Multiple sequence alignment - TraesCS7B01G156600

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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 TraesCS7B01G156600 chr7B 100.000 2285 0 0 1 2285 211694375 211696659 0.000000e+00 4220
1 TraesCS7B01G156600 chr2B 98.638 1615 19 2 1 1613 798712066 798710453 0.000000e+00 2857
2 TraesCS7B01G156600 chr2B 94.512 164 6 1 1449 1612 459254573 459254733 1.360000e-62 250
3 TraesCS7B01G156600 chr5B 98.511 1612 23 1 1 1612 123020172 123021782 0.000000e+00 2843
4 TraesCS7B01G156600 chr7A 97.582 1613 34 3 1 1612 6752977 6751369 0.000000e+00 2758
5 TraesCS7B01G156600 chr7A 93.155 672 34 2 1613 2284 250676904 250677563 0.000000e+00 976
6 TraesCS7B01G156600 chr1B 97.022 1612 45 1 1 1612 394374326 394375934 0.000000e+00 2708
7 TraesCS7B01G156600 chr1B 96.960 1612 44 3 1 1612 388170874 388169268 0.000000e+00 2700
8 TraesCS7B01G156600 chr1A 96.714 1613 46 5 1 1613 579647535 579649140 0.000000e+00 2678
9 TraesCS7B01G156600 chr6B 96.340 1612 53 4 1 1612 717064098 717065703 0.000000e+00 2645
10 TraesCS7B01G156600 chr3D 96.310 1572 54 3 1 1571 516530137 516528569 0.000000e+00 2579
11 TraesCS7B01G156600 chr6D 95.364 1510 61 6 1 1510 454964407 454962907 0.000000e+00 2392
12 TraesCS7B01G156600 chr7D 95.685 672 29 0 1613 2284 235532315 235532986 0.000000e+00 1081


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 TraesCS7B01G156600 chr7B 211694375 211696659 2284 False 4220 4220 100.000 1 2285 1 chr7B.!!$F1 2284
1 TraesCS7B01G156600 chr2B 798710453 798712066 1613 True 2857 2857 98.638 1 1613 1 chr2B.!!$R1 1612
2 TraesCS7B01G156600 chr5B 123020172 123021782 1610 False 2843 2843 98.511 1 1612 1 chr5B.!!$F1 1611
3 TraesCS7B01G156600 chr7A 6751369 6752977 1608 True 2758 2758 97.582 1 1612 1 chr7A.!!$R1 1611
4 TraesCS7B01G156600 chr7A 250676904 250677563 659 False 976 976 93.155 1613 2284 1 chr7A.!!$F1 671
5 TraesCS7B01G156600 chr1B 394374326 394375934 1608 False 2708 2708 97.022 1 1612 1 chr1B.!!$F1 1611
6 TraesCS7B01G156600 chr1B 388169268 388170874 1606 True 2700 2700 96.960 1 1612 1 chr1B.!!$R1 1611
7 TraesCS7B01G156600 chr1A 579647535 579649140 1605 False 2678 2678 96.714 1 1613 1 chr1A.!!$F1 1612
8 TraesCS7B01G156600 chr6B 717064098 717065703 1605 False 2645 2645 96.340 1 1612 1 chr6B.!!$F1 1611
9 TraesCS7B01G156600 chr3D 516528569 516530137 1568 True 2579 2579 96.310 1 1571 1 chr3D.!!$R1 1570
10 TraesCS7B01G156600 chr6D 454962907 454964407 1500 True 2392 2392 95.364 1 1510 1 chr6D.!!$R1 1509
11 TraesCS7B01G156600 chr7D 235532315 235532986 671 False 1081 1081 95.685 1613 2284 1 chr7D.!!$F1 671

