AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_ecoli_reg_100.orf -o00310_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: caiA 30 probable carnitine operon oxidoreductase Input sequences: #1 caiC 58 probable crotonobetaine/carnitine-CoA ligase #2 caiB 35 l-carnitine dehydratase #3 caiT 300 probable carnitine transporter #4 hlpA 121 histone-like protein, located in outer membrane or nucleoid #5 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #6 dnaE 36 DNA polymerase III, alpha subunit #7 ldcC 98 lysine decarboxylase 2, constitutive #8 ybcR 300 orf, hypothetical protein #9 entC 300 isochorismate hydroxymutase 2, enterochelin biosynthesis #10 lipB 166 protein of lipoate biosynthesis #11 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #12 ybeX 89 putative transport protein #13 ybeZ 113 putative ATP-binding protein in pho regulon #14 sdhC 300 succinate dehydrogenase, cytochrome b556 #15 ybjU 36 putative arylsulfatase #16 poxB 132 pyruvate oxidase #17 dmsA 300 anaerobic dimethyl sulfoxide reductase subunit A #18 htrB 224 heat shock protein #19 sohB 219 putative protease #20 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #21 ydbO 284 orf, hypothetical protein #22 ydcH 72 orf, hypothetical protein #23 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #24 rspA 205 starvation sensing protein #25 sppA 160 protease IV, a signal peptide peptidase #26 msbB 119 suppressor of htrB, heat shock protein #27 wcaA 34 putative regulator #28 BIME92 24 BIME #29 wza 300 putative polysaccharide export protein #30 yegQ 146 orf, hypothetical protein #31 gatD 47 galactitol-1-phosphate dehydrogenase #32 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #33 gatZ 28 putative tagatose 6-phosphate kinase 1 #34 gatY 197 tagatose-bisphosphate aldolase 1 #35 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #36 atoB 30 acetyl-CoA acetyltransferase #37 pdxB 98 erythronate-4-phosphate dehyrogenase #38 glyA 300 serine hydroxymethyltransferase #39 yqeF 251 putative acyltransferase #40 agaS 191 putative tagatose-6-phosphate aldose/ketose isomerase #41 yhbU 208 putative collagenase #42 yiaM 117 orf, hypothetical protein #43 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #44 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase #45 pepE 211 peptidase E, a dipeptidase where amino-terminal