Multiple sequence alignment - TraesCS5D01G207700

Loading Multiple Alignment...

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 TraesCS5D01G207700 chr5D 100.000 2730 0 0 1 2730 313521264 313518535 0.000000e+00 5042.0
1 TraesCS5D01G207700 chr5D 95.504 2113 57 6 529 2605 384519439 384517329 0.000000e+00 3341.0
2 TraesCS5D01G207700 chr5D 93.614 1519 51 14 1131 2605 401772868 401774384 0.000000e+00 2226.0
3 TraesCS5D01G207700 chr5D 98.897 544 6 0 1 544 384519919 384519376 0.000000e+00 972.0
4 TraesCS5D01G207700 chr5D 91.006 656 36 4 1075 1709 16496068 16495415 0.000000e+00 863.0
5 TraesCS5D01G207700 chr5D 93.822 259 14 1 772 1030 20273476 20273220 3.300000e-104 388.0
6 TraesCS5D01G207700 chr5D 81.098 164 14 12 588 739 20273633 20273475 6.180000e-22 115.0
7 TraesCS5D01G207700 chr5D 100.000 49 0 0 780 828 313520425 313520377 1.040000e-14 91.6
8 TraesCS5D01G207700 chr5D 100.000 49 0 0 840 888 313520485 313520437 1.040000e-14 91.6
9 TraesCS5D01G207700 chr5D 97.297 37 1 0 1026 1062 20273024 20272988 2.270000e-06 63.9
10 TraesCS5D01G207700 chr5D 93.023 43 3 0 361 403 313520784 313520742 2.270000e-06 63.9
11 TraesCS5D01G207700 chr5D 93.023 43 3 0 361 403 384519439 384519397 2.270000e-06 63.9
12 TraesCS5D01G207700 chr5D 92.857 42 3 0 360 401 313520737 313520696 8.160000e-06 62.1
13 TraesCS5D01G207700 chr6D 93.499 1569 44 10 1071 2605 452662356 452663900 0.000000e+00 2279.0
14 TraesCS5D01G207700 chr6D 91.949 1565 65 13 1070 2600 46527140 46525603 0.000000e+00 2135.0
15 TraesCS5D01G207700 chr6D 92.280 1399 59 16 527 1895 446392228 446390849 0.000000e+00 1940.0
16 TraesCS5D01G207700 chr6D 91.492 1387 61 12 1096 2427 297178747 297177363 0.000000e+00 1855.0
17 TraesCS5D01G207700 chr6D 97.978 544 11 0 1 544 446392706 446392163 0.000000e+00 944.0
18 TraesCS5D01G207700 chr6D 93.701 127 7 1 2604 2729 276112381 276112255 3.590000e-44 189.0
19 TraesCS5D01G207700 chr6D 93.878 98 6 0 194 291 46527227 46527130 6.090000e-32 148.0
20 TraesCS5D01G207700 chr6D 95.604 91 4 0 194 284 452662268 452662358 2.190000e-31 147.0
21 TraesCS5D01G207700 chr6D 96.203 79 3 0 195 273 75486495 75486573 2.210000e-26 130.0
22 TraesCS5D01G207700 chr6D 96.000 75 3 0 23 97 75486271 75486345 3.690000e-24 122.0
23 TraesCS5D01G207700 chr6D 100.000 49 0 0 780 828 446391916 446391868 1.040000e-14 91.6
24 TraesCS5D01G207700 chr6D 100.000 49 0 0 840 888 446391975 446391927 1.040000e-14 91.6
25 TraesCS5D01G207700 chr6D 97.959 49 1 0 152 200 452662117 452662165 4.840000e-13 86.1
26 TraesCS5D01G207700 chr6D 93.182 44 3 0 360 403 446392227 446392184 6.310000e-07 65.8
27 TraesCS5D01G207700 chr6D 97.297 37 1 0 1026 1062 452661951 452661987 2.270000e-06 63.9
28 TraesCS5D01G207700 chr6D 100.000 34 0 0 1029 1062 452662070 452662103 2.270000e-06 63.9
29 TraesCS5D01G207700 chr1D 93.167 1566 49 15 1074 2605 336737175 336735634 0.000000e+00 2246.0
30 TraesCS5D01G207700 chr1D 92.146 1566 67 10 1070 2605 417106074 417107613 0.000000e+00 2159.0
31 TraesCS5D01G207700 chr1D 90.877 1425 73 17 560 1949 463801550 463800148 0.000000e+00 1858.0
32 TraesCS5D01G207700 chr1D 94.519 675 27 3 1759 2427 463800281 463799611 0.000000e+00 1033.0
33 TraesCS5D01G207700 chr1D 97.482 556 13 1 1 555 463802039 463801484 0.000000e+00 948.0
34 TraesCS5D01G207700 chr1D 93.814 97 6 0 194 290 336737266 336737170 2.190000e-31 147.0
35 TraesCS5D01G207700 chr1D 92.857 98 7 0 194 291 417105987 417106084 2.830000e-30 143.0
36 TraesCS5D01G207700 chr1D 100.000 49 0 0 780 828 463801276 463801228 1.040000e-14 91.6
37 TraesCS5D01G207700 chr1D 100.000 46 0 0 155 200 336737414 336737369 4.840000e-13 86.1
38 TraesCS5D01G207700 chr1D 100.000 34 0 0 1029 1062 336737464 336737431 2.270000e-06 63.9
39 TraesCS5D01G207700 chr1D 92.857 42 1 1 372 411 463801548 463801507 2.940000e-05 60.2
40 TraesCS5D01G207700 chr3B 90.664 1671 108 18 979 2607 320731865 320730201 0.000000e+00 2178.0
41 TraesCS5D01G207700 chr3B 94.836 213 9 1 712 922 320732069 320731857 5.630000e-87 331.0
42 TraesCS5D01G207700 chr3B 93.333 45 2 1 1026 1069 318290608 318290652 6.310000e-07 65.8
43 TraesCS5D01G207700 chr2D 92.518 1537 76 7 1090 2596 397123832 397125359 0.000000e+00 2165.0
44 TraesCS5D01G207700 chr2D 94.181 1306 45 8 1153 2427 645241200 645239895 0.000000e+00 1962.0
45 TraesCS5D01G207700 chr2D 95.161 62 3 0 591 652 648988700 648988761 6.220000e-17 99.0
46 TraesCS5D01G207700 chr7B 88.895 1792 120 26 712 2427 122461222 122463010 0.000000e+00 2134.0
47 TraesCS5D01G207700 chr7B 90.150 1401 92 20 1070 2427 3651989 3653386 0.000000e+00 1781.0
48 TraesCS5D01G207700 chr7B 90.007 1401 94 11 1070 2427 44960683 44962080 0.000000e+00 1770.0
49 TraesCS5D01G207700 chr7B 92.248 258 18 2 543 799 725302046 725302302 5.560000e-97 364.0
50 TraesCS5D01G207700 chr7B 97.059 136 4 0 23 158 692732929 692733064 2.110000e-56 230.0
51 TraesCS5D01G207700 chr7B 95.161 124 5 1 23 145 725477643 725477520 7.710000e-46 195.0
52 TraesCS5D01G207700 chr7B 94.949 99 4 1 874 972 725302584 725302681 1.310000e-33 154.0
53 TraesCS5D01G207700 chr7B 94.444 72 4 0 893 964 633839172 633839243 7.990000e-21 111.0
54 TraesCS5D01G207700 chr7B 100.000 49 0 0 840 888 122461290 122461338 1.040000e-14 91.6
55 TraesCS5D01G207700 chr7B 96.154 52 2 0 774 825 122461344 122461395 4.840000e-13 86.1
56 TraesCS5D01G207700 chr3D 91.523 1569 72 13 1070 2605 330477141 330475601 0.000000e+00 2104.0
57 TraesCS5D01G207700 chr3D 90.643 1368 57 27 1128 2427 229434047 229432683 0.000000e+00 1751.0
58 TraesCS5D01G207700 chr3D 97.535 284 7 0 1 284 416544889 416545172 1.140000e-133 486.0
59 TraesCS5D01G207700 chr3D 95.312 256 10 2 775 1030 571760837 571760584 3.270000e-109 405.0
