Multiple sequence alignment - TraesCS5B01G267100

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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 TraesCS5B01G267100 chr5B 100.000 2549 0 0 1 2549 452113951 452111403 0.000000e+00 4708
1 TraesCS5B01G267100 chr5B 92.829 2022 93 22 542 2549 680230621 680228638 0.000000e+00 2883
2 TraesCS5B01G267100 chr5B 95.264 1647 63 9 912 2549 508124187 508122547 0.000000e+00 2595
3 TraesCS5B01G267100 chr5B 95.149 536 26 0 9 544 121127369 121127904 0.000000e+00 846
4 TraesCS5B01G267100 chr4B 94.156 2019 102 11 545 2549 3786342 3788358 0.000000e+00 3061
5 TraesCS5B01G267100 chr4D 94.196 2016 73 22 544 2549 43272764 43270783 0.000000e+00 3035
6 TraesCS5B01G267100 chr4D 95.329 1627 62 12 930 2549 459886113 459884494 0.000000e+00 2571
7 TraesCS5B01G267100 chr3B 93.831 2010 87 16 548 2549 548772277 548774257 0.000000e+00 2990
8 TraesCS5B01G267100 chr3B 94.692 1658 73 9 901 2549 548243263 548244914 0.000000e+00 2560
9 TraesCS5B01G267100 chr3B 93.947 413 21 3 535 944 661407788 661408199 2.790000e-174 621
10 TraesCS5B01G267100 chr1D 93.112 2018 74 23 544 2549 17040737 17038773 0.000000e+00 2896
11 TraesCS5B01G267100 chr7D 95.460 1630 62 7 930 2549 94497154 94495527 0.000000e+00 2590
12 TraesCS5B01G267100 chr7D 93.303 433 23 4 545 971 113991310 113991742 3.580000e-178 634
13 TraesCS5B01G267100 chr2B 95.956 544 22 0 1 544 434986214 434986757 0.000000e+00 883
14 TraesCS5B01G267100 chr2B 95.336 536 22 2 9 544 411015529 411014997 0.000000e+00 848
15 TraesCS5B01G267100 chr2B 94.568 405 19 2 541 942 788228854 788229258 7.740000e-175 623
16 TraesCS5B01G267100 chr6B 96.082 536 21 0 9 544 133469019 133469554 0.000000e+00 874
17 TraesCS5B01G267100 chr6B 95.037 544 26 1 1 544 296442643 296443185 0.000000e+00 854
18 TraesCS5B01G267100 chr6B 94.568 405 16 4 541 942 585915584 585915985 2.790000e-174 621
19 TraesCS5B01G267100 chr1B 95.037 544 26 1 1 544 549834933 549835475 0.000000e+00 854
20 TraesCS5B01G267100 chr1B 94.669 544 29 0 1 544 202395274 202395817 0.000000e+00 845
21 TraesCS5B01G267100 chr7B 94.679 545 26 3 1 544 224990306 224989764 0.000000e+00 843
22 TraesCS5B01G267100 chr7B 94.495 545 28 2 1 544 52598542 52599085 0.000000e+00 839
23 TraesCS5B01G267100 chr7B 94.554 404 17 3 542 942 692881449 692881850 1.000000e-173 619
24 TraesCS5B01G267100 chr3D 84.923 650 86 12 1 644 370096367 370095724 0.000000e+00 647
25 TraesCS5B01G267100 chr7A 93.365 422 21 5 525 942 39015348 39015766 3.600000e-173 617
