Multiple sequence alignment - TraesCS1A01G209200
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 | TraesCS1A01G209200 | chr1A | 100.000 | 4421 | 0 | 0 | 1 | 4421 | 371315911 | 371320331 | 0.000000e+00 | 8165 |
1 | TraesCS1A01G209200 | chr1A | 92.321 | 599 | 37 | 4 | 754 | 1350 | 562292723 | 562292132 | 0.000000e+00 | 843 |
2 | TraesCS1A01G209200 | chr5B | 94.135 | 1381 | 72 | 6 | 1347 | 2721 | 472026411 | 472025034 | 0.000000e+00 | 2093 |
3 | TraesCS1A01G209200 | chr5B | 94.649 | 598 | 31 | 1 | 754 | 1350 | 631209546 | 631210143 | 0.000000e+00 | 926 |
4 | TraesCS1A01G209200 | chr5B | 85.714 | 595 | 56 | 6 | 1 | 570 | 472027206 | 472026616 | 6.330000e-168 | 601 |
5 | TraesCS1A01G209200 | chr5B | 88.925 | 307 | 30 | 2 | 2266 | 2569 | 328278775 | 328278470 | 4.170000e-100 | 375 |
6 | TraesCS1A01G209200 | chr5B | 88.710 | 186 | 19 | 1 | 572 | 755 | 472026579 | 472026394 | 4.450000e-55 | 226 |
7 | TraesCS1A01G209200 | chr2B | 93.917 | 1381 | 75 | 6 | 1347 | 2721 | 222940147 | 222941524 | 0.000000e+00 | 2076 |
8 | TraesCS1A01G209200 | chr2B | 92.453 | 636 | 37 | 5 | 3788 | 4421 | 707739610 | 707740236 | 0.000000e+00 | 898 |
9 | TraesCS1A01G209200 | chr2B | 91.853 | 626 | 47 | 3 | 3007 | 3632 | 707737966 | 707738587 | 0.000000e+00 | 870 |
10 | TraesCS1A01G209200 | chr2B | 91.536 | 638 | 41 | 8 | 3788 | 4421 | 407885658 | 407886286 | 0.000000e+00 | 867 |
11 | TraesCS1A01G209200 | chr2B | 91.379 | 638 | 42 | 7 | 3788 | 4421 | 371367353 | 371366725 | 0.000000e+00 | 861 |
12 | TraesCS1A01G209200 | chr2B | 85.428 | 549 | 53 | 9 | 47 | 570 | 222939397 | 222939943 | 3.010000e-151 | 545 |
13 | TraesCS1A01G209200 | chr2B | 94.767 | 172 | 7 | 2 | 3632 | 3803 | 371367543 | 371367374 | 2.620000e-67 | 267 |
14 | TraesCS1A01G209200 | chr2B | 93.820 | 178 | 9 | 2 | 3626 | 3803 | 407885462 | 407885637 | 2.620000e-67 | 267 |
15 | TraesCS1A01G209200 | chr2B | 94.771 | 153 | 7 | 1 | 572 | 724 | 222939980 | 222940131 | 2.060000e-58 | 237 |
16 | TraesCS1A01G209200 | chr2B | 82.486 | 177 | 21 | 6 | 1 | 175 | 376460744 | 376460576 | 3.560000e-31 | 147 |
17 | TraesCS1A01G209200 | chr7B | 93.845 | 1381 | 79 | 4 | 1347 | 2721 | 478619336 | 478617956 | 0.000000e+00 | 2074 |
18 | TraesCS1A01G209200 | chr7B | 85.333 | 600 | 79 | 8 | 754 | 1350 | 496648404 | 496648997 | 2.920000e-171 | 612 |
19 | TraesCS1A01G209200 | chr7B | 87.292 | 480 | 60 | 1 | 92 | 570 | 478620021 | 478619542 | 8.360000e-152 | 547 |
20 | TraesCS1A01G209200 | chr7B | 94.798 | 173 | 6 | 3 | 3632 | 3803 | 43124791 | 43124621 | 2.620000e-67 | 267 |
21 | TraesCS1A01G209200 | chr7B | 88.770 | 187 | 18 | 2 | 572 | 755 | 478619505 | 478619319 | 4.450000e-55 | 226 |
