Multiple sequence alignment - TraesCS2D01G349300

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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 TraesCS2D01G349300 chr2D 100.000 2504 0 0 1 2504 446922208 446919705 0.000000e+00 4625.0
1 TraesCS2D01G349300 chr2D 91.867 996 69 6 732 1726 397900678 397899694 0.000000e+00 1380.0
2 TraesCS2D01G349300 chr2D 98.521 676 10 0 1829 2504 446905779 446905104 0.000000e+00 1194.0
3 TraesCS2D01G349300 chr2D 87.302 189 19 4 1830 2014 19004988 19005175 7.020000e-51 211.0
4 TraesCS2D01G349300 chr2D 86.772 189 20 4 1830 2014 18900758 18900945 3.260000e-49 206.0
5 TraesCS2D01G349300 chr2A 92.368 1153 65 12 674 1812 590983792 590984935 0.000000e+00 1620.0
6 TraesCS2D01G349300 chr2A 93.043 1035 61 6 693 1726 535147357 535146333 0.000000e+00 1502.0
7 TraesCS2D01G349300 chr2A 86.598 194 14 4 1 194 590982737 590982918 1.170000e-48 204.0
8 TraesCS2D01G349300 chr2B 91.631 1159 60 10 674 1830 526755045 526756168 0.000000e+00 1568.0
9 TraesCS2D01G349300 chr2B 92.575 1037 66 8 692 1726 470392561 470391534 0.000000e+00 1478.0
10 TraesCS2D01G349300 chr2B 87.943 141 9 3 31 171 526754189 526754321 2.580000e-35 159.0
11 TraesCS2D01G349300 chr3B 90.909 253 20 1 2166 2415 130123132 130122880 1.110000e-88 337.0
12 TraesCS2D01G349300 chr3B 88.688 221 16 6 1861 2075 59239944 59240161 6.870000e-66 261.0
13 TraesCS2D01G349300 chr5B 89.723 253 23 1 2166 2415 477488106 477487854 1.120000e-83 320.0
14 TraesCS2D01G349300 chr4A 85.172 290 31 11 1831 2114 611980012 611979729 1.130000e-73 287.0
15 TraesCS2D01G349300 chr1B 86.957 253 23 6 1831 2073 16797345 16797093 2.450000e-70 276.0
16 TraesCS2D01G349300 chr1B 86.695 233 25 4 1828 2054 34779287 34779055 1.150000e-63 254.0
17 TraesCS2D01G349300 chr1B 86.695 233 25 4 1828 2054 34796614 34796382 1.150000e-63 254.0
18 TraesCS2D01G349300 chr7A 82.143 252 33 9 1831 2076 323481400 323481155 3.260000e-49 206.0
19 TraesCS2D01G349300 chr7A 95.385 65 2 1 189 252 129283998 129284062 4.410000e-18 102.0
20 TraesCS2D01G349300 chrUn 82.659 173 11 6 2166 2338 296436091 296436244 4.340000e-28 135.0
21 TraesCS2D01G349300 chrUn 82.659 173 11 6 2166 2338 308695308 308695461 4.340000e-28 135.0
22 TraesCS2D01G349300 chr7B 91.304 92 7 1 283 374 91798639 91798729 9.400000e-25 124.0
23 TraesCS2D01G349300 chr7B 100.000 33 0 0 220 252 91798363 91798395 7.480000e-06 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 TraesCS2D01G349300 chr2D 446919705 446922208 2503 True 4625.0 4625 100.000 1 2504 1 chr2D.!!$R3 2503
1 TraesCS2D01G349300 chr2D 397899694 397900678 984 True 1380.0 1380 91.867 732 1726 1 chr2D.!!$R1 994
2 TraesCS2D01G349300 chr2D 446905104 446905779 675 True 1194.0 1194 98.521 1829 2504 1 chr2D.!!$R2 675
3 TraesCS2D01G349300 chr2A 535146333 535147357 1024 True 1502.0 1502 93.043 693 1726 1 chr2A.!!$R1 1033
4 TraesCS2D01G349300 chr2A 590982737 590984935 2198 False 912.0 1620 89.483 1 1812 2 chr2A.!!$F1 1811
5 TraesCS2D01G349300 chr2B 470391534 470392561 1027 True 1478.0 1478 92.575 692 1726 1 chr2B.!!$R1 1034
6 TraesCS2D01G349300 chr2B 526754189 526756168 1979 False 863.5 1568 89.787 31 1830 2 chr2B.!!$F1 1799

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
194 195 0.036306 CACCAAGTTCGGGGCTAGTT 59.964 55.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 2147 0.599558 TGCAGCAGAAAAGCATCCAC 59.4 50.0 0.0 0.0 36.85 4.02 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
61 62 8.974060 ACTCAAAGAGTATTTTCTACAACCAA 57.026 30.769 0.00 0.00 41.51 3.67
63 64 9.665264 CTCAAAGAGTATTTTCTACAACCAAAC 57.335 33.333 0.00 0.00 0.00 2.93
107 108 6.294620 GCAACTCTCAGTACACTAGTTACCTT 60.295 42.308 0.00 0.00 0.00 3.50
108 109 6.821031 ACTCTCAGTACACTAGTTACCTTG 57.179 41.667 0.00 0.00 0.00 3.61
111 112 5.944599 TCTCAGTACACTAGTTACCTTGAGG 59.055 44.000 19.81 0.00 42.17 3.86
122 123 2.174334 CCTTGAGGTCAATGCCACG 58.826 57.895 0.00 0.00 35.02 4.94
123 124 0.321564 CCTTGAGGTCAATGCCACGA 60.322 55.000 0.00 0.00 35.02 4.35
124 125 1.679944 CCTTGAGGTCAATGCCACGAT 60.680 52.381 0.00 0.00 35.02 3.73
125 126 1.399440 CTTGAGGTCAATGCCACGATG 59.601 52.381 0.00 0.00 35.02 3.84
136 137 1.442526 GCCACGATGGATCAAGCTGG 61.443 60.000 8.04 0.00 40.96 4.85
171 172 0.318441 CTTCAGGAAGACACCGCTGA 59.682 55.000 2.88 0.00 40.79 4.26
172 173 0.318441 TTCAGGAAGACACCGCTGAG 59.682 55.000 0.00 0.00 34.73 3.35
173 174 4.861310 CTTCAGGAAGACACCGCTGAGG 62.861 59.091 2.88 0.00 42.71 3.86
187 188 0.320771 CTGAGGTCACCAAGTTCGGG 60.321 60.000 0.00 0.00 0.00 5.14
