Multiple sequence alignment - TraesCS5D01G453700 
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 
      TraesCS5D01G453700 
      chr5D 
      100.000 
      2469 
      0 
      0 
      1 
      2469 
      501034069 
      501031601 
      0.000000e+00 
      4560.0 
     
    
      1 
      TraesCS5D01G453700 
      chr5D 
      88.770 
      187 
      20 
      1 
      2168 
      2354 
      490466430 
      490466615 
      6.870000e-56 
      228.0 
     
    
      2 
      TraesCS5D01G453700 
      chr5D 
      84.472 
      161 
      13 
      6 
      461 
      611 
      441592296 
      441592454 
      5.500000e-32 
      148.0 
     
    
      3 
      TraesCS5D01G453700 
      chr5D 
      84.516 
      155 
      14 
      7 
      461 
      607 
      490457390 
      490457542 
      7.120000e-31 
      145.0 
     
    
      4 
      TraesCS5D01G453700 
      chr5A 
      91.950 
      1826 
      92 
      27 
      668 
      2469 
      626274485 
      626276279 
      0.000000e+00 
      2507.0 
     
    
      5 
      TraesCS5D01G453700 
      chr5A 
      92.395 
      526 
      8 
      9 
      166 
      667 
      626273800 
      626274317 
      0.000000e+00 
      721.0 
     
    
      6 
      TraesCS5D01G453700 
      chr5A 
      82.796 
      279 
      44 
      4 
      2060 
      2337 
      612155218 
      612155493 
      1.900000e-61 
      246.0 
     
    
      7 
      TraesCS5D01G453700 
      chr5B 
      94.486 
      671 
      35 
      1 
      1799 
      2469 
      622552286 
      622551618 
      0.000000e+00 
      1033.0 
     
    
      8 
      TraesCS5D01G453700 
      chr5B 
      84.158 
      303 
      37 
      7 
      2063 
      2364 
      604881679 
      604881971 
      1.450000e-72 
      283.0 
     
    
      9 
      TraesCS5D01G453700 
      chr7D 
      83.848 
      712 
      79 
      17 
      780 
      1475 
      98409437 
      98408746 
      0.000000e+00 
      645.0 
     
    
      10 
      TraesCS5D01G453700 
      chr7D 
      77.447 
      235 
      40 
      6 
      1492 
      1720 
      98408690 
      98408463 
      7.170000e-26 
      128.0 
     
    
      11 
      TraesCS5D01G453700 
      chr7A 
      81.781 
      730 
      86 
      26 
      768 
      1475 
      100713995 
      100713291 
      3.560000e-158 
      568.0 
     
    
      12 
      TraesCS5D01G453700 
      chr7A 
      78.613 
      173 
      29 
      6 
      1487 
      1655 
      100713237 
      100713069 
      9.340000e-20 
      108.0 
     
    
      13 
      TraesCS5D01G453700 
      chr4A 
      82.258 
      310 
      43 
      9 
      2060 
      2360 
      581515400 
      581515706 
      8.760000e-65 
      257.0 
     
    
      14 
      TraesCS5D01G453700 
      chr6D 
      83.251 
      203 
      31 
      3 
      2086 
      2287 
      420258444 
      420258644 
      1.510000e-42 
      183.0 
     
    
      15 
      TraesCS5D01G453700 
      chr7B 
      79.641 
      167 
      27 
      5 
      1487 
      1650 
      53253436 
      53253274 
      2.010000e-21 
      113.0 
     
    
      16 
      TraesCS5D01G453700 
      chr7B 
      91.176 
      68 
      5 
      1 
      768 
      834 
      53254244 
      53254311 
      9.400000e-15 
      91.6 
     
   
    
 
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 
      TraesCS5D01G453700 
      chr5D 
      501031601 
      501034069 
      2468 
      True 
      4560.0 
      4560 
      100.0000 
      1 
      2469 
      1 
      chr5D.!!$R1 
      2468 
     
    
      1 
      TraesCS5D01G453700 
      chr5A 
      626273800 
      626276279 
      2479 
      False 
      1614.0 
      2507 
      92.1725 
      166 
      2469 
      2 
      chr5A.!!$F2 
      2303 
     
    
      2 
      TraesCS5D01G453700 
      chr5B 
      622551618 
      622552286 
      668 
      True 
      1033.0 
      1033 
      94.4860 
      1799 
      2469 
      1 
      chr5B.!!$R1 
      670 
     
