Multiple sequence alignment - TraesCS6B01G268800

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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 TraesCS6B01G268800 chr6B 100.000 2213 0 0 1 2213 483464128 483466340 0.000000e+00 4087
1 TraesCS6B01G268800 chr6B 94.834 1510 72 3 4 1507 177081545 177080036 0.000000e+00 2351
2 TraesCS6B01G268800 chr6B 94.707 529 27 1 1686 2213 446182350 446182878 0.000000e+00 821
3 TraesCS6B01G268800 chr4A 95.207 1690 72 5 1 1683 552223073 552221386 0.000000e+00 2663
4 TraesCS6B01G268800 chr4A 93.465 1515 90 6 1 1507 465121950 465123463 0.000000e+00 2241
5 TraesCS6B01G268800 chr4A 92.415 791 39 6 903 1685 653011942 653011165 0.000000e+00 1109
6 TraesCS6B01G268800 chr4D 95.496 1643 66 3 51 1685 45248080 45249722 0.000000e+00 2617
7 TraesCS6B01G268800 chr2A 94.103 1662 88 7 1 1655 591092070 591093728 0.000000e+00 2518
8 TraesCS6B01G268800 chr5B 93.012 1660 95 9 3 1655 41798414 41796769 0.000000e+00 2403
9 TraesCS6B01G268800 chr5B 94.329 529 28 2 1686 2213 285440250 285440777 0.000000e+00 809
10 TraesCS6B01G268800 chr5B 80.476 210 36 5 1541 1748 684237148 684237354 2.940000e-34 156
11 TraesCS6B01G268800 chr3A 94.672 1539 75 4 1 1533 664911320 664912857 0.000000e+00 2381
12 TraesCS6B01G268800 chr3A 88.511 235 24 3 1454 1686 298800590 298800823 4.650000e-72 281
13 TraesCS6B01G268800 chr1B 94.775 1512 71 4 4 1507 27643374 27644885 0.000000e+00 2348
14 TraesCS6B01G268800 chr1B 91.544 272 16 4 1421 1685 87146722 87146993 3.470000e-98 368
15 TraesCS6B01G268800 chr4B 94.044 1511 84 3 4 1508 569527595 569529105 0.000000e+00 2287
16 TraesCS6B01G268800 chr2B 92.449 1576 106 7 4 1570 686782477 686784048 0.000000e+00 2239
17 TraesCS6B01G268800 chr2B 88.136 236 25 3 1454 1687 50248593 50248827 6.020000e-71 278
18 TraesCS6B01G268800 chr3B 95.463 529 23 1 1686 2213 143146586 143146058 0.000000e+00 843
19 TraesCS6B01G268800 chr3B 94.896 529 26 1 1686 2213 193927369 193927897 0.000000e+00 826
20 TraesCS6B01G268800 chr7B 94.707 529 27 1 1686 2213 296826659 296826131 0.000000e+00 821
21 TraesCS6B01G268800 chr7B 94.518 529 28 1 1686 2213 136929314 136929842 0.000000e+00 815
22 TraesCS6B01G268800 chr7B 90.043 231 20 3 1457 1685 641951348 641951577 1.660000e-76 296
23 TraesCS6B01G268800 chr5D 94.518 529 28 1 1686 2213 502814788 502814260 0.000000e+00 815
24 TraesCS6B01G268800 chr5D 94.140 529 30 1 1686 2213 300719902 300719374 0.000000e+00 804
25 TraesCS6B01G268800 chr5D 94.140 529 30 1 1686 2213 508540880 508541408 0.000000e+00 804
26 TraesCS6B01G268800 chr7D 88.672 256 25 3 1432 1685 561631868 561631615 2.130000e-80 309
27 TraesCS6B01G268800 chr6A 88.511 235 24 3 1454 1686 585283 585516 4.650000e-72 281


