AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i316_mixed3_bsub_reg_100.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 pbpC 150 penicillin-binding protein 3 #2 pbpA 113 penicillin-binding protein 2A #3 mreC 30 cell-shape determining protein #4 mreB 90 cell-shape determining protein #5 ysxA 36 similar to DNA repair protein #6 maf 152 maf Motif number 1 AAGACAGAAAGAAGGGATAGC 1 2 0 GAAGGGATAG 0.976777 -149 TAGACTATTTGAAAAGACAGAAAGAAGGGA 1 15 0 GAAAAGACAG 0.932784 -136 TTTTGAAAATGAAGGAAAAGTTCACCGATT 1 71 0 GAAGGAAAAG 0.982039 -80 CCAATTCAATTAAGAGAAAATAACAAGTGG 1 115 1 TAAGAGAAAA 0.845002 -36 ATAACAAGTGGAAGGCAGGGGAAAGTC 1 134 1 GAAGGCAGGG 0.895813 -17 TCTATTTACAGAAAGAAAAGACACTCAAGT 2 82 0 GAAAGAAAAG 0.978255 -32 TTAATTCGACGAAAAAAAAGTG 4 3 0 GAAAAAAAAG 0.921027 -88 AAAATACCCTAAAGGGAAAAACTCATAAAC 4 44 0 AAAGGGAAAA 0.892739 -47 CTTCCTTTCTTAAAGCAAAAATACCCTAAA 4 61 0 TAAAGCAAAA 0.822286 -30 TTTGCTTTAAGAAAGGAAGATACATACAT 4 72 1 GAAAGGAAGA 0.987508 -19 CTATAAACGGGAAGGGAAAGAAAAGGAGTG 5 16 1 GAAGGGAAAG 0.994135 -21 AGCCTGTCACTAAAGGACGAAGGCTCAGGG 6 20 0 TAAAGGACGA 0.857963 -133 GTTTGCTTAAGAAAAAAAGATACTCGTTTA 6 115 0 GAAAAAAAGA 0.868594 -38 AGCAAACCCTGAAAGGATGACGAAC 6 138 1 GAAAGGATGA 0.951491 -15 ********** Masking position 7 Map Score: 19.424 Number of sites scoring better than the average of aligned sites = 3064 Number in coding regions = 2537 Number in noncoding regions = 527 Number of orfs with sites within 600 bp upstream = 525 Fraction of orfs with sites within 600 bp upstream = 0.0843238 Motif number 2 TTTCAAATAGTCTACAGCAAACGATAGGAG 1 31 1 TCTACAGCAA 0.962879 -120 GTTCACCGATTTTGCAGAAATCTCCTATCG 1 52 0 TTTGCAGAAA 0.955196 -99 CGTGCAAGATTTTTTTGAAAATGAAGGAAA 1 83 0 TTTTTTGAAA 0.92408 -68 AGATAACCCCTTTTTGGCAAAAAAA 2 6 0 TTTTTGGCAA 0.85012 -108 AAAGGGGTTATCTGTAGAAAAAAGTCGAAA 2 23 1 TCTGTAGAAA 0.958118 -91 ACCTTTTCTATTTACAGAAAGAAAAGACAC 2 88 0 TTTACAGAAA 0.960882 -26 TTACACCTCTTCTATTGAACTCCCGA 3 7 0 TCTATTGAAC 0.864569 -24 TCCCTTCCCGTTTATAGAACCG 5 3 0 TTTATAGAAC 0.917292 -34 AAAAAGTTATTTTTCTGAAATTGTGACAAG 6 67 1 TTTTCTGAAA 0.943859 -86 TATCTTTTTTTCTTAAGCAAACCCTGAAAG 6 123 1 TCTTAAGCAA 0.832533 -30 ********** Masking position 3 Map Score: 9.2528 Number of sites scoring better than the average of aligned sites = 1221 Number in coding regions = 1010 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 3 CAAAATCGGTGAACTTTTCCTTCATTTTCA 1 68 1 GAACTTTTCC 0.714435 -83 AATCTTGCACGCACCAATTCAATTAAGAGA 1 102 1 GCACCAATTC 0.901584 -49 ATGAAAACTGGCACTCTTACTTGAGTGTCT 2 64 1 GCACTCTTAC 0.861257 -50 AACATCACCTTTTCTATTTACAGA 2 100 0 TCACCTTTTC 0.989744 -14 