AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00920_ecoli_reg_300.orf -o00920_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 cysZ 229 required for sulfate transport #2 cysK 184 cysteine synthase A, O-acetylserine sulfhydrolase A #3 yfeK 104 orf, hypothetical protein #4 b2420 32 orf, hypothetical protein #5 cysM 23 cysteine synthase B, O-acetylserine sulfhydrolase B #6 BIME116 74 BIME #7 cysW 300 sulfate transport system permease W protein #8 cysD 251 ATP:sulfurylase (ATP:sulfate adenylyltransferase), subunit 2 #9 cysH 21 3'-phosphoadenosine 5'-phosphosulfate reductase #10 cysJ 300 sulfite reductase (NADPH), flavoprotein beta subunit #11 metC 103 cystathionine beta-lyase (beta-cystathionase) #12 cysE 79 serine acetyltransferase #13 secB 62 protein export; molecular chaperone; may bind to signel sequence #14 grxC 141 glutaredoxin 3 #15 yibN 244 orf, hypothetical protein #16 metB 276 cystathionine gamma-synthase #17 metA 156 homoserine transsuccinylase Motif number 1 TAACACCTTGCCACCACGGCAAACATTTACTC 1 28 1 CCACCGGCAA 0.966238 -202 TGCAGCATGTCCGGATCGGCCAGATTCTGTAA 7 44 0 CCGGCGGCCA 0.948527 -257 ATCCGGACATGCTGCACGCCATCTGGCTGACG 7 60 1 GCTGCGCCAT 0.690653 -241 ACCAGGTTTACCGGTACGGCAATCAGCGCGAT 7 98 0 CCGGCGGCAA 0.993581 -203 GCGTCACCAGCCAGGCCAGCAGAATGCCGAAC 7 130 0 CCAGCAGCAG 0.907227 -171 GGAAGTTAAAGCGCGTCACCAGCCAGGCCAGC 7 142 0 GCGCCACCAG 0.635488 -159 CTTTAACTTCCCTGGACGCCAGTTACTGCTGA 7 163 1 CCTGCGCCAG 0.957327 -138 GCAACCACCGGCGATACGGCAAACGGAATGTC 7 203 0 GCGACGGCAA 0.900857 -98 AGCAAATACACCAGACCGGCAACCACCGGCGA 7 221 0 CCAGCGGCAA 0.988133 -80 CAACCGCCGAGCGGGCCGTTAGAGCCGTAGAA 7 254 0 GCGGCGTTAG 0.900249 -47 AATTGTTTTAGCGCAGCGGCAGTTTCATACTA 8 50 0 GCGCCGGCAG 0.983534 -202 CTTTCATGATGCAGGCCGTTAGCTGCAATTAG 14 23 1 GCAGCGTTAG 0.829188 -119 ATTTCATGTTGCAGGGCGGCAGCAAAATGGAG 14 92 0 GCAGCGGCAG 0.989418 -50 GCAAATACAGCCAGCGCGTTAACTGGAATGCA 15 158 0 CCAGCGTTAA 0.812133 -87 GTATACCTGCGCGGTGCGGCAAATACAGCCAG 15 176 0 GCGGCGGCAA 0.992803 -69 GATACTTAATCCTCTTCGTCAATAAATTGAGA 16 13 1 CCTCCGTCAA 0.835194 -264 CACGGTAACGCCTGTACGGTAAACTATGCGGG 16 81 0 CCTGCGGTAA 0.919291 -196 **** ****** Masking position 7 Map Score: 24.8427 Number of sites scoring better than the average of aligned sites = 3185 Number in coding regions = 3089 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 2 AGGATATGTTCGAAAAAACAGCAAAAAGCACG 1 132 0 CGAAAAAAGC 0.993915 -98 ACAAACCTTGCCATTAAAAAGCCCGGATCGCG 6 48 0 CCATAAAAGC 0.915724 -27 CATCTGATGGCAAGAAAATAGCGGTATTGCAA 8 220 1 CAAAAAAAGC 0.978051 -32 CGATAAAACCGCCGTAGAGTAC 10 1 1 CGAAAAACGC 0.974467 -300 TTAGATAATGCGAAAAAACAGCCTTTCCGGTA 10 30 0 CGAAAAAAGC 0.993915 -271 TAGTCTTTAACAACAAAATAGATTAACCAACC 10 129 0 CAAAAAAAGA 0.897693 -172 CTGTCAGCGCCCATAAAACAGAAGAGAAGGTA 10 240 0 CCAAAAAAGA 0.931378 -61 ACAGCTGAATCGATAAAATAGCCTCTGAAGAT 15 56 1 CGAAAAAAGC 0.993915 -189 CGGGGCGCGACGAAAAAAAAGCGTAAATCTGG 15 120 0 CGAAAAAAGC 0.993915 -125 *** **** *** Masking position 6 Map Score: 16.3469 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 58 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 ACCAATCCCAGGAAAATTCTGCGTATTTTACCGG 1 185 0 GGAAAATGGT 0.948664 -45 GCCAGAATCAGGTAAAGTTTCGGTTGGATTACGA 3 41 0 GGTAAATCGT 0.967123 -64 TTGCCGTACCGGTAAACCTGGTGTTCGGCATTCT 7 108 1 GGTAAAGGGT 0.904817 -193 CCGGCGATACGGCAAACGGAATGTCCAGTAGCGT 7 194 0 GGCAAAAAGT 0.74929 -107 AAGGCAAACAGTGAGGAATCT 9 3 1 GGCAAATGGG 0.989428 -19 AGGTTAACGGGGCAAACGGTGTGGATTAAAGACG 10 206 0 GGCAAATGGG 0.989428 -95 GAAATTTCAGGGTAAAAAAACAGGAGCTAATTT 14 119 1 GGTAAAACGG 0.901048 -23 ATACTCAAGAGTCAAAATTTGCGTAATTTTACTA 15 23 1 GTCAAATGGT 0.81691 -222 ACGCCTGTACGGTAAACTATGCGGGTTTACGGTC 16 72 0 GGTAAATGGG 0.985864 -205 CAGGCACCAGAGTAAACATTGTGTTAATGGACGT 16 218 0 AGTAAATGGT 0.768775 -59 GGGCTTTGTCGGTGAAATGTCAGGCACCAGAGTA 16 238 0 GGTGAATCGG 0.86505 -39 AAAGTTTCAAGGAAAAGACTACGTTAGAATATAA 17 32 0 GGAAAATAGT 0.784429 -125 GCTCGACATTGGCAAATTTTCTGGTTATCTTCAG 17 84 1 GGCAAATCGG 0.981995 -73 ****** ** ** Masking position 6 Map Score: 12.2818 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 442 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 4 TATATTCTCTGTTGTTCTAACACCTTGCCA 1 8 1 TCTGTTCTAA 0.880763 -222 TTTACCTGATTCTGGCAGTCAAATCGGCTATCA 3 59 1 TCTGGTCAAA 0.954299 -46 GGGAAGCGCCTCCGGGCGTTTAACATTCACTCA 6 16 0 TCCGGTTTAA 0.944522 -59 CTTCCCGCGATCCGGGCTTTTTAATGGCAAGGT 6 43 1 TCCGGTTTTA 0.792296 -32 ACGCCCGAAATCCGGTGCCTTAAGCACTTTTTG 8 96 1 TCCGGCTTAA 0.855081 -156 AAACAGCCTTTCCGGTACTCTACGGCGGTTTTA 10 14 0 TCCGGTCTAC 0.963936 -287 TTTTTATACGTCTGGATGTCTAAACTAGCATGA 11 68 0 TCTGGTCTAA 0.989436 -36 ACAATAAGTCGCTGGGGGCCTAATTGCAGCTAA 14 41 0 GCTGGCCTAA 0.847932 -101 TAAAATAGCCTCTGAAGATCAAAATATACGACC 15 69 1 TCTGATCAAA 0.622874 -176 CGTCAATACATCTGGACATCTAAACTTCTTTGC 16 188 0 TCTGGTCTAA 0.989436 -89 TGGCAAATTTTCTGGTTATCTTCAGCTATCTGG 17 93 1 TCTGGTCTTC 0.879221 -64 TCTTCAGCTATCTGGATGTCTAAACGTATAAGC 17 111 1 TCTGGTCTAA 0.989436 -46 ***** ***** Masking position 2 Map Score: 12.3865 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 148 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 TCCGCATATTCTCTGAGCGGGTATGCTACCT 2 129 1 CTCGAGCGGG 0.898306 -56 AAGCCCGGATCGCGGGAAGCGCCTCCGGGCG 