AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00100_mtub_reg_300.orf -o00100_mtub_300.ace -a/home/amcguire/genomes/ORF_mtub.txt -z/home/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 idsA2 300 idsA2 #2 Rv3137 300 hypothetical protein Rv3137 #3 fadE24 79 fadE24 #4 idsB 300 idsB #5 idsA 22 idsA Motif number 1 CGAGTACTTCCATGGCCGCCAATGGGGCCA 1 20 1 CATGGCCGCC 0.871343 -281 CGCCAATGGGGCCACCGGTGGGCCGCGCCG 1 36 1 GCCACCGGTG 0.90853 -265 TTGCGCGACGCGGCGCGGCCCACCGGTGGC 1 46 0 CGGCGCGGCC 0.725873 -255 TTGGCTGGTCCGGCCCGGCCCAGGATGGCG 1 78 0 CGGCCCGGCC 0.879393 -223 TTTCCGCGAGCCCACCCGCCGAATCATCGA 1 170 1 CCCACCCGCC 0.955312 -131 CCGAATCATCGATAGCGGCCACTCGCGCCG 1 188 1 GATAGCGGCC 0.973655 -113 CAGTGTATTCCGCGCCGGCGCGAGTGGCCG 1 203 0 CGCGCCGGCG 0.540858 -98 CATTCAGGCTCAGCGCGGCGCCCCTTTCTC 1 255 0 CAGCGCGGCG 0.810331 -46 CGCTGCCGGTGCTGCCGGTGCATTCAGGCT 1 275 0 GCTGCCGGTG 0.920763 -26 CGGCAGCACCGGCAGCGGTCCAG 1 288 1 GGCAGCGGTC 0.6201 -13 CCAGTGATGATCCCGGCGATGGTGACAT 2 9 1 GATCCCGGCG 0.908076 -292 GTGACATACTGCTGGCCGCCTGCGTCCGGT 2 32 1 GCTGGCCGCC 0.922012 -269 GCCTGCGTCCGGTCGCGGGCTGACTCCGGT 2 49 1 GGTCGCGGGC 0.573156 -252 GTCGCGGGCTGACTCCGGTCACCAGGAGCG 2 60 1 GACTCCGGTC 0.653834 -241 GGGAGATCTGGCCAGCGGCACGCTCCTGGT 2 80 0 GCCAGCGGCA 0.89107 -221 GGCCAGATCTCCCCGCGGGCCGCGCGGGAT 2 97 1 CCCCGCGGGC 0.501518 -204 GGTATTTCTTGCTCCGCGGCTTATCCCGCG 2 119 0 GCTCCGCGGC 0.743179 -182 TACTCATACTGATCGCGGTCCTAGCGGTAT 2 144 0 GATCGCGGTC 0.741994 -157 AAACTCCCATCCCACCCGGCCATGGTAGGA 2 181 1 CCCACCCGGC 0.888136 -120 AACGGCTCATGCCAGCAGTCCTACCATGGC 2 199 0 GCCAGCAGTC 0.738986 -102 TCCGGAGTAAGATAGGGGTGCTTGTTAAGT 3 14 0 GATAGGGGTG 0.677675 -66 CAGCCTCGGTCATCGGGGTGATAGCGGACC 3 56 0 CATCGGGGTG 0.668057 -24 TCGAAGGCAACCTACCCGCCGTGATGGGAA 4 49 1 CCTACCCGCC 0.958111 -252 GACACGCATACCCTGCGGCGACCTATACTT 4 77 0 CCCTGCGGCG 0.658842 -224 TTGTCCAGACGCCCCGGGTCATCCACTACA 4 111 0 GCCCCGGGTC 0.519895 -190 ********** Masking position 8 Map Score: 39.3231 Number of sites scoring better than the average of aligned sites = 67273 Number in coding regions = 63260 Number in noncoding regions = 4013 Number of orfs with sites within 600 bp upstream = 1399 Fraction of orfs with sites within 600 bp upstream = 0.224703 Motif number 2 