AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00251_bsub_reg_300.orf -o00251_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 ctsR 300 transcriptional regulator #2 sms 91 DNA repair protein homolog #3 yacL 115 similar to hypothetical proteins #4 gltX 90 glutamyl-tRNA synthetase #5 glmS 300 L-glutamine-D-fructose-6-phosphate amidotransferase #6 ycgI 166 ycgI #7 nadE 139 NH3-dependent NAD+ synthetase #8 ycnG 106 similar to 4-aminobutyrate aminotransferase #9 ycnH 68 similar to succinate-semialdehyde dehydrogenase #10 yeaD 300 similar to hypothetical proteins from B. subtilis #11 yebA 196 similar to hypothetical proteins #12 guaA 232 GMP synthetase #13 purE 300 phosphoribosylaminoimidazole carboxylase I #14 purC 72 phosphoribosylaminoimidazole succinocarboxamide synthetase #15 yitV 120 similar to hypothetical proteins #16 yitW 63 similar to hypothetical proteins #17 yitX 54 yitX #18 yitY 57 similar to L-gulonolactone oxydase #19 yitZ 44 similar to multidrug resistance protein #20 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #21 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #22 ykrV 94 similar to aspartate aminotransferase #23 ileS 300 isoleucyl-tRNA synthetase #24 ylyA 77 alternate gene name: ylmK; similar to hypothetical proteins from B. subtilis #25 lsp 102 signal peptidase II #26 pyrR 273 transcriptional attenuator and uracil phosphoribosyltransferase activity (minor) #27 pyrP 171 uracil permease #28 pyrB 145 aspartate carbamoyltransferase #29 spoVK 300 alternate gene name: spoVJ; disruption leads to the production of immature spores (stage V sporulation) #30 ynbA 220 similar to GTP-binding protein protease modulator #31 ynbB 187 similar to hypothetical proteins #32 glnR 110 transcriptional regulator #33 glnA 60 glutamine synthetase #34 gltA 146 glutamate synthase (large subunit) #35 aspB 22 aspartate aminotransferase #36 ypmA 142 ypmA #37 dinG 125 ATP-dependent helicase #38 panB 245 ketopantoate hydroxymethyltransferase #39 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #40 ypjD 300 alternate gene name: jojD #41 ypcA 155 similar to glutamate dehydrogenase #42 ypbH 158 similar to negative regulation of competence MecA homolog #43 ypbG 85 similar to hypothetical proteins #44 ypbF 62 ypbF #45 ypbD 59 ypbD #46 ypbB 265 ypbB #47 yrpC 300 similar to glutamate racemase #48 ysmB 243 similar to transcriptional regulator (MarR family) #49 gerE 115 transcriptional regulator #50 ysmA 62 ysmA #51 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #52 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #53 yugG 147 similar to transcriptional regulator (Lrp/AsnC family) #54 