AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i316_mixed3_hpyl_reg_300.orf -o316_hpyl_300.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 RHP00170 300 AE000511 #2 RHP00636 119 AE000511 #3 RHP00765 42 AE000511 #4 RHP00768 171 AE000511 #5 RHP00769 300 AE000511 #6 RHP00950 87 AE000511 #7 RHP00951 74 AE000511 Motif number 1 ACTCCCCACAACAGGAATGAATTTAAGGAAACCAT 1 68 0 AAGAGATTTA 0.85341 -233 TGAAAGTGCTAGAAAAGTGCTTTAATGATGAGACG 1 158 1 AAAAGCTTAA 0.987572 -143 CTATCTTTTTAAAAAAATAACTTAAAAGAGCTATA 2 51 1 AAAAAATTAA 0.780809 -69 TAAAAGAGCTATAAAATAGCCTTAAAATACGCGAT 2 73 1 AAAAGCTTAA 0.987501 -47 ACCAACGCTAAAAATAGCGCTTTAATTGAATCCAA 4 130 1 AAAAGCTTAA 0.987561 -42 AATTGAATCCAAAACAAGGAGTTTATTTT 4 153 1 AAAAGATTTA 0.971346 -19 ATTATAAAATATAATAAGGAGTTGAGGAATGAGCA 5 137 0 AAAAGATTGA 0.965637 -164 CCAAAACTAGCGAAAATTGATTTTACCAAAATTGT 5 216 1 CAAAGATTTA 0.92865 -85 ATTGTTTGATATAATACAGAGTTTAGCTTAGAAAT 5 246 1 AAAAGATTTA 0.970387 -55 AAAAGACCGCCTTAAAACCAGCGCT 5 286 0 AAAAGCTTAA 0.986898 -15 ATAACGCTTTCTAACACAGCCTTATT 6 2 0 CAAAGCTTAT 0.778068 -86 TATTCAGCTTTTAAAATAGCTTTGATTATAACTAA 6 43 0 TAAAGCTTGA 0.863073 -45 * ** * ** **** Masking position 6 Map Score: 15.6226 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 347 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 2 TAATTTCTTGATTGTATCCAAGTTGAGATAA 1 249 0 ATTTATCCAA 0.962283 -52 AATAACCGCTATTATACCATAAGAAAACCGC 4 88 0 ATTTACCATA 0.94741 -84 AGCGTTGGTTATTCTAAAAAAATAACCGCTA 4 108 0 ATTTAAAAAA 0.880051 -64 TAGCGCTTTAATTGAATCCAAAACAAGGAGT 4 144 1 ATTAATCCAA 0.730834 -28 TAACCGAATCATTATAAAATATAATAAGGAG 5 151 0 ATTTAAAATA 0.863643 -150 AGTTATTGGGATTATATCCAAAACTAGCGAA 5 199 1 ATTTATCCAA 0.962285 -102 GCGAAAATTGATTTTACCAAAATTGTTTGAT 5 225 1 ATTTACCAAA 0.954273 -76 TAAACTCTGTATTATATCAAACAATTTTGGT 5 240 0 ATTTATCAAA 0.968763 -61 AATAGCTTTGATTATAACTAAACTTGAATAA 6 33 0 ATTTAACTAA 0.853155 -55 AGCTATTCAGCTTTTAAAATAGCTTTGATTA 6 50 0 CTTTAAAATA 0.666776 -38 ATAATCAAACATTCTAACATAAGGAGAATAA 7 20 0 ATTTAACATA 0.969525 -55 ATGTTTGATTATTGTAACATACTAAATAAAA 7 39 1 ATTTAACATA 0.969512 -36 GCTTTTATCCTATGGTTTTATT 7 63 0 CTTTATCCTA 0.874341 -12 *** ******* Masking position 6 Map Score: 15.0588 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 147 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 3 GATTGTTAGGCGTAACCGCTGTCGCGCAAG 1 20 1 CGTAACCGCT 0.923467 -281 GGAAACCATTAACAAGCGTTCTCCCCACTT 1 47 0 AACAAGCGTT 0.886881 -254 TTGCAGGGGGCACAACCGCTGTAATTATCA 1 104 1 CACAACCGCT 0.983909 -197 GCGTTTTTCATAACCCCTAATCTTATTG 1 283 0 CATAACCCCT 0.683185 -18 CGCTTTGCATAGAAACCGCTTATGCA 4 7 0 AGAAACCGCT 0.974583 -165 CATAAGCTTCAAGAAACGCTTTGCATAGAA 4 23 0 AAGAAACGCT 0.827618 -149 GTATTTGCAAAAACACCGATGCATTGCGCC 4 52 0 AAACACCGAT 0.752889 -120 TATACCATAAGAAAACCGCTCGCTTGTATT 4 77 0 GAAAACCGCT 0.934657 -95 ATTCTAAAAAAATAACCGCTATTATACCAT 4 99 0 AATAACCGCT 0.979316 -73 TTTTTAGAATAACCAACGCTAAAAATAGCG 4 119 1 AACCAACGCT 0.921295 -53 CCAACGCTAAAAATAGCGCTTTAATTGAAT 4 131 1 AAATAGCGCT 0.906029 -41 AAAAGACGCCACCTACCGCTAAAATGAGAT 5 70 1 ACCTACCGCT 0.849844 -231 ACCGCCTTAAAACCAGCGCTCAATGATTTC 5 276 0 AACCAGCGCT 0.971942 -25 AGGCTGTGTTAGAAAGCGTTATTCAAGTTT 6 15 1 AGAAAGCGTT 0.712808 -73 ********** Masking position 5 Map Score: 13.1368 Number of sites scoring better than the average of aligned sites = 1256 Number in coding regions = 1125 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 4 TGTTGTTTTATCGCGTATTTTAAGGCTATTT 2 86 0 TCGCGTTTTT 0.942267 -34 TAATCCTTTATCGTTAAATTTATAAGCGTGT 3 14 0 TCGTTAATTT 0.757514 -29 AGAAAACCGCTCGCTTGTATTTGCAAAAACA 4 67 0 TCGCTTTATT 0.846097 -105 TGGTATAATAGCGGTTATTTTTTTAGAATAA 4 100 1 GCGGTTTTTT 0.921954 -72 TTCAATTAAAGCGCTATTTTTAGCGTTGGTT 4 129 0 GCGCTATTTT 0.962086 -43 CCAAAACAAGGAGTTTATTTT 4 161 1 GAGTTTTTTT 0.745437 -11 TGGTGCGGCTGGGCTTGATTTGGAGAAATGG 5 39 0 GGGCTTATTT 0.95976 -262 TAGCGGTAGGTGGCGTCTTTTTGGTGCGGCT 5 60 0 TGGCGTTTTT 0.92176 -241 GAGATTTACTGGGATTATTTTTCTTGATTTG 5 95 1 GGGATTTTTT 0.851923 -206 TCTTGATTTGTGGTTTTATTTTGCTCATTCC 5 116 1 TGGTTTATTT 0.863808 -185 AAATCAATTTTCGCTAGTTTTGGATATAATC 5 208 0 TCGCTATTTT 0.948366 -93 AAATCATTGAGCGCTGGTTTTAAGGCGGTCT 5 277 1 GCGCTGTTTT 0.937047 -24 TTTTATCCTATGGTTTTATTTAGTATGTTAC 7 52 0 TGGTTTATTT 0.863808 -23 ****** **** Masking position 10 Map Score: 10.7769 Number of sites scoring better than the average of aligned sites = 1435 Number in coding regions = 1286 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 5 ACCCAATGCCTTCTGTGATAATTACAGCGGTT 1 117 0 TTCTGGATAT 0.919552 -184 GCTAGAAAAGTGCTTTAATGATGAGACGGGCG 1 165 1 TGCTTAATAT 0.730032 -136 TGCCTGATGAAGTTGGCATGATAACTTCTCTC 1 206 1 AGTTGCATAT 0.917349 -95 ATTGTATCCAAGTTGAGATAATTCTCCTTAAA 1 238 0 AGTTGGATAT 0.955629 -63 CCCCTAATCTTATTGTGTTAATTTCTTGATTG 1 266 0 TATTGGTTAT 0.693085 -35 GGAGAAATGGTGCTGACATTATTTGGTGGGAA 5 17 0 TGCTGCATAT 0.97441 -284 AAATGAGATTTACTGGGATTATTTTTCTTGAT 5 91 1 TACTGGATAT 0.974098 -210 GATTCGGTTAAACTTCCATCATGGTTAAGTTA 5 172 1 AACTTCATAT 0.788812 -129 ATGGTTAAGTTATTGGGATTATATCCAAAACT 5 192 1 TATTGGATAT 0.941345 -109 CTTTTAAAATAGCTTTGATTATAACTAAACTT 6 39 0 AGCTTGATAT 0.934382 -49 ***** *** ** Masking position 4 Map Score: 5.86987 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 157 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 TAGCACTTTCAAATACGCAAACCCAATGCCTTC 1 136 0 AAAGCAAACC 0.910707 -165 ATCCAAAATTAAAGGAGAAAACC 2 1 0 AAAGAAAACC 0.970714 -119 ATAAAACAACAAAAAGGAATACCC 2 106 1 AAAGAATACC 0.987046 -14 GTTTTGGATATAATCCCAATAACTTAACCATGA 5 190 0 TAACAATAAC 0.802078 -111 GATTATAACTAAACTTGAATAACGCTTTCTAAC 6 22 0 AAAGAATAAC 0.97978 -66 AGCTATTTTAAAAGCTGAATAGCTATAGTTATT 6 57 1 AAAGAATAGC 0.966013 -31 CATTCTAACATAAGGAGAATAACAATCAATT 7 9 0 TAAGAATAAC 0.95471 -66 *** ******* Masking position 9 Map Score: 2.84488 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 54 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 CAGGAATGAATTTAAGGAAACCATTAACAA 1 62 0 TTTAAGGAAA 0.890404 -239 AACTTCTCTCTTTAAGGAGAATTATCTCAA 1 228 1 TTTAAGGAGA 0.984288 -73 ACATCCAAAATTAAAGGAGAAAACC 2 6 0 TTAAAGGAGA 0.958222 -114 TATCGCGTATTTTAAGGCTATTTTATAGCT 2 79 0 TTTAAGGCTA 0.821487 -41 CACCTACCGCTAAAATGAGATTTACTGGGA 5 79 1 TAAAATGAGA 0.614875 -222 TATAAAATATAATAAGGAGTTGAGGAATGA 5 140 0 AATAAGGAGT 0.62732 -161 GAGCGCTGGTTTTAAGGCGGTCTTTT 5 285 1 TTTAAGGCGG 0.916083 -16 AACATTCTAACATAAGGAGAATAACAATCA 7 14 0 CATAAGGAGA 0.923177 -61 ********** Masking position 5 Map Score: 2.19092 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 243 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 8 ********** No masking Map Score: -3.52186e-12 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 TTAAAGCACTTTTCTAGCACTTTCAAATACGCA 1 150 0 TTTTGCCTTT 0.948355 -151 AAAAAGATAGTTTATTATACTTTAAACATCCAA 2 28 0 TTTTATCTTT 0.953368 -92 TTAAGGCTATTTTATAGCTCTTTTAAGTTATTT 2 65 0 TTTTGCCTTT 0.948355 -55 GGTATTCCTTTTTGTTGTTTTATCGCGTATTTT 2 96 0 TTTTGTTTAT 0.907297 -24 GCCCTTTCTAATCCTTTATCGTTAAAT 3 26 0 TTTTATCTTT 0.953368 -17 AGCGAGCGGTTTTCTTATGGTATAATAGCGGTT 4 83 1 TTTTATGTAT 0.783522 -89 TTTTTCTTGATTTGTGGTTTTATTTTGCTCATT 5 112 1 TTTTGTTTAT 0.907297 -189 TCCTCAACTCCTTATTATATTTTATAATGATTC 5 144 1 CTTTATTTTT 0.724454 -157 *** * ** **** Masking position 5 Map Score: 0.999128 Number of sites scoring better than the average of aligned sites = 478 Number in coding regions = 412 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 10 ********** No masking Map Score: -3.52186e-12 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: -3.52186e-12 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 12 ********** No masking Map Score: -3.52186e-12 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