Multiple sequence alignment - TraesCS3A01G475700

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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 TraesCS3A01G475700 chr3A 100.000 2390 0 0 1 2390 707127199 707124810 0.000000e+00 4414.0
1 TraesCS3A01G475700 chr3A 100.000 83 0 0 1 83 574287993 574288075 1.140000e-33 154.0
2 TraesCS3A01G475700 chr3A 97.619 42 0 1 481 521 489193178 489193137 1.190000e-08 71.3
3 TraesCS3A01G475700 chr3A 95.455 44 0 2 484 525 580599743 580599700 4.260000e-08 69.4
4 TraesCS3A01G475700 chr3B 96.738 1870 57 2 521 2390 762309326 762307461 0.000000e+00 3112.0
5 TraesCS3A01G475700 chr3B 85.246 305 33 10 101 398 762309647 762309348 1.070000e-78 303.0
6 TraesCS3A01G475700 chr3B 100.000 43 0 0 450 492 762309364 762309322 1.970000e-11 80.5
7 TraesCS3A01G475700 chr3B 100.000 40 0 0 482 521 435816885 435816924 9.160000e-10 75.0
8 TraesCS3A01G475700 chr3B 97.619 42 0 1 481 521 478078448 478078407 1.190000e-08 71.3
9 TraesCS3A01G475700 chr3D 97.236 1773 37 4 620 2390 573121775 573120013 0.000000e+00 2992.0
10 TraesCS3A01G475700 chr3D 91.837 98 5 2 522 618 573122221 573122126 1.490000e-27 134.0
11 TraesCS3A01G475700 chr3D 100.000 35 0 0 450 484 573122253 573122219 5.510000e-07 65.8
12 TraesCS3A01G475700 chr3D 87.719 57 4 3 466 520 27936547 27936602 1.980000e-06 63.9
13 TraesCS3A01G475700 chr1D 94.147 1777 86 12 620 2390 423056987 423058751 0.000000e+00 2689.0
14 TraesCS3A01G475700 chr1B 93.528 1777 94 14 620 2389 572308822 572310584 0.000000e+00 2625.0
15 TraesCS3A01G475700 chr1A 94.156 1677 76 11 718 2390 518986666 518988324 0.000000e+00 2534.0
16 TraesCS3A01G475700 chr1A 100.000 82 0 0 1 82 373317663 373317582 4.110000e-33 152.0
17 TraesCS3A01G475700 chr1A 96.226 53 1 1 398 449 554284183 554284235 4.230000e-13 86.1
18 TraesCS3A01G475700 chr1A 96.226 53 1 1 398 449 554289510 554289458 4.230000e-13 86.1
19 TraesCS3A01G475700 chr1A 97.297 37 1 0 484 520 131963584 131963620 1.980000e-06 63.9
20 TraesCS3A01G475700 chr7D 93.000 600 34 4 1797 2389 139368876 139369474 0.000000e+00 869.0
21 TraesCS3A01G475700 chr7D 95.604 91 3 1 1 90 581296273 581296363 6.890000e-31 145.0
22 TraesCS3A01G475700 chr7D 98.077 52 0 1 399 449 183786052 183786001 3.270000e-14 89.8
23 TraesCS3A01G475700 chr4A 89.867 602 52 4 1797 2389 220627174 220627775 0.000000e+00 765.0
24 TraesCS3A01G475700 chr6A 93.210 162 10 1 1797 1957 395654132 395653971 1.100000e-58 237.0
25 TraesCS3A01G475700 chr6A 100.000 82 0 0 1 82 287115369 287115450 4.110000e-33 152.0
26 TraesCS3A01G475700 chr2A 91.975 162 12 1 1797 1957 315573836 315573675 2.390000e-55 226.0
27 TraesCS3A01G475700 chr2A 93.333 45 3 0 476 520 23630478 23630434 1.530000e-07 67.6
28 TraesCS3A01G475700 chr2A 93.333 45 3 0 477 521 703708998 703709042 1.530000e-07 67.6
29 TraesCS3A01G475700 chr6B 97.727 88 2 0 1 88 459601643 459601730 4.110000e-33 152.0
30 TraesCS3A01G475700 chr6B 96.296 54 1 1 397 449 585808079 585808026 1.180000e-13 87.9
31 TraesCS3A01G475700 chr6B 94.340 53 1 2 399 450 70569397 70569448 1.970000e-11 80.5
32 TraesCS3A01G475700 chr6B 95.455 44 1 1 477 520 551951965 551951923 4.260000e-08 69.4
33 TraesCS3A01G475700 chr6D 97.674 86 2 0 1 86 91845423 91845508 5.320000e-32 148.0
34 TraesCS3A01G475700 chr7A 96.591 88 3 0 1 88 301100504 301100417 1.910000e-31 147.0
35 TraesCS3A01G475700 chr2B 94.737 95 4 1 1 95 227115837 227115930 1.910000e-31 147.0
36 TraesCS3A01G475700 chr5D 95.455 88 4 0 1 88 37920312 37920399 8.910000e-30 141.0
37 TraesCS3A01G475700 chr5D 92.063 63 2 2 388 449 225256384 225256324 4.230000e-13 86.1
38 TraesCS3A01G475700 chr4D 96.226 53 1 1 398 449 401088681 401088629 4.230000e-13 86.1
39 TraesCS3A01G475700 chr4D 96.154 52 1 1 399 449 12449216 12449267 1.520000e-12 84.2
40 TraesCS3A01G475700 chr2D 96.154 52 1 1 399 449 512770203 512770254 1.520000e-12 84.2


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 TraesCS3A01G475700 chr3A 707124810 707127199 2389 True 4414.000000 4414 100.000000 1 2390 1 chr3A.!!$R3 2389
1 TraesCS3A01G475700 chr3B 762307461 762309647 2186 True 1165.166667 3112 93.994667 101 2390 3 chr3B.!!$R2 2289
2 TraesCS3A01G475700 chr3D 573120013 573122253 2240 True 1063.933333 2992 96.357667 450 2390 3 chr3D.!!$R1 1940
3 TraesCS3A01G475700 chr1D 423056987 423058751 1764 False 2689.000000 2689 94.147000 620 2390 1 chr1D.!!$F1 1770
4 TraesCS3A01G475700 chr1B 572308822 572310584 1762 False 2625.000000 2625 93.528000 620 2389 1 chr1B.!!$F1 1769
5 TraesCS3A01G475700 chr1A 518986666 518988324 1658 False 2534.000000 2534 94.156000 718 2390 1 chr1A.!!$F2 1672
6 TraesCS3A01G475700 chr7D 139368876 139369474 598 False 869.000000 869 93.000000 1797 2389 1 chr7D.!!$F1 592
7 TraesCS3A01G475700 chr4A 220627174 220627775 601 False 765.000000 765 89.867000 1797 2389 1 chr4A.!!$F1 592


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
429 434 0.039165 GGCACAGTGGTAAAAGCTGC 60.039 55.0 1.84 0.0 33.87 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2317 2686 2.954753 GAGGTCAACAAGTGGCGCG 61.955 63.158 0.0 0.0 29.99 6.86 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.