Multiple sequence alignment - TraesCS4A01G251700

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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 TraesCS4A01G251700 chr4A 100.000 2940 0 0 1 2940 563267803 563270742 0.000000e+00 5430.0
1 TraesCS4A01G251700 chr4A 99.660 1176 4 0 1 1176 563298778 563299953 0.000000e+00 2150.0
2 TraesCS4A01G251700 chr4A 98.232 905 13 1 1171 2072 563304227 563305131 0.000000e+00 1580.0
3 TraesCS4A01G251700 chr4A 96.265 830 22 3 2120 2940 563305417 563306246 0.000000e+00 1352.0
4 TraesCS4A01G251700 chr2D 95.996 2797 98 9 1 2789 612534256 612537046 0.000000e+00 4532.0
5 TraesCS4A01G251700 chr2D 90.601 649 57 2 1025 1670 627914095 627913448 0.000000e+00 857.0
6 TraesCS4A01G251700 chr2A 89.522 649 62 5 1026 1670 758388919 758388273 0.000000e+00 817.0
7 TraesCS4A01G251700 chr2B 88.943 615 62 5 389 997 770674341 770673727 0.000000e+00 754.0
8 TraesCS4A01G251700 chr2B 90.942 552 44 3 1124 1670 748367244 748367794 0.000000e+00 737.0
9 TraesCS4A01G251700 chr2B 88.399 612 60 4 397 997 748366398 748367009 0.000000e+00 726.0
10 TraesCS4A01G251700 chr2B 90.253 554 45 4 1124 1670 770673490 770672939 0.000000e+00 715.0
11 TraesCS4A01G251700 chr2B 89.818 550 52 2 1124 1670 748216273 748216821 0.000000e+00 702.0
12 TraesCS4A01G251700 chr2B 86.297 613 72 5 397 997 748215425 748216037 0.000000e+00 656.0
13 TraesCS4A01G251700 chr2B 95.918 49 2 0 313 361 461526670 461526718 2.430000e-11 80.5
14 TraesCS4A01G251700 chr2B 95.918 49 2 0 313 361 461527098 461527146 2.430000e-11 80.5
15 TraesCS4A01G251700 chr7D 86.032 315 41 3 2342 2655 339792785 339793097 4.700000e-88 335.0
16 TraesCS4A01G251700 chr7D 95.200 125 6 0 2801 2925 494804113 494803989 6.430000e-47 198.0
17 TraesCS4A01G251700 chr7D 87.273 110 14 0 2793 2902 552768959 552768850 3.080000e-25 126.0
18 TraesCS4A01G251700 chr7D 82.114 123 19 3 2788 2908 30996559 30996680 5.180000e-18 102.0
19 TraesCS4A01G251700 chr7D 92.593 54 4 0 313 366 629435999 629435946 8.740000e-11 78.7
20 TraesCS4A01G251700 chr1D 81.095 402 68 6 2341 2738 482904832 482905229 6.120000e-82 315.0
21 TraesCS4A01G251700 chr1D 96.078 51 1 1 312 361 397389557 397389607 6.750000e-12 82.4
22 TraesCS4A01G251700 chr3A 81.330 391 63 9 2351 2737 714337367 714337751 2.850000e-80 309.0
23 TraesCS4A01G251700 chr1A 80.198 404 66 11 2344 2742 579226526 579226132 1.030000e-74 291.0
24 TraesCS4A01G251700 chr6B 79.104 402 79 5 2341 2742 536021567 536021963 3.730000e-69 272.0
25 TraesCS4A01G251700 chr6A 78.856 402 72 12 2341 2737 161044816 161044423 2.910000e-65 259.0
26 TraesCS4A01G251700 chr6A 78.934 394 74 9 2352 2742 161339426 161339039 2.910000e-65 259.0
27 TraesCS4A01G251700 chr6A 86.726 113 13 2 2788 2899 82668052 82668163 1.110000e-24 124.0
28 TraesCS4A01G251700 chr6A 87.755 98 12 0 2793 2890 25535004 25535101 6.660000e-22 115.0
29 TraesCS4A01G251700 chr6D 91.111 90 8 0 2809 2898 30454742 30454653 3.980000e-24 122.0
30 TraesCS4A01G251700 chr5A 86.792 106 12 2 2788 2892 264749390 264749494 1.850000e-22 117.0
31 TraesCS4A01G251700 chrUn 82.171 129 19 4 2788 2912 38045219 38045091 1.110000e-19 108.0
32 TraesCS4A01G251700 chr3D 94.643 56 1 2 312 366 427036977 427036923 5.220000e-13 86.1
33 TraesCS4A01G251700 chr4D 96.000 50 1 1 312 360 417477948 417477997 2.430000e-11 80.5
34 TraesCS4A01G251700 chr4D 91.667 60 2 3 313 371 457521406 457521349 2.430000e-11 80.5


