AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i243_ecoli_bsub_300.orf -o243_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yhdG 300 putative dehydrogenase #2 fis 25 site-specific DNA inversion stimulation factor; DNA-binding protein; a trans activator for transcription #3 spoIIE 300 serine phosphatase #4 yabS 84 similar to hypothetical proteins #5 yabT 88 yabT #6 yacA 103 similar to cell-cycle protein #7 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #8 yacB 194 similar to hypothetical proteins #9 yacC 85 similar to hypothetical proteins #10 yacD 46 similar to protein secretion PrsA homolog #11 cysK 75 cysteine synthetase A #12 pabB 166 para-aminobenzoate synthase (subunit A) #13 yacF 23 similar to transcriptional regulator (nitrogen regulation protein) Motif number 1 TCATTCATAAAGAAAAATTGAGAACTTACT 1 84 1 AGAAAAATTG 0.875502 -217 ATTTACACTCAAAGAAATTTGAGTAAGTTC 1 105 0 AAAGAAATTT 0.785292 -196 GGCTTCTGCAAGAGAAACCGATTTGTTAGG 3 113 0 AGAGAAACCG 0.971715 -188 TCTAAAAATGAAAAAAATCGGCTTCTGCAA 3 132 0 AAAAAAATCG 0.929733 -169 TAACAATACCAAAGAAATCTTCGACGGTTT 3 204 0 AAAGAAATCT 0.834797 -97 GTTTTTTTAGAAAGAAAGCGAA 8 3 0 AAAGAAAGCG 0.899944 -192 CTTTCTTTCTAAAAAAACTGCCGGCTGACG 8 15 1 AAAAAAACTG 0.938756 -180 TCATTTACATAAAAAAACTGCCAGCGTCAG 8 39 0 AAAAAAACTG 0.938756 -156 GCTCATTTGTAAACAAATCGATACCAGAAT 8 100 0 AAACAAATCG 0.828708 -95 AAAGTAAAGTAGAGAAACTATTCAAAAGTG 8 165 1 AGAGAAACTA 0.709111 -30 TTGATTTATGAAAGAAACCGCGTAGGAAGT 9 49 1 AAAGAAACCG 0.979073 -37 CACGAAATATAAAAAAACTCCCGGCGAACC 12 28 0 AAAAAAACTC 0.803874 -139 TATTCTTGGAAGAGAAATTCACTTTTTTCA 12 88 1 AGAGAAATTC 0.805987 -79 ********** Masking position 5 Map Score: 13.0364 Number of sites scoring better than the average of aligned sites = 575 Number in coding regions = 479 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 2 GCGAAGTGCGAGCAAGCTCACAAAAG 1 7 1 TGCGAGCAAG 0.862708 -294 ATACTGTGACTGCAAGGCGGCGTATATTAC 1 265 0 TGCAAGGCGG 0.981219 -36 TCCTCGTATTCTCCAGGAGGAATGAAT 4 68 1 CTCCAGGAGG 0.902417 -17 CCTCAAGCCGGGTACGACAAT 5 2 1 CTCAAGCCGG 0.907279 -87 ACCTGCTCATTGTGAGGAGGACATT 6 89 1 TGTGAGGAGG 0.960479 -15 ATAACCATCTCGGAAGCAGGCTGCCGA 7 8 0 CGGAAGCAGG 0.976499 -90 GTGCTTACTGTGGGAGGAGGTAAGGA 7 82 1 TGGGAGGAGG 0.974088 -16 AAACTGCCAGCGTCAGCCGGCAGTTTTTTT 8 25 0 CGTCAGCCGG 0.927893 -170 GAAAAGGGGCTGAAAGCAGGT 10 36 1 TGAAAGCAGG 0.961232 -11 AACAAATGAAAGGAGGAGAAAAA 13 7 1 TGAAAGGAGG 0.961232 -17 ********** Masking position 5 Map Score: 8.79375 Number of sites scoring better than the average of aligned sites = 1356 Number in coding regions = 1261 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 3 GAATATAACAGGTGGGAGATGAGAGGA 3 284 1 GGTGGGAGAT 0.92085 -17 GCCAGCGTCAGCCGGCAGTTTTTTTAGAAA 8 20 0 GCCGGCAGTT 0.99521 -175 GCCGGCTGACGCTGGCAGTTTTTTTATGTA 8 34 1 GCTGGCAGTT 0.989307 -161 CTCCCGGCGAACCGGGAGTTTTGGCTTTTT 12 11 0 ACCGGGAGTT 0.983095 -156 CTCCCGGTTCGCCGGGAGTTTTTTTATATT 12 23 1 GCCGGGAGTT 0.996717 -144 ********** Masking position 7 Map