189 190 2.671963 GGTCACCAAGTTCGGGGC 60.672 66.667 0.00 0.00 0.00 5.80
192 193 0.391263 GTCACCAAGTTCGGGGCTAG 60.391 60.000 0.00 0.00 0.00 3.42
193 194 0.834687 TCACCAAGTTCGGGGCTAGT 60.835 55.000 0.00 0.00 0.00 2.57
194 195 0.036306 CACCAAGTTCGGGGCTAGTT 59.964 55.000 0.00 0.00 0.00 2.24
195 196 0.769247 ACCAAGTTCGGGGCTAGTTT 59.231 50.000 0.00 0.00 0.00 2.66
196 197 1.165270 CCAAGTTCGGGGCTAGTTTG 58.835 55.000 0.00 0.00 0.00 2.93
197 198 1.165270 CAAGTTCGGGGCTAGTTTGG 58.835 55.000 0.00 0.00 0.00 3.28
198 199 0.769247 AAGTTCGGGGCTAGTTTGGT 59.231 50.000 0.00 0.00 0.00 3.67
199 200 0.769247 AGTTCGGGGCTAGTTTGGTT 59.231 50.000 0.00 0.00 0.00 3.67
200 201 1.162698 GTTCGGGGCTAGTTTGGTTC 58.837 55.000 0.00 0.00 0.00 3.62
201 202 1.061546 TTCGGGGCTAGTTTGGTTCT 58.938 50.000 0.00 0.00 0.00 3.01
202 203 1.061546 TCGGGGCTAGTTTGGTTCTT 58.938 50.000 0.00 0.00 0.00 2.52
203 204 1.165270 CGGGGCTAGTTTGGTTCTTG 58.835 55.000 0.00 0.00 0.00 3.02
204 205 1.544759 CGGGGCTAGTTTGGTTCTTGT 60.545 52.381 0.00 0.00 0.00 3.16
205 206 2.160205 GGGGCTAGTTTGGTTCTTGTC 58.840 52.381 0.00 0.00 0.00 3.18
206 207 2.160205 GGGCTAGTTTGGTTCTTGTCC 58.840 52.381 0.00 0.00 0.00 4.02
207 208 2.488347 GGGCTAGTTTGGTTCTTGTCCA 60.488 50.000 0.00 0.00 33.86 4.02
208 209 2.552743 GGCTAGTTTGGTTCTTGTCCAC 59.447 50.000 0.00 0.00 34.45 4.02
209 210 3.211045 GCTAGTTTGGTTCTTGTCCACA 58.789 45.455 0.00 0.00 34.45 4.17
210 211 3.251004 GCTAGTTTGGTTCTTGTCCACAG 59.749 47.826 0.00 0.00 34.45 3.66
211 212 3.644966 AGTTTGGTTCTTGTCCACAGA 57.355 42.857 0.00 0.00 34.45 3.41
212 213 4.170468 AGTTTGGTTCTTGTCCACAGAT 57.830 40.909 0.00 0.00 34.45 2.90
213 214 4.536765 AGTTTGGTTCTTGTCCACAGATT 58.463 39.130 0.00 0.00 34.45 2.40
214 215 4.580580 AGTTTGGTTCTTGTCCACAGATTC 59.419 41.667 0.00 0.00 34.45 2.52
215 216 3.855255 TGGTTCTTGTCCACAGATTCA 57.145 42.857 0.00 0.00 0.00 2.57
216 217 4.371624 TGGTTCTTGTCCACAGATTCAT 57.628 40.909 0.00 0.00 0.00 2.57
217 218 4.074259 TGGTTCTTGTCCACAGATTCATG 58.926 43.478 0.00 0.00 0.00 3.07
218 219 3.119708 GGTTCTTGTCCACAGATTCATGC 60.120 47.826 0.00 0.00 0.00 4.06
219 220 2.715046 TCTTGTCCACAGATTCATGCC 58.285 47.619 0.00 0.00 0.00 4.40
220 221 2.306805 TCTTGTCCACAGATTCATGCCT 59.693 45.455 0.00 0.00 0.00 4.75
221 222 2.118313 TGTCCACAGATTCATGCCTG 57.882 50.000 7.68 7.68 36.53 4.85
222 223 1.340308 TGTCCACAGATTCATGCCTGG 60.340 52.381 12.12 0.00 34.85 4.45
223 224 0.256752 TCCACAGATTCATGCCTGGG 59.743 55.000 12.12 8.86 34.85 4.45
224 225 1.389609 CCACAGATTCATGCCTGGGC 61.390 60.000 4.43 4.43 42.35 5.36
234 235 3.213264 GCCTGGGCAATGATGGTG 58.787 61.111 6.75 0.00 41.49 4.17
235 236 3.085119 GCCTGGGCAATGATGGTGC 62.085 63.158 6.75 0.00 41.49 5.01
240 241 2.497770 GCAATGATGGTGCCTGGC 59.502 61.111 12.87 12.87 35.91 4.85
241 242 2.802792 CAATGATGGTGCCTGGCG 59.197 61.111 14.98 0.00 0.00 5.69
242 243 2.048023 CAATGATGGTGCCTGGCGT 61.048 57.895 14.98 0.00 0.00 5.68
243 244 2.048023 AATGATGGTGCCTGGCGTG 61.048 57.895 14.98 0.00 0.00 5.34
244 245 4.720902 TGATGGTGCCTGGCGTGG 62.721 66.667 14.98 0.00 0.00 4.94
245 246 4.408821 GATGGTGCCTGGCGTGGA 62.409 66.667 14.98 0.00 0.00 4.02
246 247 4.722700 ATGGTGCCTGGCGTGGAC 62.723 66.667 14.98 6.25 0.00 4.02
248 249 4.722700 GGTGCCTGGCGTGGACAT 62.723 66.667 14.98 0.00 0.00 3.06
249 250 3.434319 GTGCCTGGCGTGGACATG 61.434 66.667 14.98 0.00 0.00 3.21
250 251 4.720902 TGCCTGGCGTGGACATGG 62.721 66.667 14.98 0.00 0.00 3.66
251 252 4.408821 GCCTGGCGTGGACATGGA 62.409 66.667 1.35 0.00 0.00 3.41
252 253 2.436646 CCTGGCGTGGACATGGAC 60.437 66.667 0.00 0.00 0.00 4.02
253 254 2.815211 CTGGCGTGGACATGGACG 60.815 66.667 9.17 9.17 38.63 4.79
254 255 3.589654 CTGGCGTGGACATGGACGT 62.590 63.158 13.52 0.00 37.89 4.34
255 256 2.358247 GGCGTGGACATGGACGTT 60.358 61.111 13.52 0.00 37.89 3.99
256 257 2.677003 GGCGTGGACATGGACGTTG 61.677 63.158 13.52 0.00 37.89 4.10
257 258 2.677003 GCGTGGACATGGACGTTGG 61.677 63.158 13.52 0.00 37.89 3.77
258 259 1.005512 CGTGGACATGGACGTTGGA 60.006 57.895 0.00 0.00 0.00 3.53
259 260 0.391130 CGTGGACATGGACGTTGGAT 60.391 55.000 0.00 0.00 0.00 3.41
260 261 1.134936 CGTGGACATGGACGTTGGATA 60.135 52.381 0.00 0.00 0.00 2.59
261 262 2.675603 CGTGGACATGGACGTTGGATAA 60.676 50.000 0.00 0.00 0.00 1.75
262 263 2.936498 GTGGACATGGACGTTGGATAAG 59.064 50.000 0.00 0.00 0.00 1.73
263 264 2.093181 TGGACATGGACGTTGGATAAGG 60.093 50.000 0.00 0.00 0.00 2.69
264 265 1.940613 GACATGGACGTTGGATAAGGC 59.059 52.381 0.00 0.00 0.00 4.35
265 266 1.280710 ACATGGACGTTGGATAAGGCA 59.719 47.619 0.00 0.00 0.00 4.75
266 267 1.942657 CATGGACGTTGGATAAGGCAG 59.057 52.381 0.00 0.00 0.00 4.85
