Multiple sequence alignment - TraesCS7D01G316900

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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 TraesCS7D01G316900 chr7D 100.000 2423 0 0 1 2423 403425138 403427560 0 4475
1 TraesCS7D01G316900 chr7D 96.652 2449 51 10 1 2423 440163770 440166213 0 4039
2 TraesCS7D01G316900 chr7D 95.108 2453 63 17 1 2423 590354641 590357066 0 3812
3 TraesCS7D01G316900 chr6D 96.900 2452 44 12 1 2423 449233535 449235983 0 4078
4 TraesCS7D01G316900 chr6D 96.010 2456 59 18 1 2423 418034105 418036554 0 3956
5 TraesCS7D01G316900 chr6D 96.936 2252 50 15 183 2423 60152866 60155109 0 3759
6 TraesCS7D01G316900 chr5D 96.897 2449 41 12 1 2423 473036328 473033889 0 4069
7 TraesCS7D01G316900 chr1D 96.816 2450 48 10 1 2423 155923071 155920625 0 4065
8 TraesCS7D01G316900 chr1D 96.104 770 22 6 1 770 33806306 33807067 0 1249
9 TraesCS7D01G316900 chr2D 97.835 1663 29 7 765 2423 14275576 14277235 0 2865
10 TraesCS7D01G316900 chr2D 96.673 1683 30 6 766 2423 43330494 43328813 0 2774
11 TraesCS7D01G316900 chr2D 97.276 771 16 5 1 770 43331063 43330297 0 1303
12 TraesCS7D01G316900 chr2D 96.753 770 19 6 1 770 14275010 14275773 0 1279
13 TraesCS7D01G316900 chr2D 92.922 876 54 7 1550 2423 542547946 542548815 0 1267
14 TraesCS7D01G316900 chr1A 94.705 1662 75 10 765 2423 61160759 61162410 0 2569


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 TraesCS7D01G316900 chr7D 403425138 403427560 2422 False 4475.0 4475 100.0000 1 2423 1 chr7D.!!$F1 2422
1 TraesCS7D01G316900 chr7D 440163770 440166213 2443 False 4039.0 4039 96.6520 1 2423 1 chr7D.!!$F2 2422
2 TraesCS7D01G316900 chr7D 590354641 590357066 2425 False 3812.0 3812 95.1080 1 2423 1 chr7D.!!$F3 2422
3 TraesCS7D01G316900 chr6D 449233535 449235983 2448 False 4078.0 4078 96.9000 1 2423 1 chr6D.!!$F3 2422
4 TraesCS7D01G316900 chr6D 418034105 418036554 2449 False 3956.0 3956 96.0100 1 2423 1 chr6D.!!$F2 2422
5 TraesCS7D01G316900 chr6D 60152866 60155109 2243 False 3759.0 3759 96.9360 183 2423 1 chr6D.!!$F1 2240
6 TraesCS7D01G316900 chr5D 473033889 473036328 2439 True 4069.0 4069 96.8970 1 2423 1 chr5D.!!$R1 2422
7 TraesCS7D01G316900 chr1D 155920625 155923071 2446 True 4065.0 4065 96.8160 1 2423 1 chr1D.!!$R1 2422
8 TraesCS7D01G316900 chr1D 33806306 33807067 761 False 1249.0 1249 96.1040 1 770 1 chr1D.!!$F1 769
9 TraesCS7D01G316900 chr2D 14275010 14277235 2225 False 2072.0 2865 97.2940 1 2423 2 chr2D.!!$F2 2422
10 TraesCS7D01G316900 chr2D 43328813 43331063 2250 True 2038.5 2774 96.9745 1 2423 2 chr2D.!!$R1 2422
11 TraesCS7D01G316900 chr2D 542547946 542548815 869 False 1267.0 1267 92.9220 1550 2423 1 chr2D.!!$F1 873
12 TraesCS7D01G316900 chr1A 61160759 61162410 1651 False 2569.0 2569 94.7050 765 2423 1 chr1A.!!$F1 1658

