AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00380_ecoli_reg_100.orf -o00380_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 Input sequences: #1 caiC 58 probable crotonobetaine/carnitine-CoA ligase #2 caiB 35 l-carnitine dehydratase #3 caiA 30 probable carnitine operon oxidoreductase #4 caiT 300 probable carnitine transporter #5 surA 52 survival protein #6 imp 254 organic solvent tolerance #7 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #8 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #9 entC 300 isochorismate hydroxymutase 2, enterochelin biosynthesis #10 sdhC 300 succinate dehydrogenase, cytochrome b556 #11 potF 300 periplasmic putrescine-binding protein; permease protein #12 ybjO 59 orf, hypothetical protein #13 ybjF 40 putative enzyme #14 hemA 213 enzyme in alternate path of synthesis of 5-aminolevulinate #15 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #16 tynA 247 copper amine oxidase (tyramine oxidase) #17 ydbO 284 orf, hypothetical protein #18 katE 182 catalase; hydroperoxidase HPII(III) #19 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #20 atoB 30 acetyl-CoA acetyltransferase #21 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #22 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #23 cvpA 165 membrane protein required for colicin V production #24 ygcA 56 putative enzyme #25 yqeF 251 putative acyltransferase #26 pepP 25 proline aminopeptidase P II #27 ygfB 161 orf, hypothetical protein #28 epd 284 D-erythrose 4-phosphate dehydrogenase #29 yhdT 108 orf, hypothetical protein #30 dam 106 DNA adenine methylase #31 tnaA 205 tryptophanase #32 yigN 140 putative alpha helix chain #33 ubiE 94 2-octaprenyl-6-methoxy-1,4-benzoquinone --> 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone #34 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 #35 katG 300 catalase; hydroperoxidase HPI(I) #36 yjfG 175 putative ligase Motif number 1 GGTAACGTTGCGCGTGACAAACGGTCAGAGACTAACGTAC 6 200 0 CGCGCGCAGG 0.982149 -55 TTTTGTGAACAGCCTATACTGCCGCCAGGTCTCCGGAACA 10 63 1 AGCACGCAGT 0.926432 -238 TCCTCCGGTCTGCTTGCGGGTCAGACAGCGTCCTTTCTAT 10 181 0 TGCGCGCAGG 0.985244 -120 GCTTTTATATAGCGAGCAGTGCTGGCCGGGAGAAAGTTCT 11 168 1 AGCGCGCCGG 0.979396 -133 TAACCCTTAATGCTAGCGTTACCGTCCGCTATCGTCTATG 14 45 1 TGCGCGCCGT 0.950582 -169 TTGGCAGGTGTGCCAGCTTTTCATACAGTGGATGCCCTGA 16 103 0 TGCGCTCAGG 0.983897 -145 