Multiple sequence alignment - TraesCS6B01G233100

Loading Multiple Alignment...

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 TraesCS6B01G233100 chr6B 100.000 3392 0 0 1 3392 388292742 388296133 0 6264
1 TraesCS6B01G233100 chr7B 97.853 3400 65 6 1 3392 742954445 742957844 0 5867
2 TraesCS6B01G233100 chr7B 97.736 3401 68 6 1 3392 716910718 716907318 0 5845
3 TraesCS6B01G233100 chr7B 97.707 3401 68 8 1 3392 716778901 716775502 0 5840
4 TraesCS6B01G233100 chr7A 97.825 3402 64 6 1 3392 60349353 60345952 0 5864
5 TraesCS6B01G233100 chr5A 97.824 3401 65 7 1 3392 16538875 16535475 0 5862
6 TraesCS6B01G233100 chr2B 97.648 3402 69 8 1 3392 391172737 391169337 0 5829
7 TraesCS6B01G233100 chr1B 97.529 3400 76 6 1 3392 583567255 583570654 0 5806


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 TraesCS6B01G233100 chr6B 388292742 388296133 3391 False 6264 6264 100.000 1 3392 1 chr6B.!!$F1 3391
1 TraesCS6B01G233100 chr7B 742954445 742957844 3399 False 5867 5867 97.853 1 3392 1 chr7B.!!$F1 3391
2 TraesCS6B01G233100 chr7B 716907318 716910718 3400 True 5845 5845 97.736 1 3392 1 chr7B.!!$R2 3391
3 TraesCS6B01G233100 chr7B 716775502 716778901 3399 True 5840 5840 97.707 1 3392 1 chr7B.!!$R1 3391
4 TraesCS6B01G233100 chr7A 60345952 60349353 3401 True 5864 5864 97.825 1 3392 1 chr7A.!!$R1 3391
5 TraesCS6B01G233100 chr5A 16535475 16538875 3400 True 5862 5862 97.824 1 3392 1 chr5A.!!$R1 3391
6 TraesCS6B01G233100 chr2B 391169337 391172737 3400 True 5829 5829 97.648 1 3392 1 chr2B.!!$R1 3391
7 TraesCS6B01G233100 chr1B 583567255 583570654 3399 False 5806 5806 97.529 1 3392 1 chr1B.!!$F1 3391

