Multiple sequence alignment - TraesCS5D01G033500 
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 
      TraesCS5D01G033500 
      chr5D 
      100.000 
      7458 
      0 
      0 
      1 
      7458 
      32157356 
      32149899 
      0.000000e+00 
      13773 
     
    
      1 
      TraesCS5D01G033500 
      chr5B 
      96.049 
      4176 
      125 
      23 
      3305 
      7458 
      23889434 
      23885277 
      0.000000e+00 
      6761 
     
    
      2 
      TraesCS5D01G033500 
      chr5B 
      95.916 
      3061 
      86 
      11 
      1 
      3040 
      23892470 
      23889428 
      0.000000e+00 
      4924 
     
    
      3 
      TraesCS5D01G033500 
      chr5A 
      96.892 
      3990 
      115 
      7 
      3305 
      7293 
      20819914 
      20815933 
      0.000000e+00 
      6673 
     
    
      4 
      TraesCS5D01G033500 
      chr5A 
      95.848 
      3059 
      90 
      14 
      1 
      3040 
      20822948 
      20819908 
      0.000000e+00 
      4911 
     
    
      5 
      TraesCS5D01G033500 
      chr5A 
      97.388 
      268 
      4 
      3 
      3039 
      3306 
      643338303 
      643338039 
      3.170000e-123 
      453 
     
    
      6 
      TraesCS5D01G033500 
      chr6D 
      97.761 
      268 
      3 
      3 
      3039 
      3306 
      446719523 
      446719259 
      6.820000e-125 
      459 
     
    
      7 
      TraesCS5D01G033500 
      chr4D 
      97.753 
      267 
      5 
      1 
      3039 
      3305 
      472669595 
      472669860 
      6.820000e-125 
      459 
     
    
      8 
      TraesCS5D01G033500 
      chr4D 
      97.407 
      270 
      4 
      3 
      3037 
      3306 
      349007113 
      349006847 
      2.450000e-124 
      457 
     
    
      9 
      TraesCS5D01G033500 
      chr4D 
      97.744 
      266 
      3 
      3 
      3039 
      3304 
      349005317 
      349005055 
      8.820000e-124 
      455 
     
    
      10 
      TraesCS5D01G033500 
      chr4D 
      96.377 
      276 
      5 
      5 
      3034 
      3308 
      349421729 
      349421458 
      4.100000e-122 
      449 
     
    
      11 
      TraesCS5D01G033500 
      chr7A 
      97.388 
      268 
      4 
      3 
      3039 
      3306 
      726479776 
      726480040 
      3.170000e-123 
      453 
     
    
      12 
      TraesCS5D01G033500 
      chr2A 
      97.015 
      268 
      4 
      4 
      3039 
      3306 
      723156814 
      723156551 
      1.480000e-121 
      448 
     
    
      13 
      TraesCS5D01G033500 
      chr3B 
      93.898 
      295 
      9 
      8 
      3013 
      3306 
      424123446 
      424123732 
      3.200000e-118 
      436 
     
   
    
 
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 
      TraesCS5D01G033500 
      chr5D 
      32149899 
      32157356 
      7457 
      True 
      13773.0 
      13773 
      100.0000 
      1 
      7458 
      1 
      chr5D.!!$R1 
      7457 
     
    
      1 
      TraesCS5D01G033500 
      chr5B 
      23885277 
      23892470 
      7193 
      True 
      5842.5 
      6761 
      95.9825 
      1 
      7458 
      2 
      chr5B.!!$R1 
      7457 
     
    
      2 
      TraesCS5D01G033500 
      chr5A 
      20815933 
      20822948 
      7015 
      True 
      5792.0 
      6673 
      96.3700 
      1 
      7293 
      2 
      chr5A.!!$R2 
      7292 
     
    
      3 
      TraesCS5D01G033500 
      chr4D 
      349005055 
      349007113 
      2058 
      True 
      456.0 
      457 
      97.5755 
      3037 
      3306 
      2 
      chr4D.!!$R2 
      269 
     
   
 
            
                
                     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 
     
   
  
    
      690 
      722 
      0.396001 
      GCTTTTATAACCGGGCCCCA 
      60.396 
      55.000 
      18.66 
      0.0 
      0.00 
      4.96 
      F 
     
    
      1033 
      1066 
      1.949631 
      GATCGATGGCGGGTTCGTC 
      60.950 
      63.158 
      0.54 
      0.0 
      42.06 
      4.20 
      F 
     
