AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i348_ecoli_bsub_100.orf -o348_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 csrA 234 carbon storage regulator; controls glycogen synthesis, gluconeogenesis, cell size and surface properties #2 yviE 46 yviE #3 flgM 80 anti-sigma factor repressor of sigma-D-dependent transcription #4 yvyF 73 alternate gene name: yviB; similar to flagellar protein #5 comFB 59 late competence gene #6 comFA 105 late competence protein Motif number 1 AGCGTCAGGCAATGCCGTGGACTCGCTTCA 1 15 1 AATGCCGTGG 0.990657 -220 CGTTAATGCGAATGCCGTGAAGCGAGTCCA 1 32 0 AATGCCGTGA 0.993693 -203 AACAGAATGTAATGCCATGACTGCTTAGAT 1 118 1 AATGCCATGA 0.967942 -117 TATGATGGATAATGCCGGGATACAGAGAGA 1 183 1 AATGCCGGGA 0.99598 -52 ATTCTGTTTTTATGCCGATATAATCACTAG 4 14 1 TATGCCGATA 0.941788 -60 TATTAGATAATATGCCTGTGTCAATTTCTA 4 41 0 TATGCCTGTG 0.935975 -33 TTCGAAACAGTATGCCTGAATGAATATTTT 6 72 0 TATGCCTGAA 0.924926 -34 ********** Masking position 2 Map Score: 9.76312 Number of sites scoring better than the average of aligned sites = 560 Number in coding regions = 515 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 TTAATGCGAATGCCGTGAAGCGAGTCCACG 1 30 0 TGCCGTGAAG 0.923975 -205 ACCTAAGTTTAGCCGATATACACAACTTCA 1 86 0 AGCCGATATA 0.982976 -149 GCTTACTTTTTGGCGTTATATGATGGATAA 1 165 1 TGGCGTTATA 0.975184 -70 TGATGGATAATGCCGGGATACAGAGAGACC 1 185 1 TGCCGGGATA 0.981567 -50 CTGAAAACGCAGTCGATAAAAGGGTTAAGA 3 24 1 AGTCGATAAA 0.827985 -57 TCTGTTTTTATGCCGATATAATCACTAGAA 4 16 1 TGCCGATATA 0.986874 -58 TTTCGAAAGGAGGCGTGCTAT 6 95 1 AGGCGTGCTA 0.918126 -11 ********** Masking position 5 Map Score: 4.46262 Number of sites scoring better than the average of aligned sites = 681 Number in coding regions = 623 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 3 AAAAGTAAGCAATGACAAACACATTACATCTAA 1 142 0 AAGAAAACAA 0.972098 -93 TTGCTCCTTGAAAGATTAAAAGAGTCGGGTCTC 1 209 0 AAGATAAAAA 0.957488 -26 CTACCTCCTGAACTATAAAAAAAGCGAACTCCT 2 20 0 AATAAAAAAA 0.977207 -27 GATTATATCGGCATAAAAACAGAATCAT 4 6 0 GCTAAAACAA 0.856602 -68 ATTATCTAATAAGGAGAAAAAAAG 4 60 1 AAGAAAAAAA 0.981051 -14 ATTAAAATAAGAATATAAAAAAATCTCCGCTCT 6 29 0 GATAAAAAAA 0.9665 -77 TTTTCTGTCCAACTATTAAAATAAGAATATAAA 6 43 0 AATATAAAAA 0.949106 -63 ** ** ***** * Masking position 8 Map Score: 4.33968 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 108 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 CTGACTTTATCGTTGTCGATAGCGTTAATG 1 54 0 CGTTGTCGAT 0.917208 -181 AGAGACCCGACTCTTTTAATCTTTCAAGGA 1 208 1 CTCTTTTAAT 0.873336 -27 TAGGAGTTCGCTTTTTTTATAGTTCAGGAG 2 19 1 CTTTTTTTAT 0.816765 -28 TTATCGACTGCGTTTTCAGTTAGTTTAGGG 3 13 0 CGTTTTCAGT 0.964616 -68 GGATTCCTCTCGCTTTCCGTTGCAGTCTTT 3 60 0 CGCTTTCCGT 0.870259 -21 ATGATTCTGTTTTTATGCCGATATAA 4 7 1 CTGTTTTTAT 0.813749 -67 GATAATATGCCTGTGTCAATTTCTAGTGAT 4 36 0 CTGTGTCAAT 0.910066 -38 TACTGTACCACGTTTTCAAATAATGG 5 7 0 CGTTTTCAAA 0.945467 -53 GCCAAATCTCCGTTTTTAGAGCGGAGATTT 6 12 1 CGTTTTTAGA 0.840459 -94 TTCAGGCATACTGTTTCGAAAGGAGGCGTG 6 82 1 CTGTTTCGAA 0.877612 -24 ********** Masking position 6 Map Score: 4.45244 Number of sites scoring better than the average of aligned sites = 1791 Number in coding regions = 1621 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 5 CACGGCATTGCCTGACGCTTATA 1 4 0 CCTGACGCTT 0.996208 -231 ACAACTTCAACCTGACTTTATCGTTGTCGA 1 65 0 CCTGACTTTA 0.944191 -170 TACAGAGAGACCCGACTCTTTTAATCTTTC 1 203 1 CCCGACTCTT 0.990062 -32 AGGATTCCTCTCGCTTTCCGTTGCAG 3 65 0 CCTCTCGCTT 0.974866 -16 ********** Masking position 9 Map Score: 0.859136 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 272 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 ACATTCTGTTAAACCTAAGTTTAGCCGATAT 1 97 0 AAACTAAGTT 0.916017 -138 CAAACACATTACATCTAAGCAGTCATGGCAT 1 129 0 ACACTAAGCA 0.963978 -106 TATAACGCCAAAAAGTAAGCAATGACAAACA 1 154 0 AAAGTAAGCA 0.88097 -81 TTTTACAGCTCCTCATCATCGGTTA 5 45 0 ACACTCCTCA 0.911001 -15 GGCCAAATCTCCGTTTTTAGAGCGG 6 5 1 AAACTCCGTT 0.964161 -101 GAATATAAAAAAATCTCCGCTCTAAAAACGG 6 21 0 AAACTCCGCT 0.987619 -85 *** ******* Masking position 6 Map Score: 0.0377626 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 403 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 7 ********** No masking Map Score: -7.08111e-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: -7.08111e-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: -7.08111e-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