Multiple sequence alignment - TraesCS1B01G460400

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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 TraesCS1B01G460400 chr1B 100.000 1806 0 0 1 1806 673925324 673927129 0.000000e+00 3336
1 TraesCS1B01G460400 chr1B 93.401 1864 49 36 1 1800 673892577 673894430 0.000000e+00 2693
2 TraesCS1B01G460400 chr1B 86.450 893 83 18 913 1798 673915101 673915962 0.000000e+00 944
3 TraesCS1B01G460400 chr1B 84.778 946 94 31 628 1536 673889253 673890185 0.000000e+00 904
4 TraesCS1B01G460400 chr1B 100.000 355 0 0 2054 2408 673927377 673927731 0.000000e+00 656
5 TraesCS1B01G460400 chr1B 81.081 814 110 35 624 1406 673855505 673856305 5.690000e-171 610
6 TraesCS1B01G460400 chr1B 89.513 267 17 8 32 295 673917674 673917932 6.420000e-86 327
7 TraesCS1B01G460400 chr1B 93.382 136 4 3 1534 1669 673890301 673890431 1.890000e-46 196
8 TraesCS1B01G460400 chr1D 88.022 1845 120 54 32 1798 483901380 483903201 0.000000e+00 2089
9 TraesCS1B01G460400 chr1D 80.216 925 126 38 522 1406 483865024 483865931 2.020000e-180 641
10 TraesCS1B01G460400 chr1D 81.784 807 108 25 624 1406 483680698 483681489 7.260000e-180 640
11 TraesCS1B01G460400 chr1D 82.698 630 84 17 830 1455 483895801 483896409 9.800000e-149 536
12 TraesCS1B01G460400 chr1A 91.217 1389 73 24 460 1806 580925256 580926637 0.000000e+00 1844
13 TraesCS1B01G460400 chr1A 84.249 546 72 13 830 1371 580893696 580894231 9.870000e-144 520
14 TraesCS1B01G460400 chr1A 92.394 355 21 1 2054 2408 580926679 580927027 3.570000e-138 501
15 TraesCS1B01G460400 chr1A 82.952 393 30 20 32 393 580924870 580925256 1.070000e-83 320


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 TraesCS1B01G460400 chr1B 673925324 673927731 2407 False 1996.000000 3336 100.000000 1 2408 2 chr1B.!!$F4 2407
1 TraesCS1B01G460400 chr1B 673889253 673894430 5177 False 1264.333333 2693 90.520333 1 1800 3 chr1B.!!$F2 1799
2 TraesCS1B01G460400 chr1B 673915101 673917932 2831 False 635.500000 944 87.981500 32 1798 2 chr1B.!!$F3 1766
3 TraesCS1B01G460400 chr1B 673855505 673856305 800 False 610.000000 610 81.081000 624 1406 1 chr1B.!!$F1 782
4 TraesCS1B01G460400 chr1D 483901380 483903201 1821 False 2089.000000 2089 88.022000 32 1798 1 chr1D.!!$F4 1766
5 TraesCS1B01G460400 chr1D 483865024 483865931 907 False 641.000000 641 80.216000 522 1406 1 chr1D.!!$F2 884
6 TraesCS1B01G460400 chr1D 483680698 483681489 791 False 640.000000 640 81.784000 624 1406 1 chr1D.!!$F1 782
7 TraesCS1B01G460400 chr1D 483895801 483896409 608 False 536.000000 536 82.698000 830 1455 1 chr1D.!!$F3 625
8 TraesCS1B01G460400 chr1A 580924870 580927027 2157 False 888.333333 1844 88.854333 32 2408 3 chr1A.!!$F2 2376
9 TraesCS1B01G460400 chr1A 580893696 580894231 535 False 520.000000 520 84.249000 830 1371 1 chr1A.!!$F1 541

