AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i146_NADH-formate_Dehydrogenase_mthe_reg_300.orf -o146_mthe_300.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 RTH00695 300 M.thermo #9 RTH00772 30 M.thermo #10 RTH01355 147 M.thermo #11 RTH00374 143 M.thermo #12 RTH01852 135 M.thermo #13 RTH01016 118 M.thermo Motif number 1 TATCAGTAAAAAAAAGTTTCTGTAGAGAAACCTC 1 146 1 AAAATTCTTA 0.739456 -104 AATCTTTTTAAAAAAGGTGAGTTAGACCTAAAAA 1 221 0 AAAAGTAGTA 0.699789 -29 CCCCGTAAATAATCCTGAATGAGAACATG 3 17 0 TAAAATCTAA 0.627027 -19 GGTCCATATATAAATCTTTCTTAATGGACCTCAT 7 101 0 TAAATTCTAA 0.929442 -39 AAAGCCCTTTAAACGTTTCAGAAAAATTCTGAAT 8 44 0 AAACTTAGAA 0.818238 -257 CAAGAAATTAAAAATTTTTATAAATATAACGGCA 8 83 0 AAAATTATAA 0.935883 -218 AAATGCAGATAAAATATTCATTAATTATGCAATA 8 140 1 AAAATTATAA 0.935876 -161 AATTATGCAATAACGCGTGATGAATGTATTAAAT 8 162 1 TAACGTATAA 0.91581 -139 ATGAATGTATTAAATTTTCATATAATTATTACTT 8 181 1 TAAATTATTA 0.892708 -120 CTTGCTCTAATAAAAATTAAGTAATAATTATATG 8 199 0 TAAATTAGAA 0.929793 -102 ATATGTAATAAAAAAATTAATAAAAAGTCTTAAA 8 234 1 AAAATTATAA 0.935883 -67 ATGAGGAATCTAACAGGTGAGGAATT 9 15 1 TAACGTAGAA 0.857978 -16 GTTTTCTATATAAATCGTAATAAAATAGGGGATC 10 65 0 TAAAGTATAA 0.951422 -83 TATGATAATATAAAGTTTTCTATATAAATCGTAA 10 79 0 TAAATTCTTA 0.822434 -69 AAGATCTGTTTAACTGTTAATCAAAGATGGATAT 13 39 0 TAACTTATAA 0.929795 -80 GCCTCCAGGTTAAAGAGTCATGAACTCAAATATA 13 90 0 TAAAGTATAA 0.951425 -29 **** ** ** ** Masking position 8 Map Score: 16.2387 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 49 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 2 CAGATATCAGTAAAAAAAAGTTTCTGTAGAGA 1 142 1 TAAAAAAATT 0.757384 -108 AAAGACCTCTTAATAAAATTATGGCCTTTTTT 1 191 0 TAATAAATAT 0.903483 -59 GAATATATAGATGATTACTGGT 2 1 1 GAATAATAAT 0.704552 -24 GTTTATGATAATAGAATCATTCCGGTGTTA 4 9 1 TAATAAATAT 0.903487 -33 ATTTCCTGAAAAATAAAAAAATTGAAA 7 6 0 AAATAAAAAT 0.822703 -134 GCCGTTATATTTATAAAAATTTTTAATTTCTT 8 84 1 TTATAAAATT 0.517644 -217 CATACATCGGTAATACATAAATGCAGATAAAA 8 122 1 TAATAATAAT 0.942405 -179 TAAATGCAGATAAAATATTCATTAATTATGCA 8 139 1 TAAAAATTAT 0.587586 -162 TATGAAAATTTAATACATTCATCACGCGTTAT 8 171 0 TAATAATTAT 0.851397 -130 AAAAATTAAGTAATAATTATATGAAAATTTAA 8 190 0 TAATATTAAT 0.582844 -111 ATTCTTGCTCTAATAAAAATTAAGTAATAATT 8 204 0 TAATAAAATA 0.534092 -97 CAAGAATATGTAATAAAAAAATTAATAAAAAG 8 229 1 TAATAAAAAT 0.963947 -72 ATAAAAAAATTAATAAAAAGTCTTAAATAATC 8 241 1 TAATAAAATC 0.630065 -60 TTATTTATGATAATATAAAGTTTTCTATATAA 10 86 0 TAATAAAATT 0.926175 -62 TATAGTGCTGTAATAAAAACATGAGCGTATCA 12 30 0 TAATAAAAAT 0.963947 -106 CCTCACATCTAAAAACATATATCCATCTTTGA 13 21 1 AAAAAATAAT 0.413592 -98 ***** *** ** Masking position 5 Map Score: 10.6706 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 41 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 3 AACCTCCAGGACATGATGGGGTGGGAAT 1 8 0 ACATGATGGG 0.976606 -242 AAGACATGATGTGGAATGAAAATG 