60 TraesCS5D01G207700 chr3D 94.898 98 5 0 194 291 330477228 330477131 1.310000e-33 154.0
61 TraesCS5D01G207700 chr3D 91.919 99 3 4 285 383 416545207 416545300 1.710000e-27 134.0
62 TraesCS5D01G207700 chr3D 100.000 37 0 0 1026 1062 330477331 330477295 4.880000e-08 69.4
63 TraesCS5D01G207700 chr3D 100.000 37 0 0 1026 1062 571760451 571760415 4.880000e-08 69.4
64 TraesCS5D01G207700 chr4D 90.857 1564 78 16 1104 2605 261238936 261237376 0.000000e+00 2036.0
65 TraesCS5D01G207700 chr4D 91.070 1411 62 26 1074 2427 236680725 236679322 0.000000e+00 1849.0
66 TraesCS5D01G207700 chr4D 88.023 860 65 13 1070 1895 222629957 222629102 0.000000e+00 983.0
67 TraesCS5D01G207700 chr4D 94.898 98 5 0 194 291 222630044 222629947 1.310000e-33 154.0
68 TraesCS5D01G207700 chr4D 93.814 97 6 0 194 290 236680816 236680720 2.190000e-31 147.0
69 TraesCS5D01G207700 chr4D 92.424 66 4 1 966 1030 447218802 447218737 2.890000e-15 93.5
70 TraesCS5D01G207700 chr4D 84.444 90 10 1 201 290 225341255 225341170 4.840000e-13 86.1
71 TraesCS5D01G207700 chr4A 91.595 1392 66 9 1070 2427 433609882 433608508 0.000000e+00 1875.0
72 TraesCS5D01G207700 chr4A 93.717 191 12 0 5 195 24458047 24458237 1.240000e-73 287.0
73 TraesCS5D01G207700 chr4A 94.898 98 5 0 194 291 433609969 433609872 1.310000e-33 154.0
74 TraesCS5D01G207700 chr4A 96.703 91 3 0 194 284 523832501 523832591 4.710000e-33 152.0
75 TraesCS5D01G207700 chr4A 87.778 90 10 1 683 771 723201821 723201732 1.340000e-18 104.0
76 TraesCS5D01G207700 chr5A 91.485 1374 78 13 1092 2431 178868148 178866780 0.000000e+00 1853.0
77 TraesCS5D01G207700 chr5A 96.703 273 8 1 283 555 544898369 544898640 1.150000e-123 453.0
78 TraesCS5D01G207700 chr5A 96.335 191 7 0 5 195 544897990 544898180 5.670000e-82 315.0
79 TraesCS5D01G207700 chr5A 95.263 190 9 0 5 194 384013672 384013861 4.420000e-78 302.0
80 TraesCS5D01G207700 chr5A 95.082 122 6 0 2601 2722 362673519 362673640 2.770000e-45 193.0
81 TraesCS5D01G207700 chr5A 95.082 122 6 0 531 652 544898569 544898690 2.770000e-45 193.0
82 TraesCS5D01G207700 chr5A 94.898 98 5 0 194 291 384014347 384014444 1.310000e-33 154.0
83 TraesCS5D01G207700 chr5A 100.000 37 0 0 1026 1062 384014244 384014280 4.880000e-08 69.4
84 TraesCS5D01G207700 chr7D 92.464 1327 47 14 1153 2427 17944234 17942909 0.000000e+00 1847.0
85 TraesCS5D01G207700 chr7D 95.082 122 6 0 2601 2722 1269044 1269165 2.770000e-45 193.0
86 TraesCS5D01G207700 chr7D 93.023 129 9 0 2598 2726 589133207 589133335 3.590000e-44 189.0
87 TraesCS5D01G207700 chr7D 91.729 133 11 0 2590 2722 208514157 208514289 4.640000e-43 185.0
88 TraesCS5D01G207700 chr7D 97.297 37 1 0 1026 1062 51246157 51246121 2.270000e-06 63.9
89 TraesCS5D01G207700 chr5B 91.067 1321 90 9 1132 2427 703922293 703923610 0.000000e+00 1760.0
90 TraesCS5D01G207700 chr5B 88.822 1324 105 16 1132 2427 61789258 61790566 0.000000e+00 1585.0
91 TraesCS5D01G207700 chr5B 88.652 282 12 1 23 284 399756476 399756757 2.620000e-85 326.0
92 TraesCS5D01G207700 chr5B 92.486 173 13 0 23 195 189704393 189704565 5.840000e-62 248.0
93 TraesCS5D01G207700 chr5B 96.324 136 5 0 23 158 352729607 352729472 9.840000e-55 224.0
94 TraesCS5D01G207700 chr5B 93.651 126 8 0 2604 2729 290097452 290097327 3.590000e-44 189.0
95 TraesCS5D01G207700 chr5B 90.511 137 13 0 2590 2726 244595041 244595177 6.010000e-42 182.0
96 TraesCS5D01G207700 chr5B 94.845 97 5 0 194 290 62386985 62386889 4.710000e-33 152.0
97 TraesCS5D01G207700 chr5B 96.703 91 3 0 194 284 345108554 345108644 4.710000e-33 152.0
98 TraesCS5D01G207700 chr5B 95.385 65 3 0 966 1030 598986969 598987033 1.340000e-18 104.0
99 TraesCS5D01G207700 chr5B 93.846 65 3 1 966 1030 622449842 622449779 2.240000e-16 97.1
100 TraesCS5D01G207700 chr5B 93.846 65 3 1 966 1030 622451227 622451164 2.240000e-16 97.1
101 TraesCS5D01G207700 chr2A 89.485 1417 110 16 1132 2522 599678051 599676648 0.000000e+00 1755.0
102 TraesCS5D01G207700 chr2A 88.383 1472 113 18 529 1949 259675819 259677283 0.000000e+00 1718.0
103 TraesCS5D01G207700 chr2A 87.640 1157 92 9 840 1949 259577462 259578614 0.000000e+00 1297.0
104 TraesCS5D01G207700 chr2A 89.641 946 69 11 1681 2605 259578372 259579309 0.000000e+00 1177.0
105 TraesCS5D01G207700 chr2A 91.718 652 44 2 1786 2427 605771752 605772403 0.000000e+00 896.0
106 TraesCS5D01G207700 chr2A 95.204 563 18 4 1 555 259576753 259577314 0.000000e+00 881.0
107 TraesCS5D01G207700 chr2A 97.026 269 8 0 560 828 259577242 259577510 1.150000e-123 453.0
108 TraesCS5D01G207700 chr2A 97.101 138 3 1 418 555 259675756 259675892 5.880000e-57 231.0
109 TraesCS5D01G207700 chr7A 90.738 1328 72 9 1130 2427 734436765 734438071 0.000000e+00 1724.0
110 TraesCS5D01G207700 chr7A 92.799 736 44 3 1869 2597 56066945 56067678 0.000000e+00 1057.0
111 TraesCS5D01G207700 chr7A 91.016 768 63 4 1840 2605 633711099 633710336 0.000000e+00 1031.0
112 TraesCS5D01G207700 chr7A 95.697 488 19 1 543 1030 220992640 220993125 0.000000e+00 784.0
113 TraesCS5D01G207700 chr7A 96.429 252 8 1 2354 2605 49620620 49620370 5.440000e-112 414.0
114 TraesCS5D01G207700 chr7A 96.047 253 10 0 1 253 579483581 579483329 1.960000e-111 412.0
115 TraesCS5D01G207700 chr7A 96.698 212 3 4 337 544 579483350 579483139 1.560000e-92 350.0
116 TraesCS5D01G207700 chr7A 94.000 50 3 0 1022 1071 220993318 220993367 2.920000e-10 76.8
117 TraesCS5D01G207700 chrUn 89.773 1320 97 14 1132 2427 39688772 39690077 0.000000e+00 1655.0
118 TraesCS5D01G207700 chrUn 89.517 1326 85 10 1130 2427 290561110 290559811 0.000000e+00 1629.0
119 TraesCS5D01G207700 chrUn 89.338 816 55 14 1130 1922 236925662 236926468 0.000000e+00 996.0
