Multiple sequence alignment - TraesCS3D01G260400

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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 TraesCS3D01G260400 chr3D 100.000 4020 0 0 1 4020 362433781 362429762 0.000000e+00 7424
1 TraesCS3D01G260400 chr3B 95.912 3743 80 16 1 3710 472325442 472321740 0.000000e+00 5997
2 TraesCS3D01G260400 chr3B 86.435 317 15 9 3702 4017 472321486 472321197 5.010000e-84 322
3 TraesCS3D01G260400 chr3B 82.234 197 29 5 3824 4016 828432601 828432407 8.940000e-37 165
4 TraesCS3D01G260400 chr3A 94.894 2742 105 18 1 2719 482978467 482975738 0.000000e+00 4255
5 TraesCS3D01G260400 chr3A 89.147 1161 59 17 2702 3845 482974294 482973184 0.000000e+00 1384
6 TraesCS3D01G260400 chr7A 84.834 211 27 5 3810 4017 410310963 410311171 1.460000e-49 207
7 TraesCS3D01G260400 chr6A 87.500 184 16 2 1437 1614 265783484 265783302 5.270000e-49 206
8 TraesCS3D01G260400 chr6B 88.957 163 10 3 1437 1592 542943513 542943674 1.140000e-45 195
9 TraesCS3D01G260400 chr5A 86.413 184 18 2 1437 1614 162033605 162033423 1.140000e-45 195
10 TraesCS3D01G260400 chr7D 83.500 200 24 7 3819 4015 611462072 611462265 1.150000e-40 178
11 TraesCS3D01G260400 chr7D 84.302 172 20 6 3849 4017 167511573 167511740 1.160000e-35 161
12 TraesCS3D01G260400 chr1D 83.420 193 29 2 3818 4008 437838355 437838546 4.130000e-40 176
13 TraesCS3D01G260400 chr7B 82.051 195 31 3 3825 4017 511942515 511942323 3.210000e-36 163
14 TraesCS3D01G260400 chr7B 81.188 202 33 5 3819 4017 57271410 57271609 1.500000e-34 158
15 TraesCS3D01G260400 chr5D 81.773 203 28 9 3811 4008 398468586 398468784 1.160000e-35 161


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 TraesCS3D01G260400 chr3D 362429762 362433781 4019 True 7424.0 7424 100.0000 1 4020 1 chr3D.!!$R1 4019
1 TraesCS3D01G260400 chr3B 472321197 472325442 4245 True 3159.5 5997 91.1735 1 4017 2 chr3B.!!$R2 4016
2 TraesCS3D01G260400 chr3A 482973184 482978467 5283 True 2819.5 4255 92.0205 1 3845 2 chr3A.!!$R1 3844

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
240 242 2.550606 TGCAAATAACGCGAAGGAGTTT 59.449 40.909 15.93 0.0 37.38 2.66 F
1407 1428 2.738846 GCATCATGCCATACTAGGTTCG 59.261 50.000 0.00 0.0 37.42 3.95 F
2248 2269 2.985847 GCAGGACTGGTGGTTGCC 60.986 66.667 1.01 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1459 1480 4.407296 CCTGGTAGGACAAGCTAGATTTCT 59.593 45.833 0.00 0.00 37.67 2.52 R
3007 4508 0.250166 AGGACCTTCAAACGAACCGG 60.250 55.000 0.00 0.00 0.00 5.28 R
3857 5637 0.319813 AAAAAGCATGCGCAAGGGAC 60.320 50.000 17.11 1.78 42.27 4.46 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
40 41 2.933260 GAGCTAGCTTTGCTACAGGTTC 59.067 50.000 20.42 0.00 41.30 3.62
64 66 3.576861 TCTTATCCCGGATCTGATGTGT 58.423 45.455 0.73 0.00 0.00 3.72
240 242 2.550606 TGCAAATAACGCGAAGGAGTTT 59.449 40.909 15.93 0.00 37.38 2.66
367 369 4.214971 CACATATCTTTACTGCAGCCCATC 59.785 45.833 15.27 0.00 0.00 3.51
