AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iphoB_ecoli_hinf_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 phoE 287 outer membrane pore protein E (E,Ic,NmpAB) #2 yaiB 300 orf, hypothetical protein #3 phoA 31 alkaline phosphatase #4 psiF 100 induced by phosphate starvation #5 phoB 189 positive response regulator for pho regulon, sensor is PhoR (or CreC) #6 phoR 57 positive and negative sensor protein for pho regulon #7 phoH 300 PhoB-dependent, ATP-binding pho regulon component; may be helicase; induced by P starvation #8 ugpA 97 sn-glycerol 3-phosphate transport system, integral membrane protein #9 ugpB 300 sn-glycerol 3-phosphate transport system; periplasmic binding protein #10 pstB 182 ATP-binding component of high-affinity phosphate-specific transport system #11 pstC 86 high-affinity phosphate-specific transport system, cytoplasmic membrane component #12 pstS 300 high-affinity phosphate-specific transport system; periplasmic phosphate-binding protein #13 phnQ 125 orf, hypothetical protein #14 phnL 110 ATP-binding component of phosphonate transport #15 phnE 54 membrane channel protein component of Pn transporter #16 phnD 24 periplasmic binding protein component of Pn transporter #17 phnC 132 ATP-binding component of phosphonate transport #18 phnB 300 orf, hypothetical protein #19 HI0362 300 iron (chelated) ABC transporter, periplasmic-binding protein (yfeA) #20 HI1379 300 phosphate regulon transcriptional regulatory protein (phoB) #21 HI1382 90 phosphate ABC transporter, permease protein (pstC) #22 HI1383 300 phosphate ABC transporter, periplasmic-binding protein (pstS) Motif number 1 ACGCTTGCGCGTCTTATCATGCCTACAATCAG 7 10 1 CGCATCATGC 0.962209 -291 GCGGCGTGAACGCCTTATCCAGCCTACCAAACC 7 47 0 CGCATCCAGC 0.987131 -254 AAGGCGTTCACGCCGCATCCGGCGATCGTGCAC 7 64 1 CGCATCCGGC 0.999567 -237 CGGATGCGCTTCGCTTATCCGGCCTACACGCGA 8 52 0 TCCATCCGGC 0.924502 -46 GCGGCGTAAACGCCTTATCAGGCCTACAAGATC 9 33 0 CGCATCAGGC 0.998698 -268 AAGGCGTTTACGCCGCATCCGGCATGAAACGAT 9 50 1 CGCATCCGGC 0.999567 -251 CAGGCGTTCACGCCGCATCCGGCAAAGTGTTAA 10 99 0 CGCATCCGGC 0.999567 -84 GCGGCGTGAACGCCTGATCCGGCCTACGGTAAG 10 116 1 CGCATCCGGC 0.999567 -67 CTGATGCACTTCGCTAATCAGGCTTACCGTAGG 10 138 0 TCCATCAGGC 0.802557 -45 CGGTGTTTTACGCCGCATCCGGCATTACAAAAT 