Multiple sequence alignment - TraesCS5D01G283700

Loading Multiple Alignment...

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 TraesCS5D01G283700 chr5D 100.000 2375 0 0 1 2375 384512084 384509710 0.000000e+00 4386.0
1 TraesCS5D01G283700 chr5D 94.867 2377 87 13 1 2348 29767653 29765283 0.000000e+00 3681.0
2 TraesCS5D01G283700 chr5D 96.106 1515 51 6 834 2344 401783433 401784943 0.000000e+00 2464.0
3 TraesCS5D01G283700 chr1D 96.213 2350 68 9 1 2347 336730174 336727843 0.000000e+00 3827.0
4 TraesCS5D01G283700 chr1D 96.734 888 29 0 1 888 463793609 463792722 0.000000e+00 1480.0
5 TraesCS5D01G283700 chr1D 100.000 28 0 0 2348 2375 8689386 8689359 4.000000e-03 52.8
6 TraesCS5D01G283700 chr1D 100.000 28 0 0 2348 2375 208624546 208624519 4.000000e-03 52.8
7 TraesCS5D01G283700 chr7D 95.851 2362 81 8 1 2348 51238850 51236492 0.000000e+00 3803.0
8 TraesCS5D01G283700 chr7D 92.591 1984 81 14 1 1968 103541445 103543378 0.000000e+00 2789.0
9 TraesCS5D01G283700 chr7D 94.927 749 33 4 1603 2347 79228187 79228934 0.000000e+00 1168.0
10 TraesCS5D01G283700 chr6D 95.095 2365 74 10 1 2347 297171464 297169124 0.000000e+00 3687.0
11 TraesCS5D01G283700 chr6D 95.360 819 30 7 1531 2347 446362877 446362065 0.000000e+00 1295.0
12 TraesCS5D01G283700 chr3A 92.444 2369 121 31 1 2347 702240704 702243036 0.000000e+00 3330.0
13 TraesCS5D01G283700 chr3A 88.321 137 14 2 2213 2348 669129361 669129226 1.890000e-36 163.0
14 TraesCS5D01G283700 chr2D 96.645 1550 36 3 1 1550 239256901 239258434 0.000000e+00 2560.0
15 TraesCS5D01G283700 chr2D 93.728 1435 62 19 925 2347 645235747 645234329 0.000000e+00 2126.0
16 TraesCS5D01G283700 chr2D 92.593 810 42 12 1549 2347 239258381 239259183 0.000000e+00 1147.0
17 TraesCS5D01G283700 chr4A 96.294 1376 48 3 1 1375 433607489 433606116 0.000000e+00 2255.0
18 TraesCS5D01G283700 chr4A 95.858 1376 56 1 1 1375 192323385 192322010 0.000000e+00 2224.0
19 TraesCS5D01G283700 chr2A 97.055 883 26 0 3 885 610789278 610790160 0.000000e+00 1487.0
20 TraesCS5D01G283700 chr4D 96.840 886 28 0 3 888 236672621 236671736 0.000000e+00 1482.0
21 TraesCS5D01G283700 chr4D 100.000 28 0 0 2348 2375 145228837 145228864 4.000000e-03 52.8
22 TraesCS5D01G283700 chr4D 100.000 28 0 0 2348 2375 328903667 328903694 4.000000e-03 52.8
23 TraesCS5D01G283700 chr4D 100.000 28 0 0 2348 2375 443988153 443988180 4.000000e-03 52.8
24 TraesCS5D01G283700 chr7A 96.836 885 28 0 1 885 56073933 56074817 0.000000e+00 1480.0
25 TraesCS5D01G283700 chr3D 92.112 824 36 15 1531 2347 57608750 57609551 0.000000e+00 1134.0
