AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i030_Glycerol_Uptake_synecho_reg_100.orf -o030_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 RCY34833 127 Synechocystis #2 RCY25232 300 Synechocystis #3 RCY02659 52 Synechocystis Motif number 1 GCAATTGAATGGAAAAAAGCCCCCTAAACT 1 93 0 GGAAAAAAGC 0.974219 -35 TGAGGAATAAATCGTGCAATTGA 1 115 0 GGAATAAATC 0.960046 -13 TCAAACAACAAGAAAAAATCAATTTACCCT 2 26 0 AGAAAAAATC 0.979053 -275 AAAAAACTGCAAAAATTATCCTGACTGAAT 2 83 0 AAAAATTATC 0.822765 -218 TGTCAATCCAGGGATAAATCCAGGCATATT 2 183 0 GGGATAAATC 0.848822 -118 AAAATAAGCTCAAAATAAGCTGAAATTGCT 2 267 0 CAAAATAAGC 0.898861 -34 TTTCATACTGAAAAATAAGCTCAAAATAAG 2 278 0 AAAAATAAGC 0.960483 -23 AAAATTAATCAAAAAAAATCCTTGCTCTGG 3 17 0 AAAAAAAATC 0.973192 -36 TAACCTCCGAAAAATTAATCAAAAAAAATC 3 27 0 AAAATTAATC 0.939233 -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 ATTGTCCAAACCCCCTAAAAATTGCCCAAA 1 58 1 CCCCCTAAAA 0.996446 -70 TGGAAAAAAGCCCCCTAAACTCTAACTTTG 1 84 0 CCCCCTAAAC 0.993956 -44 GTTATCAAAACTCCATAAAAAAACTGCAAA 2 100 0 CTCCATAAAA 0.936122 -201 TTGTTTTTGCCCCCCTAAGTCAGCAATGAC 2 213 1 CCCCCTAAGT 0.986213 -88 ATCCCTTACTCCCCAGCAATTTCAGCTTAT 2 253 1 CCCCAGCAAT 0.952472 -48 AGACGGTAACCTCCGAAAAATTAATCAAA 3 34 0 CCTCCGAAAA 0.972931 -19 ********** Masking position 8 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 CGCCGACCACAACTGGCATTGGCGATCGC 1 4 0 AATGATTGCT 0.638522 -124 GGTTTGGACAATGGTTATTTGGTTACCATCCGCCGA 1 34 0 ATGTTTTGTC 0.974987 -94 TTGATTTTTTCTTGTTGTTTGATCCCATTTTCCAGT 2 34 1 CTGTTTTGTC 0.987111 -267 TCCCATTTTCCAGTCTTTTTGACTTCCATTCAGTCA 2 56 1 CATTTTTGCC 0.976039 -245 CAGTTTTTTTATGGAGTTTTGATAACATTGAGCTTT 2 104 1 ATGGTTTGTC 0.969837 -197 TTTTGATAACATTGAGCTTTGCCCCCGGCGATCGCC 2 120 1 ATGGTTTGCC 0.976412 -181 TATTAGTTCACACGTTTATTGTTTATCCCTAGGCGA 2 151 0 CAGTATTGTT 0.865247 -150 CCTGGATTGACATTGTTTTTGCCCCCCTAAGTCAGC 2 201 1 CATTTTTGCC 0.976039 -100 GGATTTTCAACTCTGTCATTGCTGACTTAGGGGGGC 2 221 0 CTTTATTGTC 0.953375 -80 ** * * **** * * Masking position 9 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 CAACTGGCATTGGCGATCGC 1 1 0 TGGCGATCGC 0.996965 -127 GGTTACCATCCGCCGACCACAACTGGCATT 1 20 0 CGCCGACCAC 0.986846 -108 CAATTTACCCTGCCCATGGCAATAGT 2 7 0 TGCCCATGGC 0.978594 -294 GCTTTGCCCCCGGCGATCGCCTAGGGATAA 2 135 1 CGGCGATCGC 0.998036 -166 ********** Masking position 6 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 0.905105 -101 ACCATTGTCCAAACCCCCTAAAAATTGCCC 1 55 1 AAACCCCCTA 0.970842 -73 GAATGGAAAAAAGCCCCCTAAACTCTAACT 1 87 0 AAGCCCCCTA 0.965494 -41 CATTGAGCTTTGCCCCCGGCGATCGCCTAG 2 129 1 TGCCCCCGGC 0.971977 -172 ACATTGTTTTTGCCCCCCTAAGTCAGCAAT 2 210 1 TGCCCCCCTA 0.991454 -91 AGACGGTAACCTCCGAAAAATTAATC 3 37 0 TAACCTCCGA 0.970594 -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 GGGGCTTTTTTCCATTCAATTGCACGATTT 1 100 1 TCCATTCAAT 0.938823 -28 CTTTTTGACTTCCATTCAGTCAGGATAATT 2 70 1 TCCATTCAGT 0.987667 -231 AATCCAGGGATAAATCCAGGCATATTAGTT 2 179 0 TAAATCCAGG 0.943072 -122 AAAAACAATGTCAATCCAGGGATAAATCCA 2 191 0 TCAATCCAGG 0.988565 -110 TAAGGGATTTTCAACTCTGTCATTGCTGAC 2 231 0 TCAACTCTGT 0.910374 -70 ********** Masking position 4 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