CTGGCACACCTGCCAAACAACCTGGCAGGTGCAGGCAATC 16 127 1 TGCACGCAGT 0.951709 -121 CTGCAAAGTCTGCCTGCAAGTCTGACAGGGCAACTATTT 21 66 1 TGCGCGCAGG 0.995775 -29 AAAGGAAATATGCCTGAGCAGCAGTCAGAGACATAACTGG 25 138 0 TGCGCGCAGG 0.995775 -114 GTTTTCCCTGAGCAAATTTGCCAGACAGAGTAATCCAGCA 28 241 0 AGCACGCAGG 0.97983 -44 GGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTGGATGCTG 30 31 1 TGCGCTAAGG 0.788087 -76 ATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAT 30 65 1 AGCTCGCGGG 0.817042 -42 AATAGAATTGTGCTGTACAAACGTCCAGTTGGAAAGGCAT 32 78 0 TGCTCTCAGT 0.732396 -63 TCCGCATCTTAGCACATCGTTCATCCAGAGCGTGATTTCT 34 43 1 AGCACTCAGG 0.926432 -147 *** * * * *** * Masking position 12 Map Score: 20.0503 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 573 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 CCCCTTTGGGGAGAGGGTTAGGGTGAG 9 8 1 GGGGAGAGGG 0.961126 -293 GGAGAGGGTTAGGGTGAGGGGAACAGCCAG 9 20 1 AGGGTGAGGG 0.978838 -281 GGTGAGGGCTGGGGTGAGGGTTAATGTTCG 9 58 0 GGGGTGAGGG 0.984145 -243 TCTCCCTTCCAGGGTGAGGGCTGGGGTGAG 9 70 0 AGGGTGAGGG 0.978838 -231 TCACCCTGGAAGGGAGAGGGGGCAGAACGG 9 83 1 AGGGAGAGGG 0.948516 -218 AAGTGATTCGGGGGAGCGAACGCAGCCAAG 15 123 1 GGGGAGCGAA 0.792056 -152 TTGTTTGGCAGGTGTGCCAGCTTTTCATAC 16 117 0 GGTGTGCCAG 0.759632 -131 TTATAAAAATAGGGTGCGAAATCCGTCACA 17 153 1 AGGGTGCGAA 0.876936 -132 AATAGCAAGGGGAGTGCCAGAATGAGATTA 19 134 0 GGAGTGCCAG 0.759632 -62 GCCTTCGCTGAGGGTGCCGGTCTGGCACCC 21 12 1 AGGGTGCCGG 0.980867 -83 GTTGCAAGTCAGGGTGCCAGACCGGCACCC 21 23 0 AGGGTGCCAG 0.964228 -72 ********** Masking position 6 Map Score: 11.9236 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 213 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 ATCACATTTTTGTTTCGGGTGAATAGAGGGC 4 131 0 TGTTTCGGGG 0.7402 -170 TCATCGGTAACGTTGCGCGTGACAAACGGTC 6 214 0 CGTTGCGCGG 0.985773 -41 GACAAAATGTCGTTGCGCGCACAGTACAGCG 8 37 0 CGTTGCGCGA 0.980033 -40 CAGGACATCACATTGCGCTTATGCGAATCCA 9 115 1 CATTGCGCTA 0.874379 -186 CCTTGAGATACGTTGCAGTTATAACCCTTAA 14 24 1 CGTTGCAGTA 0.903942 -190 TTGCCGGGCGCATTGCGCTTACCCGGCTTAC 15 23 0 CATTGCGCTA 0.874379 -252 TTGCATACACCGTTGTGGGTACAGTCAGGCA 19 163 0 CGTTGTGGGA 0.804805 -33 TTTTATTCCACGTTTCGCTTATCCTAGCTGA 28 132 1 CGTTTCGCTA 0.817133 -153 CTAGCTGAAGCGTTTCAGTCGATTAAATGTT 28 155 1 CGTTTCAGTG 0.688556 -130 TCAGGGAAAACCTTGCAGGAGATCT 28 270 1 CCTTGCAGGG 0.739304 -15 AACGATAAACCATTGCGGGAGATAACCTTGA 30 11 0 CATTGCGGGG 0.963856 -96 AATGGTTTATCGTTGCGGGAGTTGCCTGAAG 