Multiple sequence alignment - TraesCS1B01G039300
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 | TraesCS1B01G039300 | chr1B | 100.000 | 5202 | 0 | 0 | 1 | 5202 | 19016819 | 19022020 | 0.000000e+00 | 9607.0 |
1 | TraesCS1B01G039300 | chr1B | 93.043 | 1308 | 61 | 9 | 2717 | 4001 | 602341449 | 602342749 | 0.000000e+00 | 1884.0 |
2 | TraesCS1B01G039300 | chr1B | 96.170 | 731 | 22 | 4 | 912 | 1641 | 602339777 | 602340502 | 0.000000e+00 | 1190.0 |
3 | TraesCS1B01G039300 | chr1B | 96.983 | 232 | 3 | 4 | 1861 | 2091 | 602340510 | 602340738 | 2.270000e-103 | 387.0 |
4 | TraesCS1B01G039300 | chr1B | 90.909 | 220 | 9 | 3 | 1 | 209 | 602338436 | 602338655 | 8.530000e-73 | 285.0 |
5 | TraesCS1B01G039300 | chr1B | 94.340 | 106 | 6 | 0 | 5097 | 5202 | 14603738 | 14603843 | 4.170000e-36 | 163.0 |
6 | TraesCS1B01G039300 | chr1B | 93.878 | 49 | 3 | 0 | 4903 | 4951 | 684201696 | 684201744 | 2.010000e-09 | 75.0 |
7 | TraesCS1B01G039300 | chr1B | 100.000 | 31 | 0 | 0 | 2687 | 2717 | 19019417 | 19019447 | 2.020000e-04 | 58.4 |
8 | TraesCS1B01G039300 | chr7D | 96.517 | 1292 | 32 | 5 | 2717 | 4001 | 553874606 | 553875891 | 0.000000e+00 | 2124.0 |
9 | TraesCS1B01G039300 | chr7D | 97.468 | 790 | 18 | 2 | 1861 | 2650 | 553873697 | 553874484 | 0.000000e+00 | 1347.0 |
10 | TraesCS1B01G039300 | chr7D | 96.986 | 730 | 18 | 1 | 912 | 1641 | 553872964 | 553873689 | 0.000000e+00 | 1223.0 |
11 | TraesCS1B01G039300 | chr7D | 90.323 | 217 | 10 | 1 | 1 | 206 | 553871630 | 553871846 | 1.850000e-69 | 274.0 |
12 | TraesCS1B01G039300 | chr7D | 90.164 | 61 | 3 | 3 | 4892 | 4951 | 311185682 | 311185740 | 5.590000e-10 | 76.8 |
13 | TraesCS1B01G039300 | chr7D | 100.000 | 31 | 0 | 0 | 2687 | 2717 | 328007910 | 328007940 | 2.020000e-04 | 58.4 |
14 | TraesCS1B01G039300 | chr4D | 96.101 | 1308 | 24 | 6 | 2717 | 4001 | 447219674 | 447218371 | 0.000000e+00 | 2108.0 |
15 | TraesCS1B01G039300 | chr4D | 98.228 | 790 | 12 | 1 | 1861 | 2650 | 447220583 | 447219796 | 0.000000e+00 | 1380.0 |
16 | TraesCS1B01G039300 | chr4D | 97.811 | 731 | 10 | 3 | 912 | 1641 | 447221316 | 447220591 | 0.000000e+00 | 1256.0 |
17 | TraesCS1B01G039300 | chr4D | 95.918 | 147 | 6 | 0 | 63 | 209 | 447222571 | 447222425 | 6.730000e-59 | 239.0 |
18 | TraesCS1B01G039300 | chr4D | 100.000 | 31 | 0 | 0 | 2687 | 2717 | 447219847 | 447219817 | 2.020000e-04 | 58.4 |
19 | TraesCS1B01G039300 | chr3D | 96.024 | 1308 | 27 | 7 | 2717 | 4001 | 250987961 | 250989266 | 0.000000e+00 | 2104.0 |
