AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_bsub_reg_300.orf -o00300_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 Purged sequences: yacF 23 similar to transcriptional regulator (nitrogen regulation protein) 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 yacB 194 similar to hypothetical proteins #7 yacC 85 similar to hypothetical proteins #8 yacD 46 similar to protein secretion PrsA homolog #9 cysK 75 cysteine synthetase A #10 pabB 166 para-aminobenzoate synthase (subunit A) #11 lysS 91 lysyl-tRNA synthetase #12 ddlA 174 D-alanyl-D-alanine ligase A #13 murF 71 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diaminopimelate-D-alanyl-D-alanyl ligase #14 patA 300 aminotransferase #15 ykuJ 300 ykuJ #16 ykuK 109 ykuK #17 ykzF 133 ykzF #18 ykuL 137 ykuL #19 ykuM 148 similar to transcriptional regulator (LysR family) #20 ykuN 111 similar to flavodoxin #21 ykuQ 24 similar to tetrahydrodipicolinate succinylase #22 ylbQ 159 similar to pyrimidine-thiamine biosynthesis #23 yllA 70 yllA #24 yllB 125 similar to hypothetical proteins #25 ylxA 69 alternate gene name: yllC; similar to hypothetical proteins #26 ftsL 39 cell-division protein #27 spoVD 116 penicillin-binding protein #28 murE 175 UDP-N-acetylmuramoylananine-D-glutamate-2,6- diaminopimelate ligase #29 ylxS 300 alternate gene name: ymxA; similar to hypothetical proteins #30 nusA 34 nusA #31 truB 81 tRNA pseudouridine 55 synthase #32 rpsO 156 ribosomal protein S15 (BS18) #33 pnpA 172 polynucleotide phosphorylase (PNPase) #34 ylxY 117 alternate gene name: ymxI; similar to deacetylase #35 ymxG 39 similar to processing protease #36 ymxH 77 similar to hypothetical proteins #37 spoVFA 185 dipicolinate synthase subunit A #38 asd 125 aspartate-semialdehyde dehydrogenase #39 dapG 91 aspartokinase I (alpha and beta subunits) #40 dapA 30 dihydrodipicolinate synthase #41 pksF 300 pksF #42 ypjD 300 alternate gene name: jojD #43 lysA 105 diaminopimelate decarboxylase #44 spoVAA 121 mutants lead to the production of immature spores (stage V sporulation) #45 spoIIAA 95 anti-anti-sigma factor (antagonist of SpoIIAB) #46 dacF 154 D-alanyl-D-alanine carboxypeptidase (penicilin binding protein) #47 drm 160 phosphodeoxyribomutase #48 ripX 300 integrase/recombinase #49 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #50 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #51 yqiS 124 similar to phosphate butyryltransferase #52 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #53 blt 116 multidrug-efflux transporter #54 bltD 168 spermine/spermidine acetyltransferase #55 lysC 175 aspartokinase II alpha subunit (aa 