Multiple sequence alignment - TraesCS7A01G380800

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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 TraesCS7A01G380800 chr7A 100.000 2862 0 0 1 2862 556142466 556139605 0.000000e+00 5286
1 TraesCS7A01G380800 chr7A 98.488 2248 33 1 616 2862 705281551 705283798 0.000000e+00 3962
2 TraesCS7A01G380800 chr5B 98.708 2244 28 1 620 2862 448586418 448588661 0.000000e+00 3982
3 TraesCS7A01G380800 chr4A 98.042 2247 24 3 617 2862 3252925 3255152 0.000000e+00 3888
4 TraesCS7A01G380800 chr1A 96.991 2260 33 7 618 2862 485328195 485330434 0.000000e+00 3764
5 TraesCS7A01G380800 chr1A 97.760 1741 19 3 620 2358 507989878 507991600 0.000000e+00 2981
6 TraesCS7A01G380800 chr1B 97.150 2246 25 3 618 2862 30529926 30532133 0.000000e+00 3757
7 TraesCS7A01G380800 chr1B 89.438 890 63 14 1986 2862 663658095 663657224 0.000000e+00 1094
8 TraesCS7A01G380800 chr2B 96.612 2273 39 14 620 2862 629108934 629111198 0.000000e+00 3736
9 TraesCS7A01G380800 chr2B 95.670 485 21 0 2377 2861 571948016 571948500 0.000000e+00 780
10 TraesCS7A01G380800 chr4B 93.008 2274 88 34 616 2861 134586683 134584453 0.000000e+00 3253
11 TraesCS7A01G380800 chr5A 97.659 1623 17 2 620 2241 666315906 666317508 0.000000e+00 2767
12 TraesCS7A01G380800 chr3B 90.277 1553 70 43 620 2116 379678261 379676734 0.000000e+00 1956
13 TraesCS7A01G380800 chr3B 96.486 370 11 2 617 985 457636051 457636419 6.780000e-171 610
14 TraesCS7A01G380800 chr7B 94.603 630 24 3 1 620 517091266 517090637 0.000000e+00 966
15 TraesCS7A01G380800 chr7D 93.590 546 21 5 47 590 488684403 488683870 0.000000e+00 802
16 TraesCS7A01G380800 chr3A 95.679 486 21 0 2377 2862 11578954 11579439 0.000000e+00 782


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 TraesCS7A01G380800 chr7A 556139605 556142466 2861 True 5286 5286 100.000 1 2862 1 chr7A.!!$R1 2861
1 TraesCS7A01G380800 chr7A 705281551 705283798 2247 False 3962 3962 98.488 616 2862 1 chr7A.!!$F1 2246
2 TraesCS7A01G380800 chr5B 448586418 448588661 2243 False 3982 3982 98.708 620 2862 1 chr5B.!!$F1 2242
3 TraesCS7A01G380800 chr4A 3252925 3255152 2227 False 3888 3888 98.042 617 2862 1 chr4A.!!$F1 2245
4 TraesCS7A01G380800 chr1A 485328195 485330434 2239 False 3764 3764 96.991 618 2862 1 chr1A.!!$F1 2244
5 TraesCS7A01G380800 chr1A 507989878 507991600 1722 False 2981 2981 97.760 620 2358 1 chr1A.!!$F2 1738
6 TraesCS7A01G380800 chr1B 30529926 30532133 2207 False 3757 3757 97.150 618 2862 1 chr1B.!!$F1 2244
7 TraesCS7A01G380800 chr1B 663657224 663658095 871 True 1094 1094 89.438 1986 2862 1 chr1B.!!$R1 876
8 TraesCS7A01G380800 chr2B 629108934 629111198 2264 False 3736 3736 96.612 620 2862 1 chr2B.!!$F2 2242
9 TraesCS7A01G380800 chr4B 134584453 134586683 2230 True 3253 3253 93.008 616 2861 1 chr4B.!!$R1 2245
10 TraesCS7A01G380800 chr5A 666315906 666317508 1602 False 2767 2767 97.659 620 2241 1 chr5A.!!$F1 1621
11 TraesCS7A01G380800 chr3B 379676734 379678261 1527 True 1956 1956 90.277 620 2116 1 chr3B.!!$R1 1496
12 TraesCS7A01G380800 chr7B 517090637 517091266 629 True 966 966 94.603 1 620 1 chr7B.!!$R1 619
13 TraesCS7A01G380800 chr7D 488683870 488684403 533 True 802 802 93.590 47 590 1 chr7D.!!$R1 543

