Multiple sequence alignment - TraesCS2A01G326800

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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 TraesCS2A01G326800 chr2A 100.000 2549 0 0 1 2549 558478259 558475711 0 4708
1 TraesCS2A01G326800 chr2A 95.614 570 25 0 1 570 34482197 34482766 0 915
2 TraesCS2A01G326800 chr2B 99.141 1978 17 0 572 2549 776222961 776224938 0 3559
3 TraesCS2A01G326800 chr2B 99.141 1978 17 0 572 2549 781094240 781096217 0 3559
4 TraesCS2A01G326800 chr6A 99.040 1979 17 2 572 2549 616131295 616133272 0 3548
5 TraesCS2A01G326800 chr3A 99.039 1978 18 1 572 2549 54951917 54953893 0 3546
6 TraesCS2A01G326800 chr3A 98.989 1979 18 1 573 2549 9952658 9954636 0 3542
7 TraesCS2A01G326800 chr3A 95.614 570 24 1 1 570 739828133 739827565 0 913
8 TraesCS2A01G326800 chr7A 98.989 1978 20 0 572 2549 39015367 39017344 0 3542
9 TraesCS2A01G326800 chr7A 95.789 570 24 0 1 570 60000582 60001151 0 920
10 TraesCS2A01G326800 chr3B 98.989 1978 19 1 572 2549 702857655 702855679 0 3541
11 TraesCS2A01G326800 chr3B 95.789 570 24 0 1 570 286251 286820 0 920
12 TraesCS2A01G326800 chr3B 95.614 570 25 0 1 570 739708964 739709533 0 915
13 TraesCS2A01G326800 chr5B 98.939 1979 20 1 572 2549 641128780 641126802 0 3537
14 TraesCS2A01G326800 chr4B 98.939 1979 19 2 572 2549 368430368 368428391 0 3537
15 TraesCS2A01G326800 chr7D 95.789 570 24 0 1 570 117244182 117243613 0 920
16 TraesCS2A01G326800 chr1B 95.614 570 25 0 1 570 151287641 151288210 0 915
17 TraesCS2A01G326800 chr1B 95.439 570 26 0 1 570 584095748 584096317 0 909
18 TraesCS2A01G326800 chr1A 95.614 570 25 0 1 570 524462334 524461765 0 915


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 TraesCS2A01G326800 chr2A 558475711 558478259 2548 True 4708 4708 100.000 1 2549 1 chr2A.!!$R1 2548
1 TraesCS2A01G326800 chr2A 34482197 34482766 569 False 915 915 95.614 1 570 1 chr2A.!!$F1 569
2 TraesCS2A01G326800 chr2B 776222961 776224938 1977 False 3559 3559 99.141 572 2549 1 chr2B.!!$F1 1977
3 TraesCS2A01G326800 chr2B 781094240 781096217 1977 False 3559 3559 99.141 572 2549 1 chr2B.!!$F2 1977
4 TraesCS2A01G326800 chr6A 616131295 616133272 1977 False 3548 3548 99.040 572 2549 1 chr6A.!!$F1 1977
5 TraesCS2A01G326800 chr3A 54951917 54953893 1976 False 3546 3546 99.039 572 2549 1 chr3A.!!$F2 1977
6 TraesCS2A01G326800 chr3A 9952658 9954636 1978 False 3542 3542 98.989 573 2549 1 chr3A.!!$F1 1976
7 TraesCS2A01G326800 chr3A 739827565 739828133 568 True 913 913 95.614 1 570 1 chr3A.!!$R1 569
8 TraesCS2A01G326800 chr7A 39015367 39017344 1977 False 3542 3542 98.989 572 2549 1 chr7A.!!$F1 1977
