Multiple sequence alignment - TraesCS4D01G067900

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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 TraesCS4D01G067900 chr4D 100.000 2549 0 0 1 2549 43273334 43270786 0.000000e+00 4708
1 TraesCS4D01G067900 chr5B 95.507 1981 83 5 571 2548 680230619 680228642 0.000000e+00 3160
2 TraesCS4D01G067900 chr5B 95.008 1983 88 6 571 2549 508124525 508122550 0.000000e+00 3103
3 TraesCS4D01G067900 chr3B 95.404 1980 84 4 575 2549 548772277 548774254 0.000000e+00 3145
4 TraesCS4D01G067900 chr3B 95.043 1977 92 5 575 2549 548242939 548244911 0.000000e+00 3103
5 TraesCS4D01G067900 chr3B 89.358 592 38 3 1 568 689531760 689532350 0.000000e+00 721
6 TraesCS4D01G067900 chr3B 94.690 113 5 1 459 571 36749530 36749419 9.370000e-40 174
7 TraesCS4D01G067900 chr3B 94.595 111 5 1 461 571 37149103 37149212 1.210000e-38 171
8 TraesCS4D01G067900 chr3B 94.595 111 5 1 461 571 37209210 37209319 1.210000e-38 171
9 TraesCS4D01G067900 chr2D 94.798 1980 75 6 570 2549 632386602 632388553 0.000000e+00 3061
10 TraesCS4D01G067900 chr2D 92.789 1983 73 20 572 2549 547242743 547240826 0.000000e+00 2806
11 TraesCS4D01G067900 chr7B 94.343 1980 103 8 572 2549 523525076 523523104 0.000000e+00 3027
12 TraesCS4D01G067900 chr7B 94.296 1981 101 8 572 2549 523399854 523397883 0.000000e+00 3022
13 TraesCS4D01G067900 chr2B 94.103 1984 81 16 572 2549 1180725 1182678 0.000000e+00 2983
14 TraesCS4D01G067900 chr2B 93.074 1978 130 7 574 2549 710554482 710552510 0.000000e+00 2887
15 TraesCS4D01G067900 chr2B 93.805 113 6 1 459 571 77577537 77577426 4.360000e-38 169
16 TraesCS4D01G067900 chr5D 90.067 594 35 2 1 571 57138669 57139261 0.000000e+00 749
17 TraesCS4D01G067900 chr5D 94.659 337 18 0 1 337 472514267 472513931 8.080000e-145 523
18 TraesCS4D01G067900 chr4A 90.170 529 24 12 1 502 703529911 703530438 0.000000e+00 664
19 TraesCS4D01G067900 chr4A 93.472 337 21 1 1 337 660868371 660868036 1.360000e-137 499
20 TraesCS4D01G067900 chr4A 85.833 360 27 9 218 553 538233091 538233450 6.700000e-96 361
21 TraesCS4D01G067900 chr2A 91.969 386 31 0 1 386 574655807 574655422 2.230000e-150 542
22 TraesCS4D01G067900 chr6D 94.595 333 17 1 1 332 396942855 396943187 4.860000e-142 514
23 TraesCS4D01G067900 chr6B 93.472 337 22 0 1 337 88567851 88567515 3.790000e-138 501
24 TraesCS4D01G067900 chr6B 93.491 338 21 1 1 337 592967401 592967738 3.790000e-138 501
25 TraesCS4D01G067900 chr1B 95.575 113 4 1 459 571 89965104 89965215 2.010000e-41 180
26 TraesCS4D01G067900 chr1B 95.575 113 4 1 459 571 286599316 286599205 2.010000e-41 180


