Multiple sequence alignment - TraesCS3B01G268900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G268900 chr3B 100.000 1747 0 0 785 2531 432847251 432845505 0.000000e+00 3227
1 TraesCS3B01G268900 chr3B 100.000 405 0 0 1 405 432848035 432847631 0.000000e+00 749
2 TraesCS3B01G268900 chr3A 95.599 1727 49 17 813 2531 451665969 451667676 0.000000e+00 2743
3 TraesCS3B01G268900 chr3D 97.559 1065 22 4 813 1873 333503403 333504467 0.000000e+00 1820
4 TraesCS3B01G268900 chr3D 88.906 640 37 19 1911 2531 333504758 333505382 0.000000e+00 758
5 TraesCS3B01G268900 chr3D 82.020 406 49 11 1 404 495496207 495496590 8.730000e-85 324
6 TraesCS3B01G268900 chr2D 87.438 406 46 5 3 405 192188315 192187912 1.770000e-126 462
7 TraesCS3B01G268900 chr2D 83.646 373 34 11 34 405 378089130 378089476 2.430000e-85 326
8 TraesCS3B01G268900 chr2D 78.803 401 53 16 1 390 536490988 536491367 9.050000e-60 241
9 TraesCS3B01G268900 chr5D 89.008 373 35 1 1 373 337685540 337685174 8.250000e-125 457
10 TraesCS3B01G268900 chr4D 86.700 406 46 4 1 405 111915686 111916084 6.420000e-121 444
11 TraesCS3B01G268900 chr5A 86.207 406 45 5 1 405 459345159 459345554 1.800000e-116 429
12 TraesCS3B01G268900 chr5A 84.066 364 40 10 50 405 548647228 548646875 4.030000e-88 335
13 TraesCS3B01G268900 chr1D 85.870 368 39 3 38 405 276243055 276243409 1.840000e-101 379
14 TraesCS3B01G268900 chr7D 82.512 406 43 10 1 405 572267573 572267951 5.220000e-87 331
15 TraesCS3B01G268900 chr6D 83.883 273 22 17 1 268 157812264 157812009 9.050000e-60 241
16 TraesCS3B01G268900 chr1B 77.750 400 59 16 2 379 249631050 249631441 4.240000e-53 219
17 TraesCS3B01G268900 chr1A 81.857 237 35 5 1 234 492130069 492130300 2.570000e-45 193


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 TraesCS3B01G268900 chr3B 432845505 432848035 2530 True 1988 3227 100.0000 1 2531 2 chr3B.!!$R1 2530
1 TraesCS3B01G268900 chr3A 451665969 451667676 1707 False 2743 2743 95.5990 813 2531 1 chr3A.!!$F1 1718
2 TraesCS3B01G268900 chr3D 333503403 333505382 1979 False 1289 1820 93.2325 813 2531 2 chr3D.!!$F2 1718

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
211 212 0.02877 TCTTTTGCACGCCGAACTTG 59.971 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2434 1.039233 CATTGCTCCATGTGGGGGAC 61.039 60.0 0.29 0.0 41.01 4.46 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
17 18 2.179018 CTGAACCAAATGCCGCCG 59.821 61.111 0.00 0.00 0.00 6.46
18 19 2.281831 TGAACCAAATGCCGCCGA 60.282 55.556 0.00 0.00 0.00 5.54
19 20 2.178273 GAACCAAATGCCGCCGAC 59.822 61.111 0.00 0.00 0.00 4.79
20 21 3.336715 GAACCAAATGCCGCCGACC 62.337 63.158 0.00 0.00 0.00 4.79
71 72 4.473520 CCACCAAGCCCGAGCGAT 62.474 66.667 0.00 0.00 46.67 4.58
72 73 3.197790 CACCAAGCCCGAGCGATG 61.198 66.667 0.00 0.00 46.67 3.84
73 74 3.390521 ACCAAGCCCGAGCGATGA 61.391 61.111 0.00 0.00 46.67 2.92
74 75 2.892425 CCAAGCCCGAGCGATGAC 60.892 66.667 0.00 0.00 46.67 3.06
75 76 3.257561 CAAGCCCGAGCGATGACG 61.258 66.667 0.00 0.00 46.67 4.35
85 86 2.648102 CGATGACGCCTCGACGAC 60.648 66.667 2.12 0.00 38.38 4.34
86 87 2.648102 GATGACGCCTCGACGACG 60.648 66.667 0.00 0.00 41.26 5.12
87 88 4.831307 ATGACGCCTCGACGACGC 62.831 66.667 8.55 8.55 39.58 5.19
97 98 4.357947 GACGACGCCCAGCACAGA 62.358 66.667 0.00 0.00 0.00 3.41
98 99 3.858868 GACGACGCCCAGCACAGAA 62.859 63.158 0.00 0.00 0.00 3.02
99 100 3.114616 CGACGCCCAGCACAGAAG 61.115 66.667 0.00 0.00 0.00 2.85
100 101 3.426568 GACGCCCAGCACAGAAGC 61.427 66.667 0.00 0.00 0.00 3.86
104 105 3.052082 CCCAGCACAGAAGCCGTG 61.052 66.667 0.00 0.00 37.43 4.94
109 110 2.434884 CACAGAAGCCGTGCCGAT 60.435 61.111 0.00 0.00 0.00 4.18
110 111 2.434884 ACAGAAGCCGTGCCGATG 60.435 61.111 0.00 0.00 0.00 3.84
111 112 3.869272 CAGAAGCCGTGCCGATGC 61.869 66.667 0.00 0.00 38.26 3.91
123 124 4.473520 CGATGCCGACCAGCCCTT 62.474 66.667 0.00 0.00 38.22 3.95
124 125 2.825836 GATGCCGACCAGCCCTTG 60.826 66.667 0.00 0.00 0.00 3.61
134 135 3.946201 AGCCCTTGCACGCTGACT 61.946 61.111 1.46 0.00 41.13 3.41
135 136 3.426568 GCCCTTGCACGCTGACTC 61.427 66.667 0.00 0.00 37.47 3.36
136 137 2.743928 CCCTTGCACGCTGACTCC 60.744 66.667 0.00 0.00 0.00 3.85
137 138 2.031012 CCTTGCACGCTGACTCCA 59.969 61.111 0.00 0.00 0.00 3.86
138 139 2.320587 CCTTGCACGCTGACTCCAC 61.321 63.158 0.00 0.00 0.00 4.02
139 140 2.280797 TTGCACGCTGACTCCACC 60.281 61.111 0.00 0.00 0.00 4.61
140 141 4.662961 TGCACGCTGACTCCACCG 62.663 66.667 0.00 0.00 0.00 4.94
141 142 4.357947 GCACGCTGACTCCACCGA 62.358 66.667 0.00 0.00 0.00 4.69
142 143 2.430921 CACGCTGACTCCACCGAC 60.431 66.667 0.00 0.00 0.00 4.79
143 144 4.039357 ACGCTGACTCCACCGACG 62.039 66.667 0.00 0.00 0.00 5.12
146 147 4.778415 CTGACTCCACCGACGCCG 62.778 72.222 0.00 0.00 0.00 6.46
