Multiple sequence alignment - TraesCS5D01G475800

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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 TraesCS5D01G475800 chr5D 100.000 2951 0 0 1 2951 515107884 515110834 0.000000e+00 5450.0
1 TraesCS5D01G475800 chr5D 86.792 159 20 1 1798 1956 268690561 268690718 3.020000e-40 176.0
2 TraesCS5D01G475800 chr5D 96.875 64 2 0 2644 2707 515110461 515110524 1.120000e-19 108.0
3 TraesCS5D01G475800 chr5D 96.875 64 2 0 2578 2641 515110527 515110590 1.120000e-19 108.0
4 TraesCS5D01G475800 chr5A 94.211 1330 46 17 670 1974 643324029 643325352 0.000000e+00 2001.0
5 TraesCS5D01G475800 chr5A 100.000 28 0 0 2291 2318 650022746 650022719 5.000000e-03 52.8
6 TraesCS5D01G475800 chr5B 95.585 521 18 4 1479 1995 647900372 647900891 0.000000e+00 830.0
7 TraesCS5D01G475800 chr5B 80.879 455 57 21 2502 2951 647901096 647901525 6.100000e-87 331.0
8 TraesCS5D01G475800 chr5B 87.850 107 13 0 767 873 647899742 647899848 3.090000e-25 126.0
9 TraesCS5D01G475800 chr7D 89.703 505 47 4 1255 1758 150492856 150493356 8.920000e-180 640.0
10 TraesCS5D01G475800 chr7D 95.276 127 6 0 1993 2119 124837897 124837771 4.990000e-48 202.0
11 TraesCS5D01G475800 chr7B 86.510 341 28 8 1418 1758 29047158 29047480 2.800000e-95 359.0
12 TraesCS5D01G475800 chr7B 77.387 199 38 4 2283 2480 702333452 702333644 8.650000e-21 111.0
13 TraesCS5D01G475800 chr7B 86.538 52 7 0 671 722 697524449 697524500 1.140000e-04 58.4
14 TraesCS5D01G475800 chr6D 96.850 127 3 1 1993 2119 426089501 426089376 8.290000e-51 211.0
15 TraesCS5D01G475800 chr6D 95.200 125 5 1 1995 2119 362301609 362301486 2.320000e-46 196.0
16 TraesCS5D01G475800 chr6D 83.333 102 16 1 555 655 30295592 30295491 3.130000e-15 93.5
17 TraesCS5D01G475800 chr6D 90.909 44 3 1 671 714 102221219 102221261 1.140000e-04 58.4
18 TraesCS5D01G475800 chr2D 96.032 126 4 1 1994 2119 15842616 15842492 1.390000e-48 204.0
19 TraesCS5D01G475800 chr2D 87.037 54 7 0 669 722 241696444 241696391 8.830000e-06 62.1
20 TraesCS5D01G475800 chr2D 94.444 36 2 0 669 704 57195240 57195275 4.110000e-04 56.5
21 TraesCS5D01G475800 chr1D 96.032 126 4 1 1995 2119 183999696 183999821 1.390000e-48 204.0
22 TraesCS5D01G475800 chr1D 89.474 152 6 1 1800 1951 381030273 381030132 1.810000e-42 183.0
23 TraesCS5D01G475800 chr4D 96.000 125 4 1 1995 2119 260686518 260686641 4.990000e-48 202.0
24 TraesCS5D01G475800 chr4D 93.130 131 7 2 1989 2119 320214303 320214175 1.080000e-44 191.0
25 TraesCS5D01G475800 chr4D 79.339 242 29 7 2281 2501 319269850 319269609 1.830000e-32 150.0
26 TraesCS5D01G475800 chr3B 95.161 124 5 1 1996 2119 753859874 753859752 8.350000e-46 195.0
27 TraesCS5D01G475800 chr3B 81.818 220 28 7 2283 2501 293740944 293741152 1.090000e-39 174.0
28 TraesCS5D01G475800 chr3B 97.222 36 1 0 669 704 477881858 477881893 8.830000e-06 62.1
29 TraesCS5D01G475800 chr1B 93.701 127 7 1 1993 2119 631621177 631621302 3.880000e-44 189.0
30 TraesCS5D01G475800 chr3D 82.273 220 26 5 2283 2501 219567580 219567787 8.400000e-41 178.0
31 TraesCS5D01G475800 chr3D 76.400 250 29 15 2276 2501 58475821 58475578 1.120000e-19 108.0
32 TraesCS5D01G475800 chr3A 81.860 215 27 6 2288 2501 259325757 259325960 1.410000e-38 171.0
33 TraesCS5D01G475800 chr3A 80.973 226 33 5 2283 2501 739144241 739144463 1.410000e-38 171.0
34 TraesCS5D01G475800 chr3A 80.093 216 38 5 2288 2501 579048982 579048770 3.940000e-34 156.0
35 TraesCS5D01G475800 chr2A 77.679 224 40 8 2281 2501 756490129 756489913 8.580000e-26 128.0
36 TraesCS5D01G475800 chr6B 85.088 114 16 1 554 666 695012816 695012703 6.680000e-22 115.0
37 TraesCS5D01G475800 chr4A 88.172 93 10 1 2411 2503 121480283 121480192 3.110000e-20 110.0
38 TraesCS5D01G475800 chr4B 85.714 84 11 1 554 636 470305664 470305581 1.460000e-13 87.9


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 TraesCS5D01G475800 chr5D 515107884 515110834 2950 False 1888.666667 5450 97.916667 1 2951 3 chr5D.!!$F2 2950
1 TraesCS5D01G475800 chr5A 643324029 643325352 1323 False 2001.000000 2001 94.211000 670 1974 1 chr5A.!!$F1 1304
2 TraesCS5D01G475800 chr5B 647899742 647901525 1783 False 429.000000 830 88.104667 767 2951 3 chr5B.!!$F1 2184
3 TraesCS5D01G475800 chr7D 150492856 150493356 500 False 640.000000 640 89.703000 1255 1758 1 chr7D.!!$F1 503


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
448 449 0.036875 ACCCTTTCTTTCTCTGGCCG 59.963 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 2653 0.179067 TGGCAACTCCGAACGTTTCT 60.179 50.0 0.46 0.0 37.8 2.52 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)



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AutoCloner maintained by Alex Coulton.