AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -icytR_tpal_opreg_100.orf -g0.528 -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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0261 114 catabolite gene activator, putative #2 TP0734 81 purine nucleoside phosphorylase (deoD) #3 TP0736 233 hydrogenase, gamma chain (hydG) #4 TP1027 121 uridine phosphorylase (udp) Motif number 1 TGCAGAGATCGTTCGCACGCCTTTTCCAGG 1 19 0 GTTCGCACGC 0.873973 -96 TCACGCGCTCCTGCGCGCACACCTGCAGAG 1 42 0 CTGCGCGCAC 0.678459 -73 CCAGAATTCACGTCACGCGCTCCTGCGCGC 1 54 0 CGTCACGCGC 0.99548 -61 TCGATAGAACGGTCATGCACTTAAGTCTTT 1 86 0 GGTCATGCAC 0.684797 -29 CGGGTGCTGCATGCGCTGAGCGTACA 2 7 1 CTGCATGCGC 0.967725 -75 TGCGCTGAGCGTACACGCGCGAGGTTACCG 2 22 1 GTACACGCGC 0.964184 -60 CGTCACTCCCTCCCTTCGTG 2 72 0 CGTCACTCCC 0.96976 -10 TGAATGAGGACTGCACGCAAAACCTGCCAG 3 74 1 CTGCACGCAA 0.936537 -160 TTTGACAAATCTGCATTCGCTGTACTATCA 3 176 1 CTGCATTCGC 0.980341 -58 GTAAGGTGCACAGCACTCCCCAGTCACGAA 4 85 0 CAGCACTCCC 0.940493 -37 ********** Masking position 4 Map Score: 14.4815 Number of sites scoring better than the average of aligned sites = 2088 Number in coding regions = 1945 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 2 CACGCCTTTTCCAGGAAAGGTGG 1 3 0 CCGGAAAGGT 0.95324 -112 TGAGCGTACACGCGCGAGGTTACCGAAACGT 2 27 1 CGGCGAGGTT 0.966561 -55 GGTCTAGGCCCCACGAAGGGAGGGAGTGACG 2 61 1 CCCGAAGGGA 0.983588 -21 GATATACGTGTCGGGGAGGTTTAC 3 4 0 TCGGGAGGTT 0.965043 -230 GCCATCGGCGCCGAGAAGGGTCCGATGAACA 3 35 0 CCAGAAGGGT 0.987847 -199 ATCATTGTTTCCTGGCAGGTTTTGCGTGCAG 3 84 0 CCGGCAGGTT 0.973416 -150 TCAGCTCTGTCGCACAAGGCAACTAACGCGC 3 132 0 CGACAAGGCA 0.809175 -102 TCGACCAAACTCTCGGAGGGATGGATGATAG 3 200 0 TCCGGAGGGA 0.953117 -34 AGAGTTTGGTCGAAGGAGGCATGGCT 3 218 1 CGAGGAGGCA 0.968902 -16 ATCCCGACCACGGGGGACGGTGACAGGTAGT 4 52 0 CGGGGACGGT 0.975717 -70 ** ******** Masking position 7 Map Score: 8.67651 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 521 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 CGTTCGCACGCCTTTTCCAGGAAAGGTGG 1 10 0 CCTTTTCCAG 0.983785 -105 GCACTTAAGTCTTTTTCCAGAATTCACGTC 1 70 0 CTTTTTCCAG 0.992623 -45 CCGACCGCTGCTTTTCTCATCATTGTTTCC 3 103 0 CTTTTCTCAT 0.961457 -131 AAAGAAAAGCCTTTCTTCAGCTCTGTCGCA 3 149 0 CTTTCTTCAG 0.982512 -85 ATCTTTTACCCTTTTTTCATAGAC 4 5 0 CTTTTTTCAT 0.982261 -117 ********** Masking position 4 Map Score: 5.84141 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 52 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 GAACGGTCATGCACTTAAGTCTTTTTCCAGA 1 79 0 GCACTTAGTC 0.883416 -36 GGTGCTGCATGCGCTGAGCGTACACGCGCGA 2 13 1 GCGCTGACGT 0.716271 -69 ACCCTTCTCGGCGCCGATGGCGTTTTGCTTG 3 45 1 GCGCCGAGGC 0.994638 -189 GCTTGAATGAGGACTGCACGCAAAACCTGCC 3 71 1 GGACTGCCGC 0.966195 -163 GGCAACTAACGCGCCGACCGCTGCTTTTCTC 3 115 0 GCGCCGACGC 0.958434 -119 GGAGTGCTGTGCACCTTACGCTTAAAGGGGA 4 96 1 GCACCTTCGC 0.97799 -26 ******* *** Masking position 4 Map Score: 3.88872 Number of sites scoring better than the average of aligned sites = 673 Number in coding regions = 621 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 CCGAAACGTGTGGGTCTAGGCCCCACGAAG 2 49 1 TGGGTCTAGG 0.979217 -33 AACAGATATACGTGTCGGGGAGGTTTAC 3 9 0 CGTGTCGGGG 0.988765 -225 CGAATGCAGATTTGTCAAAGAAAAGCCTTT 3 165 0 TTTGTCAAAG 0.873817 -69 CTCCGAGAGTTTGGTCGAAGGAGGCATGGC 3 213 1 TTGGTCGAAG 0.958005 -21 TAGTTCTCTTTTTGGCGAGGCATCTTTTAC 4 26 0 TTTGGCGAGG 0.973412 -96 CGGGATTCTTCGTGACTGGGGAGTGCTGTG 4 77 1 CGTGACTGGG 0.922315 -45 ********** Masking position 6 Map Score: 0.972811 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 163 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 ********** No masking Map Score: -8.36008e-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: -8.36008e-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: -8.36008e-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