AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i063_ecoli_bsub_100.orf -o063_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 gcvP 118 glycine decarboxylase, P protein of glycine cleavage system #2 gcvH 23 in glycine cleavage complex, carrier of aminomethyl moiety via covalently bound lipoyl cofactor #3 gcvT 300 aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system #4 yqhJ 29 similar to glycine dehydrogenase #5 yqhI 300 similar to aminomethyltransferase #6 yusH 66 similar to glycine cleavage system protein H #7 yusI 110 similar to arsenate reductase Motif number 1 CGGCTTTATTCCTCTTCTGCGGGAGAGGA 1 9 1 TTCCTCTCTG 0.847805 -110 CCTCACCCTGATCCTCTCCCGCAGAAGAGGA 1 20 0 ATCCTCCCCG 0.960052 -99 GGCATAAATTTTCCTCACCCTGATCCTCTCC 1 32 0 TTCCTCCCCT 0.990589 -87 GGAAAATTTATGCCTCACCCTCACTCTCTTC 1 49 1 TGCCTCCCCT 0.992675 -70 GAATTGTGAACCTCTCTCCTTACGAAGAGAG 1 72 0 CCTCTCCCTT 0.880101 -47 CGTTCTCTTTTGCCTGAACTTACCACCGAAA 3 183 0 TGCCTGACTT 0.762405 -118 CCAGCATCGGAGCCACTCCCGGTCCCCAACG 3 218 0 AGCCACCCCG 0.863376 -83 ATGAAAAAGTTGTCAGCCCCGCTTATTCAAT 3 271 1 TGTCAGCCCG 0.836334 -30 TTCGGTCAGGTCTCTCCCCTTGCTGTCATTC 5 36 0 TCTCTCCCTT 0.974986 -265 AAATGAAGGTTCTCTGTCCTGGCACCTGAAA 5 210 0 TCTCTGCCTG 0.947668 -91 ATGAGGTGTTTCTCTGTCCTTTTTTGTATGT 5 244 1 TCTCTGCCTT 0.946727 -57 CTAATTCCTCCCCTTTATCAACGGC 5 286 0 TTCCTCCCTT 0.987045 -15 CTTCTTCCCCCTCAATAAAATA 7 99 0 TTCTTCCCCT 0.873946 -12 ****** **** Masking position 9 Map Score: 15.5489 Number of sites scoring better than the average of aligned sites = 1261 Number in coding regions = 1021 Number in noncoding regions = 240 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 2 TTTACTTTTTTGGAGATTGATTG 2 6 1 TTTTTTGGAG 0.974271 -18 AACTGGTGTATTTTTTGGTTTTTTATTCTG 3 84 1 TTTTTTGGTT 0.828868 -217 TTTTTTGGTTTTTTATTCTGTCGCGATTTT 3 94 1 TTTTATTCTG 0.857096 -207 CGATGCTGGGTTTCGTGGTGATAATTTCAC 3 240 1 TTTCGTGGTG 0.956449 -61 CTGACAACTTTTTCATGGTGAAATTATCAC 3 257 0 TTTCATGGTG 0.979899 -44 TATTTTTTCTTGGAGAGAGGAGACA 4 6 1 TTTCTTGGAG 0.976202 -24 TCGCTCATATTTTCATGCTGTTATGGA 5 8 0 TTTCATGCTG 0.970587 -293 TTTTGTATGTTTTTTAGCTGCGCCGTTGAT 5 265 1 TTTTTAGCTG 0.840769 -36 AATCCCTCCATTTTTTACAGCACTACAATA 6 44 0 TTTTTTACAG 0.741085 -23 ACCTCGATTATTTTATTGAGGGGGAAGAAG 7 91 1 TTTTATTGAG 0.8582 -20 ********** Masking position 3 Map Score: 9.46028 Number of sites scoring better than the average of aligned sites = 761 Number in coding regions = 672 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 3 TTCCTCACCCTGATCCTCTCCCGCAGAAGA 