Multiple sequence alignment - TraesCS6B01G204000

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 TraesCS6B01G204000 chr6B 100.000 4302 0 0 1 4302 251547011 251542710 0.000000e+00 7945.0
1 TraesCS6B01G204000 chr6B 99.442 4304 19 5 1 4302 251385444 251381144 0.000000e+00 7810.0
2 TraesCS6B01G204000 chr6B 84.848 66 6 1 415 476 337834128 337834193 3.590000e-06 63.9
3 TraesCS6B01G204000 chr6B 92.683 41 3 0 436 476 232327498 232327458 4.650000e-05 60.2
4 TraesCS6B01G204000 chr7D 83.153 463 73 5 3843 4302 53522954 53523414 6.650000e-113 418.0
5 TraesCS6B01G204000 chr1D 83.937 442 62 8 3865 4302 467586050 467586486 8.610000e-112 414.0
6 TraesCS6B01G204000 chr1D 87.273 110 9 5 2465 2571 338937372 338937265 2.100000e-23 121.0
7 TraesCS6B01G204000 chr1D 95.238 42 2 0 435 476 203317131 203317172 2.780000e-07 67.6
8 TraesCS6B01G204000 chr1B 82.121 481 82 4 3823 4302 460576221 460576698 4.000000e-110 409.0
9 TraesCS6B01G204000 chr1B 89.091 110 7 5 2465 2571 24349053 24349160 9.710000e-27 132.0
10 TraesCS6B01G204000 chr1B 84.298 121 13 6 2464 2582 660672130 660672014 3.520000e-21 113.0
11 TraesCS6B01G204000 chr1B 93.478 46 3 0 3726 3771 670093980 670094025 7.720000e-08 69.4
12 TraesCS6B01G204000 chr1B 93.478 46 3 0 3726 3771 670271461 670271416 7.720000e-08 69.4
13 TraesCS6B01G204000 chr5B 81.450 469 75 11 3839 4302 540256791 540256330 1.460000e-99 374.0
14 TraesCS6B01G204000 chr7A 79.554 538 95 15 3765 4297 503451935 503452462 1.890000e-98 370.0
15 TraesCS6B01G204000 chr2D 79.558 543 91 18 3770 4302 54022248 54021716 1.890000e-98 370.0
16 TraesCS6B01G204000 chr6D 80.932 472 78 10 3839 4302 157154177 157154644 3.160000e-96 363.0
17 TraesCS6B01G204000 chr6D 80.000 110 18 2 371 476 249953702 249953811 1.280000e-10 78.7
18 TraesCS6B01G204000 chr2B 79.074 540 93 14 3770 4302 23264472 23264998 1.900000e-93 353.0
19 TraesCS6B01G204000 chr2B 84.375 128 13 7 2459 2582 28337573 28337697 7.560000e-23 119.0
20 TraesCS6B01G204000 chr3A 88.991 109 9 3 2465 2571 49871208 49871101 9.710000e-27 132.0
21 TraesCS6B01G204000 chr7B 88.182 110 8 5 2465 2571 459908919 459908812 4.520000e-25 126.0
22 TraesCS6B01G204000 chr7B 88.182 110 8 5 2465 2571 615290497 615290604 4.520000e-25 126.0
23 TraesCS6B01G204000 chr7B 93.478 46 3 0 3726 3771 122780554 122780599 7.720000e-08 69.4
24 TraesCS6B01G204000 chr4D 88.182 110 8 5 2465 2571 386984669 386984776 4.520000e-25 126.0
25 TraesCS6B01G204000 chr6A 79.817 109 15 4 374 476 346600341 346600234 5.970000e-09 73.1
26 TraesCS6B01G204000 chrUn 93.478 46 3 0 3726 3771 155121780 155121735 7.720000e-08 69.4
27 TraesCS6B01G204000 chrUn 93.478 46 3 0 3726 3771 391473853 391473808 7.720000e-08 69.4


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 TraesCS6B01G204000 chr6B 251542710 251547011 4301 True 7945 7945 100.000 1 4302 1 chr6B.!!$R3 4301
1 TraesCS6B01G204000 chr6B 251381144 251385444 4300 True 7810 7810 99.442 1 4302 1 chr6B.!!$R2 4301
2 TraesCS6B01G204000 chr7A 503451935 503452462 527 False 370 370 79.554 3765 4297 1 chr7A.!!$F1 532
3 TraesCS6B01G204000 chr2D 54021716 54022248 532 True 370 370 79.558 3770 4302 1 chr2D.!!$R1 532
4 TraesCS6B01G204000 chr2B 23264472 23264998 526 False 353 353 79.074 3770 4302 1 chr2B.!!$F1 532

