AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_bsub_mtub_100.orf -o210_bsub_mtub_100.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 ileS 300 isoleucyl-tRNA synthetase #2 ylxS 300 alternate gene name: ymxA; similar to hypothetical proteins #3 nusA 34 nusA #4 truB 81 tRNA pseudouridine 55 synthase #5 rpsO 156 ribosomal protein S15 (BS18) #6 pnpA 172 polynucleotide phosphorylase (PNPase) #7 gpsI 300 gpsI #8 rpsO 156 rpsO #9 ribF 210 ribF #10 Rv2795c 144 hypothetical protein Rv2795c #11 infB 85 infB #12 Rv2840c 126 hypothetical protein Rv2840c #13 Rv2842c 194 hypothetical protein Rv2842c Motif number 1 TACATGATTCCGGCCATCCCGGACTCTCACCA 1 91 0 CGGCACCCGG 0.509761 -210 GGCAAAGAGTGGGGAAACCCGCTCTTTTGTAT 2 156 1 GGGAACCCGC 0.856745 -145 TTAACGGTCTCCCCCCTTAAAACATT 3 19 0 CGGCTCCCCC 0.760029 -16 GCTTGGCAATCCGAAGTCACCGACGGTTGCTA 5 97 1 CCGAGCACCG 0.458167 -60 GATAAAAAAGCGGGAATCCTCCCGCTTTTTAC 6 13 0 CGGAACCTCC 0.791249 -160 ATTTGCTGGGCCGAACCGGCCCAGAACGTTCT 7 18 0 CCGACGGCCC 0.896555 -283 CTCGCTGGAACGGCACACGCGGTTCTGCGCGT 7 58 0 CGGACCGCGG 0.857668 -243 GCATATCCAAGGGAGCACCCCCGGCCTGTATC 7 97 1 GGGGCCCCCC 0.657615 -204 GCAGCCACTACCGAGGACCGCCCGATACAGGC 7 120 0 CCGGGCCGCC 0.92758 -181 GCCCCAGATCCGGAGAGCCCGGCAGCCACTAC 7 141 0 CGGGACCCGG 0.560573 -160 ATCGAAGCGGCCGACCTGCCCCAGATCCGGAG 7 158 0 CCGCCGCCCC 0.626962 -143 AGGTCTGAATGCGGCTACGGCCATCGATCGAA 7 184 0 GCGCTCGGCC 0.45382 -117 TCGCCGAACCCCGAGAGCTTCCCAGGAGAAAA 7 215 0 CCGGACTTCC 0.657207 -86 TCTCGGGGTTCGGCGAACCCGCTGGATTGCGC 7 231 1 CGGGACCCGC 0.697533 -70 GCTGGATTGCGCGTGACGACGCGAAACAGCTC 7 251 1 GCGGAGACGC 0.490344 -50 CTCAATAATCCAGAGAGGCCGCACGGACGTC 7 280 1 CAGGAGCCGC 0.806448 -21 CGGTTCTTGCGGTCGTGACCCCCGGCTGGCA 8 10 1 CGGCGGACCC 0.611976 -147 GTCGTGACCCCCGGCTGGCACCTGCGGCGTTT 8 22 1 CCGCTGCACC 0.564029 -135 TTGTGTTTGGCGGTCAACCCGCTGCTAGACTG 8 52 1 CGGCACCCGC 0.867929 -105 CTGCGGTTCGCGGTGGCCGTGCCCTGATATCC 8 104 1 CGGGGCGTGC 0.869742 -53 ACCAATCGTTCGGTATGCGCGCGCCAATTCTC 9 59 1 CGGATCGCGC 0.894788 -152 TCTCTGGGACCGGCCACGGTGCCGCCGGCGTT 9 87 1 CGGCAGGTGC 0.924711 -124 CGCAGCACGTCCGGGAACGCCGGCGGCACCGT 9 102 0 CCGGACGCCG 0.50591 -109 ACGCGGCCGCCGGACACCTGGCGCAGCACGTC 9 123 0 CGGCACTGGC 0.92073 -88 CAGGTGTCCGGCGGCCGCGTGCATGGTGTTCC 9 135 1 GCGCCCGTGC 0.547666 -76 ATGGTGTTCCCGGATCGGCCGCTGGCCAGAGC 9 157 1 CGGTCGCCGC 0.779332 -54 GGTGGTCGGCCAGGCGCCAGATTCACCG 9 