AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -icpxR9_synecho_opreg_100.orf -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ppiB 205 peptidyl-prolyl cis-trans isomerase B #2 hhoA 198 protease HhoA #3 lim 127 lipophilic protein #4 cheA 56 chemotaxis protein CheA #5 pilJ 146 methyl-accepting chemotaxis protein (MCP) #6 htrA 105 serine protease HtrA #7 1652523 300 regulatory components of sensory transduction system #8 1652728 300 hypothetical protein #9 1652730 69 hypothetical protein #10 1652731 32 hypothetical protein #11 1652734 59 hypothetical protein #12 icfg 99 ICFG #13 hhoB 113 protease HhoB #14 ycf27 154 regulatory components of sensory transduction system #15 era 300 GTP-binding protein Era #16 1001717 182 regulatory components of sensory transduction system #17 ycf27 190 regulatory components of sensory transduction system #18 1001817 118 regulatory components of sensory transduction system #19 tar 45 methyl-accepting chemotaxis protein II #20 tsr 300 methyl-accepting chemotaxis protein I #21 1001301 167 hypothetical protein #22 1653824 238 regulatory components of sensory transduction system Motif number 1 ATTGCCATTCCCGTGCTGTCAGA 1 4 1 GCCATTCCCG 0.915542 -202 TCAATTGGTCCCCATTTCCCCTAGAAAGTT 1 85 1 CCCATTTCCC 0.941363 -121 AAAATCTAATCTCCGTAATTGCTAA 1 191 0 CTAATCTCCG 0.860378 -15 GATGGATTGACTCAACCCCGG 2 2 0 CTCAACCCCG 0.961146 -197 CTAAACCCTTCCCAATCCCATCTTTGCCC 3 109 1 CCCAATCCCA 0.93813 -19 TGTCAACACACCCAACCCCGAATTTGGTCA 4 33 1 CCCAACCCCG 0.987397 -24 ACTGTTCCGACCCATTGCCCAATTGTTTTT 5 109 1 CCCATTGCCC 0.770012 -38 TAGTCATAGTCTAAACTCCCATGGAAACAG 7 194 0 CTAAACTCCC 0.669808 -107 CAAAGCGGGGGTCAGTTCCGACGGGTGACG 8 237 0 GTCAGTTCCG 0.445425 -64 CCCCCTGGTTCCCAACCTCGGAGAAATTTA 9 27 1 CCCAACCTCG 0.757026 -43 CGACAATTTCCCCAGCTCCAGTTTGTTAAA 13 65 1 CCCAGCTCCA 0.915226 -49 TCTGCCCCATCCCCATTGATACCAA 14 6 1 CCCATCCCCA 0.978726 -149 ACCAACGATACCAAACCCCCAATTTGGCTA 14 31 1 CCAAACCCCC 0.926467 -124 GTGGCAAAAAGCCATTTCCCTAAGCATATA 14 59 0 GCCATTTCCC 0.737906 -96 CAAAACTTAACCAATTTCCATTTCCTATCT 16 15 1 CCAATTTCCA 0.790671 -168 TTTTTCGTGCCCAATTTCCAGCCCTAGCGG 16 93 1 CCAATTTCCA 0.790671 -90 GTGAAAAAAGCTAATCTCCGCTAGGGCTGG 16 110 0 CTAATCTCCG 0.860378 -73 CCTGACACTGCCCAATCCCGTCGCCAATGG 20 13 1 CCCAATCCCG 