AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00660_bsub_reg_300.orf -o00660_bsub_300.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 ydaO 300 similar to hypothetical proteins #2 mutT 58 mutator protein #3 ydaP 66 similar to pyruvate oxidase #4 ylxM 176 similar to hypothetical proteins #5 rpsP 105 ribosomal protein S16 (BS17) #6 ylqD 121 ylqD #7 rplS 130 ribosomal protein L19 #8 ylqF 142 similar to hypothetical proteins #9 rnh 70 ribonuclease H #10 ylqG 31 ylqG #11 sucC 172 succinyl-CoA synthetase (beta subunit) #12 sucD 28 succinyl-CoA synthetase (alpha subunit) #13 ilvB 300 acetolactate synthase (acetohydroxy-acid synthase) (large subunit) #14 alsD 61 alpha-acetolactate decarboxylase #15 alsS 154 alpha-acetolactate synthase (pH6) Motif number 1 GATGTTATGGCACAGGGGCATCCGTTTGCCT 1 132 1 CACAGGGGAT 0.714996 -169 TTTTAATTGAAAAATGAGAAATTAAAAGGGG 1 271 1 AAAATGAGAA 0.691754 -30 ATGAGAAATTAAAAGGGGAAGACATCG 1 284 1 AAAAGGGGAG 0.968008 -17 TTTCCCGCTAAAAAGGACCAAGGTGATTCCC 2 25 0 AAAAGGACAA 0.744588 -34 TTTTAGCGGGAAAAGGAGGTATGGGG 2 43 1 AAAAGGAGTA 0.862114 -16 TTTTCAATACCACAGGAGAAAGGCTTTAAAA 3 25 0 CACAGGAGAA 0.881084 -42 GAAAAAAGGAAAAAGGAGGATACGTT 3 51 1 AAAAGGAGAT 0.881554 -16 TTTATCTTGTCAAAGCGGCGATTAACTTTTC 4 80 0 CAAAGCGGGA 0.894975 -97 TTTGACTTAACAAAGGGGAGAGCTCAA 4 160 1 CAAAGGGGGA 0.983363 -17 TGCGTGTAAAAAAAGGGGAGGTGCCGGCCCT 6 18 0 AAAAGGGGGG 0.979861 -104 TTACACGCAAAAAAAGGGTAAACTGATAGAA 6 40 1 AAAAAGGGAA 0.877155 -82 TAAAAGTTTTAAAAGCGGGGAGCTTGGTGCG 6 101 1 AAAAGCGGGA 0.943153 -21 ACAGGCCGTAAACAAGGGTGGTACCGCGGAA 13 136 1 AACAAGGGGG 0.638424 -165 TGCGATAGCTAAAAGGGGCGAAAAGGCTTTT 13 169 0 AAAAGGGGGA 0.991385 -132 ATGAAAATCCAAAAGGAGGAACTAAA 13 285 1 AAAAGGAGAA 0.975407 -16 AGCACTAAATAAAAGGAGTGAAGGGAAAT 14 43 1 AAAAGGAGGA 0.984562 -19 AAAATGCATAATAAGGAGTGAGG 15 142 1 ATAAGGAGGA 0.836668 -13 ******** ** Masking position 4 Map Score: 23.3134 Number of sites scoring better than the average of aligned sites = 1072 Number in coding regions = 705 Number in noncoding regions = 367 Number of orfs with sites within 600 bp upstream = 415 Fraction of orfs with sites within 600 bp upstream = 0.066656 Motif number 2 AATAGAACGGCTTTTTGCCGTTG 1 4 1 AGAACGGCTT 0.958754 -297 AGCCCTACCTAAAAAGGATTCACCCCAACG 1 29 0 AAAAAGGATT 0.804039 -272 ACATCATAGCAGAAAGGACTATCATCAACA 1 208 1 AGAAAGGACT 0.91171 -93 ATACCACAGGAGAAAGGCTTTAAAACCCGG 3 20 0 AGAAAGGCTT 0.984515 -47 TAGGCAAAATAGAAAAGCCTGGACGAGTAA 6 74 1 AGAAAAGCCT 0.963888 -48 ATAACGAACGAAAAGAGCTTGTTACCTGTA 8 13 1 AAAAGAGCTT 0.912245 -130 TCTGTATAAAAAAAGAGCTTGTTACAGGTA 8 35 0 AAAAGAGCTT 0.912245 -108 TACCGCGGAAAGAAAAGCCTTTTCGCCCCT 13 157 1 AGAAAAGCCT 0.963888 -144 GATTGTGGGCGGAAGGGCTTTTTTTATTGA 13 214 1 GGAAGGGCTT 0.935733 -87 ********** Masking position 4 Map Score: 8.02253 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 