Multiple sequence alignment - TraesCS3B01G510200

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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 TraesCS3B01G510200 chr3B 100.000 3493 0 0 1 3493 754458908 754462400 0 6451
1 TraesCS3B01G510200 chr3B 96.078 2907 97 14 595 3493 39619402 39622299 0 4721
2 TraesCS3B01G510200 chr2B 98.570 3497 43 6 1 3493 658224658 658221165 0 6174
3 TraesCS3B01G510200 chr2B 96.854 3497 93 15 1 3493 512426251 512422768 0 5832
4 TraesCS3B01G510200 chr2B 96.533 2163 60 14 1 2161 19851992 19854141 0 3565
5 TraesCS3B01G510200 chr2B 97.164 1340 35 3 2155 3493 19854200 19855537 0 2261
6 TraesCS3B01G510200 chr4B 98.055 3496 62 6 1 3493 608662290 608658798 0 6074
7 TraesCS3B01G510200 chr7B 97.398 3497 48 9 1 3493 693174054 693177511 0 5914
8 TraesCS3B01G510200 chr7B 99.006 2617 23 3 878 3493 180027357 180024743 0 4686
9 TraesCS3B01G510200 chrUn 97.082 3495 90 12 1 3493 76239271 76242755 0 5879
10 TraesCS3B01G510200 chr6B 96.437 2161 66 11 1 2161 319457345 319459494 0 3554
11 TraesCS3B01G510200 chr4A 97.015 1340 35 5 2155 3493 713790268 713788933 0 2248


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 TraesCS3B01G510200 chr3B 754458908 754462400 3492 False 6451 6451 100.0000 1 3493 1 chr3B.!!$F2 3492
1 TraesCS3B01G510200 chr3B 39619402 39622299 2897 False 4721 4721 96.0780 595 3493 1 chr3B.!!$F1 2898
2 TraesCS3B01G510200 chr2B 658221165 658224658 3493 True 6174 6174 98.5700 1 3493 1 chr2B.!!$R2 3492
3 TraesCS3B01G510200 chr2B 512422768 512426251 3483 True 5832 5832 96.8540 1 3493 1 chr2B.!!$R1 3492
4 TraesCS3B01G510200 chr2B 19851992 19855537 3545 False 2913 3565 96.8485 1 3493 2 chr2B.!!$F1 3492
5 TraesCS3B01G510200 chr4B 608658798 608662290 3492 True 6074 6074 98.0550 1 3493 1 chr4B.!!$R1 3492
6 TraesCS3B01G510200 chr7B 693174054 693177511 3457 False 5914 5914 97.3980 1 3493 1 chr7B.!!$F1 3492
7 TraesCS3B01G510200 chr7B 180024743 180027357 2614 True 4686 4686 99.0060 878 3493 1 chr7B.!!$R1 2615
8 TraesCS3B01G510200 chrUn 76239271 76242755 3484 False 5879 5879 97.0820 1 3493 1 chrUn.!!$F1 3492
9 TraesCS3B01G510200 chr6B 319457345 319459494 2149 False 3554 3554 96.4370 1 2161 1 chr6B.!!$F1 2160
10 TraesCS3B01G510200 chr4A 713788933 713790268 1335 True 2248 2248 97.0150 2155 3493 1 chr4A.!!$R1 1338