residue is aspartate #46 cadA 79 lysine decarboxylase 1 #47 cadB 300 transport of lysine/cadaverine #48 ampC 62 beta-lactamase; penicillin resistance #49 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit #50 hfq 85 host factor I for bacteriophage Q beta replication, a growth-related protein #51 hflX 75 GTP - binding subunit of protease specific for phage lambda cII repressor #52 hflK 85 protease specific for phage lambda cII repressor #53 sgaT 291 orf, hypothetical protein #54 yjfG 175 putative ligase #55 lplA 27 lipoate-protein ligase A #56 smp 105 orf, hypothetical protein Motif number 1 ACGCGTGGCGTCAGTCGGCTTGCCT 1 2 1 CGCGGGCCGT 0.657401 -57 GTTTGTTATTGGGCGGGCGCTAGTCAGGCAAGCC 1 27 0 GGGCGGCTGT 0.853933 -32 TTCTTTGCGTGGCCCGGCGATCTTATATTGATCG 4 58 0 GGCCGGCTTT 0.827569 -64 CTTACGATTGCGGCAGGCCGTGTTATTATTGTCG 5 53 1 CGGCGGCTTT 0.966228 -52 AAGGGTCACTTCGGTGGCCCTTTTTTATCGCCAC 7 29 1 TCGGGGCTTT 0.704959 -70 AAAAACCCGCTCGACGGCGGGTTTAAGCTGTGTG 8 156 0 TCGAGGCGTT 0.396521 -145 TTTGCCAGGCATTTGACTGGCAGACG 12 3 1 TGCCGGCTGA 0.865993 -87 CCCACCGGAACGGCAGGCCTGAGAA 13 2 0 CGGCGGCGGA 0.927188 -112 CCTGCCGTTCCGGTGGGCCTTGTTTTTTCTCTCT 13 19 1 CGGTGGCTTT 0.558079 -95 TTCCGGAGACCTGGCGGCAGTATAGGCTGTTCAC 14 67 0 CTGGGGCTTA 0.605289 -234 GTTACAACGCTGGGTGGCTCGGGATTGCAGGGTG 14 101 0 TGGGGGCGGA 0.792146 -200 GCGCCTGCGGGCGCTTTTTTTGTCTCCC 17 5 1 CTGCGGCTTT 0.773032 -296 TGCCAGGCCGCCGATCGCTGTCGT 17 287 0 TGCCGGCCGA 0.723713 -14 AAAGTAAAAATCCGCGGCATGATATAGCAATTAT 18 35 1 TCCGGGCGTA 0.466145 -190 AAGCGCAATGCGCCCGGCAATCTATACACAAAAT 20 34 1 CGCCGGCTTA 0.937921 -241 AAAAGCCGCCTGGCTGGCGGCTTAGGAAAGT 23 8 0 TGGCGGCCTA 0.892963 -55 CACGCTACCGCCCCTGGCTTTTTAGCTACCAATA 29 99 0 CCCCGGCTTA 0.808229 -202 TTGATTTCATCCGCAGGCTATTGACAGAATAATT 29 158 0 CCGCGGCTGA 0.836967 -143 AAGGTAAATGTGCATGGCGACATTGCTATTAATA 29 237 1 TGCAGGCCTT 0.440788 -64 CAACAACCCACGCCCGGCATCGTAA 30 2 0 CGCCGGCCTA 0.868859 -145 TGTAGCGCTGTGGGGGGCTCTGGTAAAGCGCCGG 30 40 0 TGGGGGCTGT 0.846385 -107 CCCACTTTAAGGGCGGGCATTGTAGCGCTGTGGG 30 60 0 GGGCGGCTTA 0.900877 -87 GCTTCCCTATCGGGAGGCCGTTTTTTTGCCTTTC 34 71 1 CGGGGGCTTT 0.927962 -127 CCATTTACATTGCAGGGCTATTTTTTATAAGATG 38 27 0 TGCAGGCTTT 0.642533 -274 CTTCAGGCTACGCAAGGCTTTGGAGAATAAAGAG 38 145 0 CGCAGGCTGA 0.634879 -156 TTAAACAAAATGGAGGGCAATTTACCATAAACCA 39 34 1 TGGAGGCTTA 0.772922 -218 TCTTAATGCCGCGCTGGCGATGTTAGGAAAATTC 