Multiple sequence alignment - TraesCS3B01G045100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


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 TraesCS3B01G045100 chr3B 100.000 5590 0 0 1 5590 22801692 22807281 0.000000e+00 10323.0
1 TraesCS3B01G045100 chr3B 88.527 1752 188 8 3060 4803 22699337 22701083 0.000000e+00 2109.0
2 TraesCS3B01G045100 chr3B 83.296 1772 257 24 3054 4797 22837088 22838848 0.000000e+00 1596.0
3 TraesCS3B01G045100 chr3B 83.895 1633 231 15 3196 4803 22788339 22789964 0.000000e+00 1530.0
4 TraesCS3B01G045100 chr3B 80.000 1875 311 41 992 2845 22831268 22833099 0.000000e+00 1327.0
5 TraesCS3B01G045100 chr3B 81.754 1266 177 33 921 2156 22784640 22785881 0.000000e+00 1009.0
6 TraesCS3B01G045100 chr3B 96.388 609 22 0 4806 5414 22822533 22823141 0.000000e+00 1003.0
7 TraesCS3B01G045100 chr3B 88.392 827 85 9 2147 2970 22786167 22786985 0.000000e+00 985.0
8 TraesCS3B01G045100 chr3B 92.105 646 47 4 848 1490 22674753 22675397 0.000000e+00 907.0
9 TraesCS3B01G045100 chr3B 79.589 1313 217 28 1562 2868 22675484 22676751 0.000000e+00 893.0
10 TraesCS3B01G045100 chr3B 96.937 457 14 0 4804 5260 811570214 811569758 0.000000e+00 767.0
11 TraesCS3B01G045100 chr3B 92.896 366 22 3 25 387 532668644 532668280 3.840000e-146 529.0
12 TraesCS3B01G045100 chr3B 91.420 338 26 3 5255 5590 810559176 810558840 1.420000e-125 460.0
13 TraesCS3B01G045100 chr3B 86.646 322 41 2 2972 3293 22788045 22788364 6.890000e-94 355.0
14 TraesCS3B01G045100 chr3B 98.864 176 2 0 5415 5590 22815705 22815880 1.170000e-81 315.0
15 TraesCS3B01G045100 chr3B 93.434 198 7 5 5396 5590 547650827 547650633 7.090000e-74 289.0
16 TraesCS3B01G045100 chr3B 73.851 348 82 8 1573 1914 22364129 22364473 4.540000e-26 130.0
17 TraesCS3B01G045100 chr3D 84.992 1779 231 18 3048 4803 15920827 15922592 0.000000e+00 1773.0
18 TraesCS3B01G045100 chr3D 79.662 1952 329 43 941 2867 15916524 15918432 0.000000e+00 1343.0
19 TraesCS3B01G045100 chr3D 79.114 948 164 21 992 1914 15331515 15332453 1.710000e-174 623.0
20 TraesCS3B01G045100 chr3D 90.313 351 28 5 5241 5590 457864266 457864611 6.600000e-124 455.0
21 TraesCS3B01G045100 chr3D 88.643 361 30 6 5237 5590 326586465 326586821 4.000000e-116 429.0
22 TraesCS3B01G045100 chr3D 80.000 100 16 3 2384 2481 15918045 15918142 2.790000e-08 71.3
23 TraesCS3B01G045100 chr3A 83.801 1747 257 16 3065 4798 20720203 20718470 0.000000e+00 1635.0
24 TraesCS3B01G045100 chr3A 79.867 1957 318 46 923 2848 20745973 20744062 0.000000e+00 1362.0
25 TraesCS3B01G045100 chr3A 80.640 1782 303 37 848 2606 20727423 20725661 0.000000e+00 1341.0
26 TraesCS3B01G045100 chr3A 82.157 1289 200 18 1692 2970 20737275 20736007 0.000000e+00 1079.0
27 TraesCS3B01G045100 chr3A 83.579 1151 166 14 3664 4796 20739030 20737885 0.000000e+00 1057.0
28 TraesCS3B01G045100 chr3A 86.425 744 92 8 3070 3810 20735853 20735116 0.000000e+00 806.0
29 TraesCS3B01G045100 chr3A 80.629 986 155 17 3843 4801 20735122 20734146 0.000000e+00 730.0
