AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icarP_hpyl_opreg_300.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 HP0919 98 carbamoyl-phosphate synthase (glutamine-hydrolysing) (pyrAb) #2 HP0920 143 conserved hypothetical integral membrane protein #3 HP1234 300 conserved hypothetical integral membrane protein #4 HP1236 78 H. pylori predicted coding region HP1236 Motif number 1 AAAGTATTTTTTATTAGGTTTTTGCGTGGCGT 1 30 0 TTATTAGTTT 0.891646 -69 GTTATCAATATTTTAAAGTATTTTTTATTAGG 1 44 0 TTTTAAGATT 0.971098 -55 TTACATTCTTTCTTTAAGGATTAGTT 1 83 1 TCTTTAGATT 0.888074 -16 TCAATTTCAATTTTAGGGGGTTTTGTTTGGTA 2 37 1 TTTTAGGGTT 0.974107 -107 AATTAAAATTATTTATTGAGTTGAATTCAAGG 2 114 1 ATTTATGGTT 0.72131 -30 TAGAAAACTCTTTTTAAGCTTTTTAAATCCC 3 10 0 TTTTTAGTTT 0.979345 -291 CCTAGACCCTTTTTAAAGGGTTTGAATGCCAC 3 45 0 TTTTAAGGTT 0.991672 -256 AGGATTCGTGTTTTTATGTTTTCATATTTCTA 3 92 1 TTTTTAGTTT 0.979345 -209 TTTCATATTTCTATAAGGAGTTTGAAATGCTG 3 111 1 CTATAAGGTT 0.857119 -190 ATCAATGCAACTTTTATGCGTTTAAAGCTTAA 3 215 1 CTTTTAGGTT 0.968158 -86 AGACTTAAAGTTTTTAAGCTTTAAACGCATAA 3 228 0 TTTTTAGTTT 0.979345 -73 TACCCTAAAATCTTTATGGGTAAAATGC 3 283 1 TCTTTAGGTA 0.829946 -18 ATAAAACGCTTTTTAAAGAATTAAT 4 4 0 TTTTAAGATT 0.971098 -75 TTAGAGTGTATTTTATCGTTTTTTAGATAAAA 4 30 0 TTTTATGTTT 0.916729 -49 TTTTATTTATTTTTAGAGTGTATTTTATCGTT 4 42 0 TTTTAGGGTA 0.867184 -37 ****** * *** Masking position 4 Map Score: 23.9882 Number of sites scoring better than the average of aligned sites = 1663 Number in coding regions = 1409 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 2 GGACGCCACGCAAAAACCTAATAAAAAATA 1 28 1 CAAAAACCTA 0.719506 -71 AATACCAAACAAAACCCCCTAAAATTGAAA 2 41 0 AAAACCCCCT 0.834345 -103 GGGATTTAAAAAGCTTAAAAAGAGTTT 3 8 1 AAAAAGCTTA 0.829107 -293 CCACTATTAGAAAACTCTTTTTAAGCTTTT 3 19 0 AAAACTCTTT 0.957927 -282 TAGTGGCATTCAAACCCTTTAAAAAGGGTC 3 43 1 CAAACCCTTT 0.930979 -258 TTTTTGAAAATAAACTCCTAGACCCTTTTT 3 63 0 TAAACTCCTA 0.947302 -238 TTCAGCATTTCAAACTCCTTATAGAAATAT 3 115 0 CAAACTCCTT 0.965027 -186 AACAAAAGGTAAAACTCCTAGAACATTGTT 3 168 1 AAAACTCCTA 0.947281 -133 TTTTAAGCTTTAAACGCATAAAAGTTGCAT 3 219 0 TAAACGCATA 0.696491 -82 GTTTAAAGCTTAAAAACTTTAAGTCTTAAT 3 234 1 TAAAAACTTT 0.779425 -67 TAGTTTAACCTAAAATCTCTAATTAAGACT 3 255 0 TAAAATCTCT 0.75312 -46 TAAACTACCCTAAAATCTTTATGGGTAAAA 3 278 1 TAAAATCTTT 0.904303 -23 TTTTTTAGATAAAACGCTTTTTAAAGAATT 4 14 0 AAAACGCTTT 0.946167 -65 ********** Masking position 4 Map Score: 15.0027 Number of sites scoring