Multiple sequence alignment - TraesCS2B01G321600

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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 TraesCS2B01G321600 chr2B 100.000 2549 0 0 1 2549 458656855 458659403 0 4708
1 TraesCS2B01G321600 chr2B 95.787 1994 77 6 560 2549 692955888 692957878 0 3210
2 TraesCS2B01G321600 chr2B 95.652 2001 76 7 559 2549 492636653 492638652 0 3203
3 TraesCS2B01G321600 chr4A 94.308 2565 126 14 1 2549 705529831 705527271 0 3910
4 TraesCS2B01G321600 chr1B 96.084 1992 70 5 565 2549 581717565 581715575 0 3240
5 TraesCS2B01G321600 chr1B 95.968 1984 73 6 569 2549 520844119 520842140 0 3214
6 TraesCS2B01G321600 chr7B 95.890 1995 75 6 561 2549 720989200 720987207 0 3223
7 TraesCS2B01G321600 chr7B 95.875 1988 74 7 568 2549 602142436 602144421 0 3210
8 TraesCS2B01G321600 chr3B 95.676 1989 80 5 566 2549 108092315 108090328 0 3192
9 TraesCS2B01G321600 chr5B 95.543 1997 81 6 559 2549 497276154 497278148 0 3188
10 TraesCS2B01G321600 chr4B 93.194 573 33 3 1 568 271012557 271011986 0 837
11 TraesCS2B01G321600 chr4B 92.832 572 35 4 1 566 372025636 372025065 0 824
12 TraesCS2B01G321600 chr4B 92.535 576 35 4 1 568 235101346 235100771 0 819
13 TraesCS2B01G321600 chr3D 92.832 572 37 2 1 568 508656402 508655831 0 826
14 TraesCS2B01G321600 chr3D 92.619 569 38 3 1 566 169686580 169687147 0 815
15 TraesCS2B01G321600 chr6B 92.933 566 37 3 1 566 558238823 558239385 0 821
16 TraesCS2B01G321600 chr6B 92.696 575 31 6 1 568 35472927 35473497 0 819
17 TraesCS2B01G321600 chr2D 92.535 576 35 3 1 568 172938059 172937484 0 819


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 TraesCS2B01G321600 chr2B 458656855 458659403 2548 False 4708 4708 100.000 1 2549 1 chr2B.!!$F1 2548
1 TraesCS2B01G321600 chr2B 692955888 692957878 1990 False 3210 3210 95.787 560 2549 1 chr2B.!!$F3 1989
2 TraesCS2B01G321600 chr2B 492636653 492638652 1999 False 3203 3203 95.652 559 2549 1 chr2B.!!$F2 1990
3 TraesCS2B01G321600 chr4A 705527271 705529831 2560 True 3910 3910 94.308 1 2549 1 chr4A.!!$R1 2548
4 TraesCS2B01G321600 chr1B 581715575 581717565 1990 True 3240 3240 96.084 565 2549 1 chr1B.!!$R2 1984
5 TraesCS2B01G321600 chr1B 520842140 520844119 1979 True 3214 3214 95.968 569 2549 1 chr1B.!!$R1 1980
6 TraesCS2B01G321600 chr7B 720987207 720989200 1993 True 3223 3223 95.890 561 2549 1 chr7B.!!$R1 1988
7 TraesCS2B01G321600 chr7B 602142436 602144421 1985 False 3210 3210 95.875 568 2549 1 chr7B.!!$F1 1981
8 TraesCS2B01G321600 chr3B 108090328 108092315 1987 True 3192 3192 95.676 566 2549 1 chr3B.!!$R1 1983
9 TraesCS2B01G321600 chr5B 497276154 497278148 1994 False 3188 3188 95.543 559 2549 1 chr5B.!!$F1 1990
10 TraesCS2B01G321600 chr4B 271011986 271012557 571 True 837 837 93.194 1 568 1 chr4B.!!$R2 567
11 TraesCS2B01G321600 chr4B 372025065 372025636 571 True 824 824 92.832 1 566 1 chr4B.!!$R3 565
12 TraesCS2B01G321600 chr4B 235100771 235101346 575 True 819 819 92.535 1 568 1 chr4B.!!$R1 567
13 TraesCS2B01G321600 chr3D 508655831 508656402 571 True 826 826 92.832 1 568 1 chr3D.!!$R1 567
14 TraesCS2B01G321600 chr3D 169686580 169687147 567 False 815 815 92.619 1 566 1 chr3D.!!$F1 565
15 TraesCS2B01G321600 chr6B 558238823 558239385 562 False 821 821 92.933 1 566 1 chr6B.!!$F2 565
16 TraesCS2B01G321600 chr6B 35472927 35473497 570 False 819 819 92.696 1 568 1 chr6B.!!$F1 567
17 TraesCS2B01G321600 chr2D 172937484 172938059 575 True 819 819 92.535 1 568 1 chr2D.!!$R1 567

