Multiple sequence alignment - TraesCS3A01G087900

Loading Multiple Alignment...

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 TraesCS3A01G087900 chr3A 100.000 3534 0 0 1 3534 56733591 56737124 0.000000e+00 6527.0
1 TraesCS3A01G087900 chr3A 91.445 1239 67 14 1161 2376 56756835 56758057 0.000000e+00 1664.0
2 TraesCS3A01G087900 chr3A 84.548 343 28 8 1 318 641015221 641014879 2.050000e-82 316.0
3 TraesCS3A01G087900 chr3A 83.673 343 31 14 1 318 640954951 640954609 2.060000e-77 300.0
4 TraesCS3A01G087900 chr3A 95.918 49 2 0 3486 3534 661484783 661484831 2.920000e-11 80.5
5 TraesCS3A01G087900 chr3B 88.889 945 70 14 1161 2091 70120962 70121885 0.000000e+00 1131.0
6 TraesCS3A01G087900 chr3B 88.070 855 63 14 1251 2091 70093051 70093880 0.000000e+00 977.0
7 TraesCS3A01G087900 chr3B 84.985 686 58 25 1413 2091 70123440 70124087 0.000000e+00 654.0
8 TraesCS3A01G087900 chr3B 86.712 444 35 10 2123 2551 70095941 70096375 4.130000e-129 472.0
9 TraesCS3A01G087900 chr3B 83.924 423 31 15 768 1166 70092514 70092923 1.550000e-98 370.0
10 TraesCS3A01G087900 chr3B 79.941 339 38 16 8 318 739069073 739068737 4.590000e-54 222.0
11 TraesCS3A01G087900 chr3B 77.509 289 29 21 889 1166 70118968 70119231 1.320000e-29 141.0
12 TraesCS3A01G087900 chr3B 94.382 89 5 0 2092 2180 70121930 70122018 1.710000e-28 137.0
13 TraesCS3A01G087900 chr3B 85.827 127 18 0 355 481 254038381 254038507 6.150000e-28 135.0
14 TraesCS3A01G087900 chr3B 87.379 103 13 0 368 470 450829676 450829778 6.200000e-23 119.0
15 TraesCS3A01G087900 chr3B 97.826 46 1 0 2093 2138 70095335 70095380 2.920000e-11 80.5
16 TraesCS3A01G087900 chr3B 92.308 52 3 1 268 318 792083175 792083124 4.890000e-09 73.1
17 TraesCS3A01G087900 chr3D 93.794 709 37 3 2828 3533 166936736 166937440 0.000000e+00 1059.0
18 TraesCS3A01G087900 chr3D 89.161 858 63 14 1251 2091 44967041 44967885 0.000000e+00 1042.0
19 TraesCS3A01G087900 chr3D 86.982 868 74 18 1161 2020 45011777 45012613 0.000000e+00 941.0
20 TraesCS3A01G087900 chr3D 85.843 445 39 5 2123 2551 44968542 44968978 5.380000e-123 451.0
21 TraesCS3A01G087900 chr3D 85.203 419 25 15 768 1166 44966504 44966905 2.560000e-106 396.0
22 TraesCS3A01G087900 chr4D 94.970 656 33 0 2828 3483 45786218 45785563 0.000000e+00 1029.0
23 TraesCS3A01G087900 chr4D 90.370 135 12 1 185 318 433350936 433350802 3.630000e-40 176.0
24 TraesCS3A01G087900 chr7A 94.970 656 32 1 2828 3483 463720417 463721071 0.000000e+00 1027.0
25 TraesCS3A01G087900 chr7A 91.339 254 21 1 2553 2805 696100083 696099830 2.610000e-91 346.0
26 TraesCS3A01G087900 chr7A 89.344 244 24 2 2566 2807 616328093 616328336 4.430000e-79 305.0
27 TraesCS3A01G087900 chr7A 82.609 184 23 8 73 250 686303287 686303107 1.700000e-33 154.0
28 TraesCS3A01G087900 chr6A 94.970 656 31 2 2828 3483 582937101 582936448 0.000000e+00 1027.0
29 TraesCS3A01G087900 chr6A 95.918 49 2 0 3486 3534 256498807 256498759 2.920000e-11 80.5
30 TraesCS3A01G087900 chr5A 94.665 656 33 1 2828 3483 34894016 34894669 0.000000e+00 1016.0
