Multiple sequence alignment - TraesCS2D01G407400

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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 TraesCS2D01G407400 chr2D 100.000 3266 0 0 1 3266 522778918 522782183 0.000000e+00 6032
1 TraesCS2D01G407400 chr2D 97.461 3269 77 3 1 3266 139702893 139699628 0.000000e+00 5572
2 TraesCS2D01G407400 chr7D 97.586 3273 70 7 1 3266 614566396 614569666 0.000000e+00 5598
3 TraesCS2D01G407400 chr6D 97.463 3271 75 5 1 3266 437005280 437008547 0.000000e+00 5574
4 TraesCS2D01G407400 chr4D 97.066 3272 89 4 1 3266 482669898 482666628 0.000000e+00 5504
5 TraesCS2D01G407400 chr3D 96.911 3270 94 4 1 3266 483312756 483309490 0.000000e+00 5472
6 TraesCS2D01G407400 chr7A 95.475 3271 140 3 3 3266 493726521 493729790 0.000000e+00 5214
7 TraesCS2D01G407400 chr7A 94.370 3268 178 3 3 3266 536365321 536368586 0.000000e+00 5011
8 TraesCS2D01G407400 chr2A 93.840 3263 165 8 3 3263 697151059 697154287 0.000000e+00 4879
9 TraesCS2D01G407400 chr6A 93.786 3267 170 9 3 3266 594022906 594026142 0.000000e+00 4878
10 TraesCS2D01G407400 chr2B 90.332 331 32 0 2936 3266 700189503 700189173 5.000000e-118 435
11 TraesCS2D01G407400 chr3B 89.124 331 36 0 2936 3266 38478098 38478428 2.340000e-111 412


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 TraesCS2D01G407400 chr2D 522778918 522782183 3265 False 6032 6032 100.000 1 3266 1 chr2D.!!$F1 3265
1 TraesCS2D01G407400 chr2D 139699628 139702893 3265 True 5572 5572 97.461 1 3266 1 chr2D.!!$R1 3265
2 TraesCS2D01G407400 chr7D 614566396 614569666 3270 False 5598 5598 97.586 1 3266 1 chr7D.!!$F1 3265
3 TraesCS2D01G407400 chr6D 437005280 437008547 3267 False 5574 5574 97.463 1 3266 1 chr6D.!!$F1 3265
4 TraesCS2D01G407400 chr4D 482666628 482669898 3270 True 5504 5504 97.066 1 3266 1 chr4D.!!$R1 3265
5 TraesCS2D01G407400 chr3D 483309490 483312756 3266 True 5472 5472 96.911 1 3266 1 chr3D.!!$R1 3265
6 TraesCS2D01G407400 chr7A 493726521 493729790 3269 False 5214 5214 95.475 3 3266 1 chr7A.!!$F1 3263
7 TraesCS2D01G407400 chr7A 536365321 536368586 3265 False 5011 5011 94.370 3 3266 1 chr7A.!!$F2 3263
8 TraesCS2D01G407400 chr2A 697151059 697154287 3228 False 4879 4879 93.840 3 3263 1 chr2A.!!$F1 3260
9 TraesCS2D01G407400 chr6A 594022906 594026142 3236 False 4878 4878 93.786 3 3266 1 chr6A.!!$F1 3263