GGGCCACCGGTGGGCCGCGCCGCGTCGCGCA 1 44 1 TGGGCCGGCC 0.957057 -257 ATCGCCATCCTGGGCCGGGCCGGACCAGCCA 1 76 1 TGGGCCGGCC 0.95706 -225 GTTTATGCTGTCTTCAGCGCCCTTGGGTTGG 1 104 0 TCTTCAGGCC 0.66785 -197 CTTGTGTGGTTTCCGCGAGCCCACCCGCCGA 1 161 1 TTCCGCGGCC 0.980188 -140 CTATCGATGATTCGGCGGGTGGGCTCGCGGA 1 172 0 TTCGGCGGTG 0.86313 -129 CCCGACAGTGTATTCCGCGCCGGCGCGAGTG 1 207 0 TATTCCGGCC 0.968553 -94 CCCTTTCTCATTTGGCGTGCCTATGGCCCGA 1 233 0 TTTGGCGGCC 0.989636 -68 GATGGTGACATACTGCTGGCCGCCTGCGTCC 2 28 1 TACTGCTGCC 0.827514 -273 CGCGGGGAGATCTGGCCAGCGGCACGCTCCT 2 83 0 TCTGGCCGCG 0.896867 -218 CTCCGCGGCTTATCCCGCGCGGCCCGCGGGG 2 107 0 TATCCCGGCG 0.982085 -194 GTGCTACTCATACTGATCGCGGTCCTAGCGG 2 147 0 TACTGATGCG 0.418258 -154 GGGATGGGAGTTTGGCGTGCTACTCATACTG 2 163 0 TTTGGCGGCT 0.903488 -138 GAGCCGTTATTACGCCGAGCGTGAACTCAGT 2 221 1 TACGCCGGCG 0.994078 -80 CAGTGCGATTTTTCGCGTGCGTTCTTGCACT 2 249 0 TTTCGCGGCG 0.977807 -52 GCCGAGCGTGTACCCAGTGCGATTTTTCGCG 2 263 0 TACCCAGGCG 0.902202 -38 GCACCATCCTTTCGCCGAGCGTGTACCCAGT 2 276 0 TTCGCCGGCG 0.994081 -25 GCAACATTCAATTGCCTGGCCTTTCTCGGAG 4 11 0 ATTGCCTGCC 0.58035 -290 AACATGTACCTATGCCCGTCGACCAACACGA 4 177 0 TATGCCCTCG 0.50833 -124 ******* *** Masking position 1 Map Score: 22.6612 Number of sites scoring better than the average of aligned sites = 10914 Number in coding regions = 9930 Number in noncoding regions = 984 Number of orfs with sites within 600 bp upstream = 658 Fraction of orfs with sites within 600 bp upstream = 0.105686 Motif number 3 GATTTGCGCGACGCGGCGCGGCCCACCGGT 1 49 0 ACGCGGCGCG 0.983509 -252 TTGTGTGGTTTCCGCGAGCCCACCCGCCGA 1 162 1 TCCGCGAGCC 0.909109 -139 CCGCCGAATCATCGATAGCGGCCACTCGCG 1 185 1 ATCGATAGCG 0.537645 -116 ATCGATAGCGGCCACTCGCGCCGGCGCGGA 1 195 1 GCCACTCGCG 0.798287 -106 CCGACAGTGTATTCCGCGCCGGCGCGAGTG 1 207 0 ATTCCGCGCC 0.711072 -94 CCTTTCTCATTTGGCGTGCCTATGGCCCGA 1 233 0 TTGGCGTGCC 0.334731 -68 GTGCATTCAGGCTCAGCGCGGCGCCCCTTT 1 258 0 GCTCAGCGCG 0.88073 -43 CACCGGCAGCACCGGCAGCGGTCCAG 1 285 1 ACCGGCAGCG 0.952769 -16 CATACTGCTGGCCGCCTGCGTCCGGTCGCG 2 36 1 GCCGCCTGCG 0.91256 -265 GCCGCCTGCGTCCGGTCGCGGGCTGACTCC 2 46 1 TCCGGTCGCG 0.94401 -255 GACTCCGGTCACCAGGAGCGTGCCGCTGGC 2 70 1 ACCAGGAGCG 0.910277 -231 GCTGGCCAGATCTCCCCGCGGGCCGCGCGG 2 94 1 TCTCCCCGCG 0.922301 -207 TCCGCGGCTTATCCCGCGCGGCCCGCGGGG 2 107 0 ATCCCGCGCG 0.983921 -194 TGCTACTCATACTGATCGCGGTCCTAGCGG 2 147 0 ACTGATCGCG 0.736482 -154 AGCCGTTATTACGCCGAGCGTGAACTCAGT 2 222 1 ACGCCGAGCG 0.976369 -79 AGTGCGATTTTTCGCGTGCGTTCTTGCACT 2 249 0 TTCGCGTGCG 0.887489 -52 CCGAGCGTGTACCCAGTGCGATTTTTCGCG 2 263 0 ACCCAGTGCG 0.955126 -38 CACCATCCTTTCGCCGAGCGTGTACCCAGT 2 276 0 TCGCCGAGCG 0.958422 -25 AAGGCAACCTACCCGCCGTGATGGGAAGTA 4 52 1 ACCCGCCGTG 0.713905 -249 GTAGTGGATGACCCGGGGCGTCTGGACAAC 4 112 1 ACCCGGGGCG 0.957388 -189 ********** Masking position 8 Map Score: 24.4959 Number of sites scoring better than the average of aligned sites = 24659 Number in coding regions = 22675 Number in noncoding regions = 1984 Number of orfs with sites within 600 bp upstream = 1005 Fraction of orfs with sites within 600 bp upstream = 0.16142 Motif number 4 CGCGGCCCACCGGTGGCCCCATTGGCGGCC 1 33 0 CGGTGGCCCC 0.887908 -268 TTGCGCGACGCGGCGCGGCCCACCGGTGGC 1 46 0 CGGCGCGGCC 0.895643 -255 TGGTCCGGCCCGGCCCAGGATGGCGATTTG 1 73 0 CGGCCCAGGA 0.837282 -228 TGGGCCGGGCCGGACCAGCCAACCCAAGGG 1 86 1 CGGACCAGCC 0.981081 -215 GGACCGCTGCCGGTGCTGCCGGTGCATTCA 1 279 0 CGGTGCTGCC 0.970915 -22 TCCTGGTGACCGGAGTCAGCCCGCGACCGG 2 57 0 CGGAGTCAGC 0.833334 -244 GGATAAGCCGCGGAGCAAGAAATACCGCTA 2 123 1 CGGAGCAAGA 0.959909 -178 ATACTGATCGCGGTCCTAGCGGTATTTCTT 2 139 0 CGGTCCTAGC 0.937867 -162 CTCATGCCAGCAGTCCTACCATGGCCGGGT 2 194 0 CAGTCCTACC 0.792612 -107 AGCGTGAACTCAGTGCAAGAACGCACGCGA 2 238 1 CAGTGCAAGA 0.736615 -63 GGCGAAAGGATGGTGCACCA 2 291 1 TGGTGCACCA 0.405615 -10 TATCTTACTCCGGAGTAAGATAGGGTGGTC 3 30 1 CGGAGTAAGA 0.751852 -50 GGGGTGATAGCGGACCACCCTATCTTACTC 3 42 0 CGGACCACCC 0.979596 -38 TCGAGTTGTCCAGACGCCCCGGGTCATCCA 4 116 0 CAGACGCCCC 0.494593 -185 TGCTTCACTTCGGAGATACCCAAATATTTC 4 220 0 CGGAGATACC 0.794465 -81 TTAACCTCACCGGAGCAACAGTGAGTCGCT 4 279 0 CGGAGCAACA 0.974881 -22 ********** Masking position 3 Map Score: 14.371 Number of sites scoring better than the average of aligned sites = 21359 Number in coding regions = 20044 Number in noncoding regions = 1315 Number of orfs with sites within 600 bp upstream = 858 Fraction of orfs with sites within 600 bp upstream = 0.137809 Motif number 5 CGACGCGGCGCGGCCCACCGGTGGCCCCAT 1 41 0 CGGCCCACCG 0.982758 -260 