Multiple sequence alignment - TraesCS3D01G521400

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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 TraesCS3D01G521400 chr3D 100.000 3711 0 0 1 3711 603153905 603157615 0.000000e+00 6854.0
1 TraesCS3D01G521400 chr3D 97.268 183 5 0 176 358 345758044 345758226 1.000000e-80 311.0
2 TraesCS3D01G521400 chr3D 94.359 195 11 0 167 361 27888475 27888669 2.170000e-77 300.0
3 TraesCS3D01G521400 chr3D 96.175 183 7 0 176 358 325025918 325026100 2.170000e-77 300.0
4 TraesCS3D01G521400 chr3D 90.217 92 4 3 359 445 31696064 31696155 8.420000e-22 115.0
5 TraesCS3D01G521400 chr3D 87.234 94 11 1 1 93 380280648 380280555 5.070000e-19 106.0
6 TraesCS3D01G521400 chr6B 97.055 2920 63 5 359 3258 269691385 269688469 0.000000e+00 4894.0
7 TraesCS3D01G521400 chr6B 92.975 1580 85 9 2105 3664 249500905 249499332 0.000000e+00 2279.0
8 TraesCS3D01G521400 chr6B 99.375 160 1 0 3552 3711 269688478 269688319 1.300000e-74 291.0
9 TraesCS3D01G521400 chr6B 94.268 157 7 2 29 184 269691525 269691370 4.790000e-59 239.0
10 TraesCS3D01G521400 chr6B 90.000 70 7 0 2105 2174 599821633 599821702 1.420000e-14 91.6
11 TraesCS3D01G521400 chr6B 93.023 43 3 0 3669 3711 249499195 249499153 3.090000e-06 63.9
12 TraesCS3D01G521400 chr2B 91.764 1627 67 8 2105 3711 34083923 34082344 0.000000e+00 2200.0
13 TraesCS3D01G521400 chr2B 79.677 310 41 8 3042 3330 315662804 315663112 1.750000e-48 204.0
14 TraesCS3D01G521400 chr2B 88.571 70 8 0 2105 2174 183532267 183532198 6.600000e-13 86.1
15 TraesCS3D01G521400 chr4B 85.556 360 46 5 1428 1784 411767872 411767516 4.530000e-99 372.0
16 TraesCS3D01G521400 chr4B 91.837 147 10 2 2313 2459 243185331 243185187 1.750000e-48 204.0
17 TraesCS3D01G521400 chr3B 85.596 361 44 7 1428 1784 792700833 792700477 4.530000e-99 372.0
18 TraesCS3D01G521400 chr3B 81.447 318 36 8 1494 1796 229467707 229468016 4.790000e-59 239.0
19 TraesCS3D01G521400 chr3B 91.837 147 10 2 2313 2459 124770568 124770424 1.750000e-48 204.0
20 TraesCS3D01G521400 chr7D 96.757 185 6 0 176 360 48555433 48555249 3.600000e-80 309.0
21 TraesCS3D01G521400 chr7D 95.676 185 8 0 176 360 229802652 229802468 7.790000e-77 298.0
22 TraesCS3D01G521400 chr7D 95.187 187 9 0 173 359 553212735 553212921 2.800000e-76 296.0
23 TraesCS3D01G521400 chr7D 86.413 184 22 3 2 184 45767495 45767676 8.130000e-47 198.0
24 TraesCS3D01G521400 chr7D 83.010 206 25 3 867 1063 528062697 528062901 1.060000e-40 178.0
25 TraesCS3D01G521400 chr7D 88.112 143 14 2 2172 2312 173701917 173702058 2.290000e-37 167.0
26 TraesCS3D01G521400 chr7D 87.234 94 11 1 1 93 33072448 33072355 5.070000e-19 106.0
27 TraesCS3D01G521400 chr1D 96.216 185 7 0 176 360 490396901 490397085 1.670000e-78 303.0
28 TraesCS3D01G521400 chr1D 88.043 92 6 3 359 445 436336426 436336517 1.820000e-18 104.0
29 TraesCS3D01G521400 chr5D 95.722 187 8 0 177 363 526241577 526241391 6.020000e-78 302.0
30 TraesCS3D01G521400 chr5D 80.968 310 36 9 3042 3330 463264195 463263888 1.340000e-54 224.0
31 TraesCS3D01G521400 chr5D 88.776 98 6 3 359 451 276297683 276297586 8.420000e-22 115.0
32 TraesCS3D01G521400 chr2D 95.238 189 8 1 177 365 51142785 51142598 7.790000e-77 298.0
33 TraesCS3D01G521400 chr2D 86.957 184 21 3 2 184 318575923 318576104 1.750000e-48 204.0
34 TraesCS3D01G521400 chrUn 84.711 242 34 2 1433 1672 403734131 403733891 4.790000e-59 239.0
35 TraesCS3D01G521400 chrUn 89.130 92 5 3 359 445 88075065 88075156 3.920000e-20 110.0
36 TraesCS3D01G521400 chrUn 90.000 70 7 0 2105 2174 77059806 77059875 1.420000e-14 91.6
37 TraesCS3D01G521400 chr3A 84.711 242 34 2 1433 1672 738467701 738467461 4.790000e-59 239.0
38 TraesCS3D01G521400 chr3A 84.711 242 34 2 1433 1672 738552583 738552343 4.790000e-59 239.0
39 TraesCS3D01G521400 chr3A 84.711 242 34 2 1433 1672 738652754 738652514 4.790000e-59 239.0
