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_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 ppiB 205 peptidyl-prolyl cis-trans isomerase B #2 ycf4 138 hypothetical protein #3 1651786 21 hypothetical protein #4 1651787 300 hypothetical protein #5 hhoA 198 protease HhoA #6 lim 127 lipophilic protein #7 cyaA 38 adenylate cyclase #8 1652045 74 hypothetical protein #9 1652046 195 esterase #10 cheA 56 chemotaxis protein CheA #11 pilJ 146 methyl-accepting chemotaxis protein (MCP) #12 1652277 32 hypothetical protein #13 1652278 106 regulatory components of sensory transduction system #14 1652279 300 regulatory components of sensory transduction system #15 1652456 46 hypothetical protein #16 1652457 198 rehydrin #17 mutL 103 DNA mismatch repair protein MutL #18 livH 184 high-affinity branched-chain amino acid transport protein #19 1652460 97 hypothetical protein #20 lacF 115 lactose transport system permease protein LacF #21 1652462 109 hypothetical protein #22 htrA 105 serine protease HtrA #23 1652523 300 regulatory components of sensory transduction system #24 1652728 300 hypothetical protein #25 1652730 69 hypothetical protein #26 1652731 32 hypothetical protein #27 1652734 59 hypothetical protein #28 icfg 99 ICFG #29 hhoB 113 protease HhoB #30 1653091 125 hypothetical protein #31 proS 168 proline-tRNA ligase #32 1653492 213 hypothetical protein #33 1653493 151 hypothetical protein #34 arsC 89 arsenate reductase #35 ycf27 154 regulatory components of sensory transduction system #36 era 300 GTP-binding protein Era #37 rnhA 80 ribonuclease H #38 1001717 182 regulatory components of sensory transduction system #39 1208480 156 hypothetical protein #40 1208481 111 hypothetical protein #41 1208482 181 hypothetical protein #42 1208483 122 hypothetical protein #43 ycf27 190 regulatory components of sensory transduction system #44 1001817 118 regulatory components of sensory transduction system #45 tar 45 methyl-accepting chemotaxis protein II #46 tsr 300 methyl-accepting chemotaxis protein I #47 1001301 167 hypothetical protein #48 cheY 137 chemotaxis protein CheY #49 1001303 249 chemotaxis protein CheY #50 1653824 238 regulatory components of sensory transduction system Motif number 1 CAATTGGTCCCCATTTCCCCTAGAAAGTTAT 1 86 1 CCTTTCCCCT 0.979435 -120 AGGTTAGACCCCAGTTCCCCTAAGGTGATCG 2 40 1 CCGTTCCCCT 0.904043 -99 TTTTCTGTGGCACTGTCCTCACGCTCGCGCG 4 71 1 CATGTCCTCA 0.5453 -230 AATTGAAACTTCATTGCCCCCTCCGTAGTCT 4 253 1 TCTTGCCCCC 0.910915 -48 CTCCTAGCACCAATTTCCCAAGACTACGGAG 4 273 