Multiple sequence alignment - TraesCS2D01G483900

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 TraesCS2D01G483900 chr2D 100.000 2357 0 0 1 2357 585391134 585393490 0.000000e+00 4353
1 TraesCS2D01G483900 chr2D 87.918 1796 141 54 2 1751 128971447 128969682 0.000000e+00 2045
2 TraesCS2D01G483900 chr2D 98.185 606 11 0 1752 2357 585409549 585410154 0.000000e+00 1059
3 TraesCS2D01G483900 chr2D 97.858 607 13 0 1751 2357 545594374 545593768 0.000000e+00 1050
4 TraesCS2D01G483900 chr2D 89.919 496 17 4 83 549 125435854 125435363 2.000000e-170 608
5 TraesCS2D01G483900 chrUn 97.091 1753 41 7 1 1751 22359657 22361401 0.000000e+00 2946
6 TraesCS2D01G483900 chr3D 96.124 1780 36 7 1 1751 284994426 284996201 0.000000e+00 2874
7 TraesCS2D01G483900 chr3D 95.591 1270 30 13 497 1751 453177516 453176258 0.000000e+00 2012
8 TraesCS2D01G483900 chr3D 94.603 1260 40 10 507 1751 540944345 540943099 0.000000e+00 1925
9 TraesCS2D01G483900 chr3D 97.419 620 13 3 1738 2357 491633565 491634181 0.000000e+00 1053
10 TraesCS2D01G483900 chr3D 98.020 606 11 1 1752 2357 35983483 35982879 0.000000e+00 1051
11 TraesCS2D01G483900 chr3D 93.506 462 19 3 1 462 83487484 83487934 0.000000e+00 676
12 TraesCS2D01G483900 chr3D 87.616 323 34 5 1 321 540944846 540944528 1.030000e-98 370
13 TraesCS2D01G483900 chr5D 95.294 1700 45 12 83 1751 486822009 486820314 0.000000e+00 2663
14 TraesCS2D01G483900 chr5D 93.443 1220 60 13 544 1751 98226413 98225202 0.000000e+00 1792
15 TraesCS2D01G483900 chr5D 97.876 612 11 2 1746 2357 281605901 281605292 0.000000e+00 1057
16 TraesCS2D01G483900 chr1D 89.039 1779 125 49 7 1751 482329662 482331404 0.000000e+00 2141
17 TraesCS2D01G483900 chr1D 98.020 606 12 0 1752 2357 47982152 47981547 0.000000e+00 1053
18 TraesCS2D01G483900 chr1D 90.734 572 16 3 1 544 1817037 1817599 0.000000e+00 728
19 TraesCS2D01G483900 chr1D 96.262 321 12 0 1 321 1827213 1826893 5.770000e-146 527
20 TraesCS2D01G483900 chr6D 95.276 1270 34 14 497 1751 454506180 454504922 0.000000e+00 1989
21 TraesCS2D01G483900 chr4A 92.766 1327 59 19 439 1751 736036809 736038112 0.000000e+00 1884
22 TraesCS2D01G483900 chr7D 96.595 793 16 4 1 792 109148856 109149638 0.000000e+00 1304
23 TraesCS2D01G483900 chr7D 98.020 606 11 1 1752 2357 73295756 73295152 0.000000e+00 1051
24 TraesCS2D01G483900 chr4D 98.020 606 11 1 1752 2357 375693210 375693814 0.000000e+00 1051
25 TraesCS2D01G483900 chr4D 97.403 616 16 0 1742 2357 374318879 374319494 0.000000e+00 1050
26 TraesCS2D01G483900 chr4B 86.615 904 93 22 38 929 37919965 37919078 0.000000e+00 974
27 TraesCS2D01G483900 chr4B 78.492 716 110 31 1 690 601276486 601275789 1.670000e-116 429
28 TraesCS2D01G483900 chr7B 91.071 616 32 8 396 1007 630811532 630812128 0.000000e+00 811
29 TraesCS2D01G483900 chr7B 87.888 322 31 7 1 316 630815590 630815271 2.860000e-99 372
30 TraesCS2D01G483900 chr7B 75.728 412 71 19 1 408 630811012 630811398 1.860000e-41 180
31 TraesCS2D01G483900 chr1B 87.812 320 31 6 1 316 669309281 669309596 3.700000e-98 368
32 TraesCS2D01G483900 chr5B 89.565 115 11 1 498 611 175994149 175994263 6.790000e-31 145


