AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i209_rpod_synecho_reg_300.orf -o209_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 RCY17385 152 Synechocystis #2 RCY16671 240 Synechocystis #3 RCY22330 51 Synechocystis #4 RCY11539 185 Synechocystis #5 RCY38294 42 Synechocystis #6 RCY35677 300 Synechocystis Motif number 1 TGGCTTTCCATCTCCCCACCACCACAGACTG 2 9 1 CCTCCCACCA 0.98484 -232 ATGGCGATCGGCAACCCCTAGCAACCACCGGCT 2 71 1 GACCCCAGCA 0.955827 -170 TATACATAACCGGCTCCCAAGCAAAGAAATCTC 2 162 1 CCTCCCAGCA 0.99213 -79 TATATGCCATGGTCCCCAAACCTGAGTCAGAGC 4 96 1 GCCCCAACCT 0.985643 -90 GCCGGATTATCCTCGCCCCCGCTTAAATTTCCC 5 14 1 CCGCCCCGCT 0.957585 -29 GGAGGGACTCGAACCCCCGACCTCGTGGTCCGT 6 36 0 GCCCCCACCT 0.995907 -265 GGGGGTTCGAGTCCCTCCAAGCCCGTTTTTTGC 6 51 1 GCCTCCAGCC 0.926967 -250 TCATCGGGCTGGGCTCCCTAGCTGGGCCCAGTT 6 100 1 GCTCCCAGCT 0.995856 -201 CTAAAGTCTACAACTCCATAGCTATAAAAAAAC 6 130 0 CCTCCAAGCT 0.985466 -171 GTGGAAACTCCTGCCCCATATCTGTGGCCTAGC 6 277 0 CCCCCAATCT 0.945295 -24 * ***** **** Masking position 7 Map Score: 13.1804 Number of sites scoring better than the average of aligned sites = 734 Number in coding regions = 672 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 2 AAATCTGTCTAGCCGGTGGTTGCTAGGGGTT 2 83 0 AGCCGGTGTT 0.965302 -158 ACCACCGGCTAGACAGATTTTTTTCAGCAAG 2 94 1 AGACAGATTT 0.885377 -147 TTTGCTTGGGAGCCGGTTATGTATATGAGTA 2 156 0 AGCCGGTTTG 0.982869 -85 TATTATTACCAGCGGAATATGT 3 2 0 AGCGGAATTG 0.822751 -50 AACAGGTCAAAGACAAATGTTGAGCGGAACA 4 149 0 AGACAAATTT 0.767245 -37 CTAGCCGGATTATCCTCGCCCCC 5 3 1 AGCCGGATAT 0.981918 -40 AGTCCCTCCAAGCCCGTTTTTTGCATCACGC 6 60 1 AGCCCGTTTT 0.979257 -241 TTTTGCATCACGCCGATTATTATCATCGGGC 6 78 1 CGCCGATTTT 0.922334 -223 TAGGGAGCCCAGCCCGATGATAATAATCGGC 6 89 0 AGCCCGATAT 0.950526 -212 CTCTGTAGATAGCCGAATCTTTGGTTTGGTC 6 201 0 AGCCGAATTT 0.988147 -100 ******** ** Masking position 2 Map Score: 8.18069 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 496 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 3 CCCCGGTGAAGGAGAGTGCAATTTGCAGATTATTC 1 32 0 GAGAGGATTG 0.991456 -121 CTCCTTCACCGGGGGGTGCTTTTTGCTGGTTGACC 1 53 1 GGGGGGTTTG 0.984711 -100 CCATGCTTGAGTAGAGCTTAAGTTGACAAGTATCT 1 86 1 GAGAGTATTG 0.978429 -67 GAGTGACGATGGGGAGAGATACTTGTCAACTTAAG 1 102 0 GGGAGGTTTG 0.991285 -51 TCACTCTTAGAAGGAGAGTAGGTTGATTTATC 1 131 1 AGGAGGATTG 0.97464 -22 CCGATCGCCATTAGAGGGGTGATTGATTCCGTTGG 2 47 0 TAGAGGTTTG 0.975131 -194 GGCCTCAAGCTCAGAGATTTCTTTGCTTGGGAGCC 2 173 0 TAGAGTTTTG 0.938751 -68 TTGGTATTAGAAAGGGTTTATTTTGCTTCTTTCCA 4 42 1 AAGGGTATTG 0.896684 -144 * **** * * *** Masking position 13 Map Score: 7.77512 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 175 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 AATCTGCAAATTGCACTCTCCTTCACCGGGG 1 36 1 TTCACTCTCC 0.966682 -117 ACTTGTCAACTTAAGCTCTACTCAAGCATGG 1 86 0 TTAGCTCTAC 0.972219 -67 ATAGCCGTTGTTCCGCTCAACATTTGTCTTT 4 141 1 TTCGCTCAAC 0.966682 -45 CCTTCAGCTTACCAAAAACAGGT 