20 | TraesCS1B01G039300 | chr3D | 93.854 | 1025 | 38 | 5 | 3000 | 4001 | 577327979 | 577329001 | 0.000000e+00 | 1520.0 |
21 | TraesCS1B01G039300 | chr3D | 97.470 | 830 | 15 | 4 | 1821 | 2650 | 250987016 | 250987839 | 0.000000e+00 | 1411.0 |
22 | TraesCS1B01G039300 | chr3D | 97.229 | 830 | 19 | 3 | 1821 | 2650 | 10523958 | 10523133 | 0.000000e+00 | 1402.0 |
23 | TraesCS1B01G039300 | chr3D | 98.358 | 731 | 7 | 3 | 912 | 1641 | 250986307 | 250987033 | 0.000000e+00 | 1279.0 |
24 | TraesCS1B01G039300 | chr3D | 97.541 | 732 | 11 | 4 | 912 | 1641 | 10524667 | 10523941 | 0.000000e+00 | 1245.0 |
25 | TraesCS1B01G039300 | chr3D | 95.599 | 409 | 11 | 2 | 3517 | 3919 | 9496301 | 9495894 | 0.000000e+00 | 649.0 |
26 | TraesCS1B01G039300 | chr3D | 91.284 | 218 | 8 | 1 | 1 | 207 | 250972601 | 250972818 | 2.370000e-73 | 287.0 |
27 | TraesCS1B01G039300 | chr3D | 95.858 | 169 | 7 | 0 | 41 | 209 | 10525950 | 10525782 | 1.850000e-69 | 274.0 |
28 | TraesCS1B01G039300 | chr3D | 82.979 | 94 | 16 | 0 | 4296 | 4389 | 596060204 | 596060111 | 9.280000e-13 | 86.1 |
29 | TraesCS1B01G039300 | chr3D | 91.111 | 45 | 2 | 2 | 8 | 52 | 10525992 | 10525950 | 5.630000e-05 | 60.2 |
30 | TraesCS1B01G039300 | chr3D | 100.000 | 31 | 0 | 0 | 2687 | 2717 | 10523184 | 10523154 | 2.020000e-04 | 58.4 |
31 | TraesCS1B01G039300 | chr3D | 100.000 | 31 | 0 | 0 | 2687 | 2717 | 250987788 | 250987818 | 2.020000e-04 | 58.4 |
32 | TraesCS1B01G039300 | chr6A | 95.336 | 1308 | 33 | 5 | 2717 | 4001 | 211315652 | 211316954 | 0.000000e+00 | 2052.0 |
33 | TraesCS1B01G039300 | chr6A | 93.437 | 1158 | 26 | 11 | 1 | 1120 | 211313289 | 211314434 | 0.000000e+00 | 1672.0 |
34 | TraesCS1B01G039300 | chr6A | 98.108 | 793 | 10 | 2 | 1861 | 2650 | 211314740 | 211315530 | 0.000000e+00 | 1376.0 |
35 | TraesCS1B01G039300 | chr6A | 85.126 | 437 | 24 | 11 | 485 | 887 | 4627299 | 4626870 | 4.850000e-110 | 409.0 |
36 | TraesCS1B01G039300 | chr6A | 99.444 | 180 | 1 | 0 | 1641 | 1820 | 605361584 | 605361405 | 1.400000e-85 | 327.0 |
37 | TraesCS1B01G039300 | chr6A | 94.839 | 155 | 7 | 1 | 222 | 375 | 4627566 | 4627412 | 1.870000e-59 | 241.0 |
38 | TraesCS1B01G039300 | chr6A | 95.098 | 102 | 5 | 0 | 5101 | 5202 | 35325937 | 35325836 | 1.500000e-35 | 161.0 |
39 | TraesCS1B01G039300 | chr6A | 93.443 | 61 | 3 | 1 | 4904 | 4963 | 346590685 | 346590625 | 7.170000e-14 | 89.8 |
40 | TraesCS1B01G039300 | chr6A | 88.710 | 62 | 6 | 1 | 263 | 323 | 4531361 | 4531422 | 2.010000e-09 | 75.0 |
41 | TraesCS1B01G039300 | chr5D | 95.336 | 1308 | 34 | 6 | 2717 | 4001 | 557863577 | 557862274 | 0.000000e+00 | 2052.0 |
