AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 map 300 methionine aminopeptidase #2 ybaN 69 putative gene 58 #3 apt 152 adenine phosphoribosyltransferase #4 dnaX 128 DNA polymerase III, tau and gamma subunits; DNA elongation factor III #5 ybaB 52 orf, hypothetical protein #6 htpG 109 chaperone Hsp90, heat shock protein C 62.5 #7 adk 180 adenylate kinase activity; pleiotropic effects on glycerol-3-phosphate acyltransferase activity #8 infA 284 protein chain initiation factor IF-1 #9 aat 41 leucyl, phenylalanyl-tRNA-protein transferase #10 cydD 122 ATP-binding component of cytochrome-related transport, Zn sensitive #11 trxB 300 thioredoxin reductase #12 yojI 75 putative ATP-binding component of a transport system #13 ada 73 O6-methylguanine-DNA methyltransferase; transcription activator/repressor #14 yojL 111 orf, hypothetical protein #15 ompC 300 outer membrane protein 1b (Ib;c) #16 usg 65 putative PTS system enzyme II A component #17 pdxB 98 erythronate-4-phosphate dehyrogenase #18 cysD 251 ATP:sulfurylase (ATP:sulfate adenylyltransferase), subunit 2 #19 rplQ 40 50S ribosomal subunit protein L17 #20 rpoA 25 RNA polymerase, alpha subunit #21 rpsD 33 30S ribosomal subunit protein S4 #22 rpsM 146 30S ribosomal subunit protein S13 #23 rpmJ 31 50S ribosomal subunit protein L36 #24 rpsH 33 30S ribosomal subunit protein S8, and regulator #25 rplN 164 50S ribosomal subunit protein L14 #26 rplC 32 50S ribosomal subunit protein L3 #27 rpsJ 237 30S ribosomal subunit protein S10 #28 yheD 179 putative export protein A for general secretion pathway (GSP) #29 fusA 27 GTP-binding protein chain elongation factor EF-G #30 rpsG 96 30S ribosomal subunit protein S7, initiates assembly #31 rpsL 125 30S ribosomal subunit protein S12 #32 yheO 154 orf, hypothetical protein #33 fkpA 220 FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase) #34 glyT 116 tRNA #35 tufB 114 protein chain elongation factor EF-Tu (duplicate of tufA) #36 secE 229 preprotein translocase #37 rplK 157 50S ribosomal subunit protein L11 #38 rplJ 300 50S ribosomal subunit protein L10 #39 rplL 66 50S ribosomal subunit protein L7/L12 #40 rpoB 300 RNA polymerase, beta subunit #41 rpoC 76 RNA polymerase, beta prime subunit #42 dnaB 82 replicative DNA helicase; part of primosome #43 ssb 253 ssDNA-binding protein #44 hfq 85 host factor I for bacteriophage Q beta replication, a growth-related protein #45 hflX 75 GTP - binding subunit of protease specific for phage lambda cII