1->408) and beta subunit (aa 246->408) #56 ask 94 ask #57 uvrC 135 excinuclease ABC (subunit C) #58 trxA 300 thioredoxin #59 ytjP 96 similar to Xaa-His dipeptidase #60 patB 80 aminotransferase #61 yutL 122 similar to diaminopimelate epimerase #62 yutK 136 similar to Na+/nucleoside cotransporter #63 yuzB 262 yuzB #64 hom 200 homoserine dehydrogenase #65 yutH 152 yutH Motif number 1 CCTAACAAATCGGTTTCTCTTGCAGAAGCC 1 113 1 CGGTTTCTCT 0.695082 -188 TTCGCTTTCTTTCTAAAAAAAC 6 3 1 CGCTTTCTTT 0.947334 -192 CGTCAGCCGGCAGTTTTTTTAGAAAGAAAG 6 15 0 CAGTTTTTTT 0.626079 -180 CTGACGCTGGCAGTTTTTTTATGTAAATGA 6 39 1 CAGTTTTTTT 0.626079 -156 ACTTCCTACGCGGTTTCTTTCATAAATCAA 7 49 0 CGGTTTCTTT 0.869573 -37 GGTTCGCCGGGAGTTTTTTTATATTTCGTG 10 28 1 GAGTTTTTTT 0.439282 -139 AAGAGAAATTCACTTTTTTCACTAACAACA 10 97 1 CACTTTTTTC 0.705772 -70 GGCAGTTTTTCTGCTTTTTTCATGAAACAA 11 50 1 CTGCTTTTTT 0.713195 -42 TACCGGCAGTGTCCTTCTTCA 13 2 0 GTCCTTCTTC 0.700537 -70 TAAAAGGGCAGTGTTTTTTCCCGTATATAC 13 30 1 GTGTTTTTTC 0.42156 -42 TAAGGTCCCTCTCTTTCTTTTGTATATACG 13 51 0 CTCTTTCTTT 0.917398 -21 CGATTGTATGCGCCTTTTTTCTAAACATAC 14 198 0 CGCCTTTTTT 0.915723 -103 TTTAGTTTGAGGCTTTTTTTGAATGTCATG 15 128 0 GGCTTTTTTT 0.857082 -173 TAGTTTTTTTCACTTTTTTTCTTTGCTTAA 15 164 1 CACTTTTTTT 0.818753 -137 TTTGAAAGGAGTCTTTTTTTAGA 15 288 1 GTCTTTTTTT 0.787363 -13 ATTATGTATGCGCTTTCTTTTTTCACTCTG 19 40 0 CGCTTTCTTT 0.947334 -109 GCGAGGTGCTGTCTTTTTTTTATTTATCTG 20 16 1 GTCTTTTTTT 0.787363 -96 GACTAGTTCAGGGTTTCTTTTTATGGGTAA 24 32 1 GGGTTTCTTT 0.757253 -94 TCTCTTGCCCCACTTTCTCTCCTTAACTCA 24 104 0 CACTTTCTCT 0.684305 -22 GCATAACGACGGCTTTCTTT 27 1 0 GGCTTTCTTT 0.893801 -116 TCGTTATGCAGGCTTTCTTTTTTTATGCCT 27 22 1 GGCTTTCTTT 0.893801 -95 ATCGTCTGTCCTCTTTCTTCGTTTATAAGA 31 32 1 CTCTTTCTTC 0.85502 -50 TCCTTCTTTTGAGTTTTTTTCTTATAAACG 31 51 0 GAGTTTTTTT 0.439282 -31 TTGCCTTTCACTCCTTCTTTTGAGTTTTTT 31 62 0 CTCCTTCTTT 0.903988 -20 CTGGGAGACCCGGCTTCTTTATTTTGAAGC 34 30 1 CGGCTTCTTT 0.84967 -88 AGGTAGAACCCGCCTGCTTTTGAAAAGCTT 34 56 0 CGCCTGCTTT 0.580903 -62 GTTCTACCTTGTCCTTCTCCTTCATAATGT 34 77 1 GTCCTTCTCC 0.444395 -41 ATAAAAGATGCGCTTTTTCCATATAAAAAA 37 79 0 CGCTTTTTCC 0.699432 -107 TCTAAACGTTCACCTTCTTTGTATATACTG 37 166 0 CACCTTCTTT 0.843124 -20 TGTCATTCCCTCTTTCTCCGCTTATGGAT 43 87 0 CTCTTTCTCC 0.668483 -19 TCACACAGCTGTCTTTTTTTATGCCCAAAA 46 52 1 GTCTTTTTTT 0.787363 -103 CAGGTGGCTGCGGCTTTTTTGTTTAGAGCG 47 14 1 CGGCTTTTTT 0.801089 -147 CTTGAAAGCCTCCTTTTTTTCTATACGTC 47 142 0 CTCCTTTTTT 0.870281 -19 TCGAACCATCCGCCTTTTTCATCCTGATCC 48 240 0 CGCCTTTTTC 0.852283 -61 ACTACATTCTCCTTTTTTCTTATCCCGG 54 151 0 CTCCTTTTTT 0.870281 -18 GGACAAAGCGCTCTTTCTCCTCACCCGCAC 55 129 1 CTCTTTCTCC 0.668483 -47 