42 | TraesCS1B01G039300 | chr5D | 95.183 | 1308 | 36 | 6 | 2717 | 4001 | 398036810 | 398038113 | 0.000000e+00 | 2041.0 |
43 | TraesCS1B01G039300 | chr5D | 95.872 | 969 | 33 | 4 | 2717 | 3684 | 16573349 | 16572387 | 0.000000e+00 | 1561.0 |
44 | TraesCS1B01G039300 | chr5D | 97.714 | 831 | 16 | 3 | 1821 | 2650 | 557864527 | 557863699 | 0.000000e+00 | 1426.0 |
45 | TraesCS1B01G039300 | chr5D | 97.349 | 830 | 20 | 1 | 1821 | 2650 | 398035861 | 398036688 | 0.000000e+00 | 1410.0 |
46 | TraesCS1B01G039300 | chr5D | 96.986 | 730 | 17 | 2 | 912 | 1641 | 398035154 | 398035878 | 0.000000e+00 | 1221.0 |
47 | TraesCS1B01G039300 | chr5D | 96.311 | 732 | 19 | 5 | 912 | 1641 | 16575021 | 16574296 | 0.000000e+00 | 1195.0 |
48 | TraesCS1B01G039300 | chr5D | 93.057 | 821 | 23 | 4 | 1861 | 2650 | 16574288 | 16573471 | 0.000000e+00 | 1170.0 |
49 | TraesCS1B01G039300 | chr5D | 92.273 | 220 | 6 | 2 | 1 | 209 | 557875331 | 557875112 | 8.470000e-78 | 302.0 |
50 | TraesCS1B01G039300 | chr5D | 89.545 | 220 | 12 | 3 | 1 | 209 | 16576369 | 16576150 | 8.590000e-68 | 268.0 |
51 | TraesCS1B01G039300 | chr5D | 96.000 | 150 | 5 | 1 | 63 | 212 | 398033892 | 398034040 | 5.200000e-60 | 243.0 |
52 | TraesCS1B01G039300 | chr5D | 97.826 | 46 | 0 | 1 | 3 | 48 | 398033851 | 398033895 | 1.550000e-10 | 78.7 |
53 | TraesCS1B01G039300 | chr5D | 100.000 | 32 | 0 | 0 | 2686 | 2717 | 16573523 | 16573492 | 5.630000e-05 | 60.2 |
54 | TraesCS1B01G039300 | chr5D | 100.000 | 31 | 0 | 0 | 2687 | 2717 | 557863750 | 557863720 | 2.020000e-04 | 58.4 |
55 | TraesCS1B01G039300 | chr2D | 94.439 | 1025 | 32 | 5 | 3000 | 4001 | 415156336 | 415157358 | 0.000000e+00 | 1554.0 |
56 | TraesCS1B01G039300 | chr2D | 94.789 | 806 | 34 | 5 | 2717 | 3518 | 420721524 | 420722325 | 0.000000e+00 | 1249.0 |
57 | TraesCS1B01G039300 | chr2D | 100.000 | 31 | 0 | 0 | 2687 | 2717 | 420721351 | 420721381 | 2.020000e-04 | 58.4 |
58 | TraesCS1B01G039300 | chr7A | 97.115 | 728 | 15 | 3 | 915 | 1641 | 151593893 | 151593171 | 0.000000e+00 | 1223.0 |
59 | TraesCS1B01G039300 | chr7A | 92.717 | 865 | 27 | 9 | 1821 | 2650 | 151593188 | 151592325 | 0.000000e+00 | 1216.0 |
60 | TraesCS1B01G039300 | chr7A | 88.636 | 220 | 14 | 7 | 1 | 209 | 151595244 | 151595025 | 1.860000e-64 | 257.0 |
61 | TraesCS1B01G039300 | chr7A | 93.103 | 58 | 4 | 0 | 4893 | 4950 | 493700531 | 493700474 | 9.280000e-13 | 86.1 |
62 | TraesCS1B01G039300 | chr2A | 94.254 | 731 | 37 | 2 | 912 | 1641 | 315961309 | 315962035 | 0.000000e+00 | 1112.0 |