repressor #46 hflK 85 protease specific for phage lambda cII repressor #47 yjeT 81 orf, hypothetical protein #48 purA 103 adenylosuccinate synthetase #49 yjeB 204 orf, hypothetical protein #50 rpsF 300 30S ribosomal subunit protein S6 #51 rplI 41 50S ribosomal subunit protein L9 Motif number 1 ATGTGCATTCAGCCTCGCCGTTCTGACGGG 4 53 1 AGCCTCGCCG 0.973077 -76 GATAGCCTTTAGGCTGCCCGGTCACCATCA 13 35 0 AGGCTGCCCG 0.989335 -39 TTCGCAAGTATGCCTGGCCGCGAGATTATG 17 34 1 TGCCTGGCCG 0.980854 -65 CGTTCTTACGTAGCTCCCCGATTGGGAGCA 27 141 0 TAGCTCCCCG 0.889853 -97 ATCATTAATGAGCCTGCCCTGAAAAGTTAA 32 115 1 AGCCTGCCCT 0.944606 -40 CTACTTAACTTTGCTGCCCGAGACAGCACT 33 46 1 TTGCTGCCCG 0.905974 -175 CGCCTCTGAGAGGCTCCCCGTGATATAAAA 37 112 0 AGGCTCCCCG 0.987307 -46 TGTTCGTTGGAGCCTGGCCTATCCAGGCCT 38 97 1 AGCCTGGCCT 0.869077 -204 GCAGGATCGCTGGCTCCCCGTGTAAAAAAA 45 23 0 TGGCTCCCCG 0.989301 -53 GCAGATATTTTGCCTGCCGGGCGAACAGTG 49 25 1 TGCCTGCCGG 0.938879 -180 ACACGTTCCTTGCCTCCCCGGGATTCGGCT 50 240 1 TGCCTCCCCG 0.991014 -61 ********** Masking position 5 Map Score: 15.2646 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 275 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 CGAAATGGATCGGAAGTCCGGCGCGCTTTATACCACA 1 86 1 CGAAGCCGCT 0.891003 -215 TGGCAGGCTCTGAAACGCTGGAAGGTGGATTCACGA 4 103 0 CGAAAGCGGT 0.918478 -26 TACTTATTTACAGAACTTCGGCATTATCTTGCCGGTT 8 226 1 CGAACTCGCT 0.943932 -59 AATGTTTTCGCAAAACACCAGGGGATTGTCAAAGCAA 11 37 1 CAAACCCGGT 0.923093 -264 TGTAAATTCCCTACAATCCTGCCCATTGTCTGCCAAC 11 259 1 CACAACCGCT 0.911659 -42 GCAGAAAACCCGGACAATGAATTACAGC 12 58 0 CGAAACCGGT 0.966584 -18 TCCTAAACGCCCGAAATCCGGTGCCTTAAGCACTTTT 18 90 1 CGAAACCGTT 0.789562 -162 CTACTGAGACCCGAAAATCAGGTCGTTAAAAATCCCC 25 113 0 CGAAATCGGT 0.931784 -52 TACTTAACCACCGAACGCAAGCGTATTGCTAGTAAAG 27 26 0 CGAACCAGCT 0.638738 -212 CTGTCAACTACGACAAGCCCGCGCATTATACATACTT 27 58 0 CACAACCGCT 0.911659 -180 CGGCATCGCCCTAAAATTCGGCGTCCTCATATTGTGT 31 45 1 CAAAATCGCT 0.925717 -81 TGCTGGAAAGCGGAACCTCCGCTGTATTAATTTAGTT 32 72 1 CGAACTCGCT 0.943931 -83 ATCCTGGAACTCGGCTACCTGATTTTCATT 34 97 0 CGGAATCGCT 0.76636 -20 TTATTGCATTCAACAAGTCGGGCATGTTGCCTGGTTG 35 43 1 CACAATCGGT 0.747489 -72 CCCAGCGATCAAAAAAGCGGCGATTTAATCGTTGCA 37 10 1 CAAAAGCGCT 0.911341 -148 AAGTTTCTTGCGAAACTCCTGCGGTCTTCGACGGAGG 38 124 0 CAAACCCGCT 0.951828 -177 CCTTACAGCGCAAAAAGGCTGGTGACTAAAAAGTCAC 40 36 0 CAAAAGCGGT 0.861957 -265 * **** ** ** * Masking position 5 Map Score: 13.172 Number of sites scoring better than the average of aligned sites = 651 Number in coding