Multiple sequence alignment - TraesCS5D01G383800

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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 TraesCS5D01G383800 chr5D 100.000 3179 0 0 1 3179 453415357 453418535 0.000000e+00 5871
1 TraesCS5D01G383800 chr5D 82.439 615 69 19 208 800 542466064 542465467 4.730000e-138 501
2 TraesCS5D01G383800 chr5D 76.471 952 202 22 809 1751 545833388 545832450 6.120000e-137 497
3 TraesCS5D01G383800 chr1D 97.479 2221 41 3 973 3179 8316598 8314379 0.000000e+00 3777
4 TraesCS5D01G383800 chr1D 90.399 802 45 12 1 792 449286212 449286991 0.000000e+00 1026
5 TraesCS5D01G383800 chr1D 82.838 606 79 17 205 800 481450906 481451496 1.310000e-143 520
6 TraesCS5D01G383800 chr1D 82.270 423 37 19 371 778 457047480 457047879 6.570000e-87 331
7 TraesCS5D01G383800 chr5A 90.034 2388 192 18 809 3179 703335570 703337928 0.000000e+00 3049
8 TraesCS5D01G383800 chr5A 85.323 511 57 12 9 505 537671441 537671947 2.190000e-141 512
9 TraesCS5D01G383800 chr4D 93.084 1793 103 8 1402 3179 417381800 417380014 0.000000e+00 2604
10 TraesCS5D01G383800 chr4D 93.538 619 26 4 809 1426 417385698 417385093 0.000000e+00 909
11 TraesCS5D01G383800 chr4D 84.477 612 58 16 208 797 437821799 437822395 1.280000e-158 569
12 TraesCS5D01G383800 chr4D 84.365 614 61 16 208 800 497693519 497692920 1.280000e-158 569
13 TraesCS5D01G383800 chr4B 83.985 2404 337 28 806 3174 472006075 472008465 0.000000e+00 2263
14 TraesCS5D01G383800 chr4B 83.443 610 61 17 212 797 567410312 567410905 6.040000e-147 531
15 TraesCS5D01G383800 chr6B 82.969 1603 232 25 1610 3179 2738959 2737365 0.000000e+00 1410
16 TraesCS5D01G383800 chr6B 82.508 606 65 24 208 800 413938877 413938300 7.920000e-136 494
17 TraesCS5D01G383800 chr6B 85.845 438 54 8 809 1242 2739398 2738965 2.890000e-125 459
18 TraesCS5D01G383800 chrUn 82.658 1603 232 29 1610 3177 276410933 276409342 0.000000e+00 1378
19 TraesCS5D01G383800 chrUn 84.440 482 46 21 9 471 308645971 308645500 6.260000e-122 448
20 TraesCS5D01G383800 chr2A 89.380 1064 99 6 2118 3167 28668349 28669412 0.000000e+00 1327
21 TraesCS5D01G383800 chr2A 80.764 785 91 25 33 790 766984052 766984803 2.770000e-155 558
22 TraesCS5D01G383800 chr7A 89.052 749 53 12 51 795 457686885 457686162 0.000000e+00 902
23 TraesCS5D01G383800 chr7A 77.554 744 160 7 1038 1777 728429579 728430319 2.910000e-120 442
24 TraesCS5D01G383800 chr7B 80.773 1061 188 11 2102 3147 651304628 651305687 0.000000e+00 815
25 TraesCS5D01G383800 chr7B 80.566 1060 191 9 2102 3147 651277553 651278611 0.000000e+00 802
26 TraesCS5D01G383800 chr7B 85.366 615 51 17 212 800 705331661 705331060 4.540000e-168 601
27 TraesCS5D01G383800 chr7B 77.600 750 160 8 1037 1782 724168035 724167290 6.260000e-122 448
28 TraesCS5D01G383800 chr7B 84.289 401 57 5 931 1329 651277088 651277484 1.380000e-103 387
29 TraesCS5D01G383800 chr7B 84.289 401 57 5 931 1329 651304163 651304559 1.380000e-103 387
30 TraesCS5D01G383800 chr7D 84.409 821 77 30 13 800 613764575 613763773 0.000000e+00 760
31 TraesCS5D01G383800 chr7D 85.631 515 49 13 8 505 236004050 236004556 4.700000e-143 518
32 TraesCS5D01G383800 chr7D 72.523 535 129 17 1051 1576 529436927 529437452 1.180000e-34 158
33 TraesCS5D01G383800 chr5B 90.306 588 38 11 1 583 339922174 339921601 0.000000e+00 752
34 TraesCS5D01G383800 chr3B 82.609 828 84 33 1 797 51905947 51906745 0.000000e+00 676
35 TraesCS5D01G383800 chr3B 83.652 575 57 13 212 763 225261919 225261359 1.020000e-139 507
36 TraesCS5D01G383800 chr6A 84.647 482 45 21 9 471 607277030 607276559 1.340000e-123 453
37 TraesCS5D01G383800 chr6A 84.440 482 46 21 9 471 607138386 607137915 6.260000e-122 448
38 TraesCS5D01G383800 chr3D 74.017 839 193 20 951 1777 395639298 395638473 5.120000e-83 318


