AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i337_bsub_mtub_300.orf -o337_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yfmT 249 similar to benzaldehyde dehydrogenase #2 yfmR 134 similar to ABC transporter (ATP-binding protein) #3 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #4 ypjD 300 alternate gene name: jojD #5 pcnA 300 pcnA Motif number 1 CGGGGATGTTTGTCCCCGGTCTC 2 3 0 TGTCCCCGGC 0.808448 -132 CGGGGACAAACATCCCCGGTCTTTTTCTTAT 2 16 1 CATCCCCGGC 0.877541 -119 TGTTCGCCCCCAAGCACATCATGA 3 18 0 TCGCCCCCAG 0.975148 -14 ACCTGTAAAACCGCCCTCAGCCAGATTGTTC 4 52 1 CCGCCCTCAC 0.983221 -249 CGCCCCGCTCCCTCGCCCAACGAATA 5 6 0 CCTCGCCCAC 0.979074 -295 GTCGCCTGCACCGCCCCGCTCCCTCGCCCAA 5 17 0 CCGCCCCGCC 0.991384 -284 TGCAGGCGACCCGCGCTGACCAATTGAGTCG 5 38 1 CCGCGCTGAC 0.962571 -263 ACCAATTGAGTCGCGCCAGTCACATCTATCA 5 56 1 TCGCGCCAGC 0.940562 -245 GGCAAATCGTGCGCCCCCGACACAGCGACTT 5 90 0 GCGCCCCCGC 0.990223 -211 CAAGACGCGACCGCACCCAAGGATTCTTAAT 5 134 1 CCGCACCCAG 0.944658 -167 CGAGGTATCGTCGTGCCCATCTCCGCGCGAC 5 182 0 TCGTGCCCAC 0.948968 -119 CGACGATACCTCGTCCCGACACCGGCCAATG 5 200 1 TCGTCCCGAA 0.691863 -101 ACCCTCGTTGCCGCACCCGTCGCATTGGCCG 5 222 0 CCGCACCCGC 0.99177 -79 CCTCCACCGACCGTCCCGGCCCACTTCGACT 5 261 1 CCGTCCCGGC 0.990892 -40 ********* * Masking position 6 Map Score: 21.7791 Number of sites scoring better than the average of aligned sites = 993 Number in coding regions = 920 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 2 TTATATGCAGTTCTTGTTGTATTATATTGTCGAA 1 50 1 TTCGTGTATA 0.844735 -200 CAATAAAATATTTTTCTGCTTTAAATGATAGAAG 1 96 1 TTTCTCTTTA 0.919088 -154 GACAACGCTGTTTCGCTTCTATCATTTAAAGCAG 1 111 0 TTTCTCTATA 0.96966 -139 TTTCTATCGGTTCATCTTGCATAAAATTGAATAT 1 176 0 TTCCTGCATA 0.982111 -74 TCGTCTGACGTTTTACTAGTTTTATTCCAGCGGC 2 65 1 TTTCTGTTTA 0.918134 -70 CTGAGGGCGGTTTTACAGGTATTACACTTTTGCT 4 38 0 TTTCAGTATA 0.887837 -263 AATTTTTTCATTTGGCTTGGTTCATTTCAATATG 4 85 0 TTTCTGGTTA 0.865462 -216 ATGAAAAAATTGCCGCTCCGATTAAAATAAAAAA 4 108 1 TGCCTCGATA 0.8326 -193 TTAATCTAATTTCTCCAAGCATCACACAAAACCC 4 150 1 TTCCAGCATA 0.928665 -151 ACAAAACCCCTTTTCCTTCCATTAGATAGCGTTT 4 175 1 TTTCTCCATA 0.97192 -126 TGTTTTCTTTTTCATCCACTATAATATAAACGCT 4 202 0 TTCCCCTATA 0.914244 -99 CCCGGCCCACTTCGACTGCCATTAGGCTGATCGA 5 275 1 TTCCTCCATA 0.982279 -26 *** ** **** * Masking position 14 Map Score: 10.3289 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 448 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 3 ATGATAGAAGCGAAACAGCGTTGTCGTATC 1 120 1 CGAAACAGCG 0.975704 -130 GAGACCGGGGACAAACATCCCCGGTCTTTT 2 11 1 ACAAACATCC 0.747615 -124 TGAACGAAACCTCCTATCATCCTC 4 287 0 CGAAACCTCC 0.980464 -14 