Multiple sequence alignment - TraesCS4D01G115200

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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 TraesCS4D01G115200 chr4D 100.000 3293 0 0 1 3293 96047755 96044463 0.000000e+00 6082
1 TraesCS4D01G115200 chr4A 95.017 1806 54 10 1518 3293 483175102 483176901 0.000000e+00 2804
2 TraesCS4D01G115200 chr4A 95.672 1525 41 12 1 1520 483173494 483174998 0.000000e+00 2427
3 TraesCS4D01G115200 chr4B 94.548 1816 51 15 1518 3293 136060096 136058289 0.000000e+00 2761
4 TraesCS4D01G115200 chr4B 95.532 1522 49 8 5 1520 136061904 136060396 0.000000e+00 2416
5 TraesCS4D01G115200 chr5A 91.111 90 8 0 1350 1439 279744962 279745051 4.460000e-24 122
6 TraesCS4D01G115200 chr5A 89.888 89 8 1 1518 1606 279745220 279745307 2.690000e-21 113
7 TraesCS4D01G115200 chr5D 90.000 90 9 0 1350 1439 214174603 214174692 2.080000e-22 117
8 TraesCS4D01G115200 chr5D 89.888 89 8 1 1518 1606 214174866 214174953 2.690000e-21 113
9 TraesCS4D01G115200 chr5B 89.362 94 7 1 1346 1439 228818573 228818663 7.470000e-22 115
10 TraesCS4D01G115200 chr5B 89.888 89 8 1 1518 1606 228818832 228818919 2.690000e-21 113


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 TraesCS4D01G115200 chr4D 96044463 96047755 3292 True 6082.0 6082 100.0000 1 3293 1 chr4D.!!$R1 3292
1 TraesCS4D01G115200 chr4A 483173494 483176901 3407 False 2615.5 2804 95.3445 1 3293 2 chr4A.!!$F1 3292
2 TraesCS4D01G115200 chr4B 136058289 136061904 3615 True 2588.5 2761 95.0400 5 3293 2 chr4B.!!$R1 3288

