Multiple sequence alignment - TraesCS6D01G247800

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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 TraesCS6D01G247800 chr6D 100.000 2195 0 0 1 2195 351111910 351114104 0.000000e+00 4054.0
1 TraesCS6D01G247800 chr6D 93.814 97 6 0 1 97 439506382 439506478 1.760000e-31 147.0
2 TraesCS6D01G247800 chr6D 92.857 98 7 0 1 98 32920165 32920262 2.270000e-30 143.0
3 TraesCS6D01G247800 chr6D 100.000 28 0 0 118 145 86854610 86854583 4.000000e-03 52.8
4 TraesCS6D01G247800 chr6A 97.424 1980 39 11 221 2195 492707186 492705214 0.000000e+00 3363.0
5 TraesCS6D01G247800 chr6B 96.906 1616 39 4 586 2195 528622262 528620652 0.000000e+00 2697.0
6 TraesCS6D01G247800 chr6B 90.511 411 24 9 180 588 528622762 528622365 1.490000e-146 529.0
7 TraesCS6D01G247800 chr5A 95.876 97 4 0 1 97 461871365 461871461 8.110000e-35 158.0
8 TraesCS6D01G247800 chr5A 100.000 30 0 0 118 147 76742153 76742182 3.040000e-04 56.5
9 TraesCS6D01G247800 chr5A 96.774 31 1 0 118 148 598868623 598868593 4.000000e-03 52.8
10 TraesCS6D01G247800 chr4D 93.878 98 6 0 1 98 386751622 386751719 4.880000e-32 148.0
11 TraesCS6D01G247800 chr4D 88.793 116 9 3 1 114 360102226 360102113 2.940000e-29 139.0
12 TraesCS6D01G247800 chr7A 92.079 101 8 0 1 101 187113609 187113509 2.270000e-30 143.0
13 TraesCS6D01G247800 chr2A 92.857 98 7 0 1 98 27741354 27741257 2.270000e-30 143.0
14 TraesCS6D01G247800 chr7D 92.079 101 7 1 1 100 277746361 277746261 8.170000e-30 141.0
15 TraesCS6D01G247800 chr7D 97.143 35 1 0 118 152 568014397 568014363 2.350000e-05 60.2
16 TraesCS6D01G247800 chr2D 92.000 100 8 0 1 100 371163956 371164055 8.170000e-30 141.0
17 TraesCS6D01G247800 chr3A 100.000 30 0 0 118 147 686178801 686178772 3.040000e-04 56.5
18 TraesCS6D01G247800 chr5D 100.000 29 0 0 117 145 6109695 6109667 1.000000e-03 54.7
19 TraesCS6D01G247800 chr5D 96.774 31 1 0 118 148 384472940 384472910 4.000000e-03 52.8
20 TraesCS6D01G247800 chr7B 96.774 31 1 0 115 145 203213350 203213380 4.000000e-03 52.8
21 TraesCS6D01G247800 chr1D 100.000 28 0 0 118 145 159982795 159982822 4.000000e-03 52.8


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 TraesCS6D01G247800 chr6D 351111910 351114104 2194 False 4054 4054 100.0000 1 2195 1 chr6D.!!$F2 2194
1 TraesCS6D01G247800 chr6A 492705214 492707186 1972 True 3363 3363 97.4240 221 2195 1 chr6A.!!$R1 1974
2 TraesCS6D01G247800 chr6B 528620652 528622762 2110 True 1613 2697 93.7085 180 2195 2 chr6B.!!$R1 2015

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
