Multiple sequence alignment - TraesCS3D01G418800

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 TraesCS3D01G418800 chr3D 100.000 4487 0 0 1 4487 531368807 531364321 0.000000e+00 8287.0
1 TraesCS3D01G418800 chr3D 96.136 3468 101 11 780 4231 426440081 426443531 0.000000e+00 5631.0
2 TraesCS3D01G418800 chr3D 96.419 391 14 0 1 391 426439157 426439547 0.000000e+00 645.0
3 TraesCS3D01G418800 chr3D 96.129 310 12 0 145 454 426439545 426439854 1.440000e-139 507.0
4 TraesCS3D01G418800 chr3D 97.701 261 6 0 4227 4487 426444828 426445088 2.460000e-122 449.0
5 TraesCS3D01G418800 chr3D 84.436 257 36 4 578 832 23088396 23088142 2.680000e-62 250.0
6 TraesCS3D01G418800 chr3B 95.378 4435 121 26 103 4486 702693492 702689091 0.000000e+00 6977.0
7 TraesCS3D01G418800 chr3B 93.750 48 1 2 3874 3919 750356583 750356536 2.240000e-08 71.3
8 TraesCS3D01G418800 chr3A 97.798 2952 61 3 965 3916 665967193 665964246 0.000000e+00 5088.0
9 TraesCS3D01G418800 chr3A 88.877 926 57 18 30 925 665968169 665967260 0.000000e+00 1098.0
10 TraesCS3D01G418800 chr3A 92.870 575 12 2 3912 4486 665963988 665963443 0.000000e+00 808.0
11 TraesCS3D01G418800 chr3A 83.817 241 30 7 549 785 32153795 32153560 2.100000e-53 220.0
12 TraesCS3D01G418800 chr1D 92.957 3081 183 17 980 4050 391317203 391320259 0.000000e+00 4457.0
13 TraesCS3D01G418800 chr1D 87.374 198 21 3 632 827 483524065 483523870 1.620000e-54 224.0
14 TraesCS3D01G418800 chr1A 92.732 3027 174 21 987 4005 493823624 493820636 0.000000e+00 4329.0
15 TraesCS3D01G418800 chr1B 94.698 2565 130 1 984 3548 531206272 531203714 0.000000e+00 3978.0
16 TraesCS3D01G418800 chr1B 84.100 522 46 18 3545 4050 531203604 531203104 1.890000e-128 470.0
17 TraesCS3D01G418800 chr4D 88.375 886 68 16 3584 4466 12419948 12420801 0.000000e+00 1033.0
18 TraesCS3D01G418800 chr4D 84.035 451 39 21 1226 1668 12419533 12419958 1.940000e-108 403.0
19 TraesCS3D01G418800 chr4A 89.244 688 63 6 991 1668 590255595 590254909 0.000000e+00 850.0
20 TraesCS3D01G418800 chr4A 87.778 540 37 8 3946 4484 590254592 590254081 4.960000e-169 604.0
21 TraesCS3D01G418800 chrUn 100.000 386 0 0 3204 3589 480559231 480559616 0.000000e+00 713.0
22 TraesCS3D01G418800 chr4B 87.645 518 52 8 3585 4099 22753569 22754077 3.870000e-165 592.0
23 TraesCS3D01G418800 chr4B 91.940 335 23 3 4117 4451 22804991 22805321 2.440000e-127 466.0
24 TraesCS3D01G418800 chr5D 84.330 351 48 6 567 916 531475426 531475082 2.000000e-88 337.0
25 TraesCS3D01G418800 chr5D 84.122 296 36 8 618 908 531470867 531470578 4.420000e-70 276.0
26 TraesCS3D01G418800 chr5B 85.333 300 37 7 620 916 669485886 669485591 2.030000e-78 303.0
27 TraesCS3D01G418800 chr5A 85.507 276 35 4 555 829 658600698 658600427 2.640000e-72 283.0
28 TraesCS3D01G418800 chr5A 80.745 161 28 3 3537 3696 450419360 450419518 6.100000e-24 122.0
29 TraesCS3D01G418800 chr5A 81.879 149 20 6 769 916 658486623 658486765 7.880000e-23 119.0


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 TraesCS3D01G418800 chr3D 531364321 531368807 4486 True 8287.000000 8287 100.000000 1 4487 1 chr3D.!!$R2 4486
1 TraesCS3D01G418800 chr3D 426439157 426445088 5931 False 1808.000000 5631 96.596250 1 4487 4 chr3D.!!$F1 4486
2 TraesCS3D01G418800 chr3B 702689091 702693492 4401 True 6977.000000 6977 95.378000 103 4486 1 chr3B.!!$R1 4383
3 TraesCS3D01G418800 chr3A 665963443 665968169 4726 True 2331.333333 5088 93.181667 30 4486 3 chr3A.!!$R2 4456
4 TraesCS3D01G418800 chr1D 391317203 391320259 3056 False 4457.000000 4457 92.957000 980 4050 1 chr1D.!!$F1 3070
5 TraesCS3D01G418800 chr1A 493820636 493823624 2988 True 4329.000000 4329 92.732000 987 4005 1 chr1A.!!$R1 3018
6 TraesCS3D01G418800 chr1B 531203104 531206272 3168 True 2224.000000 3978 89.399000 984 4050 2 chr1B.!!$R1 3066
7 TraesCS3D01G418800 chr4D 12419533 12420801 1268 False 718.000000 1033 86.205000 1226 4466 2 chr4D.!!$F1 3240
8 TraesCS3D01G418800 chr4A 590254081 590255595 1514 True 727.000000 850 88.511000 991 4484 2 chr4A.!!$R1 3493
9 TraesCS3D01G418800 chr4B 22753569 22754077 508 False 592.000000 592 87.645000 3585 4099 1 chr4B.!!$F1 514

