Multiple sequence alignment - TraesCS5B01G001100
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 | TraesCS5B01G001100 | chr5B | 100.000 | 4243 | 0 | 0 | 2461 | 6703 | 864135 | 859893 | 0.000000e+00 | 7836.0 |
1 | TraesCS5B01G001100 | chr5B | 100.000 | 2151 | 0 | 0 | 1 | 2151 | 866595 | 864445 | 0.000000e+00 | 3973.0 |
2 | TraesCS5B01G001100 | chr5B | 83.903 | 1609 | 248 | 9 | 3893 | 5494 | 44140287 | 44141891 | 0.000000e+00 | 1526.0 |
3 | TraesCS5B01G001100 | chr5B | 95.708 | 932 | 23 | 7 | 5775 | 6703 | 400664014 | 400664931 | 0.000000e+00 | 1483.0 |
4 | TraesCS5B01G001100 | chr5B | 98.758 | 322 | 4 | 0 | 1830 | 2151 | 411933655 | 411933334 | 2.100000e-159 | 573.0 |
5 | TraesCS5B01G001100 | chr5B | 93.889 | 360 | 15 | 6 | 6345 | 6701 | 407242802 | 407242447 | 2.750000e-148 | 536.0 |
6 | TraesCS5B01G001100 | chr5B | 98.286 | 175 | 3 | 0 | 2461 | 2635 | 137415231 | 137415057 | 2.350000e-79 | 307.0 |
7 | TraesCS5B01G001100 | chr5B | 94.845 | 97 | 2 | 3 | 3688 | 3782 | 13350146 | 13350051 | 1.510000e-31 | 148.0 |
8 | TraesCS5B01G001100 | chr5B | 93.814 | 97 | 2 | 3 | 3684 | 3780 | 13364611 | 13364703 | 7.010000e-30 | 143.0 |
9 | TraesCS5B01G001100 | chr5B | 92.157 | 102 | 6 | 2 | 3691 | 3792 | 687331438 | 687331339 | 7.010000e-30 | 143.0 |
10 | TraesCS5B01G001100 | chr5B | 100.000 | 56 | 0 | 0 | 3563 | 3618 | 862982 | 862927 | 3.310000e-18 | 104.0 |
11 | TraesCS5B01G001100 | chr5B | 100.000 | 56 | 0 | 0 | 3614 | 3669 | 863033 | 862978 | 3.310000e-18 | 104.0 |
12 | TraesCS5B01G001100 | chr5D | 92.653 | 2137 | 133 | 14 | 3640 | 5766 | 6822804 | 6820682 | 0.000000e+00 | 3055.0 |
13 | TraesCS5B01G001100 | chr5D | 84.217 | 1603 | 246 | 5 | 3896 | 5493 | 44571487 | 44569887 | 0.000000e+00 | 1552.0 |
14 | TraesCS5B01G001100 | chr5D | 84.484 | 1057 | 63 | 36 | 696 | 1670 | 6824192 | 6823155 | 0.000000e+00 | 950.0 |
15 | TraesCS5B01G001100 | chr5D | 87.053 | 587 | 35 | 20 | 5775 | 6346 | 72364071 | 72364631 | 5.710000e-175 | 625.0 |
16 | TraesCS5B01G001100 | chr5D | 92.222 | 360 | 21 | 6 | 6345 | 6701 | 536867438 | 536867083 | 2.790000e-138 | 503.0 |
17 | TraesCS5B01G001100 | chr5D | 80.414 | 531 | 77 | 17 | 3683 | 4190 | 3810217 | 3809691 | 4.910000e-101 | 379.0 |
18 | TraesCS5B01G001100 | chr5D | 86.879 | 282 | 14 | 11 | 3043 | 3319 | 6823114 | 6822851 | 1.830000e-75 | 294.0 |
19 | TraesCS5B01G001100 | chr5D | 96.667 | 90 | 2 | 1 | 3699 | 3788 | 544801961 | 544801873 | 1.510000e-31 | 148.0 |
20 | TraesCS5B01G001100 | chr5D | 92.157 | 102 | 6 | 2 | 3682 | 3782 | 13909890 | 13909790 | 7.010000e-30 | 143.0 |
