Multiple sequence alignment - TraesCS2B01G196700

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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 TraesCS2B01G196700 chr2B 100.000 2468 0 0 1 2468 174779829 174782296 0.000000e+00 4558
1 TraesCS2B01G196700 chr2D 88.721 1658 89 42 47 1663 121359513 121361113 0.000000e+00 1936
2 TraesCS2B01G196700 chr3B 99.128 803 7 0 1666 2468 793111068 793111870 0.000000e+00 1445
3 TraesCS2B01G196700 chr3B 98.756 804 10 0 1665 2468 674137135 674136332 0.000000e+00 1430
4 TraesCS2B01G196700 chr3B 98.269 809 8 1 1666 2468 302348920 302349728 0.000000e+00 1411
5 TraesCS2B01G196700 chr3B 98.387 806 8 4 1665 2468 651530377 651529575 0.000000e+00 1411
6 TraesCS2B01G196700 chr5B 98.637 807 8 1 1665 2468 257005634 257006440 0.000000e+00 1426
7 TraesCS2B01G196700 chr2A 98.387 806 10 1 1666 2468 748541185 748540380 0.000000e+00 1413
8 TraesCS2B01G196700 chr2A 98.269 809 8 1 1666 2468 50139710 50140518 0.000000e+00 1411
9 TraesCS2B01G196700 chr2A 89.537 1166 40 28 545 1657 125607475 125608611 0.000000e+00 1402
10 TraesCS2B01G196700 chr2A 87.568 555 37 13 36 561 125606899 125607450 4.510000e-172 614
11 TraesCS2B01G196700 chr1B 98.272 810 8 1 1665 2468 481286039 481286848 0.000000e+00 1413
12 TraesCS2B01G196700 chr6B 98.148 810 11 2 1662 2468 577926430 577927238 0.000000e+00 1410


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 TraesCS2B01G196700 chr2B 174779829 174782296 2467 False 4558 4558 100.0000 1 2468 1 chr2B.!!$F1 2467
1 TraesCS2B01G196700 chr2D 121359513 121361113 1600 False 1936 1936 88.7210 47 1663 1 chr2D.!!$F1 1616
2 TraesCS2B01G196700 chr3B 793111068 793111870 802 False 1445 1445 99.1280 1666 2468 1 chr3B.!!$F2 802
3 TraesCS2B01G196700 chr3B 674136332 674137135 803 True 1430 1430 98.7560 1665 2468 1 chr3B.!!$R2 803
4 TraesCS2B01G196700 chr3B 302348920 302349728 808 False 1411 1411 98.2690 1666 2468 1 chr3B.!!$F1 802
5 TraesCS2B01G196700 chr3B 651529575 651530377 802 True 1411 1411 98.3870 1665 2468 1 chr3B.!!$R1 803
6 TraesCS2B01G196700 chr5B 257005634 257006440 806 False 1426 1426 98.6370 1665 2468 1 chr5B.!!$F1 803
7 TraesCS2B01G196700 chr2A 748540380 748541185 805 True 1413 1413 98.3870 1666 2468 1 chr2A.!!$R1 802
8 TraesCS2B01G196700 chr2A 50139710 50140518 808 False 1411 1411 98.2690 1666 2468 1 chr2A.!!$F1 802
9 TraesCS2B01G196700 chr2A 125606899 125608611 1712 False 1008 1402 88.5525 36 1657 2 chr2A.!!$F2 1621
10 TraesCS2B01G196700 chr1B 481286039 481286848 809 False 1413 1413 98.2720 1665 2468 1 chr1B.!!$F1 803
