AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i034_synecho_ctra_300.orf -o034_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 RCY45080 251 Synechocystis #2 RCY09549 300 Synechocystis Motif number 1 TCCATGGGTCCTTCCTAGCTTTGGTGCTACCAT 1 32 0 CTCCAGCTTG 0.831516 -220 ACAGGGTTAATTTCCTTCCCTTAGCCTAACATT 1 78 0 TTCCTCCTTA 0.97476 -174 GGAAGGAAATTAACCCTGTTTTACCGCTGACAA 1 92 1 TACCTGTTTA 0.866028 -160 ATGGTATCTCTCGCCCACTATTAAAGTTAAAAT 1 171 1 TCCCACTTTA 0.935185 -81 AAAATAGGGTTTTCTGTGGATTAACCACGGACG 1 199 1 TTCTTGGTTA 0.929268 -53 ACGGACGATTTTCCCGTCGATTACATAGAGAGA 1 225 1 TTCCTCGTTA 0.967074 -27 CATGGCGTTCTCTCTGGGTCTTAGTTTTATCTT 2 12 0 TCCTGGTTTA 0.942838 -289 GGCTATCTCTTTCCCCGGCCTTAATTAAGAATC 2 103 1 TTCCGGCTTA 0.990576 -198 TTGTTTAATTTTTCTTGGCATTAGTGTTATTTT 2 155 1 TTCTGGCTTA 0.97135 -146 GTTGGGGATACTGCCGGGGGTTAATGGAGCGCT 2 200 0 CTCCGGGTTA 0.96513 -101 CCCGGCAGTATCCCCAACTGTTAACAAACTTGA 2 215 1 TCCCACTTTA 0.935184 -86 TTGTTTCATATTTCTGGCTTTTGTTGCCATTGC 2 253 1 TTCTGCTTTG 0.868215 -48 ** ** *** *** Masking position 11 Map Score: 11.9531 Number of sites scoring better than the average of aligned sites = 1438 Number in coding regions = 1232 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 2 GGTGCTACCATTTATCGCCTCCTCCTCCTC 1 13 0 TTTATCGCCT 0.913203 -239 CCATGGGTCCTTCCTAGCTTTGGTGCTACC 1 34 0 TTCCTAGCTT 0.771196 -218 CATAATCAGCTCCATGGGTCCTTCCTAGCT 1 45 0 TCCATGGGTC 0.898248 -207 GAGATACCATTCCCCCGGTCAAGCGGCGAT 1 151 0 TCCCCCGGTC 0.952081 -101 GGGAATGGTATCTCTCGCCCACTATTAAAG 1 167 1 TCTCTCGCCC 0.985147 -85 CATGGCGTTCTCTCTGGGTCTTAGTTTTAT 2 15 0 TCTCTGGGTC 0.970976 -286 CGCAGCCCCATTTCTCGACTAAGTTTTTTG 2 73 1 TTTCTCGACT 0.852258 -228 TCGACTAAGTTTTTTGGGCTATCTCTTTCC 2 87 1 TTTTTGGGCT 0.738122 -214 GGCTATCTCTTTCCCCGGCCTTAATTAAGA 2 103 1 TTCCCCGGCC 0.96611 -198 TCAACAATTTTTTAGCGCTCCATTAACCCC 2 187 1 TTTAGCGCTC 0.776983 -114 TTGTTTCATATTTCTGGCTTTTGTTGCCAT 2 253 1 TTTCTGGCTT 0.949516 -48 ********** Masking position 1 Map Score: 7.11377 Number of sites scoring better than the average of aligned sites = 2609 Number in coding regions = 2328 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 307 Fraction of orfs with sites within 600 bp upstream = 0.0493093 Motif number 3 CCTTCCTAGCTTTGGTGCTACCATTTATCGCC 1 24 0 TTGGTGCTCC 0.943057 -228 TGGAGCTGATTATGGTCAATGTTAGGCTAAGG 1 61 1 TTGGTCAAGT 0.932869 -191 CTGTTTATACTTTGGCCCTTGTCAGCGGTAAA 1 111 0 TTGGCCCTGT 0.986564 -141 TATAAACAGATTTGGCGATCGCCGCTTGACCG 1 134 1 TTGGCGATGC 0.992754 -118 ACGATTGGTGTTTGGTCATGGCGTTCTCTCTG 2 29 0 TTGGTCATGC 0.994037 -272 TTCTGGCTTTTGTTGCCATTGCAGAAACCTTT 2 264 1 TTTGCCATGC 0.975933 -37 * ******* ** Masking position 3 Map Score: 3.48658 Number of sites scoring better than the average of aligned sites = 1379 Number in coding regions = 1238 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 4 TGGAGGAGGAGGAGGCGATAAATGGTAGCA 1 10 1 AGGGGCGATA 0.99663 -242 TCCCCCGGTCAAGCGGCGATCGCCAAATCTG 1 140 0 AAGGGCGATC 0.976609 -112 TAACTTTAATAGTGGGCGAGAGATACCATTC 1 169 0 AGTGGCGAGA 0.99116 -83 GTTTGTTAACAGTTGGGGATACTGCCGGGGG 2 213 0 AGTGGGGATA 0.98619 -88 *** ******* Masking position 9 Map Score: 1.12087 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 202 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 5 CCCTTAGCCTAACATTGACCATAATCAGCTC 1 63 0 AACTTGACCA 0.92726 -189 ACCCTGTTTTACCGCTGACAAGGGCCAAAGT 1 104 1 ACCCTGACAA 0.981879 -148 AGATACCATTCCCCCGGTCAAGCGGCGATCG 1 149 0 CCCCGGTCAA 0.857446 -103 CTGTGGATTAACCACGGACGATTTTCCCGTC 1 212 1 ACCCGGACGA 0.992484 -40 CCAAACACCAATCGTTGACGACTAATTCGCA 2 46 1 ATCTTGACGA 0.962198 -255 TAGCCCAAAAAACTTAGTCGAGAAATGGGGC 2 77 0 AACTAGTCGA 0.855797 -224 CATTGCAGAAACCTTTGAGGACGATTCGTTT 2 280 1 ACCTTGAGGA 0.96182 -21 *** ******* Masking position 11 Map Score: 1.58765 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 610 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 6 ACAAGGGCCAAAGTATAAACAGATTTGGCG 1 121 1 AAGTATAAAC 0.921769 -131 CCCACTATTAAAGTTAAAATAGGGTTTTCT 1 184 1 AAGTTAAAAT 0.772682 -68 CAAGATAAAACTAAGACCCAG 2 2 1 AAGATAAAAC 0.976201 -299 GGCCTTAATTAAGAATCAACAAAAACAATC 2 119 1 AAGAATCAAC 0.889366 -182 AATGCCAAGAAAAATTAAACAACGTCAAGA 2 147 0 AAAATTAAAC 0.932708 -154 AAAATTGTTGAAAATAACACTAATGCCAAG 2 168 0 AAAATAACAC 0.835203 -133 ********** Masking position 2 Map Score: 0.394465 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 341 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 7 ********** No masking Map Score: 1.5372e-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: 1.5372e-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 ********** No masking Map Score: 1.5372e-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