Multiple sequence alignment - TraesCS3D01G491000

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 TraesCS3D01G491000 chr3D 100.000 2672 0 0 1 2672 584822490 584825161 0.000000e+00 4935.0
1 TraesCS3D01G491000 chr3D 98.677 1058 13 1 2 1059 57187228 57186172 0.000000e+00 1875.0
2 TraesCS3D01G491000 chr3D 82.574 505 88 0 1070 1574 584865071 584865575 1.890000e-121 446.0
3 TraesCS3D01G491000 chr3D 76.559 401 71 14 1358 1739 584888863 584889259 5.830000e-47 198.0
4 TraesCS3D01G491000 chr7D 98.885 1615 7 2 1059 2672 16060002 16058398 0.000000e+00 2872.0
5 TraesCS3D01G491000 chr7D 98.202 1057 18 1 2 1058 154199529 154200584 0.000000e+00 1845.0
6 TraesCS3D01G491000 chr7D 92.529 348 16 1 2325 2672 16007627 16007290 8.600000e-135 490.0
7 TraesCS3D01G491000 chr7D 92.241 348 17 1 2325 2672 16016218 16015881 4.000000e-133 484.0
8 TraesCS3D01G491000 chr7D 91.954 348 18 1 2325 2672 16019972 16019635 1.860000e-131 479.0
9 TraesCS3D01G491000 chr7D 77.241 725 135 20 1060 1760 15920221 15919503 5.360000e-107 398.0
10 TraesCS3D01G491000 chr7A 95.769 1631 52 4 1059 2672 14896011 14894381 0.000000e+00 2614.0
11 TraesCS3D01G491000 chr7A 83.622 519 85 0 1055 1573 91294798 91295316 3.090000e-134 488.0
12 TraesCS3D01G491000 chr7A 81.890 508 92 0 1070 1577 14773616 14773109 1.900000e-116 429.0
13 TraesCS3D01G491000 chr7A 87.324 71 7 2 1575 1643 14820366 14820296 2.210000e-11 80.5
14 TraesCS3D01G491000 chr4A 91.447 1555 111 10 1059 2602 718968480 718970023 0.000000e+00 2115.0
15 TraesCS3D01G491000 chr4A 91.447 1555 111 10 1059 2602 718980727 718982270 0.000000e+00 2115.0
16 TraesCS3D01G491000 chr4A 82.480 508 83 4 1070 1574 719016924 719017428 8.780000e-120 440.0
17 TraesCS3D01G491000 chr4A 74.206 252 54 7 1945 2188 719120908 719121156 7.870000e-16 95.3
18 TraesCS3D01G491000 chr7B 92.686 1463 94 5 1059 2509 711433271 711431810 0.000000e+00 2097.0
19 TraesCS3D01G491000 chr2D 98.675 1057 13 1 2 1058 284567984 284566929 0.000000e+00 1873.0
20 TraesCS3D01G491000 chr5D 98.017 1059 17 3 2 1058 361207336 361206280 0.000000e+00 1836.0
21 TraesCS3D01G491000 chr5D 97.259 1058 25 3 2 1059 397070796 397071849 0.000000e+00 1790.0
22 TraesCS3D01G491000 chr1B 97.919 1057 20 2 2 1058 637510700 637509646 0.000000e+00 1829.0
23 TraesCS3D01G491000 chr2B 97.453 1060 23 3 2 1058 543535285 543536343 0.000000e+00 1805.0
24 TraesCS3D01G491000 chr2B 96.789 1059 23 3 2 1058 580012536 580011487 0.000000e+00 1757.0
25 TraesCS3D01G491000 chr6A 95.287 1061 45 4 2 1059 480661284 480660226 0.000000e+00 1677.0
26 TraesCS3D01G491000 chrUn 91.877 357 19 1 2316 2672 457338120 457338466 8.600000e-135 490.0
27 TraesCS3D01G491000 chrUn 92.529 348 16 1 2325 2672 462295653 462295316 8.600000e-135 490.0


