AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00920_ecoli_reg_100.orf -o00920_ecoli_100.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 cysK 184 cysteine synthase A, O-acetylserine sulfhydrolase A #2 yfeK 104 orf, hypothetical protein #3 b2420 32 orf, hypothetical protein #4 cysM 23 cysteine synthase B, O-acetylserine sulfhydrolase B #5 BIME116 74 BIME #6 cysW 300 sulfate transport system permease W protein #7 cysD 251 ATP:sulfurylase (ATP:sulfate adenylyltransferase), subunit 2 #8 cysH 21 3'-phosphoadenosine 5'-phosphosulfate reductase #9 cysJ 300 sulfite reductase (NADPH), flavoprotein beta subunit #10 metC 103 cystathionine beta-lyase (beta-cystathionase) #11 cysE 79 serine acetyltransferase #12 secB 62 protein export; molecular chaperone; may bind to signel sequence #13 grxC 141 glutaredoxin 3 #14 metB 276 cystathionine gamma-synthase #15 metA 156 homoserine transsuccinylase Motif number 1 TGTTGTATCCCAATTTCATACAGTTAAGGACAGGCC 1 159 1 CACTAGGAGC 0.968163 -26 CCTTGCCATTAAAAAGCCCGGATCGCGGGAAGCGCCTCCGGGCGT 5 30 0 AACCATGGGC 0.846857 -45 GCCGGTTTTACAGAATCTGGCCGATCCGGACATGCTGCACGCCAT 6 37 1 CACGCGGAGC 0.983316 -264 GCTGCACGCCATCTGGCTGACGGTGATGATCGCGCTGATTGCCGT 6 70 1 ATCGGGGGGC 0.864561 -231 GGTGTTCGGCATTCTGCTGGCCTGGCTGGTGACGCGCTTTAACTT 6 127 1 ATCGCTGAGC 0.861693 -174 CGTCAGCAGTAACTGGCGTCCAGGGAAGTTAAAGCGCGTCACCAG 6 152 0 AACTAGGAGC 0.985093 -149 CTCGTCGAGCCAACCGCCGAGCGGGCCGTTAGAGCCGTAGAACAG 6 251 0 CACGCGGGGC 0.987868 -50 CGATAAAACCGCCGTAGAGTACCGGAAAGGCTGTTTTTTCG 9 7 1 AACTAGGAGC 0.985093 -294 TGGATGTCTAAACTAGCATGAATATTCGCGGGCGCATCCTGAAGA 10 44 0 AACTATGGGC 0.959461 -60 ACGATGAGATAATGACCGGCCCGTTCTGCGCGGGCCGGGTCATAG 11 33 0 AACGCGGGGC 0.99438 -47 TTTTACCCTGAAATTTCATGTTGCAGGGCGGCAGCAAAATGGAGT 13 91 0 AACTTGGCGC 0.884199 -51 ACTGACCGTAAACCCGCATAGTTTACCGTACAGGCGTTACCGTGA 14 69 1 AACTTTGAGC 0.88169 -208 GACATCGTGTAATGCACCTGTCGGCGTGATAATGCATATAATTTT 14 112 1 AACTCGGAGC 0.992106 -165 CTGGACATCTAAACTTCTTTGCGTATAGATTGAGCAAATCCCAAA 14 165 0 AACTCGGGGC 0.994274 -112 ** * * ** * * ** Masking position 7 Map Score: 18.1672 Number of sites scoring better than the average of aligned sites = 710 Number in coding regions = 663 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 CTTTACCTGATTCTGGCAGTCAAATCGGCTATCA 2 58 1 TCGCGTCAAA 0.914658 -47 GGGAAGCGCCTCCGGGCGTTTAACATTCACTCAA 5 15 0 TCGCTTTAAC 0.956888 -60 CTTCCCGCGATCCGGGCTTTTTAATGGCAAGGTT 5 43 1 TCGCTTTTAA 0.614402 -32 GTGCAGGCATTCAGCAAGGGGCTGA 6 2 1 TCGCTTCAGC 0.984709 -299 ATCTGGCCGATCCGGACATGCTGCACGCCATCTG 6 51 1 TCGCTGCTGC 0.909939 -250 ATCAGCGCGATCATCACCGTCAGCCAGATGGCGT 6 75 0 TACCGTCAGC 