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
131 135 0.389757 GTATCTCGAAGTGGGAGGGC 59.610 60.000 0.0 0.0 32.34 5.19 F
286 290 1.187087 CAGAGTAGTGGAGGTGGGAC 58.813 60.000 0.0 0.0 0.00 4.46 F
795 803 1.300620 CTCGGTGGTTGCTTCGACA 60.301 57.895 0.0 0.0 0.00 4.35 F
929 938 2.574322 CGCTCAATTCCGAAAACACTG 58.426 47.619 0.0 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2105 2123 1.762460 AGTAGGCTGATCCCCCACG 60.762 63.158 0.00 0.0 34.51 4.94 R
2159 2177 1.638388 CGACTCGTAGGTGGCGTACA 61.638 60.000 4.64 0.0 0.00 2.90 R
2256 2274 6.275494 TGTTTTCGTCATCACTAGTATCCA 57.725 37.500 0.00 0.0 0.00 3.41 R
3075 3094 2.258755 AGCTGTTCGCAACAACAAAAC 58.741 42.857 0.00 0.0 41.61 2.43 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
70 74 2.733218 CTTGCTTCGTCGCCGTCA 60.733 61.111 0.00 0.00 35.01 4.35
131 135 0.389757 GTATCTCGAAGTGGGAGGGC 59.610 60.000 0.00 0.00 32.34 5.19
267 271 2.614229 GCTGTGGAAGAGAGGAAGGAAC 60.614 54.545 0.00 0.00 0.00 3.62
286 290 1.187087 CAGAGTAGTGGAGGTGGGAC 58.813 60.000 0.00 0.00 0.00 4.46
394 402 4.402793 AGCATCTTAATAGACGTGTGAGGT 59.597 41.667 0.00 0.00 31.99 3.85
397 405 6.679638 GCATCTTAATAGACGTGTGAGGTACA 60.680 42.308 0.00 0.00 32.70 2.90
605 613 6.827727 AGTTTGGTAGTAGAGACATTTGTGT 58.172 36.000 0.00 0.00 0.00 3.72
795 803 1.300620 CTCGGTGGTTGCTTCGACA 60.301 57.895 0.00 0.00 0.00 4.35
807 815 2.877786 TGCTTCGACACACAACAATGAT 59.122 40.909 0.00 0.00 0.00 2.45
929 938 2.574322 CGCTCAATTCCGAAAACACTG 58.426 47.619 0.00 0.00 0.00 3.66
1334 1347 5.092554 TGTTTGGTATATCACATCACCGT 57.907 39.130 0.00 0.00 33.55 4.83
1337 1350 3.301274 TGGTATATCACATCACCGTGGA 58.699 45.455 0.00 0.00 37.50 4.02
1469 1482 6.712095 TGAAGTTTCTGAAGTAGATGCAACAT 59.288 34.615 0.00 0.00 34.80 2.71
1651 1664 7.855904 AGTTTCTTGAATTGATGTGTTAACGTC 59.144 33.333 0.26 0.17 41.90 4.34
1927 1944 6.652481 CAGTATTGAAGGTGACAAAGAGATGT 59.348 38.462 0.00 0.00 35.90 3.06
2120 2138 4.741239 ACCGTGGGGGATCAGCCT 62.741 66.667 0.00 0.00 39.97 4.58
2971 2990 2.508526 GTTTGTGAAGAGACATGGGCT 58.491 47.619 0.00 0.00 0.00 5.19
3256 3275 0.625849 ATCACTGGCCCTTAACCCTG 59.374 55.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 74 3.020984 CAACAACACAAAGTACCCACCT 58.979 45.455 0.00 0.0 0.00 4.00
267 271 1.187087 GTCCCACCTCCACTACTCTG 58.813 60.000 0.00 0.0 0.00 3.35
286 290 4.158394 AGACGGTTCCATCATTTCCATTTG 59.842 41.667 0.00 0.0 0.00 2.32
394 402 2.826128 CTGTAGAGCCTGGTGTTCTGTA 59.174 50.000 0.00 0.0 0.00 2.74
397 405 1.270907 CCTGTAGAGCCTGGTGTTCT 58.729 55.000 0.00 0.0 0.00 3.01
605 613 6.828788 ACCGATACTCTCTGAGTACTATTCA 58.171 40.000 9.27 0.0 46.06 2.57
782 790 0.730265 GTTGTGTGTCGAAGCAACCA 59.270 50.000 9.89 0.0 36.25 3.67
789 797 3.058983 GCTCATCATTGTTGTGTGTCGAA 60.059 43.478 0.00 0.0 0.00 3.71
795 803 1.237533 TGCGCTCATCATTGTTGTGT 58.762 45.000 9.73 0.0 0.00 3.72
929 938 1.523758 AGTTGAGATGGAACGGCAAC 58.476 50.000 0.00 0.0 39.17 4.17
1280 1293 2.268298 CGCATAACTGTAGAACCGCTT 58.732 47.619 0.00 0.0 0.00 4.68
1361 1374 1.813513 AGCATGGAGAGGTTGAAACG 58.186 50.000 0.00 0.0 0.00 3.60
1441 1454 5.928839 TGCATCTACTTCAGAAACTTCACTC 59.071 40.000 0.00 0.0 36.67 3.51
1469 1482 9.219603 CTGGTGAGTCAAGTTCAAAATCTATTA 57.780 33.333 0.00 0.0 0.00 0.98
1651 1664 9.915629 AATCAATTACCTATCTACTTCTTAGCG 57.084 33.333 0.00 0.0 0.00 4.26
1927 1944 1.946768 CTCCAAACCAGAACTTCGCAA 59.053 47.619 0.00 0.0 0.00 4.85
2105 2123 1.762460 AGTAGGCTGATCCCCCACG 60.762 63.158 0.00 0.0 34.51 4.94
2120 2138 4.227300 ACTCAATGAGGTAATTGGGCAGTA 59.773 41.667 15.38 0.0 41.02 2.74
2159 2177 1.638388 CGACTCGTAGGTGGCGTACA 61.638 60.000 4.64 0.0 0.00 2.90
2256 2274 6.275494 TGTTTTCGTCATCACTAGTATCCA 57.725 37.500 0.00 0.0 0.00 3.41
3075 3094 2.258755 AGCTGTTCGCAACAACAAAAC 58.741 42.857 0.00 0.0 41.61 2.43
3097 3116 4.281688 ACTTTTGAACATCCACAGGATTGG 59.718 41.667 0.00 0.0 39.79 3.16


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

AutoCloner maintained by Alex Coulton.