AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -irpoH_bsub_opreg_300.orf -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 spoIIE 300 serine phosphatase #2 yabS 84 similar to hypothetical proteins #3 yabT 88 yabT #4 yacA 103 similar to cell-cycle protein #5 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #6 ctsR 300 transcriptional regulator #7 groES 196 class I heat-shock protein (molecular chaperonin) #8 groEL 46 class I heat-shock protein (molecular chaperonin) #9 clpE 300 ATP-dependent Clp protease-like #10 ylxM 176 similar to hypothetical proteins #11 rpsP 105 ribosomal protein S16 (BS17) #12 ylqD 121 ylqD #13 rplS 130 ribosomal protein L19 #14 ylqF 142 similar to hypothetical proteins #15 rnh 70 ribonuclease H #16 ylqG 31 ylqG #17 sucC 172 succinyl-CoA synthetase (beta subunit) #18 sucD 28 succinyl-CoA synthetase (alpha subunit) #19 smf 60 DNA processing Smf protein homolog #20 topA 187 DNA topoisomerase I #21 gid 75 glucose-inhibited division protein #22 codV 67 integrase/recombinase #23 yocM 66 similar to small heat-shock protein #24 sigA 198 RNA polymerase major sigma-43 factor (sigma-A) #25 dnaG 33 DNA primase #26 yqxD 157 alternate gene name: yqfM; similar to hypothetical proteins #27 yqfL 25 similar to hypothetical proteins #28 yqzB 132 similar to hypothetical proteins #29 glyQ 296 glycyl-tRNA synthetase (alpha subunit) #30 yqxN 300 alternate gene name: yqfI; similar to hypothetical proteins #31 rpsU 163 ribosomal protein S21 #32 dnaJ 199 heat-shock protein #33 dnaK 23 class I heat-shock protein (chaperonin) #34 grpE 71 heat-shock protein #35 hrcA 119 transcriptional regulator #36 hemN 52 coproporphyrinogen III oxidase #37 lepA 133 GTP-binding protein #38 spoIIP 62 spoIIP #39 gpr 203 spore protease #40 lonA 180 class III heat-shock ATP-dependent Lon protease #41 lonB 151 Lon-like ATP-dependent protease #42 clpX 272 ATP-dependent Clp protease ATP-binding subunit (class III heat-shock protein) #43 tig 227 trigger factor (prolyl isomerase) #44 ysoA 189 ysoA #45 leuC 49 3-isopropylmalate dehydratase (large subunit) #46 ilvB 300 acetolactate synthase (acetohydroxy-acid synthase) (large subunit) #47 gapB 205 glyceraldehyde-3-phosphate dehydrogenase #48 ytcD 183 ytcD #49 gap 46 glyceraldehyde-3-phosphate dehydrogenase #50 yvbQ 297 yvbQ #51 araE 137 permease #52 clpP 300 ATP-dependent Clp protease proteolytic subunit (class III heat-shock