Multiple sequence alignment - TraesCS1D01G266800

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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 TraesCS1D01G266800 chr1D 100.000 3786 0 0 1 3786 362593425 362589640 0.000000e+00 6992.0
1 TraesCS1D01G266800 chr1D 100.000 3479 0 0 4925 8403 362588501 362585023 0.000000e+00 6425.0
2 TraesCS1D01G266800 chr1D 95.402 2436 98 14 1155 3582 142945294 142942865 0.000000e+00 3866.0
3 TraesCS1D01G266800 chr1D 94.447 2485 109 25 1154 3615 88285433 88287911 0.000000e+00 3797.0
4 TraesCS1D01G266800 chr1D 92.697 1917 98 13 5580 7491 481932355 481934234 0.000000e+00 2726.0
5 TraesCS1D01G266800 chr1D 97.697 912 21 0 7492 8403 362577898 362576987 0.000000e+00 1568.0
6 TraesCS1D01G266800 chr1D 88.309 1360 83 45 2468 3786 181032706 181031382 0.000000e+00 1561.0
7 TraesCS1D01G266800 chr1D 82.859 1266 129 57 2468 3715 20938408 20937213 0.000000e+00 1055.0
8 TraesCS1D01G266800 chr1D 97.364 569 10 1 4925 5493 397860877 397860314 0.000000e+00 963.0
9 TraesCS1D01G266800 chr1D 100.000 84 0 0 5495 5578 19957152 19957069 1.130000e-33 156.0
10 TraesCS1D01G266800 chr1D 100.000 84 0 0 5495 5578 108214451 108214368 1.130000e-33 156.0
11 TraesCS1D01G266800 chr1D 100.000 84 0 0 5495 5578 206072719 206072802 1.130000e-33 156.0
12 TraesCS1D01G266800 chr1D 100.000 84 0 0 5495 5578 483915497 483915580 1.130000e-33 156.0
13 TraesCS1D01G266800 chr1D 89.320 103 8 3 3684 3783 98144420 98144522 8.850000e-25 126.0
14 TraesCS1D01G266800 chr1D 89.773 88 5 4 3699 3783 172960064 172960150 8.920000e-20 110.0
15 TraesCS1D01G266800 chr2D 96.293 2644 51 23 1152 3751 450211824 450209184 0.000000e+00 4296.0
16 TraesCS1D01G266800 chr2D 92.465 1951 95 17 5580 7490 82210461 82208523 0.000000e+00 2741.0
17 TraesCS1D01G266800 chr2D 91.064 1287 56 29 2525 3783 384815614 384816869 0.000000e+00 1685.0
18 TraesCS1D01G266800 chr2D 97.259 912 25 0 7492 8403 386288805 386287894 0.000000e+00 1546.0
19 TraesCS1D01G266800 chr2D 97.149 912 26 0 7492 8403 155868230 155867319 0.000000e+00 1541.0
20 TraesCS1D01G266800 chr2D 96.930 912 28 0 7492 8403 386318094 386319005 0.000000e+00 1530.0
21 TraesCS1D01G266800 chr2D 94.661 899 45 2 197 1093 388079134 388078237 0.000000e+00 1391.0
22 TraesCS1D01G266800 chr2D 94.556 900 46 2 196 1093 634063866 634062968 0.000000e+00 1387.0
23 TraesCS1D01G266800 chr2D 94.444 900 47 2 196 1093 417190703 417191601 0.000000e+00 1382.0
24 TraesCS1D01G266800 chr2D 94.137 904 46 6 193 1093 589512200 589513099 0.000000e+00 1369.0
25 TraesCS1D01G266800 chr2D 98.067 569 6 3 4925 5493 450208214 450207651 0.000000e+00 985.0
26 TraesCS1D01G266800 chr2D 97.715 569 7 3 4925 5493 1745730 1746292 0.000000e+00 974.0
27 TraesCS1D01G266800 chr2D 97.364 569 10 2 4925 5493 332898810 332898247 0.000000e+00 963.0
28 TraesCS1D01G266800 chr5D 94.855 2449 99 25 1155 3590 335673970 335676404 0.000000e+00 3799.0
29 TraesCS1D01G266800 chr5D 94.256 2507 99 37 1152 3638 335682385 335684866 0.000000e+00 3790.0
30 TraesCS1D01G266800 chr5D 92.685 1367 47 33 2468 3786 480387176 480385815 0.000000e+00 1921.0
31 TraesCS1D01G266800 chr5D 89.570 1371 84 43 2441 3783 256889109 256890448 0.000000e+00 1685.0
32 TraesCS1D01G266800 chr5D 96.953 919 28 0 7485 8403 382120160 382121078 0.000000e+00 1543.0
33 TraesCS1D01G266800 chr5D 94.229 901 51 1 193 1093 70401289 70400390 0.000000e+00 1375.0
34 TraesCS1D01G266800 chr5D 97.188 569 7 4 4925 5493 122744234 122744793 0.000000e+00 953.0
35 TraesCS1D01G266800 chr5D 86.506 415 15 22 3412 3786 488326584 488326171 1.300000e-112 418.0
36 TraesCS1D01G266800 chr5D 100.000 84 0 0 5495 5578 6202160 6202243 1.130000e-33 156.0
37 TraesCS1D01G266800 chr5D 100.000 84 0 0 5495 5578 240136824 240136741 1.130000e-33 156.0
38 TraesCS1D01G266800 chr5D 96.721 61 2 0 1091 1151 503324072 503324132 1.490000e-17 102.0
39 TraesCS1D01G266800 chr4D 93.275 2617 113 48 1155 3717 12373628 12376235 0.000000e+00 3799.0
40 TraesCS1D01G266800 chr4D 94.049 2487 106 36 1152 3610 12381815 12384287 0.000000e+00 3735.0
41 TraesCS1D01G266800 chr4D 94.701 1925 80 3 5580 7491 130442841 130440926 0.000000e+00 2970.0
42 TraesCS1D01G266800 chr4D 92.654 1933 111 11 5580 7490 65098245 65096322 0.000000e+00 2754.0
43 TraesCS1D01G266800 chr4D 90.508 1338 74 36 2468 3783 3050209 3051515 0.000000e+00 1718.0
44 TraesCS1D01G266800 chr4D 89.340 1304 77 47 2468 3732 52265342 52264062 0.000000e+00 1581.0
45 TraesCS1D01G266800 chr4D 96.933 913 26 2 7492 8403 489654154 489653243 0.000000e+00 1530.0
46 TraesCS1D01G266800 chr4D 94.235 902 49 3 194 1093 479373524 479372624 0.000000e+00 1375.0
47 TraesCS1D01G266800 chr4D 96.673 571 14 5 4925 5493 418235957 418235390 0.000000e+00 944.0
48 TraesCS1D01G266800 chr4D 96.316 570 15 6 4925 5493 418228831 418228267 0.000000e+00 931.0
49 TraesCS1D01G266800 chr4D 88.785 107 8 4 3684 3786 274561659 274561553 2.460000e-25 128.0
50 TraesCS1D01G266800 chr4D 91.489 94 5 3 3693 3783 414190847 414190940 8.850000e-25 126.0
51 TraesCS1D01G266800 chr7D 94.143 2510 112 28 1149 3635 63423377 63420880 0.000000e+00 3788.0
52 TraesCS1D01G266800 chr7D 91.017 1347 57 35 2468 3786 148204523 148205833 0.000000e+00 1759.0
53 TraesCS1D01G266800 chr7D 89.428 1277 79 35 2525 3786 149584716 149583481 0.000000e+00 1559.0
54 TraesCS1D01G266800 chr7D 97.039 912 27 0 7492 8403 478936265 478935354 0.000000e+00 1535.0
55 TraesCS1D01G266800 chr7D 88.880 1295 74 40 2525 3786 208494323 208493066 0.000000e+00 1530.0
56 TraesCS1D01G266800 chr7D 98.352 546 5 2 4948 5493 459732759 459732218 0.000000e+00 955.0
57 TraesCS1D01G266800 chr7D 96.842 570 11 6 4925 5493 237504072 237504635 0.000000e+00 946.0
58 TraesCS1D01G266800 chr7D 100.000 84 0 0 5495 5578 231533282 231533199 1.130000e-33 156.0
59 TraesCS1D01G266800 chr7D 96.721 61 2 0 1091 1151 231586255 231586315 1.490000e-17 102.0
60 TraesCS1D01G266800 chr7D 96.721 61 2 0 1091 1151 231589777 231589837 1.490000e-17 102.0
61 TraesCS1D01G266800 chr7D 98.276 58 1 0 1094 1151 231592491 231592434 1.490000e-17 102.0
