Multiple sequence alignment - TraesCS5A01G003900

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 TraesCS5A01G003900 chr5A 100.000 3091 0 0 1 3091 2726321 2729411 0.000000e+00 5709.0
1 TraesCS5A01G003900 chr3B 83.594 640 66 28 995 1628 55366828 55366222 5.790000e-157 564.0
2 TraesCS5A01G003900 chr3B 97.122 278 8 0 2461 2738 17241823 17241546 1.300000e-128 470.0
3 TraesCS5A01G003900 chr3B 96.479 284 9 1 2459 2742 794632634 794632352 4.670000e-128 468.0
4 TraesCS5A01G003900 chr3D 84.459 592 64 19 995 1581 32713341 32712773 2.690000e-155 558.0
5 TraesCS5A01G003900 chr7B 98.596 285 3 1 2454 2738 221446289 221446006 1.280000e-138 503.0
6 TraesCS5A01G003900 chr3A 97.518 282 7 0 2457 2738 646678882 646678601 1.670000e-132 483.0
7 TraesCS5A01G003900 chr3A 88.473 347 34 4 995 1341 45125364 45125024 6.170000e-112 414.0
8 TraesCS5A01G003900 chr3A 93.464 153 10 0 1429 1581 45124911 45124759 8.620000e-56 228.0
9 TraesCS5A01G003900 chr5B 97.500 280 7 0 2460 2739 505567828 505567549 2.160000e-131 479.0
10 TraesCS5A01G003900 chr5B 96.797 281 9 0 2459 2739 617044667 617044947 1.300000e-128 470.0
11 TraesCS5A01G003900 chr4B 97.473 277 7 0 2463 2739 465456679 465456403 1.000000e-129 473.0
12 TraesCS5A01G003900 chr4B 96.809 282 9 0 2461 2742 203203639 203203358 3.610000e-129 472.0
13 TraesCS5A01G003900 chr4B 89.848 197 20 0 1142 1338 23414696 23414892 1.420000e-63 254.0
14 TraesCS5A01G003900 chr4B 88.832 197 22 0 1142 1338 23392661 23392465 3.080000e-60 243.0
15 TraesCS5A01G003900 chr4A 96.797 281 9 0 2458 2738 3385941 3386221 1.300000e-128 470.0
16 TraesCS5A01G003900 chr4A 89.848 197 20 0 1142 1338 589661694 589661890 1.420000e-63 254.0
17 TraesCS5A01G003900 chr4A 89.848 197 20 0 1142 1338 589835325 589835521 1.420000e-63 254.0
18 TraesCS5A01G003900 chr4A 87.817 197 24 0 1142 1338 589813275 589813471 6.670000e-57 231.0
19 TraesCS5A01G003900 chr5D 92.832 279 14 3 885 1160 3828882 3829157 1.730000e-107 399.0
20 TraesCS5A01G003900 chr5D 84.848 264 26 8 2016 2269 3829968 3830227 1.420000e-63 254.0
21 TraesCS5A01G003900 chr5D 86.224 196 15 7 2904 3091 3830505 3830696 5.230000e-48 202.0
22 TraesCS5A01G003900 chr5D 93.077 130 5 1 1429 1554 3829164 3829293 1.460000e-43 187.0
23 TraesCS5A01G003900 chr5D 76.623 154 30 4 2104 2254 3830306 3830456 2.560000e-11 80.5
24 TraesCS5A01G003900 chr4D 88.832 197 22 0 1142 1338 12668268 12668072 3.080000e-60 243.0


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 TraesCS5A01G003900 chr5A 2726321 2729411 3090 False 5709.0 5709 100.0000 1 3091 1 chr5A.!!$F1 3090
1 TraesCS5A01G003900 chr3B 55366222 55366828 606 True 564.0 564 83.5940 995 1628 1 chr3B.!!$R2 633
2 TraesCS5A01G003900 chr3D 32712773 32713341 568 True 558.0 558 84.4590 995 1581 1 chr3D.!!$R1 586
3 TraesCS5A01G003900 chr3A 45124759 45125364 605 True 321.0 414 90.9685 995 1581 2 chr3A.!!$R2 586
4 TraesCS5A01G003900 chr5D 3828882 3830696 1814 False 224.5 399 86.7208 885 3091 5 chr5D.!!$F1 2206


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
647 648 0.02877 CGCGTCTCTCTCTGTCCATC 59.971 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2577 3040 0.034756 TGGAGTGTGTGATGTTCCGG 59.965 55.0 0.0 0.0 0.0 5.14 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)



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

AutoCloner maintained by Alex Coulton.