Multiple sequence alignment - TraesCS3A01G401700

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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 TraesCS3A01G401700 chr3A 100.000 5793 0 0 1 5793 647483859 647478067 0.000000e+00 10698
1 TraesCS3A01G401700 chr3D 96.527 3686 102 12 847 4526 511350829 511347164 0.000000e+00 6074
2 TraesCS3A01G401700 chr3D 95.967 719 21 1 5083 5793 511346437 511345719 0.000000e+00 1160
3 TraesCS3A01G401700 chr3D 89.910 555 30 19 4554 5086 511347167 511346617 0.000000e+00 691
4 TraesCS3A01G401700 chr3D 84.946 465 37 13 340 784 511352716 511352265 1.920000e-119 440
5 TraesCS3A01G401700 chr3D 87.805 205 20 4 1 202 511353067 511352865 9.700000e-58 235
6 TraesCS3A01G401700 chr3D 89.423 104 7 3 340 443 511439992 511439893 1.690000e-25 128
7 TraesCS3A01G401700 chr3B 96.036 3708 126 11 827 4526 672874106 672870412 0.000000e+00 6013
8 TraesCS3A01G401700 chr3B 95.763 1251 42 4 4554 5793 672870415 672869165 0.000000e+00 2006
9 TraesCS3A01G401700 chr3B 89.899 99 8 2 328 425 683437000 683436903 6.090000e-25 126
10 TraesCS3A01G401700 chr5B 92.337 3471 207 25 1084 4525 437800085 437803525 0.000000e+00 4881
11 TraesCS3A01G401700 chr5B 97.222 288 7 1 4650 4936 437805815 437806102 2.430000e-133 486
12 TraesCS3A01G401700 chr5B 91.753 97 7 1 4551 4646 437803520 437803616 3.640000e-27 134
13 TraesCS3A01G401700 chr2A 92.079 101 5 3 340 440 475582033 475581936 7.830000e-29 139
14 TraesCS3A01G401700 chr4A 95.349 86 4 0 340 425 619145393 619145308 2.820000e-28 137
15 TraesCS3A01G401700 chr4A 94.318 88 4 1 339 425 619380493 619380580 3.640000e-27 134
16 TraesCS3A01G401700 chr4A 91.667 96 5 2 340 433 620183037 620183131 4.710000e-26 130
17 TraesCS3A01G401700 chr5D 94.318 88 4 1 340 426 548877994 548878081 3.640000e-27 134
18 TraesCS3A01G401700 chr2D 94.318 88 3 1 340 427 355449629 355449544 3.640000e-27 134
19 TraesCS3A01G401700 chr2D 85.981 107 13 2 1429 1534 23158428 23158533 4.740000e-21 113
20 TraesCS3A01G401700 chr1A 90.196 102 7 3 340 439 555799011 555799111 4.710000e-26 130
21 TraesCS3A01G401700 chr6A 84.112 107 15 2 1429 1534 578686674 578686569 1.030000e-17 102


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 TraesCS3A01G401700 chr3A 647478067 647483859 5792 True 10698.000000 10698 100.000000 1 5793 1 chr3A.!!$R1 5792
1 TraesCS3A01G401700 chr3D 511345719 511353067 7348 True 1720.000000 6074 91.031000 1 5793 5 chr3D.!!$R2 5792
2 TraesCS3A01G401700 chr3B 672869165 672874106 4941 True 4009.500000 6013 95.899500 827 5793 2 chr3B.!!$R2 4966
3 TraesCS3A01G401700 chr5B 437800085 437806102 6017 False 1833.666667 4881 93.770667 1084 4936 3 chr5B.!!$F1 3852

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
277 278 0.034896 AAGGATTGTGGAACTCGCGT 59.965 50.0 5.77 0.0 38.04 6.01 F
841 2310 0.109723 TCACAAACGGGGGAAGGAAG 59.890 55.0 0.00 0.0 0.00 3.46 F
844 2313 0.608308 CAAACGGGGGAAGGAAGGAC 60.608 60.0 0.00 0.0 0.00 3.85 F
2146 3655 0.760567 TGCTGTGAGAGTGGTGACCT 60.761 55.0 2.11 0.0 0.00 3.85 F
2471 3980 0.739112 CGTGAAGAGGGAAGCAGAGC 60.739 60.0 0.00 0.0 0.00 4.09 F
3623 5133 0.462225 CACATCCTCAGCAGCTCCAG 60.462 60.0 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 3493 1.098050 GCGTTGGCCATGATTCTCTT 58.902 50.000 6.09 0.0 0.00 2.85 R
2411 3920 0.453282 CTCAAACAAGTCCGCGCATG 60.453 55.000 8.75 0.0 0.00 4.06 R
2415 3924 1.126846 GATGTCTCAAACAAGTCCGCG 59.873 52.381 0.00 0.0 42.37 6.46 R
3152 4661 0.251077 CTTCTGCTCCTTTGCCACCT 60.251 55.000 0.00 0.0 0.00 4.00 R
3687 5197 1.073897 GGGTGCCTTCAGAAGCAGT 59.926 57.895 4.41 0.0 40.28 4.40 R
5235 9163 0.827507 AAAACCCAAGCACGGCATCT 60.828 50.000 0.00 0.0 0.00 2.90 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
25 26 6.428385 AGATAAAAAGAATCCGCAGAAGTG 57.572 37.500 0.00 0.00 0.00 3.16
39 40 4.614284 CGCAGAAGTGAAAATGACAACATC 59.386 41.667 0.00 0.00 35.50 3.06
58 59 9.300681 ACAACATCTGGAGATTAAATCAAAAGA 57.699 29.630 0.00 0.00 31.21 2.52
94 95 2.558575 GCATGAGAGGGAGGAGGCTATA 60.559 54.545 0.00 0.00 0.00 1.31
102 103 4.974399 AGGGAGGAGGCTATAATTTTTCG 58.026 43.478 0.00 0.00 0.00 3.46
104 105 5.104067 AGGGAGGAGGCTATAATTTTTCGTT 60.104 40.000 0.00 0.00 0.00 3.85
154 155 4.188948 GAATAGCTCGACACTTGCATTC 57.811 45.455 0.00 1.23 0.00 2.67
