AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i335_2_7_7_40_hpyl_reg_300.orf -o335_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 RHP00416 300 AE000511 #2 RHP00417 36 AE000511 #3 RHP00421 111 AE000511 #4 RHP00423 97 AE000511 #5 RHP01581 47 AE000511 #6 RHP00425 21 AE000511 Motif number 1 GCTTAAAATTTTTTTAGCGTTT 1 3 0 TTTTTAGCGT 0.922843 -298 GCTAAAAAAATTTTAAGCGATCTTTTAGGG 1 15 1 TTTTAAGCGA 0.973643 -286 AAACTTCATTTTTTGAATAAAACTTCATTT 1 47 0 TTTTGAATAA 0.700611 -254 AAAAATGAAGTTTTACAAAAAAGAGTTTTT 1 64 1 TTTTACAAAA 0.629389 -237 AAAAAAGAGTTTTTAAACAACAACTAAGCA 1 80 1 TTTTAAACAA 0.946969 -221 CGACCATGACTTTTTAAAAAAGCTTCAATG 1 212 1 TTTTTAAAAA 0.496104 -89 ACAAACTGATTTTTAAACATGATGATTTAA 1 271 1 TTTTAAACAT 0.860717 -30 AAACATGATGATTTAAAGGATTTCTA 1 285 1 ATTTAAAGGA 0.835168 -16 ATCTTTTATGATTTGAACGATAACCC 2 7 0 ATTTGAACGA 0.921921 -30 GTGGATAATGTTTTGCAAGAAATATCT 3 8 0 TTTTGCAAGA 0.840443 -104 CAACAAGCATTTTTTAATGAATTGCAACTC 3 53 0 TTTTTAATGA 0.930978 -59 TATTTTAAAAGAAGTTTTTAGC 4 3 1 TTTTAAAAGA 0.97118 -95 TTAAAAGAAGTTTTTAGCGTTCTTTAAAAA 4 15 1 TTTTTAGCGT 0.922843 -83 TTTTAAGGTTTTTTTAAAGAACGCTAAAAA 4 25 0 TTTTTAAAGA 0.843638 -73 AGCGATAGTTTTTTAAGCGTTTTAAGGTTT 4 44 0 TTTTAAGCGT 0.922855 -54 TTTTTAAAGATTAAATAGTA 4 88 0 TTTTTAAAGA 0.843638 -10 AGTTTAGCAAATTTTAAGGAAGTAACCATG 5 28 1 ATTTTAAGGA 0.834292 -20 ********** Masking position 4 Map Score: 25.7876 Number of sites scoring better than the average of aligned sites = 2262 Number in coding regions = 1960 Number in noncoding regions = 302 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 2 AAGATCGCTTAAAATTTTTTTAGCGTTT 1 8 0 AAAATTTTTT 0.825902 -293 TTTTTGAATAAAACTTCATTTAACCCTAAAA 1 37 0 AAACTTCTTT 0.980739 -264 CTTTTTTGTAAAACTTCATTTTTTGAATAAA 1 56 0 AAACTTCTTT 0.980739 -245 TGTTGTTTAAAAACTCTTTTTTGTAAAACTT 1 71 0 AAACTCTTTT 0.970658 -230 CTCGCGCTACAATCTCCCTTTTTGATTGCGG 1 112 1 AATCTCCTTT 0.932933 -189 ATAATCATTGAAGCTTTTTTAAAAAGTCATG 1 216 0 AAGCTTTTTA 0.945772 -85 ATGAATTGCAACTCTTTGTTTTGGTGGATGT 3 36 0 ACTCTTTTTT 0.817276 -76 ATAGCCCAACAAGCATTTTTTAATGAATTGC 3 58 0 AAGCATTTTT 0.898753 -54 AGAACGCTAAAAACTTCTTTTAAAATA 4 7 0 AAACTTCTTT 0.980569 -91 TAAGCGTTTTAAGGTTTTTTTAAAGAACGCT 4 30 0 AAGGTTTTTT 0.900986 -68 TCGCTTGATCAAGCTCTTTTACTATTTAATC 4 69 1 AAGCTCTTTA 0.916132 -29 ******* *** Masking position 1 Map Score: 15.6622 Number of sites scoring better than the average of aligned sites = 651 Number in coding regions = 530 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 