AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i106_synecho_ctra_100.orf -o106_synecho_ctra_100.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 RCY37413 300 Synechocystis #2 RCY34719 56 Synechocystis #3 RCY19962 189 Synechocystis #4 RCY15566 231 Synechocystis Motif number 1 AGGGGAAAAGTTGCAGGGGT 1 1 1 AGGGGAAAAG 0.929737 -300 TTGTTTTAGTATGGGCGGGAAGACCCCTGC 1 23 0 ATGGGCGGGA 0.940531 -278 ATCATTTGGTATAGGCAAAAGCTAAACAAC 1 86 1 ATAGGCAAAA 0.954685 -215 CAACTTTAATATAGGTAAGGAAATTGCTTA 1 112 1 ATAGGTAAGG 0.902665 -189 TGGATAAATTAGGGGCGGAATTTGATTTTT 1 218 1 AGGGGCGGAA 0.946578 -83 GTTACTGGCTATGGGAAAAAAATCAAATTC 1 235 0 ATGGGAAAAA 0.885223 -66 AATCGGATTTAAGGGTAGAGAAAAGGTAGC 2 24 0 AAGGGTAGAG 0.776483 -33 AATCTTAGGTAAAAATCGGATTTA 2 43 0 TTAGGTAAAA 0.660349 -14 AAAGATGCTTTTAGGCAAAATATCAGGTTA 3 56 0 TTAGGCAAAA 0.871193 -134 ATTTTTTTGGGGGGGCAGGGGGCGTTTGAA 3 84 0 GGGGGCAGGG 0.972245 -106 GGGAAATTTAGGGGGCAAAATAAAACCTTT 3 147 1 GGGGGCAAAA 0.954723 -43 TTGAAACATCAGAGGCAAGGGT 4 3 0 AGAGGCAAGG 0.975131 -229 GGTGTAGCTCATAGGTAAGGGAAGTTGAAT 4 94 0 ATAGGTAAGG 0.902665 -138 CTAAGTTTTCATGGGCAGGACGATAGGTCG 4 148 0 ATGGGCAGGA 0.983309 -84 GGTGATGGGGCAGAGGGGATTTGCA 4 217 0 TGGGGCAGAG 0.967651 -15 ********** Masking position 5 Map Score: 21.1646 Number of sites scoring better than the average of aligned sites = 3566 Number in coding regions = 3095 Number in noncoding regions = 471 Number of orfs with sites within 600 bp upstream = 467 Fraction of orfs with sites within 600 bp upstream = 0.075008 Motif number 2 AATATAGGTAAGGAAATTGCTTAGGCATAA 1 119 1 AGGAAATTGC 0.78954 -182 AGGTATAGAAGGGCATTTAAAAGGTATTTA 1 153 0 GGGCATTTAA 0.972199 -148 AAATTAGGGGCGGAATTTGATTTTTTTCCC 1 223 1 CGGAATTTGA 0.963165 -78 GGGGGGCAGGGGGCGTTTGAAAGATGCTTT 3 75 0 GGGCGTTTGA 0.954343 -115 AAAAATTAGGGGGAAGTTAAGTAAAAATCC 3 108 1 GGGAAGTTAA 0.976501 -82 CTCCATTATTGGGAAATTTAGGGGGCAAAA 3 137 1 GGGAAATTTA 0.914033 -53 TCATAGGTAAGGGAAGTTGAATGCAAACTC 4 86 0 GGGAAGTTGA 0.990681 -146 ACACCGGGTTGGGAATTGAAACCTTGATCC 4 119 1 GGGAATTGAA 0.935184 -113 ATGGGGCAGAGGGGATTTGCAGAAAGCAGA 4 208 0 GGGGATTTGC 0.959614 -24 ********** Masking position 7 Map Score: 8.25209 Number of sites scoring better than the average of aligned sites = 1139 Number in coding regions = 1001 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 3 AAACGAATAGATCTATCTTTTTTGTTTTAGT 1 43 0 ATCTACTTTT 0.879196 -258 TATTAAAGTTGTTTAGCTTTTGCCTATACCA 1 92 0 GTTTACTTTT 0.957944 -209 GATCCTTGGTTGCTACCTTTTCTCTACCCTT 2 13 1 TGCTACTTTT 0.937622 -44 GGTTACTTTTTCAAACTAGTT 3 1 1 GGTTATTTTT 0.954295 -189 AAACTAGTTTGGTTAATTTTTATGCTCCATT 3 23 1 GGTTATTTTT 0.954295 -167 GGCAAAGTTTTAGAGTTTTTT 3 179 0 GGCAAGTTTT 0.932652 -11 TCGTTGAACGGTCTAAGTTTTCATGGGCAGG 4 159 0 GTCTAGTTTT 0.969967 -73 ***** ***** Masking position 5 Map Score: 3.14023 Number of sites scoring better than the average of aligned sites = 652 Number in coding regions = 550 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 4 