Multiple sequence alignment - TraesCS4D01G169400

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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 TraesCS4D01G169400 chr4D 100.000 4747 0 0 1 4747 294348373 294353119 0.000000e+00 8767.0
1 TraesCS4D01G169400 chr4D 85.965 285 35 3 4083 4363 504227659 504227376 2.780000e-77 300.0
2 TraesCS4D01G169400 chr4D 82.796 93 14 2 2522 2614 432943507 432943597 1.090000e-11 82.4
3 TraesCS4D01G169400 chr4B 94.405 1841 57 14 2238 4039 362148090 362149923 0.000000e+00 2787.0
4 TraesCS4D01G169400 chr4B 92.944 1403 39 16 690 2042 362146481 362147873 0.000000e+00 1988.0
5 TraesCS4D01G169400 chr4B 94.297 263 8 1 2078 2340 362147872 362148127 3.440000e-106 396.0
6 TraesCS4D01G169400 chr4B 89.385 179 18 1 4446 4624 362149928 362150105 1.720000e-54 224.0
7 TraesCS4D01G169400 chr4B 92.982 114 8 0 60 173 362146351 362146464 2.940000e-37 167.0
8 TraesCS4D01G169400 chr4B 96.825 63 2 0 1 63 362146130 362146192 6.500000e-19 106.0
9 TraesCS4D01G169400 chr4B 82.796 93 14 2 2522 2614 531065115 531065205 1.090000e-11 82.4
10 TraesCS4D01G169400 chr4B 83.529 85 13 1 2531 2614 151438326 151438410 1.420000e-10 78.7
11 TraesCS4D01G169400 chr4A 94.558 1268 34 11 709 1953 215248974 215247719 0.000000e+00 1927.0
12 TraesCS4D01G169400 chr4A 93.810 1050 32 11 2301 3344 215225190 215224168 0.000000e+00 1548.0
13 TraesCS4D01G169400 chr4A 93.613 595 8 5 3517 4082 215224122 215223529 0.000000e+00 861.0
14 TraesCS4D01G169400 chr4A 95.380 368 16 1 4359 4726 215222071 215221705 6.850000e-163 584.0
15 TraesCS4D01G169400 chr4A 86.239 327 12 16 1968 2292 215225681 215225386 1.650000e-84 324.0
16 TraesCS4D01G169400 chr4A 95.181 166 6 1 2301 2464 215225442 215225277 1.310000e-65 261.0
17 TraesCS4D01G169400 chr4A 90.341 176 17 0 1 176 215249174 215248999 1.030000e-56 231.0
18 TraesCS4D01G169400 chr4A 85.833 120 3 7 2174 2292 215225240 215225134 1.080000e-21 115.0
19 TraesCS4D01G169400 chr6D 94.664 506 26 1 183 687 20126328 20125823 0.000000e+00 784.0
20 TraesCS4D01G169400 chr6D 92.759 511 32 4 183 688 467999190 467999700 0.000000e+00 734.0
21 TraesCS4D01G169400 chr6D 86.620 284 35 3 4083 4363 112463372 112463089 1.280000e-80 311.0
22 TraesCS4D01G169400 chr3D 93.898 508 29 2 181 688 147470269 147469764 0.000000e+00 765.0
23 TraesCS4D01G169400 chr3D 86.268 284 35 4 4083 4363 356001366 356001648 5.970000e-79 305.0
24 TraesCS4D01G169400 chr7D 93.083 506 32 3 186 688 208652075 208652580 0.000000e+00 737.0
25 TraesCS4D01G169400 chr7D 92.520 508 36 1 183 688 536979631 536980138 0.000000e+00 726.0
26 TraesCS4D01G169400 chr7D 92.644 503 33 4 186 686 178124428 178124928 0.000000e+00 721.0
27 TraesCS4D01G169400 chr7D 92.323 508 37 2 183 688 399827893 399828400 0.000000e+00 721.0
28 TraesCS4D01G169400 chr7D 89.123 285 27 2 4083 4363 236843218 236843502 7.560000e-93 351.0
29 TraesCS4D01G169400 chr7D 83.529 85 12 2 2531 2614 549545932 549546015 1.420000e-10 78.7
30 TraesCS4D01G169400 chr7D 88.889 63 6 1 4625 4686 206475797 206475859 5.090000e-10 76.8
31 TraesCS4D01G169400 chr2B 92.913 508 35 1 182 688 622655385 622655892 0.000000e+00 737.0
32 TraesCS4D01G169400 chr2B 77.492 622 99 29 1089 1698 95799173 95798581 7.610000e-88 335.0
33 TraesCS4D01G169400 chr2B 87.719 285 31 2 4083 4363 257617318 257617034 3.540000e-86 329.0
34 TraesCS4D01G169400 chr3B 92.505 507 36 2 183 688 9861712 9861207 0.000000e+00 725.0
35 TraesCS4D01G169400 chr2D 77.383 619 112 22 1089 1698 61024796 61024197 4.550000e-90 342.0
36 TraesCS4D01G169400 chr2D 85.561 187 26 1 3566 3752 61023209 61023024 1.350000e-45 195.0
37 TraesCS4D01G169400 chr2A 76.688 622 113 26 1089 1698 61491039 61490438 2.760000e-82 316.0
38 TraesCS4D01G169400 chr2A 87.425 167 21 0 3580 3746 61489405 61489239 4.850000e-45 193.0
39 TraesCS4D01G169400 chr7A 86.364 286 33 4 4083 4363 35617855 35618139 1.660000e-79 307.0
40 TraesCS4D01G169400 chr7A 79.817 109 14 6 2531 2633 635033173 635033279 6.590000e-09 73.1
