AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_rpxx_reg_300.orf -o00400_rpxx_300.ace -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -g0.29 -x5 -e 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 = 1 Input sequences: #1 RP091 174 ASPARTATE AMINOTRANSFERASE A (aatA) #2 RP415 300 DIAMINOPIMELATE EPIMERASE (dapF) #3 RP417 106 PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN (pheS) #4 RP556 300 TYROSYL-TRNA SYNTHETASE (tyrS) Motif number 1 TACTAAATTCATATTATTTACACTATAATAAAGC 1 19 1 ATATTTAACT 0.900588 -156 ATTTATTAAGATATGCTTTATTATAGTGTAAATA 1 33 0 ATATTTATAT 0.934376 -142 CAATAAAATTATTTTATTTAAAAATTTATTAAGA 1 56 0 ATTTTTAAAA 0.73943 -119 TTGAGATTAAAATTGCTGTATTATCGTTTATTAT 1 87 1 AATTTTATAT 0.504775 -88 TCGGATTCTTATATACTTTAGAATAACATTAATA 1 118 0 ATATTTAAAT 0.97781 -57 AGCACTAACAACATGAAATAAAATCAATTCA 2 8 0 ACATATAAAT 0.862863 -293 GATTGATATAATAAAGTCTAATAAAACACCAATA 2 67 0 ATAATTATAA 0.744673 -234 ACTTATTTATATATCAATTAAAATGTTATTTAGC 2 108 1 ATATATAAAT 0.945569 -193 GTCTTACTGCAAATTTTTTAAAATACTAGTTATT 2 164 1 AAATTTAAAT 0.962977 -137 TGAGGATAAAATATAGACTATTATACTAATTTCA 2 216 0 ATATATATAT 0.879929 -85 AAATTTCTTTAAATTTACTATAATGAATTGAGGA 2 244 0 AAATATAAAT 0.930404 -57 TTACATATTAAAAATTTGTATTATAGCAAATTTC 2 271 0 AAAATTATAT 0.73501 -30 TTATATATTGTATACAGGATCAACAA 3 3 1 ATATTTAACA 0.850299 -104 CAATGTTGAGATAAAATCTAAAAACAAAAAATAA 3 81 1 ATAATTAAAA 0.899575 -26 AATCATGTTAATATAATATATAGTG 4 2 0 ATATTTAAGT 0.89885 -299 TATTATATTAACATGATTTATAAATTAAGTGAGT 4 18 1 ACATTTAAAA 0.888717 -283 GATAATCAATATATCAAGTATAGACAAAGTTTTC 4 72 1 ATATATAAGA 0.743688 -229 CAAAGTTTTCATATACTTTATAATAAATTAAATA 4 96 1 ATATTTAAAT 0.977754 -205 ACTTTATAATAAATTAAATATAATGGTAATGTTA 4 110 1 AAATATAAAT 0.921285 -191 TTTATTTGTCAAAATCTCTAAAAAGACCATAAAG 4 227 1 AAAATTAAAA 0.841765 -74 TAGAAAAACCAAAAACAATATAAATAAT 4 283 1 AAAAATAAAA 0.731001 -18 **** * ** *** Masking position 9 Map Score: 24.332 Number of sites scoring better than the average of aligned sites = 1485 Number in coding regions = 895 Number in noncoding regions = 590 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 2 AGTTTAATTACTAAATTCATATTATTT 1 8 1 TTACTAAATT 0.874044 -167 AAAGCATATCTTAATAAATTTTTAAATAAA 1 48 1 TTAATAAATT 0.793637 -127 GAGATTAAAATTGCTGTATTATCGTTTATT 1 89 1 TTGCTGTATT 0.831518 -86 CATGTTGTTAGTGCTAAAAAGCTAAACACG 2 27 1 GTGCTAAAAA 0.736001 -274 TATCCTAAGATTGATATAATAAAGTCTAAT 2 79 0 TTGATATAAT 0.952757 -222 AACATTTTAATTGATATATAAATAAGTATC 2 105 0 TTGATATATA 0.952801 -196 ATAATAATCATTGCTAAATAACATTTTAAT 2 124 0 TTGCTAAATA 0.963285 -177 TTCTTTAAATTTACTATAATGAATTGAGGA 2 244 0 TTACTATAAT 0.897266 -57 TTAAAGAAATTTGCTATAATACAAATTTTT 2 266 1 TTGCTATAAT 0.973665 -35 CAACATAACTTTGCTAAATAGTCCAGTGAA 3 48 0 TTGCTAAATA 0.963285 -59 TGTAACAATGTTGAGATAAAATCTAAAAAC 3 76 1 TTGAGATAAA 0.698385 -31 ATAAATCATGTTAATATAATATATAGTG 4 9 0 TTAATATAAT 0.82816 -292 ATTAACATGATTTATAAATTAAGTGAGTTA 4 24 1 TTTATAAATT 0.673314 -277 TTGTCTATACTTGATATATTGATTATCATA 4 69 0 TTGATATATT 0.95828 -232 GGTAATGTTATTGCTATAAAACTAGACCCT 4 134 1 TTGCTATAAA 0.969407 -167 TTTAGAGATTTTGACAAATAAAGCTATTTT 4 219 0 TTGACAAATA 0.648392 -82 GTTTTTGGTTTTTCTATAAACAGTTTTCTC 4 269 0 TTTCTATAAA 0.758305 -32 ********** Masking position 8 Map Score: 21.3762 Number of sites scoring better than the average of aligned sites = 841 Number in coding regions = 607 