120 TraesCS5D01G207700 chrUn 89.677 804 41 5 1132 1893 38465374 38466177 0.000000e+00 987.0
121 TraesCS5D01G207700 chrUn 88.611 799 70 16 1130 1922 35790251 35791034 0.000000e+00 952.0
122 TraesCS5D01G207700 chrUn 86.404 787 64 15 1130 1895 264981380 264982144 0.000000e+00 821.0
123 TraesCS5D01G207700 chrUn 86.275 765 62 16 1130 1870 356709512 356708767 0.000000e+00 791.0
124 TraesCS5D01G207700 chrUn 91.087 561 28 6 1130 1669 35191660 35191101 0.000000e+00 739.0
125 TraesCS5D01G207700 chrUn 96.610 118 4 0 23 140 35789771 35789888 2.140000e-46 196.0
126 TraesCS5D01G207700 chrUn 90.099 101 8 2 102 200 35789935 35790035 2.210000e-26 130.0
127 TraesCS5D01G207700 chrUn 100.000 39 0 0 1300 1338 393375306 393375268 3.770000e-09 73.1
128 TraesCS5D01G207700 chr3A 92.839 1159 49 6 1153 2277 615143385 615142227 0.000000e+00 1650.0
129 TraesCS5D01G207700 chr3A 91.806 598 39 2 1840 2427 675995215 675995812 0.000000e+00 824.0
130 TraesCS5D01G207700 chr3A 96.457 254 8 1 2352 2605 5984346 5984094 4.200000e-113 418.0
131 TraesCS5D01G207700 chr3A 96.457 254 8 1 2352 2605 5986996 5986744 4.200000e-113 418.0
132 TraesCS5D01G207700 chr3A 96.063 254 9 1 2352 2605 733885211 733884959 1.960000e-111 412.0
133 TraesCS5D01G207700 chr3A 95.686 255 9 2 2352 2605 5983022 5982769 2.530000e-110 409.0
134 TraesCS5D01G207700 chr3A 94.444 126 7 0 2601 2726 365911887 365912012 7.710000e-46 195.0
135 TraesCS5D01G207700 chr1A 87.039 895 75 15 1096 1952 575419767 575420658 0.000000e+00 972.0
136 TraesCS5D01G207700 chr1A 94.845 97 5 0 194 290 50647834 50647738 4.710000e-33 152.0
137 TraesCS5D01G207700 chr4B 90.612 703 45 4 1070 1751 15097683 15096981 0.000000e+00 913.0
138 TraesCS5D01G207700 chr4B 95.050 303 13 1 543 845 644593701 644594001 2.460000e-130 475.0
139 TraesCS5D01G207700 chr4B 84.444 315 20 15 543 828 368724968 368725282 1.600000e-72 283.0
140 TraesCS5D01G207700 chr4B 97.059 136 4 0 837 972 644594025 644594160 2.110000e-56 230.0
141 TraesCS5D01G207700 chr4B 95.745 141 4 2 840 980 368725234 368725372 2.740000e-55 226.0
142 TraesCS5D01G207700 chr4B 95.876 97 4 0 194 290 288476855 288476759 1.010000e-34 158.0
143 TraesCS5D01G207700 chr4B 98.438 64 1 0 965 1028 644594179 644594242 2.220000e-21 113.0
144 TraesCS5D01G207700 chr4B 95.385 65 3 0 966 1030 413205120 413205184 1.340000e-18 104.0
145 TraesCS5D01G207700 chr4B 95.385 65 3 0 966 1030 413234866 413234930 1.340000e-18 104.0
146 TraesCS5D01G207700 chr4B 92.727 55 4 0 834 888 644593930 644593984 2.250000e-11 80.5
147 TraesCS5D01G207700 chr4B 90.164 61 3 2 970 1030 333374486 333374543 2.920000e-10 76.8
148 TraesCS5D01G207700 chr4B 100.000 29 0 0 375 403 644593701 644593729 1.000000e-03 54.7
149 TraesCS5D01G207700 chr6B 86.645 307 19 13 543 828 238445511 238445206 1.220000e-83 320.0
150 TraesCS5D01G207700 chr6B 93.301 209 14 0 543 751 425112513 425112721 2.640000e-80 309.0
151 TraesCS5D01G207700 chr6B 97.059 136 4 0 23 158 152492348 152492483 2.110000e-56 230.0
152 TraesCS5D01G207700 chr6B 97.674 129 3 0 902 1030 425131283 425131411 3.540000e-54 222.0
153 TraesCS5D01G207700 chr6B 94.737 133 7 0 840 972 238445254 238445122 9.910000e-50 207.0
154 TraesCS5D01G207700 chr6B 96.703 91 3 0 194 284 70625767 70625857 4.710000e-33 152.0
155 TraesCS5D01G207700 chr6B 90.909 99 7 2 104 200 152492512 152492610 6.130000e-27 132.0
156 TraesCS5D01G207700 chr6B 98.485 66 1 0 965 1030 238445103 238445038 1.720000e-22 117.0
157 TraesCS5D01G207700 chr6B 96.923 65 2 0 966 1030 483667081 483667017 2.870000e-20 110.0
158 TraesCS5D01G207700 chr6B 96.923 65 2 0 966 1030 483725222 483725158 2.870000e-20 110.0
159 TraesCS5D01G207700 chr6B 100.000 29 0 0 375 403 238445511 238445483 1.000000e-03 54.7
160 TraesCS5D01G207700 chr6B 100.000 29 0 0 375 403 425112513 425112541 1.000000e-03 54.7
161 TraesCS5D01G207700 chr6A 93.651 126 8 0 2604 2729 182414538 182414413 3.590000e-44 189.0
162 TraesCS5D01G207700 chr6A 96.000 75 3 0 23 97 445419483 445419557 3.690000e-24 122.0
163 TraesCS5D01G207700 chr6A 94.667 75 4 0 23 97 101827779 101827705 1.720000e-22 117.0
164 TraesCS5D01G207700 chr6A 93.939 66 3 1 966 1030 211316523 211316588 6.220000e-17 99.0


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 TraesCS5D01G207700 chr5D 313518535 313521264 2729 True 1070.240000 5042 97.176000 1 2730 5 chr5D.!!$R3 2729
1 TraesCS5D01G207700 chr5D 401772868 401774384 1516 False 2226.000000 2226 93.614000 1131 2605 1 chr5D.!!$F1 1474
2 TraesCS5D01G207700 chr5D 384517329 384519919 2590 True 1458.966667 3341 95.808000 1 2605 3 chr5D.!!$R4 2604
3 TraesCS5D01G207700 chr5D 16495415 16496068 653 True 863.000000 863 91.006000 1075 1709 1 chr5D.!!$R1 634
4 TraesCS5D01G207700 chr6D 297177363 297178747 1384 True 1855.000000 1855 91.492000 1096 2427 1 chr6D.!!$R2 1331
5 TraesCS5D01G207700 chr6D 46525603 46527227 1624 True 1141.500000 2135 92.913500 194 2600 2 chr6D.!!$R3 2406
6 TraesCS5D01G207700 chr6D 446390849 446392706 1857 True 626.600000 1940 96.688000 1 1895 5 chr6D.!!$R4 1894
7 TraesCS5D01G207700 chr6D 452661951 452663900 1949 False 527.980000 2279 96.871800 152 2605 5 chr6D.!!$F2 2453
8 TraesCS5D01G207700 chr1D 417105987 417107613 1626 False 1151.000000 2159 92.501500 194 2605 2 chr1D.!!$F1 2411
9 TraesCS5D01G207700 chr1D 463799611 463802039 2428 True 798.160000 1858 95.147000 1 2427 5 chr1D.!!$R2 2426
10 TraesCS5D01G207700 chr1D 336735634 336737464 1830 True 635.750000 2246 96.745250 155 2605 4 chr1D.!!$R1 2450
11 TraesCS5D01G207700 chr3B 320730201 320732069 1868 True 1254.500000 2178 92.750000 712 2607 2 chr3B.!!$R1 1895
12 TraesCS5D01G207700 chr2D 397123832 397125359 1527 False 2165.000000 2165 92.518000 1090 2596 1 chr2D.!!$F1 1506