5 4 1 ACATGATGGG 0.976606 -52 AATAAAGAGCAAATGCTGAGGTAAAGAA 6 23 1 AAATGCTGGG 0.962802 -18 TATCCATTATAACTGCGGGGGTCCTCAGCTG 7 47 1 AACTGCGGGG 0.988243 -93 TCGATCAATCAACTGAAGAGGCCATTTAGTG 8 14 0 AACTGAAGGG 0.959218 -287 ATGATTAAACACTTGAAGGGGAAGAGGCTGC 10 32 0 ACTTGAAGGG 0.920195 -116 GTTAATTGATGCCTGCGGAGGTTTATAA 11 126 1 GCCTGCGGGG 0.982794 -18 AAATCCGTATACCTGCGGCAGGTGGGACATA 12 90 0 ACCTGCGGAG 0.960023 -46 ******** ** Masking position 4 Map Score: 8.47476 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 286 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 CCCATCATGTCCTGGAGGTTCCTATGGAGTCA 1 19 1 CCGGAGGTCC 0.976124 -231 TTTACTGATATCTGAAGGGTCCCTCTACAGAA 1 124 0 TCGAAGGTCC 0.966915 -126 TTTACTAATATCTGGAGGTTTCTCTACAGAAA 1 162 0 TCGGAGGTTC 0.992567 -88 ATGTTCTCATTCAGGATTATTTACGGGG 3 18 1 TCGGATTTTT 0.803323 -18 ACCATTAACACCGGAATGATTCTATTATCATA 4 14 0 CCGAATGTTC 0.968099 -28 ATTGATCGATTCAGAATTTTTCTGAAACGTTT 8 36 1 TCGAATTTTC 0.923229 -265 TTATAAACCTCCGCAGGCATCAATTAACCTC 11 123 0 TCGCAGGATC 0.811617 -21 CATGAGCGTATCAGAATGATTCCATTTATAAG 12 11 0 TCGAATGTTC 0.977075 -125 GCCGCAGGTATACGGATTTTTCCGGAAGTGGG 12 102 1 TAGGATTTTC 0.673657 -34 GACTCTTTAACCTGGAGGCTTTGA 13 105 1 CCGGAGGTTT 0.942649 -14 ** ***** *** Masking position 6 Map Score: 7.8389 Number of sites scoring better than the average of aligned sites = 587 Number in coding regions = 548 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 ATAAATTTTAAGGATTTTCATAGTCGTTTTC 1 84 0 AGGATTTCAT 0.913302 -166 TGAAAATGGAAGGGATTTAATCAGAAAAGAG 5 27 1 AGGGTTTAAT 0.972067 -29 AAACGTTTAAAGGGCTTTAACCTTGCCGTTA 8 60 1 AGGGTTTAAC 0.986278 -241 TAAAATGAGGAATCTAACAGGTGAGGAA 9 8 1 AGGATCTAAC 0.948224 -23 AGCGACTCAGAGAAATTTAACC 11 2 0 AGAATTTAAC 0.941984 -142 CTGGAATCCCAGAAATTTAACCTCAAAGTCA 11 68 0 AGAATTTAAC 0.941984 -76 CTGGGATTCCAGGGTTTTGATGCTGTATTCT 11 87 1 AGGGTTTGAT 0.927139 -57 **** ****** Masking position 10 Map Score: 3.54571 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 71 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 GTGGATGTGACTCCATAGGAACCTCCAGGACAT 1 25 0 CTCATAGACC 0.931262 -225 ACTAAATCTTCTGTAGAGGGACCCTTCAGATAT 1 116 1 CTGAGAGACC 0.97638 -134 AAAAAAGTTTCTGTAGAGAAACCTCCAGATATT 1 155 1 CTGAGAGACC 0.97638 -95 CCCCTCTTTTCTGATTAAATCCCTTCCATTTTC 5 28 0 CTGTTAACCC 0.734288 -28 TTTTACATGGCAGCTGAGGACCCCCGCAGTTAT 7 55 0 CAGTGAGCCC 0.931413 -85 CAGTACTGTTTTCATGAGGTCCATTAAGAAAGA 7 88 1 TTCTGAGCCA 0.944678 -52 ATCGTATATTCCACAGGTCCATATATAAATC 7 119 0 TTCACAGCCA 0.691576 -21 AATTTTTAATTTCTTGAGTTACATACATCGGTA 8 101 1 TTCTGAGACA 0.914588 -200 TAGCTCCCTTCTCTTTAGTACCAATAATTAACA 10 121 0 CTCTTAGCCA 0.952003 -27 GCCGGCCTTACTGGTGAGCAACATCGCTGCAGC 11 30 0 CTGTGAGACA 0.974326 -114 *** **** *** Masking position 7 Map Score: 3.77632 Number of sites scoring better than the average of aligned sites = 882 Number in coding regions = 837 