Multiple sequence alignment - TraesCS6D01G268200

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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 TraesCS6D01G268200 chr6D 100.000 2421 0 0 1 2421 378168644 378166224 0.000000e+00 4471.0
1 TraesCS6D01G268200 chr6D 80.602 598 63 27 703 1288 377975731 377975175 1.730000e-111 412.0
2 TraesCS6D01G268200 chr6D 85.345 116 15 2 1 114 355271101 355270986 4.230000e-23 119.0
3 TraesCS6D01G268200 chr6A 93.805 2276 102 27 23 2277 519951234 519948977 0.000000e+00 3386.0
4 TraesCS6D01G268200 chr6A 80.597 603 62 28 701 1288 519596570 519596008 4.820000e-112 414.0
5 TraesCS6D01G268200 chr6A 93.519 108 7 0 2313 2420 519948766 519948659 6.930000e-36 161.0
6 TraesCS6D01G268200 chr6A 86.555 119 12 3 1555 1673 606979062 606979176 7.030000e-26 128.0
7 TraesCS6D01G268200 chr6B 91.137 2392 164 23 2 2364 564569946 564567574 0.000000e+00 3199.0
8 TraesCS6D01G268200 chr6B 80.725 524 60 22 777 1288 564509340 564508846 1.060000e-98 370.0
9 TraesCS6D01G268200 chr6B 81.452 124 19 3 1552 1675 649785519 649785400 5.510000e-17 99.0
10 TraesCS6D01G268200 chr6B 90.000 60 5 1 2362 2420 267622779 267622720 2.580000e-10 76.8
11 TraesCS6D01G268200 chr3D 81.343 268 42 6 400 662 434949468 434949732 6.780000e-51 211.0
12 TraesCS6D01G268200 chr5A 82.305 243 35 6 418 656 11374528 11374766 1.130000e-48 204.0
13 TraesCS6D01G268200 chr5A 81.781 247 35 7 422 662 590061192 590061434 5.280000e-47 198.0
14 TraesCS6D01G268200 chr5A 79.775 267 45 7 401 662 598229057 598229319 4.110000e-43 185.0
15 TraesCS6D01G268200 chr5A 86.207 116 13 2 1 115 577919815 577919928 3.270000e-24 122.0
16 TraesCS6D01G268200 chr4D 81.781 247 35 8 422 662 165929707 165929949 5.280000e-47 198.0
17 TraesCS6D01G268200 chr2D 80.216 278 36 16 396 662 353153250 353152981 8.830000e-45 191.0
18 TraesCS6D01G268200 chr2D 80.078 256 43 5 412 662 138377951 138378203 1.480000e-42 183.0
19 TraesCS6D01G268200 chr3A 89.916 119 10 2 1 117 587410805 587410923 4.170000e-33 152.0
20 TraesCS6D01G268200 chr2B 83.846 130 17 3 1545 1674 465132437 465132312 1.180000e-23 121.0
21 TraesCS6D01G268200 chr2B 82.707 133 17 5 1552 1682 600609403 600609275 1.970000e-21 113.0
22 TraesCS6D01G268200 chr2B 82.787 122 17 3 1552 1673 77819076 77818959 3.290000e-19 106.0
23 TraesCS6D01G268200 chr2A 83.077 130 18 3 1545 1674 531598665 531598540 5.470000e-22 115.0
24 TraesCS6D01G268200 chr7B 80.282 142 18 9 1538 1677 79399528 79399661 5.510000e-17 99.0
25 TraesCS6D01G268200 chr1B 94.118 51 3 0 2370 2420 59943264 59943214 7.180000e-11 78.7