CGCGGGTCGCCTGCACCGCCCCGCTCCCTC 5 23 0 CTGCACCGCC 0.904918 -278 CGTGCGCCCCCGACACAGCGACTTCTGTGA 5 84 0 CGACACAGCG 0.975225 -217 TCTCCGCGCGACAAACAGCCGGCGACAATA 5 164 0 ACAAACAGCC 0.900381 -137 ATGGGCACGACGATACCTCGTCCCGACACC 5 193 1 CGATACCTCG 0.864065 -108 TACCTCGTCCCGACACCGGCCAATGCGACG 5 206 1 CGACACCGGC 0.978597 -95 CGGTCGGTGGAGGAACCGGCAACCCTCGTT 5 244 0 AGGAACCGGC 0.881975 -57 ********** Masking position 5 Map Score: 5.58692 Number of sites scoring better than the average of aligned sites = 1293 Number in coding regions = 1146 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 4 TTTCCATGAAATTCGTCTGACGTTTTACTAG 2 53 1 ATTCGTCTGC 0.752094 -82 TACTAGTTTTATTCCAGCGGCTGATTTAAAA 2 78 1 ATTCCAGCGC 0.874858 -57 TTTTATTTTAATCGGAGCGGCAATTTTTTCA 4 109 0 ATCGGAGCGC 0.965438 -192 GGGTCGCCTGCACCGCCCCGCTCCCTCGCCC 5 19 0 CACCGCCCCC 0.887206 -282 GATAGATGTGACTGGCGCGACTCAATTGGTC 5 55 0 ACTGGCGCGC 0.877908 -246 AAGGTGGGCAAATCGTGCGCCCCCGACACAG 5 96 0 AATCGTGCGC 0.914051 -205 ATTTGCCCACCTTCGAGCGACAAGACGCGAC 5 114 1 CTTCGAGCGC 0.990355 -187 TCGTGCCCATCTCCGCGCGACAAACAGCCGG 5 172 0 CTCCGCGCGC 0.994391 -129 ACGACGATACCTCGTCCCGACACCGGCCAAT 5 199 1 CTCGTCCCGC 0.834993 -102 CCGGTTCCTCCACCGACCGTCCCGGCCCACT 5 255 1 CACCGACCGC 0.98115 -46 TCCCGGCCCACTTCGACTGCCATTAGGCTGA 5 274 1 CTTCGACTGC 0.929893 -27 ********* * Masking position 11 Map Score: 8.92488 Number of sites scoring better than the average of aligned sites = 1010 Number in coding regions = 948 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 GCACCGCCCCGCTCCCTCGCCCAACGAATA 5 8 0 GCCCCGCCCA 0.931088 -293 GCGCGGGTCGCCTGCACCGCCCCGCTCCCTCGC 5 21 0 CCCACGCCCC 0.972917 -280 CACGATTTGCCCACCTTCGAGCGACAAGACGCG 5 110 1 CCCTCGAGCG 0.994374 -191 CTTCGAGCGACAAGACGCGACCGCACCCAAGGA 5 124 1 CAACCGACCG 0.846028 -177 ATCGTCGTGCCCATCTCCGCGCGACAAACAGCC 5 174 0 CCCTCGCGCG 0.993067 -127 CCCGACACCGGCCAATGCGACGGGTGCGGCAAC 5 214 1 GCATCGACGG 0.924948 -87 TGCGACGGGTGCGGCAACGAGGGTTGCCGGTTC 5 229 1 GCCACGAGGG 0.938636 -72 GTTGCCGGTTCCTCCACCGACCGTCCCGGCCCA 5 251 1 CCCACGACCG 0.996215 -50 ACCGTCCCGGCCCACTTCGACTGCCATTAGGCT 5 270 1 CCCTCGACTG 0.9776 -31 ** ** ****** Masking position 8 Map Score: 7.13257 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 481 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 TTGCTTTATGCCCTTTTCCACATCAGCCCC 4 13 0 CCCTTTTCCA 0.961305 -288 ACAGGTATTACACTTTTGCTTTATGCCCTT 4 28 0 CACTTTTGCT 0.946766 -273 CACACAAAACCCCTTTTCCTTCCATTAGAT 4 172 1 CCCTTTTCCT 0.990167 -129 AATGTTTAAGCACGTTTGCTGTTTTCTTTT 4 225 0 CACGTTTGCT 0.965476 -76 CCTGCACCGCCCCGCTCCCTCGCCCAACGA 5 14 0 CCCGCTCCCT 0.963075 -287 AACGAGGGTTGCCGGTTCCTCCACCGACCG 5 