30 TraesCS3B01G045100 chr3A 83.793 617 90 8 3072 3684 20739821 20739211 1.350000e-160 577.0
31 TraesCS3B01G045100 chr3A 78.326 932 168 23 992 1896 20966280 20965356 6.280000e-159 571.0
32 TraesCS3B01G045100 chr3A 87.316 339 19 4 68 384 13962179 13962515 3.180000e-97 366.0
33 TraesCS3B01G045100 chr3A 69.791 1003 254 42 996 1972 20961212 20960233 1.630000e-25 128.0
34 TraesCS3B01G045100 chr7B 96.718 457 15 0 4804 5260 274230529 274230985 0.000000e+00 761.0
35 TraesCS3B01G045100 chr7B 95.931 467 19 0 4794 5260 13726356 13726822 0.000000e+00 758.0
36 TraesCS3B01G045100 chr7B 92.818 362 22 3 26 384 166985416 166985776 6.420000e-144 521.0
37 TraesCS3B01G045100 chr7B 96.111 180 5 2 5412 5590 608651360 608651182 5.480000e-75 292.0
38 TraesCS3B01G045100 chr2B 96.725 458 14 1 4804 5260 501021955 501022412 0.000000e+00 761.0
39 TraesCS3B01G045100 chr2B 93.094 362 23 2 25 386 739983945 739983586 3.840000e-146 529.0
40 TraesCS3B01G045100 chr5B 96.507 458 15 1 4804 5260 466401598 466402055 0.000000e+00 756.0
41 TraesCS3B01G045100 chr5B 86.246 618 69 12 4804 5413 494255754 494255145 0.000000e+00 656.0
42 TraesCS3B01G045100 chr5B 93.425 365 20 3 25 386 425662512 425662875 6.370000e-149 538.0
43 TraesCS3B01G045100 chr5B 94.801 327 16 1 29 355 528747706 528748031 5.000000e-140 508.0
44 TraesCS3B01G045100 chr5B 92.458 358 21 3 32 386 447006819 447006465 1.800000e-139 507.0
45 TraesCS3B01G045100 chr5B 90.536 317 26 2 71 384 703265919 703265604 3.120000e-112 416.0
46 TraesCS3B01G045100 chr4B 96.499 457 16 0 4804 5260 105647982 105648438 0.000000e+00 756.0
47 TraesCS3B01G045100 chr4B 93.664 363 22 1 25 387 407746985 407746624 4.930000e-150 542.0
48 TraesCS3B01G045100 chr4B 93.113 363 24 1 25 387 473857116 473856755 1.070000e-146 531.0
49 TraesCS3B01G045100 chr4B 80.763 655 73 36 4804 5413 448593073 448592427 3.950000e-126 462.0
50 TraesCS3B01G045100 chr4B 88.482 382 19 12 29 387 52585377 52585756 6.650000e-119 438.0
51 TraesCS3B01G045100 chr4B 86.154 390 24 10 25 386 4780513 4780900 1.460000e-105 394.0
52 TraesCS3B01G045100 chr4B 85.340 382 32 9 25 384 191194889 191195268 1.900000e-99 374.0
53 TraesCS3B01G045100 chr4B 92.903 155 9 2 232 386 602188771 602188923 2.030000e-54 224.0
54 TraesCS3B01G045100 chr4B 92.308 156 10 2 231 386 356956532 356956685 2.620000e-53 220.0
55 TraesCS3B01G045100 chr4B 90.058 171 13 4 220 390 39297205 39297039 9.430000e-53 219.0
56 TraesCS3B01G045100 chr4B 92.763 152 9 2 235 386 559293041 559293190 9.430000e-53 219.0
57 TraesCS3B01G045100 chr4B 100.000 34 0 0 801 834 662158051 662158018 4.680000e-06 63.9
58 TraesCS3B01G045100 chr1B 96.507 458 15 1 4804 5260 371340434 371339977 0.000000e+00 756.0
59 TraesCS3B01G045100 chr1B 92.832 279 18 2 106 384 649321930 649322206 2.430000e-108 403.0
60 TraesCS3B01G045100 chr1B 89.375 320 29 4 68 384 632175838 632176155 1.130000e-106 398.0
61 TraesCS3B01G045100 chr1B 100.000 31 0 0 1 31 51886203 51886173 2.180000e-04 58.4
62 TraesCS3B01G045100 chr6B 95.317 363 16 1 25 387 560194036 560193675 4.860000e-160 575.0
