Multiple sequence alignment - TraesCS3A01G081700

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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 TraesCS3A01G081700 chr3A 100.000 7839 0 0 1 7839 52725292 52733130 0.000000e+00 14477
1 TraesCS3A01G081700 chr3A 99.082 7845 65 4 1 7839 52771590 52779433 0.000000e+00 14081
2 TraesCS3A01G081700 chr3A 98.536 7853 78 8 1 7839 52819472 52827301 0.000000e+00 13830
3 TraesCS3A01G081700 chr3A 98.760 4679 37 4 3162 7839 52636720 52641378 0.000000e+00 8299
4 TraesCS3A01G081700 chr3A 99.229 4022 31 0 3574 7595 52590579 52594600 0.000000e+00 7256
5 TraesCS3A01G081700 chr3A 99.359 3900 25 0 3940 7839 52683099 52686998 0.000000e+00 7064
6 TraesCS3A01G081700 chr3A 99.401 2503 12 1 1 2500 52633443 52635945 0.000000e+00 4536
7 TraesCS3A01G081700 chr3A 99.351 2156 10 2 984 3136 52588084 52590238 0.000000e+00 3901
8 TraesCS3A01G081700 chr3A 99.939 1650 1 0 1 1650 52679461 52681110 0.000000e+00 3042
9 TraesCS3A01G081700 chr3A 99.449 1452 5 1 1688 3136 52681121 52682572 0.000000e+00 2634
10 TraesCS3A01G081700 chr3A 99.494 988 5 0 1 988 52581831 52582818 0.000000e+00 1797
11 TraesCS3A01G081700 chr3A 99.029 206 2 0 7634 7839 52594595 52594800 3.460000e-98 370
12 TraesCS3A01G081700 chr3D 91.780 2798 162 36 338 3095 41034253 41037022 0.000000e+00 3831
13 TraesCS3A01G081700 chr3D 90.152 2904 263 21 3248 6138 40912683 40915576 0.000000e+00 3757
14 TraesCS3A01G081700 chr3D 91.415 2749 203 21 3423 6154 41037289 41040021 0.000000e+00 3738
15 TraesCS3A01G081700 chr3D 90.474 2341 179 27 311 2630 40909774 40912091 0.000000e+00 3048
16 TraesCS3A01G081700 chr3D 95.856 724 24 3 6133 6855 41040031 41040749 0.000000e+00 1166
17 TraesCS3A01G081700 chr3D 93.646 724 42 2 6133 6855 40915602 40916322 0.000000e+00 1079
18 TraesCS3A01G081700 chr3D 88.542 576 41 16 2676 3250 40912090 40912641 0.000000e+00 675
19 TraesCS3A01G081700 chr3D 86.985 607 53 10 7017 7616 41040748 41041335 0.000000e+00 660
20 TraesCS3A01G081700 chr3D 80.994 463 29 28 7017 7470 40916321 40916733 5.910000e-81 313
21 TraesCS3A01G081700 chr3D 91.026 156 14 0 77 232 40909617 40909772 2.220000e-50 211
22 TraesCS3A01G081700 chr3D 87.333 150 14 5 3108 3252 41036990 41037139 4.870000e-37 167
23 TraesCS3A01G081700 chr3D 93.407 91 3 2 1 90 40909226 40909314 1.770000e-26 132
24 TraesCS3A01G081700 chrUn 99.673 1223 0 2 1024 2243 423824818 423823597 0.000000e+00 2233
25 TraesCS3A01G081700 chr2D 79.897 388 75 1 2637 3024 2891466 2891850 1.670000e-71 281
26 TraesCS3A01G081700 chr2D 92.655 177 11 2 6853 7029 83081898 83081724 3.630000e-63 254
27 TraesCS3A01G081700 chr2B 79.949 389 73 3 2637 3024 8237360 8236976 1.670000e-71 281
28 TraesCS3A01G081700 chr2B 79.692 389 74 3 2637 3024 8081894 8081510 7.750000e-70 276
29 TraesCS3A01G081700 chr2B 80.952 273 50 2 6561 6832 7909049 7908778 1.710000e-51 215
30 TraesCS3A01G081700 chr2B 80.586 273 51 2 6561 6832 8078783 8078512 7.970000e-50 209
31 TraesCS3A01G081700 chr2B 77.113 284 57 4 2156 2435 7912866 7912587 2.930000e-34 158
32 TraesCS3A01G081700 chr2B 76.056 284 60 4 2156 2435 7803519 7803240 2.950000e-29 141
33 TraesCS3A01G081700 chr1D 92.179 179 14 0 6852 7030 206955703 206955525 3.630000e-63 254
34 TraesCS3A01G081700 chr6A 93.023 172 12 0 6849 7020 276304330 276304159 1.310000e-62 252
35 TraesCS3A01G081700 chr1A 87.864 206 21 3 6853 7056 233421341 233421544 1.020000e-58 239


