AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i299_mixed14_synecho_reg_300.orf -o299_synecho_300.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY49210 300 Synechocystis #2 RCY35846 218 Synechocystis #3 RCY33500 23 Synechocystis Motif number 1 TAAGGGTGCAAAGGTGCGGTAAGAGCGCACCAG 1 66 1 AAGGTCGGTG 0.928878 -235 CTGGCTCGGTAAACCCCGGTTGGAAGCAAGGTC 1 114 1 AAACCCGGTG 0.973637 -187 GGTTGGAAGCAAGGTCGGAGGGGCAAAGGTTGG 1 131 1 AAGGTGGAGG 0.919916 -170 CGGTTCCACCAATCATGGGGCAGGAAAAAGACC 1 162 0 AATCAGGGGG 0.908423 -139 AGTTAGTCGTAAGCCGGGTTCTGTTCCAGGATG 1 250 0 AAGCCGGTTG 0.973617 -51 TGAACGTCCAAAACCCAGGGGTGGAGGATGGAT 2 19 1 AAACCAGGGG 0.990889 -200 TCAACCCAATAAAGCTAGTGTAGCGAATTGGGG 2 80 0 AAAGCAGTGG 0.972376 -139 CTTAGGGAAGAAAGCAGGGGAAGATTGTCAACC 2 107 0 AAAGCGGGGG 0.994164 -112 GCTAACAGGCAAGCTTAGGGAAGAAAGCAGGGG 2 120 0 AAGCTAGGGG 0.988021 -99 CCAACCCCAGTGACGAGATAGCAAA 2 204 0 AACCCAGTGG 0.959053 -15 ***** **** * Masking position 2 Map Score: 11.0644 Number of sites scoring better than the average of aligned sites = 1348 Number in coding regions = 1234 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 2 AGACCAACCTTTGCCCCTCCGACCTTGCTT 1 137 0 TTGCCCCTCC 0.979534 -164 GGTCTTTTTCCTGCCCCATGATTGGTGGAA 1 162 1 CTGCCCCATG 0.917999 -139 TGTTACCAAATTCCTCAAGCGGTTCCACCA 1 184 0 TTCCTCAAGC 0.950699 -117 AGATAGATAACTCCCCAAGGGTGCCTCGCA 1 222 1 CTCCCCAAGG 0.975513 -79 AAGCCGGGTTCTGTTCCAGGATGCGAGGCA 1 243 0 CTGTTCCAGG 0.784761 -58 CTCTCTTTTTTTGTCCATGGGTCCAGTGGC 1 281 1 TTGTCCATGG 0.796543 -20 TCAGAAATCCATCCTCCACCCCTGGGTTTT 2 28 0 ATCCTCCACC 0.772418 -191 CCCAAACAGATTGCCCCAATTCGCTACACT 2 67 1 TTGCCCCAAT 0.787787 -152 GGTTGACAATCTTCCCCTGCTTTCTTCCCT 2 107 1 CTTCCCCTGC 0.920071 -112 CCCTGCTTTCTTCCCTAAGCTTGCCTGTTA 2 121 1 TTCCCTAAGC 0.894604 -98 TATGGTTCGTTTGCTCATGGTATTCCCTCA 2 156 1 TTGCTCATGG 0.898933 -63 GCTCATGGTATTCCCTCAACGTTTTTCCCC 2 168 1 TTCCCTCAAC 0.807917 -51 CTCAACGTTTTTCCCCCTCCCATTTGCTAT 2 182 1 TTCCCCCTCC 0.979534 -37 ********** Masking position 2 Map Score: 11.3131 Number of sites scoring better than the average of aligned sites = 10872 Number in coding regions = 9862 Number in noncoding regions = 1010 Number of orfs with sites within 600 bp upstream = 847 Fraction of orfs with sites within 600 bp upstream = 0.136042 Motif number 3 ACCCTTTTCAGTGGTCAGTTACCAGTTAGTCAG 1 34 0 GTGGCTTACC 0.99707 -267 TACCGCACCTTTGCACCCTTACCCTTTTCAGTG 1 54 0 TTGCCTTACC 0.995362 -247 GATACTGCTGGTGCGCTCTTACCGCACCTTTGC 1 73 0 GTGCCTTACC 0.994411 -228 GGGGCAAAGGTTGGTCTTTTTCCTGCCCCATGA 1 150 1 TTGGCTTTCC 0.990224 -151 CGAGGCACCCTTGGGGAGTTATCTATCTGGGAA 1 217 0 TTGGGTTATC 0.93575 -84 CCCCTGGGTTTTGGACGTTCACCGTGGGT 2 7 0 TTGGCTCACC 0.993383 -212 **** * ***** Masking position 9 Map Score: 8.15127 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 157 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 