AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_bsub_reg_300.orf -o00550_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ybaJ 300 ybaJ #2 ybaK 185 alternate gene name: ybxH #3 cwlD 59 N-acetylmuramoyl-L-alanine amidase #4 ddlA 174 D-alanyl-D-alanine ligase A #5 murF 71 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diaminopimelate-D-alanyl-D-alanyl ligase #6 xkdH 300 PBSX prophage #7 xkdK 218 PBSX prophage #8 xkdN 91 PBSX prophage #9 xkdS 56 PBSX prophage #10 xkdV 270 PBSX prophage #11 xkdY 43 lytic exoenzyme associated with defective prophage PBSX #12 xhlA 52 xhlA #13 ylbQ 159 similar to pyrimidine-thiamine biosynthesis #14 yllA 70 yllA #15 yllB 125 similar to hypothetical proteins #16 ylxA 69 alternate gene name: yllC; similar to hypothetical proteins #17 ftsL 39 cell-division protein #18 spoVD 116 penicillin-binding protein #19 murE 175 UDP-N-acetylmuramoylananine-D-glutamate-2,6- diaminopimelate ligase #20 mraY 112 phospho-N-acetylmuramoyl-pentapeptide transferase #21 spoVE 60 spoVE #22 murG 122 UDP-N-acetylglucosamine-N-acetylmuramyl- (pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase #23 cwlC_spoVK 600 cwlC: N-acetylmuramoyl-L-alanine amidase, spoVK: alternate gene name: spoVJ; disruption leads to the production of immature spores (stage V sporulation) #24 ynbA 220 similar to GTP-binding protein protease modulator #25 ynbB 187 similar to hypothetical proteins #26 glnR 110 transcriptional regulator #27 glnA 60 glutamine synthetase #28 yqeE 186 similar to N-acetylmuramoyl-L-alanine amidase #29 cwlA 44 N-acetylmuramoyl-L-alanine amidase #30 yqxH 44 alternate gene name: yqdD; similar to holin #31 yqxG 87 alternate gene name: yqdC; similar to phage-related lytic exoenzyme #32 yqbO 181 similar to phage-related protein #33 yqbN 145 similar to phage-related protein #34 yrvJ 132 similar to N-acetylmuramoyl-L-alanine amidase #35 murC 249 UDP-N-acetyl muramate-alanine ligase #36 ytpS 159 ytpS #37 ytpP 234 similar to thioredoxin H1 #38 yubB 92 similar to bacitracin resistance protein (undecaprenol kinase) #39 yubA 181 similar to hypothetical proteins #40 lytC 38 N-acetylmuramoyl-L-alanine amidase (major autolysin) (CWBP49) #41 lytB 23 modifier protein of major autolysin LytC (CWBP76) #42 lytA 183 membrane bound lipoprotein Motif