Multiple sequence alignment - TraesCS5D01G435100

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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 TraesCS5D01G435100 chr5D 100.000 2364 0 0 1 2364 490432434 490430071 0.000000e+00 4366.0
1 TraesCS5D01G435100 chr5D 97.021 1410 28 6 961 2363 441568765 441567363 0.000000e+00 2359.0
2 TraesCS5D01G435100 chr5D 96.338 355 13 0 1 355 876523 876877 3.390000e-163 584.0
3 TraesCS5D01G435100 chr5D 94.239 243 8 3 722 961 17468037 17467798 1.340000e-97 366.0
4 TraesCS5D01G435100 chr5D 93.333 60 3 1 638 696 490431754 490431695 1.160000e-13 87.9
5 TraesCS5D01G435100 chr5D 93.333 60 3 1 681 740 490431797 490431739 1.160000e-13 87.9
6 TraesCS5D01G435100 chr5B 93.445 1434 53 10 961 2357 604857502 604856073 0.000000e+00 2089.0
7 TraesCS5D01G435100 chr7D 93.007 1430 63 7 961 2357 44716318 44714893 0.000000e+00 2052.0
8 TraesCS5D01G435100 chr7D 89.547 287 21 7 679 961 394356323 394356042 2.890000e-94 355.0
9 TraesCS5D01G435100 chr7D 96.262 214 7 1 756 968 285244590 285244377 1.340000e-92 350.0
10 TraesCS5D01G435100 chr5A 92.907 1438 55 13 961 2355 611976974 611975541 0.000000e+00 2047.0
11 TraesCS5D01G435100 chr6A 91.421 1422 67 25 961 2353 29578277 29579672 0.000000e+00 1899.0
12 TraesCS5D01G435100 chr6D 91.420 1387 59 23 961 2302 28309746 28308375 0.000000e+00 1847.0
13 TraesCS5D01G435100 chr6D 93.173 1245 58 17 961 2190 420225405 420224173 0.000000e+00 1803.0
14 TraesCS5D01G435100 chr6D 98.153 379 5 2 1 379 380025792 380025416 0.000000e+00 660.0
15 TraesCS5D01G435100 chr6D 91.165 249 19 2 713 960 428158418 428158664 3.760000e-88 335.0
16 TraesCS5D01G435100 chr6D 91.235 251 13 7 716 960 86937244 86936997 1.350000e-87 333.0
17 TraesCS5D01G435100 chr6D 91.925 161 9 2 1286 1442 13922058 13922218 3.060000e-54 222.0
18 TraesCS5D01G435100 chr6D 94.737 57 2 1 2188 2243 420224152 420224096 1.160000e-13 87.9
19 TraesCS5D01G435100 chr6D 100.000 29 0 0 2325 2353 28308373 28308345 1.000000e-03 54.7
20 TraesCS5D01G435100 chr7A 94.810 1156 44 9 961 2104 47294382 47293231 0.000000e+00 1788.0
21 TraesCS5D01G435100 chr7A 87.097 310 26 9 2060 2357 47293235 47292928 2.910000e-89 339.0
22 TraesCS5D01G435100 chr1D 97.822 597 12 1 1 597 44620307 44620902 0.000000e+00 1029.0
23 TraesCS5D01G435100 chr1D 97.260 438 11 1 1 438 103258383 103258819 0.000000e+00 741.0
24 TraesCS5D01G435100 chr1D 89.182 379 15 10 587 960 44620977 44621334 1.290000e-122 449.0
25 TraesCS5D01G435100 chr1D 82.315 311 26 14 1732 2036 310148264 310148551 2.350000e-60 243.0
26 TraesCS5D01G435100 chr4D 96.575 438 14 1 1 438 472677620 472678056 0.000000e+00 725.0
27 TraesCS5D01G435100 chr4D 95.890 438 12 2 1 432 282074997 282074560 0.000000e+00 704.0
28 TraesCS5D01G435100 chr4D 95.035 282 8 4 680 960 317191152 317190876 2.790000e-119 438.0
29 TraesCS5D01G435100 chr4D 96.279 215 6 2 746 960 458093329 458093117 3.740000e-93 351.0
30 TraesCS5D01G435100 chr2D 96.347 438 15 1 1 438 421810881 421811317 0.000000e+00 719.0
31 TraesCS5D01G435100 chr2D 97.129 418 5 2 1 417 159860036 159860447 0.000000e+00 699.0
32 TraesCS5D01G435100 chr2D 98.928 373 4 0 1 373 421784870 421784498 0.000000e+00 667.0
