Multiple sequence alignment - TraesCS4B01G117500

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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 TraesCS4B01G117500 chr4B 100.000 2487 0 0 1 2487 136488474 136490960 0 4593
1 TraesCS4B01G117500 chrUn 97.791 2490 48 4 1 2487 282364696 282362211 0 4287
2 TraesCS4B01G117500 chrUn 97.751 2490 49 4 1 2487 86510012 86507527 0 4281
3 TraesCS4B01G117500 chr6B 97.793 2492 44 8 1 2487 596620324 596622809 0 4287
4 TraesCS4B01G117500 chr3B 97.549 2489 53 5 1 2487 92317838 92320320 0 4252
5 TraesCS4B01G117500 chr3B 94.978 2489 111 9 1 2487 368696998 368699474 0 3892
6 TraesCS4B01G117500 chr2B 97.391 2491 51 11 1 2487 30670611 30668131 0 4228
7 TraesCS4B01G117500 chr6A 97.312 2493 57 5 1 2487 84434144 84436632 0 4224
8 TraesCS4B01G117500 chr5B 96.987 2489 63 5 1 2487 567270595 567268117 0 4170
9 TraesCS4B01G117500 chr3D 96.787 2490 70 6 1 2487 154704960 154702478 0 4146


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 TraesCS4B01G117500 chr4B 136488474 136490960 2486 False 4593 4593 100.000 1 2487 1 chr4B.!!$F1 2486
1 TraesCS4B01G117500 chrUn 282362211 282364696 2485 True 4287 4287 97.791 1 2487 1 chrUn.!!$R2 2486
2 TraesCS4B01G117500 chrUn 86507527 86510012 2485 True 4281 4281 97.751 1 2487 1 chrUn.!!$R1 2486
3 TraesCS4B01G117500 chr6B 596620324 596622809 2485 False 4287 4287 97.793 1 2487 1 chr6B.!!$F1 2486
4 TraesCS4B01G117500 chr3B 92317838 92320320 2482 False 4252 4252 97.549 1 2487 1 chr3B.!!$F1 2486
5 TraesCS4B01G117500 chr3B 368696998 368699474 2476 False 3892 3892 94.978 1 2487 1 chr3B.!!$F2 2486
6 TraesCS4B01G117500 chr2B 30668131 30670611 2480 True 4228 4228 97.391 1 2487 1 chr2B.!!$R1 2486
7 TraesCS4B01G117500 chr6A 84434144 84436632 2488 False 4224 4224 97.312 1 2487 1 chr6A.!!$F1 2486
8 TraesCS4B01G117500 chr5B 567268117 567270595 2478 True 4170 4170 96.987 1 2487 1 chr5B.!!$R1 2486
9 TraesCS4B01G117500 chr3D 154702478 154704960 2482 True 4146 4146 96.787 1 2487 1 chr3D.!!$R1 2486