328 329 1.478105 GATGCAAAAGCCGGGATCTTT 59.522 47.619 2.18 0.97 35.47 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1481 1.379843 GGGGTAGCAATGTGGTGGG 60.38 63.158 0.0 0.0 0.0 4.61 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
24 25 5.731591 ACTTCCTCCGTCCTAAAATAAGTG 58.268 41.667 0.00 0.00 0.00 3.16
25 26 5.482878 ACTTCCTCCGTCCTAAAATAAGTGA 59.517 40.000 0.00 0.00 0.00 3.41
26 27 5.334724 TCCTCCGTCCTAAAATAAGTGAC 57.665 43.478 0.00 0.00 0.00 3.67
27 28 5.021458 TCCTCCGTCCTAAAATAAGTGACT 58.979 41.667 0.00 0.00 0.00 3.41
28 29 5.126707 TCCTCCGTCCTAAAATAAGTGACTC 59.873 44.000 0.00 0.00 0.00 3.36
29 30 4.990257 TCCGTCCTAAAATAAGTGACTCG 58.010 43.478 0.00 0.00 0.00 4.18
30 31 4.701651 TCCGTCCTAAAATAAGTGACTCGA 59.298 41.667 0.00 0.00 0.00 4.04
31 32 5.035443 CCGTCCTAAAATAAGTGACTCGAG 58.965 45.833 11.84 11.84 0.00 4.04
32 33 5.392811 CCGTCCTAAAATAAGTGACTCGAGT 60.393 44.000 20.18 20.18 0.00 4.18
33 34 6.091437 CGTCCTAAAATAAGTGACTCGAGTT 58.909 40.000 21.08 6.08 0.00 3.01
34 35 6.585322 CGTCCTAAAATAAGTGACTCGAGTTT 59.415 38.462 21.08 12.75 0.00 2.66
35 36 7.410513 CGTCCTAAAATAAGTGACTCGAGTTTG 60.411 40.741 21.08 1.11 0.00 2.93
36 37 7.384387 GTCCTAAAATAAGTGACTCGAGTTTGT 59.616 37.037 21.08 5.70 0.00 2.83
37 38 8.579006 TCCTAAAATAAGTGACTCGAGTTTGTA 58.421 33.333 21.08 10.21 0.00 2.41
38 39 9.367444 CCTAAAATAAGTGACTCGAGTTTGTAT 57.633 33.333 21.08 11.98 0.00 2.29
43 44 9.924650 AATAAGTGACTCGAGTTTGTATTAACT 57.075 29.630 21.08 10.17 40.92 2.24
44 45 9.924650 ATAAGTGACTCGAGTTTGTATTAACTT 57.075 29.630 21.08 18.29 38.43 2.66
45 46 8.658499 AAGTGACTCGAGTTTGTATTAACTTT 57.342 30.769 21.08 0.42 38.43 2.66
46 47 8.073355 AGTGACTCGAGTTTGTATTAACTTTG 57.927 34.615 21.08 0.00 38.43 2.77
47 48 7.709613 AGTGACTCGAGTTTGTATTAACTTTGT 59.290 33.333 21.08 0.00 38.43 2.83
48 49 8.971321 GTGACTCGAGTTTGTATTAACTTTGTA 58.029 33.333 21.08 0.00 38.43 2.41
49 50 8.971321 TGACTCGAGTTTGTATTAACTTTGTAC 58.029 33.333 21.08 0.28 38.43 2.90
50 51 9.189723 GACTCGAGTTTGTATTAACTTTGTACT 57.810 33.333 21.08 0.00 38.43 2.73
74 75 9.310716 ACTAAAGTTAGTACAAAGTTGAGTCAC 57.689 33.333 1.81 0.00 41.92 3.67
75 76 9.530633 CTAAAGTTAGTACAAAGTTGAGTCACT 57.469 33.333 0.00 0.00 0.00 3.41
76 77 8.788325 AAAGTTAGTACAAAGTTGAGTCACTT 57.212 30.769 0.00 0.00 38.74 3.16
77 78 9.880157 AAAGTTAGTACAAAGTTGAGTCACTTA 57.120 29.630 0.00 0.00 35.87 2.24
83 84 9.391006 AGTACAAAGTTGAGTCACTTATTTTGA 57.609 29.630 14.62 1.37 35.87 2.69
84 85 9.651718 GTACAAAGTTGAGTCACTTATTTTGAG 57.348 33.333 14.62 0.00 35.87 3.02
85 86 8.506168 ACAAAGTTGAGTCACTTATTTTGAGA 57.494 30.769 14.62 0.00 35.87 3.27