11 30 1 CGCATCCGGC 0.999567 -57 AAGGCGTTTACGCCGCATCCGGCACCGGC 14 7 0 CGCATCCGGC 0.999567 -104 GCGGCGTAAACGCCTTATCCGGCCTACAAATGC 14 24 1 CGCATCCGGC 0.999567 -87 GACGCTGACGCGTCTTATCCGACCTACGGGGAG 14 58 0 CGCATCCGAC 0.996378 -53 GACGCGTCAGCGTCGCATCCGACACCCGAACCA 14 77 1 CGCATCCGAC 0.996378 -34 GACGCCGGGGCGTCTTATCCGACCTACGAT 15 8 0 CGCATCCGAC 0.996378 -47 GACGCCCCGGCGTCGCATCCGACAATGTGCAGG 15 27 1 CGCATCCGAC 0.996378 -28 GACGCGCAAGCGTCGCATCAGGCAGTC 18 5 0 CGCATCAGGC 0.998698 -296 GACGCTTGCGCGTCTTATCAGGCCTACAAATTC 18 24 1 CGCATCAGGC 0.998698 -277 GCGGCGTAAACGCCTTATCCGGCCTACGGAGGG 18 62 0 CGCATCCGGC 0.999567 -239 AAGGCGTTTACGCCGCATCCGGCAATGGTGCCG 18 79 1 CGCATCCGGC 0.999567 -222 GACGCGCAAGCGTCGCATCAGGCAGTCGGCACC 18 105 0 CGCATCAGGC 0.998698 -196 GACGCTTGCGCGTCTTATCAGGCCTACAAATTC 18 124 1 CGCATCAGGC 0.998698 -177 GCGGCGTAAACGCCTTATCCGGCCTACGGAGGG 18 162 0 CGCATCCGGC 0.999567 -139 AAGGCGTTTACGCCGCATCCGGCAACAGTGCCG 18 179 1 CGCATCCGGC 0.999567 -122 GACGCGCGAGCGTCGCATCAGGCAGTCGGCACT 18 205 0 CGCATCAGGC 0.998698 -96 GACGCTCGCGCGTCTTATCAGGCCGCCTCTCAT 18 224 1 CGCATCAGGC 0.998698 -77 ** * ******* Masking position 8 Map Score: 147.146 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 74 Number in noncoding regions = 536 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 GATCGCCGGATGCGGCGTGAACGCCTTATCCAGCCT 7 55 0 TGCGCGCGCT 0.999593 -246 ATTCCTGAACTGTGCCGGATGCGCTTCGCTTATCCG 8 64 0 TGTGCGCGCT 0.993864 -34 TCATGCCGGATGCGGCGTAAACGCCTTATCAGGCCT 9 41 0 TGCGCGCGCT 0.999593 -260 TTCCCTCACCCACGCCGTCACCGCCTTGTCATCTTT 9 150 1 CACGCGCGCT 0.962329 -151 CTTTGCCGGATGCGGCGTGAACGCCTGATCCGGCCT 10 105 1 TGCGCGCGCT 0.999593 -78 CGGTGCCGGATGCGGCGTAAACGCCTTATCCGGCCT 14 13 1 TGCGCGCGCT 0.999593 -98 GGGTGTCGGATGCGACGCTGACGCGTCTTATCCGAC 14 68 0 TGCGCGCGCT 0.999593 -43 CATTGTCGGATGCGACGCCGGGGCGTCTTATCCGAC 15 18 0 TGCGCGGGCT 0.995851 -37 GACTGCCTGATGCGACGCTTGCGCGTCTTATCAGGC 18 11 1 TGCGCGCGCT 0.999593 -290 CATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCT 18 70 0 TGCGCGCGCT 0.999593 -231 GACTGCCTGATGCGACGCTTGCGCGTCTTATCAGGC 18 111 1 TGCGCGCGCT 0.999593 -190 TGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCT 18 170 0 TGCGCGCGCT 0.999593 -131 GACTGCCTGATGCGACGCTCGCGCGTCTTATCAGGC 18 211 1 TGCGCGCGCT 0.999593 -90 **** ** *** * Masking