Multiple sequence alignment - TraesCS5B01G540400

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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 TraesCS5B01G540400 chr5B 100.000 3519 0 0 1 3519 695695843 695692325 0.000000e+00 6499
1 TraesCS5B01G540400 chr5B 94.336 3531 140 19 1 3519 695813463 695809981 0.000000e+00 5358
2 TraesCS5B01G540400 chr5B 80.348 2529 453 34 8 2521 695492935 695490436 0.000000e+00 1877
3 TraesCS5B01G540400 chr5B 80.506 1975 355 24 551 2515 695875781 695873827 0.000000e+00 1487
4 TraesCS5B01G540400 chr5B 79.600 500 90 11 2046 2540 695720490 695719998 7.230000e-92 348
5 TraesCS5B01G540400 chr5D 93.949 2727 138 16 2 2721 555556455 555559161 0.000000e+00 4096
6 TraesCS5B01G540400 chr5D 89.525 3093 288 18 5 3067 555636781 555639867 0.000000e+00 3884
7 TraesCS5B01G540400 chr5D 81.013 2528 444 28 12 2525 495550884 495548379 0.000000e+00 1977
8 TraesCS5B01G540400 chr5D 79.803 2540 444 52 9 2523 555063173 555065668 0.000000e+00 1784
9 TraesCS5B01G540400 chr5D 79.476 2329 448 24 164 2482 555488303 555490611 0.000000e+00 1626
10 TraesCS5B01G540400 chr5D 92.949 468 27 4 3053 3519 555643181 555643643 0.000000e+00 676
11 TraesCS5B01G540400 chr5D 82.171 258 16 7 2812 3041 555559158 555559413 9.970000e-46 195
12 TraesCS5B01G540400 chr1B 80.000 2500 463 32 8 2488 433643872 433641391 0.000000e+00 1812
13 TraesCS5B01G540400 chr6D 73.028 2510 607 54 3 2465 469067733 469070219 0.000000e+00 821
14 TraesCS5B01G540400 chr1A 78.049 779 152 11 159 930 402216081 402216847 1.140000e-129 473


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 TraesCS5B01G540400 chr5B 695692325 695695843 3518 True 6499.0 6499 100.000 1 3519 1 chr5B.!!$R2 3518
1 TraesCS5B01G540400 chr5B 695809981 695813463 3482 True 5358.0 5358 94.336 1 3519 1 chr5B.!!$R4 3518
2 TraesCS5B01G540400 chr5B 695490436 695492935 2499 True 1877.0 1877 80.348 8 2521 1 chr5B.!!$R1 2513
3 TraesCS5B01G540400 chr5B 695873827 695875781 1954 True 1487.0 1487 80.506 551 2515 1 chr5B.!!$R5 1964
4 TraesCS5B01G540400 chr5D 555636781 555643643 6862 False 2280.0 3884 91.237 5 3519 2 chr5D.!!$F4 3514
5 TraesCS5B01G540400 chr5D 555556455 555559413 2958 False 2145.5 4096 88.060 2 3041 2 chr5D.!!$F3 3039
6 TraesCS5B01G540400 chr5D 495548379 495550884 2505 True 1977.0 1977 81.013 12 2525 1 chr5D.!!$R1 2513
7 TraesCS5B01G540400 chr5D 555063173 555065668 2495 False 1784.0 1784 79.803 9 2523 1 chr5D.!!$F1 2514
8 TraesCS5B01G540400 chr5D 555488303 555490611 2308 False 1626.0 1626 79.476 164 2482 1 chr5D.!!$F2 2318
9 TraesCS5B01G540400 chr1B 433641391 433643872 2481 True 1812.0 1812 80.000 8 2488 1 chr1B.!!$R1 2480
10 TraesCS5B01G540400 chr6D 469067733 469070219 2486 False 821.0 821 73.028 3 2465 1 chr6D.!!$F1 2462
11 TraesCS5B01G540400 chr1A 402216081 402216847 766 False 473.0 473 78.049 159 930 1 chr1A.!!$F1 771

