AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -imodE_mtub_opreg_300.orf -g0.656 -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 = 0.656 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 Rv0870c 164 hypothetical protein Rv0870c #2 Rv0981 300 hypothetical protein Rv0981 #3 Rv0983 43 hypothetical protein Rv0983 #4 modA 161 modA #5 subI 124 subI #6 Rv3108 98 hypothetical protein Rv3108 #7 moaA 148 moaA #8 moaB 50 moaB #9 moaC3 184 moaC3 Motif number 1 ACAGAAGACGCGTCCCGCCTGCGCGGGACGCGATGA 1 51 1 CGCCCGCCGG 0.547689 -114 GCTCGGCGGCCGACGATCCGAGTAGGATCTTCAGAT 1 89 0 CGCGATCCGG 0.949374 -76 GATCGTCGGCCGCCGAGCACCCCTGCTTACCCCTCA 1 107 1 CGCGAGCAGC 0.971198 -58 GTAGCGCAAGCCTACCGCGTGAGGGGTAAGCAGGGG 1 126 0 CCACCGCGGG 0.697228 -39 ATCGCCTCCAGCGGTAGCGCAAGCCTACCG 1 145 0 CCCCAGCGGC 0.891526 -20 CGATCCCTGCCGTTCCACGCCTGGGCGCAGGCACAA 2 30 1 CGTCCACGGC 0.948443 -271 GTGTGCACCACGTTCCACCAATGTTGGTGCGGTTTG 2 63 0 CGTCCACCTG 0.833264 -238 TGCTGACACACGATGAGGGCAGAACCCCAGGTGCAG 2 98 0 CGTGAGGGCC 0.903 -203 GAGTTCTCGTCCGCGCGGGTTTCGCCTGCTGACACA 2 124 0 CCCGCGGGCC 0.929638 -177 GGCTAAACCTCGTCGAACAAACCCGCATACCACGGC 2 236 1 CGCGAACAGC 0.892538 -65 CCGCATACCACGGCGCGCCTCTCAGGCCAGTCTCAG 2 258 1 CGCGCGCCGG 0.997815 -43 CAGTGTCGTCGCAGCGCCTGAGACTGGCCTGA 2 279 0 CGCGCAGCAG 0.779209 -22 TTCCAGGCAACGGTCCAGGGTCTGGGTTCAGCGTTG 4 25 0 CGTCCAGGGG 0.93892 -137 CGCGTCGTGGCGGTGCGGAGTTTCCCCGAATAGCTA 4 104 0 CGTGCGGACC 0.943028 -58 CGCACCGCCACGACGCGCAGACGATCTTGGTAACCA 4 123 1 CGCGCGCATC 0.945436 -39 CCACATCAGACCGCGCACGGGTGGGGAGTCAGCGAC 5 15 0 CCCGCACGGG 0.942594 -110 GAAAGGCGATCGCTGAACATTGCAGGACTCACGAAC 5 52 0 CGTGAACAGG 0.870565 -73 ACAACGTTCCCGTAGCGGCGGAAAGGCGATCGCTGA 5 72 0 CGAGCGGCGG 0.968629 -53 GGCGACCTTCCGGTGCGGGACTTTGGACAACGTTCC 5 98 0 CGTGCGGGGG 0.992896 -27 CGTTTGAGGACGATCATGGCTCCGCCGACGACCACC 6 25 1 CGTCATGGCC 0.423664 -74 GATGGGCTATCGTCGCGGCCCTGGTGCTGGTGGTCG 6 53 0 CGCGCGGCTG 0.97888 -46 CAACGCGCCATAAACGCAGGCTCATG 7 1 1 CACGCGCCCG 0.836713 -148 CAGGCTCATGCGCTGCGCCACGATGCGCCGATGCAT 7 27 1 CGTGCGCCGC 0.99462 -122 ATCATCTTTTCGATCCTCCACTTTGGACGCAGTCGG 7 117 0 CGTCCTCCGG 0.953016 -32 GGTTCCTTCCTCAACTGTGGAGTCGTTGAT 8 31 0 CCTCCTCAGG 0.625372 -20 GACACTGAACCGCCCCGGCATGTCCGGAGACTCCAG 9 31 0 CGCCCGGCCG 0.824137 -154 AACAAGCGGTCGGTGCGGTTGACTTGTTGGACGCGC 9 70 1 CGTGCGGTTG 0.640948 -115 ACTTCGACCTCGCCGAGGCTTTCAGCGCAGTGCACG 9 131 1 CGCGAGGCGC 0.984861 -54 GCGCAGTGCACGATGAGCAATGCAGCCAGCAGGTGG 9 155 1 CGTGAGCAGC 0.950946 -30 ** ****** ** Masking position 