Score: 5.6638 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 33 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 TTACTCATAAAAATCATCATATTAGAAAATAGTGACTA 1 137 0 AATTATAAAA 0.71589 -164 GAGATGGATCAAAGAATTGCATTTAAAATGAGCGTGGT 1 182 0 AATCATTAAA 0.966489 -119 TTTTGTCAAAAGAAGGTAACAATACCAAAGAAATCTTC 3 212 0 AATCATACAA 0.968989 -89 AAAGATATTCATATCCTAACACTTTCAACCCCTCCAAG 6 46 0 AATCATTCAA 0.968989 -58 GTACCATAGAAAATCATTCCAATACAAACAATAACCAT 7 30 0 AATCATAAAA 0.966489 -68 CAGCTGAGCCAATCATTTACATAAAAAAACTGCCAGCG 8 43 0 ATTCAAAAAA 0.647586 -152 TATTATGTATATAATCTATCAATTTCAAAATTTTTTGT 11 14 0 AATCATTCAA 0.968989 -62 TAGATTATATACATAATACCAATACAAATAGTCGGAAA 11 34 1 AATCATAAAA 0.966489 -42 TAGTGAAAAAAGTGAATTTCTCTTCCAAGAATAACATT 12 83 0 ATTCTTTCAA 0.665647 -84 CACTAACAACATTGCTTTACAATTAAAAACAAGTAAAA 12 116 1 ATTCATTAAA 0.928865 -51 * * * ** ** *** Masking position 7 Map Score: 4.76389 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 50 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 TGCGTAAATAATCGGCAAATTTACGTGCCTT 1 34 0 ATGGCAAATT 0.699068 -267 TGCCGATTATTTACGCAAATTTGCGTGCCAA 1 48 1 TTCGCAAATT 0.982177 -253 ATTTGAGTAAGTTCTCAATTTTTCTTTATGA 1 88 0 GTCTCAATTT 0.846507 -213 AATTGAGAACTTACTCAAATTTCTTTGAGTG 1 99 1 TTCTCAAATT 0.971876 -202 TCTCAGAGGATTGGTCAAAGTTTGGCCTTTC 1 216 1 TTGTCAAAGT 0.798926 -85 GCGGCGTATATTACGCATTTTTTGCACGAGA 1 248 0 TTCGCATTTT 0.841182 -53 TTAGACAACATTCCGGAAATTCTTTTCATAA 3 157 1 TTCGGAAATT 0.877089 -144 ACCAAGCTGTTTACGCAATGTATAAGTGTTT 5 50 0 TTCGCAATGT 0.941811 -39 TTCAGCCCCTTTTCTCAAATTAAAAACCCGC 10 19 0 TTCTCAAATT 0.971876 -28 TTGTATCATTCCTCTATTTTCTTTTTTAC 12 148 0 TTCTCTATTT 0.768588 -19 ** ******** Masking position 2 Map Score: 4.99302 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 345 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 GCTCACAAAAGGCACGTAAATTTGCCGATTAT 1 26 1 GGCACGAATT 0.992085 -275 TGAAAATTTTGGCACGCAAATTTGCGTAAATA 1 55 0 GGCACGAATT 0.992085 -246 AAATGAGCGTGGTGCGATAATTACTCATAAAA 1 163 0 GGTGCGAATT 0.966828 -138 CCTCAAGCCGGGTACGACAATCAAAGGCAAGT 5 11 1 GGTACGAATC 0.966826 -78 TAAACAAATCGATACCAGAATTGGATGATTGT 8 89 0 GATACCAATT 0.933641 -106 TCTCGACACCTCAATTTCCGACTATT 11 60 0 GACACCAATT 0.956778 -16 ****** **** Masking position 9 Map Score: 2.60449 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 82 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 GCAAATTTGCGTGCCAAAATTTTCATTCATA 1 62 1 GTGCAAAATT 0.902642 -239 TTAGAAAATAGTGACTAAAATTTACACTCAA 1 123 0 GTGCTAAAAT 0.91781 -178 CTTTCATCTCGTGCAAAAAATGCGTAATATA 1 242 1 GTGAAAAAAT 0.922622 -59 TTCCGGAATGTTGTCTAAAAATGAAAAAAAT 3 144 0 TTGCTAAAAA 0.814411 -157 AGATAGGATTTTGTCAAAAGAAGGTAACAAT 3 227 0 TTGCAAAAGA 0.935386 -74 TGTAGAATGTTTGTAAAAAGTAAAGTAGAGA 8 149 1 TTGAAAAAGT 0.900772 -46 TTGACAAAAAATTTTGAAATT 11 1 1 TTGCAAAAAA 0.923005 -75 AATGTTGTTAGTGAAAAAAGTGAATTTCTCT 12 98 0 GTGAAAAAGT 0.93506 -69 *** ******* Masking position 7 Map Score: 2.59886 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 203 