AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ipurR_ecoli_bsub_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 carA 300 carbamoyl-phosphate synthetase, glutamine (small) subunit #2 codB 300 cytosine permease/transport #3 purE 117 phosphoribosylaminoimidazole carboxylase = AIR carboxylase, catalytic subunit #4 ppiB 173 peptidyl-prolyl cis-trans isomerase B (rotamase B) #5 ycbQ 300 putative fimbrial-like protein #6 ycbR 82 putative chaperone #7 ycbS 24 putative outer membrane protein #8 pyrD 110 dihydro-orotate dehydrogenase #9 pyrC 105 dihydro-orotase #10 yceB 133 orf, hypothetical protein #11 grxB 63 glutaredoxin 2 #12 yceL 205 orf, hypothetical protein #13 ycfC 35 orf, hypothetical protein #14 ymfC 201 orf, hypothetical protein #15 prsA 150 phosphoribosylpyrophosphate synthetase #16 hemM 213 an enzyme in main pathway of synthesis of 5-aminolevulinate, possibly glutamyl-tRNA dehydrogenase #17 purR 300 transcriptional repressor for pur regulon, glyA, glnB, prsA, speA #18 purT 133 phosphoribosylglycinamide formyltransferase 2 #19 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #20 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #21 cvpA 258 membrane protein required for colicin V production #22 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #23 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #24 dedA 82 orf, hypothetical protein #25 usg 65 putative PTS system enzyme II A component #26 pdxB 98 erythronate-4-phosphate dehyrogenase #27 purC 212 phosphoribosylaminoimidazole-succinocarboxamide synthetase = SAICAR synthetase #28 dapA 79 dihydrodipicolinate synthase #29 purM 297 phosphoribosylaminoimidazole synthetase = AIR synthetase #30 guaA 68 GMP synthetase (glutamine-hydrolyzing) #31 guaB 161 IMP dehydrogenase #32 glyA 300 serine hydroxymethyltransferase #33 glnB 60 regulatory protein P-II for glutamine synthetase #34 yfhG 164 putative alpha helix protein #35 yfhK 300 putative 2-component sensor protein #36 purL 300 phosphoribosylformyl-glycineamide synthetase = FGAM synthetase #37 gcvP 118 glycine decarboxylase, P protein of glycine cleavage system #38 gcvH 23 in glycine cleavage complex, carrier of aminomethyl moiety via covalently bound lipoyl cofactor #39 gcvT 300 aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system #40 yqgB 120 orf, hypothetical protein #41 purH 300 phosphoribosylaminoimidazolecarboxamideformyltransferase = AICAR formyltransferase; IMP cyclohydrolase #42 hfq 85 host factor I for bacteriophage Q beta replication, a growth-related protein #43 hflX 75 GTP - binding subunit of protease specific for phage lambda cII repressor #44 hflK 85 protease specific for phage lambda cII repressor #45 yjeT 81 orf, hypothetical protein #46 purA 103 adenylosuccinate synthetase #47 guaB 120 inositol-monophosphate dehydrogenase #48 metS 300 methionyl-tRNA synthetase #49 yabD 78 similar to hypothetical proteins #50 yabE 155 similar to hypothetical proteins #51 yabF 144 similar to hypothetical proteins #52 yabG 161 yabG #53 veg 210 veg #54 sspF 159 small acid-soluble spore protein (alpha/beta-type SASP) #55 yabH 147 similar to hypothetical proteins #56 purR 55 transcriptional regulator #57 spoVG 193 spoVG #58 gcaD 192 UDP-N-acetylglucosamine pyrophosphorylase #59 prs 22 phosphoribosyl pyrophosphate synthetase #60 purT 230 phosphoribosylglycinamide formyltransferase 2 #61 yclB 89 similar to phenylacrylic