Multiple sequence alignment - TraesCS2D01G215600

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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 TraesCS2D01G215600 chr2D 100.000 2666 0 0 1 2666 178504683 178507348 0.000000e+00 4924
1 TraesCS2D01G215600 chr2D 98.429 1973 23 6 699 2666 178852899 178854868 0.000000e+00 3465
2 TraesCS2D01G215600 chr2D 91.748 1636 87 24 655 2268 178667058 178668667 0.000000e+00 2230
3 TraesCS2D01G215600 chr2D 86.545 550 45 18 1 532 178666440 178666978 1.780000e-161 579
4 TraesCS2D01G215600 chr2D 87.280 511 51 10 1 500 178852075 178852582 2.980000e-159 571
5 TraesCS2D01G215600 chr2D 96.113 283 9 1 2384 2666 178668853 178669133 6.720000e-126 460
6 TraesCS2D01G215600 chr2D 89.809 157 2 2 2258 2400 178668685 178668841 3.500000e-44 189
7 TraesCS2D01G215600 chr2D 98.851 87 1 0 533 619 257754473 257754387 3.550000e-34 156
8 TraesCS2D01G215600 chr2D 98.592 71 1 0 2014 2084 178854288 178854218 2.790000e-25 126
9 TraesCS2D01G215600 chr2B 94.245 1842 71 16 836 2666 235050957 235052774 0.000000e+00 2782
10 TraesCS2D01G215600 chr2B 92.605 1163 46 13 836 1988 235585077 235586209 0.000000e+00 1635
11 TraesCS2D01G215600 chr2B 92.857 686 29 8 1985 2666 235586321 235586990 0.000000e+00 977
12 TraesCS2D01G215600 chr2B 92.661 109 5 2 680 785 235050687 235050795 1.280000e-33 154
13 TraesCS2D01G215600 chr2B 86.486 148 9 9 679 820 235584812 235584954 4.600000e-33 152
14 TraesCS2D01G215600 chr2B 100.000 71 0 0 2014 2084 235052194 235052124 5.990000e-27 132
15 TraesCS2D01G215600 chr2A 91.995 1749 79 23 947 2666 193547242 193548958 0.000000e+00 2398
16 TraesCS2D01G215600 chr2A 87.838 148 10 3 637 782 193543798 193543939 1.640000e-37 167
17 TraesCS2D01G215600 chr7A 96.809 94 2 1 528 620 48207237 48207330 3.550000e-34 156
18 TraesCS2D01G215600 chr7A 95.745 94 3 1 528 620 48192182 48192275 1.650000e-32 150
19 TraesCS2D01G215600 chr4A 96.703 91 3 0 531 621 589651907 589651997 4.600000e-33 152
20 TraesCS2D01G215600 chrUn 96.703 91 2 1 531 620 224305628 224305538 1.650000e-32 150
21 TraesCS2D01G215600 chrUn 96.703 91 2 1 531 620 375623357 375623267 1.650000e-32 150
22 TraesCS2D01G215600 chr5B 96.667 90 3 0 531 620 420005034 420005123 1.650000e-32 150
23 TraesCS2D01G215600 chr3D 96.591 88 3 0 533 620 41272483 41272570 2.140000e-31 147
24 TraesCS2D01G215600 chr1A 95.652 92 3 1 531 621 100419447 100419356 2.140000e-31 147


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 TraesCS2D01G215600 chr2D 178504683 178507348 2665 False 4924.000000 4924 100.000000 1 2666 1 chr2D.!!$F1 2665
1 TraesCS2D01G215600 chr2D 178852075 178854868 2793 False 2018.000000 3465 92.854500 1 2666 2 chr2D.!!$F3 2665
2 TraesCS2D01G215600 chr2D 178666440 178669133 2693 False 864.500000 2230 91.053750 1 2666 4 chr2D.!!$F2 2665