22 | TraesCS1A01G209200 | chr4B | 93.551 | 1380 | 81 | 6 | 1347 | 2719 | 115709337 | 115707959 | 0.000000e+00 | 2049 |
23 | TraesCS1A01G209200 | chr4B | 87.772 | 597 | 63 | 4 | 754 | 1350 | 51452078 | 51452664 | 0.000000e+00 | 689 |
24 | TraesCS1A01G209200 | chr4B | 83.878 | 490 | 55 | 11 | 105 | 570 | 115710031 | 115709542 | 3.140000e-121 | 446 |
25 | TraesCS1A01G209200 | chr4B | 93.464 | 153 | 10 | 0 | 572 | 724 | 115709505 | 115709353 | 1.240000e-55 | 228 |
26 | TraesCS1A01G209200 | chr4B | 83.750 | 160 | 17 | 5 | 20 | 177 | 434965326 | 434965478 | 4.610000e-30 | 143 |
27 | TraesCS1A01G209200 | chr4B | 82.530 | 166 | 20 | 4 | 9 | 172 | 444498535 | 444498377 | 2.140000e-28 | 137 |
28 | TraesCS1A01G209200 | chr6B | 93.560 | 1382 | 66 | 11 | 1347 | 2721 | 140954832 | 140956197 | 0.000000e+00 | 2037 |
29 | TraesCS1A01G209200 | chr6B | 91.223 | 638 | 43 | 7 | 3788 | 4421 | 308976223 | 308976851 | 0.000000e+00 | 856 |
30 | TraesCS1A01G209200 | chr6B | 90.909 | 638 | 45 | 7 | 3788 | 4421 | 570078675 | 570079303 | 0.000000e+00 | 845 |
31 | TraesCS1A01G209200 | chr6B | 91.069 | 627 | 47 | 4 | 3007 | 3632 | 308974588 | 308975206 | 0.000000e+00 | 839 |
32 | TraesCS1A01G209200 | chr6B | 95.930 | 172 | 5 | 2 | 3632 | 3803 | 361273066 | 361272897 | 1.210000e-70 | 278 |
33 | TraesCS1A01G209200 | chr6B | 91.457 | 199 | 14 | 1 | 44 | 239 | 140947314 | 140947512 | 2.030000e-68 | 270 |
34 | TraesCS1A01G209200 | chr6B | 93.820 | 178 | 8 | 3 | 3626 | 3803 | 570078480 | 570078654 | 9.430000e-67 | 265 |
35 | TraesCS1A01G209200 | chr6B | 93.258 | 178 | 10 | 2 | 3626 | 3803 | 308976027 | 308976202 | 1.220000e-65 | 261 |
36 | TraesCS1A01G209200 | chr6B | 92.258 | 155 | 12 | 0 | 570 | 724 | 140954662 | 140954816 | 2.070000e-53 | 220 |
37 | TraesCS1A01G209200 | chr6B | 83.884 | 242 | 27 | 3 | 2683 | 2924 | 293587612 | 293587841 | 2.070000e-53 | 220 |
38 | TraesCS1A01G209200 | chrUn | 93.761 | 1122 | 64 | 4 | 1605 | 2721 | 116803744 | 116802624 | 0.000000e+00 | 1679 |
39 | TraesCS1A01G209200 | chrUn | 84.538 | 595 | 67 | 10 | 1 | 570 | 116804765 | 116804171 | 2.310000e-157 | 566 |
40 | TraesCS1A01G209200 | chr1B | 94.303 | 983 | 50 | 4 | 1744 | 2721 | 278152290 | 278153271 | 0.000000e+00 | 1500 |
41 | TraesCS1A01G209200 | chr1B | 93.049 | 633 | 35 | 3 | 3788 | 4420 | 519434570 | 519433947 | 0.000000e+00 | 917 |
42 | TraesCS1A01G209200 | chr3B | 93.553 | 636 | 30 | 5 | 3788 | 4421 | 446527270 | 446527896 | 0.000000e+00 | 937 |
43 | TraesCS1A01G209200 | chr3B | 93.322 | 584 | 39 | 0 | 3049 | 3632 | 522282125 | 522281542 | 0.000000e+00 | 863 |
