AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00220_ecoli_reg_100.orf -o00220_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 Purged sequences: argI 161 ornithine carbamoyltransferase 1 Input sequences: #1 speE 105 spermidine synthase = putrescine aminopropyltransferase #2 proB 287 gamma-glutamate kinase #3 argF 300 ornithine carbamoyltransferase 2, chain F #4 speF 300 ornithine decarboxylase isozyme, inducible #5 argA 141 N-acetylglutamate synthase; amino acid acetyltransferase #6 speC 300 ornithine decarboxylase isozyme #7 ygjG 300 probable ornithine aminotransferase #8 argG 300 argininosuccinate synthetase #9 argD 85 acetylornithine delta-aminotransferase #10 pabA 31 p-aminobenzoate synthetase, component II #11 yhfG 104 orf, hypothetical protein #12 argE_argC 153 argE: acetylornithine deacetylase, argC: N-acetyl-gamma-glutamylphosphate reductase #13 argH 60 argininosuccinate lyase Motif number 1 ACCGTGCATCCGCGGTCAATGTTAGCTATTATGTTG 1 39 1 CGCGGAATTC 0.978986 -67 GCTATTATGTTGCGCCCTTTTTTTACGGGTGTTAAC 1 63 1 TGCGCTTTTC 0.793098 -43 TTTTAATTAACGCGCGAATATTCAGCGGGAGAGTCC 2 23 1 CGCGCATTCC 0.988024 -265 TTGCTGATCCCGCGCAACAAAACGCCATGCTTTGCT 2 180 1 CGCGCCAACC 0.923738 -108 CCATGCTTTGCTCGCAGATGGTTGGCAACCGACGAC 2 204 1 CTCGCATTTC 0.915122 -84 GCCTGTATTCCGCAGTGCTCATTCTCTGTTAACCCT 4 115 1 CGCAGCTTTC 0.691331 -186 AAAAGTCGCTCTCGCATAAAATTTACACTTGCACCC 5 58 1 CTCGCAATTC 0.915122 -84 GTGCCATGATTGCGCGAATTTTCTCCTCTCTGTACG 6 79 1 TGCGCATTCC 0.926947 -222 ATCGCCGTTTCGCGCGAAACGTTTCCCTTTCTATGT 6 157 1 CGCGCAATTC 0.990142 -144 CTGCAGTGAGCGTGCGTTAACTTCACCGCATGAGCA 6 196 0 CGTGCTATTC 0.713189 -105 TCGGCCCCGCTGCGGTTATCTTTAACCGATTAATTT 7 57 1 TGCGGATTTC 0.877531 -244 CGACAAAAACCGTGCAAAATAACAACAAATGTTAAC 7 252 1 CGTGCAAACC 0.570581 -49 TATAGTGATCCACGCCACATTTTGTCAACGTTTATT 8 58 1 CACGCCATTC 0.847589 -243 AATAGCGCGGTTCTTTTGTACCGGAGCCGCC 10 6 1 CGCGGCTTGC 0.888637 -26 TGATTTCTCGCGCGGGCAATCTTGCCCGCGCTTCTG 11 11 1 CGCGGAATTC 0.978986 -94 CAATCTTGCCCGCGCTTCTGCTCTCCCGGCGTAACC 11 27 1 CGCGCCTTCC 0.986848 -78 ***** ** ** * Masking position 16 Map Score: 16.3397 Number of sites scoring better than the average of aligned sites = 2039 Number in coding regions = 1949 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 2 GGGTTGCAAATGAATAATTACACATATAAAGTGA 3 237 1 TGAATATACA 0.804384 -64 CGCCACTTATTGAATTAAAATTCACTTTATATGT 3 258 0 TGAATAAACA 0.682836 -43 TGTTAACCCTTGTATTATCAGCCACCTGACTGGT 4 141 1 TGTATATACA 0.874385 -160 GCGAAAAAACAGAATAAAAATACACTAATTTCGA 5 95 1 AGAATAAACA 0.947187 -47 ACACTAATTTCGAATAATCATGCAAAGAGGTGTG 5 116 1 CGAATATACA 0.686454 -26 GCTAATCATGTGAATGAATATCCAGTTCACTTTC 8 94 1 TGAATAAACA 0.954987 -207 AAAAGATGATTAAATGAAAACTCATTTATTTTGC 8 213 1 TAAATAAACA 0.853699 -88 TCATTTATTTTGCATAAAAATTCAGTGAGAGCGG 