Multiple sequence alignment - TraesCS5B01G140400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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 TraesCS5B01G140400 chr5B 100.000 4832 0 0 1 4832 264914471 264919302 0 8924
1 TraesCS5B01G140400 chr5B 97.659 4741 76 6 123 4832 371292293 371297029 0 8107
2 TraesCS5B01G140400 chr5A 98.981 4712 43 2 126 4832 613968282 613972993 0 8431
3 TraesCS5B01G140400 chr2A 98.450 4711 71 2 123 4832 61495404 61500113 0 8294
4 TraesCS5B01G140400 chr6B 98.408 4711 71 4 123 4832 195188165 195192872 0 8281
5 TraesCS5B01G140400 chr6B 98.164 4739 52 24 126 4832 56428123 56432858 0 8237
6 TraesCS5B01G140400 chr6B 98.030 3908 68 2 123 4026 18581662 18577760 0 6782
7 TraesCS5B01G140400 chr6B 96.427 3834 125 7 123 3956 645758394 645762215 0 6311
8 TraesCS5B01G140400 chr6B 97.723 966 22 0 3867 4832 18577863 18576898 0 1663
9 TraesCS5B01G140400 chr3A 97.848 4739 73 6 123 4832 684729034 684724296 0 8159
10 TraesCS5B01G140400 chr4A 97.676 4432 90 5 402 4832 674547767 674543348 0 7601
11 TraesCS5B01G140400 chr4A 96.691 967 30 2 3867 4832 731443998 731444963 0 1607


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 TraesCS5B01G140400 chr5B 264914471 264919302 4831 False 8924.0 8924 100.0000 1 4832 1 chr5B.!!$F1 4831
1 TraesCS5B01G140400 chr5B 371292293 371297029 4736 False 8107.0 8107 97.6590 123 4832 1 chr5B.!!$F2 4709
2 TraesCS5B01G140400 chr5A 613968282 613972993 4711 False 8431.0 8431 98.9810 126 4832 1 chr5A.!!$F1 4706
3 TraesCS5B01G140400 chr2A 61495404 61500113 4709 False 8294.0 8294 98.4500 123 4832 1 chr2A.!!$F1 4709
4 TraesCS5B01G140400 chr6B 195188165 195192872 4707 False 8281.0 8281 98.4080 123 4832 1 chr6B.!!$F2 4709
5 TraesCS5B01G140400 chr6B 56428123 56432858 4735 False 8237.0 8237 98.1640 126 4832 1 chr6B.!!$F1 4706
6 TraesCS5B01G140400 chr6B 645758394 645762215 3821 False 6311.0 6311 96.4270 123 3956 1 chr6B.!!$F3 3833
7 TraesCS5B01G140400 chr6B 18576898 18581662 4764 True 4222.5 6782 97.8765 123 4832 2 chr6B.!!$R1 4709
8 TraesCS5B01G140400 chr3A 684724296 684729034 4738 True 8159.0 8159 97.8480 123 4832 1 chr3A.!!$R1 4709
9 TraesCS5B01G140400 chr4A 674543348 674547767 4419 True 7601.0 7601 97.6760 402 4832 1 chr4A.!!$R1 4430
10 TraesCS5B01G140400 chr4A 731443998 731444963 965 False 1607.0 1607 96.6910 3867 4832 1 chr4A.!!$F1 965

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.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
55 56 0.028110 GATCAGACGGCCGAAAATGC 59.972 55.000 35.90 13.09 0.00 3.56 F
85 86 0.035343 TCAGTCCGATGGTCGAGAGT 60.035 55.000 0.22 0.00 43.74 3.24 F
