AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00020_hpyl_reg_100.orf -o00020_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0026_HP0027 198 HP0026: citrate synthase (gltA), HP0027: isocitrate dehydrogenase (icd) #2 HP0193 214 fumarate reductase, cytochrome b subunit (frdC) #3 HP0779 127 aconitase B (acnB) #4 HP1325 174 fumarase (fumC) Motif number 1 TTTTTAAGGGTTATATAGTATTTTTGCGCTAGTATA 1 41 0 TTATTTTTTG 0.697037 -158 TATATAACCCTTAAAAATCTTTTTTTGAATGCGTGT 1 60 1 TTAATTTTTT 0.980777 -139 ATTTCTTTTAAAAACATTGCGTTTTTTCAAGTTATT 1 114 0 AAAAGTTTTT 0.68018 -85 AGCCAAAAAATTAAATGATTTCTTTTAAAAACATTG 1 131 0 TTAATCTTTT 0.964031 -68 TGAACGATCCTTATTTTATAGGTGGT 2 1 1 TGAATTATTT 0.729518 -214 GCTATTGTTTAAAATTTACATTTTTTAAACGCTATT 2 57 0 AAAATTTTTT 0.913236 -158 AATAGCCCCTTTGAATTGAATTTTTTCTCAATTTAG 2 87 1 TTGATTTTTT 0.903189 -128 GGTTTTGTTTATAAGAAAAATTATTTCAAATGTAGT 2 122 1 ATAATTATTT 0.906313 -93 TGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAAGCG 2 152 1 TTAAGTTTTT 0.964099 -63 CGATTTTAGGTTAATTTTGAGTTTTTAGGAGCAGTT 2 186 1 TTAAGTTTTT 0.964141 -29 TTAAAATCCTTTTTTGTATCGCATGG 3 1 1 TTAATTTTTG 0.963906 -127 TTGCCCCATGATAACAAAACTCTTTTTACTTTTAGT 3 60 0 ATAATCTTTT 0.938041 -68 TTCTCCTTTTTAAATCGCATTATTGACTAATGCCC 3 103 0 TTAATTATTG 0.869907 -25 TTGCGAACGGATAATAACCCTCTTTTGTGTAAAAAT 4 50 1 ATAATCTTTT 0.938041 -125 CTTCTACTTAAAAACCCTAATTTTTTAAACACCATT 4 92 0 AAAATTTTTT 0.840883 -83 GGTATAAGAGTTTATGCTATTTTTTTAAGGTTTTAA 4 127 1 TTTATTTTTT 0.862916 -48 **** ****** Masking position 14 Map Score: 18.032 Number of sites scoring better than the average of aligned sites = 1371 Number in coding regions = 1069 Number in noncoding regions = 302 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 2 ATTCAAAAAAAGATTTTTAAGGGTTATATA 1 60 0 AGATTTTTAA 0.610888 -139 TTTTGAATGCGTGTTTAAAAGTAGCGGTTG 1 82 1 GTGTTTAAAA 0.909839 -117 AAAAAACGCAATGTTTTTAAAAGAAATCAT 1 123 1 ATGTTTTTAA 0.920026 -76 TTTAATTTTTTGGCTTATAATTAGGAGTTG 1 152 1 TGGCTTATAA 0.835433 -47 ATATCTAATAGCGTTTAAAAAATGTAAATT 2 51 1 GCGTTTAAAA 0.786774 -164 AAAGGGGCTATTGTTTAAAATTTACATTTT 2 69 0 TTGTTTAAAA 0.911462 -146 AATTTAGGTTTTGTTTATAAGAAAAATTAT 2 116 1 TTGTTTATAA 0.934064 -99 GATACAAAAAAGGATTTTAA 3 1 0 AGGATTTTAA 0.73546 -127 TAACCCTCTTTTGTGTAAAAATTGTGGAAA 4 64 1 TTGTGTAAAA 0.781085 -111 ATTGTGGAAATGGTGTTTAAAAAATTAGGG 4 84 1 TGGTGTTTAA 0.903312 -91 TAAAAAATTAGGGTTTTTAAGTAGAAGGTA 4 101 1 GGGTTTTTAA 0.963534 -74 TATTTTTTTAAGGTTTTAAAATCAAATTTC 4 144 1 AGGTTTTAAA 0.940807 -31 ********** Masking position 9 Map Score: 10.5369 Number of sites scoring better than the average of aligned sites = 1559 Number in coding regions = 1330 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 3 TTGACTTCCTTAAGTTTTGATAG 1 186 0 ACTTCCTTAA 0.864761 -13 TCTTATAAACAAAACCTAAATTGAGAAAAA 2 108 0 AAAACCTAAA 0.946551 -107 ACGCAAAAACACTGCCTTAATTCTACTACA 2 152 0 ACTGCCTTAA 0.945773 -63 ACTGCTCCTAAAAACTCAAAATTAACCTAA 2 191 0 AAAACTCAAA 0.735028 -24 ATTATTGACTAATGCCCTAATCGTTTGCCC 3 90 0 AATGCCCTAA 0.96904 -38 CTTCTACTTAAAAACCCTAATTTTTTAAAC 4 98 0 AAAACCCTAA 0.980064 -77 ATTTGATTTTAAAACCTTAAAAAAATAGCA 4 141 0 AAAACCTTAA 0.976024 -34 ********** Masking position 9 Map Score: 4.86122 Number of sites scoring better than the average of aligned sites = 919 Number in coding regions = 822 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 4 AAACTTTAGAAAAAGGATAAACA 1 4 0 AAAAGGATAA 0.97636 -195 TGCGATACAAAAAAGGATTTTAA 3 4 0 AAAAGGATTT 0.88028 -124 TATCATGGGGCAAACGATTAGGGCATTAGT 3 83 1 CAAACGATTA 0.821405 -45 CTCCTTTTTAAATCGCATTATTGACTAATG 3 106 0 AATCGCATTA 0.751811 -22 ATGCGATTTAAAAAGGAGAA 3 118 1 AAAAGGAGAA 0.916461 -10 TTCTTGTTGCGAACGGATAATAACCCTCTT 4 44 1 GAACGGATAA 0.89531 -131 ACCTTAAAAAAATAGCATAAACTCTTATAC 4 128 0 AATAGCATAA 0.84251 -47 AATCAAATTTCAAAGGATTAGC 4 163 1 CAAAGGATTA 0.965259 -12 ********** Masking position 7 Map Score: 2.84836 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 391 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 5 TAGGAGTTGAATGCTATCAAAACTTAAGGAAG 1 173 1 ATGTACAAAA 0.987558 -26 TTTGTATCGCATGGTAGCTAAAGTTTCTTACA 3 23 1 ATGTACTAAA 0.982268 -105 AGTTTCTTACAACTTAACTAAAAGTAAAAAGA 3 44 1 AACTACTAAA 0.916526 -84 CGTTTGCCCCATGATAACAAAACTCTTTTTAC 3 67 0 ATGTACAAAA 0.987558 -61 CCTTTACATTAAGATAACAAGAAAATTCTTGT 4 19 1 AAGTACAAGA 0.961471 -156 *** ** ***** Masking position 6 Map Score: 1.63502 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 46 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 ********** No masking Map Score: -2.32047e-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: -2.32047e-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: -2.32047e-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