AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i155_synecho_ctra_300.orf -o155_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 Purged sequences: RCY39746 21 Synechocystis Input sequences: #1 RCY40720 89 Synechocystis #2 RCY45578 165 Synechocystis #3 RCY04694 45 Synechocystis #4 RCY19246 26 Synechocystis #5 RCY21450 40 Synechocystis #6 RCY45007 52 Synechocystis #7 RCY02720 300 Synechocystis Motif number 1 TAAATTCCTGAATATTTATTACAAGATCCGGCTT 1 18 1 AATATTATAA 0.765158 -72 TTTACTGCTCAAAAAATATCTAAATCAACAATAA 1 58 1 AAAAATATAA 0.85011 -32 GTCGGACAATAAAATTTGAGTCAATACAAATTGT 2 41 0 AAAATTGAAA 0.974469 -125 AAATGATGTTAAAAGTTCTTAAAAGTTCAAC 3 8 0 AAAATTCTAA 0.979869 -38 TGGCCAAAAACTCCTTTGAAAATGAA 4 7 0 AAAATCCTAA 0.938941 -20 GGTGTTTCAGAAAAGTTAACTGAGTGGATAAATT 5 17 0 AAAATTAAAG 0.85377 -24 AATCAACTAGAAAAGATCAAGCAATCACCTGATA 6 22 0 AAAAATCAAA 0.952489 -31 ATCAAAAAATCAACTAGAAAAGATCAA 6 36 0 AAAAATCAAG 0.863642 -17 AAGCAACAAAAATAGTTCAAATAAATTGCA 7 7 0 AATATTCAAA 0.920108 -294 TAGACAACGAAAAAGTTGTTTTAAGCAACAAAAA 7 29 0 AAAATTGTAA 0.970542 -272 ATCAACTTTTAAAAAGTGAGCAAATCTTTAGCTT 7 95 0 AAAAGTGAAA 0.888393 -206 CTCACTTTTTAAAAGTTGATGTAACAATGAAGGC 7 109 1 AAAATTGAAA 0.974469 -192 GGAAAAATCCTCAAAAAGGAGCAATA 7 285 0 AAAATCCTAA 0.938941 -16 **** **** ** Masking position 4 Map Score: 15.2552 Number of sites scoring better than the average of aligned sites = 635 Number in coding regions = 461 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 2 GGGATTGATTATTGTTGATTTAGATATTTT 1 70 0 TTATGTTGTT 0.989292 -20 ATTGTCCGACTTCTTGTTGGGTATTATGAAGA 2 65 1 TTCTGTTGGT 0.987032 -101 CTCATAGTTGATTAGATCAGGAG 2 153 0 TCATGTTGTT 0.966018 -13 GCTTGATCTTTTCTAGTTGATTTTTTGAT 6 34 1 TTCTGTTGTT 0.995219 -19 ATTTGAACTATTTTTGTTGCTTAAAACAACTT 7 19 1 TTTTGTTGTT 0.989292 -282 TAAAACAACTTTTTCGTTGTCTAAATTATCCC 7 40 1 TTTTGTTGCT 0.971249 -261 CGAATGGAATCTCTAGTTGGTTGCCTTCATTG 7 133 0 CTCTGTTGTT 0.984627 -168 **** **** ** Masking position 7 Map Score: 10.2413 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 69 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 GATCCGGCTTTCTATATTTACTGCTCAAAAAATATC 1 42 1 TCAATTCTCC 0.975718 -48 GGTATGACCAACCAAACTTCTTTCACAATTTGTATT 2 17 1 ACAATTTTCC 0.994026 -149 TATTTGCGTTACACCATTTATTCCACATCTCAAGAT 2 105 0 ACCATTTTCC 0.994465 -61 TAACGCAAATACTAAAATTGTTGCTCCTGATCTAAT 2 130 1 ACAATTTTCC 0.994026 -36 TTCGGTAATTTATCCACTCAGTTAACT 5 2 1 TCGATTATCC 0.940839 -39 TTGTGGAGGCACACAAATTCTTTCCCGACTAAGGGT 7 180 1 ACCATTTTCC 0.994464 -121 ** * * ** ** * * Masking position 8 Map Score: 4.64783 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 58 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 AGTCAATACAAATTGTGAAAGAAGTTTGGTT 2 26 0 AATTGGAAAG 0.987611 -140 TTGTGGGCAAGATTGTGGAGGCACACAAATT 7 168 1 GATTGGGAGG 0.973303 -133 TTTCACCCTTAGTCGGGAAAGAATTTGTGTG 7 189 0 AGTCGGAAAG 0.941796 -112 AGGTAAATTTGATTGCGAAAGTTAGCCTGAT 7 220 0 GATTGGAAAG 0.994462 -81 GATAAAAGATGATTGGGAGAGCCTAAACCAG 7 249 0 GATTGGAGAG 0.987795 -52 ***** ***** Masking position 3 Map Score: 2.11114 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 53 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 TTTTTAGGTATGACCAACCAAACTTC 2 3 1 TTTAGTACCA 0.983296 -163 GACAATAAAATTTGAGTCAATACAAATTGTGAAA 2 37 0 TTTGGTTACA 0.962108 -129 AATTTTAGTATTTGCGTTACACCATTTATTCCAC 2 115 0 TTTGGTACCA 0.99252 -51 CGGGAAAGAATTTGTGTGCCTCCACAATCTTGCC 7 173 0 TTTGGTTCCA 0.991991 -128 ATTTACCTGGTTTAGGCTCTCCCAATCATCTTTT 7 243 1 TTTAGCCCCA 0.95686 -58 **** ** **** Masking position 3 Map Score: 0.138623 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 108 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 ********** No masking Map Score: -1.4826e-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 7 TCTAAATCAACAATAATCAATCCC 1 76 1 CATAACAATC 0.953917 -14 TTTTAGGTATGACCAACCAAACTTCTTTCACA 2 12 1 GACAACAAAC 0.961981 -154 TGGGTATTATGAAGAAACTATCTATCTTGAGA 2 82 1 GAGAACTATC 0.967636 -84 AACTAGAAAAGATCAAGCAATCACCTGATACT 6 20 0 GACAACAATC 0.984893 -33 CTTTTTCGTTGTCTAAATTATCCCGATTAAGT 7 48 1 GTTAATTATC 0.808165 -253 AAATTATCCCGATTAAGTAATCGACATTGAAG 7 62 1 GATAATAATC 0.605789 -239 ** *** ***** Masking position 6 Map Score: 0.100527 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 185 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 ********** No masking Map Score: -1.4826e-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: -1.4826e-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: -1.4826e-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