Multiple sequence alignment - TraesCS3A01G526900

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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 TraesCS3A01G526900 chr3A 100.000 3369 0 0 1 3369 740746590 740749958 0.000000e+00 6222.0
1 TraesCS3A01G526900 chr3A 99.644 3370 10 2 1 3369 740715838 740719206 0.000000e+00 6156.0
2 TraesCS3A01G526900 chr3A 99.579 1661 7 0 1 1661 740684090 740685750 0.000000e+00 3029.0
3 TraesCS3A01G526900 chr3A 96.491 798 28 0 1 798 20906219 20905422 0.000000e+00 1319.0
4 TraesCS3A01G526900 chr3A 96.255 801 25 3 1 799 653302355 653303152 0.000000e+00 1308.0
5 TraesCS3A01G526900 chr3A 96.245 799 26 3 1 799 502918264 502917470 0.000000e+00 1306.0
6 TraesCS3A01G526900 chr3D 95.200 2604 74 18 792 3369 608455333 608452755 0.000000e+00 4069.0
7 TraesCS3A01G526900 chr3D 86.325 117 16 0 1115 1231 608162553 608162669 9.810000e-26 128.0
8 TraesCS3A01G526900 chr3D 81.967 122 21 1 1110 1231 608416827 608416707 5.950000e-18 102.0
9 TraesCS3A01G526900 chrUn 95.159 2169 86 5 1219 3369 43254204 43252037 0.000000e+00 3406.0
10 TraesCS3A01G526900 chrUn 94.902 1726 72 4 972 2682 43163278 43161554 0.000000e+00 2686.0
11 TraesCS3A01G526900 chrUn 95.940 1330 46 2 972 2293 43167025 43165696 0.000000e+00 2150.0
12 TraesCS3A01G526900 chrUn 96.073 1324 45 1 1219 2535 278815840 278814517 0.000000e+00 2150.0
13 TraesCS3A01G526900 chrUn 96.073 1324 45 1 1219 2535 278823055 278821732 0.000000e+00 2150.0
14 TraesCS3A01G526900 chrUn 91.749 812 57 3 2113 2916 43098015 43097206 0.000000e+00 1120.0
15 TraesCS3A01G526900 chrUn 93.892 704 35 2 2673 3369 335931595 335930893 0.000000e+00 1055.0
16 TraesCS3A01G526900 chrUn 93.750 704 36 2 2673 3369 43160361 43159659 0.000000e+00 1050.0
17 TraesCS3A01G526900 chrUn 92.507 694 40 4 2108 2790 364772375 364773067 0.000000e+00 983.0
18 TraesCS3A01G526900 chrUn 92.507 694 40 4 2108 2790 364774381 364775073 0.000000e+00 983.0
19 TraesCS3A01G526900 chrUn 92.507 694 40 4 2108 2790 364778393 364779085 0.000000e+00 983.0
20 TraesCS3A01G526900 chrUn 92.507 694 40 4 2108 2790 465410766 465410074 0.000000e+00 983.0
21 TraesCS3A01G526900 chrUn 88.803 777 78 5 1348 2115 43264523 43263747 0.000000e+00 944.0
22 TraesCS3A01G526900 chrUn 96.290 566 13 2 972 1529 471539951 471540516 0.000000e+00 922.0
23 TraesCS3A01G526900 chrUn 94.502 582 25 1 2795 3369 458607001 458606420 0.000000e+00 891.0
24 TraesCS3A01G526900 chrUn 90.886 395 28 2 2295 2682 335933181 335932788 1.070000e-144 523.0
25 TraesCS3A01G526900 chrUn 96.277 188 7 0 800 987 43168080 43167893 3.260000e-80 309.0
26 TraesCS3A01G526900 chrUn 96.277 188 7 0 800 987 371065500 371065313 3.260000e-80 309.0
27 TraesCS3A01G526900 chrUn 95.745 188 8 0 800 987 43164334 43164147 1.520000e-78 303.0
28 TraesCS3A01G526900 chr2A 97.995 798 16 0 1 798 773356189 773355392 0.000000e+00 1386.0
29 TraesCS3A01G526900 chr7D 93.383 801 44 4 9 800 20337545 20336745 0.000000e+00 1177.0
30 TraesCS3A01G526900 chr7D 92.010 801 53 8 9 799 53623251 53624050 0.000000e+00 1114.0
31 TraesCS3A01G526900 chr5D 92.786 804 49 4 6 800 425071038 425071841 0.000000e+00 1155.0
32 TraesCS3A01G526900 chr6B 92.453 53 4 0 3237 3289 80047499 80047447 3.600000e-10 76.8
33 TraesCS3A01G526900 chr7B 94.872 39 2 0 3237 3275 11450531 11450569 1.010000e-05 62.1
34 TraesCS3A01G526900 chr1A 97.222 36 1 0 3237 3272 32102251 32102216 1.010000e-05 62.1


