Multiple sequence alignment - TraesCS6D01G312400

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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 TraesCS6D01G312400 chr6D 100.000 2926 0 0 1 2926 421688293 421691218 0.000000e+00 5404.0
1 TraesCS6D01G312400 chr6D 97.294 1922 34 3 1 1922 421678954 421680857 0.000000e+00 3245.0
2 TraesCS6D01G312400 chr6D 98.625 1673 21 2 250 1922 421661214 421662884 0.000000e+00 2961.0
3 TraesCS6D01G312400 chr6D 91.618 1384 80 17 562 1922 421468282 421466912 0.000000e+00 1881.0
4 TraesCS6D01G312400 chr6D 92.006 1301 58 19 635 1922 420970525 420969258 0.000000e+00 1784.0
5 TraesCS6D01G312400 chr6D 90.179 1395 82 19 541 1913 422215061 422216422 0.000000e+00 1766.0
6 TraesCS6D01G312400 chr6D 95.870 1017 31 1 1921 2926 451921418 451920402 0.000000e+00 1635.0
7 TraesCS6D01G312400 chr6D 95.495 1021 34 2 1918 2926 457133220 457132200 0.000000e+00 1620.0
8 TraesCS6D01G312400 chr6D 90.523 1129 69 18 802 1913 422601248 422602355 0.000000e+00 1458.0
9 TraesCS6D01G312400 chr6D 92.180 601 29 10 124 719 422600537 422601124 0.000000e+00 833.0
10 TraesCS6D01G312400 chr6D 92.602 392 15 6 124 515 422214687 422215064 4.260000e-153 551.0
11 TraesCS6D01G312400 chr6D 96.063 254 2 1 1 254 421651982 421652227 9.760000e-110 407.0
12 TraesCS6D01G312400 chr6D 86.400 250 14 7 124 368 420971298 420971064 3.740000e-64 255.0
13 TraesCS6D01G312400 chr6D 93.701 127 8 0 1 127 422214507 422214633 1.070000e-44 191.0
14 TraesCS6D01G312400 chr6D 98.333 60 1 0 71 130 420971408 420971349 3.990000e-19 106.0
15 TraesCS6D01G312400 chr6A 91.289 1458 87 19 502 1922 564279239 564277785 0.000000e+00 1953.0
16 TraesCS6D01G312400 chr6A 86.989 1468 99 42 478 1913 565340013 565341420 0.000000e+00 1568.0
17 TraesCS6D01G312400 chr6A 89.459 370 26 6 124 493 565317445 565317801 3.440000e-124 455.0
18 TraesCS6D01G312400 chr6A 90.041 241 16 3 124 364 564279508 564279276 3.660000e-79 305.0
19 TraesCS6D01G312400 chr6A 95.420 131 5 1 1 130 564279700 564279570 1.060000e-49 207.0
20 TraesCS6D01G312400 chr6A 90.000 130 10 1 1 127 565317262 565317391 6.490000e-37 165.0
21 TraesCS6D01G312400 chr6B 89.915 1418 91 22 552 1922 634504304 634502892 0.000000e+00 1779.0
22 TraesCS6D01G312400 chr6B 90.531 1035 76 13 901 1932 636746185 636747200 0.000000e+00 1349.0
23 TraesCS6D01G312400 chr6B 90.496 242 12 6 124 365 636744106 636744336 2.830000e-80 309.0
24 TraesCS6D01G312400 chr6B 93.846 130 8 0 1 130 634560412 634560283 2.300000e-46 196.0
25 TraesCS6D01G312400 chr6B 91.473 129 8 1 1 126 636743923 636744051 1.080000e-39 174.0
26 TraesCS6D01G312400 chr6B 84.971 173 11 6 536 693 636744349 636744521 8.390000e-36 161.0
