AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -icrp_ctra_opreg_100.orf -g0.413 -x5 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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 CT181 300 hypothetical protein #2 pdhA 221 Pyruvate Dehydrogenase Alpha #3 CT338 283 hypothetical protein #4 yrbH 31 GutQ/KpsF Family Sugar-P Isomerase #5 sucB_2 245 Dihydrolipoamide Succinyltransferase #6 uhpC 300 Hexosphosphate Transport #7 CT565 90 hypothetical protein #8 CT569 61 predicted OMP [leader (16) peptide] #9 CT573 127 hypothetical protein #10 CT646 100 hypothetical protein Motif number 1 CCAATAAGTTAAGAAAGCTAGTAGCTCTGTGAAT 1 83 0 AAGAAAGAAG 0.924195 -218 GGAGGTGTCGAATATAGGAACGAAGAGAGCCTAT 1 153 1 AATATAGAAA 0.522356 -148 TTTTTGTTATAAGAAAAATAGTAAATAACATCAT 1 222 0 AAGAAAAAAA 0.985795 -79 GCGAGGTTATCATAAAGTAACGAAAAGCTTTTAT 1 263 1 CATAAAGAAA 0.617472 -38 ACACCCAATGCAGAAAACCAAAAATCTCGAAATA 3 158 0 CAGAAAAAAA 0.956794 -126 CTCAAAGAGGAAAAAAATGACAAATACCAGGGAA 3 205 0 AAAAAAAAAA 0.785778 -79 TTAAACCTTAAAGAAAACGAAGAGAGAAAACCCT 5 27 0 AAGAAAAAAG 0.966763 -219 TCAATATGAGAAGAAGATTATCAACTGGCTTTTA 5 177 0 AAGAAGAAAA 0.874648 -69 AGGTGTGTCAAATAAAAGAAATAATAGAGAG 6 8 0 AATAAAAAAA 0.923478 -293 TTGCTGTGTAAAGAGAGGGAGTAGGGGTGAGGAT 6 74 0 AAGAGAGAAG 0.739949 -227 CTAGAAGCTTAAGAAAAATACAAATGCATACTGA 6 247 0 AAGAAAAAAA 0.985795 -54 AGATAATTTAAATATAAACATAAAAAACCAT 7 8 0 AATATAAAAA 0.722924 -83 ATTTAATAAAAAGAAAAAAATCAGGTATGGCTT 7 68 1 AAGAAAAAAG 0.966763 -23 GGAAACTGTGAAGAAAACAAAAAAAAGAAAACAA 8 20 1 AAGAAAAAAA 0.985795 -42 AAACAAAAAAAAGAAAACAATCCATTACGTTAGT 8 34 1 AAGAAAAACA 0.931235 -28 ATTTTTACAAAAGAAAATAAGAAAAGCCGTTTTT 9 47 0 AAGAAAAAAA 0.985795 -81 TAACTGATTTGAGAAAAAAAATCAATTTTTACAA 9 71 0 GAGAAAAACA 0.617168 -57 AACAACAGAGAAACAAAAAAGAATTGTAT 9 109 0 CAGAGAAAAA 0.837882 -19 CATCTTTTTCAAGAAAAACATTAATTATAAACAG 10 21 0 AAGAAAAAAA 0.985795 -80 TCATTTTAAAAAGATAAAGAAAAACGCTAA 10 81 1 AAGATAAAAA 0.937512 -20 ******* * ** Masking position 10 Map Score: 31.4284 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 290 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 2 TTATTTACTATTTTTCTTATAACAAAAAAC 1 228 1 TTTTTCTTAT 0.801037 -73 CTCGCATGAGGTTTTTTGTTATAAGAAAAA 1 238 0 GTTTTTTGTT 0.916497 -63 GTGCCGAAAAGTTTTTTTTTGTAGCATAGA 2 51 1 GTTTTTTTTT 0.906914 -171 GAGATTTTTGGTTTTCTGCATTGGGTGTTG 3 164 1 GTTTTCTGCA 0.849329 -120 TTCTCTCTTCGTTTTCTTTAAGGTTTAAGC 5 33 1 GTTTTCTTTA 0.922708 -213 AAAGGCATTTTTTATCTGTAAAAGCCAGTT 5 159 1 TTTATCTGTA 0.691326 -87 GAAGGCTTTAGTATTCTGTTAACTCAATAT 5 204 0 