26 TraesCS5B01G267100 chr6A 93.932 412 17 6 536 942 533982332 533981924 1.300000e-172 616
27 TraesCS5B01G267100 chr4A 94.118 408 18 4 538 942 726682318 726681914 1.300000e-172 616


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 TraesCS5B01G267100 chr5B 452111403 452113951 2548 True 4708 4708 100.000 1 2549 1 chr5B.!!$R1 2548
1 TraesCS5B01G267100 chr5B 680228638 680230621 1983 True 2883 2883 92.829 542 2549 1 chr5B.!!$R3 2007
2 TraesCS5B01G267100 chr5B 508122547 508124187 1640 True 2595 2595 95.264 912 2549 1 chr5B.!!$R2 1637
3 TraesCS5B01G267100 chr5B 121127369 121127904 535 False 846 846 95.149 9 544 1 chr5B.!!$F1 535
4 TraesCS5B01G267100 chr4B 3786342 3788358 2016 False 3061 3061 94.156 545 2549 1 chr4B.!!$F1 2004
5 TraesCS5B01G267100 chr4D 43270783 43272764 1981 True 3035 3035 94.196 544 2549 1 chr4D.!!$R1 2005
6 TraesCS5B01G267100 chr4D 459884494 459886113 1619 True 2571 2571 95.329 930 2549 1 chr4D.!!$R2 1619
7 TraesCS5B01G267100 chr3B 548772277 548774257 1980 False 2990 2990 93.831 548 2549 1 chr3B.!!$F2 2001
8 TraesCS5B01G267100 chr3B 548243263 548244914 1651 False 2560 2560 94.692 901 2549 1 chr3B.!!$F1 1648
9 TraesCS5B01G267100 chr1D 17038773 17040737 1964 True 2896 2896 93.112 544 2549 1 chr1D.!!$R1 2005
10 TraesCS5B01G267100 chr7D 94495527 94497154 1627 True 2590 2590 95.460 930 2549 1 chr7D.!!$R1 1619
11 TraesCS5B01G267100 chr2B 434986214 434986757 543 False 883 883 95.956 1 544 1 chr2B.!!$F1 543
12 TraesCS5B01G267100 chr2B 411014997 411015529 532 True 848 848 95.336 9 544 1 chr2B.!!$R1 535
13 TraesCS5B01G267100 chr6B 133469019 133469554 535 False 874 874 96.082 9 544 1 chr6B.!!$F1 535
14 TraesCS5B01G267100 chr6B 296442643 296443185 542 False 854 854 95.037 1 544 1 chr6B.!!$F2 543
15 TraesCS5B01G267100 chr1B 549834933 549835475 542 False 854 854 95.037 1 544 1 chr1B.!!$F2 543
16 TraesCS5B01G267100 chr1B 202395274 202395817 543 False 845 845 94.669 1 544 1 chr1B.!!$F1 543
17 TraesCS5B01G267100 chr7B 224989764 224990306 542 True 843 843 94.679 1 544 1 chr7B.!!$R1 543
18 TraesCS5B01G267100 chr7B 52598542 52599085 543 False 839 839 94.495 1 544 1 chr7B.!!$F1 543
19 TraesCS5B01G267100 chr3D 370095724 370096367 643 True 647 647 84.923 1 644 1 chr3D.!!$R1 643

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
874 890 0.67964 ACCACAGCGAGAGAGAGAGG 60.68 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2388 2447 2.131776 ACGTTCAACTTTCCAACCCA 57.868 45.0 0.0 0.0 0.0 4.51 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