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
832 4212 0.88649 CAGATTCCCGGCATGCCTAC 60.886 60.0 33.07 16.96 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2388 5926 0.469144 TTGGGGTTGACCAAGAAGGC 60.469 55.0 2.12 0.0 45.19 4.35 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
789 4169 4.918201 CCGATGGAGGCTTCCCGC 62.918 72.222 13.07 3.17 43.33 6.13
818 4198 2.124819 CTGCCGCTGCCTCAGATT 60.125 61.111 9.39 0.00 36.33 2.40
832 4212 0.886490 CAGATTCCCGGCATGCCTAC 60.886 60.000 33.07 16.96 0.00 3.18
840 4249 2.683475 GCATGCCTACCCCCACTT 59.317 61.111 6.36 0.00 0.00 3.16
843 4252 1.084842 ATGCCTACCCCCACTTCCT 59.915 57.895 0.00 0.00 0.00 3.36
1038 4447 0.034896 ACCTCACCAACATCACGGTC 59.965 55.000 0.00 0.00 31.41 4.79
1262 4692 0.937304 CTGACCTTGTTCGGTGTGTG 59.063 55.000 0.00 0.00 37.42 3.82
1266 4696 2.162809 GACCTTGTTCGGTGTGTGTTTT 59.837 45.455 0.00 0.00 37.42 2.43
1267 4697 3.345414 ACCTTGTTCGGTGTGTGTTTTA 58.655 40.909 0.00 0.00 35.52 1.52
1268 4698 3.127376 ACCTTGTTCGGTGTGTGTTTTAC 59.873 43.478 0.00 0.00 35.52 2.01
1504 4952 8.932434 AGTATCAAAGACAGATATCAGCTAGA 57.068 34.615 5.32 2.23 31.26 2.43
1513 4961 5.777732 ACAGATATCAGCTAGAGTTTAGGGG 59.222 44.000 5.32 0.00 0.00 4.79
1729 5219 0.809636 ATATGCGTGCGTGCTTGCTA 60.810 50.000 9.56 2.29 35.36 3.49
1751 5242 3.118884 AGCTCCGTTCGTATTGGTACATT 60.119 43.478 0.00 0.00 39.30 2.71
1767 5259 7.083875 TGGTACATTAAAGCTTTGTAGATGC 57.916 36.000 22.02 6.85 0.00 3.91
2095 5587 7.537602 AAATAAAAATGTTACGTGCGTGTAC 57.462 32.000 7.55 6.24 0.00 2.90
2130 5622 2.093288 CCTGGCAGCTCTAAATCTGTCA 60.093 50.000 9.56 0.00 41.98 3.58
2141 5633 5.016831 TCTAAATCTGTCACCAGCTAGACA 58.983 41.667 13.23 13.23 42.06 3.41
2237 5775 5.894298 ACATAGCTGGACTCCATGAATTA 57.106 39.130 0.00 0.00 30.82 1.40
2239 5777 6.236409 ACATAGCTGGACTCCATGAATTATG 58.764 40.000 0.00 5.79 36.50 1.90
2266 5804 2.037901 TGATCATGAGAGCAGAGGGAC 58.962 52.381 0.09 0.00 34.77 4.46
2294 5832 1.554617 AGAGCAAGAGAGGGAAAGAGC 59.445 52.381 0.00 0.00 0.00 4.09
2303 5841 0.178891 AGGGAAAGAGCAGAGGGACA 60.179 55.000 0.00 0.00 0.00 4.02
2319 5857 2.613223 GGGACACAAAGCAGAGTAGGAC 60.613 54.545 0.00 0.00 0.00 3.85
2322 5860 2.700897 ACACAAAGCAGAGTAGGACAGT 59.299 45.455 0.00 0.00 0.00 3.55
2354 5892 6.361768 AAAACTAGAGGGGTAAAGAGAGTG 57.638 41.667 0.00 0.00 0.00 3.51
2364 5902 3.367910 GGTAAAGAGAGTGAGGCAGACAG 60.368 52.174 0.00 0.00 0.00 3.51
2388 5926 0.828677 CCTCCCTAACCTACCAACGG 59.171 60.000 0.00 0.00 0.00 4.44
2396 5934 0.036306 ACCTACCAACGGCCTTCTTG 59.964 55.000 0.00 0.00 0.00 3.02
2403 5941 0.822121 AACGGCCTTCTTGGTCAACC 60.822 55.000 0.00 0.00 41.50 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.903682 CTTTCTTGACTTGTGTATCATTTCATT 57.096 29.630 0.00 0.00 0.00 2.57
3 4 8.450578 ACTTTCTTGACTTGTGTATCATTTCA 57.549 30.769 0.00 0.00 0.00 2.69
