AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i135_ecoli_bsub_300.orf -o135_ecoli_bsub_300.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 cydA 300 cytochrome d terminal oxidase, polypeptide subunit I #2 ybgE 127 orf, hypothetical protein #3 ybgC 149 orf, hypothetical protein #4 tolA 64 membrane spanning protein, required for outer membrane integrity #5 tolB 132 periplasmic protein involved in the tonb-independent uptake of group A colicins #6 pal 34 peptidoglycan-associated lipoprotein #7 yuxL 107 similar to acylaminoacyl-peptidase #8 hom 200 homoserine dehydrogenase #9 yutH 152 yutH Motif number 1 CCTTTCTTTACGCCGTTTTTGTGTGCATTCACATGG 1 177 1 CGCCTTTTGC 0.970208 -124 GACTCCTTGCTCATCGCATGAAGACTCC 1 283 0 CTCCTGTCCA 0.790121 -18 TTGCCTGATTCGACGTGTTCAAGCGCCAGCGCGGTG 2 81 0 CGACTGTCGC 0.981522 -47 AATTTTTACGCTCCCTTAACTTGCCCTCATTCCCAA 3 55 1 CTCCTTACGC 0.987882 -95 AAAAACTGTTCGCCTGTTACCCGCTCTCTTTCAAGC 4 28 0 CGCCGTACGC 0.960824 -37 TAACATTCTGCTAAATTATCGTGGGCCATCGGTCCA 5 92 1 CTAATTTCGC 0.892359 -41 CATATCTCCCTTATCTGGACCGATGGCCCAC 5 112 0 CTCCTTTCGC 0.996137 -21 TAAATAAAAACTCCTTTATCTCCAGCAAAAAAAAGC 7 46 0 CTCCTTTCCC 0.987436 -62 GAGAAGTTTACGACTTTTTCTTGCGCCTTCTTCGGA 9 53 1 CGACTTTCGC 0.990898 -100 **** ** ** * * Masking position 1 Map Score: 7.23782 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 657 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 TGTTGAAGCAAATTTGCATTTTTCGACGGTGATCAATTT 1 60 0 ATGTTTCGAG 0.971735 -241 CCTTGCTCATCGCATGAAGACTCCGAGAGTGAACCCCGT 1 268 0 CTGGCTCGAG 0.969548 -33 TGTGGTATTTCGCATGGATTCTGGGAACGCTTCTTGCCT 2 26 1 CTGTCTGGAG 0.990746 -102 CAGATGTCTTCTTGACCGGCTTTGCCTGA 2 109 0 CTGTCTGACG 0.831436 -19 TATACGCGCGCGATTGAGGTTTGGGAATGAGGGCAAGTT 3 72 0 CTGGTTGGAG 0.990746 -78 TCGCGATGTTGACTGTTCGGACGGTCAACATCAG 5 6 1 ATGTTTGGAG 0.977083 -127 AAAGCGCCCTCCGCTGACGCTGAGGAACGCTTGGCATGA 7 12 0 CTGGTGGGAG 0.961639 -96 AGACATCATTAGGCTGAATTTTGCGAATGTAAACGCTTA 8 67 0 ATGTTTCGAG 0.971767 -134 GTTGAGTTAACAATTGTCTTTTCCAAGAGGACAATCAAA 8 155 1 CTGTTTCAAG 0.943012 -46 * ** * ** *** * Masking position 5 Map Score: 6.71721 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 61 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 TCACACGCATGCCCCAATAGAAATTTGTTTGAACA 1 224 0 GCCCCAAATT 0.975283 -77 TCACCGCGCTGGCGCTTGAACACGTCGAATCAGGC 2 80 1 GGCGCTAAGT 0.964152 -48 GGCCTGGAGCGGCCCATAATTTTTTAAAGAGAATT 3 16 0 GGCCCAATTT 0.993696 -134 GGCCGCTCCAGGCCCATAAATTTTTACGCTCCCTT 3 37 1 GGCCCAATTT 0.993696 -113 CTGGACCGATGGCCCACGATAATTTAGCAGAATGT 5 94 0 GGCCCAAATT 0.995152 -39 ATCCGAAGAAGGCGCAAGAAAAAGTCGTAAACTTC 