AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i190_ribonucleoside_diphos___synecho_reg_300.orf -o190_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 RCY49610 300 Synechocystis #2 RCY26651 230 Synechocystis Motif number 1 AATAATAGTTGGGGGGGGGAACGAACCCAAT 1 21 1 GGGGGGGGGA 0.965458 -280 ATTTTTGTTAAGATTGGGTTCGTTCCCCCCC 1 33 0 AGATTGGGTC 0.679626 -268 AATTGTTATCAGGGCAATGGCTCACCCTGGG 1 61 1 AGGGCAATGC 0.965981 -240 GGCTCACCCTGGGGTGATTTCAGACATTGAA 1 79 1 GGGGTGATTC 0.927611 -222 CCCGATCCCCAGGGGGGTGGCCTATGATAAA 1 146 1 AGGGGGGTGC 0.993672 -155 ATGTGGAGTAAGATCAGTGTCGGCCACACCA 1 184 1 AGATCAGTGC 0.797789 -117 CAAACTGACAGGGTCAAGGGCCCAAAGTGAG 1 241 0 GGGTCAAGGC 0.912004 -60 GGGACTTCGTAGGGTAGCGGAACAAACTGAC 1 263 0 AGGGTAGCGA 0.874516 -38 AAAGACAGTCAGGGGGACTTCGTAGGGTAGC 1 276 0 AGGGGGACTC 0.976426 -25 AAAAGATTGCGGGGCGGCGCCGAGCTAAACA 2 45 1 GGGGCGGCGC 0.992837 -186 AGAGTAATTTAGGTGGACTACTAAAGTCCCT 2 136 0 AGGTGGACTC 0.949362 -95 GGGTTAGAATAGGTCGGTTCACAATTTTCCT 2 195 1 AGGTCGGTTA 0.897927 -36 ********* * Masking position 2 Map Score: 11.531 Number of sites scoring better than the average of aligned sites = 5389 Number in coding regions = 5008 Number in noncoding regions = 381 Number of orfs with sites within 600 bp upstream = 380 Fraction of orfs with sites within 600 bp upstream = 0.0610344 Motif number 2 GGGTTGCTAAATTGGCTACCAAATGCCTAG 1 119 0 ATTGGCTACC 0.953211 -182 GCACTTTATCATAGGCCACCCCCCTGGGGA 1 151 0 ATAGGCCACC 0.989832 -150 GACACTGATCTTACTCCACATCTGGCACTT 1 175 0 TTACTCCACA 0.925824 -126 TAAGATCAGTGTCGGCCACACCATATCTGT 1 192 1 GTCGGCCACA 0.977015 -109 CTTAGATAAATTAAGCCACAGATATGGTGT 1 209 0 TTAAGCCACA 0.931683 -92 TGTCAGTTTGTTCCGCTACCCTACGAAGTC 1 262 1 TTCCGCTACC 0.978367 -39 TTTATGGCTCTTTCGCTACCGACAAGG 2 8 0 TTTCGCTACC 0.966753 -223 AGGGACTTTAGTAGTCCACCTAAATTACTC 2 136 1 GTAGTCCACC 0.971985 -95 ********** Masking position 8 Map Score: 9.44324 Number of sites scoring better than the average of aligned sites = 1004 Number in coding regions = 947 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 TACTCCACATCTGGCACTTTATCATAGGCC 1 164 0 CTGGCACTTT 0.994361 -137 TTTATCTAAGCTCTCACTTTGGGCCCTTGA 1 229 1 CTCTCACTTT 0.978901 -72 GCCCTTGACCCTGTCAGTTTGTTCCGCTAC 1 251 1 CTGTCAGTTT 0.983855 -50 GTCCCCCTGACTGTCTTTTTCT 1 289 1 CTGTCTTTTT 0.966323 -12 AGAATTTTTTATGGCTCTTTCGCTACCGAC 2 15 0 ATGGCTCTTT 0.95932 -216 ********** Masking position 8 Map Score: 4.30418 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 115 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 CCCCCCCCCAACTATTATTTCTTAAAAAA 1 8 0 ACTATTTTCT 0.929743 -293 TGCCCTGATAACAATTTTTGTTAAGATTGGGT 1 45 0 ACAATTTTTT 0.98362 -256 CCAAATGCCTAGAATTAATCCTTCAATGTCTG 1 99 0 AGAATTATCT 0.681089 -202 GCAATCTTTTAGAATTTTTTATGGCTCTTTCG 2 23 0 AGAATTTTAT 0.932097 -208 ACAACTCTATACAATTCTTGTTTAGCTCGGCG 2 62 0 ACAATTTTTT 0.98362 -169 CCTCTTACATAGTTTTCTTGTTCTTGTCATCT 2 107 0 AGTTTTTTTT 0.805067 -124 AGGTCGGTTCACAATTTTCCTTACTGCCCAAA 2 205 1 ACAATTTCTT 0.94867 -26 ****** ** ** Masking position 1 Map Score: 2.51632 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 148 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 5 TCACCCCAGGGTGAGCCATTGCCCTGATAA 1 66 0 GTGAGCCATT 0.98237 -235 CTGGGGTGATTTCAGACATTGAAGGATTAA 1 87 1 TTCAGACATT 0.838935 -214 AGGGCCCAAAGTGAGAGCTTAGATAAATTA 1 226 0 GTGAGAGCTT 0.972013 -75 AGCTCTCACTTTGGGCCCTTGACCCTGTCA 1 237 1 TTGGGCCCTT 0.97508 -64 GTATAGAGTTGTGTGACCTTTGTCGAGATG 2 82 1 GTGTGACCTT 0.983589 -149 AACTATGTAAGAGGGACTTTAGTAGTCCAC 2 125 1 GAGGGACTTT 0.910266 -106 ********** Masking position 9 Map Score: 1.8337 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 192 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 AGGGTGAGCCATTGCCCTGATAACAATTTT 1 59 0 ATTGCCCTGA 0.960683 -242 TTGGCTACCAAATGCCTAGAATTAATCCTT 1 108 0 AATGCCTAGA 0.939137 -193 GACAGGGTCAAGGGCCCAAAGTGAGAGCTT 1 236 0 AGGGCCCAAA 0.980315 -65 GTTGATCAAGACTGCCCAAAGAAACTGGGT 2 169 1 ACTGCCCAAA 0.994744 -62 AATTTTCCTTACTGCCCAAATTCC 2 217 1 ACTGCCCAAA 0.994744 -14 ********** Masking position 1 Map Score: 4.99139 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 333 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 ********** No masking Map Score: 3.7902e-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: 3.7902e-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: 3.7902e-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