AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -itrpR_mtub_opreg_100.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 Rv0012 93 hypothetical protein Rv0012 #2 pabA 36 pabA #3 Rv0059 179 hypothetical protein Rv0059 #4 trpE 140 trpE #5 trpC 89 trpC #6 trpB 68 trpB #7 trpD 157 trpD Motif number 1 CTACCGCCTGACCCTGCCGGCAGTCGT 2 8 0 ACCCTGCCGG 0.907305 -29 TCAGGCGGTAGCCTGTCACG 2 27 1 GCCTGTCACG 0.621264 -10 GTCTCACGGAGCGTGGCCGAATCTCACGAA 3 27 1 GCGTGGCCGA 0.918283 -153 GGACCGGTCCGCCCTGATGGCCCCATCATT 3 55 0 GCCCTGATGG 0.989709 -125 CGCCGCGGATGCGTGGACCGGTCCGCCCTG 3 69 0 GCGTGGACCG 0.987954 -111 ATCCGCGGCGGCGTTGAAGTCCCCGAGCAA 3 89 1 GCGTTGAAGT 0.800543 -91 ACGTCCTGTCGCCCTGATCTGACTCATCTC 3 140 0 GCCCTGATCT 0.90706 -40 CCGCGAAGCGGCGCGCAAGGAGTCGGGCAA 4 31 0 GCGCGCAAGG 0.987235 -110 GCGCGCCGCTTCGCGGCTGGGGGTGCCCCC 4 45 1 TCGCGGCTGG 0.960058 -96 CGCGCAAACGGCGCGCATGGGGGCACCCCC 4 63 0 GCGCGCATGG 0.992665 -78 CGTTTGCGCGGCGTGCATCGTCGTCGGGCT 4 83 1 GCGTGCATCG 0.940749 -58 GTCGGGCTACGCCCGGGCCGATCGGCGTAT 4 105 1 GCCCGGGCCG 0.989694 -36 CGGACCGCGCGCTGACGGTCGCTACCCT 5 9 1 GCGCTGACGG 0.9948 -81 AAATTGACGAGCGCGTGTGGGTGACAGTGG 5 54 1 GCGCGTGTGG 0.965235 -36 GCGCGGAAGATCCGGGGTGG 6 59 0 GCGCGGAAGA 0.97357 -10 GTCGAACTCTACCCGGGTCGGAAATTTCGG 7 37 1 ACCCGGGTCG 0.917302 -121 GCCGGGCGACACGCGGAACTGACTTACCGA 7 63 0 ACGCGGAACT 0.824404 -95 TCCGCGTGTCGCCCGGCCGTTTGGTTAGCG 7 76 1 GCCCGGCCGT 0.981602 -82 CGTGTTCAGGGCGCGGTTGGGGTTGGTTGA 7 117 1 GCGCGGTTGG 0.986839 -41 GCGCTGATGGTCCCATGAGG 7 148 0 GCGCTGATGG 0.994364 -10 ********** Masking position 2 Map Score: 40.0527 Number of sites scoring better than the average of aligned sites = 25749 Number in coding regions = 23955 Number in noncoding regions = 1794 Number of orfs with sites within 600 bp upstream = 1007 Fraction of orfs with sites within 600 bp upstream = 0.161741 Motif number 2 TTCTATCGTTGCACCCCGGGCCATTCGTCGT 1 48 0 GCCCCCGGGC 0.945585 -46 GATAGAAGTTGCAGCTGCAGGCATACCTTGT 1 72 1 GCGCTGCAGG 0.898578 -22 CATGCGGATGTGTGGGGTCTCACG 3 4 1 GCGATGTGTG 0.901738 -176 GGCCATCAGGGCGGACCGGTCCACGCATCCG 3 63 1 GCGACCGGTC 0.973103 -117 CAACGCCGCCGCGGATGCGTGGACCGGTCCG 3 74 0 GCGATGCGTG 0.983421 -106 CACGACGCGTGTTGCTCGGGGACTTCAACGC 3 99 0 GTGCTCGGGG 0.980806 -81 ACGCGTCGTGGTTGATGCGTGAGATGAGTCA 3 120 1 GTGATGCGTG 0.927823 -60 