Multiple sequence alignment - TraesCS6B01G147600

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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 TraesCS6B01G147600 chr6B 100.000 2579 0 0 1 2579 148693045 148690467 0.000000e+00 4763.0
1 TraesCS6B01G147600 chr6D 97.206 2577 52 9 8 2579 75012639 75010078 0.000000e+00 4342.0
2 TraesCS6B01G147600 chr6A 94.610 1911 86 11 8 1914 91294190 91292293 0.000000e+00 2942.0
3 TraesCS6B01G147600 chr6A 98.652 445 6 0 1904 2348 91292255 91291811 0.000000e+00 789.0
4 TraesCS6B01G147600 chr6A 98.319 238 3 1 2343 2579 91291460 91291223 1.430000e-112 416.0
5 TraesCS6B01G147600 chr6A 97.727 44 1 0 1945 1988 91292299 91292256 2.750000e-10 76.8


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 TraesCS6B01G147600 chr6B 148690467 148693045 2578 True 4763.00 4763 100.000 1 2579 1 chr6B.!!$R1 2578
1 TraesCS6B01G147600 chr6D 75010078 75012639 2561 True 4342.00 4342 97.206 8 2579 1 chr6D.!!$R1 2571
2 TraesCS6B01G147600 chr6A 91291223 91294190 2967 True 1055.95 2942 97.327 8 2579 4 chr6A.!!$R1 2571

