AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i016_ecoli_bsub_300.orf -o016_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 xylB 71 xylulokinase #2 xylA 300 D-xylose isomerase #3 xylA 300 xylose isomerase #4 xylB 150 xylulose kinase Motif number 1 CCGGTTATCGGTAGCGATACCGGGCATTTTTTTAAG 1 35 1 GCATACGGGA 0.989803 -37 CAATTTTTAGCAACTAAACAGGGGAAAACAATTAC 2 10 1 GCAAACGGGA 0.980741 -291 ATAAAATGGAATGATGAAACTGGGTAATTCCTCGAA 2 142 0 ATAAACGGGA 0.920848 -159 GATGGATGATGTCGTAATATTGGGCACTCCCTTTCA 2 243 0 GTATATGGGA 0.980349 -58 GAACACATTAGATTTAATAAAGGGAAGATTCGCTAT 3 119 0 GTATAAGGGA 0.995089 -182 TTGAATGAATTTATTTTTAAGGGGGAAATCAC 3 279 1 TTTTAAGGGA 0.877276 -22 CAATAGGAAAGGAATCATGACGGGTAATTCAGTGAC 4 45 0 GTATGAGGGA 0.990004 -106 CCTATTGCTTGTTGTTATGACGGGTAACTTCTATAA 4 74 1 GTATGAGGGA 0.990004 -77 AGAGTGAATGGTTTTTTAAAAGGGCAAGGAGTGAAA 4 123 1 GTTAAAGGGA 0.971088 -28 * * **** *** * Masking position 16 Map Score: 10.3018 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 116 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 2 ATTACGATTTTTGGTTTATTTCTTGATTTA 2 62 1 TTGGTTTATT 0.934726 -239 GACCGAGATCTTACTTTTGTTGCGCAATTG 2 93 1 TTACTTTTGT 0.90626 -208 ATTGTACTTATTGCATTTTTCTCTTCGAGG 2 119 1 TTGCATTTTT 0.864748 -182 AACTTTTGATTTACTTTTTTGACAAAGGTT 3 23 1 TTACTTTTTT 0.973261 -278 AATATTTTTTTTAGTTTTTTATGAACACAT 3 147 0 TTAGTTTTTT 0.983394 -154 TGAAAATAAGTTAGTTTGTTTAAACAACAA 3 203 1 TTAGTTTGTT 0.97552 -98 ACATCACCTATTAGTTTGTTGTTTAAACAA 3 218 0 TTAGTTTGTT 0.97552 -83 TTTAGAGTGAATGGTTTTTTAAAAGGGCAA 4 120 1 ATGGTTTTTT 0.912297 -31 ********** Masking position 6 Map Score: 8.27139 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 79 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 GTGCGCTCGCTCGCAAAATAAAATGGAATGATGAAACTGGG 2 154 0 TAAATAAAGA 0.965839 -147 AAAAAGTAAATCAAAAGTTATTATTAAAAGA 3 1 0 TAATTTAAGA 0.833109 -300 TGATACTTAATTTAAAGATTAAACAAATGGAGTGGATGAAG 3 69 0 TAAATAAAGA 0.985597 -232 TTAAATTAAGTATCAACATAGTACATAGCGAATCTTCCCTT 3 95 1 TAAATTAAGA 0.970734 -206 TTTTATGAACACATTAGATTTAATAAAGGGAAGATTCGCTA 3 120 0 ATAATAAAGA 0.910806 -181 AAAAAACTAAAAAAAATATTGAAAATACTGACGAGGTTATA 3 157 1 AAAATAAAGA 0.972288 -144 TGACGAGGTTATATAAGATGAAAATAAGTTAGTTTGTTTAA 3 185 1 AAAATAAATA 0.779125 -116 GGTGATGTACTTACTATATGAAATAAAATGCATCTGTATTT 3 240 1 TTAATAAAGC 0.893635 -61 CCATTCACTCTAAATAAATCCTAATTATAGAAGTTACCCGT 4 93 0 TTAATTAAGA 0.925118 -58 * ** ** ** * ** Masking position 9 Map Score: 3.72398 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 43 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 ATCGATCGTTCCTTAAAAAAATGCCCG 1 55 0 GTTCCTTAAA 0.95915 -17 CCCCTGTTTAGTTGCTAAAAATTG 2 5 0 GTTGCTAAAA 0.97356 -296 TCTTACTTTTGTTGCGCAATTGTACTTATT 2 101 1 GTTGCGCAAT 0.872413 -200 CTCCCTTTCAGTTGCTCAATTATGTTATTT 2 223 0 GTTGCTCAAT 0.961211 -78 AGTGGATATCGCTGATCAAACCTTTGTCAA 3 41 0 GCTGATCAAA 0.885974 -260 AATCTAATGTGTTCATAAAAAACTAAAAAA 3 141 1 GTTCATAAAA 0.846821 -160 CTATTAGTTTGTTGTTTAAACAAACTAACT 3 211 0 GTTGTTTAAA 0.949474 -90 AGAGTGAATGGTTTTTTAAAAGGGCAAGGA 4 123 1 GTTTTTTAAA 0.744236 -28 ********** Masking position 8 Map Score: 3.54717 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 468 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 5 TAAAAAAATGCCCGGTATCGCTACCGATAACCGG 1 35 0 CCCGTATGAC 0.990021 -37 AAAGGGAGTGCCCAATATTACGACATCATCCATC 2 245 1 CCCATATAAC 0.981128 -56 AGCGAATCTTCCCTTTATTAAATCTAATGTGTTC 3 121 1 CCCTTATATC 0.940488 -180 AGCTCCAGATCCTGCTATCAATACCAAGTCACTG 4 18 1 CCTGTATAAC 0.976732 -133 CACTGAATTACCCGTCATGATTCCTTTCCTATTG 4 47 1 CCCGCATACC 0.990225 -104 ATAGAAGTTACCCGTCATAACAACAAGCAATAGG 4 74 0 CCCGCATAAC 0.995487 -77 **** *** * ** Masking position 7 Map Score: 3.33412 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 129 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 ATTGTTTTCCCCTGTTTAGTTGCTAAAAATTG 2 9 0 CCTTATTGCT 0.983323 -292 ATTGGGCACTCCCTTTCAGTTGCTCAATTATGTT 2 227 0 CCTCATTGCT 0.99575 -74 TCCACTTCATCCACTCCATTTGTTTAATCTTTAA 3 65 1 CCTCATTGTT 0.990474 -236 AAGTACATCACCTATTAGTTTGTTGTTTAAACAA 3 218 0 CCTAGTTGTT 0.93884 -83 CGTCATGATTCCTTTCCTATTGCTTGTTGTTATG 4 59 1 CCTCTTTGCT 0.98933 -92 ** * ** ***** Masking position 5 Map Score: 1.21918 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 40 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 ********** No masking Map Score: -1.65313e-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 8 ********** No masking Map Score: -1.65313e-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 9 ********** No masking Map Score: -1.65313e-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