169 170 2.660552 CGACACCGCCGTTTGAGT 60.661 61.111 0.00 0.00 0.00 3.41
170 171 2.241880 CGACACCGCCGTTTGAGTT 61.242 57.895 0.00 0.00 0.00 3.01
171 172 1.768112 CGACACCGCCGTTTGAGTTT 61.768 55.000 0.00 0.00 0.00 2.66
172 173 0.316689 GACACCGCCGTTTGAGTTTG 60.317 55.000 0.00 0.00 0.00 2.93
173 174 0.745128 ACACCGCCGTTTGAGTTTGA 60.745 50.000 0.00 0.00 0.00 2.69
174 175 0.591170 CACCGCCGTTTGAGTTTGAT 59.409 50.000 0.00 0.00 0.00 2.57
175 176 0.591170 ACCGCCGTTTGAGTTTGATG 59.409 50.000 0.00 0.00 0.00 3.07
176 177 0.729140 CCGCCGTTTGAGTTTGATGC 60.729 55.000 0.00 0.00 0.00 3.91
177 178 0.040514 CGCCGTTTGAGTTTGATGCA 60.041 50.000 0.00 0.00 0.00 3.96
178 179 1.599171 CGCCGTTTGAGTTTGATGCAA 60.599 47.619 0.00 0.00 0.00 4.08
179 180 1.786579 GCCGTTTGAGTTTGATGCAAC 59.213 47.619 0.00 0.00 0.00 4.17
180 181 2.043411 CCGTTTGAGTTTGATGCAACG 58.957 47.619 0.00 0.00 0.00 4.10
181 182 1.447938 CGTTTGAGTTTGATGCAACGC 59.552 47.619 0.00 0.00 0.00 4.84
182 183 1.447938 GTTTGAGTTTGATGCAACGCG 59.552 47.619 3.53 3.53 0.00 6.01
183 184 0.660488 TTGAGTTTGATGCAACGCGT 59.340 45.000 5.58 5.58 0.00 6.01
184 185 0.660488 TGAGTTTGATGCAACGCGTT 59.340 45.000 20.79 20.79 0.00 4.84
185 186 1.318251 GAGTTTGATGCAACGCGTTC 58.682 50.000 23.92 17.01 0.00 3.95
186 187 0.384230 AGTTTGATGCAACGCGTTCG 60.384 50.000 23.92 18.16 42.43 3.95
198 199 1.658968 CGCGTTCGTCCTTTCTTTTG 58.341 50.000 0.00 0.00 0.00 2.44
199 200 1.395670 GCGTTCGTCCTTTCTTTTGC 58.604 50.000 0.00 0.00 0.00 3.68
200 201 1.268335 GCGTTCGTCCTTTCTTTTGCA 60.268 47.619 0.00 0.00 0.00 4.08
201 202 2.372350 CGTTCGTCCTTTCTTTTGCAC 58.628 47.619 0.00 0.00 0.00 4.57
202 203 2.372350 GTTCGTCCTTTCTTTTGCACG 58.628 47.619 0.00 0.00 0.00 5.34
203 204 0.306533 TCGTCCTTTCTTTTGCACGC 59.693 50.000 0.00 0.00 0.00 5.34
204 205 0.660300 CGTCCTTTCTTTTGCACGCC 60.660 55.000 0.00 0.00 0.00 5.68
205 206 0.660300 GTCCTTTCTTTTGCACGCCG 60.660 55.000 0.00 0.00 0.00 6.46
206 207 0.816018 TCCTTTCTTTTGCACGCCGA 60.816 50.000 0.00 0.00 0.00 5.54
207 208 0.030101 CCTTTCTTTTGCACGCCGAA 59.970 50.000 0.00 0.00 0.00 4.30
208 209 1.120437 CTTTCTTTTGCACGCCGAAC 58.880 50.000 0.00 0.00 0.00 3.95
209 210 0.736053 TTTCTTTTGCACGCCGAACT 59.264 45.000 0.00 0.00 0.00 3.01
210 211 0.736053 TTCTTTTGCACGCCGAACTT 59.264 45.000 0.00 0.00 0.00 2.66
211 212 0.028770 TCTTTTGCACGCCGAACTTG 59.971 50.000 0.00 0.00 0.00 3.16
212 213 0.248458 CTTTTGCACGCCGAACTTGT 60.248 50.000 0.00 0.00 0.00 3.16
213 214 0.171455 TTTTGCACGCCGAACTTGTT 59.829 45.000 0.00 0.00 0.00 2.83
214 215 1.015109 TTTGCACGCCGAACTTGTTA 58.985 45.000 0.00 0.00 0.00 2.41
215 216 1.231221 TTGCACGCCGAACTTGTTAT 58.769 45.000 0.00 0.00 0.00 1.89
216 217 1.231221 TGCACGCCGAACTTGTTATT 58.769 45.000 0.00 0.00 0.00 1.40
217 218 1.604755 TGCACGCCGAACTTGTTATTT 59.395 42.857 0.00 0.00 0.00 1.40
218 219 1.976045 GCACGCCGAACTTGTTATTTG 59.024 47.619 0.00 0.00 0.00 2.32
219 220 2.350007 GCACGCCGAACTTGTTATTTGA 60.350 45.455 0.00 0.00 0.00 2.69
220 221 3.669557 GCACGCCGAACTTGTTATTTGAT 60.670 43.478 0.00 0.00 0.00 2.57
221 222 4.088648 CACGCCGAACTTGTTATTTGATC 58.911 43.478 0.00 0.00 0.00 2.92
222 223 3.181524 ACGCCGAACTTGTTATTTGATCG 60.182 43.478 0.00 0.00 0.00 3.69
223 224 3.098636 GCCGAACTTGTTATTTGATCGC 58.901 45.455 0.00 0.00 0.00 4.58
224 225 3.680789 CCGAACTTGTTATTTGATCGCC 58.319 45.455 0.00 0.00 0.00 5.54
225 226 3.342269 CGAACTTGTTATTTGATCGCCG 58.658 45.455 0.00 0.00 0.00 6.46
226 227 3.061563 CGAACTTGTTATTTGATCGCCGA 59.938 43.478 0.00 0.00 0.00 5.54
227 228 4.434989 CGAACTTGTTATTTGATCGCCGAA 60.435 41.667 0.00 0.00 0.00 4.30
228 229 5.560966 AACTTGTTATTTGATCGCCGAAT 57.439 34.783 0.00 0.00 33.54 3.34
229 230 5.156804 ACTTGTTATTTGATCGCCGAATC 57.843 39.130 0.00 0.00 31.48 2.52
230 231 3.852471 TGTTATTTGATCGCCGAATCG 57.148 42.857 0.00 0.00 31.48 3.34
231 232 3.191669 TGTTATTTGATCGCCGAATCGT 58.808 40.909 0.82 0.00 31.48 3.73
232 233 3.000825 TGTTATTTGATCGCCGAATCGTG 59.999 43.478 0.82 0.00 31.48 4.35
233 234 0.937304 ATTTGATCGCCGAATCGTGG 59.063 50.000 0.82 0.00 0.00 4.94
234 235 0.390603 TTTGATCGCCGAATCGTGGT 60.391 50.000 0.82 0.00 0.00 4.16
235 236 0.456628 TTGATCGCCGAATCGTGGTA 59.543 50.000 0.82 0.00 0.00 3.25
236 237 0.456628 TGATCGCCGAATCGTGGTAA 59.543 50.000 0.82 0.00 0.00 2.85
237 238 0.850856 GATCGCCGAATCGTGGTAAC 59.149 55.000 0.82 0.00 0.00 2.50
246 247 3.380671 CGTGGTAACGTGATCGCC 58.619 61.111 0.00 0.00 44.93 5.54
247 248 2.502123 CGTGGTAACGTGATCGCCG 61.502 63.158 0.00 1.67 44.93 6.46
248 249 1.153978 GTGGTAACGTGATCGCCGA 60.154 57.895 11.07 0.00 41.18 5.54
249 250 0.733566 GTGGTAACGTGATCGCCGAA 60.734 55.000 11.07 0.00 41.18 4.30