GTATTCTGTT 0.681217 -42 CTCTCTATTATTTCTTTTATTTGACACA 6 9 1 TATTTCTTTT 0.636029 -292 CTAAGACCTCGTTTTTTGCTATCAGTCTAG 6 200 0 GTTTTTTGCT 0.821442 -101 TGCATTTGTATTTTTCTTAAGCTTCTAGAG 6 253 1 TTTTTCTTAA 0.609008 -48 ATGGTTTTTTATGTTTATATTTAAA 7 6 1 TTTTTATGTT 0.644376 -85 TTATATTTAAATTATCTTTTGATAATTGTT 7 25 1 ATTATCTTTT 0.490915 -66 ATACCTGATTTTTTTCTTTTTATTAAATTA 7 66 0 TTTTTCTTTT 0.966017 -25 TCTTTTTTTTGTTTTCTTCACAGTTTCCCT 8 18 0 GTTTTCTTCA 0.833439 -44 GTAATGGATTGTTTTCTTTTTTTTGTTTTC 8 32 0 GTTTTCTTTT 0.96861 -30 TAAAAGCCGATTTTTTTGTTTTTTAACAAA 9 18 1 TTTTTTTGTT 0.909999 -110 AGAAAAGCCGTTTTTTTGTTAAAAAACAAA 9 32 0 TTTTTTTGTT 0.909999 -96 GGCTTTTCTTATTTTCTTTTGTAAAAATTG 9 53 1 ATTTTCTTTT 0.842129 -75 TAAAAATTGATTTTTTTTCTCAAATCAGTT 9 74 1 TTTTTTTTCT 0.790004 -54 TTCTTTTTTGTTTCTCTGTTGTT 9 115 1 TTTCTCTGTT 0.772507 -13 AAAAGATGTTTTTATTTTTTAAAATGAGCG 10 47 1 TTTATTTTTT 0.618687 -54 TTAGCGTTTTTCTTTATCTTTTTAAA 10 85 0 TTTTTCTTTA 0.91665 -16 ********** Masking position 5 Map Score: 20.805 Number of sites scoring better than the average of aligned sites = 847 Number in coding regions = 847 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 3 GAAACCACAGAAAAGACGCTTAAACCTTAAA 5 49 0 AAAAGACGTT 0.96152 -197 TACACTCACCTGAAGGCGGTTAAGCACTCCC 5 102 0 TGAAGGCGTT 0.525206 -144 TTAAACCCTCAAAAGGCATTTTTTATCTGTA 5 148 1 AAAAGGCATT 0.866434 -98 TTTTATCTGTAAAAGCCAGTTGATAATCTTC 5 168 1 AAAAGCCATT 0.947301 -78 ACTCAATATGAGAAGAAGATTATCAACTGGC 5 182 0 AGAAGAAGTT 0.7833 -64 AATAGCTTTTAGAAGACAATACGTTTGCTGT 6 101 0 AGAAGACATA 0.8205 -200 ATTGTCTTCTAAAAGCTATTAAGCTAAATGA 6 112 1 AAAAGCTATA 0.754242 -189 ACGAGGTCTTAGAAGCTGATACTTTCGTCTC 6 218 1 AGAAGCTGTA 0.807319 -83 AACAATTATCAAAAGATAATTTAAATATAAA 7 24 0 AAAAGATATT 0.831658 -67 TTTCATATAAAAGCCGATTTTTTTGTTTT 9 9 1 AAAAGCCGTT 0.970858 -119 AGAAAATAAGAAAAGCCGTTTTTTTGTTAAA 9 39 0 AAAAGCCGTT 0.962741 -89 CAATTTTTACAAAAGAAAATAAGAAAAGCCG 9 52 0 AAAAGAAATA 0.550721 -76 TTTTTCTTGAAAAAGATGTTTTTATTTTTTA 10 37 1 AAAAGATGTT 0.901803 -64 ******** ** Masking position 4 Map Score: 11.5999 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 167 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 4 AGATCCCTAGTCATATGAATA 1 2 0 TCATATGAAT 0.63908 -299 TTCAAATAAATCTTTTGAATTTCACTCTGG 2 158 0 TCTTTTGAAT 0.864672 -64 TTCAAAAGATTTATTTGAAAGACATTCTAG 2 169 1 TTATTTGAAA 0.92553 -53 AAGACATTTTTTTAATATAGCGGTGA 4 7 1 TTTTTTTAAT 0.570693 -25 ACACTAAACATTTTTTGAAACCACAGAAAA 5 66 0 TTTTTTGAAA 0.934758 -180 ATTATTTCTTTTATTTGACACACCTTACTC 6 17 1 TTATTTGACA 0.680979 -284 