AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i078_synecho_ctra_100.orf -o078_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 RCY50877 115 Synechocystis #2 RCY13382 161 Synechocystis #3 RCY24201 240 Synechocystis #4 RCY04335 82 Synechocystis #5 RCY28320 241 Synechocystis #6 RCY18066 196 Synechocystis #7 RCY33510 30 Synechocystis Motif number 1 CTTTTAGGAATTAGCCATAGACCACAAAAAAA 2 12 0 TTACCATAGC 0.955378 -150 GAATAAAATTTTCACCATAATTA 3 2 0 TTCCCATAAT 0.862131 -239 TTTTATTCTTTTCACCATTTTCCATTCTTCAC 3 26 1 TTCCCATTTC 0.890381 -215 TTTTCCATTCTTCACCCTACTTTTCAAACACG 3 43 1 TTCCCCTACT 0.909063 -198 TAATGAAAAATTATCCCTTGTCTTATGCTTTG 3 141 0 TTACCCTTGC 0.971646 -100 GCTGTTATTTTGCTCCCTAAATAGGCTGATTA 3 185 0 TGCCCCTAAT 0.881646 -56 TTCCAGATTTTTCTCCACTGCCGGATTAATGG 4 14 1 TTCCCACTGC 0.931963 -69 ACCGACCCATTGCTCCCTTGCCCT 5 3 0 TGCCCCTTGC 0.988591 -239 AACTGTTCACTGAACCCTAGACCCAACAACAT 5 201 1 TGACCCTAGC 0.962272 -41 ATCCCATTGGTTCACCATTGATGGATAAAAAG 6 75 0 TTCCCATTGT 0.96393 -122 TGTTATCCAAATCCCCCTAGCCTGCGGCGCTA 6 165 1 ATCCCCTAGC 0.954314 -32 *** ****** * Masking position 6 Map Score: 11.09 Number of sites scoring better than the average of aligned sites = 1347 Number in coding regions = 1166 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 2 GTTCAATTCTTAATCAGGAAAAAACTCTGGA 2 74 0 TAATCGGAAA 0.975542 -88 CAGTGGAGAAAAATCTGGAAAGA 4 3 0 AAATCGGAAA 0.964595 -80 AAAATACCATTAATCCGGCAGTGGAGAAAAA 4 21 0 TAATCGGCAG 0.967822 -62 AAGAGGAATTTAATCTGTGAAC 4 71 1 TAATCGTGAA 0.945611 -12 ACCAATAAACATATCAGGCAAGTTGAGATGG 5 55 1 ATATCGGCAA 0.955198 -187 TGATGACACGAAATCAGTCAATTTACGGGCA 5 103 1 AAATCGTCAA 0.965687 -139 CATTAAAACCTAATCGAGAAATGATGGCGTA 5 140 0 TAATCAGAAA 0.860042 -102 CAGTAAGCAGGAATCGGTCAACACTGACCAT 5 168 0 GAATCGTCAA 0.92689 -74 CAGTGAACAGTTATCAGTAAGCAGGAATCGG 5 182 0 TTATCGTAAG 0.762241 -60 TGATGGATAAAAAGCAGGGAAAAGCTTTTGG 6 58 0 AAAGCGGGAA 0.809653 -139 TCCCTGCTTTTTATCCATCAATGGTGAACCA 6 69 1 TTATCATCAA 0.716584 -128 ***** ***** Masking position 3 Map Score: 9.04112 Number of sites scoring better than the average of aligned sites = 779 Number in coding regions = 674 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 3 AGGCGGAGTCAAAGCAGTTGGTCAAAGCTT 1 49 1 AAAGCAGTTG 0.938822 -67 AATGCTTAAGTTGTTGTTATTTATCT 1 100 0 TAAGTTGTTG 0.968366 -16 AAATAAAGTTTTTAAAACGCCCTA 2 148 0 AAAGTTTTTA 0.790811 -14 TCCCTTTATGTTGCTGAATCCCAGGG 3 225 0 TATGTTGCTG 0.888647 -16 AATGATGGCGTAAGCATCTGCCCGTAAATT 5 122 0 TAAGCATCTG 0.839472 -120 TGATAGCGGTTATGTTGTTGGGTCTAGGGT 5 214 0 TATGTTGTTG 0.906324 -28 TTTTACCCACAAAGTTTCTGGTAAATTGAT 6 26 1 AAAGTTTCTG 0.940604 -171 AAAGCAGGGAAAAGCTTTTGGCAATCAATT 6 49 0 AAAGCTTTTG 0.961116 -148 AGGTACAGTAAAAGCTGTTAATTTGTTATC 6 142 1 AAAGCTGTTA 0.905326 -55 ********** Masking position 2 Map Score: 6.6353 Number of sites scoring better than the average of aligned sites = 634 Number in coding regions = 548 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 4 ATTTAGGGAGCAAAATAACAGCGATTAAGCC 3 195 1 CAAATAACAG 0.962337 -46 TGCCCCATCTCAACTTGCCTGATATGTTTAT 5 59 0 CAATTGCCTG 0.974827 -183 CATCTGCCCGTAAATTGACTGATTTCGTGTC 5 107 0 TAATTGACTG 0.881901 -135 CTAGACCCAACAACATAACCGCTATCAAGAT 5 217 1 CAAATAACCG 0.937453 -25 TTTTGGCAATCAATTTACCAGAAACTTTGTG 6 33 0 CAATTACCAG 0.969677 -164 CCGATGTGCCCAAGGTGACTGTGTATTTGCG 6 108 0 CAAGTGACTG 0.962865 -89 ATTTGGATAACAAATTAACAGCTTTTACTGT 6 146 0 CAATTAACAG 0.97945 -51 *** ******* Masking position 