Multiple sequence alignment - TraesCS6B01G272600

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 TraesCS6B01G272600 chr6B 100.000 2549 0 0 1 2549 492180026 492182574 0 4708
1 TraesCS6B01G272600 chr5B 99.040 1979 15 4 573 2549 158571212 158569236 0 3546
2 TraesCS6B01G272600 chr2B 98.940 1982 16 2 573 2549 776222962 776224943 0 3539
3 TraesCS6B01G272600 chr2B 98.892 1985 17 2 570 2549 781094238 781096222 0 3539
4 TraesCS6B01G272600 chr3A 98.745 1992 20 3 563 2549 54951907 54953898 0 3535
5 TraesCS6B01G272600 chrUn 98.694 1991 21 4 563 2549 175762104 175764093 0 3528
6 TraesCS6B01G272600 chrUn 98.790 1983 20 4 570 2549 231572788 231574769 0 3526
7 TraesCS6B01G272600 chr3B 98.839 1981 19 2 573 2549 702857654 702855674 0 3528
8 TraesCS6B01G272600 chr7B 98.646 1994 19 5 562 2549 202776903 202778894 0 3526
9 TraesCS6B01G272600 chr6A 98.645 1993 19 4 563 2549 616131287 616133277 0 3524
10 TraesCS6B01G272600 chr6A 90.219 593 29 8 1 572 467041285 467041869 0 747
11 TraesCS6B01G272600 chr6D 93.750 576 27 3 1 572 328327360 328327930 0 856


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 TraesCS6B01G272600 chr6B 492180026 492182574 2548 False 4708 4708 100.000 1 2549 1 chr6B.!!$F1 2548
1 TraesCS6B01G272600 chr5B 158569236 158571212 1976 True 3546 3546 99.040 573 2549 1 chr5B.!!$R1 1976
2 TraesCS6B01G272600 chr2B 776222962 776224943 1981 False 3539 3539 98.940 573 2549 1 chr2B.!!$F1 1976
3 TraesCS6B01G272600 chr2B 781094238 781096222 1984 False 3539 3539 98.892 570 2549 1 chr2B.!!$F2 1979
4 TraesCS6B01G272600 chr3A 54951907 54953898 1991 False 3535 3535 98.745 563 2549 1 chr3A.!!$F1 1986
5 TraesCS6B01G272600 chrUn 175762104 175764093 1989 False 3528 3528 98.694 563 2549 1 chrUn.!!$F1 1986
6 TraesCS6B01G272600 chrUn 231572788 231574769 1981 False 3526 3526 98.790 570 2549 1 chrUn.!!$F2 1979
7 TraesCS6B01G272600 chr3B 702855674 702857654 1980 True 3528 3528 98.839 573 2549 1 chr3B.!!$R1 1976
8 TraesCS6B01G272600 chr7B 202776903 202778894 1991 False 3526 3526 98.646 562 2549 1 chr7B.!!$F1 1987
9 TraesCS6B01G272600 chr6A 616131287 616133277 1990 False 3524 3524 98.645 563 2549 1 chr6A.!!$F2 1986
10 TraesCS6B01G272600 chr6A 467041285 467041869 584 False 747 747 90.219 1 572 1 chr6A.!!$F1 571
11 TraesCS6B01G272600 chr6D 328327360 328327930 570 False 856 856 93.750 1 572 1 chr6D.!!$F1 571

