Multiple sequence alignment - TraesCS7A01G538400

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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 TraesCS7A01G538400 chr7A 100.000 2513 0 0 1 2513 715663716 715661204 0.000000e+00 4641
1 TraesCS7A01G538400 chr7A 98.756 1527 19 0 987 2513 715577731 715576205 0.000000e+00 2715
2 TraesCS7A01G538400 chr7A 98.441 1026 16 0 987 2012 715245929 715244904 0.000000e+00 1807
3 TraesCS7A01G538400 chr7A 98.768 893 11 0 987 1879 715333785 715332893 0.000000e+00 1589
4 TraesCS7A01G538400 chr7A 97.236 832 21 1 987 1818 715436363 715435534 0.000000e+00 1408
5 TraesCS7A01G538400 chr7A 97.206 501 14 0 2013 2513 715422627 715422127 0.000000e+00 848
6 TraesCS7A01G538400 chr7A 92.000 250 14 5 2266 2513 76575812 76576057 1.850000e-91 346
7 TraesCS7A01G538400 chr7A 96.447 197 3 2 1816 2012 715425505 715425313 3.120000e-84 322
8 TraesCS7A01G538400 chr7A 99.029 103 1 0 2194 2296 715242127 715242025 4.270000e-43 185
9 TraesCS7A01G538400 chr7A 91.111 90 7 1 2013 2102 715242213 715242125 1.220000e-23 121
10 TraesCS7A01G538400 chr7A 100.000 60 0 0 1816 1875 715329361 715329302 7.350000e-21 111
11 TraesCS7A01G538400 chr7A 93.151 73 4 1 548 619 715251496 715251424 3.420000e-19 106
12 TraesCS7A01G538400 chr7A 93.151 73 4 1 548 619 715341788 715341716 3.420000e-19 106
13 TraesCS7A01G538400 chr7A 93.151 73 4 1 548 619 715440372 715440300 3.420000e-19 106
14 TraesCS7A01G538400 chr7A 93.151 73 4 1 548 619 715581717 715581645 3.420000e-19 106
15 TraesCS7A01G538400 chr7B 92.321 1120 47 18 909 2012 716977253 716978349 0.000000e+00 1555
16 TraesCS7A01G538400 chr7B 92.111 900 28 15 916 1794 716699960 716699083 0.000000e+00 1229
17 TraesCS7A01G538400 chr7B 95.306 703 23 4 1 696 716700950 716700251 0.000000e+00 1107
18 TraesCS7A01G538400 chr7B 95.306 703 23 4 1 696 716976268 716976967 0.000000e+00 1107
19 TraesCS7A01G538400 chr7B 89.231 455 33 6 1573 2012 716984530 716984983 2.820000e-154 555
20 TraesCS7A01G538400 chr7B 90.777 206 5 5 695 896 716700137 716699942 1.920000e-66 263
21 TraesCS7A01G538400 chr7B 93.011 186 3 2 695 880 716977081 716977256 1.920000e-66 263
22 TraesCS7A01G538400 chr7B 92.899 169 12 0 1844 2012 716699070 716698902 1.930000e-61 246
23 TraesCS7A01G538400 chr7B 86.383 235 21 6 2061 2293 716988687 716988912 1.930000e-61 246
24 TraesCS7A01G538400 chr3D 96.847 222 7 0 2292 2513 15749090 15748869 3.050000e-99 372
25 TraesCS7A01G538400 chr1D 96.847 222 6 1 2292 2513 414815060 414815280 1.100000e-98 370
26 TraesCS7A01G538400 chr6D 96.396 222 8 0 2292 2513 262034477 262034698 1.420000e-97 366
