Multiple sequence alignment - TraesCS7A01G371000

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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 TraesCS7A01G371000 chr7A 100.000 3675 0 0 1 3675 544289192 544285518 0.000000e+00 6787.0
1 TraesCS7A01G371000 chr7A 92.228 193 15 0 3 195 329592475 329592667 1.300000e-69 274.0
2 TraesCS7A01G371000 chr7A 84.783 184 28 0 1242 1425 429042976 429042793 6.270000e-43 185.0
3 TraesCS7A01G371000 chr3B 98.406 1004 14 1 2674 3675 826293 827296 0.000000e+00 1764.0
4 TraesCS7A01G371000 chr3B 76.905 420 84 8 2224 2641 63389457 63389865 3.690000e-55 226.0
5 TraesCS7A01G371000 chr3B 90.769 65 2 3 523 583 20783657 20783721 2.350000e-12 84.2
6 TraesCS7A01G371000 chr2A 98.406 1004 14 2 2674 3675 30084283 30083280 0.000000e+00 1764.0
7 TraesCS7A01G371000 chr2A 93.923 181 9 1 4 184 421850413 421850235 4.680000e-69 272.0
8 TraesCS7A01G371000 chr7B 98.596 997 12 1 2681 3675 339088026 339087030 0.000000e+00 1762.0
9 TraesCS7A01G371000 chr7B 98.302 1001 15 1 2677 3675 649990212 649989212 0.000000e+00 1753.0
10 TraesCS7A01G371000 chr7B 84.805 974 106 21 1693 2643 475244684 475243730 0.000000e+00 941.0
11 TraesCS7A01G371000 chr7B 87.119 722 57 14 871 1567 475249059 475248349 0.000000e+00 785.0
12 TraesCS7A01G371000 chr7B 76.510 447 86 12 2224 2668 375394023 375393594 3.690000e-55 226.0
13 TraesCS7A01G371000 chr7B 87.500 64 5 2 523 583 592179143 592179080 1.830000e-08 71.3
14 TraesCS7A01G371000 chr7B 97.561 41 0 1 2640 2680 475243294 475243255 6.590000e-08 69.4
15 TraesCS7A01G371000 chr7B 91.667 48 4 0 1648 1695 475246350 475246303 2.370000e-07 67.6
16 TraesCS7A01G371000 chr6B 98.692 994 12 1 2683 3675 17106099 17107092 0.000000e+00 1762.0
17 TraesCS7A01G371000 chr6B 98.593 995 13 1 2682 3675 132336486 132335492 0.000000e+00 1759.0
18 TraesCS7A01G371000 chr5B 98.692 994 12 1 2683 3675 649539552 649538559 0.000000e+00 1762.0
19 TraesCS7A01G371000 chr5B 86.301 365 45 4 162 522 82467172 82466809 3.440000e-105 392.0
20 TraesCS7A01G371000 chr5B 88.060 67 6 1 523 587 652825871 652825805 1.090000e-10 78.7
21 TraesCS7A01G371000 chr5B 81.944 72 13 0 537 608 500523852 500523923 1.100000e-05 62.1
22 TraesCS7A01G371000 chr3A 98.690 992 13 0 2684 3675 606519987 606520978 0.000000e+00 1760.0
23 TraesCS7A01G371000 chr3A 95.455 176 8 0 1 176 392413836 392414011 7.770000e-72 281.0
24 TraesCS7A01G371000 chr3A 77.852 447 83 9 2224 2668 51383199 51383631 2.810000e-66 263.0
25 TraesCS7A01G371000 chr1A 98.305 1003 14 2 2676 3675 343662027 343663029 0.000000e+00 1755.0
26 TraesCS7A01G371000 chr1A 95.977 174 7 0 1 174 339537742 339537569 2.160000e-72 283.0
27 TraesCS7A01G371000 chr1A 96.471 170 6 0 3 172 230678096 230677927 7.770000e-72 281.0
28 TraesCS7A01G371000 chr7D 85.749 1228 102 32 871 2054 452262580 452261382 0.000000e+00 1230.0
29 TraesCS7A01G371000 chr7D 91.082 527 40 3 2157 2680 452259627 452259105 0.000000e+00 706.0
30 TraesCS7A01G371000 chr1B 84.022 363 53 3 162 520 632913954 632913593 9.770000e-91 344.0
31 TraesCS7A01G371000 chr1B 83.836 365 54 3 162 522 632905332 632904969 3.510000e-90 342.0
32 TraesCS7A01G371000 chr1B 83.562 365 55 3 162 522 632892724 632892361 1.630000e-88 337.0
33 TraesCS7A01G371000 chr1B 83.562 365 55 3 162 522 632898472 632898109 1.630000e-88 337.0
34 TraesCS7A01G371000 chr1B 83.562 365 55 3 162 522 632911080 632910717 1.630000e-88 337.0
35 TraesCS7A01G371000 chr1B 83.014 365 57 3 162 522 632908206 632907843 3.540000e-85 326.0
36 TraesCS7A01G371000 chr1B 95.455 176 7 1 1 176 327530309 327530483 2.790000e-71 279.0
37 TraesCS7A01G371000 chrUn 83.836 365 54 3 162 522 448650592 448650955 3.510000e-90 342.0
38 TraesCS7A01G371000 chrUn 83.562 365 55 3 162 522 8042448 8042085 1.630000e-88 337.0
39 TraesCS7A01G371000 chr5A 96.491 171 6 0 1 171 9665546 9665376 2.160000e-72 283.0
40 TraesCS7A01G371000 chr6D 92.708 192 10 4 1 191 133371795 133371607 1.300000e-69 274.0
41 TraesCS7A01G371000 chr6D 97.368 38 0 1 613 650 458333710 458333746 3.060000e-06 63.9
42 TraesCS7A01G371000 chr4D 93.443 183 10 2 1 182 211575159 211575340 1.680000e-68 270.0
43 TraesCS7A01G371000 chr3D 76.233 446 92 6 2224 2668 39590730 39591162 1.330000e-54 224.0
44 TraesCS7A01G371000 chr2D 90.909 66 2 3 523 584 78708803 78708868 6.540000e-13 86.1
45 TraesCS7A01G371000 chr5D 92.000 50 1 2 523 569 447552665 447552616 2.370000e-07 67.6
46 TraesCS7A01G371000 chr4A 87.273 55 2 3 523 572 686532705 686532651 1.430000e-04 58.4


