AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i091_Sugar_Transport_3_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 xylF 300 xylose binding protein transport system #2 xylG 77 putative ATP-binding protein of xylose transport system #3 HI1110 50 D-xylose ABC transporter, ATP-binding protein (xylG) #4 HI1111 233 D-xylose ABC transporter, periplasmic-binding protein (xylF) Motif number 1 CACACTTGTGAATTATCTCAATAGCAGTGTGA 1 33 0 AATTATCTCT 0.739633 -268 GGAATTACCCAGTTTCATCATTCCATTTTATT 1 78 0 AGTTTCATCT 0.941636 -223 TACTTATTGCATTTTTCTCTTCGAGGAATTAC 1 102 0 ATTTTTCTCC 0.984811 -199 ACAATTACAGATTTTTATCTTTCGATTACGAT 1 187 0 ATTTTTATCT 0.972285 -114 AACGTAACCAATTTTTAGCAACTAAACAGGGG 1 222 0 ATTTTTAGCC 0.81558 -79 CGGGGGCGTGATTTCTCTCCATGCCGCGTGAA 2 32 1 ATTTCTCTCT 0.938111 -46 GTAAGGGAAGAGTTTTCTCTTCCCTCTTAAAG 3 11 0 AGTTTTCTCC 0.975967 -40 AACATTTTCCTCTCTAGGTGATGAA 4 4 1 ATTTTCCTCT 0.984811 -230 AAATACGAAAAATTTCATCACCTAGAGAGGAA 4 17 0 AATTTCATCC 0.840233 -217 GAAAAACTAACTTTTCATCAATTATGTTATTT 4 53 1 CTTTTCATCT 0.802517 -181 ATGTTATTTAATTTTTCTATGTTGATTATTTG 4 76 1 ATTTTTCTAT 0.853283 -158 CAATTATAAAATCTTTCTCCATTATTACGTTT 4 137 0 ATCTTTCTCT 0.933006 -97 TCCAGTTGTTAGTTTTCACACTTTAAAAAAGG 4 173 0 AGTTTTCACT 0.864855 -61 ********* * Masking position 4 Map Score: 13.2237 Number of sites scoring better than the average of aligned sites = 798 Number in coding regions = 631 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 2 ATAACATAATTGAGCAACTGA 1 2 0 TGAGCAACTG 0.985429 -299 ATTGAGATAATTCACAAGTGTGCGCTCGCT 1 43 1 TTCACAAGTG 0.954228 -258 TTACTTTTGTTGCGCAATTGTACTTATTGC 1 124 0 TGCGCAATTG 0.957041 -177 TAACCAATTTTTAGCAACTAAACAGGGGAA 1 220 0 TTAGCAACTA 0.930247 -81 ATGTTGATTATTTGCAACTGTGGCGTGGAT 4 94 1 TTTGCAACTG 0.97319 -140 ATTACGTTTTTTCACAACTGTGATCCACGC 4 116 0 TTCACAACTG 0.989121 -118 AGTGTGAAAACTAACAACTGGAGCAATAAC 4 183 1 CTAACAACTG 0.952377 -51 AGTCCTTCACTTAACTATTGAGGTATCAAT 4 214 1 TTAACTATTG 0.786362 -20 ********** Masking position 7 Map Score: 8.78963 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 473 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 AGTTGCTCAATTATGTTATTTCACACTGCTA 1 13 1 TTATGTTATT 0.933861 -288 GACCGAGATCTTACTTTTGTTGCGCAATTGT 1 133 0 TTACTTTTTT 0.939146 -168 TATCTTTCGATTACGATTTTTGGTTTATTTC 1 173 0 TTACGATTTT 0.961091 -128 TAAAAATTGGTTACGTTTATCGCGGTGATTG 1 237 1 TTACGTTTTC 0.973411 -64 TGATGAAATTTTTCGTATTTTTGTGAAAAAC 4 29 1 TTTCGTATTT 0.836817 -205 TTTTCATCAATTATGTTATTTAATTTTTCTA 4 64 1 TTATGTTATT 0.933861 -170 TTCTCCATTATTACGTTTTTTCACAACTGTG 4 124 0 TTACGTTTTT 0.991665 -110 ******** ** Masking position 2 Map Score: 5.79935 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 174 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 4 GCGTTACGCCCCAGCGCGGAGCGG 2 5 1 TACGCCCCAG 0.996873 -73 GGAGAGAAATCACGCCCCCGCTCCGCGCTG 2 22 0 CACGCCCCCG 0.998499 -56 AACTGTGATCCACGCCACAGTTGCAAATAA 4 101 0 CACGCCACAG 0.996873 -133 ********** Masking position 2 Map Score: 3.36254 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 27 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 CTGGGTAATTCCTCGAAGAGAAAAATGCAA 1 98 1 CCTCGAAGAG 0.965885 -203 CGCCCCCGCTCCGCGCTGGGGCGTAACGC 2 10 0 CCGCGCTGGG 0.979841 -68 TTTTCTCTTCCCTCTTAAAG 3 1 0 CCTCTTAAAG 0.9541 -50 TCTTCCCTTACCTCTTAGGGAGTTACGAT 3 32 1 CCTCTTAGGG 0.990065 -19 AACATTTTCCTCTCTAGGTGATGAAATT 4 9 1 CCTCTCTAGG 0.899833 -225 ********** Masking position 4 Map Score: 2.13594 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 193 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 CAATAGCAGTGTGAAATAACATAATTGAGC 1 17 0 GTGAAATAAC 0.952308 -284 GCGCACACTTGTGAATTATCTCAATAGCAG 1 38 0 GTGAATTATC 0.854645 -263 TCCATGCCGCGTGAATGAATTGGCTTAGGT 2 49 1 GTGAATGAAT 0.962283 -29 TCCTCTCTAGGTGATGAAATTTTTCGTATT 4 18 1 GTGATGAAAT 0.818137 -216 TCGTATTTTTGTGAAAAACTAACTTTTCAT 4 41 1 GTGAAAAACT 0.961691 -193 GATCACAGTTGTGAAAAAACGTAATAATGG 4 121 1 GTGAAAAAAC 0.967343 -113 CGTAATAATGGAGAAAGATTTTATAATTGA 4 140 1 GAGAAAGATT 0.820568 -94 CAATAGTTAAGTGAAGGACTAGTTATTGCT 4 204 0 GTGAAGGACT 0.970348 -30 ********** Masking position 4 Map Score: 4.73477 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 498 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 7 ********** No masking Map Score: -1.36181e-12 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: -1.36181e-12 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: -1.36181e-12 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