27 TraesCS7A01G538400 chr4A 95.259 232 8 3 2283 2513 40568249 40568478 5.110000e-97 364
28 TraesCS7A01G538400 chr2D 95.946 222 7 2 2292 2513 184064511 184064292 2.380000e-95 359
29 TraesCS7A01G538400 chr2B 92.369 249 14 4 2267 2513 55237942 55237697 1.430000e-92 350
30 TraesCS7A01G538400 chr7D 91.129 248 16 3 2047 2293 619887518 619887760 5.180000e-87 331


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 TraesCS7A01G538400 chr7A 715661204 715663716 2512 True 4641.000000 4641 100.000000 1 2513 1 chr7A.!!$R3 2512
1 TraesCS7A01G538400 chr7A 715576205 715581717 5512 True 1410.500000 2715 95.953500 548 2513 2 chr7A.!!$R8 1965
2 TraesCS7A01G538400 chr7A 715329302 715333785 4483 True 850.000000 1589 99.384000 987 1879 2 chr7A.!!$R5 892
3 TraesCS7A01G538400 chr7A 715435534 715440372 4838 True 757.000000 1408 95.193500 548 1818 2 chr7A.!!$R7 1270
4 TraesCS7A01G538400 chr7A 715242025 715245929 3904 True 704.333333 1807 96.193667 987 2296 3 chr7A.!!$R4 1309
5 TraesCS7A01G538400 chr7A 715422127 715425505 3378 True 585.000000 848 96.826500 1816 2513 2 chr7A.!!$R6 697
6 TraesCS7A01G538400 chr7B 716976268 716978349 2081 False 975.000000 1555 93.546000 1 2012 3 chr7B.!!$F1 2011
7 TraesCS7A01G538400 chr7B 716698902 716700950 2048 True 711.250000 1229 92.773250 1 2012 4 chr7B.!!$R1 2011
8 TraesCS7A01G538400 chr7B 716984530 716988912 4382 False 400.500000 555 87.807000 1573 2293 2 chr7B.!!$F2 720

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
290 291 0.400213 CCATACTGTGTGGTGTGGGT 59.600 55.000 14.74 0.00 42.33 4.51 F
482 487 2.437716 GGATTGAAAGGCGCCCGA 60.438 61.111 26.15 8.42 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 5154 4.394712 CGCTCTTCCCGGGCTTGT 62.395 66.667 18.49 0.0 0.0 3.16 R
1795 5592 7.342581 TGCTTTAGATCCCATTGTACACAATA 58.657 34.615 7.25 0.0 44.1 1.90 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
35 36 7.040617 TCGACTATCTTACAGAAGTGTGTTTCT 60.041 37.037 0.00 0.00 37.52 2.52
72 73 8.642908 TGATGGTATTACGCTTATGCATATAC 57.357 34.615 7.36 6.14 39.64 1.47
73 74 8.254508 TGATGGTATTACGCTTATGCATATACA 58.745 33.333 7.36 0.00 39.64 2.29
214 215 4.579384 ACCACAACCACGGCCCAG 62.579 66.667 0.00 0.00 0.00 4.45
247 248 8.532186 TGTTCATAATTATTATTGTGTGCCCT 57.468 30.769 0.00 0.00 35.21 5.19
252 253 9.283768 CATAATTATTATTGTGTGCCCTGAGTA 57.716 33.333 0.00 0.00 30.69 2.59
253 254 7.807977 AATTATTATTGTGTGCCCTGAGTAG 57.192 36.000 0.00 0.00 0.00 2.57
290 291 0.400213 CCATACTGTGTGGTGTGGGT 59.600 55.000 14.74 0.00 42.33 4.51
445 450 2.871022 CGACAGTCCTACGCTGTAGTAT 59.129 50.000 12.54 0.00 45.99 2.12
465 470 5.648092 AGTATCAATGAAACCTTCTTTCCCG 59.352 40.000 0.00 0.00 0.00 5.14