26 TraesCS5D01G283700 chr3D 100.000 28 0 0 2348 2375 75431714 75431687 4.000000e-03 52.8
27 TraesCS5D01G283700 chr3D 100.000 28 0 0 2348 2375 142929007 142929034 4.000000e-03 52.8
28 TraesCS5D01G283700 chr3D 100.000 28 0 0 2348 2375 257952943 257952970 4.000000e-03 52.8
29 TraesCS5D01G283700 chr3D 100.000 28 0 0 2348 2375 346992052 346992025 4.000000e-03 52.8


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 TraesCS5D01G283700 chr5D 384509710 384512084 2374 True 4386.0 4386 100.000 1 2375 1 chr5D.!!$R2 2374
1 TraesCS5D01G283700 chr5D 29765283 29767653 2370 True 3681.0 3681 94.867 1 2348 1 chr5D.!!$R1 2347
2 TraesCS5D01G283700 chr5D 401783433 401784943 1510 False 2464.0 2464 96.106 834 2344 1 chr5D.!!$F1 1510
3 TraesCS5D01G283700 chr1D 336727843 336730174 2331 True 3827.0 3827 96.213 1 2347 1 chr1D.!!$R3 2346
4 TraesCS5D01G283700 chr1D 463792722 463793609 887 True 1480.0 1480 96.734 1 888 1 chr1D.!!$R4 887
5 TraesCS5D01G283700 chr7D 51236492 51238850 2358 True 3803.0 3803 95.851 1 2348 1 chr7D.!!$R1 2347
6 TraesCS5D01G283700 chr7D 103541445 103543378 1933 False 2789.0 2789 92.591 1 1968 1 chr7D.!!$F2 1967
7 TraesCS5D01G283700 chr7D 79228187 79228934 747 False 1168.0 1168 94.927 1603 2347 1 chr7D.!!$F1 744
8 TraesCS5D01G283700 chr6D 297169124 297171464 2340 True 3687.0 3687 95.095 1 2347 1 chr6D.!!$R1 2346
9 TraesCS5D01G283700 chr6D 446362065 446362877 812 True 1295.0 1295 95.360 1531 2347 1 chr6D.!!$R2 816
10 TraesCS5D01G283700 chr3A 702240704 702243036 2332 False 3330.0 3330 92.444 1 2347 1 chr3A.!!$F1 2346
11 TraesCS5D01G283700 chr2D 645234329 645235747 1418 True 2126.0 2126 93.728 925 2347 1 chr2D.!!$R1 1422
12 TraesCS5D01G283700 chr2D 239256901 239259183 2282 False 1853.5 2560 94.619 1 2347 2 chr2D.!!$F1 2346
13 TraesCS5D01G283700 chr4A 433606116 433607489 1373 True 2255.0 2255 96.294 1 1375 1 chr4A.!!$R2 1374
14 TraesCS5D01G283700 chr4A 192322010 192323385 1375 True 2224.0 2224 95.858 1 1375 1 chr4A.!!$R1 1374
15 TraesCS5D01G283700 chr2A 610789278 610790160 882 False 1487.0 1487 97.055 3 885 1 chr2A.!!$F1 882
16 TraesCS5D01G283700 chr4D 236671736 236672621 885 True 1482.0 1482 96.840 3 888 1 chr4D.!!$R1 885
17 TraesCS5D01G283700 chr7A 56073933 56074817 884 False 1480.0 1480 96.836 1 885 1 chr7A.!!$F1 884
18 TraesCS5D01G283700 chr3D 57608750 57609551 801 False 1134.0 1134 92.112 1531 2347 1 chr3D.!!$F1 816

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