21 | TraesCS5B01G001100 | chr5D | 92.941 | 85 | 6 | 0 | 4 | 88 | 6824767 | 6824683 | 2.540000e-24 | 124.0 |
22 | TraesCS5B01G001100 | chr5A | 94.794 | 1921 | 90 | 5 | 3842 | 5760 | 3086832 | 3088744 | 0.000000e+00 | 2985.0 |
23 | TraesCS5B01G001100 | chr5A | 83.770 | 1602 | 255 | 3 | 3896 | 5493 | 34982768 | 34981168 | 0.000000e+00 | 1513.0 |
24 | TraesCS5B01G001100 | chr5A | 85.600 | 1250 | 172 | 7 | 3880 | 5124 | 3132588 | 3133834 | 0.000000e+00 | 1304.0 |
25 | TraesCS5B01G001100 | chr5A | 81.036 | 1313 | 91 | 71 | 471 | 1670 | 3085028 | 3086295 | 0.000000e+00 | 900.0 |
26 | TraesCS5B01G001100 | chr5A | 95.495 | 111 | 4 | 1 | 3689 | 3798 | 3086722 | 3086832 | 6.910000e-40 | 176.0 |
27 | TraesCS5B01G001100 | chr5A | 96.078 | 51 | 2 | 0 | 1213 | 1263 | 34986385 | 34986335 | 4.310000e-12 | 84.2 |
28 | TraesCS5B01G001100 | chr5A | 90.476 | 63 | 5 | 1 | 3026 | 3087 | 3086561 | 3086623 | 1.550000e-11 | 82.4 |
29 | TraesCS5B01G001100 | chr6A | 96.026 | 931 | 20 | 7 | 5775 | 6703 | 107169508 | 107170423 | 0.000000e+00 | 1498.0 |
30 | TraesCS5B01G001100 | chr7A | 95.334 | 943 | 26 | 8 | 5764 | 6703 | 482328886 | 482329813 | 0.000000e+00 | 1482.0 |
31 | TraesCS5B01G001100 | chr7A | 85.566 | 1157 | 160 | 6 | 4345 | 5498 | 47511682 | 47512834 | 0.000000e+00 | 1205.0 |
32 | TraesCS5B01G001100 | chr7A | 88.756 | 587 | 43 | 13 | 5775 | 6346 | 219167424 | 219168002 | 0.000000e+00 | 697.0 |
33 | TraesCS5B01G001100 | chr7A | 98.039 | 51 | 1 | 0 | 1213 | 1263 | 47511529 | 47511579 | 9.260000e-14 | 89.8 |
34 | TraesCS5B01G001100 | chr2D | 82.884 | 1595 | 260 | 10 | 3911 | 5503 | 15991423 | 15989840 | 0.000000e+00 | 1421.0 |
35 | TraesCS5B01G001100 | chr2D | 82.127 | 1589 | 273 | 9 | 3911 | 5498 | 15935339 | 15933761 | 0.000000e+00 | 1351.0 |
36 | TraesCS5B01G001100 | chr2D | 85.802 | 324 | 29 | 12 | 5770 | 6087 | 56312282 | 56312594 | 1.800000e-85 | 327.0 |
37 | TraesCS5B01G001100 | chr4A | 82.078 | 1607 | 256 | 18 | 3901 | 5492 | 657071326 | 657072915 | 0.000000e+00 | 1343.0 |
38 | TraesCS5B01G001100 | chr4B | 94.347 | 513 | 7 | 3 | 2463 | 2975 | 672314765 | 672314275 | 0.000000e+00 | 767.0 |
39 | TraesCS5B01G001100 | chr4B | 97.455 | 393 | 10 | 0 | 2634 | 3026 | 28265887 | 28265495 | 0.000000e+00 | 671.0 |
40 | TraesCS5B01G001100 | chr4B | 97.853 | 326 | 7 | 0 | 1826 | 2151 | 479219509 | 479219184 | 1.260000e-156 | 564.0 |
41 | TraesCS5B01G001100 | chr4B | 97.826 | 322 | 7 | 0 | 1830 | 2151 | 28266972 | 28266651 | 2.110000e-154 | 556.0 |
42 | TraesCS5B01G001100 | chr4B | 98.286 | 175 | 3 | 0 | 2461 | 2635 | 479219139 | 479218965 | 2.350000e-79 | 307.0 |