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 TraesCS7A01G371000 chr7A 544285518 544289192 3674 True 6787.00 6787 100.0000 1 3675 1 chr7A.!!$R2 3674
1 TraesCS7A01G371000 chr3B 826293 827296 1003 False 1764.00 1764 98.4060 2674 3675 1 chr3B.!!$F1 1001
2 TraesCS7A01G371000 chr2A 30083280 30084283 1003 True 1764.00 1764 98.4060 2674 3675 1 chr2A.!!$R1 1001
3 TraesCS7A01G371000 chr7B 339087030 339088026 996 True 1762.00 1762 98.5960 2681 3675 1 chr7B.!!$R1 994
4 TraesCS7A01G371000 chr7B 649989212 649990212 1000 True 1753.00 1753 98.3020 2677 3675 1 chr7B.!!$R4 998
5 TraesCS7A01G371000 chr7B 475243255 475249059 5804 True 465.75 941 90.2880 871 2680 4 chr7B.!!$R5 1809
6 TraesCS7A01G371000 chr6B 17106099 17107092 993 False 1762.00 1762 98.6920 2683 3675 1 chr6B.!!$F1 992
7 TraesCS7A01G371000 chr6B 132335492 132336486 994 True 1759.00 1759 98.5930 2682 3675 1 chr6B.!!$R1 993
8 TraesCS7A01G371000 chr5B 649538559 649539552 993 True 1762.00 1762 98.6920 2683 3675 1 chr5B.!!$R2 992
9 TraesCS7A01G371000 chr3A 606519987 606520978 991 False 1760.00 1760 98.6900 2684 3675 1 chr3A.!!$F3 991
10 TraesCS7A01G371000 chr1A 343662027 343663029 1002 False 1755.00 1755 98.3050 2676 3675 1 chr1A.!!$F1 999
11 TraesCS7A01G371000 chr7D 452259105 452262580 3475 True 968.00 1230 88.4155 871 2680 2 chr7D.!!$R1 1809
12 TraesCS7A01G371000 chr1B 632904969 632913954 8985 True 337.25 344 83.6085 162 522 4 chr1B.!!$R3 360


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
283 288 0.034670 AAGGAGGAAGCCATCTGTGC 60.035 55.0 0.0 0.0 0.0 4.57 F
727 732 0.035598 TTTTGGGATCGAACGGCTGA 59.964 50.0 0.0 0.0 0.0 4.26 F
842 847 0.036765 TACGCTCGCCAAATCAGGTT 60.037 50.0 0.0 0.0 0.0 3.50 F
1906 7100 0.036858 AAGAGAAGACTTGCCGCTCC 60.037 55.0 0.0 0.0 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 6995 0.031178 CACTTCTTGTGCCCTTGTGC 59.969 55.000 0.00 0.0 40.06 4.57 R
2535 9491 0.032678 CCGTCCCATCTCAATCTCCG 59.967 60.000 0.00 0.0 0.00 4.63 R
2542 9498 0.107066 TACGTAGCCGTCCCATCTCA 60.107 55.000 0.00 0.0 46.28 3.27 R
2988 10834 1.143183 TCCGCGTATTCTTGGAGCC 59.857 57.895 4.92 0.0 0.00 4.70 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)



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AutoCloner maintained by Alex Coulton.