Multiple sequence alignment - TraesCS3A01G080300

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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 TraesCS3A01G080300 chr3A 100.000 2391 0 0 1 2391 51915014 51917404 0 4416
1 TraesCS3A01G080300 chrUn 98.162 2394 37 5 1 2391 221549562 221547173 0 4170
2 TraesCS3A01G080300 chrUn 97.953 2394 42 5 1 2391 186192560 186190171 0 4143
3 TraesCS3A01G080300 chr7B 97.703 2394 49 4 1 2391 743004918 743007308 0 4111
4 TraesCS3A01G080300 chr7B 95.652 2392 93 7 3 2391 247459906 247462289 0 3831
5 TraesCS3A01G080300 chr7A 97.160 2394 51 6 1 2391 120879312 120881691 0 4028
6 TraesCS3A01G080300 chr6D 97.969 2265 37 7 3 2263 458963807 458966066 0 3919
7 TraesCS3A01G080300 chr6A 96.072 2393 82 10 3 2391 79142535 79144919 0 3888
8 TraesCS3A01G080300 chr1B 95.527 2392 94 8 3 2391 499826047 499828428 0 3812
9 TraesCS3A01G080300 chr2B 93.815 2393 137 7 1 2391 343521117 343523500 0 3589
10 TraesCS3A01G080300 chr2B 96.232 637 21 3 3 639 357277078 357276445 0 1040


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 TraesCS3A01G080300 chr3A 51915014 51917404 2390 False 4416 4416 100.000 1 2391 1 chr3A.!!$F1 2390
1 TraesCS3A01G080300 chrUn 221547173 221549562 2389 True 4170 4170 98.162 1 2391 1 chrUn.!!$R2 2390
2 TraesCS3A01G080300 chrUn 186190171 186192560 2389 True 4143 4143 97.953 1 2391 1 chrUn.!!$R1 2390
3 TraesCS3A01G080300 chr7B 743004918 743007308 2390 False 4111 4111 97.703 1 2391 1 chr7B.!!$F2 2390
4 TraesCS3A01G080300 chr7B 247459906 247462289 2383 False 3831 3831 95.652 3 2391 1 chr7B.!!$F1 2388
5 TraesCS3A01G080300 chr7A 120879312 120881691 2379 False 4028 4028 97.160 1 2391 1 chr7A.!!$F1 2390
6 TraesCS3A01G080300 chr6D 458963807 458966066 2259 False 3919 3919 97.969 3 2263 1 chr6D.!!$F1 2260
7 TraesCS3A01G080300 chr6A 79142535 79144919 2384 False 3888 3888 96.072 3 2391 1 chr6A.!!$F1 2388
8 TraesCS3A01G080300 chr1B 499826047 499828428 2381 False 3812 3812 95.527 3 2391 1 chr1B.!!$F1 2388
9 TraesCS3A01G080300 chr2B 343521117 343523500 2383 False 3589 3589 93.815 1 2391 1 chr2B.!!$F1 2390
10 TraesCS3A01G080300 chr2B 357276445 357277078 633 True 1040 1040 96.232 3 639 1 chr2B.!!$R1 636

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
92 93 2.894126 TCTCTCTTCCAGAACCTCACAC 59.106 50.0 0.0 0.0 0.00 3.82 F
680 693 5.048013 AGGTTTACTGCTTTCTATTTGCACC 60.048 40.0 0.0 0.0 32.91 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1080 1096 0.037326 AGGAACGAAGCGCTTCATCA 60.037 50.000 40.22 0.0 39.46 3.07 R
1924 1953 2.259917 TCAACTGCTCCTCCAGAATGA 58.740 47.619 0.00 0.0 39.69 2.57 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
36 37 5.136828 TGTTGAGCAAATGAGTTTAAGGGA 58.863 37.500 0.00 0.0 0.00 4.20
92 93 2.894126 TCTCTCTTCCAGAACCTCACAC 59.106 50.000 0.00 0.0 0.00 3.82
310 314 7.541162 TCAGGCATGATAGTTTCAATTTCTTG 58.459 34.615 0.00 0.0 38.03 3.02
680 693 5.048013 AGGTTTACTGCTTTCTATTTGCACC 60.048 40.000 0.00 0.0 32.91 5.01
828 844 7.007723 TCCTTATTACTCTTCCTCCAGAGATC 58.992 42.308 4.72 0.0 42.81 2.75
1080 1096 0.460311 CGATCGAGCCCTACTTGGTT 59.540 55.000 10.26 0.0 0.00 3.67
1173 1189 2.501316 TCAAGATCTGCGGGAGAATGAA 59.499 45.455 2.54 0.0 33.12 2.57
1198 1214 8.156822 AGGAGGATCTGTTTTCTTTAGAGATT 57.843 34.615 0.00 0.0 33.73 2.40
1374 1396 7.934665 GGAGGATCTTAGAAGGGAATTAGAAAC 59.065 40.741 0.00 0.0 33.73 2.78
1656 1684 0.248621 CCCGGCGATCAAATTCTTGC 60.249 55.000 9.30 0.0 32.14 4.01
1843 1872 2.427095 GTTGTTGCCACCAAGTCTCTTT 59.573 45.455 0.00 0.0 0.00 2.52
1975 2004 7.355778 CAATTTTTAGTCTTCATCTATCGGGC 58.644 38.462 0.00 0.0 0.00 6.13
2036 2065 1.621317 TCTTCAACATGCGTGGACCTA 59.379 47.619 11.36 0.0 0.00 3.08
2125 2154 3.387947 CTTCCGGTACTGGCGGGT 61.388 66.667 16.58 0.0 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 5.930569 TCATGAAACTTCAGACACTGATGAG 59.069 40.000 17.24 9.31 40.39 2.90
310 314 2.050077 GCCGCACTTGCTTTCCAC 60.050 61.111 0.00 0.00 39.32 4.02
828 844 1.055040 CTAGAGCTTGGGGATCCTGG 58.945 60.000 12.58 0.77 0.00 4.45
1080 1096 0.037326 AGGAACGAAGCGCTTCATCA 60.037 50.000 40.22 0.00 39.46 3.07
1173 1189 7.747809 ATCTCTAAAGAAAACAGATCCTCCT 57.252 36.000 0.00 0.00 34.49 3.69
1731 1760 6.777091 CCAATTACCAAATCCACCTATCATCA 59.223 38.462 0.00 0.00 0.00 3.07
1843 1872 5.459505 ACTAAGGCTGAGCTTAATAGGAGA 58.540 41.667 3.72 0.00 0.00 3.71
1924 1953 2.259917 TCAACTGCTCCTCCAGAATGA 58.740 47.619 0.00 0.00 39.69 2.57
1972 2001 6.643388 AGAACCTAAAATTGATGAAATGCCC 58.357 36.000 0.00 0.00 0.00 5.36
2036 2065 8.200024 AGTGGTAATCTATGCATAGTCATTCT 57.800 34.615 28.51 17.32 0.00 2.40
2125 2154 9.295214 CAATCGGTTAATAACATTGTAATTGCA 57.705 29.630 5.45 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.