Multiple sequence alignment - TraesCS2D01G513000

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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 TraesCS2D01G513000 chr2D 100.000 3393 0 0 1 3393 604416906 604420298 0 6266
1 TraesCS2D01G513000 chr2D 97.526 3395 82 2 1 3393 200934935 200938329 0 5803
2 TraesCS2D01G513000 chr5D 97.761 3395 73 3 1 3393 562925174 562928567 0 5845
3 TraesCS2D01G513000 chr1A 97.437 3395 80 3 1 3393 94765603 94762214 0 5781
4 TraesCS2D01G513000 chr7A 97.290 3395 90 2 1 3393 211308107 211311501 0 5758
5 TraesCS2D01G513000 chr7A 96.996 3395 100 2 1 3393 563544632 563548026 0 5703
6 TraesCS2D01G513000 chr7A 97.418 1549 39 1 1 1549 211265010 211263463 0 2638
7 TraesCS2D01G513000 chr1D 97.261 3395 89 3 1 3393 185786577 185783185 0 5751
8 TraesCS2D01G513000 chr6D 97.684 3325 75 2 71 3393 458889921 458893245 0 5712
9 TraesCS2D01G513000 chr7D 96.583 3395 114 2 1 3393 307118245 307114851 0 5626
10 TraesCS2D01G513000 chr7B 97.700 2565 57 2 831 3393 742955280 742957844 0 4409


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 TraesCS2D01G513000 chr2D 604416906 604420298 3392 False 6266 6266 100.000 1 3393 1 chr2D.!!$F2 3392
1 TraesCS2D01G513000 chr2D 200934935 200938329 3394 False 5803 5803 97.526 1 3393 1 chr2D.!!$F1 3392
2 TraesCS2D01G513000 chr5D 562925174 562928567 3393 False 5845 5845 97.761 1 3393 1 chr5D.!!$F1 3392
3 TraesCS2D01G513000 chr1A 94762214 94765603 3389 True 5781 5781 97.437 1 3393 1 chr1A.!!$R1 3392
4 TraesCS2D01G513000 chr7A 211308107 211311501 3394 False 5758 5758 97.290 1 3393 1 chr7A.!!$F1 3392
5 TraesCS2D01G513000 chr7A 563544632 563548026 3394 False 5703 5703 96.996 1 3393 1 chr7A.!!$F2 3392
6 TraesCS2D01G513000 chr7A 211263463 211265010 1547 True 2638 2638 97.418 1 1549 1 chr7A.!!$R1 1548
7 TraesCS2D01G513000 chr1D 185783185 185786577 3392 True 5751 5751 97.261 1 3393 1 chr1D.!!$R1 3392
8 TraesCS2D01G513000 chr6D 458889921 458893245 3324 False 5712 5712 97.684 71 3393 1 chr6D.!!$F1 3322
9 TraesCS2D01G513000 chr7D 307114851 307118245 3394 True 5626 5626 96.583 1 3393 1 chr7D.!!$R1 3392
10 TraesCS2D01G513000 chr7B 742955280 742957844 2564 False 4409 4409 97.700 831 3393 1 chr7B.!!$F1 2562

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
536 537 2.045561 TGGACAACCAAAAAGCGAGA 57.954 45.0 0.0 0.0 43.91 4.04 F
1182 1184 0.252239 TGGTAGCAGAAGAGAGGGCA 60.252 55.0 0.0 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 2313 0.404040 AATCCCTTGTCGGCTTTCCA 59.596 50.000 0.0 0.0 0.0 3.53 R
2561 2564 1.202568 CGAGGCCTGTCATGATTGCTA 60.203 52.381 12.0 0.0 0.0 3.49 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
42 43 7.333423 GCTTATACCACAATGTTACTCTGACAA 59.667 37.037 0.00 0.00 0.00 3.18
362 363 4.581824 TCTTCATGAAAAAGTGCAGAAGCT 59.418 37.500 9.88 0.00 42.74 3.74