ywfB 151 alternate gene name: ipa-80d #55 ywfA 209 alternate gene name: ipa-79d; similar to chloramphenicol resistance #56 rocB 73 alternate gene name: ipa-77d #57 rocA 226 pyrroline-5 carboxylate dehydrogenase #58 yweB 176 alternate gene name: ipa-75d; similar to glutamate dehydrogenase #59 yweA 300 alternate gene name: ipa-74d; similar to hypothetical proteins from B. subtilis Motif number 1 ATATAGTGTAAGACCTCTCCCTTGTTCTAT 2 72 0 AAGACCCTCC 0.816423 -20 GGAGAACGGAAAAACCGCTTTTTACAATTGC 6 44 1 AAAACCCTTT 0.949104 -123 GAAAAGCTCCTTTAACCTTAGA 15 2 1 AAAAGCCCTT 0.780842 -119 AGAAAATAAAAAAAGCCCTCTCATCCCATAA 23 255 0 AAAAGCCTCT 0.962263 -46 ACCTTGTCCTAAAACCCCTCTATGCTCTGGC 26 210 1 AAAACCCTCT 0.973073 -64 TATAGAAGAAAAAACCCCTCCTGCCAGAGCA 26 232 0 AAAACCCTCC 0.979924 -42 ACTGTATAAAAAAACCTCTTTGCTTTTTTAC 27 104 0 AAAACCCTTT 0.949256 -68 AAGAAAAACACTTCAGGTATCTTA 29 4 1 AAAAACCTTC 0.889884 -297 AAGAAAAGCCCCCTTTATCGGGGG 37 4 1 AAAAGCCCCT 0.87299 -122 ATGGAGCGGCAAAACCGTTTTACTCTCAAAA 37 48 0 AAAACCTTTT 0.653685 -78 CTGCAAGCCAAAAAACCTTCCGTTACAACGA 38 180 0 AAAAACTTCC 0.622368 -66 TAATACCTGTAAAACCGCCCTCAGCCAGATT 40 48 1 AAAACCCCCT 0.906901 -253 AGCATCACACAAAACCCCTTTTCCTTCCATT 40 167 1 AAAACCCTTT 0.94917 -134 AAAAAACTCTCCATTCTTTTTA 43 74 0 AAAAACCTCC 0.939721 -12 TCTTACGCACAAAAGCGTTCCGTGTCTATTT 48 199 0 AAAAGCTTCC 0.784528 -45 TGTAAGAAAAAACCTCTTCCGCATGGGAG 50 9 1 AAAACCCTTC 0.96198 -54 ATTGTTTAAAAAAACCTCTCCCATGCGGAAG 50 26 0 AAAACCCTCC 0.979924 -37 TCCTATAATTAAAAACCCTTTTTAAAGGGTT 54 26 1 AAAAACCTTT 0.856664 -126 ATACAAACAAAAAAACCCTTTAAAAAGGGTT 54 39 0 AAAAACCTTT 0.856664 -113 AAAAAGCTCTCCGGGAGGCCGG 55 2 1 AAAAGCCTCC 0.971784 -208 AACACGTAAAAAAAGCTCTCCGGCCTCCCGG 55 21 0 AAAAGCCTCC 0.971784 -189 CCTCTGCAGAAAAAGCGCTTTTTCATAATTC 59 238 0 AAAAGCCTTT 0.929453 -63 ****** **** Masking position 4 Map Score: 32.0333 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 259 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 2 GCTCAATGAGCTGGGTTTTTTGTATTTTGGT 1 84 1 CGGGTTTTTT 0.881445 -217 ACCCCCACCTCCTTTTTTAACATTTTAA 3 98 0 CTCCTTTTTT 0.841362 -18 AGCAATAATCCCGTCTTCTTTTCCTATTGAG 5 20 0 CGTCTTCTTT 0.830626 -281 GCGGTTTTTCCGTTCTCCTTTCATTTCTGAT 6 31 0 CTTCTCCTTT 0.380988 -136 ACGATTGGAACAGGCTTCTTTCTCGGTTCCA 6 80 0 CGGCTTCTTT 0.818461 -87 TCCCTTTTGGCTGGTCTTTTTTTGT 6 152 1 CGGTCTTTTT 0.754226 -15 ATTTTATTTTCTGGCTTTTTTATTGCTGTGG 11 76 1 CGGCTTTTTT 0.939778 -121 ACGAAACATACAGGCTTTTTTAGTGTCTTTA 11 139 1 CGGCTTTTTT 0.939778 -58 GACGTTTCTGCTGACTTTTTTCAGGATGAG 11 177 1 CGACTTTTTT 0.706238 -20 CGGTCAAGACCATCTTCTTTTAATTAAATTT 12 53 0 CTCTTCTTTT 0.337147 -180 GAAGCTCGCTCCGCCCTCTTTGGCAAGGCCG 12 155 0 CGCCCTCTTT 0.676338 -78 