AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -icpxR_synecho_opreg_300.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 1651677 300 hypothetical protein #2 1651678 76 hypothetical protein #3 1651679 105 ABC transporter #4 1651680 105 regulatory protein PchR #5 1651681 165 ferrichrome-iron receptor #6 1651682 41 iron(III) dicitrate-binding periplasmic protein #7 1651683 173 iron(III) dicitrate-binding periplasmic protein #8 1651685 62 ABC transporter #9 ppiB 205 peptidyl-prolyl cis-trans isomerase B #10 ycf4 138 hypothetical protein #11 1651786 21 hypothetical protein #12 1651787 300 hypothetical protein #13 hhoA 198 protease HhoA #14 lim 127 lipophilic protein #15 cyaA 38 adenylate cyclase #16 1652045 74 hypothetical protein #17 1652046 195 esterase #18 cheA 56 chemotaxis protein CheA #19 pilJ 146 methyl-accepting chemotaxis protein (MCP) #20 1652277 32 hypothetical protein #21 1652278 106 regulatory components of sensory transduction system #22 1652279 300 regulatory components of sensory transduction system #23 1652456 46 hypothetical protein #24 1652457 198 rehydrin #25 mutL 103 DNA mismatch repair protein MutL #26 livH 184 high-affinity branched-chain amino acid transport protein #27 1652460 97 hypothetical protein #28 lacF 115 lactose transport system permease protein LacF #29 1652462 109 hypothetical protein #30 htrA 105 serine protease HtrA #31 1652523 300 regulatory components of sensory transduction system #32 1652728 300 hypothetical protein #33 1652730 69 hypothetical protein #34 1652731 32 hypothetical protein #35 1652734 59 hypothetical protein #36 icfg 99 ICFG #37 hhoB 113 protease HhoB #38 1653091 125 hypothetical protein #39 proS 168 proline-tRNA ligase #40 1653492 213 hypothetical protein #41 1653493 151 hypothetical protein #42 arsC 89 arsenate reductase #43 ycf27 154 regulatory components of sensory transduction system #44 era 300 GTP-binding protein Era #45 rnhA 80 ribonuclease H #46 1001717 182 regulatory components of sensory transduction system #47 1208480 156 hypothetical protein #48 1208481 111 hypothetical protein #49 1208482 181 hypothetical protein #50 1208483 122 hypothetical protein #51 ycf27 190 regulatory components of sensory transduction system #52 1001817 118 regulatory components of sensory transduction system #53 tar 45 methyl-accepting chemotaxis protein II #54 tsr 300 methyl-accepting chemotaxis protein I #55 1001301 167 hypothetical protein #56 cheY 137 chemotaxis protein CheY #57 1001303 249 chemotaxis protein CheY #58 1653824 238 regulatory components of sensory transduction system Motif number 1 CAGGCAATTATTGTGGCCCCTAGCCTAGGCTGAAC 1 260 0 TGTGCCTGCC 0.886003 -41 ATCAAAGTGATTGCCCGCCGTCCCCGTCTTACCGG 5 48 1 TGCCGCTCCC 0.968722 -118 ATGCCATACTTCCTCCCCTATCCCCGATCCAAAAT 7 32 0 TCTCCCTCCC 0.980598 -142 TATGTTCAATTGGTCCCCATTTCCCCTAGAAAGTT 9 80 1 TGTCCCTCCC 0.990074 -126 TGGTAGAGGTTAGACCCCAGTTCCCCTAAGGTGAT 10 34 1 TGACCCTCCC 0.96925 -105 