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 TraesCS6B01G268800 chr6B 483464128 483466340 2212 False 4087 4087 100.000 1 2213 1 chr6B.!!$F2 2212
1 TraesCS6B01G268800 chr6B 177080036 177081545 1509 True 2351 2351 94.834 4 1507 1 chr6B.!!$R1 1503
2 TraesCS6B01G268800 chr6B 446182350 446182878 528 False 821 821 94.707 1686 2213 1 chr6B.!!$F1 527
3 TraesCS6B01G268800 chr4A 552221386 552223073 1687 True 2663 2663 95.207 1 1683 1 chr4A.!!$R1 1682
4 TraesCS6B01G268800 chr4A 465121950 465123463 1513 False 2241 2241 93.465 1 1507 1 chr4A.!!$F1 1506
5 TraesCS6B01G268800 chr4A 653011165 653011942 777 True 1109 1109 92.415 903 1685 1 chr4A.!!$R2 782
6 TraesCS6B01G268800 chr4D 45248080 45249722 1642 False 2617 2617 95.496 51 1685 1 chr4D.!!$F1 1634
7 TraesCS6B01G268800 chr2A 591092070 591093728 1658 False 2518 2518 94.103 1 1655 1 chr2A.!!$F1 1654
8 TraesCS6B01G268800 chr5B 41796769 41798414 1645 True 2403 2403 93.012 3 1655 1 chr5B.!!$R1 1652
9 TraesCS6B01G268800 chr5B 285440250 285440777 527 False 809 809 94.329 1686 2213 1 chr5B.!!$F1 527
10 TraesCS6B01G268800 chr3A 664911320 664912857 1537 False 2381 2381 94.672 1 1533 1 chr3A.!!$F2 1532
11 TraesCS6B01G268800 chr1B 27643374 27644885 1511 False 2348 2348 94.775 4 1507 1 chr1B.!!$F1 1503
12 TraesCS6B01G268800 chr4B 569527595 569529105 1510 False 2287 2287 94.044 4 1508 1 chr4B.!!$F1 1504
13 TraesCS6B01G268800 chr2B 686782477 686784048 1571 False 2239 2239 92.449 4 1570 1 chr2B.!!$F2 1566
14 TraesCS6B01G268800 chr3B 143146058 143146586 528 True 843 843 95.463 1686 2213 1 chr3B.!!$R1 527
15 TraesCS6B01G268800 chr3B 193927369 193927897 528 False 826 826 94.896 1686 2213 1 chr3B.!!$F1 527
16 TraesCS6B01G268800 chr7B 296826131 296826659 528 True 821 821 94.707 1686 2213 1 chr7B.!!$R1 527
17 TraesCS6B01G268800 chr7B 136929314 136929842 528 False 815 815 94.518 1686 2213 1 chr7B.!!$F1 527
18 TraesCS6B01G268800 chr5D 502814260 502814788 528 True 815 815 94.518 1686 2213 1 chr5D.!!$R2 527
19 TraesCS6B01G268800 chr5D 300719374 300719902 528 True 804 804 94.140 1686 2213 1 chr5D.!!$R1 527
20 TraesCS6B01G268800 chr5D 508540880 508541408 528 False 804 804 94.140 1686 2213 1 chr5D.!!$F1 527

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
313 314 1.305213 ACGGGGATTTGGCAAGCAT 60.305 52.632 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2029 0.251916 TCTGGTAAAGGGGCGATGTG 59.748 55.0 0.0 0.0 0.0 3.21 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
27 28 4.214971 AGTCTACAAAGTTCATGCTTGCTG 59.785 41.667 0.00 0.00 0.00 4.41
33 34 2.507484 AGTTCATGCTTGCTGCTGTAA 58.493 42.857 0.00 0.00 43.37 2.41
114 115 7.560991 TCCTGTTGTTATTTGCTCCATATTGAT 59.439 33.333 0.00 0.00 0.00 2.57