193 0 CGGCAGCGCC 0.95795 -18 GCTAGGTTGGCCGAGCAGACGCAAAAGCCCCC 10 18 1 CCGGCGACGC 0.741712 -127 CATTTCGGGCCCGAAATGGGGGCTTTTGCGTC 10 35 0 CCGAAGGGGG 0.788329 -110 CATTTCGGGCCCGAAATGGGGGCTTTTGCGTC 10 49 1 CCGAAGGGGG 0.788329 -96 CCTAACGACCCGGCGAAGTGGGAACGAAATCC 10 113 0 CGGGAGTGGG 0.732938 -32 GCACACCGTGAAGTCCCGATGACAATG 11 6 1 CCGGAGTCCC 0.701543 -80 ATAGCTAAACCCGAGGCGCGGCCCACGACTGT 11 42 1 CCGGGGCGGC 0.943623 -44 GTAGCGTCACCGGGCAAGCCCGATTGCCCGGC 12 37 0 CGGCAGCCCG 0.524022 -90 CTACACTTAGCCGTGATCCAGCGCGAGCCTTC 12 65 1 CCGGACCAGC 0.910207 -62 CGCGAGCCTTCGGCCTCGGCGCATCGACGCCC 12 86 1 CGGCTGGCGC 0.621892 -41 CGGTCCGCGGGGATTATCCGGG 12 115 0 CGGCCCGGGG 0.901703 -12 ACGAATGACGCCGTGATCACGCCGTTCAACGT 13 57 0 CCGGACACGC 0.605083 -138 TCCCAGTGTCCCGCCGGCACGCAGCAGCCGGC 13 116 0 CCGCGCACGC 0.557256 -79 AGCGGAGGCGCCGCCAGGGCGGCTCCCAGTGT 13 139 0 CCGCAGGCGG 0.504146 -56 TTGAGTTGTCCGGTCATCTAGCGGAGGCGCCG 13 158 0 CGGCACTAGC 0.72026 -37 *** ** ***** Masking position 3 Map Score: 57.5997 Number of sites scoring better than the average of aligned sites = 4574 Number in coding regions = 4303 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 2 CCATTTGCTGGGCCGAACCGGCCCAGAACG 7 22 0 GGCCGAACCG 0.967688 -279 GTGCGGTACGCGCAGAACCGCGTGTGCCGT 7 51 1 CGCAGAACCG 0.833692 -250 GCATATCCAAGGGAGCACCCCCGGCCTGTA 7 97 1 GGGAGCACCC 0.697767 -204 GGGGCAGGTCGGCCGCTTCGATCGATGGCC 7 168 1 GGCCGCTTCG 0.786924 -133 TTCGATCGATGGCCGTAGCCGCATTCAGAC 7 184 1 GGCCGTAGCC 0.944957 -117 CCAGCGGGTTCGCCGAACCCCGAGAGCTTC 7 226 0 CGCCGAACCC 0.972981 -75 AATCCAGAGAGGCCGCACGGACGTC 7 286 1 GGCCGCACGG 0.985979 -15 CAAACACAAACGCCGCAGGTGCCAGCCGGG 8 31 0 CGCCGCAGGT 0.916794 -126 CACCGCGAACCGCAGCACGCACCGATGTCG 8 89 0 CGCAGCACGC 0.948888 -68 GGTTCGCGGTGGCCGTGCCCTGATATCCAT 8 108 1 GGCCGTGCCC 0.938871 -49 GCGGCACCGTGGCCGGTCCCAGAGAATTGG 9 82 0 GGCCGGTCCC 0.894074 -129 CGGGAACGCCGGCGGCACCGTGGCCGGTCC 9 93 0 GGCGGCACCG 0.970187 -118 GGACACCTGGCGCAGCACGTCCGGGAACGC 9 114 0 CGCAGCACGT 0.84417 -97 GGTGTCCGGCGGCCGCGTGCATGGTGTTCC 9 137 1 GGCCGCGTGC 0.896409 -74 TTCCCGGATCGGCCGCTGGCCAGAGCCCAC 9 163 1 GGCCGCTGGC 0.840255 -48 CGTCTGCTCACGCCGTAGCGGTTGGTCGAA 10 77 1 CGCCGTAGCG 0.906667 -68 GACAGTCGTGGGCCGCGCCTCGGGTTTAGC 11 45 0 GGCCGCGCCT 0.923346 -41 CGCCGTGCGTTATCCCACGG 12 1 1 CGCCGTGCGT 0.79431 -126 GGCGTCGATGCGCCGAGGCCGAAGGCTCGC 12 87 0 CGCCGAGGCC 0.706127 -40 