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 TraesCS4A01G251700 chr4A 563267803 563270742 2939 False 5430.0 5430 100.0000 1 2940 1 chr4A.!!$F1 2939
1 TraesCS4A01G251700 chr4A 563298778 563299953 1175 False 2150.0 2150 99.6600 1 1176 1 chr4A.!!$F2 1175
2 TraesCS4A01G251700 chr4A 563304227 563306246 2019 False 1466.0 1580 97.2485 1171 2940 2 chr4A.!!$F3 1769
3 TraesCS4A01G251700 chr2D 612534256 612537046 2790 False 4532.0 4532 95.9960 1 2789 1 chr2D.!!$F1 2788
4 TraesCS4A01G251700 chr2D 627913448 627914095 647 True 857.0 857 90.6010 1025 1670 1 chr2D.!!$R1 645
5 TraesCS4A01G251700 chr2A 758388273 758388919 646 True 817.0 817 89.5220 1026 1670 1 chr2A.!!$R1 644
6 TraesCS4A01G251700 chr2B 770672939 770674341 1402 True 734.5 754 89.5980 389 1670 2 chr2B.!!$R1 1281
7 TraesCS4A01G251700 chr2B 748366398 748367794 1396 False 731.5 737 89.6705 397 1670 2 chr2B.!!$F3 1273
8 TraesCS4A01G251700 chr2B 748215425 748216821 1396 False 679.0 702 88.0575 397 1670 2 chr2B.!!$F2 1273

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
862 881 0.681733 AGCCACATCGACACTTGACT 59.318 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2391 2826 1.069091 CATGCATCGCACACAGTTTGA 60.069 47.619 0.0 0.0 43.04 2.69 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
862 881 0.681733 AGCCACATCGACACTTGACT 59.318 50.000 0.00 0.00 0.00 3.41
1176 1355 0.172803 CCCGTGGTAGTAGCACTGTC 59.827 60.000 25.48 4.56 43.87 3.51
1471 1656 6.957631 ACTAACAAGGATATCACCAACATGA 58.042 36.000 4.83 0.00 0.00 3.07
1667 1855 6.552008 TCATATGGGAAAAGGGGAATATGAC 58.448 40.000 2.13 0.00 33.99 3.06
1915 2103 2.437281 CTCAGGTGGCTCATGGATTACT 59.563 50.000 1.12 0.00 0.00 2.24
2165 2599 6.809869 TCTCAATGATCACGTGAGTTGATAT 58.190 36.000 28.59 13.04 46.40 1.63
2349 2784 5.279708 CCAGAGGAAGAACTCACACTAATGT 60.280 44.000 0.00 0.00 39.97 2.71
2379 2814 5.530171 GGTCCTAAGACGACACATGTATAGA 59.470 44.000 0.00 0.00 44.54 1.98
2391 2826 7.055667 ACACATGTATAGAAGACCATTCGAT 57.944 36.000 0.00 0.00 0.00 3.59
2441 2876 7.909121 CGCAAACGGTATGGTTATAAAAATGTA 59.091 33.333 0.00 0.00 34.97 2.29
2469 2904 7.369607 CAATAAAATGAACTGTGTGTGATGGA 58.630 34.615 0.00 0.00 0.00 3.41
2591 3026 6.630444 ATGATTAACCAGATCAAGATGTGC 57.370 37.500 1.93 0.00 37.11 4.57
2606 3041 2.658268 TGCGCGATAGACGGCATG 60.658 61.111 12.10 0.00 40.84 4.06
2618 3053 1.022982 ACGGCATGCATGTCACTCAG 61.023 55.000 29.36 15.74 31.41 3.35
2900 3335 6.300703 CCCCAATAATTACGGTTTGGATCTA 58.699 40.000 14.54 0.00 40.89 1.98
2926 3361 8.314751 ACCCAATATTTCTAGGTCAATCTATCG 58.685 37.037 0.00 0.00 0.00 2.92
2933 3368 5.882040 TCTAGGTCAATCTATCGGATGAGT 58.118 41.667 0.00 0.00 34.45 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
862 881 2.222227 TCTGCTGTAGAGAGCTTGGA 57.778 50.000 0.00 0.00 39.90 3.53
1176 1355 7.042187 GCAATGAAATAGTCAGACTCTATGGTG 60.042 40.741 6.27 0.37 40.43 4.17
1471 1656 0.468029 CACCCCTCTTGTGCCACTTT 60.468 55.000 0.00 0.00 0.00 2.66
1567 1752 4.104738 CCCTGATGCCCTTCCTAAGAATAA 59.895 45.833 0.00 0.00 0.00 1.40
1749 1937 3.446799 GTGTGTGATGAAGCAAGCAAAA 58.553 40.909 0.00 0.00 0.00 2.44
2097 2286 9.638239 TTTGAACCATGCAATAGAGAAAATAAC 57.362 29.630 0.00 0.00 0.00 1.89
2165 2599 5.241285 TCATCAAAGCTCAGTGCAATAACAA 59.759 36.000 0.00 0.00 45.94 2.83
2379 2814 4.214119 CACACAGTTTGATCGAATGGTCTT 59.786 41.667 0.00 0.00 0.00 3.01
2391 2826 1.069091 CATGCATCGCACACAGTTTGA 60.069 47.619 0.00 0.00 43.04 2.69
2441 2876 7.523293 TCACACACAGTTCATTTTATTGGAT 57.477 32.000 0.00 0.00 0.00 3.41
2591 3026 2.023771 ATGCATGCCGTCTATCGCG 61.024 57.895 16.68 0.00 38.35 5.87
2606 3041 3.332919 ACAGTTCATCTGAGTGACATGC 58.667 45.455 0.00 0.00 46.27 4.06
2618 3053 3.248266 GGCTCATTGCAAACAGTTCATC 58.752 45.455 1.71 0.00 45.15 2.92
2806 3241 9.496710 TCCTTGGGAGTCTGTAATTAGTATAAA 57.503 33.333 0.00 0.00 0.00 1.40
2900 3335 8.314751 CGATAGATTGACCTAGAAATATTGGGT 58.685 37.037 0.00 0.00 39.76 4.51


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

AutoCloner maintained by Alex Coulton.