86 87 9.125026 ACAAAGTTGAGTCACTTATTTTGAGAT 57.875 29.630 14.62 0.00 35.87 2.75
87 88 9.390795 CAAAGTTGAGTCACTTATTTTGAGATG 57.609 33.333 5.72 0.00 35.87 2.90
88 89 7.678947 AGTTGAGTCACTTATTTTGAGATGG 57.321 36.000 0.00 0.00 0.00 3.51
89 90 7.453393 AGTTGAGTCACTTATTTTGAGATGGA 58.547 34.615 0.00 0.00 0.00 3.41
90 91 7.605691 AGTTGAGTCACTTATTTTGAGATGGAG 59.394 37.037 0.00 0.00 0.00 3.86
91 92 6.409704 TGAGTCACTTATTTTGAGATGGAGG 58.590 40.000 0.00 0.00 0.00 4.30
92 93 6.213397 TGAGTCACTTATTTTGAGATGGAGGA 59.787 38.462 0.00 0.00 0.00 3.71
93 94 7.020827 AGTCACTTATTTTGAGATGGAGGAA 57.979 36.000 0.00 0.00 0.00 3.36
94 95 7.108847 AGTCACTTATTTTGAGATGGAGGAAG 58.891 38.462 0.00 0.00 0.00 3.46
95 96 6.881602 GTCACTTATTTTGAGATGGAGGAAGT 59.118 38.462 0.00 0.00 0.00 3.01
96 97 8.041323 GTCACTTATTTTGAGATGGAGGAAGTA 58.959 37.037 0.00 0.00 0.00 2.24
97 98 8.772250 TCACTTATTTTGAGATGGAGGAAGTAT 58.228 33.333 0.00 0.00 0.00 2.12
103 104 5.991933 TGAGATGGAGGAAGTATATGAGC 57.008 43.478 0.00 0.00 0.00 4.26
104 105 5.397360 TGAGATGGAGGAAGTATATGAGCA 58.603 41.667 0.00 0.00 0.00 4.26
105 106 6.021672 TGAGATGGAGGAAGTATATGAGCAT 58.978 40.000 0.00 0.00 0.00 3.79
106 107 6.499699 TGAGATGGAGGAAGTATATGAGCATT 59.500 38.462 0.00 0.00 0.00 3.56
107 108 7.016957 TGAGATGGAGGAAGTATATGAGCATTT 59.983 37.037 0.00 0.00 0.00 2.32
108 109 8.441311 AGATGGAGGAAGTATATGAGCATTTA 57.559 34.615 0.00 0.00 0.00 1.40
109 110 8.538701 AGATGGAGGAAGTATATGAGCATTTAG 58.461 37.037 0.00 0.00 0.00 1.85
110 111 7.855784 TGGAGGAAGTATATGAGCATTTAGA 57.144 36.000 0.00 0.00 0.00 2.10
111 112 8.441311 TGGAGGAAGTATATGAGCATTTAGAT 57.559 34.615 0.00 0.00 0.00 1.98
112 113 8.535335 TGGAGGAAGTATATGAGCATTTAGATC 58.465 37.037 0.00 0.00 0.00 2.75
114 115 9.364989 GAGGAAGTATATGAGCATTTAGATCAC 57.635 37.037 0.00 0.00 46.85 3.06
115 116 8.317679 AGGAAGTATATGAGCATTTAGATCACC 58.682 37.037 0.00 0.00 46.85 4.02
116 117 8.097038 GGAAGTATATGAGCATTTAGATCACCA 58.903 37.037 0.00 0.00 46.85 4.17
117 118 9.664332 GAAGTATATGAGCATTTAGATCACCAT 57.336 33.333 0.00 0.00 46.85 3.55
137 138 9.442062 TCACCATTATATTAGTTTACAGAGGGA 57.558 33.333 0.00 0.00 0.00 4.20
138 139 9.712305 CACCATTATATTAGTTTACAGAGGGAG 57.288 37.037 0.00 0.00 0.00 4.30
139 140 9.448587 ACCATTATATTAGTTTACAGAGGGAGT 57.551 33.333 0.00 0.00 0.00 3.85
150 151 9.102453 AGTTTACAGAGGGAGTAATTTAGTTCT 57.898 33.333 0.00 0.00 32.07 3.01
151 152 9.368674 GTTTACAGAGGGAGTAATTTAGTTCTC 57.631 37.037 0.00 7.14 32.07 2.87
152 153 8.896722 TTACAGAGGGAGTAATTTAGTTCTCT 57.103 34.615 10.05 10.05 0.00 3.10
