AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i330_synecho_ctra_100.orf -o330_synecho_ctra_100.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY00269 32 Synechocystis #2 RCY43131 146 Synechocystis #3 RCY40186 300 Synechocystis Motif number 1 TGATCAGCGTCCATTGCCCAGGCTCGGCAGTCCTGG 2 53 0 CCTGCCACTG 0.996077 -94 TGGGCAATGGACGCTGATCAGCGTAGTTTTGATTTT 2 69 1 ACTGTCAGTG 0.969077 -78 GTAACTTAAACCTATGTCAATTGCAGTTGGG 2 126 1 CCTGCAAGCG 0.99679 -21 ACAGCAGGAAAAGCTGTCAAGAGCCGATACTTTTTG 3 42 1 AATGCAAGCG 0.925509 -259 CTTGATTTTTCCGTTCACCAAAGCTGTTACTGTGGA 3 122 1 CCTCCCAGCG 0.997497 -179 TCCGGCTCTGCCCCTGACCACAGTCGAACTCGCCTG 3 213 1 CCTGCCAGTG 0.998301 -88 TTTTACCCGCACTTTCACGATTCTAGGAGACTATCC 3 254 1 ACTCCGACTG 0.889563 -47 GAGACTATCCCCCATGTCCATTGCAGTTGGA 3 280 1 CCTGCCAGCG 0.999122 -21 ** ** *** ** * Masking position 10 Map Score: 13.2255 Number of sites scoring better than the average of aligned sites = 979 Number in coding regions = 898 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 2 CGATCGGTAGTCAACTACACAGAATAGCCA 2 26 1 TCAACTACAC 0.980028 -121 CCCAACTGCAATTGACATAGG 2 136 0 CCAACTGCAA 0.997175 -11 CCTCCTAAATTCAACTTCAACAGCAGGAAA 3 23 1 TCAACTTCAA 0.988184 -278 TCCAACTGCAATGGACATGGG 3 290 0 CCAACTGCAA 0.997175 -11 ********** Masking position 6 Map Score: 5.44479 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 69 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 TACACAGAATAGCCAGGACTGCCGAGCCTGG 2 41 1 AGCCAGGCTG 0.971909 -106 GGCTCTTGACAGCTTTTCCTGCTGTTGAAGT 3 36 0 AGCTTTTCTG 0.961573 -265 AGCTGTCAAGAGCCGATACTTTTTGTGTCGG 3 53 1 AGCCGATCTT 0.966018 -248 GGGTTGCTAAAACCTATTCTGAATTCTCTTG 3 95 1 AACCTATCTG 0.919721 -206 CGTTCACCAAAGCTGTTACTGTGGACTGTTA 3 133 1 AGCTGTTCTG 0.986677 -168 TAGGCAATCAATCGGGTTCTGGGTTTTGATC 3 162 1 ATCGGGTCTG 0.95594 -139 TCAGGGGCAGAGCCGGATCTGGCCATTCCCA 3 199 0 AGCCGGACTG 0.991858 -102 ******* *** Masking position 1 Map Score: 3.97712 Number of sites scoring better than the average of aligned sites = 592 Number in coding regions = 550 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 ACCGATCGCCAAACAAAGGGGAA 2 4 0 AAACAAAGGG 0.95496 -143 AGGGAATATCAAATCAAAAAATCAAAACTA 2 92 0 AAATCAAAAA 0.810119 -55 GGTTTAAGTTACTCCCAGGGAATATCAAAT 2 108 0 ACTCCCAGGG 0.874033 -39 TTAGGAGGATAAATAAAAAA 3 1 0 AAATAAAAAA 0.583036 -300 TAAACCCCCGACACAAAAAGTATCGGCTCT 3 61 0 ACACAAAAAG 0.873643 -240 TAGGTTTTAGCAACCCAAGATAAACCCCCG 3 81 0 CAACCCAAGA 0.871088 -220 GTGAACGGAAAAATCAAGAGAATTCAGAAT 3 110 0 AAATCAAGAG 0.942755 -191 CAAGGGATCAAAACCCAGAACCCGATTGAT 3 168 0 AAACCCAGAA 0.954744 -133 CTGGCCATTCCCACCAAGGGATCAAAACCC 3 182 0 CCACCAAGGG 0.963077 -119 ********** Masking position 7 Map Score: 3.68699 Number of sites scoring better than the average of aligned sites = 3482 Number in coding regions = 3111 Number in noncoding regions = 371 Number of orfs with sites within 600 bp upstream = 361 Fraction of orfs with sites within 600 bp upstream = 0.0579827 Motif number 5 TTCCCCTTTGTTTGGCGATCGGTAGTCA 2 9 1 TGTTTGGCGA 0.940999 -138 TCTGTGTAGTTGACTACCGATCGCCAAACA 2 19 0 TGACTACCGA 0.97115 -128 TCAACTACACAGAATAGCCAGGACTGCCGA 2 36 1 AGAATAGCCA 0.855714 -111 AGAATAGCCAGGACTGCCGAGCCTGGGCAA 2 46 1 GGACTGCCGA 0.990822 -101 AGAACCCGATTGATTGCCTAACAGTCCACA 3 152 0 TGATTGCCTA 0.942104 -149 TCCCTTGGTGGGAATGGCCAGATCCGGCTC 3 191 1 GGAATGGCCA 0.97955 -110 ********** Masking position 5 Map Score: 1.73961 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 512 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 6 GTTACTCCCAGGGAATATCAAATCAAAAAA 2 101 0 GGGAATATCA 0.970969 -46 GATATTCCCTGGGAGTAACTTAAACCTATG 2 112 1 GGGAGTAACT 0.937968 -35 CTTCAACAGCAGGAAAAGCTGTCAAGAGCC 3 37 1 AGGAAAAGCT 0.877098 -264 TTTGTGTCGGGGGTTTATCTTGGGTTGCTA 3 74 1 GGGTTTATCT 0.916347 -227 TTTGGTGAACGGAAAAATCAAGAGAATTCA 3 114 0 GGAAAAATCA 0.788904 -187 ATCCCTTGGTGGGAATGGCCAGATCCGGCT 3 190 1 GGGAATGGCC 0.929686 -111 GTGAAAGTGCGGGTAAAAGTTAGCAGGCGA 3 242 0 GGGTAAAAGT 0.714753 -59 ATGGACATGGGGGATAGTCTCCTAGAATCG 3 271 0 GGGATAGTCT 0.949999 -30 ********** Masking position 2 Map Score: 0.457743 Number of sites scoring better than the average of aligned sites = 3137 Number in coding regions = 2767 Number in noncoding regions = 370 Number of orfs with sites within 600 bp upstream = 369 Fraction of orfs with sites within 600 bp upstream = 0.0592676 Motif number 7 ********** No masking Map Score: -1.32571e-13 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: -1.32571e-13 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: -1.32571e-13 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