157 158 2.072298 AGCTCGACACTTGCATTCTTC 58.928 47.619 0.00 0.00 0.00 2.87
163 164 4.571984 TCGACACTTGCATTCTTCATATGG 59.428 41.667 2.13 0.00 0.00 2.74
166 167 4.641989 ACACTTGCATTCTTCATATGGTCC 59.358 41.667 2.13 0.00 0.00 4.46
172 173 6.422333 TGCATTCTTCATATGGTCCTTACAA 58.578 36.000 2.13 0.00 0.00 2.41
174 175 8.217111 TGCATTCTTCATATGGTCCTTACAATA 58.783 33.333 2.13 0.00 0.00 1.90
185 186 8.747538 ATGGTCCTTACAATATGACTTTTACC 57.252 34.615 0.00 0.00 0.00 2.85
186 187 7.691213 TGGTCCTTACAATATGACTTTTACCA 58.309 34.615 0.00 0.00 0.00 3.25
188 189 7.827729 GGTCCTTACAATATGACTTTTACCACT 59.172 37.037 0.00 0.00 0.00 4.00
189 190 9.227777 GTCCTTACAATATGACTTTTACCACTT 57.772 33.333 0.00 0.00 0.00 3.16
225 226 9.562408 TTTAAATATAATCCACGTAAGGCATCA 57.438 29.630 0.00 0.00 46.39 3.07
227 228 7.672983 AATATAATCCACGTAAGGCATCAAG 57.327 36.000 0.00 0.00 46.39 3.02
228 229 2.332063 ATCCACGTAAGGCATCAAGG 57.668 50.000 0.00 0.00 46.39 3.61
229 230 0.981183 TCCACGTAAGGCATCAAGGT 59.019 50.000 0.00 0.00 46.39 3.50
231 232 2.568062 TCCACGTAAGGCATCAAGGTTA 59.432 45.455 0.00 0.00 46.39 2.85
232 233 2.676342 CCACGTAAGGCATCAAGGTTAC 59.324 50.000 0.00 0.00 46.39 2.50
233 234 3.331150 CACGTAAGGCATCAAGGTTACA 58.669 45.455 0.00 0.00 46.39 2.41
234 235 3.370978 CACGTAAGGCATCAAGGTTACAG 59.629 47.826 0.00 0.00 46.39 2.74
235 236 3.259876 ACGTAAGGCATCAAGGTTACAGA 59.740 43.478 0.00 0.00 46.39 3.41
236 237 4.081087 ACGTAAGGCATCAAGGTTACAGAT 60.081 41.667 0.00 0.00 46.39 2.90
237 238 4.876107 CGTAAGGCATCAAGGTTACAGATT 59.124 41.667 0.00 0.00 0.00 2.40
238 239 5.220662 CGTAAGGCATCAAGGTTACAGATTG 60.221 44.000 0.00 0.00 0.00 2.67
239 240 4.307032 AGGCATCAAGGTTACAGATTGT 57.693 40.909 0.00 0.00 0.00 2.71
240 241 5.435686 AGGCATCAAGGTTACAGATTGTA 57.564 39.130 0.00 0.00 0.00 2.41
241 242 6.006275 AGGCATCAAGGTTACAGATTGTAT 57.994 37.500 0.00 0.00 32.20 2.29
242 243 6.426587 AGGCATCAAGGTTACAGATTGTATT 58.573 36.000 0.00 0.00 32.20 1.89
243 244 6.891908 AGGCATCAAGGTTACAGATTGTATTT 59.108 34.615 0.00 0.00 32.20 1.40
244 245 7.397192 AGGCATCAAGGTTACAGATTGTATTTT 59.603 33.333 0.00 0.00 32.20 1.82
245 246 7.702348 GGCATCAAGGTTACAGATTGTATTTTC 59.298 37.037 0.00 0.00 32.20 2.29
246 247 7.429340 GCATCAAGGTTACAGATTGTATTTTCG 59.571 37.037 0.00 0.00 32.20 3.46
247 248 7.372451 TCAAGGTTACAGATTGTATTTTCGG 57.628 36.000 0.00 0.00 32.20 4.30
248 249 6.373216 TCAAGGTTACAGATTGTATTTTCGGG 59.627 38.462 0.00 0.00 32.20 5.14
249 250 6.057321 AGGTTACAGATTGTATTTTCGGGA 57.943 37.500 0.00 0.00 32.20 5.14
250 251 6.478129 AGGTTACAGATTGTATTTTCGGGAA 58.522 36.000 0.00 0.00 32.20 3.97
251 252 6.943718 AGGTTACAGATTGTATTTTCGGGAAA 59.056 34.615 0.00 0.00 32.20 3.13
252 253 7.449086 AGGTTACAGATTGTATTTTCGGGAAAA 59.551 33.333 8.84 8.84 43.48 2.29
253 254 8.083462 GGTTACAGATTGTATTTTCGGGAAAAA 58.917 33.333 10.31 0.00 42.71 1.94
254 255 9.124807 GTTACAGATTGTATTTTCGGGAAAAAG 57.875 33.333 10.31 0.00 42.71 2.27
255 256 7.519032 ACAGATTGTATTTTCGGGAAAAAGA 57.481 32.000 10.31 0.27 42.71 2.52
256 257 8.122472 ACAGATTGTATTTTCGGGAAAAAGAT 57.878 30.769 10.31 3.47 42.71 2.40
257 258 8.585018 ACAGATTGTATTTTCGGGAAAAAGATT 58.415 29.630 10.31 0.00 42.71 2.40
261 262 9.869757 ATTGTATTTTCGGGAAAAAGATTAAGG 57.130 29.630 10.31 0.00 42.71 2.69
262 263 8.638629 TGTATTTTCGGGAAAAAGATTAAGGA 57.361 30.769 10.31 0.00 42.71 3.36
263 264 9.250246 TGTATTTTCGGGAAAAAGATTAAGGAT 57.750 29.630 10.31 0.00 42.71 3.24
266 267 7.533289 TTTCGGGAAAAAGATTAAGGATTGT 57.467 32.000 0.00 0.00 0.00 2.71
267 268 6.509418 TCGGGAAAAAGATTAAGGATTGTG 57.491 37.500 0.00 0.00 0.00 3.33
268 269 5.417580 TCGGGAAAAAGATTAAGGATTGTGG 59.582 40.000 0.00 0.00 0.00 4.17
269 270 5.417580 CGGGAAAAAGATTAAGGATTGTGGA 59.582 40.000 0.00 0.00 0.00 4.02
270 271 6.071616 CGGGAAAAAGATTAAGGATTGTGGAA 60.072 38.462 0.00 0.00 0.00 3.53
271 272 7.097192 GGGAAAAAGATTAAGGATTGTGGAAC 58.903 38.462 0.00 0.00 37.35 3.62
272 273 7.039011 GGGAAAAAGATTAAGGATTGTGGAACT 60.039 37.037 0.00 0.00 38.04 3.01
273 274 8.029522 GGAAAAAGATTAAGGATTGTGGAACTC 58.970 37.037 0.00 0.00 38.04 3.01
274 275 6.743575 AAAGATTAAGGATTGTGGAACTCG 57.256 37.500 0.00 0.00 38.04 4.18
275 276 4.192317 AGATTAAGGATTGTGGAACTCGC 58.808 43.478 0.00 0.00 38.04 5.03
276 277 2.004583 TAAGGATTGTGGAACTCGCG 57.995 50.000 0.00 0.00 38.04 5.87
