AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i107_aful_mthe_300.orf -o107_aful_mthe_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAG02435 213 Archaeoglobus_fulgidus #2 RAG46312 63 Archaeoglobus_fulgidus #3 RAG46188 27 Archaeoglobus_fulgidus #4 RTH00419 300 M.thermo #5 RTH00556 142 M.thermo Motif number 1 CGAGGTAACTTAAACCTTACTCGGTTTTTC 1 38 1 TAAACCTTAC 0.93903 -176 TTTTCGAACAAAAAACTTATATTTACGAGA 1 87 0 AAAAACTTAT 0.969514 -127 AAATAGAACTAAAACCTCTCAAGTGATAGA 1 114 1 AAAACCTCTC 0.870652 -100 CTTGAGACGCTAACACTTTTATAAAACCGC 2 30 1 TAACACTTTT 0.751523 -34 AGCTGCTTTTAAACCCTCATTTAGATATTC 4 105 1 AAACCCTCAT 0.97567 -196 CGGCCGCTCTAAAAACCTATATTGCAATAT 4 205 1 AAAAACCTAT 0.87556 -96 CTGCCGCTCTAAAAATTTATATTGCAATGT 4 268 1 AAAAATTTAT 0.729389 -33 GGAGTTACTGAAACCCTTATTATAAGTGGA 5 35 1 AAACCCTTAT 0.982541 -108 TATAAGTGGAAAAACCTTATTAATGATGAG 5 55 1 AAAACCTTAT 0.987102 -88 TTACTTGTGTTAAACCTCATCATTAATAAG 5 70 0 TAAACCTCAT 0.962268 -73 ********** Masking position 3 Map Score: 11.3046 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 256 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 2 TGTTCAACGACCGCTTTTACTTGAG 2 5 1 CAACACCGCT 0.959576 -59 GCGGACCTTCATCCTACCGCTGAACCTGAAC 4 44 0 ATCCACCGCT 0.987462 -257 TCCATAATAACACCAGCTGCTTTTAAACCCT 4 91 1 CACCGCTGCT 0.991992 -210 AGCTGTCTGTATGCTGCTGTTTATGGGGGAA 4 132 0 ATGCGCTGTT 0.842296 -169 CAGCATATTCCAGCGGCCGCTCTAAAAACCT 4 192 1 CAGCGCCGCT 0.995804 -109 ATATTGCAATATCCTGACGCTACTCAACTAC 4 223 1 ATCCGACGCT 0.973995 -78 ATCCACCCATAACCTGCCGCTCTAAAAATTT 4 255 1 AACCGCCGCT 0.997332 -46 **** ****** Masking position 11 Map Score: 8.73159 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 161 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 CCTCGAATAATATGAATGAATGAGGTGGTG 1 13 0 TATGAATGAA 0.948093 -201 CTGGTGTTATTATGGAAGAAAATAGCTTAA 4 77 0 TATGGAAGAA 0.902975 -224 TGCTGCTGTTTATGGGGGAATATCTAAATG 4 122 0 TATGGGGGAA 0.966089 -179 AGCGGCAGGTTATGGGTGGATAGTAGTTGA 4 246 0 TATGGGTGGA 0.993824 -55 TATATGAATGGGAACATTGCAA 4 289 0 TATGAATGGG 0.920683 -12 GATCATTTTTTATGGGTTGAGCA 5 4 0 TATGGGTTGA 0.954281 -139 AAACCCTTATTATAAGTGGAAAAACCTTAT 5 45 1 TATAAGTGGA 0.909959 -98 ********** Masking position 2 Map Score: 5.33771 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 147 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 TGTTCAACGACCGCTTTTACTTGA 2 5 1 CAACGACCGC 0.967352 -59 GCGGACCTTCATCCTACCGCTGAACCTGAA 4 45 0 ATCCTACCGC 0.966956 -256 TCCATAATAACACCAGCTGCTTTTAAACCC 4 91 1 CACCAGCTGC 0.969833 -210 ATTCCCCCATAAACAGCAGCATACAGACAG 4 131 1 AAACAGCAGC 0.899956 -170 CAGCATATTCCAGCGGCCGCTCTAAAAACC 4 192 1 CAGCGGCCGC 0.989165 -109 ATATTGCAATATCCTGACGCTACTCAACTA 4 223 1 ATCCTGACGC 0.932949 -78 ATCCACCCATAACCTGCCGCTCTAAAAATT 4 255 1 AACCTGCCGC 0.995961 -46 ********** Masking position 4 Map Score: 5.57222 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 