267 268 0.392461 TGGACGTTGGATAAGGCAGC 60.392 55.000 0.00 0.00 0.00 5.25
268 269 1.095807 GGACGTTGGATAAGGCAGCC 61.096 60.000 1.84 1.84 0.00 4.85
269 270 0.107654 GACGTTGGATAAGGCAGCCT 60.108 55.000 8.70 8.70 32.17 4.58
270 271 1.138266 GACGTTGGATAAGGCAGCCTA 59.862 52.381 16.56 3.52 32.17 3.93
271 272 1.139058 ACGTTGGATAAGGCAGCCTAG 59.861 52.381 16.56 1.70 32.17 3.02
272 273 1.598882 GTTGGATAAGGCAGCCTAGC 58.401 55.000 16.56 6.99 32.17 3.42
273 274 1.134098 GTTGGATAAGGCAGCCTAGCA 60.134 52.381 16.56 3.24 35.83 3.49
274 275 1.438469 TGGATAAGGCAGCCTAGCAT 58.562 50.000 16.56 8.68 35.83 3.79
275 276 1.072806 TGGATAAGGCAGCCTAGCATG 59.927 52.381 16.56 0.00 35.83 4.06
276 277 1.349026 GGATAAGGCAGCCTAGCATGA 59.651 52.381 16.56 0.00 35.83 3.07
277 278 2.421619 GATAAGGCAGCCTAGCATGAC 58.578 52.381 16.56 0.00 35.83 3.06
278 279 1.203237 TAAGGCAGCCTAGCATGACA 58.797 50.000 16.56 0.00 35.83 3.58
279 280 0.329261 AAGGCAGCCTAGCATGACAA 59.671 50.000 16.56 0.00 35.83 3.18
280 281 0.393537 AGGCAGCCTAGCATGACAAC 60.394 55.000 14.18 0.00 35.83 3.32
281 282 0.393537 GGCAGCCTAGCATGACAACT 60.394 55.000 3.29 0.00 35.83 3.16
282 283 1.134401 GGCAGCCTAGCATGACAACTA 60.134 52.381 3.29 0.00 35.83 2.24
283 284 2.486191 GGCAGCCTAGCATGACAACTAT 60.486 50.000 3.29 0.00 35.83 2.12
284 285 3.209410 GCAGCCTAGCATGACAACTATT 58.791 45.455 0.00 0.00 0.00 1.73
285 286 3.003068 GCAGCCTAGCATGACAACTATTG 59.997 47.826 0.00 0.00 0.00 1.90
286 287 4.445453 CAGCCTAGCATGACAACTATTGA 58.555 43.478 0.00 0.00 0.00 2.57
287 288 4.877823 CAGCCTAGCATGACAACTATTGAA 59.122 41.667 0.00 0.00 0.00 2.69
288 289 5.007430 CAGCCTAGCATGACAACTATTGAAG 59.993 44.000 0.00 0.00 0.00 3.02
289 290 5.104776 AGCCTAGCATGACAACTATTGAAGA 60.105 40.000 0.00 0.00 0.00 2.87
290 291 5.586243 GCCTAGCATGACAACTATTGAAGAA 59.414 40.000 0.00 0.00 0.00 2.52
291 292 6.238320 GCCTAGCATGACAACTATTGAAGAAG 60.238 42.308 0.00 0.00 0.00 2.85
292 293 6.259608 CCTAGCATGACAACTATTGAAGAAGG 59.740 42.308 0.00 0.00 0.00 3.46
293 294 4.397417 AGCATGACAACTATTGAAGAAGGC 59.603 41.667 0.00 0.00 0.00 4.35
294 295 4.156556 GCATGACAACTATTGAAGAAGGCA 59.843 41.667 0.00 0.00 0.00 4.75
295 296 5.335897 GCATGACAACTATTGAAGAAGGCAA 60.336 40.000 0.00 0.00 0.00 4.52
296 297 5.689383 TGACAACTATTGAAGAAGGCAAC 57.311 39.130 0.00 0.00 0.00 4.17
297 298 4.518970 TGACAACTATTGAAGAAGGCAACC 59.481 41.667 0.00 0.00 37.17 3.77
298 299 4.469657 ACAACTATTGAAGAAGGCAACCA 58.530 39.130 0.00 0.00 37.17 3.67
299 300 4.892934 ACAACTATTGAAGAAGGCAACCAA 59.107 37.500 0.00 0.00 37.17 3.67
300 301 5.362430 ACAACTATTGAAGAAGGCAACCAAA 59.638 36.000 0.00 0.00 37.17 3.28
301 302 5.453567 ACTATTGAAGAAGGCAACCAAAC 57.546 39.130 0.00 0.00 37.17 2.93
302 303 4.892934 ACTATTGAAGAAGGCAACCAAACA 59.107 37.500 0.00 0.00 37.17 2.83
303 304 3.799281 TTGAAGAAGGCAACCAAACAG 57.201 42.857 0.00 0.00 37.17 3.16
304 305 1.408702 TGAAGAAGGCAACCAAACAGC 59.591 47.619 0.00 0.00 37.17 4.40
305 306 1.683385 GAAGAAGGCAACCAAACAGCT 59.317 47.619 0.00 0.00 37.17 4.24
306 307 1.780503 AGAAGGCAACCAAACAGCTT 58.219 45.000 0.00 0.00 37.17 3.74
307 308 1.683385 AGAAGGCAACCAAACAGCTTC 59.317 47.619 0.00 0.00 37.17 3.86
308 309 1.683385 GAAGGCAACCAAACAGCTTCT 59.317 47.619 0.00 0.00 37.17 2.85
309 310 2.656947 AGGCAACCAAACAGCTTCTA 57.343 45.000 0.00 0.00 37.17 2.10
310 311 2.944129 AGGCAACCAAACAGCTTCTAA 58.056 42.857 0.00 0.00 37.17 2.10
311 312 2.887152 AGGCAACCAAACAGCTTCTAAG 59.113 45.455 0.00 0.00 37.17 2.18
312 313 2.623416 GGCAACCAAACAGCTTCTAAGT 59.377 45.455 0.00 0.00 0.00 2.24
313 314 3.550842 GGCAACCAAACAGCTTCTAAGTG 60.551 47.826 0.00 0.00 0.00 3.16
314 315 3.315191 GCAACCAAACAGCTTCTAAGTGA 59.685 43.478 0.00 0.00 0.00 3.41
315 316 4.022849 GCAACCAAACAGCTTCTAAGTGAT 60.023 41.667 0.00 0.00 0.00 3.06
316 317 5.507985 GCAACCAAACAGCTTCTAAGTGATT 60.508 40.000 0.00 0.00 0.00 2.57
317 318 5.948992 ACCAAACAGCTTCTAAGTGATTC 57.051 39.130 0.00 0.00 0.00 2.52
318 319 4.762251 ACCAAACAGCTTCTAAGTGATTCC 59.238 41.667 0.00 0.00 0.00 3.01
319 320 4.156739 CCAAACAGCTTCTAAGTGATTCCC 59.843 45.833 0.00 0.00 0.00 3.97
320 321 4.640771 AACAGCTTCTAAGTGATTCCCA 57.359 40.909 0.00 0.00 0.00 4.37
321 322 4.213564 ACAGCTTCTAAGTGATTCCCAG 57.786 45.455 0.00 0.00 0.00 4.45
322 323 3.054802 ACAGCTTCTAAGTGATTCCCAGG 60.055 47.826 0.00 0.00 0.00 4.45
323 324 2.092699 AGCTTCTAAGTGATTCCCAGGC 60.093 50.000 0.00 0.00 0.00 4.85
324 325 2.356125 GCTTCTAAGTGATTCCCAGGCA 60.356 50.000 0.00 0.00 0.00 4.75
325 326 3.274288 CTTCTAAGTGATTCCCAGGCAC 58.726 50.000 0.00 0.00 0.00 5.01
