Multiple sequence alignment - TraesCS2B01G462000

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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 TraesCS2B01G462000 chr2B 100.000 2516 0 0 1 2516 655676970 655674455 0.000000e+00 4647
1 TraesCS2B01G462000 chr2B 96.343 2516 77 11 1 2513 655681889 655684392 0.000000e+00 4122
2 TraesCS2B01G462000 chr2B 96.268 2519 85 9 2 2516 670339415 670336902 0.000000e+00 4122
3 TraesCS2B01G462000 chr2B 95.390 2516 81 16 1 2513 717661922 717664405 0.000000e+00 3971
4 TraesCS2B01G462000 chr2B 95.181 249 11 1 1 249 741199249 741199002 2.350000e-105 392
5 TraesCS2B01G462000 chr2B 94.779 249 12 1 1 249 741228996 741228749 1.090000e-103 387
6 TraesCS2B01G462000 chr4B 95.557 2521 98 12 1 2516 15528754 15526243 0.000000e+00 4023
7 TraesCS2B01G462000 chr5A 93.245 2502 124 32 38 2516 693855035 693852556 0.000000e+00 3642
8 TraesCS2B01G462000 chr5D 93.229 2496 121 22 38 2516 36575294 36572830 0.000000e+00 3629
9 TraesCS2B01G462000 chr6B 95.775 2201 80 13 325 2516 319483081 319480885 0.000000e+00 3537
10 TraesCS2B01G462000 chr6A 92.375 2505 143 30 38 2513 602785383 602787868 0.000000e+00 3524
11 TraesCS2B01G462000 chr1D 92.422 2494 129 27 38 2513 383338813 383341264 0.000000e+00 3504
12 TraesCS2B01G462000 chr2D 93.111 2395 116 23 139 2516 87968479 87966117 0.000000e+00 3463
13 TraesCS2B01G462000 chr7A 92.732 1775 98 16 38 1796 204218202 204216443 0.000000e+00 2534


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 TraesCS2B01G462000 chr2B 655674455 655676970 2515 True 4647 4647 100.000 1 2516 1 chr2B.!!$R1 2515
1 TraesCS2B01G462000 chr2B 655681889 655684392 2503 False 4122 4122 96.343 1 2513 1 chr2B.!!$F1 2512
2 TraesCS2B01G462000 chr2B 670336902 670339415 2513 True 4122 4122 96.268 2 2516 1 chr2B.!!$R2 2514
3 TraesCS2B01G462000 chr2B 717661922 717664405 2483 False 3971 3971 95.390 1 2513 1 chr2B.!!$F2 2512
4 TraesCS2B01G462000 chr4B 15526243 15528754 2511 True 4023 4023 95.557 1 2516 1 chr4B.!!$R1 2515
5 TraesCS2B01G462000 chr5A 693852556 693855035 2479 True 3642 3642 93.245 38 2516 1 chr5A.!!$R1 2478
6 TraesCS2B01G462000 chr5D 36572830 36575294 2464 True 3629 3629 93.229 38 2516 1 chr5D.!!$R1 2478
7 TraesCS2B01G462000 chr6B 319480885 319483081 2196 True 3537 3537 95.775 325 2516 1 chr6B.!!$R1 2191
8 TraesCS2B01G462000 chr6A 602785383 602787868 2485 False 3524 3524 92.375 38 2513 1 chr6A.!!$F1 2475
9 TraesCS2B01G462000 chr1D 383338813 383341264 2451 False 3504 3504 92.422 38 2513 1 chr1D.!!$F1 2475
10 TraesCS2B01G462000 chr2D 87966117 87968479 2362 True 3463 3463 93.111 139 2516 1 chr2D.!!$R1 2377
11 TraesCS2B01G462000 chr7A 204216443 204218202 1759 True 2534 2534 92.732 38 1796 1 chr7A.!!$R1 1758


