Multiple sequence alignment - TraesCS5D01G148300

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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 TraesCS5D01G148300 chr5D 100.000 7562 0 0 1 7562 235913993 235906432 0.000000e+00 13965.0
1 TraesCS5D01G148300 chr5D 97.914 911 14 2 2334 3240 487308658 487307749 0.000000e+00 1572.0
2 TraesCS5D01G148300 chr5D 93.116 1075 23 8 5804 6840 67698884 67697823 0.000000e+00 1528.0
3 TraesCS5D01G148300 chr5D 90.762 801 67 7 1 799 276679017 276678222 0.000000e+00 1062.0
4 TraesCS5D01G148300 chr2A 95.576 5018 135 32 2334 7303 377598765 377593787 0.000000e+00 7956.0
5 TraesCS5D01G148300 chr2A 93.639 1525 73 15 799 2318 377601349 377599844 0.000000e+00 2257.0
6 TraesCS5D01G148300 chr2A 91.675 1033 62 9 3239 4270 403877191 403876182 0.000000e+00 1410.0
7 TraesCS5D01G148300 chr2A 94.128 562 24 4 1201 1761 271885851 271885298 0.000000e+00 846.0
8 TraesCS5D01G148300 chr2A 90.672 536 35 3 3239 3774 401919009 401918489 0.000000e+00 699.0
9 TraesCS5D01G148300 chr2A 90.338 414 28 8 798 1201 271886307 271885896 4.020000e-147 532.0
10 TraesCS5D01G148300 chr2A 92.790 319 16 4 3952 4270 401918261 401917950 8.940000e-124 455.0
11 TraesCS5D01G148300 chr2A 92.790 319 16 4 3952 4270 403876153 403875842 8.940000e-124 455.0
12 TraesCS5D01G148300 chr2A 80.451 399 52 21 805 1199 202799456 202799080 1.610000e-71 281.0
13 TraesCS5D01G148300 chr2A 100.000 30 0 0 4241 4270 401918319 401918290 1.000000e-03 56.5
14 TraesCS5D01G148300 chr4B 94.936 5036 176 23 2334 7303 175641511 175636489 0.000000e+00 7814.0
15 TraesCS5D01G148300 chr4B 92.987 1868 58 25 5479 7303 422772912 422771075 0.000000e+00 2656.0
16 TraesCS5D01G148300 chr4B 92.118 1865 64 29 5479 7303 440443428 440445249 0.000000e+00 2553.0
17 TraesCS5D01G148300 chr4B 95.172 870 36 3 4385 5249 248831461 248832329 0.000000e+00 1369.0
18 TraesCS5D01G148300 chr4B 94.774 842 39 2 2402 3239 47618981 47618141 0.000000e+00 1306.0
19 TraesCS5D01G148300 chr4B 85.861 976 90 19 1388 2318 466378096 466377124 0.000000e+00 994.0
20 TraesCS5D01G148300 chr4B 98.134 536 9 1 2881 3416 440442364 440442898 0.000000e+00 933.0
21 TraesCS5D01G148300 chr4B 97.948 536 11 0 2881 3416 422773987 422773452 0.000000e+00 929.0
22 TraesCS5D01G148300 chr4B 97.189 498 10 1 4973 5466 422773453 422772956 0.000000e+00 839.0
23 TraesCS5D01G148300 chr4B 95.181 498 10 3 4973 5466 440442897 440443384 0.000000e+00 774.0
24 TraesCS5D01G148300 chr4B 96.907 291 5 1 2372 2658 440440126 440440416 1.140000e-132 484.0
25 TraesCS5D01G148300 chr4B 96.220 291 7 1 2372 2658 422776224 422775934 2.470000e-129 473.0
26 TraesCS5D01G148300 chr4B 89.600 250 18 4 1722 1965 178351228 178351475 2.050000e-80 311.0
27 TraesCS5D01G148300 chr4B 87.121 132 9 4 4267 4398 248831322 248831445 7.910000e-30 143.0
28 TraesCS5D01G148300 chr4B 93.750 96 5 1 1201 1296 362878368 362878462 7.910000e-30 143.0
29 TraesCS5D01G148300 chr3A 95.575 3751 98 22 3604 7303 110682627 110678894 0.000000e+00 5945.0
30 TraesCS5D01G148300 chr3A 95.556 1665 46 10 4584 6237 377489000 377487353 0.000000e+00 2639.0
31 TraesCS5D01G148300 chr3A 88.611 799 79 6 2 799 223209007 223209794 0.000000e+00 961.0
32 TraesCS5D01G148300 chr3A 97.183 71 2 0 4053 4123 164372765 164372695 3.710000e-23 121.0
33 TraesCS5D01G148300 chr1A 94.345 1892 78 10 4267 6139 254959205 254957324 0.000000e+00 2874.0
34 TraesCS5D01G148300 chr1A 90.323 62 3 2 2339 2397 335997469 335997530 2.260000e-10 78.7
35 TraesCS5D01G148300 chr1B 93.429 1872 59 22 5479 7303 499391779 499389925 0.000000e+00 2717.0
36 TraesCS5D01G148300 chr1B 92.825 1547 63 11 5804 7303 296600896 296599351 0.000000e+00 2198.0
37 TraesCS5D01G148300 chr1B 97.481 1032 24 2 3239 4270 425357447 425356418 0.000000e+00 1760.0
38 TraesCS5D01G148300 chr1B 92.436 1203 46 17 6137 7304 429719121 429720313 0.000000e+00 1676.0
39 TraesCS5D01G148300 chr1B 92.719 934 44 8 6137 7050 201925285 201926214 0.000000e+00 1327.0
40 TraesCS5D01G148300 chr1B 98.835 515 5 1 2881 3395 368082485 368082998 0.000000e+00 917.0
41 TraesCS5D01G148300 chr1B 97.201 536 14 1 2881 3416 499392853 499392319 0.000000e+00 905.0
42 TraesCS5D01G148300 chr1B 97.390 498 9 1 4973 5466 368095495 368095992 0.000000e+00 845.0
43 TraesCS5D01G148300 chr1B 96.988 498 11 1 4973 5466 499392320 499391823 0.000000e+00 833.0
44 TraesCS5D01G148300 chr1B 97.279 294 4 1 2369 2658 368080251 368080544 5.270000e-136 496.0
45 TraesCS5D01G148300 chr1B 96.907 291 5 1 2372 2658 499395525 499395235 1.140000e-132 484.0
46 TraesCS5D01G148300 chr1B 81.281 406 50 19 798 1199 193630765 193630382 9.530000e-79 305.0
47 TraesCS5D01G148300 chr7B 94.837 1530 67 6 798 2318 76841976 76840450 0.000000e+00 2377.0
48 TraesCS5D01G148300 chr7B 94.355 1435 60 11 5875 7303 215518145 215516726 0.000000e+00 2182.0
49 TraesCS5D01G148300 chr7B 94.602 1167 45 8 5875 7036 392314229 392315382 0.000000e+00 1790.0
50 TraesCS5D01G148300 chr7B 94.435 1132 48 7 1201 2318 262905734 262904604 0.000000e+00 1727.0
51 TraesCS5D01G148300 chr7B 91.111 405 33 3 798 1201 262906181 262905779 5.160000e-151 545.0
52 TraesCS5D01G148300 chr7B 79.429 350 60 9 799 1146 140714887 140714548 3.530000e-58 237.0
53 TraesCS5D01G148300 chr5B 94.421 1434 60 10 5875 7302 298161611 298160192 0.000000e+00 2187.0
54 TraesCS5D01G148300 chr5B 94.834 871 39 3 4387 5252 294279373 294280242 0.000000e+00 1354.0
55 TraesCS5D01G148300 chr5B 92.080 947 40 9 6392 7303 454129488 454130434 0.000000e+00 1301.0
56 TraesCS5D01G148300 chr5B 98.141 538 7 2 2881 3416 117938349 117938885 0.000000e+00 935.0
57 TraesCS5D01G148300 chr5B 96.599 294 6 1 2369 2658 117936166 117936459 1.140000e-132 484.0
58 TraesCS5D01G148300 chr5B 95.019 261 13 0 7302 7562 269199431 269199691 1.960000e-110 411.0
59 TraesCS5D01G148300 chr5B 86.364 132 10 5 4267 4398 294279233 294279356 3.680000e-28 137.0
60 TraesCS5D01G148300 chr4A 92.774 1467 49 18 5875 7303 181371768 181370321 0.000000e+00 2069.0
61 TraesCS5D01G148300 chr4A 94.469 669 36 1 2565 3233 569873071 569873738 0.000000e+00 1029.0