1 Map Score: 51.4036 Number of sites scoring better than the average of aligned sites = 46818 Number in coding regions = 43353 Number in noncoding regions = 3465 Number of orfs with sites within 600 bp upstream = 1289 Fraction of orfs with sites within 600 bp upstream = 0.207035 Motif number 2 CATCGCGTCCCGCGCAGGCGGGACGCGTCTTCTG 1 52 0 CGCCGGGGAC 0.989493 -113 GCAAGCCTACCGCGTGAGGGGTAAGCAGGGGTGC 1 123 0 CGCTAGGGAA 0.558402 -42 TGCCGTTCCACGCCTGGGCGCAGGCACAAACCGC 2 37 1 CGCTGGGCGG 0.982717 -264 AGTTCTCGTCCGCGCGGGTTTCGCCTGCTGACAC 2 125 0 CGCCGGTTGC 0.964559 -176 GCCTGAGACTGGCCTGAGAGGCGCGCCGTGGTAT 2 262 0 GGCTAGGGGC 0.988433 -39 TCTCAGGCCAGTCTCAGGCGCTGCGACGACACTG 2 277 1 GTCCGGGCGC 0.986206 -24 GCGTGGACTGGCATGGGTGTGGCTTTCAACAGT 3 21 0 GGCTGGGTGC 0.982384 -23 AACGGTCCAGGGTCTGGGTTCAGCGTTGAACACG 4 19 0 GGTTGGTCGC 0.902971 -143 GCATCGTGATGGCGTAAGCTCCGGTAGATGTTAC 4 63 1 GGCTAGTCGG 0.800846 -99 ATCGTCTGCGCGTCGTGGCGGTGCGGAGTTTCCC 4 114 0 CGTGGGGGGC 0.924526 -48 CATCAGACCGCGCACGGGTGGGGAGTCAGCGACA 5 14 0 CGCCGGGGGA 0.987155 -111 GGTGCTGGTGGTCGTCGGCGGAGCCATGATCGTC 6 33 0 GTCTGGGGGC 0.981042 -66 CTATCGTCGCGGCCCTGGTGCTGGTGGTCGTCGG 6 49 0 GGCCGGGCGG 0.992417 -50 GTGGCTAGCCGGTGCTGGATGGGCTATCGTCGCG 6 72 0 GGTCGGTGGC 0.965917 -27 CATAAACGCAGGCTCATGCGCTGCGCCACGATGC 7 19 1 GGCCTGGCGC 0.984442 -130 TTGTACGAAACTCTCTTGAGGCGCTCTAACCGAC 7 88 1 CTCCTGGGGC 0.922894 -61 ACTTGTTGGACGCGCCAGATGCACTGTTTGACTC 9 91 1 CGCCAGTGAC 0.856368 -94 *** * ** ** ** Masking position 8 Map Score: 29.0555 Number of sites scoring better than the average of aligned sites = 18651 Number in coding regions = 17632 Number in noncoding regions = 1019 Number of orfs with sites within 600 bp upstream = 681 Fraction of orfs with sites within 600 bp upstream = 0.10938 Motif number 3 CGATCCGTCAGACAAGCAGGTGAGACCA 1 7 0 GACAGCAGGG 0.990402 -158 GTCATCGCGTCCCGCGCAGGCGGGACGCGTCT 1 56 0 CCCCGCAGGG 0.939524 -109 CCGCGTGAGGGGTAAGCAGGGGTGCTCGGCGG 1 116 0 GGTAGCAGGG 0.965035 -49 GGTTTGTGCCTGCGCCCAGGCGTGGAACGGCA 2 37 0 TGCCCCAGGG 0.851821 -264 GATGAGGGCAGAACCCCAGGTGCAGTGTGCAC 2 91 0 GAACCCAGGG 0.728437 -210 CCTCATCGTGTGTCAGCAGGCGAAACCCGCGC 2 116 1 TGTAGCAGGG 0.762001 -185 TGGCCTGAGAGGCGCGCCGTGGTATGCGGGTT 2 255 0 GGCCGCCGTG 0.968068 -46 CAGCGCCTGAGACTGGCCTGAGAGGCGCGCCG 2 268 0 GACGGCCTGG 0.904164 -33 GCGTGGACTGGCATGGGTGTGGCTTTC 3 27 0 GACGGCATGG 0.867536 -17 GCACCGCCACGACGCGCAGACGATCTTGGTAA 4 124 1 GACCGCAGAG 0.982808 -38 TGGCGACCTTCCGGTGCGGGACTTTG 5 109 0 GACTTCCGGG 0.786782 -16 