Multiple sequence alignment - TraesCS7B01G168400

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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 TraesCS7B01G168400 chr7B 100.000 2264 0 0 1 2264 235458094 235455831 0.000000e+00 4181.0
1 TraesCS7B01G168400 chr7B 92.876 2302 116 25 1 2264 687040622 687042913 0.000000e+00 3299.0
2 TraesCS7B01G168400 chr5B 96.865 2265 68 3 1 2264 530940831 530938569 0.000000e+00 3786.0
3 TraesCS7B01G168400 chr5B 94.672 2177 71 10 1 2149 464634106 464636265 0.000000e+00 3336.0
4 TraesCS7B01G168400 chr3B 94.110 2292 93 10 1 2264 16124436 16122159 0.000000e+00 3446.0
5 TraesCS7B01G168400 chr3B 92.934 1486 65 16 814 2264 393329884 393331364 0.000000e+00 2126.0
6 TraesCS7B01G168400 chr3B 90.170 529 45 6 1738 2264 28618692 28619215 0.000000e+00 682.0
7 TraesCS7B01G168400 chr3B 87.136 412 38 8 1738 2149 112911553 112911949 9.530000e-124 453.0
8 TraesCS7B01G168400 chr3B 88.095 126 5 4 1706 1831 16201768 16201653 8.430000e-30 141.0
9 TraesCS7B01G168400 chr2B 93.848 2292 95 13 1 2264 563917140 563914867 0.000000e+00 3410.0
10 TraesCS7B01G168400 chr1B 92.268 2302 118 28 1 2264 38183391 38185670 0.000000e+00 3210.0
11 TraesCS7B01G168400 chr4B 97.429 1750 45 0 1 1750 402787203 402785454 0.000000e+00 2983.0
12 TraesCS7B01G168400 chr4A 97.171 1732 47 1 1 1732 712877478 712879207 0.000000e+00 2926.0
13 TraesCS7B01G168400 chr4A 91.403 1675 82 18 621 2264 698022900 698021257 0.000000e+00 2239.0
14 TraesCS7B01G168400 chr4A 94.778 517 27 0 1748 2264 712879259 712879775 0.000000e+00 806.0
15 TraesCS7B01G168400 chr4A 89.275 345 37 0 1920 2264 735294641 735294985 1.240000e-117 433.0
16 TraesCS7B01G168400 chr4A 94.714 227 12 0 2038 2264 712879431 712879657 9.950000e-94 353.0
17 TraesCS7B01G168400 chr4A 89.655 261 27 0 2004 2264 735294607 735294867 1.300000e-87 333.0
18 TraesCS7B01G168400 chr4A 92.174 230 18 0 1920 2149 712879549 712879778 2.170000e-85 326.0
19 TraesCS7B01G168400 chr4A 88.696 230 26 0 1920 2149 735294759 735294988 4.760000e-72 281.0
20 TraesCS7B01G168400 chr4A 87.209 86 7 2 1692 1777 514405870 514405789 6.660000e-16 95.3
21 TraesCS7B01G168400 chr7A 97.150 1719 48 1 1 1719 7487849 7486132 0.000000e+00 2902.0
22 TraesCS7B01G168400 chr6B 92.808 1752 76 19 557 2264 650646145 650644400 0.000000e+00 2492.0


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 TraesCS7B01G168400 chr7B 235455831 235458094 2263 True 4181.00 4181 100.00000 1 2264 1 chr7B.!!$R1 2263
1 TraesCS7B01G168400 chr7B 687040622 687042913 2291 False 3299.00 3299 92.87600 1 2264 1 chr7B.!!$F1 2263
2 TraesCS7B01G168400 chr5B 530938569 530940831 2262 True 3786.00 3786 96.86500 1 2264 1 chr5B.!!$R1 2263
3 TraesCS7B01G168400 chr5B 464634106 464636265 2159 False 3336.00 3336 94.67200 1 2149 1 chr5B.!!$F1 2148
4 TraesCS7B01G168400 chr3B 16122159 16124436 2277 True 3446.00 3446 94.11000 1 2264 1 chr3B.!!$R1 2263
5 TraesCS7B01G168400 chr3B 393329884 393331364 1480 False 2126.00 2126 92.93400 814 2264 1 chr3B.!!$F3 1450
6 TraesCS7B01G168400 chr3B 28618692 28619215 523 False 682.00 682 90.17000 1738 2264 1 chr3B.!!$F1 526
7 TraesCS7B01G168400 chr2B 563914867 563917140 2273 True 3410.00 3410 93.84800 1 2264 1 chr2B.!!$R1 2263
8 TraesCS7B01G168400 chr1B 38183391 38185670 2279 False 3210.00 3210 92.26800 1 2264 1 chr1B.!!$F1 2263
9 TraesCS7B01G168400 chr4B 402785454 402787203 1749 True 2983.00 2983 97.42900 1 1750 1 chr4B.!!$R1 1749
10 TraesCS7B01G168400 chr4A 698021257 698022900 1643 True 2239.00 2239 91.40300 621 2264 1 chr4A.!!$R2 1643
11 TraesCS7B01G168400 chr4A 712877478 712879778 2300 False 1102.75 2926 94.70925 1 2264 4 chr4A.!!$F1 2263
12 TraesCS7B01G168400 chr7A 7486132 7487849 1717 True 2902.00 2902 97.15000 1 1719 1 chr7A.!!$R1 1718
13 TraesCS7B01G168400 chr6B 650644400 650646145 1745 True 2492.00 2492 92.80800 557 2264 1 chr6B.!!$R1 1707


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
733 773 0.251653 TAGAGGTGGTGGTCGAGCTT 60.252 55.0 16.64 0.0 30.83 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1652 0.247736 GTCCTCCTCTCGTGCATTGT 59.752 55.0 0.0 0.0 0.0 2.71 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.