position 16 Map Score: 66.2847 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 24 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 3 CGCCTTGCTCATCGGACGCAGAGCAGGGCT 6 7 1 GCTCGGCGCA 0.932765 -51 GCTGGATAAGGCGTTCACGCCGCATCCGGCGATC 7 57 1 GCGTCGCGCA 0.999157 -244 AGGCATCAGTGCACGATCGCCGGATGCGGCGTGA 7 71 0 GCACCGCGGA 0.932765 -230 ACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGC 8 44 1 GCGTGGCGGA 0.960981 -54 GATAAGCGAAGCGCATCCGGCACAGTTCAGGAAT 8 66 1 GCGCCGCACA 0.993731 -32 GCCTGATAAGGCGTTTACGCCGCATCCGGCATGA 9 43 1 GCGTCGCGCA 0.999157 -258 GCGTGAATTCGCGCATTCGGTACAACAAGAGAGA 9 271 1 GCGCCGTACA 0.893371 -30 GCCGGATCAGGCGTTCACGCCGCATCCGGCAAAG 10 105 0 GCGTCGCGCA 0.999157 -78 TGCGTAAGCGGGGCATTTTTCTTCC 12 2 1 GCGTCGGGCA 0.989342 -299 GCCGGATAAGGCGTTTACGCCGCATCCGGCACCG 14 13 0 GCGTCGCGCA 0.999157 -98 CGGATAAGACGCGTCAGCGTCGCATCCGACACCC 14 70 1 GCGTCGCGCA 0.999157 -41 CGGATAAGACGCCCCGGCGTCGCATCCGACAATG 15 20 1 GCCCCGCGCA 0.993037 -35 CTGATAAGACGCGCAAGCGTCGCATCAGGCAGTC 18 11 0 GCGCCGCGCA 0.999412 -290 GCCGGATAAGGCGTTTACGCCGCATCCGGCAATG 18 72 1 GCGTCGCGCA 0.999157 -229 CTGATAAGACGCGCAAGCGTCGCATCAGGCAGTC 18 111 0 GCGCCGCGCA 0.999412 -190 GCCGGATAAGGCGTTTACGCCGCATCCGGCAACA 18 172 1 GCGTCGCGCA 0.999157 -129 CTGATAAGACGCGCGAGCGTCGCATCAGGCAGTC 18 211 0 GCGCCGCGCA 0.999412 -90 **** ** **** Masking position 14 Map Score: 68.885 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 104 Number in noncoding regions = 268 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 4 TGGCAGATCACGGGCGCATACGCTCATGGTTAA 4 75 1 CGGGCGACGC 0.980851 -26 ATCGCCGGATGCGGCGTGAACGCCTTATCCAGC 7 57 0 GCGGCGACGC 0.997885 -244 CACGCCGCATCCGGCGATCGTGCACTGATGCCT 7 72 1 CCGGCGGTGC 0.978405 -229 CTTCGCTTATCCGGCCTACACGCGATGCCAGGT 8 44 0 CCGGCCACGC 0.974998 -54 TTCCTGAACTGTGCCGGATGCGCTTCGCTTATC 8 66 0 GTGCCGGCGC 0.855902 -32 CATGCCGGATGCGGCGTAAACGCCTTATCAGGC 9 43 0 GCGGCGACGC 0.998166 -258 TCTCCCCAGAGGGGCGAGGGGACCGACCGAGCG 10 45 1 GGGGCGGGAC 0.807056 -138 TTTGCCGGATGCGGCGTGAACGCCTGATCCGGC 10 106 1 GCGGCGACGC 0.997885 -77 GAAGAAAAATGCCCCGCTTACGCA 12 2 0 GCCCCGACGC 0.89386 -299 TTAGGGTGAGGGGGCCAGCGCGCACATTCCCTC 13 14 0 GGGGCCGCGC 0.975657 -112 TCTCCCCAGAGGGGCGAGGGGACCGATTGTGCT 13 50 1 GGGGCGGGAC 0.807056 -76 GGTGCCGGATGCGGCGTAAACGCCTTATCCGGC 14 14 1 