AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i327_not_clear2_hpyl_reg_100.orf -o327_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 RHP01289 259 AE000511 #2 RHP01290 43 AE000511 #3 RHP01291 17 AE000511 #4 RHP00013 73 AE000511 #5 RHP00020 81 AE000511 #6 RHP00021 228 AE000511 Motif number 1 GAAGCAAAAATTAAAGGAACGCAATAACTT 1 6 0 TTAAAACAAT 0.746695 -254 TAGACTACAATTTAAGAAGCAAAAATTAAAGGAAC 1 21 0 TTTAAAAAAA 0.897155 -239 TTAAAAAGCTTTAAAAGAGGGCAAAAATTAAAGCG 1 63 1 TTAAAACAAA 0.969877 -197 TTAAAGCGATTTCAAAAAAAAAAAAAAACAATTTC 1 90 1 TTCAAAAAAA 0.968946 -170 ATAAAAGCTTTTCATTTTAATCAAACCTAGCTAAT 1 133 0 TTCATTCAAA 0.912896 -127 GACAATGAAGTTTAAACACATAAAAGCTTTTCATT 1 152 0 TTTAAAAAAA 0.910002 -108 GTGTTTAAACTTCATTGTCTTAAAACTTTTAAGAG 1 168 1 TTCATTAAAA 0.925155 -92 ACGAACGGCTTAAAAGAATGAAAATTTTATCAAG 2 10 1 TTAAAAAAAA 0.975095 -34 AATCATGCGTTTAATGGAATAAAAACCTAGTTTG 4 10 0 TTAATAAAAA 0.982012 -64 TAAAATCCTATTATTGTAGCAAAAATCATGCGTTT 4 33 0 TTATTAAAAA 0.909962 -41 TTGTCCTTTATATAATTAAAATCCTATTATT 4 53 0 TTTATAAAAA 0.927978 -21 TGGCTTTATTTGTTATAAAATTTATAGTAA 5 6 1 TTATTTAAAA 0.749392 -76 TTAAGATTTTATAATCAAAGTCAAATCATTCTTGA 5 43 1 ATAATACAAA 0.813055 -39 ATTGAACCCCTTCATGGATACCAAAAGAGAGAAAG 6 92 0 TTCATACAAA 0.97505 -137 TTCTTTTGCATTATTCCATGAAAAAAGCCACGCTT 6 130 1 TTATTAAAAA 0.909962 -99 ***** * **** Masking position 13 Map Score: 20.0605 Number of sites scoring better than the average of aligned sites = 669 Number in coding regions = 537 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 2 CCCTCTTTTAAAGCTTTTTAACCCTTTTTAG 1 53 0 AAGCTTTTAA 0.922214 -207 TTTTTTTTGAAATCGCTTTAATTTTTGCCCT 1 80 0 AATCGCTTAA 0.92123 -180 AAACACATAAAAGCTTTTCATTTTAATCAAA 1 143 0 AAGCTTTTAT 0.922214 -117 AAAAGCTTTTATGTGTTTAAACTTCATTGTC 1 156 1 ATGTGTTTAA 0.668317 -104 TTTAAACTTCATTGTCTTAAAACTTTTAAGA 1 171 1 ATTGTCTTAA 0.658054 -89 CTACTAAAAAAAGGGTTTTAAATA 1 246 1 AAGGGTTTAA 0.983745 -14 ACGAACGGCTTAAAAGAATGAAAA 2 4 1 AACGGCTTAA 0.886645 -40 AAATTTTATCAAGGTTTTAATA 2 32 1 AAGGTTTTAT 0.946241 -12 CAAACTAGGTTTTTATTCCATTAAAC 4 6 1 TAGGTTTTAT 0.600971 -68 AGCAAAAATCATGCGTTTAATGGAATAAAAA 4 20 0 ATGCGTTTAT 0.939519 -54 CTTTGTCTTTAATGGCTTCATTGAGCGTCAT 6 12 0 AATGGCTTAT 0.945544 -217 AGCGTTTTTTAAGGGCTTCATCGCAGTTAGC 6 63 0 AAGGGCTTAT 0.986586 -166 AAAAGAGAGAAAGCGTTTTTTAAGGGCTTCA 6 74 0 AAGCGTTTTT 0.77718 -155 GGTATCCATGAAGGGGTTCAATGCATTCTTT 