    
      3 
      TraesCS5D01G453700 
      chr7D 
      98408463 
      98409437 
      974 
      True 
      386.5 
      645 
      80.6475 
      780 
      1720 
      2 
      chr7D.!!$R1 
      940 
     
    
      4 
      TraesCS5D01G453700 
      chr7A 
      100713069 
      100713995 
      926 
      True 
      338.0 
      568 
      80.1970 
      768 
      1655 
      2 
      chr7A.!!$R1 
      887 
     
   
 
            
                
                     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 
     
   
  
    
      859 
      1085 
      2.817258 
      TGCCACTGTATTTGTGCTAACC 
      59.183 
      45.455 
      0.0 
      0.0 
      34.38 
      2.85 
      F 
     
   
 
	
  
    
      Position 
      MSA Position 
      Penalty 
      Sequence 
      TM 
      GC 
      Self any TH 
      Self end TH 
      Hairpin 
      End Stability 
      Orientation 
     
   
  
    
      1734 
      2033 
      1.177401 
      CAAAGGCCCTTCCAGCTTAC 
      58.823 
      55.0 
      0.0 
      0.0 
      37.29 
      2.34 
      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 
     
   
  
    
      31 
      32 
      3.960755 
      GGGGGTTCAAAATTCCTATCTGG 
      59.039 
      47.826 
      0.00 
      0.00 
      37.10 
      3.86 
     
    
      32 
      33 
      4.572007 
      GGGGGTTCAAAATTCCTATCTGGT 
      60.572 
      45.833 
      0.00 
      0.00 
      37.07 
      4.00 
     
    
      33 
      34 
      5.023452 
      GGGGTTCAAAATTCCTATCTGGTT 
      58.977 
      41.667 
      0.00 
      0.00 
      37.07 
      3.67 
     
    
      34 
      35 
      5.105351 
      GGGGTTCAAAATTCCTATCTGGTTG 
      60.105 
      44.000 
      0.00 
      0.00 
      37.07 
      3.77 
     
    
      35 
      36 
      5.714806 
      GGGTTCAAAATTCCTATCTGGTTGA 
      59.285 
      40.000 
      0.00 
      0.00 
      37.07 
      3.18 
     
    
      36 
      37 
      6.381133 
      GGGTTCAAAATTCCTATCTGGTTGAT 
      59.619 
      38.462 
      0.00 
      0.00 
      39.11 
      2.57 
     
    
      37 
      38 
      7.093333 
      GGGTTCAAAATTCCTATCTGGTTGATT 
      60.093 
      37.037 
      0.00 
      0.00 
      36.65 
      2.57 
     
    
      38 
      39 
      8.966868 
      GGTTCAAAATTCCTATCTGGTTGATTA 
      58.033 
      33.333 
      0.00 
      0.00 
      36.65 
      1.75 
     
    
      40 
      41 
      9.973661 
      TTCAAAATTCCTATCTGGTTGATTAGA 
      57.026 
      29.630 
      0.00 
      0.00 
      36.65 
      2.10 
     
    
      41 
      42 
      9.618890 
      TCAAAATTCCTATCTGGTTGATTAGAG 
      57.381 
      33.333 
      0.00 
      0.00 
      36.65 
      2.43 
     
    
      42 
      43 
      9.618890 
      CAAAATTCCTATCTGGTTGATTAGAGA 
      57.381 
      33.333 
      0.00 
      0.00 
      36.65 
      3.10 
     
    
      46 
      47 
      9.620259 
      ATTCCTATCTGGTTGATTAGAGAAAAC 
      57.380 
      33.333 
      0.00 
      0.00 
      36.65 
      2.43 
     
    
      47 
      48 
      8.146053 
      TCCTATCTGGTTGATTAGAGAAAACA 
      57.854 
      34.615 
      0.00 
      0.00 
      36.65 
      2.83 
     
    
      48 
      49 
      8.772250 
      TCCTATCTGGTTGATTAGAGAAAACAT 
      58.228 
      33.333 
      0.00 
      0.00 
      36.65 
      2.71 
     
    
      104 
      105 
      5.998454 
      AAAATACTTCCGATGATCTGCAG 
      57.002 
      39.130 
      7.63 
      7.63 
      0.00 
      4.41 
     
    
      105 
      106 
      4.944619 
      AATACTTCCGATGATCTGCAGA 
      57.055 
      40.909 
      20.79 
      20.79 
      0.00 
      4.26 
     