6 31 0 CGCGGAAGCG 0.642975 -44 GTGCAGGCATTCAGCAAGGGGCTGATGCCG 7 10 1 TTCGCAAGGG 0.626005 -291 GATCCGGACATGCTGCACGCCATCTGGCTGA 7 59 1 TGCGCACGCC 0.73808 -242 TTCGGCATTCTGCTGGCCTGGCTGGTGACGC 7 131 1 TGCGGCCTGG 0.811184 -170 TCGAGCCAACCGCCGAGCGGGCCGTTAGAGC 7 261 0 CGCGAGCGGG 0.984504 -40 GTTTTATGGGCGCTGACAGGGCGCAGAAACA 10 253 1 CGCGACAGGG 0.944143 -48 GCCCGTTCTGCGCGGGCCGGGTCATAGCGGT 12 29 0 CGCGGCCGGG 0.650877 -51 AATTTCATGTTGCAGGGCGGCAGCAAAATGG 14 94 0 TGCGGGCGGC 0.938403 -48 GGCATCGGCTTGCCGCGAGCGGTCGTATATT 15 91 0 TGCGCGAGCG 0.953745 -154 AATGCAATTTTGCGGGGCGCGACGAAAAAAA 15 133 0 TGCGGGCGCG 0.964958 -112 GTGCGGCAAATACAGCCAGCGCGTTAACTGG 15 164 0 TACGCCAGCG 0.706856 -81 GTATTTGCCGCACCGCGCAGGTATACTCCTT 15 182 1 CACGCGCAGG 0.53341 -63 TGCATTATCACGCCGACAGGTGCATTACACG 16 117 0 CGCGACAGGT 0.643641 -160 *** ******* Masking position 3 Map Score: 10.1957 Number of sites scoring better than the average of aligned sites = 4243 Number in coding regions = 4030 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 6 AATCAGGATGAGCTCCTTTTGACCAATCC 1 211 0 TGACTCCTTT 0.853754 -19 ATGTCATTATTTCCCTTCTGTATATAGATAT 2 84 1 TTCCTTCTGT 0.925025 -101 TTAATTTTTTCTCCTTGCCGATGATCC 3 7 1 TTTCTCCTTG 0.840213 -98 GTTACCTCCTGTAAATGCCTTC 4 21 0 TTACTCCTGT 0.967208 -12 TAACCTTACCTTCTCTTCTGTTTTATGGGCG 10 234 1 TTCCTTCTGT 0.925025 -67 TTTGCGAAAATTTTCTGCTTTATGCCAATTC 11 15 1 TTTCTGCTTT 0.724814 -89 CTTATTGTTATAAGCTTCTGGGGACACTCCA 14 66 1 TAACTTCTGG 0.686275 -76 AAATTAGCTCCTGTTTTTTTACCC 14 128 0 TTACTCCTGT 0.967208 -14 ACCGCGCAGGTATACTCCTTTCCTGGTTTTT 15 193 1 TATCTCCTTT 0.861183 -52 TCTGGACATCTAAACTTCTTTGCGTATAGAT 16 180 0 TAACTTCTTT 0.809421 -97 TTTCTCTCCTTTTAGTCATTCT 17 2 1 TTCCTCCTTT 0.955641 -155 *** ******* Masking position 6 Map Score: 6.09471 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 126 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 7 TACCTGATTCTGGCAGTCAAATCGGCTATCACA 3 61 1 TGGCGTCAAC 0.98287 -44 CTGGCGTCCAGGGAAGTTAAAGCGCGTCACCAG 7 152 0 GGGAGTTAAC 0.89875 -149 TTTATACGTCTGGATGTCTAAACTAGCATGAAT 11 66 0 TGGAGTCAAC 0.993668 -38 TCAATACATCTGGACATCTAAACTTCTTTGCGT 16 186 0 TGGAATCAAC 0.960437 -91 ATTGTGTTAATGGACGTCAATACATCTGGACAT 16 202 0 TGGAGTCATC 0.97482 -75 TTCAGCTATCTGGATGTCTAAACGTATAAGCGT 17 113 1 TGGAGTCAAC 0.993668 -44 **** *** ** * Masking position 7 Map Score: 4.14351 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 21 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 TTTACCGGGTAATTGCGCAATGGACAGTTA 1 163 0 AATTGCGCAA 0.956236 -67 CTGTATATAGATATGCTAAATCCTTACTTC 2 101 1 ATATGCTAAA 0.748984 -84 CGCTCAGAGAATATGCGGAAGTAAGGATTT 