62 TraesCS1D01G266800 chr6D 94.515 2425 108 18 1155 3573 271176426 271174021 0.000000e+00 3718.0
63 TraesCS1D01G266800 chr6D 89.420 1361 85 44 2468 3786 72683133 72681790 0.000000e+00 1661.0
64 TraesCS1D01G266800 chr6D 94.495 545 17 1 6960 7491 36286155 36286699 0.000000e+00 828.0
65 TraesCS1D01G266800 chr6D 84.375 352 38 13 3445 3783 243036476 243036823 6.290000e-86 329.0
66 TraesCS1D01G266800 chr6D 89.691 97 7 3 3693 3786 310097327 310097231 4.120000e-23 121.0
67 TraesCS1D01G266800 chr6D 89.474 95 5 5 3691 3783 415133486 415133577 1.920000e-21 115.0
68 TraesCS1D01G266800 chr6D 97.059 68 1 1 3720 3786 447199221 447199154 6.890000e-21 113.0
69 TraesCS1D01G266800 chr6D 85.714 98 8 5 3691 3783 299150128 299150224 1.930000e-16 99.0
70 TraesCS1D01G266800 chr6D 100.000 49 0 0 3735 3783 299158148 299158196 3.230000e-14 91.6
71 TraesCS1D01G266800 chr6D 83.077 65 5 4 3594 3656 93237823 93237763 4.000000e-03 54.7
72 TraesCS1D01G266800 chr3D 94.865 1928 76 8 5580 7490 543499449 543501370 0.000000e+00 2990.0
73 TraesCS1D01G266800 chr3D 94.813 1928 79 5 5580 7491 542834788 542836710 0.000000e+00 2987.0
74 TraesCS1D01G266800 chr3D 92.898 1929 112 12 5582 7491 126288275 126290197 0.000000e+00 2780.0
75 TraesCS1D01G266800 chr3D 90.365 1287 68 27 2525 3786 449496097 449494842 0.000000e+00 1639.0
76 TraesCS1D01G266800 chr3D 88.979 1361 77 40 2468 3786 449486381 449485052 0.000000e+00 1615.0
77 TraesCS1D01G266800 chr3D 97.043 913 26 1 7492 8403 26848452 26847540 0.000000e+00 1535.0
78 TraesCS1D01G266800 chr3D 97.039 912 26 1 7492 8403 547869279 547868369 0.000000e+00 1533.0
79 TraesCS1D01G266800 chr3D 94.568 902 46 2 194 1093 542833887 542834787 0.000000e+00 1391.0
80 TraesCS1D01G266800 chr3D 94.562 901 46 2 195 1093 543498549 543499448 0.000000e+00 1389.0
81 TraesCS1D01G266800 chr3D 93.929 906 49 5 191 1093 461558877 461559779 0.000000e+00 1363.0
82 TraesCS1D01G266800 chr3D 96.721 61 2 0 1091 1151 24158212 24158272 1.490000e-17 102.0
83 TraesCS1D01G266800 chr3D 96.721 61 2 0 1091 1151 24158723 24158783 1.490000e-17 102.0
84 TraesCS1D01G266800 chr2B 93.257 1913 112 10 5580 7491 72759906 72761802 0.000000e+00 2802.0
85 TraesCS1D01G266800 chr2B 87.265 479 32 10 7039 7490 39311630 39311154 3.480000e-143 520.0
86 TraesCS1D01G266800 chr2B 86.047 344 21 3 7175 7491 569075714 569076057 2.250000e-90 344.0
87 TraesCS1D01G266800 chr2B 86.032 315 17 3 7204 7491 439567084 439566770 6.330000e-81 313.0
88 TraesCS1D01G266800 chr6A 92.653 1960 93 10 5580 7490 594937509 594935552 0.000000e+00 2774.0
89 TraesCS1D01G266800 chr6A 92.745 1916 128 5 5580 7491 381114602 381112694 0.000000e+00 2758.0
90 TraesCS1D01G266800 chr6A 100.000 84 0 0 5495 5578 53820800 53820883 1.130000e-33 156.0
91 TraesCS1D01G266800 chr6B 90.879 1842 132 18 5581 7398 641038498 641036669 0.000000e+00 2438.0
92 TraesCS1D01G266800 chr3B 91.532 744 49 8 6749 7491 476390911 476391641 0.000000e+00 1013.0
93 TraesCS1D01G266800 chr7A 93.373 664 39 4 6829 7491 257272824 257273483 0.000000e+00 977.0
94 TraesCS1D01G266800 chrUn 84.580 441 16 31 3336 3726 474955952 474955514 2.840000e-104 390.0
95 TraesCS1D01G266800 chrUn 86.592 179 18 5 3541 3716 184828214 184828039 8.610000e-45 193.0
96 TraesCS1D01G266800 chrUn 98.276 58 1 0 1094 1151 298933341 298933284 1.490000e-17 102.0
97 TraesCS1D01G266800 chrUn 98.276 58 1 0 1094 1151 438111271 438111214 1.490000e-17 102.0
98 TraesCS1D01G266800 chrUn 83.810 105 10 6 3685 3783 274852913 274853016 8.980000e-15 93.5
99 TraesCS1D01G266800 chr1A 100.000 84 0 0 5495 5578 112776915 112776998 1.130000e-33 156.0
100 TraesCS1D01G266800 chr1A 98.276 58 1 0 1094 1151 554455168 554455111 1.490000e-17 102.0


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 TraesCS1D01G266800 chr1D 362585023 362593425 8402 True 6708.5 6992 100.0000 1 8403 2 chr1D.!!$R8 8402
1 TraesCS1D01G266800 chr1D 142942865 142945294 2429 True 3866.0 3866 95.4020 1155 3582 1 chr1D.!!$R4 2427
2 TraesCS1D01G266800 chr1D 88285433 88287911 2478 False 3797.0 3797 94.4470 1154 3615 1 chr1D.!!$F1 2461
3 TraesCS1D01G266800 chr1D 481932355 481934234 1879 False 2726.0 2726 92.6970 5580 7491 1 chr1D.!!$F5 1911
4 TraesCS1D01G266800 chr1D 362576987 362577898 911 True 1568.0 1568 97.6970 7492 8403 1 chr1D.!!$R6 911
5 TraesCS1D01G266800 chr1D 181031382 181032706 1324 True 1561.0 1561 88.3090 2468 3786 1 chr1D.!!$R5 1318
6 TraesCS1D01G266800 chr1D 20937213 20938408 1195 True 1055.0 1055 82.8590 2468 3715 1 chr1D.!!$R2 1247
7 TraesCS1D01G266800 chr1D 397860314 397860877 563 True 963.0 963 97.3640 4925 5493 1 chr1D.!!$R7 568
8 TraesCS1D01G266800 chr2D 82208523 82210461 1938 True 2741.0 2741 92.4650 5580 7490 1 chr2D.!!$R1 1910
9 TraesCS1D01G266800 chr2D 450207651 450211824 4173 True 2640.5 4296 97.1800 1152 5493 2 chr2D.!!$R7 4341
10 TraesCS1D01G266800 chr2D 384815614 384816869 1255 False 1685.0 1685 91.0640 2525 3783 1 chr2D.!!$F2 1258
11 TraesCS1D01G266800 chr2D 386287894 386288805 911 True 1546.0 1546 97.2590 7492 8403 1 chr2D.!!$R4 911
12 TraesCS1D01G266800 chr2D 155867319 155868230 911 True 1541.0 1541 97.1490 7492 8403 1 chr2D.!!$R2 911
13 TraesCS1D01G266800 chr2D 386318094 386319005 911 False 1530.0 1530 96.9300 7492 8403 1 chr2D.!!$F3 911
14 TraesCS1D01G266800 chr2D 388078237 388079134 897 True 1391.0 1391 94.6610 197 1093 1 chr2D.!!$R5 896
15 TraesCS1D01G266800 chr2D 634062968 634063866 898 True 1387.0 1387 94.5560 196 1093 1 chr2D.!!$R6 897
16 TraesCS1D01G266800 chr2D 417190703 417191601 898 False 1382.0 1382 94.4440 196 1093 1 chr2D.!!$F4 897
17 TraesCS1D01G266800 chr2D 589512200 589513099 899 False 1369.0 1369 94.1370 193 1093 1 chr2D.!!$F5 900
18 TraesCS1D01G266800 chr2D 1745730 1746292 562 False 974.0 974 97.7150 4925 5493 1 chr2D.!!$F1 568
19 TraesCS1D01G266800 chr2D 332898247 332898810 563 True 963.0 963 97.3640 4925 5493 1 chr2D.!!$R3 568
20 TraesCS1D01G266800 chr5D 335673970 335676404 2434 False 3799.0 3799 94.8550 1155 3590 1 chr5D.!!$F4 2435
