Multiple sequence alignment - TraesCS5A01G527200

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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 TraesCS5A01G527200 chr5A 100.000 3823 0 0 938 4760 687733431 687737253 0.000000e+00 7060
1 TraesCS5A01G527200 chr5A 99.685 3815 10 2 938 4751 687742348 687738535 0.000000e+00 6977
2 TraesCS5A01G527200 chr5A 100.000 863 0 0 1 863 687732494 687733356 0.000000e+00 1594
3 TraesCS5A01G527200 chr5A 98.958 864 8 1 1 863 687743471 687742608 0.000000e+00 1544
4 TraesCS5A01G527200 chr3A 98.931 3834 18 1 938 4748 11460554 11464387 0.000000e+00 6831
5 TraesCS5A01G527200 chr3A 99.435 1771 10 0 938 2708 40446830 40445060 0.000000e+00 3216
6 TraesCS5A01G527200 chr3A 89.611 2339 176 30 2042 4356 706559591 706557296 0.000000e+00 2911
7 TraesCS5A01G527200 chr3A 99.335 1504 9 1 3248 4751 40445060 40443558 0.000000e+00 2721
8 TraesCS5A01G527200 chr3A 98.958 864 8 1 1 863 11459431 11460294 0.000000e+00 1544
9 TraesCS5A01G527200 chr3A 89.205 1232 112 15 962 2184 695899438 695898219 0.000000e+00 1519
10 TraesCS5A01G527200 chr3A 98.262 863 14 1 1 863 40447977 40447116 0.000000e+00 1509
11 TraesCS5A01G527200 chr3B 99.238 2361 18 0 2388 4748 793277378 793279738 0.000000e+00 4261
12 TraesCS5A01G527200 chr3B 98.408 1445 23 0 2652 4096 29738346 29739790 0.000000e+00 2542
13 TraesCS5A01G527200 chr3B 95.611 1572 57 4 2398 3968 799582943 799584503 0.000000e+00 2510
14 TraesCS5A01G527200 chr3B 98.610 863 11 1 1 863 793275286 793276147 0.000000e+00 1526
15 TraesCS5A01G527200 chr3B 92.365 799 37 8 71 863 799580775 799581555 0.000000e+00 1116
16 TraesCS5A01G527200 chr3B 97.115 208 6 0 1 208 737880010 737880217 7.580000e-93 351
17 TraesCS5A01G527200 chr7B 93.125 2429 142 15 2042 4459 727686701 727684287 0.000000e+00 3537
18 TraesCS5A01G527200 chr7B 94.204 1225 68 2 956 2179 727687828 727686606 0.000000e+00 1866
19 TraesCS5A01G527200 chr2B 99.582 1912 8 0 2837 4748 56907339 56905428 0.000000e+00 3487
20 TraesCS5A01G527200 chr2A 89.867 2339 174 28 2042 4356 4053493 4051194 0.000000e+00 2948
21 TraesCS5A01G527200 chr7A 92.274 2058 112 21 2011 4032 12324664 12326710 0.000000e+00 2876
22 TraesCS5A01G527200 chr7A 91.885 2058 112 24 2011 4032 12267587 12269625 0.000000e+00 2824
23 TraesCS5A01G527200 chr7A 92.944 1233 77 7 956 2184 12323506 12324732 0.000000e+00 1786
24 TraesCS5A01G527200 chr7A 91.714 1231 90 6 956 2184 12266435 12267655 0.000000e+00 1698
25 TraesCS5A01G527200 chr5B 94.083 1876 75 6 989 2864 147199513 147201352 0.000000e+00 2817
26 TraesCS5A01G527200 chr5B 93.128 1659 77 18 2790 4433 147201338 147202974 0.000000e+00 2398
27 TraesCS5A01G527200 chr5B 97.535 284 7 0 248 531 534682628 534682345 1.990000e-133 486
28 TraesCS5A01G527200 chr4B 98.995 1393 14 0 3357 4749 631190708 631192100 0.000000e+00 2495
29 TraesCS5A01G527200 chr4B 98.865 793 8 1 71 863 631189790 631190581 0.000000e+00 1413
30 TraesCS5A01G527200 chr4B 98.773 163 2 0 1 163 631189755 631189917 1.680000e-74 291
31 TraesCS5A01G527200 chr6A 95.122 1230 58 2 956 2184 7125345 7126573 0.000000e+00 1938
32 TraesCS5A01G527200 chr6B 93.984 1230 72 2 956 2184 12894029 12895257 0.000000e+00 1860
33 TraesCS5A01G527200 chrUn 98.958 864 8 1 1 863 371199427 371198564 0.000000e+00 1544
34 TraesCS5A01G527200 chrUn 95.801 381 15 1 483 863 91408114 91408493 8.750000e-172 614
35 TraesCS5A01G527200 chr4A 99.243 793 6 0 71 863 646322257 646323049 0.000000e+00 1432
36 TraesCS5A01G527200 chr4A 92.045 704 30 13 153 848 708296592 708295907 0.000000e+00 966
37 TraesCS5A01G527200 chr4A 97.266 512 13 1 4239 4750 662109740 662110250 0.000000e+00 867