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
181 183 0.953727 GTGACATGCACACACACCAT 59.046 50.0 15.61 0.0 46.91 3.55 F
1219 1224 1.589716 GGTGCTCTTCGGCATTGCTT 61.590 55.0 8.82 0.0 44.34 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1253 1258 0.897401 AAGGGCCTCTTTCAAGCTGC 60.897 55.0 6.46 0.0 29.99 5.25 R
2547 2957 1.415200 TTAACCACAAAGTTGCCCCC 58.585 50.0 0.00 0.0 0.00 5.40 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
66 67 5.880332 TGCTCTAATGGTTCCTGATTACAAC 59.120 40.000 0.00 0.00 0.00 3.32
135 137 1.684983 GTGGATTCATTGCATCAGGGG 59.315 52.381 0.00 0.00 0.00 4.79
181 183 0.953727 GTGACATGCACACACACCAT 59.046 50.000 15.61 0.00 46.91 3.55
275 278 5.066505 GGCAGTGGGAATTACACTTTGATAG 59.933 44.000 11.44 3.03 46.38 2.08
460 465 4.957971 CAAAAGATAAGTTGCACGACGAT 58.042 39.130 0.00 0.00 0.00 3.73
478 483 7.841277 CACGACGATTTAATTGTCTAAGTGATG 59.159 37.037 19.49 7.20 40.76 3.07
504 509 5.811399 TTGCTAGTTGCTATGCGTAATTT 57.189 34.783 0.00 0.00 43.37 1.82
526 531 4.193826 TCTAAGTGCAAGTGATCTGGTC 57.806 45.455 0.00 0.00 0.00 4.02
649 654 7.489435 AGTTGATAAGTTGACATATGACGACTG 59.511 37.037 23.23 0.00 35.27 3.51
853 858 4.082733 TCAATGGAGTCAGACAGTACTTCG 60.083 45.833 2.66 0.00 0.00 3.79
1019 1024 5.965922 TGATATGTACTTGGATAGCATCGG 58.034 41.667 0.00 0.00 0.00 4.18
1056 1061 2.440539 ACAGGTTCAGTGATCACGAC 57.559 50.000 19.85 17.99 36.20 4.34
1154 1159 3.328382 GGGTTTTAATCCCAAAGCACC 57.672 47.619 6.24 0.00 44.05 5.01
1209 1214 3.618690 AGACATTACCAGGTGCTCTTC 57.381 47.619 0.76 0.00 0.00 2.87
1219 1224 1.589716 GGTGCTCTTCGGCATTGCTT 61.590 55.000 8.82 0.00 44.34 3.91
1235 1240 5.063186 GCATTGCTTATATGGATCTGTCTCG 59.937 44.000 0.16 0.00 0.00 4.04
1253 1258 2.802816 CTCGGGAAGAAAGTGTTGACAG 59.197 50.000 0.00 0.00 0.00 3.51
1311 1316 0.037605 CCGAAGCACTACGGTTTCCT 60.038 55.000 0.00 0.00 43.53 3.36
1363 1368 4.051237 GGCAAAGAAGTTGGAAATGTCAC 58.949 43.478 0.00 0.00 37.73 3.67
1392 1397 6.592607 CGGTTAGTATAACCAAGCTCTTCAAA 59.407 38.462 16.69 0.00 40.28 2.69
1465 1470 9.040939 TCAACATTGACAATATTACTGATACGG 57.959 33.333 0.00 0.00 31.01 4.02
1657 1662 6.536582 CAGTACTGCTTTACATGACAATAGCT 59.463 38.462 10.54 0.00 0.00 3.32
2058 2111 3.641906 CCCGGTCTCCATCTATTTGTACT 59.358 47.826 0.00 0.00 0.00 2.73
2357 2766 5.877564 AGGATGTTGCTAAACTTAGAAGAGC 59.122 40.000 0.54 0.00 37.19 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.171003 GAGGACAAATTTGAGGGGGTG 58.829 52.381 24.64 0.00 0.00 4.61
1 2 2.073776 AGAGGACAAATTTGAGGGGGT 58.926 47.619 24.64 0.44 0.00 4.95
2 3 2.450476 CAGAGGACAAATTTGAGGGGG 58.550 52.381 24.64 5.78 0.00 5.40
3 4 1.821136 GCAGAGGACAAATTTGAGGGG 59.179 52.381 24.64 9.46 0.00 4.79
5 6 4.461781 AGATTGCAGAGGACAAATTTGAGG 59.538 41.667 24.64 7.88 0.00 3.86
6 7 5.640189 AGATTGCAGAGGACAAATTTGAG 57.360 39.130 24.64 7.88 0.00 3.02
7 8 5.535783 TCAAGATTGCAGAGGACAAATTTGA 59.464 36.000 24.64 0.00 34.16 2.69
8 9 5.775686 TCAAGATTGCAGAGGACAAATTTG 58.224 37.500 16.67 16.67 0.00 2.32
9 10 6.600882 ATCAAGATTGCAGAGGACAAATTT 57.399 33.333 0.00 0.00 0.00 1.82
10 11 6.320672 CCTATCAAGATTGCAGAGGACAAATT 59.679 38.462 0.00 0.00 0.00 1.82
11 12 5.826737 CCTATCAAGATTGCAGAGGACAAAT 59.173 40.000 0.00 0.00 0.00 2.32
66 67 5.049818 AGACATGCTTCTTTGTTTTCTCTCG 60.050 40.000 0.00 0.00 0.00 4.04
135 137 6.220930 TGACACTGTACTGTCAAATACTTCC 58.779 40.000 13.83 0.00 46.04 3.46
171 173 1.597742 GCTCTGAACATGGTGTGTGT 58.402 50.000 0.00 0.00 41.14 3.72
174 176 1.830279 ATGGCTCTGAACATGGTGTG 58.170 50.000 0.00 0.00 0.00 3.82
181 183 3.632643 TTGCAGATATGGCTCTGAACA 57.367 42.857 6.43 0.00 44.48 3.18
504 509 4.284490 AGACCAGATCACTTGCACTTAGAA 59.716 41.667 0.00 0.00 0.00 2.10
649 654 1.667724 CTCATCCACCAAATGTCGAGC 59.332 52.381 0.00 0.00 0.00 5.03
853 858 6.376581 ACATTGTCTCTTTGGAGGATCAATTC 59.623 38.462 0.00 0.00 39.86 2.17
1056 1061 3.630312 CCTTGGGTAATAACATGGAACGG 59.370 47.826 0.00 0.00 34.75 4.44
1154 1159 1.065701 CTCCGACGGTTATCTGGTCAG 59.934 57.143 14.79 0.00 0.00 3.51
1209 1214 4.005650 ACAGATCCATATAAGCAATGCCG 58.994 43.478 0.00 0.00 0.00 5.69
1219 1224 5.256806 TCTTCCCGAGACAGATCCATATA 57.743 43.478 0.00 0.00 0.00 0.86
1235 1240 2.291741 CTGCTGTCAACACTTTCTTCCC 59.708 50.000 0.00 0.00 0.00 3.97
1253 1258 0.897401 AAGGGCCTCTTTCAAGCTGC 60.897 55.000 6.46 0.00 29.99 5.25
1311 1316 3.746045 AGTAACCACTTTTCGAGCTCA 57.254 42.857 15.40 0.00 0.00 4.26
1363 1368 3.387050 AGCTTGGTTATACTAACCGGGAG 59.613 47.826 6.32 5.05 43.15 4.30
1392 1397 3.331889 TCTGAGAGAGCTTTCCCCATTTT 59.668 43.478 0.00 0.00 0.00 1.82
1403 1408 6.686126 GCCTTTATGAAGAATCTGAGAGAGCT 60.686 42.308 0.00 0.00 34.71 4.09
1410 1415 6.550938 TCTCTGCCTTTATGAAGAATCTGA 57.449 37.500 0.00 0.00 34.71 3.27
1463 1468 7.081349 TGTTTTACATTTATTCTTCAGCACCG 58.919 34.615 0.00 0.00 0.00 4.94
1646 1651 7.229306 TGTTGAAGAAAACAGAGCTATTGTCAT 59.771 33.333 4.01 0.00 35.16 3.06
2357 2766 4.760530 TCTATGATTGGTTGGAGGTCTG 57.239 45.455 0.00 0.00 0.00 3.51
2547 2957 1.415200 TTAACCACAAAGTTGCCCCC 58.585 50.000 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.