CGCCCTATCATCCTAGCCCCTAGCCCTGATGGGGT 10 69 1 TCTGCCTGCC 0.797494 -70 GGTCAACTCCTAGCACCAATTTCCCAAGACTACGG 12 275 0 TGCCCATCCC 0.971434 -26 GTACGGTGCTTAGCCACTGTTACCCAGGCAGTAAA 14 53 0 TGCACTTCCC 0.874351 -75 CCTGAAACTGTTCCGACCCATTGCCCAATTGTTTT 19 103 1 TCCACCTGCC 0.949804 -44 ATGATTATCATCGTTAGCAATTGCCCAGGGGGATA 21 79 1 TGTAGCTGCC 0.610342 -28 CAAGCACCATTTCATCCCTTATCCCATTTCTTCAA 22 97 0 TCACCCACCC 0.656427 -204 CCCCATTGTCTCGCCCCCCCTAGCCTGACCTCTGA 27 41 1 TGCCCCTGCC 0.992209 -57 TCTATCTTAATGCTTCCATTTGCCCCAAAATACTG 31 162 1 TCTCCATCCC 0.863632 -139 CTTTTAAAAATCCCCCCTGGTTCCCAACCTCGGAG 33 15 1 TCCCCTTCCC 0.923226 -55 TTTCGTCCTTTGGCGACAATTTCCCCAGCTCCAGT 37 52 1 TGCACATCCC 0.908851 -62 GTTGCAGAAATAGCACCCTTTTGCCCCAGCTTTTT 38 37 1 TGCCCCTGCC 0.992209 -89 CCCCAGTATTTTGCTCCCGCTCCCCTATGATAATT 39 48 0 TGCCCCTCCC 0.996329 -121 GGAATTTTTTTCGTGCCCAATTTCCAGCCCTAGCG 46 87 1 TGTCCCTTCC 0.914579 -96 GAGTCTATTTTCCCAACCTAAACCCAGAGTTTGAT 48 40 1 TCCACCACCC 0.828276 -72 GCCTGAAAATTAGCGCCCTGTTTCCCGCGGCATTT 51 91 0 TGCCCCTTCC 0.966811 -100 TTGCGTACTTTGGCGACCCATACCCCTTTCAGGGC 57 172 1 TGCACCTCCC 0.987589 -78 * ** *** * *** Masking position 1 Map Score: 28.7525 Number of sites scoring better than the average of aligned sites = 928 Number in coding regions = 829 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 2 CCGGTAAGACGGGGACGGCGGGCAATCACTTT 5 51 0 GGGGAGCGGG 0.950796 -115 ATTTTGGATCGGGGATAGGGGAGGAAGTATGG 7 32 1 GGGGAGGGGA 0.975327 -142 CAAATTCAGGGCAGAAACGGGGGTTTGTTATG 9 52 1 GCAGACGGGG 0.870881 -154 AACTTTCTAGGGGAAATGGGGACCAATTGAAC 9 83 0 GGGAAGGGGA 0.958027 -123 CCAAATTTTGGGAGCTAGGGGACTTT 10 5 0 GGAGCGGGGA 0.953103 -134 GATCACCTTAGGGGAACTGGGGTCTAACCTCT 10 38 0 GGGGATGGGG 0.929624 -101 GGGAATCTGAGGAAAGTCCGGGCTTCCCAAAG 12 129 0 GGAAACCGGG 0.598641 -172 GAGTTAGGGAGGGAGTTGCGGATTCCTGTCAC 12 162 0 GGGAGGCGGA 0.439559 -139 ACTAGCCCAAGCAAACTTGGGGGCCGGAGTGG 13 54 0 GCAAATGGGG 0.852669 -145 GGGCAAAGATGGGATTGGGAAGGG 14 114 0 GCAAATGGGA 0.717526 -14 CTAATACAATGCAAAATGGGGATCTTCTTCGA 24 165 0 GCAAAGGGGA 0.945413 -34 GAGCTTTTAAGCGGAGAGGGAGAAAAATCATC 25 69 1 GCGGAGGGAG 0.857272 -35 ACTAAGTCCCGGAAATAGCGGGTTTGAGCCTG 26 127 1 GGAAAGCGGG 0.937938 -58 TTCTAGAATTGGAGAAAGGTGGGCCTAATCCA 26 157 0 GGAGAGGTGG 0.904305 -28 TTTAATTTAAGCAAAGCGGGGGTCAGTTCCGA 32 246 0 GCAAAGGGGG 0.975284 -55 TCCGAGGTTGGGAACCAGGGGGGATTTTTAAA 33 17 0 GGAACGGGGG 0.963945 -53 TTAACAAACTGGAGCTGGGGAAATTGTCGCCA 37 62 0 GGAGCGGGAA 0.707549 -52 GGCAGAGAGCTGGGGAAAGTGAT 39 2 1 GCAGAGCTGG 0.531787 -167 AATTATCATAGGGGAGCGGGAGCAAAATACTG 39 48 1 GGGGAGGGAG 0.914689 -121 GGATGTGAATGGAACAATGGGGGCAATGAGAT 40 60 1 GGAACTGGGG 0.796798 -154 CACGGCAACAGTAGACCGGGGACAGACCGAGT 40 133 1 GTAGAGGGGA 0.702686 -81 CCAAATTTGGGGGGCCAGGGGGGCTTTTAAAA 41 97 1 GGGGCGGGGG 0.971578 -55 TGGTATCAATGGGGATGGGGCAGA 43 3 0 GGGGAGGGCA 0.850362 -152 TCCCTCAATAGCAAACGGGGGAATTTTTTTCG 46 68 1 GCAAAGGGGA 0.945413 -115 CGCTAGGGCTGGAAATTGGGCACGAAAAAAAT 46 90 0 GGAAAGGGCA 0.816328 -93 AAATGCCGCGGGAAACAGGGCGCTAATTTTCA 51 91 1 GGAAAGGGCG 