Multiple sequence alignment - TraesCS7A01G165000

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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 TraesCS7A01G165000 chr7A 100.000 2320 0 0 1 2320 120905803 120903484 0 4285
1 TraesCS7A01G165000 chr5A 97.517 2336 30 11 1 2320 300072989 300075312 0 3967
2 TraesCS7A01G165000 chr5A 97.172 2334 38 10 1 2320 16602909 16600590 0 3919
3 TraesCS7A01G165000 chr2A 97.517 2336 30 11 1 2320 618279946 618277623 0 3967
4 TraesCS7A01G165000 chr2A 96.918 2336 43 11 1 2320 735192665 735194987 0 3888
5 TraesCS7A01G165000 chrUn 97.303 2336 35 11 1 2320 189392549 189394872 0 3940
6 TraesCS7A01G165000 chr7B 97.217 2336 37 12 1 2320 743086209 743088532 0 3928
7 TraesCS7A01G165000 chr6A 97.216 2335 37 12 1 2320 289128642 289130963 0 3927
8 TraesCS7A01G165000 chr6A 96.719 1768 28 11 465 2213 608884347 608882591 0 2916
9 TraesCS7A01G165000 chr3B 97.173 2335 37 13 1 2320 92199614 92201934 0 3919
10 TraesCS7A01G165000 chr7D 97.089 2336 40 12 1 2320 626698480 626696157 0 3912
11 TraesCS7A01G165000 chr1D 96.787 2334 49 11 1 2320 185769467 185771788 0 3871
12 TraesCS7A01G165000 chr1D 97.286 958 13 2 1 956 141321590 141320644 0 1613
13 TraesCS7A01G165000 chr4D 96.574 2335 43 15 1 2320 123412903 123415215 0 3834
14 TraesCS7A01G165000 chr6D 96.329 2343 52 16 1 2320 83976667 83974336 0 3819
15 TraesCS7A01G165000 chr6B 96.448 2224 54 10 1 2210 678547880 678550092 0 3646
16 TraesCS7A01G165000 chr5B 97.088 1992 31 10 345 2320 679659250 679661230 0 3332


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 TraesCS7A01G165000 chr7A 120903484 120905803 2319 True 4285 4285 100.000 1 2320 1 chr7A.!!$R1 2319
1 TraesCS7A01G165000 chr5A 300072989 300075312 2323 False 3967 3967 97.517 1 2320 1 chr5A.!!$F1 2319
2 TraesCS7A01G165000 chr5A 16600590 16602909 2319 True 3919 3919 97.172 1 2320 1 chr5A.!!$R1 2319
3 TraesCS7A01G165000 chr2A 618277623 618279946 2323 True 3967 3967 97.517 1 2320 1 chr2A.!!$R1 2319
4 TraesCS7A01G165000 chr2A 735192665 735194987 2322 False 3888 3888 96.918 1 2320 1 chr2A.!!$F1 2319
5 TraesCS7A01G165000 chrUn 189392549 189394872 2323 False 3940 3940 97.303 1 2320 1 chrUn.!!$F1 2319
6 TraesCS7A01G165000 chr7B 743086209 743088532 2323 False 3928 3928 97.217 1 2320 1 chr7B.!!$F1 2319
7 TraesCS7A01G165000 chr6A 289128642 289130963 2321 False 3927 3927 97.216 1 2320 1 chr6A.!!$F1 2319
8 TraesCS7A01G165000 chr6A 608882591 608884347 1756 True 2916 2916 96.719 465 2213 1 chr6A.!!$R1 1748
9 TraesCS7A01G165000 chr3B 92199614 92201934 2320 False 3919 3919 97.173 1 2320 1 chr3B.!!$F1 2319
10 TraesCS7A01G165000 chr7D 626696157 626698480 2323 True 3912 3912 97.089 1 2320 1 chr7D.!!$R1 2319
11 TraesCS7A01G165000 chr1D 185769467 185771788 2321 False 3871 3871 96.787 1 2320 1 chr1D.!!$F1 2319
12 TraesCS7A01G165000 chr1D 141320644 141321590 946 True 1613 1613 97.286 1 956 1 chr1D.!!$R1 955
13 TraesCS7A01G165000 chr4D 123412903 123415215 2312 False 3834 3834 96.574 1 2320 1 chr4D.!!$F1 2319
14 TraesCS7A01G165000 chr6D 83974336 83976667 2331 True 3819 3819 96.329 1 2320 1 chr6D.!!$R1 2319
15 TraesCS7A01G165000 chr6B 678547880 678550092 2212 False 3646 3646 96.448 1 2210 1 chr6B.!!$F1 2209
16 TraesCS7A01G165000 chr5B 679659250 679661230 1980 False 3332 3332 97.088 345 2320 1 chr5B.!!$F1 1975