protein) #53 htpG 167 class III heat-shock protein (chaperonin) #54 yxcA 116 yxcA Motif number 1 GGTATTGTTACCTTCTTTTGACAAAATCCTATCTG 1 224 1 CCTTCTTTAA 0.892661 -77 TCAACCCCCTCCTTTACTGACTTTGACTATAT 6 279 0 CCTCCTTTAT 0.986369 -22 ATGGTATGTACTCCTTTGTTAAGTGGGTTTCGTT 7 10 1 ACTCCTTTAT 0.723624 -187 TTGGGTTTGACCTTCTTTGACTATTAGTATACGGC 9 214 0 CCTTCTTTAT 0.942129 -87 TTGCCAAAACCTCCTTAATAATTTGATCATCTTT 9 277 0 CCTCCTTATT 0.823429 -24 AAAAATCCTCCTTAAAATAGGGTTCATATAC 10 7 1 CCTCCTTAAG 0.690141 -170 GACACGAACACCGCCTTTATCTTCAGTATGCATGA 14 116 0 CCGCCTTTTA 0.835784 -27 TATTCCCCATCCTTCTTTGAAATTTATGTTTTTAA 17 17 1 CCTTCTTTTT 0.892661 -156 TAGATTGACCTCCTTTTGTTAGAAAAAGCAGGA 19 38 0 CCTCCTTTAA 0.97366 -23 TTATTCAAGGCCTTCTTTTAACACACAAAGAAGGT 21 31 0 CCTTCTTTAA 0.892661 -45 AGGCAAACCTCCTTTCTATAGTTGTATGCTGG 23 8 1 CCTCCTTTAT 0.986369 -59 TATGGATCCCTCCTTCCAAAGCTTGCAACGAAT 24 176 0 CCTCCTTCGT 0.837029 -23 CACACAGCAACCGCCTTTTCTCTCT 28 1 0 CCGCCTTTTT 0.908786 -132 AAAATCCCAGCCTCTTTTTTAAAATTGCTCAAGAA 29 143 0 CCTCTTTTAT 0.723624 -154 CACAAGAAACCCACCTTTCTGTAGTTAAACTAGCT 30 99 0 CCACCTTTAT 0.830767 -202 CGGATTCACCTTCTTTACAGAAAGAAGCCGCAG 36 30 0 CCTTCTTTAA 0.892661 -23 ACAGGGGCCTCCTTCACATTAAGTACCTATAT 39 182 0 CCTCCTTCTA 0.842952 -22 CACATTGTTACCGTCTTTTTGGAAAGTATGGTAAA 42 160 1 CCGTCTTTAA 0.691504 -113 TTTAGTTCCTCCTTTTGGATTTTCATCCTTTA 46 279 0 CCTCCTTTTT 0.97366 -22 GATGTTCCTCCTTTGTAAGATGTGTTGTATG 48 7 1 CCTCCTTTGT 0.947557 -177 GATTGTTTCCTCCTTTAAATAAGTGAGAGATAT 49 24 0 CCTCCTTTAG 0.94755 -23 AATGCTCCTCCTTCACCTTTTAGGTAAGTAT 52 280 0 CCTCCTTCTT 0.913099 -21 GATACGAGACCTCCTTTTTCTATTTGTCTTCCCG 54 10 1 CCTCCTTTAT 0.986369 -107 ******** * * Masking position 7 Map Score: 25.7141 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 160 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 267 Fraction of orfs with sites within 600 bp upstream = 0.0428847 Motif number 2 TTTCCGCTCCCTTTTCCGTTAGCTTTTTCACC 7 78 0 CTTTTCGTTG 0.721583 -119 GTAACAAGCTCTTTTCGTTCGTTATCA 14 6 0 CTTTTCTTCT 0.97621 -137 AACATTCAAACTTTTACTTTATTAAAAACATA 17 41 0 CTTTTATTTT 0.647342 -132 TGGTCCCCTGCCTTTCATTCTTTC 18 3 0 CCTTTCTTCT 0.971184 -26 TGGCTTTCAACATTTCATTCTTTATCATGAAC 20 94 0 CATTTCTTCT 0.83907 -94 AGCACCTCCACTTTTCTTTCATAAGTTGACTG 29 271 0 CTTTTCTTCT 0.97621 -26 CAACCCCTTTCTTTCATTATATAGACA 31 6 1 CCTTTCTTCT 0.971184 -158 AGTGAGTTCACTTTTCCGTCATGAGTGCGACT 31 41 0 CTTTTCGTCT 0.941336 -123 GAAATGTGTTCTTTTCGGTCAGCTCCGGAAGC 