    
      2370 
      2403 
      0.323302 
      TGACGCAAAGAGCCCACATA 
      59.677 
      50.000 
      0.00 
      0.0 
      41.38 
      2.29 
      F 
     
    
      2605 
      2638 
      3.150949 
      CCAGGGAGCACTGACACA 
      58.849 
      61.111 
      0.32 
      0.0 
      40.97 
      3.72 
      F 
     
    
      4079 
      4113 
      1.000060 
      GCAGTTGAAAGCATCTTGGCA 
      60.000 
      47.619 
      0.00 
      0.0 
      35.83 
      4.92 
      F 
     
    
      4877 
      4911 
      0.254747 
      CTGACTATTTGGCCCCGGAA 
      59.745 
      55.000 
      0.73 
      0.0 
      0.00 
      4.30 
      F 
     
    
      6316 
      6354 
      2.021936 
      AGGTAACCAGCCCTATCCTTCT 
      60.022 
      50.000 
      0.00 
      0.0 
      37.17 
      2.85 
      F 
     
   
 
	
  
    
      Position 
      MSA Position 
      Penalty 
      Sequence 
      TM 
      GC 
      Self any TH 
      Self end TH 
      Hairpin 
      End Stability 
      Orientation 
     
   
  
    
      1989 
      2022 
      1.125093 
      TTGTCCTCCTTTGCCTCCGA 
      61.125 
      55.000 
      0.0 
      0.0 
      0.00 
      4.55 
      R 
     
    
      2605 
      2638 
      1.470098 
      GCGACAAGTTTCCTGATGCAT 
      59.530 
      47.619 
      0.0 
      0.0 
      0.00 
      3.96 
      R 
     
    
      3203 
      3236 
      1.066430 
      CGCTTGCTTAGGGGTCAAGTA 
      60.066 
      52.381 
      0.0 
      0.0 
      39.36 
      2.24 
      R 
     
    
      4344 
      4378 
      4.384056 
      GGGATCACCAATACTGTGAGATG 
      58.616 
      47.826 
      0.0 
      0.0 
      45.20 
      2.90 
      R 
     
    
      6019 
      6054 
      0.394352 
      CATTGGGGGCTGTAGTGACC 
      60.394 
      60.000 
      0.0 
      0.0 
      0.00 
      4.02 
      R 
     
    
      6454 
      6492 
      1.048601 
      GTCAGTCCTGGTGGTCTCAA 
      58.951 
      55.000 
      0.0 
      0.0 
      29.38 
      3.02 
      R 
     
    
      7198 
      7893 
      1.002624 
      GTGGATTTGGGTCGCTCCA 
      60.003 
      57.895 
      0.0 
      0.0 
      38.11 
      3.86 
      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 
     
   
  
    
      113 
      114 
      2.202676 
      GAGGACGGCGAGCTCAAG 
      60.203 
      66.667 
      16.62 
      6.53 
      0.00 
      3.02 
     
    
      276 
      277 
      1.811266 
      CCTGTCATCCGTCTTGGCG 
      60.811 
      63.158 
      0.00 
      0.00 
      37.80 
      5.69 
     
    
      308 
      309 
      1.812922 
      GCCTCAGTCGCATGTCCTG 
      60.813 
      63.158 
      0.00 
      0.00 
      0.00 
      3.86 
     
    
      354 
      355 
      2.203728 
      ACCAGCACGGGGTAGTGA 
      60.204 
      61.111 
      0.00 
      0.00 
      44.43 
      3.41 
     
    
      518 
      537 
      2.202453 
      GTCGTCGAAGTCTCCGCC 
      60.202 
      66.667 
      0.00 
      0.00 
      0.00 
      6.13 
     
    
      690 
      722 
      0.396001 
      GCTTTTATAACCGGGCCCCA 
      60.396 
      55.000 
      18.66 
      0.00 
      0.00 
      4.96 
     
    
      982 
      1015 
      2.429930 
      CCTTTGACCCCACGAGCA 
      59.570 
      61.111 
      0.00 
      0.00 
      0.00 
      4.26 
     
    
      1033 
      1066 
      1.949631 
      GATCGATGGCGGGTTCGTC 
      60.950 
      63.158 
      0.54 
      0.00 
      42.06 
      4.20 
     
    
      1136 
      1169 
      2.251642 
      GGACAGCGTTGGTGGACAC 
      61.252 
      63.158 
      3.74 
      0.00 
      35.13 
      3.67 
     
