AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i066_Lysine_Biosynthesis_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 lysA 105 diaminopimelate decarboxylase #2 spoVAA 121 mutants lead to the production of immature spores (stage V sporulation) #3 spoIIAA 95 anti-anti-sigma factor (antagonist of SpoIIAB) #4 dacF 154 D-alanyl-D-alanine carboxypeptidase (penicilin binding protein) #5 drm 160 phosphodeoxyribomutase #6 ripX 300 integrase/recombinase #7 yutL 122 similar to diaminopimelate epimerase #8 yutK 136 similar to Na+/nucleoside cotransporter #9 yuzB 262 yuzB Motif number 1 ATAAAACTGTCCTTTCATCCATAAGCGGAG 1 71 1 CCTTTCATCC 0.854059 -35 GCAGGCTAGCTTTTTTGTGCAAAAGCGTGG 2 19 1 TTTTTTGTGC 0.716769 -103 GATTTTGTTCTCATTCATCCGCTCGAAAAG 2 60 0 TCATTCATCC 0.713951 -62 ACAGCTGTCTTTTTTTATGCCCAAAATTCG 4 56 1 TTTTTTATGC 0.915564 -99 CAAGCGTGATGGTTTTATACGCCACTGATG 4 96 0 GGTTTTATAC 0.729185 -59 AGTATAAACCGTTTTCATTCCCGTTGACAA 5 82 0 GTTTTCATTC 0.822357 -79 TGCATTGAAAGTTTTCATCCTGTTTACCGG 6 106 1 GTTTTCATCC 0.960249 -195 ACCGCTTTGTTCTATTATGCTATGATATGG 6 140 1 TCTATTATGC 0.759636 -161 ACCGATGATAGTTTTCATACTCTTGATTCA 6 171 0 GTTTTCATAC 0.967054 -130 GAGCTTCCGGTTTATCATACCGATGATAGT 6 189 0 TTTATCATAC 0.873962 -112 ACCATCCGCCTTTTTCATCCTGATCCATTT 6 236 0 TTTTTCATCC 0.961032 -65 TTATCCCCCGTTTTTCATACATAAAAGCTC 7 40 0 TTTTTCATAC 0.967719 -83 GCTTATAATAGCTTTTATACTAAGAAAAAG 7 83 1 GCTTTTATAC 0.942082 -40 TTTTTTTAGTTCTTTTGTACGGCAAAATAA 8 37 0 TCTTTTGTAC 0.794921 -100 TAAAAAAATATCTTTTATACGATAACAATA 8 88 0 TCTTTTATAC 0.943209 -49 CTTCAATGTATCTATCATACTCTTCGGATT 9 25 0 TCTATCATAC 0.897303 -238 ACTAATTTGTGTTTTCAGGCTAAATTGTAG 9 133 0 GTTTTCAGGC 0.741989 -130 ********** Masking position 5 Map Score: 17.845 Number of sites scoring better than the average of aligned sites = 1025 Number in coding regions = 830 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 2 TGCAGGACCAAAAGACAGCTGTGTCTGATAT 4 22 1 AAAGACGCTG 0.97297 -133 GGGCATAAAAAAAGACAGCTGTGTGATATCA 4 47 0 AAAGACGCTG 0.97297 -108 CTCTAAACAAAAAAGCCGCAGCCACCTGCGG 5 11 0 AAAAGCGCAG 0.943082 -150 GTATAGAAAAAAAGGAGGCTTTCAAG 5 145 1 AAAGGAGCTT 0.800786 -16 GAAGATTCCTGAAAACAGCTGTCGATGCATT 6 81 1 GAAAACGCTG 0.873882 -220 TCAGGATGAAAAAGGCGGATGGTTCGACCGG 6 243 1 AAAGGCGATG 0.917668 -58 ACGATAAAAGCTCCTTGCGTCAGTGC 7 6 1 AAAAGCCCTT 0.957372 -117 TTTCATACATAAAAGCTCCTTGCACTGACGC 7 27 0 AAAAGCCCTT 0.957372 -96 AGAAAAGGGCCTGGACAGGCCCT 8 3 1 AAAAGGCCTG 0.96044 -134 GGCAAAATAAAAAAGGGCCTGTCCAGGCCCT 8 16 0 AAAAGGCCTG 0.96044 -121 ****** **** Masking position 3 Map Score: 9.35415 Number of sites scoring better than the average of aligned sites = 2093 Number in coding