250 251 0.733566 TGGTAACGTGATCGCCGAAC 60.734 55.000 11.07 8.35 41.18 3.95
251 252 0.457337 GGTAACGTGATCGCCGAACT 60.457 55.000 11.07 0.00 41.18 3.01
252 253 0.638746 GTAACGTGATCGCCGAACTG 59.361 55.000 11.07 0.00 41.18 3.16
253 254 0.241749 TAACGTGATCGCCGAACTGT 59.758 50.000 11.07 0.00 41.18 3.55
254 255 1.282248 AACGTGATCGCCGAACTGTG 61.282 55.000 11.07 0.00 41.18 3.66
255 256 1.443702 CGTGATCGCCGAACTGTGA 60.444 57.895 0.00 0.00 0.00 3.58
256 257 1.674611 CGTGATCGCCGAACTGTGAC 61.675 60.000 0.00 0.00 0.00 3.67
257 258 1.443702 TGATCGCCGAACTGTGACG 60.444 57.895 0.00 1.63 0.00 4.35
258 259 2.789203 GATCGCCGAACTGTGACGC 61.789 63.158 0.00 0.00 0.00 5.19
259 260 3.282745 ATCGCCGAACTGTGACGCT 62.283 57.895 0.00 0.00 0.00 5.07
260 261 3.767230 CGCCGAACTGTGACGCTG 61.767 66.667 2.86 0.00 0.00 5.18
261 262 2.355837 GCCGAACTGTGACGCTGA 60.356 61.111 0.00 0.00 0.00 4.26
262 263 1.738099 GCCGAACTGTGACGCTGAT 60.738 57.895 0.00 0.00 0.00 2.90
263 264 1.687494 GCCGAACTGTGACGCTGATC 61.687 60.000 0.00 0.00 0.00 2.92
264 265 1.406219 CCGAACTGTGACGCTGATCG 61.406 60.000 15.43 15.43 45.38 3.69
265 266 1.704582 GAACTGTGACGCTGATCGC 59.295 57.895 0.00 0.23 43.23 4.58
266 267 1.687494 GAACTGTGACGCTGATCGCC 61.687 60.000 0.00 0.00 43.23 5.54
267 268 3.250323 CTGTGACGCTGATCGCCG 61.250 66.667 3.61 3.61 43.23 6.46
268 269 3.971453 CTGTGACGCTGATCGCCGT 62.971 63.158 9.80 9.80 43.23 5.68
269 270 2.101575 GTGACGCTGATCGCCGTA 59.898 61.111 9.97 0.00 43.23 4.02
270 271 2.101575 TGACGCTGATCGCCGTAC 59.898 61.111 9.97 5.76 43.23 3.67
271 272 2.404186 TGACGCTGATCGCCGTACT 61.404 57.895 9.97 0.00 43.23 2.73
272 273 1.939785 GACGCTGATCGCCGTACTG 60.940 63.158 9.97 0.00 43.23 2.74
273 274 2.655364 CGCTGATCGCCGTACTGG 60.655 66.667 4.37 0.00 42.50 4.00
274 275 2.494918 GCTGATCGCCGTACTGGT 59.505 61.111 5.79 0.00 41.21 4.00
298 299 1.404843 TTTTTGGGAGTGGGAAACGG 58.595 50.000 0.00 0.00 0.00 4.44
299 300 0.551879 TTTTGGGAGTGGGAAACGGA 59.448 50.000 0.00 0.00 0.00 4.69
300 301 0.179012 TTTGGGAGTGGGAAACGGAC 60.179 55.000 0.00 0.00 0.00 4.79
301 302 2.059345 TTGGGAGTGGGAAACGGACC 62.059 60.000 0.00 0.00 0.00 4.46
302 303 2.522367 GGGAGTGGGAAACGGACCA 61.522 63.158 0.00 0.00 0.00 4.02
303 304 1.452801 GGAGTGGGAAACGGACCAA 59.547 57.895 0.00 0.00 38.73 3.67
304 305 0.605589 GGAGTGGGAAACGGACCAAG 60.606 60.000 0.00 0.00 38.73 3.61
305 306 0.108019 GAGTGGGAAACGGACCAAGT 59.892 55.000 0.00 0.00 38.73 3.16
306 307 0.549469 AGTGGGAAACGGACCAAGTT 59.451 50.000 0.00 0.00 38.73 2.66
307 308 1.064240 AGTGGGAAACGGACCAAGTTT 60.064 47.619 0.00 0.00 43.60 2.66
308 309 1.066454 GTGGGAAACGGACCAAGTTTG 59.934 52.381 2.59 0.00 41.32 2.93
309 310 1.064611 TGGGAAACGGACCAAGTTTGA 60.065 47.619 2.59 0.00 41.32 2.69
310 311 2.025898 GGGAAACGGACCAAGTTTGAA 58.974 47.619 2.59 0.00 41.32 2.69
311 312 2.626266 GGGAAACGGACCAAGTTTGAAT 59.374 45.455 2.59 0.00 41.32 2.57
312 313 3.069016 GGGAAACGGACCAAGTTTGAATT 59.931 43.478 2.59 0.00 41.32 2.17
313 314 4.442332 GGGAAACGGACCAAGTTTGAATTT 60.442 41.667 2.59 0.00 41.32 1.82
314 315 4.506288 GGAAACGGACCAAGTTTGAATTTG 59.494 41.667 2.59 0.00 41.32 2.32
315 316 3.092334 ACGGACCAAGTTTGAATTTGC 57.908 42.857 0.00 0.00 0.00 3.68
316 317 2.050691 CGGACCAAGTTTGAATTTGCG 58.949 47.619 0.00 0.00 0.00 4.85
317 318 2.287308 CGGACCAAGTTTGAATTTGCGA 60.287 45.455 0.00 0.00 0.00 5.10
318 319 3.049912 GGACCAAGTTTGAATTTGCGAC 58.950 45.455 0.00 0.00 0.00 5.19
319 320 2.719046 GACCAAGTTTGAATTTGCGACG 59.281 45.455 0.00 0.00 0.00 5.12
320 321 2.098443 ACCAAGTTTGAATTTGCGACGT 59.902 40.909 0.00 0.00 0.00 4.34
321 322 3.112580 CCAAGTTTGAATTTGCGACGTT 58.887 40.909 0.00 0.00 0.00 3.99
322 323 3.549873 CCAAGTTTGAATTTGCGACGTTT 59.450 39.130 0.00 0.00 0.00 3.60
323 324 4.032331 CCAAGTTTGAATTTGCGACGTTTT 59.968 37.500 0.00 0.00 0.00 2.43
324 325 4.753516 AGTTTGAATTTGCGACGTTTTG 57.246 36.364 0.00 0.00 0.00 2.44
325 326 3.549873 AGTTTGAATTTGCGACGTTTTGG 59.450 39.130 0.00 0.00 0.00 3.28
326 327 3.422417 TTGAATTTGCGACGTTTTGGA 57.578 38.095 0.00 0.00 0.00 3.53
327 328 2.993545 TGAATTTGCGACGTTTTGGAG 58.006 42.857 0.00 0.00 0.00 3.86
328 329 2.287308 TGAATTTGCGACGTTTTGGAGG 60.287 45.455 0.00 0.00 0.00 4.30
329 330 0.039527 ATTTGCGACGTTTTGGAGGC 60.040 50.000 0.00 0.00 0.00 4.70
330 331 2.381665 TTTGCGACGTTTTGGAGGCG 62.382 55.000 0.00 0.00 0.00 5.52
331 332 4.084888 GCGACGTTTTGGAGGCGG 62.085 66.667 0.00 0.00 0.00 6.13
332 333 4.084888 CGACGTTTTGGAGGCGGC 62.085 66.667 0.00 0.00 0.00 6.53
333 334 2.975799 GACGTTTTGGAGGCGGCA 60.976 61.111 13.08 0.00 33.26 5.69
334 335 3.249973 GACGTTTTGGAGGCGGCAC 62.250 63.158 13.08 4.32 33.26 5.01
335 336 4.038080 CGTTTTGGAGGCGGCACC 62.038 66.667 18.69 18.69 39.61 5.01