0.761206 -226 CAGCAAATACACCAGACCGGCAACCACCGGCGAT 6 220 0 ACGCGGCAAC 0.779447 -81 CCAACCGCCGAGCGGGCCGTTAGAGCCGTAGAAC 6 253 0 ACGCGTTAGA 0.6447 -48 GGCACCGGATTTCGGGCGTTTAGGAAGATTTGAA 7 81 0 TCGCTTTAGG 0.877974 -171 AGATTCCTCACTGTTTGCCTT 8 4 0 TCCCGTTTGC 0.945184 -18 CCGTCTTTAATCCACACCGTTTGCCCCGTTAACC 9 205 1 TCCCGTTTGC 0.945184 -96 AAGCTGTTTCTGCGCCCTGTCAGCGCCCATAAAA 9 254 0 TCCCGTCAGC 0.984681 -47 TCTTTCATGATGCAGGCCGTTAGCTGCAATTAGG 13 22 1 TCGCGTTAGC 0.98635 -120 TCCATTTTGCTGCCGCCCTGCAACATGAAATTTC 13 93 1 TCGCTGCAAC 0.928475 -49 TTGATGTGGGTACTGACCGTAAACCCGCATAGTT 14 58 1 TCGCGTAAAC 0.863263 -219 TTTCTCTCCTTTTAGTCATTCTTAT 15 2 1 TCCCTTTTAG 0.48757 -155 CCTTGAAACTTTCTCACCTTCAACATGCAGGCTC 15 54 1 TCCCTTCAAC 0.951791 -103 * * * * ****** Masking position 7 Map Score: 15.8013 Number of sites scoring better than the average of aligned sites = 2392 Number in coding regions = 2272 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 3 ATGCGGAAGTAAGGATTTAGCATATCTATATACAGA 1 100 0 AGATTTGCAC 0.986403 -85 ATACCCGCTCAGAGAATATGCGGAAGTAAGGATTTA 1 117 0 AGAATAGCAG 0.875415 -68 AAGATTTGAAATTGTTTTAGCGCAGCGGCAGTTTCA 7 55 0 AGTTTTGCAC 0.970458 -197 TTAACGGAATAACGATTTGGCAAAGCTAATATCAAA 7 125 0 AGATTTGCAC 0.986403 -127 AAGATAAATCAGCGATTTTGCGCAACAAAGTCGTTT 9 61 0 AGATTTGCAC 0.986403 -240 TGAAAAACAAATGAATTTAGCCAATCATTAAGATAA 9 90 0 AAATTTGCAC 0.953423 -211 CATAAAGCAGAAAATTTTCGCAAATGGC 10 3 0 AATTTTGCAG 0.862524 -101 TTCTTTGCGTATAGATTGAGCAAATCCCAAATAGCC 14 160 0 AGATTGGCAC 0.950663 -117 GAAGATAACCAGAAAATTTGCCAATGTCGAGCCTGC 15 80 0 AAAATTGCAG 0.862524 -77 TGGATGTCTAAACGTATAAGCGTATGTAGTGAGGTA 15 123 1 AGTATAGCAG 0.760863 -34 * ***** ** * * Masking position 7 Map Score: 8.71585 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 148 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 ATAAGCCACCCCTGTTTCACACAAACGGTT 1 32 0 CCTGTTTCAC 0.940689 -153 GGGTATGCTACCTGTTGTATCCCAATTTCA 1 147 1 CCTGTTGTAT 0.841235 -38 CGAAACTTTACCTGATTCTGGCAGTCAAAT 2 53 1 CCTGATTCTG 0.629287 -52 GGGGCTGATGCCGGTTTTACAGAATCTGGC 6 28 1 CCGGTTTTAC 0.883134 -273 TGGTGTATTTGCTGTTCTACGGCTCTAACG 6 240 1 GCTGTTCTAC 0.764591 -61 TAGCGCAGCGGCAGTTTCATACTATGGCGG 7 44 0 GCAGTTTCAT 0.689563 -208 GTACTCTACGGCGGTTTTATCG 9 3 0 GCGGTTTTAT 0.901354 -298 TACCGGAAAGGCTGTTTTTTCGCATTATCT 9 30 1 GCTGTTTTTT 0.942843 -271 GCGCAAAATCGCTGATTTATCTTAATGATT 9 74 1 GCTGATTTAT 0.844413 -227 AATCGACTAACCTGTTTTAGCAATAGTCTT 9 154 0 CCTGTTTTAG 0.95987 -147 TACCTTCTCTTCTGTTTTATGGGCGCTGAC 9 240 1 TCTGTTTTAT 0.789539 -61 AGTAAGCAAAGCTGTTTCTGCGCCCTGTCA 9 266 0 GCTGTTTCTG 0.886207 -35 GTCGGGATTCCTGTTTTTATACGTCTGGA 10 85 0 CCTGTTTTTA 0.774456 -19 AAATTAGCTCCTGTTTTTTTACCCTGAAA 13 123 0 CCTGTTTTTT 0.950399 -19 ********** Masking position 6 Map Score: 8.50733 Number of sites scoring better than the average of aligned sites = 762 Number in coding regions = 657 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 5 AGGCGCTTCCCGCGATCCGGGCTTTTTAAT 5 38 1 CGCGATCCGG 0.975116 -37 ACAGAATCTGGCCGATCCGGACATGCTGCA 6 46 1 GCCGATCCGG 0.989841 -255 ACATGCTGCACGCCATCTGGCTGACGGTGA 6 66 1 CGCCATCTGG 0.742655 -235 CACCAGGTTTACCGGTACGGCAATCAGCGC 6 101 0 ACCGGTACGG 0.856848 -200 CATTCTGCTGGCCTGGCTGGTGACGCGCTT 6 136 1 GCCTGGCTGG 0.93091 -165 GGCAACCACCGGCGATACGGCAAACGGAAT 6 206 0 GGCGATACGG 0.952075 -95 GCCGGTGGTTGCCGGTCTGGTGTATTTGCT 6 223 1 GCCGGTCTGG 0.979225 -78 CGAGCCAACCGCCGAGCGGGCCGTTAGAGC 6 261 0 GCCGAGCGGG 0.89265 -40 CGAAAAAACAGCCTTTCCGGTACTCTACGG 9 22 0 GCCTTTCCGG 0.890879 -279 TATTAGTTATCGCTATCCCGTCTTTAATCC 9 188 1 CGCTATCCCG 0.688691 -113 GCCCGTTCTGCGCGGGCCGGGTCATAGCGG 11 30 0 CGCGGGCCGG 0.976307 -50 GCCCGCGCAGAACGGGCCGGTCATTATCTC 11 43 1 AACGGGCCGG 0.690279 -37 TCACGGTAACGCCTGTACGGTAAACTATGC 14 84 0 GCCTGTACGG 0.919429 -193 TAATTTTAACGGCTATTTGGGATTTGCTCA 14 150 1 GGCTATTTGG 0.568227 -127 GGTTATCTTCAGCTATCTGGATGTCTAAAC 15 106 1 AGCTATCTGG 0.819588 -51 ********** Masking position 3 Map Score: 14.9141 Number of sites scoring better than the average of aligned sites = 3271 Number in coding regions = 3107 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 6 GGAATAAGGGGCGGCATAAGCCACCCCTGT 1 47 0 GCGGCATAAG 0.946203 -138 TTCTGTAAAACCGGCATCAGCCCCTTGCTG 6 22 0 CCGGCATCAG 0.982789 -279 AAGTTAAAGCGCGTCACCAGCCAGGCCAGC 6 142 0 GCGTCACCAG 0.982821 -159 ATGTCCAGTAGCGTCAGCAGTAACTGGCGT 6 178 0 GCGTCAGCAG 0.988144 -123 TTGTTTTAGCGCAGCGGCAGTTTCATACTA 7 50 0 GCAGCGGCAG 0.924205 -202 ATGTTGCAGGGCGGCAGCAAAATGGAGTGT 13 89 0 GCGGCAGCAA 0.975387 -53 GGTGAAATGTCAGGCACCAGAGTAAACATT 14 232 0 CAGGCACCAG 0.919012 -45 ********** Masking position 9 Map Score: 4.53165 Number of sites scoring better than the average of aligned sites = 1756 Number in coding regions = 1693 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 7 TTATACGTCTGGATGTCTAAACTAGCATGAAT 10 66 0 GGATTCTAAC 0.99236 -38 AACACTTAAGGGTTTTCTACAC 12 51 1 GGTTTCTAAC 0.975326 -12 CAATACATCTGGACATCTAAACTTCTTTGCGT 14 186 0 GGACTCTAAC 0.992921 -91 TTGTGTTAATGGACGTCAATACATCTGGACAT 14 202 0 GGACTCAAAC 0.977111 -75 TCAGCTATCTGGATGTCTAAACGTATAAGCGT 15 114 1 GGATTCTAAC 0.99236 -43 **** **** ** Masking position 6 Map Score: 4.1677 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 6 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 CTTCCGCATATTCTCTGAGCGGGTATGCTA 1 