63 | TraesCS1B01G039300 | chr2A | 92.593 | 108 | 8 | 0 | 5095 | 5202 | 650241308 | 650241201 | 6.970000e-34 | 156.0 |
64 | TraesCS1B01G039300 | chr2A | 96.078 | 51 | 2 | 0 | 4901 | 4951 | 57447057 | 57447107 | 3.340000e-12 | 84.2 |
65 | TraesCS1B01G039300 | chr2A | 91.525 | 59 | 5 | 0 | 4904 | 4962 | 569588171 | 569588113 | 1.200000e-11 | 82.4 |
66 | TraesCS1B01G039300 | chr1A | 87.486 | 919 | 87 | 10 | 4004 | 4905 | 14600699 | 14599792 | 0.000000e+00 | 1035.0 |
67 | TraesCS1B01G039300 | chr1A | 86.400 | 125 | 4 | 1 | 4960 | 5071 | 14599794 | 14599670 | 1.970000e-24 | 124.0 |
68 | TraesCS1B01G039300 | chr1A | 92.308 | 52 | 4 | 0 | 4900 | 4951 | 335543460 | 335543409 | 2.010000e-09 | 75.0 |
69 | TraesCS1B01G039300 | chr6B | 92.421 | 409 | 23 | 3 | 3517 | 3919 | 483725296 | 483724890 | 1.260000e-160 | 577.0 |
70 | TraesCS1B01G039300 | chr6B | 91.198 | 409 | 26 | 5 | 3517 | 3919 | 152441170 | 152440766 | 9.850000e-152 | 547.0 |
71 | TraesCS1B01G039300 | chr6B | 79.208 | 202 | 26 | 7 | 399 | 595 | 9380060 | 9380250 | 5.470000e-25 | 126.0 |
72 | TraesCS1B01G039300 | chr3B | 91.198 | 409 | 26 | 5 | 3517 | 3919 | 286476899 | 286477303 | 9.850000e-152 | 547.0 |
73 | TraesCS1B01G039300 | chr3B | 97.059 | 102 | 3 | 0 | 5101 | 5202 | 436561652 | 436561753 | 6.930000e-39 | 172.0 |
74 | TraesCS1B01G039300 | chr3B | 93.578 | 109 | 5 | 2 | 5094 | 5202 | 786783979 | 786784085 | 1.500000e-35 | 161.0 |
75 | TraesCS1B01G039300 | chr1D | 83.610 | 482 | 46 | 15 | 4398 | 4874 | 13355765 | 13355312 | 6.230000e-114 | 422.0 |
76 | TraesCS1B01G039300 | chr1D | 88.991 | 109 | 10 | 2 | 4999 | 5105 | 13355204 | 13355096 | 3.270000e-27 | 134.0 |
77 | TraesCS1B01G039300 | chr1D | 94.231 | 52 | 3 | 0 | 4900 | 4951 | 475911948 | 475911897 | 4.320000e-11 | 80.5 |
78 | TraesCS1B01G039300 | chr1D | 92.593 | 54 | 4 | 0 | 4903 | 4956 | 142966610 | 142966663 | 1.550000e-10 | 78.7 |
79 | TraesCS1B01G039300 | chr7B | 99.448 | 181 | 1 | 0 | 1640 | 1820 | 46028673 | 46028493 | 3.880000e-86 | 329.0 |
80 | TraesCS1B01G039300 | chr7B | 97.884 | 189 | 3 | 1 | 1639 | 1827 | 198551069 | 198551256 | 5.020000e-85 | 326.0 |
81 | TraesCS1B01G039300 | chr7B | 98.387 | 186 | 2 | 1 | 1638 | 1823 | 252794450 | 252794266 | 5.020000e-85 | 326.0 |
82 | TraesCS1B01G039300 | chr7B | 97.030 | 101 | 3 | 0 | 5102 | 5202 | 603591627 | 603591727 | 2.490000e-38 | 171.0 |
83 | TraesCS1B01G039300 | chr5B | 99.444 | 180 | 1 | 0 | 1642 | 1821 | 284367523 | 284367702 | 1.400000e-85 | 327.0 |
84 | TraesCS1B01G039300 | chr5A | 98.907 | 183 | 2 | 0 | 1639 | 1821 | 463712165 | 463712347 | 1.400000e-85 | 327.0 |
