AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -icpxR6_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 1652456 46 hypothetical protein #11 1652457 198 rehydrin #12 mutL 103 DNA mismatch repair protein MutL #13 livH 184 high-affinity branched-chain amino acid transport protein #14 1652460 97 hypothetical protein #15 lacF 115 lactose transport system permease protein LacF #16 1652462 109 hypothetical protein #17 htrA 105 serine protease HtrA #18 1652523 300 regulatory components of sensory transduction system #19 1652728 300 hypothetical protein #20 1652730 69 hypothetical protein #21 1652731 32 hypothetical protein #22 1652734 59 hypothetical protein #23 icfg 99 ICFG #24 hhoB 113 protease HhoB #25 1653091 125 hypothetical protein #26 proS 168 proline-tRNA ligase #27 1653492 213 hypothetical protein #28 1653493 151 hypothetical protein #29 arsC 89 arsenate reductase #30 ycf27 154 regulatory components of sensory transduction system #31 rnhA 80 ribonuclease H #32 1001717 182 regulatory components of sensory transduction system #33 1208480 156 hypothetical protein #34 1208481 111 hypothetical protein #35 1208482 181 hypothetical protein #36 1208483 122 hypothetical protein #37 ycf27 190 regulatory components of sensory transduction system #38 1001817 118 regulatory components of sensory transduction system #39 1653824 238 regulatory components of sensory transduction system Motif number 1 CAATTGGTCCCCATTTCCCCTAGAAAGTTAT 1 86 1 CCTTTCCCCT 0.989049 -120 AGGTTAGACCCCAGTTCCCCTAAGGTGATCG 2 40 1 CCGTTCCCCT 0.905456 -99 AATTGAAACTTCATTGCCCCCTCCGTAGTCT 4 253 1 TCTTGCCCCC 0.963584 -48 AGAAAAATTGCCATTGCCTCCGGGAAG 14 7 0 CCTTGCCTCC 0.926101 -91 TGGCAATTTTTCTTTGCCCCATTGTCTCGCC 14 25 1 TCTTGCCCCA 0.958058 -73 TTAATGCTTCCATTTGCCCCAAAATACTGTT 18 168 1 CATTGCCCCA 0.972275 -133 TCTTAAATTTCCCTTTCCCTTCAATTCACCA 22 15 1 CCTTTCCCTT 0.881498 -45 AGGACGAAAACTCTTTCCCCTTCAACCCAGC 24 30 0 CTTTTCCCCT 0.912967 -84 CCTTTGGCGACAATTTCCCCAGCTCCAGTTT 24 58 1 CATTTCCCCA 0.96018 -56 AAATAGCACCCTTTTGCCCCAGCTTTTTAGG 25 44 1 CTTTGCCCCA 0.938483 -82 GTCTAGTTATCACTTTCCCCAGCTCTCTGCC 26 11 0 CATTTCCCCA 0.96018 -158 ATTTGCTCTGTATTTTCCCCAGTATTTTGCT 26 68 0 TATTTCCCCA 0.807447 -101 TATGGAAATCTCATTGCCCCCATTGTTCCAT 27 68 0 TCTTGCCCCC 0.963584 -146 AACTTTCACTCAGTTTCCCCCCAAATTTGGG 28 77 1 CATTTCCCCC 0.965437 -75 TTAAAAGCCCCCCTGGCCCCCCAAATTTGGG 28 96 0 CCTGGCCCCC 0.969144 -56 TGGCAAAAAGCCATTTCCCTAAGCATATAGC 30 57 0 CCTTTCCCTA 0.881498 -98 TGACCTATTACCGTTGCCCCTCAACATACCA 33 121 0 CCTTGCCCCT 0.992444 -36 CCGTTTCCCCTACCTTGACCT 33 146 0 CCTTTCCCCT 0.989049 -11 CAAACCGTCACCGTGGCCTCTACCATGGGAG 36 96 1 CCTGGCCTCT 0.690703 -27 ** ******** Masking position 7 Map Score: 32.9311 Number of sites scoring better than the average of aligned sites = 1677 Number in coding regions = 1441 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 2 CATAACAAACCCCCGTTTCTGCCCTGAATTTG 1 52 0 CCCCGTCTGC 0.846466 -154 GTTCAATTGGTCCCCATTTCCCCTAGAAAGTT 1 83 1 TCCCCTTCCC 0.794723 -123 AAAGTCCCCTAGCTCCCAAAATTTGG 2 5 1 TCCCCGCTCC 0.863313 -134 CTTTGGGAAGCCCGGACTTTCCTCAGATTCCC 4 129 1 CCCGGTTTCC 0.591842 -172 CCACTCCGGCCCCCAAGTTTGCTTGGGCTAGT 5 54 1 CCCCATTTGC 0.960808 -145 ATAAAGTTTACCCCATATTTGTACGGTGCTTA 6 76 0 CCCCATTTGT 0.701231 -52 CCCTTCCCAATCCCATCTTTGCCC 6 114 1 TCCCATTTGC 0.878988 -14 TCGAAGAAGATCCCCATTTTGCATTGTATTAG 11 165 1 TCCCCTTTGC 0.958487 -34 CAGGCTCAAACCCGCTATTTCCGGGACTTAGT 13 127 0 CCCGCTTTCC 0.914673 -58 TGGATTAGGCCCACCTTTCTCCAATTCTAGAA 13 157 1 CCACCTCTCC 0.565046 -28 CATTGTCTCGCCCCCCCTAGCCTGACCTCTGA 14 44 1 CCCCCTAGCC 0.563548 -54 GGCATAAAGATCCGATTGCTGCCATGACAATG 15 43 0 TCCGAGCTGC 0.214652 -73 AGAGTCAGATCCCCCAAGTGGCCACCAAGCTC 18 242 1 CCCCCGTGGC 0.908712 -59 TCGGAACTGACCCCCGCTTTGCTTAAATTAAA 19 246 1 CCCCCTTTGC 0.98733 -55 TTTAAAAATCCCCCCTGGTTCCCAACCTCGGA 20 17 1 CCCCCGTTCC 0.976052 -53 TTATCACTTTCCCCAGCTCTCTGCC 26 4 0 CCCCATCTCT 0.551077 -165 ATCTCATTGCCCCCATTGTTCCATTCACATCC 27 60 0 CCCCAGTTCC 0.927651 -154 AGTGAAAGTTCCCCAGTATTGCGGTCGCTTTA 28 55 0 CCCCAATTGC 0.624501 -97 CTCAGTTTCCCCCCAAATTTGGGGGGCCAGGG 28 85 1 CCCCATTTGG 0.717006 -67 TTTTAAAAGCCCCCCTGGCCCCCCAAATTTGG 28 97 0 CCCCCGCCCC 0.781388 -55 CGATACCAAACCCCCAATTTGGCTATATGCTT 30 36 1 CCCCCTTTGG 0.889548 -119 CGAAAAAAATTCCCCCGTTTGCTATTGAGGGA 32 68 0 TCCCCTTTGC 0.958487 -115 ATTTTTTTCGTGCCCAATTTCCAGCCCTAGCG 32 90 1 TGCCCTTTCC 0.67641 -93 TGAAAATTAGCGCCCTGTTTCCCGCGGCATTT 37 91 0 CGCCCTTTCC 0.875854 -100 TGAATTTCATACCCCCTTTGGCAGACTGGGAA 38 42 0 ACCCCTTGGC 0.470614 -77 TACGATTTTCTCCCCCTTTTCTTCAATTTTAC 39 99 0 TCCCCTTTCT 0.688525 -140 ***** ***** Masking position 3 Map Score: 27.6837 Number of sites scoring better than the average of aligned sites = 2419 Number in coding regions = 2080 Number in noncoding regions = 339 Number of orfs with sites within 600 bp upstream = 294 Fraction of orfs with sites within 600 bp upstream = 0.0472213 Motif number 3 AAACGGATTCTTAGGTAAAATCGTCCCTGTTAG 5 123 1 TAGGAAAACG 0.876714 -76 TCCCTGTTAGAATGGCAAAAGTGAAAATTTCTG 5 146 1 ATGGAAAATG 0.905911 -53 GTTTGTTATCTTGGGTAAAAATGACTCTGTTTT 