AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i215_Ribosomal_Operon_2_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 obg 33 GTPase activity #2 spo0B 300 sporulation initiation phosphoprotein #3 rplU 146 ribosomal protein L21 (BL20) #4 spoIVFA 150 inhibitor of SpoIVFB #5 minC 52 minC #6 mreC 30 cell-shape determining protein #7 mreB 90 cell-shape determining protein #8 ysxA 36 similar to DNA repair protein #9 maf 152 maf #10 spoIIB 133 spoIIB #11 comC 139 DNA-binding protein #12 folC 59 folyl-polyglutamate synthetase #13 valS 300 valyl-tRNA synthetase Motif number 1 TCCGCATATTGCAAAAAAAACTCCAGTCAT 2 15 0 GCAAAAAAAA 0.801691 -286 AACCAAAGCCAGAAAAAAGGAACATGATAT 2 174 1 AGAAAAAAGG 0.912801 -127 GCAGGCAAAAACAAAAAAAAACCTGACACA 4 51 0 ACAAAAAAAA 0.95549 -100 ACTCATTTCGTCAAAAAAAGATAAAATCCT 5 13 0 TCAAAAAAAG 0.943607 -40 GCTTAATTCGACGAAAAAAAAGTG 7 5 0 ACGAAAAAAA 0.940345 -86 TCATGACAAAATAAAAAAAGCCTGTCACTA 9 38 0 ATAAAAAAAG 0.954694 -115 GGTTTGCTTAAGAAAAAAAGATACTCGTTT 9 116 0 AGAAAAAAAG 0.970704 -37 GCACAGGCAAAGAAAAAAAGAACAAGACTT 10 53 0 AGAAAAAAAG 0.970704 -81 TCCGGCAGAATCAAAAAAAGATTCTGCCGT 11 22 1 TCAAAAAAAG 0.943607 -118 AATTTTACACATGAAAAAAACGGCAGAATC 11 41 0 ATGAAAAAAA 0.816435 -99 CGGGAAGAGTACAAAAAAGGCGCATGCAGA 13 43 1 ACAAAAAAGG 0.95934 -258 GATTGAGTTCATGAAAAAAGGTGGTACCGC 13 200 1 ATGAAAAAAG 0.939295 -101 ATGGCTGAGAACGAAAAAAGAGCTCTTCAT 13 257 0 ACGAAAAAAG 0.982091 -44 ********** Masking position 5 Map Score: 20.8159 Number of sites scoring better than the average of aligned sites = 952 Number in coding regions = 623 Number in noncoding regions = 329 Number of orfs with sites within 600 bp upstream = 328 Fraction of orfs with sites within 600 bp upstream = 0.0526823 Motif number 2 AACGGTTTAGAACGGAGGACATT 1 21 1 AACGGAGACA 0.926556 -13 AAGCCAGAAAAAAGGAACATGATATTTCTGG 2 179 1 AAAGGACATG 0.926916 -122 GATAGAATCAAAGAGAAGAATCTGACAAAGC 4 14 1 AAGAGAGAAT 0.591119 -137 CAACGAATGCAAAGGATGATGGCA 4 137 1 AAAGGAGATG 0.978017 -14 TTTCGTCAAAAAAAGATAAAATCCTTT 5 7 0 AAAAGAAAAA 0.454418 -46 TTGCTTTAAGAAAGGAAGATACATACAT 7 73 1 AAAGGAGATA 0.940318 -18 GCCTGTCACTAAAGGACGAAGGCTCAGGGCA 9 18 0 AAAGGAGAAG 0.988477 -135 GCAAACCCTGAAAGGATGACGAAC 9 139 1 AAAGGAGACG 0.986027 -14 GGCAAAGAAAAAAAGAACAAGACTTTTGTCG 10 47 0 AAAAGACAAG 0.84125 -87 GTGTAGCATGAAAAGCCGACAAGAACGGTCA 10 89 1 AAAAGCGACA 0.67925 -45 CAAGCAAATGAAGGGAGGAAGCGGAA 10 118 1 AAGGGAGAAG 0.977428 -16 ACATGAAAAAAACGGCAGAATCTTTTTTTGA 11 32 0 AACGGCGAAT 0.722896 -108 AGAGTACAAAAAAGGCGCATGCAGAGAGAGA 13 48 1 AAAGGCCATG 0.832202 -253 ATGCACTTATAACGGATAACGGGTGTTTCCC 13 164 0 AACGGAAACG 0.818424 -137 CATCCCTGTAAAAGGACGAAAAGCTCTTTCG 13 229 0 AAAGGAGAAA 0.96813 -72 CGTCCTTTTACAGGGATGAAGAGCTCTTTTT 13 242 1 CAGGGAGAAG 0.845956 -59 ****** **** Masking position 9 Map Score: 15.7185 Number of sites scoring better than the average of aligned sites = 1721 Number in coding regions = 1377 Number in noncoding regions = 344 Number of orfs with sites within 600 bp upstream = 383 Fraction of orfs with sites within 600 bp upstream = 0.0615162 Motif number 3 TTTCTAACAAAGCCTTCTCTGTTATAATTC 2 224 1 AGCCTTCTCT 0.957075 -77 GATTGACAAACGCCTTGTATTTTGGTATAT 3 