Multiple sequence alignment - TraesCS4A01G385100

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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 TraesCS4A01G385100 chr4A 100.000 3470 0 0 1 3470 662459262 662455793 0.000000e+00 6408.0
1 TraesCS4A01G385100 chr4A 96.391 2688 78 5 1 2683 106086831 106089504 0.000000e+00 4409.0
2 TraesCS4A01G385100 chr4A 95.916 808 30 3 2664 3470 106089699 106090504 0.000000e+00 1306.0
3 TraesCS4A01G385100 chr4A 85.714 77 10 1 3394 3469 738369660 738369736 2.870000e-11 80.5
4 TraesCS4A01G385100 chr5A 99.079 3475 17 4 1 3470 599649730 599653194 0.000000e+00 6226.0
5 TraesCS4A01G385100 chr5A 96.078 663 24 2 957 1618 483709523 483708862 0.000000e+00 1079.0
6 TraesCS4A01G385100 chr5A 86.903 733 78 10 203 920 143655907 143655178 0.000000e+00 806.0
7 TraesCS4A01G385100 chr5A 94.626 521 21 3 1812 2325 483708346 483707826 0.000000e+00 800.0
8 TraesCS4A01G385100 chr5A 83.529 340 38 7 581 911 534531446 534531116 5.630000e-78 302.0
9 TraesCS4A01G385100 chr5A 84.516 155 15 6 3317 3470 119071159 119071305 1.000000e-30 145.0
10 TraesCS4A01G385100 chr1B 99.252 3341 19 4 1 3336 588477672 588474333 0.000000e+00 6026.0
11 TraesCS4A01G385100 chr1B 98.182 110 2 0 3361 3470 588473914 588473805 3.530000e-45 193.0
12 TraesCS4A01G385100 chr5B 96.682 663 20 2 957 1618 459479911 459479250 0.000000e+00 1101.0
13 TraesCS4A01G385100 chr5B 94.391 517 22 3 1816 2325 459478733 459478217 0.000000e+00 787.0
14 TraesCS4A01G385100 chr5B 94.068 118 7 0 3353 3470 257027230 257027347 2.750000e-41 180.0
15 TraesCS4A01G385100 chr5D 96.380 663 22 2 957 1618 383635474 383634813 0.000000e+00 1090.0
16 TraesCS4A01G385100 chr5D 94.434 521 22 3 1812 2325 383634293 383633773 0.000000e+00 795.0
17 TraesCS4A01G385100 chr5D 96.133 181 6 1 1632 1812 383634501 383634322 9.420000e-76 294.0
18 TraesCS4A01G385100 chr5D 86.547 223 24 4 1145 1366 538563423 538563640 1.240000e-59 241.0
19 TraesCS4A01G385100 chr6B 81.912 1161 133 38 2355 3470 247040430 247039302 0.000000e+00 909.0
20 TraesCS4A01G385100 chr6B 88.168 524 38 9 416 921 247041331 247040814 1.380000e-168 603.0
21 TraesCS4A01G385100 chr2A 80.760 842 108 29 2662 3470 363368040 363368860 2.960000e-170 608.0
22 TraesCS4A01G385100 chr2A 87.524 521 44 11 416 921 363366122 363366636 1.790000e-162 582.0
23 TraesCS4A01G385100 chr2A 88.475 295 26 4 2662 2954 6470872 6471160 1.980000e-92 350.0
24 TraesCS4A01G385100 chr2A 86.667 180 18 4 3286 3465 6471332 6471505 9.830000e-46 195.0
25 TraesCS4A01G385100 chr2A 83.978 181 27 2 2409 2587 363367833 363368013 4.600000e-39 172.0
26 TraesCS4A01G385100 chr3B 84.036 664 66 15 2399 3037 685076689 685076041 1.380000e-168 603.0
27 TraesCS4A01G385100 chr3B 99.524 210 1 0 1211 1420 793123140 793123349 1.950000e-102 383.0
28 TraesCS4A01G385100 chr3D 83.365 529 57 14 2355 2864 32173936 32174452 8.780000e-126 460.0
29 TraesCS4A01G385100 chr3D 93.377 151 10 0 41 191 138218131 138217981 1.250000e-54 224.0
30 TraesCS4A01G385100 chr3D 81.609 174 19 5 2874 3034 32176796 32176969 7.810000e-27 132.0
31 TraesCS4A01G385100 chr3D 87.500 72 8 1 3400 3470 568930106 568930035 7.980000e-12 82.4
32 TraesCS4A01G385100 chr7D 85.714 371 40 5 533 891 484185154 484184785 2.530000e-101 379.0
33 TraesCS4A01G385100 chr6D 85.946 185 19 5 1632 1810 466790725 466790908 1.270000e-44 191.0
34 TraesCS4A01G385100 chr7B 94.366 71 4 0 1 71 49418515 49418445 3.660000e-20 110.0