0.975581 -288 CACGGTCTGCCTCATCCCCGTTGATGTCAG 20 198 0 CTCATCCCCG 0.974537 -103 GAACTCAGCCCCATCTATCTCCG 20 288 0 CTCAGCCCCA 0.869871 -13 TTCCGGCTAACCAATGCCCGAGCCGATGGA 21 48 1 CCAATGCCCG 0.802769 -120 ********** Masking position 4 Map Score: 25.5226 Number of sites scoring better than the average of aligned sites = 3451 Number in coding regions = 3180 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 TCAGTGGCGTGGAAAAGCTTTGAAAACGGATT 2 100 1 GGAAAAGCTG 0.971208 -99 TGAAAATTTCTGTAAATCCTTGCTAATGCGTA 2 167 1 TGTAAATCTG 0.726098 -32 ATTAAGTTGAGCAAAAACTTTGGGGAGGCCCG 5 15 0 GCAAAAACTG 0.931063 -132 GAATGATAGCTGCAAAACGTCGAAATGGGTCG 8 61 1 TGCAAAACTG 0.951591 -240 ACTAATTTGGTGCAAAGCATAGCATAATCTCC 8 139 0 TGCAAAGCTG 0.933316 -162 TAGTTATCTTGGCAAATCATCT 8 289 1 GGCAAATCTT 0.762354 -12 ACTATGCACTGGCAAAACTTTGTTGT 12 5 0 GGCAAAACTG 0.986984 -95 AGGGTCAAGCGGAAAAACGTTAAAAACTCCAC 15 243 0 GGAAAAACTA 0.857026 -58 GGGGCAAAACTTAACCAATTTCCA 16 3 1 GGCAAAACTA 0.905608 -180 TCGTTGAATTGGCAAAGCCTAGATAGGAAATG 16 33 0 GGCAAAGCTG 0.981815 -150 TGCTATTGAGGGAAAATCGTTGAATTGGCAAA 16 49 0 GGAAAATCTG 0.965438 -134 AAAAACTCCATCTAAAACATGGGTAATCTTGT 17 22 0 TCTAAAACTG 0.561739 -169 TGGCAGACTGGGAAAATCTTGGACAAATTCCC 18 24 0 GGAAAATCTG 0.965437 -95 AGATACACAAGCAAAAACATTGGTTTCCCTGG 20 238 1 GCAAAAACTG 0.931063 -63 ******** * * Masking position 6 Map Score: 16.6614 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 384 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 AACATAACAAACCCCCGTTTCTGCCCTGAATT 1 54 0 ACCCCTTTCT 0.782793 -152 GTTCAATTGGTCCCCATTTCCCCTAGAAAGTT 1 83 1 TCCCCTTCCC 0.903607 -123 CCACTCCGGCCCCCAAGTTTGCTTGGGCTAGT 2 54 1 CCCCATTTGC 0.978528 -145 ATAAAGTTTACCCCATATTTGTACGGTGCTTA 3 76 0 CCCCATTTGT 0.883509 -52 CCCTTCCCAATCCCATCTTTGCCC 3 114 1 TCCCATTTGC 0.94767 -14 AGAGTCAGATCCCCCAAGTGGCCACCAAGCTC 7 242 1 CCCCCGTGGC 0.975608 -59 TCGGAACTGACCCCCGCTTTGCTTAAATTAAA 8 246 1 CCCCCTTTGC 0.993041 -55 TTTAAAAATCCCCCCTGGTTCCCAACCTCGGA 9 17 1 CCCCCGTTCC 0.981469 -53 GATACCAAACCCCCAATTTGGCTATATGCTTA 14 37 1 CCCCATTGGC 0.967965 -118 GTTGGGTTAACCCCACTGTGCCATTCGGTAAT 15 130 0 CCCCAGTGCC 0.918142 -171 CGAAAAAAATTCCCCCGTTTGCTATTGAGGGA 16 68 0 TCCCCTTTGC 0.982669 -115 ATTTTTTTCGTGCCCAATTTCCAGCCCTAGCG 16 90 1 TGCCCTTTCC 0.892066 -93 