Multiple sequence alignment - TraesCS6A01G177800

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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 TraesCS6A01G177800 chr6A 100.000 2366 0 0 1 2366 199235850 199233485 0.000000e+00 4370
1 TraesCS6A01G177800 chr6A 91.815 1906 119 20 496 2366 409191988 409190085 0.000000e+00 2621
2 TraesCS6A01G177800 chr2D 94.572 1879 80 8 496 2366 579027690 579025826 0.000000e+00 2885
3 TraesCS6A01G177800 chr2D 94.556 496 25 2 1 495 564727450 564726956 0.000000e+00 765
4 TraesCS6A01G177800 chr7D 94.118 1870 96 7 501 2366 503897497 503895638 0.000000e+00 2832
5 TraesCS6A01G177800 chr7D 94.086 1877 88 12 496 2366 26625729 26627588 0.000000e+00 2830
6 TraesCS6A01G177800 chr7D 93.926 1877 89 9 496 2364 13228443 13230302 0.000000e+00 2811
7 TraesCS6A01G177800 chr7D 94.908 491 22 2 8 495 416666646 416667136 0.000000e+00 765
8 TraesCS6A01G177800 chr4D 94.096 1880 79 14 496 2366 449160894 449159038 0.000000e+00 2828
9 TraesCS6A01G177800 chr4D 93.757 1874 82 16 496 2366 407162041 407163882 0.000000e+00 2780
10 TraesCS6A01G177800 chr7A 92.170 1903 113 18 496 2366 649950074 649951972 0.000000e+00 2656
11 TraesCS6A01G177800 chr7A 89.813 1286 86 19 496 1766 499621071 499622326 0.000000e+00 1607
12 TraesCS6A01G177800 chr3B 92.049 1874 134 11 496 2366 219302564 219300703 0.000000e+00 2621
13 TraesCS6A01G177800 chr7B 91.932 1884 119 21 496 2365 470044248 470042384 0.000000e+00 2606
14 TraesCS6A01G177800 chr7B 91.880 1872 136 13 498 2364 444375752 444377612 0.000000e+00 2601
15 TraesCS6A01G177800 chr3A 91.295 1907 119 27 498 2366 724427049 724428946 0.000000e+00 2558
16 TraesCS6A01G177800 chr6D 92.254 1278 85 11 496 1766 22048109 22046839 0.000000e+00 1799
17 TraesCS6A01G177800 chr6D 94.490 490 26 1 7 495 379863446 379862957 0.000000e+00 754
18 TraesCS6A01G177800 chr2B 90.584 1285 95 18 496 1766 146848568 146847296 0.000000e+00 1679
19 TraesCS6A01G177800 chr4A 96.531 490 16 1 7 496 460341640 460341152 0.000000e+00 809
20 TraesCS6A01G177800 chr2A 96.115 489 19 0 7 495 547165784 547165296 0.000000e+00 798
21 TraesCS6A01G177800 chr2A 96.203 158 5 1 496 653 234756302 234756146 8.390000e-65 257
22 TraesCS6A01G177800 chr5A 95.510 490 19 2 7 495 407472873 407472386 0.000000e+00 780
23 TraesCS6A01G177800 chr5D 94.411 501 23 2 1 496 282932985 282933485 0.000000e+00 765
24 TraesCS6A01G177800 chr5D 94.705 491 23 2 8 496 212143839 212143350 0.000000e+00 760
25 TraesCS6A01G177800 chr3D 94.705 491 23 3 7 495 268279627 268279138 0.000000e+00 760


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 TraesCS6A01G177800 chr6A 199233485 199235850 2365 True 4370 4370 100.000 1 2366 1 chr6A.!!$R1 2365
1 TraesCS6A01G177800 chr6A 409190085 409191988 1903 True 2621 2621 91.815 496 2366 1 chr6A.!!$R2 1870
2 TraesCS6A01G177800 chr2D 579025826 579027690 1864 True 2885 2885 94.572 496 2366 1 chr2D.!!$R2 1870
3 TraesCS6A01G177800 chr7D 503895638 503897497 1859 True 2832 2832 94.118 501 2366 1 chr7D.!!$R1 1865
4 TraesCS6A01G177800 chr7D 26625729 26627588 1859 False 2830 2830 94.086 496 2366 1 chr7D.!!$F2 1870
5 TraesCS6A01G177800 chr7D 13228443 13230302 1859 False 2811 2811 93.926 496 2364 1 chr7D.!!$F1 1868
6 TraesCS6A01G177800 chr4D 449159038 449160894 1856 True 2828 2828 94.096 496 2366 1 chr4D.!!$R1 1870
7 TraesCS6A01G177800 chr4D 407162041 407163882 1841 False 2780 2780 93.757 496 2366 1 chr4D.!!$F1 1870
8 TraesCS6A01G177800 chr7A 649950074 649951972 1898 False 2656 2656 92.170 496 2366 1 chr7A.!!$F2 1870
9 TraesCS6A01G177800 chr7A 499621071 499622326 1255 False 1607 1607 89.813 496 1766 1 chr7A.!!$F1 1270
10 TraesCS6A01G177800 chr3B 219300703 219302564 1861 True 2621 2621 92.049 496 2366 1 chr3B.!!$R1 1870
11 TraesCS6A01G177800 chr7B 470042384 470044248 1864 True 2606 2606 91.932 496 2365 1 chr7B.!!$R1 1869
12 TraesCS6A01G177800 chr7B 444375752 444377612 1860 False 2601 2601 91.880 498 2364 1 chr7B.!!$F1 1866
13 TraesCS6A01G177800 chr3A 724427049 724428946 1897 False 2558 2558 91.295 498 2366 1 chr3A.!!$F1 1868
14 TraesCS6A01G177800 chr6D 22046839 22048109 1270 True 1799 1799 92.254 496 1766 1 chr6D.!!$R1 1270
15 TraesCS6A01G177800 chr2B 146847296 146848568 1272 True 1679 1679 90.584 496 1766 1 chr2B.!!$R1 1270
16 TraesCS6A01G177800 chr5D 282932985 282933485 500 False 765 765 94.411 1 496 1 chr5D.!!$F1 495

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
247 248 0.180171 CACCTATCGGAACCATGCCA 59.820 55.0 0.00 0.0 0.00 4.92 F
660 686 0.735978 CACATACGCGAAGGAGCACA 60.736 55.0 15.93 0.0 36.85 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1171 1213 0.630673 TGGGCAAGGATAGCAACCAT 59.369 50.000 0.00 0.0 0.00 3.55 R
1914 2108 1.064463 TCTCCATCAACTTGGCCATCC 60.064 52.381 6.09 0.0 36.66 3.51 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
52 53 4.336280 GAGTTTGTAAGGGCAAGGAGATT 58.664 43.478 0.00 0.00 0.00 2.40
75 76 3.380637 GCCTACTTCGTGAAGATCTACCA 59.619 47.826 16.10 0.00 40.79 3.25
171 172 2.039624 AGCCCTCCATGGACTCGT 59.960 61.111 11.44 0.00 38.35 4.18
174 175 2.202797 CCTCCATGGACTCGTGCG 60.203 66.667 11.44 0.00 38.35 5.34
191 192 1.580942 CGACCGTTACCCTTCGTGA 59.419 57.895 0.00 0.00 0.00 4.35
