Multiple sequence alignment - TraesCS6B01G357100

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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 TraesCS6B01G357100 chr6B 100.000 2447 0 0 1 2447 625538254 625535808 0 4519
1 TraesCS6B01G357100 chr7B 95.933 2459 86 6 1 2447 52952796 52950340 0 3975
2 TraesCS6B01G357100 chr7B 97.075 1607 46 1 842 2447 742965082 742966688 0 2706
3 TraesCS6B01G357100 chr7B 93.690 935 28 6 1 921 327258709 327259626 0 1371
4 TraesCS6B01G357100 chr1B 94.957 2459 110 7 1 2447 286076157 286078613 0 3842
5 TraesCS6B01G357100 chr1B 95.294 935 30 8 1 921 619179149 619178215 0 1471
6 TraesCS6B01G357100 chr1B 95.080 935 32 7 1 921 583575208 583574274 0 1459
7 TraesCS6B01G357100 chr3D 97.822 1607 34 1 842 2447 202625480 202623874 0 2772
8 TraesCS6B01G357100 chr6D 97.761 1608 34 2 842 2447 430466784 430465177 0 2769
9 TraesCS6B01G357100 chr5A 97.083 1611 46 1 838 2447 162145420 162143810 0 2713
10 TraesCS6B01G357100 chr5A 95.294 935 30 7 1 921 420172524 420173458 0 1471
11 TraesCS6B01G357100 chr3B 96.951 1607 48 1 842 2447 201583761 201582155 0 2695
12 TraesCS6B01G357100 chr3B 96.826 1607 49 2 842 2447 92226626 92225021 0 2684
13 TraesCS6B01G357100 chr4D 96.762 1606 52 0 842 2447 97361819 97363424 0 2678
14 TraesCS6B01G357100 chr4D 95.396 934 31 6 1 922 398051449 398050516 0 1476
15 TraesCS6B01G357100 chr5B 95.508 935 28 7 1 921 130584989 130584055 0 1482
16 TraesCS6B01G357100 chr3A 95.396 934 30 6 1 921 247671819 247672752 0 1474
17 TraesCS6B01G357100 chr3A 95.187 935 31 7 1 921 122210600 122209666 0 1465
18 TraesCS6B01G357100 chrUn 95.080 935 32 6 1 921 222870884 222871818 0 1459
19 TraesCS6B01G357100 chrUn 93.690 935 28 6 1 921 182441251 182442168 0 1371
20 TraesCS6B01G357100 chr7A 95.080 935 32 7 1 921 60196418 60195484 0 1459
21 TraesCS6B01G357100 chr2B 94.973 935 33 5 1 921 234506708 234505774 0 1454
22 TraesCS6B01G357100 chr2D 94.861 934 36 6 1 922 200950855 200949922 0 1448


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 TraesCS6B01G357100 chr6B 625535808 625538254 2446 True 4519 4519 100.000 1 2447 1 chr6B.!!$R1 2446
1 TraesCS6B01G357100 chr7B 52950340 52952796 2456 True 3975 3975 95.933 1 2447 1 chr7B.!!$R1 2446
2 TraesCS6B01G357100 chr7B 742965082 742966688 1606 False 2706 2706 97.075 842 2447 1 chr7B.!!$F2 1605
3 TraesCS6B01G357100 chr7B 327258709 327259626 917 False 1371 1371 93.690 1 921 1 chr7B.!!$F1 920
4 TraesCS6B01G357100 chr1B 286076157 286078613 2456 False 3842 3842 94.957 1 2447 1 chr1B.!!$F1 2446
5 TraesCS6B01G357100 chr1B 619178215 619179149 934 True 1471 1471 95.294 1 921 1 chr1B.!!$R2 920
