AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_mjan_pyro_100.orf -o222_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 Input sequences: #1 RMJ00193 285 M_jannaschii_chromosome #2 RMJ10489 300 M_jannaschii_chromosome #3 RPH00451 213 Pyrococcus_OT3 Motif number 1 AAAATAAATTTTTATTAATTGAGATTATTA 1 31 1 TTTATTAATT 0.961305 -255 AATAATGAACTTTAATAATCTCAATTAATA 1 43 0 TTTAATAATC 0.909575 -243 ATATTCTTATTTTAAAAATTTTCGTCCTTC 1 150 0 TTTAAAAATT 0.893292 -136 TATTATTTTCTTTAATAAATAGATAACTAT 1 224 0 TTTAATAAAT 0.825798 -62 TTAGGAATTATTTATTTATTTAGAGGTTTT 2 31 0 TTTATTTATT 0.835324 -270 TGTTAATTGATTTATTGATTGTCTTGTTGT 2 90 0 TTTATTGATT 0.886989 -211 GATTTTCAATTTTGTTAATTGATTTATTGA 2 102 0 TTTGTTAATT 0.869612 -199 ACCCTAATAATGTAATGATAGAATAACGAT 2 137 1 TGTAATGATA 0.840027 -164 TTATAGTTTGTTTAATAATATTCTATCGTT 2 161 0 TTTAATAATA 0.964587 -140 TGTAGATAATTTTAATTATAGTTTGTTTAA 2 176 0 TTTAATTATA 0.836466 -125 ATAAACATTTTGTGATAATAAAGCTTTATT 2 215 1 TGTGATAATA 0.816986 -86 ATAATAAAGCTTTATTAAGTCAATTATCCT 2 229 1 TTTATTAAGT 0.783737 -72 AATAATTAGTTGTAATAATAGGATAATTGA 2 248 0 TGTAATAATA 0.943199 -53 TTATCTTAGTTGTAATAATTAGTTGTAATA 2 261 0 TGTAATAATT 0.966838 -40 AGGTTATACCTTTAAAAATTCTTTTTGGTA 3 175 0 TTTAAAAATT 0.893292 -39 ********** Masking position 8 Map Score: 18.21 Number of sites scoring better than the average of aligned sites = 1074 Number in coding regions = 778 Number in noncoding regions = 296 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117 Motif number 2 CAAATTAAATATTAACTACTAAAATAAATTTTT 1 8 1 AATAATCAAA 0.973291 -278 GAACTTTAATAATCTCAATTAATAAAAATTTATTTT 1 31 0 AATAATAAAA 0.834965 -255 ATTATTGGATATATCAAACTGCGAAGTCCTATTCAA 1 67 1 ATAAATCAAG 0.965575 -219 TGCCATTAAAATTTCTAATATCAAAGTTTTACAAAT 1 107 1 ATTAAACAAG 0.780878 -179 TTACAAATAGAAAAAGAAGGACGAAAATTTTTAAAA 1 135 1 AAAAAGCAAA 0.872831 -151 TTTCGTCCATATTCTTATTTTAAAAATTTTCGTCCT 1 152 0 ATTATTAAAA 0.606157 -134 AATCCCACCATACAGAACTGCTAAATTTTATTCTT 1 261 0 ATAAATCAAA 0.980458 -25 TAGAGGTTTTAAATTTAATTTCTAAGGGTT 2 5 0 AAAAATCAAG 0.953213 -296 CTCTAAATAAATAAATAATTCCTAAATACTCTCATT 2 36 1 ATAAATCAAA 0.980439 -265 AAATACTCTCATTTCTAAATTCCAAACTTATACAAC 2 59 1 ATTAATCAAA 0.980286 -242 CAATTAACAAAATTGAAAATCCTAAAACCCTAATAA 2 111 1 AATAATCAAA 0.973064 -190 CAGGTCGGACATATTAATGTACCAAAAAGAATTTTT 3 156 1 ATAATTCAAA 0.918307 -58 *** ** * * *** Masking position 7 Map Score: 14.0926 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 370 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 CGTTCAATGAAGGCGGGCGGATAATCCGGG 3 12 0 AGGCGGGCGG 0.988968 -202 TTCTCGGCAACCTCAGGCGGCCCCGGAGAC 3 45 1 CCTCAGGCGG 0.951375 -169 GAGGTGACGTCGTCGGGCGGACAGGGCCCG 3 75 0 CGTCGGGCGG 0.997148 -139 CGGCACGCTCCCTCGGTCGGGCCCCCGGGC 3 124 1 CCTCGGTCGG 0.994458 -90 TCGGTCGGGCCCCCGGGCGGCAGGTCGGAC 3 136 1 CCCCGGGCGG 0.953774 -78 ********** Masking position 6 Map Score: 11.4124 