    
      106 
      107 
      4.944619 
      ATACTTCCGATGATCTGCAGAA 
      57.055 
      40.909 
      22.50 
      5.35 
      0.00 
      3.02 
     
    
      107 
      108 
      3.834489 
      ACTTCCGATGATCTGCAGAAT 
      57.166 
      42.857 
      22.50 
      10.91 
      0.00 
      2.40 
     
    
      108 
      109 
      4.148128 
      ACTTCCGATGATCTGCAGAATT 
      57.852 
      40.909 
      22.50 
      4.69 
      0.00 
      2.17 
     
    
      109 
      110 
      4.521146 
      ACTTCCGATGATCTGCAGAATTT 
      58.479 
      39.130 
      22.50 
      3.78 
      0.00 
      1.82 
     
    
      110 
      111 
      4.946157 
      ACTTCCGATGATCTGCAGAATTTT 
      59.054 
      37.500 
      22.50 
      3.33 
      0.00 
      1.82 
     
    
      111 
      112 
      5.416952 
      ACTTCCGATGATCTGCAGAATTTTT 
      59.583 
      36.000 
      22.50 
      2.87 
      0.00 
      1.94 
     
    
      289 
      290 
      7.116736 
      TCTCTATAGCATACATGTATTCCGGA 
      58.883 
      38.462 
      15.85 
      0.00 
      0.00 
      5.14 
     
    
      377 
      378 
      6.288941 
      ACATGGATGAATCAAATTCTGCAA 
      57.711 
      33.333 
      0.00 
      0.00 
      39.96 
      4.08 
     
    
      553 
      577 
      7.049754 
      TCTCATAAATGATGAAGCTGCTACAA 
      58.950 
      34.615 
      0.90 
      0.00 
      44.14 
      2.41 
     
    
      643 
      668 
      9.171877 
      GATTAGAAAGGATTCACATTCTCTGTT 
      57.828 
      33.333 
      0.00 
      0.00 
      38.06 
      3.16 
     
    
      644 
      669 
      6.814506 
      AGAAAGGATTCACATTCTCTGTTG 
      57.185 
      37.500 
      0.00 
      0.00 
      38.06 
      3.33 
     
    
      652 
      677 
      9.764363 
      GGATTCACATTCTCTGTTGTATGTATA 
      57.236 
      33.333 
      0.00 
      0.00 
      35.29 
      1.47 
     
    
      679 
      871 
      5.645497 
      AGAATCCATCTTCAGTTGTGCTTAC 
      59.355 
      40.000 
      0.00 
      0.00 
      33.39 
      2.34 
     
    
      716 
      911 
      7.738437 
      ATTTTCATCATTTCATGTAACCCCT 
      57.262 
      32.000 
      0.00 
      0.00 
      0.00 
      4.79 
     
    
      720 
      915 
      4.666412 
      TCATTTCATGTAACCCCTTGGA 
      57.334 
      40.909 
      0.00 
      0.00 
      34.81 
      3.53 
     
    
      777 
      989 
      8.827677 
      AGTCTTGTCACATTTCTTTTAGTACAC 
      58.172 
      33.333 
      0.00 
      0.00 
      0.00 
      2.90 
     
    
      834 
      1046 
      3.010138 
      ACTGGCAAAGGCTAATCCAACTA 
      59.990 
      43.478 
      0.00 
      0.00 
      40.87 
      2.24 
     
    
      835 
      1047 
      4.016444 
      CTGGCAAAGGCTAATCCAACTAA 
      58.984 
      43.478 
      0.00 
      0.00 
      40.87 
      2.24 
     
    
      836 
      1048 
      3.761752 
      TGGCAAAGGCTAATCCAACTAAC 
      59.238 
      43.478 
      0.00 
      0.00 
      40.87 
      2.34 
     
    
      839 
      1051 
      5.402398 
      GCAAAGGCTAATCCAACTAACTTG 
      58.598 
      41.667 
      0.00 
      0.00 
      37.29 
      3.16 
     
    
      859 
      1085 
      2.817258 
      TGCCACTGTATTTGTGCTAACC 
      59.183 
      45.455 
      0.00 
      0.00 
      34.38 
      2.85 
     
    
      1122 
      1355 
      6.370718 
      GCCTTCCGAAGAAAATAAGACAAGTA 
      59.629 
      38.462 
      9.87 
      0.00 
      0.00 
      2.24 
     
