Multiple sequence alignment - TraesCS2A01G536000

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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 TraesCS2A01G536000 chr2A 100.000 2243 0 0 1 2243 750453591 750451349 0 4143
1 TraesCS2A01G536000 chr4B 97.100 2241 64 1 1 2241 209242557 209244796 0 3777
2 TraesCS2A01G536000 chr3B 97.010 2241 66 1 1 2241 483333212 483335451 0 3766
3 TraesCS2A01G536000 chr3B 96.610 2242 74 2 1 2241 575839742 575837502 0 3718
4 TraesCS2A01G536000 chr6A 96.612 2243 75 1 1 2243 155857299 155859540 0 3720
5 TraesCS2A01G536000 chr6A 96.433 2243 78 2 1 2243 375860759 375858519 0 3698
6 TraesCS2A01G536000 chr4A 96.344 2243 81 1 1 2243 350172240 350174481 0 3687
7 TraesCS2A01G536000 chr3A 96.186 2019 64 6 235 2243 230228527 230226512 0 3290
8 TraesCS2A01G536000 chr7A 97.781 1307 29 0 1 1307 60084936 60086242 0 2254
9 TraesCS2A01G536000 chr4D 97.348 1320 33 2 1 1319 123350121 123351439 0 2242
10 TraesCS2A01G536000 chr5B 97.987 1043 21 0 1201 2243 439641088 439642130 0 1810
11 TraesCS2A01G536000 chrUn 97.985 1042 20 1 1201 2241 171017238 171018279 0 1807
12 TraesCS2A01G536000 chr6B 93.122 727 47 3 1054 1779 401858415 401859139 0 1062


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 TraesCS2A01G536000 chr2A 750451349 750453591 2242 True 4143 4143 100.000 1 2243 1 chr2A.!!$R1 2242
1 TraesCS2A01G536000 chr4B 209242557 209244796 2239 False 3777 3777 97.100 1 2241 1 chr4B.!!$F1 2240
2 TraesCS2A01G536000 chr3B 483333212 483335451 2239 False 3766 3766 97.010 1 2241 1 chr3B.!!$F1 2240
3 TraesCS2A01G536000 chr3B 575837502 575839742 2240 True 3718 3718 96.610 1 2241 1 chr3B.!!$R1 2240
4 TraesCS2A01G536000 chr6A 155857299 155859540 2241 False 3720 3720 96.612 1 2243 1 chr6A.!!$F1 2242
5 TraesCS2A01G536000 chr6A 375858519 375860759 2240 True 3698 3698 96.433 1 2243 1 chr6A.!!$R1 2242
6 TraesCS2A01G536000 chr4A 350172240 350174481 2241 False 3687 3687 96.344 1 2243 1 chr4A.!!$F1 2242
7 TraesCS2A01G536000 chr3A 230226512 230228527 2015 True 3290 3290 96.186 235 2243 1 chr3A.!!$R1 2008
8 TraesCS2A01G536000 chr7A 60084936 60086242 1306 False 2254 2254 97.781 1 1307 1 chr7A.!!$F1 1306
9 TraesCS2A01G536000 chr4D 123350121 123351439 1318 False 2242 2242 97.348 1 1319 1 chr4D.!!$F1 1318
10 TraesCS2A01G536000 chr5B 439641088 439642130 1042 False 1810 1810 97.987 1201 2243 1 chr5B.!!$F1 1042
11 TraesCS2A01G536000 chrUn 171017238 171018279 1041 False 1807 1807 97.985 1201 2241 1 chrUn.!!$F1 1040
12 TraesCS2A01G536000 chr6B 401858415 401859139 724 False 1062 1062 93.122 1054 1779 1 chr6B.!!$F1 725

