Multiple sequence alignment - TraesCS2D01G195300
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 | TraesCS2D01G195300 | chr2D | 100.000 | 7448 | 0 | 0 | 1 | 7448 | 141483301 | 141475854 | 0.000000e+00 | 13754.0 |
1 | TraesCS2D01G195300 | chr2D | 91.503 | 459 | 27 | 3 | 6981 | 7429 | 553365735 | 553366191 | 8.210000e-174 | 621.0 |
2 | TraesCS2D01G195300 | chr2A | 94.336 | 3178 | 100 | 40 | 3 | 3145 | 159869419 | 159872551 | 0.000000e+00 | 4798.0 |
3 | TraesCS2D01G195300 | chr2A | 95.879 | 1990 | 63 | 13 | 4848 | 6829 | 159875437 | 159877415 | 0.000000e+00 | 3203.0 |
4 | TraesCS2D01G195300 | chr2A | 96.069 | 1094 | 26 | 6 | 3723 | 4816 | 159874359 | 159875435 | 0.000000e+00 | 1766.0 |
5 | TraesCS2D01G195300 | chr2A | 95.032 | 624 | 14 | 5 | 3125 | 3732 | 159873359 | 159873981 | 0.000000e+00 | 965.0 |
6 | TraesCS2D01G195300 | chr2A | 90.407 | 688 | 50 | 7 | 1 | 686 | 159867885 | 159868558 | 0.000000e+00 | 891.0 |
7 | TraesCS2D01G195300 | chr2A | 88.166 | 338 | 14 | 9 | 7112 | 7448 | 159877837 | 159878149 | 5.450000e-101 | 379.0 |
8 | TraesCS2D01G195300 | chr2A | 91.089 | 101 | 8 | 1 | 3724 | 3824 | 116449089 | 116448990 | 1.300000e-27 | 135.0 |
9 | TraesCS2D01G195300 | chr2B | 90.135 | 2960 | 174 | 42 | 558 | 3445 | 199010814 | 199013727 | 0.000000e+00 | 3740.0 |
10 | TraesCS2D01G195300 | chr2B | 92.877 | 1460 | 54 | 12 | 3444 | 4891 | 199013851 | 199015272 | 0.000000e+00 | 2074.0 |
11 | TraesCS2D01G195300 | chr2B | 92.269 | 983 | 44 | 10 | 5832 | 6803 | 199018695 | 199019656 | 0.000000e+00 | 1365.0 |
12 | TraesCS2D01G195300 | chr2B | 92.916 | 847 | 36 | 9 | 4889 | 5723 | 199015352 | 199016186 | 0.000000e+00 | 1210.0 |
13 | TraesCS2D01G195300 | chr2B | 89.439 | 303 | 31 | 1 | 1 | 303 | 199009485 | 199009786 | 1.520000e-101 | 381.0 |
14 | TraesCS2D01G195300 | chr2B | 88.104 | 269 | 22 | 5 | 303 | 571 | 199010539 | 199010797 | 2.020000e-80 | 311.0 |
15 | TraesCS2D01G195300 | chr2B | 89.423 | 104 | 11 | 0 | 3727 | 3830 | 519666436 | 519666333 | 1.690000e-26 | 132.0 |
16 | TraesCS2D01G195300 | chr1B | 85.289 | 1074 | 89 | 31 | 1466 | 2491 | 564711133 | 564710081 | 0.000000e+00 | 1044.0 |
17 | TraesCS2D01G195300 | chr1B | 85.343 | 846 | 75 | 31 | 4843 | 5682 | 274862561 | 274863363 | 0.000000e+00 | 830.0 |
18 | TraesCS2D01G195300 | chr1B | 87.255 | 612 | 39 | 13 | 1949 | 2559 | 564710607 | 564710034 | 0.000000e+00 | 662.0 |
19 | TraesCS2D01G195300 | chr1B | 80.733 | 737 | 85 | 34 | 5681 | 6379 | 274863394 | 274864111 | 8.560000e-144 | 521.0 |
20 | TraesCS2D01G195300 | chr1B | 85.098 | 510 | 54 | 12 | 979 | 1472 | 564716144 | 564715641 | 1.120000e-137 | 501.0 |
21 | TraesCS2D01G195300 | chr1B | 90.654 | 107 | 10 | 0 | 3724 | 3830 | 507850360 | 507850466 | 7.790000e-30 | 143.0 |
22 | TraesCS2D01G195300 | chr1B | 88.073 | 109 | 13 | 0 | 3722 | 3830 | 656252847 | 656252739 | 6.060000e-26 | 130.0 |
