Multiple sequence alignment - TraesCS1B01G065400

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 TraesCS1B01G065400 chr1B 100.000 2396 0 0 1 2396 49797222 49794827 0.000000e+00 4425
1 TraesCS1B01G065400 chr3D 97.118 2429 36 17 1 2396 202636571 202634144 0.000000e+00 4067
2 TraesCS1B01G065400 chr3D 96.910 2427 44 14 1 2396 546345430 546343004 0.000000e+00 4037
3 TraesCS1B01G065400 chr2D 97.032 2426 41 14 1 2396 634993975 634991551 0.000000e+00 4052
4 TraesCS1B01G065400 chr5B 97.070 2423 36 15 1 2393 202673967 202676384 0.000000e+00 4048
5 TraesCS1B01G065400 chr5B 96.866 2425 39 15 1 2393 695886917 695889336 0.000000e+00 4023
6 TraesCS1B01G065400 chrUn 96.947 2424 38 15 1 2393 266189282 266191700 0.000000e+00 4034
7 TraesCS1B01G065400 chrUn 96.908 2426 40 14 1 2396 246709346 246706926 0.000000e+00 4032
8 TraesCS1B01G065400 chr1D 96.903 2422 45 15 1 2393 141346068 141348488 0.000000e+00 4030
9 TraesCS1B01G065400 chr7B 96.663 2427 45 16 1 2396 698138961 698136540 0.000000e+00 4000
10 TraesCS1B01G065400 chr7B 97.199 357 7 2 1 355 47205945 47206300 3.410000e-168 601
11 TraesCS1B01G065400 chr6D 97.479 357 7 2 1 355 430480556 430480200 2.040000e-170 608
12 TraesCS1B01G065400 chr6B 97.479 357 7 2 1 355 388131151 388131507 2.040000e-170 608
13 TraesCS1B01G065400 chr6B 97.191 356 9 1 1 355 625647739 625647384 3.410000e-168 601
14 TraesCS1B01G065400 chr4D 97.191 356 9 1 1 355 135037158 135037513 3.410000e-168 601


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 TraesCS1B01G065400 chr1B 49794827 49797222 2395 True 4425 4425 100.000 1 2396 1 chr1B.!!$R1 2395
1 TraesCS1B01G065400 chr3D 202634144 202636571 2427 True 4067 4067 97.118 1 2396 1 chr3D.!!$R1 2395
2 TraesCS1B01G065400 chr3D 546343004 546345430 2426 True 4037 4037 96.910 1 2396 1 chr3D.!!$R2 2395
3 TraesCS1B01G065400 chr2D 634991551 634993975 2424 True 4052 4052 97.032 1 2396 1 chr2D.!!$R1 2395
4 TraesCS1B01G065400 chr5B 202673967 202676384 2417 False 4048 4048 97.070 1 2393 1 chr5B.!!$F1 2392
5 TraesCS1B01G065400 chr5B 695886917 695889336 2419 False 4023 4023 96.866 1 2393 1 chr5B.!!$F2 2392
6 TraesCS1B01G065400 chrUn 266189282 266191700 2418 False 4034 4034 96.947 1 2393 1 chrUn.!!$F1 2392
7 TraesCS1B01G065400 chrUn 246706926 246709346 2420 True 4032 4032 96.908 1 2396 1 chrUn.!!$R1 2395
8 TraesCS1B01G065400 chr1D 141346068 141348488 2420 False 4030 4030 96.903 1 2393 1 chr1D.!!$F1 2392
9 TraesCS1B01G065400 chr7B 698136540 698138961 2421 True 4000 4000 96.663 1 2396 1 chr7B.!!$R1 2395