326 327 1.207089 TCTAAGTGATTCCCAGGCACG 59.793 52.381 0.00 0.00 37.60 5.34
327 328 0.392461 TAAGTGATTCCCAGGCACGC 60.392 55.000 0.00 0.00 37.60 5.34
328 329 2.045926 GTGATTCCCAGGCACGCT 60.046 61.111 0.00 0.00 0.00 5.07
329 330 1.675641 GTGATTCCCAGGCACGCTT 60.676 57.895 0.00 0.00 0.00 4.68
330 331 1.377202 TGATTCCCAGGCACGCTTC 60.377 57.895 0.00 0.00 0.00 3.86
331 332 1.377202 GATTCCCAGGCACGCTTCA 60.377 57.895 0.00 0.00 0.00 3.02
332 333 1.372087 GATTCCCAGGCACGCTTCAG 61.372 60.000 0.00 0.00 0.00 3.02
333 334 2.826777 ATTCCCAGGCACGCTTCAGG 62.827 60.000 0.00 0.00 0.00 3.86
341 342 4.711949 ACGCTTCAGGCCAGGCAG 62.712 66.667 15.19 5.13 37.74 4.85
342 343 4.399395 CGCTTCAGGCCAGGCAGA 62.399 66.667 15.19 7.84 37.74 4.26
343 344 2.034687 GCTTCAGGCCAGGCAGAA 59.965 61.111 15.19 15.42 34.27 3.02
344 345 1.379576 GCTTCAGGCCAGGCAGAAT 60.380 57.895 15.19 0.00 34.27 2.40
345 346 0.107017 GCTTCAGGCCAGGCAGAATA 60.107 55.000 15.19 0.00 34.27 1.75
346 347 1.964552 CTTCAGGCCAGGCAGAATAG 58.035 55.000 15.19 2.22 0.00 1.73
347 348 0.107017 TTCAGGCCAGGCAGAATAGC 60.107 55.000 15.19 0.00 0.00 2.97
348 349 1.225426 CAGGCCAGGCAGAATAGCA 59.775 57.895 15.19 0.00 35.83 3.49
349 350 1.099879 CAGGCCAGGCAGAATAGCAC 61.100 60.000 15.19 0.00 35.83 4.40
350 351 1.825622 GGCCAGGCAGAATAGCACC 60.826 63.158 15.19 0.00 35.83 5.01
351 352 1.077501 GCCAGGCAGAATAGCACCA 60.078 57.895 6.55 0.00 35.83 4.17
352 353 1.099879 GCCAGGCAGAATAGCACCAG 61.100 60.000 6.55 0.00 35.83 4.00
353 354 0.465097 CCAGGCAGAATAGCACCAGG 60.465 60.000 0.00 0.00 35.83 4.45
354 355 0.543277 CAGGCAGAATAGCACCAGGA 59.457 55.000 0.00 0.00 35.83 3.86
355 356 1.142465 CAGGCAGAATAGCACCAGGAT 59.858 52.381 0.00 0.00 35.83 3.24
356 357 2.369860 CAGGCAGAATAGCACCAGGATA 59.630 50.000 0.00 0.00 35.83 2.59
357 358 3.008813 CAGGCAGAATAGCACCAGGATAT 59.991 47.826 0.00 0.00 35.83 1.63
358 359 3.008813 AGGCAGAATAGCACCAGGATATG 59.991 47.826 0.00 0.00 35.83 1.78
359 360 3.008375 GGCAGAATAGCACCAGGATATGA 59.992 47.826 0.00 0.00 35.83 2.15
360 361 4.505566 GGCAGAATAGCACCAGGATATGAA 60.506 45.833 0.00 0.00 35.83 2.57
361 362 4.453819 GCAGAATAGCACCAGGATATGAAC 59.546 45.833 0.00 0.00 0.00 3.18
362 363 4.999950 CAGAATAGCACCAGGATATGAACC 59.000 45.833 0.00 0.00 0.00 3.62
363 364 4.660303 AGAATAGCACCAGGATATGAACCA 59.340 41.667 0.00 0.00 0.00 3.67
364 365 5.132648 AGAATAGCACCAGGATATGAACCAA 59.867 40.000 0.00 0.00 0.00 3.67
365 366 3.737559 AGCACCAGGATATGAACCAAA 57.262 42.857 0.00 0.00 0.00 3.28
366 367 3.356290 AGCACCAGGATATGAACCAAAC 58.644 45.455 0.00 0.00 0.00 2.93
367 368 3.010584 AGCACCAGGATATGAACCAAACT 59.989 43.478 0.00 0.00 0.00 2.66
368 369 3.129287 GCACCAGGATATGAACCAAACTG 59.871 47.826 0.00 0.00 0.00 3.16
370 371 2.689983 CCAGGATATGAACCAAACTGGC 59.310 50.000 0.00 0.00 42.67 4.85
371 372 2.689983 CAGGATATGAACCAAACTGGCC 59.310 50.000 0.00 0.00 42.67 5.36
372 373 2.031870 GGATATGAACCAAACTGGCCC 58.968 52.381 0.00 0.00 42.67 5.80
373 374 2.358195 GGATATGAACCAAACTGGCCCT 60.358 50.000 0.00 0.00 42.67 5.19
374 375 2.214376 TATGAACCAAACTGGCCCTG 57.786 50.000 0.00 0.00 42.67 4.45
414 415 2.253758 GCTGCCGTGCAAGAGTGAA 61.254 57.895 0.00 0.00 38.41 3.18
417 418 0.880278 TGCCGTGCAAGAGTGAAGAC 60.880 55.000 0.00 0.00 34.76 3.01
418 419 1.891060 GCCGTGCAAGAGTGAAGACG 61.891 60.000 0.00 0.00 0.00 4.18
423 426 1.827399 GCAAGAGTGAAGACGGGGGA 61.827 60.000 0.00 0.00 0.00 4.81
430 433 1.689582 GAAGACGGGGGATGGGACT 60.690 63.158 0.00 0.00 0.00 3.85
446 449 1.677217 GGACTGGGTAGCAGAAGCAAG 60.677 57.143 0.00 0.00 45.49 4.01
453 456 1.915078 TAGCAGAAGCAAGGGGAGGC 61.915 60.000 0.00 0.00 45.49 4.70
454 457 2.437359 CAGAAGCAAGGGGAGGCG 60.437 66.667 0.00 0.00 34.54 5.52
499 691 2.652662 GCGTTTGCCTTGATCGATAG 57.347 50.000 0.00 0.00 33.98 2.08
500 692 1.333258 GCGTTTGCCTTGATCGATAGC 60.333 52.381 0.00 0.00 33.98 2.97
501 693 2.205074 CGTTTGCCTTGATCGATAGCT 58.795 47.619 0.00 0.00 0.00 3.32
502 694 2.219674 CGTTTGCCTTGATCGATAGCTC 59.780 50.000 0.00 0.00 0.00 4.09
503 695 2.140065 TTGCCTTGATCGATAGCTCG 57.860 50.000 0.00 0.00 46.41 5.03
523 715 3.056536 TCGACTCAATTGGAAGAGGACAG 60.057 47.826 5.42 0.00 36.20 3.51
624 1207 1.663643 GCAAACACGAGTTCAGTCACA 59.336 47.619 0.00 0.00 36.84 3.58
644 1227 1.611851 AGCTCAGTACCCAGCAGCT 60.612 57.895 14.45 6.21 38.18 4.24
662 1245 0.886490 CTATCCCAAGCGGCATGACC 60.886 60.000 6.80 0.00 0.00 4.02
685 1291 2.158900 GCTTCCATAGCTAGCTGACCAA 60.159 50.000 27.68 13.11 46.77 3.67
744 1350 4.082895 TCTCTTCTGTAGTTTACTGTCGCC 60.083 45.833 0.00 0.00 0.00 5.54
897 1503 9.946165 GAAATATAAGGTTATGTTTGCTGGTAC 57.054 33.333 8.64 0.00 35.49 3.34
