AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i234_sensory_cassete_hpyl_reg_300.orf -o234_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 RHP01119 235 AE000511 #2 RHP01121 46 AE000511 #3 RHP01123 74 AE000511 #4 RHP01124 60 AE000511 #5 RHP01127 300 AE000511 Motif number 1 AAGACTTTATTTTTCAATATTCCATGAAAACAAAG 1 49 1 TTTTAAATAT 0.989473 -187 TGAATTTTTATTTTTAAGATATTTTCAAGGTATCT 1 118 1 TTTTAAATTT 0.979899 -118 AGCATTTTATTATTAAAGATACCTTGAAAATATCT 1 134 0 TATTAAATTT 0.923641 -102 CTCTTAATCATTTTCAATACCTAATCTCTAAACGC 2 16 0 TTTTAAACAT 0.970217 -31 TATAAAACGCTTTTTAAAACCAATTGGCAAGGAAC 3 46 1 TTTTAAACTT 0.944119 -29 AATGGCTTTTAACAATGCTATAATGATAAGT 4 7 1 TTTTACATAT 0.946527 -54 ATGAGTGGGGTTTTGAACTTATCATTATAGCATTG 4 23 0 TTTTAATTAT 0.91587 -38 TTTTGAATCTTCTTTAACATTTTTTTTCTTTCCAA 5 89 0 TCTTAAATTT 0.910449 -212 CTCGATGCAATTATGAATATAATATTCGTAATTAT 5 127 1 TTATAAATAT 0.954624 -174 TATATTTGGTTTTTTAGCATTGCATGTTATCCCAT 5 207 1 TTTTAGATAT 0.946527 -94 GTATAGAAGTTATTTAATATGGGATAACATGCAAT 5 225 0 TATTAAATAT 0.958885 -76 CATAGTAAGCTTATCAATATGAGATTGATTAATAG 5 261 0 TTATAAATAT 0.954663 -40 **** ** ** ** Masking position 6 Map Score: 15.8796 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 263 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 AAAACGATCAAAGGAATTGTT 1 1 1 AAAACATCAA 0.848086 -235 GGAATTGTTTAAAAACATTAAAAAATAAGAC 1 23 1 AAAAAATTAA 0.967235 -213 AAAATATCTTAAAAATAAAAATTCAAAACAT 1 112 0 AAAAAAAAAA 0.887403 -124 ATTAGTCCCCTAAAACATTAACAAAGTTAAT 1 172 1 TAAAAATTAA 0.789502 -64 TGCAACTTTAAAAACGATTAACTTTGTTAAT 1 188 0 AAAACATTAA 0.954584 -48 TTAGGTATTGAAAATGATTAAGAGAAACGC 2 27 1 AAAATATTAA 0.841012 -20 AACACCAAAAAAGACAATAAATATTATTACA 5 45 0 AAGACATAAA 0.898996 -256 TTTTCTTTCCAAAAAGAATAAAACTAACACC 5 70 0 AAAAAAATAA 0.945668 -231 TCTTTTTGGAAAGAAAAAAAATGTTAAAGAA 5 84 1 AAGAAAAAAA 0.880533 -217 AAAAATGTTAAAGAAGATTCAAAAATTCTCG 5 100 1 AAGAAATTCA 0.838685 -201 ACCAAATATAAAGAATAATAACCCTGGTAAC 5 186 0 AAGAAAATAA 0.942121 -115 ***** ***** Masking position 7 Map Score: 12.3894 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 379 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 3 TAATGTTTTTAAACAATTCCTTTGATCGTTTT 1 11 0 AAACAACCTT 0.983211 -225 GAATATTGAAAAATAAAGTCTTATTTTTTAAT 1 39 0 AAATAATCTT 0.937432 -197 TATTCCATGAAAACAAAGCCTTAAATTTCCAT 1 66 1 AAACAACCTT 0.983292 -170 TAAAAATTCAAAACATTATCATAGTTATTAAT 1 96 0 AAACATTCAT 0.89774 -140 ACTTCAATTAACTCCTTCAATGATTTC 1 219 0 AATTAACCTT 0.910037 -17 CGTTTCTCTTAATCATTTTCAATACCTAATCT 2 24 0 AATCATTCAA 0.592709 -23 AAACAGAACCTTTATGAGTGGG 4 49 0 AAACAGCCTT 0.94767 -12 ATCCCATATTAAATAACTTCTATACTCTATTA 5 235 1 AAATAATCTA 0.82562 -66 ATACTCTATTAATCAATCTCATATTGATAAGC 5 256 1 AATCAATCAT 0.926359 -45 ****** **** Masking position 5 Map Score: 6.52483 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 543 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 4 AAGTCTTATTTTTTAATGTTTTTAAACAAT 1 26 0 TTTTAATGTT 0.71531 -210 AAGGCTTTGTTTTCATGGAATATTGAAAAA 1 58 0 TTTCATGGAA 0.755876 -178 TTCAAAACATTATCATAGTTATTAATGGAA 1 92 0 TATCATAGTT 0.905012 -144 TTTAAGATATTTTCAAGGTATCTTTAATAA 1 130 1 TTTCAAGGTA 0.945995 -106 CCTAAAACATTAACAAAGTTAATCGTTTTT 1 180 1 TAACAAAGTT 0.777372 -56 AGTTAATCGTTTTTAAAGTTGCAGAAATCA 1 196 1 TTTTAAAGTT 0.910591 -40 TTAAAAAGCGTTTTATAGTAACCATAATTT 3 33 0 TTTTATAGTA 0.909899 -42 TCCCTTAATCTTACATAGTAAGCTTATCAA 5 279 0 TTACATAGTA 0.904646 -22 ********** Masking position 5 Map Score: 1.81162 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 258 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 CCTAATCTCTAAACGCCATTT 2 2 0 AAACGCCATT 0.984145 -45 GGTTACTATAAAACGCTTTTTAAAACCAAT 3 40 1 AAACGCTTTT 0.620062 -35 AACGCTTTTTAAAACCAATTGGCAAGGAAC 3 51 1 AAAACCAATT 0.890014 -24 TAGCATTGTTAAAAGCCATT 4 1 0 AAAAGCCATT 0.953041 -60 GATAAGTTCAAAACCCCACTCATAAAGGTT 4 35 1 AAACCCCACT 0.970525 -26 ********** Masking position 3 Map Score: 2.03407 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 340 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 AATAATAAAATGCTAGAATTAGTCCCCTAAA 1 155 1 TGCTAAATTA 0.959707 -81 TTCAATTAACTCCTTCAATGATTTCTGCAAC 1 213 0 TCCTTAATGA 0.894801 -23 GTGCGCTAAAATGACAGCCGATAA 3 4 1 CGCTAAATGA 0.982457 -71 CTTTTAACAATGCTATAATGATAAGTTCAAA 4 16 1 TGCTAAATGA 0.991715 -45 AAATTCTCGATGCAATTATGAATATAATATT 5 122 1 TGCAATATGA 0.919925 -179 ***** ***** Masking position 8 Map Score: 1.14673 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 83 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 ********** No masking Map Score: 8.83505e-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: 8.83505e-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: 8.83505e-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