGGGAAA 0.924368 -19 TGTCCCAAGCAGATTCGGGAGGAAAGAA 18 15 1 AAGGGGGAAA 0.924369 -18 TAAGATTGGGTGTTGGGGGTGTAATTAGAGCG 19 142 1 TTGGGGTAAT 0.588514 -22 * * *** ***** Masking position 13 Map Score: 15.9628 Number of sites scoring better than the average of aligned sites = 589 Number in coding regions = 415 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 2 TTCTACCACCAAATAGACCCGGCATCAAAACA 4 13 0 AAAAGACCGG 0.98259 -78 GACCACTAGAAAAGTGATCCGGTCTTTTGA 5 9 0 AAATGACCGG 0.970825 -52 CAGATGATCCGCTCCTTATCAA 7 110 0 CAGTGACCGC 0.97829 -12 CGCTTAATAAAAAAACATCCGGAGGTAACGTA 9 11 0 AAAACACCGG 0.930793 -253 TGCAACAGGAGAACCGCCGCCGACTGC 9 247 0 CAGAGACCGC 0.987084 -17 GACAGAGAGCAAAATGAACCGCTGAAACATTT 13 88 1 AAATGACCGC 0.975423 -213 TTTTTTATTGTAGAAGAGCCGCGGAGGAGAAT 13 277 1 TAGAGACCGC 0.950585 -24 TTTCCCATGTAATGTGATTCGCGGCTGCTGAT 14 225 0 AATTGATCGC 0.708058 -76 TTACATGGGAAAAGACAACCGGCAGAAAGCTA 14 245 1 AAAACACCGG 0.930793 -56 CGAGTTCTTCCAGAAGATTCGCTGTGATGATG 16 57 0 CAGAGATCGC 0.949829 -42 ACGATGTCCCAAGCAGATTCGGGAGGAAAGAA 18 11 1 AAGAGATCGG 0.957071 -22 *** *** **** Masking position 7 Map Score: 11.2262 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 ACAGGGGGAAACCCCCGACTACCATCGGCG 1 20 0 ACCCCCGACT 0.987257 -281 GTGAGAGTAGGACGCCGCCAAGCAAGCTTA 1 48 1 GACGCCGCCA 0.864563 -253 TCAACCCCCTCCTTTACTGACTT 1 288 0 ACCCCCTCCT 0.976484 -13 ACCCCCACCTCCTTTTTTAA 3 106 0 ACCCCCACCT 0.976484 -10 GGCTGTTTACACCGCCGACAATGTGCTGTA 9 200 0 ACCGCCGACA 0.973523 -64 CAGGAGAACCGCCGCCGACTGCTTTATATG 9 239 0 GCCGCCGACT 0.982998 -25 ATCAGCCACCTCCTGCTTGCTAGT 10 5 1 GCCACCTCCT 0.886354 -117 CTCTAATTACACCCCCAACACCCAATCTTA 19 142 0 ACCCCCAACA 0.942259 -22 ********** Masking position 5 Map Score: 7.50683 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 331 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 AGCTTAAACCCAGCTCAATGAGCTGGGTTT 1 72 1 CAGCTCAATG 0.843171 -229 TTTTGTGGACCGGGAAAATGGAAATAATGA 1 189 1 CGGGAAAATG 0.938836 -112 CAGCGTAGCACAGCAAAAAGGAATATTTAA 7 70 0 CAGCAAAAAG 0.973111 -52 TGAGGCATTACAGCACATTGTCGGCGGTGT 9 192 1 CAGCACATTG 0.808491 -72 CTGTGACAGAGAGCAAAATGAACCGCTGAA 13 84 1 GAGCAAAATG 0.872786 -217 AGGTTTCATGCGGCAAAATGTTTCAGCGGT 13 105 0 CGGCAAAATG 0.982878 -196 GTGCTACTTCCAGCAAAATGAATTCCATTT 14 107 1 CAGCAAAATG 0.981476 -194 ACTTTCAATCCGGCGGAAAGAAAGACAGGA 14 161 0 CGGCGGAAAG 0.915632 -140 AAAAGACAACCGGCAGAAAGCTACTGTTTG 14 254 1 CGGCAGAAAG 0.956902 -47 GAAAAAGCTTCAGGGAAAAGAAGCATTCCT 19 12 0 CAGGGAAAAG 0.825488 -152 ********** Masking position 7 Map Score: 8.02324 Number of sites scoring better than the average of aligned sites = 795 Number in coding regions = 740 