AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_mgen_reg_100.orf -o00860_mgen_100.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MG256 166 conserved hypothetical protein #2 MG257 45 ribosomal protein L31 (rpL31) #3 MG466 25 ribosomal protein L34 (rpL34) #4 MG468.1 62 ABC transporter, ATP-binding protein #5 MG469 300 chromosomal replication initiator protein (dnaA) Motif number 1 TTAGTGGTAGAACAACAGTCTCCAAAACTGTC 1 107 1 AACAAGTCTC 0.9623 -60 ACCAATAAATATTAATATATTCACTTAA 2 7 0 ATTAATATTC 0.905454 -39 TAATCACCTGATTAATTGTTTC 3 14 1 ATTAAGTTTC 0.979782 -12 CAAAATTAAAATTTTCTAATAGTGTT 4 5 1 ATTAATTTTC 0.985509 -58 AAAATTTTCTAATAGTGTTCTCAGGGTATTTT 4 18 1 AATAGTTCTC 0.873453 -45 TTTCAAGAGGAACAAAATTTTCAATATCATAA 5 30 1 AACAATTTTC 0.980163 -271 TCAATATCATAATAATGGTTTCTTACAGCAAA 5 50 1 AATAAGTTTC 0.970663 -251 CAGCAAAAAAATCAAAATTTTCAACAACAATT 5 75 1 ATCAATTTTC 0.986609 -226 GTACACCTGTATCTAGTTTTTCTTGGCGTTCA 5 167 0 ATCTATTTTC 0.912093 -134 AAGAATGATAGTTAAAATTCTCGAAATTGGGA 5 259 0 GTTAATTCTC 0.909409 -42 ***** ***** Masking position 11 Map Score: 12.2806 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 120 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 2 CAATTTAACTAAGTTTTTATCATAAATTGGCCT 1 42 0 AAGTTTTTCT 0.96886 -125 CACTATTAGAAAATTTTAATTTTG 4 2 0 AAATTTTTTT 0.948384 -61 TTCCTCTTGAAAATATCTCTCTTTTTTTGGT 5 9 0 AAATATCTCT 0.960601 -292 ATGATATTGAAAATTTTGTTCCTCTTGAAAATA 5 27 0 AAATTTTTCT 0.985729 -274 TTGTTGTTGAAAATTTTGATTTTTTTGCTGTAA 5 72 0 AAATTTTTTT 0.949558 -229 GTTCAACAGGAACTATTCCTGGTATTTTTGTTT 5 139 0 AACTATTTGT 0.922612 -162 AGTAATTTCTAACTTTTTGTCATACTCTTTGAC 5 211 0 AACTTTTTCT 0.988153 -90 CGAGAATTTTAACTATCATTCTTGACAATGTTA 5 268 1 AACTATCTCT 0.966858 -33 ******* ** * Masking position 2 Map Score: 7.51723 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 40 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 AGGCCAATTTATGATAAAAACTTAGTTAAA 1 42 1 ATGATAAAAA 0.922028 -125 CCCCTAAAACTAGATAAAAACCTAGCAATT 1 70 0 TAGATAAAAA 0.922086 -97 TTATTGGTCTTTGTCAAAAAATAAG 2 31 1 TTGTCAAAAA 0.968946 -15 GTGTGAATTGTTGTTGAAAATTTTGATTTT 5 82 0 TTGTTGAAAA 0.784527 -219 TCCCCAACCTAAAACAAAAATACCAGGAAT 5 128 1 AAAACAAAAA 0.649201 -173 ACTTCTATACAAGTCAAAGAGTATGACAAA 5 199 1 AAGTCAAAGA 0.844573 -102 GTCAAAGAGTATGACAAAAAGTTAGAAATT 5 211 1 ATGACAAAAA 0.958757 -90 TCAAGAATGATAGTTAAAATTCTCGAAATT 5 263 0 TAGTTAAAAT 0.696555 -38 TTCTATAACATTGTCAAGAATGATAGTTAA 5 276 0 TTGTCAAGAA 0.888653 -25 ********** Masking position 7 Map Score: 4.89143 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 456 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 AAACTACACCCCCTAAAACTAGATAAAAAC 1 79 0 CCCTAAAACT 0.82436 -88 TTTGACAAAGACCAATAAATATTAATATAT 2 