242 247 1.205893 TCACCATACGTGCATGCTACA 59.794 47.619 20.33 1.62 42.69 2.74
261 266 2.616842 ACAGGACTTGCCAACTTTAACG 59.383 45.455 0.00 0.00 40.02 3.18
425 430 5.426509 TGGATGCCCATCATATTAGGACTAG 59.573 44.000 10.17 0.00 39.54 2.57
678 688 1.663739 CCGTCTCCGTCAGGTCAAA 59.336 57.895 0.00 0.00 39.05 2.69
712 722 1.462432 TTACAGGTGGGACCAGGCA 60.462 57.895 0.00 0.00 41.95 4.75
744 756 7.260603 GGCTAATTTTATTCAGACTGTTGCAT 58.739 34.615 1.59 0.00 0.00 3.96
747 759 5.450592 TTTTATTCAGACTGTTGCATGCA 57.549 34.783 18.46 18.46 0.00 3.96
874 890 0.679640 ACCACAGCGAGAGAGAGAGG 60.680 60.000 0.00 0.00 0.00 3.69
876 892 0.679640 CACAGCGAGAGAGAGAGGGT 60.680 60.000 0.00 0.00 0.00 4.34
898 914 2.982130 CGGTGGGAAGCTAGCTGT 59.018 61.111 20.16 8.62 0.00 4.40
899 915 1.448540 CGGTGGGAAGCTAGCTGTG 60.449 63.158 20.16 0.00 0.00 3.66
903 919 1.267574 TGGGAAGCTAGCTGTGGAGG 61.268 60.000 20.16 0.00 0.00 4.30
906 922 2.914777 GAAGCTAGCTGTGGAGGGCG 62.915 65.000 20.16 0.00 0.00 6.13
926 942 1.381928 CGACGGTGGGAAGCTAGCTA 61.382 60.000 19.70 0.00 0.00 3.32
1021 1066 1.913262 TCTTCCTCAAGCTCCCGCA 60.913 57.895 0.00 0.00 39.10 5.69
1133 1178 2.093447 ACACATCGAGGAACCAGAATCC 60.093 50.000 3.06 0.00 37.22 3.01
1161 1207 2.743752 CGTGTGCAGCGAGAATGGG 61.744 63.158 4.77 0.00 0.00 4.00
1174 1220 2.438392 GAGAATGGGGTAAGAATCGGGT 59.562 50.000 0.00 0.00 0.00 5.28
1179 1225 2.171870 TGGGGTAAGAATCGGGTCAATC 59.828 50.000 0.00 0.00 0.00 2.67
1282 1328 0.461548 CGATGCTCTGGCCAAGACTA 59.538 55.000 7.01 0.00 37.74 2.59
1392 1438 1.827789 GGAGGGCAAAGCACACACA 60.828 57.895 0.00 0.00 32.33 3.72
1633 1679 9.753669 GGTCAAAGTTGTTTAAATGTTGAAAAG 57.246 29.630 0.00 0.00 0.00 2.27
1745 1797 1.001746 TCTGCTCTGCCTTTCTGTCAG 59.998 52.381 0.00 0.00 0.00 3.51
1783 1836 2.565841 GGCCAAATTCAGAGCGTAGAT 58.434 47.619 0.00 0.00 0.00 1.98
1848 1901 1.532794 ATTCGGGGGTTTGCTTGCA 60.533 52.632 0.00 0.00 0.00 4.08
1923 1977 7.651704 GCTGAAACTTTTTGTGGAAGCTAATTA 59.348 33.333 0.00 0.00 0.00 1.40
2092 2146 3.389221 GTTTACACCTGGTGCCAAAATG 58.611 45.455 26.20 0.67 36.98 2.32
2235 2291 1.966451 GTGTTTAGGGCTGCGCTGT 60.966 57.895 27.01 6.59 0.00 4.40
2240 2296 0.323629 TTAGGGCTGCGCTGTTAACT 59.676 50.000 27.01 10.81 0.00 2.24
2241 2297 1.187974 TAGGGCTGCGCTGTTAACTA 58.812 50.000 27.01 4.27 0.00 2.24
2318 2375 7.542130 AGTGAGACTGTGAAATTTGTCAAAAAC 59.458 33.333 1.31 0.28 32.41 2.43
2388 2447 6.349197 CCTTTGTTTTGCACTGAAATTTTGGT 60.349 34.615 0.00 0.00 0.00 3.67
2398 2457 4.226168 ACTGAAATTTTGGTGGGTTGGAAA 59.774 37.500 0.00 0.00 0.00 3.13
