AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00730_mtub_reg_300.orf -o00730_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 thiE 129 thiE #2 thiD 26 thiD #3 thiC 151 thiC #4 Rv0424c 49 hypothetical protein Rv0424c #5 ctpH 51 ctpH #6 Rv0426c 200 hypothetical protein Rv0426c #7 def 300 def #8 Rv2979c 211 hypothetical protein Rv2979c Motif number 1 TGATCCGGATCATGCCGGCGAAGGGAGGTC 1 15 0 CATGCCGGCG 0.969014 -115 TGAGAGTGGGCGCGCCTGCCCTTACCGTCA 1 49 0 CGCGCCTGCC 0.989359 -81 ACTCTCAGACCCCGCTCCCGGGACTCCCGT 1 72 1 CCCGCTCCCG 0.937939 -58 GTGACGCTAGCGCGCTAGCGTGGAACCCTG 1 107 0 CGCGCTAGCG 0.831455 -23 TCCCGGCGGTGCCAGCGGGAG 2 16 0 CCCGGCGGTG 0.92338 -11 GCACGGACGGCCCGATGCCGCG 3 3 0 CCCGATGCCG 0.951533 -149 GCTAGCGCAGCGCGGCGCCGGTGTGCACGG 3 27 0 CGCGGCGCCG 0.992743 -125 TGGGTACCCCCACGCTAGCGCAGCGCGGCG 3 40 0 CACGCTAGCG 0.856868 -112 ACTCGGCGTGCGCTCCCGCGTGGGTACCCC 3 60 0 CGCTCCCGCG 0.592644 -92 CGCGGGAGCGCACGCCGAGTGCGCTGAGAG 3 70 1 CACGCCGAGT 0.789205 -82 ACCGTACGAACCTGACCGGGTAATGCCGGC 3 118 1 CCTGACCGGG 0.487998 -34 TTGCAACTCCCTACGCCGGCATTACCCG 3 134 0 CCCTACGCCG 0.906392 -18 CCGCACCACCCTGCACAACGG 4 2 1 CGCACCACCC 0.945675 -48 CACCACCCTGCACAACGGCAAACCCTTCGT 4 14 1 CACAACGGCA 0.673977 -36 TCAAGAGTTGCTCAACGCCGCCAGA 5 6 0 CTCAACGCCG 0.69651 -46 CTGCATCCATCGCACGGGCT 5 42 1 CGCACGGGCT 0.746432 -10 CCGCGTGCGGCGCGACTGCCGACTACCGCC 6 20 0 CGCGACTGCC 0.968549 -181 TGAGACAACGCGCAACTGCCGCGTGCGGCG 6 38 0 CGCAACTGCC 0.859448 -163 GCAAGCCTGCCACGCCGCCCTGACTGAGAC 6 62 0 CACGCCGCCC 0.995623 -139 ACCCTGCATTCGCACCGCTGACGAGATTTC 6 111 0 CGCACCGCTG 0.943926 -90 AGGATTACCGCCCGACGGTTCCTGGCGTGG 7 61 0 CCCGACGGTT 0.928066 -240 GGGCGGTAATCCTGCCCGCGAGTCGGCCGA 7 78 1 CCTGCCCGCG 0.899549 -223 CTTGCTTGCACCCGACTGCCGATCGCGGCG 7 108 1 CCCGACTGCC 0.962181 -193 CCGATCGCGGCGCGCCGGCTCATGCTCCGA 7 126 1 CGCGCCGGCT 0.997938 -175 TGCGACGCGACATGCCGGCCAGCCGTCGTG 7 166 1 CATGCCGGCC 0.956003 -135 GTGTGAACCACACGACGGCTGGCCGGCATG 7 176 0 CACGACGGCT 0.983584 -125 TCGTGTGGTTCACACCCGGCGATGATGCCC 7 191 1 CACACCCGGC 0.739415 -110 GGCGATGATGCCCGCCGCCCCGCGGCGCGC 7 208 1 CCCGCCGCCC 0.997726 -93 CCCGCCGCCCCGCGGCGCGCCTAAGCCGAT 7 218 1 CGCGGCGCGC 0.967059 -83 AAGCCGATTGCCCGCCTCCTCAGCCCGCCG 7 240 1 CCCGCCTCCT 0.974452 -61 GCCTCCTCAGCCCGCCGCCTCGCGGCGCGT 7 253 1 CCCGCCGCCT 0.996334 -48 CCCGCCGCCTCGCGGCGCGTATCGTCGGCG 7 263 1 CGCGGCGCGT 0.947884 -38 CTAGCTTAAGCGCGCCGACGATACGCGCCG 