AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00960_ecoli_reg_100.orf -o00960_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 speF 300 ornithine decarboxylase isozyme, inducible #2 tynA 247 copper amine oxidase (tyramine oxidase) #3 speC 300 ornithine decarboxylase isozyme Motif number 1 TTATTTATCAGCGGGGTAACTTTGCTTTTT 1 213 1 GCGGGGTAAC 0.945853 -88 TTAGGTAATAGCAGGTCCTCAATTTCTCGA 1 265 0 GCAGGTCCTC 0.93749 -36 TCGGTGAATGAAGGGCAACGGCGAATAGT 2 10 1 GAAGGGCAAC 0.957175 -238 TAGTGAAATAAAAGGGCAACTATTCGCCGT 2 28 0 AAAGGGCAAC 0.847247 -220 ACATCTATTTTCAGGGCATCCACTGTATGA 2 93 1 TCAGGGCATC 0.967119 -155 TGTATGAAAAGCTGGCACACCTGCCAAACA 2 116 1 GCTGGCACAC 0.854572 -132 CCTGGCAGGTGCAGGCAATCCCCTTTGCAT 2 147 1 GCAGGCAATC 0.982758 -101 GGCGGTTTAGTCAGGTTCACATTATCAGTA 2 180 0 TCAGGTTCAC 0.668768 -68 TTGCGAACAAACAAGCCATCGACGGCACCA 3 22 0 ACAAGCCATC 0.691858 -279 AGGAGAAAATTCGCGCAATCATGGCACCTT 3 76 0 TCGCGCAATC 0.707572 -225 ATGGCGTGCATCGGGCAAACTCCGTACAGA 3 107 0 TCGGGCAAAC 0.926051 -194 TTTGCCCGATGCACGCCATCTCCTTACATT 3 118 1 GCACGCCATC 0.972899 -183 AGTAACATAGAAAGGGAAACGTTTCGCGCG 3 167 0 AAAGGGAAAC 0.71515 -134 TGAAGTTAACGCACGCTCACTGCAGGACAA 3 207 1 GCACGCTCAC 0.900618 -94 CACGCTCACTGCAGGACAACAGTAAAATCA 3 218 1 GCAGGACAAC 0.954155 -83 ********** Masking position 5 Map Score: 14.5791 Number of sites scoring better than the average of aligned sites = 4559 Number in coding regions = 4171 Number in noncoding regions = 388 Number of orfs with sites within 600 bp upstream = 279 Fraction of orfs with sites within 600 bp upstream = 0.0448121 Motif number 2 TGTTAACCCTTGTATTATCAGCCACCTGACT 1 141 1 TGTATTTCAG 0.893464 -160 CAGGTAGATTGCTTTTTTCAGAATGCAGAAA 1 180 0 GCTTTTTCAG 0.947716 -121 GGGTAACTTTGCTTTTTTCCGGCACGATCGA 1 226 1 GCTTTTTCCG 0.944295 -75 CTTTATTTTAGGTAATAGCAGGTCCTCAATT 1 271 0 GGTAATGCAG 0.966506 -30 TAAAAGGGCAACTATTCGCCGTTGCCCTTCA 2 19 0 ACTATTGCCG 0.898086 -229 GATGTGTACATCTATTTTCAGGGCATCCACT 2 86 1 TCTATTTCAG 0.875493 -162 CTCTGTGGGCGGTTTAGTCAGGTTCACATTA 2 186 0 GGTTTATCAG 0.927254 -62 GCGTGCATCGGGCAAACTCCGTACAGAGAGG 3 103 0 GGCAAATCCG 0.762132 -198 ACATTCTCTCGCTTATCGCCGTTTCGCGCGA 3 143 1 GCTTATGCCG 0.930269 -158 GCAGGACAACAGTAAAATCAGAGCGTTTCTG 3 228 1 AGTAAATCAG 0.856372 -73 GCCAGACATCAGTAAAAGCAGAAACGCTCTG 3 246 0 AGTAAAGCAG 0.847933 -55 ****** **** Masking position 9 Map Score: 6.8036 Number of sites scoring better than the average of aligned sites = 1189 Number in coding regions = 1075 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 3 ACTAAGGGCACTTCAGCGTACAGGTCTTCCTGACT 1 61 1 CTACTCAGGT 0.990803 -240 CTTCCTGACTCTCTGTATTACAGGCATATGCCTGT 1 86 1 CTGATCAGGC 0.983108 -215 AGAATGAGCACTGCGGAATACAGGCATATGCCTGT 1 105 0 CTGATCAGGC 0.986538 -196 ATGCAGAAACCCTTACCAGTCAGGTGGCTGATAAT 1 154 0 CCACGCAGGT 0.975231 -147 