127 1 TTCTCTGAGC 0.923668 -58 GCGCTTTAACTTCCCTGGACGCCAGTTACT 6 160 1 TTCCCTGGAC 0.976938 -141 GTAACAAAGGTTCCCTGGGG 11 1 0 TTCCCTGGGG 0.994202 -79 ATAACAATAAGTCGCTGGGGGCCTAATTGC 13 47 0 GTCGCTGGGG 0.96659 -95 GTGATGAAGTTCCCTGGGCTTTGTCGGTG 14 258 0 TTCCCTGGGC 0.99587 -19 ********** Masking position 6 Map Score: 2.74531 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 58 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 CATCTTGCATGTCATTATTTCCCTTCTGTA 1 76 1 GTCATTATTT 0.783207 -109 GGCCTGTCCTTAACTGTATGAAATT 1 170 0 GTCCTTAACT 0.956901 -15 AGTGAGTCCTTAAATACCATGCAAA 7 6 1 GTCCTTAAAT 0.964004 -246 GAACGGGCCGGTCATTATCTCATCGTGTGG 11 52 1 GTCATTATCT 0.907868 -28 CTTAAGTGTTGTCCTTAAATACTGCGCAAT 12 31 0 GTCCTTAAAT 0.964004 -32 AATCCTCTTCGTCAATAAATTGAGACCAGA 14 20 1 GTCAATAAAT 0.906082 -257 GTTAATGGACGTCAATACATCTGGACATCT 14 200 0 GTCAATACAT 0.812947 -77 ********** Masking position 7 Map Score: 2.81522 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 36 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 ATGTCATTATTTCCCTTCTGTATATAGATA 1 84 1 TTCCCTTCTG 0.972658 -101 GTTACCTCCTGTAAATGCCTT 3 22 0 TTACCTCCTG 0.972658 -11 TAACCTTACCTTCTCTTCTGTTTTATGGGC 9 234 1 TTCTCTTCTG 0.970549 -67 CTTATTGTTATAAGCTTCTGGGGACACTCC 13 66 1 TAAGCTTCTG 0.859469 -76 AAATTAGCTCCTGTTTTTTTACC 13 129 0 TTAGCTCCTG 0.972658 -13 TTTCTCTCCTTTTAGTCATTC 15 2 1 TTCTCTCCTT 0.837712 -155 AATTTTCTGGTTATCTTCAGCTATCTGGAT 15 98 1 TTATCTTCAG 0.849972 -59 ********** Masking position 6 Map Score: 2.70311 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 111 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 GATGGAATAAGGGGCGGCATAAGCCACCCC 1 50 0 GGGGCGGCAT 0.883574 -135 ACAAAACAAGGATAAGGTAATTCA 2 91 1 GATAAGGTAA 0.816244 -14 TCCGCTTTGGGAAGGCATTTACAGGAGG 3 9 1 GGGAAGGCAT 0.942963 -24 CAGGTTTACCGGTACGGCAATCAGCGCGAT 6 98 0 GGTACGGCAA 0.981244 -203 CTGGCGTCCAGGGAAGTTAAAGCGCGTCAC 6 155 0 GGGAAGTTAA 0.839834 -146 AACCACCGGCGATACGGCAAACGGAATGTC 6 203 0 GATACGGCAA 0.944893 -98 TAAAACAGAAGAGAAGGTAAGGTTAACGGG 9 229 0 GAGAAGGTAA 0.897196 -72 CGGTAACGCCTGTACGGTAAACTATGCGGG 14 81 0 TGTACGGTAA 0.839834 -196 ATTGTGTTAATGGACGTCAATACATCTGGA 14 205 0 TGGACGTCAA 0.796195 -72 ********** Masking position 9 Map Score: 3.48395 Number of sites scoring better than the average of aligned sites = 945 Number in coding regions = 889 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 12 ********** No masking Map Score: -2.67631e-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: -2.67631e-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: -2.67631e-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