acid decarboxylase #62 yeaD 300 similar to hypothetical proteins from B. subtilis #63 yebA 196 similar to hypothetical proteins #64 guaA 232 GMP synthetase #65 purE 300 phosphoribosylaminoimidazole carboxylase I #66 purC 72 phosphoribosylaminoimidazole succinocarboxamide synthetase #67 purM 101 phosphoribosylaminoimidazole synthetase #68 yhjM 103 similar to transcriptional regulator (LacI family) #69 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #70 yitV 120 similar to hypothetical proteins #71 yitW 63 similar to hypothetical proteins #72 yitX 54 yitX #73 yitY 57 similar to L-gulonolactone oxydase #74 yitZ 44 similar to multidrug resistance protein #75 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #76 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #77 yjlC 300 yjlC #78 yjlD 39 similar to NADH dehydrogenase #79 yjmA 197 similar to glucuronate isomerase #80 yjmB 67 similar to Na+:galactoside symporter #81 yjmC 104 similar to malate dehydrogenase #82 yjmE 24 similar to D-mannonate hydrolase #83 yjmG 47 similar to hexuronate transporter #84 yjmH 87 similar to transcriptional regulator (LacI family) #85 ileS 300 isoleucyl-tRNA synthetase #86 ylyA 77 alternate gene name: ylmK; similar to hypothetical proteins from B. subtilis #87 lsp 102 signal peptidase II #88 pyrR 273 transcriptional attenuator and uracil phosphoribosyltransferase activity (minor) #89 pyrP 171 uracil permease #90 pyrB 145 aspartate carbamoyltransferase #91 yqhJ 29 similar to glycine dehydrogenase #92 yqhI 300 similar to aminomethyltransferase #93 ccpA 274 transcriptional regulator (Lacl family) #94 aroA 235 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase #95 ytxJ 23 alternate gene name: csb40; similar to general stress protein #96 ytxH 27 alternate gene name: csb40; similar to general stress protein #97 ytxG 161 alternate gene name: csb40; similar to general stress protein #98 murC 249 UDP-N-acetyl muramate-alanine ligase #99 ytpS 159 ytpS #100 ytpP 234 similar to thioredoxin H1 #101 yusH 66 similar to glycine cleavage system protein H #102 yusI 110 similar to arsenate reductase #103 yusL 267 similar to 3-hydroxyacyl-CoA dehydrogenase #104 yusM 300 similar to proline dehydrogenase #105 rbsR 300 transcriptional regulator (LacI family) #106 nrgA 281 ammonium transporter #107 glyA 206 serine hydroxymethyltransferase #108 ywlF 156 alternate gene name: ipc-32d; similar to ribose 5-phosphate epimerase (pentose phosphate) #109 ywlE 75 alternate gene name: ipc-31d; similar to protein-tyrosine-phosphatase #110 ywlD 78 alternate gene name: ipc-30d; similar to hypothetical proteins #111 ywlC 156 alternate gene name: ipc-29d; similar to hypothetical proteins #112 ywlB 66 alternate gene name: ipc-28d #113 spoIIR 140 alternate gene name: ipc-27d, csfX #114 purA 205 adenylosuccinate synthetase #115 yycE 120 yycE #116 dnaC 169 replicative DNA helicase Motif number 1 TAACCTGTTCTGGAAAACGCTTGCGCAGCAAGAA 1 67 0 TGAAACGTTC 0.902387 -234 ATATTTCCCCACGAAAACGATTGCTTTTTATCTT 2 219 1 AGAAACGTTC 0.99188 -82 AAAGAGAGCAAGGAAAACGGTTGCGTGGCTGTGA 3 33 0 AGAAACGTTC 0.99188 -85 GGCAAAAAAAACGCAAACGTTTTCCGAACCTGTT 8 11 0 AGAAACGTTC 0.99188 -100 TTTCGTGCAAAGGAAAACGTTTCCGCTTATCCTT 9 39 1 AGAAACGTTC 0.99188 -67 AGGTGTGTAAAGGCAAACGTTTACCTTGCGATTT 17 241 1 AGAAACGTTC 0.99188 -60 CGCAGTATAAACGAAAACGTTTGCGTGTGTCTTT 18 83 0 AGAAACGTTC 0.99188 -51 CTAACAGAAAAAGAAAACGTTTGCGTAGGGATTT 