21 TraesCS1D01G266800 chr5D 335682385 335684866 2481 False 3790.0 3790 94.2560 1152 3638 1 chr5D.!!$F5 2486
22 TraesCS1D01G266800 chr5D 480385815 480387176 1361 True 1921.0 1921 92.6850 2468 3786 1 chr5D.!!$R3 1318
23 TraesCS1D01G266800 chr5D 256889109 256890448 1339 False 1685.0 1685 89.5700 2441 3783 1 chr5D.!!$F3 1342
24 TraesCS1D01G266800 chr5D 382120160 382121078 918 False 1543.0 1543 96.9530 7485 8403 1 chr5D.!!$F6 918
25 TraesCS1D01G266800 chr5D 70400390 70401289 899 True 1375.0 1375 94.2290 193 1093 1 chr5D.!!$R1 900
26 TraesCS1D01G266800 chr5D 122744234 122744793 559 False 953.0 953 97.1880 4925 5493 1 chr5D.!!$F2 568
27 TraesCS1D01G266800 chr4D 12373628 12376235 2607 False 3799.0 3799 93.2750 1155 3717 1 chr4D.!!$F2 2562
28 TraesCS1D01G266800 chr4D 12381815 12384287 2472 False 3735.0 3735 94.0490 1152 3610 1 chr4D.!!$F3 2458
29 TraesCS1D01G266800 chr4D 130440926 130442841 1915 True 2970.0 2970 94.7010 5580 7491 1 chr4D.!!$R3 1911
30 TraesCS1D01G266800 chr4D 65096322 65098245 1923 True 2754.0 2754 92.6540 5580 7490 1 chr4D.!!$R2 1910
31 TraesCS1D01G266800 chr4D 3050209 3051515 1306 False 1718.0 1718 90.5080 2468 3783 1 chr4D.!!$F1 1315
32 TraesCS1D01G266800 chr4D 52264062 52265342 1280 True 1581.0 1581 89.3400 2468 3732 1 chr4D.!!$R1 1264
33 TraesCS1D01G266800 chr4D 489653243 489654154 911 True 1530.0 1530 96.9330 7492 8403 1 chr4D.!!$R8 911
34 TraesCS1D01G266800 chr4D 479372624 479373524 900 True 1375.0 1375 94.2350 194 1093 1 chr4D.!!$R7 899
35 TraesCS1D01G266800 chr4D 418235390 418235957 567 True 944.0 944 96.6730 4925 5493 1 chr4D.!!$R6 568
36 TraesCS1D01G266800 chr4D 418228267 418228831 564 True 931.0 931 96.3160 4925 5493 1 chr4D.!!$R5 568
37 TraesCS1D01G266800 chr7D 63420880 63423377 2497 True 3788.0 3788 94.1430 1149 3635 1 chr7D.!!$R1 2486
38 TraesCS1D01G266800 chr7D 148204523 148205833 1310 False 1759.0 1759 91.0170 2468 3786 1 chr7D.!!$F1 1318
39 TraesCS1D01G266800 chr7D 149583481 149584716 1235 True 1559.0 1559 89.4280 2525 3786 1 chr7D.!!$R2 1261
40 TraesCS1D01G266800 chr7D 478935354 478936265 911 True 1535.0 1535 97.0390 7492 8403 1 chr7D.!!$R7 911
41 TraesCS1D01G266800 chr7D 208493066 208494323 1257 True 1530.0 1530 88.8800 2525 3786 1 chr7D.!!$R3 1261
42 TraesCS1D01G266800 chr7D 459732218 459732759 541 True 955.0 955 98.3520 4948 5493 1 chr7D.!!$R6 545
43 TraesCS1D01G266800 chr7D 237504072 237504635 563 False 946.0 946 96.8420 4925 5493 1 chr7D.!!$F2 568
44 TraesCS1D01G266800 chr6D 271174021 271176426 2405 True 3718.0 3718 94.5150 1155 3573 1 chr6D.!!$R3 2418
45 TraesCS1D01G266800 chr6D 72681790 72683133 1343 True 1661.0 1661 89.4200 2468 3786 1 chr6D.!!$R1 1318
46 TraesCS1D01G266800 chr6D 36286155 36286699 544 False 828.0 828 94.4950 6960 7491 1 chr6D.!!$F1 531
47 TraesCS1D01G266800 chr3D 126288275 126290197 1922 False 2780.0 2780 92.8980 5582 7491 1 chr3D.!!$F1 1909
48 TraesCS1D01G266800 chr3D 543498549 543501370 2821 False 2189.5 2990 94.7135 195 7490 2 chr3D.!!$F5 7295
49 TraesCS1D01G266800 chr3D 542833887 542836710 2823 False 2189.0 2987 94.6905 194 7491 2 chr3D.!!$F4 7297
50 TraesCS1D01G266800 chr3D 449494842 449496097 1255 True 1639.0 1639 90.3650 2525 3786 1 chr3D.!!$R3 1261
51 TraesCS1D01G266800 chr3D 449485052 449486381 1329 True 1615.0 1615 88.9790 2468 3786 1 chr3D.!!$R2 1318
52 TraesCS1D01G266800 chr3D 26847540 26848452 912 True 1535.0 1535 97.0430 7492 8403 1 chr3D.!!$R1 911
53 TraesCS1D01G266800 chr3D 547868369 547869279 910 True 1533.0 1533 97.0390 7492 8403 1 chr3D.!!$R4 911
54 TraesCS1D01G266800 chr3D 461558877 461559779 902 False 1363.0 1363 93.9290 191 1093 1 chr3D.!!$F2 902
55 TraesCS1D01G266800 chr2B 72759906 72761802 1896 False 2802.0 2802 93.2570 5580 7491 1 chr2B.!!$F1 1911
56 TraesCS1D01G266800 chr6A 594935552 594937509 1957 True 2774.0 2774 92.6530 5580 7490 1 chr6A.!!$R2 1910
57 TraesCS1D01G266800 chr6A 381112694 381114602 1908 True 2758.0 2758 92.7450 5580 7491 1 chr6A.!!$R1 1911
58 TraesCS1D01G266800 chr6B 641036669 641038498 1829 True 2438.0 2438 90.8790 5581 7398 1 chr6B.!!$R1 1817
59 TraesCS1D01G266800 chr3B 476390911 476391641 730 False 1013.0 1013 91.5320 6749 7491 1 chr3B.!!$F1 742
60 TraesCS1D01G266800 chr7A 257272824 257273483 659 False 977.0 977 93.3730 6829 7491 1 chr7A.!!$F1 662

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
159 160 0.032952 GGGTGTGTGTTCGCTGAGTA 59.967 55.000 0.00 0.00 0.00 2.59 F
186 187 0.033642 GTAGGTCGCTGAATAGGGGC 59.966 60.000 0.00 0.00 40.45 5.80 F
187 188 0.105658 TAGGTCGCTGAATAGGGGCT 60.106 55.000 0.00 0.00 40.91 5.19 F
461 463 0.254747 AAATCGGCGGGAGGATTTCA 59.745 50.000 7.21 0.00 38.18 2.69 F
697 701 1.310933 GCCATGGCCTCTGTGAGTTG 61.311 60.000 27.24 0.00 34.56 3.16 F
1114 1119 2.237393 AATTTTGCAAAGCTTCCGCA 57.763 40.000 17.08 17.08 39.10 5.69 F
1127 1132 2.287009 GCTTCCGCATAATTTCCTTCGG 60.287 50.000 0.00 0.00 38.34 4.30 F
1142 1147 2.618709 CCTTCGGATTAAGCCAACATCC 59.381 50.000 10.94 0.00 34.18 3.51 F
3165 3201 1.662446 GGACGAACGGACTGCGAAA 60.662 57.895 0.00 0.00 0.00 3.46 F
5493 6112 0.104120 TGATTATCCGGGCGTCACAG 59.896 55.000 0.00 0.00 0.00 3.66 F
5834 6467 0.037303 AAGCTAGCAGCAGCAAAGGA 59.963 50.000 18.83 0.00 45.56 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1144 1149 0.038343 GGGCGTCACAGTTACCGTAA 60.038 55.000 0.00 0.00 0.00 3.18 R
1149 1154 0.322187 ATTGGGGGCGTCACAGTTAC 60.322 55.000 0.00 0.00 0.00 2.50 R
1150 1155 0.402504 AATTGGGGGCGTCACAGTTA 59.597 50.000 0.00 0.00 0.00 2.24 R
1433 1441 2.244252 GGAGTAGTTAGGAGGTCCCAGA 59.756 54.545 0.00 0.00 37.41 3.86 R
2663 2677 2.619074 GCTAGTTTTCCATCAGTGGCCT 60.619 50.000 3.32 0.00 45.63 5.19 R
2965 2997 3.682377 ACGCATCGTCATGTTATGTTTGA 59.318 39.130 0.00 0.00 33.69 2.69 R
3165 3201 1.580845 AACGACGAGACGAATCCGGT 61.581 55.000 0.00 0.00 40.78 5.28 R
5238 5857 8.519526 TCCTAACATAAATAAAACAGTGGCAAG 58.480 33.333 0.00 0.00 0.00 4.01 R
5510 6129 0.249280 TCGCGCTTTCTGACACAGAA 60.249 50.000 5.56 9.67 46.93 3.02 R
6431 7065 0.251341 ATGGCTTGTCGAAGGGCTTT 60.251 50.000 0.00 0.00 0.00 3.51 R