63 TraesCS3B01G045100 chr6B 94.475 362 19 1 29 390 607010937 607010577 1.760000e-154 556.0
64 TraesCS3B01G045100 chr6B 94.429 359 19 1 29 387 134105124 134105481 8.180000e-153 551.0
65 TraesCS3B01G045100 chr6B 92.623 366 23 2 25 387 659953566 659953202 1.780000e-144 523.0
66 TraesCS3B01G045100 chr6B 80.414 628 89 26 4804 5413 50715180 50715791 1.100000e-121 448.0
67 TraesCS3B01G045100 chr6B 97.059 34 0 1 1 33 719918655 719918688 7.820000e-04 56.5
68 TraesCS3B01G045100 chr4A 94.022 368 21 1 25 392 650062958 650062592 1.760000e-154 556.0
69 TraesCS3B01G045100 chr4A 91.837 294 20 2 97 387 705897335 705897627 1.870000e-109 407.0
70 TraesCS3B01G045100 chr4A 84.326 319 38 8 71 386 146725049 146725358 9.100000e-78 302.0
71 TraesCS3B01G045100 chr4A 95.652 46 2 0 799 844 726107129 726107174 2.160000e-09 75.0
72 TraesCS3B01G045100 chr5A 83.360 631 61 29 4804 5409 570982161 570981550 1.370000e-150 544.0
73 TraesCS3B01G045100 chr5A 100.000 30 0 0 1 30 441506395 441506424 7.820000e-04 56.5
74 TraesCS3B01G045100 chr1D 82.104 637 75 22 4804 5413 202997628 202997004 5.000000e-140 508.0
75 TraesCS3B01G045100 chr1D 87.206 383 24 7 25 384 387056128 387055748 4.030000e-111 412.0
76 TraesCS3B01G045100 chr1D 84.685 333 28 7 71 386 425542602 425542276 1.510000e-80 311.0
77 TraesCS3B01G045100 chr1D 86.286 175 21 3 215 389 23386522 23386693 2.660000e-43 187.0
78 TraesCS3B01G045100 chr1D 97.561 41 1 0 800 840 473582701 473582661 2.790000e-08 71.3
79 TraesCS3B01G045100 chr2A 80.599 634 83 28 4804 5413 24830297 24829680 2.370000e-123 453.0
80 TraesCS3B01G045100 chr7D 87.728 383 24 7 25 386 8872870 8872490 5.180000e-115 425.0
81 TraesCS3B01G045100 chr7D 100.000 35 0 0 799 833 635434171 635434137 1.300000e-06 65.8
82 TraesCS3B01G045100 chr6D 87.173 382 25 6 25 384 396006105 396006484 4.030000e-111 412.0
83 TraesCS3B01G045100 chr6D 86.136 339 23 4 71 387 283772390 283772054 1.490000e-90 344.0
84 TraesCS3B01G045100 chr6D 91.558 154 11 2 231 384 428663288 428663439 1.580000e-50 211.0
85 TraesCS3B01G045100 chr4D 87.977 341 31 7 5255 5590 307311390 307311055 1.460000e-105 394.0
86 TraesCS3B01G045100 chr4D 85.263 380 31 10 25 387 457069715 457069344 8.850000e-98 368.0
87 TraesCS3B01G045100 chr4D 84.715 386 31 10 25 384 362723803 362723420 1.480000e-95 361.0
88 TraesCS3B01G045100 chr4D 84.840 376 34 12 26 384 387090969 387091338 1.920000e-94 357.0
89 TraesCS3B01G045100 chr4D 83.158 380 43 11 25 386 19639886 19640262 1.500000e-85 327.0
90 TraesCS3B01G045100 chr4D 82.292 384 42 6 25 384 37524812 37525193 5.440000e-80 309.0
91 TraesCS3B01G045100 chr4D 82.031 384 42 10 25 384 473983693 473983313 9.100000e-78 302.0
92 TraesCS3B01G045100 chr4D 83.008 359 34 8 49 384 16453667 16454021 3.270000e-77 300.0
93 TraesCS3B01G045100 chr4D 91.176 204 11 4 25 221 504284939 504284736 2.570000e-68 270.0
94 TraesCS3B01G045100 chr4D 83.389 301 23 7 25 300 17089605 17089903 2.580000e-63 254.0
95 TraesCS3B01G045100 chr4D 82.353 255 37 7 134 386 58948379 58948627 1.220000e-51 215.0