955 1564 6.257849 GTGTCACAGTCTGTCATTTGTAGAAA 59.742 38.462 1.37 0.00 0.00 2.52
959 1568 9.554395 TCACAGTCTGTCATTTGTAGAAAAATA 57.446 29.630 1.37 0.00 0.00 1.40
981 1590 8.415950 AATATACTTCGAGGATCAGATCTTGT 57.584 34.615 10.36 0.04 33.17 3.16
987 1596 7.339721 ACTTCGAGGATCAGATCTTGTTAACTA 59.660 37.037 10.36 0.00 33.17 2.24
996 1605 5.940470 CAGATCTTGTTAACTAGGGCAACTT 59.060 40.000 15.58 0.00 0.00 2.66
1029 1638 4.574013 GCTCACATTCCTACATCTTTGGAG 59.426 45.833 0.00 0.00 33.10 3.86
1087 1696 3.933332 GTGTGCTGAGGTATCTTTGTACC 59.067 47.826 0.00 0.00 43.65 3.34
1383 1996 6.313519 TCTTTGTCTCCCTAAATGTGCTAT 57.686 37.500 0.00 0.00 0.00 2.97
1482 2099 5.359756 CAGGCTTATAAAAAGGAAATGGCC 58.640 41.667 0.00 0.00 36.51 5.36
1530 2147 3.641434 ATGGAGGACAATGACCTTCAG 57.359 47.619 17.10 0.00 44.93 3.02
1533 2150 2.616510 GGAGGACAATGACCTTCAGTGG 60.617 54.545 5.64 0.00 45.68 4.00
1542 2159 3.149196 TGACCTTCAGTGGATGCTTTTC 58.851 45.455 0.00 0.00 0.00 2.29
1571 2188 3.569194 TCCTGTGGCTTCAACTTTGTA 57.431 42.857 0.00 0.00 0.00 2.41
1596 2213 2.067365 AAGTTCCGGGCTTGTCTTTT 57.933 45.000 0.00 0.00 0.00 2.27
1597 2214 2.067365 AGTTCCGGGCTTGTCTTTTT 57.933 45.000 0.00 0.00 0.00 1.94
1777 2398 3.196207 ATGGTGTGCCTGCCTTCGT 62.196 57.895 0.00 0.00 35.27 3.85
1812 2433 3.735237 TCGATCTGGAATGTAAGGCTC 57.265 47.619 0.00 0.00 0.00 4.70
1814 2435 3.643320 TCGATCTGGAATGTAAGGCTCAT 59.357 43.478 0.00 0.00 0.00 2.90
1820 2441 3.780294 TGGAATGTAAGGCTCATACTGGT 59.220 43.478 0.00 0.00 0.00 4.00
1913 2534 4.972751 ATTGTGCCCAAAACCACTAATT 57.027 36.364 0.00 0.00 33.44 1.40
2004 2625 1.372872 GCCCATTTGTTGACGTGGC 60.373 57.895 0.00 0.00 0.00 5.01
2246 2867 3.567797 GTCGCCCGATGCTCAAGC 61.568 66.667 0.00 0.00 42.50 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.811915 TGAGTCTTCAGAGCTACGGC 59.188 55.000 0.00 0.00 39.06 5.68
17 18 7.441890 TTGAGTACTACTTGAGTCTTCAGAG 57.558 40.000 0.00 0.00 39.81 3.35
61 62 8.058498 GTTGCAAACCTTGACTAGTGTCAGTT 62.058 42.308 0.00 0.00 46.54 3.16
63 64 4.260784 GTTGCAAACCTTGACTAGTGTCAG 60.261 45.833 0.00 0.00 46.54 3.51
81 82 5.048224 GGTAACTAGTGTACTGAGAGTTGCA 60.048 44.000 12.85 0.00 35.29 4.08
107 108 0.392863 CCATCGTGGCATTGACCTCA 60.393 55.000 0.00 0.00 0.00 3.86
108 109 0.107703 TCCATCGTGGCATTGACCTC 60.108 55.000 0.00 0.00 37.47 3.85
111 112 1.667236 TGATCCATCGTGGCATTGAC 58.333 50.000 0.00 0.00 37.47 3.18
114 115 1.027357 GCTTGATCCATCGTGGCATT 58.973 50.000 0.00 0.00 37.47 3.56
118 119 0.107508 ACCAGCTTGATCCATCGTGG 60.108 55.000 0.00 0.00 39.43 4.94
119 120 1.667724 GAACCAGCTTGATCCATCGTG 59.332 52.381 0.00 0.00 0.00 4.35
120 121 1.278985 TGAACCAGCTTGATCCATCGT 59.721 47.619 0.00 0.00 0.00 3.73
121 122 1.938577 CTGAACCAGCTTGATCCATCG 59.061 52.381 0.00 0.00 0.00 3.84
136 137 3.748568 CCTGAAGACCTAAACAGCTGAAC 59.251 47.826 23.35 3.31 0.00 3.18
171 172 3.157680 CCCCGAACTTGGTGACCT 58.842 61.111 2.11 0.00 0.00 3.85
172 173 1.833787 TAGCCCCGAACTTGGTGACC 61.834 60.000 0.00 0.00 0.00 4.02
173 174 0.391263 CTAGCCCCGAACTTGGTGAC 60.391 60.000 0.00 0.00 0.00 3.67
174 175 0.834687 ACTAGCCCCGAACTTGGTGA 60.835 55.000 0.00 0.00 0.00 4.02
187 188 2.552743 GTGGACAAGAACCAAACTAGCC 59.447 50.000 0.00 0.00 39.22 3.93
189 190 4.703897 TCTGTGGACAAGAACCAAACTAG 58.296 43.478 0.00 0.00 39.22 2.57
192 193 4.338118 TGAATCTGTGGACAAGAACCAAAC 59.662 41.667 0.00 0.00 39.22 2.93
193 194 4.531854 TGAATCTGTGGACAAGAACCAAA 58.468 39.130 0.00 0.00 39.22 3.28
194 195 4.163441 TGAATCTGTGGACAAGAACCAA 57.837 40.909 0.00 0.00 39.22 3.67
195 196 3.855255 TGAATCTGTGGACAAGAACCA 57.145 42.857 0.00 0.00 34.84 3.67
196 197 3.119708 GCATGAATCTGTGGACAAGAACC 60.120 47.826 0.00 0.00 0.00 3.62
197 198 3.119708 GGCATGAATCTGTGGACAAGAAC 60.120 47.826 0.00 0.00 0.00 3.01
198 199 3.084039 GGCATGAATCTGTGGACAAGAA 58.916 45.455 0.00 0.00 0.00 2.52
199 200 2.306805 AGGCATGAATCTGTGGACAAGA 59.693 45.455 0.00 0.00 0.00 3.02
200 201 2.422479 CAGGCATGAATCTGTGGACAAG 59.578 50.000 0.00 0.00 0.00 3.16
201 202 2.439409 CAGGCATGAATCTGTGGACAA 58.561 47.619 0.00 0.00 0.00 3.18
202 203 1.340308 CCAGGCATGAATCTGTGGACA 60.340 52.381 0.00 0.00 0.00 4.02
203 204 1.386533 CCAGGCATGAATCTGTGGAC 58.613 55.000 0.00 0.00 0.00 4.02
204 205 0.256752 CCCAGGCATGAATCTGTGGA 59.743 55.000 0.00 0.00 0.00 4.02
205 206 1.389609 GCCCAGGCATGAATCTGTGG 61.390 60.000 0.00 5.76 41.49 4.17
206 207 2.112898 GCCCAGGCATGAATCTGTG 58.887 57.895 0.00 0.00 41.49 3.66
207 208 4.672251 GCCCAGGCATGAATCTGT 57.328 55.556 0.00 0.00 41.49 3.41
217 218 3.085119 GCACCATCATTGCCCAGGC 62.085 63.158 0.38 0.38 42.35 4.85