27 TraesCS6D01G312400 chr6B 84.783 92 8 2 483 569 634559733 634559643 1.440000e-13 87.9
28 TraesCS6D01G312400 chr3D 95.870 1017 30 3 1922 2926 112953494 112952478 0.000000e+00 1635.0
29 TraesCS6D01G312400 chr3D 95.020 1024 32 2 1922 2926 553355257 553354234 0.000000e+00 1591.0
30 TraesCS6D01G312400 chr2D 95.686 1020 33 1 1918 2926 577796109 577795090 0.000000e+00 1629.0
31 TraesCS6D01G312400 chr5D 95.571 1016 34 1 1922 2926 54737015 54738030 0.000000e+00 1616.0
32 TraesCS6D01G312400 chr5D 95.383 1018 35 2 1921 2926 395707192 395708209 0.000000e+00 1609.0
33 TraesCS6D01G312400 chr5D 95.285 1018 37 1 1920 2926 225855572 225856589 0.000000e+00 1604.0
34 TraesCS6D01G312400 chr5D 94.907 1021 36 6 1921 2926 507852598 507851579 0.000000e+00 1583.0
35 TraesCS6D01G312400 chr5D 93.916 1019 48 4 1918 2925 531458581 531457566 0.000000e+00 1526.0
36 TraesCS6D01G312400 chr7D 95.477 1017 32 4 1921 2925 242799627 242798613 0.000000e+00 1611.0
37 TraesCS6D01G312400 chr1D 95.472 1016 34 2 1921 2925 303224912 303225926 0.000000e+00 1611.0
38 TraesCS6D01G312400 chr1D 95.379 1017 35 2 1921 2926 31038427 31037412 0.000000e+00 1607.0
39 TraesCS6D01G312400 chr1D 95.369 1015 36 1 1922 2925 4216720 4215706 0.000000e+00 1604.0
40 TraesCS6D01G312400 chr1D 95.280 1017 36 2 1922 2926 455030362 455029346 0.000000e+00 1602.0
41 TraesCS6D01G312400 chr1D 94.395 1017 36 2 1921 2926 361169104 361168098 0.000000e+00 1543.0
42 TraesCS6D01G312400 chr1D 92.727 275 9 1 1919 2182 492579225 492579499 1.270000e-103 387.0
43 TraesCS6D01G312400 chr3B 84.818 494 61 8 1427 1913 70875183 70875669 4.380000e-133 484.0


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 TraesCS6D01G312400 chr6D 421688293 421691218 2925 False 5404.000000 5404 100.000000 1 2926 1 chr6D.!!$F4 2925
1 TraesCS6D01G312400 chr6D 421678954 421680857 1903 False 3245.000000 3245 97.294000 1 1922 1 chr6D.!!$F3 1921
2 TraesCS6D01G312400 chr6D 421661214 421662884 1670 False 2961.000000 2961 98.625000 250 1922 1 chr6D.!!$F2 1672
3 TraesCS6D01G312400 chr6D 421466912 421468282 1370 True 1881.000000 1881 91.618000 562 1922 1 chr6D.!!$R1 1360
4 TraesCS6D01G312400 chr6D 451920402 451921418 1016 True 1635.000000 1635 95.870000 1921 2926 1 chr6D.!!$R2 1005
5 TraesCS6D01G312400 chr6D 457132200 457133220 1020 True 1620.000000 1620 95.495000 1918 2926 1 chr6D.!!$R3 1008
6 TraesCS6D01G312400 chr6D 422600537 422602355 1818 False 1145.500000 1458 91.351500 124 1913 2 chr6D.!!$F6 1789
7 TraesCS6D01G312400 chr6D 422214507 422216422 1915 False 836.000000 1766 92.160667 1 1913 3 chr6D.!!$F5 1912
8 TraesCS6D01G312400 chr6D 420969258 420971408 2150 True 715.000000 1784 92.246333 71 1922 3 chr6D.!!$R4 1851