31 TraesCS3A01G087900 chr5A 94.512 656 34 2 2828 3483 352478036 352477383 0.000000e+00 1011.0
32 TraesCS3A01G087900 chr5A 81.081 185 29 6 66 246 374905519 374905701 3.680000e-30 143.0
33 TraesCS3A01G087900 chr5A 94.737 76 4 0 3404 3479 681766936 681766861 6.200000e-23 119.0
34 TraesCS3A01G087900 chr5D 94.521 657 34 1 2827 3483 281493692 281494346 0.000000e+00 1013.0
35 TraesCS3A01G087900 chr5D 88.333 180 20 1 1 179 436938356 436938177 7.680000e-52 215.0
36 TraesCS3A01G087900 chr5D 81.283 187 27 6 71 252 408654089 408653906 1.020000e-30 145.0
37 TraesCS3A01G087900 chr5D 88.235 51 5 1 497 547 378052157 378052108 3.810000e-05 60.2
38 TraesCS3A01G087900 chr2A 94.512 656 36 0 2828 3483 729252590 729251935 0.000000e+00 1013.0
39 TraesCS3A01G087900 chr6D 92.362 707 43 7 2828 3534 62817566 62818261 0.000000e+00 996.0
40 TraesCS3A01G087900 chr6D 80.597 335 38 14 8 316 351928724 351929057 2.120000e-57 233.0
41 TraesCS3A01G087900 chrUn 82.173 589 81 10 1312 1885 103768761 103768182 5.300000e-133 484.0
42 TraesCS3A01G087900 chrUn 79.249 559 96 12 1339 1884 103726365 103725814 4.310000e-99 372.0
43 TraesCS3A01G087900 chrUn 83.721 344 30 16 1 318 244965953 244965610 5.730000e-78 302.0
44 TraesCS3A01G087900 chrUn 84.821 112 17 0 355 466 225200884 225200995 2.880000e-21 113.0
45 TraesCS3A01G087900 chr6B 86.159 289 34 4 1597 1885 55597020 55596738 1.230000e-79 307.0
46 TraesCS3A01G087900 chr6B 77.515 338 47 11 8 318 90959904 90959569 3.630000e-40 176.0
47 TraesCS3A01G087900 chr6B 90.566 53 3 2 3483 3533 289825981 289825929 6.330000e-08 69.4
48 TraesCS3A01G087900 chr6B 91.489 47 2 2 3489 3533 289772078 289772032 2.950000e-06 63.9
49 TraesCS3A01G087900 chr7D 88.976 254 16 6 2553 2805 561605432 561605190 1.590000e-78 303.0
50 TraesCS3A01G087900 chr7D 81.667 240 38 5 71 306 546050450 546050687 1.000000e-45 195.0
51 TraesCS3A01G087900 chr7D 86.087 115 16 0 356 470 157664105 157663991 1.330000e-24 124.0
52 TraesCS3A01G087900 chr7B 83.721 344 30 12 1 318 687896779 687896436 5.730000e-78 302.0
53 TraesCS3A01G087900 chr7B 85.965 171 22 2 149 318 83987639 83987470 7.790000e-42 182.0
54 TraesCS3A01G087900 chr1B 80.516 349 36 13 1 317 280986718 280987066 4.560000e-59 239.0
55 TraesCS3A01G087900 chr1B 100.000 29 0 0 502 530 463525472 463525444 2.000000e-03 54.7
56 TraesCS3A01G087900 chr2D 80.290 345 34 15 1 318 388483455 388483118 2.740000e-56 230.0
57 TraesCS3A01G087900 chr2D 81.622 185 28 5 71 252 44184774 44184593 7.900000e-32 148.0
58 TraesCS3A01G087900 chr5B 78.635 337 44 8 8 318 601422127 601422461 7.740000e-47 198.0
59 TraesCS3A01G087900 chr5B 86.429 140 19 0 355 494 710225012 710225151 1.700000e-33 154.0
60 TraesCS3A01G087900 chr5B 95.918 49 2 0 3486 3534 166669509 166669461 2.920000e-11 80.5
61 TraesCS3A01G087900 chr4A 86.364 176 18 5 8 179 531236380 531236207 1.680000e-43 187.0
62 TraesCS3A01G087900 chr4B 93.878 49 3 0 3486 3534 406686483 406686435 1.360000e-09 75.0


