AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i127_synecho_ctra_300.orf -o127_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 RCY05023 300 Synechocystis #2 RCY00830 300 Synechocystis #3 RCY42642 30 Synechocystis #4 RCY10675 228 Synechocystis #5 RCY33640 38 Synechocystis #6 RCY02507 137 Synechocystis Motif number 1 GACGCGAAGGTATTATGGGAGGCGGTCCAG 1 26 1 TATTATGGGA 0.772828 -275 CCCCAGCTTTTACGATGGTTTCATGGTGCC 1 162 1 TACGATGGTT 0.584804 -139 TGGGGGGAATTGCTCTGGCAACTGATTAAT 1 250 0 TGCTCTGGCA 0.895984 -51 TTCCCCTCCATGCTCTGGGGGGAATTGCTC 1 265 0 TGCTCTGGGG 0.981439 -36 GGAAACGAGTTACGATGGGGGCGACGTTTG 2 77 0 TACGATGGGG 0.941019 -224 CCCATCGCTCTGGTCTGGGATGCAAATGGC 2 130 0 TGGTCTGGGA 0.990374 -171 CCCAGACCAGAGCGATGGGATTGACAACGC 2 141 1 AGCGATGGGA 0.920075 -160 CCTTGAAAATTGGTATGGGTCAAATCAGAT 2 204 0 TGGTATGGGT 0.971999 -97 TTTCAAGGCATGGTATAGGTGGAACTTTCC 2 226 1 TGGTATAGGT 0.814507 -75 TCAATATCTTTGGTGTGGGAAAGTTCCACC 2 243 0 TGGTGTGGGA 0.977485 -58 GAATGGAGAATGGGGTGGTGGTCGTAGCGA 4 48 1 TGGGGTGGTG 0.814004 -181 TTTGGTCTTAAAGTCTGGGAAATTAGGCTA 4 145 1 AAGTCTGGGA 0.893054 -84 TCTGGGAAATTAGGCTAGGATGTCACTCAG 4 158 1 TAGGCTAGGA 0.840541 -71 ********** Masking position 6 Map Score: 11.0454 Number of sites scoring better than the average of aligned sites = 2890 Number in coding regions = 2601 Number in noncoding regions = 289 Number of orfs with sites within 600 bp upstream = 310 Fraction of orfs with sites within 600 bp upstream = 0.0497912 Motif number 2 TGGGAGGCGGTCCAGGCAAAGTCAAAAGACAAT 1 41 1 TCCAGCAATC 0.99139 -260 AGGCAAAGTCAAAAGACAATCTGTCAAAGTTGC 1 54 1 AAAAGCAATG 0.89579 -247 ACACGCAAACAAAAACCAACGTCTTGGCGATCG 1 197 0 AAAAACAATC 0.714336 -104 CCGCTGTTAGACCAATCAAAATCAATTTGACAT 2 19 1 ACCAACAATC 0.957757 -282 CCAATATCGATACAGTCAATATCTTTGGTGTGG 2 255 0 TACAGCAATC 0.978264 -46 CCGTAAAGCAACAACCCAATATCGATACAGTCA 2 270 0 ACAACCAATC 0.843185 -31 TCTTAGCCTGACCTGACAACCTGAACCTAGGAA 4 87 1 ACCTGCAATG 0.916434 -142 TGGAGAAAAATCCAGTCAATTTGGTCTTAAAGT 4 126 1 TCCAGCAATG 0.987332 -103 AGAGGGAGTTTTCAGACAAGCTCTGAGTGACAT 4 177 0 TTCAGCAATC 0.969145 -52 CAGTTCAGTCAAGATGCGAAAAATTA 5 4 1 TTCAGCAATG 0.955079 -35 ***** *** ** Masking position 8 Map Score: 10.0298 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 462 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 3 AGGAATTGCATTGCCATGGCCACTTCACAAA 1 109 0 TTGCCTGGCC 0.990099 -192 GTCTTGGCGATCGCCATCGGCACCATGAAAC 1 179 0 TCGCCTCGGC 0.987438 -122 CTGGGGGGAATTGCTCTGGCAACTGATTAAT 1 250 0 TTGCTTGGCA 0.868459 -51 TTTCCCCTCCATGCTCTGGGGGGAATTGCTC 1 265 0 ATGCTTGGGG 0.788528 -36 AAAATTCTGCTCCCCTTGGGGGAAACGAGTT 2 96 0 TCCCCTGGGG 0.974076 -205 GTCAATCCCATCGCTCTGGTCTGGGATGCAA 2 135 0 TCGCTTGGTC 0.977965 -166 CTCCATTCATTTTCCCTCGGCGATCGCCCTG 4 25 0 TTTCCTCGGC 0.916066 -204 GTCTGAAAACTCCCTCTGGCCCGCGACAAAG 4 193 1 TCCCTTGGCC 0.976828 -36 GTGAAGCCATTCTCCGTGGTCGAATTAAGTA 6 19 1 TCTCCTGGTC 0.959658 -119 ***** ***** Masking position 7 Map Score: 6.95028 Number of sites scoring better than the average of aligned sites = 2431 Number in coding regions = 2232 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 220 Fraction of orfs with sites within 600 bp upstream = 0.0353357 Motif number 4 CTGTTTTTTATTCTTTCCCCAGCTTTTACG 1 146 1 TTCTTTCCCC 0.96603 -155 AGTTGCCAGAGCAATTCCCCCCAGAGCATG 