9 TraesCS2A01G326800 chr7A 60000582 60001151 569 False 920 920 95.789 1 570 1 chr7A.!!$F2 569
10 TraesCS2A01G326800 chr3B 702855679 702857655 1976 True 3541 3541 98.989 572 2549 1 chr3B.!!$R1 1977
11 TraesCS2A01G326800 chr3B 286251 286820 569 False 920 920 95.789 1 570 1 chr3B.!!$F1 569
12 TraesCS2A01G326800 chr3B 739708964 739709533 569 False 915 915 95.614 1 570 1 chr3B.!!$F2 569
13 TraesCS2A01G326800 chr5B 641126802 641128780 1978 True 3537 3537 98.939 572 2549 1 chr5B.!!$R1 1977
14 TraesCS2A01G326800 chr4B 368428391 368430368 1977 True 3537 3537 98.939 572 2549 1 chr4B.!!$R1 1977
15 TraesCS2A01G326800 chr7D 117243613 117244182 569 True 920 920 95.789 1 570 1 chr7D.!!$R1 569
16 TraesCS2A01G326800 chr1B 151287641 151288210 569 False 915 915 95.614 1 570 1 chr1B.!!$F1 569
17 TraesCS2A01G326800 chr1B 584095748 584096317 569 False 909 909 95.439 1 570 1 chr1B.!!$F2 569
18 TraesCS2A01G326800 chr1A 524461765 524462334 569 True 915 915 95.614 1 570 1 chr1A.!!$R1 569

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
20 21 0.037326 TCACGTCATGGAACTGCTCC 60.037 55.0 0.0 0.0 45.64 4.70 F
558 559 0.460311 CCCGAACCGAAGCTCTGTAT 59.540 55.0 0.0 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1173 1174 2.676076 GACGAAAATGGTGCAATTGCT 58.324 42.857 29.37 8.9 42.66 3.91 R
2514 2521 1.003051 GGGGGTGAGAAGCCCTCTA 59.997 63.158 12.46 0.0 43.38 2.43 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
20 21 0.037326 TCACGTCATGGAACTGCTCC 60.037 55.000 0.00 0.00 45.64 4.70
32 33 0.973632 ACTGCTCCATACCGACAACA 59.026 50.000 0.00 0.00 0.00 3.33
151 152 3.537874 GAGCCTCCCGCCGTACAT 61.538 66.667 0.00 0.00 38.78 2.29
152 153 3.792053 GAGCCTCCCGCCGTACATG 62.792 68.421 0.00 0.00 38.78 3.21
316 317 1.453379 GCAGCAGCACATCCTCCAT 60.453 57.895 0.00 0.00 41.58 3.41
402 403 3.151710 CCACCGCCTCCCATACGA 61.152 66.667 0.00 0.00 0.00 3.43
523 524 2.672996 GTGTGGGACAAGCGCCAT 60.673 61.111 2.29 0.00 44.16 4.40
524 525 2.672651 TGTGGGACAAGCGCCATG 60.673 61.111 2.29 6.50 44.16 3.66
525 526 3.443045 GTGGGACAAGCGCCATGG 61.443 66.667 7.63 7.63 44.16 3.66
526 527 3.965258 TGGGACAAGCGCCATGGT 61.965 61.111 14.67 3.31 31.92 3.55
527 528 3.134127 GGGACAAGCGCCATGGTC 61.134 66.667 14.67 11.69 0.00 4.02
528 529 3.499737 GGACAAGCGCCATGGTCG 61.500 66.667 19.99 19.99 0.00 4.79
536 537 4.856801 GCCATGGTCGCCGGTGAT 62.857 66.667 22.69 1.58 0.00 3.06
537 538 2.588877 CCATGGTCGCCGGTGATC 60.589 66.667 22.69 22.16 0.00 2.92
538 539 2.961721 CATGGTCGCCGGTGATCG 60.962 66.667 22.69 6.96 38.88 3.69
539 540 4.891727 ATGGTCGCCGGTGATCGC 62.892 66.667 22.69 8.37 37.59 4.58