15 1 CGCCTTGTAT 0.899004 -132 GCACTCCTTTTCTTTCCCTTCCC 8 24 0 CTCCTTTTCT 0.834994 -13 CTTTAGTGACAGGCTTTTTTTATTTTGTCA 9 35 1 AGGCTTTTTT 0.849278 -118 CCAAATCACGAGGCTTGTCACAATTTCAGA 9 80 0 AGGCTTGTCA 0.945256 -73 AGACTTTTGTCGCCTTGTCCAAAAAACGTT 10 29 0 CGCCTTGTCC 0.960186 -105 CCGTTCTTGTCGGCTTTTCATGCTACACAC 10 87 0 CGGCTTTTCA 0.976516 -47 GAAACCGCCCCGGCTTTTCA 12 1 0 CGGCTTTTCA 0.976516 -59 CTAGAGAAACCGCCTTGTCTTATAAAAGAG 12 30 1 CGCCTTGTCT 0.989106 -30 TCTCTGCATGCGCCTTTTTTGTACTCTTCC 13 45 0 CGCCTTTTTT 0.945857 -256 TTTCAGCAAACGGCTTCTCTCTCTGCATGC 13 64 0 CGGCTTCTCT 0.98574 -237 GTTTGCTGAAAGGCTTCTTATGTTGTCTGA 13 83 1 AGGCTTCTTA 0.765059 -218 ********** Masking position 5 Map Score: 18.6714 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 500 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 TACTCCGCATATTGCAAAAAAAACTCCAGT 2 18 0 ATTGCAAAAA 0.788669 -283 CATGATATTTCTGGGAAAAACAATTGTTTT 2 196 1 CTGGGAAAAA 0.945455 -105 AAGAACAAAGCAGGCAAAAACAAAAAAAAA 4 60 0 CAGGCAAAAA 0.978374 -91 TGTCTTGTCCATGGCAAATATTCGGTTTAG 4 92 0 ATGGCAAATA 0.876513 -59 AAATACCCTAAAGGGAAAAACTCATAAACT 7 43 0 AAGGGAAAAA 0.965951 -48 TTCCTTTCTTAAAGCAAAAATACCCTAAAG 7 60 0 AAAGCAAAAA 0.856874 -31 TATAAACGGGAAGGGAAAGAAAAGGAGTGC 8 17 1 AAGGGAAAGA 0.950224 -20 CACTTTAGCACAGGCAAAGAAAAAAAGAAC 10 60 0 CAGGCAAAGA 0.968196 -74 ********** Masking position 6 Map Score: 6.13801 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 550 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 AATGTCCTCCGTTCTAAACCGTTAAAA 1 17 0 TCCGTTCTAA 0.988059 -17 CAAAGCCTTCTCTGTTATAATTCATAATAC 2 231 1 TCTGTTATAA 0.950976 -70 GTATGTATCTTCCTTTCTTAAAGCAAAAAT 7 69 0 TCCTTTCTTA 0.824137 -22 TTTTTCTTTGCCTGTGCTAAAGTGTGTAGC 10 66 1 CCTGTGCTAA 0.89242 -68 GATAATCCCCTCTTTTATAAGACAAGGCGG 12 39 0 TCTTTTATAA 0.84106 -21 TTGTACTCTTCCCGTTCTAAGCAGGTGTAT 13 27 0 CCCGTTCTAA 0.982357 -274 ACACCCGTTATCCGTTATAAGTGCATGAAC 13 169 1 TCCGTTATAA 0.975648 -132 ********** Masking position 10 Map Score: 4.13435 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 101 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 GGCTGCAAATCAACCAAAGCCAGAAAAAAG 2 163 1 CAACCAAAGC 0.954555 -138 AATTGTTTTTCTAACAAAGCCTTCTCTGTT 2 217 1 CTAACAAAGC 0.981866 -84 AGAGAAGAATCTGACAAAGCATATGCTGTG 4 25 1 CTGACAAAGC 0.988391 -126 AAAAAAAAACCTGACACAGCATATGCTTTG 4 39 0 CTGACACAGC 0.97459 -112 CTCGTTTATCCTACCAAATCACGAGGCTTG 9 93 0 CTACCAAATC 0.929436 -60 TTTTTTGATTCTGCCGGAGCCGGATGCTT 11 10 0 CTGCCGGAGC 0.95662 -130 ********** Masking position 8 Map Score: 3.3491 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 280 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 CATATTGCAAAAAAAACTCCAGTCATCATC 2 11 0 AAAAAACTCC 0.62716 -290 ATGTGCGAGCAGACCCCGCCAAGAATGAGA 2 72 1 AGACCCCGCC 0.972877 -229 GAGCTTTTACAGCCCCCTGGTATCTGGCGA 3 100 1 AGCCCCCTGG 0.585284 -47 AAGCATCCGGCTCCGGCAGAA 11 2 1 AGCATCCGGC 0.90028 -138 TTACACATGAAAAAAACGGCAGAATCTTTT 11 37 0 AAAAAACGGC 0.797638 -103 CGGTTTCTCTAGAAACCGCCCCGGCTTTTC 12 12 0 AGAAACCGCC 0.983891 -48 CGGTTTCTAGAGAAACCGCCTTGTCTTATA 12 24 1 AGAAACCGCC 0.983891 -36 GAGCTGATAAATACACCTGCTTAGAACGGG 13 17 1 ATACACCTGC 0.809331 -284 GAAGCCTTTCAGCAAACGGCTTCTCTCTCT 