6 TraesCS6B01G357100 chr1B 583574274 583575208 934 True 1459 1459 95.080 1 921 1 chr1B.!!$R1 920
7 TraesCS6B01G357100 chr3D 202623874 202625480 1606 True 2772 2772 97.822 842 2447 1 chr3D.!!$R1 1605
8 TraesCS6B01G357100 chr6D 430465177 430466784 1607 True 2769 2769 97.761 842 2447 1 chr6D.!!$R1 1605
9 TraesCS6B01G357100 chr5A 162143810 162145420 1610 True 2713 2713 97.083 838 2447 1 chr5A.!!$R1 1609
10 TraesCS6B01G357100 chr5A 420172524 420173458 934 False 1471 1471 95.294 1 921 1 chr5A.!!$F1 920
11 TraesCS6B01G357100 chr3B 201582155 201583761 1606 True 2695 2695 96.951 842 2447 1 chr3B.!!$R2 1605
12 TraesCS6B01G357100 chr3B 92225021 92226626 1605 True 2684 2684 96.826 842 2447 1 chr3B.!!$R1 1605
13 TraesCS6B01G357100 chr4D 97361819 97363424 1605 False 2678 2678 96.762 842 2447 1 chr4D.!!$F1 1605
14 TraesCS6B01G357100 chr4D 398050516 398051449 933 True 1476 1476 95.396 1 922 1 chr4D.!!$R1 921
15 TraesCS6B01G357100 chr5B 130584055 130584989 934 True 1482 1482 95.508 1 921 1 chr5B.!!$R1 920
16 TraesCS6B01G357100 chr3A 247671819 247672752 933 False 1474 1474 95.396 1 921 1 chr3A.!!$F1 920
17 TraesCS6B01G357100 chr3A 122209666 122210600 934 True 1465 1465 95.187 1 921 1 chr3A.!!$R1 920
18 TraesCS6B01G357100 chrUn 222870884 222871818 934 False 1459 1459 95.080 1 921 1 chrUn.!!$F2 920
19 TraesCS6B01G357100 chrUn 182441251 182442168 917 False 1371 1371 93.690 1 921 1 chrUn.!!$F1 920
20 TraesCS6B01G357100 chr7A 60195484 60196418 934 True 1459 1459 95.080 1 921 1 chr7A.!!$R1 920
21 TraesCS6B01G357100 chr2B 234505774 234506708 934 True 1454 1454 94.973 1 921 1 chr2B.!!$R1 920
22 TraesCS6B01G357100 chr2D 200949922 200950855 933 True 1448 1448 94.861 1 922 1 chr2D.!!$R1 921


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
676 688 0.396435 GATGGATGTGCCCGGTATCA 59.604 55.0 0.0 0.0 34.97 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1763 0.603569 AGCTCCACGAGTCAAACGAT 59.396 50.0 0.0 0.0 31.39 3.73 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.680555 GGCACCAACCGATACAATGGA 60.681 52.381 0.00 0.00 36.75 3.41
95 96 1.729284 CAATGGAAGTTGCATTGCCC 58.271 50.000 29.54 2.61 46.27 5.36
327 329 9.893305 ATGTACGTATAGTAACCGGTTAATAAC 57.107 33.333 31.40 26.34 37.02 1.89
329 331 9.382244 GTACGTATAGTAACCGGTTAATAACAG 57.618 37.037 31.40 25.60 37.02 3.16
385 387 1.079750 GTGTCCTCTCGGCCTTGAC 60.080 63.158 0.00 0.49 0.00 3.18
434 436 3.434309 TCACACATGAGAGGTGAGATCA 58.566 45.455 0.00 0.00 39.53 2.92
440 442 6.990939 ACACATGAGAGGTGAGATCAATTATG 59.009 38.462 0.00 0.00 39.53 1.90
606 608 7.806487 GGGTCTTTCGTTTTAAAAATAGGAGTG 59.194 37.037 1.31 0.00 0.00 3.51
