AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i034_Pyruvate_Synthase_2_synecho_reg_300.orf -o034_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 RCY45080 251 Synechocystis #2 RCY09549 300 Synechocystis Motif number 1 ATGGTAGCACCAAAGCTAGGAAGGACCCATGGA 1 32 1 CAACTGGAAG 0.846304 -220 AATGTTAGGCTAAGGGAAGGAAATTAACCCTGT 1 78 1 TAAGAGGAAA 0.969081 -174 ATTTTAACTTTAATAGTGGGCGAGAGATACCAT 1 171 0 TAAGTGGCGA 0.917466 -81 CGTCCGTGGTTAATCCACAGAAAACCCTATTTT 1 199 0 TAACAAGAAA 0.932129 -53 TCTCTCTATGTAATCGACGGGAAAATCGTCCGT 1 225 0 TAAGAGGGAA 0.962759 -27 AAGATAAAACTAAGACCCAGAGAGAACGCCATG 2 12 1 TAACCAGAGA 0.956533 -289 GATTCTTAATTAAGGCCGGGGAAAGAGATAGCC 2 103 0 TAACCGGGAA 0.987481 -198 AAAATAACACTAATGCCAAGAAAAATTAAACAA 2 155 0 TAACCAGAAA 0.972326 -146 AGCGCTCCATTAACCCCCGGCAGTATCCCCAAC 2 200 1 TAACCGGCAG 0.954093 -101 TCAAGTTTGTTAACAGTTGGGGATACTGCCGGG 2 215 0 TAAGTGGGGA 0.941834 -86 GCAATGGCAACAAAAGCCAGAAATATGAAACAA 2 253 0 CAAGCAGAAA 0.918742 -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 TGGTGCTACCATTTATCGCCTCCTCCTCCT 1 14 0 ATTTATCGCC 0.93365 -238 ATTAACCCTGTTTTACCGCTGACAAGGGCC 1 100 1 TTTTACCGCT 0.893446 -152 AGAGATACCATTCCCCCGGTCAAGCGGCGA 1 152 0 TTCCCCCGGT 0.91364 -100 GGGGAATGGTATCTCTCGCCCACTATTAAA 1 166 1 ATCTCTCGCC 0.969473 -86 CCACGGACGATTTTCCCGTCGATTACATAG 1 223 1 TTTTCCCGTC 0.941981 -29 TCGCAGCCCCATTTCTCGACTAAGTTTTTT 2 72 1 ATTTCTCGAC 0.897837 -229 CTCGACTAAGTTTTTTGGGCTATCTCTTTC 2 86 1 TTTTTTGGGC 0.646269 -215 GGGCTATCTCTTTCCCCGGCCTTAATTAAG 2 102 1 TTTCCCCGGC 0.983242 -199 GTTGTTTAATTTTTCTTGGCATTAGTGTTA 2 154 1 TTTTCTTGGC 0.872327 -147 TTCAACAATTTTTTAGCGCTCCATTAACCC 2 186 1 TTTTAGCGCT 0.657834 -115 GCGCTCCATTAACCCCCGGCAGTATCCCCA 2 201 1 AACCCCCGGC 0.734021 -100 TTTGTTTCATATTTCTGGCTTTTGTTGCCA 2 252 1 ATTTCTGGCT 0.813655 -49 ********** Masking position 8 Map Score: 6.84918 Number of sites scoring better than the average of aligned sites = 4308 Number in coding regions = 3886 Number in noncoding regions = 422 Number of orfs with sites within 600 bp upstream = 421 Fraction of orfs with sites within 600 bp upstream = 0.0676197 Motif number 3 CTCTGGGTCTTAGTTTTATCTTG 2 2 0 TAGTTTATTT 0.983013 -299 AAGATTGTTTTTGTTGATTCTTAATTAAGGCC 2 119 0 TTGTTGTTTT 0.919261 -182 AATCTTGACGTTGTTTAATTTTTCTTGGCATT 2 145 1 TTGTTTATTT 0.988116 -156 TTCTTGGCATTAGTGTTATTTTCAACAATTTT 2 166 1 TAGTGTATTT 0.963158 -135 CTTGACTGCTTTGTTTCATATTTCTGGCTTTT 2 243 1 TTGTTTATTT 0.988117 -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 0.945437 -228 CCTTAGCCTAACATTGACCATAATCAGCTCCA 1 61 0 ACTTGACCAA 0.935645 -191 TTTACCGCTGACAAGGGCCAAAGTATAAACAG 1 111 1 ACAGGGCCAA 0.98715 -141 CGGTCAAGCGGCGATCGCCAAATCTGTTTATA 1 134 0 GCATCGCCAA 0.993072 -118 CAGAGAGAACGCCATGACCAAACACCAATCGT 2 29 1 GCATGACCAA 0.994299 -272 AAAGGTTTCTGCAATGGCAACAAAAGCCAGAA 2 264 0 GCATGGCAAA 0.976972 -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 GAAGGAAATTAACCCTGTTTTACCGCTGAC 1 93 1 AACCCTGTTT 0.982064 -159 GGCGATCGCCAAATCTGTTTATACTTTGGC 1 127 0 AAATCTGTTT 0.828134 -125 ATCCACAGAAAACCCTATTTTAACTTTAAT 1 190 0 AACCCTATTT 0.987113 -62 ACTAATTCGCAGCCCCATTTCTCGACTAAG 2 66 1 AGCCCCATTT 0.971391 -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 6 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 7 TGGAGGAGGAGGAGGCGATAAATGGTAGCACC 1 9 1 GAGGAGCATA 0.962369 -243 GTTAGGCTAAGGGAAGGAAATTAACCCTGTTTTA 1 81 1 GGGAAGAATA 0.98805 -171 GCTTGACCGGGGGAATGGTATCTCTCGCCCACTA 1 157 1 GGGAAGGATC 0.978287 -95 AAGACCCAGAGAGAACGCCATGACCAAACACCAA 2 23 1 GAGAAGCATC 0.990127 -278 ATTAAGGCCGGGGAAAGAGATAGCCCAAAAAACT 2 94 0 GGGAAGAATC 0.994584 -207 ***** ** ** * Masking position 5 Map Score: 1.78934 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 125 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 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