AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i275_hypothetical2_pyro_reg_300.orf -o275_pyro_300.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 RPH00884 300 Pyrococcus_OT3 #2 RPH01143 300 Pyrococcus_OT3 #3 RPH01145 147 Pyrococcus_OT3 #4 RPH01150 235 Pyrococcus_OT3 #5 RPH01151 78 Pyrococcus_OT3 #6 RPH01152 38 Pyrococcus_OT3 #7 RPH01153 136 Pyrococcus_OT3 Motif number 1 CACACTACTGAGTTCTACGGAAACAGGCAAGTG 1 51 0 AGTCTGGAAA 0.997585 -250 CGTAGAACTCAGTAGTGTGGAAAGACCTCTGGG 1 65 1 AGTGTGGAAA 0.997011 -236 CACACTACTAAGTTCTACGGAAACGGAGGTGGT 1 118 0 AGTCTGGAAA 0.997585 -183 CGTAGAACTTAGTAGTGTGGAAAGAGAACCAGT 1 132 1 AGTGTGGAAA 0.997011 -169 CACACTACTAAGTTCTACGGAAACCCAGCTGCC 1 186 0 AGTCTGGAAA 0.997585 -115 CGTAGAACTTAGTAGTGTGGAAAGCCAAACTCT 1 200 1 AGTGTGGAAA 0.997011 -101 GGCACTATTTAGTTCTACGGAAACACCATTGAG 1 253 0 AGTCTGGAAA 0.997585 -48 AATAATAACAAGTAGTTAGTAAACATACCATGC 2 178 1 AGTGTGTAAA 0.970328 -123 GTGAGTGGGTAGATCTAGGGAAGTTCCTCCATG 3 15 1 AGACTGGAAG 0.938343 -133 *** ** ***** Masking position 6 Map Score: 27.6921 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 39 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 2 AATTGGCGAAGTCTTTCCACACT 1 4 0 GTCTTTCCAC 0.985313 -297 ATTGCCGACGCCCTTTCCGACACTTGCCTG 1 31 1 CCCTTTCCGA 0.944665 -270 CGACACTTGCCTGTTTCCGTAGAACTCAGT 1 48 1 CTGTTTCCGT 0.974408 -253 TACCCCAGAGGTCTTTCCACACTACTGAGT 1 71 0 GTCTTTCCAC 0.985313 -230 AACACCACCTCCGTTTCCGTAGAACTTAGT 1 115 1 CCGTTTCCGT 0.955675 -186 GCTACTGGTTCTCTTTCCACACTACTAAGT 1 138 0 CTCTTTCCAC 0.978454 -163 GCTGGCAGCTGGGTTTCCGTAGAACTTAGT 1 183 1 GGGTTTCCGT 0.969561 -118 GGAAGAGTTTGGCTTTCCACACTACTAAGT 1 206 0 GGCTTTCCAC 0.974352 -95 CTTCTCAATGGTGTTTCCGTAGAACTAAAT 1 250 1 GTGTTTCCGT 0.982532 -51 GGTCTTTCCTAGCTTTACCTC 3 137 0 GTCTTTCCTA 0.873259 -11 ********** Masking position 5 Map Score: 15.7369 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 102 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 CGTAGAACTAAATAGTGCCTAAATCATAATTTAG 1 267 1 AATATTAAAT 0.913201 -34 TTTAAAAACCAATATTCTAAAAATGGTCAGATAA 2 46 1 AATATAAAAT 0.935351 -255 GAAAACTCTAAAAAATCTGTAATTATCTGACCAT 2 68 0 AAAATTAATT 0.868941 -233 TTATCACGAAAAAATTTCAAAAATAAGAAGTTAA 2 115 0 AAAATAAAAT 0.976039 -186 TTATTTTGCAAAAAGTTACAAAATAAATAGTATT 2 149 0 AAAATAAAAT 0.976041 -152 AATAATAACAAGTAGTTAGTAAACATACCATGCC 2 178 1 AGTATTAAAC 0.670881 -123 TACATTCATTAAAACTATCTAATTCCTTTATGCG 2 228 1 AAAATTAATT 0.868941 -73 TTACTTAATAAAATTTAAAAAATTACTCTCTTT 4 10 1 AAAATAAAAT 0.976039 -226 ATAATAACCTAAAAATACGAAAATAAAGAGAGTA 4 34 0 AAAATAAAAT 0.976041 -202 TGATTCAAGAAAAAGTTAAAAGATATAAATGCTT 4 67 1 AAAATAAGAT 0.874897 -169 ATTAGTCGTCAGAACTTAAAAAACTTATCATCCC 5 23 0 AGAATAAAAC 0.887551 -56 ACGTTCAACGAGAAGTTTATAAATCCTTAGGGGA 7 90 1 AGAATTAAAT 0.942998 -47 **** * ***** Masking position 4 Map Score: 12.2501 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 74 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 4 GCTTGAAAACAAGGAAGAGTTTGGCTTTCCAC 1 216 0 AAGAAGAGTT 0.917739 -85 AAACACCATTGAGAAGGAGCTTGAAAACAAGG 1 234 0 GAAAGGAGTT 0.852948 -67 TCAAAAATAAGAAGTTAAGTTTATGAGATCGG 2 101 0 GAGTTAAGTT 0.87804 -200 TCCTTTATGCGATGAAAAGGATTATAACATCT 2 251 1 GAGAAAAGAT 0.921347 -50 GTATGAGAACGAGGAAAAGGAAGTTCTGATAG 3 55 1 GAGAAAAGAA 0.759023 -93 AAGAGGAGACGTCATAGAGGTTCATGAGGTAA 3 112 1 GTATAGAGTT 0.599357 -36 AGAGGTTCATGAGGTAAAGCTAGGAAAGACC 3 127 1 GAGTAAAGTA 0.857816 -21 ATTATGATTCAAGAAAAAGTTAAAAGATATAA 4 63 1 AAAAAAAGTA 