ATTGAGGGATCGCTTTTTTTATTCGCCAAT 57 43 1 CGCTTTTTTT 0.927625 -93 ATGGGATATGCTCTTTTTTTAAAACACAAA 58 155 0 CTCTTTTTTT 0.887815 -146 TATAAGCCCGCTCCTGTTTTGACAAGACAT 64 100 0 CTCCTGTTTT 0.378814 -101 AGAAGTTTACGACTTTTTCTTGCGCCTTCT 65 54 1 GACTTTTTCT 0.41951 -99 CTTTTTCTTGCGCCTTCTTCGGATTAAAAT 65 66 1 CGCCTTCTTC 0.890077 -87 ********** Masking position 5 Map Score: 38.1419 Number of sites scoring better than the average of aligned sites = 2551 Number in coding regions = 2060 Number in noncoding regions = 491 Number of orfs with sites within 600 bp upstream = 488 Fraction of orfs with sites within 600 bp upstream = 0.078381 Motif number 2 ACCGCCGTGAAAGGGCGGTGTCTTAACCGCTT 1 52 0 AAGGGGGTTC 0.907727 -249 GATTTTGTCAAAAGAAGGTAACAATACCAAAG 1 220 0 AAAGAGGTAC 0.710345 -81 GAAACTATTCAAAAGTGGTGATAGAGG 6 178 1 AAAAGGGTAT 0.682455 -17 ATAAAATTCAAAAGAAGGTTTTGACAAAGTTG 15 43 1 AAAGAGGTTT 0.663784 -258 TTACTTTTGCAAAGGCGGAAGCTTGTTCCCCC 16 24 0 AAAGGGGAGC 0.701201 -86 TAGAAACAACAAAGGGGGAGATTTGT 22 5 0 AAAGGGGAAT 0.89364 -155 CGCAAAATTAAAAGGAGGTCATCAGCCT 26 22 1 AAAGGGGTAT 0.923148 -18 CAAATGTTTTAAGGGGGGAGACCGTTAA 30 17 1 AAGGGGGAAC 0.852138 -18 TCACACAACGAAGAGAGGAGTTCGTAATTGT 33 152 1 AAGAGGGATT 0.453579 -21 ATACATAGTACAAGGGGGTGACAGAC 36 62 1 CAAGGGGTAC 0.82032 -16 TAATGGAAGGAAAAGGGGTTTTGTGTGATGCT 42 167 0 AAAAGGGTTT 0.719578 -134 TAAGAGGATGATAGGAGGTTTCGTTCA 42 284 1 ATAGGGGTTC 0.55536 -17 ATAACCACCGAAAGATGGTGATCA 44 108 1 AAAGAGGTAT 0.623142 -14 GTATAGAAAAAAAGGAGGCTTTCAAG 47 145 1 AAAGGGGCTT 0.676598 -16 AGACGTAAGGGAGGATACAATC 49 7 1 AAGGGGGAAC 0.852138 -16 TTGCATAATAAAAGGCGGAGTCGAAACAAGAA 51 91 1 AAAGGGGATC 0.937023 -34 TCGAAACAAGAAAGGTGGTAACAG 51 111 1 AAAGGGGTAC 0.946852 -14 TTTTTTCATACAAAGGGGTATCGGG 52 138 1 CAAAGGGTTC 0.493747 -15 ACCGTATAGTCAAGGAGGTTTTT 53 2 0 CAAGGGGTTT 0.786114 -115 TCAATTGAGTAAAAGGGGAATTCAG 53 102 1 AAAAGGGATT 0.642205 -15 CCAAAATGTAAAGGGTGGTAATAC 55 162 1 AAGGGGGTAT 0.84745 -14 GCCTTTGGAGAAAGATGGATTCT 56 82 1 AAAGAGGATC 0.671931 -13 CAATCAAAAGAAAGGTGGAGTTTTT 64 186 1 AAAGGGGATT 0.909354 -15 ***** *** ** Masking position 7 Map Score: 18.1118 Number of sites scoring better than the average of aligned sites = 587 Number in coding regions = 323 Number in noncoding regions = 264 Number of orfs with sites within 600 bp upstream = 281 Fraction of orfs with sites within 600 bp upstream = 0.0451333 Motif number 3 TCCGGAAATTCTTTTCATAAACGAATATCAAGGCA 1 168 1 CTTTTCAAAA 0.954515 -133 TTCGCTTTCTTTCTAAAAAAACTGCCGGCTGA 6 8 1 TCTTTCAAAC 0.833557 -187 CTACGCGGTTTCTTTCATAAATCAATTCCAGCCCT 7 39 0 TCTTTCAAAA 0.927574 -47 CTTTCAGCCCCTTTTCTCAAATTAAAAACCCGCTA 8 17 0 CTTTTCAAAA 0.954515 -30 