Multiple sequence alignment - TraesCS7D01G014400 
Loading Multiple Alignment...
 BLAST Results  
BLAST Results - Input Sequence 
    
     Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this
        to extract flanking regions for cloning. If the result of the multiple sequence alignment is
        not as expected, these results could be used for further investigation. 
    
  
    
      qseqid 
      sseqid 
      percentage.identical 
      alignment.length 
      no.mismatch 
      no.gap.openings 
      qstart 
      qend 
      sstart 
      send 
      evalue 
      bitscore 
     
   
  
    
      0 
      TraesCS7D01G014400 
      chr7D 
      100.000 
      2522 
      0 
      0 
      1 
      2522 
      6401303 
      6398782 
      0.000000e+00 
      4658 
     
    
      1 
      TraesCS7D01G014400 
      chr3A 
      89.436 
      1969 
      111 
      36 
      1 
      1922 
      534323059 
      534324977 
      0.000000e+00 
      2394 
     
    
      2 
      TraesCS7D01G014400 
      chr3A 
      84.783 
      598 
      72 
      13 
      1931 
      2515 
      534325228 
      534325819 
      1.300000e-162 
      582 
     
    
      3 
      TraesCS7D01G014400 
      chr3A 
      82.904 
      427 
      58 
      7 
      2099 
      2519 
      272796324 
      272796741 
      1.100000e-98 
      370 
     
    
      4 
      TraesCS7D01G014400 
      chr3B 
      90.097 
      1858 
      107 
      31 
      1 
      1811 
      542678340 
      542676513 
      0.000000e+00 
      2340 
     
    
      5 
      TraesCS7D01G014400 
      chr3B 
      88.279 
      401 
      31 
      3 
      1931 
      2315 
      542675979 
      542675579 
      1.370000e-127 
      466 
     
    
      6 
      TraesCS7D01G014400 
      chr3B 
      82.793 
      401 
      51 
      8 
      2128 
      2522 
      349273093 
      349272705 
      2.400000e-90 
      342 
     
    
      7 
      TraesCS7D01G014400 
      chr3D 
      91.440 
      736 
      36 
      12 
      941 
      1662 
      416187028 
      416186306 
      0.000000e+00 
      985 
     
    
      8 
      TraesCS7D01G014400 
      chr3D 
      88.651 
      608 
      50 
      3 
      1931 
      2522 
      416141926 
      416141322 
      0.000000e+00 
      723 
     
    
      9 
      TraesCS7D01G014400 
      chr3D 
      85.714 
      490 
      48 
      11 
      1 
      483 
      416188129 
      416187655 
      4.840000e-137 
      497 
     
    
      10 
      TraesCS7D01G014400 
      chr3D 
      89.059 
      393 
      16 
      11 
      561 
      934 
      416187536 
      416187152 
      1.770000e-126 
      462 
     
    
      11 
      TraesCS7D01G014400 
      chr3D 
      93.436 
      259 
      14 
      3 
      1665 
      1922 
      416142434 
      416142178 
      5.090000e-102 
      381 
     
    
      12 
      TraesCS7D01G014400 
      chr4A 
      81.739 
      460 
      79 
      2 
      2064 
      2519 
      579426004 
      579426462 
      1.830000e-101 
      379 
     
    
      13 
      TraesCS7D01G014400 
      chr4D 
      82.949 
      434 
      54 
      11 
      2099 
      2522 
      315079125 
      315078702 
      8.520000e-100 
      374 
     
    
      14 
      TraesCS7D01G014400 
      chr4B 
      81.290 
      465 
      81 
      3 
      2062 
      2522 
      34729479 
      34729017 
      3.060000e-99 
      372 
     
    
      15 
      TraesCS7D01G014400 
      chr6A 
      78.988 
      514 
      91 
      7 
      2019 
      2519 
      521988528 
      521989037 
      4.020000e-88 
      335 
     
    
      16 
      TraesCS7D01G014400 
      chr1D 
      81.984 
      383 
      58 
      6 
      2138 
      2515 
      256108118 
      256108494 
      5.240000e-82 
      315 
     
    
      17 
      TraesCS7D01G014400 
      chr2B 
      77.567 
      526 
      94 
      15 
      2010 
      2519 
      21649146 
      21649663 
      1.900000e-76 
      296 
     
   
    
 
BLAST Results - HSPs grouped 
    
     These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the
        BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are
        purely upstream or downstream may be removed if they don't overlap both primers. 
    
