AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00920_bsub_reg_300.orf -o00920_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 spoIIE 300 serine phosphatase #2 yabS 84 similar to hypothetical proteins #3 yabT 88 yabT #4 yacA 103 similar to cell-cycle protein #5 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #6 yacB 194 similar to hypothetical proteins #7 yacC 85 similar to hypothetical proteins #8 yacD 46 similar to protein secretion PrsA homolog #9 cysK 75 cysteine synthetase A #10 cysE 300 serine acetyltransferase #11 yitA 300 similar to sulfate adenylyltransferase #12 yjcI 300 similar to cystathionine gamma-synthase #13 metB 300 homoserine O-succinyltransferase #14 yrhA 64 similar to cysteine synthase #15 yrrT 192 yrrT #16 ytkP 148 similar to cysteine synthase #17 yvgR 170 similar to sulfite reductase #18 yvgS 197 yvgS #19 yvgT 186 similar to hypothetical proteins #20 yvgV 119 similar to hypothetical proteins #21 yvgW 159 similar to heavy metal-transporting ATPase #22 yvgX 80 similar to heavy metal-transporting ATPase #23 yvgY 73 similar to mercuric transport protein #24 yvgZ 127 similar to hypothetical proteins Motif number 1 GGCTTCTGCAAGAGAAACCGATTTGTTAGG 1 113 0 AGAGAAACCG 0.948952 -188 TCTAAAAATGAAAAAAATCGGCTTCTGCAA 1 132 0 AAAAAAATCG 0.808552 -169 GTTTTTTTAGAAAGAAAGCGAA 6 3 0 AAAGAAAGCG 0.951041 -192 CTTTCTTTCTAAAAAAACTGCCGGCTGACG 6 15 1 AAAAAAACTG 0.848817 -180 TCATTTACATAAAAAAACTGCCAGCGTCAG 6 39 0 AAAAAAACTG 0.848817 -156 TTGATTTATGAAAGAAACCGCGTAGGAAGT 7 49 1 AAAGAAACCG 0.961283 -37 TCTACCCAATAAAAAAAGCGTCTCTGCATG 10 250 0 AAAAAAAGCG 0.97424 -51 GAAATCAGATAGAGAAACGGGGGGAAGCAT 10 281 1 AGAGAAACGG 0.829488 -20 TTGGAAGATAAGAAGAAGCGTTAAACCCCT 12 230 1 AGAAGAAGCG 0.911497 -71 CTTCTTCATAAGAAGAAGGGGTTTAACGCT 12 246 0 AGAAGAAGGG 0.729375 -55 TTGTTTTTAGAGAAAAACGGAGGAGAACGT 14 21 0 AGAAAAACGG 0.904501 -44 TAGCAAAAAAACCGATTTCGAAGT 18 5 1 AAAAAAACCG 0.979733 -193 TATTATGCAGAAAAAAACCGATTTCACTTC 18 30 0 AAAAAAACCG 0.979733 -168 CAAAAAAAGCGCCCGCGTATG 19 2 1 AAAAAAAGCG 0.97424 -185 TTTGCGAAATTAAAAAAGCGCCCGGCATAC 19 27 0 TAAAAAAGCG 0.752333 -160 TTAAAATTAAAAAAGAAGCGGATCGCAATT 20 83 0 AAAAGAAGCG 0.93223 -37 TCAATGAAAAACAAAAACCGGCATATAGCC 21 17 0 ACAAAAACCG 0.892457 -143 ********** Masking position 6 Map Score: 26.0271 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 391 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 2 GATCCCCTCCGCCGCTACCATAT 1 2 1 ATCCCTCCCC 0.992669 -299 AATGTCCTCCTCACAATGAGCAG 4 91 0 ATTCCTCCCA 0.946334 -13 TCCTTACCTCCTCCCACAGTAAGCACA 5 