379 381 3.455910 TGCAGCCCATCTTATCACTTACT 59.544 43.478 0.00 0.00 0.00 2.24
380 382 4.653801 TGCAGCCCATCTTATCACTTACTA 59.346 41.667 0.00 0.00 0.00 1.82
381 383 4.991687 GCAGCCCATCTTATCACTTACTAC 59.008 45.833 0.00 0.00 0.00 2.73
427 429 7.394077 TGTGATGTCTGGTGAATTGTTGATTAT 59.606 33.333 0.00 0.00 0.00 1.28
498 500 7.663043 AGTTTAATCGAGGACCTCTATTTCT 57.337 36.000 22.43 16.05 30.45 2.52
646 663 6.999272 TGACTGTTCTAGGACACTATATCTCC 59.001 42.308 0.00 0.00 0.00 3.71
738 755 7.777440 AGATTTTCATCCCCTAACAAGATTCTC 59.223 37.037 0.00 0.00 0.00 2.87
927 944 6.403866 TGTTTCTTTGACAAATAGGCATGT 57.596 33.333 0.05 0.00 33.13 3.21
1407 1428 2.738846 GCATCATGCCATACTAGGTTCG 59.261 50.000 0.00 0.00 37.42 3.95
1421 1442 6.540438 ACTAGGTTCGTTCATATTCTTCCA 57.460 37.500 0.00 0.00 0.00 3.53
1849 1870 4.860907 CCTCAGCAATGCAAAAACTATGAC 59.139 41.667 8.35 0.00 0.00 3.06
1955 1976 4.475135 GCTGGCCTCGGGTTCCTC 62.475 72.222 3.32 0.00 0.00 3.71
1973 1994 3.399305 TCCTCTCATGGTATCTAGCTGGA 59.601 47.826 0.82 0.82 0.00 3.86
2248 2269 2.985847 GCAGGACTGGTGGTTGCC 60.986 66.667 1.01 0.00 0.00 4.52
2839 4339 8.598924 CATACTCTACTGTAATTTGCTCTGTTG 58.401 37.037 0.00 0.00 0.00 3.33
3007 4508 2.943653 CCAAAACTCGGTGCGGAC 59.056 61.111 0.00 0.00 0.00 4.79
3282 4783 4.083565 TGCTTTTAACATGGGGTAGAACC 58.916 43.478 0.00 0.00 37.60 3.62
3294 4795 7.962003 ACATGGGGTAGAACCTTGATAGTATAT 59.038 37.037 0.00 0.00 38.64 0.86
3351 4852 7.455058 TCTTTGTAACTGCACCTTTTATCCTA 58.545 34.615 0.00 0.00 0.00 2.94
3439 4941 3.066760 GGATAAATCCTCAACAAAGCCCG 59.933 47.826 1.52 0.00 43.73 6.13
3466 4969 4.285851 GCTAGCCAGCGACAGTTT 57.714 55.556 2.29 0.00 38.22 2.66
3492 4995 5.337652 GCCCTTAGCAGATTATGGTAGGTAG 60.338 48.000 0.05 0.00 42.57 3.18
3544 5047 6.150140 TGTCACTATATCCATCTGACTGATCG 59.850 42.308 0.00 0.00 33.75 3.69
3586 5089 4.696455 CAAAATGTTTTTGGAGTGAGCCT 58.304 39.130 5.08 0.00 0.00 4.58
3640 5143 1.314730 AACCCACGAGCGTCAAAATT 58.685 45.000 0.00 0.00 0.00 1.82
3642 5145 1.679153 ACCCACGAGCGTCAAAATTTT 59.321 42.857 0.00 0.00 0.00 1.82
3643 5146 2.287368 ACCCACGAGCGTCAAAATTTTC 60.287 45.455 0.00 0.00 0.00 2.29
3649 5157 3.664025 CGAGCGTCAAAATTTTCTTCCAC 59.336 43.478 0.00 0.00 0.00 4.02
3680 5198 3.605749 GAACGCCCTAGCACCTGCA 62.606 63.158 0.00 0.00 45.16 4.41
3727 5507 1.676014 GCCACCGTGCTACTGAGAATT 60.676 52.381 0.00 0.00 0.00 2.17
3813 5593 0.171903 GGCTTGTAGCATGCTTGTGG 59.828 55.000 28.02 14.83 44.75 4.17
3845 5625 0.877071 ATTTCTGACAGGCAAGTGCG 59.123 50.000 1.81 0.00 43.26 5.34
3846 5626 1.165907 TTTCTGACAGGCAAGTGCGG 61.166 55.000 1.81 0.00 43.26 5.69
3847 5627 3.052082 CTGACAGGCAAGTGCGGG 61.052 66.667 0.00 0.00 43.26 6.13
3848 5628 4.641645 TGACAGGCAAGTGCGGGG 62.642 66.667 0.00 0.00 43.26 5.73
3972 5753 4.340097 TGTTTCTCGTGACTAGGACTTTCA 59.660 41.667 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.445450 ACATCAGATCCGGGATAAGATCG 59.555 47.826 10.08 12.19 43.03 3.69
64 66 1.226575 CACGAGAGGAACGCGCATA 60.227 57.895 5.73 0.00 45.03 3.14
