Multiple sequence alignment - TraesCS3D01G196100

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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 TraesCS3D01G196100 chr3D 100.000 2648 0 0 1 2648 193371595 193374242 0 4891
1 TraesCS3D01G196100 chrUn 97.660 2650 60 1 1 2648 171044494 171047143 0 4549
2 TraesCS3D01G196100 chrUn 97.617 1888 42 1 1 1885 45094207 45096094 0 3234
3 TraesCS3D01G196100 chr6D 97.131 2649 73 3 1 2648 283206954 283209600 0 4468
4 TraesCS3D01G196100 chr6D 96.492 2651 90 2 1 2648 425972830 425975480 0 4377
5 TraesCS3D01G196100 chr6B 96.678 2649 87 1 1 2648 388156064 388153416 0 4403
6 TraesCS3D01G196100 chr6B 96.112 2649 95 7 1 2648 388346386 388343745 0 4314
7 TraesCS3D01G196100 chr4D 96.149 2649 100 2 1 2648 241073951 241076598 0 4325
8 TraesCS3D01G196100 chr4D 95.696 2649 109 5 1 2648 241283572 241280928 0 4255
9 TraesCS3D01G196100 chr1D 95.925 2650 90 5 1 2648 351013443 351010810 0 4279
10 TraesCS3D01G196100 chr7B 95.772 2649 98 3 1 2648 247493204 247490569 0 4259


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 TraesCS3D01G196100 chr3D 193371595 193374242 2647 False 4891 4891 100.000 1 2648 1 chr3D.!!$F1 2647
1 TraesCS3D01G196100 chrUn 171044494 171047143 2649 False 4549 4549 97.660 1 2648 1 chrUn.!!$F2 2647
2 TraesCS3D01G196100 chrUn 45094207 45096094 1887 False 3234 3234 97.617 1 1885 1 chrUn.!!$F1 1884
3 TraesCS3D01G196100 chr6D 283206954 283209600 2646 False 4468 4468 97.131 1 2648 1 chr6D.!!$F1 2647
4 TraesCS3D01G196100 chr6D 425972830 425975480 2650 False 4377 4377 96.492 1 2648 1 chr6D.!!$F2 2647
5 TraesCS3D01G196100 chr6B 388153416 388156064 2648 True 4403 4403 96.678 1 2648 1 chr6B.!!$R1 2647
6 TraesCS3D01G196100 chr6B 388343745 388346386 2641 True 4314 4314 96.112 1 2648 1 chr6B.!!$R2 2647
7 TraesCS3D01G196100 chr4D 241073951 241076598 2647 False 4325 4325 96.149 1 2648 1 chr4D.!!$F1 2647
8 TraesCS3D01G196100 chr4D 241280928 241283572 2644 True 4255 4255 95.696 1 2648 1 chr4D.!!$R1 2647
9 TraesCS3D01G196100 chr1D 351010810 351013443 2633 True 4279 4279 95.925 1 2648 1 chr1D.!!$R1 2647
10 TraesCS3D01G196100 chr7B 247490569 247493204 2635 True 4259 4259 95.772 1 2648 1 chr7B.!!$R1 2647