8 21 1 TGGGAAAATG 0.749441 -54 GGGCAGGACAAAGGGCAAAAACAGAGTCATTTT 8 38 0 AGGGAAAACA 0.797286 -37 CAGCTTTGGCTATGGAAAAGTCTCTGTACAATG 9 50 0 TTGGAAAGCT 0.864359 -146 TATCAAGCTTAATGGCAAAATTTAACTTTAAAA 9 135 0 ATGGAAAATT 0.87213 -61 CGCAAAATTGTCAGGAAAAGACTGGCATTGACG 11 86 0 TAGGAAAGCT 0.780473 -113 TCAACTATGCACTGGCAAAACTTTGTTGT 23 7 0 ATGGAAAATT 0.87213 -93 CCCCAGCTTTTTAGGGAAAAATGCTATGGTCAA 25 60 1 TAGGAAAATG 0.783842 -66 AACTTACCCTCTGGAAAAAGTGATTCAAGATA 25 104 0 TTGGAAAATG 0.866661 -22 TGCTGGCAATTAGGCAAAGTTGGTTAGAGCTT 28 130 0 TAGGAAAGTG 0.719044 -22 AGTTAGTTTCAGTGGGAAAAACA 29 1 0 ATGGAAAACA 0.895251 -89 GGTTAGGGTTAATGGGAAAATCAGCGCTGGTCA 31 43 0 ATGGAAAACA 0.895251 -38 AAATCGTTGAATTGGCAAAGCCTAGATAGGAAA 32 35 0 ATGGAAAGCT 0.904212 -148 CGTTTGCTATTGAGGGAAAATCGTTGAATTGGC 32 52 0 TAGGAAAACG 0.876714 -131 TCCCCAGGATATGGGTAAAAATTGGCTTCTGAC 33 54 1 AGGGAAAATT 0.758377 -103 AGTTAAAGGGAAAATCTATAAATATTT 34 95 0 AAGGAAAACT 0.881827 -17 GTAGTAGGGTAATGGAAAAGATAGGATTTCACC 35 22 0 ATGGAAAGTA 0.754652 -160 ACCTGACATCAATGGCAAAGACAACACACCGAT 35 146 1 ATGGAAAGCA 0.857791 -36 CCTTTGGCAGACTGGGAAAATCTTGGACAAATT 38 27 0 ATGGAAAACT 0.930436 -92 * *** **** ** Masking position 7 Map Score: 17.8114 Number of sites scoring better than the average of aligned sites = 758 Number in coding regions = 638 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 4 CTGGTTTTGTCCCACGGCATTTTCGGACTA 13 101 1 CCCACGGCAT 0.963745 -84 TTTTGGCTTATCCACGGCCATTGTCATGGC 15 25 1 TCCACGGCCA 0.900236 -91 GATCTTTATGCCTAGGGCCAGCAATGGTTA 15 63 1 CCTAGGGCCA 0.914451 -53 AGTCTAAACTCCCATGGAAACAGTATTTTG 18 187 0 CCCATGGAAA 0.728177 -114 TTCCGTCCTTCCCGTGGCATCAACAT 21 17 1 CCCGTGGCAT 0.938125 -16 ACTACTTAGTCCTAGGGCCAGTCCAGTTGC 25 12 1 CCTAGGGCCA 0.914451 -114 ATTTTCATTGTCCAGGGCCATTTTGGCGAT 35 60 0 TCCAGGGCCA 0.922193 -122 TCGATCCTAGCCCATGGCAAGGGAAATTTT 35 85 0 CCCATGGCAA 0.973914 -97 CCACGGCGACCCCATGGCAATCGATCCTAG 35 105 0 CCCATGGCAA 0.973914 -77 GCAAACCGTCACCGTGGCCTCTACCATGGG 36 95 1 ACCGTGGCCT 0.6795 -28 CGCCCTGTTTCCCGCGGCATTTTTATAGTA 37 83 0 CCCGCGGCAT 0.936952 -108 CTTTCACAGTCCCAGGGCCTGAAAATTAGC 37 112 0 CCCAGGGCCT 0.982421 -79 ********** Masking position 2 Map Score: 13.1783 Number of sites scoring better than the average of aligned sites = 1448 Number in coding regions = 1338 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 5 GAACTGGGGTCTAACCTCTACCAAATTTTGGGAGCTA 2 20 0 CTCCTCACAT 0.724573 -119 GAAGCCCGGACTTTCCTCAGATTCCCTGTGACAGGAA 4 135 1 CTCCTCGACT 0.911816 -166 TTGAGTCAATCCATCCCAAGAAACCGTTCGGCAACTC 5 17 1 