Multiple sequence alignment - TraesCS3A01G106400

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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 TraesCS3A01G106400 chr3A 100.000 3165 0 0 1 3165 70715775 70712611 0.000000e+00 5845
1 TraesCS3A01G106400 chr3A 95.745 658 26 1 1 658 38419145 38419800 0.000000e+00 1059
2 TraesCS3A01G106400 chr3A 95.267 655 29 1 1 655 81661340 81661992 0.000000e+00 1037
3 TraesCS3A01G106400 chr3A 94.864 662 31 2 1 661 467776590 467777249 0.000000e+00 1031
4 TraesCS3A01G106400 chr3D 96.548 2491 60 9 693 3165 61689195 61686713 0.000000e+00 4100
5 TraesCS3A01G106400 chr3D 73.414 741 147 40 2435 3165 61681272 61680572 6.830000e-57 231
6 TraesCS3A01G106400 chr3B 92.445 1681 60 16 665 2307 99131382 99129731 0.000000e+00 2338
7 TraesCS3A01G106400 chr3B 95.708 862 34 2 2306 3165 99127812 99126952 0.000000e+00 1384
8 TraesCS3A01G106400 chr3B 72.840 729 150 32 2445 3165 99118847 99118159 4.140000e-49 206
9 TraesCS3A01G106400 chr7A 96.043 657 24 1 1 657 669859473 669860127 0.000000e+00 1068
10 TraesCS3A01G106400 chr5A 95.573 655 27 1 1 655 132905284 132905936 0.000000e+00 1048
11 TraesCS3A01G106400 chr6A 95.267 655 31 0 1 655 116954935 116955589 0.000000e+00 1038
12 TraesCS3A01G106400 chr2A 95.137 658 30 1 1 658 688226201 688225546 0.000000e+00 1037
13 TraesCS3A01G106400 chr2A 95.399 652 28 1 6 655 759116185 759116836 0.000000e+00 1037
14 TraesCS3A01G106400 chr1A 95.267 655 29 1 1 655 557159990 557159338 0.000000e+00 1037


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 TraesCS3A01G106400 chr3A 70712611 70715775 3164 True 5845 5845 100.0000 1 3165 1 chr3A.!!$R1 3164
1 TraesCS3A01G106400 chr3A 38419145 38419800 655 False 1059 1059 95.7450 1 658 1 chr3A.!!$F1 657
2 TraesCS3A01G106400 chr3A 81661340 81661992 652 False 1037 1037 95.2670 1 655 1 chr3A.!!$F2 654
3 TraesCS3A01G106400 chr3A 467776590 467777249 659 False 1031 1031 94.8640 1 661 1 chr3A.!!$F3 660
4 TraesCS3A01G106400 chr3D 61686713 61689195 2482 True 4100 4100 96.5480 693 3165 1 chr3D.!!$R2 2472
5 TraesCS3A01G106400 chr3D 61680572 61681272 700 True 231 231 73.4140 2435 3165 1 chr3D.!!$R1 730
6 TraesCS3A01G106400 chr3B 99126952 99131382 4430 True 1861 2338 94.0765 665 3165 2 chr3B.!!$R2 2500
7 TraesCS3A01G106400 chr3B 99118159 99118847 688 True 206 206 72.8400 2445 3165 1 chr3B.!!$R1 720
8 TraesCS3A01G106400 chr7A 669859473 669860127 654 False 1068 1068 96.0430 1 657 1 chr7A.!!$F1 656
9 TraesCS3A01G106400 chr5A 132905284 132905936 652 False 1048 1048 95.5730 1 655 1 chr5A.!!$F1 654
10 TraesCS3A01G106400 chr6A 116954935 116955589 654 False 1038 1038 95.2670 1 655 1 chr6A.!!$F1 654
11 TraesCS3A01G106400 chr2A 688225546 688226201 655 True 1037 1037 95.1370 1 658 1 chr2A.!!$R1 657
