Multiple sequence alignment - TraesCS2D01G275700

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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 TraesCS2D01G275700 chr2D 100.000 2614 0 0 1 2614 345250877 345253490 0.000000e+00 4828
1 TraesCS2D01G275700 chr2D 97.358 2044 40 5 582 2614 639485013 639482973 0.000000e+00 3463
2 TraesCS2D01G275700 chr2D 79.570 744 145 7 877 1615 37276739 37275998 2.300000e-145 525
3 TraesCS2D01G275700 chr1D 97.798 2044 29 6 583 2614 182580741 182582780 0.000000e+00 3511
4 TraesCS2D01G275700 chr1D 96.915 2042 51 4 583 2614 71287178 71289217 0.000000e+00 3411
5 TraesCS2D01G275700 chr1D 91.186 590 46 5 1 586 416855001 416855588 0.000000e+00 797
6 TraesCS2D01G275700 chr1D 89.060 585 54 4 1 581 289964571 289965149 0.000000e+00 717
7 TraesCS2D01G275700 chr5D 96.672 2043 54 5 583 2614 42206482 42208521 0.000000e+00 3384
8 TraesCS2D01G275700 chr7D 95.108 2044 82 9 583 2614 127375811 127377848 0.000000e+00 3205
9 TraesCS2D01G275700 chr7D 98.096 1786 25 4 583 2366 58131751 58129973 0.000000e+00 3101
10 TraesCS2D01G275700 chr7D 97.849 93 1 1 2522 2614 58129996 58129905 2.690000e-35 159
11 TraesCS2D01G275700 chr1A 88.692 1919 158 36 584 2489 546519079 546520951 0.000000e+00 2287
12 TraesCS2D01G275700 chr2A 87.773 1374 125 32 1128 2489 32113979 32115321 0.000000e+00 1567
13 TraesCS2D01G275700 chr2A 89.965 568 49 5 1 565 105483176 105482614 0.000000e+00 726
14 TraesCS2D01G275700 chr2A 90.323 558 46 6 5 557 510298431 510298985 0.000000e+00 725
15 TraesCS2D01G275700 chr2A 90.826 436 32 6 583 1013 32113534 32113966 6.270000e-161 577
16 TraesCS2D01G275700 chr4B 89.915 585 51 4 1 581 173178415 173178995 0.000000e+00 747
17 TraesCS2D01G275700 chr3B 89.863 582 53 5 1 577 733608527 733609107 0.000000e+00 743
18 TraesCS2D01G275700 chr3B 88.908 586 60 3 1 581 237102589 237103174 0.000000e+00 717
19 TraesCS2D01G275700 chr4A 89.691 582 54 5 1 577 733456940 733457520 0.000000e+00 737
20 TraesCS2D01G275700 chr1B 89.347 582 56 5 1 577 54979875 54980455 0.000000e+00 726


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 TraesCS2D01G275700 chr2D 345250877 345253490 2613 False 4828 4828 100.0000 1 2614 1 chr2D.!!$F1 2613
1 TraesCS2D01G275700 chr2D 639482973 639485013 2040 True 3463 3463 97.3580 582 2614 1 chr2D.!!$R2 2032
2 TraesCS2D01G275700 chr2D 37275998 37276739 741 True 525 525 79.5700 877 1615 1 chr2D.!!$R1 738
3 TraesCS2D01G275700 chr1D 182580741 182582780 2039 False 3511 3511 97.7980 583 2614 1 chr1D.!!$F2 2031
4 TraesCS2D01G275700 chr1D 71287178 71289217 2039 False 3411 3411 96.9150 583 2614 1 chr1D.!!$F1 2031
5 TraesCS2D01G275700 chr1D 416855001 416855588 587 False 797 797 91.1860 1 586 1 chr1D.!!$F4 585
6 TraesCS2D01G275700 chr1D 289964571 289965149 578 False 717 717 89.0600 1 581 1 chr1D.!!$F3 580
7 TraesCS2D01G275700 chr5D 42206482 42208521 2039 False 3384 3384 96.6720 583 2614 1 chr5D.!!$F1 2031