0 CATTTCCCAA 0.54267 -28 GCAACTCCCACTCCGGCCCCCAAGTTTGCTT 5 47 1 CTCGGCCCCC 0.58429 -152 TTGGGCTAGTCTATTGCCCACAAGTCAGTGG 5 76 1 CTTTGCCCAC 0.692216 -123 CTGTTCCGACCCATTGCCCAATTGTTTTTTA 11 110 1 CCTTGCCCAA 0.842545 -37 AGAAAAATTGCCATTGCCTCCGGGAAG 19 7 0 CCTTGCCTCC 0.947568 -91 TGGCAATTTTTCTTTGCCCCATTGTCTCGCC 19 25 1 TCTTGCCCCA 0.863776 -73 TGAAAAGCAGCTCTGTCCTCTACCAACATTG 23 85 0 CTTGTCCTCT 0.568141 -216 TTAATGCTTCCATTTGCCCCAAAATACTGTT 23 168 1 CATTGCCCCA 0.930067 -133 TCTTAAATTTCCCTTTCCCTTCAATTCACCA 27 15 1 CCTTTCCCTT 0.728023 -45 AGGACGAAAACTCTTTCCCCTTCAACCCAGC 29 30 0 CTTTTCCCCT 0.925444 -84 CCTTTGGCGACAATTTCCCCAGCTCCAGTTT 29 58 1 CATTTCCCCA 0.9188 -56 AAATAGCACCCTTTTGCCCCAGCTTTTTAGG 30 44 1 CTTTGCCCCA 0.930067 -82 GTCTAGTTATCACTTTCCCCAGCTCTCTGCC 31 11 0 CATTTCCCCA 0.9188 -158 ATTTGCTCTGTATTTTCCCCAGTATTTTGCT 31 68 0 TATTTCCCCA 0.58439 -101 TATGGAAATCTCATTGCCCCCATTGTTCCAT 32 68 0 TCTTGCCCCC 0.910915 -146 AACTTTCACTCAGTTTCCCCCCAAATTTGGG 33 77 1 CATTTCCCCC 0.948044 -75 TTAAAAGCCCCCCTGGCCCCCCAAATTTGGG 33 96 0 CCTGGCCCCC 0.975435 -56 TGGCAAAAAGCCATTTCCCTAAGCATATAGC 35 57 0 CCTTTCCCTA 0.709311 -98 ACCTCCTTGACTTTTTCCTCTGGTTGATTAA 36 208 1 CTTTTCCTCT 0.731632 -93 TAACCAATTTCCATTTCCTATCTAGGCTTTG 38 22 1 CCTTTCCTAT 0.523107 -161 TGACCTATTACCGTTGCCCCTCAACATACCA 39 121 0 CCTTGCCCCT 0.982449 -36 CCGTTTCCCCTACCTTGACCT 39 146 0 CCTTTCCCCT 0.979435 -11 CAAACCGTCACCGTGGCCTCTACCATGGGAG 42 96 1 CCTGGCCTCT 0.855754 -27 AGGTGAAAATCTCCTTCCCCCGCTAAGATCA 44 73 1 CTCTTCCCCC 0.712488 -46 GATTGATTTTTCCGGTCCCCCCTGGGACGGT 47 100 1 TCGGTCCCCC 0.4537 -68 CCAGCCAACACCTTTTCCTCTGATACC 47 151 1 CCTTTCCTCT 0.912739 -17 CCACAATTTTCCGGGGCCTCCTTGGGTCAAG 48 11 0 CCGGGCCTCC 0.633056 -127 ** ******** Masking position 7 Map Score: 34.4987 Number of sites scoring better than the average of aligned sites = 4014 Number in coding regions = 3568 Number in noncoding regions = 446 Number of orfs with sites within 600 bp upstream = 379 Fraction of orfs with sites within 600 bp upstream = 0.0608738 Motif number 2 CAAATTCAGGGCAGAAACGGGGGTTTGTTATG 1 52 1 GCAGACGGGG 0.83714 -154 AACTTTCTAGGGGAAATGGGGACCAATTGAAC 1 83 0 GGGAAGGGGA 0.765377 -123 CCAAATTTTGGGAGCTAGGGGACTTT 2 5 0 GGAGCGGGGA 0.737756 -134 GATCACCTTAGGGGAACTGGGGTCTAACCTCT 2 38 0 GGGGATGGGG 0.785916 -101 GGGAATCTGAGGAAAGTCCGGGCTTCCCAAAG 4 129 0 GGAAACCGGG 0.502852 -172 ACTAGCCCAAGCAAACTTGGGGGCCGGAGTGG 5 54 0 GCAAATGGGG 0.961823 -145 TAAGCACCGTACAAATATGGGGTAAACTTTAT 6 76 1 ACAAATGGGG 0.709948 -52 GGGCAAAGATGGGATTGGGAAGGG 6 114 0 GCAAATGGGA 0.817551 -14 ACGTTGACCAAATTCGGGGTTGGGTGTGT 