AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00072_mtub_reg_100.orf -o00072_mtub_100.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 fadA2 141 fadA2 #2 fadA 156 fadA #3 fadA4 300 fadA4 #4 scoA 82 scoA #5 fadD35 115 fadD35 #6 fadA6 64 fadA6 #7 Rv3557c 300 hypothetical protein Rv3557c Motif number 1 CAGCTGCCTTCCGTATCGTGTGGGGGTCGG 1 13 1 CCGTATCGTG 0.964744 -129 CGTATCGTGTGGGGGTCGGGCGCGCCAATA 1 24 1 GGGGGTCGGG 0.990107 -118 ATACACGTAACCGTATCGAGGACTAACTTA 1 51 1 CCGTATCGAG 0.945889 -91 GATCAGTTCGGGGGATCGGCCGTTGAGGGC 1 109 0 GGGGATCGGC 0.987621 -33 GCATCGTCGCCCGGATAGGCTCGACCGCC 2 10 0 CCGGATAGGC 0.930856 -147 TCGCTGCGGCGCGCATCGTCGCCCGGATAG 2 22 0 GCGCATCGTC 0.966417 -135 CAACCAACAGGTTGGCCGGGGGCCCTGTTA 2 61 1 GTTGGCCGGG 0.76152 -96 AGACTAGGTCCCGTACCGGCACCCTAACAG 2 85 0 CCGTACCGGC 0.976847 -72 GCACTGCTGGCGGTGCCGGGCTCCGCGGCG 3 14 0 CGGTGCCGGG 0.965937 -287 TCGCGGATGCCCTGATCGTCGTTGATTTCC 3 45 1 CCTGATCGTC 0.959788 -256 ATCATGCCAAGGTGGTCGTGATACCACTCG 3 87 1 GGTGGTCGTG 0.917674 -214 ATGGCAACGTCCAGGTCGGCGACCGCAATA 3 117 1 CCAGGTCGGC 0.955367 -184 GCAATACCGACGTGATCGAGTCCAGTTACC 3 141 1 CGTGATCGAG 0.878496 -160 ATCTGCTTCTCCGGGTCGGTCAGATCGGCT 3 245 1 CCGGGTCGGT 0.952711 -56 AGTCGTGTACGGAGACCGTC 5 1 0 GGAGACCGTC 0.687158 -115 AATGCCCCGTGTCGACGACGATGCGG 6 7 1 CCGTGTCGAC 0.96315 -58 GGTACCCCCACCGCATCGTCGTCGACACGG 6 17 0 CCGCATCGTC 0.975652 -48 CGATCCGCGTAGTCCGATTAGGCT 7 5 1 CCGCGTAGTC 0.778169 -296 ATATTCTTCCGCGCGTCGTCATAGCCTAAT 7 27 0 GCGCGTCGTC 0.975293 -274 GAGACATCTGGGGTATCGGCGGAGAGTGCC 7 87 0 GGGTATCGGC 0.959786 -214 GGCCCAGGTGCAGGATCGAGGGGCTTGGTA 7 128 0 CAGGATCGAG 0.771071 -173 GATCCTGCACCTGGGCCGGGCTGTGCGGGC 7 141 1 CTGGGCCGGG 0.945323 -160 TGCGCCCTTCGCTCACCGGGGCATTAGATG 7 200 0 GCTCACCGGG 0.903605 -101 CGAGGTCGCAGCTGGCCGAGCAAGCGCTTG 7 264 1 GCTGGCCGAG 0.903292 -37 ********** Masking position 8 Map Score: 38.5331 Number of sites scoring better than the average of aligned sites = 35956 Number in coding regions = 33497 Number in noncoding regions = 2459 Number of orfs with sites within 600 bp upstream = 1174 Fraction of orfs with sites within 600 bp upstream = 0.188564 Motif number 2 TTCAGCTGCCTTCCGTATCGTGTGGG 1 5 1 GCTCCTCCGT 0.722273 -137 TGGCGCGCCCGACCCCCACACGATACGGAAGG 1 19 0 GACCCCCACG 0.917577 -123 CTCAACGGCCGATCCCCCGAACTGATCAACGG 1 112 1 GATCCCGAAC 0.743575 -30 CGCCCGGATAGGCTCGACCGCC 2 1 0 GGCCGACGCC 0.616001 -156 TCCGGGCGACGATGCGCGCCGCAGCGATACCT 2 25 1 GATCGCCCGC 0.949098 -132 GCGCCGCAGCGATACCTTGCCCAACCAACAGG 2 40 1 GATCCTGCCC 0.976852 -117 ACCCTAACAGGGCCCCCGGCCAACCTGTTGGT 2 63 0 GGCCCCGCCA 0.894762 -94 GCGGTGCCGGGCTCCGCGGCGCAA 3 3 0 GCTCGCGCGC 