Multiple sequence alignment - TraesCS3B01G531800

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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 TraesCS3B01G531800 chr3B 100.000 3541 0 0 1 3541 772608503 772612043 0.000000e+00 6540
1 TraesCS3B01G531800 chr3B 96.593 3551 102 9 1 3541 170821782 170818241 0.000000e+00 5869
2 TraesCS3B01G531800 chr3B 96.229 3553 115 10 1 3541 770030508 770034053 0.000000e+00 5801
3 TraesCS3B01G531800 chr7B 97.040 3547 92 7 1 3541 379737871 379741410 0.000000e+00 5956
4 TraesCS3B01G531800 chr7B 96.955 3547 95 9 1 3541 747732800 747729261 0.000000e+00 5939
5 TraesCS3B01G531800 chr7B 96.613 3543 102 12 1 3539 81909523 81913051 0.000000e+00 5862
6 TraesCS3B01G531800 chr5B 96.928 3548 96 8 1 3541 426072393 426075934 0.000000e+00 5936
7 TraesCS3B01G531800 chr5B 95.117 3584 124 20 1 3539 450541640 450545217 0.000000e+00 5602
8 TraesCS3B01G531800 chr4B 96.074 3566 107 18 1 3541 327348197 327351754 0.000000e+00 5779
9 TraesCS3B01G531800 chr6B 95.569 3566 123 21 1 3541 526743172 526746727 0.000000e+00 5677
10 TraesCS3B01G531800 chr6B 95.322 171 8 0 1 171 8645068 8644898 4.500000e-69 272
11 TraesCS3B01G531800 chr6B 95.322 171 8 0 1 171 8690479 8690309 4.500000e-69 272
12 TraesCS3B01G531800 chr6B 95.322 171 8 0 1 171 8703596 8703426 4.500000e-69 272


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 TraesCS3B01G531800 chr3B 772608503 772612043 3540 False 6540 6540 100.000 1 3541 1 chr3B.!!$F2 3540
1 TraesCS3B01G531800 chr3B 170818241 170821782 3541 True 5869 5869 96.593 1 3541 1 chr3B.!!$R1 3540
2 TraesCS3B01G531800 chr3B 770030508 770034053 3545 False 5801 5801 96.229 1 3541 1 chr3B.!!$F1 3540
3 TraesCS3B01G531800 chr7B 379737871 379741410 3539 False 5956 5956 97.040 1 3541 1 chr7B.!!$F2 3540
4 TraesCS3B01G531800 chr7B 747729261 747732800 3539 True 5939 5939 96.955 1 3541 1 chr7B.!!$R1 3540
5 TraesCS3B01G531800 chr7B 81909523 81913051 3528 False 5862 5862 96.613 1 3539 1 chr7B.!!$F1 3538
6 TraesCS3B01G531800 chr5B 426072393 426075934 3541 False 5936 5936 96.928 1 3541 1 chr5B.!!$F1 3540
7 TraesCS3B01G531800 chr5B 450541640 450545217 3577 False 5602 5602 95.117 1 3539 1 chr5B.!!$F2 3538
8 TraesCS3B01G531800 chr4B 327348197 327351754 3557 False 5779 5779 96.074 1 3541 1 chr4B.!!$F1 3540
9 TraesCS3B01G531800 chr6B 526743172 526746727 3555 False 5677 5677 95.569 1 3541 1 chr6B.!!$F1 3540