3 TraesCS2D01G215600 chr2B 235050687 235052774 2087 False 1468.000000 2782 93.453000 680 2666 2 chr2B.!!$F1 1986
4 TraesCS2D01G215600 chr2B 235584812 235586990 2178 False 921.333333 1635 90.649333 679 2666 3 chr2B.!!$F2 1987
5 TraesCS2D01G215600 chr2A 193543798 193548958 5160 False 1282.500000 2398 89.916500 637 2666 2 chr2A.!!$F1 2029


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
653 695 0.247854 GAGCAATTTCGCCGCTCTTC 60.248 55.0 7.32 0.0 46.86 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 5728 0.612174 CAAGGACTCTCCCTCCGTCA 60.612 60.0 0.0 0.0 37.19 4.35 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
60 61 1.876799 AGGAGATAGCGAGATGTGACG 59.123 52.381 0.00 0.00 0.00 4.35
68 69 0.740868 CGAGATGTGACGGCAATGGT 60.741 55.000 0.00 0.00 0.00 3.55
88 89 4.856801 CATGGGGGCGCGCTACTT 62.857 66.667 32.29 15.84 0.00 2.24
139 140 3.384789 TGGATCTTGTTGACCTAGATCGG 59.615 47.826 12.95 0.00 43.26 4.18
142 143 5.477291 GGATCTTGTTGACCTAGATCGGATA 59.523 44.000 12.95 0.00 43.26 2.59
210 216 1.964552 CACCCAAGCTCATCTGATCC 58.035 55.000 0.00 0.00 0.00 3.36
305 313 2.228822 GTGTGTAAGGTCCTTGCCAATG 59.771 50.000 14.84 0.00 0.00 2.82
334 342 3.739519 GCATTCGGACATCTGAGTAGCTT 60.740 47.826 0.00 0.00 32.05 3.74
373 381 3.119779 GGTCCAAACAGTTCACGAACAAA 60.120 43.478 12.21 0.00 43.47 2.83
374 382 4.477780 GTCCAAACAGTTCACGAACAAAA 58.522 39.130 12.21 0.00 43.47 2.44
375 383 4.918583 GTCCAAACAGTTCACGAACAAAAA 59.081 37.500 12.21 0.00 43.47 1.94
401 419 4.383850 TTCACACACACCCTGATTTTTG 57.616 40.909 0.00 0.00 0.00 2.44
405 423 3.513515 ACACACACCCTGATTTTTGTTGT 59.486 39.130 0.00 0.00 0.00 3.32
419 437 8.077991 TGATTTTTGTTGTTGAGAGCTATTCAG 58.922 33.333 0.00 0.00 0.00 3.02
428 446 5.273674 TGAGAGCTATTCAGATGTCCAAG 57.726 43.478 0.00 0.00 29.68 3.61
525 567 2.933056 GCTGTTTACAGACAGGAGCCTC 60.933 54.545 13.83 0.00 46.59 4.70
559 601 9.408648 ACGGATCTGGATGTAATTTTTATTTCT 57.591 29.630 6.47 0.00 0.00 2.52
560 602 9.669353 CGGATCTGGATGTAATTTTTATTTCTG 57.331 33.333 0.00 0.00 0.00 3.02
561 603 9.971922 GGATCTGGATGTAATTTTTATTTCTGG 57.028 33.333 0.00 0.00 0.00 3.86
564 606 9.308000 TCTGGATGTAATTTTTATTTCTGGTGT 57.692 29.630 0.00 0.00 0.00 4.16
565 607 9.927668 CTGGATGTAATTTTTATTTCTGGTGTT 57.072 29.630 0.00 0.00 0.00 3.32
566 608 9.921637 TGGATGTAATTTTTATTTCTGGTGTTC 57.078 29.630 0.00 0.00 0.00 3.18
567 609 9.072294 GGATGTAATTTTTATTTCTGGTGTTCG 57.928 33.333 0.00 0.00 0.00 3.95
568 610 9.620660 GATGTAATTTTTATTTCTGGTGTTCGT 57.379 29.630 0.00 0.00 0.00 3.85
569 611 9.974980 ATGTAATTTTTATTTCTGGTGTTCGTT 57.025 25.926 0.00 0.00 0.00 3.85
570 612 9.239002 TGTAATTTTTATTTCTGGTGTTCGTTG 57.761 29.630 0.00 0.00 0.00 4.10
571 613 9.240159 GTAATTTTTATTTCTGGTGTTCGTTGT 57.760 29.630 0.00 0.00 0.00 3.32
573 615 8.791355 ATTTTTATTTCTGGTGTTCGTTGTAC 57.209 30.769 0.00 0.00 0.00 2.90