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 TraesCS3A01G087900 chr3A 56733591 56737124 3533 False 6527.000000 6527 100.000000 1 3534 1 chr3A.!!$F1 3533
1 TraesCS3A01G087900 chr3A 56756835 56758057 1222 False 1664.000000 1664 91.445000 1161 2376 1 chr3A.!!$F2 1215
2 TraesCS3A01G087900 chr3B 70118968 70124087 5119 False 515.750000 1131 86.441250 889 2180 4 chr3B.!!$F4 1291
3 TraesCS3A01G087900 chr3B 70092514 70096375 3861 False 474.875000 977 89.133000 768 2551 4 chr3B.!!$F3 1783
4 TraesCS3A01G087900 chr3D 166936736 166937440 704 False 1059.000000 1059 93.794000 2828 3533 1 chr3D.!!$F2 705
5 TraesCS3A01G087900 chr3D 45011777 45012613 836 False 941.000000 941 86.982000 1161 2020 1 chr3D.!!$F1 859
6 TraesCS3A01G087900 chr3D 44966504 44968978 2474 False 629.666667 1042 86.735667 768 2551 3 chr3D.!!$F3 1783
7 TraesCS3A01G087900 chr4D 45785563 45786218 655 True 1029.000000 1029 94.970000 2828 3483 1 chr4D.!!$R1 655
8 TraesCS3A01G087900 chr7A 463720417 463721071 654 False 1027.000000 1027 94.970000 2828 3483 1 chr7A.!!$F1 655
9 TraesCS3A01G087900 chr6A 582936448 582937101 653 True 1027.000000 1027 94.970000 2828 3483 1 chr6A.!!$R2 655
10 TraesCS3A01G087900 chr5A 34894016 34894669 653 False 1016.000000 1016 94.665000 2828 3483 1 chr5A.!!$F1 655
11 TraesCS3A01G087900 chr5A 352477383 352478036 653 True 1011.000000 1011 94.512000 2828 3483 1 chr5A.!!$R1 655
12 TraesCS3A01G087900 chr5D 281493692 281494346 654 False 1013.000000 1013 94.521000 2827 3483 1 chr5D.!!$F1 656
13 TraesCS3A01G087900 chr2A 729251935 729252590 655 True 1013.000000 1013 94.512000 2828 3483 1 chr2A.!!$R1 655
14 TraesCS3A01G087900 chr6D 62817566 62818261 695 False 996.000000 996 92.362000 2828 3534 1 chr6D.!!$F1 706
15 TraesCS3A01G087900 chrUn 103768182 103768761 579 True 484.000000 484 82.173000 1312 1885 1 chrUn.!!$R2 573
16 TraesCS3A01G087900 chrUn 103725814 103726365 551 True 372.000000 372 79.249000 1339 1884 1 chrUn.!!$R1 545


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
451 452 0.033642 TATCAACGTGTGTGGGCGAA 59.966 50.0 0.00 0.0 0.00 4.70 F
643 644 0.250901 GCTGTTCCAGGGAGCAAAGA 60.251 55.0 6.33 0.0 35.07 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 6482 0.586319 ACTTCCGCAACAACACGATG 59.414 50.000 0.0 0.0 0.0 3.84 R
2582 7504 2.978978 TCCCTCTCCATGTGAAGTTTGA 59.021 45.455 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)



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

AutoCloner maintained by Alex Coulton.