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
421 422 1.701847 AGACTCAAAGGGCACAGACAT 59.298 47.619 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1421 1450 0.034896 GACCCTTGACTGAGGCGAAA 59.965 55.0 0.0 0.0 35.37 3.46 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
90 91 6.942005 TCTTTGCTTCCAAGAACATAGATTCA 59.058 34.615 0.0 0.0 31.52 2.57
421 422 1.701847 AGACTCAAAGGGCACAGACAT 59.298 47.619 0.0 0.0 0.00 3.06
638 646 3.545703 CTCTCAAACCAACCAAGACAGT 58.454 45.455 0.0 0.0 0.00 3.55
739 747 3.503363 TGTTGCTTAGCTCAGTGAAATGG 59.497 43.478 5.6 0.0 0.00 3.16
740 748 3.701205 TGCTTAGCTCAGTGAAATGGA 57.299 42.857 5.6 0.0 0.00 3.41
741 749 4.019792 TGCTTAGCTCAGTGAAATGGAA 57.980 40.909 5.6 0.0 0.00 3.53
742 750 4.592942 TGCTTAGCTCAGTGAAATGGAAT 58.407 39.130 5.6 0.0 0.00 3.01
743 751 5.744171 TGCTTAGCTCAGTGAAATGGAATA 58.256 37.500 5.6 0.0 0.00 1.75
744 752 6.179756 TGCTTAGCTCAGTGAAATGGAATAA 58.820 36.000 5.6 0.0 0.00 1.40
745 753 6.317140 TGCTTAGCTCAGTGAAATGGAATAAG 59.683 38.462 5.6 0.0 0.00 1.73
746 754 6.540189 GCTTAGCTCAGTGAAATGGAATAAGA 59.460 38.462 0.0 0.0 0.00 2.10
747 755 7.066284 GCTTAGCTCAGTGAAATGGAATAAGAA 59.934 37.037 0.0 0.0 0.00 2.52
748 756 9.118300 CTTAGCTCAGTGAAATGGAATAAGAAT 57.882 33.333 0.0 0.0 0.00 2.40
749 757 7.330900 AGCTCAGTGAAATGGAATAAGAATG 57.669 36.000 0.0 0.0 0.00 2.67
1071 1080 4.638421 TCGTTTTGTTTGAGGAAGTCACAT 59.362 37.500 0.0 0.0 33.71 3.21
1227 1243 0.745845 GCTGGCTGTCGGATGTGATT 60.746 55.000 0.0 0.0 0.00 2.57
1323 1343 4.574674 AGAAGCATTGTGGAATAGTGGA 57.425 40.909 0.0 0.0 0.00 4.02
1329 1349 5.954150 AGCATTGTGGAATAGTGGAATTTCT 59.046 36.000 0.0 0.0 0.00 2.52
1406 1435 3.764434 AGCGGTCTCTGAAAGTGAATAGA 59.236 43.478 0.0 0.0 38.31 1.98
1408 1437 4.929808 GCGGTCTCTGAAAGTGAATAGAAA 59.070 41.667 0.0 0.0 38.31 2.52
1413 1442 9.436957 GGTCTCTGAAAGTGAATAGAAACATAA 57.563 33.333 0.0 0.0 38.31 1.90
1522 1566 3.067106 CCGCTCTCAATACAACAAGTGT 58.933 45.455 0.0 0.0 44.82 3.55
1806 1855 0.895530 CGGTTTCCTCTGTAGCCAGA 59.104 55.000 0.0 0.0 45.44 3.86
1942 1991 2.369394 CTTGTGGTAGAAGATTGGGCC 58.631 52.381 0.0 0.0 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 3.690460 GTCATGACCTGGGTTGAAGAAT 58.310 45.455 15.31 0.0 0.00 2.40
638 646 5.417894 TCTTGTTCTCGATAGGAACTTGCTA 59.582 40.000 14.75 0.0 42.75 3.49
742 750 9.672673 CACTTTCTCTTCCTTATTCCATTCTTA 57.327 33.333 0.00 0.0 0.00 2.10
743 751 8.166726 ACACTTTCTCTTCCTTATTCCATTCTT 58.833 33.333 0.00 0.0 0.00 2.52
744 752 7.694093 ACACTTTCTCTTCCTTATTCCATTCT 58.306 34.615 0.00 0.0 0.00 2.40
745 753 7.929941 ACACTTTCTCTTCCTTATTCCATTC 57.070 36.000 0.00 0.0 0.00 2.67
746 754 8.606830 ACTACACTTTCTCTTCCTTATTCCATT 58.393 33.333 0.00 0.0 0.00 3.16
747 755 8.043710 CACTACACTTTCTCTTCCTTATTCCAT 58.956 37.037 0.00 0.0 0.00 3.41
748 756 7.016268 ACACTACACTTTCTCTTCCTTATTCCA 59.984 37.037 0.00 0.0 0.00 3.53
749 757 7.332182 CACACTACACTTTCTCTTCCTTATTCC 59.668 40.741 0.00 0.0 0.00 3.01
1071 1080 7.136885 TCTCCTTATTTATAGGGAACAGGACA 58.863 38.462 2.70 0.0 37.96 4.02
1227 1243 3.503827 AGCGATGTGACACGAGAATAA 57.496 42.857 10.77 0.0 0.00 1.40
1406 1435 5.240623 TGAGGCGAAATCAGTTGTTATGTTT 59.759 36.000 0.00 0.0 0.00 2.83
1408 1437 4.323417 TGAGGCGAAATCAGTTGTTATGT 58.677 39.130 0.00 0.0 0.00 2.29
1418 1447 1.339055 CCCTTGACTGAGGCGAAATCA 60.339 52.381 0.00 0.0 35.37 2.57
1419 1448 1.339151 ACCCTTGACTGAGGCGAAATC 60.339 52.381 0.00 0.0 35.37 2.17
1420 1449 0.693049 ACCCTTGACTGAGGCGAAAT 59.307 50.000 0.00 0.0 35.37 2.17
1421 1450 0.034896 GACCCTTGACTGAGGCGAAA 59.965 55.000 0.00 0.0 35.37 3.46
1425 1468 0.980423 AGAAGACCCTTGACTGAGGC 59.020 55.000 0.00 0.0 35.37 4.70
1806 1855 5.581874 GTCGGCAAATGATTTGGAATTGAAT 59.418 36.000 18.52 0.0 40.94 2.57
2187 2236 7.186570 ACTAATTTTTACGGCCTCCTTAGTA 57.813 36.000 0.00 0.0 0.00 1.82


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

AutoCloner maintained by Alex Coulton.