AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -iglpR_mthe_opreg_100.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 MTH101 231 unknown #2 MTH853 22 conserved protein #3 MTH855 172 inosine-5'-monophosphate dehydrogenase related protein VIII #4 MTH1143 104 biotin synthetase (BioB) #5 MTH1145 78 conserved protein #6 MTH1147 38 conserved protein #7 MTH1850 105 fumarate reductase Motif number 1 CACAGTGGATATATGTACCTGCAGGTACTTC 1 19 1 ATATGTACTG 0.716332 -213 GTGGCAAATGTGAAGTACCTGCAGGTACATA 1 30 0 TGAAGTACTG 0.711117 -202 ATTAAAATTTTTCTGTTCATGTGGCAAATGT 1 50 0 TTCTGTTCTG 0.989071 -182 CTCTTATTAATTCTGTAGGTGGGTGCTTATG 3 34 1 TTCTGTAGTG 0.942729 -139 GTGCTTATGATTCTTTTGATGTCACACTGAA 3 56 1 TTCTTTTGTG 0.768628 -117 TATACCAGTAATCAGTTCATTTATGGATAGC 3 136 1 ATCAGTTCTT 0.952612 -37 TAACACCAGTTTCAGCTGCTTGGGATTGAAA 4 82 0 TTCAGCTGTT 0.941764 -23 TGTTTTTCTCTGCTGTTCTTTGATGGGGCCT 5 11 0 TGCTGTTCTT 0.951447 -68 TTTTGATCAGCTGTTTCCTGTTATAT 5 63 0 ATCAGCTGTT 0.851841 -16 GCTCTTTCCCTTAAGTTCATGCGTTCCATGT 6 13 0 TTAAGTTCTG 0.95233 -26 TTTCTGCTCTTTCCCTTAAGTT 6 27 0 TTCTGCTCTT 0.969334 -12 ACAATTAAAATTCAGTTCATTCTGAAGTTTT 7 71 1 TTCAGTTCTT 0.982621 -35 ******** ** Masking position 10 Map Score: 12.1447 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 534 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 2 ATTTGCCACATGAACAGAAAAATTTTAATT 1 52 1 TGAACAGAAA 0.864067 -180 ATAATCATTATAAATTGAAGTTTTTTTAGA 1 83 1 TAAATTGAAG 0.886601 -149 ACAAAAGCTTTAAATAGCAGCTATTTTCTA 1 109 0 TAAATAGCAG 0.900893 -123 GTCATCTACATTAATATCAGTTTCTAAATG 1 146 0 TTAATATCAG 0.675227 -86 CCACTGCATGTGAACTTCAGTGTGACATCA 3 72 0 TGAACTTCAG 0.974873 -101 AGTGGTTCTGTGAACTCAAAATATTTAAAT 3 97 1 TGAACTCAAA 0.755859 -76 GAAAAGTCAGTAAATTGAAGTGTAAAAATT 4 56 0 TAAATTGAAG 0.886601 -49 TTTAACACCAGTTTCAGCTGC 4 94 0 TTAACACCAG 0.842372 -11 GCCCCATCAAAGAACAGCAGAGAAAAACAG 5 13 1 AGAACAGCAG 0.936695 -66 ATGGAACGCATGAACTTAAGGGAAAGAGCA 6 15 1 TGAACTTAAG 0.960381 -24 AACTTCAGAATGAACTGAATTTTAATTGTT 7 70 0 TGAACTGAAT 0.832287 -36 ACTCATATGAAAAACTTCAGAATGAACTGA 7 82 0 AAAACTTCAG 0.787672 -24 ********** Masking position 4 Map Score: 9.45162 Number of sites scoring better than the average of aligned sites = 998 Number in coding regions = 893 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 3 GCCACATGAACAGAAAAATTTTAATTAATAATCA 1 56 1 CAAAAATTAA 0.973073 -176 AGCTATTTTCTAAAAAAACTTCAATTTATAATGA 1 87 0 TAAAAATTAA 0.930084 -145 AATGTTACAAGACAAAAGCTTTAAATAGCAGCTA 1 116 0 GAAAAATTAA 0.988404 -116 GAATTAATAAGAGAAACTTTTGAAGGCTGATGGG 3 13 0 GAAAACTTAA 0.985044 -160 GTTCTGTGAACTCAAAATATTTAAATGAACATCC 3 101 1 CTAAAATTAA 0.853675 -72 AAATTACTTGGATAAAAAAATAAATAAATTTTTC 4 27 0 GAAAAAATAA 0.939241 -78 GATTTTAACTGATAATCTTTTAAACAATACAGAC 7 13 0 GAAATCTTAA 0.934989 -93 AATATGTGTTGATAAACAATTAAAATTCAGTTCA 7 56 1 GAAAACTTAA 0.988277 -50 ** **** ** ** Masking position 5 Map Score: 8.21928 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 17 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 ATTAAATAGGTCATCTACATTAATATCAGTT 1 154 0 TCATCTCATT 0.903163 -78 TACACAGATTCCACCAATATTAAATAGGTCA 1 172 0 CCACCATATT 0.816477 -60 TAGATCACCTTCGGTAGAACTGCCC 1 217 0 TCACCTCGGT 0.974108 -15 TTCCCATCAGCCTTCAAAAGTTTC 3 4 1 CCATCACCTT 0.90916 -169 TCATAAGCACCCACCTACAGAATTAATAAGA 3 35 0 CCACCTCAGA 0.945404 -138 ACACTGAAGTTCACATGCAGTGGTTCTGTGA 3 79 1 TCACATCAGT 0.966052 -94 TTATACCACATCCGGTGCTATCCATA 3 157 0 CCACATCGGT 0.974109 -16 AAAAACAGGTCCATAAACAGTATGAACCATA 5 35 1 CCATAACAGT 0.937001 -44 TCAGTTAAAATCACAAACCTTAATATGTGTT 7 35 1 TCACAACCTT 0.88778 -71 ****** **** Masking position 3 Map Score: 5.35138 Number of sites scoring better than the average of aligned sites = 784 Number in coding regions = 720 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 GTACCTGCAGGTACATATATCCACTGTGGT 1 17 0 GTACATATAT 0.779793 -215 CCTTAGAAGGGTACACAGATTCCACCAATA 1 184 0 GTACACAGAT 0.957459 -48 AATATTTTGAGTTCACAGAACCACTGCATG 3 92 0 GTTCACAGAA 0.782141 -81 CTGATTACTGGTATATGGATGTTCATTTAA 3 121 0 GTATATGGAT 0.973135 -52 AGTGTAAAAATTACTTGGATAAAAAAATAA 4 38 0 TTACTTGGAT 0.806579 -67 GGTTCATACTGTTTATGGACCTGTTTTTCT 5 33 0 GTTTATGGAC 0.82681 -46 CTGTTTCCTGTTATATGGTTCATACTGTTT 5 49 0 TTATATGGTT 0.620156 -30 GTACATGGAACGCATGAACT 6 1 1 GTACATGGAA 0.936162 -38 ********** Masking position 2 Map Score: 0.128884 Number of sites scoring better than the average of aligned sites = 769 Number in coding regions = 712 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 ********** No masking Map Score: 1.48036e-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 7 ********** No masking Map Score: 1.48036e-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 8 ********** No masking Map Score: 1.48036e-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