Multiple sequence alignment - TraesCS3D01G356200

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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 TraesCS3D01G356200 chr3D 100.000 3853 0 0 1 3853 468650512 468646660 0 7116
1 TraesCS3D01G356200 chr7D 96.682 3858 100 16 1 3853 564196111 564192277 0 6390
2 TraesCS3D01G356200 chr7D 96.550 3855 112 13 1 3853 601716307 601712472 0 6362
3 TraesCS3D01G356200 chr6D 95.857 3862 128 20 1 3853 340966962 340963124 0 6216
4 TraesCS3D01G356200 chr6D 95.681 3867 125 22 1 3853 296393486 296389648 0 6178
5 TraesCS3D01G356200 chr6D 95.184 3862 152 24 1 3853 53655807 53651971 0 6071
6 TraesCS3D01G356200 chr6D 95.028 3862 159 21 1 3853 276418358 276422195 0 6037
7 TraesCS3D01G356200 chr5D 95.001 3861 153 27 1 3853 539497727 539501555 0 6024
8 TraesCS3D01G356200 chr4D 94.763 3876 160 29 1 3851 178593046 178589189 0 5993


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 TraesCS3D01G356200 chr3D 468646660 468650512 3852 True 7116 7116 100.000 1 3853 1 chr3D.!!$R1 3852
1 TraesCS3D01G356200 chr7D 564192277 564196111 3834 True 6390 6390 96.682 1 3853 1 chr7D.!!$R1 3852
2 TraesCS3D01G356200 chr7D 601712472 601716307 3835 True 6362 6362 96.550 1 3853 1 chr7D.!!$R2 3852
3 TraesCS3D01G356200 chr6D 340963124 340966962 3838 True 6216 6216 95.857 1 3853 1 chr6D.!!$R3 3852
4 TraesCS3D01G356200 chr6D 296389648 296393486 3838 True 6178 6178 95.681 1 3853 1 chr6D.!!$R2 3852
5 TraesCS3D01G356200 chr6D 53651971 53655807 3836 True 6071 6071 95.184 1 3853 1 chr6D.!!$R1 3852
6 TraesCS3D01G356200 chr6D 276418358 276422195 3837 False 6037 6037 95.028 1 3853 1 chr6D.!!$F1 3852
7 TraesCS3D01G356200 chr5D 539497727 539501555 3828 False 6024 6024 95.001 1 3853 1 chr5D.!!$F1 3852
8 TraesCS3D01G356200 chr4D 178589189 178593046 3857 True 5993 5993 94.763 1 3851 1 chr4D.!!$R1 3850