TGAAAATTAGCGCCCTGTTTCCCGCGGCATTT 17 91 0 CGCCCTTTCC 0.954126 -100 TGAATTTCATACCCCCTTTGGCAGACTGGGAA 18 42 0 ACCCCTTGGC 0.942371 -77 TACGATTTTCTCCCCCTTTTCTTCAATTTTAC 22 99 0 TCCCCTTTCT 0.892291 -140 ***** ***** Masking position 9 Map Score: 23.7372 Number of sites scoring better than the average of aligned sites = 1058 Number in coding regions = 942 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 4 ATTTTCACTTTTGCCATTCTAACAGGGACGATT 2 141 0 TTGCCTTAAC 0.971057 -58 AAAGTCTTTACTGCCTGGGTAACAGTGGCTAAG 3 47 1 CTGCCGTAAC 0.897197 -81 ATATTTCTCCATGCCTTGTCAACACACCCAACC 4 17 1 ATGCCGCAAC 0.881231 -40 CTACGATCAATTGCCGATCTATCTTAATGCTTC 7 145 1 TTGCCTTATC 0.915712 -156 TCGAGCTGGATTTCCTCAGTAACATTTCGTTAC 8 90 1 TTTCCATAAC 0.745622 -211 CCCGACTAAATTGCCACTGTAACGAAATGTTAC 8 108 0 TTGCCTTAAC 0.971056 -193 AGATGATTTGCCAAGATAACTAAAAGTAAT 8 281 0 TTGCCGTAAC 0.985677 -20 CTTTCCGTCCTTCCCGTGGCATCAACAT 10 15 1 TTCCCGCATC 0.784295 -18 CAACAAAGTTTTGCCAGTGCATAGTTGAAAATC 12 12 1 TTGCCTCATA 0.560619 -88 ACGAAAACTCTTTCCCCTTCAACCCAGCTAAAT 13 25 0 TTTCCTCAAC 0.953723 -89 GTGGTATTGGTTTCGGCGGTAACGC 15 3 0 TTTCGGTAAC 0.711484 -298 TATCTAGGCTTTGCCAATTCAACGATTTTCCCT 16 40 1 TTGCCTCAAC 0.976892 -143 TTATAATAGGTTGCCCCTTTAAAATCGTTTTTT 17 145 1 TTGCCTTAAA 0.757699 -46 TTGATGTCAGTTTCCTTGCCATCGCTAAACCAA 20 175 0 TTTCCGCATC 0.931923 -126 TCGGTCAAATTTTCCAGGGAAACCAATGTTTTT 20 250 0 TTTCCGAAAC 0.825155 -51 CCGGTTAATTTTTTCCGGCTAACCAATGCCCGA 21 36 1 TTTTCGTAAC 0.639423 -132 GAGCAACTGTTTTGCCAGCCAACACCTTTTCCT 21 137 1 TTTGCGCAAC 0.767729 -31 ***** * **** Masking position 11 Map Score: 12.9464 Number of sites scoring better than the average of aligned sites = 734 Number in coding regions = 643 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 5 GACGACGGTATGAAATTTTTGTGTCAGTTTT 6 51 0 TGAATTTTTG 0.787108 -55 TTAGTTCTCTTTGAATTTTTCTTTCGGAGTG 8 166 1 TTGATTTTTC 0.975753 -135 TCTGAACAGGTGAATTTTTTCAAGCCCGTCA 8 211 1 TGAATTTTTC 0.932556 -90 CATGGTGATATTGATTTTTTGGGTATCTTTT 15 57 0 TTGATTTTTG 0.914973 -244 GTTTACCTCCTTGACTTTTTCCTCTGGTTGA 15 204 1 TTGATTTTTC 0.975753 -97 ATTAACTCAGTGGAGTTTTTAACGTTTTTCC 15 234 1 TGGATTTTTA 0.78676 -67 ATTTTTAGGCTTGATTTTTTCA 15 289 1 TTGATTTTTC 0.975753 -12 TGGAAATTGGTTAAGTTTTGCCCC 16 4 0 TTAATTTTGC 0.755108 -179 