CGTGTTACACCTCTTCTATTGAACTC 3 15 0 ACACCTCTTC 0.897489 -16 GCACTCCTTTTCTTTCCCTTCC 5 25 0 ACTCCTTTTC 0.912406 -12 AAGGCTCAGGGCACTATCTC 6 1 0 GCACTATCTC 0.885003 -152 TTCAGAAAAATAACTTTTTCATGACAAAAT 6 56 0 TAACTTTTTC 0.90311 -97 ACGAGGCTTGTCACAATTTCAGAAAAATAA 6 73 0 TCACAATTTC 0.886761 -80 TAAACGAGTATCTTTTTTTCTTAAGCAAAC 6 115 1 TCTTTTTTTC 0.698173 -38 GTTCGTCATCCTTTCAGGGTTTGCT 6 138 0 TCATCCTTTC 0.893829 -15 ********** Masking position 10 Map Score: 4.54192 Number of sites scoring better than the average of aligned sites = 2713 Number in coding regions = 2257 Number in noncoding regions = 456 Number of orfs with sites within 600 bp upstream = 433 Fraction of orfs with sites within 600 bp upstream = 0.0695471 Motif number 4 TATTTGAAAAGACAGAAAGAAGGGATAGC 1 10 0 GACAGAAAGA 0.82126 -141 TTTTGAAAATGAAGGAAAAGTTCACCGATT 1 71 0 GAAGGAAAAG 0.741829 -80 TTCCTTCATTTTCAAAAAAATCTTGCACGC 1 84 1 TTCAAAAAAA 0.869223 -67 ATTCAATTAAGAGAAAATAACAAGTGGAAG 1 118 1 GAGAAAATAA 0.572848 -33 ACCCCTTTTTGGCAAAAAAA 2 1 0 GGCAAAAAAA 0.957384 -113 GGGGTTATCTGTAGAAAAAAGTCGAAAAAA 2 26 1 GTAGAAAAAA 0.954292 -88 GTAGAAAAAAGTCGAAAAAACCTTTAAAAT 2 36 1 GTCGAAAAAA 0.97878 -78 AGCTTAATTCGACGAAAAAAAAGTG 4 6 0 GACGAAAAAA 0.982082 -85 AAACGGGAAGGGAAAGAAAAGGAGTGC 5 20 1 GGAAAGAAAA 0.615955 -17 ACTTTTTCATGACAAAATAAAAAAAGCCTG 6 44 0 GACAAAATAA 0.890144 -109 TTGTCACAATTTCAGAAAAATAACTTTTTC 6 66 0 TTCAGAAAAA 0.829949 -87 TCGTGATTTGGTAGGATAAACGAGTATCTT 6 99 1 GTAGGATAAA 0.619984 -54 AGGGTTTGCTTAAGAAAAAAAGATACTCGT 6 118 0 TAAGAAAAAA 0.831633 -35 ********** Masking position 7 Map Score: 10.8036 Number of sites scoring better than the average of aligned sites = 3632 Number in coding regions = 3112 Number in noncoding regions = 520 Number of orfs with sites within 600 bp upstream = 487 Fraction of orfs with sites within 600 bp upstream = 0.0782204 Motif number 5 TTGAATTGGTGCGTGCAAGATTTTTTTGAA 1 94 0 GCGTGCAAGA 0.952673 -57 ACTTTCCCCTGCCTTCCACTTGTTATTTTC 1 130 0 GCCTTCCACT 0.977813 -21 ACTCAAGTAAGAGTGCCAGTTTTCATTTTA 2 60 0 GAGTGCCAGT 0.967996 -54 AATAAAAAAAGCCTGTCACTAAAGGACGAA 6 29 0 GCCTGTCACT 0.990298 -124 AAATCACGAGGCTTGTCACAATTTCAGAAA 6 78 0 GCTTGTCACA 0.963119 -75 ********** Masking position 4 Map Score: 0.395306 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 431 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 ********** No masking Map Score: -8.21797e-13 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 7 ********** No masking Map Score: -8.21797e-13 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 8 ********** No masking Map Score: -8.21797e-13 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