AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_mthe_reg_100.orf -o00760_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 MTH1193 146 transcriptional regulator #2 MTH1194 35 acetylpolyamine aminohydolase #3 MTH1492 51 5'-nucleotidase #4 MTH1493 78 cation transporting P-type ATPase related protein #5 MTH1494 266 conserved protein #6 MTH1510 109 NH(3)-dependent NAD+ synthetase #7 MTH1639 163 cell division control protein Cdc48 #8 MTH1832 92 quinolinate phosphoribosyltransferase Motif number 1 ATCTTCAGATAAACATTTATAAGGGAACAT 1 37 1 AAACATTTAT 0.966934 -110 AAGAAGTCATCAACTTTTATAAGATAGGGG 1 67 0 CAACTTTTAT 0.911795 -80 GACTTCTTCTAAACTTATATTCACTTAAAA 1 89 1 AAACTTATAT 0.977866 -58 GTTATATTATAAAGTTTTTTAAGTGAATAT 1 105 0 AAAGTTTTTT 0.808025 -42 TATGCCTATGAAAGTTATATTATAAAGTTT 1 118 0 AAAGTTATAT 0.967657 -29 ATACCATAAAAAACATATATTGGTCCG 4 62 1 AAACATATAT 0.966934 -17 AGAGGTAGAAAAACTTATATCAGTGATGCT 6 49 0 AAACTTATAT 0.977866 -61 ACCTCTTTTGATAGTTATATAAAATATACC 6 73 1 ATAGTTATAT 0.808025 -37 AACTTTACCGAAACATTTATATATGATTAC 7 56 1 AAACATTTAT 0.966934 -108 CTTCTGGACATAAGATTTATAATTCTTCCA 8 49 1 TAAGATTTAT 0.763274 -44 ********** Masking position 6 Map Score: 13.44 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 20 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 CATTTTCTGATTCAGGGGATAAATAAT 2 8 0 TTCAGGGGAT 0.891983 -28 AAACACCCCCCTTACAGGTTTTAACC 3 7 0 CTTACAGGTT 0.893188 -45 ATGGGTCTCGCTTACAGGTGCCACTGTATC 4 18 1 CTTACAGGTG 0.915009 -61 TATTAAGATTTTGAGAGGATACAGTGGCAC 4 35 0 TTGAGAGGAT 0.983467 -44 TGGTCCATCCTTGTGAGGAGTTCATTCATA 5 120 0 TTGTGAGGAG 0.923504 -147 GACCATGTCTTCGAGAGGATGAGGATAGTT 5 145 1 TCGAGAGGAT 0.932877 -122 CTCATTATCTCTGAGAGGTGGTGGTCTATC 5 213 0 CTGAGAGGTG 0.970705 -54 GATGATTAATTTTACAGGAGGAGTATA 6 8 0 TTTACAGGAG 0.961363 -102 TTTATATTAATTTAGGGGATCTTT 8 79 1 TTTAGGGGAT 0.94827 -14 ********** Masking position 7 Map Score: 7.1263 Number of sites scoring better than the average of aligned sites = 789 Number in coding regions = 737 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 GAAAATAAAAAAGGAGGGTAATTA 1 2 0 AAGGGGAATT 0.98671 -145 TGTTTATCTGAAGATGGGAAAATAAAAAAGGAG 1 19 0 AAGGGGAAAT 0.953787 -128 CAACTTTTATAAGATAGGGGATGTTCCCTTATA 1 54 0 AAGAGGGATG 0.924331 -93 TAAAACCTGTAAGGGGGGTGTTTTATGGCTGAA 3 14 1 AAGGGGGTTT 0.981689 -38 GGTCCCTTAAAAGAGAAGAGATCGAAGAGATAG 5 185 1 AAGAAGGATC 0.894397 -82 GATACAACTGAAGCCGTGGAATC 5 254 1 AAGGTGAATC 0.914341 -13 GGTTAAAAGTAAGTAGGGTATATTTTATATAAC 6 86 0 AAGGGGATAT 0.903339 -24 AGATCTGCAAAAGAAGAGCATTTATGAAAGAGT 8 14 0 AAGGAGATTT 0.868768 -79 ATCTTATGTCCAGAAGGGAGATCTGCAAAAGAA 8 32 0 CAGGGGGATC 0.969503 -61 CATTTATATTAATTTAGGGGATCTTT 8 77 1 AATAGGGATC 0.789813 -16 *** *** **** Masking