Multiple sequence alignment - TraesCS1B01G028700
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 | TraesCS1B01G028700 | chr1B | 100.000 | 6830 | 0 | 0 | 1 | 6830 | 13964202 | 13971031 | 0.000000e+00 | 12613.0 |
1 | TraesCS1B01G028700 | chr1B | 98.489 | 1522 | 16 | 4 | 2772 | 4289 | 556661187 | 556659669 | 0.000000e+00 | 2676.0 |
2 | TraesCS1B01G028700 | chr1B | 99.763 | 422 | 0 | 1 | 1785 | 2205 | 13967744 | 13968165 | 0.000000e+00 | 773.0 |
3 | TraesCS1B01G028700 | chr1B | 99.289 | 422 | 2 | 1 | 1785 | 2205 | 556660413 | 556659992 | 0.000000e+00 | 761.0 |
4 | TraesCS1B01G028700 | chr1B | 99.099 | 333 | 3 | 0 | 2474 | 2806 | 13968158 | 13968490 | 3.530000e-167 | 599.0 |
5 | TraesCS1B01G028700 | chr1B | 98.799 | 333 | 2 | 1 | 2474 | 2806 | 556659999 | 556659669 | 5.900000e-165 | 592.0 |
6 | TraesCS1B01G028700 | chr1B | 95.439 | 285 | 13 | 0 | 1 | 285 | 569704838 | 569705122 | 8.080000e-124 | 455.0 |
7 | TraesCS1B01G028700 | chr5B | 99.119 | 1816 | 13 | 2 | 2474 | 4289 | 697005424 | 697007236 | 0.000000e+00 | 3262.0 |
8 | TraesCS1B01G028700 | chr5B | 99.465 | 747 | 4 | 0 | 3543 | 4289 | 697005010 | 697005756 | 0.000000e+00 | 1358.0 |
9 | TraesCS1B01G028700 | chr5B | 99.526 | 422 | 1 | 1 | 1785 | 2205 | 697005010 | 697005431 | 0.000000e+00 | 767.0 |
10 | TraesCS1B01G028700 | chr5B | 99.526 | 422 | 1 | 1 | 1785 | 2205 | 697006492 | 697006913 | 0.000000e+00 | 767.0 |
11 | TraesCS1B01G028700 | chr5B | 99.399 | 333 | 0 | 1 | 2474 | 2806 | 697006906 | 697007236 | 2.730000e-168 | 603.0 |
12 | TraesCS1B01G028700 | chr5B | 95.017 | 301 | 11 | 3 | 2198 | 2498 | 451177109 | 451177405 | 2.880000e-128 | 470.0 |
13 | TraesCS1B01G028700 | chr5B | 94.700 | 283 | 15 | 0 | 3 | 285 | 56592804 | 56593086 | 2.260000e-119 | 440.0 |
14 | TraesCS1B01G028700 | chr4A | 98.789 | 1816 | 22 | 0 | 2474 | 4289 | 726804520 | 726806335 | 0.000000e+00 | 3232.0 |
15 | TraesCS1B01G028700 | chr4A | 99.197 | 747 | 6 | 0 | 3543 | 4289 | 726804106 | 726804852 | 0.000000e+00 | 1347.0 |
16 | TraesCS1B01G028700 | chr4A | 99.526 | 422 | 1 | 1 | 1785 | 2205 | 726804106 | 726804527 | 0.000000e+00 | 767.0 |
17 | TraesCS1B01G028700 | chr4A | 98.815 | 422 | 4 | 1 | 1785 | 2205 | 726805589 | 726806010 | 0.000000e+00 | 750.0 |
18 | TraesCS1B01G028700 | chr4A | 99.399 | 333 | 2 | 0 | 2474 | 2806 | 726806003 | 726806335 | 7.580000e-169 | 604.0 |
19 | TraesCS1B01G028700 | chr4A | 87.847 | 288 | 35 | 0 | 3177 | 3464 | 705905766 | 705905479 | 8.490000e-89 | 339.0 |
20 | TraesCS1B01G028700 | chr4A | 83.462 | 260 | 37 | 5 | 6355 | 6611 | 640611950 | 640612206 | 3.180000e-58 | 237.0 |