regions = 591 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 3 TCGCCGTTCTGACGGGGCTGTGTTAGCATTACC 4 67 1 GACGGGCGGT 0.77037 -62 TGTTATAATTGCGGTCGCAGAGTTGGTTACGCT 8 38 1 GCGGCGCGGT 0.978606 -247 AAATTCCTTATCGGCAGCGGGGTAATGAGCGTA 8 65 0 TCGGAGCGGT 0.722211 -220 TATCCTTAACCAGGGAGCTGATT 13 61 1 CAGGAGCGTT 0.911536 -13 TTGTTTTAGCGCAGCGGCAGTTTCATACTATGG 18 47 0 GCAGGGCGTT 0.71845 -205 TCCCCATATCGAGGGCGCGGCATTATAACACCG 25 85 0 GAGGCGCGAT 0.93021 -80 CCCGAAGGCTGTTTACTTTACTAG 27 2 1 CCGAGGCGTT 0.843081 -236 CACACAATATGAGGACGCCGAATTTTAGGGCGA 31 50 0 GAGGCGCGAT 0.93021 -76 GCCGCCTGGTCAGGCGGCGGTTCTTAATGC 32 8 0 CAGGGGCGTC 0.791796 -147 GCCGCCTGACCAGGCGGCGGTTTTTTTATTACA 32 23 1 CAGGGGCGTT 0.969648 -132 GAATGAAAATCAGGTAGCCGAGTTCCAGGAT 34 96 1 CAGGAGCGGT 0.942832 -21 GGTTTGCCTCGCGATCGCGGGGTGAAAATGTTT 36 181 1 GCGACGCGGT 0.81001 -49 GAACGGACGTCCTGTCGCAGTATATTAAGTCGT 40 133 0 CCTGCGCGAT 0.634944 -168 GGGTTAAAACCCGGCAGCGGATTGTGCTAACTC 41 38 1 CCGGAGCGTT 0.948959 -39 GCTTTTTTGCCCGGTGGCATGGTGCTACCGGCG 43 31 1 CCGGGGCTGT 0.895825 -223 CCCTGAGGATGCGGTGGCTTTATTGACCTGTAC 47 24 0 GCGGGGCTAT 0.779604 -58 CTGACCCAGACAGGAGGCTGAATAATCCGTAAG 50 268 1 CAGGGGCGAT 0.964137 -33 **** *** * ** Masking position 7 Map Score: 10.3916 Number of sites scoring better than the average of aligned sites = 1624 Number in coding regions = 1388 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 4 GCCAGTACATTCTGGCGTTTTCGAGCACAGG 3 45 1 TCTGGCTTTT 0.944125 -108 CTTCGTGTCATCCGGCATTTTTCTTTTCATC 7 27 1 TCCGGCTTTT 0.948026 -154 TTAATGAATATCTGGCATGTTGTACTAAAAA 11 82 0 TCTGGCTGTT 0.948204 -219 GCACCGGATTTCGGGCGTTTAGGAAGATTTG 18 83 0 TCGGGCTTTA 0.951394 -169 ACTAATTATATCCGGCCTGTAATAAAAAAAC 32 42 0 TCCGGCTGTA 0.89948 -113 ATTCAACAAGTCGGGCATGTTGCCTGGTTGA 35 50 1 TCGGGCTGTT 0.979094 -65 GAATACAATTTCGCGCCTTTTGTTTTTATGG 37 62 1 TCGCGCTTTT 0.920376 -96 TCTTTTATATTCTGGCTTGTTTCTGCTCACC 38 199 1 TCTGGCTGTT 0.948204 -102 AATGGTACAATCGCGCGTTTACACTTATTCA 43 206 1 TCGCGCTTTA 0.839588 -48 GGTTTCGGGCTGTTTTTTTACACGG 45 5 1 TCGGGCGTTT 0.90015 -71 ****** **** Masking position 10 Map Score: 8.87816 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 166 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 ATGTTTTCGGCACATTTCTCCC 8 3 1 GTTTTCGGCA 0.930247 -282 CGAAAAATTCCTTATCGGCAGCGGGGTAAT 8 72 0 CTTATCGGCA 0.819285 -213 TTTTTTCATTGTTTTCAGCGTACAAACTCA 14 46 1 GTTTTCAGCG 0.805421 -66 TGAAAAGCCCGTTTTCAGGATACTCAAATG 22 91 0 GTTTTCAGGA 0.915096 -56 TGAAAACGGGCTTTTCAGCATGGAACGTAC 22 104 1 CTTTTCAGCA 