Multiple sequence alignment - TraesCS3D01G298900

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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 TraesCS3D01G298900 chr3D 100.000 2828 0 0 1 2828 413678266 413675439 0.000000e+00 5223.0
1 TraesCS3D01G298900 chr3A 94.728 2864 81 29 1 2828 536895433 536898262 0.000000e+00 4388.0
2 TraesCS3D01G298900 chr3B 94.797 2806 69 26 1 2763 539944505 539941734 0.000000e+00 4301.0
3 TraesCS3D01G298900 chr3B 89.394 66 4 3 2763 2828 539941569 539941507 2.340000e-11 80.5
4 TraesCS3D01G298900 chr1A 87.119 295 35 2 1066 1360 520939480 520939771 5.840000e-87 331.0
5 TraesCS3D01G298900 chr1B 86.780 295 36 2 1066 1360 575441280 575441571 2.720000e-85 326.0


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 TraesCS3D01G298900 chr3D 413675439 413678266 2827 True 5223.00 5223 100.0000 1 2828 1 chr3D.!!$R1 2827
1 TraesCS3D01G298900 chr3A 536895433 536898262 2829 False 4388.00 4388 94.7280 1 2828 1 chr3A.!!$F1 2827
2 TraesCS3D01G298900 chr3B 539941507 539944505 2998 True 2190.75 4301 92.0955 1 2828 2 chr3B.!!$R1 2827