12 TraesCS3A01G106400 chr2A 759116185 759116836 651 False 1037 1037 95.3990 6 655 1 chr2A.!!$F1 649
13 TraesCS3A01G106400 chr1A 557159338 557159990 652 True 1037 1037 95.2670 1 655 1 chr1A.!!$R1 654

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
193 194 1.071542 TGAAGATCTTGCCAACACCGA 59.928 47.619 14.0 0.0 0.00 4.69 F
267 268 1.403814 AGATTCATCTTCGGAGGCGA 58.596 50.000 0.0 0.0 31.97 5.54 F
1805 1824 1.067212 GACCGTGCTTGATCGATACCT 59.933 52.381 0.0 0.0 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1158 1177 1.921230 GAAGAAGAAGACGCCGATGAC 59.079 52.381 0.00 0.0 0.0 3.06 R
2064 2100 2.262915 CAGGTCGGACAGGAGCAC 59.737 66.667 10.76 0.0 36.9 4.40 R
2628 4597 1.142262 CATCAGTCTGGCCATCATCCA 59.858 52.381 5.51 0.0 0.0 3.41 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
193 194 1.071542 TGAAGATCTTGCCAACACCGA 59.928 47.619 14.00 0.00 0.00 4.69
237 238 1.519234 GATGCGGTGCGTGATGAGA 60.519 57.895 0.00 0.00 0.00 3.27
267 268 1.403814 AGATTCATCTTCGGAGGCGA 58.596 50.000 0.00 0.00 31.97 5.54
324 325 5.004922 AGACGAGGAAGATGAAGATTGAC 57.995 43.478 0.00 0.00 0.00 3.18
373 374 5.798125 TTGCATTTGAACTTGGTTGGATA 57.202 34.783 0.00 0.00 0.00 2.59
489 490 1.697284 TATATGCAAAATGCCCCGCA 58.303 45.000 0.00 0.00 44.23 5.69
611 616 2.968156 AGCGCGCGTGGTAAACAA 60.968 55.556 32.35 0.00 0.00 2.83
658 663 1.939255 GCTGTTGGAGATGCTCTTAGC 59.061 52.381 0.00 0.00 42.82 3.09
672 677 3.847467 GCTCTTAGCATACAAGCATTGCG 60.847 47.826 2.38 0.00 45.93 4.85
690 695 2.512515 GCCGTGCTCTGGATCACC 60.513 66.667 0.00 0.00 0.00 4.02
816 829 4.451096 TCAGCGAGTCAACCAAAAATAGAC 59.549 41.667 0.00 0.00 0.00 2.59
956 971 8.962857 TTTTGTTGCAATTTCCTTTCTTTTTC 57.037 26.923 0.59 0.00 0.00 2.29
1230 1249 2.528743 GGTCGACGCGTCCGAGATA 61.529 63.158 31.84 9.08 36.66 1.98
1805 1824 1.067212 GACCGTGCTTGATCGATACCT 59.933 52.381 0.00 0.00 0.00 3.08
2314 4280 5.359756 ACAAAGCAAAAGGATTCAGAAACC 58.640 37.500 0.99 0.99 0.00 3.27
2343 4309 4.155462 GCAGGTCATATGCATCATACAAGG 59.845 45.833 0.19 0.00 43.31 3.61
2345 4311 5.999600 CAGGTCATATGCATCATACAAGGAA 59.000 40.000 0.19 0.00 0.00 3.36
2346 4312 6.148976 CAGGTCATATGCATCATACAAGGAAG 59.851 42.308 0.19 0.00 0.00 3.46
2441 4409 3.576356 GCACACATCCGGCCATCG 61.576 66.667 2.24 0.00 38.88 3.84
2573 4542 3.281727 TGAAGTATGGATGCAAGGGTC 57.718 47.619 0.00 0.00 0.00 4.46
2634 4603 1.054406 GGGAGTCCCCGAATGGATGA 61.054 60.000 18.55 0.00 44.02 2.92
2756 4725 0.166814 GAACGGACAAGCAGTGATGC 59.833 55.000 0.00 0.00 0.00 3.91
2804 4773 3.726517 CCAAACGGCCTGCAGACG 61.727 66.667 23.23 23.23 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 2.755064 CATTGCACCCATGGCGGA 60.755 61.111 6.09 0.00 36.56 5.54