350 351 3.252284 ACCTGAGGGTGTGGCTGG 61.252 66.667 2.38 0.00 45.43 4.85
351 352 4.039092 CCTGAGGGTGTGGCTGGG 62.039 72.222 0.00 0.00 0.00 4.45
352 353 2.930019 CTGAGGGTGTGGCTGGGA 60.930 66.667 0.00 0.00 0.00 4.37
353 354 3.249189 TGAGGGTGTGGCTGGGAC 61.249 66.667 0.00 0.00 0.00 4.46
354 355 4.394712 GAGGGTGTGGCTGGGACG 62.395 72.222 0.00 0.00 0.00 4.79
356 357 3.315949 GGGTGTGGCTGGGACGTA 61.316 66.667 0.00 0.00 0.00 3.57
357 358 2.264794 GGTGTGGCTGGGACGTAG 59.735 66.667 0.00 0.00 0.00 3.51
358 359 2.280552 GGTGTGGCTGGGACGTAGA 61.281 63.158 0.00 0.00 0.00 2.59
359 360 1.614241 GGTGTGGCTGGGACGTAGAT 61.614 60.000 0.00 0.00 0.00 1.98
360 361 0.179108 GTGTGGCTGGGACGTAGATC 60.179 60.000 0.00 0.00 0.00 2.75
361 362 1.065928 GTGGCTGGGACGTAGATCG 59.934 63.158 0.00 0.00 46.00 3.69
362 363 2.027751 GGCTGGGACGTAGATCGC 59.972 66.667 0.00 0.00 44.19 4.58
363 364 2.491022 GGCTGGGACGTAGATCGCT 61.491 63.158 0.00 0.00 44.19 4.93
364 365 1.008309 GCTGGGACGTAGATCGCTC 60.008 63.158 0.00 0.00 44.19 5.03
365 366 1.655329 CTGGGACGTAGATCGCTCC 59.345 63.158 0.00 0.00 44.19 4.70
366 367 3.040844 GGGACGTAGATCGCTCCC 58.959 66.667 0.00 10.28 45.10 4.30
367 368 3.837578 GGACGTAGATCGCTCCCA 58.162 61.111 0.00 0.00 44.19 4.37
368 369 1.655329 GGACGTAGATCGCTCCCAG 59.345 63.158 0.00 0.00 44.19 4.45
369 370 1.655329 GACGTAGATCGCTCCCAGG 59.345 63.158 0.00 0.00 44.19 4.45
370 371 1.797211 GACGTAGATCGCTCCCAGGG 61.797 65.000 0.00 0.00 44.19 4.45
371 372 2.737830 GTAGATCGCTCCCAGGGC 59.262 66.667 0.00 0.00 0.00 5.19
372 373 2.524394 TAGATCGCTCCCAGGGCC 60.524 66.667 0.00 0.00 0.00 5.80
373 374 3.088090 TAGATCGCTCCCAGGGCCT 62.088 63.158 0.00 0.00 0.00 5.19
374 375 1.726192 TAGATCGCTCCCAGGGCCTA 61.726 60.000 5.28 0.00 0.00 3.93
375 376 2.040884 ATCGCTCCCAGGGCCTAA 60.041 61.111 5.28 0.00 0.00 2.69
376 377 1.692749 ATCGCTCCCAGGGCCTAAA 60.693 57.895 5.28 0.00 0.00 1.85
377 378 1.279025 ATCGCTCCCAGGGCCTAAAA 61.279 55.000 5.28 0.00 0.00 1.52
378 379 1.001393 CGCTCCCAGGGCCTAAAAA 60.001 57.895 5.28 0.00 0.00 1.94
379 380 0.395724 CGCTCCCAGGGCCTAAAAAT 60.396 55.000 5.28 0.00 0.00 1.82
380 381 1.403814 GCTCCCAGGGCCTAAAAATC 58.596 55.000 5.28 0.00 0.00 2.17
381 382 1.680338 CTCCCAGGGCCTAAAAATCG 58.320 55.000 5.28 0.00 0.00 3.34
382 383 0.395173 TCCCAGGGCCTAAAAATCGC 60.395 55.000 5.28 0.00 0.00 4.58
383 384 1.391933 CCCAGGGCCTAAAAATCGCC 61.392 60.000 5.28 0.00 42.23 5.54
384 385 1.724582 CCAGGGCCTAAAAATCGCCG 61.725 60.000 5.28 0.00 43.99 6.46
385 386 1.453197 AGGGCCTAAAAATCGCCGG 60.453 57.895 2.82 0.00 43.99 6.13
386 387 1.452470 GGGCCTAAAAATCGCCGGA 60.452 57.895 5.05 0.00 43.99 5.14
387 388 1.721664 GGGCCTAAAAATCGCCGGAC 61.722 60.000 5.05 0.00 43.99 4.79
388 389 1.350665 GCCTAAAAATCGCCGGACG 59.649 57.895 5.05 9.12 45.62 4.79
399 400 4.137872 CCGGACGAGCGCCCTAAA 62.138 66.667 2.29 0.00 0.00 1.85
400 401 2.582498 CGGACGAGCGCCCTAAAG 60.582 66.667 2.29 0.00 0.00 1.85
401 402 2.890371 GGACGAGCGCCCTAAAGA 59.110 61.111 2.29 0.00 0.00 2.52
402 403 1.227002 GGACGAGCGCCCTAAAGAG 60.227 63.158 2.29 0.00 0.00 2.85
403 404 1.878975 GACGAGCGCCCTAAAGAGC 60.879 63.158 2.29 0.00 0.00 4.09
801 802 4.115199 GGGGGCGCAAGTGGAGAT 62.115 66.667 10.83 0.00 41.68 2.75
802 803 2.825836 GGGGCGCAAGTGGAGATG 60.826 66.667 10.83 0.00 41.68 2.90
803 804 3.512516 GGGCGCAAGTGGAGATGC 61.513 66.667 10.83 0.00 39.17 3.91
804 805 2.437359 GGCGCAAGTGGAGATGCT 60.437 61.111 10.83 0.00 40.39 3.79
805 806 2.467826 GGCGCAAGTGGAGATGCTC 61.468 63.158 10.83 0.00 40.39 4.26
806 807 1.449246 GCGCAAGTGGAGATGCTCT 60.449 57.895 0.30 0.00 40.39 4.09
807 808 1.023513 GCGCAAGTGGAGATGCTCTT 61.024 55.000 0.30 0.00 40.39 2.85
808 809 1.740380 GCGCAAGTGGAGATGCTCTTA 60.740 52.381 0.30 0.00 40.39 2.10
809 810 2.200067 CGCAAGTGGAGATGCTCTTAG 58.800 52.381 0.00 0.00 40.39 2.18
810 811 2.417924 CGCAAGTGGAGATGCTCTTAGT 60.418 50.000 0.00 0.00 40.39 2.24
811 812 2.935201 GCAAGTGGAGATGCTCTTAGTG 59.065 50.000 0.00 0.00 39.46 2.74
907 909 5.884232 TGATTATATAGATAGCACCGGTCGT 59.116 40.000 2.59 0.00 0.00 4.34
979 981 3.358076 CTCCCGCTCACTCCCGAAC 62.358 68.421 0.00 0.00 0.00 3.95
989 991 2.602267 TCCCGAACCGAAGCCTCA 60.602 61.111 0.00 0.00 0.00 3.86
1071 1073 4.731853 TCACCATCCCCCTCCGCA 62.732 66.667 0.00 0.00 0.00 5.69
1407 1409 2.214216 ACTGACCAACCTGGCGCTA 61.214 57.895 7.64 0.00 42.67 4.26
1434 1436 1.694696 GCCAAGGATCTTATCGAGGGT 59.305 52.381 0.00 0.00 0.00 4.34
1518 1520 4.699522 GGAGTCGGCGCCAAGGTT 62.700 66.667 28.98 6.42 34.50 3.50
1568 1572 4.711846 GGCTCCTTTTTCTCCCATTACATT 59.288 41.667 0.00 0.00 0.00 2.71
1616 1620 2.238646 TCCTCTTGTAATTGCCGTGGAT 59.761 45.455 0.00 0.00 0.00 3.41
1677 1687 5.591643 AGTTCATGTTCGTGTGTTGTATC 57.408 39.130 0.00 0.00 0.00 2.24