277 278 0.034896 AAGGATTGTGGAACTCGCGT 59.965 50.000 5.77 0.00 38.04 6.01
278 279 0.892755 AGGATTGTGGAACTCGCGTA 59.107 50.000 5.77 0.00 38.04 4.42
279 280 1.135083 AGGATTGTGGAACTCGCGTAG 60.135 52.381 5.77 4.90 38.04 3.51
280 281 1.278238 GATTGTGGAACTCGCGTAGG 58.722 55.000 5.77 0.00 38.04 3.18
281 282 0.606604 ATTGTGGAACTCGCGTAGGT 59.393 50.000 5.77 0.00 38.04 3.08
293 294 2.095213 TCGCGTAGGTTGAAATTGATGC 59.905 45.455 5.77 0.00 0.00 3.91
294 295 2.791158 CGCGTAGGTTGAAATTGATGCC 60.791 50.000 0.00 0.00 0.00 4.40
296 297 3.731867 GCGTAGGTTGAAATTGATGCCAG 60.732 47.826 0.00 0.00 0.00 4.85
299 300 2.232941 AGGTTGAAATTGATGCCAGCTG 59.767 45.455 6.78 6.78 0.00 4.24
300 301 2.028748 GGTTGAAATTGATGCCAGCTGT 60.029 45.455 13.81 0.00 0.00 4.40
301 302 3.248266 GTTGAAATTGATGCCAGCTGTC 58.752 45.455 13.81 0.00 0.00 3.51
302 303 2.799017 TGAAATTGATGCCAGCTGTCT 58.201 42.857 13.81 0.00 0.00 3.41
303 304 2.490509 TGAAATTGATGCCAGCTGTCTG 59.509 45.455 13.81 0.00 40.02 3.51
304 305 2.211250 AATTGATGCCAGCTGTCTGT 57.789 45.000 13.81 0.00 38.66 3.41
305 306 3.354948 AATTGATGCCAGCTGTCTGTA 57.645 42.857 13.81 0.00 38.66 2.74
307 308 0.975887 TGATGCCAGCTGTCTGTACA 59.024 50.000 13.81 0.00 38.66 2.90
308 309 1.347378 TGATGCCAGCTGTCTGTACAA 59.653 47.619 13.81 0.00 38.66 2.41
309 310 1.734465 GATGCCAGCTGTCTGTACAAC 59.266 52.381 13.81 0.00 38.66 3.32
310 311 0.467804 TGCCAGCTGTCTGTACAACA 59.532 50.000 13.81 4.04 38.66 3.33
311 312 1.072173 TGCCAGCTGTCTGTACAACAT 59.928 47.619 13.81 0.00 38.66 2.71
312 313 2.301583 TGCCAGCTGTCTGTACAACATA 59.698 45.455 13.81 0.00 38.66 2.29
313 314 2.673368 GCCAGCTGTCTGTACAACATAC 59.327 50.000 13.81 7.06 38.66 2.39
315 316 4.569943 CCAGCTGTCTGTACAACATACTT 58.430 43.478 13.81 0.00 38.66 2.24
317 318 6.163476 CCAGCTGTCTGTACAACATACTTTA 58.837 40.000 13.81 0.00 38.66 1.85
319 320 6.311445 CAGCTGTCTGTACAACATACTTTAGG 59.689 42.308 5.25 0.91 34.49 2.69
320 321 5.063564 GCTGTCTGTACAACATACTTTAGGC 59.936 44.000 10.10 5.65 34.49 3.93
321 322 5.165676 TGTCTGTACAACATACTTTAGGCG 58.834 41.667 0.00 0.00 30.91 5.52
322 323 5.166398 GTCTGTACAACATACTTTAGGCGT 58.834 41.667 0.00 0.00 0.00 5.68
323 324 5.061808 GTCTGTACAACATACTTTAGGCGTG 59.938 44.000 0.00 0.00 0.00 5.34
324 325 4.885413 TGTACAACATACTTTAGGCGTGT 58.115 39.130 0.00 0.00 0.00 4.49
325 326 4.925054 TGTACAACATACTTTAGGCGTGTC 59.075 41.667 0.00 0.00 0.00 3.67
326 327 3.332034 ACAACATACTTTAGGCGTGTCC 58.668 45.455 0.00 0.00 0.00 4.02
327 328 2.676342 CAACATACTTTAGGCGTGTCCC 59.324 50.000 0.00 0.00 34.51 4.46
328 329 1.903860 ACATACTTTAGGCGTGTCCCA 59.096 47.619 0.00 0.00 34.51 4.37
329 330 2.504175 ACATACTTTAGGCGTGTCCCAT 59.496 45.455 0.00 0.00 34.51 4.00
330 331 2.684001 TACTTTAGGCGTGTCCCATG 57.316 50.000 0.00 0.00 34.51 3.66
331 332 0.690762 ACTTTAGGCGTGTCCCATGT 59.309 50.000 0.00 0.00 34.51 3.21
332 333 1.338769 ACTTTAGGCGTGTCCCATGTC 60.339 52.381 0.00 0.00 34.51 3.06
334 335 0.687920 TTAGGCGTGTCCCATGTCAA 59.312 50.000 0.00 0.00 34.51 3.18
335 336 0.249120 TAGGCGTGTCCCATGTCAAG 59.751 55.000 0.00 0.00 34.51 3.02
336 337 2.690778 GGCGTGTCCCATGTCAAGC 61.691 63.158 10.38 10.38 38.07 4.01
337 338 3.027170 GCGTGTCCCATGTCAAGCG 62.027 63.158 0.00 0.00 30.89 4.68
338 339 2.390599 CGTGTCCCATGTCAAGCGG 61.391 63.158 0.00 0.00 0.00 5.52
357 421 1.053424 GGTCTGGGTGGTGTAGTTGA 58.947 55.000 0.00 0.00 0.00 3.18
391 455 1.003233 CTCACACACTAAAGGTCCCCC 59.997 57.143 0.00 0.00 0.00 5.40
395 459 0.689055 ACACTAAAGGTCCCCCGTTC 59.311 55.000 0.00 0.00 34.12 3.95
414 478 0.250295 CGAACCTGGGCTCAGACAAA 60.250 55.000 17.43 0.00 43.49 2.83
416 480 2.087646 GAACCTGGGCTCAGACAAATC 58.912 52.381 17.43 1.66 43.49 2.17
418 482 1.707427 ACCTGGGCTCAGACAAATCTT 59.293 47.619 17.43 0.00 43.49 2.40
419 483 2.108952 ACCTGGGCTCAGACAAATCTTT 59.891 45.455 17.43 0.00 43.49 2.52
463 535 3.445805 AGACGTTTCATCCTCCTCTCTTC 59.554 47.826 0.00 0.00 0.00 2.87
487 560 3.828451 CCCCGATAATGCTTGATTTCCAT 59.172 43.478 0.00 0.00 0.00 3.41
488 561 4.082571 CCCCGATAATGCTTGATTTCCATC 60.083 45.833 0.00 0.00 0.00 3.51
491 564 6.239120 CCCGATAATGCTTGATTTCCATCTTT 60.239 38.462 0.00 0.00 0.00 2.52
492 565 6.860023 CCGATAATGCTTGATTTCCATCTTTC 59.140 38.462 0.00 0.00 0.00 2.62