    
      1349 
      1382 
      2.103538 
      GAGTTCATCGGCGCCGTA 
      59.896 
      61.111 
      44.16 
      31.71 
      40.74 
      4.02 
     
    
      1427 
      1460 
      2.593956 
      GGACCTCGTTGGCCTCCTT 
      61.594 
      63.158 
      3.32 
      0.00 
      40.22 
      3.36 
     
    
      1463 
      1496 
      2.100989 
      GACGAGGAGGACCAACAGTAT 
      58.899 
      52.381 
      0.00 
      0.00 
      38.94 
      2.12 
     
    
      1742 
      1775 
      4.341783 
      GGCCTGCACCAGCTCAGT 
      62.342 
      66.667 
      0.00 
      0.00 
      42.74 
      3.41 
     
    
      1989 
      2022 
      1.137872 
      CTCCTGCTCGCCATAAGAACT 
      59.862 
      52.381 
      0.00 
      0.00 
      0.00 
      3.01 
     
    
      2177 
      2210 
      1.407618 
      GGGGCCCAACAAATAATCGTC 
      59.592 
      52.381 
      26.86 
      0.00 
      0.00 
      4.20 
     
    
      2370 
      2403 
      0.323302 
      TGACGCAAAGAGCCCACATA 
      59.677 
      50.000 
      0.00 
      0.00 
      41.38 
      2.29 
     
    
      2432 
      2465 
      6.091441 
      GCACATCGAGTTTAACAGAAGAATCT 
      59.909 
      38.462 
      0.00 
      0.00 
      35.88 
      2.40 
     
    
      2519 
      2552 
      3.963428 
      TCAGAAGTTAGTTGCCTCTCC 
      57.037 
      47.619 
      0.00 
      0.00 
      0.00 
      3.71 
     
    
      2561 
      2594 
      8.103948 
      AGTTCTTCTGACTTGATTGTAATTGG 
      57.896 
      34.615 
      0.00 
      0.00 
      0.00 
      3.16 
     
    
      2573 
      2606 
      4.418013 
      TTGTAATTGGTTGCTGACATCG 
      57.582 
      40.909 
      0.00 
      0.00 
      0.00 
      3.84 
     
    
      2605 
      2638 
      3.150949 
      CCAGGGAGCACTGACACA 
      58.849 
      61.111 
      0.32 
      0.00 
      40.97 
      3.72 
     
    
      2834 
      2867 
      5.445964 
      CAATATACTACCCTTTGGCAGGTT 
      58.554 
      41.667 
      1.92 
      0.00 
      42.02 
      3.50 
     
    
      2852 
      2885 
      6.206829 
      GGCAGGTTGAAAGTTTACTGACTATT 
      59.793 
      38.462 
      11.18 
      0.00 
      31.44 
      1.73 
     
    
      2890 
      2923 
      7.600375 
      TGAGAGCATAAAAAGTTCAGAGTACAG 
      59.400 
      37.037 
      0.00 
      0.00 
      0.00 
      2.74 
     
    
      3141 
      3174 
      7.063898 
      GGATTTCCTTTCTTAATTCTTGCTTGC 
      59.936 
      37.037 
      0.00 
      0.00 
      0.00 
      4.01 
     
    
      3306 
      3339 
      4.382362 
      GGCCCATTACGTACTCTAACACTT 
      60.382 
      45.833 
      0.00 
      0.00 
      0.00 
      3.16 
     
    
      3307 
      3340 
      5.173664 
      GCCCATTACGTACTCTAACACTTT 
      58.826 
      41.667 
      0.00 
      0.00 
      0.00 
      2.66 
     
    
      3308 
      3341 
      5.063060 
      GCCCATTACGTACTCTAACACTTTG 
      59.937 
      44.000 
      0.00 
      0.00 
      0.00 
      2.77 
     
    
      3309 
      3342 
      6.161381 
      CCCATTACGTACTCTAACACTTTGT 
      58.839 
      40.000 
      0.00 
      0.00 
      0.00 
      2.83 
     
    
      3310 
      3343 
      6.090358 
      CCCATTACGTACTCTAACACTTTGTG 
      59.910 
      42.308 
      0.00 
      0.00 
      39.75 
      3.33 
     
    
      3498 
      3531 
      4.363991 
      AGGTCCAATAGATGAAGATGGC 
      57.636 
      45.455 
      0.00 
      0.00 
      0.00 
      4.40 
     
