Multiple sequence alignment - TraesCS7A01G002600

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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 TraesCS7A01G002600 chr7A 100.000 4875 0 0 1 4875 1520562 1525436 0.000000e+00 9003.0
1 TraesCS7A01G002600 chr7A 81.215 1448 214 27 2371 3799 176286096 176284688 0.000000e+00 1114.0
2 TraesCS7A01G002600 chr7A 83.978 362 41 12 4439 4783 9667602 9667963 1.010000e-86 331.0
3 TraesCS7A01G002600 chr7D 87.679 1672 140 28 2250 3897 2049456 2047827 0.000000e+00 1886.0
4 TraesCS7A01G002600 chr7D 81.793 1450 207 36 2371 3803 174335514 174334105 0.000000e+00 1162.0
5 TraesCS7A01G002600 chr7D 89.922 516 44 6 4279 4786 2046441 2045926 0.000000e+00 658.0
6 TraesCS7A01G002600 chr7D 89.757 371 35 1 1 368 2050184 2049814 5.710000e-129 472.0
7 TraesCS7A01G002600 chr7D 88.142 253 16 4 4025 4268 2047689 2047442 6.170000e-74 289.0
8 TraesCS7A01G002600 chr7D 82.215 298 39 11 4465 4749 10345587 10345883 1.360000e-60 244.0
9 TraesCS7A01G002600 chr7D 85.417 240 26 2 905 1135 2049437 2049198 1.750000e-59 241.0
10 TraesCS7A01G002600 chr7D 95.420 131 5 1 4745 4875 2046014 2045885 1.780000e-49 207.0
11 TraesCS7A01G002600 chr7D 90.511 137 10 2 1737 1872 234218313 234218179 1.390000e-40 178.0
12 TraesCS7A01G002600 chr7D 82.418 182 22 8 726 900 93689896 93689718 3.040000e-32 150.0
13 TraesCS7A01G002600 chr7D 88.608 79 9 0 4796 4874 10463597 10463675 4.020000e-16 97.1
14 TraesCS7A01G002600 chr7D 100.000 34 0 0 2008 2041 36510772 36510739 4.070000e-06 63.9
15 TraesCS7A01G002600 chr7D 100.000 31 0 0 3905 3935 2047831 2047801 1.900000e-04 58.4
16 TraesCS7A01G002600 chr7D 100.000 29 0 0 3457 3485 180842532 180842504 2.000000e-03 54.7
17 TraesCS7A01G002600 chr7B 81.561 1448 209 30 2371 3799 138865245 138863837 0.000000e+00 1142.0
18 TraesCS7A01G002600 chr7B 92.193 269 17 3 1184 1450 350809027 350808761 1.280000e-100 377.0
19 TraesCS7A01G002600 chr7B 92.193 269 16 4 1184 1450 174202043 174201778 4.610000e-100 375.0
20 TraesCS7A01G002600 chr7B 80.645 186 24 8 718 900 46896933 46896757 3.060000e-27 134.0
21 TraesCS7A01G002600 chr4A 92.123 584 40 4 4297 4875 742718513 742717931 0.000000e+00 819.0
22 TraesCS7A01G002600 chr4A 83.944 355 44 9 4439 4783 728350526 728350877 1.310000e-85 327.0
23 TraesCS7A01G002600 chr4A 86.220 254 25 6 4525 4772 728354845 728355094 2.890000e-67 267.0
24 TraesCS7A01G002600 chr4A 85.283 265 29 2 4607 4871 743639363 743639109 1.040000e-66 265.0
25 TraesCS7A01G002600 chr4A 81.985 272 37 7 4525 4788 729880328 729880061 2.280000e-53 220.0
26 TraesCS7A01G002600 chr4A 87.413 143 17 1 4565 4706 743362899 743362757 3.900000e-36 163.0
27 TraesCS7A01G002600 chr4A 85.612 139 16 2 4611 4747 743636023 743635887 5.090000e-30 143.0
28 TraesCS7A01G002600 chr4A 88.542 96 10 1 4780 4875 728350827 728350921 1.110000e-21 115.0
29 TraesCS7A01G002600 chr3B 93.309 269 13 4 1184 1450 470235736 470235471 4.570000e-105 392.0
30 TraesCS7A01G002600 chrUn 93.156 263 12 5 1190 1448 136982574 136982314 9.900000e-102 381.0
31 TraesCS7A01G002600 chrUn 92.913 127 5 4 1719 1845 355880479 355880601 1.080000e-41 182.0
32 TraesCS7A01G002600 chrUn 96.875 32 1 0 3454 3485 37409962 37409993 2.000000e-03 54.7
33 TraesCS7A01G002600 chr1B 92.222 270 18 2 1183 1450 370379907 370379639 3.560000e-101 379.0
34 TraesCS7A01G002600 chr1B 92.193 269 17 3 1184 1450 78046043 78045777 1.280000e-100 377.0
35 TraesCS7A01G002600 chr1B 89.091 55 6 0 3449 3503 590092113 590092167 8.760000e-08 69.4
36 TraesCS7A01G002600 chr1B 94.444 36 2 0 2006 2041 352460707 352460742 6.820000e-04 56.5
37 TraesCS7A01G002600 chr4B 92.222 270 15 5 1184 1450 246424681 246424947 1.280000e-100 377.0
38 TraesCS7A01G002600 chr4B 92.193 269 16 4 1184 1450 47562132 47562397 4.610000e-100 375.0
39 TraesCS7A01G002600 chr4B 97.436 117 3 0 1737 1853 85349990 85349874 2.980000e-47 200.0
40 TraesCS7A01G002600 chr5B 92.193 269 16 4 1184 1450 312808058 312807793 4.610000e-100 375.0
41 TraesCS7A01G002600 chr5B 82.051 78 10 3 3449 3524 65525266 65525191 4.070000e-06 63.9
42 TraesCS7A01G002600 chr5B 100.000 32 0 0 3454 3485 567581422 567581391 5.270000e-05 60.2
43 TraesCS7A01G002600 chr3D 83.558 371 51 6 1 368 127333943 127333580 6.040000e-89 339.0
44 TraesCS7A01G002600 chr3D 100.000 28 0 0 3458 3485 709031 709058 9.000000e-03 52.8
45 TraesCS7A01G002600 chr2B 99.083 109 1 0 1739 1847 494265523 494265415 3.850000e-46 196.0
46 TraesCS7A01G002600 chr2B 95.798 119 5 0 1737 1855 475485541 475485659 4.980000e-45 193.0
47 TraesCS7A01G002600 chr2B 100.000 34 0 0 2008 2041 672819330 672819363 4.070000e-06 63.9
48 TraesCS7A01G002600 chr4D 92.593 135 8 2 1715 1848 450206644 450206777 4.980000e-45 193.0
49 TraesCS7A01G002600 chr2D 97.345 113 3 0 1739 1851 627971513 627971625 4.980000e-45 193.0
50 TraesCS7A01G002600 chr2D 82.143 84 15 0 3438 3521 5268328 5268411 6.770000e-09 73.1
51 TraesCS7A01G002600 chr5A 95.763 118 5 0 1738 1855 656477312 656477429 1.790000e-44 191.0
52 TraesCS7A01G002600 chr3A 98.165 109 2 0 1739 1847 583676591 583676699 1.790000e-44 191.0
53 TraesCS7A01G002600 chr2A 82.609 161 28 0 3402 3562 528170605 528170765 5.090000e-30 143.0
54 TraesCS7A01G002600 chr2A 83.333 84 14 0 3438 3521 3817586 3817669 1.450000e-10 78.7
55 TraesCS7A01G002600 chr2A 97.059 34 1 0 2008 2041 201087763 201087796 1.900000e-04 58.4
56 TraesCS7A01G002600 chr1A 83.673 98 16 0 3405 3502 110283285 110283188 5.200000e-15 93.5
57 TraesCS7A01G002600 chr1A 89.091 55 6 0 3449 3503 533410341 533410395 8.760000e-08 69.4
58 TraesCS7A01G002600 chr1D 89.091 55 6 0 3449 3503 436120989 436121043 8.760000e-08 69.4
59 TraesCS7A01G002600 chr5D 97.297 37 1 0 3449 3485 65010003 65010039 4.070000e-06 63.9
60 TraesCS7A01G002600 chr5D 100.000 34 0 0 2008 2041 169245945 169245978 4.070000e-06 63.9
61 TraesCS7A01G002600 chr5D 100.000 32 0 0 3454 3485 461603942 461603911 5.270000e-05 60.2
62 TraesCS7A01G002600 chr6B 94.444 36 2 0 2006 2041 345284068 345284103 6.820000e-04 56.5


