AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_mtub_reg_300.orf -o00760_mtub_300.ace -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/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 ppp 88 ppp #2 Rv0019c 123 hypothetical protein Rv0019c #3 Rv0020c 300 hypothetical protein Rv0020c #4 pntAA 300 pntAA #5 pknD 21 pknD #6 pstS 215 pstS #7 nadA 48 nadA #8 pncA 40 pncA #9 Rv2044c 85 hypothetical protein Rv2044c #10 lipT 48 lipT #11 deoD 64 deoD Motif number 1 CCCGCGCTGGCGACGATGCAGAG 1 4 1 GCGCTGGCGA 0.899429 -85 GTGGGGGCGCGCCCCCACCGCTTCTCTGCG 1 34 0 GCCCCCACCG 0.980798 -55 CGGTGGGGGCGCGCCCCCACAAGTGGGGGG 1 44 1 GCGCCCCCAC 0.975378 -45 AGTGGGGGGTACCCCCACCCGCTTGCGGGG 1 65 1 ACCCCCACCC 0.834804 -24 TCTCCCCCGCAAGCGGGTGGGG 1 77 0 TCCCCCGCAA 0.637881 -12 GCGCGGGTCAACCCCGGCAGCTTCGAGCCC 2 18 0 ACCCCGGCAG 0.84532 -106 GGGTTGACCCGCGCCGACCACCGTCAAAGT 2 34 1 GCGCCGACCA 0.986532 -90 CTCCGGCCCCGCGCTGCCGAGCACGTCAGC 2 75 0 GCGCTGCCGA 0.920626 -49 TGCACCGTCTGCTCCGGCCCCGCGCTGCCG 2 86 0 GCTCCGGCCC 0.981494 -38 AAGTCCCCCTTCGCCCACCGTACTGTGAGA 3 16 0 TCGCCCACCG 0.871686 -285 GACTTGAACCCCCACGTCCCGAAGGACACT 3 41 1 CCCACGTCCC 0.594735 -260 GTCCCGAAGGACACTGGCACCTGAAGCCAG 3 56 1 ACACTGGCAC 0.501679 -245 AATGGCAGACGCGCTGGCTTCAGGTGCCAG 3 69 0 GCGCTGGCTT 0.675468 -232 TGCCATTCCGCCACTCGCCCGCAACAACCG 3 92 1 CCACTCGCCC 0.94096 -209 ACTGTAGTAGCCGCAGGCCCCATCCGCTGC 3 134 1 CCGCAGGCCC 0.900213 -167 CAGGCCCCATCCGCTGCCAGGGGCGCCGGC 3 147 1 CCGCTGCCAG 0.905117 -154 GCTGCCAGGGGCGCCGGCGGGCTCAGTGGG 3 159 1 GCGCCGGCGG 0.501471 -142 GAAAGGGCCGGCCACGCCCACTGAGCCCGC 3 175 0 GCCACGCCCA 0.84426 -126 CCGGCCCTTTCCGCTCGCTCACACTGTCCC 3 194 1 CCGCTCGCTC 0.88712 -107 CGTTTGCCTTGCGCCGACGATGCACCAGAA 3 260 1 GCGCCGACGA 0.910635 -41 CTTTCAGCGCTCGCCTCACTGTTCTG 3 285 0 GCGCTCGCCT 0.943813 -16 AGTCGAGCTCGCGCTGCCACTTGC 4 5 0 GCGCTGCCAC 0.953391 -296 AGCTGCGATACCACTGGCCGTTGCGGTCAC 4 104 0 CCACTGGCCG 0.94779 -197 TGGTATCGCAGCTACGGCACCGAACTGTGG 4 121 1 GCTACGGCAC 0.690761 -180 CAACGACGTGCCGATCGCCGAATCCGAGCG 4 163 1 CCGATCGCCG 0.897709 -138 CGGATGCCGAGCGCGCACCGAGGTAGCGAC 4 192 0 GCGCGCACCG 0.95643 -109 TGGACAAAGCGCGCCGTCGACCCTCAGTAT 6 47 1 GCGCCGTCGA 0.594988 -169 GGTCGCCGAGCCACCGACCCGGGGTCGGTA 6 148 0 CCACCGACCC 0.935297 -68 CGGTGGCTCGGCGACCACCGGTGGCGAGTG 6 162 1 GCGACCACCG 0.927574 -54 GGTGGCGGATCCACTCGCCACCGGTGGTCG 6 173 0 CCACTCGCCA 0.893354 -43 GAGTGGATCCGCCACCACGACCCCCTCGAG 6 187 1 GCCACCACGA 0.516908 -29 