4 173 0 TTAGCTTACC 0.97222 -13 AGTTGTAGACTTTAGCTTTCCGGCCTGAGCA 6 148 1 TTAGCTTTCC 0.972219 -153 CACGAGTGCGTCAAACTCACCTTGATGCTTC 6 242 0 TCAACTCACC 0.927517 -59 ** ******** Masking position 7 Map Score: 2.23152 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 161 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 ACCAGCAAAAAGCACCCCCCGGTGAAGGAGAG 1 51 0 AGCACCCCGG 0.990835 -102 GGCAACCCCTAGCAACCACCGGCTAGACAGAT 2 80 1 AGCAACCCGG 0.988953 -161 AGCGGGGGCGAGGATAATCCGGCTAG 5 5 0 AGGATACCGG 0.944447 -38 ATCGGCGTGATGCAAAAAACGGGCTTGGAGGG 6 63 0 TGCAAAACGG 0.957521 -238 CCAGCTAGGGAGCCCAGCCCGATGATAATAAT 6 93 0 AGCCCACCGA 0.930731 -208 TAGTCCCCTGTGCTCAGGCCGGAAAGCTAAAG 6 157 0 TGCTCACCGG 0.9611 -144 TCTGTGGCCTAGCAAAACACGAGTGCGTCAAA 6 258 0 AGCAAAACGA 0.892136 -43 GGTGGAAACTCCTGCCCCATATCT 6 287 0 TGGAAACCTG 0.79565 -14 ****** **** Masking position 10 Map Score: 2.92067 Number of sites scoring better than the average of aligned sites = 696 Number in coding regions = 651 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 6 TTCTAAGAGTGACGATGGGGAGAGATACTT 1 113 0 GACGATGGGG 0.943822 -40 AGAAATCTCTGAGCTTGAGGCCAAATCCTT 2 186 1 GAGCTTGAGG 0.957532 -55 AAATTTAAGCGGGGGCGAGGATAATCCGGC 5 14 0 GGGGGCGAGG 0.972054 -29 TAGTGGATTAGAGCGCGTGGCTACGGACCA 6 14 1 GAGCGCGTGG 0.986306 -287 CGTGGCTACGGACCACGAGGTCGGGGGTTC 6 29 1 GACCACGAGG 0.988775 -272 TTTCCGGCCTGAGCACAGGGGACTATGAAT 6 164 1 GAGCACAGGG 0.965702 -137 ********** Masking position 9 Map Score: 2.30593 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 95 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 CTATTTACAAATTGTTACAATCTTGTTATA 2 125 1 ATTGTTACAA 0.902675 -116 GTATATGAGTAATATAACAAGATTGTAACA 2 137 0 AATATAACAA 0.813684 -104 TACATAAGGAATTATAACCAA 2 230 1 ATTATAACCA 0.970037 -11 ATTCAAAATTATTATTACCAGCGGAATATG 3 12 0 ATTATTACCA 0.978898 -40 CATCACGCCGATTATTATCATCGGGCTGGG 6 83 1 ATTATTATCA 0.89888 -218 ********** Masking position 5 Map Score: 0.306942 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 133 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 CCACCACCACAGACTGAAGCCCCAACGGAA 2 26 1 AGACTGAAGC 0.952579 -215 CAAAGGATTTGGCCTCAAGCTCAGAGATTT 2 188 0 GGCCTCAAGC 0.936018 -53 TTTATGAGTCGGACTTAACC 3 42 1 GGACTTAACC 0.952548 -10 TCAGGTTTGGGGACCATGGCATATATCTAC 4 91 0 GGACCATGGC 0.93141 -95 CCGACCTCGTGGTCCGTAGCCACGCGCTCT 6 23 0 GGTCCGTAGC 0.943533 -278 ATGGAGTTGTAGACTTTAGCTTTCCGGCCT 6 144 1 AGACTTTAGC 0.908871 -157 GAATTTCCCAGGACCAAACCAAAGATTCGG 6 190 1 GGACCAAACC 0.959722 -111 ********** Masking position 4 Map Score: 0.569557 Number of sites scoring better than the average of aligned sites = 497 Number in coding regions = 440 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 9 ********** No masking Map Score: -3.40817e-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: -3.40817e-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: -3.40817e-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