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
805 832 0.188342 CCCCCTTCCCCCATATGTTG 59.812 60.000 1.24 0.0 0.00 3.33 F
1083 1114 1.043673 AGATTTACGAGCCCGCCTCT 61.044 55.000 0.00 0.0 38.49 3.69 F
1275 1306 1.081242 CGTGCTGGCAAATTCGCTT 60.081 52.632 0.00 0.0 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2520 2590 0.318441 CAGGACAAGACGGAGCTGAA 59.682 55.0 0.00 0.00 0.00 3.02 R
2850 2923 0.541063 TGTGTGTCGGGAAGCTCCTA 60.541 55.0 0.00 0.00 36.57 2.94 R
2927 3000 1.494766 CGTCGGTGTCATGTTGCACA 61.495 55.0 15.48 1.44 37.35 4.57 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
175 177 7.776969 ACTTGTGATATCTGAACATATTTGGCT 59.223 33.333 3.98 0.00 0.00 4.75
721 736 7.387122 ACGATGATGATGATTTCATGGAGTTAG 59.613 37.037 0.00 0.00 45.29 2.34
805 832 0.188342 CCCCCTTCCCCCATATGTTG 59.812 60.000 1.24 0.00 0.00 3.33
927 957 5.594317 AGAAATGTAATCGCAATAGGGCTTT 59.406 36.000 0.00 0.00 0.00 3.51
1083 1114 1.043673 AGATTTACGAGCCCGCCTCT 61.044 55.000 0.00 0.00 38.49 3.69
1118 1149 3.060866 GGGACGTGGAAGACTGCT 58.939 61.111 0.00 0.00 0.00 4.24
1145 1176 1.278985 TGAGGAATCCGTGTTCTGCAT 59.721 47.619 0.00 0.00 0.00 3.96
1275 1306 1.081242 CGTGCTGGCAAATTCGCTT 60.081 52.632 0.00 0.00 0.00 4.68
1523 1559 2.812591 CTGATGCAGCAACTTCTTGTCT 59.187 45.455 5.96 0.00 0.00 3.41
1565 1601 5.037385 GGCAAAACTGAAAGAAGTGAAGAC 58.963 41.667 0.00 0.00 37.43 3.01
1567 1603 5.582550 CAAAACTGAAAGAAGTGAAGACCC 58.417 41.667 0.00 0.00 37.43 4.46
1777 1814 5.435686 ACTGCCAACATAACTAGAATGGA 57.564 39.130 0.00 0.00 0.00 3.41
2196 2262 6.141527 CACGACATTCTTTTAATTTTGACGCA 59.858 34.615 0.00 0.00 0.00 5.24
2496 2566 1.118838 TGTTTGGTGGGCCTCAAAAG 58.881 50.000 20.99 0.00 35.08 2.27
2520 2590 1.453155 GAAAGTGGATGGACGTGCAT 58.547 50.000 23.41 23.41 0.00 3.96
2612 2684 1.946745 TTGATCTTGTGCACGTGACA 58.053 45.000 22.23 17.34 0.00 3.58
2850 2923 1.198637 GGTACGACTACAACAGCTCGT 59.801 52.381 0.00 0.00 41.08 4.18
2892 2965 6.552725 ACAAGATGAACTAGATGGAGATGCTA 59.447 38.462 0.00 0.00 0.00 3.49
2906 2979 3.561143 AGATGCTACTCTCGACAAGGAT 58.439 45.455 0.00 0.00 0.00 3.24
2920 2993 2.567169 ACAAGGATGACGAGGATGACAA 59.433 45.455 0.00 0.00 0.00 3.18
2927 3000 3.099905 TGACGAGGATGACAAGGAGAAT 58.900 45.455 0.00 0.00 0.00 2.40
3159 3232 2.025898 CTAGGAGGAGGTTCGACTTCC 58.974 57.143 7.71 7.71 43.98 3.46
3302 3378 2.499756 TATGTGCAGCGAGGCGACAA 62.500 55.000 0.00 0.00 36.28 3.18
3491 3567 6.197364 AGACAGTCAAGAAGTAGGTTATCG 57.803 41.667 2.66 0.00 0.00 2.92
3588 3669 1.452110 CATCAGTCCCACATCGCAAA 58.548 50.000 0.00 0.00 0.00 3.68
3647 3730 1.538849 GCAACTCCTGCCTGTTTTTGG 60.539 52.381 0.00 0.00 46.13 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
805 832 4.609947 TGCAAACTCAACATGACATTCAC 58.390 39.130 0.00 0.00 0.00 3.18