TCATATCTGTCCTCGTTTTTTTCTGTGTCAA 12 184 1 CTCGTTTTTT 0.716463 -49 ACATGTCAGGCTGTCCTTTTTTGTT 17 5 0 CGTCCTTTTT 0.909552 -50 ACATGTGAGGCTGTCCTTTTTTACAGCTGAA 17 30 1 CGTCCTTTTT 0.909552 -25 CGCGGTCAGCCTGTTTTTTTATGCGGCTGA 20 10 1 CTGTTTTTTT 0.692331 -197 TGGAGTCGTGCTGATTTTTTTTGAGCGGAAT 20 70 1 CGATTTTTTT 0.443837 -137 GCTTTTACGCCGGGCTCTTTTGCA 24 4 0 CGGCTCTTTT 0.818461 -74 GCGTAAAAGCCGGGCTTTTTTTGTGCCAAGA 24 25 1 CGGCTTTTTT 0.939778 -53 TTCTTTACTCCAGTGCTTTTTATTGATAAAA 25 41 1 CGTGCTTTTT 0.827322 -62 AAAAAAACCTCTTTGCTTTTTTACGCAAAGA 27 97 0 CTTGCTTTTT 0.675461 -75 TATCTTAGACCGGGGTTTTTTTTCAGCCTTA 28 101 1 CGGGTTTTTT 0.881445 -45 CCCTCTGTCCCAGTCCTTTTTTGGATCAAGG 38 111 0 CGTCCTTTTT 0.909552 -135 AGCACGTTTGCTGTTTTCTTTTTCATCCACT 40 216 0 CGTTTTCTTT 0.619466 -85 CTGATTTCAGCAGTTTTTTTTCGTTAAAAAA 41 29 1 CGTTTTTTTT 0.849275 -127 ACGATAGAAACGTCTTTTTTTATTGTCCGTC 43 29 1 CTCTTTTTTT 0.63775 -57 CTTTCTGTCTCATTCTTTTTTTATCATATGA 47 269 0 CTTCTTTTTT 0.88058 -32 TGTCTATTTTCCTTCTTTTTTGAAGAAAATG 48 177 0 CTTCTTTTTT 0.88058 -67 GGAAGTTTCTCCTCGTTTTTTCTTAGCATTC 53 69 1 CTCGTTTTTT 0.716463 -79 TATAGTTTAGCATTGTTTTTTCTCTATTTAC 55 142 0 CTTGTTTTTT 0.778427 -68 AGGTGATCACCTTTCTCTTTTTCCGATCTTG 57 87 0 CTTCTCTTTT 0.680548 -140 GAGATGTTTTCAGTCTCTTTTTTTGTGGATT 58 35 1 CGTCTCTTTT 0.830626 -142 TTTTTCACCTCATTGTTTTTTTGGCCGGCTG 58 155 0 CTTGTTTTTT 0.778427 -22 GGACGATTTCCCTCTCTTTTTCTAGTAACAT 59 80 0 CTCTCTTTTT 0.510518 -221 CGCGAATTACCAGTTCTTTTTCTTAAAAATT 59 208 0 CGTTCTTTTT 0.769483 -93 * ********* Masking position 9 Map Score: 32.1529 Number of sites scoring better than the average of aligned sites = 1587 Number in coding regions = 1158 Number in noncoding regions = 429 Number of orfs with sites within 600 bp upstream = 370 Fraction of orfs with sites within 600 bp upstream = 0.0594282 Motif number 3 AGTCGGGGGTTTCCCCCTGTGAGAGTAGGA 1 30 1 TTCCCCCTGT 0.950357 -271 AGCACAGGTCTTCATTCACTGTGAACAAGA 7 25 0 TTCATTCACT 0.437013 -115 CCCAATCATTCCTCCTGTACATTTTCCC 7 122 0 TTCCTCCTGT 0.92679 -18 GTGAATATCCCCCTGTCGGTATTTTC 8 91 0 ATCCCCCTGT 0.807007 -16 AAATAAAAAATACCCGCTCTGCATTGCACT 13 246 0 TACCCGCTCT 0.43777 -55 GTTCCCTCACTCCTTTTTTCT 16 53 0 TTCCCTCACT 0.897171 -11 CATAGTGCTCTCCCTGCTGTTTTTATGACC 18 12 0 TCCCTGCTGT 0.502257 -46 AACAAGTTCACCCTCTTGGTCTTTGT 20 191 0 TTCACCCTCT 0.82811 -16 TTTCATTCCTCCACTGCATTTTTTC 23 286 0 TTCCTCCACT 0.926702 -15 AAACGTTCCTCCAGTTTACGGTTAC 25 88 0 TTCCTCCAGT 0.871119 -15 GCATTGAAGCTTCCTTCTCTTCATAACCCT 28 43 0 TTCCTTCTCT 0.915298 -103 GTTCTTTCCCCTCTCTTTTCAACTTA 28 130 0 TCCCCTCTCT 0.861157 -16 GAAAGGAGCTTCCCTTCACTTGCCGGCACA 31 27 0 TCCCTTCACT 0.686509 -161 CTCAATTTCCTCCTTTTCTTAACTTA 32 95 0 TTCCTCCTTT 0.736466 -16 TTGGTAAAATTCCTCCTCTTAAAAGGTAA 