10 38 0 CCAAACGGGG 0.461775 -19 AAAACAATTGGGCAATGGGTCGGAACAGTTTC 11 106 0 GGCAAGGTCG 0.232883 -41 CTAATACAATGCAAAATGGGGATCTTCTTCGA 16 165 0 GCAAAGGGGA 0.915278 -34 ACTAAGTCCCGGAAATAGCGGGTTTGAGCCTG 18 127 1 GGAAAGCGGG 0.852237 -58 TTCTAGAATTGGAGAAAGGTGGGCCTAATCCA 18 157 0 GGAGAGGTGG 0.727048 -28 TCAGAGGTCAGGCTAGGGGGGGCGAGACAATG 19 44 0 GGCTAGGGGG 0.797084 -54 GAGCTTGGTGGCCACTTGGGGGATCTGACTCT 23 242 0 GCCACGGGGG 0.924228 -59 TTTAATTTAAGCAAAGCGGGGGTCAGTTCCGA 24 246 0 GCAAAGGGGG 0.983803 -55 TCCGAGGTTGGGAACCAGGGGGGATTTTTAAA 25 17 0 GGAACGGGGG 0.970394 -53 AAAAAGCTGGGGCAAAAGGGTGCTATTTCTGC 30 40 0 GGCAAGGGTG 0.532072 -86 GGCAGAGAGCTGGGGAAAGTGATAA 31 4 1 AGAGATGGGG 0.61499 -165 GGATGTGAATGGAACAATGGGGGCAATGAGAT 32 60 1 GGAACTGGGG 0.931485 -154 TAAAGCGACCGCAATACTGGGGAACTTTCACT 33 55 1 GCAATTGGGG 0.565969 -97 CCCTGGCCCCCCAAATTTGGGGGGAAACTGAG 33 85 0 CCAAATGGGG 0.669877 -67 CCAAATTTGGGGGGCCAGGGGGGCTTTTAAAA 33 97 1 GGGGCGGGGG 0.779332 -55 TAAGCATATAGCCAAATTGGGGGTTTGGTATC 35 37 0 GCCAATGGGG 0.926895 -118 ATTACCGAATGGCACAGTGGGGTTAACCCAAC 36 130 1 GGCACTGGGG 0.872482 -171 TCCCTCAATAGCAAACGGGGGAATTTTTTTCG 38 68 1 GCAAAGGGGA 0.915278 -115 CGCTAGGGCTGGAAATTGGGCACGAAAAAAAT 38 90 0 GGAAAGGGCA 0.614886 -93 AAATGCCGCGGGAAACAGGGCGCTAATTTTCA 43 91 1 GGAAAGGGCG 0.899768 -100 TTCCCAGTCTGCCAAAGGGGGTATGAAATTCA 44 42 1 GCCAAGGGGT 0.493498 -77 GAGGAACCGGAGATAGATGGGGCTGAGTTC 46 281 1 AGATATGGGG 0.239276 -20 AGGAGGCCCCGGAAAATTGTGGAGTCTCCCTT 48 20 1 GGAAATGTGG 0.696003 -118 CAGGTCAACAGCAGGAGGGGGGCATATCTATA 49 211 0 GCAGGGGGGG 0.692164 -39 GTAAAATTGAAGAAAAGGGGGAGAAAATCGTA 50 99 1 AGAAAGGGGA 0.586676 -140 ***** ***** Masking position 9 Map Score: 27.918 Number of sites scoring better than the average of aligned sites = 3041 Number in coding regions = 2633 Number in noncoding regions = 408 Number of orfs with sites within 600 bp upstream = 341 Fraction of orfs with sites within 600 bp upstream = 0.0547703 Motif number 3 CCCCTCCGTAGTCTTGGGAAATTGGTGCTAGG 4 270 1 GTTGGGAAAT 0.67304 -31 CGTCCCTGTTAGAATGGCAAAAGTGAAAATTT 5 144 1 AGTGGCAAAA 0.919339 -55 TTTATCAAGCTTAATGGCAAAATTTAACTTTA 9 138 0 TTTGGCAAAA 0.954803 -58 ATCATGGCAAATGTAACAATAG 14 1 1 ATTGGCAAAT 0.841478 -300 TGCTCTTCAATCTATGGGAAATCTATCCCTTG 14 41 0 TCTGGGAAAT 0.764258 -260 ACTTTTAGTTATCTTGGCAAATCATCT 24 284 1 ATTGGCAAAT 0.841478 -17 TTTCAACTATGCACTGGCAAAACTTTGTTGT 28 10 0 GCTGGCAAAA 0.83053 -90 TGCCCCAGCTTTTTAGGGAAAAATGCTATGGT 30 58 1 TTAGGGAAAA 0.794512 -68 GGAGTTAGTTTCAGTGGGAAAAACA 34 4 0 TCTGGGAAAA 0.920102 -86 TTAGTGAAGTTTCGTGGCAAAAAGCCATTTCC 