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 TraesCS3D01G491000 chr3D 584822490 584825161 2671 False 4935.0 4935 100.0000 1 2672 1 chr3D.!!$F1 2671
1 TraesCS3D01G491000 chr3D 57186172 57187228 1056 True 1875.0 1875 98.6770 2 1059 1 chr3D.!!$R1 1057
2 TraesCS3D01G491000 chr3D 584865071 584865575 504 False 446.0 446 82.5740 1070 1574 1 chr3D.!!$F2 504
3 TraesCS3D01G491000 chr7D 16058398 16060002 1604 True 2872.0 2872 98.8850 1059 2672 1 chr7D.!!$R3 1613
4 TraesCS3D01G491000 chr7D 154199529 154200584 1055 False 1845.0 1845 98.2020 2 1058 1 chr7D.!!$F1 1056
5 TraesCS3D01G491000 chr7D 16015881 16019972 4091 True 481.5 484 92.0975 2325 2672 2 chr7D.!!$R4 347
6 TraesCS3D01G491000 chr7D 15919503 15920221 718 True 398.0 398 77.2410 1060 1760 1 chr7D.!!$R1 700
7 TraesCS3D01G491000 chr7A 14894381 14896011 1630 True 2614.0 2614 95.7690 1059 2672 1 chr7A.!!$R3 1613
8 TraesCS3D01G491000 chr7A 91294798 91295316 518 False 488.0 488 83.6220 1055 1573 1 chr7A.!!$F1 518
9 TraesCS3D01G491000 chr7A 14773109 14773616 507 True 429.0 429 81.8900 1070 1577 1 chr7A.!!$R1 507
10 TraesCS3D01G491000 chr4A 718968480 718970023 1543 False 2115.0 2115 91.4470 1059 2602 1 chr4A.!!$F1 1543
11 TraesCS3D01G491000 chr4A 718980727 718982270 1543 False 2115.0 2115 91.4470 1059 2602 1 chr4A.!!$F2 1543
12 TraesCS3D01G491000 chr4A 719016924 719017428 504 False 440.0 440 82.4800 1070 1574 1 chr4A.!!$F3 504
13 TraesCS3D01G491000 chr7B 711431810 711433271 1461 True 2097.0 2097 92.6860 1059 2509 1 chr7B.!!$R1 1450
14 TraesCS3D01G491000 chr2D 284566929 284567984 1055 True 1873.0 1873 98.6750 2 1058 1 chr2D.!!$R1 1056
15 TraesCS3D01G491000 chr5D 361206280 361207336 1056 True 1836.0 1836 98.0170 2 1058 1 chr5D.!!$R1 1056
16 TraesCS3D01G491000 chr5D 397070796 397071849 1053 False 1790.0 1790 97.2590 2 1059 1 chr5D.!!$F1 1057
17 TraesCS3D01G491000 chr1B 637509646 637510700 1054 True 1829.0 1829 97.9190 2 1058 1 chr1B.!!$R1 1056
18 TraesCS3D01G491000 chr2B 543535285 543536343 1058 False 1805.0 1805 97.4530 2 1058 1 chr2B.!!$F1 1056
19 TraesCS3D01G491000 chr2B 580011487 580012536 1049 True 1757.0 1757 96.7890 2 1058 1 chr2B.!!$R1 1056
20 TraesCS3D01G491000 chr6A 480660226 480661284 1058 True 1677.0 1677 95.2870 2 1059 1 chr6A.!!$R1 1057

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
366 368 2.612746 AGCCCGGTACCACCCAAT 60.613 61.111 13.54 0.0 33.75 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 1904 5.075448 CACTACATGCGCATTATCGAAATC 58.925 41.667 22.81 0.0 0.0 2.17 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
366 368 2.612746 AGCCCGGTACCACCCAAT 60.613 61.111 13.54 0.00 33.75 3.16
1645 1662 1.338864 CCAGCATGCTCTCTCTGTGTT 60.339 52.381 19.68 0.00 31.97 3.32
1877 1904 4.040445 TGCATTCATCATGATGTTGCTG 57.960 40.909 36.89 27.91 43.05 4.41
2002 2037 6.015772 GGGTTTCCTGTTATTGTTCAAGCTTA 60.016 38.462 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
366 368 3.294493 GCAAGGGCACGCCTCAAA 61.294 61.111 8.20 0.0 40.72 2.69
799 802 5.048364 CAGAATATCCTACAACCTCTCCTCG 60.048 48.000 0.00 0.0 0.00 4.63
1877 1904 5.075448 CACTACATGCGCATTATCGAAATC 58.925 41.667 22.81 0.0 0.00 2.17
2002 2037 6.012745 AGAGTTAGCAGGGAAATGTGAAAAT 58.987 36.000 0.00 0.0 0.00 1.82


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

AutoCloner maintained by Alex Coulton.