Multiple sequence alignment - TraesCS1D01G236800

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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 TraesCS1D01G236800 chr1D 100.000 5456 0 0 1 5456 326145728 326151183 0.000000e+00 10076
1 TraesCS1D01G236800 chr1D 100.000 3336 0 0 6062 9397 326151789 326155124 0.000000e+00 6161
2 TraesCS1D01G236800 chr1D 96.208 712 26 1 4728 5439 108259937 108259227 0.000000e+00 1164
3 TraesCS1D01G236800 chr1D 96.067 712 27 1 4728 5439 31326532 31325822 0.000000e+00 1158
4 TraesCS1D01G236800 chr1D 95.385 715 32 1 4725 5439 112169780 112170493 0.000000e+00 1136
5 TraesCS1D01G236800 chr1D 95.506 712 31 1 4725 5436 476250409 476251119 0.000000e+00 1136
6 TraesCS1D01G236800 chr1D 95.245 715 33 1 4725 5439 314435724 314436437 0.000000e+00 1131
7 TraesCS1D01G236800 chr1D 95.245 715 33 1 4725 5439 357320918 357321631 0.000000e+00 1131
8 TraesCS1D01G236800 chr1D 94.825 715 35 2 4725 5439 108369027 108369739 0.000000e+00 1114
9 TraesCS1D01G236800 chr1D 94.406 715 39 1 4725 5439 314434828 314435541 0.000000e+00 1098
10 TraesCS1D01G236800 chr1D 90.752 638 22 2 6062 6675 108258551 108257927 0.000000e+00 817
11 TraesCS1D01G236800 chr1D 91.122 597 26 2 6062 6631 143600390 143600986 0.000000e+00 784
12 TraesCS1D01G236800 chr1D 90.620 597 29 4 6062 6631 476251752 476252348 0.000000e+00 767
13 TraesCS1D01G236800 chr1D 88.333 600 37 10 6062 6631 31325266 31324670 0.000000e+00 689
14 TraesCS1D01G236800 chr1D 84.167 600 50 18 6062 6631 108370495 108371079 2.990000e-149 540
15 TraesCS1D01G236800 chr1D 90.323 372 33 1 6272 6640 412084362 412083991 1.420000e-132 484
16 TraesCS1D01G236800 chr1D 96.377 276 7 1 6359 6631 326147923 326148198 1.440000e-122 451
17 TraesCS1D01G236800 chr1D 92.027 301 19 3 6360 6656 240130794 240131093 1.460000e-112 418
18 TraesCS1D01G236800 chr1D 82.579 442 65 11 6072 6507 314436592 314437027 6.890000e-101 379
19 TraesCS1D01G236800 chr1D 81.818 451 70 11 6064 6507 357321894 357322339 1.490000e-97 368
20 TraesCS1D01G236800 chr1D 96.939 196 6 0 6062 6257 112171113 112171308 7.030000e-86 329
21 TraesCS1D01G236800 chr1D 80.556 324 48 12 8719 9031 416727978 416728297 1.580000e-57 235
22 TraesCS1D01G236800 chr1B 90.763 2176 110 31 6772 8895 439431468 439433604 0.000000e+00 2820
23 TraesCS1D01G236800 chr1B 98.109 1322 23 2 835 2155 439429985 439431305 0.000000e+00 2302
24 TraesCS1D01G236800 chr1B 96.463 820 24 3 2 821 439429189 439430003 0.000000e+00 1349
25 TraesCS1D01G236800 chr1B 85.170 499 44 13 8900 9396 439433651 439434121 1.420000e-132 484
26 TraesCS1D01G236800 chr2D 95.775 1728 55 13 3013 4727 77584728 77583006 0.000000e+00 2771
27 TraesCS1D01G236800 chr2D 95.771 1726 57 13 3013 4728 77577952 77576233 0.000000e+00 2769
28 TraesCS1D01G236800 chr2D 96.446 816 29 0 2197 3012 209031885 209031070 0.000000e+00 1347
29 TraesCS1D01G236800 chr2D 96.220 820 27 2 2194 3012 392699960 392699144 0.000000e+00 1339
30 TraesCS1D01G236800 chr2D 96.914 713 20 2 4728 5439 392699148 392698437 0.000000e+00 1194
31 TraesCS1D01G236800 chr2D 96.348 712 25 1 4728 5439 293680816 293680106 0.000000e+00 1170
32 TraesCS1D01G236800 chr2D 92.945 567 27 1 6065 6631 392698015 392697462 0.000000e+00 813
33 TraesCS1D01G236800 chr7D 95.244 1724 64 14 3013 4727 471224119 471225833 0.000000e+00 2713
34 TraesCS1D01G236800 chr7D 96.569 816 28 0 2197 3012 310992898 310993713 0.000000e+00 1352
35 TraesCS1D01G236800 chr7D 96.446 816 29 0 2197 3012 451194356 451195171 0.000000e+00 1347
36 TraesCS1D01G236800 chr7D 96.494 713 24 1 4725 5437 110570552 110569841 0.000000e+00 1177
37 TraesCS1D01G236800 chr7D 83.993 556 58 6 8718 9244 107677411 107677964 1.090000e-138 505
38 TraesCS1D01G236800 chr7D 80.100 402 42 28 8855 9244 401784027 401784402 2.010000e-66 265
39 TraesCS1D01G236800 chr1A 94.370 1723 81 14 3013 4727 115886182 115884468 0.000000e+00 2630
40 TraesCS1D01G236800 chr1A 92.216 1850 72 21 6677 8488 415583412 415585227 0.000000e+00 2553
41 TraesCS1D01G236800 chr1A 95.715 1377 43 2 835 2196 415582040 415583415 0.000000e+00 2202
42 TraesCS1D01G236800 chr1A 96.256 828 28 3 2196 3020 423920731 423919904 0.000000e+00 1354
43 TraesCS1D01G236800 chr1A 95.775 710 29 1 4728 5437 423919919 423919211 0.000000e+00 1144
44 TraesCS1D01G236800 chr1A 92.695 616 28 7 1 614 415581154 415581754 0.000000e+00 872
45 TraesCS1D01G236800 chr1A 92.630 597 17 2 6062 6631 423918797 423918201 0.000000e+00 833
46 TraesCS1D01G236800 chr1A 84.783 460 51 16 6062 6507 63753484 63753938 2.410000e-120 444
47 TraesCS1D01G236800 chr1A 89.286 196 20 1 626 821 415581864 415582058 2.620000e-60 244
48 TraesCS1D01G236800 chr1A 90.968 155 10 4 8570 8723 415585242 415585393 1.240000e-48 206
49 TraesCS1D01G236800 chr1A 92.391 92 7 0 8929 9020 116695443 116695534 2.130000e-26 132
50 TraesCS1D01G236800 chr7A 93.060 1729 98 17 3013 4727 79832457 79834177 0.000000e+00 2508
51 TraesCS1D01G236800 chr7A 97.052 814 22 2 2199 3012 269961192 269962003 0.000000e+00 1369
52 TraesCS1D01G236800 chr7A 93.333 570 23 2 6062 6631 245980241 245979687 0.000000e+00 828
53 TraesCS1D01G236800 chr7A 92.722 316 22 1 6062 6376 287474763 287474448 1.110000e-123 455
54 TraesCS1D01G236800 chr2A 92.845 1733 97 20 3010 4727 240491911 240493631 0.000000e+00 2488
55 TraesCS1D01G236800 chr2A 95.439 570 21 4 6065 6631 503463358 503462791 0.000000e+00 904
56 TraesCS1D01G236800 chr3A 92.832 1730 99 19 3010 4724 672896804 672898523 0.000000e+00 2484