374 375 5.191426 AGTGCAGAAGCTTGTATCAATGAT 58.809 37.500 2.10 0.00 42.74 2.45
383 384 5.071519 AGCTTGTATCAATGATGAGTAGGCT 59.928 40.000 5.91 5.42 39.39 4.58
456 457 4.977963 CACTGTTCGTTCGGAAAGTAAGTA 59.022 41.667 3.67 0.00 36.14 2.24
536 537 2.045561 TGGACAACCAAAAAGCGAGA 57.954 45.000 0.00 0.00 43.91 4.04
820 821 3.815809 CGGCCCCTATTGATTCTTACAA 58.184 45.455 0.00 0.00 0.00 2.41
847 848 5.360591 TCCTGTGAAAAGAAGTGTTCTCTC 58.639 41.667 0.00 0.00 39.61 3.20
1110 1111 4.817318 ATTCATTGCGGGTTGGTTATTT 57.183 36.364 0.00 0.00 0.00 1.40
1175 1177 3.002791 CGCTTTGATTGGTAGCAGAAGA 58.997 45.455 11.23 0.00 34.62 2.87
1182 1184 0.252239 TGGTAGCAGAAGAGAGGGCA 60.252 55.000 0.00 0.00 0.00 5.36
1460 1462 1.974265 TGGACCAAAGTCGCAAATCA 58.026 45.000 0.00 0.00 44.54 2.57
1509 1511 0.676782 AAAGTCGGCAAGGGGAATCG 60.677 55.000 0.00 0.00 0.00 3.34
1632 1635 2.750141 TACCCTGAGTCGGCTATTCT 57.250 50.000 0.00 0.00 0.00 2.40
1750 1753 0.795735 GCTTTCGAGCACGTACGCTA 60.796 55.000 16.72 0.00 44.01 4.26
1849 1852 0.771127 TTGTAGCAGGGCTTGGTCTT 59.229 50.000 4.02 0.00 40.44 3.01
1933 1936 3.320826 GGGCTTTGAACCTTGCTTTTCTA 59.679 43.478 0.00 0.00 0.00 2.10
1968 1971 5.929992 AGACGCTATAGCTGTGTAAAAACAA 59.070 36.000 21.98 0.00 39.32 2.83
2088 2091 6.543831 ACTCTTGACTATTGCTTGAAACAAGT 59.456 34.615 12.07 0.00 36.14 3.16
2146 2149 1.001181 GCAGCAAGAAAAGGGATGCAA 59.999 47.619 0.00 0.00 42.99 4.08
2300 2303 1.072505 GGAAGTCCTCGGCCAAACA 59.927 57.895 2.24 0.00 0.00 2.83
2310 2313 4.709397 TCCTCGGCCAAACAAATATTTCAT 59.291 37.500 2.24 0.00 0.00 2.57
2386 2389 6.276847 ACAACTCGATGAATTCAGTAGATCC 58.723 40.000 14.54 0.00 0.00 3.36
2561 2564 5.121380 ACAGTATGGCCTTCATCTTTGAT 57.879 39.130 3.32 0.00 43.62 2.57
2579 2582 2.440627 TGATAGCAATCATGACAGGCCT 59.559 45.455 0.00 0.00 37.20 5.19
2590 2593 0.750850 GACAGGCCTCGGTATTAGCA 59.249 55.000 0.00 0.00 0.00 3.49
2617 2620 3.977326 AGAAAGGAAAGGACTTGAGGTCT 59.023 43.478 0.00 0.00 43.97 3.85
2680 2683 6.711277 ACTACAACAGATAGGCATTTGAAGA 58.289 36.000 0.00 0.00 0.00 2.87
2782 2785 9.236006 AGACTGCAAAAGATAGATACAATGTTT 57.764 29.630 0.00 0.00 0.00 2.83
2858 2861 4.096682 GTCATCTACTACTGCGAAACTCCT 59.903 45.833 0.00 0.00 0.00 3.69
2866 2869 2.890766 GCGAAACTCCTGGGGGACA 61.891 63.158 0.00 0.00 36.57 4.02
2872 2875 0.478507 ACTCCTGGGGGACACTTTTG 59.521 55.000 0.00 0.00 36.57 2.44
2921 2924 3.108376 GGAAGAACACCCTCTAGACCAT 58.892 50.000 0.00 0.00 0.00 3.55
2924 2927 3.100671 AGAACACCCTCTAGACCATGAC 58.899 50.000 0.00 0.00 0.00 3.06
3111 3115 9.147732 TCATTCCTATATCGGCATGTATTATCT 57.852 33.333 5.94 0.00 30.92 1.98
3366 3370 2.667473 ACCCAAGTTAACGGATCGAG 57.333 50.000 5.17 0.00 0.00 4.04
3374 3378 3.698040 AGTTAACGGATCGAGCTAGGAAA 59.302 43.478 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 5.649831 GCCAAGACTATTTTGTCAAGGATCT 59.350 40.000 0.00 0.00 39.27 2.75