32 32 0 CTTTTCGTCG 0.899104 -168 TGAAGGACATCTTTTCCTTTTTCATATCAGAA 40 40 1 CTTTTCTTTT 0.922688 -141 CGTAGTATACCCTTTCTTTCTGATATGAAAAA 40 57 0 CCTTTCTTCG 0.949282 -124 CCTGGTGAAACCTTTCATTTCTTGTTTTTGTT 44 46 1 CCTTTCTTTT 0.907426 -144 CTTTTATTTCCTCCCTCTACCT 45 38 0 CTTTTATTCT 0.863227 -12 GGCGAAAAGGCTTTTCTTTCCGCGGTACCACC 46 152 0 CTTTTCTTCG 0.957963 -149 AAAGTACGTACTTTTATTTCTTAACGATATGT 48 116 0 CTTTTATTCT 0.863227 -68 CATATGCTGGCCTTTCTTTTCTCGCATGTTTA 54 58 0 CCTTTCTTTT 0.907426 -59 ****** *** * Masking position 5 Map Score: 18.7119 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 264 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 TCTAAAAATGAAAAAAATCGGCTTCTGCAAGAG 1 129 0 AAAAAACGCT 0.695446 -172 AAAGTTGGTCAAACAAACCGGCCTTTTTTAAAA 9 112 1 AACAAACGCC 0.970397 -189 GCTCTTGGCCACAAAAACCGGCACAGCGGAACA 13 93 0 AAAAAACGCA 0.852284 -38 TCCTTTTGTTAGAAAAAGCAGGAACAGCCTTGA 19 28 0 AAAAAACGGA 0.53202 -33 GCGGCAGCAACCAAAAAACTCCCGTCTCTATGC 29 239 0 CAAAAACCCC 0.767529 -58 AAAATTGGATAATCAAATCGGGCTAGCTCATCT 30 238 0 ATCAAACGGC 0.462924 -63 TAACTCACCCAAAAAAAGCGCCAAAAACTTCAT 35 14 0 AAAAAACCCA 0.564663 -106 GAGTTGCATGCAAAAAAACCTCCTGAGTGTTAC 41 35 0 CAAAAACTCC 0.594377 -117 TATATGTATGACAAAAAACAGCCCTGCATTAAC 42 109 0 AAAAAACGCC 0.977376 -164 CGTCCAACAAAAACAAAGCTGCCAAAGATCAGA 43 140 0 AACAAACGCC 0.970397 -88 AAGCCGCCGGACAAATACCGGCCGCTTTT 44 7 0 AAAATACGCC 0.755552 -183 TTCACCAGGCAAAAAAAGCCGCCGGACAAATAC 44 22 0 AAAAAACGCC 0.977376 -168 GGCGTAAGAACCAAAAAGCAGCCAGCGCTCCGC 47 29 0 CAAAAACGCC 0.936251 -177 TAACACATTAAAACAAATTCGCCAGTACATATT 47 127 0 AACAAATGCC 0.591323 -79 AAAAGAGCAGATTCAAATCAGCCGGCAAATGTG 48 75 1 ATCAAACGCC 0.813937 -109 TCCCGCTATGACAAAAAACGTCCCGTCATAGCC 50 236 0 AAAAAACTCC 0.81169 -62 CTTTGTCTATTTAAAAAACGGCCTCTCGAAATA 52 111 0 TAAAAACGCC 0.787075 -190 TAAAGGTCAAACAAAAAGCTGGCCTGATATGCA 52 220 0 AAAAAACGGC 0.894871 -81 ACATACAAACCTCCCAACAATTTCT 54 102 0 AACAAACCCC 0.880515 -15 * ***** * *** Masking position 7 Map Score: 17.2657 Number of sites scoring better than the average of aligned sites = 891 Number in coding regions = 725 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 4 TTTTGCGTGTAAAAAAAGGGGAGGTGCCGG 12 22 0 AAAAAAAGGG 0.943016 -100 TTTTACACGCAAAAAAAGGGTAAACTGATA 12 38 1 AAAAAAAGGG 0.943016 -84 AATTCTGTATAAAAAAAGAGCTTGTTACAG 14 38 0 AAAAAAAGAG 0.929246 -105 TAAAAAAGGGACAGCCGTCA 19 1 1 TAAAAAAGGG 0.863133 -60 TGAGCAATTTTAAAAAAGAGGCTGGGATTT 29 147 1 