26 TraesCS6D01G268200 chr1B 95.556 45 2 0 2376 2420 60036425 60036381 3.340000e-09 73.1
27 TraesCS6D01G268200 chr4B 97.727 44 1 0 2368 2411 37577931 37577974 2.580000e-10 76.8
28 TraesCS6D01G268200 chrUn 95.556 45 2 0 2376 2420 398422721 398422677 3.340000e-09 73.1
29 TraesCS6D01G268200 chr1A 97.619 42 1 0 2370 2411 291567052 291567093 3.340000e-09 73.1


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 TraesCS6D01G268200 chr6D 378166224 378168644 2420 True 4471.0 4471 100.000 1 2421 1 chr6D.!!$R3 2420
1 TraesCS6D01G268200 chr6D 377975175 377975731 556 True 412.0 412 80.602 703 1288 1 chr6D.!!$R2 585
2 TraesCS6D01G268200 chr6A 519948659 519951234 2575 True 1773.5 3386 93.662 23 2420 2 chr6A.!!$R2 2397
3 TraesCS6D01G268200 chr6A 519596008 519596570 562 True 414.0 414 80.597 701 1288 1 chr6A.!!$R1 587
4 TraesCS6D01G268200 chr6B 564567574 564569946 2372 True 3199.0 3199 91.137 2 2364 1 chr6B.!!$R3 2362

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
166 168 0.778815 GAAGCGAGACACACAAGTCG 59.221 55.0 0.0 0.0 43.24 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 1921 0.247145 GCACCGTTTGTCGCTATTCG 60.247 55.0 0.0 0.0 38.35 3.34 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
95 97 1.545136 TCGGTAGCACCACAATTACGA 59.455 47.619 0.00 0.00 38.47 3.43
166 168 0.778815 GAAGCGAGACACACAAGTCG 59.221 55.000 0.00 0.00 43.24 4.18
199 201 5.163754 AGCGGTTTCCGATCTCTTTAATTTG 60.164 40.000 12.48 0.00 44.45 2.32
372 376 8.348507 CACTTGCTAAAGAAGAAAAGATTCTGT 58.651 33.333 0.00 0.00 40.04 3.41
479 487 7.093992 AGAGTGTACTTCTATCTTTTCAGTGC 58.906 38.462 0.00 0.00 0.00 4.40
484 492 8.721478 TGTACTTCTATCTTTTCAGTGCATTTC 58.279 33.333 0.00 0.00 0.00 2.17
528 538 9.426534 TCTCTCTCATCATAAGGTAATCAAGAA 57.573 33.333 0.00 0.00 0.00 2.52
827 843 1.882989 GCAGCCTCACCTCGTTCTCT 61.883 60.000 0.00 0.00 0.00 3.10
1210 1244 4.210093 AACGTCGTGCCCGTGACA 62.210 61.111 0.00 0.00 38.77 3.58
2055 2107 6.817641 AGTTTTCATTGCAACTGATTTCAACA 59.182 30.769 0.00 0.00 31.80 3.33
2303 2357 4.740741 TCAATGGTAATGTGTGTTGTCG 57.259 40.909 0.00 0.00 0.00 4.35
2310 2364 1.305201 ATGTGTGTTGTCGGGTTCAC 58.695 50.000 0.00 0.00 0.00 3.18
2364 2593 5.162637 AGGGCATCTACATTTGAGGGTATA 58.837 41.667 0.00 0.00 0.00 1.47
2366 2595 6.275618 AGGGCATCTACATTTGAGGGTATATT 59.724 38.462 0.00 0.00 0.00 1.28
2390 2619 5.705441 TGGTGCTGGAATTTAGTCTACTTTG 59.295 40.000 0.00 0.00 0.00 2.77
2394 2623 4.595986 TGGAATTTAGTCTACTTTGGGCC 58.404 43.478 0.00 0.00 0.00 5.80
2396 2625 5.014202 GGAATTTAGTCTACTTTGGGCCAA 58.986 41.667 16.66 16.66 0.00 4.52