13 TraesCS5D01G207700 chr2D 645239895 645241200 1305 True 1962.000000 1962 94.181000 1153 2427 1 chr2D.!!$R1 1274
14 TraesCS5D01G207700 chr7B 3651989 3653386 1397 False 1781.000000 1781 90.150000 1070 2427 1 chr7B.!!$F1 1357
15 TraesCS5D01G207700 chr7B 44960683 44962080 1397 False 1770.000000 1770 90.007000 1070 2427 1 chr7B.!!$F2 1357
16 TraesCS5D01G207700 chr7B 122461222 122463010 1788 False 770.566667 2134 95.016333 712 2427 3 chr7B.!!$F5 1715
17 TraesCS5D01G207700 chr7B 725302046 725302681 635 False 259.000000 364 93.598500 543 972 2 chr7B.!!$F6 429
18 TraesCS5D01G207700 chr3D 229432683 229434047 1364 True 1751.000000 1751 90.643000 1128 2427 1 chr3D.!!$R1 1299
19 TraesCS5D01G207700 chr3D 330475601 330477331 1730 True 775.800000 2104 95.473667 194 2605 3 chr3D.!!$R2 2411
20 TraesCS5D01G207700 chr4D 261237376 261238936 1560 True 2036.000000 2036 90.857000 1104 2605 1 chr4D.!!$R2 1501
21 TraesCS5D01G207700 chr4D 236679322 236680816 1494 True 998.000000 1849 92.442000 194 2427 2 chr4D.!!$R5 2233
22 TraesCS5D01G207700 chr4D 222629102 222630044 942 True 568.500000 983 91.460500 194 1895 2 chr4D.!!$R4 1701
23 TraesCS5D01G207700 chr4A 433608508 433609969 1461 True 1014.500000 1875 93.246500 194 2427 2 chr4A.!!$R2 2233
24 TraesCS5D01G207700 chr5A 178866780 178868148 1368 True 1853.000000 1853 91.485000 1092 2431 1 chr5A.!!$R1 1339
25 TraesCS5D01G207700 chr5A 544897990 544898690 700 False 320.333333 453 96.040000 5 652 3 chr5A.!!$F3 647
26 TraesCS5D01G207700 chr7D 17942909 17944234 1325 True 1847.000000 1847 92.464000 1153 2427 1 chr7D.!!$R1 1274
27 TraesCS5D01G207700 chr5B 703922293 703923610 1317 False 1760.000000 1760 91.067000 1132 2427 1 chr5B.!!$F7 1295
28 TraesCS5D01G207700 chr5B 61789258 61790566 1308 False 1585.000000 1585 88.822000 1132 2427 1 chr5B.!!$F1 1295
29 TraesCS5D01G207700 chr2A 599676648 599678051 1403 True 1755.000000 1755 89.485000 1132 2522 1 chr2A.!!$R1 1390
30 TraesCS5D01G207700 chr2A 259675756 259677283 1527 False 974.500000 1718 92.742000 418 1949 2 chr2A.!!$F3 1531
31 TraesCS5D01G207700 chr2A 259576753 259579309 2556 False 952.000000 1297 92.377750 1 2605 4 chr2A.!!$F2 2604
32 TraesCS5D01G207700 chr2A 605771752 605772403 651 False 896.000000 896 91.718000 1786 2427 1 chr2A.!!$F1 641
33 TraesCS5D01G207700 chr7A 734436765 734438071 1306 False 1724.000000 1724 90.738000 1130 2427 1 chr7A.!!$F2 1297
34 TraesCS5D01G207700 chr7A 56066945 56067678 733 False 1057.000000 1057 92.799000 1869 2597 1 chr7A.!!$F1 728
35 TraesCS5D01G207700 chr7A 633710336 633711099 763 True 1031.000000 1031 91.016000 1840 2605 1 chr7A.!!$R2 765
36 TraesCS5D01G207700 chr7A 220992640 220993367 727 False 430.400000 784 94.848500 543 1071 2 chr7A.!!$F3 528
37 TraesCS5D01G207700 chrUn 39688772 39690077 1305 False 1655.000000 1655 89.773000 1132 2427 1 chrUn.!!$F2 1295
38 TraesCS5D01G207700 chrUn 290559811 290561110 1299 True 1629.000000 1629 89.517000 1130 2427 1 chrUn.!!$R2 1297
39 TraesCS5D01G207700 chrUn 236925662 236926468 806 False 996.000000 996 89.338000 1130 1922 1 chrUn.!!$F3 792
40 TraesCS5D01G207700 chrUn 38465374 38466177 803 False 987.000000 987 89.677000 1132 1893 1 chrUn.!!$F1 761
41 TraesCS5D01G207700 chrUn 264981380 264982144 764 False 821.000000 821 86.404000 1130 1895 1 chrUn.!!$F4 765
42 TraesCS5D01G207700 chrUn 356708767 356709512 745 True 791.000000 791 86.275000 1130 1870 1 chrUn.!!$R3 740
43 TraesCS5D01G207700 chrUn 35191101 35191660 559 True 739.000000 739 91.087000 1130 1669 1 chrUn.!!$R1 539
44 TraesCS5D01G207700 chrUn 35789771 35791034 1263 False 426.000000 952 91.773333 23 1922 3 chrUn.!!$F5 1899
45 TraesCS5D01G207700 chr3A 615142227 615143385 1158 True 1650.000000 1650 92.839000 1153 2277 1 chr3A.!!$R1 1124
46 TraesCS5D01G207700 chr3A 675995215 675995812 597 False 824.000000 824 91.806000 1840 2427 1 chr3A.!!$F2 587
47 TraesCS5D01G207700 chr3A 5982769 5986996 4227 True 415.000000 418 96.200000 2352 2605 3 chr3A.!!$R3 253
48 TraesCS5D01G207700 chr1A 575419767 575420658 891 False 972.000000 972 87.039000 1096 1952 1 chr1A.!!$F1 856
49 TraesCS5D01G207700 chr4B 15096981 15097683 702 True 913.000000 913 90.612000 1070 1751 1 chr4B.!!$R1 681

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
113 114 3.989817 GCCCTGTTGATGTTGATGTTTTC 59.01 43.478 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 2734 0.035152 TCAGCCACCACCATAGCAAG 60.035 55.0 0.0 0.0 0.0 4.01 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
113 114 3.989817 GCCCTGTTGATGTTGATGTTTTC 59.010 43.478 0.00 0.00 0.00 2.29
154 238 8.746052 TGGAATGAGTAGAAGAAGAAAACAAA 57.254 30.769 0.00 0.00 0.00 2.83
155 239 8.840321 TGGAATGAGTAGAAGAAGAAAACAAAG 58.160 33.333 0.00 0.00 0.00 2.77
156 240 8.841300 GGAATGAGTAGAAGAAGAAAACAAAGT 58.159 33.333 0.00 0.00 0.00 2.66
158 242 8.738645 ATGAGTAGAAGAAGAAAACAAAGTGT 57.261 30.769 0.00 0.00 0.00 3.55
642 884 7.095695 TGGTCCTTTTATAGTAGCAAATTGC 57.904 36.000 10.41 10.41 45.46 3.56
757 999 7.442666 AGTTTCTGAAGTAAACTGGAGATGTTC 59.557 37.037 0.69 0.00 43.66 3.18
1072 1728 6.811253 TGTGGTTACCTGAAATGTTGATAC 57.189 37.500 2.07 0.00 0.00 2.24
1432 2127 2.868253 GTGAAGGCCACATGTACCC 58.132 57.895 5.01 9.19 45.03 3.69
1653 2348 1.798223 CGACGACAACACCATGTTCAT 59.202 47.619 0.00 0.00 38.77 2.57
1702 2490 1.875813 CAGCAGCGAGGATGACGAC 60.876 63.158 0.00 0.00 0.00 4.34
1771 2706 2.728922 CCTATTCTGGCTAACGACGAC 58.271 52.381 0.00 0.00 0.00 4.34
1772 2707 2.543238 CCTATTCTGGCTAACGACGACC 60.543 54.545 0.00 0.00 0.00 4.79
1773 2708 0.175073 ATTCTGGCTAACGACGACCC 59.825 55.000 0.00 0.00 0.00 4.46