11 TraesCS2B01G196700 chr6B 577926430 577927238 808 False 1410 1410 98.1480 1662 2468 1 chr6B.!!$F1 806

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
189 202 0.248289 AAGTTACCGCTGGCGTGTAT 59.752 50.0 13.84 0.0 37.81 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 1700 0.040646 TACAGAGGCGGAAGGAAGGA 59.959 55.0 0.0 0.0 0.0 3.36 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
100 104 3.460995 GGCACGGATAGGAGGAGG 58.539 66.667 0.00 0.00 0.00 4.30
102 106 0.543174 GGCACGGATAGGAGGAGGAT 60.543 60.000 0.00 0.00 0.00 3.24
103 107 1.343069 GCACGGATAGGAGGAGGATT 58.657 55.000 0.00 0.00 0.00 3.01
104 108 2.526432 GCACGGATAGGAGGAGGATTA 58.474 52.381 0.00 0.00 0.00 1.75
105 109 2.494073 GCACGGATAGGAGGAGGATTAG 59.506 54.545 0.00 0.00 0.00 1.73
106 110 3.814676 GCACGGATAGGAGGAGGATTAGA 60.815 52.174 0.00 0.00 0.00 2.10
161 174 2.751436 ACGACGTAGGCCGGCTTA 60.751 61.111 28.56 22.00 44.70 3.09
188 201 0.668096 CAAGTTACCGCTGGCGTGTA 60.668 55.000 13.84 11.91 37.81 2.90
189 202 0.248289 AAGTTACCGCTGGCGTGTAT 59.752 50.000 13.84 0.00 37.81 2.29
203 216 1.811558 CGTGTATGATTCAGCAGGGGG 60.812 57.143 0.00 0.00 0.00 5.40
214 227 2.332654 GCAGGGGGCAGTTGTAACG 61.333 63.158 0.00 0.00 43.97 3.18
257 274 1.376037 CTGTCCCTGCCTCGTTTCC 60.376 63.158 0.00 0.00 0.00 3.13
258 275 2.111999 CTGTCCCTGCCTCGTTTCCA 62.112 60.000 0.00 0.00 0.00 3.53
263 280 0.609131 CCTGCCTCGTTTCCATTGGT 60.609 55.000 1.86 0.00 0.00 3.67
264 281 1.247567 CTGCCTCGTTTCCATTGGTT 58.752 50.000 1.86 0.00 0.00 3.67
265 282 1.613437 CTGCCTCGTTTCCATTGGTTT 59.387 47.619 1.86 0.00 0.00 3.27
294 311 2.825836 AGCAAGCGCCCTACATGC 60.826 61.111 2.29 5.76 39.83 4.06
414 432 2.021457 GTACAACAACTTGCACCAGGT 58.979 47.619 0.00 0.00 0.00 4.00
437 455 9.698309 AGGTAGTGTATAATTCTTCAATCATCG 57.302 33.333 0.00 0.00 0.00 3.84
449 474 7.158099 TCTTCAATCATCGAAGTCTCTACAA 57.842 36.000 0.00 0.00 40.63 2.41
454 479 8.184848 TCAATCATCGAAGTCTCTACAAACTAG 58.815 37.037 0.00 0.00 0.00 2.57
525 558 1.002250 CGCCATCGTATCGTACCAGC 61.002 60.000 0.00 0.00 0.00 4.85
538 572 7.044901 CGTATCGTACCAGCTTATTTATCATCG 60.045 40.741 0.00 0.00 0.00 3.84
626 714 0.891904 ACGGCCGTGGCAAGTTAATT 60.892 50.000 33.75 0.00 44.11 1.40
973 1098 3.521529 CTGAAGGCGGCGGGGATAG 62.522 68.421 9.78 0.00 0.00 2.08
1083 1219 1.668151 GTTCACGGAGGAGTGCACC 60.668 63.158 14.63 4.90 41.61 5.01
1663 1807 6.852420 ACCAATGTGTACAGAGTACATACT 57.148 37.500 12.53 0.00 39.71 2.12
