AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i203_synecho_ctra_300.orf -o203_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 RCY42235 300 Synechocystis #2 RCY05882 300 Synechocystis #3 RCY51246 183 Synechocystis #4 RCY38268 228 Synechocystis #5 RCY42426 99 Synechocystis Motif number 1 AAAGTTTTATTCCGCCCCCTAAATCCCCCA 1 44 1 TCCGCCCCCT 0.936139 -257 CGCCCCCTAAATCCCCCAATACTGGGGGAC 1 56 1 ATCCCCCAAT 0.82854 -245 CTGAATGAAAGTCCCCCAGTATTGGGGGAT 1 66 0 GTCCCCCAGT 0.894077 -235 TTTCATTCAGTTTCCCCCCAAATTTGGGAG 1 86 1 TTTCCCCCCA 0.932638 -215 TGTTCGAAAAGCTCCCCTAACCTCCCAAAT 1 107 0 GCTCCCCTAA 0.72626 -194 TTTACCGATGTCCGCCCCGATAAGTCCATT 1 156 0 TCCGCCCCGA 0.966274 -145 CGAGGAATTTTTCCCTCTGAAAAAATCAAG 2 26 1 TTCCCTCTGA 0.758164 -275 CTAACTCATCATTGCTCCATGGCGGCCAAA 2 89 0 ATTGCTCCAT 0.726684 -212 GCTAGCTTGTATTGCCCAAACCTAACTCAT 2 110 0 ATTGCCCAAA 0.851772 -191 CCAACGAATTTTTGCCCAGATTAGCGCCAA 2 162 1 TTTGCCCAGA 0.946677 -139 AAAGCAATGATTCCCCCTGAGATAAATATA 2 217 0 TTCCCCCTGA 0.927038 -84 GTTCATTAACATTCCCCTGTTCCCCAAGAT 2 278 1 ATTCCCCTGT 0.892501 -23 TGCTGGCTTTGTTGCCCTGTCAACCAAAGT 3 25 1 GTTGCCCTGT 0.894963 -159 CCTTCCCAATTCTGCTCAAATCGAGTTAAC 3 66 1 TCTGCTCAAA 0.632158 -118 TCCATAGATATTTGCCCAGTTAACTCGATT 3 84 0 TTTGCCCAGT 0.946998 -100 CCATTATTATTCCTCCCTTCTTCCTAAC 4 9 1 ATTCCTCCCT 0.698374 -220 AACCCATCCAACTGCCCCAAGGTTAGGAAG 4 30 0 ACTGCCCCAA 0.89832 -199 ATTCGATTTTTCCGCTCCCTGTTCCCTGAC 5 61 1 TCCGCTCCCT 0.783408 -39 ********** Masking position 5 Map Score: 17.0374 Number of sites scoring better than the average of aligned sites = 7975 Number in coding regions = 6987 Number in noncoding regions = 988 Number of orfs with sites within 600 bp upstream = 743 Fraction of orfs with sites within 600 bp upstream = 0.119338 Motif number 2 CCAAACATGTTCTGAAAAGTTTTTAAATTTGCT 1 11 0 TCTGAATTTT 0.852727 -290 TCAGAACATGTTTGGAAAGTTTTATTCCGCCCC 1 29 1 TTTGGATTTT 0.970186 -272 TCCCCCAGTATTGGGGGATTTAGGGGGCGGAAT 1 52 0 TTGGGATTAG 0.869531 -249 TCCCCCCAAATTTGGGAGGTTAGGGGAGCTTTT 1 98 1 TTTGGGTTAG 0.869531 -203 TAGCCAATAATTTGAACGTTATGCTATGGGAAA 1 271 0 TTTGAGTATG 0.60257 -30 CGTTCAAATTATTGGCTAATTTTTC 1 286 1 ATTGGATTTT 0.897436 -15 TTTTGATTATTTAGCCGAGGAATT 2 2 1 TTTGAATTAG 0.912644 -299 AGCCTTGACCTCTGGCGAGTTTTGTCCTAAAGA 2 54 1 TCTGGATTTT 0.932244 -247 GGAAGGACGTATTGGGAACTTTGGTTGACAGGG 3 39 0 ATTGGATTTG 0.954112 -145 ATCAGGGTCATTTGGTTAATTGTTGATGAGAAA 3 127 0 TTTGGATTGT 0.918554 -57 CTTCCTAACCTTGGGGCAGTTGGATGGGTTACC 4 30 1 TTGGGATTGG 0.877967 -199 CCTATCAGACTCTGACAATTATGGGTATTGGGG 4 160 0 TCTGAATATG 0.704831 -69 TCTTTACAAATTTTAATACTTTGCTAAATCCTA 4 189 0 TTTTAATTTG 0.777431 -40 TTTGACTAGTTTGATTGACAATT 5 1 1 TTTGAATTTG 0.970186 -99 TTGATTGACAATTTGATACTTTTAGATAATCTC 5 21 1 ATTTGATTTT 0.484329 -79 ***** * **** Masking position 10 Map Score: 10.6398 Number of sites scoring better than the average of aligned sites = 2342 Number in coding regions = 1973 Number in noncoding regions = 369 Number of orfs with sites within 600 bp upstream = 339 Fraction of orfs with sites within 600 bp upstream = 0.0544491 Motif number 3 AATAAAACTTTCCAAACATGTTCTGAAAAGTTT 1 22 0 TCCACATGTC 0.927689 -279 CTGGGGGACTTTCATTCAGTTTCCCCCCAAATT 1 77 1 TTCTCAGTTC 0.933464 -224 AGGGGAGCTTTTCGAACAGGCTCTTATAAGGTT 1 119 1 TTCACAGGTC 0.964512 -182 AAAATCAAAATCCATGCCGAATCGGGTATGAAA 1 183 1 TCCTCCGATC 0.982178 -118 CAATTCGCTATCCTATGCATGTCATGTGTTCAT 