183 184 4.752101 TGCTAGCAAGTTCAAACTCTCTTC 59.248 41.667 16.84 0.00 38.57 2.87
192 193 7.913674 AGTTCAAACTCTCTTCAATGGATAC 57.086 36.000 0.00 0.00 32.86 2.24
243 244 9.955208 ATGTTATGAATATGTTGTATGCAAGTG 57.045 29.630 0.00 0.00 34.94 3.16
313 314 1.305213 ACGGGGATTTGGCAAGCAT 60.305 52.632 0.00 0.00 0.00 3.79
318 319 2.749076 GGGGATTTGGCAAGCATTTTTC 59.251 45.455 0.00 0.00 0.00 2.29
323 324 6.128200 GGGATTTGGCAAGCATTTTTCTAAAG 60.128 38.462 0.00 0.00 0.00 1.85
362 363 3.435327 GCTCCGACATGATTTTGTGTGTA 59.565 43.478 0.00 0.00 0.00 2.90
415 416 3.003763 GAGGAACCTCCCAGGCGT 61.004 66.667 9.50 0.00 39.63 5.68
489 490 2.276306 GACGTACGAGGCGACGAC 60.276 66.667 24.41 0.00 41.60 4.34
492 493 3.490759 GTACGAGGCGACGACCGA 61.491 66.667 16.72 0.44 41.76 4.69
567 568 1.765314 GTAGCACCTGGTGATCCTGAT 59.235 52.381 30.23 3.21 35.23 2.90
666 667 1.543802 CTTATGCCTTGCCGTTGGAAA 59.456 47.619 0.00 0.00 0.00 3.13
679 680 4.749598 GCCGTTGGAAAAATGAATTCAAGT 59.250 37.500 13.09 0.28 0.00 3.16
698 699 3.482436 AGTTTTTGCAGGATCCAACGTA 58.518 40.909 15.82 0.00 0.00 3.57
761 762 9.173021 AGAGGATACGAATCATATCTCTTGTAG 57.827 37.037 0.00 0.00 46.39 2.74
866 867 7.963532 AGTATCTGTAGTTTCCAACTCTGAAA 58.036 34.615 0.00 0.00 41.77 2.69
1009 1010 1.076024 ACTTTCCTGACATGGGCACAT 59.924 47.619 0.00 0.00 37.99 3.21
1383 1389 3.409026 AAGATGGTTCTGTGACCTGAC 57.591 47.619 0.00 0.00 40.47 3.51
1405 1411 6.711194 TGACCTTATTTTTCATTGGACGTGTA 59.289 34.615 0.00 0.00 0.00 2.90
1435 1441 5.068987 TGGAAGCAACTGCATCTAACTTTTT 59.931 36.000 4.22 0.00 45.16 1.94
1469 1483 2.814805 AGTTAGTAGTAGCGTGGGGA 57.185 50.000 0.00 0.00 0.00 4.81
1517 1577 0.388907 TAGTAGCGCGGGTGTGAAAC 60.389 55.000 8.83 0.00 37.35 2.78
1617 1677 8.097078 ACTATTAGTTGTAGTGCGATACTAGG 57.903 38.462 0.00 0.00 42.37 3.02
1793 1853 4.084287 ACTGTAGGACACGACCAATAAGA 58.916 43.478 0.00 0.00 0.00 2.10
1864 1925 3.900601 CCACTCTATAGGATGGCAGACTT 59.099 47.826 9.46 0.00 0.00 3.01
1865 1926 4.262377 CCACTCTATAGGATGGCAGACTTG 60.262 50.000 9.46 0.00 0.00 3.16
1927 1988 4.039973 TGGACGACACTTGAAGGAAGTTAT 59.960 41.667 0.00 0.00 42.70 1.89
1964 2025 3.196039 TCGAAATACCAAGATTCACCGGA 59.804 43.478 9.46 0.00 0.00 5.14
1968 2029 0.037734 ACCAAGATTCACCGGAACCC 59.962 55.000 9.46 0.00 35.46 4.11
1995 2056 2.552367 CCCCTTTACCAGAAGAGGAGT 58.448 52.381 0.00 0.00 26.52 3.85
2112 2173 2.441532 GCATGGCAGCCCACATCT 60.442 61.111 9.64 0.00 45.77 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.084546 CTAGGGGCACAAACTTACAGC 58.915 52.381 0.00 0.00 0.00 4.40
33 34 0.895559 GCAAGCTAGGGGCACAAACT 60.896 55.000 0.00 0.00 44.79 2.66
130 131 7.675619 TCTCCTAACTGCATCCATCTCATTATA 59.324 37.037 0.00 0.00 0.00 0.98
