AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i203_dna_repair_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 recN 36 recN #2 ahrC 134 transcriptional regulator #3 yqiE 246 similar to hypothetical proteins #4 yqiC 85 similar to exodeoxyribonuclease VII (small subunit) #5 yqiB 137 similar to exodeoxyribonuclease VII (large subunit) #6 yqhZ 263 similar to transcription termination #7 accB 155 acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit) #8 spoIIIAC 22 spoIIIAC #9 spoIIIAA 75 spoIIIAA #10 yqhV 144 alternate gene name: yqgE #11 efp 24 elongation factor P #12 yqhS 86 similar to 3-dehydroquinate dehydratase #13 yqhR 226 yqhR #14 ytdI 185 similar to hypothetical proteins Motif number 1 GACGTTAAAAGAAAAAAAAGCAGATGTACCG 2 11 1 GAAAAAAAGC 0.966673 -124 ACATGAATGCAGAAAAAAGGAATAATAGCGC 2 52 0 AAAAAAAGGA 0.921371 -83 AGCAGTTTATATGAAAAATGAAAAGGAAAAG 3 128 1 AGAAAAATGA 0.880122 -119 AATCTCAGACATAAAAAAAGACAAACGCGCT 3 157 0 AAAAAAAAGA 0.962212 -90 CAGACGTGAAAAAAAATGAAACATGACAT 4 9 1 AAAAAAATGA 0.838729 -77 AGGGTAACGTGTAAAAAAACCAAAGGGCCGC 6 38 0 GAAAAAAACC 0.817405 -226 ATTTCAAAGCATGAAGAAAGCCGGCTTACAT 6 71 1 AGAAGAAAGC 0.903387 -193 CGGTAATAGGGTAAAAAAACCTTGATTTCAA 6 162 1 GAAAAAAACC 0.817405 -102 GAATGAGGGAAAAAAGCCCGCTAAACA 7 7 1 GGAAAAAAGC 0.97616 -149 TATGACAGCAACGCAAAAAGCCCGCTTGTTT 7 33 0 AGCAAAAAGC 0.903387 -123 GTAGTAACCTATAAAAAAAGAAATTTCATAC 7 119 1 AAAAAAAAGA 0.962212 -37 AAAGGAAAAAAGAAGTCTGTTCC 10 3 1 AGAAAAAAGA 0.972934 -142 GTTTTTGGGCACAAAAAAAGCCTGCTCCCAT 10 37 0 AAAAAAAAGC 0.981214 -108 AGCAATCCTAAAGAAATAGGCAGGTTGATAA 13 12 0 AGAAATAGGC 0.743806 -215 ATGAAATGTCAATAAAAAAGCTCACACTTTT 13 177 0 ATAAAAAAGC 0.891701 -50 GAGAGAGTTTAGGAAAAAGGAGGAGAAAAA 14 10 0 AGAAAAAGGA 0.942994 -176 * ********* Masking position 5 Map Score: 20.191 Number of sites scoring better than the average of aligned sites = 1843 Number in coding regions = 1418 Number in noncoding regions = 425 Number of orfs with sites within 600 bp upstream = 399 Fraction of orfs with sites within 600 bp upstream = 0.0640861 Motif number 2 TCGGCGGACTCTCTCTTCAAAA 3 3 1 GGCGGACTCT 0.942871 -244 AAAAAAGACAAACGCGCTTTTCCTTTTCAT 3 145 0 AACGCGCTTT 0.742874 -102 CTAAAGCCAGGGCGGGTTTTCTTTAGTTAT 5 84 1 GGCGGGTTTT 0.936031 -54 AATGCTTAGGAGAGGAGTTTTTAGAC 5 122 1 AGAGGAGTTT 0.765137 -16 CGGCTATGTAAGCCGGCTTTCTTCATGCTT 6 77 0 AGCCGGCTTT 0.983861 -187 CGGCTTACATAGCCGAGTTTCTTCATGAAC 6 92 1 AGCCGAGTTT 0.929712 -172 CCGCTTGTTTAGCGGGCTTTTTTCCCTCAT 7 13 0 AGCGGGCTTT 0.995613 -143 