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
582 583 0.390472 AGCAGCCTTGAACGACTAGC 60.390 55.0 0.00 0.00 0.0 3.42 F
2167 2203 1.078709 CTCTTGGAAAAGCATCGCGA 58.921 50.0 13.09 13.09 0.0 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 2213 7.293073 AGGAGCATGATTCCATAACTAAACAT 58.707 34.615 16.30 0.0 37.18 2.71 R
3075 6502 0.535102 CATGTATGGCCTTCGGGTCC 60.535 60.000 3.32 0.0 39.39 4.46 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
104 105 3.025978 CAGCTTATTGGCTCAATCCCAA 58.974 45.455 4.01 0.00 45.63 4.12
403 404 5.465935 GGGAATCTAGACTTCTTATCAGCG 58.534 45.833 0.00 0.00 0.00 5.18
404 405 5.010213 GGGAATCTAGACTTCTTATCAGCGT 59.990 44.000 0.00 0.00 0.00 5.07
440 441 6.430925 CAGACAACTCCAATTCCTTGTGATAA 59.569 38.462 0.00 0.00 0.00 1.75
442 443 7.671398 AGACAACTCCAATTCCTTGTGATAAAT 59.329 33.333 0.00 0.00 0.00 1.40
502 503 5.869350 GGAAACCTCAGTTCACGATTAATG 58.131 41.667 0.00 0.00 34.19 1.90
519 520 6.199531 CGATTAATGATTTTTGATGCAGGTGG 59.800 38.462 0.00 0.00 0.00 4.61
520 521 6.602410 TTAATGATTTTTGATGCAGGTGGA 57.398 33.333 0.00 0.00 0.00 4.02
544 545 3.288092 CAAGTTAATAGGTGGGCTTCCC 58.712 50.000 0.00 0.00 45.71 3.97
556 557 1.538419 GGGCTTCCCGTAGAAATCTCG 60.538 57.143 0.00 0.00 32.13 4.04
582 583 0.390472 AGCAGCCTTGAACGACTAGC 60.390 55.000 0.00 0.00 0.00 3.42
808 809 7.654568 TGTTAGAAAACATCGACTTGTCTAGA 58.345 34.615 0.00 0.00 40.69 2.43
1233 1234 8.339344 TCTCAAATCTCACATTGCAATCTTTA 57.661 30.769 9.53 0.00 0.00 1.85
1263 1264 4.643387 GGGTTGTGTGGCGCTCCT 62.643 66.667 7.64 0.00 0.00 3.69
2167 2203 1.078709 CTCTTGGAAAAGCATCGCGA 58.921 50.000 13.09 13.09 0.00 5.87
2613 2660 5.992217 CACTTAGAATAGCCACATAACTCCC 59.008 44.000 0.00 0.00 0.00 4.30
2662 2709 9.458374 CGAATTAAAATTGTATTGGGATGTACC 57.542 33.333 0.00 0.00 38.08 3.34
2910 3003 1.273606 AGCTGCAGACGTGTACTGAAT 59.726 47.619 20.43 0.00 37.54 2.57
3036 3135 6.785191 TGCAGAGAGAAACAAGTTTTAAGTG 58.215 36.000 0.00 0.00 32.11 3.16
3041 3140 7.500559 AGAGAGAAACAAGTTTTAAGTGCAGAT 59.499 33.333 0.00 0.00 32.11 2.90
3075 6502 5.934625 AGCATCAGTTTTAAGTACAGAGGTG 59.065 40.000 0.00 0.00 0.00 4.00
3140 6567 6.203723 GCCTAGATCATCACTAACATGGTTTC 59.796 42.308 0.00 0.00 0.00 2.78
3464 6893 9.347240 TGCAAATTTCCTGGATTTTCAAAAATA 57.653 25.926 0.00 0.00 38.64 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 2.906389 TGGTGAGATTGCTTAGACCAGT 59.094 45.455 0.00 0.00 0.00 4.00
178 179 7.942990 AGAGTTCCTGTATAAGACCTAATTCG 58.057 38.462 0.00 0.00 0.00 3.34
371 372 6.133356 AGAAGTCTAGATTCCCCTCTAAGTG 58.867 44.000 0.00 0.00 0.00 3.16
404 405 2.288666 GAGTTGTCTGCACTTGGACAA 58.711 47.619 13.51 13.51 46.08 3.18
440 441 6.068010 TGACACCTGTGAAAGAATTACCATT 58.932 36.000 3.94 0.00 0.00 3.16
442 443 5.042463 TGACACCTGTGAAAGAATTACCA 57.958 39.130 3.94 0.00 0.00 3.25
502 503 4.630111 TGTTTCCACCTGCATCAAAAATC 58.370 39.130 0.00 0.00 0.00 2.17
519 520 5.105877 GGAAGCCCACCTATTAACTTGTTTC 60.106 44.000 0.00 0.00 0.00 2.78
520 521 4.770531 GGAAGCCCACCTATTAACTTGTTT 59.229 41.667 0.00 0.00 0.00 2.83
544 545 5.331905 GCTGCTTATGTTCGAGATTTCTACG 60.332 44.000 0.00 0.00 0.00 3.51
556 557 2.742053 TCGTTCAAGGCTGCTTATGTTC 59.258 45.455 0.00 0.00 0.00 3.18
582 583 6.448006 CCGGTTAATAGGTTGTCATCTAGAG 58.552 44.000 0.00 0.00 0.00 2.43
808 809 7.309194 GCAGGTATCATTGAACTTAACTGGTTT 60.309 37.037 11.09 0.00 31.48 3.27
1233 1234 4.450053 CACACAACCCAACATTTCCAATT 58.550 39.130 0.00 0.00 0.00 2.32
1263 1264 2.564771 CATGGCAAAAGATCTAGGCGA 58.435 47.619 0.00 0.00 0.00 5.54
2167 2203 8.958119 TTCCATAACTAAACATATCGCTCTTT 57.042 30.769 0.00 0.00 0.00 2.52
2177 2213 7.293073 AGGAGCATGATTCCATAACTAAACAT 58.707 34.615 16.30 0.00 37.18 2.71
2613 2660 4.272504 GGTCATACACATTAACACATCCGG 59.727 45.833 0.00 0.00 0.00 5.14
2910 3003 6.772233 TGTCTGAATCAATCTTGGTTTCTTGA 59.228 34.615 0.00 0.00 30.22 3.02
3075 6502 0.535102 CATGTATGGCCTTCGGGTCC 60.535 60.000 3.32 0.00 39.39 4.46
3361 6789 9.859427 CATTTTTGCAAATCTAGGAATGTTCTA 57.141 29.630 13.65 0.00 29.41 2.10
3414 6843 8.583765 GCAAACCGTGAATATTTATTGAAACTC 58.416 33.333 0.00 0.00 0.00 3.01
3428 6857 4.057432 CAGGAAATTTGCAAACCGTGAAT 58.943 39.130 15.41 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.