43 | TraesCS5B01G001100 | chr4B | 85.874 | 269 | 22 | 10 | 5767 | 6027 | 66189475 | 66189215 | 8.570000e-69 | 272.0 |
44 | TraesCS5B01G001100 | chr4B | 94.898 | 98 | 2 | 2 | 3681 | 3778 | 14343227 | 14343321 | 4.190000e-32 | 150.0 |
45 | TraesCS5B01G001100 | chr2B | 98.219 | 393 | 7 | 0 | 2634 | 3026 | 752930639 | 752930247 | 0.000000e+00 | 688.0 |
46 | TraesCS5B01G001100 | chr2B | 97.710 | 393 | 9 | 0 | 2634 | 3026 | 617149735 | 617150127 | 0.000000e+00 | 676.0 |
47 | TraesCS5B01G001100 | chr2B | 89.041 | 438 | 29 | 8 | 5781 | 6206 | 547098842 | 547098412 | 5.950000e-145 | 525.0 |
48 | TraesCS5B01G001100 | chr2B | 97.714 | 175 | 4 | 0 | 2461 | 2635 | 617147648 | 617147822 | 1.090000e-77 | 302.0 |
49 | TraesCS5B01G001100 | chr1B | 97.975 | 395 | 8 | 0 | 2634 | 3028 | 61991509 | 61991903 | 0.000000e+00 | 686.0 |
50 | TraesCS5B01G001100 | chr1B | 98.148 | 324 | 6 | 0 | 1828 | 2151 | 61990714 | 61991037 | 3.510000e-157 | 566.0 |
51 | TraesCS5B01G001100 | chr1B | 97.714 | 175 | 4 | 0 | 2461 | 2635 | 61991093 | 61991267 | 1.090000e-77 | 302.0 |
52 | TraesCS5B01G001100 | chr6B | 97.022 | 403 | 11 | 1 | 2634 | 3035 | 704691248 | 704691650 | 0.000000e+00 | 676.0 |
53 | TraesCS5B01G001100 | chr6B | 98.137 | 322 | 4 | 1 | 1830 | 2151 | 451676786 | 451676467 | 1.630000e-155 | 560.0 |
54 | TraesCS5B01G001100 | chr6B | 96.657 | 329 | 10 | 1 | 1824 | 2151 | 693802863 | 693803191 | 4.570000e-151 | 545.0 |
55 | TraesCS5B01G001100 | chr6B | 91.922 | 359 | 23 | 5 | 6345 | 6701 | 708393038 | 708392684 | 1.300000e-136 | 497.0 |
56 | TraesCS5B01G001100 | chr6B | 97.714 | 175 | 4 | 0 | 2461 | 2635 | 670897839 | 670897665 | 1.090000e-77 | 302.0 |
57 | TraesCS5B01G001100 | chr6B | 97.714 | 175 | 4 | 0 | 2461 | 2635 | 704689161 | 704689335 | 1.090000e-77 | 302.0 |
58 | TraesCS5B01G001100 | chr3B | 97.710 | 393 | 9 | 0 | 2634 | 3026 | 671136584 | 671136192 | 0.000000e+00 | 676.0 |
59 | TraesCS5B01G001100 | chr3B | 96.970 | 396 | 12 | 0 | 2634 | 3029 | 726355859 | 726356254 | 0.000000e+00 | 665.0 |
60 | TraesCS5B01G001100 | chr3B | 97.840 | 324 | 7 | 0 | 1828 | 2151 | 49153443 | 49153766 | 1.630000e-155 | 560.0 |
61 | TraesCS5B01G001100 | chr3B | 97.714 | 175 | 4 | 0 | 2461 | 2635 | 516428580 | 516428754 | 1.090000e-77 | 302.0 |
62 | TraesCS5B01G001100 | chr7B | 97.250 | 400 | 8 | 2 | 2630 | 3028 | 698922857 | 698922460 | 0.000000e+00 | 675.0 |
63 | TraesCS5B01G001100 | chr7B | 97.215 | 395 | 9 | 1 | 2634 | 3028 | 693386471 | 693386079 | 0.000000e+00 | 667.0 |