1690 1700 7.490079 TCGTGTGTTGTATCCAATCTTGTATAC 59.510 37.037 0.00 0.00 32.54 1.47
1695 1705 9.826574 TGTTGTATCCAATCTTGTATACTTACC 57.173 33.333 4.17 0.00 32.95 2.85
1708 1718 6.818233 TGTATACTTACCGGATGTTGCATTA 58.182 36.000 9.46 0.00 0.00 1.90
1791 1802 4.099266 TGTGCATTGCCAGTTTTAGAGTTT 59.901 37.500 6.12 0.00 0.00 2.66
1829 1840 3.248602 GCGGCATATCTCTCGTTTTGATT 59.751 43.478 0.00 0.00 0.00 2.57
1924 2206 2.966516 GGATTGGAAGTATCTCCCGAGT 59.033 50.000 0.00 0.00 34.22 4.18
2139 2434 6.262273 ACAGTAATGTGAAAGTGTACCCTTTG 59.738 38.462 8.13 0.00 34.87 2.77
2303 2601 4.853924 AACCTTGATTTGCCTACTGTTG 57.146 40.909 0.00 0.00 0.00 3.33
2308 2606 3.826524 TGATTTGCCTACTGTTGTGGAA 58.173 40.909 0.00 0.00 0.00 3.53
2448 2749 4.160439 TGATGTCGCTAGACCTTCTGAATT 59.840 41.667 0.00 0.00 46.51 2.17
2484 2785 9.513727 AATGCCAAACAAATGAACAATTTAAAC 57.486 25.926 0.00 0.00 36.28 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.179018 CGGCGGCATTTGGTTCAG 59.821 61.111 10.53 0.00 0.00 3.02
1 2 2.281831 TCGGCGGCATTTGGTTCA 60.282 55.556 10.53 0.00 0.00 3.18
2 3 2.178273 GTCGGCGGCATTTGGTTC 59.822 61.111 6.63 0.00 0.00 3.62
3 4 3.370231 GGTCGGCGGCATTTGGTT 61.370 61.111 15.59 0.00 0.00 3.67
54 55 4.473520 ATCGCTCGGGCTTGGTGG 62.474 66.667 5.36 0.00 36.09 4.61
55 56 3.197790 CATCGCTCGGGCTTGGTG 61.198 66.667 5.36 0.00 36.09 4.17
56 57 3.390521 TCATCGCTCGGGCTTGGT 61.391 61.111 5.36 0.00 36.09 3.67
57 58 2.892425 GTCATCGCTCGGGCTTGG 60.892 66.667 5.36 0.00 36.09 3.61
58 59 3.257561 CGTCATCGCTCGGGCTTG 61.258 66.667 5.36 2.75 36.09 4.01
68 69 2.648102 GTCGTCGAGGCGTCATCG 60.648 66.667 7.26 10.06 41.50 3.84
69 70 2.648102 CGTCGTCGAGGCGTCATC 60.648 66.667 7.26 0.00 44.05 2.92
80 81 3.858868 TTCTGTGCTGGGCGTCGTC 62.859 63.158 0.00 0.00 0.00 4.20
81 82 3.865929 CTTCTGTGCTGGGCGTCGT 62.866 63.158 0.00 0.00 0.00 4.34
82 83 3.114616 CTTCTGTGCTGGGCGTCG 61.115 66.667 0.00 0.00 0.00 5.12
83 84 3.426568 GCTTCTGTGCTGGGCGTC 61.427 66.667 0.00 0.00 0.00 5.19
87 88 3.052082 CACGGCTTCTGTGCTGGG 61.052 66.667 0.00 0.00 43.17 4.45
106 107 4.473520 AAGGGCTGGTCGGCATCG 62.474 66.667 4.06 0.00 40.61 3.84
107 108 2.825836 CAAGGGCTGGTCGGCATC 60.826 66.667 4.06 0.00 40.61 3.91
117 118 3.890936 GAGTCAGCGTGCAAGGGCT 62.891 63.158 0.79 1.79 41.91 5.19
118 119 3.426568 GAGTCAGCGTGCAAGGGC 61.427 66.667 0.79 0.00 41.68 5.19
119 120 2.743928 GGAGTCAGCGTGCAAGGG 60.744 66.667 0.79 0.00 0.00 3.95
120 121 2.031012 TGGAGTCAGCGTGCAAGG 59.969 61.111 0.79 0.00 0.00 3.61
121 122 2.320587 GGTGGAGTCAGCGTGCAAG 61.321 63.158 0.00 0.00 0.00 4.01
122 123 2.280797 GGTGGAGTCAGCGTGCAA 60.281 61.111 0.00 0.00 0.00 4.08
129 130 4.778415 CGGCGTCGGTGGAGTCAG 62.778 72.222 0.00 0.00 0.00 3.51
152 153 1.768112 AAACTCAAACGGCGGTGTCG 61.768 55.000 13.24 7.48 36.42 4.35
153 154 0.316689 CAAACTCAAACGGCGGTGTC 60.317 55.000 13.24 0.00 0.00 3.67
154 155 0.745128 TCAAACTCAAACGGCGGTGT 60.745 50.000 13.24 0.00 0.00 4.16
155 156 0.591170 ATCAAACTCAAACGGCGGTG 59.409 50.000 13.24 9.36 0.00 4.94
156 157 0.591170 CATCAAACTCAAACGGCGGT 59.409 50.000 13.24 0.00 0.00 5.68
157 158 0.729140 GCATCAAACTCAAACGGCGG 60.729 55.000 13.24 0.00 0.00 6.13
158 159 0.040514 TGCATCAAACTCAAACGGCG 60.041 50.000 4.80 4.80 0.00 6.46
159 160 1.786579 GTTGCATCAAACTCAAACGGC 59.213 47.619 0.00 0.00 0.00 5.68
160 161 2.043411 CGTTGCATCAAACTCAAACGG 58.957 47.619 0.00 0.00 0.00 4.44
161 162 1.447938 GCGTTGCATCAAACTCAAACG 59.552 47.619 0.00 0.00 0.00 3.60
162 163 1.447938 CGCGTTGCATCAAACTCAAAC 59.552 47.619 0.00 0.00 0.00 2.93
163 164 1.064803 ACGCGTTGCATCAAACTCAAA 59.935 42.857 5.58 0.00 0.00 2.69
164 165 0.660488 ACGCGTTGCATCAAACTCAA 59.340 45.000 5.58 0.00 0.00 3.02
165 166 0.660488 AACGCGTTGCATCAAACTCA 59.340 45.000 26.00 0.00 0.00 3.41
166 167 1.318251 GAACGCGTTGCATCAAACTC 58.682 50.000 31.89 6.88 0.00 3.01
167 168 0.384230 CGAACGCGTTGCATCAAACT 60.384 50.000 31.89 0.00 0.00 2.66
168 169 2.043022 CGAACGCGTTGCATCAAAC 58.957 52.632 31.89 11.19 0.00 2.93
169 170 4.505972 CGAACGCGTTGCATCAAA 57.494 50.000 31.89 0.00 0.00 2.69
179 180 1.658968 CAAAAGAAAGGACGAACGCG 58.341 50.000 3.53 3.53 44.79 6.01
180 181 1.268335 TGCAAAAGAAAGGACGAACGC 60.268 47.619 0.00 0.00 0.00 4.84
181 182 2.372350 GTGCAAAAGAAAGGACGAACG 58.628 47.619 0.00 0.00 0.00 3.95
186 187 0.660300 CGGCGTGCAAAAGAAAGGAC 60.660 55.000 0.00 0.00 0.00 3.85
187 188 0.816018 TCGGCGTGCAAAAGAAAGGA 60.816 50.000 6.85 0.00 0.00 3.36
188 189 0.030101 TTCGGCGTGCAAAAGAAAGG 59.970 50.000 6.85 0.00 0.00 3.11
189 190 1.120437 GTTCGGCGTGCAAAAGAAAG 58.880 50.000 6.85 0.00 0.00 2.62
190 191 0.736053 AGTTCGGCGTGCAAAAGAAA 59.264 45.000 6.85 0.00 0.00 2.52
