Multiple sequence alignment - TraesCS3D01G482300

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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 TraesCS3D01G482300 chr3D 100.000 2835 0 0 1 2835 579687339 579690173 0.000000e+00 5236
1 TraesCS3D01G482300 chr3A 95.770 2246 48 12 1 2213 714787732 714789963 0.000000e+00 3578
2 TraesCS3D01G482300 chr3A 97.973 1332 25 2 882 2213 607845896 607847225 0.000000e+00 2309
3 TraesCS3D01G482300 chr3A 95.727 866 18 3 3 861 607844817 607845670 0.000000e+00 1376
4 TraesCS3D01G482300 chr3A 93.930 626 13 2 2210 2835 714789997 714790597 0.000000e+00 922
5 TraesCS3D01G482300 chr1D 92.199 1705 65 30 555 2213 439404021 439405703 0.000000e+00 2350
6 TraesCS3D01G482300 chr1D 94.606 1372 42 7 858 2213 96035256 96033901 0.000000e+00 2095
7 TraesCS3D01G482300 chr1D 93.886 1374 51 8 858 2213 64336775 64338133 0.000000e+00 2041
8 TraesCS3D01G482300 chr1D 94.675 676 28 6 1 672 96036483 96035812 0.000000e+00 1042
9 TraesCS3D01G482300 chr1D 94.659 674 30 5 1 672 64335552 64336221 0.000000e+00 1040
10 TraesCS3D01G482300 chr1D 94.127 613 22 3 2210 2816 439405737 439406341 0.000000e+00 920
11 TraesCS3D01G482300 chr1D 94.915 531 25 2 2 531 439403041 439403570 0.000000e+00 830
12 TraesCS3D01G482300 chr1D 88.315 368 37 4 498 861 96035644 96035279 1.210000e-118 436
13 TraesCS3D01G482300 chr1B 90.850 1705 69 37 555 2213 596176024 596177687 0.000000e+00 2204
14 TraesCS3D01G482300 chr7D 89.029 1750 113 32 498 2213 600063410 600065114 0.000000e+00 2095
15 TraesCS3D01G482300 chr7D 95.536 672 26 4 3 672 600062573 600063242 0.000000e+00 1072
16 TraesCS3D01G482300 chr7D 94.728 607 30 1 2210 2816 600065148 600065752 0.000000e+00 942
17 TraesCS3D01G482300 chr4A 90.313 1373 53 18 858 2213 554699030 554700339 0.000000e+00 1725
18 TraesCS3D01G482300 chr4A 89.898 1376 60 17 858 2217 557663289 557661977 0.000000e+00 1698
19 TraesCS3D01G482300 chr4A 91.013 612 47 5 2210 2819 557661947 557661342 0.000000e+00 819
20 TraesCS3D01G482300 chr4A 90.476 609 50 5 2210 2816 554700373 554700975 0.000000e+00 797
21 TraesCS3D01G482300 chr4A 88.955 335 37 0 498 832 554698641 554698975 5.650000e-112 414
22 TraesCS3D01G482300 chr2B 87.764 1373 80 19 858 2213 755330184 755331485 0.000000e+00 1524
23 TraesCS3D01G482300 chr2B 93.243 592 39 1 2226 2816 755331619 755332210 0.000000e+00 870
24 TraesCS3D01G482300 chr3B 95.022 904 41 2 1310 2213 734913177 734912278 0.000000e+00 1417
25 TraesCS3D01G482300 chr3B 88.011 1126 68 22 1117 2213 774218732 774219819 0.000000e+00 1269
26 TraesCS3D01G482300 chr3B 94.065 674 37 3 1 672 774217351 774218023 0.000000e+00 1020
27 TraesCS3D01G482300 chr3B 93.081 607 40 2 2210 2816 734912244 734911640 0.000000e+00 887
28 TraesCS3D01G482300 chr3B 87.432 366 43 3 498 861 734913987 734913623 4.370000e-113 418
29 TraesCS3D01G482300 chr3B 96.063 127 5 0 2210 2336 550787402 550787528 1.030000e-49 207
30 TraesCS3D01G482300 chr6A 94.144 905 50 3 1310 2213 121724275 121723373 0.000000e+00 1375
31 TraesCS3D01G482300 chr6A 93.575 607 39 0 2210 2816 121723339 121722733 0.000000e+00 905
32 TraesCS3D01G482300 chr6A 93.827 567 30 4 108 672 121725818 121725255 0.000000e+00 848
33 TraesCS3D01G482300 chr6A 88.315 368 38 3 498 861 121725088 121724722 1.210000e-118 436
34 TraesCS3D01G482300 chr4D 93.358 798 22 6 858 1637 42334730 42335514 0.000000e+00 1151
35 TraesCS3D01G482300 chr4D 88.859 368 36 3 498 861 42334341 42334707 5.570000e-122 448
36 TraesCS3D01G482300 chr7B 94.499 709 37 2 1505 2213 7000041 7000747 0.000000e+00 1092
37 TraesCS3D01G482300 chr7B 94.065 674 35 4 2 672 6998201 6998872 0.000000e+00 1018
38 TraesCS3D01G482300 chr7B 92.586 607 44 1 2210 2816 7000781 7001386 0.000000e+00 870
39 TraesCS3D01G482300 chr7B 90.174 631 27 4 858 1473 6999429 7000039 0.000000e+00 789
40 TraesCS3D01G482300 chr6B 89.489 333 34 1 498 830 144007234 144007565 1.210000e-113 420