57 TraesCS1D01G236800 chr3A 92.552 1732 105 17 3013 4727 551159573 551157849 0.000000e+00 2462
58 TraesCS1D01G236800 chr3A 96.446 816 27 2 2197 3012 746139829 746139016 0.000000e+00 1345
59 TraesCS1D01G236800 chr3A 94.755 572 27 1 6063 6631 675347378 675347949 0.000000e+00 887
60 TraesCS1D01G236800 chr3A 91.108 641 29 7 6062 6675 594024873 594024234 0.000000e+00 843
61 TraesCS1D01G236800 chr3A 88.542 576 51 13 6062 6631 143655511 143654945 0.000000e+00 684
62 TraesCS1D01G236800 chr3A 83.363 565 56 19 8722 9254 723562902 723562344 1.100000e-133 488
63 TraesCS1D01G236800 chr3A 86.466 399 45 5 8862 9254 159354821 159355216 6.740000e-116 429
64 TraesCS1D01G236800 chr3A 82.720 353 49 10 8911 9254 131407394 131407743 4.260000e-78 303
65 TraesCS1D01G236800 chr6A 92.366 1729 105 19 3013 4727 438370599 438372314 0.000000e+00 2436
66 TraesCS1D01G236800 chr6A 96.201 816 31 0 2197 3012 520841620 520840805 0.000000e+00 1336
67 TraesCS1D01G236800 chr6A 96.197 710 26 1 4728 5437 277277080 277276372 0.000000e+00 1160
68 TraesCS1D01G236800 chr6A 95.775 710 28 2 4728 5437 100317557 100316850 0.000000e+00 1144
69 TraesCS1D01G236800 chr6A 91.264 641 29 6 6062 6675 190606500 190607140 0.000000e+00 848
70 TraesCS1D01G236800 chr6A 95.556 450 18 2 6227 6675 309873428 309872980 0.000000e+00 719
71 TraesCS1D01G236800 chr6A 81.503 346 46 13 8911 9254 577884104 577884433 1.560000e-67 268
72 TraesCS1D01G236800 chr5D 96.083 817 31 1 2197 3012 50848648 50847832 0.000000e+00 1330
73 TraesCS1D01G236800 chr5D 89.124 662 24 7 6063 6676 50837870 50837209 0.000000e+00 780
74 TraesCS1D01G236800 chr5D 89.804 510 47 3 6062 6567 552392068 552391560 0.000000e+00 649
75 TraesCS1D01G236800 chr5D 80.115 347 45 16 8911 9254 283103629 283103304 4.390000e-58 237
76 TraesCS1D01G236800 chr5D 81.702 235 32 9 9023 9254 437449435 437449661 1.610000e-42 185
77 TraesCS1D01G236800 chr5D 80.000 270 35 16 8999 9254 556237483 556237747 2.080000e-41 182
78 TraesCS1D01G236800 chr3D 97.394 729 18 1 4728 5456 574777713 574776986 0.000000e+00 1240
79 TraesCS1D01G236800 chr3D 96.159 729 27 1 4728 5456 648547 647820 0.000000e+00 1190
80 TraesCS1D01G236800 chr3D 96.084 715 27 1 4725 5439 134500082 134500795 0.000000e+00 1164
81 TraesCS1D01G236800 chr3D 92.248 516 13 2 6143 6631 574776343 574775828 0.000000e+00 706
82 TraesCS1D01G236800 chr3D 87.500 400 41 4 8861 9254 141185180 141185576 4.000000e-123 453
83 TraesCS1D01G236800 chr4D 96.708 729 23 1 4728 5456 301752286 301751559 0.000000e+00 1212
84 TraesCS1D01G236800 chr4D 95.915 710 28 1 4728 5437 479965913 479965205 0.000000e+00 1149
85 TraesCS1D01G236800 chr4D 95.365 712 31 2 4728 5439 432423724 432423015 0.000000e+00 1131
86 TraesCS1D01G236800 chr4D 92.437 595 18 2 6064 6631 15596891 15597485 0.000000e+00 824
87 TraesCS1D01G236800 chr4D 91.584 606 24 2 6062 6640 57481228 57480623 0.000000e+00 811
88 TraesCS1D01G236800 chr4D 91.560 391 30 1 6269 6656 319267128 319267518 3.860000e-148 536
89 TraesCS1D01G236800 chr4D 88.943 407 36 7 6275 6675 101668695 101668292 2.360000e-135 494
90 TraesCS1D01G236800 chr4D 85.174 344 45 5 6072 6411 473760710 473761051 1.940000e-91 348
91 TraesCS1D01G236800 chr4D 78.589 397 64 17 8856 9240 497873992 497874379 9.430000e-60 243
92 TraesCS1D01G236800 chr4D 81.017 295 37 14 8962 9254 461466598 461466875 5.710000e-52 217
93 TraesCS1D01G236800 chr6D 94.825 715 36 1 4725 5439 11349877 11350590 0.000000e+00 1114
94 TraesCS1D01G236800 chr6D 94.233 711 40 1 4728 5438 178002507 178001798 0.000000e+00 1085
95 TraesCS1D01G236800 chr6D 93.427 715 45 2 4725 5439 375031699 375032411 0.000000e+00 1059
96 TraesCS1D01G236800 chr6D 92.426 713 33 9 4725 5437 21990828 21991519 0.000000e+00 998
97 TraesCS1D01G236800 chr6D 93.980 598 16 3 4834 5431 113461354 113461931 0.000000e+00 887
98 TraesCS1D01G236800 chr6D 92.230 592 45 1 4848 5439 424698175 424698765 0.000000e+00 837
99 TraesCS1D01G236800 chr6D 93.988 499 30 0 4725 5223 20197367 20197865 0.000000e+00 756
100 TraesCS1D01G236800 chr6D 88.552 594 31 2 6062 6631 178001107 178000527 0.000000e+00 686
101 TraesCS1D01G236800 chr6D 84.218 697 101 9 4725 5417 305356290 305356981 0.000000e+00 669
102 TraesCS1D01G236800 chr6D 83.764 696 105 8 4725 5417 262997171 262997861 0.000000e+00 652
103 TraesCS1D01G236800 chr6D 83.718 694 104 9 4728 5417 159347637 159346949 0.000000e+00 647
104 TraesCS1D01G236800 chr6D 96.875 320 7 1 6360 6676 76002881 76002562 5.000000e-147 532
105 TraesCS1D01G236800 chr6D 89.904 416 17 2 6063 6453 113462172 113462587 6.510000e-141 512
106 TraesCS1D01G236800 chr6D 95.775 284 9 1 6360 6640 20183897 20184180 1.110000e-123 455
107 TraesCS1D01G236800 chr6D 84.667 450 59 10 6062 6507 331700007 331700450 3.110000e-119 440
108 TraesCS1D01G236800 chr6D 82.046 518 78 12 8745 9254 277253661 277254171 2.430000e-115 427
109 TraesCS1D01G236800 chr6D 94.604 278 12 1 6357 6631 457729550 457729273 2.430000e-115 427
110 TraesCS1D01G236800 chr6D 89.441 322 28 4 6314 6631 9764873 9764554 1.470000e-107 401
111 TraesCS1D01G236800 chr6D 89.623 318 24 6 6360 6673 98256840 98256528 6.840000e-106 396
112 TraesCS1D01G236800 chr6D 91.034 290 22 2 6355 6640 322583003 322583292 1.140000e-103 388
113 TraesCS1D01G236800 chr6D 91.273 275 21 1 6360 6631 138815345 138815071 1.150000e-98 372
114 TraesCS1D01G236800 chr6D 97.990 199 4 0 6478 6676 113460796 113460994 6.990000e-91 346
115 TraesCS1D01G236800 chr6D 80.842 475 56 16 6062 6507 91840371 91840839 3.250000e-89 340
116 TraesCS1D01G236800 chr6D 90.417 240 20 1 6395 6631 9767270 9767031 7.080000e-81 313
