Multiple sequence alignment - TraesCS4A01G398100

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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 TraesCS4A01G398100 chr4A 100.000 4656 0 0 1 4656 673171441 673166786 0.000000e+00 8599
1 TraesCS4A01G398100 chr1B 97.682 4659 97 9 1 4656 676864558 676859908 0.000000e+00 7995
2 TraesCS4A01G398100 chr1B 97.342 4628 118 5 31 4656 567735715 567731091 0.000000e+00 7860
3 TraesCS4A01G398100 chr1B 97.026 4573 132 4 86 4656 7902887 7898317 0.000000e+00 7688
4 TraesCS4A01G398100 chr2B 97.337 4657 118 5 1 4656 785300924 785296273 0.000000e+00 7908
5 TraesCS4A01G398100 chr2B 96.597 4526 115 11 132 4656 662568037 662572524 0.000000e+00 7468
6 TraesCS4A01G398100 chr3B 97.295 4658 115 7 1 4656 667633030 667637678 0.000000e+00 7893
7 TraesCS4A01G398100 chr3B 93.714 175 10 1 4114 4288 13141456 13141629 1.280000e-65 261
8 TraesCS4A01G398100 chr5B 97.075 4649 127 4 9 4656 18261671 18257031 0.000000e+00 7823
9 TraesCS4A01G398100 chr5B 96.953 2002 47 2 2655 4656 568809872 568811859 0.000000e+00 3347
10 TraesCS4A01G398100 chr6B 97.441 4572 111 6 86 4656 572516363 572511797 0.000000e+00 7790
11 TraesCS4A01G398100 chr7B 96.564 4657 131 10 1 4656 629987442 629992070 0.000000e+00 7686
12 TraesCS4A01G398100 chr2A 94.854 4120 205 7 1 4117 773697852 773693737 0.000000e+00 6427
13 TraesCS4A01G398100 chr2A 93.548 93 6 0 1 93 773701620 773701528 6.280000e-29 139


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 TraesCS4A01G398100 chr4A 673166786 673171441 4655 True 8599 8599 100.000 1 4656 1 chr4A.!!$R1 4655
1 TraesCS4A01G398100 chr1B 676859908 676864558 4650 True 7995 7995 97.682 1 4656 1 chr1B.!!$R3 4655
2 TraesCS4A01G398100 chr1B 567731091 567735715 4624 True 7860 7860 97.342 31 4656 1 chr1B.!!$R2 4625
3 TraesCS4A01G398100 chr1B 7898317 7902887 4570 True 7688 7688 97.026 86 4656 1 chr1B.!!$R1 4570
4 TraesCS4A01G398100 chr2B 785296273 785300924 4651 True 7908 7908 97.337 1 4656 1 chr2B.!!$R1 4655
5 TraesCS4A01G398100 chr2B 662568037 662572524 4487 False 7468 7468 96.597 132 4656 1 chr2B.!!$F1 4524
6 TraesCS4A01G398100 chr3B 667633030 667637678 4648 False 7893 7893 97.295 1 4656 1 chr3B.!!$F2 4655
7 TraesCS4A01G398100 chr5B 18257031 18261671 4640 True 7823 7823 97.075 9 4656 1 chr5B.!!$R1 4647
8 TraesCS4A01G398100 chr5B 568809872 568811859 1987 False 3347 3347 96.953 2655 4656 1 chr5B.!!$F1 2001
9 TraesCS4A01G398100 chr6B 572511797 572516363 4566 True 7790 7790 97.441 86 4656 1 chr6B.!!$R1 4570
10 TraesCS4A01G398100 chr7B 629987442 629992070 4628 False 7686 7686 96.564 1 4656 1 chr7B.!!$F1 4655
11 TraesCS4A01G398100 chr2A 773693737 773701620 7883 True 3283 6427 94.201 1 4117 2 chr2A.!!$R1 4116