493 566 6.860023 CGATAATGCTTGATTTCCATCTTTCC 59.140 38.462 0.00 0.00 0.00 3.13
494 567 5.349061 AATGCTTGATTTCCATCTTTCCC 57.651 39.130 0.00 0.00 0.00 3.97
496 569 2.432146 GCTTGATTTCCATCTTTCCCCC 59.568 50.000 0.00 0.00 0.00 5.40
497 570 3.711863 CTTGATTTCCATCTTTCCCCCA 58.288 45.455 0.00 0.00 0.00 4.96
498 571 3.386932 TGATTTCCATCTTTCCCCCAG 57.613 47.619 0.00 0.00 0.00 4.45
499 572 2.925653 TGATTTCCATCTTTCCCCCAGA 59.074 45.455 0.00 0.00 0.00 3.86
501 574 4.731416 TGATTTCCATCTTTCCCCCAGATA 59.269 41.667 0.00 0.00 29.36 1.98
502 575 5.195553 TGATTTCCATCTTTCCCCCAGATAA 59.804 40.000 0.00 0.00 29.36 1.75
504 577 4.729552 TCCATCTTTCCCCCAGATAATG 57.270 45.455 0.00 0.00 29.36 1.90
505 578 3.160269 CCATCTTTCCCCCAGATAATGC 58.840 50.000 0.00 0.00 29.36 3.56
506 579 3.160269 CATCTTTCCCCCAGATAATGCC 58.840 50.000 0.00 0.00 29.36 4.40
507 580 2.502745 TCTTTCCCCCAGATAATGCCT 58.497 47.619 0.00 0.00 0.00 4.75
508 581 2.175499 TCTTTCCCCCAGATAATGCCTG 59.825 50.000 0.00 0.00 0.00 4.85
509 582 1.905839 TTCCCCCAGATAATGCCTGA 58.094 50.000 0.00 0.00 33.65 3.86
511 584 2.431997 TCCCCCAGATAATGCCTGATT 58.568 47.619 0.00 0.00 33.65 2.57
513 586 3.160269 CCCCCAGATAATGCCTGATTTC 58.840 50.000 0.00 0.00 33.65 2.17
514 587 3.181425 CCCCCAGATAATGCCTGATTTCT 60.181 47.826 0.00 0.00 33.65 2.52
515 588 4.043310 CCCCCAGATAATGCCTGATTTCTA 59.957 45.833 0.00 0.00 33.65 2.10
516 589 5.006386 CCCCAGATAATGCCTGATTTCTAC 58.994 45.833 0.00 0.00 33.65 2.59
517 590 5.456619 CCCCAGATAATGCCTGATTTCTACA 60.457 44.000 0.00 0.00 33.65 2.74
518 591 5.704515 CCCAGATAATGCCTGATTTCTACAG 59.295 44.000 0.00 0.00 33.65 2.74
520 593 7.445121 CCAGATAATGCCTGATTTCTACAGTA 58.555 38.462 0.00 0.00 33.65 2.74
600 681 9.703892 TCAATGTCAATTTGGTTCGAAATTAAT 57.296 25.926 0.00 0.00 34.46 1.40
676 759 2.905075 TCATCACATTTACTGGCCGAG 58.095 47.619 0.00 0.00 0.00 4.63
694 777 1.304381 GCCTCTGTTCCCATGCCAA 60.304 57.895 0.00 0.00 0.00 4.52
727 810 4.389687 CGATCAACATCGCATGGATAATGA 59.610 41.667 0.00 4.61 45.28 2.57
743 826 2.119801 ATGAGCTTTCGCAGACCATT 57.880 45.000 0.00 0.00 39.10 3.16
744 827 1.896220 TGAGCTTTCGCAGACCATTT 58.104 45.000 0.00 0.00 39.10 2.32
745 828 3.052455 TGAGCTTTCGCAGACCATTTA 57.948 42.857 0.00 0.00 39.10 1.40
762 845 8.322091 AGACCATTTATTAAACAGTCTAGCAGT 58.678 33.333 15.96 0.00 35.50 4.40
766 849 9.155975 CATTTATTAAACAGTCTAGCAGTGACT 57.844 33.333 0.00 1.28 44.62 3.41
780 863 1.832608 TGACTGGTGTGAGCCGAGT 60.833 57.895 0.00 0.00 0.00 4.18
784 867 1.270147 ACTGGTGTGAGCCGAGTAAAC 60.270 52.381 0.00 0.00 0.00 2.01
785 868 1.000955 CTGGTGTGAGCCGAGTAAACT 59.999 52.381 0.00 0.00 0.00 2.66
786 869 1.414919 TGGTGTGAGCCGAGTAAACTT 59.585 47.619 0.00 0.00 0.00 2.66
787 870 2.158871 TGGTGTGAGCCGAGTAAACTTT 60.159 45.455 0.00 0.00 0.00 2.66
788 871 2.223377 GGTGTGAGCCGAGTAAACTTTG 59.777 50.000 0.00 0.00 0.00 2.77
789 872 1.871039 TGTGAGCCGAGTAAACTTTGC 59.129 47.619 0.00 0.00 0.00 3.68
791 874 2.096218 GTGAGCCGAGTAAACTTTGCAG 60.096 50.000 7.33 0.00 0.00 4.41
821 2290 4.558226 TTTGATCCAAGCAGAAGAGCTA 57.442 40.909 0.00 0.00 45.89 3.32
835 2304 0.539986 GAGCTATCACAAACGGGGGA 59.460 55.000 0.00 0.00 0.00 4.81
837 2306 1.065418 AGCTATCACAAACGGGGGAAG 60.065 52.381 0.00 0.00 0.00 3.46
839 2308 1.557832 CTATCACAAACGGGGGAAGGA 59.442 52.381 0.00 0.00 0.00 3.36
840 2309 0.774908 ATCACAAACGGGGGAAGGAA 59.225 50.000 0.00 0.00 0.00 3.36
841 2310 0.109723 TCACAAACGGGGGAAGGAAG 59.890 55.000 0.00 0.00 0.00 3.46
842 2311 0.893727 CACAAACGGGGGAAGGAAGG 60.894 60.000 0.00 0.00 0.00 3.46
843 2312 1.063654 ACAAACGGGGGAAGGAAGGA 61.064 55.000 0.00 0.00 0.00 3.36
844 2313 0.608308 CAAACGGGGGAAGGAAGGAC 60.608 60.000 0.00 0.00 0.00 3.85
845 2314 1.786407 AAACGGGGGAAGGAAGGACC 61.786 60.000 0.00 0.00 39.35 4.46
846 2315 3.782443 CGGGGGAAGGAAGGACCG 61.782 72.222 0.00 0.00 44.74 4.79
847 2316 3.408853 GGGGGAAGGAAGGACCGG 61.409 72.222 0.00 0.00 44.74 5.28
848 2317 4.111053 GGGGAAGGAAGGACCGGC 62.111 72.222 0.00 0.00 44.74 6.13
849 2318 3.327404 GGGAAGGAAGGACCGGCA 61.327 66.667 0.00 0.00 44.74 5.69
850 2319 2.046217 GGAAGGAAGGACCGGCAC 60.046 66.667 0.00 0.00 44.74 5.01
923 2393 3.343326 CCCATTCCCCGTTCCCCA 61.343 66.667 0.00 0.00 0.00 4.96
924 2394 2.767352 CCATTCCCCGTTCCCCAA 59.233 61.111 0.00 0.00 0.00 4.12