514 516 3.132646 TGTTTGATTCACAGCCAGCTTTT 59.867 39.13 0.0 0.0 0.0 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 1977 0.179174 GTCCGCTATTGTTTTGGGCG 60.179 55.0 0.0 0.0 44.48 6.13 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
221 222 6.642950 AGAAAAAGTCGTGTACAATCAGAGAG 59.357 38.462 0.00 0.0 0.00 3.20
514 516 3.132646 TGTTTGATTCACAGCCAGCTTTT 59.867 39.130 0.00 0.0 0.00 2.27
733 766 7.170965 AGCCATCTTATATAGAACCACCATTG 58.829 38.462 0.00 0.0 36.22 2.82
1049 1085 3.217626 CAGAAGGTGAAGAGCCAAAGTT 58.782 45.455 0.00 0.0 0.00 2.66
1052 1088 3.018423 AGGTGAAGAGCCAAAGTTTGT 57.982 42.857 14.36 0.0 0.00 2.83
1401 1437 4.265893 TGTGCAGTTTGTCTTTGAACCTA 58.734 39.130 0.00 0.0 0.00 3.08
1445 1481 5.514500 AGTTTGAAGGCTGGGAAGTTATA 57.486 39.130 0.00 0.0 0.00 0.98
1621 1675 4.698201 TGGAACCAGTGAACTTGTGATA 57.302 40.909 0.00 0.0 0.00 2.15
1893 1992 2.324860 GTTGTCGCCCAAAACAATAGC 58.675 47.619 0.00 0.0 37.67 2.97
2067 2180 4.124238 CCGGGCTGATTCTATTTTACGAA 58.876 43.478 0.00 0.0 0.00 3.85
2091 2204 5.295045 ACTTTTCGTTTGGTCGTAATTCTGT 59.705 36.000 0.00 0.0 0.00 3.41
2201 2316 4.771590 TTGGTCATAAACGTCTACGACT 57.228 40.909 9.86 0.0 43.02 4.18
2234 2349 8.631480 AAGAAAGGTCGTTAATTCCAGTTTAT 57.369 30.769 0.00 0.0 0.00 1.40
2255 2370 0.178924 AGGGCCAGCTTTTGACCATT 60.179 50.000 6.18 0.0 29.37 3.16
2315 2430 6.560003 ATGACCATTCAGTGACCAATAGTA 57.440 37.500 0.00 0.0 34.35 1.82
2319 2434 4.572389 CCATTCAGTGACCAATAGTAGTGC 59.428 45.833 0.00 0.0 0.00 4.40
2348 2463 7.986085 AAGTTGACATATTTCTTGTAGTGCT 57.014 32.000 0.00 0.0 0.00 4.40
2349 2464 7.602517 AGTTGACATATTTCTTGTAGTGCTC 57.397 36.000 0.00 0.0 0.00 4.26
2350 2465 6.311445 AGTTGACATATTTCTTGTAGTGCTCG 59.689 38.462 0.00 0.0 0.00 5.03
2351 2466 5.961272 TGACATATTTCTTGTAGTGCTCGA 58.039 37.500 0.00 0.0 0.00 4.04
2352 2467 6.394809 TGACATATTTCTTGTAGTGCTCGAA 58.605 36.000 0.00 0.0 0.00 3.71
2353 2468 6.871492 TGACATATTTCTTGTAGTGCTCGAAA 59.129 34.615 0.00 0.0 0.00 3.46
2354 2469 7.386573 TGACATATTTCTTGTAGTGCTCGAAAA 59.613 33.333 0.00 0.0 0.00 2.29
2355 2470 7.743104 ACATATTTCTTGTAGTGCTCGAAAAG 58.257 34.615 0.00 0.0 0.00 2.27
2366 2481 0.992802 CTCGAAAAGCTACGTCAGGC 59.007 55.000 0.00 0.0 0.00 4.85
2367 2482 0.389426 TCGAAAAGCTACGTCAGGCC 60.389 55.000 0.00 0.0 0.00 5.19
2368 2483 0.669318 CGAAAAGCTACGTCAGGCCA 60.669 55.000 5.01 0.0 0.00 5.36
2369 2484 0.796927 GAAAAGCTACGTCAGGCCAC 59.203 55.000 5.01 0.0 0.00 5.01
2370 2485 0.605589 AAAAGCTACGTCAGGCCACC 60.606 55.000 5.01 0.0 0.00 4.61
2371 2486 1.481056 AAAGCTACGTCAGGCCACCT 61.481 55.000 5.01 0.0 0.00 4.00