481 486 3.876198 CGGATTGAAAGGCGCCCG 61.876 66.667 26.15 13.42 0.00 6.13
482 487 2.437716 GGATTGAAAGGCGCCCGA 60.438 61.111 26.15 8.42 0.00 5.14
503 508 7.542824 GCCCGAGCATTTTACTGTTTAAAAATA 59.457 33.333 0.00 0.00 39.53 1.40
671 679 7.388500 ACCAAATTTTGTTTTCATCCAGCTATG 59.612 33.333 8.26 0.00 0.00 2.23
808 4549 7.203910 GGAGTATTCGCCTCAGGTAATATATG 58.796 42.308 0.00 0.00 0.00 1.78
810 4551 5.683876 ATTCGCCTCAGGTAATATATGCT 57.316 39.130 0.00 0.00 0.00 3.79
813 4554 4.711846 TCGCCTCAGGTAATATATGCTCAT 59.288 41.667 0.00 0.00 0.00 2.90
817 4558 8.360390 CGCCTCAGGTAATATATGCTCATAATA 58.640 37.037 0.00 0.00 0.00 0.98
893 4634 7.692460 TTCTGCAATATTGAACAATCTGAGT 57.308 32.000 19.73 0.00 32.50 3.41
894 4635 8.791327 TTCTGCAATATTGAACAATCTGAGTA 57.209 30.769 19.73 0.00 32.50 2.59
895 4636 8.969260 TCTGCAATATTGAACAATCTGAGTAT 57.031 30.769 19.73 0.00 32.50 2.12
896 4637 8.833493 TCTGCAATATTGAACAATCTGAGTATG 58.167 33.333 19.73 0.00 32.50 2.39
897 4638 7.420002 TGCAATATTGAACAATCTGAGTATGC 58.580 34.615 19.73 0.00 32.50 3.14
898 4639 6.860023 GCAATATTGAACAATCTGAGTATGCC 59.140 38.462 19.73 0.00 32.50 4.40
899 4640 7.255381 GCAATATTGAACAATCTGAGTATGCCT 60.255 37.037 19.73 0.00 32.50 4.75
900 4641 9.276590 CAATATTGAACAATCTGAGTATGCCTA 57.723 33.333 10.04 0.00 32.50 3.93
901 4642 8.839310 ATATTGAACAATCTGAGTATGCCTAC 57.161 34.615 3.23 0.00 32.50 3.18
902 4643 5.939764 TGAACAATCTGAGTATGCCTACT 57.060 39.130 0.79 0.79 40.98 2.57
903 4644 7.418337 TTGAACAATCTGAGTATGCCTACTA 57.582 36.000 1.26 0.00 38.33 1.82
904 4645 6.806751 TGAACAATCTGAGTATGCCTACTAC 58.193 40.000 1.26 0.00 38.33 2.73
905 4646 6.607600 TGAACAATCTGAGTATGCCTACTACT 59.392 38.462 1.26 0.00 38.33 2.57
906 4647 7.778382 TGAACAATCTGAGTATGCCTACTACTA 59.222 37.037 1.26 0.00 38.33 1.82
907 4648 8.713708 AACAATCTGAGTATGCCTACTACTAT 57.286 34.615 1.26 0.00 38.33 2.12
908 4649 9.809395 AACAATCTGAGTATGCCTACTACTATA 57.191 33.333 1.26 0.00 38.33 1.31
909 4650 9.983024 ACAATCTGAGTATGCCTACTACTATAT 57.017 33.333 1.26 0.00 38.33 0.86
979 4720 3.823873 TGGTTCAAACAACAGTCAACACT 59.176 39.130 0.00 0.00 0.00 3.55
1795 5592 7.492669 CCTCGCGTATATTAGATCAATGGAAAT 59.507 37.037 5.77 0.00 0.00 2.17
2033 10547 6.921307 GGTAAAACAATGTTGGTGGAGTAAAG 59.079 38.462 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.826574 AGCGTAATACCATCAGTTAATTTCTTA 57.173 29.630 0.00 0.00 0.00 2.10
122 123 6.052360 TGGAAGAAGGTTTTTAAATGTTGGC 58.948 36.000 0.00 0.00 0.00 4.52
247 248 3.615592 GCGGTACATTTGTGTCCTACTCA 60.616 47.826 0.00 0.00 0.00 3.41
252 253 1.296056 GCGCGGTACATTTGTGTCCT 61.296 55.000 8.83 0.00 0.00 3.85
253 254 1.133869 GCGCGGTACATTTGTGTCC 59.866 57.895 8.83 0.00 0.00 4.02