191 192 0.736053 AAGTTCGGCGTGCAAAAGAA 59.264 45.000 6.85 0.00 0.00 2.52
192 193 0.028770 CAAGTTCGGCGTGCAAAAGA 59.971 50.000 6.85 0.00 0.00 2.52
193 194 0.248458 ACAAGTTCGGCGTGCAAAAG 60.248 50.000 6.85 0.00 0.00 2.27
194 195 0.171455 AACAAGTTCGGCGTGCAAAA 59.829 45.000 6.85 0.00 0.00 2.44
195 196 1.015109 TAACAAGTTCGGCGTGCAAA 58.985 45.000 6.85 0.00 0.00 3.68
196 197 1.231221 ATAACAAGTTCGGCGTGCAA 58.769 45.000 6.85 0.00 0.00 4.08
197 198 1.231221 AATAACAAGTTCGGCGTGCA 58.769 45.000 6.85 0.00 0.00 4.57
198 199 1.976045 CAAATAACAAGTTCGGCGTGC 59.024 47.619 6.85 0.48 0.00 5.34
199 200 3.529634 TCAAATAACAAGTTCGGCGTG 57.470 42.857 6.85 0.00 0.00 5.34
200 201 3.181524 CGATCAAATAACAAGTTCGGCGT 60.182 43.478 6.85 0.00 0.00 5.68
201 202 3.342269 CGATCAAATAACAAGTTCGGCG 58.658 45.455 0.00 0.00 0.00 6.46
202 203 3.098636 GCGATCAAATAACAAGTTCGGC 58.901 45.455 0.00 0.00 0.00 5.54
203 204 3.680789 GGCGATCAAATAACAAGTTCGG 58.319 45.455 0.00 0.00 0.00 4.30
204 205 3.061563 TCGGCGATCAAATAACAAGTTCG 59.938 43.478 4.99 0.00 0.00 3.95
205 206 4.593597 TCGGCGATCAAATAACAAGTTC 57.406 40.909 4.99 0.00 0.00 3.01
206 207 5.560966 ATTCGGCGATCAAATAACAAGTT 57.439 34.783 11.76 0.00 0.00 2.66
207 208 4.260212 CGATTCGGCGATCAAATAACAAGT 60.260 41.667 11.76 0.00 0.00 3.16
208 209 4.203828 CGATTCGGCGATCAAATAACAAG 58.796 43.478 11.76 0.00 0.00 3.16
209 210 3.619483 ACGATTCGGCGATCAAATAACAA 59.381 39.130 11.76 0.00 34.83 2.83
210 211 3.000825 CACGATTCGGCGATCAAATAACA 59.999 43.478 11.76 0.00 34.83 2.41
211 212 3.531982 CACGATTCGGCGATCAAATAAC 58.468 45.455 11.76 0.00 34.83 1.89
212 213 2.542178 CCACGATTCGGCGATCAAATAA 59.458 45.455 11.76 0.00 34.83 1.40
213 214 2.131972 CCACGATTCGGCGATCAAATA 58.868 47.619 11.76 0.00 34.83 1.40
214 215 0.937304 CCACGATTCGGCGATCAAAT 59.063 50.000 11.76 0.00 34.83 2.32
215 216 0.390603 ACCACGATTCGGCGATCAAA 60.391 50.000 11.76 0.00 34.83 2.69
216 217 0.456628 TACCACGATTCGGCGATCAA 59.543 50.000 11.76 0.00 34.83 2.57
217 218 0.456628 TTACCACGATTCGGCGATCA 59.543 50.000 11.76 0.00 34.83 2.92
218 219 0.850856 GTTACCACGATTCGGCGATC 59.149 55.000 11.76 9.74 34.83 3.69
219 220 2.967740 GTTACCACGATTCGGCGAT 58.032 52.632 11.76 0.10 34.83 4.58
220 221 4.481870 GTTACCACGATTCGGCGA 57.518 55.556 4.99 4.99 34.83 5.54
230 231 0.733566 TTCGGCGATCACGTTACCAC 60.734 55.000 11.76 0.00 41.98 4.16
231 232 0.733566 GTTCGGCGATCACGTTACCA 60.734 55.000 11.76 0.00 41.98 3.25
232 233 0.457337 AGTTCGGCGATCACGTTACC 60.457 55.000 19.04 0.00 41.98 2.85
233 234 0.638746 CAGTTCGGCGATCACGTTAC 59.361 55.000 19.04 8.95 41.98 2.50
234 235 0.241749 ACAGTTCGGCGATCACGTTA 59.758 50.000 19.04 0.00 41.98 3.18
235 236 1.006571 ACAGTTCGGCGATCACGTT 60.007 52.632 19.04 2.06 41.98 3.99
236 237 1.733041 CACAGTTCGGCGATCACGT 60.733 57.895 19.04 12.68 41.98 4.49
237 238 1.443702 TCACAGTTCGGCGATCACG 60.444 57.895 19.04 12.10 42.93 4.35
238 239 1.674611 CGTCACAGTTCGGCGATCAC 61.675 60.000 19.04 11.84 0.00 3.06
239 240 1.443702 CGTCACAGTTCGGCGATCA 60.444 57.895 19.04 0.00 0.00 2.92
240 241 2.789203 GCGTCACAGTTCGGCGATC 61.789 63.158 11.76 10.67 0.00 3.69
241 242 2.809601 GCGTCACAGTTCGGCGAT 60.810 61.111 11.76 0.00 0.00 4.58
242 243 3.973516 AGCGTCACAGTTCGGCGA 61.974 61.111 4.99 4.99 0.00 5.54
243 244 3.767230 CAGCGTCACAGTTCGGCG 61.767 66.667 0.00 0.00 0.00 6.46
244 245 1.687494 GATCAGCGTCACAGTTCGGC 61.687 60.000 0.00 0.00 0.00 5.54
245 246 1.406219 CGATCAGCGTCACAGTTCGG 61.406 60.000 0.00 0.00 34.64 4.30
246 247 1.983907 CGATCAGCGTCACAGTTCG 59.016 57.895 0.00 0.00 34.64 3.95
247 248 1.704582 GCGATCAGCGTCACAGTTC 59.295 57.895 0.00 0.00 43.41 3.01
248 249 3.862124 GCGATCAGCGTCACAGTT 58.138 55.556 0.00 0.00 43.41 3.16
258 259 0.108804 AACACCAGTACGGCGATCAG 60.109 55.000 16.62 2.57 39.03 2.90
259 260 0.319083 AAACACCAGTACGGCGATCA 59.681 50.000 16.62 0.00 39.03 2.92
260 261 1.435577 AAAACACCAGTACGGCGATC 58.564 50.000 16.62 5.88 39.03 3.69
261 262 1.886886 AAAAACACCAGTACGGCGAT 58.113 45.000 16.62 0.00 39.03 4.58
262 263 3.383092 AAAAACACCAGTACGGCGA 57.617 47.368 16.62 0.00 39.03 5.54
279 280 1.063867 TCCGTTTCCCACTCCCAAAAA 60.064 47.619 0.00 0.00 0.00 1.94
280 281 0.551879 TCCGTTTCCCACTCCCAAAA 59.448 50.000 0.00 0.00 0.00 2.44
281 282 0.179012 GTCCGTTTCCCACTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
282 283 1.452801 GTCCGTTTCCCACTCCCAA 59.547 57.895 0.00 0.00 0.00 4.12
283 284 2.522367 GGTCCGTTTCCCACTCCCA 61.522 63.158 0.00 0.00 0.00 4.37
284 285 2.059345 TTGGTCCGTTTCCCACTCCC 62.059 60.000 0.00 0.00 0.00 4.30
285 286 0.605589 CTTGGTCCGTTTCCCACTCC 60.606 60.000 0.00 0.00 0.00 3.85
286 287 0.108019 ACTTGGTCCGTTTCCCACTC 59.892 55.000 0.00 0.00 0.00 3.51
287 288 0.549469 AACTTGGTCCGTTTCCCACT 59.451 50.000 0.00 0.00 0.00 4.00
