AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00052_mthe_reg_100.orf -o00052_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 MTH373 142 dTDP-glucose 4,6-dehydratase related protein #2 MTH375 26 UDP-glucose 4-epimerase related protein #3 MTH380 107 UDP-glucose 4-epimerase homolog #4 MTH631 143 UDP-glucose 4-epimerase #5 MTH661 119 ammonium transporter #6 MTH662 61 nitrogen regulatory protein P-II #7 MTH663 205 ammonium transporter Motif number 1 TAAAGATTTCCTTCCCACAATATACGATTCA 1 103 0 CTTCCACAAT 0.996804 -40 TCACCTTCCATCAGTAGATTCTGCA 2 12 0 CTTCCTCAGT 0.945057 -15 CCACAAAGACCTACCCACAAAAACAGGCCAC 4 67 1 CTACCACAAA 0.953411 -77 TTCCGAAAATCTACCAACATTATAAATATCA 5 33 0 CTACCACATT 0.959527 -87 CGGTAACCTACTTCCGAAAATCTACCAACAT 5 44 0 CTTCCAAAAT 0.972093 -76 AGGAAGGTAACTTCCGACAATGAGAGTAAGA 7 130 0 CTTCCACAAT 0.996804 -76 TACCTTCCTATTTCCGACTATGATATAAATT 7 152 1 TTTCCACTAT 0.927462 -54 ATATTTTTTCTCTCCAACAATTTATATCATA 7 170 0 TCTCCACAAT 0.949875 -36 ***** ***** Masking position 5 Map Score: 10.7742 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 47 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 2 TTTCATGCCTACAGATCACCATCTGAAGCATTAA 3 10 0 ACAGATCCTG 0.91516 -98 TGAAAACCGCTCAAATCAACGGATAAGACTGATCA 3 40 1 TCAAATAATA 0.767901 -68 AACGGATAAGACTGATCAAATACTGACCGATATCA 3 57 1 ACTGATACTG 0.911228 -51 AACATCACCTCAGATTAATATATGAAATCAGACC 4 10 1 TCAGATAATG 0.981792 -134 ATGAAATCAGACCATTAAAGCTATGCAAAGGCAGA 4 32 1 ACCATTAATG 0.672068 -112 AGAAATATAGACAGAATCATATCTGTGTGATAAA 4 120 1 ACAGAAACTG 0.95801 -24 ATCTGCAATCACCAATATAAGGATGCCGGTAACCT 5 66 0 ACCAATAATG 0.941621 -54 ACACAGATTTAAACATGGTTCACAGAA 6 3 1 ACAGATAATG 0.989184 -59 AACATGGTTCACAGAAGTACTTATAAGAAATCCGG 6 22 1 ACAGAAAATA 0.900232 -40 GGATATAGTTTCAGATAAATGTATGCTGAGTAAAA 7 72 0 TCAGATAATG 0.981792 -134 TGAAACTATATCCGAAAGATTTATATATCAGCATC 7 94 1 TCCGAAAATA 0.791142 -112 ****** * *** Masking position 14 Map Score: 7.67456 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 240 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 CTCGCCATATAAATAGTTTCAATCTGTTAAGCGA 1 33 0 AATGTTTATC 0.979497 -110 CGAGTTCAATAACTAGTTTGAGTTAAACTAGGAT 1 63 1 AATGTTTATT 0.975214 -80 TGCATAGCTTTAATGGTCTGATTTCATATATTAA 4 25 0 TATGTCTATT 0.971969 -119 CTCTCTACTTTTTTTATTCTCATGATATT 5 6 1 TATTTTTATC 0.944387 -114 TAAATAAAAATAATTGTTTAATTTC 7 2 0 TATGTTTATT 0.98096 -204 TTATTATCTAAACTTGTTTTACTCAGCATACATT 7 56 1 AATGTTTATC 0.979497 -150 ATATTGTTCTTAATTATATTTTTTC 7 191 0 TATTTCTATT 0.904413 -15 ** * **** * ** Masking position 11 Map Score: 4.8168 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 4 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 TTTATTCATTCATATCATGAATA 1 130 1 CATATCATAA 0.888953 -13 TTCATGCCTACAGATCACCATCTGAAGCATT 3 13 0 CAGATCACAT 0.966221 -95 TATATGAAATCAGACCATTAAAGCTATGCAA 4 29 1 CAGACCATAA 0.989488 -115 TATGCAAAGGCAGACCACAAAGACCTACCCA 4 53 1 CAGACCACAA 0.995307 -91 CCCACAAAAACAGGCCACCAAACCTTATTTA 4 80 1 CAGGCCACAA 0.989641 -64 ******** ** Masking position 7 Map