AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mjan_pyro_100.orf -o294_mjan_pyro_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 = 0.37 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RPH01295 16 Pyrococcus_OT3 Input sequences: #1 RMJ07952 220 M_jannaschii_chromosome #2 RMJ10405 122 M_jannaschii_chromosome #3 RMJ01297 29 M_jannaschii_chromosome #4 RMJ01220 226 M_jannaschii_chromosome #5 RMJ11540 84 M_jannaschii_chromosome #6 RPH00435 225 Pyrococcus_OT3 #7 RPH01219 16 Pyrococcus_OT3 #8 RPH01220 64 Pyrococcus_OT3 #9 RPH01291 61 Pyrococcus_OT3 #10 RPH01292 23 Pyrococcus_OT3 #11 RPH01294 90 Pyrococcus_OT3 #12 RPH01750 184 Pyrococcus_OT3 Motif number 1 TAATATGCACAAAAAATAAAAAGGTGTAGTGATATTATAC 1 29 0 AAAAAAAAAT 0.816769 -192 TGTTTTGCAAAAAACTATTTTAATTCCATTTAGTTCTAAA 1 86 0 AAAATTTTAT 0.918529 -135 AGTTTTTTGCAAAACATTATTAAGATAAATAAGGCACACA 1 110 1 AAAAAATTAT 0.896804 -111 TACCTTTTGCAAAAAACTATAAATAGGGCTATTTTGT 1 194 1 AAAAAATAGT 0.673982 -27 TAATTACCTTAAAAATGATTAAGATTGATTAGGGATAGGC 2 11 0 AAAATTTAAT 0.951754 -112 ATTTTTAATGAAAATATTATACTATCAAATGTCATCAATT 2 85 0 AAAAAATAAT 0.938412 -38 ATAATTTAAAAGTGGTATTATGGAATTAAAAGGAAGA 4 8 1 AAAATTATAT 0.767494 -219 ATTTATCGATAAAATAAAATTAAAATAAATCTTCTAATAA 5 28 0 AAAAAATTAT 0.896804 -57 AAATCTATTAAAAACTTTTTTGGTGATAATT 5 64 1 AAAATTTTAT 0.918561 -21 ACCTCCACCGAAAACTACATAAATCTAACTTAAAAACTCT 6 54 0 AAAATATAAT 0.957412 -172 AACCCTTTATAAAAGACTTTCGGTAATAGTACAATCTAAA 6 157 0 AAAAATTCAT 0.736511 -69 AATCGAAAACTTTATATACTCCATTTCCTCCACTT 11 6 1 AAAATATAAT 0.957283 -85 AGAACAGAAGAAAAATTCTCAAGGGGAAGTGGAGGAAATG 11 32 0 AAAATTCAAT 0.772463 -59 TAAAGCGTTGAAAAGTCTAAAGCTATCATTATCCTTTGAC 12 86 0 AAAATAAAAT 0.868059 -99 AACCCCTACCAAAATTTATTAGCTCACAATGAAGCATTTT 12 141 1 AAAATTTAAT 0.951867 -44 **** * *** * * Masking position 4 Map Score: 14.2064 Number of sites scoring better than the average of aligned sites = 716 Number in coding regions = 516 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 2 GTATAGCAATAGAGGCTTTGCCTCTATGCTTT 4 56 0 AGGGTTTGCC 0.997392 -171 TATACTCCAGAGCGGGGTTGCCAGAGGCAACC 4 83 1 AGGGGTTGCC 0.998339 -144 CCAGATAGAAAGTGGGGTTGCCTCTGGCAACC 4 98 0 AGGGGTTGCC 0.99834 -129 CTCACTATAGAAGGGCTTTGCCCCTCTATTGG 4 138 0 AAGGTTTGCC 0.992323 -89 TACACTAATAAATAGTTTTGCCTACTTTAATC 8 37 1 AAAGTTTGCC 0.952374 -28 ACTAAACCATCGGGGTGTTGCAA 11 78 1 CGGGGTTGCA 0.97145 -13 ** ** ****** Masking position 8 Map Score: 8.8708 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 12 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 GTTCTAAATATTCAAATATTTCTATTAATA 1 64 0 TTCAAATATT 0.858424 -157 AAATAGGGCGTTCAAATATTCATATTTAAT 1 161 1 TTCAAATATT 0.858424 -60 GAAGAAGTATTTCAAAGCATAGAGGCAAAG 4 43 1 TTCAAAGCAT 0.848984 -184 CTCAGATTAATTGAAAGCTTAAGGGGGCAA 6 16 0 TTGAAAGCTT 