AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00930_synecho_reg_100.orf -o00930_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 sll0222 74 phoA; alkaline phosphatase. [EC:3.1.3.1] #2 sgl0002 42 bcp; hypothetical protein. #3 sml0004 164 ycf6; hypothetical protein. #4 sll0654 300 alkaline phosphatase. [EC:3.1.3.1] #5 slr1808 161 hemA; glutamyl-tRNA reductase (GLUTR). [EC:1.2.1.-] [SP:HEM1_SYNY3] #6 slr0942 42 aldehyde reductase. [EC:1.1.1.2] #7 slr0943 121 fda; fructose-bisphosphate aldolase. [EC:4.1.2.13] #8 sll0481 71 hypothetical protein. [SP:Y481_SYNY3] #9 sll0480 182 hypothetical protein. #10 slr1556 152 ddh; 2-hydroxyaciddehydrogenase. [EC:1.1.1.-] Motif number 1 AGTTTACGGACGCGGGGGAATTTTGCCCTC 1 29 1 CGCGGGGGAA 0.965762 -46 GGTGGTGGCACAAGAGGGCAAAATTCCCCC 1 42 0 CAAGAGGGCA 0.694632 -33 AGACTCTTAAACAACGGGAAATCCAGGTTT 2 15 0 ACAACGGGAA 0.684129 -28 CAATGATGGTTCCAGGGGAGATTAGCTCGG 3 48 1 TCCAGGGGAG 0.687953 -117 TAAAGCTTGCCTCAGGGACAAAACGCCCGA 3 74 0 CTCAGGGACA 0.842811 -91 TATCTTACGGCGATCGGGCAAAATTTTAAA 3 100 0 CGATCGGGCA 0.890208 -65 AAAAGCTAAGCTCAAGGGCGGCACTTTACT 4 48 0 CTCAAGGGCG 0.851755 -253 AATTTGCTAACTCTAGGGAAAGTTGAAGTA 4 104 0 CTCTAGGGAA 0.825124 -197 CGTCCTTCACCGATGGGGAATTTTGCTGTC 4 209 1 CGATGGGGAA 0.924404 -92 CTGGCGATCGCCAACGGACAGCAAAATTCC 4 225 0 CCAACGGACA 0.866383 -76 AGACATTAGCGCCGAGGACAACTAGGCC 5 9 0 GCCGAGGACA 0.625647 -153 CGGGGCTTTTGCCAGGGGCACCAAAGGGAA 5 68 1 GCCAGGGGCA 0.981285 -94 GCCAGGGGCACCAAAGGGAAAAACGACTCC 5 78 1 CCAAAGGGAA 0.97045 -84 AAAAACGACTCCATGGGGAACACAGAGCCA 5 96 1 CCATGGGGAA 0.967468 -66 GAAACTTATCGCAGAGGGAAGAAAGC 6 7 0 GCAGAGGGAA 0.863124 -36 ACAAGAGGATGGCAGGGGCAAGTTTCACCG 7 43 1 GGCAGGGGCA 0.955674 -79 CTTTAAGGAGCTAAGGGGCACCCGAATCAC 7 77 0 CTAAGGGGCA 0.967129 -45 CATGATTAAACCAACGGGAGCAGTATTGAT 9 75 1 CCAACGGGAG 0.919055 -108 TACCCCTCGCCCCAGGGGAAATGGCAATGG 9 121 0 CCCAGGGGAA 0.991266 -62 ********** Masking position 6 Map Score: 25.6011 Number of sites scoring better than the average of aligned sites = 5332 Number in coding regions = 4835 Number in noncoding regions = 497 Number of orfs with sites within 600 bp upstream = 461 Fraction of orfs with sites within 600 bp upstream = 0.0740443 Motif number 2 TCCCCCGCGTCCGTAAACTTTTCAACTACTCAAAA 1 13 0 CCACTTTTCA 0.785212 -62 AACAAGCTTTGCCAGCCTTTATCTTACGGCGATCG 3 114 0 GCGTTTATCT 0.940429 -51 GTCGATCCCGCCGAGGATTTTTCGCAGAATTTGCA 4 12 1 CCGTTTTTCC 0.897029 -289 CCGCCCTTGAGCTTAGCTTTTTCGTTCCCCGTTGA 4 57 1 GCATTTTTCT 0.989112 -244 TAGCAAATTTGCTTAACCTTTTCATAGTCTAACCA 4 125 1 GCACTTTTCT 0.980689 -176 CATAGTCTAACCATAAGTTTTTCTTAATTTCTCTA 4 147 1 CCATTTTTCT 0.978936 -154 ACTTGGCCCCGCTCCAGTTTTTCATAGAGAAATTA 4 171 0 GCCTTTTTCT 0.984774 -130 TGAAGGTTTTGCCCCACTTTTTCCTGATTGAGAAA 4 262 1 GCCTTTTTCT 0.984774 -39 