43 70 1 GCGCGGCTTT 0.717135 -170 TTCCTGGAATTTGCTGGCATGTTATGCAATTTGC 43 101 1 TTGCGGCGTA 0.610473 -139 TAAGAAATCACGGGAGGCATGCTACCACTGCGAA 45 173 0 CGGGGGCGTA 0.899134 -39 GGCCCGCCATAGGCGGGCCGGATTTACATTGGCG 48 16 0 AGGCGGCGTT 0.54652 -47 GGCCCGCCTATGGCGGGCCGTTTTGTATGGAAAC 48 31 1 TGGCGGCTTT 0.95006 -32 AATCCGTAATTTGCTGGCGCGATTCACCTGAGCG 54 79 0 TTGCGGCGTT 0.610473 -97 **** *** * ** Masking position 7 Map Score: 27.186 Number of sites scoring better than the average of aligned sites = 2905 Number in coding regions = 2712 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 2 CTCACCCTAACCCTCTCCCCAAAGGGG 9 8 0 CCCTCTCCCC 0.989836 -293 CTGGCTGTTCCCCTCACCCTAACCCTCTCC 9 20 0 CCCTCACCCT 0.976504 -281 CGAACATTAACCCTCACCCCAGCCCTCACC 9 58 1 CCCTCACCCC 0.989836 -243 CTCACCCCAGCCCTCACCCTGGAAGGGAGA 9 70 1 CCCTCACCCT 0.976504 -231 CCGTTCTGCCCCCTCTCCCTTCCAGGGTGA 9 83 0 CCCTCTCCCT 0.976504 -218 CGGGTAACTCCCCTCTCCTCGCTGTGATAT 10 39 1 CCCTCTCCTC 0.937756 -128 CCCATCCCTTCCCCCTCCGTCAGATGAACT 16 74 1 CCCCCTCCGT 0.935179 -59 ATTTTTCACACCCTCTCAGCATGCAGTCGT 29 54 0 CCCTCTCAGC 0.931467 -247 TTACCAGAGCCCCCCACAGCGCTACAATGC 30 48 1 CCCCCACAGC 0.853889 -99 GGGGGCACTCCCCTAACCGCTTCATCAGGT 30 91 1 CCCTAACCGC 0.872919 -56 ********** Masking position 7 Map Score: 13.1793 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 73 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 TATTTGCTCCTGAAAAATTTATGTAGC 2 19 0 TCCTGAAAAA 0.97043 -17 TTCGCAAAAGTTCTGAAAAAGGGTCACTTC 7 11 1 TTCTGAAAAA 0.945215 -88 GTGTTCCTCCTGGAAAATCCTTCCTTA 7 82 0 TCCTGGAAAA 0.884632 -17 TTAATATCCCGTCTGAAAAACGAAAATCCT 22 47 1 GTCTGAAAAA 0.764677 -26 CTGGCATCAGTCCTAAAAAAATTGATTTCA 29 183 0 TCCTAAAAAA 0.721129 -118 ATCACATTCTTTCTGAAAAACACCAAAGAA 38 61 0 TTCTGAAAAA 0.945215 -240 GGACTTTCCCTTCTGAATAAAGGTCTTCGT 43 179 1 TTCTGAATAA 0.686757 -61 AAATTCTCCTGTAAAAAACGGAATAT 45 7 1 TCCTGTAAAA 0.901214 -205 AACCTTTCGATTCTGAAAAAATTGCGCACG 50 32 0 TTCTGAAAAA 0.945215 -54 GTCATTGCCTTCCTGAAAAAATAGTGTCAG 53 64 0 TCCTGAAAAA 0.97043 -228 TAAGGCTCCTGTAAAATCGTTCGAAG 56 7 1 TCCTGTAAAA 0.901214 -99 ********** Masking position 7 Map Score: 10.5265 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 82 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 AAATTAACGAAAAAACGCCCTCTATTCACC 3 115 1 AAAAACGCCC 0.934113 -186 TATCCTGATACAAAACGGCATCTCCGTGGA 10 94 0 