0.943066 -43 TTCTTGACACCTTTTCGGCATCGCCCTAAA 31 30 1 CTTTTCGGCA 0.93936 -96 GGAGGTTCCGCTTTCCAGCACTAATTATAT 32 62 0 CTTTCCAGCA 0.916551 -93 TATTAATTTAGTTACCCGCATCATTAATGA 32 96 1 GTTACCCGCA 0.663339 -59 CTGTCGTTAACTTTTCAGGGCAGGCTCATT 32 121 0 CTTTTCAGGG 0.784198 -34 TCCTTTTCAGGAGCCTGTCGTT 32 143 0 CTTTTCAGGA 0.926031 -12 TGCGTCAAATGTTATCGGCAA 36 2 0 GTTATCGGCA 0.796045 -228 TCACCTTTCCCGGATTAAACGCTT 43 5 1 CTTTCCCGGA 0.855292 -249 GGCCAGGTTTGTTTCCCGGAACCGAGGTCA 43 152 1 GTTTCCCGGA 0.835754 -102 CAGAACGATTTTTTTCAGGAGACACGAAC 43 235 1 TTTTTCAGGA 0.582988 -19 ********** Masking position 3 Map Score: 9.0276 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 398 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 TCTCAATTTGCCCGGGTGTGATACCATTGACGGCACTTACATAT 1 230 1 CCGTGTACGC 0.974107 -71 AAGAAAGGCACCTGGGGCTGAAACGGTTAATGGCGAGATAATTT 7 73 0 CCGTGAACGC 0.986153 -108 GAGGCAATCGCCTGTTGGTGGTATCGTTTATCGCTTTTTCAAAA 7 117 1 CCGTGTATGC 0.915294 -64 ACATTTCTCCCCAGAGTGTTATAATTGCGGTCGCAGAGTTGGTT 8 22 1 CCGTTTAAGC 0.830428 -263 TGAATTACAGCCCGCAGTTTAAACATCTTCGCGCGCACAGCAAT 12 25 0 CCGTTAACGC 0.969912 -51 AGCAAAGCTCCCTGCCAATGTTACAGCAGAGAGCATGAAGAAGA 16 13 0 CCGTGTACGC 0.992766 -53 CTACGACAAGCCCGCGCATTATACATACTTAACCACCGAACGCA 27 44 0 CCGTTTACCC 0.96951 -194 ATGAGCCTGCCCTGAAAAGTTAACGACAGGCTCCTGAAAAGGA 32 122 1 CCGGTAACCC 0.738979 -33 TCGAATGGTCGCCGCGGATTCTACTTAACTTTGCTGCCCGAGAC 33 26 1 GCGTTTACGC 0.868585 -195 CACTGATGAGCCAGGTTCTGGTACGAAAGCGTGCAAAAAGGGCA 36 58 0 CCGTGTACGC 0.992668 -172 ATTTTGTTGACCGGAAAATGGAACACTTTCCGCAATGCCTGTTG 40 202 0 CCGTGAACCA 0.723314 -99 ACAAACCTGGCCAGACATTGTTACACAACACTCCGGGTAATGCA 43 120 0 CCGTGTACCC 0.985941 -134 ** * ** *** ** Masking position 13 Map Score: 10.7951 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 233 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 TATATGTAAGTGCCGTCAATGGTATCACACCC 1 243 0 TGCCGTCTGG 0.750978 -58 GCACATCTTGTGCTGTCCGTAGCGTGGGCAGC 4 27 0 TGCTGTCTAG 0.761803 -102 CAGGTGATCCTGCTCTCGTTTGC 6 2 0 TGCTCTCTTG 0.969326 -108 CAGGATCACCTGCTCTCGCTTGAAATTATTCT 6 22 1 TGCTCTCTTG 0.969326 -88 TGCTTATCGATGCTGCCGATTGCACAAATTGT 11 196 1 TGCTGCCTTG 0.955927 -105 TTCCCTACAATCCTGCCCATTGTCTGCCAACA 11 265 1 TCCTGCCTTG 0.795779 -36 CTCTTCTTCATGCTCTCTGCTGTAACATTGGC 16 12 1 TGCTCTCCTG 0.958686 -54 TGTGTCCTCTCTTTGGTACTAAGCT 20 10 0 TCCTCTCTGG 0.868014 -16 TACCTAACAATGCTCCCAATCGGGGAGCTACG 27 131 1 TGCTCCCTCG 0.910721 -107 GCGAAATGAGTGCTGTCTCGGGCAGCAAAGTT 33 52 0 TGCTGTCGGG 0.811725 -169 GGATTTGCTCCCGTCGGAGTTAGCACA 