GAAATTCACTTTTTTCACTAACAACATTGCTTTAC 10 101 1 TTTTTCAAAC 0.756954 -66 TTTTTCTGCTTTTTTCATGAAACAATATCTGTAAT 11 55 1 TTTTTCAAAA 0.888416 -37 ACATACCTTTCTTTTCAGAAAAAAAGAAGACAACC 14 169 0 CTTTTCAAAA 0.95447 -132 AAAAAAGACTCCTTTCAAAAAGCAACTTCAAATCA 15 272 0 CCTTTCAAAA 0.971219 -29 CAAGCTTCCGCCTTTGCAAAAGTAATCGAAATAAA 16 31 1 CCTTTGAAAA 0.838917 -79 CGAAAAGTTTCCTTTCAATAAAAAAGATACTCTTT 18 38 0 CCTTTCAAAA 0.971218 -100 TGAAAGGAAACTTTTCGACAAATACTGATAAAGTT 18 56 1 CTTTTCAAAC 0.891376 -82 TCTAGAACTTCCTTTCTCCAATAAATAGTTAGTGA 23 44 0 CCTTTCAAAA 0.971219 -27 ATATCAGCATTTTTTCTGCAATAAAAGAATAGGCA 28 18 0 TTTTTCAAAA 0.888416 -158 TTACAGAAAATCTTTCCCAAACTAAAAAATTCGGT 38 13 1 TCTTTCAAAA 0.927574 -113 AATTACCACGCTTTTGCACAAAAAAGCTAGCCTGC 44 19 0 CTTTTGAAAA 0.764045 -103 AATGATCCCCTTTCCGCAAGAAATGACTTGCAA 59 74 0 CCTTTCAAAA 0.971219 -23 ****** ** ** Masking position 10 Map Score: 20.2178 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 124 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 TGTATGTAATTCCTTTTTATTTTATATTAAAAT 12 35 0 TCCTTATTTT 0.940566 -140 CTCCCCCCACTACAATTCATCTTTACTATCTTA 12 125 0 TACTTATCTT 0.756406 -50 TCCCATTGATTATGGCCACGCGG 15 1 1 TCCTTATTAT 0.857767 -300 GTTTTCGACCCCTTTTCATTTTCATCATCAAT 18 116 0 CCCTTATTTT 0.713962 -22 TGTATAGTCCTCCTCCTGATTTT 21 1 0 TCCCTATTTT 0.809467 -24 GCTGATGACCTCCTTTTAATTTTGCGTTCGCGT 26 15 0 TCCTTATTTT 0.940566 -25 AAAGGATACATCCAGCTAATCTTGAAAGATATC 28 48 0 TCCCTATCTT 0.885924 -128 CATTTTTTAATCCCTTTCATCATACATAGTACA 36 41 1 TCCTTATCAT 0.916834 -37 CACCGGTATTTCCTTTTGATCATAAGATGAAGG 37 112 1 TCCTTATCAT 0.916834 -74 GTTGTTAAGCTCCCCTTCATCTTATGATCAAAA 37 125 0 TCCTTATCTT 0.966587 -61 ACTATGATTTTACGTTTTATTTTACCATAGAAT 38 60 0 TACTTATTTT 0.629449 -66 CATTTCATAATCCTTTTTATTTTTTCCAAGCGT 46 119 0 TCCTTATTTT 0.940566 -36 CAGCGGAGCTTCCGGTTTATCATACCGATGATA 48 191 0 TCCTTATCAT 0.916834 -110 GGATGGTTCGACCGGTTGATCTTTTTTTACCAA 48 259 1 ACCTTATCTT 0.844443 -42 CTTCAGAAAACCCCTTTATCTTTTCATTTCCT 52 10 1 ACCTTATCTT 0.844443 -143 *** ** ***** Masking position 9 Map Score: 13.3083 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 127 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 TATGGTAGCGGCGGAGGGGATC 1 2 0 GCGAGGGGAT 0.67412 -299 TGCTCATTGTGAGGAGGACATT 4 92 1 GAGAGGACAT 0.797546 -12 TTTAATTTGAGAAAAGGGGCTGAAAGCAGGT 8 26 1 GAAAGGGGCT 0.965102 -21 AAATGGCATTGAAAAGGAGATGTGACAT 12 8 0 GAAAGGAGAT 0.9171 -167 ACAAAAGAAAGAGAGGGACCTTAC 13 58 1 GAGGGGACCT 0.772788 -14 ATTTAAACGAGAATAGGGCTTGAATAAGAAA 19 68 1 GAAAGGGCTT 0.718757 -81 GATTTTATTAGAATGGGAGATAAGAAAAACT 19 103 1 GAAGGGAGAT 0.893552 -46 AGAAACAACAAAGGGGGAGATTTGT 22 5 0 AAGGGGAGAT 0.525546 -155 TGCTTCAAAAGAGCAGGGGCTAAAAAGTAAA 29 222 0 