better than the average of aligned sites = 1723 Number in coding regions = 1463 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 3 GTTTTACTCCTTGAATTCAACTCAAT 2 128 0 CTCCTTGAAT 0.945717 -16 TTGAATGCCACTATTAGAAAACTCTTTTTA 3 26 0 CTATTAGAAA 0.860844 -275 TGAAAATAAACTCCTAGACCCTTTTTAAAG 3 59 0 CTCCTAGACC 0.976731 -242 AACACGAATCCTTTTTGAAAATAAACTCCT 3 74 0 CTTTTTGAAA 0.881654 -227 TTTCAAACTCCTTATAGAAATATGAAAACA 3 108 0 CTTATAGAAA 0.917324 -193 AATGCTGAAGCTTCTAGAATGATTCTAGAC 3 136 1 CTTCTAGAAT 0.711389 -165 TTCTAGAATGATTCTAGACAAAACAAAAGG 3 147 1 ATTCTAGACA 0.795292 -154 AAAGGTAAAACTCCTAGAACATTGTTATAA 3 172 1 CTCCTAGAAC 0.981631 -129 ********** Masking position 8 Map Score: 7.10563 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 84 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 TAGCGCAAAATGTAGTAAAATACCAAACAAA 2 58 0 TGAGTAAAAT 0.891251 -86 AGCTGTAGGGTTAATTAAAATTATTTATTGA 2 102 1 TTATTAAAAT 0.693869 -42 AAATTATTTATTGAGTTGAATTCAAGGAGTA 2 119 1 TTAGTTGAAT 0.586485 -25 GTTGAATTCAAGGAGTAAAAC 2 133 1 AGAGTAAAAC 0.902738 -11 CCCTTTTTAAAGGGTTTGAATGCCACTATTA 3 40 0 AGGTTTGAAT 0.376856 -261 AGACAAAACAAAAGGTAAAACTCCTAGAACA 3 162 1 AAGGTAAAAC 0.900997 -139 AGTTGCATTGATTGGTAAAATCATGTTATAA 3 196 0 ATGGTAAAAT 0.972223 -105 ATTAGAGATTTTAGGTTAAACTACCCTAAAA 3 262 1 TTGGTTAAAC 0.881484 -39 TAAAATCTTTATGGGTAAAATGC 3 288 1 ATGGTAAAAT 0.972228 -13 TTATCGTTTTTTAGATAAAACGCTTTTTAAA 4 19 0 TTGATAAAAC 0.855129 -60 TTATCTAAAAAACGATAAAATACACTCTAAA 4 32 1 AAGATAAAAT 0.757362 -47 CACTCTAAAAATAAATAAAATATGCGAGAAA 4 54 1 ATAATAAAAT 0.817218 -25 ** ******** Masking position 9 Map Score: 6.86897 Number of sites scoring better than the average of aligned sites = 911 Number in coding regions = 806 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 5 AAGAATGTAAACGAAGCGTTATCAATATTT 1 63 0 ACGAAGCGTT 0.955865 -36 AACTAATCCTTAAAGAAAGAA 1 88 0 ACTAATCCTT 0.984793 -11 ACATAAAAACACGAATCCTTTTTGAAAATA 3 81 0 ACGAATCCTT 0.982513 -220 AAAATCTCTAATTAAGACTTAAAGTTTTTA 3 244 0 ATTAAGACTT 0.887563 -57 ATTAATTCTTTAAAAAGCGT 4 1 1 ATTAATTCTT 0.877255 -78 ********** Masking position 5 Map Score: 0.914802 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 110 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 ********** No masking Map Score: -9.14168e-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: -9.14168e-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: -9.14168e-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