    
      1272 
      1506 
      0.107017 
      CCTGTCTTTCATGGCCGGAT 
      60.107 
      55.000 
      5.05 
      0.00 
      0.00 
      4.18 
     
    
      1276 
      1510 
      1.416401 
      GTCTTTCATGGCCGGATCCTA 
      59.584 
      52.381 
      5.05 
      0.00 
      0.00 
      2.94 
     
    
      1356 
      1590 
      7.123997 
      ACTGTACCATGGAAATCATTAATTGCA 
      59.876 
      33.333 
      21.47 
      0.00 
      32.92 
      4.08 
     
    
      1444 
      1681 
      2.191375 
      CATGCAGAGGATGGCGGT 
      59.809 
      61.111 
      0.00 
      0.00 
      0.00 
      5.68 
     
    
      1476 
      1713 
      4.081531 
      GGAAATGGGCAAATGATGTTCAGA 
      60.082 
      41.667 
      0.00 
      0.00 
      0.00 
      3.27 
     
    
      1538 
      1822 
      8.344098 
      AGCATGTTTTTGTTGTTTTGGAATATG 
      58.656 
      29.630 
      0.00 
      0.00 
      0.00 
      1.78 
     
    
      1577 
      1861 
      2.041701 
      AGCAAGCAATGTTTCCCAGTT 
      58.958 
      42.857 
      0.00 
      0.00 
      0.00 
      3.16 
     
    
      1579 
      1863 
      3.640967 
      AGCAAGCAATGTTTCCCAGTTTA 
      59.359 
      39.130 
      0.00 
      0.00 
      0.00 
      2.01 
     
    
      1580 
      1864 
      4.100808 
      AGCAAGCAATGTTTCCCAGTTTAA 
      59.899 
      37.500 
      0.00 
      0.00 
      0.00 
      1.52 
     
    
      1581 
      1865 
      4.996758 
      GCAAGCAATGTTTCCCAGTTTAAT 
      59.003 
      37.500 
      0.00 
      0.00 
      0.00 
      1.40 
     
    
      1582 
      1866 
      5.469760 
      GCAAGCAATGTTTCCCAGTTTAATT 
      59.530 
      36.000 
      0.00 
      0.00 
      0.00 
      1.40 
     
    
      1583 
      1867 
      6.566376 
      GCAAGCAATGTTTCCCAGTTTAATTG 
      60.566 
      38.462 
      0.00 
      0.00 
      0.00 
      2.32 
     
    
      1584 
      1868 
      6.418057 
      AGCAATGTTTCCCAGTTTAATTGA 
      57.582 
      33.333 
      0.00 
      0.00 
      0.00 
      2.57 
     
    
      1585 
      1869 
      6.825610 
      AGCAATGTTTCCCAGTTTAATTGAA 
      58.174 
      32.000 
      0.00 
      0.00 
      0.00 
      2.69 
     
    
      1586 
      1870 
      7.278875 
      AGCAATGTTTCCCAGTTTAATTGAAA 
      58.721 
      30.769 
      0.00 
      0.00 
      0.00 
      2.69 
     
    
      1587 
      1871 
      7.772757 
      AGCAATGTTTCCCAGTTTAATTGAAAA 
      59.227 
      29.630 
      0.00 
      0.00 
      0.00 
      2.29 
     
    
      1588 
      1872 
      7.855409 
      GCAATGTTTCCCAGTTTAATTGAAAAC 
      59.145 
      33.333 
      9.59 
      9.59 
      39.22 
      2.43 
     
    
      1589 
      1873 
      8.887717 
      CAATGTTTCCCAGTTTAATTGAAAACA 
      58.112 
      29.630 
      16.49 
      16.49 
      40.97 
      2.83 
     
    
      1590 
      1874 
      7.835634 
      TGTTTCCCAGTTTAATTGAAAACAC 
      57.164 
      32.000 
      12.91 
      0.00 
      40.97 
      3.32 
     
    
      1734 
      2033 
      7.962964 
      ATTATCTGAATATGTGTAACCGTGG 
      57.037 
      36.000 
      0.00 
      0.00 
      34.36 
      4.94 
     
    
      1759 
      2058 
      3.033909 
      GCTGGAAGGGCCTTTGATTTAT 
      58.966 
      45.455 
      21.92 
      0.00 
      37.63 
      1.40 
     
    
      1861 
      2163 
      8.641498 
      ACTATTTTCTGTGGAAATGAAGTCAT 
      57.359 
      30.769 
      0.00 
      0.00 
      40.57 
      3.06 
     