44 | TraesCS1A01G209200 | chr3B | 87.914 | 513 | 49 | 8 | 2266 | 2768 | 522246408 | 522245899 | 3.810000e-165 | 592 |
45 | TraesCS1A01G209200 | chr3B | 85.321 | 327 | 47 | 1 | 1934 | 2259 | 434509613 | 434509939 | 1.970000e-88 | 337 |
46 | TraesCS1A01G209200 | chr3B | 87.692 | 260 | 32 | 0 | 1991 | 2250 | 383355666 | 383355407 | 2.000000e-78 | 303 |
47 | TraesCS1A01G209200 | chr3B | 94.253 | 174 | 8 | 2 | 3630 | 3803 | 446527078 | 446527249 | 9.430000e-67 | 265 |
48 | TraesCS1A01G209200 | chr3B | 79.897 | 194 | 30 | 4 | 1 | 192 | 151832024 | 151831838 | 2.770000e-27 | 134 |
49 | TraesCS1A01G209200 | chr3A | 92.982 | 627 | 41 | 3 | 3007 | 3632 | 87730092 | 87730716 | 0.000000e+00 | 911 |
50 | TraesCS1A01G209200 | chr3A | 92.453 | 636 | 36 | 9 | 3788 | 4421 | 87731752 | 87732377 | 0.000000e+00 | 898 |
51 | TraesCS1A01G209200 | chr3A | 92.453 | 636 | 35 | 8 | 3788 | 4421 | 476147871 | 476147247 | 0.000000e+00 | 896 |
52 | TraesCS1A01G209200 | chr3A | 91.759 | 631 | 49 | 3 | 3004 | 3632 | 476157134 | 476156505 | 0.000000e+00 | 874 |
53 | TraesCS1A01G209200 | chr3A | 91.547 | 627 | 49 | 3 | 3007 | 3632 | 679990336 | 679990959 | 0.000000e+00 | 861 |
54 | TraesCS1A01G209200 | chr3A | 87.173 | 421 | 38 | 12 | 1355 | 1765 | 217011965 | 217012379 | 8.660000e-127 | 464 |
55 | TraesCS1A01G209200 | chr3A | 86.682 | 428 | 39 | 15 | 1348 | 1765 | 216936493 | 216936912 | 4.030000e-125 | 459 |
56 | TraesCS1A01G209200 | chr3A | 92.697 | 178 | 11 | 2 | 3626 | 3803 | 87731556 | 87731731 | 5.670000e-64 | 255 |
57 | TraesCS1A01G209200 | chr2A | 93.802 | 597 | 36 | 1 | 754 | 1350 | 770167172 | 770166577 | 0.000000e+00 | 896 |
58 | TraesCS1A01G209200 | chr2A | 91.820 | 599 | 43 | 2 | 753 | 1350 | 477613944 | 477613351 | 0.000000e+00 | 830 |
59 | TraesCS1A01G209200 | chr2A | 80.928 | 194 | 27 | 6 | 1 | 192 | 488386288 | 488386103 | 1.280000e-30 | 145 |
60 | TraesCS1A01G209200 | chr6A | 92.151 | 637 | 37 | 9 | 3788 | 4421 | 370481494 | 370482120 | 0.000000e+00 | 887 |
61 | TraesCS1A01G209200 | chr6A | 91.707 | 627 | 47 | 5 | 3007 | 3632 | 29436178 | 29436800 | 0.000000e+00 | 865 |
62 | TraesCS1A01G209200 | chr6A | 89.202 | 639 | 31 | 12 | 3788 | 4421 | 347378769 | 347378164 | 0.000000e+00 | 763 |
63 | TraesCS1A01G209200 | chr5A | 91.879 | 628 | 47 | 4 | 3007 | 3632 | 564441686 | 564441061 | 0.000000e+00 | 874 |
64 | TraesCS1A01G209200 | chr5A | 91.261 | 595 | 45 | 2 | 754 | 1348 | 408131773 | 408131186 | 0.000000e+00 | 804 |
65 | TraesCS1A01G209200 | chr7A | 91.325 | 634 | 41 | 8 | 3788 | 4419 | 587285047 | 587284426 | 0.000000e+00 | 854 |
