AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icytR_hpyl_opreg_100.orf -g0.389 -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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP1112 109 adenylosuccinate lyase (purB) #2 HP1113 65 outer membrane protein (omp24) #3 HP1180 300 pyrimidine nucleoside transport protein (nupC) Motif number 1 TTTTTCCCCTTGATTCTTTAAACCCCTTTAA 1 52 1 TGTTCTTTAA 0.980657 -58 ATGGGATTTATGTTACTTTAAAGGGGTTTAA 1 69 0 TGTACTTTAA 0.958287 -41 TTTATAGTTTTGTTTTTATAAAAACGCGCC 2 10 0 TGTTTTATAA 0.817504 -56 CCTTAAAACTTCAATTTTTTAGCGCTTATTT 2 39 0 TCATTTTTTA 0.942508 -27 TAAAATTACATTAAACTTTTATTATCAATCC 3 48 0 TTAACTTTTA 0.730615 -253 AAAAGTTTAATGTAATTTTAATGGATTTTTA 3 59 1 TGAATTTTAA 0.934951 -242 GTAATTTTAATGGATTTTTAAGAAAGGTTTT 3 70 1 TGATTTTTAA 0.96954 -231 TTGTATAATCTCATTCTTTTATTTTTTTGTC 3 100 1 TCTTCTTTTA 0.96318 -201 ATCCGTTTAATCTTTTTTTTAGCAAAACTAA 3 232 1 TCTTTTTTTA 0.94255 -69 ACAATAGCCTTGCATCTTTTAATTTCTTGCA 3 266 1 TGATCTTTTA 0.980682 -35 ** ******** Masking position 7 Map Score: 13.1983 Number of sites scoring better than the average of aligned sites = 544 Number in coding regions = 465 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 2 TAATTAAATCAAGGGGCTTTTTTGCGCCTT 1 16 1 AAGGGGCTTT 0.988352 -94 TTAAAGAATCAAGGGGAAAAATCGCACAAG 1 43 0 AAGGGGAAAA 0.823064 -67 TGTTACTTTAAAGGGGTTTAAAGAATCAAG 1 60 0 AAGGGGTTTA 0.989692 -50 TTAAAATCAAAATGGGATTTATGTTACTTT 1 81 0 AATGGGATTT 0.987395 -29 TTGAAGTTTTAAGGGGTTTT 2 56 1 AAGGGGTTTT 0.993534 -10 ATGTAATTTTAATGGATTTTTAAGAAAGGT 3 68 1 AATGGATTTT 0.870523 -233 AAAATAAAAGAATGAGATTATACAAAAACC 3 95 0 AATGAGATTA 0.845145 -206 TGGTGTCAAGAGGGGGACTTGAACCCCCGA 3 176 0 AGGGGGACTT 0.942487 -125 ********** Masking position 1 Map Score: 9.35032 Number of sites scoring better than the average of aligned sites = 1109 Number in coding regions = 926 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 3 TTAAATCAAGGGGCTTTTTTGCGCCTTGTG 1 19 1 GGGCTTTTTT 0.991593 -91 TGCGCCTTGTGCGATTTTTCCCCTTGATTC 1 38 1 GCGATTTTTC 0.972625 -72 GGCGCGTTTTTATAAAAACAA 2 2 1 GCGCGTTTTT 0.990174 -64 CAATTTTTTAGCGCTTATTTTATAGTTTTG 2 29 0 GCGCTTATTT 0.981209 -37 GACAAAAGTTGGGCATTTTC 3 1 0 GGGCATTTTC 0.980533 -300 ********** Masking position 6 Map Score: 5.85024 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 386 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 TAGCGCTTATTTTATAGTTTTGTTTTTATA 2 21 0 TTTATAGTTT 0.873005 -45 GCGCTAAAAAATTGAAGTTTTAAGGGGTTT 2 45 1 ATTGAAGTTT 0.988017 -21 AGGATTGATAATAAAAGTTTAATGTAATTT 3 47 1 ATAAAAGTTT 0.872969 -254 ATAAAAGTTTAATGTAATTTTAATGGATTT 3 57 1 AATGTAATTT 0.871635 -244 ACGGATATTAAATGAAGTTTAAATCAAAAT 3 208 0 AATGAAGTTT 0.977833 -93 ATGCAAGGCTATTGTAGTTTAGTTTTGCTA 3 251 0 ATTGTAGTTT 0.987976 -50 ********** Masking position 6 Map Score: 5.50111 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 110 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 AAAAAGCCCCTTGATTTAATTAAAGGG 1 8 0 TTGATTTAAT 0.817372 -102 AAATCCCATTTTGATTTTAAGGATTGTCG 1 91 1 TTGATTTTAA 0.904592 -19 TAGTTTTGTTTTTATAAAAACGCGCC 2 7 0 TTTATAAAAA 0.755393 -59 CTTCCTCAAATTGATGACAAAAGTTGGGCA 3 16 0 TTGATGACAA 0.802387 -285 GGAAGTAGGATTGATAATAAAAGTTTAATG 3 41 1 TTGATAATAA 0.945693 -260 CTGAGCTACCTTGACAAAAAAATAAAAGAA 3 113 0 TTGACAAAAA 0.910671 -188 CACCATGATTTTGATTTAAACTTCATTTAA 3 201 1 TTGATTTAAA 0.912833 -100 TAGTTTAGTTTTGCTAAAAAAAAGATTAAA 3 237 0 TTGCTAAAAA 0.928491 -64 ********** Masking position 9 Map Score: 5.93773 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 484 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 6 ATTAAATCAAGGGGCTTTTTTGCGCCTTGT 1 18 1 GGGGCTTTTT 0.939247 -92 GTTACTTTAAAGGGGTTTAAAGAATCAAGG 1 59 0 AGGGGTTTAA 0.985206 -51 AAAATCAAAATGGGATTTATGTTACTTTAA 1 79 0 TGGGATTTAT 0.94456 -31 GCCGGAGGTCGGGGGTTCAAGTCCCCCTCT 3 168 1 GGGGGTTCAA 0.978904 -133 TTCTTGCATTAGGGATTTGACG 3 289 1 AGGGATTTGA 0.961908 -12 ********** Masking position 6 Map Score: 0.538088 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 574 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 7 ********** No masking Map Score: 6.56131e-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: 6.56131e-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 9 ********** No masking Map Score: 6.56131e-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