81 0 ACTCCTCCAC 0.928891 -17 TCTCTATCTGATTTCCTCTACCCAATAAAAAA 10 264 0 ATTCCTCTCC 0.946334 -37 TCTAAGGGCCAGTCCCTCCACCTCTCACGATA 12 127 0 AGCCCTCCCC 0.969358 -174 AAACATTACAATTCCCTCTTACATCTTTGAAA 13 126 1 ATCCCTCTAC 0.934696 -175 AACGGGGAGAACGTTCTCCTCCGTTTTTCTCT 14 11 1 ACTTCTCCCC 0.825044 -54 ATATGTCCTCCTCCTTAATAGAGG 14 51 0 ATTCCTCCCC 0.986147 -14 CAATAGCCGTATTCCCTCTAAATTTATCTTTT 19 71 1 ATCCCTCTAA 0.779997 -116 GAAAAAATGAATTCTCTCCGACAAT 20 4 0 ATCTCTCCAC 0.899009 -116 CAGAAGTATATACCCTCCTGATCAAATGGTA 24 10 1 ATCCCTCCGA 0.865731 -118 ** ****** ** Masking position 1 Map Score: 9.83508 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 173 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 CGGAATGTTGTCTAAAAATGAAAAAAATCGGCTTC 1 137 0 TAAATAAAAA 0.789175 -164 CTATGTTCAATAGTACCATAGAAAATCATTCCAAT 5 45 0 TTAATGAAAA 0.78985 -53 TCAGCCCCTTTTCTCAAATTAAAAACCCGCTAAAG 8 14 0 TTCATAAAAA 0.917502 -33 ATCATTTCGATTCTCACATCAAGAACCTGCCA 11 8 0 TTCATAAGAA 0.862215 -293 CTTCTTATCTTCCAAGCATAAAAAACGCTTGCTGG 12 210 0 TAAATAAAAA 0.789175 -91 TTAAACCCCTTCTTCTTATGAAGAAGGGGTTTTTA 12 250 1 TTCATAAGAA 0.862232 -51 TTTTATAGAATGATAAGATAAAAAACGAGCCATAT 13 94 0 TTAATAAAAA 0.937703 -207 GCGTGAAAATTCCTATAATGAAGAAAATTAAACGG 13 255 1 TTAATAAGAA 0.893152 -46 TCATATAATATCCTAACATAATAAACGTTTGTGCG 16 96 0 TTAATATAAA 0.562927 -53 CACAAAGTTATAAACTGATCGAAAATTGCATCTAA 17 135 0 TACATGAAAA 0.411697 -36 ATTTATCTTTTTTTCTCATGAAAATGTTATTGATT 19 92 1 TTCATAAAAT 0.645292 -95 GCGCTTGTCTTGTTAAAATAAAGAAGTGGGTCAAT 20 51 1 TTAATAAGAA 0.893134 -69 CACCTCATCGTTTTAAAATTAAAAAAGAAGCGGAT 20 90 0 TTAATAAAAA 0.937544 -30 CCCCGTAGGGTATTACAATAAAAAACGCT 23 5 0 TTAATAAAAA 0.9377 -69 TACGGGGGTATGGTAGGATGAAAATAGAAAGAATA 23 33 1 TTAATAAAAT 0.70844 -41 TAATGGGAATTAATATCATTAAACAGAGGTGTACG 24 102 1 TTAATAAACA 0.656227 -26 * ** ** ***** Masking position 8 Map Score: 11.3859 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 138 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 4 AAGCGGTTAAGACACCGCCCTTTCACGGCGG 1 52 1 GACACCGCCT 0.732635 -249 AATGTCCTCCTCACAATGAGCAGGT 4 89 0 TCCTCCTCAA 0.732302 -15 TACTAAACCTCCTATACACTTCCT 7 72 0 TAAACCTCCA 0.688246 -14 TCTCGACACCTCAATTTCCGACTAT 9 61 0 GACACCTCAT 0.921485 -15 TTCAACGTGTTCAACCTCCATTTATACGTTT 11 93 0 TCAACCTCCT 0.857323 -208 GGTTGATTAATACCCCTCCGTGGGGTTCGTT 11 128 0 TACCCCTCCT 0.877417 -173 GGCCAGTCCCTCCACCTCTCACGATAAGAAA 12 122 0 TCCACCTCTA 0.817173 -179 CTGGCCCTTAGAAACCTCAGCAACCGGCTTG 12 147 1 GAAACCTCAC 0.602384 -154 TTCTGTTGTTTCCCCCTCAACACGTATAGAT 13 211 1 TCCCCCTCAC 0.836329 -90 CGTGCCACCTCCATTATTTCCCCG 