40 TraesCS3D01G521400 chr3A 84.298 242 35 2 1433 1672 738574248 738574008 2.230000e-57 233.0
41 TraesCS3D01G521400 chr3A 87.368 95 11 1 1 94 82906194 82906288 1.410000e-19 108.0
42 TraesCS3D01G521400 chr3A 88.764 89 7 2 360 445 82906318 82906406 5.070000e-19 106.0
43 TraesCS3D01G521400 chr3A 88.571 70 8 0 2105 2174 292176037 292175968 6.600000e-13 86.1
44 TraesCS3D01G521400 chr5B 91.333 150 11 2 2310 2459 706028173 706028320 1.750000e-48 204.0
45 TraesCS3D01G521400 chr5B 87.234 94 11 1 1 93 78209297 78209390 5.070000e-19 106.0
46 TraesCS3D01G521400 chr5B 88.764 89 7 2 360 445 406550781 406550869 5.070000e-19 106.0
47 TraesCS3D01G521400 chr5B 87.368 95 4 3 359 445 459575563 459575657 6.560000e-18 102.0
48 TraesCS3D01G521400 chr5B 90.000 70 7 0 2105 2174 672538970 672538901 1.420000e-14 91.6
49 TraesCS3D01G521400 chr4A 91.837 147 11 1 2313 2459 90388393 90388248 1.750000e-48 204.0
50 TraesCS3D01G521400 chr2A 90.667 150 12 2 2310 2459 492831952 492832099 8.130000e-47 198.0
51 TraesCS3D01G521400 chr4D 85.946 185 22 4 2 184 434996530 434996348 1.050000e-45 195.0
52 TraesCS3D01G521400 chr4D 88.776 98 6 3 359 451 492828368 492828271 8.420000e-22 115.0
53 TraesCS3D01G521400 chr4D 94.444 54 3 0 1422 1475 264316930 264316877 2.380000e-12 84.2
54 TraesCS3D01G521400 chr6D 82.524 206 26 3 867 1063 69906929 69907133 4.930000e-39 172.0
55 TraesCS3D01G521400 chr7A 79.026 267 38 9 798 1061 117616955 117616704 2.290000e-37 167.0
56 TraesCS3D01G521400 chr7A 87.234 94 11 1 1 93 497658512 497658419 5.070000e-19 106.0
57 TraesCS3D01G521400 chr6A 97.222 36 1 0 128 163 256835702 256835737 1.110000e-05 62.1


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 TraesCS3D01G521400 chr3D 603153905 603157615 3710 False 6854.00 6854 100.000000 1 3711 1 chr3D.!!$F5 3710
1 TraesCS3D01G521400 chr6B 269688319 269691525 3206 True 1808.00 4894 96.899333 29 3711 3 chr6B.!!$R2 3682
2 TraesCS3D01G521400 chr6B 249499153 249500905 1752 True 1171.45 2279 92.999000 2105 3711 2 chr6B.!!$R1 1606
3 TraesCS3D01G521400 chr2B 34082344 34083923 1579 True 2200.00 2200 91.764000 2105 3711 1 chr2B.!!$R1 1606

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
219 220 0.040692 CCGTCGCTAATAGCACGCTA 60.041 55.0 22.36 0.39 42.58 4.26 F
1349 1353 0.040058 TGGAGCAGCAAACCATGGAT 59.960 50.0 21.47 2.68 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 1849 0.179156 CATGATGCACGAAGGGTTGC 60.179 55.000 0.0 0.0 0.00 4.17 R
2800 2820 3.108847 TGGTTTTTCCAAAGGTGGTCT 57.891 42.857 0.0 0.0 46.11 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.893753 TTTTGGTTTCTCCCATCTGGA 57.106 42.857 0.00 0.00 42.41 3.86
24 25 4.402616 TTTTGGTTTCTCCCATCTGGAT 57.597 40.909 0.00 0.00 44.07 3.41
25 26 4.402616 TTTGGTTTCTCCCATCTGGATT 57.597 40.909 0.00 0.00 44.07 3.01
26 27 4.402616 TTGGTTTCTCCCATCTGGATTT 57.597 40.909 0.00 0.00 44.07 2.17
27 28 3.968265 TGGTTTCTCCCATCTGGATTTC 58.032 45.455 0.00 0.00 44.07 2.17
39 40 6.239232 CCCATCTGGATTTCTGATTTGATTCC 60.239 42.308 0.00 0.00 37.39 3.01
58 59 1.538047 CAAAGTGTGGAGGTGGATGG 58.462 55.000 0.00 0.00 0.00 3.51
64 65 1.906574 TGTGGAGGTGGATGGTACTTC 59.093 52.381 0.00 0.00 0.00 3.01
73 74 2.225779 TGGATGGTACTTCAGGGAGGAA 60.226 50.000 0.00 0.00 0.00 3.36
122 123 2.741517 GCAGCGGGCACAAAATAATTTT 59.258 40.909 0.00 0.00 43.97 1.82
165 166 4.642429 GATTGGTGAGTTACAGGTCAACT 58.358 43.478 0.00 0.00 38.92 3.16
176 177 0.759346 AGGTCAACTGTGTCTCACCC 59.241 55.000 0.00 0.00 32.73 4.61
177 178 0.468226 GGTCAACTGTGTCTCACCCA 59.532 55.000 0.00 0.00 32.73 4.51
178 179 1.583054 GTCAACTGTGTCTCACCCAC 58.417 55.000 0.00 0.00 32.73 4.61
179 180 1.139058 GTCAACTGTGTCTCACCCACT 59.861 52.381 0.00 0.00 32.73 4.00
180 181 1.138859 TCAACTGTGTCTCACCCACTG 59.861 52.381 0.00 0.00 37.66 3.66
181 182 1.138859 CAACTGTGTCTCACCCACTGA 59.861 52.381 0.00 0.00 36.14 3.41
182 183 1.496060 ACTGTGTCTCACCCACTGAA 58.504 50.000 0.00 0.00 36.14 3.02