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
462 469 1.118965 TCGTTTCACAGAGGCCCAGA 61.119 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2398 0.684153 CAATCAATGGAACGGGGGCT 60.684 55.0 0.0 0.0 0.0 5.19 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
95 96 6.331845 TGTTAATCCGTCTCGCTTTGTATAA 58.668 36.000 0.00 0.00 0.00 0.98
169 170 5.238650 CCGAAGTGTTCTTGTATCAAAACCT 59.761 40.000 0.00 0.00 33.64 3.50
196 197 1.760086 CTGGATCCCGAGCTGGAGT 60.760 63.158 9.90 0.00 42.00 3.85
350 355 3.498397 CCCAATCGAATCCACGGAATTAG 59.502 47.826 0.00 0.00 0.00 1.73
426 431 3.963676 CTAGCAGCCTAGCACTCAG 57.036 57.895 0.00 0.00 35.06 3.35
462 469 1.118965 TCGTTTCACAGAGGCCCAGA 61.119 55.000 0.00 0.00 0.00 3.86
1422 1474 2.394708 CACGTCGATGACAAGTTCTGT 58.605 47.619 12.58 0.00 42.61 3.41
1437 1489 2.022129 CTGTCACTTCGCGTCCACC 61.022 63.158 5.77 0.00 0.00 4.61
1546 1598 0.318120 CATGGGGCTCAACAACAACC 59.682 55.000 0.00 0.00 0.00 3.77
1547 1599 0.188342 ATGGGGCTCAACAACAACCT 59.812 50.000 0.00 0.00 0.00 3.50
1650 1705 3.815569 CTCGGCGCAGGTCTCGATC 62.816 68.421 10.83 0.00 0.00 3.69
1686 1741 2.184020 CTCACCACTCGGCATTCCCA 62.184 60.000 0.00 0.00 34.57 4.37
1955 2010 4.576463 ACTTAATAATGCTCTCCCAAAGCG 59.424 41.667 0.00 0.00 42.83 4.68
2037 2097 3.497031 GGACAAGCCTAACCGCGC 61.497 66.667 0.00 0.00 0.00 6.86
2058 2118 5.060446 GCGCGTTCTAAAAATGTTTTATGCT 59.940 36.000 8.43 0.00 0.00 3.79
2088 2148 6.576185 ACATATGCTTAATTTGGCTTTGGAG 58.424 36.000 1.58 0.00 0.00 3.86
2108 2168 0.100146 GTTGAGCAATGCTAGCTGGC 59.900 55.000 16.23 16.23 43.58 4.85
2193 2253 7.704472 CGGTGTAATGGTTTATTGTGCAATAAT 59.296 33.333 15.44 0.00 41.34 1.28
2361 2427 5.445939 CCGTTCCATTGATTGTACTTTCTCG 60.446 44.000 0.00 0.00 0.00 4.04
2471 2537 7.068470 AGGTTCACTAGCTACCATCTAAACTAC 59.932 40.741 5.43 0.00 34.32 2.73
2529 2595 2.198426 CACACCAAGCCCCCACTT 59.802 61.111 0.00 0.00 0.00 3.16
2575 2644 2.358582 TCATATTTGCACGCATCCCAAG 59.641 45.455 0.00 0.00 0.00 3.61
2781 3015 9.232473 AGGCTAATATTACCTAATAAAAGCAGC 57.768 33.333 12.32 2.80 39.36 5.25
2782 3016 9.232473 GGCTAATATTACCTAATAAAAGCAGCT 57.768 33.333 16.30 0.00 39.36 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 4.397348 CACTTCGGTGGGAAAGGG 57.603 61.111 0.00 0.00 41.88 3.95
169 170 1.207089 CTCGGGATCCAGTGCAGTTTA 59.793 52.381 15.23 0.00 0.00 2.01
196 197 7.123547 GGAGAAGAGAGAGAAAGAGAAATGGTA 59.876 40.741 0.00 0.00 0.00 3.25
350 355 8.195436 TGTCTGTCATACAGCCTAAATTACTAC 58.805 37.037 2.12 0.00 45.54 2.73
426 431 1.907222 CGAGGGGAGGGGGTTTGTAC 61.907 65.000 0.00 0.00 0.00 2.90
462 469 2.288273 GGTCGTGCTACAAGTCTCACTT 60.288 50.000 0.00 0.00 39.39 3.16
538 551 2.088423 TGGTTGAACATATGAACCGCC 58.912 47.619 10.38 6.58 41.85 6.13
540 553 3.944650 TCCATGGTTGAACATATGAACCG 59.055 43.478 12.58 1.84 41.85 4.44
541 554 5.913137 TTCCATGGTTGAACATATGAACC 57.087 39.130 12.58 13.18 39.77 3.62
814 848 0.892755 ACCAATCAAGCATGCACCAG 59.107 50.000 21.98 6.41 0.00 4.00
1422 1474 2.915659 AGGGTGGACGCGAAGTGA 60.916 61.111 15.93 0.00 43.07 3.41
1437 1489 4.227134 CCACCATCTCCGGCGAGG 62.227 72.222 9.30 0.00 42.97 4.63
1546 1598 1.734477 CGCTGTTGACCAGTCCGAG 60.734 63.158 0.00 0.00 43.55 4.63
1547 1599 2.338620 CGCTGTTGACCAGTCCGA 59.661 61.111 0.00 0.00 43.55 4.55
1569 1624 1.091537 CGCCGGTGAAATTGTATGGT 58.908 50.000 10.20 0.00 0.00 3.55
1638 1693 2.959071 GCAGCGATCGAGACCTGC 60.959 66.667 23.30 23.30 43.10 4.85
1686 1741 1.757699 GGAGCCAAGGAGAGTAACGAT 59.242 52.381 0.00 0.00 0.00 3.73
1955 2010 6.981559 ACACTTCTACTAGCTAGCTATTTTGC 59.018 38.462 24.36 0.00 0.00 3.68
2088 2148 0.737219 CCAGCTAGCATTGCTCAACC 59.263 55.000 18.83 2.23 40.44 3.77
2108 2168 4.332637 GCACACACAGCAAGCCCG 62.333 66.667 0.00 0.00 0.00 6.13
2245 2305 8.448008 ACATACCTGGACATGGTTTCATAATAT 58.552 33.333 0.00 0.00 38.88 1.28
2247 2307 6.672593 ACATACCTGGACATGGTTTCATAAT 58.327 36.000 0.00 0.00 38.88 1.28
2292 2358 2.519377 AGCTGTAGCACGTGTAACAA 57.481 45.000 18.38 6.03 45.16 2.83
2293 2359 2.519377 AAGCTGTAGCACGTGTAACA 57.481 45.000 18.38 19.03 45.16 2.41
2332 2398 0.684153 CAATCAATGGAACGGGGGCT 60.684 55.000 0.00 0.00 0.00 5.19
2471 2537 2.092753 AGTCACTATGGCAGAATGGGTG 60.093 50.000 0.00 0.00 35.86 4.61
2575 2644 0.109132 GCCTGTAACTTGCATGTGCC 60.109 55.000 5.94 0.88 41.18 5.01
2704 2773 6.149973 CACCTTCAACTAATCATGTGTGATGT 59.850 38.462 0.00 0.00 44.20 3.06
2772 3006 1.280998 GGTACCCAGGAGCTGCTTTTA 59.719 52.381 4.36 0.00 0.00 1.52
2775 3009 0.842467 AAGGTACCCAGGAGCTGCTT 60.842 55.000 4.36 0.00 0.00 3.91
2779 3013 2.337359 TGTAAAGGTACCCAGGAGCT 57.663 50.000 8.74 0.00 0.00 4.09
2780 3014 3.279434 CAATGTAAAGGTACCCAGGAGC 58.721 50.000 8.74 0.00 0.00 4.70
2781 3015 4.569719 ACAATGTAAAGGTACCCAGGAG 57.430 45.455 8.74 0.00 0.00 3.69
2782 3016 6.645884 ATAACAATGTAAAGGTACCCAGGA 57.354 37.500 8.74 0.00 0.00 3.86
2783 3017 8.437575 AGATATAACAATGTAAAGGTACCCAGG 58.562 37.037 8.74 0.00 0.00 4.45
2784 3018 9.490379 GAGATATAACAATGTAAAGGTACCCAG 57.510 37.037 8.74 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.