GCGCCGCTTCGCGGCTGGGGGTGCCCCCATG 4 47 1 GCGCTGGGGG 0.995284 -94 CGCAAACGGCGCGCATGGGGGCACCCCCAGC 4 60 0 GCCATGGGGG 0.990337 -81 TTTGCGCGGCGTGCATCGTCGTCGGGCTACG 4 85 1 GTCATCGTCG 0.809414 -56 CTACGCCCGGGCCGATCGGCGTATCTGGGAA 4 111 1 GCGATCGGCG 0.996276 -30 GCGTATCTGGGAAGATGGTTCG 4 129 1 GAGATGGTTC 0.647558 -12 CGGACCGCGCGCTGACGGTCGCTACCCTTCA 5 11 1 GCGACGGTCG 0.966212 -79 GATGCAAGCGGCTCATCGACGG 6 2 0 GCCATCGACG 0.913073 -67 CTTGCATCTTGAGCCTCGGTGATGACAGATC 6 25 1 GACCTCGGTG 0.88533 -44 GCGCGGAAGATCCGGGGTGGATAGAT 6 53 0 GAGATCCGGG 0.953163 -16 TACCGAAATTTCCGACCCGGGTAGAGTTCGA 7 38 0 TCGACCCGGG 0.761563 -120 AGTTCCGCGTGTCGCCCGGCCGTTTGGTTAG 7 73 1 GTGCCCGGCC 0.904955 -85 GCGCTGATGGTCCCATGAGGATC 7 145 0 GCGATGGTCC 0.946444 -13 ** ******** Masking position 1 Map Score: 31.6121 Number of sites scoring better than the average of aligned sites = 27594 Number in coding regions = 25839 Number in noncoding regions = 1755 Number of orfs with sites within 600 bp upstream = 998 Fraction of orfs with sites within 600 bp upstream = 0.160296 Motif number 3 GACAAGACGACGAATGGCCCGGGGTGCAACG 1 42 1 CAATGGCCCG 0.98165 -52 ACGACTGCCGGCAGGGTCAGGCGGT 2 5 1 CGCCGGCAGG 0.965094 -32 CCGGCAGGGTCAGGCGGTAGCCTGTCACG 2 18 1 CGGCGGTAGC 0.814792 -19 CCGGTCCGCCCTGATGGCCCCATCATTCGTG 3 51 0 CGATGGCCCC 0.992162 -129 GCGGATGCGTGGACCGGTCCGCCCTGATGGC 3 64 0 GACCGGTCCG 0.890568 -116 GCATTAGTCCCACTGGTTCGACGTCCTGTC 3 160 0 CACTGGTTCG 0.841133 -20 CAGGCTACAACCGATTGCCCGACTCCTTGCG 4 17 1 CGATTGCCCG 0.916369 -124 GCACGCCGCGCAAACGGCGCGCATGGGGGCA 4 68 0 CAACGGCGCG 0.960632 -73 CCAGATACGCCGATCGGCCCGGGCGTAGCCC 4 108 0 CATCGGCCCG 0.949889 -33 CGACCGTCAGCGCGCGGTCCG 5 1 0 CCGCGGTCCG 0.536521 -89 GGACCGCGCGCTGACGGTCGCTACCCTTCAT 5 12 1 CGACGGTCGC 0.956788 -78 CGTTCCCTTCCCACTGTCACCCACACGCGCT 5 63 0 CACTGTCACC 0.667991 -27 GCCTGCCGTTCCCTTCCCACTGT 5 77 0 CGCCGTTCCC 0.962773 -13 CTATCCACCCCGGATCTTCCGCGC 6 55 1 CGATCTTCCG 0.588654 -14 TTGCGCTAACCAAACGGCCGGGCGACACGCG 7 78 0 CAACGGCCGG 0.977383 -80 GCGCTGATGGTCCCATGAGGATCA 7 144 0 CGATGGTCCC 0.987334 -14 * ********* Masking position 1 Map Score: 22.3591 Number of sites scoring better than the average of aligned sites = 24742 Number in coding regions = 23191 Number in noncoding regions = 1551 Number of orfs with sites within 600 bp upstream = 920 Fraction of