AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i292_3_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 ycsD 85 similar to hypothetical proteins from B. subtilis #2 ycsE 202 similar to hypothetical proteins from B. subtilis #3 ycsF 204 similar to lactam utilization protein #4 ycsG 203 alternate gene name: ycsH; similar to branched chain amino acids transporter #5 ycsI 23 similar to hypothetical proteins #6 ycsJ 43 similar to allophanate hydrolase Motif number 1 TGGAAAAAACACAAAAGGAGGCCGTT 1 7 0 ACAAAAGGAG 0.91123 -79 ATAATGGTCAAAAAAAGGAGATATAAA 1 69 1 AAAAAAGGAG 0.981985 -17 ACATGACAGAAAAAAAACAGCAAAACAAAC 2 53 0 AAAAAAACAG 0.985856 -150 AATAAGAGGAAAACAAACGGTGAGGTGATC 2 85 0 AAACAAACGG 0.907779 -118 CCAGCGGGACAAAAAAGCGATTTCCTATGT 2 127 0 AAAAAAGCGA 0.816763 -76 CAACAAAAAGATAAAGAGAGGTACATAT 2 185 1 ATAAAGAGAG 0.856703 -18 AAAAAGAGAGTCCTAAGATG 3 1 1 AAAAAGAGAG 0.979189 -204 CTGCCAAACTAAAAAGAGAGTCCATCTTAG 3 23 0 AAAAAGAGAG 0.979189 -182 AATAAAGTTCAAAAATTCGGAATAGTCGTT 3 125 1 AAAAATTCGG 0.789995 -80 ACATTTGCGCAAAAAATCAGAAAACAGCTC 4 66 1 AAAAAATCAG 0.962287 -138 GGAGCAGCAGAAAAAGACAGCAGGAAAAAA 4 163 1 AAAAAGACAG 0.984891 -41 AGACAGCAGGAAAAAAGCGGGCAGCTGGTC 4 177 1 AAAAAAGCGG 0.984158 -27 ********** Masking position 5 Map Score: 18.8419 Number of sites scoring better than the average of aligned sites = 1541 Number in coding regions = 1142 Number in noncoding regions = 399 Number of orfs with sites within 600 bp upstream = 388 Fraction of orfs with sites within 600 bp upstream = 0.0623193 Motif number 2 ATTTGGTTTGTTTTGCTGTTTTTTTTCTGT 2 48 1 TTTTGCTGTT 0.974684 -155 TCACCGTTTGTTTTCCTCTTATTCATTCTC 2 92 1 TTTTCCTCTT 0.942017 -111 AATCGCTTTTTTGTCCCGCTGGGTATAATG 2 135 1 TTGTCCCGCT 0.969318 -68 TATCTTTTTGTTGTGCTTCTCTCTATTCTA 2 168 0 TTGTGCTTCT 0.948456 -35 TCCAGCCGCTTTGAGCTGTTTTCTGATTTT 4 78 0 TTGAGCTGTT 0.892836 -126 CTCCATCTATTGTTCCTCCTTTATGTTGAC 4 137 0 TGTTCCTCCT 0.916938 -67 TGCTGTCTTTTTCTGCTGCTCCATCTATTG 4 155 0 TTCTGCTGCT 0.977955 -49 CTGCCCGCTTTTTTCCTGCTGTCTTTTTCT 4 171 0 TTTTCCTGCT 0.989949 -33 ********** Masking position 1 Map Score: 7.30139 Number of sites scoring better than the average of aligned sites = 1010 Number in coding regions = 912 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 3 TGTGCTCGGGGTTTTCATTTGGTTTGTTTT 2 32 1 GTTTTCATTT 0.929817 -171 CTGTTTTTTTTCTGTCATGTTTGATCACCT 2 63 1 TCTGTCATGT 0.9468 -140 CGATATGCTTTATGTCATTTATTGTCCCGA 3 162 0 TATGTCATTT 0.927745 -43 TGTGTCATTTAAAAGCGGTT 4 1 1 TGTGTCATTT 0.950076 -203 AAGCGGTTCAGTTTTCATTTATGGAGATGG 4 23 1 GTTTTCATTT 0.929817 -181 GAGCCCATGCGCTGACATTTGCGCAAAAAA 4 52 1 GCTGACATTT 0.968474 -152 TTCTGAAATAGCTGTCACTTCAATTCCAGC 4 102 0 GCTGTCACTT 0.978508 -102 CTTTTTTCCTGCTGTCTTTTTCTGCTGCTC 4 164 0 GCTGTCTTTT 0.968474 -40 ********** Masking position 3 Map Score: 8.76342 Number of sites scoring better than the average of aligned sites = 750 Number in coding regions = 684 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 4 CCTAAAGTGAAACGATAGGATATAATGGAAA 1 31 0 AACGATAGAT 0.973681 -55 CAACGACTTAACCGATCCGATTC 2 3 0 ACCGATCGAT 0.981501 -200 AGAGAAGCACAACAAAAAGATAAAGAGAGGT 2 176 1 AACAAAAGAT 0.7201 -27 TATTTCACAAACTGATATGATTCACTTATAA 3 91 1 ACTGATAGAT 0.955827 -114 TGCCAAAGCAAACGATATGCTTTATGTCATT 3 173 0 AACGATAGCT 0.978075 -32 ATAAATGAAAACTGAACCGCTTTTAAATGAC 4 14 0 ACTGAACGCT 0.944159 -190 CAGCAATGACCAGCTGCCCGCTTTT 4 189 0 AATGACCGCT 0.921702 -15 ******* *** Masking position 5 Map Score: 3.33442 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 402 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 TCCTTTTGTGTTTTTTCCATTATATCCTATCGT 1 18 1 TTTTCATTAT 0.983604 -68 TATCTCCTTTTTTTGACCATTATATCTCAGCCT 1 59 0 TTTACATTAT 0.936709 -27 TTTGTTTTCCTCTTATTCATTCTCCTCAAACAT 2 98 1 TCTTCATTCT 0.971824 -105 TTCTCTCTATTCTAATACATTATACCCAGCGGG 2 149 0 TCTTCATTAT 0.98951 -54 ATTTTTGAACTTTATTTCATTATAAGTGAATCA 3 108 0 TTTTCATTAT 0.983603 -97 CCTCTTTAATTCTCGTTCATCAGGATGACGAGA 6 13 0 TCTTCATCAG 0.926534 -31 *** * ****** Masking position 9 Map Score: 3.00288 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 59 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 TATCGTTTCACTTTAGGCTGAGATATAATGG 1 45 1 CTTTGGCTGA 0.956642 -41 TTTATATCTCCTTTTTTTGACCATTATATC 1 66 0 CCTTTTTTGA 0.863956 -20 GTTTTGCTGTTTTTTTTCTGTCATGTTTGAT 2 57 1 TTTTTTCTGT 0.797192 -146 TTGTGCTTCTCTCTATTCTAATACATTATAC 2 157 0 CTCTTTCTAA 0.85096 -46 CTCTCTTTATCTTTTTGTTGTGCTTCTCTCT 2 174 0 CTTTTGTTGT 0.854465 -29 CTAAGATGGACTCTCTTTTTAGTTTGGCAGG 3 23 1 CTCTTTTTTA 0.677181 -182 GTTTGGCAGGTTTTATTCTGGGACCATGGTA 3 44 1 TTTTTTCTGG 0.767649 -161 TTGTGAAATACTTTTGTCAGAAAACCTACCA 3 70 0 CTTTGTCAGA 0.817386 -135 CCGCTTTGAGCTGTTTTCTGATTTTTTGCGC 4 72 0 CTGTTTCTGA 0.960597 -132 TTATGTTGACCTCTGTTCTGAAATAGCTGTC 4 116 0 CTCTTTCTGA 0.984929 -88 ATTGTTCCTCCTTTATGTTGACCTCTGTTCT 4 128 0 CTTTTGTTGA 0.954794 -76 **** ****** Masking position 4 Map Score: 5.80323 Number of sites scoring better than the average of aligned sites = 1723 Number in coding regions = 1474 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 7 AACGGCCTCCTTTTGTGTTTTTTC 1 5 1 GCCTCCTTTT 0.888712 -81 ACTAAAAAGAGAGTCCATCTTAGGACTCTC 3 16 0 GAGTCCATCT 0.89417 -189 TCAGCGCATGGGCTCCATCTCCATAAATGA 4 37 0 GGCTCCATCT 0.993599 -167 CTCCATCTATTGTTCCTCCTTTATGTTGAC 4 137 0 TGTTCCTCCT 0.893696 -67 CTTTTTCTGCTGCTCCATCTATTGTTCCTC 4 149 0 TGCTCCATCT 0.989972 -55 TTTGTTTAATTGCTCCACTTATA 5 4 0 TGCTCCACTT 0.965106 -20 ********** Masking position 4 Map Score: 2.72482 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 353 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 8 ********** No masking Map Score: -7.57276e-14 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: -7.57276e-14 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: -7.57276e-14 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