Multiple sequence alignment - TraesCS4A01G159100

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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 TraesCS4A01G159100 chr4A 100.000 5130 0 0 1 5130 331627893 331633022 0.000000e+00 9474.0
1 TraesCS4A01G159100 chr4A 88.337 403 27 2 4735 5118 195472719 195472318 2.800000e-127 466.0
2 TraesCS4A01G159100 chr4A 87.437 398 30 8 4740 5118 534275915 534275519 1.700000e-119 440.0
3 TraesCS4A01G159100 chr4A 86.935 398 32 2 4740 5118 195459571 195459175 3.670000e-116 429.0
4 TraesCS4A01G159100 chr4A 86.618 411 27 6 4734 5118 534327396 534326988 3.670000e-116 429.0
5 TraesCS4A01G159100 chr4A 72.844 545 113 20 75 616 675194243 675193731 2.470000e-33 154.0
6 TraesCS4A01G159100 chr4D 94.316 1865 91 11 1824 3681 154794552 154796408 0.000000e+00 2843.0
7 TraesCS4A01G159100 chr4D 95.006 821 27 4 839 1648 154793750 154794567 0.000000e+00 1277.0
8 TraesCS4A01G159100 chr4D 95.741 634 17 3 3807 4431 154796413 154797045 0.000000e+00 1013.0
9 TraesCS4A01G159100 chr4D 75.762 656 132 21 59 707 312589457 312588822 6.450000e-79 305.0
10 TraesCS4A01G159100 chr4D 82.178 101 18 0 77 177 92065324 92065224 2.540000e-13 87.9
11 TraesCS4A01G159100 chr4B 93.710 1860 89 13 1824 3680 312787663 312785829 0.000000e+00 2761.0
12 TraesCS4A01G159100 chr4B 93.397 833 31 7 835 1648 312788475 312787648 0.000000e+00 1212.0
13 TraesCS4A01G159100 chr4B 94.879 371 11 2 3807 4169 312785823 312785453 1.600000e-159 573.0
14 TraesCS4A01G159100 chr4B 95.671 231 10 0 4167 4397 312785186 312784956 6.270000e-99 372.0
15 TraesCS4A01G159100 chr4B 77.245 646 129 13 53 689 635626105 635626741 3.780000e-96 363.0
16 TraesCS4A01G159100 chr4B 90.385 104 10 0 3704 3807 570190790 570190893 2.490000e-28 137.0
17 TraesCS4A01G159100 chr4B 90.123 81 8 0 52 132 670901703 670901783 7.020000e-19 106.0
18 TraesCS4A01G159100 chr4B 91.304 69 4 1 4388 4456 312777139 312777073 5.470000e-15 93.5
19 TraesCS4A01G159100 chr5A 88.161 397 29 6 4740 5118 347338567 347338171 1.680000e-124 457.0
20 TraesCS4A01G159100 chr5A 87.654 405 31 7 4733 5118 310864797 310864393 2.180000e-123 453.0
21 TraesCS4A01G159100 chr5A 87.909 397 30 1 4740 5118 450594364 450593968 7.830000e-123 451.0
22 TraesCS4A01G159100 chr5A 86.310 168 19 4 1648 1814 14488160 14488324 4.080000e-41 180.0
23 TraesCS4A01G159100 chr5A 76.103 272 54 9 499 763 119850578 119850311 1.160000e-26 132.0
24 TraesCS4A01G159100 chr5A 87.879 66 4 4 3741 3804 596060901 596060838 1.980000e-09 75.0
25 TraesCS4A01G159100 chr2A 87.848 395 29 4 4743 5118 421443058 421442664 3.640000e-121 446.0
26 TraesCS4A01G159100 chr2A 92.683 123 8 1 3681 3803 83914030 83913909 5.280000e-40 176.0
27 TraesCS4A01G159100 chr3A 87.250 400 32 2 4737 5118 414808122 414807724 6.100000e-119 438.0
28 TraesCS4A01G159100 chr3A 86.750 400 31 4 4740 5118 222365665 222366063 4.750000e-115 425.0
29 TraesCS4A01G159100 chr3A 75.133 563 116 17 53 613 629627468 629628008 5.130000e-60 243.0
30 TraesCS4A01G159100 chr3A 90.798 163 15 0 4740 4902 414794910 414794748 8.650000e-53 219.0