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
878 910 1.140816 GAGTGTCCGAACAGCTTCAC 58.859 55.0 0.0 0.0 35.64 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 2165 2.200092 AAACGGGGGTGCCAATGT 59.8 55.556 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 9.559732 CCAATCCCTTTTAATAAATTCATTCCC 57.440 33.333 0.00 0.0 0.00 3.97
81 82 8.950007 TTATTGGACCCAGTTTTATTCTCTTT 57.050 30.769 0.00 0.0 0.00 2.52
531 563 7.128077 ACATACCCTTTTTCCTTGATCATCAT 58.872 34.615 0.00 0.0 0.00 2.45
549 581 2.238395 TCATGGTCGTGGATTTGGATCA 59.762 45.455 0.00 0.0 33.77 2.92
616 648 3.126858 GCATTGGAAAGCATCACGTTCTA 59.873 43.478 0.00 0.0 37.01 2.10
793 825 7.974504 ACATGAAAGACTCTTTTCCTAACCTA 58.025 34.615 0.00 0.0 36.46 3.08
803 835 9.102453 ACTCTTTTCCTAACCTAACTGTTCTAT 57.898 33.333 0.00 0.0 0.00 1.98
878 910 1.140816 GAGTGTCCGAACAGCTTCAC 58.859 55.000 0.00 0.0 35.64 3.18
881 913 1.195448 GTGTCCGAACAGCTTCACATG 59.805 52.381 0.00 0.0 35.64 3.21
1105 1137 5.958380 TCTCTTTTGCCTCTCTACCAGATTA 59.042 40.000 0.00 0.0 0.00 1.75
1106 1138 6.613271 TCTCTTTTGCCTCTCTACCAGATTAT 59.387 38.462 0.00 0.0 0.00 1.28
1219 1252 2.265367 TCCACCTTTCATGGACTAGCA 58.735 47.619 0.00 0.0 41.47 3.49
1437 1471 3.347077 AAGGGAAGCAAGAGTCTCATG 57.653 47.619 1.94 1.2 0.00 3.07
1806 1843 3.300013 GGAGAGACCGAACCAGGG 58.700 66.667 0.00 0.0 35.02 4.45
1815 1853 1.752498 ACCGAACCAGGGAACAAAAAC 59.248 47.619 0.00 0.0 35.02 2.43
1906 1944 6.530019 ACAGAAACACAGGAACAAAGAAAT 57.470 33.333 0.00 0.0 0.00 2.17
2001 2039 4.018050 AGGAGTGATAGCTGGGTTTTTCAT 60.018 41.667 0.00 0.0 0.00 2.57
2393 2431 4.019174 ACTGAACCCATTCACCAATGATC 58.981 43.478 0.00 0.0 41.97 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 8.164058 TGTGTGTTTTGAGATACAATCAATCA 57.836 30.769 0.00 0.0 36.60 2.57
236 237 7.064253 CCCATTTTAGAACCGTTCACTACTAAG 59.936 40.741 13.69 0.0 0.00 2.18
522 554 3.843893 AATCCACGACCATGATGATCA 57.156 42.857 0.00 0.0 0.00 2.92
527 559 3.117926 TGATCCAAATCCACGACCATGAT 60.118 43.478 0.00 0.0 0.00 2.45
531 563 2.869101 TTGATCCAAATCCACGACCA 57.131 45.000 0.00 0.0 0.00 4.02
549 581 2.885894 TGAAGCCCGTAAAACCGAAATT 59.114 40.909 0.00 0.0 0.00 1.82
616 648 2.684881 CTGACTTCTTTTGTGTGTGGCT 59.315 45.455 0.00 0.0 0.00 4.75
793 825 5.482175 AGTGAACTAGCCAGATAGAACAGTT 59.518 40.000 0.00 0.0 0.00 3.16
803 835 4.689612 AAAGTGAAGTGAACTAGCCAGA 57.310 40.909 0.00 0.0 0.00 3.86
878 910 2.488355 CTGCGCCTTGGAAGCATG 59.512 61.111 4.18 0.0 40.35 4.06
1105 1137 2.245028 GGCCCTCTTCCTCCCTTTTTAT 59.755 50.000 0.00 0.0 0.00 1.40
1106 1138 1.639108 GGCCCTCTTCCTCCCTTTTTA 59.361 52.381 0.00 0.0 0.00 1.52
1232 1265 1.489649 CCATCTCCTGCTCCAGACATT 59.510 52.381 0.00 0.0 32.44 2.71
1437 1471 1.274703 TGTGCAGGATCTCCTTCCCC 61.275 60.000 0.00 0.0 46.09 4.81
1511 1545 4.584743 ACACGAGATAGGCAGATATGTGAA 59.415 41.667 3.61 0.0 0.00 3.18
1806 1843 8.769891 TCCTTCAGTTTTTCTTTGTTTTTGTTC 58.230 29.630 0.00 0.0 0.00 3.18
1815 1853 7.766283 AGAGAACTTCCTTCAGTTTTTCTTTG 58.234 34.615 0.00 0.0 37.11 2.77
1906 1944 3.071892 AGGACTCGTTGGTTTGGACATAA 59.928 43.478 0.00 0.0 0.00 1.90
2001 2039 4.508461 TCAATCGTACGAAGAAACTCCA 57.492 40.909 23.56 0.0 0.00 3.86
2127 2165 2.200092 AAACGGGGGTGCCAATGT 59.800 55.556 0.00 0.0 0.00 2.71
2360 2398 5.546499 TGAATGGGTTCAGTAAGGTAGAAGT 59.454 40.000 0.00 0.0 39.36 3.01


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

AutoCloner maintained by Alex Coulton.