7 275 0 CGCGCCGACG 0.990057 -26 CTGCGCGGCCACCTCTTTGCTCT 8 4 1 CGCGGCCACC 0.803575 -208 GCGAGCGGACCGCGCCAGTGTATGAGAGCA 8 28 0 CGCGCCAGTG 0.919136 -184 GCGGTCCGCTCGCGCCGGCAGTGACTCAAC 8 45 1 CGCGCCGGCA 0.990263 -167 CGTCGTCGCCCACGCCGCCTCCTTCGGCCC 8 121 0 CACGCCGCCT 0.992953 -91 GCTGGCACCCCCCGATGCGTCGTCGCCCAC 8 138 0 CCCGATGCGT 0.640938 -74 CCACTCAACCCGCAACAGCTGGCACCCCCC 8 155 0 CGCAACAGCT 0.820539 -57 GTTCCTACCGCACGCCACTGACAACTACCG 8 186 0 CACGCCACTG 0.859506 -26 ********** Masking position 1 Map Score: 83.881 Number of sites scoring better than the average of aligned sites = 48471 Number in coding regions = 45103 Number in noncoding regions = 3368 Number of orfs with sites within 600 bp upstream = 1366 Fraction of orfs with sites within 600 bp upstream = 0.219403 Motif number 2 GATCCGGATCATGCCGGCGAAGGGAGGTCA 1 14 0 ATGCCGGCGA 0.953475 -116 GTGACGGTAAGGGCAGGCGCGCCCACTCTC 1 48 1 GGGCAGGCGC 0.953879 -82 ACAGGGTTCCACGCTAGCGCGCTAGCGTCA 1 106 1 ACGCTAGCGC 0.489961 -24 TCCCGGCGGTGCCAGCGGGAGGTAGT 2 9 0 GTGCCAGCGG 0.750225 -18 CGCGGCATCGGGCCGTCCGTG 3 2 1 GCGGCATCGG 0.880188 -150 CCGTCCGTGCACACCGGCGCCGCGCTGCGC 3 23 1 ACACCGGCGC 0.612711 -129 GGGTACCCCCACGCTAGCGCAGCGCGGCGC 3 39 0 ACGCTAGCGC 0.489961 -113 CGTCCTCTCAGCGCACTCGGCGTGCGCTCC 3 74 0 GCGCACTCGG 0.901095 -78 GGACGGCTCGGGGCCGTCGACCGTACGAAC 3 99 1 GGGCCGTCGA 0.972318 -53 TGACCGGGTAATGCCGGCGTAGGGAGTTGC 3 130 1 ATGCCGGCGT 0.742613 -22 TCTGGCGGCGTTGAGCAACTC 5 2 1 CTGGCGGCGT 0.930917 -50 CGGCGGTAGTCGGCAGTCGCGCCGCACGCG 6 19 1 CGGCAGTCGC 0.928441 -182 GGCAGTCGCGCCGCACGCGGCAGTTGCGCG 6 30 1 CCGCACGCGG 0.921503 -171 TGTCTCAGTCAGGGCGGCGTGGCAGGCTTG 6 61 1 AGGGCGGCGT 0.928701 -140 TTTCTGTTCAGCGCTCTCGAAATGCAAGCC 6 85 0 GCGCTCTCGA 0.736315 -116 TGCATTCGCACCGCTGACGAGATTTCTGTT 6 107 0 CCGCTGACGA 0.583676 -94 GACTTGGCCTACGTAGGCGCTTCTTCGGCG 7 22 1 ACGTAGGCGC 0.71297 -279 ACCACGCCAGGAACCGTCGGGCGGTAATCC 7 60 1 GAACCGTCGG 0.792462 -241 GGCGGTAATCCTGCCCGCGAGTCGGCCGAC 7 79 1 CTGCCCGCGA 0.919903 -222 GCGCCGCGATCGGCAGTCGGGTGCAAGCAA 7 109 0 CGGCAGTCGG 0.91437 -192 CTCGGAGCATGAGCCGGCGCGCCGCGATCG 7 127 0 GAGCCGGCGC 0.549581 -174 ACATGCCGGCCAGCCGTCGTGTGGTTCACA 7 175 1 CAGCCGTCGT 0.900561 -126 GGCGCGCCGCGGGGCGGCGGGCATCATCGC 7 209 0 GGGGCGGCGG 0.970321 -92 GCGGCGGGCTGAGGAGGCGGGCAATCGGCT 7 241 0 GAGGAGGCGG 0.944114 -60 TACGCGCCGCGAGGCGGCGGGCTGAGGAGG 7 254 0 GAGGCGGCGG 0.965377 -47 