number 1 ACATTAAAGTAAGGAGAAGATTC 1 288 1 AAGGAGAAAT 0.764495 -13 ATTTCTAACCAAGGAGGTCATGTCATC 7 202 1 AAGGAGGTAT 0.987275 -17 TTTTAGATCAAAGGAGGATGAAG 11 31 1 AAGGAGGAGA 0.764719 -13 GGCCCTCGGAAGGGAGGTGATCTGCATGTGA 12 18 1 AGGGAGGTAT 0.934882 -35 AGAAACAACAAAGGGGGAGATTTGT 13 5 0 AAGGGGGAAT 0.886379 -155 GCAAAATTAAAAGGAGGTCATCAGCCT 17 23 1 AAGGAGGTAT 0.987275 -17 TCAACTGAAAAATGAGGAAATAACCCTTTCA 23 521 0 AATGAGGAAT 0.896407 -80 CATATCCTGTAATGAGGTGATGAAAA 23 585 1 AATGAGGTAT 0.896407 -16 TTGCTTTGAAAAGGCGGAAATACGAGCAAAA 24 37 0 AAGGCGGAAT 0.886379 -184 AAGTTAAGAAAAGGAGGAAATTGAG 26 96 1 AAGGAGGAAT 0.987275 -15 TACCTTTTAAGAGGAGGAATTTTACCAA 27 43 1 GAGGAGGATT 0.744481 -18 ATTTGCCTCGGAGGAGGTGATTAGA 30 30 1 GAGGAGGTAT 0.934882 -15 TTTTTCCTTAAAGGAGGTGGTTCCGTTGTAA 31 21 1 AAGGAGGTGT 0.944437 -67 CTACAATAGCAAGGAGGATTTATT 31 74 1 AAGGAGGATT 0.940283 -14 GAAGCGAAGAAGGGAGGTAATTAACT 32 166 1 AGGGAGGTAT 0.934882 -16 CCGAATATGAAAGGAGGTGAAATT 33 4 0 AAGGAGGTAA 0.936853 -142 TAAAAAGTAAAAGGAGTTAATAAAC 33 131 1 AAGGAGTTAT 0.764495 -15 GATCATCAGAAAGGAGGACACA 34 121 1 AAGGAGGAAC 0.896934 -12 GGATATACATAAGGAGGGATTTTTATT 37 7 0 AAGGAGGGTT 0.747807 -228 AACGCCATTTAAGGAGGAAATCAA 40 25 1 AAGGAGGAAT 0.987275 -14 GATAAAATATAATGAGGTGAAAAAA 42 169 1 AATGAGGTAA 0.623302 -15 ******** ** Masking position 6 Map Score: 29.1661 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 164 Number in noncoding regions = 221 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 2 ATCACATATCTCCTTTGTAATTTTTTTGCGTT 1 187 1 TCCTTTGATT 0.696771 -114 ATGTCACATCTCCTTTTCAATGCCATTTTAAT 4 11 1 TCCTTTTATG 0.942325 -164 TGTATGTAATTCCTTTTTATTTTATATTAAAA 4 36 0 TCCTTTTTTT 0.895288 -139 AATCCTAGACTTGTTTTCAATGGATACTCCCC 4 152 0 TTGTTTTATG 0.569645 -23 GTCCCTCTCTTTCTTTTGTATATACGGGAAAA 5 45 0 TTCTTTTATA 0.624606 -27 GTTGCCCACTCCTTTTACATGCTAAATAAAA 9 36 0 TCCTTTTATG 0.942325 -21 GCTGATGACCTCCTTTTAATTTTGCGTTCGCG 17 16 0 TCCTTTTTTT 0.895288 -24 TTATTTAGGCTTGTTTCATTTTATGCCTGAAT 18 80 0 TTGTTTCTTT 0.438304 -37 GCTGGATGTATCCTTTTATTTACGCTAAAATA 19 65 1 TCCTTTTTTA 0.800567 -111 TATAGTGAGCTTCTTTCTCATTATTTCTTTTT 23 190 1 TTCTTTCATT 0.799695 -411 TTCTCATTATTTCTTTTTCATACAACGGGCTG 23 204 1 TTCTTTTATA 0.624606 -397 AAATGGATGTTCCTTTCTTTTGCATATTGGGC 24 114 0 TCCTTTCTTG 0.909012 -107 CGGTCTACCATCGTTTCCGATTTGATTCTGGA 25 55 0 