AGGGGATTGCCTGCACCTGCCAGGTTGTTTGGCAG 2 136 0 CTACGCAGGT 0.992372 -112 GGCACCTTTGCTAAAGCGTGCAAGCCAGGACTTTG 3 49 0 CTACTCAAGC 0.966515 -252 TGGTCACCAGCTCCGACCGCCAGACATCAGTAAAA 3 260 0 CTGCGCAGAC 0.974714 -41 ** * * * ***** Masking position 12 Map Score: 4.82857 Number of sites scoring better than the average of aligned sites = 747 Number in coding regions = 697 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 ATGCCTGTAATACAGAGAGTCAGGAAGACC 1 83 0 TACAGAGAGT 0.968004 -218 TACAAGGGTTAACAGAGAATGAGCACTGCG 1 125 0 AACAGAGAAT 0.856006 -176 TTACCTAAAATAAAGAGATGAAAA 1 287 1 TAAAGAGATG 0.981394 -14 GGATGCCCTGAAAATAGATGTACACATCAT 2 84 0 AAAATAGATG 0.813899 -164 GCAAACTCCGTACAGAGAGGAGAAAATTCG 3 93 0 TACAGAGAGG 0.988954 -208 CGAGAGAATGTAAGGAGATGGCGTGCATCG 3 124 0 TAAGGAGATG 0.950706 -177 ********** Masking position 6 Map Score: 1.68111 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 161 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 AACGGGCATTGAAGAAGTGAAAGTCGAAGCT 1 21 0 GAAGAGTGAA 0.921394 -280 ACACATCATGCATAATGTGACAACGTCACAA 2 62 0 CATAAGTGAC 0.917001 -186 TCACATTATGCATGATGTGTACATCTATTTT 2 73 1 CATGAGTGTA 0.95752 -175 GCCAGCTTTTCATACAGTGGATGCCCTGAAA 2 101 0 CATACGTGGA 0.930602 -147 CATCAGTACTGATAATGTGAACCTGACTAAA 2 174 1 GATAAGTGAA 0.96471 -74 AATGTAAGGAGATGGCGTGCATCGGGCAAAC 3 117 0 GATGGGTGCA 0.919729 -184 TGTTACTGCTCATGCGGTGAAGTTAACGCAC 3 190 1 CATGCGTGAA 0.983995 -111 ***** ***** Masking position 2 Map Score: 1.30014 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 305 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 TAGTCGGTAGACTAACGGGCATTGAAGAAG 1 35 0 ACTAACGGGC 0.962626 -266 GACTAAGGGCACTTCAGCGTACAGGTCTTC 1 60 1 ACTTCAGCGT 0.730409 -241 AAAAAGCAAAGTTACCCCGCTGATAAATAA 1 213 0 GTTACCCCGC 0.855901 -88 ACTTAGTGAAATAAAAGGGCAACTATTCGC 2 31 0 ATAAAAGGGC 0.689997 -217 CACCTGCCAAACAACCTGGCAGGTGCAGGC 2 133 1 ACAACCTGGC 0.737174 -115 TGTGAACCTGACTAAACCGCCCACAGAGCG 2 189 1 ACTAAACCGC 0.970456 -59 GTTCTTGTTAGCAACCGCGCTCTGTGGGCG 2 206 0 GCAACCGCGC 0.952881 -42 CATCGACGGCACCAAACGGTCATAA 3 6 0 ACCAAACGGT 0.677322 -295 TGGCACCTTTGCTAAAGCGTGCAAGCCAGG 3 55 0 GCTAAAGCGT 0.883847 -246 AACGTTTCGCGCGAAACGGCGATAAGCGAG 3 150 0 GCGAAACGGC 0.887871 -151 GCGTGCGTTAACTTCACCGCATGAGCAGTA 3 193 0 ACTTCACCGC 0.916232 -108 ********** Masking position 9 Map Score: 2.88249 Number of sites scoring better than the average of aligned sites = 4095 Number in coding regions = 3835 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 254 Fraction of orfs with sites within 600 bp upstream = 0.0407967 Motif number 7 ********** No masking Map Score: -3.30951e-14 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: -3.30951e-14 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: -3.30951e-14 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