204 205 2.035961 CCTTCGTGAGTTGAAGTCTCCA 59.964 50.000 1.30 0.00 40.96 3.86
205 206 3.306364 CCTTCGTGAGTTGAAGTCTCCAT 60.306 47.826 1.30 0.00 40.96 3.41
206 207 3.577649 TCGTGAGTTGAAGTCTCCATC 57.422 47.619 1.30 0.00 0.00 3.51
207 208 2.890945 TCGTGAGTTGAAGTCTCCATCA 59.109 45.455 1.30 0.00 0.00 3.07
208 209 3.320826 TCGTGAGTTGAAGTCTCCATCAA 59.679 43.478 1.30 0.00 33.37 2.57
212 213 3.795561 GTTGAAGTCTCCATCAACGTG 57.204 47.619 3.24 0.00 44.01 4.49
213 214 2.455674 TGAAGTCTCCATCAACGTGG 57.544 50.000 0.00 0.00 40.76 4.94
214 215 1.967779 TGAAGTCTCCATCAACGTGGA 59.032 47.619 0.00 0.00 45.78 4.02
215 216 2.567169 TGAAGTCTCCATCAACGTGGAT 59.433 45.455 0.00 0.00 46.67 3.41
216 217 2.680312 AGTCTCCATCAACGTGGATG 57.320 50.000 23.72 23.72 46.67 3.51
217 218 1.902508 AGTCTCCATCAACGTGGATGT 59.097 47.619 27.21 9.34 46.67 3.06
218 219 3.096852 AGTCTCCATCAACGTGGATGTA 58.903 45.455 27.21 14.32 46.67 2.29
219 220 3.119101 AGTCTCCATCAACGTGGATGTAC 60.119 47.826 27.21 21.39 46.67 2.90
220 221 2.159296 TCTCCATCAACGTGGATGTACG 60.159 50.000 27.21 14.90 46.67 3.67
221 222 1.819903 TCCATCAACGTGGATGTACGA 59.180 47.619 27.21 16.74 46.46 3.43
222 223 2.429250 TCCATCAACGTGGATGTACGAT 59.571 45.455 27.21 0.00 46.46 3.73
223 224 3.633065 TCCATCAACGTGGATGTACGATA 59.367 43.478 27.21 6.69 46.46 2.92
224 225 3.981416 CCATCAACGTGGATGTACGATAG 59.019 47.826 27.21 9.84 46.46 2.08
225 226 3.074504 TCAACGTGGATGTACGATAGC 57.925 47.619 5.23 0.00 46.46 2.97
226 227 2.424246 TCAACGTGGATGTACGATAGCA 59.576 45.455 5.23 0.00 46.46 3.49
227 228 2.486951 ACGTGGATGTACGATAGCAC 57.513 50.000 5.23 0.00 46.46 4.40
228 229 1.066605 ACGTGGATGTACGATAGCACC 59.933 52.381 5.23 0.00 46.46 5.01
229 230 1.066454 CGTGGATGTACGATAGCACCA 59.934 52.381 0.00 0.00 46.46 4.17
230 231 2.470821 GTGGATGTACGATAGCACCAC 58.529 52.381 0.00 0.00 39.20 4.16
231 232 1.411246 TGGATGTACGATAGCACCACC 59.589 52.381 0.00 0.00 42.67 4.61
232 233 1.687123 GGATGTACGATAGCACCACCT 59.313 52.381 0.00 0.00 42.67 4.00
233 234 2.889045 GGATGTACGATAGCACCACCTA 59.111 50.000 0.00 0.00 42.67 3.08
234 235 3.510360 GGATGTACGATAGCACCACCTAT 59.490 47.826 0.00 0.00 42.67 2.57
235 236 4.380655 GGATGTACGATAGCACCACCTATC 60.381 50.000 0.00 0.00 40.05 2.08
240 241 3.027974 GATAGCACCACCTATCGGAAC 57.972 52.381 0.00 0.00 35.71 3.62
241 242 1.117150 TAGCACCACCTATCGGAACC 58.883 55.000 0.00 0.00 0.00 3.62
242 243 0.907704 AGCACCACCTATCGGAACCA 60.908 55.000 0.00 0.00 0.00 3.67
243 244 0.180406 GCACCACCTATCGGAACCAT 59.820 55.000 0.00 0.00 0.00 3.55
244 245 1.953559 CACCACCTATCGGAACCATG 58.046 55.000 0.00 0.00 0.00 3.66
245 246 0.180406 ACCACCTATCGGAACCATGC 59.820 55.000 0.00 0.00 0.00 4.06
246 247 0.535102 CCACCTATCGGAACCATGCC 60.535 60.000 0.00 0.00 0.00 4.40
247 248 0.180171 CACCTATCGGAACCATGCCA 59.820 55.000 0.00 0.00 0.00 4.92
248 249 0.916086 ACCTATCGGAACCATGCCAA 59.084 50.000 0.00 0.00 0.00 4.52
249 250 1.283613 ACCTATCGGAACCATGCCAAA 59.716 47.619 0.00 0.00 0.00 3.28
250 251 2.291282 ACCTATCGGAACCATGCCAAAA 60.291 45.455 0.00 0.00 0.00 2.44
251 252 2.757868 CCTATCGGAACCATGCCAAAAA 59.242 45.455 0.00 0.00 0.00 1.94
252 253 3.384467 CCTATCGGAACCATGCCAAAAAT 59.616 43.478 0.00 0.00 0.00 1.82
253 254 3.525268 ATCGGAACCATGCCAAAAATC 57.475 42.857 0.00 0.00 0.00 2.17
254 255 2.524306 TCGGAACCATGCCAAAAATCT 58.476 42.857 0.00 0.00 0.00 2.40
255 256 2.491693 TCGGAACCATGCCAAAAATCTC 59.508 45.455 0.00 0.00 0.00 2.75
256 257 2.493278 CGGAACCATGCCAAAAATCTCT 59.507 45.455 0.00 0.00 0.00 3.10
257 258 3.674138 CGGAACCATGCCAAAAATCTCTG 60.674 47.826 0.00 0.00 0.00 3.35
258 259 3.259123 GGAACCATGCCAAAAATCTCTGT 59.741 43.478 0.00 0.00 0.00 3.41
259 260 3.947910 ACCATGCCAAAAATCTCTGTG 57.052 42.857 0.00 0.00 0.00 3.66
260 261 3.233507 ACCATGCCAAAAATCTCTGTGT 58.766 40.909 0.00 0.00 0.00 3.72
261 262 3.256631 ACCATGCCAAAAATCTCTGTGTC 59.743 43.478 0.00 0.00 0.00 3.67
262 263 3.508793 CCATGCCAAAAATCTCTGTGTCT 59.491 43.478 0.00 0.00 0.00 3.41
263 264 4.380233 CCATGCCAAAAATCTCTGTGTCTC 60.380 45.833 0.00 0.00 0.00 3.36
264 265 3.149196 TGCCAAAAATCTCTGTGTCTCC 58.851 45.455 0.00 0.00 0.00 3.71
265 266 3.149196 GCCAAAAATCTCTGTGTCTCCA 58.851 45.455 0.00 0.00 0.00 3.86
266 267 3.569701 GCCAAAAATCTCTGTGTCTCCAA 59.430 43.478 0.00 0.00 0.00 3.53
267 268 4.037923 GCCAAAAATCTCTGTGTCTCCAAA 59.962 41.667 0.00 0.00 0.00 3.28
268 269 5.279156 GCCAAAAATCTCTGTGTCTCCAAAT 60.279 40.000 0.00 0.00 0.00 2.32
269 270 6.739565 GCCAAAAATCTCTGTGTCTCCAAATT 60.740 38.462 0.00 0.00 0.00 1.82
270 271 6.643770 CCAAAAATCTCTGTGTCTCCAAATTG 59.356 38.462 0.00 0.00 0.00 2.32
271 272 5.382618 AAATCTCTGTGTCTCCAAATTGC 57.617 39.130 0.00 0.00 0.00 3.56
272 273 3.490439 TCTCTGTGTCTCCAAATTGCA 57.510 42.857 0.00 0.00 0.00 4.08
273 274 4.025040 TCTCTGTGTCTCCAAATTGCAT 57.975 40.909 0.00 0.00 0.00 3.96
274 275 4.401022 TCTCTGTGTCTCCAAATTGCATT 58.599 39.130 0.00 0.00 0.00 3.56
275 276 4.828939 TCTCTGTGTCTCCAAATTGCATTT 59.171 37.500 0.00 0.00 0.00 2.32
276 277 4.873817 TCTGTGTCTCCAAATTGCATTTG 58.126 39.130 12.10 12.10 46.98 2.32
277 278 3.391965 TGTGTCTCCAAATTGCATTTGC 58.608 40.909 13.09 0.00 46.27 3.68
290 291 2.872370 GCATTTGCACACTCCAATCTC 58.128 47.619 0.00 0.00 41.59 2.75
291 292 2.229543 GCATTTGCACACTCCAATCTCA 59.770 45.455 0.00 0.00 41.59 3.27