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
356 360 2.384382 CATCGGCACACAAAAACAGAC 58.616 47.619 0.00 0.0 0.00 3.51 F
1276 1285 0.034059 CGATTAGGTAGCTGGCCCTG 59.966 60.000 4.27 0.0 32.08 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1300 1309 0.248621 GCCGGCCAAATCAATCGAAG 60.249 55.000 18.11 0.0 0.00 3.79 R
3180 3654 1.065701 GTGATCGCTGGTGTAGACGAT 59.934 52.381 0.00 0.0 43.37 3.73 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
35 36 5.086621 AGGCAACAAAGTTAGGATTCCATT 58.913 37.500 5.29 0.00 41.41 3.16
278 282 3.572682 TCCACACTTGAACACGATCTAGT 59.427 43.478 0.00 0.00 36.12 2.57
284 288 5.347907 CACTTGAACACGATCTAGTTTACCC 59.652 44.000 0.00 0.00 33.97 3.69
285 289 5.245526 ACTTGAACACGATCTAGTTTACCCT 59.754 40.000 0.00 0.00 32.63 4.34
286 290 6.435277 ACTTGAACACGATCTAGTTTACCCTA 59.565 38.462 0.00 0.00 32.63 3.53
287 291 6.446781 TGAACACGATCTAGTTTACCCTAG 57.553 41.667 0.00 0.00 36.55 3.02
289 293 4.534797 ACACGATCTAGTTTACCCTAGCT 58.465 43.478 0.00 0.00 35.43 3.32
290 294 5.688807 ACACGATCTAGTTTACCCTAGCTA 58.311 41.667 0.00 0.00 35.43 3.32
291 295 5.764192 ACACGATCTAGTTTACCCTAGCTAG 59.236 44.000 14.20 14.20 35.43 3.42
292 296 5.181622 CACGATCTAGTTTACCCTAGCTAGG 59.818 48.000 30.05 30.05 43.25 3.02
356 360 2.384382 CATCGGCACACAAAAACAGAC 58.616 47.619 0.00 0.00 0.00 3.51
746 753 4.760047 CACCCCGCCTCCTCGTTG 62.760 72.222 0.00 0.00 0.00 4.10
1032 1039 1.080839 GCGCTCGAGATCTCATCCC 60.081 63.158 22.31 6.57 0.00 3.85
1039 1046 1.472082 CGAGATCTCATCCCATCCTCG 59.528 57.143 22.31 0.97 0.00 4.63
1276 1285 0.034059 CGATTAGGTAGCTGGCCCTG 59.966 60.000 4.27 0.00 32.08 4.45
1279 1288 2.257391 TTAGGTAGCTGGCCCTGTTA 57.743 50.000 4.27 0.00 32.08 2.41
1300 1309 2.025898 TGGTTTTCGGTTTGGAAGGAC 58.974 47.619 0.00 0.00 0.00 3.85
1675 2093 1.271325 TGGCATCAACCGTGTCTGATT 60.271 47.619 0.00 0.00 29.69 2.57
1796 2214 6.546428 AGAAGGTACTCTAATTAAGCAGCA 57.454 37.500 0.00 0.00 38.49 4.41
1862 2280 7.639113 TCAAGTTGCTTAATTAATCCCGAAT 57.361 32.000 0.00 0.00 0.00 3.34
1973 2391 7.666623 TCGCTTTCATTCCTTTAATTTCCTTT 58.333 30.769 0.00 0.00 0.00 3.11
2098 2519 2.765969 CTCCAGTTGTGCCCCCAT 59.234 61.111 0.00 0.00 0.00 4.00
2216 2644 2.354109 TTCGCTCTGACAGTGATGTC 57.646 50.000 8.69 1.44 41.45 3.06
2580 3009 1.617947 AAACTCTGGGGCGAGCTAGG 61.618 60.000 0.00 0.00 34.35 3.02
2615 3044 2.364632 TCGCGAAATTTCCATGGATGT 58.635 42.857 17.06 4.23 0.00 3.06
2689 3118 0.314302 CTTCGTCACGGGTGTCTCTT 59.686 55.000 0.00 0.00 0.00 2.85
2690 3119 0.748450 TTCGTCACGGGTGTCTCTTT 59.252 50.000 0.00 0.00 0.00 2.52
2691 3120 1.608055 TCGTCACGGGTGTCTCTTTA 58.392 50.000 0.00 0.00 0.00 1.85
2692 3121 1.955778 TCGTCACGGGTGTCTCTTTAA 59.044 47.619 0.00 0.00 0.00 1.52
2693 3122 2.559668 TCGTCACGGGTGTCTCTTTAAT 59.440 45.455 0.00 0.00 0.00 1.40
2719 3148 5.746307 AAGTCTAAACCAAGAAACGGAAC 57.254 39.130 0.00 0.00 0.00 3.62
2914 3348 7.133891 TCCTCTGAACGATTCTTCATTTTTC 57.866 36.000 0.00 0.00 29.71 2.29
2915 3349 6.149474 TCCTCTGAACGATTCTTCATTTTTCC 59.851 38.462 0.00 0.00 29.71 3.13