96 TraesCS3B01G045100 chr4D 90.385 156 13 2 231 386 241952973 241953126 2.640000e-48 204.0
97 TraesCS3B01G045100 chr4D 89.103 156 15 2 231 386 165895886 165896039 5.720000e-45 193.0
98 TraesCS3B01G045100 chr4D 91.852 135 8 2 250 384 437945618 437945749 9.560000e-43 185.0
99 TraesCS3B01G045100 chr4D 87.179 156 18 2 231 386 319108855 319108702 5.760000e-40 176.0
100 TraesCS3B01G045100 chr4D 100.000 30 0 0 1 30 97505646 97505617 7.820000e-04 56.5
101 TraesCS3B01G045100 chr4D 100.000 30 0 0 1 30 379256119 379256148 7.820000e-04 56.5
102 TraesCS3B01G045100 chr4D 100.000 30 0 0 1 30 383894309 383894338 7.820000e-04 56.5
103 TraesCS3B01G045100 chr4D 100.000 30 0 0 1 30 387090700 387090729 7.820000e-04 56.5
104 TraesCS3B01G045100 chr4D 100.000 29 0 0 1 29 388820082 388820110 3.000000e-03 54.7
105 TraesCS3B01G045100 chr5D 85.829 374 34 9 30 386 331545968 331545597 4.090000e-101 379.0
106 TraesCS3B01G045100 chr5D 85.593 354 24 8 54 386 331539376 331539029 4.150000e-91 346.0
107 TraesCS3B01G045100 chr5D 85.496 131 16 3 711 840 468190054 468190182 3.510000e-27 134.0
108 TraesCS3B01G045100 chr5D 97.143 35 1 0 799 833 487453874 487453840 6.050000e-05 60.2
109 TraesCS3B01G045100 chr1A 85.233 386 32 8 25 387 568768481 568768098 1.900000e-99 374.0
110 TraesCS3B01G045100 chr1A 86.228 334 22 5 73 384 513206235 513206566 1.930000e-89 340.0
111 TraesCS3B01G045100 chr1A 86.103 331 21 7 25 332 57396190 57396518 3.230000e-87 333.0
112 TraesCS3B01G045100 chr1A 85.503 338 25 5 72 387 491117010 491116675 1.160000e-86 331.0
113 TraesCS3B01G045100 chr1A 82.461 382 42 8 25 384 559033102 559032724 1.510000e-80 311.0
114 TraesCS3B01G045100 chr1A 82.199 382 41 8 25 384 14636374 14635998 2.530000e-78 303.0
115 TraesCS3B01G045100 chr1A 81.201 383 43 12 25 390 486384431 486384801 1.190000e-71 281.0
116 TraesCS3B01G045100 chr1A 92.040 201 12 2 25 221 576643288 576643088 4.260000e-71 279.0
117 TraesCS3B01G045100 chr1A 92.000 200 13 2 25 221 15469832 15470031 1.530000e-70 278.0
118 TraesCS3B01G045100 chr1A 89.677 155 12 4 231 384 515579399 515579248 1.590000e-45 195.0
119 TraesCS3B01G045100 chr1A 89.677 155 12 4 231 384 569883963 569884114 1.590000e-45 195.0
120 TraesCS3B01G045100 chr1A 89.474 152 14 2 235 386 473961408 473961259 2.060000e-44 191.0
121 TraesCS3B01G045100 chr1A 100.000 30 0 0 1 30 15469563 15469592 7.820000e-04 56.5
122 TraesCS3B01G045100 chr1A 100.000 30 0 0 1 30 16420308 16420279 7.820000e-04 56.5
123 TraesCS3B01G045100 chr1A 100.000 30 0 0 1 30 28763967 28763938 7.820000e-04 56.5
124 TraesCS3B01G045100 chr1A 100.000 30 0 0 1 30 48595581 48595552 7.820000e-04 56.5
125 TraesCS3B01G045100 chr6A 85.185 378 31 7 29 384 594770686 594770312 1.140000e-96 364.0
126 TraesCS3B01G045100 chr6A 84.865 370 33 7 31 383 564672936 564672573 8.910000e-93 351.0
127 TraesCS3B01G045100 chr6A 83.246 382 40 6 25 384 57893370 57892991 4.170000e-86 329.0
128 TraesCS3B01G045100 chr6A 84.242 330 33 5 71 386 576197299 576196975 2.530000e-78 303.0