292 293 3.119245 GCATTTGCACACTCCAATCTCAT 60.119 43.478 0.00 0.00 41.59 2.90
293 294 4.669318 CATTTGCACACTCCAATCTCATC 58.331 43.478 0.00 0.00 0.00 2.92
294 295 3.708403 TTGCACACTCCAATCTCATCT 57.292 42.857 0.00 0.00 0.00 2.90
295 296 3.257469 TGCACACTCCAATCTCATCTC 57.743 47.619 0.00 0.00 0.00 2.75
296 297 2.836372 TGCACACTCCAATCTCATCTCT 59.164 45.455 0.00 0.00 0.00 3.10
297 298 3.262660 TGCACACTCCAATCTCATCTCTT 59.737 43.478 0.00 0.00 0.00 2.85
298 299 4.260170 GCACACTCCAATCTCATCTCTTT 58.740 43.478 0.00 0.00 0.00 2.52
299 300 5.046376 TGCACACTCCAATCTCATCTCTTTA 60.046 40.000 0.00 0.00 0.00 1.85
300 301 5.293079 GCACACTCCAATCTCATCTCTTTAC 59.707 44.000 0.00 0.00 0.00 2.01
301 302 6.401394 CACACTCCAATCTCATCTCTTTACA 58.599 40.000 0.00 0.00 0.00 2.41
302 303 7.046652 CACACTCCAATCTCATCTCTTTACAT 58.953 38.462 0.00 0.00 0.00 2.29
303 304 7.551974 CACACTCCAATCTCATCTCTTTACATT 59.448 37.037 0.00 0.00 0.00 2.71
304 305 7.768120 ACACTCCAATCTCATCTCTTTACATTC 59.232 37.037 0.00 0.00 0.00 2.67
305 306 7.986320 CACTCCAATCTCATCTCTTTACATTCT 59.014 37.037 0.00 0.00 0.00 2.40
306 307 8.547173 ACTCCAATCTCATCTCTTTACATTCTT 58.453 33.333 0.00 0.00 0.00 2.52
307 308 8.728337 TCCAATCTCATCTCTTTACATTCTTG 57.272 34.615 0.00 0.00 0.00 3.02
308 309 7.281774 TCCAATCTCATCTCTTTACATTCTTGC 59.718 37.037 0.00 0.00 0.00 4.01
309 310 7.066645 CCAATCTCATCTCTTTACATTCTTGCA 59.933 37.037 0.00 0.00 0.00 4.08
310 311 8.456471 CAATCTCATCTCTTTACATTCTTGCAA 58.544 33.333 0.00 0.00 0.00 4.08
311 312 7.369803 TCTCATCTCTTTACATTCTTGCAAC 57.630 36.000 0.00 0.00 0.00 4.17
312 313 7.164122 TCTCATCTCTTTACATTCTTGCAACT 58.836 34.615 0.00 0.00 0.00 3.16
313 314 7.663081 TCTCATCTCTTTACATTCTTGCAACTT 59.337 33.333 0.00 0.00 0.00 2.66
314 315 7.587629 TCATCTCTTTACATTCTTGCAACTTG 58.412 34.615 0.00 0.00 0.00 3.16
315 316 5.762045 TCTCTTTACATTCTTGCAACTTGC 58.238 37.500 6.82 6.82 45.29 4.01
328 329 4.635961 GCAACTTGCATGCTTTACTTTC 57.364 40.909 20.33 0.00 44.26 2.62
329 330 4.301628 GCAACTTGCATGCTTTACTTTCT 58.698 39.130 20.33 0.00 44.26 2.52
330 331 4.149396 GCAACTTGCATGCTTTACTTTCTG 59.851 41.667 20.33 5.13 44.26 3.02
331 332 3.905784 ACTTGCATGCTTTACTTTCTGC 58.094 40.909 20.33 0.00 0.00 4.26
332 333 3.571401 ACTTGCATGCTTTACTTTCTGCT 59.429 39.130 20.33 0.00 0.00 4.24
333 334 3.564235 TGCATGCTTTACTTTCTGCTG 57.436 42.857 20.33 0.00 0.00 4.41
334 335 2.257034 GCATGCTTTACTTTCTGCTGC 58.743 47.619 11.37 0.00 0.00 5.25
335 336 2.094854 GCATGCTTTACTTTCTGCTGCT 60.095 45.455 11.37 0.00 31.79 4.24
336 337 3.756069 CATGCTTTACTTTCTGCTGCTC 58.244 45.455 0.00 0.00 0.00 4.26
337 338 2.849942 TGCTTTACTTTCTGCTGCTCA 58.150 42.857 0.00 0.00 0.00 4.26
338 339 3.415212 TGCTTTACTTTCTGCTGCTCAT 58.585 40.909 0.00 0.00 0.00 2.90
339 340 4.578871 TGCTTTACTTTCTGCTGCTCATA 58.421 39.130 0.00 0.00 0.00 2.15
340 341 5.188434 TGCTTTACTTTCTGCTGCTCATAT 58.812 37.500 0.00 0.00 0.00 1.78
341 342 6.348498 TGCTTTACTTTCTGCTGCTCATATA 58.652 36.000 0.00 0.00 0.00 0.86
342 343 6.823182 TGCTTTACTTTCTGCTGCTCATATAA 59.177 34.615 0.00 0.00 0.00 0.98
343 344 7.500227 TGCTTTACTTTCTGCTGCTCATATAAT 59.500 33.333 0.00 0.00 0.00 1.28
344 345 8.014517 GCTTTACTTTCTGCTGCTCATATAATC 58.985 37.037 0.00 0.00 0.00 1.75
345 346 9.270640 CTTTACTTTCTGCTGCTCATATAATCT 57.729 33.333 0.00 0.00 0.00 2.40
346 347 9.618890 TTTACTTTCTGCTGCTCATATAATCTT 57.381 29.630 0.00 0.00 0.00 2.40
347 348 9.618890 TTACTTTCTGCTGCTCATATAATCTTT 57.381 29.630 0.00 0.00 0.00 2.52
348 349 7.928103 ACTTTCTGCTGCTCATATAATCTTTG 58.072 34.615 0.00 0.00 0.00 2.77
349 350 7.555554 ACTTTCTGCTGCTCATATAATCTTTGT 59.444 33.333 0.00 0.00 0.00 2.83
350 351 8.962884 TTTCTGCTGCTCATATAATCTTTGTA 57.037 30.769 0.00 0.00 0.00 2.41
351 352 9.565090 TTTCTGCTGCTCATATAATCTTTGTAT 57.435 29.630 0.00 0.00 0.00 2.29
352 353 8.543862 TCTGCTGCTCATATAATCTTTGTATG 57.456 34.615 0.00 0.00 36.44 2.39
353 354 7.118825 TCTGCTGCTCATATAATCTTTGTATGC 59.881 37.037 0.00 0.00 35.47 3.14
354 355 6.938596 TGCTGCTCATATAATCTTTGTATGCT 59.061 34.615 0.00 0.00 35.47 3.79
355 356 7.446319 TGCTGCTCATATAATCTTTGTATGCTT 59.554 33.333 0.00 0.00 35.47 3.91
356 357 7.749570 GCTGCTCATATAATCTTTGTATGCTTG 59.250 37.037 0.00 0.00 35.47 4.01
357 358 7.587629 TGCTCATATAATCTTTGTATGCTTGC 58.412 34.615 0.65 5.14 35.47 4.01
358 359 7.229106 TGCTCATATAATCTTTGTATGCTTGCA 59.771 33.333 0.00 0.00 35.47 4.08
359 360 8.242053 GCTCATATAATCTTTGTATGCTTGCAT 58.758 33.333 12.88 12.88 35.47 3.96
360 361 9.556030 CTCATATAATCTTTGTATGCTTGCATG 57.444 33.333 17.26 0.00 35.47 4.06
361 362 9.070179 TCATATAATCTTTGTATGCTTGCATGT 57.930 29.630 17.26 0.00 35.47 3.21
362 363 9.687210 CATATAATCTTTGTATGCTTGCATGTT 57.313 29.630 17.26 0.00 29.90 2.71
364 365 6.715344 AATCTTTGTATGCTTGCATGTTTG 57.285 33.333 17.26 5.12 0.00 2.93
365 366 5.199024 TCTTTGTATGCTTGCATGTTTGT 57.801 34.783 17.26 0.00 0.00 2.83
366 367 5.599732 TCTTTGTATGCTTGCATGTTTGTT 58.400 33.333 17.26 0.00 0.00 2.83
367 368 6.047870 TCTTTGTATGCTTGCATGTTTGTTT 58.952 32.000 17.26 0.00 0.00 2.83
368 369 5.654317 TTGTATGCTTGCATGTTTGTTTG 57.346 34.783 17.26 0.00 0.00 2.93
369 370 4.941657 TGTATGCTTGCATGTTTGTTTGA 58.058 34.783 17.26 0.00 0.00 2.69
370 371 5.539979 TGTATGCTTGCATGTTTGTTTGAT 58.460 33.333 17.26 0.00 0.00 2.57
