Multiple sequence alignment - TraesCS6B01G283500
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 | TraesCS6B01G283500 | chr6B | 100.000 | 2522 | 0 | 0 | 1 | 2522 | 511713109 | 511710588 | 0.000000e+00 | 4658.0 |
1 | TraesCS6B01G283500 | chr6B | 88.119 | 202 | 17 | 6 | 81 | 281 | 160661002 | 160660807 | 1.510000e-57 | 233.0 |
2 | TraesCS6B01G283500 | chr6B | 81.017 | 295 | 27 | 18 | 1 | 272 | 158160395 | 158160683 | 9.140000e-50 | 207.0 |
3 | TraesCS6B01G283500 | chr6B | 91.250 | 80 | 6 | 1 | 1 | 79 | 157913147 | 157913068 | 9.540000e-20 | 108.0 |
4 | TraesCS6B01G283500 | chr2B | 92.903 | 2198 | 123 | 17 | 348 | 2522 | 441885053 | 441887240 | 0.000000e+00 | 3164.0 |
5 | TraesCS6B01G283500 | chr2B | 90.183 | 927 | 66 | 7 | 352 | 1270 | 142989455 | 142988546 | 0.000000e+00 | 1184.0 |
6 | TraesCS6B01G283500 | chr2B | 94.044 | 319 | 19 | 0 | 2204 | 2522 | 534409968 | 534410286 | 3.770000e-133 | 484.0 |
7 | TraesCS6B01G283500 | chr4D | 92.179 | 2212 | 125 | 27 | 356 | 2522 | 481887026 | 481889234 | 0.000000e+00 | 3083.0 |
8 | TraesCS6B01G283500 | chr4D | 93.202 | 1927 | 105 | 14 | 354 | 2263 | 119369760 | 119367843 | 0.000000e+00 | 2809.0 |
9 | TraesCS6B01G283500 | chr4D | 92.950 | 1915 | 95 | 18 | 353 | 2239 | 486565784 | 486563882 | 0.000000e+00 | 2752.0 |
10 | TraesCS6B01G283500 | chr4D | 79.252 | 294 | 28 | 22 | 1 | 271 | 223628360 | 223628643 | 9.270000e-40 | 174.0 |
11 | TraesCS6B01G283500 | chr4D | 82.703 | 185 | 22 | 10 | 91 | 272 | 505004385 | 505004562 | 3.360000e-34 | 156.0 |
12 | TraesCS6B01G283500 | chr4D | 80.435 | 184 | 25 | 10 | 95 | 272 | 272382526 | 272382348 | 2.040000e-26 | 130.0 |
13 | TraesCS6B01G283500 | chr4D | 78.528 | 163 | 24 | 10 | 117 | 272 | 10756157 | 10755999 | 2.070000e-16 | 97.1 |
14 | TraesCS6B01G283500 | chr1D | 91.640 | 2225 | 124 | 27 | 353 | 2522 | 430108487 | 430110704 | 0.000000e+00 | 3022.0 |
15 | TraesCS6B01G283500 | chr1D | 91.712 | 2220 | 117 | 25 | 355 | 2522 | 278102468 | 278100264 | 0.000000e+00 | 3018.0 |
16 | TraesCS6B01G283500 | chr1D | 90.942 | 2208 | 140 | 24 | 355 | 2512 | 250223367 | 250225564 | 0.000000e+00 | 2915.0 |
17 | TraesCS6B01G283500 | chr1D | 93.580 | 1916 | 101 | 10 | 356 | 2255 | 303344960 | 303346869 | 0.000000e+00 | 2837.0 |
18 | TraesCS6B01G283500 | chr1D | 90.299 | 2206 | 146 | 27 | 354 | 2522 | 424634905 | 424637079 | 0.000000e+00 | 2826.0 |
19 | TraesCS6B01G283500 | chr1D | 90.901 | 1132 | 67 | 9 | 355 | 1473 | 139135263 | 139134155 | 0.000000e+00 | 1487.0 |
