AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00780_ctra_reg_300.orf -o00780_ctra_300.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 sohB 102 Protease #2 CT495 211 ADP/ATP Translocase #3 pgsA_1 300 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase #4 CT775 298 snGlycerol 3-P Acyltransferase #5 bioF 42 8-amino-7-oxononanoate synthase Motif number 1 TTGAGAAGAAAAGGACCTGGAGTATAGTATT 1 13 1 AAGGACCGGA 0.969247 -90 ATAAAAATTAAAAGACCTGGAATACTATACT 1 33 0 AAAGACCGGA 0.974497 -70 AACGGTACTAAAACAGGGGGATTATAAAAAG 1 73 0 AAACAGGGGA 0.984169 -30 TGCCCAAAGAAAAGAGGAGGCGGAGTGATCA 2 12 1 AAAGAGGGGC 0.97892 -200 CTTTCCAACGAAACAACCGGCCCAAAAAGCT 3 16 0 AAACAACGGC 0.899049 -285 CGTCCCTGCTAAGGACGCGTACCCCTTAAAG 3 68 1 AAGGACGGTA 0.844924 -233 AAAGAAACGGAAAGAGAGGGATTCGAACCCT 3 106 0 AAAGAGAGGA 0.91981 -195 TTTTGTTGATAAGCTGGGGGAAATGGCGGGA 3 175 1 AAGCTGGGGA 0.86694 -126 ACCTCTTTGCAACCAGCGGAAAAGCTT 4 7 0 AACCAGCGAA 0.775339 -292 ATTTTAACAAAACCAAGAGGAAGT 4 285 1 AACCAAGGGA 0.889526 -14 ATAATCATTCAAAGAGCAGTCC 5 2 0 AAAGAGCGTC 0.889232 -41 ******* *** Masking position 2 Map Score: 8.39948 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 248 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 GGATTATAAAAAGAATTTTTAAATAAAAATT 1 55 0 AAGAATTTTA 0.963216 -48 CGGAGTGATCAAGAACTTGAATTTTAGCAGC 2 32 1 AAGAACTTGA 0.968524 -180 GGATTTCATAAAAATCTTGTAATTATGCATT 2 85 1 AAAATCTTGA 0.843545 -127 AGACTTTGGGAAAAATTTTTGTGATGCGAGG 2 162 0 AAAAATTTTG 0.774485 -50 CTTATCAACAAAAAACATTCAAACAAACAAA 3 157 0 AAAAACATTA 0.890197 -144 GCTGGAGGCTAAGAATTTTCAAGACAAGCTT 3 267 1 AAGAATTTTA 0.963254 -34 GAGTTGCGCAAATAACTTGGATTTCTGTAAA 4 130 1 AATAACTTGA 0.912259 -169 GATTTCTGTAAAGATTATTAACGAAAAATAT 4 149 1 AAGATTATTA 0.767421 -150 ATTATTAACGAAAAATATGAAGCCACGATAT 4 162 1 AAAAATATGA 0.890203 -137 TTGGTGCAAGAATAATTTTAACAAAACCAAG 4 271 1 AATAATTTTA 0.898558 -28 ********* * Masking position 4 Map Score: 5.81645 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 149 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 AGTTCTTGATCACTCCGCCTCCTCTTTTCTTTGGG 2 14 0 CCTCGCCTCT 0.980786 -198 AGGAACCTCGCACTCTGTTGAAATTTGGGATAATT 2 130 0 CCTCGTAATT 0.973006 -82 ACACTCCTTCCTAATTTAATAAATAT 2 196 0 CCTCTTAATT 0.847935 -16 TACTTTCGACCACTCAGTCATCTTTCCAACGAAAC 3 33 0 CCTCGTCTTT 0.99596 -268 GGGATTCGAACCCTCGGTACCCTTTAAGGGGTACG 3 85 0 CCTCGTCTTT 0.99596 -216 GGGTTCGAATCCCTCTCTTTCCGTTTCTTTACATT 3 107 1 CCTCCTCGTT 0.962213 -194 CATAGCTAAACTCTCTGCTTGCTTTTGGAGTGTCT 3 208 1 CCTCGCCTTT 0.994008 -93 * *** ** **** Masking position 4 Map Score: 5.45421 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 26 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 TCTTTTAATTTTTATTTAAAAATTCTTTTT 1 49 1 TTTATTTAAA 0.559526 -54 GTTCCCTGGATTTCATAAAAATCTTGTAAT 2 78 1 TTTCATAAAA 0.920075 -134 TATTGAAGACTTTGGGAAAAATTTTTGTGA 2 169 0 TTTGGGAAAA 0.748661 -43 TCTCTTTCCGTTTCTTTACATTGTGTTTTC 3 120 1 TTTCTTTACA 0.839121 -181 CAAACAAAAATTTCAGAAAACACAATGTAA 3 135 0 TTTCAGAAAA 0.918119 -166 GAAATTTTTGTTTGTTTGAATGTTTTTTGT 3 151 1 TTTGTTTGAA 0.71017 -150 AGTGTCTATGTTTCATAATATGTGTCATTG 3 236 