371 372 6.685657 TGTATGCTTGCATGTTTGTTTGATA 58.314 32.000 17.26 0.00 0.00 2.15
372 373 7.321908 TGTATGCTTGCATGTTTGTTTGATAT 58.678 30.769 17.26 0.00 0.00 1.63
373 374 6.656314 ATGCTTGCATGTTTGTTTGATATG 57.344 33.333 7.35 0.00 0.00 1.78
374 375 5.539979 TGCTTGCATGTTTGTTTGATATGT 58.460 33.333 1.14 0.00 0.00 2.29
375 376 6.685657 TGCTTGCATGTTTGTTTGATATGTA 58.314 32.000 1.14 0.00 0.00 2.29
376 377 7.321908 TGCTTGCATGTTTGTTTGATATGTAT 58.678 30.769 1.14 0.00 0.00 2.29
377 378 7.818446 TGCTTGCATGTTTGTTTGATATGTATT 59.182 29.630 1.14 0.00 0.00 1.89
378 379 8.111836 GCTTGCATGTTTGTTTGATATGTATTG 58.888 33.333 1.14 0.00 0.00 1.90
379 380 9.142515 CTTGCATGTTTGTTTGATATGTATTGT 57.857 29.630 0.00 0.00 0.00 2.71
380 381 8.463456 TGCATGTTTGTTTGATATGTATTGTG 57.537 30.769 0.00 0.00 0.00 3.33
381 382 8.087136 TGCATGTTTGTTTGATATGTATTGTGT 58.913 29.630 0.00 0.00 0.00 3.72
382 383 8.924691 GCATGTTTGTTTGATATGTATTGTGTT 58.075 29.630 0.00 0.00 0.00 3.32
385 386 9.809096 TGTTTGTTTGATATGTATTGTGTTTGT 57.191 25.926 0.00 0.00 0.00 2.83
397 398 7.954447 TGTATTGTGTTTGTTTAAACTTGTGC 58.046 30.769 18.72 7.62 45.06 4.57
398 399 7.815068 TGTATTGTGTTTGTTTAAACTTGTGCT 59.185 29.630 18.72 1.16 45.06 4.40
399 400 6.698359 TTGTGTTTGTTTAAACTTGTGCTC 57.302 33.333 18.72 6.89 45.06 4.26
400 401 5.773575 TGTGTTTGTTTAAACTTGTGCTCA 58.226 33.333 18.72 8.91 45.06 4.26
401 402 6.216569 TGTGTTTGTTTAAACTTGTGCTCAA 58.783 32.000 18.72 0.66 45.06 3.02
402 403 6.701841 TGTGTTTGTTTAAACTTGTGCTCAAA 59.298 30.769 18.72 6.15 45.06 2.69
403 404 7.007117 GTGTTTGTTTAAACTTGTGCTCAAAC 58.993 34.615 18.72 16.41 45.06 2.93
404 405 6.926272 TGTTTGTTTAAACTTGTGCTCAAACT 59.074 30.769 18.72 0.00 45.06 2.66
405 406 7.115663 TGTTTGTTTAAACTTGTGCTCAAACTC 59.884 33.333 18.72 0.30 45.06 3.01
406 407 5.646606 TGTTTAAACTTGTGCTCAAACTCC 58.353 37.500 18.72 0.00 32.87 3.85
407 408 5.184096 TGTTTAAACTTGTGCTCAAACTCCA 59.816 36.000 18.72 0.00 32.87 3.86
408 409 3.782889 AAACTTGTGCTCAAACTCCAC 57.217 42.857 2.44 0.00 32.87 4.02
409 410 2.418368 ACTTGTGCTCAAACTCCACA 57.582 45.000 2.44 0.00 37.67 4.17
410 411 2.936202 ACTTGTGCTCAAACTCCACAT 58.064 42.857 2.44 0.00 39.03 3.21
411 412 2.880890 ACTTGTGCTCAAACTCCACATC 59.119 45.455 2.44 0.00 39.03 3.06
412 413 2.636647 TGTGCTCAAACTCCACATCA 57.363 45.000 0.00 0.00 34.82 3.07
413 414 2.929641 TGTGCTCAAACTCCACATCAA 58.070 42.857 0.00 0.00 34.82 2.57
414 415 2.618241 TGTGCTCAAACTCCACATCAAC 59.382 45.455 0.00 0.00 34.82 3.18
415 416 2.030805 GTGCTCAAACTCCACATCAACC 60.031 50.000 0.00 0.00 0.00 3.77
416 417 2.229792 GCTCAAACTCCACATCAACCA 58.770 47.619 0.00 0.00 0.00 3.67
417 418 2.622942 GCTCAAACTCCACATCAACCAA 59.377 45.455 0.00 0.00 0.00 3.67
418 419 3.068024 GCTCAAACTCCACATCAACCAAA 59.932 43.478 0.00 0.00 0.00 3.28
419 420 4.794003 GCTCAAACTCCACATCAACCAAAG 60.794 45.833 0.00 0.00 0.00 2.77
420 421 3.636300 TCAAACTCCACATCAACCAAAGG 59.364 43.478 0.00 0.00 0.00 3.11
421 422 3.593442 AACTCCACATCAACCAAAGGA 57.407 42.857 0.00 0.00 0.00 3.36
422 423 3.593442 ACTCCACATCAACCAAAGGAA 57.407 42.857 0.00 0.00 0.00 3.36
423 424 3.909732 ACTCCACATCAACCAAAGGAAA 58.090 40.909 0.00 0.00 0.00 3.13
424 425 4.482990 ACTCCACATCAACCAAAGGAAAT 58.517 39.130 0.00 0.00 0.00 2.17
425 426 4.901250 ACTCCACATCAACCAAAGGAAATT 59.099 37.500 0.00 0.00 0.00 1.82
426 427 6.074648 ACTCCACATCAACCAAAGGAAATTA 58.925 36.000 0.00 0.00 0.00 1.40
427 428 6.553100 ACTCCACATCAACCAAAGGAAATTAA 59.447 34.615 0.00 0.00 0.00 1.40
428 429 7.070571 ACTCCACATCAACCAAAGGAAATTAAA 59.929 33.333 0.00 0.00 0.00 1.52
429 430 7.796054 TCCACATCAACCAAAGGAAATTAAAA 58.204 30.769 0.00 0.00 0.00 1.52
430 431 8.267894 TCCACATCAACCAAAGGAAATTAAAAA 58.732 29.630 0.00 0.00 0.00 1.94
431 432 8.341903 CCACATCAACCAAAGGAAATTAAAAAC 58.658 33.333 0.00 0.00 0.00 2.43
432 433 9.108284 CACATCAACCAAAGGAAATTAAAAACT 57.892 29.630 0.00 0.00 0.00 2.66
433 434 9.108284 ACATCAACCAAAGGAAATTAAAAACTG 57.892 29.630 0.00 0.00 0.00 3.16
434 435 7.546778 TCAACCAAAGGAAATTAAAAACTGC 57.453 32.000 0.00 0.00 0.00 4.40
435 436 7.106239 TCAACCAAAGGAAATTAAAAACTGCA 58.894 30.769 0.00 0.00 0.00 4.41
436 437 7.607991 TCAACCAAAGGAAATTAAAAACTGCAA 59.392 29.630 0.00 0.00 0.00 4.08
437 438 7.315247 ACCAAAGGAAATTAAAAACTGCAAC 57.685 32.000 0.00 0.00 0.00 4.17
438 439 7.109501 ACCAAAGGAAATTAAAAACTGCAACT 58.890 30.769 0.00 0.00 0.00 3.16
439 440 7.609918 ACCAAAGGAAATTAAAAACTGCAACTT 59.390 29.630 0.00 0.00 0.00 2.66
440 441 8.458052 CCAAAGGAAATTAAAAACTGCAACTTT 58.542 29.630 0.00 0.00 0.00 2.66
441 442 9.838975 CAAAGGAAATTAAAAACTGCAACTTTT 57.161 25.926 9.61 9.61 0.00 2.27
443 444 9.448438 AAGGAAATTAAAAACTGCAACTTTTCT 57.552 25.926 8.31 0.00 0.00 2.52
444 445 9.448438 AGGAAATTAAAAACTGCAACTTTTCTT 57.552 25.926 8.31 3.14 0.00 2.52
445 446 9.489393 GGAAATTAAAAACTGCAACTTTTCTTG 57.511 29.630 8.31 0.00 0.00 3.02
451 452 8.424274 AAAAACTGCAACTTTTCTTGATTAGG 57.576 30.769 2.97 0.00 0.00 2.69
452 453 5.712152 ACTGCAACTTTTCTTGATTAGGG 57.288 39.130 0.00 0.00 0.00 3.53
453 454 5.140454 ACTGCAACTTTTCTTGATTAGGGT 58.860 37.500 0.00 0.00 0.00 4.34
454 455 5.241728 ACTGCAACTTTTCTTGATTAGGGTC 59.758 40.000 0.00 0.00 0.00 4.46
455 456 5.385198 TGCAACTTTTCTTGATTAGGGTCT 58.615 37.500 0.00 0.00 0.00 3.85
456 457 6.539173 TGCAACTTTTCTTGATTAGGGTCTA 58.461 36.000 0.00 0.00 0.00 2.59
