AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i038_bsub_mtub_300.orf -o038_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 galK 80 galactokinase #2 ywcC 300 alternate gene name: ipa-33d #3 galE 114 UDP-glucose 4-epimerase #4 yxkA 129 similar to hypothetical proteins #5 Rv0617 155 hypothetical protein Rv0617 #6 galT' 128 galT' Motif number 1 AATTTGTTGTACTCGCCTCCATCATCGCGC 2 16 0 ACTCGCCTCC 0.94401 -285 GGCGGCCAGGCCTCGTCGCATGAGGTCGGC 5 32 0 CCTCGTCGCA 0.974981 -124 TGCGACGAGGCCTGGCCGCCAACCGCCCTA 5 42 1 CCTGGCCGCC 0.989193 -114 GCGTCGGGACCGTCGTGACCTCCGAGGACG 5 114 1 CGTCGTGACC 0.976303 -42 TGTGCATCGTCTCCCGGCGGCGCG 6 5 1 CATCGTCTCC 0.973433 -124 GGGCGGCTCGCCGCGCCGCCGGGAGACGAT 6 16 0 CCGCGCCGCC 0.996765 -113 TATGCCTACGCATCGTGGCCCAATCGTTGG 6 51 0 CATCGTGGCC 0.985759 -78 GCTGAGGTGGCGTCGCGGCCCTCACCGGCG 6 81 1 CGTCGCGGCC 0.994445 -48 CGGCCCTCACCGGCGACACCACAGAGGATC 6 96 1 CGGCGACACC 0.924603 -33 ********** Masking position 9 Map Score: 14.2571 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 401 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 TTCTGGTTTTTATTTTTTATTCCCCTTATT 1 49 0 TATTTTTTAT 0.831861 -32 TATATTAGTCATTTTTTTAGGGAATAGGTA 2 91 0 ATTTTTTTAG 0.874126 -210 AAATAAGGTCCATTGGTTATATTAGTCATT 2 108 0 CATTGGTTAT 0.842729 -193 GTCAGTATTTAATTGTTTATTATTATAAAT 2 134 0 AATTGTTTAT 0.947743 -167 AATGAAAATAAATCATTTAGCCTATTAAAA 2 177 1 AATCATTTAG 0.661804 -124 TCCCAGGGGTCATTTTTAATAGGCTAAATG 2 190 0 CATTTTTAAT 0.749403 -111 AGTTTTTTCATATTTTTTAGC 3 2 0 TATTTTTTAG 0.872374 -113 TAAGAAGTTTAATCGTTTATTAATAGTTTT 3 26 0 AATCGTTTAT 0.901532 -89 GGTCCACATCCATTTTTAAGAAGTTTAATC 3 42 0 CATTTTTAAG 0.80513 -73 GAAAACAGGTCATTTTTTAGGAGGGTTTAC 3 92 1 CATTTTTTAG 0.952894 -23 TAAACGTAACAATTTGTTATGGATAACTTG 4 29 0 AATTTGTTAT 0.831827 -101 TTACATGCGTATTTGTTTATCACTGATTAT 4 56 1 ATTTGTTTAT 0.853427 -74 TTATACATCGATTCGTTTAGTATACCTATA 4 82 1 ATTCGTTTAG 0.802411 -48 ********** Masking position 9 Map Score: 10.3071 Number of sites scoring better than the average of aligned sites = 665 Number in coding regions = 474 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 3 CTTTCTGGTTTTTATTTTTTATTCCCCTTA 1 51 0 TTTATTTTTT 0.947865 -30 GGTTATATTAGTCATTTTTTTAGGGAATAG 2 94 0 GTCATTTTTT 0.953796 -207 TATTTAATTGTTTATTATTATAAATAAGGT 2 129 0 TTTATTATTA 0.636015 -172 GGCTAAATGATTTATTTTCATTTACATACT 2 169 0 TTTATTTTCA 0.842262 -132 TTTCCCAGGGGTCATTTTTAATAGGCTAAA 2 192 0 GTCATTTTTA 0.933776 -109 TTTAGCGGTATTTATTTCTTTAAACGGTTA 2 232 0 TTTATTTCTT 0.7913 -69 TAATAGTTTTTTCATATTTTTTAGC 3 6 0 TTCATATTTT 0.803133 -109 CCGGTCCACATCCATTTTTAAGAAGTTTAA 3 44 0 TCCATTTTTA 0.894905 -71 ATGAAAACAGGTCATTTTTTAGGAGGGTTT 3 90 1 GTCATTTTTT 0.953796 -25 AATCCCTCTCTCTATTTTCTCGTTCTATAG 4 107 0 TCTATTTTCT 0.770714 -23 ********** Masking position 5 Map Score: 6.93015 Number of sites scoring better than the