CGGGCCGGACCAGCCAACCCAAGGGCGCTG 1 91 1 CAGCCAACCC 0.99174 -210 TGGTTTCCGCGAGCCCACCCGCCGAATCAT 1 167 1 GAGCCCACCC 0.972996 -134 GCCAAACTCCCATCCCACCCGGCCATGGTA 2 178 1 CATCCCACCC 0.979391 -123 GGGGTGATAGCGGACCACCCTATCTTACTC 3 42 0 CGGACCACCC 0.987248 -38 TTGTCGAAGGCAACCTACCCGCCGTGATGG 4 46 1 CAACCTACCC 0.981423 -255 TACCCTGCGGCGACCTATACTTCCCATCAC 4 69 0 CGACCTATAC 0.61798 -232 GAGATCATTGCTAACAACCCTGATGGTCGT 4 151 1 CTAACAACCC 0.819194 -150 CTATGCCCGTCGACCAACACGACCATCAGG 4 169 0 CGACCAACAC 0.959422 -132 ********** Masking position 7 Map Score: 11.5265 Number of sites scoring better than the average of aligned sites = 2597 Number in coding regions = 2389 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 6 GCACGCCAAATGAGAAAGGGGCGCCGCGCT 1 244 1 TGAGAAAGGG 0.990155 -57 TACTCCGGAGTAAGATAGGGGTGCTTGTTA 3 17 0 TAAGATAGGG 0.984852 -63 TACTCCGGAGTAAGATAGGGTGGTCCGCTA 3 35 1 TAAGATAGGG 0.984852 -45 CTCCGAGAAAGGCCAGGCAATTG 4 4 1 CGAGAAAGGC 0.956534 -297 ********** Masking position 5 Map Score: 1.90852 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 9 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 AGCGGCCACTCGCGCCGGCGCGGAATACAC 1 201 1 CGCGCCGGCG 0.900566 -100 AATACACTGTCGGGCCATAGGCACGCCAAA 1 224 1 CGGGCCATAG 0.977987 -77 GCGGGGAGATCTGGCCAGCGGCACGCTCCT 2 83 0 CTGGCCAGCG 0.984227 -218 CCCATCCCACCCGGCCATGGTAGGACTGCT 2 186 1 CCGGCCATGG 0.951263 -115 GGTAGGACTGCTGGCATGAGCCGTTATTAC 2 204 1 CTGGCATGAG 0.910786 -97 CGAGAAAGGCCAGGCAATTGAATGTTGCAG 4 14 1 CAGGCAATTG 0.789482 -287 TGTTGGTCGACGGGCATAGGTACATGTTGC 4 180 1 CGGGCATAGG 0.891411 -121 TTTCAGCGAACGAGCAATCGGCGATATTGC 4 247 0 CGAGCAATCG 0.958916 -54 TGCGTGAATCTAGCATTCGCTC 5 4 0 CTAGCATTCG 0.875771 -19 ********** Masking position 5 Map Score: 3.43261 Number of sites scoring better than the average of aligned sites = 6405 Number in coding regions = 5975 Number in noncoding regions = 430 Number of orfs with sites within 600 bp upstream = 385 Fraction of orfs with sites within 600 bp upstream = 0.0618375 Motif number 8 ********** No masking Map Score: -1.07759e-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: -1.07759e-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: -1.07759e-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