1317 2790 4.925861 GCGGAGATCAGGCAGGCC 62.926 72.222 0.97 0.97 0.00 5.19
1754 3263 4.120755 GAAGCTGGCCTCCCCCTG 62.121 72.222 3.32 0.00 0.00 4.45
1827 3336 2.187946 CTCCGCTACCTTGCCCTG 59.812 66.667 0.00 0.00 0.00 4.45
2146 3655 0.760567 TGCTGTGAGAGTGGTGACCT 60.761 55.000 2.11 0.00 0.00 3.85
2226 3735 2.501610 GATGAGAGGGTGGTCGCC 59.498 66.667 0.00 0.00 0.00 5.54
2411 3920 8.315554 CATTTCAATGCAAAGAACTACGATAC 57.684 34.615 3.92 0.00 0.00 2.24
2415 3924 4.857871 TGCAAAGAACTACGATACATGC 57.142 40.909 0.00 0.00 0.00 4.06
2471 3980 0.739112 CGTGAAGAGGGAAGCAGAGC 60.739 60.000 0.00 0.00 0.00 4.09
2590 4099 2.956132 TGATCCCTCTCCTCATCACTC 58.044 52.381 0.00 0.00 0.00 3.51
2610 4119 8.677148 TCACTCCATTAAATAATCTTGCCTAC 57.323 34.615 0.00 0.00 0.00 3.18
2622 4131 2.561419 TCTTGCCTACTGCTTCTTACGT 59.439 45.455 0.00 0.00 42.00 3.57
2626 4135 3.243941 TGCCTACTGCTTCTTACGTTTGA 60.244 43.478 0.00 0.00 42.00 2.69
2635 4144 6.791303 TGCTTCTTACGTTTGACTCAAAATT 58.209 32.000 5.76 0.00 35.03 1.82
2749 4258 5.123979 GGTATTGTTTGCTAACCCAGAAGAG 59.876 44.000 8.56 0.00 33.15 2.85
2782 4291 9.293404 AGATCAAAATTCATCTTCAGAAGAACA 57.707 29.630 17.00 3.78 41.63 3.18
2842 4351 2.562298 GGTTGCATTGACTTCAATCCCA 59.438 45.455 1.28 0.55 44.10 4.37
2844 4353 2.874014 TGCATTGACTTCAATCCCACA 58.126 42.857 1.28 0.00 44.10 4.17
3071 4580 2.109126 GGATGTCTGACCTTGGCGC 61.109 63.158 0.00 0.00 0.00 6.53
3081 4590 3.804193 CTTGGCGCGGAAGGCTTC 61.804 66.667 18.98 18.98 40.44 3.86
3098 4607 1.547372 CTTCTTTGGCAATGGACCTGG 59.453 52.381 12.54 0.00 0.00 4.45
3126 4635 1.268539 CGTGAACTGAACTGGTTTGCC 60.269 52.381 0.00 0.00 0.00 4.52
3127 4636 1.748493 GTGAACTGAACTGGTTTGCCA 59.252 47.619 0.00 0.00 43.73 4.92
3152 4661 6.003950 GCAATAGCTGGAATATGGGTAGAAA 58.996 40.000 0.00 0.00 37.91 2.52
3298 4807 2.497138 TGAGTGTCACTTCCATGCTTG 58.503 47.619 7.00 0.00 0.00 4.01
3518 5028 2.852075 TGGCCCTCGGGTTCAGTT 60.852 61.111 0.00 0.00 37.65 3.16
3623 5133 0.462225 CACATCCTCAGCAGCTCCAG 60.462 60.000 0.00 0.00 0.00 3.86
3687 5197 5.896678 TCCCATCTTCTCAAACTTGGAAAAA 59.103 36.000 0.00 0.00 0.00 1.94
3894 5404 2.145397 TCGACAAGCCTACCAGATCT 57.855 50.000 0.00 0.00 0.00 2.75
4038 5548 7.180766 GGATGAAGATGGGATTAGATCTCTCTT 59.819 40.741 0.00 0.00 33.16 2.85
4142 5652 0.109597 GTGAACATGCTTTGCTCGGG 60.110 55.000 0.00 0.00 0.00 5.14
4218 5728 0.826715 TAGCATGTCTCAGCCTGTCC 59.173 55.000 0.00 0.00 0.00 4.02
4234 5744 9.503369 TCAGCCTGTCCTAGTATAGTATAGATA 57.497 37.037 0.00 0.00 36.82 1.98
4320 5830 1.406539 GGTTGCATATGACAGGCCAAG 59.593 52.381 5.01 0.00 31.20 3.61
4351 5861 9.757227 GTCTGATTTACATCTCTAGTAAGCATT 57.243 33.333 0.00 0.00 33.44 3.56
4380 5891 5.657474 TCTTTGTCGATAGTAACCATGTCC 58.343 41.667 0.00 0.00 37.40 4.02
4387 5898 5.532032 TCGATAGTAACCATGTCCGTGAATA 59.468 40.000 0.00 0.00 37.40 1.75
4421 5932 4.886489 TGATGTGTAGGAGAGATGACTGAG 59.114 45.833 0.00 0.00 0.00 3.35
4433 5944 8.035394 GGAGAGATGACTGAGTGTTTGTAATAA 58.965 37.037 0.00 0.00 0.00 1.40
4435 5946 9.209175 AGAGATGACTGAGTGTTTGTAATAAAC 57.791 33.333 0.00 0.00 0.00 2.01
4436 5947 8.902540 AGATGACTGAGTGTTTGTAATAAACA 57.097 30.769 0.00 1.42 37.76 2.83
4437 5948 9.507329 AGATGACTGAGTGTTTGTAATAAACAT 57.493 29.630 8.26 0.00 41.51 2.71
4439 5950 9.897744 ATGACTGAGTGTTTGTAATAAACATTG 57.102 29.630 8.26 3.26 41.51 2.82
4480 5999 5.047377 GGATTTGTTCAGGCAACCTTTATGA 60.047 40.000 0.00 0.00 33.51 2.15
4494 6013 7.432869 CAACCTTTATGACCATTTTCTGTCAA 58.567 34.615 0.00 0.00 44.04 3.18
4498 6017 9.143631 CCTTTATGACCATTTTCTGTCAAATTC 57.856 33.333 0.00 0.00 44.04 2.17
4499 6018 9.695526 CTTTATGACCATTTTCTGTCAAATTCA 57.304 29.630 0.00 0.00 44.04 2.57
4522 6041 4.100373 ACTAATCTCCTGATGCCCCTATC 58.900 47.826 0.00 0.00 32.44 2.08
4523 6042 2.729383 ATCTCCTGATGCCCCTATCA 57.271 50.000 0.00 0.00 35.83 2.15
4524 6043 2.729383 TCTCCTGATGCCCCTATCAT 57.271 50.000 0.00 0.00 36.55 2.45
4525 6044 2.995746 TCTCCTGATGCCCCTATCATT 58.004 47.619 0.00 0.00 36.55 2.57
4526 6045 3.330198 TCTCCTGATGCCCCTATCATTT 58.670 45.455 0.00 0.00 36.55 2.32
4527 6046 3.723681 TCTCCTGATGCCCCTATCATTTT 59.276 43.478 0.00 0.00 36.55 1.82
4528 6047 3.825014 CTCCTGATGCCCCTATCATTTTG 59.175 47.826 0.00 0.00 36.55 2.44
4529 6048 3.205056 TCCTGATGCCCCTATCATTTTGT 59.795 43.478 0.00 0.00 36.55 2.83