41 TraesCS4D01G169400 chr7B 85.965 285 36 3 4083 4363 403790394 403790110 7.720000e-78 302.0
42 TraesCS4D01G169400 chr7B 75.728 206 31 11 2410 2614 593922696 593922883 8.460000e-13 86.1
43 TraesCS4D01G169400 chr5D 85.614 285 37 3 4083 4363 210601126 210601410 3.590000e-76 296.0
44 TraesCS4D01G169400 chr5D 86.765 68 8 1 4625 4691 253391518 253391451 1.830000e-09 75.0
45 TraesCS4D01G169400 chr5A 85.512 283 36 4 4083 4363 505027711 505027990 1.670000e-74 291.0
46 TraesCS4D01G169400 chr5A 83.824 68 10 1 4625 4691 336039433 336039366 3.970000e-06 63.9
47 TraesCS4D01G169400 chr1B 87.662 154 19 0 3596 3749 155748362 155748209 3.770000e-41 180.0
48 TraesCS4D01G169400 chr1A 86.861 137 18 0 1279 1415 92565366 92565502 2.290000e-33 154.0
49 TraesCS4D01G169400 chr6B 85.401 137 18 2 1279 1415 616722130 616722264 1.780000e-29 141.0
50 TraesCS4D01G169400 chr6A 97.368 38 1 0 2577 2614 615704344 615704307 1.100000e-06 65.8
51 TraesCS4D01G169400 chr6A 82.353 68 11 1 4625 4691 404997327 404997260 1.850000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G169400 chr4D 294348373 294353119 4746 False 8767.000000 8767 100.0000 1 4747 1 chr4D.!!$F1 4746
1 TraesCS4D01G169400 chr4B 362146130 362150105 3975 False 944.666667 2787 93.4730 1 4624 6 chr4B.!!$F3 4623
2 TraesCS4D01G169400 chr4A 215247719 215249174 1455 True 1079.000000 1927 92.4495 1 1953 2 chr4A.!!$R2 1952
3 TraesCS4D01G169400 chr4A 215221705 215225681 3976 True 615.500000 1548 91.6760 1968 4726 6 chr4A.!!$R1 2758
4 TraesCS4D01G169400 chr6D 20125823 20126328 505 True 784.000000 784 94.6640 183 687 1 chr6D.!!$R1 504
5 TraesCS4D01G169400 chr6D 467999190 467999700 510 False 734.000000 734 92.7590 183 688 1 chr6D.!!$F1 505
6 TraesCS4D01G169400 chr3D 147469764 147470269 505 True 765.000000 765 93.8980 181 688 1 chr3D.!!$R1 507
7 TraesCS4D01G169400 chr7D 208652075 208652580 505 False 737.000000 737 93.0830 186 688 1 chr7D.!!$F3 502
8 TraesCS4D01G169400 chr7D 536979631 536980138 507 False 726.000000 726 92.5200 183 688 1 chr7D.!!$F6 505
9 TraesCS4D01G169400 chr7D 178124428 178124928 500 False 721.000000 721 92.6440 186 686 1 chr7D.!!$F1 500
10 TraesCS4D01G169400 chr7D 399827893 399828400 507 False 721.000000 721 92.3230 183 688 1 chr7D.!!$F5 505
11 TraesCS4D01G169400 chr2B 622655385 622655892 507 False 737.000000 737 92.9130 182 688 1 chr2B.!!$F1 506
12 TraesCS4D01G169400 chr2B 95798581 95799173 592 True 335.000000 335 77.4920 1089 1698 1 chr2B.!!$R1 609
13 TraesCS4D01G169400 chr3B 9861207 9861712 505 True 725.000000 725 92.5050 183 688 1 chr3B.!!$R1 505
14 TraesCS4D01G169400 chr2D 61023024 61024796 1772 True 268.500000 342 81.4720 1089 3752 2 chr2D.!!$R1 2663
15 TraesCS4D01G169400 chr2A 61489239 61491039 1800 True 254.500000 316 82.0565 1089 3746 2 chr2A.!!$R1 2657

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
136 299 0.527565 GTGCTTCATTCCGTGCCAAT 59.472 50.0 0.00 0.0 0.00 3.16 F
806 996 0.725784 GTTTCTGATGGTTGCGCACG 60.726 55.0 11.12 0.0 0.00 5.34 F
1419 1675 0.036010 CATGGACGGCAAGGTCTCTT 60.036 55.0 0.00 0.0 37.12 2.85 F
1538 1796 0.036388 AAATCGCTGTGATCGTGGGT 60.036 50.0 3.89 0.0 35.84 4.51 F
1941 2223 0.401356 TCAACTTGCCATCTCAGCCA 59.599 50.0 0.00 0.0 0.00 4.75 F
2648 3323 0.403271 AGCCTTGAACCTGCACATCT 59.597 50.0 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1328 1558 1.219124 GAGGCGCTTCAGGATCACA 59.781 57.895 15.47 0.0 0.00 3.58 R
2055 2375 1.356124 AGTTCTGGGCACATCAGTCT 58.644 50.000 0.00 0.0 34.15 3.24 R
2393 3067 1.675641 GGTGTGGTCACTGCCATCC 60.676 63.158 2.66 0.0 43.41 3.51 R
3182 3995 2.388735 TCACGATATTCAGAGCACCCT 58.611 47.619 0.00 0.0 0.00 4.34 R
3510 4494 3.312718 GGGCCAGTTGCAATGCCA 61.313 61.111 27.95 0.0 45.83 4.92 R
4103 5142 0.243907 ATGTGTCTTGGTCTCCGTCG 59.756 55.000 0.00 0.0 0.00 5.12 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
36 37 7.447374 TCTCATGAATTTTAACACGAACCAT 57.553 32.000 0.00 0.00 0.00 3.55
119 282 5.723672 TTAGTCCTTCCTGTCTTACTGTG 57.276 43.478 0.00 0.00 0.00 3.66
125 288 4.564406 CCTTCCTGTCTTACTGTGCTTCAT 60.564 45.833 0.00 0.00 0.00 2.57
