AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i127_Transmembrane_Transport_1_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 yurN 57 similar to sugar permease #2 yurO 80 similar to multiple sugar-binding protein #3 yurP 215 similar to opine catabolism #4 msmX 120 multiple sugar-binding transport ATP-binding protein Motif number 1 GCATTAGACTATAATGTTATATAACATTAT 2 33 1 ATAATGTTAT 0.557391 -48 ACATTAGACTATAATGTTATATAACATTAT 2 43 0 ATAATGTTAT 0.557391 -38 ATAACATTATATATTGTTATATTAAAGTCC 3 161 0 ATATTGTTAT 0.836281 -55 ATAACAATATATAATGTTATATAACGTTAT 3 171 1 ATAATGTTAT 0.557391 -45 ATAATGTTATATAACGTTATATAATAAAAA 3 181 1 ATAACGTTAT 0.499953 -35 ********** Masking position 7 Map Score: 13.4531 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 6 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 2 GCGAAGCTTCACCTTTTCTTTGAT 1 5 0 ACCTTTTCTT 0.991401 -53 GAAGCTTCGCACCTTTTCTTTTTATAAAGG 1 25 1 ACCTTTTCTT 0.991401 -33 TCGCATATAGACCCTTTGTCTGTCATCCGA 3 83 1 ACCCTTTGTC 0.987707 -133 GTTATTGTAAACGCTTTCTTATATTGAGTG 4 86 0 ACGCTTTCTT 0.986627 -35 CTAACATCCCCCTTTGTTATTGTAAACG 4 103 0 CCCCTTTGTT 0.987707 -18 ********** Masking position 5 Map Score: 7.03802 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 60 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 3 GTTATATAACATTATAGTCTAATGCATAAT 2 28 0 ATTATAGTCT 0.992371 -53 GTTATATAACATTATAGTCTAATGTCCAGA 2 48 1 ATTATAGTCT 0.992371 -33 GATTGTCAATATTATTTTCTGAAATTTCTC 3 123 0 ATTATTTTCT 0.9285 -93 ATATTGTTATATTAAAGTCCGCGGGTAGGA 3 151 0 ATTAAAGTCC 0.968109 -65 ********** Masking position 4 Map Score: 3.26838 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 28 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 GACGTCAGTCTGCGGATTGAACAGCGAA 3 5 1 TCAGCGCGAT 0.988685 -211 TGACTTAAGCTCTGGCTTCGCTGTTCAATCCGCA 3 21 0 TCTGCTCGTT 0.991456 -195 TAAGTCAAGTTCTGGCTTTTGATTTGGGCATTTT 3 48 1 TCTGCTTTAT 0.804201 -168 AGACCCTTTGTCTGTCATCCGAATAAATTATTGA 3 91 1 TCTGCTCCAT 0.979992 -125 TATTGACAATCCTACCCGCGGACTTTAATATAAC 3 142 1 CCTACGCGAT 0.852739 -74 ATCCTTCACTCCTCGTTTTTATTATATAA 3 197 0 TCACCTCGTT 0.98548 -19 GTTCATAAAATCACCCAGCCATTTTTCGTGCATA 4 19 0 TCACCGCCTT 0.965601 -102 CTAACATCCCCCTTTGTTATTGTAAACGCT 4 101 0 TCCCCTTGTT 0.901046 -20 **** * *** * * Masking position 14 Map Score: 1.88061 Number of sites scoring better than the average of aligned sites = 808 Number in coding regions = 736 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 TATAGTCTAATGTCCAGAGGAGGCCAACCC 2 60 1 TGTCCAGAGG 0.967575 -21 TTGAACAGCGAAGCCAGAGCTTAAGTCAAG 3 27 1 AAGCCAGAGC 0.995078 -189 CCCAAATCAAAAGCCAGAACTTGACTTAAG 3 46 0 AAGCCAGAAC 0.980729 -170 CTGCCCATTTTAGCGAGAGGGAATTGCTGT 4 54 1 TAGCGAGAGG 0.986915 -67 ********** Masking position 6 Map Score: 1.12628 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 114 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 TATAACATTATAGTCTAATGCATAATGGTT 2 24 0 TAGTCTAATG 0.990963 -57 TATAACATTATAGTCTAATGTCCAGAGGAG 2 52 1 TAGTCTAATG 0.990963 -29 CTCAATAATTTATTCGGATGACAGACAAAG 3 96 0 TATTCGGATG 0.951416 -120 ********** Masking position 8 Map Score: 0.743591 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 3 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 ********** No masking Map Score: -8.28903e-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: -8.28903e-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: -8.28903e-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