    
      1893 
      2195 
      2.224621 
      GCACAGGAGGCACATGGTATAT 
      60.225 
      50.000 
      1.10 
      0.00 
      34.35 
      0.86 
     
    
      1918 
      2220 
      6.545666 
      TGATGTACAGAATTCAACACTTGGTT 
      59.454 
      34.615 
      8.44 
      0.00 
      41.47 
      3.67 
     
    
      1950 
      2252 
      2.500098 
      TGCTTGCTTAGGGTTCGATACT 
      59.500 
      45.455 
      0.00 
      0.00 
      0.00 
      2.12 
     
    
      2029 
      2331 
      0.036952 
      AGGACGAGCCATTGTGTCAG 
      60.037 
      55.000 
      0.00 
      0.00 
      40.02 
      3.51 
     
    
      2030 
      2332 
      0.037326 
      GGACGAGCCATTGTGTCAGA 
      60.037 
      55.000 
      0.00 
      0.00 
      36.34 
      3.27 
     
    
      2031 
      2333 
      1.608025 
      GGACGAGCCATTGTGTCAGAA 
      60.608 
      52.381 
      0.00 
      0.00 
      36.34 
      3.02 
     
    
      2032 
      2334 
      2.143122 
      GACGAGCCATTGTGTCAGAAA 
      58.857 
      47.619 
      0.00 
      0.00 
      0.00 
      2.52 
     
    
      2058 
      2360 
      7.573968 
      AAAACAGAGGATAAGGCACATTATC 
      57.426 
      36.000 
      6.52 
      6.52 
      40.13 
      1.75 
     
    
      2059 
      2361 
      5.894298 
      ACAGAGGATAAGGCACATTATCA 
      57.106 
      39.130 
      14.78 
      0.00 
      41.82 
      2.15 
     
    
      2310 
      2624 
      4.877823 
      ACCATCTACAGCAACATGTATGTG 
      59.122 
      41.667 
      17.13 
      9.67 
      41.61 
      3.21 
     
    
      2406 
      2720 
      2.629137 
      TCCTGCAACATCAGCAAACAAT 
      59.371 
      40.909 
      0.00 
      0.00 
      42.17 
      2.71 
     
    
      2410 
      2724 
      3.573538 
      TGCAACATCAGCAAACAATAGGT 
      59.426 
      39.130 
      0.00 
      0.00 
      39.39 
      3.08 
     
    
      2442 
      2756 
      5.569355 
      TCTTTCATTCAAGCTTGGACCATA 
      58.431 
      37.500 
      25.73 
      2.68 
      0.00 
      2.74 
     
   
	 
    
		
  
    
      Position 
      MSA Position 
      Penalty 
      Sequence 
      TM 
      GC 
      Self any TH 
      Self end TH 
      Hairpin 
      End Stability 
     
   
  
    
      9 
      10 
      3.960755 
      CCAGATAGGAATTTTGAACCCCC 
      59.039 
      47.826 
      0.00 
      0.00 
      41.22 
      5.40 
     
    
      10 
      11 
      4.610333 
      ACCAGATAGGAATTTTGAACCCC 
      58.390 
      43.478 
      0.00 
      0.00 
      41.22 
      4.95 
     
    
      11 
      12 
      5.714806 
      TCAACCAGATAGGAATTTTGAACCC 
      59.285 
      40.000 
      0.00 
      0.00 
      41.22 
      4.11 
     
    
      12 
      13 
      6.834168 
      TCAACCAGATAGGAATTTTGAACC 
      57.166 
      37.500 
      0.00 
      0.00 
      41.22 
      3.62 
     
    
      14 
      15 
      9.973661 
      TCTAATCAACCAGATAGGAATTTTGAA 
      57.026 
      29.630 
      0.00 
      0.00 
      41.22 
      2.69 
     
    
      15 
      16 
      9.618890 
      CTCTAATCAACCAGATAGGAATTTTGA 
      57.381 
      33.333 
      0.00 
      0.00 
      41.22 
      2.69 
     
    
      16 
      17 
      9.618890 
      TCTCTAATCAACCAGATAGGAATTTTG 
      57.381 
      33.333 
      0.00 
      0.00 
      41.22 
      2.44 
     
    
      20 
      21 
      9.620259 
      GTTTTCTCTAATCAACCAGATAGGAAT 
      57.380 
      33.333 
      0.00 
      0.00 
      41.22 
      3.01 
     