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 TraesCS3D01G482300 chr3D 579687339 579690173 2834 False 5236.000000 5236 100.000000 1 2835 1 chr3D.!!$F1 2834
1 TraesCS3D01G482300 chr3A 714787732 714790597 2865 False 2250.000000 3578 94.850000 1 2835 2 chr3A.!!$F2 2834
2 TraesCS3D01G482300 chr3A 607844817 607847225 2408 False 1842.500000 2309 96.850000 3 2213 2 chr3A.!!$F1 2210
3 TraesCS3D01G482300 chr1D 64335552 64338133 2581 False 1540.500000 2041 94.272500 1 2213 2 chr1D.!!$F1 2212
4 TraesCS3D01G482300 chr1D 439403041 439406341 3300 False 1366.666667 2350 93.747000 2 2816 3 chr1D.!!$F2 2814
5 TraesCS3D01G482300 chr1D 96033901 96036483 2582 True 1191.000000 2095 92.532000 1 2213 3 chr1D.!!$R1 2212
6 TraesCS3D01G482300 chr1B 596176024 596177687 1663 False 2204.000000 2204 90.850000 555 2213 1 chr1B.!!$F1 1658
7 TraesCS3D01G482300 chr7D 600062573 600065752 3179 False 1369.666667 2095 93.097667 3 2816 3 chr7D.!!$F1 2813
8 TraesCS3D01G482300 chr4A 557661342 557663289 1947 True 1258.500000 1698 90.455500 858 2819 2 chr4A.!!$R1 1961
9 TraesCS3D01G482300 chr4A 554698641 554700975 2334 False 978.666667 1725 89.914667 498 2816 3 chr4A.!!$F1 2318
10 TraesCS3D01G482300 chr2B 755330184 755332210 2026 False 1197.000000 1524 90.503500 858 2816 2 chr2B.!!$F1 1958
11 TraesCS3D01G482300 chr3B 774217351 774219819 2468 False 1144.500000 1269 91.038000 1 2213 2 chr3B.!!$F2 2212
12 TraesCS3D01G482300 chr3B 734911640 734913987 2347 True 907.333333 1417 91.845000 498 2816 3 chr3B.!!$R1 2318
13 TraesCS3D01G482300 chr6A 121722733 121725818 3085 True 891.000000 1375 92.465250 108 2816 4 chr6A.!!$R1 2708
14 TraesCS3D01G482300 chr4D 42334341 42335514 1173 False 799.500000 1151 91.108500 498 1637 2 chr4D.!!$F1 1139
15 TraesCS3D01G482300 chr7B 6998201 7001386 3185 False 942.250000 1092 92.831000 2 2816 4 chr7B.!!$F1 2814