30 28 1 CGTTGCGGGG 0.990372 -79 ACTCCATAAACATTGCAGGGAAAGTTTT 36 8 0 CATTGCAGGA 0.81683 -168 TTGTTAAGATTGTTGCGGTCGCTTTACTCCA 36 33 0 TGTTGCGGTG 0.903524 -143 ATAATCTCAATGTTGCGCTCAGGTGAATCGC 36 64 1 TGTTGCGCTA 0.817133 -112 ********* * Masking position 4 Map Score: 12.2859 Number of sites scoring better than the average of aligned sites = 1668 Number in coding regions = 1581 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 4 TTTTGTTCGTTTGTTATTGGGCGGG 1 44 0 TGTCGTTTTT 0.893454 -15 GGGTGAATAGAGGGCGTTTTTTCGTTAATTTT 4 114 0 AGGCGTTTTT 0.64433 -187 TTATTTTGCGTTCCCGTTTGTTTTATTTTTGT 4 251 0 TTCCGTTTTT 0.949475 -50 CGTGTTATTATTGTCGTTTCTTATATTTTGAC 7 71 1 TTGCGTTTTT 0.817459 -34 GTTGACATAGTGCGCGTTTGCTTTTAGGTTAG 9 220 1 TGCCGTTTCT 0.855336 -81 CGGGAGAAAGTTCTCTTTTCTTACACCGCGCC 11 194 1 TTCCTTTTTT 0.877032 -107 ATAAAAAATATGCACGTTTATTGCATATCTTT 11 227 1 TGCCGTTTTT 0.95948 -74 TGACAACTTTTGTTCGTTTGTTAACGAACTTT 11 264 1 TGTCGTTTTT 0.893454 -37 AAAGGGGGCGCTCTCTTTTATTGATCTTACGC 14 135 1 CTCCTTTTTT 0.782632 -79 CCGGGCCGTATGCCCGTTTATTTCTGGCGACA 15 190 0 TGCCGTTTTT 0.95948 -85 GGCGAATAGTTGCCCTTTTATTTCACTAAGTT 16 30 1 TGCCTTTTTT 0.899869 -218 TACGCAAACGTTTTCTTTTTCTGTTAGAATGC 23 103 1 TTTCTTTTCT 0.386757 -63 TGTGATAAAAATCACTTTTTTTAAACAATTAA 25 177 1 ATCCTTTTTT 0.696027 -75 AACACTCTCCTTACGTTTTTTGTTT 26 5 0 CTTCGTTTTT 0.770621 -21 CTGGACAAACATTCCTTTTATTCCACGTTTCG 28 117 1 ATTCTTTTTT 0.447786 -168 CAAAGGTCATCTCTCGTTTATTTACTTGTTTT 31 97 1 CTCCGTTTTT 0.904641 -109 *** ***** ** Masking position 7 Map Score: 11.6679 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 208 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 5 GTGCGCGCAACGACATTTTGTCCGAGTCGTG 8 46 1 CGACATTTGT 0.890089 -31 GCGACATGCGCGGCATTATGTAGCCAGGTTG 12 27 0 CGGCATTTGT 0.981331 -33 GCGCATGTCGCGGCATTGTTTTC 12 47 1 CGGCATTTTT 0.965081 -13 TTATTTCTGGCGACATTCTTTATATACACTT 15 174 0 CGACATTTTT 0.809807 -101 CCGGAAAATCCGGCCTTTTGACGCTTTAGCA 29 14 0 CGGCCTTTGA 0.945955 -95 CCGGATTTTCCGGCCTTTTTTATTACTGGGG 29 32 1 CGGCCTTTTT 0.973746 -77 CCGAACGCGTCGGCCTTCAGACAGGAGAAGA 32 14 0 CGGCCTTAGA 0.711218 -127 CCGACGCGTTCGGCCTTTTGTATTTTTGCGT 32 32 1 CGGCCTTTGT 0.986022 -109 GTGATCAGATCGGCATTTCTTTAATCTTTTG 34 90 1 CGGCATTCTT 0.852153 -100 CATTTCGAGGCAGCATTTTGTGCTCTGTTTA 35 25 0 CAGCATTTGT 0.890089 -276 ATAAGGTTATCAGCCTTGTTTTCTCCCTCAT 35 67 1 CAGCCTTTTT 0.851055 -234 ******* *** Masking position 6 Map