288 289 1.066454 CAAACTTGGTCCGTTTCCCAC 59.934 52.381 0.00 0.00 32.64 4.61
289 290 1.064611 TCAAACTTGGTCCGTTTCCCA 60.065 47.619 0.00 0.00 32.64 4.37
290 291 1.682740 TCAAACTTGGTCCGTTTCCC 58.317 50.000 0.00 0.00 32.64 3.97
291 292 4.316205 AATTCAAACTTGGTCCGTTTCC 57.684 40.909 0.00 0.00 32.64 3.13
292 293 4.026062 GCAAATTCAAACTTGGTCCGTTTC 60.026 41.667 0.00 0.00 32.64 2.78
293 294 3.868661 GCAAATTCAAACTTGGTCCGTTT 59.131 39.130 0.00 0.00 35.12 3.60
294 295 3.453424 GCAAATTCAAACTTGGTCCGTT 58.547 40.909 0.00 0.00 0.00 4.44
295 296 2.542824 CGCAAATTCAAACTTGGTCCGT 60.543 45.455 0.00 0.00 0.00 4.69
296 297 2.050691 CGCAAATTCAAACTTGGTCCG 58.949 47.619 0.00 0.00 0.00 4.79
297 298 3.049912 GTCGCAAATTCAAACTTGGTCC 58.950 45.455 0.00 0.00 0.00 4.46
298 299 2.719046 CGTCGCAAATTCAAACTTGGTC 59.281 45.455 0.00 0.00 0.00 4.02
299 300 2.098443 ACGTCGCAAATTCAAACTTGGT 59.902 40.909 0.00 0.00 0.00 3.67
300 301 2.726633 ACGTCGCAAATTCAAACTTGG 58.273 42.857 0.00 0.00 0.00 3.61
301 302 4.753516 AAACGTCGCAAATTCAAACTTG 57.246 36.364 0.00 0.00 0.00 3.16
302 303 4.032331 CCAAAACGTCGCAAATTCAAACTT 59.968 37.500 0.00 0.00 0.00 2.66
303 304 3.549873 CCAAAACGTCGCAAATTCAAACT 59.450 39.130 0.00 0.00 0.00 2.66
304 305 3.548268 TCCAAAACGTCGCAAATTCAAAC 59.452 39.130 0.00 0.00 0.00 2.93
305 306 3.770666 TCCAAAACGTCGCAAATTCAAA 58.229 36.364 0.00 0.00 0.00 2.69
306 307 3.367607 CTCCAAAACGTCGCAAATTCAA 58.632 40.909 0.00 0.00 0.00 2.69
307 308 2.287308 CCTCCAAAACGTCGCAAATTCA 60.287 45.455 0.00 0.00 0.00 2.57
308 309 2.315901 CCTCCAAAACGTCGCAAATTC 58.684 47.619 0.00 0.00 0.00 2.17
309 310 1.601914 GCCTCCAAAACGTCGCAAATT 60.602 47.619 0.00 0.00 0.00 1.82
310 311 0.039527 GCCTCCAAAACGTCGCAAAT 60.040 50.000 0.00 0.00 0.00 2.32
311 312 1.357334 GCCTCCAAAACGTCGCAAA 59.643 52.632 0.00 0.00 0.00 3.68
312 313 2.887889 CGCCTCCAAAACGTCGCAA 61.888 57.895 0.00 0.00 0.00 4.85
313 314 3.342627 CGCCTCCAAAACGTCGCA 61.343 61.111 0.00 0.00 0.00 5.10
314 315 4.084888 CCGCCTCCAAAACGTCGC 62.085 66.667 0.00 0.00 0.00 5.19
315 316 4.084888 GCCGCCTCCAAAACGTCG 62.085 66.667 0.00 0.00 0.00 5.12
316 317 2.975799 TGCCGCCTCCAAAACGTC 60.976 61.111 0.00 0.00 0.00 4.34
317 318 3.284449 GTGCCGCCTCCAAAACGT 61.284 61.111 0.00 0.00 0.00 3.99
318 319 4.038080 GGTGCCGCCTCCAAAACG 62.038 66.667 0.00 0.00 0.00 3.60
319 320 2.597510 AGGTGCCGCCTCCAAAAC 60.598 61.111 0.00 0.00 46.96 2.43
320 321 2.597217 CAGGTGCCGCCTCCAAAA 60.597 61.111 0.00 0.00 46.96 2.44
321 322 3.551496 CTCAGGTGCCGCCTCCAAA 62.551 63.158 0.00 0.00 46.96 3.28
322 323 4.020617 CTCAGGTGCCGCCTCCAA 62.021 66.667 0.00 0.00 46.96 3.53
334 335 4.039092 CCCAGCCACACCCTCAGG 62.039 72.222 0.00 0.00 40.04 3.86
335 336 2.930019 TCCCAGCCACACCCTCAG 60.930 66.667 0.00 0.00 0.00 3.35
336 337 3.249189 GTCCCAGCCACACCCTCA 61.249 66.667 0.00 0.00 0.00 3.86
337 338 4.394712 CGTCCCAGCCACACCCTC 62.395 72.222 0.00 0.00 0.00 4.30
338 339 3.839046 TACGTCCCAGCCACACCCT 62.839 63.158 0.00 0.00 0.00 4.34
339 340 3.310860 CTACGTCCCAGCCACACCC 62.311 68.421 0.00 0.00 0.00 4.61
340 341 1.614241 ATCTACGTCCCAGCCACACC 61.614 60.000 0.00 0.00 0.00 4.16
341 342 0.179108 GATCTACGTCCCAGCCACAC 60.179 60.000 0.00 0.00 0.00 3.82
342 343 1.663379 CGATCTACGTCCCAGCCACA 61.663 60.000 0.00 0.00 37.22 4.17
343 344 1.065928 CGATCTACGTCCCAGCCAC 59.934 63.158 0.00 0.00 37.22 5.01
344 345 2.782222 GCGATCTACGTCCCAGCCA 61.782 63.158 0.00 0.00 44.60 4.75
345 346 2.027751 GCGATCTACGTCCCAGCC 59.972 66.667 0.00 0.00 44.60 4.85
346 347 1.008309 GAGCGATCTACGTCCCAGC 60.008 63.158 0.00 0.00 44.60 4.85
347 348 1.655329 GGAGCGATCTACGTCCCAG 59.345 63.158 0.00 0.00 44.60 4.45
348 349 3.837578 GGAGCGATCTACGTCCCA 58.162 61.111 0.00 0.00 44.60 4.37
349 350 3.040844 GGGAGCGATCTACGTCCC 58.959 66.667 0.00 0.00 46.27 4.46
350 351 1.655329 CTGGGAGCGATCTACGTCC 59.345 63.158 0.00 0.00 44.60 4.79
351 352 1.655329 CCTGGGAGCGATCTACGTC 59.345 63.158 0.00 0.00 44.60 4.34
352 353 1.828660 CCCTGGGAGCGATCTACGT 60.829 63.158 7.01 0.00 44.60 3.57
353 354 3.043419 CCCTGGGAGCGATCTACG 58.957 66.667 7.01 0.00 45.66 3.51
354 355 2.737830 GCCCTGGGAGCGATCTAC 59.262 66.667 19.27 0.00 0.00 2.59
355 356 1.726192 TAGGCCCTGGGAGCGATCTA 61.726 60.000 19.27 4.76 0.00 1.98
356 357 2.605535 TTAGGCCCTGGGAGCGATCT 62.606 60.000 19.27 5.72 0.00 2.75
357 358 1.696097 TTTAGGCCCTGGGAGCGATC 61.696 60.000 19.27 0.00 0.00 3.69
358 359 1.279025 TTTTAGGCCCTGGGAGCGAT 61.279 55.000 19.27 0.00 0.00 4.58
359 360 1.493854 TTTTTAGGCCCTGGGAGCGA 61.494 55.000 19.27 0.00 0.00 4.93
360 361 0.395724 ATTTTTAGGCCCTGGGAGCG 60.396 55.000 19.27 0.00 0.00 5.03
361 362 1.403814 GATTTTTAGGCCCTGGGAGC 58.596 55.000 19.27 0.75 0.00 4.70