TAAAAAAGAG 0.833469 -150 TTAAAGAACTGGAAAAAGAGAACATGGAAA 30 192 1 GGAAAAAGAG 0.886793 -109 CTATATAATGAAAGAAAGGGGTTG 31 5 0 AAAGAAAGGG 0.783806 -159 ATCCCGGGCAAGAAAAAAAGTCAAAGCCAA 32 106 0 AGAAAAAAAG 0.442915 -94 TAACTCACCCAAAAAAAGCGCCAAAAACTT 35 17 0 AAAAAAAGCG 0.732545 -103 TTCATATCAGAAAGAAAGGGTATACTACGA 40 60 1 AAAGAAAGGG 0.783806 -121 TATTGCCCCAAGAAAAAGAGATAACTCATA 42 77 0 AGAAAAAGAG 0.944512 -196 TGCCGGTAAAAGAAAAAGTGAGACAAGATT 42 240 1 AGAAAAAGTG 0.705463 -33 ACCGCCTTGTGGAAAAAGGG 44 180 1 GGAAAAAGGG 0.908007 -10 GCTATATAAATAAAAAAGAGCAGATTCAAA 48 62 1 TAAAAAAGAG 0.833469 -122 GGGGAAAATGGGAAAAAGAGACGACTTTGC 52 193 1 GGAAAAAGAG 0.886793 -108 CTCATTCTCATAAAAAAGAGAGGCTTCA 53 9 0 TAAAAAAGAG 0.833469 -159 AGAATGAGTGAGAAAAAGAGTGAAAACAAA 53 31 1 AGAAAAAGAG 0.944512 -137 GAAGACAAATAGAAAAAGGAGGTCTCGTAT 54 12 0 AGAAAAAGGA 0.500453 -105 ********** Masking position 5 Map Score: 18.3049 Number of sites scoring better than the average of aligned sites = 783 Number in coding regions = 591 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 5 TCAAGCGGTTAAGACACCGCCCTTTCACGGC 1 50 1 AGACACCGCC 0.934682 -251 CTGTGAGAGTAGGACGCCGCCAAGCAAGCTT 6 46 1 AGACGCCGCC 0.888229 -255 GTTTACAAGACCTCCTCAAATGTTT 8 32 0 AAAGACCTCC 0.840596 -15 TTGCCAAAACCTCCTTAATAATTT 9 287 0 CAAAACCTCC 0.87308 -14 TTTACTAGCACCTCCGAAAATATTT 11 91 0 CAGCACCTCC 0.954112 -15 AGGGAGAGGGCCGGCACCTCCCCTTTTTTTA 12 12 1 CGGCACCTCC 0.967053 -110 GTGACACGAACACCGCCTTTATCTTCA 14 126 0 CAACACCGCC 0.954112 -17 TTTAAAAAGGTGCCTCCTTGTCCATGG 16 15 0 AGGTGCCTCC 0.578729 -17 GCCTAATACCTCCCCAGGAAGGG 22 55 0 CAATACCTCC 0.827608 -13 TCATCCTTAGCTTACACCGCCCTAAGGTCGC 29 95 0 CTACACCGCC 0.76623 -202 TTCAAGCACCTCCACTTTTCTTT 29 284 0 CAGCACCTCC 0.954112 -13 ACAGGGGCCTCCTTCACATTAA 39 192 0 CGGGGCCTCC 0.863928 -12 GTGACTGACACCTCCGTGACTTTAG 40 166 0 CGACACCTCC 0.975126 -15 GTTGCATGCAAAAAAACCTCCTGAGTGTTAC 41 35 0 AAAAACCTCC 0.770308 -117 CACCAGGCAAAAAAAGCCGCCGGACAAATAC 44 22 0 AAAAGCCGCC 0.582363 -168 GATACGAGACCTCCTTTTTCTATT 54 4 1 AGAGACCTCC 0.881577 -113 * ********* Masking position 7 Map Score: 15.1701 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 215 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 CGGTTAAGACACCGCCCTTTCACGGCGGTAA 1 55 1 ACGCCCTTTC 0.949661 -246 ACTAAAATAGACTGCGCTTTCATTCTATAAT 17 124 0 ATGCGCTTTC 0.705954 -49 ATACCATTTAAAAGCCCTTCCTGGGGAGGTA 22 41 1 AAGCCCTTCC 0.975867 -27 TCACACAGCAACCGCCTTTTCTCTCT 28 6 0 ACGCCTTTTC 