1774 2709 0.896940 TTCTGGCTAACGACGACCCT 60.897 55.000 0.00 0.00 0.00 4.34
1775 2710 1.153823 CTGGCTAACGACGACCCTG 60.154 63.158 0.00 0.00 0.00 4.45
1776 2711 2.508663 GGCTAACGACGACCCTGC 60.509 66.667 0.00 0.00 0.00 4.85
1777 2712 2.572284 GCTAACGACGACCCTGCT 59.428 61.111 0.00 0.00 0.00 4.24
1778 2713 1.660560 GGCTAACGACGACCCTGCTA 61.661 60.000 0.00 0.00 0.00 3.49
1779 2714 0.384669 GCTAACGACGACCCTGCTAT 59.615 55.000 0.00 0.00 0.00 2.97
1780 2715 1.864435 GCTAACGACGACCCTGCTATG 60.864 57.143 0.00 0.00 0.00 2.23
1781 2716 0.742505 TAACGACGACCCTGCTATGG 59.257 55.000 0.00 0.00 0.00 2.74
1782 2717 1.255667 AACGACGACCCTGCTATGGT 61.256 55.000 0.00 0.00 39.32 3.55
1783 2718 1.226974 CGACGACCCTGCTATGGTG 60.227 63.158 0.00 0.00 35.85 4.17
1784 2719 1.144057 GACGACCCTGCTATGGTGG 59.856 63.158 0.00 0.00 35.85 4.61
1785 2720 1.612442 ACGACCCTGCTATGGTGGT 60.612 57.895 0.00 2.62 39.63 4.16
1786 2721 1.153369 CGACCCTGCTATGGTGGTG 60.153 63.158 0.00 0.00 35.85 4.17
1787 2722 1.224592 GACCCTGCTATGGTGGTGG 59.775 63.158 0.00 0.00 35.85 4.61
1788 2723 2.124151 CCCTGCTATGGTGGTGGC 60.124 66.667 0.00 0.00 0.00 5.01
1789 2724 2.514592 CCTGCTATGGTGGTGGCG 60.515 66.667 0.00 0.00 0.00 5.69
1790 2725 2.514592 CTGCTATGGTGGTGGCGG 60.515 66.667 0.00 0.00 0.00 6.13
1791 2726 3.006133 TGCTATGGTGGTGGCGGA 61.006 61.111 0.00 0.00 0.00 5.54
1792 2727 2.329539 CTGCTATGGTGGTGGCGGAT 62.330 60.000 0.00 0.00 34.22 4.18
1793 2728 1.893808 GCTATGGTGGTGGCGGATG 60.894 63.158 0.00 0.00 0.00 3.51
1794 2729 1.829456 CTATGGTGGTGGCGGATGA 59.171 57.895 0.00 0.00 0.00 2.92
1795 2730 0.532862 CTATGGTGGTGGCGGATGAC 60.533 60.000 0.00 0.00 0.00 3.06
1808 2743 1.871080 GGATGACGACCTTGCTATGG 58.129 55.000 0.00 0.00 0.00 2.74
1809 2744 1.139058 GGATGACGACCTTGCTATGGT 59.861 52.381 0.00 0.00 41.07 3.55
1810 2745 2.205074 GATGACGACCTTGCTATGGTG 58.795 52.381 0.00 0.00 38.03 4.17
1811 2746 0.249120 TGACGACCTTGCTATGGTGG 59.751 55.000 0.00 2.87 38.03 4.61
1812 2747 0.249398 GACGACCTTGCTATGGTGGT 59.751 55.000 9.72 9.72 46.54 4.16
1813 2748 0.036388 ACGACCTTGCTATGGTGGTG 60.036 55.000 9.30 0.19 43.23 4.17
1814 2749 0.744414 CGACCTTGCTATGGTGGTGG 60.744 60.000 0.86 0.00 38.03 4.61
1815 2750 1.000896 ACCTTGCTATGGTGGTGGC 60.001 57.895 0.00 0.00 36.30 5.01
1816 2751 1.304282 CCTTGCTATGGTGGTGGCT 59.696 57.895 0.00 0.00 0.00 4.75
1817 2752 1.033746 CCTTGCTATGGTGGTGGCTG 61.034 60.000 0.00 0.00 0.00 4.85
1818 2753 0.035152 CTTGCTATGGTGGTGGCTGA 60.035 55.000 0.00 0.00 0.00 4.26
1819 2754 0.322456 TTGCTATGGTGGTGGCTGAC 60.322 55.000 0.00 0.00 0.00 3.51
1820 2755 1.815421 GCTATGGTGGTGGCTGACG 60.815 63.158 0.00 0.00 0.00 4.35
1821 2756 1.897423 CTATGGTGGTGGCTGACGA 59.103 57.895 0.00 0.00 0.00 4.20
1822 2757 0.179100 CTATGGTGGTGGCTGACGAG 60.179 60.000 0.00 0.00 0.00 4.18
1823 2758 1.613317 TATGGTGGTGGCTGACGAGG 61.613 60.000 0.00 0.00 0.00 4.63
1824 2759 3.311110 GGTGGTGGCTGACGAGGA 61.311 66.667 0.00 0.00 0.00 3.71
1827 2762 4.083862 GGTGGCTGACGAGGACCC 62.084 72.222 0.00 0.00 0.00 4.46
1835 2770 1.043116 TGACGAGGACCCTGCTATGG 61.043 60.000 0.00 0.00 0.00 2.74
1843 2778 2.514592 CCTGCTATGGTGGTGGCG 60.515 66.667 0.00 0.00 0.00 5.69
2109 3561 7.590279 TGTTAAGCATGTTAGGTTTAAGCTTC 58.410 34.615 0.00 0.00 40.78 3.86
2306 3772 0.040514 TCGGTTTTTGTGCATGCTCG 60.041 50.000 20.33 9.51 0.00 5.03
2607 8053 3.916761 TGATATGGCCGTATCCGTTAAC 58.083 45.455 32.80 14.47 31.47 2.01
2608 8054 3.321396 TGATATGGCCGTATCCGTTAACA 59.679 43.478 32.80 16.57 31.47 2.41
2609 8055 2.922740 ATGGCCGTATCCGTTAACAT 57.077 45.000 6.39 0.00 0.00 2.71
2610 8056 1.942677 TGGCCGTATCCGTTAACATG 58.057 50.000 6.39 0.00 0.00 3.21
2611 8057 1.481363 TGGCCGTATCCGTTAACATGA 59.519 47.619 6.39 1.80 0.00 3.07
2612 8058 2.093606 TGGCCGTATCCGTTAACATGAA 60.094 45.455 6.39 0.00 0.00 2.57
2613 8059 2.937799 GGCCGTATCCGTTAACATGAAA 59.062 45.455 6.39 0.00 0.00 2.69
2614 8060 3.374678 GGCCGTATCCGTTAACATGAAAA 59.625 43.478 6.39 0.00 0.00 2.29
2615 8061 4.495184 GGCCGTATCCGTTAACATGAAAAG 60.495 45.833 6.39 0.00 0.00 2.27
2616 8062 4.093850 GCCGTATCCGTTAACATGAAAAGT 59.906 41.667 6.39 0.00 0.00 2.66
2617 8063 5.291614 GCCGTATCCGTTAACATGAAAAGTA 59.708 40.000 6.39 0.00 0.00 2.24
2618 8064 6.183360 GCCGTATCCGTTAACATGAAAAGTAA 60.183 38.462 6.39 0.00 0.00 2.24
2619 8065 7.175410 CCGTATCCGTTAACATGAAAAGTAAC 58.825 38.462 6.39 0.00 0.00 2.50
2620 8066 7.148606 CCGTATCCGTTAACATGAAAAGTAACA 60.149 37.037 6.39 0.00 0.00 2.41
2621 8067 8.385111 CGTATCCGTTAACATGAAAAGTAACAT 58.615 33.333 6.39 0.00 0.00 2.71
2623 8069 8.964420 ATCCGTTAACATGAAAAGTAACATTG 57.036 30.769 6.39 0.00 0.00 2.82
2624 8070 6.858993 TCCGTTAACATGAAAAGTAACATTGC 59.141 34.615 6.39 0.00 0.00 3.56
2625 8071 6.088883 CCGTTAACATGAAAAGTAACATTGCC 59.911 38.462 6.39 0.00 0.00 4.52
2626 8072 6.088883 CGTTAACATGAAAAGTAACATTGCCC 59.911 38.462 6.39 0.00 0.00 5.36
2627 8073 5.806654 AACATGAAAAGTAACATTGCCCT 57.193 34.783 0.00 0.00 0.00 5.19
2628 8074 5.806654 ACATGAAAAGTAACATTGCCCTT 57.193 34.783 0.00 0.00 0.00 3.95
2629 8075 5.540911 ACATGAAAAGTAACATTGCCCTTG 58.459 37.500 0.00 0.00 0.00 3.61
2630 8076 3.988819 TGAAAAGTAACATTGCCCTTGC 58.011 40.909 0.00 0.00 38.26 4.01
2631 8077 3.640967 TGAAAAGTAACATTGCCCTTGCT 59.359 39.130 0.00 0.00 38.71 3.91
2632 8078 3.665745 AAAGTAACATTGCCCTTGCTG 57.334 42.857 0.00 0.00 38.71 4.41
2633 8079 0.890683 AGTAACATTGCCCTTGCTGC 59.109 50.000 0.00 0.00 38.71 5.25
2634 8080 0.602562 GTAACATTGCCCTTGCTGCA 59.397 50.000 0.00 0.00 38.71 4.41
2638 8084 2.443577 TTGCCCTTGCTGCAACCA 60.444 55.556 11.69 6.28 43.36 3.67
2639 8085 2.062777 TTGCCCTTGCTGCAACCAA 61.063 52.632 11.69 11.78 43.36 3.67
2640 8086 1.409251 TTGCCCTTGCTGCAACCAAT 61.409 50.000 11.69 0.00 43.36 3.16
