Multiple sequence alignment - TraesCS5D01G540900

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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 TraesCS5D01G540900 chr5D 100.000 3213 0 0 1 3213 552029660 552026448 0.000000e+00 5934
1 TraesCS5D01G540900 chr5D 96.607 2623 54 9 615 3211 78602935 78600322 0.000000e+00 4318
2 TraesCS5D01G540900 chr5D 97.612 2052 30 9 616 2654 555413536 555415581 0.000000e+00 3500
3 TraesCS5D01G540900 chr4D 97.369 2623 41 6 616 3213 491381490 491384109 0.000000e+00 4436
4 TraesCS5D01G540900 chr4D 90.761 368 32 2 246 612 497518056 497517690 1.040000e-134 490
5 TraesCS5D01G540900 chr7D 97.327 2619 50 7 610 3213 531067732 531065119 0.000000e+00 4431
6 TraesCS5D01G540900 chr3D 97.294 2624 41 9 616 3213 334133 336752 0.000000e+00 4425
7 TraesCS5D01G540900 chr3D 98.039 1020 15 3 2195 3213 610059709 610058694 0.000000e+00 1768
8 TraesCS5D01G540900 chr3D 87.017 362 46 1 255 616 522779647 522779287 1.070000e-109 407
9 TraesCS5D01G540900 chr3D 87.850 214 24 2 13 225 522779859 522779647 1.910000e-62 250
10 TraesCS5D01G540900 chr1D 97.180 2624 43 8 616 3213 316243968 316241350 0.000000e+00 4407
11 TraesCS5D01G540900 chr6D 97.060 2619 52 5 616 3213 420171217 420173831 0.000000e+00 4386
12 TraesCS5D01G540900 chr2D 96.839 2626 52 9 614 3213 617340743 617343363 0.000000e+00 4361
13 TraesCS5D01G540900 chr2D 96.729 2629 49 10 616 3213 130079133 130076511 0.000000e+00 4344
14 TraesCS5D01G540900 chr2D 90.251 359 33 2 255 612 614342488 614342131 4.850000e-128 468
15 TraesCS5D01G540900 chr4A 96.179 2617 76 10 616 3213 731637348 731634737 0.000000e+00 4257
16 TraesCS5D01G540900 chr4A 95.888 2602 85 9 616 3213 478227133 478229716 0.000000e+00 4193
17 TraesCS5D01G540900 chr1A 95.351 2624 79 21 616 3213 77263366 77265972 0.000000e+00 4130
18 TraesCS5D01G540900 chr1A 95.401 2609 90 17 615 3213 25271007 25268419 0.000000e+00 4126
19 TraesCS5D01G540900 chr3A 95.229 2620 73 20 616 3213 693613629 693611040 0.000000e+00 4098
20 TraesCS5D01G540900 chr6A 95.008 2624 89 20 616 3213 587986824 587984217 0.000000e+00 4082
21 TraesCS5D01G540900 chr6A 84.976 619 70 11 1 616 584891972 584892570 9.860000e-170 606
22 TraesCS5D01G540900 chr5A 94.643 2632 92 22 615 3213 540625171 540622556 0.000000e+00 4034
23 TraesCS5D01G540900 chr5A 94.212 2626 105 14 616 3213 666200505 666197899 0.000000e+00 3964
24 TraesCS5D01G540900 chr6B 87.833 600 70 3 18 616 75644480 75643883 0.000000e+00 701
25 TraesCS5D01G540900 chr1B 87.333 600 73 3 18 616 682167963 682168560 0.000000e+00 684
26 TraesCS5D01G540900 chr2A 84.843 607 71 12 7 612 718930953 718930367 2.760000e-165 592
27 TraesCS5D01G540900 chr2A 84.176 613 75 12 1 610 524593296 524593889 2.780000e-160 575