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 TraesCS5D01G383800 chr5D 453415357 453418535 3178 False 5871.0 5871 100.0000 1 3179 1 chr5D.!!$F1 3178
1 TraesCS5D01G383800 chr5D 542465467 542466064 597 True 501.0 501 82.4390 208 800 1 chr5D.!!$R1 592
2 TraesCS5D01G383800 chr5D 545832450 545833388 938 True 497.0 497 76.4710 809 1751 1 chr5D.!!$R2 942
3 TraesCS5D01G383800 chr1D 8314379 8316598 2219 True 3777.0 3777 97.4790 973 3179 1 chr1D.!!$R1 2206
4 TraesCS5D01G383800 chr1D 449286212 449286991 779 False 1026.0 1026 90.3990 1 792 1 chr1D.!!$F1 791
5 TraesCS5D01G383800 chr1D 481450906 481451496 590 False 520.0 520 82.8380 205 800 1 chr1D.!!$F3 595
6 TraesCS5D01G383800 chr5A 703335570 703337928 2358 False 3049.0 3049 90.0340 809 3179 1 chr5A.!!$F2 2370
7 TraesCS5D01G383800 chr5A 537671441 537671947 506 False 512.0 512 85.3230 9 505 1 chr5A.!!$F1 496
8 TraesCS5D01G383800 chr4D 417380014 417385698 5684 True 1756.5 2604 93.3110 809 3179 2 chr4D.!!$R2 2370
9 TraesCS5D01G383800 chr4D 437821799 437822395 596 False 569.0 569 84.4770 208 797 1 chr4D.!!$F1 589
10 TraesCS5D01G383800 chr4D 497692920 497693519 599 True 569.0 569 84.3650 208 800 1 chr4D.!!$R1 592
11 TraesCS5D01G383800 chr4B 472006075 472008465 2390 False 2263.0 2263 83.9850 806 3174 1 chr4B.!!$F1 2368
12 TraesCS5D01G383800 chr4B 567410312 567410905 593 False 531.0 531 83.4430 212 797 1 chr4B.!!$F2 585
13 TraesCS5D01G383800 chr6B 2737365 2739398 2033 True 934.5 1410 84.4070 809 3179 2 chr6B.!!$R2 2370
14 TraesCS5D01G383800 chr6B 413938300 413938877 577 True 494.0 494 82.5080 208 800 1 chr6B.!!$R1 592
15 TraesCS5D01G383800 chrUn 276409342 276410933 1591 True 1378.0 1378 82.6580 1610 3177 1 chrUn.!!$R1 1567
16 TraesCS5D01G383800 chr2A 28668349 28669412 1063 False 1327.0 1327 89.3800 2118 3167 1 chr2A.!!$F1 1049
17 TraesCS5D01G383800 chr2A 766984052 766984803 751 False 558.0 558 80.7640 33 790 1 chr2A.!!$F2 757
18 TraesCS5D01G383800 chr7A 457686162 457686885 723 True 902.0 902 89.0520 51 795 1 chr7A.!!$R1 744
19 TraesCS5D01G383800 chr7A 728429579 728430319 740 False 442.0 442 77.5540 1038 1777 1 chr7A.!!$F1 739
20 TraesCS5D01G383800 chr7B 651304163 651305687 1524 False 601.0 815 82.5310 931 3147 2 chr7B.!!$F2 2216
21 TraesCS5D01G383800 chr7B 705331060 705331661 601 True 601.0 601 85.3660 212 800 1 chr7B.!!$R1 588
22 TraesCS5D01G383800 chr7B 651277088 651278611 1523 False 594.5 802 82.4275 931 3147 2 chr7B.!!$F1 2216
23 TraesCS5D01G383800 chr7B 724167290 724168035 745 True 448.0 448 77.6000 1037 1782 1 chr7B.!!$R2 745
24 TraesCS5D01G383800 chr7D 613763773 613764575 802 True 760.0 760 84.4090 13 800 1 chr7D.!!$R1 787
25 TraesCS5D01G383800 chr7D 236004050 236004556 506 False 518.0 518 85.6310 8 505 1 chr7D.!!$F1 497
26 TraesCS5D01G383800 chr5B 339921601 339922174 573 True 752.0 752 90.3060 1 583 1 chr5B.!!$R1 582
27 TraesCS5D01G383800 chr3B 51905947 51906745 798 False 676.0 676 82.6090 1 797 1 chr3B.!!$F1 796
28 TraesCS5D01G383800 chr3B 225261359 225261919 560 True 507.0 507 83.6520 212 763 1 chr3B.!!$R1 551
29 TraesCS5D01G383800 chr3D 395638473 395639298 825 True 318.0 318 74.0170 951 1777 1 chr3D.!!$R1 826

