AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i117_mjan_pyro_100.orf -o117_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 RPH00319 174 Pyrococcus_OT3 #2 RPH00318 41 Pyrococcus_OT3 #3 RPH01298 250 Pyrococcus_OT3 #4 RPH01299 117 Pyrococcus_OT3 #5 RPH01808 198 Pyrococcus_OT3 Motif number 1 AGTTTTGGACTTTCAATTCGACAAATTTA 1 1 1 ATTTCTTTTC 0.960949 -174 GATATGTTAAAATTTAACCCTATATTTTTGAATAAATTT 1 33 0 ATTTCTATTT 0.86313 -142 CACTAATGCAATCTTGAGAATCTATGATCTTCAATGCCA 1 71 1 ACTTATCATC 0.897696 -104 GTATATTTAATTTTTATGGATCGGAATTTGGCATTGAAG 1 99 0 TTTTATCTTT 0.851411 -76 CGACGTACATAGTTTTAAGATTTAAAATTGGGGGTAATC 1 142 1 ATTTATTATT 0.848944 -33 GTGGTGTATCATTTTGATCATAAAACATTCAAAAACATC 3 46 1 ATTTATAATT 0.609848 -205 AGTGTAAATGAACTTCATAATTTTATTACTAATTGTTAT 3 120 1 ACTTATTTAC 0.74566 -131 TAATTGTTATAATTTGGATCTTCTATTTTCCACAAAGTG 3 149 1 ATTTCTTTTT 0.957778 -102 CTCGCTAATAAGCTTTTCGATCTTGGTTCACTTTGTGGA 3 177 0 ACTTATCTTC 0.970268 -74 TAATCTTTCTTCTCTCTTTTCTTTATTGCCC 4 3 1 ACTTCTCTTC 0.972528 -115 ATTTGCCCCTCCTTGTACATTCTTGTTCTATAACATCG 4 90 0 TCTTATTTTC 0.895955 -28 CCTCCCCTTTAGTTTTCTCCTTGATTTTTAAATTTTAGA 5 16 1 ATTTCTTTTT 0.957781 -183 TTCTCGTTAGTTCTTTCGGCTTATCGTTTAGATGACTTT 5 76 1 TCTTCTTTTT 0.895955 -123 TTGTAAAACTACCTTATATATCTTACTTTCGAAAGTCAT 5 107 0 ACTTATCTTT 0.967828 -92 TGAAGGAACAAGTTTGAACATTATCTTTTTCAAGCTTGT 5 142 0 ATTTATTTTT 0.954364 -57 * *** *** *** Masking position 11 Map Score: 14.3713 Number of sites scoring better than the average of aligned sites = 876 Number in coding regions = 710 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 2 CCTATATTTTTGAATAAATTTGTCGAATTGAA 1 22 0 TGAAAATTTG 0.735884 -153 ATTAGTGATATGTTAAAATTTAACCCTATATT 1 46 0 TGTTAATTTA 0.937174 -129 TTACCCCCAATTTTAAATCTTAAAACTATGTA 1 147 0 TTTTAACTTA 0.80404 -28 GCTTATTGTTTCACCTTGAAGATGCTTA 3 7 1 TGTTCACTTG 0.983014 -244 AAATCAGTGGTGTATCATTTTGATCATAAAAC 3 40 1 TGTACATTTG 0.930786 -211 TTTTTTGAGATGTTTAACCTAGTGTAAATGAA 3 100 1 TGTTAACTAG 0.954839 -151 TATTACTAATTGTTATAATTTGGATCTTCTAT 3 143 1 TGTTTATTTG 0.913366 -108 TTTTCGATCTTGGTTCACTTTGTGGAAAATAG 3 171 0 TGGTCATTTG 0.877912 -80 AAAATTTTGGTGTTTAAATAAGGGCAATAAAG 4 31 0 TGTTAATAAG 0.619561 -87 TGCCCCTCCTTGTACATTCTTGTTCTATAACA 4 93 0 TGTAATCTTG 0.779577 -25 TCTCCTTGATTTTTAAATTTTAGAAACCCTTC 5 31 1 TTTTAATTTA 0.748099 -168 AACATTATCTTTTTCAAGCTTGTAAAACTACC 5 133 0 TTTTAACTTG 0.953724 -66 AAAAAGATAATGTTCAAACTTGTTCCTTCAAA 5 151 1 TGTTAACTTG 0.990432 -48 **** ** **** Masking position 1 Map Score: 12.1017 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 299 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 CAACAAAGAAAAGGGGAATAAAAATAAAAA 2 7 0 AAGGGTAAAA 0.993168 -35 