Multiple sequence alignment - TraesCS3B01G189400

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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 TraesCS3B01G189400 chr3B 100.000 2447 0 0 1 2447 201584602 201582156 0 4519
1 TraesCS3B01G189400 chr3B 98.121 2448 44 2 1 2447 92236950 92239396 0 4265
2 TraesCS3B01G189400 chr3B 98.038 2447 46 2 1 2447 92227466 92225022 0 4252
3 TraesCS3B01G189400 chr2B 97.793 2447 46 1 1 2447 87959280 87961718 0 4213
4 TraesCS3B01G189400 chr2B 98.827 2301 26 1 1 2300 449203847 449201547 0 4098
5 TraesCS3B01G189400 chr1B 97.185 2451 59 5 1 2447 135100555 135098111 0 4135
6 TraesCS3B01G189400 chr1B 97.418 1820 42 2 1 1816 135059518 135057700 0 3096
7 TraesCS3B01G189400 chr1B 97.624 926 17 3 1 922 339012800 339013724 0 1583
8 TraesCS3B01G189400 chr1B 97.300 926 18 4 1 922 338937103 338938025 0 1565
9 TraesCS3B01G189400 chr7B 98.034 1933 38 0 515 2447 742964755 742966687 0 3360
10 TraesCS3B01G189400 chr3D 98.381 1606 26 0 842 2447 202625480 202623875 0 2822
11 TraesCS3B01G189400 chr6D 98.320 1607 26 1 842 2447 430466784 430465178 0 2817
12 TraesCS3B01G189400 chr5A 97.634 1606 38 0 842 2447 162145416 162143811 0 2756
13 TraesCS3B01G189400 chr6B 97.192 926 19 3 1 922 388026212 388027134 0 1559


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 TraesCS3B01G189400 chr3B 201582156 201584602 2446 True 4519 4519 100.000 1 2447 1 chr3B.!!$R2 2446
1 TraesCS3B01G189400 chr3B 92236950 92239396 2446 False 4265 4265 98.121 1 2447 1 chr3B.!!$F1 2446
2 TraesCS3B01G189400 chr3B 92225022 92227466 2444 True 4252 4252 98.038 1 2447 1 chr3B.!!$R1 2446
3 TraesCS3B01G189400 chr2B 87959280 87961718 2438 False 4213 4213 97.793 1 2447 1 chr2B.!!$F1 2446
4 TraesCS3B01G189400 chr2B 449201547 449203847 2300 True 4098 4098 98.827 1 2300 1 chr2B.!!$R1 2299
5 TraesCS3B01G189400 chr1B 135098111 135100555 2444 True 4135 4135 97.185 1 2447 1 chr1B.!!$R2 2446
6 TraesCS3B01G189400 chr1B 135057700 135059518 1818 True 3096 3096 97.418 1 1816 1 chr1B.!!$R1 1815
7 TraesCS3B01G189400 chr1B 339012800 339013724 924 False 1583 1583 97.624 1 922 1 chr1B.!!$F2 921
8 TraesCS3B01G189400 chr1B 338937103 338938025 922 False 1565 1565 97.300 1 922 1 chr1B.!!$F1 921
9 TraesCS3B01G189400 chr7B 742964755 742966687 1932 False 3360 3360 98.034 515 2447 1 chr7B.!!$F1 1932
10 TraesCS3B01G189400 chr3D 202623875 202625480 1605 True 2822 2822 98.381 842 2447 1 chr3D.!!$R1 1605
11 TraesCS3B01G189400 chr6D 430465178 430466784 1606 True 2817 2817 98.320 842 2447 1 chr6D.!!$R1 1605
12 TraesCS3B01G189400 chr5A 162143811 162145416 1605 True 2756 2756 97.634 842 2447 1 chr5A.!!$R1 1605
13 TraesCS3B01G189400 chr6B 388026212 388027134 922 False 1559 1559 97.192 1 922 1 chr6B.!!$F1 921