GAGAGGGGCT 0.954513 -79 ATCATAAGATGAAGGGGAGCTTAACAACTAG 37 130 1 GAAGGGAGCT 0.905225 -56 GGCTGATGTGGAAAAGGGCATAAAGCAAAAG 42 15 1 GAAAGGGCAT 0.919396 -286 CTAATGGAAGGAAAAGGGGTTTTGTGTGATG 42 169 0 GAAAGGGGTT 0.844858 -132 TAAAAGCATAAAGGAGGGGCTTGA 50 60 1 AAGAGGGGCT 0.784914 -14 ACATGACAGTGAAGAGGAGATGTGATCTTAT 58 66 1 GAAAGGAGAT 0.9171 -235 TAGCGTGAACGAATGGGAGATGCTATACTAA 58 248 1 GAAGGGAGAT 0.893552 -53 CATTTCTTGCGGAAAGGGGATCATT 59 82 1 GGAAGGGGAT 0.73163 -15 TATGTATGAAAAACGGGGGATAATTGTATTG 61 47 1 AAAGGGGGAT 0.762315 -76 AGAAAAGGGCCTGGACAGGCCC 62 2 1 GAAAGGGCCT 0.928462 -135 CGGCAAAATAAAAAAGGGCCTGTCCAGGCCC 62 17 0 AAAAGGGCCT 0.692971 -120 *** ******* Masking position 11 Map Score: 16.9806 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 247 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 6 ACAGGCAACGAATATAACAGGTGGGAGATGAGAGG 1 275 1 AAAACAGTGG 0.587308 -26 AAACAAGTAAAAAAGAAAATAGAGGAATGATACAA 10 142 1 AAAAAAAGGG 0.971507 -25 ACTAGCAGTGAGCAGCAAATAGAGGTGAGTA 11 7 0 AACAAAAGGG 0.822258 -85 AGAGGTATTCAGTATAAAACAGGGGGCCTGA 17 113 1 AAAAAAAGGG 0.971507 -21 AAACTTATTGATAACAAAAAGGAGGACGAC 19 129 1 AAAAAAGGGG 0.9682 -20 ACGCGAACGCAAAATTAAAAGGAGGTCATCAGCCT 26 15 1 AATAAAGGGG 0.735954 -25 TCTCCTGTTCAATACAAAAGAGCGGGTTTCCCCAC 29 164 0 AAAAAAAGGG 0.971507 -137 TCGCTTTAATACGATAAAAAAGCGGGAATCCTCCC 33 22 0 AAAAAAAGGG 0.971507 -151 CTTTTTCCATATAAAAAAACATCGGCTCCGGCAGC 37 62 0 AAAAAAATGG 0.872262 -124 AATAAAAAGGATTATGAAATGGAGGGCTTTTGAG 46 131 1 AAGAAAGGGG 0.805106 -24 AATAGACGTATAGAAAAAAAGGAGGCTTTCAAG 47 138 1 TAAAAAGGGG 0.709761 -23 ATCATAGCATAATAGAACAAAGCGGTAAAACCGGT 48 131 0 AAAACAAGGG 0.888362 -170 CATTTTTAAAAGCATAAAGGAGGGGCTTGA 50 54 1 AAAAAGAGGG 0.802327 -20 GGATACCGGGATAAGAAAAAAGGAGAATGTAGT 54 146 1 AAAAAAAGAG 0.628378 -23 TACTAAGAAAAAGAAAAAAAGTTGGAGGCACCT 61 100 1 AAAAAAGTGG 0.859109 -23 TTTGTACGGCAAAATAAAAAAGGGCCTGTCCAGGC 62 19 0 AAAAAAAGGC 0.714785 -118 TGTATAAACTAGTAAAAAAGATTGGGTGAAGCTG 65 10 0 AAAAAAATGG 0.872262 -143 * * **** ** ** Masking position 7 Map Score: 14.323 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 192 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 7 CCGTGTTACCGCCGTGAAAGGGCGGTGTCTTAA 1 58 0 GCGTGAAAGC 0.954062 -243 CATGAAAAAAGCAGAAAAACTGCCAGCGTAAAA 11 41 0 GCGAAAAAGC 0.951203 -51 TATTAAAATGGCATTGAAAAGGAGATGTGACAT 12 11 0 GCTTGAAAGA 0.626837 -164 AGATCATTTTCCGGTGAAAATGATAAGATAGTA 12 102 1 CCGTGAAAGA 0.464357 -73 AAGGACACTGCCGGTAAAAGGGCAGTGTTTTTT 13 16 1 CCGTAAAAGC 0.814927 -56 ATCTTTGGCAGCATTAAGAATGCCTTTTTGCAA 15 72 0 GCTTAAGAGC 0.415389 -229 CTTAAATTCAGCAGTGAAAATGCCATCCTGTCC 15 189 1 GCGTGAAAGC 0.953965 -112 TCCTCTGAAGGCATAAAAAAAGAAAGCCTGCAT 27 27 0 