21 189 0 AGAAACGTTC 0.99188 -70 TTTCCTGCAGACGCACACGTTTGCGTATCATATC 27 46 0 AGACACGTTC 0.935657 -167 CTAACAGGGAAAGCAAACGTTTGCGAGACTGCTT 29 221 0 AGAAACGTTC 0.99188 -77 AAAGGGGTAGATGCAATCGGTTACGCTCTGTATA 31 93 1 AGAATCGTTC 0.902387 -69 AAAGGAATTTACGCAAACGATTACCTTCAGGCTA 32 169 0 AGAAACGTTC 0.99188 -132 TTTTATTTCCACGCAAACGGTTTCGTCAGCGCAT 36 209 1 AGAAACGTTC 0.99188 -92 GTTCAGGCAAAAGAGAACGATTGCGTTGGGGACC 39 195 1 AGGAACGTTC 0.93198 -106 CCGCATTGTAACGAAAACGTTTGCGCAACGCTCG 41 180 0 AGAAACGTTC 0.99188 -121 TATAAAAACCAAGTATACGTTTTCATCATCTATA 93 69 1 AGATACGTTC 0.907505 -206 TAATCTATCTATGTAAACGGTTACATAAACAAGG 105 267 1 AGAAACGTTC 0.99188 -34 GCACCATTTTATTAAAACGCTTTCAATTTTTCAT 115 77 0 ATAAACGTTC 0.850871 -44 * * ***** ** * Masking position 11 Map Score: 47.6359 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 5 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 2 TGCATGAAATAAAAACGAGCAGAAAAAAGTGG 1 32 0 AAAAACGACG 0.808746 -269 TTATCGGTGTAAAAACAGTGGGTAGGCCTGAT 2 148 0 AAAAACAGGG 0.866648 -153 ATCATATCAGAAAAAAGGGCCGGATGATTCCA 27 22 0 AAAAAAGGCG 0.952511 -191 CCCCGTGTAAAAAAACAGCCCGAAACC 43 6 0 AAAAACAGCG 0.952511 -70 ACAAAAAACAGACTGATCGAGGTCA 46 4 1 AAAAACAGCG 0.952511 -100 TAATGAAAATAAAAAAAGTCTGTTCGTGTCGA 48 99 0 AAAAAAAGCG 0.952641 -202 TTATAACGAAAAAAACAGAGGGCGCAAAACCC 51 31 0 AAAAACAGGG 0.866648 -114 ATATCCAAAATAAAAAAACCAGGGAACAGCAC 55 29 0 TAAAAAAACG 0.481594 -119 AAAATATTTTAAAAACGAGCAGGATTTCAGAA 57 115 1 AAAAACGACG 0.808746 -79 AATCAGAATTAAAAAAGGACCGCCGGCAAAAG 58 55 0 AAAAAAGGCG 0.952511 -138 GAAGCCTGAAAAGAACGGAGCGGATACAAGGC 62 86 0 AAGAACGGGG 0.458834 -215 TAAACCAAGGAAAAACGAGCCGTTTGGCGCGG 62 265 0 AAAAACGACG 0.808746 -36 CCCACAGCAATAAAAAAGCCAGAAAATAAAAT 63 76 0 TAAAAAAGCG 0.814599 -121 ATAAAGACACTAAAAAAGCCTGTATGTTTCGT 63 139 0 TAAAAAAGCG 0.814599 -58 TATACTGTAGAAAAAAGGAGTGAGGGAAC 71 45 1 AAAAAAGGGG 0.866648 -19 AACAAAAAAGGACAGCCTGACATGT 72 4 1 AAAAAAGGCG 0.952511 -51 TTTCAGCTGTAAAAAAGGACAGCCTCACATGT 72 30 0 AAAAAAGGCG 0.952511 -25 AGCCGCATAAAAAAACAGGCTGACCGCG 75 7 0 AAAAACAGCG 0.952511 -200 AATTCCGCTCAAAAAAAATCAGCACGACTCCA 75 70 0 AAAAAAAACG 0.809635 -137 CTCTTGGCACAAAAAAAGCCCGGCTTTTACGC 86 25 0 AAAAAAAGCG 0.952641 -53 TTAAGGCTGAAAAAAAACCCCGGTCTAAGATA 90 101 0 AAAAAAACCG 0.530436 -45 AAAAACATACAAAAAAGGACAGAGAAACACCT 92 247 0 AAAAAAGGCG 0.952511 -54 GAGAAAGCATAAAAAAAGGCCGCACGGCGGCC 93 26 0 AAAAAAAGCG 0.952641 -249 TTTAGGTTTTTAAAACAAACTGTGTTAAAATA 102 59 1 TAAAACAACG 0.480875 -52 GGTACGAGAGAAAAAAAATCCGTCTTCAGCGG 103 148 0 AAAAAAAACG 0.809635 -120 AGACTTTGTCAAAAAAAGAGTGAAAACCTTAA 105 160 1 AAAAAAAGGG 0.866981 -141 CTTAAAATAAAAGAAAAGACTGGCTATGCAGT 107 15 0 AAGAAAAGCG 0.724655 -192 ACGCATAGGCTAAAAAAGCGGGGCGTGTCCAA 110 42 1 TAAAAAAGGG 0.5874 -37 GAAAGAACGCAAAAACGGGGTGAACGG 112 50 1 AAAAACGGGG 0.866315 -17 ******** * * Masking position 5 Map Score: 35.9992 Number of sites scoring better than the average of aligned sites = 451 Number in coding regions = 344 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 3 AACGCGTCAGCGTCGCATCAGGCATCGGCACAC 2 19 0 CGCCATCAGC 0.991314 -282 GCGACGCGAGCGCCTTATCCGACCTACGGTTCA 2 70 0 CGCTATCCGC 0.98805 -231 AAGGCGCTCGCGTCGCATCCGACACCATGCTCA 2 87 1 CGCCATCCGC 0.994555 -214 GACGCGTCAGCGTCGCATCAGGCATCTGAGCAT 2 113 0 CGCCATCAGC 0.991314 -188 GACGCTGACGCGTCTTATCAGGCCTACCCACTG 2 132 1 CGCTATCAGC 0.981009 -169 GACGCGCCAGCGTCGCATCAGGCAAGACCGTA 21 10 0 CGCCATCAGC 0.991314 -249 GACGCTGGCGCGTCTTATCAGGCCTACGCAGGG 21 29 