    
      3772 
      3805 
      4.507756 
      GGCTTTGGTTTGTTCATTTCTCAC 
      59.492 
      41.667 
      0.00 
      0.00 
      0.00 
      3.51 
     
    
      3995 
      4029 
      8.960591 
      CCAATGGTGAGTTTTAATCATTAGTCT 
      58.039 
      33.333 
      0.00 
      0.00 
      0.00 
      3.24 
     
    
      4079 
      4113 
      1.000060 
      GCAGTTGAAAGCATCTTGGCA 
      60.000 
      47.619 
      0.00 
      0.00 
      35.83 
      4.92 
     
    
      4122 
      4156 
      3.054655 
      AGCTCGTAACCCATTTGTGGTAT 
      60.055 
      43.478 
      0.00 
      0.00 
      34.15 
      2.73 
     
    
      4344 
      4378 
      3.081710 
      ACTGGTAAGTTACAATGCCCC 
      57.918 
      47.619 
      14.81 
      0.00 
      30.14 
      5.80 
     
    
      4345 
      4379 
      2.377193 
      ACTGGTAAGTTACAATGCCCCA 
      59.623 
      45.455 
      14.81 
      1.16 
      30.14 
      4.96 
     
    
      4677 
      4711 
      4.933400 
      GTGCTGCAGAATGATTTGGATTTT 
      59.067 
      37.500 
      20.43 
      0.00 
      39.69 
      1.82 
     
    
      4739 
      4773 
      7.885922 
      TCAAAGGTTGGTCTTATAAATAGCACA 
      59.114 
      33.333 
      0.00 
      0.00 
      0.00 
      4.57 
     
    
      4768 
      4802 
      0.610174 
      TCTGGTCCAGATGTCAGCAC 
      59.390 
      55.000 
      18.15 
      0.00 
      35.39 
      4.40 
     
    
      4825 
      4859 
      1.059681 
      AACGTGCACACAAACGACG 
      59.940 
      52.632 
      18.64 
      1.42 
      42.32 
      5.12 
     
    
      4877 
      4911 
      0.254747 
      CTGACTATTTGGCCCCGGAA 
      59.745 
      55.000 
      0.73 
      0.00 
      0.00 
      4.30 
     
    
      4903 
      4937 
      2.330216 
      ACTAGGGATGAGCCATGGTAC 
      58.670 
      52.381 
      14.67 
      8.43 
      40.59 
      3.34 
     
    
      4920 
      4954 
      5.333299 
      TGGTACGTATGCTTCTTATGTGT 
      57.667 
      39.130 
      0.00 
      0.00 
      0.00 
      3.72 
     
    
      5112 
      5147 
      7.454694 
      TGAGCATCCACAGGTAGTATTATGTAT 
      59.545 
      37.037 
      0.00 
      0.00 
      0.00 
      2.29 
     
    
      5266 
      5301 
      2.634940 
      CTGAAAGGAGGAAGACTGGTCA 
      59.365 
      50.000 
      3.51 
      0.00 
      0.00 
      4.02 
     
    
      5906 
      5941 
      5.622378 
      CAACTAAAAGACTGCCTCGAATTC 
      58.378 
      41.667 
      0.00 
      0.00 
      0.00 
      2.17 
     
    
      5913 
      5948 
      2.670414 
      GACTGCCTCGAATTCAAGTCTG 
      59.330 
      50.000 
      6.22 
      0.00 
      0.00 
      3.51 
     
    
      5998 
      6033 
      3.346631 
      CTTTGCCTGCCGTCATGCC 
      62.347 
      63.158 
      0.00 
      0.00 
      33.62 
      4.40 
     
    
      6143 
      6178 
      6.447084 
      ACAGATTAATCCCTCTTAACTTCCCA 
      59.553 
      38.462 
      11.92 
      0.00 
      0.00 
      4.37 
     
    
      6314 
      6352 
      2.509964 
      CAAGGTAACCAGCCCTATCCTT 
      59.490 
      50.000 
      0.00 
      0.00 
      34.69 
      3.36 
     
    
      6315 
      6353 
      2.409570 
      AGGTAACCAGCCCTATCCTTC 
      58.590 
      52.381 
      0.00 
      0.00 
      37.17 
      3.46 
     
    
      6316 
      6354 
      2.021936 
      AGGTAACCAGCCCTATCCTTCT 
      60.022 
      50.000 
      0.00 
      0.00 
      37.17 
      2.85 
     