position 2 Map Score: 5.67977 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 290 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 AACATTTATAAGGGAACATCCCCTATCTTAT 1 48 1 AGGGAACTCC 0.989618 -99 TATCGGCGGCAGGGTGCCTCCAG 5 3 0 AGGGTGCTCC 0.99328 -264 TCATAGTATAAGGATCCTTCCAGTCATCTGT 5 40 0 AGGATCCTCC 0.984121 -227 ACGTCCTGGTGGGGTACATGCTATCAGCTCC 5 88 0 GGGGTACTGC 0.971421 -179 TCTCGAAGACATGGTCCATCCTTGTGAGGAG 5 130 0 ATGGTCCTCC 0.984125 -137 TTCTCTTTTAAGGGACCTTGTCCGGCTAACT 5 171 0 AGGGACCTGT 0.945553 -96 ******* *** Masking position 9 Map Score: 3.60248 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 352 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 TTTCCCATCTTCAGATAAACATTTATAAGGGA 1 31 1 TCATAAACAT 0.814047 -116 TGAATCAGAAAATGATAACCAT 2 24 1 AAATAACCAT 0.917851 -12 TGTAAGCGAGACCCATAAACATC 4 2 0 ACATAAACAT 0.954723 -77 GCACCCTGCCGCCGATAATCATCACAGATGAC 5 17 1 GCATAATCAT 0.937165 -250 CTCCTCCTGTAAAATTAATCATCGATCCAAGA 6 15 1 AATTAATCAT 0.882478 -95 TAATACATGTACAGGTAATCATATATAAATGT 7 68 0 ACGTAATCAT 0.970247 -96 ATTAAATATCAACCGGAATCATAATAATAATC 7 134 1 AAGGAATCAT 0.845245 -30 CCGGAATCATAATAATAATCATAAAGAG 7 146 1 AAATAATCAT 0.968297 -18 ** ******** Masking position 7 Map Score: 2.70996 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 44 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 CCCCTGAATCAGAAAATGATAACCAT 2 20 1 AGAAAATGAT 0.947098 -16 CTAGATTATGCTCAGTTCAGCC 3 40 0 AGATTATGCT 0.867434 -12 TATGGTATTAAGATTTTGAGAGGATACAGT 4 40 0 AGATTTTGAG 0.937966 -39 TATGAGTGATAGAAATTGATATGGAGCTGA 5 66 1 AGAAATTGAT 0.905654 -201 CATGTCTTCGAGAGGATGAGGATAGTTAGC 5 148 1 AGAGGATGAG 0.932926 -119 CACCTCTCAGAGATAATGAGGATACTGAAC 5 223 1 AGATAATGAG 0.975859 -44 ********** Masking position 7 Map Score: 0.599795 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 150 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 GATAAACATTTATAAGGGAACATCCCCTAT 1 44 1 TATAAGGGAA 0.911389 -103 TATAAAGTTTTTTAAGTGAATATAAGTTTA 1 98 0 TTTAAGTGAA 0.874034 -49 ATCCTTATACTATGAGTGATAGAAATTGAT 5 56 1 TATGAGTGAT 0.955121 -211 CCAGGACGTATATGAATGAACTCCTCACAA 5 110 1 TATGAATGAA 0.93064 -157 GAAAAACTTATATCAGTGATGCTGATCTTG 6 42 0 TATCAGTGAT 0.92041 -68 CCGAAACATTTATATATGATTACCTGTACA 7 63 1 TATATATGAT 0.720702 -101 CCTAAATTAATATAAATGGAAGAATTATAA 8 65 0 TATAAATGGA 0.832773 -28 ********** Masking position 3 Map Score: 0.735978 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 122 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 ********** No masking Map Score: 1.21035e-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: 1.21035e-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: 1.21035e-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