  
    
      query 
      scaffold 
      start 
      end 
      length 
      rev.comp 
      avg.bitscore 
      max.bitscore 
      avg.percent.identical 
      query.start 
      query.end 
      num_hsp 
      groupid 
      homo_length 
     
   
  
    
      0 
      TraesCS7D01G014400 
      chr7D 
      6398782 
      6401303 
      2521 
      True 
      4658 
      4658 
      100.000000 
      1 
      2522 
      1 
      chr7D.!!$R1 
      2521 
     
    
      1 
      TraesCS7D01G014400 
      chr3A 
      534323059 
      534325819 
      2760 
      False 
      1488 
      2394 
      87.109500 
      1 
      2515 
      2 
      chr3A.!!$F2 
      2514 
     
    
      2 
      TraesCS7D01G014400 
      chr3B 
      542675579 
      542678340 
      2761 
      True 
      1403 
      2340 
      89.188000 
      1 
      2315 
      2 
      chr3B.!!$R2 
      2314 
     
    
      3 
      TraesCS7D01G014400 
      chr3D 
      416186306 
      416188129 
      1823 
      True 
      648 
      985 
      88.737667 
      1 
      1662 
      3 
      chr3D.!!$R2 
      1661 
     
    
      4 
      TraesCS7D01G014400 
      chr3D 
      416141322 
      416142434 
      1112 
      True 
      552 
      723 
      91.043500 
      1665 
      2522 
      2 
      chr3D.!!$R1 
      857 
     
    
      5 
      TraesCS7D01G014400 
      chr6A 
      521988528 
      521989037 
      509 
      False 
      335 
      335 
      78.988000 
      2019 
      2519 
      1 
      chr6A.!!$F1 
      500 
     
    
      6 
      TraesCS7D01G014400 
      chr2B 
      21649146 
      21649663 
      517 
      False 
      296 
      296 
      77.567000 
      2010 
      2519 
      1 
      chr2B.!!$F1 
      509 
     
   
 
            
                
                     AutoCloner calculated primer pairs  
                     These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3),
                        whilst remaining within the specified product range where possible. 
                 
                
                    
                 
             
        
	Forward
		Primers 
	Reverse
		Primers 
	
  
    
      Position 
      MSA Position 
      Penalty 
      Sequence 
      TM 
      GC 
      Self any TH 
      Self end TH 
      Hairpin 
      End Stability 
      Orientation 
     
   
  
    
      856 
      955 
      0.108804 
      TCGGGTGCTCGATTCTCAAC 
      60.109 
      55.0 
      0.0 
      0.0 
      33.92 
      3.18 
      F 
     
   
 
	
  
    
      Position 
      MSA Position 
      Penalty 
      Sequence 
      TM 
      GC 
      Self any TH 
      Self end TH 
      Hairpin 
      End Stability 
      Orientation 
     
   
  
    
      2210 
      2956 
      0.46729 
      TTGCAGTTGTTCCTGGACCC 
      60.467 
      55.0 
      0.0 
      0.0 
      32.08 
      4.46 
      R 
     
   
 
        
            
                 All possible primers  
                 Listed here are all possible primers based on the multiple sequence alignment and SNPs generated
                    previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work
                    during PCR or sequencing,
                    these could be used as alternatives. 
             
            
                
             
         
    
    
        Forward
            Primers 
        Reverse
            Primers 
    
    
		
  
    
      Position 
      MSA Position 
      Penalty 
      Sequence 
      TM 
      GC 
      Self any TH 
      Self end TH 
      Hairpin 
      End Stability 
     
   
  
    
      67 
      68 
      9.569122 
      GCCTAATTTTATATTTCTGTAGGGTCA 
      57.431 
      33.333 
      0.00 
      0.00 
      0.00 
      4.02 
     
    
      82 
      83 
      6.411376 
      TGTAGGGTCATTGTAATAGTTGTGG 
      58.589 
      40.000 
      0.00 
      0.00 
      0.00 
      4.17 
     
    
      121 
      127 
      3.581437 
      TCCTTGGGGACTGTTGGTA 
      57.419 
      52.632 
      0.00 
      0.00 
      36.57 
      3.25 
     
    
      163 
      169 
      1.258458 
      CTTGCATTGCACAAAACACCG 
      59.742 
      47.619 
      11.66 
      0.00 
      38.71 
      4.94 
     
    
      208 
      216 
      2.981859 
      TTCTTCTGCCGGGATAACTC 
      57.018 
      50.000 
      2.18 
      0.00 
      0.00 
      3.01 
     
    
      233 
      243 
      1.068472 
      ACTTAACGCGGTCACTCTCTG 
      60.068 
      52.381 
      12.47 
      0.00 
      0.00 
      3.35 
     
    
      273 
      283 
      0.463654 
      TTGATATGACAGTGGCGGGC 
      60.464 
      55.000 
      0.00 
      0.00 
      0.00 
      6.13 
     
