Multiple sequence alignment - TraesCS2B01G434300

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 TraesCS2B01G434300 chr2B 100.000 2828 0 0 1 2828 624356768 624353941 0.000000e+00 5223
1 TraesCS2B01G434300 chr2D 92.321 1719 73 24 142 1830 527294933 527293244 0.000000e+00 2388
2 TraesCS2B01G434300 chr2D 94.199 362 15 3 2472 2828 527292647 527292287 5.330000e-152 547
3 TraesCS2B01G434300 chr2D 90.808 359 17 7 1923 2267 527293210 527292854 1.530000e-127 466
4 TraesCS2B01G434300 chr2A 92.000 1325 76 18 585 1889 672293169 672291855 0.000000e+00 1832
5 TraesCS2B01G434300 chr2A 88.473 347 25 11 142 484 672293579 672293244 3.390000e-109 405
6 TraesCS2B01G434300 chr2A 86.761 355 26 12 1931 2267 672291850 672291499 2.660000e-100 375
7 TraesCS2B01G434300 chr2A 83.123 397 29 15 2470 2828 672291278 672290882 7.550000e-86 327
8 TraesCS2B01G434300 chr6D 89.575 259 27 0 1285 1543 326540360 326540618 2.100000e-86 329
9 TraesCS2B01G434300 chr6D 85.714 266 35 2 1285 1550 326760711 326760973 7.720000e-71 278
10 TraesCS2B01G434300 chr6B 89.575 259 27 0 1285 1543 495806711 495806453 2.100000e-86 329
11 TraesCS2B01G434300 chr6B 86.090 266 34 2 1285 1550 495543773 495543511 1.660000e-72 283
12 TraesCS2B01G434300 chr6A 89.575 259 27 0 1285 1543 465231917 465232175 2.100000e-86 329
13 TraesCS2B01G434300 chr6A 88.211 246 29 0 1285 1530 465389787 465390032 7.660000e-76 294
14 TraesCS2B01G434300 chr1A 85.606 264 33 4 1283 1542 388849402 388849664 3.590000e-69 272


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 TraesCS2B01G434300 chr2B 624353941 624356768 2827 True 5223.000000 5223 100.000000 1 2828 1 chr2B.!!$R1 2827
1 TraesCS2B01G434300 chr2D 527292287 527294933 2646 True 1133.666667 2388 92.442667 142 2828 3 chr2D.!!$R1 2686
2 TraesCS2B01G434300 chr2A 672290882 672293579 2697 True 734.750000 1832 87.589250 142 2828 4 chr2A.!!$R1 2686


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
95 96 0.034767 TAGTCTCCCGTCGATGGTGT 60.035 55.0 22.05 4.57 0.0 4.16 F
96 97 0.034767 AGTCTCCCGTCGATGGTGTA 60.035 55.0 22.05 6.67 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1098 1168 0.252239 TCTTGGGGAGCTCTAGCACA 60.252 55.000 14.64 0.83 45.16 4.57 R
2061 2138 1.225704 CCAGGGAAGTCCATCCTGC 59.774 63.158 0.00 0.00 44.87 4.85 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.