Multiple sequence alignment - TraesCS2D01G522300

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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 TraesCS2D01G522300 chr2D 100.000 2549 0 0 1 2549 610930060 610932608 0.000000e+00 4708
1 TraesCS2D01G522300 chr2D 96.101 1975 42 13 596 2537 64508696 64510668 0.000000e+00 3188
2 TraesCS2D01G522300 chr2D 91.107 596 45 7 1 594 637624826 637624237 0.000000e+00 800
3 TraesCS2D01G522300 chr2D 90.452 597 47 9 1 594 184062076 184062665 0.000000e+00 778
4 TraesCS2D01G522300 chr2D 90.252 595 51 6 1 594 457144392 457144980 0.000000e+00 771
5 TraesCS2D01G522300 chr1B 95.831 1943 65 6 598 2537 672221813 672223742 0.000000e+00 3125
6 TraesCS2D01G522300 chr1B 95.637 1948 82 3 592 2537 582666195 582664249 0.000000e+00 3123
7 TraesCS2D01G522300 chr1B 94.306 2002 68 20 592 2549 542264933 542266932 0.000000e+00 3024
8 TraesCS2D01G522300 chr4B 95.277 1969 76 6 593 2549 534922957 534920994 0.000000e+00 3105
9 TraesCS2D01G522300 chr4B 96.335 382 14 0 588 969 372353127 372352746 1.660000e-176 628
10 TraesCS2D01G522300 chrUn 95.457 1959 54 18 596 2521 60558709 60560665 0.000000e+00 3092
11 TraesCS2D01G522300 chr5B 94.475 1991 71 21 592 2549 26059383 26057399 0.000000e+00 3031
12 TraesCS2D01G522300 chr5B 94.580 1974 79 10 598 2549 680910064 680908097 0.000000e+00 3027
13 TraesCS2D01G522300 chr5B 96.825 378 10 1 596 971 317969013 317969390 4.630000e-177 630
14 TraesCS2D01G522300 chr7B 94.389 1907 89 8 603 2507 54520694 54518804 0.000000e+00 2913
15 TraesCS2D01G522300 chr3A 90.861 1127 69 8 598 1722 120653865 120654959 0.000000e+00 1480
16 TraesCS2D01G522300 chr7D 92.230 592 45 1 6 597 306569474 306570064 0.000000e+00 837
17 TraesCS2D01G522300 chr7D 91.933 595 45 1 4 595 159685247 159684653 0.000000e+00 830
18 TraesCS2D01G522300 chr5D 91.275 596 44 4 4 595 74028827 74028236 0.000000e+00 806
19 TraesCS2D01G522300 chr6D 90.909 594 48 5 2 594 249346177 249346765 0.000000e+00 793
20 TraesCS2D01G522300 chr6D 90.252 595 52 5 1 594 56112478 56113067 0.000000e+00 773
21 TraesCS2D01G522300 chr4D 90.167 600 54 2 1 595 85720056 85720655 0.000000e+00 776
22 TraesCS2D01G522300 chr2A 92.279 544 36 3 596 1138 695806754 695806216 0.000000e+00 767


