Multiple sequence alignment - TraesCS7B01G318600

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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 TraesCS7B01G318600 chr7B 100.000 2514 0 0 1 2514 568626964 568629477 0.000000e+00 4643
1 TraesCS7B01G318600 chr4B 94.913 2536 93 15 1 2514 615791950 615789429 0.000000e+00 3936
2 TraesCS7B01G318600 chr4B 94.633 2534 105 14 1 2514 379060538 379063060 0.000000e+00 3897
3 TraesCS7B01G318600 chr2D 94.741 2548 83 20 6 2514 46525238 46527773 0.000000e+00 3916
4 TraesCS7B01G318600 chr3D 94.619 2546 92 22 6 2514 360444229 360441692 0.000000e+00 3901
5 TraesCS7B01G318600 chr2B 94.401 2536 101 16 8 2514 648798367 648800890 0.000000e+00 3858
6 TraesCS7B01G318600 chr2B 93.799 2532 112 19 4 2514 646053826 646051319 0.000000e+00 3764
7 TraesCS7B01G318600 chr2B 92.894 2547 116 31 1 2514 77597115 77594601 0.000000e+00 3640
8 TraesCS7B01G318600 chr2B 94.039 1879 83 15 7 1867 143026817 143024950 0.000000e+00 2822
9 TraesCS7B01G318600 chr2B 93.717 1878 92 14 6 1867 692983954 692982087 0.000000e+00 2791
10 TraesCS7B01G318600 chr2B 92.173 1712 72 27 6 1700 705424348 705422682 0.000000e+00 2362
11 TraesCS7B01G318600 chr2B 91.886 1713 74 28 6 1700 522167165 522165500 0.000000e+00 2333
12 TraesCS7B01G318600 chr2B 94.748 476 13 2 2051 2514 778522945 778523420 0.000000e+00 730
13 TraesCS7B01G318600 chr6B 93.718 2531 124 15 6 2514 234533902 234531385 0.000000e+00 3760
14 TraesCS7B01G318600 chr5B 93.283 2531 138 20 1 2511 523701170 523698652 0.000000e+00 3703
15 TraesCS7B01G318600 chr5B 94.671 319 6 2 2206 2514 281167320 281167003 3.760000e-133 484
16 TraesCS7B01G318600 chrUn 93.099 2536 140 16 1 2514 37646455 37643933 0.000000e+00 3681
17 TraesCS7B01G318600 chrUn 93.099 2536 140 16 1 2514 251163518 251166040 0.000000e+00 3681
18 TraesCS7B01G318600 chr5D 96.285 2019 65 9 5 2016 391883826 391881811 0.000000e+00 3304
19 TraesCS7B01G318600 chr5D 95.360 431 9 2 2094 2514 391881811 391881382 0.000000e+00 675
20 TraesCS7B01G318600 chr7A 94.089 1878 87 13 6 1867 452019727 452021596 0.000000e+00 2832
21 TraesCS7B01G318600 chr5A 93.667 1879 92 14 6 1867 580225358 580223490 0.000000e+00 2785
22 TraesCS7B01G318600 chr3A 93.237 1878 98 16 6 1867 654166975 654168839 0.000000e+00 2737
23 TraesCS7B01G318600 chr3B 94.962 794 24 3 1737 2514 497581350 497580557 0.000000e+00 1230
24 TraesCS7B01G318600 chr6D 94.574 516 15 2 2012 2514 434427850 434428365 0.000000e+00 785