574 616 7.556733 TTTTATTTCTGGTGTTCGTTGTACT 57.443 32.000 0.00 0.00 0.00 2.73
575 617 8.659925 TTTTATTTCTGGTGTTCGTTGTACTA 57.340 30.769 0.00 0.00 0.00 1.82
576 618 8.836268 TTTATTTCTGGTGTTCGTTGTACTAT 57.164 30.769 0.00 0.00 0.00 2.12
577 619 6.963049 ATTTCTGGTGTTCGTTGTACTATC 57.037 37.500 0.00 0.00 0.00 2.08
578 620 5.456548 TTCTGGTGTTCGTTGTACTATCA 57.543 39.130 0.00 0.00 0.00 2.15
579 621 5.654603 TCTGGTGTTCGTTGTACTATCAT 57.345 39.130 0.00 0.00 0.00 2.45
580 622 5.407502 TCTGGTGTTCGTTGTACTATCATG 58.592 41.667 0.00 0.00 0.00 3.07
581 623 5.184287 TCTGGTGTTCGTTGTACTATCATGA 59.816 40.000 0.00 0.00 0.00 3.07
582 624 5.972935 TGGTGTTCGTTGTACTATCATGAT 58.027 37.500 13.81 13.81 0.00 2.45
583 625 6.403049 TGGTGTTCGTTGTACTATCATGATT 58.597 36.000 14.65 0.00 0.00 2.57
584 626 6.312672 TGGTGTTCGTTGTACTATCATGATTG 59.687 38.462 14.65 14.58 0.00 2.67
585 627 6.533723 GGTGTTCGTTGTACTATCATGATTGA 59.466 38.462 21.64 1.13 36.00 2.57
586 628 7.064134 GGTGTTCGTTGTACTATCATGATTGAA 59.936 37.037 21.64 5.14 34.96 2.69
587 629 8.110612 GTGTTCGTTGTACTATCATGATTGAAG 58.889 37.037 21.64 12.40 34.96 3.02
588 630 8.032451 TGTTCGTTGTACTATCATGATTGAAGA 58.968 33.333 21.64 6.21 34.96 2.87
589 631 9.035607 GTTCGTTGTACTATCATGATTGAAGAT 57.964 33.333 21.64 4.07 34.96 2.40
590 632 8.579682 TCGTTGTACTATCATGATTGAAGATG 57.420 34.615 21.64 10.62 34.96 2.90
591 633 8.413229 TCGTTGTACTATCATGATTGAAGATGA 58.587 33.333 21.64 12.27 34.96 2.92
592 634 9.034544 CGTTGTACTATCATGATTGAAGATGAA 57.965 33.333 21.64 4.00 34.96 2.57
602 644 9.856162 TCATGATTGAAGATGAATAGATTGGAA 57.144 29.630 0.00 0.00 0.00 3.53
604 646 9.863650 ATGATTGAAGATGAATAGATTGGAAGT 57.136 29.630 0.00 0.00 0.00 3.01
605 647 9.690913 TGATTGAAGATGAATAGATTGGAAGTT 57.309 29.630 0.00 0.00 0.00 2.66
653 695 0.247854 GAGCAATTTCGCCGCTCTTC 60.248 55.000 7.32 0.00 46.86 2.87
658 700 0.997196 ATTTCGCCGCTCTTCGTTAC 59.003 50.000 0.00 0.00 36.19 2.50
1760 5280 1.968493 ACTCACCACGCTTTCCTTCTA 59.032 47.619 0.00 0.00 0.00 2.10
2024 5668 2.830651 AGTCATTACTCCCTCCGTCT 57.169 50.000 0.00 0.00 0.00 4.18
2038 5682 4.322801 CCCTCCGTCTCAAAATAAGTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
2039 5683 4.627467 CCTCCGTCTCAAAATAAGTGTCTG 59.373 45.833 0.00 0.00 0.00 3.51
2040 5684 4.566004 TCCGTCTCAAAATAAGTGTCTGG 58.434 43.478 0.00 0.00 0.00 3.86
2041 5685 4.282449 TCCGTCTCAAAATAAGTGTCTGGA 59.718 41.667 0.00 0.00 0.00 3.86
2042 5686 5.046591 TCCGTCTCAAAATAAGTGTCTGGAT 60.047 40.000 0.00 0.00 0.00 3.41
2045 5689 7.333423 CCGTCTCAAAATAAGTGTCTGGATTTA 59.667 37.037 0.00 0.00 0.00 1.40
2072 5728 4.759516 AAATCGGCGACACTTATTTTGT 57.240 36.364 13.76 0.00 0.00 2.83
2478 6207 6.240894 TGTTCTGAGCAGGAAACAAGAATAT 58.759 36.000 3.20 0.00 0.00 1.28
2479 6208 7.394016 TGTTCTGAGCAGGAAACAAGAATATA 58.606 34.615 3.20 0.00 0.00 0.86