0.895171 -127 AACATAACACATAGCGCTTTCAACTATATGG 43 17 0 AAGCGCTTTC 0.944636 -211 AATGAACTGCAAAGCCTGTCCAACCGTATTT 43 87 0 AAGCCTGTCC 0.758583 -141 CGCGGAAAGAAAAGCCTTTTCGCCCCTTTTA 46 160 1 AAGCCTTTTC 0.956989 -141 TTCAATAAAAAAAGCCCTTCCGCCCACAATC 46 214 0 AAGCCCTTCC 0.975867 -87 CTTTAATGAAACAGCCCTTTCTACGGGAAGG 50 16 1 AAGCCCTTTC 0.980062 -282 CCCAATATAAACAGCCCTTCCCGTAGAAAGG 50 31 0 AAGCCCTTCC 0.975867 -267 AATGTTGAGTAAAGCGTTTTCATTTAAACCT 51 102 0 AAGCGTTTTC 0.885363 -36 ACCATTATGTAAACCCTTTTCAGCATCTATT 53 131 0 AACCCTTTTC 0.702923 -37 * ********* Masking position 1 Map Score: 13.8173 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 109 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 ATTCATTCCTCCTGGAGAATAC 2 73 0 TTATTCCTCC 0.905414 -12 CCTAACACTTTCAACCCCTCCAAGCAAAGAA 4 39 0 TCACCCCTCC 0.866217 -65 TCCTTACCTCCTCCCACAGTAAGC 5 84 0 TTCCTCCTCC 0.741918 -14 TACATCATTCTTTTCCGCTCCCTTTTCCGTT 7 90 0 TTTCCGCTCC 0.830191 -107 AAGCGATCTATTTGCTCCTCCGCAAGGAATC 24 44 0 TTGCTCCTCC 0.910088 -155 TATGGATCCCTCCTTCCAAAGCT 24 186 0 TGATCCCTCC 0.919891 -13 TATAAACCTCTTGGCCGCTCCTGCTTGAGGA 30 270 1 TTGCCGCTCC 0.862906 -31 TCTCTTTCCCTCCCTCCGAATAC 31 151 0 TCTTCCCTCC 0.887429 -13 TGAATCCCTCCAGCGCTTGTC 38 52 0 TGATCCCTCC 0.919891 -11 GGTGGTCCCTCCTGAAAAACAA 41 140 0 GTGTCCCTCC 0.798928 -12 GTGTTTCCCTCCAAAAATCTAT 43 216 0 TGTTCCCTCC 0.919891 -12 CTTTTATTTCCTCCCTCTACCTAG 45 36 0 TTTTTCCTCC 0.905414 -14 TTTAGTTCCTCCTTTTGGATTT 46 289 0 TTGTTCCTCC 0.924947 -12 GATTGTTTCCTCCTTTAAATAAG 49 34 0 TTTTTCCTCC 0.905414 -13 TCTTGATCGCTCCTTTACCATTA 53 155 0 TTATCGCTCC 0.856167 -13 ** ******** Masking position 9 Map Score: 11.9757 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 123 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 8 AGCCGGGTACGACAATCAAAGGCAAGTGGAATGG 3 16 1 GCAATAAGCA 0.907321 -73 TAAGATTAAAGTCAAATATAGTCAAAGTCAGTAA 6 264 1 GCAAAAAGCA 0.981193 -37 AGACTTGAAAGTCAAAGATAGTCAGAGTATACTA 9 72 1 GCAAAAAGCA 0.981193 -229 AAATCAATTGGTCAAAGATAGTCAAATATTCAGT 9 143 1 GCAAAAAGCA 0.981193 -158 TATACTAATAGTCAAAGAAGGTCAAACCCAATAG 9 218 1 GCAAAAGGCA 0.960013 -83 ACTTTCATTGGTCAAAGATGATCAAATTATTAAG 9 264 1 GCAAAAGACA 0.894761 -37 AATGTTGAAAGCCAAATAAAGACAGCTGCAAAAA 20 112 1 GCAAAAAGCA 0.981193 -76 TGATTAGAAAGTCAAAGTCAGGCATCTCTTGGCT 32 78 1 GCAAATAGCA 0.836994 -122 ACCCGTTATACACAAATACAACCACTATATTATA 43 47 0 CCAAAAAACA 0.625027 -181 ATTCGGCTTCGTCCAACAAAAACAAAGCTGCCAA 43 148 0 GCCAAAAACA 