111 112 0.397816 ATTCTGAGAGACCTCGGGGG 60.398 60.000 6.13 0.00 44.20 5.40 F
715 720 1.123861 AGGAGGAGCAACAGCTGTGA 61.124 55.000 22.49 0.00 39.10 3.58 F
1502 1507 1.144057 GTGGTCCTGATACTGGGCG 59.856 63.158 0.00 0.00 0.00 6.13 F
2877 2882 1.187567 ACTTGCCAGCAATTGACCCC 61.188 55.000 10.34 0.00 35.20 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 1984 0.036388 TGAAGTCAGGTTCGGATGCC 60.036 55.000 0.0 0.0 0.00 4.40 R
2706 2711 2.034879 GCGCTGTTGGCTCTGCTTA 61.035 57.895 0.0 0.0 39.13 3.09 R
2877 2882 7.916077 TCCCTTCTTTCTCTTAGTATTAGGG 57.084 40.000 0.0 0.0 39.95 3.53 R
3449 3454 1.677576 TGTTGAGCACTGCCTCTTTTG 59.322 47.619 0.0 0.0 33.02 2.44 R
3563 3568 1.192146 TCTGCCCCTACTTGTTCGCT 61.192 55.000 0.0 0.0 0.00 4.93 R
4353 4502 1.115467 CCTGCCTCATCTAAGTCCGT 58.885 55.000 0.0 0.0 0.00 4.69 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.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.814294 GCCTCGATCCAACGGCGT 62.814 66.667 6.77 6.77 32.22 5.68
19 20 2.802792 CCTCGATCCAACGGCGTA 59.197 61.111 15.20 0.00 0.00 4.42
20 21 1.299165 CCTCGATCCAACGGCGTAG 60.299 63.158 15.20 8.52 0.00 3.51
21 22 1.299165 CTCGATCCAACGGCGTAGG 60.299 63.158 15.20 9.01 0.00 3.18
22 23 2.001361 CTCGATCCAACGGCGTAGGT 62.001 60.000 15.20 3.68 0.00 3.08
23 24 1.588139 CGATCCAACGGCGTAGGTC 60.588 63.158 15.20 13.16 0.00 3.85
24 25 1.514087 GATCCAACGGCGTAGGTCA 59.486 57.895 15.20 0.00 0.00 4.02
25 26 0.104304 GATCCAACGGCGTAGGTCAT 59.896 55.000 15.20 0.80 0.00 3.06
26 27 0.104304 ATCCAACGGCGTAGGTCATC 59.896 55.000 15.20 0.00 0.00 2.92
27 28 0.968901 TCCAACGGCGTAGGTCATCT 60.969 55.000 15.20 0.00 0.00 2.90
28 29 0.742505 CCAACGGCGTAGGTCATCTA 59.257 55.000 15.20 0.00 0.00 1.98
29 30 1.269102 CCAACGGCGTAGGTCATCTAG 60.269 57.143 15.20 0.00 0.00 2.43
30 31 1.674441 CAACGGCGTAGGTCATCTAGA 59.326 52.381 15.20 0.00 0.00 2.43
31 32 2.048444 ACGGCGTAGGTCATCTAGAA 57.952 50.000 12.58 0.00 0.00 2.10
32 33 1.948145 ACGGCGTAGGTCATCTAGAAG 59.052 52.381 12.58 0.00 0.00 2.85
33 34 1.335142 CGGCGTAGGTCATCTAGAAGC 60.335 57.143 0.00 0.00 0.00 3.86
34 35 1.957877 GGCGTAGGTCATCTAGAAGCT 59.042 52.381 0.00 0.00 0.00 3.74
35 36 2.362717 GGCGTAGGTCATCTAGAAGCTT 59.637 50.000 0.00 0.00 0.00 3.74
36 37 3.376540 GCGTAGGTCATCTAGAAGCTTG 58.623 50.000 2.10 0.00 0.00 4.01
37 38 3.066900 GCGTAGGTCATCTAGAAGCTTGA 59.933 47.826 2.10 0.00 0.00 3.02
38 39 4.261825 GCGTAGGTCATCTAGAAGCTTGAT 60.262 45.833 2.10 0.00 0.00 2.57
39 40 5.457140 CGTAGGTCATCTAGAAGCTTGATC 58.543 45.833 2.10 0.00 0.00 2.92
40 41 5.009110 CGTAGGTCATCTAGAAGCTTGATCA 59.991 44.000 2.10 0.00 0.00 2.92
41 42 5.534207 AGGTCATCTAGAAGCTTGATCAG 57.466 43.478 2.10 0.00 0.00 2.90
