Multiple sequence alignment - TraesCS3B01G606100

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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 TraesCS3B01G606100 chr3B 100.000 4036 0 0 1 4036 825318001 825313966 0.000000e+00 7454.0
1 TraesCS3B01G606100 chr3B 98.184 3854 55 11 186 4036 825491911 825495752 0.000000e+00 6715.0
2 TraesCS3B01G606100 chr3B 93.436 2864 155 11 632 3468 824008561 824005704 0.000000e+00 4217.0
3 TraesCS3B01G606100 chr3B 91.029 836 54 9 2633 3468 824048280 824047466 0.000000e+00 1109.0
4 TraesCS3B01G606100 chr3B 90.625 576 30 6 3485 4036 823985455 823984880 0.000000e+00 743.0
5 TraesCS3B01G606100 chr3B 94.964 278 12 2 3585 3862 824027504 824027229 6.190000e-118 435.0
6 TraesCS3B01G606100 chr3B 95.789 190 8 0 1 190 825491440 825491629 1.410000e-79 307.0
7 TraesCS3B01G606100 chr3B 90.141 213 20 1 10 222 824009135 824008924 3.970000e-70 276.0
8 TraesCS3B01G606100 chrUn 96.408 2060 49 6 426 2468 211800407 211802458 0.000000e+00 3371.0
9 TraesCS3B01G606100 chrUn 97.050 1661 48 1 2376 4036 43085119 43083460 0.000000e+00 2795.0
10 TraesCS3B01G606100 chrUn 92.308 273 6 7 1 271 211800017 211800276 1.370000e-99 374.0
11 TraesCS3B01G606100 chrUn 100.000 52 0 0 353 404 211800282 211800333 3.320000e-16 97.1


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 TraesCS3B01G606100 chr3B 825313966 825318001 4035 True 7454.0 7454 100.000000 1 4036 1 chr3B.!!$R4 4035
1 TraesCS3B01G606100 chr3B 825491440 825495752 4312 False 3511.0 6715 96.986500 1 4036 2 chr3B.!!$F1 4035
2 TraesCS3B01G606100 chr3B 824005704 824009135 3431 True 2246.5 4217 91.788500 10 3468 2 chr3B.!!$R5 3458
3 TraesCS3B01G606100 chr3B 824047466 824048280 814 True 1109.0 1109 91.029000 2633 3468 1 chr3B.!!$R3 835
4 TraesCS3B01G606100 chr3B 823984880 823985455 575 True 743.0 743 90.625000 3485 4036 1 chr3B.!!$R1 551
5 TraesCS3B01G606100 chrUn 43083460 43085119 1659 True 2795.0 2795 97.050000 2376 4036 1 chrUn.!!$R1 1660
6 TraesCS3B01G606100 chrUn 211800017 211802458 2441 False 1280.7 3371 96.238667 1 2468 3 chrUn.!!$F1 2467