    
      294 
      304 
      4.142600 
      GGCTTCGTGTCTTGCTATTTTCAT 
      60.143 
      41.667 
      0.00 
      0.00 
      0.00 
      2.57 
     
    
      354 
      383 
      5.410355 
      AAAAAGATCCACCATTGTCCATG 
      57.590 
      39.130 
      0.00 
      0.00 
      0.00 
      3.66 
     
    
      356 
      385 
      3.287867 
      AGATCCACCATTGTCCATGTC 
      57.712 
      47.619 
      0.00 
      0.00 
      0.00 
      3.06 
     
    
      358 
      387 
      1.071434 
      TCCACCATTGTCCATGTCCA 
      58.929 
      50.000 
      0.00 
      0.00 
      0.00 
      4.02 
     
    
      364 
      393 
      4.039004 
      CACCATTGTCCATGTCCAAAAGAA 
      59.961 
      41.667 
      0.00 
      0.00 
      0.00 
      2.52 
     
    
      365 
      394 
      4.653341 
      ACCATTGTCCATGTCCAAAAGAAA 
      59.347 
      37.500 
      0.00 
      0.00 
      0.00 
      2.52 
     
    
      366 
      395 
      5.307716 
      ACCATTGTCCATGTCCAAAAGAAAT 
      59.692 
      36.000 
      0.00 
      0.00 
      0.00 
      2.17 
     
    
      367 
      396 
      6.183361 
      ACCATTGTCCATGTCCAAAAGAAATT 
      60.183 
      34.615 
      0.00 
      0.00 
      0.00 
      1.82 
     
    
      368 
      397 
      7.016072 
      ACCATTGTCCATGTCCAAAAGAAATTA 
      59.984 
      33.333 
      0.00 
      0.00 
      0.00 
      1.40 
     
    
      369 
      398 
      7.546667 
      CCATTGTCCATGTCCAAAAGAAATTAG 
      59.453 
      37.037 
      0.00 
      0.00 
      0.00 
      1.73 
     
    
      370 
      399 
      6.588719 
      TGTCCATGTCCAAAAGAAATTAGG 
      57.411 
      37.500 
      0.00 
      0.00 
      0.00 
      2.69 
     
    
      461 
      490 
      3.682858 
      TCGGGAAAAAGTCGCTATCTTTG 
      59.317 
      43.478 
      0.00 
      0.00 
      37.05 
      2.77 
     
    
      483 
      512 
      3.184683 
      GGTTGCTCGCTCGCTCTG 
      61.185 
      66.667 
      0.00 
      0.00 
      0.00 
      3.35 
     
    
      598 
      668 
      9.743057 
      TGTTAACAGAAAAACAAATGATACCAG 
      57.257 
      29.630 
      3.59 
      0.00 
      32.86 
      4.00 
     
    
      600 
      670 
      5.783111 
      ACAGAAAAACAAATGATACCAGCC 
      58.217 
      37.500 
      0.00 
      0.00 
      0.00 
      4.85 
     
    
      601 
      671 
      5.170748 
      CAGAAAAACAAATGATACCAGCCC 
      58.829 
      41.667 
      0.00 
      0.00 
      0.00 
      5.19 
     
    
      687 
      765 
      1.501582 
      GGCTCAACTCCCCTATCACT 
      58.498 
      55.000 
      0.00 
      0.00 
      0.00 
      3.41 
     
    
      796 
      895 
      7.442666 
      GGTTAACCAAGCAATATTCAAAACCAA 
      59.557 
      33.333 
      20.12 
      0.00 
      33.38 
      3.67 
     
    
      799 
      898 
      5.221702 
      ACCAAGCAATATTCAAAACCAAGCT 
      60.222 
      36.000 
      0.00 
      0.00 
      0.00 
      3.74 
     
    
      855 
      954 
      0.824109 
      ATCGGGTGCTCGATTCTCAA 
      59.176 
      50.000 
      0.54 
      0.00 
      46.23 
      3.02 
     
    
      856 
      955 
      0.108804 
      TCGGGTGCTCGATTCTCAAC 
      60.109 
      55.000 
      0.00 
      0.00 
      33.92 
      3.18 
     
    
      857 
      956 
      1.084370 
      CGGGTGCTCGATTCTCAACC 
      61.084 
      60.000 
      0.00 
      0.00 
      34.33 
      3.77 
     
    
      858 
      957 
      0.250513 
      GGGTGCTCGATTCTCAACCT 
      59.749 
      55.000 
      4.55 
      0.00 
      34.82 
      3.50 
     
    
      859 
      958 
      1.646189 
      GGTGCTCGATTCTCAACCTC 
      58.354 
      55.000 
      0.00 
      0.00 
      0.00 
      3.85 
     
