Multiple sequence alignment - TraesCS7D01G299600

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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 TraesCS7D01G299600 chr7D 100.000 5139 0 0 1 5139 379572346 379567208 0.000000e+00 9491
1 TraesCS7D01G299600 chr7D 96.364 220 7 1 1 220 221660589 221660807 1.360000e-95 361
2 TraesCS7D01G299600 chr7D 95.909 220 8 1 1 220 42752398 42752180 6.330000e-94 355
3 TraesCS7D01G299600 chr7D 88.095 126 13 2 4418 4542 222777619 222777743 1.150000e-31 148
4 TraesCS7D01G299600 chr7B 92.786 3535 170 34 898 4411 374727097 374723627 0.000000e+00 5036
5 TraesCS7D01G299600 chr7B 74.914 291 47 20 4755 5036 624187579 624187852 5.440000e-20 110
6 TraesCS7D01G299600 chr7A 91.289 1986 105 16 310 2283 427822408 427820479 0.000000e+00 2647
7 TraesCS7D01G299600 chr7A 89.877 1877 141 32 2542 4411 427820019 427818185 0.000000e+00 2368
8 TraesCS7D01G299600 chr7A 95.503 467 12 3 2042 2499 427820481 427820015 0.000000e+00 737
9 TraesCS7D01G299600 chr7A 92.045 528 28 8 4625 5139 670181455 670181981 0.000000e+00 730
10 TraesCS7D01G299600 chr7A 92.505 507 21 9 4642 5139 36305997 36305499 0.000000e+00 710
11 TraesCS7D01G299600 chr7A 90.393 229 21 1 4417 4644 36306269 36306041 3.010000e-77 300
12 TraesCS7D01G299600 chr7A 80.952 231 29 13 4417 4644 681253116 681252898 8.850000e-38 169
13 TraesCS7D01G299600 chr3D 93.699 730 12 5 4417 5139 477408578 477407876 0.000000e+00 1062
14 TraesCS7D01G299600 chr3D 85.233 386 50 6 315 695 9273061 9272678 1.730000e-104 390
15 TraesCS7D01G299600 chr3D 96.364 220 7 1 1 220 428692347 428692129 1.360000e-95 361
16 TraesCS7D01G299600 chr3D 87.097 124 13 3 4417 4539 8307743 8307864 2.500000e-28 137
17 TraesCS7D01G299600 chr3D 86.614 127 14 3 4417 4542 517801285 517801409 2.500000e-28 137
18 TraesCS7D01G299600 chr6A 94.499 509 16 6 4641 5139 521470301 521469795 0.000000e+00 774
19 TraesCS7D01G299600 chr3B 93.137 510 15 12 4641 5139 17348440 17348940 0.000000e+00 730
20 TraesCS7D01G299600 chr3A 93.528 479 16 7 4675 5139 689387235 689386758 0.000000e+00 699
21 TraesCS7D01G299600 chr3A 76.549 452 59 30 4697 5138 725331931 725332345 2.430000e-48 204
22 TraesCS7D01G299600 chr1B 85.572 402 45 10 310 702 610971064 610971461 4.790000e-110 409
23 TraesCS7D01G299600 chr4B 85.422 391 51 3 310 695 647764455 647764844 8.010000e-108 401
24 TraesCS7D01G299600 chr4B 82.222 405 63 8 310 708 39046779 39047180 1.770000e-89 340
25 TraesCS7D01G299600 chr6D 85.166 391 51 4 310 695 15694443 15694055 1.340000e-105 394
26 TraesCS7D01G299600 chr6D 95.909 220 8 1 1 220 307313935 307313717 6.330000e-94 355
27 TraesCS7D01G299600 chr2A 84.211 399 56 4 310 703 431581739 431581343 1.040000e-101 381
28 TraesCS7D01G299600 chr4A 83.374 409 59 5 308 708 16961681 16961274 2.260000e-98 370
29 TraesCS7D01G299600 chr1D 96.789 218 6 1 4 221 211858977 211858761 3.780000e-96 363
30 TraesCS7D01G299600 chr1D 83.503 394 56 6 308 695 16676089 16675699 4.890000e-95 359
31 TraesCS7D01G299600 chr2D 96.364 220 7 1 1 220 386374135 386373917 1.360000e-95 361
32 TraesCS7D01G299600 chr2D 96.330 218 7 1 1 218 268474185 268474401 1.760000e-94 357
33 TraesCS7D01G299600 chr2D 86.508 126 13 4 4417 4541 361422419 361422297 8.980000e-28 135
34 TraesCS7D01G299600 chr5B 96.330 218 7 1 1 218 287455865 287456081 1.760000e-94 357
35 TraesCS7D01G299600 chr4D 95.909 220 8 1 1 220 222130280 222130498 6.330000e-94 355
36 TraesCS7D01G299600 chr2B 87.903 124 10 5 4417 4538 784729288 784729168 1.930000e-29 141
37 TraesCS7D01G299600 chr5D 87.805 123 10 4 4417 4537 53896877 53896758 6.940000e-29 139