0.829401 -298 CGCGGAGCCCGGCACCGCCAGCAGTGCCTCGC 3 17 1 GGCCCGCAGC 0.91349 -284 GTGCCTCGCGGATGCCCTGATCGTCGTTGATT 3 40 1 GATCCCGATC 0.74205 -261 CGGAGAAGCAGATTCTTTCCCTTCAGGTTACC 3 226 0 GATCTTCCCT 0.402163 -75 TCGGCTTTCGGGTGCGCTGAGGAGGTAGTCAT 3 269 1 GGTCGCGAGG 0.855576 -32 GGTCCCTAGACGCACCGCGGGG 4 1 1 GGTCCTGACG 0.906792 -82 TCCTCCGCCTGGTGCCTACCGCATGTCTGACT 5 91 0 GGTCCTCCGC 0.985458 -25 GGTTCCTCCGCCTGGTGCCTAC 5 104 0 GGTCCTCGCC 0.94774 -12 GCCAGTGAGTGGTACCCCCACCGCATCGTCGT 6 25 0 GGTCCCCACC 0.989606 -40 AACCGCTCCTCTCCCGTTGCCAGTGA 6 49 0 GCTCTCCCCG 0.803551 -16 CAGAACGCTAGGCACTCTCCGCCGATACCCCA 7 77 1 GGCCTCCCGC 0.948889 -224 CCCGTGATCAGGTACCAAGCCCCTCGATCCTG 7 116 1 GGTCCAGCCC 0.963865 -185 GCGCTGGATGGACGCCTTGCCCGCACAGCCCG 7 157 0 GACCCTGCCC 0.97 -144 CGCATCTAATGCCCCGGTGAGCGAAGGGCGCA 7 198 1 GCCCGGGAGC 0.530626 -103 CGAATTCCCGGATTCCCACCCCATCGAGGTCG 7 240 1 GATCCCCCCC 0.99213 -61 *** *** **** Masking position 5 Map Score: 25.7839 Number of sites scoring better than the average of aligned sites = 17595 Number in coding regions = 16256 Number in noncoding regions = 1339 Number of orfs with sites within 600 bp upstream = 803 Fraction of orfs with sites within 600 bp upstream = 0.128975 Motif number 3 GGCCGATCCCCCGAACTGATCAACGGAGAA 1 118 1 CCGAACTGAT 0.806435 -24 ACGATGCGCGCCGCAGCGATACCTTGCCCA 2 33 1 CCGCAGCGAT 0.955124 -124 TTGCGCCGCGGAGCCCGGCACCGCC 3 6 1 CCGCGGAGCC 0.984066 -295 CCGGCACCGCCAGCAGTGCCTCGCGGATGC 3 25 1 CAGCAGTGCC 0.945763 -276 GACCGCAATACCGACGTGATCGAGTCCAGT 3 137 1 CCGACGTGAT 0.866776 -164 CACCCGAAAGCCGATCTGACCGACCCGGAG 3 253 0 CCGATCTGAC 0.868644 -48 ACCATTGCCCCCGCGGTGCGTCTAGGGACC 4 11 0 CCGCGGTGCG 0.895509 -72 ACCGCAGAGCCTCCTAGCATT 4 72 0 CCGCAGAGCC 0.992147 -11 TGACGATTAACCGAAGTGTCCAGCATGAGT 5 28 0 CCGAAGTGTC 0.935501 -88 GGTACCCCCACCGCATCGTCGTCGACACGG 6 17 0 CCGCATCGTC 0.74693 -48 TAGGCACTCTCCGCCGATACCCCAGATGTC 7 85 1 CCGCCGATAC 0.825391 -216 GACGCCTTGCCCGCACAGCCCGGCCCAGGT 7 149 0 CCGCACAGCC 0.982936 -152 CTTGCTCGGCCAGCTGCGACCTCGATGGGG 7 258 0 CAGCTGCGAC 0.796899 -43 CCGACCAGACTATCAACCAA 7 291 0 CCGACCAGAC 0.926136 -10 ********** Masking position 1 Map Score: 16.9186 Number of sites scoring better than the average of aligned sites = 12206 Number in coding regions = 11349 Number in noncoding regions = 857 Number of orfs with sites within 600 bp upstream = 628 Fraction of orfs with sites within 600 bp upstream = 0.100867 Motif number 4 TTCAGCTGCCTTCCGTATCGTGTGGG 1 7 1 TGCCTTCCGT 0.909986 -135 AAGGTATCGCTGCGGCGCGCATCGTCGCCC 2 28 0 TGCGGCGCGC 0.968908 -129 TTGCGCCGCGGAGCCCGGCAC 3 2 1 TGCGCCGCGG 0.968908 -299 CCGCCAGCAGTGCCTCGCGGATGCCCTGAT 3 