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
189 204 3.577848 TGCAACTTCCCTGTGCATTAAAT 59.422 39.13 0.0 0.0 0.0 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1694 2111 1.003118 CGGGATTCCTTGGTGAGAACA 59.997 52.381 2.01 0.0 0.0 3.18 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
154 156 6.309980 CAGATGTGAGAACATGTCAACTCTAC 59.690 42.308 20.29 17.29 0.00 2.59
189 204 3.577848 TGCAACTTCCCTGTGCATTAAAT 59.422 39.130 0.00 0.00 0.00 1.40
190 207 4.769488 TGCAACTTCCCTGTGCATTAAATA 59.231 37.500 0.00 0.00 0.00 1.40
254 271 8.035984 AGAGAGGTAGAAAGTATTAACTTGCAC 58.964 37.037 0.00 0.00 45.37 4.57
261 278 7.570161 AGAAAGTATTAACTTGCACGTGTTAC 58.430 34.615 18.38 0.49 45.37 2.50
403 421 4.257267 TGCTACATTCCATATGGTCTCG 57.743 45.455 21.28 10.89 36.34 4.04
876 1289 8.443953 AGAAGATATGAATTGCCTCTGTTTAC 57.556 34.615 0.00 0.00 0.00 2.01
1349 1763 0.590195 CGCTATGCTTTGATGGAGGC 59.410 55.000 0.00 0.00 0.00 4.70
1354 1770 1.167851 TGCTTTGATGGAGGCTTTCG 58.832 50.000 0.00 0.00 0.00 3.46
2292 2800 1.652124 CGGAGTTGATTGTTCCGTACG 59.348 52.381 8.69 8.69 46.56 3.67
2321 2829 2.308570 AGCCATCCATAACCACTGTTCA 59.691 45.455 0.00 0.00 35.87 3.18
2361 2869 9.390795 CAACTAAAGACATTGACATTGAAGAAG 57.609 33.333 4.40 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 84 1.374758 GCTACGGTTGCACAGCTCT 60.375 57.895 9.66 0.00 0.00 4.09
154 156 5.473504 AGGGAAGTTGCATGTGTTTTAGTAG 59.526 40.000 0.00 0.00 0.00 2.57
213 230 7.005296 TCTACCTCTCTCTGTAACTTGAGTTT 58.995 38.462 1.20 0.00 39.31 2.66
225 242 9.796120 CAAGTTAATACTTTCTACCTCTCTCTG 57.204 37.037 0.00 0.00 41.85 3.35
229 246 7.009357 CGTGCAAGTTAATACTTTCTACCTCTC 59.991 40.741 0.00 0.00 41.85 3.20
254 271 0.306533 AAAAGCTGTGCGGTAACACG 59.693 50.000 0.00 0.00 43.74 4.49
261 278 0.523072 ACATAGCAAAAGCTGTGCGG 59.477 50.000 15.00 11.73 46.86 5.69
738 952 6.401367 GCATGCATGACCTTTTATGAACAAAC 60.401 38.462 30.64 1.71 0.00 2.93
876 1289 4.522789 ACACTTGTTTGGGCAACTATAAGG 59.477 41.667 0.00 0.00 36.21 2.69
943 1357 1.001068 CCACAAAAGCATGCATGACCA 59.999 47.619 30.64 0.00 0.00 4.02
1349 1763 6.633668 AGACGTATTTGACTTGATCGAAAG 57.366 37.500 0.00 0.00 34.20 2.62
1354 1770 6.812160 ACCTGTAAGACGTATTTGACTTGATC 59.188 38.462 0.00 0.00 34.07 2.92
1686 2103 4.942944 TCCTTGGTGAGAACAGAGGTATA 58.057 43.478 0.00 0.00 0.00 1.47
1694 2111 1.003118 CGGGATTCCTTGGTGAGAACA 59.997 52.381 2.01 0.00 0.00 3.18
2292 2800 2.294512 GGTTATGGATGGCTTTAGCTGC 59.705 50.000 0.00 0.00 41.70 5.25
2361 2869 4.976116 CACCTTGCAAAAGTAGTTTAGTGC 59.024 41.667 11.27 11.27 32.99 4.40


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

AutoCloner maintained by Alex Coulton.