Multiple sequence alignment - TraesCS7D01G255200

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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 TraesCS7D01G255200 chr7D 100.000 2339 0 0 1 2339 231566590 231564252 0.000000e+00 4320.0
1 TraesCS7D01G255200 chr1A 99.051 1264 11 1 394 1656 554448043 554449306 0.000000e+00 2266.0
2 TraesCS7D01G255200 chr5D 98.972 1264 12 1 394 1656 503330813 503329550 0.000000e+00 2261.0
3 TraesCS7D01G255200 chr5D 98.418 1264 18 2 394 1656 6235998 6237260 0.000000e+00 2222.0
4 TraesCS7D01G255200 chr5D 98.903 638 5 1 1654 2291 196431613 196430978 0.000000e+00 1138.0
5 TraesCS7D01G255200 chr5D 97.809 639 8 4 1654 2291 503253491 503252858 0.000000e+00 1098.0
6 TraesCS7D01G255200 chr5D 97.496 639 13 2 1654 2291 432406342 432406978 0.000000e+00 1088.0
7 TraesCS7D01G255200 chr5D 100.000 393 0 0 1 393 503238112 503238504 0.000000e+00 726.0
8 TraesCS7D01G255200 chr5D 99.746 393 1 0 1 393 503228334 503228726 0.000000e+00 721.0
9 TraesCS7D01G255200 chr5D 99.746 393 1 0 1 393 503268216 503267824 0.000000e+00 721.0
10 TraesCS7D01G255200 chr3B 98.814 1265 13 2 394 1656 201492906 201491642 0.000000e+00 2252.0
11 TraesCS7D01G255200 chr3B 97.969 640 9 3 1654 2291 201554711 201555348 0.000000e+00 1107.0
12 TraesCS7D01G255200 chr1D 98.813 1264 13 2 394 1656 254476900 254475638 0.000000e+00 2250.0
13 TraesCS7D01G255200 chr1D 98.497 1264 17 2 394 1656 290507069 290505807 0.000000e+00 2228.0
14 TraesCS7D01G255200 chr1D 97.310 1264 33 1 394 1656 180356492 180357755 0.000000e+00 2145.0
15 TraesCS7D01G255200 chr1D 96.598 1264 40 2 394 1656 244201194 244199933 0.000000e+00 2093.0
16 TraesCS7D01G255200 chr1D 96.364 1265 36 6 394 1656 244768383 244767127 0.000000e+00 2073.0
17 TraesCS7D01G255200 chr1D 99.746 393 1 0 1 393 51917171 51916779 0.000000e+00 721.0
18 TraesCS7D01G255200 chr1D 100.000 51 0 0 2289 2339 51913098 51913048 6.880000e-16 95.3
19 TraesCS7D01G255200 chr1D 100.000 51 0 0 2289 2339 254380974 254380924 6.880000e-16 95.3
20 TraesCS7D01G255200 chr1D 100.000 51 0 0 2289 2339 254526634 254526684 6.880000e-16 95.3
21 TraesCS7D01G255200 chr1D 100.000 51 0 0 2289 2339 446752599 446752549 6.880000e-16 95.3
22 TraesCS7D01G255200 chr3D 99.216 638 3 1 1654 2291 158931579 158930944 0.000000e+00 1149.0
23 TraesCS7D01G255200 chr3D 98.746 638 5 1 1654 2291 589248922 589248288 0.000000e+00 1131.0
24 TraesCS7D01G255200 chr3D 98.592 639 4 3 1654 2291 158937693 158937059 0.000000e+00 1125.0
25 TraesCS7D01G255200 chr3D 99.746 393 1 0 1 393 589266437 589266045 0.000000e+00 721.0
26 TraesCS7D01G255200 chrUn 98.746 638 5 1 1654 2291 371791124 371790490 0.000000e+00 1131.0
27 TraesCS7D01G255200 chrUn 99.746 393 1 0 1 393 440226778 440226386 0.000000e+00 721.0
28 TraesCS7D01G255200 chrUn 100.000 51 0 0 2289 2339 365940123 365940173 6.880000e-16 95.3
29 TraesCS7D01G255200 chr5A 97.809 639 10 2 1654 2291 482023302 482023937 0.000000e+00 1099.0
30 TraesCS7D01G255200 chr6D 99.746 393 1 0 1 393 389254255 389254647 0.000000e+00 721.0
31 TraesCS7D01G255200 chr6D 100.000 51 0 0 2289 2339 25672601 25672551 6.880000e-16 95.3
32 TraesCS7D01G255200 chr6D 100.000 51 0 0 2289 2339 172742548 172742498 6.880000e-16 95.3
33 TraesCS7D01G255200 chr6D 100.000 51 0 0 2289 2339 389244795 389244745 6.880000e-16 95.3
34 TraesCS7D01G255200 chr6D 100.000 51 0 0 2289 2339 398830732 398830782 6.880000e-16 95.3
35 TraesCS7D01G255200 chr3A 99.746 393 1 0 1 393 593311774 593312166 0.000000e+00 721.0
36 TraesCS7D01G255200 chr7B 99.746 393 0 1 1 393 663102338 663101947 0.000000e+00 719.0