2607 6336 4.532834 ACCCAACACTTCATACAACAAGT 58.467 39.130 0.00 0.00 32.87 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.545582 GCATATGTTGTTGGTGGCAGT 59.454 47.619 4.29 0.00 0.00 4.40
35 36 0.114168 ATCTCGCTATCTCCTGCCCT 59.886 55.000 0.00 0.00 0.00 5.19
45 46 0.459899 TTGCCGTCACATCTCGCTAT 59.540 50.000 0.00 0.00 0.00 2.97
60 61 3.472726 CCCCATGCCACCATTGCC 61.473 66.667 0.00 0.00 0.00 4.52
174 180 6.707440 TTGGGTGCATAAATGAATATTCGT 57.293 33.333 10.80 7.66 0.00 3.85
305 313 2.094894 CAGATGTCCGAATGCACTGAAC 59.905 50.000 0.00 0.00 0.00 3.18
334 342 3.131223 TGGACCGATTTTGTTTTGCTGAA 59.869 39.130 0.00 0.00 0.00 3.02
375 383 5.612725 AATCAGGGTGTGTGTGAATTTTT 57.387 34.783 0.00 0.00 0.00 1.94
376 384 5.612725 AAATCAGGGTGTGTGTGAATTTT 57.387 34.783 0.00 0.00 0.00 1.82
377 385 5.612725 AAAATCAGGGTGTGTGTGAATTT 57.387 34.783 0.00 0.00 0.00 1.82
378 386 5.104982 ACAAAAATCAGGGTGTGTGTGAATT 60.105 36.000 0.00 0.00 0.00 2.17
379 387 4.405358 ACAAAAATCAGGGTGTGTGTGAAT 59.595 37.500 0.00 0.00 0.00 2.57
401 419 5.293079 GGACATCTGAATAGCTCTCAACAAC 59.707 44.000 0.00 0.00 0.00 3.32
405 423 5.668471 CTTGGACATCTGAATAGCTCTCAA 58.332 41.667 0.00 0.00 0.00 3.02
419 437 1.089920 ATTCAGCGTGCTTGGACATC 58.910 50.000 0.00 0.00 0.00 3.06
428 446 0.589729 CGTGCCAATATTCAGCGTGC 60.590 55.000 3.25 0.00 0.00 5.34
504 545 1.002544 AGGCTCCTGTCTGTAAACAGC 59.997 52.381 5.21 2.04 44.34 4.40
534 576 9.669353 CAGAAATAAAAATTACATCCAGATCCG 57.331 33.333 0.00 0.00 0.00 4.18
535 577 9.971922 CCAGAAATAAAAATTACATCCAGATCC 57.028 33.333 0.00 0.00 0.00 3.36
538 580 9.308000 ACACCAGAAATAAAAATTACATCCAGA 57.692 29.630 0.00 0.00 0.00 3.86
539 581 9.927668 AACACCAGAAATAAAAATTACATCCAG 57.072 29.630 0.00 0.00 0.00 3.86
540 582 9.921637 GAACACCAGAAATAAAAATTACATCCA 57.078 29.630 0.00 0.00 0.00 3.41
541 583 9.072294 CGAACACCAGAAATAAAAATTACATCC 57.928 33.333 0.00 0.00 0.00 3.51
542 584 9.620660 ACGAACACCAGAAATAAAAATTACATC 57.379 29.630 0.00 0.00 0.00 3.06
543 585 9.974980 AACGAACACCAGAAATAAAAATTACAT 57.025 25.926 0.00 0.00 0.00 2.29
544 586 9.239002 CAACGAACACCAGAAATAAAAATTACA 57.761 29.630 0.00 0.00 0.00 2.41
545 587 9.240159 ACAACGAACACCAGAAATAAAAATTAC 57.760 29.630 0.00 0.00 0.00 1.89
547 589 9.240159 GTACAACGAACACCAGAAATAAAAATT 57.760 29.630 0.00 0.00 0.00 1.82
548 590 8.626526 AGTACAACGAACACCAGAAATAAAAAT 58.373 29.630 0.00 0.00 0.00 1.82
549 591 7.987649 AGTACAACGAACACCAGAAATAAAAA 58.012 30.769 0.00 0.00 0.00 1.94
550 592 7.556733 AGTACAACGAACACCAGAAATAAAA 57.443 32.000 0.00 0.00 0.00 1.52
551 593 8.836268 ATAGTACAACGAACACCAGAAATAAA 57.164 30.769 0.00 0.00 0.00 1.40
552 594 8.089597 TGATAGTACAACGAACACCAGAAATAA 58.910 33.333 0.00 0.00 0.00 1.40
553 595 7.604549 TGATAGTACAACGAACACCAGAAATA 58.395 34.615 0.00 0.00 0.00 1.40
554 596 6.460781 TGATAGTACAACGAACACCAGAAAT 58.539 36.000 0.00 0.00 0.00 2.17