183 184 6.872628 AACTGCACTATGATGTATCCATTG 57.127 37.500 0.00 0.00 0.00 2.82
192 193 5.752472 CACTTCTCCTAACTGCACTATGATG 59.248 44.000 0.00 0.00 0.00 3.07
243 244 6.578919 GCTGAACTTTTTCTAATACACACTGC 59.421 38.462 0.00 0.00 32.36 4.40
313 314 9.974980 AAATCGCCATAAACTTCTTTAGAAAAA 57.025 25.926 0.00 0.00 33.07 1.94
318 319 6.555315 AGCAAATCGCCATAAACTTCTTTAG 58.445 36.000 0.00 0.00 44.04 1.85
323 324 3.695816 GGAGCAAATCGCCATAAACTTC 58.304 45.455 0.00 0.00 44.04 3.01
362 363 5.419788 TCATCTTGTTGAGCTGCCAAAATAT 59.580 36.000 0.00 0.00 0.00 1.28
415 416 0.895530 CTTGGACGGAGGAGTTGCTA 59.104 55.000 0.00 0.00 0.00 3.49
511 512 1.750018 CCTCATCGGCATGTTGGCA 60.750 57.895 0.00 0.00 43.94 4.92
532 533 1.142870 TGCTACCTGTTTGTGGCTCTT 59.857 47.619 1.38 0.00 42.57 2.85
567 568 4.692625 GCAGAATTCTGAAGCACTCTGTTA 59.307 41.667 34.43 0.00 46.59 2.41
666 667 7.173735 GGATCCTGCAAAAACTTGAATTCATTT 59.826 33.333 9.40 5.09 0.00 2.32
679 680 3.126171 CGATACGTTGGATCCTGCAAAAA 59.874 43.478 14.23 0.00 26.96 1.94
698 699 1.153289 CACAGCCAGCCTTAGCGAT 60.153 57.895 0.00 0.00 46.67 4.58
761 762 3.374988 TGTTCCATGAAACGATCAGATGC 59.625 43.478 0.00 0.00 42.53 3.91
965 966 5.235616 TGAAAACTTGTTAGTTAGCGTCCAG 59.764 40.000 0.00 0.00 43.74 3.86
1009 1010 0.604073 TAGTCCGCGTCAATCAACCA 59.396 50.000 4.92 0.00 0.00 3.67
1038 1040 1.072159 GAAGAGCACACTGCCCACT 59.928 57.895 0.00 0.00 46.52 4.00
1383 1389 7.910162 CAGATACACGTCCAATGAAAAATAAGG 59.090 37.037 0.00 0.00 0.00 2.69
1405 1411 2.502142 TGCAGTTGCTTCCATCAGAT 57.498 45.000 5.62 0.00 42.66 2.90
1469 1483 8.059798 TCCTAAATACTAGTAGCGAGTTGTTT 57.940 34.615 8.85 4.25 0.00 2.83
1517 1577 2.434884 CCACCCACGCTACTGCTG 60.435 66.667 0.00 0.00 36.97 4.41
1550 1610 2.928116 CCCGCACTACTACTAACTTTGC 59.072 50.000 0.00 0.00 0.00 3.68
1606 1666 2.637589 CGCGCTCCTAGTATCGCA 59.362 61.111 5.56 0.00 46.95 5.10
1632 1692 3.541632 GGTAAAATGGCTACTAGCAGCA 58.458 45.455 16.76 3.69 44.75 4.41
1793 1853 5.276440 AGAGAAGAGTGACCTATGGTTCAT 58.724 41.667 0.00 0.00 35.25 2.57
1864 1925 2.165437 GGTTGTGCAAACTTGTTCCTCA 59.835 45.455 10.28 0.00 0.00 3.86
1865 1926 2.794631 CGGTTGTGCAAACTTGTTCCTC 60.795 50.000 10.28 0.00 0.00 3.71
1878 1939 0.517316 GTGTCTTCATCCGGTTGTGC 59.483 55.000 12.19 2.78 0.00 4.57
1927 1988 8.076910 TGGTATTTCGATGTTTAGGTACCTAA 57.923 34.615 27.27 27.27 36.81 2.69
1964 2025 0.323087 GTAAAGGGGCGATGTGGGTT 60.323 55.000 0.00 0.00 0.00 4.11
1968 2029 0.251916 TCTGGTAAAGGGGCGATGTG 59.748 55.000 0.00 0.00 0.00 3.21
1995 2056 4.641396 ACTTGAACTCGAATCATCCAACA 58.359 39.130 1.78 0.00 0.00 3.33
2112 2173 1.224315 CTCCAATGCGTCCCATGGA 59.776 57.895 15.22 0.00 33.49 3.41


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

AutoCloner maintained by Alex Coulton.