62 TraesCS5D01G148300 chr4A 93.194 191 9 1 2396 2582 569872688 569872878 2.080000e-70 278.0
63 TraesCS5D01G148300 chr4A 85.950 121 11 3 1256 1370 356605445 356605325 2.860000e-24 124.0
64 TraesCS5D01G148300 chr6D 93.605 1204 39 10 6137 7303 181406047 181404845 0.000000e+00 1762.0
65 TraesCS5D01G148300 chr6D 93.333 1200 45 13 6137 7303 172392411 172393608 0.000000e+00 1740.0
66 TraesCS5D01G148300 chr6D 88.593 263 22 4 4784 5039 226913229 226912968 5.700000e-81 313.0
67 TraesCS5D01G148300 chr6B 92.123 1206 54 18 6137 7303 259711843 259713046 0.000000e+00 1663.0
68 TraesCS5D01G148300 chr6B 84.311 784 78 21 4267 5049 422991193 422991932 0.000000e+00 725.0
69 TraesCS5D01G148300 chr6B 88.973 263 21 4 4784 5039 421001468 421001207 1.220000e-82 318.0
70 TraesCS5D01G148300 chr3D 92.013 1202 36 10 6137 7303 306826139 306824963 0.000000e+00 1633.0
71 TraesCS5D01G148300 chr3D 92.010 801 56 8 2 798 106352783 106353579 0.000000e+00 1118.0
72 TraesCS5D01G148300 chr3D 91.386 801 61 8 2 798 106373597 106374393 0.000000e+00 1090.0
73 TraesCS5D01G148300 chr3D 90.785 803 62 6 4 800 256569517 256568721 0.000000e+00 1062.0
74 TraesCS5D01G148300 chr2B 93.987 948 50 4 3302 4246 331216568 331217511 0.000000e+00 1428.0
75 TraesCS5D01G148300 chr2B 95.189 873 36 3 4385 5252 169701528 169700657 0.000000e+00 1375.0
76 TraesCS5D01G148300 chr2B 97.205 787 14 5 2460 3240 516170612 516169828 0.000000e+00 1325.0
77 TraesCS5D01G148300 chr2B 90.673 847 69 7 5300 6139 339206181 339205338 0.000000e+00 1118.0
78 TraesCS5D01G148300 chr2B 90.437 847 71 7 5300 6139 331503572 331502729 0.000000e+00 1107.0
79 TraesCS5D01G148300 chr2B 97.619 42 1 0 2826 2867 91804767 91804808 1.050000e-08 73.1
80 TraesCS5D01G148300 chr4D 92.180 1023 53 14 1306 2312 231927684 231928695 0.000000e+00 1421.0
81 TraesCS5D01G148300 chr4D 92.824 850 47 4 2402 3239 32763620 32762773 0.000000e+00 1219.0
82 TraesCS5D01G148300 chr4D 91.646 802 55 9 1 799 150619309 150618517 0.000000e+00 1099.0
83 TraesCS5D01G148300 chr4D 87.685 406 38 9 799 1201 231927178 231927574 5.350000e-126 462.0
84 TraesCS5D01G148300 chr4D 94.595 259 14 0 7302 7560 307934368 307934110 1.180000e-107 401.0
85 TraesCS5D01G148300 chr4D 94.595 259 14 0 7302 7560 432797639 432797381 1.180000e-107 401.0
86 TraesCS5D01G148300 chr4D 94.595 259 14 0 7302 7560 482317306 482317048 1.180000e-107 401.0
87 TraesCS5D01G148300 chr4D 81.948 349 49 12 801 1146 357305576 357305913 4.470000e-72 283.0
88 TraesCS5D01G148300 chr4D 91.176 68 0 2 1201 1268 231927618 231927679 3.760000e-13 87.9
89 TraesCS5D01G148300 chr4D 92.593 54 4 0 2344 2397 126505035 126505088 2.260000e-10 78.7
90 TraesCS5D01G148300 chr3B 90.909 847 66 8 5300 6139 326265860 326265018 0.000000e+00 1127.0
91 TraesCS5D01G148300 chr3B 98.321 536 8 1 2881 3416 678843003 678842469 0.000000e+00 939.0
92 TraesCS5D01G148300 chr3B 84.184 784 79 21 4267 5049 39599960 39600699 0.000000e+00 719.0
93 TraesCS5D01G148300 chr3B 82.895 760 74 24 4267 5026 814624994 814625697 3.850000e-177 632.0
94 TraesCS5D01G148300 chr3B 97.264 329 3 2 2334 2658 678844528 678844202 3.080000e-153 553.0
95 TraesCS5D01G148300 chr7D 92.000 800 60 4 2 799 305424487 305425284 0.000000e+00 1120.0
96 TraesCS5D01G148300 chr7D 94.981 259 13 0 7302 7560 212760707 212760965 2.540000e-109 407.0
97 TraesCS5D01G148300 chr7D 88.129 278 23 5 5026 5296 321939010 321939284 9.470000e-84 322.0
98 TraesCS5D01G148300 chr7D 95.312 64 3 0 2334 2397 46355999 46355936 1.340000e-17 102.0
99 TraesCS5D01G148300 chr1D 91.304 805 62 4 1 798 200031725 200032528 0.000000e+00 1092.0
100 TraesCS5D01G148300 chr1D 94.981 259 13 0 7302 7560 41005661 41005403 2.540000e-109 407.0
101 TraesCS5D01G148300 chr1D 94.961 258 13 0 7302 7559 414616938 414617195 9.140000e-109 405.0
102 TraesCS5D01G148300 chr5A 88.323 805 85 8 1 800 207282753 207283553 0.000000e+00 957.0
103 TraesCS5D01G148300 chrUn 94.595 259 14 0 7302 7560 45434826 45434568 1.180000e-107 401.0
104 TraesCS5D01G148300 chrUn 94.595 259 14 0 7302 7560 91574255 91574513 1.180000e-107 401.0


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 TraesCS5D01G148300 chr5D 235906432 235913993 7561 True 13965.000000 13965 100.000000 1 7562 1 chr5D.!!$R2 7561
1 TraesCS5D01G148300 chr5D 487307749 487308658 909 True 1572.000000 1572 97.914000 2334 3240 1 chr5D.!!$R4 906
2 TraesCS5D01G148300 chr5D 67697823 67698884 1061 True 1528.000000 1528 93.116000 5804 6840 1 chr5D.!!$R1 1036
3 TraesCS5D01G148300 chr5D 276678222 276679017 795 True 1062.000000 1062 90.762000 1 799 1 chr5D.!!$R3 798
4 TraesCS5D01G148300 chr2A 377593787 377601349 7562 True 5106.500000 7956 94.607500 799 7303 2 chr2A.!!$R3 6504
5 TraesCS5D01G148300 chr2A 403875842 403877191 1349 True 932.500000 1410 92.232500 3239 4270 2 chr2A.!!$R5 1031
6 TraesCS5D01G148300 chr2A 271885298 271886307 1009 True 689.000000 846 92.233000 798 1761 2 chr2A.!!$R2 963
7 TraesCS5D01G148300 chr2A 401917950 401919009 1059 True 403.500000 699 94.487333 3239 4270 3 chr2A.!!$R4 1031
8 TraesCS5D01G148300 chr4B 175636489 175641511 5022 True 7814.000000 7814 94.936000 2334 7303 1 chr4B.!!$R2 4969
9 TraesCS5D01G148300 chr4B 47618141 47618981 840 True 1306.000000 1306 94.774000 2402 3239 1 chr4B.!!$R1 837
10 TraesCS5D01G148300 chr4B 422771075 422776224 5149 True 1224.250000 2656 96.086000 2372 7303 4 chr4B.!!$R4 4931
11 TraesCS5D01G148300 chr4B 440440126 440445249 5123 False 1186.000000 2553 95.585000 2372 7303 4 chr4B.!!$F4 4931
12 TraesCS5D01G148300 chr4B 466377124 466378096 972 True 994.000000 994 85.861000 1388 2318 1 chr4B.!!$R3 930
13 TraesCS5D01G148300 chr4B 248831322 248832329 1007 False 756.000000 1369 91.146500 4267 5249 2 chr4B.!!$F3 982
14 TraesCS5D01G148300 chr3A 110678894 110682627 3733 True 5945.000000 5945 95.575000 3604 7303 1 chr3A.!!$R1 3699
15 TraesCS5D01G148300 chr3A 377487353 377489000 1647 True 2639.000000 2639 95.556000 4584 6237 1 chr3A.!!$R3 1653
16 TraesCS5D01G148300 chr3A 223209007 223209794 787 False 961.000000 961 88.611000 2 799 1 chr3A.!!$F1 797
17 TraesCS5D01G148300 chr1A 254957324 254959205 1881 True 2874.000000 2874 94.345000 4267 6139 1 chr1A.!!$R1 1872
