AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i034_Pyruvate_Synthase_2_synecho_reg_100.orf -o034_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 RCY45080 251 Synechocystis #2 RCY09549 300 Synechocystis Motif number 1 ATGGTAGCACCAAAGCTAGGAAGGACCCATGGA 1 32 1 CAACTGGAAG 0.859287 -220 AATGTTAGGCTAAGGGAAGGAAATTAACCCTGT 1 78 1 TAAGAGGAAA 0.972036 -174 ATTTTAACTTTAATAGTGGGCGAGAGATACCAT 1 171 0 TAAGTGGCGA 0.924971 -81 CGTCCGTGGTTAATCCACAGAAAACCCTATTTT 1 199 0 TAACAAGAAA 0.93839 -53 TCTCTCTATGTAATCGACGGGAAAATCGTCCGT 1 225 0 TAAGAGGGAA 0.966297 -27 AAGATAAAACTAAGACCCAGAGAGAACGCCATG 2 12 1 TAACCAGAGA 0.960638 -289 GATTCTTAATTAAGGCCGGGGAAAGAGATAGCC 2 103 0 TAACCGGGAA 0.988698 -198 AAAATAACACTAATGCCAAGAAAAATTAAACAA 2 155 0 TAACCAGAAA 0.974979 -146 AGCGCTCCATTAACCCCCGGCAGTATCCCCAAC 2 200 1 TAACCGGCAG 0.958418 -101 TCAAGTTTGTTAACAGTTGGGGATACTGCCGGG 2 215 0 TAAGTGGGGA 0.94725 -86 GCAATGGCAACAAAAGCCAGAAATATGAAACAA 2 253 0 CAAGCAGAAA 0.92614 -48 *** ** ***** Masking position 3 Map Score: 10.7432 Number of sites scoring better than the average of aligned sites = 1109 Number in coding regions = 950 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 2 AGGAGGAGGAGGCGATAAATGGTAGCACCA 1 14 1 GGCGATAAAT 0.933705 -238 GGCCCTTGTCAGCGGTAAAACAGGGTTAAT 1 100 0 AGCGGTAAAA 0.907458 -152 TCGCCGCTTGACCGGGGGAATGGTATCTCT 1 152 1 ACCGGGGGAA 0.926128 -100 TTTAATAGTGGGCGAGAGATACCATTCCCC 1 166 0 GGCGAGAGAT 0.972686 -86 CTATGTAATCGACGGGAAAATCGTCCGTGG 1 223 0 GACGGGAAAA 0.943403 -29 AAAAAACTTAGTCGAGAAATGGGGCTGCGA 2 72 0 GTCGAGAAAT 0.897918 -229 CTTAATTAAGGCCGGGGAAAGAGATAGCCC 2 102 0 GCCGGGGAAA 0.981976 -199 TAACACTAATGCCAAGAAAAATTAAACAAC 2 154 0 GCCAAGAAAA 0.826559 -147 GGGTTAATGGAGCGCTAAAAAATTGTTGAA 2 186 0 AGCGCTAAAA 0.692152 -115 TGGGGATACTGCCGGGGGTTAATGGAGCGC 2 201 0 GCCGGGGGTT 0.784882 -100 TGGCAACAAAAGCCAGAAATATGAAACAAA 2 252 0 AGCCAGAAAT 0.730092 -49 ********** Masking position 3 Map Score: 7.06171 Number of sites scoring better than the average of aligned sites = 3823 Number in coding regions = 3478 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 357 Fraction of orfs with sites within 600 bp upstream = 0.0573402 Motif number 3 CAAGATAAAACTAAGACCCAGAG 2 2 1 AAATAAACTA 0.981358 -299 GGCCTTAATTAAGAATCAACAAAAACAATCTT 2 119 1 AAAACAACAA 0.911913 -182 AATGCCAAGAAAAATTAAACAACGTCAAGATT 2 145 0 AAATAAACAA 0.986946 -156 AAAATTGTTGAAAATAACACTAATGCCAAGAA 2 166 0 AAATACACTA 0.95963 -135 AAAAGCCAGAAATATGAAACAAAGCAGTCAAG 2 243 0 AAATAAACAA 0.986946 -58 ** ** ****** Masking position 4 Map Score: 2.47088 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 30 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 GGCGATAAATGGTAGCACCAAAGCTAGGAAGG 1 24 1 GGAGCACCAA 0.944277 -228 CCTTAGCCTAACATTGACCATAATCAGCTCCA 1 61 0 ACTTGACCAA 0.934292 -191 TTTACCGCTGACAAGGGCCAAAGTATAAACAG 1 111 1 ACAGGGCCAA 0.986865 -141 CGGTCAAGCGGCGATCGCCAAATCTGTTTATA 1 134 0 GCATCGCCAA 0.992917 -118 CAGAGAGAACGCCATGACCAAACACCAATCGT 2 29 1 GCATGACCAA 0.994171 -272 AAAGGTTTCTGCAATGGCAACAAAAGCCAGAA 2 264 0 GCATGGCAAA 0.976466 -37 ** ******* * Masking position 10 Map Score: 3.48658 Number of sites scoring better than the average of aligned sites = 1516 Number in coding regions = 1372 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 5 TGGTGCTACCATTTATCGCCTCCTCCTCCTCCA 1 9 0 ATATCTCCTC 0.945549 -243 GTAAAACAGGGTTAATTTCCTTCCCTTAGCCTAAC 1 81 0 GTATCTTCCC 0.99288 -171 ATAGTGGGCGAGAGATACCATTCCCCCGGTCAAGC 1 157 0 AGATCTTCCC 0.985406 -95 ATTGGTGTTTGGTCATGGCGTTCTCTCTGGGTCTT 2 23 0 GGATCTTCTC 0.990932 -278 AAGTTTTTTGGGCTATCTCTTTCCCCGGCCTTAAT 2 93 1 GGATCTTCCC 0.995274 -208 ** ** * ***** Masking position 6 Map Score: 3.29787 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 114 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 6 GAAGGAAATTAACCCTGTTTTACCGCTGAC 1 93 1 AACCCTGTTT 0.982724 -159 GGCGATCGCCAAATCTGTTTATACTTTGGC 1 127 0 AAATCTGTTT 0.822667 -125 ATCCACAGAAAACCCTATTTTAACTTTAAT 1 190 0 AACCCTATTT 0.985291 -62 ACTAATTCGCAGCCCCATTTCTCGACTAAG 2 66 1 AGCCCCATTT 0.964747 -235 ********** Masking position 8 Map Score: 0.738217 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 138 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 TTAGTCGTCAACGATTGGTGTTTGGTCATG 2 41 0 ACGATTGGTG 0.954754 -260 TTTCTCGACTAAGTTTTTTGGGCTATCTCT 2 83 1 AAGTTTTTTG 0.932908 -218 AAACAACGTCAAGATTGTTTTTGTTGATTC 2 131 0 AAGATTGTTT 0.963175 -170 GGAGCGCTAAAAAATTGTTGAAAATAACAC 2 178 0 AAAATTGTTG 0.952194 -123 CAAAGCAGTCAAGTTTGTTAACAGTTGGGG 2 226 0 AAGTTTGTTA 0.948091 -75 ********** Masking position 5 Map Score: 0.257552 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 316 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 8 ********** No masking Map Score: 1.5372e-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 9 ********** No masking Map Score: 1.5372e-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 10 ********** No masking Map Score: 1.5372e-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