183 184 1.837439 ACTGTGTCTCACCCACTGAAA 59.163 47.619 0.00 0.00 36.14 2.69
184 185 2.238646 ACTGTGTCTCACCCACTGAAAA 59.761 45.455 0.00 0.00 36.14 2.29
185 186 3.278574 CTGTGTCTCACCCACTGAAAAA 58.721 45.455 0.00 0.00 34.73 1.94
203 204 2.144482 AAAATAGCGCGCTATACCGT 57.856 45.000 43.81 30.08 38.20 4.83
204 205 1.694639 AAATAGCGCGCTATACCGTC 58.305 50.000 43.81 10.26 38.20 4.79
205 206 0.453950 AATAGCGCGCTATACCGTCG 60.454 55.000 43.81 0.00 38.20 5.12
206 207 2.845861 ATAGCGCGCTATACCGTCGC 62.846 60.000 43.42 16.23 46.16 5.19
207 208 4.977126 GCGCGCTATACCGTCGCT 62.977 66.667 26.67 0.00 45.87 4.93
208 209 2.552768 CGCGCTATACCGTCGCTA 59.447 61.111 5.56 0.00 45.87 4.26
209 210 1.082561 CGCGCTATACCGTCGCTAA 60.083 57.895 5.56 0.00 45.87 3.09
210 211 0.453950 CGCGCTATACCGTCGCTAAT 60.454 55.000 5.56 0.00 45.87 1.73
211 212 1.201954 CGCGCTATACCGTCGCTAATA 60.202 52.381 5.56 0.00 45.87 0.98
212 213 2.438583 GCGCTATACCGTCGCTAATAG 58.561 52.381 0.00 0.00 44.79 1.73
213 214 2.438583 CGCTATACCGTCGCTAATAGC 58.561 52.381 15.91 15.91 42.10 2.97
214 215 2.159612 CGCTATACCGTCGCTAATAGCA 60.160 50.000 21.37 0.00 44.51 3.49
215 216 3.169733 GCTATACCGTCGCTAATAGCAC 58.830 50.000 13.15 8.59 43.98 4.40
216 217 2.327081 ATACCGTCGCTAATAGCACG 57.673 50.000 21.46 21.46 42.58 5.34
217 218 0.317269 TACCGTCGCTAATAGCACGC 60.317 55.000 22.36 8.84 42.58 5.34
218 219 1.299165 CCGTCGCTAATAGCACGCT 60.299 57.895 22.36 0.00 42.58 5.07
219 220 0.040692 CCGTCGCTAATAGCACGCTA 60.041 55.000 22.36 0.39 42.58 4.26
220 221 1.401148 CCGTCGCTAATAGCACGCTAT 60.401 52.381 22.36 5.72 42.58 2.97
221 222 2.159612 CCGTCGCTAATAGCACGCTATA 60.160 50.000 22.36 1.16 42.58 1.31
222 223 3.092135 CGTCGCTAATAGCACGCTATAG 58.908 50.000 18.51 10.32 42.58 1.31
223 224 2.847133 GTCGCTAATAGCACGCTATAGC 59.153 50.000 15.09 15.09 42.58 2.97
238 239 5.209944 GCTATAGCGTATTGAGAATTGCC 57.790 43.478 9.40 0.00 0.00 4.52
239 240 4.932200 GCTATAGCGTATTGAGAATTGCCT 59.068 41.667 9.40 0.00 0.00 4.75
240 241 5.409826 GCTATAGCGTATTGAGAATTGCCTT 59.590 40.000 9.40 0.00 0.00 4.35
241 242 5.679734 ATAGCGTATTGAGAATTGCCTTG 57.320 39.130 0.00 0.00 0.00 3.61
242 243 2.098117 AGCGTATTGAGAATTGCCTTGC 59.902 45.455 0.00 0.00 0.00 4.01
243 244 2.098117 GCGTATTGAGAATTGCCTTGCT 59.902 45.455 0.00 0.00 0.00 3.91
244 245 3.312421 GCGTATTGAGAATTGCCTTGCTA 59.688 43.478 0.00 0.00 0.00 3.49
245 246 4.201910 GCGTATTGAGAATTGCCTTGCTAA 60.202 41.667 0.00 0.00 0.00 3.09
246 247 5.676079 GCGTATTGAGAATTGCCTTGCTAAA 60.676 40.000 0.00 0.00 0.00 1.85
247 248 6.498304 CGTATTGAGAATTGCCTTGCTAAAT 58.502 36.000 0.00 0.00 0.00 1.40
248 249 7.639039 CGTATTGAGAATTGCCTTGCTAAATA 58.361 34.615 0.00 0.00 0.00 1.40
249 250 8.292448 CGTATTGAGAATTGCCTTGCTAAATAT 58.708 33.333 0.00 0.00 0.00 1.28
253 254 8.922931 TGAGAATTGCCTTGCTAAATATATCA 57.077 30.769 0.00 0.00 0.00 2.15
254 255 9.006839 TGAGAATTGCCTTGCTAAATATATCAG 57.993 33.333 0.00 0.00 0.00 2.90
255 256 8.930846 AGAATTGCCTTGCTAAATATATCAGT 57.069 30.769 0.00 0.00 0.00 3.41
256 257 8.790718 AGAATTGCCTTGCTAAATATATCAGTG 58.209 33.333 0.00 0.00 0.00 3.66
257 258 8.469309 AATTGCCTTGCTAAATATATCAGTGT 57.531 30.769 0.00 0.00 0.00 3.55
258 259 9.573166 AATTGCCTTGCTAAATATATCAGTGTA 57.427 29.630 0.00 0.00 0.00 2.90
259 260 7.962964 TGCCTTGCTAAATATATCAGTGTAC 57.037 36.000 0.00 0.00 0.00 2.90
260 261 7.505258 TGCCTTGCTAAATATATCAGTGTACA 58.495 34.615 0.00 0.00 0.00 2.90
261 262 7.990314 TGCCTTGCTAAATATATCAGTGTACAA 59.010 33.333 0.00 0.00 0.00 2.41
262 263 9.003658 GCCTTGCTAAATATATCAGTGTACAAT 57.996 33.333 0.00 0.00 0.00 2.71
266 267 9.489084 TGCTAAATATATCAGTGTACAATGTCC 57.511 33.333 21.56 0.00 0.00 4.02
267 268 8.936864 GCTAAATATATCAGTGTACAATGTCCC 58.063 37.037 21.56 0.00 0.00 4.46
268 269 7.962964 AAATATATCAGTGTACAATGTCCCG 57.037 36.000 21.56 0.00 0.00 5.14
269 270 2.024176 ATCAGTGTACAATGTCCCGC 57.976 50.000 21.56 0.00 0.00 6.13