35 70 0 TTTGGCAAAA 0.954803 -85 AAGGTTAGGGTTAATGGGAAAATCAGCGCTGG 37 46 0 TTTGGGAAAA 0.95013 -35 CCCGTTTGCTATTGAGGGAAAATCGTTGAATT 38 55 0 ATAGGGAAAA 0.77534 -128 AACAGCAAACTTTTTGGCAAAATAATGACATG 38 140 0 TTTGGCAAAA 0.954802 -43 CTCTGGGTTTAGGTTGGGAAAATAGACTCGGT 40 37 0 AGTGGGAAAA 0.91134 -75 AGTTAAAGGGAAAATCTATAAATA 40 98 0 TTAGGGAAAA 0.794513 -14 CCCCTTTGGCAGACTGGGAAAATCTTGGACAA 44 30 0 AGTGGGAAAA 0.91134 -89 CTCTCCATCGATGGTGGCAAAAGAAGCGCTGG 46 114 0 ATTGGCAAAA 0.949638 -187 GAAAAGGTGTTGGCTGGCAAAACAGTTGCTCC 47 136 0 TGTGGCAAAA 0.927374 -32 CACCGAGGGGACTTTGGCAAAAGCTTTTGTAT 49 123 0 ACTGGCAAAA 0.919339 -127 ** ******** Masking position 9 Map Score: 20.5389 Number of sites scoring better than the average of aligned sites = 576 Number in coding regions = 485 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 4 CAGAGACTTTTCCATAGCCAAAGCTGGTTT 9 57 1 TCCATAGCCA 0.541281 -139 TGGTATCCCCCTGGGCAATTGCTAACGA 13 89 0 CCCTGGGCAA 0.881609 -18 TTGCATTGTTCCCATAGCAAAGTGATCAAC 14 171 1 CCCATAGCAA 0.731212 -130 CTGGTTTTGTCCCACGGCATTTTCGGACTA 18 101 1 CCCACGGCAT 0.92814 -84 TTTTGGCTTATCCACGGCCATTGTCATGGC 20 25 1 TCCACGGCCA 0.92198 -91 GATCTTTATGCCTAGGGCCAGCAATGGTTA 20 63 1 CCTAGGGCCA 0.872298 -53 AGTCTAAACTCCCATGGAAACAGTATTTTG 23 187 0 CCCATGGAAA 0.731212 -114 TTCCGTCCTTCCCGTGGCATCAACAT 26 17 1 CCCGTGGCAT 0.841855 -16 ACTACTTAGTCCTAGGGCCAGTCCAGTTGC 30 12 1 CCTAGGGCCA 0.872298 -114 ATTTTCATTGTCCAGGGCCATTTTGGCGAT 41 60 0 TCCAGGGCCA 0.974193 -122 TCGATCCTAGCCCATGGCAAGGGAAATTTT 41 85 0 CCCATGGCAA 0.970614 -97 CCACGGCGACCCCATGGCAATCGATCCTAG 41 105 0 CCCATGGCAA 0.970614 -77 CGCCCTGTTTCCCGCGGCATTTTTATAGTA 43 83 0 CCCGCGGCAT 0.814501 -108 CTTTCACAGTCCCAGGGCCTGAAAATTAGC 43 112 0 CCCAGGGCCT 0.975197 -79 GCTAAACCAATCCAGGGCATCCCCTACCTC 46 155 0 TCCAGGGCAT 0.949441 -146 GGTCAAATTTTCCAGGGAAACCAATGTTTT 46 251 0 TCCAGGGAAA 0.765396 -50 TCCACAATTTTCCGGGGCCTCCTTGGGTCA 48 13 0 TCCGGGGCCT 0.858833 -125 CTCCCTTGATTCCAGGCCAATACTTTTGCG 48 45 1 TCCAGGCCAA 0.721558 -93 CCATACCCCTTTCAGGGCAAGCTATAGATA 49 189 1 TTCAGGGCAA 0.636158 -61 ********** Masking position 2 Map Score: 19.4017 Number of sites scoring better than the average of aligned sites = 2603 Number in coding regions = 2436 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 5 ATTGCCATTCCCGTGCTGTCAGATTTCACT 1 10 1 CCCGTGCTGC 0.948595 -196 TAACAAACCCCCGTTTCTGCCCTGAATTTGG 1 51 0 CCGTTTCTGC 0.727522 -155 AACTTGCCAATGCTGACTACGGTGATG 12 7 1 CCAATGCTGC 0.861964 -26 TGTTCAACCGCCATTGTTGTCCC 14 288 1 CCATTGTTGC 0.883761 -13 AAATTTGTTACCCGTGATACCAAGAGCGAGC 18 