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
777 4551 2.282603 GTTTGGCAACGGGGGCTA 60.283 61.111 0.00 0.0 42.51 3.93 F
1751 5532 3.242739 GCACCGGCAATGTAAGTCAATAG 60.243 47.826 0.00 0.0 40.72 1.73 F
2320 6102 2.918600 CGTGTTTCAATGATACGGACGA 59.081 45.455 9.75 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 5992 0.033208 GGCCATTCTCCATCCCAACA 60.033 55.000 0.0 0.0 0.00 3.33 R
2866 6650 1.374885 CCACGGTTCGGTGTGCATA 60.375 57.895 0.0 0.0 36.16 3.14 R
4276 8065 2.340210 TTCTACAGCAAAGTGTGGCA 57.660 45.000 0.0 0.0 31.46 4.92 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
300 4074 5.066634 TGTGCATTGACCGAAAGAAAACTAA 59.933 36.000 0.00 0.00 0.00 2.24
318 4092 4.901868 ACTAAATAAAGGAGTCAACGGCA 58.098 39.130 0.00 0.00 0.00 5.69
777 4551 2.282603 GTTTGGCAACGGGGGCTA 60.283 61.111 0.00 0.00 42.51 3.93
946 4720 3.578282 GGTGGAAAAATTCACACCCAGAT 59.422 43.478 14.62 0.00 41.33 2.90
1000 4774 6.126863 ACTGTATGTTGAGAATTCCTTCCA 57.873 37.500 0.65 0.00 31.27 3.53
1087 4862 8.691661 ATTTATTATTCGGCCAAATACAGACT 57.308 30.769 2.24 0.00 0.00 3.24
1591 5372 6.019801 CGACTAGTTGTGTTTACTATCATGCC 60.020 42.308 0.00 0.00 0.00 4.40
1659 5440 5.400066 TGATCCTTTGTCTCGTGAATACA 57.600 39.130 0.00 0.00 0.00 2.29
1751 5532 3.242739 GCACCGGCAATGTAAGTCAATAG 60.243 47.826 0.00 0.00 40.72 1.73
2209 5991 8.994170 TGATGAATTTGTTAATGTACGTCAAGA 58.006 29.630 0.00 0.00 0.00 3.02
2210 5992 9.988350 GATGAATTTGTTAATGTACGTCAAGAT 57.012 29.630 0.00 0.00 0.00 2.40
2320 6102 2.918600 CGTGTTTCAATGATACGGACGA 59.081 45.455 9.75 0.00 0.00 4.20
2389 6171 5.232414 GTGACGCTACTGATCCTTTCATTAC 59.768 44.000 0.00 0.00 32.72 1.89
2430 6212 4.191544 CCCATGTTCGTCATCAACTGTAT 58.808 43.478 0.00 0.00 34.09 2.29
2866 6650 2.029828 ACTCTCGCATCGACAAAGAAGT 60.030 45.455 0.00 0.00 0.00 3.01
3714 7500 6.579666 AAGCTGATCACACATGTTTATTGT 57.420 33.333 0.00 0.00 0.00 2.71
4064 7850 4.757657 ACTACACATTTAAATGCGTGTGGA 59.242 37.500 27.36 17.89 44.61 4.02
4082 7870 7.462724 GCGTGTGGACAAATAATATTTTTCTGC 60.463 37.037 10.55 5.90 0.00 4.26
4276 8065 0.310854 GTGTGGCGCTTGTTTTAGCT 59.689 50.000 7.64 0.00 39.03 3.32
4325 8114 6.279513 TGTAGAAATTTGCCCCTAAATGTG 57.720 37.500 0.00 0.00 31.05 3.21
4326 8115 5.777732 TGTAGAAATTTGCCCCTAAATGTGT 59.222 36.000 0.00 0.00 31.05 3.72
4349 8138 2.605837 TGTTGTTGTTCCTACTCGCA 57.394 45.000 0.00 0.00 0.00 5.10
4398 8187 2.338620 CGTCCTGAGTTGGTGCGA 59.661 61.111 0.00 0.00 0.00 5.10
4429 8218 1.004277 ACCTGCACAATATCCCACGTT 59.996 47.619 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.966246 TGCATGCAAGTTTTCATAATTTTCT 57.034 28.000 20.30 0.00 0.00 2.52
159 3933 5.163723 TGCATATTCTTCAAAAAGAGAGCCG 60.164 40.000 0.00 0.00 42.36 5.52
300 4074 2.073816 CGTGCCGTTGACTCCTTTATT 58.926 47.619 0.00 0.00 0.00 1.40
729 4503 2.345991 GGTTAGTCGTGGCAGCCA 59.654 61.111 11.22 11.22 0.00 4.75
777 4551 3.588336 GTCTAGACGAGCACCGGT 58.412 61.111 7.22 0.00 43.93 5.28
1375 5152 1.067212 GATAGCGTTCACGTCCTCCAT 59.933 52.381 0.62 0.00 42.22 3.41
1591 5372 8.709646 GCTCAACTTTTTCCCAGTATATATACG 58.290 37.037 15.57 11.05 38.28 3.06
1659 5440 3.329520 TCTGGCCAGTTAACCATTAGTGT 59.670 43.478 31.58 0.00 34.82 3.55
1751 5532 7.582667 ATTTGCAACCAATAAGGACTATACC 57.417 36.000 0.00 0.00 41.22 2.73
2209 5991 1.412074 GGCCATTCTCCATCCCAACAT 60.412 52.381 0.00 0.00 0.00 2.71
2210 5992 0.033208 GGCCATTCTCCATCCCAACA 60.033 55.000 0.00 0.00 0.00 3.33
2320 6102 2.047274 CCGTGTCATCAACGGGCT 60.047 61.111 7.10 0.00 42.70 5.19
2389 6171 4.006989 TGGGGACTTTTCATTATCGTGTG 58.993 43.478 0.00 0.00 0.00 3.82
2430 6212 6.518493 ACATAGACGGAAACTCTTTTGTACA 58.482 36.000 0.00 0.00 0.00 2.90
2537 6319 0.539438 TGTTGCTCTTTGCCGGGAAT 60.539 50.000 10.01 0.00 42.00 3.01
2866 6650 1.374885 CCACGGTTCGGTGTGCATA 60.375 57.895 0.00 0.00 36.16 3.14
3593 7379 2.484417 GCCACGATGAGACATCTGGAAT 60.484 50.000 21.90 0.00 0.00 3.01
3991 7777 6.037172 CGTGGAAAATTGTCGAAATCTATCCT 59.963 38.462 0.00 0.00 0.00 3.24
4082 7870 5.888161 AGAGGCAAACTGATACATTTTAGGG 59.112 40.000 0.00 0.00 0.00 3.53
4276 8065 2.340210 TTCTACAGCAAAGTGTGGCA 57.660 45.000 0.00 0.00 31.46 4.92
4325 8114 4.584394 CGAGTAGGAACAACAACAACAAC 58.416 43.478 0.00 0.00 0.00 3.32
4326 8115 3.064271 GCGAGTAGGAACAACAACAACAA 59.936 43.478 0.00 0.00 0.00 2.83
4398 8187 6.040842 GGATATTGTGCAGGTTTTATCCACAT 59.959 38.462 12.70 0.00 36.61 3.21
4429 8218 1.676635 GCTGCTGCCACCAGAATCA 60.677 57.895 3.85 0.00 41.77 2.57
4462 8251 0.813610 CGCACGGCCTGGAATATTCA 60.814 55.000 17.07 3.07 0.00 2.57


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

AutoCloner maintained by Alex Coulton.