AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i226_Glycyl_TRNA_synthase_synecho_reg_100.orf -o226_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 RCY00779 241 Synechocystis #2 RCY09718 300 Synechocystis #3 RCY10327 39 Synechocystis Motif number 1 GAACCCTAGACCCAACAACATAACCGCTATCAAG 1 17 0 CCCACACAAC 0.997063 -225 TCGGTCAACACTGACCATTAAAACCTAATCGAGA 1 77 1 CTGACATAAC 0.891648 -165 CTGATTTCGTGTCATCATCAAAAATCTCTATGCC 1 143 1 GTCACACAAA 0.957291 -99 GAAGGCAAAAGCCACCACCAATAAACATATCAGG 1 190 0 GCCACACAAA 0.985589 -52 GTAATAATCCCCCAGCCCCTCAACAAATATAACG 2 51 0 CCCACCCTAC 0.988643 -250 CTAGTCAATTCCCAGCCGTACAACAGGGCCACCA 2 132 0 CCCACCTAAC 0.9883 -169 TGAATTTTACCCCAGCATTACCAACATTGACCTA 2 170 0 CCCACATAAA 0.985412 -131 GGCAACTCAGCAATTGAACCAGATTTAGA 2 282 0 CTCACATTAC 0.967436 -19 AGAAAGCCAACAACTTGATGCTAAATGAT 3 21 0 GCCACACTAT 0.934204 -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 TATGTTGTTGGGTCTAGGGTTCAGTGAACAGT 1 29 1 GGTCTAGGTC 0.877889 -213 AGGTTTTAATGGTCAGTGTTGACCGATTCCTG 1 71 0 GGTCAGTGGA 0.928324 -171 TGCCTGATATGTTTATTGGTGGTGGCTTTTGC 1 188 1 GTTTATTGGG 0.735335 -54 GCAATGGGTCGGTTAGGGAAGGCAAAAGCCAC 1 209 0 GGTTAGGGGG 0.978112 -33 AGGGCAAGGGAGCAATGGGTCGG 1 229 0 GGGCAAGGGC 0.992328 -13 AACCCCTATTGGGTTTGGTAGGATTGACCCTA 2 18 1 GGGTTTGGGG 0.955378 -283 GAATCTTCCTTGGCATGGCCGCCCTCACGGTC 2 99 1 TGGCATGGGC 0.94774 -202 CCGCCCTCACGGTCTTGGTGGCCCTGTTGTAC 2 117 1 GGTCTTGGGC 0.992482 -184 CTAGCCGTTAGGTCAATGTTGGTAATGCTGGG 2 162 1 GGTCAATGGG 0.984279 -139 AAACTGTTGTGATCATTGCCGCAGGTTTGTTC 2 210 1 GATCATTGGC 0.924225 -91 ******** ** Masking position 8 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 3 GGGTCTAGGGTTCAGTGAACAGTTATCAGTAAGCAGG 1 38 1 TTGACAGTTC 0.992479 -204 GGGCAGATGCTTACGCCATCATTTCTCGATTAGGTTT 1 97 0 TTGACATTTC 0.993757 -145 ATATGTTTATTGGTGGTGGCTTTTGCCTTCCCTAACC 1 194 1 TGGGCTTTTC 0.9225 -48 CCTGCGGCAATGATCACAACAGTTTGCGGTCTGAATT 2 198 0 TGCACAGTTC 0.982812 -103 TTTGTTCGTTTTTGCTTAACATTTAACTCTGTTTCCG 2 235 1 TTCACATTTC 0.988122 -66 TCCTTTAGTAATCATTTAGCATCAAGTTGT 3 4 1 TTGACATTTC 0.993757 -36 ** * * ***** * Masking position 13 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 4 TAGACCCAACAACATAACCGCTATCAAGAT 1 15 0 AACATAACCG 0.986289 -227 TGACCATTAAAACCTAATCGAGAAATGATG 1 88 1 AACCTAATCG 0.975921 -154 ACCACCAATAAACATATCAGGCAAGTTGAG 1 181 0 AACATATCAG 0.90474 -61 GCTTTTGCCTTCCCTAACCGACCCATTGCT 1 212 1 TCCCTAACCG 0.930566 -30 AATCCTACCAAACCCAATAGGGGTTTTCCA 2 13 0 AACCCAATAG 0.945488 -288 TACCAACATTGACCTAACGGCTAGTCAATT 2 156 0 GACCTAACGG 0.952975 -145 TGCGGCAATGATCACAACAGTTTGCGGTCT 2 203 0 ATCACAACAG 0.883649 -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 5 TCAGTAAGCAGGAATCGGTCAACACTGACC 1 63 1 GGAATCGGTC 0.990694 -179 ATGATGACACGAAATCAGTCAATTTACGGG 1 131 0 GAAATCAGTC 0.969576 -111 CAGGCAAGTTGAGATGGGGCATAGAGATTT 1 164 0 GAGATGGGGC 0.97756 -78 GGGCAAGGGAGCAATGGGTCGGTTAGGGAA 1 221 0 GCAATGGGTC 0.990687 -21 ********** Masking position 5 Map Score: 0.708489 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 195 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 TATAACGCTAGGGTCAATCCTACCAAACCCA 2 27 0 GGGTAATCCT 0.967143 -274 TTGAGGGGCTGGGGGATTATTACCTTTTTAC 2 62 1 GGGGATTATT 0.980808 -239 CTTTTTACCTGGGGGAATCTTCCTTGGCATG 2 85 1 GGGGAATCTT 0.995018 -216 TGGTAATGCTGGGGTAAAATTCAGACCGCAA 2 181 1 GGGGAAAATT 0.980807 -120 **** ****** Masking position 6 Map Score: 0.14832 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 141 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 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 Motif number 9 ********** 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