Multiple sequence alignment - TraesCS3A01G076100

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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 TraesCS3A01G076100 chr3A 100.000 2450 0 0 1 2450 47065170 47067619 0.000000e+00 4525
1 TraesCS3A01G076100 chr7A 97.718 2454 34 4 1 2450 563485579 563483144 0.000000e+00 4202
2 TraesCS3A01G076100 chr5A 97.617 2056 44 4 399 2450 438798068 438796014 0.000000e+00 3520
3 TraesCS3A01G076100 chr5A 97.619 2058 37 6 398 2450 626202561 626200511 0.000000e+00 3518
4 TraesCS3A01G076100 chr6A 97.522 2058 45 4 398 2450 708750 710806 0.000000e+00 3513
5 TraesCS3A01G076100 chr2A 97.472 2057 43 4 398 2450 632421465 632423516 0.000000e+00 3502
6 TraesCS3A01G076100 chr2A 95.965 2057 45 9 398 2450 58986214 58988236 0.000000e+00 3304
7 TraesCS3A01G076100 chr2A 93.917 411 9 6 1 407 58985873 58986271 7.490000e-170 606
8 TraesCS3A01G076100 chr2A 97.006 334 6 2 75 407 632421192 632421522 2.130000e-155 558
9 TraesCS3A01G076100 chr1A 97.376 2058 46 6 398 2450 381110281 381108227 0.000000e+00 3494
10 TraesCS3A01G076100 chr1A 97.279 2058 50 4 398 2450 242736444 242734388 0.000000e+00 3485
11 TraesCS3A01G076100 chr1A 94.377 409 11 4 1 407 381110622 381110224 3.460000e-173 617
12 TraesCS3A01G076100 chr1A 98.209 335 4 1 75 407 242736721 242736387 3.510000e-163 584
13 TraesCS3A01G076100 chr3B 92.382 2468 97 30 1 2450 513952174 513954568 0.000000e+00 3432
14 TraesCS3A01G076100 chr2B 97.080 411 7 3 1 407 692622201 692621792 0.000000e+00 688
15 TraesCS3A01G076100 chr4A 95.620 411 9 6 1 407 49220858 49220453 0.000000e+00 651
16 TraesCS3A01G076100 chr7B 96.078 357 11 2 53 406 126217867 126217511 1.630000e-161 579
17 TraesCS3A01G076100 chr4B 94.400 375 16 3 1 371 639149073 639148700 2.730000e-159 571


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 TraesCS3A01G076100 chr3A 47065170 47067619 2449 False 4525.0 4525 100.0000 1 2450 1 chr3A.!!$F1 2449
1 TraesCS3A01G076100 chr7A 563483144 563485579 2435 True 4202.0 4202 97.7180 1 2450 1 chr7A.!!$R1 2449
2 TraesCS3A01G076100 chr5A 438796014 438798068 2054 True 3520.0 3520 97.6170 399 2450 1 chr5A.!!$R1 2051
3 TraesCS3A01G076100 chr5A 626200511 626202561 2050 True 3518.0 3518 97.6190 398 2450 1 chr5A.!!$R2 2052
4 TraesCS3A01G076100 chr6A 708750 710806 2056 False 3513.0 3513 97.5220 398 2450 1 chr6A.!!$F1 2052
5 TraesCS3A01G076100 chr2A 632421192 632423516 2324 False 2030.0 3502 97.2390 75 2450 2 chr2A.!!$F2 2375
6 TraesCS3A01G076100 chr2A 58985873 58988236 2363 False 1955.0 3304 94.9410 1 2450 2 chr2A.!!$F1 2449
7 TraesCS3A01G076100 chr1A 381108227 381110622 2395 True 2055.5 3494 95.8765 1 2450 2 chr1A.!!$R2 2449
8 TraesCS3A01G076100 chr1A 242734388 242736721 2333 True 2034.5 3485 97.7440 75 2450 2 chr1A.!!$R1 2375
9 TraesCS3A01G076100 chr3B 513952174 513954568 2394 False 3432.0 3432 92.3820 1 2450 1 chr3B.!!$F1 2449