    
      860 
      959 
      1.066858 
      GGTGCTCGATTCTCAACCTCA 
      60.067 
      52.381 
      0.00 
      0.00 
      0.00 
      3.86 
     
    
      880 
      979 
      1.777941 
      ACCCAGAGATAACGGAGACC 
      58.222 
      55.000 
      0.00 
      0.00 
      0.00 
      3.85 
     
    
      893 
      992 
      1.242665 
      GGAGACCTCCGTCGAGTTGT 
      61.243 
      60.000 
      0.00 
      0.00 
      44.28 
      3.32 
     
    
      964 
      1181 
      1.194547 
      CCGTCTGTGTTTCATTGTCGG 
      59.805 
      52.381 
      0.00 
      0.00 
      0.00 
      4.79 
     
    
      965 
      1182 
      1.864711 
      CGTCTGTGTTTCATTGTCGGT 
      59.135 
      47.619 
      0.00 
      0.00 
      0.00 
      4.69 
     
    
      966 
      1183 
      2.096909 
      CGTCTGTGTTTCATTGTCGGTC 
      60.097 
      50.000 
      0.00 
      0.00 
      0.00 
      4.79 
     
    
      967 
      1184 
      2.096909 
      GTCTGTGTTTCATTGTCGGTCG 
      60.097 
      50.000 
      0.00 
      0.00 
      0.00 
      4.79 
     
    
      1005 
      1222 
      1.269309 
      CCTAGTACGCAGCAGATGACC 
      60.269 
      57.143 
      0.00 
      0.00 
      0.00 
      4.02 
     
    
      1528 
      1745 
      2.202311 
      CTCGATCGTGACGCGTGT 
      60.202 
      61.111 
      20.70 
      0.00 
      42.13 
      4.49 
     
    
      1529 
      1746 
      1.796355 
      CTCGATCGTGACGCGTGTT 
      60.796 
      57.895 
      20.70 
      0.00 
      42.13 
      3.32 
     
    
      1537 
      1754 
      0.041312 
      GTGACGCGTGTTTGCAAGAT 
      60.041 
      50.000 
      20.70 
      0.00 
      34.15 
      2.40 
     
    
      1539 
      1756 
      0.234625 
      GACGCGTGTTTGCAAGATGA 
      59.765 
      50.000 
      20.70 
      0.00 
      34.15 
      2.92 
     
    
      1577 
      1795 
      7.170998 
      GCTGTGTACAAAACTAGCTTCTAGAAA 
      59.829 
      37.037 
      6.63 
      0.00 
      36.60 
      2.52 
     
    
      1578 
      1796 
      8.589335 
      TGTGTACAAAACTAGCTTCTAGAAAG 
      57.411 
      34.615 
      6.63 
      3.93 
      0.00 
      2.62 
     
    
      1579 
      1797 
      8.202137 
      TGTGTACAAAACTAGCTTCTAGAAAGT 
      58.798 
      33.333 
      6.63 
      4.59 
      0.00 
      2.66 
     
    
      1624 
      1856 
      3.603294 
      CGTTCTCGTGATTTCTTCGTC 
      57.397 
      47.619 
      0.00 
      0.00 
      0.00 
      4.20 
     
    
      1757 
      1989 
      6.072508 
      AGTGATAATGTGACATGAACACCAAC 
      60.073 
      38.462 
      16.89 
      1.86 
      37.45 
      3.77 
     
    
      1765 
      1997 
      3.751518 
      ACATGAACACCAACCTCCTAAC 
      58.248 
      45.455 
      0.00 
      0.00 
      0.00 
      2.34 
     
    
      1834 
      2069 
      8.308931 
      TGTCGTTCTTTAGCTTTAGGATCTAAA 
      58.691 
      33.333 
      0.00 
      0.98 
      33.05 
      1.85 
     
    
      1835 
      2070 
      9.315525 
      GTCGTTCTTTAGCTTTAGGATCTAAAT 
      57.684 
      33.333 
      0.00 
      0.00 
      33.45 
      1.40 
     
    
      1913 
      2148 
      6.262944 
      TGTGCAAACATTCTTATCTGACAAGT 
      59.737 
      34.615 
      0.00 
      0.00 
      0.00 
      3.16 
     
    
      1922 
      2157 
      6.500684 
      TCTTATCTGACAAGTTTGGAATGC 
      57.499 
      37.500 
      0.00 
      0.00 
      0.00 
      3.56 
     
    
      1923 
      2158 
      5.415701 
      TCTTATCTGACAAGTTTGGAATGCC 
      59.584 
      40.000 
      0.00 
      0.00 
      0.00 
      4.40 
     
