Multiple sequence alignment - TraesCS3B01G294300

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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 TraesCS3B01G294300 chr3B 100.000 2991 0 0 1 2991 473235661 473238651 0 5524
1 TraesCS3B01G294300 chr3B 85.273 1426 172 21 1 1392 766341707 766343128 0 1435
2 TraesCS3B01G294300 chr4B 96.761 2995 91 5 1 2991 321542009 321545001 0 4988
3 TraesCS3B01G294300 chr4B 97.201 2179 57 2 814 2989 587099150 587101327 0 3683
4 TraesCS3B01G294300 chr4B 96.530 778 24 3 1 777 587098372 587099147 0 1284
5 TraesCS3B01G294300 chr7B 96.400 3000 95 8 1 2991 51883776 51886771 0 4929
6 TraesCS3B01G294300 chr7B 85.494 1427 168 25 1 1392 73167740 73169162 0 1452
7 TraesCS3B01G294300 chr6B 96.396 2997 85 8 1 2991 48079472 48082451 0 4915
8 TraesCS3B01G294300 chr7A 94.735 3001 105 21 1 2991 126148520 126151477 0 4617
9 TraesCS3B01G294300 chr6A 95.100 2408 84 12 1 2402 182420386 182418007 0 3762
10 TraesCS3B01G294300 chr6A 94.404 1644 55 15 1354 2991 137393776 137392164 0 2492
11 TraesCS3B01G294300 chr6A 94.428 1364 55 8 1 1361 137493485 137492140 0 2078
12 TraesCS3B01G294300 chr6A 92.424 726 46 9 2271 2991 182418174 182417453 0 1027
13 TraesCS3B01G294300 chr2A 94.645 2409 80 10 1 2402 778648763 778651129 0 3688
14 TraesCS3B01G294300 chr2A 91.542 733 50 12 2264 2991 778650957 778651682 0 1000
15 TraesCS3B01G294300 chr5A 82.681 2298 299 55 198 2442 514149471 514147220 0 1947
16 TraesCS3B01G294300 chr6D 94.175 1133 39 9 1871 2991 16251411 16252528 0 1701
17 TraesCS3B01G294300 chr3A 95.853 844 34 1 1 844 153362656 153363498 0 1363
18 TraesCS3B01G294300 chr3A 94.755 591 25 4 2402 2991 644687580 644686995 0 915


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 TraesCS3B01G294300 chr3B 473235661 473238651 2990 False 5524.0 5524 100.0000 1 2991 1 chr3B.!!$F1 2990
1 TraesCS3B01G294300 chr3B 766341707 766343128 1421 False 1435.0 1435 85.2730 1 1392 1 chr3B.!!$F2 1391
2 TraesCS3B01G294300 chr4B 321542009 321545001 2992 False 4988.0 4988 96.7610 1 2991 1 chr4B.!!$F1 2990
3 TraesCS3B01G294300 chr4B 587098372 587101327 2955 False 2483.5 3683 96.8655 1 2989 2 chr4B.!!$F2 2988
4 TraesCS3B01G294300 chr7B 51883776 51886771 2995 False 4929.0 4929 96.4000 1 2991 1 chr7B.!!$F1 2990
5 TraesCS3B01G294300 chr7B 73167740 73169162 1422 False 1452.0 1452 85.4940 1 1392 1 chr7B.!!$F2 1391
6 TraesCS3B01G294300 chr6B 48079472 48082451 2979 False 4915.0 4915 96.3960 1 2991 1 chr6B.!!$F1 2990
7 TraesCS3B01G294300 chr7A 126148520 126151477 2957 False 4617.0 4617 94.7350 1 2991 1 chr7A.!!$F1 2990
8 TraesCS3B01G294300 chr6A 137392164 137393776 1612 True 2492.0 2492 94.4040 1354 2991 1 chr6A.!!$R1 1637
9 TraesCS3B01G294300 chr6A 182417453 182420386 2933 True 2394.5 3762 93.7620 1 2991 2 chr6A.!!$R3 2990
10 TraesCS3B01G294300 chr6A 137492140 137493485 1345 True 2078.0 2078 94.4280 1 1361 1 chr6A.!!$R2 1360
11 TraesCS3B01G294300 chr2A 778648763 778651682 2919 False 2344.0 3688 93.0935 1 2991 2 chr2A.!!$F1 2990
12 TraesCS3B01G294300 chr5A 514147220 514149471 2251 True 1947.0 1947 82.6810 198 2442 1 chr5A.!!$R1 2244
13 TraesCS3B01G294300 chr6D 16251411 16252528 1117 False 1701.0 1701 94.1750 1871 2991 1 chr6D.!!$F1 1120
14 TraesCS3B01G294300 chr3A 153362656 153363498 842 False 1363.0 1363 95.8530 1 844 1 chr3A.!!$F1 843
15 TraesCS3B01G294300 chr3A 644686995 644687580 585 True 915.0 915 94.7550 2402 2991 1 chr3A.!!$R1 589