8295 9030 1.376609 GACGGTGATGGGTTGGATGC 61.377 60.000 0.00 0.00 0.00 3.91 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
97 98 1.819905 AAAAACAAGGTGCCACGGG 59.180 52.632 0.00 0.00 0.00 5.28
125 126 2.807622 GGTCGGCCCAAATCATGC 59.192 61.111 0.00 0.00 0.00 4.06
126 127 2.051518 GGTCGGCCCAAATCATGCA 61.052 57.895 0.00 0.00 0.00 3.96
127 128 1.139520 GTCGGCCCAAATCATGCAC 59.860 57.895 0.00 0.00 0.00 4.57
128 129 2.102749 CGGCCCAAATCATGCACG 59.897 61.111 0.00 0.00 0.00 5.34
129 130 2.495866 GGCCCAAATCATGCACGG 59.504 61.111 0.00 0.00 0.00 4.94
130 131 2.051518 GGCCCAAATCATGCACGGA 61.052 57.895 0.00 0.00 0.00 4.69
131 132 1.434696 GCCCAAATCATGCACGGAG 59.565 57.895 0.00 0.00 0.00 4.63
132 133 2.008268 GCCCAAATCATGCACGGAGG 62.008 60.000 0.00 0.00 0.00 4.30
133 134 0.394216 CCCAAATCATGCACGGAGGA 60.394 55.000 0.00 0.00 0.00 3.71
134 135 1.019673 CCAAATCATGCACGGAGGAG 58.980 55.000 0.00 0.00 0.00 3.69
135 136 1.407299 CCAAATCATGCACGGAGGAGA 60.407 52.381 0.00 0.00 0.00 3.71
136 137 1.938577 CAAATCATGCACGGAGGAGAG 59.061 52.381 0.00 0.00 0.00 3.20
137 138 1.489481 AATCATGCACGGAGGAGAGA 58.511 50.000 0.00 0.00 0.00 3.10
138 139 1.039068 ATCATGCACGGAGGAGAGAG 58.961 55.000 0.00 0.00 0.00 3.20
139 140 1.039785 TCATGCACGGAGGAGAGAGG 61.040 60.000 0.00 0.00 0.00 3.69
140 141 1.760086 ATGCACGGAGGAGAGAGGG 60.760 63.158 0.00 0.00 0.00 4.30
141 142 3.151022 GCACGGAGGAGAGAGGGG 61.151 72.222 0.00 0.00 0.00 4.79
142 143 2.443016 CACGGAGGAGAGAGGGGG 60.443 72.222 0.00 0.00 0.00 5.40
143 144 2.947785 ACGGAGGAGAGAGGGGGT 60.948 66.667 0.00 0.00 0.00 4.95
144 145 2.443016 CGGAGGAGAGAGGGGGTG 60.443 72.222 0.00 0.00 0.00 4.61
145 146 2.781406 GGAGGAGAGAGGGGGTGT 59.219 66.667 0.00 0.00 0.00 4.16
146 147 1.687493 GGAGGAGAGAGGGGGTGTG 60.687 68.421 0.00 0.00 0.00 3.82
147 148 1.079438 GAGGAGAGAGGGGGTGTGT 59.921 63.158 0.00 0.00 0.00 3.72
148 149 1.229336 AGGAGAGAGGGGGTGTGTG 60.229 63.158 0.00 0.00 0.00 3.82
149 150 1.536662 GGAGAGAGGGGGTGTGTGT 60.537 63.158 0.00 0.00 0.00 3.72
150 151 1.128188 GGAGAGAGGGGGTGTGTGTT 61.128 60.000 0.00 0.00 0.00 3.32
151 152 0.321996 GAGAGAGGGGGTGTGTGTTC 59.678 60.000 0.00 0.00 0.00 3.18
152 153 1.004918 GAGAGGGGGTGTGTGTTCG 60.005 63.158 0.00 0.00 0.00 3.95
153 154 2.668550 GAGGGGGTGTGTGTTCGC 60.669 66.667 0.00 0.00 0.00 4.70
154 155 3.168528 AGGGGGTGTGTGTTCGCT 61.169 61.111 0.00 0.00 0.00 4.93
155 156 2.978010 GGGGGTGTGTGTTCGCTG 60.978 66.667 0.00 0.00 0.00 5.18
156 157 2.110213 GGGGTGTGTGTTCGCTGA 59.890 61.111 0.00 0.00 0.00 4.26
157 158 1.961277 GGGGTGTGTGTTCGCTGAG 60.961 63.158 0.00 0.00 0.00 3.35
158 159 1.227556 GGGTGTGTGTTCGCTGAGT 60.228 57.895 0.00 0.00 0.00 3.41
159 160 0.032952 GGGTGTGTGTTCGCTGAGTA 59.967 55.000 0.00 0.00 0.00 2.59
160 161 1.337823 GGGTGTGTGTTCGCTGAGTAT 60.338 52.381 0.00 0.00 0.00 2.12
161 162 1.993370 GGTGTGTGTTCGCTGAGTATC 59.007 52.381 0.00 0.00 0.00 2.24
162 163 1.993370 GTGTGTGTTCGCTGAGTATCC 59.007 52.381 0.00 0.00 0.00 2.59
163 164 1.616374 TGTGTGTTCGCTGAGTATCCA 59.384 47.619 0.00 0.00 0.00 3.41
164 165 2.036604 TGTGTGTTCGCTGAGTATCCAA 59.963 45.455 0.00 0.00 0.00 3.53
165 166 2.412089 GTGTGTTCGCTGAGTATCCAAC 59.588 50.000 0.00 0.00 0.00 3.77
166 167 1.654105 GTGTTCGCTGAGTATCCAACG 59.346 52.381 0.00 0.00 0.00 4.10
167 168 1.278238 GTTCGCTGAGTATCCAACGG 58.722 55.000 0.00 0.00 0.00 4.44
168 169 0.892755 TTCGCTGAGTATCCAACGGT 59.107 50.000 0.00 0.00 0.00 4.83
169 170 1.753930 TCGCTGAGTATCCAACGGTA 58.246 50.000 0.00 0.00 0.00 4.02
170 171 1.674441 TCGCTGAGTATCCAACGGTAG 59.326 52.381 0.00 0.00 0.00 3.18
171 172 1.269102 CGCTGAGTATCCAACGGTAGG 60.269 57.143 0.00 0.00 0.00 3.18
172 173 1.755380 GCTGAGTATCCAACGGTAGGT 59.245 52.381 0.00 0.00 0.00 3.08
173 174 2.223758 GCTGAGTATCCAACGGTAGGTC 60.224 54.545 0.00 0.00 0.00 3.85
174 175 2.019249 TGAGTATCCAACGGTAGGTCG 58.981 52.381 0.00 0.00 0.00 4.79
175 176 0.743097 AGTATCCAACGGTAGGTCGC 59.257 55.000 0.00 0.00 0.00 5.19
176 177 0.743097 GTATCCAACGGTAGGTCGCT 59.257 55.000 0.00 0.00 0.00 4.93
177 178 0.742505 TATCCAACGGTAGGTCGCTG 59.257 55.000 0.00 0.00 0.00 5.18
178 179 0.968901 ATCCAACGGTAGGTCGCTGA 60.969 55.000 0.00 0.00 0.00 4.26
179 180 1.180456 TCCAACGGTAGGTCGCTGAA 61.180 55.000 0.00 0.00 0.00 3.02
180 181 0.108329 CCAACGGTAGGTCGCTGAAT 60.108 55.000 0.00 0.00 0.00 2.57
181 182 1.135527 CCAACGGTAGGTCGCTGAATA 59.864 52.381 0.00 0.00 0.00 1.75
182 183 2.460918 CAACGGTAGGTCGCTGAATAG 58.539 52.381 0.00 0.00 0.00 1.73
183 184 1.030457 ACGGTAGGTCGCTGAATAGG 58.970 55.000 0.00 0.00 0.00 2.57
184 185 0.314302 CGGTAGGTCGCTGAATAGGG 59.686 60.000 0.00 0.00 38.16 3.53
185 186 0.680061 GGTAGGTCGCTGAATAGGGG 59.320 60.000 0.00 0.00 37.46 4.79
186 187 0.033642 GTAGGTCGCTGAATAGGGGC 59.966 60.000 0.00 0.00 40.45 5.80
187 188 0.105658 TAGGTCGCTGAATAGGGGCT 60.106 55.000 0.00 0.00 40.91 5.19
188 189 1.069935 GGTCGCTGAATAGGGGCTC 59.930 63.158 0.00 0.00 40.91 4.70
189 190 1.069935 GTCGCTGAATAGGGGCTCC 59.930 63.158 0.00 0.00 38.35 4.70
341 342 2.435410 GGAAACGCCCGAATCGGT 60.435 61.111 21.12 0.42 46.80 4.69
461 463 0.254747 AAATCGGCGGGAGGATTTCA 59.745 50.000 7.21 0.00 38.18 2.69
555 557 3.014085 TTCGAGCTTTCCCGCCGAT 62.014 57.895 0.00 0.00 34.39 4.18
590 592 4.697756 AGCAGGTAAGCGGCGCAA 62.698 61.111 35.02 19.15 40.15 4.85
697 701 1.310933 GCCATGGCCTCTGTGAGTTG 61.311 60.000 27.24 0.00 34.56 3.16
700 704 2.507484 CATGGCCTCTGTGAGTTGAAA 58.493 47.619 3.32 0.00 0.00 2.69
763 768 4.040217 CAGCTAGGGTTTGATCTAGATGCT 59.960 45.833 10.74 6.28 41.17 3.79
797 802 4.026052 TGGTCTGATCTGTGAGCTGATAA 58.974 43.478 0.00 0.00 34.14 1.75
831 836 3.243128 GCGGTTGCAATTTGTGGC 58.757 55.556 0.59 0.00 42.15 5.01
854 859 3.019564 GGGCTAGATGTTCAAGCATGTT 58.980 45.455 0.00 0.00 38.01 2.71
921 926 7.011763 GCTTGTGTTGAATCATGCTTAGATCTA 59.988 37.037 0.00 0.00 33.79 1.98
968 973 4.383850 TTGTAGCATGCTGTTTGTTGTT 57.616 36.364 30.42 1.88 0.00 2.83
997 1002 3.519107 TGTTCCTGCTCATAGATTGTCCA 59.481 43.478 0.00 0.00 0.00 4.02
1029 1034 4.328440 GGTATGATAGCGATGAAGCATGTC 59.672 45.833 0.00 0.00 40.15 3.06
1093 1098 4.450976 CTTTCATGGATTGTCCGGTATGA 58.549 43.478 0.00 0.00 40.17 2.15