154 155 6.954684 ACAGAGGGAGTAATTTAGTTCTCTGA 59.045 38.462 28.77 0.00 45.60 3.27
155 156 7.123547 ACAGAGGGAGTAATTTAGTTCTCTGAG 59.876 40.741 28.77 16.93 45.60 3.35
156 157 7.123547 CAGAGGGAGTAATTTAGTTCTCTGAGT 59.876 40.741 23.78 0.00 45.60 3.41
157 158 8.337739 AGAGGGAGTAATTTAGTTCTCTGAGTA 58.662 37.037 4.32 0.00 0.00 2.59
158 159 9.138596 GAGGGAGTAATTTAGTTCTCTGAGTAT 57.861 37.037 4.32 0.00 0.00 2.12
159 160 9.138596 AGGGAGTAATTTAGTTCTCTGAGTATC 57.861 37.037 4.32 0.00 0.00 2.24
177 178 8.096621 TGAGTATCATTTCTTATACCCAACCA 57.903 34.615 0.00 0.00 42.56 3.67
178 179 8.553153 TGAGTATCATTTCTTATACCCAACCAA 58.447 33.333 0.00 0.00 42.56 3.67
196 197 3.758554 ACCAAGAAGAATATGCTTTGCGT 59.241 39.130 0.00 0.00 0.00 5.24
207 208 3.980646 TGCTTTGCGTAACACAGAAAT 57.019 38.095 0.00 0.00 0.00 2.17
214 215 6.462073 TTGCGTAACACAGAAATCTTCTAC 57.538 37.500 0.00 0.00 38.11 2.59
215 216 5.779922 TGCGTAACACAGAAATCTTCTACT 58.220 37.500 0.00 0.00 38.11 2.57
218 219 7.868922 TGCGTAACACAGAAATCTTCTACTAAA 59.131 33.333 0.00 0.00 38.11 1.85
219 220 8.160976 GCGTAACACAGAAATCTTCTACTAAAC 58.839 37.037 0.00 0.00 38.11 2.01
245 246 6.188871 CGCTGCATAAAATACGATGTGTTAA 58.811 36.000 0.00 0.00 0.00 2.01
280 281 9.401058 CTAATGATGTTTAAAAGAGGGAGATGT 57.599 33.333 0.00 0.00 0.00 3.06
284 285 4.522789 TGTTTAAAAGAGGGAGATGTTGCC 59.477 41.667 0.00 0.00 37.61 4.52
303 304 2.512286 ATCGGCTGTGTGCATCGG 60.512 61.111 0.00 0.00 45.15 4.18
328 329 1.478105 GATGCAAAAGCCGGGATCTTT 59.522 47.619 2.18 0.97 35.47 2.52
397 398 4.202111 ACATGCCCCTATGTTTAATTTCGC 60.202 41.667 0.00 0.00 38.05 4.70
404 405 4.642885 CCTATGTTTAATTTCGCAAGGGGA 59.357 41.667 0.00 0.00 38.47 4.81
469 470 3.482786 CAATCAAAGTTACAGCGACTGC 58.517 45.455 6.74 0.00 43.24 4.40
523 526 2.560504 CACCAAAGGCTGTATATGCGA 58.439 47.619 0.00 0.00 0.00 5.10
771 881 2.992689 TGGTGCTCGGCGACCTTA 60.993 61.111 15.97 0.00 33.31 2.69
861 971 3.624300 CTCGCCATCAGCTTCGCG 61.624 66.667 0.00 0.00 45.76 5.87
924 1034 1.560923 GGATCAACTCGTCGGTGATG 58.439 55.000 11.63 2.16 0.00 3.07
1044 1154 1.349357 ACAAGCTTGGACCTCTCTTCC 59.651 52.381 29.18 0.00 0.00 3.46
1056 1166 1.306482 CTCTTCCTCCCCAGGCAGA 60.306 63.158 0.00 0.00 39.56 4.26
1251 1361 8.166706 CAGAATTAAAGAAATGTCAAATGCTGC 58.833 33.333 0.00 0.00 28.01 5.25
1252 1362 7.874016 AGAATTAAAGAAATGTCAAATGCTGCA 59.126 29.630 4.13 4.13 0.00 4.41
1609 1719 8.641498 AGTCAAATAACTGATGAATCTTGGTT 57.359 30.769 0.00 0.00 0.00 3.67
1793 1909 1.070445 CTTGCTGCCATTGTTTTCCCA 59.930 47.619 0.00 0.00 0.00 4.37
1997 2113 2.149803 TAGCACGTGAAGGGACACCG 62.150 60.000 22.23 0.00 43.47 4.94