66 | TraesCS1A01G209200 | chr7A | 91.200 | 625 | 51 | 4 | 3009 | 3632 | 587286694 | 587286073 | 0.000000e+00 | 846 |
67 | TraesCS1A01G209200 | chr2D | 91.333 | 600 | 42 | 4 | 754 | 1350 | 303501395 | 303500803 | 0.000000e+00 | 811 |
68 | TraesCS1A01G209200 | chr2D | 87.648 | 421 | 36 | 14 | 1355 | 1765 | 161651795 | 161651381 | 4.000000e-130 | 475 |
69 | TraesCS1A01G209200 | chr4D | 90.297 | 639 | 24 | 14 | 3788 | 4421 | 255552770 | 255553375 | 0.000000e+00 | 802 |
70 | TraesCS1A01G209200 | chr4D | 85.464 | 571 | 65 | 13 | 2443 | 3006 | 448360124 | 448359565 | 2.960000e-161 | 579 |
71 | TraesCS1A01G209200 | chr4D | 93.258 | 178 | 10 | 2 | 3626 | 3803 | 255552574 | 255552749 | 1.220000e-65 | 261 |
72 | TraesCS1A01G209200 | chr3D | 90.847 | 590 | 46 | 4 | 754 | 1342 | 227670788 | 227670206 | 0.000000e+00 | 784 |
73 | TraesCS1A01G209200 | chr3D | 84.393 | 346 | 50 | 2 | 14 | 356 | 236112470 | 236112814 | 1.970000e-88 | 337 |
74 | TraesCS1A01G209200 | chr6D | 89.671 | 639 | 28 | 12 | 3788 | 4421 | 225586819 | 225586214 | 0.000000e+00 | 780 |
75 | TraesCS1A01G209200 | chr6D | 87.173 | 421 | 38 | 14 | 1355 | 1765 | 197263410 | 197263824 | 8.660000e-127 | 464 |
76 | TraesCS1A01G209200 | chr6D | 86.041 | 437 | 46 | 13 | 1356 | 1782 | 338138541 | 338138110 | 5.210000e-124 | 455 |
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 | TraesCS1A01G209200 | chr1A | 371315911 | 371320331 | 4420 | False | 8165.000000 | 8165 | 100.000000 | 1 | 4421 | 1 | chr1A.!!$F1 | 4420 |
1 | TraesCS1A01G209200 | chr1A | 562292132 | 562292723 | 591 | True | 843.000000 | 843 | 92.321000 | 754 | 1350 | 1 | chr1A.!!$R1 | 596 |
2 | TraesCS1A01G209200 | chr5B | 472025034 | 472027206 | 2172 | True | 973.333333 | 2093 | 89.519667 | 1 | 2721 | 3 | chr5B.!!$R2 | 2720 |
3 | TraesCS1A01G209200 | chr5B | 631209546 | 631210143 | 597 | False | 926.000000 | 926 | 94.649000 | 754 | 1350 | 1 | chr5B.!!$F1 | 596 |
4 | TraesCS1A01G209200 | chr2B | 222939397 | 222941524 | 2127 | False | 952.666667 | 2076 | 91.372000 | 47 | 2721 | 3 | chr2B.!!$F1 | 2674 |
5 | TraesCS1A01G209200 | chr2B | 707737966 | 707740236 | 2270 | False | 884.000000 | 898 | 92.153000 | 3007 | 4421 | 2 | chr2B.!!$F3 | 1414 |
6 | TraesCS1A01G209200 | chr2B | 407885462 | 407886286 | 824 | False | 567.000000 | 867 | 92.678000 | 3626 | 4421 | 2 | chr2B.!!$F2 | 795 |
7 | TraesCS1A01G209200 | chr2B | 371366725 | 371367543 | 818 | True | 564.000000 | 861 | 93.073000 | 3632 | 4421 | 2 | chr2B.!!$R2 | 789 |
8 | TraesCS1A01G209200 | chr7B | 478617956 | 478620021 | 2065 | True | 949.000000 | 2074 | 89.969000 | 92 | 2721 | 3 | chr7B.!!$R2 | 2629 |