    
      21 
      22 
      8.602424 
      TGTTTTCTCTAATCAACCAGATAGGAA 
      58.398 
      33.333 
      0.00 
      0.00 
      41.22 
      3.36 
     
    
      22 
      23 
      8.146053 
      TGTTTTCTCTAATCAACCAGATAGGA 
      57.854 
      34.615 
      0.00 
      0.00 
      41.22 
      2.94 
     
    
      23 
      24 
      8.970859 
      ATGTTTTCTCTAATCAACCAGATAGG 
      57.029 
      34.615 
      0.00 
      0.00 
      45.67 
      2.57 
     
    
      81 
      82 
      6.115446 
      TCTGCAGATCATCGGAAGTATTTTT 
      58.885 
      36.000 
      13.74 
      0.00 
      0.00 
      1.94 
     
    
      82 
      83 
      5.674525 
      TCTGCAGATCATCGGAAGTATTTT 
      58.325 
      37.500 
      13.74 
      0.00 
      0.00 
      1.82 
     
    
      83 
      84 
      5.282055 
      TCTGCAGATCATCGGAAGTATTT 
      57.718 
      39.130 
      13.74 
      0.00 
      0.00 
      1.40 
     
    
      84 
      85 
      4.944619 
      TCTGCAGATCATCGGAAGTATT 
      57.055 
      40.909 
      13.74 
      0.00 
      0.00 
      1.89 
     
    
      85 
      86 
      4.944619 
      TTCTGCAGATCATCGGAAGTAT 
      57.055 
      40.909 
      19.04 
      0.00 
      0.00 
      2.12 
     
    
      86 
      87 
      4.944619 
      ATTCTGCAGATCATCGGAAGTA 
      57.055 
      40.909 
      19.04 
      0.00 
      31.86 
      2.24 
     
    
      87 
      88 
      3.834489 
      ATTCTGCAGATCATCGGAAGT 
      57.166 
      42.857 
      19.04 
      0.00 
      31.86 
      3.01 
     
    
      88 
      89 
      5.496133 
      AAAATTCTGCAGATCATCGGAAG 
      57.504 
      39.130 
      19.04 
      0.00 
      31.86 
      3.46 
     
    
      89 
      90 
      5.902613 
      AAAAATTCTGCAGATCATCGGAA 
      57.097 
      34.783 
      19.04 
      0.00 
      32.76 
      4.30 
     
    
      183 
      184 
      2.294233 
      TGTCCTTGCAAATCTCAAGCAC 
      59.706 
      45.455 
      0.00 
      0.00 
      39.54 
      4.40 
     
    
      329 
      330 
      4.157840 
      GGATCACACCAAGGGTTAATGAAC 
      59.842 
      45.833 
      0.00 
      0.00 
      31.02 
      3.18 
     
    
      402 
      403 
      4.626042 
      AGAAAGCAACACACAACAAAACA 
      58.374 
      34.783 
      0.00 
      0.00 
      0.00 
      2.83 
     
    
      403 
      404 
      6.090129 
      TCTAGAAAGCAACACACAACAAAAC 
      58.910 
      36.000 
      0.00 
      0.00 
      0.00 
      2.43 
     
    
      404 
      405 
      6.260870 
      TCTAGAAAGCAACACACAACAAAA 
      57.739 
      33.333 
      0.00 
      0.00 
      0.00 
      2.44 
     
    
      553 
      577 
      7.437267 
      GCTTCAAGCATAATACAGCATTTGAAT 
      59.563 
      33.333 
      3.89 
      0.00 
      41.89 
      2.57 
     
    
      652 
      677 
      6.421485 
      AGCACAACTGAAGATGGATTCTTAT 
      58.579 
      36.000 
      0.00 
      0.00 
      44.88 
      1.73 
     
    
      660 
      685 
      3.325870 
      TCGTAAGCACAACTGAAGATGG 
      58.674 
      45.455 
      0.00 
      0.00 
      37.18 
      3.51 
     
    
      671 
      863 
      1.272313 
      ACCCCTCTACTCGTAAGCACA 
      60.272 
      52.381 
      0.00 
      0.00 
      37.18 
      4.57 
     
    
      679 
      871 
      5.531122 
      TGATGAAAATACCCCTCTACTCG 
      57.469 
      43.478 
      0.00 
      0.00 
      0.00 
      4.18 
     
    
      716 
      911 
      7.294720 
      AGGACATACACCATTTATCCTATCCAA 
      59.705 
      37.037 
      0.00 
      0.00 
      33.29 
      3.53 
     
