AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i330_synecho_ctra_300.orf -o330_synecho_ctra_300.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 0.996241 -94 TGGGCAATGGACGCTGATCAGCGTAGTTTTGATTTT 2 69 1 ACTGTCAGTG 0.970333 -78 GTAACTTAAACCTATGTCAATTGCAGTTGGG 2 126 1 CCTGCAAGCG 0.996924 -21 ACAGCAGGAAAAGCTGTCAAGAGCCGATACTTTTTG 3 42 1 AATGCAAGCG 0.927928 -259 CTTGATTTTTCCGTTCACCAAAGCTGTTACTGTGGA 3 122 1 CCTCCCAGCG 0.9976 -179 TCCGGCTCTGCCCCTGACCACAGTCGAACTCGCCTG 3 213 1 CCTGCCAGTG 0.998346 -88 TTTTACCCGCACTTTCACGATTCTAGGAGACTATCC 3 254 1 ACTCCGACTG 0.893697 -47 GAGACTATCCCCCATGTCCATTGCAGTTGGA 3 280 1 CCTGCCAGCG 0.999159 -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 TGGCTATTCTGTGTAGTTGACTACCGATCG 2 26 0 GTGTAGTTGA 0.975412 -121 CCTATGTCAATTGCAGTTGGG 2 136 1 TTGCAGTTGG 0.996508 -11 TTTCCTGCTGTTGAAGTTGAATTTAGGAGG 3 23 0 TTGAAGTTGA 0.985427 -278 CCCATGTCCATTGCAGTTGGA 3 290 1 TTGCAGTTGG 0.996508 -11 ********** Masking position 5 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 0.968625 -106 GGCTCTTGACAGCTTTTCCTGCTGTTGAAGT 3 36 0 AGCTTTTCTG 0.957134 -265 AGCTGTCAAGAGCCGATACTTTTTGTGTCGG 3 53 1 AGCCGATCTT 0.962072 -248 GGGTTGCTAAAACCTATTCTGAATTCTCTTG 3 95 1 AACCTATCTG 0.910895 -206 CGTTCACCAAAGCTGTTACTGTGGACTGTTA 3 133 1 AGCTGTTCTG 0.985092 -168 TAGGCAATCAATCGGGTTCTGGGTTTTGATC 3 162 1 ATCGGGTCTG 0.950883 -139 TCAGGGGCAGAGCCGGATCTGGCCATTCCCA 3 199 0 AGCCGGACTG 0.990885 -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 TTCCCCTTTGTTTGGCGATCGGT 2 4 1 CCCTTTGTTT 0.95496 -143 TAGTTTTGATTTTTTGATTTGATATTCCCT 2 92 1 TTTTTGATTT 0.810119 -55 ATTTGATATTCCCTGGGAGTAACTTAAACC 2 108 1 CCCTGGGAGT 0.874033 -39 TTTTTTATTTATCCTCCTAA 3 1 1 TTTTTTATTT 0.583036 -300 AGAGCCGATACTTTTTGTGTCGGGGGTTTA 3 61 1 CTTTTTGTGT 0.873643 -240 CGGGGGTTTATCTTGGGTTGCTAAAACCTA 3 81 1 TCTTGGGTTG 0.871088 -220 ATTCTGAATTCTCTTGATTTTTCCGTTCAC 3 110 1 CTCTTGATTT 0.942755 -191 ATCAATCGGGTTCTGGGTTTTGATCCCTTG 3 168 1 TTCTGGGTTT 0.954744 -133 GGGTTTTGATCCCTTGGTGGGAATGGCCAG 3 182 1 CCCTTGGTGG 0.963077 -119 ********** Masking position 4 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 TGACTACCGATCGCCAAACAAAGGGGAA 2 9 0 TCGCCAAACA 0.945671 -138 TGTTTGGCGATCGGTAGTCAACTACACAGA 2 19 1 TCGGTAGTCA 0.973483 -128 TCGGCAGTCCTGGCTATTCTGTGTAGTTGA 2 36 0 TGGCTATTCT 0.866162 -111 TTGCCCAGGCTCGGCAGTCCTGGCTATTCT 2 46 0 TCGGCAGTCC 0.991584 -101 TGTGGACTGTTAGGCAATCAATCGGGTTCT 3 152 1 TAGGCAATCA 0.946694 -149 GAGCCGGATCTGGCCATTCCCACCAAGGGA 3 191 0 TGGCCATTCC 0.981229 -110 ********** Masking position 6 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 TTTTTTGATTTGATATTCCCTGGGAGTAAC 2 101 1 TGATATTCCC 0.970969 -46 CATAGGTTTAAGTTACTCCCAGGGAATATC 2 112 0 AGTTACTCCC 0.937968 -35 GGCTCTTGACAGCTTTTCCTGCTGTTGAAG 3 37 0 AGCTTTTCCT 0.877098 -264 TAGCAACCCAAGATAAACCCCCGACACAAA 3 74 0 AGATAAACCC 0.916347 -227 TGAATTCTCTTGATTTTTCCGTTCACCAAA 3 114 1 TGATTTTTCC 0.788904 -187 AGCCGGATCTGGCCATTCCCACCAAGGGAT 3 190 0 GGCCATTCCC 0.929686 -111 TCGCCTGCTAACTTTTACCCGCACTTTCAC 3 242 1 ACTTTTACCC 0.714753 -59 CGATTCTAGGAGACTATCCCCCATGTCCAT 3 271 1 AGACTATCCC 0.949999 -30 ********** Masking position 9 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