0.910122 -100 ACCCCCTTTGGCAGACTGGGAAAATCTTGGAC 52 32 0 GCAGAGGGAA 0.781221 -87 AGGAGGCCCCGGAAAATTGTGGAGTCTCCCTT 56 20 1 GGAAATGTGG 0.444523 -118 CAGGTCAACAGCAGGAGGGGGGCATATCTATA 57 211 0 GCAGGGGGGG 0.916286 -39 ***** ***** Masking position 1 Map Score: 31.9131 Number of sites scoring better than the average of aligned sites = 3197 Number in coding regions = 2754 Number in noncoding regions = 443 Number of orfs with sites within 600 bp upstream = 359 Fraction of orfs with sites within 600 bp upstream = 0.0576614 Motif number 3 CTCAATTAATCCCCTTGCCTAGCCATAATA 1 23 1 CCCCTTGCCT 0.956744 -278 ATTATTGTGGCCCCTAGCCTAGGCTGAACT 1 259 0 CCCCTAGCCT 0.945891 -42 CATACTTCCTCCCCTATCCCCGATCCAAAA 7 33 0 CCCCTATCCC 0.936461 -141 CAATTGGTCCCCATTTCCCCTAGAAAGTTA 9 86 1 CCATTTCCCC 0.877908 -120 AAAGTCCCCTAGCTCCCAAAATTTG 10 6 1 CCCCTAGCTC 0.845243 -133 ATCATCCTAGCCCCTAGCCCTGATGGGGTA 10 75 1 CCCCTAGCCC 0.984235 -64 ACTCCTAGCACCAATTTCCCAAGACTACGG 12 275 0 CCAATTTCCC 0.466454 -26 TCTGTTTTTGCCCTTTGTCCTGCCCAGGCA 16 46 1 CCCTTTGTCC 0.587088 -29 ACTGTTCCGACCCATTGCCCAATTGTTTTT 19 109 1 CCCATTGCCC 0.958289 -38 ACCATTTCATCCCTTATCCCATTTCTTCAA 22 97 0 CCCTTATCCC 0.892737 -204 TGTCTCGCCCCCCCTAGCCTGACCTCTGAC 27 47 1 CCCCTAGCCT 0.945891 -51 CTTAATGCTTCCATTTGCCCCAAAATACTG 31 167 1 CCATTTGCCC 0.877908 -134 TCTTAAATTTCCCTTTCCCTTCAATTCACC 35 15 1 CCCTTTCCCT 0.925872 -45 AGGACGAAAACTCTTTCCCCTTCAACCCAG 37 31 0 CTCTTTCCCC 0.803082 -83 GAAATAGCACCCTTTTGCCCCAGCTTTTTA 38 43 1 CCTTTTGCCC 0.639501 -83 GTCTAGTTATCACTTTCCCCAGCTCTCTGC 39 12 0 CACTTTCCCC 0.617452 -157 TTATGGAAATCTCATTGCCCCCATTGTTCC 40 70 0 CTCATTGCCC 0.677465 -144 TTTAAAAGCCCCCCTGGCCCCCCAAATTTG 41 98 0 CCCCTGGCCC 0.91466 -54 TCTGCCCCATCCCCATTGATACCA 43 5 1 CCCCATCCCC 0.803481 -150 TGGCAAAAAGCCATTTCCCTAAGCATATAG 43 58 0 CCATTTCCCT 0.668145 -97 CCAATTTTTACCCATATCCTGGGGAGTTAG 47 49 0 CCCATATCCT 0.545505 -108 CCGTTTCCCCTACCTTGACCTATTAC 47 141 0 CCCCTACCTT 0.604634 -16 CCTATCTTTTCCATTACCCTACTACGGGCG 49 30 1 CCATTACCCT 0.614089 -152 AGGTGAAAATCTCCTTCCCCCGCTAAGATC 52 73 1 CTCCTTCCCC 0.878374 -46 TCCAGGGCATCCCCTACCTCACTTTTATCC 54 145 0 CCCCTACCTC 0.845243 -156 ACTTTGGCGACCCATACCCCTTTCAGGGCA 57 178 1 CCCATACCCC 0.947803 -72 ********** Masking position 1 Map Score: 29.5044 Number of sites scoring better than the average of aligned sites = 2444 Number in coding regions = 2124 Number in noncoding regions = 320 Number of orfs with sites within 600 bp upstream = 287 Fraction of orfs with sites within 600 bp upstream = 0.046097 Motif number 4 TTTGTCGGGAATTGTGAGGTCAAGAAATTAGCC 3 44 1 ATTGAGGCAA 0.715533 -62 AAAAATTAAGACATAGGGGTTAAAAAGTGTGGG 8 32 0 AAAGGGGTAA 0.73192 -31 TGTCACAGGGAATCTGAGGAAAGTCCGGGCTTC 12 135 0 ATTGAGGAAG 0.449758 -166 TCCCAAGACTACGGAGGGGGCAATGAAGTTTCA 12 256 0 AGAGGGGCAA 0.803409 -45 GCACCGTACAAATATGGGGTAAACTTTATCCTA 14 79 1 ATTGGGGAAA 0.96558 -49 GGCGTAACTTAAACTGGGGATAAACCAGCTTTG 17 75 0 AATGGGGTAA 0.937899 -121 TTTTAGAAATAGTATGGGGTTAAACTCTACTCA 22 133 1 ATTGGGGTAA 0.955159 -168 