Multiple sequence alignment - TraesCS7A01G095600

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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 TraesCS7A01G095600 chr7A 100.000 2339 0 0 1 2339 58646316 58648654 0.000000e+00 4320
1 TraesCS7A01G095600 chr7A 92.559 981 70 2 1 980 482164081 482163103 0.000000e+00 1404
2 TraesCS7A01G095600 chr7A 92.253 981 73 2 1 980 456270882 456269904 0.000000e+00 1387
3 TraesCS7A01G095600 chr6A 93.079 968 63 3 14 980 228507832 228508796 0.000000e+00 1413
4 TraesCS7A01G095600 chr3A 92.574 983 66 6 1 980 57845778 57846756 0.000000e+00 1404
5 TraesCS7A01G095600 chr3A 85.938 128 18 0 1449 1576 103690653 103690780 1.130000e-28 137
6 TraesCS7A01G095600 chr4A 92.464 982 70 3 1 980 497792954 497791975 0.000000e+00 1400
7 TraesCS7A01G095600 chr2A 92.665 968 68 2 14 980 422379352 422380317 0.000000e+00 1391
8 TraesCS7A01G095600 chr5A 92.253 981 73 2 1 980 275746382 275747360 0.000000e+00 1387
9 TraesCS7A01G095600 chr5A 94.368 799 35 7 1548 2338 244006587 244007383 0.000000e+00 1218
10 TraesCS7A01G095600 chr5A 95.960 99 4 0 1449 1547 267960427 267960525 6.690000e-36 161
11 TraesCS7A01G095600 chr1A 92.253 981 72 3 1 980 486295185 486296162 0.000000e+00 1387
12 TraesCS7A01G095600 chr1A 94.421 466 20 5 978 1439 168449425 168448962 0.000000e+00 712
13 TraesCS7A01G095600 chr1D 92.159 982 72 4 1 980 452436272 452437250 0.000000e+00 1382
14 TraesCS7A01G095600 chr1D 94.250 800 37 6 1546 2338 476655567 476654770 0.000000e+00 1214
15 TraesCS7A01G095600 chr1D 96.137 466 14 2 978 1439 254499141 254499606 0.000000e+00 758
16 TraesCS7A01G095600 chr1D 94.545 165 9 0 1449 1613 296448143 296448307 2.980000e-64 255
17 TraesCS7A01G095600 chr1D 94.949 99 5 0 1449 1547 258868825 258868727 3.110000e-34 156
18 TraesCS7A01G095600 chr2D 94.074 810 38 7 1537 2338 113574955 113574148 0.000000e+00 1221
19 TraesCS7A01G095600 chr2D 94.257 801 36 7 1546 2338 73366578 73365780 0.000000e+00 1216
20 TraesCS7A01G095600 chr2D 93.604 813 42 7 1534 2338 155302254 155303064 0.000000e+00 1205
21 TraesCS7A01G095600 chr3D 94.382 801 34 9 1547 2339 320311055 320311852 0.000000e+00 1219
22 TraesCS7A01G095600 chr3D 94.949 99 5 0 1449 1547 118333725 118333823 3.110000e-34 156
23 TraesCS7A01G095600 chr4D 94.161 805 35 9 1543 2338 100851151 100851952 0.000000e+00 1216
24 TraesCS7A01G095600 chr4D 94.361 798 36 7 1548 2338 346107527 346108322 0.000000e+00 1216
25 TraesCS7A01G095600 chr4D 93.991 466 24 2 978 1439 19917636 19918101 0.000000e+00 702
26 TraesCS7A01G095600 chr4D 94.949 99 5 0 1449 1547 111655045 111655143 3.110000e-34 156
27 TraesCS7A01G095600 chr3B 90.434 899 75 7 1449 2338 681809313 681808417 0.000000e+00 1173
28 TraesCS7A01G095600 chr3B 95.708 466 16 2 978 1439 201515823 201516288 0.000000e+00 747
29 TraesCS7A01G095600 chrUn 96.352 466 13 2 978 1439 30306208 30305743 0.000000e+00 763
30 TraesCS7A01G095600 chrUn 94.949 99 5 0 1449 1547 74033645 74033743 3.110000e-34 156
31 TraesCS7A01G095600 chr5D 96.137 466 14 4 978 1439 560873611 560874076 0.000000e+00 758
32 TraesCS7A01G095600 chr5D 95.708 466 16 2 978 1439 6200139 6199674 0.000000e+00 747
33 TraesCS7A01G095600 chr5D 95.717 467 14 4 978 1439 329163320 329163785 0.000000e+00 747
34 TraesCS7A01G095600 chr5D 94.949 99 5 0 1449 1547 358264257 358264355 3.110000e-34 156
35 TraesCS7A01G095600 chr6B 95.708 466 16 2 978 1439 121821134 121820669 0.000000e+00 747


