Multiple sequence alignment - TraesCS7D01G469600

Loading Multiple Alignment...

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 TraesCS7D01G469600 chr7D 100.000 2402 0 0 1 2402 582667852 582665451 0.000000e+00 4436.0
1 TraesCS7D01G469600 chr7D 98.433 2425 13 3 1 2402 582562548 582560126 0.000000e+00 4244.0
2 TraesCS7D01G469600 chr7D 90.671 686 49 7 1726 2402 582797913 582797234 0.000000e+00 898.0
3 TraesCS7D01G469600 chr7D 84.178 967 100 22 707 1644 582748171 582747229 0.000000e+00 889.0
4 TraesCS7D01G469600 chr7D 88.011 367 17 3 1 341 583052112 583051747 2.220000e-110 409.0
5 TraesCS7D01G469600 chr7D 84.864 403 31 9 1 374 84416006 84416407 1.740000e-101 379.0
6 TraesCS7D01G469600 chr7A 91.860 1376 99 7 685 2056 674802818 674801452 0.000000e+00 1908.0
7 TraesCS7D01G469600 chr7A 90.131 1378 105 11 685 2056 674672194 674670842 0.000000e+00 1762.0
8 TraesCS7D01G469600 chr7A 90.192 938 78 5 685 1611 674608774 674607840 0.000000e+00 1210.0
9 TraesCS7D01G469600 chr7A 93.013 229 12 3 454 681 674672486 674672261 4.950000e-87 331.0
10 TraesCS7D01G469600 chr7A 91.703 229 15 3 454 681 674803110 674802885 4.980000e-82 315.0
11 TraesCS7D01G469600 chr7A 91.818 220 16 1 464 681 674609060 674608841 3.000000e-79 305.0
12 TraesCS7D01G469600 chr7A 91.818 220 16 1 464 681 674797421 674797202 3.000000e-79 305.0
13 TraesCS7D01G469600 chr7B 92.090 1201 79 8 685 1881 650574298 650573110 0.000000e+00 1677.0
14 TraesCS7D01G469600 chr7B 91.923 1201 81 7 685 1881 650550918 650549730 0.000000e+00 1666.0
15 TraesCS7D01G469600 chr7B 91.757 1201 79 9 685 1881 650585224 650584040 0.000000e+00 1652.0
16 TraesCS7D01G469600 chr7B 91.424 1201 87 7 685 1881 650540368 650539180 0.000000e+00 1633.0
17 TraesCS7D01G469600 chr7B 91.257 1201 76 9 685 1881 650562443 650561268 0.000000e+00 1609.0
18 TraesCS7D01G469600 chr7B 84.635 384 30 12 16 371 388160966 388160584 2.940000e-94 355.0
19 TraesCS7D01G469600 chr7B 92.308 195 15 0 487 681 650540629 650540435 6.540000e-71 278.0
20 TraesCS7D01G469600 chr7B 92.308 195 15 0 487 681 650551179 650550985 6.540000e-71 278.0
21 TraesCS7D01G469600 chr7B 92.308 195 15 0 487 681 650551886 650551692 6.540000e-71 278.0
22 TraesCS7D01G469600 chr7B 92.308 195 15 0 487 681 650562704 650562510 6.540000e-71 278.0
23 TraesCS7D01G469600 chr7B 80.571 175 22 10 1673 1837 650246396 650246224 9.020000e-25 124.0
24 TraesCS7D01G469600 chr7B 80.571 175 22 10 1673 1837 650260970 650260798 9.020000e-25 124.0
25 TraesCS7D01G469600 chr7B 80.571 175 22 10 1673 1837 650273331 650273159 9.020000e-25 124.0
26 TraesCS7D01G469600 chr7B 92.308 65 3 1 685 749 650551625 650551563 9.140000e-15 91.6
27 TraesCS7D01G469600 chr1D 85.894 397 25 16 1 367 366007457 366007062 6.220000e-106 394.0
28 TraesCS7D01G469600 chr1D 82.323 396 42 17 1 369 365549326 365548932 3.850000e-83 318.0
29 TraesCS7D01G469600 chr1D 85.714 210 8 8 7 194 470651920 470651711 4.050000e-48 202.0
30 TraesCS7D01G469600 chr1D 90.361 83 6 2 341 423 454645979 454645899 9.080000e-20 108.0
31 TraesCS7D01G469600 chr1D 96.610 59 1 1 366 424 387054733 387054676 1.970000e-16 97.1
32 TraesCS7D01G469600 chr1D 100.000 28 0 0 421 448 400181647 400181674 4.000000e-03 52.8
33 TraesCS7D01G469600 chr6D 87.870 338 34 5 92 423 377888917 377889253 8.050000e-105 390.0
34 TraesCS7D01G469600 chr6D 82.161 398 34 14 1 363 341150397 341150792 8.340000e-80 307.0
35 TraesCS7D01G469600 chr6D 83.750 80 10 3 1995 2073 328746907 328746984 3.310000e-09 73.1
36 TraesCS7D01G469600 chr4B 83.156 469 36 20 1 427 464540610 464541077 2.900000e-104 388.0
37 TraesCS7D01G469600 chr2A 84.576 389 31 7 6 367 657060705 657061091 2.270000e-95 359.0
38 TraesCS7D01G469600 chr2A 100.000 28 0 0 422 449 677949561 677949534 4.000000e-03 52.8
39 TraesCS7D01G469600 chr4A 82.183 449 47 13 9 425 731488564 731489011 2.940000e-94 355.0
40 TraesCS7D01G469600 chr2D 87.948 307 30 4 122 423 460639954 460640258 2.940000e-94 355.0
41 TraesCS7D01G469600 chr1A 82.183 449 43 12 6 423 556100645 556101087 3.800000e-93 351.0
42 TraesCS7D01G469600 chr1A 82.870 216 14 10 1 194 564350348 564350134 3.170000e-39 172.0
43 TraesCS7D01G469600 chr6A 83.005 406 32 10 1 370 483545827 483545423 1.380000e-87 333.0
44 TraesCS7D01G469600 chr4D 96.907 97 3 0 2 98 58983830 58983734 1.910000e-36 163.0
45 TraesCS7D01G469600 chr4D 100.000 29 0 0 422 450 100318382 100318410 1.000000e-03 54.7
46 TraesCS7D01G469600 chr5B 91.176 68 6 0 362 429 82466649 82466582 2.540000e-15 93.5
47 TraesCS7D01G469600 chr5D 89.041 73 7 1 357 428 510874543 510874471 3.290000e-14 89.8
48 TraesCS7D01G469600 chr5A 100.000 28 0 0 422 449 650141352 650141325 4.000000e-03 52.8