117 TraesCS1D01G236800 chr6D 85.000 280 18 3 6062 6317 98255097 98254818 7.240000e-66 263
118 TraesCS1D01G236800 chr6D 81.556 347 39 16 8911 9254 431264291 431264615 7.240000e-66 263
119 TraesCS1D01G236800 chr5A 92.020 614 32 5 6062 6675 126271225 126271821 0.000000e+00 846
120 TraesCS1D01G236800 chr5A 95.625 320 13 1 6062 6381 484442263 484441945 6.510000e-141 512
121 TraesCS1D01G236800 chr5A 92.181 243 17 2 10 251 478834159 478833918 9.040000e-90 342
122 TraesCS1D01G236800 chr5A 83.976 337 44 5 8911 9239 268586624 268586290 1.970000e-81 315
123 TraesCS1D01G236800 chr5A 82.596 339 44 11 8912 9242 121421172 121421503 1.540000e-72 285
124 TraesCS1D01G236800 chrUn 94.653 505 24 1 6130 6631 32961258 32960754 0.000000e+00 780
125 TraesCS1D01G236800 chrUn 84.753 669 73 6 4768 5436 458839145 458838506 2.210000e-180 643
126 TraesCS1D01G236800 chrUn 82.081 692 107 11 4730 5420 39709953 39709278 8.180000e-160 575
127 TraesCS1D01G236800 chrUn 87.789 475 56 2 4728 5201 344843440 344842967 1.070000e-153 555
128 TraesCS1D01G236800 chrUn 82.099 648 106 9 4728 5370 78995488 78994846 6.420000e-151 545
129 TraesCS1D01G236800 chrUn 86.842 456 58 2 4725 5179 26909685 26910139 8.420000e-140 508
130 TraesCS1D01G236800 chrUn 86.184 456 61 2 4725 5179 60487452 60487906 8.480000e-135 492
131 TraesCS1D01G236800 chrUn 88.564 376 31 2 6268 6640 26910842 26911208 6.690000e-121 446
132 TraesCS1D01G236800 chrUn 83.800 500 48 10 8761 9229 333409811 333410308 2.410000e-120 444
133 TraesCS1D01G236800 chrUn 80.220 546 68 22 8718 9254 126718529 126719043 3.200000e-99 374
134 TraesCS1D01G236800 chrUn 91.135 282 9 1 6359 6640 26908900 26909165 1.490000e-97 368
135 TraesCS1D01G236800 chrUn 82.597 362 51 10 6323 6677 60489025 60489381 9.160000e-80 309
136 TraesCS1D01G236800 chrUn 87.405 262 26 7 6400 6656 434355734 434355475 2.570000e-75 294
137 TraesCS1D01G236800 chrUn 82.440 336 48 9 6347 6676 60486645 60486975 5.550000e-72 283
138 TraesCS1D01G236800 chrUn 79.302 430 59 20 8848 9254 323779897 323780319 3.340000e-69 274
139 TraesCS1D01G236800 chrUn 82.019 317 37 16 6326 6631 39708725 39708418 1.570000e-62 252
140 TraesCS1D01G236800 chrUn 84.583 240 23 11 6400 6631 39710722 39710489 9.490000e-55 226
141 TraesCS1D01G236800 chrUn 96.552 87 1 2 6596 6680 32960763 32960677 9.840000e-30 143
142 TraesCS1D01G236800 chrUn 98.750 80 0 1 6596 6675 39708427 39708349 3.540000e-29 141
143 TraesCS1D01G236800 chrUn 97.531 81 1 1 6596 6676 39710498 39710419 4.580000e-28 137
144 TraesCS1D01G236800 chr3B 86.264 546 66 5 8718 9256 781433337 781432794 1.360000e-162 584
145 TraesCS1D01G236800 chr6B 86.245 538 64 5 8720 9249 17069396 17069931 8.180000e-160 575
146 TraesCS1D01G236800 chr6B 85.165 546 71 6 8718 9254 648100868 648100324 1.380000e-152 551
147 TraesCS1D01G236800 chr6B 85.549 173 22 3 8720 8890 216359004 216358833 2.700000e-40 178
148 TraesCS1D01G236800 chr2B 83.700 546 76 8 8718 9254 627945583 627945042 3.920000e-138 503
149 TraesCS1D01G236800 chr2B 83.768 499 50 8 8761 9229 530792693 530793190 2.410000e-120 444
150 TraesCS1D01G236800 chr2B 83.800 500 48 10 8761 9229 530838586 530839083 2.410000e-120 444
151 TraesCS1D01G236800 chr4B 82.149 549 64 12 8717 9254 98742429 98741904 3.110000e-119 440
152 TraesCS1D01G236800 chr4B 80.058 346 49 13 8912 9254 623985400 623985072 1.220000e-58 239
153 TraesCS1D01G236800 chr4B 76.739 417 52 21 8850 9254 460159439 460159056 3.460000e-44 191
154 TraesCS1D01G236800 chr4A 92.490 253 17 1 1 251 38728566 38728818 2.490000e-95 361
155 TraesCS1D01G236800 chr5B 80.882 340 55 5 8911 9242 704904862 704905199 9.360000e-65 259
156 TraesCS1D01G236800 chr7B 81.102 254 38 6 9001 9244 730055844 730055591 2.680000e-45 195


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 TraesCS1D01G236800 chr1D 326145728 326155124 9396 False 5562.666667 10076 98.792333 1 9397 3 chr1D.!!$F7 9396
1 TraesCS1D01G236800 chr1D 108257927 108259937 2010 True 990.500000 1164 93.480000 4728 6675 2 chr1D.!!$R3 1947
2 TraesCS1D01G236800 chr1D 476250409 476252348 1939 False 951.500000 1136 93.063000 4725 6631 2 chr1D.!!$F9 1906
3 TraesCS1D01G236800 chr1D 31324670 31326532 1862 True 923.500000 1158 92.200000 4728 6631 2 chr1D.!!$R2 1903
4 TraesCS1D01G236800 chr1D 314434828 314437027 2199 False 869.333333 1131 90.743333 4725 6507 3 chr1D.!!$F6 1782
5 TraesCS1D01G236800 chr1D 108369027 108371079 2052 False 827.000000 1114 89.496000 4725 6631 2 chr1D.!!$F4 1906
6 TraesCS1D01G236800 chr1D 143600390 143600986 596 False 784.000000 784 91.122000 6062 6631 1 chr1D.!!$F1 569
7 TraesCS1D01G236800 chr1D 357320918 357322339 1421 False 749.500000 1131 88.531500 4725 6507 2 chr1D.!!$F8 1782
8 TraesCS1D01G236800 chr1D 112169780 112171308 1528 False 732.500000 1136 96.162000 4725 6257 2 chr1D.!!$F5 1532
9 TraesCS1D01G236800 chr1B 439429189 439434121 4932 False 1738.750000 2820 92.626250 2 9396 4 chr1B.!!$F1 9394
10 TraesCS1D01G236800 chr2D 77583006 77584728 1722 True 2771.000000 2771 95.775000 3013 4727 1 chr2D.!!$R2 1714
11 TraesCS1D01G236800 chr2D 77576233 77577952 1719 True 2769.000000 2769 95.771000 3013 4728 1 chr2D.!!$R1 1715
12 TraesCS1D01G236800 chr2D 209031070 209031885 815 True 1347.000000 1347 96.446000 2197 3012 1 chr2D.!!$R3 815
13 TraesCS1D01G236800 chr2D 293680106 293680816 710 True 1170.000000 1170 96.348000 4728 5439 1 chr2D.!!$R4 711
14 TraesCS1D01G236800 chr2D 392697462 392699960 2498 True 1115.333333 1339 95.359667 2194 6631 3 chr2D.!!$R5 4437