2120 2236 7.767261 AGGCAAATGCGTTAATTGTATAAGAA 58.233 30.769 0.00 0.00 43.26 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.664816 TCACTTATTTTAGGACGGAGGAAGTA 59.335 38.462 0.00 0.00 0.00 2.24
1 2 5.482878 TCACTTATTTTAGGACGGAGGAAGT 59.517 40.000 0.00 0.00 0.00 3.01
2 3 5.811100 GTCACTTATTTTAGGACGGAGGAAG 59.189 44.000 0.00 0.00 0.00 3.46
3 4 5.482878 AGTCACTTATTTTAGGACGGAGGAA 59.517 40.000 0.00 0.00 33.84 3.36
4 5 5.021458 AGTCACTTATTTTAGGACGGAGGA 58.979 41.667 0.00 0.00 33.84 3.71
5 6 5.340439 AGTCACTTATTTTAGGACGGAGG 57.660 43.478 0.00 0.00 33.84 4.30
6 7 5.035443 CGAGTCACTTATTTTAGGACGGAG 58.965 45.833 0.00 0.00 33.84 4.63
7 8 4.701651 TCGAGTCACTTATTTTAGGACGGA 59.298 41.667 0.00 0.00 33.84 4.69
8 9 4.990257 TCGAGTCACTTATTTTAGGACGG 58.010 43.478 0.00 0.00 33.84 4.79
9 10 5.638783 ACTCGAGTCACTTATTTTAGGACG 58.361 41.667 13.58 0.00 33.84 4.79
10 11 7.384387 ACAAACTCGAGTCACTTATTTTAGGAC 59.616 37.037 20.33 0.00 0.00 3.85
11 12 7.439381 ACAAACTCGAGTCACTTATTTTAGGA 58.561 34.615 20.33 0.00 0.00 2.94
12 13 7.653767 ACAAACTCGAGTCACTTATTTTAGG 57.346 36.000 20.33 0.00 0.00 2.69
17 18 9.924650 AGTTAATACAAACTCGAGTCACTTATT 57.075 29.630 20.33 18.91 34.60 1.40
18 19 9.924650 AAGTTAATACAAACTCGAGTCACTTAT 57.075 29.630 20.33 10.35 38.76 1.73
19 20 9.754382 AAAGTTAATACAAACTCGAGTCACTTA 57.246 29.630 20.33 8.44 38.76 2.24
20 21 8.548721 CAAAGTTAATACAAACTCGAGTCACTT 58.451 33.333 20.33 6.87 38.76 3.16
21 22 7.709613 ACAAAGTTAATACAAACTCGAGTCACT 59.290 33.333 20.33 0.00 38.76 3.41
22 23 7.848491 ACAAAGTTAATACAAACTCGAGTCAC 58.152 34.615 20.33 5.87 38.76 3.67
23 24 8.971321 GTACAAAGTTAATACAAACTCGAGTCA 58.029 33.333 20.33 5.05 38.76 3.41
24 25 9.189723 AGTACAAAGTTAATACAAACTCGAGTC 57.810 33.333 20.33 2.53 38.76 3.36
48 49 9.310716 GTGACTCAACTTTGTACTAACTTTAGT 57.689 33.333 6.85 6.85 45.39 2.24
49 50 9.530633 AGTGACTCAACTTTGTACTAACTTTAG 57.469 33.333 0.00 0.00 36.82 1.85
50 51 9.880157 AAGTGACTCAACTTTGTACTAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
51 52 8.788325 AAGTGACTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
57 58 9.391006 TCAAAATAAGTGACTCAACTTTGTACT 57.609 29.630 0.00 0.00 40.77 2.73
58 59 9.651718 CTCAAAATAAGTGACTCAACTTTGTAC 57.348 33.333 0.00 0.00 40.77 2.90
59 60 9.607988 TCTCAAAATAAGTGACTCAACTTTGTA 57.392 29.630 0.00 0.00 40.77 2.41
60 61 8.506168 TCTCAAAATAAGTGACTCAACTTTGT 57.494 30.769 0.00 0.00 40.77 2.83
61 62 9.390795 CATCTCAAAATAAGTGACTCAACTTTG 57.609 33.333 0.00 0.00 40.77 2.77
62 63 8.571336 CCATCTCAAAATAAGTGACTCAACTTT 58.429 33.333 0.00 0.00 40.77 2.66