3010 3449 2.284190 GGCTCTTCATCAGGCACTAAC 58.716 52.381 0.00 0.00 36.02 2.34
3040 3479 0.101399 AAACAACATGCGTTCGCCAA 59.899 45.000 14.44 0.00 31.13 4.52
3180 3654 1.048601 AGACGACCAAGAAGAAGCCA 58.951 50.000 0.00 0.00 0.00 4.75
3276 3750 3.130160 CCGCAGCCAAGCTTCCTC 61.130 66.667 0.00 0.00 36.40 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 6.925211 AGAATTGACTCGTCTAGATTGAACA 58.075 36.000 0.00 0.00 0.00 3.18
278 282 2.767960 CCCGTTTCCTAGCTAGGGTAAA 59.232 50.000 34.43 25.83 43.79 2.01
284 288 3.132289 TGATGTTCCCGTTTCCTAGCTAG 59.868 47.826 14.20 14.20 0.00 3.42
285 289 3.101437 TGATGTTCCCGTTTCCTAGCTA 58.899 45.455 0.00 0.00 0.00 3.32
286 290 1.906574 TGATGTTCCCGTTTCCTAGCT 59.093 47.619 0.00 0.00 0.00 3.32
287 291 2.396590 TGATGTTCCCGTTTCCTAGC 57.603 50.000 0.00 0.00 0.00 3.42
289 293 4.837093 AAGATGATGTTCCCGTTTCCTA 57.163 40.909 0.00 0.00 0.00 2.94
290 294 3.721087 AAGATGATGTTCCCGTTTCCT 57.279 42.857 0.00 0.00 0.00 3.36
291 295 3.673323 GCAAAGATGATGTTCCCGTTTCC 60.673 47.826 0.00 0.00 0.00 3.13
292 296 3.191371 AGCAAAGATGATGTTCCCGTTTC 59.809 43.478 0.00 0.00 0.00 2.78
356 360 2.286772 CGTTTTTGTTTCTCGTCCCCAG 60.287 50.000 0.00 0.00 0.00 4.45
561 568 2.600475 CGTGTGAAAACCGGACGGG 61.600 63.158 9.46 6.67 43.62 5.28
1236 1245 2.201732 GCGAAATCGATTACCTGAGCA 58.798 47.619 11.83 0.00 43.02 4.26
1276 1285 4.278919 TCCTTCCAAACCGAAAACCATAAC 59.721 41.667 0.00 0.00 0.00 1.89
1279 1288 2.626266 GTCCTTCCAAACCGAAAACCAT 59.374 45.455 0.00 0.00 0.00 3.55
1300 1309 0.248621 GCCGGCCAAATCAATCGAAG 60.249 55.000 18.11 0.00 0.00 3.79
1675 2093 1.197055 GCGCGAATCGTGTCAGAATA 58.803 50.000 17.69 0.00 39.70 1.75
1862 2280 0.325933 CATGTCCTTCTCCTGCACCA 59.674 55.000 0.00 0.00 0.00 4.17
1973 2391 4.475747 ACTAATAATGGACGGGGAAAAGGA 59.524 41.667 0.00 0.00 0.00 3.36
2098 2519 1.166129 GCGTGACTGTAGTCCTCTCA 58.834 55.000 9.37 0.00 44.15 3.27
2216 2644 6.757010 GGCACATAGAGTATATTATTGTCCGG 59.243 42.308 0.00 0.00 0.00 5.14
2315 2743 1.868997 CGGACGCATCAGCAAGTTT 59.131 52.632 0.00 0.00 42.27 2.66
2419 2847 2.898840 CATGGCCGCTACCTGCAG 60.899 66.667 6.78 6.78 43.06 4.41
2691 3120 8.905850 TCCGTTTCTTGGTTTAGACTTTAAATT 58.094 29.630 0.00 0.00 0.00 1.82
2692 3121 8.454570 TCCGTTTCTTGGTTTAGACTTTAAAT 57.545 30.769 0.00 0.00 0.00 1.40
2693 3122 7.862512 TCCGTTTCTTGGTTTAGACTTTAAA 57.137 32.000 0.00 0.00 0.00 1.52
2910 3344 4.283467 TCCAGATCTGTCGAAAGAGGAAAA 59.717 41.667 21.11 0.00 43.49 2.29
2914 3348 3.876274 TTCCAGATCTGTCGAAAGAGG 57.124 47.619 21.11 7.22 43.49 3.69
2915 3349 4.560128 TGTTTCCAGATCTGTCGAAAGAG 58.440 43.478 20.77 6.29 43.49 2.85
3010 3449 8.512297 CGAACGCATGTTGTTTAACTATTATTG 58.488 33.333 6.87 0.00 38.78 1.90
3040 3479 2.798847 GCGAGAAAACTAGTGTTCCGTT 59.201 45.455 24.87 10.65 34.96 4.44
3180 3654 1.065701 GTGATCGCTGGTGTAGACGAT 59.934 52.381 0.00 0.00 43.37 3.73
3258 3732 3.909086 GAGGAAGCTTGGCTGCGGT 62.909 63.158 2.10 0.00 39.62 5.68


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

AutoCloner maintained by Alex Coulton.