AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i334_1_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 hemA 213 enzyme in alternate path of synthesis of 5-aminolevulinate #2 prfA 41 peptide chain release factor RF-1 #3 yrdD 62 putative DNA topoisomerase #4 smf_2 53 orf, fragment 2 #5 smf_1 129 orf, fragment 1 #6 HI0658 160 ABC transporter, ATP-binding protein #7 HI1560 22 H. influenzae predicted coding region HI1560 #8 HI1561 106 peptide chain release factor 1 (prfA) Motif number 1 TTAGATTCTGGCAATTAAGACAACTTGAAC 1 84 0 GCAATTAAGA 0.924992 -130 TGCGTAAGATCAATAAAAGAGAGCGCCCCC 1 138 0 CAATAAAAGA 0.835921 -76 ATGCACCCTGTAAAAAAAGAAAATGATGTA 2 14 0 TAAAAAAAGA 0.864128 -28 AACTTATGCTGAATTAAAGAAATGA 3 6 0 GAATTAAAGA 0.919885 -57 GATTTGTCTAGAATAGAAGAAATAATCTTT 5 40 0 GAATAGAAGA 0.86671 -90 ATAATAAGACGCAATAAAAACTATTTATAA 6 39 0 GCAATAAAAA 0.799435 -122 GATTTTCTAGTCAAAAAAGCCACGTATAAT 6 64 0 TCAAAAAAGC 0.551979 -97 ACTGTTCCGAGAAAAGAAAAAATATTGCAA 6 110 1 GAAAAGAAAA 0.801485 -51 AAAATAGCCTCAAATTAAGACCTATGTAGA 6 138 1 CAAATTAAGA 0.907303 -23 GGGTAAATCACAAATAAAGCGTCTGAGATT 8 12 1 CAAATAAAGC 0.832391 -95 CAGCGAAAAGGAAATTAAGAATCTCAGACG 8 31 0 GAAATTAAGA 0.956636 -76 GTAAGTCACCGAAAATAAAATCGGCGTATT 8 85 0 GAAAATAAAA 0.829642 -22 ********** Masking position 7 Map Score: 8.95469 Number of sites scoring better than the average of aligned sites = 853 Number in coding regions = 694 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 2 TAGCGGACGGTAACGCTAGCATTAAGGGTTA 1 45 0 TACGCTAGCA 0.937115 -169 GCAAGCAGACTAACCCTATCAACGTTGGTAT 1 179 1 TACCCTATCA 0.983598 -35 AGGCGTAAATGCACCCTGTAAAAAAAGAAAA 2 21 0 GACCCTGTAA 0.85537 -21 ACAGTGCTGATTTCGCCATAACAACTTATGC 3 27 0 TTCGCCATAA 0.818799 -36 GATTGGTCAGTGATGCTGTCAATCAGAGGGG 5 70 0 TATGCTGTCA 0.850497 -60 CCTTATCTCCCTGCCATAAGCAGCCT 5 114 0 TTCCCTGCCA 0.966973 -16 TGAAATCAGATGTCCCTATCA 7 1 0 TTCCCTATCA 0.986607 -22 TTAATTTCCTTTTCGCTGTCAATTTTCCCTA 8 43 1 TTCGCTGTCA 0.986234 -64 CGCTGTCAATTTTCCCTAAAATCGGCTAGAA 8 56 1 TTCCCTAAAA 0.834119 -51 * ********* Masking position 11 Map Score: 6.45476 Number of sites scoring better than the average of aligned sites = 759 Number in coding regions = 681 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 3 TAAAAGAGAGCGCCCCCTTTTGGAGTAATT 1 125 0 CGCCCCCTTT 0.983195 -89 ATTGATCTTACGCATCCTGTATGATGCAAG 1 154 1 CGCATCCTGT 0.992359 -60 AGGCGTAAATGCACCCTGTAAAAAAAGAA 2 23 0 TGCACCCTGT 0.992359 -19 TATTACGCACCGTGAACAGTGCTGA 3 48 0 CGCACCGTGA 0.987155 -15 AAGAATCGCACCTTGTTTTATTAACC 4 38 0 CGCACCTTGT 0.994172 -16 ********** Masking position 8 Map Score: 6.21504 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 151 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 GCACCGTGAACAGTGCTGATTTCGCCATAACAA 3 34 0 CAGTGCTGTC 0.991008 -29 TTTTATTAACCAGTGAGGCCCTTCGCTTCCCGG 4 16 0 CAGTGAGGTT 0.988963 -38 AAATCTCCAGAGATGTGTTCAGGAGTTAGA 5 8 1 CAGAGATGTC 0.992449 -122 TGCTGTCAATCAGAGGGGGATTTGTCTAGAATA 5 55 0 CAGAGGGGTT 0.97364 -75 TGCGATTGGTCAGTGATGCTGTCAATCAGAGGG 5 71 0 CAGTGATGTC 0.994697 -59 ******** ** Masking position 2 Map Score: 2.05585 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 97 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 CTTGAACATAGACGATAGCGGACGGTAACGC 1 60 0 GACGATAGCG 0.946257 -154 TGGAGTAATTGCCGAAAGCCGTTAGATTCTG 1 104 0 GCCGAAAGCG 0.991642 -110 CATCCTGTATGATGCAAGCAGACTAACCCTA 1 166 1 GATGCAAGCG 0.950148 -48 AAGTTGTTATGGCGAAATCAGCACTGTTCAC 3 31 1 GGCGAAATCG 0.965403 -32 TTATCTCCCTGCCATAAGCAGCCTTAGCAAT 5 107 0 GCCATAAGCG 0.939501 -23 CTAGAAAATCGATAAAATCGGAATAGACTGT 6 84 1 GATAAAATCG 0.960969 -77 GTCAATTTTCCCTAAAATCGGCTAGAATACG 8 60 1 CCTAAAATCG 0.851086 -47 AGTCACCGAAAATAAAATCGGCGTATTCTAG 8 81 0 AATAAAATCG 0.761537 -26 ********* * Masking position 7 Map Score: 3.32353 Number of sites scoring better than the average of aligned sites = 1547 Number in coding regions = 1457 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 6 ATTTCTTCTATTCTAGACAAATCCCCCTCT 5 47 1 TTCTAGACAA 0.984046 -83 TTTATCGATTTTCTAGTCAAAAAAGCCACG 6 70 0 TTCTAGTCAA 0.985232 -91 AATCGGCGTATTCTAGCCGATTTTAGGGAA 8 67 0 TTCTAGCCGA 0.988198 -40 ********** Masking position 5 Map Score: 0.244432 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: 4.85601e-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: 4.85601e-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 9 ********** No masking Map Score: 4.85601e-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