0.725726 -210 ATATTCGGCGATCAACGATTTTAGATTGTA 6 138 1 ATCAACGATT 0.873836 -88 CTATTAGCCTTTCAACCCTTTATAAAAGAC 6 180 0 TTCAACCCTT 0.957271 -46 TTTTCTTTTCTTCACCTATTAGCCTTTCAA 6 195 0 TTCACCTATT 0.898978 -31 TTCAAGGATTAAAGTAGGCA 8 55 0 TTCAAGGATT 0.842927 -10 GATCATCACCCCTTGATCGTGAAC 12 5 1 ATCACCCCTT 0.776863 -180 CTTTAGACTTTTCAACGCTTTACTTATTCA 12 104 1 TTCAACGCTT 0.981513 -81 TTGGTAGGGGTTCACCTCATGAATAAGTAA 12 123 0 TTCACCTCAT 0.807673 -62 ********** Masking position 4 Map Score: 7.37254 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 305 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 TAGTGATATTATACATATAATGTAAGTTGGGC 1 8 0 ATACATTATA 0.7115 -213 GCATATTAATAGAAATATTTGAATATTTAGAACTA 1 61 1 AGAAATTTAA 0.791613 -160 TGCAAAAGGTATAAATTAAATATGAATATTTGAAC 1 170 0 ATAAATAATA 0.763387 -51 TTTGTTTAACACAAATTTTATATAATTAGGTAATT 2 51 0 ACAAATTTTA 0.839424 -72 ATCAAATGTCATCAATTTTGTTTAACACAAATTTT 2 67 0 ATCAATTTTA 0.826603 -56 TTTAATAAATTTTTAATGAAAATATTATA 2 104 0 ATAAATTTTA 0.965241 -19 AGAGAATTGCATAAATTATTGGTGAAACT 3 11 1 ATAAATATTA 0.861532 -19 TAAAATTAAAATAAATCTTCTAATAAAAGAATGAT 5 19 0 ATAAATTTAA 0.952768 -66 TATTTTATCGATAAATCTATTAAAAACTTTTTTGG 5 52 1 ATAAATTAAA 0.912757 -33 CGAAAACTACATAAATCTAACTTAAAAACTCTAGA 6 51 0 ATAAATTATA 0.935073 -175 TGAAGTGAGCATAAATATTTATAAACCTAGTTCAA 12 48 0 ATAAATTTAA 0.952768 -137 TTGTGAGCTAATAAATTTTGGTAGGGGTTCACCTC 12 135 0 ATAAATTTAG 0.77593 -50 ****** ** * * Masking position 5 Map Score: 7.22544 Number of sites scoring better than the average of aligned sites = 384 Number in coding regions = 261 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 5 TCTATTGGGATACTCCCCAGATAGAAAGTG 4 116 0 TACTCCCCAG 0.929534 -111 TACCTCTTAACACTCCCCTTNCTAACGCTC 4 172 1 CACTCCCCTT 0.982915 -55 TTCTCACACCCCCTGA 7 3 0 CACACCCCCT 0.98289 -14 CTTAAAAGTTAACTCCCCAAACGCCGATGG 9 32 1 AACTCCCCAA 0.975403 -30 GGTTCGCTCCCCATCGGCGTTTGG 9 48 0 CGCTCCCCAT 0.980497 -14 CCATTTCCTCCACTTCCCCTTGAGAATTTT 11 31 1 CACTTCCCCT 0.946014 -60 TTGCAACACCCCGATGGTTTAGTT 11 77 0 AACACCCCGA 0.867368 -14 TTCCAATCCCCAATAAAATGCTT 12 172 0 CAATCCCCAA 0.941971 -13 ********** Masking position 6 Map Score: 5.76403 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 101 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 ACATATAATGTAAGTTGGGC 1 1 0 TAAGTTGGGC 0.966845 -220 ATTATTAAGATAAATAAGGCACACAATGAA 1 125 1 TAAATAAGGC 0.976601 -96 ATGAACGTCCCAAATAGGGCGTTCAAATAT 1 150 1 CAAATAGGGC 0.959995 -71 CAAAAAACTATAAATAGGGCTATTTTGT 1 203 1 TAAATAGGGC 0.984991 -18 TTCAAGGATTAAAGTAGGCAAAACTATTT 8 46 0 TAAAGTAGGC 0.891059 -19 ACCTCATGAATAAGTAAAGCGTTGAAAAGT 12 110 0 TAAGTAAAGC 0.842592 -75 ********** Masking position 3 Map Score: 3.68455 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 54 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 