AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i291_bsub_mtub_300.orf -o291_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 guaB 120 inositol-monophosphate dehydrogenase #2 dacA 152 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5) #3 yaaD 196 similar to hypothetical proteins #4 yaaE 21 similar to hypothetical proteins #5 tesB2 28 tesB2 #6 Rv2606c 127 hypothetical protein Rv2606c Motif number 1 CCAAGAGCATGTCAAGGAAGCGGGAAAGAGTTGA 1 46 0 GCAGAACGGG 0.993473 -75 ATAATATTTTGCCGAAAAGAGGGGGATTTACTA 1 98 1 GCAAAGGGGG 0.981766 -23 GAACCCGCGACGAGCAGACGGTCATCGC 5 9 1 GCAGAGCGGT 0.993473 -20 CAGCCGTGCAGCACCGGAGGCCGGA 6 2 0 GACGAGCCGG 0.99278 -126 TCAGGGGCGTGGCCAGGACGCCGATTGGTAAATT 6 46 0 GCAGACCCGA 0.963727 -82 GCCCCTGAGTGGCTAGCAGACCGGCGCGGTAGCG 6 72 1 GCAGAGCCGG 0.998667 -56 GGTAGCGGTCGTATCGTAGTGGGGACAAGAGGAG 6 99 1 GACGAGGGGG 0.987048 -29 * * ** ** **** Masking position 8 Map Score: 6.82619 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 172 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 2 GTATATTTCTTAATCCTTTCCGTTATCTAA 1 11 1 TAATCCTTTC 0.724048 -110 CTAAATATTTCAACTCTTTCCCGCTTCCTT 1 37 1 CAACTCTTTC 0.934761 -84 ACAGAGTCAGAGACCCTGTCAAATGTTTTT 2 27 0 AGACCCTGTC 0.904071 -126 ACAGGGTCTCTGACTCTGTCTATTTTTTTT 2 38 1 TGACTCTGTC 0.961084 -115 AAGCCGTTAAGGACATTTTCAATGCACAAC 2 94 0 GGACATTTTC 0.879165 -59 ACATCCATCAGAGCTCTTTCAATTGA 3 7 0 GAGCTCTTTC 0.980174 -190 ATGGATGTTAGGGCTCTTTCGCGTAATATA 3 29 1 GGGCTCTTTC 0.992157 -168 ATTAAAAATTGGGTTTTTTCAGTATATTAC 3 51 0 GGGTTTTTTC 0.868739 -146 ********** Masking position 7 Map Score: 4.08484 Number of sites scoring better than the average of aligned sites = 866 Number in coding regions = 734 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 3 CTTTTCGGCAAAATATTATATGTAGATTAT 1 87 0 AAATATTATA 0.840364 -34 ATTTTATCATAATCAGTATAAAAAAAATAG 2 57 0 AATCAGTATA 0.906191 -96 TTTCAATGCACAACAGTATAAATTTTATCA 2 78 0 CAACAGTATA 0.87734 -75 TATACTGAAAAAACCCAATTTTTAATAAAA 3 55 1 AAACCCAATT 0.838845 -142 AAAGCGCTAAAAACCGAATAAAATAGTATA 3 95 1 AAACCGAATA 0.969098 -102 AAACCGAATAAAATAGTATATATGCATATG 3 105 1 AAATAGTATA 0.939647 -92 TGTATCCTAGAAATCCAATAATTCATATGC 3 128 0 AAATCCAATA 0.893478 -69 TATGATTTCTAATCCTTATTGTATCCTAGA 3 147 0 AATCCTTATT 0.666279 -50 TAAGGATTAGAAATCATATAACTATACCTT 3 159 1 AAATCATATA 0.854356 -38 ********** Masking position 8 Map Score: 2.60898 Number of sites scoring better than the average of aligned sites = 726 Number in coding regions = 594 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 4 CTAGCCAAGAGCATGTCAAGGAAGCGGGAAA 1 53 0 GCTGTCAAGG 0.965529 -68 CATTGAAAATGTCCTTAACGGCTTAATTATA 2 100 1 GTCTTAACGG 0.851792 -53 ATGACCGTCTGCTCGTCGCGGGTTC 5 5 0 GCCGTCGCGG 0.988456 -24 CCGGCCTCCGGTGCTGCACGGCTGAGGGATT 6 12 1 GTCTGCACGG 0.983133 -116 CCACTCAGGGGCGTGGCCAGGACGCCGATTG 6 53 0 GCTGGCCAGG 0.962131 -75 GTGGCTAGCAGACCGGCGCGGTAGCGGTCGT 6 80 1 GACGGCGCGG 0.990607 -48 ** ******** Masking position 10 Map Score: 1.77051 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 388 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 GTATATTTCTTAATCCTTTCCGTTA 1 6 1 TTTCTTAATC 0.977428 -115 CTCTTGGCTAGTTGATAATCTACATATAAT 1 73 1 GTTGATAATC 0.938193 -48 GTATAAATTTTATCATAATCAGTATAAAAA 2 63 0 TATCATAATC 0.948433 -90 CGTATTTCATTTTCTTCATCTATAATTAAG 2 121 0 TTTCTTCATC 0.951027 -32 TTTTTAGCGCTTTGAAAATCATTTTTTATT 3 78 0 TTTGAAAATC 0.928057 -119 ********** Masking position 3 Map Score: 0.755329 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 264 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 6 ATGAAATACGGAGGTCGTACGA 2 141 1 GAGGTCTACG 0.989622 -12 TCAATTGAAAGAGCTCTGATGGATGTTAGGG 3 11 1 GAGCTCGATG 0.983037 -186 ATGGATGTTAGGGCTCTTTCGCGTAATATAC 3 29 1 GGGCTCTTCG 0.972591 -168 GTCAGCAGCGCTCCTATGTTC 4 4 0 GCGCTCTATG 0.995001 -18 CGGCGCGGTAGCGGTCGTATCGTAGTGGGGA 6 93 1 GCGGTCTATC 0.974878 -35 ****** **** Masking position 5 Map Score: 1.23108 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 57 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 ********** No masking Map Score: -2.10731e-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: -2.10731e-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 9 ********** No masking Map Score: -2.10731e-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