9 55 0 GGCGCAAAGT 0.99234 -98 GTTGAATTAGGGCTCATCACATCGTAGTCATACAC 9 116 0 GGCTCAATGT 0.973316 -37 ****** * * ** Masking position 9 Map Score: 6.08478 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 92 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 AGATAAATTGTTCTCGATCAAATTGGCTG 1 4 1 TAATTGCATC 0.965056 -297 AATTTATAGCTAAATTACCGCCTTTCAGCCAATTTG 1 29 0 TAATTACTTC 0.96818 -272 AATTTAGCTATAAATTGATCACCGTCGAAAAATGCA 1 49 1 TAATTGCGTC 0.976122 -252 TTTTATTAACATGTTTGCAACCTTTCTTTACGCCGT 1 157 1 ATGTTGCTTC 0.895337 -144 CAATAGAAATTTGTTTGAACACTTTCATCATACCAT 1 209 0 TTGTTGCTTC 0.97948 -92 TACGCTCCCTTAACTTGCCCTCATTCCCAAACCTCA 3 61 1 TAATTGCTTC 0.992519 -89 TTGTGTATTTTAGTTTGTTAACATTCTGCTAAATTA 5 74 1 TAGTTGCTTC 0.992388 -59 CACAGACATATAAGTTACAAACATTATATAAGCCCG 8 120 0 TAATTACTTA 0.77231 -81 *** *** * *** Masking position 6 Map Score: 3.05938 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 87 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 5 AGCTAAATTACCGCCTTTCAGCCAATTTGA 1 28 0 CCGCCTTTCA 0.935505 -273 AACATGTTTGCAACCTTTCTTTACGCCGTT 1 164 1 CAACCTTTCT 0.977828 -137 ATGCGAAATACCACATTTTTAGCTCCTTAC 2 11 0 CCACATTTTT 0.927749 -117 ATTCATCTCCTCCTTTTTACATGTATTT 7 90 0 CCTCCTTTTT 0.961873 -18 AAAAACTCCACCTTTCTTTTGATTGTC 8 184 0 CCACCTTTCT 0.992396 -17 CAGCTTCACCCAATCTTTTTTACTAGTTTA 9 11 1 CAATCTTTTT 0.812696 -142 ********** Masking position 6 Map Score: 2.92524 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 184 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 CATCATACCATGTGAATGCACACAAAAACG 1 190 0 TGTGAATGCA 0.825213 -111 TAGAAATTTGTTTGAACACTTTCATCATAC 1 212 0 TTTGAACACT 0.786012 -89 GCATGGATTCTGGGAACGCTTCTTGCCTGT 2 37 1 TGGGAACGCT 0.990208 -91 AGTTAGAGCTTTTAAACGCTGCTACTATAC 3 106 0 TTTAAACGCT 0.932028 -44 TTTCAAGCAAGGGAAACGCAGATGT 4 6 0 GGGAAACGCA 0.934831 -59 CGCTGACGCTGAGGAACGCTTGGCATGAT 7 10 0 GAGGAACGCT 0.928829 -98 ATTTTGCGAATGTAAACGCTTAACGCATTG 8 59 0 TGTAAACGCT 0.975945 -142 ********** Masking position 5 Map Score: 2.27708 Number of sites scoring better than the average of aligned sites = 630 Number in coding regions = 580 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 GATAAATTGTTCTCGATCAAATTGGCTGAAAGGCG 1 12 1 TCTCGAAAGG 0.944663 -289 GCCGCAAAATCCTTACAATAAACAGGTTTTTGTTG 1 94 0 CCTTACAAAG 0.847245 -207 CGAGAGTGAACCCCGTTAGAAAGGGTCACACGCAT 1 249 0 CCCCGTAAGG 0.932661 -52 GCGGTGATTACCCCAAACGAACAGGCAAGAAGCGT 2 52 0 CCCCAAAAGG 0.97097 -76 TCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAAC 4 14 1 CCTTGCAAAG 0.944164 -51 ACTACCAGAACCCCGTGGCAACCGGTGCCTGATGT 5 38 0 