457 458 7.175104 TGCAACTTTTCTTGATTAGGGTCTAT 58.825 34.615 0.00 0.00 0.00 1.98
458 459 7.669722 TGCAACTTTTCTTGATTAGGGTCTATT 59.330 33.333 0.00 0.00 0.00 1.73
459 460 8.184848 GCAACTTTTCTTGATTAGGGTCTATTC 58.815 37.037 0.00 0.00 0.00 1.75
460 461 9.231297 CAACTTTTCTTGATTAGGGTCTATTCA 57.769 33.333 0.00 0.00 0.00 2.57
461 462 8.794335 ACTTTTCTTGATTAGGGTCTATTCAC 57.206 34.615 0.00 0.00 0.00 3.18
462 463 7.829706 ACTTTTCTTGATTAGGGTCTATTCACC 59.170 37.037 0.00 0.00 35.42 4.02
483 484 3.621682 CCCCCTATAGACACCTCTTCT 57.378 52.381 0.00 0.00 0.00 2.85
484 485 3.502356 CCCCCTATAGACACCTCTTCTC 58.498 54.545 0.00 0.00 0.00 2.87
485 486 3.150767 CCCCTATAGACACCTCTTCTCG 58.849 54.545 0.00 0.00 0.00 4.04
486 487 3.181442 CCCCTATAGACACCTCTTCTCGA 60.181 52.174 0.00 0.00 0.00 4.04
487 488 4.507691 CCCCTATAGACACCTCTTCTCGAT 60.508 50.000 0.00 0.00 0.00 3.59
488 489 4.698304 CCCTATAGACACCTCTTCTCGATC 59.302 50.000 0.00 0.00 0.00 3.69
489 490 4.698304 CCTATAGACACCTCTTCTCGATCC 59.302 50.000 0.00 0.00 0.00 3.36
490 491 2.818751 AGACACCTCTTCTCGATCCT 57.181 50.000 0.00 0.00 0.00 3.24
491 492 3.094484 AGACACCTCTTCTCGATCCTT 57.906 47.619 0.00 0.00 0.00 3.36
492 493 3.436243 AGACACCTCTTCTCGATCCTTT 58.564 45.455 0.00 0.00 0.00 3.11
493 494 3.445805 AGACACCTCTTCTCGATCCTTTC 59.554 47.826 0.00 0.00 0.00 2.62
494 495 3.165875 ACACCTCTTCTCGATCCTTTCA 58.834 45.455 0.00 0.00 0.00 2.69
660 686 0.735978 CACATACGCGAAGGAGCACA 60.736 55.000 15.93 0.00 36.85 4.57
686 714 3.637273 GCCGTCCCTGGTTGACCT 61.637 66.667 1.34 0.00 36.82 3.85
741 769 3.848019 CGCATTTTGATTCACACTACAGC 59.152 43.478 0.00 0.00 0.00 4.40
811 839 2.091541 ACATTTGACCCCATTACTGCG 58.908 47.619 0.00 0.00 0.00 5.18
815 843 1.252215 TGACCCCATTACTGCGACGA 61.252 55.000 0.00 0.00 0.00 4.20
1016 1056 4.971125 GATGCTCTACCCCGCCGC 62.971 72.222 0.00 0.00 0.00 6.53
1049 1089 2.825982 CACCCTTCGTGTGTGGGA 59.174 61.111 4.11 0.00 43.47 4.37
1171 1213 0.606944 GGTCATGCACAACGGGGTTA 60.607 55.000 0.00 0.00 0.00 2.85
1210 1252 0.605589 CTTCACCAACCCCTTCGACC 60.606 60.000 0.00 0.00 0.00 4.79
1351 1393 1.543650 CGTACCCCATCAACAACACCA 60.544 52.381 0.00 0.00 0.00 4.17
1352 1394 2.588620 GTACCCCATCAACAACACCAA 58.411 47.619 0.00 0.00 0.00 3.67
1863 2057 1.411977 CTTGATGGAGGAGCAGATCGT 59.588 52.381 0.00 0.00 0.00 3.73
1889 2083 2.717809 GAGAACGCCGACTTCGTGC 61.718 63.158 0.00 0.46 40.36 5.34
1914 2108 4.554363 CGGCGGCGACTAGGTCAG 62.554 72.222 29.19 0.00 32.09 3.51
1935 2129 2.019984 GATGGCCAAGTTGATGGAGAC 58.980 52.381 10.96 0.00 43.54 3.36
1938 2132 0.329596 GCCAAGTTGATGGAGACCCT 59.670 55.000 3.87 0.00 43.54 4.34
2110 2310 3.402681 CCAGCCCGTGGGACAGAT 61.403 66.667 9.72 0.00 43.63 2.90
2132 2332 0.038166 ATGTGGTGGGCGTTCAGATT 59.962 50.000 0.00 0.00 0.00 2.40
2254 2454 4.436998 GGAGGACAGTGGTCGCGG 62.437 72.222 6.13 0.00 45.28 6.46
2287 2487 0.035056 CCGTTCTCCATGCTTCCCTT 60.035 55.000 0.00 0.00 0.00 3.95
2306 2506 3.522731 CCGCTCCCCTCGTCTGAG 61.523 72.222 0.00 0.00 42.18 3.35
2329 2529 1.455248 TGGCGGTACCATTGTTTAGC 58.545 50.000 13.54 4.08 46.36 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.441500 TGGTTCAACTCCACAATCTTGTTA 58.558 37.500 0.00 0.00 39.91 2.41
5 6 4.277476 TGGTTCAACTCCACAATCTTGTT 58.723 39.130 0.00 0.00 39.91 2.83
52 53 3.380637 GGTAGATCTTCACGAAGTAGGCA 59.619 47.826 0.00 0.00 41.61 4.75
162 163 1.588824 TAACGGTCGCACGAGTCCAT 61.589 55.000 5.60 0.00 37.61 3.41
171 172 2.259204 CGAAGGGTAACGGTCGCA 59.741 61.111 0.00 0.00 36.85 5.10
174 175 0.600057 ACTCACGAAGGGTAACGGTC 59.400 55.000 0.00 0.00 37.60 4.79
204 205 3.067601 TGCTATCGTACATCCACGTTGAT 59.932 43.478 0.00 0.00 42.51 2.57
205 206 2.424246 TGCTATCGTACATCCACGTTGA 59.576 45.455 0.00 0.00 42.51 3.18
206 207 2.534349 GTGCTATCGTACATCCACGTTG 59.466 50.000 0.00 0.00 42.51 4.10
207 208 2.480759 GGTGCTATCGTACATCCACGTT 60.481 50.000 0.00 0.00 42.51 3.99
208 209 1.066605 GGTGCTATCGTACATCCACGT 59.933 52.381 0.00 0.00 42.51 4.49
209 210 1.066454 TGGTGCTATCGTACATCCACG 59.934 52.381 0.00 0.00 43.28 4.94
210 211 2.470821 GTGGTGCTATCGTACATCCAC 58.529 52.381 0.00 0.00 37.33 4.02
211 212 1.411246 GGTGGTGCTATCGTACATCCA 59.589 52.381 0.00 0.00 0.00 3.41
212 213 1.687123 AGGTGGTGCTATCGTACATCC 59.313 52.381 0.00 0.00 0.00 3.51
213 214 4.672024 CGATAGGTGGTGCTATCGTACATC 60.672 50.000 3.96 0.00 45.51 3.06
214 215 3.190744 CGATAGGTGGTGCTATCGTACAT 59.809 47.826 3.96 0.00 45.51 2.29
215 216 2.551032 CGATAGGTGGTGCTATCGTACA 59.449 50.000 3.96 0.00 45.51 2.90
216 217 3.198863 CGATAGGTGGTGCTATCGTAC 57.801 52.381 3.96 0.00 45.51 3.67
231 232 4.339247 AGATTTTTGGCATGGTTCCGATAG 59.661 41.667 0.00 0.00 0.00 2.08
232 233 4.277476 AGATTTTTGGCATGGTTCCGATA 58.723 39.130 0.00 0.00 0.00 2.92
233 234 3.099141 AGATTTTTGGCATGGTTCCGAT 58.901 40.909 0.00 0.00 0.00 4.18
234 235 2.491693 GAGATTTTTGGCATGGTTCCGA 59.508 45.455 0.00 0.00 0.00 4.55
235 236 2.493278 AGAGATTTTTGGCATGGTTCCG 59.507 45.455 0.00 0.00 0.00 4.30
236 237 3.259123 ACAGAGATTTTTGGCATGGTTCC 59.741 43.478 0.00 0.00 0.00 3.62
237 238 4.240096 CACAGAGATTTTTGGCATGGTTC 58.760 43.478 0.00 0.00 0.00 3.62
238 239 3.642848 ACACAGAGATTTTTGGCATGGTT 59.357 39.130 0.00 0.00 0.00 3.67
239 240 3.233507 ACACAGAGATTTTTGGCATGGT 58.766 40.909 0.00 0.00 0.00 3.55