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
253 263 1.340017 ACCGATCAAGGTTGGGTGATG 60.340 52.381 0.0 0.0 43.00 3.07 F
256 266 3.605634 CGATCAAGGTTGGGTGATGTAA 58.394 45.455 0.0 0.0 34.61 2.41 F
1690 1793 3.445096 ACATAGCAACTGGAGAAAATGCC 59.555 43.478 0.0 0.0 37.73 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 1793 1.580845 CTGCCTCACCAAAGCCTTCG 61.581 60.000 0.00 0.0 0.00 3.79 R
1914 2017 3.648339 ATTGTGTCACATTGTTGAGCC 57.352 42.857 6.48 0.0 0.00 4.70 R
2914 3153 5.576563 TCCAAGACATCCTTTAACCAGAA 57.423 39.130 0.00 0.0 31.42 3.02 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 3.297736 CAGAACCTATACCCGAGGACTT 58.702 50.000 0.00 0.00 37.53 3.01
182 192 3.585862 TGTAGAATTGTCTTGGAGCGTC 58.414 45.455 0.00 0.00 35.12 5.19
253 263 1.340017 ACCGATCAAGGTTGGGTGATG 60.340 52.381 0.00 0.00 43.00 3.07
256 266 3.605634 CGATCAAGGTTGGGTGATGTAA 58.394 45.455 0.00 0.00 34.61 2.41
792 834 6.010294 ACTTCTATCTCAACTTCGAACGAA 57.990 37.500 9.22 9.22 0.00 3.85
1626 1729 3.877735 GCAAAGGGATTGTATGGTGTCCT 60.878 47.826 0.00 0.00 41.32 3.85
1690 1793 3.445096 ACATAGCAACTGGAGAAAATGCC 59.555 43.478 0.00 0.00 37.73 4.40
1914 2017 2.938451 TGCTTCAAGATGTCAATAGCCG 59.062 45.455 0.00 0.00 0.00 5.52
1988 2092 3.596066 ATGGCACGAGAAGCAGCGT 62.596 57.895 0.00 0.00 42.11 5.07
2191 2298 8.094548 GGTATCCTTTTGCTAAACTCCAAAATT 58.905 33.333 0.00 0.00 39.40 1.82
2195 2302 7.926018 TCCTTTTGCTAAACTCCAAAATTTCTC 59.074 33.333 0.00 0.00 39.40 2.87
2303 2424 7.008021 TGCTAGTATATGATTTGCCATCTCA 57.992 36.000 0.00 0.00 0.00 3.27
2621 2852 2.574450 TGCAATCAGAGTGCTTGTTCA 58.426 42.857 22.66 0.00 42.69 3.18
2812 3045 1.114722 TGGCCTTTGGACTTGCCTTG 61.115 55.000 3.32 0.00 44.32 3.61
2914 3153 6.403866 TGCATTTTAGAAGTGGTGTCAAAT 57.596 33.333 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 9.473007 TGAAATATTTCCATTTACCATCTGTGA 57.527 29.630 22.42 0.00 36.36 3.58
182 192 0.740868 CCCTACGTGTGTGCCATCTG 60.741 60.000 0.00 0.00 0.00 2.90
253 263 8.347035 ACACACACCTAACACATTTGTATTTAC 58.653 33.333 0.00 0.00 33.55 2.01
256 266 6.734137 CACACACACCTAACACATTTGTATT 58.266 36.000 0.00 0.00 33.55 1.89
566 600 1.421646 CCCACTGACCCTTGAGTCTTT 59.578 52.381 0.00 0.00 37.66 2.52
623 665 2.880268 GCCATGATGATTCGACATTGGA 59.120 45.455 9.72 0.00 32.82 3.53
792 834 4.772100 AGAACATTCCGGAAATTTGTCCAT 59.228 37.500 23.08 6.39 37.56 3.41
1626 1729 4.693566 CCAACTGCTCAAAGTACGGAAATA 59.306 41.667 0.00 0.00 0.00 1.40
1690 1793 1.580845 CTGCCTCACCAAAGCCTTCG 61.581 60.000 0.00 0.00 0.00 3.79
1914 2017 3.648339 ATTGTGTCACATTGTTGAGCC 57.352 42.857 6.48 0.00 0.00 4.70
1988 2092 4.964897 TGATTTCTGCTGAGGATCCTCTTA 59.035 41.667 35.84 22.72 43.12 2.10
2191 2298 6.940739 AGCTGATAAGAGTTTAGCAAGAGAA 58.059 36.000 0.00 0.00 35.00 2.87
2195 2302 7.369803 TCAAAGCTGATAAGAGTTTAGCAAG 57.630 36.000 0.00 0.00 35.00 4.01
2303 2424 5.525378 GCATATACTAGCAGCAAGTCAACTT 59.475 40.000 0.00 0.00 36.45 2.66
2844 3077 6.073602 TCAGACTTCAACAACAATTCGAGATG 60.074 38.462 0.00 0.00 0.00 2.90
2914 3153 5.576563 TCCAAGACATCCTTTAACCAGAA 57.423 39.130 0.00 0.00 31.42 3.02


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

AutoCloner maintained by Alex Coulton.