950 980 0.819582 GTCGGTGAATCCCTCGGTTA 59.180 55.000 0.00 0.00 0.00 2.85
951 981 1.595357 GTCGGTGAATCCCTCGGTT 59.405 57.895 0.00 0.00 0.00 4.44
1083 1114 2.847449 TCCCGGAATCACAAATTCCCTA 59.153 45.455 0.73 0.00 43.48 3.53
1118 1149 4.466370 AGAACACGGATTCCTCATCTAACA 59.534 41.667 0.30 0.00 31.67 2.41
1275 1306 1.559368 CATGGGTTTTCATGCCCTCA 58.441 50.000 7.54 0.00 45.06 3.86
1488 1522 4.439057 CTGCATCAGAAATCAAAATGGGG 58.561 43.478 0.00 0.00 32.44 4.96
1523 1559 2.797792 GCCTGCACGACACAAATTTCAA 60.798 45.455 0.00 0.00 0.00 2.69
1565 1601 5.713025 CAATGAACTTACACCAATTCAGGG 58.287 41.667 0.00 0.00 34.71 4.45
1567 1603 4.853196 CGCAATGAACTTACACCAATTCAG 59.147 41.667 0.00 0.00 34.71 3.02
1668 1704 4.401925 AGCTAGGAGTGTTTGCAAAAGAT 58.598 39.130 14.67 1.22 0.00 2.40
1931 1995 4.771577 TCAGTTGCCATCATGGTATTTTGT 59.228 37.500 5.31 0.00 40.46 2.83
1997 2063 8.127481 CCATAGTGGACAGATCAAGACGATCA 62.127 46.154 4.98 0.00 46.08 2.92
2019 2085 4.235372 CCTCCTATCCCAGTAAAGTCCAT 58.765 47.826 0.00 0.00 0.00 3.41
2052 2118 2.599973 CAGAAACAGCAAACTTGTGTGC 59.400 45.455 7.78 7.78 41.22 4.57
2214 2281 3.772619 CGGTTGTCGTATGGGGATT 57.227 52.632 0.00 0.00 0.00 3.01
2320 2387 7.394641 GGAAGAGGATAGAAGTTTCAAAATGGT 59.605 37.037 0.00 0.00 0.00 3.55
2375 2443 7.173863 ACAATGAACACTAACTAACAGTTCG 57.826 36.000 0.00 0.00 40.95 3.95
2496 2566 2.031157 CACGTCCATCCACTTTCCAAAC 60.031 50.000 0.00 0.00 0.00 2.93
2520 2590 0.318441 CAGGACAAGACGGAGCTGAA 59.682 55.000 0.00 0.00 0.00 3.02
2565 2637 9.866655 ATGAACCAAACACAACCATAGATATAT 57.133 29.630 0.00 0.00 0.00 0.86
2566 2638 9.693739 AATGAACCAAACACAACCATAGATATA 57.306 29.630 0.00 0.00 0.00 0.86
2589 2661 3.665409 GTCACGTGCACAAGATCAAAATG 59.335 43.478 18.64 0.00 0.00 2.32
2612 2684 5.163693 GCAGCAGTAACCAAACCGTATTAAT 60.164 40.000 0.00 0.00 0.00 1.40
2850 2923 0.541063 TGTGTGTCGGGAAGCTCCTA 60.541 55.000 0.00 0.00 36.57 2.94
2892 2965 1.822506 TCGTCATCCTTGTCGAGAGT 58.177 50.000 0.00 0.00 38.24 3.24
2906 2979 2.215942 TCTCCTTGTCATCCTCGTCA 57.784 50.000 0.00 0.00 0.00 4.35
2912 2985 2.715046 TGCACATTCTCCTTGTCATCC 58.285 47.619 0.00 0.00 0.00 3.51
2920 2993 2.816087 GTGTCATGTTGCACATTCTCCT 59.184 45.455 11.03 0.00 36.53 3.69
2927 3000 1.494766 CGTCGGTGTCATGTTGCACA 61.495 55.000 15.48 1.44 37.35 4.57
3302 3378 0.317479 GTAACTGCTCGTCCACCAGT 59.683 55.000 0.00 0.00 41.26 4.00
3491 3567 7.042925 GCAATATGGCAATGAAGAAAGAACATC 60.043 37.037 0.00 0.00 0.00 3.06
3588 3669 3.446442 AGAGCATGGGAGAAACAACAT 57.554 42.857 0.00 0.00 0.00 2.71
3647 3730 1.098050 CCTGGTTAGCAGTTGCCATC 58.902 55.000 10.62 0.00 43.38 3.51


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

AutoCloner maintained by Alex Coulton.