Multiple sequence alignment - TraesCS4A01G078500

Loading Multiple Alignment...

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 TraesCS4A01G078500 chr4A 100.000 2468 0 0 1 2468 78261409 78263876 0.000000e+00 4558.0
1 TraesCS4A01G078500 chr4A 97.431 545 14 0 56 600 395039274 395038730 0.000000e+00 929.0
2 TraesCS4A01G078500 chr4A 91.329 346 27 3 59 403 225315962 225315619 1.030000e-128 470.0
3 TraesCS4A01G078500 chr1A 98.129 1871 34 1 599 2468 551926452 551928322 0.000000e+00 3260.0
4 TraesCS4A01G078500 chr1A 89.840 561 46 9 44 600 10088168 10088721 0.000000e+00 710.0
5 TraesCS4A01G078500 chr1A 78.020 1010 149 45 602 1560 208704418 208705405 3.560000e-158 568.0
6 TraesCS4A01G078500 chr1A 80.860 721 97 29 873 1571 14167136 14167837 1.680000e-146 529.0
7 TraesCS4A01G078500 chr1A 79.549 709 119 20 1780 2468 14168056 14168758 1.330000e-132 483.0
8 TraesCS4A01G078500 chr1A 79.549 709 119 20 1780 2468 208705633 208706335 1.330000e-132 483.0
9 TraesCS4A01G078500 chr1A 76.520 954 168 32 601 1539 249035855 249036767 1.030000e-128 470.0
10 TraesCS4A01G078500 chr5A 97.802 546 11 1 55 600 529184546 529184002 0.000000e+00 941.0
11 TraesCS4A01G078500 chr5A 97.222 36 1 0 1384 1419 622384678 622384643 7.370000e-06 62.1
12 TraesCS4A01G078500 chr3A 83.080 987 129 28 601 1566 728041898 728040929 0.000000e+00 863.0
13 TraesCS4A01G078500 chr3A 82.877 987 131 28 601 1566 728026866 728025897 0.000000e+00 852.0
14 TraesCS4A01G078500 chr3A 82.696 994 127 30 601 1566 729682395 729683371 0.000000e+00 841.0
15 TraesCS4A01G078500 chr3B 82.477 993 136 26 600 1571 84451267 84452242 0.000000e+00 835.0
16 TraesCS4A01G078500 chr3B 81.755 1014 124 31 601 1571 705352515 705353510 0.000000e+00 791.0
17 TraesCS4A01G078500 chr3D 89.890 455 21 10 794 1224 501426127 501426580 1.660000e-156 562.0
18 TraesCS4A01G078500 chr3D 89.500 200 20 1 599 798 501418193 501418391 4.070000e-63 252.0
19 TraesCS4A01G078500 chr7B 91.795 195 16 0 79 273 657905170 657904976 3.130000e-69 272.0
20 TraesCS4A01G078500 chr2B 90.909 88 8 0 599 686 794581826 794581913 4.310000e-23 119.0
21 TraesCS4A01G078500 chr1B 97.368 38 0 1 48 85 316608793 316608757 2.050000e-06 63.9


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 TraesCS4A01G078500 chr4A 78261409 78263876 2467 False 4558.0 4558 100.0000 1 2468 1 chr4A.!!$F1 2467
1 TraesCS4A01G078500 chr4A 395038730 395039274 544 True 929.0 929 97.4310 56 600 1 chr4A.!!$R2 544
2 TraesCS4A01G078500 chr1A 551926452 551928322 1870 False 3260.0 3260 98.1290 599 2468 1 chr1A.!!$F3 1869