TAGCTTAAGCGCGCCGACGATACGCGCCGC 7 274 0 GCGCCGACGA 0.691388 -27 GAGCAAAGAGGTGGCCGCGCAG 8 3 0 GTGGCCGCGC 0.959535 -209 TTGCTCTCATACACTGGCGCGGTCCGCTCG 8 27 1 ACACTGGCGC 0.66309 -185 AGTTGAGTCACTGCCGGCGCGAGCGGACCG 8 46 0 CTGCCGGCGC 0.55831 -166 CGGGCCGAAGGAGGCGGCGTGGGCGACGAC 8 120 1 GAGGCGGCGT 0.949591 -92 ACCCCCCGATGCGTCGTCGCCCACGCCGCC 8 132 0 GCGTCGTCGC 0.713885 -80 ********** Masking position 8 Map Score: 59.3169 Number of sites scoring better than the average of aligned sites = 54437 Number in coding regions = 51459 Number in noncoding regions = 2978 Number of orfs with sites within 600 bp upstream = 1163 Fraction of orfs with sites within 600 bp upstream = 0.186797 Motif number 3 GGATCATGCCGGCGAAGGGAGGTCAAGG 1 6 0 GGCGGGGAGT 0.613637 -124 CCGGCATGATCCGGATCAGGTGTGACGGTAAGG 1 27 1 CCGGCAGGGT 0.93864 -103 TCTCAGACCCCGCTCCCGGGACTCCCGTGTCTA 1 74 1 CGCTCGGGCT 0.933026 -56 TCCCGGCGGTGCCAGCGGGAGGTAGT 2 8 0 CGGTCAGCGG 0.712709 -19 CGCGGCATCGGGCCGTCCGTGCACAC 3 4 1 GGCAGGGCGT 0.908903 -148 GCACACCGGCGCCGCGCTGCGCTAGCGTGGGGG 3 31 1 GCCGCTGCCT 0.91803 -121 CGTGGGGGTACCCACGCGGGAGCGCACGCCGAG 3 56 1 CCCACGGGGC 0.944921 -96 GTCCTCTCAGCGCACTCGGCGTGCGCTCCCGCG 3 70 0 CGCACGGCTG 0.796424 -82 CTGAGAGGACGGCTCGGGGCCGTCGACCGTACG 3 93 1 GGCTGGGCGT 0.929217 -59 GCCGGCATTACCCGGTCAGGTTCGTACGGTCGA 3 115 0 CCCGCAGGTC 0.883442 -37 GCGGCGTACGGCGGTAGTCGGCAGT 6 3 1 GGCGCGGCGT 0.994333 -198 GCAGTCGCGCCGCACGCGGCAGTTGCGCGTTGT 6 31 1 CGCACGGCGT 0.987089 -170 AGTCAGGGCGGCGTGGCAGGCTTGCATTTCGAG 6 67 1 GCGTCAGGTT 0.530477 -134 CTCGTTAACCCGCACCCTGCATTCGCACCGCTG 6 121 0 CGCACTGCTT 0.870342 -80 GACTCCCTGGCCCAAACTGCATTCGTTTACAAA 6 175 0 CCCACTGCTT 0.843429 -26 TACCGCCCGACGGTTCCTGGCGTGGTTCAATAT 7 53 0 CGGTCTGGGT 0.833022 -248 TCGGCCGACTCGCGGGCAGGATTACCGCCCGAC 7 75 0 CGCGCAGGTT 0.947529 -226 GCCGGCGCGCCGCGATCGGCAGTCGGGTGCAAG 7 112 0 CGCGCGGCGT 0.996179 -189 CCGGCATGTCGCGTCGCAGGATTCACACTCGGA 7 151 0 GCGTCAGGTT 0.530477 -150 GACGCGACATGCCGGCCAGCCGTCGTGTGGTTC 7 169 1 GCCGCAGCGT 0.979449 -132 GCTTAGGCGCGCCGCGGGGCGGCGGGCATCATC 7 211 0 GCCGGGGCGC 0.61431 -90 GACGATACGCGCCGCGAGGCGGCGGGCTGAGGA 7 256 0 GCCGAGGCGC 0.725189 -45 CTGCGCGGCCACCTCTTTGCTCTCAT 8 4 1 CGCGCACCCT 0.733057 -208 TGGCGCGGTCCGCTCGCGCCGGCAGTGACTCAA 8 41 1 CGCTCGCCGC 0.819957 -171 GAACACCTCGCCCGACCTGCGGTAAGTTGAGTC 8 67 0 CCCGCTGCGT 0.984524 -145 CCTCCTTCGGCCCGTTCTGGCCCTGTGGACCTT 8 101 0 CCCGCTGGCC 0.827633 -111 ACGCATCGGGGGGTGCCAGCTGTTGCGGGTTGA 8 148 1 GGGTCAGCGT 0.904906 -64 **** **** ** Masking position 9 Map Score: 40.3744 Number of sites scoring better than the average of aligned sites = 43194 Number in coding regions = 40308 Number in noncoding regions = 2886 Number of orfs with sites within 600 bp upstream = 1255 Fraction of orfs with sites within 600 bp upstream = 0.201574 Motif number 4 AGGTGTGACGGTAAGGGCAGGCGCGCCCAC 1 44 1 GTAAGGGCAG 0.457261 -86 CGGGAGTCCCGGGAGCGGGGTCTGAGAGTG 1 71 0 GGGAGCGGGG 0.850998 -59 GAACCCTGTAGACACGGGAGTCCCGGGAGC 1 85 0 GACACGGGAG 0.178926 -45 ACCTCCCGCTGGCACCGCCGGGA 2 14 1 GGCACCGCCG 0.982877 -13 CGCGGCATCGGGCCGTCCGTGCACACCGG 3 10 1 GGGCCGTCCG 0.569139 -142 CCCACGCTAGCGCAGCGCGGCGCCGGTGTG 3 32 0 CGCAGCGCGG 0.752068 -120 AGCGCACGCCGAGTGCGCTGAGAGGACGGC 3 76 1 GAGTGCGCTG 0.67096 -76 CAGTAACGAAGGGTTTGCCGTTGTGCAGGG 4 19 0 GGGTTTGCCG 0.488285 -31 GGTAGTCGGCAGTCGCGCCGCACGCGGCAG 6 23 1 AGTCGCGCCG 0.781501 -178 GAGACAACGCGCAACTGCCGCGTGCGGCGC 6 37 0 GCAACTGCCG 0.280079 -164 CGTTGTCTCAGTCAGGGCGGCGTGGCAGGC 6 58 1 GTCAGGGCGG 0.705043 -143 CTTGCATTTCGAGAGCGCTGAACAGAAATC 6 87 1 GAGAGCGCTG 0.836156 -114 CAGAAATCTCGTCAGCGGTGCGAATGCAGG 6 109 1 GTCAGCGGTG 0.47682 -92 TATTCGCCGAAGAAGCGCCTACGTAGGCCA 7 26 0 AGAAGCGCCT 0.304705 -275 GCGTGGTTCAATATTCGCCGAAGAAGCGCC 7 37 0 ATATTCGCCG 0.203183 -264 AACCACGCCAGGAACCGTCGGGCGGTAATC 7 59 1 GGAACCGTCG 0.527959 -242 TCCTGCCCGCGAGTCGGCCGACTTGCTTGC 7 87 1 GAGTCGGCCG 0.842075 -214 CTGCCGATCGCGGCGCGCCGGCTCATGCTC 7 123 1 CGGCGCGCCG 0.499814 -178 AACCACACGACGGCTGGCCGGCATGTCGCG 7 171 0 CGGCTGGCCG 0.588844 -130 CCCGGCGATGATGCCCGCCGCCCCGCGGCG 7 205 1 ATGCCCGCCG 0.880162 -96 CAATCGGCTTAGGCGCGCCGCGGGGCGGCG 7 220 0 AGGCGCGCCG 0.623795 -81 CCCGCCTCCTCAGCCCGCCGCCTCGCGGCG 7 250 1 CAGCCCGCCG 0.560816 -51 CGCGCCGACGATACGCGCCGCGAGGCGGCG 7 265 0 ATACGCGCCG 0.891672 -36 GGGCTAGCTTAAGCGCGCCGACGATACGCG 7 278 0 AAGCGCGCCG 0.859893 -23 GCAAAGAGGTGGCCGCGCAG 8 1 0 GGCCGCGCAG 0.91004 -211 GGCGCGAGCGGACCGCGCCAGTGTATGAGA 8 31 0 GACCGCGCCA 0.615371 -181 GGTAAGTTGAGTCACTGCCGGCGCGAGCGG 8 50 0 GTCACTGCCG 0.750277 -162 AACTTACCGCAGGTCGGGCGAGGTGTTCGA 8 72 1 AGGTCGGGCG 0.501562 -140 CACAGGGCCAGAACGGGCCGAAGGAGGCGG 8 107 1 GAACGGGCCG 0.931774 -105 ACGGGCCGAAGGAGGCGGCGTGGGCGACGA 8 119 1 GGAGGCGGCG 0.691855 -93 GTCGGTAGTTGTCAGTGGCGTGCGGTAGGA 8 184 1 GTCAGTGGCG 0.578484 -28 ********** Masking position 