240 241 3.508793 AGACACAGAGATTTTTGGCATGG 59.491 43.478 0.00 0.00 0.00 3.66
241 242 4.380233 GGAGACACAGAGATTTTTGGCATG 60.380 45.833 0.00 0.00 0.00 4.06
242 243 3.760684 GGAGACACAGAGATTTTTGGCAT 59.239 43.478 0.00 0.00 0.00 4.40
243 244 3.149196 GGAGACACAGAGATTTTTGGCA 58.851 45.455 0.00 0.00 0.00 4.92
244 245 3.149196 TGGAGACACAGAGATTTTTGGC 58.851 45.455 0.00 0.00 33.40 4.52
245 246 5.772825 TTTGGAGACACAGAGATTTTTGG 57.227 39.130 0.00 0.00 42.67 3.28
246 247 6.145048 GCAATTTGGAGACACAGAGATTTTTG 59.855 38.462 0.00 0.00 42.67 2.44
247 248 6.183360 TGCAATTTGGAGACACAGAGATTTTT 60.183 34.615 0.00 0.00 42.67 1.94
248 249 5.302568 TGCAATTTGGAGACACAGAGATTTT 59.697 36.000 0.00 0.00 42.67 1.82
249 250 4.828939 TGCAATTTGGAGACACAGAGATTT 59.171 37.500 0.00 0.00 42.67 2.17
250 251 4.401022 TGCAATTTGGAGACACAGAGATT 58.599 39.130 0.00 0.00 42.67 2.40
251 252 4.025040 TGCAATTTGGAGACACAGAGAT 57.975 40.909 0.00 0.00 42.67 2.75
252 253 3.490439 TGCAATTTGGAGACACAGAGA 57.510 42.857 0.00 0.00 42.67 3.10
253 254 4.778534 AATGCAATTTGGAGACACAGAG 57.221 40.909 0.00 0.00 42.67 3.35
270 271 2.229543 TGAGATTGGAGTGTGCAAATGC 59.770 45.455 0.00 0.00 42.50 3.56
271 272 4.398358 AGATGAGATTGGAGTGTGCAAATG 59.602 41.667 0.00 0.00 29.75 2.32
272 273 4.597004 AGATGAGATTGGAGTGTGCAAAT 58.403 39.130 0.00 0.00 29.75 2.32
273 274 4.005650 GAGATGAGATTGGAGTGTGCAAA 58.994 43.478 0.00 0.00 29.75 3.68
274 275 3.262660 AGAGATGAGATTGGAGTGTGCAA 59.737 43.478 0.00 0.00 30.73 4.08
275 276 2.836372 AGAGATGAGATTGGAGTGTGCA 59.164 45.455 0.00 0.00 0.00 4.57
276 277 3.540314 AGAGATGAGATTGGAGTGTGC 57.460 47.619 0.00 0.00 0.00 4.57
277 278 6.401394 TGTAAAGAGATGAGATTGGAGTGTG 58.599 40.000 0.00 0.00 0.00 3.82
278 279 6.611613 TGTAAAGAGATGAGATTGGAGTGT 57.388 37.500 0.00 0.00 0.00 3.55
279 280 7.986320 AGAATGTAAAGAGATGAGATTGGAGTG 59.014 37.037 0.00 0.00 0.00 3.51
280 281 8.088463 AGAATGTAAAGAGATGAGATTGGAGT 57.912 34.615 0.00 0.00 0.00 3.85
281 282 8.828644 CAAGAATGTAAAGAGATGAGATTGGAG 58.171 37.037 0.00 0.00 0.00 3.86
282 283 7.281774 GCAAGAATGTAAAGAGATGAGATTGGA 59.718 37.037 0.00 0.00 0.00 3.53
283 284 7.066645 TGCAAGAATGTAAAGAGATGAGATTGG 59.933 37.037 0.00 0.00 0.00 3.16
284 285 7.982224 TGCAAGAATGTAAAGAGATGAGATTG 58.018 34.615 0.00 0.00 0.00 2.67
285 286 8.457261 GTTGCAAGAATGTAAAGAGATGAGATT 58.543 33.333 0.00 0.00 32.75 2.40
286 287 7.828223 AGTTGCAAGAATGTAAAGAGATGAGAT 59.172 33.333 0.00 0.00 32.75 2.75
287 288 7.164122 AGTTGCAAGAATGTAAAGAGATGAGA 58.836 34.615 0.00 0.00 32.75 3.27
288 289 7.375106 AGTTGCAAGAATGTAAAGAGATGAG 57.625 36.000 0.00 0.00 32.75 2.90
289 290 7.587629 CAAGTTGCAAGAATGTAAAGAGATGA 58.412 34.615 0.00 0.00 32.75 2.92
290 291 6.307318 GCAAGTTGCAAGAATGTAAAGAGATG 59.693 38.462 22.90 0.00 44.26 2.90
291 292 6.385033 GCAAGTTGCAAGAATGTAAAGAGAT 58.615 36.000 22.90 0.00 44.26 2.75
292 293 5.762045 GCAAGTTGCAAGAATGTAAAGAGA 58.238 37.500 22.90 0.00 44.26 3.10
307 308 4.149396 CAGAAAGTAAAGCATGCAAGTTGC 59.851 41.667 21.98 21.17 45.29 4.17
308 309 4.149396 GCAGAAAGTAAAGCATGCAAGTTG 59.851 41.667 21.98 0.00 33.92 3.16
309 310 4.038402 AGCAGAAAGTAAAGCATGCAAGTT 59.962 37.500 21.98 13.07 36.15 2.66
310 311 3.571401 AGCAGAAAGTAAAGCATGCAAGT 59.429 39.130 21.98 6.75 36.15 3.16
311 312 3.918591 CAGCAGAAAGTAAAGCATGCAAG 59.081 43.478 21.98 0.00 36.15 4.01
312 313 3.858129 GCAGCAGAAAGTAAAGCATGCAA 60.858 43.478 21.98 1.32 36.15 4.08
313 314 2.352030 GCAGCAGAAAGTAAAGCATGCA 60.352 45.455 21.98 0.00 36.15 3.96
314 315 2.094854 AGCAGCAGAAAGTAAAGCATGC 60.095 45.455 10.51 10.51 34.02 4.06
315 316 3.189910 TGAGCAGCAGAAAGTAAAGCATG 59.810 43.478 0.00 0.00 0.00 4.06
316 317 3.415212 TGAGCAGCAGAAAGTAAAGCAT 58.585 40.909 0.00 0.00 0.00 3.79
317 318 2.849942 TGAGCAGCAGAAAGTAAAGCA 58.150 42.857 0.00 0.00 0.00 3.91
318 319 5.747951 ATATGAGCAGCAGAAAGTAAAGC 57.252 39.130 0.00 0.00 0.00 3.51
319 320 9.270640 AGATTATATGAGCAGCAGAAAGTAAAG 57.729 33.333 0.00 0.00 0.00 1.85
320 321 9.618890 AAGATTATATGAGCAGCAGAAAGTAAA 57.381 29.630 0.00 0.00 0.00 2.01
321 322 9.618890 AAAGATTATATGAGCAGCAGAAAGTAA 57.381 29.630 0.00 0.00 0.00 2.24
322 323 9.049523 CAAAGATTATATGAGCAGCAGAAAGTA 57.950 33.333 0.00 0.00 0.00 2.24
323 324 7.555554 ACAAAGATTATATGAGCAGCAGAAAGT 59.444 33.333 0.00 0.00 0.00 2.66
324 325 7.928103 ACAAAGATTATATGAGCAGCAGAAAG 58.072 34.615 0.00 0.00 0.00 2.62
325 326 7.870509 ACAAAGATTATATGAGCAGCAGAAA 57.129 32.000 0.00 0.00 0.00 2.52
326 327 8.996271 CATACAAAGATTATATGAGCAGCAGAA 58.004 33.333 0.00 0.00 0.00 3.02
327 328 7.118825 GCATACAAAGATTATATGAGCAGCAGA 59.881 37.037 0.00 0.00 0.00 4.26
328 329 7.119407 AGCATACAAAGATTATATGAGCAGCAG 59.881 37.037 0.00 0.00 0.00 4.24
329 330 6.938596 AGCATACAAAGATTATATGAGCAGCA 59.061 34.615 0.00 0.00 0.00 4.41
330 331 7.375106 AGCATACAAAGATTATATGAGCAGC 57.625 36.000 0.00 0.00 0.00 5.25
331 332 7.749570 GCAAGCATACAAAGATTATATGAGCAG 59.250 37.037 0.00 0.00 0.00 4.24
332 333 7.229106 TGCAAGCATACAAAGATTATATGAGCA 59.771 33.333 0.00 0.00 32.61 4.26
333 334 7.587629 TGCAAGCATACAAAGATTATATGAGC 58.412 34.615 0.00 0.00 0.00 4.26
334 335 9.556030 CATGCAAGCATACAAAGATTATATGAG 57.444 33.333 7.29 0.00 34.91 2.90
335 336 9.070179 ACATGCAAGCATACAAAGATTATATGA 57.930 29.630 7.29 0.00 34.91 2.15