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 TraesCS4D01G067900 chr4D 43270786 43273334 2548 True 4708 4708 100.000 1 2549 1 chr4D.!!$R1 2548
1 TraesCS4D01G067900 chr5B 680228642 680230619 1977 True 3160 3160 95.507 571 2548 1 chr5B.!!$R2 1977
2 TraesCS4D01G067900 chr5B 508122550 508124525 1975 True 3103 3103 95.008 571 2549 1 chr5B.!!$R1 1978
3 TraesCS4D01G067900 chr3B 548772277 548774254 1977 False 3145 3145 95.404 575 2549 1 chr3B.!!$F4 1974
4 TraesCS4D01G067900 chr3B 548242939 548244911 1972 False 3103 3103 95.043 575 2549 1 chr3B.!!$F3 1974
5 TraesCS4D01G067900 chr3B 689531760 689532350 590 False 721 721 89.358 1 568 1 chr3B.!!$F5 567
6 TraesCS4D01G067900 chr2D 632386602 632388553 1951 False 3061 3061 94.798 570 2549 1 chr2D.!!$F1 1979
7 TraesCS4D01G067900 chr2D 547240826 547242743 1917 True 2806 2806 92.789 572 2549 1 chr2D.!!$R1 1977
8 TraesCS4D01G067900 chr7B 523523104 523525076 1972 True 3027 3027 94.343 572 2549 1 chr7B.!!$R2 1977
9 TraesCS4D01G067900 chr7B 523397883 523399854 1971 True 3022 3022 94.296 572 2549 1 chr7B.!!$R1 1977
10 TraesCS4D01G067900 chr2B 1180725 1182678 1953 False 2983 2983 94.103 572 2549 1 chr2B.!!$F1 1977
11 TraesCS4D01G067900 chr2B 710552510 710554482 1972 True 2887 2887 93.074 574 2549 1 chr2B.!!$R2 1975
12 TraesCS4D01G067900 chr5D 57138669 57139261 592 False 749 749 90.067 1 571 1 chr5D.!!$F1 570
13 TraesCS4D01G067900 chr4A 703529911 703530438 527 False 664 664 90.170 1 502 1 chr4A.!!$F2 501