1 TTTCATAATA 0.792885 -65 AGAGAGATAGTTTCTTAGCAAGAGCAGAGC 4 93 1 TTTCTTAGCA 0.777109 -206 ATAACTTGGATTTCTGTAAAGATTATTAAC 4 141 1 TTTCTGTAAA 0.908807 -158 ACGATATCTTTTTGATAATAAATGAAAAGA 4 186 1 TTTGATAATA 0.690607 -113 ACAGGTTTGCATTCTGAAAAGAACTATTCT 4 213 0 ATTCTGAAAA 0.690338 -86 TCCTCTTGGTTTTGTTAAAATTATTCTTGC 4 276 0 TTTGTTAAAA 0.931195 -23 ********** Masking position 10 Map Score: 5.1936 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 511 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 TAGCAACAAAACGGTACTAAAACAGG 1 87 0 CAAAACGGTA 0.895131 -16 ACAACCGGCCCAAAAAGCTCCGAA 3 5 0 CAAAAAGCTC 0.908159 -296 CATAGACACTCCAAAAGCAAGCAGAGAGTT 3 216 0 CCAAAAGCAA 0.918988 -85 CCGCTGGTTGCAAAGAGGTAACAATCACTC 4 19 1 CAAAGAGGTA 0.980759 -280 ACATCCTAACCAGAGAGATAGTTTCTTAGC 4 82 1 CAGAGAGATA 0.857325 -217 CATTTATTATCAAAAAGATATCGTGGCTTC 4 180 0 CAAAAAGATA 0.934483 -119 TTTAACAAAACCAAGAGGAAGT 4 287 1 CCAAGAGGAA 0.947349 -12 TATAATCATTCAAAGAGCAGTCC 5 4 0 CAAAGAGCAG 0.90721 -39 ********** Masking position 4 Map Score: 3.38001 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 133 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 CTGGAATACTATACTCCAGGTCCTTTTCTTC 1 17 0 ATATCCAGGT 0.981436 -86 CTGGAGTATAGTATTCCAGGTCTTTTAATTT 1 29 1 GTATCCAGGT 0.991675 -74 ACTTGCTGCTAAAATTCAAGTTCTTGATCAC 2 36 0 AAATTCAAGT 0.865643 -176 AGATTTTTATGAAATCCAGGGAACTAGAATA 2 71 0 GAATCCAGGG 0.987162 -141 AATCTTTACAGAAATCCAAGTTATTTGCGCA 4 134 0 GAATCCAAGT 0.986972 -165 *** ******* Masking position 5 Map Score: 1.57184 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 22 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 ACTAAAACAGGGGGATTATAAAAAGAATTTTT 1 66 0 GGGGATATAA 0.860577 -37 TGTTGAAATTTGGGATAATTACTGGATGCTTG 2 118 0 TGGGATATAC 0.962084 -94 GTTGTTTCGTTGGAAAGATGACTGAGTGGTCG 3 30 1 TGGAAAATAC 0.967854 -271 TTGATAAGCTGGGGGAAATGGCGGGAAACATA 3 180 1 GGGGGAATGC 0.977169 -121 GGGAAATGGCGGGAAACATAGCTAAACTCTCT 3 192 1 GGGAAAATGC 0.986744 -109 AATTTGGATATGGAAATATTGCACTCTTTGGT 4 244 1 TGGAAAATGC 0.979313 -55 ****** ** ** Masking position 8 Map Score: 1.16628 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 67 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 ACACTCCTTCCTAATTTAAT 2 202 0 ACACTCCTTC 0.887067 -10 ACCGAGGGTTCGAATCCCTCTCTTTCCGTT 3 102 1 CGAATCCCTC 0.879798 -199 CAAAGAGGTAACAATCACTCATTATAGGGA 4 29 1 ACAATCACTC 0.976862 -270 CACTACAGCAACATTCGCTCCCTATAATGA 4 47 0 ACATTCGCTC 0.951805 -252 TTGCTAAGAAACTATCTCTCTGGTTAGGAT 4 84 0 ACTATCTCTC 0.81099 -215 GCGCAACTCTACAATAGCTCTGCTCTTGCT 4 109 0 ACAATAGCTC 0.956059 -190 ATAAATGAAAAGAATAGTTCTTTTCAGAAT 4 203 1 AGAATAGTTC 0.782076 -96 CCTCATAGCTATAATCATTCAAAGAGCAGT 5 13 0 ATAATCATTC 0.718554 -30 ********** Masking position 5 Map Score: 0.452513 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 247 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: -2.18604e-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: -2.18604e-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 11 ********** No masking Map Score: -2.18604e-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