CAAAACGGCA 0.88194 -73 GTTAGTTAATCAAAACGCCGTCGTTAATCA 12 50 0 CAAAACGCCG 0.932832 -40 CACGCCACAGGAAAAAGGCGCAAGCATTGC 13 70 0 GAAAAAGGCG 0.703424 -44 TTCCAGATGCGAAAACGACACGTTACAACG 14 126 0 GAAAACGACA 0.561338 -175 GTGGTTTGGTAAAAACGACAGCGATCGGCG 17 273 1 AAAAACGACA 0.786886 -28 TGCAGTTGTTAAAAAAGCCGCCTGGCTGGC 23 24 0 AAAAAAGCCG 0.888259 -39 AGTGATCACAAAAAAAGGCGTATATTTGCG 24 98 0 AAAAAAGGCG 0.872508 -108 ATAAAGATCGAAAAAAGCCGGAGTGATCAC 24 119 0 AAAAAAGCCG 0.888259 -87 GCACCAAATAAAAAAAGCCGGTACTGACTG 26 36 0 AAAAAAGCCG 0.888259 -84 TGAAAGGCAAAAAAACGGCCTCCCGATAGG 34 76 0 AAAAACGGCC 0.924275 -122 TAACGATCACAAAAACGACAATATGAAAAT 34 117 0 AAAAACGACA 0.786886 -81 GTCTTATGCCAAAAACGCCACGTGTTTACG 43 15 1 AAAAACGCCA 0.929008 -225 GATATAAAAGCAAAACGCCACGTAAACACG 43 35 0 CAAAACGCCA 0.896663 -205 ATCTCCAGGTAAAAAAGGCCCCTCCCAACA 46 54 0 AAAAAAGGCC 0.822457 -26 GGTTTCCATACAAAACGGCCCGCCATAGGC 48 36 0 CAAAACGGCC 0.890029 -27 ********** Masking position 5 Map Score: 16.3864 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 565 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 5 GGTTCCTGCGAGATGGGAAAGTAAAAATCCGC 18 18 1 AGAGGGAAGT 0.952647 -207 GAGATGTTATTGCAGCGAAAGTATGACAAAGT 19 130 0 TGCGCGAAGT 0.875453 -90 TTGTTCTGTAAGCCGGGTAAGCGCAATGCGCC 20 16 1 AGCGGGAAGC 0.938464 -259 TTTTATTTGGTGCGGGGCAAGTTGCGCCGCTA 26 53 1 TGCGGGAAGT 0.98821 -67 TTCAATTAACTGCAAGGTAAATGTGCATGGCG 29 224 1 TGCAGGAAAT 0.599569 -77 TTTTTACCTGAGGGGGAGGTTATCCCCCTT 31 9 1 TGAGGGAGGT 0.896006 -39 ACCCACCAATAGAGGGGTAGATAGGGCGTTAA 39 84 0 AGAGGGAGAT 0.492861 -168 ACCTTTATTCAGAAGGGAAAGTCCGTTCCAAA 43 171 0 AGAGGGAAGT 0.952647 -69 CAGTATAGTCTGATGGATAAGTCTGAAATTTG 49 169 0 TGAGGAAAGT 0.626801 -126 AGCCACGTACTTCAGGGTAAGTACCTGAAAGT 49 244 0 TTCGGGAAGT 0.825863 -51 TAAATAGATCAGCGGGGAACGCAGGATCGCTG 51 41 0 AGCGGGACGC 0.706349 -35 TTTGACTTTTTGCCAGGGAAGTTGTTGTTGAT 53 99 1 TGCAGGAAGT 0.89997 -193 CCATAAACATTGCAGGGAAAGTTTT 54 4 0 TGCGGGAAGT 0.98821 -172 TTTACGCATATGTCGGGCAAGTGAGAAACGCA 54 122 0 TGTGGGAAGT 0.87985 -54 AATCGTTCGAAGCAGGGAAAATAACGCATGAG 56 25 1 AGCGGGAAAT 0.904346 -81 *** *** **** Masking position 9 Map Score: 9.21143 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 290 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 AAAATAAATATTCGTTTTCACAGTGGAATTAACT 3 276 1 TTCGTTTAGT 0.477198 -25 TGTATTTGTAGTGGTGTTTTCAATACTCGGTAGC 8 50 1 GTGGTGTAAT 