GCGGCGACGC 0.998166 -97 GGTGTCGGATGCGACGCTGACGCGTCTTATCCG 14 70 0 GCGACGACGC 0.976655 -41 ATTGTCGGATGCGACGCCGGGGCGTCTTATCCG 15 20 0 GCGACGGGGC 0.824621 -35 CCCGCCGGGAGGCCCGCCCTCCC 17 1 1 CCCGCCAGGC 0.538488 -132 ACTGCCTGATGCGACGCTTGCGCGTCTTATCAG 18 12 1 GCGACGGCGC 0.993248 -289 ATTGCCGGATGCGGCGTAAACGCCTTATCCGGC 18 72 0 GCGGCGACGC 0.998166 -229 TACGCCGCATCCGGCAATGGTGCCGACTGCCTG 18 87 1 CCGGCAGTGC 0.788641 -214 ACTGCCTGATGCGACGCTTGCGCGTCTTATCAG 18 112 1 GCGACGGCGC 0.993248 -189 GTTGCCGGATGCGGCGTAAACGCCTTATCCGGC 18 172 0 GCGGCGACGC 0.998166 -129 TACGCCGCATCCGGCAACAGTGCCGACTGCCTG 18 187 1 CCGGCAGTGC 0.788651 -114 ACTGCCTGATGCGACGCTCGCGCGTCTTATCAG 18 212 1 GCGACGGCGC 0.993248 -89 ****** **** Masking position 5 Map Score: 62.6503 Number of sites scoring better than the average of aligned sites = 1914 Number in coding regions = 1590 Number in noncoding regions = 324 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 5 AAAAAACCACCCGGCAGCGAAAATTCACTGC 4 22 0 CCGGCAGCGA 0.649846 -79 GCCTACCAAACCCGCACTGATTGTAGGCATG 7 28 0 CCCGCACTGT 0.746902 -273 CTCCCATTTTCCCTCACCCACGCCGTCACCG 9 142 1 CCCTCACCCC 0.995701 -159 CTCACCCACGCCGTCACCGCCTTGTCATCTT 9 154 1 CCGTCACCGC 0.969067 -147 CACGGTTTTCCCCTCACCCTAACCCTCTCCC 10 20 1 CCCTCACCCA 0.994781 -163 CTCACCCTAACCCTCTCCCCAGAGGGGCGAG 10 32 1 CCCTCTCCCA 0.98086 -151 TCGGTCGGTCCCCTCGCCCCTCTGGGGAGAG 10 44 0 CCCTCGCCCT 0.956588 -139 CGCGCTGGCCCCCTCACCCTAACCCTCTCCC 13 25 1 CCCTCACCCA 0.994781 -101 CTCACCCTAACCCTCTCCCCAGAGGGGCGAG 13 37 1 CCCTCTCCCA 0.98086 -89 ACAATCGGTCCCCTCGCCCCTCTGGGGAGAG 13 49 0 CCCTCGCCCT 0.956588 -77 CTCGTTTTCTCCCTCTCCCCATTGGGGTGAG 13 100 1 CCCTCTCCCA 0.98086 -26 CGCCCCTCACCCCAATGGGGAGAG 13 112 0 CCCTCACCCA 0.994781 -14 TACGCCGCATCCGGCACCGGC 14 1 0 CCGGCACCGC 0.968426 -110 AGCGTCGCATCCGACACCCGAACCACGAGGC 14 85 1 CCGACACCCA 0.884961 -26 GGCCCGCCCTCCCGCACTGTCATCGAATTCC 17 21 1 CCCGCACTGC 0.900042 -112 CCTACAAATTCCCGCACCCTCCGTAGGCCGG 18 46 1 CCCGCACCCC 0.995612 -255 CCTACAAATTCCCGCACCCTCCGTAGGCCGG 18 146 1 CCCGCACCCC 0.995612 -155 ********* * Masking position 5 Map Score: 41.4549 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 206 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 CAACCGACGACAGTCCTGCTAAAACGTTCGT 1 49 0 CAGTCCTGCA 0.674898 -239 GCGGGATCAGCAAGCCTAGCGGCAGTTGTTT 