36 0 CCCGTGATAC 0.688795 -149 CATAAAGATCCGATTGCTGCCATGACAATGG 20 42 0 CGATTGCTGC 0.827516 -74 ACTAACATAACCATTGCTGGCCCTAGGCATA 20 69 0 CCATTGCTGC 0.980058 -47 TGCCCCATCCCCATTGATACCAACGATACCA 35 13 1 CCATTGATAC 0.85496 -142 GTTGTCTTTGCCATTGATGTCAGGTGGTTAA 41 140 0 CCATTGATGC 0.976972 -42 AATGGCGAGACCCTTGATGGCGCTCTTTTTA 46 38 1 CCCTTGATGC 0.978707 -263 TGCCTCATCCCCGTTGATGTCAGTTTCCTTG 46 190 0 CCGTTGATGC 0.972218 -111 TGTGGAGTCTCCCTTGATTCCAGGCCAATAC 48 37 1 CCCTTGATTC 0.783628 -101 CGCATTTACACCGTTGATGGCAGGGATCAAT 49 55 1 CCGTTGATGC 0.972218 -195 ********* * Masking position 5 Map Score: 12.6384 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 368 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 ACCAAATTCAGGGCAGAAACGGGGGTTTGT 1 50 1 GGGCAGAAAC 0.900699 -156 GCAGGACAAAGGGCAAAAACAGAGTCATTT 8 39 0 GGGCAAAAAC 0.974888 -36 AGATTAAGTTGAGCAAAAACTTTGGGGAGG 11 19 0 GAGCAAAAAC 0.967901 -128 ATAGATTGAAGAGCAAAAACGATTAGTCAT 14 58 1 GAGCAAAAAC 0.967901 -243 TACCAAGAGCGAGCTAAAACGCCAATGGTT 18 20 0 GAGCTAAAAC 0.940539 -165 GGAAAATACAGAGCAAATACATCCCCGGAT 31 81 1 GAGCAAATAC 0.826194 -88 AATCTAAGCGAGGCTAAAACT 34 79 1 AGGCTAAAAC 0.8004 -11 GCTCAGGGGCTAAAACTAAAGGAAAA 43 175 0 GGGCTAAAAC 0.953193 -16 GCAGATACACAAGCAAAAACATTGGTTTCC 46 236 1 AAGCAAAAAC 0.855861 -65 ********** Masking position 7 Map Score: 10.3051 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 114 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 7 CCAAGACTACGGAGGGGGCAATGAAGTTTCA 4 256 0 GGAGGGGCAA 0.931045 -45 GGCAAAGATGGGATTGGGAAGGGTTTAGGAT 6 106 0 GGATGGGAAG 0.921454 -22 AATTAACGCTGCCTGGGCAGGACAAAGGGC 8 55 0 TGCTGGGCAG 0.869553 -20 CAAATTTATGGAACGGAGCAGGGTTAACTAT 18 60 1 GAAGGAGCAG 0.650476 -125 GTTGGTCGATTGAGGGGGCAGAATAAAACTT 33 24 0 TGAGGGGCAG 0.969308 -128 GTATCAATGGGGATGGGGCAGA 35 2 0 GGAGGGGCAG 0.995146 -153 GTCTGATCTTAGCGGGGGAAGGAGATTTTCA 44 76 0 AGCGGGGAAG 0.821967 -43 ATTGGCGACGGGATTGGGCAGTGTCAGGAC 46 10 0 GGATGGGCAG 0.983313 -291 CCGACGATTCGTCCTGGGCAGCGGCCGTGTC 46 80 0 GTCTGGGCAG 0.756371 -221 ACATCAACGGGGATGAGGCAGACCGTGGAAT 46 201 1 GGAGAGGCAG 0.962876 -100 AACCGGAGATAGATGGGGCTGAGTTC 46 285 1 AGAGGGGCTG 0.770687 -16 GGTGGCTGGAGAAGTTTGCCTTAG 49 4 1 GGCGGAGAAG 0.791308 -246 TTAATCAAAGGAAGAGGCAGGTCAACAGCA 49 230 0 GGAGAGGCAG 0.962876 -20 *** ******* Masking position 8 Map Score: 10.9985 Number of sites scoring better than the average of aligned sites = 919 Number in coding regions = 860 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 8 TCTAAAAAGGGCGGTATTTTTCTGTGGCACTGT 4 54 1 GGGATTTTTT 0.840668 -247 