33 42 0 TTCCTCCTCT 0.959481 -19 AAAAGCGGATTTCCCGCTCTGTGATACTAG 36 62 1 TTCCCGCTCT 0.88263 -81 TTTTTCATCCTCCAGTTTGAACAAAT 36 127 0 ATCCTCCAGT 0.596185 -16 GGCGAGTTTCATCCCTCTGTCCCAGTCCTT 38 124 0 ATCCCTCTGT 0.65615 -122 TGTTTTCTTTTTCATCCACTATAATATAAA 40 206 0 TTCATCCACT 0.629764 -95 GAAACCTCCTATCATCCTCTTACATGTTAG 40 276 0 ATCATCCTCT 0.410335 -25 TTTTCGTAATTTCATCCACTGACTCTGGAA 47 15 1 TTCATCCACT 0.629764 -286 CTTGCCGGTATTCCTTCTTTTGGAAGGAGC 48 13 1 TTCCTTCTTT 0.560498 -231 CGTGTCTATTTTCCTTCTTTTTTGAAGAAA 48 180 0 TTCCTTCTTT 0.560498 -64 TTGTCCATCCCTCACTCAAGGATCTC 48 228 0 ATCCCTCACT 0.655857 -16 ATCTGTCTCCCCTCTCTCCTGCGTATA 52 8 1 TCCCCTCTCT 0.861157 -285 TCTGTAATCCTCCCCCCTGTTTGAGCTATA 52 39 0 TCCCCCCTGT 0.879024 -254 GCTAAATCTCTTCCCCCACTTCTTTCAATT 52 240 0 TTCCCCCACT 0.950296 -53 TACTTTACCCCCTGTTTGATAAGTG 52 278 0 TACCCCCTGT 0.664673 -15 AATGGACGATTTCCCTCTCTTTTTCTAGTA 59 84 0 TTCCCTCTCT 0.942334 -217 ********** Masking position 10 Map Score: 31.3008 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 458 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 4 GTAGTCGGGGGTTTCCCCCTGTGAGAGTAG 1 28 1 GTTTCCCCCT 0.948813 -273 TGTATGCCTCATTTCCGTCTTCTATA 2 7 0 ATTTCCGTCT 0.895825 -85 GTGAATATCCCCCTGTCGGTATTT 8 93 0 ATATCCCCCT 0.975128 -14 GATGATTTCCCCCTGATTGTTGAC 27 158 0 ATTTCCCCCT 0.989943 -14 TTTTGCTCGTATTTCCGCCTTTTCAAAGCA 30 37 1 ATTTCCGCCT 0.977614 -184 ACAGTATGACATATCCGGCTATGTCCAAGA 31 111 1 ATATCCGGCT 0.841224 -77 CTCAATTTCCTCCTTTTCTTAACT 32 97 0 ATTTCCTCCT 0.916608 -14 TTAAAAGCGGATTTCCCGCTCTGTGATACT 36 60 1 ATTTCCCGCT 0.967722 -83 TATCTACATAACATCCCCCTTAATGATGAC 46 161 1 ACATCCCCCT 0.880714 -105 CAAATGGACGATTTCCCTCTCTTTTTCTAG 59 86 0 ATTTCCCTCT 0.950937 -215 GACATTTCCCCCTAATTGATTGT 59 288 0 ATTTCCCCCT 0.989943 -13 ********** Masking position 4 Map Score: 12.1214 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 62 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 TATCCTTCATTATTTCCATTTTCCCGGTCCA 1 194 0 TATTTCCATT 0.744804 -107 GCAATTGTGTTTTATCCATTTGCCTGAAGCC 10 112 0 TTTATCCATT 0.880334 -189 GCTTCTGCGATATATCCATGTCAGTTTTATC 13 165 0 TATATCCATT 0.664215 -136 CAGTGTAGCTTTTTACCATCTTTATTGTCTA 15 56 1 TTTTACCATT 0.744804 -65 ATTTAATATTTTTATTCATTTATAAATTTTC 20 113 0 TTTATTCATT 0.899568 -94 TGAATTAATTTTTATTCATGTTATAATGTTA 20 151 1 TTTATTCATT 0.899568 -56 TTTTCTTTACTTTTTTCATTTAACCATATAT 22 29 1 TTTTTTCATT 0.929654 -66 CTTTCAACCGTTTTTTCATCTGAATTTATGA 23 18 0 TTTTTTCATT 0.929654 -283 AGATTTTGTTTTTAATCATTTTGTCAGAGTA 29 110 0 TTTAATCATT 0.706608 -191 GGAGCGGCAATTTTTTCATTTGGCTTGGTTC 40 96 0 TTTTTTCATT 0.929654 -205 AAACGTTATGTTTTTCCATGTTTTTTAACGA 41 49 0 TTTTTCCATT 0.915642 -107 CTCATTCTTTTTTTATCATATGACTTTATAT 