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 TraesCS5A01G527200 chr5A 687732494 687737253 4759 False 4327.000000 7060 100.000000 1 4760 2 chr5A.!!$F1 4759
1 TraesCS5A01G527200 chr5A 687738535 687743471 4936 True 4260.500000 6977 99.321500 1 4751 2 chr5A.!!$R1 4750
2 TraesCS5A01G527200 chr3A 11459431 11464387 4956 False 4187.500000 6831 98.944500 1 4748 2 chr3A.!!$F1 4747
3 TraesCS5A01G527200 chr3A 706557296 706559591 2295 True 2911.000000 2911 89.611000 2042 4356 1 chr3A.!!$R2 2314
4 TraesCS5A01G527200 chr3A 40443558 40447977 4419 True 2482.000000 3216 99.010667 1 4751 3 chr3A.!!$R3 4750
5 TraesCS5A01G527200 chr3A 695898219 695899438 1219 True 1519.000000 1519 89.205000 962 2184 1 chr3A.!!$R1 1222
6 TraesCS5A01G527200 chr3B 793275286 793279738 4452 False 2893.500000 4261 98.924000 1 4748 2 chr3B.!!$F3 4747
7 TraesCS5A01G527200 chr3B 29738346 29739790 1444 False 2542.000000 2542 98.408000 2652 4096 1 chr3B.!!$F1 1444
8 TraesCS5A01G527200 chr3B 799580775 799584503 3728 False 1813.000000 2510 93.988000 71 3968 2 chr3B.!!$F4 3897
9 TraesCS5A01G527200 chr7B 727684287 727687828 3541 True 2701.500000 3537 93.664500 956 4459 2 chr7B.!!$R1 3503
10 TraesCS5A01G527200 chr2B 56905428 56907339 1911 True 3487.000000 3487 99.582000 2837 4748 1 chr2B.!!$R1 1911
11 TraesCS5A01G527200 chr2A 4051194 4053493 2299 True 2948.000000 2948 89.867000 2042 4356 1 chr2A.!!$R1 2314
12 TraesCS5A01G527200 chr7A 12323506 12326710 3204 False 2331.000000 2876 92.609000 956 4032 2 chr7A.!!$F2 3076
13 TraesCS5A01G527200 chr7A 12266435 12269625 3190 False 2261.000000 2824 91.799500 956 4032 2 chr7A.!!$F1 3076
14 TraesCS5A01G527200 chr5B 147199513 147202974 3461 False 2607.500000 2817 93.605500 989 4433 2 chr5B.!!$F1 3444
15 TraesCS5A01G527200 chr4B 631189755 631192100 2345 False 1399.666667 2495 98.877667 1 4749 3 chr4B.!!$F1 4748
16 TraesCS5A01G527200 chr6A 7125345 7126573 1228 False 1938.000000 1938 95.122000 956 2184 1 chr6A.!!$F1 1228
17 TraesCS5A01G527200 chr6B 12894029 12895257 1228 False 1860.000000 1860 93.984000 956 2184 1 chr6B.!!$F1 1228
18 TraesCS5A01G527200 chrUn 371198564 371199427 863 True 1544.000000 1544 98.958000 1 863 1 chrUn.!!$R1 862
19 TraesCS5A01G527200 chr4A 646322257 646323049 792 False 1432.000000 1432 99.243000 71 863 1 chr4A.!!$F1 792
20 TraesCS5A01G527200 chr4A 708295907 708296592 685 True 966.000000 966 92.045000 153 848 1 chr4A.!!$R1 695
21 TraesCS5A01G527200 chr4A 662109740 662110250 510 False 867.000000 867 97.266000 4239 4750 1 chr4A.!!$F2 511

