AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i014_Glycolysis_1_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 tpi 30 triose phosphate isomerase #2 pgk 300 phosphoglycerate kinase #3 gap 46 glyceraldehyde-3-phosphate dehydrogenase #4 yvbQ 297 yvbQ #5 araE 137 permease Motif number 1 AAAACTGCTATAAGGAAGTGGAACAG 1 15 1 TAAGGAAGTG 0.749487 -16 GGTTCTTTCGAATAGAAGCGCTATAATGAA 2 21 1 AATAGAAGCG 0.885323 -280 GAAGCGCTATAATGAAAGCGGACAAGGGAA 2 35 1 AATGAAAGCG 0.958619 -266 GAAAGCGGACAAGGGAAGGGGACGGACTCC 2 48 1 AAGGGAAGGG 0.974454 -253 TTCATGGAAAAAGGGAAAGGGAGTCCGTCC 2 67 0 AAGGGAAAGG 0.954269 -234 AGACCGGCTTTCAGAAAACGCTCTGTGATA 2 96 1 TCAGAAAACG 0.890873 -205 CGCTCTGTGATAGAGAAACGACCGCGTTTT 2 114 1 TAGAGAAACG 0.743927 -187 TGCATACAGCACGAAAAACGTGAAACCGTC 2 253 0 ACGAAAAACG 0.892502 -48 AGCCCTTTCTACGGGAAGGGCTGTTTATAT 4 28 1 ACGGGAAGGG 0.976403 -270 TTTATCTTATACAGAAAGCGCCAAATGGTG 4 65 0 ACAGAAAGCG 0.982301 -233 TAAAATAATTAAAGAAAGCAGAAATGATTT 4 201 1 AAAGAAAGCA 0.845955 -97 TCCCGCTATGACAAAAAACGTCCCGTCATA 4 239 0 ACAAAAAACG 0.87756 -59 GTCCAGCAAAAAAGGAAGGAACGTTTGAGT 4 277 1 AAAGGAAGGA 0.77947 -21 TGACAGAAAATGCAAACAAGAT 5 3 1 ACAGAAAATG 0.823862 -135 TGAAGGTTTAAATGAAAACGCTTTACTCAA 5 99 1 AATGAAAACG 0.926862 -39 ********** Masking position 6 Map Score: 19.388 Number of sites scoring better than the average of aligned sites = 3393 Number in coding regions = 3002 Number in noncoding regions = 391 Number of orfs with sites within 600 bp upstream = 389 Fraction of orfs with sites within 600 bp upstream = 0.0624799 Motif number 2 ATGGAAAAAGGGAAAGGGAGTCCGTCCCCT 2 64 0 GGAAAGGGAG 0.822168 -237 GGCCTTAGGCGAAAGCGCCGGCAAAGCTGC 2 146 0 GAAAGCGCCG 0.978178 -155 GGCGCTTTCGCCTAAGGCCGCTGCCCTGGC 2 157 1 CCTAAGGCCG 0.8028 -144 TCGTCTAAAAGCCAGGGCAGCGGCCTTAGG 2 167 0 GCCAGGGCAG 0.992856 -134 TCTTTTTCGGCACAGGGCAGTTCGTCTAAA 2 188 0 CACAGGGCAG 0.968528 -113 CGATAACTCCGCTAGGGCAGATCGCAGTCT 2 215 0 GCTAGGGCAG 0.988993 -86 CCTTCCCGTAGAAAGGGCTGTTTCATTAAA 4 17 0 GAAAGGGCTG 0.986738 -281 CCTTTCTACGGGAAGGGCTGTTTATATTGG 4 31 1 GGAAGGGCTG 0.988993 -267 ATCTTATACAGAAAGCGCCAAATGGTGCAT 4 62 0 GAAAGCGCCA 0.7966 -236 CTCAACATTCGGGAGGGCAGGGAA 5 124 1 GGGAGGGCAG 0.986931 -14 ********** Masking position 4 Map Score: 12.933 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 488 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 TATAATGAAAGCGGACAAGGGAAGGGGACG 2 42 1 GCGGACAAGG 0.976028 -259 AGGCGAAAGCGCCGGCAAAGCTGCTTAAAA 2 140 0 GCCGGCAAAG 0.942065 -161 ACTGCCCTGTGCCGAAAAAGACTGCGATCT 2 197 1 GCCGAAAAAG 0.977659 -104 ATTAAAGAAAGCAGAAATGATTTTTTTTGG 4 208 1 GCAGAAATGA 0.852459 -90 TCCCGTCATAGCCAAAAAAAATCATTTCTG 4 219 0 GCCAAAAAAA 0.911181 -79 