15 TraesCS1D01G236800 chr7D 471224119 471225833 1714 False 2713.000000 2713 95.244000 3013 4727 1 chr7D.!!$F5 1714
16 TraesCS1D01G236800 chr7D 310992898 310993713 815 False 1352.000000 1352 96.569000 2197 3012 1 chr7D.!!$F2 815
17 TraesCS1D01G236800 chr7D 451194356 451195171 815 False 1347.000000 1347 96.446000 2197 3012 1 chr7D.!!$F4 815
18 TraesCS1D01G236800 chr7D 110569841 110570552 711 True 1177.000000 1177 96.494000 4725 5437 1 chr7D.!!$R1 712
19 TraesCS1D01G236800 chr7D 107677411 107677964 553 False 505.000000 505 83.993000 8718 9244 1 chr7D.!!$F1 526
20 TraesCS1D01G236800 chr1A 115884468 115886182 1714 True 2630.000000 2630 94.370000 3013 4727 1 chr1A.!!$R1 1714
21 TraesCS1D01G236800 chr1A 415581154 415585393 4239 False 1215.400000 2553 92.176000 1 8723 5 chr1A.!!$F3 8722
22 TraesCS1D01G236800 chr1A 423918201 423920731 2530 True 1110.333333 1354 94.887000 2196 6631 3 chr1A.!!$R2 4435
23 TraesCS1D01G236800 chr7A 79832457 79834177 1720 False 2508.000000 2508 93.060000 3013 4727 1 chr7A.!!$F1 1714
24 TraesCS1D01G236800 chr7A 269961192 269962003 811 False 1369.000000 1369 97.052000 2199 3012 1 chr7A.!!$F2 813
25 TraesCS1D01G236800 chr7A 245979687 245980241 554 True 828.000000 828 93.333000 6062 6631 1 chr7A.!!$R1 569
26 TraesCS1D01G236800 chr2A 240491911 240493631 1720 False 2488.000000 2488 92.845000 3010 4727 1 chr2A.!!$F1 1717
27 TraesCS1D01G236800 chr2A 503462791 503463358 567 True 904.000000 904 95.439000 6065 6631 1 chr2A.!!$R1 566
28 TraesCS1D01G236800 chr3A 672896804 672898523 1719 False 2484.000000 2484 92.832000 3010 4724 1 chr3A.!!$F3 1714
29 TraesCS1D01G236800 chr3A 551157849 551159573 1724 True 2462.000000 2462 92.552000 3013 4727 1 chr3A.!!$R2 1714
30 TraesCS1D01G236800 chr3A 746139016 746139829 813 True 1345.000000 1345 96.446000 2197 3012 1 chr3A.!!$R5 815
31 TraesCS1D01G236800 chr3A 675347378 675347949 571 False 887.000000 887 94.755000 6063 6631 1 chr3A.!!$F4 568
32 TraesCS1D01G236800 chr3A 594024234 594024873 639 True 843.000000 843 91.108000 6062 6675 1 chr3A.!!$R3 613
33 TraesCS1D01G236800 chr3A 143654945 143655511 566 True 684.000000 684 88.542000 6062 6631 1 chr3A.!!$R1 569
34 TraesCS1D01G236800 chr3A 723562344 723562902 558 True 488.000000 488 83.363000 8722 9254 1 chr3A.!!$R4 532
35 TraesCS1D01G236800 chr6A 438370599 438372314 1715 False 2436.000000 2436 92.366000 3013 4727 1 chr6A.!!$F2 1714
36 TraesCS1D01G236800 chr6A 520840805 520841620 815 True 1336.000000 1336 96.201000 2197 3012 1 chr6A.!!$R4 815
37 TraesCS1D01G236800 chr6A 277276372 277277080 708 True 1160.000000 1160 96.197000 4728 5437 1 chr6A.!!$R2 709
38 TraesCS1D01G236800 chr6A 100316850 100317557 707 True 1144.000000 1144 95.775000 4728 5437 1 chr6A.!!$R1 709
39 TraesCS1D01G236800 chr6A 190606500 190607140 640 False 848.000000 848 91.264000 6062 6675 1 chr6A.!!$F1 613
40 TraesCS1D01G236800 chr5D 50847832 50848648 816 True 1330.000000 1330 96.083000 2197 3012 1 chr5D.!!$R2 815
41 TraesCS1D01G236800 chr5D 50837209 50837870 661 True 780.000000 780 89.124000 6063 6676 1 chr5D.!!$R1 613
42 TraesCS1D01G236800 chr5D 552391560 552392068 508 True 649.000000 649 89.804000 6062 6567 1 chr5D.!!$R4 505
43 TraesCS1D01G236800 chr3D 647820 648547 727 True 1190.000000 1190 96.159000 4728 5456 1 chr3D.!!$R1 728
44 TraesCS1D01G236800 chr3D 134500082 134500795 713 False 1164.000000 1164 96.084000 4725 5439 1 chr3D.!!$F1 714
45 TraesCS1D01G236800 chr3D 574775828 574777713 1885 True 973.000000 1240 94.821000 4728 6631 2 chr3D.!!$R2 1903
46 TraesCS1D01G236800 chr4D 301751559 301752286 727 True 1212.000000 1212 96.708000 4728 5456 1 chr4D.!!$R3 728
47 TraesCS1D01G236800 chr4D 479965205 479965913 708 True 1149.000000 1149 95.915000 4728 5437 1 chr4D.!!$R5 709
48 TraesCS1D01G236800 chr4D 432423015 432423724 709 True 1131.000000 1131 95.365000 4728 5439 1 chr4D.!!$R4 711
49 TraesCS1D01G236800 chr4D 15596891 15597485 594 False 824.000000 824 92.437000 6064 6631 1 chr4D.!!$F1 567
50 TraesCS1D01G236800 chr4D 57480623 57481228 605 True 811.000000 811 91.584000 6062 6640 1 chr4D.!!$R1 578
51 TraesCS1D01G236800 chr6D 11349877 11350590 713 False 1114.000000 1114 94.825000 4725 5439 1 chr6D.!!$F1 714
52 TraesCS1D01G236800 chr6D 375031699 375032411 712 False 1059.000000 1059 93.427000 4725 5439 1 chr6D.!!$F11 714
53 TraesCS1D01G236800 chr6D 21990828 21991519 691 False 998.000000 998 92.426000 4725 5437 1 chr6D.!!$F4 712
54 TraesCS1D01G236800 chr6D 178000527 178002507 1980 True 885.500000 1085 91.392500 4728 6631 2 chr6D.!!$R7 1903
55 TraesCS1D01G236800 chr6D 424698175 424698765 590 False 837.000000 837 92.230000 4848 5439 1 chr6D.!!$F12 591
56 TraesCS1D01G236800 chr6D 305356290 305356981 691 False 669.000000 669 84.218000 4725 5417 1 chr6D.!!$F8 692
57 TraesCS1D01G236800 chr6D 262997171 262997861 690 False 652.000000 652 83.764000 4725 5417 1 chr6D.!!$F6 692
58 TraesCS1D01G236800 chr6D 159346949 159347637 688 True 647.000000 647 83.718000 4728 5417 1 chr6D.!!$R3 689
59 TraesCS1D01G236800 chr6D 113460796 113462587 1791 False 581.666667 887 93.958000 4834 6676 3 chr6D.!!$F14 1842
60 TraesCS1D01G236800 chr6D 277253661 277254171 510 False 427.000000 427 82.046000 8745 9254 1 chr6D.!!$F7 509
61 TraesCS1D01G236800 chr6D 9764554 9767270 2716 True 357.000000 401 89.929000 6314 6631 2 chr6D.!!$R5 317
62 TraesCS1D01G236800 chr6D 98254818 98256840 2022 True 329.500000 396 87.311500 6062 6673 2 chr6D.!!$R6 611