23 | TraesCS2D01G195300 | chr1B | 89.744 | 78 | 4 | 2 | 2554 | 2627 | 564697708 | 564697631 | 6.150000e-16 | 97.1 |
24 | TraesCS2D01G195300 | chr7B | 84.623 | 1021 | 105 | 26 | 979 | 1959 | 424554668 | 424553660 | 0.000000e+00 | 968.0 |
25 | TraesCS2D01G195300 | chr7B | 88.567 | 691 | 47 | 16 | 1942 | 2627 | 424553648 | 424552985 | 0.000000e+00 | 809.0 |
26 | TraesCS2D01G195300 | chr7B | 88.197 | 466 | 36 | 13 | 4862 | 5320 | 16921783 | 16921330 | 8.500000e-149 | 538.0 |
27 | TraesCS2D01G195300 | chr4A | 86.777 | 847 | 83 | 15 | 4843 | 5682 | 423377456 | 423376632 | 0.000000e+00 | 917.0 |
28 | TraesCS2D01G195300 | chr4A | 80.711 | 731 | 87 | 32 | 5681 | 6379 | 423376178 | 423375470 | 3.080000e-143 | 520.0 |
29 | TraesCS2D01G195300 | chr4A | 86.047 | 387 | 36 | 8 | 5296 | 5682 | 423376578 | 423376210 | 4.190000e-107 | 399.0 |
30 | TraesCS2D01G195300 | chr6B | 88.741 | 675 | 56 | 15 | 4843 | 5509 | 557774459 | 557773797 | 0.000000e+00 | 808.0 |
31 | TraesCS2D01G195300 | chr6B | 85.178 | 533 | 65 | 9 | 5852 | 6379 | 557773166 | 557772643 | 1.100000e-147 | 534.0 |
32 | TraesCS2D01G195300 | chr6B | 83.558 | 371 | 49 | 6 | 5838 | 6202 | 275770013 | 275769649 | 3.330000e-88 | 337.0 |
33 | TraesCS2D01G195300 | chr6B | 83.851 | 322 | 31 | 15 | 4843 | 5157 | 275771188 | 275770881 | 3.400000e-73 | 287.0 |
34 | TraesCS2D01G195300 | chr5B | 86.479 | 710 | 73 | 14 | 4857 | 5559 | 247686610 | 247685917 | 0.000000e+00 | 758.0 |
35 | TraesCS2D01G195300 | chr5B | 87.027 | 370 | 32 | 10 | 4872 | 5236 | 346440375 | 346440733 | 3.240000e-108 | 403.0 |
36 | TraesCS2D01G195300 | chr1A | 89.114 | 542 | 24 | 13 | 6921 | 7429 | 451522055 | 451521516 | 6.300000e-180 | 641.0 |
37 | TraesCS2D01G195300 | chr1A | 90.088 | 454 | 31 | 6 | 6986 | 7429 | 552086825 | 552087274 | 1.800000e-160 | 577.0 |
38 | TraesCS2D01G195300 | chr1A | 96.721 | 61 | 1 | 1 | 6921 | 6980 | 552086735 | 552086795 | 4.760000e-17 | 100.0 |
39 | TraesCS2D01G195300 | chrUn | 91.921 | 458 | 23 | 6 | 6984 | 7429 | 22375968 | 22375513 | 4.900000e-176 | 628.0 |
40 | TraesCS2D01G195300 | chr6D | 91.410 | 454 | 26 | 4 | 6986 | 7429 | 19564985 | 19564535 | 1.780000e-170 | 610.0 |
41 | TraesCS2D01G195300 | chr6D | 96.364 | 55 | 1 | 1 | 6921 | 6974 | 19565074 | 19565020 | 1.030000e-13 | 89.8 |
42 | TraesCS2D01G195300 | chr5A | 90.529 | 454 | 31 | 4 | 6986 | 7429 | 19264402 | 19264853 | 2.310000e-164 | 590.0 |
43 | TraesCS2D01G195300 | chr5A | 86.777 | 121 | 15 | 1 | 3711 | 3831 | 119997825 | 119997706 | 4.690000e-27 | 134.0 |
44 | TraesCS2D01G195300 | chr5A | 93.333 | 60 | 3 | 1 | 6921 | 6979 | 19264311 | 19264370 | 3.700000e-13 | 87.9 |
45 | TraesCS2D01G195300 | chr3B | 86.852 | 540 | 47 | 14 | 4996 | 5530 | 217400104 | 217400624 | 3.870000e-162 | 582.0 |
