Multiple sequence alignment - TraesCS4A01G459600

Loading Multiple Alignment...

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 TraesCS4A01G459600 chr4A 100.000 2312 0 0 1 2312 725264615 725266926 0.000000e+00 4270.0
1 TraesCS4A01G459600 chr1B 90.794 1499 38 19 39 1476 592426462 592427921 0.000000e+00 1912.0
2 TraesCS4A01G459600 chr1B 96.318 842 12 3 1478 2312 592428167 592428996 0.000000e+00 1365.0
3 TraesCS4A01G459600 chr1B 100.000 37 0 0 1 37 592426442 592426478 4.120000e-08 69.4
4 TraesCS4A01G459600 chr3D 88.133 1205 59 21 27 1177 157365895 157364721 0.000000e+00 1356.0
5 TraesCS4A01G459600 chr3D 91.493 576 30 11 1525 2090 157360465 157359899 0.000000e+00 774.0
6 TraesCS4A01G459600 chr3D 91.480 223 7 5 1318 1540 157360694 157360484 1.740000e-76 296.0
7 TraesCS4A01G459600 chr3D 85.887 248 20 5 2071 2311 157359886 157359647 1.370000e-62 250.0
8 TraesCS4A01G459600 chr3D 92.683 41 3 0 1246 1286 157363467 157363427 2.480000e-05 60.2
9 TraesCS4A01G459600 chr2B 84.151 877 90 18 321 1177 773777637 773778484 0.000000e+00 804.0
10 TraesCS4A01G459600 chr7A 80.965 1098 114 45 304 1356 652761734 652762781 0.000000e+00 782.0
11 TraesCS4A01G459600 chr3B 87.719 285 24 9 659 942 672581291 672581017 2.870000e-84 322.0
12 TraesCS4A01G459600 chr3B 78.212 358 46 9 85 426 672581729 672581388 1.400000e-47 200.0


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 TraesCS4A01G459600 chr4A 725264615 725266926 2311 False 4270.000000 4270 100.0000 1 2312 1 chr4A.!!$F1 2311
1 TraesCS4A01G459600 chr1B 592426442 592428996 2554 False 1115.466667 1912 95.7040 1 2312 3 chr1B.!!$F1 2311
2 TraesCS4A01G459600 chr3D 157359647 157365895 6248 True 547.240000 1356 89.9352 27 2311 5 chr3D.!!$R1 2284
3 TraesCS4A01G459600 chr2B 773777637 773778484 847 False 804.000000 804 84.1510 321 1177 1 chr2B.!!$F1 856
4 TraesCS4A01G459600 chr7A 652761734 652762781 1047 False 782.000000 782 80.9650 304 1356 1 chr7A.!!$F1 1052
5 TraesCS4A01G459600 chr3B 672581017 672581729 712 True 261.000000 322 82.9655 85 942 2 chr3B.!!$R1 857

