Multiple sequence alignment - TraesCS3D01G356100

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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 TraesCS3D01G356100 chr3D 100.000 2512 0 0 1 2512 468644857 468642346 0.000000e+00 4639
1 TraesCS3D01G356100 chr3D 92.250 2529 139 29 1 2512 223107509 223109997 0.000000e+00 3531
2 TraesCS3D01G356100 chr2D 96.671 2523 48 11 1 2512 460887128 460884631 0.000000e+00 4161
3 TraesCS3D01G356100 chr2D 92.484 2528 135 25 1 2512 412482555 412485043 0.000000e+00 3565
4 TraesCS3D01G356100 chr7D 96.384 2544 51 21 1 2512 535917336 535919870 0.000000e+00 4150
5 TraesCS3D01G356100 chr7D 96.552 2523 51 7 1 2512 313362172 313359675 0.000000e+00 4145
6 TraesCS3D01G356100 chr1D 93.624 2525 112 23 1 2512 146648661 146651149 0.000000e+00 3725
7 TraesCS3D01G356100 chr1D 93.188 2525 125 19 1 2512 234890744 234888254 0.000000e+00 3666
8 TraesCS3D01G356100 chr1A 92.506 2522 140 22 1 2512 76798939 76801421 0.000000e+00 3565
9 TraesCS3D01G356100 chr4A 92.436 2525 141 22 1 2512 684875989 684878476 0.000000e+00 3559
10 TraesCS3D01G356100 chr4A 92.109 2522 144 27 4 2512 440207886 440205407 0.000000e+00 3504
11 TraesCS3D01G356100 chr4A 91.112 2554 167 28 1 2512 500424076 500421541 0.000000e+00 3404
12 TraesCS3D01G356100 chr5B 88.087 2535 249 41 1 2512 69065301 69062797 0.000000e+00 2959
13 TraesCS3D01G356100 chr5B 82.073 357 56 7 2159 2512 416005290 416004939 5.250000e-77 298


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 TraesCS3D01G356100 chr3D 468642346 468644857 2511 True 4639 4639 100.000 1 2512 1 chr3D.!!$R1 2511
1 TraesCS3D01G356100 chr3D 223107509 223109997 2488 False 3531 3531 92.250 1 2512 1 chr3D.!!$F1 2511
2 TraesCS3D01G356100 chr2D 460884631 460887128 2497 True 4161 4161 96.671 1 2512 1 chr2D.!!$R1 2511
3 TraesCS3D01G356100 chr2D 412482555 412485043 2488 False 3565 3565 92.484 1 2512 1 chr2D.!!$F1 2511
4 TraesCS3D01G356100 chr7D 535917336 535919870 2534 False 4150 4150 96.384 1 2512 1 chr7D.!!$F1 2511
5 TraesCS3D01G356100 chr7D 313359675 313362172 2497 True 4145 4145 96.552 1 2512 1 chr7D.!!$R1 2511
6 TraesCS3D01G356100 chr1D 146648661 146651149 2488 False 3725 3725 93.624 1 2512 1 chr1D.!!$F1 2511
7 TraesCS3D01G356100 chr1D 234888254 234890744 2490 True 3666 3666 93.188 1 2512 1 chr1D.!!$R1 2511
8 TraesCS3D01G356100 chr1A 76798939 76801421 2482 False 3565 3565 92.506 1 2512 1 chr1A.!!$F1 2511
9 TraesCS3D01G356100 chr4A 684875989 684878476 2487 False 3559 3559 92.436 1 2512 1 chr4A.!!$F1 2511
10 TraesCS3D01G356100 chr4A 440205407 440207886 2479 True 3504 3504 92.109 4 2512 1 chr4A.!!$R1 2508
11 TraesCS3D01G356100 chr4A 500421541 500424076 2535 True 3404 3404 91.112 1 2512 1 chr4A.!!$R2 2511
12 TraesCS3D01G356100 chr5B 69062797 69065301 2504 True 2959 2959 88.087 1 2512 1 chr5B.!!$R1 2511