21 | TraesCS1B01G028700 | chr4A | 83.333 | 258 | 37 | 6 | 6357 | 6611 | 656555847 | 656556101 | 4.120000e-57 | 233.0 |
22 | TraesCS1B01G028700 | chr3B | 98.681 | 1820 | 21 | 2 | 2474 | 4292 | 623943009 | 623944826 | 0.000000e+00 | 3225.0 |
23 | TraesCS1B01G028700 | chr3B | 85.706 | 1749 | 183 | 29 | 4297 | 6017 | 154439019 | 154440728 | 0.000000e+00 | 1783.0 |
24 | TraesCS1B01G028700 | chr3B | 98.527 | 747 | 9 | 1 | 3543 | 4289 | 623942595 | 623943339 | 0.000000e+00 | 1317.0 |
25 | TraesCS1B01G028700 | chr3B | 98.595 | 427 | 4 | 2 | 1780 | 2205 | 623942591 | 623943016 | 0.000000e+00 | 754.0 |
26 | TraesCS1B01G028700 | chr3B | 98.815 | 422 | 4 | 1 | 1785 | 2205 | 623944076 | 623944497 | 0.000000e+00 | 750.0 |
27 | TraesCS1B01G028700 | chr3B | 77.937 | 1396 | 161 | 74 | 481 | 1782 | 154437672 | 154439014 | 0.000000e+00 | 736.0 |
28 | TraesCS1B01G028700 | chr3B | 99.700 | 333 | 1 | 0 | 2474 | 2806 | 623944490 | 623944822 | 1.630000e-170 | 610.0 |
29 | TraesCS1B01G028700 | chr3B | 95.341 | 279 | 12 | 1 | 1 | 279 | 647231603 | 647231880 | 6.290000e-120 | 442.0 |
30 | TraesCS1B01G028700 | chr3B | 84.556 | 259 | 32 | 8 | 6357 | 6611 | 199545418 | 199545164 | 4.090000e-62 | 250.0 |
31 | TraesCS1B01G028700 | chr3B | 78.261 | 414 | 66 | 17 | 2624 | 3026 | 792724280 | 792724680 | 1.900000e-60 | 244.0 |
32 | TraesCS1B01G028700 | chr3B | 94.828 | 58 | 3 | 0 | 350 | 407 | 154437632 | 154437575 | 2.620000e-14 | 91.6 |
33 | TraesCS1B01G028700 | chr3B | 81.373 | 102 | 17 | 2 | 999 | 1099 | 810251036 | 810251136 | 1.580000e-11 | 82.4 |
34 | TraesCS1B01G028700 | chr3B | 94.595 | 37 | 2 | 0 | 1065 | 1101 | 28699254 | 28699290 | 2.660000e-04 | 58.4 |
35 | TraesCS1B01G028700 | chr3B | 94.595 | 37 | 2 | 0 | 1065 | 1101 | 823809284 | 823809320 | 2.660000e-04 | 58.4 |
36 | TraesCS1B01G028700 | chrUn | 94.118 | 1615 | 81 | 8 | 4291 | 5893 | 96549742 | 96551354 | 0.000000e+00 | 2444.0 |
37 | TraesCS1B01G028700 | chrUn | 89.104 | 1340 | 76 | 15 | 481 | 1784 | 96548440 | 96549745 | 0.000000e+00 | 1602.0 |
38 | TraesCS1B01G028700 | chrUn | 99.059 | 744 | 7 | 0 | 3546 | 4289 | 181270282 | 181269539 | 0.000000e+00 | 1336.0 |
39 | TraesCS1B01G028700 | chrUn | 96.791 | 748 | 17 | 2 | 3543 | 4289 | 104669849 | 104669108 | 0.000000e+00 | 1242.0 |
40 | TraesCS1B01G028700 | chrUn | 99.045 | 419 | 3 | 1 | 1788 | 2205 | 181270282 | 181269864 | 0.000000e+00 | 750.0 |
41 | TraesCS1B01G028700 | chrUn | 99.701 | 335 | 1 | 0 | 2474 | 2808 | 181269871 | 181269537 | 1.260000e-171 | 614.0 |
42 | TraesCS1B01G028700 | chrUn | 87.395 | 119 | 9 | 1 | 5888 | 6006 | 96555081 | 96555193 | 1.550000e-26 | 132.0 |