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 TraesCS7A01G095600 chr7A 58646316 58648654 2338 False 4320 4320 100.000 1 2339 1 chr7A.!!$F1 2338
1 TraesCS7A01G095600 chr7A 482163103 482164081 978 True 1404 1404 92.559 1 980 1 chr7A.!!$R2 979
2 TraesCS7A01G095600 chr7A 456269904 456270882 978 True 1387 1387 92.253 1 980 1 chr7A.!!$R1 979
3 TraesCS7A01G095600 chr6A 228507832 228508796 964 False 1413 1413 93.079 14 980 1 chr6A.!!$F1 966
4 TraesCS7A01G095600 chr3A 57845778 57846756 978 False 1404 1404 92.574 1 980 1 chr3A.!!$F1 979
5 TraesCS7A01G095600 chr4A 497791975 497792954 979 True 1400 1400 92.464 1 980 1 chr4A.!!$R1 979
6 TraesCS7A01G095600 chr2A 422379352 422380317 965 False 1391 1391 92.665 14 980 1 chr2A.!!$F1 966
7 TraesCS7A01G095600 chr5A 275746382 275747360 978 False 1387 1387 92.253 1 980 1 chr5A.!!$F3 979
8 TraesCS7A01G095600 chr5A 244006587 244007383 796 False 1218 1218 94.368 1548 2338 1 chr5A.!!$F1 790
9 TraesCS7A01G095600 chr1A 486295185 486296162 977 False 1387 1387 92.253 1 980 1 chr1A.!!$F1 979
10 TraesCS7A01G095600 chr1D 452436272 452437250 978 False 1382 1382 92.159 1 980 1 chr1D.!!$F3 979
11 TraesCS7A01G095600 chr1D 476654770 476655567 797 True 1214 1214 94.250 1546 2338 1 chr1D.!!$R2 792
12 TraesCS7A01G095600 chr2D 113574148 113574955 807 True 1221 1221 94.074 1537 2338 1 chr2D.!!$R2 801
13 TraesCS7A01G095600 chr2D 73365780 73366578 798 True 1216 1216 94.257 1546 2338 1 chr2D.!!$R1 792
14 TraesCS7A01G095600 chr2D 155302254 155303064 810 False 1205 1205 93.604 1534 2338 1 chr2D.!!$F1 804
15 TraesCS7A01G095600 chr3D 320311055 320311852 797 False 1219 1219 94.382 1547 2339 1 chr3D.!!$F2 792
16 TraesCS7A01G095600 chr4D 100851151 100851952 801 False 1216 1216 94.161 1543 2338 1 chr4D.!!$F2 795
17 TraesCS7A01G095600 chr4D 346107527 346108322 795 False 1216 1216 94.361 1548 2338 1 chr4D.!!$F4 790
18 TraesCS7A01G095600 chr3B 681808417 681809313 896 True 1173 1173 90.434 1449 2338 1 chr3B.!!$R1 889


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
320 322 0.380378 TGTGCCTTCGAAGTTGTTGC 59.620 50.000 23.03 18.23 0.00 4.17 F
348 350 1.337387 GGCGCTAGAACGATAGACCTT 59.663 52.381 7.64 0.00 41.38 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1165 1168 0.030638 CCTGCACCAGTTCGTTTTGG 59.969 55.0 0.0 1.31 40.38 3.28 R
1770 1777 0.037046 GGTGCTTTTGCCCTGAATGG 60.037 55.0 0.0 0.00 46.87 3.16 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.