0.72937 -80 GGTTTCACCAGGCAAAAAAAGCCGCCGGACAAAT 44 24 0 GCAAAAAGCG 0.88386 -166 TCCCGTCATAGCCAAAAAAAATCATTTCTGCTTT 50 215 0 GCAAAAAACA 0.948653 -83 TACATTTTTGGTCAATAAAGGTCAAACAAAAAGC 52 234 0 GCAATAGGCA 0.818354 -67 ATAGCGGGAAGACAAATAGAAAAAGGAGGTCTCG 54 15 0 GCAAAAAAAA 0.529332 -102 * **** * ** ** Masking position 5 Map Score: 15.3306 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 111 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 TTCCGGAATGTTGTCTAAAAATGAAAAAAATC 1 143 0 TTGTTAAAAT 0.626115 -158 TGGTTATTGTTTGTATTGGAATGATTTTCTAT 5 31 1 TTGTTTGAAT 0.850761 -67 CCCGTACCGATTATGTTACAATAGCTGTAGAT 7 46 0 TTATTTAAAT 0.82993 -151 TCTTCCAGTATTATTATAGAATGAAAGCGCAG 17 112 1 TTATATAAAT 0.530244 -61 TTTGTGAAGTTTGTATTATAATAAAAAATTGT 26 75 1 TTGTTTAAAT 0.917348 -83 TAATAAAAAATTGTGATAAAATGATTAATTTT 26 93 1 TTGTATAAAT 0.719672 -65 TACAAGATATTTACGTTATAATATGGATTGTT 28 79 1 TTACTTAAAT 0.532474 -54 GGTGGGTTTCTTGTGTTGAATTTTACCTGGAA 30 119 1 TTGTTTGATT 0.462401 -182 GACTGATGGCTTATATTATAATGTCAAAGTAC 31 83 1 TTATTTAAAT 0.82993 -81 TTTGATACTTTTGTTATAGAATTAGCACTCGC 35 68 1 TTGTATAAAT 0.719672 -52 TTTCTCTTTCTTGTTTTACATTGAATCTTTAC 37 52 1 TTGTTTAATT 0.626115 -82 CCTCCAGCGCTTGTCTAGTAATTACTCTATGA 38 35 0 TTGTTAGAAT 0.462401 -28 TACTTTACATTTATATTGCAATCTAAAGGTGT 39 98 0 TTATTTGAAT 0.714811 -106 GATGAAAAAGTTGTATTATAATGGTTCATACT 40 136 1 TTGTTTAAAT 0.917348 -45 GCGCTATGTGTTATGTTATAATATAGTGGTTG 43 31 1 TTATTTAAAT 0.82993 -197 AGCCGAATGATTGCTTTAGAATGGAAGACCGA 43 174 1 TTGCTTAAAT 0.721475 -54 TTGTACGTACTTATATTAAAATTTAACGAAAA 51 66 0 TTATTTAAAT 0.82993 -72 **** *** *** Masking position 10 Map Score: 8.84624 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 68 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 10 TGAAAAATTTTTTATCTTATCACTTGAAATTG 7 125 1 TTTTCTTTCA 0.925991 -72 ACATGTTTTCTTCGTCTTTTCAAGGA 9 5 0 TTCTCTTTCA 0.931379 -296 CTGTCAAGTTTTTATCTTGTCAAAGCGGCGAT 10 89 0 TTTTCTTTCA 0.925991 -88 TGTAAAGTGTTTTTTCTTAACAACGGTTTTAT 11 24 0 TTTTCTTACA 0.865664 -82 TTTCTCTTCTCCCTTACTGTAT 15 59 0 TTTTCTTTCC 0.841019 -12 AGAGGTGTTCTCTCTCTTTTCAAGATATTTCA 20 152 0 TCTTCTTTCA 0.770583 -36 CTCATCATGAATTGTCATTTCATTATTCGCAC 24 78 1 ATTTCATTCA 0.527941 -121 GTGATCGGTAATCGTCTTTTCCCCATTTATAA 28 33 1 ATCTCTTTCC 0.747194 -100 AATTCTTACCTTTATCTTGACCAGATGTCCTC 30 54 0 TTTTCTTACC 0.731512 -247 CGGATTCACCTTCTTTACAGAAAGAAGCC 36 34 0 ACCTCTTACA 0.49149 -19 TTAAGGTTAAATCTTCTTCACAATAGAACAAA 39 50 1 ATCTCTTACA 