AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i130_synecho_ctra_100.orf -o130_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 RCY28537 38 Synechocystis #2 RCY13382 161 Synechocystis #3 RCY44868 300 Synechocystis #4 RCY30726 96 Synechocystis Motif number 1 CATCCGCAGAAAACTGACAACTTTTAGGAAT 2 33 0 AAACTGCAAC 0.847616 -129 AGTTTTTAAAACGCCCTAACCAGATAGCGTA 2 135 0 ACGCCCAACC 0.971221 -27 CACCCGTAACAAACCGTTACTTGATCGACCG 3 101 0 AAACCGTACT 0.966917 -200 CCAACCCTTAACACCCGTAACAAACCGTTAC 3 112 0 ACACCCTAAC 0.985575 -189 CTTATCCAACAAACCCCCAACCCTTAACACC 3 128 0 AAACCCCAAC 0.98948 -173 TCCTAATCGAGAACCGACACTCATCAGCTTA 3 155 0 GAACCGCACT 0.856617 -146 GCGTTGAAACAAGCCCTTAATGGGTAACGGT 4 20 1 AAGCCCTAAT 0.950685 -77 CACCCGTAACAAACCGTTACCCATTAAGGGC 4 32 0 AAACCGTACC 0.990438 -65 CCAACCCCTAACACCCGTAACAAACCGTTAC 4 43 0 ACACCCTAAC 0.985575 -54 ATACCCAACCAAGCCCCAACCCCTAACACCC 4 58 0 AAGCCCAACC 0.979338 -39 ****** **** Masking position 9 Map Score: 14.1403 Number of sites scoring better than the average of aligned sites = 1032 Number in coding regions = 947 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 2 TTTTTGCTACGCCCAAAGGCCCATGG 1 5 0 GCCCAAGCCC 0.98161 -34 AAACCCCCAACCCTTAACACCCGTAACAAACC 3 117 0 CCCTAACCCC 0.995106 -184 TCAGCTTATCCAACAAACCCCCAACCCTTAAC 3 131 0 CAACAACCCC 0.987574 -170 GAATGATAATCACTCAACACGTTTGTATTTAA 3 265 1 CACTAACCGT 0.946604 -36 TCACTAAAGGCGTTGAAACAAGC 4 2 1 CACTAAGCGT 0.946604 -95 AAACCGTTACCCATTAAGGGCTTGTTTCAACG 4 21 0 CCATAAGGCT 0.837183 -76 CAAGCCCCAACCCCTAACACCCGTAACAAACC 4 48 0 CCCCAACCCC 0.996909 -49 CCAGCATACCCAACCAAGCCCCAACCCCTAAC 4 62 0 CAACAAGCCC 0.987574 -35 **** *** *** Masking position 6 Map Score: 8.63501 Number of sites scoring better than the average of aligned sites = 1215 Number in coding regions = 1016 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 3 AACCAGATAGCGTAAGCTTACCAGACAAAGCCAAA 2 114 0 CGAGCTTCAA 0.983897 -48 TCAAGAGCATCGCCTAGTTTACGAAG 3 2 1 CAAGCATCCA 0.997639 -299 TGTCAGTTGTCGTTATCATTACCGATAGCATTAAT 3 59 1 CGATCATCCA 0.988707 -242 AACCGACACTCATCAGCTTATCCAACAAACCCCCA 3 140 0 CAAGCTTCCA 0.996626 -161 AAGCATTAGCCACCAGCATACCCAACCAAGCCCCA 4 71 0 CAAGCATCCA 0.997643 -26 ** ***** ** * Masking position 9 Map Score: 4.54067 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 28 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 ACTTGAGGTCAATTTTTGCTACGCCCAA 1 21 0 GTCAATTTTG 0.959243 -18 CCTAAAAGTTGTCAGTTTTCTGCGGATGAGT 2 36 1 GTCAGTTTCT 0.989419 -126 CATTCGTGTTGTCAGTTGTCGTTATCATTAC 3 50 1 GTCAGTTTCG 0.997316 -251 GCTGATGAGTGTCGGTTCTCGATTAGGATTC 3 158 1 GTCGGTTTCG 0.995432 -143 ******* *** Masking position 6 Map Score: 3.03049 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 12 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 TCGATCAAGTAACGGTTTGTTACGGGTGTT 3 104 1 AACGGTTTGT 0.994428 -197 TACGGGTGTTAAGGGTTGGGGGTTTGTTGG 3 124 1 AAGGGTTGGG 0.983984 -177 GTTACCCATTAAGGGCTTGTTTCAACGCCT 4 18 0 AAGGGCTTGT 0.990534 -79 CTTAATGGGTAACGGTTTGTTACGGGTGTT 4 35 1 AACGGTTTGT 0.994428 -62 ********** Masking position 7 Map Score: 4.21154 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 12 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 AATTATTTTTTTGGCTTTGTCTGGTAAGCT 2 105 1 TTGGCTTTGT 0.987646 -57 GAAATCATCGGTGACTTCGTAAACTAGGCG 3 21 0 GTGACTTCGT 0.97912 -280 GTTAAGGGTTGGGGGTTTGTTGGATAAGCT 3 131 1 GGGGGTTTGT 0.982215 -170 TATATTGACTTTGTTTAAATACAA 3 287 0 TTGACTTTGT 0.97259 -14 GTTAGGGGTTGGGGCTTGGTTGGGTATGCT 4 62 1 GGGGCTTGGT 0.991309 -35 ********** Masking position 6 Map Score: 4.22195 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 166 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 AGGTCAATTTTTGCTACGCCCAAAGGCCCA 1 14 0 TTGCTACGCC 0.9902 -25 AATAAAGTTTTTAAAACGCCCTAACCAGAT 2 141 0 TTAAAACGCC 0.977815 -21 TAAGGGCTTGTTTCAACGCCTTTAGTGA 4 9 0 TTTCAACGCC 0.99175 -88 ********** Masking position 6 Map Score: 0.203273 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 32 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 CAACTTTTAGGAATTAGCCATAGACCACAA 2 17 0 GAATTAGCCA 0.975593 -145 GTGACTTCGTAAACTAGGCGATGCTCTTGA 3 11 0 AAACTAGGCG 0.948195 -290 TCGGGTGGAAAATTTAGGCAAAAAGTACAT 3 208 1 AATTTAGGCA 0.91962 -93 ACATGATTGGTCACTAGGCAGAAGGAAGGG 3 234 1 TCACTAGGCA 0.961029 -67 AAAGCATTAGCCACCAGCATACC 4 84 0 GCATTAGCCA 0.97735 -13 ********** Masking position 5 Map Score: 0.0910564 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 149 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 ********** No masking Map Score: 1.44541e-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: 1.44541e-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 11 ********** No masking Map Score: 1.44541e-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