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
96 120 0.040499 ACTCACTCTCACTCTCCCCC 59.96 60.0 0.0 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2015 1.005215 CCCTCCTCCTTGCATCTTTGT 59.995 52.381 0.0 0.0 0.0 2.83 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
90 114 0.455972 GCGCTCACTCACTCTCACTC 60.456 60.000 0.00 0.00 0.00 3.51
91 115 1.164411 CGCTCACTCACTCTCACTCT 58.836 55.000 0.00 0.00 0.00 3.24
92 116 1.130373 CGCTCACTCACTCTCACTCTC 59.870 57.143 0.00 0.00 0.00 3.20
93 117 1.472480 GCTCACTCACTCTCACTCTCC 59.528 57.143 0.00 0.00 0.00 3.71
94 118 2.091541 CTCACTCACTCTCACTCTCCC 58.908 57.143 0.00 0.00 0.00 4.30
95 119 1.181786 CACTCACTCTCACTCTCCCC 58.818 60.000 0.00 0.00 0.00 4.81
96 120 0.040499 ACTCACTCTCACTCTCCCCC 59.960 60.000 0.00 0.00 0.00 5.40
945 1005 4.814234 GTGAATTGTGGTGTAGTTCAGTGA 59.186 41.667 0.00 0.00 30.27 3.41
964 1024 1.000396 GTTGATCCTGCCTGGCCTT 60.000 57.895 17.53 0.00 35.26 4.35
1263 1323 4.357918 AAGGCTAGCAAAAGAACAGAGA 57.642 40.909 18.24 0.00 0.00 3.10
1576 1636 7.820872 TGTTTAAGTTATGGTAACTAGAGTGGC 59.179 37.037 0.00 0.00 37.61 5.01
1671 1734 9.797556 GTGAACTGTTTTATTTCTTTAGGTTGT 57.202 29.630 0.00 0.00 0.00 3.32
1742 1805 3.953612 CCATTATGTACACATTGTGGGCT 59.046 43.478 20.33 2.89 37.94 5.19
1765 1828 7.046033 GCTTAGACTGGGCTGTTTTATTACTA 58.954 38.462 0.00 0.00 0.00 1.82
1918 1985 4.510024 GGATCCTGGAGAGGTCATAGATGA 60.510 50.000 3.84 0.00 40.76 2.92
2126 2194 2.715763 TCCCTTTCAGGTCACTAGGT 57.284 50.000 0.00 0.00 31.93 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.964373 CGTTTTGACCTGGTCGGGG 60.964 63.158 21.15 5.69 34.95 5.73
93 117 1.687493 GGGAGTGAGAGTGAGGGGG 60.687 68.421 0.00 0.00 0.00 5.40
94 118 1.687493 GGGGAGTGAGAGTGAGGGG 60.687 68.421 0.00 0.00 0.00 4.79
95 119 1.687493 GGGGGAGTGAGAGTGAGGG 60.687 68.421 0.00 0.00 0.00 4.30
96 120 4.042251 GGGGGAGTGAGAGTGAGG 57.958 66.667 0.00 0.00 0.00 3.86
885 944 7.933577 AGTTTGATCAGAGAACACATACTTCAA 59.066 33.333 10.56 0.00 0.00 2.69
945 1005 1.504275 AAGGCCAGGCAGGATCAACT 61.504 55.000 15.19 0.00 41.22 3.16
964 1024 7.418337 TGATGAGGCAGTTCTTAAGTACATA 57.582 36.000 13.87 0.00 0.00 2.29
1215 1275 2.699321 CTCCATCTTCATCTCCAGCTCA 59.301 50.000 0.00 0.00 0.00 4.26
1263 1323 1.143813 CCTGGGCCTGAAGGATACAT 58.856 55.000 12.58 0.00 35.40 2.29
1576 1636 2.996621 CAGACTTAGCAAAGGTTCTCCG 59.003 50.000 0.00 0.00 37.01 4.63
1671 1734 5.301551 TCAGCATTGCTACTTTCAGGAAAAA 59.698 36.000 11.55 0.00 36.40 1.94
1742 1805 7.820872 GTGTAGTAATAAAACAGCCCAGTCTAA 59.179 37.037 0.00 0.00 0.00 2.10
1765 1828 1.355112 GGTTGGTGGTAGGTAGGTGT 58.645 55.000 0.00 0.00 0.00 4.16
1948 2015 1.005215 CCCTCCTCCTTGCATCTTTGT 59.995 52.381 0.00 0.00 0.00 2.83
2126 2194 4.883021 ACAGAATCCTAGTCCACCTCTA 57.117 45.455 0.00 0.00 0.00 2.43
2400 2468 7.823745 AACTTAAAACATCAAGATCACCAGT 57.176 32.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.