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
152 154 1.256010 AGAGGGAGGGTAATAGGGCT 58.744 55.0 0.00 0.0 0.00 5.19 F
565 587 1.533625 GGAGCAGTGCACCAATAACA 58.466 50.0 24.73 0.0 39.08 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 1234 0.772124 TGAGGGCTGGGGAGTTCTTT 60.772 55.000 0.0 0.0 0.00 2.52 R
1699 1737 2.188817 GGAGCCTTCCTGTCCTTCTTA 58.811 52.381 0.0 0.0 40.58 2.10 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
152 154 1.256010 AGAGGGAGGGTAATAGGGCT 58.744 55.000 0.00 0.00 0.00 5.19
155 157 2.905085 GAGGGAGGGTAATAGGGCTAAC 59.095 54.545 0.00 0.00 0.00 2.34
173 175 9.617053 AGGGCTAACTATAGGATAGTTTTGTAT 57.383 33.333 15.14 0.69 38.55 2.29
565 587 1.533625 GGAGCAGTGCACCAATAACA 58.466 50.000 24.73 0.00 39.08 2.41
586 608 2.829720 AGGGTACAAGCGTATGAGAACA 59.170 45.455 0.00 0.00 0.00 3.18
772 795 3.157087 CATAGTTGCCCCAGTTTCACTT 58.843 45.455 0.00 0.00 0.00 3.16
819 842 7.682741 GCATAAGTTGCCTATGTTGTGATGAAT 60.683 37.037 0.00 0.00 46.15 2.57
855 884 7.013834 TCCCTTTTGCTAATTCCCTTTTTCTA 58.986 34.615 0.00 0.00 0.00 2.10
981 1012 4.949856 GGAAGAGAATTTGGTGGCATTCTA 59.050 41.667 0.54 0.00 39.41 2.10
991 1022 3.585289 TGGTGGCATTCTAGACCTTGTAA 59.415 43.478 0.00 0.00 0.00 2.41
1203 1234 9.665719 ATGTACAGTATTTACAACATCACATCA 57.334 29.630 0.33 0.00 33.22 3.07
1216 1247 3.423539 TCACATCAAAGAACTCCCCAG 57.576 47.619 0.00 0.00 0.00 4.45
1357 1388 1.142060 TTCCCCAAAGAGTTTCCCGA 58.858 50.000 0.00 0.00 0.00 5.14
1457 1490 1.896660 GGCGTGCCAACAAGAAGGA 60.897 57.895 5.89 0.00 35.81 3.36
1656 1694 1.339727 GCCAATCCCGAACTTGGTACT 60.340 52.381 10.28 0.00 43.18 2.73
1673 1711 3.504906 GGTACTAAGGGTTTCAGTTTGGC 59.495 47.826 0.00 0.00 0.00 4.52
1828 1870 7.775053 ACCATTTTTAGAGTAGGCAATTCAA 57.225 32.000 0.00 0.00 0.00 2.69
2487 2551 3.761218 TCGCCATTTGTACATTCAACCAT 59.239 39.130 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 199 2.250031 AGTGGGCAATGAAAAGCATCA 58.750 42.857 0.00 0.0 35.78 3.07
464 482 8.974060 TGTACAGGAAGAACATAAAAACTTCT 57.026 30.769 0.00 0.0 38.78 2.85
565 587 2.829720 TGTTCTCATACGCTTGTACCCT 59.170 45.455 0.00 0.0 0.00 4.34
761 784 2.030805 GGCAACTGCTAAGTGAAACTGG 60.031 50.000 1.06 0.0 44.60 4.00
772 795 2.284754 TCATTGTTGGGCAACTGCTA 57.715 45.000 1.06 0.0 41.67 3.49
819 842 3.653164 AGCAAAAGGGAAGGGAAAAAGA 58.347 40.909 0.00 0.0 0.00 2.52
903 934 3.251972 CCTTGTTCAACTTGAAGAGCCTC 59.748 47.826 4.36 0.0 37.00 4.70
981 1012 3.676324 GCATGCTACTCGTTACAAGGTCT 60.676 47.826 11.37 0.0 0.00 3.85
991 1022 2.758327 TCCGGGCATGCTACTCGT 60.758 61.111 18.92 0.0 0.00 4.18
1203 1234 0.772124 TGAGGGCTGGGGAGTTCTTT 60.772 55.000 0.00 0.0 0.00 2.52
1216 1247 0.895100 TTGCACCATTCTGTGAGGGC 60.895 55.000 0.00 0.0 38.55 5.19
1357 1388 1.559219 TCCATTGACATCCATGACCGT 59.441 47.619 0.00 0.0 0.00 4.83
1656 1694 4.219115 TGAATGCCAAACTGAAACCCTTA 58.781 39.130 0.00 0.0 0.00 2.69
1699 1737 2.188817 GGAGCCTTCCTGTCCTTCTTA 58.811 52.381 0.00 0.0 40.58 2.10
1828 1870 5.726980 TTACCTTGCATGCTCTTTCAAAT 57.273 34.783 20.33 0.0 0.00 2.32



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

AutoCloner maintained by Alex Coulton.