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
779 789 1.991965 CGTTGCTGTGTTGTTTGCTTT 59.008 42.857 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2597 2686 1.538687 GCCTTCCTTGCTGCACCATT 61.539 55.0 0.0 0.0 0.0 3.16 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
242 246 5.493133 ACGTTGCTTCAAAACATACTGAA 57.507 34.783 0.00 0.00 0.00 3.02
276 281 3.192422 ACACACAAACTTGCTGCTGTAAA 59.808 39.130 0.00 0.00 0.00 2.01
277 282 4.172505 CACACAAACTTGCTGCTGTAAAA 58.827 39.130 0.00 0.00 0.00 1.52
779 789 1.991965 CGTTGCTGTGTTGTTTGCTTT 59.008 42.857 0.00 0.00 0.00 3.51
926 938 3.761897 TGGCTTGCCTGTATTTACTGTT 58.238 40.909 13.18 0.00 0.00 3.16
941 953 8.947115 GTATTTACTGTTCTACTTGCTTCCATT 58.053 33.333 0.00 0.00 0.00 3.16
1081 1094 3.693085 ACATGCTACTGGAAATGCAGAAG 59.307 43.478 9.02 0.00 38.87 2.85
1283 1296 1.671054 CCGGTGGCACTGTTGGTAG 60.671 63.158 24.01 4.80 0.00 3.18
1323 1336 3.753815 TGATGATGAAGCTTGGTCACAA 58.246 40.909 2.10 0.00 34.87 3.33
1684 1697 5.706833 TGCAAAGCTAAGATGATTGTGAAGA 59.293 36.000 0.00 0.00 0.00 2.87
2064 2081 5.260424 TGCCTAATTTGTTTCTGGATGCTA 58.740 37.500 0.00 0.00 0.00 3.49
2597 2686 5.015178 AGGGTTGAGAATATTTTCTGGGTCA 59.985 40.000 2.90 0.00 42.34 4.02
2813 2902 4.100498 CCTTCCTTGAGGCAATGCATAATT 59.900 41.667 7.79 0.00 34.44 1.40
3166 3256 0.319900 AGTCAACTCAACGCAGCGAT 60.320 50.000 24.65 6.83 0.00 4.58
3264 3354 5.755409 ATCCAAACACACATACTAGTCCA 57.245 39.130 0.00 0.00 0.00 4.02
3292 3382 3.402628 TCAAAAGACTACAGGACAGCC 57.597 47.619 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 9.469807 CAACAAAGGTAAATTGTACTATGCAAA 57.530 29.630 0.00 0.00 39.98 3.68
158 160 2.503356 TGGCTTTTTCCTCCTTTTGCAA 59.497 40.909 0.00 0.00 0.00 4.08
242 246 6.257630 GCAAGTTTGTGTGTTTTTGGATATGT 59.742 34.615 0.00 0.00 0.00 2.29
389 394 8.685838 AGCATGTTTAGTGTTAGGAAAAACTA 57.314 30.769 0.00 0.00 34.81 2.24
779 789 4.461781 GCTAGTACCACACTAAACTCAGGA 59.538 45.833 0.00 0.00 39.28 3.86
926 938 3.369892 GCAGAGGAATGGAAGCAAGTAGA 60.370 47.826 0.00 0.00 0.00 2.59
941 953 2.634940 AGTAAAGCAAGTCAGCAGAGGA 59.365 45.455 0.00 0.00 36.85 3.71
1081 1094 1.816074 TTAGGTGATTCCGCCACAAC 58.184 50.000 0.00 0.00 45.32 3.32
1283 1296 2.102252 TCATTTTCAGCACCCAAACCAC 59.898 45.455 0.00 0.00 0.00 4.16
1323 1336 1.677552 CACGTAAGGCTCCTTGGGT 59.322 57.895 11.25 6.10 46.39 4.51
1684 1697 4.226846 CACCTCCCATCTGCCATCTATTAT 59.773 45.833 0.00 0.00 0.00 1.28
2187 2270 7.495279 ACACATGAGCAAAATACACAAAACAAT 59.505 29.630 0.00 0.00 0.00 2.71
2597 2686 1.538687 GCCTTCCTTGCTGCACCATT 61.539 55.000 0.00 0.00 0.00 3.16
2813 2902 2.897271 ATGATGTTGGTGGGCACTAA 57.103 45.000 0.00 0.00 0.00 2.24
3166 3256 3.420893 CTTAAGGACAGCATTGAACCCA 58.579 45.455 0.00 0.00 0.00 4.51
3264 3354 3.328050 CCTGTAGTCTTTTGAACCCTCCT 59.672 47.826 0.00 0.00 0.00 3.69
3292 3382 5.390885 CGACCACATTTCAGTCTGTAAATGG 60.391 44.000 25.22 21.67 43.96 3.16


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

AutoCloner maintained by Alex Coulton.