63 TraesCS1D01G236800 chr5A 126271225 126271821 596 False 846.000000 846 92.020000 6062 6675 1 chr5A.!!$F2 613
64 TraesCS1D01G236800 chrUn 458838506 458839145 639 True 643.000000 643 84.753000 4768 5436 1 chrUn.!!$R4 668
65 TraesCS1D01G236800 chrUn 78994846 78995488 642 True 545.000000 545 82.099000 4728 5370 1 chrUn.!!$R1 642
66 TraesCS1D01G236800 chrUn 32960677 32961258 581 True 461.500000 780 95.602500 6130 6680 2 chrUn.!!$R5 550
67 TraesCS1D01G236800 chrUn 26908900 26911208 2308 False 440.666667 508 88.847000 4725 6640 3 chrUn.!!$F4 1915
68 TraesCS1D01G236800 chrUn 126718529 126719043 514 False 374.000000 374 80.220000 8718 9254 1 chrUn.!!$F1 536
69 TraesCS1D01G236800 chrUn 60486645 60489381 2736 False 361.333333 492 83.740333 4725 6677 3 chrUn.!!$F5 1952
70 TraesCS1D01G236800 chrUn 39708349 39710722 2373 True 266.200000 575 88.992800 4730 6676 5 chrUn.!!$R6 1946
71 TraesCS1D01G236800 chr3B 781432794 781433337 543 True 584.000000 584 86.264000 8718 9256 1 chr3B.!!$R1 538
72 TraesCS1D01G236800 chr6B 17069396 17069931 535 False 575.000000 575 86.245000 8720 9249 1 chr6B.!!$F1 529
73 TraesCS1D01G236800 chr6B 648100324 648100868 544 True 551.000000 551 85.165000 8718 9254 1 chr6B.!!$R2 536
74 TraesCS1D01G236800 chr2B 627945042 627945583 541 True 503.000000 503 83.700000 8718 9254 1 chr2B.!!$R1 536
75 TraesCS1D01G236800 chr4B 98741904 98742429 525 True 440.000000 440 82.149000 8717 9254 1 chr4B.!!$R1 537

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
685 786 1.597742 CCCACAGGGCATATTTCTCG 58.402 55.000 0.00 0.00 35.35 4.04 F
1024 1140 4.099266 TGGACTGGTTGAAGGAACAATTTG 59.901 41.667 0.00 0.00 36.12 2.32 F
2099 2215 1.001746 CAAGAGAAGTGGAGCTCAGCA 59.998 52.381 17.19 1.78 33.62 4.41 F
2925 3047 0.620556 ACGGTGATTCCTGCTGGATT 59.379 50.000 13.72 9.96 42.81 3.01 F
4019 4148 0.382515 TTGTTTTGGTCGCCGGAAAG 59.617 50.000 5.05 0.00 0.00 2.62 F
4207 4340 0.326713 AGGGAGAGTCCTAAAGGGGC 60.327 60.000 0.00 0.00 40.74 5.80 F
4596 4763 1.019278 CGACTCCATCAACCCCGTTG 61.019 60.000 0.00 0.00 43.99 4.10 F
4662 4833 1.187087 CCTTCCCTCTCGTTGCTAGT 58.813 55.000 0.00 0.00 0.00 2.57 F
4663 4834 2.025605 TCCTTCCCTCTCGTTGCTAGTA 60.026 50.000 0.00 0.00 0.00 1.82 F
6434 7517 2.304831 TGGGACGGGGCATTGATCA 61.305 57.895 0.00 0.00 0.00 2.92 F
6905 8136 1.425066 AGTTCATCACAAGGGCCAGAA 59.575 47.619 6.18 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 1715 0.250252 TGCTTGAGTGGCAATCGACA 60.250 50.000 10.64 5.42 36.71 4.35 R
2781 2903 0.612174 TCACCTCAGCCGAGCTACTT 60.612 55.000 0.00 0.00 36.40 2.24 R
3204 3326 0.625316 TCCAATGTCCATGGTCAGGG 59.375 55.000 19.77 19.77 39.09 4.45 R
4119 4250 0.534877 CATATAGGCCAAGGCGCACA 60.535 55.000 10.83 0.00 43.06 4.57 R
6516 7625 2.595095 CTATTGCCCGGCTCCCAA 59.405 61.111 11.61 0.00 0.00 4.12 R
6678 7851 9.034544 CAGATCGATGACAATGTTCACTAATAA 57.965 33.333 0.54 0.00 0.00 1.40 R
6763 7936 1.887854 TGGCATCACAAATGTCCACAG 59.112 47.619 0.00 0.00 0.00 3.66 R
6810 8036 3.550842 GGCAACGATCTGAGCAAAAGTTT 60.551 43.478 0.00 0.00 0.00 2.66 R
6905 8136 3.950397 TCGGAACAACAATAATCCTGCT 58.050 40.909 0.00 0.00 0.00 4.24 R
7261 8492 0.239347 ATCAACTGCGCAGACAAAGC 59.761 50.000 42.03 0.00 0.00 3.51 R
9121 10528 0.040514 TGCAATTTGACGTGCCGAAG 60.041 50.000 0.00 0.00 40.14 3.79 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 7.325694 CCCTTTCAGAAAAATATGCTGAACAT 58.674 34.615 0.00 0.00 45.30 2.71
132 133 7.876936 AGTATCAGTTAATCAGTAGGTCGAA 57.123 36.000 0.00 0.00 0.00 3.71
519 522 4.122776 CTGATCCCTTGACATAGAAACCG 58.877 47.826 0.00 0.00 0.00 4.44
540 543 3.544682 CGAATAACACGTGTCTTGCGATA 59.455 43.478 23.61 9.12 0.00 2.92
685 786 1.597742 CCCACAGGGCATATTTCTCG 58.402 55.000 0.00 0.00 35.35 4.04
802 903 4.457810 CGTTATCTTTCTGCTGTGTGTTG 58.542 43.478 0.00 0.00 0.00 3.33
803 904 4.211164 CGTTATCTTTCTGCTGTGTGTTGA 59.789 41.667 0.00 0.00 0.00 3.18
804 905 5.106948 CGTTATCTTTCTGCTGTGTGTTGAT 60.107 40.000 0.00 0.00 0.00 2.57
805 906 6.566564 CGTTATCTTTCTGCTGTGTGTTGATT 60.567 38.462 0.00 0.00 0.00 2.57
806 907 7.360017 CGTTATCTTTCTGCTGTGTGTTGATTA 60.360 37.037 0.00 0.00 0.00 1.75
807 908 6.882610 ATCTTTCTGCTGTGTGTTGATTAA 57.117 33.333 0.00 0.00 0.00 1.40
808 909 6.882610 TCTTTCTGCTGTGTGTTGATTAAT 57.117 33.333 0.00 0.00 0.00 1.40
810 911 8.389779 TCTTTCTGCTGTGTGTTGATTAATTA 57.610 30.769 0.00 0.00 0.00 1.40
812 913 8.969121 TTTCTGCTGTGTGTTGATTAATTATG 57.031 30.769 0.00 0.00 0.00 1.90
813 914 7.686438 TCTGCTGTGTGTTGATTAATTATGT 57.314 32.000 0.00 0.00 0.00 2.29
814 915 8.109705 TCTGCTGTGTGTTGATTAATTATGTT 57.890 30.769 0.00 0.00 0.00 2.71
816 917 8.109705 TGCTGTGTGTTGATTAATTATGTTCT 57.890 30.769 0.00 0.00 0.00 3.01
817 918 8.022550 TGCTGTGTGTTGATTAATTATGTTCTG 58.977 33.333 0.00 0.00 0.00 3.02
827 928 7.717436 TGATTAATTATGTTCTGATTACCCGCA 59.283 33.333 0.00 0.00 0.00 5.69
828 929 7.867305 TTAATTATGTTCTGATTACCCGCAA 57.133 32.000 0.00 0.00 0.00 4.85
829 930 6.767524 AATTATGTTCTGATTACCCGCAAA 57.232 33.333 0.00 0.00 0.00 3.68
830 931 6.767524 ATTATGTTCTGATTACCCGCAAAA 57.232 33.333 0.00 0.00 0.00 2.44
1024 1140 4.099266 TGGACTGGTTGAAGGAACAATTTG 59.901 41.667 0.00 0.00 36.12 2.32
1110 1226 4.517285 CTGCATACCTCACTGTTGGTATT 58.483 43.478 15.51 4.00 44.46 1.89
1111 1227 4.260985 TGCATACCTCACTGTTGGTATTG 58.739 43.478 15.51 12.87 44.46 1.90
1137 1253 8.617809 GTCAGTCTTTTGATGTTTTTGTACCTA 58.382 33.333 0.00 0.00 0.00 3.08
1185 1301 5.413833 CAGTGTAAGCTGGATGAAAGTGATT 59.586 40.000 0.00 0.00 33.11 2.57
1602 1718 2.562912 CAACGGCTGGTGCATGTC 59.437 61.111 0.00 0.00 41.91 3.06