1 116 1 CAAGCCTAGG 0.678443 -172 CGCGTCTTATCATGCCTACAATCAGTGCGGG 7 18 1 CATGCCTACA 0.877251 -283 AACGCCTTATCCAGCCTACCAAACCCGCACT 7 41 0 CCAGCCTACA 0.962755 -260 CTTCGCTTATCCGGCCTACACGCGATGCCAG 8 46 0 CCGGCCTACC 0.980477 -52 AACGCCTTATCAGGCCTACAAGATCGTGCAA 9 27 0 CAGGCCTACA 0.991554 -274 GAGTTTGATTCAGACCTTCTATATTTTCCCG 9 95 1 CAGACCTTCA 0.657894 -206 AACGCCTGATCCGGCCTACGGTAAGCCTGAT 10 124 1 CCGGCCTACG 0.996186 -59 AACACCGTACCCGGCCTGGAGTTTTA 11 6 0 CCGGCCTGGG 0.915424 -81 AACGCCTTATCCGGCCTACAAATGCGCTCCC 14 32 1 CCGGCCTACA 0.995865 -79 CGCGTCTTATCCGACCTACGGGGAGCGCATT 14 52 0 CCGACCTACG 0.977512 -59 GGCGTCTTATCCGACCTACGAT 15 2 0 CCGACCTACA 0.975656 -53 CGCGTCTTATCAGGCCTACAAATTCCCGCAC 18 32 1 CAGGCCTACA 0.991554 -269 AACGCCTTATCCGGCCTACGGAGGGTGCGGG 18 56 0 CCGGCCTACG 0.996186 -245 CGCGTCTTATCAGGCCTACAAATTCCCGCAC 18 132 1 CAGGCCTACA 0.991554 -169 AACGCCTTATCCGGCCTACGGAGGGTGCGGG 18 156 0 CCGGCCTACG 0.996186 -145 ********* * Masking position 7 Map Score: 40.0535 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 134 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 7 TGGTAATTTATTAAATCTGTAATAAAAGCGTAA 1 145 0 TTTCTGTAAT 0.894937 -143 TAAGAATATTATTAATCTGTAATATATCTTTAA 1 183 1 ATTCTGTAAT 0.942595 -105 GCGCAAAGTATTTCCTTTGTCATAAAAATAATA 2 209 1 TTTTTGTCAT 0.734654 -92 CGAGCTTTTCATAAATCTGTCATAAATCTGACG 5 114 1 ATTCTGTCAT 0.986736 -76 CATCACTGTCATCACTCTGTCATCTTTCCAGTA 7 139 1 ATTCTGTCAT 0.986662 -162 CCGCCTTGTCATCTTTCTGACACCTTACTATCT 9 170 1 ATTCTGACAC 0.828105 -131 CAAAAAAGTTATTTTTCTGTAATTCGAGCATGT 9 214 1 ATTCTGTAAT 0.942605 -87 TTCGGCTACTTTTTCTCTGTCACAGAATGAAAA 12 88 1 TTTCTGTCAC 0.955697 -213 CAGAATGAAAATTTTTCTGTCATCTCTTCGTTA 12 110 1 ATTCTGTCAT 0.986736 -191 TGAAGACTTTATCTCTCTGTCATAAAACTGTCA 12 189 1 ATTCTGTCAT 0.986728 -112 TATTCCTTACATATAACTGTCACCTGTTTGTCC 12 222 1 ATACTGTCAC 0.828104 -79 GTTGTTTTGGTTTGTTCTGTCATTTTAGGTTTA 19 42 1 TTTCTGTCAT 0.974739 -259 ** ******** Masking position 12 Map Score: 16.7194 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 40 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 8 GCTTTTATTACAGATTTAATAAATTACCACATTTT 1 149 1 CAGAAAAATT 0.961999 -139 AGATATATTACAGATTAATAATATTCTTAAAATGT 1 177 0 CAGAATAATT 0.814591 -111 TATAAGTTAACGAAGAGAATATATTTCATAACTTT 2 76 1 CGAAAAAATT 0.759974 -225 CGCTGGTAATCAAACAAAAAATATTTGCGCAAAGT 2 183 1 CAAAAAAATT 0.958908 -118 ATTTTTATGACAAAGGAAATACTTTGCGCAAATAT 2 203 0 CAAAAAATTT 0.898917 -98 CAAGATCGTGCAAATTCAACATATTGCCA 9 5 0 CAAAAAAATT 0.958908 -296 AGGTCTGAATCAAACTCTACAGATTGCTCATCGTT 9 77 0 CAAATAAATT 0.68115 -224 GCTCGAATTACAGAAAAATAACTTTTTTGTTACAT 9 208 0 CAGAATATTT 0.626065 -93 TTCTCTGTCACAGAATGAAAATTTTTCTGTCATCT 12 100 1 CAGAAAATTT 0.906076 -201 TTATTTAAATCAGACTGAAGACTTTATCTCTCTGT 12 174 1 CAGAAAATTT 0.906076 -127 TGTGTTTGACCAAATTCAACTAATTCACCCAAATA 20 118 0 CAAAAATATT 0.68115 -183 TGAATTTGGTCAAACACAACAAATTTTTGATAGAC 20 135 1 CAAAAAAATT 0.958908 -166 AAAGTGAAGTGAGAAATAATACATTCTCACCAAAC 20 248 0 GAGAAAAATT 0.71192 -53 AAGTGCGGTATAAAATAAAGAGATT 21 1 0 TAAAAAAATT 0.730483 -90 ATTTTATGCATAAACATAACAAATTCTCCTTGAGT 22 51 0 TAAAAAAATT 0.730483 -250 **** ** * *** Masking position 4 Map Score: 9.92508 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 86 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 9 ATAATATTCTTAAAATGTGGTAATTTATTAA 1 164 0 TAAAATGGGT 0.937265 -124 TGATCTGCCATTAAGTCTGGTTGCTAACAGC 4 54 0 TTAAGTCGGT 0.828881 -47 TTATGATTTCTTAACTGGAGTATCTTAC 6 40 1 TTAACTGAGT 0.866444 -18 GAGAAGCCAGTTAAGTGTAGTTCGAAATTTA 18 262 0 TTAAGTGAGT 0.913457 -39 CTGGCTTCTCTTAACTGAGGTCACCATC 18 283 1 TTAACTGGGT 0.95832 -18 AAAACNNGATTATACTGTGGTTATAGTAACT 20 39 1 TATACTGGGT 0.825679 -262 ATATTCGCGGTAAAATGGGGTAGTTATTTTG 20 194 1 TAAAATGGGT 0.937265 -107 TTTATGGCATAAAAGTGAAGTGAGAAATAAT 20 263 0 AAAAGTGAGT 0.684974 -38 AGGTTTTGTATAAAGTGCGGTATAAAATAAA 21 17 0 TAAAGTGGGT 0.982068 -74 TTAACATTAATAAAGTGCGGTTATCTTAAAT 21 53 1 TAAAGTGGGT 0.982068 -38 ******* *** Masking position 6 Map Score: 6.41457 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 55 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 GAAAATTCACTGCCGGGCGCGGTT 4 5 0 TGCCGGGCGC 0.936386 -96 GAATTTTCGCTGCCGGGTGGTTTTTTTGCT 4 27 1 TGCCGGGTGG 0.900807 -74 AGTGCACGATCGCCGGATGCGGCGTGAACG 7 68 0 CGCCGGATGC 0.984392 -233 CGTGCACTGATGCCTGATGCAAATCCTGCT 7 90 1 TGCCTGATGC 0.98676 -211 TCAGTGTAATGTCGGATGCGTTTCGCTTA 8 10 1 TGTCGGATGC 0.98676 -88 TCCTGAACTGTGCCGGATGCGCTTCGCTTA 8 68 0 TGCCGGATGC 0.998322 -30 CATCGTTTCATGCCGGATGCGGCGTAAACG 9 54 0 TGCCGGATGC 0.998322 -247 TCTCTTGTTGTACCGAATGCGCGAATTCAC 9 273 0 TACCGAATGC 