Multiple sequence alignment - TraesCS1B01G463200

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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 TraesCS1B01G463200 chr1B 100.000 2537 0 0 1 2537 675546575 675544039 0.000000e+00 4686.0
1 TraesCS1B01G463200 chr1B 76.900 1000 196 20 621 1603 675555222 675554241 3.710000e-148 534.0
2 TraesCS1B01G463200 chr1B 94.207 328 17 1 1 328 561638789 561639114 1.360000e-137 499.0
3 TraesCS1B01G463200 chr1B 93.976 332 17 2 1 332 613249018 613249346 1.360000e-137 499.0
4 TraesCS1B01G463200 chr1B 92.694 219 12 2 404 622 605270048 605270262 1.890000e-81 313.0
5 TraesCS1B01G463200 chr1B 92.035 226 9 2 404 621 605440152 605440376 2.450000e-80 309.0
6 TraesCS1B01G463200 chr1B 94.030 201 11 1 366 566 615700097 615699898 1.140000e-78 303.0
7 TraesCS1B01G463200 chr1B 91.556 225 10 2 404 620 605433740 605433517 4.100000e-78 302.0
8 TraesCS1B01G463200 chr1B 92.228 193 14 1 329 521 571700675 571700866 3.220000e-69 272.0
9 TraesCS1B01G463200 chr1B 79.149 235 27 16 2315 2537 675377561 675377337 2.630000e-30 143.0
10 TraesCS1B01G463200 chr1B 88.889 81 1 2 548 620 615699897 615699817 2.690000e-15 93.5
11 TraesCS1B01G463200 chr1D 92.906 1029 56 7 621 1639 485092927 485091906 0.000000e+00 1480.0
12 TraesCS1B01G463200 chr1D 90.379 634 48 10 1914 2537 485091567 485090937 0.000000e+00 821.0
13 TraesCS1B01G463200 chr1D 77.008 996 194 22 621 1602 485102797 485101823 2.870000e-149 538.0
14 TraesCS1B01G463200 chr1D 93.262 282 16 2 1638 1919 485091877 485091599 1.820000e-111 412.0
15 TraesCS1B01G463200 chr1D 84.444 270 22 10 366 626 296590210 296589952 5.420000e-62 248.0
16 TraesCS1B01G463200 chr1A 91.139 1027 74 8 621 1639 582361480 582360463 0.000000e+00 1376.0
17 TraesCS1B01G463200 chr1A 89.292 607 53 9 1940 2537 582360009 582359406 0.000000e+00 750.0
18 TraesCS1B01G463200 chr1A 77.186 995 194 19 621 1602 582415479 582414505 1.330000e-152 549.0
19 TraesCS1B01G463200 chr1A 92.116 241 13 4 1638 1873 582360434 582360195 4.040000e-88 335.0
20 TraesCS1B01G463200 chr1A 87.166 187 17 5 2351 2537 582413176 582412997 3.310000e-49 206.0
21 TraesCS1B01G463200 chr1A 83.133 166 16 7 2380 2537 582280212 582280051 9.460000e-30 141.0
22 TraesCS1B01G463200 chr1A 84.071 113 18 0 1489 1601 582281949 582281837 2.670000e-20 110.0
23 TraesCS1B01G463200 chr2B 96.012 326 12 1 4 329 787789253 787788929 1.730000e-146 529.0
24 TraesCS1B01G463200 chr2B 90.909 330 26 4 1 326 151461421 151461092 8.330000e-120 440.0
25 TraesCS1B01G463200 chr2B 95.522 67 3 0 2471 2537 94929404 94929470 9.600000e-20 108.0
26 TraesCS1B01G463200 chr2A 94.012 334 18 2 1 332 765191035 765191368 2.910000e-139 505.0
27 TraesCS1B01G463200 chr5B 93.578 327 21 0 1 327 244132257 244132583 2.930000e-134 488.0
28 TraesCS1B01G463200 chr4A 93.293 328 22 0 1 328 674455928 674456255 3.790000e-133 484.0
29 TraesCS1B01G463200 chr4D 92.378 328 18 5 12 336 370527333 370527010 6.390000e-126 460.0
30 TraesCS1B01G463200 chr6B 90.419 334 28 4 1 331 703960923 703960591 1.080000e-118 436.0
31 TraesCS1B01G463200 chr6B 95.122 82 2 1 329 410 660463529 660463608 7.370000e-26 128.0
32 TraesCS1B01G463200 chr6B 100.000 45 0 0 332 376 114127379 114127335 1.620000e-12 84.2
33 TraesCS1B01G463200 chr4B 92.478 226 8 2 404 621 7772731 7772955 5.270000e-82 315.0
34 TraesCS1B01G463200 chr7A 88.722 266 12 3 363 620 611335633 611335888 2.450000e-80 309.0
35 TraesCS1B01G463200 chr7A 90.090 222 12 3 363 584 611329941 611330152 1.920000e-71 279.0
36 TraesCS1B01G463200 chr2D 85.768 267 21 8 366 620 58803181 58802920 1.500000e-67 267.0
37 TraesCS1B01G463200 chr7B 100.000 32 0 0 591 622 376804145 376804114 2.730000e-05 60.2


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 TraesCS1B01G463200 chr1B 675544039 675546575 2536 True 4686.000000 4686 100.000000 1 2537 1 chr1B.!!$R3 2536
1 TraesCS1B01G463200 chr1B 675554241 675555222 981 True 534.000000 534 76.900000 621 1603 1 chr1B.!!$R4 982
2 TraesCS1B01G463200 chr1D 485090937 485092927 1990 True 904.333333 1480 92.182333 621 2537 3 chr1D.!!$R3 1916
3 TraesCS1B01G463200 chr1D 485101823 485102797 974 True 538.000000 538 77.008000 621 1602 1 chr1D.!!$R2 981
4 TraesCS1B01G463200 chr1A 582359406 582361480 2074 True 820.333333 1376 90.849000 621 2537 3 chr1A.!!$R2 1916
5 TraesCS1B01G463200 chr1A 582412997 582415479 2482 True 377.500000 549 82.176000 621 2537 2 chr1A.!!$R3 1916


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
274 275 0.035036 TTGTAATCGTGGCCGGTTGA 59.965 50.0 1.9 0.0 38.06 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 2315 0.394565 ATGGCCACGGAGAGCTTATC 59.605 55.0 8.16 0.0 0.0 1.75 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.