2641 8087 0.541530 TGCCCTTGCTGCAACCAATA 60.542 50.000 11.69 0.00 38.71 1.90
2642 8088 0.607620 GCCCTTGCTGCAACCAATAA 59.392 50.000 11.69 0.00 33.53 1.40
2643 8089 1.672737 GCCCTTGCTGCAACCAATAAC 60.673 52.381 11.69 0.00 33.53 1.89
2644 8090 1.617850 CCCTTGCTGCAACCAATAACA 59.382 47.619 11.69 0.00 0.00 2.41
2645 8091 2.353011 CCCTTGCTGCAACCAATAACAG 60.353 50.000 11.69 0.00 0.00 3.16
2649 8095 0.532115 CTGCAACCAATAACAGCCCC 59.468 55.000 0.00 0.00 0.00 5.80
2650 8096 0.114168 TGCAACCAATAACAGCCCCT 59.886 50.000 0.00 0.00 0.00 4.79
2651 8097 0.532115 GCAACCAATAACAGCCCCTG 59.468 55.000 0.00 0.00 37.52 4.45
2652 8098 0.532115 CAACCAATAACAGCCCCTGC 59.468 55.000 0.00 0.00 34.37 4.85
2653 8099 0.114168 AACCAATAACAGCCCCTGCA 59.886 50.000 0.00 0.00 41.13 4.41
2654 8100 0.323725 ACCAATAACAGCCCCTGCAG 60.324 55.000 6.78 6.78 41.13 4.41
2655 8101 0.323725 CCAATAACAGCCCCTGCAGT 60.324 55.000 13.81 0.00 39.11 4.40
2656 8102 1.064758 CCAATAACAGCCCCTGCAGTA 60.065 52.381 13.81 0.00 36.02 2.74
2657 8103 2.423373 CCAATAACAGCCCCTGCAGTAT 60.423 50.000 13.81 0.00 36.02 2.12
2658 8104 3.290710 CAATAACAGCCCCTGCAGTATT 58.709 45.455 13.81 5.38 36.02 1.89
2659 8105 2.710096 TAACAGCCCCTGCAGTATTC 57.290 50.000 13.81 0.00 36.02 1.75
2660 8106 0.698238 AACAGCCCCTGCAGTATTCA 59.302 50.000 13.81 0.00 36.02 2.57
2661 8107 0.698238 ACAGCCCCTGCAGTATTCAA 59.302 50.000 13.81 0.00 41.13 2.69
2662 8108 1.075374 ACAGCCCCTGCAGTATTCAAA 59.925 47.619 13.81 0.00 41.13 2.69
2663 8109 2.170166 CAGCCCCTGCAGTATTCAAAA 58.830 47.619 13.81 0.00 41.13 2.44
2664 8110 2.562298 CAGCCCCTGCAGTATTCAAAAA 59.438 45.455 13.81 0.00 41.13 1.94
2665 8111 2.827921 AGCCCCTGCAGTATTCAAAAAG 59.172 45.455 13.81 0.00 41.13 2.27
2666 8112 2.094026 GCCCCTGCAGTATTCAAAAAGG 60.094 50.000 13.81 2.05 37.47 3.11
2667 8113 2.497273 CCCCTGCAGTATTCAAAAAGGG 59.503 50.000 13.81 7.95 42.21 3.95
2668 8114 3.165071 CCCTGCAGTATTCAAAAAGGGT 58.835 45.455 13.81 0.00 38.47 4.34
2669 8115 3.193479 CCCTGCAGTATTCAAAAAGGGTC 59.807 47.826 13.81 0.00 38.47 4.46
2670 8116 4.082125 CCTGCAGTATTCAAAAAGGGTCT 58.918 43.478 13.81 0.00 0.00 3.85
2671 8117 5.253330 CCTGCAGTATTCAAAAAGGGTCTA 58.747 41.667 13.81 0.00 0.00 2.59
2672 8118 5.123979 CCTGCAGTATTCAAAAAGGGTCTAC 59.876 44.000 13.81 0.00 0.00 2.59
2673 8119 5.007682 TGCAGTATTCAAAAAGGGTCTACC 58.992 41.667 0.00 0.00 40.67 3.18
2674 8120 5.007682 GCAGTATTCAAAAAGGGTCTACCA 58.992 41.667 0.81 0.00 43.89 3.25
2675 8121 5.475564 GCAGTATTCAAAAAGGGTCTACCAA 59.524 40.000 0.81 0.00 43.89 3.67
2676 8122 6.349363 GCAGTATTCAAAAAGGGTCTACCAAG 60.349 42.308 0.81 0.00 43.89 3.61
2677 8123 6.151144 CAGTATTCAAAAAGGGTCTACCAAGG 59.849 42.308 0.81 0.00 43.89 3.61
2678 8124 4.799715 TTCAAAAAGGGTCTACCAAGGA 57.200 40.909 0.81 0.00 43.89 3.36
2679 8125 5.333566 TTCAAAAAGGGTCTACCAAGGAT 57.666 39.130 0.81 0.00 43.89 3.24
2680 8126 4.662278 TCAAAAAGGGTCTACCAAGGATG 58.338 43.478 0.81 0.00 43.89 3.51
2681 8127 4.352595 TCAAAAAGGGTCTACCAAGGATGA 59.647 41.667 0.81 0.00 43.89 2.92
2682 8128 5.015178 TCAAAAAGGGTCTACCAAGGATGAT 59.985 40.000 0.81 0.00 43.89 2.45
2683 8129 4.779993 AAAGGGTCTACCAAGGATGATC 57.220 45.455 0.81 0.00 43.89 2.92
2684 8130 2.320781 AGGGTCTACCAAGGATGATCG 58.679 52.381 0.81 0.00 43.89 3.69
2685 8131 2.091278 AGGGTCTACCAAGGATGATCGA 60.091 50.000 0.81 0.00 43.89 3.59
2686 8132 2.036089 GGGTCTACCAAGGATGATCGAC 59.964 54.545 0.81 0.00 39.85 4.20
2687 8133 2.693591 GGTCTACCAAGGATGATCGACA 59.306 50.000 0.00 0.00 35.64 4.35
2688 8134 3.322254 GGTCTACCAAGGATGATCGACAT 59.678 47.826 0.00 0.00 37.71 3.06
2689 8135 4.523173 GGTCTACCAAGGATGATCGACATA 59.477 45.833 0.00 0.00 36.20 2.29
2690 8136 5.462405 GTCTACCAAGGATGATCGACATAC 58.538 45.833 0.00 0.00 39.56 2.39
2698 8144 3.982058 GGATGATCGACATACTTTCGTCC 59.018 47.826 5.64 5.64 39.56 4.79
2699 8145 4.261656 GGATGATCGACATACTTTCGTCCT 60.262 45.833 12.06 0.00 38.76 3.85
2700 8146 4.288670 TGATCGACATACTTTCGTCCTC 57.711 45.455 0.00 0.00 37.73 3.71
2701 8147 2.819422 TCGACATACTTTCGTCCTCG 57.181 50.000 0.00 0.00 37.73 4.63
2702 8148 1.399440 TCGACATACTTTCGTCCTCGG 59.601 52.381 0.00 0.00 37.73 4.63
2703 8149 1.533338 CGACATACTTTCGTCCTCGGG 60.533 57.143 0.00 0.00 37.69 5.14
2704 8150 1.747355 GACATACTTTCGTCCTCGGGA 59.253 52.381 0.00 0.00 37.69 5.14
2705 8151 2.165030 GACATACTTTCGTCCTCGGGAA 59.835 50.000 0.00 0.00 37.69 3.97
2706 8152 2.764572 ACATACTTTCGTCCTCGGGAAT 59.235 45.455 0.00 0.00 37.69 3.01
2707 8153 3.956199 ACATACTTTCGTCCTCGGGAATA 59.044 43.478 0.00 0.00 37.69 1.75
2708 8154 4.587684 ACATACTTTCGTCCTCGGGAATAT 59.412 41.667 0.00 0.00 37.69 1.28
2709 8155 3.729862 ACTTTCGTCCTCGGGAATATC 57.270 47.619 0.00 0.00 37.69 1.63
2710 8156 3.028850 ACTTTCGTCCTCGGGAATATCA 58.971 45.455 0.00 0.00 37.69 2.15
2711 8157 3.449737 ACTTTCGTCCTCGGGAATATCAA 59.550 43.478 0.00 0.00 37.69 2.57
2712 8158 3.728076 TTCGTCCTCGGGAATATCAAG 57.272 47.619 0.00 0.00 37.69 3.02
2713 8159 2.940158 TCGTCCTCGGGAATATCAAGA 58.060 47.619 0.00 0.00 37.69 3.02
2714 8160 3.293337 TCGTCCTCGGGAATATCAAGAA 58.707 45.455 0.00 0.00 37.69 2.52
2715 8161 3.895656 TCGTCCTCGGGAATATCAAGAAT 59.104 43.478 0.00 0.00 37.69 2.40
2716 8162 5.074804 TCGTCCTCGGGAATATCAAGAATA 58.925 41.667 0.00 0.00 37.69 1.75
2717 8163 5.183331 TCGTCCTCGGGAATATCAAGAATAG 59.817 44.000 0.00 0.00 37.69 1.73
2718 8164 5.172205 GTCCTCGGGAATATCAAGAATAGC 58.828 45.833 0.00 0.00 31.38 2.97
2719 8165 4.838423 TCCTCGGGAATATCAAGAATAGCA 59.162 41.667 0.00 0.00 0.00 3.49
2720 8166 5.306937 TCCTCGGGAATATCAAGAATAGCAA 59.693 40.000 0.00 0.00 0.00 3.91
2721 8167 5.997746 CCTCGGGAATATCAAGAATAGCAAA 59.002 40.000 0.00 0.00 0.00 3.68
