Multiple sequence alignment - TraesCS7B01G397500

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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 TraesCS7B01G397500 chr7B 100.000 2645 0 0 1 2645 663683513 663686157 0.000000e+00 4885.0
1 TraesCS7B01G397500 chr7B 98.753 2646 20 4 1 2645 663630363 663632996 0.000000e+00 4691.0
2 TraesCS7B01G397500 chr7B 98.262 2647 27 6 1 2645 663597548 663600177 0.000000e+00 4615.0
3 TraesCS7B01G397500 chr7B 99.125 1943 16 1 704 2645 663706720 663708662 0.000000e+00 3493.0
4 TraesCS7B01G397500 chr7B 98.587 1345 14 1 385 1729 663652799 663654138 0.000000e+00 2374.0
5 TraesCS7B01G397500 chr7B 98.065 620 8 2 1 619 663706048 663706664 0.000000e+00 1075.0
6 TraesCS7B01G397500 chr7B 98.028 355 4 1 1 355 663652453 663652804 4.840000e-172 614.0
7 TraesCS7B01G397500 chr7B 100.000 30 0 0 1306 1335 226333860 226333889 3.680000e-04 56.5
8 TraesCS7B01G397500 chr7D 78.057 1153 191 32 388 1507 589195246 589196369 0.000000e+00 671.0
9 TraesCS7B01G397500 chr7D 85.836 586 55 13 162 736 589338040 589338608 4.870000e-167 597.0
10 TraesCS7B01G397500 chr7D 77.083 240 46 5 449 688 609947236 609947006 2.140000e-26 130.0
11 TraesCS7B01G397500 chr7D 75.904 249 51 5 440 688 607931246 607931485 4.620000e-23 119.0
12 TraesCS7B01G397500 chr7D 100.000 30 0 0 1306 1335 249375641 249375670 3.680000e-04 56.5
13 TraesCS7B01G397500 chr1B 74.308 253 58 3 441 687 632209438 632209689 1.680000e-17 100.0
14 TraesCS7B01G397500 chr7A 100.000 30 0 0 1306 1335 271792934 271792905 3.680000e-04 56.5


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 TraesCS7B01G397500 chr7B 663683513 663686157 2644 False 4885 4885 100.0000 1 2645 1 chr7B.!!$F4 2644
1 TraesCS7B01G397500 chr7B 663630363 663632996 2633 False 4691 4691 98.7530 1 2645 1 chr7B.!!$F3 2644
2 TraesCS7B01G397500 chr7B 663597548 663600177 2629 False 4615 4615 98.2620 1 2645 1 chr7B.!!$F2 2644
3 TraesCS7B01G397500 chr7B 663706048 663708662 2614 False 2284 3493 98.5950 1 2645 2 chr7B.!!$F6 2644
4 TraesCS7B01G397500 chr7B 663652453 663654138 1685 False 1494 2374 98.3075 1 1729 2 chr7B.!!$F5 1728
5 TraesCS7B01G397500 chr7D 589195246 589196369 1123 False 671 671 78.0570 388 1507 1 chr7D.!!$F2 1119
6 TraesCS7B01G397500 chr7D 589338040 589338608 568 False 597 597 85.8360 162 736 1 chr7D.!!$F3 574

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
337 349 2.075355 AACACCTCCGGCCAATCCAA 62.075 55.000 2.24 0.0 34.01 3.53 F
1096 1135 2.084546 AGGCTTGGAGCGATTTGTTAC 58.915 47.619 0.00 0.0 43.62 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1359 1401 1.862123 ACGAAGTTGTGATGCTGCG 59.138 52.632 0.00 0.0 37.78 5.18 R
2486 2529 4.503741 ACGAGTTACTGCGGTAAGTTTA 57.496 40.909 23.47 0.0 40.46 2.01 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
89 90 2.294512 GGAAATGGAAGGCGATGAATCC 59.705 50.000 0.00 0.0 0.00 3.01
337 349 2.075355 AACACCTCCGGCCAATCCAA 62.075 55.000 2.24 0.0 34.01 3.53
698 713 3.653122 TTCCTCCCTAGCCCCACCC 62.653 68.421 0.00 0.0 0.00 4.61
702 717 3.786257 CCCTAGCCCCACCCCCTA 61.786 72.222 0.00 0.0 0.00 3.53
1096 1135 2.084546 AGGCTTGGAGCGATTTGTTAC 58.915 47.619 0.00 0.0 43.62 2.50
1359 1401 7.699812 GGATTGCTCACTTTCTCAATTAATGAC 59.300 37.037 0.00 0.0 33.47 3.06
1624 1666 2.196742 TACCAGCTTCCCTCCATCAT 57.803 50.000 0.00 0.0 0.00 2.45
1680 1722 7.473735 TTCATTGCACAACCTTATTATTCCA 57.526 32.000 0.00 0.0 0.00 3.53
2486 2529 6.865834 TCCTTTTGGCCAACATGTTATAAT 57.134 33.333 20.35 0.0 40.12 1.28
2604 2647 8.834465 GTGATTGTGATGCAGATCTAACTTAAT 58.166 33.333 0.00 0.0 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 7.930865 TGTCAATTTGGGAAGAAAAATAACCAG 59.069 33.333 0.00 0.00 0.00 4.00
295 305 2.613977 GGAGCGGCGGATACTAGTACTA 60.614 54.545 9.78 1.89 0.00 1.82
296 306 1.521580 GAGCGGCGGATACTAGTACT 58.478 55.000 9.78 0.00 0.00 2.73
297 307 0.520847 GGAGCGGCGGATACTAGTAC 59.479 60.000 9.78 0.00 0.00 2.73
381 393 3.781307 CCATCTTCCGGCCGGTCA 61.781 66.667 41.57 28.30 36.47 4.02
698 713 2.017559 GAGCAGCGTGTAGGGTAGGG 62.018 65.000 0.00 0.00 0.00 3.53
699 714 1.437986 GAGCAGCGTGTAGGGTAGG 59.562 63.158 0.00 0.00 0.00 3.18
700 715 1.437986 GGAGCAGCGTGTAGGGTAG 59.562 63.158 0.00 0.00 0.00 3.18
701 716 2.056223 GGGAGCAGCGTGTAGGGTA 61.056 63.158 0.00 0.00 0.00 3.69
702 717 3.391382 GGGAGCAGCGTGTAGGGT 61.391 66.667 0.00 0.00 0.00 4.34
886 901 4.436998 GAGTGCGTCCCTCACCGG 62.437 72.222 0.00 0.00 35.14 5.28
1096 1135 1.226859 CAATTGGCATGCCGCAGAG 60.227 57.895 30.87 15.89 45.17 3.35
1359 1401 1.862123 ACGAAGTTGTGATGCTGCG 59.138 52.632 0.00 0.00 37.78 5.18
1624 1666 4.532126 ACTTCATACTGTCCTGGATGACAA 59.468 41.667 0.00 0.00 44.19 3.18
1680 1722 8.655935 AGTGATAACCAAGGAAATGAAGAAAT 57.344 30.769 0.00 0.00 0.00 2.17
2351 2394 5.046910 TCAAAGAGAATCAAAATGTCCGC 57.953 39.130 0.00 0.00 37.82 5.54
2486 2529 4.503741 ACGAGTTACTGCGGTAAGTTTA 57.496 40.909 23.47 0.00 40.46 2.01


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

AutoCloner maintained by Alex Coulton.