1094 1099 4.705110 TTCATGGATTGTCCGGTATGAT 57.295 40.909 0.00 0.00 40.17 2.45
1095 1100 5.816955 TTCATGGATTGTCCGGTATGATA 57.183 39.130 0.00 0.00 40.17 2.15
1096 1101 5.816955 TCATGGATTGTCCGGTATGATAA 57.183 39.130 0.00 0.00 40.17 1.75
1097 1102 6.373005 TCATGGATTGTCCGGTATGATAAT 57.627 37.500 0.00 0.00 40.17 1.28
1098 1103 6.778821 TCATGGATTGTCCGGTATGATAATT 58.221 36.000 0.00 0.00 40.17 1.40
1099 1104 7.230747 TCATGGATTGTCCGGTATGATAATTT 58.769 34.615 0.00 0.00 40.17 1.82
1100 1105 7.723616 TCATGGATTGTCCGGTATGATAATTTT 59.276 33.333 0.00 0.00 40.17 1.82
1101 1106 7.270757 TGGATTGTCCGGTATGATAATTTTG 57.729 36.000 0.00 0.00 40.17 2.44
1102 1107 6.149633 GGATTGTCCGGTATGATAATTTTGC 58.850 40.000 0.00 0.00 0.00 3.68
1103 1108 6.238897 GGATTGTCCGGTATGATAATTTTGCA 60.239 38.462 0.00 0.00 0.00 4.08
1104 1109 6.516739 TTGTCCGGTATGATAATTTTGCAA 57.483 33.333 0.00 0.00 0.00 4.08
1105 1110 6.516739 TGTCCGGTATGATAATTTTGCAAA 57.483 33.333 8.05 8.05 0.00 3.68
1106 1111 6.559810 TGTCCGGTATGATAATTTTGCAAAG 58.440 36.000 12.41 0.00 0.00 2.77
1107 1112 5.458779 GTCCGGTATGATAATTTTGCAAAGC 59.541 40.000 12.41 0.00 0.00 3.51
1108 1113 5.359576 TCCGGTATGATAATTTTGCAAAGCT 59.640 36.000 12.41 6.18 0.00 3.74
1109 1114 6.042143 CCGGTATGATAATTTTGCAAAGCTT 58.958 36.000 12.41 12.22 0.00 3.74
1110 1115 6.198966 CCGGTATGATAATTTTGCAAAGCTTC 59.801 38.462 12.41 8.84 0.00 3.86
1111 1116 6.198966 CGGTATGATAATTTTGCAAAGCTTCC 59.801 38.462 12.41 4.27 0.00 3.46
1112 1117 6.198966 GGTATGATAATTTTGCAAAGCTTCCG 59.801 38.462 12.41 0.00 0.00 4.30
1113 1118 3.925913 TGATAATTTTGCAAAGCTTCCGC 59.074 39.130 12.41 12.66 0.00 5.54
1114 1119 2.237393 AATTTTGCAAAGCTTCCGCA 57.763 40.000 17.08 17.08 39.10 5.69
1115 1120 2.460757 ATTTTGCAAAGCTTCCGCAT 57.539 40.000 20.48 6.90 39.10 4.73
1116 1121 3.591196 ATTTTGCAAAGCTTCCGCATA 57.409 38.095 20.48 14.65 39.10 3.14
1117 1122 3.377346 TTTTGCAAAGCTTCCGCATAA 57.623 38.095 20.48 18.63 39.10 1.90
1118 1123 3.591196 TTTGCAAAGCTTCCGCATAAT 57.409 38.095 20.48 0.00 39.10 1.28
1119 1124 3.591196 TTGCAAAGCTTCCGCATAATT 57.409 38.095 20.48 0.00 39.10 1.40
1120 1125 3.591196 TGCAAAGCTTCCGCATAATTT 57.409 38.095 17.08 0.00 39.10 1.82
1121 1126 3.510719 TGCAAAGCTTCCGCATAATTTC 58.489 40.909 17.08 0.00 39.10 2.17
1122 1127 2.860136 GCAAAGCTTCCGCATAATTTCC 59.140 45.455 14.24 0.00 39.10 3.13
1123 1128 3.429410 GCAAAGCTTCCGCATAATTTCCT 60.429 43.478 14.24 0.00 39.10 3.36
1124 1129 4.747810 CAAAGCTTCCGCATAATTTCCTT 58.252 39.130 0.00 0.00 39.10 3.36
1125 1130 4.639135 AAGCTTCCGCATAATTTCCTTC 57.361 40.909 0.00 0.00 39.10 3.46
1126 1131 2.614057 AGCTTCCGCATAATTTCCTTCG 59.386 45.455 0.00 0.00 39.10 3.79
1127 1132 2.287009 GCTTCCGCATAATTTCCTTCGG 60.287 50.000 0.00 0.00 38.34 4.30
1128 1133 2.992124 TCCGCATAATTTCCTTCGGA 57.008 45.000 0.00 0.00 42.86 4.55
1129 1134 3.485463 TCCGCATAATTTCCTTCGGAT 57.515 42.857 0.00 0.00 40.62 4.18
1130 1135 3.815809 TCCGCATAATTTCCTTCGGATT 58.184 40.909 0.00 0.00 40.62 3.01
1131 1136 4.963373 TCCGCATAATTTCCTTCGGATTA 58.037 39.130 0.00 0.00 40.62 1.75
1132 1137 5.369833 TCCGCATAATTTCCTTCGGATTAA 58.630 37.500 0.00 0.00 40.62 1.40
1133 1138 5.468746 TCCGCATAATTTCCTTCGGATTAAG 59.531 40.000 0.00 0.00 40.62 1.85
1134 1139 5.147162 CGCATAATTTCCTTCGGATTAAGC 58.853 41.667 0.00 0.00 30.72 3.09
1135 1140 5.461526 GCATAATTTCCTTCGGATTAAGCC 58.538 41.667 0.00 0.00 28.85 4.35
1136 1141 5.009610 GCATAATTTCCTTCGGATTAAGCCA 59.990 40.000 10.94 0.00 28.85 4.75
1137 1142 6.460953 GCATAATTTCCTTCGGATTAAGCCAA 60.461 38.462 10.94 2.77 28.85 4.52
1138 1143 4.983671 ATTTCCTTCGGATTAAGCCAAC 57.016 40.909 10.94 0.00 0.00 3.77
1139 1144 3.426787 TTCCTTCGGATTAAGCCAACA 57.573 42.857 10.94 0.00 0.00 3.33
1140 1145 3.644966 TCCTTCGGATTAAGCCAACAT 57.355 42.857 10.94 0.00 0.00 2.71
1141 1146 3.541632 TCCTTCGGATTAAGCCAACATC 58.458 45.455 10.94 0.00 0.00 3.06
1142 1147 2.618709 CCTTCGGATTAAGCCAACATCC 59.381 50.000 10.94 0.00 34.18 3.51
1147 1152 4.547406 GGATTAAGCCAACATCCGTTAC 57.453 45.455 4.48 0.00 32.75 2.50
1148 1153 3.001939 GGATTAAGCCAACATCCGTTACG 59.998 47.826 4.48 0.00 32.75 3.18
1166 1171 2.745037 GTAACTGTGACGCCCCCA 59.255 61.111 0.00 0.00 0.00 4.96
1292 1297 3.424703 CATCATAATACAAGCCAGGGGG 58.575 50.000 0.00 0.00 37.18 5.40
1565 1574 3.312736 AAAGAGGGAGAAAAGCAACCA 57.687 42.857 0.00 0.00 0.00 3.67
1871 1882 7.201670 GGAAGGGTGTGTTTTATTAAGTATCCG 60.202 40.741 0.00 0.00 0.00 4.18
2663 2677 3.244078 ACAGCAGACGGACAAGAATGTAA 60.244 43.478 0.00 0.00 40.74 2.41
2828 2843 9.058174 GCAGTATAGAGAAGAATAGGCGATATA 57.942 37.037 0.00 0.00 0.00 0.86
2965 2997 7.246027 AGGGGGAAGAAACAGTAAATACAATT 58.754 34.615 0.00 0.00 0.00 2.32
3165 3201 1.662446 GGACGAACGGACTGCGAAA 60.662 57.895 0.00 0.00 0.00 3.46
5031 5649 3.981051 GGGGGTTCCTCCTTTCTTC 57.019 57.895 0.00 0.00 36.25 2.87
5034 5652 2.110188 GGGGGTTCCTCCTTTCTTCTTT 59.890 50.000 0.00 0.00 36.25 2.52
5035 5653 3.438078 GGGGGTTCCTCCTTTCTTCTTTT 60.438 47.826 0.00 0.00 36.25 2.27
5077 5696 7.992180 TCTCTGTTGCATTTTCTTTTCTTTC 57.008 32.000 0.00 0.00 0.00 2.62
5493 6112 0.104120 TGATTATCCGGGCGTCACAG 59.896 55.000 0.00 0.00 0.00 3.66
5494 6113 0.104304 GATTATCCGGGCGTCACAGT 59.896 55.000 0.00 0.00 0.00 3.55
5495 6114 1.338973 GATTATCCGGGCGTCACAGTA 59.661 52.381 0.00 0.00 0.00 2.74
5496 6115 1.184431 TTATCCGGGCGTCACAGTAA 58.816 50.000 0.00 0.00 0.00 2.24
5497 6116 0.457035 TATCCGGGCGTCACAGTAAC 59.543 55.000 0.00 0.00 0.00 2.50
5498 6117 2.234913 ATCCGGGCGTCACAGTAACC 62.235 60.000 0.00 0.00 0.00 2.85
5499 6118 2.433664 CGGGCGTCACAGTAACCC 60.434 66.667 0.00 0.00 37.19 4.11
5500 6119 2.939261 CGGGCGTCACAGTAACCCT 61.939 63.158 0.00 0.00 38.50 4.34
5501 6120 1.373812 GGGCGTCACAGTAACCCTT 59.626 57.895 0.00 0.00 37.59 3.95
5502 6121 0.672711 GGGCGTCACAGTAACCCTTC 60.673 60.000 0.00 0.00 37.59 3.46
5503 6122 0.320697 GGCGTCACAGTAACCCTTCT 59.679 55.000 0.00 0.00 0.00 2.85
5504 6123 1.547372 GGCGTCACAGTAACCCTTCTA 59.453 52.381 0.00 0.00 0.00 2.10
5505 6124 2.416972 GGCGTCACAGTAACCCTTCTAG 60.417 54.545 0.00 0.00 0.00 2.43