20 | TraesCS6B01G283500 | chr1D | 91.434 | 1004 | 64 | 8 | 354 | 1345 | 446540375 | 446541368 | 0.000000e+00 | 1358.0 |
21 | TraesCS6B01G283500 | chr1D | 90.661 | 696 | 48 | 8 | 354 | 1037 | 441745115 | 441744425 | 0.000000e+00 | 909.0 |
22 | TraesCS6B01G283500 | chr1D | 88.889 | 459 | 40 | 5 | 2075 | 2522 | 236097094 | 236096636 | 2.830000e-154 | 555.0 |
23 | TraesCS6B01G283500 | chr1D | 88.489 | 278 | 19 | 5 | 357 | 623 | 398866615 | 398866340 | 8.700000e-85 | 324.0 |
24 | TraesCS6B01G283500 | chr1D | 82.990 | 194 | 16 | 13 | 82 | 271 | 475624161 | 475623981 | 2.600000e-35 | 159.0 |
25 | TraesCS6B01G283500 | chr1D | 82.105 | 190 | 22 | 11 | 90 | 272 | 337212309 | 337212493 | 4.350000e-33 | 152.0 |
26 | TraesCS6B01G283500 | chr1D | 81.026 | 195 | 17 | 16 | 92 | 273 | 478935222 | 478935035 | 1.220000e-28 | 137.0 |
27 | TraesCS6B01G283500 | chr1D | 80.435 | 184 | 25 | 10 | 95 | 272 | 462009682 | 462009860 | 2.040000e-26 | 130.0 |
28 | TraesCS6B01G283500 | chr1D | 81.657 | 169 | 18 | 11 | 110 | 274 | 50989390 | 50989549 | 7.320000e-26 | 128.0 |
29 | TraesCS6B01G283500 | chr1D | 80.000 | 195 | 16 | 21 | 82 | 273 | 111980057 | 111980231 | 3.410000e-24 | 122.0 |
30 | TraesCS6B01G283500 | chr1D | 88.298 | 94 | 10 | 1 | 179 | 272 | 66379350 | 66379442 | 7.370000e-21 | 111.0 |
31 | TraesCS6B01G283500 | chr1D | 86.735 | 98 | 7 | 6 | 179 | 273 | 250703682 | 250703776 | 1.230000e-18 | 104.0 |
32 | TraesCS6B01G283500 | chr1D | 84.466 | 103 | 10 | 6 | 176 | 275 | 208854896 | 208854995 | 2.070000e-16 | 97.1 |
33 | TraesCS6B01G283500 | chr6D | 91.434 | 2218 | 125 | 27 | 354 | 2522 | 325418870 | 325416669 | 0.000000e+00 | 2983.0 |
34 | TraesCS6B01G283500 | chr6D | 90.836 | 2117 | 112 | 33 | 355 | 2420 | 447882347 | 447880262 | 0.000000e+00 | 2760.0 |
35 | TraesCS6B01G283500 | chr6D | 92.451 | 1934 | 113 | 17 | 352 | 2263 | 347439908 | 347437986 | 0.000000e+00 | 2732.0 |
36 | TraesCS6B01G283500 | chr6D | 92.901 | 1296 | 66 | 8 | 353 | 1627 | 421840966 | 421842256 | 0.000000e+00 | 1860.0 |
37 | TraesCS6B01G283500 | chr6D | 92.668 | 1132 | 60 | 13 | 354 | 1473 | 41924608 | 41923488 | 0.000000e+00 | 1609.0 |
38 | TraesCS6B01G283500 | chr6D | 78.596 | 285 | 34 | 20 | 4 | 273 | 83174870 | 83174598 | 2.010000e-36 | 163.0 |
39 | TraesCS6B01G283500 | chr6D | 81.579 | 190 | 23 | 9 | 89 | 273 | 412196980 | 412197162 | 2.020000e-31 | 147.0 |
40 | TraesCS6B01G283500 | chr6D | 79.042 | 167 | 20 | 13 | 117 | 274 | 139575054 | 139574894 | 1.600000e-17 | 100.0 |