    
      752 
      947 
      8.827677 
      AGTGTACTAAAAGAAATGTGACAAGAC 
      58.172 
      33.333 
      0.00 
      0.00 
      0.00 
      3.01 
     
    
      777 
      989 
      8.836413 
      ACATACCGATACAACCAAATTATCAAG 
      58.164 
      33.333 
      0.00 
      0.00 
      0.00 
      3.02 
     
    
      827 
      1039 
      4.634012 
      ATACAGTGGCAAGTTAGTTGGA 
      57.366 
      40.909 
      1.75 
      0.00 
      36.56 
      3.53 
     
    
      834 
      1046 
      2.958355 
      AGCACAAATACAGTGGCAAGTT 
      59.042 
      40.909 
      0.00 
      0.00 
      37.46 
      2.66 
     
    
      835 
      1047 
      2.586425 
      AGCACAAATACAGTGGCAAGT 
      58.414 
      42.857 
      0.00 
      0.00 
      37.46 
      3.16 
     
    
      836 
      1048 
      4.475944 
      GTTAGCACAAATACAGTGGCAAG 
      58.524 
      43.478 
      0.00 
      0.00 
      37.46 
      4.01 
     
    
      839 
      1051 
      2.159572 
      CGGTTAGCACAAATACAGTGGC 
      60.160 
      50.000 
      0.00 
      0.00 
      37.46 
      5.01 
     
    
      859 
      1085 
      5.741388 
      ATAAGCAATAGAGCAAAACCTCG 
      57.259 
      39.130 
      0.00 
      0.00 
      36.95 
      4.63 
     
    
      951 
      1181 
      8.485392 
      TGATAATCAGAATCTGTCACCATACAA 
      58.515 
      33.333 
      10.36 
      0.00 
      32.61 
      2.41 
     
    
      1122 
      1355 
      2.706190 
      AGGCAGAAAGTAACACTCAGGT 
      59.294 
      45.455 
      0.00 
      0.00 
      0.00 
      4.00 
     
    
      1272 
      1506 
      4.415224 
      AAGGTAAGTGGTTCCTCTAGGA 
      57.585 
      45.455 
      0.00 
      0.00 
      43.73 
      2.94 
     
    
      1276 
      1510 
      6.758806 
      TTTCTTAAGGTAAGTGGTTCCTCT 
      57.241 
      37.500 
      1.85 
      0.00 
      37.10 
      3.69 
     
    
      1356 
      1590 
      9.999009 
      CGATGAAGCAAAATAGATATGCATAAT 
      57.001 
      29.630 
      11.13 
      5.29 
      42.45 
      1.28 
     
    
      1444 
      1681 
      0.187117 
      TGCCCATTTCCCAGACAACA 
      59.813 
      50.000 
      0.00 
      0.00 
      0.00 
      3.33 
     
    
      1476 
      1713 
      3.577805 
      ACTTAACAGCAACAGAAGGGT 
      57.422 
      42.857 
      0.00 
      0.00 
      0.00 
      4.34 
     
    
      1538 
      1822 
      4.931082 
      GCTTTCGTCAGCAAGTTAAAAC 
      57.069 
      40.909 
      4.04 
      0.00 
      39.83 
      2.43 
     
    
      1562 
      1846 
      7.489574 
      TTTCAATTAAACTGGGAAACATTGC 
      57.510 
      32.000 
      0.00 
      0.00 
      0.00 
      3.56 
     
    
      1577 
      1861 
      6.155393 
      AGGGACAAGGTTGTGTTTTCAATTAA 
      59.845 
      34.615 
      0.00 
      0.00 
      42.43 
      1.40 
     
    
      1579 
      1863 
      4.469586 
      AGGGACAAGGTTGTGTTTTCAATT 
      59.530 
      37.500 
      0.00 
      0.00 
      42.43 
      2.32 
     
    
      1580 
      1864 
      4.030216 
      AGGGACAAGGTTGTGTTTTCAAT 
      58.970 
      39.130 
      0.00 
      0.00 
      42.43 
      2.57 
     
    
      1581 
      1865 
      3.194542 
      CAGGGACAAGGTTGTGTTTTCAA 
      59.805 
      43.478 
      0.00 
      0.00 
      42.43 
      2.69 
     
    
      1582 
      1866 
      2.757868 
      CAGGGACAAGGTTGTGTTTTCA 
      59.242 
      45.455 
      0.00 
      0.00 
      42.43 
      2.69 
     