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 TraesCS3A01G081700 chr3A 52725292 52733130 7838 False 14477.000000 14477 100.000000 1 7839 1 chr3A.!!$F2 7838
1 TraesCS3A01G081700 chr3A 52771590 52779433 7843 False 14081.000000 14081 99.082000 1 7839 1 chr3A.!!$F3 7838
2 TraesCS3A01G081700 chr3A 52819472 52827301 7829 False 13830.000000 13830 98.536000 1 7839 1 chr3A.!!$F4 7838
3 TraesCS3A01G081700 chr3A 52633443 52641378 7935 False 6417.500000 8299 99.080500 1 7839 2 chr3A.!!$F6 7838
4 TraesCS3A01G081700 chr3A 52679461 52686998 7537 False 4246.666667 7064 99.582333 1 7839 3 chr3A.!!$F7 7838
5 TraesCS3A01G081700 chr3A 52588084 52594800 6716 False 3842.333333 7256 99.203000 984 7839 3 chr3A.!!$F5 6855
6 TraesCS3A01G081700 chr3A 52581831 52582818 987 False 1797.000000 1797 99.494000 1 988 1 chr3A.!!$F1 987
7 TraesCS3A01G081700 chr3D 41034253 41041335 7082 False 1912.400000 3831 90.673800 338 7616 5 chr3D.!!$F2 7278
8 TraesCS3A01G081700 chr3D 40909226 40916733 7507 False 1316.428571 3757 89.748714 1 7470 7 chr3D.!!$F1 7469
9 TraesCS3A01G081700 chrUn 423823597 423824818 1221 True 2233.000000 2233 99.673000 1024 2243 1 chrUn.!!$R1 1219
10 TraesCS3A01G081700 chr2B 8078512 8081894 3382 True 242.500000 276 80.139000 2637 6832 2 chr2B.!!$R4 4195

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
2561 2941 3.717707 TCTTAGTATGCATGCCTTCGAC 58.282 45.455 16.68 5.86 0.00 4.20 F
4755 5452 1.303724 CCAACACCCCGCCATTGTA 60.304 57.895 0.00 0.00 0.00 2.41 F
5857 6572 4.635223 TGATCTTTTATCTGGATCTGCCG 58.365 43.478 0.00 0.00 40.66 5.69 F
6332 7917 1.479323 GTAGGCGGACCAACACTATCA 59.521 52.381 0.00 0.00 39.06 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3572 4116 6.942532 TTAGTCTTTTGAGCTGTTGATGTT 57.057 33.333 0.00 0.0 0.00 2.71 R
6332 7917 1.028330 CGCCTGCCATCACACTCAAT 61.028 55.000 0.00 0.0 0.00 2.57 R
6801 8689 0.462225 TAGGCTCTCGACAGTCTCCG 60.462 60.000 0.00 0.0 28.82 4.63 R
7773 9839 6.495181 GGGATCTAGTATCCAATCTCTTGTCA 59.505 42.308 17.64 0.0 39.93 3.58 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
2561 2941 3.717707 TCTTAGTATGCATGCCTTCGAC 58.282 45.455 16.68 5.86 0.00 4.20
4755 5452 1.303724 CCAACACCCCGCCATTGTA 60.304 57.895 0.00 0.00 0.00 2.41
4766 5463 5.163131 ACCCCGCCATTGTAGTTAATTAGAT 60.163 40.000 0.00 0.00 0.00 1.98
5128 5830 8.478775 TGAACGTAGGTAGTACTCTAGGTATA 57.521 38.462 14.03 6.81 34.69 1.47
5633 6347 8.102047 TGGATTGTGATTTGCATATTCCTTTTT 58.898 29.630 6.43 0.00 38.34 1.94
5857 6572 4.635223 TGATCTTTTATCTGGATCTGCCG 58.365 43.478 0.00 0.00 40.66 5.69
5909 6624 6.241207 TGAGCACAAACAAGCTAATAGAAC 57.759 37.500 0.00 0.00 42.04 3.01
6332 7917 1.479323 GTAGGCGGACCAACACTATCA 59.521 52.381 0.00 0.00 39.06 2.15
6801 8689 5.756347 TGTACACAACAAGTACACATCTTCC 59.244 40.000 2.34 0.00 44.86 3.46
6886 8937 9.947433 TCCGTTCCTAAATATTTGTCTTTCTAA 57.053 29.630 11.05 0.00 0.00 2.10
7773 9839 4.638421 TGTCTTCATTGTTGGTTTCGTCTT 59.362 37.500 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3572 4116 6.942532 TTAGTCTTTTGAGCTGTTGATGTT 57.057 33.333 0.00 0.0 0.00 2.71
4766 5463 4.285775 TGTGGTGGATGTATCTTGAACTCA 59.714 41.667 0.00 0.0 0.00 3.41
5128 5830 5.887598 TGCATCAAATACTAGCCAACTTCAT 59.112 36.000 0.00 0.0 0.00 2.57
5633 6347 2.266279 AGGAGTTGTAGGCTAAGGCAA 58.734 47.619 0.00 0.0 40.87 4.52
5663 6377 8.331931 ACCTGATTTGTATTGAACCCTAGATA 57.668 34.615 0.00 0.0 0.00 1.98
5857 6572 7.159322 TGTTTCTAGATGAAGACCTACTGAC 57.841 40.000 0.00 0.0 35.89 3.51
5909 6624 6.145535 GGCACAAAAGAAAATAGTGAGACAG 58.854 40.000 0.00 0.0 32.14 3.51
6332 7917 1.028330 CGCCTGCCATCACACTCAAT 61.028 55.000 0.00 0.0 0.00 2.57
6801 8689 0.462225 TAGGCTCTCGACAGTCTCCG 60.462 60.000 0.00 0.0 28.82 4.63
6886 8937 9.214957 TCGTATGTAGTCATTTGTTGAAATCTT 57.785 29.630 0.00 0.0 35.70 2.40
7085 9146 4.104102 ACATGACTCACTGGGGAAAGTAAA 59.896 41.667 0.00 0.0 0.00 2.01
7773 9839 6.495181 GGGATCTAGTATCCAATCTCTTGTCA 59.505 42.308 17.64 0.0 39.93 3.58


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

AutoCloner maintained by Alex Coulton.