31 TraesCS4A01G159100 chr3A 72.324 654 134 32 84 722 115620552 115619931 1.480000e-35 161.0
32 TraesCS4A01G159100 chr1A 86.902 397 34 10 4740 5118 334537484 334537880 3.670000e-116 429.0
33 TraesCS4A01G159100 chr1A 88.889 54 3 2 3642 3693 153340523 153340575 4.290000e-06 63.9
34 TraesCS4A01G159100 chr1A 97.222 36 1 0 3645 3680 335033491 335033526 1.540000e-05 62.1
35 TraesCS4A01G159100 chr3D 78.120 681 137 11 81 757 177775172 177774500 6.140000e-114 422.0
36 TraesCS4A01G159100 chr3D 74.601 689 147 22 75 754 495912824 495913493 1.410000e-70 278.0
37 TraesCS4A01G159100 chr3D 79.211 279 40 12 4461 4731 569469683 569469415 1.470000e-40 178.0
38 TraesCS4A01G159100 chr3D 89.831 59 6 0 4398 4456 61758703 61758645 5.510000e-10 76.8
39 TraesCS4A01G159100 chr7D 77.692 650 126 15 53 698 98032919 98033553 3.750000e-101 379.0
40 TraesCS4A01G159100 chr7D 100.000 35 0 0 3646 3680 112131325 112131359 1.190000e-06 65.8
41 TraesCS4A01G159100 chr5D 80.720 389 63 10 4740 5118 388285843 388285457 5.020000e-75 292.0
42 TraesCS4A01G159100 chr5D 91.803 183 11 4 1646 1827 353404164 353404343 8.530000e-63 252.0
43 TraesCS4A01G159100 chr5D 85.093 161 21 3 1648 1808 565262397 565262240 1.480000e-35 161.0
44 TraesCS4A01G159100 chr5D 83.333 132 16 5 4600 4728 463930336 463930208 3.250000e-22 117.0
45 TraesCS4A01G159100 chr7B 75.671 596 129 15 76 666 690288193 690287609 3.020000e-72 283.0
46 TraesCS4A01G159100 chr7B 87.879 66 4 3 3741 3804 192109593 192109656 1.980000e-09 75.0
47 TraesCS4A01G159100 chr6D 78.641 412 80 8 259 667 298155673 298155267 3.050000e-67 267.0
48 TraesCS4A01G159100 chr6D 74.080 679 139 30 75 746 83251732 83252380 1.430000e-60 244.0
49 TraesCS4A01G159100 chr6D 72.601 719 170 20 59 758 412012045 412011335 1.450000e-50 211.0
50 TraesCS4A01G159100 chr2B 91.061 179 14 2 1649 1827 768012399 768012575 1.850000e-59 241.0
51 TraesCS4A01G159100 chr2B 84.177 158 12 10 1648 1798 557339950 557340101 1.930000e-29 141.0
52 TraesCS4A01G159100 chr2B 85.135 74 7 4 3735 3804 154350449 154350522 7.130000e-09 73.1
53 TraesCS4A01G159100 chr7A 90.503 179 15 2 1649 1827 639691685 639691861 8.590000e-58 235.0
54 TraesCS4A01G159100 chr7A 73.833 707 132 33 53 757 165225019 165225674 1.110000e-56 231.0
55 TraesCS4A01G159100 chr7A 100.000 35 0 0 3646 3680 117087385 117087419 1.190000e-06 65.8
56 TraesCS4A01G159100 chr1D 86.503 163 18 4 1649 1809 359835324 359835484 5.280000e-40 176.0
57 TraesCS4A01G159100 chr1D 88.235 68 6 2 3741 3806 311255638 311255705 4.260000e-11 80.5
58 TraesCS4A01G159100 chr1D 90.000 60 6 0 4393 4452 464869687 464869746 1.530000e-10 78.7
59 TraesCS4A01G159100 chr1D 97.368 38 0 1 3643 3680 481618372 481618336 4.290000e-06 63.9
60 TraesCS4A01G159100 chr1D 100.000 28 0 0 770 797 451865880 451865907 9.000000e-03 52.8
61 TraesCS4A01G159100 chrUn 84.868 152 18 5 1648 1797 204478498 204478646 1.150000e-31 148.0
62 TraesCS4A01G159100 chrUn 84.211 152 17 7 1649 1797 231014845 231014992 1.930000e-29 141.0
63 TraesCS4A01G159100 chrUn 100.000 28 0 0 770 797 26965647 26965674 9.000000e-03 52.8
