Multiple sequence alignment - TraesCS5B01G340700

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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 TraesCS5B01G340700 chr5B 100.000 2468 0 0 1 2468 525550046 525547579 0.000000e+00 4558
1 TraesCS5B01G340700 chr2B 96.733 2479 48 6 1 2468 109886727 109889183 0.000000e+00 4098
2 TraesCS5B01G340700 chr2B 97.833 2030 44 0 439 2468 614643420 614645449 0.000000e+00 3506
3 TraesCS5B01G340700 chr2B 91.957 373 9 2 1 373 614642696 614643047 1.020000e-138 503
4 TraesCS5B01G340700 chr1B 95.530 2483 72 8 1 2468 126921410 126923868 0.000000e+00 3934
5 TraesCS5B01G340700 chr1D 92.888 1645 77 10 1 1626 288858320 288859943 0.000000e+00 2353
6 TraesCS5B01G340700 chr1D 97.476 832 21 0 1637 2468 288860317 288861148 0.000000e+00 1421
7 TraesCS5B01G340700 chr1D 85.714 399 25 13 6 400 265145762 265145392 2.300000e-105 392
8 TraesCS5B01G340700 chr2A 93.493 1583 64 14 1 1567 354528936 354530495 0.000000e+00 2316
9 TraesCS5B01G340700 chr2A 93.363 1582 68 7 4 1570 494101281 494099722 0.000000e+00 2305
10 TraesCS5B01G340700 chr2A 96.635 832 22 1 1637 2468 354530501 354531326 0.000000e+00 1376
11 TraesCS5B01G340700 chr2A 96.170 235 8 1 1637 1871 494099719 494099486 1.380000e-102 383
12 TraesCS5B01G340700 chr2A 87.317 205 16 6 436 630 62918524 62918728 2.470000e-55 226
13 TraesCS5B01G340700 chr7A 92.744 1585 71 12 1 1567 320507546 320509104 0.000000e+00 2250
14 TraesCS5B01G340700 chr7A 96.635 832 28 0 1637 2468 320509110 320509941 0.000000e+00 1382
15 TraesCS5B01G340700 chr7D 91.413 1642 95 12 5 1629 61524199 61522587 0.000000e+00 2209
16 TraesCS5B01G340700 chr7D 97.596 832 20 0 1637 2468 61522216 61521385 0.000000e+00 1426
17 TraesCS5B01G340700 chr1A 91.289 1653 93 15 1 1626 408631033 408632661 0.000000e+00 2207
18 TraesCS5B01G340700 chr4D 97.236 832 23 0 1637 2468 382847075 382846244 0.000000e+00 1410
19 TraesCS5B01G340700 chr4D 89.011 364 18 3 4 366 382849336 382848994 4.880000e-117 431
20 TraesCS5B01G340700 chr6D 93.741 703 34 4 1775 2468 93876313 93877014 0.000000e+00 1046


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 TraesCS5B01G340700 chr5B 525547579 525550046 2467 True 4558.0 4558 100.0000 1 2468 1 chr5B.!!$R1 2467
1 TraesCS5B01G340700 chr2B 109886727 109889183 2456 False 4098.0 4098 96.7330 1 2468 1 chr2B.!!$F1 2467
2 TraesCS5B01G340700 chr2B 614642696 614645449 2753 False 2004.5 3506 94.8950 1 2468 2 chr2B.!!$F2 2467
3 TraesCS5B01G340700 chr1B 126921410 126923868 2458 False 3934.0 3934 95.5300 1 2468 1 chr1B.!!$F1 2467
4 TraesCS5B01G340700 chr1D 288858320 288861148 2828 False 1887.0 2353 95.1820 1 2468 2 chr1D.!!$F1 2467
5 TraesCS5B01G340700 chr2A 354528936 354531326 2390 False 1846.0 2316 95.0640 1 2468 2 chr2A.!!$F2 2467
6 TraesCS5B01G340700 chr2A 494099486 494101281 1795 True 1344.0 2305 94.7665 4 1871 2 chr2A.!!$R1 1867
7 TraesCS5B01G340700 chr7A 320507546 320509941 2395 False 1816.0 2250 94.6895 1 2468 2 chr7A.!!$F1 2467
8 TraesCS5B01G340700 chr7D 61521385 61524199 2814 True 1817.5 2209 94.5045 5 2468 2 chr7D.!!$R1 2463
9 TraesCS5B01G340700 chr1A 408631033 408632661 1628 False 2207.0 2207 91.2890 1 1626 1 chr1A.!!$F1 1625
10 TraesCS5B01G340700 chr4D 382846244 382849336 3092 True 920.5 1410 93.1235 4 2468 2 chr4D.!!$R1 2464
11 TraesCS5B01G340700 chr6D 93876313 93877014 701 False 1046.0 1046 93.7410 1775 2468 1 chr6D.!!$F1 693