832 4212 1.348775 GGGATCTGAGGAAGTGGGGG 61.349 65.000 0.00 0.00 0.00 5.40
840 4249 2.066393 CAAGCCGGGGATCTGAGGA 61.066 63.158 2.18 0.00 0.00 3.71
843 4252 3.797353 GGCAAGCCGGGGATCTGA 61.797 66.667 2.18 0.00 0.00 3.27
1245 4654 1.375551 AACACACACCGAACAAGGTC 58.624 50.000 0.00 0.00 43.89 3.85
1255 4685 8.120465 GCACATATATACAGTAAAACACACACC 58.880 37.037 0.00 0.00 0.00 4.16
1262 4692 9.046296 AGAAGCAGCACATATATACAGTAAAAC 57.954 33.333 0.00 0.00 0.00 2.43
1266 4696 8.421002 TCAAAGAAGCAGCACATATATACAGTA 58.579 33.333 0.00 0.00 0.00 2.74
1267 4697 7.275183 TCAAAGAAGCAGCACATATATACAGT 58.725 34.615 0.00 0.00 0.00 3.55
1268 4698 7.719778 TCAAAGAAGCAGCACATATATACAG 57.280 36.000 0.00 0.00 0.00 2.74
1486 4934 7.232534 CCCTAAACTCTAGCTGATATCTGTCTT 59.767 40.741 10.85 1.37 0.00 3.01
1490 4938 5.777732 ACCCCTAAACTCTAGCTGATATCTG 59.222 44.000 3.98 4.68 0.00 2.90
1504 4952 3.095332 GAGACGTCCTAACCCCTAAACT 58.905 50.000 13.01 0.00 0.00 2.66
1513 4961 5.470777 AGCTACATATGAGAGACGTCCTAAC 59.529 44.000 13.01 2.35 0.00 2.34
1567 5038 4.142381 TGACGGAGATCTTACATGACTGTG 60.142 45.833 0.00 0.00 36.79 3.66
1729 5219 1.820519 TGTACCAATACGAACGGAGCT 59.179 47.619 0.00 0.00 33.60 4.09
1738 5228 8.875803 TCTACAAAGCTTTAATGTACCAATACG 58.124 33.333 12.25 0.00 33.60 3.06
1751 5242 6.172630 TGAGTCATGCATCTACAAAGCTTTA 58.827 36.000 12.25 0.00 0.00 1.85
1767 5259 4.999950 AGAGGTAGCAAAAGTTGAGTCATG 59.000 41.667 0.00 0.00 0.00 3.07
2075 5567 3.311871 TGGTACACGCACGTAACATTTTT 59.688 39.130 0.00 0.00 34.15 1.94
2076 5568 2.871022 TGGTACACGCACGTAACATTTT 59.129 40.909 0.00 0.00 34.15 1.82
2077 5569 2.481854 TGGTACACGCACGTAACATTT 58.518 42.857 0.00 0.00 34.15 2.32
2078 5570 2.151881 TGGTACACGCACGTAACATT 57.848 45.000 0.00 0.00 34.15 2.71
2079 5571 3.890145 TGGTACACGCACGTAACAT 57.110 47.368 0.00 0.00 34.15 2.71
2095 5587 0.947244 GCCAGGATAACGAGCAATGG 59.053 55.000 0.00 0.00 0.00 3.16
2130 5622 8.409358 AAAATCTTTATTTGTGTCTAGCTGGT 57.591 30.769 0.00 0.00 35.46 4.00
2211 5749 3.118629 TCATGGAGTCCAGCTATGTTGTC 60.119 47.826 18.69 0.00 36.75 3.18
2237 5775 2.554462 GCTCTCATGATCAAGCATGCAT 59.446 45.455 21.98 4.57 44.08 3.96
2239 5777 1.947456 TGCTCTCATGATCAAGCATGC 59.053 47.619 14.39 10.51 44.08 4.06
2266 5804 1.805345 CCTCTCTTGCTCTGCTTTGTG 59.195 52.381 0.00 0.00 0.00 3.33
2294 5832 1.071385 ACTCTGCTTTGTGTCCCTCTG 59.929 52.381 0.00 0.00 0.00 3.35
2303 5841 2.965831 TCACTGTCCTACTCTGCTTTGT 59.034 45.455 0.00 0.00 0.00 2.83
2334 5872 4.325501 CCTCACTCTCTTTACCCCTCTAGT 60.326 50.000 0.00 0.00 0.00 2.57
2364 5902 1.343431 GGTAGGTTAGGGAGGGTGGC 61.343 65.000 0.00 0.00 0.00 5.01
2388 5926 0.469144 TTGGGGTTGACCAAGAAGGC 60.469 55.000 2.12 0.00 45.19 4.35


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

AutoCloner maintained by Alex Coulton.