548 549 4.137872 GGTGATCGCCCGAACCGA 62.138 66.667 14.81 0.00 39.24 4.69
549 550 2.125832 GTGATCGCCCGAACCGAA 60.126 61.111 0.00 0.00 38.31 4.30
550 551 2.165301 GTGATCGCCCGAACCGAAG 61.165 63.158 0.00 0.00 38.31 3.79
551 552 3.262686 GATCGCCCGAACCGAAGC 61.263 66.667 0.00 0.00 38.31 3.86
552 553 3.718210 GATCGCCCGAACCGAAGCT 62.718 63.158 0.00 0.00 38.31 3.74
553 554 3.718210 ATCGCCCGAACCGAAGCTC 62.718 63.158 0.00 0.00 38.31 4.09
554 555 4.436998 CGCCCGAACCGAAGCTCT 62.437 66.667 0.00 0.00 0.00 4.09
555 556 2.815647 GCCCGAACCGAAGCTCTG 60.816 66.667 0.00 0.00 0.00 3.35
556 557 2.657237 CCCGAACCGAAGCTCTGT 59.343 61.111 0.00 0.00 0.00 3.41
557 558 1.888018 CCCGAACCGAAGCTCTGTA 59.112 57.895 0.00 0.00 0.00 2.74
558 559 0.460311 CCCGAACCGAAGCTCTGTAT 59.540 55.000 0.00 0.00 0.00 2.29
559 560 1.679680 CCCGAACCGAAGCTCTGTATA 59.320 52.381 0.00 0.00 0.00 1.47
560 561 2.543238 CCCGAACCGAAGCTCTGTATAC 60.543 54.545 0.00 0.00 0.00 1.47
561 562 2.543238 CCGAACCGAAGCTCTGTATACC 60.543 54.545 0.00 0.00 0.00 2.73
562 563 2.098607 CGAACCGAAGCTCTGTATACCA 59.901 50.000 0.00 0.00 0.00 3.25
563 564 3.428452 CGAACCGAAGCTCTGTATACCAA 60.428 47.826 0.00 0.00 0.00 3.67
564 565 4.694339 GAACCGAAGCTCTGTATACCAAT 58.306 43.478 0.00 0.00 0.00 3.16
565 566 4.755266 ACCGAAGCTCTGTATACCAATT 57.245 40.909 0.00 0.00 0.00 2.32
566 567 5.864418 ACCGAAGCTCTGTATACCAATTA 57.136 39.130 0.00 0.00 0.00 1.40
567 568 6.420913 ACCGAAGCTCTGTATACCAATTAT 57.579 37.500 0.00 0.00 0.00 1.28
568 569 6.827727 ACCGAAGCTCTGTATACCAATTATT 58.172 36.000 0.00 0.00 0.00 1.40
569 570 6.706270 ACCGAAGCTCTGTATACCAATTATTG 59.294 38.462 0.00 0.00 0.00 1.90
688 689 1.001597 GACTCGTTCCGTGAACTCTGT 60.002 52.381 12.80 9.18 40.05 3.41
794 795 2.197324 GTGGCTTGTGGGACCCAA 59.803 61.111 16.98 0.00 34.18 4.12
912 913 2.045829 AGAGAGAGAGCACGGCGA 60.046 61.111 16.62 0.00 0.00 5.54
1173 1174 2.364324 CGAGAATGGGGTAAGAATCGGA 59.636 50.000 0.00 0.00 0.00 4.55
1430 1432 6.018343 GCTATTGAGCTTAGGATGTTGAAGAC 60.018 42.308 0.00 0.00 45.98 3.01
1819 1822 0.664761 CTAATGGGCCAACTGCATCG 59.335 55.000 11.89 0.00 43.89 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.037139 TCCCCGTTGTTGTCGGTATG 60.037 55.000 3.78 0.00 45.63 2.39
23 24 1.227734 CTTCCCCGTTGTTGTCGGT 60.228 57.895 3.78 0.00 45.63 4.69
27 28 1.228154 GCCTCTTCCCCGTTGTTGT 60.228 57.895 0.00 0.00 0.00 3.32
32 33 2.732619 GGATCGCCTCTTCCCCGTT 61.733 63.158 0.00 0.00 0.00 4.44
239 240 0.396811 CCCTGAAGGTGAGGTTCGTT 59.603 55.000 0.00 0.00 0.00 3.85
288 289 1.228337 TGCTGCTGCAGGTGTCAAT 60.228 52.632 29.05 0.00 45.31 2.57
316 317 3.171828 TTGCTTCTCGGGGCGTTGA 62.172 57.895 0.00 0.00 0.00 3.18
