Multiple sequence alignment - TraesCS3D01G305700

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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 TraesCS3D01G305700 chr3D 100.000 3171 0 0 1 3171 419636634 419633464 0.000000e+00 5856.0
1 TraesCS3D01G305700 chr3D 99.117 3171 23 2 1 3171 355120147 355116982 0.000000e+00 5696.0
2 TraesCS3D01G305700 chr7D 99.022 3171 31 0 1 3171 575648113 575651283 0.000000e+00 5685.0
3 TraesCS3D01G305700 chr5D 98.581 3172 42 3 1 3171 564866755 564869924 0.000000e+00 5605.0
4 TraesCS3D01G305700 chr5D 98.171 3171 56 2 1 3171 409714061 409717229 0.000000e+00 5533.0
5 TraesCS3D01G305700 chr5D 99.197 1245 10 0 1 1245 90284646 90285890 0.000000e+00 2244.0
6 TraesCS3D01G305700 chr5D 99.330 1044 7 0 2128 3171 90285891 90286934 0.000000e+00 1890.0
7 TraesCS3D01G305700 chrUn 98.234 3171 56 0 1 3171 70176444 70173274 0.000000e+00 5546.0
8 TraesCS3D01G305700 chr6A 93.938 1600 90 4 855 2453 121671112 121672705 0.000000e+00 2410.0
9 TraesCS3D01G305700 chr6A 88.489 278 32 0 2761 3038 558144639 558144362 1.410000e-88 337.0
10 TraesCS3D01G305700 chr6A 96.094 128 5 0 3044 3171 121672811 121672938 3.210000e-50 209.0
11 TraesCS3D01G305700 chr6B 92.502 1547 91 9 929 2453 139417828 139416285 0.000000e+00 2191.0
12 TraesCS3D01G305700 chr6B 90.923 650 51 2 573 1220 707972939 707973582 0.000000e+00 867.0
13 TraesCS3D01G305700 chr6B 93.061 245 14 3 331 574 707972653 707972895 3.890000e-94 355.0
14 TraesCS3D01G305700 chr6B 88.129 278 33 0 2761 3038 100913703 100913426 6.560000e-87 331.0
15 TraesCS3D01G305700 chr6B 96.875 128 4 0 3044 3171 707975031 707975158 6.890000e-52 215.0
16 TraesCS3D01G305700 chr2B 93.681 1266 75 4 929 2193 652607746 652606485 0.000000e+00 1890.0
17 TraesCS3D01G305700 chr2B 96.313 217 8 0 2237 2453 652606483 652606267 1.080000e-94 357.0
18 TraesCS3D01G305700 chr3B 93.602 1266 76 4 929 2193 741391162 741389901 0.000000e+00 1884.0
19 TraesCS3D01G305700 chr2A 88.325 394 44 2 2125 2516 438725357 438724964 3.700000e-129 472.0
20 TraesCS3D01G305700 chr2A 94.776 134 7 0 3038 3171 744804129 744803996 3.210000e-50 209.0
21 TraesCS3D01G305700 chr3A 88.129 278 33 0 2761 3038 27732899 27733176 6.560000e-87 331.0
22 TraesCS3D01G305700 chr2D 75.085 590 105 25 2 568 88614489 88615059 1.470000e-58 237.0
23 TraesCS3D01G305700 chr1B 81.928 83 10 2 2573 2655 84368176 84368253 7.340000e-07 65.8