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 8 CCATATTTGTTTGGCCCGTTGGTCAAGCGG 3 28 1 TTGGCCCGTT 0.937216 -273 GGGCGGTGTCTTAACCGCTTGACCAACGGG 3 42 0 TTAACCGCTT 0.911833 -259 AATTCCATTGGCCCCTTTACCAAGCTG 5 72 0 TTGGCCCCTT 0.976846 -17 CCTAACACTTTCAACCCCTCCAAGCAAAGA 6 40 0 TCAACCCCTC 0.963181 -64 CCATACACGATCAGCGGCTCATTTGTAAAC 8 116 0 TCAGCGGCTC 0.945525 -79 GCTCTTTAGCGGGTTTTTAATTTGA 10 6 1 TTAGCGGGTT 0.797975 -41 ACCTGCTTTCAGCCCCTTTTCTCAAATT 10 29 0 TCAGCCCCTT 0.985565 -18 TCTCGACACCTCAATTTCCGAC 11 64 0 TCGACACCTC 0.79866 -12 ********** Masking position 9 Map Score: 2.36229 Number of sites scoring better than the average of aligned sites = 695 Number in coding regions = 609 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 9 AAAAGAAGGTAACAATACCAAAGAAATCTT 3 213 0 AACAATACCA 0.951447 -88 GTATAAGTGTTTCCATTCCACTTGCCTTTG 5 32 0 TTCCATTCCA 0.813821 -57 AGAAAATCATTCCAATACAAACAATAACCA 7 31 0 TCCAATACAA 0.812081 -67 TTGTAAACAAATCGATACCAGAATTGGATG 8 94 0 ATCGATACCA 0.918369 -101 ACAAACATTCTACAATACCATACACGATCA 8 133 0 TACAATACCA 0.924329 -62 TCTTTCATAAATCAATTCCAGCCCTTTTAG 9 34 0 ATCAATTCCA 0.957963 -52 TATATAATCTATCAATTTCAAAATTTTTTG 11 15 0 ATCAATTTCA 0.717916 -61 TATACATAATACCAATACAAATAGTCGGAA 11 41 1 ACCAATACAA 0.873945 -35 ********** Masking position 5 Map Score: 2.08085 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 476 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 AAAGGGCGGTGTCTTAACCGCTTGACCAAC 3 45 0 GTCTTAACCG 0.85393 -256 CCGTACGGGATTCGAACCCGTGTTACCGCC 3 78 0 TTCGAACCCG 0.931606 -223 GGTTTCTCTTGCAGAAGCCGATTTTTTTCA 3 124 1 GCAGAAGCCG 0.978913 -177 GAATATCAAGGCAGAAACCGTCGAAGATTT 3 190 1 GCAGAAACCG 0.967753 -111 GCCTTTGATTGTCGTACCCGGCTTGAGG 5 9 0 GTCGTACCCG 0.979249 -80 TTGGATGATTGTAAAAGCCGCAGCTGAGCC 8 71 0 GTAAAAGCCG 0.914748 -124 ********** Masking position 6 Map Score: 0.162763 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 663 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 AACTTACTCAAATTTCTTTGAGTGTAAATT 1 106 1 AATTTCTTTG 0.782765 -195 CGCCGCTACCATATTTGTTTGGCCCGTTGG 3 20 1 ATATTTGTTT 0.832548 -281 AACATTCCGGAAATTCTTTTCATAAACGAA 3 163 1 AAATTCTTTT 0.833051 -138 TTCTGCCTTGATATTCGTTTATGAAAAGAA 3 176 0 ATATTCGTTT 0.920951 -125 CCCACCTGTTATATTCGTTGCCTGTCATTA 3 270 0 ATATTCGTTG 0.948925 -31 TCGCCAGAAGAAATTTGATTTATACGGAAG 4 13 0 AAATTTGATT 0.605945 -72 TATTGGAATGATTTTCTATGGTACTATTGA 7 44 1 ATTTTCTATG 0.704903 -54 ATCAATTTCAAAATTTTTTGTCAA 11 5 0 AAATTTTTTG 0.772521 -71 CAGACATGGCATATTTGATGCACGAAATAT 12 48 0 ATATTTGATG 0.782142 -119 TCATTCCTCTATTTTCTTTTTTACTTGTTT 12 142 0 ATTTTCTTTT 0.767876 -25 ********** Masking position 5 Map Score: 3.77677 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 304 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 12 ********** No masking Map Score: 1.49457e-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: 1.49457e-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: 1.49457e-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