0.501262 -251 GTTGCATCTGGTTGTGGTTACAATGAAAATGAGA 9 157 0 GTTGTGTAAT 0.828158 -144 ATCAGGGATTTTCGTTTTCATAATGGCTCACTCA 17 211 0 TTCGTTTAAT 0.621729 -90 GACGTTGTCTGTCGCGCTGCCAGTGTACTTTATG 19 25 1 GTCGCGTAGT 0.658089 -195 CTTTTTATGATTCGCGATTTAACTATTAGCAACA 21 38 0 TTCGCGTACT 0.712342 -247 ACATACAAAATTTGTGATTTTACTTAACTATTGT 21 189 1 TTTGTGTACT 0.774949 -96 AACAATGTGATTCGTGTTTTTAATTAATTCACGA 21 236 1 TTCGTGTAAT 0.929162 -49 AAGGCGTATATTTGCGCTGTGAATGGTTGACAAA 24 80 0 TTTGCGTAAT 0.784325 -126 ATTAACTCCTGTCGTGATATTTATTCACAAAATT 25 14 1 GTCGTGTTAT 0.686034 -147 TATTGTCGTTTTTGTGATCGTTATCTCGATATTT 34 124 1 TTTGTGTTAT 0.6963 -74 GTTTGTGTTACCTGTATGAGACGAG 37 84 0 TTTGTGTTGT 0.560103 -15 TCTTTTCAGGTTTGTGATGCAAATTTTTCACTTC 38 91 0 TTTGTGTAAT 0.890642 -210 GCATATTTCCTTTGTGATAAAAATCACTTTTTTT 39 165 1 TTTGTGTAAT 0.890638 -87 AATAAAGGTCTTCGTGGTTATACTTCTGCTAATA 43 194 1 TTCGTGTACT 0.847231 -46 AAGTGTGTATTTTGTGTTAAAAATATGCAAACAA 44 118 0 TTTGTGTAAT 0.890641 -72 TTGTCTCGCCGTCGCGTTGCGAGTAGACTTC 49 8 0 GTCGCGTAGT 0.658089 -287 GTTTGTGCTCCATATTTGTTATGCG 52 71 0 TTTGTGTTAT 0.6963 -15 GGATAATTGTTTCGTTGTGTGAATCCCACTCTAT 53 189 1 TTCGTTTAAT 0.621729 -103 ****** * *** Masking position 8 Map Score: 7.26281 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 147 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 CAACTCGGGGTTGCATCTGGTTGTGGTTACAA 9 168 0 TTGCACTGGT 0.847571 -133 AACCGAAACTGGATAGATAACTAC 11 3 1 CCGAACTGGT 0.719249 -22 CGTGTCGTTTTCGCATCTGGAAGCAGTGTTTT 14 134 1 TCGCACTGGA 0.971938 -167 GCAGCCAATACCGCATCAGGGATTTTCGTTTT 17 227 0 CCGCACAGGA 0.953887 -74 TGCGGTGTTATCGCCCCAGGCTGATTGAAATG 19 90 0 TCGCCCAGGT 0.752001 -130 GGCTCACAGTTTACAACAGGCATGTTAAGCCG 19 169 0 TTACACAGGA 0.374892 -51 TAACATCCATTCGCAGCCGGTACGCAGTCAGT 26 12 1 TCGCACCGGA 0.961067 -108 TTTGCCTTATCCGAAACTGGAAAAGC 26 104 1 CCGAACTGGA 0.870512 -16 AGACACGCTACCGCCCCTGGCTTTTTAGCTAC 29 104 0 CCGCCCTGGT 0.774192 -197 TATGTTTACACCGCATCCGGCATAAAAACACG 34 25 1 CCGCACCGGA 0.952999 -173 AATAAAGAGCTTGCAACCGGAAACGGATTTCT 38 122 0 TTGCACCGGA 0.912195 -179 AGGATGATTGTTGAAACAGGGAGTAAAACTC 41 10 0 TTGAACAGGA 0.714459 -199 ATGTCGCACATTGCTTCTGGAAAGTGATTTGA 45 114 0 TTGCTCTGGA 0.748739 -98 GTAAAATCGTTCGAAGCAGGGAAAATAACGCA 56 21 1 TCGAACAGGA 0.856014 -85 CTTGTATCCATTGCTTCTGGCAACATTAAGTC 56 62 1 TTGCTCTGGA 0.748755 -44 ***** **** * Masking position 7 Map Score: 