128 291 3.686726 CCTGTCTTACTGTGCTTCATTCC 59.313 47.826 0.00 0.00 0.00 3.01
129 292 3.325870 TGTCTTACTGTGCTTCATTCCG 58.674 45.455 0.00 0.00 0.00 4.30
136 299 0.527565 GTGCTTCATTCCGTGCCAAT 59.472 50.000 0.00 0.00 0.00 3.16
138 301 2.358898 GTGCTTCATTCCGTGCCAATAT 59.641 45.455 0.00 0.00 0.00 1.28
176 339 8.589335 TTGAAACGACTTGAGATATATTAGCC 57.411 34.615 0.00 0.00 0.00 3.93
177 340 7.952671 TGAAACGACTTGAGATATATTAGCCT 58.047 34.615 0.00 0.00 0.00 4.58
178 341 7.867909 TGAAACGACTTGAGATATATTAGCCTG 59.132 37.037 0.00 0.00 0.00 4.85
179 342 7.526142 AACGACTTGAGATATATTAGCCTGA 57.474 36.000 0.00 0.00 0.00 3.86
180 343 6.915349 ACGACTTGAGATATATTAGCCTGAC 58.085 40.000 0.00 0.00 0.00 3.51
181 344 6.717540 ACGACTTGAGATATATTAGCCTGACT 59.282 38.462 0.00 0.00 0.00 3.41
318 481 4.271816 CGTCGGCGGCAGCTAGAT 62.272 66.667 13.62 0.00 44.37 1.98
324 487 3.610669 CGGCAGCTAGATCGGGCT 61.611 66.667 9.16 9.16 39.60 5.19
418 581 2.345244 CTGGTTGAGGAGCACGCT 59.655 61.111 0.00 0.00 0.00 5.07
468 631 2.352805 CTGGTTGGGACCTCAGGC 59.647 66.667 0.00 0.00 46.66 4.85
496 659 0.978151 TTAGGTTTGGCTGCGAGGTA 59.022 50.000 0.00 0.00 0.00 3.08
545 708 2.224621 CGCCCCTTCATCAACTGGATAT 60.225 50.000 0.00 0.00 33.95 1.63
579 747 1.301716 TTGCTCAGACGGTGGCTTC 60.302 57.895 0.00 0.00 0.00 3.86
806 996 0.725784 GTTTCTGATGGTTGCGCACG 60.726 55.000 11.12 0.00 0.00 5.34
875 1066 1.684869 CCCAACACAACACAGGTTCCT 60.685 52.381 0.00 0.00 34.21 3.36
923 1115 3.371063 GAGTCGACTCCACCGCCA 61.371 66.667 31.24 0.00 37.02 5.69
1328 1558 1.202976 ACCAAGAGCCAGTTCAATGCT 60.203 47.619 0.00 0.00 38.24 3.79
1419 1675 0.036010 CATGGACGGCAAGGTCTCTT 60.036 55.000 0.00 0.00 37.12 2.85
1470 1728 4.618489 CGTGATTAGGTTCGTTTCGTTACT 59.382 41.667 0.00 0.00 0.00 2.24
1514 1772 1.363744 CGATTCTGGAAGTGCAGGAC 58.636 55.000 0.00 0.00 33.76 3.85
1538 1796 0.036388 AAATCGCTGTGATCGTGGGT 60.036 50.000 3.89 0.00 35.84 4.51
1689 1947 2.753029 GTGCTCCTCTTGGCCAGT 59.247 61.111 5.11 0.00 0.00 4.00
1853 2111 9.486857 GTTACTAGACTTCTTTTTGTTGTTGTC 57.513 33.333 0.00 0.00 0.00 3.18
1857 2115 3.192633 ACTTCTTTTTGTTGTTGTCGGCT 59.807 39.130 0.00 0.00 0.00 5.52
1859 2141 2.750166 TCTTTTTGTTGTTGTCGGCTCA 59.250 40.909 0.00 0.00 0.00 4.26
1941 2223 0.401356 TCAACTTGCCATCTCAGCCA 59.599 50.000 0.00 0.00 0.00 4.75
2042 2362 2.079158 CACCATGGTGCTACTGTCTTG 58.921 52.381 31.13 3.98 39.39 3.02
2043 2363 1.089920 CCATGGTGCTACTGTCTTGC 58.910 55.000 2.57 0.00 0.00 4.01
2044 2364 1.611410 CCATGGTGCTACTGTCTTGCA 60.611 52.381 2.57 0.00 0.00 4.08
2045 2365 2.153645 CATGGTGCTACTGTCTTGCAA 58.846 47.619 0.00 0.00 38.50 4.08
2046 2366 1.882912 TGGTGCTACTGTCTTGCAAG 58.117 50.000 20.81 20.81 38.50 4.01
2047 2367 1.140852 TGGTGCTACTGTCTTGCAAGT 59.859 47.619 25.19 10.16 38.50 3.16
2048 2368 2.367241 TGGTGCTACTGTCTTGCAAGTA 59.633 45.455 25.19 14.77 38.50 2.24
2049 2369 2.996621 GGTGCTACTGTCTTGCAAGTAG 59.003 50.000 25.19 23.81 38.50 2.57
2050 2370 2.996621 GTGCTACTGTCTTGCAAGTAGG 59.003 50.000 25.19 17.24 38.50 3.18
2051 2371 2.897326 TGCTACTGTCTTGCAAGTAGGA 59.103 45.455 25.19 18.05 35.92 2.94
2052 2372 3.056536 TGCTACTGTCTTGCAAGTAGGAG 60.057 47.826 27.20 27.20 35.92 3.69
2053 2373 3.193691 GCTACTGTCTTGCAAGTAGGAGA 59.806 47.826 31.77 18.67 35.92 3.71
2054 2374 4.142049 GCTACTGTCTTGCAAGTAGGAGAT 60.142 45.833 31.77 17.66 35.92 2.75
2055 2375 5.067936 GCTACTGTCTTGCAAGTAGGAGATA 59.932 44.000 31.77 17.78 35.92 1.98
2056 2376 5.590530 ACTGTCTTGCAAGTAGGAGATAG 57.409 43.478 25.19 14.86 34.67 2.08
2057 2377 5.265191 ACTGTCTTGCAAGTAGGAGATAGA 58.735 41.667 25.19 0.00 33.32 1.98
2058 2378 5.126384 ACTGTCTTGCAAGTAGGAGATAGAC 59.874 44.000 25.19 12.87 33.32 2.59
2059 2379 5.265191 TGTCTTGCAAGTAGGAGATAGACT 58.735 41.667 25.19 0.00 33.67 3.24
2060 2380 5.126222 TGTCTTGCAAGTAGGAGATAGACTG 59.874 44.000 25.19 0.00 33.67 3.51
2061 2381 5.358442 GTCTTGCAAGTAGGAGATAGACTGA 59.642 44.000 25.19 0.00 0.00 3.41
2062 2382 6.040391 GTCTTGCAAGTAGGAGATAGACTGAT 59.960 42.308 25.19 0.00 0.00 2.90