270 271 0.973632 TCAGTGTACAATGTCCCGCT 59.026 50.000 21.56 0.00 0.00 5.52
271 272 2.172679 TCAGTGTACAATGTCCCGCTA 58.827 47.619 21.56 0.00 0.00 4.26
272 273 2.563620 TCAGTGTACAATGTCCCGCTAA 59.436 45.455 21.56 0.00 0.00 3.09
273 274 3.196901 TCAGTGTACAATGTCCCGCTAAT 59.803 43.478 21.56 0.00 0.00 1.73
274 275 4.403113 TCAGTGTACAATGTCCCGCTAATA 59.597 41.667 21.56 0.00 0.00 0.98
275 276 4.745125 CAGTGTACAATGTCCCGCTAATAG 59.255 45.833 15.00 0.00 0.00 1.73
276 277 3.493503 GTGTACAATGTCCCGCTAATAGC 59.506 47.826 1.41 1.41 38.02 2.97
277 278 3.133183 TGTACAATGTCCCGCTAATAGCA 59.867 43.478 13.15 0.00 42.58 3.49
278 279 2.561569 ACAATGTCCCGCTAATAGCAC 58.438 47.619 13.15 3.79 42.58 4.40
279 280 1.526887 CAATGTCCCGCTAATAGCACG 59.473 52.381 13.15 1.23 42.58 5.34
280 281 0.600255 ATGTCCCGCTAATAGCACGC 60.600 55.000 13.15 0.19 42.58 5.34
281 282 1.067582 GTCCCGCTAATAGCACGCT 59.932 57.895 13.15 0.00 42.58 5.07
282 283 0.313043 GTCCCGCTAATAGCACGCTA 59.687 55.000 13.15 0.39 42.58 4.26
283 284 1.067776 GTCCCGCTAATAGCACGCTAT 60.068 52.381 13.15 5.72 42.58 2.97
284 285 2.163010 GTCCCGCTAATAGCACGCTATA 59.837 50.000 13.15 1.16 42.58 1.31
285 286 2.422479 TCCCGCTAATAGCACGCTATAG 59.578 50.000 13.15 10.32 42.58 1.31
286 287 2.186076 CCGCTAATAGCACGCTATAGC 58.814 52.381 15.09 15.09 42.58 2.97
301 302 2.879002 ATAGCGCGATATAGCATGCT 57.121 45.000 25.99 25.99 37.52 3.79
302 303 3.990318 ATAGCGCGATATAGCATGCTA 57.010 42.857 28.72 28.72 39.25 3.49
303 304 2.654749 AGCGCGATATAGCATGCTAA 57.345 45.000 30.06 19.16 33.28 3.09
304 305 3.170791 AGCGCGATATAGCATGCTAAT 57.829 42.857 30.06 22.48 33.28 1.73
305 306 4.307443 AGCGCGATATAGCATGCTAATA 57.693 40.909 30.06 21.15 33.28 0.98
306 307 4.294232 AGCGCGATATAGCATGCTAATAG 58.706 43.478 30.06 22.19 33.28 1.73
307 308 3.121194 GCGCGATATAGCATGCTAATAGC 60.121 47.826 30.06 27.58 38.28 2.97
322 323 5.622378 GCTAATAGCATATTTTGAGGTCGC 58.378 41.667 7.49 0.00 41.89 5.19
323 324 5.390991 GCTAATAGCATATTTTGAGGTCGCC 60.391 44.000 7.49 0.00 41.89 5.54
324 325 1.299541 AGCATATTTTGAGGTCGCCG 58.700 50.000 0.00 0.00 0.00 6.46
325 326 0.317020 GCATATTTTGAGGTCGCCGC 60.317 55.000 0.00 0.00 0.00 6.53
326 327 1.299541 CATATTTTGAGGTCGCCGCT 58.700 50.000 1.93 0.00 0.00 5.52
327 328 2.479837 CATATTTTGAGGTCGCCGCTA 58.520 47.619 1.93 0.00 0.00 4.26
328 329 2.902705 TATTTTGAGGTCGCCGCTAT 57.097 45.000 1.93 0.00 0.00 2.97
329 330 2.038387 ATTTTGAGGTCGCCGCTATT 57.962 45.000 1.93 0.00 0.00 1.73
330 331 1.816074 TTTTGAGGTCGCCGCTATTT 58.184 45.000 1.93 0.00 0.00 1.40
331 332 1.816074 TTTGAGGTCGCCGCTATTTT 58.184 45.000 1.93 0.00 0.00 1.82
332 333 1.083489 TTGAGGTCGCCGCTATTTTG 58.917 50.000 1.93 0.00 0.00 2.44
333 334 1.352056 GAGGTCGCCGCTATTTTGC 59.648 57.895 0.00 0.00 0.00 3.68
334 335 1.078426 AGGTCGCCGCTATTTTGCT 60.078 52.632 0.00 0.00 0.00 3.91
335 336 1.062525 GGTCGCCGCTATTTTGCTG 59.937 57.895 0.00 0.00 0.00 4.41
336 337 1.644786 GGTCGCCGCTATTTTGCTGT 61.645 55.000 0.00 0.00 0.00 4.40
337 338 1.003851 GTCGCCGCTATTTTGCTGTA 58.996 50.000 0.00 0.00 0.00 2.74
338 339 1.004927 GTCGCCGCTATTTTGCTGTAG 60.005 52.381 0.00 0.00 0.00 2.74
339 340 0.316196 CGCCGCTATTTTGCTGTAGC 60.316 55.000 0.00 0.00 39.86 3.58
457 461 6.498303 AGGGATATCATGTACAGTGCTAATCA 59.502 38.462 4.83 0.00 0.00 2.57
478 482 4.161565 TCACCTAATGCGATTTAGACCAGT 59.838 41.667 6.42 0.00 32.02 4.00
605 609 5.835113 TTCATATTGTTCTTTAGCCCTGC 57.165 39.130 0.00 0.00 0.00 4.85
659 663 7.913423 TGCTCAGATGAAAGAATAATTTCTCG 58.087 34.615 1.41 0.00 41.42 4.04
764 768 4.189231 GCATCGTTAGTAACCACTGGAAT 58.811 43.478 7.45 0.00 36.14 3.01
765 769 4.634443 GCATCGTTAGTAACCACTGGAATT 59.366 41.667 7.45 0.00 36.14 2.17
797 801 6.462552 TCAGTCAGTCTCTTTGATATCCAG 57.537 41.667 0.00 0.00 0.00 3.86
865 869 4.335037 GGGCTTTTCTAGAAGATGCTCTTG 59.665 45.833 18.87 0.97 36.73 3.02
918 922 9.490663 GTAATGTGTTCTTTGAAATCTAATCGG 57.509 33.333 0.00 0.00 0.00 4.18