244 1 GCCGGTTCCT 0.942381 -57 ********** Masking position 6 Map Score: 2.24821 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 360 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 7 AATGATTAGAATATTTTGAATATTTCTAGGA 1 21 0 ATATTTTAAT 0.95311 -229 AAGCAGAAAAATATTTTATTGACTACGTCAA 1 86 0 ATATTTTTTG 0.786805 -164 GGGCGAATCTATTTTTTCTATCGGTTCATCT 1 193 0 ATTTTTTTAT 0.871641 -57 AGATTCGCCCATATTTTGATTTGCGGTTATA 1 214 1 ATATTTTATT 0.939822 -36 GTTCATGTGTACATTTTAAATCAGCCGCTGG 2 91 0 ACATTTTAAT 0.862177 -44 CGGAGCGGCAATTTTTTCATTTGGCTTGGTT 4 97 0 ATTTTTTATT 0.871697 -204 ATTAAAAAACATATTTTTTATTTTAATCGGA 4 124 0 ATATTTTTAT 0.939776 -177 ******* *** Masking position 1 Map Score: 2.09966 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 193 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 8 ********** No masking Map Score: -2.59815e-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 AAAATTACTATCCTATGATACGACAACGCTGTTT 1 132 0 TCCTTTACGC 0.953244 -118 GGTCAGCATCTCCTTTATAACCGCAAATCAAAAT 1 226 0 TCCTTAACCC 0.995767 -24 GGTTCCTATCAATCCTCACGTAAGTTC 2 118 0 TCCTTATCCC 0.993969 -17 AAAGTGTAATACCTGTAAAACCGCCCTCAGCCAG 4 42 1 ACCTTAACCC 0.98626 -259 TTTGCTGTTTTCTTTTTCATCCACTATAATATAA 4 207 0 TCTTTATCCC 0.969311 -94 **** * **** * Masking position 6 Map Score: 0.534142 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 35 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 ********** No masking Map Score: -2.59815e-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 CCTCCTAGAAATATTCAAAATATTCTAATC 1 19 1 ATATTCAAAA 0.853265 -231 AGATGAACCGATAGAAAAAATAGATTCGCC 1 193 1 ATAGAAAAAA 0.688065 -57 GAAATGCAGGATAAGAAAAAGACCGGGGAT 2 27 0 ATAAGAAAAA 0.814967 -108 GTTCATTTCAATATGCAGAACAATCTGGCT 4 70 0 ATATGCAGAA 0.85447 -231 GAACCAAGCCAAATGAAAAAATTGCCGCTC 4 96 1 AAATGAAAAA 0.91447 -205 GCTCCGATTAAAATAAAAAATATGTTTTTT 4 122 1 AAATAAAAAA 0.783212 -179 TGGAGAAATTAGATTAAAAAACATATTTTT 4 137 0 AGATTAAAAA 0.888982 -164 ATATTATAGTGGATGAAAAAGAAAACAGCA 4 209 1 GGATGAAAAA 0.794412 -92 GCCGGCGACAATATTAAGAATCCTTGGGTG 5 147 0 ATATTAAGAA 0.853284 -154 ********** Masking position 7 Map Score: 0.511216 Number of sites scoring better than the average of aligned sites = 1537 Number in coding regions = 1198 Number in noncoding regions = 339 Number of orfs with sites within 600 bp upstream = 354 Fraction of orfs with sites within 600 bp upstream = 0.0568583 Motif number 12 ********** No masking Map Score: -2.59815e-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: -2.59815e-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: -2.59815e-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