Multiple sequence alignment - TraesCS7A01G284100

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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 TraesCS7A01G284100 chr7A 100.000 2432 0 0 1 2432 320507574 320510005 0.000000e+00 4492
1 TraesCS7A01G284100 chr2A 95.195 2435 100 9 1 2429 354528964 354531387 0.000000e+00 3832
2 TraesCS7A01G284100 chr2A 94.820 1776 82 8 1 1771 494101256 494099486 0.000000e+00 2761
3 TraesCS7A01G284100 chr1D 94.665 1537 75 6 1 1531 288858349 288859884 0.000000e+00 2377
4 TraesCS7A01G284100 chr1D 96.231 902 34 0 1528 2429 288860308 288861209 0.000000e+00 1478
5 TraesCS7A01G284100 chr1B 94.340 1537 75 9 1 1531 126921437 126922967 0.000000e+00 2346
6 TraesCS7A01G284100 chr1B 95.633 893 39 0 1537 2429 126923037 126923929 0.000000e+00 1434
7 TraesCS7A01G284100 chr2B 93.502 1539 81 15 1 1531 109886755 109888282 0.000000e+00 2270
8 TraesCS7A01G284100 chr2B 95.221 1130 49 4 406 1531 614643420 614644548 0.000000e+00 1783
9 TraesCS7A01G284100 chr2B 96.753 893 29 0 1537 2429 109888352 109889244 0.000000e+00 1489
10 TraesCS7A01G284100 chr2B 96.305 893 33 0 1537 2429 614644618 614645510 0.000000e+00 1467
11 TraesCS7A01G284100 chr7D 92.857 1540 95 9 1 1534 61524176 61522646 0.000000e+00 2220
12 TraesCS7A01G284100 chr7D 96.354 905 33 0 1528 2432 61522225 61521321 0.000000e+00 1489
13 TraesCS7A01G284100 chr1A 92.631 1547 93 9 1 1531 408631061 408632602 0.000000e+00 2206
14 TraesCS7A01G284100 chr5B 92.628 1560 71 12 1 1534 525550018 525548477 0.000000e+00 2204
15 TraesCS7A01G284100 chr5B 96.540 896 31 0 1537 2432 525548410 525547515 0.000000e+00 1483
16 TraesCS7A01G284100 chr4D 96.022 905 36 0 1528 2432 382847084 382846180 0.000000e+00 1472
17 TraesCS7A01G284100 chr6D 93.586 764 39 3 1675 2429 93876313 93877075 0.000000e+00 1131
18 TraesCS7A01G284100 chr6A 94.509 346 16 3 4 348 87409822 87409479 4.600000e-147 531
19 TraesCS7A01G284100 chr3A 94.000 350 18 3 1 348 34899554 34899206 5.960000e-146 527


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 TraesCS7A01G284100 chr7A 320507574 320510005 2431 False 4492.0 4492 100.0000 1 2432 1 chr7A.!!$F1 2431
1 TraesCS7A01G284100 chr2A 354528964 354531387 2423 False 3832.0 3832 95.1950 1 2429 1 chr2A.!!$F1 2428
2 TraesCS7A01G284100 chr2A 494099486 494101256 1770 True 2761.0 2761 94.8200 1 1771 1 chr2A.!!$R1 1770
3 TraesCS7A01G284100 chr1D 288858349 288861209 2860 False 1927.5 2377 95.4480 1 2429 2 chr1D.!!$F1 2428
4 TraesCS7A01G284100 chr1B 126921437 126923929 2492 False 1890.0 2346 94.9865 1 2429 2 chr1B.!!$F1 2428
5 TraesCS7A01G284100 chr2B 109886755 109889244 2489 False 1879.5 2270 95.1275 1 2429 2 chr2B.!!$F1 2428
6 TraesCS7A01G284100 chr2B 614643420 614645510 2090 False 1625.0 1783 95.7630 406 2429 2 chr2B.!!$F2 2023
7 TraesCS7A01G284100 chr7D 61521321 61524176 2855 True 1854.5 2220 94.6055 1 2432 2 chr7D.!!$R1 2431