340 341 1.079127 CGGAAGGACAAGATGGCGT 60.079 57.895 0.00 0.00 0.00 5.68
402 403 1.728069 CGATCCTCGACGTCCACAT 59.272 57.895 10.58 0.00 43.74 3.21
436 437 0.963962 GGACAACTACACGGTCTGGA 59.036 55.000 0.00 0.00 0.00 3.86
522 523 4.891727 GCGATCACCGGCGACCAT 62.892 66.667 9.30 0.00 39.04 3.55
531 532 3.652539 TTCGGTTCGGGCGATCACC 62.653 63.158 0.00 0.00 0.00 4.02
532 533 2.125832 TTCGGTTCGGGCGATCAC 60.126 61.111 0.00 0.00 0.00 3.06
533 534 2.183300 CTTCGGTTCGGGCGATCA 59.817 61.111 0.00 0.00 0.00 2.92
534 535 3.262686 GCTTCGGTTCGGGCGATC 61.263 66.667 0.00 0.00 0.00 3.69
535 536 3.718210 GAGCTTCGGTTCGGGCGAT 62.718 63.158 0.00 0.00 33.37 4.58
536 537 4.430765 GAGCTTCGGTTCGGGCGA 62.431 66.667 0.00 0.00 33.37 5.54
537 538 4.436998 AGAGCTTCGGTTCGGGCG 62.437 66.667 0.00 0.00 33.37 6.13
538 539 2.221906 TACAGAGCTTCGGTTCGGGC 62.222 60.000 0.00 0.00 0.00 6.13
539 540 0.460311 ATACAGAGCTTCGGTTCGGG 59.540 55.000 0.00 0.00 0.00 5.14
540 541 2.543238 GGTATACAGAGCTTCGGTTCGG 60.543 54.545 5.01 0.00 0.00 4.30
541 542 2.098607 TGGTATACAGAGCTTCGGTTCG 59.901 50.000 5.01 0.00 0.00 3.95
542 543 3.795623 TGGTATACAGAGCTTCGGTTC 57.204 47.619 5.01 0.00 0.00 3.62
543 544 4.755266 ATTGGTATACAGAGCTTCGGTT 57.245 40.909 5.01 0.00 0.00 4.44
544 545 4.755266 AATTGGTATACAGAGCTTCGGT 57.245 40.909 5.01 0.00 0.00 4.69
545 546 6.147821 CCAATAATTGGTATACAGAGCTTCGG 59.852 42.308 5.01 0.00 45.93 4.30
546 547 7.121974 CCAATAATTGGTATACAGAGCTTCG 57.878 40.000 5.01 0.00 45.93 3.79
564 565 8.700973 GCAAAAGGATAATTAACCCTCCAATAA 58.299 33.333 8.09 0.00 0.00 1.40
565 566 7.289084 GGCAAAAGGATAATTAACCCTCCAATA 59.711 37.037 8.09 0.00 0.00 1.90
566 567 6.099701 GGCAAAAGGATAATTAACCCTCCAAT 59.900 38.462 8.09 0.00 0.00 3.16
567 568 5.423931 GGCAAAAGGATAATTAACCCTCCAA 59.576 40.000 8.09 0.00 0.00 3.53
568 569 4.959839 GGCAAAAGGATAATTAACCCTCCA 59.040 41.667 8.09 0.00 0.00 3.86
569 570 4.344102 GGGCAAAAGGATAATTAACCCTCC 59.656 45.833 8.09 1.73 31.84 4.30
570 571 5.208890 AGGGCAAAAGGATAATTAACCCTC 58.791 41.667 8.09 0.00 41.34 4.30
742 743 6.127842 GGTCTGAATAAAATTGGCCGTTTCTA 60.128 38.462 0.00 0.00 0.00 2.10
794 795 0.106708 TCTGCTCAACGGCTCTTTGT 59.893 50.000 0.00 0.00 0.00 2.83
912 913 1.608717 CTCCACAGCTAGCTTCCCGT 61.609 60.000 16.46 7.10 0.00 5.28
1173 1174 2.676076 GACGAAAATGGTGCAATTGCT 58.324 42.857 29.37 8.90 42.66 3.91
1430 1432 3.926616 TCTTCAAGCTTCCTAACCTTCG 58.073 45.455 0.00 0.00 0.00 3.79
2514 2521 1.003051 GGGGGTGAGAAGCCCTCTA 59.997 63.158 12.46 0.00 43.38 2.43


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

AutoCloner maintained by Alex Coulton.