8 234 1 TGCATAAACA 0.674771 -67 CCACAAAATATGCATAAAAAATCACTAAATGGCA 9 19 0 TGCATAAACA 0.952495 -67 GCAGTATTTATGAATAAAAATACACTAACGTTGA 12 91 0 TGAATAAACA 0.81996 -63 TGGTCATGATAGTATCAATATTCATGCAGTATTT 12 116 0 AGTATAAACA 0.848675 -38 ***** ** * ** Masking position 7 Map Score: 14.0267 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 47 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 3 TTTCATTCCTGATTTTAATTAACGCG 2 6 1 TTCCTGTTTT 0.945542 -282 GTTAAAAACTTTCCTGTTTTCAACGGGACTC 2 53 0 TTCCTGTTTC 0.972688 -235 CGAGGCTTGCTGCCTTACTTCATTACTTCAG 3 12 0 TGCCTTCTTC 0.743847 -289 ATCCAATGTCTTTCTGCTTCTGCAGAGAATC 3 135 1 TTTCTGTTCT 0.738875 -166 CGTACAGGTCTTCCTGACTCTCTGTATTACA 4 77 1 TTCCTGCTCT 0.801335 -224 TACAGGCATATGCCTGTATTCCGCAGTGCTC 4 104 1 TGCCTGATTC 0.863941 -197 CTGGTAAGGGTTTCTGCATTCTGAAAAAAGC 4 170 1 TTTCTGATTC 0.801947 -131 ATCAGGTAGATTGCTTTTTTCAGAATGCAGA 4 182 0 TTGCTTTTTC 0.711679 -119 CGGGGTAACTTTGCTTTTTTCCGGCACGATC 4 224 1 TTGCTTTTTC 0.711679 -77 AATCAGAGCGTTTCTGCTTTTACTGATGTCT 6 243 1 TTTCTGTTTT 0.860116 -58 ACAAATCTAATTCCTTGATTTAAAATACTTT 7 121 1 TTCCTTATTT 0.618498 -180 GGGCAATAATTGCCTGATTTTTGGGCAAGAT 7 181 0 TGCCTGTTTT 0.906035 -120 CACTAAACTCTTCCTGTCTCCGATAAAAGAT 8 189 1 TTCCTGCTCC 0.892168 -112 TTTCTGATTGCCATTTAGTGA 9 1 1 TTTCTGTTGC 0.799382 -85 CACCTTCTTATGTCTGGTTGCCAGGTTAAAC 12 21 1 TGTCTGTTGC 0.688748 -133 AACTCTGTTTCCTTATTTTGAAATTCAAT 13 42 0 TTCCTTTTTT 0.834705 -19 ****** **** Masking position 5 Map Score: 13.7588 Number of sites scoring better than the average of aligned sites = 971 Number in coding regions = 824 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 4 AAATATTGACCGTGCATCCGCGGTCAATGTTAG 1 31 1 CGATCCGCGG 0.929542 -75 ACTCTCCCGCTGAATATTCGCGCGTTAATTAAA 2 24 0 TGATTCGCGC 0.975144 -264 CAAAGCATGGCGTTTTGTTGCGCGGGATCAGCA 2 181 0 CGTGTTGCGC 0.946937 -107 ATTTTTATTCTGTTTTTTCGCAGGGTGCAAGTG 5 83 0 TGTTTCGCAG 0.667397 -59 TACAGAGAGGAGAAAATTCGCGCAATCATGGCA 6 80 0 AGATTCGCGC 0.906357 -221 TCTCGCTTATCGCCGTTTCGCGCGAAACGTTTC 6 149 1 CGTTTCGCGC 0.990359 -152 GCCCTGAAAACGTGCATTTGCGCAGCAATCATC 7 208 1 CGATTTGCGC 0.971244 -93 TAACATTTGTTGTTATTTTGCACGGTTTTTGTC 7 253 0 TGTTTTGCAC 0.808655 -48 ATGATGAGCCTGGATTTCCGCTCTCACTGAATT 8 252 0 TGTTCCGCTC 0.884804 -49 TGATTTCTCGCGCGGGCAATCTT 11 1 1 TGTCTCGCGC 0.918457 -104 CAATCTTGCCCGCGCTTCTGCTCTCCCGGCGTA 11 27 1 CGTTCTGCTC 0.868638 -78 AATTCAATGCCGGAAAGCTGCGCCTCCGGCCAA 13 17 0 CGAGCTGCGC 0.914268 -44 ** ******** Masking position 11 Map Score: 8.43736 Number of sites scoring better than the average of aligned sites = 1884 Number in coding regions = 1795 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 5 GCGGGATCAGCAAGCCTAGCGGCAGTTGTTTACGCTT 2 156 0 CGCCGGCATT 0.952379 -132 AACGTTTTAGCAGGACTGTCGTCGGTTGCCAACCATC 