GGCAAAAACAGAGTCATTTTTACCCAAGATAAC 8 25 0 GGTATTTTTC 0.908031 -50 TGAAATTTTTGTGTCAGTTTTTCAGGACAAGGT 22 39 0 GGTAGTTTTC 0.878786 -67 GTTCTGAACAGGTGAATTTTTTCAAGCCCGTCA 24 209 1 GTGATTTTTC 0.947405 -92 GAATTTTTAGGCTTGATTTTTTCA 36 287 1 GTTATTTTTC 0.906447 -14 CCCTAACCTTGCTGAATTTGTCC 37 68 1 GTGATTTGTC 0.739659 -13 AATGGAAATTGGTTAAGTTTTGCCCC 38 4 0 GTTAGTTTTC 0.876767 -179 ATAGCAAACGGGGGAATTTTTTTCGTGCCCAAT 38 75 1 GGGATTTTTT 0.840668 -108 CCATGTTTTAGATGGAGTTTTTCTTGGTCATGA 43 32 1 GTGAGTTTTC 0.929712 -159 CCTGTTTCCCGCGGCATTTTTATAGTAATTATA 43 77 0 GGGATTTTTT 0.840668 -114 CTTTCTTTCCGGTTAATTTTTTCCGGCTAACCA 47 28 1 GTTATTTTTC 0.906447 -140 TACTAAAGCTGATTGATTTTTCCGGTCCCCCCT 47 90 1 GTTATTTTTC 0.906447 -78 CGGTGAGGTCGATGAAGTTTTCTTGCGTACTTT 49 150 1 GTGAGTTTTT 0.791756 -100 * ** ****** * Masking position 6 Map Score: 9.06386 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 239 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 Motif number 9 TTGGTAGAGGTTAGACCCCAGTTCCCCTAAG 2 33 1 TTAACCCCAG 0.771913 -106 AACCATTGAATTTTACCCCATCAGGGCTAGG 2 87 0 TTTACCCCAT 0.892761 -52 ACAGGGACGATTTTACCTAAGAATCCGTTTT 5 122 0 TTTACCTAAG 0.595741 -77 TTAGGATAAAGTTTACCCCATATTTGTACGG 6 82 0 GTTACCCCAT 0.634522 -46 ACAGAGTCATTTTTACCCAAGATAACAAACT 8 20 0 TTTACCCAAG 0.916902 -55 CCAAAGCTGGTTTATCCCCAGTTTAAGTTAC 9 74 1 TTTTCCCCAG 0.878328 -122 ATGAGTAGAGTTTAACCCCATACTATTTCTA 14 136 0 TTTACCCCAT 0.892761 -165 TTGCCTTTGACCTAAGGCGATCGCCT 16 6 1 TTTACCTAAG 0.595737 -193 AAGGCGATCGCCTTACCCCAGACTAACTGGC 16 24 1 CCTACCCCAG 0.953477 -175 GGCAATTTTTCTTTGCCCCATTGTCTCGCCC 19 26 1 CTTGCCCCAT 0.7237 -72 ACTCTTTCCCCTTCAACCCAGCTAAATGGCA 29 21 0 CTTAACCCAG 0.882707 -93 AATAGCACCCTTTTGCCCCAGCTTTTTAGGG 30 45 1 TTTGCCCCAG 0.917805 -81 TTTGCTCTGTATTTTCCCCAGTATTTTGCTC 31 67 0 ATTTCCCCAG 0.503907 -102 TTGAATGCCCCTTTACCTAAGGCAGCGGAGG 32 31 1 CTTACCTAAG 0.649965 -183 AAAATTGGCTTCTGACCCCAGTATAATTCCC 39 71 1 TCTACCCCAG 0.942079 -86 ATTTTCCCAACCTAAACCCAGAGTTTGATCA 40 46 1 CCTAACCCAG 0.732418 -66 CGGCCGTGTCCGTCAACCCAGTAAAAAGAGC 46 59 0 CGTAACCCAG 0.505214 -242 CTTGACCCAAGGAGGCCCCGG 48 1 1 CTTACCCAAG 0.932479 -137 *** ******* Masking position 10 Map Score: 10.0103 Number of sites scoring better than the average of aligned sites = 1313 Number in coding regions = 1155 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 10 GGCCCCTAGAATTTGGCTCCGATGCTGGGG 6 12 0 ATTTGGCTCC 0.918436 -116 TATTTCCTTTAGTTTTCTCCGGTGG 7 6 0 AGTTTTCTCC 0.859707 -33 GCGGAAATATTTCTCCATGCCTTGTC 10 7 1 ATATTTCTCC 0.805242 -50 AGGGTAGATGATTTTTCTCCCTCTCCGCTT 17 77 0 