AAAATAGTTAACTTTAGGGCTAATAATTATTGA 22 222 1 ATTAGGGTAA 0.765992 -79 CTGGCCAGTTAGTCTGGGGTAAGGCGATCGCCT 24 25 0 ATTGGGGAAG 0.917211 -174 GGGGGGCGAGACAATGGGGCAAAGAAAAATTGC 27 27 0 AATGGGGAAA 0.95213 -71 TGGAAACAGTATTTTGGGGCAAATGGAAGCATT 31 170 0 ATTGGGGAAA 0.96558 -131 GACAGTCTAGGGACAATTAAAATGTC 32 4 1 ATTAGGGCAA 0.839722 -297 TTTCCCTAAAAAGCTGGGGCAAAAGGGTGCTAT 38 46 0 AGTGGGGAAA 0.948982 -80 CGGGAGCAAAATACTGGGGAAAATACAGAGCAA 39 64 1 AATGGGGAAA 0.95213 -105 TGTGAATGGAACAATGGGGGCAATGAGATTTCC 40 63 1 AATGGGGCAA 0.960275 -151 TAGTTGGTCGATTGAGGGGGCAGAATAAAACTT 41 24 0 ATAGGGGCAG 0.708801 -128 TGGCCCCCCAAATTTGGGGGGAAACTGAGTGAA 41 81 0 ATTGGGGGAA 0.867625 -71 ACCGAATGGCACAGTGGGGTTAACCCAACATAT 44 133 1 AATGGGGTAA 0.937899 -168 AAATTCAGCAAGGTTAGGGTTAATGGGAAAATC 45 54 0 AGTAGGGTAA 0.684591 -27 TTAGGGAATTATACTGGGGTCAGAAGCCAATTT 47 72 0 AATGGGGCAG 0.905184 -85 GTAATAGGTCAAGGTAGGGGAAACGG 47 141 1 AGTAGGGAAA 0.740828 -16 * * ***** *** Masking position 12 Map Score: 22.7152 Number of sites scoring better than the average of aligned sites = 710 Number in coding regions = 560 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 5 AAGTATGGCATTCCCCGCTTGCGCTTTGCT 7 56 1 TTCCCCGCTT 0.772105 -118 AACATAACAAACCCCCGTTTCTGCCCTGAA 9 56 0 ACCCCCGTTT 0.931928 -150 GTTCAATTGGTCCCCATTTCCCCTAGAAAG 9 83 1 TCCCCATTTC 0.714602 -123 TAGAGGTTAGACCCCAGTTCCCCTAAGGTG 10 37 1 ACCCCAGTTC 0.896044 -102 CCCCCAGCATCGGAGCCAAA 14 1 1 CCCCCAGCAT 0.760353 -127 AGCTGGTTTATCCCCAGTTTAAGTTACGCC 17 78 1 TCCCCAGTTT 0.97665 -118 TCGAAGAAGATCCCCATTTTGCATTGTATT 24 165 1 TCCCCATTTT 0.839775 -34 GTCGGAACTGACCCCCGCTTTGCTTAAATT 32 245 1 ACCCCCGCTT 0.946649 -56 GGCGACAATTTCCCCAGCTCCAGTTTGTTA 37 63 1 TCCCCAGCTC 0.962823 -51 GCACCCTTTTGCCCCAGCTTTTTAGGGAAA 38 49 1 GCCCCAGCTT 0.895293 -77 GTTATCACTTTCCCCAGCTCTCTGCC 39 7 0 TCCCCAGCTC 0.962823 -162 CTCTGTATTTTCCCCAGTATTTTGCTCCCG 39 64 0 TCCCCAGTAT 0.93947 -105 GAGTGAAAGTTCCCCAGTATTGCGGTCGCT 41 58 0 TCCCCAGTAT 0.93947 -94 CCTGCTTATGATCCCAGCTTGACCAGCGCT 45 24 1 ATCCCAGCTT 0.658237 -57 CGAAAAAAATTCCCCCGTTTGCTATTGAGG 46 70 0 TCCCCCGTTT 0.969454 -113 ACCAGCTAACTCCCCAGGATATGGGTAAAA 47 44 1 TCCCCAGGAT 0.745085 -113 TTGGCTTCTGACCCCAGTATAATTCCCTAA 47 75 1 ACCCCAGTAT 0.870045 -82 AAAATCTCCTTCCCCCGCTAAGATCAGACC 52 78 1 TCCCCCGCTA 0.790167 -41 TACGATTTTCTCCCCCTTTTCTTCAATTTT 58 101 0 TCCCCCTTTT 0.799075 -138 ********** Masking position 5 Map Score: 22.2919 Number of sites scoring better than the average of aligned sites = 813 Number in coding regions = 703 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 6 GTCAGTGGCGTGGAAAAGCTTTGAAAACGG 13 99 1 TGGAAAAGCT 0.828129 -100 CCTGTTAGAATGGCAAAAGTGAAAATTTCT 13 148 1 TGGCAAAAGT 0.904803 -51 TCAAGCTTAATGGCAAAATTTAACTTTAAA 17 136 0 TGGCAAAATT 0.756987 -60 ATCATGGCAAATGTAACAATAGAT 22 5 1 TGGCAAATGT 0.884537 -296 CTTCAATCTATGGGAAATCTATCCCTTGGG 22 39 0 TGGGAAATCT 0.616029 -262 TTAGTTATCTTGGCAAATCATCT 32 288 1 TGGCAAATCA 0.917251 -13 AACTATGCACTGGCAAAACTTTGTTGT 36 8 0 TGGCAAAACT 0.949283 -92 