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
417 418 1.270907 CCACTCAACCTCAGCCTAGT 58.729 55.0 0.0 0.0 0.0 2.57 F
1627 1638 0.392461 GCATTTACCCTGAGTCGGCA 60.392 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2276 2288 0.032515 TGGCCGAGGACTTCCATAGA 60.033 55.0 0.00 0.0 38.89 1.98 R
2561 2574 0.740868 CCGCGACCTGTCATGATTGT 60.741 55.0 8.23 0.0 0.00 2.71 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
118 119 3.389329 AGATGAATTAGCGGATCACAGGT 59.611 43.478 0.00 0.00 0.00 4.00
417 418 1.270907 CCACTCAACCTCAGCCTAGT 58.729 55.000 0.00 0.00 0.00 2.57
419 420 1.620819 CACTCAACCTCAGCCTAGTGT 59.379 52.381 0.00 0.00 31.82 3.55
519 521 5.479306 TCGTCTCCTTTAACTGATTCAAGG 58.521 41.667 0.00 0.00 39.62 3.61
599 601 7.060633 GTGAAAATGACAACGCTAAATCGAAAT 59.939 33.333 0.00 0.00 0.00 2.17
776 778 3.309410 CCTCTTCCTCCACCCATGATTTT 60.309 47.826 0.00 0.00 0.00 1.82
795 797 8.517062 TGATTTTGTTTTCCCATTGACAAATT 57.483 26.923 0.00 0.00 40.44 1.82
825 827 6.312399 AGACGAACTTGCATTTGTTGAATA 57.688 33.333 5.23 0.00 0.00 1.75
872 882 3.132289 TCCAGTGAAAAGAACAGTCTCGT 59.868 43.478 0.00 0.00 30.70 4.18
1013 1023 2.017623 GCTCAGCATGTCTGGAAGCAT 61.018 52.381 17.79 0.00 40.46 3.79
1359 1370 2.285834 GCTGTTTGGATTAGATGTCGCG 60.286 50.000 0.00 0.00 0.00 5.87
1459 1470 1.974265 TGGACCAAAGTCGCAAATCA 58.026 45.000 0.00 0.00 44.54 2.57
1627 1638 0.392461 GCATTTACCCTGAGTCGGCA 60.392 55.000 0.00 0.00 0.00 5.69
1820 1831 8.153550 TGAAAAAGAAATCTAGCAGTCTCTTCT 58.846 33.333 0.00 0.00 0.00 2.85
1882 1893 5.574188 AGATACCAACAGAAGCTTGGAAAT 58.426 37.500 2.10 0.00 40.76 2.17
1933 1944 3.320826 GGGCTTTGAACCTTGCTTTTCTA 59.679 43.478 0.00 0.00 0.00 2.10
1949 1960 8.797350 TGCTTTTCTATCAAATTCTCAGATGA 57.203 30.769 0.00 0.00 0.00 2.92
2114 2126 1.196808 GCAATGGAAAGAAGCGAACGA 59.803 47.619 0.00 0.00 0.00 3.85
2276 2288 6.409349 GGCCTACCTAGTTGAAATAGGAACAT 60.409 42.308 23.81 5.36 42.15 2.71
2350 2362 6.821031 TTTTCTTAATAACTGGGCGCTTTA 57.179 33.333 7.64 0.36 0.00 1.85
2353 2365 8.508883 TTTCTTAATAACTGGGCGCTTTAATA 57.491 30.769 7.64 0.00 0.00 0.98
2354 2366 8.685838 TTCTTAATAACTGGGCGCTTTAATAT 57.314 30.769 7.64 0.00 0.00 1.28
2499 2512 7.785033 TGACACACATATGAGAATCTGTACAT 58.215 34.615 10.38 0.00 34.92 2.29
2517 2530 8.803201 CTGTACATGATACAGAATAACGACAT 57.197 34.615 21.31 0.00 45.69 3.06
2561 2574 4.701651 CAGTATGGCCTTCATCTTTGACAA 59.298 41.667 3.32 0.00 37.30 3.18
2661 2674 2.093128 CGCCTTTGGGGACTACTACAAT 60.093 50.000 0.00 0.00 37.91 2.71
2719 2732 2.110011 ACTTTGACACCCAGCCCTTAAT 59.890 45.455 0.00 0.00 0.00 1.40
2778 2791 7.826252 ACAGACTGCAAAAGATAGATACAATGT 59.174 33.333 1.25 0.00 0.00 2.71
3031 3044 3.552890 GGCGGCCCTCATTATTGAATTTC 60.553 47.826 8.12 0.00 0.00 2.17
3040 3053 6.183360 CCTCATTATTGAATTTCTCCGCCTTT 60.183 38.462 0.00 0.00 0.00 3.11
3064 3077 7.172868 TGATGCAACCAAATTCACTATTGAT 57.827 32.000 0.00 0.00 0.00 2.57
3266 3279 6.873997 TGCTATTCCTTCAAGAAAGTATCGA 58.126 36.000 0.00 0.00 32.69 3.59
3290 3303 1.947456 GCAAAAAGGGACTCGTTCACT 59.053 47.619 0.00 0.00 41.15 3.41