    
      1583 
      1867 
      2.758423 
      ACAGGGACAAGGTTGTGTTTTC 
      59.242 
      45.455 
      0.00 
      0.00 
      42.43 
      2.29 
     
    
      1584 
      1868 
      2.495669 
      CACAGGGACAAGGTTGTGTTTT 
      59.504 
      45.455 
      0.00 
      0.00 
      42.43 
      2.43 
     
    
      1585 
      1869 
      2.099405 
      CACAGGGACAAGGTTGTGTTT 
      58.901 
      47.619 
      0.00 
      0.00 
      42.43 
      2.83 
     
    
      1586 
      1870 
      1.762708 
      CACAGGGACAAGGTTGTGTT 
      58.237 
      50.000 
      0.00 
      0.00 
      42.43 
      3.32 
     
    
      1587 
      1871 
      0.623723 
      ACACAGGGACAAGGTTGTGT 
      59.376 
      50.000 
      0.00 
      3.48 
      46.62 
      3.72 
     
    
      1588 
      1872 
      1.676006 
      GAACACAGGGACAAGGTTGTG 
      59.324 
      52.381 
      0.00 
      2.23 
      42.43 
      3.33 
     
    
      1589 
      1873 
      1.409661 
      GGAACACAGGGACAAGGTTGT 
      60.410 
      52.381 
      0.00 
      0.00 
      45.65 
      3.32 
     
    
      1590 
      1874 
      1.133792 
      AGGAACACAGGGACAAGGTTG 
      60.134 
      52.381 
      0.00 
      0.00 
      0.00 
      3.77 
     
    
      1734 
      2033 
      1.177401 
      CAAAGGCCCTTCCAGCTTAC 
      58.823 
      55.000 
      0.00 
      0.00 
      37.29 
      2.34 
     
    
      1844 
      2146 
      9.994432 
      GTAATCTTTATGACTTCATTTCCACAG 
      57.006 
      33.333 
      0.00 
      0.00 
      37.76 
      3.66 
     
    
      1861 
      2163 
      3.263170 
      TGCCTCCTGTGCTGTAATCTTTA 
      59.737 
      43.478 
      0.00 
      0.00 
      0.00 
      1.85 
     
    
      1893 
      2195 
      6.061441 
      ACCAAGTGTTGAATTCTGTACATCA 
      58.939 
      36.000 
      7.05 
      0.00 
      0.00 
      3.07 
     
    
      1918 
      2220 
      5.069781 
      ACCCTAAGCAAGCACATTTTTGTAA 
      59.930 
      36.000 
      0.00 
      0.00 
      0.00 
      2.41 
     
    
      1950 
      2252 
      9.065798 
      TGTGTCTGAAATGATCATTGTTTTCTA 
      57.934 
      29.630 
      21.39 
      6.42 
      37.44 
      2.10 
     
    
      2058 
      2360 
      3.877559 
      TCAGAGTCCATGCCTAACATTG 
      58.122 
      45.455 
      0.00 
      0.00 
      36.64 
      2.82 
     
    
      2059 
      2361 
      4.164796 
      TGATCAGAGTCCATGCCTAACATT 
      59.835 
      41.667 
      0.00 
      0.00 
      36.64 
      2.71 
     
    
      2287 
      2601 
      4.877823 
      CACATACATGTTGCTGTAGATGGT 
      59.122 
      41.667 
      2.30 
      0.00 
      39.39 
      3.55 
     
    
      2310 
      2624 
      1.248785 
      TGCCGACTGGAGAGGTACAC 
      61.249 
      60.000 
      0.00 
      0.00 
      37.49 
      2.90 
     
    
      2406 
      2720 
      7.094634 
      GCTTGAATGAAAGAACTGAATGACCTA 
      60.095 
      37.037 
      0.00 
      0.00 
      0.00 
      3.08 
     
    
      2410 
      2724 
      6.889301 
      AGCTTGAATGAAAGAACTGAATGA 
      57.111 
      33.333 
      0.00 
      0.00 
      0.00 
      2.57 
     
    
      2442 
      2756 
      5.242393 
      CACTTGGAAGAATCATCACTGGTTT 
      59.758 
      40.000 
      0.00 
      0.00 
      0.00 
      3.27 
     
   
	 
	
 Based at the University of Bristol  with support from BBSRC .
AutoCloner maintained by Alex Coulton.