ACTTACCCTCTGGAAAAAGTGATTCAAGAT 38 105 0 TGGAAAAAGT 0.828962 -21 TGTCTTCCGATGGAAAAGGAGCAAAATAGA 40 105 0 TGGAAAAGGA 0.642565 -109 TAGTTTCAGTGGGAAAAACA 42 1 0 GGGAAAAACA 0.784527 -89 ATAAGCAGGATGGAAAATCAGA 45 3 0 TGGAAAATCA 0.849679 -78 TAGGGTTAATGGGAAAATCAGCGCTGGTCA 45 43 0 GGGAAAATCA 0.745848 -38 GGGGCAAAACTTAACCAATTT 46 2 1 GGGCAAAACT 0.906697 -181 ATCGTTGAATTGGCAAAGCCTAGATAGGAA 46 36 0 TGGCAAAGCC 0.749071 -147 GCAAACTTTTTGGCAAAATAATGACATGGT 46 138 0 TGGCAAAATA 0.695933 -45 AGTTAAAGGGAAAATCTATAAATATTT 48 95 0 GGGAAAATCT 0.799764 -17 TTGGCAGACTGGGAAAATCTTGGACAAATT 52 27 0 GGGAAAATCT 0.799764 -92 CCATCGATGGTGGCAAAAGAAGCGCTGGTT 54 112 0 TGGCAAAAGA 0.87474 -189 TTGGTTTCCCTGGAAAATTTGACCGAGGAA 54 257 1 TGGAAAATTT 0.561462 -44 AGGTGTTGGCTGGCAAAACAGTTGCTCCTA 55 134 0 TGGCAAAACA 0.932215 -34 GAGGGGACTTTGGCAAAAGCTTTTGTATTA 57 121 0 TGGCAAAAGC 0.750172 -129 ********** Masking position 5 Map Score: 14.6851 Number of sites scoring better than the average of aligned sites = 773 Number in coding regions = 682 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 7 TTGCTATTATGGCTAGGCAAGGGGATTAATTGA 1 24 0 GGCTGGAAGG 0.923222 -277 ATGCAGTTCAGCCTAGGCTAGGGGCCACAATAA 1 255 1 GCCTGGTAGG 0.911849 -46 GCACCAATTTCCCAAGACTACGGAGGGGGCAAT 12 265 0 CCCAGATAGG 0.757264 -36 GCGTGGAAAAGCTTTGAAAACGGATTCTTAGGT 13 106 1 GCTTGAAAGG 0.784362 -93 AGTCTTTACTGCCTGGGTAACAGTGGCTAAGCA 14 49 1 GCCTGGAAAG 0.841814 -79 ACGCTGCCTGGGCAGGACAAAGGGCAAAAACAG 16 47 0 GGCAGAAAGG 0.842914 -28 GGATAAACCAGCTTTGGCTATGGAAAAGTCTCT 17 58 0 GCTTGGTAGG 0.638842 -138 TGGTATCCCCCTGGGCAATTGCTAACGATGA 21 86 0 CCCTGGAATG 0.906991 -21 GGAAATCTATCCCTTGGGAAGTATCTATTGTTA 22 24 0 CCCTGGAATA 0.548671 -277 TCCGATTGCTGCCATGACAATGGCCGTGGATAA 28 32 0 GCCAGAAAGG 0.964459 -84 GTATGACAGGGCTATGACGACGGTATGAAATTT 30 64 0 GCTAGAGAGG 0.553665 -42 AGTCTAAACTCCCATGGAAACAGTATTTTGGGG 31 184 0 CCCAGGAAAG 0.818739 -117 AGATGATTTGCCAAGATAACTAAAAGTAATCA 32 279 0 GCCAGAAATA 0.446939 -22 ATGTTGATGCCACGGGAAGGACGGAAAGGTT 34 12 0 GCCAGGAAGA 0.905647 -21 TCCTCCGCTGCCTTAGGTAAAGGGGCATTCAAC 40 30 0 CCTTGGAAGG 0.873699 -184 GCCGTGTCTTCCGATGGAAAAGGAGCAAAATAG 40 106 0 CCGAGGAAGG 0.762068 -108 TTGGCTATATGCTTAGGGAAATGGCTTTTTGCC 43 54 1 GCTTGGAATG 0.711428 -101 TTCCACAAGGGCCAAGATGAAGGATTACCGAAT 44 107 1 GCCAGAGAGG 0.879727 -194 TAAACTATCCGCCTGGAAAACGGCTTGCCAGCT 44 176 0 GCCTGAAAGG 0.955452 -125 GCCAAAATGGCCCTGGACAATGAAAATTTCCCT 49 63 1 CCCTGAAAGA 0.642045 -119 TCGATCCTAGCCCATGGCAAGGGAAATTTTCAT 49 82 0 CCCAGGAAGG 0.975318 -100 CCACGGCGACCCCATGGCAATCGATCCTAGCCC 49 102 0 CCCAGGAACG 0.791506 -80 TCCGGCTAGGCGCAAGGAAAGTGAAAATTTTAA 50 39 0 CGCAGGAATG 0.709279 -84 CATGGTAGAGGCCACGGTGACGGTTTGCTGCAA 50 90 0 GCCAGGGAGG 0.95403 -33 GTTTAGCGATGGCAAGGAAACTGACATCAACGG 54 178 1 GGCAGGAATG 0.784336 -123 **** ** ** ** Masking position 10 Map Score: 19.7864 Number of sites scoring better than the average of aligned sites = 2894 Number in coding regions = 2636 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 283 Fraction