18 TraesCS5D01G148300 chr1B 296599351 296600896 1545 True 2198.000000 2198 92.825000 5804 7303 1 chr1B.!!$R2 1499
19 TraesCS5D01G148300 chr1B 425356418 425357447 1029 True 1760.000000 1760 97.481000 3239 4270 1 chr1B.!!$R3 1031
20 TraesCS5D01G148300 chr1B 429719121 429720313 1192 False 1676.000000 1676 92.436000 6137 7304 1 chr1B.!!$F3 1167
21 TraesCS5D01G148300 chr1B 201925285 201926214 929 False 1327.000000 1327 92.719000 6137 7050 1 chr1B.!!$F1 913
22 TraesCS5D01G148300 chr1B 499389925 499395525 5600 True 1234.750000 2717 96.131250 2372 7303 4 chr1B.!!$R4 4931
23 TraesCS5D01G148300 chr1B 368080251 368082998 2747 False 706.500000 917 98.057000 2369 3395 2 chr1B.!!$F4 1026
24 TraesCS5D01G148300 chr7B 76840450 76841976 1526 True 2377.000000 2377 94.837000 798 2318 1 chr7B.!!$R1 1520
25 TraesCS5D01G148300 chr7B 215516726 215518145 1419 True 2182.000000 2182 94.355000 5875 7303 1 chr7B.!!$R3 1428
26 TraesCS5D01G148300 chr7B 392314229 392315382 1153 False 1790.000000 1790 94.602000 5875 7036 1 chr7B.!!$F1 1161
27 TraesCS5D01G148300 chr7B 262904604 262906181 1577 True 1136.000000 1727 92.773000 798 2318 2 chr7B.!!$R4 1520
28 TraesCS5D01G148300 chr5B 298160192 298161611 1419 True 2187.000000 2187 94.421000 5875 7302 1 chr5B.!!$R1 1427
29 TraesCS5D01G148300 chr5B 454129488 454130434 946 False 1301.000000 1301 92.080000 6392 7303 1 chr5B.!!$F2 911
30 TraesCS5D01G148300 chr5B 294279233 294280242 1009 False 745.500000 1354 90.599000 4267 5252 2 chr5B.!!$F4 985
31 TraesCS5D01G148300 chr5B 117936166 117938885 2719 False 709.500000 935 97.370000 2369 3416 2 chr5B.!!$F3 1047
32 TraesCS5D01G148300 chr4A 181370321 181371768 1447 True 2069.000000 2069 92.774000 5875 7303 1 chr4A.!!$R1 1428
33 TraesCS5D01G148300 chr4A 569872688 569873738 1050 False 653.500000 1029 93.831500 2396 3233 2 chr4A.!!$F1 837
34 TraesCS5D01G148300 chr6D 181404845 181406047 1202 True 1762.000000 1762 93.605000 6137 7303 1 chr6D.!!$R1 1166
35 TraesCS5D01G148300 chr6D 172392411 172393608 1197 False 1740.000000 1740 93.333000 6137 7303 1 chr6D.!!$F1 1166
36 TraesCS5D01G148300 chr6B 259711843 259713046 1203 False 1663.000000 1663 92.123000 6137 7303 1 chr6B.!!$F1 1166
37 TraesCS5D01G148300 chr6B 422991193 422991932 739 False 725.000000 725 84.311000 4267 5049 1 chr6B.!!$F2 782
38 TraesCS5D01G148300 chr3D 306824963 306826139 1176 True 1633.000000 1633 92.013000 6137 7303 1 chr3D.!!$R2 1166
39 TraesCS5D01G148300 chr3D 106352783 106353579 796 False 1118.000000 1118 92.010000 2 798 1 chr3D.!!$F1 796
40 TraesCS5D01G148300 chr3D 106373597 106374393 796 False 1090.000000 1090 91.386000 2 798 1 chr3D.!!$F2 796
41 TraesCS5D01G148300 chr3D 256568721 256569517 796 True 1062.000000 1062 90.785000 4 800 1 chr3D.!!$R1 796
42 TraesCS5D01G148300 chr2B 331216568 331217511 943 False 1428.000000 1428 93.987000 3302 4246 1 chr2B.!!$F2 944
43 TraesCS5D01G148300 chr2B 169700657 169701528 871 True 1375.000000 1375 95.189000 4385 5252 1 chr2B.!!$R1 867
44 TraesCS5D01G148300 chr2B 516169828 516170612 784 True 1325.000000 1325 97.205000 2460 3240 1 chr2B.!!$R4 780
45 TraesCS5D01G148300 chr2B 339205338 339206181 843 True 1118.000000 1118 90.673000 5300 6139 1 chr2B.!!$R3 839
46 TraesCS5D01G148300 chr2B 331502729 331503572 843 True 1107.000000 1107 90.437000 5300 6139 1 chr2B.!!$R2 839
47 TraesCS5D01G148300 chr4D 32762773 32763620 847 True 1219.000000 1219 92.824000 2402 3239 1 chr4D.!!$R1 837
48 TraesCS5D01G148300 chr4D 150618517 150619309 792 True 1099.000000 1099 91.646000 1 799 1 chr4D.!!$R2 798
49 TraesCS5D01G148300 chr4D 231927178 231928695 1517 False 656.966667 1421 90.347000 799 2312 3 chr4D.!!$F3 1513
50 TraesCS5D01G148300 chr3B 326265018 326265860 842 True 1127.000000 1127 90.909000 5300 6139 1 chr3B.!!$R1 839
51 TraesCS5D01G148300 chr3B 678842469 678844528 2059 True 746.000000 939 97.792500 2334 3416 2 chr3B.!!$R2 1082
52 TraesCS5D01G148300 chr3B 39599960 39600699 739 False 719.000000 719 84.184000 4267 5049 1 chr3B.!!$F1 782
53 TraesCS5D01G148300 chr3B 814624994 814625697 703 False 632.000000 632 82.895000 4267 5026 1 chr3B.!!$F2 759
54 TraesCS5D01G148300 chr7D 305424487 305425284 797 False 1120.000000 1120 92.000000 2 799 1 chr7D.!!$F2 797
55 TraesCS5D01G148300 chr1D 200031725 200032528 803 False 1092.000000 1092 91.304000 1 798 1 chr1D.!!$F1 797
56 TraesCS5D01G148300 chr5A 207282753 207283553 800 False 957.000000 957 88.323000 1 800 1 chr5A.!!$F1 799

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
81 82 0.182061 ATTGCTCCGCTGTGATGGAT 59.818 50.000 0.00 0.00 32.83 3.41 F
859 917 0.824759 CTCCCTCGATCGGTTCCTTT 59.175 55.000 16.41 0.00 0.00 3.11 F
1659 1804 1.078426 GCAGGGAATGTAGCGGTGT 60.078 57.895 0.00 0.00 0.00 4.16 F
2438 3706 0.605083 ACGTGCAGATCAGCTCTTCA 59.395 50.000 11.68 0.00 34.99 3.02 F
3011 8244 7.306574 GCATTGGAGCTAAAGTTTTGTTGTTAC 60.307 37.037 0.00 0.00 0.00 2.50 F
3738 8975 3.053291 CCTGGCGGCGCAGTTTTA 61.053 61.111 34.36 10.79 0.00 1.52 F
4837 10460 0.636647 TGCAGAGGAGAGGGGATACA 59.363 55.000 0.00 0.00 39.74 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1142 1217 0.980231 GAGGACAGATGCAGGAGGGT 60.980 60.000 0.00 0.0 0.00 4.34 R
1767 1939 1.741706 CTGGCGCTTGAATTGATCTGT 59.258 47.619 7.64 0.0 0.00 3.41 R
3219 8453 5.481615 ACCAAGGTAATGGGGTTCATAAT 57.518 39.130 0.00 0.0 45.18 1.28 R
3738 8975 0.174162 GCATGAAAGAGCGGGCAAAT 59.826 50.000 0.00 0.0 0.00 2.32 R
4324 9909 1.080569 CGGGCAAAGCAACATGGAC 60.081 57.895 0.00 0.0 0.00 4.02 R
5296 10924 0.737715 GCACTCTGGTAGAGCAACGG 60.738 60.000 5.78 0.0 46.12 4.44 R
6575 12292 1.153449 TAATCTCCCGTTGCGCCAG 60.153 57.895 4.18 0.0 0.00 4.85 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
58 59 2.060980 GTCTGGAGATGGAGCCCGT 61.061 63.158 0.00 0.00 0.00 5.28
63 64 1.122019 GGAGATGGAGCCCGTGGTAT 61.122 60.000 0.00 0.00 0.00 2.73
81 82 0.182061 ATTGCTCCGCTGTGATGGAT 59.818 50.000 0.00 0.00 32.83 3.41
246 247 4.607293 AAATACATCAGCCGCTCATCTA 57.393 40.909 0.00 0.00 0.00 1.98
263 264 6.920758 GCTCATCTATGAACTTAACTGTCGAT 59.079 38.462 0.00 0.00 36.18 3.59