2541 2612 3.507162 TGAATGAAACAGAGGGCTTCA 57.493 42.857 0.00 0.00 33.82 3.02
2543 2614 2.206576 ATGAAACAGAGGGCTTCACC 57.793 50.000 0.00 0.00 32.19 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 74 5.106277 GCTTCGAGGGCTAATAAACTTTTGT 60.106 40.000 0.00 0.00 0.00 2.83
242 247 1.607148 GCGTTAAAGTTGGCAAGTCCT 59.393 47.619 8.24 1.57 35.26 3.85
425 430 8.603181 CATGGTAATTTGCTTTGGCTATAAAAC 58.397 33.333 0.00 0.00 39.59 2.43
433 438 2.674357 CAGCATGGTAATTTGCTTTGGC 59.326 45.455 0.00 0.00 46.71 4.52
520 528 4.431416 TCTTTTTAGAGCAAGGTGGTGA 57.569 40.909 0.00 0.00 0.00 4.02
678 688 1.418637 TGTAAGGGCCGAGTCAAAAGT 59.581 47.619 0.00 0.00 0.00 2.66
722 734 7.600960 TGCATGCAACAGTCTGAATAAAATTA 58.399 30.769 20.30 0.00 0.00 1.40
744 756 2.283101 GGTCCCACAAGCCATGCA 60.283 61.111 0.00 0.00 0.00 3.96
747 759 2.765969 CTGGGTCCCACAAGCCAT 59.234 61.111 6.47 0.00 45.28 4.40
876 892 2.362760 TAGCTTCCCACCGCCGTA 60.363 61.111 0.00 0.00 0.00 4.02
906 922 2.202756 CTAGCTTCCCACCGTCGC 60.203 66.667 0.00 0.00 0.00 5.19
909 925 0.753262 CATAGCTAGCTTCCCACCGT 59.247 55.000 24.88 0.00 0.00 4.83
1061 1106 0.389817 CCGCGGACAGATGAAGACAA 60.390 55.000 24.07 0.00 0.00 3.18
1161 1207 1.865340 GCGATTGACCCGATTCTTACC 59.135 52.381 0.00 0.00 0.00 2.85
1174 1220 1.198867 CCACGAAAATGGTGCGATTGA 59.801 47.619 0.00 0.00 34.77 2.57
1282 1328 6.376299 TGCTCTTCTTGCAGTTCATTTATCAT 59.624 34.615 0.00 0.00 35.31 2.45
1392 1438 2.754552 CTCAACAGCTAGCTCTCTGTCT 59.245 50.000 16.15 8.41 42.19 3.41
1633 1679 6.625873 ATGTTGGTCACTTCTTCTCTTTTC 57.374 37.500 0.00 0.00 0.00 2.29
1674 1724 7.025520 TCTGAATTCCTCATTTCTTCTCCTT 57.974 36.000 2.27 0.00 32.14 3.36
1783 1836 2.231716 TAGTCTAGCCTGCACTTGGA 57.768 50.000 0.00 0.00 0.00 3.53
1841 1894 6.985645 ACAGAAAATAGAAAAACATGCAAGCA 59.014 30.769 0.00 0.00 0.00 3.91
1842 1895 7.412137 ACAGAAAATAGAAAAACATGCAAGC 57.588 32.000 0.00 0.00 0.00 4.01
1932 1986 9.528489 AATTCTAACCTTAATTGTTTGGCTCTA 57.472 29.630 0.00 0.00 0.00 2.43
2235 2291 5.955959 TCTTGCCATCTGTCCTAGTAGTTAA 59.044 40.000 0.00 0.00 0.00 2.01
2240 2296 3.982516 AGTCTTGCCATCTGTCCTAGTA 58.017 45.455 0.00 0.00 0.00 1.82
2241 2297 2.826488 AGTCTTGCCATCTGTCCTAGT 58.174 47.619 0.00 0.00 0.00 2.57
2318 2375 5.621422 CAAACATTCACGGTCTCACTATTG 58.379 41.667 0.00 0.00 0.00 1.90
2388 2447 2.131776 ACGTTCAACTTTCCAACCCA 57.868 45.000 0.00 0.00 0.00 4.51
2398 2457 3.548014 GCAGTGCAAACATACGTTCAACT 60.548 43.478 11.09 0.00 32.91 3.16


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

AutoCloner maintained by Alex Coulton.