AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_ctra_reg_100.orf -o00190_ctra_100.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 atpK 41 ATP Synthase Subunit K #2 CT309 166 hypothetical protein #3 atpE 108 ATP Synthase Subunit E #4 sdhB 236 Succinate Dehydrogenase #5 sdhC 25 Succinate Dehydrogenase #6 CT593.1 221 hypothetical protein-possible frameshift with CT593 #7 CT663 300 hypothetical protein #8 CT665 43 hypothetical protein #9 CT666 26 hypothetical protein #10 fliI 73 Flagellum-specific ATP Synthase #11 fliF 272 Flagellar M-Ring Protein #12 ppa 247 Inorganic Pyrophosphatase Motif number 1 GGCTAATTTGAAAGAGACATTTATTTTGAATA 4 171 1 AAAGAGCTTT 0.983526 -66 TTGAATATTTATAGAGGCGTTCCTGGGAAATA 4 196 1 ATAGAGCTTC 0.963621 -41 AATTAGGGATGGAAGCCTTTCAGTTGAGGG 6 9 1 ATGGAACTTT 0.703126 -213 GCCCTTCCATAAAGAGCCCTCCTCAAACATCA 6 88 0 AAAGAGCTCC 0.951579 -134 GACAGCGAATAAGGAGGCGTTCATATGAGGAG 6 133 1 AAGGAGCTTC 0.987437 -89 AAATCAAAAGAACGAGTCGTTCGTGCCCGATT 7 75 1 AACGAGCTTC 0.967017 -226 CATCTCGATAGAGGAGCCTTTTCTGTTTTCTC 7 150 0 GAGGAGCTTT 0.954908 -151 TCTGTAACAAAAAGAGGCTATTAAAAACAATA 11 60 0 AAAGAGCATT 0.893705 -213 CTCTCAATTAAAAGAGCCCTTTTGTCTTCTGT 11 87 0 AAAGAGCTTT 0.952677 -186 TTGTTCACAAGAAGAAGCCTTCTTTTTCATCC 11 162 1 GAAGAACTTC 0.875816 -111 ****** * *** Masking position 5 Map Score: 9.76605 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 144 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 CATATTCTGTAGATGAGCCAGAAATTTCATA 4 26 1 AGATGGCCAG 0.900043 -211 TCATCATGATGTTTGAGGAGGGCTCTTTATG 6 82 1 GTTTGGGAGG 0.888276 -140 GGCTCTTTATGGAAGGGCAGGAACCATGAGG 6 102 1 GGAAGGCAGG 0.956402 -120 GGAGGCGTTCATATGAGGAGGGAGATAGTAC 6 145 1 ATATGGGAGG 0.879506 -77 GAATGAGTTGATTTGTGCCGGGAAAATGTGT 7 26 1 ATTTGGCCGG 0.967462 -275 AGAACGAGTCGTTCGTGCCCGATTTTTTTCT 7 83 1 GTTCGGCCCG 0.866493 -218 TCTCAGTTAGAGATGAGCACGTGAATAC 7 283 1 AGATGGCACG 0.957326 -18 ATAGAGCAAGGGTAGAGCCCGCTAAGTATCC 11 205 0 GGTAGGCCCG 0.924891 -68 CTGCAAAATAATATGAGCCGGACGTAGGAT 12 10 0 ATATGGCCGG 0.977544 -238 CGAATAAGCCGGATGCGCAGGATAATTGCGC 12 199 1 GGATGGCAGG 0.985799 -49 ***** ***** Masking position 5 Map Score: 8.44013 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 68 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 TATGCGTTGAGAAAAGAAGAACTATCTCTG 2 101 1 GAAAAGAAGA 0.962448 -66 ATCTGATACCAAGAAAAACAACGTTTA 3 92 0 ACCAAGAAAA 0.862379 -17 CTGAAGAGAAAAAATTCTCTCT 5 14 0 GAAGAGAAAA 0.84732 -12 GAAAGGGATGAAAGAGAAAACAGAAAAGGC 7 137 1 AAAGAGAAAA 0.870901 -164 TACCTACTTTAAAAAGAAAAACGATTTCTC 7 181 0 AAAAAGAAAA 0.951136 -120 TGTCTTCTGTAACAAAAAGAGGCTATTAAA 11 67 0 AACAAAAAGA 0.67648 -206 TCTTCTTGTGAACAAGAAGAAAATTAGCAT 11 147 0 AACAAGAAGA 0.969462 -126 TCTTCTTGTTCACAAGAAGAAGCCTTCTTT 11 157 1 CACAAGAAGA 0.881198 -116 GAAAAGGATGAAAAAGAAGGCTTCTTCTTG 11 169 0 AAAAAGAAGG 0.907771 -104 TAAGTATCCTACAAAGAAAAGGATGAAAAA 11 184 0 ACAAAGAAAA 0.86013 -89 TTTTCACAATGACAAGAATAAAAGCAAAAA 12 109 1 GACAAGAATA 0.772084 -139 