GCTAAAAAGA 0.611778 -90 TTCTTTTATTGCAGAAAAAATGCTGATATCTTT 28 24 1 GCGAAAAAGC 0.951205 -152 GCATACATAAGCGCAAAAAGTGCCATCGTAATA 29 19 1 GCCAAAAAGC 0.620473 -282 TAAAAACCCTGCTTCAAAAGAGCAGGGGCTAAA 29 229 0 GCTCAAAAGC 0.573699 -72 ATATGATTTGGAGGTGAAACAGG 32 144 1 GAGTGAAAGG 0.409823 -13 TGATGAAAGGGATTAAAAAATGCCTGCTCCATT 36 30 0 GATAAAAAGC 0.570722 -48 AAGTGTAATACCTGTAAAACCGCCCTCAGCCAG 42 43 1 CCGTAAAAGC 0.81488 -258 TCGCATTGAAACTGACTGAAGAGTA 43 3 1 GCTTGAAAGA 0.626836 -103 TCATCCATAAGCGGAGAAAGAGGGAATGACA 43 85 1 GCGAGAAAGG 0.79 -21 CGAATTTTGGGCATAAAAAAAGACAGCTGTGTG 46 53 0 GCTAAAAAGA 0.611778 -102 ATAGAACAAAGCGGTAAAACCGGTAAACAGGAT 48 122 0 GCGTAAAAGG 0.806924 -179 TTTGCAGAATAAACGCAAACATCTGC 51 4 1 GCGAATAAGC 0.52279 -121 TCGTGCGGGTGAGGAGAAAGAGCGCTTTGTCCA 55 128 0 GAGAGAAAGC 0.764039 -48 CACAATTGGCGAATAAAAAAAGCGATCCCTCAA 57 44 0 GATAAAAAGC 0.570722 -92 TGTTTTAAAACCTGAAAAAGAGCGCCGGCATG 58 10 0 CCGAAAAAGC 0.801811 -291 TAATTTGTAAGCATTAAAATAGCGTGAACGAAT 58 229 1 GCTTAAAAGC 0.895091 -72 GGACATATGTGAGGTGAAACCGC 63 250 1 GAGTGAAAGC 0.778969 -13 ** ****** ** Masking position 9 Map Score: 18.8788 Number of sites scoring better than the average of aligned sites = 1537 Number in coding regions = 1388 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 8 CCGGAAATTCTTTTCATAAACGAATATCAA 1 169 1 TTTTCATAAA 0.59153 -132 TACGCGGTTTCTTTCATAAATCAATTCCAG 7 43 0 CTTTCATAAA 0.586536 -43 CCCCTTTTCATTTTCATCATCAATACATTC 18 110 0 TTTTCATCAT 0.748838 -28 ACTACGAAAACTATCATACTAAAAATCGTG 32 55 0 CTATCATACT 0.736168 -102 TTTTTAATCCCTTTCATCATACATAGTACA 36 44 1 CTTTCATCAT 0.744938 -34 TATAGGTATATTTTCATAATATTCAAACTT 41 17 0 TTTTCATAAT 0.702926 -284 GCTGTTTTCTTTTTCATCCACTATAATATA 42 208 0 TTTTCATCCA 0.862525 -93 ACGAAACCTCCTATCATCCTCTTACATGTT 42 278 0 CTATCATCCT 0.77856 -23 AAGACATACATTATCATACTCTTCAGTCAG 43 22 0 TTATCATACT 0.740155 -84 TAAAACTGTCCTTTCATCCATAAGCGGAGA 43 72 1 CTTTCATCCA 0.86006 -34 GCATTGAAAGTTTTCATCCTGTTTACCGGT 48 107 1 TTTTCATCCT 0.911121 -194 CCGATGATAGTTTTCATACTCTTGATTCAC 48 170 0 TTTTCATACT 0.890538 -131 CCATCCGCCTTTTTCATCCTGATCCATTTC 48 235 0 TTTTCATCCT 0.911121 -66 TGTGCAAATTTTTTCATACAAAGGGGTATC 52 130 1 TTTTCATACA 0.832754 -23 TATCCCCCGTTTTTCATACATAAAAGCTCC 61 39 0 TTTTCATACA 0.832754 -84 TTCAATGTATCTATCATACTCTTCGGATTA 63 24 0 CTATCATACT 0.736168 -239 ********** Masking position 6 Map Score: 12.4986 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 214 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 9 GTTTGTATTGGAATGATTTTCTATGGTACT 5 39 1 GAATGATTTT 0.77857 -59 GAAAATGATCTAATTATTTTTGGGCATGCT 12 83 0 TAATTATTTT 0.744543 -92 TTAACAAATATAATGAGTTTATCCTATTTT 14 270 0 TAATGAGTTT 0.77857 -31 