AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i228_6_1_1_17_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 ctsR 300 transcriptional regulator #2 sms 91 DNA repair protein homolog #3 yacL 115 similar to hypothetical proteins #4 gltX 90 glutamyl-tRNA synthetase #5 ywfO 161 alternate gene name: ipa-93d; similar to hypothetical proteins #6 ywzC 214 ywzC Motif number 1 TCTCGCTCTATCCTTCATTATTTCCATTTT 1 203 0 TCCTTCATTA 0.786705 -98 TCAACCCCCTCCTTTACTGACTTTG 1 286 0 CCCCTCCTTT 0.992133 -15 ACATGCTGTATGCCTCATTTCCGTCTTCTA 2 13 0 TGCCTCATTT 0.962851 -79 TGTAAGTGTATGCCTCACTTTCATATCAAG 2 40 1 TGCCTCACTT 0.917658 -52 TAGTGTAAGACCTCTCCCTTGTTCTATTTC 2 69 0 CCTCTCCCTT 0.825705 -23 ACCCCCACCTCCTTTTTTAACATTT 3 101 0 CACCTCCTTT 0.980117 -15 TTTCAAATACTTCCTTTCATGTCATGT 4 74 0 TACTTCCTTT 0.929535 -17 CGTCATTCCCTCTTTTTTTTAGCCGT 5 146 0 TCCCTCTTTT 0.938093 -16 AATCACATCACACTTCATTTTACAAGGATT 6 130 0 CACTTCATTT 0.942329 -85 ACGTACGCTTCCCTTCATTTCTATGTTCAT 6 194 0 CCCTTCATTT 0.976636 -21 ********** Masking position 5 Map Score: 12.6791 Number of sites scoring better than the average of aligned sites = 725 Number in coding regions = 450 Number in noncoding regions = 275 Number of orfs with sites within 600 bp upstream = 315 Fraction of orfs with sites within 600 bp upstream = 0.0505943 Motif number 2 ATCCTTCATTATTTCCATTTTCCCGGTCCACAAAACCTG 1 185 0 ATTTCTCGTC 0.80574 -116 TTCTCGAGAATTTTCAACTTTCTCGCTCTATCCTTCATT 1 214 0 TTTTCTCGTT 0.963886 -87 GACCTCTCCCTTGTTCTATTTCTTGATATGAAAGTGAGG 2 52 0 TTGTTTCGTT 0.963883 -40 TTAATGTTGGTTTTTGTTTATTCTGATATTCGTAGGATG 3 42 1 TTTTTTTGTT 0.845666 -74 CTTGTTTTGATGCCGGGTCTATTTGGTGGT 4 2 1 TTGTTACGTT 0.957375 -89 AAACATATTTTTTCTTAGCCTCGGCCCTCAGGTCAGG 5 9 1 TTTTTACGCC 0.933632 -153 AGGTCAGGCTTTTTTGCTTCACAAGATGTGTTTTTCATG 5 40 1 TTTTTTCGTT 0.985824 -122 TCATTCCCTCTTTTTTTTAGCCGTGTTTCTATTATATCG 5 131 0 TTTTTACGTC 0.973442 -31 CTCAACTCCCATTTTTCTTTTCATGGTATTAGAATGTCC 6 15 1 ATTTTTCGTT 0.94522 -200 TTTGTATAAATATTTTCCAACCTGGACATTCTAATACCA 6 38 0 TATTTACGCT 0.740518 -177 GTGATGTGATTTTTTTTGAAACGTGATTTTAGGTTATTC 6 149 1 TTTTTACGTT 0.983199 -66 ***** * * * * * Masking position 4 Map Score: 8.53376 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 373 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 3 AAGCAAGCTTAAACCCAGCTCAATGAGCTG 1 67 1 AAACCCAGCT 0.992094 -234 AAAATACAAAAAACCCAGCTCATTGAGCTG 1 82 0 AAACCCAGCT 0.992094 -219 AAAATTCTCGAGAAACGGCTTATAGTAAGA 1 239 1 AGAAACGGCT 0.941388 -62 ACCACCAAATAGACCCGGCATCAAAACAAG 4 11 0 AGACCCGGCA 0.975718 -80 TCTTCATGAAAAACACATCTTGTGAAGCAA 5 53 0 AAACACATCT 0.925041 -109 GATATAATAGAAACACGGCTAAAAAAAAGA 5 132 1 AAACACGGCT 0.992027 -30 ********** Masking position 3 Map Score: 7.70412 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 164 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 GTATTTTGGTTTATTGGTATCATAAAATTCCACT 1 105 1 TTTGGTATAA 0.97826 -196 