471 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 3 GTTGGGGTGAATCCTTTTTAGGTAGGGCTA 1 30 1 ATCCTTTTTA 0.637222 -271 CCCCATACCTCCTTTTCCCGCTAAA 2 44 0 TACCTCCTTT 0.785774 -15 ATCCTCCTTTTTCCTTTTTTCAATACCACA 3 42 0 TTCCTTTTTT 0.761365 -25 AACGTATCCTCCTTTTTCCTTTTTT 3 52 0 ATCCTCCTTT 0.980032 -15 AAAAATCCTCCTTAAAATAGGGTT 4 5 1 ATCCTCCTTA 0.953526 -172 TACGCTAAATATCATCCAATTTATTCCGAT 4 45 0 ATCATCCAAT 0.416954 -132 AATATTCCCCATCCTTCTTTGAAATTTATG 11 15 1 ATCCTTCTTT 0.958637 -158 AAATCTTTTAATCCTTCTAAACATTCAAAC 11 62 0 ATCCTTCTAA 0.801988 -111 AGACTGCGCTTTCATTCTATAATAATACTG 11 117 0 TTCATTCTAT 0.722631 -56 TTCCCATCCTCCTAACTTATGTAAC 11 158 0 ATCCTCCTAA 0.895584 -15 TCCCCTGCCTTTCATTCTTTC 12 2 0 TTCATTCTTT 0.861729 -27 TCCTTTAAAGATCATCTTTTCATTAGCTAG 13 256 0 ATCATCTTTT 0.759101 -45 CTTTTGGATTTTCATCCTTTAAAGATCATC 13 270 0 TTCATCCTTT 0.929567 -31 TTTAGTTCCTCCTTTTGGATTTTCA 13 286 0 TTCCTCCTTT 0.973868 -15 ********** Masking position 5 Map Score: 16.9846 Number of sites scoring better than the average of aligned sites = 1170 Number in coding regions = 698 Number in noncoding regions = 472 Number of orfs with sites within 600 bp upstream = 544 Fraction of orfs with sites within 600 bp upstream = 0.0873755 Motif number 4 CAAAAATGAACAACAAAAAACACAGAGGCA 1 158 0 CAACAAAAAA 0.903634 -143 ATGCGATTTGCATTCAAAAATGAACAACAA 1 172 0 CATTCAAAAA 0.740974 -129 TCAATTAAAACAATAAAACATCCATCAGTG 1 251 0 CAATAAAACA 0.788809 -50 GCCGCTTTGACAAGATAAAAACTTGACAGT 4 92 1 CAAGATAAAA 0.92818 -85 TCGGTTATACATGATAAAACCGTTGTTAA 5 10 1 CATGATAAAA 0.825515 -96 AAACCGTTGTTAAGAAAAAACACTTTACAA 5 27 1 TAAGAAAAAA 0.800371 -79 CCTTTTTTTACACGCAAAAAAAGGGTAAAC 6 33 1 CACGCAAAAA 0.860161 -89 TCGGTTCAGCCAAGAAAAAATAAAGACCCG 9 26 0 CAAGAAAAAA 0.976132 -45 GCTGATTATTCAATAAAAAAAGCCCTTCCG 13 223 0 CAATAAAAAA 0.941128 -78 ********** Masking position 7 Map Score: 3.58391 Number of sites scoring better than the average of aligned sites = 777 Number in coding regions = 569 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 5 CGCACCAAGCTCCCCGCTTTTA 6 110 0 GCACAAGCTC 0.993733 -12 GGGCTTATCCGCTGCAAGCTTGAAAACGATG 7 64 1 GCTCAAGCTT 0.90238 -67 CTTGTTACAGGTAACAAGCTCTTTTCGTTCG 8 17 0 GTACAAGCTC 0.990348 -126 CTTGTTACCTGTAACAAGCTCTTTTTTTATA 8 30 1 GTACAAGCTC 0.990348 -113 AGTAACGAGTGAATCAAGTTCACCCGGCCAA 13 70 0 GAACAAGTTC 0.917649 -231 *** ******* Masking position 6 Map Score: 2.43791 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 83 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 GGGCTAACTCTCATATGCCCGAATCCGTCAGC 1 54 1 TCAAGCCCGA 0.735323 -247 CTTTTTAGCGGGAAAAGGAGGTATGGGG 2 41 1 GGAAGGAGGT 0.874719 -18 AAGGGAGAGGGCCGGCACCTCCCCT 6 4 1 GGAAGGCCGG 0.995386 -118 AGCTTGCAGCGGATAAGCCCGCTTAAGCCACA 7 52 0 GGAAGCCCGC 0.983082 -79 ATACAGAATTTGAAAATGCCGGACAGGCATCG 8 58 1 TGAATGCCGG 