Multiple sequence alignment - TraesCS3D01G243100

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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 TraesCS3D01G243100 chr3D 100.000 5434 0 0 1 5434 338355084 338349651 0.000000e+00 10035.0
1 TraesCS3D01G243100 chr3D 91.205 307 22 4 443 748 569242261 569242563 3.920000e-111 412.0
2 TraesCS3D01G243100 chr3D 93.889 180 10 1 5256 5434 338321160 338321339 2.490000e-68 270.0
3 TraesCS3D01G243100 chr3D 89.252 214 14 3 171 384 569242056 569242260 5.400000e-65 259.0
4 TraesCS3D01G243100 chr3D 92.683 123 5 2 26 147 569241947 569242066 2.010000e-39 174.0
5 TraesCS3D01G243100 chr3D 97.436 39 1 0 405 443 338354758 338354720 3.510000e-07 67.6
6 TraesCS3D01G243100 chr3B 97.799 1817 38 2 2281 4095 436731002 436729186 0.000000e+00 3133.0
7 TraesCS3D01G243100 chr3B 93.153 1329 60 20 4123 5434 436729189 436727875 0.000000e+00 1921.0
8 TraesCS3D01G243100 chr3B 92.857 1246 61 14 1031 2272 436732259 436731038 0.000000e+00 1783.0
9 TraesCS3D01G243100 chr3B 95.429 175 8 0 5260 5434 436574737 436574911 4.140000e-71 279.0
10 TraesCS3D01G243100 chr3A 93.742 1582 58 16 2571 4121 456704751 456703180 0.000000e+00 2335.0
11 TraesCS3D01G243100 chr3A 94.158 1472 61 10 804 2272 456719141 456717692 0.000000e+00 2218.0
12 TraesCS3D01G243100 chr3A 88.955 1349 78 32 4116 5434 456701779 456700472 0.000000e+00 1600.0
13 TraesCS3D01G243100 chr3A 95.541 314 11 3 2281 2592 456717656 456717344 2.920000e-137 499.0
14 TraesCS3D01G243100 chr3A 94.444 180 9 1 5256 5434 456452188 456452367 5.360000e-70 276.0
15 TraesCS3D01G243100 chr3A 95.833 48 1 1 766 812 456722019 456721972 5.840000e-10 76.8
16 TraesCS3D01G243100 chr4B 90.265 339 32 1 405 743 604701394 604701731 5.000000e-120 442.0
17 TraesCS3D01G243100 chr4B 85.556 360 48 3 1 359 604701070 604701426 1.850000e-99 374.0
18 TraesCS3D01G243100 chr7D 92.508 307 19 3 443 748 458936053 458935750 2.320000e-118 436.0
19 TraesCS3D01G243100 chr7D 89.252 214 14 3 171 384 140818471 140818267 5.400000e-65 259.0
20 TraesCS3D01G243100 chr7D 88.318 214 16 3 171 384 458936258 458936054 1.170000e-61 248.0
21 TraesCS3D01G243100 chr7D 92.405 158 6 4 1 157 458936392 458936240 2.550000e-53 220.0
22 TraesCS3D01G243100 chr7D 90.506 158 9 4 1 157 140818605 140818453 2.570000e-48 204.0
23 TraesCS3D01G243100 chr6D 87.855 387 23 5 364 748 413994648 413994284 3.010000e-117 433.0
24 TraesCS3D01G243100 chr6D 91.857 307 21 3 443 748 437343647 437343950 5.030000e-115 425.0
25 TraesCS3D01G243100 chr6D 89.252 214 14 3 171 384 413994792 413994588 5.400000e-65 259.0
26 TraesCS3D01G243100 chr6D 89.252 214 14 3 171 384 437343442 437343646 5.400000e-65 259.0
27 TraesCS3D01G243100 chr6D 93.919 148 5 2 1 147 437343308 437343452 2.550000e-53 220.0
28 TraesCS3D01G243100 chr6D 91.772 158 7 4 1 157 413994926 413994774 1.190000e-51 215.0
29 TraesCS3D01G243100 chr5D 87.855 387 23 5 364 748 118855792 118855428 3.010000e-117 433.0
30 TraesCS3D01G243100 chr5D 87.855 387 23 5 364 748 518001000 518000636 3.010000e-117 433.0
31 TraesCS3D01G243100 chr5D 90.187 214 12 3 171 384 518001144 518000940 2.490000e-68 270.0
32 TraesCS3D01G243100 chr5D 89.252 214 14 3 171 384 118855936 118855732 5.400000e-65 259.0
33 TraesCS3D01G243100 chr5D 92.405 158 6 4 1 157 518001278 518001126 2.550000e-53 220.0
34 TraesCS3D01G243100 chr5D 90.769 130 6 4 29 157 118856042 118855918 9.360000e-38 169.0
35 TraesCS3D01G243100 chrUn 91.531 307 21 4 443 748 315029799 315029497 8.420000e-113 418.0
36 TraesCS3D01G243100 chrUn 88.785 214 15 3 171 384 315030004 315029800 2.510000e-63 254.0
37 TraesCS3D01G243100 chrUn 91.538 130 5 4 29 157 315030110 315029986 2.010000e-39 174.0
38 TraesCS3D01G243100 chr6B 86.994 346 35 5 405 748 461950565 461950902 1.100000e-101 381.0
39 TraesCS3D01G243100 chr2B 96.429 56 2 0 5379 5434 637775928 637775983 5.800000e-15 93.5