8 TraesCS7A01G284100 chr1A 408631061 408632602 1541 False 2206.0 2206 92.6310 1 1531 1 chr1A.!!$F1 1530
9 TraesCS7A01G284100 chr5B 525547515 525550018 2503 True 1843.5 2204 94.5840 1 2432 2 chr5B.!!$R1 2431
10 TraesCS7A01G284100 chr4D 382846180 382847084 904 True 1472.0 1472 96.0220 1528 2432 1 chr4D.!!$R1 904
11 TraesCS7A01G284100 chr6D 93876313 93877075 762 False 1131.0 1131 93.5860 1675 2429 1 chr6D.!!$F1 754

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
369 406 0.032615 GCTCCCTTCTCCTCCTCTCA 60.033 60.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 3264 0.038618 TTGTCGGACCTCACATCACG 60.039 55.0 5.55 0.0 0.0 4.35 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
116 121 9.220635 GGTTTTCCATTTTCTTTTTGAATTTCG 57.779 29.630 0.00 0.00 40.31 3.46
119 124 7.176285 TCCATTTTCTTTTTGAATTTCGCAG 57.824 32.000 0.00 0.00 34.24 5.18
329 366 1.272985 GGTCATTTTCCATCCACCCCA 60.273 52.381 0.00 0.00 0.00 4.96
369 406 0.032615 GCTCCCTTCTCCTCCTCTCA 60.033 60.000 0.00 0.00 0.00 3.27
371 408 1.287739 CTCCCTTCTCCTCCTCTCACT 59.712 57.143 0.00 0.00 0.00 3.41
398 435 4.415332 TTCTCTGTCGCGACGCCC 62.415 66.667 31.88 11.18 0.00 6.13
442 479 2.016315 TCTCCCCCGATCCCACCTA 61.016 63.158 0.00 0.00 0.00 3.08
496 543 2.190578 GCCTCCAGATCCAACCCG 59.809 66.667 0.00 0.00 0.00 5.28
519 566 1.151677 AAGCCCAACTCCTACCCCA 60.152 57.895 0.00 0.00 0.00 4.96
581 628 1.551019 GGTGGCTAGGGTTTCGGTCT 61.551 60.000 0.00 0.00 0.00 3.85
636 683 3.151958 GAGCCCTCAAGCGCCGATA 62.152 63.158 2.29 0.00 38.01 2.92
656 705 2.569059 ACATCTTCGATGGCCTTGATG 58.431 47.619 3.32 9.51 37.77 3.07
770 820 0.919289 GGTCTCCCCCTCCCAAATCA 60.919 60.000 0.00 0.00 0.00 2.57
820 870 1.141881 CAAGGTCCGACCCATCTCG 59.858 63.158 14.32 0.00 39.75 4.04
912 964 1.671054 TGCTTGTAGCGGCTGTTCC 60.671 57.895 13.86 0.00 46.26 3.62
963 1015 2.258591 GTCCACTCGAGCGAGCAA 59.741 61.111 18.80 2.96 45.54 3.91
1100 1153 0.462581 ATCACGGCGCACATCAAGAT 60.463 50.000 10.83 0.00 0.00 2.40
1149 1203 6.441924 CCCCAAATCTATAGCCTCTGAATCTA 59.558 42.308 0.00 0.00 0.00 1.98
1201 1255 7.360438 GCAAGAGAAAGAACGATGTACTTGAAT 60.360 37.037 0.00 0.00 35.67 2.57
1436 1490 3.430862 GCGGCCGTGCTGATTTGA 61.431 61.111 28.70 0.00 37.02 2.69
1454 1508 9.388506 CTGATTTGATCTGTAGGTTTAAGTGAT 57.611 33.333 0.00 0.00 0.00 3.06
1503 1557 5.633655 TTTTCCTGGTCTGTAGGTTTACA 57.366 39.130 0.00 0.00 37.45 2.41
1592 2506 6.317642 TCCATTTATACTTCCACATGGTTTCG 59.682 38.462 0.00 0.00 34.05 3.46
1615 2529 9.480861 TTCGGAATCTGGATAGAATCACTATAT 57.519 33.333 0.00 0.00 41.32 0.86
1644 2558 2.736721 GTGATTCGTTCTGTAGCTTGCA 59.263 45.455 0.00 0.00 0.00 4.08
1645 2559 3.186409 GTGATTCGTTCTGTAGCTTGCAA 59.814 43.478 0.00 0.00 0.00 4.08
1652 2566 4.083537 CGTTCTGTAGCTTGCAATTGGTAA 60.084 41.667 7.72 0.00 0.00 2.85
1855 2770 7.284261 TCCATGGTGCGATTTAATTAGATTCAA 59.716 33.333 12.58 0.00 0.00 2.69
1884 2799 3.740397 CCAGGGCGTGTGCATGTG 61.740 66.667 6.43 0.00 45.35 3.21