TCGTTTCATT 0.864682 -133 GATCCGGCTGTCCTTTTTTATTTGCCTCGGAG 30 11 1 TCCTTTTATT 0.940306 -34 AATTTCACCTCCTTTCATATTCGGAGGATAA 33 10 1 TCCTTTCATT 0.946654 -136 GTTTATTAACTCCTTTTACTTTTTAGTTTTGG 33 124 0 TCCTTTTTTT 0.895288 -22 TATCGTAAAGTCCTTTCTGATTTTTAAATAAA 34 66 0 TCCTTTCATT 0.946654 -67 TGTGTCCTCCTTTCTGATGATCATTAAAA 34 114 0 TCCTTTCATG 0.94847 -19 ATCAGGTTATTTCTTTCCGATTAAACCCAGAT 35 107 0 TTCTTTCATT 0.799695 -143 TTCACATGATTCGTTTTTTTTGGCGGATTTAT 36 17 0 TCGTTTTTTG 0.761532 -143 ATTATCAAGCTCGTTTCGTTTAACATCGTGTA 37 60 0 TCGTTTCTTA 0.61954 -175 TCGTATCGCTCCTTTTGCATGATATAGCTAA 39 10 1 TCCTTTTATG 0.942325 -172 CCTAAAATAGTCGTTTTTTATAAAAAAAAGTT 42 94 1 TCGTTTTATA 0.727008 -90 ******* *** Masking position 6 Map Score: 24.5452 Number of sites scoring better than the average of aligned sites = 775 Number in coding regions = 571 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 3 TTAGAGGGGCTGCTTTTTTCATAACCAATT 2 25 1 TGCTTTTTTC 0.910596 -161 TCTCAGAAAGGTCTGTTTTTTAAAGATGAA 8 42 1 GTCTGTTTTT 0.802546 -50 GCTCTACTATTTCTGTTTTTTGGCCGTTGA 10 73 0 TTCTGTTTTT 0.864656 -198 AAATCGAGTGTTCTGTTTTCGCTGACGTCC 10 224 0 TTCTGTTTTC 0.824288 -47 GGCTTTTTTATTTTGCCTGT 11 1 1 GGCTTTTTTA 0.834249 -43 AGTTCAGGGTTTCTTTTTATGGGTAAACAG 15 36 1 TTCTTTTTAT 0.743009 -90 TATGCAGGCTTTCTTTTTTTATGCCTTCAG 18 26 1 TTCTTTTTTT 0.930424 -91 TTCTAATTCGTTCTTTTTATCATTGAAGTC 19 137 0 TTCTTTTTAT 0.743009 -39 TTCTTTTTTCCCCCAGTCTA 22 113 0 TTCTTTTTTC 0.907575 -10 TCGAAACAATTGCTTTTTTCGGGAACAATA 23 56 1 TGCTTTTTTC 0.910596 -545 TGAAGTGTTTTTCTTTTTTTCGATTTATAA 23 273 1 TTCTTTTTTT 0.930424 -328 TTTTTGAGAGGTCTGTTTTTTGCTCGTATT 24 20 1 GTCTGTTTTT 0.802546 -201 AAGAACACAATTCTTTTTTACCTCATAAAA 28 114 1 TTCTTTTTTA 0.884088 -73 GCCAGTGGCTTTTTTTATCTTACTGA 29 7 1 GGCTTTTTTT 0.898215 -38 GGCTTTTTTATTTTTCCTTA 31 1 1 GGCTTTTTTA 0.834249 -87 AGTATGAATGTGCTTTTTTTCTTGTCCAAA 33 99 1 TGCTTTTTTT 0.932754 -47 TAAACAAGAATGCTTTTTTAATGATCATCA 34 99 1 TGCTTTTTTA 0.887782 -34 TGTGATTTTGTTCTTTTTAAGCTATAATTT 39 40 0 TTCTTTTTAA 0.622499 -142 ********** Masking position 6 Map Score: 19.2656 Number of sites scoring better than the average of aligned sites = 1016 Number in coding regions = 724 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 277 Fraction of orfs with sites within 600 bp upstream = 0.0444908 Motif number 4 