    
      1925 
      2160 
      3.499338 
      TCTGACAAGTTTGGAATGCCAT 
      58.501 
      40.909 
      0.00 
      0.00 
      45.46 
      4.40 
     
    
      1926 
      2161 
      3.507233 
      TCTGACAAGTTTGGAATGCCATC 
      59.493 
      43.478 
      0.00 
      0.00 
      45.46 
      3.51 
     
    
      1928 
      2163 
      2.228822 
      GACAAGTTTGGAATGCCATCGT 
      59.771 
      45.455 
      0.00 
      0.00 
      45.46 
      3.73 
     
    
      1929 
      2164 
      2.030007 
      ACAAGTTTGGAATGCCATCGTG 
      60.030 
      45.455 
      0.00 
      1.51 
      45.46 
      4.35 
     
    
      1935 
      2660 
      0.099436 
      GGAATGCCATCGTGTGAAGC 
      59.901 
      55.000 
      0.00 
      0.00 
      0.00 
      3.86 
     
    
      2075 
      2816 
      3.173151 
      TGGATAACAGGTTCTGCTCTGA 
      58.827 
      45.455 
      0.00 
      0.00 
      34.37 
      3.27 
     
    
      2078 
      2819 
      5.003804 
      GGATAACAGGTTCTGCTCTGAAAA 
      58.996 
      41.667 
      0.00 
      0.00 
      34.37 
      2.29 
     
    
      2110 
      2851 
      4.046286 
      TCACCCACATGCTTAAATTCCT 
      57.954 
      40.909 
      0.00 
      0.00 
      0.00 
      3.36 
     
    
      2116 
      2857 
      3.689161 
      CACATGCTTAAATTCCTGACCGA 
      59.311 
      43.478 
      0.00 
      0.00 
      0.00 
      4.69 
     
    
      2157 
      2899 
      1.710244 
      TCCTCCACAATCATGTTGGGT 
      59.290 
      47.619 
      11.15 
      0.00 
      37.82 
      4.51 
     
    
      2187 
      2929 
      2.173519 
      CAAGTTGCCATCACCTTCCAT 
      58.826 
      47.619 
      0.00 
      0.00 
      0.00 
      3.41 
     
    
      2210 
      2956 
      0.392193 
      GCCTCTGGATCCCATATGCG 
      60.392 
      60.000 
      9.90 
      0.00 
      30.82 
      4.73 
     
    
      2262 
      3008 
      1.813513 
      CACTTCAAATGCCCTCTCGT 
      58.186 
      50.000 
      0.00 
      0.00 
      0.00 
      4.18 
     
    
      2303 
      3053 
      2.435372 
      TGTCTTTGGGCAAAGTGAGT 
      57.565 
      45.000 
      0.00 
      0.00 
      45.88 
      3.41 
     
    
      2352 
      3102 
      1.079127 
      CTTGACGAAGGTCGCCCAT 
      60.079 
      57.895 
      0.00 
      0.00 
      46.49 
      4.00 
     
    
      2361 
      3111 
      1.507140 
      AGGTCGCCCATGAAGGATAA 
      58.493 
      50.000 
      0.00 
      0.00 
      41.22 
      1.75 
     
    
      2366 
      3116 
      5.010282 
      GGTCGCCCATGAAGGATAAATATT 
      58.990 
      41.667 
      0.00 
      0.00 
      41.22 
      1.28 
     
    
      2409 
      3161 
      6.238566 
      CCATGTTGTACTCATGACCATTGATC 
      60.239 
      42.308 
      23.17 
      0.00 
      43.47 
      2.92 
     
    
      2436 
      3190 
      1.538047 
      TGCATGAAAGAGCTTGTCCC 
      58.462 
      50.000 
      0.00 
      0.00 
      0.00 
      4.46 
     
    
      2437 
      3191 
      1.202915 
      TGCATGAAAGAGCTTGTCCCA 
      60.203 
      47.619 
      0.00 
      0.00 
      0.00 
      4.37 
     
    
      2501 
      3255 
      1.627864 
      TGTCATTGTGAGACCCGAGA 
      58.372 
      50.000 
      0.00 
      0.00 
      35.15 
      4.04 
     
    
      2519 
      3273 
      4.563580 
      CCGAGAATCCCAAAGAAAGAGTGA 
      60.564 
      45.833 
      0.00 
      0.00 
      0.00 
      3.41 
     
   
	 
    
		
  
    
      Position 
      MSA Position 
      Penalty 
      Sequence 
      TM 
      GC 
      Self any TH 
      Self end TH 
      Hairpin 
      End Stability 
     
   
  
    
      82 
      83 
      4.644234 
      GGACCTAGGTAGAAGTGGTTACTC 
      59.356 
      50.000 
      16.29 
      0.00 
      35.69 
      2.59 
     