63 64 7.939039 TCCATCTCAAAATAAGTGACTCAACTT 59.061 33.333 0.00 0.00 42.89 2.66
64 65 7.453393 TCCATCTCAAAATAAGTGACTCAACT 58.547 34.615 0.00 0.00 0.00 3.16
65 66 7.148340 CCTCCATCTCAAAATAAGTGACTCAAC 60.148 40.741 0.00 0.00 0.00 3.18
66 67 6.881065 CCTCCATCTCAAAATAAGTGACTCAA 59.119 38.462 0.00 0.00 0.00 3.02
67 68 6.213397 TCCTCCATCTCAAAATAAGTGACTCA 59.787 38.462 0.00 0.00 0.00 3.41
68 69 6.644347 TCCTCCATCTCAAAATAAGTGACTC 58.356 40.000 0.00 0.00 0.00 3.36
69 70 6.627087 TCCTCCATCTCAAAATAAGTGACT 57.373 37.500 0.00 0.00 0.00 3.41
70 71 6.881602 ACTTCCTCCATCTCAAAATAAGTGAC 59.118 38.462 0.00 0.00 0.00 3.67
71 72 7.020827 ACTTCCTCCATCTCAAAATAAGTGA 57.979 36.000 0.00 0.00 0.00 3.41
72 73 8.970859 ATACTTCCTCCATCTCAAAATAAGTG 57.029 34.615 0.00 0.00 0.00 3.16
77 78 7.882271 GCTCATATACTTCCTCCATCTCAAAAT 59.118 37.037 0.00 0.00 0.00 1.82
78 79 7.147497 TGCTCATATACTTCCTCCATCTCAAAA 60.147 37.037 0.00 0.00 0.00 2.44
79 80 6.327365 TGCTCATATACTTCCTCCATCTCAAA 59.673 38.462 0.00 0.00 0.00 2.69
80 81 5.840693 TGCTCATATACTTCCTCCATCTCAA 59.159 40.000 0.00 0.00 0.00 3.02
81 82 5.397360 TGCTCATATACTTCCTCCATCTCA 58.603 41.667 0.00 0.00 0.00 3.27
82 83 5.991933 TGCTCATATACTTCCTCCATCTC 57.008 43.478 0.00 0.00 0.00 2.75
83 84 6.949117 AATGCTCATATACTTCCTCCATCT 57.051 37.500 0.00 0.00 0.00 2.90
84 85 8.535335 TCTAAATGCTCATATACTTCCTCCATC 58.465 37.037 0.00 0.00 0.00 3.51
85 86 8.441311 TCTAAATGCTCATATACTTCCTCCAT 57.559 34.615 0.00 0.00 0.00 3.41
86 87 7.855784 TCTAAATGCTCATATACTTCCTCCA 57.144 36.000 0.00 0.00 0.00 3.86
87 88 8.535335 TGATCTAAATGCTCATATACTTCCTCC 58.465 37.037 0.00 0.00 0.00 4.30
88 89 9.364989 GTGATCTAAATGCTCATATACTTCCTC 57.635 37.037 0.00 0.00 0.00 3.71
89 90 8.317679 GGTGATCTAAATGCTCATATACTTCCT 58.682 37.037 0.00 0.00 0.00 3.36
90 91 8.097038 TGGTGATCTAAATGCTCATATACTTCC 58.903 37.037 0.00 0.00 0.00 3.46
91 92 9.664332 ATGGTGATCTAAATGCTCATATACTTC 57.336 33.333 0.00 0.00 0.00 3.01
111 112 9.442062 TCCCTCTGTAAACTAATATAATGGTGA 57.558 33.333 0.00 0.00 0.00 4.02
112 113 9.712305 CTCCCTCTGTAAACTAATATAATGGTG 57.288 37.037 0.00 0.00 0.00 4.17
113 114 9.448587 ACTCCCTCTGTAAACTAATATAATGGT 57.551 33.333 0.00 0.00 0.00 3.55
124 125 9.102453 AGAACTAAATTACTCCCTCTGTAAACT 57.898 33.333 0.00 0.00 34.20 2.66
125 126 9.368674 GAGAACTAAATTACTCCCTCTGTAAAC 57.631 37.037 0.00 0.00 34.20 2.01
126 127 9.322769 AGAGAACTAAATTACTCCCTCTGTAAA 57.677 33.333 0.00 0.00 34.20 2.01
127 128 8.750298 CAGAGAACTAAATTACTCCCTCTGTAA 58.250 37.037 0.00 0.00 40.61 2.41