41 60 0 TGCTCCCCGG 0.970299 -17 TGTTATGCGGTGATCCCTGTTGTCTTTCGACG 46 48 0 TGATCCCTTG 0.700407 -38 TGTGCTCTCCTCTGTGATGATCTT 50 3 1 TGCTCTCCTG 0.958686 -298 CGAATTGCTCCTTACGGATTATTCAGC 50 284 0 TGCTCCTCGG 0.665396 -17 ******* *** Masking position 1 Map Score: 8.22446 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 379 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 TGATTAACCCTCATTAATCAGTCGGCAAGTCCA 15 225 0 TCATTTCAGC 0.97406 -76 AATAAACGGCTCATTTCTGAGCCGTTTATTCGT 25 30 0 TCATTTGAGC 0.978952 -135 ACGAAAATGATTACTCCTCAGACCCATTACGAT 27 188 0 TTACTTCAGC 0.672092 -50 GTTACCCGCATCATTAATGAGCCTGCCCTGAAA 32 106 1 TCATTTGAGC 0.978952 -49 ACAAAGAAAATCACTGATGAGCCAGGTTCTGGT 36 80 0 TCACTTGAGC 0.957868 -150 TTTGTCATAATCATTGCTGAGACAGGCTCTGTT 36 108 1 TCATTTGAGC 0.978952 -122 GCCATCAGCCTGATTTCTCAGGC 40 1 0 TGATTTCAGC 0.861395 -300 CTGATCGAGGTCATTTTTGAGTGCAAAAAGTGC 48 23 1 TCATTTGAGG 0.871102 -81 CTATAACGCGTCATTTTTCAGCCGACCTTTAAC 50 209 1 TCATTTCAGC 0.97406 -92 ***** **** * Masking position 8 Map Score: 6.88302 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 21 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 AAGAATACTGTTTTTTTTCTTCCTCGAAT 11 8 1 CGTTTTTTTC 0.753454 -293 AATCGTCATACTCTTTTTTTACGTCTGTAAAT 11 234 1 CCTTTTTTTC 0.868231 -67 GGCCTGCGGGCCCTTTTTTCATTGTTTTCAGC 14 33 1 CCTTTTTTCT 0.936949 -79 CGTACAAACTCAGTTTTTTGGTGTACTCTTGC 14 64 1 CGTTTTTTGT 0.800657 -48 TTTGCAATACCGCTATTTTCTTGCCATCAGAT 18 221 0 CCTATTTTCT 0.720595 -31 GACCAGGCGGCGGTTTTTTTATTACAGGCCGG 32 30 1 CGTTTTTTTT 0.757266 -125 TATTTTCAGACTCTTTTTGTTTAAATTAGTTT 33 92 0 CCTTTTTGTT 0.724539 -129 TTTCTCCTCCCTGTTTTTTCCTTCTGTTTATT 35 16 1 CGTTTTTTCT 0.873293 -99 TCATTTGATGCCCTTTTTGCACGCTTTCGTAC 36 50 1 CCTTTTTGCC 0.850573 -180 ATTAAATCGCCGCTTTTTTGATCGCTGGG 37 8 0 CCTTTTTTGT 0.896478 -150 GTTTGTGCAACACTATTTTGTTGACCGGAAAA 40 228 0 CCTATTTTGT 0.60047 -73 CCGGATTAAACGCTTTTTTGCCCGGTGGCATG 43 20 1 CCTTTTTTGC 0.894548 -234 TCTCTCTTTTCCTTATATGCTTA 44 73 0 CCTCTTTTCT 0.684314 -13 GGTTTCGGGCTGTTTTTTTACACGGGGAGCC 45 10 1 CGTTTTTTTC 0.753454 -66 AGAGTTACAGCACTTTTTGCACTCAAAAATGA 48 33 0 CCTTTTTGCC 0.850573 -71 GTTAAATCCTCGCTTTTTTCCTTCCCCGAACT 49 101 1 CCTTTTTTCT 0.936949 -104 * ******** * Masking position 6 Map Score: 12.6812 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 269 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 10 ACACACACGTATCGGCACATATTCCGGGGT 1 12 0 ATCGGCACAT 0.805774 -289 TTTCAAAAAATTCGACACATTTTAAGGGGA 7 153 1 TTCGACACAT 0.953295 -28 