85 | TraesCS1B01G039300 | chr5A | 94.444 | 108 | 5 | 1 | 5096 | 5202 | 611639848 | 611639955 | 1.160000e-36 | 165.0 |
86 | TraesCS1B01G039300 | chr4A | 98.907 | 183 | 2 | 0 | 1639 | 1821 | 662286867 | 662287049 | 1.400000e-85 | 327.0 |
87 | TraesCS1B01G039300 | chr4B | 99.441 | 179 | 1 | 0 | 1642 | 1820 | 128540849 | 128540671 | 5.020000e-85 | 326.0 |
88 | TraesCS1B01G039300 | chr4B | 98.901 | 182 | 2 | 0 | 1642 | 1823 | 588430996 | 588430815 | 5.020000e-85 | 326.0 |
89 | TraesCS1B01G039300 | chr4B | 95.146 | 103 | 3 | 1 | 5100 | 5202 | 95717029 | 95717129 | 1.500000e-35 | 161.0 |
90 | TraesCS1B01G039300 | chr4B | 100.000 | 38 | 0 | 0 | 3964 | 4001 | 160257975 | 160258012 | 2.600000e-08 | 71.3 |
91 | TraesCS1B01G039300 | chr4B | 100.000 | 31 | 0 | 0 | 2687 | 2717 | 236163731 | 236163701 | 2.020000e-04 | 58.4 |
92 | TraesCS1B01G039300 | chr3A | 96.970 | 99 | 3 | 0 | 5104 | 5202 | 580564995 | 580565093 | 3.220000e-37 | 167.0 |
93 | TraesCS1B01G039300 | chr6D | 100.000 | 30 | 0 | 0 | 4716 | 4745 | 453996308 | 453996279 | 7.280000e-04 | 56.5 |
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 | TraesCS1B01G039300 | chr1B | 19016819 | 19022020 | 5201 | False | 4832.700000 | 9607 | 100.000000 | 1 | 5202 | 2 | chr1B.!!$F3 | 5201 |
1 | TraesCS1B01G039300 | chr1B | 602338436 | 602342749 | 4313 | False | 936.500000 | 1884 | 94.276250 | 1 | 4001 | 4 | chr1B.!!$F4 | 4000 |
2 | TraesCS1B01G039300 | chr7D | 553871630 | 553875891 | 4261 | False | 1242.000000 | 2124 | 95.323500 | 1 | 4001 | 4 | chr7D.!!$F3 | 4000 |
3 | TraesCS1B01G039300 | chr4D | 447218371 | 447222571 | 4200 | True | 1008.280000 | 2108 | 97.611600 | 63 | 4001 | 5 | chr4D.!!$R1 | 3938 |
4 | TraesCS1B01G039300 | chr3D | 577327979 | 577329001 | 1022 | False | 1520.000000 | 1520 | 93.854000 | 3000 | 4001 | 1 | chr3D.!!$F2 | 1001 |
5 | TraesCS1B01G039300 | chr3D | 250986307 | 250989266 | 2959 | False | 1213.100000 | 2104 | 97.963000 | 912 | 4001 | 4 | chr3D.!!$F3 | 3089 |
6 | TraesCS1B01G039300 | chr3D | 10523133 | 10525992 | 2859 | True | 607.920000 | 1402 | 96.347800 | 8 | 2717 | 5 | chr3D.!!$R3 | 2709 |
7 | TraesCS1B01G039300 | chr6A | 211313289 | 211316954 | 3665 | False | 1700.000000 | 2052 | 95.627000 | 1 | 4001 | 3 | chr6A.!!$F2 | 4000 |
8 | TraesCS1B01G039300 | chr6A | 4626870 | 4627566 | 696 | True | 325.000000 | 409 | 89.982500 | 222 | 887 | 2 | chr6A.!!$R4 | 665 |
9 | TraesCS1B01G039300 | chr5D | 557862274 | 557864527 | 2253 | True | 1178.800000 | 2052 | 97.683333 | 1821 | 4001 | 3 | chr5D.!!$R3 | 2180 |