13 287 0 GCCACCTCCT 0.967893 -14 ATATGTCCTCCTCCTTAATAGAGGTT 14 49 0 TCCTCCTCCT 0.88132 -16 CGTATCCACCTCACAAAGTTATAAA 17 156 0 TCCACCTCAA 0.924296 -15 TCCGACACCTCATCGTTTTAAAAT 20 106 0 GACACCTCAC 0.893121 -14 GCGTACACCTCTGTTTAATGATAT 24 114 0 TACACCTCTT 0.825292 -14 ********* * Masking position 6 Map Score: 7.752 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 243 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 5 AATTCCATTGGCCCCTTTACCAAGCTGTT 3 70 0 TGCCCCTTTA 0.929848 -19 ATTGGCTCAGCTGCGGCTTTTACAATCATCC 6 68 1 CGCGGCTTTT 0.95638 -127 AAATCAATTCCAGCCCTTTTAGGGTTAAGAA 7 25 0 CGCCCTTTTA 0.864748 -61 GCTCTTTAGCGGGTTTTTAATTTGAGA 8 7 1 TGCGGGTTTT 0.79817 -40 ACCTGCTTTCAGCCCCTTTTCTCAAATTAA 8 27 0 CGCCCCTTTT 0.976471 -20 GTAACGGCGGCGGCCGCCTTTGAATACTGAT 10 141 0 CGCCGCCTTT 0.86512 -160 CAGAGTGGAACCGCGCGGTTAAAGCGTCTCT 10 209 1 CGCGCGGTTA 0.595942 -92 AGTTTGACATCAGCGCCTTAACATCATTTCG 11 34 0 CGCGCCTTAA 0.756524 -267 TCGGCGGCTACAGCCCGTTAACAGGTTTTTT 11 246 1 CGCCCGTTAA 0.790943 -55 TCTATCCGCACAGCCTCTTTATTGATAAAAT 16 42 0 CGCCTCTTTA 0.822518 -107 ACATGAAGCATAGCCGTTTTATCATTAGGAT 17 42 1 TGCCGTTTTA 0.69934 -129 CCGGCATACGCGGGCGCTTTTTTTG 19 5 0 CGGCGCTTTT 0.879457 -182 CCGCGTATGCCGGGCGCTTTTTTAATTTCGC 19 23 1 CGGCGCTTTT 0.879457 -164 AACCGGCATATAGCCGGTTTT 21 1 0 TGCCGGTTTT 0.89503 -159 AACCGGCTATATGCCGGTTTTTGTTTTTCAT 21 13 1 AGCCGGTTTT 0.677788 -147 TTCAAGGTATCGCGCCTTTAGGGAGGCGCG 22 10 1 TGCGCCTTTA 0.860093 -71 * ********* Masking position 9 Map Score: 9.22118 Number of sites scoring better than the average of aligned sites = 2091 Number in coding regions = 1881 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 6 CGCGCACCCTTCAAAATGGCATGCGGGATCACA 11 161 0 TAAAGGCATG 0.879958 -140 CTCTTTCACAACGGAATGATAATCTTTT 11 283 0 TAAAGGAATG 0.950248 -18 GTTTTTATTTTGAAAAGGGAAGGTGTCAGCTAT 12 278 1 TAAAGGAAGG 0.782461 -23 TTACTGTGAAACCAAAAGGCGTGTCAGTGCGTT 13 164 1 ACAAGGCGTG 0.817017 -137 TAGGAATTATTAAATATGGAGTGTGACAAAT 15 172 1 TATAGGAGTG 0.868515 -21 AATAGCTGTCAAAGAAGGGAGTGTCAGACGG 16 9 0 AAAAGGAGTG 0.98407 -140 CTTGTTTTATTCAGAAAGGAATGACA 16 133 1 TAAAGGAATG 0.950248 -16 AGAGAAGGGAGTCCTTCTCTTTT 17 1 1 AAAAGGAGTC 0.936393 -170 TTTAACAAACATAAAAGGGAGTCATCAGA 19 168 1 AAAAGGAGTC 0.936393 -19 TGTCTTGTTAAAATAAAGAAGTGGGTCAATTGC 20 56 1 AAAAGAAGTG 0.829572 -64 CCCCAGGTGTATATAAAGGAGTGAGT 22 65 1 AAAAGGAGTG 0.98407 -16 * * ** ****** Masking position 6 Map Score: 6.2555 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 229 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 7 