322 342 5.399301 CGAAACTGAATTTTGCTGTCGAAAT 59.601 36.000 0.00 0.00 37.79 2.17
331 370 1.535028 TGCTGTCGAAATTGAACGCAT 59.465 42.857 0.00 0.00 0.00 4.73
618 668 7.015682 CACCCTGAACCATAAGATAGATAGTGT 59.984 40.741 0.00 0.00 0.00 3.55
681 739 1.153349 CTTAACTCTGGCGAGCCCC 60.153 63.158 12.05 0.00 41.09 5.80
699 757 1.304052 CCCCACCCGCTGAAAATCA 60.304 57.895 0.00 0.00 0.00 2.57
750 808 2.418368 ATGTAGCCAAATCGGAGCAA 57.582 45.000 0.00 0.00 36.56 3.91
859 917 0.824759 CTCCCTCGATCGGTTCCTTT 59.175 55.000 16.41 0.00 0.00 3.11
868 926 3.373565 GGTTCCTTTGCTGGCCGG 61.374 66.667 7.41 7.41 0.00 6.13
874 932 1.451927 CTTTGCTGGCCGGCAGATA 60.452 57.895 36.44 24.52 43.39 1.98
878 936 1.153168 GCTGGCCGGCAGATAAAGA 60.153 57.895 32.13 0.00 0.00 2.52
882 940 3.679389 CTGGCCGGCAGATAAAGATAAT 58.321 45.455 30.85 0.00 0.00 1.28
896 954 3.040147 AGATAATATTCCCACCACGCG 57.960 47.619 3.53 3.53 0.00 6.01
1142 1217 4.077184 CCACGAACCCTAGCCGCA 62.077 66.667 0.00 0.00 0.00 5.69
1535 1666 4.414956 AGGAGATGGGGGTCGCCA 62.415 66.667 9.19 9.19 40.15 5.69
1659 1804 1.078426 GCAGGGAATGTAGCGGTGT 60.078 57.895 0.00 0.00 0.00 4.16
1987 2167 7.333921 ACAATGATGACATGTTTGTTGTTGTTT 59.666 29.630 0.00 0.00 35.79 2.83
2329 2534 8.921353 ATGAAATGCTAATTCTATGAAGAGCT 57.079 30.769 14.06 0.00 31.96 4.09
2331 2536 9.836864 TGAAATGCTAATTCTATGAAGAGCTAA 57.163 29.630 14.06 1.53 31.96 3.09
2438 3706 0.605083 ACGTGCAGATCAGCTCTTCA 59.395 50.000 11.68 0.00 34.99 3.02
3011 8244 7.306574 GCATTGGAGCTAAAGTTTTGTTGTTAC 60.307 37.037 0.00 0.00 0.00 2.50
3080 8313 7.782897 TTCTCCTGGATGATTAAGACGATAT 57.217 36.000 0.00 0.00 0.00 1.63
3738 8975 3.053291 CCTGGCGGCGCAGTTTTA 61.053 61.111 34.36 10.79 0.00 1.52
4084 9666 3.569701 CCTGTGTATGTTCTGTTTTGCCT 59.430 43.478 0.00 0.00 0.00 4.75
4312 9897 3.625764 CACCTCCCCGTGTTTTATATGTG 59.374 47.826 0.00 0.00 0.00 3.21
4324 9909 6.968904 GTGTTTTATATGTGAGCAATCACCTG 59.031 38.462 5.97 0.00 39.72 4.00
4325 9910 6.658816 TGTTTTATATGTGAGCAATCACCTGT 59.341 34.615 5.97 0.00 39.72 4.00
4404 10026 8.086522 GCTACTGGATAACCGTTATTGATCTAA 58.913 37.037 5.26 0.00 39.42 2.10
4733 10356 8.523915 AAAATCCATAATATGAAGCTGTGTCA 57.476 30.769 1.10 0.00 0.00 3.58
4750 10373 2.825532 TGTCAGCTGCATCAGTACAGTA 59.174 45.455 9.47 0.00 36.26 2.74
4837 10460 0.636647 TGCAGAGGAGAGGGGATACA 59.363 55.000 0.00 0.00 39.74 2.29
4862 10485 2.045926 GCGGAGGTCAGGCATTGT 60.046 61.111 0.00 0.00 0.00 2.71
4937 10560 3.056328 GGCTCCTGTTTGGCGGTC 61.056 66.667 0.00 0.00 35.26 4.79
5296 10924 3.190118 ACTTTTGTCAGCTTCTAGCATGC 59.810 43.478 10.51 10.51 45.56 4.06
6124 11821 4.065789 GGTGCTGCCAGGATATTAAGTAC 58.934 47.826 0.00 0.00 37.17 2.73
6526 12237 3.940852 CCATATGTGCTTGCTCAACACTA 59.059 43.478 1.24 0.00 35.33 2.74
6575 12292 0.517316 GTGTGGGTCTGTTCGCAATC 59.483 55.000 0.00 0.00 32.43 2.67
6640 12360 3.689347 TGACATGGTCTTGAAATGGGAG 58.311 45.455 0.00 0.00 33.15 4.30
6860 12618 0.756903 GTCCCCTGCCGCTTCTTATA 59.243 55.000 0.00 0.00 0.00 0.98
6941 12699 5.524535 GCTATCCTAATACCTCCTGATCCT 58.475 45.833 0.00 0.00 0.00 3.24
6976 12736 7.007367 CGTATATGCACAACAAAGACATGTTTC 59.993 37.037 0.00 0.00 41.44 2.78
7304 13080 1.693083 CGCAACGGCCAACTAGTAGC 61.693 60.000 2.24 8.90 36.38 3.58
7305 13081 0.672401 GCAACGGCCAACTAGTAGCA 60.672 55.000 17.03 0.00 0.00 3.49
7306 13082 1.803334 CAACGGCCAACTAGTAGCAA 58.197 50.000 17.03 0.00 0.00 3.91
7307 13083 1.732259 CAACGGCCAACTAGTAGCAAG 59.268 52.381 17.03 12.95 0.00 4.01
7308 13084 1.263356 ACGGCCAACTAGTAGCAAGA 58.737 50.000 17.03 0.00 0.00 3.02
7309 13085 1.204941 ACGGCCAACTAGTAGCAAGAG 59.795 52.381 17.03 9.13 0.00 2.85
7310 13086 1.657822 GGCCAACTAGTAGCAAGAGC 58.342 55.000 17.03 4.26 42.56 4.09
7311 13087 1.066143 GGCCAACTAGTAGCAAGAGCA 60.066 52.381 17.03 0.00 45.49 4.26
7312 13088 2.275318 GCCAACTAGTAGCAAGAGCAG 58.725 52.381 11.85 0.00 45.49 4.24
7313 13089 2.093973 GCCAACTAGTAGCAAGAGCAGA 60.094 50.000 11.85 0.00 45.49 4.26
7314 13090 3.516615 CCAACTAGTAGCAAGAGCAGAC 58.483 50.000 0.00 0.00 45.49 3.51
7315 13091 3.516615 CAACTAGTAGCAAGAGCAGACC 58.483 50.000 0.00 0.00 45.49 3.85
7316 13092 2.808919 ACTAGTAGCAAGAGCAGACCA 58.191 47.619 0.00 0.00 45.49 4.02
7317 13093 2.757868 ACTAGTAGCAAGAGCAGACCAG 59.242 50.000 0.00 0.00 45.49 4.00
7318 13094 0.901124 AGTAGCAAGAGCAGACCAGG 59.099 55.000 0.00 0.00 45.49 4.45
7319 13095 0.742635 GTAGCAAGAGCAGACCAGGC 60.743 60.000 0.00 0.00 45.49 4.85
7320 13096 1.194121 TAGCAAGAGCAGACCAGGCA 61.194 55.000 0.00 0.00 45.49 4.75
7321 13097 2.039405 GCAAGAGCAGACCAGGCAG 61.039 63.158 0.00 0.00 41.58 4.85
7322 13098 1.376942 CAAGAGCAGACCAGGCAGG 60.377 63.158 0.00 0.00 45.67 4.85
7323 13099 2.600729 AAGAGCAGACCAGGCAGGG 61.601 63.158 0.00 0.00 43.89 4.45
7324 13100 4.106925 GAGCAGACCAGGCAGGGG 62.107 72.222 0.00 0.00 43.89 4.79
7325 13101 4.664267 AGCAGACCAGGCAGGGGA 62.664 66.667 0.00 0.00 43.89 4.81
7326 13102 4.416738 GCAGACCAGGCAGGGGAC 62.417 72.222 0.00 0.00 43.89 4.46
7338 13114 2.896443 GGGGACCGAGAGCAAGAG 59.104 66.667 0.00 0.00 40.86 2.85
7339 13115 1.985116 GGGGACCGAGAGCAAGAGT 60.985 63.158 0.00 0.00 40.86 3.24
7340 13116 0.683504 GGGGACCGAGAGCAAGAGTA 60.684 60.000 0.00 0.00 40.86 2.59
7341 13117 0.741915 GGGACCGAGAGCAAGAGTAG 59.258 60.000 0.00 0.00 0.00 2.57
7342 13118 1.682394 GGGACCGAGAGCAAGAGTAGA 60.682 57.143 0.00 0.00 0.00 2.59
7343 13119 1.673920 GGACCGAGAGCAAGAGTAGAG 59.326 57.143 0.00 0.00 0.00 2.43
7344 13120 1.064952 GACCGAGAGCAAGAGTAGAGC 59.935 57.143 0.00 0.00 0.00 4.09
7345 13121 1.098869 CCGAGAGCAAGAGTAGAGCA 58.901 55.000 0.00 0.00 0.00 4.26
7346 13122 1.065401 CCGAGAGCAAGAGTAGAGCAG 59.935 57.143 0.00 0.00 0.00 4.24
7347 13123 1.533756 CGAGAGCAAGAGTAGAGCAGC 60.534 57.143 0.00 0.00 0.00 5.25
7348 13124 1.476085 GAGAGCAAGAGTAGAGCAGCA 59.524 52.381 0.00 0.00 0.00 4.41
7349 13125 1.477700 AGAGCAAGAGTAGAGCAGCAG 59.522 52.381 0.00 0.00 0.00 4.24
7350 13126 1.476085 GAGCAAGAGTAGAGCAGCAGA 59.524 52.381 0.00 0.00 0.00 4.26
7351 13127 1.477700 AGCAAGAGTAGAGCAGCAGAG 59.522 52.381 0.00 0.00 0.00 3.35
7352 13128 1.925229 CAAGAGTAGAGCAGCAGAGC 58.075 55.000 0.00 0.00 0.00 4.09
