AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i001_Purine_Biosynthesis_synecho_reg_100.orf -o001_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 RCY47787 137 Synechocystis #2 RCY28877 111 Synechocystis #3 RCY49648 201 Synechocystis #4 RCY50816 270 Synechocystis #5 RCY04887 215 Synechocystis #6 RCY09060 300 Synechocystis #7 RCY24689 228 Synechocystis #8 RCY13788 142 Synechocystis #9 RCY02057 58 Synechocystis Motif number 1 TGAAATCTGAGCCCCAACCCGGAATACCTTT 1 34 0 GCCCCACCCG 0.988198 -104 GGGGCTCAGATTTCAAACCCGGTGGACACTA 1 50 1 TTTCAACCCG 0.774586 -88 AGGGATTAATGCCCATCTCCGCTAAAATCA 2 92 1 GCCCACTCCG 0.968304 -20 GAGTTATTTATCTCCGCCCCCCCACTTTCC 3 10 0 TCTCCCCCCC 0.982695 -192 AATAGCAATGGCTCACCTCCGGCGATCGAAC 3 179 0 GCTCACTCCG 0.868772 -23 ATCTATACATTCCCCTGTCCCCTGACAACTA 4 49 1 TCCCCGTCCC 0.988193 -222 AAGAAGCAGTGCCCACACCGCAGTGTTTGGT 4 97 0 GCCCAACCGC 0.799396 -174 CGTCATTGCCTTCCCTGTCTGGCGGGAATCC 4 178 1 TTCCCGTCTG 0.802025 -93 TTGCTCCGGGGCCCAAGCCCCTAATTTTTAA 5 93 1 GCCCAGCCCC 0.989654 -123 TGAGTTTTATTTCCCCCCCCGTTGCTTTAGG 5 158 1 TTCCCCCCCG 0.987049 -58 TAGGGAATATTCCCCAACCCCGCTGTTTATC 5 185 1 TCCCCACCCC 0.991137 -31 TAACCCAGAATTCCCGGCCTCAAACCTCTCC 6 212 1 TTCCCGCCTC 0.926924 -89 GAGTTAACAATCTCCTGCCCGAATTTTACAA 6 251 0 TCTCCGCCCG 0.982695 -50 CTATGATGGATCCCATCGCCCAGACTGCTTC 8 29 0 TCCCACGCCC 0.937185 -114 TTATTTATCTTCCCCCGTCTGAAAATCTGAA 8 120 1 TCCCCGTCTG 0.933017 -23 TTGGTAATTTTTCCATCCCCCATTATCCCCC 9 26 0 TTCCACCCCC 0.973793 -33 ***** ***** Masking position 4 Map Score: 26.0974 Number of sites scoring better than the average of aligned sites = 3814 Number in coding regions = 3513 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 282 Fraction of orfs with sites within 600 bp upstream = 0.0452939 Motif number 2 GGGTTTGATGACCCCATTGGCCTAGGGAGAAA 2 25 0 ACCCCATGCC 0.973156 -87 GGGTCATCAAACCCCACATCACCATGGTAATC 2 43 1 ACCCCAATAC 0.791795 -69 TATCTCCGCCCCCCCACTTTCC 3 1 0 CCCCCATTCC 0.993925 -201 TGGCGGGAATCCACCAATTCCCATAGTCTAAG 4 197 1 CCACCATTCC 0.981403 -74 TTTTATTTCCCCCCCCGTTGCTTTAGGGAATA 5 162 1 CCCCCCTTCT 0.796026 -54 CTGCCACTAACCCACAAAACACTTTCAAGCAG 6 74 1 CCCACAAAAC 0.746802 -227 GCCATAGGGGCCAACAATGGCCACGTTGCGGA 6 121 1 CCAACATGCC 0.954226 -180 ATGAACAACCCCACCAATGAATCCCTCCGCAA 6 146 0 CCACCATGAT 0.790421 -155 CTGAGCCTAACCCAGAATTCCCGGCCTCAAAC 6 205 1 CCCAGATTCC 0.811678 -96 CTTCTAAGCGCCCCCATAGAAC 8 1 0 CCCCCAAGAC 0.977603 -142 GCGATGGGATCCATCATAGTCCCTTGGCTCAG 8 41 1 CCATCAAGCC 