Multiple sequence alignment - TraesCS2A01G306600

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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 TraesCS2A01G306600 chr2A 100.000 4052 0 0 1 4052 527465042 527460991 0.000000e+00 7483
1 TraesCS2A01G306600 chr2B 97.398 3267 71 4 779 4032 461984300 461981035 0.000000e+00 5550
2 TraesCS2A01G306600 chr2D 97.326 3179 81 2 875 4052 390735888 390732713 0.000000e+00 5397
3 TraesCS2A01G306600 chr2D 93.162 117 4 3 779 894 390895629 390895516 6.970000e-38 169
4 TraesCS2A01G306600 chr7B 98.597 784 6 1 1 779 258957466 258958249 0.000000e+00 1382
5 TraesCS2A01G306600 chr6B 98.597 784 6 2 1 779 554796503 554795720 0.000000e+00 1382
6 TraesCS2A01G306600 chr6A 98.597 784 6 1 1 779 39498779 39497996 0.000000e+00 1382
7 TraesCS2A01G306600 chr6A 98.595 783 7 1 1 779 115019319 115020101 0.000000e+00 1382
8 TraesCS2A01G306600 chr5B 98.597 784 5 2 1 779 254544993 254544211 0.000000e+00 1382
9 TraesCS2A01G306600 chr4A 98.597 784 6 1 1 779 693884624 693885407 0.000000e+00 1382
10 TraesCS2A01G306600 chr1B 98.597 784 6 1 1 779 69841644 69842427 0.000000e+00 1382
11 TraesCS2A01G306600 chr1B 98.597 784 6 1 1 779 405928398 405929181 0.000000e+00 1382
12 TraesCS2A01G306600 chr1B 98.597 784 6 1 1 779 516020890 516021673 0.000000e+00 1382


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 TraesCS2A01G306600 chr2A 527460991 527465042 4051 True 7483 7483 100.000 1 4052 1 chr2A.!!$R1 4051
1 TraesCS2A01G306600 chr2B 461981035 461984300 3265 True 5550 5550 97.398 779 4032 1 chr2B.!!$R1 3253
2 TraesCS2A01G306600 chr2D 390732713 390735888 3175 True 5397 5397 97.326 875 4052 1 chr2D.!!$R1 3177
3 TraesCS2A01G306600 chr7B 258957466 258958249 783 False 1382 1382 98.597 1 779 1 chr7B.!!$F1 778
4 TraesCS2A01G306600 chr6B 554795720 554796503 783 True 1382 1382 98.597 1 779 1 chr6B.!!$R1 778
5 TraesCS2A01G306600 chr6A 39497996 39498779 783 True 1382 1382 98.597 1 779 1 chr6A.!!$R1 778
6 TraesCS2A01G306600 chr6A 115019319 115020101 782 False 1382 1382 98.595 1 779 1 chr6A.!!$F1 778
7 TraesCS2A01G306600 chr5B 254544211 254544993 782 True 1382 1382 98.597 1 779 1 chr5B.!!$R1 778
8 TraesCS2A01G306600 chr4A 693884624 693885407 783 False 1382 1382 98.597 1 779 1 chr4A.!!$F1 778
9 TraesCS2A01G306600 chr1B 69841644 69842427 783 False 1382 1382 98.597 1 779 1 chr1B.!!$F1 778
10 TraesCS2A01G306600 chr1B 405928398 405929181 783 False 1382 1382 98.597 1 779 1 chr1B.!!$F2 778
11 TraesCS2A01G306600 chr1B 516020890 516021673 783 False 1382 1382 98.597 1 779 1 chr1B.!!$F3 778