41 | TraesCS6B01G283500 | chr6D | 78.528 | 163 | 25 | 10 | 117 | 272 | 63718777 | 63718936 | 5.740000e-17 | 99.0 |
42 | TraesCS6B01G283500 | chr6D | 78.916 | 166 | 20 | 11 | 112 | 275 | 147894399 | 147894247 | 5.740000e-17 | 99.0 |
43 | TraesCS6B01G283500 | chr2D | 90.769 | 2210 | 157 | 19 | 354 | 2522 | 644015512 | 644013309 | 0.000000e+00 | 2907.0 |
44 | TraesCS6B01G283500 | chr2D | 92.499 | 1933 | 94 | 18 | 354 | 2263 | 500667213 | 500665309 | 0.000000e+00 | 2719.0 |
45 | TraesCS6B01G283500 | chr2D | 91.505 | 671 | 38 | 6 | 355 | 1011 | 50139065 | 50138400 | 0.000000e+00 | 905.0 |
46 | TraesCS6B01G283500 | chr2D | 83.889 | 180 | 19 | 9 | 97 | 272 | 26455785 | 26455958 | 2.010000e-36 | 163.0 |
47 | TraesCS6B01G283500 | chr2D | 85.542 | 83 | 4 | 5 | 272 | 354 | 21532136 | 21532210 | 2.080000e-11 | 80.5 |
48 | TraesCS6B01G283500 | chr7D | 93.691 | 1918 | 94 | 16 | 354 | 2255 | 85019321 | 85021227 | 0.000000e+00 | 2846.0 |
49 | TraesCS6B01G283500 | chr7D | 91.297 | 1195 | 67 | 12 | 353 | 1533 | 56936786 | 56937957 | 0.000000e+00 | 1596.0 |
50 | TraesCS6B01G283500 | chr7B | 93.584 | 1917 | 101 | 9 | 355 | 2255 | 442357638 | 442359548 | 0.000000e+00 | 2839.0 |
51 | TraesCS6B01G283500 | chr7B | 91.635 | 526 | 25 | 9 | 2016 | 2522 | 8457989 | 8457464 | 0.000000e+00 | 710.0 |
52 | TraesCS6B01G283500 | chr7B | 87.000 | 200 | 15 | 9 | 80 | 277 | 1880477 | 1880287 | 5.460000e-52 | 215.0 |
53 | TraesCS6B01G283500 | chrUn | 93.184 | 1922 | 100 | 13 | 355 | 2258 | 105335964 | 105334056 | 0.000000e+00 | 2795.0 |
54 | TraesCS6B01G283500 | chrUn | 90.511 | 822 | 55 | 10 | 351 | 1160 | 108802910 | 108803720 | 0.000000e+00 | 1064.0 |
55 | TraesCS6B01G283500 | chrUn | 80.928 | 194 | 19 | 16 | 82 | 272 | 32325533 | 32325355 | 1.220000e-28 | 137.0 |
56 | TraesCS6B01G283500 | chrUn | 86.139 | 101 | 9 | 5 | 179 | 275 | 410432203 | 410432302 | 1.230000e-18 | 104.0 |
57 | TraesCS6B01G283500 | chr5B | 89.428 | 2204 | 184 | 32 | 356 | 2522 | 615401475 | 615399284 | 0.000000e+00 | 2734.0 |
58 | TraesCS6B01G283500 | chr5B | 89.955 | 2011 | 155 | 18 | 356 | 2325 | 635767314 | 635765310 | 0.000000e+00 | 2551.0 |
59 | TraesCS6B01G283500 | chr5B | 89.060 | 521 | 42 | 7 | 353 | 871 | 128209013 | 128208506 | 1.270000e-177 | 632.0 |
60 | TraesCS6B01G283500 | chr5B | 87.766 | 188 | 15 | 6 | 85 | 272 | 158732819 | 158732998 | 1.970000e-51 | 213.0 |
61 | TraesCS6B01G283500 | chr5B | 89.634 | 164 | 10 | 5 | 108 | 271 | 105756185 | 105756341 | 4.250000e-48 | 202.0 |