0.914997 -85 ATCACCATGGACAAGGAGGCACCTTTTTAA 10 9 1 GGAAGGAGGC 0.950111 -23 GAAAGAATGAAAGGCAGGGGACCAAATA 12 8 1 TGAAGCAGGG 0.905279 -21 AATGACAGTAGGACTTGGCCGGGTGAACTTGA 13 56 1 GGATGGCCGG 0.971435 -245 GAAATATCCATGAGACGGCCGATTAACAGGCC 13 111 1 TGAAGGCCGA 0.973755 -190 *** * ****** Masking position 3 Map Score: 3.31121 Number of sites scoring better than the average of aligned sites = 761 Number in coding regions = 704 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 AGCGTATTTTGGAAAAGTTAATCGCCGCTT 4 69 1 GGAAAAGTTA 0.844117 -108 CTATCTTGTTGAAATATTTTCGGAGGTGCT 5 80 1 GAAATATTTT 0.729267 -26 GCCTGGACGAGTAAAAGTTTTAAAAGCGGG 6 90 1 GTAAAAGTTT 0.953124 -32 AGAAGGATGGGGAATATTTTAG 11 3 0 GGAATATTTT 0.881884 -170 TTTTAATAAAGTAAAAGTTTGAATGTTTAG 11 46 1 GTAAAAGTTT 0.953124 -127 CATTTTAAACGTAAAATTTTAAATATCTTG 15 118 0 GTAAAATTTT 0.928207 -37 ********** Masking position 6 Map Score: 0.846069 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 90 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 CCGTCAGCTAACCTCGTAAGCGTTCGTGAG 1 78 1 ACCTCGTAAG 0.93721 -223 TGTCATTAAAACCGTGTAAACTAAGTTATC 4 121 1 ACCGTGTAAA 0.9556 -56 TTTACTAGCACCTCCGAAAATATTTCAAC 5 87 0 ACCTCCGAAA 0.946492 -19 AATCTTTTAATCCTTCTAAACATTCAAACT 11 61 0 TCCTTCTAAA 0.769985 -112 AGGCGAGTTCACCTTGTAAAGCTTCGCCG 13 10 0 ACCTTGTAAA 0.962909 -291 CAAGGGTGGTACCGCGGAAAGAAAAGCCTT 13 148 1 ACCGCGGAAA 0.965585 -153 ********** Masking position 8 Map Score: 0.621285 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 52 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 CACAATTTCATAGCCTATGCAATAAAAT 7 7 0 TAGCTATGAA 0.965808 -124 TGATAACGAACGAAAAGAGCTTGTT 8 4 1 TAACAACGAA 0.918572 -139 CCCATCCTCCTAACTTATGTAACAAAACTAAA 11 149 0 TAACTATGAA 0.964545 -24 ATCAGCTATCTAGCTAATGAAAAGATGATCTT 13 247 1 TAGCAATGAA 0.964408 -54 TACGAATTATTAACCTATGGAAAGGAATGCAT 15 16 0 TAACTATGAA 0.972181 -139 **** **** ** Masking position 7 Map Score: 0.276804 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 17 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 GAATGAAACCTGTGTTCGATGTTATGGCACA 1 115 1 TGTGTTGATG 0.885925 -186 AGAGCAAGACACTGATGGATGTTTTATTGTT 1 242 1 ACTGATGATG 0.971323 -59 AAAAGGGTAAACTGATAGAAGCTTAGGCAAA 6 51 1 ACTGATGAAG 0.94779 -71 GCCAAGAGCATCTGTTGGAAGGAG 7 117 1 TCTGTTGAAG 0.94779 -14 AGAATTGTCTACAGTTCGATGCAAAATCTTT 11 84 0 ACAGTTGATG 0.939726 -89 GCATCACGACACTGTTTTATGAACAGCACTA 14 19 1 ACTGTTTATG 0.907206 -43 ****** **** Masking position 6 Map Score: 0.220547 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 154 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 ********** No masking Map Score: 5.23913e-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: 5.23913e-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: 5.23913e-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