of orfs with sites within 600 bp upstream = 0.0454545 Motif number 8 GCCATTATTACCCTTGTGTTCAGGTCTCCATCA 3 74 1 CCCTTGGTCG 0.888083 -32 TTATCAGATGCCATGGCCGGCTGTCTCAACTAA 5 128 1 CCATGGCGCG 0.951487 -38 ATTGCCATTCCCGTGCTGTCAGATTTCACTAC 9 10 1 CCCGTGTGCG 0.966981 -196 TGTTCAACCGCCATTGTTGTCCC 22 288 1 CCATTGTGCC 0.968779 -13 AGAAAAATTGCCATTGCCTCCGGGAAG 27 5 0 CCATTGCTCG 0.925081 -93 ACTAACATAACCATTGCTGGCCCTAGGCATAAA 28 67 0 CCATTGTGCC 0.968779 -49 GTTGTCTTTGCCATTGATGTCAGGTGGTTAACT 49 138 0 CCATTGTGCG 0.990012 -44 AAGGGTCTCGCCATTGGCGACGGGATTGGGCAG 54 20 0 CCATTGCGCG 0.983927 -281 AATGGCGAGACCCTTGATGGCGCTCTTTTTACT 54 38 1 CCCTTGTGCC 0.966687 -263 TGCCTCATCCCCGTTGATGTCAGTTTCCTTGCC 54 188 0 CCGTTGTGCG 0.979777 -113 AAAAACCGTCCCAGGGGGGACCGGAAAAATCAA 55 102 0 CCAGGGGGCG 0.809665 -66 TGTGGAGTCTCCCTTGATTCCAGGCCAATACTT 56 37 1 CCCTTGTTCG 0.948598 -101 CGCATTTACACCGTTGATGGCAGGGATCAATCC 57 55 1 CCGTTGTGCG 0.979777 -195 ****** ** * * Masking position 11 Map Score: 13.8804 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 267 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 GAAATTAAAAAAAATCAGGGTTAAGG 3 1 0 AAAAGGGTGG 0.979996 -105 TGAATTTTACCCCATCAGGGCTAGGGGCTAGGATGA 10 76 0 CCCAGGGTGG 0.919684 -63 GGCACACTAGAAAAAGAGAGTTAGGGAGGGAGTTGC 12 175 0 AAAAGAGTGG 0.820341 -126 CTAGCCCAAGCAAACTTGGGGGCCGGAGTGGGAGTT 13 49 0 CAAAGGGGGG 0.959563 -150 GGGCAAAGATGGGATTGGGAAGGGTTTAG 14 109 0 CAAAGGGTGG 0.988814 -19 ACGTTGACCAAATTCGGGGTTGGGTGTGTTGACA 18 33 0 CAAAGGGTGG 0.988811 -24 GTAATTAAAAAACAATTGGGCAATGGGTCGGAACAG 19 110 0 AACAGGGAGG 0.874736 -37 CTGATCGTTGAAGAAATGGGATAAGGGATGAAATGG 22 90 1 AAGAGGGTGG 0.944377 -211 TTAATTTAAGCAAAGCGGGGGTCAGTTCCGACGGGT 32 241 0 CAAAGGGTGT 0.814253 -60 TTAACTTTAACAAACTGGAGCTGGGGAAATTGTCGC 37 64 0 CAAAGAGTGG 0.891762 -50 GAGAAAAATTATCATAGGGGAGCGGGAGCAAAATAC 39 42 1 ATCAGGGGGG 0.790878 -127 TATCGTTGGTATCAATGGGGATGGGGCAGA 43 5 0 ATCAGGGTGG 0.93372 -150 AGCATATAGCCAAATTGGGGGTTTGGTATCGTTGGT 43 31 0 CAAAGGGTGG 0.988814 -124 ACAAGTTAATCAAAGGAGGGTTGTGGATCTTGGAAA 43 109 1 CAAAGGGTGG 0.988814 -46 GTCAATGATCAAACTCTGGGTTTAGGTTGGGAAAAT 48 46 0 AAACGGGTGG 0.853625 -66 GGAAACTGACATCAACGGGGATGAGGCAGACCGTGG 54 193 1 ATCAGGGTGG 0.93372 -108 ATAGCTTGCCCTGAAAGGGGTATGGGTCGCCAAAGT 57 178 0 CTGAGGGAGG 0.650536 -72 **** *** * ** Masking position 8 Map Score: 20.8598 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 254 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 10 TGTTATCAGATGCCATGGCCGGCTGTCTCAA 5 126 1 TGCCATGGCG 0.980375 -40 TTTTCTAGTGTGCCATTGATTAGAGCCATAG 12 197 1 TGCCATTGAT 0.594367 -104 TAGCCACTGTTACCCAGGCAGTAAAGACTTT 14 47 0 TACCCAGGCG 0.710961 -81 CCCTTTGTCCTGCCCAGGCAGCGTTAATT 16 56 1 TGCCCAGGCG 0.958179 -19 AACTTGCCAATGCTGACTACGGTGA 20 5 1 TGCCAATGCG 0.878423 -28 CGTTAGCAATTGCCCAGGGGGATACCA 21 90 1 TGCCCAGGGG 0.958021 -17 AAAGAAAAATTGCCATTGCCTCCGGGAAG 27 9 0 TGCCATTGCT 0.77443 -89 CCACGGCCATTGTCATGGCAGCAATCGGATC 28 36 1 TGTCATGGCG 0.725532 -80 AAAATACTGTTTCCATGGGAGTTTAGACTAT 31 188 1 