9 | TraesCS1A01G209200 | chr7B | 496648404 | 496648997 | 593 | False | 612.000000 | 612 | 85.333000 | 754 | 1350 | 1 | chr7B.!!$F1 | 596 |
10 | TraesCS1A01G209200 | chr4B | 115707959 | 115710031 | 2072 | True | 907.666667 | 2049 | 90.297667 | 105 | 2719 | 3 | chr4B.!!$R2 | 2614 |
11 | TraesCS1A01G209200 | chr4B | 51452078 | 51452664 | 586 | False | 689.000000 | 689 | 87.772000 | 754 | 1350 | 1 | chr4B.!!$F1 | 596 |
12 | TraesCS1A01G209200 | chr6B | 140954662 | 140956197 | 1535 | False | 1128.500000 | 2037 | 92.909000 | 570 | 2721 | 2 | chr6B.!!$F3 | 2151 |
13 | TraesCS1A01G209200 | chr6B | 308974588 | 308976851 | 2263 | False | 652.000000 | 856 | 91.850000 | 3007 | 4421 | 3 | chr6B.!!$F4 | 1414 |
14 | TraesCS1A01G209200 | chr6B | 570078480 | 570079303 | 823 | False | 555.000000 | 845 | 92.364500 | 3626 | 4421 | 2 | chr6B.!!$F5 | 795 |
15 | TraesCS1A01G209200 | chrUn | 116802624 | 116804765 | 2141 | True | 1122.500000 | 1679 | 89.149500 | 1 | 2721 | 2 | chrUn.!!$R1 | 2720 |
16 | TraesCS1A01G209200 | chr1B | 278152290 | 278153271 | 981 | False | 1500.000000 | 1500 | 94.303000 | 1744 | 2721 | 1 | chr1B.!!$F1 | 977 |
17 | TraesCS1A01G209200 | chr1B | 519433947 | 519434570 | 623 | True | 917.000000 | 917 | 93.049000 | 3788 | 4420 | 1 | chr1B.!!$R1 | 632 |
18 | TraesCS1A01G209200 | chr3B | 522281542 | 522282125 | 583 | True | 863.000000 | 863 | 93.322000 | 3049 | 3632 | 1 | chr3B.!!$R4 | 583 |
19 | TraesCS1A01G209200 | chr3B | 446527078 | 446527896 | 818 | False | 601.000000 | 937 | 93.903000 | 3630 | 4421 | 2 | chr3B.!!$F2 | 791 |
20 | TraesCS1A01G209200 | chr3B | 522245899 | 522246408 | 509 | True | 592.000000 | 592 | 87.914000 | 2266 | 2768 | 1 | chr3B.!!$R3 | 502 |
21 | TraesCS1A01G209200 | chr3A | 476147247 | 476147871 | 624 | True | 896.000000 | 896 | 92.453000 | 3788 | 4421 | 1 | chr3A.!!$R1 | 633 |
22 | TraesCS1A01G209200 | chr3A | 476156505 | 476157134 | 629 | True | 874.000000 | 874 | 91.759000 | 3004 | 3632 | 1 | chr3A.!!$R2 | 628 |
23 | TraesCS1A01G209200 | chr3A | 679990336 | 679990959 | 623 | False | 861.000000 | 861 | 91.547000 | 3007 | 3632 | 1 | chr3A.!!$F3 | 625 |
24 | TraesCS1A01G209200 | chr3A | 87730092 | 87732377 | 2285 | False | 688.000000 | 911 | 92.710667 | 3007 | 4421 | 3 | chr3A.!!$F4 | 1414 |
25 | TraesCS1A01G209200 | chr2A | 770166577 | 770167172 | 595 | True | 896.000000 | 896 | 93.802000 | 754 | 1350 | 1 | chr2A.!!$R3 | 596 |
26 | TraesCS1A01G209200 | chr2A | 477613351 | 477613944 | 593 | True | 830.000000 | 830 | 91.820000 | 753 | 1350 | 1 | chr2A.!!$R1 | 597 |