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
116 117 1.443828 GCCTCTCCCCTTCATCGAC 59.556 63.158 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4092 4939 2.559698 TCGGACAGCATTTCCTTTGA 57.44 45.0 0.0 0.0 0.0 2.69 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
46 47 3.371595 CCAAACCCTAACCCTTCATCGAT 60.372 47.826 0.00 0.0 0.00 3.59
116 117 1.443828 GCCTCTCCCCTTCATCGAC 59.556 63.158 0.00 0.0 0.00 4.20
370 414 6.382570 AGTGCTGAACTTAGATAGGTGATCTT 59.617 38.462 0.00 0.0 44.81 2.40
3538 4370 3.088532 TGGTGGTATGTTTGCCATCTTC 58.911 45.455 0.00 0.0 39.34 2.87
4510 5376 2.028190 CGATCGGCAGCTACCTGG 59.972 66.667 7.38 0.0 39.54 4.45
4751 5617 2.258591 CGTGTCCACCCTGAGTCG 59.741 66.667 0.00 0.0 0.00 4.18
4752 5618 2.048127 GTGTCCACCCTGAGTCGC 60.048 66.667 0.00 0.0 0.00 5.19
4753 5619 3.311110 TGTCCACCCTGAGTCGCC 61.311 66.667 0.00 0.0 0.00 5.54
4754 5620 4.436998 GTCCACCCTGAGTCGCCG 62.437 72.222 0.00 0.0 0.00 6.46
4755 5621 4.988716 TCCACCCTGAGTCGCCGT 62.989 66.667 0.00 0.0 0.00 5.68
4756 5622 4.742201 CCACCCTGAGTCGCCGTG 62.742 72.222 0.00 0.0 0.00 4.94
4757 5623 3.991051 CACCCTGAGTCGCCGTGT 61.991 66.667 0.00 0.0 0.00 4.49
4758 5624 3.681835 ACCCTGAGTCGCCGTGTC 61.682 66.667 0.00 0.0 0.00 3.67
4759 5625 4.778415 CCCTGAGTCGCCGTGTCG 62.778 72.222 0.00 0.0 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 1.045911 GTCGATGAAGGGGAGAGGCT 61.046 60.000 0.00 0.0 0.00 4.58
65 66 1.736586 CCGTCGATGAAGGGGAGAG 59.263 63.158 6.11 0.0 0.00 3.20
370 414 7.987458 AGTTTCTTGTTCAAACACTAGATCTCA 59.013 33.333 0.00 0.0 38.92 3.27
4092 4939 2.559698 TCGGACAGCATTTCCTTTGA 57.440 45.000 0.00 0.0 0.00 2.69
4510 5376 9.013490 CATATTTAGCTGTTGTTTATGCAGTTC 57.987 33.333 0.00 0.0 33.18 3.01


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

AutoCloner maintained by Alex Coulton.