Multiple sequence alignment - TraesCS4D01G152100

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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 TraesCS4D01G152100 chr4D 100.000 2489 0 0 1 2489 179916667 179919155 0 4597
1 TraesCS4D01G152100 chr7D 95.257 2488 111 6 4 2489 122700572 122698090 0 3934
2 TraesCS4D01G152100 chr5D 93.710 2496 136 14 1 2489 464310001 464312482 0 3720
3 TraesCS4D01G152100 chr2D 92.431 2497 146 19 1 2489 554138639 554136178 0 3524
4 TraesCS4D01G152100 chr2B 92.136 2505 170 20 1 2489 366591349 366588856 0 3509
5 TraesCS4D01G152100 chr6D 92.947 2226 139 12 1 2218 426960113 426957898 0 3225
6 TraesCS4D01G152100 chr6A 88.960 2509 238 27 1 2489 178096002 178093513 0 3062
7 TraesCS4D01G152100 chr6A 88.570 2511 249 30 1 2489 401500577 401498083 0 3013
8 TraesCS4D01G152100 chr4A 88.814 2512 237 36 1 2484 45263349 45265844 0 3042
9 TraesCS4D01G152100 chr2A 88.471 2524 236 39 1 2489 490628578 490631081 0 2998
10 TraesCS4D01G152100 chr3D 93.004 1115 53 7 1399 2489 116350039 116348926 0 1604


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 TraesCS4D01G152100 chr4D 179916667 179919155 2488 False 4597 4597 100.000 1 2489 1 chr4D.!!$F1 2488
1 TraesCS4D01G152100 chr7D 122698090 122700572 2482 True 3934 3934 95.257 4 2489 1 chr7D.!!$R1 2485
2 TraesCS4D01G152100 chr5D 464310001 464312482 2481 False 3720 3720 93.710 1 2489 1 chr5D.!!$F1 2488
3 TraesCS4D01G152100 chr2D 554136178 554138639 2461 True 3524 3524 92.431 1 2489 1 chr2D.!!$R1 2488
4 TraesCS4D01G152100 chr2B 366588856 366591349 2493 True 3509 3509 92.136 1 2489 1 chr2B.!!$R1 2488
5 TraesCS4D01G152100 chr6D 426957898 426960113 2215 True 3225 3225 92.947 1 2218 1 chr6D.!!$R1 2217
6 TraesCS4D01G152100 chr6A 178093513 178096002 2489 True 3062 3062 88.960 1 2489 1 chr6A.!!$R1 2488
7 TraesCS4D01G152100 chr6A 401498083 401500577 2494 True 3013 3013 88.570 1 2489 1 chr6A.!!$R2 2488
8 TraesCS4D01G152100 chr4A 45263349 45265844 2495 False 3042 3042 88.814 1 2484 1 chr4A.!!$F1 2483
9 TraesCS4D01G152100 chr2A 490628578 490631081 2503 False 2998 2998 88.471 1 2489 1 chr2A.!!$F1 2488
10 TraesCS4D01G152100 chr3D 116348926 116350039 1113 True 1604 1604 93.004 1399 2489 1 chr3D.!!$R1 1090