1689 1805 2.249844 TTCTTTCCCCACTTCACGTC 57.750 50.000 0.00 0.00 0.00 4.34
1900 2016 4.946646 TCAGAGGGCCAAGGAATTAAAAT 58.053 39.130 6.18 0.00 0.00 1.82
2099 2215 1.001746 CAAGAGAAGTGGAGCTCAGCA 59.998 52.381 17.19 1.78 33.62 4.41
2142 2258 3.576550 GGCTACATTTCCTTTTGAACCCA 59.423 43.478 0.00 0.00 31.05 4.51
2696 2818 2.673368 CCTTCGGAATGTAGTCTGCAAC 59.327 50.000 0.00 0.00 0.00 4.17
2881 3003 4.845580 CCTGCGCGGAATCTGGCT 62.846 66.667 20.25 0.00 33.16 4.75
2925 3047 0.620556 ACGGTGATTCCTGCTGGATT 59.379 50.000 13.72 9.96 42.81 3.01
3005 3127 2.432628 CCGAAGCTCCACGTCCAC 60.433 66.667 0.00 0.00 0.00 4.02
3006 3128 2.805353 CGAAGCTCCACGTCCACG 60.805 66.667 0.00 0.00 46.33 4.94
3204 3326 6.292168 CGTTGATCAATAGATGGTTACGGTTC 60.292 42.308 12.12 0.00 33.72 3.62
3376 3502 1.002134 AGATTGTGCAACTCCCGGG 60.002 57.895 16.85 16.85 38.04 5.73
3685 3814 2.168936 TCGGGCAAGTAACATACCGATT 59.831 45.455 0.00 0.00 44.53 3.34
3692 3821 6.375377 GCAAGTAACATACCGATTGACAAAA 58.625 36.000 0.00 0.00 0.00 2.44
3896 4025 4.760715 TGACGCTAGGGTTGTAGAGATATC 59.239 45.833 14.33 0.00 0.00 1.63
4019 4148 0.382515 TTGTTTTGGTCGCCGGAAAG 59.617 50.000 5.05 0.00 0.00 2.62
4207 4340 0.326713 AGGGAGAGTCCTAAAGGGGC 60.327 60.000 0.00 0.00 40.74 5.80
4276 4430 2.860971 AGGAAGGGCCAAGGCTGT 60.861 61.111 11.40 0.00 41.60 4.40
4330 4492 1.979155 GGAAGGGAGGGCAGCAAAC 60.979 63.158 0.00 0.00 0.00 2.93
4520 4687 1.866880 GCTCCGTACGTGTGTTGAACT 60.867 52.381 15.21 0.00 0.00 3.01
4596 4763 1.019278 CGACTCCATCAACCCCGTTG 61.019 60.000 0.00 0.00 43.99 4.10
4646 4817 3.658725 AGGGTATGTAGATGCACTCCTT 58.341 45.455 0.00 0.00 0.00 3.36
4649 4820 3.244249 GGTATGTAGATGCACTCCTTCCC 60.244 52.174 0.00 0.00 0.00 3.97
4650 4821 2.254152 TGTAGATGCACTCCTTCCCT 57.746 50.000 0.00 0.00 0.00 4.20
4651 4822 2.111384 TGTAGATGCACTCCTTCCCTC 58.889 52.381 0.00 0.00 0.00 4.30
4662 4833 1.187087 CCTTCCCTCTCGTTGCTAGT 58.813 55.000 0.00 0.00 0.00 2.57
4663 4834 2.025605 TCCTTCCCTCTCGTTGCTAGTA 60.026 50.000 0.00 0.00 0.00 1.82
4664 4835 2.758979 CCTTCCCTCTCGTTGCTAGTAA 59.241 50.000 0.00 0.00 0.00 2.24
6434 7517 2.304831 TGGGACGGGGCATTGATCA 61.305 57.895 0.00 0.00 0.00 2.92
6516 7625 2.368011 GCTAGGGTTCCGGCTCCTT 61.368 63.158 13.78 9.38 32.46 3.36
6678 7851 2.425668 GCTAAACCGGCCATAACACATT 59.574 45.455 0.00 0.00 0.00 2.71
6728 7901 7.206687 TGCTGTTTTCCTTTATTTACCAGTTG 58.793 34.615 0.00 0.00 0.00 3.16
6763 7936 3.222603 ACCAATTGAAAGGTCACTCCAC 58.777 45.455 7.12 0.00 39.02 4.02
6810 8036 5.570205 TTAATCACACAACCCACCTTAGA 57.430 39.130 0.00 0.00 0.00 2.10
6905 8136 1.425066 AGTTCATCACAAGGGCCAGAA 59.575 47.619 6.18 0.00 0.00 3.02
7046 8277 1.615392 GTTGCAATTCTTCCAGCTGGT 59.385 47.619 31.58 10.06 36.34 4.00
7202 8433 8.504005 GTTACAGTAGAAGATAAGCAAGCAAAA 58.496 33.333 0.00 0.00 0.00 2.44
7204 8435 7.588512 ACAGTAGAAGATAAGCAAGCAAAAAG 58.411 34.615 0.00 0.00 0.00 2.27
7205 8436 7.229506 ACAGTAGAAGATAAGCAAGCAAAAAGT 59.770 33.333 0.00 0.00 0.00 2.66
7261 8492 9.543231 TCTAGGTAGGTTAGGTATGGATATTTG 57.457 37.037 0.00 0.00 0.00 2.32
7262 8493 7.017319 AGGTAGGTTAGGTATGGATATTTGC 57.983 40.000 0.00 0.00 0.00 3.68
7266 8519 7.823745 AGGTTAGGTATGGATATTTGCTTTG 57.176 36.000 0.00 0.00 0.00 2.77
7271 8524 5.300286 AGGTATGGATATTTGCTTTGTCTGC 59.700 40.000 0.00 0.00 0.00 4.26
7284 8537 0.950555 TGTCTGCGCAGTTGATCCAC 60.951 55.000 34.70 23.80 0.00 4.02
7285 8538 0.950555 GTCTGCGCAGTTGATCCACA 60.951 55.000 34.70 11.47 0.00 4.17
7294 8547 4.033358 CGCAGTTGATCCACAGAACTTATC 59.967 45.833 0.00 0.00 0.00 1.75
7303 8556 5.500234 TCCACAGAACTTATCTTTCCATGG 58.500 41.667 4.97 4.97 35.73 3.66
7307 8560 5.940470 ACAGAACTTATCTTTCCATGGTGAC 59.060 40.000 12.58 0.00 35.73 3.67
7308 8561 6.176183 CAGAACTTATCTTTCCATGGTGACT 58.824 40.000 12.58 0.00 35.73 3.41
7309 8562 6.093219 CAGAACTTATCTTTCCATGGTGACTG 59.907 42.308 12.58 7.49 35.73 3.51
7310 8563 5.762179 ACTTATCTTTCCATGGTGACTGA 57.238 39.130 12.58 5.01 0.00 3.41
7324 8577 2.029290 GTGACTGACAGGTATCGGTTGT 60.029 50.000 7.51 0.00 38.36 3.32
7330 8583 0.930310 CAGGTATCGGTTGTGATGCG 59.070 55.000 0.00 0.00 32.45 4.73
7400 8659 6.980416 AGTTCTACAGTCAGGTAGTTTCTT 57.020 37.500 0.00 0.00 41.20 2.52
7409 8668 6.147821 CAGTCAGGTAGTTTCTTTACCACATG 59.852 42.308 4.45 0.00 42.47 3.21
7457 8717 6.424812 CGCTGATCAGGATATTTACATTGTCA 59.575 38.462 23.89 0.00 0.00 3.58
7475 8735 5.666969 TGTCATCTTTTGGTGTCTAAACG 57.333 39.130 0.00 0.00 0.00 3.60
7523 8783 2.193536 AAACGGTGTGCCTTGAGCC 61.194 57.895 0.00 0.00 42.71 4.70
7543 8803 4.079253 GCCCTTCTCATTTTACAAGGTCA 58.921 43.478 0.00 0.00 34.62 4.02
7703 8973 8.429641 TGAGATTGATATACCAGAGGTTTAACC 58.570 37.037 5.91 5.91 37.09 2.85
7741 9011 7.573843 GCGACTATTATACGTACCACCACTATT 60.574 40.741 0.00 0.00 0.00 1.73
7788 9058 1.757118 CAGGATTCAGAAGGCGTCCTA 59.243 52.381 3.14 0.00 37.20 2.94
7929 9199 3.491598 AACTTGGCACCTGGGGACG 62.492 63.158 0.00 0.00 0.00 4.79
7971 9241 5.624715 TTAGCGTATAACATTTTCGTCGG 57.375 39.130 0.00 0.00 0.00 4.79
7976 9246 6.143438 AGCGTATAACATTTTCGTCGGATAAG 59.857 38.462 0.00 0.00 0.00 1.73
8006 9276 4.096984 GCTGGAGGATGGATAAACAACAAG 59.903 45.833 0.00 0.00 0.00 3.16
8027 9297 7.234355 ACAAGAGAGTTGGATTTTATCAGGTT 58.766 34.615 0.00 0.00 0.00 3.50
8065 9335 1.152881 GGATCGCTCAGGGCCAATT 60.153 57.895 6.18 0.00 37.74 2.32
8087 9357 1.215647 CAAGCTACGGTTCTCGGCT 59.784 57.895 0.00 0.00 44.45 5.52
8199 9491 3.059325 GTCTGCGACTATGATGATTTGGC 60.059 47.826 0.00 0.00 0.00 4.52
8202 9494 3.313249 TGCGACTATGATGATTTGGCAAG 59.687 43.478 0.00 0.00 0.00 4.01