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 0 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 CAAATTAAATATTAACTACTAAA 1 4 1 ATTAAATATT 0.820004 -282 ATCTCAATTAATAAAAATTTATTTTAGTAG 1 26 0 ATAAAAATTT 0.759578 -260 AAAGATTGCCATTAAAATTTCTAATATCAA 1 101 1 ATTAAAATTT 0.907756 -185 ATATCAAAGTTTTACAAATAGAAAAAGAAG 1 124 1 TTTACAAATA 0.78257 -162 ATATTCTTATTTTAAAAATTTTCGTCCTTC 1 150 0 TTTAAAAATT 0.820005 -136 TCAACCCATGTTTAAATCTACAATTCATCA 1 189 0 TTTAAATCTA 0.763881 -97 TATAAAAAGAATAAAATTTAGCAGTTCTGT 1 255 1 ATAAAATTTA 0.69595 -31 ACCCTTAGAAATTAAATTTAAAACCTCTAA 2 12 1 ATTAAATTTA 0.876992 -289 ACAAACTATAATTAAAATTATCTACAGACT 2 180 1 ATTAAAATTA 0.939026 -121 TTATCCTATTATTACAACTAATTATTACAA 2 252 1 ATTACAACTA 0.883997 -49 ACAACTAATTATTACAACTAAGATAAAAAA 2 265 1 ATTACAACTA 0.883997 -36 TACAACTAAGATAAAAAATACTGCTGGTGA 2 277 1 ATAAAAAATA 0.831772 -24 AGGTTATACCTTTAAAAATTCTTTTTGGTA 3 175 0 TTTAAAAATT 0.820005 -39 ********** Masking position 6 Map Score: 13.0513 Number of sites scoring better than the average of aligned sites = 1449 Number in coding regions = 986 Number in noncoding regions = 463 Number of orfs with sites within 600 bp upstream = 405 Fraction of orfs with sites within 600 bp upstream = 0.0650498 Motif number 5 GCAACCTCAGGCGGCCCCGGAGACCGGGCC 3 51 1 GCGGCCCCGG 0.963749 -163 CCCCGGAGACCGGGCCCTGTCCGCCCGACG 3 65 1 CGGGCCCTGT 0.994398 -149 ATTCTCGGCACGCTCCCTCGGTCGGGCCCC 3 119 1 CGCTCCCTCG 0.980446 -95 CTCCCTCGGTCGGGCCCCCGGGCGGCAGGT 3 131 1 CGGGCCCCCG 0.769005 -83 GTTCGCACCCTGTGAGGTAAGGT 3 201 0 CGCACCCTGT 0.970192 -13 ********** Masking position 5 Map Score: 1.87386 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 2 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 TTATTTTAAAAATTTTCGTCCTTCTTTTTC 1 144 0 AATTTTCGTC 0.912321 -142 TACAATTCATCAGTTTCGTCCATATTCTTA 1 171 0 CAGTTTCGTC 0.983226 -115 AAATTATCTACAGACTCGTATATAAACATT 2 194 1 CAGACTCGTA 0.884955 -107 CATTGAACGCCATTCTCGGCAACCTCAGGC 3 33 1 CATTCTCGGC 0.992485 -181 CATTGCGCGCCATTCTCGGCACGCTCCCTC 3 108 1 CATTCTCGGC 0.992485 -106 ********** Masking position 6 Map Score: 3.17492 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 11 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 CGAAGTCCTATTCAAAGATTGCCATTAAAATTTCT 1 88 1 TTCAGGCCAT 0.997201 -198 TCCGCCCGCCTTCATTGAACGCCATTCTCGGCAAC 3 21 1 TTCAGGCCAT 0.997201 -193 CGTCACCTCGTTCATTGCGCGCCATTCTCGGCACG 3 96 1 TTCAGGCCAT 0.997201 -118 ATAACCTTACCTCACAGGGTGCGAAC 3 198 1 CTCAGGCGAA 0.966849 -16 **** * ***** Masking position 4 Map Score: 0.0882165 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 5 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 ********** No masking Map Score: 1.77879e-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: 1.77879e-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: 1.77879e-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