Score: 10.3155 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 217 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 TCCTGAAAAATTTATGTAGCGCATGACT 2 7 0 TTTTGTGCGC 0.731319 -29 GCTACATAAATTTTTCAGGAGCAAATA 2 19 1 TTTTCAGAGC 0.921843 -17 TCTCTGACCGTTTGTCACGCGCAACGTTACCG 6 209 1 TTTTCAGCGC 0.89828 -46 TTTGTCGGGTTTTATCCTGAACAGTGAT 10 7 0 TTTTCCGAAC 0.597011 -294 TTGTAATGATTTTGTGAACAGCCTATACTGCC 10 54 1 TTTTGACAGC 0.790068 -247 TCCTTTGCTTTTTATGATTCGCGATTTAACTA 17 47 0 TTTTGATCGC 0.772664 -238 ACTGTGCAAATTTCTGCATAGCAAGTTTTGGT 19 12 0 TTTTGCTAGC 0.915153 -184 AGTGCGCAATTTTCTGCATAGCCGCTCATTCT 19 41 1 TTTTGCTAGC 0.915153 -155 GCGTTGAATATTTTTTCAGCGCCATTTTTATT 23 50 1 TTTTTCGCGC 0.731319 -116 AGCGCCATTTTTATTGATGCGCGGGAAGGAAA 23 67 1 TTATGAGCGC 0.545499 -99 TCCTGCAAGGTTTTCCCTGAGCAAATTTGCCA 28 258 0 TTTCCCGAGC 0.780431 -27 CTGTCGGAGCTTTCTCCACAGCCGGAGAAGGT 30 68 1 TTTTCCCAGC 0.857622 -39 GCCTTTTGTATTTTTGCGTAGCGCCTCGCAGG 32 44 1 TTTTGCTAGC 0.915161 -97 CTGGAACAATTTTTTGATGAGCAGGCATTGAG 33 73 1 TTTTGAGAGC 0.945979 -22 TAGCACATCGTTCATCCAGAGCGTGATTTCTG 34 52 1 TTCTCCGAGC 0.791787 -138 CAGAGCGTGATTTCTGCCGAGCGTGATCAGAT 34 68 1 TTTTGCGAGC 0.976532 -122 *** *** **** Masking position 2 Map Score: 12.0189 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 643 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 CCTTTATATTGTGGGAGATAGCCCTGATAT 6 34 0 GTGGGAGATA 0.501647 -221 GCGGTCAATTGTGGGACATCGCCTATAATT 6 85 1 GTGGGACATC 0.688658 -170 TACGATTGCGGCAGGCCGTGTTATTATTGT 7 55 1 GCAGGCCGTG 0.623459 -50 GCAGAACGGCGCAGGACATCACATTGCGCT 9 104 1 GCAGGACATC 0.94362 -197 CAGACCGGAGGAAGGAAATCCCGACGTCTC 10 209 1 GAAGGAAATC 0.71997 -92 GTCTGCGGGAAATAATACCAACGT 14 200 0 GCGGGAAATA 0.86592 -14 CCTGGCAGGTGCAGGCAATCCCCTTTGCAT 16 147 1 GCAGGCAATC 0.848917 -101 TACACGCAAAGCGGGACGTACAGGGGCTAA 18 44 0 GCGGGACGTA 0.688525 -139 CAGGATTTCGGCGGGAGTTGCAAGTCAGGG 21 39 0 GCGGGAGTTG 0.885573 -56 GGCAGACTTTGCAGGATTTCGGCGGGAGTT 21 50 0 GCAGGATTTC 0.683065 -45 TGATGCGCGGGAAGGAAATCCCTACGCAAA 23 81 1 GAAGGAAATC 0.71997 -85 GGAAAACCTTGCAGGAGATCT 28 274 1 GCAGGAGATC 0.953985 -11 ATAAACCATTGCGGGAGATAACCTTGA 30 8 0 GCGGGAGATA 0.896554 -99 GTTTATCGTTGCGGGAGTTGCCTGAAGCGC 30 32 1 GCGGGAGTTG 0.885573 -75 GTAGCGCCTCGCAGGAAATGCCTTTCCAAC 32 61 1 GCAGGAAATG 0.930071 -80 TTTTTGATGAGCAGGCATTGAG 33 83 1 GCAGGCATTG 0.648314 -12 CTCATTACTTGAAGGATATGAAGCTAAAAC 35 93 1 GAAGGATATG 0.447611 -208 ********** Masking position 9 Map Score: 8.18547 Number of sites scoring better than the average of aligned sites = 1470 Number in coding regions = 1390 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 Motif number 8 TTACTCACAACAGAGCATAACAAACTGATT 4 77 1 CAGAGCATAA 0.866037 -224 GACAAACGGTCAGAGACTAACGTACTCGTC 6 195 0 CAGAGACTAA 0.749899 -60 AAGAATGAGACAGGCCGTAAAGTTTGGCGA 7 26 0 CAGGCCGTAA 0.755112 -79 CCGTAGTCCCCAGGGAATAATAAGAACAGC 10 266 1 CAGGGAATAA 0.652883 -35 TTGTGAACGTCAGGGCGCAGAGATCCCCGG 15 218 0 CAGGGCGCAG 0.931166 -57 AAACCGCCCACAGAGCGCGGTTGCTAACAA 16 202 1 CAGAGCGCGG 0.695243 -46 GCGGGACGTACAGGGGCTAAATCGGCTAAA 18 34 0 CAGGGGCTAA 0.738391 -149 GAAATTTGCACAGTGCGCAATTTTCTGCAT 19 30 1 CAGTGCGCAA 0.850135 -166 AACAGGATGACAGGGCGTAAAATCGTGGGA 23 141 1 CAGGGCGTAA 0.973523 -25 TCTGGTCCACCAGGGCCCAAAGTGGTAGCA 27 112 1 CAGGGCCCAA 0.973198 -50 CTTCACCCATCAGGGACAAAAA 29 97 1 CAGGGACAAA 0.603262 -12 TAGCCATCACCAGAGCCAAACCGATTAGAT 31 23 1 CAGAGCCAAA 0.83939 -183 ATCGTTCATCCAGAGCGTGATTTCTGCCGA 34 58 1 CAGAGCGTGA 0.860156 -132 AAATTTTAAACAGAGCACAAAATGCTGCCT 35 19 1 CAGAGCACAA 0.899311 -282 CGCGATTCACCTGAGCGCAACATTGAGATT 36 66 0 CTGAGCGCAA 0.743439 -110 ********** Masking position 3 Map Score: 7.55869 Number of sites scoring better than the average of aligned sites = 752 Number in coding regions = 697 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 9 ACCACGTAATCCGCAGTGCGGTTAATTGAAA 5 22 1 CCCAGTGCGG 0.682094 -31 TTGACCGCAGCCGGAAAACGGTAAAAGCACC 6 62 0 CCGAAAACGG 0.769288 -193 CTAACCCTCTCCCCAAAGGGG 9 1 0 CCCAAAGGGG 0.978018 -300 CCAGCCCTCACCCTGGAAGGGAGAGGGGGCA 9 76 1 CCTGGAAGGG 0.615 -225 TCGGCAATTACTCCAAAAGGGGGCGCTCTCT 14 120 1 CTCAAAAGGG 0.928426 -94 ATCAGTACTGATGCAAAGGGGATTGCCTGCA 16 156 0 ATCAAAGGGG 0.761388 -92 ACTAAACCGCCCACAGAGCGCGGTTGCTAAC 16 199 1 CCCAGAGCGC 0.729453 -49 TATGAAATACACGCAAAGCGGGACGTACAGG 18 50 0 ACCAAAGCGG 0.792333 -133 CCAGAATAGTCTCCGAAGCGGGATCTGGCTG 18 90 1 CTCGAAGCGG 0.877136 -93 GACCCATGGTCTGCGAAGGGGCGACACTATA 27 51 1 CTCGAAGGGG 0.926694 -111 CCCTGGTGGACCAGAAAAGGGCTTGTCTCTT 27 96 0 CCGAAAAGGG 0.855167 -66 ATAAAGCTTCCCACAAAAGGGGATAAAAGTG 28 56 1 CCCAAAAGGG 0.964865 -229 CTGGTGATGGCTACAGAAGGGCAAA 31 5 0 CTCAGAAGGG 0.921874 -201 AACGGTAACACTGTAGAGGGGAGCACATTG 35 281 1 CTTAGAGGGG 0.776368 -20 ** ******** Masking position 10 Map Score: 7.57542 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 319 