62 | TraesCS6B01G283500 | chr5B | 87.500 | 168 | 15 | 6 | 106 | 273 | 106354658 | 106354497 | 3.310000e-44 | 189.0 |
63 | TraesCS6B01G283500 | chr3D | 93.763 | 1443 | 70 | 10 | 353 | 1781 | 576579536 | 576578100 | 0.000000e+00 | 2148.0 |
64 | TraesCS6B01G283500 | chr3D | 92.581 | 1240 | 67 | 8 | 341 | 1567 | 580656345 | 580657572 | 0.000000e+00 | 1757.0 |
65 | TraesCS6B01G283500 | chr3D | 89.950 | 398 | 25 | 9 | 354 | 740 | 515671975 | 515672368 | 1.350000e-137 | 499.0 |
66 | TraesCS6B01G283500 | chr3D | 93.691 | 317 | 20 | 0 | 2206 | 2522 | 576576212 | 576575896 | 2.270000e-130 | 475.0 |
67 | TraesCS6B01G283500 | chr3D | 81.481 | 189 | 25 | 9 | 89 | 274 | 2253483 | 2253302 | 2.020000e-31 | 147.0 |
68 | TraesCS6B01G283500 | chr3D | 80.874 | 183 | 24 | 5 | 92 | 273 | 231161742 | 231161570 | 1.570000e-27 | 134.0 |
69 | TraesCS6B01G283500 | chr5A | 89.736 | 341 | 20 | 8 | 353 | 682 | 655728954 | 655729290 | 3.000000e-114 | 422.0 |
70 | TraesCS6B01G283500 | chr5A | 88.563 | 341 | 24 | 8 | 353 | 682 | 655800047 | 655800383 | 1.410000e-107 | 399.0 |
71 | TraesCS6B01G283500 | chr5A | 87.683 | 341 | 26 | 9 | 353 | 682 | 655646392 | 655646727 | 1.420000e-102 | 383.0 |
72 | TraesCS6B01G283500 | chr5A | 82.734 | 278 | 34 | 11 | 1 | 272 | 404664799 | 404665068 | 4.190000e-58 | 235.0 |
73 | TraesCS6B01G283500 | chr5A | 84.043 | 188 | 20 | 9 | 93 | 273 | 338409852 | 338410036 | 3.340000e-39 | 172.0 |
74 | TraesCS6B01G283500 | chr5A | 83.516 | 182 | 20 | 9 | 95 | 271 | 624753090 | 624753266 | 7.220000e-36 | 161.0 |
75 | TraesCS6B01G283500 | chr4B | 90.391 | 281 | 25 | 2 | 353 | 633 | 554219909 | 554220187 | 3.960000e-98 | 368.0 |
76 | TraesCS6B01G283500 | chr4B | 87.329 | 292 | 12 | 10 | 1 | 273 | 436261598 | 436261313 | 6.770000e-81 | 311.0 |
77 | TraesCS6B01G283500 | chr4B | 83.158 | 190 | 23 | 7 | 90 | 272 | 242718651 | 242718838 | 5.580000e-37 | 165.0 |
78 | TraesCS6B01G283500 | chr3B | 85.811 | 296 | 14 | 11 | 1 | 272 | 741431653 | 741431944 | 3.170000e-74 | 289.0 |
79 | TraesCS6B01G283500 | chr3B | 90.674 | 193 | 11 | 3 | 80 | 271 | 16836340 | 16836154 | 1.500000e-62 | 250.0 |
80 | TraesCS6B01G283500 | chr3B | 89.175 | 194 | 15 | 5 | 80 | 273 | 539563880 | 539563693 | 1.170000e-58 | 237.0 |
81 | TraesCS6B01G283500 | chr3B | 82.432 | 296 | 23 | 15 | 1 | 273 | 466660491 | 466660780 | 5.430000e-57 | 231.0 |
82 | TraesCS6B01G283500 | chr3B | 89.071 | 183 | 13 | 5 | 92 | 272 | 254847583 | 254847760 | 1.170000e-53 | 220.0 |
