Multiple sequence alignment - TraesCS3D01G323200

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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 TraesCS3D01G323200 chr3D 100.000 2416 0 0 1 2416 436043575 436045990 0.000000e+00 4462.0
1 TraesCS3D01G323200 chr3D 96.322 2420 83 5 1 2416 436162789 436165206 0.000000e+00 3971.0
2 TraesCS3D01G323200 chr3D 77.181 149 30 4 2270 2415 427443555 427443702 1.540000e-12 84.2
3 TraesCS3D01G323200 chr3A 96.154 2418 86 5 1 2416 574865319 574867731 0.000000e+00 3943.0
4 TraesCS3D01G323200 chr3A 84.052 232 30 3 150 380 614561321 614561096 1.450000e-52 217.0
5 TraesCS3D01G323200 chr3A 80.645 248 42 6 132 376 439278499 439278743 1.140000e-43 187.0
6 TraesCS3D01G323200 chr3A 91.304 46 4 0 340 385 661496202 661496157 2.010000e-06 63.9
7 TraesCS3D01G323200 chr3B 94.798 2422 109 10 1 2416 571810746 571813156 0.000000e+00 3759.0
8 TraesCS3D01G323200 chr3B 81.443 194 33 3 129 320 95455265 95455457 3.220000e-34 156.0
9 TraesCS3D01G323200 chr3B 100.000 28 0 0 2379 2406 188248151 188248178 4.000000e-03 52.8
10 TraesCS3D01G323200 chr2D 78.947 190 36 3 2223 2410 628016870 628017057 2.520000e-25 126.0
11 TraesCS3D01G323200 chr7B 82.482 137 17 6 2274 2408 125379680 125379549 1.960000e-21 113.0
12 TraesCS3D01G323200 chr5B 82.727 110 15 4 2309 2416 312276698 312276591 7.110000e-16 95.3
13 TraesCS3D01G323200 chr2A 76.923 169 20 8 190 357 689197614 689197464 7.160000e-11 78.7


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 TraesCS3D01G323200 chr3D 436043575 436045990 2415 False 4462 4462 100.000 1 2416 1 chr3D.!!$F2 2415
1 TraesCS3D01G323200 chr3D 436162789 436165206 2417 False 3971 3971 96.322 1 2416 1 chr3D.!!$F3 2415
2 TraesCS3D01G323200 chr3A 574865319 574867731 2412 False 3943 3943 96.154 1 2416 1 chr3A.!!$F2 2415
3 TraesCS3D01G323200 chr3B 571810746 571813156 2410 False 3759 3759 94.798 1 2416 1 chr3B.!!$F3 2415

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
224 226 0.887933 ACGCGAGGATGGCAATTTTT 59.112 45.000 15.93 0.0 41.24 1.94 F
599 602 1.670967 GCTGCATTTGTTGAGAAGGGC 60.671 52.381 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1077 1080 2.102588 GCACTCTCGGATTAGCCCTTTA 59.897 50.000 0.0 0.0 0.00 1.85 R
2233 2242 2.749776 CGTAATATGACGCATGGTCCA 58.250 47.619 0.0 0.0 45.46 4.02 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
181 182 1.154150 GAGCACATGCCAACTTCGC 60.154 57.895 0.00 0.00 43.38 4.70
224 226 0.887933 ACGCGAGGATGGCAATTTTT 59.112 45.000 15.93 0.00 41.24 1.94
298 300 4.955925 TCGTGTGTCACTGAAATTTGTT 57.044 36.364 4.27 0.00 31.34 2.83
498 501 5.302313 TGAAATATATGCTGCAAATGCCTCA 59.698 36.000 6.36 3.63 41.18 3.86
595 598 8.522003 TCATTAAATAGCTGCATTTGTTGAGAA 58.478 29.630 15.50 5.88 30.84 2.87
599 602 1.670967 GCTGCATTTGTTGAGAAGGGC 60.671 52.381 0.00 0.00 0.00 5.19
720 723 3.438781 ACGCAACAAAGAAACAGAAGTGA 59.561 39.130 0.00 0.00 0.00 3.41
724 727 6.092748 GCAACAAAGAAACAGAAGTGAAGAA 58.907 36.000 0.00 0.00 0.00 2.52
1077 1080 2.559668 TGAAGATTGTACCGTCGACCTT 59.440 45.455 10.58 4.54 0.00 3.50
1343 1346 8.579006 TGTATTATGTACCCCTAATACTTGTCG 58.421 37.037 19.85 0.00 39.71 4.35
1348 1351 5.422970 TGTACCCCTAATACTTGTCGTGAAT 59.577 40.000 0.00 0.00 0.00 2.57
1488 1491 4.298626 AGGCCTCTATGTTGACTGGATTA 58.701 43.478 0.00 0.00 0.00 1.75
1489 1492 4.910304 AGGCCTCTATGTTGACTGGATTAT 59.090 41.667 0.00 0.00 0.00 1.28
1760 1765 5.175859 AGTCCTTTGTGATATTGTACGGTG 58.824 41.667 0.00 0.00 0.00 4.94
2139 2148 0.878416 GAATTGGTGTTGGCGCTACA 59.122 50.000 7.64 9.73 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 1.115467 CTCGGGGCAGTGAGATTAGT 58.885 55.000 0.00 0.00 34.04 2.24
224 226 1.069427 GTTGCCATGCTTGCCAACA 59.931 52.632 18.16 1.31 0.00 3.33
269 271 6.671614 TTTCAGTGACACACGATAAGTTTT 57.328 33.333 8.59 0.00 39.64 2.43
298 300 4.098349 GGCAATTCCAGTCATGCAAAGATA 59.902 41.667 0.00 0.00 40.51 1.98
595 598 2.675658 ATGTTTGTTGTACTGGCCCT 57.324 45.000 0.00 0.00 0.00 5.19
599 602 5.238432 TGAGCACTTATGTTTGTTGTACTGG 59.762 40.000 0.00 0.00 0.00 4.00
720 723 5.011329 TGGTTCCTATGTAGACACGTTTCTT 59.989 40.000 9.91 0.00 0.00 2.52
724 727 4.282703 ACTTGGTTCCTATGTAGACACGTT 59.717 41.667 0.00 0.00 0.00 3.99
962 965 1.553706 TCGGTTGGTTACCTCTCTCC 58.446 55.000 2.07 0.00 45.40 3.71
973 976 7.569240 ACTACTACTACTAGTAATCGGTTGGT 58.431 38.462 3.76 0.00 35.43 3.67
1077 1080 2.102588 GCACTCTCGGATTAGCCCTTTA 59.897 50.000 0.00 0.00 0.00 1.85
2044 2049 5.917541 TTTTTGTACTGACCGATCTCAAC 57.082 39.130 0.00 0.00 0.00 3.18
2072 2081 7.163441 GGGTTTGTCTTGTAGTAACCTATGAA 58.837 38.462 0.00 0.00 38.59 2.57
2233 2242 2.749776 CGTAATATGACGCATGGTCCA 58.250 47.619 0.00 0.00 45.46 4.02


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

AutoCloner maintained by Alex Coulton.