Multiple sequence alignment - TraesCS2D01G269300

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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 TraesCS2D01G269300 chr2D 100.000 2549 0 0 1 2549 331196607 331199155 0 4708
1 TraesCS2D01G269300 chr7D 95.808 1980 68 9 573 2549 574727118 574725151 0 3182
2 TraesCS2D01G269300 chr7D 96.510 573 18 2 2 572 506759339 506759911 0 946
3 TraesCS2D01G269300 chr7D 95.629 572 24 1 2 572 141575482 141576053 0 917
4 TraesCS2D01G269300 chr5D 95.709 1981 75 8 573 2549 520497539 520495565 0 3179
5 TraesCS2D01G269300 chr5D 95.562 1983 73 9 572 2549 336262623 336264595 0 3160
6 TraesCS2D01G269300 chr5D 95.819 574 22 2 1 572 425726513 425727086 0 926
7 TraesCS2D01G269300 chrUn 95.571 1987 73 10 573 2549 93726510 93724529 0 3168
8 TraesCS2D01G269300 chr6D 95.398 1999 77 11 556 2549 109963195 109965183 0 3168
9 TraesCS2D01G269300 chr6D 95.804 572 24 0 1 572 450383323 450383894 0 924
10 TraesCS2D01G269300 chr7A 94.935 1994 85 15 563 2549 701581933 701583917 0 3109
11 TraesCS2D01G269300 chr1D 95.060 1984 84 10 570 2549 26486135 26488108 0 3109
12 TraesCS2D01G269300 chr1D 95.804 572 24 0 1 572 189428631 189429202 0 924
13 TraesCS2D01G269300 chr7B 95.013 1985 84 13 573 2549 552932143 552930166 0 3103
14 TraesCS2D01G269300 chr6B 94.927 1991 85 14 566 2549 660437750 660435769 0 3103
15 TraesCS2D01G269300 chr3D 96.147 571 21 1 2 572 400440118 400439549 0 931
16 TraesCS2D01G269300 chr3D 95.645 574 23 2 1 572 440903833 440903260 0 920
17 TraesCS2D01G269300 chr4D 95.986 573 21 2 1 572 292472879 292473450 0 929
18 TraesCS2D01G269300 chr4D 95.812 573 22 2 1 572 121888819 121888248 0 924


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 TraesCS2D01G269300 chr2D 331196607 331199155 2548 False 4708 4708 100.000 1 2549 1 chr2D.!!$F1 2548
1 TraesCS2D01G269300 chr7D 574725151 574727118 1967 True 3182 3182 95.808 573 2549 1 chr7D.!!$R1 1976
2 TraesCS2D01G269300 chr7D 506759339 506759911 572 False 946 946 96.510 2 572 1 chr7D.!!$F2 570
3 TraesCS2D01G269300 chr7D 141575482 141576053 571 False 917 917 95.629 2 572 1 chr7D.!!$F1 570
4 TraesCS2D01G269300 chr5D 520495565 520497539 1974 True 3179 3179 95.709 573 2549 1 chr5D.!!$R1 1976
5 TraesCS2D01G269300 chr5D 336262623 336264595 1972 False 3160 3160 95.562 572 2549 1 chr5D.!!$F1 1977
6 TraesCS2D01G269300 chr5D 425726513 425727086 573 False 926 926 95.819 1 572 1 chr5D.!!$F2 571
7 TraesCS2D01G269300 chrUn 93724529 93726510 1981 True 3168 3168 95.571 573 2549 1 chrUn.!!$R1 1976