218 219 3.213264 GCACCATCATTGCCCAGG 58.787 61.111 0.00 0.00 33.58 4.45
223 224 2.497770 GCCAGGCACCATCATTGC 59.502 61.111 6.55 0.00 39.41 3.56
224 225 2.048023 ACGCCAGGCACCATCATTG 61.048 57.895 13.30 0.00 0.00 2.82
225 226 2.048023 CACGCCAGGCACCATCATT 61.048 57.895 13.30 0.00 0.00 2.57
226 227 2.438975 CACGCCAGGCACCATCAT 60.439 61.111 13.30 0.00 0.00 2.45
227 228 4.720902 CCACGCCAGGCACCATCA 62.721 66.667 13.30 0.00 0.00 3.07
228 229 4.408821 TCCACGCCAGGCACCATC 62.409 66.667 13.30 0.00 0.00 3.51
229 230 4.722700 GTCCACGCCAGGCACCAT 62.723 66.667 13.30 0.00 0.00 3.55
231 232 4.722700 ATGTCCACGCCAGGCACC 62.723 66.667 13.30 0.00 0.00 5.01
232 233 3.434319 CATGTCCACGCCAGGCAC 61.434 66.667 13.30 1.99 0.00 5.01
233 234 4.720902 CCATGTCCACGCCAGGCA 62.721 66.667 13.30 0.00 0.00 4.75
234 235 4.408821 TCCATGTCCACGCCAGGC 62.409 66.667 0.00 0.00 0.00 4.85
235 236 2.436646 GTCCATGTCCACGCCAGG 60.437 66.667 0.00 0.00 0.00 4.45
236 237 2.815211 CGTCCATGTCCACGCCAG 60.815 66.667 0.00 0.00 0.00 4.85
237 238 3.171828 AACGTCCATGTCCACGCCA 62.172 57.895 8.54 0.00 39.73 5.69
238 239 2.358247 AACGTCCATGTCCACGCC 60.358 61.111 8.54 0.00 39.73 5.68
239 240 2.677003 CCAACGTCCATGTCCACGC 61.677 63.158 8.54 0.00 39.73 5.34
240 241 0.391130 ATCCAACGTCCATGTCCACG 60.391 55.000 7.36 7.36 41.90 4.94
241 242 2.684001 TATCCAACGTCCATGTCCAC 57.316 50.000 0.00 0.00 0.00 4.02
242 243 2.093181 CCTTATCCAACGTCCATGTCCA 60.093 50.000 0.00 0.00 0.00 4.02
243 244 2.561569 CCTTATCCAACGTCCATGTCC 58.438 52.381 0.00 0.00 0.00 4.02
244 245 1.940613 GCCTTATCCAACGTCCATGTC 59.059 52.381 0.00 0.00 0.00 3.06
245 246 1.280710 TGCCTTATCCAACGTCCATGT 59.719 47.619 0.00 0.00 0.00 3.21
246 247 1.942657 CTGCCTTATCCAACGTCCATG 59.057 52.381 0.00 0.00 0.00 3.66
247 248 1.747206 GCTGCCTTATCCAACGTCCAT 60.747 52.381 0.00 0.00 0.00 3.41
248 249 0.392461 GCTGCCTTATCCAACGTCCA 60.392 55.000 0.00 0.00 0.00 4.02
249 250 1.095807 GGCTGCCTTATCCAACGTCC 61.096 60.000 12.43 0.00 0.00 4.79
250 251 0.107654 AGGCTGCCTTATCCAACGTC 60.108 55.000 17.22 0.00 0.00 4.34
251 252 1.139058 CTAGGCTGCCTTATCCAACGT 59.861 52.381 28.55 0.03 34.61 3.99
252 253 1.871080 CTAGGCTGCCTTATCCAACG 58.129 55.000 28.55 1.89 34.61 4.10
253 254 1.134098 TGCTAGGCTGCCTTATCCAAC 60.134 52.381 28.55 4.04 34.61 3.77
254 255 1.212375 TGCTAGGCTGCCTTATCCAA 58.788 50.000 28.55 6.45 34.61 3.53
255 256 1.072806 CATGCTAGGCTGCCTTATCCA 59.927 52.381 28.55 17.91 34.61 3.41
256 257 1.349026 TCATGCTAGGCTGCCTTATCC 59.651 52.381 28.55 12.89 34.61 2.59
257 258 2.224378 TGTCATGCTAGGCTGCCTTATC 60.224 50.000 28.55 16.00 34.61 1.75
258 259 1.770658 TGTCATGCTAGGCTGCCTTAT 59.229 47.619 28.55 15.83 34.61 1.73
259 260 1.203237 TGTCATGCTAGGCTGCCTTA 58.797 50.000 28.55 14.17 34.61 2.69
260 261 0.329261 TTGTCATGCTAGGCTGCCTT 59.671 50.000 28.55 11.17 34.61 4.35
261 262 0.393537 GTTGTCATGCTAGGCTGCCT 60.394 55.000 26.52 26.52 37.71 4.75
262 263 0.393537 AGTTGTCATGCTAGGCTGCC 60.394 55.000 11.65 11.65 0.00 4.85
263 264 2.315925 TAGTTGTCATGCTAGGCTGC 57.684 50.000 0.00 0.00 0.00 5.25
264 265 4.445453 TCAATAGTTGTCATGCTAGGCTG 58.555 43.478 0.00 0.00 0.00 4.85
265 266 4.760530 TCAATAGTTGTCATGCTAGGCT 57.239 40.909 0.00 0.00 0.00 4.58
266 267 5.118990 TCTTCAATAGTTGTCATGCTAGGC 58.881 41.667 0.00 0.00 0.00 3.93
267 268 6.259608 CCTTCTTCAATAGTTGTCATGCTAGG 59.740 42.308 0.00 0.00 0.00 3.02
268 269 6.238320 GCCTTCTTCAATAGTTGTCATGCTAG 60.238 42.308 0.00 0.00 0.00 3.42
269 270 5.586243 GCCTTCTTCAATAGTTGTCATGCTA 59.414 40.000 0.00 0.00 0.00 3.49
270 271 4.397417 GCCTTCTTCAATAGTTGTCATGCT 59.603 41.667 0.00 0.00 0.00 3.79
271 272 4.156556 TGCCTTCTTCAATAGTTGTCATGC 59.843 41.667 0.00 0.00 0.00 4.06
272 273 5.885230 TGCCTTCTTCAATAGTTGTCATG 57.115 39.130 0.00 0.00 0.00 3.07
273 274 5.183904 GGTTGCCTTCTTCAATAGTTGTCAT 59.816 40.000 0.00 0.00 0.00 3.06
274 275 4.518970 GGTTGCCTTCTTCAATAGTTGTCA 59.481 41.667 0.00 0.00 0.00 3.58
275 276 4.518970 TGGTTGCCTTCTTCAATAGTTGTC 59.481 41.667 0.00 0.00 0.00 3.18
276 277 4.469657 TGGTTGCCTTCTTCAATAGTTGT 58.530 39.130 0.00 0.00 0.00 3.32
277 278 5.452078 TTGGTTGCCTTCTTCAATAGTTG 57.548 39.130 0.00 0.00 0.00 3.16
278 279 5.362430 TGTTTGGTTGCCTTCTTCAATAGTT 59.638 36.000 0.00 0.00 0.00 2.24
279 280 4.892934 TGTTTGGTTGCCTTCTTCAATAGT 59.107 37.500 0.00 0.00 0.00 2.12
280 281 5.452078 TGTTTGGTTGCCTTCTTCAATAG 57.548 39.130 0.00 0.00 0.00 1.73
281 282 4.261994 GCTGTTTGGTTGCCTTCTTCAATA 60.262 41.667 0.00 0.00 0.00 1.90
282 283 3.493176 GCTGTTTGGTTGCCTTCTTCAAT 60.493 43.478 0.00 0.00 0.00 2.57
283 284 2.159114 GCTGTTTGGTTGCCTTCTTCAA 60.159 45.455 0.00 0.00 0.00 2.69