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
292 293 2.940994 TACAGGTGCAAGGCTTACAA 57.059 45.0 0.79 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 1572 0.973632 GAAAAACAGGCCCCGGATTT 59.026 50.0 0.73 0.0 0.0 2.17 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
20 21 3.402628 AACACAAGCTGGAGACGTATT 57.597 42.857 0.00 0.00 0.00 1.89
275 276 3.491267 GCGACTCAGGCATTACTCAATAC 59.509 47.826 0.00 0.00 0.00 1.89
292 293 2.940994 TACAGGTGCAAGGCTTACAA 57.059 45.000 0.79 0.00 0.00 2.41
304 305 2.972021 AGGCTTACAAAAGTGCCCAAAT 59.028 40.909 0.00 0.00 45.94 2.32
519 520 7.823745 ACCAGATGCTTCTTTAAAAGAAAGA 57.176 32.000 0.00 2.94 46.13 2.52
544 545 6.924111 ACTTTGCCTTACCTGTGAATTAATG 58.076 36.000 0.00 0.00 0.00 1.90
618 619 6.335781 ACTGAACCCCAATAGGCTATTTTA 57.664 37.500 16.95 0.00 0.00 1.52
1108 1112 1.468520 CTTTGATTCATTCCGTGGCGT 59.531 47.619 0.00 0.00 0.00 5.68
1109 1113 1.083489 TTGATTCATTCCGTGGCGTC 58.917 50.000 0.00 0.00 0.00 5.19
1348 1354 2.962859 TCCGATGGATGAATGAGGAGA 58.037 47.619 0.00 0.00 0.00 3.71
1395 1402 4.022676 GGATTCTGCTTTTCGGTTAAACCA 60.023 41.667 0.00 0.00 38.47 3.67
1501 1508 4.868171 CGAAAGACCCGATGAGTATTTTCA 59.132 41.667 0.00 0.00 29.30 2.69
1565 1572 6.461092 CCACTAGGCGAGACATAAGTTATCAA 60.461 42.308 0.28 0.00 0.00 2.57
1826 1833 3.475174 ACCTATCTCTTCCCCCTAATGGA 59.525 47.826 0.00 0.00 35.39 3.41
1872 1879 0.532640 TATCGTTGCTGCATCGCCAT 60.533 50.000 24.00 16.86 0.00 4.40
1912 1920 2.912771 TCCGAACTGCTTGTTTTCTCA 58.087 42.857 0.00 0.00 39.30 3.27
2104 2120 6.231211 TGGGAAAGAAGAGCAAGTAAGTAAG 58.769 40.000 0.00 0.00 0.00 2.34
2105 2121 6.183361 TGGGAAAGAAGAGCAAGTAAGTAAGT 60.183 38.462 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.710244 CATTGGTGGGGATATAGGCCA 59.290 52.381 5.01 0.0 0.00 5.36
275 276 2.362077 ACTTTTGTAAGCCTTGCACCTG 59.638 45.455 0.00 0.0 34.60 4.00
292 293 4.972751 ATTGTGGTTATTTGGGCACTTT 57.027 36.364 0.00 0.0 0.00 2.66
304 305 5.882040 TGGAAGTGGTTCATATTGTGGTTA 58.118 37.500 0.00 0.0 33.93 2.85
361 362 1.204704 TCGATCACAGAAGCCGTTGAT 59.795 47.619 0.00 0.0 0.00 2.57
519 520 6.969993 TTAATTCACAGGTAAGGCAAAGTT 57.030 33.333 0.00 0.0 0.00 2.66
554 555 2.424523 CCTACATCTCCGAGTAAGGGGT 60.425 54.545 0.00 0.0 32.31 4.95
566 567 5.739959 AGAAAAGCCTTCTTCCTACATCTC 58.260 41.667 0.00 0.0 0.00 2.75
721 724 2.694616 GGCTGGGTGGGGTATCCA 60.695 66.667 0.00 0.0 44.79 3.41
1108 1112 6.602410 TTGTTTAGCCAATGATGGATTTGA 57.398 33.333 0.00 0.0 44.90 2.69
1109 1113 7.042950 TGATTGTTTAGCCAATGATGGATTTG 58.957 34.615 0.00 0.0 44.90 2.32
1395 1402 1.944024 TGAATCGCCGACTTGTGTTTT 59.056 42.857 0.00 0.0 0.00 2.43
1501 1508 6.443849 TGACTAAGAAGATTGGAAGGTGGTAT 59.556 38.462 0.00 0.0 0.00 2.73
1565 1572 0.973632 GAAAAACAGGCCCCGGATTT 59.026 50.000 0.73 0.0 0.00 2.17
1872 1879 4.000988 GGAAAAGCAAGTCAGGAATACGA 58.999 43.478 0.00 0.0 0.00 3.43
1912 1920 2.433446 CAACTGGACTGCAGCCCT 59.567 61.111 20.60 0.0 0.00 5.19
2037 2045 2.684943 TGGATTGTAGGCCCTCGATAA 58.315 47.619 0.00 0.0 0.00 1.75
2038 2046 2.391926 TGGATTGTAGGCCCTCGATA 57.608 50.000 0.00 0.0 0.00 2.92


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

AutoCloner maintained by Alex Coulton.