3 TraesCS4A01G078500 chr1A 10088168 10088721 553 False 710.0 710 89.8400 44 600 1 chr1A.!!$F1 556
4 TraesCS4A01G078500 chr1A 208704418 208706335 1917 False 525.5 568 78.7845 602 2468 2 chr1A.!!$F5 1866
5 TraesCS4A01G078500 chr1A 14167136 14168758 1622 False 506.0 529 80.2045 873 2468 2 chr1A.!!$F4 1595
6 TraesCS4A01G078500 chr1A 249035855 249036767 912 False 470.0 470 76.5200 601 1539 1 chr1A.!!$F2 938
7 TraesCS4A01G078500 chr5A 529184002 529184546 544 True 941.0 941 97.8020 55 600 1 chr5A.!!$R1 545
8 TraesCS4A01G078500 chr3A 728040929 728041898 969 True 863.0 863 83.0800 601 1566 1 chr3A.!!$R2 965
9 TraesCS4A01G078500 chr3A 728025897 728026866 969 True 852.0 852 82.8770 601 1566 1 chr3A.!!$R1 965
10 TraesCS4A01G078500 chr3A 729682395 729683371 976 False 841.0 841 82.6960 601 1566 1 chr3A.!!$F1 965
11 TraesCS4A01G078500 chr3B 84451267 84452242 975 False 835.0 835 82.4770 600 1571 1 chr3B.!!$F1 971
12 TraesCS4A01G078500 chr3B 705352515 705353510 995 False 791.0 791 81.7550 601 1571 1 chr3B.!!$F2 970

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
29 30 0.094558 TCTGCAAAATTAGCGCGACG 59.905 50.0 12.1 0.0 33.85 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 1854 1.153329 GGTGTGACGTGGACCAACA 60.153 57.895 0.0 0.0 0.0 3.33 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
23 24 4.925646 CAGGGACTTTTCTGCAAAATTAGC 59.074 41.667 0.00 0.00 34.60 3.09
24 25 3.920412 GGGACTTTTCTGCAAAATTAGCG 59.080 43.478 0.00 0.00 30.91 4.26
25 26 3.364920 GGACTTTTCTGCAAAATTAGCGC 59.635 43.478 0.00 0.00 30.91 5.92
26 27 2.979813 ACTTTTCTGCAAAATTAGCGCG 59.020 40.909 0.00 0.00 30.91 6.86
27 28 2.979401 TTTCTGCAAAATTAGCGCGA 57.021 40.000 12.10 0.00 33.85 5.87
28 29 2.241259 TTCTGCAAAATTAGCGCGAC 57.759 45.000 12.10 0.04 33.85 5.19
29 30 0.094558 TCTGCAAAATTAGCGCGACG 59.905 50.000 12.10 0.00 33.85 5.12
30 31 0.857311 CTGCAAAATTAGCGCGACGG 60.857 55.000 12.10 0.00 33.85 4.79
31 32 1.292571 TGCAAAATTAGCGCGACGGA 61.293 50.000 12.10 0.00 33.85 4.69
32 33 0.856080 GCAAAATTAGCGCGACGGAC 60.856 55.000 12.10 0.00 0.00 4.79
33 34 0.247537 CAAAATTAGCGCGACGGACC 60.248 55.000 12.10 0.00 0.00 4.46
34 35 1.689352 AAAATTAGCGCGACGGACCG 61.689 55.000 12.10 13.61 0.00 4.79
35 36 2.546645 AAATTAGCGCGACGGACCGA 62.547 55.000 23.38 0.00 0.00 4.69
36 37 2.345880 AATTAGCGCGACGGACCGAT 62.346 55.000 23.38 4.57 0.00 4.18
37 38 1.509644 ATTAGCGCGACGGACCGATA 61.510 55.000 23.38 0.45 0.00 2.92
38 39 1.713937 TTAGCGCGACGGACCGATAA 61.714 55.000 23.38 6.61 33.61 1.75
39 40 1.509644 TAGCGCGACGGACCGATAAT 61.510 55.000 23.38 0.00 0.00 1.28
40 41 2.362800 GCGCGACGGACCGATAATC 61.363 63.158 23.38 6.52 0.00 1.75