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 ATTATATTATACAGTTAAGTGGAATTTTATGATACCAATAAACC 1 112 0 AATAATTAAA 0.960925 -189 TTGCTGATTTAAAATTCGGTATAAAGTTATTATATTATACAGTT 1 140 0 AATAATTAAA 0.960925 -161 GACTTTGACTATATTTGACTTTAATCTTACTATAAGCCGTTTCT 1 249 0 AATAATTAAA 0.96091 -52 ATGTAAGTGTATGCCTCACTTTCATATCAAGAAATAGAACAAGG 2 39 1 AGTCATCAAA 0.891946 -53 ACAAAGTCTTATGCATCCTACGAATATCAGAATAAACAAAAACC 3 50 0 AGTAATCAAA 0.898236 -66 AAAATATACGAAAAGTTCTAAAAATTTTATGAAAAAT 7 4 0 AATAATTAAA 0.960925 -118 GCAAAAAGGAATATTTAAGATACATGTTATAAAATGTAACAAAA 7 44 0 AATCATTAAA 0.95833 -78 GCTCCTTATCAAATGTTTTTTCCAGCGTAGCACAGCAAAAAGGA 7 78 0 AATCAGTAAA 0.812419 -44 AATGGTATAGAAATGTAGCTCAAAGTTCAAAAAATCGCCGAATT 11 14 0 AATAATCAAA 0.95833 -108 TATCCTGTCAAAATGTTTGTATCAGATCATTAAAGAGGGTGTAA 12 35 1 AATCATCAAA 0.955571 -37 TAGAATTGTGCTAAAATTTACTACAAATCTAAAAA 14 2 1 AATAATTAAA 0.960925 -299 * * * ** *** * * Masking position 14 Map Score: 7.87542 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 103 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 CCAATAAACCAAAATACAAAAAACCCAGCTCA 1 90 0 AAATAAAAAA 0.960928 -211 ACTTAACTGTATAATATAATAACTTTATACCG 1 136 1 AAATAAATAA 0.814927 -165 TACGAATATCAGAATAAACAAAAACCAACATT 3 44 0 AAATAACAAA 0.923205 -72 AAAATGTAACAAAATATACGAAAAGTTCTAAA 7 26 0 AAATAACGAA 0.761508 -96 TTGGATACGCTTAATAAAAAAACATCCGGAGG 9 18 0 TAATAAAAAA 0.794953 -246 TTTTCTTTGCATAATATAAAAAAATCATTGAG 13 23 1 AAATAAAAAA 0.960923 -278 CGGCTCTTCTACAATAAAAAAACCCATTTCAT 13 266 0 AAATAAAAAA 0.960928 -35 TTTACCTCTTAAAATAAAAAACTTTCAATCCG 14 179 0 AAATAAAAAC 0.851769 -122 TTCTTATGCTATATTAGAAAAAGCTTCAGGGA 19 26 0 AATTAAAAAA 0.794953 -138 * **** ***** Masking position 6 Map Score: 4.60897 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 131 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 7 AACATTTTAATTTCACAAAGTCTTATGCAT 3 78 0 TTTCACAAAG 0.96033 -38 ATTTTTCATAAAATTTTTAGAAC 7 4 1 TTTCATAAAA 0.628343 -118 TGTTATAAAATGTAACAAAATATACGAAAA 7 34 0 TGTAACAAAA 0.679006 -88 GCATTAAACGTGTCACAAAAACTTACACAT 8 89 0 TGTCACAAAA 0.960335 -91 TTAAAAATTATGTCACAATGCATTGTTAAC 8 119 0 TGTCACAATG 0.963468 -61 ATCAATTGAACTTCACAATGAGGCATTACA 9 174 1 CTTCACAATG 0.775227 -90 AATGATATCCTGTCAAAATGTTTGTATCAG 12 30 1 TGTCAAAATG 0.838533 -42 TTTTGCTCTCTGTCACAGAAAGGTCTGCTT 13 72 0 TGTCACAGAA 0.834694 -229 AGCCCTTATCTTTCAAAATGGAATTCATTT 14 122 0 TTTCAAAATG 0.765066 -179 ACATAGTTTCTTTCACAAAATGTGAACAGA 19 66 0 TTTCACAAAA 0.938176 -98 ********** Masking position 5 Map Score: 4.3363 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 374 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 GCAATCAGGTTTTGTGGACCGGGAAAATGGAA 