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
114 115 1.406539 CTCAAAGCCCAATTAGCGCAT 59.593 47.619 11.47 0.0 34.64 4.73 F
847 849 2.107204 GGTCAACCAGGCCAGATCATAT 59.893 50.000 5.01 0.0 43.39 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1171 1174 0.184211 AAAGGTACAACGGCCCAAGT 59.816 50.0 0.0 0.0 0.0 3.16 R
2293 2311 0.109272 CGCGGCAGAGAACTAGACAA 60.109 55.0 0.0 0.0 0.0 3.18 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
56 57 4.407621 TGGAACAGTTTAGGACAGAACAGA 59.592 41.667 0.00 0.00 0.00 3.41
114 115 1.406539 CTCAAAGCCCAATTAGCGCAT 59.593 47.619 11.47 0.00 34.64 4.73
223 224 6.371271 CCGCCAAGTCCATAATTCAAAAATTT 59.629 34.615 0.00 0.00 36.49 1.82
274 275 7.085052 AGGCGATTACCAAATCTACTTTTTC 57.915 36.000 0.00 0.00 39.56 2.29
288 289 7.807977 TCTACTTTTTCAGCATCTTGAAACT 57.192 32.000 1.02 0.00 44.33 2.66
563 565 7.118680 ACAACAAACTATCGATACACCGAAAAT 59.881 33.333 0.00 0.00 42.22 1.82
606 608 2.462723 TGGAGACATCGTGGATTACCA 58.537 47.619 0.00 0.00 38.79 3.25
745 747 6.240549 AGTGAGGATTCCATTCGAAGTAAT 57.759 37.500 3.35 3.12 32.78 1.89
776 778 4.464008 AGCACCATCTTCAAAACTTCTCA 58.536 39.130 0.00 0.00 0.00 3.27
847 849 2.107204 GGTCAACCAGGCCAGATCATAT 59.893 50.000 5.01 0.00 43.39 1.78
1067 1070 5.476614 GTTCGGATTGTTACAACCTCTAGT 58.523 41.667 0.00 0.00 0.00 2.57
1110 1113 7.448748 TCTAAAAGAACCTATTTCACCAAGC 57.551 36.000 0.00 0.00 36.57 4.01
1171 1174 6.821665 GGCTACATTTATGTTAAGTCTGGTCA 59.178 38.462 0.02 0.00 41.97 4.02
1253 1256 9.586435 GCTACTTTATTTGTTTGCCATATCTTT 57.414 29.630 0.00 0.00 0.00 2.52
1414 1419 1.129058 GGCTTACAAGGCTAGGGCTA 58.871 55.000 8.19 0.00 46.98 3.93
1464 1469 1.228154 GGTCACTTTTCTGGGCCGT 60.228 57.895 0.00 0.00 0.00 5.68
1468 1473 1.202879 TCACTTTTCTGGGCCGTGATT 60.203 47.619 5.70 0.00 30.41 2.57
1520 1525 2.362397 TCTCCTCGCACCTCATATCAAC 59.638 50.000 0.00 0.00 0.00 3.18
1656 1667 6.997239 TGATGGATGAAAGAACATGAGAAG 57.003 37.500 0.00 0.00 0.00 2.85
1659 1670 4.043310 TGGATGAAAGAACATGAGAAGGGT 59.957 41.667 0.00 0.00 0.00 4.34
1661 1672 5.124617 GGATGAAAGAACATGAGAAGGGTTC 59.875 44.000 0.00 0.00 40.84 3.62
1734 1747 0.106369 TTGCCTAGCCTCGCCTACTA 60.106 55.000 0.00 0.00 0.00 1.82
1858 1871 7.695618 GCTCGACGTTAATTAAGAGAGTAAAGA 59.304 37.037 13.57 6.10 0.00 2.52
2061 2074 2.554142 CGTAAATCAGAGAGCATGCCA 58.446 47.619 15.66 0.00 0.00 4.92
2126 2140 6.237313 ACGCAAAGAATTAAAGTACCTGAC 57.763 37.500 0.00 0.00 0.00 3.51
2127 2141 5.180680 ACGCAAAGAATTAAAGTACCTGACC 59.819 40.000 0.00 0.00 0.00 4.02
2128 2142 5.391629 CGCAAAGAATTAAAGTACCTGACCC 60.392 44.000 0.00 0.00 0.00 4.46
2129 2143 5.105877 GCAAAGAATTAAAGTACCTGACCCC 60.106 44.000 0.00 0.00 0.00 4.95
2293 2311 0.249741 ACAAAGGTACGCTCGCTTGT 60.250 50.000 0.00 0.00 0.00 3.16
2299 2317 1.401931 GGTACGCTCGCTTGTTGTCTA 60.402 52.381 0.00 0.00 0.00 2.59
2322 2340 4.473520 CTGCCGCGGACTGGGATT 62.474 66.667 33.48 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 1.551452 AGCTCGCTTTCTACTGAGGT 58.449 50.000 0.00 0.00 34.59 3.85
252 253 6.469275 GCTGAAAAAGTAGATTTGGTAATCGC 59.531 38.462 0.00 0.00 43.99 4.58
274 275 3.570926 ATGTGCAGTTTCAAGATGCTG 57.429 42.857 0.00 0.00 40.62 4.41
563 565 8.493607 TCCATTTTATGTATCCATCTTGACTCA 58.506 33.333 0.00 0.00 32.29 3.41
606 608 3.055675 TGTCCTATCGTCGTCCCAATTTT 60.056 43.478 0.00 0.00 0.00 1.82
745 747 2.637382 TGAAGATGGTGCTCCTGTTACA 59.363 45.455 6.34 0.00 34.23 2.41
776 778 4.748277 TTATCGAAAAACTCCGGATCCT 57.252 40.909 3.57 0.00 0.00 3.24
847 849 3.930229 CGACCCGATCAAACTATTTCACA 59.070 43.478 0.00 0.00 0.00 3.58
1110 1113 7.687941 TCTAAAAAGGGAGAAATTAGCACTG 57.312 36.000 0.00 0.00 0.00 3.66
1171 1174 0.184211 AAAGGTACAACGGCCCAAGT 59.816 50.000 0.00 0.00 0.00 3.16
1414 1419 9.933723 CTTGATGAATGAAAGAAAGGGTTTATT 57.066 29.630 0.00 0.00 0.00 1.40
1464 1469 8.690203 TTTTTATGACTTCCACTTCTCAATCA 57.310 30.769 0.00 0.00 0.00 2.57
1503 1508 2.101415 TCCTGTTGATATGAGGTGCGAG 59.899 50.000 0.00 0.00 0.00 5.03
1545 1550 9.620259 AGAAAGCTAGAATTTCCAATAGTTAGG 57.380 33.333 14.06 0.00 37.37 2.69
1584 1595 2.545946 GCGTTGACAAAGAAGAAGAGCT 59.454 45.455 5.22 0.00 0.00 4.09
1656 1667 8.577048 ACTTTCTAGCCTTTTATTTAGAACCC 57.423 34.615 0.00 0.00 33.28 4.11
1734 1747 2.423577 ACTCGCTCGCCTACAAAAATT 58.576 42.857 0.00 0.00 0.00 1.82
1858 1871 6.906901 TGGTTCTTCTATGTAGGGTATTCCTT 59.093 38.462 0.00 0.00 45.47 3.36
2192 2210 0.460311 AAACTCCGATTCGATCCGCT 59.540 50.000 7.83 0.00 0.00 5.52
2293 2311 0.109272 CGCGGCAGAGAACTAGACAA 60.109 55.000 0.00 0.00 0.00 3.18
2299 2317 2.992114 AGTCCGCGGCAGAGAACT 60.992 61.111 23.51 15.27 0.00 3.01
2442 2460 3.494336 ACGCCTAGACGACGACCG 61.494 66.667 5.13 0.00 45.44 4.79
2443 2461 2.099831 CACGCCTAGACGACGACC 59.900 66.667 5.13 0.00 36.70 4.79


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

AutoCloner maintained by Alex Coulton.