    
      6343 
      6381 
      5.474532 
      CCACAATCTTTGAATCTTGTCCTCA 
      59.525 
      40.000 
      0.00 
      0.00 
      29.74 
      3.86 
     
    
      6418 
      6456 
      7.278203 
      GCATCGATGAATTATGATCTGATGACT 
      59.722 
      37.037 
      29.20 
      0.00 
      34.78 
      3.41 
     
    
      6454 
      6492 
      6.424883 
      AGATCCTTTGCAATCTTCAAGATCT 
      58.575 
      36.000 
      0.00 
      1.64 
      32.89 
      2.75 
     
    
      6470 
      6508 
      2.183679 
      GATCTTGAGACCACCAGGACT 
      58.816 
      52.381 
      0.00 
      0.00 
      42.73 
      3.85 
     
    
      6919 
      6960 
      6.440647 
      TGGAACATTTGAGATACTAGACAGGT 
      59.559 
      38.462 
      0.00 
      0.00 
      0.00 
      4.00 
     
    
      6962 
      7003 
      2.420642 
      CCTACAGAATCCATCATGGCG 
      58.579 
      52.381 
      0.00 
      0.00 
      37.47 
      5.69 
     
    
      7012 
      7053 
      5.957842 
      TTGGGTCAATAGTGAAACATGTC 
      57.042 
      39.130 
      0.00 
      0.00 
      41.43 
      3.06 
     
    
      7198 
      7893 
      1.671845 
      GTCGTCGTCATCTTCCTAGCT 
      59.328 
      52.381 
      0.00 
      0.00 
      0.00 
      3.32 
     
    
      7230 
      7925 
      3.277142 
      AATCCACTTATTGTCGGACCC 
      57.723 
      47.619 
      5.55 
      0.00 
      31.90 
      4.46 
     
    
      7409 
      8165 
      7.587037 
      AACTCCAATGAAAAATGAGAGAACA 
      57.413 
      32.000 
      0.00 
      0.00 
      0.00 
      3.18 
     
   
	 
    
		
  
    
      Position 
      MSA Position 
      Penalty 
      Sequence 
      TM 
      GC 
      Self any TH 
      Self end TH 
      Hairpin 
      End Stability 
     
   
  
    
      96 
      97 
      2.202676 
      CTTGAGCTCGCCGTCCTC 
      60.203 
      66.667 
      9.64 
      0.99 
      0.00 
      3.71 
     
    
      217 
      218 
      4.373116 
      GTCGGTGGAGAAGGCGCA 
      62.373 
      66.667 
      10.83 
      0.00 
      0.00 
      6.09 
     
    
      507 
      526 
      4.415332 
      TGTCGCGGCGGAGACTTC 
      62.415 
      66.667 
      23.46 
      3.88 
      42.66 
      3.01 
     
    
      518 
      537 
      3.478394 
      CACGGTGATGGTGTCGCG 
      61.478 
      66.667 
      0.74 
      0.00 
      38.25 
      5.87 
     
    
      867 
      900 
      2.124320 
      AATGGATGGCGAACCCGG 
      60.124 
      61.111 
      0.00 
      0.00 
      35.87 
      5.73 
     
    
      929 
      962 
      1.774046 
      GAGGATCCTCCGTCGTCGTC 
      61.774 
      65.000 
      28.84 
      2.46 
      42.75 
      4.20 
     
    
      930 
      963 
      1.818785 
      GAGGATCCTCCGTCGTCGT 
      60.819 
      63.158 
      28.84 
      0.00 
      42.75 
      4.34 
     
    
      931 
      964 
      3.023950 
      GAGGATCCTCCGTCGTCG 
      58.976 
      66.667 
      28.84 
      0.00 
      42.75 
      5.12 
     
    
      982 
      1015 
      1.888436 
      ATGATCTCACACCACCGCGT 
      61.888 
      55.000 
      4.92 
      0.00 
      0.00 
      6.01 
     
    
      1101 
      1134 
      2.202260 
      CTTCTGCACGCACGCATG 
      60.202 
      61.111 
      0.00 
      0.00 
      42.06 
      4.06 
     
    
      1102 
      1135 
      3.425713 
      CCTTCTGCACGCACGCAT 
      61.426 
      61.111 
      0.00 
      0.00 
      42.06 
      4.73 
     
    
      1103 
      1136 
      4.600576 
      TCCTTCTGCACGCACGCA 
      62.601 
      61.111 
      0.00 
      0.00 
      40.32 
      5.24 
     