237 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 TCGAACAAAAAACTTATATTTACGAGAGCA 1 84 0 AACTTATATT 0.957495 -130 TACTCATCGAAATTTATTTTTTGGTTCAGG 4 21 1 AATTTATTTT 0.916414 -280 GTCCGCTGTTAAGCTATTTTCTTCCATAAT 4 69 1 AAGCTATTTT 0.920914 -232 CCGCTCTAAAAACCTATATTGCAATATCCT 4 208 1 AACCTATATT 0.959858 -93 CCGCTCTAAAAATTTATATTGCAATGTTCC 4 271 1 AATTTATATT 0.869034 -30 ********** Masking position 5 Map Score: 2.67013 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 9 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 CTCACCACCTCATTCATTCATATT 1 5 1 CCACCTCATT 0.988462 -209 GGTCAGAGCCCCACATCACGGCTTTTCTAT 1 147 1 CCACATCACG 0.980317 -67 TTCAGTAACTCCAGATCATTTTTTATGGGT 5 17 0 CCAGATCATT 0.981805 -126 TTGTGTTAAACCTCATCATTAATAAGGTTT 5 66 0 CCTCATCATT 0.982885 -77 ********** Masking position 6 Map Score: 1.54121 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 45 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 GTTTTTCCGTTGTAGGGAAAGAATGCTCTCG 1 61 1 TGTAGGAAAG 0.949804 -153 ATAAGTTTTTTGTTCGAAAATAGAACTAAAA 1 97 1 TGTTGAAAAT 0.915087 -117 ACCTCTCAAGTGATAGAAAAGGTCAGAGCCC 1 127 1 TGATGAAAAG 0.871221 -87 TTCTTCGTATTGTTTGGCAATTCTGGTTTAT 1 184 0 TGTTGGCAAT 0.819501 -30 TAGAGAAGTTTGGGGAGAAAGAAGAT 3 12 1 TGGGAGAAAG 0.907689 -16 GGTGTTATTATGGAAGAAAATAGCTTAACAG 4 74 0 TGGAGAAAAT 0.939517 -227 CTGCTGTTTATGGGGGAATATCTAAATGAGG 4 119 0 TGGGGAATAT 0.927603 -182 CGGCAGGTTATGGGTGGATAGTAGTTGAGTA 4 243 0 TGGGGGATAG 0.969912 -58 **** ****** Masking position 10 Map Score: 1.92696 Number of sites scoring better than the average of aligned sites = 605 Number in coding regions = 570 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 AAAACTTATATTTACGAGAGCATTCTTTCC 1 76 0 TTTACGAGAG 0.953258 -138 GACCTTTTCTATCACTTGAGAGGTTTTAGT 1 121 0 ATCACTTGAG 0.948125 -93 AACGACCGCTTTTACTTGAGACGCTAACAC 2 16 1 TTTACTTGAG 0.988582 -48 GTAAGTGGTGTTTACTTGTGTTAAACCTCA 5 81 0 TTTACTTGTG 0.972269 -62 ********** Masking position 4 Map Score: 0.711534 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 19 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 TTTTATAAAACCGCAATCCAGAAGTGGT 2 46 1 CCGCAATCCA 0.98202 -18 TACCGCTGAACCTGAACCAAAAAATAAATT 4 31 0 CCTGAACCAA 0.980927 -270 TGCTCAACCCATAAAAAATGA 5 2 1 GCTCAACCCA 0.939436 -141 ATCAATGTAACCGGTATCAATGTAAGTGGT 5 102 0 CCGGTATCAA 0.939863 -41 TTGATTTTTCCCTGAATCTAGAAGGT 5 127 1 CCTGAATCTA 0.964309 -16 ********** Masking position 6 Map Score: 0.232988 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 157 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 ********** No masking Map Score: 6.91659e-13 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: 6.91659e-13 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 12 ********** No masking Map Score: 6.91659e-13 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