Multiple sequence alignment - TraesCS7D01G317000

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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 TraesCS7D01G317000 chr7D 100.000 2493 0 0 1 2493 403463713 403466205 0.000000e+00 4604.0
1 TraesCS7D01G317000 chr7D 98.017 2521 16 9 1 2493 567321998 567324512 0.000000e+00 4348.0
2 TraesCS7D01G317000 chr7D 97.819 2522 23 6 1 2493 589613511 589610993 0.000000e+00 4324.0
3 TraesCS7D01G317000 chr7D 97.521 2501 43 14 1 2493 118751757 118754246 0.000000e+00 4257.0
4 TraesCS7D01G317000 chr1D 98.487 2512 17 4 1 2493 143269200 143266691 0.000000e+00 4409.0
5 TraesCS7D01G317000 chr1D 97.976 2520 21 6 1 2493 203582848 203585364 0.000000e+00 4344.0
6 TraesCS7D01G317000 chr1D 97.738 2520 23 7 1 2493 19993794 19991282 0.000000e+00 4307.0
7 TraesCS7D01G317000 chr1D 98.172 1696 10 4 817 2493 49896494 49898187 0.000000e+00 2940.0
8 TraesCS7D01G317000 chr1D 98.300 1647 9 2 865 2493 58905405 58903760 0.000000e+00 2868.0
9 TraesCS7D01G317000 chr1D 98.208 893 4 2 1 882 58906231 58905340 0.000000e+00 1550.0
10 TraesCS7D01G317000 chr1D 97.059 34 0 1 2428 2461 78960528 78960560 3.460000e-04 56.5
11 TraesCS7D01G317000 chr2D 98.249 2513 21 6 1 2493 54792981 54790472 0.000000e+00 4375.0
12 TraesCS7D01G317000 chr5D 98.056 2521 16 10 1 2493 55023998 55021483 0.000000e+00 4353.0
13 TraesCS7D01G317000 chr5D 97.977 2521 19 8 1 2493 335823507 335826023 0.000000e+00 4344.0
14 TraesCS7D01G317000 chr5D 97.611 2511 16 6 1 2493 80828717 80831201 0.000000e+00 4265.0
15 TraesCS7D01G317000 chr5D 98.118 1647 9 5 865 2493 442642101 442643743 0.000000e+00 2850.0
16 TraesCS7D01G317000 chr3D 98.016 2520 19 5 1 2493 68827263 68824748 0.000000e+00 4348.0
17 TraesCS7D01G317000 chr3D 97.870 892 8 3 1 882 414811280 414810390 0.000000e+00 1531.0
18 TraesCS7D01G317000 chr4D 97.738 2520 25 6 1 2493 433308257 433305743 0.000000e+00 4309.0
19 TraesCS7D01G317000 chr4D 97.569 2509 36 17 1 2493 529834 532333 0.000000e+00 4272.0
20 TraesCS7D01G317000 chr4D 97.463 2523 29 10 1 2493 502304550 502307067 0.000000e+00 4272.0
21 TraesCS7D01G317000 chr6D 97.660 2521 27 9 1 2493 42264550 42262034 0.000000e+00 4300.0
22 TraesCS7D01G317000 chr6D 97.650 2511 29 8 1 2493 5280197 5277699 0.000000e+00 4283.0
23 TraesCS7D01G317000 chr6A 100.000 35 0 0 2459 2493 461950127 461950161 5.760000e-07 65.8
24 TraesCS7D01G317000 chr1A 100.000 35 0 0 2459 2493 549991722 549991688 5.760000e-07 65.8