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
838 839 0.036875 AGGACGGGCAAAAAGAGAGG 59.963 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2569 2579 0.696501 GCCTTTCTAGGTTGGTGGGA 59.303 55.0 0.0 0.0 44.0 4.37 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
78 79 4.649674 AGAATCAGGCTCCGTAATCAAGTA 59.350 41.667 0.00 0.00 0.00 2.24
88 89 3.499048 CGTAATCAAGTACTCGCTGTGT 58.501 45.455 0.00 0.00 0.00 3.72
703 704 9.527157 TCCCATACTTTTTATCATTTCAGAACA 57.473 29.630 0.00 0.00 0.00 3.18
725 726 3.319137 TCAGCATACTGTGTGACTTCC 57.681 47.619 8.84 0.00 44.77 3.46
732 733 0.667487 CTGTGTGACTTCCGCGTGAT 60.667 55.000 4.92 0.00 0.00 3.06
769 770 4.520078 GTTTGTTGCTTTGCATGAACATG 58.480 39.130 10.04 10.04 38.76 3.21
838 839 0.036875 AGGACGGGCAAAAAGAGAGG 59.963 55.000 0.00 0.00 0.00 3.69
841 842 0.698818 ACGGGCAAAAAGAGAGGGAT 59.301 50.000 0.00 0.00 0.00 3.85
919 920 4.586841 ACAACTGCACTAGAGAGAAAGAGT 59.413 41.667 0.00 0.00 0.00 3.24
949 950 4.833390 ACTAAGGAAATGCAGTACCTGTC 58.167 43.478 8.71 0.00 33.43 3.51
982 983 2.672961 TCATGCAAAGCTAGCGTAGT 57.327 45.000 9.55 0.00 33.85 2.73
1034 1035 4.691216 AGAACGCAGAAGTAAGGAAATGAC 59.309 41.667 0.00 0.00 0.00 3.06
1074 1075 7.968014 AAAATTTCATAAGCAGATCTTCCCT 57.032 32.000 0.00 0.00 36.25 4.20
1192 1198 1.943340 GTTCAATTCGGATCCCTCTGC 59.057 52.381 6.06 0.00 0.00 4.26
1419 1425 6.362248 GTTAAACATTCTATTAGGGAGCCCA 58.638 40.000 8.53 0.00 38.92 5.36
1462 1468 2.279582 TCATTCTCGTTCGGCTCTTC 57.720 50.000 0.00 0.00 0.00 2.87
1540 1546 2.380571 ATTGCCCCCAACCGTTTCCT 62.381 55.000 0.00 0.00 32.95 3.36
1541 1547 2.203582 GCCCCCAACCGTTTCCTT 60.204 61.111 0.00 0.00 0.00 3.36
1705 1711 1.256812 AAAAGAATGTTGAGCCGGGG 58.743 50.000 2.18 0.00 0.00 5.73
1919 1927 0.179000 GGGTAGCACCACCAGATCTG 59.821 60.000 16.24 16.24 41.02 2.90
1946 1954 6.001460 ACAAGGTGGAAATTCTCGTATTTCA 58.999 36.000 16.31 6.00 43.24 2.69
2004 2012 8.838452 AGTTATTTATATCGCGACAGCTATAC 57.162 34.615 12.93 4.16 42.32 1.47
2054 2062 2.372172 TCCCCTTTTTCTTCGCTCTTCT 59.628 45.455 0.00 0.00 0.00 2.85
2077 2086 3.404899 GAACCGGTACAGAAATTGGTGA 58.595 45.455 8.00 0.00 0.00 4.02
2226 2235 4.141981 TGCATTTTCAAAAGCTTCCTGTCA 60.142 37.500 0.00 0.00 34.04 3.58
2253 2262 3.494398 GGCTCCTATTTCAATCCGTGCTA 60.494 47.826 0.00 0.00 0.00 3.49
2520 2530 5.419760 AAAAACCTAGTTCGCTCTCAAAC 57.580 39.130 0.00 0.00 0.00 2.93
2569 2579 1.822990 CATGGCTGAATGGTGAAAGCT 59.177 47.619 0.00 0.00 35.93 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 2.560542 AGATCTTCTTCACACAGCGAGT 59.439 45.455 0.00 0.00 0.00 4.18
88 89 5.163405 GGTACATGCCTGTAGATCTTCTTCA 60.163 44.000 0.00 0.00 38.51 3.02
363 364 8.607459 GTTGAAGATCAATTCATATCGACAAGT 58.393 33.333 0.00 0.00 38.79 3.16
531 532 4.737946 GCAAGACAAGACACGGCTAGATAT 60.738 45.833 0.00 0.00 0.00 1.63
703 704 4.256920 GGAAGTCACACAGTATGCTGATT 58.743 43.478 18.40 0.37 45.28 2.57
725 726 3.345714 GAAATGCAAGAACTATCACGCG 58.654 45.455 3.53 3.53 0.00 6.01
732 733 4.737765 GCAACAAACGAAATGCAAGAACTA 59.262 37.500 0.00 0.00 38.63 2.24
769 770 7.070074 TCAGGGAGTTCTCTTTCCAATATCTAC 59.930 40.741 0.00 0.00 35.09 2.59
838 839 3.640029 TGATCCGGGTAGTTAGTCAATCC 59.360 47.826 0.00 0.00 0.00 3.01
841 842 4.682320 GCATTGATCCGGGTAGTTAGTCAA 60.682 45.833 0.00 0.00 0.00 3.18
906 907 5.584913 AGTTGGATCCACTCTTTCTCTCTA 58.415 41.667 15.91 0.00 0.00 2.43
919 920 4.263905 ACTGCATTTCCTTAGTTGGATCCA 60.264 41.667 11.44 11.44 35.83 3.41
949 950 1.202568 TGCATGATTAGCTCCGACAGG 60.203 52.381 0.00 0.00 39.46 4.00
982 983 2.449031 ATTCACTTCGACGGCTGGCA 62.449 55.000 0.00 0.00 0.00 4.92
1034 1035 7.969387 TGAAATTTTTCAAGAAAGAGTCGTG 57.031 32.000 3.31 0.00 43.62 4.35
1074 1075 2.631160 AACTCGTGATTGGTGTGGAA 57.369 45.000 0.00 0.00 0.00 3.53
1192 1198 3.542648 GTTCGGGAGGAAAGGGAAATAG 58.457 50.000 0.00 0.00 36.14 1.73
1419 1425 3.034635 ACCACACAGAAGAGTCAAGACT 58.965 45.455 1.68 1.68 45.84 3.24
1462 1468 1.012086 CCACTGCTGGATGTGATTCG 58.988 55.000 0.00 0.00 40.55 3.34
1540 1546 8.445361 AACCCTTCTGTTTCTATAGAGGTAAA 57.555 34.615 2.02 0.00 0.00 2.01
1541 1547 8.445361 AAACCCTTCTGTTTCTATAGAGGTAA 57.555 34.615 2.02 0.00 33.24 2.85
1705 1711 1.296727 GCTGAACTTACATACCCGGC 58.703 55.000 0.00 0.00 0.00 6.13
1919 1927 2.293399 ACGAGAATTTCCACCTTGTTGC 59.707 45.455 0.00 0.00 0.00 4.17
2004 2012 6.406400 TTTGTTAATGGGAACAAGGAACTGTG 60.406 38.462 2.36 0.00 46.88 3.66
2054 2062 2.106857 ACCAATTTCTGTACCGGTTCCA 59.893 45.455 15.04 9.68 0.00 3.53
2226 2235 3.288092 GGATTGAAATAGGAGCCGGTTT 58.712 45.455 1.90 0.00 0.00 3.27
2520 2530 5.917541 TTAGCGAGTGAACTAGGTTTTTG 57.082 39.130 0.66 0.00 31.95 2.44
2569 2579 0.696501 GCCTTTCTAGGTTGGTGGGA 59.303 55.000 0.00 0.00 44.00 4.37


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

AutoCloner maintained by Alex Coulton.