27 | TraesCS1A01G209200 | chr6A | 370481494 | 370482120 | 626 | False | 887.000000 | 887 | 92.151000 | 3788 | 4421 | 1 | chr6A.!!$F2 | 633 |
28 | TraesCS1A01G209200 | chr6A | 29436178 | 29436800 | 622 | False | 865.000000 | 865 | 91.707000 | 3007 | 3632 | 1 | chr6A.!!$F1 | 625 |
29 | TraesCS1A01G209200 | chr6A | 347378164 | 347378769 | 605 | True | 763.000000 | 763 | 89.202000 | 3788 | 4421 | 1 | chr6A.!!$R1 | 633 |
30 | TraesCS1A01G209200 | chr5A | 564441061 | 564441686 | 625 | True | 874.000000 | 874 | 91.879000 | 3007 | 3632 | 1 | chr5A.!!$R2 | 625 |
31 | TraesCS1A01G209200 | chr5A | 408131186 | 408131773 | 587 | True | 804.000000 | 804 | 91.261000 | 754 | 1348 | 1 | chr5A.!!$R1 | 594 |
32 | TraesCS1A01G209200 | chr7A | 587284426 | 587286694 | 2268 | True | 850.000000 | 854 | 91.262500 | 3009 | 4419 | 2 | chr7A.!!$R1 | 1410 |
33 | TraesCS1A01G209200 | chr2D | 303500803 | 303501395 | 592 | True | 811.000000 | 811 | 91.333000 | 754 | 1350 | 1 | chr2D.!!$R2 | 596 |
34 | TraesCS1A01G209200 | chr4D | 448359565 | 448360124 | 559 | True | 579.000000 | 579 | 85.464000 | 2443 | 3006 | 1 | chr4D.!!$R1 | 563 |
35 | TraesCS1A01G209200 | chr4D | 255552574 | 255553375 | 801 | False | 531.500000 | 802 | 91.777500 | 3626 | 4421 | 2 | chr4D.!!$F1 | 795 |
36 | TraesCS1A01G209200 | chr3D | 227670206 | 227670788 | 582 | True | 784.000000 | 784 | 90.847000 | 754 | 1342 | 1 | chr3D.!!$R1 | 588 |
37 | TraesCS1A01G209200 | chr6D | 225586214 | 225586819 | 605 | True | 780.000000 | 780 | 89.671000 | 3788 | 4421 | 1 | chr6D.!!$R1 | 633 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
704 | 767 | 0.103208 | AGATAAGCTTGTCCGGCTCG | 59.897 | 55.0 | 18.49 | 0.0 | 39.30 | 5.03 | F |
746 | 809 | 0.250295 | CTTCCCGCAGTTCAAGGACA | 60.250 | 55.0 | 0.00 | 0.0 | 0.00 | 4.02 | F |
747 | 810 | 0.250295 | TTCCCGCAGTTCAAGGACAG | 60.250 | 55.0 | 0.00 | 0.0 | 0.00 | 3.51 | F |
1724 | 1793 | 0.322456 | GGGAGCCACTGTGCATTACA | 60.322 | 55.0 | 1.29 | 0.0 | 37.78 | 2.41 | F |
2847 | 2928 | 0.110295 | CATGTCCCAGTGTCCCACAA | 59.890 | 55.0 | 0.00 | 0.0 | 36.74 | 3.33 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1699 | 1768 | 0.543749 | GCACAGTGGCTCCCTTATCT | 59.456 | 55.0 | 1.84 | 0.0 | 0.00 | 1.98 | R |
1967 | 2038 | 0.999406 | AGATGTTCGTCGCATTTCGG | 59.001 | 50.0 | 0.00 | 0.0 | 39.05 | 4.30 | R |
2010 | 2081 | 2.094894 | CGAATTCTCACTGTGTGGATGC | 59.905 | 50.0 | 7.79 | 3.4 | 33.87 | 3.91 | R |
2974 | 3055 | 0.037139 | TGTTCCATTCCCGTGTACCG | 60.037 | 55.0 | 0.00 | 0.0 | 0.00 | 4.02 | R |
4375 | 5355 | 0.463620 | GAGGAGCTTGTAGAGGCAGG | 59.536 | 60.0 | 0.00 | 0.0 | 0.00 | 4.85 | 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.