AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -ipurR_rpxx_opreg_100.orf -g0.290 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP541 62 3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE (ubiX) #2 RP743 79 SERINE HYDROXYMETHYLTRANSFERASE (glyA) #3 RP744 102 unknown #4 RP760 300 unknown Motif number 1 ATATAAATATATTTTATATTGTTTTT 1 6 1 AATTATTTTA 0.713443 -57 TATTTTATATTGTTTTTATTATATACTAAAT 1 20 1 TGTTTTATTA 0.974983 -43 TTTAATTCATTAAATTTAGTATATAATAAAA 1 33 0 TAATTTAGTA 0.918848 -30 CATCCTCATATGTTTTTAGTATTTATCTGTA 2 58 0 TGTTTTAGTA 0.981242 -22 ATATTAAAGTTGAGTATATTAAATGAATAGC 3 50 0 TGATATATTA 0.931271 -53 CTTTATTTCATATGTTTATTACTTTAATATT 3 76 0 TATTTTATTA 0.934727 -27 AGATAAAAACAGAATTTTTTATTATGAAAGC 4 47 0 AGATTTTTTA 0.871408 -254 AACATCTTATAATTTTTATTAAATAATGATG 4 107 1 AATTTTATTA 0.944498 -194 TATACTGATGAGAATATAGTACTGCTTAATT 4 243 0 AGATATAGTA 0.955772 -58 TATTCTCATCAGTATATAGTACTGTTGAAGG 4 258 1 AGTTATAGTA 0.973441 -43 CTGTTGAAGGAGTTTTTAGAAAAGGTTATAT 4 279 1 AGTTTTAGAA 0.887622 -22 *** ******* Masking position 11 Map Score: 12.2976 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 353 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 2 CAATATAAAATATATTTATAT 1 2 0 TATATTTATA 0.716437 -61 TATTTTATATTGTTTTTATTATATACTAAA 1 20 1 TGTTTTTATT 0.98156 -43 TCTAGTCGTTTATTTTTCTTTGTACTGTAG 2 19 1 TATTTTTCTT 0.849639 -61 CATCCTCATATGTTTTTAGTATTTATCTGT 2 59 0 TGTTTTTAGT 0.974295 -21 CTTTATTTCATATGTTTATTACTTTAATAT 3 77 0 TATGTTTATT 0.929768 -26 TAAAAACAGAATTTTTTATTATGAAAGCAG 4 45 0 ATTTTTTATT 0.788541 -256 TAAAAAATTCTGTTTTTATCTTGACAAAAG 4 57 1 TGTTTTTATC 0.942463 -244 TATAAGATGTTGTGTTTAGAGCACATTAAT 4 88 0 TGTGTTTAGA 0.906705 -213 AACATCTTATAATTTTTATTAAATAATGAT 4 107 1 AATTTTTATT 0.924581 -194 CTGTTGAAGGAGTTTTTAGAAAAGGTTATA 4 279 1 AGTTTTTAGA 0.900029 -22 ********** Masking position 5 Map Score: 9.29304 Number of sites scoring better than the average of aligned sites = 795 Number in coding regions = 498 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 3 ACAAAGAGCCTATACTGTAGCACTTA 3 6 0 TATATGTAGC 0.9899 -97 ATTAGCAAGTTATATTGTGACACCACGTATC 4 15 1 TATATGTGAC 0.989964 -286 AATGATGGCTAATATTATGGCACCGATAAAT 4 131 1 AATATATGGC 0.92829 -170 TGGCGTATATTATAAGGTAACCACTTACAAT 4 201 0 TATAGGTAAC 0.951741 -100 TTAATTTATGTATAATGTGGCGTATATTATA 4 218 0 TATATGTGGC 0.995521 -83 **** ****** Masking position 4 Map Score: 3.7192 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 8 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 TTATTATATACTAAATTTAATGAATTAAAG 1 35 1 CTAAATTTAA 0.910452 -28 TTAAATTTCTTTAATTCATTAAATTTAG 1 45 0 CTTTAATTCA 0.927429 -18 GGTTTACTTTATTTCATATGTTTATT 3 87 0 CTTTATTTCA 0.981058 -16 TATTAGCCATCATTATTTAATAAAAATTAT 4 115 0 CATTATTTAA 0.922104 -186 TGCGTTATACCTATATTTGACAATGAAATT 4 174 1 CTATATTTGA 0.937769 -127 TATAGTACTGCTTAATTTATGTATAATGTG 4 230 0 CTTAATTTAT 0.862807 -71 ********** Masking position 5 Map Score: 2.30076 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 106 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 TTCATTAAATTTAGTATATAATAAAAACAA 1 29 0 TTAGTATATA 0.973323 -34 TTAGTATTTATCTGTATATGTGTTACTACA 2 44 0 TCTGTATATG 0.861935 -36 TCATATGTTTTTAGTATTTATCTGTATATG 2 54 0 TTAGTATTTA 0.883373 -26 ATATTAAAGTTGAGTATATTAAATGAATAG 3 51 0 TGAGTATATT 0.933017 -52 ATACGTGGTGTCACAATATAACTTGCTAAT 4 15 0 TCACAATATA 0.873066 -286 TATATACTGATGAGAATATAGTACTGCTTA 4 246 0 TGAGAATATA 0.960879 -55 TATATTCTCATCAGTATATAGTACTGTTGA 4 256 1 TCAGTATATA 0.987975 -45 ********** Masking position 6 Map Score: 5.52058 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 103 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 ********** No masking Map Score: 4.50646e-14 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: 4.50646e-14 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: 4.50646e-14 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