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 TraesCS3A01G526900 chr3A 740746590 740749958 3368 False 6222.0 6222 100.0000 1 3369 1 chr3A.!!$F4 3368
1 TraesCS3A01G526900 chr3A 740715838 740719206 3368 False 6156.0 6156 99.6440 1 3369 1 chr3A.!!$F3 3368
2 TraesCS3A01G526900 chr3A 740684090 740685750 1660 False 3029.0 3029 99.5790 1 1661 1 chr3A.!!$F2 1660
3 TraesCS3A01G526900 chr3A 20905422 20906219 797 True 1319.0 1319 96.4910 1 798 1 chr3A.!!$R1 797
4 TraesCS3A01G526900 chr3A 653302355 653303152 797 False 1308.0 1308 96.2550 1 799 1 chr3A.!!$F1 798
5 TraesCS3A01G526900 chr3A 502917470 502918264 794 True 1306.0 1306 96.2450 1 799 1 chr3A.!!$R2 798
6 TraesCS3A01G526900 chr3D 608452755 608455333 2578 True 4069.0 4069 95.2000 792 3369 1 chr3D.!!$R2 2577
7 TraesCS3A01G526900 chrUn 43252037 43254204 2167 True 3406.0 3406 95.1590 1219 3369 1 chrUn.!!$R2 2150
8 TraesCS3A01G526900 chrUn 278814517 278815840 1323 True 2150.0 2150 96.0730 1219 2535 1 chrUn.!!$R4 1316
9 TraesCS3A01G526900 chrUn 278821732 278823055 1323 True 2150.0 2150 96.0730 1219 2535 1 chrUn.!!$R5 1316
10 TraesCS3A01G526900 chrUn 43159659 43168080 8421 True 1299.6 2686 95.3228 800 3369 5 chrUn.!!$R9 2569
11 TraesCS3A01G526900 chrUn 43097206 43098015 809 True 1120.0 1120 91.7490 2113 2916 1 chrUn.!!$R1 803
12 TraesCS3A01G526900 chrUn 364772375 364779085 6710 False 983.0 983 92.5070 2108 2790 3 chrUn.!!$F2 682
13 TraesCS3A01G526900 chrUn 465410074 465410766 692 True 983.0 983 92.5070 2108 2790 1 chrUn.!!$R8 682
14 TraesCS3A01G526900 chrUn 43263747 43264523 776 True 944.0 944 88.8030 1348 2115 1 chrUn.!!$R3 767
15 TraesCS3A01G526900 chrUn 471539951 471540516 565 False 922.0 922 96.2900 972 1529 1 chrUn.!!$F1 557
16 TraesCS3A01G526900 chrUn 458606420 458607001 581 True 891.0 891 94.5020 2795 3369 1 chrUn.!!$R7 574
17 TraesCS3A01G526900 chrUn 335930893 335933181 2288 True 789.0 1055 92.3890 2295 3369 2 chrUn.!!$R10 1074
18 TraesCS3A01G526900 chr2A 773355392 773356189 797 True 1386.0 1386 97.9950 1 798 1 chr2A.!!$R1 797
19 TraesCS3A01G526900 chr7D 20336745 20337545 800 True 1177.0 1177 93.3830 9 800 1 chr7D.!!$R1 791
20 TraesCS3A01G526900 chr7D 53623251 53624050 799 False 1114.0 1114 92.0100 9 799 1 chr7D.!!$F1 790
21 TraesCS3A01G526900 chr5D 425071038 425071841 803 False 1155.0 1155 92.7860 6 800 1 chr5D.!!$F1 794

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
1661 6330 3.067106 GTTGACGATTGGAAGCTCAGAA 58.933 45.455 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2489 13180 2.946947 CCAGCCACACCTGGTAAAG 58.053 57.895 0.0 0.0 45.87 1.85 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
1661 6330 3.067106 GTTGACGATTGGAAGCTCAGAA 58.933 45.455 0.00 0.0 0.00 3.02
2489 13180 1.137513 CACCGACGTGAAAACCTCTC 58.862 55.000 0.00 0.0 43.14 3.20
2491 13182 1.411612 ACCGACGTGAAAACCTCTCTT 59.588 47.619 0.00 0.0 0.00 2.85
2546 13244 1.550327 TCCTCAGTGAGATGCTCGTT 58.450 50.000 22.09 0.0 32.35 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1661 6330 4.664677 GTCTCGTGCCAGCACCGT 62.665 66.667 16.69 0.0 43.49 4.83
2489 13180 2.946947 CCAGCCACACCTGGTAAAG 58.053 57.895 0.00 0.0 45.87 1.85


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

AutoCloner maintained by Alex Coulton.