3 Map Score: 4.27102 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 218 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 GAAACTGTTACAAACCCGAGGTG 1 3 0 CAAACCCGAG 0.909246 -113 ATAGCGTAAGCTTACCAGACAAAGCCAAAAA 2 112 0 CTTACCAGAA 0.907482 -50 TTAAAACGCCCTAACCAGATAGCGTAAGCTT 2 130 0 CTAACCAGAA 0.948189 -32 TTTTCCATTCTTCACCCTACTTTTCAAACAC 3 43 1 TTCACCCTAT 0.766337 -198 TTTGTAAGGTTTCACTCGATAATTCCCCCAA 3 114 0 TTCACTCGAA 0.850002 -127 TTAGGGTTACGACACCCGAAAAAATACCATT 4 41 0 GACACCCGAA 0.944421 -42 TTCGGGTGTCGTAACCCTAAAGAGGAATTTA 4 52 1 GTAACCCTAA 0.905352 -31 AACTGTTCACTGAACCCTAGACCCAACAACA 5 201 1 TGAACCCTAA 0.753972 -41 TGGCAATCAATTTACCAGAAACTTTGTGGGT 6 30 0 TTTACCAGAA 0.860799 -167 TTTACTGTACCTCACCCGATGTGCCCAAGGT 6 123 0 CTCACCCGAG 0.980502 -74 ********* * Masking position 4 Map Score: 2.4796 Number of sites scoring better than the average of aligned sites = 538 Number in coding regions = 471 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 TACTAAATCCAGAGTTTTTTCCTGATTAAG 2 67 1 AGAGTTTTTT 0.79561 -95 CTATCTGGTTAGGGCGTTTTAAAAACTTTA 2 139 1 AGGGCGTTTT 0.974498 -23 AAATAAAGTTTTTAAAACGCCC 2 150 0 ATAAAGTTTT 0.648616 -12 ATAGATCCTAAGAGCGTGTTTGAAAAGTAG 3 59 0 AGAGCGTGTT 0.947202 -182 GATGGGGCATAGAGATTTTTGATGATGACA 5 81 1 AGAGATTTTT 0.907552 -161 ATTGAGTAAAGAAAGTTTTACCCACAAAG 6 10 1 AGAAAGTTTT 0.938297 -187 GCCGCAGGCTAGGGGGATTTGGATAACAAA 6 163 0 AGGGGGATTT 0.839476 -34 GGGAAAGAAAGAACGATTTGGTTAAATAA 7 12 0 AGAACGATTT 0.904141 -19 ********** Masking position 1 Map Score: 1.89614 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 351 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 7 ********** No masking Map Score: -1.09891e-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 ********** No masking Map Score: -1.09891e-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 9 TTTTTTTTGTGGTCTATGGCTA 2 2 1 TTTTTTTGGG 0.966925 -160 AAAGTTGTCAGTTTTCTGCGGATGAGTTACT 2 40 1 GTTTTCTGGG 0.948924 -122 TAAATCCAGAGTTTTTTCCTGATTAAGAATT 2 70 1 GTTTTTTCTG 0.892506 -92 ATTGAACAATTATTTTTTTGGCTTTGTCTGG 2 98 1 TATTTTTTGG 0.883537 -64 GGATTAATGGTATTTTTTCGGGTGTCGTAAC 4 36 1 TATTTTTTGG 0.883537 -47 TGCCTGATATGTTTATTGGTGGTGGCTTTTG 5 44 0 GTTTATTGTG 0.858543 -198 GGGGCATAGAGATTTTTGATGATGACACGAA 5 84 1 GATTTTTGTG 0.957359 -158 ******** ** Masking position 7 Map Score: 0.734936 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 425 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 10 ACAACTTTTAGGAATTAGCCATAGACCACAA 2 17 0 GGAATTAGCA 0.91638 -145 AAAAAACTCTGGATTTAGTAACTCATCCGCA 2 56 0 GGATTTAGAA 0.965194 -106 TAAGCCCCTGGGATTCAGCAACATAAAGGGA 3 220 1 GGATTCAGAA 0.977771 -21 TCAGTAAGCAGGAATCGGTCAACACTGACCA 5 169 0 GGAATCGGCA 0.965 -73 GTTGGGTCTAGGGTTCAGTGAACAGTTATCA 5 197 0 GGGTTCAGGA 0.872658 -45 TGAACCAATGGGATTCGCAAATACACAGTCA 6 93 1 GGATTCGCAA 0.9203 -104 CAGGCTAGGGGGATTTGGATAACAAATTAAC 6 158 0 GGATTTGGTA 0.968451 -39 AAAGAAAGAACGATTTGGTTAAATAAA 7 7 0 CGATTTGGTA 0.835541 -24 ******** ** Masking position 11 Map Score: 3.01537 Number of sites scoring better than the average of aligned sites = 728 Number in coding regions = 659 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 11 ********** No masking Map Score: -1.09891e-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: -1.09891e-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 13 ********** No masking Map Score: -1.09891e-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