47 261 0 TTTTATCATT 0.780387 -40 CTTTTTTCATCTCCTTATTGTT 50 51 0 TTTTTTCATT 0.929654 -12 TAAGTTTTATTATTTTCATTTAAATCCCATT 55 92 0 TATTTTCATT 0.780387 -118 TTCTTGCATTTTTATTCATATGCGAAGATAT 57 180 1 TTTATTCATT 0.899568 -47 ********* * Masking position 8 Map Score: 13.8641 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 273 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 6 GAGAAACGCGTAAAACAAAAACCAGCTGAC 10 29 0 TAAAACAAAA 0.834991 -272 AAAAAAGCCAGAAAATAAAATAACAGCAAG 11 67 0 GAAAATAAAA 0.915587 -130 TTTGTTTTCAGAAAATAAAAAATACCCGCT 13 258 0 GAAAATAAAA 0.915587 -43 TTTATTTTCTGAAAACAAAAGCATTAGAAG 13 269 1 GAAAACAAAA 0.80631 -32 CATTTTTTCAGAAAATAAAAAAAGCCCTCT 23 265 0 GAAAATAAAA 0.915587 -36 TGAGTCATCCTAAAATGAAAGTCAACAATC 27 138 1 TAAAATGAAA 0.820449 -34 CTCAAAATCTTAAAAGAAAACCCCCGATAA 37 25 0 TAAAAGAAAA 0.733308 -101 CCGCTCCGATTAAAATAAAAAATATGTTTT 40 120 1 TAAAATAAAA 0.929502 -181 TATATGAACGTAAAATAAAAATAATACC 44 9 0 TAAAATAAAA 0.929502 -54 TGAAATCTGTTAAAATAAAAAGAGCAAATC 46 211 1 TAAAATAAAA 0.929502 -55 TATATATTGATAAAATAAAATTTTTCAATC 52 106 1 TAAAATAAAA 0.929502 -187 GAGGGAGGAGTAAAATGAAATTGTCAATAA 52 191 1 TAAAATGAAA 0.820449 -102 ********** Masking position 5 Map Score: 9.66382 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 138 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 7 TCAACCCCCTCCTTTACTGACTTTGA 1 285 0 CCCCTCCTTA 0.78111 -16 TAGTGTAAGACCTCTCCCTTGTTCTATTTCT 2 68 0 CCTCTCCCTG 0.85989 -24 ACCCCCACCTCCTTTTTTAACAT 3 103 0 CCCCACCTCT 0.728882 -13 TTTCAATCGTCCCCTCCTACATGTTTTTTGG 5 222 0 CCCCTCCTCA 0.95868 -79 TTACGCCCAGCCTGTCCCCCGCATGCAATTG 10 136 0 CCTGTCCCCG 0.745735 -165 AGCGCCTAAGCCACTCCCACAGCAATAAAAA 11 92 0 CCACTCCCCA 0.697557 -105 TCTGTTCCCCACCTTCTAATGCTTTTG 13 284 0 CCCCACCTCT 0.728882 -17 AATGTGCCCCTCCTTAGGATAACCATA 15 104 0 CCCCTCCTAG 0.814081 -17 GAAGAAAAAACCCCTCCTGCCAGAGCATAGA 26 228 0 CCCCTCCTCC 0.95058 -46 AATTCCTCTCCCCCGATCAATTTCC 34 132 0 CCTCTCCCCG 0.975551 -15 AACGTTCCCTCCTGCCTCTACTTGCA 42 143 0 TCCCTCCTCC 0.733329 -16 GTCCTCTATTTCTCTCCTGCGAGTCTTGCAT 48 149 1 TCTCTCCTCG 0.833713 -95 TTGTAAACGTCACCTCCTGCGCCCTTCTTAC 49 21 1 CACCTCCTCG 0.791761 -95 TTTAAAAAAACCTCTCCCATGCGGAAGAGGT 50 22 0 CCTCTCCCTG 0.85989 -41 GATAGCCCCTCTCCCTCTAGTAATCTAG 51 16 0 CCTCTCCCCT 0.908122 -18 CTGTCTCCCCTCTCTCCTGCGTATATTATAG 52 13 1 TCTCTCCTCG 0.833713 -280 TTTCATTTTACTCCTCCCTCAAAAGGGCGTC 52 180 0 CTCCTCCCCA 0.582531 -113 ******** ** Masking position 6 Map Score: 12.7852 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 123 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 8 AGACCCGGCATCAAAACAAG 4 1 0 TCAAAACAAG 0.782332 -90 AAACATGAAATCAAAACACGACCTCATATA 13 65 1 