129 TraesCS3B01G045100 chr6A 91.026 156 12 2 231 386 436405694 436405847 5.670000e-50 209.0
130 TraesCS3B01G045100 chr6A 90.385 156 13 2 231 386 443344568 443344415 2.640000e-48 204.0
131 TraesCS3B01G045100 chrUn 83.436 326 40 11 71 384 1909374 1909051 1.970000e-74 291.0
132 TraesCS3B01G045100 chrUn 81.383 376 44 11 31 387 321526260 321525892 3.300000e-72 283.0
133 TraesCS3B01G045100 chrUn 79.942 344 42 9 64 384 105230735 105230396 1.570000e-55 228.0
134 TraesCS3B01G045100 chrUn 77.807 383 45 17 25 386 1796666 1797029 3.420000e-47 200.0
135 TraesCS3B01G045100 chrUn 77.807 383 45 17 25 386 245571097 245571460 3.420000e-47 200.0
136 TraesCS3B01G045100 chrUn 87.261 157 18 2 231 387 332225062 332224908 1.600000e-40 178.0
137 TraesCS3B01G045100 chrUn 87.261 157 18 2 231 387 332227876 332227722 1.600000e-40 178.0
138 TraesCS3B01G045100 chrUn 86.310 168 12 5 220 387 335191997 335191841 7.450000e-39 172.0
139 TraesCS3B01G045100 chrUn 86.164 159 19 3 226 384 17895624 17895779 9.630000e-38 169.0
140 TraesCS3B01G045100 chrUn 84.416 154 22 2 231 384 5440866 5441017 3.490000e-32 150.0
141 TraesCS3B01G045100 chrUn 88.235 68 4 4 25 90 105230717 105230652 1.670000e-10 78.7
142 TraesCS3B01G045100 chrUn 97.222 36 1 0 31 66 1909395 1909360 1.680000e-05 62.1
143 TraesCS3B01G045100 chrUn 97.143 35 1 0 799 833 165283289 165283323 6.050000e-05 60.2
144 TraesCS3B01G045100 chrUn 97.143 35 1 0 799 833 165314480 165314514 6.050000e-05 60.2
145 TraesCS3B01G045100 chrUn 97.143 35 1 0 799 833 312829874 312829908 6.050000e-05 60.2
146 TraesCS3B01G045100 chrUn 97.143 35 1 0 799 833 330053982 330053948 6.050000e-05 60.2
147 TraesCS3B01G045100 chrUn 97.143 35 1 0 799 833 350835692 350835726 6.050000e-05 60.2
148 TraesCS3B01G045100 chrUn 100.000 30 0 0 1 30 105230986 105230957 7.820000e-04 56.5
149 TraesCS3B01G045100 chrUn 96.875 32 1 0 799 830 289620961 289620930 3.000000e-03 54.7
150 TraesCS3B01G045100 chrUn 100.000 29 0 0 799 827 299514317 299514345 3.000000e-03 54.7
151 TraesCS3B01G045100 chr7A 82.759 145 24 1 711 854 150119321 150119465 1.630000e-25 128.0
152 TraesCS3B01G045100 chr7A 100.000 31 0 0 1 31 89648492 89648522 2.180000e-04 58.4
153 TraesCS3B01G045100 chr7A 100.000 31 0 0 1 31 162397203 162397233 2.180000e-04 58.4
154 TraesCS3B01G045100 chr7A 100.000 31 0 0 1 31 657885117 657885087 2.180000e-04 58.4


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 TraesCS3B01G045100 chr3B 22801692 22807281 5589 False 10323.000000 10323 100.000000 1 5590 1 chr3B.!!$F3 5589
1 TraesCS3B01G045100 chr3B 22699337 22701083 1746 False 2109.000000 2109 88.527000 3060 4803 1 chr3B.!!$F2 1743
2 TraesCS3B01G045100 chr3B 22831268 22838848 7580 False 1461.500000 1596 81.648000 992 4797 2 chr3B.!!$F8 3805
3 TraesCS3B01G045100 chr3B 22822533 22823141 608 False 1003.000000 1003 96.388000 4806 5414 1 chr3B.!!$F5 608
4 TraesCS3B01G045100 chr3B 22784640 22789964 5324 False 969.750000 1530 85.171750 921 4803 4 chr3B.!!$F7 3882
