AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i189_synecho_ctra_300.orf -o189_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 RCY08506 300 Synechocystis #2 RCY33560 226 Synechocystis Motif number 1 AGGGGATACCTCTCCCCCCTGTCAATCGACT 1 168 0 TCTCCCCCCG 0.988289 -133 GGGGGAGAGGTATCCCCTAGGCTTAGGCTTA 1 181 1 TATCCCCTAG 0.944377 -120 ATTGTTGATCAATTGCCCAAGCTGAGCTGGT 1 230 0 AATTGCCCAG 0.986482 -71 GGCGGTGTTTAATTCCCCATCAACTTTTGAG 2 23 0 AATTCCCCAC 0.98331 -204 CTAGTGACAATCTTGCCCAACTTCAATTCCC 2 63 1 TCTTGCCCAC 0.97776 -164 GCCCAACTTCAATTCCCCCCCTATCTCCCAC 2 77 1 AATTCCCCCC 0.970899 -150 ATTCCCCCCCTATCTCCCACGGACAGTAGAA 2 88 1 TATCTCCCAG 0.966815 -139 TGATGGTGAAACACGCCCAGGGTAAGGCATT 2 169 0 ACACGCCCAG 0.953123 -58 ********* * Masking position 6 Map Score: 8.16676 Number of sites scoring better than the average of aligned sites = 1697 Number in coding regions = 1517 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 2 ATTGAGAAATGTTGAGACTGGCCAAGCTAAA 1 128 1 GTTAGACTGG 0.970927 -173 CTTTGCCAGACTTTAGCTTGGCCAGTCTCAA 1 139 0 CTTAGCTTGG 0.991189 -162 GGAAAATAAGCCTAAGCCTAGGGGATACCTC 1 187 0 CCTAGCCTAG 0.990676 -114 CGGTCGACCAGCTCAGCTTGGGCAATTGATC 1 224 1 GCTAGCTTGG 0.994294 -77 GGGATAAATGCCTTACCCTGGGCGTGTTTCA 2 163 1 CCTACCCTGG 0.993579 -64 *** ******* Masking position 5 Map Score: 3.91765 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 295 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 3 TTATGGTTTTCTGACAAACACAATTTTGTT 1 32 1 CTGACAAACA 0.95807 -269 ATTTCAACCTAGGTCAAACAAAATTGTGTT 1 48 0 AGGTCAAACA 0.986224 -253 TTCCGGCCTCCGGTCGACCAGCTCAGCTTG 1 214 1 CGGTCGACCA 0.632505 -87 ACAATCATCGTTGTCAACCATAGGGATAAA 2 141 1 TTGTCAACCA 0.927265 -86 TCGTCAGTGATGGTGAAACACGCCCAGGGT 2 177 0 TGGTGAAACA 0.953411 -50 AGGAAAAACAATGGGACAAT 2 217 0 AGGAAAAACA 0.89335 -10 ********** Masking position 7 Map Score: 3.06684 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 384 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 TAAGGGAACTGTGGTAAATGCCTG 1 1 0 GGTAATGCCG 0.996029 -300 TGAAATTTTTGTCTTAACTGCCCGGATTTTTAGA 1 72 1 GCTAATGCCG 0.997983 -229 CCTAGGCTTAGGCTTATTTTCCGGCCTCCGGTCG 1 196 1 GCTATTTCCG 0.985114 -105 TTGTCACTAGGACTTATCTGGCGGTGTTTAATTC 2 39 0 GCTATTGGCG 0.989909 -188 GTCAACCATAGGGATAAATGCCTTACCCTGGGCG 2 153 1 GGTAATGCCT 0.984827 -74 * * *** **** * Masking position 6 Map Score: 3.6143 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 44 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 GTGAATACATGATCTAAAAATCCGGGCAGTTAA 1 85 0 GATAAAAACC 0.950798 -216 TCATTCCATAGAACTAATCAATGCGTGTTTGTG 1 261 1 GATAATCATG 0.978392 -40 AGTTGATGGGGAATTAAACACCGCCAGATAAGT 2 29 1 GATAAACACG 0.996014 -198 ACGGACAGTAGAAATAAACAACGTTACAATTAG 2 106 1 GATAAACACG 0.996019 -121 GTTACAATTAGATACAATCATCGTTGTCAACCA 2 128 1 GACAATCACG 0.980012 -99 CACTGACGACGGCATAAAAATTGTCCCATTGTT 2 198 1 GGTAAAAATG 0.912593 -29 ** ****** ** Masking position 7 Map Score: 3.53818 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 141 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 AAATGTTGAGACTGGCCAAGCTAAAGTCTG 1 134 1 ACTGGCCAAG 0.982195 -167 CAAGCTAAAGTCTGGCAAAGTCGATTGACA 1 150 1 TCTGGCAAAG 0.936783 -151 CTAGGACTTATCTGGCGGTGTTTAATTCCC 2 37 0 TCTGGCGGTG 0.989162 -190 GTTTATTTCTACTGTCCGTGGGAGATAGGG 2 95 0 ACTGTCCGTG 0.973347 -132 AATGCCTTACCCTGGGCGTGTTTCACCATC 2 169 1 CCTGGGCGTG 0.962028 -58 TTTCACCATCACTGACGACGGCATAAAAAT 2 189 1 ACTGACGACG 0.903437 -38 ********** Masking position 3 Map Score: 2.47559 Number of sites scoring better than the average of aligned sites = 949 Number in coding regions = 881 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 ********** No masking Map Score: -1.75204e-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 8 ********** No masking Map Score: -1.75204e-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: -1.75204e-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