10 | TraesCS1B01G039300 | chr5D | 398033851 | 398038113 | 4262 | False | 998.740000 | 2041 | 96.668800 | 3 | 4001 | 5 | chr5D.!!$F1 | 3998 |
11 | TraesCS1B01G039300 | chr5D | 16572387 | 16576369 | 3982 | True | 850.840000 | 1561 | 94.957000 | 1 | 3684 | 5 | chr5D.!!$R2 | 3683 |
12 | TraesCS1B01G039300 | chr2D | 415156336 | 415157358 | 1022 | False | 1554.000000 | 1554 | 94.439000 | 3000 | 4001 | 1 | chr2D.!!$F1 | 1001 |
13 | TraesCS1B01G039300 | chr2D | 420721351 | 420722325 | 974 | False | 653.700000 | 1249 | 97.394500 | 2687 | 3518 | 2 | chr2D.!!$F2 | 831 |
14 | TraesCS1B01G039300 | chr7A | 151592325 | 151595244 | 2919 | True | 898.666667 | 1223 | 92.822667 | 1 | 2650 | 3 | chr7A.!!$R2 | 2649 |
15 | TraesCS1B01G039300 | chr2A | 315961309 | 315962035 | 726 | False | 1112.000000 | 1112 | 94.254000 | 912 | 1641 | 1 | chr2A.!!$F2 | 729 |
16 | TraesCS1B01G039300 | chr1A | 14599670 | 14600699 | 1029 | True | 579.500000 | 1035 | 86.943000 | 4004 | 5071 | 2 | chr1A.!!$R2 | 1067 |
17 | TraesCS1B01G039300 | chr1D | 13355096 | 13355765 | 669 | True | 278.000000 | 422 | 86.300500 | 4398 | 5105 | 2 | chr1D.!!$R2 | 707 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
141 | 153 | 1.374758 | GCAACTCCAGTCACTCCCG | 60.375 | 63.158 | 0.0 | 0.0 | 0.00 | 5.14 | F |
1768 | 2460 | 0.107831 | TTCCAGGACTTGAACCCGTG | 59.892 | 55.000 | 0.0 | 0.0 | 0.00 | 4.94 | F |
1777 | 2469 | 0.107831 | TTGAACCCGTGACCTCTTGG | 59.892 | 55.000 | 0.0 | 0.0 | 39.83 | 3.61 | F |
2097 | 2822 | 0.108804 | GTCACGAGATCCTTTCCGCA | 60.109 | 55.000 | 0.0 | 0.0 | 0.00 | 5.69 | F |
2664 | 3398 | 0.109412 | GTGAAGCATGAGCCAAGCAC | 60.109 | 55.000 | 0.0 | 0.0 | 43.56 | 4.40 | F |
2668 | 3402 | 0.323087 | AGCATGAGCCAAGCACATCA | 60.323 | 50.000 | 0.0 | 0.0 | 37.73 | 3.07 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1810 | 2502 | 0.100861 | CGTACTCTTCGAAGGGGAGC | 59.899 | 60.0 | 28.03 | 15.97 | 32.01 | 4.70 | R |
2645 | 3379 | 0.109412 | GTGCTTGGCTCATGCTTCAC | 60.109 | 55.0 | 12.12 | 2.33 | 39.59 | 3.18 | R |
2649 | 3383 | 0.323087 | TGATGTGCTTGGCTCATGCT | 60.323 | 50.0 | 11.00 | 0.00 | 41.77 | 3.79 | R |
3871 | 4992 | 0.942962 | GATCAGCATCAAGGGCTTCG | 59.057 | 55.0 | 0.00 | 0.00 | 40.23 | 3.79 | R |
4138 | 5261 | 0.107800 | CTCATCAGTGGCAGGGACAG | 60.108 | 60.0 | 0.00 | 0.00 | 0.00 | 3.51 | R |
4413 | 5551 | 0.637195 | TAGGCTGGAAGGTCCTAGCT | 59.363 | 55.0 | 11.19 | 0.00 | 39.23 | 3.32 | 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.