AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i226_Glycyl_TRNA_synthase_synecho_reg_300.orf -o226_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 RCY00779 241 Synechocystis #2 RCY09718 300 Synechocystis #3 RCY10327 39 Synechocystis Motif number 1 GAACCCTAGACCCAACAACATAACCGCTATCAAG 1 17 0 CCCACACAAC 0.996529 -225 TCGGTCAACACTGACCATTAAAACCTAATCGAGA 1 77 1 CTGACATAAC 0.874341 -165 CTGATTTCGTGTCATCATCAAAAATCTCTATGCC 1 143 1 GTCACACAAA 0.94988 -99 GAAGGCAAAAGCCACCACCAATAAACATATCAGG 1 190 0 GCCACACAAA 0.983002 -52 GTAATAATCCCCCAGCCCCTCAACAAATATAACG 2 51 0 CCCACCCTAC 0.986597 -250 CTAGTCAATTCCCAGCCGTACAACAGGGCCACCA 2 132 0 CCCACCTAAC 0.986192 -169 TGAATTTTACCCCAGCATTACCAACATTGACCTA 2 170 0 CCCACATAAA 0.982793 -131 GGCAACTCAGCAATTGAACCAGATTTAGA 2 282 0 CTCACATTAC 0.961715 -19 AGAAAGCCAACAACTTGATGCTAAATGAT 3 21 0 GCCACACTAT 0.923109 -19 **** ** ** ** Masking position 4 Map Score: 10.6148 Number of sites scoring better than the average of aligned sites = 1103 Number in coding regions = 1039 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 GGTCAGTGTTGACCGATTCCTGCTTACTGATAA 1 60 0 GACGATTCTC 0.985849 -182 TCAATTTACGGGCAGATGCTTACGCCATCATTT 1 110 0 GGCGATGTTC 0.980318 -132 TTCCCTAACCGACCCATTGCTCCCTTGCCCT 1 221 1 GACCATTCTC 0.961296 -21 TATAACGCTAGGGTCAATCCTACCAAACCCAAT 2 25 0 GGGCAATCTC 0.9772 -276 TTGAGGGGCTGGGGGATTATTACCTTTTTACCT 2 62 1 GGGGATTTTC 0.990584 -239 CTTTTTACCTGGGGGAATCTTCCTTGGCATGGC 2 85 1 GGGGAATTTC 0.764284 -216 ACAGTTTGCGGTCTGAATTTTACCCCAGCATTA 2 184 0 GTCGAATTTC 0.963833 -117 *** **** ** * Masking position 6 Map Score: 5.89997 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 243 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 ACTGTTCACTGAACCCTAGACCCAACAACATA 1 29 0 GACCTAGACC 0.858208 -213 CAGGAATCGGTCAACACTGACCATTAAAACCT 1 71 1 TCCACTGACC 0.915994 -171 GCAAAAGCCACCACCAATAAACATATCAGGCA 1 188 0 CCCAATAAAC 0.700517 -54 GTGGCTTTTGCCTTCCCTAACCGACCCATTGC 1 209 1 CCCCCTAACC 0.974108 -33 CCGACCCATTGCTCCCTTGCCCT 1 229 1 GCCCTTGCCC 0.990901 -13 TAGGGTCAATCCTACCAAACCCAATAGGGGTT 2 18 0 CCCCAAACCC 0.947438 -283 GACCGTGAGGGCGGCCATGCCAAGGAAGATTC 2 99 0 GCCCATGCCA 0.938529 -202 GTACAACAGGGCCACCAAGACCGTGAGGGCGG 2 117 0 GCCCAAGACC 0.991082 -184 CCCAGCATTACCAACATTGACCTAACGGCTAG 2 162 0 CCCATTGACC 0.981382 -139 GAACAAACCTGCGGCAATGATCACAACAGTTT 2 210 0 GCCAATGATC 0.911257 -91 ** ******** Masking position 5 Map Score: 8.87183 Number of sites scoring better than the average of aligned sites = 3098 Number in coding regions = 2840 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 240 Fraction of orfs with sites within 600 bp upstream = 0.038548 Motif number 4 CCTGCTTACTGATAACTGTTCACTGAACCCTAGACCC 1 38 0 GAACTGTCAA 0.992844 -204 AAACCTAATCGAGAAATGATGGCGTAAGCATCTGCCC 1 97 1 GAAATGTCAA 0.99406 -145 GGTTAGGGAAGGCAAAAGCCACCACCAATAAACATAT 1 194 0 GAAAAGCCCA 0.926008 -48 AATTCAGACCGCAAACTGTTGTGATCATTGCCGCAGG 2 198 1 GAACTGTGCA 0.983638 -103 CGGAAACAGAGTTAAATGTTAAGCAAAAACGAACAAA 2 235 0 GAAATGTGAA 0.988697 -66 ACAACTTGATGCTAAATGATTACTAAAGGA 3 4 0 GAAATGTCAA 0.99406 -36 * ***** * * ** Masking position 5 Map Score: 2.72599 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 61 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 TAGACCCAACAACATAACCGCTATCAAGAT 1 15 0 AACATAACCG 0.983621 -227 TGACCATTAAAACCTAATCGAGAAATGATG 1 88 1 AACCTAATCG 0.971293 -154 ACCACCAATAAACATATCAGGCAAGTTGAG 1 181 0 AACATATCAG 0.888003 -61 GCTTTTGCCTTCCCTAACCGACCCATTGCT 1 212 1 TCCCTAACCG 0.917955 -30 AATCCTACCAAACCCAATAGGGGTTTTCCA 2 13 0 AACCCAATAG 0.935398 -288 TACCAACATTGACCTAACGGCTAGTCAATT 2 156 0 GACCTAACGG 0.94419 -145 TGCGGCAATGATCACAACAGTTTGCGGTCT 2 203 0 ATCACAACAG 0.863763 -98 ********** Masking position 6 Map Score: 2.36958 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 424 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 ********** No masking Map Score: 1.24588e-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 7 ********** No masking Map Score: 1.24588e-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 ********** No masking Map Score: 1.24588e-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