83 | TraesCS6B01G283500 | chr3B | 95.312 | 64 | 3 | 0 | 1 | 64 | 16836687 | 16836624 | 4.440000e-18 | 102.0 |
84 | TraesCS6B01G283500 | chr1B | 93.000 | 200 | 7 | 3 | 80 | 277 | 573413411 | 573413217 | 4.110000e-73 | 285.0 |
85 | TraesCS6B01G283500 | chr1B | 84.512 | 297 | 18 | 10 | 1 | 273 | 7335756 | 7336048 | 4.140000e-68 | 268.0 |
86 | TraesCS6B01G283500 | chr1B | 83.217 | 286 | 30 | 16 | 1 | 272 | 161379874 | 161379593 | 1.940000e-61 | 246.0 |
87 | TraesCS6B01G283500 | chr1B | 81.145 | 297 | 26 | 16 | 1 | 273 | 130105834 | 130106124 | 7.070000e-51 | 211.0 |
88 | TraesCS6B01G283500 | chr1B | 87.135 | 171 | 16 | 5 | 106 | 273 | 6578746 | 6578913 | 3.310000e-44 | 189.0 |
89 | TraesCS6B01G283500 | chr1B | 87.059 | 170 | 16 | 5 | 105 | 271 | 562470704 | 562470538 | 1.190000e-43 | 187.0 |
90 | TraesCS6B01G283500 | chr4A | 86.705 | 173 | 13 | 7 | 105 | 271 | 651086437 | 651086605 | 1.540000e-42 | 183.0 |
91 | TraesCS6B01G283500 | chr4A | 83.770 | 191 | 22 | 9 | 86 | 273 | 512026073 | 512026257 | 3.340000e-39 | 172.0 |
92 | TraesCS6B01G283500 | chr4A | 100.000 | 27 | 0 | 0 | 1 | 27 | 436436890 | 436436916 | 1.600000e-02 | 51.0 |
93 | TraesCS6B01G283500 | chr1A | 79.667 | 300 | 25 | 21 | 4 | 272 | 513590144 | 513589850 | 1.540000e-42 | 183.0 |
94 | TraesCS6B01G283500 | chr1A | 83.436 | 163 | 13 | 12 | 112 | 271 | 492136526 | 492136677 | 3.380000e-29 | 139.0 |
95 | TraesCS6B01G283500 | chr1A | 83.226 | 155 | 17 | 8 | 118 | 271 | 269576126 | 269575980 | 1.570000e-27 | 134.0 |
96 | TraesCS6B01G283500 | chr6A | 79.522 | 293 | 29 | 19 | 1 | 268 | 457611361 | 457611075 | 1.990000e-41 | 180.0 |
97 | TraesCS6B01G283500 | chr6A | 82.812 | 192 | 23 | 9 | 95 | 281 | 609673185 | 609673371 | 2.010000e-36 | 163.0 |
98 | TraesCS6B01G283500 | chr6A | 77.517 | 298 | 36 | 20 | 4 | 275 | 161148984 | 161148692 | 1.560000e-32 | 150.0 |
99 | TraesCS6B01G283500 | chr6A | 97.674 | 43 | 1 | 0 | 1 | 43 | 102139846 | 102139804 | 9.680000e-10 | 75.0 |
100 | TraesCS6B01G283500 | chr5D | 86.585 | 164 | 14 | 8 | 112 | 271 | 459140553 | 459140712 | 9.270000e-40 | 174.0 |
101 | TraesCS6B01G283500 | chr5D | 85.629 | 167 | 13 | 10 | 117 | 281 | 110346009 | 110346166 | 5.580000e-37 | 165.0 |
102 | TraesCS6B01G283500 | chr5D | 82.162 | 185 | 20 | 12 | 95 | 272 | 484783402 | 484783580 | 2.020000e-31 | 147.0 |
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 | TraesCS6B01G283500 | chr6B | 511710588 | 511713109 | 2521 | True | 4658.0 | 4658 | 100.000 | 1 | 2522 | 1 | chr6B.!!$R3 | 2521 |
