Multiple sequence alignment - TraesCS3B01G458700

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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 TraesCS3B01G458700 chr3B 100.000 2439 0 0 1 2439 701413640 701411202 0.000000e+00 4505
1 TraesCS3B01G458700 chr3B 94.595 74 2 2 149 221 701413428 701413356 1.980000e-21 113
2 TraesCS3B01G458700 chr3B 94.595 74 2 2 213 285 701413492 701413420 1.980000e-21 113
3 TraesCS3B01G458700 chr3D 86.694 2202 130 71 213 2309 531051339 531049196 0.000000e+00 2292
4 TraesCS3B01G458700 chr3D 97.409 193 4 1 1 193 531051487 531051296 6.500000e-86 327
5 TraesCS3B01G458700 chr3D 89.773 88 8 1 2305 2392 76229514 76229428 7.130000e-21 111
6 TraesCS3B01G458700 chr3A 89.283 1605 75 36 771 2303 664690661 664689082 0.000000e+00 1921
7 TraesCS3B01G458700 chr3A 85.417 432 33 13 213 635 664691355 664690945 2.900000e-114 422
8 TraesCS3B01G458700 chr3A 91.593 226 12 7 1 221 664691504 664691281 3.050000e-79 305
9 TraesCS3B01G458700 chr4B 95.402 87 4 0 2306 2392 97072392 97072306 3.270000e-29 139
10 TraesCS3B01G458700 chr4B 91.765 85 7 0 2308 2392 657004655 657004739 4.260000e-23 119
11 TraesCS3B01G458700 chr6B 93.023 86 6 0 2307 2392 412149449 412149364 2.550000e-25 126
12 TraesCS3B01G458700 chr6B 90.217 92 7 1 2301 2392 347591188 347591277 4.260000e-23 119
13 TraesCS3B01G458700 chr6D 89.773 88 9 0 2305 2392 424720011 424719924 1.980000e-21 113
14 TraesCS3B01G458700 chr5B 90.588 85 8 0 2308 2392 535055271 535055355 1.980000e-21 113
15 TraesCS3B01G458700 chr4D 90.588 85 8 0 2308 2392 266952288 266952372 1.980000e-21 113
16 TraesCS3B01G458700 chr2A 89.130 92 8 2 2300 2391 156368672 156368761 1.980000e-21 113


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 TraesCS3B01G458700 chr3B 701411202 701413640 2438 True 1577.000000 4505 96.396667 1 2439 3 chr3B.!!$R1 2438
1 TraesCS3B01G458700 chr3D 531049196 531051487 2291 True 1309.500000 2292 92.051500 1 2309 2 chr3D.!!$R2 2308
2 TraesCS3B01G458700 chr3A 664689082 664691504 2422 True 882.666667 1921 88.764333 1 2303 3 chr3A.!!$R1 2302

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
249 251 0.030908 GATCGTCGGTCTCATCCACC 59.969 60.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 1664 1.293924 CCTCATTCATCACACTCGGC 58.706 55.0 0.0 0.0 0.0 5.54 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
43 45 2.225596 CCCCCAACGACCCAGGTTA 61.226 63.158 0.00 0.00 0.00 2.85
48 50 1.201414 CCAACGACCCAGGTTAAATGC 59.799 52.381 0.00 0.00 0.00 3.56
175 177 0.040870 CTCCATCTCACGATCGTCGG 60.041 60.000 19.84 13.85 45.59 4.79
193 195 1.827969 CGGTCTCATCCACCTTCTCTT 59.172 52.381 0.00 0.00 0.00 2.85
195 197 3.307059 CGGTCTCATCCACCTTCTCTTTT 60.307 47.826 0.00 0.00 0.00 2.27
196 198 4.006319 GGTCTCATCCACCTTCTCTTTTG 58.994 47.826 0.00 0.00 0.00 2.44
198 200 5.280011 GGTCTCATCCACCTTCTCTTTTGTA 60.280 44.000 0.00 0.00 0.00 2.41
199 201 6.231211 GTCTCATCCACCTTCTCTTTTGTAA 58.769 40.000 0.00 0.00 0.00 2.41
206 208 7.893658 TCCACCTTCTCTTTTGTAAGTAGTAG 58.106 38.462 0.00 0.00 32.98 2.57
211 213 7.329717 CCTTCTCTTTTGTAAGTAGTAGCAGTG 59.670 40.741 0.00 0.00 32.98 3.66
212 214 6.688578 TCTCTTTTGTAAGTAGTAGCAGTGG 58.311 40.000 0.00 0.00 32.98 4.00
213 215 6.492429 TCTCTTTTGTAAGTAGTAGCAGTGGA 59.508 38.462 0.00 0.00 32.98 4.02
214 216 7.014905 TCTCTTTTGTAAGTAGTAGCAGTGGAA 59.985 37.037 0.00 0.00 32.98 3.53
215 217 7.676947 TCTTTTGTAAGTAGTAGCAGTGGAAT 58.323 34.615 0.00 0.00 32.98 3.01
216 218 7.817962 TCTTTTGTAAGTAGTAGCAGTGGAATC 59.182 37.037 0.00 0.00 32.98 2.52
217 219 5.244785 TGTAAGTAGTAGCAGTGGAATCG 57.755 43.478 0.00 0.00 0.00 3.34
218 220 2.873133 AGTAGTAGCAGTGGAATCGC 57.127 50.000 0.00 0.00 0.00 4.58
219 221 1.409427 AGTAGTAGCAGTGGAATCGCC 59.591 52.381 0.00 0.00 37.10 5.54
220 222 1.409427 GTAGTAGCAGTGGAATCGCCT 59.591 52.381 0.00 0.00 37.63 5.52
221 223 0.461961 AGTAGCAGTGGAATCGCCTC 59.538 55.000 0.00 0.00 37.63 4.70
222 224 0.530870 GTAGCAGTGGAATCGCCTCC 60.531 60.000 0.00 0.00 37.63 4.30
223 225 0.975556 TAGCAGTGGAATCGCCTCCA 60.976 55.000 1.49 1.49 43.45 3.86
228 230 2.914908 TGGAATCGCCTCCATCTCA 58.085 52.632 1.49 0.00 40.71 3.27
229 231 0.465705 TGGAATCGCCTCCATCTCAC 59.534 55.000 1.49 0.00 40.71 3.51
230 232 0.598680 GGAATCGCCTCCATCTCACG 60.599 60.000 0.00 0.00 35.36 4.35
231 233 0.385751 GAATCGCCTCCATCTCACGA 59.614 55.000 0.00 0.00 37.15 4.35
232 234 1.000283 GAATCGCCTCCATCTCACGAT 60.000 52.381 0.00 0.00 44.68 3.73