33 TraesCS5D01G435100 chr2D 98.153 379 5 2 1 379 490572341 490571965 0.000000e+00 660.0
34 TraesCS5D01G435100 chr3D 94.607 445 16 3 1 438 330284519 330284962 0.000000e+00 682.0
35 TraesCS5D01G435100 chr3D 87.500 304 15 18 670 960 540242729 540242436 1.750000e-86 329.0
36 TraesCS5D01G435100 chr4A 80.055 722 114 23 963 1673 542044196 542043494 2.100000e-140 508.0
37 TraesCS5D01G435100 chr3A 78.275 603 68 33 1732 2285 128521175 128520587 1.750000e-86 329.0
38 TraesCS5D01G435100 chr1A 94.083 169 8 2 2021 2187 389877111 389877279 3.020000e-64 255.0
39 TraesCS5D01G435100 chr1A 90.909 99 5 2 2188 2285 389877469 389877564 1.910000e-26 130.0
40 TraesCS5D01G435100 chr4B 88.957 163 13 1 963 1125 81992516 81992673 1.850000e-46 196.0
41 TraesCS5D01G435100 chrUn 82.741 197 14 2 1270 1446 71289805 71289609 8.750000e-35 158.0


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 TraesCS5D01G435100 chr5D 490430071 490432434 2363 True 1513.933333 4366 95.555333 1 2364 3 chr5D.!!$R3 2363
1 TraesCS5D01G435100 chr5D 441567363 441568765 1402 True 2359.000000 2359 97.021000 961 2363 1 chr5D.!!$R2 1402
2 TraesCS5D01G435100 chr5B 604856073 604857502 1429 True 2089.000000 2089 93.445000 961 2357 1 chr5B.!!$R1 1396
3 TraesCS5D01G435100 chr7D 44714893 44716318 1425 True 2052.000000 2052 93.007000 961 2357 1 chr7D.!!$R1 1396
4 TraesCS5D01G435100 chr5A 611975541 611976974 1433 True 2047.000000 2047 92.907000 961 2355 1 chr5A.!!$R1 1394
5 TraesCS5D01G435100 chr6A 29578277 29579672 1395 False 1899.000000 1899 91.421000 961 2353 1 chr6A.!!$F1 1392
6 TraesCS5D01G435100 chr6D 28308345 28309746 1401 True 950.850000 1847 95.710000 961 2353 2 chr6D.!!$R3 1392
7 TraesCS5D01G435100 chr6D 420224096 420225405 1309 True 945.450000 1803 93.955000 961 2243 2 chr6D.!!$R4 1282
8 TraesCS5D01G435100 chr7A 47292928 47294382 1454 True 1063.500000 1788 90.953500 961 2357 2 chr7A.!!$R1 1396
9 TraesCS5D01G435100 chr1D 44620307 44621334 1027 False 739.000000 1029 93.502000 1 960 2 chr1D.!!$F3 959
10 TraesCS5D01G435100 chr4A 542043494 542044196 702 True 508.000000 508 80.055000 963 1673 1 chr4A.!!$R1 710
11 TraesCS5D01G435100 chr3A 128520587 128521175 588 True 329.000000 329 78.275000 1732 2285 1 chr3A.!!$R1 553

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
409 410 0.385751 GAACGGGATGCTCGATCTGA 59.614 55.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1480 1599 5.925506 TCCATTTGATGAAGCAATGACAT 57.074 34.783 0.0 0.0 0.0 3.06 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
126 127 1.878734 GCCTCATCAGCAATCTTAGCC 59.121 52.381 0.00 0.0 0.00 3.93
409 410 0.385751 GAACGGGATGCTCGATCTGA 59.614 55.000 0.00 0.0 0.00 3.27
447 448 4.379243 AGTCGGGCAGGCGTCAAG 62.379 66.667 0.00 0.0 0.00 3.02
476 477 3.319198 GAGACCGGTTGGGGAGCA 61.319 66.667 9.42 0.0 41.60 4.26
518 519 4.828296 GCCTCGTCCCTCCCCGTA 62.828 72.222 0.00 0.0 0.00 4.02
542 543 1.301716 GTTCTGCAGGAACCGCTCA 60.302 57.895 15.13 0.0 46.17 4.26
550 551 2.666190 GAACCGCTCAGCACAGCA 60.666 61.111 0.00 0.0 39.62 4.41
556 557 2.046507 CTCAGCACAGCAGGTCCC 60.047 66.667 0.00 0.0 0.00 4.46
557 558 2.848679 TCAGCACAGCAGGTCCCA 60.849 61.111 0.00 0.0 0.00 4.37
631 717 3.069318 GAGCGGGAGGGAAGACGT 61.069 66.667 0.00 0.0 0.00 4.34