CCCCGTAAGG 0.990151 -95 CTCCTTTATCTCCAGCAAAAAAAAGCGCCCTCCGC 7 37 0 TCCAGCAAAG 0.768097 -71 CCTAATGATGTCTTGTCAAAACAGGAGCGGGCTTA 8 93 1 TCTTGTAAGG 0.91494 -108 ATGTGATGAGCCCTAATTCAACAGGCAGGTGATC 9 129 1 CCCTAAAAGG 0.954767 -24 ****** ** ** Masking position 10 Map Score: 2.33817 Number of sites scoring better than the average of aligned sites = 726 Number in coding regions = 603 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 8 GCTATAAATTGATCACCGTCGAAAAATGCA 1 55 1 GATCACCGTC 0.92785 -246 CGTTAGAAAGGGTCACACGCATGCCCCAAT 1 241 0 GGTCACACGC 0.912688 -60 TTCTAACGGGGTTCACTCTCGGAGTCTTCA 1 263 1 GTTCACTCTC 0.86119 -38 CAGATGTCTTCTTGACCGGCTTTGCCTGAT 2 108 0 CTTGACCGGC 0.886742 -20 TTTACGCTCCCTTAACTTGCCCTCATTCCC 3 59 1 CTTAACTTGC 0.607085 -91 AAAGAGAGCGGGTAACAGGCGAACAGTTTT 4 33 1 GGTAACAGGC 0.906396 -32 GGTGCCTGATGTTGACCGTCCGAACAGTCA 5 20 0 GTTGACCGTC 0.948349 -113 ATTTTAGTTTGTTAACATTCTGCTAAATTA 5 80 1 GTTAACATTC 0.871141 -53 TGCGTTAAGCGTTTACATTCGCAAAATTCA 8 62 1 GTTTACATTC 0.727934 -139 GATCACCTGCCTGTTGAATT 9 143 0 GATCACCTGC 0.928209 -10 ********** Masking position 5 Map Score: 2.09651 Number of sites scoring better than the average of aligned sites = 1988 Number in coding regions = 1885 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 9 TGATCACCGTCGAAAAATGCAAATTTGCTT 1 64 1 CGAAAAATGC 0.97138 -237 TATATTACGCCGCAAAATCCTTACAATAAA 1 107 0 CGCAAAATCC 0.987092 -194 AAGAAGCGTTCCCAGAATCCATGCGAAATA 2 31 0 CCCAGAATCC 0.959092 -97 CGTTTACATTCGCAAAATTCAGCCTAATGA 8 71 1 CGCAAAATTC 0.965561 -130 TATTTTAATCCGAAGAAGGCGCAAGAAAAA 9 67 0 CGAAGAAGGC 0.942873 -86 ********** Masking position 6 Map Score: 0.745329 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 203 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 GAACACTTTCATCATACCATGTGAATGCACA 1 198 0 ATCATACCAG 0.934593 -103 TCTCGGAGTCTTCATGCGATGAGCAAGGAGT 1 279 1 TTCATGCGAG 0.938479 -22 AACACGTCGAATCAGGCAAAGCCGGTCAAGA 2 98 1 ATCAGGCAAG 0.981266 -30 CCCGCTCTCTTTCAAGCAAGGGAAACGCAGA 4 14 0 TTCAAGCAAG 0.911445 -51 GACGGTCAACATCAGGCACCGGTTGCCACGG 5 30 1 ATCAGGCACG 0.972411 -103 ATCATGCCAAGCGTTCCTCAG 7 1 1 ATCATGCCAG 0.981266 -107 TCACATCGTAGTCATACACAGCCGGAATTAT 9 104 0 GTCATACACG 0.83935 -49 ********* * Masking position 4 Map Score: 2.22042 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 291 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 ********** No masking Map Score: -1.90893e-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: -1.90893e-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: -1.90893e-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