233 235 0.600557 ATCGCCTCCATCTCACGATC 59.399 55.000 0.00 0.00 39.06 3.69
234 236 1.371022 CGCCTCCATCTCACGATCG 60.371 63.158 14.88 14.88 0.00 3.69
235 237 1.736586 GCCTCCATCTCACGATCGT 59.263 57.895 16.60 16.60 0.00 3.73
236 238 0.318275 GCCTCCATCTCACGATCGTC 60.318 60.000 19.84 0.00 0.00 4.20
237 239 0.040870 CCTCCATCTCACGATCGTCG 60.041 60.000 19.84 14.06 46.93 5.12
238 240 0.040870 CTCCATCTCACGATCGTCGG 60.041 60.000 19.84 13.85 45.59 4.79
239 241 0.746923 TCCATCTCACGATCGTCGGT 60.747 55.000 19.84 5.85 45.59 4.69
240 242 0.317103 CCATCTCACGATCGTCGGTC 60.317 60.000 19.84 0.00 45.59 4.79
241 243 0.658368 CATCTCACGATCGTCGGTCT 59.342 55.000 19.84 0.00 45.59 3.85
242 244 0.938713 ATCTCACGATCGTCGGTCTC 59.061 55.000 19.84 0.00 45.59 3.36
243 245 0.390735 TCTCACGATCGTCGGTCTCA 60.391 55.000 19.84 0.00 45.59 3.27
244 246 0.658368 CTCACGATCGTCGGTCTCAT 59.342 55.000 19.84 0.00 45.59 2.90
245 247 0.656259 TCACGATCGTCGGTCTCATC 59.344 55.000 19.84 0.00 45.59 2.92
246 248 0.317103 CACGATCGTCGGTCTCATCC 60.317 60.000 19.84 0.00 45.59 3.51
247 249 0.746923 ACGATCGTCGGTCTCATCCA 60.747 55.000 16.60 0.00 45.59 3.41
248 250 0.317103 CGATCGTCGGTCTCATCCAC 60.317 60.000 7.03 0.00 36.00 4.02
249 251 0.030908 GATCGTCGGTCTCATCCACC 59.969 60.000 0.00 0.00 0.00 4.61
250 252 0.395862 ATCGTCGGTCTCATCCACCT 60.396 55.000 0.00 0.00 0.00 4.00
251 253 0.611062 TCGTCGGTCTCATCCACCTT 60.611 55.000 0.00 0.00 0.00 3.50
252 254 0.179134 CGTCGGTCTCATCCACCTTC 60.179 60.000 0.00 0.00 0.00 3.46
253 255 0.179134 GTCGGTCTCATCCACCTTCG 60.179 60.000 0.00 0.00 0.00 3.79
254 256 1.519455 CGGTCTCATCCACCTTCGC 60.519 63.158 0.00 0.00 0.00 4.70
255 257 1.901085 GGTCTCATCCACCTTCGCT 59.099 57.895 0.00 0.00 0.00 4.93
256 258 0.250513 GGTCTCATCCACCTTCGCTT 59.749 55.000 0.00 0.00 0.00 4.68
257 259 1.339151 GGTCTCATCCACCTTCGCTTT 60.339 52.381 0.00 0.00 0.00 3.51
258 260 2.427506 GTCTCATCCACCTTCGCTTTT 58.572 47.619 0.00 0.00 0.00 2.27
259 261 2.160417 GTCTCATCCACCTTCGCTTTTG 59.840 50.000 0.00 0.00 0.00 2.44
260 262 2.154462 CTCATCCACCTTCGCTTTTGT 58.846 47.619 0.00 0.00 0.00 2.83
261 263 3.007506 TCTCATCCACCTTCGCTTTTGTA 59.992 43.478 0.00 0.00 0.00 2.41
262 264 3.745799 TCATCCACCTTCGCTTTTGTAA 58.254 40.909 0.00 0.00 0.00 2.41
263 265 3.751175 TCATCCACCTTCGCTTTTGTAAG 59.249 43.478 0.00 0.00 34.36 2.34
264 266 3.202829 TCCACCTTCGCTTTTGTAAGT 57.797 42.857 0.00 0.00 33.74 2.24
265 267 4.339872 TCCACCTTCGCTTTTGTAAGTA 57.660 40.909 0.00 0.00 33.74 2.24
266 268 4.312443 TCCACCTTCGCTTTTGTAAGTAG 58.688 43.478 0.00 0.00 33.74 2.57
267 269 4.062991 CCACCTTCGCTTTTGTAAGTAGT 58.937 43.478 0.00 0.00 33.74 2.73
268 270 5.010922 TCCACCTTCGCTTTTGTAAGTAGTA 59.989 40.000 0.00 0.00 33.74 1.82
269 271 5.347907 CCACCTTCGCTTTTGTAAGTAGTAG 59.652 44.000 0.00 0.00 33.74 2.57
270 272 4.928020 ACCTTCGCTTTTGTAAGTAGTAGC 59.072 41.667 0.00 0.00 33.74 3.58
271 273 4.927425 CCTTCGCTTTTGTAAGTAGTAGCA 59.073 41.667 0.00 0.00 33.74 3.49
292 294 4.369182 CAGTGGAATCGTCCTAACCATAC 58.631 47.826 0.00 0.00 45.22 2.39
325 327 1.192980 CAAAGCTGCCGCACAAATTTC 59.807 47.619 2.05 0.00 39.10 2.17
341 343 7.095899 GCACAAATTTCATTCTTCTTCTTGACC 60.096 37.037 0.00 0.00 0.00 4.02
350 352 6.433847 TTCTTCTTCTTGACCCTTGTGATA 57.566 37.500 0.00 0.00 0.00 2.15
356 358 7.050377 TCTTCTTGACCCTTGTGATAATGATC 58.950 38.462 0.00 0.00 0.00 2.92
357 359 6.566079 TCTTGACCCTTGTGATAATGATCT 57.434 37.500 0.00 0.00 32.79 2.75
358 360 7.675161 TCTTGACCCTTGTGATAATGATCTA 57.325 36.000 0.00 0.00 32.79 1.98
385 388 9.268268 CTAGACAGTACTACAATTTTCCAAACA 57.732 33.333 0.00 0.00 0.00 2.83
394 397 5.359756 ACAATTTTCCAAACAGAAGAAGCC 58.640 37.500 0.00 0.00 0.00 4.35
404 407 7.233348 TCCAAACAGAAGAAGCCTGATTTTTAT 59.767 33.333 0.00 0.00 35.69 1.40
426 429 0.531532 CCTGACTGATGATCCGGTGC 60.532 60.000 0.00 0.00 0.00 5.01
432 435 3.809374 GATGATCCGGTGCCCGTCC 62.809 68.421 0.00 2.70 46.80 4.79
485 488 2.479566 TTGTCCTAGGCTCTTGCAAG 57.520 50.000 20.81 20.81 41.91 4.01
486 489 1.644509 TGTCCTAGGCTCTTGCAAGA 58.355 50.000 26.87 26.87 41.91 3.02
487 490 2.191400 TGTCCTAGGCTCTTGCAAGAT 58.809 47.619 28.57 16.99 41.91 2.40
488 491 2.169352 TGTCCTAGGCTCTTGCAAGATC 59.831 50.000 28.57 23.91 41.91 2.75
597 604 3.141767 TCGTCCACATCGAGATCCTAT 57.858 47.619 0.00 0.00 33.38 2.57
635 642 4.645535 TCAGGAGCAATTATCATAGGCAC 58.354 43.478 0.00 0.00 0.00 5.01
636 643 4.349048 TCAGGAGCAATTATCATAGGCACT 59.651 41.667 0.00 0.00 46.37 4.40
