Multiple sequence alignment - TraesCS3A01G485600

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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 TraesCS3A01G485600 chr3A 100.000 4341 0 0 1 4341 714591684 714587344 0.000000e+00 8017
1 TraesCS3A01G485600 chr3A 89.119 2463 190 36 1633 4044 714645540 714647975 0.000000e+00 2992
2 TraesCS3A01G485600 chr3A 90.465 1248 113 5 1 1248 714643673 714644914 0.000000e+00 1640
3 TraesCS3A01G485600 chr3A 87.805 779 82 5 794 1571 714627773 714628539 0.000000e+00 900
4 TraesCS3A01G485600 chr3A 88.757 676 67 5 2717 3391 714602902 714602235 0.000000e+00 819
5 TraesCS3A01G485600 chr3A 90.811 185 15 2 1230 1414 714644930 714645112 3.350000e-61 246
6 TraesCS3A01G485600 chr3D 89.864 3374 293 23 4 3350 579423874 579420523 0.000000e+00 4290
7 TraesCS3A01G485600 chr3D 89.651 2464 185 39 1633 4045 579587107 579589551 0.000000e+00 3073
8 TraesCS3A01G485600 chr3D 94.249 1339 74 3 1 1339 579396187 579394852 0.000000e+00 2043
9 TraesCS3A01G485600 chr3D 91.960 1393 107 5 1 1393 579585292 579586679 0.000000e+00 1947
10 TraesCS3A01G485600 chr3D 91.067 1265 71 15 1364 2609 579394855 579393614 0.000000e+00 1672
11 TraesCS3A01G485600 chr3D 93.868 848 44 6 2605 3449 579383798 579382956 0.000000e+00 1271
12 TraesCS3A01G485600 chr3D 86.622 299 34 6 4046 4341 579379623 579379328 4.190000e-85 326
13 TraesCS3A01G485600 chr3D 91.703 229 7 2 3562 3779 579382959 579382732 1.520000e-79 307
14 TraesCS3A01G485600 chr3D 92.179 179 14 0 3169 3347 579367490 579367312 2.000000e-63 254
15 TraesCS3A01G485600 chr3B 88.419 3402 321 27 24 3390 773761067 773757704 0.000000e+00 4032
16 TraesCS3A01G485600 chr3B 91.165 1777 128 17 1628 3387 773900177 773901941 0.000000e+00 2385
17 TraesCS3A01G485600 chr3B 91.203 1239 106 2 8 1246 773898620 773899855 0.000000e+00 1681
18 TraesCS3A01G485600 chr3B 95.770 662 22 4 2686 3345 773743745 773743088 0.000000e+00 1062
19 TraesCS3A01G485600 chr3B 89.189 185 18 2 1230 1414 773899873 773900055 3.380000e-56 230
20 TraesCS3A01G485600 chr3B 90.722 97 8 1 3384 3479 773730251 773730155 1.270000e-25 128


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 TraesCS3A01G485600 chr3A 714587344 714591684 4340 True 8017.000000 8017 100.000000 1 4341 1 chr3A.!!$R1 4340
1 TraesCS3A01G485600 chr3A 714643673 714647975 4302 False 1626.000000 2992 90.131667 1 4044 3 chr3A.!!$F2 4043
2 TraesCS3A01G485600 chr3A 714627773 714628539 766 False 900.000000 900 87.805000 794 1571 1 chr3A.!!$F1 777
3 TraesCS3A01G485600 chr3A 714602235 714602902 667 True 819.000000 819 88.757000 2717 3391 1 chr3A.!!$R2 674
4 TraesCS3A01G485600 chr3D 579420523 579423874 3351 True 4290.000000 4290 89.864000 4 3350 1 chr3D.!!$R2 3346
5 TraesCS3A01G485600 chr3D 579585292 579589551 4259 False 2510.000000 3073 90.805500 1 4045 2 chr3D.!!$F1 4044
6 TraesCS3A01G485600 chr3D 579393614 579396187 2573 True 1857.500000 2043 92.658000 1 2609 2 chr3D.!!$R4 2608
7 TraesCS3A01G485600 chr3D 579379328 579383798 4470 True 634.666667 1271 90.731000 2605 4341 3 chr3D.!!$R3 1736
8 TraesCS3A01G485600 chr3B 773757704 773761067 3363 True 4032.000000 4032 88.419000 24 3390 1 chr3B.!!$R3 3366
9 TraesCS3A01G485600 chr3B 773898620 773901941 3321 False 1432.000000 2385 90.519000 8 3387 3 chr3B.!!$F1 3379
10 TraesCS3A01G485600 chr3B 773743088 773743745 657 True 1062.000000 1062 95.770000 2686 3345 1 chr3B.!!$R2 659


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 0.106918 GACCCACAAGACACACCCAA 60.107 55.0 0.00 0.0 0.00 4.12 F
1331 1400 0.316204 GCATGACAACTTGCTGCCTT 59.684 50.0 0.00 0.0 41.77 4.35 F
1778 2272 0.451783 CCTTGTATGGTTCCGCAAGC 59.548 55.0 11.92 0.0 37.56 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1581 0.034574 AACAACATGGGGATAGCGCA 60.035 50.000 11.47 0.0 0.00 6.09 R
2495 3018 2.047274 AATCGTGTCGGCCAGTGG 60.047 61.111 4.20 4.2 0.00 4.00 R
3559 4112 0.034896 AGTGATCACGGGGACACAAC 59.965 55.000 19.85 0.0 35.97 3.32 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.