43 | TraesCS1B01G028700 | chr1A | 92.757 | 1643 | 100 | 10 | 4290 | 5914 | 10971416 | 10969775 | 0.000000e+00 | 2357.0 |
44 | TraesCS1B01G028700 | chr1A | 86.832 | 1086 | 61 | 30 | 617 | 1656 | 10972546 | 10971497 | 0.000000e+00 | 1138.0 |
45 | TraesCS1B01G028700 | chr1A | 89.241 | 158 | 17 | 0 | 481 | 638 | 10972751 | 10972594 | 1.500000e-46 | 198.0 |
46 | TraesCS1B01G028700 | chr1A | 97.727 | 88 | 1 | 1 | 1697 | 1784 | 10971498 | 10971412 | 4.270000e-32 | 150.0 |
47 | TraesCS1B01G028700 | chr1A | 83.486 | 109 | 15 | 2 | 3467 | 3572 | 44315092 | 44314984 | 1.570000e-16 | 99.0 |
48 | TraesCS1B01G028700 | chr1D | 90.847 | 1464 | 90 | 27 | 4493 | 5928 | 9645684 | 9644237 | 0.000000e+00 | 1921.0 |
49 | TraesCS1B01G028700 | chr1D | 87.520 | 625 | 42 | 23 | 607 | 1209 | 9646753 | 9646143 | 0.000000e+00 | 689.0 |
50 | TraesCS1B01G028700 | chr1D | 92.453 | 265 | 19 | 1 | 4903 | 5167 | 9642495 | 9642232 | 1.800000e-100 | 377.0 |
51 | TraesCS1B01G028700 | chr1D | 92.827 | 237 | 11 | 4 | 1201 | 1431 | 9645963 | 9645727 | 8.490000e-89 | 339.0 |
52 | TraesCS1B01G028700 | chr3D | 86.070 | 1608 | 171 | 21 | 4290 | 5866 | 103789051 | 103790636 | 0.000000e+00 | 1679.0 |
53 | TraesCS1B01G028700 | chr3D | 79.519 | 1372 | 146 | 60 | 481 | 1785 | 103787753 | 103789056 | 0.000000e+00 | 852.0 |
54 | TraesCS1B01G028700 | chr3D | 86.819 | 349 | 44 | 1 | 3118 | 3464 | 500139670 | 500139322 | 8.310000e-104 | 388.0 |
55 | TraesCS1B01G028700 | chr3D | 90.217 | 92 | 7 | 2 | 350 | 439 | 103667353 | 103667262 | 1.200000e-22 | 119.0 |
56 | TraesCS1B01G028700 | chr3D | 78.947 | 95 | 20 | 0 | 1005 | 1099 | 603634715 | 603634621 | 1.590000e-06 | 65.8 |
57 | TraesCS1B01G028700 | chr3D | 78.788 | 99 | 17 | 2 | 1005 | 1101 | 602449605 | 602449509 | 5.720000e-06 | 63.9 |
58 | TraesCS1B01G028700 | chr3A | 85.081 | 1173 | 132 | 15 | 4797 | 5933 | 552539231 | 552538066 | 0.000000e+00 | 1157.0 |
59 | TraesCS1B01G028700 | chr3A | 91.766 | 668 | 50 | 4 | 2733 | 3395 | 660004770 | 660004103 | 0.000000e+00 | 924.0 |
60 | TraesCS1B01G028700 | chr3A | 91.467 | 668 | 52 | 4 | 2733 | 3395 | 660014867 | 660014200 | 0.000000e+00 | 913.0 |
61 | TraesCS1B01G028700 | chr3A | 95.677 | 532 | 20 | 3 | 3345 | 3875 | 9487511 | 9488040 | 0.000000e+00 | 852.0 |
62 | TraesCS1B01G028700 | chr3A | 85.579 | 527 | 51 | 8 | 4290 | 4805 | 552542761 | 552542249 | 4.690000e-146 | 529.0 |
63 | TraesCS1B01G028700 | chr3A | 78.953 | 898 | 94 | 48 | 933 | 1785 | 552543603 | 552542756 | 2.180000e-144 | 523.0 |
64 | TraesCS1B01G028700 | chr3A | 97.173 | 283 | 8 | 0 | 2199 | 2481 | 724060669 | 724060387 | 4.790000e-131 | 479.0 |