ATAATGTCCAGCAAAAAAGGAAGGAACGTT 4 272 1 GCAAAAAAGG 0.965314 -26 GACAGAAAATGCAAACAAGATTATTCTATA 5 12 1 GCAAACAAGA 0.942103 -126 ********** Masking position 7 Map Score: 3.73476 Number of sites scoring better than the average of aligned sites = 920 Number in coding regions = 843 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 TCTCAAAACTGCTATAAGGAAGTGGAACAG 1 10 1 TGCTATAGGA 0.850356 -21 CGAATAGAAGCGCTATAATGAAAGCGGACAA 2 29 1 CGCTATATGA 0.976024 -272 GAAACGACCGCGTTTTAAGCAGCTTTGCCGG 2 128 1 CGTTTTAGCA 0.97178 -173 AAACGCTTTAATGAAACAGCCCTT 4 4 1 CGCTTTATGA 0.981464 -294 CATGCCGCGTCGTTTTATCCAGCAATATTTT 4 107 0 CGTTTTACCA 0.973252 -191 AAAAACGTCCCGTCATAGCCAAAAAAAATCA 4 225 0 CGTCATACCA 0.895827 -73 TAAATGAAAACGCTTTACTCAACATTCGGGA 5 107 1 CGCTTTATCA 0.985802 -31 ******* *** Masking position 7 Map Score: 4.25795 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 235 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 GGCTTTTAGACGAACTGCCCTGTGCCGAAA 2 184 1 CGAACTGCCC 0.994599 -117 AAAAAGACTGCGATCTGCCCTAGCGGAGTT 2 211 1 CGATCTGCCC 0.982448 -90 AAATGGTTTGCATACAGCACGAAAAACGTG 2 261 0 CATACAGCAC 0.934373 -40 ACGCTTTAATGAAACAGCCCTTTCTACGGG 4 13 1 GAAACAGCCC 0.989153 -285 CATCCCAATATAAACAGCCCTTCCCGTAGA 4 35 0 TAAACAGCCC 0.984007 -263 ********** Masking position 5 Map Score: 3.58466 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 256 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 CTGTTCCACTTCCTTATAGCAGTTTTGA 1 13 0 TCCCTCTATA 0.939178 -18 GACCTGACTTGGTTCTTTCGAATAGAAGCGCTAT 2 10 1 TGTCTCAATA 0.994249 -291 AAGCGCCAAATGGTGCATCCCAATATAAACAGCCC 4 45 0 TGTCTCAATA 0.994249 -253 TACATTTAATTAGTACGTACAAATATAGAATAATC 5 30 0 TGTCTCAATA 0.994215 -108 AAACCTTCAATTGTACGTACTTATATTAAAATTTA 5 73 0 TGTCTCTATA 0.991782 -65 * ** * * * **** Masking position 8 Map Score: 3.07369 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 18 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 TAGGAGATCCTCCTTCAAAATGGTTTGCAT 2 278 0 TCCTTCAAAA 0.8689 -23 TCCCTCAATATAAATATCTC 3 1 1 TCCCTCAATA 0.980053 -46 CGTCGTTTTATCCAGCAATATTTTATCCTA 4 101 0 TCCAGCAATA 0.984705 -197 ACAAAAAACGTCCCGTCATAGCCAAAAAAA 4 229 0 TCCCGTCATA 0.910181 -69 ACATTATATGTCCCGCTATGACAAAAAACG 4 249 0 TCCCGCTATG 0.941724 -49 ACATATAATGTCCAGCAAAAAAGGAAGGAA 4 268 1 TCCAGCAAAA 0.971865 -30 ********** Masking position 8 Map Score: 2.83763 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 414 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 8 ********** No masking Map Score: 1.76458e-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: 1.76458e-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: 1.76458e-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