336 337 9.687210 AACATGCAAGCATACAAAGATTATATG 57.313 29.630 7.29 0.00 34.91 1.78
338 339 9.518906 CAAACATGCAAGCATACAAAGATTATA 57.481 29.630 7.29 0.00 34.91 0.98
339 340 8.036575 ACAAACATGCAAGCATACAAAGATTAT 58.963 29.630 7.29 0.00 34.91 1.28
340 341 7.377398 ACAAACATGCAAGCATACAAAGATTA 58.623 30.769 7.29 0.00 34.91 1.75
341 342 6.225318 ACAAACATGCAAGCATACAAAGATT 58.775 32.000 7.29 0.00 34.91 2.40
342 343 5.786311 ACAAACATGCAAGCATACAAAGAT 58.214 33.333 7.29 0.00 34.91 2.40
343 344 5.199024 ACAAACATGCAAGCATACAAAGA 57.801 34.783 7.29 0.00 34.91 2.52
344 345 5.910637 AACAAACATGCAAGCATACAAAG 57.089 34.783 7.29 0.00 34.91 2.77
345 346 5.814188 TCAAACAAACATGCAAGCATACAAA 59.186 32.000 7.29 0.00 34.91 2.83
346 347 5.354767 TCAAACAAACATGCAAGCATACAA 58.645 33.333 7.29 0.00 34.91 2.41
347 348 4.941657 TCAAACAAACATGCAAGCATACA 58.058 34.783 7.29 0.00 34.91 2.29
348 349 7.276218 ACATATCAAACAAACATGCAAGCATAC 59.724 33.333 7.29 0.00 34.91 2.39
349 350 7.321908 ACATATCAAACAAACATGCAAGCATA 58.678 30.769 7.29 0.00 34.91 3.14
350 351 6.167685 ACATATCAAACAAACATGCAAGCAT 58.832 32.000 0.86 0.86 37.08 3.79
351 352 5.539979 ACATATCAAACAAACATGCAAGCA 58.460 33.333 0.00 0.00 0.00 3.91
352 353 7.760131 ATACATATCAAACAAACATGCAAGC 57.240 32.000 0.00 0.00 0.00 4.01
353 354 9.142515 ACAATACATATCAAACAAACATGCAAG 57.857 29.630 0.00 0.00 0.00 4.01
354 355 8.923683 CACAATACATATCAAACAAACATGCAA 58.076 29.630 0.00 0.00 0.00 4.08
355 356 8.087136 ACACAATACATATCAAACAAACATGCA 58.913 29.630 0.00 0.00 0.00 3.96
356 357 8.464770 ACACAATACATATCAAACAAACATGC 57.535 30.769 0.00 0.00 0.00 4.06
359 360 9.809096 ACAAACACAATACATATCAAACAAACA 57.191 25.926 0.00 0.00 0.00 2.83
371 372 8.599774 GCACAAGTTTAAACAAACACAATACAT 58.400 29.630 20.06 0.00 35.20 2.29
372 373 7.815068 AGCACAAGTTTAAACAAACACAATACA 59.185 29.630 20.06 0.00 35.20 2.29
373 374 8.180317 AGCACAAGTTTAAACAAACACAATAC 57.820 30.769 20.06 0.00 35.20 1.89
374 375 8.029522 TGAGCACAAGTTTAAACAAACACAATA 58.970 29.630 20.06 0.00 35.20 1.90
375 376 6.870965 TGAGCACAAGTTTAAACAAACACAAT 59.129 30.769 20.06 0.00 35.20 2.71
376 377 6.216569 TGAGCACAAGTTTAAACAAACACAA 58.783 32.000 20.06 0.00 35.20 3.33
377 378 5.773575 TGAGCACAAGTTTAAACAAACACA 58.226 33.333 20.06 8.38 35.20 3.72
378 379 6.698359 TTGAGCACAAGTTTAAACAAACAC 57.302 33.333 20.06 6.81 35.20 3.32
379 380 6.926272 AGTTTGAGCACAAGTTTAAACAAACA 59.074 30.769 20.06 7.47 44.19 2.83
380 381 7.346208 AGTTTGAGCACAAGTTTAAACAAAC 57.654 32.000 20.06 16.62 43.01 2.93
381 382 6.588373 GGAGTTTGAGCACAAGTTTAAACAAA 59.412 34.615 20.06 6.67 37.06 2.83
382 383 6.096695 GGAGTTTGAGCACAAGTTTAAACAA 58.903 36.000 20.06 0.68 37.06 2.83
383 384 5.184096 TGGAGTTTGAGCACAAGTTTAAACA 59.816 36.000 20.06 0.00 37.06 2.83
384 385 5.515270 GTGGAGTTTGAGCACAAGTTTAAAC 59.485 40.000 10.47 10.47 35.59 2.01
385 386 5.184096 TGTGGAGTTTGAGCACAAGTTTAAA 59.816 36.000 0.00 0.00 37.32 1.52
386 387 4.702612 TGTGGAGTTTGAGCACAAGTTTAA 59.297 37.500 0.00 0.00 37.32 1.52
387 388 4.265893 TGTGGAGTTTGAGCACAAGTTTA 58.734 39.130 0.00 0.00 37.32 2.01
388 389 3.088532 TGTGGAGTTTGAGCACAAGTTT 58.911 40.909 0.00 0.00 37.32 2.66
389 390 2.722094 TGTGGAGTTTGAGCACAAGTT 58.278 42.857 0.00 0.00 37.32 2.66
390 391 2.418368 TGTGGAGTTTGAGCACAAGT 57.582 45.000 0.00 0.00 37.32 3.16
391 392 2.880268 TGATGTGGAGTTTGAGCACAAG 59.120 45.455 0.00 0.00 37.32 3.16
392 393 2.929641 TGATGTGGAGTTTGAGCACAA 58.070 42.857 0.00 0.00 0.00 3.33
393 394 2.618241 GTTGATGTGGAGTTTGAGCACA 59.382 45.455 0.00 0.00 0.00 4.57
394 395 2.030805 GGTTGATGTGGAGTTTGAGCAC 60.031 50.000 0.00 0.00 0.00 4.40
395 396 2.229792 GGTTGATGTGGAGTTTGAGCA 58.770 47.619 0.00 0.00 0.00 4.26
396 397 2.229792 TGGTTGATGTGGAGTTTGAGC 58.770 47.619 0.00 0.00 0.00 4.26
397 398 4.261741 CCTTTGGTTGATGTGGAGTTTGAG 60.262 45.833 0.00 0.00 0.00 3.02
398 399 3.636300 CCTTTGGTTGATGTGGAGTTTGA 59.364 43.478 0.00 0.00 0.00 2.69
399 400 3.636300 TCCTTTGGTTGATGTGGAGTTTG 59.364 43.478 0.00 0.00 0.00 2.93
400 401 3.909732 TCCTTTGGTTGATGTGGAGTTT 58.090 40.909 0.00 0.00 0.00 2.66
401 402 3.593442 TCCTTTGGTTGATGTGGAGTT 57.407 42.857 0.00 0.00 0.00 3.01
402 403 3.593442 TTCCTTTGGTTGATGTGGAGT 57.407 42.857 0.00 0.00 0.00 3.85
403 404 5.473066 AATTTCCTTTGGTTGATGTGGAG 57.527 39.130 0.00 0.00 0.00 3.86
404 405 6.985653 TTAATTTCCTTTGGTTGATGTGGA 57.014 33.333 0.00 0.00 0.00 4.02
405 406 8.341903 GTTTTTAATTTCCTTTGGTTGATGTGG 58.658 33.333 0.00 0.00 0.00 4.17
406 407 9.108284 AGTTTTTAATTTCCTTTGGTTGATGTG 57.892 29.630 0.00 0.00 0.00 3.21
407 408 9.108284 CAGTTTTTAATTTCCTTTGGTTGATGT 57.892 29.630 0.00 0.00 0.00 3.06
408 409 8.069574 GCAGTTTTTAATTTCCTTTGGTTGATG 58.930 33.333 0.00 0.00 0.00 3.07
409 410 7.772757 TGCAGTTTTTAATTTCCTTTGGTTGAT 59.227 29.630 0.00 0.00 0.00 2.57
410 411 7.106239 TGCAGTTTTTAATTTCCTTTGGTTGA 58.894 30.769 0.00 0.00 0.00 3.18
411 412 7.313951 TGCAGTTTTTAATTTCCTTTGGTTG 57.686 32.000 0.00 0.00 0.00 3.77
412 413 7.609918 AGTTGCAGTTTTTAATTTCCTTTGGTT 59.390 29.630 0.00 0.00 0.00 3.67
413 414 7.109501 AGTTGCAGTTTTTAATTTCCTTTGGT 58.890 30.769 0.00 0.00 0.00 3.67
414 415 7.552458 AGTTGCAGTTTTTAATTTCCTTTGG 57.448 32.000 0.00 0.00 0.00 3.28
415 416 9.838975 AAAAGTTGCAGTTTTTAATTTCCTTTG 57.161 25.926 8.07 0.00 26.81 2.77