65 | TraesCS1B01G028700 | chr3A | 80.492 | 569 | 93 | 15 | 6054 | 6616 | 518710369 | 518709813 | 2.950000e-113 | 420.0 |
66 | TraesCS1B01G028700 | chr3A | 87.365 | 277 | 32 | 3 | 1 | 276 | 50966198 | 50966472 | 1.430000e-81 | 315.0 |
67 | TraesCS1B01G028700 | chr3A | 84.291 | 261 | 35 | 5 | 6355 | 6612 | 747097723 | 747097980 | 4.090000e-62 | 250.0 |
68 | TraesCS1B01G028700 | chr3A | 83.908 | 261 | 36 | 5 | 6355 | 6612 | 747137834 | 747138091 | 1.900000e-60 | 244.0 |
69 | TraesCS1B01G028700 | chr3A | 83.525 | 261 | 37 | 5 | 6355 | 6612 | 747117855 | 747118112 | 8.850000e-59 | 239.0 |
70 | TraesCS1B01G028700 | chr3A | 78.641 | 103 | 18 | 4 | 999 | 1099 | 732419297 | 732419397 | 1.590000e-06 | 65.8 |
71 | TraesCS1B01G028700 | chr7D | 83.378 | 1131 | 122 | 44 | 2693 | 3787 | 277899251 | 277900351 | 0.000000e+00 | 987.0 |
72 | TraesCS1B01G028700 | chr2A | 92.357 | 628 | 44 | 3 | 2771 | 3395 | 174035209 | 174035835 | 0.000000e+00 | 891.0 |
73 | TraesCS1B01G028700 | chr2A | 98.540 | 274 | 4 | 0 | 2201 | 2474 | 650241299 | 650241026 | 1.030000e-132 | 484.0 |
74 | TraesCS1B01G028700 | chr2A | 95.088 | 285 | 14 | 0 | 1 | 285 | 733425774 | 733426058 | 3.760000e-122 | 449.0 |
75 | TraesCS1B01G028700 | chr6B | 97.193 | 285 | 8 | 0 | 1 | 285 | 27117982 | 27117698 | 3.700000e-132 | 483.0 |
76 | TraesCS1B01G028700 | chr6B | 88.413 | 397 | 38 | 6 | 3178 | 3571 | 712477061 | 712476670 | 8.020000e-129 | 472.0 |
77 | TraesCS1B01G028700 | chr6B | 95.439 | 285 | 13 | 0 | 2199 | 2483 | 49551605 | 49551321 | 8.080000e-124 | 455.0 |
78 | TraesCS1B01G028700 | chr6B | 80.620 | 129 | 14 | 8 | 3484 | 3607 | 712477494 | 712477372 | 9.430000e-14 | 89.8 |
79 | TraesCS1B01G028700 | chr5A | 97.491 | 279 | 7 | 0 | 2199 | 2477 | 650689305 | 650689583 | 1.720000e-130 | 477.0 |
80 | TraesCS1B01G028700 | chr5A | 87.500 | 288 | 36 | 0 | 3174 | 3461 | 555170976 | 555171263 | 3.950000e-87 | 333.0 |
81 | TraesCS1B01G028700 | chr6D | 96.491 | 285 | 10 | 0 | 1 | 285 | 106666825 | 106666541 | 8.020000e-129 | 472.0 |
82 | TraesCS1B01G028700 | chr7A | 96.491 | 285 | 9 | 1 | 2194 | 2478 | 660936838 | 660936555 | 2.880000e-128 | 470.0 |
83 | TraesCS1B01G028700 | chr7A | 82.437 | 279 | 40 | 9 | 6345 | 6620 | 26582877 | 26583149 | 1.150000e-57 | 235.0 |
84 | TraesCS1B01G028700 | chr2B | 97.445 | 274 | 7 | 0 | 2201 | 2474 | 748596579 | 748596852 | 1.040000e-127 | 468.0 |
85 | TraesCS1B01G028700 | chr2B | 83.525 | 261 | 36 | 6 | 6355 | 6612 | 115052015 | 115052271 | 3.180000e-58 | 237.0 |
86 | TraesCS1B01G028700 | chr2B | 79.381 | 291 | 50 | 9 | 2693 | 2979 | 116257736 | 116257452 | 5.400000e-46 | 196.0 |