CCGCTAAACAAGCGGGCTTTTTGCGTTGCT 7 28 1 AGCGGGCTTT 0.995613 -128 ATCTTACAGGAGCGGACTTGTGAATTCAAC 7 69 0 AGCGGACTTG 0.957404 -87 TATGATGTGAGGCAGACTTTATGACAAGCC 9 16 0 GGCAGACTTT 0.962853 -60 CCCAAATGGGAGCAGGCTTTTTTTGTGCCC 10 32 1 AGCAGGCTTT 0.982606 -113 CTAGAGGTTTAGCGGTGTTTCCTGTACAAT 13 62 0 AGCGGTGTTT 0.911264 -165 TCATTTTTTGGGCACACTTTAACTGGAGGT 13 204 1 GGCACACTTT 0.835333 -23 ********** Masking position 8 Map Score: 18.093 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 653 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 3 TTCTCTGCACATTGTACATGAATGCAGAAAA 2 67 0 ATTTACATGA 0.770526 -68 TCAAAAAGACCTTTTATATGAGCTTTGTGAT 3 27 1 CTTTATATGA 0.945675 -220 TGATACATGTCTTTTGCATGCCGAGCTGACA 3 190 0 CTTTGCATGC 0.801213 -57 ATCAACTCACTTTCAGCATGAATTTCTGCAA 3 221 0 TTTAGCATGA 0.865279 -26 GTTTACCCGCCTTGAATATGAGCACGATACC 5 38 1 CTTAATATGA 0.945675 -100 CATAGCCGAGTTTCTTCATGAACGTGAAATC 6 99 1 TTTTTCATGA 0.551719 -165 TTTTCACACACCTTAATATGATTATTCGGAT 6 127 0 CCTAATATGA 0.812963 -137 AAAACCTTGATTTCAATATGCGGATACGAAA 6 177 1 TTTAATATGC 0.809222 -87 GTGAATTCAACTCTAATATGACAGCAACGCA 7 49 0 CTCAATATGA 0.871911 -107 CAATCGCACTCCTATGTATGAAATTTCTTTT 7 134 0 CCTTGTATGA 0.724314 -22 ACCTCCCATTTTTTTATATGATATGCTCTAG 10 112 0 TTTTATATGA 0.915592 -33 TATAATCCTTTTCCAGTATGATAAAATGTTC 12 13 1 TTCAGTATGA 0.719408 -74 AAGTGAACATTTTTTACATGAGAAACCCTCG 12 49 1 TTTTACATGA 0.913984 -38 AGCCTTGCTTTTCCTACATGCATTATACCCG 13 117 1 TTCTACATGC 0.619019 -110 TCATTATACGATTCAATATGAAAAATGTTTC 14 39 1 ATTAATATGA 0.774154 -147 GGCAGAAAAACTTAAATATGACAGCAAAGGG 14 155 1 CTTAATATGA 0.945675 -31 *** ******* Masking position 8 Map Score: 13.6317 Number of sites scoring better than the average of aligned sites = 548 Number in coding regions = 443 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 4 ACAGCATTACACCTCTTATCTTTGTTAGA 1 18 0 CACCTCTTAT 0.732284 -19 GTAAGCACCTCTATTTCCAAGCTTA 2 120 0 CACCTCTATT 0.780782 -15 CTAAAAACTCCTCTCCTAAGCATTCCTGCA 5 116 0 CTCTCCTAAG 0.826041 -22 AAGGGCCGCCCTCCCCTTGGTTTCGTGTTA 6 17 0 CTCCCCTTGG 0.949532 -247 TTTCTTTCTCCTTTGATCCTCTTTA 6 249 0 TTCTCCTTTG 0.804278 -15 ACAATCGCACTCCTATGTATGAAATTT 7 139 0 CACTCCTATG 0.812335 -17 CAGAGCCTCCTCCTTTCTACCGATTG 9 60 0 CTCCTCCTTT 0.894182 -16 AAAAAGCCTGCTCCCATTTGGGAACAGACT 10 24 0 CTCCCATTTG 0.962825 -121 CTCTCCCAACCTCCCATTTTTTTATATGAT 10 121 0 CTCCCATTTT 0.955178 -24 GTTTAATGTCCTCCTATATTCCAA 11 5 0 CTCCTATATT 0.759319 -20 ACAATCTCTCCTTTTCGCGAGGGTT 12 72 0 CTCTCCTTTT 0.96679 -15 TTTTTCTCCTCCTTTTTCCTAAACT 14 6 1 CTCCTCCTTT 