7353 13129 0.455410 AAGAGTAGAGCAGCAGAGCG 59.545 55.000 0.00 0.00 40.15 5.03
7354 13130 0.393673 AGAGTAGAGCAGCAGAGCGA 60.394 55.000 0.00 0.00 40.15 4.93
7355 13131 0.029300 GAGTAGAGCAGCAGAGCGAG 59.971 60.000 0.00 0.00 40.15 5.03
7356 13132 0.679640 AGTAGAGCAGCAGAGCGAGT 60.680 55.000 0.00 0.00 40.15 4.18
7357 13133 0.525242 GTAGAGCAGCAGAGCGAGTG 60.525 60.000 0.00 0.00 40.15 3.51
7358 13134 0.678048 TAGAGCAGCAGAGCGAGTGA 60.678 55.000 0.00 0.00 40.15 3.41
7359 13135 1.516821 GAGCAGCAGAGCGAGTGAG 60.517 63.158 0.00 0.00 40.15 3.51
7360 13136 1.932011 GAGCAGCAGAGCGAGTGAGA 61.932 60.000 0.00 0.00 40.15 3.27
7361 13137 1.516821 GCAGCAGAGCGAGTGAGAG 60.517 63.158 0.00 0.00 0.00 3.20
7362 13138 1.516821 CAGCAGAGCGAGTGAGAGC 60.517 63.158 0.00 0.00 0.00 4.09
7364 13140 0.393673 AGCAGAGCGAGTGAGAGCTA 60.394 55.000 0.00 0.00 44.69 3.32
7365 13141 0.453793 GCAGAGCGAGTGAGAGCTAA 59.546 55.000 0.00 0.00 44.69 3.09
7366 13142 1.135257 GCAGAGCGAGTGAGAGCTAAA 60.135 52.381 0.00 0.00 44.69 1.85
7367 13143 2.796304 CAGAGCGAGTGAGAGCTAAAG 58.204 52.381 0.00 0.00 44.69 1.85
7368 13144 1.134175 AGAGCGAGTGAGAGCTAAAGC 59.866 52.381 0.00 0.00 44.69 3.51
7369 13145 0.891373 AGCGAGTGAGAGCTAAAGCA 59.109 50.000 4.54 0.00 42.60 3.91
7370 13146 1.273606 AGCGAGTGAGAGCTAAAGCAA 59.726 47.619 4.54 0.00 42.60 3.91
7371 13147 1.391826 GCGAGTGAGAGCTAAAGCAAC 59.608 52.381 4.54 0.00 45.16 4.17
7372 13148 2.677199 CGAGTGAGAGCTAAAGCAACA 58.323 47.619 4.54 0.00 45.16 3.33
7373 13149 2.665537 CGAGTGAGAGCTAAAGCAACAG 59.334 50.000 4.54 0.00 45.16 3.16
7374 13150 2.414825 GAGTGAGAGCTAAAGCAACAGC 59.585 50.000 4.54 0.00 45.16 4.40
7375 13151 2.146342 GTGAGAGCTAAAGCAACAGCA 58.854 47.619 4.54 0.00 45.16 4.41
7376 13152 2.159234 GTGAGAGCTAAAGCAACAGCAG 59.841 50.000 4.54 0.00 45.16 4.24
7377 13153 1.130186 GAGAGCTAAAGCAACAGCAGC 59.870 52.381 4.54 0.00 45.16 5.25
7378 13154 1.163554 GAGCTAAAGCAACAGCAGCT 58.836 50.000 4.54 0.00 44.95 4.24
7379 13155 1.163554 AGCTAAAGCAACAGCAGCTC 58.836 50.000 4.54 0.00 42.53 4.09
7380 13156 0.169894 GCTAAAGCAACAGCAGCTCC 59.830 55.000 0.00 0.00 42.53 4.70
7381 13157 1.818642 CTAAAGCAACAGCAGCTCCT 58.181 50.000 0.00 0.00 42.53 3.69
7382 13158 2.936993 GCTAAAGCAACAGCAGCTCCTA 60.937 50.000 0.00 0.00 42.53 2.94
7383 13159 2.276732 AAAGCAACAGCAGCTCCTAA 57.723 45.000 0.00 0.00 42.53 2.69
7384 13160 2.503895 AAGCAACAGCAGCTCCTAAT 57.496 45.000 0.00 0.00 42.53 1.73
7385 13161 1.747709 AGCAACAGCAGCTCCTAATG 58.252 50.000 0.00 0.00 38.01 1.90
7386 13162 1.280133 AGCAACAGCAGCTCCTAATGA 59.720 47.619 0.00 0.00 38.01 2.57
7387 13163 1.669779 GCAACAGCAGCTCCTAATGAG 59.330 52.381 0.00 0.00 44.47 2.90
7388 13164 2.286872 CAACAGCAGCTCCTAATGAGG 58.713 52.381 0.00 0.00 45.35 3.86
7396 13172 3.118905 GCTCCTAATGAGGTGGATGTC 57.881 52.381 0.00 0.00 44.19 3.06
7397 13173 2.546795 GCTCCTAATGAGGTGGATGTCG 60.547 54.545 0.00 0.00 44.19 4.35
7398 13174 1.412710 TCCTAATGAGGTGGATGTCGC 59.587 52.381 0.00 0.00 44.19 5.19
7399 13175 1.541233 CCTAATGAGGTGGATGTCGCC 60.541 57.143 0.00 0.00 46.19 5.54
7419 13195 4.813526 CGAGGGAGCGACGTCGTG 62.814 72.222 35.48 12.84 42.03 4.35
7420 13196 4.477975 GAGGGAGCGACGTCGTGG 62.478 72.222 35.48 12.08 42.22 4.94
7422 13198 4.477975 GGGAGCGACGTCGTGGAG 62.478 72.222 35.48 11.31 42.22 3.86
7423 13199 4.477975 GGAGCGACGTCGTGGAGG 62.478 72.222 35.48 10.56 42.22 4.30
7424 13200 3.429141 GAGCGACGTCGTGGAGGA 61.429 66.667 35.48 0.00 42.22 3.71
7425 13201 2.974489 GAGCGACGTCGTGGAGGAA 61.974 63.158 35.48 0.00 42.22 3.36
7426 13202 2.504244 GCGACGTCGTGGAGGAAG 60.504 66.667 35.48 8.32 42.22 3.46
7427 13203 2.952245 CGACGTCGTGGAGGAAGT 59.048 61.111 29.08 0.00 34.11 3.01
7428 13204 1.442184 CGACGTCGTGGAGGAAGTG 60.442 63.158 29.08 0.00 34.11 3.16
7429 13205 1.080705 GACGTCGTGGAGGAAGTGG 60.081 63.158 0.63 0.00 0.00 4.00
7430 13206 2.432628 CGTCGTGGAGGAAGTGGC 60.433 66.667 0.00 0.00 0.00 5.01
7431 13207 2.047179 GTCGTGGAGGAAGTGGCC 60.047 66.667 0.00 0.00 0.00 5.36
7432 13208 3.691342 TCGTGGAGGAAGTGGCCG 61.691 66.667 0.00 0.00 0.00 6.13
7433 13209 4.760047 CGTGGAGGAAGTGGCCGG 62.760 72.222 0.00 0.00 0.00 6.13
7480 13256 2.809010 GTCGGCTCAGGACCTAGC 59.191 66.667 12.16 12.16 38.03 3.42
7481 13257 2.829003 TCGGCTCAGGACCTAGCG 60.829 66.667 13.49 10.35 39.71 4.26
7482 13258 4.577246 CGGCTCAGGACCTAGCGC 62.577 72.222 0.00 0.00 39.71 5.92
7483 13259 4.228567 GGCTCAGGACCTAGCGCC 62.229 72.222 2.29 10.95 39.71 6.53
7484 13260 4.577246 GCTCAGGACCTAGCGCCG 62.577 72.222 2.29 0.00 0.00 6.46
7485 13261 3.905678 CTCAGGACCTAGCGCCGG 61.906 72.222 2.29 7.98 0.00 6.13
7490 13266 4.752879 GACCTAGCGCCGGCAACA 62.753 66.667 28.98 9.11 43.41 3.33
7501 13277 3.474806 GGCAACACCGTGAGATCG 58.525 61.111 5.28 0.00 0.00 3.69
7502 13278 1.080093 GGCAACACCGTGAGATCGA 60.080 57.895 5.28 0.00 0.00 3.59
7503 13279 0.669318 GGCAACACCGTGAGATCGAA 60.669 55.000 5.28 0.00 0.00 3.71
7504 13280 1.359848 GCAACACCGTGAGATCGAAT 58.640 50.000 5.28 0.00 0.00 3.34
7505 13281 1.324736 GCAACACCGTGAGATCGAATC 59.675 52.381 5.28 0.00 0.00 2.52
7506 13282 2.606108 CAACACCGTGAGATCGAATCA 58.394 47.619 5.28 0.00 0.00 2.57
7507 13283 2.993220 CAACACCGTGAGATCGAATCAA 59.007 45.455 5.28 0.00 0.00 2.57
7508 13284 2.881074 ACACCGTGAGATCGAATCAAG 58.119 47.619 5.28 7.44 0.00 3.02
7509 13285 2.492088 ACACCGTGAGATCGAATCAAGA 59.508 45.455 15.26 0.00 0.00 3.02
7510 13286 3.056821 ACACCGTGAGATCGAATCAAGAA 60.057 43.478 15.26 0.00 0.00 2.52
7511 13287 3.549471 CACCGTGAGATCGAATCAAGAAG 59.451 47.826 15.26 6.43 0.00 2.85
7512 13288 3.444034 ACCGTGAGATCGAATCAAGAAGA 59.556 43.478 15.26 0.00 0.00 2.87
7513 13289 4.082190 ACCGTGAGATCGAATCAAGAAGAA 60.082 41.667 15.26 0.00 0.00 2.52
7514 13290 4.864806 CCGTGAGATCGAATCAAGAAGAAA 59.135 41.667 15.26 0.00 0.00 2.52
7515 13291 5.348724 CCGTGAGATCGAATCAAGAAGAAAA 59.651 40.000 15.26 0.00 0.00 2.29
7516 13292 6.036517 CCGTGAGATCGAATCAAGAAGAAAAT 59.963 38.462 15.26 0.00 0.00 1.82
7517 13293 6.898716 CGTGAGATCGAATCAAGAAGAAAATG 59.101 38.462 10.14 0.00 0.00 2.32
7518 13294 6.686253 GTGAGATCGAATCAAGAAGAAAATGC 59.314 38.462 5.36 0.00 0.00 3.56