Score: 3.55281 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 29 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 TAGGATATACTCTGAATCGTATATTGTGGGAA 1 91 1 TCTGAATGTT 0.887161 -52 AACATCACCTCAGATTAATATATGAAATCAG 4 10 1 TCAGATTATT 0.944623 -134 TTACATGTTAACAGAAATATAGACAGAATCAT 4 108 1 ACAGAAAATG 0.842966 -36 AGAAATATAGACAGAATCATATCTGTGTGATA 4 120 1 ACAGAATATT 0.965814 -24 AACCTCAATTACTGAAATATGTTAAATAAAAA 7 26 0 ACTGAAAATT 0.933742 -180 GGATATAGTTTCAGATAAATGTATGCTGAGTA 7 75 0 TCAGATAATT 0.932609 -131 TGAAACTATATCCGAAAGATTTATATATCAGC 7 94 1 TCCGAAAATT 0.94125 -112 GATTTATATATCAGCATCATCTTACTCTCATT 7 111 1 TCAGCATATT 0.926537 -95 ATATTGTTCTTAATTATATTTTTTCTCTC 7 187 0 TCTTAATATT 0.767328 -19 ******* ** * Masking position 10 Map Score: 3.35535 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 109 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 AACTCGCCATATAAATAGTTTCAATCTGTT 1 39 0 ATAAATAGTT 0.968277 -104 GGCGAGTTCAATAACTAGTTTGAGTTAAAC 1 61 1 ATAACTAGTT 0.962019 -82 TCATGAGAATAAAAAAAGTAGAGAG 5 6 0 AAAAAAAGTA 0.801586 -114 TATGTTAAATAAAAATAATTGTTTAATTTC 7 11 0 AAAAATAATT 0.824833 -195 TATGCTGAGTAAAACAAGTTTAGATAATAA 7 56 0 AAAACAAGTT 0.931392 -150 CGACTATGATATAAATTGTTGGAGAGAAAA 7 166 1 ATAAATTGTT 0.882287 -40 ********** Masking position 4 Map Score: 1.54077 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 13 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 7 TATTCATGATATGAATGAATAA 1 131 0 TTCATGATAT 0.690096 -12 AATGGTCTGATTTCATATATTAATCTGAGG 4 18 0 TTTCATATAT 0.739533 -126 TCTGTCTATATTTCTGTTAACATGTAAATA 4 105 0 TTTCTGTTAA 0.723099 -39 GTTGGTAGATTTTCGGAAGTAGGTTACCGG 5 46 1 TTTCGGAAGT 0.618815 -74 ATATTGGTGATTGCAGATATGTTAGGCACA 5 83 1 TTGCAGATAT 0.943996 -37 CTTAACCGGATTTCTTATAAGTACTTCTGT 6 32 0 TTTCTTATAA 0.618232 -30 AGAAATCCGGTTAAGGATATTTAAG 6 47 1 TTAAGGATAT 0.773286 -15 ATAACCTCAATTACTGAAATATGTTAAATA 7 30 0 TTACTGAAAT 0.728922 -176 ATTTCAGTAATTGAGGTTATTATCTAAACT 7 40 1 TTGAGGTTAT 0.632608 -166 TCGGATATAGTTTCAGATAAATGTATGCTG 7 79 0 TTTCAGATAA 0.87901 -127 TATATAAATCTTTCGGATATAGTTTCAGAT 7 91 0 TTTCGGATAT 0.976855 -115 GAGTAAGATGATGCTGATATATAAATCTTT 7 108 0 ATGCTGATAT 0.75799 -98 ********** Masking position 2 Map Score: 2.97981 Number of sites scoring better than the average of aligned sites = 791 Number in coding regions = 707 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 8 TTCTCTCTGGCGAGGGATGGATTCGCTT 1 9 1 GGCGAGGGAT 0.995441 -134 TTCATCAGCCGGACAGGGATAAT 3 95 1 GGACAGGGAT 0.992968 -13 ACATCCAAAAGGAGAGTGAT 5 110 1 GGAGAGTGAT 0.989614 -10 ********** Masking position 5 Map Score: 1.18528 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 20 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 ********** No masking Map Score: 7.69818e-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 10 ********** No masking Map Score: 7.69818e-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 11 ********** No masking Map Score: 7.69818e-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