1 CGCTATCAGC 0.981009 -230 GCGGCGTAAACGCCTTATCCGACCTACGGTTCT 21 64 0 CGCTATCCGC 0.98805 -195 AAGGCGTTTACGCCGCATCCGACACGCATTGCC 21 81 1 CGCCATCCGC 0.994555 -178 GCGGCGTGAACGCCTTATCCGAACTACGTCCGA 27 117 0 CGCTATCCGA 0.855752 -96 AAGGCGTTCACGCCGCATCCGACAAAACATCCG 27 134 1 CGCCATCCGC 0.994555 -79 ACAAAACATCCGGCACACCAGACAGCAAAAGAT 27 155 1 CGCCACCAGC 0.951436 -58 ** * ****** * Masking position 7 Map Score: 28.1166 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 84 Number in noncoding regions = 563 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 4 TGATAAAACGCGTCAGCGTCGCATCAGGCATC 2 26 0 CGAGCGTCGC 0.984343 -275 TCGGATAAGGCGCTCGCGTCGCATCCGACACC 2 81 1 CGCGCGTCGC 0.991371 -220 TGATAAGACGCGTCAGCGTCGCATCAGGCATC 2 120 0 CGAGCGTCGC 0.984343 -181 CGAATACAGGCTGCCGCGGCGGGTCAGGA 10 8 0 CTCGCGGCGG 0.695434 -126 TGATAAGACGCGCCAGCGTCGCATCAGGCAAG 21 17 0 CGAGCGTCGC 0.984343 -242 CATAAAAAGTCGATGGCGTTGAATATTTTTTC 21 128 1 CGGGCGTTGA 0.527384 -131 CTTTTCCCCAGGCGCGCGGCGAAAGAAGACTT 29 169 0 GGCGCGGCGA 0.870522 -129 TTCTCTGTGTCGTGCGCGTCCCAGCTTGAAAA 36 62 1 CGCGCGTCCC 0.893923 -239 AGCCATTGGCGGCACGCGTTGCTAATTCACGA 36 171 1 GGCGCGTTGC 0.837777 -130 GAGAAAAATTCGCGAGCGTTGCGCAAACGTTT 41 168 1 CGAGCGTTGC 0.926427 -133 GCCCAAAGGACGAGAGCGGCGATAAGTGCAAA 48 243 0 CGAGCGGCGA 0.942399 -58 TAAATCGAGACGGAGGCCGCGCCAAACGGCTC 62 249 1 CGGGCCGCGC 0.863912 -52 CGAAAGCGGTGCAACAGAAACT 83 1 1 CGAGCGGTGC 0.947555 -47 CCATATCCTCGGGAAGCGGCGCTTCAAATTCG 88 35 0 GGAGCGGCGC 0.952758 -239 TTTCAATTTGCGACCGCGGCGGCTGAAAAGCC 98 179 0 CGCGCGGCGG 0.971352 -71 TCTCCCTTTACGCTCGCCGCGCTGACTGCCGC 103 120 1 CGCGCCGCGC 0.95965 -148 AGCAAGAACTCGACCGCGTCGGACACATGCAT 104 40 0 CGCGCGTCGG 0.962628 -261 ** ******** Masking position 6 Map Score: 21.3708 Number of sites scoring better than the average of aligned sites = 1062 Number in coding regions = 913 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 CTTTCTTTAGTTTATTTTCAGAAAAAGATAC 5 63 0 TTTTTTTCAG 0.893076 -238 TTTCTATTCTGCATTGCCGCT 12 195 0 TTTTATTCTG 0.829884 -11 ATACAGTATATTTCTTTTCGGTTGAGAAATC 18 40 1 TTTTTTTCGG 0.689292 -94 CGCAAACGTTTTCTTTTTCTGTTAGAATGCG 21 198 1 TTCTTTTCTG 0.854978 -61 ATAAAGTTATTTTATATTCAGATGGTTATGA 29 96 1 TTTTATTCAG 0.743385 -202 CGGAAACGGATTTCTTTTCAGGTTTGTGATG 32 106 0 TTTTTTTCAG 0.893076 -195 ATTTTTTGGTTTTTTATTCTGTCGCGATTTT 39 93 1 TTTTATTCTG 0.829884 -208 ACTTTGAACCTTTCGATTCTGAAAAAATTGC 42 37 0 TTTGATTCTG 0.671566 -49 ATTTTAATTATTCTTTTTCAGGGCGTATGTA 48 141 1 TTCTTTTCAG 0.777823 -160 TTGCTGTTATTTTATTTTCTGGCTTTTTTAT 63 68 1 TTTTTTTCTG 0.933623 -129 AGCCTGTATGTTTCGTTTCAGTAAAACTGTC 63 124 0 TTTGTTTCAG 0.777823 -73 GCGGGTATTTTTTATTTTCTGAAAACAAAAG 65 259 1 TTTTTTTCTG 0.933623 -42 AAGTGCCTCCTTCCTTTTCAGTTTTTTGGGC 81 82 0 TTCTTTTCAG 0.777823 -23 CCTATGTTGGTTCAGTTTCTGTTGCACCGCT 83 15 0 TTCGTTTCTG 0.711907 -33 GAGGGCTTTTTTTATTTTCTGAAAAAATGCA 85 266 1 TTTTTTTCTG 0.933623 -35 TGACAGAGGGTTTCTTTTCTGAAATAATAAA 88 99 1 TTTTTTTCTG 0.933623 -175 TAGACCGGGGTTTTTTTTCAGCCTTAAGTTG 90 106 1 TTTTTTTCAG 0.893076 -40 GTGATCCTCCTTTGGTTTCTGTTCATTTTAT 104 218 1 TTTGTTTCTG 0.854978 -83 TAATAATTGCTTTTTATTCTGAAAGATACGG 106 250 1 TTTTATTCTG 0.829884 -32 AATTTTTCTATTTTTTTTCTGTAGAAATGGT 116 105 1 TTTTTTTCTG 0.933623 -65 *** ******* Masking position 7 Map Score: 23.1503 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 42 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 6 GCTGCGCAAGCGTTTTCCAGAACAGGTTAG 1 72 1 CGTTTTCCAG 0.625683 -229 