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
606 617 1.835531 GGATAGTTCGGGTTGAAGGGA 59.164 52.381 0.0 0.0 37.23 4.20 F
881 914 3.660959 TCCCCATTCGTAAATCCCTAGT 58.339 45.455 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 1884 4.584743 GGCTAACCAAATTTCCCTCCTATG 59.415 45.833 0.0 0.0 35.26 2.23 R
2712 2932 4.465512 GCTCGTTACGCCGGTCGA 62.466 66.667 22.1 14.1 41.67 4.20 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
399 400 2.041265 GGAGGGGCTGAGGAGGAA 59.959 66.667 0.0 0.0 0.00 3.36
488 491 2.362889 CCATGGCTTCCCCGCTTT 60.363 61.111 0.0 0.0 35.87 3.51
554 557 2.768344 GATGGAAGGCGGGGGAGA 60.768 66.667 0.0 0.0 0.00 3.71
578 589 3.023949 GCGGAGAGGACAGCACCAT 62.024 63.158 0.0 0.0 0.00 3.55
606 617 1.835531 GGATAGTTCGGGTTGAAGGGA 59.164 52.381 0.0 0.0 37.23 4.20
662 673 4.293901 ACATAAACTTGTAGGGGTGGGAAT 59.706 41.667 0.0 0.0 0.00 3.01
881 914 3.660959 TCCCCATTCGTAAATCCCTAGT 58.339 45.455 0.0 0.0 0.00 2.57
1382 1480 3.890756 TCAATGGCAGTGACAAAAGTGAT 59.109 39.130 14.4 0.0 0.00 3.06
1772 1884 4.161377 ACAAGAAGGAGATCAGAACTAGGC 59.839 45.833 0.0 0.0 0.00 3.93
1822 1934 0.179037 TCTGCTGCTCTGCACTGTTT 60.179 50.000 0.0 0.0 38.12 2.83
1950 2082 8.492415 TCAGTGGCTACCTATTATCTATGTTT 57.508 34.615 0.0 0.0 0.00 2.83
2032 2183 7.065324 TGTTCAGTGTTCTGTTTACTTAACTGG 59.935 37.037 0.0 0.0 41.91 4.00
2712 2932 0.818040 GTTTCTGCCACCCTCAACGT 60.818 55.000 0.0 0.0 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.456280 GCTCTTCTCAGGTATGCTTCAG 58.544 50.000 0.00 0.0 0.00 3.02
440 441 4.925861 GAGCATGCGCCTCCCCTC 62.926 72.222 13.01 0.0 39.83 4.30
484 485 0.969149 CCACCAGGAAAAGGGAAAGC 59.031 55.000 0.00 0.0 36.89 3.51
485 486 2.158460 ACTCCACCAGGAAAAGGGAAAG 60.158 50.000 0.00 0.0 45.19 2.62
488 491 1.529744 AACTCCACCAGGAAAAGGGA 58.470 50.000 0.00 0.0 45.19 4.20
521 524 0.943673 CATCTCCACAAACACGCACA 59.056 50.000 0.00 0.0 0.00 4.57
554 557 4.316823 TGTCCTCTCCGCCCCACT 62.317 66.667 0.00 0.0 0.00 4.00
578 589 5.132502 TCAACCCGAACTATCCGTTATCTA 58.867 41.667 0.00 0.0 35.56 1.98
606 617 7.238486 TGGTATTAACTCAAATGCCAAACAT 57.762 32.000 4.23 0.0 45.18 2.71
685 697 0.404426 GGAGGGCTAGTTTTGTGGGT 59.596 55.000 0.00 0.0 0.00 4.51
881 914 3.702048 CAAAGGGGAGGGCGACGA 61.702 66.667 0.00 0.0 0.00 4.20
1136 1233 0.537600 TCCGGTGATTTTCGCCCAAA 60.538 50.000 0.00 0.0 43.95 3.28
1564 1665 5.536538 TGTATCATAACCCTGCAAAACACAA 59.463 36.000 0.00 0.0 0.00 3.33
1772 1884 4.584743 GGCTAACCAAATTTCCCTCCTATG 59.415 45.833 0.00 0.0 35.26 2.23
1822 1934 5.731957 TCACTAGTGCTACAACACCATAA 57.268 39.130 18.45 0.0 41.67 1.90
2161 2370 7.524294 AACTTAACTGAAATTTGCACTGTTG 57.476 32.000 0.00 0.0 0.00 3.33
2461 2681 7.507277 AGTTAGGTCTGCTGATCTATATGTTGA 59.493 37.037 13.68 0.0 35.98 3.18
2712 2932 4.465512 GCTCGTTACGCCGGTCGA 62.466 66.667 22.10 14.1 41.67 4.20


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

AutoCloner maintained by Alex Coulton.