    
      192 
      200 
      1.140852 
      CATGGAGTTATCCCGGCAGAA 
      59.859 
      52.381 
      0.00 
      0.00 
      46.04 
      3.02 
     
    
      193 
      201 
      0.758734 
      CATGGAGTTATCCCGGCAGA 
      59.241 
      55.000 
      0.00 
      0.00 
      46.04 
      4.26 
     
    
      194 
      202 
      0.758734 
      TCATGGAGTTATCCCGGCAG 
      59.241 
      55.000 
      0.00 
      0.00 
      46.04 
      4.85 
     
    
      195 
      203 
      0.468226 
      GTCATGGAGTTATCCCGGCA 
      59.532 
      55.000 
      0.00 
      0.00 
      46.04 
      5.69 
     
    
      196 
      204 
      0.759346 
      AGTCATGGAGTTATCCCGGC 
      59.241 
      55.000 
      0.00 
      0.00 
      46.04 
      6.13 
     
    
      197 
      205 
      4.377897 
      GTTAAGTCATGGAGTTATCCCGG 
      58.622 
      47.826 
      0.00 
      0.00 
      46.04 
      5.73 
     
    
      198 
      206 
      4.049186 
      CGTTAAGTCATGGAGTTATCCCG 
      58.951 
      47.826 
      0.00 
      0.00 
      46.04 
      5.14 
     
    
      201 
      209 
      3.489785 
      CCGCGTTAAGTCATGGAGTTATC 
      59.510 
      47.826 
      4.92 
      0.00 
      29.16 
      1.75 
     
    
      208 
      216 
      0.719465 
      GTGACCGCGTTAAGTCATGG 
      59.281 
      55.000 
      16.92 
      0.00 
      44.34 
      3.66 
     
    
      273 
      283 
      7.805071 
      AGAAAATGAAAATAGCAAGACACGAAG 
      59.195 
      33.333 
      0.00 
      0.00 
      0.00 
      3.79 
     
    
      294 
      304 
      3.222603 
      GGCAACTGGGAAAGAGAGAAAA 
      58.777 
      45.455 
      0.00 
      0.00 
      0.00 
      2.29 
     
    
      337 
      366 
      2.301346 
      GGACATGGACAATGGTGGATC 
      58.699 
      52.381 
      0.00 
      0.00 
      40.94 
      3.36 
     
    
      338 
      367 
      1.640149 
      TGGACATGGACAATGGTGGAT 
      59.360 
      47.619 
      0.00 
      0.00 
      40.94 
      3.41 
     
    
      339 
      368 
      1.071434 
      TGGACATGGACAATGGTGGA 
      58.929 
      50.000 
      0.00 
      0.00 
      40.94 
      4.02 
     
    
      354 
      383 
      6.934083 
      TGGCATTTTCCTAATTTCTTTTGGAC 
      59.066 
      34.615 
      0.00 
      0.00 
      38.69 
      4.02 
     
    
      356 
      385 
      6.149308 
      GGTGGCATTTTCCTAATTTCTTTTGG 
      59.851 
      38.462 
      0.00 
      0.00 
      0.00 
      3.28 
     
    
      358 
      387 
      6.836242 
      TGGTGGCATTTTCCTAATTTCTTTT 
      58.164 
      32.000 
      0.00 
      0.00 
      0.00 
      2.27 
     
    
      364 
      393 
      5.248020 
      TGACAATGGTGGCATTTTCCTAATT 
      59.752 
      36.000 
      0.00 
      0.00 
      38.09 
      1.40 
     
    
      365 
      394 
      4.776837 
      TGACAATGGTGGCATTTTCCTAAT 
      59.223 
      37.500 
      0.00 
      0.00 
      38.09 
      1.73 
     
    
      366 
      395 
      4.155709 
      TGACAATGGTGGCATTTTCCTAA 
      58.844 
      39.130 
      0.00 
      0.00 
      38.09 
      2.69 
     
    
      367 
      396 
      3.763360 
      CTGACAATGGTGGCATTTTCCTA 
      59.237 
      43.478 
      0.00 
      0.00 
      43.72 
      2.94 
     
    
      368 
      397 
      2.564062 
      CTGACAATGGTGGCATTTTCCT 
      59.436 
      45.455 
      0.00 
      0.00 
      43.72 
      3.36 
     
    
      369 
      398 
      2.562298 
      TCTGACAATGGTGGCATTTTCC 
      59.438 
      45.455 
      0.00 
      0.00 
      43.72 
      3.13 
     
    
      370 
      399 
      3.940209 
      TCTGACAATGGTGGCATTTTC 
      57.060 
      42.857 
      0.00 
      0.00 
      43.72 
      2.29 
     