627 630 2.752903 GTTCGGGTCTAGTTTACCGGTA 59.247 50.000 11.16 11.16 45.97 4.02
676 688 0.396435 GATGGATGTGCCCGGTATCA 59.604 55.000 0.00 0.00 34.97 2.15
718 730 4.092821 CGACGCAGGATTTCAATAGAACAA 59.907 41.667 0.00 0.00 32.39 2.83
761 774 3.171528 GGATAGGTACTTATTCCCGGCT 58.828 50.000 0.00 0.00 41.75 5.52
1097 1113 3.978759 CGAGAGTTCGTGCTATTGTTTG 58.021 45.455 0.00 0.00 41.84 2.93
1232 1248 7.016661 AGGTACTATTTATGATGTTCCTGGGAG 59.983 40.741 0.00 0.00 36.02 4.30
1287 1303 1.034292 GTTGGATCCTTGGAGCAGCC 61.034 60.000 14.23 1.32 37.10 4.85
1316 1332 6.814506 ACGACGTATAAGCTACAGGATAAT 57.185 37.500 0.00 0.00 0.00 1.28
1491 1507 7.244886 TCTTCCTCATTCAGTCATACTCAAA 57.755 36.000 0.00 0.00 0.00 2.69
1580 1597 4.287067 TCATACTCCCCCTTCATTCATAGC 59.713 45.833 0.00 0.00 0.00 2.97
1683 1700 4.039730 CCTCACCTCAGGTCGAATGAATAT 59.960 45.833 0.00 0.00 31.02 1.28
1724 1741 8.920174 TCAAATCAATAAGCCATGAATGAAGAT 58.080 29.630 0.00 0.00 0.00 2.40
1739 1756 2.912956 TGAAGATGTAGTGGGCCTTTCT 59.087 45.455 4.53 3.32 0.00 2.52
1746 1763 4.627015 TGTAGTGGGCCTTTCTCCTTATA 58.373 43.478 4.53 0.00 0.00 0.98
1771 1788 0.884514 TGACTCGTGGAGCTGAGAAG 59.115 55.000 5.84 0.00 36.11 2.85
1828 1845 1.074405 AGAACAAGCAAGGGATGAGCA 59.926 47.619 0.00 0.00 0.00 4.26
1838 1855 2.265739 GATGAGCACACGGGAGCA 59.734 61.111 10.41 0.00 32.55 4.26
1857 1874 1.452145 AAAATCTGTTGCGCCCACGT 61.452 50.000 4.18 0.00 42.83 4.49
1948 1966 1.380650 TTTTTCCCCTATGCCGCCC 60.381 57.895 0.00 0.00 0.00 6.13
2172 2190 1.404717 CGATCCCCTATTCTGCATCCG 60.405 57.143 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.620108 GCCATTTCTTCTCTTGGAGGCT 60.620 50.000 0.00 0.00 36.72 4.58
52 53 1.280421 CAGCTTCCCTGGAACTAGCTT 59.720 52.381 7.91 0.00 37.93 3.74
88 89 2.224113 ACTCAAAAGCAACTGGGCAATG 60.224 45.455 0.00 0.00 35.83 2.82
95 96 5.273170 TCAAATCGAACTCAAAAGCAACTG 58.727 37.500 0.00 0.00 0.00 3.16
327 329 7.094291 CGAGATTAGTATTAGGGACCCTTACTG 60.094 44.444 26.03 11.08 31.81 2.74
329 331 6.944862 TCGAGATTAGTATTAGGGACCCTTAC 59.055 42.308 20.96 16.09 34.61 2.34
416 418 6.990939 ACATAATTGATCTCACCTCTCATGTG 59.009 38.462 0.00 0.00 35.01 3.21
434 436 6.465464 CCTCCATCTGTCTCCATCACATAATT 60.465 42.308 0.00 0.00 0.00 1.40
440 442 2.364970 CTCCTCCATCTGTCTCCATCAC 59.635 54.545 0.00 0.00 0.00 3.06
494 496 5.508489 CCGTCTCAAGAGTTGTACACCTTAA 60.508 44.000 0.00 0.00 0.00 1.85
551 553 5.395682 AAATTATGGCGCAATGCTATGAT 57.604 34.783 10.83 0.00 45.40 2.45
606 608 1.546029 ACCGGTAAACTAGACCCGAAC 59.454 52.381 4.49 0.00 43.01 3.95
627 630 4.807304 ACTATTTCACTTTTCACACGACGT 59.193 37.500 0.00 0.00 0.00 4.34