7.44071 Number of sites scoring better than the average of aligned sites = 1516 Number in coding regions = 1032 Number in noncoding regions = 484 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 8 TCATTTATATTTTCGGTCGCTAACCTAAAAGCAAAC 9 235 0 TTTCCGCTCT 0.903249 -66 TCGGGATTTCCTTCCTCCGGTCTGCTTGCGGGTCAG 14 197 0 CTTCCGGTCT 0.686851 -104 GCGCCTGCGGGCGCTTTTTTTGTCTCCCTT 17 5 1 CTGCCGCTTT 0.765776 -296 TCTGCCTTGGCTGCGTTCGCTCCCCCGAATCACTTA 20 122 0 CTGCCGCTCC 0.990164 -153 CGACGCCTGCATTCGCACCGCCCC 28 7 1 CTGCCGCACC 0.921009 -18 GGGTTGTTGGCGTCCGGCGCTTTACCAGAGCCCCCC 30 27 1 CGTCCGCTCC 0.886648 -120 CACGCGCACTTTGCTACGGCTTCCCTATCGGGAGGC 34 53 1 TTGCGGCTCT 0.815928 -145 CACGTAAGGTTTGCAACCACTAACCCACCAATAGAG 39 102 0 TTGCCACTCC 0.765776 -150 TTAAAAGTATTTTCCGAGGCTCCTCCTTTCATTTTG 46 11 1 TTTCGGCTCC 0.815928 -69 AAGTTACGGTCTGCGAACGCTATTCCACTGCTCCTT 49 212 0 CTGCCGCTCC 0.990164 -83 TGACTCCACGCTTCAGACGCTACGCCG 52 2 0 CTTCCGCTCC 0.978525 -84 GTTAAGATTGTTGCGGTCGCTTTACTCCATAAACAT 54 26 0 TTGCCGCTCT 0.953757 -150 **** **** ** Masking position 4 Map Score: 5.97017 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 439 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 CGCAGGACATCACATTGCGCTTATGCGAAT 9 113 1 CACATTGCGC 0.979061 -188 CAAGAGTTGACATAGTGCGCGTTTGCTTTT 9 215 1 CATAGTGCGC 0.934263 -86 GATTGCCGGGCGCATTGCGCTTACCCGGCT 20 26 0 CGCATTGCGC 0.925481 -249 TTTGTTACAGCACAGTCCGCAATTCCTGCT 25 63 1 CACAGTCCGC 0.924671 -98 TGGTGCGGGGCAAGTTGCGCCGCTACACTA 26 60 1 CAAGTTGCGC 0.857412 -60 GAAGCCGTAGCAAAGTGCGCGTGTTTTTAT 34 46 0 CAAAGTGCGC 0.972907 -152 CAGAAATTTGCACAGTGCGCAATTTTCTGC 35 28 1 CACAGTGCGC 0.986696 -168 CGATTCTGAAAAAATTGCGCACGATACGTC 50 25 0 AAAATTGCGC 0.716565 -61 ********** Masking position 6 Map Score: 4.68418 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 231 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 10 ATGTTAACAAAAATAAAACAAACGGGAACGCAAAATA 3 245 1 AAAAAAAAGA 0.805262 -56 TGTTCTCCACAAAGGAATGTAGTGGTAGTGTAGCGAT 4 12 1 AAAGAAAGGA 0.951548 -110 TATCATCTACAAATTAAACAAAATGGAGGGCAATTTA 39 21 1 AAATAAAAGA 0.805262 -231 AAGAAAAGATAAAGGAAGCAAAAGGGAT 40 2 0 AAAGAAAAGA 0.954545 -190 CAATGGAGAAAAAAGAAATAAAACGAAATTTGTGATC 40 44 0 AAAGAAAAGA 0.954545 -148 TCACCAAGTGAAATGAAACGAAAGGCAAGTGAAAGCG 40 124 1 AAAGAAAAGA 0.954545 -68 CCATATCAGAAAAATAACATAGCGGTATAAATCAACA 41 48 1 AAATAAAGGA 0.794541 -161 