TTTCACCTTGAAGATGCTTAAAAATCAGTGGTGT 3 19 1 AAGATTAAAA 0.903676 -232 CTCAAAAAATAAGGGAATTAGAGAGATGTTTTTG 3 75 0 AAGGGTAGAA 0.987998 -176 AGGTTATCCAAAGAGATATAACCAGGCACCTCGC 3 211 0 AAGAGTAACA 0.917571 -40 GTGTTTAAATAAGGGCAATAAAGAAAAGAGAGAA 4 20 0 AAGGGTAAAA 0.993168 -98 GAGAAAACTAAAGGGGAGGAGAAA 5 1 0 AAGGGGAGAA 0.956264 -198 AGCTTAAGAGAAGGGTTTCTAAAATTTAAAAATC 5 38 0 AAGGGCTAAA 0.95295 -161 ACTAACGAGAAAGAGAGCTTAAGAGAAGGGTTTC 5 53 0 AAGAGTTAAA 0.961527 -146 TAAGATATATAAGGTAGTTTTACAAGCTTGAAAA 5 121 1 AAGGTTTTAA 0.757128 -78 ***** **** * Masking position 2 Map Score: 7.94923 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 222 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 AAATATAGGGTTAAATTTTAACATATCACT 1 45 1 TTAAATTTTA 0.867852 -130 AAGCGTATATTTAATTTTTATGGATCGGAA 1 112 0 TTAATTTTTA 0.959239 -63 ACCCCCAATTTTAAATCTTAAAACTATGTA 1 147 0 TTAAATCTTA 0.94229 -28 TTTTTATTTTTATTCCCCTTTT 2 3 1 TTTATTTTTA 0.899314 -39 TCCTTGATTTTTAAATTTTAGAAACCCTTC 5 33 1 TTAAATTTTA 0.867852 -166 ********** Masking position 6 Map Score: 5.49854 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 109 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 5 TCATAGATTCTCAAGATTGCATTAGTGATAT 1 67 0 TCAAGTTGCA 0.94009 -108 TTAAGCATCTTCAAGGTGAAACAATAAGC 3 9 0 TCAAGTGAAA 0.930622 -242 GTTCATTTACACTAGGTTAAACATCTCAAAA 3 102 0 ACTAGTTAAA 0.823058 -149 ACAAAGTGAACCAAGATCGAAAAGCTTATTA 3 180 1 CCAAGTCGAA 0.916233 -71 ATGTTATAGAACAAGAATGTACAAGGAGGGG 4 92 1 ACAAGATGTA 0.834624 -26 AATTTAAAAATCAAGGAGAAAACTAAAGGGG 5 19 0 TCAAGAGAAA 0.830813 -180 AGGTAGTTTTACAAGCTTGAAAAAGATAATG 5 132 1 ACAAGTTGAA 0.985164 -67 TTTTGAAGGAACAAGTTTGAACATTATCTTT 5 153 0 ACAAGTTGAA 0.985164 -46 ***** ***** Masking position 4 Map Score: 4.09258 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 88 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TTTTTATTTTTATTCCCCTTTTCTTTGT 2 9 1 TTTATTCCCC 0.973457 -33 AAAACATCTCTCTAATTCCCTTATTTTTTG 3 77 1 TCTAATTCCC 0.968313 -174 ATTTGGATCTTCTATTTTCCACAAAGTGAA 3 160 1 TCTATTTTCC 0.939592 -91 CTCTCTTTTCTTTATTGCCCTTATTTAAAC 4 22 1 TTTATTGCCC 0.952217 -96 TTTCTCCTCCCCTTTAGTTTTC 5 3 1 TCTCCTCCCC 0.975924 -196 TCTCTTAAGCTCTCTTTCTCGTTAGTTCTT 5 61 1 TCTCTTTCTC 0.928032 -138 ********** Masking position 6 Map Score: 2.57106 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 109 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ********** No masking Map Score: -2.67574e-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 8 ********** No masking Map Score: -2.67574e-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 9 ********** No masking Map Score: -2.67574e-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