Multiple sequence alignment - TraesCS1D01G183400

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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 TraesCS1D01G183400 chr1D 100.000 2444 0 0 1 2444 254525594 254523151 0 4477
1 TraesCS1D01G183400 chr1D 94.634 1491 64 13 961 2444 397109464 397110945 0 2296
2 TraesCS1D01G183400 chr1D 98.423 951 14 1 1 950 254382033 254382983 0 1672
3 TraesCS1D01G183400 chrUn 98.187 1489 17 9 961 2444 93411068 93412551 0 2591
4 TraesCS1D01G183400 chrUn 97.576 949 16 6 1498 2444 403667276 403668219 0 1618
5 TraesCS1D01G183400 chrUn 97.332 787 14 6 1660 2444 93414138 93414919 0 1330
6 TraesCS1D01G183400 chr2D 98.051 1488 19 10 961 2444 272795331 272796812 0 2579
7 TraesCS1D01G183400 chr2D 98.739 952 10 1 1 950 591984598 591983647 0 1690
8 TraesCS1D01G183400 chr2D 97.679 948 15 6 1498 2444 635584530 635585471 0 1622
9 TraesCS1D01G183400 chr6D 97.782 1488 22 9 961 2444 168250103 168248623 0 2555
10 TraesCS1D01G183400 chr6D 98.739 952 10 1 1 950 389245833 389246784 0 1690
11 TraesCS1D01G183400 chr5D 97.649 1489 23 12 961 2444 503216781 503215300 0 2545
12 TraesCS1D01G183400 chr5D 97.308 1486 31 9 961 2444 329121544 329123022 0 2514
13 TraesCS1D01G183400 chr5D 98.842 950 11 0 1 950 503265316 503266265 0 1694
14 TraesCS1D01G183400 chr5D 98.739 952 10 1 1 950 503245261 503244310 0 1690
15 TraesCS1D01G183400 chr3A 97.579 1487 27 7 961 2444 672911446 672912926 0 2538
16 TraesCS1D01G183400 chr3A 98.843 951 10 1 1 950 66005144 66006094 0 1694
17 TraesCS1D01G183400 chr6A 96.376 1490 41 10 961 2444 260117717 260119199 0 2440
18 TraesCS1D01G183400 chr2A 96.974 1388 33 9 961 2345 335829459 335828078 0 2322
19 TraesCS1D01G183400 chr2A 98.739 952 10 1 1 950 726906466 726907417 0 1690
20 TraesCS1D01G183400 chr3D 99.158 950 8 0 1 950 589263537 589264486 0 1711
21 TraesCS1D01G183400 chr3D 97.635 888 14 6 1559 2444 24171316 24170434 0 1517
22 TraesCS1D01G183400 chr3D 98.881 447 4 1 1999 2444 24169339 24168893 0 797
23 TraesCS1D01G183400 chr7B 98.634 952 11 1 1 950 663099436 663100387 0 1685
24 TraesCS1D01G183400 chr7D 98.528 951 13 1 1 950 231554437 231555387 0 1677