28 TraesCS5D01G540900 chr3B 79.755 652 87 23 1 613 16755727 16756372 6.370000e-117 431


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 TraesCS5D01G540900 chr5D 552026448 552029660 3212 True 5934.0 5934 100.0000 1 3213 1 chr5D.!!$R2 3212
1 TraesCS5D01G540900 chr5D 78600322 78602935 2613 True 4318.0 4318 96.6070 615 3211 1 chr5D.!!$R1 2596
2 TraesCS5D01G540900 chr5D 555413536 555415581 2045 False 3500.0 3500 97.6120 616 2654 1 chr5D.!!$F1 2038
3 TraesCS5D01G540900 chr4D 491381490 491384109 2619 False 4436.0 4436 97.3690 616 3213 1 chr4D.!!$F1 2597
4 TraesCS5D01G540900 chr7D 531065119 531067732 2613 True 4431.0 4431 97.3270 610 3213 1 chr7D.!!$R1 2603
5 TraesCS5D01G540900 chr3D 334133 336752 2619 False 4425.0 4425 97.2940 616 3213 1 chr3D.!!$F1 2597
6 TraesCS5D01G540900 chr3D 610058694 610059709 1015 True 1768.0 1768 98.0390 2195 3213 1 chr3D.!!$R1 1018
7 TraesCS5D01G540900 chr3D 522779287 522779859 572 True 328.5 407 87.4335 13 616 2 chr3D.!!$R2 603
8 TraesCS5D01G540900 chr1D 316241350 316243968 2618 True 4407.0 4407 97.1800 616 3213 1 chr1D.!!$R1 2597
9 TraesCS5D01G540900 chr6D 420171217 420173831 2614 False 4386.0 4386 97.0600 616 3213 1 chr6D.!!$F1 2597
10 TraesCS5D01G540900 chr2D 617340743 617343363 2620 False 4361.0 4361 96.8390 614 3213 1 chr2D.!!$F1 2599
11 TraesCS5D01G540900 chr2D 130076511 130079133 2622 True 4344.0 4344 96.7290 616 3213 1 chr2D.!!$R1 2597
12 TraesCS5D01G540900 chr4A 731634737 731637348 2611 True 4257.0 4257 96.1790 616 3213 1 chr4A.!!$R1 2597
13 TraesCS5D01G540900 chr4A 478227133 478229716 2583 False 4193.0 4193 95.8880 616 3213 1 chr4A.!!$F1 2597
14 TraesCS5D01G540900 chr1A 77263366 77265972 2606 False 4130.0 4130 95.3510 616 3213 1 chr1A.!!$F1 2597
15 TraesCS5D01G540900 chr1A 25268419 25271007 2588 True 4126.0 4126 95.4010 615 3213 1 chr1A.!!$R1 2598
16 TraesCS5D01G540900 chr3A 693611040 693613629 2589 True 4098.0 4098 95.2290 616 3213 1 chr3A.!!$R1 2597
17 TraesCS5D01G540900 chr6A 587984217 587986824 2607 True 4082.0 4082 95.0080 616 3213 1 chr6A.!!$R1 2597
18 TraesCS5D01G540900 chr6A 584891972 584892570 598 False 606.0 606 84.9760 1 616 1 chr6A.!!$F1 615
19 TraesCS5D01G540900 chr5A 540622556 540625171 2615 True 4034.0 4034 94.6430 615 3213 1 chr5A.!!$R1 2598
20 TraesCS5D01G540900 chr5A 666197899 666200505 2606 True 3964.0 3964 94.2120 616 3213 1 chr5A.!!$R2 2597
21 TraesCS5D01G540900 chr6B 75643883 75644480 597 True 701.0 701 87.8330 18 616 1 chr6B.!!$R1 598
22 TraesCS5D01G540900 chr1B 682167963 682168560 597 False 684.0 684 87.3330 18 616 1 chr1B.!!$F1 598
23 TraesCS5D01G540900 chr2A 718930367 718930953 586 True 592.0 592 84.8430 7 612 1 chr2A.!!$R1 605