266 267 3.195002 CCACACAGTATGGCGCGG 61.195 66.667 8.83 0.00 43.62 6.46
290 291 6.121776 ACTCTCTCTAACTCTCTCAACAGA 57.878 41.667 0.00 0.00 0.00 3.41
333 334 1.139058 GTCCATGCCGACTAGTTCCAT 59.861 52.381 0.00 0.00 0.00 3.41
445 450 3.153919 CCGGGAAAGAAGGTTTCATTGA 58.846 45.455 0.00 0.00 0.00 2.57
465 470 2.437716 TCGGGCGCCTTTCAATCC 60.438 61.111 28.56 5.59 0.00 3.01
650 658 6.040209 TGCATAGCTGGATGAAAACAAAAT 57.960 33.333 0.00 0.00 0.00 1.82
671 679 2.784889 AATTTGCCCACGTGCCATGC 62.785 55.000 10.91 10.14 0.00 4.06
817 4558 9.807649 GCAGAAAACCAACAGAATCATAATATT 57.192 29.630 0.00 0.00 0.00 1.28
818 4559 8.131100 CGCAGAAAACCAACAGAATCATAATAT 58.869 33.333 0.00 0.00 0.00 1.28
820 4561 6.150976 TCGCAGAAAACCAACAGAATCATAAT 59.849 34.615 0.00 0.00 0.00 1.28
821 4562 5.471797 TCGCAGAAAACCAACAGAATCATAA 59.528 36.000 0.00 0.00 0.00 1.90
823 4564 3.820467 TCGCAGAAAACCAACAGAATCAT 59.180 39.130 0.00 0.00 0.00 2.45
824 4565 3.003275 GTCGCAGAAAACCAACAGAATCA 59.997 43.478 0.00 0.00 39.69 2.57
825 4566 3.251004 AGTCGCAGAAAACCAACAGAATC 59.749 43.478 0.00 0.00 39.69 2.52
880 4621 5.939764 AGTAGGCATACTCAGATTGTTCA 57.060 39.130 4.95 0.00 37.75 3.18
881 4622 7.045126 AGTAGTAGGCATACTCAGATTGTTC 57.955 40.000 15.39 0.00 41.46 3.18
882 4623 8.713708 ATAGTAGTAGGCATACTCAGATTGTT 57.286 34.615 15.39 0.00 41.46 2.83
883 4624 9.983024 ATATAGTAGTAGGCATACTCAGATTGT 57.017 33.333 15.39 0.00 41.46 2.71
893 4634 9.848710 GGACAGTGATATATAGTAGTAGGCATA 57.151 37.037 0.00 0.00 0.00 3.14
894 4635 8.336987 TGGACAGTGATATATAGTAGTAGGCAT 58.663 37.037 0.00 0.00 0.00 4.40
895 4636 7.610692 GTGGACAGTGATATATAGTAGTAGGCA 59.389 40.741 0.00 0.00 0.00 4.75
896 4637 7.610692 TGTGGACAGTGATATATAGTAGTAGGC 59.389 40.741 0.00 0.00 0.00 3.93
897 4638 9.516546 TTGTGGACAGTGATATATAGTAGTAGG 57.483 37.037 0.00 0.00 0.00 3.18
910 4651 9.113838 GAAATACTCAATATTGTGGACAGTGAT 57.886 33.333 18.89 5.53 33.53 3.06
911 4652 7.552687 GGAAATACTCAATATTGTGGACAGTGA 59.447 37.037 18.89 4.89 33.53 3.41
912 4653 7.336679 TGGAAATACTCAATATTGTGGACAGTG 59.663 37.037 18.89 0.00 33.53 3.66
913 4654 7.336931 GTGGAAATACTCAATATTGTGGACAGT 59.663 37.037 18.89 14.59 33.53 3.55
914 4655 7.336679 TGTGGAAATACTCAATATTGTGGACAG 59.663 37.037 18.89 10.13 33.53 3.51
979 4720 5.526111 CCATCGATCAATCTGCATGCATATA 59.474 40.000 22.97 10.46 0.00 0.86
1379 5154 4.394712 CGCTCTTCCCGGGCTTGT 62.395 66.667 18.49 0.00 0.00 3.16
1795 5592 7.342581 TGCTTTAGATCCCATTGTACACAATA 58.657 34.615 7.25 0.00 44.10 1.90
2033 10547 8.703336 GGATCTTTTGTAAAGCAAGAACATTTC 58.297 33.333 0.00 0.00 38.47 2.17


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

AutoCloner maintained by Alex Coulton.