CCCCCAGACT 0.852025 -182 GGGCAATAGACTAGCCCAAGCAAACTTGGGGGCCGGA 5 58 0 CTCCCAGCAT 0.952238 -141 CAGGGACGATTTTACCTAAGAATCCGTTTTCAAAGCT 5 115 0 TTCCTAGACT 0.22697 -84 TATCCTAAACCCTTCCCAATCCCATCTTTGCCC 6 105 1 CCCCCATCAT 0.45378 -23 TGCCCTTTGTCCTGCCCAGGCAGCGTTAATT 8 54 1 CCCCCAGCCT 0.932345 -21 CAAAGCTGGTTTATCCCCAGTTTAAGTTACGCCATTA 9 75 1 TTCCCCGTAT 0.592414 -121 AGGCGATCGCCTTACCCCAGACTAACTGGCCAGGTGT 11 25 1 CTCCCCGAAT 0.970343 -174 CCCCCCTAGCCTGACCTCTGACCAAATTTAGCTTCAG 14 55 1 CTCCTCGAAT 0.940027 -43 AAAAGCAGCTCTGTCCTCTACCAACATTGAGACGAAA 18 77 0 CTCCTCACAT 0.724573 -224 CCCGTCGGAACTGACCCCCGCTTTGCTTAAATTAAAC 19 242 1 CTCCCCGCTT 0.921967 -59 CCCCTGGTTCCCAACCTCGGAGAAATTTATTCCTCAT 20 28 1 CCCCTCGAAT 0.942603 -42 TTTGGCGACAATTTCCCCAGCTCCAGTTTGTTAAAGT 24 60 1 ATCCCCGCCT 0.800823 -54 CTAGTTATCACTTTCCCCAGCTCTCTGCC 26 3 0 CTCCCCGCTG 0.664554 -166 TTTGCTCCCGCTCCCCTATGATAATTTTTCTCGTCTA 26 37 0 CTCCTAGAAT 0.799632 -132 TGTTCCATTCACATCCTCCGCTGCCTTAGGTAAAGGG 27 39 0 ACCCTCGCCT 0.668684 -175 TCAACTCGGTCTGTCCCCGGTCTACTGTTGCCGTGTC 27 131 0 CTCCCCGTAG 0.686046 -83 AGATCCACAACCCTCCTTTGATTAACTTGTATAACGA 30 102 0 CCCCTTGAAT 0.604873 -53 TGCCCAATTTCCAGCCCTAGCGGAGATTAGCTTTTTT 32 100 1 CCCCCTGCAT 0.884353 -83 AAATTGGCTTCTGACCCCAGTATAATTCCCTAAATAG 33 72 1 CTCCCCGTAT 0.928736 -85 GTGAAAATCTCCTTCCCCCGCTAAGATCAGACCGTTA 38 75 1 CCCCCCGCAT 0.987959 -44 CTTTTCTCTATCAACCTCAGCTTACCTGAAGGGGTGA 39 201 0 TCCCTCGCAT 0.814268 -38 ** **** ** * * Masking position 6 Map Score: 17.5275 Number of sites scoring better than the average of aligned sites = 1610 Number in coding regions = 1455 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 6 GCCCTGATGGGGTAAAATTCAATGGTTAGT 2 91 1 GGTAAAATTC 0.561134 -48 ACAGTGCCACAGAAAAATACCGCCCTTTTT 4 57 0 AGAAAAATAC 0.822839 -244 CCAGCATCGGAGCCAAATTCTAGGGGCCAT 6 14 1 AGCCAAATTC 0.843983 -114 AAAACTTAATAGAAAAATTGTTTTGTTTCT 9 167 1 AGAAAAATTG 0.902073 -29 AATGGGGCAAAGAAAAATTGCCATTGCCTC 14 18 0 AGAAAAATTG 0.902073 -80 GCACTCCGAAAGAAAAATTCAAAGAGAACT 19 168 0 AGAAAAATTC 0.924173 -133 TAACTAGACGAGAAAAATTATCATAGGGGA 26 33 1 AGAAAAATTA 0.544386 -136 GGGGAGCGGGAGCAAAATACTGGGGAAAAT 26 58 1 AGCAAAATAC 0.773268 -111 TGTTTTATCAGAAAAATAGGTTGAATGCC 27 10 1 AGAAAAATAG 0.778288 -204 ATGGAAAAGGAGCAAAATAGAGTACTTTAT 27 96 0 AGCAAAATAG 0.720487 -118 CTAAGCATATAGCCAAATTGGGGGTTTGGT 30 40 0 AGCCAAATTG 0.80348 -115 GGACAAATTCAGCAAGGTTA 31 71 0 GGACAAATTC 0.756975 -10 ATCATGACCAAGAAAAACTCCATCTAAAAC 37 36 0 AGAAAAACTC 0.623162 -155 GGAAAATCTTGGACAAATTCCCAATTTGAG 38 16 0 GGACAAATTC 0.756975 -103 ATCCTAACAAAGTAAAATTGAAGAAAAGGG 39 88 1 AGTAAAATTG 0.695641 -151 ********** Masking position 5 Map Score: 8.88202 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 274 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 7 CATTTCCCCTAGAAAGTTATCTAAAGTGGAC 1 97 1 AGAAAGTTAC 0.645324 -109 TCATCGTTTATGTAAATTAACCAACTTTAAA 1 147 0 TGTAAATTAC 0.669386 -59 ATTGTTGGCTTGCAAATCAACCACACCATTA 12 36 1 TGCAAATCAC 0.907206 -68 CGGTTGTTGTTGAAAAGCAGCTCTGTCCTCT 18 95 0 TGAAAAGCAC 0.738565 -206 GAAAATAATTAGAAAATTAACTACGATCAAT 18 125 1 AGAAAATTAC 0.798133 -176 TAGTTATCTTGGCAAATCATCT 19 289 1 GGCAAATCAC 0.845335 -12 AGTGCATAGTTGAAAATCAACCGCATAAATG 23 27 1 TGAAAATCAC 0.950899 -73 AGGGTTAATGGGAAAATCAGCGCTGGTCAAG 31 41 0 GGAAAATCAC 0.915444 -40 AGCTGGTGCGTGAAAGTTATCCAATTGTTGA 33 20 0 TGAAAGTTAC 0.879995 -137 CCCTGGACAATGAAAATTTCCCTTGCCATGG 35 73 1 TGAAAATTTC 0.748928 -109 GACGGTTTGCTGCAAATTATCGTTCCTGGGT 36 74 0 TGCAAATTAC 0.889433 -49 TCCCAGGGCCTGAAAATTAGCGCCCTGTTTC 37 102 0 TGAAAATTAC 0.940949 -89 GAAATTCAGGTGAAAATCTCCTTCCCCCGCT 38 66 1 TGAAAATCTC 0.7842 -53 TAAAGAAATCGGAAAGTTAGCTGATGCGACT 39 129 1 GGAAAGTTAC 0.803841 -110 ********* * Masking position 5 Map Score: 9.81412 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 211 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 TAGTGAAATCTGACAGCACGGGAATGGCAAT 1 4 0 TGCAAATGGC 0.882569 -202 GCTAGTCTATTGCCCACAAGTCAGTGGCGTGGAAAAGC 5 80 1 TGCCAATGGC 0.983444 -119 TAGGTAAAATCGTCCCTGTTAGAATGGCAAAAGTGAAA 5 134 1 CGCCGATGGC 0.96658 -65 AAGTCTTTACTGCCTGGGTAACAGTGGCTAAGCACCGT 6 48 1 TGCTGATGGC 0.75785 -80 GGTAAGGCGATCGCCTTAGGTCAAAGGCAA 11 3 0 TCCCAAAGGC 0.890101 -196 GCGATCGCCTTACCCCAGACTAACTGGCCAGGTGTTGT 11 27 1 TACCGATGGC 0.870931 -172 AACGCAAAATTGTCAGGAAAAGACTGGCATTGACGCAA 11 83 0 TGCAAATGGC 0.882569 -116 ATCGCCTTCAACCATTGGCGTTTTAGCTC 13 2 1 TCCCCATGGC 0.944939 -183 CTTCCCGGAGGCAATGGCAATTTTTCTT 14 1 1 CTCCGATGGC 0.817328 -97 TGATGGAATTCCCCCATATCGTAGTGGAAGAAAAGGAA 16 71 1 CCCCAATGGA 0.768594 -39 CATAGCATAATCTCCCGACTAAATTGCCACTGTAACGA 19 116 0 TCCCAATGCC 0.881296 -185 TCTTTCCCCTTCAACCCAGCTAAATGGCAGCGCAAAAC 24 12 0 TCACAATGGC 0.83359 -102 AGCAAATACATCCCCGGATTCAAGTGGCACTCCGATTT 26 92 1 TCCCAATGGC 0.987991 -77 GTTCAGTTAACCACCTGACATCAATGGCAAAGACAACA 35 134 1 CCCCAATGGC 0.982003 -48 ** ** * * **** Masking position 13 Map Score: 10.8003 Number of sites scoring better than the average of aligned sites = 490 Number in coding regions = 443 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 CCACCGGAGAAAACTAAAGGAAATA 7 6 1 GGAGAAAACT 