AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i146_NADH-formate_Dehydrogenase_mthe_reg_100.orf -o146_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH00407 249 M.thermo #2 RTH00771 24 M.thermo #3 RTH00911 35 M.thermo #4 RTH01399 41 M.thermo #5 RTH01500 55 M.thermo #6 RTH01705 40 M.thermo #7 RTH01266 139 M.thermo #8 RTH00772 30 M.thermo #9 RTH01355 147 M.thermo #10 RTH01016 118 M.thermo Motif number 1 CTCTACAGAAGATTTAGTAATAAATTTTAAGGATT 1 99 0 GATTTAAAAT 0.970766 -151 GGACCCTTCAGATATCAGTAAAAAAAAGTTTCTGT 1 134 1 GATTGAAAAA 0.976048 -116 GAAACCTCCAGATATTAGTAAAAAAGGCCATAATT 1 172 1 GATTGAAAAA 0.976048 -78 ACCTAAAAAAGACCTCTTAATAAAATTATGGCCTT 1 195 0 GACTTAAAAA 0.969694 -55 ATATAAATCTTTTTAAAAAAGGTGAGTTAG 1 230 0 AATTTAAAAA 0.890948 -20 AAGACATGATGTGGAATGAAAATGGAAGGGAT 5 8 1 GATTATAAAA 0.769979 -48 AAATGGAAGGGATTTAATCAGAAAAGAGGGGATTT 5 30 1 GATTTAAAAA 0.988147 -26 TATCCTCACGTATTTCCTGAAAAATAAAAAAATTG 7 14 0 TATTTAAAAT 0.851589 -126 TTTCTTAATGGACCTCATGAAAACAGTACTGTTTT 7 84 0 GACTTAAACA 0.857664 -56 ATTTTATTACGATTTATATAGAAAACTTTATATTA 9 73 1 GATTAAAAAA 0.963429 -75 TAGAAAACTTTATATTATCATAAATAATCATGTTA 9 91 1 TATTTAAAAT 0.851642 -57 *** * * * **** Masking position 12 Map Score: 11.5437 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 67 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 ATTCCCACCCCATCATGTCCTGGAGGTTCC 1 8 1 CCCCTCATCC 0.995209 -242 CTGTAGAGGGACCCTTCAGATATCAGTAAAAAA 1 126 1 ACCCTCATAT 0.928349 -124 CATTTTCATTCCACATCATGTCTT 5 2 0 CCACTCATCT 0.989249 -54 TAAATCCCCTCTTTTCTGATTAAATCC 5 39 0 TCCCTCTTCT 0.882191 -17 TTCTTTACCTCAGCATTTGCTCTTTATTGA 6 21 0 CCTCGCATGC 0.847627 -20 CAGCTGAGGACCCCCGCAGTTATAATGGATATC 7 45 0 CCCCGCATAT 0.982676 -95 GCCGTAATAACCCCATGAGTCCT 9 1 0 CCCCTGACCT 0.935237 -147 GCAGCCTCTTCCCCTTCAAGTGTTTAATCATCG 9 32 1 CCCCTCATGT 0.993414 -116 ACACCCACCACCTCACATCTAAAAACATAT 10 8 1 CCACTCATCT 0.989815 -111 **** *** *** Masking position 4 Map Score: 8.84818 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 340 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 3 ATGTCCTGGAGGTTCCTATGGAGTCACATCCA 1 25 1 GGTTCCTTGA 0.98822 -225 TCCACTTACCGGTTTCTGTGAATATAATCACG 1 53 1 GGTTTCTTGA 0.975971 -197 ATATCTGAAGGGTCCCTCTACAGAAGATTTAG 1 117 0 GGTCCCTTAA 0.993401 -133 AATATCTGGAGGTTTCTCTACAGAAACTTTTT 1 156 0 GGTTTCTTAA 0.983702 -94 GTTTTCATGAGGTCCATTAAGAAAGATTTATA 7 95 1 GGTCCATAAA 0.895021 -45 ATATTCCACAGGTCCATATATAAATCTTTCTT 7 113 0 GGTCCATTAA 0.976227 -27 ATAATATAAAGTTTTCTATATAAATCGTAATA 9 77 0 GTTTTCTTAA 0.88674 -71 ******* ** * Masking position 12 Map Score: 6.82493 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 160 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 CCCATCATGTCCTGGAGGTTCCTATGGAGT 1 19 1 CCTGGAGGTT 0.994264 -231 TTTACTAATATCTGGAGGTTTCTCTACAGA 1 164 0 TCTGGAGGTT 0.970776 -86 TGAATGAGAACATGGAAGCC 3 1 0 CATGGAAGCC 0.971957 -35 TACTGTTTTACATGGCAGCTGAGGACCCCC 7 63 0 CATGGCAGCT 0.971957 -77 GACTCTTTAACCTGGAGGCTTTGA 10 105 1 CCTGGAGGCT 0.997446 -14 ********** Masking position 3 Map Score: 4.39837 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 369 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 TCATGTCCTGGAGGTTCCTATGGAGTCACAT 1 23 1 GAGGTTCCTT 0.971498 -227 CATCCACTTACCGGTTTCTGTGAATATAATC 1 51 1 CCGGTTTCTT 0.922835 -199 CTAATATCTGGAGGTTTCTCTACAGAAACTT 1 159 0 GAGGTTTCTT 0.976373 -91 ATTTTATTAAGAGGTCTTTTTTAGGTCTAAC 1 204 1 GAGGTCTTTT 0.910672 -46 TGTTCTCATTCAGGATTATTTACGGGG 3 19 1 CAGGATTATT 0.944221 -17 CTGTTTTCATGAGGTCCATTAAGAAAGATTT 7 93 1 GAGGTCCATA 0.81348 -47 GTATATTCCACAGGTCCATATATAAATCTTT 7 116 0 CAGGTCCATT 0.971647 -24 CAATAATTAACATGATTATTTATGATAATAT 9 102 0 CATGATTATT 0.769232 -46 TATTTGAGTTCATGACTCTTTAACCTGGAGG 10 92 1 CATGACTCTT 0.871908 -27 ********* * Masking position 9 Map Score: 4.097 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 526 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 TAGGTCTAACTCACCTTTTTTAAAAAGATTTAT 1 225 1 TCACTTTTAA 0.96469 -25 TAAATCCCCTCTTTTCTGATTAAATCC 5 39 0 TCCCTTTTCT 0.953825 -17 TTTCAATTTTTTTATTTTTCAGGAA 7 3 1 TCAATTTTAT 0.965911 -137 ATGGATATCCTCACGTATTTCCTGAAAAATAAA 7 21 0 TCACTTTTCT 0.976884 -119 AATTCCTCACCTGTTAGATTCCTCATTTT 8 12 0 TCACTTTAAT 0.96469 -19 CTCTTCCCCTTCAAGTGTTTAATCATCGGATCC 9 37 1 TCAATTTTAT 0.965911 -111 AATCATCGGATCCCCTATTTTATTACGATTTAT 9 57 1 TCCCTTTTAT 0.976884 -91 ACCCACCACCTCACATCTAAAAACATATATCCA 10 13 1 TCACTTAAAA 0.731776 -106 AGTCATGAACTCAAATATATTATAGATTAAGGA 10 76 0 TCAATTATAT 0.899538 -43 **** * *** ** Masking position 6 Map Score: 9.96876 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 84 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 ********** No masking Map Score: -6.939e-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: -6.939e-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: -6.939e-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