632 718 3.358076 GAGCGGGAGGGAAGACGTG 62.358 68.421 0.00 0.0 0.00 4.49
633 719 4.452733 GCGGGAGGGAAGACGTGG 62.453 72.222 0.00 0.0 0.00 4.94
634 720 2.678934 CGGGAGGGAAGACGTGGA 60.679 66.667 0.00 0.0 0.00 4.02
635 721 2.979649 GGGAGGGAAGACGTGGAC 59.020 66.667 0.00 0.0 0.00 4.02
636 722 1.609794 GGGAGGGAAGACGTGGACT 60.610 63.158 0.00 0.0 0.00 3.85
637 723 1.605971 GGGAGGGAAGACGTGGACTC 61.606 65.000 0.00 0.0 0.00 3.36
638 724 1.507174 GAGGGAAGACGTGGACTCG 59.493 63.158 0.00 0.0 0.00 4.18
639 725 1.935327 GAGGGAAGACGTGGACTCGG 61.935 65.000 0.00 0.0 34.94 4.63
640 726 2.572284 GGAAGACGTGGACTCGGG 59.428 66.667 0.00 0.0 34.94 5.14
641 727 1.975407 GGAAGACGTGGACTCGGGA 60.975 63.158 0.00 0.0 34.94 5.14
642 728 1.507174 GAAGACGTGGACTCGGGAG 59.493 63.158 0.00 0.0 34.94 4.30
643 729 1.935327 GAAGACGTGGACTCGGGAGG 61.935 65.000 0.00 0.0 34.94 4.30
644 730 3.450115 GACGTGGACTCGGGAGGG 61.450 72.222 0.00 0.0 34.94 4.30
856 954 4.202503 ACTTGTATTCCCATGAGGCCATAG 60.203 45.833 5.01 0.0 34.51 2.23
885 985 8.683615 CGATATATATACATGTACAGGTGTGGT 58.316 37.037 22.69 11.8 0.00 4.16
910 1010 5.372661 ACATATGCAGGAAACCCCTTATACT 59.627 40.000 1.58 0.0 44.85 2.12
931 1031 6.317663 ACTACGGGATAAATACAAAAGGGT 57.682 37.500 0.00 0.0 0.00 4.34
932 1032 7.436320 ACTACGGGATAAATACAAAAGGGTA 57.564 36.000 0.00 0.0 0.00 3.69
1146 1248 3.641436 ACATCTCGCTGGAATATGTACCA 59.359 43.478 0.00 0.0 30.89 3.25
1318 1421 1.212935 GGCCAGCCCTTCTCTAAATCA 59.787 52.381 0.00 0.0 0.00 2.57
1468 1578 8.198109 AGTGTATGTTCGAGTAGCAGATTTTAT 58.802 33.333 0.00 0.0 0.00 1.40
1680 1800 7.095857 GCATCTGTATTCTGTAGTTCTGTATGC 60.096 40.741 0.00 0.0 0.00 3.14
2039 2211 3.363787 GGAATGACCTTGCTTGGGT 57.636 52.632 1.00 0.0 40.13 4.51
2287 2526 4.396166 ACAATGCATAGGTCAAGTGTTAGC 59.604 41.667 0.00 0.0 0.00 3.09
2302 2541 9.772973 TCAAGTGTTAGCTTTCTGAAACTATTA 57.227 29.630 0.00 0.0 0.00 0.98
2363 2602 2.747460 GGCCAACATCGAGCTGCA 60.747 61.111 0.00 0.0 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 203 4.363990 CTGCTGTCCGCCACGTCT 62.364 66.667 0.00 0.00 38.05 4.18
363 364 3.713003 TGGAAGGTCTGATCTCTGCTAA 58.287 45.455 0.00 0.00 0.00 3.09
409 410 1.522668 CCTCGATCGATCTCTCTGCT 58.477 55.000 19.78 0.00 0.00 4.24
447 448 2.435059 GGTCTCGTTCCCTGCTGC 60.435 66.667 0.00 0.00 0.00 5.25
518 519 2.427320 TTCCTGCAGAACAGCGCT 59.573 55.556 17.39 2.64 45.78 5.92
542 543 2.113986 GTTGGGACCTGCTGTGCT 59.886 61.111 0.00 0.00 35.29 4.40
612 698 4.516195 GTCTTCCCTCCCGCTCGC 62.516 72.222 0.00 0.00 0.00 5.03
652 738 2.747855 CAGCTTGCGGTTCCTCCC 60.748 66.667 0.00 0.00 0.00 4.30
695 793 4.785453 CAGCTTGCGGTCCCTCCC 62.785 72.222 0.00 0.00 0.00 4.30
856 954 7.145985 CACCTGTACATGTATATATATCGGCC 58.854 42.308 9.18 0.00 0.00 6.13
910 1010 8.932610 TGTATACCCTTTTGTATTTATCCCGTA 58.067 33.333 0.00 0.00 33.58 4.02
1146 1248 5.559770 TCCACACATCAACACATGTTATCT 58.440 37.500 0.00 0.00 34.60 1.98
1480 1599 5.925506 TCCATTTGATGAAGCAATGACAT 57.074 34.783 0.00 0.00 0.00 3.06
1872 2006 7.445402 TCAAGACACCAAAAAGATTTAGGAGAG 59.555 37.037 4.32 0.00 0.00 3.20
2039 2211 8.321353 ACAACAATATCATAACAGAGAAGGTCA 58.679 33.333 0.00 0.00 0.00 4.02
2302 2541 6.070538 AGGAAGTTAGCATCAGTTCACAGTAT 60.071 38.462 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.