284 285 1.408702 GCTGTTTGGTTGCCTTCTTCA 59.591 47.619 0.00 0.00 0.00 3.02
285 286 1.683385 AGCTGTTTGGTTGCCTTCTTC 59.317 47.619 0.00 0.00 0.00 2.87
286 287 1.780503 AGCTGTTTGGTTGCCTTCTT 58.219 45.000 0.00 0.00 0.00 2.52
287 288 1.683385 GAAGCTGTTTGGTTGCCTTCT 59.317 47.619 0.00 0.00 36.40 2.85
288 289 1.683385 AGAAGCTGTTTGGTTGCCTTC 59.317 47.619 0.00 0.00 36.40 3.46
289 290 1.780503 AGAAGCTGTTTGGTTGCCTT 58.219 45.000 0.00 0.00 36.40 4.35
290 291 2.656947 TAGAAGCTGTTTGGTTGCCT 57.343 45.000 0.00 0.00 36.40 4.75
291 292 2.623416 ACTTAGAAGCTGTTTGGTTGCC 59.377 45.455 0.00 0.00 36.40 4.52
292 293 3.315191 TCACTTAGAAGCTGTTTGGTTGC 59.685 43.478 0.00 0.00 36.40 4.17
293 294 5.695851 ATCACTTAGAAGCTGTTTGGTTG 57.304 39.130 0.00 0.00 36.40 3.77
294 295 5.241728 GGAATCACTTAGAAGCTGTTTGGTT 59.758 40.000 0.00 0.00 39.32 3.67
295 296 4.762251 GGAATCACTTAGAAGCTGTTTGGT 59.238 41.667 0.00 0.00 0.00 3.67
296 297 4.156739 GGGAATCACTTAGAAGCTGTTTGG 59.843 45.833 0.00 0.00 0.00 3.28
297 298 4.761739 TGGGAATCACTTAGAAGCTGTTTG 59.238 41.667 0.00 0.00 0.00 2.93
298 299 4.985538 TGGGAATCACTTAGAAGCTGTTT 58.014 39.130 0.00 0.00 0.00 2.83
299 300 4.566488 CCTGGGAATCACTTAGAAGCTGTT 60.566 45.833 0.00 0.00 0.00 3.16
300 301 3.054802 CCTGGGAATCACTTAGAAGCTGT 60.055 47.826 0.00 0.00 0.00 4.40
301 302 3.539604 CCTGGGAATCACTTAGAAGCTG 58.460 50.000 0.00 0.00 0.00 4.24
302 303 2.092699 GCCTGGGAATCACTTAGAAGCT 60.093 50.000 0.00 0.00 0.00 3.74
303 304 2.293170 GCCTGGGAATCACTTAGAAGC 58.707 52.381 0.00 0.00 0.00 3.86
304 305 3.274288 GTGCCTGGGAATCACTTAGAAG 58.726 50.000 0.00 0.00 0.00 2.85
305 306 2.354704 CGTGCCTGGGAATCACTTAGAA 60.355 50.000 0.00 0.00 0.00 2.10
306 307 1.207089 CGTGCCTGGGAATCACTTAGA 59.793 52.381 0.00 0.00 0.00 2.10
307 308 1.656652 CGTGCCTGGGAATCACTTAG 58.343 55.000 0.00 0.00 0.00 2.18
308 309 0.392461 GCGTGCCTGGGAATCACTTA 60.392 55.000 0.00 0.00 0.00 2.24
309 310 1.675641 GCGTGCCTGGGAATCACTT 60.676 57.895 0.00 0.00 0.00 3.16
310 311 2.045926 GCGTGCCTGGGAATCACT 60.046 61.111 0.00 0.00 0.00 3.41
311 312 1.648467 GAAGCGTGCCTGGGAATCAC 61.648 60.000 0.00 0.00 0.00 3.06
312 313 1.377202 GAAGCGTGCCTGGGAATCA 60.377 57.895 0.00 0.00 0.00 2.57
313 314 1.372087 CTGAAGCGTGCCTGGGAATC 61.372 60.000 0.00 0.00 0.00 2.52
314 315 1.377725 CTGAAGCGTGCCTGGGAAT 60.378 57.895 0.00 0.00 0.00 3.01
315 316 2.032528 CTGAAGCGTGCCTGGGAA 59.967 61.111 0.00 0.00 0.00 3.97
316 317 4.020617 CCTGAAGCGTGCCTGGGA 62.021 66.667 0.00 0.00 0.00 4.37
320 321 4.711949 CTGGCCTGAAGCGTGCCT 62.712 66.667 3.32 0.00 45.56 4.75
324 325 4.711949 CTGCCTGGCCTGAAGCGT 62.712 66.667 17.53 0.00 45.17 5.07
325 326 3.783020 TATTCTGCCTGGCCTGAAGCG 62.783 57.143 22.27 4.20 45.17 4.68
326 327 0.107017 TATTCTGCCTGGCCTGAAGC 60.107 55.000 22.27 7.56 42.60 3.86
327 328 1.964552 CTATTCTGCCTGGCCTGAAG 58.035 55.000 22.27 12.37 0.00 3.02
328 329 0.107017 GCTATTCTGCCTGGCCTGAA 60.107 55.000 17.53 19.59 0.00 3.02
329 330 1.273986 TGCTATTCTGCCTGGCCTGA 61.274 55.000 17.53 11.73 0.00 3.86
330 331 1.099879 GTGCTATTCTGCCTGGCCTG 61.100 60.000 17.53 9.35 0.00 4.85
331 332 1.225704 GTGCTATTCTGCCTGGCCT 59.774 57.895 17.53 0.66 0.00 5.19
332 333 1.825622 GGTGCTATTCTGCCTGGCC 60.826 63.158 17.53 0.00 0.00 5.36
333 334 1.077501 TGGTGCTATTCTGCCTGGC 60.078 57.895 12.87 12.87 0.00 4.85
334 335 0.465097 CCTGGTGCTATTCTGCCTGG 60.465 60.000 0.00 0.00 34.58 4.45
335 336 0.543277 TCCTGGTGCTATTCTGCCTG 59.457 55.000 0.00 0.00 0.00 4.85
336 337 1.516110 ATCCTGGTGCTATTCTGCCT 58.484 50.000 0.00 0.00 0.00 4.75
337 338 3.008375 TCATATCCTGGTGCTATTCTGCC 59.992 47.826 0.00 0.00 0.00 4.85
338 339 4.277515 TCATATCCTGGTGCTATTCTGC 57.722 45.455 0.00 0.00 0.00 4.26
339 340 4.999950 GGTTCATATCCTGGTGCTATTCTG 59.000 45.833 0.00 0.00 0.00 3.02
340 341 4.660303 TGGTTCATATCCTGGTGCTATTCT 59.340 41.667 0.00 0.00 0.00 2.40
341 342 4.973168 TGGTTCATATCCTGGTGCTATTC 58.027 43.478 0.00 0.00 0.00 1.75
342 343 5.387113 TTGGTTCATATCCTGGTGCTATT 57.613 39.130 0.00 0.00 0.00 1.73
343 344 5.103940 AGTTTGGTTCATATCCTGGTGCTAT 60.104 40.000 0.00 0.00 0.00 2.97
344 345 4.227300 AGTTTGGTTCATATCCTGGTGCTA 59.773 41.667 0.00 0.00 0.00 3.49
345 346 3.010584 AGTTTGGTTCATATCCTGGTGCT 59.989 43.478 0.00 0.00 0.00 4.40
346 347 3.129287 CAGTTTGGTTCATATCCTGGTGC 59.871 47.826 0.00 0.00 0.00 5.01
347 348 3.696051 CCAGTTTGGTTCATATCCTGGTG 59.304 47.826 0.00 0.00 34.63 4.17
348 349 3.877735 GCCAGTTTGGTTCATATCCTGGT 60.878 47.826 0.00 0.00 40.46 4.00
349 350 2.689983 GCCAGTTTGGTTCATATCCTGG 59.310 50.000 0.00 0.00 40.46 4.45