AGAATGCCGCCGTTTGCCAGAAATTCGTCG 1 200 1 CGTTTGCCAG 0.785539 -101 AAAAAGCAATCGTTTTCGTGGGGAAATATA 2 218 0 CGTTTTCGTG 0.898989 -83 GCCACGCAACCGTTTTCCTTGCTCTCTTTC 3 38 1 CGTTTTCCTT 0.860607 -80 GTTCGGAAAACGTTTGCGTTTTTTTTGCCG 8 16 1 CGTTTGCGTT 0.886474 -95 TAAGCGGAAACGTTTTCCTTTGCACGAAAA 9 38 0 CGTTTTCCTT 0.860607 -68 GTTGCATATGCGTTTGCGTCCTGCGATACG 14 55 1 CGTTTGCGTC 0.900452 -147 GCAAGGTAAACGTTTGCCTTTACACACCTT 17 240 0 CGTTTGCCTT 0.931173 -61 TAAACGAAAACGTTTGCGTGTGTCTTTATT 18 80 0 CGTTTGCGTG 0.951226 -54 ACGTCTTTTTCCTCGTTAAGCCAC 20 23 0 CTTTTTCCTC 0.5355 -14 CCTACGCAAACGTTTTCTTTTTCTGTTAGA 21 194 1 CGTTTTCTTT 0.534743 -65 CAGACGCACACGTTTGCGTATCATATCAGA 27 43 0 CGTTTGCGTA 0.779529 -170 GCTAAAATCGCGTTTTCCTGCAGACGCACA 27 63 0 CGTTTTCCTG 0.939099 -150 GTCTCGCAAACGTTTGCTTTCCCTGTTAGA 29 226 1 CGTTTGCTTT 0.715794 -72 TGAAGGTAATCGTTTGCGTAAATTCCTTTG 32 174 1 CGTTTGCGTA 0.779529 -127 CTGACGAAACCGTTTGCGTGGAAATAAAAT 36 208 0 CGTTTGCGTG 0.951226 -93 CAATCGTTCTCTTTTGCCTGAACTTACCAC 39 188 0 CTTTTGCCTG 0.844884 -113 GTTGCGCAAACGTTTTCGTTACAATGCGGG 41 185 1 CGTTTTCGTT 0.780866 -116 TCAAAATCACCGTTTGCTTAAAAATGGATT 46 81 0 CGTTTGCTTA 0.532803 -23 TGACATAAGCCTTTTGCCGGCGGTCCTTTT 58 45 1 CTTTTGCCGG 0.570874 -148 GTGTTTTATCCATTTGCCTGAAGCCTGAAA 62 107 0 CATTTGCCTG 0.573332 -194 TTGGCAAGGCCGTTTGCCGGAGTCAGGCCA 64 137 0 CGTTTGCCGG 0.891925 -96 CAAGCATACACTTTTTCCTCTTGAGCATCG 85 181 0 CTTTTTCCTC 0.5355 -120 AGCAAGAGTTCTTTTGCCTGAGAGATTCAC 92 105 0 CTTTTGCCTG 0.844884 -196 GCTGTTTACCCGTTTTCTTCAATCATAAAC 97 114 0 CGTTTTCTTC 0.571074 -48 TTGACTTGTCCGTTTTCCGCCGCCGTAATG 103 74 1 CGTTTTCCGC 0.635938 -194 ********** Masking position 5 Map Score: 21.81 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 555 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 AAATAATATAAAAAATCCCGCCATTAAGTTGA 1 148 1 AAAAACCGCC 0.964601 -153 TTTGAAACCCAAAAAATCCGCCGCATTCTATT 2 259 0 AAAAACCGCC 0.964601 -42 ATCATTAACAAAAAATTGCTCTAAAGCATCCG 14 83 0 AAAAAGCTCT 0.548738 -119 GCGCATCAATAAAAATGGCGCTGAAAAAATAT 21 150 0 AAAAAGCGCT 0.845674 -109 CAGGTTTACGCAAAATGCCGCTCATTTATGAG 36 118 0 CAAAACCGCT 0.818606 -183 CATTCCCCAGCAAAAGCCCGCTTTATACCTTT 41 49 1 CAAAACCGCT 0.818606 -252 ATTTTTCGCGAAAAACTCAGCTAACGCCCCTA 41 236 0 AAAAACAGCT 0.803306 -65 GTTTTTCGCGAAAAATTCAGCTAACGCTCTCT 41 252 1 AAAAACAGCT 0.803306 -49 TCGATTCTGAAAAAATTGCGCACGATACGTCT 42 24 0 AAAAAGCGCA 0.770314 -62 CTCCCCGTGTAAAAAAACAGCCCGAAACC 43 8 0 AAAAACAGCC 0.878525 -68 GGACTCAGCGAAAAAAGGCGCTTTCTCAAGGC 52 95 1 AAAAAGCGCT 0.845674 -67 TATGTAAAATAAAAAACCCGCATAGCTCTCCT 53 28 0 AAAAACCGCA 0.904009 -183 AAGGTAAATAAAAAAGTGATCCCGGCTCTCCC 57 27 0 AAAAAGATCC 0.363675 -167 TCAGAATTAAAAAAGGACCGCCGGCAAAAGGC 58 53 0 AAAAGCCGCC 0.66787 -140 ACGCGTAAAACAAAAACCAGCTGACAAAGCCG 62 22 0 CAAAACAGCT 0.544991 -279 CTCATCCTGAAAAAAGTCAGCAGAAACGTCAA 63 175 0 AAAAACAGCA 0.714248 -22 TTCCGCTCAAAAAAAATCAGCACGACTCCAGC 75 68 0 AAAAACAGCA 0.714248 -139 ACCCTTTCCAAAAAAATCAGCAAACTGCTTAT 77 261 1 AAAAACAGCA 0.714248 -40 TTGTATCATCAAACATACCGCCTCTCCCACTA 84 21 0 AAACACCGCC 0.66787 -67 CAGAAAATAAAAAAAGCCCTCTCATCCCATAA 85 255 0 AAAAACCTCT 0.773481 -46 ATATAGAAGAAAAAACCCCTCCTGCCAGAGCA 88 232 0 AAAAACCTCC 0.858091 -42 ATGACTGTATAAAAAAACCTCTTTGCTTTTTT 89 106 0 AAAAACCTCT 0.773481 -66 TTGAACAATCCAAAAGGCCGCCGTGCGGCCTT 93 11 1 CAAAACCGCC 0.888784 -264 GAAAGCATAAAAAAAGGCCGCACGGCGGCCTT 93 24 0 AAAAACCGCA 0.904009 -251 GTTTTTTACAAAAAAAAGCGCCAGATGATATC 94 24 0 AAAAAGCGCC 0.906575 -212 AATAAAAATCCCTCCTTATGTATAT 