    
      1104 
      1137 
      4.077188 
      GTCCTTCTGCACGCACGC 
      62.077 
      66.667 
      0.00 
      0.00 
      0.00 
      5.34 
     
    
      1105 
      1138 
      2.661537 
      TGTCCTTCTGCACGCACG 
      60.662 
      61.111 
      0.00 
      0.00 
      0.00 
      5.34 
     
    
      1106 
      1139 
      2.959357 
      GCTGTCCTTCTGCACGCAC 
      61.959 
      63.158 
      0.00 
      0.00 
      40.09 
      5.34 
     
    
      1349 
      1382 
      3.080319 
      GAGCCTGATGAACTTGCTCTTT 
      58.920 
      45.455 
      0.00 
      0.00 
      43.85 
      2.52 
     
    
      1989 
      2022 
      1.125093 
      TTGTCCTCCTTTGCCTCCGA 
      61.125 
      55.000 
      0.00 
      0.00 
      0.00 
      4.55 
     
    
      2177 
      2210 
      2.042686 
      TCATCCTTGGCTTTCCATCG 
      57.957 
      50.000 
      0.00 
      0.00 
      43.05 
      3.84 
     
    
      2370 
      2403 
      4.209538 
      TCAGGATGATGAAATTCCGCATT 
      58.790 
      39.130 
      0.00 
      0.00 
      42.56 
      3.56 
     
    
      2432 
      2465 
      6.596497 
      CGTTATCATGATCCATTGATCCATCA 
      59.404 
      38.462 
      12.53 
      0.00 
      45.74 
      3.07 
     
    
      2441 
      2474 
      7.716560 
      TGAGACAAATCGTTATCATGATCCATT 
      59.283 
      33.333 
      12.53 
      3.75 
      0.00 
      3.16 
     
    
      2553 
      2586 
      3.188254 
      CACGATGTCAGCAACCAATTACA 
      59.812 
      43.478 
      0.00 
      0.00 
      0.00 
      2.41 
     
    
      2605 
      2638 
      1.470098 
      GCGACAAGTTTCCTGATGCAT 
      59.530 
      47.619 
      0.00 
      0.00 
      0.00 
      3.96 
     
    
      2775 
      2808 
      9.455847 
      GCCATCAAAGAAGCTTAGTTTATTATG 
      57.544 
      33.333 
      0.00 
      7.26 
      0.00 
      1.90 
     
    
      2834 
      2867 
      8.035394 
      CCTCTAGCAATAGTCAGTAAACTTTCA 
      58.965 
      37.037 
      0.00 
      0.00 
      0.00 
      2.69 
     
    
      2890 
      2923 
      3.830679 
      CTCAAGTCCTCCAGTGAGC 
      57.169 
      57.895 
      0.00 
      0.00 
      37.29 
      4.26 
     
    
      3040 
      3073 
      1.069204 
      CTCCTTCTAGCAGCGCCATAA 
      59.931 
      52.381 
      2.29 
      0.00 
      0.00 
      1.90 
     
    
      3041 
      3074 
      0.676184 
      CTCCTTCTAGCAGCGCCATA 
      59.324 
      55.000 
      2.29 
      0.00 
      0.00 
      2.74 
     
    
      3042 
      3075 
      1.445095 
      CTCCTTCTAGCAGCGCCAT 
      59.555 
      57.895 
      2.29 
      0.00 
      0.00 
      4.40 
     
    
      3043 
      3076 
      2.725312 
      CCTCCTTCTAGCAGCGCCA 
      61.725 
      63.158 
      2.29 
      0.00 
      0.00 
      5.69 
     
    
      3124 
      3157 
      9.013229 
      TCAATCTAAGCAAGCAAGAATTAAGAA 
      57.987 
      29.630 
      0.00 
      0.00 
      0.00 
      2.52 
     
    
      3172 
      3205 
      4.974399 
      CTTGGGAGTCAAGTAAACCTCTT 
      58.026 
      43.478 
      0.00 
      0.00 
      45.81 
      2.85 
     
    
      3203 
      3236 
      1.066430 
      CGCTTGCTTAGGGGTCAAGTA 
      60.066 
      52.381 
      0.00 
      0.00 
      39.36 
      2.24 
     
    
      3276 
      3309 
      2.370849 
      AGTACGTAATGGGCCTAATGGG 
      59.629 
      50.000 
      4.53 
      0.00 
      38.36 
      4.00 
     