555 597 5.845103 TGATAGTACAACGAACACCAGAAA 58.155 37.500 0.00 0.00 0.00 2.52
556 598 5.456548 TGATAGTACAACGAACACCAGAA 57.543 39.130 0.00 0.00 0.00 3.02
557 599 5.184287 TCATGATAGTACAACGAACACCAGA 59.816 40.000 0.00 0.00 0.00 3.86
558 600 5.407502 TCATGATAGTACAACGAACACCAG 58.592 41.667 0.00 0.00 0.00 4.00
559 601 5.394224 TCATGATAGTACAACGAACACCA 57.606 39.130 0.00 0.00 0.00 4.17
560 602 6.533723 TCAATCATGATAGTACAACGAACACC 59.466 38.462 9.04 0.00 0.00 4.16
561 603 7.520119 TCAATCATGATAGTACAACGAACAC 57.480 36.000 9.04 0.00 0.00 3.32
562 604 8.032451 TCTTCAATCATGATAGTACAACGAACA 58.968 33.333 9.04 0.00 34.96 3.18
563 605 8.407457 TCTTCAATCATGATAGTACAACGAAC 57.593 34.615 9.04 0.00 34.96 3.95
564 606 9.034544 CATCTTCAATCATGATAGTACAACGAA 57.965 33.333 9.04 2.03 34.96 3.85
565 607 8.413229 TCATCTTCAATCATGATAGTACAACGA 58.587 33.333 9.04 0.00 34.96 3.85
566 608 8.579682 TCATCTTCAATCATGATAGTACAACG 57.420 34.615 9.04 0.00 34.96 4.10
576 618 9.856162 TTCCAATCTATTCATCTTCAATCATGA 57.144 29.630 0.00 0.00 0.00 3.07
578 620 9.863650 ACTTCCAATCTATTCATCTTCAATCAT 57.136 29.630 0.00 0.00 0.00 2.45
579 621 9.690913 AACTTCCAATCTATTCATCTTCAATCA 57.309 29.630 0.00 0.00 0.00 2.57
632 674 2.045926 AGCGGCGAAATTGCTCCT 60.046 55.556 12.98 0.00 32.44 3.69
653 695 7.797819 AGCAGATCTTAAGAAAAACAGTAACG 58.202 34.615 9.71 0.00 0.00 3.18
658 700 8.862550 AACAAAGCAGATCTTAAGAAAAACAG 57.137 30.769 9.71 0.68 33.88 3.16
852 4064 4.049546 TCATACGTAGCGTAAAGGCAAT 57.950 40.909 0.08 0.00 45.39 3.56
859 4071 7.990541 ATTTGTACAATCATACGTAGCGTAA 57.009 32.000 9.56 0.00 45.39 3.18
1447 4965 1.736032 GCGTAGGAACAGCAACTCGAT 60.736 52.381 0.00 0.00 0.00 3.59
1760 5280 6.376581 ACAGTAAGTAGTACCAAGTAAGCGAT 59.623 38.462 0.00 0.00 32.58 4.58
2038 5682 6.201425 GTGTCGCCGATTTAGTATTAAATCCA 59.799 38.462 19.41 11.47 46.51 3.41
2039 5683 6.423001 AGTGTCGCCGATTTAGTATTAAATCC 59.577 38.462 19.41 9.63 46.51 3.01
2040 5684 7.404139 AGTGTCGCCGATTTAGTATTAAATC 57.596 36.000 16.74 16.74 46.08 2.17
2041 5685 7.781548 AAGTGTCGCCGATTTAGTATTAAAT 57.218 32.000 3.09 3.09 41.12 1.40
2042 5686 8.876275 ATAAGTGTCGCCGATTTAGTATTAAA 57.124 30.769 0.00 0.00 33.54 1.52
2045 5689 7.781548 AAATAAGTGTCGCCGATTTAGTATT 57.218 32.000 0.00 0.00 0.00 1.89
2056 5712 2.412325 CCGTCACAAAATAAGTGTCGCC 60.412 50.000 7.29 0.00 43.59 5.54
2058 5714 3.122948 CCTCCGTCACAAAATAAGTGTCG 59.877 47.826 0.00 0.00 44.19 4.35
2072 5728 0.612174 CAAGGACTCTCCCTCCGTCA 60.612 60.000 0.00 0.00 37.19 4.35
2127 5785 1.199789 GAGCCATCGTGCAAAACATCA 59.800 47.619 0.00 0.00 0.00 3.07
2479 6208 9.672673 GATTGTGCATCAGGGTTATAAGTATAT 57.327 33.333 0.00 0.00 0.00 0.86
2607 6336 5.066375 CAGAACTCAAAGTGATTGGTGTGAA 59.934 40.000 0.00 0.00 39.62 3.18



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

AutoCloner maintained by Alex Coulton.