AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i005_Pyrimidine_Biosynthesis_synecho_reg_300.orf -o005_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 RCY08561 119 Synechocystis #2 RCY01957 241 Synechocystis #3 RCY27506 300 Synechocystis #4 RCY30833 46 Synechocystis #5 RCY01603 300 Synechocystis #6 RCY37071 155 Synechocystis Motif number 1 TAGCAAAGTTGGGCAACCTTTCCGGATTCTGGGGGTTAAC 1 39 0 GGGCTCCGTT 0.909796 -81 GGGGATTTTTGTGCCGTCGTTCCCCCGAGGTTAAAAGGTT 1 88 1 GTGCTCCCGG 0.981212 -32 AGAGCGTTACTGCCGATGCTAATGCTTTGCA 2 2 1 GAGCTCCGGA 0.93879 -240 TATCATCAGAGTACTGCTTTTCCCGGGCCGGCAAATTGTG 2 111 1 GTACTCCCGG 0.927978 -131 CTAACTAATGGGGCCGTTGTCACCAAGCTTCCTAATAGAA 3 23 1 GGGCTACCGT 0.843304 -278 AATTAGGGCAAAAGCTAAACACCGTTGGCGCATTTCAGAA 3 118 1 AAAGCCCGGG 0.527312 -183 CCCATGTATTTAGCTAAAAGTCCGTGGTATTCTGAAATGC 3 147 0 TAGCGCCGGT 0.876221 -154 GCTACACTAGGGAGGAACGTTCCCATGTATTTAGCTAAAA 3 168 0 GGAGTCCCGT 0.856659 -133 TTGCATTAACTGGCGATCGCCCCCAATATGGATCCCTGGG 3 219 1 TGGCCCCCTG 0.895051 -82 GATATGGGGCAGGCGGTAGTCCCCAGGGATCCATATTGGG 3 240 0 AGGCTCCCGT 0.962202 -61 TATCCGTAAAAGACCTCTGCACCGCCGACGGGTCTGGATT 5 60 1 AGACCCCGGG 0.925112 -241 AATCACAGTCGAGCCAGACTACCCCTGGAGGTAAACTCCG 5 109 1 GAGCTCCCGG 0.990055 -192 CTAATCTTTATGGCTCCAGCCCCGGAGTTTACCTCCAGGG 5 131 0 TGGCCCCGGT 0.976287 -170 AGGGTGAACAGAGGAGACTTTCCCCTGTTACAGTGTCAGT 5 232 1 GAGGTCCCGA 0.763091 -69 AACAACTTTTTGGCATCGGTGCAGGTGGTGAGCC 5 277 1 TGGCTCAGGG 0.819365 -24 AACCACATATTAGCAGATTCGCCCCTGTCGTCTGTTCCAC 6 29 0 TAGCCCCCGG 0.976206 -127 CTGTGCTCCTTTGCCCGGCCGCCGCCGAATCAACCACATA 6 60 0 TTGCCCCGGT 0.912758 -96 AGCTGGAATAGGACCATTCGGCCGTAGTGGGAAAAAGTTA 6 123 0 GGACGCCGGG 0.952898 -33 **** * *** * * Masking position 12 Map Score: 20.6008 Number of sites scoring better than the average of aligned sites = 4119 Number in coding regions = 3884 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117 Motif number 2 ATTGGCTCAACCCAAAAGTACAGTTAACCCC 1 17 1 CCCAAAGTAC 0.927431 -103 TACAGTTAACCCCCAGAATCCGGAAAGGTTG 1 35 1 CCCCAAATCC 0.994134 -85 ACAAAAATCCCCCTAAAATCCTAGCAAAGTT 1 69 0 CCCTAAATCC 0.977092 -51 GGAACGACGGCACAAAAATCCCCCTAAAATC 1 80 0 CACAAAATCC 0.947228 -40 TAGATTGGAGCCCAAATATCATCAGAGTACT 2 95 1 CCCAATATCA 0.850122 -147 CATGTATTTAGCTAAAAGTCCGTGGTATTCT 3 154 0 GCTAAAGTCC 0.795611 -147 GGCGGTAGTCCCCAGGGATCCATATTGGGGG 3 238 0 CCCAGGATCC 0.919225 -63 AGGTTTATTGACCAAAAATCCGGGTCCGAAT 4 12 0 ACCAAAATCC 0.958233 -35 TGTGATTATTGCCCATAATCCAGACCCGTCG 5 85 0 GCCCAAATCC 0.980994 -216 CATACCACGCCCCCACTGTCCGGCAGGGTGA 5 208 1 CCCCATGTCC 0.974443 -93 ***** ***** Masking position 9 Map Score: 9.79449 Number of sites scoring better than the average of aligned sites = 889 Number in coding regions = 780 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 3 CTAATTTGACTGCCTTTGACTATGACCACC 3 94 0 TGCCTTTGAC 0.975661 -207 TGCCTTAGATTGCCTTAGATAGATATGGGG 3 271 0 TGCCTTAGAT 0.995571 -30 TGCCTTAGATTGCCTTAGATTGCCTTAGAT 3 281 0 TGCCTTAGAT 0.995571 -20 TGCCTTAGATTGCCTTAGAT 3 291 0 TGCCTTAGAT 0.995571 -10 AAAGGAGCACAGCCTTGGATAAGACTCCAA 6 88 1 AGCCTTGGAT 0.975377 -68 ********** Masking position 5 Map Score: 8.96422 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 27 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 GGATTCATTCCCCTCTTTTTCAGTGTACCGTGCACTTCC 2 47 1 CTCTATGTAC 0.995469 -195 TGCACTTCCTCGTTCCACTAGATTGGAGCCCAAATATCA 2 77 1 CTCCATGGAC 0.992146 -165 TACATGGGAACGTTCCTCCCTAGTGTAGCGAGGAAAAGA 3 179 1 CTCCATGTAC 0.997113 -122 AATGCTCCAATCGCCTTGATTGTATCGAATGATGCA 5 8 1 CTCCATGTAC 0.997114 -293 TCGAATGATGCAGTCTCTAAAATTGTATCCGTAAAAGAC 5 35 1 CTCTATGTAC 0.995469 -266 AAAAGTTGTTTTGTCACTGACACTGTAACAGGGGAAAGT 5 248 0 TTCTATGTAC 0.971393 -53 * ** * * **** * Masking position 12 Map Score: 7.2757 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 3 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 AGTGGAACGAGGAAGTGCACGGTACACTGA 2 66 0 GGAAGTGCAC 0.829981 -176 GCCCGGGAAAAGCAGTACTCTGATGATATT 2 109 0 AGCAGTACTC 0.830236 -133 AACAAAAGTTGGCAGTGAACAATTCATTCC 2 161 1 GGCAGTGAAC 0.952722 -81 TAACTAATGGGGCCGTTGTCACCAAGCTTC 3 24 1 GGCCGTTGTC 0.930728 -277 GCAAATGGGTTGCGGTGGTCATAGTCAAAG 3 81 1 TGCGGTGGTC 0.956391 -220 ATATGGGGCAGGCGGTAGTCCCCAGGGATC 3 249 0 GGCGGTAGTC 0.987584 -52 CCGTCGGCGGTGCAGAGGTCTTTTACGGAT 5 61 0 TGCAGAGGTC 0.739782 -240 CTGGATTATGGGCAATAATCACAGTCGAGC 5 93 1 GGCAATAATC 0.71426 -208 GACTACCCCTGGAGGTAAACTCCGGGGCTG 5 125 1 GGAGGTAAAC 0.656145 -176 TCTTATCCAAGGCTGTGCTCCTTTGCCCGG 6 82 0 GGCTGTGCTC 0.951516 -74 AGGACCATTCGGCCGTAGTGGGAAAAAGTT 6 124 0 GGCCGTAGTG 0.86446 -32 ********** Masking position 2 Map Score: 4.9525 Number of sites scoring better than the average of aligned sites = 1896 Number in coding regions = 1779 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 6 AAACTTGCCGCGACAGTTCTATTAGGAAGCTTG 3 46 0 CGAAGTCTAT 0.886582 -255 ACAATCAAGGCGATTGGAGCATT 5 1 0 CGATGAGCAT 0.97198 -300 TTGATTGTATCGAATGATGCAGTCTCTAAAATT 5 26 1 CGATGTGCAT 0.992938 -275 TCTAGAACGTCGATTGTTACATTTCTTAATGAA 5 174 0 CGATGTACAT 0.980971 -127 TCGCCCCTGTCGTCTGTTCCACTAATGTCAAAT 6 18 0 CGTTGTCCAT 0.980593 -138 CCACTACGGCCGAATGGTCCTATTCCAGCTACC 6 133 1 CGATGTCCTT 