GCCGCCCCTTCCGCGCTCCAACAGGTTTTC 7 28 0 CCGCGCTCCA 0.692362 -21 GCAAACTGCCCGGGCAGTCGCCCGAAC 8 8 1 GCCCGGGCAG 0.924119 -33 AGGTCGCGGCGCTCCGGCCACTGACAGAAA 9 15 0 GCTCCGGCCA 0.971698 -71 CAGGCTAGCCGCCCCGCCCCCATTCCTGCA 10 16 1 GCCCCGCCCC 0.988465 -33 TCATCGACGAGCACCCGCTCCCCGGCGAGC 11 23 1 GCACCCGCTC 0.886471 -42 CTTAACTGAGCCGCTCGCCGGGGAGCGGGT 11 35 0 CCGCTCGCCG 0.98588 -30 GCTCAGTTAAGCTCGCCCAGT 11 54 1 GCTCGCCCAG 0.520427 -11 ********** Masking position 8 Map Score: 55.0864 Number of sites scoring better than the average of aligned sites = 54311 Number in coding regions = 50832 Number in noncoding regions = 3479 Number of orfs with sites within 600 bp upstream = 1425 Fraction of orfs with sites within 600 bp upstream = 0.228879 Motif number 2 TGCATCGTCGCCAGCGCGGG 1 1 0 CCAGCGCGGG 0.629219 -88 TGGCGACGATGCAGAGCGCAGAGAAGCGGT 1 18 1 GCAGAGCGCA 0.959176 -71 AGAAGCGGTGGGGGCGCGCCCCCACAAGTG 1 39 1 GGGGCGCGCC 0.779421 -50 TTGACGGTGGTCGGCGCGGGTCAACCCCGG 2 31 0 TCGGCGCGGG 0.833524 -93 GACGTGCTCGGCAGCGCGGGGCCGGAGCAG 2 78 1 GCAGCGCGGG 0.663721 -46 GCACCTGAAGCCAGCGCGTCTGCCATTCCG 3 72 1 CCAGCGCGTC 0.924814 -229 ACTGAGCCCGCCGGCGCCCCTGGCAGCGGA 3 156 0 CCGGCGCCCC 0.502993 -145 CTTTCAGCGCTCGCCTCACTGTT 3 288 0 TCAGCGCTCG 0.532139 -13 GCAAGTGGCAGCGCGAGCTCGACTATT 4 8 1 GCAGCGCGAG 0.967975 -293 CACCGAGGTAGCGACGCTCGGATTCGGCGA 4 177 0 GCGACGCTCG 0.811078 -124 ACTCGGATGCCGAGCGCGCACCGAGGTAGC 4 195 0 CGAGCGCGCA 0.860984 -106 TACCGGGCTACCAGAGCGGTATTTCCTGGC 4 228 0 CCAGAGCGGT 0.890655 -73 CTGAGGGTCGACGGCGCGCTTTGTCCAAGG 6 44 0 ACGGCGCGCT 0.92462 -172 AAAACCTGTTGGAGCGCGGAAGGGGCGGCA 7 29 1 GGAGCGCGGA 0.789195 -20 TTTCCAGGTCGCGGCGCTCCGGCCACTGAC 9 20 0 GCGGCGCTCC 0.520313 -66 AGGAATGGGGGCGGGGCGGCTAGCCTGTCG 10 13 0 GCGGGGCGGC 0.967344 -36 GCCGCTCGCCGGGGAGCGGGTGCTCGTCGA 11 26 0 GGGGAGCGGG 0.964362 -39 ********** Masking position 6 Map Score: 34.085 Number of sites scoring better than the average of aligned sites = 13568 Number in coding regions = 12546 Number in noncoding regions = 1022 Number of orfs with sites within 600 bp upstream = 664 Fraction of orfs with sites within 600 bp upstream = 0.10665 Motif number 3 CCCGCGCTGGCGACGATGCAGAGC 1 2 1 CCGCGGCGAC 0.920537 -87 GCGCAGAGAAGCGGTGGGGGCGCGCCCCCACAA 1 33 1 GCGGGGGCGC 0.799557 -56 ACCTACTGGGCTCGAAGCTGCCGGGGTT 2 6 1 CTGGCGAAGC 0.843446 -118 GATACTTTGACGGTGGTCGGCGCGGGTCAACCC 2 34 0 CGGTCGGCGC 0.561558 -90 GCTCGGCAGCGCGGGGCCGGAGCAGACGGTGCA 2 83 1 