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 TraesCS7D01G317000 chr7D 403463713 403466205 2492 False 4604 4604 100.000 1 2493 1 chr7D.!!$F2 2492
1 TraesCS7D01G317000 chr7D 567321998 567324512 2514 False 4348 4348 98.017 1 2493 1 chr7D.!!$F3 2492
2 TraesCS7D01G317000 chr7D 589610993 589613511 2518 True 4324 4324 97.819 1 2493 1 chr7D.!!$R1 2492
3 TraesCS7D01G317000 chr7D 118751757 118754246 2489 False 4257 4257 97.521 1 2493 1 chr7D.!!$F1 2492
4 TraesCS7D01G317000 chr1D 143266691 143269200 2509 True 4409 4409 98.487 1 2493 1 chr1D.!!$R2 2492
5 TraesCS7D01G317000 chr1D 203582848 203585364 2516 False 4344 4344 97.976 1 2493 1 chr1D.!!$F3 2492
6 TraesCS7D01G317000 chr1D 19991282 19993794 2512 True 4307 4307 97.738 1 2493 1 chr1D.!!$R1 2492
7 TraesCS7D01G317000 chr1D 49896494 49898187 1693 False 2940 2940 98.172 817 2493 1 chr1D.!!$F1 1676
8 TraesCS7D01G317000 chr1D 58903760 58906231 2471 True 2209 2868 98.254 1 2493 2 chr1D.!!$R3 2492
9 TraesCS7D01G317000 chr2D 54790472 54792981 2509 True 4375 4375 98.249 1 2493 1 chr2D.!!$R1 2492
10 TraesCS7D01G317000 chr5D 55021483 55023998 2515 True 4353 4353 98.056 1 2493 1 chr5D.!!$R1 2492
11 TraesCS7D01G317000 chr5D 335823507 335826023 2516 False 4344 4344 97.977 1 2493 1 chr5D.!!$F2 2492
12 TraesCS7D01G317000 chr5D 80828717 80831201 2484 False 4265 4265 97.611 1 2493 1 chr5D.!!$F1 2492
13 TraesCS7D01G317000 chr5D 442642101 442643743 1642 False 2850 2850 98.118 865 2493 1 chr5D.!!$F3 1628
14 TraesCS7D01G317000 chr3D 68824748 68827263 2515 True 4348 4348 98.016 1 2493 1 chr3D.!!$R1 2492
15 TraesCS7D01G317000 chr3D 414810390 414811280 890 True 1531 1531 97.870 1 882 1 chr3D.!!$R2 881
16 TraesCS7D01G317000 chr4D 433305743 433308257 2514 True 4309 4309 97.738 1 2493 1 chr4D.!!$R1 2492
17 TraesCS7D01G317000 chr4D 529834 532333 2499 False 4272 4272 97.569 1 2493 1 chr4D.!!$F1 2492
18 TraesCS7D01G317000 chr4D 502304550 502307067 2517 False 4272 4272 97.463 1 2493 1 chr4D.!!$F2 2492
19 TraesCS7D01G317000 chr6D 42262034 42264550 2516 True 4300 4300 97.660 1 2493 1 chr6D.!!$R2 2492
20 TraesCS7D01G317000 chr6D 5277699 5280197 2498 True 4283 4283 97.650 1 2493 1 chr6D.!!$R1 2492

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
635 676 1.273606 GCTACTGCACTGTCCTTCTCA 59.726 52.381 0.0 0.0 39.41 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1821 3.30572 ACGAGCTAGGGTATGATCCAAA 58.694 45.455 0.0 0.0 0.0 3.28 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
635 676 1.273606 GCTACTGCACTGTCCTTCTCA 59.726 52.381 0.00 0.00 39.41 3.27
1090 1227 1.503818 GAACTTTGGGCGCGAGTTCA 61.504 55.000 28.92 9.24 45.30 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
635 676 1.353022 TGGGGCAGATCGTAAAAACCT 59.647 47.619 0.0 0.0 0.0 3.50
1684 1821 3.305720 ACGAGCTAGGGTATGATCCAAA 58.694 45.455 0.0 0.0 0.0 3.28


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

AutoCloner maintained by Alex Coulton.