417 418 9.448438 AGAAAAGTTGCAGTTTTTAATTTCCTT 57.552 25.926 9.50 0.00 31.40 3.36
418 419 9.448438 AAGAAAAGTTGCAGTTTTTAATTTCCT 57.552 25.926 9.50 1.41 31.40 3.36
419 420 9.489393 CAAGAAAAGTTGCAGTTTTTAATTTCC 57.511 29.630 9.50 0.00 31.40 3.13
425 426 9.528018 CCTAATCAAGAAAAGTTGCAGTTTTTA 57.472 29.630 9.50 0.00 31.40 1.52
426 427 7.495606 CCCTAATCAAGAAAAGTTGCAGTTTTT 59.504 33.333 9.50 9.37 31.40 1.94
427 428 6.986231 CCCTAATCAAGAAAAGTTGCAGTTTT 59.014 34.615 8.23 8.23 33.74 2.43
428 429 6.098266 ACCCTAATCAAGAAAAGTTGCAGTTT 59.902 34.615 0.00 0.00 0.00 2.66
429 430 5.598417 ACCCTAATCAAGAAAAGTTGCAGTT 59.402 36.000 0.00 0.00 0.00 3.16
430 431 5.140454 ACCCTAATCAAGAAAAGTTGCAGT 58.860 37.500 0.00 0.00 0.00 4.40
431 432 5.474876 AGACCCTAATCAAGAAAAGTTGCAG 59.525 40.000 0.00 0.00 0.00 4.41
432 433 5.385198 AGACCCTAATCAAGAAAAGTTGCA 58.615 37.500 0.00 0.00 0.00 4.08
433 434 5.966742 AGACCCTAATCAAGAAAAGTTGC 57.033 39.130 0.00 0.00 0.00 4.17
434 435 9.231297 TGAATAGACCCTAATCAAGAAAAGTTG 57.769 33.333 0.00 0.00 0.00 3.16
435 436 9.232473 GTGAATAGACCCTAATCAAGAAAAGTT 57.768 33.333 0.00 0.00 0.00 2.66
436 437 7.829706 GGTGAATAGACCCTAATCAAGAAAAGT 59.170 37.037 0.00 0.00 0.00 2.66
437 438 8.214721 GGTGAATAGACCCTAATCAAGAAAAG 57.785 38.462 0.00 0.00 0.00 2.27
463 464 3.502356 GAGAAGAGGTGTCTATAGGGGG 58.498 54.545 0.00 0.00 30.45 5.40
464 465 3.150767 CGAGAAGAGGTGTCTATAGGGG 58.849 54.545 0.00 0.00 30.45 4.79
465 466 4.088056 TCGAGAAGAGGTGTCTATAGGG 57.912 50.000 0.00 0.00 30.45 3.53
466 467 4.698304 GGATCGAGAAGAGGTGTCTATAGG 59.302 50.000 0.00 0.00 30.45 2.57
467 468 5.556915 AGGATCGAGAAGAGGTGTCTATAG 58.443 45.833 0.00 0.00 30.45 1.31
468 469 5.570205 AGGATCGAGAAGAGGTGTCTATA 57.430 43.478 0.00 0.00 30.45 1.31
469 470 4.447138 AGGATCGAGAAGAGGTGTCTAT 57.553 45.455 0.00 0.00 30.45 1.98
470 471 3.935818 AGGATCGAGAAGAGGTGTCTA 57.064 47.619 0.00 0.00 30.45 2.59
471 472 2.818751 AGGATCGAGAAGAGGTGTCT 57.181 50.000 0.00 0.00 32.81 3.41
472 473 3.193691 TGAAAGGATCGAGAAGAGGTGTC 59.806 47.826 0.00 0.00 0.00 3.67
473 474 3.165875 TGAAAGGATCGAGAAGAGGTGT 58.834 45.455 0.00 0.00 0.00 4.16
474 475 3.779759 CTGAAAGGATCGAGAAGAGGTG 58.220 50.000 0.00 0.00 0.00 4.00
475 476 2.167487 GCTGAAAGGATCGAGAAGAGGT 59.833 50.000 0.00 0.00 0.00 3.85
476 477 2.430332 AGCTGAAAGGATCGAGAAGAGG 59.570 50.000 0.00 0.00 0.00 3.69
477 478 3.446799 CAGCTGAAAGGATCGAGAAGAG 58.553 50.000 8.42 0.00 0.00 2.85
478 479 2.417924 GCAGCTGAAAGGATCGAGAAGA 60.418 50.000 20.43 0.00 0.00 2.87
479 480 1.932511 GCAGCTGAAAGGATCGAGAAG 59.067 52.381 20.43 0.00 0.00 2.85
480 481 1.406069 GGCAGCTGAAAGGATCGAGAA 60.406 52.381 20.43 0.00 0.00 2.87
481 482 0.176680 GGCAGCTGAAAGGATCGAGA 59.823 55.000 20.43 0.00 0.00 4.04
482 483 0.107993 TGGCAGCTGAAAGGATCGAG 60.108 55.000 20.43 0.00 0.00 4.04
483 484 0.543277 ATGGCAGCTGAAAGGATCGA 59.457 50.000 20.43 0.00 0.00 3.59
484 485 0.661552 CATGGCAGCTGAAAGGATCG 59.338 55.000 20.43 0.00 0.00 3.69
485 486 0.384669 GCATGGCAGCTGAAAGGATC 59.615 55.000 20.43 0.00 0.00 3.36
486 487 0.323999 TGCATGGCAGCTGAAAGGAT 60.324 50.000 20.43 0.00 33.32 3.24
487 488 0.323999 ATGCATGGCAGCTGAAAGGA 60.324 50.000 20.43 5.17 43.65 3.36
488 489 0.179111 CATGCATGGCAGCTGAAAGG 60.179 55.000 20.43 7.16 43.65 3.11
489 490 0.806102 GCATGCATGGCAGCTGAAAG 60.806 55.000 27.34 4.64 43.65 2.62
490 491 1.216977 GCATGCATGGCAGCTGAAA 59.783 52.632 27.34 4.25 43.65 2.69
491 492 2.889617 GCATGCATGGCAGCTGAA 59.110 55.556 27.34 4.69 43.65 3.02
492 493 3.514362 CGCATGCATGGCAGCTGA 61.514 61.111 27.34 0.00 43.65 4.26
493 494 3.822192 ACGCATGCATGGCAGCTG 61.822 61.111 27.34 10.11 43.65 4.24
494 495 3.822192 CACGCATGCATGGCAGCT 61.822 61.111 27.34 1.40 43.65 4.24
677 704 0.320374 GTCATCGGTCAGGTCAACCA 59.680 55.000 1.33 0.00 36.53 3.67
686 714 0.464036 GCCCTATGTGTCATCGGTCA 59.536 55.000 0.00 0.00 0.00 4.02
741 769 1.006571 AGTGTACACGCGTGGGAAG 60.007 57.895 39.21 17.81 36.20 3.46
950 981 2.668632 CCCGGTGTACTGCATGGT 59.331 61.111 0.00 0.00 0.00 3.55
1016 1056 1.511464 GTGCTCTCGACGTACACCG 60.511 63.158 0.00 0.00 44.03 4.94
1049 1089 1.566298 GCCCCTCCACCTTGACATCT 61.566 60.000 0.00 0.00 0.00 2.90
1171 1213 0.630673 TGGGCAAGGATAGCAACCAT 59.369 50.000 0.00 0.00 0.00 3.55
1210 1252 2.783288 GGCCGAGGAGGTAGAACGG 61.783 68.421 0.00 0.00 45.26 4.44
1351 1393 1.846712 GCCCTTCACTGCTCCTCCTT 61.847 60.000 0.00 0.00 0.00 3.36
1352 1394 2.297129 GCCCTTCACTGCTCCTCCT 61.297 63.158 0.00 0.00 0.00 3.69
1907 2101 1.281867 CAACTTGGCCATCCTGACCTA 59.718 52.381 6.09 0.00 0.00 3.08
1914 2108 1.064463 TCTCCATCAACTTGGCCATCC 60.064 52.381 6.09 0.00 36.66 3.51
1923 2117 3.245052 CCAAGAAAGGGTCTCCATCAACT 60.245 47.826 0.00 0.00 34.56 3.16
1935 2129 7.151976 CCTTATGTTGTTAAACCAAGAAAGGG 58.848 38.462 0.00 0.00 35.25 3.95
1938 2132 7.113658 TGCCTTATGTTGTTAAACCAAGAAA 57.886 32.000 0.00 0.00 35.25 2.52
2109 2309 2.283101 AACGCCCACCACATGCAT 60.283 55.556 0.00 0.00 0.00 3.96
2110 2310 2.983030 GAACGCCCACCACATGCA 60.983 61.111 0.00 0.00 0.00 3.96
2132 2332 1.489481 CAGTGGATGCTCTACCCTGA 58.511 55.000 0.00 0.00 31.20 3.86
2329 2529 1.410004 TAGGAGTGGGGATGCTTACG 58.590 55.000 0.00 0.00 0.00 3.18
2336 2536 3.734344 AGGAAGATTAGGAGTGGGGAT 57.266 47.619 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.