1 23 0 TGATCCTCTC 0.983639 -96 TGCCTCACCCTCACTCTCTTCGTAAGGAGA 1 59 1 TCACTCTCTT 0.883236 -60 CAGTGAATTGTGAACCTCTCTCCTTACGAA 1 77 0 TGAACCTCTC 0.988525 -42 TTATTCAAATTGACTTTCTCATCACATCAT 3 43 1 TGACTTTCTC 0.947163 -258 CCCCTTGCTGTCATTCGCTCATATTTTCAT 5 22 0 TCATTCGCTC 0.932365 -279 AACTGCGGAGTGAATCTCTCAGGCAAAAGA 5 96 1 TGAATCTCTC 0.99225 -205 TTGAATCCCTCCATTTTTTAC 6 56 0 TGAATCCCTC 0.979085 -11 ********** Masking position 3 Map Score: 6.77669 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 124 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 GTGAGGAAAATTTATGCCTCACCCTCACTCT 1 45 1 TTTATGCCTA 0.910048 -74 ATCACATTAGCTTATGGTTAAAAAATGCAAA 3 122 0 CTTATGGTTA 0.966388 -179 TCAATTTTACCTTATGGTTAACAGTCTGTTT 3 155 1 CTTATGGTTA 0.966388 -146 CAATCGTTCTCTTTTGCCTGAACTTACCACC 3 187 0 CTTTTGCCTA 0.98358 -114 AGCAAGAGTTCTTTTGCCTGAGAGATTCACT 5 104 0 CTTTTGCCTA 0.98358 -197 GGCAAAAGAACTCTTGCTCGACGCAACTCTG 5 117 1 CTCTTGCTCA 0.929242 -184 GCATGCGGAGCTCATGGCCAA 7 1 0 CTCATGGCCA 0.964143 -110 ********* * Masking position 11 Map Score: 5.41225 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 86 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 CGGCTTTATTCCTCTTCTGCGGGA 1 5 1 TTTATTCCTC 0.946969 -114 GTGAGGAAAATTTATGCCTCACCCTCACTC 1 45 1 TTTATGCCTC 0.955682 -74 CAATCGTTCTCTTTTGCCTGAACTTACCAC 3 188 0 CTTTTGCCTG 0.987042 -113 GGGCTGACAACTTTTTCATGGTGAAATTAT 3 260 0 CTTTTTCATG 0.907048 -41 TATTTTTTCTTGGAGAGAGGAG 4 3 1 TTTTTTCTTG 0.825319 -27 AGCAAGAGTTCTTTTGCCTGAGAGATTCAC 5 105 0 CTTTTGCCTG 0.987042 -196 CTAATTCCTCCCCTTTATCA 5 291 0 CTAATTCCTC 0.884483 -10 ********** Masking position 5 Map Score: 5.06433 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 429 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 6 CAATTCACTGCACGTTTCAGGAACCATCGC 1 97 1 CACGTTTCAG 0.904743 -22 CAATCAATCTCCAAAAAAGTAAA 2 10 0 CAATCTCCAA 0.94457 -14 GTGTTGTCTCCTCTCTCCAAGAAAAAATA 4 10 0 CTCTCTCCAA 0.964508 -20 CTGAGAGATTCACTCCGCAGTTTGCTCCTT 5 88 0 CACTCCGCAG 0.959392 -213 TCCGCACAAACACTCTCCAGAGTTGCGTCG 5 135 0 CACTCTCCAG 0.99426 -166 GAAGATACCACACTTTTCAAAAAAAATTTA 6 13 0 CACTTTTCAA 0.942921 -54 ********** Masking position 9 Map Score: 2.22904 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 341 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 CTATACAAAGATGATGTGATGAGAAAGTCAATTTG 3 48 0 ATATGTGTGA 0.797652 -253 TAACCATAAGCTAATGTGATGATCAATTTTACCTT 3 133 1 CTATGTGTGA 0.975734 -168 GGTTAACAGTCTGTTTCGGTGGTAAGTTCAGGCAA 3 170 1 CTTTTCGTGA 0.884185 -131 