2413 2642 3.270027 GCCAACCCAATAGCAATTTTCC 58.730 45.455 0.00 0.00 0.00 3.13
2420 2649 7.019656 ACCCAATAGCAATTTTCCAAATTCT 57.980 32.000 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 77 1.545136 TCGTAATTGTGGTGCTACCGA 59.455 47.619 0.00 0.00 42.58 4.69
84 86 1.136085 CCGTTGCACTCGTAATTGTGG 60.136 52.381 9.14 0.00 34.99 4.17
128 130 2.108168 TCTCTATCAACTGGAACGGGG 58.892 52.381 0.00 0.00 40.47 5.73
199 201 0.874607 CATCCGTTGCCGCCTAGTAC 60.875 60.000 0.00 0.00 0.00 2.73
457 465 7.602517 ATGCACTGAAAAGATAGAAGTACAC 57.397 36.000 0.00 0.00 0.00 2.90
458 466 8.621532 AAATGCACTGAAAAGATAGAAGTACA 57.378 30.769 0.00 0.00 0.00 2.90
462 470 9.125906 CTTTGAAATGCACTGAAAAGATAGAAG 57.874 33.333 7.62 0.00 0.00 2.85
514 524 9.967451 TGAATGGTATTGTTCTTGATTACCTTA 57.033 29.630 0.00 0.00 0.00 2.69
516 526 8.739972 GTTGAATGGTATTGTTCTTGATTACCT 58.260 33.333 0.00 0.00 0.00 3.08
528 538 6.319658 GGAGATCATGTGTTGAATGGTATTGT 59.680 38.462 0.00 0.00 38.03 2.71
534 544 7.578310 ATTAAGGAGATCATGTGTTGAATGG 57.422 36.000 0.00 0.00 38.03 3.16
1205 1239 3.357079 CTGCACCCGCCTTGTCAC 61.357 66.667 0.00 0.00 37.32 3.67
1351 1385 1.362717 CTCGTCGGTGAACACTGGT 59.637 57.895 12.85 0.00 38.23 4.00
1586 1626 8.612619 AGACATGTTTTAATGTTCGATACATCC 58.387 33.333 0.00 2.72 46.75 3.51
1646 1686 5.127356 ACTCCCTCACTTCGTCCTAAATTAG 59.873 44.000 0.00 0.00 0.00 1.73
1653 1693 1.355043 AGTACTCCCTCACTTCGTCCT 59.645 52.381 0.00 0.00 0.00 3.85
1662 1702 8.004801 TCTGAATATGTCATTAGTACTCCCTCA 58.995 37.037 0.00 0.00 35.07 3.86
1696 1737 4.221924 TCCTATCCGAAGACATTCACACAA 59.778 41.667 0.00 0.00 34.94 3.33
1875 1921 0.247145 GCACCGTTTGTCGCTATTCG 60.247 55.000 0.00 0.00 38.35 3.34
1934 1980 7.926018 GGTTAAATTGAGGTTCAGACACAAATT 59.074 33.333 0.00 0.00 31.31 1.82
1998 2044 6.787085 ACCACGTTTTCTTAAATCTCTCAG 57.213 37.500 0.00 0.00 0.00 3.35
2167 2221 9.207868 TGAAAAGATTAAAGGAAAAGGGAAAGA 57.792 29.630 0.00 0.00 0.00 2.52
2289 2343 2.873472 GTGAACCCGACAACACACATTA 59.127 45.455 0.00 0.00 34.05 1.90
2291 2345 1.134220 AGTGAACCCGACAACACACAT 60.134 47.619 0.00 0.00 35.97 3.21
2303 2357 3.681593 TGTTGCAACCTATAGTGAACCC 58.318 45.455 26.14 0.00 0.00 4.11
2310 2364 8.500753 TTGTATTAACCTGTTGCAACCTATAG 57.499 34.615 26.14 16.22 0.00 1.31
2364 2593 6.067217 AGTAGACTAAATTCCAGCACCAAT 57.933 37.500 0.00 0.00 0.00 3.16
2366 2595 5.499004 AAGTAGACTAAATTCCAGCACCA 57.501 39.130 0.00 0.00 0.00 4.17
2394 2623 7.391275 AGAATTTGGAAAATTGCTATTGGGTTG 59.609 33.333 2.82 0.00 0.00 3.77
2396 2625 7.019656 AGAATTTGGAAAATTGCTATTGGGT 57.980 32.000 2.82 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.