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
82 85 1.457009 GGCGTGGCCTGGTTGTTAAA 61.457 55.000 3.32 0.0 46.69 1.52 F
357 376 1.672356 GCACCACCCTGTAGCACTG 60.672 63.158 0.00 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 2490 7.036220 TCAAAAGAATACCTCTCTCGACATTC 58.964 38.462 0.0 0.0 31.02 2.67 R
2356 3313 3.682718 CGGGGATGAGCAACATAAAGTCT 60.683 47.826 0.0 0.0 39.56 3.24 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
82 85 1.457009 GGCGTGGCCTGGTTGTTAAA 61.457 55.000 3.32 0.00 46.69 1.52
189 193 6.036517 GTGGAGAATACTGCTTATGAACTGTG 59.963 42.308 0.00 0.00 35.49 3.66
357 376 1.672356 GCACCACCCTGTAGCACTG 60.672 63.158 0.00 0.00 0.00 3.66
404 570 8.518430 ACCAAAAGAAATTAAAATTGCCAAGT 57.482 26.923 0.00 0.00 0.00 3.16
846 1401 9.453572 GGGTATATGATGATTGTTCACACATAT 57.546 33.333 15.24 15.24 41.96 1.78
853 1408 9.406113 TGATGATTGTTCACACATATAATTCCA 57.594 29.630 0.00 0.00 33.85 3.53
856 1411 8.136800 TGATTGTTCACACATATAATTCCATGC 58.863 33.333 0.00 0.00 31.06 4.06
1473 2282 7.990886 TGGTTACTTCAACAACTTAATCTCACT 59.009 33.333 0.00 0.00 39.04 3.41
1679 2490 1.774254 TGGGTGGATGTATAGGCAAGG 59.226 52.381 0.00 0.00 0.00 3.61
1813 2639 9.398170 CCATTTGTGTACTTCTATTTGTTCTTG 57.602 33.333 0.00 0.00 0.00 3.02
2356 3313 1.864263 TTCCCTCTCCTCTCGCCTCA 61.864 60.000 0.00 0.00 0.00 3.86
2436 3393 5.180367 TGATTTGTCATTTTGCTCGTTCA 57.820 34.783 0.00 0.00 0.00 3.18
2826 3790 2.279851 CGTGTTCACGGTGGAGCA 60.280 61.111 16.17 2.46 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 85 2.291540 CCCCCATGACCAGTAACAACAT 60.292 50.000 0.0 0.0 0.00 2.71
189 193 8.090831 TGAGTCAATCATATTAGTAGTCCATGC 58.909 37.037 0.0 0.0 31.12 4.06
357 376 6.934645 TGGTTATGGCAGTTAAGATAGCATAC 59.065 38.462 0.0 0.0 0.00 2.39
794 1309 9.093970 CGTCCAGTACAATGATTAGAACAATTA 57.906 33.333 0.0 0.0 0.00 1.40
799 1314 4.809426 CCCGTCCAGTACAATGATTAGAAC 59.191 45.833 0.0 0.0 0.00 3.01
1679 2490 7.036220 TCAAAAGAATACCTCTCTCGACATTC 58.964 38.462 0.0 0.0 31.02 2.67
2356 3313 3.682718 CGGGGATGAGCAACATAAAGTCT 60.683 47.826 0.0 0.0 39.56 3.24
2436 3393 3.005554 CACTTCAAGGCAGATGAATCGT 58.994 45.455 0.0 0.0 36.30 3.73


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

AutoCloner maintained by Alex Coulton.