AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00730_hpyl_reg_300.orf -o00730_hpyl_300.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 HP0845 44 thiamin phosphate pyrophosphorylase/hyroxyethylthiazole kinase (thiM) #2 HP0846 290 type I restriction enzyme R protein (hsdR) #3 HP0848 101 type I restriction enzyme S protein (hsdS) #4 HP0850 173 type I restriction enzyme M protein (hsdM) Motif number 1 TAAACGGCGCTTTTTTTGAGCCTTA 1 30 0 GGCGCTTTTT 0.986954 -15 AAAGGGCGTTTATTAAGCTTTTAG 2 5 1 GGCGTTTATT 0.978613 -286 TCTTCTTTGTGGATTTTTTTAAATTCATAG 2 45 0 GGATTTTTTT 0.968159 -246 CTTTTCTAACTGCTCTTTTAAATTGTCTTT 2 82 0 TGCTCTTTTA 0.749645 -209 ATGATCATTAAGCTTTTCTAACTGCTCTTT 2 94 0 AGCTTTTCTA 0.741778 -197 GGATCTTCTTGGATCTTTTTCGTTTTAGCC 2 192 0 GGATCTTTTT 0.976079 -99 ATTAAAAATCGGATCTTCTTGGATCTTTTT 2 202 0 GGATCTTCTT 0.98132 -89 GCGTTTCTATGGATATTTTTCTTATCAATG 2 270 0 GGATATTTTT 0.917567 -21 GGCGTTTCTATGGATATTTT 2 281 0 GGCGTTTCTA 0.978893 -10 CCAATTATTTGGATTTTCTTTAATAATTGA 3 19 0 GGATTTTCTT 0.975091 -83 GATTAAAGAGGGAATTTATTCAATCAAACC 3 51 1 GGAATTTATT 0.815592 -51 ATTTTAAAAAGGCGATTATATCTTATTTGC 4 32 1 GGCGATTATA 0.914558 -142 ACACAAAAAAGGGGCTTATATC 4 162 1 GGGGCTTATA 0.882949 -12 ********** Masking position 6 Map Score: 17.9946 Number of sites scoring better than the average of aligned sites = 1326 Number in coding regions = 1227 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 2 AAACGGCGCTTTTTTTGAGCCTTAATGCAAAAG 1 21 0 TTTTGAGCTT 0.946246 -24 TTAATTCTTCTTCTTTGTGGATTTTTTTAAATT 2 50 0 TTTTGTGGTT 0.976803 -241 CTCTTTTAAATTGTCTTTTAATTCTTCTTCTTT 2 67 0 TTTTTTTATT 0.754712 -224 TAGTCATCGTTTTTATTAGCGATGAATTGAGAA 2 156 0 TTTTTAGCAT 0.924702 -135 TGGATCTTTTTCGTTTTAGCCTTATAGTCATCG 2 180 0 TCTTTAGCTT 0.867843 -111 AATGATTTTAATGTTTTTGGTTTTCCCGTTCTC 2 241 0 ATTTTTGGTT 0.944967 -50 CTATGGATATTTTTCTTATCAATGATTTTAATG 2 261 0 TTTTTATCAT 0.76097 -30 TTAATCGCCCAATTATTTGGATTTTCTTTAATA 3 24 0 AATTTTGGTT 0.778125 -78 AATACTATTTTTTTATTTGGTTTGATTGAATAA 3 66 0 TTTTTTGGTT 0.98919 -36 ATTCCTTGCGTTTTCTGTGCGTTTGTGGGGCAA 4 58 0 TTTTGTGCTT 0.976803 -116 GCAAAGAATATTATTTTTTTATTCCTTGCGTTT 4 78 0 TTTTTTTTTT 0.754713 -96 AAAAAAATAATATTCTTTGCTATAATGAAACCT 4 91 1 TATTTTGCAT 0.857144 -83 TGATTGGCGGTTCTGTTTGGCGTTGTCAGCCTT 4 127 0 TTTTTTGGGT 0.945151 -47 AGCCCCTTTTTTGTGTTTTGATTGGCGGTTCTG 4 145 0 TTTTTTTGTT 0.959549 -29 ** * ***** ** Masking position 6 Map Score: 14.2867 Number of sites scoring better than the average of aligned sites = 1308 Number in coding regions = 1111 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 3 GTGGATTTTTTTAAATTCATAGCCTTGTTTTT 2 35 0 TTAAATTCTG 0.98857 -256 TAAATTGTCTTTTAATTCTTCTTCTTTGTGGA 2 62 0 TTTAATTCTT 0.878681 -229 CGTTTTAGCCTTATAGTCATCGTTTTTATTAG 2 170 0 TTATAGTCTG 0.951726 -121 ACCAAAAACATTAAAATCATTGATAAGAAAAA 2 253 1 TTAAAATCTG 0.974099 -38 TAAAAATCTTGGAAATACTATT 3 90 0 TAAAAATCTG 0.959109 -12 ATCGCCTTTTTAAAATTCATTTTTTAAAGGGG 4 16 0 TAAAATTCTT 0.924995 -158 AATATTATTTTTTTATTCCTTGCGTTTTCTGT 4 73 0 TTTTATTCTG 0.951781 -101 AATAAAAAAATAATATTCTTTGCTATAATGAA 4 88 1 TAATATTCTG 0.971106 -86 ******** * * Masking position 5 Map Score: 8.72951 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 197 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 TTTTTCTAAAAGCTTAATAAACGCCCTTT 2 7 0 AGTTAATAAG 0.837359 -284 CATTCTTTCACGCCTAAAGAATGGGACACTCTT 2 121 1 CGCTAAAGAG 0.988185 -170 CGATGAATTGAGAATAAAGAGTGTCCCATTCTT 2 137 0 AGATAAAGAG 0.942381 -154 CTCTAGCGTGAGATTAAAAATCGGATCTTCTTG 2 211 0 AGTTAAAAAG 0.971046 -80 TTTTAATCTCACGCTAGAGAACGGGAAAACCAA 2 225 1 ACCTAGAGAG 0.924567 -66 AATAATTGGGCGATTAAAGAGGGAATTTATTCA 3 40 1 CGTTAAAGAG 0.988166 -62 TCAAACCCCTTTAAAAAATGAATTTTAAAA 4 8 1 CCTTAAAAAG 0.971975 -166 TATAATGAAACCTTTAAAGGCTGACAACGCCAA 4 111 1 CCTTAAAGGG 0.941508 -63 GCCAATCAAAACACAAAAAAGGGGCTTATATC 4 152 1 ACCAAAAAAG 0.808032 -22 ** ******* * Masking position 6 Map Score: 6.20381 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 439 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 ********** No masking Map Score: 2.93755e-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 6 ********** No masking Map Score: 2.93755e-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: 2.93755e-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