AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_heat_shock_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 spoVK 300 alternate gene name: spoVJ; disruption leads to the production of immature spores (stage V sporulation) #2 ynbA 220 similar to GTP-binding protein protease modulator #3 ynbB 187 similar to hypothetical proteins #4 glnR 110 transcriptional regulator #5 dnaJ 199 heat-shock protein #6 dnaK 23 class I heat-shock protein (chaperonin) #7 grpE 71 heat-shock protein #8 hrcA 119 transcriptional regulator #9 hemN 52 coproporphyrinogen III oxidase #10 lepA 133 GTP-binding protein #11 spoIIP 62 spoIIP #12 gpr 203 spore protease Motif number 1 AGCCCGTTGTATGAAAAAGAAATAATGAGAAA 1 64 1 AGAAAAGAAA 0.969387 -237 TTTTTTCGGGAACAATAAGGAATCCTGCGCTT 1 198 0 ACAAAAGGAA 0.752403 -103 ACTGCCCAATATGCAAAAGAAAGGAACATCCA 2 111 1 AGCAAAGAAA 0.963032 -110 ATCCATTTGAACGAACAAGAAACGATTCAGGA 2 138 1 AGAAAAGAAA 0.969387 -83 ACAAGAAACGATTCAGGAGAAAGCCATTTTAG 2 152 1 ATCAGAGAAA 0.825088 -69 TATTTTAATGAAGAAAATGAACAGTATGACAT 3 91 1 AGAAATGAAC 0.867383 -97 TTAACATCAAATCCAGGAGAAATTTTTAAAAA 4 13 0 ACCAGAGAAA 0.906913 -98 CGGGGCTGACACTAAAAAGAAC 5 1 0 ATAAAAGAAC 0.849159 -199 TCCGGAGCTGACCGAAAAGAACACATTTCATA 5 35 1 ACGAAAGAAC 0.922166 -165 AATCTGATTCAATGATTAGAAAGTCAAAGTCA 5 66 1 ATGATAGAAA 0.695489 -134 CCCGGGATAAAAGGAATTGAAAAATCATAATT 5 128 1 AGGATTGAAA 0.726295 -72 CTCAAAGTGTAAGGAGAAGGACAGGTGCTGCC 7 37 0 AGGAAAGGAC 0.870546 -35 TTACACTTTGAGGGAGGTGAACACA 7 57 1 AGGAGTGAAC 0.858396 -15 AAAAGTATCAAACCACAAGAAAAATGTCAATT 8 48 0 ACCAAAGAAA 0.914614 -72 GTACGTGAAAGAGAAAAGCAACCCAG 10 5 1 GGAAGAGAAA 0.774194 -129 AATGTAAAACAAGAAAGAGAAAAGTTCCCTAT 10 42 0 AGAAGAGAAA 0.966445 -92 AACAAGCTAGAGGAAGTAGAACTGT 11 4 0 AGAATAGAAC 0.909528 -59 * *** ****** Masking position 5 Map Score: 15.4736 Number of sites scoring better than the average of aligned sites = 1123 Number in coding regions = 953 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 2 AGAAATAATGAGAAAGAAGCTCACTATAAT 1 81 1 AGAAAGAAGC 0.968832 -220 TGCGCTTTCCCGAGAAATACTTTATTTCTT 1 175 0 CGAGAAATAC 0.510654 -126 TTATTGTTCCCGAAAAAAGCAATTGTTTCG 1 212 1 CGAAAAAAGC 0.953846 -89 AATATGCAAAAGAAAGGAACATCCATTTGA 2 118 1 AGAAAGGAAC 0.773056 -103 ATTTGATTCTGGAAAGGAGCTTCCCTTCAC 3 38 0 GGAAAGGAGC 0.814469 -150 TTCTTCATTAAAATAGAAGCGGTCTACCAT 3 76 0 AAATAGAAGC 0.640176 -112 CGGCTATGTCCAAGAAGAGCAAAGTATCAT 3 126 1 CAAGAAGAGC 0.864913 -62 CGGAGCTGACCGAAAAGAACACATTTCATA 5 37 1 CGAAAAGAAC 0.693696 -163 AAGTCAAAGCCAAGAGATGCCTGACTTTGA 5 89 0 CAAGAGATGC 0.77067 -111 GAAATTCGGGAGAGTGAAGCGAG 5 187 1 AGAGTGAAGC 0.820358 -13 ATAACTCACCCAAAAAAAGCGCCAAAAACT 8 18 0 CAAAAAAAGC 0.86843 -102 CCTTCTTTACAGAAAGAAGCCGCAGTACAA 9 25 0 AGAAAGAAGC 0.968832 -28 GTACGTGAAAGAGAAAAGCAACCCAGATA 10 10 1 AGAGAAAAGC 0.964651 -124 AAAACAAGAAAGAGAAAAGTTCCCTATCAT 10 39 0 AGAGAAAAGT 0.60693 -95 ATCATGCTAAAAAGAGAACCTTCAATGAAA 12 132 0 AAAGAGAACC 0.628847 -72 ********** Masking