637 644 4.694509 CAGGAGCAATTATCATAGGCACTC 59.305 45.833 0.00 0.00 41.75 3.51
666 687 1.472276 GAGTGAGTATGAACGCGCCG 61.472 60.000 5.73 0.00 36.68 6.46
674 695 3.824510 GAACGCGCCGAAGTCGAC 61.825 66.667 7.70 7.70 43.02 4.20
702 723 1.209127 GTGATTTCAACACGGGCCG 59.791 57.895 27.06 27.06 0.00 6.13
703 724 1.969064 TGATTTCAACACGGGCCGG 60.969 57.895 31.78 21.03 0.00 6.13
704 725 3.336715 GATTTCAACACGGGCCGGC 62.337 63.158 31.78 21.18 0.00 6.13
705 726 4.877619 TTTCAACACGGGCCGGCA 62.878 61.111 31.78 0.51 0.00 5.69
736 757 8.978539 CACATCATGTGCGTATTATTTACTACT 58.021 33.333 4.43 0.00 41.89 2.57
737 758 8.978539 ACATCATGTGCGTATTATTTACTACTG 58.021 33.333 0.00 0.00 0.00 2.74
744 913 5.116680 GCGTATTATTTACTACTGCCACTCG 59.883 44.000 0.00 0.00 0.00 4.18
750 919 2.614829 ACTACTGCCACTCGTGTTTT 57.385 45.000 0.00 0.00 0.00 2.43
755 933 1.798813 CTGCCACTCGTGTTTTCTACC 59.201 52.381 0.00 0.00 0.00 3.18
765 943 1.414919 TGTTTTCTACCAGCGTCCACT 59.585 47.619 0.00 0.00 0.00 4.00
1035 1235 0.107752 CCAAGCTGCTCTTCCTCCTC 60.108 60.000 1.00 0.00 31.27 3.71
1093 1296 3.369997 GGTAAGCCTTCCTCTTCCTCTTG 60.370 52.174 0.00 0.00 0.00 3.02
1134 1345 2.036256 GGCCCTGACATTGCCTGT 59.964 61.111 7.87 0.00 42.01 4.00
1411 1628 2.525629 TCCTTCACGCCCAGGTCA 60.526 61.111 0.00 0.00 0.00 4.02
1447 1664 1.624865 GCAACGTCTGAGCTCTGCTG 61.625 60.000 16.19 12.06 39.88 4.41
1449 1666 2.508887 CGTCTGAGCTCTGCTGCC 60.509 66.667 16.19 2.80 39.88 4.85
1451 1668 2.677875 TCTGAGCTCTGCTGCCGA 60.678 61.111 16.19 0.00 39.88 5.54
1452 1669 2.202770 CTGAGCTCTGCTGCCGAG 60.203 66.667 16.19 15.65 39.88 4.63
1453 1670 2.993840 TGAGCTCTGCTGCCGAGT 60.994 61.111 19.90 8.86 39.88 4.18
1454 1671 2.508887 GAGCTCTGCTGCCGAGTG 60.509 66.667 19.90 4.17 39.88 3.51
1455 1672 3.293901 GAGCTCTGCTGCCGAGTGT 62.294 63.158 19.90 9.69 39.88 3.55
1456 1673 3.117171 GCTCTGCTGCCGAGTGTG 61.117 66.667 19.90 0.00 0.00 3.82
1457 1674 2.653115 CTCTGCTGCCGAGTGTGA 59.347 61.111 12.29 0.00 0.00 3.58
1458 1675 1.217511 CTCTGCTGCCGAGTGTGAT 59.782 57.895 12.29 0.00 0.00 3.06
1459 1676 1.079612 TCTGCTGCCGAGTGTGATG 60.080 57.895 0.00 0.00 0.00 3.07
1460 1677 1.079612 CTGCTGCCGAGTGTGATGA 60.080 57.895 0.00 0.00 0.00 2.92
1468 1700 1.208052 CCGAGTGTGATGAATGAGGGT 59.792 52.381 0.00 0.00 0.00 4.34
1478 1710 6.115446 GTGATGAATGAGGGTAATGTTGAGA 58.885 40.000 0.00 0.00 0.00 3.27
1502 1741 9.339850 AGAGCGATAGTAAGTATTTTAGAGTGA 57.660 33.333 0.00 0.00 39.35 3.41
1670 1914 6.969993 TTGGTTGGTTATTAGCAAAGAGTT 57.030 33.333 0.00 0.00 42.84 3.01
1676 1920 6.065374 TGGTTATTAGCAAAGAGTTGGTGAA 58.935 36.000 1.59 0.00 44.96 3.18
1707 1978 1.980765 TGCTCTGTTTCCTCTCATGGT 59.019 47.619 0.00 0.00 0.00 3.55
1739 2010 2.860735 GTCGCGTGCTTTCTCTTGATAT 59.139 45.455 5.77 0.00 0.00 1.63
1775 2046 1.841450 CGCGGAGATTCAGTACCTTC 58.159 55.000 0.00 0.00 0.00 3.46
1781 2052 4.404715 CGGAGATTCAGTACCTTCCCTTTA 59.595 45.833 0.00 0.00 0.00 1.85
1788 2059 5.497474 TCAGTACCTTCCCTTTAAATGCTC 58.503 41.667 0.00 0.00 0.00 4.26
1793 2064 3.626217 CCTTCCCTTTAAATGCTCGGTAC 59.374 47.826 0.00 0.00 0.00 3.34
1806 2082 2.438411 CTCGGTACCTCTTGTGTCTCT 58.562 52.381 10.90 0.00 0.00 3.10
1811 2087 5.129980 TCGGTACCTCTTGTGTCTCTATCTA 59.870 44.000 10.90 0.00 0.00 1.98
1818 2094 7.400339 ACCTCTTGTGTCTCTATCTATTTCCAA 59.600 37.037 0.00 0.00 0.00 3.53
1846 2122 3.214328 AGTAAAACTGAACTGCACAGGG 58.786 45.455 7.62 0.00 39.38 4.45
1870 2146 5.048434 GCATTTAGAAGGCTGTGTTCTTCTT 60.048 40.000 10.28 0.00 45.01 2.52
1871 2147 6.606768 CATTTAGAAGGCTGTGTTCTTCTTC 58.393 40.000 10.28 0.00 45.01 2.87
1872 2148 5.552870 TTAGAAGGCTGTGTTCTTCTTCT 57.447 39.130 10.28 0.00 45.01 2.85
1873 2149 4.429854 AGAAGGCTGTGTTCTTCTTCTT 57.570 40.909 0.00 0.00 45.01 2.52
1874 2150 4.384940 AGAAGGCTGTGTTCTTCTTCTTC 58.615 43.478 0.00 0.00 45.01 2.87
1875 2151 4.102367 AGAAGGCTGTGTTCTTCTTCTTCT 59.898 41.667 0.00 0.00 45.01 2.85
1876 2152 4.429854 AGGCTGTGTTCTTCTTCTTCTT 57.570 40.909 0.00 0.00 0.00 2.52
1877 2153 4.384940 AGGCTGTGTTCTTCTTCTTCTTC 58.615 43.478 0.00 0.00 0.00 2.87
1912 2188 7.121759 ACCATTTATACATGCCTGCAGATATTC 59.878 37.037 17.39 0.00 0.00 1.75
1982 2264 4.404073 TCCTCTTAGCACCTTCTGAAGATC 59.596 45.833 18.68 7.11 0.00 2.75
2133 2426 4.067896 ACACATTGTCTGCTCCTTTACTG 58.932 43.478 0.00 0.00 0.00 2.74
2191 2484 3.711190 TGAATTCAGTAGGCAGCATCCTA 59.289 43.478 3.38 0.38 37.66 2.94
2233 2526 6.265422 AGCCTTGCAGTTGTTTTAATAGAACT 59.735 34.615 3.13 3.13 0.00 3.01
