AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i297_mixed12_hpyl_reg_300.orf -o297_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 RHP00234 300 AE000511 #2 RHP00864 26 AE000511 #3 RHP00871 104 AE000511 #4 RHP00872 138 AE000511 Motif number 1 GCGTCAGGACATTTTAATGAAAAAGTTGAT 1 35 1 ATTTTAATGA 0.94982 -266 ATAACTTAGCATTTTAATCAACTTTTTCAT 1 51 0 ATTTTAATCA 0.957579 -250 TTTGAACTTTATTTTTAACATTCTGTTTTT 1 162 1 ATTTTTAACA 0.981159 -139 AAAAGTGTTTCATTTTATAAAAAAGAAAAA 1 187 0 CATTTTATAA 0.600796 -114 AAATGAAACACTTTTTAAGTTTATTTATTT 1 202 1 CTTTTTAAGT 0.779626 -99 GCGATTCTTTCTTTTAAACACCAATATTAA 1 234 0 CTTTTAAACA 0.969944 -67 AATCGCTATAATTTGAAACAATTTAAATCT 1 258 1 ATTTGAAACA 0.852388 -43 TGAAGGCTTGATTTTTAAAAGTTAGGCTTA 3 17 1 ATTTTTAAAA 0.943683 -88 AAAATCTCAGAATTTTAACATAAAAGATTA 3 45 0 AATTTTAACA 0.907291 -60 TTTAAAGAGAGTTTTAAAAA 4 1 0 GTTTTAAAAA 0.838708 -138 TTAAAGTAAAATTTTAAAGAGAGTTTTAAA 4 13 0 ATTTTAAAGA 0.969601 -126 ATAATGAGCCATTTTTATCAAACAACGCTT 4 51 1 ATTTTTATCA 0.967475 -88 TCAAACAACGCTTTTTAAGAGTGGCTCAAG 4 68 1 CTTTTTAAGA 0.972947 -71 TTAGAACAAGGTTTTTATGACGAT 4 125 1 GTTTTTATGA 0.914705 -14 ********** Masking position 7 Map Score: 21.8028 Number of sites scoring better than the average of aligned sites = 1261 Number in coding regions = 1006 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 2 ACCTTAATTGAGAAAGCAAG 1 1 0 AGAAAGCAAG 0.964015 -300 GTTATAGTAAAGAAAGAAGGAATATAATAC 1 76 1 AGAAAGAAGG 0.927563 -225 GCATTATACCAAAAAAAAAAAAAACGATGT 1 130 1 AAAAAAAAAA 0.898257 -171 ACAGAATGTTAAAAATAAAGTTCAAATAAC 1 158 0 AAAAATAAAG 0.977692 -143 TCATTTTATAAAAAAGAAAAACAGAATGTT 1 178 0 AAAAAGAAAA 0.982779 -123 TATTGGTGTTTAAAAGAAAGAATCGCTATA 1 238 1 TAAAAGAAAG 0.946453 -63 CAAGCCATGAAAAAAGAAAAGTC 2 14 1 AAAAAGAAAA 0.982779 -13 CCTAACTTTTAAAAATCAAGCCTTCAAAAA 3 13 0 AAAAATCAAG 0.955403 -92 ACCTAACGATAAATATAAAATATATAAAAT 3 70 0 AAATATAAAA 0.778594 -35 ********** Masking position 5 Map Score: 11.7869 Number of sites scoring better than the average of aligned sites = 1114 Number in coding regions = 936 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 3 CTTTCTTTACTATAACTTAGCATTTTAATCAACT 1 58 0 TATAACCATT 0.954698 -243 AAAGAAGGAATATAATACGCCTTTCGCTCTTACC 1 88 1 TATAATCTTT 0.960169 -213 ATAAAGTTCAAATAACATCGTTTTTTTTTTTTTT 1 140 0 AATAACTTTT 0.739647 -161 AATAAACTTAAAAAGTGTTTCATTTTATAAAAAA 1 193 0 AAAAGTCATT 0.732664 -108 TGTTTCAAATTATAGCGATTCTTTCTTTTAAACA 1 244 0 TATAGCCTTT 0.966817 -57 CCTAACTTTTAAAAATCAAGCCTTCAAAAACC 3 9 0 AAAAATCCTT 0.721033 -96 ACATAAAAGATTAAGCCTAACTTTTAAAAATCAA 3 24 0 TTAAGCCTTT 0.804048 -81 AAACTCTCTTTAAAATTTTACTTTAAGATACCAT 4 17 1 TAAAATCTTT 0.960751 -122 TAAGATACCATATAATGAGCCATTTTTATCAAAC 4 40 1 TATAATCATT 0.916693 -99 GCCATTTTTATCAAACAACGCTTTTTAAGAGTGG 4 58 1 TCAAACCTTT 0.90663 -81 AGACCACTATTAGAACAAGGTTTTTATGACGAT 4 116 1 TAGAACTTTT 0.72341 -23 ****** **** Masking position 4 Map Score: 3.22217 Number of sites scoring better than the average of aligned sites = 1371 Number in coding regions = 1162 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 4 GTTCAAATAACATCGTTTTTTTTTTTTTTG 1 139 0 CATCGTTTTT 0.982936 -162 TTTCTTTTTTCATGGCTTGTCT 2 3 0 CATGGCTTGT 0.981224 -24 TTTTATCAAACAACGCTTTTTAAGAGTGGC 4 63 1 CAACGCTTTT 0.987118 -76 ACTATTAGAACAAGGTTTTTATGACGAT 4 121 1 CAAGGTTTTT 0.982861 -18 ********** Masking position 7 Map Score: 2.38943 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 155 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 AATGTCCTGACGCTCTTACCTTAATTGAGA 1 18 0 CGCTCTTACC 0.997326 -283 ATACGCCTTTCGCTCTTACCTTCGCCGAGC 1 102 1 CGCTCTTACC 0.997326 -199 GCCCTTGAGCCACTCTTAAAAAGCGTTGTT 4 71 0 CACTCTTAAA 0.948408 -68 ********** Masking position 8 Map Score: 1.7526 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 17 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 ********** No masking Map Score: 1.48747e-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: 1.48747e-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 8 ********** No masking Map Score: 1.48747e-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