19 0 ACCAATAAAT 0.883032 -27 ATTGGTCTTTGTCAAAAAATAAG 2 33 1 GTCAAAAAAT 0.869712 -13 TCATTAAGTCATCTAAAAAAATACCCTGAG 4 37 0 ATCTAAAAAA 0.908423 -26 ACCAAAAAAAGAGAGATATT 5 1 1 ACCAAAAAAA 0.983147 -300 GGTTTCTTACAGCAAAAAAATCAAAATTTT 5 66 1 AGCAAAAAAA 0.930439 -235 TTCCTCCCCAACCTAAAACAAAAATACCAG 5 124 1 ACCTAAAACA 0.953686 -177 CCTGTTGAACGCCAAGAAAAACTAGATACA 5 162 1 GCCAAGAAAA 0.923541 -139 ********** Masking position 5 Map Score: 4.00204 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 331 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 TTAAGTGAATATATTAATATTTATTGGTCTT 2 11 1 ATATAATATT 0.881163 -35 CTATTAGAAAATTTTAATTTTG 4 2 0 ATTTAATTTT 0.944536 -61 AGAAACCATTATTATGATATTGAAAATTTTG 5 42 0 ATTTGATATT 0.971441 -259 GTTGTTGAAAATTTTGATTTTTTTGCTGTAA 5 72 0 ATTTGATTTT 0.974495 -229 AATTCTCGAAATTGGGATATTAACTGCTTTG 5 245 0 ATTGGATATT 0.961289 -56 *** ******* Masking position 7 Map Score: 2.06017 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 25 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 AGAGGAGTTGAACCTCTATTTACTGA 1 7 0 AACCTCTATT 0.916451 -160 TGAATATATTAATATTTATTGGTCTTTGTC 2 16 1 AATATTTATT 0.583217 -30 GAAACAATTAATCAGGTGATTA 3 14 0 AACAATTAAT 0.894428 -12 AAACAATCATTAAGTCATCTA 4 52 0 AACAATCATT 0.957204 -11 TGCTGTAAGAAACCATTATTATGATATTGA 5 50 0 AACCATTATT 0.957204 -251 CAAAATTTTCAACAACAATTCACACAACCA 5 87 1 AACAACAATT 0.898501 -214 CGAGAATTTTAACTATCATTCTTGACAATG 5 268 1 AACTATCATT 0.914394 -33 ********** Masking position 8 Map Score: 3.19609 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 144 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 AGGAATCGAACCCACACAGACAGTTTTGGAG 1 126 0 CCACACAGAC 0.978641 -41 TCGATTCCTTCCACCCCCGCCATTTACAG 1 148 1 CCCCCCCGCC 0.998479 -19 ACAATTCACACAACCACAGCCTATTCCTCCC 5 101 1 CACCACAGCC 0.994537 -200 ACAGCCTATTCCTCCCCAACCTAAAACAAAA 5 116 1 CCCCCCAACC 0.996461 -185 ** ******** Masking position 5 Map Score: 1.56632 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 1 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 TCAGTAAATAGAGGTTCAACTCCTCTA 1 8 1 ATAGAGGTTC 0.927652 -159 TTGGCCTTCCCTAGAGGAGTTGAACCTCTA 1 19 0 CTAGAGGAGT 0.972643 -148 GAAAAACTAGATACAGGTGTACACTTCTAT 5 177 1 ATACAGGTGT 0.96822 -124 TTTGACTTGTATAGAAGTGTACACCTGTAT 5 187 0 ATAGAAGTGT 0.980407 -114 TGACAATGTTATAGAAGAATA 5 290 1 ATAGAAGAAT 0.898078 -11 ********** Masking position 5 Map Score: 0.434471 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 17 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 ********** 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 10 ********** 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 11 ********** 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