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
442 443 0.546747 TCCCCGAGACCTTTCCACAT 60.547 55.000 0.0 0.0 0.00 3.21 F
1307 1324 2.202492 CGTCCGTGCTCTCTTCGG 60.202 66.667 0.0 0.0 44.76 4.30 F
1481 1498 2.203788 TGCCGTGGAGAAGGACCT 60.204 61.111 0.0 0.0 0.00 3.85 F
2540 2557 3.133003 AGATACTTTCGGTCCATGACTGG 59.867 47.826 0.0 0.0 44.64 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 1565 0.952497 ACATGTCCAAGAGCGCACTG 60.952 55.000 11.47 2.91 0.00 3.66 R
2540 2557 3.054065 GGATGGAGTTATCCCATGATCCC 60.054 52.174 0.00 0.00 46.04 3.85 R
2872 2889 4.302455 CTGCCTATCTCAATCCAACTACG 58.698 47.826 0.00 0.00 0.00 3.51 R
3898 3917 1.916181 GGGATTTGGGGAGAGTCAGAA 59.084 52.381 0.00 0.00 0.00 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
323 324 2.447047 ACTCTGAACATCCCCCTTGTTT 59.553 45.455 0.00 0.0 37.43 2.83
442 443 0.546747 TCCCCGAGACCTTTCCACAT 60.547 55.000 0.00 0.0 0.00 3.21
452 453 2.649312 ACCTTTCCACATCTCAATGGGA 59.351 45.455 0.00 0.0 38.71 4.37
749 755 7.510675 TCTTATAGATGTCCCTTTCACCTTT 57.489 36.000 0.00 0.0 0.00 3.11
827 833 4.524316 TCAAAACATGGCAATCAGGAAG 57.476 40.909 0.00 0.0 0.00 3.46
841 847 6.352516 CAATCAGGAAGAGTATTTGCCTAGT 58.647 40.000 0.00 0.0 0.00 2.57
847 853 5.361285 GGAAGAGTATTTGCCTAGTCTCAGA 59.639 44.000 0.00 0.0 31.57 3.27
849 855 6.463995 AGAGTATTTGCCTAGTCTCAGAAG 57.536 41.667 0.00 0.0 27.26 2.85
854 860 8.157476 AGTATTTGCCTAGTCTCAGAAGAAAAA 58.843 33.333 0.00 0.0 31.93 1.94
908 914 2.417339 TCTGGCGCGTATTCAGTATC 57.583 50.000 8.43 0.0 0.00 2.24
919 925 4.260212 CGTATTCAGTATCGCCCTTGTTTG 60.260 45.833 0.00 0.0 0.00 2.93
971 977 2.825836 CCGCCTTCTGCCACCATC 60.826 66.667 0.00 0.0 36.24 3.51
1044 1061 2.680352 GTCTCCCACCTCCGAGCA 60.680 66.667 0.00 0.0 0.00 4.26
1307 1324 2.202492 CGTCCGTGCTCTCTTCGG 60.202 66.667 0.00 0.0 44.76 4.30
1481 1498 2.203788 TGCCGTGGAGAAGGACCT 60.204 61.111 0.00 0.0 0.00 3.85
1962 1979 4.629200 GTCTCTGAAACATCACTCATCACC 59.371 45.833 0.00 0.0 0.00 4.02
2439 2456 7.750229 TCTTTTTGAGAGAATGTTATGCAGT 57.250 32.000 0.00 0.0 0.00 4.40
2540 2557 3.133003 AGATACTTTCGGTCCATGACTGG 59.867 47.826 0.00 0.0 44.64 4.00
2872 2889 0.680921 TGTCATTAAGCAGCCTGGCC 60.681 55.000 16.57 0.0 0.00 5.36
2952 2969 2.435805 TCCCTGCAGGAATGAGATACAC 59.564 50.000 34.91 0.0 43.78 2.90
3266 3284 0.461870 TGCGTGCTGACAACTTGACT 60.462 50.000 0.00 0.0 0.00 3.41
3321 3339 6.154877 TGGACTCGGTGTATAAAGGTGAAATA 59.845 38.462 0.00 0.0 0.00 1.40
3322 3340 7.147620 TGGACTCGGTGTATAAAGGTGAAATAT 60.148 37.037 0.00 0.0 0.00 1.28