301 302 7.437713 TCATCTGTCTTGGAGTTATACCATT 57.562 36.000 0.00 0.00 37.26 3.16
308 309 6.132658 AGAGCTATCATCTGTCTTGGAGTTA 58.867 40.000 0.00 0.00 0.00 2.24
362 363 5.130975 ACCAGCCTACTCATCATTGATACAA 59.869 40.000 0.00 0.00 0.00 2.41
383 384 6.808321 ATTTACTATCTTCTGCTGGTACCA 57.192 37.500 15.39 15.39 0.00 3.25
456 457 4.175962 TGGGGAGAACAATCTTTAGGAGT 58.824 43.478 0.00 0.00 35.54 3.85
536 537 0.456312 CGCCGCTCTCTTACTCGTTT 60.456 55.000 0.00 0.00 0.00 3.60
609 610 5.129485 AGTGGTCTCTCTCTTCTTTTCACAA 59.871 40.000 0.00 0.00 0.00 3.33
677 678 5.236911 TGCTTTTGGTAACGAACTTACGAAT 59.763 36.000 0.00 0.00 40.58 3.34
820 821 7.340487 AGAGAACACTTCTTTTCACAGGATTTT 59.660 33.333 0.00 0.00 40.87 1.82
847 848 2.734079 GACTGTTCTTTTCGCTGGAGAG 59.266 50.000 0.00 0.00 0.00 3.20
971 972 7.665559 TGAGCTCTACCAATTTTTGTACATTCT 59.334 33.333 16.19 0.00 0.00 2.40
1182 1184 1.039856 AAAATGAAGGCTGGCAACGT 58.960 45.000 3.38 0.00 42.51 3.99
1230 1232 8.457261 AGTTTGAAGTTCTCTCATATGCATTTC 58.543 33.333 3.54 0.00 0.00 2.17
1509 1511 3.418684 TGACTAAACAGCCCTTTCTCC 57.581 47.619 0.00 0.00 0.00 3.71
1632 1635 6.434028 CCACATACCTTTCCTTTCTGAATCAA 59.566 38.462 0.00 0.00 0.00 2.57
1869 1872 4.437682 TCCTTCTTCTTTCCAAGCTTCA 57.562 40.909 0.00 0.00 0.00 3.02
1893 1896 2.124403 ACGGAGCGGTAGGTCGAT 60.124 61.111 0.00 0.00 45.26 3.59
2088 2091 3.550639 CGCTTCTTTCCATTGCTTCAACA 60.551 43.478 0.00 0.00 0.00 3.33
2146 2149 5.393027 GCATATCCGATTTTTGGACACTTGT 60.393 40.000 0.00 0.00 38.60 3.16
2300 2303 5.913137 TGTCGGCTTTCCATGAAATATTT 57.087 34.783 0.00 0.00 30.85 1.40
2310 2313 0.404040 AATCCCTTGTCGGCTTTCCA 59.596 50.000 0.00 0.00 0.00 3.53
2377 2380 3.970640 AGGCCTCCTAAAAGGATCTACTG 59.029 47.826 0.00 0.00 44.81 2.74
2386 2389 3.282885 GTCATGGAAGGCCTCCTAAAAG 58.717 50.000 5.23 0.00 45.64 2.27
2561 2564 1.202568 CGAGGCCTGTCATGATTGCTA 60.203 52.381 12.00 0.00 0.00 3.49
2579 2582 6.971726 TCCTTTCTCTAATGCTAATACCGA 57.028 37.500 0.00 0.00 0.00 4.69
2590 2593 6.273495 ACCTCAAGTCCTTTCCTTTCTCTAAT 59.727 38.462 0.00 0.00 0.00 1.73
2617 2620 6.368779 AGCTTTATTAGTTGTAGGTGGACA 57.631 37.500 0.00 0.00 0.00 4.02
2680 2683 2.105993 GTCCTCAGTAGGTGGTTTGGTT 59.894 50.000 0.00 0.00 44.09 3.67
2782 2785 1.637338 TTGCATGCATGGTGGGTAAA 58.363 45.000 27.34 0.00 0.00 2.01
2858 2861 2.423660 CCAGTTACAAAAGTGTCCCCCA 60.424 50.000 0.00 0.00 39.30 4.96
2866 2869 5.691896 AGAGGCTAAACCAGTTACAAAAGT 58.308 37.500 0.00 0.00 43.14 2.66
2872 2875 5.394333 CCACTCTAGAGGCTAAACCAGTTAC 60.394 48.000 23.50 0.00 43.14 2.50
2924 2927 8.629986 CGCTTTGTCAATTGAATTAGTAAGTTG 58.370 33.333 10.35 2.45 0.00 3.16
3111 3115 1.419381 TGTCTCACAACCAGCCTACA 58.581 50.000 0.00 0.00 0.00 2.74
3366 3370 6.357367 TGGTTCTATTCATCCTTTTCCTAGC 58.643 40.000 0.00 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.