AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i005_Pyrimidine_Biosynthesis_hpyl_reg_100.orf -o005_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP01210 111 AE000511 #2 RHP01211 72 AE000511 #3 RHP01212 53 AE000511 #4 RHP00334 98 AE000511 #5 RHP00335 143 AE000511 #6 RHP00488 66 AE000511 #7 RHP00630 300 AE000511 #8 RHP00632 78 AE000511 Motif number 1 TAGAGCTTTGATCAAAATGGTTTTTGGCTAAAT 1 43 0 ATAAAATGTT 0.793144 -69 TATTAGAAGATTTAAAAAGGCTTTT 1 97 1 TTAAAAAGTT 0.972995 -15 GCGTTTTAAAAACCTTTGAGGGTTAAA 2 5 1 TTAAAAACTT 0.948176 -68 CCTTTGAGGGTTAAAATAGTGTAAAATAGTAAA 2 23 1 TTAAATAGTA 0.769579 -50 CTTTTTGAGTTTTAAAATCTTTACTATTTTACA 2 42 0 TTAAAATCTA 0.900741 -31 GATTTTAAAACTCAAAAAGGATTGATA 2 56 1 CTAAAAAGTT 0.987525 -17 TTTTGTTATCCTAAAAAAGACAAGAAATGGTTA 3 13 1 CTAAAAAGAA 0.938912 -41 ATGGTTATTTTTGAAAAAGGATTGA 3 39 1 TTAAAAAGTT 0.972995 -15 AAATTGAAGTCTGAAAATAGGATAATAGTTACG 5 11 0 CTAAAATAAT 0.621228 -133 ACAAAACCCCCTAAAATTGAAATTGAAGTCTGA 5 30 0 CTAAATTGAT 0.640488 -114 TTTATTTTAGCTAAAAATGGCATGGGTTTTAGC 6 16 0 CTAAAATGAT 0.933868 -51 ATTTAAAAAGCTTAAAAAGAGTTTTCTAATAGT 7 14 1 CTAAAAAGTT 0.987525 -287 ATTCAAACCCTTTAAAAAGGGTCTAGGAGTTTA 7 50 1 TTAAAAAGTC 0.860827 -251 GGAGTTTATTTTCAAAAAGGATTCGTGTTTTTA 7 75 1 TTAAAAAGTT 0.972995 -226 GCGTTTAAAGCTTAAAAACTTTAAGTCTTAATT 7 232 1 CTAAAAACTA 0.96725 -69 GGTAGTTTAACCTAAAATCTCTAATTAAGACTT 7 254 0 CCAAAATCTA 0.795535 -47 GTTAAACTACCCTAAAATCTTTATGGGTAAAAT 7 276 1 CCAAAATCTA 0.795535 -25 ATTAATTCTTTAAAAAGCGTTTTATCTAAAA 8 9 1 TTAAAAAGTT 0.972995 -70 AGCGTTTTATCTAAAAAACGATAAAATACACTC 8 26 1 CTAAAAACTA 0.96725 -53 AAAATACACTCTAAAAATAAATAAAATATGCGA 8 48 1 CTAAAATATA 0.820152 -31 ** ****** ** Masking position 6 Map Score: 30.2324 Number of sites scoring better than the average of aligned sites = 1564 Number in coding regions = 1305 Number in noncoding regions = 259 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 2 TTATTTAGCCAAAAACCATTTTGATCAAAG 1 41 1 AAAAACCATT 0.623474 -71 GCGTTTTAAAAACCTTTGAGGGTTAA 2 7 1 TAAAAACCTT 0.872198 -66 GTAAAGATTTTAAAACTCAAAAAGGATTGA 2 51 1 TAAAACTCAA 0.614646 -22 AATACCAAACAAAACCCCCTAAAATTGAAA 5 41 0 AAAACCCCCT 0.913764 -103 TCCTTGCTAAAACCCATGCCATTTTTA 6 8 1 TAAAACCCAT 0.968576 -59 AAAACCCCCTTTTAGTTATA 6 57 0 AAAACCCCCT 0.913764 -10 GGGATTTAAAAAGCTTAAAAAGAGTT 7 7 1 TAAAAAGCTT 0.778616 -294 GCCACTATTAGAAAACTCTTTTTAAGCTTT 7 20 0 GAAAACTCTT 0.865643 -281 ATAGTGGCATTCAAACCCTTTAAAAAGGGT 7 42 1 TCAAACCCTT 0.953193 -259 CTTTTTGAAAATAAACTCCTAGACCCTTTT 7 64 0 ATAAACTCCT 0.811332 -237 CTTCAGCATTTCAAACTCCTTATAGAAATA 7 116 0 TCAAACTCCT 0.934932 -185 AAACAAAAGGTAAAACTCCTAGAACATTGT 7 167 1 TAAAACTCCT 0.976448 -134 TTTTTAAGCTTTAAACGCATAAAAGTTGCA 7 220 0 TTAAACGCAT 0.780654 -81 GTTTTTTAGATAAAACGCTTTTTAAAGAAT 8 15 0 TAAAACGCTT 0.968032 -64 ********** Masking position 4 Map Score: 13.8261 Number of sites scoring better than the average of aligned sites = 2064 Number in coding regions = 1768 Number in noncoding regions = 296 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 3 TCTCATTCATGCTCCATGACGATC 1 5 0 GCTCCATGAC 0.961268 -107 GTTTTACTCCTTGAATTCAACTCAA 5 129 0 ACTCCTTGAA 0.976012 -15 TTGAAAATAAACTCCTAGACCCTTTTTAAA 7 60 0 ACTCCTAGAC 0.991692 -241 AAATGCTGAAGCTTCTAGAATGATTCTAGA 7 135 1 GCTTCTAGAA 0.975807 -166 CTTCTAGAATGATTCTAGACAAAACAAAAG 7 146 1 GATTCTAGAC 0.907508 -155 AAAAGGTAAAACTCCTAGAACATTGTTATA 7 171 1 ACTCCTAGAA 0.986998 -130 ********** Masking position 3 Map Score: 6.12532 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 29 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 CTTTGAGGGTTAAAATAGTGTAAAATAGTAAAGAT 2 24 1 TAAAATAAAA 0.986452 -49 TTTGTTATCCTAAAAAAGACAAGAAATGGTTATTT 3 14 1 TAAAAAAAAA 0.919864 -40 AAACCTAATAAAAAATACTTTAAAATATTGATAAC 4 41 1 AAAAATAAAA 0.919864 -58 CAAAATGTAGTAAAATACCAAACAAAACCCCCTAA 5 49 0 TAAAATAAAA 0.986453 -95 CTAGGTCCAATATAATAGCGCAAAATGTAGTAAAA 5 69 0 TATAATAAAA 0.919864 -75 CATTTTTAGCTAAAATAAAATCTATATTATAACTA 6 30 1 TAAAATACAT 0.848734 -37 GATTTTAGGTTAAACTACCCTAAAATCTTTATGGG 7 268 1 TAAACTAAAA 0.944484 -33 TAAAAAACGATAAAATACACTCTAAAAATAAATAA 8 37 1 TAAAATACAA 0.972672 -42 TAAAAATAAATAAAATATGCGAGAAAAATC 8 59 1 TAAAATAAAA 0.986453 -20 ******* * ** Masking position 7 Map Score: 10.6903 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 67 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 TGGCCTTTATTTAGCCAAAAACCATTTTGATC 1 35 1 TTACCAAAAC 0.887014 -77 TACACTATTTTAACCCTCAAAGGTTTTTAAAA 2 14 0 TAACCCAAAG 0.973658 -59 GTAAAGATTTTAAAACTCAAAAAGGATTGATA 2 51 1 TAAACCAAAA 0.73992 -22 GGTTTTGTTATCCTAAAAAAGACAAGAAA 3 8 1 TTACCAAAAA 0.930477 -46 AACTAATCCTTAAAGAAAGAATGTA 4 84 0 TAACCTAAAG 0.98212 -15 ATAATTTTAATTAACCCTACAGCTAGGTCCAA 5 94 0 TTACCTACAG 0.919711 -50 TTTATGCGTTTAAAGCTTAAAAACTTTAAGTC 7 227 1 TAAGCTAAAA 0.780391 -74 AATCTCTAATTAAGACTTAAAGTTTTTAAGCT 7 240 0 TAAACTAAAG 0.915369 -61 TTAGGGTAGTTTAACCTAAAATCTCTAATTAA 7 259 0 TTACCAAAAT 0.841192 -42 GCATTTTACCCATAAAGATTTTAGGGT 7 284 0 TTACCTAAAG 0.98212 -17 *** ** ***** Masking position 9 Map Score: 8.18623 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 539 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 6 AAAACCTTTGAGGGTTAAAATAGTGTAAAAT 