1 180 1 TTGTGACCGG 0.949197 -121 GTTAAAACCTTATGAATACGGGTATATTAATG 3 16 1 TTGATACGGG 0.877175 -100 CTTGTTTTGATGCCGGGTCTATTTGGT 4 6 1 TTGAGCCGGG 0.989776 -85 TCAAAAGACCGGATCACTTTTC 5 1 1 TAAAGACCGG 0.840288 -60 CTCAGCTGAATCTGAAGCCCGAAGCCATTGTT 9 72 1 TTGAGCCCGA 0.964513 -192 TCCGCTCTCCTGTAACGCCAGGTTATGCGCCT 13 170 0 TTAAGCCAGG 0.881339 -131 GGACTGGACCTATGAAGCCCGGCAACCTGCAT 14 65 1 TTGAGCCCGG 0.993691 -236 TCCCATGTAATGTGATTCGCGGCTGCTGATAT 14 223 0 TTGATCGCGG 0.779034 -78 TGCGTTCTTCTCAGATGCCGGAATGCAAGCGA 16 22 1 TAGAGCCGGA 0.883417 -77 TTTTATTCAGTTGACAGGAGTTGAGGCA 17 7 1 TAGTGACAGG 0.697636 -23 * *** ****** Masking position 1 Map Score: 4.38498 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 384 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 TTCTCGCTCTATCCTTCATTATTTCCATTT 1 204 0 ATCCTTCATT 0.970746 -97 TACATGCTGTATGCCTCATTTCCGTCTTCT 2 14 0 ATGCCTCATT 0.981355 -78 ATGTAAGTGTATGCCTCACTTTCATATCAA 2 39 1 ATGCCTCACT 0.933243 -53 TTTTCTAGTGGTCCTTCATTTTTTACAGTG 5 28 1 GTCCTTCATT 0.949471 -33 CCCCTTTCTAGACCCTCATTATTTTACATT 8 17 1 GACCCTCATT 0.842301 -163 ATGGTCCTATATCCTTGATTCAGAAAATGT 8 42 0 ATCCTTGATT 0.845965 -138 ATGTGCTGTAATGCCTCATTGTGAAGTTCA 9 180 0 ATGCCTCATT 0.981355 -84 TAGGAATGCTTCTTTTCCCTGAAGC 19 6 1 ATGCTTCTTT 0.856045 -158 ********** Masking position 6 Map Score: 4.82832 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 106 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 TTTCAAATACTTCCTTTCATGTCATGT 4 74 0 AATACCCTTT 0.958352 -17 AAGATTCCCCTTTCTAGACCCT 8 1 1 AAGATCCCTT 0.744265 -179 GTATCAGACCTCCTTTGGCGAAGCTC 8 164 0 CAGACCCTTT 0.982964 -16 CCTATATCTCCATGCGTCCTTTCTATTGTAGC 9 119 0 CATGCCCTTT 0.982965 -145 CAATTTTTCCCATACTACCTTTAGAAAGGCGA 10 91 1 CATACCCTTT 0.983298 -31 ACAGGAACAGCATGCAGCCCTTATCTTTCAAA 14 135 0 CATGCCCCTT 0.970279 -166 TGCTGATATACAGATAGCCTTTTTACCTCTTA 14 200 0 CAGATCCTTT 0.929572 -101 TAGGAATGCTTCTTTTCCCTGAAGCT 19 5 1 AATGCCTTTT 0.715793 -159 ***** ***** Masking position 2 Map Score: 2.63012 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 189 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 11 GTCAAAGTCAGTAAAGGAGGGGGTTGA 1 284 1 GTAAAGGAGG 0.928718 -17 TAAAATGTTAAAAAAGGAGGTGGGGGT 3 99 1 AAAAAGGAGG 0.897862 -17 ATACATGACATGAAAGGAAGTATTTGAAA 4 72 1 TGAAAGGAAG 0.828812 -19 ACGAGCTTCGCCAAAGGAGGTCTGATAC 8 162 1 CCAAAGGAGG 0.94024 -18 ATGCTACAATAGAAAGGACGCATGGAGATA 9 117 1 AGAAAGGACG 0.883621 -147 ACGCATGGAGATATAGGAGGTTTTTATTCT 9 134 1 ATATAGGAGG 0.802745 -130 CCTCGCCTTTCTAAAGGTAGTATGGGAAAA 10 95 0 CTAAAGGTAG 0.756934 -27 GGTTGCCGTATGAAAGGTGGAAATCAG 11 105 1 TGAAAGGTGG 0.917581 -17 AGCGCGTTCAATCAAGGTGGTACCACGGAA 