Multiple sequence alignment - TraesCS6B01G037900

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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 TraesCS6B01G037900 chr6B 100.000 2117 0 0 1 2117 22425839 22427955 0 3910
1 TraesCS6B01G037900 chr5D 97.159 1584 38 6 4 1585 6201381 6199803 0 2669
2 TraesCS6B01G037900 chr5D 96.708 1519 46 4 67 1583 329162138 329163654 0 2525
3 TraesCS6B01G037900 chr5D 97.272 1393 36 2 194 1585 560872556 560873947 0 2361
4 TraesCS6B01G037900 chr1D 96.912 1587 46 3 1 1585 254497892 254499477 0 2656
5 TraesCS6B01G037900 chr1D 93.750 1584 83 11 4 1585 244484149 244482580 0 2362
6 TraesCS6B01G037900 chr1A 95.641 1583 59 6 4 1585 168450664 168449091 0 2532
7 TraesCS6B01G037900 chr1A 97.207 537 10 3 1585 2117 554452032 554452567 0 904
8 TraesCS6B01G037900 chr4D 95.523 1586 66 5 1 1585 19916391 19917972 0 2531
9 TraesCS6B01G037900 chr7A 94.058 1582 90 4 4 1585 352194124 352192547 0 2398
10 TraesCS6B01G037900 chr3D 96.827 1229 35 3 1 1226 21904520 21905747 0 2050
11 TraesCS6B01G037900 chr3D 97.222 540 8 2 1585 2117 24161354 24160815 0 907
12 TraesCS6B01G037900 chr3B 97.414 580 14 1 1007 1585 201515580 201516159 0 987
13 TraesCS6B01G037900 chr3B 97.403 539 8 2 1585 2117 201488914 201488376 0 913
14 TraesCS6B01G037900 chr3A 97.579 537 7 3 1586 2117 273159631 273160166 0 915
15 TraesCS6B01G037900 chr3A 96.840 538 11 3 1585 2117 524024374 524023838 0 894
16 TraesCS6B01G037900 chr7B 97.398 538 9 2 1585 2117 662741829 662742366 0 911
17 TraesCS6B01G037900 chr7B 97.378 534 11 1 1585 2115 397631124 397630591 0 905
18 TraesCS6B01G037900 chr2D 97.026 538 9 2 1585 2115 630263054 630262517 0 898
19 TraesCS6B01G037900 chr2B 97.020 537 11 3 1585 2117 683741638 683741103 0 898


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 TraesCS6B01G037900 chr6B 22425839 22427955 2116 False 3910 3910 100.000 1 2117 1 chr6B.!!$F1 2116
1 TraesCS6B01G037900 chr5D 6199803 6201381 1578 True 2669 2669 97.159 4 1585 1 chr5D.!!$R1 1581
2 TraesCS6B01G037900 chr5D 329162138 329163654 1516 False 2525 2525 96.708 67 1583 1 chr5D.!!$F1 1516
3 TraesCS6B01G037900 chr5D 560872556 560873947 1391 False 2361 2361 97.272 194 1585 1 chr5D.!!$F2 1391
4 TraesCS6B01G037900 chr1D 254497892 254499477 1585 False 2656 2656 96.912 1 1585 1 chr1D.!!$F1 1584
5 TraesCS6B01G037900 chr1D 244482580 244484149 1569 True 2362 2362 93.750 4 1585 1 chr1D.!!$R1 1581
6 TraesCS6B01G037900 chr1A 168449091 168450664 1573 True 2532 2532 95.641 4 1585 1 chr1A.!!$R1 1581
7 TraesCS6B01G037900 chr1A 554452032 554452567 535 False 904 904 97.207 1585 2117 1 chr1A.!!$F1 532
8 TraesCS6B01G037900 chr4D 19916391 19917972 1581 False 2531 2531 95.523 1 1585 1 chr4D.!!$F1 1584
9 TraesCS6B01G037900 chr7A 352192547 352194124 1577 True 2398 2398 94.058 4 1585 1 chr7A.!!$R1 1581
10 TraesCS6B01G037900 chr3D 21904520 21905747 1227 False 2050 2050 96.827 1 1226 1 chr3D.!!$F1 1225
11 TraesCS6B01G037900 chr3D 24160815 24161354 539 True 907 907 97.222 1585 2117 1 chr3D.!!$R1 532
12 TraesCS6B01G037900 chr3B 201515580 201516159 579 False 987 987 97.414 1007 1585 1 chr3B.!!$F1 578
13 TraesCS6B01G037900 chr3B 201488376 201488914 538 True 913 913 97.403 1585 2117 1 chr3B.!!$R1 532
14 TraesCS6B01G037900 chr3A 273159631 273160166 535 False 915 915 97.579 1586 2117 1 chr3A.!!$F1 531
15 TraesCS6B01G037900 chr3A 524023838 524024374 536 True 894 894 96.840 1585 2117 1 chr3A.!!$R1 532
16 TraesCS6B01G037900 chr7B 662741829 662742366 537 False 911 911 97.398 1585 2117 1 chr7B.!!$F1 532
17 TraesCS6B01G037900 chr7B 397630591 397631124 533 True 905 905 97.378 1585 2115 1 chr7B.!!$R1 530
18 TraesCS6B01G037900 chr2D 630262517 630263054 537 True 898 898 97.026 1585 2115 1 chr2D.!!$R1 530
19 TraesCS6B01G037900 chr2B 683741103 683741638 535 True 898 898 97.020 1585 2117 1 chr2B.!!$R1 532