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 TraesCS2D01G483900 chr2D 585391134 585393490 2356 False 4353.0 4353 100.0000 1 2357 1 chr2D.!!$F1 2356
1 TraesCS2D01G483900 chr2D 128969682 128971447 1765 True 2045.0 2045 87.9180 2 1751 1 chr2D.!!$R2 1749
2 TraesCS2D01G483900 chr2D 585409549 585410154 605 False 1059.0 1059 98.1850 1752 2357 1 chr2D.!!$F2 605
3 TraesCS2D01G483900 chr2D 545593768 545594374 606 True 1050.0 1050 97.8580 1751 2357 1 chr2D.!!$R3 606
4 TraesCS2D01G483900 chrUn 22359657 22361401 1744 False 2946.0 2946 97.0910 1 1751 1 chrUn.!!$F1 1750
5 TraesCS2D01G483900 chr3D 284994426 284996201 1775 False 2874.0 2874 96.1240 1 1751 1 chr3D.!!$F2 1750
6 TraesCS2D01G483900 chr3D 453176258 453177516 1258 True 2012.0 2012 95.5910 497 1751 1 chr3D.!!$R2 1254
7 TraesCS2D01G483900 chr3D 540943099 540944846 1747 True 1147.5 1925 91.1095 1 1751 2 chr3D.!!$R3 1750
8 TraesCS2D01G483900 chr3D 491633565 491634181 616 False 1053.0 1053 97.4190 1738 2357 1 chr3D.!!$F3 619
9 TraesCS2D01G483900 chr3D 35982879 35983483 604 True 1051.0 1051 98.0200 1752 2357 1 chr3D.!!$R1 605
10 TraesCS2D01G483900 chr5D 486820314 486822009 1695 True 2663.0 2663 95.2940 83 1751 1 chr5D.!!$R3 1668
11 TraesCS2D01G483900 chr5D 98225202 98226413 1211 True 1792.0 1792 93.4430 544 1751 1 chr5D.!!$R1 1207
12 TraesCS2D01G483900 chr5D 281605292 281605901 609 True 1057.0 1057 97.8760 1746 2357 1 chr5D.!!$R2 611
13 TraesCS2D01G483900 chr1D 482329662 482331404 1742 False 2141.0 2141 89.0390 7 1751 1 chr1D.!!$F2 1744
14 TraesCS2D01G483900 chr1D 47981547 47982152 605 True 1053.0 1053 98.0200 1752 2357 1 chr1D.!!$R2 605
15 TraesCS2D01G483900 chr1D 1817037 1817599 562 False 728.0 728 90.7340 1 544 1 chr1D.!!$F1 543
16 TraesCS2D01G483900 chr6D 454504922 454506180 1258 True 1989.0 1989 95.2760 497 1751 1 chr6D.!!$R1 1254
17 TraesCS2D01G483900 chr4A 736036809 736038112 1303 False 1884.0 1884 92.7660 439 1751 1 chr4A.!!$F1 1312
18 TraesCS2D01G483900 chr7D 109148856 109149638 782 False 1304.0 1304 96.5950 1 792 1 chr7D.!!$F1 791
19 TraesCS2D01G483900 chr7D 73295152 73295756 604 True 1051.0 1051 98.0200 1752 2357 1 chr7D.!!$R1 605
20 TraesCS2D01G483900 chr4D 375693210 375693814 604 False 1051.0 1051 98.0200 1752 2357 1 chr4D.!!$F2 605
21 TraesCS2D01G483900 chr4D 374318879 374319494 615 False 1050.0 1050 97.4030 1742 2357 1 chr4D.!!$F1 615
22 TraesCS2D01G483900 chr4B 37919078 37919965 887 True 974.0 974 86.6150 38 929 1 chr4B.!!$R1 891
23 TraesCS2D01G483900 chr4B 601275789 601276486 697 True 429.0 429 78.4920 1 690 1 chr4B.!!$R2 689
24 TraesCS2D01G483900 chr7B 630811012 630812128 1116 False 495.5 811 83.3995 1 1007 2 chr7B.!!$F1 1006