128 129 8.114102 TCAGAGAACTAAATTACTCCCTCTGTA 58.886 37.037 18.37 9.15 43.87 2.74
129 130 6.954684 TCAGAGAACTAAATTACTCCCTCTGT 59.045 38.462 18.37 0.00 43.87 3.41
130 131 7.123547 ACTCAGAGAACTAAATTACTCCCTCTG 59.876 40.741 3.79 15.33 44.45 3.35
131 132 7.186268 ACTCAGAGAACTAAATTACTCCCTCT 58.814 38.462 3.79 0.00 0.00 3.69
132 133 7.412853 ACTCAGAGAACTAAATTACTCCCTC 57.587 40.000 3.79 0.00 0.00 4.30
133 134 9.138596 GATACTCAGAGAACTAAATTACTCCCT 57.861 37.037 3.79 0.00 0.00 4.20
134 135 8.915036 TGATACTCAGAGAACTAAATTACTCCC 58.085 37.037 3.79 0.00 0.00 4.30
146 147 9.699703 GGGTATAAGAAATGATACTCAGAGAAC 57.300 37.037 3.79 0.00 30.60 3.01
147 148 9.434275 TGGGTATAAGAAATGATACTCAGAGAA 57.566 33.333 3.79 0.00 34.73 2.87
148 149 9.434275 TTGGGTATAAGAAATGATACTCAGAGA 57.566 33.333 3.79 0.00 39.56 3.10
149 150 9.482627 GTTGGGTATAAGAAATGATACTCAGAG 57.517 37.037 0.00 0.00 39.56 3.35
150 151 8.429641 GGTTGGGTATAAGAAATGATACTCAGA 58.570 37.037 0.00 0.00 39.56 3.27
151 152 8.210946 TGGTTGGGTATAAGAAATGATACTCAG 58.789 37.037 0.00 0.00 39.56 3.35
152 153 8.096621 TGGTTGGGTATAAGAAATGATACTCA 57.903 34.615 0.00 0.00 37.26 3.41
153 154 8.974060 TTGGTTGGGTATAAGAAATGATACTC 57.026 34.615 0.00 0.00 30.84 2.59
154 155 8.778059 TCTTGGTTGGGTATAAGAAATGATACT 58.222 33.333 0.00 0.00 0.00 2.12
155 156 8.974060 TCTTGGTTGGGTATAAGAAATGATAC 57.026 34.615 0.00 0.00 0.00 2.24
156 157 9.627123 CTTCTTGGTTGGGTATAAGAAATGATA 57.373 33.333 0.00 0.00 38.32 2.15
157 158 8.336235 TCTTCTTGGTTGGGTATAAGAAATGAT 58.664 33.333 0.00 0.00 38.32 2.45
158 159 7.695055 TCTTCTTGGTTGGGTATAAGAAATGA 58.305 34.615 0.00 0.00 38.32 2.57
159 160 7.938140 TCTTCTTGGTTGGGTATAAGAAATG 57.062 36.000 0.00 0.00 38.32 2.32
162 163 9.627123 CATATTCTTCTTGGTTGGGTATAAGAA 57.373 33.333 0.00 0.00 36.96 2.52
163 164 7.719633 GCATATTCTTCTTGGTTGGGTATAAGA 59.280 37.037 0.00 0.00 0.00 2.10
164 165 7.721399 AGCATATTCTTCTTGGTTGGGTATAAG 59.279 37.037 0.00 0.00 0.00 1.73
165 166 7.582719 AGCATATTCTTCTTGGTTGGGTATAA 58.417 34.615 0.00 0.00 0.00 0.98
166 167 7.149202 AGCATATTCTTCTTGGTTGGGTATA 57.851 36.000 0.00 0.00 0.00 1.47
167 168 6.018433 AGCATATTCTTCTTGGTTGGGTAT 57.982 37.500 0.00 0.00 0.00 2.73
168 169 5.450818 AGCATATTCTTCTTGGTTGGGTA 57.549 39.130 0.00 0.00 0.00 3.69
169 170 4.322057 AGCATATTCTTCTTGGTTGGGT 57.678 40.909 0.00 0.00 0.00 4.51
170 171 5.413499 CAAAGCATATTCTTCTTGGTTGGG 58.587 41.667 0.00 0.00 31.96 4.12
171 172 4.866486 GCAAAGCATATTCTTCTTGGTTGG 59.134 41.667 0.00 0.00 31.96 3.77
172 173 4.560035 CGCAAAGCATATTCTTCTTGGTTG 59.440 41.667 0.00 0.00 31.96 3.77