13 70 0 AGCAAACGGC 0.924642 -231 CATAACCCTCCAGCATGTTTA 13 290 0 ATAACCCTCC 0.831006 -11 ********** Masking position 1 Map Score: 3.76159 Number of sites scoring better than the average of aligned sites = 1280 Number in coding regions = 1106 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 8 TTTATGTATTACTGCTTGGGGAACATATCC 2 122 0 ACTGCTTGGG 0.979369 -179 TAAGAAATTAAATGATTGGGAGTGCGAAA 2 282 1 AATGATTGGG 0.952573 -19 AACTGATTGACAAACGCCTTG 3 2 1 ACTGATTGAC 0.9591 -145 ACACACCTTTACTCATTGAGTTCTGGTATG 11 115 0 ACTCATTGAG 0.949828 -25 TCTTATGTTGTCTGATTGGAAGGTCGCCCG 13 98 1 TCTGATTGGA 0.859883 -203 AAGTGCATGAACTGATTGAGTTCATGAAAA 13 187 1 ACTGATTGAG 0.988033 -114 ********** Masking position 6 Map Score: 2.67534 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 137 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 GTAGCAATGGTGCTACATCCATAACATTAA 3 48 0 TGCTACATCC 0.984881 -99 GTAGCACCATTGCTACAACCGCTCAGTACA 3 62 1 TGCTACAACC 0.991367 -85 CGGCTTTTCATGCTACACACTTTAGCACAG 10 77 0 TGCTACACAC 0.972538 -57 ATGTCCATTTTGCTACAATCCATACCAGAA 11 95 1 TGCTACAATC 0.976817 -45 ********** Masking position 5 Map Score: 2.3921 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 9 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 10 GCTCTTAACACCTGTACTGAGCGGTTGTAG 3 74 0 CCTGTACTGA 0.971213 -73 TTTTTCTTTGCCTGTGCTAAAGTGTGTAGC 10 66 1 CCTGTGCTAA 0.894041 -68 AAATGGACATCCTGAGCTCCAATTGGGAAT 11 75 0 CCTGAGCTCC 0.946358 -65 ACAATCCATACCAGAACTCAATGAGTAAAG 11 109 1 CCAGAACTCA 0.946475 -31 AGACAACACACCTTTACTCATTGAGTTCTG 11 120 0 CCTTTACTCA 0.894601 -20 GTTATAAGTGCATGAACTGATTGAGTTCAT 13 182 1 CATGAACTGA 0.923946 -119 CACCTTTTTTCATGAACTCAATCAGTTCAT 13 193 0 CATGAACTCA 0.958752 -108 ********** Masking position 8 Map Score: 3.11472 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 157 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 TTTAACGGTTTAGAACGGAGGACATT 1 18 1 TAGAACGGAG 0.963716 -16 TATTATGAATTATAACAGAGAAGGCTTTGT 2 230 0 TATAACAGAG 0.98202 -71 CGAATTAAGCTATAATAGAGTTTATGAGTT 7 25 1 TATAATAGAG 0.932189 -66 CGCCTTGTCTTATAAAAGAGGGGATTATCA 12 40 1 TATAAAAGAG 0.932189 -20 TTCATGCACTTATAACGGATAACGGGTGTT 13 168 0 TATAACGGAT 0.918687 -133 ********** Masking position 5 Map Score: 1.14045 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 20 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 TTAGGAGTCTGTATAAGTGTGTATTATGAA 2 251 0 GTATAAGTGT 0.82654 -50 CAACCGCTCAGTACAGGTGTTAAGAGCTTT 3 77 1 GTACAGGTGT 0.978564 -70 TGAGTATGTTGTTGAGGTGAATATT 5 38 1 GTTGAGGTGA 0.836423 -15 GAGTTCAATAGAAGAGGTGTAACACG 6 15 1 GAAGAGGTGT 0.978274 -16 GGAAGGGAAAGAAAAGGAGTGC 8 25 1 GAAAAGGAGT 0.877775 -12 AACTCAATGAGTAAAGGTGTGTTGTCT 11 123 1 GTAAAGGTGT 0.981921 -17 ********** Masking position 5 Map Score: 1.05818 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 62 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 13 ********** No masking Map Score: 3.19987e-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 14 ********** No masking Map Score: 3.19987e-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 15 ********** No masking Map Score: 3.19987e-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