139 141 1.067142 ACAAGGCGCTCGACTATTTGA 60.067 47.619 7.64 0.00 30.17 2.69
222 224 4.062991 ACAGAAACTCCTTCGCGTTATTT 58.937 39.130 5.77 0.00 39.22 1.40
240 242 3.214328 GCAAGAACAAAGGAGGAACAGA 58.786 45.455 0.00 0.00 0.00 3.41
345 347 3.931907 TGGGCTGCAGTAAAGATATGT 57.068 42.857 16.64 0.00 0.00 2.29
367 369 9.419297 TGCTTAAACAGTGTAGTAAGTGATAAG 57.581 33.333 19.97 9.83 32.62 1.73
379 381 8.462811 TCACATTTCTTTTGCTTAAACAGTGTA 58.537 29.630 0.00 0.00 0.00 2.90
380 382 7.319646 TCACATTTCTTTTGCTTAAACAGTGT 58.680 30.769 0.00 0.00 0.00 3.55
381 383 7.754069 TCACATTTCTTTTGCTTAAACAGTG 57.246 32.000 0.00 0.00 0.00 3.66
498 500 3.191669 CACACAACAGAAGGTACGAACA 58.808 45.455 0.00 0.00 0.00 3.18
587 589 1.477700 GATAACATGGGCTGCAGCAAA 59.522 47.619 37.63 25.84 44.36 3.68
646 663 3.402110 TGTGTGCTGTAGATGTTCAAGG 58.598 45.455 0.00 0.00 0.00 3.61
1260 1277 6.552008 AGGAGGTTCATGAAAATAAACAGGA 58.448 36.000 10.35 0.00 0.00 3.86
1407 1428 7.062605 CACAAACTTGCATGGAAGAATATGAAC 59.937 37.037 30.84 0.00 0.00 3.18
1459 1480 4.407296 CCTGGTAGGACAAGCTAGATTTCT 59.593 45.833 0.00 0.00 37.67 2.52
1849 1870 5.414360 TCTTGCAGTTTAGAGTATCAGCAG 58.586 41.667 0.00 0.00 37.82 4.24
1955 1976 6.994496 TGATTTTTCCAGCTAGATACCATGAG 59.006 38.462 0.00 0.00 0.00 2.90
1973 1994 9.034544 CCTCTTCGATCAAAAACTTTGATTTTT 57.965 29.630 14.14 0.00 41.38 1.94
2839 4339 8.916628 AAAGAAGATAATGATCCTAGCTTTCC 57.083 34.615 0.00 0.00 31.81 3.13
3007 4508 0.250166 AGGACCTTCAAACGAACCGG 60.250 55.000 0.00 0.00 0.00 5.28
3294 4795 6.650807 GTCACAGATCATCAGGAACTTAACAA 59.349 38.462 0.00 0.00 34.60 2.83
3351 4852 4.931914 TCTACCTACTTGCTACAACCTCT 58.068 43.478 0.00 0.00 0.00 3.69
3507 5010 9.784531 ATGGATATAGTGACAATTAACCAGAAG 57.215 33.333 0.00 0.00 0.00 2.85
3508 5011 9.778741 GATGGATATAGTGACAATTAACCAGAA 57.221 33.333 0.00 0.00 0.00 3.02
3509 5012 9.159254 AGATGGATATAGTGACAATTAACCAGA 57.841 33.333 0.00 0.00 0.00 3.86
3544 5047 2.687935 TGGGATTTGAAAGCCTATTCGC 59.312 45.455 12.37 0.00 37.07 4.70
3586 5089 4.169204 TGGGATGGAGGGGCTATATTTA 57.831 45.455 0.00 0.00 0.00 1.40
3813 5593 1.275291 TCAGAAATCCTGTCCCGTGAC 59.725 52.381 0.00 0.00 43.38 3.67
3847 5627 4.410400 CAAGGGACTCGGTGCCCC 62.410 72.222 10.22 2.28 45.38 5.80
3851 5631 3.958147 ATGCGCAAGGGACTCGGTG 62.958 63.158 17.11 0.00 38.49 4.94
3852 5632 3.706373 ATGCGCAAGGGACTCGGT 61.706 61.111 17.11 0.00 38.49 4.69
3853 5633 3.197790 CATGCGCAAGGGACTCGG 61.198 66.667 17.11 0.00 38.49 4.63
3854 5634 3.869272 GCATGCGCAAGGGACTCG 61.869 66.667 17.11 0.00 38.49 4.18
3855 5635 1.589716 AAAGCATGCGCAAGGGACTC 61.590 55.000 17.11 0.00 42.27 3.36
3856 5636 1.181098 AAAAGCATGCGCAAGGGACT 61.181 50.000 17.11 4.51 42.27 3.85
3857 5637 0.319813 AAAAAGCATGCGCAAGGGAC 60.320 50.000 17.11 1.78 42.27 4.46
3954 5735 7.313646 TCTTATTTGAAAGTCCTAGTCACGAG 58.686 38.462 0.00 0.00 0.00 4.18
3955 5736 7.223260 TCTTATTTGAAAGTCCTAGTCACGA 57.777 36.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.