0.894182 -180 TTCCTAAACTCTCTCATTATACGATTCAAT 14 26 1 CTCTCATTAT 0.707849 -160 ATCCCATTTCCCCTTTGCTGTCATATT 14 169 0 TTCCCCTTTG 0.920658 -17 ********** Masking position 3 Map Score: 10.2275 Number of sites scoring better than the average of aligned sites = 1466 Number in coding regions = 973 Number in noncoding regions = 493 Number of orfs with sites within 600 bp upstream = 496 Fraction of orfs with sites within 600 bp upstream = 0.0796659 Motif number 5 GAACAGATAAGCTTGGAAATAGAGGTGCTTAC 2 113 1 GCTGAAAAAG 0.92215 -22 TTGTATCAAAGCTTGAAGAGGGAGAT 4 70 1 GCTGAGAGAG 0.961479 -16 GGCTTTAGGAGCCTGAAGAAGCGGGTATCGTGCT 5 58 0 GCCGAGAGGG 0.977336 -80 CTTTCTTCATGCTTTGAAATAAAGGGTAACGTGT 6 57 0 GCTTAAAAAG 0.671883 -207 AAGAAACTCGGCTATGTAAGCCGGCTTTCTTCAT 6 81 0 GCTTTAACGG 0.841999 -183 AGGGAAAAAAGCCCGCTAAACAAGCGGGCTTTTT 7 16 1 GCCGTAACAG 0.978436 -140 ATATGCTCTAGCTTGCTGAAGTAGTCTTGTCATT 10 89 0 GCTGTGAGAG 0.952961 -56 AATTTTTTCAGCCTGTCAATCTAGAGGTTTAGCG 13 78 0 GCCGCAACAG 0.95336 -149 TTTGCCGGCAGCCCGTTAAGCCGGAGCTTTCTCA 14 76 0 GCCGTAACGG 0.98005 -110 TTAACGGGCTGCCGGCAAACGTGGTACACTTATG 14 91 1 GCCGAAAGGG 0.983756 -95 *** * *** * ** Masking position 9 Map Score: 7.16929 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 519 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 CATCTGCTTTTTTTTCTTTTAACGTC 2 7 0 TTTTTCTTTT 0.819161 -128 CCAAGCTTATCTGTTCTTTTATGTTATATG 2 99 0 CTGTTCTTTT 0.85245 -36 GCTCATATAAAAGGTCTTTTTGAAGAGAGA 3 20 0 AAGGTCTTTT 0.541073 -227 CGCGCTTTTCCTTTTCATTTTTCATATAAA 3 133 0 CTTTTCATTT 0.915125 -114 GAAAAGCGCGTTTGTCTTTTTTTATGTCTG 3 153 1 TTTGTCTTTT 0.821932 -94 TGCAATGATACATGTCTTTTGCATGCCGAG 3 196 0 CATGTCTTTT 0.955728 -51 TGTCATGTTTCATTTTTTTTCACGTCTG 4 9 0 CATTTTTTTT 0.582527 -77 AAAAATGAAACATGACATTTGAAGAAGCGA 4 22 1 CATGACATTT 0.57528 -64 CTATGTATGAAATTTCTTTTTTTATAGGTT 7 124 0 AATTTCTTTT 0.785511 -32 ACAGACTTCTTTTTTCCTTT 10 1 0 TTTTTCCTTT 0.688878 -144 CTGAAGTAGTCTTGTCATTTCCGTATAAAA 10 78 0 CTTGTCATTT 0.916575 -67 GATTGCTAACCATTTCCTTTCACTCTATTG 13 36 1 CATTTCCTTT 0.911935 -191 TTTTTATTGACATTTCATTTTTTGGGCACA 13 190 1 CATTTCATTT 0.925875 -37 ********** Masking position 8 Map Score: 9.32093 Number of sites scoring better than the average of aligned sites = 1290 Number in coding regions = 1058 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 232 Fraction of orfs with sites within 600 bp upstream = 0.0372631 Motif number 7 CGCCCTATTATTCCGGTACATCTGCTTTTT 2 25 0 TTCCGGTACA 0.970751 -110 TTTTTCTGCATTCATGTACAATGTGCAGAG 2 66 1 TTCATGTACA 