4530 6049 4.415179 TCCTGATGCCCCTATCATTTTGTA 59.585 41.667 0.00 0.00 36.55 2.41
4531 6050 4.763793 CCTGATGCCCCTATCATTTTGTAG 59.236 45.833 0.00 0.00 36.55 2.74
4532 6051 5.380043 CTGATGCCCCTATCATTTTGTAGT 58.620 41.667 0.00 0.00 36.55 2.73
4533 6052 5.765510 TGATGCCCCTATCATTTTGTAGTT 58.234 37.500 0.00 0.00 32.39 2.24
4534 6053 6.905736 TGATGCCCCTATCATTTTGTAGTTA 58.094 36.000 0.00 0.00 32.39 2.24
4535 6054 7.526041 TGATGCCCCTATCATTTTGTAGTTAT 58.474 34.615 0.00 0.00 32.39 1.89
4536 6055 8.664992 TGATGCCCCTATCATTTTGTAGTTATA 58.335 33.333 0.00 0.00 32.39 0.98
4537 6056 8.863872 ATGCCCCTATCATTTTGTAGTTATAC 57.136 34.615 0.00 0.00 0.00 1.47
4538 6057 8.041143 TGCCCCTATCATTTTGTAGTTATACT 57.959 34.615 0.00 0.00 32.75 2.12
4539 6058 9.161572 TGCCCCTATCATTTTGTAGTTATACTA 57.838 33.333 0.00 0.00 32.75 1.82
4571 6090 8.903820 GGCATTACCATTCAAACTATTCTAGTT 58.096 33.333 0.00 0.00 44.14 2.24
4604 6123 5.934781 AGAGGGGCAGAAATACATAAAGAG 58.065 41.667 0.00 0.00 0.00 2.85
4616 6138 6.997942 ATACATAAAGAGGGTAAGGACTCC 57.002 41.667 0.00 0.00 34.27 3.85
4873 8591 0.681733 GCTGACCTGGTGTCTTCAGA 59.318 55.000 14.63 0.00 44.75 3.27
5021 8765 5.134202 TCGATGTGACATGTACAGAAAGT 57.866 39.130 1.23 0.00 0.00 2.66
5116 9044 8.004087 TGCCGATATATAGGGTATAACAAGAC 57.996 38.462 13.15 0.00 0.00 3.01
5118 9046 7.646314 CCGATATATAGGGTATAACAAGACGG 58.354 42.308 4.01 0.00 0.00 4.79
5127 9055 5.916320 GGGTATAACAAGACGGTTTTTGTTG 59.084 40.000 23.43 9.39 44.63 3.33
5333 9261 8.464404 CAATTGCACTATATGGGAATAGGAATG 58.536 37.037 0.00 0.00 34.34 2.67
5397 9325 3.822167 CCATGGCATGTGCATATACAGAA 59.178 43.478 24.80 0.00 44.36 3.02
5446 9374 7.028962 CCATTATATTGCATCAACATAACCGG 58.971 38.462 0.00 0.00 27.74 5.28
5478 9406 5.125356 TGTCTAATCAGGCAACATGGTATG 58.875 41.667 0.00 0.00 32.05 2.39
5578 9514 2.161855 TGCATGCTCCGAGTTTTCAAT 58.838 42.857 20.33 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.064060 TCTCCAGATGTTGTCATTTTCACTT 58.936 36.000 0.00 0.00 34.06 3.16
39 40 7.066766 CCCACTCTCTTTTGATTTAATCTCCAG 59.933 40.741 6.50 0.04 0.00 3.86
58 59 1.081833 ATGCACTCCCTCCCACTCT 59.918 57.895 0.00 0.00 0.00 3.24
94 95 6.976636 TTTTGAAGCTTCCAACGAAAAATT 57.023 29.167 23.42 0.00 0.00 1.82
142 143 5.220931 GGACCATATGAAGAATGCAAGTGTC 60.221 44.000 3.65 0.00 0.00 3.67
145 146 5.121380 AGGACCATATGAAGAATGCAAGT 57.879 39.130 3.65 0.00 0.00 3.16
154 155 9.784531 AAGTCATATTGTAAGGACCATATGAAG 57.215 33.333 3.65 0.00 45.34 3.02
163 164 8.788325 AGTGGTAAAAGTCATATTGTAAGGAC 57.212 34.615 0.00 0.00 0.00 3.85
200 201 9.562408 TTGATGCCTTACGTGGATTATATTTAA 57.438 29.630 0.00 0.00 0.00 1.52
202 203 7.174946 CCTTGATGCCTTACGTGGATTATATTT 59.825 37.037 0.00 0.00 0.00 1.40
203 204 6.655003 CCTTGATGCCTTACGTGGATTATATT 59.345 38.462 0.00 0.00 0.00 1.28
204 205 6.173339 CCTTGATGCCTTACGTGGATTATAT 58.827 40.000 0.00 0.00 0.00 0.86
208 209 2.026262 ACCTTGATGCCTTACGTGGATT 60.026 45.455 0.00 0.00 0.00 3.01
209 210 1.559682 ACCTTGATGCCTTACGTGGAT 59.440 47.619 0.00 0.00 0.00 3.41
211 212 1.821216 AACCTTGATGCCTTACGTGG 58.179 50.000 0.00 0.00 0.00 4.94
212 213 3.331150 TGTAACCTTGATGCCTTACGTG 58.669 45.455 0.00 0.00 0.00 4.49
214 215 3.857052 TCTGTAACCTTGATGCCTTACG 58.143 45.455 0.00 0.00 0.00 3.18
215 216 5.648092 ACAATCTGTAACCTTGATGCCTTAC 59.352 40.000 0.00 0.00 0.00 2.34
216 217 5.815581 ACAATCTGTAACCTTGATGCCTTA 58.184 37.500 0.00 0.00 0.00 2.69
218 219 4.307032 ACAATCTGTAACCTTGATGCCT 57.693 40.909 0.00 0.00 0.00 4.75
220 221 7.429340 CGAAAATACAATCTGTAACCTTGATGC 59.571 37.037 0.00 0.00 36.31 3.91
221 222 7.910162 CCGAAAATACAATCTGTAACCTTGATG 59.090 37.037 0.00 0.00 36.31 3.07
223 224 6.373216 CCCGAAAATACAATCTGTAACCTTGA 59.627 38.462 0.00 0.00 36.31 3.02
224 225 6.373216 TCCCGAAAATACAATCTGTAACCTTG 59.627 38.462 0.00 0.00 36.31 3.61
225 226 6.478129 TCCCGAAAATACAATCTGTAACCTT 58.522 36.000 0.00 0.00 36.31 3.50
227 228 6.746745 TTCCCGAAAATACAATCTGTAACC 57.253 37.500 0.00 0.00 36.31 2.85
228 229 9.124807 CTTTTTCCCGAAAATACAATCTGTAAC 57.875 33.333 3.58 0.00 39.69 2.50
229 230 9.069082 TCTTTTTCCCGAAAATACAATCTGTAA 57.931 29.630 3.58 0.00 39.69 2.41
231 232 7.519032 TCTTTTTCCCGAAAATACAATCTGT 57.481 32.000 3.58 0.00 39.69 3.41
232 233 8.986477 AATCTTTTTCCCGAAAATACAATCTG 57.014 30.769 3.58 0.00 39.69 2.90
