AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i021_bsub_mtub_100.orf -o021_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 sucC 172 succinyl-CoA synthetase (beta subunit) #2 sucD 28 succinyl-CoA synthetase (alpha subunit) #3 sucC 300 sucC Motif number 1 ACGGGCGATACGGTGCTGGGACAAATCT 3 3 1 GGCGACGTCG 0.986379 -298 ATGGTCACGATCCGAGGACATTTCAGATTTGTCCCA 3 27 0 TCGAACATCG 0.943747 -274 CCATCCGGTTGCGGATAACGTCTCAGGGTCCAGATA 3 68 0 GGGAACGCCG 0.995466 -233 GCGCTGAAGTTGCCACTACCATCCGGTTGCGGATAA 3 86 0 TCCAACCTCG 0.971712 -215 CACAATCACAGCCGAATTCCGCGCTGAAGTTGCCAC 3 106 0 GCGATCCCCG 0.995317 -195 TGATTGTGAGTTGGATCACGTTTCGGCTGGACAAAC 3 134 1 TGGAACGTCG 0.982417 -167 TTAACTCCGCGGCCGCATCCACCCGGTGTGGCACAG 3 181 0 GCCGTCCCCG 0.989052 -120 GGAGTTAATCGGCGGTCTCGATACAGTTCTCCGTGC 3 209 1 GCGGTCGTCG 0.995506 -92 CGTGCGAGTCGCCGATTTCGGCACCGCCTACCTATT 3 240 1 GCGATCGCCG 0.997116 -61 * *** *** * * * Masking position 9 Map Score: 14.1454 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 480 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 2 CTAAAATATTCCCCATCCTTCTTTGAAAT 1 10 1 TCCCCATCCT 0.994917 -163 TTCCCATCCTCCTAACTTAT 1 163 0 TTCCCATCCT 0.956252 -10 TATTTGGTCCCCTGCCTTTCATTCTTT 2 12 0 TCCCCTGCCT 0.97931 -17 AACGTTATGGTCACGATCCGAGGACATTTC 3 39 0 TCACGATCCG 0.938436 -262 TGAGACGTTATCCGCAACCGGATGGTAGTG 3 79 1 TCCGCAACCG 0.966553 -222 CCGATATGTTTGTCCAGCCGAAACGTGATC 3 147 0 TGTCCAGCCG 0.944502 -154 GCCGATTAACTCCGCGGCCGCATCCACCCG 3 192 0 TCCGCGGCCG 0.991192 -109 TCGATACAGTTCTCCGTGCGAGTCGCCGAT 3 226 1 TCTCCGTGCG 0.937269 -75 GGGCTCACCGTCTTCGCTCGGCTT 3 287 0 TCACCGTCTT 0.836895 -14 ********** Masking position 1 Map Score: 9.23678 Number of sites scoring better than the average of aligned sites = 1289 Number in coding regions = 1139 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 3 TAAATTTCAAAGAAGGATGGGGAATATTTT 1 13 0 AGAAGGATGG 0.995354 -160 TTGAATGTTTAGAAGGATTAAAAGATTTTG 1 64 1 AGAAGGATTA 0.937697 -109 GTATTATTATAGAATGAAAGCGCAGTCTAT 1 119 1 AGAATGAAAG 0.97722 -54 TACATAAGTTAGGAGGATGGGAA 1 160 1 AGGAGGATGG 0.989744 -13 GAAAGAATGAAAGGCAGGGGACC 2 4 1 AGAATGAAAG 0.97722 -25 ********** Masking position 4 Map Score: 4.60147 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 144 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 4 ACGGGCGATACGGTGCTGGG 3 1 1 ACGGGCGATA 0.855336 -300 GACGTTATCCGCAACCGGATGGTAGTGGCA 3 82 1 GCAACCGGAT 0.854546 -219 ACTCACAATCACAGCCGAATTCCGCGCTGA 3 115 0 ACAGCCGAAT 0.981512 -186 ATATGTTTGTCCAGCCGAAACGTGATCCAA 3 144 0 CCAGCCGAAA 0.97277 -157 TGTGGCACAGCTCACCGATATGTTTGTCCA 3 161 0 CTCACCGATA 0.746109 -140 GATTAACTCCGCGGCCGCATCCACCCGGTG 3 189 0 GCGGCCGCAT 0.965191 -112 CTGTATCGAGACCGCCGATTAACTCCGCGG 3 205 0 ACCGCCGATT 0.988163 -96 CTCCGTGCGAGTCGCCGATTTCGGCACCGC 3 237 1 GTCGCCGATT 0.967766 -64 ********** Masking position 6 Map Score: 4.18676 Number of sites scoring better than the average of aligned sites = 2683 Number in coding regions = 2496 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 5 ATTATAGAATGAAAGCGCAGTCTATTTTAG 1 124 1 GAAAGCGCAG 0.970565 -49 AAACATATCGGTGAGCTGTGCCACACCGGG 3 166 1 GTGAGCTGTG 0.934974 -135 AGGCGGTGCCGAAATCGGCGACTCGCACGG 3 239 0 GAAATCGGCG 0.958661 -62 CGACCAATAGGTAGGCGGTGCCGAAATCGG 3 251 0 GTAGGCGGTG 0.994182 -50 TGGTCGAGCAGTAAGCCGAGCGAAGACGGT 3 275 1 GTAAGCCGAG 0.976085 -26 TAAGCCGAGCGAAGACGGTGAGCCC 3 286 1 GAAGACGGTG 0.970393 -15 ********** Masking position 6 Map Score: 2.98887 Number of sites scoring better than the average of aligned sites = 910 Number in coding regions = 869 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 ********** No masking Map Score: 4.14547e-13 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 7 ********** No masking Map Score: 4.14547e-13 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: 4.14547e-13 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