ATGTTTTAGATGGAGTTTTTCTTGGTCATGA 17 34 1 TGGATTTTTC 0.974117 -157 TTCTTTCCGGTTAATTTTTTCCGGCTAACCA 21 30 1 TTAATTTTTC 0.93665 -138 CTAAAGCTGATTGATTTTTCCGGTCCCCCCT 21 92 1 TTGATTTTCC 0.893533 -76 **** ****** Masking position 4 Map Score: 11.2611 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 131 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 CTCCCACTCCGGCCCCCAAGTTTGCTTGGG 2 51 1 GGCCCCCAAG 0.691118 -148 AAAGCTTTTCCACGCCACTGACTTGTGGGC 2 91 0 CACGCCACTG 0.830725 -108 CTTAGGTAAAATCGTCCCTGTTAGAATGGC 2 132 1 ATCGTCCCTG 0.709573 -67 TTATCGGGCCTCCCCAAAGTTTTTGCTCA 5 10 1 CTCCCCAAAG 0.814781 -137 TCATAGTCTAAACTCCCATGGAAACAGTAT 7 191 0 AACTCCCATG 0.754204 -110 TTAGAGTCAGATCCCCCAAGTGGCCACCAA 7 240 1 ATCCCCCAAG 0.941794 -61 TCCCGACTAAATTGCCACTGTAACGAAATG 8 112 0 ATTGCCACTG 0.633794 -189 ACTTTTAAAAATCCCCCCTGGTTCCCAACC 9 14 1 ATCCCCCCTG 0.985536 -56 TGGGGAAATTGTCGCCAAAGGACGAAAACT 13 49 0 GTCGCCAAAG 0.842109 -65 TCTGCCCCATCCCCATTGATACCAACGA 14 9 1 ATCCCCATTG 0.843507 -146 ATGTTGGGTTAACCCCACTGTGCCATTCGG 15 134 0 AACCCCACTG 0.952781 -167 AAACGTTAAAAACTCCACTGAGTTAATCAA 15 231 0 AACTCCACTG 0.777192 -70 GCCCAATCCCGTCGCCAATGGCGAGACCCT 20 22 1 GTCGCCAATG 0.933314 -279 ACTTTATATCCCCCATGCTTTCTTTCC 21 8 1 ATCCCCCATG 0.97699 -160 GATTTTTCCGGTCCCCCCTGGGACGGTTTT 21 104 1 GTCCCCCCTG 0.980405 -64 ********** Masking position 6 Map Score: 11.685 Number of sites scoring better than the average of aligned sites = 1791 Number in coding regions = 1580 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 7 CAATTGGTCCCCATTTCCCCTAGAAAGTTAT 1 86 1 CCATTCCCCT 0.673426 -120 TGTTAGGAACCTTAGTCCACTTTAGATAACT 1 111 0 CTTATCCACT 0.564198 -95 GCAACTCCCACTCCGGCCCCCAAGTTTGCTT 2 47 1 CTCCGCCCCC 0.678552 -152 TTAATCCTTACTTTTTCACCTTAACAGAGTC 5 54 1 CTTTTCACCT 0.810506 -93 ACAACTTTTAGTTTGTCCACTAGATCAGATA 7 24 1 GTTTTCCACT 0.592537 -277 TGAAAAGCAGCTCTGTCCTCTACCAACATTG 7 85 0 CTCTTCCTCT 0.910358 -216 GGGGATGTTTTCTCAACTCTAGCAAGAA 7 283 0 TTTTTCAACT 0.332602 -18 TACTAATATTCTATCTCCTCCATTTATGCGG 12 47 0 CTATTCCTCC 0.824257 -53 AGGACGAAAACTCTTTCCCCTTCAACCCAGC 13 30 0 CTCTTCCCCT 0.962344 -84 ACCTCCTTGACTTTTTCCTCTGGTTGATTAA 15 208 1 CTTTTCCTCT 0.931338 -93 CGGAGATTAGCTTTTTTCACCATGTCATTAT 16 120 1 CTTTTTCACC 0.456697 -63 TTTCCTTTAGTTTTAGCCCCTGAGC 17 176 1 