Multiple sequence alignment - TraesCS6D01G023200

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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 TraesCS6D01G023200 chr6D 100.000 4220 0 0 1 4220 8838768 8834549 0.000000e+00 7793.0
1 TraesCS6D01G023200 chr6D 99.430 2282 6 4 1940 4220 8497544 8499819 0.000000e+00 4135.0
2 TraesCS6D01G023200 chr6D 94.576 2360 90 13 89 2414 10439628 10441983 0.000000e+00 3615.0
3 TraesCS6D01G023200 chr6D 99.434 1945 8 1 1 1942 8488547 8490491 0.000000e+00 3528.0
4 TraesCS6D01G023200 chr6D 90.674 697 37 6 3077 3764 10442807 10443484 0.000000e+00 902.0
5 TraesCS6D01G023200 chr6D 91.770 486 15 3 3759 4220 25576 25092 0.000000e+00 652.0
6 TraesCS6D01G023200 chr6D 90.835 491 13 5 3759 4220 455680799 455681286 2.770000e-176 628.0
7 TraesCS6D01G023200 chr6D 82.599 431 32 17 2685 3079 10442340 10442763 1.450000e-89 340.0
8 TraesCS6D01G023200 chr6D 81.765 340 57 4 987 1323 10435736 10436073 3.210000e-71 279.0
9 TraesCS6D01G023200 chr6D 74.027 874 136 53 2745 3565 10437508 10438343 5.380000e-69 272.0
10 TraesCS6D01G023200 chr6D 72.987 559 119 25 1693 2228 26250407 26250956 2.610000e-37 167.0
11 TraesCS6D01G023200 chr6D 92.727 55 2 1 1 53 10439589 10439643 1.260000e-10 78.7
12 TraesCS6D01G023200 chr6B 93.347 2495 122 22 461 2925 19196693 19199173 0.000000e+00 3648.0
13 TraesCS6D01G023200 chr6B 87.193 734 48 16 3037 3764 19199184 19199877 0.000000e+00 793.0
14 TraesCS6D01G023200 chr6B 89.223 399 30 11 2981 3367 21082958 21082561 1.760000e-133 486.0
15 TraesCS6D01G023200 chr6B 77.491 542 96 15 1679 2206 19153776 19154305 6.860000e-78 302.0
16 TraesCS6D01G023200 chr6B 82.370 346 35 14 3427 3764 21082534 21082207 1.160000e-70 278.0
17 TraesCS6D01G023200 chr6B 76.722 421 86 5 987 1396 19153071 19153490 1.530000e-54 224.0
18 TraesCS6D01G023200 chr6B 85.185 216 27 3 470 681 21083846 21083632 2.560000e-52 217.0
19 TraesCS6D01G023200 chr6B 91.139 158 11 3 1902 2056 21083174 21083017 1.190000e-50 211.0
20 TraesCS6D01G023200 chr6B 85.246 183 20 5 281 457 21084231 21084050 9.320000e-42 182.0
21 TraesCS6D01G023200 chr6B 79.386 228 44 3 1997 2223 42506283 42506508 1.570000e-34 158.0
22 TraesCS6D01G023200 chr6B 98.214 56 1 0 1 56 19168109 19168164 9.660000e-17 99.0
23 TraesCS6D01G023200 chr6A 95.805 1645 58 4 837 2470 12048730 12050374 0.000000e+00 2645.0
24 TraesCS6D01G023200 chr6A 93.790 628 31 5 2957 3580 12052377 12053000 0.000000e+00 937.0
25 TraesCS6D01G023200 chr6A 96.957 460 11 2 2462 2920 12051916 12052373 0.000000e+00 769.0
26 TraesCS6D01G023200 chr6A 88.774 579 54 7 273 844 12018619 12019193 0.000000e+00 699.0
27 TraesCS6D01G023200 chr6A 78.634 454 57 21 2981 3415 12017255 12017687 9.000000e-67 265.0
28 TraesCS6D01G023200 chr6A 92.366 131 10 0 2410 2540 542709477 542709347 2.000000e-43 187.0
29 TraesCS6D01G023200 chr6A 81.461 178 32 1 1040 1216 4335469 4335292 1.220000e-30 145.0
30 TraesCS6D01G023200 chr7D 93.004 486 9 9 3759 4220 17324518 17325002 0.000000e+00 686.0
31 TraesCS6D01G023200 chr7D 92.798 486 10 3 3759 4220 422141194 422140710 0.000000e+00 680.0
32 TraesCS6D01G023200 chr7D 92.197 487 12 4 3759 4220 28430466 28429981 0.000000e+00 665.0
33 TraesCS6D01G023200 chr7D 91.975 486 12 5 3759 4220 36262040 36262522 0.000000e+00 656.0
34 TraesCS6D01G023200 chr7D 89.041 292 8 2 3759 4026 18446893 18447184 1.450000e-89 340.0
35 TraesCS6D01G023200 chr7D 92.366 131 10 0 2413 2543 30043630 30043760 2.000000e-43 187.0
36 TraesCS6D01G023200 chrUn 92.387 486 10 5 3759 4220 440304474 440304956 0.000000e+00 667.0
37 TraesCS6D01G023200 chrUn 91.770 486 14 4 3759 4220 257833741 257834224 0.000000e+00 652.0
38 TraesCS6D01G023200 chrUn 81.977 172 30 1 1037 1207 62558083 62558254 1.220000e-30 145.0
39 TraesCS6D01G023200 chrUn 81.977 172 30 1 1037 1207 62614022 62614193 1.220000e-30 145.0
40 TraesCS6D01G023200 chrUn 81.395 172 31 1 1037 1207 62312589 62312760 5.690000e-29 139.0
41 TraesCS6D01G023200 chrUn 80.814 172 32 1 1037 1207 62429742 62429913 2.650000e-27 134.0
42 TraesCS6D01G023200 chr1D 91.975 486 12 5 3759 4220 289575976 289576458 0.000000e+00 656.0
43 TraesCS6D01G023200 chr3D 91.564 486 15 4 3759 4220 550624790 550624307 0.000000e+00 647.0
44 TraesCS6D01G023200 chr3D 90.144 487 20 6 3759 4220 593844001 593844484 3.610000e-170 608.0
45 TraesCS6D01G023200 chr3D 88.520 331 11 4 3759 4065 2966328 2966001 3.980000e-100 375.0
46 TraesCS6D01G023200 chr3D 76.793 474 85 17 1739 2201 557764217 557763758 4.220000e-60 243.0
47 TraesCS6D01G023200 chr3D 79.394 330 54 11 991 1318 557914249 557914566 1.980000e-53 220.0
48 TraesCS6D01G023200 chr3D 82.569 218 34 3 1000 1217 557921034 557921247 5.570000e-44 189.0
49 TraesCS6D01G023200 chr2D 91.564 486 16 3 3759 4220 610486090 610485606 0.000000e+00 647.0
50 TraesCS6D01G023200 chr2D 93.548 124 8 0 2411 2534 300887315 300887438 7.210000e-43 185.0
51 TraesCS6D01G023200 chr5D 90.741 486 20 4 3759 4220 543413125 543413609 3.580000e-175 625.0
52 TraesCS6D01G023200 chr3B 80.415 337 51 12 984 1318 740514541 740514864 4.220000e-60 243.0
53 TraesCS6D01G023200 chr4D 93.023 129 9 0 2413 2541 333267241 333267369 5.570000e-44 189.0
54 TraesCS6D01G023200 chr4D 100.000 33 0 0 1106 1138 455618768 455618800 1.270000e-05 62.1
55 TraesCS6D01G023200 chr5B 90.580 138 13 0 2408 2545 327750233 327750370 2.590000e-42 183.0
56 TraesCS6D01G023200 chr2B 88.158 152 14 4 2413 2561 543430305 543430155 1.210000e-40 178.0
57 TraesCS6D01G023200 chr5A 83.607 183 26 3 1036 1216 655072315 655072135 7.260000e-38 169.0
58 TraesCS6D01G023200 chr1B 83.815 173 28 0 1035 1207 645707448 645707620 9.390000e-37 165.0
59 TraesCS6D01G023200 chr1A 83.240 179 30 0 1035 1213 560181261 560181083 9.390000e-37 165.0