    
      483 
      512 
      5.457148 
      TGTGTCAACGATGCAATTGTAAAAC 
      59.543 
      36.000 
      7.40 
      0.00 
      41.01 
      2.43 
     
    
      600 
      670 
      1.070786 
      ACGCATATGTAAGCCGGGG 
      59.929 
      57.895 
      2.18 
      0.00 
      0.00 
      5.73 
     
    
      601 
      671 
      1.841663 
      GCACGCATATGTAAGCCGGG 
      61.842 
      60.000 
      2.18 
      0.99 
      0.00 
      5.73 
     
    
      687 
      765 
      4.079500 
      TGTGATGTATTTTGGGGCCATAGA 
      60.080 
      41.667 
      4.39 
      0.00 
      0.00 
      1.98 
     
    
      796 
      895 
      1.291588 
      CTTGTGCAGTCGAGGAGCT 
      59.708 
      57.895 
      0.00 
      0.00 
      0.00 
      4.09 
     
    
      799 
      898 
      3.137687 
      TGCTTGTGCAGTCGAGGA 
      58.862 
      55.556 
      0.00 
      0.00 
      45.31 
      3.71 
     
    
      855 
      954 
      1.831736 
      CCGTTATCTCTGGGTTGAGGT 
      59.168 
      52.381 
      0.00 
      0.00 
      34.98 
      3.85 
     
    
      856 
      955 
      2.101582 
      CTCCGTTATCTCTGGGTTGAGG 
      59.898 
      54.545 
      0.00 
      0.00 
      34.98 
      3.86 
     
    
      857 
      956 
      3.024547 
      TCTCCGTTATCTCTGGGTTGAG 
      58.975 
      50.000 
      0.00 
      0.00 
      35.52 
      3.02 
     
    
      858 
      957 
      2.758979 
      GTCTCCGTTATCTCTGGGTTGA 
      59.241 
      50.000 
      0.00 
      0.00 
      0.00 
      3.18 
     
    
      859 
      958 
      2.159085 
      GGTCTCCGTTATCTCTGGGTTG 
      60.159 
      54.545 
      0.00 
      0.00 
      0.00 
      3.77 
     
    
      860 
      959 
      2.108970 
      GGTCTCCGTTATCTCTGGGTT 
      58.891 
      52.381 
      0.00 
      0.00 
      0.00 
      4.11 
     
    
      880 
      979 
      5.293814 
      TCTTTATAGAGACAACTCGACGGAG 
      59.706 
      44.000 
      0.00 
      0.00 
      46.64 
      4.63 
     
    
      964 
      1181 
      2.027625 
      CGTGGAGGTTGCTTCCGAC 
      61.028 
      63.158 
      0.00 
      0.00 
      37.54 
      4.79 
     
    
      965 
      1182 
      2.342279 
      CGTGGAGGTTGCTTCCGA 
      59.658 
      61.111 
      0.00 
      0.00 
      37.54 
      4.55 
     
    
      966 
      1183 
      3.423154 
      GCGTGGAGGTTGCTTCCG 
      61.423 
      66.667 
      0.00 
      0.00 
      37.54 
      4.30 
     
    
      967 
      1184 
      2.032681 
      AGCGTGGAGGTTGCTTCC 
      59.967 
      61.111 
      0.00 
      0.00 
      34.80 
      3.46 
     
    
      1528 
      1745 
      1.285668 
      TACGCGCGTCATCTTGCAAA 
      61.286 
      50.000 
      41.35 
      15.51 
      0.00 
      3.68 
     
    
      1529 
      1746 
      1.682867 
      CTACGCGCGTCATCTTGCAA 
      61.683 
      55.000 
      41.35 
      17.88 
      0.00 
      4.08 
     
    
      1577 
      1795 
      0.629058 
      AAACTGGTGTGTTGGGGACT 
      59.371 
      50.000 
      0.00 
      0.00 
      0.00 
      3.85 
     
    
      1578 
      1796 
      1.407618 
      GAAAACTGGTGTGTTGGGGAC 
      59.592 
      52.381 
      0.00 
      0.00 
      0.00 
      4.46 
     
    
      1579 
      1797 
      1.286553 
      AGAAAACTGGTGTGTTGGGGA 
      59.713 
      47.619 
      0.00 
      0.00 
      0.00 
      4.81 
     
    
      1757 
      1989 
      2.420129 
      CCTGATTTCACGGGTTAGGAGG 
      60.420 
      54.545 
      0.00 
      0.00 
      0.00 
      4.30 
     