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 TraesCS7D01G299600 chr7D 379567208 379572346 5138 True 9491.000000 9491 100.000 1 5139 1 chr7D.!!$R2 5138
1 TraesCS7D01G299600 chr7B 374723627 374727097 3470 True 5036.000000 5036 92.786 898 4411 1 chr7B.!!$R1 3513
2 TraesCS7D01G299600 chr7A 427818185 427822408 4223 True 1917.333333 2647 92.223 310 4411 3 chr7A.!!$R3 4101
3 TraesCS7D01G299600 chr7A 670181455 670181981 526 False 730.000000 730 92.045 4625 5139 1 chr7A.!!$F1 514
4 TraesCS7D01G299600 chr7A 36305499 36306269 770 True 505.000000 710 91.449 4417 5139 2 chr7A.!!$R2 722
5 TraesCS7D01G299600 chr3D 477407876 477408578 702 True 1062.000000 1062 93.699 4417 5139 1 chr3D.!!$R3 722
6 TraesCS7D01G299600 chr6A 521469795 521470301 506 True 774.000000 774 94.499 4641 5139 1 chr6A.!!$R1 498
7 TraesCS7D01G299600 chr3B 17348440 17348940 500 False 730.000000 730 93.137 4641 5139 1 chr3B.!!$F1 498


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
990 999 0.035820 TCGTTTCCCCAATTCCCTCG 60.036 55.000 0.00 0.00 0.00 4.63 F
991 1000 0.322187 CGTTTCCCCAATTCCCTCGT 60.322 55.000 0.00 0.00 0.00 4.18 F
994 1003 0.330267 TTCCCCAATTCCCTCGTTCC 59.670 55.000 0.00 0.00 0.00 3.62 F
995 1004 1.076995 CCCCAATTCCCTCGTTCCC 60.077 63.158 0.00 0.00 0.00 3.97 F
996 1005 1.076995 CCCAATTCCCTCGTTCCCC 60.077 63.158 0.00 0.00 0.00 4.81 F
1029 1038 1.078848 CCACAAGAAGAGGAGCCCG 60.079 63.158 0.00 0.00 0.00 6.13 F
2046 2060 2.094026 CCTAAAGTTGGCTTCATTGGGC 60.094 50.000 0.00 0.00 33.01 5.36 F
4015 4334 0.105778 GGATAGCAGGACTCCAGCAC 59.894 60.000 14.46 5.71 38.55 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 2706 1.580845 GGCATATCATGTCGCCTGCC 61.581 60.000 10.21 10.21 41.50 4.85 R
2517 2826 3.266636 TCAGAAACGTCAAACTTGAGCA 58.733 40.909 0.00 0.00 37.98 4.26 R
2856 3167 3.751698 AGAGATCAACGCCCAAACTAAAC 59.248 43.478 0.00 0.00 0.00 2.01 R
3011 3322 8.034313 TGGACTAGAGAAACCATTATTAGCAT 57.966 34.615 0.00 0.00 0.00 3.79 R
3063 3374 3.243101 CCTGCATCACATCATCAAGCTTC 60.243 47.826 0.00 0.00 0.00 3.86 R
3084 3395 1.303309 CCTTCTCGTTGCATCCATCC 58.697 55.000 0.00 0.00 0.00 3.51 R
4115 4434 0.376152 CATCACAGCACGCATTCTCC 59.624 55.000 0.00 0.00 0.00 3.71 R
4885 5254 5.063204 ACTCTCGTCCAACAAATCAAATGA 58.937 37.500 0.00 0.00 0.00 2.57 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.