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
832 838 1.89756 ACTACAAGGAAACAGGCAGC 58.102 50.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1895 4.650972 ATTGTAGTAAAACCTGGCCTGA 57.349 40.909 11.88 0.0 0.0 3.86 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
361 365 9.218525 ACATCCCATCTTTAGAGATAAAGAAGA 57.781 33.333 12.90 10.78 45.66 2.87
624 630 2.180432 AGACCGGGCTACTTTGAAAC 57.820 50.000 9.02 0.00 0.00 2.78
703 709 4.630894 TTGCTTTGCTCTTCTTTTTCGA 57.369 36.364 0.00 0.00 0.00 3.71
758 764 5.088739 CGAGATGTTTTTGCTGGTATTGAC 58.911 41.667 0.00 0.00 0.00 3.18
832 838 1.897560 ACTACAAGGAAACAGGCAGC 58.102 50.000 0.00 0.00 0.00 5.25
918 924 6.040842 TCCCATCCTTTCTTTGACTCTTTTTG 59.959 38.462 0.00 0.00 0.00 2.44
922 928 9.154847 CATCCTTTCTTTGACTCTTTTTGTTTT 57.845 29.630 0.00 0.00 0.00 2.43
970 976 8.780846 ATTACAAATGAATACGTGTGGAAGTA 57.219 30.769 0.00 0.00 27.91 2.24
1022 1028 5.751243 ATGGAAGCATTGGTTTATACGTC 57.249 39.130 2.14 0.00 0.00 4.34
1164 1171 6.042208 CCAGATAGGGGGACTTCTTACTTAAG 59.958 46.154 0.00 0.00 34.65 1.85
1338 1345 9.838339 AGATTACAATGGATCTACGAAAAGATT 57.162 29.630 0.00 0.00 36.33 2.40
1450 1459 1.612676 AACCTAGGCCAAAACGAACC 58.387 50.000 9.30 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
265 269 3.012274 TCTGAATAATCCCCCTTTTGCCA 59.988 43.478 0.00 0.00 0.00 4.92
361 365 1.003223 GGCGTACAAAAAGCTCACGTT 60.003 47.619 0.00 0.00 35.17 3.99
624 630 1.666888 GCTGCGAAAAACACCATCAGG 60.667 52.381 0.00 0.00 42.21 3.86
703 709 1.374505 GCGCCATGCCAAATGTGTT 60.375 52.632 0.00 0.00 37.76 3.32
758 764 2.426024 CACTTGAGCATCCAAATCTGGG 59.574 50.000 0.00 0.00 43.71 4.45
947 953 8.780846 ATTACTTCCACACGTATTCATTTGTA 57.219 30.769 0.00 0.00 0.00 2.41
1022 1028 5.554070 TCCCTAAAGTCGAAACTAAAAGGG 58.446 41.667 11.07 11.07 43.71 3.95
1050 1057 7.362142 GGTTCTTGGAAGAAGATAGCGAAAAAT 60.362 37.037 1.96 0.00 45.01 1.82
1164 1171 3.549299 TCGAAGAACACGGAGACTAAC 57.451 47.619 0.00 0.00 0.00 2.34
1338 1345 9.524106 CTATTCCGTTGTAGATGTAAATACACA 57.476 33.333 0.00 0.00 39.30 3.72
1350 1359 8.959548 TGACTTTGTATACTATTCCGTTGTAGA 58.040 33.333 4.17 0.00 0.00 2.59
1450 1459 2.736144 TCAGTAAACTACCTGCACCG 57.264 50.000 0.00 0.00 0.00 4.94
1876 1895 4.650972 ATTGTAGTAAAACCTGGCCTGA 57.349 40.909 11.88 0.00 0.00 3.86
2054 2073 8.477419 ACCTTTTGATCTTTGGTTATCTTTCA 57.523 30.769 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.