24 TraesCS5D01G540900 chr2A 524593296 524593889 593 False 575.0 575 84.1760 1 610 1 chr2A.!!$F1 609
25 TraesCS5D01G540900 chr3B 16755727 16756372 645 False 431.0 431 79.7550 1 613 1 chr3B.!!$F1 612

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
302 342 0.105453 ACGCATATCTCCCCTCTGGT 60.105 55.0 0.0 0.0 34.77 4.00 F
314 354 0.322648 CCTCTGGTGATGACAGTGCA 59.677 55.0 0.0 0.0 37.25 4.57 F
340 380 1.110442 CACAACAACCTCCCTGCAAA 58.890 50.0 0.0 0.0 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 1826 1.133025 CCTTTGCAGAATTACAGGCCG 59.867 52.381 0.00 0.0 0.00 6.13 R
1969 2092 3.928727 TGAAGCTCAATCTTTGCTTGG 57.071 42.857 4.12 0.0 45.56 3.61 R
2338 2474 2.371510 CCCCACACCAACCAAAATGATT 59.628 45.455 0.00 0.0 0.00 2.57 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
127 138 2.125552 CGCTGCGGTTCCTGATCA 60.126 61.111 15.40 0.00 0.00 2.92
130 141 0.391661 GCTGCGGTTCCTGATCAAGA 60.392 55.000 0.00 0.00 0.00 3.02
138 149 3.263425 GGTTCCTGATCAAGACTTGGGTA 59.737 47.826 15.13 0.00 0.00 3.69
139 150 4.263331 GGTTCCTGATCAAGACTTGGGTAA 60.263 45.833 15.13 0.00 0.00 2.85
261 301 2.654912 CGCGTGGTTGTCGGAGTTC 61.655 63.158 0.00 0.00 0.00 3.01
299 339 0.188587 TCCACGCATATCTCCCCTCT 59.811 55.000 0.00 0.00 0.00 3.69
302 342 0.105453 ACGCATATCTCCCCTCTGGT 60.105 55.000 0.00 0.00 34.77 4.00
304 344 1.722034 GCATATCTCCCCTCTGGTGA 58.278 55.000 0.00 0.00 40.75 4.02
314 354 0.322648 CCTCTGGTGATGACAGTGCA 59.677 55.000 0.00 0.00 37.25 4.57
340 380 1.110442 CACAACAACCTCCCTGCAAA 58.890 50.000 0.00 0.00 0.00 3.68
361 401 7.836685 TGCAAAGGGTCCATTGTAATCTATTTA 59.163 33.333 6.80 0.00 0.00 1.40
391 431 8.650143 TCTAGGGTAATCTTTGCAATTTTTCT 57.350 30.769 0.00 0.00 0.00 2.52
409 450 3.782656 TCTGGGACCCTTTTGTTAGTC 57.217 47.619 13.00 0.00 0.00 2.59
449 490 3.871074 GCCCCATGTCTAACTTAACGGTT 60.871 47.826 0.00 0.00 0.00 4.44
484 525 2.747446 GACCGTTTTATGCCATGTCAGT 59.253 45.455 0.00 0.00 0.00 3.41
492 533 2.268762 TGCCATGTCAGTGCTTACAA 57.731 45.000 0.00 0.00 0.00 2.41
1054 1126 2.259618 ACAACGATGACGAGTACATGC 58.740 47.619 0.00 0.00 42.66 4.06
1118 1190 3.394274 CTCAGTCTATCCTCTCCCTCTCA 59.606 52.174 0.00 0.00 0.00 3.27
1253 1360 5.728471 CAAACTCCTGACACTGTGATAGAT 58.272 41.667 15.86 0.00 0.00 1.98
1460 1567 6.267496 ACAGACTGTTTAGTTGCTGTTTTT 57.733 33.333 1.07 0.00 38.25 1.94
1503 1610 6.599244 TCTGGAAACATTGGTATGTCTGAATC 59.401 38.462 0.00 0.00 44.14 2.52
1504 1611 6.244654 TGGAAACATTGGTATGTCTGAATCA 58.755 36.000 0.00 0.00 44.14 2.57
1515 1622 7.979537 TGGTATGTCTGAATCATGTACTTGTAC 59.020 37.037 8.46 4.14 0.00 2.90
1969 2092 4.384940 AGAAGAAGAAGCAACTTGAGGAC 58.615 43.478 0.34 0.00 0.00 3.85
1972 2095 3.117888 AGAAGAAGCAACTTGAGGACCAA 60.118 43.478 0.00 0.00 0.00 3.67
