AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i107_synecho_ctra_300.orf -o107_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 RCY33232 300 Synechocystis #2 RCY47152 92 Synechocystis #3 RCY47847 21 Synechocystis #4 RCY01442 89 Synechocystis #5 RCY26797 100 Synechocystis #6 RCY18346 231 Synechocystis #7 RCY20248 131 Synechocystis Motif number 1 ATAGGACAATTGCTCGACAATCTTTCTAAA 1 57 0 TGCTCGACAA 0.974322 -244 ATCATCGAGGCGATCGCCATTTGGTAGGGG 1 144 0 CGATCGCCAT 0.987677 -157 GATTGTGGCTTGATCAACTTCGAGGTCATT 1 171 1 TGATCAACTT 0.898774 -130 CGGCTAATTTTGCTCAACTTTTGCGGGACT 2 30 0 TGCTCAACTT 0.896937 -63 CGGTTGTACACGATCGCCGTTTTGATTCAG 5 25 0 CGATCGCCGT 0.967003 -76 TTGTAACTTCTGATCGCCACTCAGGGTAA 5 82 1 TGATCGCCAC 0.981043 -19 TGCTTAGACATGATCGCCATAGGTATTTAT 6 35 0 TGATCGCCAT 0.992984 -197 GTAAAGTTACTGCTCGACAAGGTTAAGGCT 6 165 1 TGCTCGACAA 0.974322 -67 ********** Masking position 4 Map Score: 9.71617 Number of sites scoring better than the average of aligned sites = 3694 Number in coding regions = 3335 Number in noncoding regions = 359 Number of orfs with sites within 600 bp upstream = 329 Fraction of orfs with sites within 600 bp upstream = 0.0528429 Motif number 2 TACCTTTTGTCCCCTACCAAATGGCGATCG 1 134 1 CCCCTACCAA 0.882712 -167 GTTGATCAAGCCACAATCATCGAGGCGATC 1 159 0 CCACAATCAT 0.711115 -142 AATAACTATACCCACATCTAATGACCTCGA 1 190 0 CCCACATCTA 0.778328 -111 CTCCCCTAAACCAAACTCAATAACTATACC 1 208 0 CCAAACTCAA 0.84459 -93 TGGGGTGAACCTCCCCTAAACCAAACTCAA 1 218 0 CTCCCCTAAA 0.738717 -83 TTAGGGGAGGTTCACCCCAATGCCACCTTT 1 229 1 TTCACCCCAA 0.687609 -72 GGGGCATAATTCACCCTCAAATTGTCGGTA 6 197 0 TCACCCTCAA 0.978255 -35 GTTGCTTACTCAACCCTCAAATTTCCCCAT 7 33 1 CAACCCTCAA 0.906919 -99 CCCTCAAATTTCCCCATCAAACCTTGGTGG 7 46 1 TCCCCATCAA 0.984167 -86 TGGTGGCCAATCCCCACCAAGGTTTGATGG 7 59 0 TCCCCACCAA 0.972027 -73 TGGGGATTGGCCACCATCAATTTTCGTGAA 7 73 1 CCACCATCAA 0.988479 -59 TGAACTTCCATTACAATCAAGCCTGTTATC 7 99 1 TTACAATCAA 0.704392 -33 ********** Masking position 9 Map Score: 8.35956 Number of sites scoring better than the average of aligned sites = 4305 Number in coding regions = 3961 Number in noncoding regions = 344 Number of orfs with sites within 600 bp upstream = 336 Fraction of orfs with sites within 600 bp upstream = 0.0539672 Motif number 3 TTCTGAGGGCAACTAAATTTGA 1 2 1 TCTGGGGCAA 0.989849 -299 CTTGATCAACTTCGAGGTCATTAGATGTGGG 1 179 1 TTCGGGTCAT 0.831563 -122 TTGCTCAACTTTTGCGGGACTTAGATTAAAG 2 20 0 TTTGGGGACT 0.93959 -73 ACATAATATTTCTGTTGGTCTGTATTCAATC 4 24 1 TCTGTGGTCT 0.816291 -66 TCACTATCTGTCTGTGGTAAATACA 6 5 0 TCTGGGTAAA 0.882854 -227 TTACCGACAATTTGAGGGTGAATTATGCCCC 6 196 1 TTTGGGGTGA 0.852987 -36 GGGTTCAGACTCCGGGGGCATAATTCACCCT 6 210 0 TCCGGGGCAT 0.982213 -22 GGGTCTGTGGGCCAAAATTCTAGT 7 4 1 TCTGGGGCCA 0.991579 -128 **** ****** Masking position 1 Map Score: 3.87755 Number of sites