CTTACCTATATTAAAGTTGTTTAGCTTTTGCC 1 99 0 TTAAAGTTTT 0.972095 -202 GAAGGGCATTTAAAAGGTATTTATAGATTATG 1 144 0 TAAAAGTTTT 0.951445 -157 CTATACCTTGTGAAAGTTCATTTATCACAGCA 1 175 1 TGAAAGTATT 0.959791 -126 AGGGGGCGTTTGAAAGATGCTTTTAGGCAAAA 3 66 0 TGAAAGTCTT 0.972515 -124 AGAGTTTTTTTGAAAGGTTTTATTTTGCCCCC 3 157 0 TGAAAGTTTA 0.944038 -33 GGCAAAGTTTTAGAGTTTTTTTGAAAGGTTT 3 169 0 TTAGAGTTTT 0.926922 -21 ****** * *** Masking position 5 Map Score: 2.12582 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 43 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 CCTATACCAAATGATATAGAAGTAATTAAA 1 71 0 ATGATATAGA 0.960449 -230 GAACTTTCACAAGGTATAGAAGGGCATTTA 1 164 0 AAGGTATAGA 0.97448 -137 CAGCAAACTGATGATATGGATAAATTAGGG 1 202 1 ATGATATGGA 0.952679 -99 TGTTTTGATGATGGTTTGGAGATGACAAAA 1 277 1 ATGGTTTGGA 0.960493 -24 ATCGGATTTAAGGGTAGAGAAAAGGTAGCA 2 23 0 AGGGTAGAGA 0.921478 -34 GGCAAAGTTTTAGAGTTTTTTTGA 3 176 0 AAGTTTTAGA 0.837427 -14 ********** Masking position 5 Map Score: 2.32074 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 100 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 GATTTTTTTCCCATAGCCAGTAACCCCCAC 1 241 1 CCATAGCCAG 0.922593 -60 CTCTGGCTAACCATGGCCCGTAGGCGATCG 4 59 0 CCATGGCCCG 0.99597 -173 GGAATTGAAACCTTGATCCGACCTATCGTC 4 130 1 CCTTGATCCG 0.967861 -102 GAGGGGCCTGCCTCGGTCCGTCGTTGAACG 4 180 0 CCTCGGTCCG 0.99414 -52 CTGCAAATCCCCTCTGCCCCATCACC 4 216 1 CCTCTGCCCC 0.964695 -16 ********** Masking position 8 Map Score: 1.84433 Number of sites scoring better than the average of aligned sites = 716 Number in coding regions = 676 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 CAAATTCCGCCCCTAATTTATCCATATCATC 1 211 0 CCCTAATTAT 0.877792 -90 TAGGGGCGGAATTTGATTTTTTTCCCATAGC 1 227 1 ATTTGATTTT 0.843533 -74 CTACCCTTAAATCCGATTTTTACCTAAGATT 2 36 1 ATCCGATTTT 0.927231 -21 TCCATTACTAACCTGATATTTTGCCTAAAAG 3 48 1 ACCTGATTTT 0.982078 -142 CTTAACTTCCCCCTAATTTTTTTGGGGGGGC 3 98 0 CCCTAATTTT 0.966794 -92 ACCCTTGCCTCTGATGTTTCAAGCAAAAA 4 9 1 CTCTGATTTT 0.982078 -223 ******* *** Masking position 6 Map Score: 1.56493 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 181 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 8 CACAAGGTATAGAAGGGCATTTAAAAGGTA 1 157 0 AGAAGGGCAT 0.945735 -144 AAACAGGATAAGTGGGGGTTACTGGCTATG 1 252 0 AGTGGGGGTT 0.981809 -49 TCAGGTTAGTAATGGAGCATAAAAATTAAC 3 34 0 AATGGAGCAT 0.927864 -156 ATTTCCCAATAATGGAGGATTTTTACTTAA 3 124 0 AATGGAGGAT 0.898276 -66 TGCAGAAAGCAGAGGGGCCTGCCTCGGTCC 4 191 0 AGAGGGGCCT 0.985092 -41 GTGATGGGGCAGAGGGGATTTGCAGAAAGC 4 211 0 AGAGGGGATT 0.951894 -21 ********** Masking position 1 Map Score: 2.23755 Number of sites scoring better than the average of aligned sites = 485 Number in coding regions = 376 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 9 ********** No masking Map Score: 7.69818e-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: 7.69818e-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: 7.69818e-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