2 118 0 ATATGCGGAA 0.826537 -67 TCGTTTTAGATAATGCGAAAAAACAGCCTT 10 37 0 TAATGCGAAA 0.831445 -264 AAATCAGCGATTTTGCGCAACAAAGTCGTT 10 62 0 TTTTGCGCAA 0.955722 -239 TGTTAAAGACTATTGCTAAAACAGGTTAGT 10 149 1 TATTGCTAAA 0.726153 -152 GCCATTTGCGAAAATTTTCTGCT 11 4 1 ATTTGCGAAA 0.952445 -100 TGTCCTTAAATACTGCGCAATGTAATGCCA 13 22 0 TACTGCGCAA 0.821174 -41 AAGAGTCAAAATTTGCGTAATTTTACTACA 15 29 1 ATTTGCGTAA 0.859596 -216 GCTATTTGGGATTTGCTCAATCTATACGCA 16 161 1 ATTTGCTCAA 0.900244 -116 ********** Masking position 4 Map Score: 4.18945 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 374 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 9 AATCAGGATGAGCTCCTTTTGAC 1 217 0 ATCAGGAAGC 0.85836 -13 GCAAGATGGAATAAGGGGCGGCATAAGCCACC 2 52 0 ATAAGGGGGC 0.887492 -133 CAGAAGGGAAATAATGACATGCAAGATGGAAT 2 72 0 ATAATGATGC 0.85746 -113 TTTCATACAGTTAAGGACAGGCC 2 172 1 TTAAGGAGGC 0.972413 -13 AATCTGGCCGATCCGGACATGCTGCACGCCAT 7 50 1 ATCCGGATGC 0.742508 -251 TGCATGGTATTTAAGGACTCACT 8 2 0 TTAAGGACAC 0.786523 -250 CGTTATTCCGTTAAGGAACTACTCATTCTAAT 8 147 1 TTAAGGATAC 0.773397 -105 CTGATTTATCTTAATGATTGGCTAAATTCATT 10 85 1 TTAATGAGGC 0.928318 -216 ATGCCAATTCTTCAGGATGCGCCCGCGAATAT 11 36 1 TTCAGGACGC 0.932931 -68 ACACGATGAGATAATGACCGGCCCGTTCTGCG 12 48 0 ATAATGAGGC 0.938985 -32 AACGGCCTGCATCATGAAAGACGACAGGTAAA 14 11 0 ATCATGAGAC 0.780944 -131 ******* *** Masking position 2 Map Score: 3.72429 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 376 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 10 AAAGCCCGGATCGCGGGAAGCGCCTCCGGG 6 33 0 TCGCGGGAAG 0.877205 -42 GTAACTGGCGTCCAGGGAAGTTAAAGCGCG 7 159 0 TCCAGGGAAG 0.962687 -142 ACACCGTTTGCCCCGTTAACCTTACCTTCT 10 218 1 CCCCGTTAAC 0.921733 -83 CCCCAGGGAACCTTTGTTACC 12 2 1 CCCAGGGAAC 0.986637 -78 AAAATTGCATTCCAGTTAACGCGCTGGCTG 15 153 1 TCCAGTTAAC 0.889817 -92 TTACACGATGTCACGGTAACGCCTGTACGG 16 94 0 TCACGGTAAC 0.846873 -183 ACCGACAAAGCCCAGGGAACTTCATCAC 16 259 1 CCCAGGGAAC 0.986637 -18 ********** Masking position 8 Map Score: 2.4481 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 211 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 CTAAGAGTATTTGCCGATTACCTCAAGTGC 1 61 1 TTGCCGATTA 0.934014 -169 CAATCTACCGGTTATTTTGTAAAC 2 5 1 CTACCGGTTA 0.696037 -180 TTTTTTCTCCTTGCCGATGATCCTCATCGT 3 15 1 TTGCCGATGA 0.973061 -90 CGCCATCTGGCTGACGGTGATGATCGCGCT 7 76 1 CTGACGGTGA 0.962183 -225 AATTTGCAGGTTATGCTCGTCGA 7 288 0 TTGCAGGTTA 0.892426 -13 TCTCAATTTATTGACGAAGAGGATTAAGTA 16 15 0 TTGACGAAGA 0.758891 -262 TCCCTGGGCTTTGTCGGTGAAATGTCAGGC 16 247 0 TTGTCGGTGA 0.946538 -30 AGCCTGCATGTTGAAGGTGAGAAAGTTTCA 17 57 0 