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 TraesCS3D01G305700 chr3D 419633464 419636634 3170 True 5856.0 5856 100.000000 1 3171 1 chr3D.!!$R2 3170
1 TraesCS3D01G305700 chr3D 355116982 355120147 3165 True 5696.0 5696 99.117000 1 3171 1 chr3D.!!$R1 3170
2 TraesCS3D01G305700 chr7D 575648113 575651283 3170 False 5685.0 5685 99.022000 1 3171 1 chr7D.!!$F1 3170
3 TraesCS3D01G305700 chr5D 564866755 564869924 3169 False 5605.0 5605 98.581000 1 3171 1 chr5D.!!$F2 3170
4 TraesCS3D01G305700 chr5D 409714061 409717229 3168 False 5533.0 5533 98.171000 1 3171 1 chr5D.!!$F1 3170
5 TraesCS3D01G305700 chr5D 90284646 90286934 2288 False 2067.0 2244 99.263500 1 3171 2 chr5D.!!$F3 3170
6 TraesCS3D01G305700 chrUn 70173274 70176444 3170 True 5546.0 5546 98.234000 1 3171 1 chrUn.!!$R1 3170
7 TraesCS3D01G305700 chr6A 121671112 121672938 1826 False 1309.5 2410 95.016000 855 3171 2 chr6A.!!$F1 2316
8 TraesCS3D01G305700 chr6B 139416285 139417828 1543 True 2191.0 2191 92.502000 929 2453 1 chr6B.!!$R2 1524
9 TraesCS3D01G305700 chr6B 707972653 707975158 2505 False 479.0 867 93.619667 331 3171 3 chr6B.!!$F1 2840
10 TraesCS3D01G305700 chr2B 652606267 652607746 1479 True 1123.5 1890 94.997000 929 2453 2 chr2B.!!$R1 1524
11 TraesCS3D01G305700 chr3B 741389901 741391162 1261 True 1884.0 1884 93.602000 929 2193 1 chr3B.!!$R1 1264
12 TraesCS3D01G305700 chr2D 88614489 88615059 570 False 237.0 237 75.085000 2 568 1 chr2D.!!$F1 566


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
99 100 4.159506 GCTTCAGTCCTCACTATCTTCACT 59.840 45.833 0.0 0.0 0.0 3.41 F
1664 1839 0.547712 AGCTCTGAAGTTGCCCCCTA 60.548 55.000 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 1904 1.468054 GCACCATCGAGCAATTCCAAC 60.468 52.381 0.00 0.00 0.0 3.77 R
2852 3049 0.111061 AACCACTGAAGCATGCTGGA 59.889 50.000 23.48 9.96 0.0 3.86 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
99 100 4.159506 GCTTCAGTCCTCACTATCTTCACT 59.840 45.833 0.00 0.0 0.00 3.41
937 1004 4.638304 TCGTCCTTTCCTTTTCGATTTCT 58.362 39.130 0.00 0.0 0.00 2.52
1157 1224 1.896220 TTCTGTTTTGCTCCATCGCT 58.104 45.000 0.00 0.0 0.00 4.93
1180 1247 3.917988 GCTTATTTGCCTTGCTTCTGTT 58.082 40.909 0.00 0.0 0.00 3.16
1664 1839 0.547712 AGCTCTGAAGTTGCCCCCTA 60.548 55.000 0.00 0.0 0.00 3.53
1729 1904 5.050634 TGTGACGGTTACTTTCATTTCTTCG 60.051 40.000 4.63 0.0 0.00 3.79
2297 2494 3.250744 GAGCAAGATGTGTGTACGCTTA 58.749 45.455 8.10 0.0 0.00 3.09
2813 3010 1.458639 GGCAGCACCTCAAAGCAACT 61.459 55.000 0.00 0.0 34.51 3.16
2852 3049 3.010584 AGCCTTTGGTCAATGTATCCTGT 59.989 43.478 0.00 0.0 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 2.225491 GGCGATTGTTACTTGTCTTGCA 59.775 45.455 0.00 0.00 0.00 4.08
937 1004 2.290641 GAGGAGAAAGCAAACGAAGCAA 59.709 45.455 0.00 0.00 0.00 3.91
1664 1839 6.992715 GGGCATATCTTGTGATAGTAAGTTGT 59.007 38.462 0.00 0.00 38.42 3.32
1729 1904 1.468054 GCACCATCGAGCAATTCCAAC 60.468 52.381 0.00 0.00 0.00 3.77
2297 2494 1.419387 AGAGGCAGCAAGTGAAGACTT 59.581 47.619 0.00 0.00 43.63 3.01
2696 2893 5.813672 GTGCTTGACGGTGGTTAGATTATTA 59.186 40.000 0.00 0.00 0.00 0.98
2813 3010 7.093024 ACCAAAGGCTAGCAGTAACTATTTCTA 60.093 37.037 18.24 0.00 0.00 2.10
2852 3049 0.111061 AACCACTGAAGCATGCTGGA 59.889 50.000 23.48 9.96 0.00 3.86



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

AutoCloner maintained by Alex Coulton.