AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -ipurR_rpxx_opreg_300.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 RP745 52 GLUTAREDOXIN-LIKE PROTEIN GRLA (grxC2) #5 RP760 300 unknown Motif number 1 ATATAAATATATTTTATATTGTTTTT 1 6 1 AATTATTTTA 0.786334 -57 TATTTTATATTGTTTTTATTATATACTAAAT 1 20 1 TGTTTTATTA 0.969779 -43 TTTAATTCATTAAATTTAGTATATAATAAAA 1 33 0 TAATTTAGTA 0.861425 -30 CATCCTCATATGTTTTTAGTATTTATCTGTA 2 58 0 TGTTTTAGTA 0.973806 -22 ATATTAAAGTTGAGTATATTAAATGAATAGC 3 50 0 TGATATATTA 0.923609 -53 CTTTATTTCATATGTTTATTACTTTAATATT 3 76 0 TATTTTATTA 0.911901 -27 TGCTATAGAAAGTGTATTTTAGAAAATAATA 4 15 1 AGTTATTTTA 0.91942 -38 AGATAAAAACAGAATTTTTTATTATGAAAGC 5 47 0 AGATTTTTTA 0.890672 -254 AACATCTTATAATTTTTATTAAATAATGATG 5 107 1 AATTTTATTA 0.934424 -194 TATACTGATGAGAATATAGTACTGCTTAATT 5 243 0 AGATATAGTA 0.950694 -58 TATTCTCATCAGTATATAGTACTGTTGAAGG 5 258 1 AGTTATAGTA 0.973806 -43 CTGTTGAAGGAGTTTTTAGAAAAGGTTATAT 5 279 1 AGTTTTAGAA 0.855656 -22 *** ******* Masking position 11 Map Score: 14.3474 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 337 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 2 ATATAAATATATTTTATATTGT 1 1 1 ATAAAAATAT 0.678462 -62 TTAGTATATAATAAAAACAATATAAAATATAT 1 17 0 ATAAAAAATA 0.875421 -46 TTTTTATTATATACTAAATTTAATGAATTAAA 1 32 1 ATATAATTTA 0.618634 -31 TTAATGAATTAAAGAAATTTAA 1 51 1 AAAAAATTAA 0.77582 -12 ACTACAGTACAAAGAAAAATAAACGACTAGAT 2 18 0 AAAAAAATAA 0.870465 -62 GTAGTAACACATATACAGATAAATACTAAAAA 2 45 1 ATAACAATAA 0.943087 -35 GATAAATACTAAAAACATATGAGGATGC 2 62 1 AAAACAATGA 0.813694 -18 TATTAAAGTAATAAACATATGAAATAAAGTAA 3 78 1 ATAACAATGA 0.942004 -25 ATATTGCTATAGAAAGTGTATTTTAGAAAA 4 9 1 ATAAAATGTA 0.848444 -44 TCAAAACCTGATATAAATATTATTTTCTAAAA 4 31 0 ATAAAAATTA 0.971615 -22 TTTTGTCAAGATAAAAACAGAATTTTTTATTA 5 54 0 ATAAAAAGAA 0.887586 -247 TCATTATTTAATAAAAATTATAAGATGTTGTG 5 104 0 ATAAAATATA 0.783506 -197 GGTATAACGCATTTAAAGTTTACATTTATCGG 5 153 0 ATTAAATTTA 0.618634 -148 ACGCCACATTATACATAAATTAAGCAGTACTA 5 226 1 ATAATAATTA 0.813831 -75 CAACAGTACTATATACTGATGAGAATATAGTA 5 253 0 ATAACTATGA 0.597903 -48 *** *** **** Masking position 1 Map Score: 10.4995 Number of sites scoring better than the average of aligned sites = 1349 Number in coding regions = 835 Number in noncoding regions = 514 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 3 ATATAAATATATTTTATATTG 1 2 1 TATAAATATA 0.711164 -61 TAGTAACACATATACAGATAAATACTAAAA 2 46 1 TATACAGATA 0.948775 -34 ATAAATACTAAAAACATATGAGGATGC 2 63 1 AAAACATATG 0.87549 -17 ATTAAAGTAATAAACATATGAAATAAAGTA 3 79 1 TAAACATATG 0.939457 -24 CAAAACCTGATATAAATATTATTTTCTAAA 4 32 0 TATAAATATT 0.638949 -21 ATTATTTAATAAAAATTATAAGATGTTGTG 5 104 0 AAAAATTATA 0.52847 -197 ATTTTTATTAAATAATGATGGCTAATATTA 5 118 1 AATAATGATG 0.71093 -183 TTAAATGCGTTATACCTATATTTGACAATG 5 169 1 TATACCTATA 0.858279 -132 TACGCCACATTATACATAAATTAAGCAGTA 5 225 1 TATACATAAA 0.788458 -76 AACAGTACTATATACTGATGAGAATATAGT 5 254 0 TATACTGATG 0.926929 -47 ********** Masking position 4 Map Score: 4.78174 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 285 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 4 ATTTTATATTGTTTTTATTATATACTAAAT 1 21 1 GTTTTTATTA 0.861276 -42 GTATCTAGTCGTTTATTTTTCTTTGTACTG 2 16 1 GTTTATTTTT 0.909924 -64 TATTAAAGTTGAGTATATTAAATGAATAGC 3 50 0 GAGTATATTA 0.889053 -53 GGTTTACTTTATTTCATATGT 3 92 0 GTTTACTTTA 0.947649 -11 GCTATAGAAAGTGTATTTTAGAAAATAATA 4 16 1 GTGTATTTTA 0.963461 -37 AATAATGATGGCTAATATTATGGCACCGAT 5 128 1 GCTAATATTA 0.858866 -173 CGCATTTAAAGTTTACATTTATCGGTGCCA 5 148 0 GTTTACATTT 0.875739 -153 GTATAATGTGGCGTATATTATAAGGTAACC 5 210 0 GCGTATATTA 0.96955 -91 ATATAGTACTGCTTAATTTATGTATAATGT 5 231 0 GCTTAATTTA 0.866756 -70 ********** Masking position 8 Map Score: 7.15222 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 187 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 5 GTATATGTGTTACTACAGTACAAAGAAAAA 2 31 0 TACTACAGTA 0.708832 -49 TAAGTGCTACAGTATAGGCTCTTT 3 5 1 TGCTACAGTA 0.963303 -98 TCAACTTTAATATTAAAGTAATAAACATAT 3 68 1 TATTAAAGTA 0.773409 -35 ATATTGCTATAGAAAGTGTATTTT 4 5 1 TGCTATAGAA 0.624982 -48 AAATATTATTTTCTAAAATACACTTTCTAT 4 19 0 TTCTAAAATA 0.817959 -34 CAATATAACTTGCTAATGTAT 5 2 0 TGCTAATGTA 0.940795 -299 TAAAAACTCCTTCAACAGTACTATATACTG 5 267 0 TTCAACAGTA 0.901474 -34 ********** Masking position 5 Map Score: 4.4232 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 189 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 ********** No masking Map Score: -7.08111e-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: -7.08111e-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: -7.08111e-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