2 220 0 CGCCGTCGTT 0.944263 -68 CAAGCCTCGCCATGTTCTCCGCCATTTTAGAAGCATA 3 34 1 CGTCGCCATT 0.991114 -267 TGAAAATAATCGTATCTGCCTCCGATTCTCTGCAGAA 3 152 0 CACCTCCGTT 0.77282 -149 CACACACGGACGGGTTTGCCTCCACCTTTGTAAGAAA 3 187 1 CGTCTCCACT 0.947817 -114 TTTATCCTCGCATGGCGAACGCCACTTATTGAATTAA 3 274 0 CGCCGCCATT 0.991792 -27 ACGGAGTTTGCCCGATGCACGCCATCTCCTTACATTC 6 112 1 CGTCGCCACT 0.987564 -189 CTTACATTCTCTCGCTTATCGCCGTTTCGCGCGAAAC 6 140 1 CGTCGCCGTT 0.987564 -161 AGATATGGGTCAAACTGGTCACCAGCTCCGACCGCCA 6 273 0 CATCACCACT 0.758448 -28 AGCGGAAATCCAGGCTCATCATCAGTTAATTAAGCAG 8 263 1 CGTCATCATT 0.833978 -38 * * * ***** ** Masking position 17 Map Score: 6.20681 Number of sites scoring better than the average of aligned sites = 695 Number in coding regions = 664 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 CGCGGGATCAGCAAGCCTAGCGGCAGTTGTT 2 163 0 GCAAGCCTGC 0.866778 -125 CCAACCATCTGCGAGCAAAGCATGGCGTTTT 2 198 0 GCGAGCAAGC 0.962771 -90 AAGTAAGGCAGCAAGCCTCGCCATGTTCTCC 3 23 1 GCAAGCCTGC 0.598409 -278 GCTAAAGCGTGCAAGCCAGGACTTTGCGAAC 6 44 0 GCAAGCCAGA 0.935757 -257 GAAAATTCGCGCAATCATGGCACCTTTGCTA 6 71 0 GCAATCATGC 0.932504 -230 CAAAAATCAGGCAATTATTGCCCTGAAAACG 7 189 1 GCAATTATGC 0.555856 -112 AGGCATTATAGTGATCCACGCCACATTTTGT 8 52 1 GTGATCCAGC 0.857672 -249 AGTGAGAGCGGAAATCCAGGCTCATCATCAG 8 257 1 GAAATCCAGC 0.914413 -44 ******** ** Masking position 4 Map Score: 4.52581 Number of sites scoring better than the average of aligned sites = 750 Number in coding regions = 674 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 7 AGAAATATTGACCGTGCATCCGCGGTCAAT 1 29 1 ACCGTGCATC 0.86157 -77 GTCCTGCTAAAACGTTCGTTTGATATCATT 2 241 1 AACGTTCGTT 0.906308 -47 TCGGTAGACTAACGGGCATTGAAGAAGTGA 4 32 0 AACGGGCATT 0.952126 -269 AAGAATGTTTACCGTTTATTAG 5 3 0 ACCGTTTATT 0.806316 -139 GACGGCACCAAACGGTCATAA 6 2 0 AACGGTCATA 0.737896 -299 TCCTGCAGTGAGCGTGCGTTAACTTCACCG 6 204 0 AGCGTGCGTT 0.860458 -97 ACTATACGAAAACGTTAATTATCTTGCCCA 7 161 1 AACGTTAATT 0.806532 -140 TTGCCCTGAAAACGTGCATTTGCGCAGCAA 7 206 1 AACGTGCATT 0.975621 -95 ACATTTTGTCAACGTTTATTGCTAATCATG 8 74 1 AACGTTTATT 0.88025 -227 ********** Masking position 9 Map Score: 2.18612 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 274 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 8 CTAAAATTGAATGGCAGAGAATC 2 275 1 ATGGCAGAGA 0.71154 -13 TGCTTCTAAAATGGCGGAGAACATGGCGAG 3 39 0 ATGGCGGAGA 0.961775 -262 GAAATCGATCGTGCCGGAAAAAAGCAAAGT 4 231 0 GTGCCGGAAA 0.941604 -70 TTTATCAGTAATGCCGTGAATATAAAAAGA 5 29 0 ATGCCGTGAA 0.96032 -113 TGACCGTTTGGTGCCGTCGATGGCTTGTTT 6 14 1 GTGCCGTCGA 0.899936 -287 ATGTAAGGAGATGGCGTGCATCGGGCAAAC 6 117 0 ATGGCGTGCA 0.898002 -184 GTTACTGCTCATGCGGTGAAGTTAACGCAC 6 191 1 ATGCGGTGAA 0.778634 -110 TTGACAAAATGTGGCGTGGATCACTATAAT 8 56 0 GTGGCGTGGA 0.962363 -245 TTGAAATTCAATGCCGGAAAGCTGCGCCTC 13 24 0 ATGCCGGAAA 0.951287 -37 ********** Masking position 2 Map Score: 3.09091 Number of sites scoring better than the average of aligned sites = 1141 Number in coding regions = 1061 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 9 TTATTCGAAATTAGTGTATTTTTATTCTGTT 5 102 0 TTAGTGTTTT 0.978611 -40 CAGGAAGAGTTTAGTGTGTTTTTTGTAAAAT 8 174 0 TTAGTGTTTT 0.978611 -127 TGATTGCCATTTAGTGATTTTTTATGCATAT 9 15 1 TTAGTGATTT 0.947665 -71 ACGCTCAACGTTAGTGTATTTTTATTCATAA 12 87 1 TTAGTGTTTT 0.978611 -67 ******* *** Masking position 5 Map Score: 1.84979 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 3 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 TGATATCAAACGAACGTTTTAGCAGGACTG 2 239 0 CGAACGTTTT 0.791192 -49 AGTCCTGGCTTGCACGCTTTAGCAAAGGTG 6 52 1 TGCACGCTTT 0.954154 -249 GTCCTGTGCAGGTTATATGGTTGTTA 7 7 1 TGCAGGTTAT 0.716553 -294 GGCAAGATAATTAACGTTTTCGTATAGTAA 7 159 0 TTAACGTTTT 0.613489 -142 GCTGCGCAAATGCACGTTTTCAGGGCAATA 7 204 0 TGCACGTTTT 0.977052 -97 GTTGTTATTTTGCACGGTTTTTGTCGGGTA 7 248 0 TGCACGGTTT 0.918757 -53 CTATAATGCCTGCAGATTTTACGTCCCGTC 8 33 0 TGCAGATTTT 0.835236 -268 TTTCATTTGTTGAATACTTTTGCCTTCTCC 8 124 1 TGAATACTTT 0.494839 -177 TGATTTTTTATGCATATTTTGTGGTTATAA 9 29 1 TGCATATTTT 0.824436 -57 AGCCGTAAGGTGAATGTTTTACGTTTAACC 12 44 0 TGAATGTTTT 0.876578 -110 ********** Masking position 4 Map Score: 2.94014 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 512 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 11 GAGAATCGGAGGCAGATACGATTATTTTCA 3 159 1 GGCAGATACG 0.951301 -142 CAAAGGTGGAGGCAAACCCGTCCGTGTGTG 3 187 0 GGCAAACCCG 0.979941 -114 CAGAGTTTATGTCGGCCCCGCTGCGGTTAT 7 46 1 GTCGGCCCCG 0.960899 -255 GGCGGCTCCGGTACAAAAGA 10 22 0 GGCGGCTCCG 0.991393 -10 AAGTATAAGCGGCAAATCCGGGTTACGCCG 11 53 0 GGCAAATCCG 0.978381 -52 ********** Masking position 3 Map Score: 0.520665 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 395 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 TCCCTGATACCTTTTTGTAG 1 1 1 TCCCTGATAC 0.910703 -105 CAGTGCTCATTCTCTGTTAACCCTTGTATT 4 127 1 TCTCTGTTAA 0.885243 -174 CGTTTCCCTTTCTATGTTACTGCTCATGCG 6 176 1 TCTATGTTAC 0.885243 -125 AAATACTTTCACTCTGTTACTATACGAAAA 7 143 1 ACTCTGTTAC 0.98034 -158 CTCATGATCACCCTGTTACGCATAAACAA 9 67 0 ACCCTGTTAC 0.976381 -19 AACTCTGTTTCCTTATTTTGA 13 50 0 ACTCTGTTTC 0.924821 -11 ********** Masking position 5 Map Score: 1.91662 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 45 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 ********** No masking Map Score: 6.21968e-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: 6.21968e-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 15 ********** No masking Map Score: 6.21968e-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