2063 2383 5.781210 TGCAAGTAGGAGATAGACTGATG 57.219 43.478 0.00 0.00 0.00 3.07
2064 2384 5.204292 TGCAAGTAGGAGATAGACTGATGT 58.796 41.667 0.00 0.00 0.00 3.06
2065 2385 5.068329 TGCAAGTAGGAGATAGACTGATGTG 59.932 44.000 0.00 0.00 0.00 3.21
2066 2386 5.527951 CAAGTAGGAGATAGACTGATGTGC 58.472 45.833 0.00 0.00 0.00 4.57
2067 2387 4.148838 AGTAGGAGATAGACTGATGTGCC 58.851 47.826 0.00 0.00 0.00 5.01
2068 2388 2.324541 AGGAGATAGACTGATGTGCCC 58.675 52.381 0.00 0.00 0.00 5.36
2069 2389 2.042464 GGAGATAGACTGATGTGCCCA 58.958 52.381 0.00 0.00 0.00 5.36
2070 2390 2.036992 GGAGATAGACTGATGTGCCCAG 59.963 54.545 0.00 0.00 37.64 4.45
2071 2391 2.961741 GAGATAGACTGATGTGCCCAGA 59.038 50.000 0.00 0.00 35.69 3.86
2072 2392 3.378512 AGATAGACTGATGTGCCCAGAA 58.621 45.455 0.00 0.00 35.69 3.02
2073 2393 3.133721 AGATAGACTGATGTGCCCAGAAC 59.866 47.826 0.00 0.00 35.69 3.01
2074 2394 1.356124 AGACTGATGTGCCCAGAACT 58.644 50.000 0.00 0.00 35.69 3.01
2075 2395 2.540383 AGACTGATGTGCCCAGAACTA 58.460 47.619 0.00 0.00 35.69 2.24
2076 2396 2.499289 AGACTGATGTGCCCAGAACTAG 59.501 50.000 0.00 0.00 35.69 2.57
2077 2397 2.234908 GACTGATGTGCCCAGAACTAGT 59.765 50.000 0.00 0.00 35.69 2.57
2078 2398 2.639839 ACTGATGTGCCCAGAACTAGTT 59.360 45.455 8.13 8.13 35.69 2.24
2134 2548 9.353999 GATTGTTTCTTGAGTACAGTTTGTTTT 57.646 29.630 0.00 0.00 0.00 2.43
2141 2555 6.114221 TGAGTACAGTTTGTTTTCCTTTCG 57.886 37.500 0.00 0.00 0.00 3.46
2178 2592 2.202236 CTGCACAGTGCTACCCCCAT 62.202 60.000 25.83 0.00 45.31 4.00
2209 2623 7.652909 GTCAGATCACAATCCTATGAAGAAGAG 59.347 40.741 0.00 0.00 31.78 2.85
2230 2644 2.755103 GACCCCCAATTTCTGTGCTTAG 59.245 50.000 0.00 0.00 0.00 2.18
2231 2645 2.378547 ACCCCCAATTTCTGTGCTTAGA 59.621 45.455 0.00 0.00 0.00 2.10
2232 2646 3.011708 ACCCCCAATTTCTGTGCTTAGAT 59.988 43.478 0.00 0.00 0.00 1.98
2233 2647 3.382546 CCCCCAATTTCTGTGCTTAGATG 59.617 47.826 0.00 0.00 0.00 2.90
2234 2648 4.019174 CCCCAATTTCTGTGCTTAGATGT 58.981 43.478 0.00 0.00 0.00 3.06
2235 2649 4.463891 CCCCAATTTCTGTGCTTAGATGTT 59.536 41.667 0.00 0.00 0.00 2.71
2236 2650 5.393461 CCCCAATTTCTGTGCTTAGATGTTC 60.393 44.000 0.00 0.00 0.00 3.18
2289 2703 4.577834 TGTCACTTGTGATTGAGTCGTA 57.422 40.909 6.74 0.00 0.00 3.43
2393 3067 8.586570 TGTAGTAACAAAATTTGCATTGGAAG 57.413 30.769 5.52 0.00 30.91 3.46
2640 3315 1.944177 TAGCTCTGAGCCTTGAACCT 58.056 50.000 25.09 7.47 43.77 3.50
2648 3323 0.403271 AGCCTTGAACCTGCACATCT 59.597 50.000 0.00 0.00 0.00 2.90
2888 3584 8.138365 TCAGTCAAATGTTCTAACAACACTAC 57.862 34.615 0.00 0.00 43.03 2.73
2905 3601 6.104146 ACACTACCTCTCTCCTTTTTCTTC 57.896 41.667 0.00 0.00 0.00 2.87
3138 3951 2.366266 ACTTGAAAATGCATGCACCTGT 59.634 40.909 25.37 8.44 0.00 4.00
3182 3995 9.890629 ATCTGTTGACAAATACTGCTTATTCTA 57.109 29.630 0.00 0.00 29.39 2.10
3209 4022 6.870965 GGTGCTCTGAATATCGTGATTCTATT 59.129 38.462 11.50 0.00 36.86 1.73
3346 4325 4.728882 GCCTTGATGTTTGAATGCTAGTCG 60.729 45.833 0.00 0.00 0.00 4.18
3399 4380 5.425862 TGTATTGCCCCTATTGTGTGTAGTA 59.574 40.000 0.00 0.00 0.00 1.82
4043 5057 1.050421 AAGGCTGGCTTTTGGTTGCT 61.050 50.000 11.07 0.00 0.00 3.91
4077 5091 0.679960 AGGCGGTACCAAATCAAGGC 60.680 55.000 13.54 5.93 43.14 4.35
4080 5094 0.675522 CGGTACCAAATCAAGGCCGT 60.676 55.000 13.54 0.00 33.87 5.68
4081 5095 1.092348 GGTACCAAATCAAGGCCGTC 58.908 55.000 7.15 0.00 0.00 4.79
4091 5130 5.353394 AATCAAGGCCGTCTTATGTAAGA 57.647 39.130 0.00 0.00 39.82 2.10
4094 5133 4.161565 TCAAGGCCGTCTTATGTAAGATGT 59.838 41.667 16.64 1.30 44.13 3.06
4099 5138 8.135382 AGGCCGTCTTATGTAAGATGTATTAT 57.865 34.615 16.64 1.33 44.13 1.28
4100 5139 8.594550 AGGCCGTCTTATGTAAGATGTATTATT 58.405 33.333 16.64 0.12 44.13 1.40
4130 5176 7.434492 ACGGAGACCAAGACACATAATTATAG 58.566 38.462 0.00 0.00 0.00 1.31
4151 5197 4.501071 AGACATGTTACGGCGAAATTACT 58.499 39.130 16.62 0.01 0.00 2.24
4157 5203 6.817270 TGTTACGGCGAAATTACTCTTATC 57.183 37.500 16.62 0.00 0.00 1.75
4175 5221 9.349713 ACTCTTATCAAATTTGTTGGTTAGTGA 57.650 29.630 17.47 0.00 0.00 3.41
4196 5242 7.155328 AGTGACAAGTAAATCAGTTAGTCCAG 58.845 38.462 0.00 0.00 0.00 3.86
