Multiple sequence alignment - TraesCS2B01G165900

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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 TraesCS2B01G165900 chr2B 100.000 2264 0 0 1 2264 138731795 138734058 0 4181
1 TraesCS2B01G165900 chr2B 94.776 2278 85 9 1 2263 563917154 563914896 0 3517
2 TraesCS2B01G165900 chr2B 93.890 491 28 2 1772 2260 717653793 717654283 0 739
3 TraesCS2B01G165900 chr3B 95.040 2278 83 6 1 2263 16124450 16122188 0 3554
4 TraesCS2B01G165900 chr3B 95.593 1702 68 6 562 2260 28617486 28619183 0 2721
5 TraesCS2B01G165900 chr4A 94.748 2285 90 12 1 2260 712877464 712879743 0 3528
6 TraesCS2B01G165900 chr5B 95.761 2194 61 6 1 2180 464634092 464636267 0 3507
7 TraesCS2B01G165900 chr5B 95.000 780 17 7 1 759 426532809 426533587 0 1205
8 TraesCS2B01G165900 chr5B 93.509 493 31 1 1772 2263 530939090 530938598 0 732
9 TraesCS2B01G165900 chr7B 94.471 2279 80 9 1 2263 235458108 235455860 0 3469
10 TraesCS2B01G165900 chr7B 93.599 2281 118 12 1 2260 687040608 687042881 0 3378
11 TraesCS2B01G165900 chr7B 92.271 2277 133 18 1 2260 27326600 27328850 0 3190
12 TraesCS2B01G165900 chr7B 93.724 733 39 3 1 727 685201816 685202547 0 1092
13 TraesCS2B01G165900 chr7B 93.279 491 31 2 1772 2260 130335701 130336191 0 723
14 TraesCS2B01G165900 chr1B 93.208 2282 113 17 1 2260 38183377 38185638 0 3317
15 TraesCS2B01G165900 chr1B 94.512 820 25 4 1 800 357902145 357901326 0 1247
16 TraesCS2B01G165900 chr1B 94.534 494 25 2 1772 2263 550438357 550437864 0 761
17 TraesCS2B01G165900 chr4B 95.844 1997 56 3 1 1983 402787217 402785234 0 3203
18 TraesCS2B01G165900 chr6B 94.627 1433 54 7 561 1984 687513878 687512460 0 2198
19 TraesCS2B01G165900 chr6B 94.512 820 25 5 1 800 650646679 650645860 0 1247
20 TraesCS2B01G165900 chr6B 92.198 769 47 10 1 757 578524299 578525066 0 1075
21 TraesCS2B01G165900 chr6B 92.713 494 34 2 1772 2263 114143093 114142600 0 712
22 TraesCS2B01G165900 chr1D 95.429 700 28 3 1 697 490888797 490889495 0 1112