scoring better than the average of aligned sites = 1017 Number in coding regions = 918 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 4 TTGAAACTTAGAAAGGTTAATACTGGTTTT 1 29 1 GAAAGGTTAA 0.979989 -272 GGTAGGGGACAAAAGGTAAAGAAACATAAA 1 122 0 AAAAGGTAAA 0.960503 -179 GGACTTAGATTAAAGGATAACGTT 2 5 0 TAAAGGATAA 0.905875 -88 TATGGGAACTGAAAGGATAAATGAGCAGAG 2 64 1 GAAAGGATAA 0.963305 -29 AAGCTCGATCAAAATGTAAAGTTACTGCTC 6 150 1 AAAATGTAAA 0.790007 -82 TTACTGCTCGACAAGGTTAAGGCTTTTACC 6 171 1 ACAAGGTTAA 0.943148 -61 ********** Masking position 4 Map Score: 3.38954 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 130 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 TTCTGAGGGCAACTAAATTTGA 1 3 1 CTGAGGGCAA 0.97343 -298 AGGTCATTAGATGTGGGTATAGTTATTGAG 1 193 1 ATGTGGGTAT 0.883313 -108 GCAAAATTAGCCGGGGATATGGGAACTGAA 2 47 1 CCGGGGATAT 0.766949 -46 CATAATATTTCTGTTGGTCTGTATTCAATC 4 25 1 CTGTTGGTCT 0.881235 -65 CTGATCGCCACTCAGGGTAA 5 91 1 CTCAGGGTAA 0.792655 -10 GGTTCAGACTCCGGGGGCATAATTCACCCT 6 210 0 CCGGGGGCAT 0.979055 -22 GGGTCTGTGGGCCAAAATTCTAGT 7 5 1 CTGTGGGCCA 0.980936 -127 ACGAAAATTGATGGTGGCCAATCCCCACCA 7 70 0 ATGGTGGCCA 0.8089 -62 ********** Masking position 6 Map Score: 0.950593 Number of sites scoring better than the average of aligned sites = 3172 Number in coding regions = 2881 Number in noncoding regions = 291 Number of orfs with sites within 600 bp upstream = 316 Fraction of orfs with sites within 600 bp upstream = 0.0507549 Motif number 6 AAGGGAACGATAGGGCTTTAACAATACGAGAT 4 52 0 TAGGCTTTAC 0.970547 -38 ATACAATTCTTAATGCTTAGACATGATCGCCA 6 46 0 TAAGCTTAAC 0.99055 -186 TTGAACTAAATAAAGCTGAAAGTGAATCAGGA 6 98 1 TAAGCTGAAG 0.930606 -134 TAATCTTCTGTAATGCTTATCCTGATTCACTT 6 117 0 TAAGCTTACC 0.979261 -115 TCGACAAGGTTAAGGCTTTTACCGACAATTTG 6 178 1 TAAGCTTTAC 0.986514 -54 *** ***** ** Masking position 7 Map Score: 0.247148 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 42 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 CCTATTTCACTTTTGATAATTCAGTATATTTTGCT 1 82 1 TTTATTTCAT 0.8735 -219 AGTGATTTCCTCTGCTCATTTATCCTTTCA 2 73 0 TTTTCCTCAT 0.878623 -20 TAACATAATATTTCTGTTGGTCTGTATTCAATCTC 4 22 1 TTTGTGTCTT 0.929458 -68 TATCGTTCCCTTTATTTTTGTCAATCCT 4 72 1 TTTTTGTCAT 0.988072 -18 CGATCGCCGTTTTGATTCAGTCAGTTCAAATCAT 5 10 0 TTTTTGTCAT 0.988055 -91 AGTTCAATTATTTTTTTACGTCTTTCCATACAATT 6 70 0 TTTTTGTCTT 0.972999 -162 CACTTTCAGCTTTATTTAGTTCAATTATTTTTTTA 6 87 0 TTTTTTTCAT 0.965504 -145 *** ** **** * Masking position 11 Map Score: 2.04487 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 74 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 ********** No masking Map Score: -3.50765e-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: -3.50765e-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: -3.50765e-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