Multiple sequence alignment - TraesCS2A01G245600

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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 TraesCS2A01G245600 chr2A 100.000 2468 0 0 1 2468 354528929 354531396 0.000000e+00 4558
1 TraesCS2A01G245600 chr2A 95.467 1809 71 6 1 1801 494101291 494099486 0.000000e+00 2876
2 TraesCS2A01G245600 chr2A 93.059 389 24 3 1 388 745975882 745975496 1.280000e-157 566
3 TraesCS2A01G245600 chr7A 95.200 2479 102 9 1 2468 320507539 320510011 0.000000e+00 3903
4 TraesCS2A01G245600 chr1D 95.105 1573 70 6 1 1567 288858313 288859884 0.000000e+00 2471
5 TraesCS2A01G245600 chr1D 96.487 911 26 1 1564 2468 288860308 288861218 0.000000e+00 1500
6 TraesCS2A01G245600 chr1B 95.032 1570 70 6 1 1567 126921403 126922967 0.000000e+00 2460
7 TraesCS2A01G245600 chr1B 95.898 902 31 1 1573 2468 126923037 126923938 0.000000e+00 1456
8 TraesCS2A01G245600 chr2B 94.148 1572 78 11 1 1567 109886720 109888282 0.000000e+00 2381
9 TraesCS2A01G245600 chr2B 96.454 1128 38 2 441 1567 614643422 614644548 0.000000e+00 1860
10 TraesCS2A01G245600 chr2B 96.452 902 26 1 1573 2468 109888352 109889253 0.000000e+00 1483
11 TraesCS2A01G245600 chr2B 96.341 902 27 1 1573 2468 614644618 614645519 0.000000e+00 1478
12 TraesCS2A01G245600 chr7D 94.088 1573 82 8 1 1570 61524210 61522646 0.000000e+00 2379
13 TraesCS2A01G245600 chr7D 96.597 911 25 1 1564 2468 61522225 61521315 0.000000e+00 1506
14 TraesCS2A01G245600 chr5B 93.471 1593 65 14 1 1570 525550053 525548477 0.000000e+00 2329
15 TraesCS2A01G245600 chr5B 96.452 902 26 1 1573 2468 525548410 525547509 0.000000e+00 1483
16 TraesCS2A01G245600 chr1A 93.295 1581 87 8 2 1567 408631026 408632602 0.000000e+00 2314
17 TraesCS2A01G245600 chr4D 96.378 911 27 1 1564 2468 382847084 382846174 0.000000e+00 1495
18 TraesCS2A01G245600 chr6D 93.661 773 39 5 1705 2468 93876313 93877084 0.000000e+00 1147
19 TraesCS2A01G245600 chr6A 92.857 392 20 8 1 388 87409859 87409472 1.660000e-156 562
20 TraesCS2A01G245600 chr3A 92.640 394 21 6 1 388 34899590 34899199 5.960000e-156 560


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 TraesCS2A01G245600 chr2A 354528929 354531396 2467 False 4558.0 4558 100.0000 1 2468 1 chr2A.!!$F1 2467
1 TraesCS2A01G245600 chr2A 494099486 494101291 1805 True 2876.0 2876 95.4670 1 1801 1 chr2A.!!$R1 1800
2 TraesCS2A01G245600 chr7A 320507539 320510011 2472 False 3903.0 3903 95.2000 1 2468 1 chr7A.!!$F1 2467
3 TraesCS2A01G245600 chr1D 288858313 288861218 2905 False 1985.5 2471 95.7960 1 2468 2 chr1D.!!$F1 2467
4 TraesCS2A01G245600 chr1B 126921403 126923938 2535 False 1958.0 2460 95.4650 1 2468 2 chr1B.!!$F1 2467
5 TraesCS2A01G245600 chr2B 109886720 109889253 2533 False 1932.0 2381 95.3000 1 2468 2 chr2B.!!$F1 2467
6 TraesCS2A01G245600 chr2B 614643422 614645519 2097 False 1669.0 1860 96.3975 441 2468 2 chr2B.!!$F2 2027
7 TraesCS2A01G245600 chr7D 61521315 61524210 2895 True 1942.5 2379 95.3425 1 2468 2 chr7D.!!$R1 2467
8 TraesCS2A01G245600 chr5B 525547509 525550053 2544 True 1906.0 2329 94.9615 1 2468 2 chr5B.!!$R1 2467
9 TraesCS2A01G245600 chr1A 408631026 408632602 1576 False 2314.0 2314 93.2950 2 1567 1 chr1A.!!$F1 1565
10 TraesCS2A01G245600 chr4D 382846174 382847084 910 True 1495.0 1495 96.3780 1564 2468 1 chr4D.!!$R1 904
11 TraesCS2A01G245600 chr6D 93876313 93877084 771 False 1147.0 1147 93.6610 1705 2468 1 chr6D.!!$F1 763

