Multiple sequence alignment - TraesCS5B01G262600

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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 TraesCS5B01G262600 chr5B 100.000 2538 0 0 1 2538 447277045 447279582 0.000000e+00 4687
1 TraesCS5B01G262600 chr5B 98.572 1961 24 2 580 2538 446268499 446266541 0.000000e+00 3463
2 TraesCS5B01G262600 chr7A 91.126 586 34 6 1 577 466868372 466868948 0.000000e+00 778
3 TraesCS5B01G262600 chr7A 91.126 586 33 7 1 576 470684436 470683860 0.000000e+00 776
4 TraesCS5B01G262600 chr7A 90.801 587 34 7 1 577 545166055 545165479 0.000000e+00 767
5 TraesCS5B01G262600 chr7A 90.816 588 33 8 1 577 548906503 548905926 0.000000e+00 767
6 TraesCS5B01G262600 chr7A 90.492 589 35 8 1 578 549463302 549462724 0.000000e+00 758
7 TraesCS5B01G262600 chr7A 90.323 589 35 9 1 578 553946822 553947399 0.000000e+00 752
8 TraesCS5B01G262600 chr7A 90.411 584 36 7 4 577 544696513 544695940 0.000000e+00 750
9 TraesCS5B01G262600 chr7A 88.567 586 36 6 1 577 469827865 469828428 0.000000e+00 682
10 TraesCS5B01G262600 chr6D 91.126 586 33 7 1 577 145011175 145011750 0.000000e+00 776
11 TraesCS5B01G262600 chr6B 90.785 586 33 9 1 577 240907544 240908117 0.000000e+00 763
12 TraesCS5B01G262600 chr6B 89.643 589 39 9 1 579 328535526 328534950 0.000000e+00 730
13 TraesCS5B01G262600 chr1B 90.444 586 29 11 1 577 334347047 334347614 0.000000e+00 747
14 TraesCS5B01G262600 chr7B 86.382 492 33 10 1 481 172370634 172371102 8.100000e-140 507
15 TraesCS5B01G262600 chr7B 96.667 60 2 0 519 578 172371102 172371161 1.610000e-17 100


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 TraesCS5B01G262600 chr5B 447277045 447279582 2537 False 4687.0 4687 100.0000 1 2538 1 chr5B.!!$F1 2537
1 TraesCS5B01G262600 chr5B 446266541 446268499 1958 True 3463.0 3463 98.5720 580 2538 1 chr5B.!!$R1 1958
2 TraesCS5B01G262600 chr7A 466868372 466868948 576 False 778.0 778 91.1260 1 577 1 chr7A.!!$F1 576
3 TraesCS5B01G262600 chr7A 470683860 470684436 576 True 776.0 776 91.1260 1 576 1 chr7A.!!$R1 575
4 TraesCS5B01G262600 chr7A 545165479 545166055 576 True 767.0 767 90.8010 1 577 1 chr7A.!!$R3 576
5 TraesCS5B01G262600 chr7A 548905926 548906503 577 True 767.0 767 90.8160 1 577 1 chr7A.!!$R4 576
6 TraesCS5B01G262600 chr7A 549462724 549463302 578 True 758.0 758 90.4920 1 578 1 chr7A.!!$R5 577
7 TraesCS5B01G262600 chr7A 553946822 553947399 577 False 752.0 752 90.3230 1 578 1 chr7A.!!$F3 577
8 TraesCS5B01G262600 chr7A 544695940 544696513 573 True 750.0 750 90.4110 4 577 1 chr7A.!!$R2 573
9 TraesCS5B01G262600 chr7A 469827865 469828428 563 False 682.0 682 88.5670 1 577 1 chr7A.!!$F2 576
10 TraesCS5B01G262600 chr6D 145011175 145011750 575 False 776.0 776 91.1260 1 577 1 chr6D.!!$F1 576
11 TraesCS5B01G262600 chr6B 240907544 240908117 573 False 763.0 763 90.7850 1 577 1 chr6B.!!$F1 576
12 TraesCS5B01G262600 chr6B 328534950 328535526 576 True 730.0 730 89.6430 1 579 1 chr6B.!!$R1 578
13 TraesCS5B01G262600 chr1B 334347047 334347614 567 False 747.0 747 90.4440 1 577 1 chr1B.!!$F1 576
14 TraesCS5B01G262600 chr7B 172370634 172371161 527 False 303.5 507 91.5245 1 578 2 chr7B.!!$F1 577