2260 2556 5.410067 AGTTTTCATGACAAACACTGGTTG 58.590 37.500 23.38 5.20 37.30 3.77
2310 2606 9.587772 CTGCACACAGTTTAGTTATTATCTACT 57.412 33.333 0.00 0.00 39.22 2.57
2311 2607 9.582431 TGCACACAGTTTAGTTATTATCTACTC 57.418 33.333 0.00 0.00 0.00 2.59
2312 2608 9.032420 GCACACAGTTTAGTTATTATCTACTCC 57.968 37.037 0.00 0.00 0.00 3.85
2313 2609 9.530633 CACACAGTTTAGTTATTATCTACTCCC 57.469 37.037 0.00 0.00 0.00 4.30
2314 2610 9.490083 ACACAGTTTAGTTATTATCTACTCCCT 57.510 33.333 0.00 0.00 0.00 4.20
2315 2611 9.968870 CACAGTTTAGTTATTATCTACTCCCTC 57.031 37.037 0.00 0.00 0.00 4.30
2316 2612 9.939424 ACAGTTTAGTTATTATCTACTCCCTCT 57.061 33.333 0.00 0.00 0.00 3.69
2318 2614 9.939424 AGTTTAGTTATTATCTACTCCCTCTGT 57.061 33.333 0.00 0.00 0.00 3.41
2320 2616 8.937207 TTAGTTATTATCTACTCCCTCTGTCC 57.063 38.462 0.00 0.00 0.00 4.02
2321 2617 6.316513 AGTTATTATCTACTCCCTCTGTCCC 58.683 44.000 0.00 0.00 0.00 4.46
2322 2618 4.834406 ATTATCTACTCCCTCTGTCCCA 57.166 45.455 0.00 0.00 0.00 4.37
2323 2619 4.620086 TTATCTACTCCCTCTGTCCCAA 57.380 45.455 0.00 0.00 0.00 4.12
2324 2620 3.491766 ATCTACTCCCTCTGTCCCAAA 57.508 47.619 0.00 0.00 0.00 3.28
2325 2621 3.269592 TCTACTCCCTCTGTCCCAAAA 57.730 47.619 0.00 0.00 0.00 2.44
2326 2622 3.803340 TCTACTCCCTCTGTCCCAAAAT 58.197 45.455 0.00 0.00 0.00 1.82
2327 2623 4.955335 TCTACTCCCTCTGTCCCAAAATA 58.045 43.478 0.00 0.00 0.00 1.40
2328 2624 5.538877 TCTACTCCCTCTGTCCCAAAATAT 58.461 41.667 0.00 0.00 0.00 1.28
2329 2625 6.689561 TCTACTCCCTCTGTCCCAAAATATA 58.310 40.000 0.00 0.00 0.00 0.86
2330 2626 7.136885 TCTACTCCCTCTGTCCCAAAATATAA 58.863 38.462 0.00 0.00 0.00 0.98
2331 2627 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
2332 2628 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
2333 2629 6.126739 ACTCCCTCTGTCCCAAAATATAAGAC 60.127 42.308 0.00 0.00 0.00 3.01
2334 2630 5.729229 TCCCTCTGTCCCAAAATATAAGACA 59.271 40.000 0.00 0.00 36.16 3.41
2335 2631 5.823045 CCCTCTGTCCCAAAATATAAGACAC 59.177 44.000 0.00 0.00 34.03 3.67
2336 2632 6.353082 CCCTCTGTCCCAAAATATAAGACACT 60.353 42.308 0.00 0.00 34.03 3.55
2337 2633 7.112779 CCTCTGTCCCAAAATATAAGACACTT 58.887 38.462 0.00 0.00 34.03 3.16
2338 2634 7.611855 CCTCTGTCCCAAAATATAAGACACTTT 59.388 37.037 0.00 0.00 34.03 2.66
2339 2635 8.934023 TCTGTCCCAAAATATAAGACACTTTT 57.066 30.769 0.00 0.00 34.03 2.27
2340 2636 9.362151 TCTGTCCCAAAATATAAGACACTTTTT 57.638 29.630 0.00 0.00 34.03 1.94
2341 2637 9.410556 CTGTCCCAAAATATAAGACACTTTTTG 57.589 33.333 0.00 0.00 37.14 2.44
2342 2638 9.137459 TGTCCCAAAATATAAGACACTTTTTGA 57.863 29.630 7.74 0.00 38.79 2.69
2345 2641 8.872845 CCCAAAATATAAGACACTTTTTGATGC 58.127 33.333 7.74 0.00 38.79 3.91
2346 2642 9.643693 CCAAAATATAAGACACTTTTTGATGCT 57.356 29.630 7.74 0.00 38.79 3.79
2352 2648 6.882610 AAGACACTTTTTGATGCTATCACA 57.117 33.333 0.00 0.00 39.39 3.58
2353 2649 6.492007 AGACACTTTTTGATGCTATCACAG 57.508 37.500 0.00 0.00 39.39 3.66
2354 2650 6.000219 AGACACTTTTTGATGCTATCACAGT 59.000 36.000 0.00 0.00 39.39 3.55
2355 2651 6.148480 AGACACTTTTTGATGCTATCACAGTC 59.852 38.462 0.00 0.00 39.39 3.51
2356 2652 6.000219 ACACTTTTTGATGCTATCACAGTCT 59.000 36.000 0.00 0.00 39.39 3.24
2357 2653 6.148480 ACACTTTTTGATGCTATCACAGTCTC 59.852 38.462 0.00 0.00 39.39 3.36
2358 2654 6.148315 CACTTTTTGATGCTATCACAGTCTCA 59.852 38.462 0.00 0.00 39.39 3.27
2359 2655 6.712095 ACTTTTTGATGCTATCACAGTCTCAA 59.288 34.615 0.00 0.00 39.39 3.02
2360 2656 7.229306 ACTTTTTGATGCTATCACAGTCTCAAA 59.771 33.333 0.00 0.00 39.39 2.69
2361 2657 7.509141 TTTTGATGCTATCACAGTCTCAAAA 57.491 32.000 0.00 0.00 40.51 2.44
2362 2658 7.509141 TTTGATGCTATCACAGTCTCAAAAA 57.491 32.000 0.00 0.00 39.39 1.94
2381 2677 4.737353 AAAACGTCTTACATTTCGGGAC 57.263 40.909 0.00 0.00 0.00 4.46
2395 2691 3.294904 GGGACGGAGGGAGTAAAGA 57.705 57.895 0.00 0.00 0.00 2.52
2396 2692 1.565067 GGGACGGAGGGAGTAAAGAA 58.435 55.000 0.00 0.00 0.00 2.52
2397 2693 1.206610 GGGACGGAGGGAGTAAAGAAC 59.793 57.143 0.00 0.00 0.00 3.01
2398 2694 1.897802 GGACGGAGGGAGTAAAGAACA 59.102 52.381 0.00 0.00 0.00 3.18
2399 2695 2.353505 GGACGGAGGGAGTAAAGAACAC 60.354 54.545 0.00 0.00 0.00 3.32
2400 2696 1.271656 ACGGAGGGAGTAAAGAACACG 59.728 52.381 0.00 0.00 0.00 4.49
2401 2697 1.723220 GGAGGGAGTAAAGAACACGC 58.277 55.000 0.00 0.00 32.79 5.34
2402 2698 1.275573 GGAGGGAGTAAAGAACACGCT 59.724 52.381 0.00 0.00 43.09 5.07
2403 2699 2.494870 GGAGGGAGTAAAGAACACGCTA 59.505 50.000 0.00 0.00 41.04 4.26
2404 2700 3.132467 GGAGGGAGTAAAGAACACGCTAT 59.868 47.826 0.00 0.00 41.04 2.97