8226 9518 3.424170 GCTCTGCTTTTTCTAACTCTGCG 60.424 47.826 0.00 0.00 0.00 5.18
8346 9638 1.273606 AGACCAGTCAAGTGATCACGG 59.726 52.381 19.85 15.58 36.20 4.94
8535 9838 3.625649 TTTTTGAGGCAGGCTGTTTTT 57.374 38.095 17.16 0.00 0.00 1.94
8609 9912 3.189495 CAGTGTGGTTGTTGTGTTGTGTA 59.811 43.478 0.00 0.00 0.00 2.90
8613 9916 4.034163 TGTGGTTGTTGTGTTGTGTATACG 59.966 41.667 0.00 0.00 0.00 3.06
8643 9946 3.064207 GTCTTTGTGCAGTCACGGAATA 58.936 45.455 0.00 0.00 46.01 1.75
8692 9995 7.271511 AGGAAGATGATGTTCTTGTCTGATAC 58.728 38.462 2.24 0.00 36.10 2.24
8693 9996 7.125507 AGGAAGATGATGTTCTTGTCTGATACT 59.874 37.037 2.24 0.00 36.10 2.12
8694 9997 8.417106 GGAAGATGATGTTCTTGTCTGATACTA 58.583 37.037 2.24 0.00 36.10 1.82
9052 10459 8.996988 AATAACAGTACAACAAACATACAACG 57.003 30.769 0.00 0.00 0.00 4.10
9072 10479 1.003331 GTCATGCGTTTTGTCGTCCAA 60.003 47.619 0.00 0.00 0.00 3.53
9077 10484 1.662026 GCGTTTTGTCGTCCAATCCAC 60.662 52.381 0.00 0.00 31.81 4.02
9104 10511 4.100189 CACCACTCCTCGATTAGATCCTTT 59.900 45.833 1.48 0.00 0.00 3.11
9121 10528 2.919229 CCTTTTGAAGTTCATCATGCGC 59.081 45.455 6.36 0.00 0.00 6.09
9181 10591 2.301738 CCACCCTCTCAACCCTCCC 61.302 68.421 0.00 0.00 0.00 4.30
9182 10592 1.229658 CACCCTCTCAACCCTCCCT 60.230 63.158 0.00 0.00 0.00 4.20
9325 10738 4.491409 GGAAGAGGGGGAAGCGGC 62.491 72.222 0.00 0.00 0.00 6.53
9326 10739 4.840005 GAAGAGGGGGAAGCGGCG 62.840 72.222 0.51 0.51 0.00 6.46
9383 10869 1.066908 GTCGCTGAAGAGGATGAGGAG 59.933 57.143 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
540 543 1.200716 CGTCCATTGCAAGTGAAGCAT 59.799 47.619 4.94 0.00 42.33 3.79
685 786 5.127356 AGACTCACAGGTTATTAGCTACACC 59.873 44.000 7.58 7.58 0.00 4.16
802 903 8.094798 TGCGGGTAATCAGAACATAATTAATC 57.905 34.615 0.00 0.00 0.00 1.75
803 904 8.458573 TTGCGGGTAATCAGAACATAATTAAT 57.541 30.769 0.00 0.00 0.00 1.40
804 905 7.867305 TTGCGGGTAATCAGAACATAATTAA 57.133 32.000 0.00 0.00 0.00 1.40
805 906 7.867305 TTTGCGGGTAATCAGAACATAATTA 57.133 32.000 0.00 0.00 0.00 1.40
806 907 6.767524 TTTGCGGGTAATCAGAACATAATT 57.232 33.333 0.00 0.00 0.00 1.40
807 908 6.767524 TTTTGCGGGTAATCAGAACATAAT 57.232 33.333 0.00 0.00 0.00 1.28
808 909 6.576662 TTTTTGCGGGTAATCAGAACATAA 57.423 33.333 0.00 0.00 0.00 1.90
867 968 7.039784 ACCTTGCAAATGCTTAATAAACTCTCA 60.040 33.333 0.00 0.00 42.66 3.27
1024 1140 8.342634 ACTGTACAAACTGAACATAAACATGTC 58.657 33.333 0.00 0.00 32.87 3.06
1110 1226 7.122055 AGGTACAAAAACATCAAAAGACTGACA 59.878 33.333 0.00 0.00 0.00 3.58
1111 1227 7.480810 AGGTACAAAAACATCAAAAGACTGAC 58.519 34.615 0.00 0.00 0.00 3.51
1185 1301 0.183971 TTCTCCTTTTTGACCGGGCA 59.816 50.000 5.41 5.41 0.00 5.36
1392 1508 5.126869 CCTCTGAGAGTTTGAAGAGCAGATA 59.873 44.000 8.88 0.00 35.80 1.98
1599 1715 0.250252 TGCTTGAGTGGCAATCGACA 60.250 50.000 10.64 5.42 36.71 4.35
1602 1718 0.806868 ACATGCTTGAGTGGCAATCG 59.193 50.000 10.64 0.00 43.14 3.34
1689 1805 3.373565 GGCTTGTTCTTGGCCCCG 61.374 66.667 0.00 0.00 39.96 5.73
1900 2016 3.286353 TCTGAACACTGCCAACATTTGA 58.714 40.909 0.00 0.00 0.00 2.69
2142 2258 1.696336 AGAAGTGTCATGACCTGCACT 59.304 47.619 22.85 15.98 41.15 4.40
2222 2344 1.550130 CCCTACAACCTCCGGAGCAA 61.550 60.000 26.87 7.54 0.00 3.91
2678 2800 1.899814 AGGTTGCAGACTACATTCCGA 59.100 47.619 0.00 0.00 0.00 4.55
2696 2818 0.741915 GCGACTCTTCTACCTGGAGG 59.258 60.000 0.00 0.00 42.17 4.30
2781 2903 0.612174 TCACCTCAGCCGAGCTACTT 60.612 55.000 0.00 0.00 36.40 2.24
2902 3024 2.124695 GCAGGAATCACCGTCCCC 60.125 66.667 0.00 0.00 44.74 4.81
2949 3071 2.965462 GCCATGTACTACGCCCGC 60.965 66.667 0.00 0.00 0.00 6.13
2950 3072 2.279918 GGCCATGTACTACGCCCG 60.280 66.667 0.00 0.00 35.23 6.13
3005 3127 2.384382 GCATATTTCCAACAATCCGCG 58.616 47.619 0.00 0.00 0.00 6.46
3006 3128 2.545742 GGGCATATTTCCAACAATCCGC 60.546 50.000 0.00 0.00 0.00 5.54
3008 3130 5.385198 TCTAGGGCATATTTCCAACAATCC 58.615 41.667 0.00 0.00 0.00 3.01
3011 3133 4.792068 CCTCTAGGGCATATTTCCAACAA 58.208 43.478 0.00 0.00 0.00 2.83
3117 3239 8.934023 TGTCTATGTATCCACACATGTATCTA 57.066 34.615 0.00 0.00 39.46 1.98
3204 3326 0.625316 TCCAATGTCCATGGTCAGGG 59.375 55.000 19.77 19.77 39.09 4.45
3376 3502 2.285977 CCCAAAGCATTCCTACGGTAC 58.714 52.381 0.00 0.00 0.00 3.34
3685 3814 5.806818 TCCCGTATACAATTCCTTTTGTCA 58.193 37.500 3.32 0.00 40.25 3.58
3692 3821 6.837312 TCAATCAATCCCGTATACAATTCCT 58.163 36.000 3.32 0.00 0.00 3.36
4019 4148 1.210870 TACCGATAATGCGCGAAACC 58.789 50.000 12.10 0.00 0.00 3.27
4119 4250 0.534877 CATATAGGCCAAGGCGCACA 60.535 55.000 10.83 0.00 43.06 4.57
4239 4393 4.660938 AAGGAAGGGTGCGGCCAC 62.661 66.667 2.24 0.00 41.32 5.01
4286 4443 4.656112 CACTATATATAGGGCCAAGGGAGG 59.344 50.000 21.20 0.00 34.69 4.30
4646 4817 3.428532 AGTTTACTAGCAACGAGAGGGA 58.571 45.455 0.00 0.00 0.00 4.20
4649 4820 4.436242 TGGAGTTTACTAGCAACGAGAG 57.564 45.455 0.00 0.00 0.00 3.20
4650 4821 5.884232 TCTATGGAGTTTACTAGCAACGAGA 59.116 40.000 0.00 0.00 0.00 4.04
4651 4822 6.132791 TCTATGGAGTTTACTAGCAACGAG 57.867 41.667 0.00 0.00 0.00 4.18
4662 4833 8.089625 TCACCAAGATCAATCTATGGAGTTTA 57.910 34.615 19.34 3.42 37.92 2.01
4663 4834 6.962182 TCACCAAGATCAATCTATGGAGTTT 58.038 36.000 19.34 3.87 37.92 2.66
4664 4835 6.566079 TCACCAAGATCAATCTATGGAGTT 57.434 37.500 19.34 4.10 37.92 3.01
6516 7625 2.595095 CTATTGCCCGGCTCCCAA 59.405 61.111 11.61 0.00 0.00 4.12
6678 7851 9.034544 CAGATCGATGACAATGTTCACTAATAA 57.965 33.333 0.54 0.00 0.00 1.40
6728 7901 8.872845 CCTTTCAATTGGTAAGCATAAATTCAC 58.127 33.333 5.42 0.00 0.00 3.18
6763 7936 1.887854 TGGCATCACAAATGTCCACAG 59.112 47.619 0.00 0.00 0.00 3.66
