AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -imelR_mthe_opreg_300.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH1142 300 H(2)-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase Motif number 1 ATTATTAAGATATTAATATCACGGATCTGTG 1 58 0 TTTAATATCA 0.959816 -243 ATTATGATTATTTTCATATAATATTATATGG 1 87 1 TTTCATATAA 0.980662 -214 TACCATCCATTATCCATATAATATTATATGA 1 100 0 TTCCATATAA 0.988301 -201 TTAAGCAATGTTTTCATTTTATCCTCCTTTG 1 140 0 TTTCATTTTA 0.832823 -161 TTTCAGGGTAAGTCAATTTAAGCAATGTTTT 1 157 0 ATCAATTTAA 0.771553 -144 TATTCACCTGTGGCAATTTCAGGGTAAGTCA 1 173 0 TGCAATTTCA 0.840176 -128 GTGAATAAATTCTCCTTATAAGTTTTTTGAT 1 197 1 TTCCTTATAA 0.922437 -104 TTTTTGATAATTTTCAAATCAAAAAACTTAT 1 214 0 TTTCAAATCA 0.860144 -87 ATTAATCGGTTTCCAATATAAATATATTTTT 1 241 0 TCCAATATAA 0.932689 -60 TCTGTACTACTAATAATATAAGTAGTATTAC 1 271 1 TATAATATAA 0.74807 -30 * ********* Masking position 9 Map Score: 7.70249 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 316 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 2 GTGATCCTAACTGGAAGGCTGCCCTTAA 1 9 0 CTGGAAGGCT 0.972869 -292 TGCTTCAATCCAGTGATCCTAACTGGAAGG 1 21 0 CAGTGATCCT 0.960306 -280 GGATCTGTGGCTGAGCTGCTTCAATCCAGT 1 37 0 CTGAGCTGCT 0.984266 -264 ACCGATTAATCTGTACTACTAATAATATAA 1 262 1 CTGTACTACT 0.989551 -39 TCCATTTCTGTAATACTACTTATATTA 1 284 0 CTGTAATACT 0.98873 -17 ********** Masking position 10 Map Score: 2.50691 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 125 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 TAATATTATATGAAAATAATCATAATTATTA 1 82 0 TGAAAAAATC 0.992864 -219 GAGGATAAAATGAAAACATTGCTTAAATTGA 1 145 1 TGAAAAATTG 0.981099 -156 TTGCCACAGGTGAATAAATTCTCCTTATAAG 1 188 1 TGAATAATTC 0.982164 -113 TTTTTTGATTTGAAAATTATCAAAAAATATA 1 219 1 TGAAAATATC 0.982161 -82 ****** **** Masking position 6 Map Score: 2.17523 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 10 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 TTTACCATCCATTATCCATATAATATTATA 1 103 0 ATTATCCATA 0.896491 -198 TTTTCATTTTATCCTCCTTTGGGAAGCCTT 1 131 0 ATCCTCCTTT 0.976439 -170 AGGAGAATTTATTCACCTGTGGCAATTTCA 1 183 0 ATTCACCTGT 0.985776 -118 AGGTGAATAAATTCTCCTTATAAGTTTTTT 1 195 1 ATTCTCCTTA 0.984663 -106 TTGGAAACCGATTAATCTGTACTACTAATA 1 256 1 ATTAATCTGT 0.854954 -45 ********** Masking position 2 Map Score: 1.16224 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 428 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 TATATTATTAGTAGTACAGATTAATCGGTT 1 261 0 GTAGTACAGA 0.994586 -40 AATATAAGTAGTATTACAGAAATGGA 1 285 1 GTATTACAGA 0.992678 -16 ********** Masking position 5 Map Score: 0.114646 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 = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 ********** No masking Map Score: 7.91135e-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 7 ********** No masking Map Score: 7.91135e-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: 7.91135e-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