AGATCGCTTAAAATTTTTTTAGCGTTT 1 8 0 AAATTTTTTT 0.765843 -293 AAAAATTTTAAGCGATCTTTTAGGGTTAAA 1 20 1 AGCGATCTTT 0.506926 -281 TTTTGAATAAAACTTCATTTAACCCTAAAA 1 37 0 AACTTCATTT 0.883606 -264 TTTTTTGTAAAACTTCATTTTTTGAATAAA 1 56 0 AACTTCATTT 0.883606 -245 GTTGTTTAAAAACTCTTTTTTGTAAAACTT 1 71 0 AACTCTTTTT 0.962479 -230 TCGCGCTACAATCTCCCTTTTTGATTGCGG 1 113 1 ATCTCCCTTT 0.763136 -188 TAATCATTGAAGCTTTTTTAAAAAGTCATG 1 216 0 AGCTTTTTTA 0.9289 -85 TAGAAATCCTTTAAATCATCATG 1 288 0 AAATCCTTTA 0.551946 -13 AATGAATTGCAACTCTTTGTTTTGGTGGAT 3 38 0 AACTCTTTGT 0.776844 -74 TAGCCCAACAAGCATTTTTTAATGAATTGC 3 58 0 AGCATTTTTT 0.784869 -54 GAACGCTAAAAACTTCTTTTAAAATA 4 7 0 AACTTCTTTT 0.968353 -91 AGAAGTTTTTAGCGTTCTTTAAAAAAACCT 4 20 1 AGCGTTCTTT 0.879621 -78 AAGCGTTTTAAGGTTTTTTTAAAGAACGCT 4 30 0 AGGTTTTTTT 0.769944 -68 CGCTTGATCAAGCTCTTTTACTATTTAATC 4 70 1 AGCTCTTTTA 0.922378 -28 CATGGTTACTTCCTTAAAATTTGCTA 5 32 0 TACTTCCTTA 0.439426 -16 ********** Masking position 8 Map Score: 9.66303 Number of sites scoring better than the average of aligned sites = 2656 Number in coding regions = 2206 Number in noncoding regions = 450 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 4 GCGCGCACCCTTGGGGTGGGTGAGGTCGTG 1 163 1 TTGGGGTGGG 0.997824 -138 ATCAGTTTGTTTGGTGTGATTATATAATGA 1 251 0 TTGGTGTGAT 0.907551 -50 CAACTCTTTGTTTTGGTGGATGTGGATAAT 3 29 0 TTTTGGTGGA 0.907551 -83 TTTTCGCCCCTTTGTGTGGGGCTATTCTGT 3 90 1 TTTGTGTGGG 0.989051 -22 TAGGGGTGGGTCGTTAGTCG 6 1 1 TAGGGGTGGG 0.992877 -21 ********** Masking position 7 Map Score: 4.24434 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 186 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 GGAGATTGTAGCGCGAGTTTGCTTAGTTGTT 1 98 0 GCGCGATTTG 0.975098 -203 ATCAGGCTGCGCCATACTCCGCAATCAAAAA 1 130 0 GCCATATCCG 0.919526 -171 CCAAGGGTGCGCGCTAATCAGGCTGCGCCAT 1 146 0 GCGCTATCAG 0.987635 -155 GGTTTGAATCCCGCTACTCCGACCATGACTT 1 193 1 CCGCTATCCG 0.976459 -108 AATGCTTGTTGGGCTATTTTTTCGCCCCTTT 3 72 1 GGGCTATTTT 0.936098 -40 CCTTTGTGTGGGGCTATTCTGTTA 3 98 1 GGGCTATCTG 0.991063 -14 GCTTGATCAAGCGATAGTTTTTTAAGCGTTT 4 52 0 GCGATATTTT 0.904493 -46 ****** **** Masking position 6 Map Score: 3.92392 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 221 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 ********** No masking Map Score: 2.227e-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: 2.227e-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: 2.227e-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