1 257 1 GCAATTCCCC 0.987557 -44 TCCAAAAGCTGACTTTCCCCTCCATGCTCT 1 279 0 GACTTTCCCC 0.962062 -22 CCATCGTAACTCGTTTCCCCCAAGGGGAGC 2 89 1 TCGTTTCCCC 0.967328 -212 CATTCTCCATTCATTTTCCCTCGGCGATCG 4 30 0 TCATTTTCCC 0.920285 -199 CGACCACCACCCCATTCTCCATTCATTTTC 4 42 0 CCCATTCTCC 0.962602 -187 ACATCCTAGCCTAATTTCCCAGACTTTAAG 4 151 0 CTAATTTCCC 0.772713 -78 TGGTGGTGAAGCCATTCTCCGTGGTCGAAT 6 14 1 GCCATTCTCC 0.974021 -124 ********** Masking position 5 Map Score: 5.66313 Number of sites scoring better than the average of aligned sites = 1852 Number in coding regions = 1630 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 250 Fraction of orfs with sites within 600 bp upstream = 0.0401542 Motif number 5 ATTCTTTCCCCAGCTTTTACGATGGTTTCA 1 155 1 CAGCTTTTAC 0.750318 -146 ATGGTGCCGATGGCGATCGCCAAGACGTTG 1 184 1 TGGCGATCGC 0.908206 -117 TGCGTGTCTTGGGCTGTTGCTCAGTGGATT 1 223 1 GGGCTGTTGC 0.96483 -78 GGTCTAACAGCGGTGTTTACC 2 2 0 CGGTGTTTAC 0.928233 -299 ACGATGGGGGCGACGTTTGCTTTGTTTGCG 2 66 0 CGACGTTTGC 0.959532 -235 TATCGATATTGGGTTGTTGCTTTACGGTTT 2 276 1 GGGTTGTTGC 0.89991 -25 TGTTGCTTTACGGTTTTTGCG 2 290 1 CGGTTTTTGC 0.968408 -11 CATTTTCCCTCGGCGATCGCCCTGTCTAGA 4 19 0 CGGCGATCGC 0.98706 -210 GTGGTCGTAGCGACTATCACCATCTTAGCC 4 65 1 CGACTATCAC 0.792686 -164 ********** Masking position 7 Map Score: 5.28084 Number of sites scoring better than the average of aligned sites = 7130 Number in coding regions = 6512 Number in noncoding regions = 618 Number of orfs with sites within 600 bp upstream = 401 Fraction of orfs with sites within 600 bp upstream = 0.0644073 Motif number 6 TCAAAGTTGCGGTCAAGCTAAAATTGGCTA 1 77 1 GGTCAAGCTA 0.988368 -224 AATTGGTATGGGTCAAATCAGATAGTTCTT 2 197 0 GGTCAAATCA 0.938033 -104 GCATGGTATAGGTGGAACTTTCCCACACCA 2 233 1 GGTGGAACTT 0.852433 -68 CAGGTTGTCAGGTCAGGCTAAGATGGTGAT 4 80 0 GGTCAGGCTA 0.968817 -149 TTATGGTGGTGAAGCCATTCTCCGTGG 6 8 1 GGTGAAGCCA 0.973558 -130 CATTCTCCGTGGTCGAATTAAGTACCCATT 6 26 1 GGTCGAATTA 0.938033 -112 ********** Masking position 3 Map Score: 1.47969 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 269 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 GGATAAAGTCTTCAAGACGCGAAGGT 1 7 1 AGTCTTCAAG 0.9416 -294 AGTCCAAAAGCTGACTTTCC 1 291 0 AGTCCAAAAG 0.967828 -10 GATTTTGATTGGTCTAACAGCGGTGTTTAC 2 12 0 GGTCTAACAG 0.96145 -289 CAAAATTAGTAGTCAAAAAGAACTATCTGA 2 180 1 AGTCAAAAAG 0.953045 -121 CAGTCAATTTGGTCTTAAAGTCTGGGAAAT 4 138 1 GGTCTTAAAG 0.974771 -91 ********** Masking position 3 Map Score: 1.11551 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 42 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 CTCTGGCAACTGATTAATCCACTGAGCAAC 1 238 0 TGATTAATCC 0.855424 -63 ACAATAATGGAGAAAAATCCAGTCAATTTG 4 119 1 AGAAAAATCC 0.937007 -110 AGAGCTTGTCTGAAAACTCCCTCTGGCCCG 4 186 1 TGAAAACTCC 0.957188 -43 GACAAAGATTTGATTAATCCCT 4 217 1 TGATTAATCC 0.855424 -12 ********** Masking position 6 Map Score: 0.589431 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 61 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 ********** No masking Map Score: 1.63668e-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 10 ********** No masking Map Score: 1.63668e-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: 1.63668e-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