GCGGCGGAGC 0.968264 -41 ACGGTGCAGGACGGAAAGGACGCCAG 2 108 1 ACGGGGACGC 0.875779 -16 CGGGCGAGTGGCGGAATGGCAGACGCGCTGGCT 3 80 0 GCGGGGCAGA 0.634638 -221 GACCATACCACTGTAGTAGCCGCAGGCCCCATC 3 125 1 CTGTAGCCGC 0.465595 -176 GCCCCATCCGCTGCCAGGGGCGCCGGCGGGCTC 3 150 1 CTGCGGGCGC 0.908906 -151 AGCGAGCGGAAAGGGCCGGCCACGCCCACTGAG 3 180 0 AAGGGGCCAC 0.88555 -121 TCAATCAATCATGGTATCGGGACAGTGTGAGCG 3 209 0 ATGGCGGGAC 0.878307 -92 CTTTCAGCGCTCGCCTCACTGTTCTGG 3 284 0 CAGCCGCCTC 0.710105 -17 GCAAGTGGCAGCGCGAGCTCGACTATT 4 5 1 GTGGCGCGAG 0.797274 -296 TGCGGTTGTCGTGGAAGCTCCACAAACTCTTGC 4 44 0 GTGGCTCCAC 0.784167 -257 GGGATTCGTACTGGAACCGCATCGCAATGCGGT 4 71 0 CTGGCGCATC 0.922609 -230 AGTACGAATCCCGTGACCGCAACGGCCAGTGGT 4 92 1 CCGTCGCAAC 0.83099 -209 GCAACGGCCAGTGGTATCGCAGCTACGGCACCG 4 110 1 GTGGCGCAGC 0.979656 -191 GTCGTTGATGCTGGCTTCGCCACAGTTCGGTGC 4 137 0 CTGGCGCCAC 0.778122 -164 AGCGCGCACCGAGGTAGCGACGCTCGGATTCGG 4 180 0 GAGGCGACGC 0.854933 -121 CTCTGGTAGCCCGGTAGGGTGTCTGAGCAAATC 4 242 1 CCGGGGTGTC 0.539414 -59 TCCTAGCGTTCAGGAGGGGCCGCTGATACTGAG 6 69 0 CAGGGGCCGC 0.817571 -147 TCGATGCACAACGGTGACGGCTCGAATACCGAC 6 122 1 ACGGCGGCTC 0.895717 -94 CCCCGGGTCGGTGGCTCGGCGACCACCGGTGGC 6 154 1 GTGGGGCGAC 0.949325 -62 CCGGTGGCGAGTGGATCCGCCACCACGACCCCC 6 179 1 GTGGCGCCAC 0.832264 -37 CTGTTGGAGCGCGGAAGGGGCGGCA 7 34 1 GCGGGGGCGG 0.855915 -15 CGTCCACCATACGTTCGGGCGACTGCCCGGGCA 8 17 0 ACGTGGCGAC 0.699076 -24 CCAGGTCGCGGCGCTCCGGCCACTGACAGAAAA 9 14 0 GCGCGGCCAC 0.743996 -72 GCGCCGCGACCTGGAAAGGCAACCCGAGAGATG 9 33 1 CTGGGGCAAC 0.957453 -53 CAGTGCAGGAATGGGGGCGGGGCGGCTAGCCTG 10 16 0 ATGGCGGGGC 0.926558 -33 TCGCCGGGGAGCGGGTGCTCGTCGATGAGATAC 11 18 0 GCGGCTCGTC 0.620519 -47 **** ****** Masking position 3 Map Score: 45.1503 Number of sites scoring better than the average of aligned sites = 40298 Number in coding regions = 37756 Number in noncoding regions = 2542 Number of orfs with sites within 600 bp upstream = 1134 Fraction of orfs with sites within 600 bp upstream = 0.182139 Motif number 4 CGACGATGCAGAGCGCAGAGAAGCGGTGGG 1 21 1 GAGCGCAGAG 0.852953 -68 TGACGGTGGTCGGCGCGGGTCAACCCCGGC 2 30 0 CGGCGCGGGT 0.988338 -94 ACGTGCTCGGCAGCGCGGGGCCGGAGCAGA 2 79 1 CAGCGCGGGG 0.98176 -45 CCGGAGCAGACGGTGCAGGACGGAAAGGAC 2 99 1 CGGTGCAGGA 0.977567 -25 ACAGTACGGTGGGCGAAGGGGGACTTGAAC 3 20 1 GGGCGAAGGG 0.961119 -281 CGGGACGTGGGGGTTCAAGTCCCCCTTCGC 3 32 0 GGGTTCAAGT 0.409512 -269 CCGCTGCCAGGGGCGCCGGCGGGCTCAGTG 3 157 1 GGGCGCCGGC 0.96268 -144 