TTTTGCCCCT 0.728825 -15 AGGTGAAAATCTCCTTCCCCCGCTAAGATCA 18 73 1 CTCCTCCCCC 0.86868 -46 ACCAGCGCTTCTTTTGCCACCATCGATGGAG 20 113 1 CTTTGCCACC 0.8587 -188 CCTACCTCACTTTTATCCTCTCCATCGATGG 20 132 0 TTTTTCCTCT 0.769947 -169 ACTTTATATCCCCCATGCTTTCTT 21 4 1 TTATTCCCCC 0.744391 -164 CCAGCCAACACCTTTTCCTCTGATACC 21 151 1 CCTTTCCTCT 0.736837 -17 TTCTTTACGATTTTCTCCCCCTTTTCTTCAA 22 105 0 TTTTTCCCCC 0.908683 -134 TTGTGCTTTTCTCTATCAACCTCAGCTTACC 22 212 0 CTCTTCAACC 0.641147 -27 **** ****** Masking position 10 Map Score: 10.0981 Number of sites scoring better than the average of aligned sites = 2132 Number in coding regions = 1846 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 304 Fraction of orfs with sites within 600 bp upstream = 0.0488275 Motif number 8 AAACTTTATCCTAAACCCTTCCCAATCCCATCT 3 99 1 CTAAACCTCC 0.97077 -29 ATCGTTAATCCTGAAACTGTTCCGACCCATTGC 5 94 1 CTGAAACTCC 0.935643 -53 AAAAAGCCCTCTAAAACAATGACCTTGTCCTGA 6 18 1 CTAAAACTAC 0.952161 -88 TGACCTTGTCCTGAAAAACTGACACAAAAATTT 6 37 1 CTGAAAATAC 0.671696 -69 CGCCAAAGGACGAAAACTCTTTCCCCTTCAACC 13 34 0 CGAAAACTTC 0.69322 -80 TTTGTTAAAGTTAAAACACTGACTATTAACAAT 13 86 1 TTAAAACTAC 0.547833 -28 GCGTTACCGCCGAAACCAATACCACGCTCCTAC 15 11 1 CGAAACCTCC 0.938589 -290 AGCCGCATAGCTAAAAAGATACCCAAAAAATCA 15 44 1 CTAAAAATCC 0.946632 -257 AAATTGGGCACGAAAAAAATTCCCCCGTTTGCT 16 77 0 CGAAAAATCC 0.890862 -106 TCTATAATTACTATAAAAATGCCGCGGGAAACA 17 75 1 CTATAAATCC 0.635806 -116 AAATGTATAACTAAACCCATAACCGACATTCAA 19 18 1 CTAAACCTAC 0.929565 -28 CTTGCCATCGCTAAACCAATCCAGGGCATCCCC 20 161 0 CTAAACCTCA 0.669057 -140 ACAGTTGCTCCTAAAAACCGTCCCAGGGGGGAC 21 114 0 CTAAAAAGCC 0.721252 -54 GCTGATGCGACTAAAACTGTTACATTTCGCAAC 22 148 1 CTAAAACTAC 0.952159 -91 ******* * ** Masking position 5 Map Score: 8.74652 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 505 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 9 TTTAAAGTTGGTTAATTTACATAAACGATG 1 147 1 GTTAATTTAC 0.724963 -59 TTAACAGAGTCTTAATTTTCATCGTTAATC 5 74 1 CTTAATTTTC 0.804253 -73 AGAGGACAGAGCTGCTTTTCAACAACAACC 7 95 1 GCTGCTTTTC 0.856766 -206 ATTGATCGTAGTTAATTTTCTAATTATTTT 7 126 0 GTTAATTTTC 0.922021 -175 AATGGGTCGAGCTGGATTTCCTCAGTAACA 8 84 1 GCTGGATTTC 0.732275 -217 ATTGTCTTAAATTTCCCTTTCCCTT 11 6 1 CTTAAATTTC 0.77566 -54 CATTTATGCGGTTGATTTTCAACTATGCAC 