4201 5247 9.403583 ACAAGTAAATCAGTTAGTCCAGAAAAA 57.596 29.630 0.00 0.00 0.00 1.94
4210 5256 9.658799 TCAGTTAGTCCAGAAAAATAAGAGATG 57.341 33.333 0.00 0.00 0.00 2.90
4219 5311 7.494625 CCAGAAAAATAAGAGATGCATGCAATT 59.505 33.333 26.68 15.56 0.00 2.32
4226 5318 3.628032 AGAGATGCATGCAATTGACAGAG 59.372 43.478 26.68 5.39 0.00 3.35
4274 5366 8.370940 ACAAGAAGAGATACAGACAATCAAGAA 58.629 33.333 0.00 0.00 0.00 2.52
4275 5367 9.381033 CAAGAAGAGATACAGACAATCAAGAAT 57.619 33.333 0.00 0.00 0.00 2.40
4313 5405 3.206464 TGGGAGGGATAACAAGGGAATT 58.794 45.455 0.00 0.00 0.00 2.17
4315 5407 4.167307 TGGGAGGGATAACAAGGGAATTAC 59.833 45.833 0.00 0.00 0.00 1.89
4316 5408 4.167307 GGGAGGGATAACAAGGGAATTACA 59.833 45.833 0.00 0.00 0.00 2.41
4318 5410 6.373759 GGAGGGATAACAAGGGAATTACAAT 58.626 40.000 0.00 0.00 0.00 2.71
4337 5429 9.807649 ATTACAATGAATTAGAAGAAATGCACC 57.192 29.630 0.00 0.00 26.90 5.01
4338 5430 7.472334 ACAATGAATTAGAAGAAATGCACCT 57.528 32.000 0.00 0.00 26.90 4.00
4339 5431 7.899973 ACAATGAATTAGAAGAAATGCACCTT 58.100 30.769 0.00 0.00 26.90 3.50
4340 5432 9.023962 ACAATGAATTAGAAGAAATGCACCTTA 57.976 29.630 0.00 0.00 26.90 2.69
4341 5433 9.512435 CAATGAATTAGAAGAAATGCACCTTAG 57.488 33.333 0.00 0.00 26.90 2.18
4342 5434 9.466497 AATGAATTAGAAGAAATGCACCTTAGA 57.534 29.630 0.00 0.00 26.90 2.10
4343 5435 9.638176 ATGAATTAGAAGAAATGCACCTTAGAT 57.362 29.630 0.00 0.00 26.90 1.98
4344 5436 9.466497 TGAATTAGAAGAAATGCACCTTAGATT 57.534 29.630 0.00 0.00 0.00 2.40
4345 5437 9.943163 GAATTAGAAGAAATGCACCTTAGATTC 57.057 33.333 0.00 1.34 0.00 2.52
4346 5438 9.692325 AATTAGAAGAAATGCACCTTAGATTCT 57.308 29.630 0.00 0.00 0.00 2.40
4347 5439 6.998968 AGAAGAAATGCACCTTAGATTCTG 57.001 37.500 0.00 0.00 0.00 3.02
4349 5441 5.441718 AGAAATGCACCTTAGATTCTGGA 57.558 39.130 0.00 0.00 0.00 3.86
4350 5442 5.819991 AGAAATGCACCTTAGATTCTGGAA 58.180 37.500 0.00 0.00 0.00 3.53
4351 5443 6.430007 AGAAATGCACCTTAGATTCTGGAAT 58.570 36.000 0.00 0.00 0.00 3.01
4352 5444 6.894103 AGAAATGCACCTTAGATTCTGGAATT 59.106 34.615 0.00 0.00 0.00 2.17
4353 5445 7.398332 AGAAATGCACCTTAGATTCTGGAATTT 59.602 33.333 0.00 1.07 0.00 1.82
4354 5446 7.486407 AATGCACCTTAGATTCTGGAATTTT 57.514 32.000 0.00 0.00 0.00 1.82
4355 5447 8.593945 AATGCACCTTAGATTCTGGAATTTTA 57.406 30.769 0.00 0.00 0.00 1.52
4356 5448 8.773033 ATGCACCTTAGATTCTGGAATTTTAT 57.227 30.769 0.00 0.00 0.00 1.40
4357 5449 8.225603 TGCACCTTAGATTCTGGAATTTTATC 57.774 34.615 0.00 0.00 0.00 1.75
4440 6639 4.941263 TGACATGCCAGGTACTAACAAATC 59.059 41.667 0.00 0.00 36.02 2.17
4441 6640 4.917385 ACATGCCAGGTACTAACAAATCA 58.083 39.130 0.00 0.00 36.02 2.57
4565 6764 6.552008 TCCTCTGGATGGTCTTAAAACATTT 58.448 36.000 0.00 0.00 0.00 2.32
4617 6816 2.436417 GAGCCAGATGCCAAACAAGTA 58.564 47.619 0.00 0.00 42.71 2.24
4631 6830 6.821665 GCCAAACAAGTAGATCATAAGTGGTA 59.178 38.462 0.00 0.00 0.00 3.25
4639 6838 8.783660 AGTAGATCATAAGTGGTAAGGAATGA 57.216 34.615 0.00 0.00 0.00 2.57
4640 6839 9.213777 AGTAGATCATAAGTGGTAAGGAATGAA 57.786 33.333 0.00 0.00 0.00 2.57
4726 6925 3.309954 GTGGTCCTAAGAAATGTCGCATC 59.690 47.826 0.00 0.00 0.00 3.91
4727 6926 2.872858 GGTCCTAAGAAATGTCGCATCC 59.127 50.000 0.00 0.00 0.00 3.51
4728 6927 3.432326 GGTCCTAAGAAATGTCGCATCCT 60.432 47.826 0.00 0.00 0.00 3.24
4729 6928 4.202223 GGTCCTAAGAAATGTCGCATCCTA 60.202 45.833 0.00 0.00 0.00 2.94
4730 6929 4.745620 GTCCTAAGAAATGTCGCATCCTAC 59.254 45.833 0.00 0.00 0.00 3.18
4731 6930 4.404394 TCCTAAGAAATGTCGCATCCTACA 59.596 41.667 0.00 0.00 0.00 2.74
4732 6931 5.105106 TCCTAAGAAATGTCGCATCCTACAA 60.105 40.000 0.00 0.00 0.00 2.41
4733 6932 5.584649 CCTAAGAAATGTCGCATCCTACAAA 59.415 40.000 0.00 0.00 0.00 2.83
4734 6933 5.551760 AAGAAATGTCGCATCCTACAAAG 57.448 39.130 0.00 0.00 0.00 2.77
4735 6934 4.832248 AGAAATGTCGCATCCTACAAAGA 58.168 39.130 0.00 0.00 0.00 2.52
4736 6935 4.872691 AGAAATGTCGCATCCTACAAAGAG 59.127 41.667 0.00 0.00 0.00 2.85
4737 6936 3.895232 ATGTCGCATCCTACAAAGAGT 57.105 42.857 0.00 0.00 0.00 3.24
4738 6937 3.678056 TGTCGCATCCTACAAAGAGTT 57.322 42.857 0.00 0.00 0.00 3.01