GCGACCTGTTAGAGGGGCTGCTTTTTTCATAAC 2 17 1 AAGGCTGCTT 0.498178 -169 CATTGATAAAAAATCAGCTTTCTGCAGGGTGAG 2 70 0 AAAGCTTTCT 0.874536 -116 GCAGCGGATCATACAAGCTGTCTTCAAAGCGGT 6 53 0 AAAGCTGTCT 0.861376 -248 CAAACAACAGAAGAAGGCTGTACATACAAAGAG 7 25 1 AGGGCTGTAC 0.705676 -194 AGCCTGCATAACGACGGCTTTCTTT 18 3 0 AGGGCTTTCT 0.932735 -114 AGCCGTCGTTATGCAGGCTTTCTTTTTTTATGC 18 17 1 AGGGCTTTCT 0.922757 -100 GTCTTGAAGTAAATCGGCAGCCCTAATGACTTT 21 17 1 AAGGCAGCCC 0.715772 -44 GTCTTTAATGAAAGGAGCTTTCCTCATCAATTT 23 309 1 AAAGCTTTCC 0.926347 -292 ACATCCGACTAAAATGGCTTTCTCCTGAATCGT 24 159 0 AAGGCTTTCT 0.949345 -62 TTGATTCTGGAAAGGAGCTTCCCTTCACTTGCC 25 33 0 AAAGCTTCCC 0.86595 -155 TTACCTCATAAAAAAGGCTGTCCATCTCTCTGT 28 131 1 AAGGCTGTCC 0.96973 -56 AGACGGGGACAAAGAGGCTGTATACCTTTACTA 32 15 1 AAGGCTGTAT 0.658637 -167 GATGATCATTAAAAAAGCATTCTTGTTTAATAT 34 95 0 AAAGCATTCT 0.512467 -38 TACGCCGCTAAGGGAGGCTTTTCAGCCGCCGCG 35 164 1 AGGGCTTTTC 0.728736 -86 TGAATATGTAAGATTGGCTTTCCCATTATCATT 37 108 0 AAGGCTTTCC 0.973239 -127 TAGTTATATAAGACGGGCTTTCCATTTATGGGA 38 21 1 AAGGCTTTCC 0.973185 -72 TTTTTACATAACGGGAGCTTCCCATAAATGGAA 38 40 0 AGAGCTTCCC 0.816301 -53 * * ******** Masking position 1 Map Score: 15.2427 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 511 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 GATTGATATCGCTTTCCCTTTGCATATTTAGA 1 233 0 GCTTTCCCTG 0.97146 -68 TTCCCCTCCCGCTTGTCCGTTATTACATAACT 3 35 0 GCTTGTCCTA 0.894347 -25 CTTTAGTAAAGCTTGCCCAGTATTTTGCGCTT 6 107 1 GCTTGCCCTA 0.955161 -194 GCTTTTTCGGTAACATGCTATA 14 1 1 GCTTTTTCTA 0.772213 -70 GGAATCCTGCGCTTTCCCGAGAAATACTTTAT 23 87 1 GCTTTCCCGA 0.976868 -514 TGAATTGTGCGCTTTCCCGAGAAATAATTTCT 23 484 1 GCTTTCCCGA 0.976868 -117 GACTAAAATGGCTTTCTCCTGAATCGTTTCTT 24 154 0 GCTTTCTCGA 0.842351 -67 TTTTGAATGTGCTTTCCATATAATTCATGTAT 33 67 0 GCTTTCCATA 0.950936 -79 GCTAAGGGAGGCTTTTCAGCCGCCGCGGTCGC 35 170 1 GCTTTTCACG 0.625717 -80 GGGCTTAGCGGCTTTTCACATGATTCGTTTTT 36 31 0 GCTTTTCATG 0.795418 -129 TGTAAGATTGGCTTTCCCATTATCATTATCAT 37 103 0 GCTTTCCCTA 0.985386 -132 TATAAGACGGGCTTTCCATTTATGGGAAGCTC 38 27 1 GCTTTCCATA 0.950936 -66 AACCGAGAAAGCTTTTCCAGCAATTAACGGTT 39 94 1 GCTTTTCCCA 0.920133 -88 ******** ** Masking position 4 Map Score: 12.6933 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 178 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 