regions = 1851 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 3 AGGACCAAAAGACAGCTGTGTCTGATATCA 4 25 1 GACAGCTGTG 0.682251 -130 CATAAAAAAAGACAGCTGTGTGATATCAGA 4 45 0 GACAGCTGTG 0.682251 -110 TCAATGCATCGACAGCTGTTTTCAGGAATC 6 84 0 GACAGCTGTT 0.676863 -217 CGCGATAATGGACATATGTGAGGTGAAACC 9 241 1 GACATATGTG 0.906072 -22 ********** Masking position 4 Map Score: 5.21517 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 12 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 TTCATAATCCTTTTTATTTTTTCCAAGCGTGA 4 117 0 TTTTTTTTTT 0.714396 -38 ATATTGAAGTTTCTCATTATTTCCAAATACAT 5 51 1 TTTCTTATTT 0.640414 -110 GTTCGACCGGTTGATCTTTTTTTACCAAAACG 6 264 1 TTATTTTTTT 0.899984 -37 TTTTGATGTCTACACATTTTTTTAGTTCTTTT 8 51 0 TAACTTTTTT 0.903651 -86 TACGATAACAATAATATTTTTTGATGTCTACA 8 69 0 ATATTTTTTT 0.859771 -68 TATCGTATAAAAGATATTTTTTTAAATAAAAT 8 94 1 AAATTTTTTT 0.899674 -43 GTACACCTCTTAAATTTTATTTAAAAAAATAT 8 107 0 TAATTTATTT 0.929446 -30 GATATAATTCTAGATGTTATTTTACATAGTTC 9 62 0 TAATTTATTT 0.929448 -201 ACAAATTAGTAAAACGTTATTTGAGAAATAAT 9 153 1 AAACTTATTT 0.864907 -110 TTATTATCGTAACATATTATTTCTCAAATAAC 9 168 0 AAATTTATTT 0.899898 -95 ** ** ****** Masking position 7 Map Score: 4.31543 Number of sites scoring better than the average of aligned sites = 478 Number in coding regions = 313 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 5 GAGAACAAAATCGAACCACATACTACATATA 2 78 1 TCGAACACAT 0.809866 -44 TCCGTCGAAATCGAAACACTCATTATCCGAT 3 55 1 TCGAACACTC 0.96161 -41 TGGTCCTGCATTGATTCATAT 4 1 0 TTGATCATAT 0.662236 -154 TGCCCAAAATTCGAAACATTTTCCATCAGTG 4 73 1 TCGAACATTT 0.932211 -82 CATGTCCTAATCGATCCTTTCCCTATGGTTC 6 49 0 TCGATCTTTC 0.831938 -252 AAAACAGCTGTCGATGCATTGAAAGTTTTCA 6 92 1 TCGATCATTG 0.936888 -209 TTTCATACTCTTGATTCACCCATATCATAGC 6 158 0 TTGATCACCC 0.889462 -143 GATCAACCGGTCGAACCATCCGCCTTTTTCA 6 249 0 TCGAACATCC 0.971818 -52 AAGAGTATGATAGATACATTGAAGAAAATAC 9 31 1 TAGATCATTG 0.658182 -232 ATAATAAATTTTGAATCATCCGTTGTCTTTG 9 193 1 TTGAACATCC 0.918709 -70 ***** ***** Masking position 4 Map Score: 4.14279 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 358 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 CATACATTATCATACTCTTCAGTCAGTTTC 1 18 0 CATACTCTTC 0.977331 -88 TGAAAGTTTTCATCCTGTTTACCGGTTTTA 6 111 1 CATCCTGTTT 0.89993 -190 TGATAGTTTTCATACTCTTGATTCACCCAT 6 166 0 CATACTCTTG 0.967312 -135 TCCGGTTTATCATACCGATGATAGTTTTCA 6 184 0 CATACCGATG 0.851757 -117 CCGCCTTTTTCATCCTGATCCATTTCAACA 6 231 0 CATCCTGATC 0.949702 -70 ATGTATCTATCATACTCTTCGGATTAAAGG 9 20 0 CATACTCTTC 0.977331 -243 ********** Masking position 3 Map Score: 2.63616 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 152 