3296 3309 2.803956 AGGGACTCGTTCACTGTATCA 58.196 47.619 0.00 0.00 36.20 2.15
3352 3365 4.833390 CCAACTGGTAAACAAAACCCAAA 58.167 39.130 0.00 0.00 36.06 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 1.824852 TCTGGCATGCTTCGACTTAGA 59.175 47.619 18.92 6.09 0.00 2.10
776 778 6.263392 TCGTCTAATTTGTCAATGGGAAAACA 59.737 34.615 0.00 0.00 0.00 2.83
795 797 3.570926 ATGCAAGTTCGTCTTCGTCTA 57.429 42.857 0.00 0.00 38.33 2.59
832 836 5.465056 CACTGGAGAAAGAGAACACTTCTTC 59.535 44.000 0.00 0.00 40.87 2.87
912 922 9.680315 CGGGAAAACTAGACTATATAAGAGTTG 57.320 37.037 0.00 0.00 0.00 3.16
1013 1023 1.188219 AGCAGAAGAGCGTTCTCCCA 61.188 55.000 0.98 0.00 40.22 4.37
1056 1066 9.953565 GGTATAGTAATGCTATGAATAACCCAA 57.046 33.333 1.01 0.00 40.41 4.12
1359 1370 5.467705 AGCGGAAATACTACAACCGATATC 58.532 41.667 0.00 0.00 45.31 1.63
1627 1638 6.318112 ACCTTTCCTTTCTGAATCAGGAATT 58.682 36.000 19.21 8.47 44.49 2.17
1820 1831 2.951642 GCCCTGCTACAATTCATTGCTA 59.048 45.455 0.00 0.00 41.38 3.49
1867 1878 5.880901 TCCTTCTTATTTCCAAGCTTCTGT 58.119 37.500 0.00 0.00 0.00 3.41
1882 1893 3.379372 CGGTAGGTCGACATTCCTTCTTA 59.621 47.826 21.11 0.00 35.51 2.10
1933 1944 9.438228 CACAGCTATATCATCTGAGAATTTGAT 57.562 33.333 2.94 2.94 33.59 2.57
2088 2100 3.507233 TCGCTTCTTTCCATTGCTTCAAT 59.493 39.130 0.00 0.00 34.04 2.57
2276 2288 0.032515 TGGCCGAGGACTTCCATAGA 60.033 55.000 0.00 0.00 38.89 1.98
2350 2362 9.927668 AAATTCATCGAGTTGTTCCAAAATATT 57.072 25.926 0.00 0.00 0.00 1.28
2353 2365 8.576442 ACTAAATTCATCGAGTTGTTCCAAAAT 58.424 29.630 0.00 0.00 0.00 1.82
2354 2366 7.936584 ACTAAATTCATCGAGTTGTTCCAAAA 58.063 30.769 0.00 0.00 0.00 2.44
2499 2512 5.741982 CGTGTCATGTCGTTATTCTGTATCA 59.258 40.000 0.00 0.00 0.00 2.15
2517 2530 5.066968 TGTAGTCATAAGATTGCGTGTCA 57.933 39.130 0.00 0.00 0.00 3.58
2561 2574 0.740868 CCGCGACCTGTCATGATTGT 60.741 55.000 8.23 0.00 0.00 2.71
2661 2674 5.708736 TTGGTCCTTCAAATGCCTATCTA 57.291 39.130 0.00 0.00 0.00 1.98
2695 2708 1.603739 GGCTGGGTGTCAAAGTCCC 60.604 63.158 0.00 0.00 41.41 4.46
2719 2732 6.121776 TCCCAAAGTTGTAGATTCTGCTTA 57.878 37.500 3.38 0.00 0.00 3.09
2778 2791 0.894141 GCATGCATGGTGGGTAACAA 59.106 50.000 27.34 0.00 39.74 2.83
3031 3044 1.243342 TGGTTGCATCAAAGGCGGAG 61.243 55.000 0.00 0.00 0.00 4.63
3040 3053 6.587206 TCAATAGTGAATTTGGTTGCATCA 57.413 33.333 0.00 0.00 0.00 3.07
3064 3077 5.871465 TGAAGCATGCATAAACTCGTAAA 57.129 34.783 21.98 0.00 0.00 2.01
3182 3195 8.635765 ACATTGCAAAGAATCTAAAAGAGGTA 57.364 30.769 8.96 0.00 0.00 3.08
3195 3208 3.551863 CCCGCACTAAACATTGCAAAGAA 60.552 43.478 8.96 0.00 0.00 2.52
3266 3279 3.445805 TGAACGAGTCCCTTTTTGCTTTT 59.554 39.130 0.00 0.00 0.00 2.27
3290 3303 5.934043 GCATAGCTGTATTGGATGTGATACA 59.066 40.000 0.00 0.00 36.64 2.29
3296 3309 3.117926 TGTGGCATAGCTGTATTGGATGT 60.118 43.478 0.00 0.00 0.00 3.06
3352 3365 5.418209 CCTATTCCTAGGTCGATCCGTTAAT 59.582 44.000 9.08 0.00 39.89 1.40


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

AutoCloner maintained by Alex Coulton.