924 928 7.065803 TGTTCTTTGAAATCTAATCGGTCCATC 59.934 37.037 0.00 0.00 0.00 3.51
993 997 4.165950 TCAACTTGAGTATATGGTGCCCAT 59.834 41.667 10.96 10.96 46.99 4.00
1084 1088 3.697439 TTATGGGCCTGCTCCGTGC 62.697 63.158 4.53 0.00 43.25 5.34
1184 1188 3.019003 AACTCCATCCTGGCCGACG 62.019 63.158 0.00 0.00 37.47 5.12
1207 1211 1.976474 GGGCGAATGCTGGTTTCCA 60.976 57.895 0.00 0.00 42.25 3.53
1213 1217 2.238521 GAATGCTGGTTTCCAAGGTGA 58.761 47.619 0.00 0.00 30.80 4.02
1224 1228 4.669866 TTCCAAGGTGAGGTAGTCTCTA 57.330 45.455 0.00 0.00 42.86 2.43
1240 1244 5.580998 AGTCTCTATGTCCACTAACTCCAA 58.419 41.667 0.00 0.00 0.00 3.53
1323 1327 2.224769 GGTGGTTCTCCCAGTCAATGAA 60.225 50.000 0.00 0.00 46.45 2.57
1349 1353 0.040058 TGGAGCAGCAAACCATGGAT 59.960 50.000 21.47 2.68 0.00 3.41
1366 1370 1.407979 GGATGATTTGGAGGCTGCTTG 59.592 52.381 7.74 0.00 0.00 4.01
1563 1567 5.184479 ACAATGAAAGATCCATGAGGTTGTG 59.816 40.000 0.00 0.00 35.89 3.33
1567 1571 0.753111 GATCCATGAGGTTGTGGGGC 60.753 60.000 0.00 0.00 36.15 5.80
1657 1661 6.871492 TGTCTCTTGATGTCGCTAATTTTGTA 59.129 34.615 0.00 0.00 0.00 2.41
1661 1665 7.909267 TCTTGATGTCGCTAATTTTGTATGAG 58.091 34.615 0.00 0.00 0.00 2.90
1845 1849 0.741221 GGAGCAACAGGTAAGGAGCG 60.741 60.000 0.00 0.00 0.00 5.03
1855 1859 1.079405 TAAGGAGCGCAACCCTTCG 60.079 57.895 25.13 0.00 41.53 3.79
1898 1902 2.738521 CCAGAACAGGCGACCACG 60.739 66.667 0.00 0.00 42.93 4.94
1982 1986 4.840716 ATTGCTTCTCTTGGTCATCTCT 57.159 40.909 0.00 0.00 0.00 3.10
1983 1987 3.606595 TGCTTCTCTTGGTCATCTCTG 57.393 47.619 0.00 0.00 0.00 3.35
2035 2039 7.035004 TGTGGCAACTAATTTATGCTTCATTC 58.965 34.615 0.00 0.00 39.94 2.67
2260 2264 7.539034 AACCATTTCCTGCAAACTAAACTAT 57.461 32.000 0.00 0.00 0.00 2.12
2549 2569 1.202498 TCTGCTGCTGAAGGATGATCG 60.202 52.381 6.77 0.00 0.00 3.69
2604 2624 1.661341 GTAGGTCTGGAGCTTGCATG 58.339 55.000 7.61 0.00 40.09 4.06
2767 2787 4.202141 TGGCAAGTGTTTTCTCATTTCCAG 60.202 41.667 0.00 0.00 0.00 3.86
3013 3035 6.916360 AGTGTTCCACCATTGATTGTTAAT 57.084 33.333 0.00 0.00 34.49 1.40
3207 3235 5.440207 AAGGCAATTGATTTTGGGCTATT 57.560 34.783 10.34 0.00 33.67 1.73
3282 3310 9.717942 AATCTAGATCTGCTAAAATAAGCGATT 57.282 29.630 5.51 0.00 45.85 3.34
3360 3388 6.536941 GGCAAATGTGGAAACTCTTGTTAAAA 59.463 34.615 0.00 0.00 34.96 1.52
3410 3438 4.540359 TTTGCTTGATTTTCCATCCCTG 57.460 40.909 0.00 0.00 0.00 4.45
3420 3448 4.474303 TTTCCATCCCTGCATAATGGAT 57.526 40.909 19.68 11.75 46.23 3.41
3535 3564 6.717289 TGAAACTGTAGGCAAACCATACTAT 58.283 36.000 0.00 0.00 39.06 2.12
3646 3675 2.224548 ACCTTTACTTGTGTGGCCTCTC 60.225 50.000 3.32 1.31 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.191804 TCCAGATGGGAGAAACCAAAAA 57.808 40.909 0.00 0.00 45.13 1.94
3 4 3.893753 TCCAGATGGGAGAAACCAAAA 57.106 42.857 0.00 0.00 45.13 2.44
14 15 6.239232 GGAATCAAATCAGAAATCCAGATGGG 60.239 42.308 0.00 0.00 35.41 4.00
15 16 6.322969 TGGAATCAAATCAGAAATCCAGATGG 59.677 38.462 0.00 0.00 34.55 3.51
16 17 7.342769 TGGAATCAAATCAGAAATCCAGATG 57.657 36.000 0.00 0.00 34.55 2.90
17 18 7.966339 TTGGAATCAAATCAGAAATCCAGAT 57.034 32.000 0.00 0.00 38.22 2.90
18 19 7.452501 ACTTTGGAATCAAATCAGAAATCCAGA 59.547 33.333 0.00 0.00 41.45 3.86
19 20 7.544566 CACTTTGGAATCAAATCAGAAATCCAG 59.455 37.037 0.00 0.00 41.45 3.86
20 21 7.015487 ACACTTTGGAATCAAATCAGAAATCCA 59.985 33.333 0.00 0.00 41.45 3.41
21 22 7.330208 CACACTTTGGAATCAAATCAGAAATCC 59.670 37.037 0.00 0.00 41.45 3.01
22 23 8.236084 CACACTTTGGAATCAAATCAGAAATC 57.764 34.615 0.00 0.00 41.45 2.17
39 40 1.202927 ACCATCCACCTCCACACTTTG 60.203 52.381 0.00 0.00 0.00 2.77
64 65 0.178992 TGCAACCAACTTCCTCCCTG 60.179 55.000 0.00 0.00 0.00 4.45
73 74 4.842574 ACAAAAGGAAATTGCAACCAACT 58.157 34.783 0.00 0.00 32.95 3.16
122 123 1.610522 GCTGAAAGAAAGCTTGCCTGA 59.389 47.619 0.00 0.00 37.69 3.86
157 158 0.759346 GGGTGAGACACAGTTGACCT 59.241 55.000 0.00 0.00 35.86 3.85