ACTTAAGGTCAAAAAAACAGAAGGGTAAAAA 44 5 0 AAAAAAAAGA 0.805262 -185 ACATGGGACAAAATGAAAGGAGGAGCCTCGGAAAATA 46 18 0 AAAGAAAGGC 0.787161 -62 CCAAATTCAAAAATGAAATTAGGAGAAGAGC 47 280 1 AAAGAAAGGA 0.951548 -21 TCAATTAACTAAATGAATTTAAATGGATAATTGTTTC 53 165 1 AAAGAAAAGA 0.954545 -127 *** *** ** * * Masking position 7 Map Score: 5.62552 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 28 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 CGTGGCGTCAGTCGGCTTGCCTGACTAGCGCCC 1 14 1 GCGTTGCCTG 0.952984 -45 CCAACGGCGGGGACGTCTGCCAGTCAAATGCCT 12 17 0 GAGCTGCCAG 0.856372 -73 GACGTTGTCTGTCGCGCTGCCAGTGTACTTTAT 19 25 1 GCCCTGCCAG 0.780403 -195 ATGACTTTGGGGCTTTATGCCTGAAACAGAAGG 19 56 1 GCTATGCCTG 0.968864 -164 GAGATCCCCGGGCCGTATGCCCGTTTATTTCTG 20 196 0 GCGATGCCCG 0.950901 -79 TGCATCGCTTGTCGTGATGCATGAAATCTACGC 24 172 0 GCTATGCATG 0.690664 -34 GCGGTAGCGTGTCTGGATGCCTGAAAGACCAGT 29 122 1 GCGATGCCTG 0.986471 -179 AATTTTTTTAGGACTGATGCCAGTTAAATTTTT 29 190 1 GATATGCCAG 0.855442 -111 TGAAATCTTCGCAAGTATGCCTGGCCGCGAGAT 37 27 1 GAGATGCCTG 0.959215 -72 TTATCACAAAGGAAATATGCCTGAGCAGCAGTC 39 152 0 GAAATGCCTG 0.753122 -100 AATCGTCTACGCCAGAACGCCTGGGTAATGTTA 42 17 1 GCGACGCCTG 0.926022 -101 ACCATTTTTTGACTTTTTGCCAGGGAAGTTGTT 53 92 1 GCTTTGCCAG 0.836067 -200 * * * ******* Masking position 10 Map Score: 5.64055 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 513 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 12 ACTCCTTACCATCCCATTTGCACCGGAGGGT 4 96 0 ATCCCATTGC 0.911592 -26 GAAAACGAAAATCCCTGATGCGGTATTGGCT 17 226 1 ATCCCTATGC 0.911592 -75 ATGACAAAGTATCCATTTTGCGGTGTTATCG 19 109 0 ATCCATTTGC 0.86509 -111 ACGGCTTAACATGCCTGTTGTAAACTGTGAG 19 168 1 ATGCCTTTGT 0.780124 -52 ATGAAATAGAATACCTTTTGTCAGCTGACAC 24 47 0 ATACCTTTGT 0.705352 -159 TTTTTATCCCTCTTGCATACACCGTT 35 180 0 ATCCCTTTGC 0.984942 -16 ATCCCTTTTGCTTCCTTTATC 40 1 1 ATCCCTTTGC 0.984942 -191 GTGATAATTTAGCCCTCTTGCGCACTAAAAA 49 126 1 AGCCCTTTGC 0.938584 -169 TTATGCGGTGATCCCTGTTGTCTTTCGACGC 52 47 0 ATCCCTTTGT 0.955431 -39 ****** **** Masking position 9 Map Score: 5.70116 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 79 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 13 TGGTAGTGTAGCGATGACTTTAGGCGATCAATAT 4 34 1 GCGACTTAGG 0.974853 -88 GTTGCAGATTGCGTTACCTCAAGAGTTGACATAG 9 196 1 GCGCCTCAGA 0.855608 -105 CCTGTGACAGGTGTGACCTTAAGTTGGGAGAATA 25 136 1 GTGCCTTAGT 