8 TraesCS2D01G275700 chr7D 127375811 127377848 2037 False 3205 3205 95.1080 583 2614 1 chr7D.!!$F1 2031
9 TraesCS2D01G275700 chr7D 58129905 58131751 1846 True 1630 3101 97.9725 583 2614 2 chr7D.!!$R1 2031
10 TraesCS2D01G275700 chr1A 546519079 546520951 1872 False 2287 2287 88.6920 584 2489 1 chr1A.!!$F1 1905
11 TraesCS2D01G275700 chr2A 32113534 32115321 1787 False 1072 1567 89.2995 583 2489 2 chr2A.!!$F2 1906
12 TraesCS2D01G275700 chr2A 105482614 105483176 562 True 726 726 89.9650 1 565 1 chr2A.!!$R1 564
13 TraesCS2D01G275700 chr2A 510298431 510298985 554 False 725 725 90.3230 5 557 1 chr2A.!!$F1 552
14 TraesCS2D01G275700 chr4B 173178415 173178995 580 False 747 747 89.9150 1 581 1 chr4B.!!$F1 580
15 TraesCS2D01G275700 chr3B 733608527 733609107 580 False 743 743 89.8630 1 577 1 chr3B.!!$F2 576
16 TraesCS2D01G275700 chr3B 237102589 237103174 585 False 717 717 88.9080 1 581 1 chr3B.!!$F1 580
17 TraesCS2D01G275700 chr4A 733456940 733457520 580 False 737 737 89.6910 1 577 1 chr4A.!!$F1 576
18 TraesCS2D01G275700 chr1B 54979875 54980455 580 False 726 726 89.3470 1 577 1 chr1B.!!$F1 576

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
173 177 0.037605 TCGAGGCGAAAAAGGAGGTC 60.038 55.0 0.0 0.0 31.06 3.85 F
574 582 0.109532 TCATCAGTTTGAACCGGCCA 59.890 50.0 0.0 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1392 1407 2.929903 GCCCATTTTGCTGCACCGA 61.930 57.895 0.0 0.0 0.0 4.69 R
1785 1809 5.533903 ACCATCAGTTCATCCATAGCATTTC 59.466 40.000 0.0 0.0 0.0 2.17 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
57 58 2.028484 GACCGGCAGTTGTCGTCA 59.972 61.111 0.00 0.00 42.34 4.35
75 76 4.069232 CTCCCGGCAAGAGCGACA 62.069 66.667 0.00 0.00 43.41 4.35
119 120 0.179134 GAGAGCATCCGCAGTACGTT 60.179 55.000 0.00 0.00 42.27 3.99
149 150 0.679505 TGGAGCACTACTGAAAGCGT 59.320 50.000 0.00 0.00 37.60 5.07
164 168 2.427905 CGTGACGTCGAGGCGAAA 60.428 61.111 11.62 0.00 37.72 3.46
169 173 0.665369 GACGTCGAGGCGAAAAAGGA 60.665 55.000 3.46 0.00 37.72 3.36
173 177 0.037605 TCGAGGCGAAAAAGGAGGTC 60.038 55.000 0.00 0.00 31.06 3.85
233 238 1.763968 TCAAGTCGTCGGATGAGGAT 58.236 50.000 0.00 0.00 40.76 3.24
260 265 3.332395 TCCGAGGAGGAGGACGAT 58.668 61.111 0.00 0.00 45.98 3.73
339 344 6.257411 CGACGAGGAGTAGTTTCATCTAGTAA 59.743 42.308 0.00 0.00 0.00 2.24
447 453 5.528320 TCGTTTTAATCTTCGTTTTGGACCT 59.472 36.000 0.00 0.00 0.00 3.85
449 455 6.141685 CGTTTTAATCTTCGTTTTGGACCTTG 59.858 38.462 0.00 0.00 0.00 3.61
458 464 3.365969 CGTTTTGGACCTTGTATTGGAGC 60.366 47.826 0.00 0.00 0.00 4.70
514 522 9.295825 TCATCTATTGAAGTTAAGCCTTTTTCA 57.704 29.630 0.00 0.00 0.00 2.69
552 560 8.655970 AGCACTTTTTAGTGTTTCAAATTTGAC 58.344 29.630 20.35 11.27 41.53 3.18
554 562 8.930760 CACTTTTTAGTGTTTCAAATTTGACCA 58.069 29.630 20.35 16.23 34.60 4.02
555 563 9.665719 ACTTTTTAGTGTTTCAAATTTGACCAT 57.334 25.926 20.35 11.69 36.83 3.55
557 565 9.658799 TTTTTAGTGTTTCAAATTTGACCATCA 57.341 25.926 20.35 13.28 36.83 3.07