9 TraesCS6D01G312400 chr6A 565340013 565341420 1407 False 1568.000000 1568 86.989000 478 1913 1 chr6A.!!$F1 1435
10 TraesCS6D01G312400 chr6A 564277785 564279700 1915 True 821.666667 1953 92.250000 1 1922 3 chr6A.!!$R1 1921
11 TraesCS6D01G312400 chr6A 565317262 565317801 539 False 310.000000 455 89.729500 1 493 2 chr6A.!!$F2 492
12 TraesCS6D01G312400 chr6B 634502892 634504304 1412 True 1779.000000 1779 89.915000 552 1922 1 chr6B.!!$R1 1370
13 TraesCS6D01G312400 chr6B 636743923 636747200 3277 False 498.250000 1349 89.367750 1 1932 4 chr6B.!!$F1 1931
14 TraesCS6D01G312400 chr3D 112952478 112953494 1016 True 1635.000000 1635 95.870000 1922 2926 1 chr3D.!!$R1 1004
15 TraesCS6D01G312400 chr3D 553354234 553355257 1023 True 1591.000000 1591 95.020000 1922 2926 1 chr3D.!!$R2 1004
16 TraesCS6D01G312400 chr2D 577795090 577796109 1019 True 1629.000000 1629 95.686000 1918 2926 1 chr2D.!!$R1 1008
17 TraesCS6D01G312400 chr5D 54737015 54738030 1015 False 1616.000000 1616 95.571000 1922 2926 1 chr5D.!!$F1 1004
18 TraesCS6D01G312400 chr5D 395707192 395708209 1017 False 1609.000000 1609 95.383000 1921 2926 1 chr5D.!!$F3 1005
19 TraesCS6D01G312400 chr5D 225855572 225856589 1017 False 1604.000000 1604 95.285000 1920 2926 1 chr5D.!!$F2 1006
20 TraesCS6D01G312400 chr5D 507851579 507852598 1019 True 1583.000000 1583 94.907000 1921 2926 1 chr5D.!!$R1 1005
21 TraesCS6D01G312400 chr5D 531457566 531458581 1015 True 1526.000000 1526 93.916000 1918 2925 1 chr5D.!!$R2 1007
22 TraesCS6D01G312400 chr7D 242798613 242799627 1014 True 1611.000000 1611 95.477000 1921 2925 1 chr7D.!!$R1 1004
23 TraesCS6D01G312400 chr1D 303224912 303225926 1014 False 1611.000000 1611 95.472000 1921 2925 1 chr1D.!!$F1 1004
24 TraesCS6D01G312400 chr1D 31037412 31038427 1015 True 1607.000000 1607 95.379000 1921 2926 1 chr1D.!!$R2 1005
25 TraesCS6D01G312400 chr1D 4215706 4216720 1014 True 1604.000000 1604 95.369000 1922 2925 1 chr1D.!!$R1 1003
26 TraesCS6D01G312400 chr1D 455029346 455030362 1016 True 1602.000000 1602 95.280000 1922 2926 1 chr1D.!!$R4 1004
27 TraesCS6D01G312400 chr1D 361168098 361169104 1006 True 1543.000000 1543 94.395000 1921 2926 1 chr1D.!!$R3 1005

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
231 308 1.976404 TGGATCTCCAGCTCCATGATC 59.024 52.381 0.0 6.87 42.01 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 3920 0.915364 GAGGATTGAGCCAGTTCCCT 59.085 55.0 0.0 0.0 0.0 4.2 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
231 308 1.976404 TGGATCTCCAGCTCCATGATC 59.024 52.381 0.00 6.87 42.01 2.92
1074 3031 4.015406 AAGTCACCGGCGATGGCA 62.015 61.111 9.28 0.00 42.47 4.92