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
786 1133 0.390124 TCGCGGGCGGATTTATAAGT 59.610 50.0 13.60 0.00 40.25 2.24 F
1643 2042 0.315382 CGCTTGTTTGATCGGATCGC 60.315 55.0 12.99 8.09 0.00 4.58 F
2009 2408 0.445436 GCACAGAGCAATCAGAACGG 59.555 55.0 0.00 0.00 44.79 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 2408 0.882484 GAATAGCTCGAAGGCCTGCC 60.882 60.0 5.69 0.0 0.00 4.85 R
2851 3250 2.437281 CAGATGGTGCTGAAGGGATACT 59.563 50.0 0.00 0.0 38.14 2.12 R
3871 4422 1.831580 ACATCAAGAAGCAAGCCTCC 58.168 50.0 0.00 0.0 0.00 4.30 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
153 156 5.349543 CCTCCGTACATTTAACTGGTACAAC 59.650 44.000 0.00 0.00 38.70 3.32
173 176 3.356290 ACTACATGGGGAAATTGTGCTC 58.644 45.455 0.00 0.00 0.00 4.26
569 880 9.939424 AATAGAAGTAAGGACCTATCTGTAAGT 57.061 33.333 0.00 0.00 33.76 2.24
602 913 0.458025 CGAGGGCGTGGAAGTAAGAC 60.458 60.000 0.00 0.00 0.00 3.01
622 933 0.998928 ACCAGGGCCATATGTGTGAA 59.001 50.000 6.18 0.00 0.00 3.18
786 1133 0.390124 TCGCGGGCGGATTTATAAGT 59.610 50.000 13.60 0.00 40.25 2.24
1054 1438 1.660355 GTCTCTCACCACACTCGCA 59.340 57.895 0.00 0.00 0.00 5.10
1339 1735 4.309950 GGGTGTTCGACGGGCTGT 62.310 66.667 0.00 0.00 0.00 4.40
1602 2001 0.963856 TCGACGCCTACTCCATGTGT 60.964 55.000 0.00 0.00 0.00 3.72
1627 2026 4.393155 TCGGTGATGCAAGGCGCT 62.393 61.111 7.64 0.00 43.06 5.92
1643 2042 0.315382 CGCTTGTTTGATCGGATCGC 60.315 55.000 12.99 8.09 0.00 4.58
2009 2408 0.445436 GCACAGAGCAATCAGAACGG 59.555 55.000 0.00 0.00 44.79 4.44
2025 2424 3.470888 GGGCAGGCCTTCGAGCTA 61.471 66.667 0.00 0.00 36.10 3.32
2561 2960 9.565213 GATATTTGAAACTCAGAAAGAACATGG 57.435 33.333 0.00 0.00 0.00 3.66
2851 3250 6.405065 GCATGATGCTCTGAACTTTATTGGAA 60.405 38.462 10.72 0.00 40.96 3.53
2852 3251 6.748333 TGATGCTCTGAACTTTATTGGAAG 57.252 37.500 0.00 0.00 0.00 3.46
3689 4222 9.234827 TCTCTCAACAACATTTGTATTCATCAT 57.765 29.630 0.00 0.00 44.59 2.45
3767 4310 3.920231 ATGCTTGCTTGATCTGGACTA 57.080 42.857 0.00 0.00 0.00 2.59
3835 4381 8.748380 ACGTATCTCATTGTGATGTATATGTG 57.252 34.615 10.69 0.00 34.68 3.21
3881 4432 0.893447 GAAAATGCAGGAGGCTTGCT 59.107 50.000 12.07 0.00 45.15 3.91
3953 4766 7.576236 CAAGATACAACACACACTAGAAAAGG 58.424 38.462 0.00 0.00 0.00 3.11
3954 4767 7.062749 AGATACAACACACACTAGAAAAGGA 57.937 36.000 0.00 0.00 0.00 3.36
3955 4768 7.155328 AGATACAACACACACTAGAAAAGGAG 58.845 38.462 0.00 0.00 0.00 3.69
4061 4876 1.707427 GTGGGCCTCATCCCTGATTAT 59.293 52.381 4.53 0.00 46.67 1.28
4090 4905 2.237392 AGCCCTCTCCAGAATGTTACAC 59.763 50.000 0.00 0.00 0.00 2.90
4407 6546 6.478673 CACCTTCAATTTGTTTTCCTGGTTAC 59.521 38.462 0.00 0.00 0.00 2.50
4452 6591 2.033407 CAGGTGCGAATATTGAAGCTCG 60.033 50.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.640147 TCCCCACAGAATGAAACTTGTAAT 58.360 37.500 0.00 0.00 39.69 1.89