orfs with sites within 600 bp upstream = 0.147767 Motif number 4 AGTCCCGCCAGATCCCGAGGAAAGTG 1 7 0 GATCCCGAGG 0.832065 -87 CATTCGTCGTCTTGTCGAGGTAGTCCCGCC 1 28 0 CTTGTCGAGG 0.794417 -66 TCTATCGTTGCACCCCGGGCCATTCGTCGT 1 48 0 CACCCCGGGC 0.964151 -46 GGACTTCAACGCCGCCGCGGATGCGTGGAC 3 81 0 GCCGCCGCGG 0.928631 -99 CGGCGTTGAAGTCCCCGAGCAACACGCGTC 3 97 1 GTCCCCGAGC 0.991628 -83 AGGGCGACAGGACGTCGAACCAGTGGGACT 3 155 1 GACGTCGAAC 0.959902 -25 AGTCGTCAGGCTACAACCGAT 4 2 1 GTCGTCAGGC 0.922095 -139 CGGCGCGCAAGGAGTCGGGCAATCGGTTGT 4 23 0 GGAGTCGGGC 0.726538 -118 CGCATGGGGGCACCCCCAGCCGCGAAGCGG 4 50 0 CACCCCCAGC 0.821221 -91 GACGACGATGCACGCCGCGCAAACGGCGCG 4 78 0 CACGCCGCGC 0.975062 -63 GGCGTGCATCGTCGTCGGGCTACGCCCGGG 4 92 1 GTCGTCGGGC 0.994044 -49 CGGACCGCGCGCTGACGGTCGC 5 3 1 GACCGCGCGC 0.89582 -87 CTTCATGGACGTCGTCGAAATTGACGAGCG 5 37 1 GTCGTCGAAA 0.699803 -53 CCGTCGATGAGCCGCTTGCATC 6 3 1 GTCGATGAGC 0.642394 -66 ACGCTTTGTAGTTGTCGAACTCTACCCGGG 7 24 1 GTTGTCGAAC 0.843986 -134 AGTTCCGCGTGTCGCCCGGCCGTTTGGTTA 7 73 1 GTCGCCCGGC 0.975777 -85 GTTAGCGCAAGTCGTCGACGTGTTCAGGGC 7 99 1 GTCGTCGACG 0.87704 -59 ********** Masking position 6 Map Score: 19.2629 Number of sites scoring better than the average of aligned sites = 36228 Number in coding regions = 33882 Number in noncoding regions = 2346 Number of orfs with sites within 600 bp upstream = 1168 Fraction of orfs with sites within 600 bp upstream = 0.1876 Motif number 5 GACGAATGGCCCGGGGTGCAACGATAGAAG 1 50 1 CCGGGGTGCA 0.95644 -44 AGAAGTTGCAGCTGCAGGCATACCTTGTT 1 75 1 GCTGCAGGCA 0.979564 -19 ACCGCCTGACCCTGCCGGCAGTCGT 2 6 0 CCTGCCGGCA 0.953729 -31 TCATTCGTGAGATTCGGCCACGCTCCGTGA 3 30 0 GATTCGGCCA 0.928336 -150 TCTCACGAATGATGGGGCCATCAGGGCGGA 3 48 1 GATGGGGCCA 0.979466 -132 CGCCGCCGCGGATGCGTGGACCGGTCCGCC 3 72 0 GATGCGTGGA 0.903489 -108 GGCGCGCAAGGAGTCGGGCAATCGGTTGTA 4 22 0 GAGTCGGGCA 0.968455 -119 CAGCCGCGAAGCGGCGCGCAAGGAGTCGGG 4 34 0 GCGGCGCGCA 0.980081 -107 AAACGGCGCGCATGGGGGCACCCCCAGCCG 4 58 0 CATGGGGGCA 0.985975 -83 CGCCGTTTGCGCGGCGTGCATCGTCGTCGG 4 80 1 GCGGCGTGCA 0.98822 -61 CGAGGCTCAAGATGCAAGCGGCTCATCGAC 6 13 0 GATGCAAGCG 0.619015 -56 GGTTGATCCTCATGGGACCATCAGCGC 7 141 1 CATGGGACCA 0.848058 -17 ********** Masking position 10 Map Score: 15.1354 Number of sites scoring better than the average of aligned sites = 10663 Number