41 42 2.073220 CGCGACGGACCGATAATCG 61.073 63.158 23.38 19.86 40.07 3.34
42 43 3.824806 CGACGGACCGATAATCGC 58.175 61.111 23.38 0.00 38.82 4.58
46 47 2.602933 CGACGGACCGATAATCGCTTTA 60.603 50.000 23.38 0.00 38.82 1.85
50 51 5.717119 ACGGACCGATAATCGCTTTATTAT 58.283 37.500 23.38 0.00 38.82 1.28
251 255 2.080286 AACACGACATTTAGCGAGCT 57.920 45.000 2.25 2.25 0.00 4.09
686 691 4.559251 GGATTCGCACTCACTATAATAGCG 59.441 45.833 0.00 0.00 44.45 4.26
687 692 4.563337 TTCGCACTCACTATAATAGCGT 57.437 40.909 0.00 0.00 43.63 5.07
692 697 4.554134 GCACTCACTATAATAGCGTCGTCA 60.554 45.833 0.00 0.00 0.00 4.35
724 730 5.183140 TGCTTTCCAACTTTAGTATTCCTGC 59.817 40.000 0.00 0.00 0.00 4.85
771 777 1.202557 AGTACAACGCGTTTTCTCCCA 60.203 47.619 24.21 0.00 0.00 4.37
871 877 0.976641 ACACGCTCCTCATTTCCTCA 59.023 50.000 0.00 0.00 0.00 3.86
1208 1302 7.201661 GCACGAGTGGGTATGTCATTTTATTTA 60.202 37.037 5.32 0.00 0.00 1.40
1390 1486 2.202932 CATCCCGCGAAGACAGGG 60.203 66.667 8.23 0.00 46.40 4.45
1816 1962 1.035139 CAAAAGCCTGCTCCAACAGT 58.965 50.000 0.00 0.00 35.83 3.55
2078 2239 1.300620 GGCAACCAAAAGCCGGAAC 60.301 57.895 5.05 0.00 41.70 3.62
2224 2385 0.618458 GGTCTAGCCCCAACATCACA 59.382 55.000 0.00 0.00 0.00 3.58
2330 2491 4.503991 GGGATACTTAAGCTCCCATCACTG 60.504 50.000 27.48 0.00 46.70 3.66
2460 2621 7.781056 AGATGTTCATAAAGTTTTTGGTGTGT 58.219 30.769 6.26 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.925646 GCTAATTTTGCAGAAAAGTCCCTG 59.074 41.667 0.00 0.00 34.53 4.45
1 2 4.321230 CGCTAATTTTGCAGAAAAGTCCCT 60.321 41.667 0.00 0.00 34.53 4.20
2 3 3.920412 CGCTAATTTTGCAGAAAAGTCCC 59.080 43.478 0.00 0.00 34.53 4.46
3 4 3.364920 GCGCTAATTTTGCAGAAAAGTCC 59.635 43.478 0.00 0.00 34.53 3.85
4 5 3.058129 CGCGCTAATTTTGCAGAAAAGTC 59.942 43.478 5.56 0.00 34.53 3.01
5 6 2.979813 CGCGCTAATTTTGCAGAAAAGT 59.020 40.909 5.56 0.00 34.53 2.66
6 7 3.058129 GTCGCGCTAATTTTGCAGAAAAG 59.942 43.478 5.56 0.00 34.53 2.27
7 8 2.977169 GTCGCGCTAATTTTGCAGAAAA 59.023 40.909 5.56 0.00 35.52 2.29
8 9 2.580589 GTCGCGCTAATTTTGCAGAAA 58.419 42.857 5.56 0.00 0.00 2.52
9 10 1.463363 CGTCGCGCTAATTTTGCAGAA 60.463 47.619 5.56 0.00 0.00 3.02
10 11 0.094558 CGTCGCGCTAATTTTGCAGA 59.905 50.000 5.56 0.00 0.00 4.26
11 12 0.857311 CCGTCGCGCTAATTTTGCAG 60.857 55.000 5.56 0.00 0.00 4.41
12 13 1.133664 CCGTCGCGCTAATTTTGCA 59.866 52.632 5.56 0.00 0.00 4.08
13 14 0.856080 GTCCGTCGCGCTAATTTTGC 60.856 55.000 5.56 0.00 0.00 3.68
14 15 0.247537 GGTCCGTCGCGCTAATTTTG 60.248 55.000 5.56 0.00 0.00 2.44
15 16 1.689352 CGGTCCGTCGCGCTAATTTT 61.689 55.000 5.56 0.00 0.00 1.82