0.782624 -154 CATCTTTTCCTTTTTCATATCAGAAAGAAAGG 40 47 1 TTTTCATTCA 0.684689 -134 AATTTTTGCGTTTTTCTTGTCATGCGTCATAC 44 127 0 TTTTCTTTCA 0.925991 -63 TCCTTTAAAGATCATCTTTTCATTAGCTAGAT 46 254 0 ATCTCTTTCA 0.874851 -47 CAATTTCTAATTCATCTTAACATATGCTGGCC 54 78 0 TTCTCTTACA 0.874851 -39 *** **** *** Masking position 5 Map Score: 8.53955 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 213 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 11 TCATATCCTAACACTTTCAACCCCTCCAAGCA 4 44 0 ACTTTCAACC 0.707435 -60 TTTTCCGTTAGCTTTTTCACCCCCGTACCGAT 7 67 0 GCTTTCACCC 0.982599 -130 GAGTTCTCCCGCGGTTCCACCCTAGTTGCTGA 29 182 0 GCTTCCACCC 0.986976 -115 ATAACACATAGCGCTTTCAACTATATGGCGCG 43 13 0 GCTTTCAACT 0.683036 -215 GAACTGCAAAGCCTGTCCAACCGTATTTCTTA 43 83 0 GCGTCCAACC 0.92161 -145 GCACTCTGAGGCGAGTTCACCTTGTAAAGCTT 46 16 0 GCGTTCACCT 0.84493 -285 AACGAGTGAATCAAGTTCACCCGGCCAAGTCC 46 66 0 TCGTTCACCC 0.776149 -235 TTTTCTTTCCGCGGTACCACCCTTGTTTACGG 46 141 0 GCTACCACCC 0.905915 -160 GGAAAGAAAAGCCTTTTCGCCCCTTTTAGCTA 46 163 1 GCTTTCGCCC 0.955894 -138 AATAAAAAAAGCCCTTCCGCCCACAATCAGCC 46 210 0 GCTTCCGCCC 0.96676 -91 AGTTGAATAAACAATTCCACCCTGTTAAAATA 50 176 1 ACTTCCACCC 0.929079 -122 ** ******** Masking position 8 Map Score: 6.07061 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 121 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 12 TGTTTGGCCCGTTGGTCAAGCGGTTAAGACACCGCC 1 35 1 GTTCAAGGGA 0.882014 -266 GCGTAAACAGCTTGGTAAAGGGGCCAATGGAATT 3 65 1 CTTAAAGGGA 0.984149 -24 AAGTTTTTATCTTGTCAAAGCGGCGATTAACTTTTC 10 80 0 CTTAAAGGGA 0.984149 -97 AGGGATTTGACTTAACAAAGGGGAGAGCTCAA 10 155 1 CTTAAAGGGA 0.984149 -22 ACGAGTAAAAGTTTTAAAAGCGGGGAGCTTGGTGCG 12 96 1 GTTAAAGGGA 0.969693 -26 ATAATACAAACTTCACAAAGATGCTATTGTTTTTCA 26 58 0 CTTAAAGTGA 0.873945 -100 AAACAAAAAACTTATAAATGGGGAAAAGACGATTAC 28 40 0 CTTAATGGGA 0.907298 -93 TTTTCCAGTTCTTTAAAAAGAAGATACGTATCAACA 30 172 0 CTTAAAGAGA 0.873945 -129 TGATTCACTCGTTACTAAAGCGGATAGAAATATCCA 46 85 1 GTTAAAGGGA 0.969693 -216 *** **** ** * Masking position 8 Map Score: 5.17762 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 52 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 GATTCATATATTCCCATCTTCGCCAGAAGAA 2 31 0 TTCCCATTTC 0.96883 -54 TCCTTCATTATTTCCATTTTCCCGGTCCACA 6 192 0 TTTCCATTTC 0.960227 -109 TTCCCATCCTCCTAACTTATG 17 162 0 TTCCCATCTC 0.878966 -11 TCTTCGGGTCTTTCCATGTTCTCTTTTTCCA 30 201 0 TTTCCATTTC 0.960227 -100 AAGGACATCTTTTCCTTTTTCATATCAGAAA 40 42 