42 43 5.207354 AGGTCATCTAGAAGCTTGATCAGA 58.793 41.667 2.10 0.75 0.00 3.27
43 44 5.068987 AGGTCATCTAGAAGCTTGATCAGAC 59.931 44.000 2.10 5.56 0.00 3.51
44 45 4.975502 GTCATCTAGAAGCTTGATCAGACG 59.024 45.833 2.10 0.00 0.00 4.18
45 46 4.037327 TCATCTAGAAGCTTGATCAGACGG 59.963 45.833 2.10 0.00 0.00 4.79
46 47 2.099921 TCTAGAAGCTTGATCAGACGGC 59.900 50.000 2.10 0.00 0.00 5.68
47 48 0.107945 AGAAGCTTGATCAGACGGCC 60.108 55.000 2.10 0.00 0.00 6.13
48 49 1.424493 GAAGCTTGATCAGACGGCCG 61.424 60.000 26.86 26.86 0.00 6.13
49 50 1.888436 AAGCTTGATCAGACGGCCGA 61.888 55.000 35.90 10.13 0.00 5.54
50 51 1.447838 GCTTGATCAGACGGCCGAA 60.448 57.895 35.90 13.03 0.00 4.30
51 52 1.019278 GCTTGATCAGACGGCCGAAA 61.019 55.000 35.90 14.20 0.00 3.46
52 53 1.438651 CTTGATCAGACGGCCGAAAA 58.561 50.000 35.90 14.60 0.00 2.29
53 54 2.009774 CTTGATCAGACGGCCGAAAAT 58.990 47.619 35.90 18.92 0.00 1.82
54 55 1.368641 TGATCAGACGGCCGAAAATG 58.631 50.000 35.90 22.80 0.00 2.32
55 56 0.028110 GATCAGACGGCCGAAAATGC 59.972 55.000 35.90 13.09 0.00 3.56
56 57 0.676466 ATCAGACGGCCGAAAATGCA 60.676 50.000 35.90 13.61 0.00 3.96
57 58 0.676466 TCAGACGGCCGAAAATGCAT 60.676 50.000 35.90 6.14 0.00 3.96
58 59 0.248215 CAGACGGCCGAAAATGCATC 60.248 55.000 35.90 16.59 0.00 3.91
59 60 0.676466 AGACGGCCGAAAATGCATCA 60.676 50.000 35.90 0.00 0.00 3.07
60 61 0.170116 GACGGCCGAAAATGCATCAA 59.830 50.000 35.90 0.00 0.00 2.57
61 62 0.171007 ACGGCCGAAAATGCATCAAG 59.829 50.000 35.90 0.00 0.00 3.02
62 63 0.526096 CGGCCGAAAATGCATCAAGG 60.526 55.000 24.07 2.76 0.00 3.61
63 64 0.179103 GGCCGAAAATGCATCAAGGG 60.179 55.000 0.00 0.73 0.00 3.95
64 65 0.179103 GCCGAAAATGCATCAAGGGG 60.179 55.000 0.00 0.00 0.00 4.79
65 66 1.473258 CCGAAAATGCATCAAGGGGA 58.527 50.000 0.00 0.00 0.00 4.81
66 67 2.034124 CCGAAAATGCATCAAGGGGAT 58.966 47.619 0.00 0.00 36.39 3.85
67 68 2.035066 CCGAAAATGCATCAAGGGGATC 59.965 50.000 0.00 0.00 32.57 3.36
68 69 2.689471 CGAAAATGCATCAAGGGGATCA 59.311 45.455 0.00 0.00 32.57 2.92
69 70 3.243301 CGAAAATGCATCAAGGGGATCAG 60.243 47.826 0.00 0.00 32.57 2.90
70 71 3.393426 AAATGCATCAAGGGGATCAGT 57.607 42.857 0.00 0.00 32.57 3.41
71 72 2.653234 ATGCATCAAGGGGATCAGTC 57.347 50.000 0.00 0.00 32.57 3.51
72 73 0.548031 TGCATCAAGGGGATCAGTCC 59.452 55.000 0.00 0.00 44.29 3.85
73 74 0.533755 GCATCAAGGGGATCAGTCCG 60.534 60.000 0.00 0.00 46.09 4.79
74 75 1.123077 CATCAAGGGGATCAGTCCGA 58.877 55.000 0.00 0.00 46.09 4.55
75 76 1.696336 CATCAAGGGGATCAGTCCGAT 59.304 52.381 0.00 0.00 46.09 4.18
76 77 1.123077 TCAAGGGGATCAGTCCGATG 58.877 55.000 0.00 0.00 46.09 3.84