ATCAGAAAGACGCCGCTACGAAGGCAGGCG 13 25 1 CGCCGCTACG 0.702042 -170 CCCGCCGGCACGCAGCAGCCGGCGTAGCTA 13 109 0 CGCAGCAGCC 0.74489 -86 GCGCCGCCAGGGCGGCTCCCAGTGTCCCGC 13 134 0 GGCGGCTCCC 0.929486 -61 GAGCCGCCCTGGCGGCGCCTCCGCTAGATG 13 146 1 GGCGGCGCCT 0.925009 -49 ********** Masking position 5 Map Score: 40.965 Number of sites scoring better than the average of aligned sites = 1628 Number in coding regions = 1526 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 TTTTCTAAAAGGGTGGTACCGCGAGATAAGCTTTCTC 1 213 1 GGGGTCGGGT 0.968911 -88 AGAGAGGATAGGCGTATATCGTCTGTCCTCTTTCTTC 4 15 1 GGCTTCGCGC 0.989773 -67 GAGCACCCCCGGCCTGTATCGGGCGGTCCTCGGTAGT 7 109 1 GGCTTCGGGT 0.991189 -192 ATCAATGGTCGGCGTAAAGCTTGAGACCAATCGTTCG 9 34 1 GGCTACTGGC 0.978093 -177 ATTCACCGGTGGGCTCTGGCCAGCGGCCGATCCGGGA 9 164 0 GGGTTCCGGC 0.963054 -47 CCCGAAATGGGGGCTTTTGCGTCTGCTCGGCCAACCT 10 21 0 GGGTTCGCGT 0.969352 -124 CCCGAAATGGGGGCTTTTGCGTCTGCTCACGCCGTAG 10 58 1 GGGTTCGCGT 0.969352 -87 CTGTCCATGAGGCGACAGTCGTGGGCCGCGCCTCGGG 11 51 0 GGCAACGGGC 0.960193 -35 GATGCGCCGAGGCCGAAGGCTCGCGCTGGATCACGGC 12 74 0 GGCGACTGGT 0.878101 -53 CGGTCCGCGGGGATTATCCGGGCGTCGATGCGCCGA 12 101 0 GGGTACGGGC 0.992385 -26 CCTTCGTAGCGGCGTCTTTCTGATGGCAGGATGTTGC 13 12 0 GGCTTCTAGC 0.857773 -183 GCGTGATCACGGCGTCATTCGTGATTCCTGGCGTATC 13 67 1 GGCTACGGTC 0.928334 -128 *** * * ** * * * Masking position 10 Map Score: 14.4877 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 172 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 ACCCTTTTAGAAAAAGCAAGCATACACTTT 1 197 0 AAAAAGCAAG 0.790354 -104 TGCTTTTTCTAAAAGGGTGGTACCGCGAGA 1 209 1 AAAAGGGTGG 0.675413 -92 CTCATCCCATAAGGGACGAGAAAGCTTATC 1 237 0 AAGGGACGAG 0.816863 -64 TTACCGAGGCAAAGAGTGGGGAAACCCGCT 2 149 1 AAAGAGTGGG 0.807025 -152 GTTCAATACAAAAGAGCGGGTTTCCCCACT 2 163 0 AAAGAGCGGG 0.969917 -138 CCCTGCTTCAAAAGAGCAGGGGCTAAAAAG 2 226 0 AAAGAGCAGG 0.927599 -75 TCGACAGCACAAGGAGGAAGAAC 2 288 1 AAGGAGGAAG 0.864713 -13 CAAATGTTTTAAGGGGGGAGACCGTTAA 3 17 1 AAGGGGGGAG 0.93602 -18 AAAAAGAGAGGATAGGCGTAT 4 2 1 AAAAGAGAGG 0.749183 -80 CTTATAAACGAAGAAAGAGGACAGACGATA 4 31 0 AAGAAAGAGG 0.749183 -51 AAAAAACTCAAAAGAAGGAGTGAAAGGCAA 4 62 1 AAAGAAGGAG 0.86231 -20 TCGTAAAAAGCGGGAGGATTCCCG 6 5 1 AAAAAGCGGG 0.952586 -168 TAATACGATAAAAAAGCGGGAATCCTCCCG 6 21 0 AAAAAGCGGG 0.952586 -152 TCACACAACGAAGAGAGGAGTTCGTAATTG 6 152 1 AAGAGAGGAG 0.763506 -21 ********** Masking