ATTTTTCTCC 0.958457 -27 ACCAAAAGTAATTTAGCTCCTTACTAATAT 28 69 0 ATTTAGCTCC 0.883686 -31 CCCTATGATAATTTTTCTCGTCTAGTTATC 31 31 0 ATTTTTCTCG 0.792468 -138 TTTCCCCAGTATTTTGCTCCCGCTCCCCTA 31 56 0 ATTTTGCTCC 0.973401 -113 AAAGTACTCTATTTTGCTCCTTTTCCATCG 32 98 1 ATTTTGCTCC 0.973401 -116 ********** Masking position 1 Map Score: 3.98646 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 93 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 11 AGACCCCAGTTCCCCTAAGGTGATCGCCCT 2 45 1 TCCCCTAAGG 0.694712 -94 AAGTCCGGGCTTCCCAAAGGCCAAACTTGC 4 118 0 TTCCCAAAGG 0.923773 -183 TTATCGGGCCTCCCCAAAGTTTTTGCTCAA 11 11 1 TCCCCAAAGT 0.792673 -136 TCGTTAGCAATTGCCCAGGGGGATACCA 13 89 1 TTGCCCAGGG 0.771309 -18 CAATAGATACTTCCCAAGGGATAGATTTCC 14 27 1 TTCCCAAGGG 0.951096 -274 GCGAGCTAAAACGCCAATGGTTGAAGGCGA 18 12 0 ACGCCAATGG 0.516549 -173 GTCAATATGTCCCCCAAGGGCT 21 3 0 CCCCCAAGGG 0.944028 -107 AGAGTCAGATCCCCCAAGTGGCCACCAAGC 23 242 1 CCCCCAAGTG 0.471324 -59 GGGGAAATTGTCGCCAAAGGACGAAAACTC 29 48 0 TCGCCAAAGG 0.969487 -66 ATTAAGGGATTCCACAAGGGCCAAGATGAA 36 98 1 TCCACAAGGG 0.678309 -203 AAAATTTCCCTTGCCATGGGCTAGGATCGA 41 85 1 TTGCCATGGG 0.800507 -97 CTAGGATCGATTGCCATGGGGTCGCCGTGG 41 105 1 TTGCCATGGG 0.800507 -77 TTTTCCCAGTCTGCCAAAGGGGGTATGAAA 44 40 1 CTGCCAAAGG 0.867535 -79 CCCAATCCCGTCGCCAATGGCGAGACCCTT 46 23 1 TCGCCAATGG 0.909422 -278 ACAAAAGCTTTTGCCAAAGTCCCCTCGGTG 49 125 1 TTGCCAAAGT 0.704354 -125 GGGGTATGGGTCGCCAAAGTACGCAAGAAA 49 168 0 TCGCCAAAGT 0.830129 -82 ********** Masking position 5 Map Score: 10.406 Number of sites scoring better than the average of aligned sites = 1731 Number in coding regions = 1549 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 12 TTAGCAATTACGGAGATTAGATTTT 1 191 1 CGGAGATTAG 0.84468 -15 CCGGGGTTGAGTCAATCCATC 5 2 1 CGGGGTTGAG 0.981318 -197 CATATTTGTACGGTGCTTAGCCACTGTTAC 6 65 0 CGGTGCTTAG 0.867853 -63 TGACCAAATTCGGGGTTGGGTGTGTTGACA 10 33 0 CGGGGTTGGG 0.908192 -24 ATGCTGACTACGGTGATGAGGTT 12 20 1 CGGTGATGAG 0.911845 -13 CCGCTATTTCCGGGACTTAGTCCGAAAATG 18 118 0 CGGGACTTAG 0.744495 -67 CCGGAAATAGCGGGTTTGAGCCTGGATTAG 18 135 1 CGGGTTTGAG 0.821087 -50 CCAGCCCTAGCGGAGATTAGCTTTTTTCAC 38 110 1 CGGAGATTAG 0.84468 -73 TGATCAAACTCTGGGTTTAGGTTGGGAAAA 40 47 0 CTGGGTTTAG 0.68515 -65 CTGACATCAACGGGGATGAGGCAGACCGTG 46 198 1 CGGGGATGAG 0.981318 -103 CGGAGATAGATGGGGCTGAGTTC 46 288 1 TGGGGCTGAG 0.833282 -13 ********** Masking position 7 Map Score: 6.85201 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 317 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 13 ACTGTGTATATTTGGTTAACATTGGACCAT 