AATTCCATTGGCCCCTTTACCAAGCT 3 73 0 ATTGGCCCCT 0.795944 -16 TCCTAACACTTTCAACCCCTCCAAGCAAAG 4 41 0 TTCAACCCCT 0.837817 -63 ACCATACACGATCAGCGGCTCATTTGTAAA 6 117 0 ATCAGCGGCT 0.974225 -78 ACCTGCTTTCAGCCCCTTTTCTCAAAT 8 30 0 TTCAGCCCCT 0.9576 -17 AAAGTTTGACATCAGCGCCTTAACATCATT 11 37 0 ATCAGCGCCT 0.984047 -264 AGGGGTATTAATCAACCGCTGTGATCCCGC 11 142 1 ATCAACCGCT 0.896602 -159 GCTTATTGCGATCGGCGGCTACAGCCCGTT 11 235 1 ATCGGCGGCT 0.953754 -66 GGGTTTTCTTATCAGCGCTTGTCTTGTTAA 20 37 1 ATCAGCGCTT 0.873246 -83 ********** Masking position 2 Map Score: 4.81309 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 374 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 GGTTTCTCTTGCAGAAGCCGATTTTTTTCATT 1 124 1 GCGAAGCCGT 0.93993 -177 GAATATCAAGGCAGAAACCGTCGAAGATTTCT 1 190 1 GCGAAACCGC 0.981233 -111 TCGGCAGCCTGCTTCCGAGATG 5 1 1 TCGCAGCCTC 0.942324 -97 AAAACTGCCAGCGTCAGCCGGCAGTTTTTTTA 6 24 0 GCTCAGCCGC 0.961268 -171 GTATTCAAAGGCGGCCGCCGCCGTTACAGGCT 10 145 1 GCGCCGCCGC 0.991902 -156 AGTTGGGAGAGCAGAAGTCTGCTTTTCAAACA 10 179 1 GCGAAGTCTC 0.78174 -122 CTGTTAACGGGCTGTAGCCGCCGATCGCAATA 11 238 0 GCGTAGCCGC 0.979801 -63 CTTAGAAACCTCAGCAACCGGCTTGTTTTGCA 12 153 1 TCGCAACCGC 0.942324 -148 ATAGCTGACACCTTCCCTTTTCAAA 12 286 0 GCGACACCTC 0.893369 -15 ** ******* * Masking position 9 Map Score: 6.25283 Number of sites scoring better than the average of aligned sites = 696 Number in coding regions = 639 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 GAAGATTTCTTTGGTATTGTTACCTTCTTT 1 212 1 TTGGTATTGT 0.945129 -89 ATGGTTATTGTTTGTATTGGAATGATTTTC 5 30 1 TTTGTATTGG 0.967169 -68 CTGATCGTGTATGGTATTGTAGAATGTTTG 6 132 1 ATGGTATTGT 0.781467 -63 TTTCCGACTATTTGTATTGGTATTATGTAT 9 42 0 TTTGTATTGG 0.967169 -34 AGAGACGCTTTTTTTATTGGGTAGAGGAAA 10 255 1 TTTTTATTGG 0.889336 -46 CAAACCTTGATTGGTATTGGGTGAATGTGC 18 69 1 TTGGTATTGG 0.972659 -129 AGCGTTTTTTATTGTAATACCCTAC 23 6 1 TTTTTATTGT 0.795545 -68 ********** Masking position 6 Map Score: 4.63294 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 46 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 CCGGAAATTCTTTTCATAAACGAATATCAA 1 169 1 TTTTCATAAA 0.626294 -132 GAGCCAATCATTTACATAAAAAAACTGCCA 6 46 0 TTTACATAAA 0.821208 -149 AGCTGCGGCTTTTACAATCATCCAATTCTG 6 76 1 TTTACAATCA 0.677869 -119 TACTTTACTTTTTACAAACATTCTACAATA 6 146 0 TTTACAAACA 0.937253 -49 TTGACAAAAAATTTTGAAAT 9 1 1 TTGACAAAAA 0.649225 -75 AGAAGTCTGCTTTTCAAACAGAGTGGAACC 10 191 1 TTTTCAAACA 0.841637 -110 CTCTGTCATGTTTACATGCAGAGACGCTTT 10 236 1 TTTACATGCA 0.851625 -65 TGCGAGAGTGTTTTCATACACTGTTCCTCT 16 70 0 TTTTCATACA 0.841518 -79 