Multiple sequence alignment - TraesCS3A01G080100

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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 TraesCS3A01G080100 chr3A 100.000 2273 0 0 454 2726 51868198 51870470 0.000000e+00 4198
1 TraesCS3A01G080100 chr3A 97.800 2273 48 2 454 2726 633112276 633114546 0.000000e+00 3919
2 TraesCS3A01G080100 chr3A 100.000 128 0 0 1 128 51867745 51867872 1.260000e-58 237
3 TraesCS3A01G080100 chr4D 98.374 2275 34 2 454 2726 123300913 123303186 0.000000e+00 3993
4 TraesCS3A01G080100 chr4D 97.405 2274 52 5 454 2726 123717533 123719800 0.000000e+00 3866
5 TraesCS3A01G080100 chr7D 98.110 2275 40 2 454 2726 203516501 203518774 0.000000e+00 3960
6 TraesCS3A01G080100 chr7D 96.124 129 4 1 1 128 306908842 306908970 2.750000e-50 209
7 TraesCS3A01G080100 chr7B 98.022 2275 42 3 454 2726 644468466 644470739 0.000000e+00 3949
8 TraesCS3A01G080100 chr7A 98.021 2274 43 2 454 2726 60122542 60120270 0.000000e+00 3949
9 TraesCS3A01G080100 chr7A 95.349 129 5 1 1 128 211274390 211274262 1.280000e-48 204
10 TraesCS3A01G080100 chr6B 97.713 2274 50 2 454 2726 306994964 306992692 0.000000e+00 3910
11 TraesCS3A01G080100 chr6B 97.656 128 3 0 1 128 306995169 306995042 1.270000e-53 220
12 TraesCS3A01G080100 chr1B 97.449 2274 55 3 454 2726 638699639 638697368 0.000000e+00 3875
13 TraesCS3A01G080100 chr1B 95.349 129 5 1 1 128 638699845 638699717 1.280000e-48 204
14 TraesCS3A01G080100 chr2B 97.405 2274 57 2 454 2726 391111816 391109544 0.000000e+00 3871
15 TraesCS3A01G080100 chr2B 95.312 128 4 1 1 128 391112019 391111894 4.600000e-48 202
16 TraesCS3A01G080100 chrUn 96.875 128 4 0 1 128 225929074 225929201 5.910000e-52 215
17 TraesCS3A01G080100 chrUn 96.875 128 3 1 1 128 393315426 393315300 2.130000e-51 213
18 TraesCS3A01G080100 chrUn 96.094 128 3 1 1 128 454685499 454685374 9.890000e-50 207
19 TraesCS3A01G080100 chr3D 96.094 128 2 1 1 128 501932984 501932860 3.560000e-49 206


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 TraesCS3A01G080100 chr3A 51867745 51870470 2725 False 2217.5 4198 100.0000 1 2726 2 chr3A.!!$F2 2725
1 TraesCS3A01G080100 chr3A 633112276 633114546 2270 False 3919.0 3919 97.8000 454 2726 1 chr3A.!!$F1 2272
2 TraesCS3A01G080100 chr4D 123300913 123303186 2273 False 3993.0 3993 98.3740 454 2726 1 chr4D.!!$F1 2272
3 TraesCS3A01G080100 chr4D 123717533 123719800 2267 False 3866.0 3866 97.4050 454 2726 1 chr4D.!!$F2 2272
4 TraesCS3A01G080100 chr7D 203516501 203518774 2273 False 3960.0 3960 98.1100 454 2726 1 chr7D.!!$F1 2272
5 TraesCS3A01G080100 chr7B 644468466 644470739 2273 False 3949.0 3949 98.0220 454 2726 1 chr7B.!!$F1 2272
6 TraesCS3A01G080100 chr7A 60120270 60122542 2272 True 3949.0 3949 98.0210 454 2726 1 chr7A.!!$R1 2272
7 TraesCS3A01G080100 chr6B 306992692 306995169 2477 True 2065.0 3910 97.6845 1 2726 2 chr6B.!!$R1 2725
8 TraesCS3A01G080100 chr1B 638697368 638699845 2477 True 2039.5 3875 96.3990 1 2726 2 chr1B.!!$R1 2725
9 TraesCS3A01G080100 chr2B 391109544 391112019 2475 True 2036.5 3871 96.3585 1 2726 2 chr2B.!!$R1 2725

