AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i301_mixed16_hpyl_reg_300.orf -o301_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 RHP00970 121 AE000511 #2 RHP01128 300 AE000511 #3 RHP01129 16 AE000511 #4 RHP01130 21 AE000511 Motif number 1 AGTGTAAAATAACGCCATTATAACAAAAAGAAATGCAAGAAT 1 24 1 AAAATAAAAA 0.990895 -98 TTTTAAAAACAAACGAATTTTAATCAAAATGAGATTTAAGGG 1 83 1 AAATTAAAAA 0.992596 -39 AAAGAGAATGCATACAACAATAATTACGAATATTATATTCAT 2 11 1 CAAATAAAAA 0.966561 -290 TTTGGAAAGAAAAAAAATGTTAAAGAAGATTCAAAAATTCTC 2 62 0 AAATTAAAAC 0.969059 -239 TTTTCTTTCCAAAAAGAATAAAACTAACACCAAAAAAGACAA 2 91 1 AAAAAAAAAA 0.971744 -210 ACTAACACCAAAAAAGACAATAAATATTATTACAACATCTGA 2 113 1 AAAATAAAAA 0.990894 -188 TGATCACAGAAAACTCACATTAAAGAGTAAGAAATGCTTAAA 2 193 0 AAATTAAAAA 0.992596 -108 ATTCACATTATAGCAAATTTAAAACAAAATCAGCTATCATGA 2 232 0 TAATAAAAAA 0.883627 -69 AATTTGCTATAATGTGAATTTAATGATGAAAATTAGTTTAGA 2 255 1 AAATTAAAAA 0.992596 -46 ** * **** * * * Masking position 12 Map Score: 12.9957 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 87 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 CATTTTGATTAAAATTCGTTTGTTTTTAAAA 1 83 0 AAATTCGTTT 0.955459 -39 AATTTTAATCAAAATGAGATTTAAGGGTTAA 1 98 1 AAATGAGATT 0.896546 -24 AATAATTACGAATATTATATTCATAATTGCA 2 29 1 AAATTATATT 0.651574 -272 AATCTTCTTTAACATTTTTTTTCTTTCCAAA 2 73 1 AAATTTTTTT 0.839317 -228 CTTACTCTTTAATGTGAGTTTTCTGTGATCA 2 204 1 AAGTGAGTTT 0.976028 -97 AATTTGCTATAATGTGAATTTAATGATGAAA 2 255 1 AAGTGAATTT 0.904272 -46 TTTAATGATGAAAATTAGTTTAGAGTGGAGA 2 273 1 AAATTAGTTT 0.90889 -28 ** ******** Masking position 2 Map Score: 4.29036 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 237 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 3 ATAATGGCGTTATTTTACACTTTAAAGGGCTTTC 1 5 0 TTTCCTAAAC 0.977411 -117 ATTTTAGCTATGATAAGCGTTTTAAAAACAAACGAATTTT 1 64 1 TATCTTAAAA 0.958801 -58 TCTTTAACCCTTAAATCTCATTTTGATTAA 1 102 0 TTTCCTAATA 0.983508 -20 TCTTTAACATTTTTTTTCTTTCCAAAAAGAATAAAACTAA 2 78 1 TTTCTTAAAA 0.96129 -223 AGGCGAACACTTTTACCCGCTTTGAATGGAATGAATAACT 2 154 1 TTTCCTGAAA 0.977411 -147 AAATCAGCTATCATGATCACAGAAAACTCACATTAAAGAG 2 208 0 TATCCAAAAA 0.914431 -93 TCTAAACTAATTTTCATCATTAAATTCACATTATAGCAAA 2 257 0 TTTCTTATTA 0.806853 -44 TGTGTGTTCTCCACTCTAAACTAATTTTCATCAT 2 277 0 TTTCCTAAAA 0.993898 -24 * ** * ** *** * Masking position 4 Map Score: 5.05796 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 284 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 CGCCATTATAACAAAAAGAAATGCAAGAAT 1 36 1 ACAAAAAGAA 0.984566 -86 GAGAATGCATACAACAATAATTACGAATAT 2 14 1 ACAACAATAA 0.930124 -287 CTTTTTGGAAAGAAAAAAAATGTTAAAGAA 2 77 0 AGAAAAAAAA 0.866518 -224 TTTTTTCTTTCCAAAAAGAATAAAACTAAC 2 89 1 CCAAAAAGAA 0.985686 -212 AAAACTAACACCAAAAAAGACAATAAATAT 2 110 1 CCAAAAAAGA 0.962032 -191 TCAACAAGGAAAGAGTGTAA 4 1 1 TCAACAAGGA 0.945509 -21 ********** Masking position 6 Map Score: 3.8546 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 368 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 ATTTTACACTTTAAAGGGCTTTC 1 3 0 TTAAAGGCTT 0.959412 -119 CTTATCATAGCTAAAATTCTTGCATTTCTTT 1 50 0 CTAAATTCTT 0.977057 -72 TCGTTTGTTTTTAAAACGCTTATCATAGCTA 1 68 0 TTAAACGCTT 0.977529 -54 CTCATTTTGATTAAAATTCGTTTGTTTTTAA 1 85 0 TTAAATTCGT 0.958578 -37 TCTTTAACCCTTAAATCTCATTTTGATTAAA 1 101 0 TTAAACTCAT 0.928289 -21 TAAGAAATGCTTAAAGTTATTCATTCCATTC 2 177 0 TTAAATTATT 0.945251 -124 GTTCTCCACTCTAAACTAATTTTCATCATTA 2 275 0 CTAAATAATT 0.779317 -26 ***** ***** Masking position 5 Map Score: 2.70051 Number of sites scoring better than the average of aligned sites = 509 Number in coding regions = 422 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 6 ********** No masking Map Score: 2.72438e-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: 2.72438e-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: 2.72438e-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