5506 6125 2.416972 GCGTCACAGTAACCCTTCTAGG 60.417 54.545 0.00 0.00 34.30 3.02
5518 6137 3.828875 CCTTCTAGGGGATTCTGTGTC 57.171 52.381 0.00 0.00 0.00 3.67
5519 6138 3.107601 CCTTCTAGGGGATTCTGTGTCA 58.892 50.000 0.00 0.00 0.00 3.58
5520 6139 3.133721 CCTTCTAGGGGATTCTGTGTCAG 59.866 52.174 0.00 0.00 0.00 3.51
5521 6140 3.757947 TCTAGGGGATTCTGTGTCAGA 57.242 47.619 0.00 0.00 38.87 3.27
5528 6147 2.225348 TTCTGTGTCAGAAAGCGCG 58.775 52.632 0.00 0.00 45.84 6.86
5529 6148 0.249280 TTCTGTGTCAGAAAGCGCGA 60.249 50.000 12.10 0.00 45.84 5.87
5530 6149 0.249280 TCTGTGTCAGAAAGCGCGAA 60.249 50.000 12.10 0.00 37.57 4.70
5531 6150 0.792640 CTGTGTCAGAAAGCGCGAAT 59.207 50.000 12.10 0.00 32.44 3.34
5532 6151 1.992667 CTGTGTCAGAAAGCGCGAATA 59.007 47.619 12.10 0.00 32.44 1.75
5533 6152 2.604914 CTGTGTCAGAAAGCGCGAATAT 59.395 45.455 12.10 0.00 32.44 1.28
5534 6153 3.000041 TGTGTCAGAAAGCGCGAATATT 59.000 40.909 12.10 0.00 0.00 1.28
5535 6154 3.435327 TGTGTCAGAAAGCGCGAATATTT 59.565 39.130 12.10 4.31 0.00 1.40
5536 6155 4.627900 TGTGTCAGAAAGCGCGAATATTTA 59.372 37.500 12.10 0.00 0.00 1.40
5537 6156 5.293324 TGTGTCAGAAAGCGCGAATATTTAT 59.707 36.000 12.10 0.00 0.00 1.40
5538 6157 6.183360 TGTGTCAGAAAGCGCGAATATTTATT 60.183 34.615 12.10 0.00 0.00 1.40
5539 6158 6.687105 GTGTCAGAAAGCGCGAATATTTATTT 59.313 34.615 12.10 0.00 0.00 1.40
5540 6159 6.905076 TGTCAGAAAGCGCGAATATTTATTTC 59.095 34.615 12.10 3.16 0.00 2.17
5541 6160 6.905076 GTCAGAAAGCGCGAATATTTATTTCA 59.095 34.615 12.10 0.00 0.00 2.69
5542 6161 7.587757 GTCAGAAAGCGCGAATATTTATTTCAT 59.412 33.333 12.10 0.00 0.00 2.57
5543 6162 8.128582 TCAGAAAGCGCGAATATTTATTTCATT 58.871 29.630 12.10 0.00 0.00 2.57
5544 6163 8.412676 CAGAAAGCGCGAATATTTATTTCATTC 58.587 33.333 12.10 0.00 0.00 2.67
5545 6164 7.591426 AGAAAGCGCGAATATTTATTTCATTCC 59.409 33.333 12.10 0.00 0.00 3.01
5546 6165 6.312399 AGCGCGAATATTTATTTCATTCCA 57.688 33.333 12.10 0.00 0.00 3.53
5547 6166 6.913170 AGCGCGAATATTTATTTCATTCCAT 58.087 32.000 12.10 0.00 0.00 3.41
5548 6167 7.370383 AGCGCGAATATTTATTTCATTCCATT 58.630 30.769 12.10 0.00 0.00 3.16
5549 6168 8.511321 AGCGCGAATATTTATTTCATTCCATTA 58.489 29.630 12.10 0.00 0.00 1.90
5550 6169 9.123709 GCGCGAATATTTATTTCATTCCATTAA 57.876 29.630 12.10 0.00 0.00 1.40
5597 6216 8.038351 TCATAAGTTTGTGTGCTATGCTTACTA 58.962 33.333 0.00 0.00 0.00 1.82
5598 6217 6.481954 AAGTTTGTGTGCTATGCTTACTAC 57.518 37.500 0.00 0.00 0.00 2.73
5649 6268 1.203928 CGCAGACGCAAGATCTTAGG 58.796 55.000 7.86 5.54 43.62 2.69
5654 6274 0.905357 ACGCAAGATCTTAGGCAGGT 59.095 50.000 7.86 0.46 43.62 4.00
5755 6376 0.669318 GGTGTTCGCGTCTGATTCCA 60.669 55.000 5.77 0.00 0.00 3.53
5834 6467 0.037303 AAGCTAGCAGCAGCAAAGGA 59.963 50.000 18.83 0.00 45.56 3.36
6118 6751 5.075493 GGGATGAGAACATTTGCTCCATAT 58.925 41.667 0.00 0.00 36.82 1.78
6183 6817 4.228210 TCACAGCCCTCTTCCTTTTCATAT 59.772 41.667 0.00 0.00 0.00 1.78
6257 6891 4.717313 GACCACCCAAGGGACGCC 62.717 72.222 13.15 0.00 38.96 5.68
6270 6904 2.049433 ACGCCGAGTTCCTCAACG 60.049 61.111 0.00 0.00 37.61 4.10
6392 7026 2.125225 GACTTCCCTGGGACCCCT 59.875 66.667 16.85 0.00 36.94 4.79
6539 7173 0.955428 GCATGACTGAGGCGGTGAAA 60.955 55.000 0.00 0.00 0.00 2.69
6588 7222 2.038329 CCCTGGACGTCCACCCTA 59.962 66.667 33.23 12.45 42.01 3.53
6703 7337 3.361977 GTTCGTTGCCATGGCCGT 61.362 61.111 33.44 0.00 41.09 5.68
6740 7374 2.284921 CTCAGGACCTGGCTGGGA 60.285 66.667 21.56 0.00 41.11 4.37
6787 7421 1.153289 GTGAGCGTGCATGATCCCT 60.153 57.895 20.81 2.50 0.00 4.20
6832 7478 1.129251 GAGGACGATGACGACGTACAA 59.871 52.381 0.00 0.00 45.58 2.41
7140 7831 1.203994 CGTGTTCATCGGTAAGGTCCT 59.796 52.381 0.00 0.00 0.00 3.85
7227 7918 1.203313 AGGGTTCAAGACTAGGCAGGA 60.203 52.381 0.00 0.00 0.00 3.86
7384 8108 4.988486 GCTGTGCTGTGGCGTTGC 62.988 66.667 0.00 0.00 42.25 4.17
7521 8254 2.104281 ACAAGTATAGGGGATCGCAACC 59.896 50.000 12.32 0.00 0.00 3.77
7707 8441 6.517605 TGTAGTGATTGTAACAGTAGCAACA 58.482 36.000 0.00 0.00 0.00 3.33
7776 8511 6.680148 TTGGATCGGTGATGGAGAATTATA 57.320 37.500 0.00 0.00 0.00 0.98
7777 8512 6.874278 TGGATCGGTGATGGAGAATTATAT 57.126 37.500 0.00 0.00 0.00 0.86
7871 8606 8.718102 AATGTAGGCATGTATTCCGAATATAC 57.282 34.615 4.15 3.11 35.15 1.47
8124 8859 7.947332 TGACTATAGACTTGCAAGATAGGATCT 59.053 37.037 32.50 23.29 42.61 2.75
8126 8861 9.238368 ACTATAGACTTGCAAGATAGGATCTAC 57.762 37.037 32.50 9.75 39.08 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 1.819905 CCCGTGGCACCTTGTTTTT 59.180 52.632 12.86 0.00 0.00 1.94
80 81 3.532501 CCCGTGGCACCTTGTTTT 58.467 55.556 12.86 0.00 0.00 2.43
108 109 2.051518 TGCATGATTTGGGCCGACC 61.052 57.895 0.00 0.00 40.81 4.79
109 110 1.139520 GTGCATGATTTGGGCCGAC 59.860 57.895 0.00 0.00 0.00 4.79
110 111 2.405805 CGTGCATGATTTGGGCCGA 61.406 57.895 0.00 0.00 0.00 5.54
111 112 2.102749 CGTGCATGATTTGGGCCG 59.897 61.111 0.00 0.00 0.00 6.13
112 113 2.008268 CTCCGTGCATGATTTGGGCC 62.008 60.000 7.72 0.00 0.00 5.80
113 114 1.434696 CTCCGTGCATGATTTGGGC 59.565 57.895 7.72 0.00 0.00 5.36
114 115 0.394216 TCCTCCGTGCATGATTTGGG 60.394 55.000 7.72 2.21 0.00 4.12
115 116 1.019673 CTCCTCCGTGCATGATTTGG 58.980 55.000 7.72 3.97 0.00 3.28
116 117 1.938577 CTCTCCTCCGTGCATGATTTG 59.061 52.381 7.72 0.00 0.00 2.32
117 118 1.833630 TCTCTCCTCCGTGCATGATTT 59.166 47.619 7.72 0.00 0.00 2.17
118 119 1.411977 CTCTCTCCTCCGTGCATGATT 59.588 52.381 7.72 0.00 0.00 2.57
119 120 1.039068 CTCTCTCCTCCGTGCATGAT 58.961 55.000 7.72 0.00 0.00 2.45
120 121 1.039785 CCTCTCTCCTCCGTGCATGA 61.040 60.000 7.72 0.00 0.00 3.07
121 122 1.440893 CCTCTCTCCTCCGTGCATG 59.559 63.158 0.00 0.00 0.00 4.06
122 123 1.760086 CCCTCTCTCCTCCGTGCAT 60.760 63.158 0.00 0.00 0.00 3.96
123 124 2.363018 CCCTCTCTCCTCCGTGCA 60.363 66.667 0.00 0.00 0.00 4.57
124 125 3.151022 CCCCTCTCTCCTCCGTGC 61.151 72.222 0.00 0.00 0.00 5.34
125 126 2.443016 CCCCCTCTCTCCTCCGTG 60.443 72.222 0.00 0.00 0.00 4.94
126 127 2.947785 ACCCCCTCTCTCCTCCGT 60.948 66.667 0.00 0.00 0.00 4.69
127 128 2.443016 CACCCCCTCTCTCCTCCG 60.443 72.222 0.00 0.00 0.00 4.63
128 129 1.687493 CACACCCCCTCTCTCCTCC 60.687 68.421 0.00 0.00 0.00 4.30
