Multiple sequence alignment - TraesCS3B01G247400

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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 TraesCS3B01G247400 chr3B 100.000 2614 0 0 1 2614 393335185 393332572 0.000000e+00 4828.0
1 TraesCS3B01G247400 chr5B 98.699 2614 34 0 1 2614 658090117 658087504 0.000000e+00 4639.0
2 TraesCS3B01G247400 chr5B 97.972 2614 53 0 1 2614 426537740 426535127 0.000000e+00 4534.0
3 TraesCS3B01G247400 chr5B 95.973 149 6 0 2417 2565 246980571 246980423 2.600000e-60 243.0
4 TraesCS3B01G247400 chrUn 98.508 2614 39 0 1 2614 17588023 17585410 0.000000e+00 4612.0
5 TraesCS3B01G247400 chr6B 98.432 2614 40 1 1 2614 650640567 650643179 0.000000e+00 4599.0
6 TraesCS3B01G247400 chr6B 97.652 2385 49 1 1 2378 114138771 114141155 0.000000e+00 4087.0
7 TraesCS3B01G247400 chr1B 97.711 2621 52 2 1 2614 357896040 357898659 0.000000e+00 4501.0
8 TraesCS3B01G247400 chr1B 97.684 2375 48 1 1 2368 550434056 550436430 0.000000e+00 4074.0
9 TraesCS3B01G247400 chr1B 98.947 95 1 0 2471 2565 550436429 550436523 1.240000e-38 171.0
10 TraesCS3B01G247400 chr1B 98.000 50 1 0 2565 2614 550436613 550436662 1.290000e-13 87.9
11 TraesCS3B01G247400 chr7B 97.438 2615 42 2 1 2614 335933193 335930603 0.000000e+00 4434.0
12 TraesCS3B01G247400 chr7B 97.928 2365 41 2 1 2357 687046585 687044221 0.000000e+00 4089.0
13 TraesCS3B01G247400 chr2B 96.471 2635 71 10 1 2614 711449337 711451970 0.000000e+00 4331.0
14 TraesCS3B01G247400 chr4B 100.000 84 0 0 2482 2565 291841402 291841319 3.480000e-34 156.0
15 TraesCS3B01G247400 chr4B 100.000 47 0 0 2568 2614 49109129 49109083 1.290000e-13 87.9
16 TraesCS3B01G247400 chr4B 98.000 50 1 0 2565 2614 291841229 291841180 1.290000e-13 87.9
17 TraesCS3B01G247400 chr7A 97.619 42 1 0 2417 2458 719949051 719949092 3.610000e-09 73.1


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 TraesCS3B01G247400 chr3B 393332572 393335185 2613 True 4828.0 4828 100.000000 1 2614 1 chr3B.!!$R1 2613
1 TraesCS3B01G247400 chr5B 658087504 658090117 2613 True 4639.0 4639 98.699000 1 2614 1 chr5B.!!$R3 2613
2 TraesCS3B01G247400 chr5B 426535127 426537740 2613 True 4534.0 4534 97.972000 1 2614 1 chr5B.!!$R2 2613
3 TraesCS3B01G247400 chrUn 17585410 17588023 2613 True 4612.0 4612 98.508000 1 2614 1 chrUn.!!$R1 2613
4 TraesCS3B01G247400 chr6B 650640567 650643179 2612 False 4599.0 4599 98.432000 1 2614 1 chr6B.!!$F2 2613
5 TraesCS3B01G247400 chr6B 114138771 114141155 2384 False 4087.0 4087 97.652000 1 2378 1 chr6B.!!$F1 2377
6 TraesCS3B01G247400 chr1B 357896040 357898659 2619 False 4501.0 4501 97.711000 1 2614 1 chr1B.!!$F1 2613
7 TraesCS3B01G247400 chr1B 550434056 550436662 2606 False 1444.3 4074 98.210333 1 2614 3 chr1B.!!$F2 2613
8 TraesCS3B01G247400 chr7B 335930603 335933193 2590 True 4434.0 4434 97.438000 1 2614 1 chr7B.!!$R1 2613
9 TraesCS3B01G247400 chr7B 687044221 687046585 2364 True 4089.0 4089 97.928000 1 2357 1 chr7B.!!$R2 2356
10 TraesCS3B01G247400 chr2B 711449337 711451970 2633 False 4331.0 4331 96.471000 1 2614 1 chr2B.!!$F1 2613