2405 2701 4.382793 GGAGGGAGTAAAGAACACGCTATT 60.383 45.833 0.00 0.00 41.04 1.73
2406 2702 5.161943 AGGGAGTAAAGAACACGCTATTT 57.838 39.130 0.00 0.00 39.59 1.40
2407 2703 5.176592 AGGGAGTAAAGAACACGCTATTTC 58.823 41.667 0.00 0.00 39.59 2.17
2408 2704 4.933400 GGGAGTAAAGAACACGCTATTTCA 59.067 41.667 0.00 0.00 0.00 2.69
2409 2705 5.163884 GGGAGTAAAGAACACGCTATTTCAC 60.164 44.000 0.00 0.00 0.00 3.18
2410 2706 5.638234 GGAGTAAAGAACACGCTATTTCACT 59.362 40.000 0.00 0.00 0.00 3.41
2411 2707 6.810182 GGAGTAAAGAACACGCTATTTCACTA 59.190 38.462 0.00 0.00 0.00 2.74
2412 2708 7.330208 GGAGTAAAGAACACGCTATTTCACTAA 59.670 37.037 0.00 0.00 0.00 2.24
2413 2709 8.015409 AGTAAAGAACACGCTATTTCACTAAC 57.985 34.615 0.00 0.00 0.00 2.34
2414 2710 7.871463 AGTAAAGAACACGCTATTTCACTAACT 59.129 33.333 0.00 0.00 0.00 2.24
2415 2711 7.492352 AAAGAACACGCTATTTCACTAACTT 57.508 32.000 0.00 0.00 0.00 2.66
2416 2712 8.597662 AAAGAACACGCTATTTCACTAACTTA 57.402 30.769 0.00 0.00 0.00 2.24
2417 2713 8.773404 AAGAACACGCTATTTCACTAACTTAT 57.227 30.769 0.00 0.00 0.00 1.73
2418 2714 9.865321 AAGAACACGCTATTTCACTAACTTATA 57.135 29.630 0.00 0.00 0.00 0.98
2419 2715 9.517609 AGAACACGCTATTTCACTAACTTATAG 57.482 33.333 0.00 0.00 0.00 1.31
2420 2716 9.298774 GAACACGCTATTTCACTAACTTATAGT 57.701 33.333 0.00 0.00 0.00 2.12
2421 2717 9.649167 AACACGCTATTTCACTAACTTATAGTT 57.351 29.630 0.00 0.00 41.97 2.24
2422 2718 9.649167 ACACGCTATTTCACTAACTTATAGTTT 57.351 29.630 0.00 0.00 39.51 2.66
2424 2720 9.865321 ACGCTATTTCACTAACTTATAGTTTCA 57.135 29.630 0.00 0.00 39.51 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
175 177 4.646572 ACAAAAGAGAAGGTGGATGAGAC 58.353 43.478 0.00 0.00 0.00 3.36
193 195 6.097356 CGATTCCACTGCTACTACTTACAAA 58.903 40.000 0.00 0.00 0.00 2.83
195 197 4.439700 GCGATTCCACTGCTACTACTTACA 60.440 45.833 0.00 0.00 0.00 2.41
196 198 4.043073 GCGATTCCACTGCTACTACTTAC 58.957 47.826 0.00 0.00 0.00 2.34
198 200 2.159085 GGCGATTCCACTGCTACTACTT 60.159 50.000 0.00 0.00 34.01 2.24
199 201 1.409427 GGCGATTCCACTGCTACTACT 59.591 52.381 0.00 0.00 34.01 2.57
206 208 2.268920 TGGAGGCGATTCCACTGC 59.731 61.111 4.39 0.00 42.24 4.40
211 213 0.598680 CGTGAGATGGAGGCGATTCC 60.599 60.000 0.00 0.00 37.77 3.01
212 214 0.385751 TCGTGAGATGGAGGCGATTC 59.614 55.000 0.00 0.00 33.31 2.52
213 215 2.504920 TCGTGAGATGGAGGCGATT 58.495 52.632 0.00 0.00 33.31 3.34
214 216 4.259952 TCGTGAGATGGAGGCGAT 57.740 55.556 0.00 0.00 33.31 4.58
225 227 0.658368 ATGAGACCGACGATCGTGAG 59.342 55.000 28.12 18.48 38.40 3.51
226 228 0.656259 GATGAGACCGACGATCGTGA 59.344 55.000 28.12 2.25 38.40 4.35
227 229 0.317103 GGATGAGACCGACGATCGTG 60.317 60.000 28.12 15.01 38.40 4.35
228 230 0.746923 TGGATGAGACCGACGATCGT 60.747 55.000 22.97 22.97 38.40 3.73
229 231 0.317103 GTGGATGAGACCGACGATCG 60.317 60.000 14.88 14.88 40.07 3.69
230 232 0.030908 GGTGGATGAGACCGACGATC 59.969 60.000 0.00 0.00 0.00 3.69
231 233 0.395862 AGGTGGATGAGACCGACGAT 60.396 55.000 0.00 0.00 38.64 3.73
232 234 0.611062 AAGGTGGATGAGACCGACGA 60.611 55.000 0.00 0.00 38.64 4.20
233 235 0.179134 GAAGGTGGATGAGACCGACG 60.179 60.000 0.00 0.00 38.64 5.12
234 236 0.179134 CGAAGGTGGATGAGACCGAC 60.179 60.000 0.00 0.00 38.64 4.79
235 237 1.945354 GCGAAGGTGGATGAGACCGA 61.945 60.000 0.00 0.00 38.64 4.69
236 238 1.519455 GCGAAGGTGGATGAGACCG 60.519 63.158 0.00 0.00 38.64 4.79
237 239 0.250513 AAGCGAAGGTGGATGAGACC 59.749 55.000 0.00 0.00 39.47 3.85
238 240 2.100605 AAAGCGAAGGTGGATGAGAC 57.899 50.000 0.00 0.00 39.47 3.36
239 241 2.224523 ACAAAAGCGAAGGTGGATGAGA 60.225 45.455 0.00 0.00 39.47 3.27
240 242 2.154462 ACAAAAGCGAAGGTGGATGAG 58.846 47.619 0.00 0.00 39.47 2.90
241 243 2.270352 ACAAAAGCGAAGGTGGATGA 57.730 45.000 0.00 0.00 39.47 2.92
242 244 3.502211 ACTTACAAAAGCGAAGGTGGATG 59.498 43.478 0.00 0.00 39.47 3.51
243 245 3.751518 ACTTACAAAAGCGAAGGTGGAT 58.248 40.909 0.00 0.00 39.47 3.41
244 246 3.202829 ACTTACAAAAGCGAAGGTGGA 57.797 42.857 0.00 0.00 39.47 4.02
245 247 4.062991 ACTACTTACAAAAGCGAAGGTGG 58.937 43.478 0.00 0.00 39.47 4.61
246 248 5.163982 GCTACTACTTACAAAAGCGAAGGTG 60.164 44.000 0.00 0.00 39.47 4.00
247 249 4.928020 GCTACTACTTACAAAAGCGAAGGT 59.072 41.667 0.00 0.00 44.60 3.50
248 250 4.927425 TGCTACTACTTACAAAAGCGAAGG 59.073 41.667 0.00 0.00 36.05 3.46
249 251 5.634020 ACTGCTACTACTTACAAAAGCGAAG 59.366 40.000 0.00 0.00 36.05 3.79
250 252 5.404366 CACTGCTACTACTTACAAAAGCGAA 59.596 40.000 0.00 0.00 36.05 4.70