9 23 1 TTTGGTTAAC 0.570141 -173 GGTTTGGTCAGAAACAAAACAA 9 184 0 TTTGGTCAGA 0.950501 -12 CAACCCCGAATTTGGTCAACGT 10 45 1 TTTGGTCAAC 0.884214 -12 GGCGATCGCCTTAGGTCAAAGGCAA 16 6 0 TTAGGTCAAA 0.737492 -193 TGAAGCTAAATTTGGTCAGAGGTCAGGCTA 19 61 0 TTTGGTCAGA 0.950501 -37 CAAAACACTGCTTGGTTAGAGTCAGATCCC 23 225 1 CTTGGTTAGA 0.783586 -76 GATTTCACCTCTTGGTCAAA 41 1 0 CTTGGTCAAA 0.950425 -181 CTGGGAAAATCTTGGACAAATTCCCAATTT 44 19 0 CTTGGACAAA 0.730899 -100 TAGTTATACATTTGGTCAGA 45 1 0 TTTGGTCAGA 0.950501 -45 TCTCCGGTTCCTCGGTCAAATTTTCCAGGG 46 264 0 CTCGGTCAAA 0.818729 -37 ********** Masking position 8 Map Score: 3.61803 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 219 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 14 TTCCCAATCCCATCTTTGCCC 6 117 1 CACTTTGCCC 0.848534 -11 CCTTGGGGGACATATTGACCCTGACTGAAAA 21 14 1 CAATTGACCC 0.940506 -96 TGAGGAAATCCAGCTCGACCCATTTCGACGT 24 77 0 CACTCGACCC 0.893774 -224 ATATTCAAGACACATTGACCATAGCATTTTT 30 76 0 CAATTGACCA 0.877385 -50 TTTTAAAAGCCCCCCTGGCCCCCCAAATTTG 33 98 0 CCCCTGGCCC 0.744521 -54 GGTAATCCTTCATCTTGGCCCTTGTGGAATC 36 105 0 CACTTGGCCC 0.975799 -196 AACGGCTTGCCAGCTTGACAAAAAAATATGT 36 160 0 CACTTGACAA 0.61417 -141 TAACGTTTTTCCGCTTGACCCTCCATAAACT 36 253 1 CCCTTGACCC 0.944402 -48 CTTATGATCCCAGCTTGACCAGCGCTGATTT 37 28 1 CACTTGACCA 0.956869 -53 GGGCGATCGCCAAAATGGCCCTGGACAATGA 41 55 1 CAAATGGCCC 0.763414 -127 TTTAATCGTCCAAATTTACCA 42 1 0 CAATTTACCA 0.498546 -122 GACTTGCGAGCATCATGACCAAGAAAAACTC 43 46 0 CACATGACCA 0.846262 -145 ** ******** Masking position 9 Map Score: 5.30331 Number of sites scoring better than the average of aligned sites = 478 Number in coding regions = 438 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 15 GCGGAAATATTTCTCCATGCCTTGTCAACAC 10 8 1 TATTCTCCTC 0.846702 -49 TAATCCTTACTTTTTCACCTTAACAGAGTCTTAA 11 55 1 TTTTCACCTC 0.917162 -92 GGGTAGATGATTTTTCTCCCTCTCCGCTTAAAAG 17 72 0 TTTTCTCCTC 0.972251 -32 CCAAAAGTAATTTAGCTCCTTACTAATATTCTAT 28 64 0 TTTACTCCTT 0.676463 -36 TTCCCCAGTATTTTGCTCCCGCTCCCCTATGATA 31 51 0 TTTTCTCCGC 0.961459 -118 AAGTACTCTATTTTGCTCCTTTTCCATCGGAAGA 32 99 1 TTTTCTCCTC 0.972251 -115 AGGCGGATAGTTTACCTCCTTGACTTTTTCCTCT 36 195 1 TTTACTCCTC 0.95989 -106 GAGATTAGCTTTTTTCACCATGTCATTATTTTGC 38 122 1 TTTTCACCTC 0.917162 -61 TTCCTTTAGTTTTAGCCCCTGAGC 43 177 1 TTTACCCCGC 0.819029 -14 CTCAGCCCCATCTATCTCCGGTTCCTCGGTCAAA 46 274 0 TCTACTCCGC 0.799243 -27 **** **** * * Masking position 3 Map Score: 2.89469 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 158 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542