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
342 346 0.107831 CGTCCTCAACCCTTCCACAA 59.892 55.0 0.0 0.0 0.0 3.33 F
1302 1628 0.323302 TGATTTGGACGGCTGCACTA 59.677 50.0 0.5 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1456 1782 1.134877 CAGACCAGATCAGCACGACAT 60.135 52.381 0.0 0.0 0.00 3.06 R
2345 3537 1.943693 CAAAACAACAGCGTGGCCG 60.944 57.895 0.0 0.0 37.07 6.13 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
214 218 9.664332 GGCAACTATGATCTATTTAGATGACAT 57.336 33.333 4.85 6.07 42.79 3.06
342 346 0.107831 CGTCCTCAACCCTTCCACAA 59.892 55.000 0.00 0.00 0.00 3.33
375 380 3.591527 ACCCTAGTCATTTTCCATCCACA 59.408 43.478 0.00 0.00 0.00 4.17
639 961 4.880537 CTCGATCCCGCGCTGCTT 62.881 66.667 5.56 0.00 35.37 3.91
811 1134 0.630673 CCCCTCCCAAATCCATCACA 59.369 55.000 0.00 0.00 0.00 3.58
941 1266 1.068264 CACTCTCTGTGCTTGTAGCGA 60.068 52.381 0.00 0.00 46.26 4.93
1302 1628 0.323302 TGATTTGGACGGCTGCACTA 59.677 50.000 0.50 0.00 0.00 2.74
1682 2862 8.660373 GCTATTGAAGATCCATTTATACTTCCG 58.340 37.037 0.00 0.00 36.96 4.30
1743 2929 3.990092 TGTGATTCGTTCTGTAGCTTGT 58.010 40.909 0.00 0.00 0.00 3.16
2345 3537 3.895232 TCTTCAGGGCTATGAGTTGAC 57.105 47.619 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 106 4.580580 GGAAAACCTTCTCATTGTGTCACT 59.419 41.667 4.27 0.00 0.00 3.41
216 220 9.793252 GATGTTGTGAAATTATGTCAGCTATTT 57.207 29.630 0.00 0.00 0.00 1.40
217 221 8.959548 TGATGTTGTGAAATTATGTCAGCTATT 58.040 29.630 0.00 0.00 0.00 1.73
218 222 8.510243 TGATGTTGTGAAATTATGTCAGCTAT 57.490 30.769 0.00 0.00 0.00 2.97
219 223 7.920160 TGATGTTGTGAAATTATGTCAGCTA 57.080 32.000 0.00 0.00 0.00 3.32
220 224 6.822667 TGATGTTGTGAAATTATGTCAGCT 57.177 33.333 0.00 0.00 0.00 4.24
221 225 8.400947 AGTATGATGTTGTGAAATTATGTCAGC 58.599 33.333 0.00 0.00 0.00 4.26
222 226 9.712359 CAGTATGATGTTGTGAAATTATGTCAG 57.288 33.333 0.00 0.00 39.69 3.51
223 227 8.183536 GCAGTATGATGTTGTGAAATTATGTCA 58.816 33.333 0.00 0.00 39.69 3.58
224 228 8.183536 TGCAGTATGATGTTGTGAAATTATGTC 58.816 33.333 0.00 0.00 39.69 3.06
225 229 7.970061 GTGCAGTATGATGTTGTGAAATTATGT 59.030 33.333 0.00 0.00 39.69 2.29
226 230 8.186163 AGTGCAGTATGATGTTGTGAAATTATG 58.814 33.333 0.00 0.00 39.69 1.90
227 231 8.284945 AGTGCAGTATGATGTTGTGAAATTAT 57.715 30.769 0.00 0.00 39.69 1.28
228 232 7.607607 AGAGTGCAGTATGATGTTGTGAAATTA 59.392 33.333 0.00 0.00 39.69 1.40
229 233 6.432162 AGAGTGCAGTATGATGTTGTGAAATT 59.568 34.615 0.00 0.00 39.69 1.82
230 234 5.942236 AGAGTGCAGTATGATGTTGTGAAAT 59.058 36.000 0.00 0.00 39.69 2.17
231 235 5.179929 CAGAGTGCAGTATGATGTTGTGAAA 59.820 40.000 10.74 0.00 39.69 2.69
232 236 4.692155 CAGAGTGCAGTATGATGTTGTGAA 59.308 41.667 10.74 0.00 39.69 3.18
342 346 5.952347 AATGACTAGGGTTTCGGAGTTAT 57.048 39.130 0.00 0.00 0.00 1.89
375 380 1.379146 GAAAGAAAGGAGGCGGGGT 59.621 57.895 0.00 0.00 0.00 4.95
811 1134 2.476199 CAGAGGGAGATTTGGGAGACT 58.524 52.381 0.00 0.00 0.00 3.24
971 1297 2.338984 GAGTGGACGAACAGCCGT 59.661 61.111 0.00 0.00 46.43 5.68
1302 1628 4.020751 CCATGGATCATATCGAACTCCTGT 60.021 45.833 5.56 0.00 0.00 4.00
1456 1782 1.134877 CAGACCAGATCAGCACGACAT 60.135 52.381 0.00 0.00 0.00 3.06
1459 1785 1.745653 CTACAGACCAGATCAGCACGA 59.254 52.381 0.00 0.00 0.00 4.35
1682 2862 5.371526 TCTATCCAGATTCTGAAACCATGC 58.628 41.667 15.36 0.00 32.44 4.06
1743 2929 7.883391 TTCTGTTATTTCCAAGTACCAAACA 57.117 32.000 0.00 0.00 0.00 2.83
1886 3072 6.672357 GCAAGTACTAGTAAATCTTTGCACCG 60.672 42.308 20.59 6.42 0.00 4.94
2345 3537 1.943693 CAAAACAACAGCGTGGCCG 60.944 57.895 0.00 0.00 37.07 6.13
2356 3548 6.985117 AGAATTATCAAGCAGAGCAAAACAA 58.015 32.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.