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 TraesCS7A01G002600 chr7A 1520562 1525436 4874 False 9003.000000 9003 100.000000 1 4875 1 chr7A.!!$F1 4874
1 TraesCS7A01G002600 chr7A 176284688 176286096 1408 True 1114.000000 1114 81.215000 2371 3799 1 chr7A.!!$R1 1428
2 TraesCS7A01G002600 chr7D 174334105 174335514 1409 True 1162.000000 1162 81.793000 2371 3803 1 chr7D.!!$R3 1432
3 TraesCS7A01G002600 chr7D 2045885 2050184 4299 True 544.485714 1886 90.905286 1 4875 7 chr7D.!!$R6 4874
4 TraesCS7A01G002600 chr7B 138863837 138865245 1408 True 1142.000000 1142 81.561000 2371 3799 1 chr7B.!!$R2 1428
5 TraesCS7A01G002600 chr4A 742717931 742718513 582 True 819.000000 819 92.123000 4297 4875 1 chr4A.!!$R2 578
6 TraesCS7A01G002600 chr4A 728350526 728355094 4568 False 236.333333 327 86.235333 4439 4875 3 chr4A.!!$F1 436
7 TraesCS7A01G002600 chr4A 743635887 743639363 3476 True 204.000000 265 85.447500 4607 4871 2 chr4A.!!$R4 264


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
585 722 0.034756 TCGAGGCACTTGCTTGCTTA 59.965 50.0 0.38 0.00 41.55 3.09 F
1145 1282 0.035458 CCCGCCACTCTATCATTCCC 59.965 60.0 0.00 0.00 0.00 3.97 F
1725 1862 0.109781 GTGCCCGTGCTTTGTGTATG 60.110 55.0 0.00 0.00 38.71 2.39 F
1935 2072 0.166814 CGCAACTGTTAGCTTCTGCC 59.833 55.0 0.00 0.00 40.80 4.85 F
3247 3487 0.179026 CTATGCTGCAGCCAGGTCAT 60.179 55.0 34.64 22.14 39.54 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1444 1581 0.033699 AGTGTCCCTCCGGTAGTACC 60.034 60.0 9.50 9.5 34.05 3.34 R
2251 2461 0.316522 CGTGATGATCCGGCTCTGAT 59.683 55.0 6.88 0.0 0.00 2.90 R
3122 3362 0.324943 CCGTCTCTCCACCATGGTTT 59.675 55.0 16.84 0.0 39.03 3.27 R
3598 3841 0.392461 TGCTCGGTGCCATCTTAACC 60.392 55.0 0.00 0.0 42.00 2.85 R
4275 4601 0.185901 ACCACCACCAGCATGTTTCT 59.814 50.0 0.00 0.0 0.00 2.52 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)



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AutoCloner maintained by Alex Coulton.