ATCGAGGCGGAAGCAGAAGCGGCTCTCATCAC 6 16 1 AACAGAACGG 0.827959 -285 CGTATGACGAAATCAGAAGCCAACCAATTGAT 7 164 1 AACAGAACCA 0.935796 -55 CTGTTTTTTAAAGATGAAACCAAACAATAGAC 8 54 1 AAATGAACCA 0.857928 -38 CTGATCTAAAAAGCAGAATCGATCACGTGCTG 10 40 1 AACAGAACGA 0.941196 -231 GTTTACCCATAAAAAGAAACCCTGAACTAGTC 15 32 0 AAAAGAACCC 0.763144 -94 GAAGGCATAAAAAAAGAAAGCCTGCATAACGA 18 22 0 AAAAGAAGCC 0.676028 -95 ATTCAGGCATAAAATGAAACAAGCCTAAATAA 18 80 1 AAATGAACAA 0.456233 -37 CTTCAATGATAAAAAGAACGAATTAGAATGTT 19 139 1 AAAAGAAGAA 0.584118 -37 TGCTTGATTTAATATGAACGCAAAGCTTAAAA 23 352 1 AAATGAAGCA 0.796371 -249 CGCACAATTCAACATGAAGCGACAACAGATAC 23 463 0 AAATGAACGA 0.868961 -138 ATAATCGTACAAGCAGAAGCCGTGTTTTTTCA 23 555 1 AACAGAACCG 0.814213 -46 GCCCAATATGCAAAAGAAAGGAACATCCATTT 24 114 1 CAAAGAAGGA 0.739906 -107 CATTTGAACGAACAAGAAACGATTCAGGAGAA 24 141 1 AAAAGAACGA 0.944875 -80 TCCAGAATCAAATCGGAAACGATGGTAGACCG 25 55 1 AACGGAACGA 0.655809 -133 TTCTTCATTAAAATAGAAGCGGTCTACCATCG 25 74 0 AATAGAACGG 0.32056 -114 CCTCCCTATTAATAAGAATGCAGAAAACAGAG 28 158 0 AAAAGAAGCA 0.909982 -29 GAGCTGTTAGAAAAAGAAGCGAAGAAGGGAGG 32 151 1 AAAAGAACGA 0.944875 -31 TTATCCTCCGAATATGAAAGGAGGTGAAATT 33 10 0 AAATGAAGGA 0.811132 -136 TTTATTTAAAAATCAGAAAGGACTTTACGATA 34 66 1 AACAGAAGGA 0.912018 -67 TACGATATTAAACAAGAATGCTTTTTTAATGA 34 91 1 AAAAGAAGCT 0.433436 -42 TTTTAATGATCATCAGAAAGGAGGACACA 34 114 1 CACAGAAGGA 0.726509 -19 GTTTGGTGTGAAAATGAACCCATA 35 3 0 AAATGAACCA 0.857928 -247 ATTAAGCTATCAGCAGAAACCAAGCCGCTAAA 36 66 0 CACAGAACCA 0.788814 -94 ** ***** *** Masking position 7 Map Score: 18.1728 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 546 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 7 CAACCGAATTCGGGCATTGTTTCATCATCCAAACC 2 128 1 CGCTTGTTCT 0.701412 -58 ATAAATTCACTCTCCTTTTACCGATTATTTTGAG 2 162 0 CCCTTTTCCA 0.630557 -24 GGAAAAAACACTGCCCTTTTACCGGCAGTGTCCTT 5 16 0 CGCTTTTCCG 0.922283 -56 GTAAGGTCCCTCTCTTTCTTTTGTATATACGGGA 5 48 0 CCCTTCTTTT 0.730729 -24 TAGGAATAATCCCCCATTTTCTCATACTGATAGCT 6 166 0 CCCTTTTTCT 0.948831 -135 AAAGATCTCACCTTCAGTCTGGAGGATTCAG 6 280 0 CCCTTCATCG 0.793788 -21 GTTGCCCACTCCTTTTACATGCTAAATAAAA 9 36 0 CCCTTTTCAG 0.764773 -21 TGATGTCTTCCTCACGTTTTGTCAGAACGGTGACT 10 122 0 CCCTTTTTCG 0.974382 -149 ACGTCCAGGTCAGTCTTTCTCTCTGTGATCACATT 10 195 0 CGCTTCTTCG 0.966792 -76 GATCTCTTGCCCCACTTTCTCTCCTTAACTCACCA 