193 194 1.086067 CGCATCATGTGAAGCTCCGT 61.086 55.000 8.36 0.00 36.69 4.69
373 374 4.686191 TCAAAATCATGCCCACAAGTTT 57.314 36.364 0.00 0.00 0.00 2.66
489 490 1.289109 AAATACAGTGCGCGCGACTT 61.289 50.000 37.18 22.36 0.00 3.01
500 501 2.095567 CAGCAGAGCGCAAAAATACAGT 60.096 45.455 11.47 0.00 46.13 3.55
572 577 3.645975 CTGGTTTTGCGCGTCCGT 61.646 61.111 8.43 0.00 36.67 4.69
658 663 1.298563 CGGCCGCAATGCTTGTATG 60.299 57.895 14.67 0.00 0.00 2.39
659 664 1.748879 ACGGCCGCAATGCTTGTAT 60.749 52.632 28.58 0.00 0.00 2.29
660 665 2.359354 ACGGCCGCAATGCTTGTA 60.359 55.556 28.58 0.00 0.00 2.41
661 666 4.041917 CACGGCCGCAATGCTTGT 62.042 61.111 28.58 0.00 0.00 3.16
672 677 2.512515 GTGATCCAGAGCACGGCC 60.513 66.667 0.00 0.00 38.00 6.13
690 695 1.741770 GCCCAAGTGCAGAGTACCG 60.742 63.158 0.00 0.00 0.00 4.02
781 794 0.642291 CTCGCTGATACACTGCAACG 59.358 55.000 0.00 0.00 42.30 4.10
886 899 1.169034 GCCCCAATTCGAGATGGAGC 61.169 60.000 17.47 13.22 39.12 4.70
956 971 4.499183 AGTTCTCTGCCTAAGATCAAACG 58.501 43.478 0.00 0.00 33.29 3.60
1158 1177 1.921230 GAAGAAGAAGACGCCGATGAC 59.079 52.381 0.00 0.00 0.00 3.06
1195 1214 3.361977 CTGGAAAACGCACCCGGG 61.362 66.667 22.25 22.25 39.22 5.73
1300 1319 3.110178 GTCGTCGGGCAACTTCGG 61.110 66.667 0.00 0.00 0.00 4.30
1326 1345 2.378084 GGTCGACCGCTCCGAAAAC 61.378 63.158 20.85 0.00 37.81 2.43
1694 1713 3.472943 GAGCTGCCGATGGAGCCAT 62.473 63.158 0.71 0.71 39.69 4.40
1695 1714 4.166888 GAGCTGCCGATGGAGCCA 62.167 66.667 0.00 0.00 35.69 4.75
1805 1824 3.153024 GCCAGTCTGCGGATGTAAA 57.847 52.632 0.00 0.00 0.00 2.01
2064 2100 2.262915 CAGGTCGGACAGGAGCAC 59.737 66.667 10.76 0.00 36.90 4.40
2314 4280 5.952526 TGATGCATATGACCTGCTAAATG 57.047 39.130 6.97 0.00 40.34 2.32
2343 4309 7.764443 TGGTTGTCTTGCTAGATTATGTACTTC 59.236 37.037 0.05 0.00 31.86 3.01
2345 4311 7.182817 TGGTTGTCTTGCTAGATTATGTACT 57.817 36.000 0.05 0.00 31.86 2.73
2346 4312 9.712305 ATATGGTTGTCTTGCTAGATTATGTAC 57.288 33.333 0.05 0.00 31.86 2.90
2410 4378 3.338676 GTGCCTACTATGCGCCGC 61.339 66.667 4.18 0.00 33.19 6.53
2573 4542 0.744414 CGATGGGGTACTTGGCAGTG 60.744 60.000 0.00 0.00 34.06 3.66
2628 4597 1.142262 CATCAGTCTGGCCATCATCCA 59.858 52.381 5.51 0.00 0.00 3.41
2629 4598 1.893544 CATCAGTCTGGCCATCATCC 58.106 55.000 5.51 0.00 0.00 3.51
2630 4599 1.236628 GCATCAGTCTGGCCATCATC 58.763 55.000 5.51 0.00 0.00 2.92
2634 4603 1.453379 GCTGCATCAGTCTGGCCAT 60.453 57.895 5.51 0.00 33.43 4.40
2672 4641 5.076182 TGTTCTTTTCCATGCTGATACCAA 58.924 37.500 0.00 0.00 0.00 3.67
2804 4773 4.214971 CCTATGCCTCTGTATGAAACATGC 59.785 45.833 0.00 0.00 37.50 4.06
2809 4778 3.071602 GCCTCCTATGCCTCTGTATGAAA 59.928 47.826 0.00 0.00 0.00 2.69
2813 4782 2.158249 TGAGCCTCCTATGCCTCTGTAT 60.158 50.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.