TTCCATGGGG 0.752655 -113 AAATTTCCCTTGCCATGGGCTAGGATCGATT 49 86 1 TGCCATGGGT 0.934043 -96 TAGGATCGATTGCCATGGGGTCGCCGTGGTT 49 106 1 TGCCATGGGT 0.935648 -76 GTGTTGTCTTTGCCATTGATGTCAGGTGGTT 49 142 0 TGCCATTGAG 0.834378 -40 CCGTGGCCTCTACCATGGGAGGGTTTT 50 106 1 TACCATGGGG 0.842878 -17 TTTCCCAGTCTGCCAAAGGGGGTATGAAATT 52 41 1 TGCCAAAGGG 0.687124 -78 ACACGGCCGCTGCCCAGGACGAATCGTCGGA 54 81 1 TGCCCAGGAG 0.906654 -220 AGGTAGGGGATGCCCTGGATTGGTTTAGCGA 54 156 1 TGCCCTGGAT 0.822892 -145 ********* * Masking position 1 Map Score: 12.7683 Number of sites scoring better than the average of aligned sites = 1425 Number in coding regions = 1340 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 11 GTTATCAGATGCCATGGCCGGCTGTCTCAA 5 127 1 GCCATGGCCG 0.919661 -39 ACAAAGAAAAGCCATTGGTTTTTTAACAAT 7 135 0 GCCATTGGTT 0.840788 -39 ACGCTCGCGCGCACTGGGCGTTACCCAGCA 12 91 1 GCACTGGGCG 0.506566 -210 TTTCTAGTGTGCCATTGATTAGAGCCATAG 12 198 1 GCCATTGATT 0.577882 -103 AACTTGCCAATGCTGACTACGGTGA 20 6 1 GCCAATGCTG 0.703452 -27 GTTAGCAATTGCCCAGGGGGATACCA 21 91 1 GCCCAGGGGG 0.913554 -16 TTGTTCAACCGCCATTGTTGTCCC 22 287 1 GCCATTGTTG 0.683555 -14 GAGCTAAAACGCCAATGGTTGAAGGCGAT 26 10 0 GCCAATGGTT 0.662115 -175 AAGAAAAATTGCCATTGCCTCCGGGAAG 27 9 0 GCCATTGCCT 0.750004 -89 AGCCCTTGGGGGACATATTGA 29 2 1 GCCCTTGGGG 0.956266 -108 AATTTGGGGGGCCAGGGGGGCTTTTAAAAC 41 100 1 GCCAGGGGGG 0.814384 -52 CTTCATCTTGGCCCTTGTGGAATCCCTTAA 44 99 0 GCCCTTGTGG 0.753401 -202 CCAATTTCCAGCCCTAGCGGAGATTAGCTT 46 103 1 GCCCTAGCGG 0.669515 -80 AATTTCCCTTGCCATGGGCTAGGATCGATT 49 87 1 GCCATGGGCT 0.904365 -95 AGGATCGATTGCCATGGGGTCGCCGTGGTT 49 107 1 GCCATGGGGT 0.916556 -75 TGTTGTCTTTGCCATTGATGTCAGGTGGTT 49 142 0 GCCATTGATG 0.801206 -40 TTCCCAGTCTGCCAAAGGGGGTATGAAATT 52 42 1 GCCAAAGGGG 0.674705 -77 CAAGGGTCTCGCCATTGGCGACGGGATTGG 54 24 0 GCCATTGGCG 0.955515 -277 CACGGCCGCTGCCCAGGACGAATCGTCGGA 54 82 1 GCCCAGGACG 0.702408 -219 GGTAGGGGATGCCCTGGATTGGTTTAGCGA 54 157 1 GCCCTGGATT 0.609963 -144 ********** Masking position 7 Map Score: 12.0566 Number of sites scoring better than the average of aligned sites = 3077 Number in coding regions = 2872 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 12 GCTTTTCTTTGTTTTTGCCCAACTGCTCCT 7 153 1 GTTTTTGCCC 0.981112 -21 ACAAACCCCCGTTTCTGCCCTGAATTTGGT 9 50 0 GTTTCTGCCC 0.91549 -156 AAATGACTCTGTTTTTGCCCTTTGTCCTGC 16 39 1 GTTTTTGCCC 0.981112 -36 CCTCCCCAAAGTTTTTGCTCAACTTAATCT 19 19 1 GTTTTTGCTC 0.970214 -128 ATGACTAATCGTTTTTGCTCTTCAATCTAT 22 58 0 GTTTTTGCTC 0.970214 -243 AACCATTGGCGTTTTAGCTCGCTCTTGGTA 26 20 1 GTTTTAGCTC 0.936505 -165 ATCCGGGGATGTATTTGCTCTGTATTTTCC 39 81 0 GTATTTGCTC 0.820895 -88 AGTTTTAGCCTCGCTTAGATT 42 79 0 GTTTTAGCCT 0.802607 -11 TTTTCCTTTAGTTTTAGCCCCTGAGC 51 175 1 GTTTTAGCCC 0.959218 -16 GGAAACCAATGTTTTTGCTTGTGTATCTGC 54 236 0 GTTTTTGCTT 0.849191 -65 ********** Masking position 4 Map Score: 14.1842 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 101 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 13 TTAATTTATTGAAAATAGTTATCAATTGCTATT 