165 166 3.358111 TTTTTCAGTGGGTGAGACACA 57.642 42.857 0.00 0.00 41.21 3.72
183 184 2.473984 GACGGTATAGCGCGCTATTTTT 59.526 45.455 46.76 31.77 39.65 1.94
184 185 2.056577 GACGGTATAGCGCGCTATTTT 58.943 47.619 46.76 32.19 39.65 1.82
185 186 1.694639 GACGGTATAGCGCGCTATTT 58.305 50.000 46.76 32.85 39.65 1.40
186 187 0.453950 CGACGGTATAGCGCGCTATT 60.454 55.000 46.76 33.83 39.65 1.73
187 188 1.134075 CGACGGTATAGCGCGCTAT 59.866 57.895 44.16 44.16 41.58 2.97
188 189 2.552768 CGACGGTATAGCGCGCTA 59.447 61.111 39.72 39.72 0.00 4.26
189 190 4.977126 GCGACGGTATAGCGCGCT 62.977 66.667 35.56 38.01 43.85 5.92
192 193 5.789944 TGCTATTAGCGACGGTATAGCGC 62.790 52.174 23.33 14.87 46.26 5.92
193 194 2.159612 TGCTATTAGCGACGGTATAGCG 60.160 50.000 25.51 21.96 46.26 4.26
194 195 3.169733 GTGCTATTAGCGACGGTATAGC 58.830 50.000 25.09 25.09 46.26 2.97
195 196 3.414464 CGTGCTATTAGCGACGGTATAG 58.586 50.000 22.11 11.85 46.26 1.31
196 197 2.413239 GCGTGCTATTAGCGACGGTATA 60.413 50.000 26.64 0.00 46.26 1.47
197 198 1.665161 GCGTGCTATTAGCGACGGTAT 60.665 52.381 26.64 1.45 46.26 2.73
198 199 0.317269 GCGTGCTATTAGCGACGGTA 60.317 55.000 26.64 1.96 46.26 4.02
199 200 1.588139 GCGTGCTATTAGCGACGGT 60.588 57.895 26.64 4.41 46.26 4.83
200 201 0.040692 TAGCGTGCTATTAGCGACGG 60.041 55.000 26.64 16.35 46.26 4.79
201 202 1.965083 ATAGCGTGCTATTAGCGACG 58.035 50.000 23.96 23.96 46.26 5.12
202 203 2.847133 GCTATAGCGTGCTATTAGCGAC 59.153 50.000 18.62 9.06 46.26 5.19
203 204 3.132629 GCTATAGCGTGCTATTAGCGA 57.867 47.619 18.62 0.92 46.26 4.93
216 217 4.932200 AGGCAATTCTCAATACGCTATAGC 59.068 41.667 15.09 15.09 37.78 2.97
217 218 6.619446 GCAAGGCAATTCTCAATACGCTATAG 60.619 42.308 0.00 0.00 0.00 1.31
218 219 5.179368 GCAAGGCAATTCTCAATACGCTATA 59.821 40.000 0.00 0.00 0.00 1.31
219 220 4.023707 GCAAGGCAATTCTCAATACGCTAT 60.024 41.667 0.00 0.00 0.00 2.97
220 221 3.312421 GCAAGGCAATTCTCAATACGCTA 59.688 43.478 0.00 0.00 0.00 4.26
221 222 2.098117 GCAAGGCAATTCTCAATACGCT 59.902 45.455 0.00 0.00 0.00 5.07
222 223 2.098117 AGCAAGGCAATTCTCAATACGC 59.902 45.455 0.00 0.00 0.00 4.42
223 224 5.484173 TTAGCAAGGCAATTCTCAATACG 57.516 39.130 0.00 0.00 0.00 3.06
227 228 9.353431 TGATATATTTAGCAAGGCAATTCTCAA 57.647 29.630 0.00 0.00 0.00 3.02
228 229 8.922931 TGATATATTTAGCAAGGCAATTCTCA 57.077 30.769 0.00 0.00 0.00 3.27
229 230 9.007901 ACTGATATATTTAGCAAGGCAATTCTC 57.992 33.333 0.00 0.00 0.00 2.87
230 231 8.790718 CACTGATATATTTAGCAAGGCAATTCT 58.209 33.333 0.00 0.00 0.00 2.40
231 232 8.571336 ACACTGATATATTTAGCAAGGCAATTC 58.429 33.333 0.00 0.00 0.00 2.17
232 233 8.469309 ACACTGATATATTTAGCAAGGCAATT 57.531 30.769 0.00 0.00 0.00 2.32
233 234 9.003658 GTACACTGATATATTTAGCAAGGCAAT 57.996 33.333 0.00 0.00 0.00 3.56
234 235 7.990314 TGTACACTGATATATTTAGCAAGGCAA 59.010 33.333 0.00 0.00 0.00 4.52
235 236 7.505258 TGTACACTGATATATTTAGCAAGGCA 58.495 34.615 0.00 0.00 0.00 4.75
236 237 7.962964 TGTACACTGATATATTTAGCAAGGC 57.037 36.000 0.00 0.00 0.00 4.35
240 241 9.489084 GGACATTGTACACTGATATATTTAGCA 57.511 33.333 19.02 0.00 0.00 3.49
241 242 8.936864 GGGACATTGTACACTGATATATTTAGC 58.063 37.037 19.02 0.00 0.00 3.09
242 243 9.140286 CGGGACATTGTACACTGATATATTTAG 57.860 37.037 19.02 0.00 0.00 1.85
243 244 7.601130 GCGGGACATTGTACACTGATATATTTA 59.399 37.037 19.02 0.00 0.00 1.40
244 245 6.426937 GCGGGACATTGTACACTGATATATTT 59.573 38.462 19.02 0.00 0.00 1.40
245 246 5.932303 GCGGGACATTGTACACTGATATATT 59.068 40.000 19.02 0.00 0.00 1.28
246 247 5.246203 AGCGGGACATTGTACACTGATATAT 59.754 40.000 19.02 0.00 0.00 0.86
247 248 4.587262 AGCGGGACATTGTACACTGATATA 59.413 41.667 19.02 0.00 0.00 0.86
248 249 3.388024 AGCGGGACATTGTACACTGATAT 59.612 43.478 19.02 0.00 0.00 1.63
249 250 2.764010 AGCGGGACATTGTACACTGATA 59.236 45.455 19.02 0.00 0.00 2.15
250 251 1.555075 AGCGGGACATTGTACACTGAT 59.445 47.619 19.02 4.41 0.00 2.90