251 253 4.921515 CACTGCTACTACTTACAAAAGCGA 59.078 41.667 0.00 0.00 36.05 4.93
252 254 4.091509 CCACTGCTACTACTTACAAAAGCG 59.908 45.833 0.00 0.00 36.05 4.68
253 255 5.235516 TCCACTGCTACTACTTACAAAAGC 58.764 41.667 0.00 0.00 36.05 3.51
254 256 7.201444 CGATTCCACTGCTACTACTTACAAAAG 60.201 40.741 0.00 0.00 38.77 2.27
255 257 6.588756 CGATTCCACTGCTACTACTTACAAAA 59.411 38.462 0.00 0.00 0.00 2.44
256 258 6.097356 CGATTCCACTGCTACTACTTACAAA 58.903 40.000 0.00 0.00 0.00 2.83
257 259 5.184479 ACGATTCCACTGCTACTACTTACAA 59.816 40.000 0.00 0.00 0.00 2.41
258 260 4.703575 ACGATTCCACTGCTACTACTTACA 59.296 41.667 0.00 0.00 0.00 2.41
259 261 5.246145 ACGATTCCACTGCTACTACTTAC 57.754 43.478 0.00 0.00 0.00 2.34
260 262 4.337555 GGACGATTCCACTGCTACTACTTA 59.662 45.833 0.00 0.00 42.30 2.24
261 263 3.130693 GGACGATTCCACTGCTACTACTT 59.869 47.826 0.00 0.00 42.30 2.24
262 264 2.688958 GGACGATTCCACTGCTACTACT 59.311 50.000 0.00 0.00 42.30 2.57
263 265 2.688958 AGGACGATTCCACTGCTACTAC 59.311 50.000 0.00 0.00 45.72 2.73
264 266 3.014304 AGGACGATTCCACTGCTACTA 57.986 47.619 0.00 0.00 45.72 1.82
265 267 1.853963 AGGACGATTCCACTGCTACT 58.146 50.000 0.00 0.00 45.72 2.57
266 268 3.445857 GTTAGGACGATTCCACTGCTAC 58.554 50.000 0.00 0.00 45.72 3.58
267 269 2.429610 GGTTAGGACGATTCCACTGCTA 59.570 50.000 0.00 0.00 45.72 3.49
268 270 1.207329 GGTTAGGACGATTCCACTGCT 59.793 52.381 0.00 0.00 45.72 4.24
269 271 1.066430 TGGTTAGGACGATTCCACTGC 60.066 52.381 0.00 0.00 45.72 4.40
270 272 3.543680 ATGGTTAGGACGATTCCACTG 57.456 47.619 0.00 0.00 45.72 3.66
271 273 3.067742 CGTATGGTTAGGACGATTCCACT 59.932 47.826 0.00 0.00 45.72 4.00
292 294 0.321122 AGCTTTGAGAGGAAGTGCCG 60.321 55.000 0.00 0.00 43.43 5.69
325 327 5.065914 TCACAAGGGTCAAGAAGAAGAATG 58.934 41.667 0.00 0.00 0.00 2.67
341 343 8.855110 ACTGTCTAGTAGATCATTATCACAAGG 58.145 37.037 2.51 0.00 34.74 3.61
358 360 9.269453 GTTTGGAAAATTGTAGTACTGTCTAGT 57.731 33.333 5.39 0.00 40.99 2.57
374 376 4.895297 TCAGGCTTCTTCTGTTTGGAAAAT 59.105 37.500 0.00 0.00 34.15 1.82
376 378 3.897239 TCAGGCTTCTTCTGTTTGGAAA 58.103 40.909 0.00 0.00 34.15 3.13
377 379 3.576078 TCAGGCTTCTTCTGTTTGGAA 57.424 42.857 0.00 0.00 34.15 3.53
378 380 3.795688 ATCAGGCTTCTTCTGTTTGGA 57.204 42.857 0.00 0.00 34.15 3.53
385 388 7.671398 TCAGGAAATAAAAATCAGGCTTCTTCT 59.329 33.333 0.00 0.00 0.00 2.85
394 397 9.947669 GATCATCAGTCAGGAAATAAAAATCAG 57.052 33.333 0.00 0.00 0.00 2.90
404 407 2.093500 CACCGGATCATCAGTCAGGAAA 60.093 50.000 9.46 0.00 35.31 3.13
433 436 2.453379 TTAAACCTGGACGGGCGGAC 62.453 60.000 0.00 0.00 36.97 4.79
438 441 1.877443 CTGTTGTTAAACCTGGACGGG 59.123 52.381 0.00 0.00 35.25 5.28
485 488 4.755411 TGTTTGTTACAGGGAGATCGATC 58.245 43.478 17.91 17.91 31.68 3.69
486 489 4.819105 TGTTTGTTACAGGGAGATCGAT 57.181 40.909 0.00 0.00 31.68 3.59
553 556 1.620589 ATGGGTCACTGGGATGGCT 60.621 57.895 0.00 0.00 0.00 4.75
554 557 1.152881 GATGGGTCACTGGGATGGC 60.153 63.158 0.00 0.00 0.00 4.40
555 558 0.182061 CTGATGGGTCACTGGGATGG 59.818 60.000 0.00 0.00 0.00 3.51
556 559 0.465097 GCTGATGGGTCACTGGGATG 60.465 60.000 0.00 0.00 0.00 3.51
652 669 0.801067 GACTTCGGCGCGTTCATACT 60.801 55.000 8.43 0.00 0.00 2.12
674 695 3.564027 GAAATCACGCGCCCTCCG 61.564 66.667 5.73 0.00 40.75 4.63
677 698 1.599518 TGTTGAAATCACGCGCCCT 60.600 52.632 5.73 0.00 0.00 5.19
685 706 1.969064 CCGGCCCGTGTTGAAATCA 60.969 57.895 0.85 0.00 0.00 2.57
701 722 3.879682 CATGATGTGCCGGTGCCG 61.880 66.667 1.90 3.25 36.33 5.69
702 723 2.751436 ACATGATGTGCCGGTGCC 60.751 61.111 1.90 0.00 36.33 5.01
703 724 2.486504 CACATGATGTGCCGGTGC 59.513 61.111 13.15 0.00 41.89 5.01
734 755 2.480845 GTAGAAAACACGAGTGGCAGT 58.519 47.619 8.19 0.00 34.19 4.40
735 756 1.798813 GGTAGAAAACACGAGTGGCAG 59.201 52.381 8.19 0.00 34.19 4.85
736 757 1.139256 TGGTAGAAAACACGAGTGGCA 59.861 47.619 8.19 0.00 34.19 4.92
737 758 1.798813 CTGGTAGAAAACACGAGTGGC 59.201 52.381 8.19 0.00 34.19 5.01
744 913 1.529865 GTGGACGCTGGTAGAAAACAC 59.470 52.381 0.00 0.00 0.00 3.32
750 919 2.044555 CCGAGTGGACGCTGGTAGA 61.045 63.158 0.00 0.00 37.49 2.59
821 1000 0.659957 GGCTACGGTAGTACACTCGG 59.340 60.000 16.05 0.00 0.00 4.63
823 1002 2.613133 CAGAGGCTACGGTAGTACACTC 59.387 54.545 16.05 16.21 33.84 3.51
824 1003 2.641305 CAGAGGCTACGGTAGTACACT 58.359 52.381 16.05 10.49 0.00 3.55
828 1007 0.549950 AGGCAGAGGCTACGGTAGTA 59.450 55.000 16.05 0.00 40.87 1.82
829 1008 0.324460 AAGGCAGAGGCTACGGTAGT 60.324 55.000 16.05 0.00 37.50 2.73