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 10 TTACATGTTTTTAACAAAATAA 8 2 1 TACATGTTTT 0.67829 -75 AACTCGGGGTTGCATCTGGTTGTGGTTACAA 9 168 0 TGCATCTGTT 0.874695 -133 ACAATTAACCTACATATAGTTTGTCGGGTTT 10 27 0 TACATATGTT 0.834569 -274 GCAATAAACGTGCATATTTTTTATCGGCGCG 11 220 0 TGCATATTTT 0.952236 -81 GCACGTTTATTGCATATCTTTCAGTGTGACA 11 238 1 TGCATATTTT 0.952236 -63 GTTCACAAACTGCATATATCTGATAGACGTG 15 240 1 TGCATATTCT 0.789667 -35 GCATGATGTGTACATCTATTTTCAGGGCATC 16 82 1 TACATCTTTT 0.849667 -166 TCGATGGCGTTGAATATTTTTTCAGCGCCAT 23 44 1 TGAATATTTT 0.588554 -122 TGATGGTGCTTGCATATATATCTGGCGAATT 31 135 1 TGCATATTAT 0.716963 -71 ATCTTTTGTTTGCATATTTTTAACACAAAAT 34 113 1 TGCATATTTT 0.952236 -77 CAATTTGATCTACATCTCTTTAACCAACAAT 35 181 1 TACATCTTTT 0.849667 -120 GTTGAGATCTTACATATTGTTGGTTAAAGAG 35 196 0 TACATATGTT 0.834569 -105 ******* *** Masking position 4 Map Score: 6.26204 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 66 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 ACCAGTGCTGGCTGTTCCCCTCACCCTAACC 9 26 0 GCGTTCCCCT 0.957496 -275 GCAACTATTCGCCGTTGCCCTTCATTCACCG 16 12 0 GCGTTGCCCT 0.981613 -236 GCAACGGCGAATAGTTGCCCTTTTATTTCAC 16 25 1 ATGTTGCCCT 0.955836 -223 TTTTCATACAGTGGATGCCCTGAAAATAGAT 16 95 0 GTGATGCCCT 0.983852 -153 AAATAGTTGCCCTGTCAGACTTG 21 82 0 ATGTTGCCCT 0.955836 -13 TATGGGGGTTGTCGATCCCCAGTAATAAAAA 29 48 0 GTGATCCCCA 0.842211 -61 CAGATTGGGCGTCGATGCCCTAGATTTCTAC 33 34 0 GTGATGCCCT 0.983853 -61 ** ******** Masking position 6 Map Score: 4.25583 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 74 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 CGTGGCGTCAGTCGGCTTGCCTGACTAGCG 1 14 1 GTCGGCTTGC 0.970075 -45 ACCGTTTTCCGGCTGCGGTCAATTGTGGGA 6 71 1 GGCTGCGGTC 0.862481 -184 CCTTCCTCCGGTCTGCTTGCGGGTCAGACA 10 194 0 GTCTGCTTGC 0.975204 -107 GATAGGGTTAGTCTGCTTGCATCATACAGG 14 169 0 GTCTGCTTGC 0.975204 -45 GTCTGCGGGAAATAATACCA 14 204 0 GTCTGCGGGA 0.820522 -10 CCTCTGCCTTGGCTGCGTTCGCTCCCCCGA 15 130 0 GGCTGCGTTC 0.927745 -145 CCAAGGCAGAGGCGGCTTGAAGGATGAAGT 15 148 1 GGCGGCTTGA 0.840497 -127 ATCCTGCAAAGTCTGCCTGCAAGTCTGACA 21 63 1 GTCTGCCTGC 0.970211 -32 GGCCGAACGCGTCGGCCTTCAGACAGGAGA 32 17 0 GTCGGCCTTC 0.897748 -124 ********** Masking position 6 Map Score: 6.32357 Number of sites scoring better than the average of aligned sites = 524 Number in coding regions = 502 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 AATTGACCGCAGCCGGAAAACGGTAAAAGC 