AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i256_heat_shock1_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 hslV 92 heat shock protein hslVU, proteasome-related peptidase subunit #2 ftsN 91 essential cell division protein #3 cytR 155 regulator for deo operon, udp, cdd, tsx, nupC, and nupG #4 priA 202 primosomal protein N'(= factor Y)(putative helicase) Motif number 1 GTAAACCTTTAAGACTGCCGTGACTGGTCAA 2 12 1 AGACTGCCGT 0.946151 -80 GACTGGTCAAAGGCCCGCCGCTTAAGTAACA 2 33 1 AGCCCGCCGC 0.996365 -59 ATTCGTTCGTCAGCCCGCCATGTTACTTAAG 2 53 0 CGCCCGCCAT 0.956077 -39 ACCGCTCACGATGCGAGGCGGATCGAAAAAT 3 11 1 AGCGAGGCGG 0.879596 -145 TGGATGTAGTACGCCTGACGTGCCAGGCGAG 3 127 1 AGCCTGACGT 0.574279 -29 CTGACGTGCCAGGCGAGGAGTGAGT 3 141 1 AGCGAGGAGT 0.940441 -15 TTAGGGCTGGAAGAGCGACGCGGCCTTAAAC 4 23 0 AGAGCGACGC 0.975101 -180 TCCAGCCCTAACGCCAGACACCACGCGATGT 4 43 1 AGCCAGACAC 0.915723 -160 TTTCGTACGAAGGCGCGAAATCATACAGAAA 4 99 1 AGCGCGAAAT 0.92905 -104 * ********* Masking position 7 Map Score: 7.54931 Number of sites scoring better than the average of aligned sites = 3647 Number in coding regions = 3481 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 2 TAATTGCATTATGCCCCGTACTTTTGTACG 1 35 1 ATGCCCCGTA 0.98101 -58 TACAGAGTACAAACCCCGTACAAAAGTACG 1 51 0 AAACCCCGTA 0.97953 -42 TTGGTTACGAATACAGAGTACAAACCCCGT 1 62 0 ATACAGAGTA 0.870995 -31 GAACGAATAAATACAGCGAAACGATA 2 76 1 ATACAGCGAA 0.975594 -16 ATTTCGTACGAAGGCGCGAAATCATACAGA 4 98 1 AAGGCGCGAA 0.908678 -105 TACAGAAATTAACCAGCGTATGCAAACTGA 4 122 1 AACCAGCGTA 0.982482 -81 GTGTATACTAACCCACCGAATTTCAAGTCA 4 173 1 ACCCACCGAA 0.950669 -30 ********** Masking position 1 Map Score: 3.72512 Number of sites scoring better than the average of aligned sites = 1195 Number in coding regions = 1106 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 3 GCATTATGCCCCGTACTTTTGTACGGGGTT 1 40 1 CCGTACTTTT 0.985633 -53 TCAATATTCATCACACTTTTCATGAAAATT 3 42 1 TCACACTTTT 0.964838 -114 TTCACATCGGCAACATTTTTAGCAGATAGC 3 90 0 CAACATTTTT 0.873464 -66 CGTATTGAAGCTATACTTTTAACATCGCGT 4 65 0 CTATACTTTT 0.941163 -138 GCAAACTGATCCGCACTCTTCTACGGCAAT 4 143 1 CCGCACTCTT 0.985843 -60 ********** Masking position 5 Map Score: 0.838228 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 473 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 4 GTACAAACCCCGTACAAAAGTACGGGGCATA 1 44 0 CGTACAAAGT 0.886409 -49 TGTATTTATTCGTTCGTCAGCCCGCCATGTT 2 60 0 CGTTCGCAGC 0.983242 -32 ATTCTGTAACCGTTTTCACGCGCTATCTGCT 3 69 1 CGTTTTACGC 0.892022 -87 GCACGTCAGGCGTACTACATCCATGTTTACT 3 119 0 CGTACTCATC 0.966647 -37 ACGAAATGATCGTATTGAAGCTATACTTTTA 4 74 0 CGTATTAAGC 0.984046 -129 TTCGCGCCTTCGTACGAAATGATCGTATTGA 4 87 0 CGTACGAATG 0.939461 -116 AATTAACCAGCGTATGCAAACTGATCCGCAC 4 128 1 CGTATGAAAC 0.948969 -75 ****** **** Masking position 3 Map Score: 0.981001 Number of sites scoring better than the average of aligned sites = 948 Number in coding regions = 895 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 GCGGATCGAAAAATTCAATATTCATCACAC 3 28 1 AAATTCAATA 0.91629 -128 CTTTTCATGAAAATTCTGTAACCGTTTTCA 3 57 1 AAATTCTGTA 0.987131 -99 TACGCTGGTTAATTTCTGTATGATTTCGCG 4 112 0 AATTTCTGTA 0.96811 -91 TCCTGACTTGAAATTCGGTGGGTTAGTATA 4 176 0 AAATTCGGTG 0.974239 -27 ********** Masking position 5 Map Score: 0.669499 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 67 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 ********** No masking Map Score: 1.42352e-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: 1.42352e-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: 1.42352e-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