AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icoldbox_ecoli_hinf_100.orf -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 cspB 300 cold shock protein; may affect transcription #2 deaD 128 inducible ATP-independent RNA helicase #3 cspA 280 cold shock protein 7.4, transcriptional activator of hns #4 HI0231 120 ATP-dependent RNA helicase (deaD) Motif number 1 TTATCAGTATTAAGGAATTTTT 1 3 0 TAAGGAATTT 0.916989 -298 ATAGCTTTCTTCAGGAACGTGTGTATAGTG 1 40 0 TCAGGAACGT 0.988549 -261 TTGAACATATGAAGCAATGTTTATTTTAGA 1 102 0 GAAGCAATGT 0.867118 -199 AGGCTCAAGTTAAGGAATGTAGA 1 288 1 TAAGGAATGT 0.986241 -13 GAAATTGATCAGCAATTTTCATTGAAAA 2 111 0 TCAGCAATTT 0.800957 -18 GGTCCTGTCATCAGGACCGTAAACAGCAAT 3 26 0 TCAGGACCGT 0.970649 -255 GGTCCTGATGACAGGACCGTTTTCCAACCG 3 38 1 ACAGGACCGT 0.900499 -243 TGATGTGCATTAAGCCACGCATTGGCGGGT 3 102 0 TAAGCCACGC 0.841188 -179 AGCAGTGTAGTAAGGCAAGTCCCTTCAAGA 3 156 1 TAAGGCAAGT 0.922909 -125 TTGAAGCGTTAAAGGAATGTGCACTACGAG 3 202 0 AAAGGAATGT 0.952071 -79 CGAATATAAATAAGGAAAGCTCAAAGAGGC 4 92 0 TAAGGAAAGC 0.922915 -29 ********** Masking position 3 Map Score: 11.5141 Number of sites scoring better than the average of aligned sites = 669 Number in coding regions = 559 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 2 ACTGATAACTTGGCGCACTATACACACGTTCCTGAA 1 25 1 TGGACACACA 0.940227 -276 ATGATTGCGTCGGTTTGAAGAACAGACGATATACGA 1 142 1 CGGGAACAGA 0.992567 -159 CGTACTTAATTGGAGAGACTCAAAGAAGGAATAAGT 1 217 0 TGGGAAAAGA 0.981567 -84 TCGGCATAAATGGTTTGCATAACAGAAACGACTTCG 1 251 0 TGGGCACAGA 0.997117 -50 GTTAAGGTGATGGCAATCAAAAAAGATTACGGGCTG 2 24 0 TGGTCAAAGA 0.9547 -105 TGCACATCAACGGTTTGACGTACAGACCATTAAAGC 3 123 1 CGGGAACAGA 0.992567 -158 TTCGGCGATATGGCGTGCTTTACAGATTTTGAAGCG 3 224 0 TGGGCACAGA 0.997138 -57 TTTTTCTATTCGTTCTACTGCAAAGAGCGGTAAGTT 4 23 0 CGTACAAAGA 0.80267 -98 *** ** ***** Masking position 12 Map Score: 8.81576 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 404 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 ATATGTTCAACTATGCGTTAATGATTGCGTCGG 1 122 1 CTTGCTTATG 0.896344 -179 TTCTTTGAGTCTCTCCAATTAAGTACGAAGTCG 1 226 1 CTTCCATAAG 0.943415 -75 TTCTGTTATGCAAACCATTTATGCCGAAAGGCT 1 260 1 CAACCTTATG 0.985214 -41 CAACAACGCCCTCACCCGTTAAGGTGATGGCAA 2 44 0 CTACCGTAAG 0.944782 -85 CAGGACCGTAAACAGCAATAAAGTGGATAAAAG 3 12 0 AAAGCATAAG 0.701407 -269 GTCTGTACGTCAAACCGTTGATGTGCATTAAGC 3 117 0 CAACCTTATG 0.985226 -164 GTTTGACGTACAGACCATTAAAGCAGTGTAGTA 3 135 1 CAACCTTAAG 0.990734 -146 GTAGTAAGGCAAGTCCCTTCAAGAGTTATCGTT 3 162 1 AATCCTTAAG 0.944749 -119 TCGTAGTGCACATTCCTTTAACGCTTCAAAATC 3 203 1 CATCCTTACG 0.969452 -78 ** *** ** *** Masking position 9 Map Score: 7.75786 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 417 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 GTTTTTTGATGGGGTTGAAGATGGCTGGAT 1 71 1 GGGGTTGAAG 0.979705 -230 ATGATTGCGTCGGTTTGAAGAACAGACGAT 1 142 1 CGGTTTGAAG 0.993689 -159 AAAAAGATTACGGGCTGATGTGTACGTCAG 2 11 0 CGGGCTGATG 0.968054 -118 TATGATTAATCGGTTGGAAAACGGTCCTGT 3 48 0 CGGTTGGAAA 0.931469 -233 TGCACATCAACGGTTTGACGTACAGACCAT 3 123 1 CGGTTTGACG 0.989285 -158 ********** Masking position 8 Map Score: 3.04523 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 160 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 TCCTTAACTTGAGCCTTTCGGCATAAATGG 1 274 0 GAGCCTTTCG 0.987874 -27 AACCGTTGATGTGCATTAAGCCACGCATTG 3 108 0 GTGCATTAAG 0.912564 -173 TTAAAGGAATGTGCACTACGAGGGGTATCA 3 194 0 GTGCACTACG 0.982435 -87 GCGATATGGCGTGCTTTACAGATTTTGAAG 3 226 0 GTGCTTTACA 0.855466 -55 ATAATTAAGTGTGCCTTTCGGCGATATGGC 3 246 0 GTGCCTTTCG 0.993464 -35 AAAGCTCAAAGAGGCCTTCGGTTTATTAAG 4 77 0 GAGGCCTTCG 0.939344 -44 ********** Masking position 7 Map Score: 3.46629 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 325 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 AATTGGAGAGACTCAAAGAAGGAATAAGTG 1 216 0 ACTCAAAGAA 0.931634 -85 ATGCCGAAAGGCTCAAGTTAAGGAATGTAG 1 280 1 GCTCAAGTTA 0.963674 -21 GTGTGAACCGGCTCAAAGTAGGTGTATTAA 2 81 0 GCTCAAAGTA 0.990282 -48 CATTCGCTCTGCTCAACTTAATAAACCGAA 4 61 1 GCTCAACTTA 0.963674 -60 AATAAGGAAAGCTCAAAGAGGCCTTCGGTT 4 84 0 GCTCAAAGAG 0.96973 -37 ********** Masking position 5 Map Score: 2.16073 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 77 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 GGATGTCTAAAATAAACATTGCTTCATATGTT 1 97 1 AATAAATTGC 0.954429 -204 ACTATGCGTTAATGATTGCGTCGGTTTGAAGA 1 131 1 AATGAGCGTC 0.872668 -170 TAACACCTGAAATGAGAACTGCTTTAGTAAAC 1 182 0 AATGAACTGC 0.980911 -119 CACACTTTTCAATGAAAATTGCTGATCAATTT 2 106 1 AATGAATTGC 0.984122 -23 AAATATGAAAAATAATTGTTGCATCACCCGCC 3 77 1 AATAAGTTGC 0.957643 -204 GAGCAGAGCGAATGAATTTTTCTATTCGTTCT 4 43 0 AATGATTTTC 0.892336 -78 ***** ***** Masking position 5 Map Score: 0.449741 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 218 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 ********** No masking Map Score: 1.08246e-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 9 ********** No masking Map Score: 1.08246e-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: 1.08246e-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