362 363 1.680338 CGATTTTTAGGCCCTGGGAG 58.320 55.000 19.27 0.00 0.00 4.30
363 364 0.395173 GCGATTTTTAGGCCCTGGGA 60.395 55.000 19.27 0.00 0.00 4.37
364 365 1.391933 GGCGATTTTTAGGCCCTGGG 61.392 60.000 8.86 8.86 41.01 4.45
365 366 1.724582 CGGCGATTTTTAGGCCCTGG 61.725 60.000 0.00 0.00 43.99 4.45
366 367 1.724582 CCGGCGATTTTTAGGCCCTG 61.725 60.000 9.30 0.00 43.99 4.45
367 368 1.453197 CCGGCGATTTTTAGGCCCT 60.453 57.895 9.30 0.00 43.99 5.19
368 369 1.452470 TCCGGCGATTTTTAGGCCC 60.452 57.895 9.30 0.00 43.99 5.80
369 370 1.725665 GTCCGGCGATTTTTAGGCC 59.274 57.895 9.30 0.00 43.42 5.19
370 371 1.085501 TCGTCCGGCGATTTTTAGGC 61.086 55.000 9.30 0.00 45.68 3.93
371 372 3.053662 TCGTCCGGCGATTTTTAGG 57.946 52.632 9.30 0.00 45.68 2.69
382 383 4.137872 TTTAGGGCGCTCGTCCGG 62.138 66.667 6.54 0.00 46.16 5.14
383 384 2.582498 CTTTAGGGCGCTCGTCCG 60.582 66.667 6.54 0.00 46.16 4.79
384 385 1.227002 CTCTTTAGGGCGCTCGTCC 60.227 63.158 6.54 4.52 40.91 4.79
385 386 1.878975 GCTCTTTAGGGCGCTCGTC 60.879 63.158 6.54 0.00 0.00 4.20
386 387 2.184579 GCTCTTTAGGGCGCTCGT 59.815 61.111 6.54 1.44 0.00 4.18
387 388 2.956964 CGCTCTTTAGGGCGCTCG 60.957 66.667 11.45 0.00 44.64 5.03
784 785 4.115199 ATCTCCACTTGCGCCCCC 62.115 66.667 4.18 0.00 0.00 5.40
785 786 2.825836 CATCTCCACTTGCGCCCC 60.826 66.667 4.18 0.00 0.00 5.80
786 787 3.512516 GCATCTCCACTTGCGCCC 61.513 66.667 4.18 0.00 0.00 6.13
787 788 2.437359 AGCATCTCCACTTGCGCC 60.437 61.111 4.18 0.00 43.61 6.53
788 789 3.096791 GAGCATCTCCACTTGCGC 58.903 61.111 0.00 0.00 43.61 6.09
795 796 7.956408 ATGGGATCCACTAAGAGCATCTCCA 62.956 48.000 15.23 0.00 40.40 3.86
796 797 5.549665 ATGGGATCCACTAAGAGCATCTCC 61.550 50.000 15.23 0.00 40.40 3.71
797 798 3.582208 ATGGGATCCACTAAGAGCATCTC 59.418 47.826 15.23 0.00 40.40 2.75
798 799 3.596101 ATGGGATCCACTAAGAGCATCT 58.404 45.455 15.23 0.00 42.68 2.90
799 800 4.070716 CAATGGGATCCACTAAGAGCATC 58.929 47.826 15.23 0.00 35.80 3.91
800 801 3.181436 CCAATGGGATCCACTAAGAGCAT 60.181 47.826 15.23 1.90 35.80 3.79
801 802 2.173356 CCAATGGGATCCACTAAGAGCA 59.827 50.000 15.23 0.00 35.80 4.26
802 803 2.856222 CCAATGGGATCCACTAAGAGC 58.144 52.381 15.23 0.00 35.80 4.09
803 804 2.441001 AGCCAATGGGATCCACTAAGAG 59.559 50.000 15.23 0.00 35.80 2.85
804 805 2.492025 AGCCAATGGGATCCACTAAGA 58.508 47.619 15.23 0.00 35.80 2.10
805 806 3.303351 AAGCCAATGGGATCCACTAAG 57.697 47.619 15.23 0.00 35.80 2.18
806 807 3.364549 CAAAGCCAATGGGATCCACTAA 58.635 45.455 15.23 0.00 35.80 2.24
807 808 2.949963 GCAAAGCCAATGGGATCCACTA 60.950 50.000 15.23 0.00 35.80 2.74
808 809 1.856629 CAAAGCCAATGGGATCCACT 58.143 50.000 15.23 0.00 35.80 4.00
809 810 0.176449 GCAAAGCCAATGGGATCCAC 59.824 55.000 15.23 3.53 35.80 4.02
810 811 0.041535 AGCAAAGCCAATGGGATCCA 59.958 50.000 15.23 0.00 38.19 3.41
811 812 0.749049 GAGCAAAGCCAATGGGATCC 59.251 55.000 1.92 1.92 35.59 3.36
907 909 0.780637 AGATGAGGCGAGGGGATAGA 59.219 55.000 0.00 0.00 0.00 1.98
979 981 1.153469 GGAGCTCTTGAGGCTTCGG 60.153 63.158 14.64 0.00 40.40 4.30
989 991 0.033699 GGAAGCCATTGGGAGCTCTT 60.034 55.000 14.64 0.00 38.74 2.85
1407 1409 3.181450 CGATAAGATCCTTGGCCTCCTTT 60.181 47.826 3.32 0.00 0.00 3.11
1434 1436 2.304180 CTCCTTGAGCTTCTTTGGGAGA 59.696 50.000 11.18 0.00 40.68 3.71
1518 1520 3.014304 ACCTAGTCTCACGCTATGGAA 57.986 47.619 0.00 0.00 0.00 3.53
1616 1620 6.966632 GCGCACTAATCTCATATGAAACAAAA 59.033 34.615 6.90 0.00 0.00 2.44
1677 1687 6.522054 ACATCCGGTAAGTATACAAGATTGG 58.478 40.000 0.00 0.04 33.45 3.16
1690 1700 7.490962 TCTAAATAATGCAACATCCGGTAAG 57.509 36.000 0.00 0.00 0.00 2.34
1695 1705 7.206981 AGGAATCTAAATAATGCAACATCCG 57.793 36.000 0.00 0.00 0.00 4.18
1791 1802 2.158827 TGCCGCTCTATTGCTCCAATAA 60.159 45.455 0.00 0.00 36.14 1.40
1829 1840 7.233389 ACTGAGAGCTATTACAGACTCAAAA 57.767 36.000 13.27 0.00 38.12 2.44
1996 2279 2.143876 ATGATTAGCAACACCCCACC 57.856 50.000 0.00 0.00 0.00 4.61
1998 2281 4.308526 TGTAATGATTAGCAACACCCCA 57.691 40.909 0.00 0.00 0.00 4.96
2057 2340 7.823799 TCATGTAGCATTCTTGAACAATGTAGA 59.176 33.333 0.00 0.00 34.27 2.59
2139 2434 1.039233 CATTGCTCCATGTGGGGGAC 61.039 60.000 0.29 0.00 41.01 4.46
2303 2601 2.687935 TGTGAAGCCTGAAGTTTTCCAC 59.312 45.455 0.00 0.00 0.00 4.02
2308 2606 2.092429 TCCAGTGTGAAGCCTGAAGTTT 60.092 45.455 0.00 0.00 0.00 2.66
2448 2749 9.770097 TTCATTTGTTTGGCATTATACTTCAAA 57.230 25.926 0.00 0.00 0.00 2.69
2484 2785 5.993106 GGTACAGCCTAAAAAGCATAGAG 57.007 43.478 0.00 0.00 0.00 2.43
2496 2797 5.737413 GCTGACTGCAAAGGTACAGCCTA 62.737 52.174 0.00 0.00 44.12 3.93
2498 2799 1.160137 CTGACTGCAAAGGTACAGCC 58.840 55.000 0.00 0.00 37.42 4.85


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

AutoCloner maintained by Alex Coulton.