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 TraesCS1D01G183400 chr1D 254523151 254525594 2443 True 4477.0 4477 100.0000 1 2444 1 chr1D.!!$R1 2443
1 TraesCS1D01G183400 chr1D 397109464 397110945 1481 False 2296.0 2296 94.6340 961 2444 1 chr1D.!!$F2 1483
2 TraesCS1D01G183400 chr1D 254382033 254382983 950 False 1672.0 1672 98.4230 1 950 1 chr1D.!!$F1 949
3 TraesCS1D01G183400 chrUn 93411068 93414919 3851 False 1960.5 2591 97.7595 961 2444 2 chrUn.!!$F2 1483
4 TraesCS1D01G183400 chrUn 403667276 403668219 943 False 1618.0 1618 97.5760 1498 2444 1 chrUn.!!$F1 946
5 TraesCS1D01G183400 chr2D 272795331 272796812 1481 False 2579.0 2579 98.0510 961 2444 1 chr2D.!!$F1 1483
6 TraesCS1D01G183400 chr2D 591983647 591984598 951 True 1690.0 1690 98.7390 1 950 1 chr2D.!!$R1 949
7 TraesCS1D01G183400 chr2D 635584530 635585471 941 False 1622.0 1622 97.6790 1498 2444 1 chr2D.!!$F2 946
8 TraesCS1D01G183400 chr6D 168248623 168250103 1480 True 2555.0 2555 97.7820 961 2444 1 chr6D.!!$R1 1483
9 TraesCS1D01G183400 chr6D 389245833 389246784 951 False 1690.0 1690 98.7390 1 950 1 chr6D.!!$F1 949
10 TraesCS1D01G183400 chr5D 503215300 503216781 1481 True 2545.0 2545 97.6490 961 2444 1 chr5D.!!$R1 1483
11 TraesCS1D01G183400 chr5D 329121544 329123022 1478 False 2514.0 2514 97.3080 961 2444 1 chr5D.!!$F1 1483
12 TraesCS1D01G183400 chr5D 503265316 503266265 949 False 1694.0 1694 98.8420 1 950 1 chr5D.!!$F2 949
13 TraesCS1D01G183400 chr5D 503244310 503245261 951 True 1690.0 1690 98.7390 1 950 1 chr5D.!!$R2 949
14 TraesCS1D01G183400 chr3A 672911446 672912926 1480 False 2538.0 2538 97.5790 961 2444 1 chr3A.!!$F2 1483
15 TraesCS1D01G183400 chr3A 66005144 66006094 950 False 1694.0 1694 98.8430 1 950 1 chr3A.!!$F1 949
16 TraesCS1D01G183400 chr6A 260117717 260119199 1482 False 2440.0 2440 96.3760 961 2444 1 chr6A.!!$F1 1483
17 TraesCS1D01G183400 chr2A 335828078 335829459 1381 True 2322.0 2322 96.9740 961 2345 1 chr2A.!!$R1 1384
18 TraesCS1D01G183400 chr2A 726906466 726907417 951 False 1690.0 1690 98.7390 1 950 1 chr2A.!!$F1 949
19 TraesCS1D01G183400 chr3D 589263537 589264486 949 False 1711.0 1711 99.1580 1 950 1 chr3D.!!$F1 949
20 TraesCS1D01G183400 chr3D 24168893 24171316 2423 True 1157.0 1517 98.2580 1559 2444 2 chr3D.!!$R1 885
21 TraesCS1D01G183400 chr7B 663099436 663100387 951 False 1685.0 1685 98.6340 1 950 1 chr7B.!!$F1 949
22 TraesCS1D01G183400 chr7D 231554437 231555387 950 False 1677.0 1677 98.5280 1 950 1 chr7D.!!$F1 949

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
436 442 3.056107 CCGATTCAAACAGGAGGAGTACA 60.056 47.826 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1841 1856 9.587772 TTTGTAGATCTTTCTCTAATTCTTCGG 57.412 33.333 0.0 0.0 33.17 4.3 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
357 363 9.699703 GAATAGAAAGTTAGATCTACATGGGAC 57.300 37.037 0.67 0.00 31.35 4.46
436 442 3.056107 CCGATTCAAACAGGAGGAGTACA 60.056 47.826 0.00 0.00 0.00 2.90
777 783 5.014228 AGCTTGGTCTTACTTCACCCTAAAT 59.986 40.000 0.00 0.00 0.00 1.40
1961 4345 9.440773 CCTAACATTCTTGCAGAATATATAGCA 57.559 33.333 9.96 3.97 42.67 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 261 4.901849 TCTCGAGAATCCATACATCCCTTT 59.098 41.667 14.01 0.00 0.00 3.11
357 363 1.987807 ATGGGGCGATTCAGGTGAGG 61.988 60.000 0.00 0.00 0.00 3.86
436 442 1.005805 TCCAAGGCACATTAGCATGGT 59.994 47.619 1.62 1.62 41.25 3.55
777 783 7.020827 ACTTGGATATGGAAGTCTTCTTTCA 57.979 36.000 12.31 2.81 42.55 2.69
1841 1856 9.587772 TTTGTAGATCTTTCTCTAATTCTTCGG 57.412 33.333 0.00 0.00 33.17 4.30
2039 4424 9.908152 CACAATTTTTACTTTTACTCCCCTTAG 57.092 33.333 0.00 0.00 0.00 2.18


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

AutoCloner maintained by Alex Coulton.