7519 13295 5.804173 AGATCGAATCAAGAAGAAAATGCG 58.196 37.500 0.00 0.00 0.00 4.73
7520 13296 4.340894 TCGAATCAAGAAGAAAATGCGG 57.659 40.909 0.00 0.00 0.00 5.69
7521 13297 2.848302 CGAATCAAGAAGAAAATGCGGC 59.152 45.455 0.00 0.00 0.00 6.53
7522 13298 2.549633 ATCAAGAAGAAAATGCGGCG 57.450 45.000 0.51 0.51 0.00 6.46
7523 13299 1.518325 TCAAGAAGAAAATGCGGCGA 58.482 45.000 12.98 0.00 0.00 5.54
7524 13300 2.083774 TCAAGAAGAAAATGCGGCGAT 58.916 42.857 12.98 0.00 0.00 4.58
7525 13301 2.487762 TCAAGAAGAAAATGCGGCGATT 59.512 40.909 12.98 4.80 0.00 3.34
7526 13302 3.687212 TCAAGAAGAAAATGCGGCGATTA 59.313 39.130 12.98 0.00 0.00 1.75
7527 13303 3.951979 AGAAGAAAATGCGGCGATTAG 57.048 42.857 12.98 0.00 0.00 1.73
7528 13304 3.270877 AGAAGAAAATGCGGCGATTAGT 58.729 40.909 12.98 0.00 0.00 2.24
7529 13305 3.063997 AGAAGAAAATGCGGCGATTAGTG 59.936 43.478 12.98 0.00 0.00 2.74
7530 13306 2.356135 AGAAAATGCGGCGATTAGTGT 58.644 42.857 12.98 0.00 0.00 3.55
7531 13307 3.527533 AGAAAATGCGGCGATTAGTGTA 58.472 40.909 12.98 0.00 0.00 2.90
7532 13308 3.308866 AGAAAATGCGGCGATTAGTGTAC 59.691 43.478 12.98 0.00 0.00 2.90
7533 13309 2.303163 AATGCGGCGATTAGTGTACA 57.697 45.000 12.98 0.00 0.00 2.90
7534 13310 2.303163 ATGCGGCGATTAGTGTACAA 57.697 45.000 12.98 0.00 0.00 2.41
7535 13311 1.352114 TGCGGCGATTAGTGTACAAC 58.648 50.000 12.98 0.00 0.00 3.32
7536 13312 0.648958 GCGGCGATTAGTGTACAACC 59.351 55.000 12.98 0.00 0.00 3.77
7537 13313 1.738030 GCGGCGATTAGTGTACAACCT 60.738 52.381 12.98 0.00 0.00 3.50
7538 13314 2.190981 CGGCGATTAGTGTACAACCTC 58.809 52.381 0.00 0.00 0.00 3.85
7539 13315 2.159282 CGGCGATTAGTGTACAACCTCT 60.159 50.000 0.00 0.00 0.00 3.69
7540 13316 3.675228 CGGCGATTAGTGTACAACCTCTT 60.675 47.826 0.00 0.00 0.00 2.85
7541 13317 4.251268 GGCGATTAGTGTACAACCTCTTT 58.749 43.478 0.00 0.00 0.00 2.52
7542 13318 4.092968 GGCGATTAGTGTACAACCTCTTTG 59.907 45.833 0.00 0.00 41.49 2.77
7543 13319 4.435651 GCGATTAGTGTACAACCTCTTTGC 60.436 45.833 0.00 0.00 39.01 3.68
7544 13320 4.929808 CGATTAGTGTACAACCTCTTTGCT 59.070 41.667 0.00 0.00 39.01 3.91
7545 13321 5.163953 CGATTAGTGTACAACCTCTTTGCTG 60.164 44.000 0.00 0.00 39.01 4.41
7546 13322 2.851195 AGTGTACAACCTCTTTGCTGG 58.149 47.619 0.00 0.00 39.01 4.85
7547 13323 1.266989 GTGTACAACCTCTTTGCTGGC 59.733 52.381 0.00 0.00 39.01 4.85
7548 13324 0.517316 GTACAACCTCTTTGCTGGCG 59.483 55.000 0.00 0.00 39.01 5.69
7549 13325 1.234615 TACAACCTCTTTGCTGGCGC 61.235 55.000 0.00 0.00 39.01 6.53
7550 13326 2.985847 AACCTCTTTGCTGGCGCC 60.986 61.111 22.73 22.73 34.43 6.53
7553 13329 2.821366 CTCTTTGCTGGCGCCGAT 60.821 61.111 23.90 0.00 34.43 4.18
7554 13330 2.359850 TCTTTGCTGGCGCCGATT 60.360 55.556 23.90 0.00 34.43 3.34
7555 13331 1.078778 TCTTTGCTGGCGCCGATTA 60.079 52.632 23.90 2.23 34.43 1.75
7556 13332 1.089481 TCTTTGCTGGCGCCGATTAG 61.089 55.000 23.90 14.94 34.43 1.73
7557 13333 2.051804 CTTTGCTGGCGCCGATTAGG 62.052 60.000 23.90 6.90 44.97 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 0.878523 CTGCTCCAACGACGAAACCA 60.879 55.000 0.00 0.00 0.00 3.67
263 264 9.872757 GTTCAGTTTCGACAGTTAAATTCAATA 57.127 29.630 0.00 0.00 0.00 1.90
265 266 7.981142 AGTTCAGTTTCGACAGTTAAATTCAA 58.019 30.769 0.00 0.00 0.00 2.69
322 342 5.616866 GCTTTTCTGCTACTAATGCGTTCAA 60.617 40.000 0.00 0.00 0.00 2.69
331 370 5.147330 TGCTACTGCTTTTCTGCTACTAA 57.853 39.130 0.00 0.00 40.48 2.24
397 436 0.879765 CCGGTAGTGTCAGTCGACTT 59.120 55.000 17.26 3.27 43.06 3.01
603 653 8.896658 AGAGAGGTACCACACTATCTATCTTAT 58.103 37.037 15.94 0.00 33.85 1.73
681 739 0.897863 TTGATTTTCAGCGGGTGGGG 60.898 55.000 7.42 0.00 0.00 4.96
689 747 4.320608 TTTGGGTCAGTTGATTTTCAGC 57.679 40.909 0.00 0.00 0.00 4.26
699 757 5.374071 ACTAAATCGACTTTTGGGTCAGTT 58.626 37.500 0.00 0.00 36.12 3.16
731 789 2.017049 GTTGCTCCGATTTGGCTACAT 58.983 47.619 0.00 0.00 37.80 2.29
750 808 1.205655 TCTTGCTCTTGCTAGCGATGT 59.794 47.619 10.77 0.00 45.85 3.06
757 815 1.133982 CTCTCGCTCTTGCTCTTGCTA 59.866 52.381 0.00 0.00 40.48 3.49
780 838 4.669842 TGCTCTTGCTCGCGCTGT 62.670 61.111 5.56 0.00 40.48 4.40
859 917 1.451927 CTTTATCTGCCGGCCAGCA 60.452 57.895 26.77 14.24 41.50 4.41
868 926 7.148407 CGTGGTGGGAATATTATCTTTATCTGC 60.148 40.741 0.00 0.00 0.00 4.26
874 932 3.813166 CGCGTGGTGGGAATATTATCTTT 59.187 43.478 0.00 0.00 0.00 2.52
878 936 2.367567 AGACGCGTGGTGGGAATATTAT 59.632 45.455 20.70 0.00 0.00 1.28
882 940 1.514087 GAGACGCGTGGTGGGAATA 59.486 57.895 20.70 0.00 0.00 1.75
975 1033 0.891373 ACATGACAGACTCCACCGAG 59.109 55.000 0.00 0.00 42.32 4.63
983 1041 2.092753 CCCAGCCAATACATGACAGACT 60.093 50.000 0.00 0.00 0.00 3.24
987 1045 2.040947 TGAACCCAGCCAATACATGACA 59.959 45.455 0.00 0.00 0.00 3.58
1142 1217 0.980231 GAGGACAGATGCAGGAGGGT 60.980 60.000 0.00 0.00 0.00 4.34
1535 1666 2.435586 GTGCGGCTGTGCTCATCT 60.436 61.111 0.00 0.00 35.36 2.90
1651 1796 2.656069 GGAGAGGCCAACACCGCTA 61.656 63.158 5.01 0.00 40.28 4.26
1659 1804 2.041265 GGGGAGAGGAGAGGCCAA 59.959 66.667 5.01 0.00 40.02 4.52
1767 1939 1.741706 CTGGCGCTTGAATTGATCTGT 59.258 47.619 7.64 0.00 0.00 3.41
2320 2525 9.624373 ATCATGTACTTTCAATTAGCTCTTCAT 57.376 29.630 0.00 0.00 0.00 2.57
2321 2526 8.886719 CATCATGTACTTTCAATTAGCTCTTCA 58.113 33.333 0.00 0.00 0.00 3.02
2323 2528 8.798859 ACATCATGTACTTTCAATTAGCTCTT 57.201 30.769 0.00 0.00 0.00 2.85
2324 2529 8.043113 TGACATCATGTACTTTCAATTAGCTCT 58.957 33.333 0.00 0.00 0.00 4.09
2325 2530 8.119226 GTGACATCATGTACTTTCAATTAGCTC 58.881 37.037 0.00 0.00 0.00 4.09
2326 2531 7.066284 GGTGACATCATGTACTTTCAATTAGCT 59.934 37.037 0.00 0.00 0.00 3.32
2327 2532 7.148255 TGGTGACATCATGTACTTTCAATTAGC 60.148 37.037 0.00 0.00 33.40 3.09
2328 2533 8.177663 GTGGTGACATCATGTACTTTCAATTAG 58.822 37.037 0.00 0.00 46.14 1.73
2329 2534 7.148490 CGTGGTGACATCATGTACTTTCAATTA 60.148 37.037 0.00 0.00 46.14 1.40
2330 2535 6.348458 CGTGGTGACATCATGTACTTTCAATT 60.348 38.462 0.00 0.00 46.14 2.32
2331 2536 5.122239 CGTGGTGACATCATGTACTTTCAAT 59.878 40.000 0.00 0.00 46.14 2.57
2332 2537 4.450757 CGTGGTGACATCATGTACTTTCAA 59.549 41.667 0.00 0.00 46.14 2.69
2438 3706 3.441572 AGCAACATAGCGCTTGAAAGAAT 59.558 39.130 18.68 0.00 40.15 2.40