0.766887 -28 GTTAACACTTTGCCGGATGCGGCGTGAACG 10 98 1 TGCCGGATGC 0.998322 -85 TTCCTCATCGTGCCTGATGCACTTCGCTAA 10 154 0 TGCCTGATGC 0.98676 -29 CATTTTGTAATGCCGGATGCGGCGTAAAAC 11 34 0 TGCCGGATGC 0.998322 -53 GCCGGTGCCGGATGCGGCGTAAACG 14 6 1 TGCCGGATGC 0.998322 -105 GTGGTTCGGGTGTCGGATGCGACGCTGACG 14 81 0 TGTCGGATGC 0.98676 -30 GCCTGCACATTGTCGGATGCGACGCCGGGG 15 31 0 TGTCGGATGC 0.98676 -24 GACTGCCTGATGCGACGCTTGCG 18 4 1 TGCCTGATGC 0.98676 -297 TCGGCACCATTGCCGGATGCGGCGTAAACG 18 83 0 TGCCGGATGC 0.998322 -218 CCGGCAATGGTGCCGACTGCCTGATGCGAC 18 97 1 TGCCGACTGC 0.945636 -204 TCGGCACTGTTGCCGGATGCGGCGTAAACG 18 183 0 TGCCGGATGC 0.998322 -118 CCGGCAACAGTGCCGACTGCCTGATGCGAC 18 197 1 TGCCGACTGC 0.945636 -104 ********** Masking position 4 Map Score: 77.6598 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 270 Number in noncoding regions = 277 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 11 TCATTCCTGATTTTAATTAACGCGCGAATA 1 266 0 TTTTAATTAA 0.884661 -22 CTTCGTTAACTTATAATTAAGAGAAAAAAA 2 61 0 TTATAATTAA 0.865721 -240 TCAACCTTTATTATAAATAAAAGTTATGAA 2 100 0 TTATAAATAA 0.879628 -201 TAATAAAGGTTGATAATTAAAAGCCTATAT 2 117 1 TGATAATTAA 0.735127 -184 CGTTTCTCTTATTTAAATAATTACCCACAC 2 150 0 ATTTAAATAA 0.693398 -151 CTTCAGTCTGATTTAAATAAGCGTTGATAT 12 164 0 ATTTAAATAA 0.693398 -137 TGTTAGTCACTTTTAATTAACCAAATCGTC 17 67 1 TTTTAATTAA 0.884661 -66 TACGAAATAATTATAAATAAATCTATTATT 19 158 1 TTATAAATAA 0.879628 -143 AATCTATCTTTTTTAAATAAGGACATCTT 19 282 1 TTTTAAATAA 0.900993 -19 AGTGCGGTTATCTTAAATAATTTTGGAAAA 21 66 1 TCTTAAATAA 0.680471 -25 ACCGATGGATTGATAATTAACTTTATTCCC 22 218 0 TGATAATTAA 0.735127 -83 ********** Masking position 5 Map Score: 5.50679 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 36 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 12 TACTTCCAGACACTATGAAGTTGTGAAACA 2 240 1 CACTATGAAG 0.873965 -61 GATAGTCAGTCACTATGGAGATCGCGG 7 284 1 CACTATGGAG 0.961839 -17 GTCCCCTCGCCCCTCTGGGGAGAGGGTTAG 10 38 0 CCCTCTGGGG 0.972156 -145 GTGCATCAGGCACGATGAGGAAAAGATTGC 10 162 1 CACGATGAGG 0.922192 -21 GTCCCCTCGCCCCTCTGGGGAGAGGGTTAG 13 43 0 CCCTCTGGGG 0.972156 -83 CGCCCCTCACCCCAATGGGGAGAGGGAGAA 13 106 0 CCCAATGGGG 0.858816 -20 AATAATCCGCCACGATGGAGCCACTTTTTT 17 99 1 CACGATGGAG 0.95439 -34 ********** Masking position 6 Map Score: 4.64419 