AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i151_synecho_ctra_300.orf -o151_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY26449 200 Synechocystis #2 RCY32207 26 Synechocystis #3 RCY00731 247 Synechocystis #4 RCY50499 40 Synechocystis Motif number 1 CCTGAGCAGTCCTTACCCATCTTACGGGGAC 1 20 1 CCTTACCATC 0.987666 -181 TGACCCAATTCCTATTCCATCAATAACCGAC 1 63 1 CCTATCCATC 0.877435 -138 CACAAATTAGCCTTAACGGTCGGTTATTGAT 1 81 0 CCTTACGGTC 0.952768 -120 TGGCCCCAAACTTTGGCGATCGCCTTACTAT 1 142 1 CTTTGCGATC 0.946486 -59 AGTTTTTGTTTCTTGTCCATTTATTGAAGCC 3 20 0 TCTTGCCATT 0.979843 -228 AAAGCTGAGGCCTTGGGGATTATTTTTAGCT 3 60 0 CCTTGGGATT 0.938269 -188 CTGGTTGGCTTCTTGATCATCAAACTGGTAG 3 119 1 TCTTGTCATC 0.914276 -129 GATAAGCATCGCTTGTCCGTTCAACCAACAA 3 172 1 GCTTGCCGTT 0.973513 -76 ATAAGCTTTTGCTTGACCATTTTTTGTTGGT 3 195 0 GCTTGCCATT 0.986865 -53 ***** ***** Masking position 3 Map Score: 8.99778 Number of sites scoring better than the average of aligned sites = 1636 Number in coding regions = 1466 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 2 ACGGAGGTCTTGATCTGCATAGTAAGGCGA 1 161 0 TGATCTGCAT 0.92196 -40 AAACAAAAACTTTTAAGCAAAGCTAAAAAT 3 40 1 TTTTAAGCAA 0.826365 -208 TTAGAGAATTTGAAAAGCTTTTAGAACTAT 3 89 1 TGAAAAGCTT 0.884227 -159 GTTGGCTTCTTGATCATCAAACTGGTAGTC 3 122 1 TGATCATCAA 0.895298 -126 GGTACTCCTATGATAAGCATCGCTTGTCCG 3 161 1 TGATAAGCAT 0.991483 -87 TTGCTTAACTTGATAAGCTTTTGCTTGACC 3 208 0 TGATAAGCTT 0.977074 -40 AAGCTTATCAAGTTAAGCAATTTCTCAATC 3 218 1 AGTTAAGCAA 0.884227 -30 TTACTTAAATTGATAACCAATTACCACTAA 4 15 1 TGATAACCAA 0.95723 -26 ********** Masking position 8 Map Score: 6.30024 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 317 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 ACCTTTACGCTGTCCCCGTAAGATGGGTAAG 1 31 0 TGTCCCGTAA 0.970259 -170 GGAAAAAAATCAAAGTAAACACGGAGGT 1 183 0 AATCAAGTAA 0.941791 -18 TTTTGTTTCTTGTCCATTTATTGAAGCCTTA 3 17 0 TGTCCATTAT 0.930621 -231 TCAAACTGGTAGTCACCGTATTTGGTACTCC 3 138 1 AGTCACGTAT 0.918729 -110 AGCAAAAGCTTATCAAGTTAAGCAATTTCTC 3 213 1 TATCAATTAA 0.950491 -35 GGTAATTGGTTATCAATTTAAGTAAAGGA 4 9 0 TATCAATTAA 0.950491 -32 ****** **** Masking position 3 Map Score: 0.656386 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 91 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 CTCCTGAGCAGTCCTTACCCATCTTACGGGGA 1 18 1 GTCCTCCCAT 0.925203 -183 ATAGGAATTGGGTCAAACCTTTACGCTGTCCC 1 46 0 GGTCACCTTT 0.981825 -155 CAAAGTTTGGGGCCAATCCTTTGCATTGCTTT 1 125 0 GGCCACCTTT 0.996465 -76 CCCAAACTTTGGCGATCGCCTTACTATGCAGA 1 146 1 GGCGAGCCTT 0.983426 -55 TAATCCCCAAGGCCTCAGCTTTAGAGAATTTG 3 69 1 GGCCTGCTTT 0.99265 -179 ***** ***** Masking position 12 Map Score: 0.540317 Number of sites scoring better than the average of aligned sites = 726 Number in coding regions = 682 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 ATTCCTATTCCATCAATAACCGACCGTTAA 1 70 1 CATCAATAAC 0.932512 -131 TGTGAGTAAACAAATATAAAGCAATGCAAA 1 108 1 CAAATATAAA 0.825921 -93 GGAAAAAAATCAAAGTAAACACG 1 188 0 AAAAAATCAA 0.772974 -13 AATTCCTATTAAAAAATAAAA 2 2 0 AAAAAATAAA 0.917118 -25 CCTAATAAGGCTTCAATAAATGGACAAGAA 3 12 1 CTTCAATAAA 0.80999 -236 AATGGACAAGAAACAAAAACTTTTAAGCAA 3 30 1 AAACAAAAAC 0.869963 -218 TCCGTTCAACCAACAAAAAATGGTCAAGCA 3 187 1 CAACAAAAAA 0.953561 -61 ********** Masking position 6 Map Score: 0.407047 Number of sites scoring better than the average of aligned sites = 997 Number in coding regions = 811 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 6 GGACTGCTCAGGAGGGAACCT 1 2 0 GGAGGGAACC 0.938022 -199 AATAGGAATTGGGTCAAACCTTTACGCTGT 1 49 0 GGGTCAAACC 0.955133 -152 GCCAAAGTTTGGGGCCAATCCTTTGCATTG 1 129 0 GGGGCCAATC 0.988682 -72 TGATGATCAAGAAGCCAACCAGATAGTTCT 3 111 0 GAAGCCAACC 0.983967 -137 ********** Masking position 7 Map Score: 0.148418 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 468 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 ********** No masking Map Score: -8.36008e-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: -8.36008e-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: -8.36008e-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