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 AAGACCATAAATTACCACGCTTTTGCACAAAAAA 2 29 0 ATACCCCTTT 0.978767 -93 TTATGCCGAATGACCACTAGTTTTGTCACGGTG 3 10 1 ATACCCATTT 0.982421 -86 ATCCTGATCCATTTCAACAACTTTTACAGCGGAG 6 216 0 ATTCACATTT 0.828106 -85 ACACAATACAATTATCCCCCGTTTTTCATACATA 7 47 0 ATATCCCTTT 0.95912 -76 ATATTTTTTGATGTCTACACATTTTTTTAGTTCT 8 54 0 ATTCTCCTTT 0.798942 -83 AACATCTAGAATTATATCGAATTTGATCTAAAAT 9 76 1 ATATACATTT 0.88578 -187 TAGTTTCAAAATAACCTACAATTTAGCCTGAAAA 9 118 1 ATACCAATTT 0.916694 -145 AAGACAACGGATGATTCAAAATTTATTATCGTAA 9 188 0 ATATTAATTT 0.60442 -75 ACATATGTCCATTATCGCGAATTTTTCACTATTC 9 226 0 ATATCCATTT 0.965717 -37 ** *** * * *** Masking position 12 Map Score: 3.19825 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 292 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 8 AAGCGGAGAAAGAGGGAATGACA 1 93 1 AGAGGAATGA 0.969134 -13 ATGGTCTTTTCGAGCGGATGAATGAGAACAA 2 55 1 CGACGGATGA 0.981961 -67 ACATATATAACCACCGAAAGATGGTGATCA 2 102 1 CCACGAAAGA 0.921427 -20 TTATGCCGAATGACCACTAGTTT 3 3 1 ATGCGAATGA 0.72122 -93 GTTTCGATTTCGACGGAATGAATTCCTTCAC 3 41 0 CGAGGAATGA 0.971443 -55 GATCATATCAAGGAGGAATGAGC 3 83 1 AGGGGAATGA 0.931038 -13 TTTTTTGTTTAGAGCGACAGAAAATATTGAA 5 28 1 AGACGACAGA 0.830719 -133 ATCGATTAGGACATGGGAAGATTCCTGAAAA 6 65 1 ACAGGGAAGA 0.888117 -236 GCGGATGGTTCGACCGGTTGATCTTTTTTTA 6 257 1 CGACGGTTGA 0.895648 -44 TTCGTCAAAGACAACGGATGATTCAAAATTT 9 198 0 ACACGGATGA 0.962715 -65 *** ******* Masking position 11 Map Score: 6.8324 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 346 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 TCGCATTGAAACTGACTGAAGA 1 3 1 GCATTGAAAC 0.890254 -103 TCATCCATAAGCGGAGAAAGAGGGAATGAC 1 85 1 GCGGAGAAAG 0.952356 -21 TCTGCAGTGCAGGCTAGCTTTTT 2 4 1 GCAGTGCAGG 0.950232 -118 TAGTTTTGTCACGGTGAAGGAATTCATTCC 3 28 1 ACGGTGAAGG 0.873758 -68 AGCTGTCGATGCATTGAAAGTTTTCATCCT 6 97 1 GCATTGAAAG 0.940269 -204 ATAGAACAAAGCGGTAAAACCGGTAAACAG 6 125 0 GCGGTAAAAC 0.927806 -176 CGGAAGCTCCGCTGTAAAAGTTGTTGAAAT 6 210 1 GCTGTAAAAG 0.827068 -91 GCTCCTTGCGTCAGTGCAAGGAGCTTTTAT 7 20 1 TCAGTGCAAG 0.813558 -103 GGACATATGTGAGGTGAAACCGC 9 250 1 GAGGTGAAAC 0.864977 -13 ********** Masking position 8 Map Score: 2.21607 Number of sites scoring better than the average of aligned sites = 1223 Number in coding regions = 1122 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 10 ********** No masking Map Score: 3.40593e-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 11 ********** No masking Map Score: 3.40593e-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 12 ********** No masking Map Score: 3.40593e-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