AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i081_PTS_cellobiose_specific_Transport_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 licB 127 phosphotransferase system (PTS) lichenan-specific enzyme IIB component #2 licR 162 transcriptional regulator (antiterminator) #3 yxzF 28 yxzF #4 yxlJ 128 similar to DNA-3-methyladenine glycosidase Motif number 1 ATTTTGTAATGTCCTGCTGTTGCTATCATC 1 82 0 GTCCTGCTGT 0.809788 -46 TCCCGGCTGTTTTTTTATAG 2 1 1 TCCCGGCTGT 0.954108 -162 AGGTCAGTTTTCCCTCTAGTCCTCCGGATG 2 29 1 TCCCTCTAGT 0.934081 -134 GACTTGCCATTCTCTCCATTATAGAATTTA 2 65 1 TCTCTCCATT 0.976873 -98 ACATTTCGCATCCCTTCATCATCCTTTCTG 2 98 1 TCCCTTCATC 0.966752 -65 CCCTTCATCATCCTTTCTGCCTATTCACTG 2 109 1 TCCTTTCTGC 0.844862 -54 ATTCACTGAATCCCTGCATCTACTAGTTAG 2 131 1 TCCCTGCATC 0.984966 -32 TGGTTGGCCCTCCTTTTTTGAACGGT 4 7 1 GCCCTCCTTT 0.986519 -122 TGTTTTAAAATCTTTCCATTCAGGGAATAT 4 41 0 TCTTTCCATT 0.879548 -88 GAATCGACCTCTCCTTTTACCGATTTT 4 112 0 CCTCTCCTTT 0.918162 -17 ********** Masking position 5 Map Score: 8.81986 Number of sites scoring better than the average of aligned sites = 2135 Number in coding regions = 1657 Number in noncoding regions = 478 Number of orfs with sites within 600 bp upstream = 493 Fraction of orfs with sites within 600 bp upstream = 0.0791841 Motif number 2 CGCAGCAACGGAAAAAAGGTATATACAGGC 1 13 0 GAAAAAAGGT 0.875663 -115 CGTTGCTGCGGAAAAACCCTGAGTGTTTAT 1 33 1 GAAAAACCCT 0.965962 -95 GTAAAAGACCCCCTAGAGTTTG 1 116 0 AAAAGACCCC 0.937244 -12 CTGACCTATAAAAAAACAGCCGGGA 2 6 0 AAAAAACAGC 0.958971 -157 GAGAAAAACCTCCTAACTAGTA 2 151 0 GAAAAACCTC 0.955532 -12 AGCAGATCAAAAAAAACGGCTGTTTTAAAA 4 61 0 AAAAAACGGC 0.989346 -68 TACAATGTACAAAAATCGGTAAAAGGAGAG 4 101 1 AAAAATCGGT 0.903235 -28 ********** Masking position 4 Map Score: 4.99384 Number of sites scoring better than the average of aligned sites = 1943 Number in coding regions = 1670 Number in noncoding regions = 273 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 3 TTATGAAATCGCTTTCATAAACACTCAGGG 1 49 0 GCTTTCATAA 0.977871 -79 TTATGAAAGCGATTTCATAATATGATGATA 1 59 1 GATTTCATAA 0.957431 -69 TCCTGCTGTTGCTATCATCATATTATGAAA 1 71 0 GCTATCATCA 0.9189 -57 AACAGCAGGACATTACAAAATTGATCAAAC 1 91 1 CATTACAAAA 0.844012 -37 GGAAAACTGACCTATAAAAAAACAGCCGGG 2 12 0 CCTATAAAAA 0.797987 -151 CATTTCGCATCCCTTCATCATCCTTTCTGC 2 99 1 CCCTTCATCA 0.891686 -64 AATATTGTTACCGTTCAAAAAAGGAGGGCC 4 16 0 CCGTTCAAAA 0.974481 -113 TGAATGGAAAGATTTTAAAACAGCCGTTTT 4 49 1 GATTTTAAAA 0.755759 -80 ATTCCCGAAGCAGATCAAAAAAAACGGCTG 4 69 0 CAGATCAAAA 0.910679 -60 ********** Masking position 7 Map Score: 5.14777 Number of sites scoring better than the average of aligned sites = 2201 Number in coding regions = 1894 Number in noncoding regions = 307 Number of orfs with sites within 600 bp upstream = 330 Fraction of orfs with sites within 600 bp upstream = 0.0530035 Motif number 4 TGCGGAAAAACCCTGAGTGTTTATGAAAGC 1 39 1 CCCTGAGTGT 0.991746 -89 TCTGCCTATTCACTGAATCCCTGCATCTAC 2 124 1 CACTGAATCC 0.973435 -39 TCCCCTGATTGCCTCTTCCTTA 3 17 0 CCCTGATTGC 0.995495 -12 TAACAATATTCCCTGAATGGAAAGATTTTA 4 36 1 CCCTGAATGG 0.993071 -93 ********** Masking position 6 Map Score: 3.30023 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 37 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 CAGCCTGTATATACCTTTTTTCCGTTGC 1 9 1 ATATACCTTT 0.928385 -119 AGTCCTCCGGATGTTCATTGACTTGCCATT 2 46 1 ATGTTCATTG 0.974559 -117 TATAGAATTTATATACATTTCGCATCCCTT 2 84 1 ATATACATTT 0.939795 -79 TCCTTTCTGCCTATTCACTGAATCCCTGCA 2 119 1 CTATTCACTG 0.945194 -44 AACGGTAACAATATTCCCTGAATGGAAAGA 4 31 1 ATATTCCCTG 0.969518 -98 TTACCGATTTTTGTACATTGTACCATTCCC 4 93 0 TTGTACATTG 0.921016 -36 ********** Masking position 4 Map Score: 2.67842 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 234 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 6 ********** No masking Map Score: 5.42445e-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 7 ********** No masking Map Score: 5.42445e-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: 5.42445e-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