TCCACTTAACTGTATAATATAATAACTTTATACC 1 133 1 TGTAATATAA 0.743775 -168 CAAAACCTGATTGCTGATTTAAAATTCGGTATAA 1 160 0 TTTGATTTAA 0.891611 -141 CTTGTTCTATTTCTTGATATGAAAGTGAGGCATA 2 48 0 TTTGATATAA 0.978679 -44 TGCATAAGACTTTGTGAAATTAAAATGTTAAAAA 3 79 1 TTTGAAATAA 0.943836 -37 CCGGGTCTATTTGGTGGTAGAATAGATTCATACA 4 23 1 TTTGGTAGAA 0.962238 -68 CATTTTTCTTTTCATGGTATTAGAATGTCCAGGT 6 24 1 TTTGGTATAA 0.97826 -191 TTATACAAATTGGCTGAAAGAATAGGAGATACGA 6 68 1 TGTGAAAGAA 0.843486 -147 ** ****** * * Masking position 12 Map Score: 3.62637 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 145 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 TTCGGTTAAAACCTTATGAATACGGGTATA 3 12 1 ACCTTATGAA 0.82596 -104 GATGCATAAGACTTTGTGAAATTAAAATGT 3 77 1 ACTTTGTGAA 0.943389 -39 TGAAAAACACATCTTGTGAAGCAAAAAAGC 5 47 0 ATCTTGTGAA 0.906473 -115 TTGTTCCATCTTCATGAAAAACACATCTTG 5 61 0 TTCATGAAAA 0.694176 -101 TCGACTCTATTCTTTGAAAACATCCTTGAA 5 104 0 TCTTTGAAAA 0.86736 -58 ACATTCTAATACCATGAAAAGAAAAATGGG 6 22 0 ACCATGAAAA 0.912616 -193 AACAGTCGAATCCTTGTAAAATGAAGTGTG 6 122 1 TCCTTGTAAA 0.963916 -93 TCTATGTTCATCTATGTGAATAACCTAAAA 6 175 0 TCTATGTGAA 0.911664 -40 ********** Masking position 9 Map Score: 3.07423 Number of sites scoring better than the average of aligned sites = 675 Number in coding regions = 579 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 6 CGACTACCATCGGCGCTGAAGAGC 1 4 0 CGGCCTGAAG 0.977398 -297 AGTAGGACGCCGCCAAGCAAGCTTAAACCCA 1 53 1 CGCCAGCAAG 0.946788 -248 AATTTTAAATCAGCAATCAGGTTTTGTGGAC 1 168 1 CAGCATCAGG 0.977364 -133 TATAGAAGACGGAAATGAGGCATACAGCAT 2 10 1 CGGAATGAGG 0.914724 -82 ATGAGGCATACAGCATGTAAGTGTATGCCTC 2 25 1 CAGCTGTAAG 0.771499 -67 TTCTTAGCCTCGGCCCTCAGGTCAGGCTTTT 5 22 1 CGGCCTCAGG 0.994182 -140 AAGGATGGAGCGGCTTGCAGGAACAGTCGAA 6 101 1 CGGCTGCAGG 0.99256 -114 **** ****** Masking position 9 Map Score: 3.18904 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 642 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 CTGTGAGAGTAGGACGCCGCCAAGCAAGCT 1 46 1 AGGACGCCGC 0.851479 -255 GTGGACCGGGAAAATGGAAATAATGAAGGA 1 193 1 AAAATGGAAA 0.710584 -108 GAAATAATGAAGGATAGAGCGAGAAAGTTG 1 209 1 AGGATAGAGC 0.923261 -92 TATAGAAGACGGAAATGAGGCATAC 2 6 1 AAGACGGAAA 0.925652 -86 TGATATTCGTAGGATGCATAAGACTTTGTG 3 65 1 AGGATGCATA 0.858127 -51 GTTTTTCATGAAGATGGAACAAATCGCCGG 5 69 1 AAGATGGAAC 0.972125 -93 TAGAATGTCCAGGTTGGAAAATATTTATAC 6 44 1 AGGTTGGAAA 0.909747 -171 GGAGATACGAAGGATGGAGCGGCTTGCAGG 6 92 1 AGGATGGAGC 0.990804 -123 ********** Masking position 1 Map Score: 1.91932 Number of sites scoring better than the average of aligned sites = 926 Number in coding regions = 781 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 8 ********** No masking Map Score: 1.77168e-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: 1.77168e-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: 1.77168e-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