251 252 0.973632 AGCGGGACATTGTACACTGA 59.026 50.000 19.02 0.00 0.00 3.41
252 253 2.665649 TAGCGGGACATTGTACACTG 57.334 50.000 11.37 11.37 0.00 3.66
253 254 3.906720 ATTAGCGGGACATTGTACACT 57.093 42.857 0.57 0.33 0.00 3.55
254 255 3.493503 GCTATTAGCGGGACATTGTACAC 59.506 47.826 0.57 0.00 0.00 2.90
255 256 3.133183 TGCTATTAGCGGGACATTGTACA 59.867 43.478 10.94 0.00 46.26 2.90
256 257 3.493503 GTGCTATTAGCGGGACATTGTAC 59.506 47.826 10.94 0.00 46.26 2.90
257 258 3.724374 GTGCTATTAGCGGGACATTGTA 58.276 45.455 10.94 0.00 46.26 2.41
258 259 2.561569 GTGCTATTAGCGGGACATTGT 58.438 47.619 10.94 0.00 46.26 2.71
259 260 1.526887 CGTGCTATTAGCGGGACATTG 59.473 52.381 10.94 0.00 46.26 2.82
260 261 1.865865 CGTGCTATTAGCGGGACATT 58.134 50.000 10.94 0.00 46.26 2.71
261 262 0.600255 GCGTGCTATTAGCGGGACAT 60.600 55.000 10.94 0.00 46.26 3.06
262 263 1.227147 GCGTGCTATTAGCGGGACA 60.227 57.895 10.94 0.00 46.26 4.02
263 264 0.313043 TAGCGTGCTATTAGCGGGAC 59.687 55.000 10.94 3.28 46.26 4.46
264 265 1.254026 ATAGCGTGCTATTAGCGGGA 58.746 50.000 8.54 0.00 46.26 5.14
265 266 2.798680 CTATAGCGTGCTATTAGCGGG 58.201 52.381 18.62 6.35 46.26 6.13
266 267 2.186076 GCTATAGCGTGCTATTAGCGG 58.814 52.381 18.62 6.68 46.26 5.52
280 281 3.894920 AGCATGCTATATCGCGCTATAG 58.105 45.455 25.40 25.40 35.61 1.31
281 282 3.990318 AGCATGCTATATCGCGCTATA 57.010 42.857 21.21 4.63 0.00 1.31
282 283 2.879002 AGCATGCTATATCGCGCTAT 57.121 45.000 21.21 7.70 0.00 2.97
283 284 3.775661 TTAGCATGCTATATCGCGCTA 57.224 42.857 27.35 7.05 30.90 4.26
284 285 2.654749 TTAGCATGCTATATCGCGCT 57.345 45.000 27.35 0.82 32.62 5.92
285 286 3.121194 GCTATTAGCATGCTATATCGCGC 60.121 47.826 27.35 18.57 41.89 6.86
286 287 4.621526 GCTATTAGCATGCTATATCGCG 57.378 45.455 27.35 13.61 41.89 5.87
299 300 5.390991 GGCGACCTCAAAATATGCTATTAGC 60.391 44.000 8.80 8.80 42.82 3.09
300 301 5.163953 CGGCGACCTCAAAATATGCTATTAG 60.164 44.000 0.00 0.00 0.00 1.73
301 302 4.688879 CGGCGACCTCAAAATATGCTATTA 59.311 41.667 0.00 0.00 0.00 0.98
302 303 3.498397 CGGCGACCTCAAAATATGCTATT 59.502 43.478 0.00 0.00 0.00 1.73
303 304 3.067106 CGGCGACCTCAAAATATGCTAT 58.933 45.455 0.00 0.00 0.00 2.97
304 305 2.479837 CGGCGACCTCAAAATATGCTA 58.520 47.619 0.00 0.00 0.00 3.49
305 306 1.299541 CGGCGACCTCAAAATATGCT 58.700 50.000 0.00 0.00 0.00 3.79
306 307 0.317020 GCGGCGACCTCAAAATATGC 60.317 55.000 12.98 0.00 0.00 3.14
307 308 1.299541 AGCGGCGACCTCAAAATATG 58.700 50.000 12.98 0.00 0.00 1.78
308 309 2.902705 TAGCGGCGACCTCAAAATAT 57.097 45.000 12.98 0.00 0.00 1.28
309 310 2.902705 ATAGCGGCGACCTCAAAATA 57.097 45.000 12.98 0.00 0.00 1.40
310 311 2.038387 AATAGCGGCGACCTCAAAAT 57.962 45.000 12.98 0.00 0.00 1.82
311 312 1.816074 AAATAGCGGCGACCTCAAAA 58.184 45.000 12.98 0.00 0.00 2.44
312 313 1.466950 CAAAATAGCGGCGACCTCAAA 59.533 47.619 12.98 0.00 0.00 2.69
313 314 1.083489 CAAAATAGCGGCGACCTCAA 58.917 50.000 12.98 0.00 0.00 3.02
314 315 1.366111 GCAAAATAGCGGCGACCTCA 61.366 55.000 12.98 0.00 0.00 3.86
315 316 1.090052 AGCAAAATAGCGGCGACCTC 61.090 55.000 12.98 0.00 40.15 3.85
316 317 1.078426 AGCAAAATAGCGGCGACCT 60.078 52.632 12.98 0.56 40.15 3.85
317 318 1.062525 CAGCAAAATAGCGGCGACC 59.937 57.895 12.98 0.00 40.15 4.79
318 319 1.003851 TACAGCAAAATAGCGGCGAC 58.996 50.000 12.98 1.23 40.15 5.19
319 320 1.286501 CTACAGCAAAATAGCGGCGA 58.713 50.000 12.98 0.00 40.15 5.54
320 321 0.316196 GCTACAGCAAAATAGCGGCG 60.316 55.000 0.51 0.51 41.59 6.46
321 322 3.533913 GCTACAGCAAAATAGCGGC 57.466 52.632 0.00 0.00 41.59 6.53
348 349 4.792068 AGTGAGGTGAGACCAATGAAAAA 58.208 39.130 0.00 0.00 41.95 1.94
349 350 4.437682 AGTGAGGTGAGACCAATGAAAA 57.562 40.909 0.00 0.00 41.95 2.29
350 351 5.560722 TTAGTGAGGTGAGACCAATGAAA 57.439 39.130 0.00 0.00 41.95 2.69
351 352 5.560722 TTTAGTGAGGTGAGACCAATGAA 57.439 39.130 0.00 0.00 41.95 2.57
352 353 5.624509 CGATTTAGTGAGGTGAGACCAATGA 60.625 44.000 0.00 0.00 41.95 2.57