6 7 4.935352 TTTCCCCACAGAATGAAACTTG 57.065 40.909 0.00 0.00 39.69 3.16
17 18 2.315176 TCCAACACAATTTCCCCACAG 58.685 47.619 0.00 0.00 0.00 3.66
153 156 2.355756 CGAGCACAATTTCCCCATGTAG 59.644 50.000 0.00 0.00 0.00 2.74
229 234 8.275632 TGATGATTCATGTTATTTCGTTCGATC 58.724 33.333 3.32 0.00 0.00 3.69
403 694 5.667539 TCAATTTTGTGAACCAACTTGGA 57.332 34.783 15.14 0.00 40.96 3.53
473 784 1.893801 CACTTACGAACTGGTCCTCCT 59.106 52.381 0.00 0.00 34.23 3.69
499 810 0.813610 CGCAGTCCTGTTGGTGTTGA 60.814 55.000 0.00 0.00 34.23 3.18
531 842 5.605488 CCTTACTTCTATTTGTAGCCCCCTA 59.395 44.000 0.00 0.00 0.00 3.53
569 880 1.593196 CCCTCGCTTCTTTGTGAACA 58.407 50.000 0.00 0.00 0.00 3.18
602 913 0.255604 TCACACATATGGCCCTGGTG 59.744 55.000 7.80 6.70 35.66 4.17
622 933 0.310854 CGCGCAGGTCCTTTTTCTTT 59.689 50.000 8.75 0.00 0.00 2.52
777 1088 4.638865 GCGAGTTCCACCCAACTTATAAAT 59.361 41.667 0.00 0.00 36.71 1.40
786 1133 1.301401 CGAAGCGAGTTCCACCCAA 60.301 57.895 0.00 0.00 0.00 4.12
1318 1714 4.308458 CCCGTCGAACACCCTGCA 62.308 66.667 0.00 0.00 0.00 4.41
1339 1735 2.264480 CACCATGTTCCGCTCCGA 59.736 61.111 0.00 0.00 0.00 4.55
1602 2001 2.033448 GCATCACCGACAACCCCA 59.967 61.111 0.00 0.00 0.00 4.96
1627 2026 1.087202 CCCGCGATCCGATCAAACAA 61.087 55.000 8.23 0.00 40.02 2.83
1643 2042 2.469516 GCAACGGCATCCTTACCCG 61.470 63.158 0.00 0.00 46.97 5.28
2009 2408 0.882484 GAATAGCTCGAAGGCCTGCC 60.882 60.000 5.69 0.00 0.00 4.85
2851 3250 2.437281 CAGATGGTGCTGAAGGGATACT 59.563 50.000 0.00 0.00 38.14 2.12
2852 3251 2.843701 CAGATGGTGCTGAAGGGATAC 58.156 52.381 0.00 0.00 38.14 2.24
3689 4222 6.177610 CCAACCTAGCACATTAAGGTAGAAA 58.822 40.000 0.00 0.00 42.86 2.52
3767 4310 6.588719 TCTATTGCATGTTTACCTTTGCTT 57.411 33.333 0.00 0.00 36.10 3.91
3835 4381 3.425659 AGAAAAACATTCTGGAGAGGGC 58.574 45.455 0.00 0.00 0.00 5.19
3871 4422 1.831580 ACATCAAGAAGCAAGCCTCC 58.168 50.000 0.00 0.00 0.00 4.30
3872 4423 4.637534 TCAATACATCAAGAAGCAAGCCTC 59.362 41.667 0.00 0.00 0.00 4.70
3953 4766 8.207545 ACTAATCTTTCTCTCTCTCTCTCTCTC 58.792 40.741 0.00 0.00 0.00 3.20
3954 4767 7.989741 CACTAATCTTTCTCTCTCTCTCTCTCT 59.010 40.741 0.00 0.00 0.00 3.10
3955 4768 7.254932 GCACTAATCTTTCTCTCTCTCTCTCTC 60.255 44.444 0.00 0.00 0.00 3.20
4061 4876 2.144450 TCTGGAGAGGGCTATCAGGTA 58.856 52.381 0.00 0.00 0.00 3.08
4090 4905 8.733458 TCAATTGATGTTTTCTGTATCCTTCAG 58.267 33.333 3.38 0.00 0.00 3.02
4407 6546 5.289434 GGTCAACTTTTCAAAACTTCAGCAG 59.711 40.000 0.00 0.00 0.00 4.24
4452 6591 9.813080 GTATGTTTCATCGATCCTAAATTTAGC 57.187 33.333 18.18 5.64 0.00 3.09


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

AutoCloner maintained by Alex Coulton.