2722 8168 6.656693 CCTCGGGAATATCAAGAATAGCAAAT 59.343 38.462 0.00 0.00 0.00 2.32
2723 8169 7.175641 CCTCGGGAATATCAAGAATAGCAAATT 59.824 37.037 0.00 0.00 0.00 1.82
2724 8170 8.099364 TCGGGAATATCAAGAATAGCAAATTC 57.901 34.615 4.14 4.14 0.00 2.17
2725 8171 7.939039 TCGGGAATATCAAGAATAGCAAATTCT 59.061 33.333 8.16 8.16 39.82 2.40
2726 8172 9.219603 CGGGAATATCAAGAATAGCAAATTCTA 57.780 33.333 13.00 1.97 37.38 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 4.275689 TCATTCCATATTTTGCTAGCACCG 59.724 41.667 19.17 2.13 0.00 4.94
154 238 4.199432 TGGCAAAAACATCAACAACACT 57.801 36.364 0.00 0.00 0.00 3.55
155 239 5.081888 GATGGCAAAAACATCAACAACAC 57.918 39.130 0.00 0.00 43.21 3.32
642 884 6.203808 TCAATCTCAATCTCAATGGCAAAG 57.796 37.500 0.00 0.00 0.00 2.77
757 999 3.244976 GGACAGCAACCATCAAATTTCG 58.755 45.455 0.00 0.00 0.00 3.46
1298 1971 1.591703 CAGCGAGGGTCAAGCAGTA 59.408 57.895 0.00 0.00 0.00 2.74
1519 2214 1.601903 TGTCAAACATCTTCACGGTGC 59.398 47.619 2.51 0.00 0.00 5.01
1653 2348 2.036992 CCTGGCCAAATGCAACAAAGTA 59.963 45.455 7.01 0.00 43.89 2.24
1692 2435 1.999071 GCTCTGCTCGTCGTCATCCT 61.999 60.000 0.00 0.00 0.00 3.24
1702 2490 3.531207 TCATCCCCGCTCTGCTCG 61.531 66.667 0.00 0.00 0.00 5.03
1763 2698 1.255667 ACCATAGCAGGGTCGTCGTT 61.256 55.000 0.00 0.00 31.49 3.85
1766 2701 1.144057 CCACCATAGCAGGGTCGTC 59.856 63.158 0.00 0.00 36.19 4.20
1767 2702 1.612442 ACCACCATAGCAGGGTCGT 60.612 57.895 0.00 0.00 36.19 4.34
1768 2703 1.153369 CACCACCATAGCAGGGTCG 60.153 63.158 0.00 0.00 36.19 4.79
1769 2704 1.224592 CCACCACCATAGCAGGGTC 59.775 63.158 0.00 0.00 36.19 4.46
1770 2705 2.983879 GCCACCACCATAGCAGGGT 61.984 63.158 0.00 0.00 39.88 4.34
1771 2706 2.124151 GCCACCACCATAGCAGGG 60.124 66.667 0.00 0.00 0.00 4.45
1772 2707 2.514592 CGCCACCACCATAGCAGG 60.515 66.667 0.00 0.00 0.00 4.85
1773 2708 2.329539 ATCCGCCACCACCATAGCAG 62.330 60.000 0.00 0.00 0.00 4.24
1774 2709 2.374525 ATCCGCCACCACCATAGCA 61.375 57.895 0.00 0.00 0.00 3.49
1775 2710 1.893808 CATCCGCCACCACCATAGC 60.894 63.158 0.00 0.00 0.00 2.97
1776 2711 0.532862 GTCATCCGCCACCACCATAG 60.533 60.000 0.00 0.00 0.00 2.23
1777 2712 1.524961 GTCATCCGCCACCACCATA 59.475 57.895 0.00 0.00 0.00 2.74
1778 2713 2.272146 GTCATCCGCCACCACCAT 59.728 61.111 0.00 0.00 0.00 3.55
1779 2714 4.386951 CGTCATCCGCCACCACCA 62.387 66.667 0.00 0.00 0.00 4.17
1780 2715 4.077184 TCGTCATCCGCCACCACC 62.077 66.667 0.00 0.00 36.19 4.61
1781 2716 2.813908 GTCGTCATCCGCCACCAC 60.814 66.667 0.00 0.00 36.19 4.16
1782 2717 4.077184 GGTCGTCATCCGCCACCA 62.077 66.667 0.00 0.00 34.46 4.17
1783 2718 3.310860 AAGGTCGTCATCCGCCACC 62.311 63.158 0.00 0.00 35.87 4.61
1784 2719 2.100631 CAAGGTCGTCATCCGCCAC 61.101 63.158 0.00 0.00 35.87 5.01
1785 2720 2.264480 CAAGGTCGTCATCCGCCA 59.736 61.111 0.00 0.00 35.87 5.69
1786 2721 2.292794 TAGCAAGGTCGTCATCCGCC 62.293 60.000 0.00 0.00 36.19 6.13
1787 2722 0.249489 ATAGCAAGGTCGTCATCCGC 60.249 55.000 0.00 0.00 36.19 5.54
1788 2723 1.491670 CATAGCAAGGTCGTCATCCG 58.508 55.000 0.00 0.00 38.13 4.18
1789 2724 1.139058 ACCATAGCAAGGTCGTCATCC 59.861 52.381 0.00 0.00 32.90 3.51
1790 2725 2.205074 CACCATAGCAAGGTCGTCATC 58.795 52.381 0.00 0.00 37.23 2.92
1791 2726 1.134401 CCACCATAGCAAGGTCGTCAT 60.134 52.381 0.00 0.00 37.23 3.06
1792 2727 0.249120 CCACCATAGCAAGGTCGTCA 59.751 55.000 0.00 0.00 37.23 4.35
1793 2728 0.249398 ACCACCATAGCAAGGTCGTC 59.751 55.000 0.00 0.00 37.23 4.20
1794 2729 0.036388 CACCACCATAGCAAGGTCGT 60.036 55.000 0.00 0.00 37.23 4.34
1795 2730 0.744414 CCACCACCATAGCAAGGTCG 60.744 60.000 0.00 0.00 37.23 4.79
1796 2731 1.032114 GCCACCACCATAGCAAGGTC 61.032 60.000 0.00 0.00 37.23 3.85
1797 2732 1.000896 GCCACCACCATAGCAAGGT 60.001 57.895 0.00 0.00 40.85 3.50
1798 2733 1.033746 CAGCCACCACCATAGCAAGG 61.034 60.000 0.00 0.00 0.00 3.61
1799 2734 0.035152 TCAGCCACCACCATAGCAAG 60.035 55.000 0.00 0.00 0.00 4.01
1800 2735 0.322456 GTCAGCCACCACCATAGCAA 60.322 55.000 0.00 0.00 0.00 3.91
1801 2736 1.299648 GTCAGCCACCACCATAGCA 59.700 57.895 0.00 0.00 0.00 3.49
1802 2737 1.815421 CGTCAGCCACCACCATAGC 60.815 63.158 0.00 0.00 0.00 2.97
1803 2738 0.179100 CTCGTCAGCCACCACCATAG 60.179 60.000 0.00 0.00 0.00 2.23
1804 2739 1.613317 CCTCGTCAGCCACCACCATA 61.613 60.000 0.00 0.00 0.00 2.74
1805 2740 2.665000 CTCGTCAGCCACCACCAT 59.335 61.111 0.00 0.00 0.00 3.55
1806 2741 3.625897 CCTCGTCAGCCACCACCA 61.626 66.667 0.00 0.00 0.00 4.17
1807 2742 3.311110 TCCTCGTCAGCCACCACC 61.311 66.667 0.00 0.00 0.00 4.61
1808 2743 2.048127 GTCCTCGTCAGCCACCAC 60.048 66.667 0.00 0.00 0.00 4.16
1809 2744 3.311110 GGTCCTCGTCAGCCACCA 61.311 66.667 0.00 0.00 0.00 4.17
1810 2745 4.083862 GGGTCCTCGTCAGCCACC 62.084 72.222 0.00 0.00 0.00 4.61
1811 2746 2.997897 AGGGTCCTCGTCAGCCAC 60.998 66.667 0.00 0.00 33.49 5.01
1812 2747 2.997315 CAGGGTCCTCGTCAGCCA 60.997 66.667 0.00 0.00 33.49 4.75
1813 2748 4.459089 GCAGGGTCCTCGTCAGCC 62.459 72.222 0.00 0.00 0.00 4.85
1814 2749 1.395826 ATAGCAGGGTCCTCGTCAGC 61.396 60.000 0.00 0.00 0.00 4.26
1815 2750 0.387202 CATAGCAGGGTCCTCGTCAG 59.613 60.000 0.00 0.00 0.00 3.51
1816 2751 1.043116 CCATAGCAGGGTCCTCGTCA 61.043 60.000 0.00 0.00 0.00 4.35
1817 2752 1.043673 ACCATAGCAGGGTCCTCGTC 61.044 60.000 0.00 0.00 31.49 4.20
1818 2753 1.001760 ACCATAGCAGGGTCCTCGT 59.998 57.895 0.00 0.00 31.49 4.18
1819 2754 1.443407 CACCATAGCAGGGTCCTCG 59.557 63.158 0.00 0.00 36.19 4.63
1820 2755 0.983378 ACCACCATAGCAGGGTCCTC 60.983 60.000 0.00 0.00 36.19 3.71
1821 2756 1.082954 ACCACCATAGCAGGGTCCT 59.917 57.895 0.00 0.00 36.19 3.85
1822 2757 1.224592 CACCACCATAGCAGGGTCC 59.775 63.158 0.00 0.00 36.19 4.46
1823 2758 1.224592 CCACCACCATAGCAGGGTC 59.775 63.158 0.00 0.00 36.19 4.46
