AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00473_rpxx_reg_300.orf -o00473_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 RP095 300 ALANINE RACEMASE (alr) #2 RP246 54 unknown #3 RP247 182 UDP-N-ACETYLMURAMATE--ALANINE LIGASE (murC) #4 RP249 115 D-ALANINE--D-ALANINE LIGASE (ddlB) Motif number 1 AATTGTCATTATTGAAAAGAAATTATCA 1 1 1 AATTATTAAA 0.930487 -300 ATTATCAATCAAATAAAATTAGTAAAAACAAGAGTATC 1 32 1 AATAATTAAA 0.842037 -269 GTTCTTTTAAAAATTTTTCTGCTTTTAATATTGTCATC 1 114 0 AATTTTTTAA 0.948087 -187 TCTTCCTACCATTTATAAAAAATTGTAAATTTGGTAGT 1 183 1 ATTTAATTAA 0.936164 -118 ATTTGGTAGTAGATCAGATTTTTGTTAATGATACTCTA 1 211 1 AGTAATTTAA 0.82343 -90 TATCTGACTTATCTATAAATTTTCATAATATTATAGTG 1 253 1 ATTTATTTAA 0.980429 -48 ATTTTTATTTCATTTAAAGTAAAAATGT 2 1 1 ATTTTTTAAA 0.922768 -54 TAAAGTAAAAATGTCTTAATATTCTTAAATATATAATT 2 25 1 ATTTATTTAA 0.980435 -30 TTCAAAATTGATCTTGTTATAATTATAACGTTT 3 6 0 ATTGTTTTAA 0.947089 -177 TAATACTATAATTTTGCTTACTTATTAAGTATATGCCT 3 67 0 ATTGTATTAA 0.839715 -116 GTAGTGCATCAATTATTATACTTTATAACATAGGTAAT 3 115 1 AATTAATTAA 0.903578 -68 TAATAATTTAAAATTGAATTCGTCATAAAGATCATTAC 3 148 0 AATGATTTAA 0.952505 -35 CGATAAAGTAATATCAGTATGTTTGAAAAGCCTTTTCC 4 49 0 ATTATTTAAA 0.826355 -67 TCGCAACTTAATATTTTAGTCATACTAATAAAAAAGTA 4 84 1 ATTTATTTAA 0.980435 -32 ** * * * * * *** Masking position 17 Map Score: 15.7497 Number of sites scoring better than the average of aligned sites = 868 Number in coding regions = 555 Number in noncoding regions = 313 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 2 TATTGAAAAGAAATTATCAATCAAATAAAA 1 20 1 AAATTATCAA 0.922231 -281 CAATCAAATAAAATTAGTAAAAACAAGAGT 1 37 1 AAATTAGTAA 0.817859 -264 AGTAAAAACAAGAGTATCAATCAATTGAGA 1 52 1 AGAGTATCAA 0.918855 -249 TTCATTGATGACAATATTAAAAGCAGAAAA 1 108 1 ACAATATTAA 0.544976 -193 AAAAGCAGAAAAATTTTTAAAAGAACATGT 1 126 1 AAATTTTTAA 0.833377 -175 ATCTACTACCAAATTTACAATTTTTTATAA 1 195 0 AAATTTACAA 0.698471 -106 AGATACTTCTAGAGTATCATTAACAAAAAT 1 228 0 AGAGTATCAT 0.879789 -73 ACTTATCTATAAATTTTCATAATATTATAG 1 259 1 AAATTTTCAT 0.79711 -42 TATTTCATTTAAAGTAAAAATGTCTTAATA 2 16 1 AAAGTAAAAA 0.781915 -39 TATATATTTAAGAATATTAAGACATTTTTA 2 30 0 AGAATATTAA 0.808305 -25 AAAATTATATATTTAAGAAT 2 45 0 AAAATTATAT 0.508981 -10 GGATTCCTTGAGAGTTTCAAAATTGATCTT 3 29 0 AGAGTTTCAA 0.853036 -154 CCTATGTTATAAAGTATAATAATTGATGCA 3 119 0 AAAGTATAAT 0.858776 -64 TTAATAATTTAAAATTGAATTCGTCATAAA 3 157 0 AAAATTGAAT 0.393679 -26 ATTCAATTTTAAATTATTAAACTTAA 3 167 1 AAATTATTAA 0.907029 -16 AAGTTGCGATAAAGTAATATCAGTATGTTT 4 63 0 AAAGTAATAT 0.817062 -53 TAGTATGACTAAAATATTAAGTTGCGATAA 4 81 0 AAAATATTAA 0.891404 -35 TACTAATAAAAAAGTAGAAT 4 106 1 AAAGTAGAAT 0.736731 -10 ********** Masking position 5 Map Score: 17.0169 Number of sites scoring better than the average of aligned sites = 2072 Number in coding regions = 1375 Number in noncoding regions = 697 Number of orfs with sites within 600 bp upstream = 277 Fraction of orfs with sites within 600 bp upstream = 0.0444908 Motif number 3 AAAAGAAATTATCAATCAAATAAAATTAGT 1 25 1 ATCAATCAAA 0.939363 -276 AAACAAGAGTATCAATCAATTGAGATTATA 1 57 1 ATCAATCAAT 0.971025 -244 TTGAGATTATATCAATACTAGGTATAGTTA 1 76 1 ATCAATACTA 0.838229 -225 TAATATTGTCATCAATGAATATAACTATAC 1 97 0 ATCAATGAAT 0.949262 -204 TGCTTTTGTAATCAATTCTTCCTACCATTT 1 167 1 ATCAATTCTT 0.921165 -134 TATCTGACTTATCTATAAATTTTCATAATA 1 253 1 ATCTATAAAT 0.821141 -48 TTTGTAGTGCATCAATTATTATACTTTATA 3 112 1 ATCAATTATT 0.945107 -71 ********** Masking position 5 Map Score: 4.60411 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 170 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 AATTGTCATTATTGAAAAGAAA 1 3 1 TTGTCATTAT 0.718984 -298 CTCTTGTTTTTACTAATTTTATTTGATTGA 1 36 0 TACTAATTTT 0.859048 -265 ATACTAGGTATAGTTATATTCATTGATGAC 1 90 1 TAGTTATATT 0.836835 -211 TTAAAAATTTTTCTGCTTTTAATATTGTCA 1 116 0 TTCTGCTTTT 0.869462 -185 GTGATTCAGTTAGTGCTTTTGTAATCAATT 1 154 1 TAGTGCTTTT 0.918678 -147 AGATTTTTGTTAATGATACTCTAGAAGTAT 1 226 1 TAATGATACT 0.5344 -75 AGTATATACTCATTTTATAACACTAT 1 285 0 TACTCATTTT 0.932121 -16 AAAATTGATCTTGTTATAATTATAACGTTT 3 11 0 TTGTTATAAT 0.488642 -172 TTTTCAAACATACTGATATTACTTTATCGC 4 58 1 TACTGATATT 0.938189 -58 CTTAATATTTTAGTCATACTAATAAAAAAG 4 90 1 TAGTCATACT 0.84959 -26 ATTCTACTTTTTTATTAGTAT 4 105 0 TTCTACTTTT 0.692368 -11 ********** Masking position 4 Map Score: 3.1203 Number of sites scoring better than the average of aligned sites = 829 Number in coding regions = 577 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 5 ********** No masking Map Score: 1.24588e-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 6 ********** No masking Map Score: 1.24588e-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 7 ********** No masking Map Score: 1.24588e-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