AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i117_Oligopeptide_Transport_pyro_reg_100.orf -o117_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RPH00319 174 Pyrococcus_OT3 #2 RPH00318 41 Pyrococcus_OT3 #3 RPH01298 250 Pyrococcus_OT3 #4 RPH01299 117 Pyrococcus_OT3 #5 RPH01808 198 Pyrococcus_OT3 Motif number 1 TGTCGAATTGAAAGTCCAAAACT 1 3 0 AAAGTCAAAA 0.848796 -172 TCCGATCCATAAAAATTAAATATACGCTTCG 1 113 1 AAAAATAAAT 0.796998 -62 ACATAGTTTTAAGATTTAAAATTGGGGGTAA 1 148 1 AAGATTAAAA 0.976894 -27 AAAGGGGAATAAAAATAAAAA 2 1 0 AAAAATAAAA 0.924408 -41 CACCTTGAAGATGCTTAAAAATCAGTGGTGT 3 22 1 ATGCTTAAAA 0.883564 -229 TGAATGTTTTATGATCAAAATGATACACCAC 3 46 0 ATGATCAAAT 0.816197 -205 TTGATCATAAAACATTCAAAAACATCTCTCT 3 59 1 AACATTAAAA 0.890448 -192 TGGAAAATAGAAGATCCAAATTATAACAATT 3 150 0 AAGATCAAAT 0.932577 -101 AAAGTGAACCAAGATCGAAAAGCTTATTAGC 3 182 1 AAGATCAAAA 0.977315 -69 GCCCTTATTTAAACACCAAAATTTTTATTTA 4 38 1 AAACACAAAA 0.874474 -80 ATATTATCGCATAAATAAAAATTTTGGTGTT 4 49 0 ATAAATAAAA 0.796998 -69 AAGGGTTTCTAAAATTTAAAAATCAAGGAGA 5 31 0 AAAATTAAAA 0.963524 -168 GTAGTTTTACAAGCTTGAAAAAGATAATGTT 5 134 1 AAGCTTAAAA 0.959409 -65 ****** **** Masking position 8 Map Score: 14.5615 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 276 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 2 TTTATTTTTATTCCCCTTTTCTTTGTTGGAGGTG 2 13 1 TTCCCTCTTT 0.981939 -29 ATCTCTCTAATTCCCTTATTTTTTGAGATGTTTA 3 82 1 TTCCCTTTTT 0.982291 -169 TAATCTTTCTTCTCTCTTTTCTTTATTGCC 4 7 1 TTCTTTTTTT 0.957273 -111 ATTTGCCCCTCCTTGTACATTCTTGTTCTATAA 4 95 0 TCCTTTTTCT 0.853646 -23 TTTCTCCTCCCCTTTAGTTTTCTCC 5 2 1 TTCTCTCTTT 0.989692 -197 CCCTTTAGTTTTCTCCTTGATTTTTAAATTTTAG 5 20 1 TTCTCTTTTT 0.989894 -179 TTAGAAACCCTTCTCTTAAGCTCTCTTTCTCGTT 5 50 1 TTCTCTCTCT 0.989486 -149 TAAGCTCTCTTTCTCGTTAGTTCTTTCGGCTTAT 5 66 1 TTCTCTTTCT 0.989692 -133 ***** * **** Masking position 7 Map Score: 10.8725 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 207 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 TTCAATTCGACAAATTTATTCAAAAATATAGG 1 22 1 CAAATTTACA 0.929637 -153 TAAGCATCTTCAAGGTGAAACAATAAGC 3 7 0 CAAGGTGACA 0.994937 -244 GTTTTATGATCAAAATGATACACCACTGATTT 3 40 0 CAAAATGACA 0.922387 -211 TTCATTTACACTAGGTTAAACATCTCAAAAAA 3 100 0 CTAGGTTACA 0.956905 -151 CTATTTTCCACAAAGTGAACCAAGATCGAAAA 3 171 1 CAAAGTGACA 0.98715 -80 CATCACCAGGGAAGGTTATCCAAAGAGATATA 3 225 0 GAAGGTTACA 0.953503 -26 CAAGAATGTACAAGGAGGGGCAAAT 4 103 1 CAAGGAGGCA 0.952253 -15 TTTGAAGGAACAAGTTTGAACATTATCTTTTT 5 151 0 CAAGTTTGCA 0.950348 -48 ******** ** Masking position 3 Map Score: 7.31274 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 103 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 CAAGATTGCATTAGTGATATGTTAAAATTTA 1 56 0 TTAGGATATG 0.954626 -119 CCCTTTTCTTTGTTGGAGGTGAGAGA 2 26 1 TGTTGAGGTG 0.94298 -16 AATAAGGGAATTAGAGAGATGTTTTTGAATG 3 71 0 TTAGGAGATG 0.990974 -180 ATTCCCTTATTTTTTGAGATGTTTAACCTAG 3 91 1 TTTTGAGATG 0.971435 -160 GAAAAGCTTATTAGCGAGGTGCCTGGTTATA 3 198 1 TTAGGAGGTG 0.991633 -53 **** ****** Masking position 7 Map Score: 2.21044 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 88 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 AATTTATTCAAAAATATAGGGTTAAATTTT 1 34 1 AAAATATAGG 0.942871 -141 AAGGGGAATAAAAATAAAAA 2 1 0 AAAATAAAAA 0.697174 -41 TCACCTCCAACAAAGAAAAGGGGAATAAAA 2 18 0 CAAAGAAAAG 0.876163 -24 CTTCAAGGTGAAACAATAAGC 3 2 0 AAACAATAAG 0.877748 -249 TAAACATCTCAAAAAATAAGGGAATTAGAG 3 86 0 AAAAAATAAG 0.919766 -165 CACTTTGTGGAAAATAGAAGATCCAAATTA 3 158 0 AAAATAGAAG 0.905972 -93 ATAAGGGCAATAAAGAAAAGAGAGAAGAAA 4 16 0 TAAAGAAAAG 0.826799 -102 ATCAAGGAGAAAACTAAAGGGGAGGAGAAA 5 11 0 AAACTAAAGG 0.911793 -188 CTAAAATTTAAAAATCAAGGAGAAAACTAA 5 24 0 AAAATCAAGG 0.756578 -175 AAAGTCATCTAAACGATAAGCCGAAAGAAC 5 85 0 AAACGATAAG 0.955053 -114 ACAAGCTTGAAAAAGATAATGTTCAAACTT 5 142 1 AAAAGATAAT 0.747728 -57 ********** Masking position 3 Map Score: 6.30647 Number of sites scoring better than the average of aligned sites = 662 Number in coding regions = 561 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 6 ATAGGGTTAAATTTTAACATATCACTAATG 1 49 1 ATTTTAACAT 0.878811 -126 GACGTACATAGTTTTAAGATTTAAAATTGG 1 143 1 GTTTTAAGAT 0.965603 -32 AAAAATCAGTGGTGTATCATTTTGATCATA 3 38 1 GGTGTATCAT 0.899692 -213 GTTTTTGAATGTTTTATGATCAAAATGATA 3 52 0 GTTTTATGAT 0.939214 -199 ATTTACACTAGGTTAAACATCTCAAAAAAT 3 99 0 GGTTAAACAT 0.932933 -152 GAAGGAACAAGTTTGAACATTATCTTTTTC 5 150 0 GTTTGAACAT 0.9613 -49 ********** Masking position 6 Map Score: 0.985283 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 67 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ********** No masking Map Score: -2.67574e-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: -2.67574e-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 9 ********** No masking Map Score: -2.67574e-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