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
502 582 5.998981 TGGCGTTGGTATTTCTTTTAAGAGA 59.001 36.0 0.0 0.0 36.22 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2232 5701 2.200067 CTGCCTCATGAGATCACGAAC 58.8 52.381 24.62 3.62 0.0 3.95 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
502 582 5.998981 TGGCGTTGGTATTTCTTTTAAGAGA 59.001 36.000 0.00 0.00 36.22 3.10
505 585 7.065923 GGCGTTGGTATTTCTTTTAAGAGAGAT 59.934 37.037 4.69 4.69 36.22 2.75
715 821 6.749923 AATGCAACCTAGAAGAGCTAAAAG 57.250 37.500 0.00 0.00 0.00 2.27
800 906 7.661040 ACTCACCATCAAAATTAAACAGGAAG 58.339 34.615 0.00 0.00 0.00 3.46
801 907 7.287696 ACTCACCATCAAAATTAAACAGGAAGT 59.712 33.333 0.00 0.00 0.00 3.01
802 908 8.698973 TCACCATCAAAATTAAACAGGAAGTA 57.301 30.769 0.00 0.00 0.00 2.24
803 909 8.573035 TCACCATCAAAATTAAACAGGAAGTAC 58.427 33.333 0.00 0.00 0.00 2.73
804 910 8.356657 CACCATCAAAATTAAACAGGAAGTACA 58.643 33.333 0.00 0.00 0.00 2.90
805 911 8.919145 ACCATCAAAATTAAACAGGAAGTACAA 58.081 29.630 0.00 0.00 0.00 2.41
806 912 9.757227 CCATCAAAATTAAACAGGAAGTACAAA 57.243 29.630 0.00 0.00 0.00 2.83
1024 1141 2.488355 GAACGCTGTCGGGATCGA 59.512 61.111 0.00 0.00 43.86 3.59
1238 1366 1.737793 GGCGAAGGACGTGAAAATCAT 59.262 47.619 0.00 0.00 44.60 2.45
2005 5473 0.746659 GGGAAACACAAGCAAGCAGT 59.253 50.000 0.00 0.00 0.00 4.40
2232 5701 4.796231 CCGCGACGGTTCAGGAGG 62.796 72.222 8.23 0.00 42.73 4.30
2658 6128 3.398184 CGCAAATGGACGCATTCAA 57.602 47.368 0.00 0.00 0.00 2.69
2714 6184 2.301346 GCTATGTTGGAAGTGGATGGG 58.699 52.381 0.00 0.00 0.00 4.00
2829 6299 6.035843 CAGCAGTACTTGAACACAAAAATGT 58.964 36.000 0.00 0.00 0.00 2.71
3035 6519 3.061848 GGCCACATGGGACCAACG 61.062 66.667 0.00 0.00 39.68 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
373 428 8.650143 AATACCAATTCCACTATTCACTTGTT 57.350 30.769 0.00 0.00 0.00 2.83
374 429 9.747898 TTAATACCAATTCCACTATTCACTTGT 57.252 29.630 0.00 0.00 0.00 3.16
673 776 7.552458 TGCATTTTTCCTTTTCCTTTTTCTC 57.448 32.000 0.00 0.00 0.00 2.87
715 821 0.453390 CGAATTGCTTCTTGGGCTCC 59.547 55.000 0.00 0.00 0.00 4.70
800 906 3.119209 CCTAACGAGAGGGGAGTTTGTAC 60.119 52.174 0.00 0.00 32.39 2.90
801 907 3.094572 CCTAACGAGAGGGGAGTTTGTA 58.905 50.000 0.00 0.00 32.39 2.41
802 908 1.900486 CCTAACGAGAGGGGAGTTTGT 59.100 52.381 0.00 0.00 32.39 2.83
803 909 2.674796 CCTAACGAGAGGGGAGTTTG 57.325 55.000 0.00 0.00 32.39 2.93
1024 1141 2.624838 CCAGATCAGTTGTTTTGGTGCT 59.375 45.455 0.00 0.00 0.00 4.40
1238 1366 6.099269 GGTGTAGAGGTTATCTTCCAATGGTA 59.901 42.308 0.00 0.00 39.64 3.25
2005 5473 4.659172 CGGGGGAGGCAACAGCAA 62.659 66.667 0.00 0.00 41.41 3.91
2232 5701 2.200067 CTGCCTCATGAGATCACGAAC 58.800 52.381 24.62 3.62 0.00 3.95
2658 6128 3.493334 CCACATGTATCCAATGCATCCT 58.507 45.455 0.00 0.00 33.12 3.24
2714 6184 5.650543 TCCAGACACTTTCTTTTCAAAAGC 58.349 37.500 4.87 0.00 37.26 3.51
2829 6299 2.035961 GGTAGATGATCGCTGGTTGCTA 59.964 50.000 0.00 0.00 40.11 3.49


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

AutoCloner maintained by Alex Coulton.