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 TraesCS7B01G318600 chr7B 568626964 568629477 2513 False 4643.0 4643 100.0000 1 2514 1 chr7B.!!$F1 2513
1 TraesCS7B01G318600 chr4B 615789429 615791950 2521 True 3936.0 3936 94.9130 1 2514 1 chr4B.!!$R1 2513
2 TraesCS7B01G318600 chr4B 379060538 379063060 2522 False 3897.0 3897 94.6330 1 2514 1 chr4B.!!$F1 2513
3 TraesCS7B01G318600 chr2D 46525238 46527773 2535 False 3916.0 3916 94.7410 6 2514 1 chr2D.!!$F1 2508
4 TraesCS7B01G318600 chr3D 360441692 360444229 2537 True 3901.0 3901 94.6190 6 2514 1 chr3D.!!$R1 2508
5 TraesCS7B01G318600 chr2B 648798367 648800890 2523 False 3858.0 3858 94.4010 8 2514 1 chr2B.!!$F1 2506
6 TraesCS7B01G318600 chr2B 646051319 646053826 2507 True 3764.0 3764 93.7990 4 2514 1 chr2B.!!$R4 2510
7 TraesCS7B01G318600 chr2B 77594601 77597115 2514 True 3640.0 3640 92.8940 1 2514 1 chr2B.!!$R1 2513
8 TraesCS7B01G318600 chr2B 143024950 143026817 1867 True 2822.0 2822 94.0390 7 1867 1 chr2B.!!$R2 1860
9 TraesCS7B01G318600 chr2B 692982087 692983954 1867 True 2791.0 2791 93.7170 6 1867 1 chr2B.!!$R5 1861
10 TraesCS7B01G318600 chr2B 705422682 705424348 1666 True 2362.0 2362 92.1730 6 1700 1 chr2B.!!$R6 1694
11 TraesCS7B01G318600 chr2B 522165500 522167165 1665 True 2333.0 2333 91.8860 6 1700 1 chr2B.!!$R3 1694
12 TraesCS7B01G318600 chr6B 234531385 234533902 2517 True 3760.0 3760 93.7180 6 2514 1 chr6B.!!$R1 2508
13 TraesCS7B01G318600 chr5B 523698652 523701170 2518 True 3703.0 3703 93.2830 1 2511 1 chr5B.!!$R2 2510
14 TraesCS7B01G318600 chrUn 37643933 37646455 2522 True 3681.0 3681 93.0990 1 2514 1 chrUn.!!$R1 2513
15 TraesCS7B01G318600 chrUn 251163518 251166040 2522 False 3681.0 3681 93.0990 1 2514 1 chrUn.!!$F1 2513
16 TraesCS7B01G318600 chr5D 391881382 391883826 2444 True 1989.5 3304 95.8225 5 2514 2 chr5D.!!$R1 2509
17 TraesCS7B01G318600 chr7A 452019727 452021596 1869 False 2832.0 2832 94.0890 6 1867 1 chr7A.!!$F1 1861
18 TraesCS7B01G318600 chr5A 580223490 580225358 1868 True 2785.0 2785 93.6670 6 1867 1 chr5A.!!$R1 1861
19 TraesCS7B01G318600 chr3A 654166975 654168839 1864 False 2737.0 2737 93.2370 6 1867 1 chr3A.!!$F1 1861
20 TraesCS7B01G318600 chr3B 497580557 497581350 793 True 1230.0 1230 94.9620 1737 2514 1 chr3B.!!$R1 777
21 TraesCS7B01G318600 chr6D 434427850 434428365 515 False 785.0 785 94.5740 2012 2514 1 chr6D.!!$F1 502

