AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i174_Biotin_Biosynthesis_bsub_reg_100.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 yngI 43 similar to long-chain acyl-CoA synthetase #2 yngJ 90 similar to butyryl-CoA dehydrogenase #3 ynzE 270 ynzE #4 accB 155 acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit) Motif number 1 GACGACTTAGAAAGCCGTCCTTCTCATTTC 3 11 0 AAAGCCGTCC 0.992923 -260 CTTTTTAAAAAAAGACGACTTAGAAAGCCG 3 24 0 AAAGACGACT 0.957031 -247 GTAAATGTCCAAACACCGCCTCCATATTCA 3 119 0 AAACACCGCC 0.990649 -152 AATCGAAGAGAAACACGTACAGGACGTGTT 3 189 1 AAACACGTAC 0.919861 -82 TGAAAACGTAAAACACGTCCTGTACGTGTT 3 200 0 AAACACGTCC 0.988822 -71 ATGAGGGAAAAAAGCCCGCTAAACAAGCGG 4 13 1 AAAGCCCGCT 0.987854 -143 AGCAACGCAAAAAGCCCGCTTGTTTAGCGG 4 28 0 AAAGCCCGCT 0.987854 -128 ********** Masking position 3 Map Score: 10.6506 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 292 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 AAATGTAAACGCTTTCCTATC 1 1 1 AAATGAAACG 0.989611 -43 GATGTTACAAAGATGTGAAGGAGGAAACGAT 2 70 1 AGATGGAAGG 0.93756 -21 GAAATGAGAAGGACGGCTTTCT 3 2 1 AAATGGAAGG 0.979919 -269 ATCACTTTTTAAAAAAAGACGACTTAGAAAG 3 27 0 AAAAAAGACG 0.860596 -244 GAATTTTTTAAAAAACAAAGGTGAGATTCAC 3 87 1 AAAAAAAAGG 0.938555 -184 TACTAAATAAAAATAAAATCGAAGAGAAACA 3 173 1 AAATAAATCG 0.905434 -98 ACCAGACTAGAAATGAAAACGTAAAACACGT 3 212 0 AAATGAAACG 0.989611 -59 ***** ***** Masking position 3 Map Score: 5.54541 Number of sites scoring better than the average of aligned sites = 575 Number in coding regions = 467 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 3 GTAAACGCTTTCCTATCATTAAGAAAGGAG 1 15 1 TCCTATCATT 0.740479 -29 TTCAGACTTTTCTTGTCAGGGAATGATTAT 2 24 1 TCTTGTCAGG 0.973329 -67 CTTTGTAACATCCTATTAGGCGAGTTCTAT 2 52 0 TCCTATTAGG 0.946953 -39 TACCATCGTTTCCTGTCCCAAAATCACTTT 3 50 0 TCCTGTCCCA 0.935027 -221 GTAAAACACGTCCTGTACGTGTTTCTCTTC 3 193 0 TCCTGTACGT 0.946394 -78 TCATTTCTAGTCTGGTTAGGTGCCACATTA 3 227 1 TCTGGTTAGG 0.806704 -44 TTATTTTTTGTGCTGTTCGGAGATGCT 3 254 1 TGCTGTTCGG 0.957996 -17 CTTTTTGCGTTGCTGTCATATTAGAGTTGA 4 44 1 TGCTGTCATA 0.863467 -112 ACAAGTCCGCTCCTGTAAGATGAACATAGT 4 78 1 TCCTGTAAGA 0.966552 -78 ********** Masking position 6 Map Score: 4.512 Number of sites scoring better than the average of aligned sites = 1659 Number in coding regions = 1491 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 4 GAGTTCTATAATCATTCCCTGACAAGAAAA 2 31 0 ATCATTCCCT 0.987576 -60 ATCGTTTCCTCCTTCACATC 2 81 0 ATCGTTTCCT 0.996139 -10 GCGGTTTACCATCGTTTCCTGTCCCAAAAT 3 56 0 ATCGTTTCCT 0.996139 -215 ********** Masking position 1 Map Score: 3.03193 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 25 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 TATCATTAAGAAAGGAGGAACAATGA 1 28 1 AAAGGAGGAA 0.985251 -16 ACAAAGATGTGAAGGAGGAAACGAT 2 76 1 GAAGGAGGAA 0.99057 -15 GAAATGAGAAGGACGGCTTTCTAAGTC 3 8 1 GAAGGACGGC 0.98622 -263 ACTTTTTAAAAAAAGACGACTTAGAAAGCC 3 25 0 AAAAGACGAC 0.847253 -246 TTTAAAAAACAAAGGTGAGATTCACATGAA 3 93 1 AAAGGTGAGA 0.800358 -178 GAATGAGGGAAAAAAGCCCG 4 1 1 GAATGAGGGA 0.969372 -155 ********** Masking position 3 Map Score: 3.46876 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 461 Number in noncoding regions = 253 Number of orfs with sites within 600 bp upstream = 302 Fraction of orfs with sites within 600 bp upstream = 0.0485063 Motif number 6 TCATTGTTCCTCCTTTCTTAATG 1 31 0 TTGTTCCTCC 0.799263 -13 TAATTTTCAGACTTTTCTTGTCAGGGAATG 2 19 1 ACTTTTCTTG 0.800023 -72 AGTTCTATAATCATTCCCTGACAAGAAAAG 2 30 0 TCATTCCCTG 0.979617 -61 ATCGTTTCCTCCTTCACATCT 2 80 0 TCGTTTCCTC 0.985564 -11 CGGTTTACCATCGTTTCCTGTCCCAAAATC 3 55 0 TCGTTTCCTG 0.988971 -216 TTTTACGTTTTCATTTCTAGTCTGGTTAGG 3 217 1 TCATTTCTAG 0.826207 -54 TTAGCGGGCTTTTTTCCCTCATTC 4 5 0 TTTTTCCCTC 0.90894 -151 ********** Masking position 5 Map Score: 2.27428 Number of sites scoring better than the average of aligned sites = 1032 Number in coding regions = 894 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 7 ********** No masking Map Score: -1.11312e-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: -1.11312e-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: -1.11312e-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