6 65 0 AGCCGGAAAA 0.892325 -190 GAGCAGTGCTGGCCGGGAGAAAGTTCTCTT 11 181 1 GGCCGGGAGA 0.967313 -120 TTGTTCTGTAAGCCGGGTAAGCGCAATGCG 15 16 1 AGCCGGGTAA 0.957549 -259 ACGGGCATACGGCCCGGGGATCTCTGCGCC 15 205 1 GGCCCGGGGA 0.822293 -70 CCAGCAAATCGTCCGGGGAAACCTTACCTG 28 217 0 GTCCGGGGAA 0.934895 -68 TAATAAAAAAGGCCGGAAAATCCGGCCTTT 29 27 0 GGCCGGAAAA 0.951026 -82 CTTTCTCCACAGCCGGAGAAGGTGTAATTA 30 77 1 AGCCGGAGAA 0.909154 -30 ATTCTATTTTGTGCGGGTAAGTTGTTGCGT 32 110 1 GTGCGGGTAA 0.709578 -31 GGAGTAGTTAAGCCGGGTAGAAATCTAGGG 33 18 1 AGCCGGGTAG 0.824687 -77 CTCGAAATGAGGGCGGGAAAATAAGGTTAT 35 47 1 GGGCGGGAAA 0.948463 -254 ********** Masking position 4 Map Score: 3.6412 Number of sites scoring better than the average of aligned sites = 765 Number in coding regions = 570 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 14 TTCCGCAGTTGCTATACAGATCGCATAGTT 17 96 0 GCTATACAGA 0.661064 -189 GCCAGATCCCGCTTCGGAGACTATTCTGGA 18 89 0 GCTTCGGAGA 0.821692 -94 ACCAAAACTTGCTATGCAGAAATTTGCACA 19 12 1 GCTATGCAGA 0.952136 -184 AGAATGAGCGGCTATGCAGAAAATTGCGCA 19 43 0 GCTATGCAGA 0.952136 -153 TGCCTTCGCTGAGGGTGCCGGT 21 3 1 CCTTCGCTGA 0.801501 -92 GAAGGAAATCCCTACGCAAACGTTTTCTTT 23 91 1 CCTACGCAAA 0.911835 -75 TAGTGTCGCCCCTTCGCAGACCATGGGTCT 27 50 0 CCTTCGCAGA 0.962364 -112 CGAGAGATGACCTTTGCAAAAGGCAAAATT 31 83 0 CCTTTGCAAA 0.810346 -123 CCTGCGAGGCGCTACGCAAAAATACAAAAG 32 46 0 GCTACGCAAA 0.927592 -95 ********** Masking position 3 Map Score: 3.32136 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 205 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 15 AGGCAAGCCGACTGACGCCACGCGT 1 6 0 ACTGACGCCA 0.943815 -53 GCCTAACACCACTGACGCTATTCGGACAGG 6 145 1 ACTGACGCTA 0.86031 -110 AATAACACGGCCTGCCGCAATCGTAAGAAT 7 50 0 CCTGCCGCAA 0.978357 -55 GTAACCACAACCAGATGCAACCCCGAGTTG 9 170 1 CCAGATGCAA 0.685123 -131 AACAGCCTATACTGCCGCCAGGTCTCCGGA 10 70 1 ACTGCCGCCA 0.932687 -231 CACTTGCCGCCTTGATGCAACTTGAATGAT 15 66 0 CTTGATGCAA 0.574648 -209 CATTATCAGTACTGATGCAAAGGGGATTGC 16 161 0 ACTGATGCAA 0.906514 -87 GGAAACCTTACCTGTCGCAAACTGCGACTG 28 201 0 CCTGTCGCAA 0.91921 -84 GCTTCAGGCAACTCCCGCAACGATAAACCA 30 30 0 ACTCCCGCAA 0.785894 -77 AACGCCTCCTGACGCAACAACTTACCC 32 124 0 CCTGACGCAA 0.98208 -17 ********** Masking position 10 Map Score: 5.85371 Number of sites scoring better than the average of aligned sites = 731 Number in coding regions = 684 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454