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 TraesCS4A01G385100 chr4A 662455793 662459262 3469 True 6408.000000 6408 100.000000 1 3470 1 chr4A.!!$R1 3469
1 TraesCS4A01G385100 chr4A 106086831 106090504 3673 False 2857.500000 4409 96.153500 1 3470 2 chr4A.!!$F2 3469
2 TraesCS4A01G385100 chr5A 599649730 599653194 3464 False 6226.000000 6226 99.079000 1 3470 1 chr5A.!!$F2 3469
3 TraesCS4A01G385100 chr5A 483707826 483709523 1697 True 939.500000 1079 95.352000 957 2325 2 chr5A.!!$R3 1368
4 TraesCS4A01G385100 chr5A 143655178 143655907 729 True 806.000000 806 86.903000 203 920 1 chr5A.!!$R1 717
5 TraesCS4A01G385100 chr1B 588473805 588477672 3867 True 3109.500000 6026 98.717000 1 3470 2 chr1B.!!$R1 3469
6 TraesCS4A01G385100 chr5B 459478217 459479911 1694 True 944.000000 1101 95.536500 957 2325 2 chr5B.!!$R1 1368
7 TraesCS4A01G385100 chr5D 383633773 383635474 1701 True 726.333333 1090 95.649000 957 2325 3 chr5D.!!$R1 1368
8 TraesCS4A01G385100 chr6B 247039302 247041331 2029 True 756.000000 909 85.040000 416 3470 2 chr6B.!!$R1 3054
9 TraesCS4A01G385100 chr2A 363366122 363368860 2738 False 454.000000 608 84.087333 416 3470 3 chr2A.!!$F2 3054
10 TraesCS4A01G385100 chr2A 6470872 6471505 633 False 272.500000 350 87.571000 2662 3465 2 chr2A.!!$F1 803
11 TraesCS4A01G385100 chr3B 685076041 685076689 648 True 603.000000 603 84.036000 2399 3037 1 chr3B.!!$R1 638
12 TraesCS4A01G385100 chr3D 32173936 32176969 3033 False 296.000000 460 82.487000 2355 3034 2 chr3D.!!$F1 679

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
307 318 4.410228 TGAATGATAGGACCAAGGAAGGAG 59.590 45.833 0.0 0.0 0.00 3.69 F
412 423 7.066284 GGTCTGTATGAACATATCAAGCAAGTT 59.934 37.037 0.0 0.0 42.54 2.66 F
1892 2548 8.908786 AATTTGTATGTGAGAACTGAGAAGAA 57.091 30.769 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 2548 1.191535 TACGGCCTGCAGTTGATAGT 58.808 50.000 13.81 6.38 0.00 2.12 R
2185 2844 7.868922 TGAAAGCGACAATACTCTTACTTGTTA 59.131 33.333 0.00 0.00 33.46 2.41 R
2930 6299 1.302511 GGAGCAAGGCGTGGAAAGA 60.303 57.895 1.91 0.00 0.00 2.52 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
307 318 4.410228 TGAATGATAGGACCAAGGAAGGAG 59.590 45.833 0.0 0.0 0.00 3.69
412 423 7.066284 GGTCTGTATGAACATATCAAGCAAGTT 59.934 37.037 0.0 0.0 42.54 2.66
1892 2548 8.908786 AATTTGTATGTGAGAACTGAGAAGAA 57.091 30.769 0.0 0.0 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
207 218 1.063174 GATTGTCCAGCGATCAGTTGC 59.937 52.381 0.00 0.00 37.81 4.17
412 423 3.613030 TGAATGAAGCATTGCTAGCAGA 58.387 40.909 18.45 9.64 38.25 4.26
1892 2548 1.191535 TACGGCCTGCAGTTGATAGT 58.808 50.000 13.81 6.38 0.00 2.12
2185 2844 7.868922 TGAAAGCGACAATACTCTTACTTGTTA 59.131 33.333 0.00 0.00 33.46 2.41
2930 6299 1.302511 GGAGCAAGGCGTGGAAAGA 60.303 57.895 1.91 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.