0.810573 -102 ATTTTTCCATCCCCCATTATCCCCCAGGAGTT 9 19 0 CCCCCATACC 0.986145 -40 ****** ** ** Masking position 2 Map Score: 10.5354 Number of sites scoring better than the average of aligned sites = 2771 Number in coding regions = 2519 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 268 Fraction of orfs with sites within 600 bp upstream = 0.0430453 Motif number 3 TTGTTTTTAGGCAATGTCAGATAAAATGAG 1 112 1 GCAATGTCAG 0.966756 -26 AATTTTTCCAGCAGTTGTAGAGGTTACAGT 3 90 1 GCAGTTGTAG 0.913106 -112 ACAGTCCATGAAAGTGGCAGTTATTGGTAG 3 115 1 AAAGTGGCAG 0.723387 -87 GCAATAGCAATGGCTCACCT 3 192 0 GCAATAGCAA 0.794271 -10 TGCCCACACCGCAGTGTTTGGTTCTTGGCC 4 89 0 GCAGTGTTTG 0.713566 -182 ACCTATGTCGGCTATGTCAGATTTGTCGAA 5 123 1 GCTATGTCAG 0.803609 -93 AACACAGTGAGCGATAGCAGCCCTGAGGCC 6 13 0 GCGATAGCAG 0.76473 -288 TGGGTTAGTGGCAGTGTCAGCCGTAAGGGG 6 58 0 GCAGTGTCAG 0.987524 -243 GGCCCCTATGGCAGTGGTAAAACCACCCTG 6 103 0 GCAGTGGTAA 0.929671 -198 GGCAGGATTAACAGTGGCAGATTCCCCGGT 7 199 1 ACAGTGGCAG 0.970752 -30 CCTTGGCTCAGCAGTTGCAATAGTGGAGTC 8 62 1 GCAGTTGCAA 0.913106 -81 ********** Masking position 5 Map Score: 8.41808 Number of sites scoring better than the average of aligned sites = 1702 Number in coding regions = 1591 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 4 TCAAGGTAGAATGTGCCTAGTGTCCACCGG 1 68 0 ATGTGCCTAG 0.899385 -70 GTCAGATAAAATGAGCCTGGA 1 127 1 ATGAGCCTGG 0.953574 -11 TGATGACCCCATTGGCCTAGGGAGAAAGAG 2 22 0 ATTGGCCTAG 0.849796 -90 ACTAGACCGACTTGGCCAAGAACCAAACAC 4 76 1 CTTGGCCAAG 0.499226 -195 TTTCTCTACCCTGATCCAGGAAGATTGCCG 4 249 1 CTGATCCAGG 0.854375 -22 GCTCTTATTGCTGAGCCTAACCCAGAATTC 6 195 1 CTGAGCCTAA 0.954875 -106 TTCCAAGGCACTTAGCCAAATTATGCTGAA 7 60 0 CTTAGCCAAA 0.874717 -169 ATTGCAACTGCTGAGCCAAGGGACTATGAT 8 53 0 CTGAGCCAAG 0.952093 -90 ********** Masking position 2 Map Score: 5.32718 Number of sites scoring better than the average of aligned sites = 700 Number in coding regions = 636 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 GATTAACAGAATGGCCGGAGTTGACTGGAGT 3 37 0 AGGCCGGAGT 0.992785 -165 CGTTAGTTCGATCGCCGGAGGTGAGCCATTG 3 174 1 ACGCCGGAGG 0.962999 -28 TAGCCCGTTGAGGGCAGGATTGCTCCGGGGC 5 74 1 AGGCAGGATT 0.982106 -142 GTTGGCCCCTATGGCAGTGGTAAAACCACCC 6 105 0 AGGCAGTGGT 0.806386 -196 TTGTAAAATTCGGGCAGGAGATTGTTAACTC 6 251 1 CGGCAGGAGA 0.942885 -50 ACTGCTAAAGAGCGCCGGATTATTTTGTGCA 7 107 0 ACGCCGGATT 0.970636 -122 AAGACTTTCTAAGGCAGGATTAACAGTGGCA 7 187 1 AGGCAGGATT 0.982087 -42 CCCCCATTATCCCCCAGGAGTTGGTCTCCC 