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 TraesCS2B01G165900 chr2B 138731795 138734058 2263 False 4181 4181 100.000 1 2264 1 chr2B.!!$F1 2263
1 TraesCS2B01G165900 chr2B 563914896 563917154 2258 True 3517 3517 94.776 1 2263 1 chr2B.!!$R1 2262
2 TraesCS2B01G165900 chr3B 16122188 16124450 2262 True 3554 3554 95.040 1 2263 1 chr3B.!!$R1 2262
3 TraesCS2B01G165900 chr3B 28617486 28619183 1697 False 2721 2721 95.593 562 2260 1 chr3B.!!$F1 1698
4 TraesCS2B01G165900 chr4A 712877464 712879743 2279 False 3528 3528 94.748 1 2260 1 chr4A.!!$F1 2259
5 TraesCS2B01G165900 chr5B 464634092 464636267 2175 False 3507 3507 95.761 1 2180 1 chr5B.!!$F2 2179
6 TraesCS2B01G165900 chr5B 426532809 426533587 778 False 1205 1205 95.000 1 759 1 chr5B.!!$F1 758
7 TraesCS2B01G165900 chr7B 235455860 235458108 2248 True 3469 3469 94.471 1 2263 1 chr7B.!!$R1 2262
8 TraesCS2B01G165900 chr7B 687040608 687042881 2273 False 3378 3378 93.599 1 2260 1 chr7B.!!$F4 2259
9 TraesCS2B01G165900 chr7B 27326600 27328850 2250 False 3190 3190 92.271 1 2260 1 chr7B.!!$F1 2259
10 TraesCS2B01G165900 chr7B 685201816 685202547 731 False 1092 1092 93.724 1 727 1 chr7B.!!$F3 726
11 TraesCS2B01G165900 chr1B 38183377 38185638 2261 False 3317 3317 93.208 1 2260 1 chr1B.!!$F1 2259
12 TraesCS2B01G165900 chr1B 357901326 357902145 819 True 1247 1247 94.512 1 800 1 chr1B.!!$R1 799
13 TraesCS2B01G165900 chr4B 402785234 402787217 1983 True 3203 3203 95.844 1 1983 1 chr4B.!!$R1 1982
14 TraesCS2B01G165900 chr6B 687512460 687513878 1418 True 2198 2198 94.627 561 1984 1 chr6B.!!$R3 1423
15 TraesCS2B01G165900 chr6B 650645860 650646679 819 True 1247 1247 94.512 1 800 1 chr6B.!!$R2 799
16 TraesCS2B01G165900 chr6B 578524299 578525066 767 False 1075 1075 92.198 1 757 1 chr6B.!!$F1 756
17 TraesCS2B01G165900 chr1D 490888797 490889495 698 False 1112 1112 95.429 1 697 1 chr1D.!!$F1 696

