AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i038_Galactose_Metabolism__bsub_reg_100.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 galK 80 galactokinase #2 ywcC 300 alternate gene name: ipa-33d #3 galE 114 UDP-glucose 4-epimerase Motif number 1 TATTTCTTCATAGAAAACGGCAGATCATAT 1 23 0 TAGAAAACGG 0.899533 -58 ATAAGGGGAATAAAAAATAAAAACCAGAAA 1 50 1 TAAAAAATAA 0.969009 -31 CCTATTCCCTAAAAAAATGACTAATATAAC 2 93 1 AAAAAAATGA 0.952384 -208 TTGTTTATTATTATAAATAAGGTCCATTGG 2 122 0 TTATAAATAA 0.873258 -179 TTATTTATAATAATAAACAATTAAATACTG 2 132 1 TAATAAACAA 0.890803 -169 TAGTATGTAAATGAAAATAAATCATTTAGC 2 168 1 ATGAAAATAA 0.823624 -133 ATTTAGCCTATTAAAAATGACCCCTGGGAA 2 191 1 TTAAAAATGA 0.965039 -110 ATAACCGTTTAAAGAAATAAATACCGCTAA 2 231 1 AAAGAAATAA 0.75119 -70 GCTAAAAAATATGAAAAAACTA 3 3 1 TAAAAAATAT 0.81482 -112 AAAAAACTATTAATAAACGATTAAACTTCT 3 24 1 TAATAAACGA 0.918558 -91 ATTAAACTTCTTAAAAATGGATGTGGACCG 3 43 1 TTAAAAATGG 0.93915 -72 ACACTATATAATGAAAACAGGTCATTTTTT 3 80 1 ATGAAAACAG 0.657187 -35 TAAACCCTCCTAAAAAATGACCTGTTTTCA 3 91 0 TAAAAAATGA 0.977378 -24 ********** Masking position 5 Map Score: 14.274 Number of sites scoring better than the average of aligned sites = 2131 Number in coding regions = 1578 Number in noncoding regions = 553 Number of orfs with sites within 600 bp upstream = 550 Fraction of orfs with sites within 600 bp upstream = 0.0883392 Motif number 2 GTTTTCTATGAAGAAATAAGGGGAATAAAA 1 35 1 AAGAAATAAG 0.8573 -46 GGGAATAAAAAATAAAAACCAGAAAGGTGA 1 55 1 AATAAAAACC 0.958179 -26 CACAAACTGAAGGAAAAACCACCTACCTAT 2 68 1 AGGAAAAACC 0.88681 -233 CCTTATTTATAATAATAAACAATTAAATAC 2 130 1 AATAATAAAC 0.839838 -171 ATAATAAACAATTAAATACTGACTGGATAG 2 141 1 ATTAAATACT 0.750221 -160 TGTAAATGAAAATAAATCATTTAGCCTATT 2 173 1 AATAAATCAT 0.520631 -128 CATTTAGCCTATTAAAAATGACCCCTGGGA 2 190 1 ATTAAAAATG 0.693489 -111 CGTTTAAAGAAATAAATACCGCTAAAGATT 2 236 1 AATAAATACC 0.93104 -65 GCTAAAAAATATGAAAAAACTATTAATAAA 3 11 1 ATGAAAAAAC 0.951866 -104 TGAAAAAACTATTAATAAACGATTAAACTT 3 22 1 ATTAATAAAC 0.839484 -93 ACACTATATAATGAAAACAGGTCATTTTTT 3 80 1 ATGAAAACAG 0.796405 -35 ********** Masking position 5 Map Score: 5.52707 Number of sites scoring better than the average of aligned sites = 2664 Number in coding regions = 2096 Number in noncoding regions = 568 Number of orfs with sites within 600 bp upstream = 516 Fraction of orfs with sites within 600 bp upstream = 0.0828783 Motif number 3 CTATGAAGAAATAAGGGGAATAAAAAATAAA 1 40 1 ATAAGGGAAT 0.989141 -41 ATTATTATAAATAAGGTCCATTGGTTATATT 2 115 0 ATAAGGTCAT 0.974242 -186 GTCATTTTTAATAGGCTAAATGATTTATTTT 2 181 0 ATAGGCTAAT 0.934226 -120 CCGGTGTAAGATAAGGGTAATCATTACCGCC 2 269 1 ATAAGGGAAT 0.988724 -32 TCCATTTTTAAGAAGTTTAATCGTTTATTAA 3 33 0 AGAAGTTAAT 0.905621 -82 ******* *** Masking position 3 Map Score: 0.970329 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 61 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 TTCACACATAGTTGCTCGGTGTTCACAAAC 2 45 1 GTTGCTCGGT 0.966761 -256 AAACGGTTATGCTATTCGGTTTCCCAGGGG 2 211 0 GCTATTCGGT 0.938506 -90 TATTTATTTCTTTAAACGGTTATGCTATTC 2 224 0 TTTAAACGGT 0.937709 -77 CCGCTAAAGATTGATCCGGTGTAAGATAAG 2 254 1 TTGATCCGGT 0.959606 -47 TTTTAAGAAGTTTAATCGTTTATTAATAGT 3 29 0 TTTAATCGTT 0.854742 -86 AAAAATGGATGTGGACCGGTTCTAAACACT 3 55 1 GTGGACCGGT 0.977961 -60 ********** Masking position 10 Map Score: 0.422932 Number of sites scoring better than the average of aligned sites = 488 Number in coding regions = 442 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 ********** No masking Map Score: 5.21128e-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: 5.21128e-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: 5.21128e-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