558 566 9.829507 TTTTAGTGTTTCAAATTTGACCATCAT 57.170 25.926 20.35 11.90 36.83 2.45
559 567 9.474920 TTTAGTGTTTCAAATTTGACCATCATC 57.525 29.630 20.35 8.35 36.83 2.92
560 568 7.053316 AGTGTTTCAAATTTGACCATCATCA 57.947 32.000 20.35 8.17 36.83 3.07
561 569 7.149973 AGTGTTTCAAATTTGACCATCATCAG 58.850 34.615 20.35 0.00 36.83 2.90
562 570 6.925165 GTGTTTCAAATTTGACCATCATCAGT 59.075 34.615 20.35 0.00 36.83 3.41
563 571 7.439056 GTGTTTCAAATTTGACCATCATCAGTT 59.561 33.333 20.35 0.00 36.83 3.16
564 572 7.986320 TGTTTCAAATTTGACCATCATCAGTTT 59.014 29.630 20.35 0.00 36.83 2.66
565 573 7.949903 TTCAAATTTGACCATCATCAGTTTG 57.050 32.000 20.35 0.00 37.36 2.93
566 574 7.287512 TCAAATTTGACCATCATCAGTTTGA 57.712 32.000 16.91 11.27 39.77 2.69
567 575 7.724287 TCAAATTTGACCATCATCAGTTTGAA 58.276 30.769 16.91 0.00 39.48 2.69
568 576 7.652909 TCAAATTTGACCATCATCAGTTTGAAC 59.347 33.333 16.91 0.00 39.48 3.18
569 577 5.452078 TTTGACCATCATCAGTTTGAACC 57.548 39.130 0.00 0.00 0.00 3.62
570 578 3.073678 TGACCATCATCAGTTTGAACCG 58.926 45.455 0.00 0.00 0.00 4.44
571 579 2.420022 GACCATCATCAGTTTGAACCGG 59.580 50.000 0.00 0.00 0.00 5.28
572 580 1.133025 CCATCATCAGTTTGAACCGGC 59.867 52.381 0.00 0.00 0.00 6.13
573 581 1.133025 CATCATCAGTTTGAACCGGCC 59.867 52.381 0.00 0.00 0.00 6.13
574 582 0.109532 TCATCAGTTTGAACCGGCCA 59.890 50.000 0.00 0.00 0.00 5.36
575 583 0.958091 CATCAGTTTGAACCGGCCAA 59.042 50.000 0.00 3.03 0.00 4.52
576 584 1.339610 CATCAGTTTGAACCGGCCAAA 59.660 47.619 15.95 15.95 0.00 3.28
577 585 1.698506 TCAGTTTGAACCGGCCAAAT 58.301 45.000 20.84 10.62 36.14 2.32
578 586 2.865079 TCAGTTTGAACCGGCCAAATA 58.135 42.857 20.84 10.47 36.14 1.40
579 587 3.426615 TCAGTTTGAACCGGCCAAATAT 58.573 40.909 20.84 12.71 36.14 1.28
580 588 4.590918 TCAGTTTGAACCGGCCAAATATA 58.409 39.130 20.84 9.94 36.14 0.86
725 733 1.597027 CGGGCAAGAGACGTTGGTT 60.597 57.895 0.00 0.00 0.00 3.67
727 735 0.818040 GGGCAAGAGACGTTGGTTGT 60.818 55.000 0.00 0.00 0.00 3.32
845 856 4.006319 ACGGTGAGGTACAGTAAGTAGTC 58.994 47.826 0.00 0.00 35.89 2.59
897 908 0.687354 ACGGTTGCTTCTGGATCTGT 59.313 50.000 0.00 0.00 0.00 3.41
946 957 0.620700 AAACCCTAGACTCGCCCCAT 60.621 55.000 0.00 0.00 0.00 4.00
1533 1548 1.003839 GCGTCCATCAACCTGGTCA 60.004 57.895 0.00 0.00 37.57 4.02
1785 1809 4.502645 TGCAGATGTAATGTCGTGTTATCG 59.497 41.667 0.00 0.00 0.00 2.92
1874 1898 5.365314 GTCAGAATGGGAGTTAGGAGAGAAT 59.635 44.000 0.00 0.00 36.16 2.40
1878 1902 3.034635 TGGGAGTTAGGAGAGAATGCTC 58.965 50.000 0.00 0.00 41.62 4.26
1997 2022 7.116075 AGCCATTGTTTGTATGCAGATATTT 57.884 32.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 4.070552 GTCGCTCTTGCCGGGAGT 62.071 66.667 2.18 0.00 35.36 3.85
149 150 0.942410 CCTTTTTCGCCTCGACGTCA 60.942 55.000 17.16 1.87 34.89 4.35
164 168 2.640332 GTCCTCCTTCTTGACCTCCTTT 59.360 50.000 0.00 0.00 0.00 3.11
169 173 1.551452 CTCGTCCTCCTTCTTGACCT 58.449 55.000 0.00 0.00 0.00 3.85