TCAAAACACG 0.904489 -236 TGTAAGTAAGGCAAAACAAGCAAAATCTAA 15 28 0 GCAAAACAAG 0.852495 -93 GGAATTCCGCTCAAAAAAAATCAGCACGAC 20 74 0 TCAAAAAAAA 0.680505 -133 GGAAATACGAGCAAAAAACAGACCTCTCAA 30 23 0 GCAAAAAACA 0.900242 -198 TGCCCAATATGCAAAAGAAAGGAACATCCA 30 113 1 GCAAAAGAAA 0.738056 -108 CACATGTGCTTCAAAAGACG 31 1 0 TCAAAAGACG 0.904489 -187 CTCCCACACCGCAAAAGCCGCTTTATGCGG 36 14 0 GCAAAAGCCG 0.791769 -129 CTCGACTATATCAAAACCCATTCGTTTCTG 49 61 1 TCAAAACCCA 0.535489 -55 AATACAACCATCAAAAAAAGGGAGTGACAC 53 14 0 TCAAAAAAAG 0.813743 -134 TTAGCATTCGTCAAAAAACGTGATATAATG 53 91 1 TCAAAAAACG 0.920073 -57 ATCAATATTTTCAAAAAACATTGACAGTTC 54 80 1 TCAAAAAACA 0.848761 -72 TGCTCTTTACGCAAAAAACAAATGCAAAAT 57 33 0 GCAAAAAACA 0.900242 -194 TGCGTAAAGAGCAAAAAACGCAAAATAAAT 57 50 1 GCAAAAAACG 0.948746 -177 AGTTTTTTCAGCAAAAGACAAGAAAATGGC 57 146 1 GCAAAAGACA 0.88129 -81 TTAAAAAAGGGCAAAAAAAGTCGAAGATGC 59 19 0 GCAAAAAAAG 0.875394 -282 ********** Masking position 5 Map Score: 11.7212 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 460 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 CGTAAAACAAAAACCAGCTGACAAAGCCGCC 10 20 0 AAACCGCTGA 0.929475 -281 AAAACAAATTAAAATGGCTGACATTATCACA 19 17 1 AAAATGCTGA 0.86931 -28 CCGCATAAAAAAACAGGCTGACCGCG 20 6 0 AAACAGCTGA 0.72185 -201 ACTCCAGCACAAAAACGTTGATGCGGTGCCG 20 45 0 AAAAAGTTGA 0.743612 -162 TTCAGATGAAAAAACGGTTGAAAGGGACAGT 23 25 1 AAAACGTTGA 0.936419 -276 AACCTCAGAAAAAACGGTTGACAGAGGGTTT 26 81 1 AAAACGTTGA 0.936419 -193 TGTATATAGCAAAACAGTTGCTAACGGA 33 8 0 AAAACGTTGC 0.716592 -53 CTTGCAGAAGAAAACGGCAGATCATCTCCTC 38 204 1 AAAACGCAGA 0.731944 -42 AATGCAACGGAAAACTGCTGATTTCAGCAGT 41 12 1 AAAACGCTGA 0.959307 -144 TTAACGAAAAAAAACTGCTGAAATCAGCAGT 41 25 0 AAAACGCTGA 0.959307 -131 CTTCCTGACAAAAATCGTTGATTTGCTCTTT 46 229 0 AAAATGTTGA 0.806047 -37 TTTGCTGAAAAAACTTGTTGAATCGAACAGA 57 130 0 AAACTGTTGA 0.699098 -97 ***** ***** Masking position 3 Map Score: 9.03556 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 180 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 GGCCTTGTATCCGCTCCGTTCTTTTCAGGCTT 10 85 1 CCGCTCGTCT 0.968086 -216 CACCTAATCTCCTCTAAGTTTTTTGACACAGA 12 205 0 CCTCTAGTTT 0.839302 -28 TAAAAAATACCCGCTCTGCATTGCACTTATGA 13 241 0 CCGCTCGATT 0.907662 -60 TCCTTCTCAGCCTCTCTGGACTGTTTTAAAGA 26 145 0 CCTCTCGACT 0.965686 -129 TCCTAAAACCCCTCTATGCTCTGGCAGGAGGG 26 216 1 CCTCTAGTCT 0.893156 -58 TGTGTGACACCTCACAGTTCATATAGAAGAA 26 253 0 CCTCACGTCA 0.584745 -21 CTCTTTGCAACCTCTCTGGATTGCTTAAAAAG 27 19 0 CCTCTCGATT 0.946188 -153 TATAAAAAAACCTCTTTGCTTTTTTACGCAAA 27 99 0 CCTCTTGTTT 0.747594 -73 CCCTTCCAAGCCTCTCTGGACTTTCATTAAAA 28 15 0 CCTCTCGACT 0.965686 -131 CTTCACCTCTCTGTTCTCTCTATATGA 29 284 0 CCTCTCGTCT 0.981904 -17 