position 3 Map Score: 10.9195 Number of sites scoring better than the average of aligned sites = 2207 Number in coding regions = 1953 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 3 CAGCCCGTTGTATGAAAAAGAAATAATGAGAAAGA 1 63 1 TTGAAAGAAA 0.811202 -238 TATAATACTCTGACAAAATGATTAAAAACAAAATC 1 105 1 TACAAAGATA 0.866063 -196 CTCTCTGTTCTCTCTATATGATATTCAAGCGGATG 1 270 0 TTCTAAGATT 0.700882 -31 AATCGATTGCTTTGAAAAGGCGGAAATACGAGCAA 2 39 0 TTGAAAGCGA 0.942742 -182 AGAATTTTCAAAATGCTCATCCGTGATATG 2 201 0 TTCAAAGCTT 0.936928 -20 CCGATTTGATTCTGGAAAGGAGCTTCCCTTCACTT 3 36 0 TTGGAAGAGT 0.710951 -152 TTATATTATGTGTCAATACGATGTAAGGATTCTTA 4 42 0 TTCAAAGATA 0.969381 -69 GAAACTAAGTTAAGAAAAGGAGGAAATTGAG 4 90 1 TAGAAAGAGA 0.820777 -21 AAAAATCATAATTCAAAATGATACAATCTAATTTA 5 147 1 ATCAAAGATA 0.77112 -53 CTGTTAGCACTCTCAATAAGCGAGTGCTAATTCTA 8 84 0 TTCAAAGCGT 0.924359 -36 GCTTAGATTATATCAATAGGATTGTAAAGATTCAA 10 72 0 TTCAAAGATT 0.952897 -62 GTAATTACTCTATGAACAAGCTAGAGGAAGTAGAA 11 15 0 TTGAAAGCTA 0.952413 -48 TTTGTTCTATTGTGAAGAAGATTTAACCTTAAGAC 12 47 0 TTGAAAGATA 0.964609 -157 * **** * *** * Masking position 8 Map Score: 8.22938 Number of sites scoring better than the average of aligned sites = 545 Number in coding regions = 469 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 4 TCCGTGATATGCGGCAGCTGACATCCGACTA 2 181 0 GCGCAGCTGA 0.964475 -40 CGTCTTTTGAAGCACATGTGCCGGCAAGT 3 9 1 GAGCACATGT 0.918458 -179 TTATCGAAGGGCAGCACCTGTCCTTCTCCTT 7 28 1 GCGCACCTGT 0.990757 -44 AAGCCGCCGCAGTCTTGTACTGC 9 3 1 GCGCCGCAGT 0.988378 -50 TTTACAGAAAGAAGCCGCAGTACAAGACTGC 9 19 0 GAGCCGCAGT 0.983385 -34 TAATGTGAAGGAGGCCCCTGT 12 193 1 GAGCCCCTGT 0.99134 -11 ** ******** Masking position 5 Map Score: 4.69138 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 269 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 CTTAACTTAGTTTCATTATAGGTGATGTTATA 4 72 0 TTTCATAAGG 0.961229 -39 TTACATAGCAGGAGGTTATTCA 6 1 1 TTACATGAGG 0.975331 -23 TTTTGGCAAATTTTATCGAAGGGCAGCACCTG 7 16 1 TTTTATGAGG 0.968464 -56 GTATTTTGCGTTTAATAGTAGGAGTGATAGAT 10 111 1 TTTAATGAGG 0.968463 -23 CTACAGGTTGTATCTTAGGAGGTGAAACAC 12 9 0 TATCTTGAGG 0.907006 -195 GTAAAGTATTTTTCATTGAAGGTTCTCTTTTT 12 122 1 TTTCATGAGG 0.993799 -82 ****** * *** Masking position 6 Map Score: 2.72296 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 95 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 CTTCACCTCTCTGTTCTCTC 1 291 0 CTTCACCTCT 0.98272 -10 CATAATATAACATCACCTATAATGAAACTA 4 67 1 CATCACCTAT 0.871076 -44 TTGAATAACCTCCTGCTATGTAA 6 11 0 AATAACCTCC 0.838524 -13 TGTGTTCACCTCCCTCAAAGTGT 7 59 0 GTTCACCTCC 0.977686 -13 CATCATCACCTCTGTTAGCACTC 8 107 0 CATCACCTCT 0.977616 -13 CGGATTCACCTTCTTTACAGAAA 9 40 0 ATTCACCTTC 0.88968 -13 GTGTTTCACCTCCTAAGATACAA 12 4 1 TTTCACCTCC 0.96728 -200 ********** Masking position 5 Map Score: 4.43952 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 137 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 7 AGGATTCTTAACATCAAATCCAGGAGAAAT 