129 130 1.079438 ACACACCCCCTCTCTCCTC 59.921 63.158 0.00 0.00 0.00 3.71
130 131 1.229336 CACACACCCCCTCTCTCCT 60.229 63.158 0.00 0.00 0.00 3.69
131 132 1.128188 AACACACACCCCCTCTCTCC 61.128 60.000 0.00 0.00 0.00 3.71
132 133 0.321996 GAACACACACCCCCTCTCTC 59.678 60.000 0.00 0.00 0.00 3.20
133 134 1.472662 CGAACACACACCCCCTCTCT 61.473 60.000 0.00 0.00 0.00 3.10
134 135 1.004918 CGAACACACACCCCCTCTC 60.005 63.158 0.00 0.00 0.00 3.20
135 136 3.148084 CGAACACACACCCCCTCT 58.852 61.111 0.00 0.00 0.00 3.69
136 137 2.668550 GCGAACACACACCCCCTC 60.669 66.667 0.00 0.00 0.00 4.30
137 138 3.168528 AGCGAACACACACCCCCT 61.169 61.111 0.00 0.00 0.00 4.79
138 139 2.978010 CAGCGAACACACACCCCC 60.978 66.667 0.00 0.00 0.00 5.40
139 140 1.961277 CTCAGCGAACACACACCCC 60.961 63.158 0.00 0.00 0.00 4.95
140 141 0.032952 TACTCAGCGAACACACACCC 59.967 55.000 0.00 0.00 0.00 4.61
141 142 1.993370 GATACTCAGCGAACACACACC 59.007 52.381 0.00 0.00 0.00 4.16
142 143 1.993370 GGATACTCAGCGAACACACAC 59.007 52.381 0.00 0.00 0.00 3.82
143 144 1.616374 TGGATACTCAGCGAACACACA 59.384 47.619 0.00 0.00 37.61 3.72
144 145 2.363788 TGGATACTCAGCGAACACAC 57.636 50.000 0.00 0.00 37.61 3.82
145 146 2.683968 GTTGGATACTCAGCGAACACA 58.316 47.619 0.00 0.00 30.16 3.72
146 147 1.654105 CGTTGGATACTCAGCGAACAC 59.346 52.381 0.00 0.00 42.52 3.32
147 148 1.403647 CCGTTGGATACTCAGCGAACA 60.404 52.381 2.90 0.00 42.52 3.18
148 149 1.278238 CCGTTGGATACTCAGCGAAC 58.722 55.000 2.90 0.00 42.52 3.95
149 150 0.892755 ACCGTTGGATACTCAGCGAA 59.107 50.000 2.90 0.00 42.52 4.70
150 151 1.674441 CTACCGTTGGATACTCAGCGA 59.326 52.381 2.90 0.00 42.52 4.93
151 152 1.269102 CCTACCGTTGGATACTCAGCG 60.269 57.143 0.00 0.00 40.25 5.18
152 153 1.755380 ACCTACCGTTGGATACTCAGC 59.245 52.381 5.98 0.00 37.61 4.26
153 154 2.033049 CGACCTACCGTTGGATACTCAG 59.967 54.545 5.98 0.00 37.61 3.35
154 155 2.019249 CGACCTACCGTTGGATACTCA 58.981 52.381 5.98 0.00 37.61 3.41
155 156 1.268948 GCGACCTACCGTTGGATACTC 60.269 57.143 5.98 0.00 37.61 2.59
156 157 0.743097 GCGACCTACCGTTGGATACT 59.257 55.000 5.98 0.00 37.61 2.12
157 158 0.743097 AGCGACCTACCGTTGGATAC 59.257 55.000 5.98 0.00 0.00 2.24
158 159 0.742505 CAGCGACCTACCGTTGGATA 59.257 55.000 5.98 0.00 37.17 2.59
159 160 0.968901 TCAGCGACCTACCGTTGGAT 60.969 55.000 5.98 0.00 40.39 3.41
160 161 1.180456 TTCAGCGACCTACCGTTGGA 61.180 55.000 5.98 0.00 40.39 3.53
161 162 0.108329 ATTCAGCGACCTACCGTTGG 60.108 55.000 0.00 0.00 40.39 3.77
162 163 2.460918 CTATTCAGCGACCTACCGTTG 58.539 52.381 0.00 0.00 41.15 4.10
163 164 1.407979 CCTATTCAGCGACCTACCGTT 59.592 52.381 0.00 0.00 0.00 4.44
164 165 1.030457 CCTATTCAGCGACCTACCGT 58.970 55.000 0.00 0.00 0.00 4.83
165 166 0.314302 CCCTATTCAGCGACCTACCG 59.686 60.000 0.00 0.00 0.00 4.02
166 167 0.680061 CCCCTATTCAGCGACCTACC 59.320 60.000 0.00 0.00 0.00 3.18
167 168 0.033642 GCCCCTATTCAGCGACCTAC 59.966 60.000 0.00 0.00 0.00 3.18
168 169 0.105658 AGCCCCTATTCAGCGACCTA 60.106 55.000 0.00 0.00 0.00 3.08
169 170 1.383248 AGCCCCTATTCAGCGACCT 60.383 57.895 0.00 0.00 0.00 3.85
170 171 1.069935 GAGCCCCTATTCAGCGACC 59.930 63.158 0.00 0.00 0.00 4.79
171 172 1.069935 GGAGCCCCTATTCAGCGAC 59.930 63.158 0.00 0.00 0.00 5.19
172 173 2.140792 GGGAGCCCCTATTCAGCGA 61.141 63.158 3.16 0.00 41.34 4.93
173 174 2.427753 GGGAGCCCCTATTCAGCG 59.572 66.667 3.16 0.00 41.34 5.18
189 190 1.074248 AACCAAACACGCCCTAGGG 59.926 57.895 24.89 24.89 38.57 3.53
246 247 3.470433 GGCAACCAAACAGGCCAT 58.530 55.556 5.01 0.00 45.70 4.40
282 283 2.505866 CTTTAAGTTTCGTGCGATGCC 58.494 47.619 0.00 0.00 0.00 4.40
376 377 2.126424 GAGAAGCGCGTCGTCCTT 60.126 61.111 17.57 0.94 0.00 3.36
439 441 2.721425 AATCCTCCCGCCGATTTTTA 57.279 45.000 0.00 0.00 0.00 1.52
461 463 3.222855 CTCGGCGGGAGATGAGCT 61.223 66.667 0.00 0.00 46.23 4.09
697 701 3.413327 GAACAGAGAGAAAGGGGGTTTC 58.587 50.000 0.00 0.00 44.48 2.78
700 704 1.132365 AGGAACAGAGAGAAAGGGGGT 60.132 52.381 0.00 0.00 0.00 4.95
763 768 5.013079 ACAGATCAGACCACTAATCAACCAA 59.987 40.000 0.00 0.00 0.00 3.67
797 802 1.382522 CGCACCATAGCAATCAACCT 58.617 50.000 0.00 0.00 0.00 3.50
831 836 2.408271 TGCTTGAACATCTAGCCCTG 57.592 50.000 10.46 0.00 43.03 4.45
854 859 9.339850 CAAACTCTACTACTAATCTAGCCTACA 57.660 37.037 0.00 0.00 0.00 2.74
921 926 5.133221 GGACCACCAATAGCTACAAATCAT 58.867 41.667 0.00 0.00 35.97 2.45
968 973 6.676990 ATCTATGAGCAGGAACATACATCA 57.323 37.500 0.00 0.00 0.00 3.07
997 1002 5.185828 TCATCGCTATCATACCAAGCATACT 59.814 40.000 0.00 0.00 35.98 2.12
1029 1034 8.370940 ACATGGTTCATCACTATCATAGTAAGG 58.629 37.037 0.00 0.00 37.23 2.69
1122 1127 3.971032 GGATGTTGGCTTAATCCGAAG 57.029 47.619 0.00 0.00 31.11 3.79
1126 1131 3.001939 CGTAACGGATGTTGGCTTAATCC 59.998 47.826 0.00 3.66 39.12 3.01
1127 1132 4.191662 CGTAACGGATGTTGGCTTAATC 57.808 45.455 0.00 0.00 39.12 1.75
1142 1147 0.704551 GCGTCACAGTTACCGTAACG 59.295 55.000 14.35 11.93 43.29 3.18
1143 1148 1.063031 GGCGTCACAGTTACCGTAAC 58.937 55.000 12.73 12.73 38.94 2.50
1144 1149 0.038343 GGGCGTCACAGTTACCGTAA 60.038 55.000 0.00 0.00 0.00 3.18
1145 1150 1.586028 GGGCGTCACAGTTACCGTA 59.414 57.895 0.00 0.00 0.00 4.02
1146 1151 2.341176 GGGCGTCACAGTTACCGT 59.659 61.111 0.00 0.00 0.00 4.83
1147 1152 2.433664 GGGGCGTCACAGTTACCG 60.434 66.667 0.00 0.00 0.00 4.02
1148 1153 2.046604 GGGGGCGTCACAGTTACC 60.047 66.667 0.00 0.00 0.00 2.85
1149 1154 0.322187 ATTGGGGGCGTCACAGTTAC 60.322 55.000 0.00 0.00 0.00 2.50
1150 1155 0.402504 AATTGGGGGCGTCACAGTTA 59.597 50.000 0.00 0.00 0.00 2.24
1151 1156 0.469144 AAATTGGGGGCGTCACAGTT 60.469 50.000 0.00 0.00 0.00 3.16
1152 1157 1.152830 AAATTGGGGGCGTCACAGT 59.847 52.632 0.00 0.00 0.00 3.55
1166 1171 5.645929 TGCATGATTAGTGTACGGTCAAATT 59.354 36.000 0.00 0.00 0.00 1.82
1433 1441 2.244252 GGAGTAGTTAGGAGGTCCCAGA 59.756 54.545 0.00 0.00 37.41 3.86
1871 1882 5.875359 CCTTGACCTTATGACAACTAGAACC 59.125 44.000 0.00 0.00 0.00 3.62
2663 2677 2.619074 GCTAGTTTTCCATCAGTGGCCT 60.619 50.000 3.32 0.00 45.63 5.19
2965 2997 3.682377 ACGCATCGTCATGTTATGTTTGA 59.318 39.130 0.00 0.00 33.69 2.69