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
42 43 3.383185 TGGTTCCAACATGAAAGGACAAC 59.617 43.478 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 1896 0.395311 TCGGAGGCGAGGAAGTACAT 60.395 55.0 0.0 0.0 0.0 2.29 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 3.383185 TGGTTCCAACATGAAAGGACAAC 59.617 43.478 0.00 0.00 0.00 3.32
250 251 6.837312 TCTTACTTGACAATCTCCCAAAAGA 58.163 36.000 0.00 0.00 0.00 2.52
322 323 3.423539 AAAGAGTGTGCAGCCTATCAA 57.576 42.857 0.00 0.00 0.00 2.57
667 669 6.033341 CAGAATTTCCTTCAAAACGTCAACA 58.967 36.000 0.00 0.00 36.24 3.33
1188 1191 1.808945 GATAGATTGAATGGCCTGGCG 59.191 52.381 13.40 0.00 0.00 5.69
1276 1279 1.265635 CACGAAATGCCCGAAGAAACA 59.734 47.619 0.00 0.00 0.00 2.83
1744 1754 0.174845 GGCAGCACTACCACGTGATA 59.825 55.000 19.30 2.24 37.06 2.15
1754 1764 3.478857 ACCACGTGATAAACTTCACCA 57.521 42.857 19.30 0.00 42.46 4.17
2044 2060 1.241990 ACTACTTCTGCAGCGACGGA 61.242 55.000 9.47 0.00 0.00 4.69
2069 2085 0.318762 ACTCAAAGTCTGGTCGCTCC 59.681 55.000 0.00 0.00 0.00 4.70
2125 2141 2.492090 GCCGTGAGAGTCAGCGAT 59.508 61.111 0.00 0.00 0.00 4.58
2134 2150 0.524392 GAGTCAGCGATGTCGTGGAG 60.524 60.000 0.00 0.00 42.22 3.86
2135 2151 1.517257 GTCAGCGATGTCGTGGAGG 60.517 63.158 0.00 0.00 42.22 4.30
2136 2152 2.202797 CAGCGATGTCGTGGAGGG 60.203 66.667 4.20 0.00 42.22 4.30
2137 2153 4.148825 AGCGATGTCGTGGAGGGC 62.149 66.667 4.20 0.00 42.22 5.19
2139 2155 4.873129 CGATGTCGTGGAGGGCGG 62.873 72.222 0.00 0.00 34.11 6.13
2173 2195 3.645660 TTCCTGGCGATGCACCCA 61.646 61.111 0.00 0.00 0.00 4.51
2186 2208 1.817099 CACCCAGAGAATCAGGCGC 60.817 63.158 0.00 0.00 41.03 6.53
2188 2210 0.687757 ACCCAGAGAATCAGGCGCTA 60.688 55.000 7.64 0.00 41.03 4.26
2202 2224 3.005897 CAGGCGCTAGTCTACATATGGTT 59.994 47.826 7.64 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.307776 TGTTGGAACCATTGTCATAACCTTA 58.692 36.000 0.00 0.00 0.00 2.69
42 43 1.502231 CGACTCTGAACACCTTGGTG 58.498 55.000 17.34 17.34 0.00 4.17
250 251 6.775594 AAGGCTTGAGAGTTAGTTTTGTTT 57.224 33.333 0.00 0.00 0.00 2.83
322 323 7.573710 TGAAATTACATGGATAGCTTGGTACT 58.426 34.615 0.00 0.00 0.00 2.73
667 669 6.185511 TCATCATGATGCCTCTTTCTTTTCT 58.814 36.000 27.68 0.00 38.65 2.52
1099 1102 4.102367 AGAGAAACTTCTTTCAGCTGAGGT 59.898 41.667 17.43 9.14 38.67 3.85
1188 1191 2.362736 TCCTTCTCAATGCAGCACATC 58.637 47.619 0.00 0.00 38.34 3.06
1619 1629 2.578981 GACGTAGAACTCCGGCGC 60.579 66.667 0.00 0.00 0.00 6.53
1877 1887 1.067582 GGAAGTACATAGCGCCGCT 59.932 57.895 18.67 18.67 43.41 5.52
1886 1896 0.395311 TCGGAGGCGAGGAAGTACAT 60.395 55.000 0.00 0.00 0.00 2.29
2044 2060 1.903183 GACCAGACTTTGAGTAGCCCT 59.097 52.381 0.00 0.00 0.00 5.19
2098 2114 1.687494 CTCTCACGGCGTGCTTTAGC 61.687 60.000 33.59 0.00 42.50 3.09
2101 2117 1.664965 GACTCTCACGGCGTGCTTT 60.665 57.895 33.59 17.80 32.98 3.51
2173 2195 2.065899 AGACTAGCGCCTGATTCTCT 57.934 50.000 2.29 0.00 0.00 3.10
2186 2208 4.299155 CACGGCAACCATATGTAGACTAG 58.701 47.826 1.24 0.00 0.00 2.57
2188 2210 2.158957 CCACGGCAACCATATGTAGACT 60.159 50.000 1.24 0.00 0.00 3.24
2202 2224 4.351938 CGACGACCTTCCACGGCA 62.352 66.667 0.00 0.00 37.38 5.69


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

AutoCloner maintained by Alex Coulton.