8 TraesCS2D01G269300 chr6D 109963195 109965183 1988 False 3168 3168 95.398 556 2549 1 chr6D.!!$F1 1993
9 TraesCS2D01G269300 chr6D 450383323 450383894 571 False 924 924 95.804 1 572 1 chr6D.!!$F2 571
10 TraesCS2D01G269300 chr7A 701581933 701583917 1984 False 3109 3109 94.935 563 2549 1 chr7A.!!$F1 1986
11 TraesCS2D01G269300 chr1D 26486135 26488108 1973 False 3109 3109 95.060 570 2549 1 chr1D.!!$F1 1979
12 TraesCS2D01G269300 chr1D 189428631 189429202 571 False 924 924 95.804 1 572 1 chr1D.!!$F2 571
13 TraesCS2D01G269300 chr7B 552930166 552932143 1977 True 3103 3103 95.013 573 2549 1 chr7B.!!$R1 1976
14 TraesCS2D01G269300 chr6B 660435769 660437750 1981 True 3103 3103 94.927 566 2549 1 chr6B.!!$R1 1983
15 TraesCS2D01G269300 chr3D 400439549 400440118 569 True 931 931 96.147 2 572 1 chr3D.!!$R1 570
16 TraesCS2D01G269300 chr3D 440903260 440903833 573 True 920 920 95.645 1 572 1 chr3D.!!$R2 571
17 TraesCS2D01G269300 chr4D 292472879 292473450 571 False 929 929 95.986 1 572 1 chr4D.!!$F1 571
18 TraesCS2D01G269300 chr4D 121888248 121888819 571 True 924 924 95.812 1 572 1 chr4D.!!$R1 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
987 1001 0.250234 CAGCGTTGAGATCCCCTTCA 59.75 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 1855 0.988832 AATACGCAAGAGAACCCCCA 59.011 50.0 0.0 0.0 43.62 4.96 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 1.001974 CAAGACCTCCCGATGAACACA 59.998 52.381 0.00 0.00 0.00 3.72
113 114 0.662077 CCATGAACACGACGACGACA 60.662 55.000 15.32 8.67 42.66 4.35
288 289 1.154357 CTACTACGACACGTGCGCA 60.154 57.895 25.05 5.66 41.39 6.09
411 412 0.811616 CGAAGATGTAGCTGGTGGGC 60.812 60.000 0.00 0.00 0.00 5.36
614 619 0.473755 AGTGGTGTCCATGTGCTCAA 59.526 50.000 0.00 0.00 35.28 3.02
631 636 2.494471 CTCAATTTTGCCCTCAGATGCA 59.506 45.455 0.00 0.00 35.27 3.96
658 663 1.003696 GCTCAGTTTTGCCCCTAGTCT 59.996 52.381 0.00 0.00 0.00 3.24
672 677 1.241990 TAGTCTGAGCGCACCGACTT 61.242 55.000 29.75 17.37 37.80 3.01
677 682 1.664965 GAGCGCACCGACTTGTTCT 60.665 57.895 11.47 0.00 0.00 3.01
727 732 2.618045 CCTTTTGACTCGGCCCTTACAT 60.618 50.000 0.00 0.00 0.00 2.29
877 884 2.182791 CACGGCGACAGAGAGCAT 59.817 61.111 16.62 0.00 34.54 3.79
893 900 4.697756 ATGGCGGTGACCACGGTG 62.698 66.667 1.11 0.00 44.17 4.94
987 1001 0.250234 CAGCGTTGAGATCCCCTTCA 59.750 55.000 0.00 0.00 0.00 3.02
1321 1336 4.660168 AGAAGAGCATGAAGAATGGTTGT 58.340 39.130 0.00 0.00 46.95 3.32
1694 1717 8.482852 AAAAGGAGAAGAAATGAGGAATTCAA 57.517 30.769 7.93 0.00 39.77 2.69
1723 1746 4.632538 TGATCAATGAAATGCAGCTCTG 57.367 40.909 0.00 0.00 0.00 3.35