235 236 9.869757 CCTTAATCTTTTTCCCGAAAATACAAT 57.130 29.630 3.58 0.00 39.69 2.71
236 237 9.080097 TCCTTAATCTTTTTCCCGAAAATACAA 57.920 29.630 3.58 0.00 39.69 2.41
237 238 8.638629 TCCTTAATCTTTTTCCCGAAAATACA 57.361 30.769 3.58 0.00 39.69 2.29
240 241 8.593679 ACAATCCTTAATCTTTTTCCCGAAAAT 58.406 29.630 3.58 0.00 39.69 1.82
241 242 7.870445 CACAATCCTTAATCTTTTTCCCGAAAA 59.130 33.333 0.00 0.00 38.40 2.29
242 243 7.375053 CACAATCCTTAATCTTTTTCCCGAAA 58.625 34.615 0.00 0.00 0.00 3.46
243 244 6.071616 CCACAATCCTTAATCTTTTTCCCGAA 60.072 38.462 0.00 0.00 0.00 4.30
244 245 5.417580 CCACAATCCTTAATCTTTTTCCCGA 59.582 40.000 0.00 0.00 0.00 5.14
245 246 5.417580 TCCACAATCCTTAATCTTTTTCCCG 59.582 40.000 0.00 0.00 0.00 5.14
246 247 6.850752 TCCACAATCCTTAATCTTTTTCCC 57.149 37.500 0.00 0.00 0.00 3.97
247 248 7.896811 AGTTCCACAATCCTTAATCTTTTTCC 58.103 34.615 0.00 0.00 0.00 3.13
248 249 7.750903 CGAGTTCCACAATCCTTAATCTTTTTC 59.249 37.037 0.00 0.00 0.00 2.29
249 250 7.593825 CGAGTTCCACAATCCTTAATCTTTTT 58.406 34.615 0.00 0.00 0.00 1.94
250 251 6.349363 GCGAGTTCCACAATCCTTAATCTTTT 60.349 38.462 0.00 0.00 0.00 2.27
251 252 5.123979 GCGAGTTCCACAATCCTTAATCTTT 59.876 40.000 0.00 0.00 0.00 2.52
252 253 4.636206 GCGAGTTCCACAATCCTTAATCTT 59.364 41.667 0.00 0.00 0.00 2.40
253 254 4.192317 GCGAGTTCCACAATCCTTAATCT 58.808 43.478 0.00 0.00 0.00 2.40
254 255 3.001330 CGCGAGTTCCACAATCCTTAATC 59.999 47.826 0.00 0.00 0.00 1.75
255 256 2.936498 CGCGAGTTCCACAATCCTTAAT 59.064 45.455 0.00 0.00 0.00 1.40
256 257 2.289195 ACGCGAGTTCCACAATCCTTAA 60.289 45.455 15.93 0.00 46.40 1.85
257 258 1.274167 ACGCGAGTTCCACAATCCTTA 59.726 47.619 15.93 0.00 46.40 2.69
258 259 0.034896 ACGCGAGTTCCACAATCCTT 59.965 50.000 15.93 0.00 46.40 3.36
259 260 0.892755 TACGCGAGTTCCACAATCCT 59.107 50.000 15.93 0.00 46.40 3.24
260 261 1.278238 CTACGCGAGTTCCACAATCC 58.722 55.000 15.93 0.00 46.40 3.01
261 262 1.278238 CCTACGCGAGTTCCACAATC 58.722 55.000 15.93 0.00 46.40 2.67
262 263 0.606604 ACCTACGCGAGTTCCACAAT 59.393 50.000 15.93 0.00 46.40 2.71
263 264 0.390124 AACCTACGCGAGTTCCACAA 59.610 50.000 15.93 0.00 46.40 3.33
264 265 0.319211 CAACCTACGCGAGTTCCACA 60.319 55.000 15.93 0.00 46.40 4.17
265 266 0.038892 TCAACCTACGCGAGTTCCAC 60.039 55.000 15.93 0.00 46.40 4.02
266 267 0.675083 TTCAACCTACGCGAGTTCCA 59.325 50.000 15.93 0.00 46.40 3.53
267 268 1.787012 TTTCAACCTACGCGAGTTCC 58.213 50.000 15.93 0.00 46.40 3.62
268 269 3.430895 TCAATTTCAACCTACGCGAGTTC 59.569 43.478 15.93 0.00 46.40 3.01
269 270 3.395639 TCAATTTCAACCTACGCGAGTT 58.604 40.909 15.93 10.80 46.40 3.01
271 272 3.785505 GCATCAATTTCAACCTACGCGAG 60.786 47.826 15.93 5.77 0.00 5.03
272 273 2.095213 GCATCAATTTCAACCTACGCGA 59.905 45.455 15.93 0.00 0.00 5.87
273 274 2.440501 GCATCAATTTCAACCTACGCG 58.559 47.619 3.53 3.53 0.00 6.01
274 275 2.163412 TGGCATCAATTTCAACCTACGC 59.837 45.455 0.00 0.00 0.00 4.42
275 276 3.731867 GCTGGCATCAATTTCAACCTACG 60.732 47.826 0.00 0.00 0.00 3.51
276 277 3.445096 AGCTGGCATCAATTTCAACCTAC 59.555 43.478 0.00 0.00 0.00 3.18
277 278 3.444742 CAGCTGGCATCAATTTCAACCTA 59.555 43.478 5.57 0.00 0.00 3.08
278 279 2.232941 CAGCTGGCATCAATTTCAACCT 59.767 45.455 5.57 0.00 0.00 3.50
279 280 2.028748 ACAGCTGGCATCAATTTCAACC 60.029 45.455 19.93 0.00 0.00 3.77
280 281 3.057033 AGACAGCTGGCATCAATTTCAAC 60.057 43.478 24.55 0.00 0.00 3.18
281 282 3.057104 CAGACAGCTGGCATCAATTTCAA 60.057 43.478 24.55 0.00 38.51 2.69
293 294 4.193826 AGTATGTTGTACAGACAGCTGG 57.806 45.455 19.93 2.38 42.36 4.85
294 295 6.311445 CCTAAAGTATGTTGTACAGACAGCTG 59.689 42.308 13.48 13.48 42.36 4.24
296 297 5.063564 GCCTAAAGTATGTTGTACAGACAGC 59.936 44.000 13.66 10.11 42.36 4.40
299 300 5.061808 CACGCCTAAAGTATGTTGTACAGAC 59.938 44.000 0.00 0.00 40.38 3.51
300 301 5.165676 CACGCCTAAAGTATGTTGTACAGA 58.834 41.667 0.00 0.00 0.00 3.41
301 302 4.927425 ACACGCCTAAAGTATGTTGTACAG 59.073 41.667 0.00 0.00 0.00 2.74
302 303 4.885413 ACACGCCTAAAGTATGTTGTACA 58.115 39.130 0.00 0.00 0.00 2.90
303 304 4.328169 GGACACGCCTAAAGTATGTTGTAC 59.672 45.833 0.00 0.00 0.00 2.90
304 305 4.497300 GGACACGCCTAAAGTATGTTGTA 58.503 43.478 0.00 0.00 0.00 2.41
305 306 3.332034 GGACACGCCTAAAGTATGTTGT 58.668 45.455 0.00 0.00 0.00 3.32
307 308 2.303600 TGGGACACGCCTAAAGTATGTT 59.696 45.455 0.00 0.00 36.66 2.71