GAATAAAAGCAAAAAGAAAGGCTGCCGATA 12 124 1 AAAAAGAAAG 0.86013 -124 TTTACTGCGAGAACAGAAGACTAAAACTAT 12 164 1 GAACAGAAGA 0.828372 -84 ********** Masking position 5 Map Score: 10.1735 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 490 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 TATGTTGGTTAAATCGTTATTGGGAAAATTCGTTGACGATG 2 32 1 AAATTGAATC 0.98289 -135 CTTCAACTAAGAAACTCTCTAGACAGCTCTCCAGAGATAGT 2 121 0 GAATTGACTC 0.946234 -46 AAACTACGATCGCTACATATTCTGTAGATGA 4 1 1 AAAGTGAATT 0.836502 -236 GCGTTCCTGGGAAATAATATTGGGAAAGTTTTGAG 4 212 1 GAATTGAATT 0.94582 -25 TCATATAATGAAACGAATGTAGGAAGATTTTTGTACTATCT 6 167 0 AAATTGAATT 0.960664 -55 TGTGCCGGGAAAATGTGTTTTGGGAGATGTCTTTAGAAATC 7 39 1 AAATTGAATC 0.982902 -262 TTAAAGTACAAAAGAATTTTAGAAAAAAATCGGGCACGAAC 7 93 0 AAATTGAATC 0.98289 -208 TTTCTTTTTAAAGTAGGTATTGGCATAACTCAGCATAAGGT 7 192 1 AAGTTGAATC 0.92301 -109 AAACTGATTCAAAATCCTATCGAAATCTTTCTTAGATAACC 11 19 1 AAATTGACTC 0.960835 -254 CAACCTATACGTAGAGCTTTTGTAAGAACTTACTTCATGGA 11 240 1 GTATTGAATT 0.710801 -33 *** * * * * * ** Masking position 10 Map Score: 6.55798 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 57 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 CTATTTTTTTCAAAAAAACGCACATCAACC 1 19 0 CAAAAAAACG 0.981589 -23 TCAACGCATACAAAAAAACTCCGAGTTTGC 2 81 0 CAAAAAAACT 0.929609 -86 AAGGTTAGATCATAACAACGTTTAAAATCA 3 24 0 CATAACAACG 0.924382 -85 ACGTTTATCTTAAAAAAACGATCAATTATG 3 69 0 TAAAAAAACG 0.856189 -40 TGATACCAAGAAAAACAACGTTTATCTTAA 3 86 0 AAAAACAACG 0.925418 -23 TCTCCCTCCTCATATGAACGCCTCCTTATT 6 140 0 CATATGAACG 0.675566 -82 TTTCCCGGCACAAATCAACTCATTCAGAGC 7 21 0 CAAATCAACT 0.729933 -280 CTTTAGAAATCAAAAGAACGAGTCGTTCGT 7 69 1 CAAAAGAACG 0.967939 -232 AGAATTTTAGAAAAAAATCGGGCACGAACG 7 92 0 AAAAAAATCG 0.679147 -209 CTACTTTAAAAAGAAAAACGATTTCTCATC 7 178 0 AAGAAAAACG 0.778502 -123 GTCTTTCGTACAAAAAACCTGTCTGAAAGG 12 54 1 CAAAAAACCT 0.733627 -194 ********** Masking position 4 Map Score: 6.66792 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 192 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 TTGAGAAAAGAAGAACTATCTCTGGAGAGCTG 2 107 1 AGAACATCTC 0.827889 -60 CCTTCAACTAAGAAACTCTCTAGACAGCTCTC 2 131 0 AAAACCTCTA 0.877292 -36 TGAAGAGAAAAAATTCTCTCTCCC 5 3 0 AATTCCTCTC 0.975556 -23 AGATTTTTGTACTATCTCCCTCCTCATATGAA 6 152 0 ATATCCCCTC 0.899438 -70 TCTGGGTCCGAAATACTCCCTCCCTAGCTATT 7 249 0 AATACCCCTC 0.957626 -52 AGATACCCTCTCTTTTACCGTT 9 15 0 AATACCTCTC 0.975556 -12 ATTTTGCAGTACAATCACTCTCGTCTTTCGTA 12 32 1 AAATCCTCTC 0.984621 -216 AAGATCACTCTCTATTAAAGTG 12 236 0 AGATCCTCTC 0.977307 -12 * **** ***** Masking position 1 Map Score: 5.41486 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 93 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 AATTAGGGATGGAAGCCTTTCAGT 6 4 1 TAGGGAGGAA 0.799324 -218 CCTTTCAGTTGAGGGATATAGCTGCTGTTTG 6 26 1 GAGGGAATAG 0.978557 -196 CAAACATCATGATGAACAGCGCACTTAATCG 6 66 0 GATGAAAGCG 0.799324 -156 CAGGAACCATGAGGGACAGCGAATAAGGAGG 6 119 1 GAGGGAAGCG 0.991195 -103 