Multiple sequence alignment - TraesCS3A01G480800

Loading Multiple Alignment...

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 TraesCS3A01G480800 chr3A 100.000 2624 0 0 1 2624 711578029 711575406 0 4846
1 TraesCS3A01G480800 chr3A 97.187 2631 65 7 1 2624 745750330 745752958 0 4440
2 TraesCS3A01G480800 chr6A 97.073 2631 69 5 1 2624 494425300 494427929 0 4425
3 TraesCS3A01G480800 chr6A 96.467 2632 85 5 1 2624 554915088 554917719 0 4338
4 TraesCS3A01G480800 chr2A 96.882 2630 75 4 1 2624 733070589 733073217 0 4396
5 TraesCS3A01G480800 chr2A 96.768 2630 70 8 1 2624 58510412 58507792 0 4372
6 TraesCS3A01G480800 chr1A 96.505 2632 82 7 1 2624 21073548 21070919 0 4342
7 TraesCS3A01G480800 chr1A 95.784 2633 98 10 1 2624 10682135 10684763 0 4235
8 TraesCS3A01G480800 chr4A 96.814 2574 73 6 1 2567 37320265 37322836 0 4290
9 TraesCS3A01G480800 chr5A 95.822 2633 98 9 1 2624 33905187 33907816 0 4242


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 TraesCS3A01G480800 chr3A 711575406 711578029 2623 True 4846 4846 100.000 1 2624 1 chr3A.!!$R1 2623
1 TraesCS3A01G480800 chr3A 745750330 745752958 2628 False 4440 4440 97.187 1 2624 1 chr3A.!!$F1 2623
2 TraesCS3A01G480800 chr6A 494425300 494427929 2629 False 4425 4425 97.073 1 2624 1 chr6A.!!$F1 2623
3 TraesCS3A01G480800 chr6A 554915088 554917719 2631 False 4338 4338 96.467 1 2624 1 chr6A.!!$F2 2623
4 TraesCS3A01G480800 chr2A 733070589 733073217 2628 False 4396 4396 96.882 1 2624 1 chr2A.!!$F1 2623
5 TraesCS3A01G480800 chr2A 58507792 58510412 2620 True 4372 4372 96.768 1 2624 1 chr2A.!!$R1 2623
6 TraesCS3A01G480800 chr1A 21070919 21073548 2629 True 4342 4342 96.505 1 2624 1 chr1A.!!$R1 2623
7 TraesCS3A01G480800 chr1A 10682135 10684763 2628 False 4235 4235 95.784 1 2624 1 chr1A.!!$F1 2623
8 TraesCS3A01G480800 chr4A 37320265 37322836 2571 False 4290 4290 96.814 1 2567 1 chr4A.!!$F1 2566
9 TraesCS3A01G480800 chr5A 33905187 33907816 2629 False 4242 4242 95.822 1 2624 1 chr5A.!!$F1 2623