ATGTTTTCGGCACATTTCTCCCCAG 8 6 1 TTCGGCACAT 0.943926 -279 AACAAACAGGTTCGGCACATTACTCCGAAA 8 175 0 TTCGGCACAT 0.943926 -110 AAAAAATAAAGGCGACCCATAGTCGCATGG 10 47 0 GGCGACCCAT 0.857508 -76 GCTCCCTATAGTCGAAACATCTGATGGCAA 18 203 1 GTCGAAACAT 0.662311 -49 CGTTTATTTTTTCTACCCATATCCTTGAAG 25 55 1 TTCTACCCAT 0.720367 -110 TCGCTGACAAGTCGACCCATCTGTCCATTG 40 268 0 GTCGACCCAT 0.962625 -33 ATGATAAAGTTTCGACCCATTCTTTATCTC 42 47 1 TTCGACCCAT 0.963338 -36 ********** Masking position 9 Map Score: 5.41022 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 37 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 TTATTCTCCCTTGTCCCCATCTCTCCCACAT 6 47 1 TGTCCCCATC 0.742569 -63 TTAGGCTGCCCGGTCACCATCACGCAAAAAC 13 26 0 CGTCACCATC 0.959153 -48 GAAATGAGTGCTGTCTCGGGCAGCAAAGTTA 33 51 0 CGTCTCGGGC 0.935649 -170 AGCGAACTTATCGTCTCGGGCTACGCCATCG 34 23 0 TGTCTCGGGC 0.884321 -94 GAAGCCAACGCCGTCACAAGCTGAATAGCGA 38 51 1 CGTCACAAGC 0.779163 -250 TCTTAGCGTTCTGTCACCGTCTACGCAGGGG 38 164 0 CGTCACCGTC 0.974082 -137 GGTGACTAAAAAGTCACCAGCCATCAGCCTG 40 22 0 AGTCACCAGC 0.779163 -279 GGTGACTTTTTAGTCACCAGCCTTTTTGCGC 40 35 1 TGTCACCAGC 0.934647 -266 CCAGAACGTATCGTCAGGGTCTGCTTCATAT 42 18 1 TGTCAGGGTC 0.780737 -65 GCATCAGAAATGGTCACCATCAACTTCTTTA 50 57 0 TGTCACCATC 0.925071 -244 ATTCAGCCTCCTGTCTGGGTCAGCCGAATCC 50 260 0 CGTCTGGGTC 0.729551 -41 TCGGTCACGGTCCATTAATACG 51 2 1 CGTCACGGTC 0.969242 -40 * ********* Masking position 4 Map Score: 5.38267 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 529 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 12 CGTTTCAGCCCCAGGTGCCTTTCTTGAGGCAAT 7 92 1 CCAGGTGCTC 0.932998 -89 GTAACATTGGCAGGGAGCTTTGCTATTTCTGGA 16 33 1 CAGGGAGCGC 0.906911 -33 AAAGCTAAAACCAGGAGCTATTTA 31 112 1 CCAGGAGCTT 0.896213 -14 TCCTTTTCAGGAGCCTGTCGTTAACTTTT 32 136 0 TCAGGAGCTC 0.949863 -19 CCATATCTCCAGGATCGGGGCATCTCACCCC 33 200 0 CCAGGATCGC 0.927793 -21 ATCCTGGAACTCGGCTACCTGATTT 34 102 0 CCTGGAACGC 0.669482 -15 GCCAGGAGCATAGCTAACTATGTG 38 2 1 CCAGGAGCGC 0.993246 -299 TGGCAAACATCCAGGAGCAAAGCTA 38 286 1 CCAGGAGCGC 0.993246 -15 CTGTAAGGCGCCAGTAGCGTTTCACACTGTTTG 40 65 1 CCAGTAGCTC 0.896213 -236 GCTAACTCCGACGGGAGCAAATCC 41 63 1 ACGGGAGCTC 0.822053 -14 GAATAATCCGTAAGGAGCAATTCG 50 287 1 TAAGGAGCTC 0.744813 -14 ******** ** Masking position 8 Map Score: 5.99459 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 228 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 TTTTTCGCGTCAGGTAACGCCCATCGTTTAT 8 95 1 CAGGAACGCC 0.914455 -190 CTTATCGTCTCGGGCTACGCCATCGCGTGGC 34 17 0 CGGGTACGCC 0.967907 -100 AATCGTTTTACGGGCAAGGCCATAAAAACAA 37 81 0 CGGGAAGGCC 0.990847 -77 CGACGGAGGCCTGGATAGGCCAGGCTCCAAC 38 102 0 CTGGTAGGCC 0.837142 -199 CACAACACTCCGGGTAATGCATTCCAATACT 43 110 0 CGGGAATGCA 0.928964 -144 AATAGATCAGCGGGGAACGCAGGATCGCTGG 45 40 0 CGGGAACGCA 0.981113 -36 ATTGCTGTGTCGGGTAAGCCATTACGCTATC 49 61 1 CGGGAAGCCA 0.918558 -144 TATTTCAGTTCGGGGAAGGAAAAAAGCGAGG 49 108 0 CGGGAAGGAA 0.884007 -97 **** ****** Masking position 7 Map Score: 2.75757 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 209 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 14 TGAAACGGTTAATGGCGAGATAATTTGCGGAAA 7 66 0 ATGGGAATAA 0.836966 -115 CCTTATCGGCAGCGGGGTAATGAGCGTAACCAA 8 60 0 ACGGGTATGA 0.690999 -225 CGTATAAGGGAGCGGTGAGATAAACGATGGGCG 8 112 0 ACGGGAATAA 0.975947 -173 CGTAATTTGAACCGGCAAGATAATGCCGAAGTT 8 239 0 ACGGAAATAA 0.727705 -46 GCAATGTTACAACGGGGAAAAAATAAAGGCGAC 10 61 0 ACGGGAAAAA 0.837543 -62 ATTATTGCGGAATGGCGAAATAAGCACCTAACA 15 80 0 ATGGGAATAA 0.836966 -221 ATATCCTTGAAGCGGTGTTATAATGCCGCGCCC 25 73 1 ACGGGTATAA 0.928706 -92 CTAAAAGATAAACGAGGAAACAA 29 15 1 ACGAGAACAA 0.801669 -13 ACACGGATAAATCGGTGATATCACCACATCAAC 35 76 0 ACGGGAATCA 0.874458 -39 CGATCAAAAAAGCGGCGATTTAATCGTTGCACA 37 16 1 ACGGGATTAA 0.928706 -142 GCTTGTTTCTATCGACGACTTAATATACTGCGA 40 119 1 ACGAGATTAA 0.789224 -182 GTTTCCCGGAACCGAGGTCACAACATAGTAAAA 43 162 1 ACGAGTACAA 0.564781 -92 GAAGGAAAAAAGCGAGGATTTAACACTGTGTCG 49 92 0 ACGAGATTAA 0.789224 -113 * *** ** **** Masking position 1 Map Score: 3.87313 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 306 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 15 TTTTGCGTGATGGTGACCGGGCAGCCTAAA 13 28 1 TGGTGACCGG 0.865155 -46 TTGGTCGCCCGAGAAGTTACG 23 2 1 TGGTCGCCCG 0.944532 -30 TTTTGTCGAATGGTCGCCGCGGATTCTACT 33 21 1 TGGTCGCCGC 0.892997 -200 GCCGCTTTTTTGATCGCTGGG 37 2 0 TGATCGCTGG 0.959495 -156 AGAAAAGATTTGTTCGTTGGAGCCTGGCCT 38 87 1 TGTTCGTTGG 0.589056 -214 GAAATCAGGCTGATGGCTGGTGACTTTTTA 40 17 1 TGATGGCTGG 0.932453 -284 AACACTATTTTGTTGACCGGAAAATGGAAC 40 222 0 TGTTGACCGG 0.75648 -79 TAACCGTTTGTGATCGCCGGTAGCACCATG 43 48 0 TGATCGCCGG 0.978287 -206 GGGGAACGCAGGATCGCTGGCTCCCCGTGT 45 30 0 GGATCGCTGG 0.816883 -46 TGTATCACACTGTTCGCCCGGCAGGCAAAA 49 32 0 TGTTCGCCCG 0.891839 -173 GCGACACAGCTTGTGGCTGGTTTATCATCA 49 144 1 TTGTGGCTGG 0.633062 -61 ********** Masking position 4 Map Score: 3.66649 Number of sites scoring better than the average of aligned sites = 1161 Number in coding regions = 1100 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207