31 1 TGCCTCGCGG 0.995699 -270 CGTCGTTGATTTCCTCGTGGACCAGGATCA 3 61 1 TTCCTCGTGG 0.853619 -240 AGCCAGCATGTGACGGGCGTGGACTTGATC 3 179 1 TGACGGGCGT 0.868724 -122 GTGTCCAGCATGAGTCGTGTACGGAGACCG 5 13 0 TGAGTCGTGT 0.835673 -103 ACCGCATGTCTGACTCGCGTTAACATCGAA 5 76 0 TGACTCGCGT 0.987893 -40 CTCCGCCTGGTGCCTACCGCATGTCTGACT 5 91 0 TGCCTACCGC 0.884595 -25 AATGCCCCGTGTCGACGACGAT 6 3 1 TGCCCCGTGT 0.969364 -62 GCGCATATTCTTCCGCGCGTCGTCATAGCC 7 31 0 TTCCGCGCGT 0.966987 -270 CGGCGGAGAGTGCCTAGCGTTCTGGGCATT 7 71 0 TGCCTAGCGT 0.982742 -230 ATACCCCAGATGTCTCCCGTGATCAGGTAC 7 101 1 TGTCTCCCGT 0.909986 -200 ********** Masking position 1 Map Score: 19.119 Number of sites scoring better than the average of aligned sites = 4060 Number in coding regions = 3657 Number in noncoding regions = 403 Number of orfs with sites within 600 bp upstream = 326 Fraction of orfs with sites within 600 bp upstream = 0.0523611 Motif number 5 GGGGGATCGGCCGTTGAGGGCCATACTACC 1 100 0 CCGTTGAGGG 0.975798 -42 GGGCCCCCGGCCAACCTGTTGGTTGGGCAA 2 56 0 CCAACCTGTT 0.548552 -101 GAAATCAACGACGATCAGGGCATCCGCGAG 3 44 0 ACGATCAGGG 0.765816 -257 CTGGACGTTGCCATCGAGTGGTATCACGAC 3 101 0 CCATCGAGTG 0.967274 -200 CTCGATGGCAACGTCCAGGTCGGCGACCGC 3 113 1 ACGTCCAGGT 0.838895 -188 AGTCCAGTTACCAACGAGGTAGCCAGCATG 3 159 1 CCAACGAGGT 0.934429 -142 CTTCAGGTTACCGTTGTGTGATGACGACCG 3 208 0 CCGTTGTGTG 0.87313 -93 CAGATTCTTTCCCTTCAGGTTACCGTTGTG 3 220 0 CCCTTCAGGT 0.841142 -81 TCTCCCGTTGCCAGTGAGTGGTACCCCCAC 6 36 0 CCAGTGAGTG 0.917993 -29 GGCAAGGCGTCCATCCAGCGCCAGCAACGT 7 168 1 CCATCCAGCG 0.956213 -133 ATCTAATGCCCCGGTGAGCGAAGGGCGCAT 7 201 1 CCGGTGAGCG 0.925673 -100 GATTCCCACCCCATCGAGGTCGCAGCTGGC 7 250 1 CCATCGAGGT 0.924921 -51 ********** Masking position 2 Map Score: 10.278 Number of sites scoring better than the average of aligned sites = 5708 Number in coding regions = 5301 Number in noncoding regions = 407 Number of orfs with sites within 600 bp upstream = 351 Fraction of orfs with sites within 600 bp upstream = 0.0563765 Motif number 6 GCCGATCCCCCGAACTGATCAACGGAGAAA 1 119 1 CGAACTGATC 0.926003 -23 TGCCGGTACGGGACCTAGTCTTGAAGAAGG 2 94 1 GGACCTAGTC 0.936241 -63 TCCTGGTCCACGAGGAAATCAACGACGATC 3 58 0 CGAGGAAATC 0.621467 -243 AGGATCATGCCAAGGTGGTCGTGATACCAC 3 84 1 CAAGGTGGTC 0.84398 -217 TTGCGGTCGCCGACCTGGACGTTGCCATCG 3 115 0 CGACCTGGAC 0.911749 -186 ACCGCAATACCGACGTGATCGAGTCCAGTT 3 138 1 CGACGTGATC 0.975305 -163 CAGTTACCAACGAGGTAGCCAGCATGTGAC 3 163 1 CGAGGTAGCC 0.951468 -138 TGACGGGCGTGGACTTGATCGGTCGTCATC 3 189 1 GGACTTGATC 0.743109 -112 ACCCGAAAGCCGATCTGACCGACCCGGAGA 3 252 0 CGATCTGACC 0.838999 -49 GGTGCGCTGAGGAGGTAGTCATAACGACAT 3 279 1 