6 105 1 AAGGGGTTAA 0.962994 -124 AGCCACTTGAATGCGGTTGATTTTAACCGAA 6 164 0 ATGCGGTTAT 0.869781 -65 ACCGCATTCAAGTGGCTTTAAGATCCCATGA 6 178 1 AGTGGCTTAA 0.748791 -51 ******** ** Masking position 7 Map Score: 19.6255 Number of sites scoring better than the average of aligned sites = 2782 Number in coding regions = 2485 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 3 AGCTTTTTAACCCTTTTTAGACTACAATTTAAG 1 40 0 CCTTTTTAAT 0.965243 -220 AATTTTTGCCCTCTTTTAAAGCTTTTTAACCCT 1 59 0 CCTTTTAAGT 0.975425 -201 AAAATTAAAGCGATTTCAAAAAAAAAAAAAAAC 1 86 1 CATTTCAAAA 0.776439 -174 CTTTTAAGAGCAATTTTAAAATTCGTTGGCGTA 1 193 1 CATTTTAAAT 0.918122 -67 TATTTAAAACCCTTTTTTTAGTAGTTCATTCA 1 238 0 CCTTTTTTAT 0.935766 -22 AAAACTCTACTCTTTCAAGAATGATTTGACTT 5 60 0 CCTTTCAAAT 0.985325 -22 TCGCAGTTAGCGATTTCTACGATTTCATAAACT 6 41 0 CATTTCTAGT 0.958373 -188 ATGCATTGAACCCCTTCATGGATACCAAAAGAG 6 98 0 CCCTTCATGT 0.913829 -131 ACGCTTTCTTTGATGACAAGGTAT 6 215 0 CCTTTCTTGT 0.973579 -14 * ******* * * Masking position 6 Map Score: 6.90198 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 417 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 CCTTTAATTTTTGCTTCTTAAATTGTAGTCTAA 1 24 1 TTCTTTAAAT 0.74564 -236 AATTTTAAAATTGCTCTTAAAAGTTTTAAGACA 1 183 0 TTCTTAAAAG 0.950072 -77 TTTTTAGTAGTTCATTCAAAACGGATATTATAC 1 223 0 TTATAAAACG 0.692033 -37 TTTGAATGAACTACTAAAAAAAGGGTTTTAAAT 1 236 1 CTCTAAAAAG 0.750868 -24 AATCATGCGTTTAATGGAATAAAAACCTAGTTT 4 12 0 TTATAATAAA 0.753699 -62 CGCATGATTTTTGCTACAATAATAGGATTTTAA 4 36 1 TTCTAATAAT 0.919457 -38 TAATAGGATTTTAATTATATAAAGGACAA 4 55 1 TTATTATAAA 0.731265 -19 TGTTATAAAATTTATAGTAAAATTAAGATTTTA 5 21 1 TTATTAAAAT 0.939908 -61 TGATTTGACTTTGATTATAAAATCTTAATTTTA 5 38 0 TTATTAAAAT 0.944911 -44 CGTGGCTTTTTTCATGGAATAATGCAAAAGAAT 6 129 0 TTATAATAAT 0.894933 -100 AAAGCCACGCTTTCGGTTAAAATCAACCGCATT 6 153 1 TTCGTAAAAT 0.8129 -76 ** ** ****** Masking position 11 Map Score: 3.58804 Number of sites scoring better than the average of aligned sites = 841 Number in coding regions = 625 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 5 ********** No masking Map Score: -1.76682e-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 6 ********** No masking Map Score: -1.76682e-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 7 ********** No masking Map Score: -1.76682e-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