3219 8453 5.481615 ACCAAGGTAATGGGGTTCATAAT 57.518 39.130 0.00 0.00 45.18 1.28
3689 8925 6.780457 AATTGGGATCACAAAAGACATAGG 57.220 37.500 15.71 0.00 33.48 2.57
3738 8975 0.174162 GCATGAAAGAGCGGGCAAAT 59.826 50.000 0.00 0.00 0.00 2.32
3912 9149 4.260784 GCAACATGATTTACATCGTCCCTC 60.261 45.833 0.00 0.00 37.07 4.30
4084 9666 7.201835 TGACATGAAGTGTACACGTTTAACTA 58.798 34.615 19.93 3.44 42.36 2.24
4312 9897 2.119801 ACATGGACAGGTGATTGCTC 57.880 50.000 0.00 0.00 0.00 4.26
4324 9909 1.080569 CGGGCAAAGCAACATGGAC 60.081 57.895 0.00 0.00 0.00 4.02
4325 9910 1.228398 TCGGGCAAAGCAACATGGA 60.228 52.632 0.00 0.00 0.00 3.41
4404 10026 7.724061 ACCTGTAGTGTTATGATTCCTTTTTGT 59.276 33.333 0.00 0.00 0.00 2.83
4645 10268 8.925161 TCATCAAAGGAAACAGTTTAAACTTG 57.075 30.769 18.25 15.15 37.08 3.16
4733 10356 4.319139 CATCTACTGTACTGATGCAGCT 57.681 45.455 2.53 0.00 41.96 4.24
4782 10405 8.376270 TCTCTCCTCGATCTCAACTAATACATA 58.624 37.037 0.00 0.00 0.00 2.29
4837 10460 4.974438 TGACCTCCGCCCACCCTT 62.974 66.667 0.00 0.00 0.00 3.95
4862 10485 2.483877 CACTCTGCCGCAAATCTGTTAA 59.516 45.455 0.00 0.00 0.00 2.01
4937 10560 2.680913 CGGCACCCTTCTCTTTGCG 61.681 63.158 0.00 0.00 35.74 4.85
5296 10924 0.737715 GCACTCTGGTAGAGCAACGG 60.738 60.000 5.78 0.00 46.12 4.44
5710 11372 5.684704 TGGCTATTGCTATAGAAAAGCTGT 58.315 37.500 17.84 0.05 40.73 4.40
6124 11821 7.526608 ACGTGGTTTATACAACTTCATGAATG 58.473 34.615 8.96 8.04 0.00 2.67
6549 12260 1.274167 GAACAGACCCACACCATACGA 59.726 52.381 0.00 0.00 0.00 3.43
6575 12292 1.153449 TAATCTCCCGTTGCGCCAG 60.153 57.895 4.18 0.00 0.00 4.85
6941 12699 9.203421 CTTTGTTGTGCATATACGGAGATATAA 57.797 33.333 0.00 0.00 0.00 0.98
7293 13068 3.516615 GTCTGCTCTTGCTACTAGTTGG 58.483 50.000 0.00 0.00 40.48 3.77
7304 13080 1.376942 CCTGCCTGGTCTGCTCTTG 60.377 63.158 0.00 0.00 0.00 3.02
7305 13081 2.600729 CCCTGCCTGGTCTGCTCTT 61.601 63.158 0.00 0.00 0.00 2.85
7306 13082 3.007920 CCCTGCCTGGTCTGCTCT 61.008 66.667 0.00 0.00 0.00 4.09
7307 13083 4.106925 CCCCTGCCTGGTCTGCTC 62.107 72.222 0.00 0.00 0.00 4.26
7308 13084 4.664267 TCCCCTGCCTGGTCTGCT 62.664 66.667 0.00 0.00 0.00 4.24
7309 13085 4.416738 GTCCCCTGCCTGGTCTGC 62.417 72.222 0.00 0.00 0.00 4.26
7310 13086 3.721706 GGTCCCCTGCCTGGTCTG 61.722 72.222 0.00 0.00 0.00 3.51
7315 13091 3.465403 CTCTCGGTCCCCTGCCTG 61.465 72.222 0.00 0.00 0.00 4.85
7318 13094 3.672295 CTTGCTCTCGGTCCCCTGC 62.672 68.421 0.00 0.00 0.00 4.85
7319 13095 1.954362 CTCTTGCTCTCGGTCCCCTG 61.954 65.000 0.00 0.00 0.00 4.45
7320 13096 1.684049 CTCTTGCTCTCGGTCCCCT 60.684 63.158 0.00 0.00 0.00 4.79
7321 13097 0.683504 TACTCTTGCTCTCGGTCCCC 60.684 60.000 0.00 0.00 0.00 4.81
7322 13098 0.741915 CTACTCTTGCTCTCGGTCCC 59.258 60.000 0.00 0.00 0.00 4.46
7323 13099 1.673920 CTCTACTCTTGCTCTCGGTCC 59.326 57.143 0.00 0.00 0.00 4.46
7324 13100 1.064952 GCTCTACTCTTGCTCTCGGTC 59.935 57.143 0.00 0.00 0.00 4.79
7325 13101 1.099689 GCTCTACTCTTGCTCTCGGT 58.900 55.000 0.00 0.00 0.00 4.69
7326 13102 1.065401 CTGCTCTACTCTTGCTCTCGG 59.935 57.143 0.00 0.00 0.00 4.63
7327 13103 1.533756 GCTGCTCTACTCTTGCTCTCG 60.534 57.143 0.00 0.00 0.00 4.04
7328 13104 1.476085 TGCTGCTCTACTCTTGCTCTC 59.524 52.381 0.00 0.00 0.00 3.20
7329 13105 1.477700 CTGCTGCTCTACTCTTGCTCT 59.522 52.381 0.00 0.00 0.00 4.09
7330 13106 1.476085 TCTGCTGCTCTACTCTTGCTC 59.524 52.381 0.00 0.00 0.00 4.26
7331 13107 1.477700 CTCTGCTGCTCTACTCTTGCT 59.522 52.381 0.00 0.00 0.00 3.91
7332 13108 1.925229 CTCTGCTGCTCTACTCTTGC 58.075 55.000 0.00 0.00 0.00 4.01
7333 13109 1.798446 CGCTCTGCTGCTCTACTCTTG 60.798 57.143 0.00 0.00 0.00 3.02
7334 13110 0.455410 CGCTCTGCTGCTCTACTCTT 59.545 55.000 0.00 0.00 0.00 2.85
7335 13111 0.393673 TCGCTCTGCTGCTCTACTCT 60.394 55.000 0.00 0.00 0.00 3.24
7336 13112 0.029300 CTCGCTCTGCTGCTCTACTC 59.971 60.000 0.00 0.00 0.00 2.59
7337 13113 0.679640 ACTCGCTCTGCTGCTCTACT 60.680 55.000 0.00 0.00 0.00 2.57
7338 13114 0.525242 CACTCGCTCTGCTGCTCTAC 60.525 60.000 0.00 0.00 0.00 2.59
7339 13115 0.678048 TCACTCGCTCTGCTGCTCTA 60.678 55.000 0.00 0.00 0.00 2.43
7340 13116 1.936436 CTCACTCGCTCTGCTGCTCT 61.936 60.000 0.00 0.00 0.00 4.09
7341 13117 1.516821 CTCACTCGCTCTGCTGCTC 60.517 63.158 0.00 0.00 0.00 4.26
7342 13118 1.936436 CTCTCACTCGCTCTGCTGCT 61.936 60.000 0.00 0.00 0.00 4.24
7343 13119 1.516821 CTCTCACTCGCTCTGCTGC 60.517 63.158 0.00 0.00 0.00 5.25
7344 13120 1.516821 GCTCTCACTCGCTCTGCTG 60.517 63.158 0.00 0.00 0.00 4.41
7345 13121 0.393673 TAGCTCTCACTCGCTCTGCT 60.394 55.000 0.00 0.00 37.68 4.24
7346 13122 0.453793 TTAGCTCTCACTCGCTCTGC 59.546 55.000 0.00 0.00 37.68 4.26
7347 13123 2.796304 CTTTAGCTCTCACTCGCTCTG 58.204 52.381 0.00 0.00 37.68 3.35
7348 13124 1.134175 GCTTTAGCTCTCACTCGCTCT 59.866 52.381 0.00 0.00 37.68 4.09
7349 13125 1.135257 TGCTTTAGCTCTCACTCGCTC 60.135 52.381 3.10 0.00 42.66 5.03
7350 13126 0.891373 TGCTTTAGCTCTCACTCGCT 59.109 50.000 3.10 0.00 42.66 4.93
7351 13127 1.391826 GTTGCTTTAGCTCTCACTCGC 59.608 52.381 3.10 0.00 42.66 5.03
7352 13128 2.665537 CTGTTGCTTTAGCTCTCACTCG 59.334 50.000 3.10 0.00 42.66 4.18
7353 13129 2.414825 GCTGTTGCTTTAGCTCTCACTC 59.585 50.000 3.10 0.00 42.66 3.51
7354 13130 2.224378 TGCTGTTGCTTTAGCTCTCACT 60.224 45.455 3.10 0.00 42.66 3.41
7355 13131 2.146342 TGCTGTTGCTTTAGCTCTCAC 58.854 47.619 3.10 0.00 42.66 3.51
7356 13132 2.420642 CTGCTGTTGCTTTAGCTCTCA 58.579 47.619 3.10 0.00 42.66 3.27
7357 13133 1.130186 GCTGCTGTTGCTTTAGCTCTC 59.870 52.381 3.10 0.00 42.66 3.20
7358 13134 1.163554 GCTGCTGTTGCTTTAGCTCT 58.836 50.000 3.10 0.00 42.66 4.09
7359 13135 1.163554 AGCTGCTGTTGCTTTAGCTC 58.836 50.000 0.00 0.00 40.56 4.09
7360 13136 1.163554 GAGCTGCTGTTGCTTTAGCT 58.836 50.000 7.01 0.00 45.02 3.32
7361 13137 0.169894 GGAGCTGCTGTTGCTTTAGC 59.830 55.000 7.01 0.00 41.30 3.09
7362 13138 1.818642 AGGAGCTGCTGTTGCTTTAG 58.181 50.000 7.07 0.00 41.30 1.85
7363 13139 3.417069 TTAGGAGCTGCTGTTGCTTTA 57.583 42.857 19.25 0.00 41.30 1.85
7364 13140 2.276732 TTAGGAGCTGCTGTTGCTTT 57.723 45.000 19.25 0.00 41.30 3.51
7365 13141 2.089980 CATTAGGAGCTGCTGTTGCTT 58.910 47.619 19.25 0.00 41.30 3.91
7366 13142 1.280133 TCATTAGGAGCTGCTGTTGCT 59.720 47.619 19.25 6.70 44.24 3.91