0.678583 -25 AGGCATACTTGCGAAGATTTCAGGTATAAGGATA 37 15 0 GCGATTTAGG 0.791685 -84 CCAAAGCCTTGCGTAGCCTGAAGGTAATCGTTTG 38 156 1 GCGCCTGAGG 0.941617 -145 CGTTTTGATAGCGCAACCTTCAGGAAAAATT 41 188 1 GCGCCTTAGG 0.988458 -21 AGCTATTCCTTGAGGCTATGTCTGT 42 103 0 GCTCCTTAGG 0.860044 -15 AACATCGCCAGCGCGGCATTAAGATTACAGATAT 43 60 0 GCGCATTAGA 0.886289 -180 GTGCTAAGATGCGGAGACTTAAGGTCAAAAAAAC 44 24 0 GCGACTTAGG 0.974853 -166 GTTTCTGTAAGTGAGAACTTGAGGTTTTTTATTA 47 141 0 GTGACTTAGG 0.895372 -160 ATGTGTACAATTGAGACGTATCGTGC 50 3 1 GTGAATTAGA 0.437827 -83 ATTCACCTGAGCGCAACATTGAGATTATTTGTTA 54 58 0 GCGCATTAGA 0.886289 -118 *** **** *** Masking position 12 Map Score: 4.51886 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 157 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 14 TCAAACCGTGGCGATAAAAAAGGGCCACCG 7 40 0 GCGATAAAAA 0.692835 -59 TGGGGATAAAGAGAGAAAAAACAAGGCCCA 13 32 0 GAGAGAAAAA 0.769502 -82 GGGAAGGGATGGGAGAGAAAGGAGGCACTA 16 57 0 GGGAGAGAAA 0.888348 -76 CGGTATCAAAGGGAGACAAAAAAAGCGCCC 17 19 0 GGGAGACAAA 0.936071 -282 TTTTGGTTGCGGGCGAAAAAATGCGACAAT 18 166 1 GGGCGAAAAA 0.865101 -59 CTCATAAGCCGGGAGAACAACCT 27 22 1 GGGAGAACAA 0.865101 -13 GTATGCAAGAGGGATAAAAA 35 186 1 GGGATAAAAA 0.894015 -10 GAAAGTTCAATGGAGAAAAAAGAAATAAAA 40 58 0 TGGAGAAAAA 0.728496 -134 TGTTGAAACAGGGAGTAAAACTC 41 4 0 GGGAGTAAAA 0.812273 -205 CAACGCGACGGCGAGACAAATTTTACGCAG 49 23 1 GCGAGACAAA 0.796557 -272 ACGTGGCTGTGGGATAAAAACAATCTGGAG 49 268 1 GGGATAAAAA 0.894015 -27 ********** Masking position 9 Map Score: 4.32567 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 181 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 15 GTTATCACATTCAGGAGATGGAGAACC 16 116 1 TAGGAGAGAG 0.903422 -17 TATTGGCTGCTGAGGTGAGTCGCCGTGGTTTGG 17 249 1 TAGGTGATGC 0.935085 -52 ATGTGAAACATCTGGAGAGTAGCG 21 2 0 TTGGAGATGC 0.812345 -283 AACCGCTTCATCAGGTGAAGCGGATCTGACCTG 30 105 1 TAGGTGAGGG 0.937391 -42 TGGGGATTTATAAGGAGAATGAGCGGCTATGCA 35 55 0 TAGGAGATAG 0.87902 -141 GTTAGCTGAGTCAGGAGATGCGG 38 288 1 TAGGAGAGGG 0.96615 -13 CCTTGCGGATTCAGGAGACTGAC 44 177 1 TAGGAGATAC 0.899999 -13 AAAAATGAAATTAGGAGAAGAGC 47 288 1 TAGGAGAGGC 0.972493 -13 AATGTTGCGCTCAGGTGAATCGCGCCAGCAAAT 54 72 1 TAGGTGATGC 0.935085 -104 * ****** * ** Masking position 8 Map Score: 2.35376 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 24 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678