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
103 106 1.003866 GCGTTAGCAATTAAGCCGGAG 60.004 52.381 5.05 0.0 44.35 4.63 F
304 699 5.975939 GTGTAGTATTCCTTGGTCATACGTC 59.024 44.000 0.00 0.0 0.00 4.34 F
2722 3212 2.029828 AGATTCGCGTTTCTGTCTCACT 60.030 45.455 5.77 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2659 3149 2.322355 ATCTGCCTCGACATCTTTGG 57.678 50.000 0.0 0.0 0.0 3.28 R
2899 3389 3.181429 ACTCTTCTTTTCCTCCAATGCCA 60.181 43.478 0.0 0.0 0.0 4.92 R
3532 4031 0.461693 GGGCTCAGCTCATGTGTCTC 60.462 60.000 0.0 0.0 0.0 3.36 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
38 39 2.030862 GGGTTAACACGTCGCCCA 59.969 61.111 8.10 0.0 39.13 5.36
103 106 1.003866 GCGTTAGCAATTAAGCCGGAG 60.004 52.381 5.05 0.0 44.35 4.63
280 675 6.140110 ACGATTAAACAAAAACGACATGAGG 58.860 36.000 0.00 0.0 0.00 3.86
304 699 5.975939 GTGTAGTATTCCTTGGTCATACGTC 59.024 44.000 0.00 0.0 0.00 4.34
2659 3149 3.842869 CTGAGGAAGCAGGGTACAC 57.157 57.895 0.00 0.0 32.26 2.90
2722 3212 2.029828 AGATTCGCGTTTCTGTCTCACT 60.030 45.455 5.77 0.0 0.00 3.41
2899 3389 4.105697 TGGTGAGAATGGGAAACTAAAGGT 59.894 41.667 0.00 0.0 0.00 3.50
2938 3428 5.190528 AGAAGAGTGAGATTGATGCCCTTAA 59.809 40.000 0.00 0.0 0.00 1.85
3096 3586 9.450807 GTGAATAGTTGGTATTATGCAATGAAC 57.549 33.333 0.00 0.0 30.93 3.18
3213 3709 1.007445 AGGGGTGGATATGGGCCTT 59.993 57.895 4.53 0.0 0.00 4.35
3322 3818 5.238650 CCCCTAAATTAAGGACTATGCAACG 59.761 44.000 0.00 0.0 39.15 4.10
3326 3822 8.621286 CCTAAATTAAGGACTATGCAACGATTT 58.379 33.333 0.00 0.0 39.15 2.17
3368 3864 5.241506 ACATTTGATGACAAAGTACCACAGG 59.758 40.000 0.00 0.0 46.84 4.00
3405 3904 5.885230 TGGACAGATGCTTAGAACATTTG 57.115 39.130 0.00 0.0 36.12 2.32
3500 3999 3.383698 TGATCGGACCCTCTAGTTTCT 57.616 47.619 0.00 0.0 0.00 2.52
3532 4031 1.154016 ACGCGAGATGTCTTGGACG 60.154 57.895 15.93 0.0 34.95 4.79
3611 4110 2.146920 ACCTTCCCTCCTCTACTTCG 57.853 55.000 0.00 0.0 0.00 3.79
3686 4185 3.135348 TCCATGTATGCCTTCTCTCCTTG 59.865 47.826 0.00 0.0 0.00 3.61
3809 4308 2.264794 GCATGAAGGACGACGGGT 59.735 61.111 0.00 0.0 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 106 1.082104 GGCGTATTTATGGCTGCGC 60.082 57.895 0.00 0.00 43.46 6.09
280 675 5.899299 ACGTATGACCAAGGAATACTACAC 58.101 41.667 0.00 0.00 0.00 2.90
2659 3149 2.322355 ATCTGCCTCGACATCTTTGG 57.678 50.000 0.00 0.00 0.00 3.28
2899 3389 3.181429 ACTCTTCTTTTCCTCCAATGCCA 60.181 43.478 0.00 0.00 0.00 4.92
2938 3428 2.104792 TGTAGCTGCTCCTTGTCTTTGT 59.895 45.455 4.91 0.00 0.00 2.83
3128 3624 6.436847 ACATCCCAATGAATGTAACATGAACA 59.563 34.615 0.00 3.70 36.67 3.18
3220 3716 0.325860 ACCTAGGGTCGTGGGCATAA 60.326 55.000 14.81 0.00 0.00 1.90
3322 3818 4.548991 TGTTTGTTTGGCATGCAAAATC 57.451 36.364 22.75 16.02 34.47 2.17
3326 3822 2.703416 TGTTGTTTGTTTGGCATGCAA 58.297 38.095 21.36 4.92 0.00 4.08
3368 3864 4.681744 TCTGTCCATTTTGCTTGTGTTTC 58.318 39.130 0.00 0.00 0.00 2.78
3405 3904 3.937706 AGCTCTCATGCATGTAGTGAAAC 59.062 43.478 25.43 13.51 34.99 2.78
3468 3967 3.069016 GGGTCCGATCAAAACCAAACTTT 59.931 43.478 9.60 0.00 34.62 2.66
3469 3968 2.626266 GGGTCCGATCAAAACCAAACTT 59.374 45.455 9.60 0.00 34.62 2.66
3515 4014 0.863538 CTCGTCCAAGACATCTCGCG 60.864 60.000 0.00 0.00 32.09 5.87
3532 4031 0.461693 GGGCTCAGCTCATGTGTCTC 60.462 60.000 0.00 0.00 0.00 3.36
3611 4110 0.693049 ATGGAGTGTTGGTGAGGGAC 59.307 55.000 0.00 0.00 0.00 4.46
3686 4185 1.680249 GGAGTGTCAATGAGGAAGGCC 60.680 57.143 0.00 0.00 0.00 5.19
3809 4308 3.655486 TCGTCGAAGGTAAAAGATGCAA 58.345 40.909 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.