100 4 1 AAAAACCTCC 0.858091 -231 GTGCTTCTTAAAAAAGAGCTCCGCGCATGCGG 102 24 0 AAAAAGCTCC 0.682878 -87 ***** ***** Masking position 3 Map Score: 28.5831 Number of sites scoring better than the average of aligned sites = 796 Number in coding regions = 625 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 8 TATGAATGAGTGCAAAAAGGTGGGGGAAAA 2 181 0 TGCAAAAAGG 0.932014 -120 GGTTTCAAACAGCAAAAAGGGGGAATTTC 2 282 1 AGCAAAAAGG 0.704075 -19 ATTCCCGGTGTGCAAACCGGGGGCGTATTA 8 79 0 TGCAAACCGG 0.644352 -32 GACACTTGTTTGCACAGAGGATGGCCC 28 63 1 TGCACAGAGG 0.837081 -17 GGAAAAGACGTGCAAAAAGGTTGTGTAAAG 29 194 1 TGCAAAAAGG 0.932014 -104 AAGCATTTTTTGCAAAAAGGGGTAGATGCA 31 78 1 TGCAAAAAGG 0.932014 -84 AAACGGCCTTGCCAAAGAGGGCGGAGCGAG 64 152 1 GCCAAAGAGG 0.669225 -81 ATAAGTGCAATGCAGAGCGGGTATTTTTTA 65 243 1 TGCAGAGCGG 0.80851 -58 TTTAAAACAGTCCAGAGAGGCTGAGAAGGA 88 147 1 TCCAGAGAGG 0.885089 -127 TTTTAAGCAATCCAGAGAGGTTGCAAAGAG 89 21 1 TCCAGAGAGG 0.885089 -151 CCAGAGAGGTTGCAAAGAGGTGCACAACAA 89 32 1 TGCAAAGAGG 0.970217 -140 TGCTTTTTTACGCAAAGAGGCATACAAAGA 89 85 0 CGCAAAGAGG 0.826147 -87 TGCGTAAAAAAGCAAAGAGGTTTTTTTATA 89 101 1 AGCAAAGAGG 0.849707 -71 TTAATGAAAGTCCAGAGAGGCTTGGAAGGG 90 17 1 TCCAGAGAGG 0.885089 -129 TCAGAAAATCTGCAAACAGGTCATTTGCAA 108 15 1 TGCAAACAGG 0.885883 -142 CCTATGCGTGTCCAAAAAGGGTTAGAACAT 110 21 0 TCCAAAAAGG 0.853731 -58 AATAAAATGGTGCAAAAAGGAGATGGTAAC 115 98 1 TGCAAAAAGG 0.932014 -23 ********** Masking position 6 Map Score: 15.609 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 95 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 GGCTGCCGCGGCGGGTCAGGA 10 1 0 GGGGTCAGGA 0.84178 -133 CGAAAACTGTGCGGGCCAGGCATGATCCTTT 15 87 0 GGGGCCAGGC 0.904726 -64 CGCTGAGGGTGCCGGTCTGGCACCCTGACTT 19 17 1 GCGGTCTGGC 0.586565 -78 GCCATAATCTCGCGGCCAGGCATACTTGCGA 26 35 0 CCGGCCAGGC 0.788874 -64 ATTACGCCCACTGGGATAGGCTTTAAGTCTG 34 138 1 CGGGATAGGC 0.780415 -27 TTCCTCTTCTGCGGGAGAGGATCAGGGTGAG 37 19 1 GGGGAGAGGA 0.940173 -100 GGGAGAGGATCAGGGTGAGGAAAATTTATGC 37 31 1 CGGGTGAGGA 0.905819 -88 CGAAGAGAGTGAGGGTGAGGCATAAATTTTC 37 50 0 GGGGTGAGGC 0.968067 -69 GCGTTGGGGACCGGGAGTGGCTCCGATGCTG 39 217 1 CGGGAGTGGC 0.914594 -84 AAAAGTGATTCTGGGAGAGCCGGGATCACTT 57 15 1 CGGGAGAGCC 0.912297 -179 AATTGCATGCGGGGGACAGGCTGGGCGTAAC 62 137 1 GGGGACAGGC 0.964786 -164 TTTTATTGCTGTGGGAGTGGCTTAGGCGCTT 63 93 1 GGGGAGTGGC 0.914594 -104 ATAAAAACAGCAGGGAGAGCACTATGAAAAA 73 16 1 CGGGAGAGCA 0.767453 -42 CGCGGTCAGCCTGTTTTTTTA 75 1 1 CCGGTCAGCC 0.580835 -206 AAGCGTGAGACAGGGAGAGGCACTACCCTTT 77 237 1 CGGGAGAGGC 0.980211 -64 TAGAATGAAAGACGGTGAGGAC 79 186 1 GCGGTGAGGA 0.790989 -12 TGGAAATATAGTGGGAGAGGCGGTATGTTTG 84 13 1 GGGGAGAGGC 0.980211 -75 AGAAACAAAGCACGGAGAGGAACGGTGGGGA 113 117 1 CCGGAGAGGA 0.860791 -24 * ********* Masking position 5 Map Score: 16.3241 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 321 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 10 CTAAAAGTCAACTTAATGGCGGGATTTTTTATATT 1 152 0 AATGGCGGAT 0.860748 -149 ATCCCCTCCAGAACACTGGAGGGGTACTAATTAAT 6 31 0 GATGGAGGGT 0.831867 -52 TGAACTGACAGCCAAATGGAGGAGTCAC 11 46 1 GATGGAGGGT 0.831867 -18 TTGCCGCCTTGAAGAAAGGAGGTATAATCCGTCGA 29 19 0 GAAGGAGGAT 0.83829 -279 AACTTATTACAGCCATTGGCGGCACGCGTTGCTAA 36 161 1 AATGGCGGAC 0.809596 -140 AACTTGCGGAACATAATTGAGGAATCATAGAATTT 53 79 1 AATTGAGGAT 0.567746 -132 AGACCACCACACCGACAGGAGGCATCCC 60 4 0 AAAGGAGGAT 0.909852 -227 ATGGTTTGGAACAGATAGGAGGGGCAAAG 60 212 1 AAAGGAGGGC 0.716325 -19 