77 78 0.107456 CAAGGGGATCAGTCCGATGG 59.893 60.000 0.00 0.00 46.09 3.51
78 79 0.326618 AAGGGGATCAGTCCGATGGT 60.327 55.000 0.00 0.00 46.09 3.55
79 80 0.760945 AGGGGATCAGTCCGATGGTC 60.761 60.000 0.00 0.00 46.09 4.02
80 81 1.364171 GGGATCAGTCCGATGGTCG 59.636 63.158 0.00 0.00 46.09 4.79
81 82 1.107538 GGGATCAGTCCGATGGTCGA 61.108 60.000 0.22 0.00 46.09 4.20
82 83 0.312416 GGATCAGTCCGATGGTCGAG 59.688 60.000 0.22 0.00 43.74 4.04
83 84 1.309950 GATCAGTCCGATGGTCGAGA 58.690 55.000 0.22 0.00 43.74 4.04
84 85 1.265635 GATCAGTCCGATGGTCGAGAG 59.734 57.143 0.22 0.00 43.74 3.20
85 86 0.035343 TCAGTCCGATGGTCGAGAGT 60.035 55.000 0.22 0.00 43.74 3.24
86 87 0.811915 CAGTCCGATGGTCGAGAGTT 59.188 55.000 0.22 0.00 43.74 3.01
87 88 0.811915 AGTCCGATGGTCGAGAGTTG 59.188 55.000 0.22 0.00 43.74 3.16
88 89 0.802607 GTCCGATGGTCGAGAGTTGC 60.803 60.000 0.22 0.00 43.74 4.17
89 90 0.965866 TCCGATGGTCGAGAGTTGCT 60.966 55.000 0.22 0.00 43.74 3.91
90 91 0.738975 CCGATGGTCGAGAGTTGCTA 59.261 55.000 0.22 0.00 43.74 3.49
91 92 1.134367 CCGATGGTCGAGAGTTGCTAA 59.866 52.381 0.22 0.00 43.74 3.09
92 93 2.416836 CCGATGGTCGAGAGTTGCTAAA 60.417 50.000 0.22 0.00 43.74 1.85
93 94 3.448686 CGATGGTCGAGAGTTGCTAAAT 58.551 45.455 0.00 0.00 43.74 1.40
94 95 3.865745 CGATGGTCGAGAGTTGCTAAATT 59.134 43.478 0.00 0.00 43.74 1.82
95 96 4.026475 CGATGGTCGAGAGTTGCTAAATTC 60.026 45.833 0.00 0.00 43.74 2.17
96 97 4.537135 TGGTCGAGAGTTGCTAAATTCT 57.463 40.909 0.00 0.00 35.25 2.40
97 98 4.245660 TGGTCGAGAGTTGCTAAATTCTG 58.754 43.478 0.00 0.00 32.89 3.02
98 99 4.021456 TGGTCGAGAGTTGCTAAATTCTGA 60.021 41.667 0.00 0.00 32.89 3.27
99 100 4.564769 GGTCGAGAGTTGCTAAATTCTGAG 59.435 45.833 0.00 0.00 32.89 3.35
100 101 5.403246 GTCGAGAGTTGCTAAATTCTGAGA 58.597 41.667 0.00 0.00 32.89 3.27
101 102 5.514914 GTCGAGAGTTGCTAAATTCTGAGAG 59.485 44.000 0.00 0.00 32.89 3.20
102 103 5.416013 TCGAGAGTTGCTAAATTCTGAGAGA 59.584 40.000 0.00 0.00 32.89 3.10
103 104 5.514914 CGAGAGTTGCTAAATTCTGAGAGAC 59.485 44.000 0.00 0.00 32.89 3.36
104 105 5.729510 AGAGTTGCTAAATTCTGAGAGACC 58.270 41.667 0.00 0.00 31.64 3.85
105 106 5.483583 AGAGTTGCTAAATTCTGAGAGACCT 59.516 40.000 0.00 0.00 31.64 3.85
106 107 5.729510 AGTTGCTAAATTCTGAGAGACCTC 58.270 41.667 0.00 0.00 39.86 3.85
107 108 4.377839 TGCTAAATTCTGAGAGACCTCG 57.622 45.455 0.00 0.00 42.33 4.63
108 109 3.131223 TGCTAAATTCTGAGAGACCTCGG 59.869 47.826 0.00 0.00 45.18 4.63
109 110 3.491792 GCTAAATTCTGAGAGACCTCGGG 60.492 52.174 0.00 0.00 44.20 5.14
110 111 1.490574 AATTCTGAGAGACCTCGGGG 58.509 55.000 0.00 0.00 44.20 5.73
111 112 0.397816 ATTCTGAGAGACCTCGGGGG 60.398 60.000 6.13 0.00 44.20 5.40