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 3 TTATAGTGTAAATAATATGAATTTAGTAAT 1 17 0 AATAATATGA 0.918886 -158 TTTTAATCTCAATAAAATTATTTTATTTAA 1 69 0 AATAAAATTA 0.786405 -106 TATACTTTAGAATAACATTAATAATAAACG 1 111 0 AATAACATTA 0.970562 -64 TTTTAGCACTAACAACATGAAATAAAATCA 2 16 0 AACAACATGA 0.962072 -285 ACTTTATTATATCAATCTTAGGATACTTAT 2 84 1 ATCAATCTTA 0.714997 -217 ATCATTGCTAAATAACATTTTAATTGATAT 2 118 0 AATAACATTT 0.792481 -183 TGTATACAGGATCAACAATATTGTATTGAT 3 19 1 ATCAACAATA 0.695314 -88 TATATATTATATTAACATGATTTATAAATT 4 14 1 ATTAACATGA 0.957261 -287 AAGTGAGTTAATTAATATGAGCTTGTATGA 4 44 1 ATTAATATGA 0.891645 -257 GTTTTATAGCAATAACATTACCATTATATT 4 126 0 AATAACATTA 0.970562 -175 GCTTTTTAAAATTAACCTTAAGGCCTTATT 4 168 0 ATTAACCTTA 0.892476 -133 AAAAACCAAAAACAATATAAATAAT 4 286 1 AACAATATAA 0.641039 -15 ********** Masking position 5 Map Score: 12.4711 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 283 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 4 TTTTATTTAAAAATTTATTAAGATATGCTT 1 49 0 AAATTTATTA 0.841032 -126 TATTGAGATTAAAATTGCTGTATTATCGTT 1 85 1 AAAATTGCTG 0.955295 -90 AAAGATAATAATCATTGCTAAATAACATTT 2 128 0 ATCATTGCTA 0.776949 -173 GTATTTTAAAAAATTTGCAGTAAGACAAAA 2 160 0 AAATTTGCAG 0.814884 -141 AAATTTCTTTAAATTTACTATAATGAATTG 2 248 0 AAATTTACTA 0.92536 -53 AAATTTAAAGAAATTTGCTATAATACAAAT 2 262 1 AAATTTGCTA 0.977748 -39 GAATCAATACAATATTGTTGATCCTGTATA 3 21 0 AATATTGTTG 0.654363 -86 GTTACAACATAACTTTGCTAAATAGTCCAG 3 52 0 AACTTTGCTA 0.973149 -55 ATTTTATCTCAACATTGTTACAACATAACT 3 68 0 AACATTGTTA 0.913528 -39 AAGCAGCAATAAATTTATTAGCAGGAAAAT 4 194 1 AAATTTATTA 0.841032 -107 ********** Masking position 5 Map Score: 8.50919 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 379 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 ATAAATTTTTAAATAAAATAATTTTATTGAG 1 61 1 AAAAAAATAA 0.822516 -114 AAGTCTAATAAAACACCAATACTTAAAAAGA 2 57 0 AAAACCAATA 0.907229 -244 AGACAAAAATAAAGATAATAATCATTGCTAA 2 137 0 AAAATAATAA 0.822517 -164 AAATTTGCAGTAAGACAAAAATAAAGATAAT 2 149 0 TAAACAAAAA 0.890087 -152 GATAAAATCTAAAAACAAAAAATAATT 3 90 1 AAAACAAAAA 0.975004 -17 AAATCTCTAAAAAGACCATAAAGTGTCTGTA 4 238 1 AAAACCATAA 0.9731 -63 CTGTTTATAGAAAAACCAAAAACAATATAAA 4 276 1 AAAACCAAAA 0.979212 -25 *** ******* Masking position 5 Map Score: 4.20509 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 108 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 TAAATAATATGAATTTAGTAATTAAACT 1 8 0 GAATTAGTAA 0.91915 -167 ATAAGAATCCGAATTCAGTATTTTAAGATTC 1 140 1 GAATTAGTAT 0.986324 -35 TGAATTGATTTTATTTCATGTT 2 2 1 GAATTATTTT 0.852472 -299 TGTTTTATTAGACTTTATTATATCAATCTTA 2 73 1 GACTTATTAT 0.895579 -228 AATTGATATATAAATAAGTATCCTAAGATTG 2 96 0 TAAATAGTAT 0.881614 -205 ATGTTATTTAGCAATGATTATTATCTTTATT 2 130 1 GCAATATTAT 0.81813 -171 TAAGAAGCATGAAATTAGTATAATAGTCTAT 2 207 1 GAAATAGTAT 0.974238 -94 TTACTATAATGAATTGAGGATAAAATATAGA 2 233 0 GAATTAGGAT 0.94398 -68 CCATTATATTTAATTTATTATAAAGTATATG 4 105 0 TAATTATTAT 0.878441 -196 ***** ***** Masking position 5 Map Score: 6.84365 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 132 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 ********** No masking Map Score: -1.44708e-12 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: -1.44708e-12 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: -1.44708e-12 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