0.980593 -23 *** ** **** * Masking position 13 Map Score: 1.92776 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 57 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 TTAACCTTTTAACCTCGGGGGAAC 1 106 0 TACTTTTACC 0.829459 -14 GGATTCATTCCCCTCTTTTTCAGTGTACCGTGC 2 47 1 CCCTTTTCAG 0.811855 -195 TACCGTGCACTTCCTCGTTCCACTAGATTGGAG 2 72 1 TCTCGTTCAC 0.750652 -170 ATCATCAGAGTACTGCTTTTCCCGGGCCGGCAA 2 112 1 TCGCTTTCCC 0.900738 -130 TGAGAAAAATTTCACTTTTCCAGGGAGTTGATT 2 208 1 TCCTTTTCAG 0.958182 -34 CCAACGGTGTTTAGCTTTTGCCCTAATTTGACT 3 113 0 TACTTTTCCC 0.969297 -188 GGGGAAAGTCTCCTCTGTTCACCCTGCCGGACA 5 224 0 TCCTGTTACC 0.941591 -77 GAGGAGACTTTCCCCTGTTACAGTGTCAGTGAC 5 242 1 TCCTGTTCAG 0.955414 -59 TTCGCCCCTGTCGTCTGTTCCACTAATGTCAAA 6 19 0 TGCTGTTCAC 0.901044 -137 TCCAAGGCTGTGCTCCTTTGCCCGGCCGCCGCC 6 74 0 TCCCTTTCCC 0.985931 -82 CTCCAAGGACTTAACTTTTTCCCACTACGGCCG 6 112 1 TACTTTTCCC 0.969297 -44 * * ***** *** Masking position 8 Map Score: 7.2928 Number of sites scoring better than the average of aligned sites = 1471 Number in coding regions = 1294 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 8 TGAAAAAGAGGGGAATGAATCCTCTTCTGCA 2 38 0 GGGAAGAATC 0.987554 -204 CATCTTAGGAGGGAATGAATTGTTCACTGCC 2 171 0 GGGAAGAATT 0.974658 -71 AGTGTAGCGAGGAAAAGACTTGCATTAACTG 3 200 1 GGAAAGACTT 0.926845 -101 CCAAAAATCCGGGTCCGAATC 4 1 0 GGGTCGAATC 0.974242 -46 CACCGCCGACGGGTCTGGATTATGGGCAATA 5 79 1 GGGTCGGATT 0.879038 -222 ACTGTAACAGGGGAAAGTCTCCTCTGTTCAC 5 235 0 GGGAAGTCTC 0.959004 -66 GCACAGCCTTGGATAAGACTCCAAGGACTTA 6 94 1 GGATAGACTC 0.952515 -62 ***** ***** Masking position 10 Map Score: 4.17554 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 214 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 TTTGTGCCGTCGTTCCCCCGAGGTTAAAAGG 1 95 1 CGTTCCCCGA 0.971923 -25 GAAGAGGATTCATTCCCCTCTTTTTCAGTGT 2 42 1 CATTCCCTCT 0.982961 -200 GTGAACAATTCATTCCCTCCTAAGATGCCAT 2 175 1 CATTCCCCCT 0.989096 -67 TACATGGGAACGTTCCTCCCTAGTGTAGCGA 3 179 1 CGTTCCTCCT 0.969343 -122 CCGTTCCCATATCCAGGTTTAT 4 35 0 CGTTCCCTAT 0.97034 -12 ACAGAGGAGACTTTCCCCTGTTACAGTGTCA 5 239 1 CTTTCCCTGT 0.957374 -62 ******* *** Masking position 4 Map Score: 4.16068 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 137 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 ********** No masking Map Score: 3.35619e-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 11 ********** No masking Map Score: 3.35619e-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 12 ********** No masking Map Score: 3.35619e-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