870 1059 0.976073 ACGGACGACTTGGGATGGAT 60.976 55.000 0.00 0.00 0.00 3.41
916 1115 1.990614 GGTGGGGAGTGAGGTCCTC 60.991 68.421 12.40 12.40 37.64 3.71
1411 1628 2.267006 CAGTGGAGGCAGTCGCAT 59.733 61.111 0.00 0.00 41.24 4.73
1447 1664 1.293924 CCTCATTCATCACACTCGGC 58.706 55.000 0.00 0.00 0.00 5.54
1449 1666 2.680312 ACCCTCATTCATCACACTCG 57.320 50.000 0.00 0.00 0.00 4.18
1451 1668 5.441718 ACATTACCCTCATTCATCACACT 57.558 39.130 0.00 0.00 0.00 3.55
1452 1669 5.647658 TCAACATTACCCTCATTCATCACAC 59.352 40.000 0.00 0.00 0.00 3.82
1453 1670 5.814481 TCAACATTACCCTCATTCATCACA 58.186 37.500 0.00 0.00 0.00 3.58
1454 1671 6.115446 TCTCAACATTACCCTCATTCATCAC 58.885 40.000 0.00 0.00 0.00 3.06
1455 1672 6.312141 TCTCAACATTACCCTCATTCATCA 57.688 37.500 0.00 0.00 0.00 3.07
1456 1673 5.238214 GCTCTCAACATTACCCTCATTCATC 59.762 44.000 0.00 0.00 0.00 2.92
1457 1674 5.128919 GCTCTCAACATTACCCTCATTCAT 58.871 41.667 0.00 0.00 0.00 2.57
1458 1675 4.517285 GCTCTCAACATTACCCTCATTCA 58.483 43.478 0.00 0.00 0.00 2.57
1459 1676 3.557595 CGCTCTCAACATTACCCTCATTC 59.442 47.826 0.00 0.00 0.00 2.67
1460 1677 3.197766 TCGCTCTCAACATTACCCTCATT 59.802 43.478 0.00 0.00 0.00 2.57
1478 1710 9.900710 CATCACTCTAAAATACTTACTATCGCT 57.099 33.333 0.00 0.00 0.00 4.93
1529 1768 1.559682 GTTGGGGGAACTCTCATGCTA 59.440 52.381 0.00 0.00 0.00 3.49
1670 1914 3.084039 GAGCAATGTCTCCAATTCACCA 58.916 45.455 0.00 0.00 0.00 4.17
1676 1920 3.760684 GGAAACAGAGCAATGTCTCCAAT 59.239 43.478 8.40 0.00 39.66 3.16
1739 2010 7.854557 TCTCCGCGCTATTAACTAATCTATA 57.145 36.000 5.56 0.00 0.00 1.31
1756 2027 1.536284 GGAAGGTACTGAATCTCCGCG 60.536 57.143 0.00 0.00 40.86 6.46
1775 2046 3.118371 AGAGGTACCGAGCATTTAAAGGG 60.118 47.826 6.18 0.00 0.00 3.95
1781 2052 2.038557 ACACAAGAGGTACCGAGCATTT 59.961 45.455 6.18 0.00 0.00 2.32
1788 2059 4.200874 AGATAGAGACACAAGAGGTACCG 58.799 47.826 6.18 0.00 0.00 4.02
1793 2064 7.353414 TGGAAATAGATAGAGACACAAGAGG 57.647 40.000 0.00 0.00 0.00 3.69
1846 2122 4.457257 AGAAGAACACAGCCTTCTAAATGC 59.543 41.667 0.00 0.00 45.05 3.56
1870 2146 9.745880 GTATAAATGGTTCGACTATGAAGAAGA 57.254 33.333 0.00 0.00 0.00 2.87
1871 2147 9.529325 TGTATAAATGGTTCGACTATGAAGAAG 57.471 33.333 0.00 0.00 0.00 2.85
1873 2149 9.476202 CATGTATAAATGGTTCGACTATGAAGA 57.524 33.333 0.00 0.00 0.00 2.87
1874 2150 8.223769 GCATGTATAAATGGTTCGACTATGAAG 58.776 37.037 5.03 0.00 0.00 3.02
1875 2151 7.172532 GGCATGTATAAATGGTTCGACTATGAA 59.827 37.037 5.03 0.00 0.00 2.57
1876 2152 6.649141 GGCATGTATAAATGGTTCGACTATGA 59.351 38.462 5.03 0.00 0.00 2.15
1877 2153 6.650807 AGGCATGTATAAATGGTTCGACTATG 59.349 38.462 5.03 0.00 0.00 2.23
1912 2188 7.270365 CCAACACAACGCACACTAATTAATAAG 59.730 37.037 0.00 0.00 0.00 1.73
1918 2194 2.946329 TCCAACACAACGCACACTAATT 59.054 40.909 0.00 0.00 0.00 1.40
1982 2264 6.741500 GCGTAACAAAATTGTGAAGCAATAG 58.258 36.000 14.31 0.00 46.29 1.73
2101 2383 6.300354 AGCAGACAATGTGTTAAACTACAC 57.700 37.500 0.00 0.00 46.71 2.90
2133 2426 4.262617 CCAACTAGGCTTCCTTAAAGGTC 58.737 47.826 0.00 0.00 36.53 3.85
2228 2521 7.542130 GTGTTTGTCATGAAAACTTCAAGTTCT 59.458 33.333 22.52 0.00 43.95 3.01
2233 2526 6.098679 CCAGTGTTTGTCATGAAAACTTCAA 58.901 36.000 22.52 10.83 43.95 2.69
2271 2567 5.213913 CTGTGTGCAGTAGAATGAATGTC 57.786 43.478 0.00 0.00 37.92 3.06
2286 2582 9.032420 GGAGTAGATAATAACTAAACTGTGTGC 57.968 37.037 0.00 0.00 0.00 4.57
2296 2592 7.074623 TGGGACAGAGGGAGTAGATAATAACTA 59.925 40.741 0.00 0.00 0.00 2.24
2303 2599 4.620086 TTTGGGACAGAGGGAGTAGATA 57.380 45.455 0.00 0.00 42.39 1.98
2304 2600 3.491766 TTTGGGACAGAGGGAGTAGAT 57.508 47.619 0.00 0.00 42.39 1.98
2305 2601 3.269592 TTTTGGGACAGAGGGAGTAGA 57.730 47.619 0.00 0.00 42.39 2.59
2306 2602 5.896073 ATATTTTGGGACAGAGGGAGTAG 57.104 43.478 0.00 0.00 42.39 2.57
2307 2603 7.070821 GTCTTATATTTTGGGACAGAGGGAGTA 59.929 40.741 0.00 0.00 42.39 2.59
2308 2604 5.970640 TCTTATATTTTGGGACAGAGGGAGT 59.029 40.000 0.00 0.00 42.39 3.85
2309 2605 6.126768 TGTCTTATATTTTGGGACAGAGGGAG 60.127 42.308 0.00 0.00 42.39 4.30
2310 2606 5.729229 TGTCTTATATTTTGGGACAGAGGGA 59.271 40.000 0.00 0.00 42.39 4.20
2311 2607 5.823045 GTGTCTTATATTTTGGGACAGAGGG 59.177 44.000 0.00 0.00 42.39 4.30
2312 2608 6.653989 AGTGTCTTATATTTTGGGACAGAGG 58.346 40.000 0.00 0.00 42.39 3.69
2313 2609 8.567285 AAAGTGTCTTATATTTTGGGACAGAG 57.433 34.615 0.00 0.00 42.39 3.35
2314 2610 8.934023 AAAAGTGTCTTATATTTTGGGACAGA 57.066 30.769 0.00 0.00 42.39 3.41