0.911895 -33 TTGTTATCTTGGGTAAAAATGACTCTGTTT 8 23 1 GGGTAAAAAT 0.834257 -52 CCATTAAGCTTGATAAAACTTAATAGAAAA 9 153 1 TGATAAAACT 0.56561 -43 TAAACCTTGAGGTTAAAAATTATTAAAACA 10 24 0 GGTTAAAAAT 0.648551 -23 AAGCGGAGAGGGAGAAAAATCATCTACCCT 12 77 1 GGAGAAAAAT 0.791782 -27 GTCGCCAAAGGACGAAAACTCTTTCCCCTT 24 39 0 GACGAAAACT 0.802627 -75 TGAGGGGGCAGAATAAAACTTTCCAAACAC 28 15 0 GAATAAAACT 0.803667 -137 ATCTAAGCGAGGCTAAAACT 29 80 1 GGCTAAAACT 0.963251 -10 CCCAGGATATGGGTAAAAATTGGCTTCTGA 33 56 1 GGGTAAAAAT 0.834257 -101 GCTCAGGGGCTAAAACTAAAGGAAAAA 37 174 0 GGCTAAAACT 0.963251 -17 TAGCTGATGCGACTAAAACTGTTACATTTC 39 146 1 GACTAAAACT 0.866538 -93 ********** Masking position 5 Map Score: 5.04525 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 306 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 10 TCATCCTAGCCCCTAGCCCTGATGGGGTAAA 2 76 1 CCTAGCCCTG 0.982474 -63 ATTGCCCCCTCCGTAGTCTTGGGAAATTGGT 4 265 1 CCTAGTCTTG 0.920134 -36 CTGTTTTTGCCCTTTGTCCTGCCCAGGCAGC 8 47 1 CCTTGTCCTG 0.980388 -28 TTTCTTTGCCCCATTGTCTCGCCCCCCCTAG 14 33 1 CCTTGTCTCG 0.882346 -65 TTATCCACGGCCATTGTCATGGCAGCAATCG 15 32 1 CCTTGTCATG 0.951315 -84 TAAAACAATGACCTTGTCCTGAAAAACTGAC 17 29 1 ACTTGTCCTG 0.813691 -77 CATACCGTCGTCATAGCCCTGTCATACTCGT 17 70 1 TCTAGCCCTG 0.830441 -36 TTCCCATTAACCCTAACCTTGCTGAATTTGT 31 58 1 CCTAACCTTG 0.633238 -23 TGACCTATTACCGTTGCCCCTCAACATACCA 33 121 0 CCTTGCCCCT 0.741951 -36 ATGAAAATTTCCCTTGCCATGGGCTAGGATC 35 82 1 CCTTGCCATG 0.973798 -100 GGGCTAGGATCGATTGCCATGGGGTCGCCGT 35 102 1 CGTTGCCATG 0.81274 -80 ** ******** Masking position 4 Map Score: 3.82553 Number of sites scoring better than the average of aligned sites = 1011 Number in coding regions = 934 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 11 CTTTAGATAACTTTCTAGGGGAAATGGGGA 1 93 0 CTTTCTAGGG 0.77642 -113 AGATCAGATAATATTGAGGGGCTTTTACTT 18 45 1 ATATTGAGGG 0.922266 -256 TTTGCCCCAGCTTTTTAGGGAAAAATGCTA 25 56 1 CTTTTTAGGG 0.918608 -70 TTTAGTTGGTCGATTGAGGGGGCAGAATAA 28 29 0 CGATTGAGGG 0.930469 -123 CCCCCGTTTGCTATTGAGGGAAAATCGTTG 32 59 0 CTATTGAGGG 0.977523 -124 ATTGTTCCTTCTATTTAGGGAATTATACTG 33 89 0 CTATTTAGGG 0.954664 -68 CAATTGTGGTATGTTGAGGGGCAACGGTAA 33 115 1 ATGTTGAGGG 0.842388 -42 ********** Masking position 7 Map Score: 1.57173 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 33 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 TAGGATGATAGGGCGATCACCTTAGGGGAAC 2 53 0 GGGCGATCCC 0.992917 -86 CGCGCGCACTGGGCGTTACCCAGCAAGTTTG 4 96 1 GGGCGTTACC 0.959258 -205 ACTGACTTGTGGGCAATAGACTAGCCCAAGC 5 74 0 GGGCAATAAC 0.844918 -125 GTCTGGGGTAAGGCGATCGCCTTAGGTCAAA 11 16 0 AGGCGATCCC 0.956237 -183 TTAGGTAAAGGGGCATTCAACCTATTTTTCT 27 20 0 GGGCATTCAC 0.896248 -194 ACCCTACTACGGGCGATCGCCAAAATGGCCC 35 45 1 GGGCGATCCC 0.992917 -137 ******** ** Masking position 7 Map Score: 1.98963 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 757 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 13 ACAGCGGCCTATGGCTCTAATCAATGGCACAC 4 204 0 AGGCTCAATC 0.834702 -97 GGGCCTAATCCAGGCTCAAACCCGCTATTTCC 13 137 0 CGGCTCAACC 0.987716 -48 CTTGGGGGATCTGACTCTAACCAAGCAGTGTT 18 228 0 CGACTCAACC 0.956397 -73 AAGTGGCCACCAAGCTCTAATCTAAATTCTTG 18 257 1 CAGCTCAATC 0.969914 -44 CTGAGGAAATCCAGCTCGACCCATTTCGACGT 19 77 0 CAGCTCACCC 0.953461 -224 GCTTTTAAAACAAGCTCTAACCAACTTTGCCT 28 119 1 CAGCTCAACC 0.985203 -33 CCCACTGAAACTAACTCCAATCACTCCAATTT 29 18 1 CAACTCAATC 0.897901 -72 * ***** **** Masking position 9 Map Score: 2.92045 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 48 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 AATTCAATGGTTAGTTTCGTTGTAATTATT 2 106 1 TTAGTTTCGT 0.855918 -33 GGCCCCCAAGTTTGCTTGGGCTAGTCTATT 5 61 1 TTTGCTTGGG 0.644036 -138 AGATAGTTTGTTATCTTGGGTAAAAATGAC 8 16 1 TTATCTTGGG 0.682653 -59 ACCTGGCCAGTTAGTCTGGGGTAAGGCGAT 11 30 0 TTAGTCTGGG 0.765237 -169 CTGACCAAATTTAGCTTCAGCCTTTTTTAT 14 72 1 TTAGCTTCAG 0.901429 -26 AATGGTTATGTTAGTTTGATGTAGTCCTAC 15 85 1 TTAGTTTGAT 0.76164 -31 GGGCTTTTACTTAGTTTCGTCTCAATGTTG 18 63 1 TTAGTTTCGT 0.855918 -238 AATTTTCTAATTATTTTCGGTTGTTGTTGA 18 113 0 TTATTTTCGG 0.723362 -188 GTGATTGGAGTTAGTTTCAGTGGGAAAAAC 29 12 0 TTAGTTTCAG 0.917467 -78 CTTAGATTAATTAGTTTGATTAATTAATTG 29 57 0 TTAGTTTGAT 0.76164 -33 AACTCTGGGTTTAGGTTGGGAAAATAGACT 34 41 0 TTAGGTTGGG 0.828433 -71 TTAGCTTCAGCACAAGATTA 37 1 1 TTAGCTTCAG 0.901429 -190 TTTTTTTCCTTTAGTTTTAGCCCCTGAGC 37 172 1 TTAGTTTTAG 0.590483 -19 ********** Masking position 7 Map Score: 3.248 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 267 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 15 GGGTCTAACCTCTACCAAATTTTGGGAGCT 2 21 0 TCTACCAAAT 0.884939 -118 TTCTAACAATTCGTCCAAATTCTGTATCTG 11 121 1 TCGTCCAAAT 0.924237 -78 AGCTCTGTCCTCTACCAACATTGAGACGAA 18 78 0 TCTACCAACA 0.86634 -223 GCCCCCTCAATCGACCAACTAAAGCGACCG 28 36 1 TCGACCAACT 0.972819 -116 TCGGTAAATTTCGACCAACACAGCCCAGAA 34 12 0 TCGACCAACA 0.950452 -100 TAGCATTTAATCGTCCAAATTTACCA 36 7 0 TCGTCCAAAT 0.924237 -116 ********** Masking position 7 Map Score: 0.933435 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 27 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084