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
787 814 3.915437 AATACTGGGCAACTTTGTTCG 57.085 42.857 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 1941 4.029861 CGATAACTTTCACTAACCGTGTCG 59.97 45.833 0.0 0.0 44.16 4.35 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
131 133 7.279981 AGCTGTACGATATTGTCAAGCATTTTA 59.720 33.333 22.71 0.00 34.54 1.52
297 310 9.507329 TTTGCTTAGTAGAGACATGATTCTTTT 57.493 29.630 0.00 0.00 0.00 2.27
491 504 4.202336 TGTCCCAACAAAACAATCATGCAT 60.202 37.500 0.00 0.00 30.70 3.96
658 676 4.388773 TGTTTTGTCAGTAGCTATGCTTCG 59.611 41.667 0.00 0.00 40.44 3.79
787 814 3.915437 AATACTGGGCAACTTTGTTCG 57.085 42.857 0.00 0.00 0.00 3.95
832 859 8.804688 TTTAATTACACATGGCAACTAAACAC 57.195 30.769 0.00 0.00 37.61 3.32
919 950 8.116753 CCGGCGATATCTTTACATATCATTTTC 58.883 37.037 9.30 0.00 36.04 2.29
1022 1059 3.052082 CCAGGAGCTTGCACCACG 61.052 66.667 11.34 2.41 0.00 4.94
1433 1475 1.993391 GGGAAGGTCGATGGGTCCA 60.993 63.158 8.92 0.00 0.00 4.02
1465 1507 1.153745 GCAATGGTCGTCGAGCTCT 60.154 57.895 23.53 9.69 0.00 4.09
1467 1509 0.803768 CAATGGTCGTCGAGCTCTGG 60.804 60.000 23.53 6.76 0.00 3.86
1489 1531 7.715249 TCTGGAAAATATACACATGGAACTAGC 59.285 37.037 0.00 0.00 0.00 3.42
1501 1543 6.094464 CACATGGAACTAGCTGATGAATGAAA 59.906 38.462 0.00 0.00 0.00 2.69
1548 1591 4.142271 CGAGAGTTCATAGAGGAAGCTGTT 60.142 45.833 0.00 0.00 0.00 3.16
1845 1902 4.135747 CCAGTTGGGTGTTTTTGAATGT 57.864 40.909 0.00 0.00 0.00 2.71
1884 1941 4.989279 ACATGGCAAATGTAGTTGATCC 57.011 40.909 2.62 0.00 0.00 3.36
1979 2041 4.848357 AGCATGGTAGTTCATAAGCAGTT 58.152 39.130 0.00 0.00 0.00 3.16
2099 2208 5.240183 CGGAAATCTACATGATGGCAGATTT 59.760 40.000 24.77 24.77 41.60 2.17
2116 2225 9.860650 TGGCAGATTTAGTATAAATAACATGGT 57.139 29.630 0.00 0.00 0.00 3.55
2139 2248 7.715249 TGGTAGATTCAGTAGAAATAACATGGC 59.285 37.037 0.00 0.00 37.29 4.40
2180 2289 7.798596 ACATGGCAGATTCAGTAGAAATAAG 57.201 36.000 0.00 0.00 37.29 1.73
2430 2543 1.739067 CTTGAATCTCCAACCCCGAC 58.261 55.000 0.00 0.00 0.00 4.79
2484 2597 3.393106 GAACGGGGCGGGTTCCTA 61.393 66.667 7.77 0.00 38.23 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.129555 CTCACAGAACCAGGGGTGGG 62.130 65.000 0.00 0.00 35.34 4.61
62 64 2.766263 TGACTTCGGGCTCATAGTCATT 59.234 45.455 12.45 0.00 41.34 2.57
131 133 1.813513 CTGTTGGACCTCGCATTTCT 58.186 50.000 0.00 0.00 0.00 2.52
314 327 5.918576 GGTTTTGTCCAAACATTAGCTGTAC 59.081 40.000 0.00 0.00 46.01 2.90
322 335 6.232581 TGATCTTGGTTTTGTCCAAACATT 57.767 33.333 2.31 0.00 46.01 2.71
491 504 5.182950 CCATATTTTGCAGGTCACACTGTAA 59.817 40.000 0.00 0.00 40.52 2.41
787 814 5.391312 AAAAGAAGTTGCCATCCATGTAC 57.609 39.130 0.00 0.00 0.00 2.90
832 859 3.071023 TCCAAAAGTACACCCACAGAGAG 59.929 47.826 0.00 0.00 0.00 3.20
919 950 7.151308 TCAAAAACAGCAATTATGTAGTTGGG 58.849 34.615 13.23 0.00 30.89 4.12
930 961 6.477688 CAGAGTTCACATCAAAAACAGCAATT 59.522 34.615 0.00 0.00 0.00 2.32
968 1002 9.317827 ACAGTACCTACAAAGTAAGATAAAGGA 57.682 33.333 0.00 0.00 0.00 3.36
1022 1059 1.032014 ACACTTGTCATGTGGGTTGC 58.968 50.000 19.70 0.00 39.52 4.17
1433 1475 0.800631 CATTGCAGCTGTGACGACAT 59.199 50.000 16.64 0.00 0.00 3.06
1465 1507 7.498900 CAGCTAGTTCCATGTGTATATTTTCCA 59.501 37.037 0.00 0.00 0.00 3.53
1467 1509 8.662781 TCAGCTAGTTCCATGTGTATATTTTC 57.337 34.615 0.00 0.00 0.00 2.29
1489 1531 6.519315 GCGTGTTGAAATTTTCATTCATCAG 58.481 36.000 12.39 10.83 39.84 2.90
1501 1543 1.739338 TTGGCCCGCGTGTTGAAATT 61.739 50.000 4.92 0.00 0.00 1.82
1548 1591 6.826741 ACTTGTACTTCTTGTTGGCTTTCTTA 59.173 34.615 0.00 0.00 0.00 2.10
1838 1895 5.101648 TCAGGCATCATAGACACATTCAA 57.898 39.130 0.00 0.00 0.00 2.69
1845 1902 4.641541 CCATGTTTTCAGGCATCATAGACA 59.358 41.667 0.00 0.00 0.00 3.41
1884 1941 4.029861 CGATAACTTTCACTAACCGTGTCG 59.970 45.833 0.00 0.00 44.16 4.35
2047 2110 7.139896 TCAGTCAACGCATTTTATTACACAT 57.860 32.000 0.00 0.00 0.00 3.21
2116 2225 8.704668 TCTGCCATGTTATTTCTACTGAATCTA 58.295 33.333 0.00 0.00 31.56 1.98
2131 2240 9.109393 GTTATTTCTACTGAATCTGCCATGTTA 57.891 33.333 0.00 0.00 31.56 2.41
2132 2241 7.611467 TGTTATTTCTACTGAATCTGCCATGTT 59.389 33.333 0.00 0.00 31.56 2.71
2133 2242 7.112122 TGTTATTTCTACTGAATCTGCCATGT 58.888 34.615 0.00 0.00 31.56 3.21
2139 2248 7.496920 TCTGCCATGTTATTTCTACTGAATCTG 59.503 37.037 0.00 0.00 31.56 2.90
2180 2289 7.792374 TGTTATTTCTACTGAATCTGCCATC 57.208 36.000 0.00 0.00 31.56 3.51
2331 2441 4.707448 TGTAACTTGGTTGTTGGTGACATT 59.293 37.500 0.00 0.00 42.32 2.71
2430 2543 4.627467 CGTCCAAAAGAGGTGAGATACAAG 59.373 45.833 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.