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
425 427 1.302949 GTATTGTGAGCCAGCCCCA 59.697 57.895 0.00 0.0 0.00 4.96 F
1418 1424 0.038166 GGACTGGCTTCCACCAATCA 59.962 55.000 1.28 0.0 37.69 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1431 0.608856 ACCACCATCTGAAATGCGCA 60.609 50.000 14.96 14.96 0.00 6.09 R
2341 2356 3.055819 TCTTGTTTCCAGAAGATCTCGGG 60.056 47.826 0.00 0.34 40.57 5.14 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
121 122 2.567615 CCCTATGATCCCGGTAAAGAGG 59.432 54.545 0.00 0.00 0.00 3.69
282 283 2.354203 GGAGATGAAGAAGCGACTTGGT 60.354 50.000 3.40 0.00 0.00 3.67
358 360 4.998033 GCCCTATACATAGAAAGAAGTGCC 59.002 45.833 0.00 0.00 32.05 5.01
425 427 1.302949 GTATTGTGAGCCAGCCCCA 59.697 57.895 0.00 0.00 0.00 4.96
517 519 1.428869 AAGATCTTGGCTCGCCCTAT 58.571 50.000 7.30 0.00 34.56 2.57
648 654 4.243008 TGTTTCACGGGCAGCCGA 62.243 61.111 5.00 0.00 36.94 5.54
715 721 4.592485 ACGTGATTGTCTTCTCTCACTT 57.408 40.909 0.00 0.00 36.67 3.16
751 757 6.323482 TGACAAAGATGACCCATTCTTTTTCA 59.677 34.615 9.13 9.13 36.89 2.69
904 910 1.978580 TCCTTTCTCTTTTCGGGAGCT 59.021 47.619 0.00 0.00 0.00 4.09
1418 1424 0.038166 GGACTGGCTTCCACCAATCA 59.962 55.000 1.28 0.00 37.69 2.57
1425 1431 2.893489 GGCTTCCACCAATCAGAGTTTT 59.107 45.455 0.00 0.00 0.00 2.43
2104 2119 7.067496 TGTTAGATCTCCAAACTGAACTTCT 57.933 36.000 0.00 0.00 0.00 2.85
2171 2186 2.540383 AGCGATCCCCTATTCTGCATA 58.460 47.619 0.00 0.00 0.00 3.14
2341 2356 3.149196 TCATGGAAGCTTCAGAAACCAC 58.851 45.455 27.02 8.32 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 3.259625 ACCTGAGAAGAGCTTAGTTGGAC 59.740 47.826 0.00 0.00 0.00 4.02
358 360 7.989741 AGATAGAATGTTGATACCAGTGGAAAG 59.010 37.037 18.40 0.00 0.00 2.62
366 368 8.033178 TGATTCCAGATAGAATGTTGATACCA 57.967 34.615 0.00 0.00 36.60 3.25
425 427 2.453521 TGGAGGTGCGTAGTGTCTTAT 58.546 47.619 0.00 0.00 0.00 1.73
648 654 2.354328 TCACAACCTTCCCCTATTGGT 58.646 47.619 0.00 0.00 0.00 3.67
684 690 5.179555 AGAAGACAATCACGTTCTTAAAGCC 59.820 40.000 0.00 0.00 0.00 4.35
715 721 8.106462 TGGGTCATCTTTGTCAATTGATAACTA 58.894 33.333 16.24 8.59 0.00 2.24
751 757 4.703093 CCATACCATTGTCGTTTTTAGGGT 59.297 41.667 0.00 0.00 0.00 4.34
904 910 4.090761 ACTGTCCATCTTTTTCAGCTCA 57.909 40.909 0.00 0.00 0.00 4.26
1118 1124 1.609932 TACATCGCGTTCAGTTCGAC 58.390 50.000 5.77 0.00 34.92 4.20
1418 1424 3.366679 CCATCTGAAATGCGCAAAACTCT 60.367 43.478 17.11 0.00 0.00 3.24
1425 1431 0.608856 ACCACCATCTGAAATGCGCA 60.609 50.000 14.96 14.96 0.00 6.09
2171 2186 2.722201 GGGCCGTCTGATCTTCGGT 61.722 63.158 18.93 0.00 45.11 4.69
2300 2315 9.130661 TCCATGATCTTGTAAAAGAAAGAAACA 57.869 29.630 0.00 0.00 36.09 2.83
2341 2356 3.055819 TCTTGTTTCCAGAAGATCTCGGG 60.056 47.826 0.00 0.34 40.57 5.14


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

AutoCloner maintained by Alex Coulton.