TAGATTATAAAATCATTGGAGGTACTGTTC 68 6 0 AATGGAGGAC 0.947967 -98 TTTTATTATAAGGAAATGGAGGTACACTTTAAAAC 69 43 0 AATGGAGGAC 0.947967 -81 TTCTGAAAAAATGCAGTGGAGGAATGAAA 85 282 1 AATGGAGGAT 0.963616 -19 TAAAGTAACCGTAAACTGGAGGAACGTTT 87 84 1 GATGGAGGAC 0.903452 -19 TGCGCCGTTGATAAAGGGGAGGAATTAG 92 283 1 AAGGGAGGAT 0.893246 -18 AGAAAAAAATACTAAGAGGAGGAATA 96 12 1 AAAGGAGGAT 0.909852 -16 TAAGAACATAAACAACTGGAGGGATATGAA 100 215 1 AATGGAGGAT 0.963616 -20 GTAGTGCTGTAAAAAATGGAGGGATTCAA 101 48 1 AATGGAGGAT 0.963616 -19 ATGCAATAAAACATAAGGGAGGAATGAAAG 116 6 0 AAGGGAGGAT 0.893246 -164 * * ****** ** Masking position 5 Map Score: 15.0983 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 19 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 AACGCGCATCTTTCATGACGGCAAACAATA 14 141 0 TTTCATGACG 0.637258 -61 TTATCCAAAGTTTCGGGCTGTTATGTTTTA 23 39 1 TTTCGGGCTG 0.922281 -117 GCTCGGAACATTTCAGGCTGTAGCCAACGT 24 21 1 TTTCAGGCTG 0.968099 -62 ACTCGTCATCTTTCAGGCTGTAACTACGTT 24 46 0 TTTCAGGCTG 0.968099 -37 TATTACGTTTTTTCAAGCTGGGACGCGCAC 36 73 0 TTTCAAGCTG 0.726126 -228 CGATGCTGGGTTTCGTGGTGATAATTTCAC 39 240 1 TTTCGTGGTG 0.759883 -61 CTGACAACTTTTTCATGGTGAAATTATCAC 39 257 0 TTTCATGGTG 0.890024 -44 GGTTTCGGGCTGTTTTTTTACA 43 3 1 TTTCGGGCTG 0.922281 -73 AATTATTCTTTTTCAGGGCGTATGTATATA 48 146 1 TTTCAGGGCG 0.914382 -155 AGGCTCTTTCTTTCATGATGAGGCTTAGTC 52 123 1 TTTCATGATG 0.759812 -39 ATGTTTCAGGGCGGCTTTGTCAG 62 4 1 TTTCAGGGCG 0.914382 -297 GCTCCGTTCTTTTCAGGCTTCAGGCAAATG 62 97 1 TTTCAGGCTT 0.615984 -204 TGCTGACTTTTTTCAGGATGAG 63 185 1 TTTCAGGATG 0.882589 -12 CAGCCTCACATGTCAGGCTGTCCTTTTTTG 72 13 0 TGTCAGGCTG 0.793752 -42 TCGCTCATATTTTCATGCTGTTATGGA 92 8 0 TTTCATGCTG 0.927383 -293 AAAAAGCGCATTTCATGGCGCAGCAGTGCC 104 87 0 TTTCATGGCG 0.817995 -214 ********** Masking position 3 Map Score: 12.5172 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 235 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 CACGCAACCGTTTTCCTTGCTCTCTTTCCGTGCT 3 40 1 TTTTCCTCTC 0.795917 -78 TGTCCCACGATTTTACGCCCTGTCATCCTGTTCG 21 232 0 TTTTCCTGTC 0.795917 -27 TCTCTTCTTCATGCTCTCTGCTGTAACA 25 5 1 TTCTCCTCTC 0.930075 -61 AATCGACGGATTATACCTCCTTTCTTCAAGGCGG 29 17 1 TTATCCTTTC 0.593155 -281 ACGCTCCGGTTTCTCCGCGCTGTCCATGTCCAGA 34 92 1 TTCTCCTGTC 0.930075 -73 TTCTCGTGGTTTCGCCGAACTTTCACACTTACGT 40 89 1 TTCGCCTTTC 0.878071 -32 TCAGTCATTTTTCTGCAATTTTTCTATTGCGG 41 9 0 TTCTCTTTTC 0.796247 -292 GTATATTTCTTAATCCTTTCCGTTATCTAA 47 7 1 TTCTACTTTC 0.500523 -114 TCTATAAAAGTTCTACATGCTTTCTTCTCCTCAT 50 59 1 TTCTCCTTTC 0.959921 -97 CGACAAGTCTTTCTTCCGTTTCTCAGTGTATTTC 50 106 1 TTCTCTTCTC 0.684566 -50 GACATAAGCCTTTTGCCGGCGGTCCTTTTTTAAT 58 46 1 TTTTCCGGTC 0.539729 -147 TTTTACGCGTTTCTCCCTTTTGTCTTGTATGCCG 62 44 1 TTCTCTTGTC 0.684566 -257 GGCAGCGCAGTTCGGCTGCCTTTCTCTTTCTGCC 67 31 1 TTCGCCTTTC 0.878071 -71 GCCTTTCTCTTTCTGCCCTCGTTCGGGGAGATAT 67 48 1 TTCTCCGTTC 0.878071 -54 AAGATTTTTCCTTTCGTTCTAAAGGATGT 86 59 0 TTTTCCGTTC 0.678615 -19 GCGCTTCAAATTCGACATATTCTCCTGTTCGTGG 88 15 0 TTCGCTTCTC 0.394872 -259 TTTTTTCATCCTTTCCCTGCACATT 94 221 0 TTTTCCTTTC 0.875352 -15 AAAAATGCCATTCTCCTTCCTTTCCATCCCTCGA 106 137 1 TTCTCCTTTC 0.959921 -145 TTCACCCCGTTTTTGCGTTCTTTCTTCCAATCTA 112 40 0 TTTTCCTTTC 0.875352 -27 CGAACGTCATTTCTTCCATCTTTCGAATGAAAAA 115 35 0 TTCTCCTTTC 0.959921 -86 **** * ***** Masking position 2 Map Score: 14.5329 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 128 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 13 CGATAATTTTTCCCCCACCTTTTTGCACTCA 2 