173 177 1.219393 GGCCTCGTCCTCCTTCTTG 59.781 63.158 0.00 0.00 0.00 3.02
200 204 3.769844 ACGACTTGATAGGGATCACAGTT 59.230 43.478 0.00 0.00 41.92 3.16
233 238 1.609501 CTCCTCGGAGTCACCCCAA 60.610 63.158 4.02 0.00 37.47 4.12
447 453 7.466746 AAATAAAAGAGCAGCTCCAATACAA 57.533 32.000 19.40 0.00 0.00 2.41
449 455 7.985476 TGTAAATAAAAGAGCAGCTCCAATAC 58.015 34.615 19.40 12.40 0.00 1.89
494 502 9.264719 CATCTTTGAAAAAGGCTTAACTTCAAT 57.735 29.630 22.31 12.07 36.27 2.57
503 511 7.552330 TGCTTTTTACATCTTTGAAAAAGGCTT 59.448 29.630 16.53 0.00 44.63 4.35
536 544 7.053316 TGATGATGGTCAAATTTGAAACACT 57.947 32.000 22.07 13.17 39.21 3.55
540 548 8.202811 TCAAACTGATGATGGTCAAATTTGAAA 58.797 29.630 22.07 13.91 38.73 2.69
552 560 1.133025 GCCGGTTCAAACTGATGATGG 59.867 52.381 1.90 0.00 37.48 3.51
554 562 1.271871 TGGCCGGTTCAAACTGATGAT 60.272 47.619 1.90 0.00 37.48 2.45
555 563 0.109532 TGGCCGGTTCAAACTGATGA 59.890 50.000 1.90 0.00 37.48 2.92
556 564 0.958091 TTGGCCGGTTCAAACTGATG 59.042 50.000 1.90 0.00 37.48 3.07
557 565 1.698506 TTTGGCCGGTTCAAACTGAT 58.301 45.000 17.13 0.00 37.48 2.90
558 566 1.698506 ATTTGGCCGGTTCAAACTGA 58.301 45.000 21.34 5.95 37.00 3.41
559 567 3.866883 ATATTTGGCCGGTTCAAACTG 57.133 42.857 21.34 0.00 37.00 3.16
560 568 4.274950 CGATATATTTGGCCGGTTCAAACT 59.725 41.667 21.34 15.75 37.00 2.66
561 569 4.273969 TCGATATATTTGGCCGGTTCAAAC 59.726 41.667 21.34 11.30 37.00 2.93
562 570 4.452825 TCGATATATTTGGCCGGTTCAAA 58.547 39.130 21.23 21.23 38.30 2.69
563 571 4.074627 TCGATATATTTGGCCGGTTCAA 57.925 40.909 1.90 5.74 0.00 2.69
564 572 3.755112 TCGATATATTTGGCCGGTTCA 57.245 42.857 1.90 0.00 0.00 3.18
565 573 6.920569 ATTATCGATATATTTGGCCGGTTC 57.079 37.500 5.84 0.00 0.00 3.62
566 574 6.404293 GCAATTATCGATATATTTGGCCGGTT 60.404 38.462 5.84 0.00 32.91 4.44
567 575 5.065988 GCAATTATCGATATATTTGGCCGGT 59.934 40.000 5.84 0.00 32.91 5.28
568 576 5.296780 AGCAATTATCGATATATTTGGCCGG 59.703 40.000 5.84 0.00 32.91 6.13
569 577 6.363577 AGCAATTATCGATATATTTGGCCG 57.636 37.500 5.84 0.00 32.91 6.13
570 578 7.520614 GCCTAGCAATTATCGATATATTTGGCC 60.521 40.741 5.84 0.00 32.91 5.36
571 579 7.355778 GCCTAGCAATTATCGATATATTTGGC 58.644 38.462 5.84 10.43 32.91 4.52
572 580 7.567571 CGCCTAGCAATTATCGATATATTTGG 58.432 38.462 5.84 4.82 32.91 3.28
725 733 3.620300 CTCGTCTAACGCCGGCACA 62.620 63.158 28.98 9.52 42.21 4.57
727 735 4.124351 CCTCGTCTAACGCCGGCA 62.124 66.667 28.98 5.90 42.21 5.69
749 760 1.136280 GCGCGTTACATAAACACCGTT 60.136 47.619 8.43 0.00 38.03 4.44
897 908 1.003646 TTTGGGGATCGAATGGGGAA 58.996 50.000 0.00 0.00 0.00 3.97
946 957 4.038271 TGGGACGACCTAGAAGAAACTA 57.962 45.455 3.44 0.00 41.11 2.24
1392 1407 2.929903 GCCCATTTTGCTGCACCGA 61.930 57.895 0.00 0.00 0.00 4.69
1533 1548 6.772716 CCAATTACCAGGTTTGCTACTGATAT 59.227 38.462 0.00 0.00 36.86 1.63
1785 1809 5.533903 ACCATCAGTTCATCCATAGCATTTC 59.466 40.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.