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
701 761 0.465642 CCCTTTTACGATCTGCCCCC 60.466 60.0 0.0 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 1663 3.987547 ACTGCATACATTCAGAGATCGG 58.012 45.455 0.0 0.0 34.57 4.18 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
107 108 9.618890 CAGATCCTTCTTATTCACTCCAAAATA 57.381 33.333 0.00 0.0 0.00 1.40
229 236 4.095483 GGTGATAGCTCATTTGTGTGAAGG 59.905 45.833 0.00 0.0 32.98 3.46
269 278 8.588290 ATGACCTGCACCAAGTTTATATTTTA 57.412 30.769 0.00 0.0 0.00 1.52
272 285 9.869757 GACCTGCACCAAGTTTATATTTTATTT 57.130 29.630 0.00 0.0 0.00 1.40
367 392 8.647143 AAAACATTTGAAGTTGATTTCGACAT 57.353 26.923 0.99 0.0 32.64 3.06
425 460 9.433153 CTCCCCTATACCGAGTTTATATTTTTC 57.567 37.037 0.00 0.0 0.00 2.29
701 761 0.465642 CCCTTTTACGATCTGCCCCC 60.466 60.000 0.00 0.0 0.00 5.40
870 932 2.028658 TCGAGCAGATCTTGAGCAGTTT 60.029 45.455 6.33 0.0 31.59 2.66
1229 1298 3.057969 AGATCGTGAAGAAATGCCACA 57.942 42.857 0.00 0.0 0.00 4.17
1304 1373 0.918983 TTCGAGGGGGAATGCAATCT 59.081 50.000 1.01 0.0 0.00 2.40
1332 1401 0.700564 AATCTGCCCCATGACAGTGT 59.299 50.000 0.00 0.0 35.37 3.55
1340 1409 1.212751 CATGACAGTGTCGCTCCGA 59.787 57.895 18.17 0.0 34.95 4.55
1341 1410 0.388520 CATGACAGTGTCGCTCCGAA 60.389 55.000 18.17 0.0 37.72 4.30
1427 1496 5.128919 AGATGAACAAGAACTTCAAGCAGT 58.871 37.500 0.00 0.0 31.48 4.40
1727 1796 2.239400 TGGATCATACCCTAGCTCGTG 58.761 52.381 0.00 0.0 0.00 4.35
2122 2205 0.037590 TGGCTTAGTTTGGCGGTGAT 59.962 50.000 0.00 0.0 0.00 3.06
2388 2486 7.478520 AGCCGTGTACAATATGTTCTTATTC 57.521 36.000 0.00 0.0 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
269 278 6.538742 CCGTATGTGACAAGGTTATGAGAAAT 59.461 38.462 0.00 0.00 0.00 2.17
272 285 4.679639 GCCGTATGTGACAAGGTTATGAGA 60.680 45.833 0.00 0.00 0.00 3.27
354 379 8.948853 TTTTGAAGTGATATGTCGAAATCAAC 57.051 30.769 7.67 0.00 34.06 3.18
390 416 7.019656 ACTCGGTATAGGGGAGTTTTAAAAA 57.980 36.000 1.31 0.00 37.76 1.94
391 417 6.625532 ACTCGGTATAGGGGAGTTTTAAAA 57.374 37.500 0.00 0.00 37.76 1.52
392 418 6.625532 AACTCGGTATAGGGGAGTTTTAAA 57.374 37.500 7.02 0.00 45.90 1.52
400 432 9.162733 AGAAAAATATAAACTCGGTATAGGGGA 57.837 33.333 0.00 0.00 0.00 4.81
425 460 7.230108 TCCGTTTATGAGACCTAGTTACCATAG 59.770 40.741 0.00 0.00 0.00 2.23
870 932 4.599241 AGAAGATGGGGAAAGAAACAGAGA 59.401 41.667 0.00 0.00 0.00 3.10
971 1038 1.003839 CCATACACTGGCCACGTGT 60.004 57.895 30.63 30.63 46.45 4.49
1177 1246 6.753107 AATCACGTAACCTAAATCCCAAAG 57.247 37.500 0.00 0.00 0.00 2.77
1229 1298 6.356556 TGTAATCATCCATCCACTCGAAATT 58.643 36.000 0.00 0.00 0.00 1.82
1304 1373 1.377202 GGGGCAGATTGAACTCGCA 60.377 57.895 0.00 0.00 0.00 5.10
1340 1409 2.401766 CCGGATGCGCTTCTGCTTT 61.402 57.895 23.09 0.00 36.97 3.51
1341 1410 2.803155 TTCCGGATGCGCTTCTGCTT 62.803 55.000 23.09 0.00 36.97 3.91
1347 1416 1.227853 GGGTATTCCGGATGCGCTT 60.228 57.895 4.15 0.55 31.89 4.68
1427 1496 5.535783 TGGATTGCTTCTTCAACTCAATCAA 59.464 36.000 13.15 1.90 42.67 2.57
1594 1663 3.987547 ACTGCATACATTCAGAGATCGG 58.012 45.455 0.00 0.00 34.57 4.18
1727 1796 5.955488 TCAAGTACTGCTTACTGTCATCTC 58.045 41.667 0.00 0.00 40.44 2.75
1930 2003 5.298276 AGAACAAAGCAATCGTTCCTAAACA 59.702 36.000 0.00 0.00 39.89 2.83


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

AutoCloner maintained by Alex Coulton.