position 2 Map Score: 11.542 Number of sites scoring better than the average of aligned sites = 1481 Number in coding regions = 1010 Number in noncoding regions = 471 Number of orfs with sites within 600 bp upstream = 441 Fraction of orfs with sites within 600 bp upstream = 0.070832 Motif number 5 TTACTTTTTAGCCCCTGCTCTTTTGAAGCA 2 223 1 GCCCCTGCTC 0.979119 -78 ATCATATTTAGCCCCAGTTACCTAGCAACC 5 121 0 GCCCCAGTTA 0.915622 -36 CGGCCGACCTGCCCCAGATCCGGAGAGCCC 7 153 0 GCCCCAGATC 0.973287 -148 CGGTATGCGCGCGCCAATTCTCTGGGACCG 9 69 1 GCGCCAATTC 0.912839 -142 CGGACGTGCTGCGCCAGGTGTCCGGCGGCC 9 121 1 GCGCCAGGTG 0.804255 -90 GCTCTGGCCAGCGGCCGATCCGGGAACACC 9 159 0 GCGGCCGATC 0.872053 -52 GGTCGGCCAGGCGCCAGATTCACCGGTGGG 9 188 0 GCGCCAGATT 0.922728 -23 GGGGGCTTTTGCGTCTGCTCGGCCAACCTA 10 20 0 GCGTCTGCTC 0.920752 -125 AGACGCAAAAGCCCCCATTTCGGGCCCGAA 10 34 1 GCCCCCATTT 0.815467 -111 AGACGCAAAAGCCCCCATTTCGGGCCCGAA 10 52 0 GCCCCCATTT 0.815467 -93 GGGGGCTTTTGCGTCTGCTCACGCCGTAGC 10 66 1 GCGTCTGCTC 0.920752 -79 CCCTGGCGGCGCCTCCGCTAGATGACCGGA 13 152 1 GCCTCCGCTA 0.845893 -43 ********** Masking position 9 Map Score: 7.48801 Number of sites scoring better than the average of aligned sites = 891 Number in coding regions = 822 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 CAGGGTTTTTATGCAGAGTGACGAGACGAAT 2 251 1 ATGCAGAGGA 0.907341 -50 GCGTGTGCCGTTCCAGCGAGTCACTATGCAT 7 70 1 TTCCAGCGGT 0.985724 -231 GTCACGCGCAATCCAGCGGGTTCGCCGAACC 7 237 0 ATCCAGCGGT 0.993731 -64 CAGCTCAATAATCCAGAGAGGCCGCACGGAC 7 277 1 ATCCAGAGGG 0.951232 -24 TTGGACAGTCTAGCAGCGGGTTGACCGCCAA 8 58 0 TAGCAGCGGT 0.858128 -99 TGGGAACGAAATCCAGCCAGTTCGACCAACC 10 96 0 ATCCAGCCGT 0.968267 -49 CTTAGCCGTGATCCAGCGCGAGCCTTCGGCC 12 70 1 ATCCAGCGGA 0.98838 -57 ******** ** Masking position 5 Map Score: 4.85685 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 76 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 AGAAAATAAAAAAAGCCCTCTCATCCCATA 1 256 0 AAAAGCCCTC 0.987396 -45 GAGCAGACGCAAAAGCCCCCATTTCGGGCC 10 30 1 AAAAGCCCCC 0.995346 -115 GAGCAGACGCAAAAGCCCCCATTTCGGGCC 10 56 0 AAAAGCCCCC 0.995346 -89 ********** Masking position 4 Map Score: 2.42875 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 4 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 TTTCCTTCAGGCCTTCATAGCGACCCGGAG 1 60 1 GCCTTCATAG 0.81738 -241 CGCAAAAAGTGCCATCGTAATATTAGAGTT 2 30 1 GCCATCGTAA 0.74489 -271 AATAAAATTTGCGTGCGTTGCAAG 5 5 0 GCGTGCGTTG 0.897538 -152 TAGTATGATAGTTTTCGTAGTCTTAAAACC 5 64 1 GTTTTCGTAG 0.304972 -93 CGGTTCTTGCGGTCGTGACCCCCGGCTG 8 9 1 GCGGTCGTGA 0.861932 -148 CTGATCAATGGTCGGCGTAAAGCTTGAGAC 9 31 1 GTCGGCGTAA 0.873574 -180 CCACGGTGCCGCCGGCGTTCCCGGACGTGC 9 100 1 GCCGGCGTTC 0.876231 -111 TCCGGCGGCCGCGTGCATGGTGTTCCCGGA 9 141 1 GCGTGCATGG 0.732718 -70 ACCCTAACGACCCGGCGAAGTGGGAACGAA 10 117 0 CCCGGCGAAG 0.646514 -28 CGTCTCGCCTGCCTTCGTAGCGGCGTCTTT 13 30 0 GCCTTCGTAG 0.969892 -165 GCACGCAGCAGCCGGCGTAGCTACCAACGA 13 102 0 GCCGGCGTAG 0.992666 -93 GCTGCTGCGTGCCGGCGGGACACTGGGAGC 13 120 1 GCCGGCGGGA 0.869567 -75 ********** Masking position 6 Map Score: 1.84597 Number of sites scoring better than the average of aligned sites = 1170 Number in coding regions = 1084 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 AAAACGGTTGAAAGGGACAGTCATGTTTCC 1 35 1 AAAGGGACAG 0.926903 -266 CATACCTAAGCAAGTGACAGAAACTCTAAT 2 51 0 CAAGTGACAG 0.948635 -250 TAAACGAAGAAAGAGGACAGACGATATACG 4 27 0 AAGAGGACAG 0.853061 -55 ACAAACGCCGCAGGTGCCAGCCGGGGGTCA 8 26 0 CAGGTGCCAG 0.973382 -131 GGTGGTCGGCCAGGCGCCAGATTCACCGGT 9 191 0 CAGGCGCCAG 0.861523 -20 TCCTGTCCATGAGGCGACAGTCGTGGGCCG 11 60 0 GAGGCGACAG 0.969086 -26 ********** Masking position 2 Map Score: 1.35587 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 153 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 AGCAAATGGTGCGGTACGCGCAGAACCGCG 7 43 1 GCGGTACGCG 0.990357 -258 CCTGTATCGGGCGGTCCTCGGTAGTGGCTG 7 121 1 GCGGTCCTCG 0.94664 -180 CTGTTTCGCGTCGTCACGCGCAATCCAGCG 7 250 0 TCGTCACGCG 0.829518 -51 TCCAACGACATCGGTGCGTGCTGCGGTTCG 8 84 1 TCGGTGCGTG 0.917931 -73 GGTGCGTGCTGCGGTTCGCGGTGGCCGTGC 8 96 1 GCGGTTCGCG 0.990357 -61 TCTCCATCAATGGGTTCGCGATCATGGATA 8 131 0 TGGGTTCGCG 0.936895 -26 TCCCAGAGAATTGGCGCGCGCATACCGAAC 9 66 0 TTGGCGCGCG 0.948416 -145 GGCGACAGTCGTGGGCCGCGCCTCGGGTTT 11 48 0 GTGGGCCGCG 0.940641 -38 ********** Masking position 7 Map Score: 4.12751 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 160 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 ********** No masking Map Score: -6.3214e-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 12 ********** No masking Map Score: -6.3214e-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 13 ********** No masking Map Score: -6.3214e-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