16 17 2.162754 CGGTCCGTCGCGCTAATTT 61.163 57.895 5.56 0.00 0.00 1.82
17 18 2.345880 ATCGGTCCGTCGCGCTAATT 62.346 55.000 11.88 0.00 0.00 1.40
18 19 1.509644 TATCGGTCCGTCGCGCTAAT 61.510 55.000 11.88 0.00 0.00 1.73
19 20 1.713937 TTATCGGTCCGTCGCGCTAA 61.714 55.000 11.88 0.00 0.00 3.09
20 21 1.509644 ATTATCGGTCCGTCGCGCTA 61.510 55.000 11.88 0.00 0.00 4.26
21 22 2.728427 GATTATCGGTCCGTCGCGCT 62.728 60.000 11.88 0.00 0.00 5.92
22 23 2.354305 ATTATCGGTCCGTCGCGC 60.354 61.111 11.88 0.00 0.00 6.86
23 24 2.073220 CGATTATCGGTCCGTCGCG 61.073 63.158 11.88 0.00 36.00 5.87
24 25 3.824806 CGATTATCGGTCCGTCGC 58.175 61.111 11.88 0.00 36.00 5.19
25 26 3.824806 GCGATTATCGGTCCGTCG 58.175 61.111 16.59 15.48 40.84 5.12
46 47 8.411683 ACGTGCAAGCTTACTAGTAGTAATAAT 58.588 33.333 20.44 8.94 39.68 1.28
50 51 5.396484 CACGTGCAAGCTTACTAGTAGTAA 58.604 41.667 19.32 19.32 38.28 2.24
161 165 9.542462 GTCTATCATTAAGTGGCTTGTAATGTA 57.458 33.333 11.61 6.05 36.83 2.29
220 224 8.774586 GCTAAATGTCGTGTTTCCTAATGATAT 58.225 33.333 0.00 0.00 0.00 1.63
251 255 7.561021 TTATGTTCTCACTAAAGTTGCACAA 57.439 32.000 0.00 0.00 0.00 3.33
296 300 8.981647 GTTATTGTGAGATTGATTGTTTGCTTT 58.018 29.630 0.00 0.00 0.00 3.51
297 301 8.143193 TGTTATTGTGAGATTGATTGTTTGCTT 58.857 29.630 0.00 0.00 0.00 3.91
686 691 3.932710 TGGAAAGCAGTGAATATGACGAC 59.067 43.478 0.00 0.00 0.00 4.34
687 692 4.200838 TGGAAAGCAGTGAATATGACGA 57.799 40.909 0.00 0.00 0.00 4.20
692 697 9.686683 ATACTAAAGTTGGAAAGCAGTGAATAT 57.313 29.630 0.00 0.00 0.00 1.28
724 730 2.201732 GTGATATACCCACACTGTGCG 58.798 52.381 7.90 0.00 34.81 5.34
771 777 6.011122 AGGAGATGCATTTTTCTGGACTAT 57.989 37.500 0.00 0.00 0.00 2.12
871 877 0.687354 ACTGAGGATTGAGCCGTTGT 59.313 50.000 0.00 0.00 0.00 3.32
1208 1302 7.540745 GCAACAAAACGGTACTGAATAAATGAT 59.459 33.333 9.17 0.00 0.00 2.45
1390 1486 2.096069 CGATGATGATGCGGTGGAATTC 60.096 50.000 0.00 0.00 0.00 2.17
1708 1854 1.153329 GGTGTGACGTGGACCAACA 60.153 57.895 0.00 0.00 0.00 3.33
1816 1962 4.720046 TGGTTACACAGTGGCAATTAAGA 58.280 39.130 5.31 0.00 0.00 2.10
2078 2239 6.530567 TGAACATATTGCGAAAGTTAAGACG 58.469 36.000 0.00 0.00 0.00 4.18
2091 2252 6.576185 ACATCCTGGAAAATGAACATATTGC 58.424 36.000 0.00 0.00 0.00 3.56
2208 2369 1.003580 AGTGTGTGATGTTGGGGCTAG 59.996 52.381 0.00 0.00 0.00 3.42
2224 2385 4.939439 AGACAACTTTTGTTACCGAAGTGT 59.061 37.500 2.15 3.40 45.52 3.55
2325 2486 1.629043 AGGTTAAGACGAGCCAGTGA 58.371 50.000 0.00 0.00 0.00 3.41
2330 2491 2.643933 AACGTAGGTTAAGACGAGCC 57.356 50.000 10.51 0.00 41.60 4.70


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

AutoCloner maintained by Alex Coulton.