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
895 914 2.317609 GCTGACGGTGCATGTTCGT 61.318 57.895 9.19 9.19 39.99 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 1902 0.321671 TCAGTAAGCAGTGCCTCACC 59.678 55.0 12.58 0.0 34.49 4.02 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
82 83 7.596749 TTCATCGAACCTCTTGATCTTTTAC 57.403 36.000 0.00 0.00 0.00 2.01
197 199 6.071952 CCACCAATAGCGCCTTCATATTTATT 60.072 38.462 2.29 0.00 0.00 1.40
198 200 7.120579 CCACCAATAGCGCCTTCATATTTATTA 59.879 37.037 2.29 0.00 0.00 0.98
199 201 8.511321 CACCAATAGCGCCTTCATATTTATTAA 58.489 33.333 2.29 0.00 0.00 1.40
200 202 9.243105 ACCAATAGCGCCTTCATATTTATTAAT 57.757 29.630 2.29 0.00 0.00 1.40
247 249 8.943085 AGTATTTGAGAATAATGAGAGATGGGT 58.057 33.333 0.00 0.00 29.89 4.51
294 296 9.685276 ATACAAACCATCTAATCATGACTTGAA 57.315 29.630 0.00 0.00 38.03 2.69
496 515 6.041409 TGGAAGTGGTAAATGAAGCAAATCAA 59.959 34.615 0.00 0.00 32.06 2.57
497 516 6.928492 GGAAGTGGTAAATGAAGCAAATCAAA 59.072 34.615 0.00 0.00 32.06 2.69
748 767 9.470399 TCTAGTATAAAGGTGATCAGTGTGTAA 57.530 33.333 0.00 0.00 0.00 2.41
780 799 8.486210 AGCAGACCTGAAGTAATGATGTTATAA 58.514 33.333 0.47 0.00 0.00 0.98
895 914 2.317609 GCTGACGGTGCATGTTCGT 61.318 57.895 9.19 9.19 39.99 3.85
916 935 4.528504 GTTTTCCTTTCTTCTCTTCGTGC 58.471 43.478 0.00 0.00 0.00 5.34
1366 1385 1.054231 CCCATCATCCTAGCAGAGCA 58.946 55.000 0.00 0.00 0.00 4.26
1475 1494 8.576936 TTTGTCACCGTAATTTTTGGTAAATC 57.423 30.769 0.00 0.00 33.82 2.17
1502 1521 3.127030 GTGCTTGCATCTACTTTGGGTAC 59.873 47.826 0.00 0.00 0.00 3.34
1847 1866 5.945191 ACCTGCATTTGGAAAATTATTTGGG 59.055 36.000 0.00 0.00 0.00 4.12
1883 1902 7.905604 TTAGAGTTGTATGTCAAGTGAATGG 57.094 36.000 0.00 0.00 39.50 3.16
1935 1954 5.897377 AGTGCAGTAAACACTTGTTTCTT 57.103 34.783 10.58 0.00 46.01 2.52
2159 2178 5.431420 TGCGTCAAACAAAGTGAATATGT 57.569 34.783 0.00 0.00 0.00 2.29
2270 2289 2.029200 TGTGTGGCTGGCACAAATTATG 60.029 45.455 34.26 0.00 42.96 1.90
2279 2298 5.679382 GCTGGCACAAATTATGACATTGCTA 60.679 40.000 7.31 1.53 38.70 3.49
2329 2348 6.016693 GCTTAGGGGAATAAAAGCAAGAGATC 60.017 42.308 1.27 0.00 43.00 2.75
2396 2415 7.912949 TGATGAGCGTGCATTAATATTTTTC 57.087 32.000 0.00 0.00 0.00 2.29
2473 2494 4.384846 ACACAACGTTCTAGAAAGCATACG 59.615 41.667 17.03 13.45 35.34 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 7.938140 TCTCCTTCGAAATTTTCCAATACAT 57.062 32.000 0.00 0.00 0.00 2.29
303 306 6.444704 AGTGATCTAGGAGAAAGGGATTACA 58.555 40.000 0.00 0.00 0.00 2.41
427 442 6.500589 AAATGGACAGTAGGTATGTAGCAT 57.499 37.500 0.00 0.00 0.00 3.79
531 550 0.940126 CGGGCTAGCATGTAAAGCAG 59.060 55.000 18.24 7.16 38.01 4.24
748 767 0.394565 ACTTCAGGTCTGCTTTCGCT 59.605 50.000 0.00 0.00 36.97 4.93
895 914 4.196193 TGCACGAAGAGAAGAAAGGAAAA 58.804 39.130 0.00 0.00 0.00 2.29
916 935 5.375417 TTTGTGGCTTGTCAAGATACATG 57.625 39.130 16.99 0.00 0.00 3.21
1158 1177 2.048222 CGTCGTGTGGATGCAGGT 60.048 61.111 0.00 0.00 0.00 4.00
1366 1385 1.140312 TCAGAGGCCTCACTTTTGGT 58.860 50.000 33.90 8.39 0.00 3.67
1475 1494 0.176680 AGTAGATGCAAGCACGGGAG 59.823 55.000 0.00 0.00 0.00 4.30
1504 1523 1.664321 ATACACGGAGACAGGCGACC 61.664 60.000 0.00 0.00 0.00 4.79
1847 1866 3.610911 ACAACTCTAATAAGCTGTGGGC 58.389 45.455 0.00 0.00 42.19 5.36
1883 1902 0.321671 TCAGTAAGCAGTGCCTCACC 59.678 55.000 12.58 0.00 34.49 4.02
1935 1954 2.088104 AGGGCATCTCGGTTCTGATA 57.912 50.000 0.00 0.00 0.00 2.15
2307 2326 5.163088 GGGATCTCTTGCTTTTATTCCCCTA 60.163 44.000 0.00 0.00 36.38 3.53
2329 2348 8.388484 TGAATTTTTGGACATTGTTTATTGGG 57.612 30.769 0.00 0.00 0.00 4.12
2372 2391 7.479150 TGAAAAATATTAATGCACGCTCATCA 58.521 30.769 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.