average of aligned sites = 1418 Number in coding regions = 1106 Number in noncoding regions = 312 Number of orfs with sites within 600 bp upstream = 325 Fraction of orfs with sites within 600 bp upstream = 0.0522004 Motif number 4 CCTCCATCATCGCGCTGGCT 2 1 0 CGCGCTGGCT 0.833338 -300 CTCGTCGCATGAGGTCGGCGACCGTTTCAC 5 21 0 GAGGTCGGCG 0.903908 -135 TTGGCGGCCAGGCCTCGTCGCATGAGGTCG 5 34 0 GGCCTCGTCG 0.950325 -122 CGGTAGGGCGGTTGGCGGCCAGGCCTCGTC 5 45 0 GTTGGCGGCC 0.684952 -111 ACCGCCCTACCGCGTTGTCCTCAGACCCCA 5 63 1 CGCGTTGTCC 0.836795 -93 GGTGAGCGTCGGGACCGTCGTGACCTCCGA 5 109 1 GGGACCGTCG 0.965332 -47 TGTGCATCGTCTCCCGGCGGCG 6 3 1 TGCATCGTCT 0.756071 -126 CGTCTCCCGGCGGCGCGGCGAGCCGCCCCA 6 18 1 CGGCGCGGCG 0.604262 -111 TCGTTGGTTTTGGGGCGGCTCGCCGCGCCG 6 28 0 TGGGGCGGCT 0.908707 -101 GCTATGCCTACGCATCGTGGCCCAATCGTT 6 53 0 CGCATCGTGG 0.824201 -76 GCATAGCTGAGGTGGCGTCGCGGCCCTCAC 6 76 1 GGTGGCGTCG 0.949628 -53 CGTCGCGGCCCTCACCGGCGACACCACAGA 6 91 1 CTCACCGGCG 0.910751 -38 CGGATCGGCCCGAGATCCTC 6 119 0 CGGATCGGCC 0.970431 -10 ********** Masking position 7 Map Score: 5.61007 Number of sites scoring better than the average of aligned sites = 3939 Number in coding regions = 3735 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 5 GATCATATGCTGCAGTCCTC 1 1 0 TGCAGTCCTC 0.963858 -80 GCATATGATCTGCCGTTTTCTATGAAGAAA 1 21 1 TGCCGTTTTC 0.835784 -60 CTCTCTATTTTCTCGTTCTATAGGTATACT 4 100 0 TCTCGTTCTA 0.724047 -30 GTGAAACGGTCGCCGACCTCATGCGACGAG 5 21 1 CGCCGACCTC 0.915999 -135 GCGGTTGGCGGCCAGGCCTCGTCGCATGAG 5 38 0 GCCAGGCCTC 0.941597 -118 CCAAAGGCAATCCCGTTCTGGGGTCTGAGG 5 81 0 TCCCGTTCTG 0.934449 -75 TCTAATGAACGCACGTCCTCGGAGGTCACG 5 127 0 GCACGTCCTC 0.972557 -29 TGCTCGTCCTCTAATGAACGC 5 145 0 GCTCGTCCTC 0.98425 -11 ********** Masking position 9 Map Score: 2.00142 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 624 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 6 TTCACACATAGTTGCTCGGTGTTCACAAAC 2 45 1 GTTGCTCGGT 0.882997 -256 AAACGGTTATGCTATTCGGTTTCCCAGGGG 2 211 0 GCTATTCGGT 0.927879 -90 TATTTATTTCTTTAAACGGTTATGCTATTC 2 224 0 TTTAAACGGT 0.909062 -77 CCGCTAAAGATTGATCCGGTGTAAGATAAG 2 254 1 TTGATCCGGT 0.949586 -47 TTTTAAGAAGTTTAATCGTTTATTAATAGT 3 29 0 TTTAATCGTT 0.810105 -86 AAAAATGGATGTGGACCGGTTCTAAACACT 3 55 1 GTGGACCGGT 0.956577 -60 TGATTATACATCGATTCGTTTAGTATACCT 4 79 1 TCGATTCGTT 0.746367 -51 CGCACGTTGAGTGAAACGGTCGCCGACCTC 5 11 1 GTGAAACGGT 0.961759 -145 ********** Masking position 10 Map Score: 1.44291 Number of sites scoring better than the average of aligned sites = 679 Number in coding regions = 625 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 ********** No masking Map Score: -8.78641e-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: -8.78641e-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: -8.78641e-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