1824 2759 2.983879 GCCACCACCATAGCAGGGT 61.984 63.158 0.00 0.00 39.88 4.34
1827 2762 2.514592 CCGCCACCACCATAGCAG 60.515 66.667 0.00 0.00 0.00 4.24
1843 2778 1.065928 CATAGCAGGGTCGTCGTCC 59.934 63.158 0.00 0.00 0.00 4.79
1854 2939 0.745845 GTCAGCCACCACCATAGCAG 60.746 60.000 0.00 0.00 0.00 4.24
2109 3561 8.939929 ACATTGACATGTTCAGATTACACTAAG 58.060 33.333 0.00 0.00 41.16 2.18
2288 3754 0.317770 ACGAGCATGCACAAAAACCG 60.318 50.000 21.98 11.46 0.00 4.44
2450 6566 3.063316 CCACATTTGATGATGTTACGCGA 59.937 43.478 15.93 0.00 38.15 5.87
2607 8053 4.389687 GCAAGGGCAATGTTACTTTTCATG 59.610 41.667 0.00 0.00 40.72 3.07
2608 8054 4.284234 AGCAAGGGCAATGTTACTTTTCAT 59.716 37.500 0.00 0.00 44.61 2.57
2609 8055 3.640967 AGCAAGGGCAATGTTACTTTTCA 59.359 39.130 0.00 0.00 44.61 2.69
2610 8056 3.989817 CAGCAAGGGCAATGTTACTTTTC 59.010 43.478 0.00 0.00 44.61 2.29
2611 8057 3.803368 GCAGCAAGGGCAATGTTACTTTT 60.803 43.478 0.00 0.00 44.61 2.27
2612 8058 2.289010 GCAGCAAGGGCAATGTTACTTT 60.289 45.455 0.00 0.00 44.61 2.66
2613 8059 1.273327 GCAGCAAGGGCAATGTTACTT 59.727 47.619 0.00 0.00 44.61 2.24
2614 8060 0.890683 GCAGCAAGGGCAATGTTACT 59.109 50.000 0.00 0.00 44.61 2.24
2615 8061 0.602562 TGCAGCAAGGGCAATGTTAC 59.397 50.000 0.00 0.00 44.61 2.50
2616 8062 1.336131 TTGCAGCAAGGGCAATGTTA 58.664 45.000 2.83 0.00 45.57 2.41
2617 8063 2.134991 TTGCAGCAAGGGCAATGTT 58.865 47.368 2.83 0.00 45.57 2.71
2618 8064 3.873910 TTGCAGCAAGGGCAATGT 58.126 50.000 2.83 0.00 45.57 2.71
2622 8068 0.541530 TATTGGTTGCAGCAAGGGCA 60.542 50.000 8.49 0.00 44.61 5.36
2623 8069 0.607620 TTATTGGTTGCAGCAAGGGC 59.392 50.000 8.49 0.00 39.11 5.19
2624 8070 1.617850 TGTTATTGGTTGCAGCAAGGG 59.382 47.619 8.49 0.00 39.11 3.95
2625 8071 2.950433 CTGTTATTGGTTGCAGCAAGG 58.050 47.619 8.49 0.00 39.11 3.61
2630 8076 0.532115 GGGGCTGTTATTGGTTGCAG 59.468 55.000 0.00 0.00 0.00 4.41
2631 8077 0.114168 AGGGGCTGTTATTGGTTGCA 59.886 50.000 0.00 0.00 0.00 4.08
2632 8078 0.532115 CAGGGGCTGTTATTGGTTGC 59.468 55.000 0.00 0.00 0.00 4.17
2633 8079 0.532115 GCAGGGGCTGTTATTGGTTG 59.468 55.000 0.00 0.00 36.96 3.77
2634 8080 0.114168 TGCAGGGGCTGTTATTGGTT 59.886 50.000 0.00 0.00 41.91 3.67
2635 8081 0.323725 CTGCAGGGGCTGTTATTGGT 60.324 55.000 5.57 0.00 41.91 3.67
2636 8082 2.496942 CTGCAGGGGCTGTTATTGG 58.503 57.895 5.57 0.00 41.91 3.16
2643 8089 1.838112 TTTGAATACTGCAGGGGCTG 58.162 50.000 19.93 0.00 43.82 4.85
2644 8090 2.603075 TTTTGAATACTGCAGGGGCT 57.397 45.000 19.93 0.00 41.91 5.19
2645 8091 2.094026 CCTTTTTGAATACTGCAGGGGC 60.094 50.000 19.93 4.94 41.68 5.80
2646 8092 2.497273 CCCTTTTTGAATACTGCAGGGG 59.503 50.000 19.93 10.73 36.57 4.79
2647 8093 3.165071 ACCCTTTTTGAATACTGCAGGG 58.835 45.455 19.93 8.23 44.60 4.45
2648 8094 4.082125 AGACCCTTTTTGAATACTGCAGG 58.918 43.478 19.93 0.00 0.00 4.85
2649 8095 5.123979 GGTAGACCCTTTTTGAATACTGCAG 59.876 44.000 13.48 13.48 0.00 4.41
2650 8096 5.007682 GGTAGACCCTTTTTGAATACTGCA 58.992 41.667 0.00 0.00 0.00 4.41
2651 8097 5.007682 TGGTAGACCCTTTTTGAATACTGC 58.992 41.667 0.00 0.00 34.29 4.40
2652 8098 6.151144 CCTTGGTAGACCCTTTTTGAATACTG 59.849 42.308 0.00 0.00 34.29 2.74
2653 8099 6.045106 TCCTTGGTAGACCCTTTTTGAATACT 59.955 38.462 0.00 0.00 34.29 2.12
2654 8100 6.243148 TCCTTGGTAGACCCTTTTTGAATAC 58.757 40.000 0.00 0.00 34.29 1.89
2655 8101 6.457159 TCCTTGGTAGACCCTTTTTGAATA 57.543 37.500 0.00 0.00 34.29 1.75
2656 8102 5.333566 TCCTTGGTAGACCCTTTTTGAAT 57.666 39.130 0.00 0.00 34.29 2.57
2657 8103 4.799715 TCCTTGGTAGACCCTTTTTGAA 57.200 40.909 0.00 0.00 34.29 2.69
2658 8104 4.352595 TCATCCTTGGTAGACCCTTTTTGA 59.647 41.667 0.00 0.00 34.29 2.69
2659 8105 4.662278 TCATCCTTGGTAGACCCTTTTTG 58.338 43.478 0.00 0.00 34.29 2.44
2660 8106 5.510430 GATCATCCTTGGTAGACCCTTTTT 58.490 41.667 0.00 0.00 34.29 1.94
2661 8107 4.384208 CGATCATCCTTGGTAGACCCTTTT 60.384 45.833 0.00 0.00 34.29 2.27
2662 8108 3.134804 CGATCATCCTTGGTAGACCCTTT 59.865 47.826 0.00 0.00 34.29 3.11
2663 8109 2.700897 CGATCATCCTTGGTAGACCCTT 59.299 50.000 0.00 0.00 34.29 3.95
2664 8110 2.091278 TCGATCATCCTTGGTAGACCCT 60.091 50.000 0.00 0.00 34.29 4.34
2665 8111 2.036089 GTCGATCATCCTTGGTAGACCC 59.964 54.545 0.00 0.00 33.79 4.46
2666 8112 2.693591 TGTCGATCATCCTTGGTAGACC 59.306 50.000 0.00 0.00 37.69 3.85
2667 8113 4.592485 ATGTCGATCATCCTTGGTAGAC 57.408 45.455 0.00 0.00 38.62 2.59
2668 8114 5.386060 AGTATGTCGATCATCCTTGGTAGA 58.614 41.667 4.15 0.00 37.91 2.59
2669 8115 5.713792 AGTATGTCGATCATCCTTGGTAG 57.286 43.478 4.15 0.00 37.91 3.18
2670 8116 6.479972 AAAGTATGTCGATCATCCTTGGTA 57.520 37.500 4.15 0.00 33.91 3.25
2671 8117 5.359194 AAAGTATGTCGATCATCCTTGGT 57.641 39.130 4.15 0.00 33.91 3.67
2672 8118 5.914085 GAAAGTATGTCGATCATCCTTGG 57.086 43.478 4.15 0.00 33.91 3.61
2690 8136 3.728076 TGATATTCCCGAGGACGAAAG 57.272 47.619 0.00 0.00 42.66 2.62
2691 8137 3.702548 TCTTGATATTCCCGAGGACGAAA 59.297 43.478 0.00 0.00 42.66 3.46
2692 8138 3.293337 TCTTGATATTCCCGAGGACGAA 58.707 45.455 0.00 0.00 42.66 3.85
2693 8139 2.940158 TCTTGATATTCCCGAGGACGA 58.060 47.619 0.00 0.00 42.66 4.20
2694 8140 3.728076 TTCTTGATATTCCCGAGGACG 57.272 47.619 0.00 0.00 39.43 4.79
2695 8141 5.172205 GCTATTCTTGATATTCCCGAGGAC 58.828 45.833 0.00 0.00 0.00 3.85
2696 8142 4.838423 TGCTATTCTTGATATTCCCGAGGA 59.162 41.667 0.00 0.00 0.00 3.71
2697 8143 5.152623 TGCTATTCTTGATATTCCCGAGG 57.847 43.478 0.00 0.00 0.00 4.63
2698 8144 7.678947 ATTTGCTATTCTTGATATTCCCGAG 57.321 36.000 0.00 0.00 0.00 4.63
2699 8145 7.939039 AGAATTTGCTATTCTTGATATTCCCGA 59.061 33.333 8.32 0.00 34.99 5.14
2700 8146 8.103948 AGAATTTGCTATTCTTGATATTCCCG 57.896 34.615 8.32 0.00 34.99 5.14


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

AutoCloner maintained by Alex Coulton.