1 | TraesCS6B01G283500 | chr2B | 441885053 | 441887240 | 2187 | False | 3164.0 | 3164 | 92.903 | 348 | 2522 | 1 | chr2B.!!$F1 | 2174 |
2 | TraesCS6B01G283500 | chr2B | 142988546 | 142989455 | 909 | True | 1184.0 | 1184 | 90.183 | 352 | 1270 | 1 | chr2B.!!$R1 | 918 |
3 | TraesCS6B01G283500 | chr4D | 481887026 | 481889234 | 2208 | False | 3083.0 | 3083 | 92.179 | 356 | 2522 | 1 | chr4D.!!$F2 | 2166 |
4 | TraesCS6B01G283500 | chr4D | 119367843 | 119369760 | 1917 | True | 2809.0 | 2809 | 93.202 | 354 | 2263 | 1 | chr4D.!!$R2 | 1909 |
5 | TraesCS6B01G283500 | chr4D | 486563882 | 486565784 | 1902 | True | 2752.0 | 2752 | 92.950 | 353 | 2239 | 1 | chr4D.!!$R4 | 1886 |
6 | TraesCS6B01G283500 | chr1D | 430108487 | 430110704 | 2217 | False | 3022.0 | 3022 | 91.640 | 353 | 2522 | 1 | chr1D.!!$F10 | 2169 |
7 | TraesCS6B01G283500 | chr1D | 278100264 | 278102468 | 2204 | True | 3018.0 | 3018 | 91.712 | 355 | 2522 | 1 | chr1D.!!$R3 | 2167 |
8 | TraesCS6B01G283500 | chr1D | 250223367 | 250225564 | 2197 | False | 2915.0 | 2915 | 90.942 | 355 | 2512 | 1 | chr1D.!!$F5 | 2157 |
9 | TraesCS6B01G283500 | chr1D | 303344960 | 303346869 | 1909 | False | 2837.0 | 2837 | 93.580 | 356 | 2255 | 1 | chr1D.!!$F7 | 1899 |
10 | TraesCS6B01G283500 | chr1D | 424634905 | 424637079 | 2174 | False | 2826.0 | 2826 | 90.299 | 354 | 2522 | 1 | chr1D.!!$F9 | 2168 |
11 | TraesCS6B01G283500 | chr1D | 139134155 | 139135263 | 1108 | True | 1487.0 | 1487 | 90.901 | 355 | 1473 | 1 | chr1D.!!$R1 | 1118 |
12 | TraesCS6B01G283500 | chr1D | 446540375 | 446541368 | 993 | False | 1358.0 | 1358 | 91.434 | 354 | 1345 | 1 | chr1D.!!$F11 | 991 |
13 | TraesCS6B01G283500 | chr1D | 441744425 | 441745115 | 690 | True | 909.0 | 909 | 90.661 | 354 | 1037 | 1 | chr1D.!!$R5 | 683 |
14 | TraesCS6B01G283500 | chr6D | 325416669 | 325418870 | 2201 | True | 2983.0 | 2983 | 91.434 | 354 | 2522 | 1 | chr6D.!!$R5 | 2168 |
15 | TraesCS6B01G283500 | chr6D | 447880262 | 447882347 | 2085 | True | 2760.0 | 2760 | 90.836 | 355 | 2420 | 1 | chr6D.!!$R7 | 2065 |
16 | TraesCS6B01G283500 | chr6D | 347437986 | 347439908 | 1922 | True | 2732.0 | 2732 | 92.451 | 352 | 2263 | 1 | chr6D.!!$R6 | 1911 |
17 | TraesCS6B01G283500 | chr6D | 421840966 | 421842256 | 1290 | False | 1860.0 | 1860 | 92.901 | 353 | 1627 | 1 | chr6D.!!$F3 | 1274 |
18 | TraesCS6B01G283500 | chr6D | 41923488 | 41924608 | 1120 | True | 1609.0 | 1609 | 92.668 | 354 | 1473 | 1 | chr6D.!!$R1 | 1119 |