9 10 0 CCCCAGGAGT 0.886398 -49 * ********* Masking position 5 Map Score: 4.98735 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 357 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 6 AGGAGGAAAGGAAAGATTACCATGGTGATGT 2 58 0 GAAAGATTCC 0.981352 -54 TATGGGAATTGGTGGATTCCCGCCAGACAGG 4 191 0 GGTGGATTCC 0.947065 -80 CCCTGATCCAGGAAGATTGCCGCC 4 257 1 GGAAGATTCC 0.962477 -14 GCGGGGTTGGGGAATATTCCCTAAAGCAACG 5 177 0 GGAATATTCC 0.963596 -39 GATTAACAGTGGCAGATTCCCCGGTAAGGCC 7 204 1 GGCAGATTCC 0.981213 -25 ATGGGGGATGGAAAAATTACCAAGAGGAGAA 9 34 1 GAAAAATTCC 0.900265 -25 ******** ** Masking position 6 Map Score: 5.0024 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 75 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 GCCGTTCTCAAGATTAACAGAATGGCCGGA 3 49 0 AGATTAACAG 0.848449 -153 TTGCTAGTATGGGTTAACGATTAACAATTG 4 127 1 GGGTTAACGA 0.944227 -144 TAGCCGACATAGGTTAAAAATTAGGGGCTT 5 107 0 AGGTTAAAAA 0.851006 -109 TATCCCAAGGGATAAACAGCGGGGTTGGG 5 197 0 GGATAAACAG 0.899607 -19 AACTTAACCAGAGTTAACAATCTCCTGCCC 6 262 0 GAGTTAACAA 0.87695 -39 AAGTTTCAGTGGGTAAAAAACGAC 6 287 1 GGGTAAAAAA 0.901401 -14 ACTTTGAGTTGGGTTAAAAACTGACAACTA 7 13 0 GGGTTAAAAA 0.961493 -216 TTCTAAGGCAGGATTAACAGTGGCAGATTC 7 193 1 GGATTAACAG 0.960745 -36 ********** Masking position 6 Map Score: 3.73949 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 524 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 8 CTAACCGGATTGTTTTTAGGCAATGTCAGATA 1 103 1 TGTTTTGGCA 0.882958 -35 GGCTCCTCTTTCTCCCTAGGCCAATGGGGTCA 2 17 1 TCCCCTGGCC 0.930391 -95 CCGCAGTGTTTGGTTCTTGGCCAAGTCGGTCT 4 79 0 TGTTCTGGCC 0.984803 -192 GTGTGGGCACTGCTTCTTTGCTAGTATGGGTT 4 110 1 TGTTCTTGCT 0.688767 -161 AGGGCAGGATTGCTCCGGGGCCCAAGCCCCTA 5 84 1 TGTCCGGGCC 0.972647 -132 GAGCGATAGCAGCCCTGAGGCCAA 6 3 0 AGCCTGGGCC 0.902866 -298 GATTGCGGAGAGGTTTGAGGCCGGGAATTCTG 6 217 0 AGTTTGGGCC 0.953398 -84 TTCGAGATCTAGATTTGGGGCTAGTCTTGCCG 7 152 1 AGTTTGGGCT 0.888663 -77 CCTTAGAAAGTCTTTCTCGGCAAGACTAGCCC 7 169 0 TCTTCTGGCA 0.825396 -60 GATCCATCATAGTCCCTTGGCTCAGCAGTTGC 8 48 1 AGCCCTGGCT 0.929951 -95 ** **** **** Masking position 11 Map Score: 3.73543 Number of sites scoring better than the average of aligned sites = 1018 Number in coding regions = 913 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 9 TGGCCTAGGGAGAAAGAGGAGCCAATCAG 2 9 0 AGAAGAGGAG 0.938328 -103 TGATTTTAGCGGAGATGGGCATTA 2 98 0 TTTAGCGGAG 0.83592 -14 TGGCAGTTATTGGTAGCGGTGGACGGGAACA 3 129 1 TGTAGCGGTG 0.906828 -73 CAAGAACCAAACACTGCGGTGTGGGCACTGC 4 92 1 ACCTGCGGTG 0.901169 -179 CGATGGCGATAGAATGGGGAGCGATGTCTTT 5 32 0 AGATGGGGAG 0.927474 -184 AACAATGGCCACGTTGCGGAGGGATTCATTG 6 133 1 ACTTGCGGAG 0.982235 -168 ATTTTACAAGAGATTGCGGAGAGGTTTGAGG 6 229 0 AGTTGCGGAG 0.986417 -72 TGGAAAAATTACCAAGAGGAGAAGGCA 9 42 1 ACAAGAGGAG 0.920531 -17 ** ******** Masking position 6 Map Score: 2.06982 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 270 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 TGATTTTAGCGGAGATGGGCATTAATCCCT 2 92 0 AGCGATGGGC 0.951341 -20 CTAACGACCAAGCCAAAGTATGTTCCCGTCCAC 3 147 0 AGCCATATGT 0.984329 -55 AATCTGACATAGCCGACATAGGTTAAAAATTAG 5 113 0 AGCCATAGGT 0.985464 -103 CAAGGCACTTAGCCAAATTATGCTGAAAATAAG 7 54 0 AGCCATATGC 0.992982 -175 GAATCAATAAAGCCTAGTTATGCACAAAATAAT 7 87 1 AGCCATATGC 0.992985 -142 **** * ***** Masking position 6 Map Score: 0.795144 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 41 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 AGTTTTAAAAAAGGTATTCCGGGTTGGGGCTCAG 1 25 1 AGTTCCGGGT 0.963782 -113 GAATGTGCCTAGTGTCCACCGGGTTTGAAATCTG 1 56 0 AGTACCGGGT 0.988707 -82 ACGATTAACAATTGATTAAGGGGTCTAGACCCGT 4 143 1 AGAAAGGGGT 0.959708 -128 CAGGGAAGGCAATGACGAACGGGTCTAGACCCCT 4 161 0 AGAAACGGGT 0.990466 -110 GGATCAGGGTAGAGAAAAACGGGTACAGAAACTA 4 232 0 AGAAACGGGT 0.990466 -39 CTTTACTGCTAAAGAGCGCCGGATTATTTTGTGC 7 108 0 AGAGCCGGAT 0.919251 -121 * ** ******* Masking position 1 Map Score: 1.09263 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 63 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 TCCGGGTTGGGGCTCAGATTTCAAACCCGG 1 42 1 GGCTCAGATT 0.987111 -96 TCCAGGCTCATTTTATCTGACATT 1 124 0 GGCTCATTTT 0.952094 -14 AATTCCCATAGTCTAAGATTTAGTTTCTGT 4 212 1 GTCTAAGATT 0.827878 -59 GCCCTCAACGGGCTAACTTTGACATCCGAT 5 59 0 GGCTAACTTT 0.889965 -157 ATACCTGAAAGGCTCTTATTGCTGAGCCTA 6 184 1 GGCTCTTATT 0.843078 -117 TGTTAACTCTGGTTAAGTTTCAGTGGGTAA 6 273 1 GGTTAAGTTT 0.885957 -28 GGTTCAGATTTTCAGACGGG 8 133 0 GGTTCAGATT 0.954322 -10 ********** Masking position 4 Map Score: 2.96286 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 301 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 13 ********** No masking Map Score: -2.57684e-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 14 ********** No masking Map Score: -2.57684e-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 15 ********** No masking Map Score: -2.57684e-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