TTCATATGAGGAGGGAGATAGTACAAAAATC 6 152 1 GAGGGAATAG 0.978557 -70 TTCCAATAGCTAGGGAGGGAGTATTTCGGAC 7 245 1 TAGGGAGGAG 0.968462 -56 CGTATAGGTTGAGGAATAGAGCAAGGGTAGA 11 220 0 GAGGAAAGAG 0.978557 -53 ****** **** Masking position 6 Map Score: 3.90283 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 140 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 TAGCACGACATCTTTTGCTCCCTGTCGAGT 4 103 0 TCTTTTGCTC 0.798866 -134 GCTGGAATATTCTCTAGCACGACATCTTTT 4 117 0 TCTCTAGCAC 0.909962 -120 GAGAAAAAATTCTCTCTCCC 5 1 0 TCTCTCTCCC 0.906381 -25 TTTCTAAAATTCTTTTGTACTTTAAATTGA 7 109 1 TCTTTTGTAC 0.942611 -192 TTCTGTTTTCTCTTTCATCCCTTTCAATTT 7 132 0 TCTTTCATCC 0.779321 -169 AGATACCCTCTCTTTTACCGTTTACA 9 9 0 TCTCTTTTAC 0.87665 -18 TTTTTTAGGATCTCTCGTACGTAATGTTTG 10 25 0 TCTCTCGTAC 0.981754 -49 ATCACTCTCGTCTTTCGTACAAAAAACCTG 12 45 1 TCTTTCGTAC 0.971366 -203 ********** Masking position 5 Map Score: 3.76985 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 81 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 TATAGGAGGCTAATTTGAAAGAGACATTTAT 4 164 1 TATTTGAAAG 0.892742 -73 GCTATATCCCTCAACTGAAAGGCTTCCATCC 6 17 0 TAACTGAAAG 0.965482 -205 TTTTGTACTTTAAATTGAAAGGGATGAAAGA 7 121 1 TAATTGAAAG 0.971213 -180 GTGCTCATCTCTAACTGAGAGCTCTGGGTCC 7 272 0 CAACTGAGAG 0.941325 -29 AAGGGCTCTTTTAATTGAGAGTCCCTTTTGA 11 98 1 TAATTGAGAG 0.981499 -175 ATAAAACACTTTAATAGAGAGTGATCTT 12 230 1 TAATAGAGAG 0.929016 -18 * ********* Masking position 8 Map Score: 2.0754 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 19 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 AAAGTAGATACCCGCTATGTGAATCCAGAAT 4 61 1 CCCGCTAGTG 0.975547 -176 CGAGATTACACTCGACAGGGAGCAAAAGATG 4 94 1 CTCGACAGGA 0.918091 -143 ATATTCATTTCCCGATATAGGAGGCTAATTT 4 149 1 CCCGATAAGG 0.979649 -88 ACATCCCGATACGGAATGAATACAT 6 207 0 CCCGATAGGA 0.988206 -15 GATTTCTCATCTCGATAGAGGAGCCTTTTCT 7 158 0 CTCGATAAGG 0.942155 -143 AAGGGTAGAGCCCGCTAAGTATCCTACAAAG 11 198 0 CCCGCTAGTA 0.96214 -75 ******* *** Masking position 7 Map Score: 1.71909 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 23 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 11 AGCTCTCCAGAGATAGTTCTTCTTTTCTCA 2 108 0 AGATAGTTCT 0.904225 -59 GAAACTCTCTAGACAGCTCTCCAGAGATAG 2 122 0 AGACAGCTCT 0.878269 -45 AATAATATTGGGAAAGTTTTGAG 4 224 1 GGAAAGTTTT 0.840202 -13 AAACGAATGTAGGAAGATTTTTGTACTATC 6 168 0 AGGAAGATTT 0.765524 -54 AGGTTATCTAAGAAAGATTTCGATAGGATT 11 31 0 AGAAAGATTT 0.913683 -242 TCTCCATGAAGTAAGTTCTTACAAAAGCT 11 254 0 AGTAAGTTCT 0.800638 -19 CAATCCTTTCAGACAGGTTTTTTGTACGAA 12 58 0 AGACAGGTTT 0.880736 -190 TTATTCGTCCAGATAGTTTTAGTCTTCTGT 12 176 0 AGATAGTTTT 0.913683 -72 ********** Masking position 5 Map Score: 0.330313 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 182 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: 2.40407e-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: 2.40407e-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: 2.40407e-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