12 28 0 GTTGATTTTC 0.906866 -72 TTAGTAAGGAGCTAAATTACTTTTGGTAAA 12 72 1 GCTAAATTAC 0.781272 -28 GAAACAGGGCGCTAATTTTCAGGCCCTGGG 17 102 1 GCTAATTTTC 0.949851 -89 GAGATTTTCACCTGAATTTCATACCCCCTT 18 56 0 CCTGAATTTC 0.819903 -63 AGTCGCATCAGCTAACTTTCCGATTTCTTT 22 130 0 GCTAACTTTC 0.853571 -109 GACTAAAACTGTTACATTTCGCAACATGAA 22 156 1 GTTACATTTC 0.792655 -83 ********** Masking position 7 Map Score: 5.41784 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 287 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 10 GATTTCACTACCAAGAACACCAAATTCAGGG 1 32 1 CCAAGAAACC 0.96185 -174 TCAATCCATCCCAAGAAACCGTTCGGCAACT 2 22 1 CCAAGAACCG 0.956962 -177 ACGATTTTACCTAAGAATCCGTTTTCAAAGC 2 116 0 CTAAGAACCG 0.660168 -83 AGGATTAAGACCAAGATTAAGTTGAGCAAAA 5 31 0 CCAAGATAAG 0.951247 -116 AGATGATTTGCCAAGATAACTAAAAGTAATC 8 280 0 CCAAGATACT 0.876132 -21 TTATTGGTTTCCAAGATCCACAACCCTCCTT 14 121 0 CCAAGATCAC 0.918137 -34 ATCAATATCACCATGATGACGAATCATTAAG 15 73 1 CCATGATACG 0.865471 -228 TCCACAAGGGCCAAGATGAAGGATTACCGAA 15 108 1 CCAAGATAAG 0.951247 -193 TAGCTTCAGCACAAGATTACCCATGTTTTAG 17 12 1 ACAAGATACC 0.763305 -179 AGCATCATGACCAAGAAAAACTCCATCTAAA 17 38 0 CCAAGAAAAC 0.914961 -153 ******* *** Masking position 6 Map Score: 6.05259 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 162 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 11 TTAGTCCACTTTAGATAACTTTCTAGGGGAA 1 100 0 TTAGTAACTT 0.879959 -106 TTTATGTAAATTAACCAACTTTAAAGTCCTT 1 141 0 TTAACAACTT 0.791422 -65 ACGTTGACCAAATTCGGGGTTGGG 4 43 0 TTGACAAATT 0.75489 -14 CCCAAAGTTTTTGCTCAACTTAATCTTGGTC 5 23 1 TTGCCAACTT 0.898813 -124 CAGATTCCATTGGACAACTTTTAGTTTGTC 7 10 1 TTGGCAACTT 0.970776 -291 GACCCCCGCTTTGCTTAAATTAAACTGATTA 8 254 1 TTGCTAAATT 0.614052 -47 CTGATTACTTTTAGTTATCTTGGCAAATCAT 8 278 1 TTAGTATCTT 0.579051 -23 CAACCCTCCTTTGATTAACTTGTATAACGAT 14 101 0 TTGATAACTT 0.869732 -54 TATTGATTTTTTGGGTATCTTTTTAGCTATG 15 49 0 TTGGTATCTT 0.795264 -252 GAAATGGAAATTGGTTAAGTTTTGCCCC 16 8 0 TTGGTAAGTT 0.728288 -175 TGGGAAAATCTTGGACAAATTCCCAATTTGA 18 17 0 TTGGCAAATT 0.9052 -102 CTCCGGTTCCTCGGTCAAATTTTCCAGGGAA 20 262 0 TCGGCAAATT 0.73486 -39 TGGCTGGACATTAAACAACTTTTAAGTTTAA 22 26 0 TTAACAACTT 0.791422 -213 TTTAGTCGCATCAGCTAACTTTCCGATTTCT 22 132 0 TCAGTAACTT 0.680285 -107 **** ****** Masking position 7 Map Score: 6.91742 Number of sites scoring better than the average of aligned sites = 861 Number in coding regions = 754 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 12 CAGAAATTTTCACTTTTGCCATTCTAACAGG 2 148 0 CATTTTGCCA 0.912098 -51 CGGTATGAAATTTTTGTGTCAGTTTTTCAGG 6 46 0 TTTTGTGTCA 0.611341 -60 AGATGATTTGCCAAGATAACTAA 8 288 0 ATATTTGCCA 0.74284 -13 ACAACAAAGTTTTGCCAGTGCATAGTT 12 7 1 AATTTTGCCA 0.870267 -93 TAGGGAAATGGCTTTTTGCCACGAAACTTCA 14 67 1 GCTTTTGCCA 0.825755 -88 ACCCAACATATTTTTTTGTCAAGCTGGCAAG 15 155 1 TTTTTTGTCA 0.870672 -146 CACCATGTCATTATTTTGCCAAAAAGTTTGC 16 137 1 TTTTTTGCCA 0.971582 -46 AAACCAGCGCTTCTTTTGCCACCATCGATGG 20 111 1 TTTTTTGCCA 0.971582 -190 TTAGGAGCAACTGTTTTGCCAGCCAACACCT 21 133 1 CTTTTTGCCA 0.965921 -35 ** ******** Masking position 5 Map Score: 2.70059 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 302 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 13 TTAAGGTGAAAAAGTAAGGATTAAGACCAA 5 48 0 AAAGTAAGGA 0.966433 -99 GGCGATTAAAAGTAATTAAAAAACAATT 5 129 0 AAAGTAATTA 0.807241 -18 CATTGAGACGAAACTAAGTAAAAGCCCCTC 7 60 0 AAACTAAGTA 0.866275 -241 AAGATAACTAAAAGTAATCAGTTTAATTTA 8 269 0 AAAGTAATCA 0.818871 -32 GGAAACCAATAAAGAAAGGATATTG 14 140 1 AAAGAAAGGA 0.913345 -15 GACCCTCCATAAACTAAGGAATTTTTAGGC 15 269 1 AAACTAAGGA 0.910605 -32 AATTAACCGGAAAGAAAGCATGGGGGATAT 21 16 0 AAAGAAAGCA 0.878581 -152 AGATAAAGTTAGTAATTAAACTTA 22 5 1 AAAGTTAGTA 0.766425 -234 ********** Masking position 7 Map Score: 0.644864 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 74 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 14 ATTTTCTAATTATTTTCGGTTGTTGTTGAAA 7 111 0 TTTTTCGGTT 0.921186 -190 GTTTTTAACGTTTTTCCGCTTGACCCTCCAT 15 248 1 TTTTCCGCTT 0.945424 -53 CAGCCCCATCTATCTCCGGTTCCTCGGTCAA 20 275 0 TTCTCCGGTT 0.965066 -26 CCCCATGCTTTCTTTCCGGTTAATTTTTTCC 21 21 1 TTTTCCGGTT 0.986937 -147 TCCGGTTAATTTTTTCCGGCTAACCAATGCC 21 35 1 TTTTCCGGCT 0.965066 -133 AGCTGATTGATTTTTCCGGTCCCCCCTGGGA 21 96 1 TTTTCCGGTC 0.965066 -72 * ********* Masking position 5 Map Score: 2.89327 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 38 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 15 ********** No masking Map Score: 5.54467e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0