15 101 0 CCCTTCTTCT 0.958958 -25 TTGTGTTGGTCCCACCTTTTATCAGGATGAATTGA 16 44 0 CCCTTTTTCG 0.974382 -26 CGTCGTTATGCAGGCTTTCTTTTTTTATGCCTTCA 18 20 1 CGCTTCTTTT 0.622425 -97 CATTCTAATTCGTTCTTTTTATCATTGAAGTCACA 19 134 0 CTCTTTTTCT 0.593671 -42 ATAAAAAAGGCTGTCCATCTCTCTGTTTTCTGCAT 28 138 1 CGCATCTTCG 0.70045 -49 ATACCCTCTCTCCTTCTGTCAGTAAGATAAAA 29 23 0 CCCTTCTTCG 0.979561 -22 GATCCGGCTGTCCTTTTTTATTTGCCTCGGAG 30 8 1 CGCTTTTTAT 0.652127 -37 TCGTATCGCTCCTTTTGCATGATATAGCTAA 39 7 1 CCCTTTTCAG 0.764773 -175 * * * **** ** * Masking position 8 Map Score: 10.3799 Number of sites scoring better than the average of aligned sites = 650 Number in coding regions = 562 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 8 TGTATCAAATAGAGCTTCCCGGCTCTTTGT 7 50 0 AGAGCTTCCC 0.959871 -169 CAGAAATAGTAGAGCTCGCCATTGACGGTG 10 88 1 AGAGCTCGCC 0.675755 -183 TAAGGAATCCTGCGCTTTCCCGAGAAATAC 23 84 1 TGCGCTTTCC 0.959234 -517 TTTAATGAAAGGAGCTTTCCTCATCAATTT 23 312 1 GGAGCTTTCC 0.981959 -289 TGTTGAATTGTGCGCTTTCCCGAGAAATAA 23 481 1 TGCGCTTTCC 0.959234 -120 ATTCTGGAAAGGAGCTTCCCTTCACTTGCC 25 33 0 GGAGCTTCCC 0.981718 -155 ACTTTTTGAATGTGCTTTCCATATAATTCA 33 72 0 TGTGCTTTCC 0.896125 -74 TTATATAAGACGGGCTTTCCATTTATGGGA 38 24 1 CGGGCTTTCC 0.882352 -69 TTACATAACGGGAGCTTCCCATAAATGGAA 38 40 0 GGAGCTTCCC 0.981718 -53 ********** Masking position 6 Map Score: 6.1197 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 159 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 GTTAGAGGGGCTGCTTTTTTCATAACCAATT 2 24 1 CTGTTTTTTC 0.721527 -162 GATAAAAAATCAGCTTTCTGCAGGGTGAGGA 2 68 0 CAGTTTCTGC 0.891288 -118 CTTTTACCGGCAGTGTCCTTCTTCA 5 5 0 CAGGTCCTTC 0.65784 -67 AGAGCCGCTTCTGCTTCCGCCTCGATGATAT 6 11 0 CTGTTCCGCC 0.915628 -290 CCTCAGGCCGCTGAATCCTGCCTTCTCCGGA 6 208 0 CTGATCCTGC 0.926689 -93 GGCTACGTCCCTGAATCCTCCAGACTGAAGG 6 270 1 CTGATCCTCC 0.885968 -31 TGGTTGGCTTCTGATTTCGTCATACGTGGTT 7 159 0 CTGTTTCGTC 0.802675 -60 TTTTCTCCTCCTGTTTCTTTCAAACGACATA 20 87 0 CTGTTCTTTC 0.851282 -26 TTAACCTGCACTGATTCCTGCTGGTTTTAAG 23 377 0 CTGTTCCTGC 0.980749 -224 TTTGAGAGGTCTGTTTTTTGCTCGTATTTCC 24 22 1 CTGTTTTTGC 0.835812 -199 GTCCATCTCTCTGTTTTCTGCATTCTTATTA 28 150 1 CTGTTTCTGC 0.958438 -37 AATTTCAGGTTCCTCCCTATATC 41 8 0 CAGTTCCTCC 0.917579 -16 *** ******* Masking position 6 Map Score: 7.00198 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 