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
564 606 3.181477 GCTGCATAATATGTGGCAACCAA 60.181 43.478 12.09 0.0 34.18 3.67 F
1286 1347 0.528470 CTCCCAGGAACGTCTGACTC 59.472 60.000 6.21 0.0 36.93 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1519 1.069513 ACACGGATTCCTCGTTCAACA 59.930 47.619 0.3 0.0 38.94 3.33 R
2756 2835 0.034337 ACAACCCGTATTGCAGTCGT 59.966 50.000 0.0 0.0 32.47 4.34 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
506 548 7.596248 GCAAATAGAATGTGAACACAATGTCTT 59.404 33.333 11.60 1.51 45.41 3.01
529 571 3.354467 TGCCACAATGCAGATATGACAA 58.646 40.909 0.00 0.00 36.04 3.18
554 596 4.449743 GTGGCAAATTGGCTGCATAATATG 59.550 41.667 20.08 0.00 44.10 1.78
555 597 4.101274 TGGCAAATTGGCTGCATAATATGT 59.899 37.500 20.08 0.00 44.10 2.29
564 606 3.181477 GCTGCATAATATGTGGCAACCAA 60.181 43.478 12.09 0.00 34.18 3.67
723 765 4.248859 GTGATATCTGAACACACTGTGCT 58.751 43.478 9.20 0.00 36.98 4.40
743 787 5.569059 GTGCTTGTTTTCAGGTTATCGATTG 59.431 40.000 1.71 0.00 0.00 2.67
1147 1204 4.388469 CCGATTTTTGTTATTGGTTGGCAG 59.612 41.667 0.00 0.00 0.00 4.85
1286 1347 0.528470 CTCCCAGGAACGTCTGACTC 59.472 60.000 6.21 0.00 36.93 3.36
1323 1384 1.298667 CCGACGATCAAAAGGGGGT 59.701 57.895 0.00 0.00 0.00 4.95
1458 1519 2.971452 GGGACGCGGAAGACTTCT 59.029 61.111 12.47 0.00 0.00 2.85
1517 1578 3.430929 GCCTCGTGGACATATCAAAGTCT 60.431 47.826 7.92 0.00 35.18 3.24
1518 1579 4.759782 CCTCGTGGACATATCAAAGTCTT 58.240 43.478 0.00 0.00 35.18 3.01
1759 1820 8.831550 GTGAATGATCCATCCTTTCTACTTTAC 58.168 37.037 0.00 0.00 0.00 2.01
2306 2378 3.055675 CCCATGATGGCAACTGACATTTT 60.056 43.478 5.79 0.00 45.42 1.82
2446 2518 0.108585 ACCATCAACGCTGTCAAGGT 59.891 50.000 0.00 0.00 0.00 3.50
2451 2523 0.732571 CAACGCTGTCAAGGTTGTGT 59.267 50.000 7.26 0.00 37.01 3.72
2630 2702 4.502259 GCCAAGCATGCTATAGACTACAGT 60.502 45.833 23.00 0.00 0.00 3.55
2756 2835 4.884458 TTACTTGTTGATGTCACGCAAA 57.116 36.364 0.00 0.00 0.00 3.68
3041 3120 4.657013 AGATGATGTAGATGGAGACGCTA 58.343 43.478 0.00 0.00 0.00 4.26
3070 3149 3.795488 GCAAGGATGACGACGATGACATA 60.795 47.826 0.00 0.00 0.00 2.29
3190 3270 5.220989 CGGAGAAAGTGATAGAACATACGGA 60.221 44.000 0.00 0.00 0.00 4.69
3486 3567 0.461548 TGGATGAGCAGCTACGAAGG 59.538 55.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
506 548 3.762823 TGTCATATCTGCATTGTGGCAAA 59.237 39.130 0.00 0.0 44.40 3.68
529 571 0.616371 ATGCAGCCAATTTGCCACAT 59.384 45.000 0.00 0.0 40.81 3.21
564 606 2.036475 TGGCACAATTGGTACGCAAATT 59.964 40.909 10.83 0.0 31.92 1.82
723 765 7.390440 ACATCTCAATCGATAACCTGAAAACAA 59.610 33.333 0.00 0.0 0.00 2.83
1147 1204 7.194278 TGACAGACGACTACAAAAGATATAGC 58.806 38.462 0.00 0.0 0.00 2.97
1237 1298 2.284417 GCGAACACGTTTCTTCTTCTGT 59.716 45.455 0.00 0.0 0.00 3.41
1286 1347 5.115472 CGTCGGTGAATTTTTCAATCAACAG 59.885 40.000 0.00 0.0 42.15 3.16
1323 1384 1.748244 GCATACCCATCTCAGCAGCAA 60.748 52.381 0.00 0.0 0.00 3.91
1458 1519 1.069513 ACACGGATTCCTCGTTCAACA 59.930 47.619 0.30 0.0 38.94 3.33
1517 1578 6.038936 TCGATCTCATTATTGACCTCGTACAA 59.961 38.462 11.08 0.0 34.58 2.41
1518 1579 5.529800 TCGATCTCATTATTGACCTCGTACA 59.470 40.000 11.08 0.0 34.58 2.90
1759 1820 3.693578 GGAGCCAGAAGATTGAAGGAAAG 59.306 47.826 0.00 0.0 0.00 2.62
1830 1892 1.795162 GCCGCATCAGAAATCAAACGG 60.795 52.381 0.00 0.0 42.19 4.44
2116 2183 6.179756 TCAGTATGACAGTTGCCATATTGTT 58.820 36.000 9.52 0.0 42.56 2.83
2446 2518 1.723608 CCTGTCTGCGGCAAACACAA 61.724 55.000 4.76 0.0 0.00 3.33
2647 2719 4.923281 CGTCCATCCACTTTCCAAATTTTC 59.077 41.667 0.00 0.0 0.00 2.29
2756 2835 0.034337 ACAACCCGTATTGCAGTCGT 59.966 50.000 0.00 0.0 32.47 4.34
3041 3120 1.220206 CGTCATCCTTGCTGAGGCT 59.780 57.895 0.00 0.0 45.87 4.58
3070 3149 3.461061 CGTGTCCTGATGCACATTATCT 58.539 45.455 0.00 0.0 35.51 1.98
3160 3240 1.139058 CTATCACTTTCTCCGGTGGGG 59.861 57.143 0.00 0.0 34.57 4.96
3161 3241 2.108168 TCTATCACTTTCTCCGGTGGG 58.892 52.381 0.00 0.0 34.57 4.61
3162 3242 3.056107 TGTTCTATCACTTTCTCCGGTGG 60.056 47.826 0.00 0.0 34.57 4.61
3380 3461 3.736100 CCATTGCCGCGCTTGACA 61.736 61.111 5.56 0.0 0.00 3.58
3471 3552 0.966179 TGTTCCTTCGTAGCTGCTCA 59.034 50.000 4.91 0.0 0.00 4.26


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

AutoCloner maintained by Alex Coulton.