AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i190_ribonucleoside_diphos___synecho_reg_100.orf -o190_synecho_100.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 ATTGGGTTCGTTCCCCCCCCCAACTATTATT 1 21 0 TCCCCCCCCC 0.958695 -280 GGGGGGGAACGAACCCAATCTTAACAAAAAT 1 33 1 GACCCAATCT 0.637886 -268 CCCAGGGTGAGCCATTGCCCTGATAACAATT 1 61 0 GCATTGCCCT 0.959316 -240 TTCAATGTCTGAAATCACCCCAGGGTGAGCC 1 79 0 GAATCACCCC 0.914096 -222 TTTATCATAGGCCACCCCCCTGGGGATCGGG 1 146 0 GCACCCCCCT 0.992389 -155 TGGTGTGGCCGACACTGATCTTACTCCACAT 1 184 0 GCACTGATCT 0.766147 -117 CTCACTTTGGGCCCTTGACCCTGTCAGTTTG 1 241 1 GCCTTGACCC 0.895903 -60 GTCAGTTTGTTCCGCTACCCTACGAAGTCCC 1 263 1 TCGCTACCCT 0.852663 -38 GCTACCCTACGAAGTCCCCCTGACTGTCTTT 1 276 1 GAGTCCCCCT 0.971747 -25 TGTTTAGCTCGGCGCCGCCCCGCAATCTTTT 2 45 0 GCGCCGCCCC 0.992252 -186 AGGGACTTTAGTAGTCCACCTAAATTACTCT 2 136 1 GAGTCCACCT 0.939644 -95 AGGAAAATTGTGAACCGACCTATTCTAACCC 2 195 0 TAACCGACCT 0.87959 -36 * ********* Masking position 10 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 CTAGGCATTTGGTAGCCAATTTAGCAACCC 1 119 1 GGTAGCCAAT 0.958839 -182 TCCCCAGGGGGGTGGCCTATGATAAAGTGC 1 151 1 GGTGGCCTAT 0.991099 -150 AAGTGCCAGATGTGGAGTAAGATCAGTGTC 1 175 1 TGTGGAGTAA 0.934719 -126 ACAGATATGGTGTGGCCGACACTGATCTTA 1 192 0 TGTGGCCGAC 0.979063 -109 ACACCATATCTGTGGCTTAATTTATCTAAG 1 209 1 TGTGGCTTAA 0.9398 -92 GACTTCGTAGGGTAGCGGAACAAACTGACA 1 262 0 GGTAGCGGAA 0.981088 -39 CCTTGTCGGTAGCGAAAGAGCCATAAA 2 8 1 GGTAGCGAAA 0.970843 -223 GAGTAATTTAGGTGGACTACTAAAGTCCCT 2 136 0 GGTGGACTAC 0.975475 -95 ********** Masking position 9 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 AAAATTGTTATCAGGGCAATGGCTCACCCT 1 59 1 TCAGGGCAAT 0.967021 -242 AAGGATTAATTCTAGGCATTTGGTAGCCAA 1 108 1 TCTAGGCATT 0.948798 -193 AAGCTCTCACTTTGGGCCCTTGACCCTGTC 1 236 1 TTTGGGCCCT 0.983554 -65 ACCCAGTTTCTTTGGGCAGTCTTGATCAAC 2 169 0 TTTGGGCAGT 0.995485 -62 GGAATTTGGGCAGTAAGGAAAATT 2 217 0 TTTGGGCAGT 0.995485 -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 4 AATAGTTGGGGGGGGGAACGAACCCAATCT 1 24 1 GGGGGGAACG 0.982871 -277 GGCTCACCCTGGGGTGATTTCAGACATTGA 1 79 1 GGGGTGATTT 0.885686 -222 GATCCCCAGGGGGGTGGCCTATGATAAAGT 1 149 1 GGGGTGGCCT 0.997124 -152 CCACAGATATGGTGTGGCCGACACTGATCT 1 194 0 GGTGTGGCCG 0.989346 -107 AAAGACAGTCAGGGGGACTTCGTAGGGTAG 1 277 0 AGGGGGACTT 0.883589 -24 AAGATTGCGGGGCGGCGCCGAGCTAAACAA 2 47 1 GGCGGCGCCG 0.926803 -184 TGTATAGAGTTGTGTGACCTTTGTCGAGAT 2 81 1 TGTGTGACCT 0.942177 -150 AAGAGTAATTTAGGTGGACTACTAAAGTCC 2 138 0 TAGGTGGACT 0.742678 -93 ********** Masking position 4 Map Score: 4.29301 Number of sites scoring better than the average of aligned sites = 2234 Number in coding regions = 2079 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 5 TTTTTTAAGAAATAATAGTTGGGGGGGGG 1 8 1 AGAAAATAGT 0.928988 -293 ACCCAATCTTAACAAAAATTGTTATCAGGGCA 1 45 1 AAAAAATTGT 0.982917 -256 CAGACATTGAAGGATTAATTCTAGGCATTTGG 1 99 1 AGATAATTCT 0.682439 -202 CGAAAGAGCCATAAAAAATTCTAAAAGATTGC 2 23 1 ATAAAATTCT 0.929405 -208 CGCCGAGCTAAACAAGAATTGTATAGAGTTGT 2 62 1 AAAAAATTGT 0.982917 -169 AGATGACAAGAACAAGAAAACTATGTAAGAGG 2 107 1 AAAAAAAACT 0.79827 -124 TTTGGGCAGTAAGGAAAATTGTGAACCGACCT 2 205 0 AAGAAATTGT 0.946547 -26 ** ** ****** Masking position 7 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 6 TTGCTAAATTGGCTACCAAATGCCTAGAAT 1 116 0 GGCTACCAAA 0.977379 -185 CTGGGGATCGGGTTGCTAAATTGGCTACCA 1 128 0 GGTTGCTAAA 0.964883 -173 AATTTAGGTGGACTACTAAAGTCCCTCTTA 2 132 0 GACTACTAAA 0.945873 -99 AATTACTCTTGGTTGATCAAGACTGCCCAA 2 158 1 GGTTGATCAA 0.869865 -73 GGTTGATCAAGACTGCCCAAAGAAACTGGG 2 168 1 GACTGCCCAA 0.99224 -63 CAATTTTCCTTACTGCCCAAATTCC 2 216 1 TACTGCCCAA 0.95188 -15 ********** Masking position 4 Map Score: 4.24435 Number of sites scoring better than the average of aligned sites = 791 Number in coding regions = 718 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 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