3165 3201 1.580845 AACGACGAGACGAATCCGGT 61.581 55.000 0.00 0.00 40.78 5.28
5238 5857 8.519526 TCCTAACATAAATAAAACAGTGGCAAG 58.480 33.333 0.00 0.00 0.00 4.01
5384 6003 8.994881 GTTCAAAACCGATTCAAAATTCAAAAC 58.005 29.630 0.00 0.00 0.00 2.43
5497 6116 5.961959 CTGACACAGAATCCCCTAGAAGGG 61.962 54.167 4.90 4.90 44.02 3.95
5498 6117 3.107601 TGACACAGAATCCCCTAGAAGG 58.892 50.000 0.00 0.00 34.30 3.46
5499 6118 4.026744 TCTGACACAGAATCCCCTAGAAG 58.973 47.826 0.00 0.00 37.57 2.85
5500 6119 4.061131 TCTGACACAGAATCCCCTAGAA 57.939 45.455 0.00 0.00 37.57 2.10
5501 6120 3.757947 TCTGACACAGAATCCCCTAGA 57.242 47.619 0.00 0.00 37.57 2.43
5510 6129 0.249280 TCGCGCTTTCTGACACAGAA 60.249 50.000 5.56 9.67 46.93 3.02
5511 6130 0.249280 TTCGCGCTTTCTGACACAGA 60.249 50.000 5.56 0.00 38.87 3.41
5512 6131 0.792640 ATTCGCGCTTTCTGACACAG 59.207 50.000 5.56 0.00 0.00 3.66
5513 6132 2.073117 TATTCGCGCTTTCTGACACA 57.927 45.000 5.56 0.00 0.00 3.72
5514 6133 3.658351 AATATTCGCGCTTTCTGACAC 57.342 42.857 5.56 0.00 0.00 3.67
5515 6134 5.984233 ATAAATATTCGCGCTTTCTGACA 57.016 34.783 5.56 0.00 0.00 3.58
5516 6135 6.905076 TGAAATAAATATTCGCGCTTTCTGAC 59.095 34.615 5.56 0.00 0.00 3.51
5517 6136 7.010697 TGAAATAAATATTCGCGCTTTCTGA 57.989 32.000 5.56 0.00 0.00 3.27
5518 6137 7.842525 ATGAAATAAATATTCGCGCTTTCTG 57.157 32.000 5.56 0.00 0.00 3.02
5519 6138 7.591426 GGAATGAAATAAATATTCGCGCTTTCT 59.409 33.333 5.56 0.00 32.88 2.52
5520 6139 7.378461 TGGAATGAAATAAATATTCGCGCTTTC 59.622 33.333 5.56 5.93 32.88 2.62
5521 6140 7.199766 TGGAATGAAATAAATATTCGCGCTTT 58.800 30.769 5.56 0.66 32.88 3.51
5522 6141 6.734137 TGGAATGAAATAAATATTCGCGCTT 58.266 32.000 5.56 0.00 32.88 4.68
5523 6142 6.312399 TGGAATGAAATAAATATTCGCGCT 57.688 33.333 5.56 0.00 32.88 5.92
5524 6143 7.566858 AATGGAATGAAATAAATATTCGCGC 57.433 32.000 0.00 0.00 32.88 6.86
5543 6162 9.874205 CAGAATTGGCTTCTTATTTTTAATGGA 57.126 29.630 0.00 0.00 41.60 3.41
5544 6163 9.657419 ACAGAATTGGCTTCTTATTTTTAATGG 57.343 29.630 0.00 0.00 41.60 3.16
5552 6171 9.247861 ACTTATGAACAGAATTGGCTTCTTATT 57.752 29.630 0.00 0.00 41.60 1.40
5553 6172 8.814038 ACTTATGAACAGAATTGGCTTCTTAT 57.186 30.769 0.00 0.00 41.60 1.73
5554 6173 8.635765 AACTTATGAACAGAATTGGCTTCTTA 57.364 30.769 0.00 0.00 41.60 2.10
5555 6174 7.530426 AACTTATGAACAGAATTGGCTTCTT 57.470 32.000 0.00 0.00 41.60 2.52
5556 6175 7.014615 ACAAACTTATGAACAGAATTGGCTTCT 59.985 33.333 0.00 0.00 45.34 2.85
5557 6176 7.115378 CACAAACTTATGAACAGAATTGGCTTC 59.885 37.037 0.00 0.00 0.00 3.86
5558 6177 6.925165 CACAAACTTATGAACAGAATTGGCTT 59.075 34.615 0.00 0.00 0.00 4.35
5559 6178 6.040842 ACACAAACTTATGAACAGAATTGGCT 59.959 34.615 0.00 0.00 0.00 4.75
5560 6179 6.144402 CACACAAACTTATGAACAGAATTGGC 59.856 38.462 0.00 0.00 0.00 4.52
5561 6180 6.144402 GCACACAAACTTATGAACAGAATTGG 59.856 38.462 0.00 0.00 0.00 3.16
5562 6181 6.919662 AGCACACAAACTTATGAACAGAATTG 59.080 34.615 0.00 0.00 0.00 2.32
5563 6182 7.042797 AGCACACAAACTTATGAACAGAATT 57.957 32.000 0.00 0.00 0.00 2.17
5564 6183 6.639632 AGCACACAAACTTATGAACAGAAT 57.360 33.333 0.00 0.00 0.00 2.40
5565 6184 7.584108 CATAGCACACAAACTTATGAACAGAA 58.416 34.615 0.00 0.00 0.00 3.02
5566 6185 6.348458 GCATAGCACACAAACTTATGAACAGA 60.348 38.462 0.00 0.00 0.00 3.41
5567 6186 5.796935 GCATAGCACACAAACTTATGAACAG 59.203 40.000 0.00 0.00 0.00 3.16
5568 6187 5.473162 AGCATAGCACACAAACTTATGAACA 59.527 36.000 0.00 0.00 0.00 3.18
5569 6188 5.942872 AGCATAGCACACAAACTTATGAAC 58.057 37.500 0.00 0.00 0.00 3.18
5570 6189 6.573664 AAGCATAGCACACAAACTTATGAA 57.426 33.333 0.00 0.00 0.00 2.57
5571 6190 6.878923 AGTAAGCATAGCACACAAACTTATGA 59.121 34.615 0.00 0.00 0.00 2.15
5572 6191 7.076842 AGTAAGCATAGCACACAAACTTATG 57.923 36.000 0.00 0.00 0.00 1.90
5573 6192 7.280205 GGTAGTAAGCATAGCACACAAACTTAT 59.720 37.037 0.00 0.00 0.00 1.73
5574 6193 6.592607 GGTAGTAAGCATAGCACACAAACTTA 59.407 38.462 0.00 0.00 0.00 2.24
5575 6194 5.411669 GGTAGTAAGCATAGCACACAAACTT 59.588 40.000 0.00 0.00 0.00 2.66
5576 6195 4.935808 GGTAGTAAGCATAGCACACAAACT 59.064 41.667 0.00 0.00 0.00 2.66
5577 6196 4.693566 TGGTAGTAAGCATAGCACACAAAC 59.306 41.667 0.00 0.00 0.00 2.93
5578 6197 4.900684 TGGTAGTAAGCATAGCACACAAA 58.099 39.130 0.00 0.00 0.00 2.83
5597 6216 0.726827 CAATCGTAGCACGCATTGGT 59.273 50.000 16.33 0.00 42.21 3.67
5598 6217 0.726827 ACAATCGTAGCACGCATTGG 59.273 50.000 21.69 12.99 42.21 3.16
5649 6268 1.668151 GGACACGACAAGGACCTGC 60.668 63.158 0.00 0.00 0.00 4.85
5755 6376 2.035193 CGAGCACTACTGGCACATAGAT 59.965 50.000 7.80 0.00 38.20 1.98
5834 6467 4.041198 TGTTCGACCTACCATCCTTCTTTT 59.959 41.667 0.00 0.00 0.00 2.27
6118 6751 1.276421 GTAGTGCTCTGCCTCCAGAAA 59.724 52.381 0.00 0.00 46.84 2.52
6183 6817 1.004277 GGAGTAGGCAATGGTGGACAA 59.996 52.381 0.00 0.00 0.00 3.18
6270 6904 2.084546 GTTGTAGTTCTGGATGGGTGC 58.915 52.381 0.00 0.00 0.00 5.01
6348 6982 0.912006 GGAGAACCAAGAGGCTCCCT 60.912 60.000 11.71 0.00 37.90 4.20
6392 7026 0.526211 CATCAAGGACCTCGACGTCA 59.474 55.000 17.16 1.87 34.24 4.35
6431 7065 0.251341 ATGGCTTGTCGAAGGGCTTT 60.251 50.000 0.00 0.00 0.00 3.51
6575 7209 1.190178 ACAGGTTAGGGTGGACGTCC 61.190 60.000 28.17 28.17 0.00 4.79
6588 7222 0.253044 ATGACAGCGCCATACAGGTT 59.747 50.000 2.29 0.00 40.61 3.50
6703 7337 2.821685 ACAGCACCTTGTGAGCGA 59.178 55.556 0.00 0.00 35.23 4.93
6762 7396 3.541950 ATGCACGCTCACAGGCAGT 62.542 57.895 0.00 0.00 39.95 4.40
6814 7448 2.184385 ATTGTACGTCGTCATCGTCC 57.816 50.000 0.00 0.00 41.72 4.79
6832 7478 4.650972 TTTGAGCCCTAGGTACACAAAT 57.349 40.909 15.86 0.00 0.00 2.32
7140 7831 6.214278 TCTTCCCATGAACTATAAACCCCTA 58.786 40.000 0.00 0.00 0.00 3.53
7227 7918 4.523558 ACTCGGAGTAAGCTTGTTCTACTT 59.476 41.667 9.33 0.00 0.00 2.24
7384 8108 1.676014 GCTTACCCACACCTAGCACAG 60.676 57.143 0.00 0.00 0.00 3.66
7521 8254 4.990257 TGAATACTCTACCCTCGAAAACG 58.010 43.478 0.00 0.00 0.00 3.60
7550 8283 4.941263 TCCCCTTGTGTCGAATCAATAAAG 59.059 41.667 4.42 0.00 0.00 1.85
7871 8606 6.313905 AGTTCTTTTCCATAAGCACGTATGAG 59.686 38.462 5.32 0.00 33.97 2.90
8295 9030 1.376609 GACGGTGATGGGTTGGATGC 61.377 60.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.