1 49 0 GAAAAAGTAC 0.920842 -252 TTCACTACTTGAAAATATTTATCATTAAAATTT 4 33 1 GAAAAATTAC 0.927478 -73 ACAGCAACCAGTAAACAGTTAACAGGGTTTTTC 12 19 0 GTAAAAGTAC 0.804918 -282 GCCCTTTTTAGAAAACAGCAACCAGTAAACAGT 12 33 0 GAAAAAGCAC 0.913714 -268 TTAAGATTAAGAAAATAGTTAACTTTAGGGCTA 22 211 1 GAAAAAGTAC 0.92088 -90 TGACGGGCTTGAAAAAATTCACCTGTTCAGAAC 32 209 0 GAAAAATTAC 0.927523 -92 TGAAAAAATCAAGCCTAAAAATTC 44 287 0 GAAAAATCAC 0.920901 -14 AATAGACTCGGTAAATTTCGACCAACACAGCCC 48 16 0 GTAAATTCAC 0.570613 -96 CAAGGAAAGTGAAAATTTTAACCTAGCATTTAA 50 27 0 GAAAATTTAC 0.804284 -96 TCATGACCAAGAAAAACTCCATCTAAAACATGG 51 32 0 GAAAACTCAC 0.686766 -159 TGGTTTCCCTGGAAAATTTGACCGAGGAACCGG 54 258 1 GGAAATTTAC 0.611953 -43 TGGTTAGCCGGAAAAAATTAACCGGAAAGAAAG 55 28 0 GAAAAATTAC 0.927523 -140 AGGGGGGACCGGAAAAATCAATCAGCTTTAGTA 55 90 0 GGAAAATCAC 0.817129 -78 AAAGTGAACGGTAAATAGTAAACAGTTATAGAT 56 87 0 GTAAAAGTAC 0.805419 -51 ***** *** * * Masking position 5 Map Score: 8.69833 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 109 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 14 TCCCCTTGCCTAGCCATAATAGCAATTGATAACTA 1 32 1 TAGCAAACAA 0.836661 -269 AGTCAAGGTTTACCTAATTAACCAATTGAGTTGAA 2 13 0 TACCTTACAA 0.568753 -64 CAGATTTCACTACCAAGAACACCAAATTCAGGGCA 9 30 1 TACCAAACAA 0.959775 -176 GAGTCATTTTTACCCAAGATAACAAACTATCTACC 16 13 0 TACCGAACAA 0.978439 -62 ATTGTTCCCATAGCAAAGTGATCAACTATAGTTAA 22 175 1 TAGCGTACAA 0.68605 -126 ATAAATTTGTTACCCGTGATACCAAGAGCGAGCTA 26 34 0 TACCGAACAA 0.978439 -151 TCCCCATTGATACCAACGATACCAAACCCCCAATT 43 20 1 TACCGAACAA 0.978439 -135 GCGTTACCGCCGAAACCAATACCACGCTC 44 5 1 TACCGAACAA 0.978439 -296 GCTAAAAAGATACCCAAAAAATCAATATCACCATG 44 53 1 TACCAAACAA 0.959775 -248 TTCAACGATTTTCCCTCAATAGCAAACGGGGGAAT 46 57 1 TTCCAAACAA 0.842416 -126 CGGTCAAATTTTCCAGGGAAACCAATGTTTTTGCT 54 247 0 TTCCGAACAA 0.910457 -54 TCCCAGGGGGGACCGGAAAAATCAATCAGCTTTAG 55 92 0 GACCAAACAA 0.803768 -76 **** ** * *** Masking position 11 Map Score: 9.59112 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 47 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 15 CACTTTTTAACCCCTATGTCTTAATTTTTT 8 36 1 CCCCTATGTC 0.723328 -27 TTCCTCAGATTCCCTGTGACAGGAATCCGC 12 147 1 TCCCTGTGAC 0.772869 -154 CTCTGTTTTTGCCCTTTGTCCTGCCCAGGC 16 45 1 GCCCTTTGTC 0.699889 -30 TAAGGCGATCGCCTTAGGTCAAAGGCAA 24 9 0 GCCTTAGGTC 0.759303 -190 GTCCGAAAATGCCGTGGGACAAAACCAGGT 26 99 0 GCCGTGGGAC 0.934746 -86 TTAAAAATCCCCCCTGGTTCCCAACCTCGG 33 18 1 CCCCTGGTTC 0.8784 -52 AACTGGACTGGCCCTAGGACTAAGTAGTT 38 10 0 GCCCTAGGAC 0.918973 -116 CCATGGGGTCGCCGTGGTTCAGTTAACCAC 49 118 1 GCCGTGGTTC 0.813213 -64 GAAAATTAGCGCCCTGTTTCCCGCGGCATT 51 92 0 GCCCTGTTTC 0.840038 -99 TAATTTTCAGGCCCTGGGACTGTGAAAGCC 51 114 1 GCCCTGGGAC 0.981379 -77 TTTCCGGTCCCCCCTGGGACGGTTTTTAGG 55 108 1 CCCCTGGGAC 0.959624 -60 TTCCGGGGCCTCCTTGGGTCAAG 56 4 0 TCCTTGGGTC 0.715153 -134 ********** Masking position 5 Map Score: 6.89321 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 662 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887