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
730 904 0.541063 TGCTAGAGGTGGTGGTCGAA 60.541 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 2374 0.036388 GGCGTCTGGATGTCCTTCAA 60.036 55.0 0.09 0.0 36.82 2.69 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
165 166 5.350504 ACATGTTTGTGATGGAAAAACCA 57.649 34.783 0.00 0.00 43.40 3.67
316 317 2.024273 TGGAGACGAAGGGTAGAAGGAT 60.024 50.000 0.00 0.00 0.00 3.24
527 542 1.469335 GGAAGAGGTGACGGTGGTGA 61.469 60.000 0.00 0.00 0.00 4.02
534 549 2.125673 GACGGTGGTGATGGTCGG 60.126 66.667 0.00 0.00 0.00 4.79
550 565 1.071471 CGGGGAAGCACAAGTGTCT 59.929 57.895 1.79 0.00 0.00 3.41
559 574 1.070134 GCACAAGTGTCTGAGGTGGTA 59.930 52.381 1.79 0.00 0.00 3.25
730 904 0.541063 TGCTAGAGGTGGTGGTCGAA 60.541 55.000 0.00 0.00 0.00 3.71
872 1046 2.031683 CGGCCTTCGGTTATTTGCTTAG 59.968 50.000 0.00 0.00 34.75 2.18
1206 1380 2.021457 AGGTTTTTCGTGTGTCCCAAG 58.979 47.619 0.00 0.00 0.00 3.61
1254 1428 3.552132 AACGCATATGACATACCACCA 57.448 42.857 6.97 0.00 0.00 4.17
1349 1524 1.151810 TCCCCTCCTCCACTTTGCT 60.152 57.895 0.00 0.00 0.00 3.91
1491 1666 1.216710 GTGAGAAGGAGGCTCGTGG 59.783 63.158 10.92 0.00 35.15 4.94
1549 1724 1.859302 AGGAGGCTCGTCAAGAAGAT 58.141 50.000 8.69 0.00 0.00 2.40
1657 1833 2.380064 AGACAAATGGAAAGGCACCA 57.620 45.000 0.00 0.00 41.83 4.17
1689 1865 5.234329 TGATGAACTGTCGAGACTTTGTTTC 59.766 40.000 4.78 4.36 0.00 2.78
1700 1876 6.704050 TCGAGACTTTGTTTCATGTATGAACA 59.296 34.615 6.79 6.36 45.63 3.18
1876 2069 7.986889 TGAGACTAGCATGCTTTGTTCATATTA 59.013 33.333 28.02 1.36 0.00 0.98
2016 2246 1.071385 CAGGAGACCAGACAAGCTGTT 59.929 52.381 0.00 0.00 43.33 3.16
2025 2255 2.164219 CAGACAAGCTGTTTGGTGTGTT 59.836 45.455 9.07 0.00 41.25 3.32
2143 2374 1.668419 GACAAGCTGTCTGGTGTGTT 58.332 50.000 8.50 0.00 43.73 3.32
2147 2378 2.418368 AGCTGTCTGGTGTGTTTGAA 57.582 45.000 0.00 0.00 0.00 2.69
2200 2432 4.263572 CCCACACCCAGACGCCAA 62.264 66.667 0.00 0.00 0.00 4.52
2205 2437 2.847234 ACCCAGACGCCAAGGACA 60.847 61.111 0.00 0.00 0.00 4.02
2263 2496 4.193826 GACACCTGTCTGATGTGTATGT 57.806 45.455 9.55 0.00 42.89 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
316 317 4.136341 TCACCCCTGAACCTCTTAGTTA 57.864 45.455 0.00 0.0 0.00 2.24
527 542 1.002134 CTTGTGCTTCCCCGACCAT 60.002 57.895 0.00 0.0 0.00 3.55
534 549 1.517242 CTCAGACACTTGTGCTTCCC 58.483 55.000 0.10 0.0 0.00 3.97
550 565 0.762418 CAACCACCACTACCACCTCA 59.238 55.000 0.00 0.0 0.00 3.86
559 574 1.645710 CTCCCTCTACAACCACCACT 58.354 55.000 0.00 0.0 0.00 4.00
730 904 5.024118 ACCACCTCTAGTATTTGTGCTAGT 58.976 41.667 0.00 0.0 36.84 2.57
742 916 0.966370 GCTCGACCACCACCTCTAGT 60.966 60.000 0.00 0.0 0.00 2.57
1035 1209 1.296392 CATGTCCTCTTGGTCCGCA 59.704 57.895 0.00 0.0 34.23 5.69
1206 1380 2.472861 CCTTCGACGATCATGTGCATAC 59.527 50.000 0.00 0.0 0.00 2.39
1286 1460 8.902540 TTGTTAGACATATGAGTGACAACTTT 57.097 30.769 10.38 0.0 36.52 2.66
1349 1524 7.052248 TCGTGATCTATCCAAGTGAAGTACTA 58.948 38.462 0.00 0.0 39.18 1.82
1507 1682 1.630244 CTTTGCGTGCCCTCTCTTCG 61.630 60.000 0.00 0.0 0.00 3.79
1657 1833 1.795525 CGACAGTTCATCATCGACGCT 60.796 52.381 0.00 0.0 36.70 5.07
1700 1876 5.385198 ACCACACAAGGTCTTGAATAACAT 58.615 37.500 16.55 0.0 42.93 2.71
1876 2069 3.427503 GCAACTTGTAGCACACACTGTTT 60.428 43.478 0.00 0.0 36.69 2.83
2016 2246 2.428890 GGTTGTCCATCAAACACACCAA 59.571 45.455 0.00 0.0 42.74 3.67
2025 2255 0.605319 GGCGTCTGGTTGTCCATCAA 60.605 55.000 0.00 0.0 43.43 2.57
2143 2374 0.036388 GGCGTCTGGATGTCCTTCAA 60.036 55.000 0.09 0.0 36.82 2.69
2147 2378 1.599047 CTTGGCGTCTGGATGTCCT 59.401 57.895 0.09 0.0 36.82 3.85
2200 2432 4.008933 GCCAGACGCCAGTGTCCT 62.009 66.667 7.70 0.0 39.77 3.85


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

AutoCloner maintained by Alex Coulton.