632 635 8.128582 TCACATCAACTATTTCACTTTTCACAC 58.871 33.333 0.00 0.00 0.00 3.82
633 636 8.219546 TCACATCAACTATTTCACTTTTCACA 57.780 30.769 0.00 0.00 0.00 3.58
634 637 9.121517 CATCACATCAACTATTTCACTTTTCAC 57.878 33.333 0.00 0.00 0.00 3.18
676 688 3.063997 GTCGAGCCGATGTTTCATTGATT 59.936 43.478 0.67 0.00 38.42 2.57
718 730 5.479375 TCCCTCTACTACTGACGATGTTTTT 59.521 40.000 0.00 0.00 0.00 1.94
761 774 1.270305 GGAGCAGCAATGATACCGCTA 60.270 52.381 0.00 0.00 33.82 4.26
801 814 9.419297 GATTGATATTTCACATAAGCATTGCAT 57.581 29.630 11.91 0.71 0.00 3.96
821 834 6.142817 CGAAACGAAGAAGTTTTGGATTGAT 58.857 36.000 0.00 0.00 43.54 2.57
1097 1113 3.501062 AGCTAGGCGGTGAAAAGTTTTAC 59.499 43.478 0.00 0.83 0.00 2.01
1232 1248 0.535335 TTGACGATCCCTGGCTACAC 59.465 55.000 0.00 0.00 0.00 2.90
1287 1303 5.229469 CCTGTAGCTTATACGTCGTTTGAAG 59.771 44.000 1.78 6.24 0.00 3.02
1316 1332 8.316946 TCTCAGCAAATGAAGATTTCTCTAAGA 58.683 33.333 0.00 0.00 37.52 2.10
1328 1344 5.277876 GCATCCAGTATCTCAGCAAATGAAG 60.278 44.000 0.00 0.00 37.52 3.02
1491 1507 6.097129 TCCGGGTCAAACATTTCTTACTTTTT 59.903 34.615 0.00 0.00 0.00 1.94
1542 1558 5.445964 GGAGTATGAGGAAGGCCAATTTTA 58.554 41.667 5.01 0.00 36.29 1.52
1548 1564 0.694444 GGGGAGTATGAGGAAGGCCA 60.694 60.000 5.01 0.00 36.29 5.36
1683 1700 4.945411 TGATTTGATTGATCCCCCTTTCA 58.055 39.130 0.00 0.00 0.00 2.69
1724 1741 1.742308 AAGGAGAAAGGCCCACTACA 58.258 50.000 0.00 0.00 0.00 2.74
1739 1756 4.641541 TCCACGAGTCAAACGATATAAGGA 59.358 41.667 0.00 0.00 34.70 3.36
1746 1763 0.603569 AGCTCCACGAGTCAAACGAT 59.396 50.000 0.00 0.00 31.39 3.73
1771 1788 6.014925 ACTCTTTCCCTCTCTTTGAAGTAGAC 60.015 42.308 0.00 0.00 0.00 2.59
1828 1845 1.608590 CAACAGATTTTGCTCCCGTGT 59.391 47.619 0.00 0.00 0.00 4.49
1838 1855 1.285641 CGTGGGCGCAACAGATTTT 59.714 52.632 10.83 0.00 0.00 1.82
1857 1874 3.417101 ACCCATCAAGAAAACGTATGCA 58.583 40.909 0.00 0.00 0.00 3.96
1873 1890 8.704668 ACAAAAACTTTCTGAGAAATTACCCAT 58.295 29.630 8.23 0.00 0.00 4.00
1903 1921 7.056635 CACAACACCTAGGAATAGGAATCAAT 58.943 38.462 17.98 0.00 39.60 2.57
1948 1966 6.463049 CCAATCCTACTCCACTAGTACCAATG 60.463 46.154 0.00 0.00 39.80 2.82
2073 2091 9.994432 GTTCAGTTTGGAGATCTAACAATTATG 57.006 33.333 11.76 10.80 34.35 1.90
2074 2092 9.965902 AGTTCAGTTTGGAGATCTAACAATTAT 57.034 29.630 11.76 1.40 34.35 1.28
2075 2093 9.793259 AAGTTCAGTTTGGAGATCTAACAATTA 57.207 29.630 11.76 0.00 34.35 1.40
2172 2190 1.144936 CTGGGCCGTCTGATCTTCC 59.855 63.158 0.00 0.00 0.00 3.46
2254 2272 5.987347 CGTGGACCAAAAGACTAAGAAACTA 59.013 40.000 0.00 0.00 0.00 2.24



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

AutoCloner maintained by Alex Coulton.