AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i188_synecho_ctra_100.orf -o188_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 RCY04876 200 Synechocystis #2 RCY05831 277 Synechocystis #3 RCY37144 238 Synechocystis Motif number 1 TGATCTGCATAGTAAGGCGATCGCCAAAGTTTGGG 1 41 1 AAAGGGAGCC 0.830433 -160 ATAAAGCAATGCAAAGGATTGGCCCCAAACTTTGG 1 64 0 GAAGGTTCCC 0.991279 -137 CGGGGACAGCGTAAAGGTTTGACCCAATTCCTATT 1 143 0 GAAGGTTCCC 0.991279 -58 GGTAAGGACTGCTCAGGAGGGAACCT 1 185 1 GCAGGGGACC 0.935714 -16 AGCTTGGAAGGCTAAGGTTTTACCACTAAACTACA 2 81 0 GAAGGTTCCA 0.951575 -197 ACCCAAAGCGGGTGAGGGGAATCGAACCCCTATCA 2 118 0 GGAGGGACGA 0.919298 -160 TGGGTAATGGGTACAGCGGTCTCCGAAACTCGATA 2 148 1 GCAGCGTCCG 0.94442 -130 GATGACGGTCGAGGAGGGGTGTCGCAACGGACATC 2 212 0 GGAGGGTCGC 0.993174 -66 TGGACAGTCGGCACAGCATTACCCCTCGAACAAAT 3 120 0 GCAGCTTCCC 0.977254 -119 GGCAGGTTTTGCACAGGCGATCGCCTAGGTCATTG 3 182 0 GCAGGGAGCC 0.989942 -57 TACCTTTTCAGCAGAGGAGTCCGGCAGGTTTTGCA 3 204 0 GGAGGGTGGC 0.984748 -35 * **** ** *** Masking position 5 Map Score: 10.8343 Number of sites scoring better than the average of aligned sites = 1575 Number in coding regions = 1469 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 2 GCATAGTAAGGCGATCGCCAAAGTTTGGGG 1 47 1 GCGATCGCCA 0.991585 -154 CCATCAATAACCGACCGTTAAGGCTAATTT 1 113 0 CCGACCGTTA 0.897912 -88 TGATAGGGGTTCGATTCCCCTCACCCGCTT 2 118 1 TCGATTCCCC 0.882625 -160 TTGATAATTTCTGATCGTCCCTGATGTCCG 2 190 1 CTGATCGTCC 0.915513 -88 GATGTCCGTTGCGACACCCCTCCTCGACCG 2 212 1 GCGACACCCC 0.918955 -66 ACACCCCTCCTCGACCGTCATCCATGCTCC 2 225 1 TCGACCGTCA 0.975502 -53 TAATGCTGTGCCGACTGTCCACTGCTCCAA 3 134 1 CCGACTGTCC 0.98234 -105 TGCTCCAACTGCGATTGTCAAGCCCCCAAT 3 156 1 GCGATTGTCA 0.97281 -83 AATGACCTAGGCGATCGCCTGTGCAAAACC 3 183 1 GCGATCGCCT 0.972839 -56 ********** Masking position 4 Map Score: 8.52505 Number of sites scoring better than the average of aligned sites = 8223 Number in coding regions = 7531 Number in noncoding regions = 692 Number of orfs with sites within 600 bp upstream = 468 Fraction of orfs with sites within 600 bp upstream = 0.0751686 Motif number 3 CCAAAGTTTGGGGCCAATCCTTTGCATTGC 1 64 1 GGGCCAATCC 0.984234 -137 AATAGGAATTGGGTCAAACCTTTACGCTGT 1 143 1 GGGTCAAACC 0.986273 -58 TGTAGTTTAGTGGTAAAACCTTAGCCTTCC 2 81 1 TGGTAAAACC 0.966232 -197 CAGATAACCGTGCAGAACCGAGGAATTAT 2 259 0 GTGCAGAACC 0.968717 -19 CCAACTGCGATTGTCAAGCCCCCAATGACC 3 160 1 TTGTCAAGCC 0.928062 -79 GCGATCGCCTGTGCAAAACCTGCCGGACTC 3 193 1 GTGCAAAACC 0.988338 -46 ********** Masking position 7 Map Score: 5.70604 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 543 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 GTCGGTTATTGATGGAATAGGAATTGGGTCA 1 128 1 GATGGATAGG 0.887035 -73 GTCCCCGTAAGATGGGTAAGGACTGCTCAGG 1 171 1 GATGGGAAGG 0.986721 -30 CCTCACCCGCTTTGGGTAATGGGTACAGCGG 2 136 1 TTTGGGAATG 0.935062 -142 CGATAATTTTGATTGATAATTTCTGATCGTC 2 178 1 GATTGAAATT 0.747423 -100 AGGAATTATCGAGGGAGCATGGATGACGGTC 2 237 0 GAGGGACATG 0.955392 -41 AATCCTCGTGGGGCAATTTTGCAAACAA 3 8 1 GTGGGGAATT 0.951849 -231 TATTACAACTTTTTGGAAATGTTCTTAAGAT 3 62 1 TTTTGGAATG 0.739272 -177 AAATTTGTTCGAGGGGTAATGCTGTGCCGAC 3 118 1 GAGGGGAATG 0.986722 -121 GACAATCGCAGTTGGAGCAGTGGACAGTCGG 3 144 0 GTTGGACAGT 0.850692 -95 ****** **** Masking position 9 Map Score: 4.17729 Number of sites scoring better than the average of aligned sites = 2545 Number in coding regions = 2268 Number in noncoding regions = 277 Number of orfs with sites within 600 bp upstream = 289 Fraction of orfs with sites within 600 bp upstream = 0.0464182 Motif number 5 GCGATCGCCTTACTATGCAGATCAAGACCT 1 35 0 TACTATGCAG 0.871271 -166 ATTGGCCCCAAACTTTGGCGATCGCCTTAC 1 52 0 AACTTTGGCG 0.977894 -149 TTGTCAGGAGAACTTTCCCG 2 1 0 AACTTTCCCG 0.958542 -277 TATCAATCAAAATTATCGAGTTTCGGAGAC 2 166 0 AATTATCGAG 0.946627 -112 AGAACCGAGGAATTATCGAGGGAGCATGGA 2 245 0 AATTATCGAG 0.946627 -33 CAATTTTGCAAACAATGGCGGTTTTTTCTC 3 24 1 AACAATGGCG 0.953186 -215 ********** Masking position 6 Map Score: 1.92135 Number of sites scoring better than the average of aligned sites = 378 Number in coding regions = 343 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 ********** No masking Map Score: -4.67335e-15 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 7 ********** No masking Map Score: -4.67335e-15 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: -4.67335e-15 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