AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i128_Transmembrane_Transport_2_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 ytsC 101 similar to ABC transporter (ATP-binding protein) #2 yusC 300 similar to ABC transporter (ATP-binding protein) Motif number 1 AAAATGTCACATGCTTTTCTTTTTTGTTCG 1 13 1 ATGCTTTTCT 0.969047 -89 ATAAAAAGGAATGCCGGGCTTTTCCTTCGA 1 48 0 ATGCCGGGCT 0.995091 -54 ATTTAATCATTCGCCGTGCTATTCTACATT 2 37 1 TCGCCGTGCT 0.985709 -264 GTGTTGATGGTTGCCGGGCTTCATAGGGCA 2 125 0 TTGCCGGGCT 0.990358 -176 CTTATATAAAATGCCTTTCTCTCATCTTTC 2 194 0 ATGCCTTTCT 0.995873 -107 CATTTTATATAAGCCTTTCTGCTCAAGTGT 2 211 1 AAGCCTTTCT 0.992328 -90 TGCAAAAGAAAAGCCTTTCTGCACACTTGA 2 233 0 AAGCCTTTCT 0.992328 -68 ********** Masking position 10 Map Score: 14.7173 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 267 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 CGAAAATGTCACATGCTTTTCTTTTTTGTTC 1 11 1 AATGCTTTTC 0.948003 -91 TTATAAAAAGGAATGCCGGGCTTTTCCTTCG 1 49 0 GATGCCGGGC 0.984716 -53 ACATTTAATCATTCGCCGTGCTATTCTACAT 2 35 1 ATCGCCGTGC 0.9756 -266 CAGTGTTGATGGTTGCCGGGCTTCATAGGGC 2 126 0 GTTGCCGGGC 0.97585 -175 GGCTTATATAAAATGCCTTTCTCTCATCTTT 2 195 0 AATGCCTTTC 0.990428 -106 GGCATTTTATATAAGCCTTTCTGCTCAAGTG 2 209 1 AAAGCCTTTC 0.984416 -92 TCTGCAAAAGAAAAGCCTTTCTGCACACTTG 2 234 0 AAAGCCTTTC 0.95426 -67 * ********* Masking position 6 Map Score: 8.53818 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 554 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 3 CGGCGAACAAAAAAGAAAAGCATGTGACAT 1 16 0 AAAAGAAAAG 0.967882 -86 TCGCCGTATCGAAGGAAAAGCCCGGCATTC 1 40 1 GAAGGAAAAG 0.938563 -62 TCTCATTATAAAAAGGAATGCCGGGCTTTT 1 55 0 AAAAGGAATG 0.922961 -47 AAATGTCAATAAAATAAATGATGTCAACTT 2 11 0 AAAATAAATG 0.849212 -290 CTCTCTTGATAAGAGAAATATATAGTCTTT 2 84 0 AAGAGAAATA 0.888936 -217 TTCTCTTATCAAGAGAGGTGGAGGGAAGTG 2 97 1 AAGAGAGGTG 0.965573 -204 AAGAGAGGTGGAGGGAAGTGCCCTATGAAG 2 107 1 GAGGGAAGTG 0.970646 -194 TTTGAAAGATGAGAGAAAGGCATTTTATAT 2 191 1 GAGAGAAAGG 0.95254 -110 TTTTTTCTGCAAAAGAAAAGCCTTTCTGCA 2 240 0 AAAAGAAAAG 0.967882 -61 GAATAGTGTTAAGGCAGGTGATTGCT 2 285 1 AAGGCAGGTG 0.74369 -16 ********** Masking position 2 Map Score: 9.89645 Number of sites scoring better than the average of aligned sites = 2635 Number in coding regions = 2131 Number in noncoding regions = 504 Number of orfs with sites within 600 bp upstream = 501 Fraction of orfs with sites within 600 bp upstream = 0.080469 Motif number 4 CGAAAATGTCACATGCTTTTC 1 2 1 GAAAATGTCA 0.945067 -100 CTTTATATTGGATAATCTCATTATAAAAAG 1 70 0 GATAATCTCA 0.941438 -32 CAATAAAATAAATGATGTCAACTT 2 5 0 AATGATGTCA 0.982639 -296 ACACTGTTGAAATGGTGCCAATTCACACGA 2 151 1 AATGGTGCCA 0.964946 -150 GATTTCTTAGAATAGTGTTAAGGCAGGTGA 2 276 1 AATAGTGTTA 0.915592 -25 ********** Masking position 6 Map Score: 0.175117 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 555 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 ********** No masking Map Score: 6.84553e-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: 6.84553e-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: 6.84553e-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