112 113 3.151022 CTGAGAGACCTCGGGGGC 61.151 72.222 6.13 0.16 42.33 5.80
120 121 4.787280 CCTCGGGGGCTCCTGTCT 62.787 72.222 12.38 0.00 40.36 3.41
121 122 2.685380 CTCGGGGGCTCCTGTCTT 60.685 66.667 12.38 0.00 40.36 3.01
182 183 4.549668 TCGGGAACTATAGTACCCATTGT 58.450 43.478 19.83 0.00 42.16 2.71
715 720 1.123861 AGGAGGAGCAACAGCTGTGA 61.124 55.000 22.49 0.00 39.10 3.58
1502 1507 1.144057 GTGGTCCTGATACTGGGCG 59.856 63.158 0.00 0.00 0.00 6.13
1829 1834 1.302192 CGCAGAGGGTTTTCCGGAA 60.302 57.895 14.35 14.35 41.82 4.30
1880 1885 6.030849 CCGTGAAATGTGTTGAAACAAGTTA 58.969 36.000 0.00 0.00 41.21 2.24
2877 2882 1.187567 ACTTGCCAGCAATTGACCCC 61.188 55.000 10.34 0.00 35.20 4.95
3283 3288 3.839490 TCCTACCGATGGTTTTGGTTCTA 59.161 43.478 0.00 0.00 39.26 2.10
3449 3454 3.007635 CCTTCGTGTCCCCATACTTTTC 58.992 50.000 0.00 0.00 0.00 2.29
3563 3568 0.982852 ATCCCGCATCCAGACCTTCA 60.983 55.000 0.00 0.00 0.00 3.02
3737 3742 0.317160 TCGACGAGTGCTTCCACATT 59.683 50.000 0.00 0.00 44.53 2.71
3789 3794 3.371063 GGTCGTGGCAGTCGAGGA 61.371 66.667 0.00 0.00 37.99 3.71
3964 4081 9.733556 TTTGTAATATGTCAGGACTATGTTTGT 57.266 29.630 0.65 0.00 0.00 2.83
3992 4109 9.733556 TTTGTAATATGTCAGGACTATGTTTGT 57.266 29.630 0.65 0.00 0.00 2.83
4353 4502 5.103982 ACATTGGATGAGTGGATTGATGGTA 60.104 40.000 0.00 0.00 0.00 3.25
4450 4599 7.284944 GTCACTCCTTACCTGCTTAGTAGATAA 59.715 40.741 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.420214 TACGCCGTTGGATCGAGGC 62.420 63.158 0.00 1.15 45.67 4.70
2 3 1.299165 CTACGCCGTTGGATCGAGG 60.299 63.158 0.00 0.00 0.00 4.63
3 4 1.299165 CCTACGCCGTTGGATCGAG 60.299 63.158 12.49 0.00 30.33 4.04
4 5 1.996786 GACCTACGCCGTTGGATCGA 61.997 60.000 24.02 0.00 33.00 3.59
5 6 1.588139 GACCTACGCCGTTGGATCG 60.588 63.158 24.02 0.00 33.00 3.69
6 7 0.104304 ATGACCTACGCCGTTGGATC 59.896 55.000 24.02 16.48 33.00 3.36
7 8 0.104304 GATGACCTACGCCGTTGGAT 59.896 55.000 24.02 8.12 33.00 3.41
8 9 0.968901 AGATGACCTACGCCGTTGGA 60.969 55.000 24.02 3.04 33.00 3.53
9 10 0.742505 TAGATGACCTACGCCGTTGG 59.257 55.000 16.10 16.10 34.76 3.77
10 11 1.674441 TCTAGATGACCTACGCCGTTG 59.326 52.381 0.00 0.00 0.00 4.10
11 12 2.048444 TCTAGATGACCTACGCCGTT 57.952 50.000 0.00 0.00 0.00 4.44
12 13 1.948145 CTTCTAGATGACCTACGCCGT 59.052 52.381 0.00 0.00 0.00 5.68
13 14 1.335142 GCTTCTAGATGACCTACGCCG 60.335 57.143 9.72 0.00 0.00 6.46
14 15 1.957877 AGCTTCTAGATGACCTACGCC 59.042 52.381 9.72 0.00 0.00 5.68
15 16 3.066900 TCAAGCTTCTAGATGACCTACGC 59.933 47.826 9.72 0.00 0.00 4.42
16 17 4.902443 TCAAGCTTCTAGATGACCTACG 57.098 45.455 9.72 0.00 0.00 3.51
17 18 6.264292 TCTGATCAAGCTTCTAGATGACCTAC 59.736 42.308 9.72 0.00 0.00 3.18