350 351 2.689983 GGCCAGTTTGGTTCATATCCTG 59.310 50.000 0.00 0.00 40.46 3.86
351 352 2.358195 GGGCCAGTTTGGTTCATATCCT 60.358 50.000 4.39 0.00 40.46 3.24
352 353 2.031870 GGGCCAGTTTGGTTCATATCC 58.968 52.381 4.39 0.00 40.46 2.59
353 354 2.689983 CAGGGCCAGTTTGGTTCATATC 59.310 50.000 6.18 0.00 40.46 1.63
354 355 2.624029 CCAGGGCCAGTTTGGTTCATAT 60.624 50.000 6.18 0.00 40.46 1.78
355 356 1.272425 CCAGGGCCAGTTTGGTTCATA 60.272 52.381 6.18 0.00 40.46 2.15
356 357 0.542702 CCAGGGCCAGTTTGGTTCAT 60.543 55.000 6.18 0.00 40.46 2.57
357 358 1.152567 CCAGGGCCAGTTTGGTTCA 60.153 57.895 6.18 0.00 40.46 3.18
358 359 1.152546 ACCAGGGCCAGTTTGGTTC 60.153 57.895 9.28 0.00 42.36 3.62
359 360 1.152546 GACCAGGGCCAGTTTGGTT 60.153 57.895 15.60 1.21 44.88 3.67
361 362 2.672996 CGACCAGGGCCAGTTTGG 60.673 66.667 6.18 7.22 41.55 3.28
362 363 3.365265 GCGACCAGGGCCAGTTTG 61.365 66.667 6.18 0.00 0.00 2.93
409 410 1.995626 CCCATCCCCCGTCTTCACT 60.996 63.158 0.00 0.00 0.00 3.41
414 415 2.365635 CAGTCCCATCCCCCGTCT 60.366 66.667 0.00 0.00 0.00 4.18
417 418 3.707025 TACCCAGTCCCATCCCCCG 62.707 68.421 0.00 0.00 0.00 5.73
418 419 1.770518 CTACCCAGTCCCATCCCCC 60.771 68.421 0.00 0.00 0.00 5.40
423 426 1.207791 CTTCTGCTACCCAGTCCCAT 58.792 55.000 0.00 0.00 42.38 4.00
430 433 1.685224 CCCTTGCTTCTGCTACCCA 59.315 57.895 0.00 0.00 40.48 4.51
495 687 4.938080 TCTTCCAATTGAGTCGAGCTATC 58.062 43.478 7.12 0.00 0.00 2.08
496 688 4.202202 CCTCTTCCAATTGAGTCGAGCTAT 60.202 45.833 7.12 0.00 0.00 2.97
497 689 3.131223 CCTCTTCCAATTGAGTCGAGCTA 59.869 47.826 7.12 0.00 0.00 3.32
498 690 2.093764 CCTCTTCCAATTGAGTCGAGCT 60.094 50.000 7.12 0.00 0.00 4.09
499 691 2.093973 TCCTCTTCCAATTGAGTCGAGC 60.094 50.000 7.12 0.00 0.00 5.03
500 692 3.056536 TGTCCTCTTCCAATTGAGTCGAG 60.057 47.826 7.12 6.97 0.00 4.04
501 693 2.897326 TGTCCTCTTCCAATTGAGTCGA 59.103 45.455 7.12 0.00 0.00 4.20
502 694 3.257393 CTGTCCTCTTCCAATTGAGTCG 58.743 50.000 7.12 0.00 0.00 4.18
503 695 3.006247 GCTGTCCTCTTCCAATTGAGTC 58.994 50.000 7.12 0.00 0.00 3.36
504 696 2.373169 TGCTGTCCTCTTCCAATTGAGT 59.627 45.455 7.12 0.00 0.00 3.41
505 697 2.746362 GTGCTGTCCTCTTCCAATTGAG 59.254 50.000 7.12 0.00 0.00 3.02
506 698 2.783135 GTGCTGTCCTCTTCCAATTGA 58.217 47.619 7.12 0.00 0.00 2.57
507 699 1.466167 CGTGCTGTCCTCTTCCAATTG 59.534 52.381 0.00 0.00 0.00 2.32
508 700 1.347707 TCGTGCTGTCCTCTTCCAATT 59.652 47.619 0.00 0.00 0.00 2.32
509 701 0.976641 TCGTGCTGTCCTCTTCCAAT 59.023 50.000 0.00 0.00 0.00 3.16
510 702 0.318441 CTCGTGCTGTCCTCTTCCAA 59.682 55.000 0.00 0.00 0.00 3.53
523 715 0.794981 CTGTCACTACTCGCTCGTGC 60.795 60.000 0.00 0.00 0.00 5.34
581 853 8.668510 TGCTGTTTATAAAAATGAAAAAGGCA 57.331 26.923 0.00 0.00 0.00 4.75
624 1207 1.978473 CTGCTGGGTACTGAGCTGT 59.022 57.895 14.95 0.00 35.38 4.40
644 1227 1.148273 GGTCATGCCGCTTGGGATA 59.852 57.895 6.43 0.00 42.75 2.59
685 1291 0.323178 CTTGGGCAGAATCCAGCTGT 60.323 55.000 13.81 0.00 35.48 4.40
744 1350 5.006358 GTGTTTGTAATATCTGTAGGGCACG 59.994 44.000 0.00 0.00 0.00 5.34
884 1490 3.513680 TCGATACGTACCAGCAAACAT 57.486 42.857 0.00 0.00 0.00 2.71
897 1503 0.318360 TGGCGCCTAACATCGATACG 60.318 55.000 29.70 0.00 0.00 3.06
955 1564 8.865090 ACAAGATCTGATCCTCGAAGTATATTT 58.135 33.333 13.83 0.00 0.00 1.40
959 1568 6.723298 AACAAGATCTGATCCTCGAAGTAT 57.277 37.500 13.83 0.00 0.00 2.12
981 1590 4.830046 TGCATGAAAAGTTGCCCTAGTTAA 59.170 37.500 0.00 0.00 0.00 2.01
987 1596 0.971386 CCTGCATGAAAAGTTGCCCT 59.029 50.000 0.00 0.00 0.00 5.19
996 1605 1.820519 GGAATGTGAGCCTGCATGAAA 59.179 47.619 0.00 0.00 0.00 2.69
1029 1638 1.707427 AGGGTTAGATGGGGATGCATC 59.293 52.381 18.81 18.81 0.00 3.91
1087 1696 3.388308 CATCAGATAGAGCCAAAGGTCG 58.612 50.000 0.00 0.00 45.43 4.79
1383 1996 4.576463 GCTTTCTGAGTTTCACAAGGAGAA 59.424 41.667 0.00 0.00 0.00 2.87
1482 2099 7.581959 CGAAGCTATGATTCATTTTCTTTCTCG 59.418 37.037 4.14 3.51 0.00 4.04
1530 2147 0.599558 TGCAGCAGAAAAGCATCCAC 59.400 50.000 0.00 0.00 36.85 4.02
1533 2150 2.165845 AGGATTGCAGCAGAAAAGCATC 59.834 45.455 0.00 0.00 38.19 3.91
1542 2159 1.248785 AAGCCACAGGATTGCAGCAG 61.249 55.000 0.00 0.00 26.61 4.24
1571 2188 1.828595 ACAAGCCCGGAACTTTGTTTT 59.171 42.857 0.73 0.00 0.00 2.43
1735 2356 6.452242 TCATCACTAACTCGCTCTTTTACAA 58.548 36.000 0.00 0.00 0.00 2.41
1777 2398 1.463056 GATCGAACGGCACAAATGACA 59.537 47.619 0.00 0.00 30.51 3.58
2004 2625 1.595489 CGTCTATCCCGAACCGTTACG 60.595 57.143 0.00 0.00 0.00 3.18
2464 3085 1.758514 GAGCTGATGGGAGGTCCGA 60.759 63.158 0.00 0.00 38.76 4.55


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

AutoCloner maintained by Alex Coulton.