1791 1816 1.079819 GCGTAGAGCCAAGTGCAGA 60.080 57.895 0.00 0.00 44.83 4.26
1830 1855 2.761809 TGCATCCAATTAGGCCCATTT 58.238 42.857 0.00 0.00 37.29 2.32
1855 1880 4.939439 GGGGTTCTCTTGCGTATTTTTCTA 59.061 41.667 0.00 0.00 0.00 2.10
1985 2012 6.189859 TGGAGCTGTTAATCAATCCAATTCT 58.810 36.000 0.00 0.00 38.34 2.40
2032 2059 8.776376 AATACCAAAATGTCATGGAAAATGTC 57.224 30.769 0.00 0.00 39.12 3.06
2074 2101 3.744238 ACACCTGGTGCCAAAATAAAC 57.256 42.857 26.20 0.00 36.98 2.01
2213 2241 1.078708 GGTGTTTAGGGCTGCGCTA 60.079 57.895 20.82 20.82 0.00 4.26
2502 2532 9.979578 TTTGCATGTTAGTTCATGACTTATTTT 57.020 25.926 10.28 0.00 45.41 1.82
2503 2533 8.969121 TGCATGTTAGTTCATGACTTATTTTG 57.031 30.769 10.28 0.00 45.41 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 0.320421 CGTTGTGTTCATCGGGAGGT 60.320 55.000 0.00 0.00 34.40 3.85
264 265 0.671781 ACGTGTCGTAGTAGAGGCGT 60.672 55.000 0.00 0.00 38.73 5.68
288 289 3.899726 ACATACTGGTCGATGTAGAGGT 58.100 45.455 0.00 0.00 34.52 3.85
631 636 2.485302 GGGGCAAAACTGAGCACAATTT 60.485 45.455 0.00 0.00 35.37 1.82
658 663 1.954146 GAACAAGTCGGTGCGCTCA 60.954 57.895 9.73 0.00 0.00 4.26
672 677 4.141846 GGAGATGGCTGAGTTCATAGAACA 60.142 45.833 11.92 0.00 0.00 3.18
677 682 2.362397 GACGGAGATGGCTGAGTTCATA 59.638 50.000 0.00 0.00 0.00 2.15
893 900 0.390124 CTGCCATGCTCTCTCTCTCC 59.610 60.000 0.00 0.00 0.00 3.71
969 983 0.539051 CTGAAGGGGATCTCAACGCT 59.461 55.000 0.00 0.00 0.00 5.07
1694 1717 7.227910 AGCTGCATTTCATTGATCAAAAGTTTT 59.772 29.630 13.09 0.00 0.00 2.43
1723 1746 1.597742 TTGACAGAAAGGCAGAGCAC 58.402 50.000 0.00 0.00 35.94 4.40
1791 1816 3.053693 TGCAATTGGCCCATTAGTCTAGT 60.054 43.478 7.72 0.00 43.89 2.57
1830 1855 0.988832 AATACGCAAGAGAACCCCCA 59.011 50.000 0.00 0.00 43.62 4.96
1960 1987 6.664816 AGAATTGGATTGATTAACAGCTCCAA 59.335 34.615 16.82 16.82 46.23 3.53
1974 2001 6.918892 TCACGGTGTATTAGAATTGGATTG 57.081 37.500 8.17 0.00 0.00 2.67
2032 2059 2.819477 CCTCTACCAGAGCTGAGGG 58.181 63.158 7.49 0.97 40.98 4.30
2213 2241 2.032620 CCATCTGTCCTAGCGGTTACT 58.967 52.381 0.00 0.00 0.00 2.24
2499 2529 5.584251 GCCCTCTGTTTCATTCAAAACAAAA 59.416 36.000 4.04 0.00 45.67 2.44
2500 2530 5.104982 AGCCCTCTGTTTCATTCAAAACAAA 60.105 36.000 4.04 0.00 45.67 2.83
2501 2531 4.405358 AGCCCTCTGTTTCATTCAAAACAA 59.595 37.500 4.04 0.00 45.67 2.83
2502 2532 3.960102 AGCCCTCTGTTTCATTCAAAACA 59.040 39.130 2.60 2.60 44.59 2.83
2503 2533 4.590850 AGCCCTCTGTTTCATTCAAAAC 57.409 40.909 0.00 0.00 39.16 2.43


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

AutoCloner maintained by Alex Coulton.