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
39 40 0.175073 GTGTCGTGTAAGGCTAGGGG 59.825 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1778 1.344114 GAATTTGGCCCAAGAGCAACA 59.656 47.619 0.0 0.0 0.0 3.33 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
35 36 3.192001 AGATTTCGTGTCGTGTAAGGCTA 59.808 43.478 0.00 0.0 0.00 3.93
37 38 0.806868 TCGTGTCGTGTAAGGCTAGG 59.193 55.000 0.00 0.0 0.00 3.02
39 40 0.175073 GTGTCGTGTAAGGCTAGGGG 59.825 60.000 0.00 0.0 0.00 4.79
97 98 4.336433 ACAGTACATGACCAAATATGCAGC 59.664 41.667 0.00 0.0 0.00 5.25
152 156 3.084039 ACAAACATAGATGGGCACAGTG 58.916 45.455 0.00 0.0 0.00 3.66
240 247 1.531149 CGCTGGCTAAATCAATACCCG 59.469 52.381 0.00 0.0 0.00 5.28
280 287 3.713650 ACCATCACCCGGTCTCAG 58.286 61.111 0.00 0.0 27.30 3.35
374 391 1.366854 GGGACCGCCATTTCTTCGAC 61.367 60.000 0.00 0.0 35.15 4.20
479 501 4.616953 TCGGCAAAACATTTTCTCTTTCC 58.383 39.130 0.00 0.0 0.00 3.13
516 538 4.096231 TGAACGCTTTGCACATTATAGCAT 59.904 37.500 0.00 0.0 40.94 3.79
517 539 4.637483 ACGCTTTGCACATTATAGCATT 57.363 36.364 0.00 0.0 40.94 3.56
551 573 1.218196 TCCCCCAAACTTTTGCCTACA 59.782 47.619 0.00 0.0 36.86 2.74
552 574 1.618343 CCCCCAAACTTTTGCCTACAG 59.382 52.381 0.00 0.0 36.86 2.74
553 575 2.316108 CCCCAAACTTTTGCCTACAGT 58.684 47.619 0.00 0.0 36.86 3.55
554 576 2.035832 CCCCAAACTTTTGCCTACAGTG 59.964 50.000 0.00 0.0 36.86 3.66
555 577 2.545742 CCCAAACTTTTGCCTACAGTGC 60.546 50.000 0.00 0.0 36.86 4.40
592 614 6.728632 TCTTTGGGTTAATTATCCTTTTGCCT 59.271 34.615 11.51 0.0 0.00 4.75
638 660 0.659957 GCCCTCAGATGCGAATTGTC 59.340 55.000 0.00 0.0 0.00 3.18
791 813 4.988598 CGCGTGGCTTGTGGGACT 62.989 66.667 0.00 0.0 0.00 3.85
1469 1493 6.299805 TGAAGATCAAGCACTACCAATACT 57.700 37.500 0.00 0.0 0.00 2.12
2201 2228 1.065109 GCGTGGGTTTGTGGTGTTC 59.935 57.895 0.00 0.0 0.00 3.18
2210 2237 0.840617 TTGTGGTGTTCAGGGCTACA 59.159 50.000 0.00 0.0 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.787280 CCTGGAGGAGTCGCCCCT 62.787 72.222 0.00 0.00 37.37 4.79
37 38 1.262640 TTTACCTGGAGGAGTCGCCC 61.263 60.000 0.00 0.00 38.94 6.13
39 40 0.460459 GCTTTACCTGGAGGAGTCGC 60.460 60.000 0.00 0.00 38.94 5.19
129 133 4.883585 CACTGTGCCCATCTATGTTTGTAT 59.116 41.667 0.00 0.00 0.00 2.29
152 156 0.179081 CCGGCCTAGCAAGTTCCTAC 60.179 60.000 0.00 0.00 0.00 3.18
177 181 2.860735 CCTCTACTACATGCAAAGTCGC 59.139 50.000 0.00 0.00 0.00 5.19
240 247 0.108138 ACTCCTACATGCAAGTCGGC 60.108 55.000 7.71 0.00 0.00 5.54
280 287 4.404715 TCTTTCTGTATGTAGGGTACAGGC 59.595 45.833 11.94 0.00 45.70 4.85
374 391 1.206849 GCAGAACCAAGAGAGAGGAGG 59.793 57.143 0.00 0.00 0.00 4.30
479 501 2.808543 AGCGTTCAGGCTGTTTTCTAAG 59.191 45.455 15.27 0.39 42.86 2.18
516 538 6.045577 AGTTTGGGGGATTAGAGAGAAAAGAA 59.954 38.462 0.00 0.00 0.00 2.52
517 539 5.551977 AGTTTGGGGGATTAGAGAGAAAAGA 59.448 40.000 0.00 0.00 0.00 2.52
530 552 2.158234 TGTAGGCAAAAGTTTGGGGGAT 60.158 45.455 5.95 0.00 38.57 3.85
592 614 0.473755 AGCACATGGACACCACTGAA 59.526 50.000 0.00 0.00 35.80 3.02
638 660 1.340114 GGACTAGGGGCAAAACTGAGG 60.340 57.143 0.00 0.00 0.00 3.86
1087 1111 2.125673 CCTTCGATCAACGCCCGT 60.126 61.111 0.00 0.00 42.26 5.28
1469 1493 4.965814 TGCCCAAAAGTATTTGCAAATGA 58.034 34.783 30.43 14.27 43.73 2.57
1752 1778 1.344114 GAATTTGGCCCAAGAGCAACA 59.656 47.619 0.00 0.00 0.00 3.33
2159 2186 2.284405 GGGTTCGAGTCCCCAGGA 60.284 66.667 14.49 0.00 40.88 3.86
2201 2228 0.108329 CGGTTACCAGTGTAGCCCTG 60.108 60.000 1.13 0.00 43.38 4.45
2210 2237 1.183549 CTGTCCTAGCGGTTACCAGT 58.816 55.000 1.13 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.