    
      3306 
      3339 
      6.939730 
      TGAATCAGAAGTATTAAGTGGCACAA 
      59.060 
      34.615 
      21.41 
      6.63 
      44.16 
      3.33 
     
    
      3307 
      3340 
      6.472016 
      TGAATCAGAAGTATTAAGTGGCACA 
      58.528 
      36.000 
      21.41 
      0.00 
      0.00 
      4.57 
     
    
      3308 
      3341 
      6.985188 
      TGAATCAGAAGTATTAAGTGGCAC 
      57.015 
      37.500 
      10.29 
      10.29 
      0.00 
      5.01 
     
    
      3309 
      3342 
      8.579850 
      AAATGAATCAGAAGTATTAAGTGGCA 
      57.420 
      30.769 
      0.00 
      0.00 
      0.00 
      4.92 
     
    
      3498 
      3531 
      5.104259 
      AGCTTACACTATTCTCCAAAGGG 
      57.896 
      43.478 
      0.00 
      0.00 
      0.00 
      3.95 
     
    
      4079 
      4113 
      5.010516 
      AGCTGATATTAAGATGTCACGCTCT 
      59.989 
      40.000 
      0.00 
      0.00 
      35.31 
      4.09 
     
    
      4122 
      4156 
      4.826733 
      ACCATGCTGAACATTCAACTTACA 
      59.173 
      37.500 
      0.00 
      0.00 
      36.64 
      2.41 
     
    
      4344 
      4378 
      4.384056 
      GGGATCACCAATACTGTGAGATG 
      58.616 
      47.826 
      0.00 
      0.00 
      45.20 
      2.90 
     
    
      4345 
      4379 
      4.696479 
      GGGATCACCAATACTGTGAGAT 
      57.304 
      45.455 
      0.00 
      0.00 
      45.20 
      2.75 
     
    
      4563 
      4597 
      7.848223 
      AAAAATCTCAAAACACAAAGGGAAG 
      57.152 
      32.000 
      0.00 
      0.00 
      0.00 
      3.46 
     
    
      4634 
      4668 
      7.278868 
      GCAGCACAACATAACTTAAGACTAGAT 
      59.721 
      37.037 
      10.09 
      0.00 
      0.00 
      1.98 
     
    
      4768 
      4802 
      2.234661 
      TGATTGTCACCCACTAGAGCAG 
      59.765 
      50.000 
      0.00 
      0.00 
      0.00 
      4.24 
     
    
      4825 
      4859 
      1.174712 
      TGTCTGCTTTTGCCTCTGCC 
      61.175 
      55.000 
      0.00 
      0.00 
      46.87 
      4.85 
     
    
      4877 
      4911 
      4.780021 
      CCATGGCTCATCCCTAGTAGTATT 
      59.220 
      45.833 
      0.00 
      0.00 
      0.00 
      1.89 
     
    
      5112 
      5147 
      7.508687 
      TGCTACTAGGATCAATAAATCAAGCA 
      58.491 
      34.615 
      0.00 
      0.00 
      0.00 
      3.91 
     
    
      5132 
      5167 
      6.426937 
      TCCAACAGAAAAGAAGTGTATGCTAC 
      59.573 
      38.462 
      0.00 
      0.00 
      0.00 
      3.58 
     
    
      5266 
      5301 
      8.771286 
      AGGGGTGAATAAATAGCAAATCATTTT 
      58.229 
      29.630 
      0.00 
      0.00 
      0.00 
      1.82 
     
    
      5611 
      5646 
      9.476202 
      AGTTGAAATAACAATTTTAGCTTGGAC 
      57.524 
      29.630 
      0.00 
      0.00 
      32.36 
      4.02 
     
    
      5752 
      5787 
      5.064198 
      GCATATTTCAGTTAGCGTGGTTACA 
      59.936 
      40.000 
      0.00 
      0.00 
      0.00 
      2.41 
     
    
      5998 
      6033 
      1.451567 
      CTCATCAGCAGCACCCCAG 
      60.452 
      63.158 
      0.00 
      0.00 
      0.00 
      4.45 
     
    
      6019 
      6054 
      0.394352 
      CATTGGGGGCTGTAGTGACC 
      60.394 
      60.000 
      0.00 
      0.00 
      0.00 
      4.02 
     
    
      6168 
      6203 
      3.879998 
      TGTGAGGTGACTGCTGTAAAAA 
      58.120 
      40.909 
      0.00 
      0.00 
      44.43 
      1.94 
     