CTTTAAATGATAATGATTTTCATTGTCAAC 20 45 0 TAATGATTTT 0.944009 -67 CATTAGTTGATAATGATTTTCAATATCATA 20 82 0 TAATGATTTT 0.944009 -30 AATGATGTGGTAATGATTTTAAGCATACAG 28 101 0 TAATGATTTT 0.944009 -75 GGGATTATTTTAATGATTTTTATAGGTATA 41 37 0 TAATGATTTT 0.944009 -264 CGTACCATTTTAATGATTATTGGGGCAATT 58 101 1 TAATGATTAT 0.703471 -200 CAATGTGAAATGATGATTTTTAGTATAGCA 58 268 0 TGATGATTTT 0.77857 -33 CTTTATTTTCTAATTATTTTTGTCAGATTT 64 16 0 TAATTATTTT 0.744543 -185 ********** Masking position 6 Map Score: 6.35074 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 44 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 ACCATCTCGGAAGCAGGCTGCCGA 5 5 0 AAGCAGGCTG 0.647407 -93 CTGCCAGCGTCAGCCGGCAGTTTTTTTAGA 6 22 0 CAGCCGGCAG 0.771117 -173 CTGCCGGCTGACGCTGGCAGTTTTTTTATG 6 32 1 ACGCTGGCAG 0.931434 -163 TGCTAGTTTTACGCTGGCAGTTTTTCTGCT 11 35 1 ACGCTGGCAG 0.931434 -57 CCCCATAATGGAGCAGGCATTTTTTAATCC 36 24 1 GAGCAGGCAT 0.822871 -54 AAAAACATCGGCTCCGGCAGCCGATGTTTC 37 53 0 GCTCCGGCAG 0.938883 -133 TAACAGAAGAGAGCAGGCTGATAGCGCCTT 39 46 0 GAGCAGGCTG 0.836146 -46 TATGCAGAACAATCTGGCTGAGGGCGGTTT 42 59 0 AATCTGGCTG 0.49331 -242 GCACCCTTAAGAGCTGGCATGGAACTTGCA 51 66 1 GAGCTGGCAT 0.881673 -59 AATCGGAATCGCTCTGGCATGTAAGCAGCG 57 16 0 GCTCTGGCAT 0.793766 -120 CTGAAAAAGAGCGCCGGCATG 58 2 0 GCGCCGGCAT 0.938497 -299 TTTTAAAACAGCTCCGGCAGGGCATGGTAA 58 33 1 GCTCCGGCAG 0.938883 -268 ********** Masking position 4 Map Score: 7.18303 Number of sites scoring better than the average of aligned sites = 687 Number in coding regions = 641 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 11 TGCTTACTGTGGGAGGAGGTAAGGA 5 83 1 GGGAGGAGGT 0.843924 -15 AGACAGCGAGGTGCTGTCTTTTTTT 20 6 1 GCGAGGTGCT 0.948445 -106 AAGTTGTGGAGCGAAGTGGTGAATAGTGGT 24 75 1 GCGAAGTGGT 0.771703 -51 ACCAATATTTGCGAGGTGCTTCCTGAATTA 41 118 1 GCGAGGTGCT 0.948445 -183 AGTTAGTTGAGCTAGGAGCTGACTCTGTAG 41 176 1 GCTAGGAGCT 0.937916 -125 GTAAGAGGATGATAGGAGGTTTCGTTCA 42 283 1 GATAGGAGGT 0.756974 -18 CTATTGTATCGCTAAGAGGTCTGACAACTC 47 113 0 GCTAAGAGGT 0.735159 -48 GTCGAAACAAGAAAGGTGGTAACAG 51 110 1 GAAAGGTGGT 0.70513 -15 TACCGTATAGTCAAGGAGGTTTTT 53 5 0 TCAAGGAGGT 0.648953 -112 TTGCACTGACGCAAGGAGCTTTTATCGT 61 9 0 GCAAGGAGCT 0.951624 -114 TTGCGTCAGTGCAAGGAGCTTTTATGTATG 61 25 1 GCAAGGAGCT 0.951624 -98 ********** Masking position 4 Map Score: 5.92815 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 81 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 AGCCGGGTACGACAATCAAAGGCAAGTGGA 3 16 1 GACAATCAAA 0.970725 -73 ATACAATAAAGACAATCAAATCGCTGGTTG 14 144 1 GACAATCAAA 0.970725 -157 TTATGTGCATGACATTCAAAAAAAGCCTCA 15 121 1 GACATTCAAA 0.891074 -180 TTTATCTGTTGACAATGAAAATCATTATCA 20 38 1 GACAATGAAA 