ACCTCTCAGTTTTTGAGAGGTCT 30 2 1 CCTCTCGTTT 0.971348 -219 GAAAAAATTGCCGCTCCGATTAAAATAAAAAA 40 110 1 CCGCTCGTTA 0.809393 -191 ****** * *** Masking position 4 Map Score: 11.5422 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 69 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 AAGTGTATGCCTCACTTTCATATCAAGAAATAGAACAAGG 2 43 1 CCATTTACAA 0.465856 -49 CTTTCTTCGTCTCCTTTTACAATCTTAGGAGGAAGAAAAA 5 270 1 CCCTTTCCTA 0.554917 -31 TTTGTAGTTTCTCCTTCTGATACCATCAAAAAGTTATAAT 8 11 1 CCCTCTACAA 0.907347 -96 ATTGTGTTTTATCCATTTGCCTGAAGCCTGAAAAGAACGG 10 100 0 ACCTTTCAAG 0.419247 -201 AATCTTCAATCACCATATACCATCAGCGGAAATGGCAGCT 10 185 0 CCCTATCCAA 0.623203 -116 CGTCATGCTCCGTTTAAACCAAGGAAAAACGAGCCGT 10 274 0 CCCTTTAAAA 0.911237 -27 GTTCCCTCACTCCTTTTTTCTACAGTATAACGTAAATTC 16 35 0 CCCTTTTCAA 0.683398 -29 CTATTCTCACCTTCTAAAAAAATCTTGAAATGATAGT 22 68 0 CCCTCTAAAG 0.704139 -27 CTCGCGGTACCACCCTTTTAGAAAAAGCAAGCATACACTT 23 198 0 CCCTTTAAAA 0.905905 -103 AAATAAAAAAAGCCCTCTCATCCCATAAGGGACGAGAAAG 23 243 0 ACCTCTACAG 0.438618 -58 TAGATCACCTTTTTAAGCAATCCAGAGAGGTTGCA 27 6 1 CCCTTTAAAG 0.842015 -166 AACCTTTTAATGAAAGTCCAGAGAGGCTTG 28 1 1 ACCTTTAAAA 0.612037 -145 GGTTTGTCCACCCCATGTCCGTGAATACAATAAGAAATAA 29 144 1 CCCTGTCAAA 0.534336 -157 CTCGTATTTCCGCCTTTTCAAAGCAATCGATTTGTGGTAT 30 42 1 CCCTTTACAA 0.956392 -179 AGAAAGGAACATCCATTTGAACGAACAAGAAACGATTCAG 30 128 1 ACCTTTAAAA 0.612043 -93 GTTAGTCATACTCCATTTCAGGACACGCCATACTAGTATC 36 84 0 CCCTTTACAA 0.955674 -59 GGTTTTGCCGCTCCATTTCCGTACAAAACGTGTTACACTT 37 63 1 CCCTTTCCAG 0.909334 -63 TCACACAAAACCCCTTTTCCTTCCATTAGATAGCGTTTAT 40 171 1 CCCTTTCCAA 0.950811 -130 TTCTCACATGCTCCCTTTCAGAGAATAGTATACACCTTCA 41 99 0 CCCTTTAAAA 0.911231 -57 ACGTTCCCTCCTGCCTCTACTTGCACACAAATCATATAAC 42 128 0 CGCTCTCCAA 0.496225 -31 AGATCCGTACCAGCTTTTGAATCCACAAAAAAAGAGACTG 58 45 0 CGCTTTACAA 0.714519 -132 * ** *** * ** * Masking position 8 Map Score: 10.1382 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 322 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 12 ACAGTCATGATTCATTTTCATTGATTTAGGG 7 75 1 TCATTTTCAT 0.929472 -65 AGCAGACCCGGCCATTTTCTTTCCAATGA 9 9 0 GCATTTTCTT 0.777422 -60 TTTATTTTCTGGCTTTTTTATTGCTGTGGGA 11 78 1 GCTTTTTTAT 0.383613 -119 TGCAAGCAATTTCTTTTTCATAGTGCTCTCC 18 29 0 TCTTTTTCAT 0.911876 -29 GGCATAAAAATTCATTTTTATAATTAATTAT 21 28 1 TCATTTTTAT 0.669638 -43 AGTGTATGCTTGCTTTTTCTAAAAGGGTGGT 23 199 1 TCTTTTTCTA 0.530985 -102 TTCTCATTATTTCTTTTTCATACAACGGGCT 29 64 0 TCTTTTTCAT 0.911876 -237 TGTCATACTGTTCATTTTCTTCATTAAAATA 31 91 0 TCATTTTCTT 0.899317 -97 GTTTGCTGTTTTCTTTTTCATCCACTATAAT 40 211 0 TCTTTTTCAT 0.911876 -90 TCACACCTTGTCCATTTTCATTGCTACAATA 44 37 0 TCATTTTCAT 0.929472 -26 TAAATACTCCTACATTTTCAAAGCTAATTTG 