4739 6938 3.325870 TGTCGCATCCTACAAAGAGTTG 58.674 45.455 0.00 0.00 40.84 3.16
4741 6940 4.021807 TGTCGCATCCTACAAAGAGTTGTA 60.022 41.667 0.00 0.00 46.33 2.41
4742 6941 4.927425 GTCGCATCCTACAAAGAGTTGTAA 59.073 41.667 1.38 0.00 46.91 2.41
4743 6942 4.927425 TCGCATCCTACAAAGAGTTGTAAC 59.073 41.667 1.38 0.00 46.91 2.50
4744 6943 4.929808 CGCATCCTACAAAGAGTTGTAACT 59.070 41.667 0.00 0.00 46.91 2.24
4745 6944 5.163953 CGCATCCTACAAAGAGTTGTAACTG 60.164 44.000 1.35 0.00 46.91 3.16
4746 6945 5.122396 GCATCCTACAAAGAGTTGTAACTGG 59.878 44.000 1.35 0.00 46.91 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 8.421784 AGTATATGTCTCGCTCCAAAAGAAATA 58.578 33.333 0.00 0.00 0.00 1.40
44 45 5.131067 ACAGTAGTATATGTCTCGCTCCAA 58.869 41.667 0.00 0.00 0.00 3.53
119 282 2.618241 TCATATTGGCACGGAATGAAGC 59.382 45.455 0.00 0.00 0.00 3.86
125 288 2.288666 GAAGCTCATATTGGCACGGAA 58.711 47.619 0.00 0.00 0.00 4.30
128 291 1.600957 CAGGAAGCTCATATTGGCACG 59.399 52.381 0.00 0.00 0.00 5.34
129 292 2.648059 ACAGGAAGCTCATATTGGCAC 58.352 47.619 0.00 0.00 0.00 5.01
136 299 5.810587 GTCGTTTCAATACAGGAAGCTCATA 59.189 40.000 0.00 0.00 0.00 2.15
138 301 3.994392 GTCGTTTCAATACAGGAAGCTCA 59.006 43.478 0.00 0.00 0.00 4.26
173 336 3.950395 GGCAAGATAAATCAAGTCAGGCT 59.050 43.478 0.00 0.00 0.00 4.58
176 339 6.095860 TCAATGGGCAAGATAAATCAAGTCAG 59.904 38.462 0.00 0.00 0.00 3.51
177 340 5.951148 TCAATGGGCAAGATAAATCAAGTCA 59.049 36.000 0.00 0.00 0.00 3.41
178 341 6.455360 TCAATGGGCAAGATAAATCAAGTC 57.545 37.500 0.00 0.00 0.00 3.01
179 342 6.608405 TCATCAATGGGCAAGATAAATCAAGT 59.392 34.615 0.00 0.00 0.00 3.16
180 343 6.921857 GTCATCAATGGGCAAGATAAATCAAG 59.078 38.462 0.00 0.00 0.00 3.02
181 344 6.459985 CGTCATCAATGGGCAAGATAAATCAA 60.460 38.462 0.00 0.00 0.00 2.57
318 481 1.464376 GCTGCATCTACCTAGCCCGA 61.464 60.000 0.00 0.00 0.00 5.14
324 487 4.023980 AGTTGTACTGCTGCATCTACCTA 58.976 43.478 1.31 0.00 0.00 3.08
468 631 3.378427 GCAGCCAAACCTAACATCTAAGG 59.622 47.826 0.00 0.00 38.93 2.69
496 659 7.512746 TGATAGTCTAGGCCTAATACCAAACAT 59.487 37.037 14.85 4.20 0.00 2.71
545 708 1.546029 AGCAACATCTGTCGCTACTCA 59.454 47.619 0.00 0.00 31.60 3.41
566 734 0.034059 AAGACTGAAGCCACCGTCTG 59.966 55.000 5.81 0.00 36.88 3.51
688 859 4.096382 CACTTTGTACTGGGACAATATGCC 59.904 45.833 0.00 0.00 39.04 4.40
773 944 0.460284 AGAAACATCAGCTACCGCCG 60.460 55.000 0.00 0.00 36.60 6.46
806 996 1.329906 CAGATTCAGATGTTGCCGAGC 59.670 52.381 0.00 0.00 0.00 5.03
875 1066 2.656646 CGCACCAGCACTAGGTCA 59.343 61.111 0.00 0.00 42.27 4.02
923 1115 6.573289 CGAAAGAGTGAGGCATATATAGGCTT 60.573 42.308 18.06 11.47 42.47 4.35
1249 1444 2.279120 GGGATGAGACGCTGCTCG 60.279 66.667 0.00 0.00 45.38 5.03
1328 1558 1.219124 GAGGCGCTTCAGGATCACA 59.781 57.895 15.47 0.00 0.00 3.58
1419 1675 3.305398 AAACACCAAAGCAAACGAACA 57.695 38.095 0.00 0.00 0.00 3.18
1514 1772 1.464608 ACGATCACAGCGATTTGGTTG 59.535 47.619 0.00 0.00 33.17 3.77
1538 1796 3.346315 TCTCTTGTCGTCGGTTATGGTA 58.654 45.455 0.00 0.00 0.00 3.25
1689 1947 2.352388 GGCAGCAGAAATTACCGTGTA 58.648 47.619 0.00 0.00 0.00 2.90
1789 2047 3.502211 GGATCACCGGTTAGGCATTATTG 59.498 47.826 2.97 0.00 46.52 1.90
1857 2115 5.650703 TCTGAAATAGTACGGTCAGACATGA 59.349 40.000 13.42 0.00 41.13 3.07
1859 2141 6.239064 GGATCTGAAATAGTACGGTCAGACAT 60.239 42.308 17.39 7.86 46.80 3.06
2042 2362 5.527951 CACATCAGTCTATCTCCTACTTGC 58.472 45.833 0.00 0.00 0.00 4.01
2043 2363 5.508825 GGCACATCAGTCTATCTCCTACTTG 60.509 48.000 0.00 0.00 0.00 3.16
2044 2364 4.586841 GGCACATCAGTCTATCTCCTACTT 59.413 45.833 0.00 0.00 0.00 2.24
2045 2365 4.148838 GGCACATCAGTCTATCTCCTACT 58.851 47.826 0.00 0.00 0.00 2.57
2046 2366 3.257127 GGGCACATCAGTCTATCTCCTAC 59.743 52.174 0.00 0.00 0.00 3.18
2047 2367 3.117131 TGGGCACATCAGTCTATCTCCTA 60.117 47.826 0.00 0.00 0.00 2.94
2048 2368 2.324541 GGGCACATCAGTCTATCTCCT 58.675 52.381 0.00 0.00 0.00 3.69
2049 2369 2.036992 CTGGGCACATCAGTCTATCTCC 59.963 54.545 0.00 0.00 0.00 3.71
2050 2370 2.961741 TCTGGGCACATCAGTCTATCTC 59.038 50.000 0.00 0.00 34.15 2.75