GGGCGCCGGCGGGCTCAGTGGGCGTGGCCG 3 167 1 GGGCTCAGTG 0.936132 -134 GGTGCATCGTCGGCGCAAGGCAAACGACTC 3 256 0 CGGCGCAAGG 0.984223 -45 CGCCACAGTTCGGTGCCGTAGCTGCGATAC 4 123 0 CGGTGCCGTA 0.769037 -178 CGGCGCAGGGTACTACATGC 6 1 1 CGGCGCAGGG 0.998137 -215 GTGCAGGAATGGGGGCGGGGCGGCTAGCCT 10 17 0 GGGGGCGGGG 0.9671 -32 GCGGCATGCGCAGTGCAGGAATGGGGGCGG 10 29 0 CAGTGCAGGA 0.887643 -20 CCCCGGCGAGCGGCTCAGTTAAGCTCGCCC 11 42 1 CGGCTCAGTT 0.845486 -23 ********** Masking position 3 Map Score: 20.8461 Number of sites scoring better than the average of aligned sites = 10893 Number in coding regions = 10101 Number in noncoding regions = 792 Number of orfs with sites within 600 bp upstream = 543 Fraction of orfs with sites within 600 bp upstream = 0.0872149 Motif number 5 GCAGAGAAGCGGTGGGGGCGCGCCCCCACAA 1 35 1 GGTGGGGCGC 0.954785 -54 TCCGGCCCCGCGCTGCCGAGCACGTCAGCAA 2 73 0 CGCGCCGAGC 0.921827 -51 TCGGCAGCGCGGGGCCGGAGCAGACGGTGCA 2 85 1 GGGCCGGAGC 0.968564 -39 CAGGCGAGTCGTTTGCCTTGCGCCGACGATG 3 251 1 GTTGCCTTGC 0.74024 -50 CACCAGAACAGTGAGGCGAGCGCTGAAAG 3 282 1 GTGGGCGAGC 0.846172 -19 CTACGCAAGAGTTTGTGGAGCTTCCACGACA 4 40 1 GTTGTGGAGC 0.898674 -261 ATCGCAATGCGGTTGTCGTGGAAGCTCCACA 4 53 0 GGTGTCGTGG 0.630412 -248 GCCACAGTTCGGTGCCGTAGCTGCGATACCA 4 121 0 GGTCCGTAGC 0.905409 -180 TGCCGATCGCCGAATCCGAGCGTCGCTACCT 4 171 1 CGATCCGAGC 0.700145 -130 GGCCATACTCGGATGCCGAGCGCGCACCGAG 4 200 0 GGAGCCGAGC 0.989773 -101 AGCCCGGTAGGGTGTCTGAGCAAATCTATCG 4 249 1 GGTTCTGAGC 0.87386 -52 ACCCGGGGTCGGTATTCGAGCCGTCACCGTT 6 131 0 GGTTTCGAGC 0.929556 -85 CGCCACCGGTGGTCGCCGAGCCACCGACCCG 6 157 0 GGTGCCGAGC 0.983999 -59 AGGGGGTCGTGGTGGCGGATCCACTCGCCAC 6 182 0 GGTGCGGATC 0.97199 -34 TGCCTTTCCAGGTCGCGGCGCTCCGGCCACT 9 23 0 GGTGCGGCGC 0.990408 -63 ACATCTCTCGGGTTGCCTTTCCAGGTCGCGG 9 36 0 GGTGCCTTTC 0.650094 -50 GTGCAGGAATGGGGGCGGGGCGGCTAGCCTG 10 16 0 GGGGCGGGGC 0.967156 -33 *** ******* Masking position 11 Map Score: 22.4016 Number of sites scoring better than the average of aligned sites = 10965 Number in coding regions = 10177 Number in noncoding regions = 788 Number of orfs with sites within 600 bp upstream = 578 Fraction of orfs with sites within 600 bp upstream = 0.0928365 Motif number 6 CTGCTCCGGCCCCGCGCTGCCGAGCACGTC 2 78 0 CCCGCGCTGC 0.979585 -46 AATAGTCGAGCTCGCGCTGCCACTTGC 4 8 0 CTCGCGCTGC 0.994511 -293 TCCACAAACTCTTGCGTAGCGAATAGTCGA 4 29 0 CTTGCGTAGC 0.974837 -272 CGACAACCGCATTGCGATGCGGTTCCAGTA 4 66 1 ATTGCGATGC 0.921993 -235 GGAAATACCGCTCTGGTAGCCCGGTAGGGT 4 232 1 CTCTGGTAGC 0.896271 -69 CTACATGCTCCTTGGGATGCTCCTTGGACA 6 23 1 CTTGGGATGC 0.984862 -193 GATCAGACCTCTTTCGATGCACAACGGTGA 6 109 1 CTTTCGATGC 0.96033 -107 TCGTACATCTCTCGGGTTGCCTTTCCAGGT 9 41 0 CTCGGGTTGC 0.990402 -45 ********** Masking position 6 Map Score: 11.3112 Number of sites scoring better than the average of aligned sites = 1420 Number in coding regions = 1310 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 7 GGGTTGACCCGCGCCGACCACCGTCAAAGT 2 34 1 GCGCCGACCA 0.892657 -90 ATTGATTGACACGACATACAGGCGAGTCGT 3 233 1 ACGACATACA 0.285277 -68 CCAGAACAGTGAGGCGAGCGCTGAAAG 3 284 1 GAGGCGAGCG 0.902906 -17 TGGAGCTTCCACGACAACCGCATTGCGATG 4 55 1 ACGACAACCG 0.845055 -246 GCCAGCATCAACGACGTGCCGATCGCCGAA 4 155 1 ACGACGTGCC 0.865225 -146 CACCGAGGTAGCGACGCTCGGATTCGGCGA 4 177 0 GCGACGCTCG 0.795167 -124 CGGTGCGCGCTCGGCATCCGAGTATGGCCA 4 202 1 TCGGCATCCG 0.919329 -99 AGCAAATCTATCGGCGTTCAGTAAGGAAAG 4 267 1 TCGGCGTTCA 0.862579 -34 GGTCGGTGGCTCGGCGACCACCGGTGGCGA 6 159 1 TCGGCGACCA 0.962331 -57 TGGGGGCGGGGCGGCTAGCCTGTCGGG 10 8 0 GCGGCTAGCC 0.83042 -41 GCGGCATGCGCAGTGCAGGA 10 39 0 GCGGCATGCG 0.970656 -10 CAGTATCTCATCGACGAGCACCCGCTCCCC 11 16 1 TCGACGAGCA 0.944756 -49 CACCCGCTCCCCGGCGAGCGGCTCAGTTAA 11 34 1 CCGGCGAGCG 0.970034 -31 ********** Masking position 5 Map Score: 8.53129 Number of sites scoring better than the average of aligned sites = 18069 Number in coding regions = 16875 Number in noncoding regions = 1194 Number of orfs with sites within 600 bp upstream = 734 Fraction of orfs with sites within 600 bp upstream = 0.117893 Motif number 8 GTACGGTGGGCGAAGGGGGACTTGAACCCC 3 23 1 CGAAGGGGGA 0.950484 -278 CCGCAACAACCGGAGGACCATACCACTGTA 3 110 1 CGGAGGACCA 0.950482 -191 AAGGAGCATCCCAAGGAGCATGTAGTACCC 6 18 0 CCAAGGAGCA 0.990194 -198 CGCGCTTTGTCCAAGGAGCATCCCAAGGAG 6 30 0 CCAAGGAGCA 0.990194 -186 GTTGGAGCGCGGAAGGGGCGGCA 7 36 1 GGAAGGGGCG 0.940877 -13 GAGCCGCTCGCCGGGGAGCGGGTGCTCGTC 11 28 0 CCGGGGAGCG 0.962089 -37 ********** Masking position 5 Map Score: 1.93062 Number of sites scoring better than the average of aligned sites = 363 Number in coding regions = 314 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 9 ********** No masking Map Score: 9.53751e-15 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: 9.53751e-15 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: 9.53751e-15 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