13 211 1 ATCAAGGTGG 0.731986 -90 TGTTTGTCTCCGAAAGGAGGAAAGAAGAA 14 282 1 CGAAAGGAGG 0.982269 -19 ********** Masking position 5 Map Score: 4.24013 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 167 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 320 Fraction of orfs with sites within 600 bp upstream = 0.0513974 Motif number 12 ATCAAGAAATAGAACAAGGGAGAGGTCTTA 2 64 1 AGAACAAGGG 0.962131 -28 CAGAAAATGTAAAATAATGAGGGTCTAGAA 8 22 0 AAAATAATGA 0.700771 -158 TCTTTTCCAGAAAATAATGGTCCTATATCC 8 58 0 AAAATAATGG 0.938035 -122 CTTCCGAACAAGAACAATGGCTTCGGGCTT 9 86 0 AGAACAATGG 0.954626 -178 CTAGTATATCAAAACAATGGTATAAGTTTC 10 30 1 AAAACAATGG 0.969007 -92 CCATTTGCCTAAAACAAGGTATAGTGTAAT 11 53 1 AAAACAAGGT 0.853823 -69 TCCATTTTGAAAGATAAGGGCTGCATGCTG 14 130 1 AAGATAAGGG 0.849057 -171 ********** Masking position 6 Map Score: 2.07454 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 199 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 13 GGGGGAAACCCCCGACTACCATCGGCGCTG 1 17 0 CCCGACTACC 0.905554 -284 ACCAAATAGACCCGGCATCAAAACAAG 4 8 0 CCCGGCATCA 0.962688 -83 CCACCTTTCATACGGCAACCATACGTTCGT 11 95 0 TACGGCAACC 0.966312 -27 AAGGTGGTACCACGGAAACCCATTTCGTCC 13 224 1 CACGGAAACC 0.929241 -77 ACCTATGAAGCCCGGCAACCTGCATAGTTT 14 72 1 CCCGGCAACC 0.996035 -229 TCGCTTGCATTCCGGCATCTGAGAAGAACG 16 24 0 TCCGGCATCT 0.897102 -75 ********** Masking position 4 Map Score: 1.24299 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 262 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 14 CTACCATCGGCGCTGAAGAGC 1 2 0 CGCTGAAGAG 0.982641 -299 CAAAAACTATCATTGAGGAGGAATGGAC 6 14 1 CATTGAGGAG 0.962859 -18 TGTATCAGATCATTAAAGAGGGTGTAAACA 12 52 1 CATTAAAGAG 0.821477 -20 AATCATTGAGCGTTGAAGAGGATTAGTAAG 13 45 1 CGTTGAAGAG 0.981836 -256 GTAGAAGAGCCGCGGAGGAGAATAA 13 286 1 CGCGGAGGAG 0.96599 -15 ********** Masking position 6 Map Score: 0.63263 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 38 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 CCAGCTCATTGAGCTGGGTTTAAGCTTGCT 1 68 0 GAGCTGGGTT 0.987943 -233 CCAGCTCAATGAGCTGGGTTTTTTGTATTT 1 81 1 GAGCTGGGTT 0.987943 -220 GTTAAAAAAGGAGGTGGGGGT 3 105 1 GAGGTGGGGG 0.968823 -11 AGATTCAGCTGAGATGGTTGTAATCTGGAC 9 55 0 GAGATGGTTG 0.906113 -209 TAGCAAGCAGGAGGTGGCTGAT 10 3 0 GAGGTGGCTG 0.957432 -119 TTAGAAAGGCGAGGTGAGTTC 10 111 1 GAGGTGAGTT 0.930212 -11 TCATAAGGACGAAATGGGTTTCCGTGGTAC 13 230 0 GAAATGGGTT 0.945541 -71 GAATCAGGATGAAATGGGTTTTTTTATTGT 13 258 1 GAAATGGGTT 0.945541 -43 ********** Masking position 2 Map Score: 7.33107 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 47 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617