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
482 511 0.175531 GGGTGCTTGTTGTGCAACTT 59.824 50.0 14.97 0.0 46.36 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 2302 1.06825 GCCATCTGTCCTAGCGGTC 59.932 63.158 0.0 0.0 0.0 4.79 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
57 58 4.190772 CAAGGCAAAAATGTTGGTGAAGT 58.809 39.130 0.00 0.00 0.00 3.01
132 133 2.680841 CTGGTGAACAAACCTTCGTTGA 59.319 45.455 0.00 0.00 41.16 3.18
179 180 3.181496 GCATTTCTCCGGATGAAAAGGAC 60.181 47.826 23.72 14.20 37.05 3.85
214 215 9.102757 CATCTTGTATAACTGCAACTTGACTAT 57.897 33.333 0.00 0.00 0.00 2.12
240 241 6.672657 AGGTGTGTTTCTATATCCCTTACAGT 59.327 38.462 0.00 0.00 0.00 3.55
258 259 9.198475 CCTTACAGTATTAAGTTTCCCTCTAGA 57.802 37.037 0.00 0.00 0.00 2.43
292 293 4.040584 TGCAACTGTTATGGTACTGGTGTA 59.959 41.667 0.00 0.00 37.11 2.90
337 339 4.398319 CAACTAGTGTCCAACTTCCCATT 58.602 43.478 0.00 0.00 40.56 3.16
338 340 4.724279 ACTAGTGTCCAACTTCCCATTT 57.276 40.909 0.00 0.00 40.56 2.32
360 362 1.327303 GGCACCAGGTTTTGATGTGA 58.673 50.000 0.00 0.00 0.00 3.58
463 492 2.297701 AGGTTAGTGTGCAACCACTTG 58.702 47.619 14.44 0.00 46.60 3.16
482 511 0.175531 GGGTGCTTGTTGTGCAACTT 59.824 50.000 14.97 0.00 46.36 2.66
559 588 1.842381 AAGGTGCAGCTAGGTGTCCC 61.842 60.000 20.51 20.19 0.00 4.46
618 647 4.578928 GTGGTGTCCATGTACTCAGTTTTT 59.421 41.667 0.00 0.00 35.28 1.94
736 765 1.785353 GCCCTTACAGGTGGGACCAA 61.785 60.000 1.75 0.00 46.15 3.67
793 822 2.197324 GTGGCTTGTGGGACCCAA 59.803 61.111 16.98 0.00 34.18 4.12
869 898 4.953868 CGGTGACCACGGCGACAA 62.954 66.667 16.62 0.00 0.00 3.18
1394 1431 4.347453 GGGCAAAGCACGCACTGG 62.347 66.667 0.00 0.00 0.00 4.00
1558 1596 5.128033 TGGAAAGGCATGAATTATGGAGA 57.872 39.130 0.00 0.00 37.26 3.71
1579 1617 9.206870 TGGAGAAATTTGTAATCTTGAAATTGC 57.793 29.630 0.00 0.00 31.31 3.56
1631 1669 8.833231 TGGTCAAAGTTGTTTAAATGTTGAAA 57.167 26.923 0.00 0.00 0.00 2.69
1658 1700 7.410120 AAAGAGAAGAAGTGACCAACATTTT 57.590 32.000 0.00 0.00 0.00 1.82
2201 2269 1.911766 GGACTCGAACCCAGGACCA 60.912 63.158 0.00 0.00 0.00 4.02
2234 2302 2.359850 TTTAGGGCTGCGCTGGTG 60.360 61.111 27.01 1.29 0.00 4.17
2271 2340 3.356290 GGCAAGACTTTGACATGGGTAT 58.644 45.455 0.00 0.00 42.21 2.73
2297 2366 6.015265 GGAAGGAAGGTATACATAGTGAGACC 60.015 46.154 5.01 0.00 0.00 3.85
2344 2418 3.525059 CGTGAATGTTTGCACACGT 57.475 47.368 14.91 4.56 46.75 4.49
2515 2591 7.878477 AATTTGCATGTTAGTTCATGACTTG 57.122 32.000 10.28 0.00 45.41 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.625315 CTCCCATCGCCCATCTATCAA 59.375 52.381 0.00 0.00 0.00 2.57
132 133 3.591527 TGGTGGGATCTCAAGTATTTGGT 59.408 43.478 0.00 0.00 34.97 3.67
179 180 5.003778 GCAGTTATACAAGATGCGCAAAAAG 59.996 40.000 17.11 8.05 0.00 2.27
214 215 7.842743 ACTGTAAGGGATATAGAAACACACCTA 59.157 37.037 0.00 0.00 39.30 3.08
240 241 7.186972 TGGACTGTCTAGAGGGAAACTTAATA 58.813 38.462 7.85 0.00 0.00 0.98
292 293 5.530915 TGCACACTTAAGACATTTTAGCTGT 59.469 36.000 10.09 0.00 0.00 4.40
295 296 6.438763 AGTTGCACACTTAAGACATTTTAGC 58.561 36.000 10.09 2.51 27.32 3.09
337 339 1.415659 CATCAAAACCTGGTGCCCAAA 59.584 47.619 0.00 0.00 30.80 3.28
338 340 1.047002 CATCAAAACCTGGTGCCCAA 58.953 50.000 0.00 0.00 30.80 4.12
463 492 0.175531 AAGTTGCACAACAAGCACCC 59.824 50.000 15.40 0.00 42.54 4.61
482 511 4.085357 AGTTGCACAGTGAAGGTAATCA 57.915 40.909 4.15 0.00 0.00 2.57
559 588 6.324770 AGGATAATTAACCCTTGCAGGAAATG 59.675 38.462 8.09 0.00 37.67 2.32
618 647 2.013563 GCACAATTCGCATCTGAGGGA 61.014 52.381 0.00 0.00 0.00 4.20
671 700 1.300620 CGGCAGAGTTCACGGAACA 60.301 57.895 15.94 0.00 44.11 3.18
736 765 2.172483 AATTGGTCGTCTCTGCCGCT 62.172 55.000 0.00 0.00 0.00 5.52
793 822 1.181741 TCTGCTCAACGGCTCTCTGT 61.182 55.000 0.00 0.00 0.00 3.41
869 898 2.045926 GGTCACCGCCATGCTCTT 60.046 61.111 0.00 0.00 0.00 2.85
1394 1431 1.925229 CTCAACAGCTAGCTCTCTGC 58.075 55.000 16.15 4.35 43.29 4.26
1889 1934 7.359514 GCTTCCACAAAAAGTTTCAGCATTATC 60.360 37.037 0.00 0.00 0.00 1.75
2201 2269 2.424246 CCTAAACACCACAAAACCACGT 59.576 45.455 0.00 0.00 0.00 4.49
2207 2275 1.410882 GCAGCCCTAAACACCACAAAA 59.589 47.619 0.00 0.00 0.00 2.44
2234 2302 1.068250 GCCATCTGTCCTAGCGGTC 59.932 63.158 0.00 0.00 0.00 4.79
2271 2340 6.550108 GTCTCACTATGTATACCTTCCTTCCA 59.450 42.308 0.00 0.00 0.00 3.53
2318 2392 1.069227 GCAAACATTCACGGTCTCACC 60.069 52.381 0.00 0.00 34.05 4.02
2344 2418 3.963129 ACAAAGGAAAACCACTCTCACA 58.037 40.909 0.00 0.00 0.00 3.58
2522 2600 4.565652 GGTGAGAAGCCCTCTGTTTCATTA 60.566 45.833 5.47 0.00 42.44 1.90


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

AutoCloner maintained by Alex Coulton.