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
175 177 0.393077 CGGCCTTCCTATCAACGGAT 59.607 55.0 0.0 0.0 37.55 4.18 F
334 336 0.469144 AAACACCAATCCGTGCCCTT 60.469 50.0 0.0 0.0 37.25 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1460 1463 0.674895 AATCTTGTGCAGTCTCCGGC 60.675 55.000 0.00 0.0 0.00 6.13 R
1843 1853 2.028839 CACCATGGCAAGAAAGCATTGA 60.029 45.455 13.04 0.0 35.83 2.57 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
96 97 1.306141 TTGGAGGCCGGAGACTCAT 60.306 57.895 5.05 0.0 34.00 2.90
175 177 0.393077 CGGCCTTCCTATCAACGGAT 59.607 55.000 0.00 0.0 37.55 4.18
311 313 3.586470 TTCCTGGCTAAAACTGGTCAA 57.414 42.857 0.00 0.0 0.00 3.18
334 336 0.469144 AAACACCAATCCGTGCCCTT 60.469 50.000 0.00 0.0 37.25 3.95
415 417 7.411808 ACTAACCAAGGTAGTCTTCTCAGATA 58.588 38.462 0.00 0.0 32.41 1.98
430 432 2.901192 TCAGATACAACCGGGAACTCAA 59.099 45.455 6.32 0.0 0.00 3.02
1123 1126 7.695055 TGGAAGAAGACAAGGTATTCCAATTA 58.305 34.615 2.11 0.0 42.29 1.40
1373 1376 5.814188 TCACAATCAGTCAGCATATCAGAAC 59.186 40.000 0.00 0.0 0.00 3.01
1399 1402 0.650512 GTGTGGTATGCGGATCGTTG 59.349 55.000 0.00 0.0 0.00 4.10
1460 1463 1.613925 TCGGAGTTGGTGTCTGAAGAG 59.386 52.381 0.00 0.0 0.00 2.85
1477 1480 2.159819 GAGCCGGAGACTGCACAAGA 62.160 60.000 5.05 0.0 43.87 3.02
1827 1837 2.238942 TGCAGAAGTTCAAGAAGCGA 57.761 45.000 5.50 0.0 0.00 4.93
1843 1853 5.068636 AGAAGCGATTTCATAAGATGGCAT 58.931 37.500 0.00 0.0 38.31 4.40
2168 2178 7.680730 AGCAAGAAAGGTAGAAAGAAGACATA 58.319 34.615 0.00 0.0 0.00 2.29
2369 2403 1.830408 CTTGTTCCGGTTTGGCCCA 60.830 57.895 0.00 0.0 37.80 5.36
2430 2464 7.418337 TTGGTGTCTTATGTGCTATCTTCTA 57.582 36.000 0.00 0.0 0.00 2.10
2566 2613 5.279506 GGTGTAGTCTCTTTCCATGAACTCA 60.280 44.000 0.00 0.0 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.004398 CGTCGCTTAAACTGCAACACA 60.004 47.619 0.00 0.0 0.00 3.72
96 97 1.890876 CACATGGAAGGTGGAACGAA 58.109 50.000 0.00 0.0 46.42 3.85
175 177 0.961019 ACACGACCGGTAACAGCTTA 59.039 50.000 7.34 0.0 0.00 3.09
311 313 0.958822 GCACGGATTGGTGTTTCCTT 59.041 50.000 0.00 0.0 40.08 3.36
334 336 0.998928 ACCACATCATTGGCACCCTA 59.001 50.000 0.00 0.0 40.77 3.53
415 417 1.149854 GGGTTGAGTTCCCGGTTGT 59.850 57.895 0.00 0.0 35.27 3.32
430 432 1.912043 CTCCAAGAACATCCAGAGGGT 59.088 52.381 0.00 0.0 34.93 4.34
694 696 2.171003 CCATGAGGGGGTTCTTGAAAC 58.829 52.381 0.00 0.0 0.00 2.78
1123 1126 3.591079 AGAATTTCCTCCTTGCTCTCCTT 59.409 43.478 0.00 0.0 0.00 3.36
1399 1402 0.960861 AGGCTTCAGCTTTAACCGGC 60.961 55.000 0.00 0.0 41.70 6.13
1460 1463 0.674895 AATCTTGTGCAGTCTCCGGC 60.675 55.000 0.00 0.0 0.00 6.13
1477 1480 5.481473 ACAGCCATGTTGAAGGTTTGATAAT 59.519 36.000 1.85 0.0 35.63 1.28
1843 1853 2.028839 CACCATGGCAAGAAAGCATTGA 60.029 45.455 13.04 0.0 35.83 2.57
2143 2153 5.930135 TGTCTTCTTTCTACCTTTCTTGCT 58.070 37.500 0.00 0.0 0.00 3.91
2168 2178 4.253685 CGGACTATGGAATTGTGTGTTCT 58.746 43.478 0.00 0.0 30.89 3.01


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

AutoCloner maintained by Alex Coulton.