18 19 6.264292 GTCTGATCAAGCTTCTAGATGACCTA 59.736 42.308 9.72 0.00 0.00 3.08
19 20 5.068987 GTCTGATCAAGCTTCTAGATGACCT 59.931 44.000 9.72 0.00 0.00 3.85
20 21 5.288804 GTCTGATCAAGCTTCTAGATGACC 58.711 45.833 9.72 0.00 0.00 4.02
21 22 4.975502 CGTCTGATCAAGCTTCTAGATGAC 59.024 45.833 9.72 1.34 0.00 3.06
22 23 4.037327 CCGTCTGATCAAGCTTCTAGATGA 59.963 45.833 9.72 3.11 0.00 2.92
23 24 4.297510 CCGTCTGATCAAGCTTCTAGATG 58.702 47.826 0.00 3.75 0.00 2.90
24 25 3.243704 GCCGTCTGATCAAGCTTCTAGAT 60.244 47.826 0.00 0.00 0.00 1.98
25 26 2.099921 GCCGTCTGATCAAGCTTCTAGA 59.900 50.000 0.00 0.00 0.00 2.43
26 27 2.468831 GCCGTCTGATCAAGCTTCTAG 58.531 52.381 0.00 0.00 0.00 2.43
27 28 1.137086 GGCCGTCTGATCAAGCTTCTA 59.863 52.381 0.00 0.00 0.00 2.10
28 29 0.107945 GGCCGTCTGATCAAGCTTCT 60.108 55.000 0.00 0.00 0.00 2.85
29 30 1.424493 CGGCCGTCTGATCAAGCTTC 61.424 60.000 19.50 0.00 0.00 3.86
30 31 1.448540 CGGCCGTCTGATCAAGCTT 60.449 57.895 19.50 0.00 0.00 3.74
31 32 1.888436 TTCGGCCGTCTGATCAAGCT 61.888 55.000 27.15 0.00 0.00 3.74
32 33 1.019278 TTTCGGCCGTCTGATCAAGC 61.019 55.000 27.15 0.00 0.00 4.01
33 34 1.438651 TTTTCGGCCGTCTGATCAAG 58.561 50.000 27.15 0.00 0.00 3.02
34 35 1.737236 CATTTTCGGCCGTCTGATCAA 59.263 47.619 27.15 7.12 0.00 2.57
35 36 1.368641 CATTTTCGGCCGTCTGATCA 58.631 50.000 27.15 0.00 0.00 2.92
36 37 0.028110 GCATTTTCGGCCGTCTGATC 59.972 55.000 27.15 8.20 0.00 2.92
37 38 0.676466 TGCATTTTCGGCCGTCTGAT 60.676 50.000 27.15 12.31 0.00 2.90
38 39 0.676466 ATGCATTTTCGGCCGTCTGA 60.676 50.000 27.15 10.38 0.00 3.27
39 40 0.248215 GATGCATTTTCGGCCGTCTG 60.248 55.000 27.15 18.20 0.00 3.51
40 41 0.676466 TGATGCATTTTCGGCCGTCT 60.676 50.000 27.15 5.31 0.00 4.18
41 42 0.170116 TTGATGCATTTTCGGCCGTC 59.830 50.000 27.15 13.26 0.00 4.79
42 43 0.171007 CTTGATGCATTTTCGGCCGT 59.829 50.000 27.15 1.49 0.00 5.68
43 44 0.526096 CCTTGATGCATTTTCGGCCG 60.526 55.000 22.12 22.12 0.00 6.13
44 45 0.179103 CCCTTGATGCATTTTCGGCC 60.179 55.000 0.00 0.00 0.00 6.13
45 46 0.179103 CCCCTTGATGCATTTTCGGC 60.179 55.000 0.00 0.00 0.00 5.54
46 47 1.473258 TCCCCTTGATGCATTTTCGG 58.527 50.000 0.00 0.00 0.00 4.30
47 48 2.689471 TGATCCCCTTGATGCATTTTCG 59.311 45.455 0.00 0.00 32.41 3.46
48 49 3.703052 ACTGATCCCCTTGATGCATTTTC 59.297 43.478 0.00 0.00 32.41 2.29
49 50 3.703052 GACTGATCCCCTTGATGCATTTT 59.297 43.478 0.00 0.00 32.41 1.82
50 51 3.294214 GACTGATCCCCTTGATGCATTT 58.706 45.455 0.00 0.00 32.41 2.32
51 52 2.423947 GGACTGATCCCCTTGATGCATT 60.424 50.000 0.00 0.00 39.39 3.56
52 53 1.144503 GGACTGATCCCCTTGATGCAT 59.855 52.381 0.00 0.00 39.39 3.96
53 54 0.548031 GGACTGATCCCCTTGATGCA 59.452 55.000 0.00 0.00 39.39 3.96