GGAGGTAGTC 0.937803 -22 GACGATTAACCGAAGTGTCCAGCATGAGTC 5 27 0 CGAAGTGTCC 0.743334 -89 TAACGTAGCACGAGCTATTCGATGTTAACG 5 59 1 CGAGCTATTC 0.876439 -57 GAGGGGCTTGGTACCTGATCACGGGAGACA 7 111 0 GTACCTGATC 0.650211 -190 CATCGAGGTCGCAGCTGGCCGAGCAAGCGC 7 261 1 GCAGCTGGCC 0.794318 -40 ********** Masking position 3 Map Score: 9.11046 Number of sites scoring better than the average of aligned sites = 11821 Number in coding regions = 11310 Number in noncoding regions = 511 Number of orfs with sites within 600 bp upstream = 418 Fraction of orfs with sites within 600 bp upstream = 0.0671378 Motif number 7 AGGTATCGCTGCGGCGCGCATCGTCGCCCG 2 27 0 GCGGCGCGCA 0.926666 -130 TTGCGCCGCGGAGCCCGGCACC 3 3 1 GCGCCGCGGA 0.991433 -298 CGCCAGCAGTGCCTCGCGGATGCCCTGATC 3 32 1 GCCTCGCGGA 0.949947 -269 GTCGTTGATTTCCTCGTGGACCAGGATCAT 3 62 1 TCCTCGTGGA 0.652106 -239 AATACCATTGCCCCCGCGGTGCGTCTAGGG 4 14 0 CCCCCGCGGT 0.941693 -69 ATGCTAGGAGGCTCTGCGGT 4 73 1 GCTCTGCGGT 0.708474 -10 TGTCCAGCATGAGTCGTGTACGGAGACCGT 5 12 0 GAGTCGTGTA 0.738335 -104 CCGCATGTCTGACTCGCGTTAACATCGAAT 5 75 0 GACTCGCGTT 0.94454 -41 AATGCCCCGTGTCGACGACGATG 6 4 1 GCCCCGTGTC 0.825109 -61 GGCAACGGGAGAGGAGCGGTT 6 54 1 GAGGAGCGGT 0.755913 -11 CGATCCGCGTAGTCCGATTAG 7 2 1 GATCCGCGTA 0.884116 -299 AGGCTATGACGACGCGCGGAAGAATATGCG 7 30 1 GACGCGCGGA 0.642221 -271 GGCGGAGAGTGCCTAGCGTTCTGGGCATTC 7 70 0 GCCTAGCGTT 0.860615 -231 ********** Masking position 6 Map Score: 12.7354 Number of sites scoring better than the average of aligned sites = 10600 Number in coding regions = 9712 Number in noncoding regions = 888 Number of orfs with sites within 600 bp upstream = 577 Fraction of orfs with sites within 600 bp upstream = 0.0926759 Motif number 8 ACCTGTTGGTTGGGCAAGGTATCGCTGCGGC 2 42 0 TGGCAAGGTA 0.79276 -115 GACCTAGTCTTGAAGAAGGATCCAAACCCCC 2 105 1 TGAGAAGGAT 0.849602 -52 GTGGAATTTGTGGAACAGGAAATCGAC 2 140 1 TGGACAGGAA 0.95861 -17 GATTTCCTCGTGGACCAGGATCATGCCAAGG 3 68 1 TGGCCAGGAT 0.984417 -233 GGTAGGCACCAGGCGGAGGAACC 5 103 1 AGGGGAGGAA 0.939634 -13 AGCCCGGCCCAGGTGCAGGATCGAGGGGCTT 7 132 0 AGGGCAGGAT 0.982081 -169 GCGACGTTGCTGGCGCTGGATGGACGCCTTG 7 170 0 TGGGCTGGAT 0.968829 -131 GCGACCTCGATGGGGTGGGAATCCGGGAATT 7 242 0 TGGGTGGGAA 0.898242 -59 *** ******* Masking position 8 Map Score: 2.55148 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 492 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 ********** No masking Map Score: 1.1393e-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: 1.1393e-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 11 ********** No masking Map Score: 1.1393e-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