CTTTTTTCTATTTACATGAAGCATAGCCGT 17 29 1 TTTACATGAA 0.649103 -142 CAGAAAATAGTTGACAAACATAGATGAAAT 18 166 0 TTGACAAACA 0.851629 -32 GTCAGAAAATTTAACAAACATAAAAGGGAG 19 159 1 TTAACAAACA 0.677869 -28 ACTCACTCCTTTATATACACCTGGGGGGT 22 62 0 TTTATATACA 0.51323 -19 ********** Masking position 6 Map Score: 4.12051 Number of sites scoring better than the average of aligned sites = 593 Number in coding regions = 472 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 11 ATGGTGCAAACTGCAGAGCCTAT 4 4 1 GTGCAAACTG 0.980691 -100 AGATCACTCAGTGCAAGCTGATCCAGCTCT 11 202 0 GTGCAAGCTG 0.982087 -99 CATATGACTTGTGAAAGCTGGAGGGTCAAG 15 13 0 GTGAAAGCTG 0.948788 -180 CGATTTCGAAGTGAAATCGGTTTTTTTCTG 18 23 1 GTGAAATCGG 0.849194 -175 TAAATATATGATGCAAACTGGCAAATACAA 18 108 0 ATGCAAACTG 0.8871 -90 TATACTGATTGTCCAAACGGTTGTCTAAGC 24 74 0 GTCCAAACGG 0.906144 -54 ********** Masking position 5 Map Score: 0.713062 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 100 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 ********** No masking Map Score: 2.41828e-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 GAATATCAAGGCAGAAACCGTCGAAGATTTC 1 190 1 GCAGAAACCT 0.833266 -111 GGTGCAAACTGCAGAGCCTATGCTTCTTCTT 4 13 1 GCAGAGCCTT 0.960202 -91 TGTAAACATGACAGAGACGCTTTAACCGCGC 10 221 0 ACAGAGACGT 0.861624 -80 ATGTTTACATGCAGAGACGCTTTTTTTATTG 10 243 1 GCAGAGACGT 0.982382 -58 TTCTTCGTGTGCCGAACCGTTTAAAGAGAGA 12 28 0 GCCGAACCGT 0.901792 -273 TCCTCTATCCGCACAGCCTCTTTATTGATAA 16 45 0 GCACAGCCTT 0.910562 -104 AAACACTCTCGCACAAACGTTTATTATGTTA 16 87 1 GCACAAACGT 0.901934 -62 TTTACATGAAGCATAGCCGTTTTATCATTAG 17 39 1 GCATAGCCGT 0.931892 -132 ********* * Masking position 5 Map Score: 1.35888 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 282 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 14 TCTCAAATTAAAAACCCGCTAAAGAGC 8 8 0 AAAACCCGCT 0.865735 -39 TACTGATTTCAAAAAACGTTCTTCAAAGGT 10 118 0 AAAAAACGTT 0.906378 -183 TTCCAAGCATAAAAAACGCTTGCTGGATTT 12 206 0 AAAAAACGCT 0.961191 -95 GGGAAACAACAGAAAACTCTTTAAATAAAA 13 195 0 AGAAAACTCT 0.719995 -106 AGCAGGTACTAAAACACTTTGTGTATTTTA 15 86 0 AAAACACTTT 0.787647 -107 ACAGTGTATGAAAACACTCTCGCACAAACG 16 76 1 AAAACACTCT 0.904664 -73 ATCCTAACATAATAAACGTTTGTGCGAGAG 16 92 0 AATAAACGTT 0.634363 -57 GTATTACAATAAAAAACGCT 23 1 0 AAAAAACGCT 0.961191 -73 ********** Masking position 4 Map Score: 1.76333 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 270 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 15 ********** No masking Map Score: 2.41828e-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