2 251 1 TCCAGCATTC 0.79408 -50 TCCCAATACGTCCTTCCCAATTCTGCTCAAATC 3 55 1 TCCTCCAATC 0.955639 -129 TATGGATTACTCCTTCCCATTTCTCATCAACAA 3 108 1 TCCTCCATTC 0.955639 -76 TCGATCTTCCTTCCATCAGGGTCATTTGGTTAA 3 141 0 TTCACAGGTC 0.964512 -43 CTTTGCTAAATCCTATCAGACTCTGACAATTAT 4 171 0 TCCACAGATC 0.981392 -58 *** * **** ** Masking position 12 Map Score: 6.37911 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 241 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 CCCCCAATACTGGGGGACTTTCATTCAGTTT 1 68 1 TGGGGGCTTT 0.783995 -233 CGTTATGCTATGGGAAACTGTCGTTACGATA 1 257 0 TGGGAACTGT 0.944064 -44 AAAATCTTGGGGAACAGGGGAATGTTAA 2 283 0 TGGGGACAGG 0.990371 -18 TTGGGAACTTTGGTTGACAGGGCAACAAAGC 3 30 0 TGGTTGCAGG 0.83295 -154 TGAGCAGAATTGGGAAGGACGTATTGGGAAC 3 53 0 TGGGAAGACG 0.841016 -131 TGATGAGAAATGGGAAGGAGTAATCCATAGA 3 106 0 TGGGAAGAGT 0.942089 -78 TGCATTGACATTGGAGCCAGTACCGGGGTAG 4 106 1 TTGGAGCAGT 0.953838 -123 ATTATGGGTATTGGGGCCAGGGCACAAAAAT 4 145 0 TTGGGGCAGG 0.975485 -84 GCGAGATCCTAGGGAGTCAGGGAACAGGGAG 5 75 0 AGGGAGCAGG 0.970149 -25 ****** **** Masking position 3 Map Score: 3.91516 Number of sites scoring better than the average of aligned sites = 1608 Number in coding regions = 1409 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 211 Fraction of orfs with sites within 600 bp upstream = 0.0338901 Motif number 5 AGCAAATTTAAAAACTTTTCAG 1 3 1 CAAATTTAAA 0.87828 -298 AATATAAGTGCAAAATAAAGTACGTCAGCC 1 216 0 CAAAATAAAG 0.832678 -85 GCATAACGTTCAAATTATTGGCTAATTTTT 1 280 1 CAAATTATTG 0.901804 -21 CGAAAACCAACGAATTTTTGCCCAGATTAG 2 156 1 CGAATTTTTG 0.853488 -145 AGATTAGCGCCAAAATTAAGCGGAGCAGTG 2 179 1 CAAAATTAAG 0.899049 -122 GGTAGGGAAACAAATTTTTGTGCCCTGGCC 4 132 1 CAAATTTTTG 0.727791 -97 ATTTTCTTTACAAATTTTAATACTTTGCTA 4 196 0 CAAATTTTAA 0.903252 -33 ********** Masking position 4 Map Score: 2.20511 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 458 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 6 GGAGCTTTTCGAACAGGCTCTTATAAGGTT 1 122 1 GAACAGGCTC 0.925921 -179 ATTAAGCGGAGCAGTGGGTCAAAATATATT 2 193 1 GCAGTGGGTC 0.969518 -108 TTGTAGTCATTCACTGGGTCGATCTTCCTT 3 162 0 TCACTGGGTC 0.97911 -22 CCCTACCCCGGTACTGGCTCCAATGTCAAT 4 109 0 GTACTGGCTC 0.980704 -120 AAATTTTTGTGCCCTGGCCCCAATACCCAT 4 143 1 GCCCTGGCCC 0.987679 -86 CGCTCCCTGTTCCCTGACTCCCTAGGATCT 5 73 1 TCCCTGACTC 0.920028 -27 ********** Masking position 6 Map Score: 1.78515 Number of sites scoring better than the average of aligned sites = 634 Number in coding regions = 582 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 7 ********** No masking Map Score: 2.81618e-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 8 CAATACTGGGGGACTTTCATTCAGTTTCCCC 1 72 1 GGACTTTATT 0.966026 -229 GATTCGGCATGGATTTTGATTTTACCGATGT 1 175 0 GGATTTTATT 0.963424 -126 ACTTTATTTTGCACTTATATTCTAGACTTAG 1 225 1 GCACTTAATT 0.966561 -76 TGGTGGGATTGCATTGACATTGGAGCCAGTA 4 97 1 GCATTGAATT 0.923444 -132 AACTCGCATTTTAATTTTCTTTACAA 4 213 0 GCATTTTATT 0.974599 -16 ******* *** Masking position 5 Map Score: 0.326704 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 42 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 ********** No masking Map Score: 2.81618e-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: 2.81618e-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: 2.81618e-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