2315 2611 9.410556 CAAAAAGTGTCTTATATTTTGGGACAG 57.589 33.333 0.00 0.00 42.39 3.51
2316 2612 9.137459 TCAAAAAGTGTCTTATATTTTGGGACA 57.863 29.630 8.80 0.00 39.94 4.02
2319 2615 8.872845 GCATCAAAAAGTGTCTTATATTTTGGG 58.127 33.333 8.80 4.40 39.94 4.12
2320 2616 9.643693 AGCATCAAAAAGTGTCTTATATTTTGG 57.356 29.630 8.80 0.00 39.94 3.28
2326 2622 9.665719 TGTGATAGCATCAAAAAGTGTCTTATA 57.334 29.630 1.17 0.00 41.69 0.98
2327 2623 8.565896 TGTGATAGCATCAAAAAGTGTCTTAT 57.434 30.769 1.17 0.00 41.69 1.73
2328 2624 7.661437 ACTGTGATAGCATCAAAAAGTGTCTTA 59.339 33.333 1.17 0.00 41.69 2.10
2329 2625 6.488006 ACTGTGATAGCATCAAAAAGTGTCTT 59.512 34.615 1.17 0.00 41.69 3.01
2330 2626 6.000219 ACTGTGATAGCATCAAAAAGTGTCT 59.000 36.000 1.17 0.00 41.69 3.41
2331 2627 6.148480 AGACTGTGATAGCATCAAAAAGTGTC 59.852 38.462 11.52 0.00 41.69 3.67
2332 2628 6.000219 AGACTGTGATAGCATCAAAAAGTGT 59.000 36.000 11.52 7.65 41.69 3.55
2333 2629 6.148315 TGAGACTGTGATAGCATCAAAAAGTG 59.852 38.462 11.52 0.00 41.69 3.16
2334 2630 6.233434 TGAGACTGTGATAGCATCAAAAAGT 58.767 36.000 1.17 5.65 41.69 2.66
2335 2631 6.732531 TGAGACTGTGATAGCATCAAAAAG 57.267 37.500 1.17 3.22 41.69 2.27
2336 2632 7.509141 TTTGAGACTGTGATAGCATCAAAAA 57.491 32.000 4.64 0.00 41.69 1.94
2337 2633 7.509141 TTTTGAGACTGTGATAGCATCAAAA 57.491 32.000 12.86 12.86 43.96 2.44
2338 2634 7.509141 TTTTTGAGACTGTGATAGCATCAAA 57.491 32.000 3.27 3.27 41.69 2.69
2359 2655 4.318974 CGTCCCGAAATGTAAGACGTTTTT 60.319 41.667 0.00 0.00 43.89 1.94
2360 2656 3.184986 CGTCCCGAAATGTAAGACGTTTT 59.815 43.478 0.00 0.00 43.89 2.43
2361 2657 2.733026 CGTCCCGAAATGTAAGACGTTT 59.267 45.455 2.88 0.00 43.89 3.60
2362 2658 2.331194 CGTCCCGAAATGTAAGACGTT 58.669 47.619 2.88 0.00 43.89 3.99
2363 2659 1.403249 CCGTCCCGAAATGTAAGACGT 60.403 52.381 9.63 0.00 46.62 4.34
2365 2661 2.537401 CTCCGTCCCGAAATGTAAGAC 58.463 52.381 0.00 0.00 0.00 3.01
2366 2662 1.479323 CCTCCGTCCCGAAATGTAAGA 59.521 52.381 0.00 0.00 0.00 2.10
2367 2663 1.472728 CCCTCCGTCCCGAAATGTAAG 60.473 57.143 0.00 0.00 0.00 2.34
2368 2664 0.538118 CCCTCCGTCCCGAAATGTAA 59.462 55.000 0.00 0.00 0.00 2.41
2369 2665 0.324552 TCCCTCCGTCCCGAAATGTA 60.325 55.000 0.00 0.00 0.00 2.29
2370 2666 1.611261 TCCCTCCGTCCCGAAATGT 60.611 57.895 0.00 0.00 0.00 2.71
2371 2667 1.144057 CTCCCTCCGTCCCGAAATG 59.856 63.158 0.00 0.00 0.00 2.32
2372 2668 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17
2373 2669 0.251742 TTACTCCCTCCGTCCCGAAA 60.252 55.000 0.00 0.00 0.00 3.46
2374 2670 0.251742 TTTACTCCCTCCGTCCCGAA 60.252 55.000 0.00 0.00 0.00 4.30
2375 2671 0.682209 CTTTACTCCCTCCGTCCCGA 60.682 60.000 0.00 0.00 0.00 5.14
2376 2672 0.682209 TCTTTACTCCCTCCGTCCCG 60.682 60.000 0.00 0.00 0.00 5.14
2377 2673 1.206610 GTTCTTTACTCCCTCCGTCCC 59.793 57.143 0.00 0.00 0.00 4.46
2378 2674 1.897802 TGTTCTTTACTCCCTCCGTCC 59.102 52.381 0.00 0.00 0.00 4.79
2379 2675 2.670509 CGTGTTCTTTACTCCCTCCGTC 60.671 54.545 0.00 0.00 0.00 4.79
2380 2676 1.271656 CGTGTTCTTTACTCCCTCCGT 59.728 52.381 0.00 0.00 0.00 4.69
2381 2677 1.992170 CGTGTTCTTTACTCCCTCCG 58.008 55.000 0.00 0.00 0.00 4.63
2382 2678 1.275573 AGCGTGTTCTTTACTCCCTCC 59.724 52.381 0.00 0.00 0.00 4.30
2383 2679 2.745515 AGCGTGTTCTTTACTCCCTC 57.254 50.000 0.00 0.00 0.00 4.30
2384 2680 4.820894 AATAGCGTGTTCTTTACTCCCT 57.179 40.909 0.00 0.00 0.00 4.20
2385 2681 4.933400 TGAAATAGCGTGTTCTTTACTCCC 59.067 41.667 0.00 0.00 0.00 4.30
2386 2682 5.638234 AGTGAAATAGCGTGTTCTTTACTCC 59.362 40.000 0.00 0.00 0.00 3.85
2387 2683 6.707599 AGTGAAATAGCGTGTTCTTTACTC 57.292 37.500 0.00 0.00 0.00 2.59
2388 2684 7.871463 AGTTAGTGAAATAGCGTGTTCTTTACT 59.129 33.333 0.00 0.00 0.00 2.24
2389 2685 8.015409 AGTTAGTGAAATAGCGTGTTCTTTAC 57.985 34.615 0.00 0.00 0.00 2.01
2390 2686 8.597662 AAGTTAGTGAAATAGCGTGTTCTTTA 57.402 30.769 0.00 0.00 0.00 1.85
2391 2687 7.492352 AAGTTAGTGAAATAGCGTGTTCTTT 57.508 32.000 0.00 0.00 0.00 2.52
2392 2688 8.773404 ATAAGTTAGTGAAATAGCGTGTTCTT 57.227 30.769 0.00 0.00 0.00 2.52
2393 2689 9.517609 CTATAAGTTAGTGAAATAGCGTGTTCT 57.482 33.333 0.00 0.00 0.00 3.01
2394 2690 9.298774 ACTATAAGTTAGTGAAATAGCGTGTTC 57.701 33.333 0.00 0.00 0.00 3.18
2395 2691 9.649167 AACTATAAGTTAGTGAAATAGCGTGTT 57.351 29.630 0.00 0.00 36.52 3.32
2396 2692 9.649167 AAACTATAAGTTAGTGAAATAGCGTGT 57.351 29.630 0.00 0.00 37.47 4.49
2398 2694 9.865321 TGAAACTATAAGTTAGTGAAATAGCGT 57.135 29.630 0.00 0.00 37.47 5.07


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

AutoCloner maintained by Alex Coulton.