Multiple sequence alignment - TraesCS1D01G386200

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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 TraesCS1D01G386200 chr1D 100.000 4717 0 0 1 4717 459031806 459027090 0.000000e+00 8711.0
1 TraesCS1D01G386200 chr1D 85.738 4130 532 41 198 4300 459042393 459038294 0.000000e+00 4311.0
2 TraesCS1D01G386200 chr1B 86.053 4223 511 38 108 4300 631203975 631199801 0.000000e+00 4464.0
3 TraesCS1D01G386200 chr1B 84.898 4443 580 65 1 4392 631222282 631217880 0.000000e+00 4403.0
4 TraesCS1D01G386200 chr1A 87.285 3311 368 33 235 3508 551463775 551460481 0.000000e+00 3733.0
5 TraesCS1D01G386200 chr1A 80.824 1700 268 37 2975 4658 551443294 551441637 0.000000e+00 1280.0
6 TraesCS1D01G386200 chr1A 83.705 718 109 4 3492 4208 551458803 551458093 0.000000e+00 671.0
7 TraesCS1D01G386200 chr1A 86.607 112 14 1 85 195 551463774 551463663 6.410000e-24 122.0
8 TraesCS1D01G386200 chr3D 78.573 3953 735 72 355 4245 428251410 428255312 0.000000e+00 2505.0
9 TraesCS1D01G386200 chr3D 78.166 3980 738 95 282 4187 428245383 428249305 0.000000e+00 2414.0
10 TraesCS1D01G386200 chr3D 89.655 58 4 1 1 58 428245239 428245294 6.550000e-09 73.1
11 TraesCS1D01G386200 chr3A 78.270 3953 748 70 355 4245 557413361 557409458 0.000000e+00 2438.0
12 TraesCS1D01G386200 chr3A 77.199 3991 765 93 360 4268 557419092 557415165 0.000000e+00 2194.0
13 TraesCS1D01G386200 chr3B 77.613 4114 766 106 282 4319 559880868 559884902 0.000000e+00 2351.0
14 TraesCS1D01G386200 chr3B 79.643 2019 336 48 355 2329 559886830 559888817 0.000000e+00 1382.0
15 TraesCS1D01G386200 chr3B 89.474 57 4 1 2 58 559880726 559880780 2.350000e-08 71.3
16 TraesCS1D01G386200 chr6D 77.018 3951 788 93 358 4259 469800194 469804073 0.000000e+00 2156.0
17 TraesCS1D01G386200 chrUn 76.577 3962 805 94 358 4270 62079784 62075897 0.000000e+00 2061.0
18 TraesCS1D01G386200 chr4A 75.172 3923 843 86 391 4238 734385227 734389093 0.000000e+00 1727.0
19 TraesCS1D01G386200 chr4A 74.828 3790 808 99 385 4091 736896812 736900538 0.000000e+00 1580.0
20 TraesCS1D01G386200 chr7B 75.872 3067 648 74 1140 4175 746528352 746525347 0.000000e+00 1480.0
21 TraesCS1D01G386200 chr7B 76.977 1985 399 39 380 2330 744260778 744258818 0.000000e+00 1081.0
22 TraesCS1D01G386200 chr7B 76.542 1978 404 38 380 2322 743738228 743740180 0.000000e+00 1027.0
23 TraesCS1D01G386200 chr2D 73.194 1052 253 21 3142 4182 633216738 633217771 2.090000e-93 353.0
24 TraesCS1D01G386200 chr2B 78.796 382 78 2 358 739 776410740 776411118 2.180000e-63 254.0


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 TraesCS1D01G386200 chr1D 459027090 459031806 4716 True 8711.000000 8711 100.000000 1 4717 1 chr1D.!!$R1 4716
1 TraesCS1D01G386200 chr1D 459038294 459042393 4099 True 4311.000000 4311 85.738000 198 4300 1 chr1D.!!$R2 4102
2 TraesCS1D01G386200 chr1B 631199801 631203975 4174 True 4464.000000 4464 86.053000 108 4300 1 chr1B.!!$R1 4192
3 TraesCS1D01G386200 chr1B 631217880 631222282 4402 True 4403.000000 4403 84.898000 1 4392 1 chr1B.!!$R2 4391
4 TraesCS1D01G386200 chr1A 551458093 551463775 5682 True 1508.666667 3733 85.865667 85 4208 3 chr1A.!!$R2 4123
5 TraesCS1D01G386200 chr1A 551441637 551443294 1657 True 1280.000000 1280 80.824000 2975 4658 1 chr1A.!!$R1 1683
6 TraesCS1D01G386200 chr3D 428245239 428255312 10073 False 1664.033333 2505 82.131333 1 4245 3 chr3D.!!$F1 4244
7 TraesCS1D01G386200 chr3A 557409458 557419092 9634 True 2316.000000 2438 77.734500 355 4268 2 chr3A.!!$R1 3913
8 TraesCS1D01G386200 chr3B 559880726 559888817 8091 False 1268.100000 2351 82.243333 2 4319 3 chr3B.!!$F1 4317
9 TraesCS1D01G386200 chr6D 469800194 469804073 3879 False 2156.000000 2156 77.018000 358 4259 1 chr6D.!!$F1 3901
10 TraesCS1D01G386200 chrUn 62075897 62079784 3887 True 2061.000000 2061 76.577000 358 4270 1 chrUn.!!$R1 3912
11 TraesCS1D01G386200 chr4A 734385227 734389093 3866 False 1727.000000 1727 75.172000 391 4238 1 chr4A.!!$F1 3847
12 TraesCS1D01G386200 chr4A 736896812 736900538 3726 False 1580.000000 1580 74.828000 385 4091 1 chr4A.!!$F2 3706
13 TraesCS1D01G386200 chr7B 746525347 746528352 3005 True 1480.000000 1480 75.872000 1140 4175 1 chr7B.!!$R2 3035
14 TraesCS1D01G386200 chr7B 744258818 744260778 1960 True 1081.000000 1081 76.977000 380 2330 1 chr7B.!!$R1 1950
15 TraesCS1D01G386200 chr7B 743738228 743740180 1952 False 1027.000000 1027 76.542000 380 2322 1 chr7B.!!$F1 1942
16 TraesCS1D01G386200 chr2D 633216738 633217771 1033 False 353.000000 353 73.194000 3142 4182 1 chr2D.!!$F1 1040


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
438 608 0.031857 CTCCTCGCTGATGCTTCGAT 59.968 55.0 0.00 0.00 36.97 3.59 F
1468 7416 0.952280 CAGAGATCTTAGCCGGCGTA 59.048 55.0 23.20 12.37 0.00 4.42 F
3085 15044 0.657312 GCAATTGATGGCATCGACGA 59.343 50.0 19.47 0.00 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 7909 0.238289 GCATGGTATTTCCGCCATCG 59.762 55.0 0.0 0.0 43.05 3.84 R
3360 15334 0.036294 GGACCTCTTTGGACGGAAGG 60.036 60.0 0.0 0.0 39.71 3.46 R
4522 18204 0.108615 AAGAGTGGAAGGACGATGCG 60.109 55.0 0.0 0.0 0.00 4.73 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)



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AutoCloner maintained by Alex Coulton.