64 TraesCS4A01G159100 chr3B 76.493 268 58 2 53 319 227823201 227823464 1.930000e-29 141.0
65 TraesCS4A01G159100 chr6A 91.176 102 8 1 3703 3804 586897787 586897887 2.490000e-28 137.0
66 TraesCS4A01G159100 chr6B 87.692 65 6 2 3741 3803 359755678 359755614 1.980000e-09 75.0
67 TraesCS4A01G159100 chr6B 86.364 66 5 4 3741 3803 665290683 665290619 9.220000e-08 69.4
68 TraesCS4A01G159100 chr1B 100.000 36 0 0 3645 3680 345325194 345325229 3.310000e-07 67.6
69 TraesCS4A01G159100 chr1B 97.222 36 1 0 3645 3680 631859370 631859405 1.540000e-05 62.1


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 TraesCS4A01G159100 chr4A 331627893 331633022 5129 False 9474.0 9474 100.00000 1 5130 1 chr4A.!!$F1 5129
1 TraesCS4A01G159100 chr4D 154793750 154797045 3295 False 1711.0 2843 95.02100 839 4431 3 chr4D.!!$F1 3592
2 TraesCS4A01G159100 chr4D 312588822 312589457 635 True 305.0 305 75.76200 59 707 1 chr4D.!!$R2 648
3 TraesCS4A01G159100 chr4B 312784956 312788475 3519 True 1229.5 2761 94.41425 835 4397 4 chr4B.!!$R2 3562
4 TraesCS4A01G159100 chr4B 635626105 635626741 636 False 363.0 363 77.24500 53 689 1 chr4B.!!$F2 636
5 TraesCS4A01G159100 chr3A 629627468 629628008 540 False 243.0 243 75.13300 53 613 1 chr3A.!!$F2 560
6 TraesCS4A01G159100 chr3D 177774500 177775172 672 True 422.0 422 78.12000 81 757 1 chr3D.!!$R2 676
7 TraesCS4A01G159100 chr3D 495912824 495913493 669 False 278.0 278 74.60100 75 754 1 chr3D.!!$F1 679
8 TraesCS4A01G159100 chr7D 98032919 98033553 634 False 379.0 379 77.69200 53 698 1 chr7D.!!$F1 645
9 TraesCS4A01G159100 chr7B 690287609 690288193 584 True 283.0 283 75.67100 76 666 1 chr7B.!!$R1 590
10 TraesCS4A01G159100 chr6D 83251732 83252380 648 False 244.0 244 74.08000 75 746 1 chr6D.!!$F1 671
11 TraesCS4A01G159100 chr6D 412011335 412012045 710 True 211.0 211 72.60100 59 758 1 chr6D.!!$R2 699
12 TraesCS4A01G159100 chr7A 165225019 165225674 655 False 231.0 231 73.83300 53 757 1 chr7A.!!$F2 704


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
24 25 0.041238 TCATCGGAGGAGGTGGAACT 59.959 55.0 0.00 0.0 36.74 3.01 F
820 861 0.108520 GACGCCGGATAACCTGAACA 60.109 55.0 5.05 0.0 0.00 3.18 F
1722 1782 0.178981 AACAGGCAGCATCCAACAGT 60.179 50.0 0.00 0.0 0.00 3.55 F
1773 1833 0.178068 GCCGAAGCCCAAGTGAGATA 59.822 55.0 0.00 0.0 0.00 1.98 F
1787 1847 0.179045 GAGATACATGCAACCGGCCT 60.179 55.0 0.00 0.0 43.89 5.19 F
2704 2766 0.250209 CCTGACTGTCTTGCTGCTGT 60.250 55.0 9.51 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1814 0.178068 TATCTCACTTGGGCTTCGGC 59.822 55.0 0.00 0.0 40.88 5.54 R
1768 1828 0.179045 AGGCCGGTTGCATGTATCTC 60.179 55.0 1.90 0.0 43.89 2.75 R
3688 3765 0.395312 GAAAGACCGGGTGTGAAGGA 59.605 55.0 3.30 0.0 0.00 3.36 R
3689 3766 0.396811 AGAAAGACCGGGTGTGAAGG 59.603 55.0 3.30 0.0 0.00 3.46 R
3697 3774 0.875059 GCAACAGAAGAAAGACCGGG 59.125 55.0 6.32 0.0 0.00 5.73 R
4635 4990 0.034477 ACGGGGGTGGTGATTGATTC 60.034 55.0 0.00 0.0 0.00 2.52 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)



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AutoCloner maintained by Alex Coulton.