AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00480_ecoli_reg_100.orf -o00480_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 icdA 201 isocitrate dehydrogenase, specific for NADP+ #2 gst 105 glutathionine S-transferase #3 zwf 300 glucose-6-phosphate dehydrogenase #4 gshA 72 gamma-glutamate-cysteine ligase #5 yqaB 280 putative phosphatase #6 galP 300 galactose-proton symport of transport system #7 sprT 76 orf, hypothetical protein #8 endA 94 DNA-specific endonuclease I #9 yggJ 52 orf, hypothetical protein #10 ggt 119 gamma-glutamyltranspeptidase #11 yhiR 202 orf, hypothetical protein #12 gor 71 glutathione oxidoreductase Motif number 1 ATAACGCGCATCTTTCATGACGGCAAACAATAGGG 1 50 1 TCTCTCGGCA 0.910342 -152 GGTTTGCTCGTCTGCCACCACGTTGCATATGCGTT 1 154 0 TCTCCCGTTG 0.951696 -48 TTTACAAGCCGCTAACTTTTCGTTAGCGGCTTTTT 2 27 1 GCTCTCGTTA 0.984633 -79 GGTTAATACCGCTATCTCTTCGATACCTTCATTGC 5 29 0 GCTCCCGATA 0.987007 -252 TCGGGCCGTTGCTGGCGCAACGTTATCCTTCCTGG 5 71 0 GCTCCCGTTA 0.991861 -210 AAGCAATTACGCTAAAGTAGCGTCATATTTTTCGA 5 242 1 GCTATCGTCA 0.902264 -39 GCAAGAGGTGGCTTCCTCCGCGATGGGAGGAAGCT 7 19 0 GCTCCCGATG 0.98612 -58 TACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTT 8 53 1 GCTCCCGTTG 0.991302 -42 CTTTAAGTTTACTCGCTTCCCGACAAAACGATGAT 10 35 1 ACTCTCGACA 0.785494 -85 GAAACGTTACGCTTTCGCGGCGGCGGCCTCTTTTC 11 105 1 GCTCCCGGCG 0.990519 -98 TACGTCTCGCGCTACAATCGCGGTAATCAACGATA 12 34 1 GCTATCGGTA 0.906329 -38 *** * * ***** Masking position 3 Map Score: 13.3782 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 581 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 ACCACGTTGCATATGCGTTTGCGTCCTGCG 1 143 0 ATATGCGTTT 0.690845 -59 AGCGGCTTGTAAAAGAGTTTCCCTGAATT 2 10 0 AAAAGAGTTT 0.582532 -96 ATGCAGTTTTGTCAGATATTACGCCTGTGT 3 26 1 GTCAGATATT 0.612504 -275 CAACTTTTTTATCTGCTTTTGTCATTAACA 3 60 0 ATCTGCTTTT 0.690843 -241 CATGATCAGTGTCAGATTTTTACCCAATGG 3 106 1 GTCAGATTTT 0.854614 -195 TGATAAAAAAATCATCGTTTTCCATTGGGT 3 127 0 ATCATCGTTT 0.943621 -174 GCACGGGTGGATAAGCGTTTACAGTTTTCG 3 191 1 ATAAGCGTTT 0.927302 -110 CCCGCCTGTCAAAATCGTTTTAATTAGCAT 4 45 0 AAAATCGTTT 0.645453 -28 CTAAAGTAGCGTCATATTTTTCGACTTGCG 5 253 1 GTCATATTTT 0.762798 -28 ACAAAGATTTGTAATATTTTCATATTATTA 6 59 1 GTAATATTTT 0.574991 -242 AATTGCAGATAACAGCGTTTAATCTATGAT 6 131 1 AACAGCGTTT 0.890871 -170 GAGTTATATCATCATAGATTAAACGCTGTT 6 141 0 ATCATAGATT 0.654474 -160 AAATGTTAGTGTAAGCGATTACACTGATGT 6 205 1 GTAAGCGATT 0.789743 -96 ACCTCTTGCAGTCATCTTTTCTTCGCTCTA 7 45 1 GTCATCTTTT 0.884277 -32 CTCTGAATTAATCATCGTTTTGTCGGGAAG 10 50 0 ATCATCGTTT 0.943621 -70 ********** Masking position 9 Map Score: 9.55043 Number of sites scoring better than the average of aligned sites = 1816 Number in coding regions = 1654 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 3 TGCTCGTCTGCCACCACGTTGCATATGCGTT 1 154 0 CCACCACGTG 0.845442 -48 TCACCTCTCCTTCGAGCGCTACTG 1 188 0 CCTCTCCTCG 0.835332 -14 AAACGCTTATCCACCCGTGCGATTACGGGAA 3 180 0 CCACCCGTCG 0.936494 -121 ATTGACCTCCCGCCTGTCAAAATCGT 4 57 0 CCTCCCGCTG 0.984708 -16 GCAACGTTATCCTTCCTGGTGCCTGCGGTTA 5 59 0 CCTTCCTGTG 0.802602 -222 TGACGTTCGCCCTTCGGGCCGTTGCTGGCGC 5 88 0 CCTTCGGGCG 0.944688 -193 AGTGAGTCATCCTCCCGGATGCACCATCTTC 5 118 1 CCTCCCGGTG 0.937399 -163 GAGGTGGCTTCCTCCGCGATGGGAGGAAGCT 7 19 0 CCTCCGCGTG 0.983292 -58 TTTGTTAACCCCTACCCCACGCGTACAACCG 9 31 1 CCTACCCCCG 0.935927 -22 CGAAAAGAGGCCGCCGCCGCGAAAGCGTAAC 11 110 0 CCGCCGCCCG 0.947108 -93 ******** ** Masking position 2 Map Score: 6.93086 Number of sites scoring better than the average of aligned sites = 693 Number in coding regions = 627 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 4 TTTTTTTTTGTTCAGCAACGCACTACCATA 2 57 1 TTCAGCAACG 0.97905 -49 CTCCGTAACCTTCAGCAATGAAGGTATCGA 5 15 1 TTCAGCAATG 0.927266 -266 ATAACGTTGCGCCAGCAACGGCCCGAAGGG 5 80 1 GCCAGCAACG 0.997182 -201 CTTCTCCTTCGCCATCAGCGACAAAATCAA 5 214 1 GCCATCAGCG 0.967426 -67 GTTAAAACGAGCCAGCAACGTAGCGAAAGC 8 63 0 GCCAGCAACG 0.997182 -32 CGTAATAGGTGCCAGCAATGGCTGCAA 12 8 0 GCCAGCAATG 0.989746 -64 TACAATCGCGGTAATCAACGATAAGGACAC 12 46 1 GTAATCAACG 0.858393 -26 ********** Masking position 4 Map Score: 10.3335 Number of sites scoring better than the average of aligned sites = 914 Number in coding regions = 869 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 TTACGGTGCACTGTACTGCTTTTACGAGCT 3 223 0 CTGTACTGCT 0.863354 -78 ATTAGCATAACTGTAATGGTGACCATATGT 4 23 0 CTGTAATGGT 0.809992 -50 GCAACGTTATCCTTCCTGGTGCCTGCGGTT 5 60 0 CCTTCCTGGT 0.789225 -221 TAATCGGTTTCAGTTGTGATGATAATCTGC 6 14 0 CAGTTGTGAT 0.8356 -287 AAATCTTTGTCTGTTGTGGTTGGTGTAATC 6 39 0 CTGTTGTGGT 0.969326 -262 AGCGATTACACTGATGTGATTTGCTTCACA 6 218 1 CTGATGTGAT 0.693553 -83 CTATCAGGAACTTTCCTGATCTGGCTGATT 8 20 1 CTTTCCTGAT 0.877682 -75 GTAGCGAAAGCTGTTTTGGTATGCAATCAG 8 44 0 CTGTTTTGGT 0.888315 -51 TCGCGCAGTCCTGGTTAAAGAGGTT 11 6 1 CAGTCCTGGT 0.962645 -197 TTTCGGTATACTGTCCTGATACGCTTTTGT 11 136 1 CTGTCCTGAT 0.976475 -67 ********** Masking position 7 Map Score: 4.32622 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 553 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 AACAATAGGGTAGTATTGACAAGCCAATTAC 1 75 1 TAGTATTGCA 0.614912 -127 CGAGCGCTACTGGTTTGCTCGTCTGCCACCA 1 169 0 TGGTTTGCCG 0.812629 -33 AATCGAAATGCAGTTTTGTCAGATATTACGC 3 19 1 CAGTTTTGCA 0.959844 -282 CTTTTTTATCTGCTTTTGTCATTAACACGGC 3 56 0 TGCTTTTGCA 0.899696 -245 ATTTTTTTATCAGTTTTGCCGCACTTTGCGC 3 145 1 CAGTTTTGCG 0.969767 -156 GCACTTTGCGCGCTTTTCCCGTAATCGCACG 3 165 1 CGCTTTTCCG 0.930268 -136 TAAGCGTTTACAGTTTTCGCAAGCTCGTAAA 3 202 1 CAGTTTTCCA 0.933018 -99 CTAATTAAAACGATTTTGACAGGCGGGAGGT 4 48 1 CGATTTTGCA 0.916868 -25 CGTAATTGCTTGATTTTGTCGCTGATGGCGA 5 222 0 TGATTTTGCG 0.886128 -59 TATTATTATTCGGTTTTCACAGTTGTTACAT 6 81 1 CGGTTTTCCA 0.970273 -220 GAATTAATCATCGTTTTGTCGGGAAGCGAGT 10 45 0 TCGTTTTGCG 0.883686 -75 ******** ** Masking position 6 Map Score: 7.79774 Number of sites scoring better than the average of aligned sites = 1367 Number in coding regions = 1293 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 7 TATTCTCCGTAACCTTCAGCAATGAAG 5 4 1 TCTCCAATTC 0.987502 -277 TACCGCTATCTCTTCGATACCTTCATTGCTGAAG 5 24 0 TCTTCTATTC 0.811429 -257 CGGGAGGATGACTCACTGACGTTCGCCCTTCGGG 5 101 0 ACTCAGATTC 0.86315 -180 TGCACCATCTTCTCCAAAAAATTTCCTTCAAAAA 5 137 1 TCTCCAATTT 0.931782 -144 CCTTTATCCATTTCCTGAATTTTCTTCTCCTTCG 5 191 1 TTTCCAATTC 0.898201 -90 TGATGATATAACTCAATTATTTTCATGCACTTAA 6 157 1 ACTCATATTC 0.85386 -144 TCTCCCCAAGCTTCCTCCCATCGC 7 1 1 TCTCCAATTC 0.987502 -76 CCATCTGAACTATCAGGAACTTTCCTGATCTGGC 8 11 1 TATCAAATTC 0.869105 -84 CCTCTGAAGATATCCTTTAAGTTTACTCGCTTCC 10 21 1 TATCCTATTT 0.626387 -99 GCGTAACGTTTCTCATTGAAATTCACTACACTTA 11 83 0 TCTCAGATTC 0.957788 -120 ***** ** *** Masking position 9 Map Score: 3.61327 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 203 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 8 CGGTAACTCCTTTTGTCTGTGGT 2 93 0 TAACTCCTTT 0.9584 -13 TGAAAAAAAATAACAACTTTTTTATCTGCT 3 73 0 TAACAACTTT 0.950182 -228 CATTTCTAAATAACTCCTTTATCCATTTCC 5 176 1 TAACTCCTTT 0.9584 -105 AAAAGAAATGTAACAACTGTGAAAACCGAA 6 89 0 TAACAACTGT 0.854447 -212 GTGATTTGCTTCACATCTTTTTACGTCGTA 6 233 1 TCACATCTTT 0.854444 -68 AGCGCTTCCTTAACCTCTTTAACCAGGACT 11 17 0 TAACCTCTTT 0.895772 -186 TTACTTACCGGAACACCTTTACCC 11 189 1 GAACACCTTT 0.92971 -14 ********** Masking position 3 Map Score: 2.68471 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 92 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 9 TGTCAATACTACCCTATTGTTTGCCGTCATGAAA 1 62 0 ACCTTTGTGC 0.990084 -140 ATTCAGGGAAACTCTTTTACAAGCCGCTAACTTT 2 12 1 ACCTTTACGC 0.977797 -94 AAAAATAACAACTTTTTTATCTGCTTTTGTCATT 3 64 0 ACTTTTATGC 0.949063 -237 CATAGATTAAACGCTGTTATCTGCAATTAAGACT 6 125 0 ACCTTTATGC 0.991765 -176 TGATGATATAACTCAATTATTTTCATGCACTTAA 6 157 1 ACCATTATTC 0.821323 -144 CTGTCCTGATACGCTTTTGTGCGCCCCGAATACG 11 146 1 ACCTTTGTGC 0.990078 -57 ** ** **** ** Masking position 7 Map Score: 1.99564 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 13 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 10 AAAAAGCCGCTAACGAAAAGTTAGCGGCTTG 2 31 0 TACGAAAAGT 0.811348 -75 TTAGTTAACTTAAGGAGAATGAC 3 288 1 TAGGAGAATG 0.750193 -13 TGCTGAAGGTTACGGAGAATA 5 1 0 TAGGAGAATA 0.935065 -280 GCAATGAAGGTATCGAAGAGATAGCGGTATT 5 29 1 TACGAAGAGA 0.851975 -252 AAGGAAATTTTTTGGAGAAGATGGTGCATCC 5 134 0 TTGGAGAAGA 0.941725 -147 CGCTGATGGCGAAGGAGAAGAAAATTCAGGA 5 203 0 GAGGAGAAGA 0.916302 -78 ATTTTTCGACTTGCGAGAAGACC 5 268 1 TTCGAGAAGA 0.941725 -13 ATTAAGACTTTACTGAAAAGAAATGTAACAA 6 103 0 TATGAAAAGA 0.825433 -198 GGGTAGGGGTTAACAAAAAGAATCCCGCTAG 9 17 0 TACAAAAAGA 0.706599 -36 CCCCTTAATCTCTGGAGAATAACG 10 106 1 TCGGAGAATA 0.770874 -14 CAGGACAGTATACCGAAAAGAGGCCGCCGCC 11 123 0 TACGAAAAGA 0.968319 -80 ** ******** Masking position 6 Map Score: 2.78084 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 339 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 11 ********** No masking Map Score: -4.28214e-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: -4.28214e-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: -4.28214e-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