TTGAAGGTGA 0.911325 -100 ********** Masking position 10 Map Score: 1.66586 Number of sites scoring better than the average of aligned sites = 1233 Number in coding regions = 1163 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 12 CCGGAGGCGCTTCCCGCGATCCGGGCTTTT 6 34 1 TTCCCGCGAT 0.954592 -41 GCAAATTTTTTTACCGCCATAGTATGAAAC 8 31 1 TTACCGCCAT 0.979137 -221 TTCCTTTGCAATACCGCTATTTTCTTGCCA 8 227 0 ATACCGCTAT 0.924705 -25 TGGTTATTAGTTATCGCTATCCCGTCTTTA 10 184 1 TTATCGCTAT 0.93702 -117 GGAACCTTTGTTACCGCTATGACCCGGCCC 12 17 1 TTACCGCTAT 0.98542 -63 ********** Masking position 2 Map Score: 1.9266 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 119 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 GAAGCGCCTCCGGGCGTTTAACATTCACTC 6 17 0 CGGGCGTTTA 0.992374 -58 TCCCGCGATCCGGGCTTTTTAATGGCAAGG 6 45 1 CGGGCTTTTT 0.883445 -30 AACCGCCGAGCGGGCCGTTAGAGCCGTAGA 7 255 0 CGGGCCGTTA 0.943343 -46 CACCGGATTTCGGGCGTTTAGGAAGATTTG 8 83 0 CGGGCGTTTA 0.992374 -169 TGAATATTCGCGGGCGCATCCTGAAGAATT 11 41 0 CGGGCGCATC 0.934013 -63 TTGCCGCGAGCGGTCGTATATTTTGATCTT 15 83 0 CGGTCGTATA 0.915185 -162 ********** Masking position 9 Map Score: 1.78322 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 220 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 14 TCTGGCAGTCAAATCGGCTATCACAAAACAAG 3 69 1 AAATCGCATC 0.971529 -36 CAGATTCTGTAAAACCGGCATCAGCCCCTTGC 7 24 0 AAAACGGATC 0.969224 -277 GTTCCTTTGCAATACCGCTATTTTCTTGCCAT 8 226 0 AATACGCATT 0.755933 -26 ATAATGCGAAAAAACAGCCTTTCCGGTACTCT 10 26 0 AAAACGCTTT 0.81703 -275 TCATTAAGATAAATCAGCGATTTTGCGCAACA 10 70 0 AAATCGCATT 0.942934 -231 CAGACGTATAAAAACAGGAATCCCGAC 11 87 1 AAAACGGATC 0.970718 -17 AAAAAAGCGTAAATCTGGCATCGGCTTGCCGC 15 106 0 AAATCGGATC 0.962906 -139 ***** ** *** Masking position 2 Map Score: 2.22215 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 190 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 15 ATATAGATATGCTAAATCCTTACTTCCGCATA 2 105 1 GCTAATCTTA 0.938827 -80 CTGCCGCTGCGCTAAAACAATTTCAAATCTTC 8 60 1 GCTAAACATT 0.882529 -192 TATTAGCTTTGCCAAATCGTTATTCCGTTAAG 8 130 1 GCCAATCTTA 0.803005 -122 TTAATGATTGGCTAAATTCATTTGTTTTTCAT 10 95 1 GCTAATTATT 0.82398 -206 TCATTAGGTTGGTTAATCTATTTTGTTGTTAA 10 123 1 GGTAATCATT 0.936836 -178 TGCTAAAACAGGTTAGTCGATTTGGTTATTAG 10 162 1 GGTAGTCATT 0.797548 -139 TTTTACTACAGCTGAATCGATAAAATAGCCTC 15 49 1 GCTAATCATA 0.976702 -196 TTTGGGATTTGCTCAATCTATACGCAAAGAAG 16 165 1 GCTAATCATA 0.976702 -112 *** **** *** Masking position 5 Map Score: 0.380051 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 151 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282