AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i122_Arsenical_Resistance_Pump_synecho_reg_100.orf -o122_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 RCY08201 100 Synechocystis #2 RCY43438 300 Synechocystis #3 RCY15995 213 Synechocystis Motif number 1 GTATTATCGTTTTTTGCTCCTCTCACCGTG 1 26 1 TTTTTGCTCC 0.984062 -75 CTTCAGGAAGTTTTTGTCCCCTGGGCTGAC 1 58 1 TTTTTGTCCC 0.955461 -43 GTGGTGGATATTTTTGATCCAAAC 2 5 0 TTTTTGATCC 0.858215 -296 TGTAGCCAAATTCTTGCCCCCAAAAAGTAA 2 83 0 TTCTTGCCCC 0.987656 -218 GAATTTGGCTACATTTCCCCAGCATCTAAC 2 100 1 ACATTTCCCC 0.910319 -201 TTGAACGGAATCTTTGCCCAATCAGCCTGC 2 143 1 TCTTTGCCCA 0.960958 -158 TCTAGCTACGACATTACCCCACTGTGCAGG 2 168 0 ACATTACCCC 0.910319 -133 AAAAATAGGTTGAATGCCCCTTTACCTAAG 3 22 1 TGAATGCCCC 0.901363 -192 TATGGAAATCTCATTGCCCCCATTGTTCCA 3 69 0 TCATTGCCCC 0.995646 -145 AAAGTACTCTATTTTGCTCCTTTTCCATCG 3 98 1 ATTTTGCTCC 0.965466 -116 ********** Masking position 5 Map Score: 14.0111 Number of sites scoring better than the average of aligned sites = 2124 Number in coding regions = 1880 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 272 Fraction of orfs with sites within 600 bp upstream = 0.0436878 Motif number 2 GGAATCTTTGCCCAATCAGCCTGCACAGTG 2 149 1 CCCAATCAGC 0.886657 -152 ACGACATTACCCCACTGTGCAGGCTGATTG 2 161 0 CCCACTGTGC 0.92097 -140 CCATTCACCCCCCATCTAGCTACGACATTA 2 182 0 CCCATCTAGC 0.956081 -119 GTGAATTGATCCCATTCACCCCCCATCTAG 2 193 0 CCCATTCACC 0.98489 -108 TTAATATCCTCATATTTTTCTATATTGTC 2 282 1 CATATTTTTC 0.616063 -19 GGGCATTCAACCTATTTTTCTGATAAAACA 3 11 0 CCTATTTTTC 0.890695 -203 AGGTTGAATGCCCCTTTACCTAAGGCAGCG 3 28 1 CCCCTTTACC 0.966209 -186 TTGTTCCATTCACATCCTCCGCTGCCTTAG 3 47 0 CACATCCTCC 0.889864 -167 TCTCATTGCCCCCATTGTTCCATTCACATC 3 61 0 CCCATTGTTC 0.969437 -153 CTCTATTTTGCTCCTTTTCCATCGGAAGAC 3 104 1 CTCCTTTTCC 0.823778 -110 ********** Masking position 1 Map Score: 6.78896 Number of sites scoring better than the average of aligned sites = 2464 Number in coding regions = 2143 Number in noncoding regions = 321 Number of orfs with sites within 600 bp upstream = 331 Fraction of orfs with sites within 600 bp upstream = 0.0531642 Motif number 3 GACAAAAACTTCCTGAAGCTCACGGTGAGAGGAGCAAAAAAC 1 34 0 TCCCTGTGAG 0.993495 -67 AAGTTTTTGTCCCCTGGGCTGACTCTGCCTGGCTTTGCTTAA 1 65 1 CCCCTTTGCG 0.995548 -36 ATCAAAAATATCCACCACGAAAGGTAGCACTGTTTTGTCAAA 2 17 1 TCCGAGAGCG 0.922237 -284 CAGCATCTAACCCACTCCCTAGTTTTGAACGGAATCTTTGCC 2 119 1 CCCCTTTGAG 0.993124 -182 TACGACATTACCCCACTGTGCAGGCTGATTGGGCAAAGATTC 2 150 0 CCCTGGTGAG 0.945862 -151 GGTTGAATGCCCCTTTACCTAAGGCAGCGGAGGATGTGAATG 3 29 1 CCCCTGAGCG 0.985819 -185 ACTCGGTCTGTCCCCGGTCTACTGTTGCCGTGTCTTCCGATG 3 123 0 TCCCTGTGCG 0.9973 -91 GTAAGATTATTCCATCAAGTTTTTTTGATGAGTTGTC 3 187 1 TCCGTTTGAG 0.974601 -27 *** ** * *** * Masking position 17 Map Score: 7.15858 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 221 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 GATTTTGTACAAAATTTGACAAAACAGTGC 2 43 0 AAAATTTGAC 0.987135 -258 AAAATCAACGAAAATTTTACTTTTTGGGGG 2 67 1 AAAATTTTAC 0.922292 -234 TTTGGGGGCAAGAATTTGGCTACATTTCCC 2 89 1 AGAATTTGGC 0.911183 -212 ACAATATAGAAAAATATGAGGATATTAAAA 2 280 0 AAAATATGAG 0.875952 -21 TTACATCAAAAAAACTTGATATGTCAACTC 3 161 0 AAAACTTGAT 0.96579 -53 ACTCATCAAAAAAACTTGATGGAATAATCT 3 190 0 AAAACTTGAT 0.96579 -24 ********** Masking position 4 Map Score: 2.9717 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 359 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 5 GAATGCCCCTTTACCTAAGGCAGCGGAGGA 3 33 1 TTACCTAAGG 0.884265 -181 GCAATGAGATTTCCATAAAGTACTCTATTT 3 82 1 TTCCATAAAG 0.97241 -132 TTTGCTCCTTTTCCATCGGAAGACACGGCA 3 110 1 TTCCATCGGA 0.943189 -104 TGGAATAATCTTACATCAAAAAAACTTGAT 3 171 0 TTACATCAAA 0.93985 -43 TGTAAGATTATTCCATCAAGTTTTTTTGAT 3 186 1 TTCCATCAAG 0.987498 -28 ********** Masking position 6 Map Score: 0.595358 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 197 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 GGGGACAAAAACTTCCTGAAGCTCACGGTG 1 49 0 ACTTCCTGAA 0.786848 -52 TGGATCAAAAATATCCACCACGAAAGGTAG 2 14 1 ATATCCACCA 0.952629 -287 ATTTGGCTACATTTCCCCAGCATCTAACCC 2 102 1 ATTTCCCCAG 0.92634 -199 ACACCATAATACATCCAGAGCTTTTCGGTG 2 221 1 ACATCCAGAG 0.961705 -80 TTTCTTGCGGATAACCACCGAAAAGCTCTG 2 236 0 ATAACCACCG 0.925124 -65 ATTATTTTTAATATCCTCATATTTTTCTAT 2 275 1 ATATCCTCAT 0.904247 -26 TGTTCCATTCACATCCTCCGCTGCCTTAGG 3 46 0 ACATCCTCCG 0.986277 -168 ********** Masking position 1 Map Score: 2.41376 Number of sites scoring better than the average of aligned sites = 1028 Number in coding regions = 952 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 7 ********** No masking Map Score: 1.58694e-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 8 AAGTTTTTGTCCCCTGGGCTGACTCTGCCTG 1 65 1 CCCCTGGCTG 0.953923 -36 TCAAAAATATCCACCACGAAAGGTAGCACTG 2 18 1 CCACCAGAAA 0.935221 -283 CAAATTCTTGCCCCCAAAAAGTAAAATTTTC 2 76 0 CCCCCAAAAG 0.984877 -225 CGACATTACCCCACTGTGCAGGCTGATTGGG 2 159 0 CCACTGGCAG 0.981635 -142 TCCCATTCACCCCCCATCTAGCTACGACATT 2 183 0 CCCCCACTAG 0.955877 -118 TTGCGGATAACCACCGAAAAGCTCTGGATGT 2 231 0 CCACCGAAAG 0.984872 -70 ****** **** Masking position 4 Map Score: 0.877239 Number of sites scoring better than the average of aligned sites = 1052 Number in coding regions = 976 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 9 ********** No masking Map Score: 1.58694e-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: 1.58694e-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: 1.58694e-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