TGTCCTCGGCGCTAATGTCTTTCTCGACAATTCTA 5 19 1 GCATCTTTCC 0.923563 -143 CCAAATTTCTGCTAAAACCTATCCTTAACACCCCC 9 22 0 GCACCTATCT 0.862211 -161 CCTAGTAACAGCTACGATTTATCGTACTATCGATC 10 16 1 GCCTTTATCT 0.958325 -137 CCTTTTATTACCAGATATTTTTCCTAAAAATGAAG 10 81 0 CCATTTTTCT 0.978936 -72 ** * ****** * Masking position 10 Map Score: 15.8602 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 217 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 CGGACGCGGGGGAATTTTGCCCTCTTGTGCC 1 35 1 GGATTTTGCC 0.985877 -40 TGGTTCCAGGGGAGATTAGCTCGGGCGTTTT 3 54 1 GGAATTAGCT 0.892131 -111 GTTGACAATGGCGGTTTTACTTCAACTTTCC 4 87 1 GCGTTTTACT 0.909086 -214 CCTAGAGTTAGCAAATTTGCTTAACCTTTTC 4 117 1 GCAATTTGCT 0.94229 -184 TCACCGATGGGGAATTTTGCTGTCCGTTGGC 4 215 1 GGATTTTGCT 0.992123 -86 GAATCTGGCGGGGCTTTTGCCAGGGGCACCA 5 60 1 GGGTTTTGCC 0.985897 -102 TAAAGGTATGGGATTTTTACTTAACATGGA 7 102 1 GGATTTTACT 0.966481 -20 AAATGGCAATGGGTTTATGCTCGCTCCAATC 9 102 0 GGGTTATGCT 0.956789 -81 *** ******* Masking position 6 Map Score: 8.50369 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 432 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 4 CCTTTATCTTACGGCGATCGGGCAAAATTT 3 104 0 ACGGCGATCG 0.98067 -61 TCGTTCCCCGTTGACAATGGCGGTTTTACT 4 78 1 TTGACAATGG 0.798258 -223 TTGCTGTCCGTTGGCGATCGCCAGCACCGA 4 231 1 TTGGCGATCG 0.991671 -70 TCAAACTGGAATGGCAATTGATAAAGGCGT 8 39 0 ATGGCAATTG 0.934671 -33 TGGTTTAATCATGGTGACGGCCATAGCTAG 9 58 0 ATGGTGACGG 0.898316 -125 CCCAGGGGAAATGGCAATGGGTTTATGCTC 9 111 0 ATGGCAATGG 0.982712 -72 ACCTTTTATAATGGCGATCGCCCTTTAATC 9 155 1 ATGGCGATCG 0.994792 -28 CGGCACTACCTTGGTGATCGATAGTACGAT 10 36 0 TTGGTGATCG 0.964581 -117 ********** Masking position 7 Map Score: 10.6191 Number of sites scoring better than the average of aligned sites = 5007 Number in coding regions = 4524 Number in noncoding regions = 483 Number of orfs with sites within 600 bp upstream = 407 Fraction of orfs with sites within 600 bp upstream = 0.065371 Motif number 5 GGTTTCTAGCTTTGGGGGAGAAAAA 3 6 1 CTAGCTTTGG 0.996384 -159 CCAATAAAAACAAGCTTTGCCAGCCTTTAT 3 127 0 CAAGCTTTGC 0.950692 -38 CTCGACAATTCTAGCTTAGGAATCTGGCGG 5 41 1 CTAGCTTAGG 0.98556 -121 GAACACAGAGCCAGTTTTGGGACATTTATT 5 113 1 CCAGTTTTGG 0.950237 -49 AGAGCTAGAGCTACCTTTGGGAGGGATT 8 9 0 CTACCTTTGG 0.984466 -63 GAAATTTGGACTAGCTATGGCCGTCACCAT 9 48 1 CTAGCTATGG 0.985546 -135 ********** Masking position 6 Map Score: 7.33262 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 127 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 AAGTTATCACAGGGGTGGTGGCA 1 62 0 GTTATACAGG 0.970408 -13 GGTATCAAAGACTCTTAAACA 2 32 0 GGTATAAAGA 0.91527 -11 AGCTTTGGGGGAGAAAAAAGGGGATAGAGAC 3 18 1 GAGAAAAAGG 0.904371 -147 CGACTCCATGGGGAACACAGAGCCAGTTTTG 5 101 1 GGGAAACAGA 0.73403 -61 ACCTTAAGATATTACAGAAACTTATCGC 6 25 0 GATATACAGA 0.891937 -18 