47 48 1 TCATTTTCAA 0.680245 -253 AGTAAAATGGTTCTTTTTCGTTTGATTCAGA 47 228 1 TCTTTTTCGT 0.683342 -73 CTGCGAGTCTTGCATTTTCTTCAAAAAAGAA 48 165 1 TCATTTTCTT 0.899317 -79 CAAGAATCATGCCATTTTCTTGTCTTTTGCT 57 155 0 GCATTTTCTT 0.777422 -72 GCATGATTCTTGCATTTTTATTCATATGCGA 57 174 1 TCATTTTTAT 0.669638 -53 GAATTACCAGTTCTTTTTCTTAAAAATTAAT 59 205 0 TCTTTTTCTT 0.875208 -96 * ********* Masking position 6 Map Score: 11.5029 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 501 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 13 GTCCACAAAACCTGATTGCTGATTTAAAAT 1 169 0 CCTGATTGCT 0.916751 -132 ATGATTTCCCCCTGATTGTTGACTTTCATT 27 151 0 CCTGATTGTT 0.972818 -21 GCGCAGGATTCCTTATTGTTCCCGAAAAAA 29 200 1 CCTTATTGTT 0.923624 -101 CCGCCCTCAGCCAGATTGTTCTGCATATTG 40 62 1 CCAGATTGTT 0.939647 -239 ATAAAACCTCCCAGATTGTTCTTGGTGGAA 46 13 1 CCAGATTGTT 0.939647 -253 TTTTTCATCTCCTTATTGTTTAAAAAAACC 50 41 0 CCTTATTGTT 0.923624 -22 CTTTTTCACCTCATTGTTTTTTTGGCCG 58 159 0 CCTCATTGTT 0.910429 -18 ********** Masking position 5 Map Score: 4.19028 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 23 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 CTTACTATAAGCCGTTTCTCGAGAATTTTCAAC 1 235 0 GCCGTTTCGG 0.991145 -66 CGTCAACTAAGCCTTTTTCCGGGCGCTTAGTTC 5 72 0 GCCTTTTCGG 0.96829 -229 GGAAAAACGAGCCGTTTGGCGCGGCCTCCGTCT 10 256 0 GCCGTTTCGG 0.991139 -45 CTTTGGCAAGGCCGTTTGCCGGAGTCAGGCCAA 12 136 0 GCCGTTTCGA 0.968277 -97 AATTTGAAGCGCCGCTTCCCGAGGATATGGCAG 26 37 1 GCCGCTTCGG 0.992656 -237 GTCTTTGTATGCCTCTTTGCGTAAAAAAGCAAA 27 84 1 GCCTCTTCGA 0.909578 -88 CACCGCAAAAGCCGCTTTATGCGGCTT 36 5 0 GCCGCTTTGG 0.946043 -138 ******* ** * Masking position 7 Map Score: 4.74913 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 55 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 15 AAAATGTACAGGAGGAATGATTGGG 7 125 1 GGAGGAATGA 0.919964 -15 GGTATCAGAAGGAGAAACTACAAA 8 5 0 GGAGAAACTA 0.857576 -102 AAGACAAAAGGGAGAAACGCGTAAAACAAA 10 40 0 GGAGAAACGC 0.77895 -261 TTTAAACCAAGGAAAAACGAGCCGTTTGGC 10 269 0 GGAAAAACGA 0.572472 -32 AAAATGCAGTGGAGGAATGAAA 23 289 1 GGAGGAATGA 0.919964 -12 ACCGTAAACTGGAGGAACGTTT 25 91 1 GGAGGAACGT 0.948267 -12 ATCAAATCCAGGAGAAATTTTTAAAAAAT 32 10 0 GGAGAAATTT 0.842068 -101 GTTAAGAAAAGGAGGAAATTGAG 32 98 1 GGAGGAAATT 0.63921 -13 CCTTTTAAGAGGAGGAATTTTACCAA 33 45 1 GGAGGAATTT 0.895111 -16 TGTGATGCTTGGAGAAATTAGATTAAAAAA 40 146 0 GGAGAAATTA 0.817747 -155 ATTTTTGTCAGGAAGAATGTAGGTGGATAG 46 245 1 GGAAGAATGT 0.654909 -21 GAAAAAACGAGGAGAAACTTCCGCTAGAAT 53 61 0 GGAGAAACTT 0.87738 -87 ********** Masking position 6 Map Score: 4.64223 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 214 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098