6810 8036 3.550842 GGCAACGATCTGAGCAAAAGTTT 60.551 43.478 0.00 0.00 0.00 2.66
6905 8136 3.950397 TCGGAACAACAATAATCCTGCT 58.050 40.909 0.00 0.00 0.00 4.24
7046 8277 4.263905 ACCCTTGAAAGATCATTGCCAGTA 60.264 41.667 0.00 0.00 34.96 2.74
7246 8477 6.486657 GCAGACAAAGCAAATATCCATACCTA 59.513 38.462 0.00 0.00 0.00 3.08
7247 8478 5.300286 GCAGACAAAGCAAATATCCATACCT 59.700 40.000 0.00 0.00 0.00 3.08
7250 8481 4.261155 GCGCAGACAAAGCAAATATCCATA 60.261 41.667 0.30 0.00 0.00 2.74
7251 8482 3.489738 GCGCAGACAAAGCAAATATCCAT 60.490 43.478 0.30 0.00 0.00 3.41
7252 8483 2.159393 GCGCAGACAAAGCAAATATCCA 60.159 45.455 0.30 0.00 0.00 3.41
7253 8484 2.159393 TGCGCAGACAAAGCAAATATCC 60.159 45.455 5.66 0.00 38.01 2.59
7254 8485 3.103738 CTGCGCAGACAAAGCAAATATC 58.896 45.455 33.66 0.00 40.63 1.63
7255 8486 2.489329 ACTGCGCAGACAAAGCAAATAT 59.511 40.909 42.03 13.56 40.63 1.28
7256 8487 1.879380 ACTGCGCAGACAAAGCAAATA 59.121 42.857 42.03 0.00 40.63 1.40
7257 8488 0.670162 ACTGCGCAGACAAAGCAAAT 59.330 45.000 42.03 14.36 40.63 2.32
7259 8490 0.248580 CAACTGCGCAGACAAAGCAA 60.249 50.000 42.03 0.00 40.63 3.91
7260 8491 1.094650 TCAACTGCGCAGACAAAGCA 61.095 50.000 42.03 15.87 39.25 3.91
7261 8492 0.239347 ATCAACTGCGCAGACAAAGC 59.761 50.000 42.03 0.00 0.00 3.51
7262 8493 1.135859 GGATCAACTGCGCAGACAAAG 60.136 52.381 42.03 24.38 0.00 2.77
7266 8519 0.950555 TGTGGATCAACTGCGCAGAC 60.951 55.000 42.03 27.06 31.48 3.51
7271 8524 1.800805 AGTTCTGTGGATCAACTGCG 58.199 50.000 1.02 0.00 0.00 5.18
7284 8537 6.093219 CAGTCACCATGGAAAGATAAGTTCTG 59.907 42.308 21.47 10.97 33.93 3.02
7285 8538 6.013379 TCAGTCACCATGGAAAGATAAGTTCT 60.013 38.462 21.47 2.94 35.70 3.01
7294 8547 2.224621 ACCTGTCAGTCACCATGGAAAG 60.225 50.000 21.47 8.04 0.00 2.62
7303 8556 2.029290 ACAACCGATACCTGTCAGTCAC 60.029 50.000 0.00 0.00 0.00 3.67
7307 8560 3.190079 CATCACAACCGATACCTGTCAG 58.810 50.000 0.00 0.00 0.00 3.51
7308 8561 2.676750 GCATCACAACCGATACCTGTCA 60.677 50.000 0.00 0.00 0.00 3.58
7309 8562 1.933853 GCATCACAACCGATACCTGTC 59.066 52.381 0.00 0.00 0.00 3.51
7310 8563 1.739035 CGCATCACAACCGATACCTGT 60.739 52.381 0.00 0.00 0.00 4.00
7324 8577 0.592637 CAAGTGCAACCTTCGCATCA 59.407 50.000 0.00 0.00 42.32 3.07
7330 8583 3.988379 TGAATGTCAAGTGCAACCTTC 57.012 42.857 0.00 0.00 37.80 3.46
7400 8659 5.420739 TGTATGAGACTGCTACATGTGGTAA 59.579 40.000 9.11 0.00 0.00 2.85
7409 8668 6.470160 CGTTTTTCATGTATGAGACTGCTAC 58.530 40.000 0.00 0.00 38.19 3.58
7457 8717 6.713450 ACCAATACGTTTAGACACCAAAAGAT 59.287 34.615 0.00 0.00 0.00 2.40
7463 8723 4.339872 ACACCAATACGTTTAGACACCA 57.660 40.909 0.00 0.00 0.00 4.17
7523 8783 7.538678 CGAAAATGACCTTGTAAAATGAGAAGG 59.461 37.037 0.00 0.00 43.82 3.46
7543 8803 6.073222 ACAGAAGAGAAATGCGTAACGAAAAT 60.073 34.615 0.00 0.00 0.00 1.82
7788 9058 1.549203 AGCTTGGGATGTTCGCAATT 58.451 45.000 7.35 0.00 46.03 2.32
7872 9142 5.014858 ACTTCAAGCATCTTGTCATGGATT 58.985 37.500 6.47 0.00 0.00 3.01
7945 9215 6.561533 CGACGAAAATGTTATACGCTAATGCT 60.562 38.462 0.00 0.00 36.97 3.79
7946 9216 5.555191 CGACGAAAATGTTATACGCTAATGC 59.445 40.000 0.00 0.00 0.00 3.56
7949 9219 5.339177 TCCGACGAAAATGTTATACGCTAA 58.661 37.500 0.00 0.00 0.00 3.09
7954 9224 7.169035 TGCTTATCCGACGAAAATGTTATAC 57.831 36.000 0.00 0.00 0.00 1.47
7976 9246 0.960364 TCCATCCTCCAGCGTTTTGC 60.960 55.000 0.00 0.00 46.98 3.68
8006 9276 5.946377 ACCAACCTGATAAAATCCAACTCTC 59.054 40.000 0.00 0.00 0.00 3.20
8015 9285 6.149474 CACGAGAAAGACCAACCTGATAAAAT 59.851 38.462 0.00 0.00 0.00 1.82
8027 9297 2.733218 CGCGCACGAGAAAGACCA 60.733 61.111 8.75 0.00 43.93 4.02
8065 9335 1.134367 CCGAGAACCGTAGCTTGATCA 59.866 52.381 0.00 0.00 36.31 2.92
8087 9357 1.758592 CACCTGAACCGGGAAAGGA 59.241 57.895 21.46 0.00 33.36 3.36
8199 9491 5.238214 AGAGTTAGAAAAAGCAGAGCACTTG 59.762 40.000 0.00 0.00 0.00 3.16
8202 9494 4.612486 GCAGAGTTAGAAAAAGCAGAGCAC 60.612 45.833 0.00 0.00 0.00 4.40
8226 9518 0.594028 TGAACGACACGAGCACAGAC 60.594 55.000 0.00 0.00 0.00 3.51
8346 9638 2.883253 GGCTCTCTTCTGCGACGC 60.883 66.667 14.19 14.19 0.00 5.19
8471 9764 0.250858 TACCACCGTCGAGGACAAGA 60.251 55.000 6.70 0.00 45.00 3.02
8609 9912 4.181578 GCACAAAGACCTACATCACGTAT 58.818 43.478 0.00 0.00 0.00 3.06
8613 9916 3.403038 ACTGCACAAAGACCTACATCAC 58.597 45.455 0.00 0.00 0.00 3.06
8692 9995 4.214545 TGTTTCAACGTGGGCAAATACTAG 59.785 41.667 0.00 0.00 0.00 2.57
8693 9996 4.135306 TGTTTCAACGTGGGCAAATACTA 58.865 39.130 0.00 0.00 0.00 1.82
8694 9997 2.952978 TGTTTCAACGTGGGCAAATACT 59.047 40.909 0.00 0.00 0.00 2.12
8729 10032 2.202518 GCCGTAGCGCGTCTGTTA 60.203 61.111 8.43 0.00 39.32 2.41
8805 10110 0.746063 CAGCACCTGGTGAAGCAAAA 59.254 50.000 30.23 0.00 45.66 2.44
8806 10111 2.417978 CAGCACCTGGTGAAGCAAA 58.582 52.632 30.23 0.00 45.66 3.68
8884 10230 7.706179 CCACATTTAAATACTATTTGTGCTGGG 59.294 37.037 0.00 0.00 33.44 4.45
9052 10459 0.584396 TGGACGACAAAACGCATGAC 59.416 50.000 0.00 0.00 36.70 3.06
9072 10479 3.717294 GGAGTGGTGGGCGTGGAT 61.717 66.667 0.00 0.00 0.00 3.41
9077 10484 1.672854 TAATCGAGGAGTGGTGGGCG 61.673 60.000 0.00 0.00 0.00 6.13
9104 10511 2.159667 CGAAGCGCATGATGAACTTCAA 60.160 45.455 20.44 0.00 37.24 2.69
9121 10528 0.040514 TGCAATTTGACGTGCCGAAG 60.041 50.000 0.00 0.00 40.14 3.79
9133 10541 4.025360 TGTTGCCTCCTATCATGCAATTT 58.975 39.130 0.00 0.00 44.57 1.82
9356 10788 0.108898 CCTCTTCAGCGACCAGTCAG 60.109 60.000 0.00 0.00 0.00 3.51
9361 10846 0.820226 CTCATCCTCTTCAGCGACCA 59.180 55.000 0.00 0.00 0.00 4.02
9368 10854 1.769026 CGACCTCCTCATCCTCTTCA 58.231 55.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.