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
409 708 1.540267 CTGATGTGCTGCTGCTTTTCT 59.46 47.619 17.0 0.0 40.48 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 2416 1.201414 TCGAGCACTTGTATTCGAGCA 59.799 47.619 5.19 0.0 37.18 4.26 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
409 708 1.540267 CTGATGTGCTGCTGCTTTTCT 59.460 47.619 17.00 0.0 40.48 2.52
435 790 5.491982 GGAATCACTCCTGCTTTTCTTCTA 58.508 41.667 0.00 0.0 41.61 2.10
648 1131 1.743772 CGTCCAGCCATCCTCGAAATT 60.744 52.381 0.00 0.0 0.00 1.82
1092 1595 3.879932 GCGTGGAATAGTTTCTATGCC 57.120 47.619 6.80 6.8 44.94 4.40
1141 1656 2.233431 GAGGAGAAAGCAGAGCAAGAGA 59.767 50.000 0.00 0.0 0.00 3.10
1142 1657 2.234414 AGGAGAAAGCAGAGCAAGAGAG 59.766 50.000 0.00 0.0 0.00 3.20
1376 1893 8.822805 TCAGTAGATTCCTGTGGTAGTATTTTT 58.177 33.333 0.00 0.0 0.00 1.94
1481 1998 7.618964 TCGTACGATGTATCTTATTTTCAGC 57.381 36.000 15.28 0.0 0.00 4.26
1555 2075 6.183360 GGCATTTTCTTTCCCTCCACTAATAC 60.183 42.308 0.00 0.0 0.00 1.89
1740 2260 0.108615 CTCTTGCCCTTCGACGATGT 60.109 55.000 0.00 0.0 0.00 3.06
2240 2760 7.093640 GGGTATATGTGTAAAGGACCATATCGA 60.094 40.741 0.00 0.0 35.39 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.969196 CAGGTGCCACGTGTCGCT 62.969 66.667 15.65 0.0 0.00 4.93
1092 1595 2.202311 TTCTCGCGTCGCTCTTCG 60.202 61.111 16.36 0.0 40.15 3.79
1141 1656 8.008513 TCCGCATAGTATTCTTTTAACTCTCT 57.991 34.615 0.00 0.0 0.00 3.10
1142 1657 7.095982 GCTCCGCATAGTATTCTTTTAACTCTC 60.096 40.741 0.00 0.0 0.00 3.20
1263 1780 5.512921 CCTTTCTTTCTTTCTCTGCCTCTCT 60.513 44.000 0.00 0.0 0.00 3.10
1481 1998 2.925578 TCCATTACGACACGGTACAG 57.074 50.000 0.00 0.0 0.00 2.74
1555 2075 3.684305 TGTAGTTCTTGCATGATGTTCGG 59.316 43.478 2.75 0.0 0.00 4.30
1641 2161 8.070034 TCCAGTTCTACCGTTTAATTCAGATA 57.930 34.615 0.00 0.0 0.00 1.98
1740 2260 2.429610 GGGGCGTCACATAAGAGTTCTA 59.570 50.000 0.00 0.0 0.00 2.10
1893 2413 2.996621 GAGCACTTGTATTCGAGCACTT 59.003 45.455 0.00 0.0 0.00 3.16
1896 2416 1.201414 TCGAGCACTTGTATTCGAGCA 59.799 47.619 5.19 0.0 37.18 4.26
2240 2760 3.264193 TGGCATTCTGTAGTTCAGTCCAT 59.736 43.478 0.00 0.0 43.97 3.41
2286 2806 2.351447 CCAGAAGCGTAGTCTTCGACAA 60.351 50.000 2.72 0.0 42.44 3.18


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

AutoCloner maintained by Alex Coulton.