ACCTCTCGATACTGCTGGTGCGCTCTTACC 1 83 0 ACTGCTGGTG 0.961681 -218 GGCTCGGTAAACCCCGGTTGGAAGCAAGGT 1 116 1 ACCCCGGTTG 0.912001 -185 CGGTTCCACCAATCATGGGGCAGGAAAAAG 1 165 0 AATCATGGGG 0.842031 -136 GATTGGTGGAACCGCTTGAGGAATTTGGTA 1 181 1 ACCGCTTGAG 0.89536 -120 GATGCGAGGCACCCTTGGGGAGTTATCTAT 1 224 0 ACCCTTGGGG 0.939484 -77 GCCACTGGACCCATGGACAAAAAAAGAG 1 283 0 ACCCATGGAC 0.925636 -18 ACCCACGGTGAACGTCCAAA 2 1 1 ACCCACGGTG 0.967402 -218 TCCATCCTCCACCCCTGGGTTTTGGACGTT 2 21 0 ACCCCTGGGT 0.520488 -198 ********** Masking position 1 Map Score: 4.65903 Number of sites scoring better than the average of aligned sites = 2649 Number in coding regions = 2418 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 5 TGGTCAGTTACCAGTTAGTCAGCAGAAAAACC 1 24 0 CCAGTTGTAG 0.96632 -277 CTCGGTAAACCCCGGTTGGAAGCAAGGTCGGA 1 118 1 CCCGGTGGAG 0.987797 -183 GGGTTCTGTTCCAGGATGCGAGGCACCCTTGG 1 236 0 CCAGGAGCAG 0.978853 -65 ACAGATTGCCCCAATTCGCTACACTAGCTTTA 2 72 1 CCAATTGCAC 0.962363 -147 CCTAAGCTTGCCTGTTAGCGATTATGGTTCGT 2 134 1 CCTGTTGCAT 0.961263 -85 TTTTCCCCCTCCCATTTGCTATCTCGTCACTG 2 190 1 CCCATTGCAT 0.979522 -29 CCAACCCCAGTGACGAGATAGCAAATG 2 202 0 CCCAGTACAG 0.956777 -17 ****** ** ** Masking position 11 Map Score: 2.68085 Number of sites scoring better than the average of aligned sites = 763 Number in coding regions = 707 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 6 TTTCTGCTGACTAACTGGTAACTGACCACT 1 28 1 CTAACTGGTA 0.961455 -273 GACCTTGCTTCCAACCGGGGTTTACCGAGC 1 117 0 CCAACCGGGG 0.983336 -184 GGGGAGTTATCTATCTGGGAAATTTGTTAC 1 208 0 CTATCTGGGA 0.970993 -93 GCTAGTGTAGCGAATTGGGGCAATCTGTTT 2 70 0 CGAATTGGGG 0.931349 -149 ACCATAATCGCTAACAGGCAAGCTTAGGGA 2 132 0 CTAACAGGCA 0.901192 -87 TGACGAGATAGCAAATGGGAGGGGGAAAAA 2 189 0 GCAAATGGGA 0.897182 -30 TTGCTATCTCGTCACTGGGGTTGG 2 205 1 GTCACTGGGG 0.961948 -14 ********** Masking position 7 Map Score: 1.39368 Number of sites scoring better than the average of aligned sites = 1309 Number in coding regions = 1205 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 7 TAAGGGTGCAAAGGTGCGGTAAGAGCGCAC 1 66 1 AAGGTGCGGT 0.950555 -235 CTCGATACTGCTGGTGCGCTCTTACCGCAC 1 79 0 CTGGTGCGCT 0.991787 -222 TCGAGAGGTACTGGCTCGGTAAACCCCGGT 1 104 1 CTGGCTCGGT 0.978284 -197 CGAGGCACCCTTGGGGAGTTATCTATCTGG 1 220 0 TTGGGGAGTT 0.893952 -81 GGCAATCTGTTTGGGTCGCTAAGGTCAGAA 2 52 0 TTGGGTCGCT 0.981686 -167 GTTAGCGATTATGGTTCGTTTGCTCATGGT 2 147 1 ATGGTTCGTT 0.969781 -72 ********** Masking position 10 Map Score: 2.97005 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 413 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 ********** No masking Map Score: 2.36911e-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 9 ********** No masking Map Score: 2.36911e-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: 2.36911e-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