0.800381 -69 GTTATATGATTCTCTGCACATTGTACATGA 2 77 0 TCTCTGCACA 0.878589 -58 CTCCTAAGCATTCCTGCACCATAACTAAAG 5 104 0 TTCCTGCACC 0.919861 -34 CCTGCTCCCATTTGGGAACAGACTTCTTTT 10 18 0 TTTGGGAACA 0.863101 -127 AGATTCTGTTTTTGGGCACAAAAAAAGCCT 10 45 0 TTTGGGCACA 0.97047 -100 TTAGCGGTGTTTCCTGTACAATAGAGTGAA 13 54 0 TTCCTGTACA 0.954388 -173 CATTTCATTTTTTGGGCACACTTTAACTGG 13 200 1 TTTGGGCACA 0.97047 -27 ********** Masking position 8 Map Score: 4.35998 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 321 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 CACGAGGGTATGGTAAAATGTAAGCAGTTTA 3 106 1 TGGTAAATGT 0.948538 -141 CTTCAAGCTTTGATACAATGCTCTCAAGCCC 4 57 0 TGATAAATGC 0.87701 -29 CTGAAGAAGCGGGTATCGTGCTCATATTCAA 5 49 0 GGGTACGTGC 0.980202 -89 GCCCTCCCCTTGGTTTCGTGTTAAGCCAT 6 9 0 TGGTTCGTGT 0.828062 -255 TTGAAATAAAGGGTAACGTGTAAAAAAACCA 6 47 0 GGGTACGTGT 0.961831 -217 TGTTCCCAAATGGGAGCAGGCTTTTTTTGTG 10 28 1 TGGGACAGGC 0.841885 -117 AATGGGAGGTTGGGAGAGTGCT 10 133 1 TGGGAAGTGC 0.957964 -12 TTTTCCAGTATGATAAAATGTTCACGAGAAG 12 21 1 TGATAAATGT 0.783991 -66 TGAAAATAACGGGTATAATGCATGTAGGAAA 13 126 0 GGGTAAATGC 0.967605 -101 ***** ***** Masking position 2 Map Score: 3.49982 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 169 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 ATGGTAAAATGTAAGCAGTTTATATGAAAA 3 115 1 GTAAGCAGTT 0.919223 -132 TTCAAGGCGGGTAAACATTTCGCCTGTGAA 5 24 0 GTAAACATTT 0.959018 -114 TTCACTTCTCGTGAACATTTTATCATACTG 12 26 0 GTGAACATTT 0.981387 -61 TTCACGAGAAGTGAACATTTTTTACATGAG 12 41 1 GTGAACATTT 0.981387 -46 GCCAAAAAGTGTGAGCTTTTTTATTGACAT 13 173 1 GTGAGCTTTT 0.945351 -54 ********** Masking position 4 Map Score: 2.44752 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 21 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 GTCTGAGATTATTGTCAGCTCGGCATGCAAAAGA 3 178 1 ATTTCGCTGC 0.985091 -69 TTTGATCCTCTTTATCCGCTTGTCGTTAAGCCAC 6 229 0 TTTTCGCTGC 0.989548 -35 ATTATCAACCTGCCTATTTCTTTA 13 1 1 ATTTCACCGC 0.966134 -226 CTATGGCAATTTTTTCAGCCTGTCAATCTAGAGG 13 85 0 TTTTCGCCGC 0.995334 -142 CATATTTAAGTTTTTCTGCCATCCAGTATTTGTG 14 141 0 TTTTCGCCTC 0.976121 -45 *** ** *** * * Masking position 5 Map Score: 0.326851 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 106 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 ********** No masking Map Score: 2.07011e-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: 2.07011e-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: 2.07011e-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