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 TraesCS2D01G522300 chr2D 610930060 610932608 2548 False 4708 4708 100.000 1 2549 1 chr2D.!!$F4 2548
1 TraesCS2D01G522300 chr2D 64508696 64510668 1972 False 3188 3188 96.101 596 2537 1 chr2D.!!$F1 1941
2 TraesCS2D01G522300 chr2D 637624237 637624826 589 True 800 800 91.107 1 594 1 chr2D.!!$R1 593
3 TraesCS2D01G522300 chr2D 184062076 184062665 589 False 778 778 90.452 1 594 1 chr2D.!!$F2 593
4 TraesCS2D01G522300 chr2D 457144392 457144980 588 False 771 771 90.252 1 594 1 chr2D.!!$F3 593
5 TraesCS2D01G522300 chr1B 672221813 672223742 1929 False 3125 3125 95.831 598 2537 1 chr1B.!!$F2 1939
6 TraesCS2D01G522300 chr1B 582664249 582666195 1946 True 3123 3123 95.637 592 2537 1 chr1B.!!$R1 1945
7 TraesCS2D01G522300 chr1B 542264933 542266932 1999 False 3024 3024 94.306 592 2549 1 chr1B.!!$F1 1957
8 TraesCS2D01G522300 chr4B 534920994 534922957 1963 True 3105 3105 95.277 593 2549 1 chr4B.!!$R2 1956
9 TraesCS2D01G522300 chrUn 60558709 60560665 1956 False 3092 3092 95.457 596 2521 1 chrUn.!!$F1 1925
10 TraesCS2D01G522300 chr5B 26057399 26059383 1984 True 3031 3031 94.475 592 2549 1 chr5B.!!$R1 1957
11 TraesCS2D01G522300 chr5B 680908097 680910064 1967 True 3027 3027 94.580 598 2549 1 chr5B.!!$R2 1951
12 TraesCS2D01G522300 chr7B 54518804 54520694 1890 True 2913 2913 94.389 603 2507 1 chr7B.!!$R1 1904
13 TraesCS2D01G522300 chr3A 120653865 120654959 1094 False 1480 1480 90.861 598 1722 1 chr3A.!!$F1 1124
14 TraesCS2D01G522300 chr7D 306569474 306570064 590 False 837 837 92.230 6 597 1 chr7D.!!$F1 591
15 TraesCS2D01G522300 chr7D 159684653 159685247 594 True 830 830 91.933 4 595 1 chr7D.!!$R1 591
16 TraesCS2D01G522300 chr5D 74028236 74028827 591 True 806 806 91.275 4 595 1 chr5D.!!$R1 591
17 TraesCS2D01G522300 chr6D 249346177 249346765 588 False 793 793 90.909 2 594 1 chr6D.!!$F2 592
18 TraesCS2D01G522300 chr6D 56112478 56113067 589 False 773 773 90.252 1 594 1 chr6D.!!$F1 593
19 TraesCS2D01G522300 chr4D 85720056 85720655 599 False 776 776 90.167 1 595 1 chr4D.!!$F1 594
20 TraesCS2D01G522300 chr2A 695806216 695806754 538 True 767 767 92.279 596 1138 1 chr2A.!!$R1 542