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 TraesCS6D01G023200 chr6D 8834549 8838768 4219 True 7793.000000 7793 100.000000 1 4220 1 chr6D.!!$R2 4219
1 TraesCS6D01G023200 chr6D 8497544 8499819 2275 False 4135.000000 4135 99.430000 1940 4220 1 chr6D.!!$F2 2280
2 TraesCS6D01G023200 chr6D 8488547 8490491 1944 False 3528.000000 3528 99.434000 1 1942 1 chr6D.!!$F1 1941
3 TraesCS6D01G023200 chr6D 10435736 10443484 7748 False 914.450000 3615 86.061333 1 3764 6 chr6D.!!$F5 3763
4 TraesCS6D01G023200 chr6B 19196693 19199877 3184 False 2220.500000 3648 90.270000 461 3764 2 chr6B.!!$F4 3303
5 TraesCS6D01G023200 chr6B 21082207 21084231 2024 True 274.800000 486 86.632600 281 3764 5 chr6B.!!$R1 3483
6 TraesCS6D01G023200 chr6B 19153071 19154305 1234 False 263.000000 302 77.106500 987 2206 2 chr6B.!!$F3 1219
7 TraesCS6D01G023200 chr6A 12048730 12053000 4270 False 1450.333333 2645 95.517333 837 3580 3 chr6A.!!$F2 2743
8 TraesCS6D01G023200 chr6A 12017255 12019193 1938 False 482.000000 699 83.704000 273 3415 2 chr6A.!!$F1 3142