    
      1765 
      1997 
      3.886123 
      ACCTTTATCCTGATTTCACGGG 
      58.114 
      45.455 
      0.00 
      0.00 
      37.63 
      5.28 
     
    
      1834 
      2069 
      8.650143 
      AGATCGCAAATAACCCCAATTAATAT 
      57.350 
      30.769 
      0.00 
      0.00 
      0.00 
      1.28 
     
    
      1835 
      2070 
      8.356657 
      CAAGATCGCAAATAACCCCAATTAATA 
      58.643 
      33.333 
      0.00 
      0.00 
      0.00 
      0.98 
     
    
      1836 
      2071 
      6.976934 
      AGATCGCAAATAACCCCAATTAAT 
      57.023 
      33.333 
      0.00 
      0.00 
      0.00 
      1.40 
     
    
      1922 
      2157 
      3.624326 
      TTGAAAAGCTTCACACGATGG 
      57.376 
      42.857 
      0.00 
      0.00 
      41.34 
      3.51 
     
    
      1923 
      2158 
      7.621832 
      TTTTATTGAAAAGCTTCACACGATG 
      57.378 
      32.000 
      0.00 
      0.00 
      41.34 
      3.84 
     
    
      1925 
      2160 
      8.564574 
      ACTATTTTATTGAAAAGCTTCACACGA 
      58.435 
      29.630 
      0.00 
      0.00 
      41.34 
      4.35 
     
    
      1926 
      2161 
      8.728088 
      ACTATTTTATTGAAAAGCTTCACACG 
      57.272 
      30.769 
      0.00 
      0.00 
      41.34 
      4.49 
     
    
      1954 
      2679 
      9.903682 
      ATGTCTGAATAAGTTGAACTCAAATTG 
      57.096 
      29.630 
      13.76 
      0.00 
      42.96 
      2.32 
     
    
      2075 
      2816 
      7.342799 
      AGCATGTGGGTGATTCTATACAATTTT 
      59.657 
      33.333 
      0.00 
      0.00 
      0.00 
      1.82 
     
    
      2078 
      2819 
      5.945310 
      AGCATGTGGGTGATTCTATACAAT 
      58.055 
      37.500 
      0.00 
      0.00 
      0.00 
      2.71 
     
    
      2110 
      2851 
      3.744719 
      CGGAGTTCGCCTCGGTCA 
      61.745 
      66.667 
      0.00 
      0.00 
      41.46 
      4.02 
     
    
      2157 
      2899 
      5.356751 
      GGTGATGGCAACTTGTGTGATTATA 
      59.643 
      40.000 
      0.00 
      0.00 
      37.61 
      0.98 
     
    
      2187 
      2929 
      2.391926 
      TATGGGATCCAGAGGCGTTA 
      57.608 
      50.000 
      15.23 
      0.00 
      36.75 
      3.18 
     
    
      2210 
      2956 
      0.467290 
      TTGCAGTTGTTCCTGGACCC 
      60.467 
      55.000 
      0.00 
      0.00 
      32.08 
      4.46 
     
    
      2262 
      3008 
      6.240894 
      ACAAGAAATGTGCTAGAAAGGATGA 
      58.759 
      36.000 
      0.00 
      0.00 
      41.93 
      2.92 
     
    
      2303 
      3053 
      6.306199 
      TCTGATCAAATGGGTGAGAAAAGAA 
      58.694 
      36.000 
      0.00 
      0.00 
      0.00 
      2.52 
     
    
      2320 
      3070 
      5.221322 
      CCTTCGTCAAGACCATATCTGATCA 
      60.221 
      44.000 
      0.00 
      0.00 
      37.88 
      2.92 
     
    
      2366 
      3116 
      7.998383 
      ACAACATGGGCTATTATCTTTGTGATA 
      59.002 
      33.333 
      0.00 
      0.00 
      36.65 
      2.15 
     
    
      2409 
      3161 
      2.738846 
      AGCTCTTTCATGCAACTACACG 
      59.261 
      45.455 
      0.00 
      0.00 
      0.00 
      4.49 
     
    
      2436 
      3190 
      1.991965 
      GTTTGCAAGGTTGTGTGTGTG 
      59.008 
      47.619 
      0.00 
      0.00 
      0.00 
      3.82 
     
    
      2437 
      3191 
      1.615883 
      TGTTTGCAAGGTTGTGTGTGT 
      59.384 
      42.857 
      0.00 
      0.00 
      0.00 
      3.72 
     
    
      2478 
      3232 
      2.002586 
      CGGGTCTCACAATGACATCAC 
      58.997 
      52.381 
      0.00 
      0.00 
      36.26 
      3.06 
     
   
	 
	
 Based at the University of Bristol  with support from BBSRC .
AutoCloner maintained by Alex Coulton.