AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i257_ecoli_bsub_300.orf -o257_ecoli_bsub_300.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 mopB 275 GroES, 10 Kd chaperone binds to Hsp60 in pres. Mg-ATP, suppressing its ATPase activity #2 mopA 43 GroEL, chaperone Hsp60, peptide-dependent ATPase, heat shock protein #3 groES 196 class I heat-shock protein (molecular chaperonin) #4 groEL 46 class I heat-shock protein (molecular chaperonin) Motif number 1 TCATCGCAATTTCTTCATCGCCGTCATAAG 1 82 0 TTCTTCATCG 0.83094 -194 GTGAATCAGGGTTTTCACCCGATTTTGTGC 1 120 1 GTTTTCACCC 0.995049 -156 ATTTTTTTTCTTTTTCCCCCTTGAAGGGGC 1 158 1 TTTTTCCCCC 0.988427 -118 ATGGGGATGAGGCTTCGCCCCTTCAAGGGG 1 174 0 GGCTTCGCCC 0.986046 -102 GAGCTTACGTGGTTTCCCGGCTGGTGACCA 1 209 0 GGTTTCCCGG 0.943249 -67 CGTAAGCTCCGGCGTCACCCATAACAGATA 1 230 1 GGCGTCACCC 0.980732 -46 TTCCGTTAGCTTTTTCACCCCCGTACCGAT 3 67 0 TTTTTCACCC 0.992182 -130 AGATAAAAAATTTTTCACGCTTACATCATT 3 112 0 TTTTTCACGC 0.978216 -85 ********** Masking position 5 Map Score: 9.99777 Number of sites scoring better than the average of aligned sites = 977 Number in coding regions = 909 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 AGTTGCCCAAAATTTGGGCGCAATCGGACATC 1 16 0 AATTTGGGCA 0.950191 -260 GGCGATGAAGAAATTGCGATGAAATGTGAGGT 1 90 1 AAATTGGTGA 0.9844 -186 ATTGCGATGAAATGTGAGGTGAATCAGGGTTT 1 102 1 AATGTGGTGA 0.982236 -174 TTTTCACCCGATTTTGTGCTGATCAGAATTTT 1 131 1 ATTTTGGTGA 0.944628 -145 GTGACCAGAGAAATGGGGATGAGGCTTCGCCC 1 184 0 AAATGGGTGA 0.987048 -92 AGCTAACGGAAAAGGGAGCGGAAAAGAATGAT 3 86 1 AAAGGGGGGA 0.984109 -111 TATCACTTGAAATTGGAAGGGAGATTCTTTAT 3 142 1 AATTGGAGGA 0.939552 -55 ****** * *** Masking position 1 Map Score: 6.02551 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 260 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 GATGTCCGATTGCGCCCAAATTTTGGGCAAC 1 16 1 TGCGCCAAAT 0.870559 -260 ACCTCACATTTCATCGCAATTTCTTCATCGC 1 91 0 TCATCCAATT 0.913905 -185 AAACCCTGATTCACCTCACATTTCATCGCAA 1 103 0 TCACCCACAT 0.960482 -173 AAAATTCTGATCAGCACAAAATCGGGTGAAA 1 132 0 TCAGCCAAAA 0.970366 -144 GGGCGAAGCCTCATCCCCATTTCTCTGGTCA 1 184 1 TCATCCCATT 0.931816 -92 TCCGCGCACGACACTGAACAT 2 1 1 TCCGCCACGA 0.914506 -43 GTTAGCTTTTTCACCCCCGTACCGATTATGT 3 62 0 TCACCCCGTA 0.866159 -135 ATCATTCTTTTCCGCTCCCTTTTCCGTTAGC 3 87 0 TCCGCCCCTT 0.978151 -110 ATAAAGAATCTCCCTTCCAATTTCAAGTGAT 3 143 0 TCCCTCCAAT 0.782175 -54 TCAGCACTAAAGAGTGCTAAC 3 186 0 TCAGCCTAAA 0.889849 -11 ***** ***** Masking position 1 Map Score: 4.21661 Number of sites scoring better than the average of aligned sites = 2221 Number in coding regions = 2052 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 4 CATCGCCGTCATAAGCGAATCTGATTGTGCT 1 66 0 ATAACGAATC 0.966417 -210 GGCGTCACCCATAACAGATACGGACTTTCTC 1 240 1 ATAAAGATAC 0.962905 -36 ATAGCTGTAGATGAACGAAACCCACTTAACA 3 27 0 ATGACGAAAC 0.977091 -170 CTATTGTAACATAATCGGTACGGGGGTGAAA 3 54 1 ATAACGGTAC 0.98389 -143 TTCTTAAATAAACAATACTTAAAACATT 4 8 1 ATAACAATAC 0.962955 -39 **** ****** Masking position 4 Map Score: 1.4679 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 153 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 AATTTTGGGCAACTGCGTAGATTTTCGATG 1 34 1 AACTGCGTAG 0.915362 -242 ATTCGCTTATGACGGCGATGAAGAAATTGC 1 77 1 GACGGCGATG 0.993679 -199 GCGATGAAGAAATTGCGATGAAATGTGAGG 1 91 1 AATTGCGATG 0.944948 -185 TGACCAGAGAAATGGGGATGAGGCTTCGCC 1 185 0 AATGGGGATG 0.963788 -91 TGTTATGGGTGACGCCGGAGCTTACGTGGT 1 226 0 GACGCCGGAG 0.955753 -50 ACATAATCGGTACGGGGGTGAAAAAGCTAA 3 62 1 TACGGGGGTG 0.971032 -135 ********** Masking position 2 Map Score: 1.90559 Number of sites scoring better than the average of aligned sites = 2227 Number in coding regions = 2136 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 6 TTTCACCCGATTTTGTGCTGATCAGAATTT 1 132 1 TTTTGTGCTG 0.973873 -144 TGATCAGAATTTTTTTTCTTTTTCCCCCTT 1 150 1 TTTTTTTCTT 0.953871 -126 TATCTTTATTCCTTAAATTCGTAT 2 30 0 TTTATTCCTT 0.923836 -14 CGTGAAAAATTTTTTATCTTATCACTTGAA 3 123 1 TTTTTATCTT 0.862733 -74 GTTAGCACTCTTTAGTGCTGA 3 186 1 TTTAGTGCTG 0.962981 -11 ********** Masking position 3 Map Score: 0.0849277 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 337 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 7 ********** No masking Map Score: 1.48747e-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: 1.48747e-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: 1.48747e-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