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 87 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 13 TTAAATAAGAGAAACGTTTCGCTGGTAATCAAA 2 164 1 GAACTTCGCT 0.91376 -137 CCCAAACAGATGTGCCATTTGCTTTTTTCTGCG 5 48 1 TTGCTTTGCT 0.910429 -142 TGTAATGTCGGATGCGTTTCGCTTATCTGACCT 8 15 1 GTGCTTCGCT 0.992484 -83 AACTGTGCCGGATGCGCTTCGCTTATCCGGCCT 8 60 0 GTGCTTCGCT 0.992484 -38 CATCGTGCCTGATGCACTTCGCTAATCAGGCTT 10 146 0 GTGCTTCGCT 0.992484 -37 TATGCAACAAGCTACACGTTGCTCCGACTATAC 20 75 1 GTACGTTGCT 0.859914 -226 ACAATTATTTTCTACACTTCGCTACGCAATCTA 22 12 1 TTACTTCGCT 0.929751 -289 CCTTAGGTACGTTACCTTTTGCTCAAGCTAATA 22 111 1 GTACTTTGCT 0.963333 -190 CAGCACCAGTGATGCTATTAGCTTGAGCAAAAG 22 126 0 GTGCTTAGCT 0.953334 -175 * *** ****** Masking position 9 Map Score: 10.1704 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 86 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 TGGCAATATGTTGAATTTGCACGATCTTG 9 10 1 GTTGAATTTG 0.734717 -291 GCATAAAACGCGTGAATTCGCGCATTCGGT 9 262 1 CGTGAATTCG 0.958763 -39 GAAGAGTTAACGGGAATTCGATGACAGTGC 17 34 0 CGGGAATTCG 0.973375 -99 ACGGAGGGTGCGGGAATTTGTAGGCCTGAT 18 40 0 CGGGAATTTG 0.977827 -261 ACGGAGGGTGCGGGAATTTGTAGGCCTGAT 18 140 0 CGGGAATTTG 0.977827 -161 TATGTATTTGGGTGAATTAGTTGAATTTGG 20 114 1 GGTGAATTAG 0.866485 -187 TAACACTCAAGGAGAATTTGTTATGTTTAT 22 47 1 GGAGAATTTG 0.894185 -254 ********** Masking position 5 Map Score: 3.63011 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 82 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 AGGCTTGCTGATCCCGCGCAACAAAACGCCA 1 102 0 ACCCGCGCAA 0.877118 -186 GATTTTAATTAACGCGCGAATATTCAGCGGG 1 257 0 ACGCGCGAAT 0.968447 -31 TTTGGGTATAATCGCGCCCATGCTTTTTCGC 5 23 0 ACGCGCCCAT 0.955501 -167 GGCCTACAAGATCGTGCAAATTCAACATATT 9 15 0 ACGTGCAAAT 0.649863 -286 TGTTGTACCGAATGCGCGAATTCACGCGTTT 9 267 0 ATGCGCGAAT 0.750558 -34 GAGGGGACCGACCGAGCGCCTTTTTGACTCT 10 60 1 ACGAGCGCCT 0.89532 -123 TGAGGGGGCCAGCGCGCACATTCCCTCTCA 13 10 0 ACGCGCACAT 0.973409 -116 AATATTCAATATCGAGCACAATCGGTCCCCT 13 66 0 ACGAGCACAA 0.882436 -60 AGAGGGAGAAAACGAGCGCAATATTCAATAT 13 85 0 ACGAGCGCAA 0.950501 -41 * ********* Masking position 1 Map Score: 2.50637 Number of sites scoring better than the average of aligned sites = 707 Number in coding regions = 670 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529