87 | TraesCS1B01G028700 | chr7B | 96.085 | 281 | 9 | 1 | 2194 | 2474 | 81417492 | 81417770 | 2.250000e-124 | 457.0 |
88 | TraesCS1B01G028700 | chr4B | 96.057 | 279 | 11 | 0 | 2199 | 2477 | 479214971 | 479214693 | 8.080000e-124 | 455.0 |
89 | TraesCS1B01G028700 | chr4B | 93.684 | 285 | 16 | 1 | 1 | 285 | 424063294 | 424063012 | 6.330000e-115 | 425.0 |
90 | TraesCS1B01G028700 | chr5D | 93.684 | 285 | 18 | 0 | 1 | 285 | 377296672 | 377296388 | 1.760000e-115 | 427.0 |
91 | TraesCS1B01G028700 | chr4D | 83.333 | 258 | 38 | 5 | 6357 | 6612 | 302780375 | 302780629 | 4.120000e-57 | 233.0 |
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 | TraesCS1B01G028700 | chr1B | 13964202 | 13971031 | 6829 | False | 4661.666667 | 12613 | 99.620667 | 1 | 6830 | 3 | chr1B.!!$F2 | 6829 |
1 | TraesCS1B01G028700 | chr1B | 556659669 | 556661187 | 1518 | True | 1343.000000 | 2676 | 98.859000 | 1785 | 4289 | 3 | chr1B.!!$R1 | 2504 |
2 | TraesCS1B01G028700 | chr5B | 697005010 | 697007236 | 2226 | False | 1351.400000 | 3262 | 99.407000 | 1785 | 4289 | 5 | chr5B.!!$F3 | 2504 |
3 | TraesCS1B01G028700 | chr4A | 726804106 | 726806335 | 2229 | False | 1340.000000 | 3232 | 99.145200 | 1785 | 4289 | 5 | chr4A.!!$F3 | 2504 |
4 | TraesCS1B01G028700 | chr3B | 623942591 | 623944826 | 2235 | False | 1331.200000 | 3225 | 98.863600 | 1780 | 4292 | 5 | chr3B.!!$F7 | 2512 |
5 | TraesCS1B01G028700 | chr3B | 154437672 | 154440728 | 3056 | False | 1259.500000 | 1783 | 81.821500 | 481 | 6017 | 2 | chr3B.!!$F6 | 5536 |
6 | TraesCS1B01G028700 | chrUn | 96548440 | 96555193 | 6753 | False | 1392.666667 | 2444 | 90.205667 | 481 | 6006 | 3 | chrUn.!!$F1 | 5525 |
7 | TraesCS1B01G028700 | chrUn | 104669108 | 104669849 | 741 | True | 1242.000000 | 1242 | 96.791000 | 3543 | 4289 | 1 | chrUn.!!$R1 | 746 |
8 | TraesCS1B01G028700 | chrUn | 181269537 | 181270282 | 745 | True | 900.000000 | 1336 | 99.268333 | 1788 | 4289 | 3 | chrUn.!!$R2 | 2501 |
9 | TraesCS1B01G028700 | chr1A | 10969775 | 10972751 | 2976 | True | 960.750000 | 2357 | 91.639250 | 481 | 5914 | 4 | chr1A.!!$R2 | 5433 |
10 | TraesCS1B01G028700 | chr1D | 9642232 | 9646753 | 4521 | True | 831.500000 | 1921 | 90.911750 | 607 | 5928 | 4 | chr1D.!!$R1 | 5321 |
11 | TraesCS1B01G028700 | chr3D | 103787753 | 103790636 | 2883 | False | 1265.500000 | 1679 | 82.794500 | 481 | 5866 | 2 | chr3D.!!$F1 | 5385 |
12 | TraesCS1B01G028700 | chr3A | 660004103 | 660004770 | 667 | True | 924.000000 | 924 | 91.766000 | 2733 | 3395 | 1 | chr3A.!!$R2 | 662 |
13 | TraesCS1B01G028700 | chr3A | 660014200 | 660014867 | 667 | True | 913.000000 | 913 | 91.467000 | 2733 | 3395 | 1 | chr3A.!!$R3 | 662 |