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 TraesCS3D01G243100 chr3D 338349651 338355084 5433 True 5051.300000 10035 98.718000 1 5434 2 chr3D.!!$R1 5433
1 TraesCS3D01G243100 chr3D 569241947 569242563 616 False 281.666667 412 91.046667 26 748 3 chr3D.!!$F2 722
2 TraesCS3D01G243100 chr3B 436727875 436732259 4384 True 2279.000000 3133 94.603000 1031 5434 3 chr3B.!!$R1 4403
3 TraesCS3D01G243100 chr3A 456700472 456704751 4279 True 1967.500000 2335 91.348500 2571 5434 2 chr3A.!!$R1 2863
4 TraesCS3D01G243100 chr3A 456717344 456722019 4675 True 931.266667 2218 95.177333 766 2592 3 chr3A.!!$R2 1826
5 TraesCS3D01G243100 chr4B 604701070 604701731 661 False 408.000000 442 87.910500 1 743 2 chr4B.!!$F1 742
6 TraesCS3D01G243100 chr7D 458935750 458936392 642 True 301.333333 436 91.077000 1 748 3 chr7D.!!$R2 747
7 TraesCS3D01G243100 chr6D 413994284 413994926 642 True 302.333333 433 89.626333 1 748 3 chr6D.!!$R1 747
8 TraesCS3D01G243100 chr6D 437343308 437343950 642 False 301.333333 425 91.676000 1 748 3 chr6D.!!$F1 747
9 TraesCS3D01G243100 chr5D 518000636 518001278 642 True 307.666667 433 90.149000 1 748 3 chr5D.!!$R2 747
10 TraesCS3D01G243100 chr5D 118855428 118856042 614 True 287.000000 433 89.292000 29 748 3 chr5D.!!$R1 719
11 TraesCS3D01G243100 chrUn 315029497 315030110 613 True 282.000000 418 90.618000 29 748 3 chrUn.!!$R1 719


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
474 476 0.036858 GATAGGATCGAGCAAGGGCC 60.037 60.0 1.84 0.0 42.56 5.80 F
1077 3919 0.463295 CGAATCAGCATCCACAGCCT 60.463 55.0 0.00 0.0 0.00 4.58 F
1758 4601 0.102844 TGTTTCTGTTGCTTGGCTGC 59.897 50.0 0.00 0.0 0.00 5.25 F
2964 5850 0.737367 TTCATCAAGTCAGCGAGCGG 60.737 55.0 0.00 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 4562 0.102300 GCCCGCACACATAAAATCCC 59.898 55.0 0.00 0.0 0.00 3.85 R
2414 5291 0.319986 TCGCAGAATACCGCACAACA 60.320 50.0 0.00 0.0 0.00 3.33 R
3549 6436 0.231279 CTAACACCACGACGTGCAAC 59.769 55.0 22.46 0.0 37.25 4.17 R
4459 8774 0.466189 ACAACAACTGCCACCTGGAG 60.466 55.0 0.00 0.0 37.39 3.86 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)



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AutoCloner maintained by Alex Coulton.