64 | TraesCS5B01G001100 | chr7B | 97.516 | 322 | 8 | 0 | 1828 | 2149 | 693387279 | 693386958 | 9.820000e-153 | 551.0 |
65 | TraesCS5B01G001100 | chr7B | 97.508 | 321 | 8 | 0 | 1831 | 2151 | 6895944 | 6895624 | 3.530000e-152 | 549.0 |
66 | TraesCS5B01G001100 | chr7B | 97.714 | 175 | 4 | 0 | 2461 | 2635 | 246382919 | 246383093 | 1.090000e-77 | 302.0 |
67 | TraesCS5B01G001100 | chrUn | 87.415 | 588 | 49 | 12 | 5775 | 6349 | 49961906 | 49961331 | 0.000000e+00 | 652.0 |
68 | TraesCS5B01G001100 | chr7D | 85.110 | 591 | 41 | 20 | 5775 | 6349 | 4171625 | 4171066 | 1.630000e-155 | 560.0 |
69 | TraesCS5B01G001100 | chr7D | 92.244 | 361 | 19 | 8 | 6345 | 6701 | 586687459 | 586687814 | 2.790000e-138 | 503.0 |
70 | TraesCS5B01G001100 | chr7D | 89.091 | 385 | 25 | 6 | 5777 | 6150 | 552324313 | 552323935 | 4.740000e-126 | 462.0 |
71 | TraesCS5B01G001100 | chr7D | 91.513 | 271 | 17 | 5 | 6082 | 6349 | 431154176 | 431153909 | 1.060000e-97 | 368.0 |
72 | TraesCS5B01G001100 | chr7D | 87.307 | 323 | 26 | 10 | 5770 | 6087 | 33694291 | 33694603 | 8.270000e-94 | 355.0 |
73 | TraesCS5B01G001100 | chr7D | 88.119 | 303 | 26 | 5 | 5771 | 6069 | 431164695 | 431164399 | 1.070000e-92 | 351.0 |
74 | TraesCS5B01G001100 | chr7D | 91.633 | 251 | 15 | 5 | 6098 | 6346 | 586687159 | 586687405 | 6.440000e-90 | 342.0 |
75 | TraesCS5B01G001100 | chr3A | 92.244 | 361 | 19 | 8 | 6345 | 6701 | 357059041 | 357059396 | 2.790000e-138 | 503.0 |
76 | TraesCS5B01G001100 | chr2A | 91.413 | 361 | 23 | 7 | 6345 | 6701 | 733098018 | 733098374 | 7.810000e-134 | 488.0 |
77 | TraesCS5B01G001100 | chr4D | 87.133 | 443 | 23 | 12 | 5775 | 6206 | 400894868 | 400894449 | 7.870000e-129 | 472.0 |
78 | TraesCS5B01G001100 | chr4D | 87.133 | 443 | 22 | 16 | 5775 | 6206 | 472925584 | 472925166 | 2.830000e-128 | 470.0 |
79 | TraesCS5B01G001100 | chr4D | 80.526 | 190 | 37 | 0 | 3906 | 4095 | 11867190 | 11867001 | 5.420000e-31 | 147.0 |
80 | TraesCS5B01G001100 | chr4D | 96.512 | 86 | 3 | 0 | 3687 | 3772 | 7904979 | 7905064 | 7.010000e-30 | 143.0 |
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 | TraesCS5B01G001100 | chr5B | 859893 | 866595 | 6702 | True | 3004.25 | 7836 | 100.000000 | 1 | 6703 | 4 | chr5B.!!$R6 | 6702 |
1 | TraesCS5B01G001100 | chr5B | 44140287 | 44141891 | 1604 | False | 1526.00 | 1526 | 83.903000 | 3893 | 5494 | 1 | chr5B.!!$F2 | 1601 |
2 | TraesCS5B01G001100 | chr5B | 400664014 | 400664931 | 917 | False | 1483.00 | 1483 | 95.708000 | 5775 | 6703 | 1 | chr5B.!!$F3 | 928 |
3 | TraesCS5B01G001100 | chr5D | 44569887 | 44571487 | 1600 | True | 1552.00 | 1552 | 84.217000 | 3896 | 5493 | 1 | chr5D.!!$R3 | 1597 |