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
347 348 0.521735 GGAAAAGTCACGACCATGGC 59.478 55.000 13.04 3.65 0.0 4.40 F
389 393 3.823304 ACAAAAGTGGGAAGAAGATCAGC 59.177 43.478 0.00 0.00 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1208 1307 1.745087 CGGAACAGATCAACCCATTGG 59.255 52.381 0.00 0.0 36.39 3.16 R
2032 2138 1.927487 TCTGTCCTAGCGGTTACCAA 58.073 50.000 1.13 0.0 0.00 3.67 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
112 113 3.068560 GGGTACACGCTAAACATGTGAA 58.931 45.455 0.00 0.00 37.08 3.18
115 116 3.247563 ACACGCTAAACATGTGAAACG 57.752 42.857 0.00 4.52 42.39 3.60
129 130 8.044060 ACATGTGAAACGATGTTTCTTCATAT 57.956 30.769 19.59 12.26 42.39 1.78
137 138 3.553828 TGTTTCTTCATATCCGACCCC 57.446 47.619 0.00 0.00 0.00 4.95
195 196 1.272490 GGAGCATCGTCGGAATGGATA 59.728 52.381 0.00 0.00 34.37 2.59
221 222 1.134560 GCCAACGAGGAAGACTACGAT 59.865 52.381 2.86 0.00 41.22 3.73
227 228 4.706035 ACGAGGAAGACTACGATCAGTAT 58.294 43.478 0.00 0.00 34.34 2.12
292 293 8.023050 ACATACGTCAAAAGAAGAATGAAGAG 57.977 34.615 0.00 0.00 0.00 2.85
293 294 7.872993 ACATACGTCAAAAGAAGAATGAAGAGA 59.127 33.333 0.00 0.00 0.00 3.10
294 295 6.777526 ACGTCAAAAGAAGAATGAAGAGAG 57.222 37.500 0.00 0.00 0.00 3.20
347 348 0.521735 GGAAAAGTCACGACCATGGC 59.478 55.000 13.04 3.65 0.00 4.40
389 393 3.823304 ACAAAAGTGGGAAGAAGATCAGC 59.177 43.478 0.00 0.00 0.00 4.26
429 433 3.826157 CCCAAGCTGACAAACTAATCCAA 59.174 43.478 0.00 0.00 0.00 3.53
462 470 9.811995 TGTGTGTATCTATTTTGTATACCACTC 57.188 33.333 0.00 0.00 33.35 3.51
1208 1307 0.245539 TCGTGGTCGGGATCTTTGAC 59.754 55.000 0.00 0.00 37.69 3.18
1474 1573 4.523083 TCAAGCACTACCAATACCCATTC 58.477 43.478 0.00 0.00 0.00 2.67
1593 1692 9.778993 ATCTTGAAATTGTATGAGAAATTCACG 57.221 29.630 0.00 0.00 38.99 4.35
1757 1863 6.574269 GCCAGAGCCAAACAATTAAGGTTAAT 60.574 38.462 0.00 0.00 34.98 1.40
2032 2138 1.599797 GTGGTGTTTAGGGCTGCGT 60.600 57.895 0.00 0.00 0.00 5.24
2358 2471 3.003763 GCTTCTCACCCCCTCCGT 61.004 66.667 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.856156 TGGTAGTGAAATGTCGGTTTTCTA 58.144 37.500 7.02 0.0 34.80 2.10
112 113 4.809426 GGTCGGATATGAAGAAACATCGTT 59.191 41.667 0.00 0.0 0.00 3.85
115 116 4.065789 GGGGTCGGATATGAAGAAACATC 58.934 47.826 0.00 0.0 0.00 3.06
129 130 3.407967 GGGATTGCTGGGGTCGGA 61.408 66.667 0.00 0.0 0.00 4.55
195 196 0.895530 TCTTCCTCGTTGGCGATTCT 59.104 50.000 0.00 0.0 46.80 2.40
221 222 2.893489 CCTCATCGGATCACCATACTGA 59.107 50.000 0.00 0.0 35.59 3.41
227 228 1.123077 CTTCCCTCATCGGATCACCA 58.877 55.000 0.00 0.0 35.59 4.17
293 294 9.289782 GGATTACAATCTTTCATAGGTAATGCT 57.710 33.333 0.00 0.0 36.92 3.79
294 295 8.515414 GGGATTACAATCTTTCATAGGTAATGC 58.485 37.037 0.00 0.0 38.21 3.56
374 375 1.956869 TCAGGCTGATCTTCTTCCCA 58.043 50.000 14.43 0.0 0.00 4.37
389 393 3.147294 CGACAACGACGCTTCAGG 58.853 61.111 0.00 0.0 42.66 3.86
503 511 9.745018 CAATAACACCATTTATCCTCTGGATAT 57.255 33.333 7.09 0.0 43.26 1.63
519 527 3.500448 TCTGTTGGAGCAATAACACCA 57.500 42.857 0.00 0.0 0.00 4.17
609 619 1.611977 GGACACCACTAAGGGCAAAAC 59.388 52.381 0.00 0.0 43.89 2.43
699 709 1.795286 GAGACGCCAAAGTTCACAGAG 59.205 52.381 0.00 0.0 0.00 3.35
1208 1307 1.745087 CGGAACAGATCAACCCATTGG 59.255 52.381 0.00 0.0 36.39 3.16
1448 1547 4.966168 TGGGTATTGGTAGTGCTTGATCTA 59.034 41.667 0.00 0.0 0.00 1.98
1474 1573 4.324974 CAAATGCCCAAAAGTATTTGCG 57.675 40.909 2.86 0.0 43.73 4.85
1593 1692 8.920509 ACAACTTTGACCAACATTTAAACTAC 57.079 30.769 0.00 0.0 0.00 2.73
1792 1898 7.696453 CACGGTGTATTTGAATTGGATTACTTC 59.304 37.037 0.00 0.0 0.00 3.01
2032 2138 1.927487 TCTGTCCTAGCGGTTACCAA 58.073 50.000 1.13 0.0 0.00 3.67


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

AutoCloner maintained by Alex Coulton.