353 354 4.568359 CGATTTAGTGAGGTGAGACCAATG 59.432 45.833 0.00 0.00 41.95 2.82
354 355 4.383118 CCGATTTAGTGAGGTGAGACCAAT 60.383 45.833 0.00 0.00 41.95 3.16
355 356 3.056107 CCGATTTAGTGAGGTGAGACCAA 60.056 47.826 0.00 0.00 41.95 3.67
356 357 2.496070 CCGATTTAGTGAGGTGAGACCA 59.504 50.000 0.00 0.00 41.95 4.02
357 358 2.159085 CCCGATTTAGTGAGGTGAGACC 60.159 54.545 0.00 0.00 38.99 3.85
358 359 2.496470 ACCCGATTTAGTGAGGTGAGAC 59.504 50.000 0.00 0.00 0.00 3.36
359 360 2.816411 ACCCGATTTAGTGAGGTGAGA 58.184 47.619 0.00 0.00 0.00 3.27
360 361 3.195825 AGAACCCGATTTAGTGAGGTGAG 59.804 47.826 0.00 0.00 0.00 3.51
361 362 3.170717 AGAACCCGATTTAGTGAGGTGA 58.829 45.455 0.00 0.00 0.00 4.02
362 363 3.056107 TGAGAACCCGATTTAGTGAGGTG 60.056 47.826 0.00 0.00 0.00 4.00
363 364 3.170717 TGAGAACCCGATTTAGTGAGGT 58.829 45.455 0.00 0.00 0.00 3.85
364 365 3.887621 TGAGAACCCGATTTAGTGAGG 57.112 47.619 0.00 0.00 0.00 3.86
365 366 3.557595 GCATGAGAACCCGATTTAGTGAG 59.442 47.826 0.00 0.00 0.00 3.51
457 461 4.161565 TCACTGGTCTAAATCGCATTAGGT 59.838 41.667 7.06 0.00 34.36 3.08
478 482 6.478512 ACAAAGGCCAAAATAGAAAACTCA 57.521 33.333 5.01 0.00 0.00 3.41
605 609 8.761575 AAATGCAAACTGAACCATACAAATAG 57.238 30.769 0.00 0.00 0.00 1.73
797 801 9.006839 TCATTCATCTATTTAGATTGACCATGC 57.993 33.333 0.00 0.00 40.91 4.06
865 869 4.756084 AGCAGCAATGAACAGTTAACTC 57.244 40.909 4.77 0.00 0.00 3.01
993 997 6.084060 TCCTCACCTGATATCCATCACAATA 58.916 40.000 0.00 0.00 36.22 1.90
1084 1088 2.923035 ACCGTGGTGACTCCCTGG 60.923 66.667 0.00 0.00 36.11 4.45
1135 1139 1.300233 GGCGCCATCCTCGAGTTAG 60.300 63.158 24.80 0.00 0.00 2.34
1184 1188 3.830192 CCAGCATTCGCCCTTGCC 61.830 66.667 0.00 0.00 39.72 4.52
1207 1211 4.017407 TGGACATAGAGACTACCTCACCTT 60.017 45.833 0.00 0.00 44.40 3.50
1213 1217 6.330178 AGTTAGTGGACATAGAGACTACCT 57.670 41.667 0.00 0.00 0.00 3.08
1224 1228 3.009143 GGAAGGTTGGAGTTAGTGGACAT 59.991 47.826 0.00 0.00 0.00 3.06
1240 1244 6.129874 AGCTAACAGAAAAGAAAAGGAAGGT 58.870 36.000 0.00 0.00 0.00 3.50
1323 1327 1.614317 GGTTTGCTGCTCCATACCACT 60.614 52.381 0.00 0.00 36.97 4.00
1349 1353 0.612732 CCCAAGCAGCCTCCAAATCA 60.613 55.000 0.00 0.00 0.00 2.57
1366 1370 0.961019 TGTTTCACTGCTTCATGCCC 59.039 50.000 0.00 0.00 42.00 5.36
1437 1441 6.205464 GCCTGCTGCAATCTTCAAGTATATTA 59.795 38.462 3.02 0.00 40.77 0.98
1546 1550 1.285962 CCCCACAACCTCATGGATCTT 59.714 52.381 0.00 0.00 38.34 2.40
1637 1641 6.630443 GCTCATACAAAATTAGCGACATCAAG 59.370 38.462 0.00 0.00 0.00 3.02
1657 1661 5.089434 TGATGATGGTCACCTATAGCTCAT 58.911 41.667 0.00 0.00 0.00 2.90
1661 1665 5.157940 ACATGATGATGGTCACCTATAGC 57.842 43.478 0.00 0.00 33.39 2.97
1751 1755 9.868277 AAATTGTTATCTGACAAAACAGTGAAA 57.132 25.926 0.00 0.00 42.29 2.69
1758 1762 6.398517 CGGCGAAAATTGTTATCTGACAAAAC 60.399 38.462 0.00 0.00 42.29 2.43
1832 1836 1.003718 GGTTGCGCTCCTTACCTGT 60.004 57.895 9.73 0.00 0.00 4.00
1845 1849 0.179156 CATGATGCACGAAGGGTTGC 60.179 55.000 0.00 0.00 0.00 4.17
1898 1902 1.776034 GATCAACCATTCGCTCGCCC 61.776 60.000 0.00 0.00 0.00 6.13
1901 1905 1.926561 TCAGATCAACCATTCGCTCG 58.073 50.000 0.00 0.00 0.00 5.03
1982 1986 1.227943 GGTGGCTGTCAGAAGCACA 60.228 57.895 3.32 0.00 45.43 4.57
1983 1987 1.227943 TGGTGGCTGTCAGAAGCAC 60.228 57.895 3.32 0.00 45.43 4.40
2175 2179 4.915704 AGTGTGACAACAAAACCATTACG 58.084 39.130 0.00 0.00 38.27 3.18
2800 2820 3.108847 TGGTTTTTCCAAAGGTGGTCT 57.891 42.857 0.00 0.00 46.11 3.85
3013 3035 5.656480 GTGGAACAAAAAGCTGGACTAAAA 58.344 37.500 0.00 0.00 44.16 1.52
3207 3235 4.974645 ATACCAGTCCTGAAGAACACAA 57.025 40.909 0.00 0.00 0.00 3.33
3454 3482 4.112634 TCTGGGGCAAAAATGTCTTACT 57.887 40.909 0.00 0.00 0.00 2.24
3535 3564 0.832135 GGTGATCCTCTCGGGCCATA 60.832 60.000 4.39 0.00 34.39 2.74
3646 3675 1.187087 ACCTAAAGGACTCCTCAGCG 58.813 55.000 2.23 0.00 38.94 5.18


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

AutoCloner maintained by Alex Coulton.