    
      6314 
      6352 
      5.302568 
      ACAAGATTCAAAGATTGTGGCAAGA 
      59.697 
      36.000 
      0.00 
      0.00 
      34.71 
      3.02 
     
    
      6315 
      6353 
      5.535333 
      ACAAGATTCAAAGATTGTGGCAAG 
      58.465 
      37.500 
      0.00 
      0.00 
      34.71 
      4.01 
     
    
      6316 
      6354 
      5.509501 
      GGACAAGATTCAAAGATTGTGGCAA 
      60.510 
      40.000 
      0.00 
      0.00 
      36.08 
      4.52 
     
    
      6343 
      6381 
      7.741554 
      ATAGAGGGAAAGATGTTAACTCACT 
      57.258 
      36.000 
      7.22 
      1.54 
      0.00 
      3.41 
     
    
      6418 
      6456 
      5.182487 
      TGCAAAGGATCTTCGTTATGCTTA 
      58.818 
      37.500 
      0.00 
      0.00 
      34.36 
      3.09 
     
    
      6454 
      6492 
      1.048601 
      GTCAGTCCTGGTGGTCTCAA 
      58.951 
      55.000 
      0.00 
      0.00 
      29.38 
      3.02 
     
    
      6470 
      6508 
      1.144708 
      TGTTGCTGAGGGAATTGGTCA 
      59.855 
      47.619 
      0.00 
      0.00 
      0.00 
      4.02 
     
    
      6919 
      6960 
      3.346028 
      TCCCAGGGAGAGATCTATGGTA 
      58.654 
      50.000 
      3.01 
      0.00 
      0.00 
      3.25 
     
    
      6962 
      7003 
      4.573201 
      TGTACAACACAAACAGCTAGGTTC 
      59.427 
      41.667 
      0.00 
      0.00 
      32.95 
      3.62 
     
    
      7012 
      7053 
      2.434884 
      ACAGATCCAACCTGCGCG 
      60.435 
      61.111 
      0.00 
      0.00 
      35.14 
      6.86 
     
    
      7022 
      7063 
      3.276857 
      AGTGATCAATGTGCACAGATCC 
      58.723 
      45.455 
      30.90 
      24.66 
      36.84 
      3.36 
     
    
      7198 
      7893 
      1.002624 
      GTGGATTTGGGTCGCTCCA 
      60.003 
      57.895 
      0.00 
      0.00 
      38.11 
      3.86 
     
    
      7230 
      7925 
      7.962918 
      CCCTGTCAACATTAAAATAAGAAGACG 
      59.037 
      37.037 
      0.00 
      0.00 
      0.00 
      4.18 
     
    
      7330 
      8086 
      7.225145 
      CCTTGCTCTCTCTCTCTTCATTTATTG 
      59.775 
      40.741 
      0.00 
      0.00 
      0.00 
      1.90 
     
    
      7333 
      8089 
      5.719085 
      ACCTTGCTCTCTCTCTCTTCATTTA 
      59.281 
      40.000 
      0.00 
      0.00 
      0.00 
      1.40 
     
    
      7337 
      8093 
      3.168035 
      ACCTTGCTCTCTCTCTCTTCA 
      57.832 
      47.619 
      0.00 
      0.00 
      0.00 
      3.02 
     
    
      7338 
      8094 
      3.509575 
      TCAACCTTGCTCTCTCTCTCTTC 
      59.490 
      47.826 
      0.00 
      0.00 
      0.00 
      2.87 
     
    
      7339 
      8095 
      3.505386 
      TCAACCTTGCTCTCTCTCTCTT 
      58.495 
      45.455 
      0.00 
      0.00 
      0.00 
      2.85 
     
    
      7340 
      8096 
      3.168035 
      TCAACCTTGCTCTCTCTCTCT 
      57.832 
      47.619 
      0.00 
      0.00 
      0.00 
      3.10 
     
    
      7341 
      8097 
      3.258123 
      ACTTCAACCTTGCTCTCTCTCTC 
      59.742 
      47.826 
      0.00 
      0.00 
      0.00 
      3.20 
     
    
      7350 
      8106 
      2.887152 
      GGTTCATGACTTCAACCTTGCT 
      59.113 
      45.455 
      6.30 
      0.00 
      37.24 
      3.91 
     
   
	 
	
 Based at the University of Bristol  with support from BBSRC .
AutoCloner maintained by Alex Coulton.