54 55 0.533755 CGGACTGATCCCCTTGATGC 60.534 60.000 0.00 0.00 42.83 3.91
55 56 1.123077 TCGGACTGATCCCCTTGATG 58.877 55.000 0.00 0.00 42.83 3.07
56 57 1.696336 CATCGGACTGATCCCCTTGAT 59.304 52.381 0.00 0.00 42.83 2.57
57 58 1.123077 CATCGGACTGATCCCCTTGA 58.877 55.000 0.00 0.00 42.83 3.02
58 59 0.107456 CCATCGGACTGATCCCCTTG 59.893 60.000 0.00 0.00 42.83 3.61
59 60 0.326618 ACCATCGGACTGATCCCCTT 60.327 55.000 0.00 0.00 42.83 3.95
60 61 0.760945 GACCATCGGACTGATCCCCT 60.761 60.000 0.00 0.00 42.83 4.79
61 62 1.749033 GACCATCGGACTGATCCCC 59.251 63.158 0.00 0.00 42.83 4.81
62 63 1.107538 TCGACCATCGGACTGATCCC 61.108 60.000 0.00 0.00 42.83 3.85
63 64 0.312416 CTCGACCATCGGACTGATCC 59.688 60.000 0.00 0.00 40.88 3.36
64 65 1.265635 CTCTCGACCATCGGACTGATC 59.734 57.143 0.00 0.00 40.88 2.92
65 66 1.313772 CTCTCGACCATCGGACTGAT 58.686 55.000 0.00 0.00 40.88 2.90
66 67 0.035343 ACTCTCGACCATCGGACTGA 60.035 55.000 0.00 0.00 40.88 3.41
67 68 0.811915 AACTCTCGACCATCGGACTG 59.188 55.000 0.00 0.00 40.88 3.51
68 69 0.811915 CAACTCTCGACCATCGGACT 59.188 55.000 0.00 0.00 40.88 3.85
69 70 0.802607 GCAACTCTCGACCATCGGAC 60.803 60.000 0.00 0.00 40.88 4.79
70 71 0.965866 AGCAACTCTCGACCATCGGA 60.966 55.000 0.00 0.00 40.88 4.55
71 72 0.738975 TAGCAACTCTCGACCATCGG 59.261 55.000 0.00 0.00 40.88 4.18
72 73 2.561733 TTAGCAACTCTCGACCATCG 57.438 50.000 0.00 0.00 42.10 3.84
73 74 5.006165 CAGAATTTAGCAACTCTCGACCATC 59.994 44.000 0.00 0.00 0.00 3.51
74 75 4.872691 CAGAATTTAGCAACTCTCGACCAT 59.127 41.667 0.00 0.00 0.00 3.55
75 76 4.021456 TCAGAATTTAGCAACTCTCGACCA 60.021 41.667 0.00 0.00 0.00 4.02
76 77 4.495422 TCAGAATTTAGCAACTCTCGACC 58.505 43.478 0.00 0.00 0.00 4.79
77 78 5.403246 TCTCAGAATTTAGCAACTCTCGAC 58.597 41.667 0.00 0.00 0.00 4.20
78 79 5.416013 TCTCTCAGAATTTAGCAACTCTCGA 59.584 40.000 0.00 0.00 0.00 4.04
79 80 5.514914 GTCTCTCAGAATTTAGCAACTCTCG 59.485 44.000 0.00 0.00 0.00 4.04
80 81 5.810074 GGTCTCTCAGAATTTAGCAACTCTC 59.190 44.000 0.00 0.00 0.00 3.20
81 82 5.483583 AGGTCTCTCAGAATTTAGCAACTCT 59.516 40.000 0.00 0.00 0.00 3.24
82 83 5.729510 AGGTCTCTCAGAATTTAGCAACTC 58.270 41.667 0.00 0.00 0.00 3.01
83 84 5.623368 CGAGGTCTCTCAGAATTTAGCAACT 60.623 44.000 0.00 0.00 39.95 3.16
84 85 4.564769 CGAGGTCTCTCAGAATTTAGCAAC 59.435 45.833 0.00 0.00 39.95 4.17
85 86 4.382040 CCGAGGTCTCTCAGAATTTAGCAA 60.382 45.833 0.00 0.00 39.95 3.91
86 87 3.131223 CCGAGGTCTCTCAGAATTTAGCA 59.869 47.826 0.00 0.00 39.95 3.49
87 88 3.491792 CCCGAGGTCTCTCAGAATTTAGC 60.492 52.174 0.00 0.00 39.95 3.09
88 89 3.068873 CCCCGAGGTCTCTCAGAATTTAG 59.931 52.174 0.00 0.00 39.95 1.85