2051 2371 3.037851 TCTGGGCACATCAGTCTATCT 57.962 47.619 0.00 0.00 34.15 1.98
2052 2372 3.133721 AGTTCTGGGCACATCAGTCTATC 59.866 47.826 0.00 0.00 34.15 2.08
2053 2373 3.110705 AGTTCTGGGCACATCAGTCTAT 58.889 45.455 0.00 0.00 34.15 1.98
2054 2374 2.540383 AGTTCTGGGCACATCAGTCTA 58.460 47.619 0.00 0.00 34.15 2.59
2055 2375 1.356124 AGTTCTGGGCACATCAGTCT 58.644 50.000 0.00 0.00 34.15 3.24
2056 2376 2.234908 ACTAGTTCTGGGCACATCAGTC 59.765 50.000 0.00 0.00 34.15 3.51
2057 2377 2.260822 ACTAGTTCTGGGCACATCAGT 58.739 47.619 0.00 0.00 34.15 3.41
2058 2378 3.340814 AACTAGTTCTGGGCACATCAG 57.659 47.619 1.12 0.00 0.00 2.90
2059 2379 3.788227 AAACTAGTTCTGGGCACATCA 57.212 42.857 8.95 0.00 0.00 3.07
2060 2380 6.456988 CGATTAAAACTAGTTCTGGGCACATC 60.457 42.308 8.95 2.37 0.00 3.06
2061 2381 5.354234 CGATTAAAACTAGTTCTGGGCACAT 59.646 40.000 8.95 0.00 0.00 3.21
2062 2382 4.693566 CGATTAAAACTAGTTCTGGGCACA 59.306 41.667 8.95 0.00 0.00 4.57
2063 2383 4.436986 GCGATTAAAACTAGTTCTGGGCAC 60.437 45.833 8.95 0.00 0.00 5.01
2064 2384 3.687698 GCGATTAAAACTAGTTCTGGGCA 59.312 43.478 8.95 0.00 0.00 5.36
2065 2385 3.939592 AGCGATTAAAACTAGTTCTGGGC 59.060 43.478 8.95 8.18 0.00 5.36
2066 2386 6.984474 TCATAGCGATTAAAACTAGTTCTGGG 59.016 38.462 8.95 0.00 0.00 4.45
2067 2387 7.707035 AGTCATAGCGATTAAAACTAGTTCTGG 59.293 37.037 8.95 0.00 0.00 3.86
2068 2388 8.635877 AGTCATAGCGATTAAAACTAGTTCTG 57.364 34.615 8.95 0.00 0.00 3.02
2069 2389 7.921745 GGAGTCATAGCGATTAAAACTAGTTCT 59.078 37.037 8.95 0.00 0.00 3.01
2070 2390 7.705325 TGGAGTCATAGCGATTAAAACTAGTTC 59.295 37.037 8.95 0.00 0.00 3.01
2071 2391 7.553334 TGGAGTCATAGCGATTAAAACTAGTT 58.447 34.615 1.12 1.12 0.00 2.24
2072 2392 7.108841 TGGAGTCATAGCGATTAAAACTAGT 57.891 36.000 0.00 0.00 0.00 2.57
2073 2393 7.203910 ACTGGAGTCATAGCGATTAAAACTAG 58.796 38.462 0.00 0.00 0.00 2.57
2074 2394 7.108841 ACTGGAGTCATAGCGATTAAAACTA 57.891 36.000 0.00 0.00 0.00 2.24
2075 2395 5.978814 ACTGGAGTCATAGCGATTAAAACT 58.021 37.500 0.00 0.00 0.00 2.66
2076 2396 6.421202 CCTACTGGAGTCATAGCGATTAAAAC 59.579 42.308 0.00 0.00 34.57 2.43
2077 2397 6.513180 CCTACTGGAGTCATAGCGATTAAAA 58.487 40.000 0.00 0.00 34.57 1.52
2078 2398 5.509163 GCCTACTGGAGTCATAGCGATTAAA 60.509 44.000 0.00 0.00 34.57 1.52
2134 2548 3.197766 ACCAATATGCTCAGACGAAAGGA 59.802 43.478 0.00 0.00 0.00 3.36
2141 2555 2.611292 GCAGACACCAATATGCTCAGAC 59.389 50.000 0.00 0.00 35.78 3.51
2178 2592 3.708403 AGGATTGTGATCTGACAAGCA 57.292 42.857 14.00 0.00 42.74 3.91
2209 2623 1.632589 AAGCACAGAAATTGGGGGTC 58.367 50.000 0.00 0.00 0.00 4.46
2230 2644 6.591834 CCAAATGGGATAGTAGATCGAACATC 59.408 42.308 0.00 5.20 40.01 3.06
2231 2645 6.043243 ACCAAATGGGATAGTAGATCGAACAT 59.957 38.462 4.17 0.00 41.15 2.71
2232 2646 5.365605 ACCAAATGGGATAGTAGATCGAACA 59.634 40.000 4.17 0.00 41.15 3.18
2233 2647 5.696724 CACCAAATGGGATAGTAGATCGAAC 59.303 44.000 4.17 0.00 41.15 3.95
2234 2648 5.365605 ACACCAAATGGGATAGTAGATCGAA 59.634 40.000 4.17 0.00 41.15 3.71
2235 2649 4.899457 ACACCAAATGGGATAGTAGATCGA 59.101 41.667 4.17 0.00 41.15 3.59
2236 2650 5.215252 ACACCAAATGGGATAGTAGATCG 57.785 43.478 4.17 0.00 41.15 3.69
2289 2703 7.730332 TGGGATAGTAGATCTATGTTGACACAT 59.270 37.037 5.57 0.00 46.07 3.21
2393 3067 1.675641 GGTGTGGTCACTGCCATCC 60.676 63.158 2.66 0.00 43.41 3.51
2640 3315 8.843262 CATTAATGATCCTAGAAAAGATGTGCA 58.157 33.333 10.04 0.00 0.00 4.57
2888 3584 5.012561 TCAGGAAGAAGAAAAAGGAGAGAGG 59.987 44.000 0.00 0.00 0.00 3.69
2905 3601 9.388506 ACTATTGAAACTACATCATTCAGGAAG 57.611 33.333 0.00 0.00 34.80 3.46
3182 3995 2.388735 TCACGATATTCAGAGCACCCT 58.611 47.619 0.00 0.00 0.00 4.34
3209 4022 4.679197 GCAATGCACGAAAACATTTCTACA 59.321 37.500 0.00 0.00 34.32 2.74
3249 4212 8.761575 AAGTGTAGGTTTTTATTGCATCAATG 57.238 30.769 2.57 0.00 35.54 2.82
3399 4380 3.433274 CGCAACAGTGTACAGACATGAAT 59.567 43.478 0.00 0.00 38.04 2.57
3510 4494 3.312718 GGGCCAGTTGCAATGCCA 61.313 61.111 27.95 0.00 45.83 4.92
3807 4796 8.397906 CGAACAAAATTTAGATGATCCTAGCAA 58.602 33.333 0.00 0.00 0.00 3.91