173 174 4.218417 ACGCAAAGCATATTCTTCTTGGTT 59.782 37.500 0.00 0.00 32.86 3.67
174 175 3.758554 ACGCAAAGCATATTCTTCTTGGT 59.241 39.130 0.00 0.00 0.00 3.67
175 176 4.361451 ACGCAAAGCATATTCTTCTTGG 57.639 40.909 0.00 0.00 0.00 3.61
176 177 6.249260 GTGTTACGCAAAGCATATTCTTCTTG 59.751 38.462 0.00 0.00 0.00 3.02
177 178 6.072728 TGTGTTACGCAAAGCATATTCTTCTT 60.073 34.615 0.00 0.00 0.00 2.52
178 179 5.411361 TGTGTTACGCAAAGCATATTCTTCT 59.589 36.000 0.00 0.00 0.00 2.85
196 197 7.816031 CGGGTTTAGTAGAAGATTTCTGTGTTA 59.184 37.037 1.71 0.00 40.94 2.41
207 208 1.897133 TGCAGCGGGTTTAGTAGAAGA 59.103 47.619 0.00 0.00 0.00 2.87
214 215 4.271533 TCGTATTTTATGCAGCGGGTTTAG 59.728 41.667 0.00 0.00 0.00 1.85
215 216 4.190001 TCGTATTTTATGCAGCGGGTTTA 58.810 39.130 0.00 0.00 0.00 2.01
218 219 2.319136 TCGTATTTTATGCAGCGGGT 57.681 45.000 0.00 0.00 0.00 5.28
219 220 2.548057 ACATCGTATTTTATGCAGCGGG 59.452 45.455 0.00 0.00 0.00 6.13
253 254 9.618890 CATCTCCCTCTTTTAAACATCATTAGA 57.381 33.333 0.00 0.00 0.00 2.10
256 257 8.526147 CAACATCTCCCTCTTTTAAACATCATT 58.474 33.333 0.00 0.00 0.00 2.57
269 270 0.755686 GATCGGCAACATCTCCCTCT 59.244 55.000 0.00 0.00 0.00 3.69
284 285 2.863853 CGATGCACACAGCCGATCG 61.864 63.158 8.51 8.51 44.83 3.69
328 329 5.515106 TCTCCTTTTTCTTTTGTGAAGGGA 58.485 37.500 0.00 0.00 37.92 4.20
357 358 5.170021 GGCATGTTTGTATCAGCAAAATCA 58.830 37.500 0.00 0.00 39.65 2.57
375 376 4.202101 TGCGAAATTAAACATAGGGGCATG 60.202 41.667 0.00 0.00 0.00 4.06
397 398 4.141158 ACCAATATTTAGAGCCTCCCCTTG 60.141 45.833 0.00 0.00 0.00 3.61
404 405 5.615925 AACTCGACCAATATTTAGAGCCT 57.384 39.130 6.29 0.00 0.00 4.58
523 526 6.325919 TCGGCATTTTCTGTTCTATTTGTT 57.674 33.333 0.00 0.00 0.00 2.83
924 1034 0.466124 AGAAGATAGCGGTGAAGGGC 59.534 55.000 0.00 0.00 0.00 5.19
1056 1166 2.101582 CGATGAGGTTCTCGAATTCCCT 59.898 50.000 0.00 0.00 37.05 4.20
1251 1361 4.992688 TGTTTTGCCTTTACTCAACTGTG 58.007 39.130 0.00 0.00 0.00 3.66
1252 1362 5.852282 ATGTTTTGCCTTTACTCAACTGT 57.148 34.783 0.00 0.00 0.00 3.55
1259 1369 8.184304 TGTTGGTAATATGTTTTGCCTTTACT 57.816 30.769 0.00 0.00 33.04 2.24
1371 1481 1.379843 GGGGTAGCAATGTGGTGGG 60.380 63.158 0.00 0.00 0.00 4.61
1436 1546 8.609176 GTGATTTTGCAGCATTTGATATTTCAT 58.391 29.630 0.00 0.00 0.00 2.57
1609 1719 2.434336 ACCATTAGGATCGCAAGCAGTA 59.566 45.455 0.00 0.00 38.69 2.74
1997 2113 1.413077 CGAGGGAAGTATCCTTGGTCC 59.587 57.143 0.00 0.00 45.77 4.46
2018 2134 4.538917 CATCACTGATCAGAGAGTCATCG 58.461 47.826 29.27 8.48 31.84 3.84
2120 2236 8.780846 ATATTTTTCATTTGTGCATGTGATGT 57.219 26.923 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.