438 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 TGTTCTGTAATTGGTTATGAAAAAAGCAGC 2 33 0 TTGGTTATGA 0.715699 -153 AAATGCTAAATTGGGTGTGACATC 13 146 1 TTGGGTGTGA 0.971105 -14 TACCACATCATTTGATGTGACTTCAATGAT 19 119 1 TTTGATGTGA 0.811517 -57 ACATGCAGGGTTTGGTATGATAATACTACT 24 84 1 TTTGGTATGA 0.930916 -137 ATCACCTAAGTTGGGAGTGACCATAGAC 28 9 0 TTGGGAGTGA 0.874646 -178 TCATACCATGTTTGGTGTGAAAATGAACCC 35 14 0 TTTGGTGTGA 0.965315 -236 CCTCAAGCAGTTTGGTATGATCCAAATGGA 37 164 1 TTTGGTATGA 0.930916 -71 ********** Masking position 10 Map Score: 2.66304 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 27 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 GTTCGGTCAATGTTTATTAACGTTATGTGATCAGCCCA 1 27 1 TGTTTACTGT 0.959595 -274 AGGAGATATGTGATTTATATCATCAGATTTACTTTTAC 1 163 0 TGTTTACTAT 0.699544 -138 GATGTGGTAATGATTTTAAGCATACAGTTCATATTTTA 19 90 0 TGTTAACTGT 0.97839 -86 GCAGCCCTAATGACTTTAAGCTTGGGGTGTCGATTGCT 21 33 1 TGCTAACTGT 0.913631 -28 CGAATGTATTTCCAAGCCTCCTGTCTAACATGAA 22 7 1 TATTAACTGT 0.816126 -116 TCGCATCAATTGTTTCCAAGCTTCATGTTAGACAGGAG 22 28 0 TGTTAACTGT 0.97839 -95 CATGAGATTTTGTTTTTAATCATTTTGTCAGAGTATTA 23 154 1 TGTTAACTGT 0.97839 -447 TGATTCCTGCTGGTTTTAAGCTTTGCGTTCATATTAAA 23 359 0 TGTTAACTGT 0.97839 -242 AAAGCATTCTTGTTTAATATCGTAAAGTCCTTTCTGAT 34 77 0 TGTTTACTGT 0.959595 -56 ** ** ** * * ** Masking position 9 Map Score: 6.48834 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 20 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 CCCTTCCCCTCCCGCTTGTCCGTT 3 46 0 CCTTCCTCCG 0.987071 -14 GCCGAACAGTTCCTTCGCGTGCTTAATCAAATCC 7 82 0 TCTTCCTGCT 0.842583 -137 AAAAGCAGAATCGATCACGTGCTGCTCAACGGCC 10 48 1 TCATCCTGCG 0.830183 -223 CTCTCACTCCTCCTTCACATGCAGATCACCTCCC 12 29 0 TCTTCCTGCG 0.972023 -24 TGTCCTTTTCTCCTCCTGTTTCTTTCAA 20 95 0 CTTTCCTCCG 0.92164 -18 AGGAAATAACCCTTTCACATCCAGAAATTATTTC 23 504 0 CCTTCCTCCG 0.987071 -97 GAAGCCGTGTTTTTTCATATCCTGTAATGAGGTG 23 570 1 TTTTCTTCCG 0.517 -31 AATGGATGTTCCTTTCTTTTGCATATTGGGCAGT 24 111 0 CCTTCTTGCT 0.783021 -110 AAAGGAGCTTCCCTTCACTTGCCGGCACATGTGC 25 22 0 CCTTCCTGCG 0.989536 -166 ATACCCTCTCTCCTTCTGTCAGTAAGAT 29 27 0 CCCTCCTTCG 0.843258 -18 AATTTCACCTCCTTTCATATTCGGAGGATAAGCT 33 11 1 CCTTCTTTCG 0.864683 -135 ** *** * *** * Masking position 5 Map Score: 6.05401 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 