2229 3150 8.848474 TGACCCTATTAGTTCTTTCTTTCTTG 57.152 34.615 0.00 0.00 0.00 3.02
2251 3172 2.283145 GGCTATGAGTTGATGGCCAT 57.717 50.000 20.96 20.96 46.59 4.40
2263 3184 1.477700 GATGGCCATGCTGCTGTTTTA 59.522 47.619 26.56 0.00 0.00 1.52
2429 3353 9.006839 TCTTCTTCACATCATATCATATTTGCC 57.993 33.333 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 121 4.276678 TCATGCAGCTATTTTATGACCTGC 59.723 41.667 0.00 0.00 44.26 4.85
119 124 9.748708 TTAAAATCATGCAGCTATTTTATGACC 57.251 29.630 17.43 0.00 35.87 4.02
229 256 0.664466 CGGCGTATGATGCACGATCT 60.664 55.000 0.00 0.00 41.91 2.75
329 366 1.134438 AGGAAAGAAAGGAGGCGGGT 61.134 55.000 0.00 0.00 0.00 5.28
371 408 2.755650 GCGACAGAGAAGACTTGGAAA 58.244 47.619 0.00 0.00 0.00 3.13
398 435 0.249489 GATCGAATCGTGGGAGGTGG 60.249 60.000 1.52 0.00 0.00 4.61
476 513 2.670148 GGTTGGATCTGGAGGCCGT 61.670 63.158 0.00 0.00 0.00 5.68
581 628 2.423898 GCGGGATCGAGTTGGAGGA 61.424 63.158 0.00 0.00 39.00 3.71
636 683 2.092753 ACATCAAGGCCATCGAAGATGT 60.093 45.455 5.01 11.71 45.12 3.06
942 994 1.429825 CTCGCTCGAGTGGACGAAT 59.570 57.895 24.88 0.00 41.67 3.34
963 1015 1.611965 GCCTTCCCTTCCAGCATCT 59.388 57.895 0.00 0.00 0.00 2.90
1050 1103 1.081641 GAGGACGTCGAAGCGTTCA 60.082 57.895 9.92 0.00 45.79 3.18
1100 1153 3.153919 GGTATTGGCAAGTTTCTCACCA 58.846 45.455 5.96 0.00 0.00 4.17
1149 1203 5.536916 AGACTGTCTCTAGCTTGTTACTTGT 59.463 40.000 4.06 0.00 0.00 3.16
1201 1255 4.873259 TGCGCAACTAACTGCTGATTTATA 59.127 37.500 8.16 0.00 40.33 0.98
1306 1360 2.362120 GAAGCTGCAGCCCACCAT 60.362 61.111 34.39 12.93 43.38 3.55
1421 1475 0.379669 CAGATCAAATCAGCACGGCC 59.620 55.000 0.00 0.00 0.00 6.13
1433 1487 8.822805 ACCTTATCACTTAAACCTACAGATCAA 58.177 33.333 0.00 0.00 0.00 2.57
1436 1490 8.375493 TCACCTTATCACTTAAACCTACAGAT 57.625 34.615 0.00 0.00 0.00 2.90
1454 1508 5.222079 TCACAAGTTGTATGCTCACCTTA 57.778 39.130 8.49 0.00 0.00 2.69
1503 1557 3.433314 GCCACCATCAGATCAGAACTCAT 60.433 47.826 0.00 0.00 0.00 2.90
1615 2529 5.050363 GCTACAGAACGAATCACAAAACTGA 60.050 40.000 0.00 0.00 0.00 3.41
1621 2535 3.186409 GCAAGCTACAGAACGAATCACAA 59.814 43.478 0.00 0.00 0.00 3.33
1698 2613 6.885922 AGAAAGGCGGTTTTCAGTATACTAT 58.114 36.000 4.74 0.00 39.08 2.12
1855 2770 0.394352 CGCCCTGGCCTATCAAAGTT 60.394 55.000 3.32 0.00 37.98 2.66
1880 2795 7.829211 AGTAGTAATTGTTCCATGCTAACACAT 59.171 33.333 10.40 6.35 36.61 3.21
2103 3024 8.340443 CACATCATTCAGTCACAAGGTATAATG 58.660 37.037 0.00 0.00 0.00 1.90
2214 3135 4.445557 AGCCCTCAAGAAAGAAAGAACT 57.554 40.909 0.00 0.00 0.00 3.01
2229 3150 1.544314 GGCCATCAACTCATAGCCCTC 60.544 57.143 0.00 0.00 34.23 4.30
2251 3172 2.260844 AGCAGAGTAAAACAGCAGCA 57.739 45.000 0.00 0.00 0.00 4.41
2263 3184 8.854614 ACAGTAAAAGAATTATCAAGCAGAGT 57.145 30.769 0.00 0.00 0.00 3.24
2340 3264 0.038618 TTGTCGGACCTCACATCACG 60.039 55.000 5.55 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.