4 | TraesCS5B01G001100 | chr5D | 6820682 | 6824767 | 4085 | True | 1105.75 | 3055 | 89.239250 | 4 | 5766 | 4 | chr5D.!!$R6 | 5762 |
5 | TraesCS5B01G001100 | chr5D | 72364071 | 72364631 | 560 | False | 625.00 | 625 | 87.053000 | 5775 | 6346 | 1 | chr5D.!!$F1 | 571 |
6 | TraesCS5B01G001100 | chr5D | 3809691 | 3810217 | 526 | True | 379.00 | 379 | 80.414000 | 3683 | 4190 | 1 | chr5D.!!$R1 | 507 |
7 | TraesCS5B01G001100 | chr5A | 3132588 | 3133834 | 1246 | False | 1304.00 | 1304 | 85.600000 | 3880 | 5124 | 1 | chr5A.!!$F1 | 1244 |
8 | TraesCS5B01G001100 | chr5A | 3085028 | 3088744 | 3716 | False | 1035.85 | 2985 | 90.450250 | 471 | 5760 | 4 | chr5A.!!$F2 | 5289 |
9 | TraesCS5B01G001100 | chr5A | 34981168 | 34986385 | 5217 | True | 798.60 | 1513 | 89.924000 | 1213 | 5493 | 2 | chr5A.!!$R1 | 4280 |
10 | TraesCS5B01G001100 | chr6A | 107169508 | 107170423 | 915 | False | 1498.00 | 1498 | 96.026000 | 5775 | 6703 | 1 | chr6A.!!$F1 | 928 |
11 | TraesCS5B01G001100 | chr7A | 482328886 | 482329813 | 927 | False | 1482.00 | 1482 | 95.334000 | 5764 | 6703 | 1 | chr7A.!!$F2 | 939 |
12 | TraesCS5B01G001100 | chr7A | 219167424 | 219168002 | 578 | False | 697.00 | 697 | 88.756000 | 5775 | 6346 | 1 | chr7A.!!$F1 | 571 |
13 | TraesCS5B01G001100 | chr7A | 47511529 | 47512834 | 1305 | False | 647.40 | 1205 | 91.802500 | 1213 | 5498 | 2 | chr7A.!!$F3 | 4285 |
14 | TraesCS5B01G001100 | chr2D | 15989840 | 15991423 | 1583 | True | 1421.00 | 1421 | 82.884000 | 3911 | 5503 | 1 | chr2D.!!$R2 | 1592 |
15 | TraesCS5B01G001100 | chr2D | 15933761 | 15935339 | 1578 | True | 1351.00 | 1351 | 82.127000 | 3911 | 5498 | 1 | chr2D.!!$R1 | 1587 |
16 | TraesCS5B01G001100 | chr4A | 657071326 | 657072915 | 1589 | False | 1343.00 | 1343 | 82.078000 | 3901 | 5492 | 1 | chr4A.!!$F1 | 1591 |
17 | TraesCS5B01G001100 | chr4B | 28265495 | 28266972 | 1477 | True | 613.50 | 671 | 97.640500 | 1830 | 3026 | 2 | chr4B.!!$R3 | 1196 |
18 | TraesCS5B01G001100 | chr4B | 479218965 | 479219509 | 544 | True | 435.50 | 564 | 98.069500 | 1826 | 2635 | 2 | chr4B.!!$R4 | 809 |
19 | TraesCS5B01G001100 | chr2B | 617147648 | 617150127 | 2479 | False | 489.00 | 676 | 97.712000 | 2461 | 3026 | 2 | chr2B.!!$F1 | 565 |
20 | TraesCS5B01G001100 | chr1B | 61990714 | 61991903 | 1189 | False | 518.00 | 686 | 97.945667 | 1828 | 3028 | 3 | chr1B.!!$F1 | 1200 |
21 | TraesCS5B01G001100 | chr6B | 704689161 | 704691650 | 2489 | False | 489.00 | 676 | 97.368000 | 2461 | 3035 | 2 | chr6B.!!$F2 | 574 |
22 | TraesCS5B01G001100 | chr7B | 693386079 | 693387279 | 1200 | True | 609.00 | 667 | 97.365500 | 1828 | 3028 | 2 | chr7B.!!$R3 | 1200 |