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
222 225 0.461548 TGCATGTTGGCCAAAAACGA 59.538 45.000 22.47 1.22 0.00 3.85 F
995 1004 1.888512 GCAGCATCCAAGAACAAGGAA 59.111 47.619 0.00 0.00 37.48 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1201 1210 0.604780 TGGCTCTCTGACTGCAAAGC 60.605 55.0 0.0 0.00 0.0 3.51 R
2537 2553 0.248012 TCCTATGAAAGGCGCGAACA 59.752 50.0 12.1 1.52 46.1 3.18 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
190 193 6.649155 TCTAGCCAACTGAATGCATTAACTA 58.351 36.000 12.97 1.62 0.00 2.24
221 224 1.194997 CATGCATGTTGGCCAAAAACG 59.805 47.619 22.47 11.98 0.00 3.60
222 225 0.461548 TGCATGTTGGCCAAAAACGA 59.538 45.000 22.47 1.22 0.00 3.85
266 269 5.010922 AGCTGAGACATCTATTCTAGCCAAG 59.989 44.000 0.00 0.00 0.00 3.61
373 376 6.568462 CGAAAACCAGAAATCTGTAGTGCAAT 60.568 38.462 9.43 0.00 42.27 3.56
589 592 7.013655 CCAATTCTTCTTTCTTCTTTCACCTGA 59.986 37.037 0.00 0.00 0.00 3.86
609 612 8.359642 CACCTGAATTTTCCTTCTCAAATGTAA 58.640 33.333 0.00 0.00 0.00 2.41
995 1004 1.888512 GCAGCATCCAAGAACAAGGAA 59.111 47.619 0.00 0.00 37.48 3.36
1182 1191 2.439156 GGCCAGTCATCAGCCCAC 60.439 66.667 0.00 0.00 41.00 4.61
1404 1413 8.579850 TTCAAATTGCTAAGGATCACTACAAT 57.420 30.769 0.00 0.00 32.12 2.71
1417 1426 6.349445 GGATCACTACAATAGCTACGCACTAT 60.349 42.308 0.00 0.00 31.60 2.12
1425 1434 0.951040 GCTACGCACTATGGATGGGC 60.951 60.000 0.00 0.00 33.49 5.36
1513 1522 2.754552 TGCTGCAACAAGTTCAAGAAGT 59.245 40.909 0.00 0.00 0.00 3.01
1586 1595 7.831691 TTCCAGATCCAAAATCTGTTAACAA 57.168 32.000 10.03 1.56 42.88 2.83
1752 1766 1.278637 CGCACTTTGTTCGTGACCC 59.721 57.895 0.00 0.00 34.35 4.46
1779 1793 0.099791 CCGCTTGTGAACAAACCGTT 59.900 50.000 12.14 0.00 41.86 4.44
2273 2289 2.405559 TGGATCTGAGATGATGGTGCT 58.594 47.619 0.00 0.00 0.00 4.40
2356 2372 6.408548 GGAGGGTGATCTGATTGAGACAATTA 60.409 42.308 0.00 0.00 31.75 1.40
2487 2503 0.597637 CTTATGCGGAGGCGTACCAG 60.598 60.000 0.00 0.00 44.10 4.00
2536 2552 7.768582 CCTACATGACCAACTTGTACAATATGA 59.231 37.037 9.13 0.00 37.85 2.15
2537 2553 9.330063 CTACATGACCAACTTGTACAATATGAT 57.670 33.333 9.13 0.00 37.85 2.45
2547 2563 1.953559 ACAATATGATGTTCGCGCCT 58.046 45.000 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 148 6.252599 AGAATATATGTCTCAGTTGGCCAA 57.747 37.500 16.05 16.05 0.00 4.52
221 224 3.934579 CTGGCCAGGTTGCATTTATTTTC 59.065 43.478 26.14 0.00 0.00 2.29
222 225 3.869526 GCTGGCCAGGTTGCATTTATTTT 60.870 43.478 33.46 0.00 0.00 1.82
266 269 7.206687 TCCAGTTGGACATTCAATGTTTTTAC 58.793 34.615 4.04 1.72 45.03 2.01
373 376 8.744652 TGGACAAAAGTTCTTGTGATTTTTCTA 58.255 29.630 9.39 0.00 39.63 2.10
381 384 3.068024 GCCATGGACAAAAGTTCTTGTGA 59.932 43.478 18.40 0.00 39.63 3.58
589 592 8.869109 TGGATGTTACATTTGAGAAGGAAAATT 58.131 29.630 0.00 0.00 0.00 1.82
609 612 7.762615 CAGATTTTTCTGCACATAATTGGATGT 59.237 33.333 0.00 0.00 40.78 3.06
655 658 6.774673 TGTTGTAATGATCTGTAGGTTTCCA 58.225 36.000 0.00 0.00 0.00 3.53
1190 1199 1.202927 ACTGCAAAGCCACCACTACAT 60.203 47.619 0.00 0.00 0.00 2.29
1201 1210 0.604780 TGGCTCTCTGACTGCAAAGC 60.605 55.000 0.00 0.00 0.00 3.51
1417 1426 3.657610 TCTTGATAGAGAAGCCCATCCA 58.342 45.455 0.00 0.00 0.00 3.41
1425 1434 7.111247 AGAGGTGTTCATCTTGATAGAGAAG 57.889 40.000 0.00 0.00 30.03 2.85
1513 1522 2.172082 CTCCTCCATCATCAGCTTTGGA 59.828 50.000 0.00 0.00 36.81 3.53
1586 1595 4.725810 AGGTTCTTTCCATCTCCTCATCAT 59.274 41.667 0.00 0.00 0.00 2.45
1688 1702 4.278170 CAGCTTCACCAACATTTTCACCTA 59.722 41.667 0.00 0.00 0.00 3.08
1752 1766 1.811965 TGTTCACAAGCGGATGATTGG 59.188 47.619 0.00 0.00 45.62 3.16
1779 1793 7.054124 GTGGGATCTCAAGTATTTGGACAATA 58.946 38.462 0.00 0.00 34.97 1.90
1903 1917 2.122768 CTGGACTGCCTAGAGGGAAAT 58.877 52.381 0.00 0.00 34.22 2.17
2033 2047 6.136071 GTGTAGTTGCACAGTAAAGACAATG 58.864 40.000 0.00 0.00 39.07 2.82
2243 2259 7.038870 CCATCATCTCAGATCCATAGAACTCTT 60.039 40.741 0.00 0.00 0.00 2.85
2273 2289 2.554893 GTTATTGCCTTTGGTCCGAACA 59.445 45.455 0.00 0.00 0.00 3.18
2356 2372 6.811253 TTTTTGTATATCCTTGAAGTGCGT 57.189 33.333 0.00 0.00 0.00 5.24
2487 2503 3.376859 TGGTGTCAAACGATATGCAATCC 59.623 43.478 0.00 0.00 0.00 3.01
2536 2552 1.134521 TCCTATGAAAGGCGCGAACAT 60.135 47.619 12.10 9.55 46.10 2.71
2537 2553 0.248012 TCCTATGAAAGGCGCGAACA 59.752 50.000 12.10 1.52 46.10 3.18
2547 2563 5.298276 GCCATGTCGGTTTATTCCTATGAAA 59.702 40.000 0.00 0.00 36.97 2.69


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

AutoCloner maintained by Alex Coulton.