Multiple sequence alignment - TraesCS4B01G312500

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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 TraesCS4B01G312500 chr4B 100.000 2609 0 0 1 2609 602293337 602290729 0.000000e+00 4819
1 TraesCS4B01G312500 chr4B 90.177 1812 123 30 840 2608 194219979 194221778 0.000000e+00 2309
2 TraesCS4B01G312500 chr4B 87.630 865 55 30 1 850 194219098 194219925 0.000000e+00 957
3 TraesCS4B01G312500 chr6D 91.682 2633 154 33 1 2608 14045561 14048153 0.000000e+00 3589
4 TraesCS4B01G312500 chr5D 90.964 2634 154 39 1 2608 373747708 373750283 0.000000e+00 3469
5 TraesCS4B01G312500 chr6A 86.556 2648 258 54 1 2608 74674998 74677587 0.000000e+00 2828
6 TraesCS4B01G312500 chr5B 91.553 2060 135 19 558 2608 445131422 445133451 0.000000e+00 2804
7 TraesCS4B01G312500 chr5B 90.929 1797 118 24 854 2608 420718032 420719825 0.000000e+00 2374
8 TraesCS4B01G312500 chr5B 90.221 1810 124 29 840 2608 179227840 179229637 0.000000e+00 2313
9 TraesCS4B01G312500 chr5B 88.051 862 54 22 1 850 179226962 179227786 0.000000e+00 976
10 TraesCS4B01G312500 chr5B 87.963 864 54 26 1 850 406870655 406869828 0.000000e+00 974
11 TraesCS4B01G312500 chr5B 87.826 575 51 10 1 562 445111491 445112059 0.000000e+00 656
12 TraesCS4B01G312500 chr2D 93.764 1764 99 9 849 2608 617164184 617162428 0.000000e+00 2638
13 TraesCS4B01G312500 chr2D 93.140 860 39 12 1 850 617165088 617164239 0.000000e+00 1243
14 TraesCS4B01G312500 chr1D 93.718 1767 97 12 848 2608 485158460 485160218 0.000000e+00 2636
15 TraesCS4B01G312500 chr1D 94.416 591 27 5 263 850 485157818 485158405 0.000000e+00 904
16 TraesCS4B01G312500 chr2A 92.325 1772 104 18 848 2608 17676655 17674905 0.000000e+00 2490
17 TraesCS4B01G312500 chr2A 87.935 862 54 23 1 850 719453738 719454561 0.000000e+00 970
18 TraesCS4B01G312500 chr2A 87.703 862 58 23 1 850 43380232 43381057 0.000000e+00 961
19 TraesCS4B01G312500 chr2A 94.247 591 29 4 263 850 17677299 17676711 0.000000e+00 898
20 TraesCS4B01G312500 chr7B 90.558 1811 122 26 840 2608 68098241 68100044 0.000000e+00 2351
21 TraesCS4B01G312500 chr7B 88.079 864 52 24 1 850 528879444 528880270 0.000000e+00 977
22 TraesCS4B01G312500 chr3B 90.492 1809 123 23 840 2608 552478977 552480776 0.000000e+00 2342
23 TraesCS4B01G312500 chr3B 88.208 865 52 23 1 851 552478097 552478925 0.000000e+00 987
24 TraesCS4B01G312500 chr7A 90.387 1810 121 29 840 2608 171419456 171421253 0.000000e+00 2329
25 TraesCS4B01G312500 chr7A 85.681 866 53 35 1 850 171418592 171419402 0.000000e+00 846
26 TraesCS4B01G312500 chr1A 90.306 1795 126 29 854 2608 567477295 567475509 0.000000e+00 2307
27 TraesCS4B01G312500 chr1A 85.658 509 36 21 2131 2608 567471887 567471385 3.880000e-138 501
28 TraesCS4B01G312500 chr6B 87.963 864 53 26 1 850 704850743 704849917 0.000000e+00 972


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 TraesCS4B01G312500 chr4B 602290729 602293337 2608 True 4819.0 4819 100.0000 1 2609 1 chr4B.!!$R1 2608
1 TraesCS4B01G312500 chr4B 194219098 194221778 2680 False 1633.0 2309 88.9035 1 2608 2 chr4B.!!$F1 2607
2 TraesCS4B01G312500 chr6D 14045561 14048153 2592 False 3589.0 3589 91.6820 1 2608 1 chr6D.!!$F1 2607
3 TraesCS4B01G312500 chr5D 373747708 373750283 2575 False 3469.0 3469 90.9640 1 2608 1 chr5D.!!$F1 2607
4 TraesCS4B01G312500 chr6A 74674998 74677587 2589 False 2828.0 2828 86.5560 1 2608 1 chr6A.!!$F1 2607
5 TraesCS4B01G312500 chr5B 445131422 445133451 2029 False 2804.0 2804 91.5530 558 2608 1 chr5B.!!$F3 2050
6 TraesCS4B01G312500 chr5B 420718032 420719825 1793 False 2374.0 2374 90.9290 854 2608 1 chr5B.!!$F1 1754
7 TraesCS4B01G312500 chr5B 179226962 179229637 2675 False 1644.5 2313 89.1360 1 2608 2 chr5B.!!$F4 2607
8 TraesCS4B01G312500 chr5B 406869828 406870655 827 True 974.0 974 87.9630 1 850 1 chr5B.!!$R1 849
9 TraesCS4B01G312500 chr5B 445111491 445112059 568 False 656.0 656 87.8260 1 562 1 chr5B.!!$F2 561
10 TraesCS4B01G312500 chr2D 617162428 617165088 2660 True 1940.5 2638 93.4520 1 2608 2 chr2D.!!$R1 2607
11 TraesCS4B01G312500 chr1D 485157818 485160218 2400 False 1770.0 2636 94.0670 263 2608 2 chr1D.!!$F1 2345
12 TraesCS4B01G312500 chr2A 17674905 17677299 2394 True 1694.0 2490 93.2860 263 2608 2 chr2A.!!$R1 2345
13 TraesCS4B01G312500 chr2A 719453738 719454561 823 False 970.0 970 87.9350 1 850 1 chr2A.!!$F2 849
14 TraesCS4B01G312500 chr2A 43380232 43381057 825 False 961.0 961 87.7030 1 850 1 chr2A.!!$F1 849
15 TraesCS4B01G312500 chr7B 68098241 68100044 1803 False 2351.0 2351 90.5580 840 2608 1 chr7B.!!$F1 1768
16 TraesCS4B01G312500 chr7B 528879444 528880270 826 False 977.0 977 88.0790 1 850 1 chr7B.!!$F2 849
17 TraesCS4B01G312500 chr3B 552478097 552480776 2679 False 1664.5 2342 89.3500 1 2608 2 chr3B.!!$F1 2607
18 TraesCS4B01G312500 chr7A 171418592 171421253 2661 False 1587.5 2329 88.0340 1 2608 2 chr7A.!!$F1 2607
19 TraesCS4B01G312500 chr1A 567471385 567477295 5910 True 1404.0 2307 87.9820 854 2608 2 chr1A.!!$R1 1754
20 TraesCS4B01G312500 chr6B 704849917 704850743 826 True 972.0 972 87.9630 1 850 1 chr6B.!!$R1 849


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
172 187 1.681229 TGAAAGAGGGGGTAGGCAAT 58.319 50.0 0.0 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1862 1.627329 TCCCATCTGCCATCTATCAGC 59.373 52.381 0.0 0.0 0.0 4.26 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)



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AutoCloner maintained by Alex Coulton.