14 | TraesCS1B01G028700 | chr3A | 9487511 | 9488040 | 529 | False | 852.000000 | 852 | 95.677000 | 3345 | 3875 | 1 | chr3A.!!$F1 | 530 |
15 | TraesCS1B01G028700 | chr3A | 552538066 | 552543603 | 5537 | True | 736.333333 | 1157 | 83.204333 | 933 | 5933 | 3 | chr3A.!!$R5 | 5000 |
16 | TraesCS1B01G028700 | chr3A | 518709813 | 518710369 | 556 | True | 420.000000 | 420 | 80.492000 | 6054 | 6616 | 1 | chr3A.!!$R1 | 562 |
17 | TraesCS1B01G028700 | chr7D | 277899251 | 277900351 | 1100 | False | 987.000000 | 987 | 83.378000 | 2693 | 3787 | 1 | chr7D.!!$F1 | 1094 |
18 | TraesCS1B01G028700 | chr2A | 174035209 | 174035835 | 626 | False | 891.000000 | 891 | 92.357000 | 2771 | 3395 | 1 | chr2A.!!$F1 | 624 |
19 | TraesCS1B01G028700 | chr6B | 712476670 | 712477494 | 824 | True | 280.900000 | 472 | 84.516500 | 3178 | 3607 | 2 | chr6B.!!$R3 | 429 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
461 | 462 | 0.039074 | CGCAGTGTTCGTCTCCTCTT | 60.039 | 55.000 | 0.00 | 0.00 | 0.00 | 2.85 | F |
474 | 475 | 0.104855 | TCCTCTTTGATGCCGATCGG | 59.895 | 55.000 | 30.03 | 30.03 | 38.57 | 4.18 | F |
475 | 476 | 0.104855 | CCTCTTTGATGCCGATCGGA | 59.895 | 55.000 | 37.64 | 21.99 | 37.50 | 4.55 | F |
1227 | 1541 | 0.109132 | CTGTTGAAAGGAATGCCGGC | 60.109 | 55.000 | 22.73 | 22.73 | 39.96 | 6.13 | F |
2208 | 2583 | 0.110295 | TGTGTGCTGTTAGGGCATGT | 59.890 | 50.000 | 0.00 | 0.00 | 41.86 | 3.21 | F |
2452 | 2827 | 1.005097 | TCCTACGTGGCACTCCTAAGA | 59.995 | 52.381 | 16.72 | 2.12 | 35.26 | 2.10 | F |
4106 | 4520 | 1.282157 | GTGGTAGCCAAGGGAAGTGAT | 59.718 | 52.381 | 0.00 | 0.00 | 34.18 | 3.06 | F |
4467 | 4894 | 1.021390 | AAGAGCATCCCGTTCGCTTG | 61.021 | 55.000 | 0.00 | 0.00 | 35.75 | 4.01 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
2454 | 2829 | 0.332632 | AGGGCATGTACAATGGTGCT | 59.667 | 50.000 | 16.47 | 0.0 | 37.70 | 4.40 | R |
2470 | 2845 | 1.079127 | CACACTCGGCCACTAAGGG | 60.079 | 63.158 | 2.24 | 0.0 | 38.09 | 3.95 | R |
2471 | 2846 | 1.079127 | CCACACTCGGCCACTAAGG | 60.079 | 63.158 | 2.24 | 0.0 | 41.84 | 2.69 | R |
2987 | 3381 | 0.036732 | GGCCTGTCACCATCTTGTCA | 59.963 | 55.000 | 0.00 | 0.0 | 0.00 | 3.58 | R |
4106 | 4520 | 1.003118 | AGACACGATAGCTTTGCCCAA | 59.997 | 47.619 | 0.00 | 0.0 | 42.67 | 4.12 | R |
4443 | 4870 | 2.803492 | GCGAACGGGATGCTCTTAAGAT | 60.803 | 50.000 | 5.44 | 0.0 | 0.00 | 2.40 | R |
5116 | 8586 | 0.035439 | TTGACCCGCCTCCAAATCTC | 60.035 | 55.000 | 0.00 | 0.0 | 0.00 | 2.75 | R |
6036 | 13286 | 0.103026 | TGACCATCGAGGCGATCTTG | 59.897 | 55.000 | 0.00 | 0.0 | 45.19 | 3.02 | 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.