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
826 842 0.104304 ATAGATCCGTTGCGGGTGTC 59.896 55.0 7.76 4.47 42.08 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2012 0.318762 GCAGTCTTGGGTTCGAGTCT 59.681 55.0 0.0 0.0 0.0 3.24 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
342 343 5.801720 ATAATTGGGGATGAGCATATCCA 57.198 39.130 17.73 1.35 46.89 3.41
413 414 5.682943 TCGGAATGAGTTTGTTAACAAGG 57.317 39.130 19.72 4.32 37.15 3.61
449 450 8.313292 CCTTGTTAATGGATTCCTTTTGATGAA 58.687 33.333 8.94 0.00 0.00 2.57
458 459 8.054572 TGGATTCCTTTTGATGAACATGAGATA 58.945 33.333 0.00 0.00 0.00 1.98
488 489 6.534634 AGTTAGAAAGCACAACCTTCTGTAT 58.465 36.000 0.00 0.00 0.00 2.29
655 669 1.351017 CTCAGTTTTGCCCCTAGTCCA 59.649 52.381 0.00 0.00 0.00 4.02
812 826 3.243367 GCAGAGAGTCGTTGAGCATAGAT 60.243 47.826 1.67 0.00 0.00 1.98
826 842 0.104304 ATAGATCCGTTGCGGGTGTC 59.896 55.000 7.76 4.47 42.08 3.67
1012 1030 0.809241 GAGCTCCATGTCTTCCGCAG 60.809 60.000 0.87 0.00 0.00 5.18
1212 1230 0.536460 GGTCGGGGTCTTTGAGCAAA 60.536 55.000 0.00 0.00 0.00 3.68
1879 1903 5.163364 CCTCAGCTCTGGTAGATGTTTACAT 60.163 44.000 0.00 0.00 42.45 2.29
1986 2012 2.435418 AAAAATTGGTGCGGCTGGA 58.565 47.368 0.00 0.00 0.00 3.86
2003 2029 1.258676 GGAGACTCGAACCCAAGACT 58.741 55.000 0.00 0.00 0.00 3.24
2006 2032 0.033504 GACTCGAACCCAAGACTGCA 59.966 55.000 0.00 0.00 0.00 4.41
2163 2191 3.640407 GGTGCAGCTGGGGACTCA 61.640 66.667 17.12 0.00 0.00 3.41
2319 2350 0.316937 CGTGAATGTTTGCACACGCT 60.317 50.000 11.57 0.00 46.38 5.07
2349 2380 3.373748 GGTTTTCCTTTGTTTTGCACTGG 59.626 43.478 0.00 0.00 36.94 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.603707 ACAACAGGCACATCCTCACG 60.604 55.000 0.00 0.00 45.52 4.35
59 60 9.542462 CTCGGGAATATCAAGAATAACAAAGTA 57.458 33.333 0.00 0.00 0.00 2.24
106 107 6.715264 CAGTATTCAAAAAGGGTCTACCAAGT 59.285 38.462 0.81 0.00 43.89 3.16
166 167 9.237187 TGCTCATTACCATTAACATGAAAAGTA 57.763 29.630 0.00 0.00 31.07 2.24
322 323 4.202749 ACATGGATATGCTCATCCCCAATT 60.203 41.667 12.79 0.00 43.43 2.32
342 343 7.039882 CGAATAACACTAGGTTACCTCAACAT 58.960 38.462 7.39 0.00 44.36 2.71
413 414 5.643379 TCCATTAACAAGGTTGATCAAGC 57.357 39.130 26.43 26.43 38.96 4.01
449 450 8.481314 TGCTTTCTAACTTCATCTATCTCATGT 58.519 33.333 0.00 0.00 0.00 3.21
458 459 5.625150 AGGTTGTGCTTTCTAACTTCATCT 58.375 37.500 0.00 0.00 0.00 2.90
655 669 1.010935 CAGAACGAGTCAGTGCGCAT 61.011 55.000 15.91 0.00 0.00 4.73
826 842 1.736032 GCTGTCGCCCGCTAATATAGG 60.736 57.143 0.00 0.00 0.00 2.57
850 868 2.910479 TCTGTCGCCGTGGTCACT 60.910 61.111 0.00 0.00 0.00 3.41
889 907 1.237954 TGTCGTGCTCTCGCTCTCTT 61.238 55.000 0.00 0.00 36.97 2.85
908 926 0.838122 ACAGCTAGCTTCCCACCACT 60.838 55.000 16.46 0.00 0.00 4.00
1049 1067 0.532573 GAAGACAGGCATCTCCACGA 59.467 55.000 0.00 0.00 37.29 4.35
1050 1068 0.803768 CGAAGACAGGCATCTCCACG 60.804 60.000 0.00 0.00 37.29 4.94
1986 2012 0.318762 GCAGTCTTGGGTTCGAGTCT 59.681 55.000 0.00 0.00 0.00 3.24
2003 2029 2.373335 AAACACCACTAACCCATGCA 57.627 45.000 0.00 0.00 0.00 3.96
2006 2032 3.075432 AGCCTTAAACACCACTAACCCAT 59.925 43.478 0.00 0.00 0.00 4.00
2151 2179 1.774217 TGGGTTTGAGTCCCCAGCT 60.774 57.895 1.71 0.00 46.06 4.24
2163 2191 2.406002 ATCCACGCGGTCTTGGGTTT 62.406 55.000 12.47 0.00 32.85 3.27
2319 2350 5.993748 AAACAAAGGAAAACCACTCTCAA 57.006 34.783 0.00 0.00 0.00 3.02
2349 2380 3.239449 ACCTTCCAACCCTCCAAAATTC 58.761 45.455 0.00 0.00 0.00 2.17
2511 2544 2.701551 TCAAAAGAGGGGGTGAGAAGA 58.298 47.619 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.