GACGATCATGGCTCCGCCGACGACCACCAGCA 6 33 1 GCTCGCCGAG 0.917493 -66 GTGGTGGCTAGCCGGTGCTGGATGGGC 6 82 0 GGCAGCCGGG 0.994531 -17 GCTGCGCCACGATGCGCCGATGCATTTCGGTA 7 38 1 GATCGCCGAG 0.946767 -111 GGAGTCTCCGGACATGCCGGGGCGGTTCAGTG 9 33 1 GACTGCCGGG 0.980618 -152 GTCGACTTCGACCTCGCCGAGGCTTTCAGCGC 9 127 1 ACCCGCCGAG 0.856534 -58 TGAGCAATGCAGCCAGCAGGTGGCACG 9 168 1 AGCAGCAGGG 0.935184 -17 *** ****** * Masking position 12 Map Score: 24.6829 Number of sites scoring better than the average of aligned sites = 15148 Number in coding regions = 14110 Number in noncoding regions = 1038 Number of orfs with sites within 600 bp upstream = 694 Fraction of orfs with sites within 600 bp upstream = 0.111468 Motif number 4 TGGTGCGGTTTGTGCCTGCGCCCAGGCGTG 2 45 0 TGTGCCTGCG 0.971059 -256 GCCCTCATCGTGTGTCAGCAGGCGAAACCC 2 114 1 TGTGTCAGCA 0.938537 -187 TCCAGGGTCTGGGTTCAGCGTTGAACACGA 4 18 0 GGGTTCAGCG 0.954522 -144 GCACGGGTGGGGAGTCAGCGACAACA 5 7 0 GGAGTCAGCG 0.995791 -118 GCTGATGGTGTCAGCGTTTGAGGACG 6 7 1 GGTGTCAGCG 0.995791 -92 GCGCAGCGCATGAGCCTGCGTTTATGGCGC 7 15 0 TGAGCCTGCG 0.971059 -134 TCCAAGAACTGGAGTCTCCGGACATGCCGG 9 23 1 GGAGTCTCCG 0.947463 -162 CCTCGCCGAGGCTTTCAGCGCAGTGCACGA 9 138 1 GCTTTCAGCG 0.934173 -47 GATGAGCAATGCAGCCAGCAGGTGGCACG 9 166 1 GCAGCCAGCA 0.921295 -19 ********** Masking position 6 Map Score: 11.8132 Number of sites scoring better than the average of aligned sites = 5239 Number in coding regions = 4974 Number in noncoding regions = 265 Number of orfs with sites within 600 bp upstream = 233 Fraction of orfs with sites within 600 bp upstream = 0.0374237 Motif number 5 TGGTCTCACCTGCTTGTCTGACGGATCG 1 9 1 CCTGCTTGTC 0.974475 -156 GAAGACGCGTCCCGCCTGCGCGGGACGCGA 1 54 1 CCCGCCTGCG 0.925544 -111 GCCGAGCACCCCTGCTTACCCCTCACGCGG 1 118 1 CCTGCTTACC 0.953463 -47 AGCGGTAGCGCAAGCCTACCGCGTGAGGGG 1 136 0 CAAGCCTACC 0.710972 -29 TCGGACGATCCCTGCCGTTCCACGCCTGGG 2 25 1 CCTGCCGTTC 0.825878 -276 GTCGAACAAACCCGCATACCACGGCGCGCC 2 247 1 CCCGCATACC 0.880799 -54 GCGCGCCTCTCAGGCCAGTCTCAGGCGCTG 2 270 1 CAGGCCAGTC 0.905241 -31 AAGCCACACCCATGCCAGTCCACGC 3 29 1 CATGCCAGTC 0.906945 -15 CCATCCAGCACCGGCTAGCCACCAC 6 84 1 CCGGCTAGCC 0.973914 -15 CTGAACCGCCCCGGCATGTCCGGAGACTCC 9 33 0 CCGGCATGTC 0.952508 -152 CGTGCCACCTGCTGGCTGCATTGCTCA 9 168 0 CCTGCTGGCT 0.782248 -17 ********** Masking position 5 Map Score: 7.45033 Number of sites scoring better than the average of aligned sites = 9099 Number in coding regions = 8434 Number in noncoding regions = 665 Number of orfs with sites