4 22 0 ACATCAAATC 0.80035 -89 GACTTTCTAATCATTGAATCAGATTATGAA 5 61 0 TCATTGAATC 0.848169 -139 CACATAAATTAGATTGTATCATTTTGAATT 5 156 0 AGATTGTATC 0.964467 -44 TTCTTGTTTTACATTGAATCTTTACAATCC 10 59 1 ACATTGAATC 0.964168 -75 ACACTAGCTTAGATTATATCAATAGGATTG 10 83 0 AGATTATATC 0.929288 -51 ACTGTGCTACAGGTTGTATCTTAGGAGGTG 12 17 0 AGGTTGTATC 0.948091 -187 CAGTGTCTTAAGGTTAAATCTTCTTCACAA 12 43 1 AGGTTAAATC 0.920096 -161 ********** Masking position 8 Map Score: 2.2852 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 74 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 TAGTGAGCTTCTTTCTCATTATTTCTTTTT 1 77 0 CTTTCTCATT 0.861724 -224 AAGGAGCTTCCCTTCACTTGCCGGCACATG 3 25 0 CCTTCACTTG 0.934585 -163 AGATGCCTGACTTTGACTTTCTAATCATTG 5 75 0 CTTTGACTTT 0.96099 -125 CATCTCTTGGCTTTGACTTTTTTTCTTGCC 5 100 1 CTTTGACTTT 0.96099 -100 TGTCCTTCTCCTTACACTTTGAGGGAGGTG 7 46 1 CTTACACTTT 0.920808 -26 ACAGGGGCCTCCTTCACATTAAGTACCTAT 12 184 0 CCTTCACATT 0.954425 -20 ********** Masking position 3 Map Score: 1.69869 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 137 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 9 GACATGGGGTGGACAAACCATGAGATTTTGTTT 1 130 0 GGCAACCTGA 0.827314 -171 GTATTTCTCGGGAAAGCGCAGGATTCCTTATTG 1 185 1 GGAACGCGGA 0.992424 -116 TGTCACAATCGGCATCCGCTTGAATATCATATA 1 258 1 GGATCGCTGA 0.949356 -43 CGACTAAAATGGCTTTCTCCTGAATCGTTTCTT 2 154 0 GGTTCTCTGA 0.73395 -67 TGCTCTTCTTGGACATAGCCGGATATGTCATAC 3 114 0 GGCAAGCGGA 0.977352 -74 TGTTCTTTTCGGTCAGCTCCGGAAGCGGGGCTG 5 25 0 GGCACTCGGA 0.987112 -175 TAATTTATGTGAGAAATTCGGGAGAGTGAAGCG 5 175 1 GAAATTCGGA 0.691768 -25 GTAATTACTAGACAAGCGCTGGAGGGATTCA 11 42 1 GAAACGCGGA 0.967703 -21 ** ** *** *** Masking position 13 Map Score: 0.417003 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 311 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 10 ********** No masking Map Score: 1.10377e-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 AGATACCTGAAGTGTTTTTCTT 1 3 0 AGTGTTTTTC 0.898679 -298 TAAGAAATAAAGTATTTCTCGGGAAAGCGC 1 174 1 AGTATTTCTC 0.800645 -127 TCGAAACAATTGCTTTTTTCGGGAACAATA 1 213 0 TGCTTTTTTC 0.821436 -88 TTGAGAGGTCTGTTTTTTGCTCGTATTTCC 2 23 1 TGTTTTTTGC 0.941996 -198 TTATGAAATGTGTTCTTTTCGGTCAGCTCC 5 38 0 TGTTCTTTTC 0.821436 -162 CTTGGCTTTGACTTTTTTTCTTGCCCGGGA 5 105 1 ACTTTTTTTC 0.778984 -95 GCAATGAAGTTTTTGGCGCTTTTTTTG 8 8 1 AGTTTTTGGC 0.841631 -112 TCTAAGCTAGTGTATTTTGCGTTTAATAGT 10 100 1 TGTATTTTGC 0.9101 -34 ATAAATGTAAAGTATTTTTCATTGAAGGTT 12 116 1 AGTATTTTTC 0.937969 -88 ********** Masking position 6 Map Score: 2.83131 Number of sites scoring better than the average of aligned sites = 676 Number in coding regions = 543 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 12 ********** No masking Map Score: 1.10377e-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: 1.10377e-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: 1.10377e-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