291 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 13 TCCTTGGTTAGAAATGTTTGAATCAATTGG 7 187 0 GAAATGTTTG 0.789155 -32 ACCTTTCTGAGAAAGGTCTGCGTATGGGCT 8 24 0 GAAAGGTCTG 0.977741 -68 ACCTTTCTCAGAAAGGTCTGTTTTTTAAAG 8 37 1 GAAAGGTCTG 0.977741 -55 TTAGAATGTTGAGAGGTTTGATACG 19 161 1 GAGAGGTTTG 0.954636 -15 CTCAGTTTTTGAGAGGTCTGTTTTTTGCTC 24 15 1 GAGAGGTCTG 0.979285 -206 ********** Masking position 4 Map Score: 2.06517 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 6 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 14 TTCAGGGGGCTTTATTTGGCGTGGATCAACCA 7 132 1 TTTATTTGCT 0.942637 -87 CGAAGGGGTTTTTATTTAGCATGTAAAAGGAG 9 27 1 TTTATTTGCT 0.942637 -30 GGCTTTTTTATTTTGCCTGTTTTTAGAT 11 7 1 TTTATTTGCT 0.942637 -37 TGACCTCCTTTTAATTTTGCGTTCGCGTTTCG 17 11 0 TTAATTTGCT 0.770448 -29 CGAGAAATACTTTATTTCTTATTGTATTCACG 23 104 1 TTTATTTTTT 0.536415 -497 TTTCTCATTATTTCTTTTTCATACAACGGGCT 23 203 1 TTTCTTTTCT 0.848231 -398 TGGATGTTCCTTTCTTTTGCATATTGGGCAGT 24 111 0 TTTCTTTGCT 0.850638 -110 GTCTTTATATTTCCTTCCTACATAT 25 173 0 TTTATATTCT 0.63183 -15 GCCAGTGGCTTTTTTTATCTTACTGACAGAA 29 10 1 TTTTTTTTCT 0.672028 -35 GGCTTTTTTATTTTTCCTTAAAGGAGGT 31 7 1 TTTATTTTCT 0.941611 -81 AACAAATCATTTTATTTTTATTTAAAAATCAG 34 50 1 TTTATTTTAT 0.536415 -83 ATTAACGGTTTTTATTTTTCATTATAGGGACG 39 116 1 TTTATTTTCT 0.941611 -66 TCATTGTTTCTTAATTTTTCTTTAAAATATAA 42 126 1 TTAATTTTCT 0.767102 -58 ******* ** * Masking position 7 Map Score: 8.33721 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 90 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 15 TGATTCTTAACCCGGAGAAACAATAGCTCT 1 107 1 CCCGGAGAAA 0.968532 -194 TAGATCATTTTCCGGTGAAAATGATAAGAT 4 101 1 TCCGGTGAAA 0.908476 -74 CTACACGGTTTCCGGAGAAGGCAGGATTCA 6 198 1 TCCGGAGAAG 0.936353 -103 TCCTTATTGTTCCCGAAAAAAGCAATTGTT 23 60 0 TCCCGAAAAA 0.760833 -541 TCCTGCGCTTTCCCGAGAAATACTTTATTT 23 91 1 TCCCGAGAAA 0.970104 -510 TTGTGCGCTTTCCCGAGAAATAATTTCTGG 23 488 1 TCCCGAGAAA 0.970104 -113 AAGAAACGATTCAGGAGAAAGCCATTTTAG 24 154 1 TCAGGAGAAA 0.953782 -67 AACATCAAATCCAGGAGAAATTTTTAAAAA 26 13 0 CCAGGAGAAA 0.909806 -98 GATTAAGCTATCAGCAGAAACCAAGCCGCT 36 69 0 TCAGCAGAAA 0.749905 -91 ********** Masking position 8 Map Score: 6.73208 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 160 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049