2 19 1 AGGGTAAAAT 0.823909 -54 ATAGTGTAAAATAGTAAAGATTTTAAAACTC 2 38 1 ATAGAAAGAT 0.696648 -35 TTTGAAAAAATAGGGGGGGAC 4 1 1 TTTGAAAAAT 0.801261 -98 AGCTGTAGGGTTAATTAAAATTATTTATTGA 5 102 1 TTAATAAAAT 0.872586 -42 CATGCCATTTTTAGCTAAAATAAAATCTATA 6 25 1 TTAGTAAAAT 0.975382 -42 AAACCCCCTTTTAGTTATAATATAGATTTTA 6 45 0 TTAGTATAAT 0.847887 -22 AGTTGCATTGATTGGTAAAATCATGTTATAA 7 196 0 ATTGTAAAAT 0.935415 -105 TAAAATCTTTATGGGTAAAATGC 7 288 1 ATGGTAAAAT 0.957328 -13 TTATCGTTTTTTAGATAAAACGCTTTTTAAA 8 19 0 TTAGTAAAAC 0.892041 -60 CACTCTAAAAATAAATAAAATATGCGAGAAA 8 54 1 ATAATAAAAT 0.872588 -25 **** ****** Masking position 7 Map Score: 5.11524 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 438 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 7 TATCAATCCTTTTTGAGTTTT 2 62 0 ATCAATCCTT 0.973524 -11 TTCAAAAATAACCATTTCTTGTCTTTTTTA 3 24 0 ACCATTTCTT 0.918158 -30 AACTAATCCTTAAAGAAAGAA 4 88 0 ACTAATCCTT 0.981626 -11 ACATAAAAACACGAATCCTTTTTGAAAATA 7 81 0 ACGAATCCTT 0.974431 -220 ATTAATTCTTTAAAAAGCGT 8 1 1 ATTAATTCTT 0.911542 -78 ********** Masking position 6 Map Score: 2.0717 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 44 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 8 CTCTTGATTTTAGAGCTTTGATCAAAATGGT 1 55 0 TAGAGTTTGA 0.970162 -57 ATCAAGAGCATAGAAAATTTATTAGAAGATT 1 78 1 TAGAAATTTA 0.904565 -34 GAAAATTTATTAGAAGATTTAAAAAGGCTTT 1 90 1 TAGAAATTTA 0.904565 -22 TGTAAAATAGTAAAGATTTTAAAACTCAAAA 2 42 1 TAAAGTTTTA 0.585432 -31 TTAAAACTCAAAAAGGATTGATA 2 60 1 AAAAGATTGA 0.78245 -13 TTATTTTTGAAAAAGGATTGA 3 43 1 AAAAGATTGA 0.78245 -11 AAAAATACTTTAAAATATTGATAACGCTTCG 4 51 1 TAAAAATTGA 0.891632 -48 TTAGTTATAATATAGATTTTATTTTAGCTAA 6 35 0 TATAGTTTTA 0.706074 -32 AAACTCCTTATAGAAATATGAAAACATAAAA 7 103 0 TAGAATATGA 0.56178 -198 AGAATCATTCTAGAAGCTTCAGCATTTCAAA 7 131 0 TAGAACTTCA 0.414443 -170 GTAAAACTCCTAGAACATTGTTATAACATGA 7 176 1 TAGAAATTGT 0.561798 -125 AATTAAGACTTAAAGTTTTTAAGCTTTAAAC 7 234 0 TAAAGTTTTA 0.585432 -67 AAGTCTTAATTAGAGATTTTAGGTTAAACTA 7 254 1 TAGAGTTTTA 0.929639 -47 ATTTTACCCATAAAGATTTTAGGGTAGTTTA 7 278 0 TAAAGTTTTA 0.585432 -23 AAACGCTTTTTAAAGAATTAAT 8 2 0 TAAAGATTAA 0.727781 -77 ***** ***** Masking position 4 Map Score: 16.2488 Number of sites scoring better than the average of aligned sites = 671 Number in coding regions = 610 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 ********** No masking Map Score: 4.64285e-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: 4.64285e-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: 4.64285e-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