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 TAATAAAATTATGGCCTTTTTTACTAATAT 1 183 0 ATGGCCTTTT 0.916259 -67 TAAATCCCCTCTTTTCTGATTAA 5 43 0 ATCCCCTCTT 0.982788 -13 ATCGTATATTCCACAGGTCC 7 130 0 ATCGTATATT 0.734394 -10 TGGCACTAAATGGCCTCTTCAGTTGATTG 8 10 1 ATGGCCTCTT 0.967579 -291 TAATCATCGGATCCCCTATTTTATTACGAT 10 56 1 ATCCCCTATT 0.981445 -92 CTTATAACTTATCCCATATTAATATCTATA 12 58 0 ATCCCATATT 0.947014 -78 ********** Masking position 7 Map Score: 1.84991 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 57 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 ATATAAATCTTTTTAAAAAA 1 240 0 ATATAAATCT 0.963 -10 ACAGGTCCATATATAAATCTTTCTTAATGG 7 108 0 ATATAAATCT 0.963 -32 TTCTTGAGTTACATACATCGGTAATACATA 8 111 1 ACATACATCG 0.932579 -190 AAAGTTTTCTATATAAATCGTAATAAAATA 10 72 0 ATATAAATCG 0.966024 -76 CTAAAAACATATATCCATCTTTGATTAACA 13 29 1 ATATCCATCT 0.927201 -90 ********** Masking position 4 Map Score: 1.44439 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 13 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 CAGAAAAATTCTGAATCGATCAATCAACTGA 8 29 0 CTGATCGATC 0.978434 -272 TTAAATTTCTCTGAGTCGCTGCAGCGATGTT 11 13 1 CTGATCGCTG 0.992926 -131 ATGCTGTATTCTGACTTGAGGTTAATTGATG 11 106 1 CTGATTGAGG 0.92964 -38 TGGAATCATTCTGATACGCTCATGTTTTTAT 12 19 1 CTGAACGCTC 0.968815 -117 CTGAATTGCTGGCCCACTTCC 12 125 0 CTGATTGCTG 0.984916 -11 **** ****** Masking position 4 Map Score: 1.31999 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 21 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 GGCTTCCATGTTCTCATTCAG 3 2 1 GCTTCCATGT 0.989429 -34 TGATTAAATCCCTTCCATTTTCATTCCACA 5 20 0 CCTTCCATTT 0.931739 -36 GGGGTCCTCAGCTGCCATGTAAAACAGTAC 7 64 1 GCTGCCATGT 0.987278 -76 ATCAACTGAAGAGGCCATTTAGTGCCA 8 8 0 GAGGCCATTT 0.882526 -293 GTATCAGAATGATTCCATTTATAAG 12 6 0 GATTCCATTT 0.952642 -130 TCAAAGCCTCCAGGTTAAAGAGTCA 13 104 0 GCCTCCAGGT 0.93907 -15 ********** Masking position 7 Map Score: 1.8512 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 104 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 TATTCACAGAAACCGGTAAGTGGATGTGAC 1 47 0 AACCGGTAAG 0.943601 -203 TCACCAGTAATCATCTATATA 2 14 0 CACCAGTAAT 0.978004 -11 CTCATCACCATTAACACCGGAATGA 4 27 0 CACCATTAAC 0.852541 -15 GAGTTACATACATCGGTAATACATAAATGC 8 116 1 CATCGGTAAT 0.881313 -185 AATTCCTCACCTGTTAGATTCCTCATT 9 14 0 CACCTGTTAG 0.90725 -17 CGATGTTGCTCACCAGTAAGGCCGGCGCCA 11 37 1 CACCAGTAAG 0.990117 -107 ********** Masking position 7 Map Score: 1.29229 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 190 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 ********** No masking Map Score: 2.67407e-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 13 ********** No masking Map Score: 2.67407e-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 14 ********** No masking Map Score: 2.67407e-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