1762 1908 4.280019 GGGTTGTGCCGGTTCCCT 62.280 66.667 1.90 0.00 38.44 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 2.565645 CCTCCTCCTATCCGTGCCG 61.566 68.421 0.00 0.00 0.00 5.69
161 174 0.328258 AGCGGTAACTTGCAAGGGAT 59.672 50.000 29.18 17.28 0.00 3.85
188 201 1.229359 CTGCCCCCTGCTGAATCAT 59.771 57.895 0.00 0.00 41.11 2.45
189 202 1.792757 AACTGCCCCCTGCTGAATCA 61.793 55.000 0.00 0.00 41.11 2.57
203 216 3.678072 TGTCTATTGCTCGTTACAACTGC 59.322 43.478 0.00 0.00 0.00 4.40
214 227 1.328986 GCTTCGCCTTGTCTATTGCTC 59.671 52.381 0.00 0.00 0.00 4.26
246 259 1.611491 GAAACCAATGGAAACGAGGCA 59.389 47.619 6.16 0.00 0.00 4.75
257 274 4.279169 TGCTGAAGGAAGAAGAAACCAATG 59.721 41.667 0.00 0.00 0.00 2.82
258 275 4.473444 TGCTGAAGGAAGAAGAAACCAAT 58.527 39.130 0.00 0.00 0.00 3.16
263 280 2.549754 CGCTTGCTGAAGGAAGAAGAAA 59.450 45.455 14.93 0.00 44.86 2.52
264 281 2.146342 CGCTTGCTGAAGGAAGAAGAA 58.854 47.619 14.93 0.00 44.86 2.52
265 282 1.800805 CGCTTGCTGAAGGAAGAAGA 58.199 50.000 14.93 0.00 44.86 2.87
366 384 0.530744 AAGAAGATGTGACGGCGCTA 59.469 50.000 6.90 0.00 0.00 4.26
437 455 7.393841 TTCTAGGCTAGTTTGTAGAGACTTC 57.606 40.000 20.45 0.00 29.16 3.01
442 460 6.100668 GGTGTTTCTAGGCTAGTTTGTAGAG 58.899 44.000 20.45 0.00 0.00 2.43
449 474 3.244457 GGTGTGGTGTTTCTAGGCTAGTT 60.244 47.826 20.45 0.00 0.00 2.24
454 479 1.235724 GTGGTGTGGTGTTTCTAGGC 58.764 55.000 0.00 0.00 0.00 3.93
493 526 2.631696 GATGGCGCCGTGTTTGATCG 62.632 60.000 29.48 0.00 0.00 3.69
505 538 1.002250 CTGGTACGATACGATGGCGC 61.002 60.000 0.00 0.00 42.48 6.53
538 572 0.591741 CGCCTCGTTATCTCGTGGAC 60.592 60.000 10.57 2.77 44.05 4.02
606 693 1.303091 ATTAACTTGCCACGGCCGTC 61.303 55.000 31.80 19.75 41.09 4.79
672 773 1.885850 GTCCCGTCGTTGCTTGTGT 60.886 57.895 0.00 0.00 0.00 3.72
765 871 3.702048 GAGGCCTGCCACGTGGTA 61.702 66.667 33.92 29.33 38.92 3.25
776 882 1.486310 TGCGACTGAATTATGAGGCCT 59.514 47.619 3.86 3.86 0.00 5.19
851 968 2.029560 GTCCGGAGTCCGTATTTATCCC 60.030 54.545 28.98 0.00 46.80 3.85
955 1080 3.521529 CTATCCCCGCCGCCTTCAG 62.522 68.421 0.00 0.00 0.00 3.02
956 1081 3.546543 CTATCCCCGCCGCCTTCA 61.547 66.667 0.00 0.00 0.00 3.02
1558 1699 0.836400 ACAGAGGCGGAAGGAAGGAA 60.836 55.000 0.00 0.00 0.00 3.36
1559 1700 0.040646 TACAGAGGCGGAAGGAAGGA 59.959 55.000 0.00 0.00 0.00 3.36
1560 1701 0.902531 TTACAGAGGCGGAAGGAAGG 59.097 55.000 0.00 0.00 0.00 3.46
1561 1702 2.762535 TTTACAGAGGCGGAAGGAAG 57.237 50.000 0.00 0.00 0.00 3.46
1762 1908 5.192927 CCATGTAAGACAATAGGCTTTGGA 58.807 41.667 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.