2083 2206 0.750911 GGAAGGCCATGAAGGAGCTG 60.751 60.000 5.01 0.00 41.22 4.24
2338 2474 6.195600 ACCTAAGAACTGTAATGGGTTCAA 57.804 37.500 8.24 0.00 42.76 2.69
3087 3268 1.064060 GTTGCATAGCGTTGGTCCATC 59.936 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 138 0.475044 TTGGCGGTTACCCAAGTCTT 59.525 50.000 0.00 0.00 37.43 3.01
138 149 2.597510 GGTTGCTCCTTGGCGGTT 60.598 61.111 0.00 0.00 34.52 4.44
251 291 4.667420 GGAAAGCGAACTCCGACA 57.333 55.556 0.00 0.00 41.76 4.35
287 327 3.116590 TGTCATCACCAGAGGGGAGATAT 60.117 47.826 0.00 0.00 44.11 1.63
299 339 0.879839 CGTGTGCACTGTCATCACCA 60.880 55.000 19.41 0.00 0.00 4.17
302 342 1.301637 CCCGTGTGCACTGTCATCA 60.302 57.895 19.41 0.00 0.00 3.07
304 344 2.669569 GCCCGTGTGCACTGTCAT 60.670 61.111 19.41 0.00 0.00 3.06
314 354 1.822186 GAGGTTGTTGTGCCCGTGT 60.822 57.895 0.00 0.00 0.00 4.49
340 380 9.936329 AAACATAAATAGATTACAATGGACCCT 57.064 29.630 0.00 0.00 0.00 4.34
361 401 7.961326 ATTGCAAAGATTACCCTAGAAACAT 57.039 32.000 1.71 0.00 0.00 2.71
377 417 3.071457 AGGGTCCCAGAAAAATTGCAAAG 59.929 43.478 11.55 0.00 0.00 2.77
391 431 2.107552 CTGGACTAACAAAAGGGTCCCA 59.892 50.000 11.55 0.00 45.29 4.37
409 450 1.389609 GCCCACCAATCATCAGCTGG 61.390 60.000 15.13 0.00 36.24 4.85
564 607 6.070481 GCCCCAAAAATCTACCAATTTCCTTA 60.070 38.462 0.00 0.00 0.00 2.69
570 613 2.093711 GCGCCCCAAAAATCTACCAATT 60.094 45.455 0.00 0.00 0.00 2.32
572 615 0.892063 GCGCCCCAAAAATCTACCAA 59.108 50.000 0.00 0.00 0.00 3.67
601 644 0.038166 ACACTCGGATTTGCCACCAT 59.962 50.000 0.00 0.00 35.94 3.55
1036 1108 1.545759 CGCATGTACTCGTCATCGTT 58.454 50.000 0.00 0.00 38.33 3.85
1054 1126 2.398429 CATGCTGCTGAACTCGCG 59.602 61.111 0.00 0.00 0.00 5.87
1118 1190 5.187967 CCTAACCCTAGAACAGAACAGACAT 59.812 44.000 0.00 0.00 0.00 3.06
1253 1360 2.054799 ACAAGCCCACAGAAACTAGGA 58.945 47.619 0.00 0.00 0.00 2.94
1313 1420 3.910490 GCCACAAACTTGCCCGCA 61.910 61.111 0.00 0.00 0.00 5.69
1503 1610 6.311445 CCAGTGCTCTTTAGTACAAGTACATG 59.689 42.308 12.43 0.00 40.50 3.21
1504 1611 6.210784 TCCAGTGCTCTTTAGTACAAGTACAT 59.789 38.462 12.43 1.44 40.50 2.29
1515 1622 7.615582 TTCATATGTTTCCAGTGCTCTTTAG 57.384 36.000 1.90 0.00 0.00 1.85
1703 1826 1.133025 CCTTTGCAGAATTACAGGCCG 59.867 52.381 0.00 0.00 0.00 6.13
1969 2092 3.928727 TGAAGCTCAATCTTTGCTTGG 57.071 42.857 4.12 0.00 45.56 3.61
1972 2095 4.525487 TCCATTTGAAGCTCAATCTTTGCT 59.475 37.500 0.00 0.00 36.11 3.91
2338 2474 2.371510 CCCCACACCAACCAAAATGATT 59.628 45.455 0.00 0.00 0.00 2.57
2887 3068 1.383109 AGATCATCGCCCCACCAGA 60.383 57.895 0.00 0.00 0.00 3.86
3087 3268 1.153667 GACTGAGGAGAAGCAGCGG 60.154 63.158 0.00 0.00 35.57 5.52


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

AutoCloner maintained by Alex Coulton.