ATTTAAATTATCTTTTGATAATTGTTTAGT 7 29 1 TCTTTTGATA 0.697443 -62 ATTTTTTTCTTTTTATTAAATTAATCTCGT 7 59 0 TTTTATTAAA 0.569329 -32 AAATCGGCTTTTATATGAAA 9 1 0 TTATATGAAA 0.798402 -127 TTTCTTATTTTCTTTTGTAAAAATTGATTT 9 57 1 TCTTTTGTAA 0.679267 -71 AATTAATGTTTTTCTTGAAAAAGATGTTTT 10 29 1 TTTCTTGAAA 0.68305 -72 TGAAGAGCGCTCATTTTAAAAAATAAAAAC 10 54 0 TCATTTTAAA 0.831596 -47 TGAGCGCTCTTCATTTTAAAAAGATAAAGA 10 71 1 TCATTTTAAA 0.831596 -30 ********** Masking position 6 Map Score: 5.76407 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 369 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 5 ATCTGCTCGAGAGAAAGCACTTCTACCGGT 3 27 0 GAGAAAGCAC 0.965504 -257 CGTGGAACTTTAGCAAACACTTCTTCCCAA 3 72 0 TAGCAAACAC 0.954761 -212 AAAACGAAGAGAGAAAACCCTCTTCGTTAA 5 18 0 GAGAAAACCC 0.965594 -228 TAAGCTTCTAGAGCAAACACACTTGAATCG 6 270 1 GAGCAAACAC 0.990967 -31 CACTTGAATCGAGCTAACACCT 6 289 1 GAGCTAACAC 0.957272 -12 GGAAACTGTGAAGAAAACAAAAAAAAGAAA 8 20 1 AAGAAAACAA 0.893718 -42 AAACAAAAAAAAGAAAACAATCCATTACGT 8 34 1 AAGAAAACAA 0.893718 -28 ********** Masking position 6 Map Score: 4.62682 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 64 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 6 TACACAGAACCCGACCATCCTAACAAGGAG 1 34 1 CCGACCATCC 0.97729 -267 TAGATATTTACAAGCCTTCTCATAGGCTCT 1 178 0 CAAGCCTTCT 0.901647 -123 AACTTCAAACCAACTTCATCTCTAT 2 6 1 CAAACCAACT 0.717217 -216 CCGGAAAGGTCCGGCCTTCGCAAATATAAT 2 101 0 CCGGCCTTCG 0.950539 -121 CTTTTCCGCGCCGGCCTTGCATAGCCAGAG 2 134 1 CCGGCCTTGC 0.928616 -88 CCTACCAACTCAAACCATCCTCTGGGCAAC 3 102 0 CAAACCATCC 0.945218 -182 CTGCTTGAGACAGACCTACCAACTCAAACC 3 116 0 CAGACCTACC 0.952799 -168 ********** Masking position 5 Map Score: 0.803047 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 84 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 7 TTCGTTCCTATATTCGACACCTCCCGCGTTTCATTC 1 141 0 TTTCCACCCG 0.991219 -160 AAAAAAAAACTTTTCGGCACTACCCAGAAAAATGGA 2 35 0 TTTCCACCCA 0.990528 -187 CAGCTTGTTCTAAACAACCGGTAGAAGTGCT 3 6 1 TTTCAACCCG 0.990528 -278 GGGAAATCAGTATTCTCAACACCCAATGCAGAAAAC 3 174 0 TTTCAACCCA 0.989782 -110 CTATTTCGCGTTATCCGAACGTCCAAATGGCTCAAA 3 233 0 TATCAACCCA 0.967152 -51 * *** *** ** * Masking position 9 Map Score: 0.379223 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 13 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: -4.7582e-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: -4.7582e-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 10 ********** No masking Map Score: -4.7582e-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