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 TraesCS7D01G255200 chr7D 231564252 231566590 2338 True 4320.00 4320 100.000 1 2339 1 chr7D.!!$R1 2338
1 TraesCS7D01G255200 chr1A 554448043 554449306 1263 False 2266.00 2266 99.051 394 1656 1 chr1A.!!$F1 1262
2 TraesCS7D01G255200 chr5D 503329550 503330813 1263 True 2261.00 2261 98.972 394 1656 1 chr5D.!!$R4 1262
3 TraesCS7D01G255200 chr5D 6235998 6237260 1262 False 2222.00 2222 98.418 394 1656 1 chr5D.!!$F1 1262
4 TraesCS7D01G255200 chr5D 196430978 196431613 635 True 1138.00 1138 98.903 1654 2291 1 chr5D.!!$R1 637
5 TraesCS7D01G255200 chr5D 503252858 503253491 633 True 1098.00 1098 97.809 1654 2291 1 chr5D.!!$R2 637
6 TraesCS7D01G255200 chr5D 432406342 432406978 636 False 1088.00 1088 97.496 1654 2291 1 chr5D.!!$F2 637
7 TraesCS7D01G255200 chr3B 201491642 201492906 1264 True 2252.00 2252 98.814 394 1656 1 chr3B.!!$R1 1262
8 TraesCS7D01G255200 chr3B 201554711 201555348 637 False 1107.00 1107 97.969 1654 2291 1 chr3B.!!$F1 637
9 TraesCS7D01G255200 chr1D 254475638 254476900 1262 True 2250.00 2250 98.813 394 1656 1 chr1D.!!$R4 1262
10 TraesCS7D01G255200 chr1D 290505807 290507069 1262 True 2228.00 2228 98.497 394 1656 1 chr1D.!!$R5 1262
11 TraesCS7D01G255200 chr1D 180356492 180357755 1263 False 2145.00 2145 97.310 394 1656 1 chr1D.!!$F1 1262
12 TraesCS7D01G255200 chr1D 244199933 244201194 1261 True 2093.00 2093 96.598 394 1656 1 chr1D.!!$R1 1262
13 TraesCS7D01G255200 chr1D 244767127 244768383 1256 True 2073.00 2073 96.364 394 1656 1 chr1D.!!$R2 1262
14 TraesCS7D01G255200 chr1D 51913048 51917171 4123 True 408.15 721 99.873 1 2339 2 chr1D.!!$R7 2338
15 TraesCS7D01G255200 chr3D 158930944 158931579 635 True 1149.00 1149 99.216 1654 2291 1 chr3D.!!$R1 637
16 TraesCS7D01G255200 chr3D 589248288 589248922 634 True 1131.00 1131 98.746 1654 2291 1 chr3D.!!$R3 637
17 TraesCS7D01G255200 chr3D 158937059 158937693 634 True 1125.00 1125 98.592 1654 2291 1 chr3D.!!$R2 637
18 TraesCS7D01G255200 chrUn 371790490 371791124 634 True 1131.00 1131 98.746 1654 2291 1 chrUn.!!$R1 637
19 TraesCS7D01G255200 chr5A 482023302 482023937 635 False 1099.00 1099 97.809 1654 2291 1 chr5A.!!$F1 637

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
191 192 1.680338 CCCCTTTGCCTTAGGATTCG 58.32 55.0 0.69 0.0 34.56 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1466 4264 4.385825 TGAACCACCTCATGTTTGACTAC 58.614 43.478 0.0 0.0 0.0 2.73 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
191 192 1.680338 CCCCTTTGCCTTAGGATTCG 58.320 55.000 0.69 0.0 34.56 3.34
467 2075 3.422473 GCGCTCGTTTTTGTTGTTTTTGT 60.422 39.130 0.00 0.0 0.00 2.83
1362 2975 3.589288 AGAGGGGCTCTTTTGTGTAGAAT 59.411 43.478 0.00 0.0 37.60 2.40
1466 4264 3.636764 GCAGGGTTGGTTATCTAATTGGG 59.363 47.826 0.00 0.0 0.00 4.12
2157 5140 3.985925 GTGGCAGCATTCTTGAAAAAGAG 59.014 43.478 0.00 0.0 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 192 5.232414 CGTCCCATCGAGAAAGAGAATTAAC 59.768 44.000 0.00 0.0 0.00 2.01
467 2075 5.240121 GGTATAGAAAGACGGTTTCCACAA 58.760 41.667 8.46 0.0 0.00 3.33
1094 2707 8.879427 AAGTTTTGTTAGGGCATCTATAACTT 57.121 30.769 0.00 0.0 31.99 2.66
1362 2975 7.238486 TGAAAGATTGCCCTGCTTTTTATTA 57.762 32.000 0.00 0.0 32.45 0.98
1466 4264 4.385825 TGAACCACCTCATGTTTGACTAC 58.614 43.478 0.00 0.0 0.00 2.73


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

AutoCloner maintained by Alex Coulton.