5 TraesCS3B01G045100 chr3B 22674753 22676751 1998 False 900.000000 907 85.847000 848 2868 2 chr3B.!!$F6 2020
6 TraesCS3B01G045100 chr3D 15916524 15922592 6068 False 1062.433333 1773 81.551333 941 4803 3 chr3D.!!$F4 3862
7 TraesCS3B01G045100 chr3D 15331515 15332453 938 False 623.000000 623 79.114000 992 1914 1 chr3D.!!$F1 922
8 TraesCS3B01G045100 chr3A 20718470 20720203 1733 True 1635.000000 1635 83.801000 3065 4798 1 chr3A.!!$R1 1733
9 TraesCS3B01G045100 chr3A 20744062 20745973 1911 True 1362.000000 1362 79.867000 923 2848 1 chr3A.!!$R3 1925
10 TraesCS3B01G045100 chr3A 20725661 20727423 1762 True 1341.000000 1341 80.640000 848 2606 1 chr3A.!!$R2 1758
11 TraesCS3B01G045100 chr3A 20734146 20739821 5675 True 849.800000 1079 83.316600 1692 4801 5 chr3A.!!$R6 3109
12 TraesCS3B01G045100 chr3A 20965356 20966280 924 True 571.000000 571 78.326000 992 1896 1 chr3A.!!$R5 904
13 TraesCS3B01G045100 chr5B 494255145 494255754 609 True 656.000000 656 86.246000 4804 5413 1 chr5B.!!$R2 609
14 TraesCS3B01G045100 chr4B 448592427 448593073 646 True 462.000000 462 80.763000 4804 5413 1 chr4B.!!$R3 609
15 TraesCS3B01G045100 chr6B 50715180 50715791 611 False 448.000000 448 80.414000 4804 5413 1 chr6B.!!$F1 609
16 TraesCS3B01G045100 chr5A 570981550 570982161 611 True 544.000000 544 83.360000 4804 5409 1 chr5A.!!$R1 605
17 TraesCS3B01G045100 chr1D 202997004 202997628 624 True 508.000000 508 82.104000 4804 5413 1 chr1D.!!$R1 609
18 TraesCS3B01G045100 chr2A 24829680 24830297 617 True 453.000000 453 80.599000 4804 5413 1 chr2A.!!$R1 609
19 TraesCS3B01G045100 chr4D 387090700 387091338 638 False 206.750000 357 92.420000 1 384 2 chr4D.!!$F12 383

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
481 742 0.031616 CAGGAGCCCTAGGAGGTTCT 60.032 60.000 11.48 7.4 37.31 3.01 F
529 790 0.032952 ACGAAGTGCACCGAAAGCTA 59.967 50.000 20.13 0.0 42.51 3.32 F
1581 1909 0.036010 ACTTTCAGATCCTGGTGGCG 60.036 55.000 0.00 0.0 31.51 5.69 F
1953 2293 0.322277 CAGGACATGTGCTCAGCCTT 60.322 55.000 17.98 0.0 0.00 4.35 F
2303 2938 0.520404 CTGTCAATCACTGGCTGCAC 59.480 55.000 0.50 0.0 0.00 4.57 F
2415 3050 1.080569 CGCAATTGGCAACCTGACC 60.081 57.895 13.74 0.0 45.17 4.02 F
4127 14495 0.999712 CATGGTTGGGGGTACTTCCT 59.000 55.000 0.00 0.0 36.25 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2278 0.111061 TGGAAAGGCTGAGCACATGT 59.889 50.000 6.82 0.00 0.00 3.21 R
2084 2424 0.907486 TGAGGATTGAGGCTCCACAG 59.093 55.000 12.86 0.00 35.08 3.66 R
3068 13299 0.890996 CTGGAAGTTCCCCTGCACAC 60.891 60.000 19.42 0.00 35.03 3.82 R
3552 13920 1.267121 AGGCTACTGTTCCATGTCGT 58.733 50.000 0.00 0.00 0.00 4.34 R
3672 14040 1.283321 AGGAATCTGCCCCTGAAGTTC 59.717 52.381 0.00 0.00 0.00 3.01 R
4286 14654 1.337071 GCCATCATTGATGTCAGCCTG 59.663 52.381 21.95 8.64 38.28 4.85 R
5470 15945 0.107456 CCCTCTCGTTGCTATGCCAT 59.893 55.000 0.00 0.00 0.00 4.40 R

All possible primers

Listed 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.

Download all possible primers: (Forward) (Reverse)


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.