3874 4863 7.086230 AGAGAGGTTAAACAGTACAGTATCG 57.914 40.000 0.00 0.00 0.00 2.92
4043 5057 3.059982 CCTGTTGAGAGGCCACGA 58.940 61.111 5.01 0.00 0.00 4.35
4091 5130 5.909477 TGGTCTCCGTCGAAAATAATACAT 58.091 37.500 0.00 0.00 0.00 2.29
4094 5133 6.038356 GTCTTGGTCTCCGTCGAAAATAATA 58.962 40.000 0.00 0.00 0.00 0.98
4099 5138 1.409790 TGTCTTGGTCTCCGTCGAAAA 59.590 47.619 0.00 0.00 0.00 2.29
4100 5139 1.034356 TGTCTTGGTCTCCGTCGAAA 58.966 50.000 0.00 0.00 0.00 3.46
4103 5142 0.243907 ATGTGTCTTGGTCTCCGTCG 59.756 55.000 0.00 0.00 0.00 5.12
4104 5143 3.587797 TTATGTGTCTTGGTCTCCGTC 57.412 47.619 0.00 0.00 0.00 4.79
4130 5176 4.565564 AGAGTAATTTCGCCGTAACATGTC 59.434 41.667 0.00 0.00 0.00 3.06
4139 5185 7.696453 ACAAATTTGATAAGAGTAATTTCGCCG 59.304 33.333 24.64 0.00 30.17 6.46
4151 5197 9.126151 TGTCACTAACCAACAAATTTGATAAGA 57.874 29.630 24.64 6.84 0.00 2.10
4157 5203 8.918961 TTACTTGTCACTAACCAACAAATTTG 57.081 30.769 16.67 16.67 32.89 2.32
4167 5213 8.828688 ACTAACTGATTTACTTGTCACTAACC 57.171 34.615 0.00 0.00 0.00 2.85
4175 5221 8.974060 TTTTCTGGACTAACTGATTTACTTGT 57.026 30.769 0.00 0.00 0.00 3.16
4196 5242 8.325997 GTCAATTGCATGCATCTCTTATTTTTC 58.674 33.333 23.37 6.03 0.00 2.29
4201 5247 5.826208 TCTGTCAATTGCATGCATCTCTTAT 59.174 36.000 23.37 7.94 0.00 1.73
4210 5256 5.943706 ATATCTCTCTGTCAATTGCATGC 57.056 39.130 11.82 11.82 0.00 4.06
4249 5341 8.768957 TTCTTGATTGTCTGTATCTCTTCTTG 57.231 34.615 0.00 0.00 0.00 3.02
4293 5385 3.973472 AATTCCCTTGTTATCCCTCCC 57.027 47.619 0.00 0.00 0.00 4.30
4294 5386 5.382664 TGTAATTCCCTTGTTATCCCTCC 57.617 43.478 0.00 0.00 0.00 4.30
4295 5387 7.060421 TCATTGTAATTCCCTTGTTATCCCTC 58.940 38.462 0.00 0.00 0.00 4.30
4296 5388 6.980577 TCATTGTAATTCCCTTGTTATCCCT 58.019 36.000 0.00 0.00 0.00 4.20
4297 5389 7.654022 TTCATTGTAATTCCCTTGTTATCCC 57.346 36.000 0.00 0.00 0.00 3.85
4313 5405 8.579850 AGGTGCATTTCTTCTAATTCATTGTA 57.420 30.769 0.00 0.00 0.00 2.41
4315 5407 9.512435 CTAAGGTGCATTTCTTCTAATTCATTG 57.488 33.333 0.00 0.00 0.00 2.82
4316 5408 9.466497 TCTAAGGTGCATTTCTTCTAATTCATT 57.534 29.630 0.00 0.00 0.00 2.57
4318 5410 9.466497 AATCTAAGGTGCATTTCTTCTAATTCA 57.534 29.630 0.00 0.00 0.00 2.57
4331 5423 8.773033 ATAAAATTCCAGAATCTAAGGTGCAT 57.227 30.769 0.00 0.00 0.00 3.96
4332 5424 7.833682 TGATAAAATTCCAGAATCTAAGGTGCA 59.166 33.333 0.00 0.00 0.00 4.57
4333 5425 8.225603 TGATAAAATTCCAGAATCTAAGGTGC 57.774 34.615 0.00 0.00 0.00 5.01
4340 5432 8.974238 TGCATTTCTGATAAAATTCCAGAATCT 58.026 29.630 0.00 0.00 43.71 2.40
4341 5433 9.028185 GTGCATTTCTGATAAAATTCCAGAATC 57.972 33.333 0.00 0.00 43.71 2.52
4342 5434 7.983484 GGTGCATTTCTGATAAAATTCCAGAAT 59.017 33.333 0.00 0.00 43.71 2.40
4343 5435 7.178983 AGGTGCATTTCTGATAAAATTCCAGAA 59.821 33.333 0.00 0.00 42.93 3.02
4344 5436 6.664816 AGGTGCATTTCTGATAAAATTCCAGA 59.335 34.615 0.00 0.00 35.38 3.86
4345 5437 6.870769 AGGTGCATTTCTGATAAAATTCCAG 58.129 36.000 0.00 0.00 0.00 3.86
4346 5438 6.855763 AGGTGCATTTCTGATAAAATTCCA 57.144 33.333 0.00 0.00 0.00 3.53
4347 5439 8.686334 TCTAAGGTGCATTTCTGATAAAATTCC 58.314 33.333 0.00 0.00 0.00 3.01
4351 5443 9.466497 AGAATCTAAGGTGCATTTCTGATAAAA 57.534 29.630 0.00 0.00 0.00 1.52
4352 5444 8.896744 CAGAATCTAAGGTGCATTTCTGATAAA 58.103 33.333 4.84 0.00 41.47 1.40
4353 5445 7.500227 CCAGAATCTAAGGTGCATTTCTGATAA 59.500 37.037 11.03 0.00 41.47 1.75
4354 5446 6.994496 CCAGAATCTAAGGTGCATTTCTGATA 59.006 38.462 11.03 0.00 41.47 2.15
4355 5447 5.826737 CCAGAATCTAAGGTGCATTTCTGAT 59.173 40.000 11.03 5.10 41.47 2.90
4356 5448 5.045651 TCCAGAATCTAAGGTGCATTTCTGA 60.046 40.000 11.03 3.40 41.47 3.27
4357 5449 5.188434 TCCAGAATCTAAGGTGCATTTCTG 58.812 41.667 0.00 0.00 39.66 3.02
4565 6764 8.862325 AATTTATGTTGACACATAGAAGGACA 57.138 30.769 0.00 0.00 44.94 4.02
4682 6881 9.601217 ACCACAATGTAAGACTTGTCTATTATC 57.399 33.333 3.52 0.00 33.45 1.75
4687 6886 5.542635 AGGACCACAATGTAAGACTTGTCTA 59.457 40.000 3.52 0.00 33.45 2.59
4691 6890 6.464222 TCTTAGGACCACAATGTAAGACTTG 58.536 40.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.