19 | TraesCS6B01G283500 | chr2D | 644013309 | 644015512 | 2203 | True | 2907.0 | 2907 | 90.769 | 354 | 2522 | 1 | chr2D.!!$R3 | 2168 |
20 | TraesCS6B01G283500 | chr2D | 500665309 | 500667213 | 1904 | True | 2719.0 | 2719 | 92.499 | 354 | 2263 | 1 | chr2D.!!$R2 | 1909 |
21 | TraesCS6B01G283500 | chr2D | 50138400 | 50139065 | 665 | True | 905.0 | 905 | 91.505 | 355 | 1011 | 1 | chr2D.!!$R1 | 656 |
22 | TraesCS6B01G283500 | chr7D | 85019321 | 85021227 | 1906 | False | 2846.0 | 2846 | 93.691 | 354 | 2255 | 1 | chr7D.!!$F2 | 1901 |
23 | TraesCS6B01G283500 | chr7D | 56936786 | 56937957 | 1171 | False | 1596.0 | 1596 | 91.297 | 353 | 1533 | 1 | chr7D.!!$F1 | 1180 |
24 | TraesCS6B01G283500 | chr7B | 442357638 | 442359548 | 1910 | False | 2839.0 | 2839 | 93.584 | 355 | 2255 | 1 | chr7B.!!$F1 | 1900 |
25 | TraesCS6B01G283500 | chr7B | 8457464 | 8457989 | 525 | True | 710.0 | 710 | 91.635 | 2016 | 2522 | 1 | chr7B.!!$R2 | 506 |
26 | TraesCS6B01G283500 | chrUn | 105334056 | 105335964 | 1908 | True | 2795.0 | 2795 | 93.184 | 355 | 2258 | 1 | chrUn.!!$R2 | 1903 |
27 | TraesCS6B01G283500 | chrUn | 108802910 | 108803720 | 810 | False | 1064.0 | 1064 | 90.511 | 351 | 1160 | 1 | chrUn.!!$F1 | 809 |
28 | TraesCS6B01G283500 | chr5B | 615399284 | 615401475 | 2191 | True | 2734.0 | 2734 | 89.428 | 356 | 2522 | 1 | chr5B.!!$R3 | 2166 |
29 | TraesCS6B01G283500 | chr5B | 635765310 | 635767314 | 2004 | True | 2551.0 | 2551 | 89.955 | 356 | 2325 | 1 | chr5B.!!$R4 | 1969 |
30 | TraesCS6B01G283500 | chr5B | 128208506 | 128209013 | 507 | True | 632.0 | 632 | 89.060 | 353 | 871 | 1 | chr5B.!!$R2 | 518 |
31 | TraesCS6B01G283500 | chr3D | 580656345 | 580657572 | 1227 | False | 1757.0 | 1757 | 92.581 | 341 | 1567 | 1 | chr3D.!!$F2 | 1226 |
32 | TraesCS6B01G283500 | chr3D | 576575896 | 576579536 | 3640 | True | 1311.5 | 2148 | 93.727 | 353 | 2522 | 2 | chr3D.!!$R3 | 2169 |
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. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
198 | 199 | 0.109964 | GTGTTTGTGCGTGTGTGTGT | 60.11 | 50.0 | 0.0 | 0.0 | 0.0 | 3.72 | F |
200 | 201 | 0.109964 | GTTTGTGCGTGTGTGTGTGT | 60.11 | 50.0 | 0.0 | 0.0 | 0.0 | 3.72 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1259 | 1350 | 1.004745 | ACCTCTGGTTATGGCCAACAG | 59.995 | 52.381 | 10.96 | 16.16 | 38.18 | 3.16 | R |
2090 | 3615 | 1.350684 | TGGCCAGAGCTAACAACATCA | 59.649 | 47.619 | 0.00 | 0.00 | 39.73 | 3.07 | 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.