2372 2487 0.613853 AAGCTACGTCAGGCCACCTA 60.614 55.000 5.01 0.0 29.64 3.08
2373 2488 0.397254 AGCTACGTCAGGCCACCTAT 60.397 55.000 5.01 0.0 29.64 2.57
2374 2489 0.464452 GCTACGTCAGGCCACCTATT 59.536 55.000 5.01 0.0 29.64 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
221 222 1.275291 TGTGTAGTGCCTGGAACTAGC 59.725 52.381 15.09 11.30 30.90 3.42
396 397 0.879090 GGGTGGCCTTAAACAAGTCG 59.121 55.000 3.32 0.00 0.00 4.18
514 516 5.900865 TCATCAAAGCATCAAACAGCATA 57.099 34.783 0.00 0.00 0.00 3.14
1049 1085 6.526325 CACTTCTTCGACAATTTCAACAACAA 59.474 34.615 0.00 0.00 0.00 2.83
1052 1088 5.034152 GCACTTCTTCGACAATTTCAACAA 58.966 37.500 0.00 0.00 0.00 2.83
1197 1233 1.550072 GCTTGAAGCTCAGACCTCTCT 59.450 52.381 10.44 0.00 38.45 3.10
1401 1437 3.603532 ACGACAAACTGCATCAGATCAT 58.396 40.909 0.29 0.00 35.18 2.45
1445 1481 5.505324 GCATAAGTTCACGACCTACTACGAT 60.505 44.000 0.00 0.00 0.00 3.73
1621 1675 2.027377 AGCTTCAGAACTGCACATAGCT 60.027 45.455 0.00 0.00 45.94 3.32
1804 1901 4.407296 TGGATGCAACCTTTTACCAACTTT 59.593 37.500 14.77 0.00 0.00 2.66
1819 1917 5.704978 GGCCTTTTTATTTTCTTGGATGCAA 59.295 36.000 0.00 0.00 0.00 4.08
1878 1977 0.179174 GTCCGCTATTGTTTTGGGCG 60.179 55.000 0.00 0.00 44.48 6.13
1968 2074 6.455360 TTTCTCTTTGTTTTGCTCATCTGT 57.545 33.333 0.00 0.00 0.00 3.41
2028 2141 1.376812 GGTCCATTTCGGCCGTCTT 60.377 57.895 27.15 7.91 33.14 3.01
2067 2180 5.295045 ACAGAATTACGACCAAACGAAAAGT 59.705 36.000 0.00 0.00 37.03 2.66
2074 2187 3.492011 ACGTGACAGAATTACGACCAAAC 59.508 43.478 4.79 0.00 40.01 2.93
2091 2204 2.661537 CGTGGCAAGCTGACGTGA 60.662 61.111 0.00 0.00 0.00 4.35
2201 2316 7.551617 GGAATTAACGACCTTTCTTCTGGAATA 59.448 37.037 0.00 0.00 33.53 1.75
2234 2349 1.228552 GGTCAAAAGCTGGCCCTCA 60.229 57.895 0.00 0.00 44.93 3.86
2315 2430 8.671921 CAAGAAATATGTCAACTTATGAGCACT 58.328 33.333 0.00 0.00 39.19 4.40
2348 2463 0.389426 GGCCTGACGTAGCTTTTCGA 60.389 55.000 11.42 0.00 0.00 3.71
2349 2464 0.669318 TGGCCTGACGTAGCTTTTCG 60.669 55.000 3.32 0.00 0.00 3.46
2350 2465 0.796927 GTGGCCTGACGTAGCTTTTC 59.203 55.000 3.32 0.00 0.00 2.29
2351 2466 0.605589 GGTGGCCTGACGTAGCTTTT 60.606 55.000 3.32 0.00 0.00 2.27
2352 2467 1.003718 GGTGGCCTGACGTAGCTTT 60.004 57.895 3.32 0.00 0.00 3.51
2353 2468 0.613853 TAGGTGGCCTGACGTAGCTT 60.614 55.000 3.32 0.00 34.61 3.74
2354 2469 0.397254 ATAGGTGGCCTGACGTAGCT 60.397 55.000 3.32 0.00 34.61 3.32
2355 2470 0.464452 AATAGGTGGCCTGACGTAGC 59.536 55.000 3.32 0.00 34.61 3.58


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

AutoCloner maintained by Alex Coulton.