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
669 671 0.806492 TTGTTACGCGCGATATGCCA 60.806 50.0 39.36 19.56 42.08 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2552 2559 0.394488 TGACAAACGAACAAGGGGCA 60.394 50.0 0.0 0.0 0.0 5.36 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
57 58 3.568007 CGACCTTTCATTCCCTTGTTTCA 59.432 43.478 0.00 0.00 0.00 2.69
92 94 4.994756 CCCCACAAGCACCCCCAC 62.995 72.222 0.00 0.00 0.00 4.61
669 671 0.806492 TTGTTACGCGCGATATGCCA 60.806 50.000 39.36 19.56 42.08 4.92
675 677 2.521771 GCGCGATATGCCAACGACA 61.522 57.895 12.10 0.00 42.08 4.35
770 772 1.982958 GGTCTGAACCTTTGGGTAGGA 59.017 52.381 0.00 0.00 46.67 2.94
1342 1345 5.946377 ATCAAAAAGATACTCCGAAGGCTTT 59.054 36.000 0.00 0.00 41.54 3.51
1374 1377 3.131400 GTCTCATTAGCCGAAGAAGACCT 59.869 47.826 0.00 0.00 31.11 3.85
1435 1438 6.620877 ACAGAGACATAGTAAATTGGTCCA 57.379 37.500 0.00 0.00 0.00 4.02
1477 1480 0.895530 GTCCTACTACAGGTGCTGCA 59.104 55.000 0.00 0.00 45.71 4.41
1479 1482 2.093447 GTCCTACTACAGGTGCTGCAAT 60.093 50.000 2.77 0.00 45.71 3.56
1563 1567 1.340889 GCCCACAAGCACAAATCTTCA 59.659 47.619 0.00 0.00 0.00 3.02
1910 1917 1.064389 GCCCTCCATGCCTCTTTAGTT 60.064 52.381 0.00 0.00 0.00 2.24
1922 1929 7.923414 TGCCTCTTTAGTTTTTCTAATCCTC 57.077 36.000 0.00 0.00 38.27 3.71
1926 1933 7.554476 CCTCTTTAGTTTTTCTAATCCTCAGGG 59.446 40.741 0.00 0.00 38.27 4.45
2210 2217 2.731571 GCACCTATCAGGCCCGACA 61.732 63.158 0.00 0.00 39.63 4.35
2284 2291 0.257039 CAGGAGGTTGGCTGCCTATT 59.743 55.000 21.03 5.03 36.29 1.73
2378 2385 6.860790 TTCTATATATATGGGTCCGTGCAA 57.139 37.500 5.44 0.00 0.00 4.08
2394 2401 4.614555 GTGCAACATTTCCACGATATCA 57.385 40.909 3.12 0.00 36.32 2.15
2452 2459 4.145052 TCTTGCCTCTATCATTAGCTCGA 58.855 43.478 0.00 0.00 0.00 4.04
2552 2559 0.546598 CTACTCCCCGAAAATGCCCT 59.453 55.000 0.00 0.00 0.00 5.19
2571 2578 0.394488 TGCCCCTTGTTCGTTTGTCA 60.394 50.000 0.00 0.00 0.00 3.58
2594 2601 2.503765 TGGGGATTCATTGCTCGTTCTA 59.496 45.455 0.00 0.00 0.00 2.10
2693 2700 3.846405 AACACCCTCTCCTCCGGCA 62.846 63.158 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 94 2.167398 TTTCTGGTCTCCCCTTCGCG 62.167 60.000 0.00 0.00 0.00 5.87
669 671 3.698040 ACGATTCCCAGTAGTATGTCGTT 59.302 43.478 0.00 0.00 37.77 3.85
675 677 2.698797 CACCCACGATTCCCAGTAGTAT 59.301 50.000 0.00 0.00 0.00 2.12
726 728 4.163458 GGATTGTAGGAAGTGGGTGATACA 59.837 45.833 0.00 0.00 0.00 2.29
770 772 3.744940 ATGGTTGTTGATCCTGTGGAT 57.255 42.857 0.00 0.00 46.28 3.41
844 846 0.750546 TGTATGGGAGTCGTCCTCGG 60.751 60.000 0.00 0.00 43.36 4.63
1182 1184 2.885113 CCCGATCGTGAGACTGCA 59.115 61.111 15.09 0.00 46.97 4.41
1342 1345 1.964223 GCTAATGAGACCTCGATCCCA 59.036 52.381 0.00 0.00 0.00 4.37
1435 1438 1.299926 GACTTATCGCGATGCCCGT 60.300 57.895 31.05 20.27 41.15 5.28
1477 1480 4.692155 CGTTCGGACTTGGTAAAGGTTATT 59.308 41.667 0.00 0.00 37.76 1.40
1479 1482 3.320541 TCGTTCGGACTTGGTAAAGGTTA 59.679 43.478 0.00 0.00 37.76 2.85
1563 1567 5.148651 ACTTTAGGATTATATTCCGCGCT 57.851 39.130 5.56 0.00 40.94 5.92
1910 1917 5.480422 GGAAAAAGCCCTGAGGATTAGAAAA 59.520 40.000 0.00 0.00 42.30 2.29
1922 1929 4.813750 ATGAATGAAGGAAAAAGCCCTG 57.186 40.909 0.00 0.00 33.55 4.45
1926 1933 5.376537 CGCAAAATGAATGAAGGAAAAAGC 58.623 37.500 0.00 0.00 0.00 3.51
2098 2105 2.619931 CCCCCTTTTCCTTTGACCAAT 58.380 47.619 0.00 0.00 0.00 3.16
2192 2199 2.109181 GTCGGGCCTGATAGGTGC 59.891 66.667 19.55 0.00 37.80 5.01
2210 2217 4.379243 CAGCTCCGTGGACCGCTT 62.379 66.667 3.03 0.00 34.38 4.68
2284 2291 7.698912 TCTTTTTGGAAATGGGAAGATCTAGA 58.301 34.615 0.00 0.00 0.00 2.43
2378 2385 9.506018 TTGATCATAATGATATCGTGGAAATGT 57.494 29.630 0.00 0.00 37.20 2.71
2394 2401 7.038799 GGCCAAGTCCCATTAATTGATCATAAT 60.039 37.037 0.00 0.00 0.00 1.28
2452 2459 0.974383 CACCTGAAACGGGGACTACT 59.026 55.000 0.00 0.00 33.40 2.57
2552 2559 0.394488 TGACAAACGAACAAGGGGCA 60.394 50.000 0.00 0.00 0.00 5.36
2571 2578 2.442236 ACGAGCAATGAATCCCCAAT 57.558 45.000 0.00 0.00 0.00 3.16
2594 2601 4.734695 GCTGGCTACGTTACTTATAACCGT 60.735 45.833 0.00 0.00 37.94 4.83


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

AutoCloner maintained by Alex Coulton.