AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i030_synecho_ctra_100.orf -o030_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 RCY34833 127 Synechocystis #2 RCY25232 300 Synechocystis #3 RCY02659 52 Synechocystis Motif number 1 GCAATTGAATGGAAAAAAGCCCCCTAAACT 1 93 0 GGAAAAAAGC 0.977029 -35 TGAGGAATAAATCGTGCAATTGA 1 115 0 GGAATAAATC 0.964343 -13 TCAAACAACAAGAAAAAATCAATTTACCCT 2 26 0 AGAAAAAATC 0.981346 -275 AAAAAACTGCAAAAATTATCCTGACTGAAT 2 83 0 AAAAATTATC 0.839341 -218 TGTCAATCCAGGGATAAATCCAGGCATATT 2 183 0 GGGATAAATC 0.863383 -118 AAAATAAGCTCAAAATAAGCTGAAATTGCT 2 267 0 CAAAATAAGC 0.909119 -34 TTTCATACTGAAAAATAAGCTCAAAATAAG 2 278 0 AAAAATAAGC 0.964737 -23 AAAATTAATCAAAAAAAATCCTTGCTCTGG 3 17 0 AAAAAAAATC 0.976111 -36 TAACCTCCGAAAAATTAATCAAAAAAAATC 3 27 0 AAAATTAATC 0.945643 -26 ********** Masking position 4 Map Score: 10.3706 Number of sites scoring better than the average of aligned sites = 713 Number in coding regions = 569 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 2 TTTGGGCAATTTTTAGGGGGTTTGGACAAT 1 58 0 TTTTAGGGGG 0.996856 -70 CAAAGTTAGAGTTTAGGGGGCTTTTTTCCA 1 84 1 GTTTAGGGGG 0.994653 -44 TTTGCAGTTTTTTTATGGAGTTTTGATAAC 2 100 1 TTTTATGGAG 0.943109 -201 GTCATTGCTGACTTAGGGGGGCAAAAACAA 2 213 0 ACTTAGGGGG 0.987792 -88 ATAAGCTGAAATTGCTGGGGAGTAAGGGAT 2 253 0 ATTGCTGGGG 0.957751 -48 TTTGATTAATTTTTCGGAGGTTACCGTCT 3 34 1 TTTTCGGAGG 0.975992 -19 ********** Masking position 3 Map Score: 7.14153 Number of sites scoring better than the average of aligned sites = 758 Number in coding regions = 558 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 3 GCGATCGCCAATGCCAGTTGTGGTCGGCG 1 4 1 AGCAATCATT 0.659142 -124 TCGGCGGATGGTAACCAAATAACCATTGTCCAAACC 1 34 1 GACAAAACAT 0.977103 -94 ACTGGAAAATGGGATCAAACAACAAGAAAAAATCAA 2 34 0 GACAAAACAG 0.988213 -267 TGACTGAATGGAAGTCAAAAAGACTGGAAAATGGGA 2 56 0 GGCAAAAATG 0.978067 -245 AAAGCTCAATGTTATCAAAACTCCATAAAAAAACTG 2 104 0 GACAAACCAT 0.972375 -197 GGCGATCGCCGGGGGCAAAGCTCAATGTTATCAAAA 2 120 0 GGCAAACCAT 0.97841 -181 TCGCCTAGGGATAAACAATAAACGTGTGAACTAATA 2 151 1 AACAATACTG 0.875456 -150 GCTGACTTAGGGGGGCAAAAACAATGTCAATCCAGG 2 201 0 GGCAAAAATG 0.978067 -100 GCCCCCCTAAGTCAGCAATGACAGAGTTGAAAATCC 2 221 1 GACAATAAAG 0.957238 -80 * * **** * * ** Masking position 8 Map Score: 5.5269 Number of sites scoring better than the average of aligned sites = 936 Number in coding regions = 833 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 4 GCGATCGCCAATGCCAGTTG 1 1 1 GCGATCGCCA 0.997058 -127 AATGCCAGTTGTGGTCGGCGGATGGTAACC 1 20 1 GTGGTCGGCG 0.987245 -108 ACTATTGCCATGGGCAGGGTAAATTG 2 7 1 GCCATGGGCA 0.979239 -294 TTATCCCTAGGCGATCGCCGGGGGCAAAGC 2 135 0 GCGATCGCCG 0.998096 -166 ********** Masking position 5 Map Score: 2.65508 Number of sites scoring better than the average of aligned sites = 6292 Number in coding regions = 5737 Number in noncoding regions = 555 Number of orfs with sites within 600 bp upstream = 353 Fraction of orfs with sites within 600 bp upstream = 0.0566977 Motif number 5 GTTATTTGGTTACCATCCGCCGACCACAAC 1 27 0 TACCATCCGC 0.912137 -101 ACCATTGTCCAAACCCCCTAAAAATTGCCC 1 55 1 AAACCCCCTA 0.973147 -73 GAATGGAAAAAAGCCCCCTAAACTCTAACT 1 87 0 AAGCCCCCTA 0.968207 -41 CATTGAGCTTTGCCCCCGGCGATCGCCTAG 2 129 1 TGCCCCCGGC 0.974195 -172 ACATTGTTTTTGCCCCCCTAAGTCAGCAAT 2 210 1 TGCCCCCCTA 0.992143 -91 AGACGGTAACCTCCGAAAAATTAATC 3 37 0 TAACCTCCGA 0.972918 -16 ********** Masking position 4 Map Score: 2.42115 Number of sites scoring better than the average of aligned sites = 1498 Number in coding regions = 1353 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 6 AAATCGTGCAATTGAATGGAAAAAAGCCCC 1 100 0 ATTGAATGGA 0.93392 -28 AATTATCCTGACTGAATGGAAGTCAAAAAG 2 70 0 ACTGAATGGA 0.986623 -231 AACTAATATGCCTGGATTTATCCCTGGATT 2 179 1 CCTGGATTTA 0.938487 -122 TGGATTTATCCCTGGATTGACATTGTTTTT 2 191 1 CCTGGATTGA 0.987596 -110 GTCAGCAATGACAGAGTTGAAAATCCCTTA 2 231 1 ACAGAGTTGA 0.903425 -70 ********** Masking position 7 Map Score: 1.07299 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 254 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 7 ********** No masking Map Score: -3.03101e-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: -3.03101e-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: -3.03101e-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