89 90 3.031736 CCCCGAGGTCTCTCAGAATTTA 58.968 50.000 0.00 0.00 39.95 1.40
90 91 1.834263 CCCCGAGGTCTCTCAGAATTT 59.166 52.381 0.00 0.00 39.95 1.82
91 92 1.490574 CCCCGAGGTCTCTCAGAATT 58.509 55.000 0.00 0.00 39.95 2.17
92 93 0.397816 CCCCCGAGGTCTCTCAGAAT 60.398 60.000 0.00 0.00 39.95 2.40
93 94 1.000486 CCCCCGAGGTCTCTCAGAA 60.000 63.158 0.00 0.00 39.95 3.02
94 95 2.684104 CCCCCGAGGTCTCTCAGA 59.316 66.667 0.00 0.00 39.95 3.27
95 96 3.151022 GCCCCCGAGGTCTCTCAG 61.151 72.222 0.00 0.00 39.95 3.35
96 97 3.663815 GAGCCCCCGAGGTCTCTCA 62.664 68.421 0.00 0.00 39.95 3.27
97 98 2.835895 GAGCCCCCGAGGTCTCTC 60.836 72.222 0.00 0.00 36.44 3.20
98 99 4.467107 GGAGCCCCCGAGGTCTCT 62.467 72.222 0.00 0.00 38.28 3.10
99 100 4.467107 AGGAGCCCCCGAGGTCTC 62.467 72.222 0.00 0.00 40.87 3.36
100 101 4.787280 CAGGAGCCCCCGAGGTCT 62.787 72.222 0.00 0.00 40.87 3.85
103 104 4.787280 AGACAGGAGCCCCCGAGG 62.787 72.222 0.00 0.00 40.87 4.63
104 105 2.685380 AAGACAGGAGCCCCCGAG 60.685 66.667 0.00 0.00 40.87 4.63
105 106 2.822643 ATCAAGACAGGAGCCCCCGA 62.823 60.000 0.00 0.00 40.87 5.14
106 107 1.915078 AATCAAGACAGGAGCCCCCG 61.915 60.000 0.00 0.00 40.87 5.73
107 108 0.332972 AAATCAAGACAGGAGCCCCC 59.667 55.000 0.00 0.00 0.00 5.40
108 109 2.222227 AAAATCAAGACAGGAGCCCC 57.778 50.000 0.00 0.00 0.00 5.80
182 183 9.778741 GACAAGGTCATATTTCTGGTATATTCA 57.221 33.333 0.00 0.00 32.09 2.57
204 205 2.732016 CCACCACGAGACCGACAA 59.268 61.111 0.00 0.00 39.50 3.18
265 266 3.221222 GGCCTACAGCTGGACGAT 58.779 61.111 19.93 0.00 43.05 3.73
715 720 0.252467 CTCCTCACCACCTCCTCCTT 60.252 60.000 0.00 0.00 0.00 3.36
1267 1272 1.714794 CAGCGTCTTAACAGGGACAG 58.285 55.000 0.00 0.00 33.19 3.51
1502 1507 6.095720 AGCTAATATTATCGACTGGCTACTCC 59.904 42.308 0.00 0.00 0.00 3.85
1829 1834 6.959639 AGTTTGTTGGACTTGATATGTGTT 57.040 33.333 0.00 0.00 0.00 3.32
1880 1885 2.671070 CGTGCACCTTCCCAGGAT 59.329 61.111 12.15 0.00 44.19 3.24
1979 1984 0.036388 TGAAGTCAGGTTCGGATGCC 60.036 55.000 0.00 0.00 0.00 4.40
2706 2711 2.034879 GCGCTGTTGGCTCTGCTTA 61.035 57.895 0.00 0.00 39.13 3.09
2877 2882 7.916077 TCCCTTCTTTCTCTTAGTATTAGGG 57.084 40.000 0.00 0.00 39.95 3.53
3283 3288 3.069586 TCGTGTGTCTTCACCTCATTTCT 59.930 43.478 0.00 0.00 43.26 2.52
3449 3454 1.677576 TGTTGAGCACTGCCTCTTTTG 59.322 47.619 0.00 0.00 33.02 2.44
3563 3568 1.192146 TCTGCCCCTACTTGTTCGCT 61.192 55.000 0.00 0.00 0.00 4.93
3737 3742 2.202946 TTGTTGTCGCAGCCGTCA 60.203 55.556 0.00 0.00 35.54 4.35
4353 4502 1.115467 CCTGCCTCATCTAAGTCCGT 58.885 55.000 0.00 0.00 0.00 4.69
4450 4599 1.293062 ATGTGTCTCTGGCCTCCATT 58.707 50.000 3.32 0.00 30.82 3.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.