1 TTTCCTTTTC 0.812259 -139 AAACGGCATGGTTCCATTTTCTATAAAACAG 40 95 0 GTTCCATTTC 0.849414 -86 AAAACGTTTATTCCCGTCTTCTATGGGAGAT 41 75 1 TTCCCGTTTC 0.891957 -77 AATAATCTTGTTTGCATTTTCTGTCA 51 6 0 TTTGCATTTC 0.778166 -132 TCGTCTCTTTTTCCCATTTTCCCCAAAAATA 52 186 0 TTCCCATTTC 0.96883 -115 ******* *** Masking position 7 Map Score: 5.60636 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 49 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 TAGATTGACCTCCTTTTGTTAGAA 19 47 0 TTGACCTCCT 0.63687 -14 TGCCAATAAATGCTCCTCATCAGTTCTCCA 24 12 0 TGCTCCTCAT 0.876863 -187 GCGATCTATTTGCTCCTCCGCAAGGAATCA 24 43 0 TGCTCCTCCG 0.826321 -156 AGTACTTGCGTTTACCTCATGAAAGCGACC 29 71 1 TTTACCTCAT 0.609191 -226 TTTCGTTGCGTGCTCATCCTTAGCTTACAC 29 109 0 TGCTCATCCT 0.833892 -188 TGTGTTCACCTCCCTCAAAGTGTA 34 58 0 TTCACCTCCC 0.754652 -14 GTGTTTCACCTCCTAAGATACAAC 39 5 1 TTCACCTCCT 0.913768 -199 TAATACAACTTTTTCATCCTTGTACAATAA 40 124 0 TTTTCATCCT 0.742514 -57 AAATTATTCCTTTTCCTCATCTGAAGACCG 44 154 1 TTTTCCTCAT 0.803555 -36 TCCTTTTGGATTTTCATCCTTTAAAGATCA 46 272 0 TTTTCATCCT 0.742514 -29 TTTAGTTCCTCCTTTTGGATTTT 46 288 0 AGTTCCTCCT 0.649126 -13 GATGTTCCTCCTTTGTAAGATG 48 3 1 TGTTCCTCCT 0.949487 -181 ACAATCCATTCTCCTCACAGGCACCAAA 48 166 0 TTCTCCTCAC 0.655815 -18 GATTGTTTCCTCCTTTAAATAAGT 49 33 0 GTTTCCTCCT 0.716523 -14 AATGCTCCTCCTTCACCTTTTA 52 289 0 TGCTCCTCCT 0.967913 -12 ********** Masking position 7 Map Score: 6.32224 Number of sites scoring better than the average of aligned sites = 564 Number in coding regions = 333 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 15 GGTTAAGACACCGCCCTTTCACGGCGGTAA 1 56 1 CCGCCCTTTC 0.92299 -245 GGGGAGGTGCCGGCCCTCTCCCTT 12 5 0 CGGCCCTCTC 0.882445 -117 CTAAAATAGACTGCGCTTTCATTCTATAAT 17 124 0 CTGCGCTTTC 0.863764 -49 TACCATTTAAAAGCCCTTCCTGGGGAGGTA 22 42 1 AAGCCCTTCC 0.905702 -26 AGGACAGGTGCTGCCCTTCGATAAAATTTG 34 22 0 CTGCCCTTCG 0.923424 -50 TCAATAAAAAAAGCCCTTCCGCCCACAATC 46 214 0 AAGCCCTTCC 0.905702 -87 AAAAAGCAGCCAGCGCTCCGCACTGACTGC 47 20 0 CAGCGCTCCG 0.689043 -186 TTTAATGAAACAGCCCTTTCTACGGGAAGG 50 17 1 CAGCCCTTTC 0.970395 -281 CCAATATAAACAGCCCTTCCCGTAGAAAGG 50 31 0 CAGCCCTTCC 0.984213 -267 TTCCCTGCCCTCCCGAATGTTGAG 51 124 0 CTGCCCTCCC 0.969413 -14 TTAACATATGCTGGCCTTTCTTTTCTCGCA 54 64 0 CTGGCCTTTC 0.756515 -53 ********** Masking position 7 Map Score: 7.69087 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 193 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185