AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i291_hish_mthe_reg_300.orf -o291_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH01560 125 M.thermo #2 RTH00070 26 M.thermo #3 RTH01863 142 M.thermo #4 RTH00604 99 M.thermo #5 RTH00031 136 M.thermo Motif number 1 CATGAGAACACTTCAAGAGGAATTTAA 1 8 0 CTTCAAGAGG 0.968462 -118 GATCATTCAGCTTCATGAGAACACTTCAAG 1 21 0 CTTCATGAGA 0.917934 -105 GCTGAATGATCTGCATGGGATAATATTTTA 1 40 1 CTGCATGGGA 0.950377 -86 CTCATATGGGATGTCCTGAT 2 1 1 CTCATATGGG 0.815696 -26 GCTCCTATCTGAAATAGGGGAACCCGCT 3 9 1 CTGAAATAGG 0.963336 -134 TGTTGAACAGCTCATTGAGGCCCTTGATGA 3 38 1 CTCATTGAGG 0.957501 -105 AGGGGTTCAACTGCTCTGGGATCTCCAATG 3 113 0 CTGCTCTGGG 0.857829 -30 AGCCTTTATGAGGGGTTCAACTG 3 130 0 CTTTATGAGG 0.867975 -13 TGCATTCAACCTCCCTGAGGTCATTTCCTT 4 62 1 CTCCCTGAGG 0.950846 -38 GGGGTTACTGAAAGATGGAAGGAAATG 4 83 0 CTGAAAGATG 0.854036 -17 CCATGAACTGCTGCAATAGATATTTAACCC 5 70 1 CTGCAATAGA 0.917034 -67 AATGATCATTCTGATGGAGGAGATTTATC 5 118 1 CTGATGGAGG 0.946168 -19 ********** Masking position 2 Map Score: 11.985 Number of sites scoring better than the average of aligned sites = 2696 Number in coding regions = 2585 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 TCATAAAAACCCCCAGCTTCCAAACTATTTTT 1 83 0 CCCCGCTCCA 0.995982 -43 CTCATTGAGGCCCTTGATGACAGTGACAAATC 3 48 1 CCCTGATACA 0.983678 -95 TGCTGCGGCCCCCCTCCTAACAGATTTGTCAC 3 70 0 CCCCCCTACA 0.997937 -73 GCCGCAGCAGCCCTGGGTAACATTGGAGATCC 3 93 1 CCCTGGTACA 0.980641 -50 GTAAACCCTTCACCCCATCACACTGAACCGGA 4 11 0 CACCCATACA 0.978071 -89 TCCCTGAGGTCATTTCCTTCCATCTTTCAGTA 4 73 1 CATTCCTCCA 0.847982 -27 ATTTAAGAATCCCCACCATATAATTCACAGTT 5 20 0 CCCCCCAATA 0.928722 -117 **** *** *** Masking position 12 Map Score: 4.98515 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 371 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 AGCTGAATGATCTGCATGGGATAATATTTT 1 39 1 TCTGCATGGG 0.838641 -87 AAATAGTTTGGAAGCTGGGGGTTTTTATGA 1 85 1 GAAGCTGGGG 0.988539 -41 GCTCCTATCTGAAATAGGGGAACCCGCTGT 3 11 1 GAAATAGGGG 0.826537 -132 AATGAGCTGTTCAACAGCGGGTTCCCCTAT 3 24 0 TCAACAGCGG 0.871482 -119 GACAAATCTGTTAGGAGGGGGGCCGCAGCA 3 72 1 TTAGGAGGGG 0.977101 -71 GTTACCCAGGGCTGCTGCGGCCCCCCTCCT 3 84 0 GCTGCTGCGG 0.962436 -59 AGCCTTTATGAGGGGTTCAACTGCT 3 128 0 TTATGAGGGG 0.826537 -15 AATGCACACTGAAGGTCCGGCCATGGTAAA 4 38 0 GAAGGTCCGG 0.873216 -62 CTGTGAATTATATGGTGGGGATTCTTAAAT 5 22 1 TATGGTGGGG 0.978615 -115 TGATCATTCTGATGGAGGAGATTTATC 5 120 1 GATGGAGGAG 0.903235 -17 ********** Masking position 10 Map Score: 6.45988 Number of sites scoring better than the average of aligned sites = 2261 Number in coding regions = 2125 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 4 TTAAATTCCTCTTGAAGTGT 1 1 1 TTAAATTCCT 0.981691 -125 GTGGGGATTCTTAAATACCTTGTGCATACC 5 36 1 TTAAATACCT 0.989577 -101 AAATAAAGGGTTAAATATCTATTGCAGCAG 5 77 0 TTAAATATCT 0.972007 -60 ********** Masking position 5 Map Score: 1.60949 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 5 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 CTCTTGAAGTGTTCTCATGAAGCTGAATGA 1 19 1 GTTCTCATGA 0.936273 -107 GGAATATGAAGACATCATAAAAACCCCCAG 1 99 0 GACATCATAA 0.902559 -27 TCAGATATCAGGACATCCCATAT 2 14 0 GATATCAGGA 0.975173 -13 ATTTGTCACTGTCATCAAGGGCCTCAATGA 3 49 0 GTCATCAAGG 0.929084 -94 TAACATTGGAGATCCCAGAGCAGTTGAACC 3 110 1 GATCCCAGAG 0.923072 -33 GGAAGGAAATGACCTCAGGGAGGTTGAATG 4 64 0 GACCTCAGGG 0.993494 -36 ********** Masking position 7 Map Score: 1.52215 Number of sites scoring better than the average of aligned sites = 1763 Number in coding regions = 1702 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 6 ********** No masking Map Score: -5.09159e-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: -5.09159e-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: -5.09159e-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