AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_Polysaccharide_Biosynthesis_1_bsub_reg_300.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 yvfB 149 yvfB #2 yveR 24 similar to spore coat polysaccharide biosynthesis #3 yveM 258 similar to capsular polysaccharide biosynthesis #4 yveK 245 similar to capsular polysaccharide biosynthesis #5 spsA 300 alternate gene name: ipa-63d Motif number 1 TCTGATGGCGGGCTTCGGCGCTGCACCATT 1 84 1 GGCTTCGGCG 0.952685 -66 ACCATTTTATGCCAACCGCCTTTATATCAC 1 108 1 GCCAACCGCC 0.930832 -42 CAGCATCTAAGGCAGCAACTTCAGCTGCCC 3 68 0 GGCAGCAACT 0.958731 -191 GCCAGCGACGACCAGCATCTAAGGCAGCAA 3 80 0 ACCAGCATCT 0.818726 -179 CTCACGCCCCGCCAGCGACGACCAGCATCT 3 90 0 GCCAGCGACG 0.983254 -169 CCAAAAAATCGGCAGCAGCTAAACCGACAA 3 163 0 GGCAGCAGCT 0.669852 -96 TTATCGGTTTAGCTGCGGCGGTTTTCGTCT 3 195 0 AGCTGCGGCG 0.877534 -64 GGCGCGGGAAGCCAGCCGCGGGAAGGCTGA 4 213 1 GCCAGCCGCG 0.994392 -33 GTATTCATAGCCTTCAGCCTTCCCGCGGC 4 227 0 GCCTTCAGCC 0.914144 -19 TAAAAATCGCACCAGCGACTAAGATCGTTT 5 76 0 ACCAGCGACT 0.93633 -225 GCATAATCCAAGCATCAGCCTCATAAGGTG 5 113 0 AGCATCAGCC 0.879301 -188 TTTCGCTCTGGGCAGCCGCTGTTTTTCAGA 5 169 1 GGCAGCCGCT 0.918732 -132 ********** Masking position 6 Map Score: 19.0675 Number of sites scoring better than the average of aligned sites = 2672 Number in coding regions = 2498 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 2 CAGCACACTGCCGATTAAAATCGACAAACGCA 1 38 0 CCGAAAAATC 0.987984 -112 ATTTTTTGGAGAGACGAAAACCGCCGCAGCTA 3 184 1 GAGAAAAACC 0.971349 -75 TGCAGTAAATTAGAGGAAAATCATGATTTTGT 4 99 1 TAGAAAAATC 0.954779 -147 GTTCTCTTTAGAGAACAAAATCATGATTTTCC 4 113 0 GAGAAAAATC 0.991003 -133 TGACTCACCTCCGATGGAAAACGATCTTAGTC 5 58 1 CCGAGAAAAC 0.906247 -243 AATCGCACCAGCGACTAAGATCGTTTTCCATC 5 70 0 GCGAAAGATC 0.966313 -231 TAAGGTGAAAGAGATAAAAATCGCACCAGCGA 5 88 0 GAGAAAAATC 0.990998 -213 AGCGGCTGCCCAGAGCGAAATCTGATCGGTCC 5 157 0 CAGAGAAATC 0.979382 -144 **** ****** Masking position 8 Map Score: 9.37472 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 124 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 ATGTGCCGCAAGCGCTTTTGGCA 1 3 1 GTGCCGCAGC 0.966268 -147 AAACGCACATCTGCCAAAAGCGCTTGCGGCA 1 14 0 CTGCCAAAGC 0.99139 -136 TTAAAATAAACAGCACACTGCCGATTAAAAT 1 49 0 CAGCACATGC 0.886961 -101 GCACCATTTTATGCCAACCGCCTTTATATCA 1 106 1 ATGCCAACGC 0.908593 -44 GCCCACAGCAGAGCCGAGTGCCTCCATTGAT 3 41 0 GAGCCGATGC 0.955956 -218 GCAACTTCAGCTGCCCACAGCAGAGCCGAGT 3 53 0 CTGCCCAAGC 0.99616 -206 AAAACAGCGGCTGCCCAGAGCGAAATCTGAT 5 163 0 CTGCCCAAGC 0.99616 -138 ******* *** Masking position 4 Map Score: 6.22685 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 273 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 AGATGTGCGTTTGTCGATTTTAATCGGCAGT 1 33 1 TTGTCGATTT 0.568185 -117 GCGGGGCGTGAGGATGGGTTAAATGCCCACT 3 108 1 AGGATGGTTA 0.871639 -151 ATAGGACGTATTGTCGGTTTAGCTGCTGCCG 3 153 1 TTGTCGGTTA 0.960134 -106 