0.883761 -74 TTTTTTCAAGTACAATCAAATCATAAGGTA 53 41 0 TACAATCAAA 0.836862 -76 TTTCCAAGAGGACAATCAAAAGAAAGGTGG 64 174 1 GACAATCAAA 0.970725 -27 ********** Masking position 6 Map Score: 2.9489 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 28 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 AAACAGCTTGGTAAAGGGGCCAATGGAATT 3 69 1 GTAAAGGGGC 0.874722 -20 TTCTTAACCCTAAAAGGGCTGGAATTGATT 7 25 1 TAAAAGGGCT 0.83035 -61 TTTAATTTGAGAAAAGGGGCTGAAAGCAGG 8 26 1 GAAAAGGGGC 0.975746 -21 AAATGGCATTGAAAAGGAGATGTGACAT 12 9 0 GAAAAGGAGA 0.821777 -166 ACACTGCCGGTAAAAGGGCAGTGTTTTTTC 13 20 1 TAAAAGGGCA 0.853292 -52 GTAAATCCTTGAAAAGGAGTGTCGTG 16 94 1 GAAAAGGAGT 0.79509 -16 TGATGAAAATGAAAAGGGGTCGAAAAC 18 121 1 GAAAAGGGGT 0.961872 -17 ATTTAAACGAGAATAGGGCTTGAATAAGAA 19 68 1 GAATAGGGCT 0.567337 -81 ATGAAAACATAAAAGGAGCCTGGGAGACC 34 10 1 TAAAAGGAGC 0.66401 -108 GGCTGATGTGGAAAAGGGCATAAAGCAAAA 42 15 1 GAAAAGGGCA 0.947946 -286 CTAATGGAAGGAAAAGGGGTTTTGTGTGAT 42 170 0 GAAAAGGGGT 0.961872 -131 TTCAATTGAGTAAAAGGGGAATTCAG 53 101 1 TAAAAGGGGA 0.905435 -16 CATTTCTTGCGGAAAGGGGATCATT 59 82 1 GGAAAGGGGA 0.813888 -15 AGAAAAGGGCCTGGACAGGCC 62 2 1 GAAAAGGGCC 0.96069 -135 CGGCAAAATAAAAAAGGGCCTGTCCAGGCC 62 18 0 AAAAAGGGCC 0.658189 -119 ACTCTTCGGATTAAAGGGGAATTCAA 63 7 0 TTAAAGGGGA 0.624304 -256 ********** Masking position 5 Map Score: 15.6918 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 171 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 14 GTGAGCAGCAAATAGAGGTGAGTA 11 2 0 AATAGGTGAT 0.975615 -90 CGAAGTGGTGAATAGTGGTGAGTTAAGGAGAGA 24 86 1 AATAGGTGAT 0.975615 -40 ATCAAAAGGAAATACCGGTGAATATAAAAGATG 37 99 0 AATAGGTGAT 0.975611 -87 GCACCTCGCAAATATTGGTGATTAATACTTCAA 41 104 0 AATAGGTGAT 0.975613 -197 CGGGGTGAAAAACATCGGTGAATTAGCTGAGGT 41 273 1 AACAGGTGAT 0.936017 -28 ATTATGCTATGATATGGGTGAATCAAGAGTATG 48 153 1 GATAGGTGAT 0.936018 -148 **** ***** * Masking position 9 Map Score: 1.75899 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 13 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 15 GTATTCTCCAGGAGGAATGAAT 2 73 1 GGAGGAATGA 0.970597 -12 AAAAGAAAATAGAGGAATGATACAA 10 152 1 AGAGGAATGA 0.786609 -15 ACTATTTATTGGAGAAAGGAAGTTCTAGAA 23 50 1 GGAGAAAGGA 0.816564 -21 GACAGCACAAGGAGGAAGAAC 29 290 1 GGAGGAAGAA 0.901163 -11 TCTTTGAATAGGAGGAACAAAT 35 28 1 GGAGGAACAA 0.772792 -12 GAAGCTGATTGGCGGAAGGAGTTTTACAG 38 107 1 GGCGGAAGGA 0.913703 -19 CTTTTCGAGCGGATGAATGAGAACAAAATC 44 60 1 GGATGAATGA 0.786609 -62 ATCATATCAAGGAGGAATGAGC 45 84 1 GGAGGAATGA 0.970597 -12 ********** Masking position 6 Map Score: 2.32339 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 91 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282