CAAAAGAGAACGATTGCGTTGGGGACCGGGAGTGG 3 202 1 CGTTGCGTGA 0.980359 -99 GTCAGCCCCGCTTATTCAATGAGGACAAG 3 282 1 CTATTCATGA 0.887866 -19 AGTGTTTGTGCGGATGCGCAAACCACCTTTGGGGA 5 151 1 CGATGCGAAA 0.961899 -150 GACGTCTTTGCGTATGCAAAGTAAACTTTCAGGTG 5 184 1 CGATGCAAGA 0.976754 -117 AGAGAAACACCTCATGTAAAATGAAGGTTCTCTGT 5 224 0 CTATGTAAAA 0.678074 -77 AAGAGCTCCGCGCATGCGGAGCTCATGGCCAA 7 8 0 CGATGCGAGA 0.992261 -103 ** ***** ** * Masking position 5 Map Score: 2.22887 Number of sites scoring better than the average of aligned sites = 1555 Number in coding regions = 1187 Number in noncoding regions = 368 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 8 GGGGACCGGGAGTGGCTCCGATGCTGGGTTT 3 222 1 ATGGCTCCGA 0.966597 -79 TGAAAAAGTTGTCAGCCCCGCTTATTCAATG 3 272 1 GCAGCCCCGC 0.969519 -29 ACCTCGGGATACAGGCGCCGAAGGAGCAAAC 5 68 1 AAGGCGCCGA 0.96897 -233 CCCCTTTATCAACGGCGCAGCTAAAAAACAT 5 271 0 ACGGCGCAGC 0.975006 -30 TTGGCCATGAGCTCCGCATGCGCGGAG 7 7 1 AGAGCTCCGC 0.993312 -104 CTTCTTAAAAAAGAGCTCCGCGCATGCGGAG 7 22 0 AGAGCTCCGC 0.993312 -89 * ********* Masking position 6 Map Score: 2.12469 Number of sites scoring better than the average of aligned sites = 718 Number in coding regions = 683 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 9 TCTTCTGCGGGAGAGGATCAGGGTGAGGAA 1 23 1 GAGAGGATCA 0.822393 -96 GAGGATCAGGGTGAGGAAAATTTATGCCTC 1 35 1 GTGAGGAAAA 0.95856 -84 TTCCTGAAACGTGCAGTGAATTGTGAACCT 1 90 0 GTGCAGTGAA 0.825511 -29 CAAAGATGATGTGATGAGAAAGTCAATTTG 3 48 0 GTGATGAGAA 0.977354 -253 ATAAGCTAATGTGATGATCAATTTTACCTT 3 138 1 GTGATGATCA 0.964162 -163 GCTGGGTTTCGTGGTGATAATTTCACCATG 3 244 1 GTGGTGATAA 0.947397 -57 TCTTATTGTAGTGCTGTAAAAAATGGAGGG 6 41 1 GTGCTGTAAA 0.909607 -26 ********** Masking position 10 Map Score: 1.14465 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 504 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 10 AGTTCAGGCAAAAGAGAACGATTGCGTTGG 3 194 1 AAAGAGAACG 0.942578 -107 GAGAGACCTGACCGAAAACCTCGGGATACA 5 51 1 ACCGAAAACC 0.962702 -250 AGGTGCCAGGACAGAGAACCTTCATTTTAC 5 214 1 ACAGAGAACC 0.994313 -87 ACAAAAAAGGACAGAGAAACACCTCATGTA 5 241 0 ACAGAGAAAC 0.977779 -60 ********** Masking position 5 Map Score: 0.526489 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 112 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 ********** No masking Map Score: 6.56131e-13 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: 6.56131e-13 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: 6.56131e-13 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