CCTAATTCTTTTATCGGTTTAGCTGCGGCGG 3 204 0 TTATCGGTTA 0.949101 -55 AGGGGGGAAAAGGTTGAGTTACCGGAGAAGA 3 232 1 AGGTTGATTA 0.808536 -27 TAAAGAGAACTTATTGGCTTATTTTGCAATT 4 135 1 TTATTGGTTA 0.963335 -111 TTTCTGTTAATGATTGGATTATAAAAGAAAA 4 180 0 TGATTGGTTA 0.976589 -66 GAACATGTTTTGAATGGTTTT 5 1 0 TGAATGGTTT 0.786357 -300 ATGAGGCTGATGCTTGGATTATGCTGAAAAA 5 119 1 TGCTTGGTTA 0.93873 -182 AACTTTTCGCATATTGGTTTGTATCCCTAGC 5 209 1 ATATTGGTTG 0.759629 -92 ******* *** Masking position 9 Map Score: 4.19984 Number of sites scoring better than the average of aligned sites = 575 Number in coding regions = 488 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 TCGGCAGTGTGCTGTTTATTTTAACGTTTCTGATGGCG 1 56 1 GCTTTATTAT 0.944002 -94 TTATGCCAACCGCCTTTATATCACCAGTTCCATTCAGG 1 114 1 CGCTTATTAT 0.973424 -36 GGGTTAAATGCCCACTTATCTCATATATACATAGGACG 3 123 1 CCCTTATTAT 0.990646 -136 CCTTTTCCCCCCTAATTCTTTTATCGGTTTAGCTGCGG 3 207 0 CCTTTCTTAT 0.983328 -52 ACTGCACTTCCCTTATTATTTTAAATTTTATAAAGAAC 4 67 0 CCTTTATTAT 0.988726 -179 TAAAAGAAAACGTTATTATTTAAAAATTGCAAAATAAG 4 152 0 CGTTTATTAT 0.973517 -94 GCTTCCCGCGCCCCTTTCTGTTAATGATTGGATTATAA 4 187 0 CCCTTCTTAT 0.986162 -59 *** **** * * * Masking position 13 Map Score: 4.59829 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 62 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 GCAGCGCCGAAGCCCGCCATCAGAAACGTT 1 78 0 AGCCCGCCAT 0.907663 -72 TTGCACCGCCTGAATGGAACTG 1 138 0 GCACCGCCTG 0.992307 -12 AATGACCGGCTCCTCGTGCATAAA 2 7 0 GCTCCTCGTG 0.957948 -18 CCATCCTCACGCCCCGCCAGCGACGACCAG 3 95 0 GCCCCGCCAG 0.995013 -164 ATAGGTGAACGCTCCGCGATGACTCACCTC 5 39 1 GCTCCGCGAT 0.977207 -262 ATCCTACACCTCCTTCTTGGAACTT 5 286 0 ACACCTCCTT 0.903529 -15 ********** Masking position 5 Map Score: 2.14087 Number of sites scoring better than the average of aligned sites = 623 Number in coding regions = 576 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 7 CAGAAACGTTAAAATAAACAGCACACTGCC 1 58 0 AAAATAAACA 0.692224 -92 AAAATTCCTTATAATGAACGAAATAACGAC 4 35 0 ATAATGAACG 0.928964 -211 TTTAAATTTTATAAAGAACGAAAAATTCCT 4 56 0 ATAAAGAACG 0.972768 -190 TTTGTTCTCTAAAGAGAACTTATTGGCTTA 4 126 1 AAAGAGAACT 0.844158 -120 TTGGATTATAAAAGAAAACGTTATTATTTA 4 168 0 AAAGAAAACG 0.956663 -78 CTCACCTCCGATGGAAAACGATCTTAGTCG 5 61 1 ATGGAAAACG 0.854295 -240 GGTGAAAGAGATAAAAATCGCACCAGCGAC 5 87 0 ATAAAAATCG 0.801428 -214 GATTATGCTGAAAAAGAACAGCGGACCGAT 5 135 1 AAAAAGAACA 0.906932 -166 ********** Masking position 7 Map Score: 2.44024 Number of sites scoring better than the average of aligned sites = 733 Number in coding regions = 599 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 8 ********** No masking Map Score: -7.43638e-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: -7.43638e-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 10 ********** No masking Map Score: -7.43638e-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