within 600 bp upstream = 489 Fraction of orfs with sites within 600 bp upstream = 0.0785416 Motif number 6 CTGCTTGTCTGACGGATCGCTCGGATTGGC 1 20 1 GACGGATCGC 0.855169 -145 GTCTTCTGTTGCCAATCCGAGCGATCCGTC 1 30 0 GCCAATCCGA 0.428177 -135 GGGACGCGATGACGATCTGAAGATCCTACT 1 75 1 GACGATCTGA 0.765386 -90 CTCGGCGGCCGACGATCCGAGTAGGATCTT 1 94 0 GACGATCCGA 0.962663 -71 CGTTTATTCGGACGATCCCTGCCGTTCCAC 2 18 1 GACGATCCCT 0.58471 -283 TGGGCGCAGGCACAAACCGCACCAACATTG 2 51 1 CACAAACCGC 0.958282 -250 CGCCAAGCAGCACAAATCGCCCTACTCTTG 2 163 1 CACAAATCGC 0.818946 -138 ACCCGCATACCACGGCGCGCCTCTCAGGCC 2 256 1 CACGGCGCGC 0.962673 -45 CTTACGCCATCACGATGCGATTCCAGGCAA 4 51 0 CACGATGCGA 0.970551 -111 TCCGCACCGCCACGACGCGCAGACGATCTT 4 121 1 CACGACGCGC 0.982469 -41 TTGCAGGACTCACGAACTCCACATCAGACC 5 39 0 CACGAACTCC 0.723959 -86 TGCGCTGCGCCACGATGCGCCGATGCATTT 7 35 1 CACGATGCGC 0.991353 -114 AAGTCAACCGCACCGACCGCTTGTTATGGA 9 65 0 CACCGACCGC 0.861123 -120 CAGCGCAGTGCACGATGAGCAATGCAGCCA 9 153 1 CACGATGAGC 0.891618 -32 ********** Masking position 3 Map Score: 13.3383 Number of sites scoring better than the average of aligned sites = 6962 Number in coding regions = 6378 Number in noncoding regions = 584 Number of orfs with sites within 600 bp upstream = 465 Fraction of orfs with sites within 600 bp upstream = 0.0746868 Motif number 7 TTGTTTGGTGGTCAAGAGTAGGGCGATTTGTGC 2 172 0 GTCAAAGTGG 0.986968 -129 CCAGGCAACGGTCCAGGGTCTGGGTTCAGCGTT 4 26 0 GTCCAGGTTG 0.978217 -136 CGGGAACGTTGTCCAAAGTCCCGCACCGGAAGG 5 96 1 GTCCAAGTCG 0.993277 -29 AACCGACTGCGTCCAAAGTGGAGGATCGAAAAG 7 115 1 GTCCAAGTGG 0.986895 -34 TGATCAACGACTCCACAGTTGAGGAAGGAACC 8 29 1 CTCCAAGTGG 0.6177 -22 ***** *** * * Masking position 5 Map Score: 2.62386 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 32 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 CGTCCGAATAAACGGTTACCC 2 2 0 AACGGTTACC 0.989699 -299 GGCCAAACCTAATGGTTACCAAGATCGTCT 4 141 0 AATGGTTACC 0.991327 -21 GTTAACTAACAATCGTTACCGAAATGCATC 7 56 0 AATCGTTACC 0.977085 -93 AGTTTCGTACAAGGGTTAACTAACAATCGT 7 70 0 AAGGGTTAAC 0.960288 -79 ********** Masking position 6 Map Score: 1.67033 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 12 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 TGCACCACGTTCCACCAATGTTGGTGCGGT 2 66 0 TCCACCAATG 0.958422 -235 AGTTCGTGAGTCCTGCAATGTTCAGCGATC 5 51 1 TCCTGCAATG 0.981477 -74 TTGTCCAAAGTCCCGCACCGGAAGGTCGCC 5 104 1 TCCCGCACCG 0.979832 -21 GCCATGATCGTCCTCAAACGCTGACACCAT 6 15 0 TCCTCAAACG 0.922357 -84 