174 1 TCCCCCCCTT 0.793481 -127 AATAAAAGAGAGCGCCCCCTTTTGGAGTAAT 16 78 1 AGCGCCCCTT 0.913706 -136 CGAAAAGAATATTGCCGCCTTGAAGAAAGGA 29 34 0 ATTGCCCCTT 0.56873 -264 TGACGCCCGTTTCCCCCCCTTGGGTACACCG 36 257 1 TTCCCCCCTT 0.942676 -44 AGTAGTTCACCACCTTTTCCCTATAT 57 178 0 TTCACCCCTT 0.589611 -16 CTTTGCCCCTCCTATCTGTTCCAA 60 217 0 TGCCCCCCTA 0.679886 -14 AAGAAAGCGCCTCCTTATCATACCTT 61 6 1 AGCGCCCCTT 0.913706 -84 TCTGTTCCCCACCTTCTAATGCTTT 65 286 0 TTCCCCCCTT 0.942676 -15 GCAGCCGAACTGCGCTGCCTTTATGTCATTT 67 19 0 TGCGCTCCTT 0.799479 -83 ATTTTCCCTTCCTTAAAAAAGTTG 68 90 0 TTCCCTCCTT 0.814485 -14 AATGTGCCCCTCCTTAGGATAACCA 70 106 0 TGCCCCCCTT 0.963561 -15 GCAAGTGCCTCCTTCCTTTTCAGT 81 91 0 AGTGCCCCTT 0.679544 -14 CTAATTCCCTTCCTTATCATACCGG 84 73 0 TTCCCTCCTT 0.814485 -15 GACTCAAGCTCTTCCTTCCCTGC 95 7 0 AGCTCTCCTT 0.435398 -17 AACAGCTCCTCCTTGTTTATGTAA 105 287 0 AGCTCCCCTT 0.742826 -14 CTTTCATTCCTCCCTTATGTTTTATT 116 6 1 ATTCCTCCTT 0.384021 -164 TTATTGCATTTTTCCCGCCTTGTTACTGTCC 116 32 1 TTTCCCCCTT 0.767085 -138 ****** **** Masking position 10 Map Score: 10.0727 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 142 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 14 ACGAAAACGATTGCTTTTTATCTTCAGATG 2 229 1 TTGCTTTTTA 0.740669 -72 TTCCCCCTTTTTGCTGTTTGAAACCCAAAA 2 277 0 TTGCTGTTTG 0.763463 -24 ACCCGCAACTTTGCTGATTTCACAGCCACG 3 14 1 TTGCTGATTT 0.685847 -104 ACTGAATAACCTGCTGATTTAGAATTTGAT 31 20 0 CTGCTGATTT 0.797538 -142 AGTGCATTTTCTGCTTATTAGACGCTCGAT 51 70 1 CTGCTTATTA 0.741944 -75 CTTTTGTTTACTGCTTTTTGTTTTGCCCTT 54 23 1 CTGCTTTTTG 0.763463 -137 TCAGCAGTCCTTGCTTTTTGGTTATTTT 58 9 0 TTGCTTTTTG 0.641425 -184 TTGTATGATGTTGCTGTTTAGGAATAGAGA 60 72 1 TTGCTGTTTA 0.837487 -159 AGTGCTCTCCCTGCTGTTTTTATGACCA 73 9 0 CTGCTGTTTT 0.87594 -49 TATAAGCAGTTTGCTGATTTTTTTGGAAAG 77 264 0 TTGCTGATTT 0.685847 -37 AAAAACCTCTTTGCTTTTTTACGCAAAGAG 89 96 0 TTGCTTTTTT 0.684412 -76 AGTGAGATCACTGCTTTTTA 97 1 0 CTGCTTTTTA 0.837487 -161 AGTGATCTCACTGCTTTTTATTTATCTGAT 97 19 1 CTGCTTTTTA 0.837487 -143 GCAGGATATACTGCTGTTTACCCGTTTTCT 97 126 0 CTGCTGTTTA 0.902899 -36 GTTTTTTATACTGCTGATTTTGACTTGTCC 103 55 1 CTGCTGATTT 0.797538 -213 TTTGAGATTGCTGCTGATTATCCATTGTGA 104 192 1 CTGCTGATTA 0.838391 -109 AATATAATAATTGCTTTTTATTCTGAAAGA 106 246 1 TTGCTTTTTA 0.740669 -36 ********** Masking position 5 Map Score: 11.0918 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 413 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 15 TCACGAGGGCGCATTCGCGCCCTTTA 9 7 1 GGGCGCATTC 0.89444 -99 CTCCAAAAGGGGGCGCTCTCTTTTATTGAT 16 75 0 GGGCGCTCTC 0.954068 -139 ATCCTGTTCGGGGCGCATTCTAACAGAAAA 21 212 0 GGGCGCATTC 0.89444 -47 GACTGAACAAGGGCGCTCTTGTAAAAACAA 40 54 1 GGGCGCTCTT 0.9283 -67 TCCTTTGGGCGGGAGCTTTTTGACATTCTG 48 265 1 GGGAGCTTTT 0.765684 -36 CAGCGAAAAAAGGCGCTTTCTCAAGGCTCT 52 100 1 AGGCGCTTTC 0.94721 -62 CGCTTTCTCAAGGCTCTTTCTTTCATGATG 52 113 1 AGGCTCTTTC 0.694213 -49 TATGATAAGGAGGCGCTTTCTT 61 3 0 AGGCGCTTTC 0.94721 -87 CACTCCTTTAAGGCGCTTTTCAAAATATCT 67 76 0 AGGCGCTTTT 0.917905 -26 CTAAGGTTAAAGGAGCTTTTC 70 2 0 AGGAGCTTTT 0.564949 -119 TCAGTTTTTTGGGCACTCTCCAAGCGAAAC 81 66 0 GGGCACTCTC 0.598549 -39 CTTTTACGCCGGGCTCTTTTGCA 86 4 0 GGGCTCTTTT 0.780702 -74 GATGATATCTGGACGCTTTTTT 94 3 0 GGACGCTTTT 0.631371 -233 AGATATCATCTGGCGCTTTTTTTTGTAAAA 94 23 1 TGGCGCTTTT 0.733929 -213 ********** Masking position 9 Map Score: 8.27457 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 336 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344