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 TraesCS7D01G469600 chr7D 582665451 582667852 2401 True 4436.0 4436 100.00000 1 2402 1 chr7D.!!$R2 2401
1 TraesCS7D01G469600 chr7D 582560126 582562548 2422 True 4244.0 4244 98.43300 1 2402 1 chr7D.!!$R1 2401
2 TraesCS7D01G469600 chr7D 582797234 582797913 679 True 898.0 898 90.67100 1726 2402 1 chr7D.!!$R4 676
3 TraesCS7D01G469600 chr7D 582747229 582748171 942 True 889.0 889 84.17800 707 1644 1 chr7D.!!$R3 937
4 TraesCS7D01G469600 chr7A 674801452 674803110 1658 True 1111.5 1908 91.78150 454 2056 2 chr7A.!!$R4 1602
5 TraesCS7D01G469600 chr7A 674670842 674672486 1644 True 1046.5 1762 91.57200 454 2056 2 chr7A.!!$R3 1602
6 TraesCS7D01G469600 chr7A 674607840 674609060 1220 True 757.5 1210 91.00500 464 1611 2 chr7A.!!$R2 1147
7 TraesCS7D01G469600 chr7B 650573110 650574298 1188 True 1677.0 1677 92.09000 685 1881 1 chr7B.!!$R5 1196
8 TraesCS7D01G469600 chr7B 650584040 650585224 1184 True 1652.0 1652 91.75700 685 1881 1 chr7B.!!$R6 1196
9 TraesCS7D01G469600 chr7B 650539180 650540629 1449 True 955.5 1633 91.86600 487 1881 2 chr7B.!!$R7 1394
10 TraesCS7D01G469600 chr7B 650561268 650562704 1436 True 943.5 1609 91.78250 487 1881 2 chr7B.!!$R9 1394
11 TraesCS7D01G469600 chr7B 650549730 650551886 2156 True 578.4 1666 92.21175 487 1881 4 chr7B.!!$R8 1394

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
364 388 2.429927 GCAAATATGAGGGGTGCCC 58.57 57.895 0.0 0.0 45.9 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2906 3.189702 CAGTATCTTAGAGGCGCTCCTAC 59.81 52.174 7.64 0.0 44.46 3.18 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
243 267 3.372206 CCCGATCTTGTGCTTCTTTGTAG 59.628 47.826 0.0 0.0 0.00 2.74
259 283 6.503524 TCTTTGTAGCTCAATTTTGTTGTCC 58.496 36.000 0.0 0.0 35.84 4.02
364 388 2.429927 GCAAATATGAGGGGTGCCC 58.570 57.895 0.0 0.0 45.90 5.36
1531 2362 1.735198 CAAGCGTTTGCATGGGCTG 60.735 57.895 0.0 0.0 46.23 4.85
2074 2906 2.358247 GCACACACACCCTACCGG 60.358 66.667 0.0 0.0 37.81 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 267 2.286772 ACGACGGACAACAAAATTGAGC 60.287 45.455 0.00 0.00 0.00 4.26
259 283 3.972950 ATCCTACAAGATCAGACGACG 57.027 47.619 0.00 0.00 0.00 5.12
380 404 1.533625 CAAATCCGGCTCCTCAAACA 58.466 50.000 0.00 0.00 0.00 2.83
1936 2768 5.709631 TGTACATATGGCATGCGGAATAATT 59.290 36.000 12.44 4.16 0.00 1.40
2074 2906 3.189702 CAGTATCTTAGAGGCGCTCCTAC 59.810 52.174 7.64 0.00 44.46 3.18


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

AutoCloner maintained by Alex Coulton.