Multiple sequence alignment - TraesCS5B01G508500

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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 TraesCS5B01G508500 chr5B 100.000 2959 0 0 944 3902 673679865 673682823 0.000000e+00 5465.0
1 TraesCS5B01G508500 chr5B 100.000 648 0 0 1 648 673678922 673679569 0.000000e+00 1197.0
2 TraesCS5B01G508500 chr5B 81.126 604 54 16 944 1543 673636177 673636724 2.790000e-116 429.0
3 TraesCS5B01G508500 chr5B 85.498 331 36 7 944 1274 673670126 673670444 6.250000e-88 335.0
4 TraesCS5B01G508500 chr5B 89.510 143 13 2 1275 1417 673670682 673670822 3.100000e-41 180.0
5 TraesCS5B01G508500 chr5B 86.275 102 6 3 1827 1921 673638691 673638791 1.920000e-18 104.0
6 TraesCS5B01G508500 chr5B 91.667 72 4 2 1446 1517 673671539 673671608 8.920000e-17 99.0
7 TraesCS5B01G508500 chr5B 85.870 92 10 3 3247 3336 568731929 568732019 1.150000e-15 95.3
8 TraesCS5B01G508500 chr5D 89.638 2210 145 37 1602 3779 533631269 533633426 0.000000e+00 2736.0
9 TraesCS5B01G508500 chr5D 90.772 531 23 8 1021 1543 533630701 533631213 0.000000e+00 686.0
10 TraesCS5B01G508500 chr5D 82.011 378 34 17 1131 1506 533576168 533576513 1.370000e-74 291.0
11 TraesCS5B01G508500 chr5D 85.965 114 10 2 535 642 533629834 533629947 2.460000e-22 117.0
12 TraesCS5B01G508500 chr5D 95.455 44 2 0 1290 1333 533545493 533545536 1.950000e-08 71.3
13 TraesCS5B01G508500 chr5D 100.000 29 0 0 1572 1600 533631215 533631243 2.000000e-03 54.7
14 TraesCS5B01G508500 chr4A 86.177 1823 125 69 1600 3366 638221797 638220046 0.000000e+00 1853.0
15 TraesCS5B01G508500 chr4A 88.816 608 39 16 947 1543 638222450 638221861 0.000000e+00 719.0
16 TraesCS5B01G508500 chr4A 93.750 432 26 1 3458 3889 638220044 638219614 0.000000e+00 647.0
17 TraesCS5B01G508500 chr4A 82.550 149 13 6 3510 3645 395039389 395039537 6.850000e-23 119.0
18 TraesCS5B01G508500 chr6B 79.545 528 77 21 3372 3876 392492463 392491944 8.020000e-92 348.0
19 TraesCS5B01G508500 chr4D 79.480 346 38 15 3470 3796 215447003 215446672 8.490000e-52 215.0
20 TraesCS5B01G508500 chr2D 80.612 196 22 8 3697 3889 33723871 33724053 1.890000e-28 137.0
21 TraesCS5B01G508500 chr2D 86.667 105 14 0 436 540 562580333 562580437 2.460000e-22 117.0
22 TraesCS5B01G508500 chr7D 80.982 163 22 7 3199 3353 125879369 125879208 1.900000e-23 121.0
23 TraesCS5B01G508500 chr7D 80.982 163 22 7 3199 3353 125886276 125886115 1.900000e-23 121.0
24 TraesCS5B01G508500 chr7D 94.737 38 2 0 2544 2581 32644811 32644848 4.210000e-05 60.2
25 TraesCS5B01G508500 chr2B 100.000 28 0 0 423 450 52720464 52720491 7.000000e-03 52.8


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 TraesCS5B01G508500 chr5B 673678922 673682823 3901 False 3331.000000 5465 100.000000 1 3902 2 chr5B.!!$F4 3901
1 TraesCS5B01G508500 chr5B 673636177 673638791 2614 False 266.500000 429 83.700500 944 1921 2 chr5B.!!$F2 977
2 TraesCS5B01G508500 chr5B 673670126 673671608 1482 False 204.666667 335 88.891667 944 1517 3 chr5B.!!$F3 573
3 TraesCS5B01G508500 chr5D 533629834 533633426 3592 False 898.425000 2736 91.593750 535 3779 4 chr5D.!!$F3 3244
4 TraesCS5B01G508500 chr4A 638219614 638222450 2836 True 1073.000000 1853 89.581000 947 3889 3 chr4A.!!$R1 2942
5 TraesCS5B01G508500 chr6B 392491944 392492463 519 True 348.000000 348 79.545000 3372 3876 1 chr6B.!!$R1 504


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
520 521 0.028505 CGAGCCGCATGAATTCAAGG 59.971 55.0 13.09 16.32 0.00 3.61 F
1234 1787 0.175760 ATACGCATGCACGTCCTTCT 59.824 50.0 19.57 0.00 44.43 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2219 5534 0.179145 CCTTATTGTGCTGCTGCTGC 60.179 55.0 22.51 22.51 40.48 5.25 R
3196 6536 0.031994 AACCATTGCCGTGTTGAAGC 59.968 50.0 0.00 0.00 0.00 3.86 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.