7367 13143 1.669779 CTCATTAGGAGCTGCTGTTGC 59.330 52.381 19.25 0.00 36.69 4.17
7380 13156 1.869754 CGGCGACATCCACCTCATTAG 60.870 57.143 0.00 0.00 0.00 1.73
7381 13157 0.104120 CGGCGACATCCACCTCATTA 59.896 55.000 0.00 0.00 0.00 1.90
7382 13158 1.153369 CGGCGACATCCACCTCATT 60.153 57.895 0.00 0.00 0.00 2.57
7383 13159 2.501128 CGGCGACATCCACCTCAT 59.499 61.111 0.00 0.00 0.00 2.90
7384 13160 4.451150 GCGGCGACATCCACCTCA 62.451 66.667 12.98 0.00 0.00 3.86
7402 13178 4.813526 CACGACGTCGCTCCCTCG 62.814 72.222 35.92 12.70 44.43 4.63
7403 13179 4.477975 CCACGACGTCGCTCCCTC 62.478 72.222 35.92 0.00 44.43 4.30
7405 13181 4.477975 CTCCACGACGTCGCTCCC 62.478 72.222 35.92 0.00 44.43 4.30
7406 13182 4.477975 CCTCCACGACGTCGCTCC 62.478 72.222 35.92 0.00 44.43 4.70
7407 13183 2.852431 CTTCCTCCACGACGTCGCTC 62.852 65.000 35.92 0.00 44.43 5.03
7408 13184 2.979197 CTTCCTCCACGACGTCGCT 61.979 63.158 35.92 20.88 44.43 4.93
7409 13185 2.504244 CTTCCTCCACGACGTCGC 60.504 66.667 35.92 0.00 44.43 5.19
7410 13186 1.442184 CACTTCCTCCACGACGTCG 60.442 63.158 34.58 34.58 46.33 5.12
7411 13187 1.080705 CCACTTCCTCCACGACGTC 60.081 63.158 5.18 5.18 0.00 4.34
7412 13188 3.048602 CCACTTCCTCCACGACGT 58.951 61.111 0.00 0.00 0.00 4.34
7413 13189 2.432628 GCCACTTCCTCCACGACG 60.433 66.667 0.00 0.00 0.00 5.12
7414 13190 2.047179 GGCCACTTCCTCCACGAC 60.047 66.667 0.00 0.00 0.00 4.34
7415 13191 3.691342 CGGCCACTTCCTCCACGA 61.691 66.667 2.24 0.00 0.00 4.35
7416 13192 4.760047 CCGGCCACTTCCTCCACG 62.760 72.222 2.24 0.00 0.00 4.94
7459 13235 3.775654 GGTCCTGAGCCGACCTGG 61.776 72.222 1.23 0.00 45.41 4.45
7463 13239 2.809010 GCTAGGTCCTGAGCCGAC 59.191 66.667 0.00 0.00 32.25 4.79
7464 13240 2.829003 CGCTAGGTCCTGAGCCGA 60.829 66.667 0.00 0.00 35.13 5.54
7465 13241 4.577246 GCGCTAGGTCCTGAGCCG 62.577 72.222 0.00 0.00 35.13 5.52
7466 13242 4.228567 GGCGCTAGGTCCTGAGCC 62.229 72.222 16.21 16.21 35.13 4.70
7467 13243 4.577246 CGGCGCTAGGTCCTGAGC 62.577 72.222 7.64 6.01 35.24 4.26
7468 13244 3.905678 CCGGCGCTAGGTCCTGAG 61.906 72.222 7.64 0.00 0.00 3.35
7473 13249 4.752879 TGTTGCCGGCGCTAGGTC 62.753 66.667 23.90 14.09 35.36 3.85
7484 13260 0.669318 TTCGATCTCACGGTGTTGCC 60.669 55.000 8.17 0.00 0.00 4.52
7485 13261 1.324736 GATTCGATCTCACGGTGTTGC 59.675 52.381 8.17 0.00 0.00 4.17
7486 13262 2.606108 TGATTCGATCTCACGGTGTTG 58.394 47.619 8.17 3.02 0.00 3.33
7487 13263 3.056821 TCTTGATTCGATCTCACGGTGTT 60.057 43.478 8.17 0.00 0.00 3.32
7488 13264 2.492088 TCTTGATTCGATCTCACGGTGT 59.508 45.455 8.17 0.00 0.00 4.16
7489 13265 3.150848 TCTTGATTCGATCTCACGGTG 57.849 47.619 0.56 0.56 0.00 4.94
7490 13266 3.444034 TCTTCTTGATTCGATCTCACGGT 59.556 43.478 0.00 0.00 0.00 4.83
7491 13267 4.033990 TCTTCTTGATTCGATCTCACGG 57.966 45.455 0.00 0.00 0.00 4.94
7492 13268 6.395089 TTTTCTTCTTGATTCGATCTCACG 57.605 37.500 0.00 0.00 0.00 4.35
7493 13269 6.686253 GCATTTTCTTCTTGATTCGATCTCAC 59.314 38.462 0.00 0.00 0.00 3.51
7494 13270 6.456047 CGCATTTTCTTCTTGATTCGATCTCA 60.456 38.462 0.00 0.00 0.00 3.27
7495 13271 5.900789 CGCATTTTCTTCTTGATTCGATCTC 59.099 40.000 0.00 0.00 0.00 2.75
7496 13272 5.220739 CCGCATTTTCTTCTTGATTCGATCT 60.221 40.000 0.00 0.00 0.00 2.75
7497 13273 4.966366 CCGCATTTTCTTCTTGATTCGATC 59.034 41.667 0.00 0.00 0.00 3.69
7498 13274 4.731773 GCCGCATTTTCTTCTTGATTCGAT 60.732 41.667 0.00 0.00 0.00 3.59
7499 13275 3.426159 GCCGCATTTTCTTCTTGATTCGA 60.426 43.478 0.00 0.00 0.00 3.71
7500 13276 2.848302 GCCGCATTTTCTTCTTGATTCG 59.152 45.455 0.00 0.00 0.00 3.34
7501 13277 2.848302 CGCCGCATTTTCTTCTTGATTC 59.152 45.455 0.00 0.00 0.00 2.52
7502 13278 2.487762 TCGCCGCATTTTCTTCTTGATT 59.512 40.909 0.00 0.00 0.00 2.57
7503 13279 2.083774 TCGCCGCATTTTCTTCTTGAT 58.916 42.857 0.00 0.00 0.00 2.57
7504 13280 1.518325 TCGCCGCATTTTCTTCTTGA 58.482 45.000 0.00 0.00 0.00 3.02
7505 13281 2.549633 ATCGCCGCATTTTCTTCTTG 57.450 45.000 0.00 0.00 0.00 3.02
7506 13282 3.689649 ACTAATCGCCGCATTTTCTTCTT 59.310 39.130 0.00 0.00 0.00 2.52
7507 13283 3.063997 CACTAATCGCCGCATTTTCTTCT 59.936 43.478 0.00 0.00 0.00 2.85
7508 13284 3.181510 ACACTAATCGCCGCATTTTCTTC 60.182 43.478 0.00 0.00 0.00 2.87
7509 13285 2.747446 ACACTAATCGCCGCATTTTCTT 59.253 40.909 0.00 0.00 0.00 2.52
7510 13286 2.356135 ACACTAATCGCCGCATTTTCT 58.644 42.857 0.00 0.00 0.00 2.52
7511 13287 2.825086 ACACTAATCGCCGCATTTTC 57.175 45.000 0.00 0.00 0.00 2.29
7512 13288 3.004171 TGTACACTAATCGCCGCATTTT 58.996 40.909 0.00 0.00 0.00 1.82
7513 13289 2.623535 TGTACACTAATCGCCGCATTT 58.376 42.857 0.00 0.00 0.00 2.32
7514 13290 2.303163 TGTACACTAATCGCCGCATT 57.697 45.000 0.00 0.00 0.00 3.56
7515 13291 1.931172 GTTGTACACTAATCGCCGCAT 59.069 47.619 0.00 0.00 0.00 4.73
7516 13292 1.352114 GTTGTACACTAATCGCCGCA 58.648 50.000 0.00 0.00 0.00 5.69
7517 13293 0.648958 GGTTGTACACTAATCGCCGC 59.351 55.000 0.00 0.00 0.00 6.53
7518 13294 2.159282 AGAGGTTGTACACTAATCGCCG 60.159 50.000 0.00 0.00 0.00 6.46
7519 13295 3.521947 AGAGGTTGTACACTAATCGCC 57.478 47.619 0.00 0.00 0.00 5.54
7520 13296 4.435651 GCAAAGAGGTTGTACACTAATCGC 60.436 45.833 0.00 0.00 39.63 4.58
7521 13297 4.929808 AGCAAAGAGGTTGTACACTAATCG 59.070 41.667 0.00 0.00 39.63 3.34
7522 13298 5.122396 CCAGCAAAGAGGTTGTACACTAATC 59.878 44.000 0.00 0.00 39.63 1.75
7523 13299 5.003804 CCAGCAAAGAGGTTGTACACTAAT 58.996 41.667 0.00 0.00 39.63 1.73
7524 13300 4.385825 CCAGCAAAGAGGTTGTACACTAA 58.614 43.478 0.00 0.00 39.63 2.24
7525 13301 3.805807 GCCAGCAAAGAGGTTGTACACTA 60.806 47.826 0.00 0.00 39.63 2.74
7526 13302 2.851195 CCAGCAAAGAGGTTGTACACT 58.149 47.619 0.00 0.00 39.63 3.55
7527 13303 1.266989 GCCAGCAAAGAGGTTGTACAC 59.733 52.381 0.00 0.00 39.63 2.90
7528 13304 1.604604 GCCAGCAAAGAGGTTGTACA 58.395 50.000 0.00 0.00 39.63 2.90
7529 13305 0.517316 CGCCAGCAAAGAGGTTGTAC 59.483 55.000 0.00 0.00 39.63 2.90
7530 13306 1.234615 GCGCCAGCAAAGAGGTTGTA 61.235 55.000 0.00 0.00 44.35 2.41
7531 13307 2.555547 GCGCCAGCAAAGAGGTTGT 61.556 57.895 0.00 0.00 44.35 3.32
7532 13308 2.256461 GCGCCAGCAAAGAGGTTG 59.744 61.111 0.00 0.00 44.35 3.77


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

AutoCloner maintained by Alex Coulton.