23 | TraesCS5B01G001100 | chrUn | 49961331 | 49961906 | 575 | True | 652.00 | 652 | 87.415000 | 5775 | 6349 | 1 | chrUn.!!$R1 | 574 |
24 | TraesCS5B01G001100 | chr7D | 4171066 | 4171625 | 559 | True | 560.00 | 560 | 85.110000 | 5775 | 6349 | 1 | chr7D.!!$R1 | 574 |
25 | TraesCS5B01G001100 | chr7D | 586687159 | 586687814 | 655 | False | 422.50 | 503 | 91.938500 | 6098 | 6701 | 2 | chr7D.!!$F2 | 603 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
227 | 323 | 0.039798 | GCAATATGGTGCATCCGCTG | 60.040 | 55.000 | 0.00 | 0.0 | 44.29 | 5.18 | F |
1039 | 1228 | 0.039437 | CTACCTACCTATGTGCGCCG | 60.039 | 60.000 | 4.18 | 0.0 | 0.00 | 6.46 | F |
1294 | 1533 | 0.179207 | GCATGCACATGTCACACTCG | 60.179 | 55.000 | 14.21 | 0.0 | 40.80 | 4.18 | F |
1628 | 1890 | 0.409092 | TGAGTGCCCACAATCCCATT | 59.591 | 50.000 | 0.82 | 0.0 | 40.16 | 3.16 | F |
1799 | 2226 | 0.443869 | GAGCGAAATCATGTGCGTGT | 59.556 | 50.000 | 0.00 | 0.0 | 0.00 | 4.49 | F |
3426 | 5833 | 0.856982 | TTTCCTCTTCCTTTGGGGCA | 59.143 | 50.000 | 0.00 | 0.0 | 34.39 | 5.36 | F |
3492 | 5899 | 0.396435 | ACTGTCGCTGAAATGGGTGA | 59.604 | 50.000 | 0.00 | 0.0 | 0.00 | 4.02 | F |
3493 | 5900 | 1.202758 | ACTGTCGCTGAAATGGGTGAA | 60.203 | 47.619 | 0.00 | 0.0 | 0.00 | 3.18 | F |
4130 | 8672 | 1.490490 | GCCACCATGTCCTCCTTCATA | 59.510 | 52.381 | 0.00 | 0.0 | 0.00 | 2.15 | F |
5549 | 10107 | 0.905337 | ACAGCCCGAAGAAGCCTAGT | 60.905 | 55.000 | 0.00 | 0.0 | 0.00 | 2.57 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1606 | 1868 | 0.034186 | GGGATTGTGGGCACTCATCA | 60.034 | 55.000 | 0.00 | 0.00 | 0.00 | 3.07 | R |
2997 | 5373 | 0.811219 | CCAACAGCTGCGCTATAGCA | 60.811 | 55.000 | 23.99 | 6.02 | 45.96 | 3.49 | R |
3039 | 5415 | 1.552792 | AGCTACACAGGAAAGAGAGGC | 59.447 | 52.381 | 0.00 | 0.00 | 0.00 | 4.70 | R |
3473 | 5880 | 0.396435 | TCACCCATTTCAGCGACAGT | 59.604 | 50.000 | 0.00 | 0.00 | 0.00 | 3.55 | R |
3474 | 5881 | 1.522668 | TTCACCCATTTCAGCGACAG | 58.477 | 50.000 | 0.00 | 0.00 | 0.00 | 3.51 | R |
5015 | 9570 | 1.207593 | CTTTGTGAAGCGGCGAAGG | 59.792 | 57.895 | 12.98 | 0.00 | 0.00 | 3.46 | R |
5436 | 9994 | 1.613836 | AAGTAGACGAGGTTCACGGT | 58.386 | 50.000 | 0.00 | 0.00 | 34.93 | 4.83 | R |
5504 | 10062 | 1.219124 | GAGCTCAACATCTCCGGCA | 59.781 | 57.895 | 9.40 | 0.00 | 0.00 | 5.69 | R |
5651 | 10215 | 0.172127 | CGGGATCGATCGATGAGCAT | 59.828 | 55.000 | 33.86 | 11.11 | 39.00 | 3.79 | R |
6384 | 11038 | 2.543777 | AGTTGCAACCGCTAAGAGAA | 57.456 | 45.000 | 25.62 | 0.00 | 39.64 | 2.87 | 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.