CGATAGCCCATCCAGCACCGGCTAGCCACC 6 77 1 TCCAGCACCG 0.982994 -22 ATCTTTTCGATCCTCCACTTTGGACGCAGT 7 120 0 TCCTCCACTT 0.938033 -29 GGTTCCTTCCTCAACTGTGGAGTCGTT 8 34 0 TCCTCAACTG 0.968755 -17 GCATTGCTCATCGTGCACTGCGCTGAAAGC 9 148 0 TCGTGCACTG 0.957302 -37 ********** Masking position 7 Map Score: 9.57096 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 501 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 TTGTCTGACGGATCGCTCGGATTGGCAACA 1 24 1 GATCGCTCGG 0.928971 -141 GGGTAAGCAGGGGTGCTCGGCGGCCGACGA 1 109 0 GGGTGCTCGG 0.892421 -56 GGGTAACCGTTTATTCGGACGATCCCTG 2 9 1 GTTTATTCGG 0.826442 -292 TTCCACCAATGTTGGTGCGGTTTGTGCCTG 2 57 0 GTTGGTGCGG 0.989933 -244 AAGAGTTCTCGTCCGCGCGGGTTTCGCCTG 2 132 0 GTCCGCGCGG 0.987577 -169 TGGTATGCGGGTTTGTTCGACGAGGTTTAG 2 238 0 GTTTGTTCGA 0.826442 -63 TGCGCGTCGTGGCGGTGCGGAGTTTCCCCG 4 112 0 GGCGGTGCGG 0.982007 -50 TCAATCGACTGTTCGTTCGGC 8 2 0 GTTCGTTCGG 0.987076 -49 ATAACAAGCGGTCGGTGCGGTTGACTTGTT 9 68 1 GTCGGTGCGG 0.989731 -117 ********** Masking position 8 Map Score: 11.2283 Number of sites scoring better than the average of aligned sites = 3307 Number in coding regions = 3031 Number in noncoding regions = 276 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 11 CTTCAGATCGTCATCGCGTCCCGCGCAGGC 1 67 0 TCATCGCGTC 0.969822 -98 CTGAAGATCCTACTCGGATCGTCGGCCGCC 1 91 1 TACTCGGATC 0.694646 -74 ACTGGCCTGAGAGGCGCGCCGTGGTATGCG 2 259 0 GAGGCGCGCC 0.874702 -42 CAGTGTCGTCGCAGCGCCTGAGACT 2 286 0 TCGTCGCAGC 0.977548 -15 CCGTTGCCTGGAATCGCATCGTGATGGCGT 4 48 1 GAATCGCATC 0.888209 -114 ACCAAGATCGTCTGCGCGTCGTGGCGGTGC 4 124 0 TCTGCGCGTC 0.831684 -38 CTGGTGGTCGTCGGCGGAGCCATGATCGTC 6 33 0 TCGGCGGAGC 0.933176 -66 GGATGGGCTATCGTCGCGGCCCTGGTGCTG 6 60 0 TCGTCGCGGC 0.98286 -39 GCATCGTGGCGCAGCGCATGAGCCTGCGTT 7 23 0 GCAGCGCATG 0.773839 -126 CCGAAATGCATCGGCGCATCGTGGCGCAGC 7 38 0 TCGGCGCATC 0.985231 -111 TGCACTGTTTGACTCGCGTCGACTTCGACC 9 110 1 GACTCGCGTC 0.741686 -75 ********** Masking position 5 Map Score: 11.4946 Number of sites scoring better than the average of aligned sites = 9082 Number in coding regions = 8294 Number in noncoding regions = 788 Number of orfs with sites within 600 bp upstream = 540 Fraction of orfs with sites within 600 bp upstream = 0.0867331 Motif number 12 ********** No masking Map Score: -1.93735e-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: -1.93735e-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 14 ********** No masking Map Score: -1.93735e-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