Multiple sequence alignment - TraesCS4A01G159100
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 pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
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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 primersListed 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. |
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Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.