0.494772 -173 ATTTATGTATGAAGTAGAGTTTGAAATAGAGC 4 125 1 GAGTAGAGTT 0.960537 -111 AGTAGAGTTTGAAATAGAGCTTATAACCCTTG 4 137 1 GAATAGAGTT 0.896047 -99 TAACCAGAGGGAACAAGAGATTGAGGCTTTCT 4 176 1 GACAAGAGTT 0.859541 -60 CAATTTGTGGGATGATAAGTTTTTTAAGTTCT 5 15 1 GAGATAAGTT 0.933272 -64 ACTAATGGTAGTTGATAAGTTTCAATTAGGTG 5 51 1 GTGATAAGTT 0.708234 -28 TAAGTATATTAAAAAAAAGAATAATAAAGATA 6 13 0 AAAAAAAGAT 0.494772 -26 TACAACGTTCAACGAGAAGTTTATAAATCCTT 7 86 1 AAGAGAAGTT 0.780906 -51 ** ****** ** Masking position 8 Map Score: 9.61429 Number of sites scoring better than the average of aligned sites = 1357 Number in coding regions = 1257 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 5 TCTTTCCACACTACTGAGTTCTACGGAAACA 1 59 0 CTACTGAGTC 0.984099 -242 GCAAGTCATACCCCAGAGGTCTTTCCACACT 1 78 0 CCCCAGAGTC 0.924546 -223 TCTTTCCACACTACTAAGTTCTACGGAAACG 1 126 0 CTACTAAGTC 0.986835 -175 GCTTTCCACACTACTAAGTTCTACGGAAACC 1 194 0 CTACTAAGTC 0.986835 -107 CAAGACCATAACACTCAGCTCTTCATATTTA 2 12 1 ACACTCAGTC 0.861196 -289 TTCAACAAGCCTCCTACGCTCTAAGAAAGCA 4 214 0 CTCCTACGTC 0.971409 -22 ACGAACATTGATACAACGTTCAACGAGAAGT 7 75 1 ATACAACGTC 0.856978 -62 ******** ** Masking position 10 Map Score: 3.5316 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 69 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 TAGTGTGGAAAGAGAACCAGTAGCCTGTTA 1 144 1 AGAGAACCAG 0.983214 -157 AGAAGGAGCTTGAAAACAAGGAAGAGTTTG 1 225 0 TGAAAACAAG 0.877121 -76 GAAACACCATTGAGAAGGAGCTTGAAAACA 1 237 0 TGAGAAGGAG 0.869374 -64 ATCATAATTTAGGTGACCAGGG 1 289 1 AGGTGACCAG 0.810085 -12 TTTTGCAAAATAATAACAAGTAGTTAGTAA 2 170 1 TAATAACAAG 0.668223 -131 AGCAGAGGTATGAGAACGAGGAAAAGGAAG 3 48 1 TGAGAACGAG 0.975735 -100 CCCTTGCAAGAGATAACCAGAGGGAACAAG 4 163 1 AGATAACCAG 0.96594 -73 AGATAACCAGAGGGAACAAGAGATTGAGGC 4 173 1 AGGGAACAAG 0.954739 -63 ********** Masking position 6 Map Score: 3.47994 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 137 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 ATTTAGGCACTATTTAGTTCTACGGAAACA 1 261 0 TATTTAGTTC 0.816773 -40 CAGCTCTTCATATTTAGTGTTTAAAAACCA 2 27 1 TATTTAGTGT 0.923139 -274 GATAAAATACTATTTATTTTGTAACTTTTT 2 144 1 TATTTATTTT 0.923058 -157 AAAATTACTCTCTTTATTTTCGTATTTTTA 4 29 1 TCTTTATTTT 0.961207 -207 ATTGAGGCTTTCTTTAGTGTGCTTTCTTAG 4 195 1 TCTTTAGTGT 0.961249 -41 GTTATCTTTATTATTCTTTTTTTT 6 5 1 TCTTTATTAT 0.882781 -34 TCTTTATTATTCTTTTTTTTAATATACTTA 6 15 1 TCTTTTTTTT 0.83724 -24 ********** Masking position 5 Map Score: 2.79717 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 87 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 AACTAAATAGTGCCTAAATCATAATTTAGGTGA 1 272 1 TCTAATCATA 0.978081 -29 GAGAGAAGAGTACATTCATTAAAACTATCTAAT 2 218 1 TCTCATTAAA 0.847587 -83 TTTTAACTTTTTCTTGAATCATAATAACCTAAA 4 55 0 TCTAATCATA 0.978081 -181 AAGATATAAATGCTTTAATTATATCTTGAATTA 4 86 1 TCTAATTATA 0.965961 -150 CTCTACTTCATACATAAATTATCACTAATTCAA 4 111 0 TCTAATTATC 0.959228 -125 TGTATCAATGTTCGTTAATCAACGATATTAGAT 7 57 0 TCTAATCAAC 0.951986 -80 * * * ******* Masking position 8 Map Score: 0.742142 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 20 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 ********** No masking Map Score: 3.15071e-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 10 ********** No masking Map Score: 3.15071e-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 11 ********** No masking Map Score: 3.15071e-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