AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i337_weak_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 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 Motif number 1 TTATATGCAGTTCTTGTTGTATTATATTGTCGAA 1 50 1 TTCGTGTATA 0.896321 -200 CAATAAAATATTTTTCTGCTTTAAATGATAGAAG 1 96 1 TTTCTCTTTA 0.948432 -154 GACAACGCTGTTTCGCTTCTATCATTTAAAGCAG 1 111 0 TTTCTCTATA 0.978828 -139 TTTCTATCGGTTCATCTTGCATAAAATTGAATAT 1 176 0 TTCCTGCATA 0.983494 -74 TCGTCTGACGTTTTACTAGTTTTATTCCAGCGGC 2 65 1 TTTCTGTTTA 0.954353 -70 CTGAGGGCGGTTTTACAGGTATTACACTTTTGCT 4 38 0 TTTCAGTATA 0.938304 -263 AATTTTTTCATTTGGCTTGGTTCATTTCAATATG 4 85 0 TTTCTGGTTA 0.925514 -216 ATGAAAAAATTGCCGCTCCGATTAAAATAAAAAA 4 108 1 TGCCTCGATA 0.868778 -193 TTAATCTAATTTCTCCAAGCATCACACAAAACCC 4 150 1 TTCCAGCATA 0.937014 -151 ACAAAACCCCTTTTCCTTCCATTAGATAGCGTTT 4 175 1 TTTCTCCATA 0.974424 -126 TGTTTTCTTTTTCATCCACTATAATATAAACGCT 4 202 0 TTCCCCTATA 0.935348 -99 *** ** **** * Masking position 14 Map Score: 9.41831 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 443 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 2 GGTCAGCATCTCCTTTATAACCGC 1 236 0 AGCATCTCCT 0.936973 -14 ACCGGGGACAAACATCCCCGGTCTTTTTCT 2 14 1 AACATCCCCG 0.962387 -121 TACATTTTAAATCAGCCGCTGGAATAAAAC 2 83 0 ATCAGCCGCT 0.978881 -52 CCTTTTCCACATCAGCCCCTC 4 2 0 ATCAGCCCCT 0.99456 -299 TGTTTTCTTTTTCATCCACTATAATATAAA 4 206 0 TTCATCCACT 0.934623 -95 GAAACCTCCTATCATCCTCTTACATGTTAG 4 276 0 ATCATCCTCT 0.983029 -25 ********** Masking position 4 Map Score: 4.64204 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 203 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 TCCTAGAAATATTCAAAATATTCTAATCATT 1 21 1 ATTAAAATAT 0.969743 -229 TTGACGTAGTCAATAAAATATTTTTCTGCTT 1 86 1 CAAAAAATAT 0.853435 -164 AGATGAACCGATAGAAAAAATAGATTCGCCC 1 193 1 ATAAAAAAAT 0.91458 -57 TATAACCGCAAATCAAAATATGGGCGAATCT 1 214 0 AATAAAATAT 0.961 -36 CCAGCGGCTGATTTAAAATGTACACATGAAC 2 91 1 ATTAAAATGT 0.907976 -44 AACCAAGCCAAATGAAAAAATTGCCGCTCCG 4 97 1 AATAAAAAAT 0.914673 -204 TCCGATTAAAATAAAAAATATGTTTTTTAAT 4 124 1 ATAAAAATAT 0.960925 -177 *** ******* Masking position 6 Map Score: 4.63249 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 4 GGGGCTGATGTGGAAAAGGGCATAAAGCAA 4 13 1 TGGAAAAGGG 0.983666 -288 AAGGGCATAAAGCAAAAGTGTAATACCTGT 4 28 1 AGCAAAAGTG 0.989937 -273 ATCTAATGGAAGGAAAAGGGGTTTTGTGTG 4 172 0 AGGAAAAGGG 0.993471 -129 AAAAGAAAACAGCAAACGTGCTTAAACATT 4 225 1 AGCAAACGTG 0.982965 -76 ********** Masking position 5 Map Score: 3.25498 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 96 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 CAATAAAATATTTTTCTGCTTTAAATGATAG 1 96 1 TTTTCTGCTT 0.909155 -154 TTCTATCGGTTCATCTTGCATAAAATTGAAT 1 178 0 TCTCTTGCAT 0.983347 -72 GGTCTTTTTCTTATCCTGCATTTCCATGAAA 2 33 1 TTTCCTGCAT 0.973326 -102 TCCATGAAATTCGTCTGACGTTTTACTAGTT 2 55 1 TCTCTGACGT 0.769123 -80 CTCAGCCAGATTGTTCTGCATATTGAAATGA 4 67 1 TTTTCTGCAT 0.958342 -234 GGCAATTTTTTCATTTGGCTTGGTTCATTTC 4 91 0 TCTTTGGCTT 0.901678 -210 GTTTGCTGTTTTCTTTTTCATCCACTATAAT 4 211 0 TTTTTTTCAT 0.784058 -90 CCTCCTATCATCCTCTTACATGTTAGCTAAT 4 271 0 TCTCTTACAT 0.941548 -30 ** ******** Masking position 4 Map Score: 3.28006 Number of sites scoring better than the average of aligned sites = 895 Number in coding regions = 784 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 6 GAGACCGGGGACAAACATCCC 2 2 1 AGACCGGGGA 0.997411 -133 GATAAGAAAAAGACCGGGGATGTTTGTCCC 2 18 0 AGACCGGGGA 0.997411 -117 ********** Masking position 3 Map Score: 1.40487 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 5 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 CGACAACGCTGTTTCGCTTCTATCATTTAAAGC 1 113 0 GTTTCGCTAT 0.98797 -137 AGAAAAAATAGATTCGCCCATATTTTGATTTGC 1 205 1 GATTCGCTAT 0.977785 -45 CCCATATTTTGATTTGCGGTTATAAAGGAGATG 1 221 1 GATTTGCTAT 0.976063 -29 TTCGTCTGACGTTTTACTAGTTTTATTCCAGCG 2 64 1 GTTTTACTTT 0.93633 -71 GCTGAGGGCGGTTTTACAGGTATTACACTTTTG 4 40 0 GTTTTACTAT 0.979751 -261 ATTCAGATACGTTTGACAAATGTTTAAGCACGT 4 240 0 GTTTGACTGT 0.927458 -61 ******* *** Masking position 4 Map Score: 1.26289 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 104 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 ********** No masking Map Score: -1.19128e-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: -1.19128e-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: -1.19128e-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