TATCACTACACCTTTTTATTTTTTGTGCAT 1 35 1 CCTTTTTATT 0.935914 -186 AATATTCAAATATTTCTATTAATATGCACA 1 58 0 TATTTCTATT 0.601847 -163 TATTTTAATTCCATTTAGTTCTAAATATTC 1 81 0 CCATTTAGTT 0.672444 -140 TGCAAAAAACTATTTTAATTCCATTTAGTT 1 91 0 TATTTTAATT 0.847158 -130 TATAATTAGGTAATTTAATTACCTTAAAAA 2 36 0 TAATTTAATT 0.698536 -87 CAAATGTCATCAATTTTGTTTAACACAAAT 2 70 0 CAATTTTGTT 0.524769 -53 GATAGTATAATATTTTCATTAAAAATTTAT 2 99 1 TATTTTCATT 0.595505 -24 AATACTTCTTCCTTTTAATTCCATAATACC 4 24 0 CCTTTTAATT 0.94419 -203 ATAAAAGAATGATTTTTATTT 5 2 0 GATTTTTATT 0.824245 -83 TTAGAAGATTTATTTTAATTTTATTTTATC 5 31 1 TATTTTAATT 0.847158 -54 GCCCCCTTAAGCTTTCAATTAATCTGAGTT 6 18 1 GCTTTCAATT 0.733654 -208 GTCTCTCCTTTTTAGTATTTAAC 10 7 1 CCTTTTTAGT 0.809124 -17 TATCCTTTGACCTTTGAAGTGAGCATAAAT 12 67 0 CCTTTGAAGT 0.457415 -118 TCACAATGAAGCATTTTATTGGGGATTGGA 12 164 1 GCATTTTATT 0.758816 -21 ********** Masking position 5 Map Score: 4.54473 Number of sites scoring better than the average of aligned sites = 1375 Number in coding regions = 1045 Number in noncoding regions = 330 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 8 TTTGCAAAACATTATTAAGATAAATAAGGCA 1 115 1 ATATTAAGAT 0.608607 -106 TACCTTAAAAATGATTAAGATTGATTAGGGA 2 16 0 AGATTAAGAT 0.862591 -107 TAGAAGGGGAGTGTTAAGAGGTATCCTCAC 4 165 0 ATGTTAAGAG 0.860201 -62 AAATTTTCTTATGATTGAGGGATTATT 4 210 1 AGATTGAGGG 0.948717 -17 GATTAATTGAAAGCTTAAGGGGGCAAAAAAG 6 11 0 AGCTTAAGGG 0.979273 -215 TCTTTTATAAAGGGTTGAAAGGCTAATAGGT 6 181 1 AGGTTGAAAG 0.777911 -45 TTCAAGGATTAAAGTAGGCAAAACT 8 50 0 AGATTAAAGT 0.814357 -15 CTTCTCAAGAAAGCTTAAAAGTTAACTCCCC 9 19 1 AGCTTAAAAG 0.901248 -43 CAGAAGAAAAATTCTCAAGGGGAAGTGGAGG 11 37 0 ATCTCAAGGG 0.879951 -54 CCATCGGTTCACGATCAAGGGGTGATGATC 12 10 0 AGATCAAGGG 0.967938 -175 GCTCACTTCAAAGGTCAAAGGATAATGATAG 12 73 1 AGGTCAAAGG 0.915767 -112 * ********* Masking position 8 Map Score: 6.00373 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 277 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 AGTTTCACCAATAATTTATG 3 20 0 AGTTTCACCA 0.921533 -10 AATTATCACCAAAAAAGTTTT 5 74 0 ATTATCACCA 0.93972 -11 GTAATGTCTTAGTACCTCCACCGAAAACTA 6 77 0 AGTACCTCCA 0.981923 -149 AAATGCTATCATTACCTACATATATTCGGC 6 117 1 ATTACCTACA 0.906053 -109 TATATACTCCATTTCCTCCACTTCCCCTTG 11 23 1 ATTTCCTCCA 0.972318 -68 ********** Masking position 3 Map Score: 0.823441 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 142 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 ********** No masking Map Score: 3.24961e-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 11 ********** No masking Map Score: 3.24961e-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 12 ********** No masking Map Score: 3.24961e-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