TTTTTTGAATGATATTAAAGGGTAAAGTCAG 7 12 1 GATATAAAGG 0.968286 -110 GGCGATCGCCATTATAAAAGGTGAGTTACCC 9 146 0 ATTATAAAGG 0.795815 -37 GGCTTGGTGATTAAAGGGCGATCGCCA 9 166 0 GTGATAAAGG 0.97498 -17 AAAATATCTGGTAATAAAAGGCTAAAAAATT 10 95 1 GTAATAAAGG 0.907477 -58 ***** ***** Masking position 7 Map Score: 4.88705 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 214 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 AATTTTAAAGCTTGCCTCAGGGACAAAACG 3 79 0 CTTGCCTCAG 0.977185 -86 ATCACTTGGCCCCGCTCCAGTTTTTCATAG 4 179 0 CCCGCTCCAG 0.990033 -122 CACGGTGAAACTTGCCCCTGCCATCCTCTT 7 45 0 CTTGCCCCTG 0.985379 -77 TGGGTTTATGCTCGCTCCAATCAATACTGC 9 94 0 CTCGCTCCAA 0.977185 -89 TGAGTTACCCCTCGCCCCAGGGGAAATGGC 9 126 0 CTCGCCCCAG 0.995638 -57 ********** Masking position 5 Map Score: 5.32062 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 173 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 TGCCCTCTTGTGCCACCACCCCTGTGATAA 1 52 1 TGCCACCACC 0.928497 -23 AGCTCAAGGGCGGCACTTTACTGTGCAAAT 4 40 0 CGGCACTTTA 0.576465 -261 GAAGTAAAACCGCCATTGTCAACGGGGAAC 4 80 0 CGCCATTGTC 0.94252 -221 CGTTGGCGATCGCCAGCACCGATTGAAGGT 4 239 1 CGCCAGCACC 0.960418 -62 GCAAAAGCCCCGCCAGATTCCTAAGCTAGA 5 50 0 CGCCAGATTC 0.739365 -112 AACTTGCCCCTGCCATCCTCTTGTCTGACT 7 37 0 TGCCATCCTC 0.887564 -85 TCTAGCTCTACGCCTTTATCAATTGCCATT 8 30 1 CGCCTTTATC 0.850704 -42 CTTTATCAATTGCCATTCCAGTTTGAAAGG 8 43 1 TGCCATTCCA 0.786305 -29 ATAAACCCATTGCCATTTCCCCTGGGGCGA 9 115 1 TGCCATTTCC 0.932352 -68 AAAGGGCGATCGCCATTATAAAAGGTGAGT 9 151 0 CGCCATTATA 0.917413 -32 ATAGTATTAACGGCACTACCTTGGTGATCG 10 46 0 CGGCACTACC 0.922054 -107 ********** Masking position 4 Map Score: 3.97234 Number of sites scoring better than the average of aligned sites = 2983 Number in coding regions = 2795 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 9 ********** No masking Map Score: -2.27841e-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 AAAACAAGCTTTGCCAGCCTTTATCTTACGGC 3 119 0 TTGCAGCTTT 0.909253 -46 CCGAGGATTTTTCGCAGAATTTGCACAGTAAA 4 22 1 TTCCAGATTT 0.923939 -279 TTATTGACAGTTAGCTGAAATTCATTAACAAG 5 138 1 TTACTGAATT 0.953936 -24 ATTTTTTGAATGATATTAAAGGGTAAA 7 6 1 TTGATGAATT 0.808567 -116 TGCCATCCTCTTGTCTGACTTTACCCTTTAAT 7 25 0 TTGCTGATTT 0.96155 -97 AGGATAGGTTTTAGCAGAAATTTGGACTAGCT 9 32 1 TTACAGAATT 0.964241 -151 TAGCCTTTTATTACCAGATATTTTTCCTAAAA 10 87 0 TTACAGAATT 0.964241 -66 *** **** *** Masking position 2 Map Score: 1.67933 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 217 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 ********** No masking Map Score: -2.27841e-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: -2.27841e-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 13 ********** No masking Map Score: -2.27841e-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