7 Map Score: 29.7727 Number of sites scoring better than the average of aligned sites = 75943 Number in coding regions = 71155 Number in noncoding regions = 4788 Number of orfs with sites within 600 bp upstream = 1579 Fraction of orfs with sites within 600 bp upstream = 0.253614 Motif number 5 CCCGGGAGCGGGGTCTGAGAGTGGGCGCGCC 1 63 0 GGGTCTGAGG 0.908774 -67 CAAACCCTTCGTTACTGAAAGGCAAATG 4 32 1 GTTACTGAAG 0.874312 -18 CAGGGTGCGGGTTAACGAGTGTAGAACTGTA 6 135 1 GTTAACGAGG 0.954404 -66 TAAACCATTTGTAAACGAATGCAGTTTGGGC 6 168 1 GTAAACGAAG 0.907661 -33 TGTGTACGAATGACTTGGCCTA 7 2 1 GTGTACGAAG 0.985249 -299 GACCGCGCCAGTGTATGAGAGCAAAGAGGTG 8 20 0 GTGTATGAGG 0.975034 -192 GTCGGGCGAGGTGTTCGAAGGTCCACAGGGC 8 84 1 GTGTTCGAAG 0.953055 -128 ********* * Masking position 8 Map Score: 1.71346 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 355 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 CCCTTCGCCGGCATGATCCGGATCAGGTGTG 1 20 1 GCATATCCGG 0.941987 -110 ACCTCCCGCTGGCACCGCCGGGA 2 14 1 GGCACGCCGG 0.84883 -13 CCACGCGGGAGCGCACGCCGAGTGCGCTGAG 3 67 1 GCGCCGCCGA 0.94315 -85 CCCTACGCCGGCATTACCCGGTCAGGTTCGT 3 123 0 GCATACCCGG 0.971046 -29 GCGGCGTACGGCGGTAGTCGGCAG 6 4 1 GCGTCGGCGG 0.969675 -197 CGGCAGTCGCGCCGCACGCGGCAGTTGCGCG 6 29 1 GCCGACGCGG 0.819317 -172 CGAAATGCAAGCCTGCCACGCCGCCCTGACT 6 67 0 GCCTCCACGC 0.842485 -134 CCGAAGAAGCGCCTACGTAGGCCAAGTCATT 7 19 0 GCCTCGTAGG 0.887822 -282 CACACTCGGAGCATGAGCCGGCGCGCCGCGA 7 130 0 GCATAGCCGG 0.982919 -171 CCCGCGGCGCGCCTAAGCCGATTGCCCGCCT 7 226 1 GCCTAGCCGA 0.971893 -75 CCGATTGCCCGCCTCCTCAGCCCGCCGCCTC 7 243 1 GCCTCTCAGC 0.775441 -58 GGCGCGGTCCGCTCGCGCCGGCAGTGACTCA 8 42 1 GCTCCGCCGG 0.965022 -170 CGCCCACGCCGCCTCCTTCGGCCCGTTCTGG 8 114 0 GCCTCTTCGG 0.95056 -98 GCAACAGCTGGCACCCCCCGATGCGTCGTCG 8 143 0 GCACCCCCGA 0.921174 -69 **** ****** Masking position 10 Map Score: 15.0078 Number of sites scoring better than the average of aligned sites = 16818 Number in coding regions = 15837 Number in noncoding regions = 981 Number of orfs with sites within 600 bp upstream = 648 Fraction of orfs with sites within 600 bp upstream = 0.10408 Motif number 7 ********** No masking Map Score: -2.61947e-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 8 ********** No masking Map Score: -2.61947e-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: -2.61947e-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