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
1669 5808 0.17576 GACCGTAGATGGCAAGCTCA 59.824 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3922 11173 5.575957 CCTGAACACTTTCACATATGCATC 58.424 41.667 0.19 0.0 36.79 3.91 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
1669 5808 0.175760 GACCGTAGATGGCAAGCTCA 59.824 55.000 0.00 0.0 0.00 4.26
1671 5810 1.003118 ACCGTAGATGGCAAGCTCAAA 59.997 47.619 0.00 0.0 0.00 2.69
2031 6179 3.181476 GGGACAATGCTGAGTTTGTGTTT 60.181 43.478 7.48 0.0 36.25 2.83
2194 6351 0.740737 GGATGATCCGGCAAGGTTTG 59.259 55.000 0.00 0.0 41.99 2.93
3615 9801 1.399440 CATGCATTCTCTGAACCACGG 59.601 52.381 0.00 0.0 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1669 5808 0.899720 TCATCCGGCCGACTAAGTTT 59.100 50.000 30.73 0.00 0.00 2.66
1671 5810 0.460311 CTTCATCCGGCCGACTAAGT 59.540 55.000 30.73 2.02 0.00 2.24
1869 6017 3.863142 ATTTGAAGCTCCTTGACATGC 57.137 42.857 0.00 0.00 0.00 4.06
2031 6179 0.461870 CGCATCGACCCATCTCCAAA 60.462 55.000 0.00 0.00 0.00 3.28
2194 6351 2.100749 ACCATATAAAGGCGCAAAAGGC 59.899 45.455 10.83 0.00 39.90 4.35
2195 6352 3.632145 AGACCATATAAAGGCGCAAAAGG 59.368 43.478 10.83 1.88 0.00 3.11
2196 6353 4.601019 CAGACCATATAAAGGCGCAAAAG 58.399 43.478 10.83 0.00 0.00 2.27
2197 6354 3.181491 GCAGACCATATAAAGGCGCAAAA 60.181 43.478 10.83 0.00 0.00 2.44
2198 6355 2.357637 GCAGACCATATAAAGGCGCAAA 59.642 45.455 10.83 0.00 0.00 3.68
2199 6356 1.946768 GCAGACCATATAAAGGCGCAA 59.053 47.619 10.83 0.00 0.00 4.85
2200 6357 1.134250 TGCAGACCATATAAAGGCGCA 60.134 47.619 10.83 0.00 0.00 6.09
2201 6358 1.593196 TGCAGACCATATAAAGGCGC 58.407 50.000 0.00 0.00 0.00 6.53
2202 6359 4.389992 CACTATGCAGACCATATAAAGGCG 59.610 45.833 0.00 0.00 35.91 5.52
3922 11173 5.575957 CCTGAACACTTTCACATATGCATC 58.424 41.667 0.19 0.00 36.79 3.91
4139 11390 4.455366 ACGCTACAGGGTTAGGCT 57.545 55.556 0.00 0.00 38.04 4.58


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

AutoCloner maintained by Alex Coulton.