in coding regions = 9889 Number in noncoding regions = 774 Number of orfs with sites within 600 bp upstream = 556 Fraction of orfs with sites within 600 bp upstream = 0.0893029 Motif number 6 ACTTTCCTCGGGATCTGGCGGGACTACCTC 1 12 1 GGATCTGGCG 0.994402 -82 ACTGCCGGCAGGGTCAGGCGGTAGCCTGTC 2 14 1 GGGTCAGGCG 0.952241 -23 CGGATGTGTGGGGTCTCACGGAGCGTGGCC 3 15 1 GGGTCTCACG 0.987504 -165 GAGCGTGGCCGAATCTCACGAATGATGGGG 3 35 1 GAATCTCACG 0.969056 -145 CCTGTCGCCCTGATCTGACTCATCTCACGC 3 136 0 TGATCTGACT 0.86552 -44 CAATCGGTTGTAGCCTGACGACT 4 4 0 TAGCCTGACG 0.808992 -137 CGGACCGCGCGCTGACGGTCG 5 2 1 GGACCGCGCG 0.923733 -88 GGACGTCGTCGAAATTGACGAGCGCGTGTG 5 43 1 GAAATTGACG 0.660276 -47 TATCCACCCCGGATCTTCCGCGC 6 56 1 GGATCTTCCG 0.895785 -13 GGCGACACGCGGAACTGACTTACCGAAATT 7 59 0 GGAACTGACT 0.931645 -99 ********** Masking position 9 Map Score: 6.58961 Number of sites scoring better than the average of aligned sites = 5375 Number in coding regions = 4936 Number in noncoding regions = 439 Number of orfs with sites within 600 bp upstream = 312 Fraction of orfs with sites within 600 bp upstream = 0.0501124 Motif number 7 CATGCGGATGTGTGGGGTCTCACGGAGCG 3 10 1 GTGTGGGGTC 0.937459 -170 ATCTCACGAATGATGGGGCCATCAGGGCGG 3 47 1 TGATGGGGCC 0.960125 -133 CAACCACGACGCGTGTTGCTCGGGGACTTC 3 104 0 GCGTGTTGCT 0.880211 -76 GCCGCTTCGCGGCTGGGGGTGCCCCCATGC 4 49 1 GGCTGGGGGT 0.950716 -92 CAAACGGCGCGCATGGGGGCACCCCCAGCC 4 59 0 GCATGGGGGC 0.990267 -82 GCGTGCATCGTCGTCGGGCTACGCCCGGGC 4 93 1 TCGTCGGGCT 0.906591 -48 ATTGACGAGCGCGTGTGGGTGACAGTGGGA 5 56 1 GCGTGTGGGT 0.978755 -34 AGTCAGTTCCGCGTGTCGCCCGGCCGTTTG 7 69 1 GCGTGTCGCC 0.945556 -89 TTCAGGGCGCGGTTGGGGTTGGTTGATCCT 7 121 1 GGTTGGGGTT 0.852451 -37 TGGTTGATCCTCATGGGACCATCAGCGC 7 140 1 TCATGGGACC 0.803227 -18 ********** Masking position 4 Map Score: 5.81619 Number of sites scoring better than the average of aligned sites = 5048 Number in coding regions = 4536 Number in noncoding regions = 512 Number of orfs with sites within 600 bp upstream = 414 Fraction of orfs with sites within 600 bp upstream = 0.0664953 Motif number 8 ********** No masking Map Score: 1.17483e-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: 1.17483e-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: 1.17483e-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