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
357 358 2.586079 CGTGCAGGTAGGATGGCG 60.586 66.667 0.00 0.0 0.00 5.69 F
655 657 4.627467 AGAGAAGATTGTTACATGCACGTC 59.373 41.667 0.00 0.0 0.00 4.34 F
1724 1726 3.383505 CGTAGTGTGGTGAGGATTATCCA 59.616 47.826 14.30 0.0 39.61 3.41 F
2588 2590 5.472137 TCCGTATTGCAATCTATAAAAGGGC 59.528 40.000 16.86 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1380 1382 3.285484 CCCGTTTCTGCTAGACCTAGTA 58.715 50.000 0.00 0.88 35.65 1.82 R
2602 2604 4.142160 GCTTTTGTCCAATGTATTCCCTCC 60.142 45.833 0.00 0.00 0.00 4.30 R
2743 2745 2.296471 ACATAGCTACGCCATAGTGTCC 59.704 50.000 0.00 0.00 37.94 4.02 R
4217 4236 2.435805 AGAAGTTTGAGTCAGTGCTCCA 59.564 45.455 10.72 0.00 34.74 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.825160 GACTCGTGTTGGCCAGGCA 62.825 63.158 15.19 6.78 0.00 4.75
357 358 2.586079 CGTGCAGGTAGGATGGCG 60.586 66.667 0.00 0.00 0.00 5.69
655 657 4.627467 AGAGAAGATTGTTACATGCACGTC 59.373 41.667 0.00 0.00 0.00 4.34
1724 1726 3.383505 CGTAGTGTGGTGAGGATTATCCA 59.616 47.826 14.30 0.00 39.61 3.41
2588 2590 5.472137 TCCGTATTGCAATCTATAAAAGGGC 59.528 40.000 16.86 0.00 0.00 5.19
2950 2952 8.698973 TTGTGTTAGAATTTCTGGAAATGGTA 57.301 30.769 9.22 2.60 40.57 3.25
3063 3065 9.581289 TTTTTGATAAGATCCCTCTGTTTACAA 57.419 29.630 0.00 0.00 0.00 2.41
3989 4003 2.029110 CACGTGGAAATGCCCAGAAAAT 60.029 45.455 7.95 0.00 36.78 1.82
4132 4148 0.404040 AATTTTCCTCCGCCTGTCCA 59.596 50.000 0.00 0.00 0.00 4.02
4217 4236 0.035056 AGGCAGCCATTTCTAACGCT 60.035 50.000 15.80 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.683365 ATGGATGCCTGGCCAACAC 60.683 57.895 17.53 0.00 37.78 3.32
161 162 0.833287 GGATTGCTCCCTGTGCTCTA 59.167 55.000 0.00 0.00 35.28 2.43
192 193 1.191647 CGTGTCGGCTAGTTTGTTCAC 59.808 52.381 0.00 0.00 0.00 3.18
357 358 2.063378 CCTCTCAGGGGCTCTCCAC 61.063 68.421 0.00 0.00 37.22 4.02
1319 1321 6.701145 TTGCGGGCTAATATTGTAAAATCA 57.299 33.333 0.00 0.00 0.00 2.57
1380 1382 3.285484 CCCGTTTCTGCTAGACCTAGTA 58.715 50.000 0.00 0.88 35.65 1.82
1724 1726 4.663592 TCTTTTTCTTAGTCCCCCTTGTCT 59.336 41.667 0.00 0.00 0.00 3.41
2602 2604 4.142160 GCTTTTGTCCAATGTATTCCCTCC 60.142 45.833 0.00 0.00 0.00 4.30
2743 2745 2.296471 ACATAGCTACGCCATAGTGTCC 59.704 50.000 0.00 0.00 37.94 4.02
3423 3425 9.710979 TTCATTACTTTTACAAGAACAAGAACG 57.289 29.630 0.00 0.00 33.72 3.95
3989 4003 4.735132 CGAGCTTCGGACCGCCAA 62.735 66.667 9.66 0.00 36.00 4.52
4217 4236 2.435805 AGAAGTTTGAGTCAGTGCTCCA 59.564 45.455 10.72 0.00 34.74 3.86


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

AutoCloner maintained by Alex Coulton.