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
656 777 0.106167 ATAGGGCTCGCACTCCTACA 60.106 55.0 0.0 0.0 36.15 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 6514 0.179078 GCATGCTCTCCAGACTCCAG 60.179 60.0 11.37 0.0 0.0 3.86 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
118 123 2.906897 ACAACTTGCGGTGCAGGG 60.907 61.111 5.88 0.00 40.00 4.45
250 260 0.606096 ACATGGACGACGTGGATCAA 59.394 50.000 4.58 0.00 40.51 2.57
288 308 2.358247 GGTTTTCTCCGAGCGCCA 60.358 61.111 2.29 0.00 0.00 5.69
315 345 3.301222 AATGGGCGGGCTGAATGGT 62.301 57.895 0.00 0.00 0.00 3.55
543 588 1.511305 GAAGATCGTCTGGCCGTCA 59.489 57.895 0.00 0.00 0.00 4.35
656 777 0.106167 ATAGGGCTCGCACTCCTACA 60.106 55.000 0.00 0.00 36.15 2.74
657 778 0.752009 TAGGGCTCGCACTCCTACAG 60.752 60.000 0.00 0.00 32.46 2.74
658 779 2.202810 GGCTCGCACTCCTACAGC 60.203 66.667 0.00 0.00 0.00 4.40
659 780 2.202810 GCTCGCACTCCTACAGCC 60.203 66.667 0.00 0.00 0.00 4.85
660 781 2.716017 GCTCGCACTCCTACAGCCT 61.716 63.158 0.00 0.00 0.00 4.58
661 782 1.384989 GCTCGCACTCCTACAGCCTA 61.385 60.000 0.00 0.00 0.00 3.93
662 783 0.382515 CTCGCACTCCTACAGCCTAC 59.617 60.000 0.00 0.00 0.00 3.18
815 942 0.176680 CACTGGGCGAGCTGTATTCT 59.823 55.000 0.00 0.00 0.00 2.40
872 1000 8.565896 TTTCTTCACATTGCTCAACATACTAT 57.434 30.769 0.00 0.00 0.00 2.12
1315 5341 2.586079 CCGTGATGCGCTAGGTGG 60.586 66.667 9.73 0.98 39.71 4.61
1316 5342 2.184322 CGTGATGCGCTAGGTGGT 59.816 61.111 9.73 0.00 0.00 4.16
1317 5343 2.167219 CGTGATGCGCTAGGTGGTG 61.167 63.158 9.73 0.00 0.00 4.17
1408 5434 1.346068 AGGTGCTGACTGTTCCTTCTC 59.654 52.381 0.00 0.00 0.00 2.87
1732 6036 9.582648 AAAAGGTCTTAACTATGTTAACCATGT 57.417 29.630 2.48 0.00 34.86 3.21
1734 6038 9.662947 AAGGTCTTAACTATGTTAACCATGTAC 57.337 33.333 2.48 0.00 34.86 2.90
1735 6039 8.818860 AGGTCTTAACTATGTTAACCATGTACA 58.181 33.333 0.00 0.00 34.86 2.90
1926 6240 5.045213 TGGTATTCTGGTGTACATGGTGAAT 60.045 40.000 0.00 9.62 0.00 2.57
1927 6241 6.157123 TGGTATTCTGGTGTACATGGTGAATA 59.843 38.462 0.00 8.72 0.00 1.75
2099 6449 1.169661 TTGTGTTTTCGGCATCGGCT 61.170 50.000 0.00 0.00 40.87 5.52
2163 6514 2.607892 GCCGTGTCACACTTCTGCC 61.608 63.158 6.33 0.00 31.34 4.85
2164 6515 1.069765 CCGTGTCACACTTCTGCCT 59.930 57.895 6.33 0.00 31.34 4.75
2165 6516 1.224069 CCGTGTCACACTTCTGCCTG 61.224 60.000 6.33 0.00 31.34 4.85
2166 6517 1.224069 CGTGTCACACTTCTGCCTGG 61.224 60.000 6.33 0.00 31.34 4.45
2167 6518 0.106708 GTGTCACACTTCTGCCTGGA 59.893 55.000 0.00 0.00 0.00 3.86
2168 6519 0.394192 TGTCACACTTCTGCCTGGAG 59.606 55.000 0.00 0.00 0.00 3.86
2169 6520 0.394565 GTCACACTTCTGCCTGGAGT 59.605 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 3.660111 GTGTGCACAGAACCCCGC 61.660 66.667 22.40 1.29 0.00 6.13
188 193 1.343142 TGACGAAGCTTTGTAGGCAGA 59.657 47.619 19.49 0.00 0.00 4.26
250 260 2.069165 GACAACCTTGCCCACCTCCT 62.069 60.000 0.00 0.00 0.00 3.69
288 308 4.431131 CCGCCCATTGTCCAGGCT 62.431 66.667 0.00 0.00 44.84 4.58
543 588 2.943978 CGTCCTTGCCGACCCTTCT 61.944 63.158 0.00 0.00 0.00 2.85
815 942 2.058798 GCACGTCGTGAGAAGATGAAA 58.941 47.619 28.83 0.00 45.01 2.69
872 1000 1.611977 ACGATCGAAGAAGTGTGTGGA 59.388 47.619 24.34 0.00 43.58 4.02
1315 5341 0.447801 CGCACATCCAAACCTAGCAC 59.552 55.000 0.00 0.00 0.00 4.40
1316 5342 1.305219 GCGCACATCCAAACCTAGCA 61.305 55.000 0.30 0.00 0.00 3.49
1317 5343 1.305219 TGCGCACATCCAAACCTAGC 61.305 55.000 5.66 0.00 0.00 3.42
1460 5486 1.468054 GCTAAGCAAACTTGATGGCGG 60.468 52.381 0.00 0.00 36.57 6.13
1462 5488 1.200020 ACGCTAAGCAAACTTGATGGC 59.800 47.619 0.00 0.00 36.57 4.40
1600 5904 1.000955 TGGTCGCTCCTTCTCTTGTTC 59.999 52.381 0.00 0.00 37.07 3.18
1926 6240 4.037446 AGAAACTCGGCAGCAACAAAAATA 59.963 37.500 0.00 0.00 0.00 1.40
1927 6241 2.888834 AACTCGGCAGCAACAAAAAT 57.111 40.000 0.00 0.00 0.00 1.82
2099 6449 1.455822 GGATCCCACCCATAATCCCA 58.544 55.000 0.00 0.00 33.06 4.37
2163 6514 0.179078 GCATGCTCTCCAGACTCCAG 60.179 60.000 11.37 0.00 0.00 3.86
2164 6515 1.620739 GGCATGCTCTCCAGACTCCA 61.621 60.000 18.92 0.00 0.00 3.86
2165 6516 1.145819 GGCATGCTCTCCAGACTCC 59.854 63.158 18.92 0.00 0.00 3.85
2166 6517 1.407936 TAGGCATGCTCTCCAGACTC 58.592 55.000 18.92 0.00 0.00 3.36
2167 6518 1.871418 TTAGGCATGCTCTCCAGACT 58.129 50.000 18.92 5.85 0.00 3.24
2168 6519 2.559440 CTTTAGGCATGCTCTCCAGAC 58.441 52.381 18.92 0.00 0.00 3.51
2169 6520 1.134280 GCTTTAGGCATGCTCTCCAGA 60.134 52.381 18.92 0.00 41.35 3.86
2279 6637 4.164294 CAGCAAGCAAAGACAGCTAAATC 58.836 43.478 0.00 0.00 42.53 2.17


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

AutoCloner maintained by Alex Coulton.