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
706 754 0.393132 TGATCTGCTCGAGGACGACT 60.393 55.0 15.58 2.18 43.81 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 2872 0.796312 CAAACCATTGTCGGACCTCG 59.204 55.0 5.55 0.0 40.9 4.63 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
219 245 6.428159 GGCAACTATGACCTATTTAGATGGTG 59.572 42.308 0.00 0.00 33.74 4.17
323 349 2.593956 GGCCGTCCTCAACCCTTCT 61.594 63.158 0.00 0.00 0.00 2.85
383 421 1.271379 CCCGCCTTCTTTCTTTCCTCA 60.271 52.381 0.00 0.00 0.00 3.86
415 453 2.008400 TCCTCTCCCCTTCCAAGTCTA 58.992 52.381 0.00 0.00 0.00 2.59
548 596 1.211457 CAGCTCAAGCCCAACTCCTAT 59.789 52.381 0.00 0.00 43.38 2.57
676 724 1.068753 CAAGCGCCGATCCATCTCT 59.931 57.895 2.29 0.00 0.00 3.10
706 754 0.393132 TGATCTGCTCGAGGACGACT 60.393 55.000 15.58 2.18 43.81 4.18
723 771 2.030540 CGACTGGTTCTTCGTCAACCTA 60.031 50.000 12.16 1.91 43.43 3.08
812 861 0.546122 CCCTCCCAAATCCATCACGA 59.454 55.000 0.00 0.00 0.00 4.35
829 878 2.171448 CACGATCTCCCAAATCTCCCTT 59.829 50.000 0.00 0.00 0.00 3.95
871 920 3.481559 TCTCCCCTCTCAGATTTCAGT 57.518 47.619 0.00 0.00 0.00 3.41
968 1019 2.602676 CCCAACCTCCGGTCCATGT 61.603 63.158 0.00 0.00 33.12 3.21
1111 1163 2.358369 TCGACGTCCTCGACTGCT 60.358 61.111 10.58 0.00 46.75 4.24
1193 1246 4.500499 AGCCTCTGAATCTGCAAGTAAT 57.500 40.909 0.00 0.00 33.76 1.89
1282 1335 2.158769 AGTGCTGCCGAATGATTGGATA 60.159 45.455 0.00 0.00 30.72 2.59
1723 2209 9.829507 ATAGAAATTTGGAATTTTGTTGACACA 57.170 25.926 0.00 0.00 0.00 3.72
1731 2217 6.041409 TGGAATTTTGTTGACACACCATGTAT 59.959 34.615 0.00 0.00 43.56 2.29
1750 2236 7.442969 CCATGTATTATACTGAAAACCGCCTTA 59.557 37.037 3.92 0.00 0.00 2.69
1762 2248 0.595310 CCGCCTTACTTCTAGCGCTC 60.595 60.000 16.34 0.00 46.90 5.03
2075 2567 9.350357 CAGATTGTTTTCATAAACCATTCTCAG 57.650 33.333 0.00 0.00 42.39 3.35
2179 2671 9.443323 TGATGTGTTATTTAGTTAGCTAAGCAA 57.557 29.630 6.38 0.89 38.31 3.91
2461 2956 8.913487 TCTTCACATCATATCATATTTGCACT 57.087 30.769 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 245 6.615264 ATCAGAATGCAGTATGATGTTGTC 57.385 37.500 22.12 0.00 38.34 3.18
323 349 5.648247 ACCTAGGGTTTCAGAGTTAGTGTA 58.352 41.667 14.81 0.00 27.29 2.90
370 408 4.235372 AGAAGGGAGTGAGGAAAGAAAGA 58.765 43.478 0.00 0.00 0.00 2.52
383 421 0.634465 GGAGAGGAGGAGAAGGGAGT 59.366 60.000 0.00 0.00 0.00 3.85
439 477 3.243907 GGAGAGGATTGGATCGAATCGTT 60.244 47.826 21.55 13.86 33.75 3.85
480 518 2.283529 GGTTGAGAGGAGGTCGCCA 61.284 63.158 0.00 0.00 0.00 5.69
676 724 1.228228 GCAGATCAAGGCCATCCCA 59.772 57.895 5.01 0.00 35.39 4.37
706 754 3.493699 CCTTGTAGGTTGACGAAGAACCA 60.494 47.826 14.47 2.27 44.71 3.67
767 816 1.771746 ATCCTGGTCGCCATGGGAT 60.772 57.895 15.13 11.42 34.85 3.85
812 861 2.584498 AGCAAAGGGAGATTTGGGAGAT 59.416 45.455 1.80 0.00 39.94 2.75
829 878 1.671742 GTCGGACCTTGAGGAGCAA 59.328 57.895 3.59 0.00 38.94 3.91
1193 1246 4.767409 TCTTGCAAGACTGTCTCTAGCTTA 59.233 41.667 25.16 13.54 0.00 3.09
1282 1335 0.322816 AGTGCAGCCGTCCAAATCAT 60.323 50.000 0.00 0.00 0.00 2.45
1310 1363 1.601759 GGGCCATGGATCATGTCGG 60.602 63.158 18.40 0.00 39.94 4.79
1715 2201 8.487313 TTCAGTATAATACATGGTGTGTCAAC 57.513 34.615 0.00 0.00 42.29 3.18
1723 2209 5.529800 GGCGGTTTTCAGTATAATACATGGT 59.470 40.000 0.00 0.00 0.00 3.55
1731 2217 6.704310 AGAAGTAAGGCGGTTTTCAGTATAA 58.296 36.000 0.00 0.00 0.00 0.98
1750 2236 1.835494 TGTGTAGGAGCGCTAGAAGT 58.165 50.000 11.50 0.00 0.00 3.01
1762 2248 6.161855 TCATCCTAACTAGCATTGTGTAGG 57.838 41.667 0.00 0.00 0.00 3.18
2377 2872 0.796312 CAAACCATTGTCGGACCTCG 59.204 55.000 5.55 0.00 40.90 4.63


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

AutoCloner maintained by Alex Coulton.