46 | TraesCS2D01G195300 | chr7A | 90.088 | 454 | 33 | 4 | 6986 | 7429 | 606317847 | 606317396 | 5.010000e-161 | 579.0 |
47 | TraesCS2D01G195300 | chr7A | 89.427 | 454 | 31 | 7 | 6986 | 7429 | 110398630 | 110399076 | 2.350000e-154 | 556.0 |
48 | TraesCS2D01G195300 | chr7A | 95.082 | 61 | 2 | 1 | 6921 | 6980 | 606317938 | 606317878 | 2.210000e-15 | 95.3 |
49 | TraesCS2D01G195300 | chr7A | 93.333 | 60 | 3 | 1 | 6921 | 6979 | 110398540 | 110398599 | 3.700000e-13 | 87.9 |
50 | TraesCS2D01G195300 | chr4B | 90.066 | 453 | 33 | 4 | 6987 | 7429 | 279320883 | 279320433 | 1.800000e-160 | 577.0 |
51 | TraesCS2D01G195300 | chr7D | 88.140 | 430 | 40 | 10 | 4846 | 5270 | 632829695 | 632830118 | 1.120000e-137 | 501.0 |
52 | TraesCS2D01G195300 | chr7D | 91.480 | 223 | 13 | 6 | 5309 | 5530 | 632830115 | 632830332 | 1.210000e-77 | 302.0 |
53 | TraesCS2D01G195300 | chr6A | 91.228 | 114 | 9 | 1 | 3723 | 3836 | 465229028 | 465228916 | 3.600000e-33 | 154.0 |
54 | TraesCS2D01G195300 | chr6A | 85.366 | 123 | 13 | 5 | 3724 | 3843 | 50253385 | 50253265 | 1.010000e-23 | 122.0 |
55 | TraesCS2D01G195300 | chr3D | 90.654 | 107 | 10 | 0 | 3724 | 3830 | 450875292 | 450875186 | 7.790000e-30 | 143.0 |
56 | TraesCS2D01G195300 | chr1D | 89.720 | 107 | 11 | 0 | 3724 | 3830 | 128528616 | 128528722 | 3.620000e-28 | 137.0 |
57 | TraesCS2D01G195300 | chr1D | 90.196 | 102 | 10 | 0 | 3724 | 3825 | 379139897 | 379139998 | 4.690000e-27 | 134.0 |
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 | TraesCS2D01G195300 | chr2D | 141475854 | 141483301 | 7447 | True | 13754.000000 | 13754 | 100.000000 | 1 | 7448 | 1 | chr2D.!!$R1 | 7447 |
1 | TraesCS2D01G195300 | chr2A | 159867885 | 159878149 | 10264 | False | 2000.333333 | 4798 | 93.314833 | 1 | 7448 | 6 | chr2A.!!$F1 | 7447 |
2 | TraesCS2D01G195300 | chr2B | 199009485 | 199019656 | 10171 | False | 1513.500000 | 3740 | 90.956667 | 1 | 6803 | 6 | chr2B.!!$F1 | 6802 |
3 | TraesCS2D01G195300 | chr1B | 564710034 | 564711133 | 1099 | True | 853.000000 | 1044 | 86.272000 | 1466 | 2559 | 2 | chr1B.!!$R4 | 1093 |
4 | TraesCS2D01G195300 | chr1B | 274862561 | 274864111 | 1550 | False | 675.500000 | 830 | 83.038000 | 4843 | 6379 | 2 | chr1B.!!$F2 | 1536 |
5 | TraesCS2D01G195300 | chr1B | 564715641 | 564716144 | 503 | True | 501.000000 | 501 | 85.098000 | 979 | 1472 | 1 | chr1B.!!$R2 | 493 |
6 | TraesCS2D01G195300 | chr7B | 424552985 | 424554668 | 1683 | True | 888.500000 | 968 | 86.595000 | 979 | 2627 | 2 | chr7B.!!$R2 | 1648 |
7 | TraesCS2D01G195300 | chr4A | 423375470 | 423377456 | 1986 | True | 612.000000 | 917 | 84.511667 | 4843 | 6379 | 3 | chr4A.!!$R1 | 1536 |
8 | TraesCS2D01G195300 | chr6B | 557772643 | 557774459 | 1816 | True | 671.000000 | 808 | 86.959500 | 4843 | 6379 | 2 | chr6B.!!$R2 | 1536 |
9 | TraesCS2D01G195300 | chr6B | 275769649 | 275771188 | 1539 | True | 312.000000 | 337 | 83.704500 | 4843 | 6202 | 2 | chr6B.!!$R1 | 1359 |