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
385 393 0.03601 CTGGGTGATCTTGCCGAGTT 60.036 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 1644 1.067635 GTAAGGTAGGCGTTCGGTCAA 60.068 52.381 0.0 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
385 393 0.036010 CTGGGTGATCTTGCCGAGTT 60.036 55.000 0.00 0.00 0.00 3.01
420 428 7.010183 CACTCGGTAAAATGTCGAAGAATGTAT 59.990 37.037 0.00 0.00 39.69 2.29
536 544 2.091610 TGACTTCCACCACAAAATCCCA 60.092 45.455 0.00 0.00 0.00 4.37
608 616 5.123227 TGTGTGAGTACTCCTTCCTTTTTG 58.877 41.667 20.11 0.00 0.00 2.44
609 617 4.023963 GTGTGAGTACTCCTTCCTTTTTGC 60.024 45.833 20.11 0.00 0.00 3.68
610 618 4.134563 GTGAGTACTCCTTCCTTTTTGCA 58.865 43.478 20.11 0.00 0.00 4.08
611 619 4.023963 GTGAGTACTCCTTCCTTTTTGCAC 60.024 45.833 20.11 3.78 0.00 4.57
613 621 4.729868 AGTACTCCTTCCTTTTTGCACAT 58.270 39.130 0.00 0.00 0.00 3.21
614 622 5.140454 AGTACTCCTTCCTTTTTGCACATT 58.860 37.500 0.00 0.00 0.00 2.71
618 628 5.817296 ACTCCTTCCTTTTTGCACATTTTTC 59.183 36.000 0.00 0.00 0.00 2.29
698 713 1.949525 GTGACAGCTGTTTCATGTGGT 59.050 47.619 22.65 0.00 0.00 4.16
927 954 7.595819 TCTTTACATGTCATTTTCCCAACTT 57.404 32.000 0.00 0.00 0.00 2.66
941 969 7.831691 TTTCCCAACTTCATCATTTCTGTTA 57.168 32.000 0.00 0.00 0.00 2.41
963 993 7.391554 TGTTATTAATGTGAGCTCTGCTTCTTT 59.608 33.333 16.19 7.33 39.88 2.52
964 994 6.830873 ATTAATGTGAGCTCTGCTTCTTTT 57.169 33.333 16.19 0.62 39.88 2.27
973 1003 5.625150 AGCTCTGCTTCTTTTCTTTCCTTA 58.375 37.500 0.00 0.00 33.89 2.69
1011 1043 1.153539 TGTTCCCCATGTTCCAGGAA 58.846 50.000 0.00 0.00 36.05 3.36
1332 1370 6.377327 TTTGTCACCTCTGAATTGAAGTTC 57.623 37.500 0.00 0.00 0.00 3.01
1483 1526 1.080093 TCGTCGAGCTCCGCAAAAT 60.080 52.632 8.47 0.00 38.37 1.82
1601 1644 0.681733 AAGTGATCACGTGGTGCTCT 59.318 50.000 19.85 8.59 31.07 4.09
1903 1964 6.534475 AACATGGCAAATGTAGTTGATCAT 57.466 33.333 0.00 0.00 0.00 2.45
1919 1980 8.408043 AGTTGATCATTCATGGTTAGTGAAAA 57.592 30.769 0.00 0.00 38.89 2.29
1948 2009 5.445806 CGTTCTTTCTTGTTTGGCTTTTTGG 60.446 40.000 0.00 0.00 0.00 3.28
2064 2131 2.790433 TCCCATAGTTTGCACCAGAAC 58.210 47.619 0.00 0.00 0.00 3.01
2282 2443 4.334552 TCAGTAGAAATTGCATGGCAGAA 58.665 39.130 0.00 0.00 40.61 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 3.144657 TCATGTGATTGCTGTTGGACT 57.855 42.857 0.00 0.00 0.00 3.85
385 393 0.759959 TTTACCGAGTGGCCTCACAA 59.240 50.000 3.32 0.00 45.91 3.33
420 428 3.229293 TGAAGTCAATCCCACATGCAAA 58.771 40.909 0.00 0.00 0.00 3.68
448 456 3.440127 TCGGGAGACATATCCATATGCA 58.560 45.455 6.49 0.00 42.98 3.96
553 561 1.820519 TGAGCTTGAAATCACCATGCC 59.179 47.619 0.00 0.00 35.92 4.40
608 616 2.827921 ACATGGGAGGAGAAAAATGTGC 59.172 45.455 0.00 0.00 0.00 4.57
609 617 6.780457 ATAACATGGGAGGAGAAAAATGTG 57.220 37.500 0.00 0.00 0.00 3.21
610 618 7.797121 AAATAACATGGGAGGAGAAAAATGT 57.203 32.000 0.00 0.00 0.00 2.71
698 713 5.009631 AGTCATTTTACATGGCAGCTGTTA 58.990 37.500 16.64 4.96 0.00 2.41
927 954 9.399797 AGCTCACATTAATAACAGAAATGATGA 57.600 29.630 1.59 1.94 35.18 2.92
941 969 6.658391 AGAAAAGAAGCAGAGCTCACATTAAT 59.342 34.615 17.77 0.00 38.25 1.40
963 993 7.826744 ACCTGCAAACAAAAATTAAGGAAAGAA 59.173 29.630 0.00 0.00 0.00 2.52
964 994 7.334858 ACCTGCAAACAAAAATTAAGGAAAGA 58.665 30.769 0.00 0.00 0.00 2.52
973 1003 5.353956 GGAACAAGACCTGCAAACAAAAATT 59.646 36.000 0.00 0.00 0.00 1.82
1011 1043 2.203153 GGGTCGTGTGGTGCAAGT 60.203 61.111 0.00 0.00 0.00 3.16
1483 1526 5.830457 TCATCAACCAGTTCCATGTGTAAAA 59.170 36.000 0.00 0.00 0.00 1.52
1601 1644 1.067635 GTAAGGTAGGCGTTCGGTCAA 60.068 52.381 0.00 0.00 0.00 3.18
1903 1964 9.226606 AGAACGATAATTTTCACTAACCATGAA 57.773 29.630 0.00 0.00 34.27 2.57
1919 1980 6.575162 AGCCAAACAAGAAAGAACGATAAT 57.425 33.333 0.00 0.00 0.00 1.28
2146 2237 4.941263 TGAATCTGCCATGTTAGTTGTACC 59.059 41.667 0.00 0.00 0.00 3.34
2282 2443 6.594788 ATTTGCCATGTTACTTGAACTGAT 57.405 33.333 0.00 0.00 38.98 2.90
2442 2627 4.202050 ACAACATTGGAGCACTTTGACTTC 60.202 41.667 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.