AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i130_synecho_ctra_300.orf -o130_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 RCY28537 38 Synechocystis #2 RCY25783 171 Synechocystis #3 RCY43089 119 Synechocystis #4 RCY42092 106 Synechocystis #5 RCY13382 161 Synechocystis #6 RCY44868 300 Synechocystis #7 RCY30726 96 Synechocystis Motif number 1 GATAATCCTATTTTAATGGGTAGCTTACTTTGGCGATCGCCATTG 2 116 0 TATGGTCTTG 0.931787 -56 AGTAGTAGTAGTATTTAGTCACTCTTTTTATTGGATGGGGTCA 3 87 0 TATTGTCTTG 0.969483 -33 GTCAGTTTTCTGCGGATGAGTTACTAAATCCAGAGTTTTTTCCTG 5 46 1 TGTGGTCCCG 0.963342 -116 CAATTATTTTTTTGGCTTTGTCTGGTAAGCTTACGCTATCTGGTT 5 104 1 TGTTGTGCTG 0.994984 -58 GTCGATCAAGTAACGGTTTGTTACGGGTGTTAAGGGTTGGGGGTT 6 103 1 TGTTGTCTTG 0.994588 -198 TGTTAAGGGTTGGGGGTTTGTTGGATAAGCTGATGAGTGTCGGTT 6 130 1 TGTTGTGCTG 0.994984 -171 ATGTCGGACGTGATGATTCGGGTGGAAAATTTAGGCAAAAAGTAC 6 191 1 TGTTGGGTTG 0.962881 -110 CGTTACCCATTAAGGGCTTGTTTCAACGCCTTTAGTGA 7 4 0 TGCTGTCCTG 0.983901 -93 CCTTAATGGGTAACGGTTTGTTACGGGTGTTAGGGGTTGGGGCTT 7 34 1 TGTTGTCTTG 0.994588 -63 TGTTAGGGGTTGGGGCTTGGTTGGGTATGCTGGTGGCTAATGCTT 7 61 1 TGTTGTGCTG 0.994984 -36 * * ** ** * ** * Masking position 1 Map Score: 14.2127 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 76 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 GTTGAACAATGGCGATCGCCAAAGTAAGCT 2 110 1 GGCGATCGCC 0.499996 -62 AGGCGATCGCCTAGGAATTTG 3 2 1 GGCGATCGCC 0.499996 -118 CATTGTAATGGGCAAATTCCTAGGCGATCG 3 14 0 GGCAAATTCC 0.902178 -106 TAGATTTTCTGGCTGACCCCATCCAATAAA 3 74 1 GGCTGACCCC 0.959899 -46 TCCTCTAGAGGGCGATCGCCAAATGAAAAC 4 11 1 GGCGATCGCC 0.499996 -96 TGTGGTCTATGGCTAATTCCTAAAAGTTGT 5 18 1 GGCTAATTCC 0.974202 -144 GTATGCTGGTGGCTAATGCTTT 7 85 1 GGCTAATGCT 0.942714 -12 ********** Masking position 3 Map Score: 10.8561 Number of sites scoring better than the average of aligned sites = 5914 Number in coding regions = 5358 Number in noncoding regions = 556 Number of orfs with sites within 600 bp upstream = 336 Fraction of orfs with sites within 600 bp upstream = 0.0539672 Motif number 3 AACAAACAAATGGTTTTATGAGCTATTGAAGGATTTTA 2 18 1 TGTATAGCTG 0.987006 -154 GGTTTGACCGTGGCACAAGTTGCTCAGGTTGAACAGTT 2 75 1 TGCAGTGCTG 0.951865 -97 TTTTTTGGCTTTGTCTGGTAAGCTTACGCTATCTGGTT 5 111 1 TGTGTAGCTG 0.99488 -51 ATGATTTCATTCGTGTTGTCAGTTGTCGTTATCATTAC 6 43 1 TGTGTAGTTG 0.987006 -258 AAGTAACGGTTTGTTACGGGTGTTAAGGGTTGGGGGTT 6 110 1 TGTGGTGTTG 0.986746 -191 GGTTGGGGGTTTGTTGGATAAGCTGATGAGTGTCGGTT 6 137 1 TGTATAGCTG 0.987006 -164 GGGTAACGGTTTGTTACGGGTGTTAGGGGTTGGGGCTT 7 41 1 TGTGGTGTTG 0.986746 -56 GGTTGGGGCTTGGTTGGGTATGCTGGTGGCTAATGCTT 7 68 1 TGTGTTGCTG 0.99488 -29 * ** ** **** * Masking position 14 Map Score: 10.4405 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 47 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 TTGAGGTCAATTTTTGCTACGCCCAAAGGCCC 1 15 0 TTTTTGTAGC 0.940766 -24 ACAAACAAATGGTTTTATGAGCTATTGAAGGA 2 19 1 GGTTTTTGGC 0.952988 -153 CTTCTCTCCATTTTTGATGTGGTTAGATTTTC 3 51 1 TTTTTGTGGG 0.96215 -69 TCACTCTTTTTATTGGATGGGGTCAGCCAGAA 3 80 0 TATTGGTGGG 0.863036 -40 TTTTTTTTGTGGTCTATGGCTA 5 1 1 TTTTTTTGGG 0.862953 -161 AAAAGTTGTCAGTTTTCTGCGGATGAGTTACT 5 39 1 AGTTTTTGGG 0.822477 -123 TTTTTGGCTTTGTCTGGTAAGCTTACGCTATC 5 112 1 TGTCTGTAGC 0.913795 -50 ATCAAGTAACGGTTTGTTACGGGTGTTAAGGG 6 107 1 GGTTTGTAGG 0.986438 -194 GTTGGGGGTTTGTTGGATAAGCTGATGAGTGT 6 138 1 TGTTGGTAGC 0.972417 -163 AATGGGTAACGGTTTGTTACGGGTGTTAGGGG 7 38 1 GGTTTGTAGG 0.986438 -59 GTTGGGGCTTGGTTGGGTATGCTGGTGGCTAA 7 69 1 GGTTGGTAGC 0.974487 -28 ****** ** ** Masking position 8 Map Score: 11.9599 Number of sites scoring better than the average of aligned sites = 671 Number in coding regions = 603 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 GAACAATGGCGATCGCCAAAGTAAGCTACC 2 113 1 GATCGCCAAA 0.989847 -59 AGGCGATCGCCTAGGAATTTGCCC 3 5 1 GATCGCCTAG 0.98841 -115 TCTAGAGGGCGATCGCCAAATGAAAACCAA 4 14 1 GATCGCCAAA 0.989847 -93 GCTTACCAGACAAAGCCAAAAAAATAATTG 5 104 0 CAAAGCCAAA 0.898073 -58 GCCCTAACCAGATAGCGTAAGCTTACCAGA 5 124 0 GATAGCGTAA 0.869444 -38 TCAAGAGCATCGCCTAGTTTACGAAGT 6 8 1 CATCGCCTAG 0.984591 -293 AACCAAGCCCCAACCCCTAACACCCGTAAC 7 53 0 CAACCCCTAA 0.889938 -44 ********** Masking position 2 Map Score: 7.09034 Number of sites scoring better than the average of aligned sites = 1999 Number in coding regions = 1774 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 6 ATGGCAACAAACAAATGGTTTTATGAGCTA 2 13 1 ACAAATGGTT 0.969931 -159 ATTAATTTTAACAATTGGTTTTCATTTGGC 4 28 0 ACAATTGGTT 0.927361 -79 AACACCCGTAACAAACCGTTACTTGATCGA 6 104 0 ACAAACCGTT 0.990642 -197 AGGCGTTGAAACAAGCCCTTAATGGGTAAC 7 18 1 ACAAGCCCTT 0.946343 -79 AACACCCGTAACAAACCGTTACCCATTAAG 7 35 0 ACAAACCGTT 0.990642 -62 ********** Masking position 4 Map Score: 3.472 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 32 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 CATCCAATAAAAAGAGTGACTAAATACTACT 3 93 1 AAAGAGTGAT 0.948458 -27 GTGCAGCTTAGAAGAGTGAATTAATTTTAAC 4 46 0 GAAGAGTGAT 0.991662 -61 GTTTTCTGCGGATGAGTTACTAAATCCAGAG 5 50 1 GATGAGTTAT 0.948465 -112 TGGATAAGCTGATGAGTGTCGGTTCTCGATT 6 151 1 GATGAGTGTG 0.914762 -150 TAGGCAGAAGGAAGGGTGAATGATAATCACT 6 248 1 GAAGGGTGAT 0.977529 -53 ATACAAACGTGTTGAGTGATTATCATTCACC 6 262 0 GTTGAGTGAT 0.967016 -39 ********* * Masking position 7 Map Score: 3.32845 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 21 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 TGCCCATTACAATGAAATCATCTTCTCTCC 3 30 1 AATGAAATCA 0.932256 -90 GCGATCGCCAAATGAAAACCAATTGTTAAA 4 22 1 AATGAAAACC 0.965178 -85 TGACAACACGAATGAAATCATCGGTGACTT 6 34 0 AATGAAATCA 0.932256 -267 TGCTATCGGTAATGATAACGACAACTGACA 6 59 0 AATGATAACG 0.968756 -242 AAATACGATTAATGCTATCGGTAATGATAA 6 71 0 AATGCTATCG 0.941258 -230 AGGAAGGGTGAATGATAATCACTCAACACG 6 256 1 AATGATAATC 0.73411 -45 ACTTTGTTTAAATACAAACGTGTTGAGTGA 6 274 0 AATACAAACG 0.778956 -27 ********** Masking position 7 Map Score: 2.6311 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 222 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 GGTCAAACCCAATTCAGGCAACTGTATTTAA 2 53 0 AATCAGGCAA 0.852319 -119 ATGGGTAGCTTACTTTGGCGATCGCCATTGT 2 115 0 TATTTGGCGA 0.956404 -57 AATGGGCAAATTCCTAGGCGATCGCCT 3 7 0 TTCTAGGCGA 0.946599 -113 CAATTGGTTTTCATTTGGCGATCGCCCTCTA 4 16 0 TCTTTGGCGA 0.947625 -91 GTGACTTCGTAAACTAGGCGATGCTCTTGA 6 10 0 AACTAGGCGA 0.979061 -291 TCGGGTGGAAAATTTAGGCAAAAAGTACATG 6 208 1 AATTAGGCAA 0.949385 -93 ACATGATTGGTCACTAGGCAGAAGGAAGGGT 6 234 1 TCCTAGGCAG 0.882571 -67 ** ******** Masking position 7 Map Score: 0.8879 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 510 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 10 ********** No masking Map Score: 2.54618e-12 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: 2.54618e-12 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 12 ********** No masking Map Score: 2.54618e-12 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