3376 3394 3.751175 CAGATTTTACGGCTGACTTCCAA 59.249 43.478 0.00 0.0 0.00 3.53
3467 3486 9.660180 GTAGAAATTGGAAGTAAAGAGACTCAT 57.340 33.333 5.02 0.0 0.00 2.90
3505 3524 2.376808 AAGTTCAGGAGCATGAGTCG 57.623 50.000 0.00 0.0 0.00 4.18
3530 3549 0.900182 AAGCTAGCAAACAAGCCCCC 60.900 55.000 18.83 0.0 39.64 5.40
3898 3917 5.677319 TGTTACTCCTTAAGCAGCTATGT 57.323 39.130 0.00 0.0 0.00 2.29
3907 3926 5.395103 CCTTAAGCAGCTATGTTCTGACTCT 60.395 44.000 0.00 0.0 33.54 3.24
3914 3933 3.055094 GCTATGTTCTGACTCTCCCCAAA 60.055 47.826 0.00 0.0 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
213 214 4.320202 GCACCGCTTAAGAAGAATGACAAA 60.320 41.667 6.67 0.00 0.00 2.83
323 324 9.976511 CGGAGTATATTAGTACCAATCTTCAAA 57.023 33.333 0.00 0.00 0.00 2.69
442 443 4.689705 GCCCTGATTGTATTCCCATTGAGA 60.690 45.833 0.00 0.00 0.00 3.27
452 453 1.819305 GCGATGGGCCCTGATTGTATT 60.819 52.381 25.70 0.00 34.80 1.89
749 755 0.320073 CCAACGGTTAGGCACGAAGA 60.320 55.000 0.00 0.00 0.00 2.87
827 833 6.458232 TCTTCTGAGACTAGGCAAATACTC 57.542 41.667 0.00 0.00 0.00 2.59
854 860 4.553330 TCGGAGAGGCAAATACTCTTTT 57.447 40.909 0.00 0.00 44.89 2.27
855 861 4.254492 GTTCGGAGAGGCAAATACTCTTT 58.746 43.478 0.00 0.00 44.89 2.52
908 914 0.041312 CGAACTGACAAACAAGGGCG 60.041 55.000 0.00 0.00 0.00 6.13
919 925 0.880278 TGCCAGCAGAACGAACTGAC 60.880 55.000 15.12 8.17 39.94 3.51
971 977 2.315901 GTGCCTCCGTTTGAAAATTCG 58.684 47.619 0.00 0.00 0.00 3.34
1548 1565 0.952497 ACATGTCCAAGAGCGCACTG 60.952 55.000 11.47 2.91 0.00 3.66
1962 1979 2.813908 GCAGACCTTGCGTACCCG 60.814 66.667 0.00 0.00 44.09 5.28
2439 2456 4.081420 GTGACAGAATCTGGGCTCTCTTTA 60.081 45.833 15.38 0.00 35.51 1.85
2540 2557 3.054065 GGATGGAGTTATCCCATGATCCC 60.054 52.174 0.00 0.00 46.04 3.85
2872 2889 4.302455 CTGCCTATCTCAATCCAACTACG 58.698 47.826 0.00 0.00 0.00 3.51
2952 2969 6.128607 GCATCTGAATGATTCTCAAGGTATCG 60.129 42.308 6.73 0.00 34.61 2.92
3364 3382 9.736023 CAGTTATTTTATAATTGGAAGTCAGCC 57.264 33.333 0.00 0.00 0.00 4.85
3448 3466 9.436957 GACAATAATGAGTCTCTTTACTTCCAA 57.563 33.333 9.69 0.00 0.00 3.53
3483 3502 3.406764 GACTCATGCTCCTGAACTTTGT 58.593 45.455 0.00 0.00 0.00 2.83
3505 3524 3.120025 GGCTTGTTTGCTAGCTTCTCTTC 60.120 47.826 17.23 0.61 41.90 2.87
3530 3549 2.697751 AGGGATCTCGAGGAAGTCAATG 59.302 50.000 13.56 0.00 0.00 2.82
3898 3917 1.916181 GGGATTTGGGGAGAGTCAGAA 59.084 52.381 0.00 0.00 0.00 3.02
3907 3926 2.324541 CACTGTTTTGGGATTTGGGGA 58.675 47.619 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.