AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -ifruR_rpxx_opreg_100.orf -g0.290 -x5 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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP265 102 ISOCITRATE DEHYDROGENASE (icd) #2 RP492 300 PYRUVATE,PHOSPHATE DIKINASE PRECURSOR (ppdK) #3 RP707 194 unknown Motif number 1 TTTGTTACCAAGTTGATTGTATAAGTAGACTA 1 21 1 AGTGATGTAT 0.929758 -82 TCGTAAACCAATGTTAAATTACCATTGTTTAT 1 61 0 ATTTAATTAC 0.815757 -42 GTTTACGAAAAGATGAGAGTATTTTAAT 1 85 1 AGTGAAGTAT 0.936825 -18 AAGCTAATTGAAATTCTTTTAACATATTATTG 2 93 0 AATTCTTTAA 0.565336 -208 CTGAGGGGAAAATTTATTGTAATTATTGTACA 2 133 1 AATTATGTAA 0.72079 -168 TTGTTATTATAATTGTAATTATATTGTGTGTA 2 161 0 AATGTATTAT 0.896094 -140 ACATTATGGAATTTGTTATTATAATTGTAATT 2 173 0 ATTGTATTAT 0.931015 -128 TTCTTTAAAGAATTGACATTATGGAATTTGTT 2 188 0 AATGAATTAT 0.943645 -113 AAATTAAGATATCTTTCTTTAAAGAATTGACA 2 202 0 ATTTTTTTAA 0.751543 -99 AATAGTAGCAATGTTAAATTAAGATATCTTTC 2 217 0 ATTTAATTAA 0.86807 -84 CTAATAGTGTATATGTTTTTAAGTACTACATT 2 268 0 ATTGTTTTAA 0.861198 -33 ATGTGAATTGAGTTAATATTATTATACCGTAA 3 44 1 AGTAAATTAT 0.653192 -151 TGATCTATATAACTTATTGTATCAGATCTGGA 3 88 1 AATTATGTAT 0.833675 -107 AAAACTGAATATGTGCTTTTATCTAGGTGATT 3 143 1 ATTGCTTTAT 0.890187 -52 GCTTTTATCTAGGTGATTTTATGTAATAACAC 3 157 1 AGTGATTTAT 0.950599 -38 TCTAAAATACATGTGTTATTACATAAAATCAC 3 169 0 ATTGTATTAC 0.823866 -26 TAACACATGTATTTTAGAGTAT 3 183 1 ATTTAAGTAT 0.897803 -12 ** *** ***** Masking position 4 Map Score: 13.9536 Number of sites scoring better than the average of aligned sites = 1038 Number in coding regions = 698 Number in noncoding regions = 340 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 2 ATTTAACATTGGTTTACGAAAAGATGAGAGTA 1 74 1 GTTTAGAAAA 0.754645 -29 ACGACCATTTAGATTATGGTAGCTTTTCTTAA 2 55 1 AATTAGGTAG 0.94985 -246 ATTATTGACTAATTTAAGAAAAGCTACCATAA 2 68 0 ATTTAGAAAA 0.906851 -233 AAATTAGTCAATAATATGTTAAAAGAATTTCA 2 85 1 AAATAGTTAA 0.691955 -216 CTGAGGGGAAAATTTATTGTAATTATTGTACA 2 133 1 ATTTATGTAA 0.635479 -168 TAAAGAATTGACATTATGGAATTTGTTATTAT 2 183 0 AATTAGGAAT 0.955285 -118 TAGCAATGTTAAATTAAGATATCTTTCTTTAA 2 212 0 AATTAGATAT 0.954474 -89 CATTATTTATACATTAGGAAAAAAATAGTAGC 2 240 0 AATTAGAAAA 0.918556 -61 CCATATCAACGTATTAGGATAGATGTGAATTG 3 22 1 GATTAGATAG 0.789576 -173 ACTCGATTAAAGTTTACGGTATAATAATATTA 3 57 0 ATTTAGGTAT 0.966524 -138 CAGATCTGATACAATAAGTTATATAGATCACT 3 86 0 AAATAGTTAT 0.727546 -109 TATCTAGGTGATTTTATGTAATAACACATGTA 3 162 1 ATTTAGTAAT 0.874781 -33 TAACACATGTATTTTAGAGTAT 3 183 1 ATTTAAGTAT 0.674028 -12 * **** ***** Masking position 6 Map Score: 8.19368 Number of sites scoring better than the average of aligned sites = 713 Number in coding regions = 491 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 3 AAGTAGACTATGCAAAAAATAAACAATGGT 1 43 1 TGCAAAAAAT 0.761076 -60 ATTAAAATACTCTCATCTTTT 1 92 0 TTAAAATACT 0.871779 -11 CAATAATATGTTAAAAGAATTTCAATTAGC 2 93 1 TTAAAAGAAT 0.862372 -208 TATATTGTGTGTACAATAATTACAATAAAT 2 144 0 GTACAATAAT 0.878913 -157 TTATACATTAGGAAAAAAATAGTAGCAATG 2 236 0 GGAAAAAAAT 0.964011 -65 AATGTAGTACTTAAAAACATATACACTATT 2 268 1 TTAAAAACAT 0.764698 -33 ACGTTGATATGGAAAATAATAGT 3 4 0 GGAAAATAAT 0.964011 -191 AAAGTTTACGGTATAATAATATTAACTCAA 3 51 0 GTATAATAAT 0.830433 -144 ACGTGGTGACGAAAAAAACTGAATATGTGC 3 129 1 GAAAAAAACT 0.767198 -66 ********** Masking position 5 Map Score: 2.59419 Number of sites scoring better than the average of aligned sites = 648 Number in coding regions = 453 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 4 ********** No masking Map Score: 6.06393e-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 5 ********** No masking Map Score: 6.06393e-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 6 ********** No masking Map Score: 6.06393e-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