10 | TraesCS2D01G195300 | chr5B | 247685917 | 247686610 | 693 | True | 758.000000 | 758 | 86.479000 | 4857 | 5559 | 1 | chr5B.!!$R1 | 702 |
11 | TraesCS2D01G195300 | chr1A | 451521516 | 451522055 | 539 | True | 641.000000 | 641 | 89.114000 | 6921 | 7429 | 1 | chr1A.!!$R1 | 508 |
12 | TraesCS2D01G195300 | chr1A | 552086735 | 552087274 | 539 | False | 338.500000 | 577 | 93.404500 | 6921 | 7429 | 2 | chr1A.!!$F1 | 508 |
13 | TraesCS2D01G195300 | chr6D | 19564535 | 19565074 | 539 | True | 349.900000 | 610 | 93.887000 | 6921 | 7429 | 2 | chr6D.!!$R1 | 508 |
14 | TraesCS2D01G195300 | chr5A | 19264311 | 19264853 | 542 | False | 338.950000 | 590 | 91.931000 | 6921 | 7429 | 2 | chr5A.!!$F1 | 508 |
15 | TraesCS2D01G195300 | chr3B | 217400104 | 217400624 | 520 | False | 582.000000 | 582 | 86.852000 | 4996 | 5530 | 1 | chr3B.!!$F1 | 534 |
16 | TraesCS2D01G195300 | chr7A | 606317396 | 606317938 | 542 | True | 337.150000 | 579 | 92.585000 | 6921 | 7429 | 2 | chr7A.!!$R1 | 508 |
17 | TraesCS2D01G195300 | chr7A | 110398540 | 110399076 | 536 | False | 321.950000 | 556 | 91.380000 | 6921 | 7429 | 2 | chr7A.!!$F1 | 508 |
18 | TraesCS2D01G195300 | chr7D | 632829695 | 632830332 | 637 | False | 401.500000 | 501 | 89.810000 | 4846 | 5530 | 2 | chr7D.!!$F1 | 684 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
149 | 150 | 0.673644 | CCATCGGCGAAGAACCAACT | 60.674 | 55.000 | 15.93 | 0.00 | 0.00 | 3.16 | F |
900 | 3231 | 1.118356 | CCTCCCTTCCTCCATCTCCG | 61.118 | 65.000 | 0.00 | 0.00 | 0.00 | 4.63 | F |
2608 | 5037 | 0.622665 | CCTTCCACTTGAGATGGCCT | 59.377 | 55.000 | 3.32 | 0.00 | 37.13 | 5.19 | F |
3822 | 7631 | 1.135315 | CGACAACTAATTCCGGACGGA | 60.135 | 52.381 | 1.83 | 9.76 | 43.52 | 4.69 | F |
3824 | 7633 | 1.206371 | ACAACTAATTCCGGACGGAGG | 59.794 | 52.381 | 13.64 | 8.21 | 46.06 | 4.30 | F |
4350 | 8167 | 2.643551 | CAAAATGGTAGCTCGTGGGAT | 58.356 | 47.619 | 0.00 | 0.00 | 0.00 | 3.85 | F |
5904 | 13534 | 2.582172 | TGATGATTTCCCACTGTCCCAT | 59.418 | 45.455 | 0.00 | 0.00 | 0.00 | 4.00 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1314 | 3677 | 0.111253 | AGCAAGGGGCCATGTATAGC | 59.889 | 55.000 | 4.39 | 0.00 | 46.50 | 2.97 | R |
2864 | 5299 | 1.655484 | TGTCAACCATATGCAGAGCG | 58.345 | 50.000 | 0.00 | 0.00 | 0.00 | 5.03 | R |
4050 | 7867 | 1.893544 | TTGCCCAAACAATGCAATGG | 58.106 | 45.000 | 6.73 | 3.05 | 39.86 | 3.16 | R |
5477 | 10294 | 0.954452 | GAAACACAAGGGCCACAGAG | 59.046 | 55.000 | 6.18 | 0.00 | 0.00 | 3.35 | R |
5787 | 13384 | 5.915758 | GCACAAGAGTCGTCATACCTAATAG | 59.084 | 44.000 | 0.00 | 0.00 | 0.00 | 1.73 | R |
6249 | 13898 | 1.446792 | ACGCGCACTGGATGAAGAG | 60.447 | 57.895 | 5.73 | 0.00 | 0.00 | 2.85 | R |
7389 | 15239 | 0.234884 | CCGGAAATTAGCGCGGATTC | 59.765 | 55.000 | 8.83 | 5.74 | 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.