1345 3317 0.679960 ATCAAGGTAACGGCAAGCCC 60.680 55.000 5.34 0.00 46.39 5.19
1803 3784 5.514279 GCAAGCACACATTATATTCTGGTC 58.486 41.667 0.00 0.00 0.00 4.02
1812 3793 8.408601 ACACATTATATTCTGGTCAATTTCTGC 58.591 33.333 0.00 0.00 0.00 4.26
1913 3894 3.393089 AGCACTACAACTCCAGAAGTG 57.607 47.619 0.00 0.00 38.58 3.16
1970 3951 0.040204 CAATCCTCAAAGGGGTGGCT 59.960 55.000 0.00 0.00 35.59 4.75
1987 3980 8.938883 AGGGGTGGCTTATCACATATATATAAG 58.061 37.037 8.49 8.49 39.27 1.73
2070 4063 4.016479 AGTCTAACACCCTCCCTCAATCTA 60.016 45.833 0.00 0.00 0.00 1.98
2112 4105 1.202698 GGAGGTTGAGATTGCGCCTAT 60.203 52.381 4.18 0.00 0.00 2.57
2176 4180 8.787852 GTTGATCTTTTGAAGAGATAAACCTGT 58.212 33.333 12.67 0.00 41.61 4.00
2443 4447 4.395583 GCTTGCGTGCACTCCAGC 62.396 66.667 16.00 16.00 0.00 4.85
2445 4449 4.560743 TTGCGTGCACTCCAGCCA 62.561 61.111 16.19 0.00 0.00 4.75
2552 4558 3.669536 CAGAAAGAACTCCAGAGGAACC 58.330 50.000 0.00 0.00 0.00 3.62
2686 4694 1.415659 CCGCAAAGGAGAGATCAGGAT 59.584 52.381 0.00 0.00 45.00 3.24
2785 4794 0.183492 AGCAGCAGAAAGGGTGTCAA 59.817 50.000 0.00 0.00 38.49 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
231 308 2.126580 GCAGCCGCAAAGCTCAAG 60.127 61.111 0.00 0.00 42.61 3.02
992 2949 3.222173 ACACAAGGACCATAACTGCAA 57.778 42.857 0.00 0.00 0.00 4.08
1074 3031 3.751698 GCTCCATACTTTCCGACAAAACT 59.248 43.478 0.00 0.00 0.00 2.66
1345 3317 2.235016 AGCAAGAGATACTAGAGGCCG 58.765 52.381 0.00 0.00 0.00 6.13
1640 3620 6.691818 CGGTAGAGCAAGGTATATATAAAGCG 59.308 42.308 0.00 0.00 0.00 4.68
1913 3894 3.865446 ACCTACGTTTTACACCCATAGC 58.135 45.455 0.00 0.00 0.00 2.97
1939 3920 0.915364 GAGGATTGAGCCAGTTCCCT 59.085 55.000 0.00 0.00 0.00 4.20
1987 3980 5.680619 TGGTATTGGACTTGTATGTCATCC 58.319 41.667 0.00 0.00 38.61 3.51
2023 4016 4.336433 TCGTATTGTAGCCCTACTGTGTAC 59.664 45.833 6.96 0.00 37.00 2.90
2070 4063 6.494952 TCCTAGATACTTCAGGAGTGAGTTT 58.505 40.000 0.00 0.00 39.48 2.66
2176 4180 4.202212 TGTTGCACAGAAGCTACTACAAGA 60.202 41.667 0.00 0.00 40.21 3.02
2267 4271 0.370273 CATCGGTGCTACGTTTCTGC 59.630 55.000 0.00 0.00 34.94 4.26
2359 4363 0.032403 GCCAATGCAACTGCTGAACA 59.968 50.000 2.95 0.00 42.66 3.18
2443 4447 4.778213 TCTTGGGTCCTAATCTGATTGG 57.222 45.455 13.01 9.81 0.00 3.16
2445 4449 5.014123 TGTGTTCTTGGGTCCTAATCTGATT 59.986 40.000 8.14 8.14 0.00 2.57
2592 4599 3.173599 TGTGAAGCGCATACTACGTTAC 58.826 45.455 11.47 0.00 0.00 2.50
2598 4605 1.476488 TCTGCTGTGAAGCGCATACTA 59.524 47.619 11.47 0.00 35.32 1.82
2686 4694 1.533965 GCAGTATCTGACGATCACGCA 60.534 52.381 0.66 0.00 36.03 5.24
2785 4794 1.410850 CCTACGCCCATGTCCTCCAT 61.411 60.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.