308 309 1.903860 TGGGACACGCCTAAAGTATGT 59.096 47.619 0.00 0.00 36.66 2.29
309 310 2.684001 TGGGACACGCCTAAAGTATG 57.316 50.000 0.00 0.00 36.66 2.39
322 323 2.350895 CCCGCTTGACATGGGACA 59.649 61.111 6.93 0.00 46.41 4.02
323 324 1.745489 GACCCGCTTGACATGGGAC 60.745 63.158 13.32 5.13 46.41 4.46
324 325 1.918293 AGACCCGCTTGACATGGGA 60.918 57.895 13.32 0.00 46.41 4.37
326 327 1.746615 CCAGACCCGCTTGACATGG 60.747 63.158 0.00 0.00 0.00 3.66
327 328 1.746615 CCCAGACCCGCTTGACATG 60.747 63.158 0.00 0.00 0.00 3.21
328 329 2.224159 ACCCAGACCCGCTTGACAT 61.224 57.895 0.00 0.00 0.00 3.06
329 330 2.847234 ACCCAGACCCGCTTGACA 60.847 61.111 0.00 0.00 0.00 3.58
330 331 2.358737 CACCCAGACCCGCTTGAC 60.359 66.667 0.00 0.00 0.00 3.18
331 332 3.636231 CCACCCAGACCCGCTTGA 61.636 66.667 0.00 0.00 0.00 3.02
332 333 3.953775 ACCACCCAGACCCGCTTG 61.954 66.667 0.00 0.00 0.00 4.01
334 335 3.839046 TACACCACCCAGACCCGCT 62.839 63.158 0.00 0.00 0.00 5.52
335 336 3.310860 CTACACCACCCAGACCCGC 62.311 68.421 0.00 0.00 0.00 6.13
336 337 1.477685 AACTACACCACCCAGACCCG 61.478 60.000 0.00 0.00 0.00 5.28
337 338 0.036306 CAACTACACCACCCAGACCC 59.964 60.000 0.00 0.00 0.00 4.46
338 339 1.053424 TCAACTACACCACCCAGACC 58.947 55.000 0.00 0.00 0.00 3.85
357 421 6.268825 AGTGTGTGAGACTAACGTGATAAT 57.731 37.500 0.00 0.00 0.00 1.28
391 455 1.738099 CTGAGCCCAGGTTCGAACG 60.738 63.158 21.34 9.05 36.77 3.95
395 459 0.250295 TTTGTCTGAGCCCAGGTTCG 60.250 55.000 0.00 0.00 40.76 3.95
425 489 8.835467 TGAAACGTCTTAAAAATGAAAGACTG 57.165 30.769 12.00 8.68 46.10 3.51
426 490 9.665264 GATGAAACGTCTTAAAAATGAAAGACT 57.335 29.630 12.00 0.00 46.10 3.24
428 492 8.846211 AGGATGAAACGTCTTAAAAATGAAAGA 58.154 29.630 0.00 0.00 0.00 2.52
429 493 9.118236 GAGGATGAAACGTCTTAAAAATGAAAG 57.882 33.333 0.00 0.00 0.00 2.62
442 514 3.429684 GGAAGAGAGGAGGATGAAACGTC 60.430 52.174 0.00 0.00 0.00 4.34
468 541 6.860023 GGAAAGATGGAAATCAAGCATTATCG 59.140 38.462 0.00 0.00 0.00 2.92
487 560 2.175499 CAGGCATTATCTGGGGGAAAGA 59.825 50.000 0.00 0.00 0.00 2.52
488 561 2.175499 TCAGGCATTATCTGGGGGAAAG 59.825 50.000 0.00 0.00 33.36 2.62
491 564 2.138535 ATCAGGCATTATCTGGGGGA 57.861 50.000 0.00 0.00 33.36 4.81
492 565 2.986534 AATCAGGCATTATCTGGGGG 57.013 50.000 0.00 0.00 33.36 5.40
493 566 4.109877 AGAAATCAGGCATTATCTGGGG 57.890 45.455 0.00 0.00 33.36 4.96
494 567 5.624159 TGTAGAAATCAGGCATTATCTGGG 58.376 41.667 0.00 0.00 33.36 4.45
496 569 8.893219 TTACTGTAGAAATCAGGCATTATCTG 57.107 34.615 0.00 0.00 37.25 2.90
497 570 9.905713 TTTTACTGTAGAAATCAGGCATTATCT 57.094 29.630 0.00 0.00 37.25 1.98
499 572 9.905713 TCTTTTACTGTAGAAATCAGGCATTAT 57.094 29.630 0.00 0.00 37.25 1.28
501 574 8.103305 TCTCTTTTACTGTAGAAATCAGGCATT 58.897 33.333 0.00 0.00 37.25 3.56
502 575 7.624549 TCTCTTTTACTGTAGAAATCAGGCAT 58.375 34.615 0.00 0.00 37.25 4.40
504 577 9.771534 ATATCTCTTTTACTGTAGAAATCAGGC 57.228 33.333 0.00 0.00 37.25 4.85
515 588 8.908903 CAGACCTACAGATATCTCTTTTACTGT 58.091 37.037 1.03 0.00 40.74 3.55
516 589 8.908903 ACAGACCTACAGATATCTCTTTTACTG 58.091 37.037 1.03 11.02 0.00 2.74
556 637 9.527157 TGACATTGATTACCTTTTAGGAATTCA 57.473 29.630 7.93 0.00 37.67 2.57
576 657 9.150348 GGATTAATTTCGAACCAAATTGACATT 57.850 29.630 0.00 0.00 36.75 2.71
581 662 8.532977 AAGTGGATTAATTTCGAACCAAATTG 57.467 30.769 0.00 0.00 36.75 2.32
600 681 3.244387 TGGAATGAACGTGATGAAGTGGA 60.244 43.478 0.00 0.00 0.00 4.02
658 741 1.668419 GCTCGGCCAGTAAATGTGAT 58.332 50.000 2.24 0.00 0.00 3.06
686 769 3.229276 TCGCTTTACAAATTGGCATGG 57.771 42.857 0.00 0.00 0.00 3.66
762 845 0.538746 TACTCGGCTCACACCAGTCA 60.539 55.000 0.00 0.00 0.00 3.41
766 849 1.045407 AGTTTACTCGGCTCACACCA 58.955 50.000 0.00 0.00 0.00 4.17
803 1995 4.057432 GTGATAGCTCTTCTGCTTGGATC 58.943 47.826 0.00 0.00 43.74 3.36
806 2275 3.257469 TGTGATAGCTCTTCTGCTTGG 57.743 47.619 0.00 0.00 43.74 3.61
821 2290 0.774908 TTCCTTCCCCCGTTTGTGAT 59.225 50.000 0.00 0.00 0.00 3.06
835 2304 4.016706 CCGTGCCGGTCCTTCCTT 62.017 66.667 1.90 0.00 42.73 3.36
910 2380 2.618449 GGGATTGGGGAACGGGGAA 61.618 63.158 0.00 0.00 0.00 3.97
911 2381 3.018805 GGGATTGGGGAACGGGGA 61.019 66.667 0.00 0.00 0.00 4.81
912 2382 4.137615 GGGGATTGGGGAACGGGG 62.138 72.222 0.00 0.00 0.00 5.73
913 2383 3.343326 TGGGGATTGGGGAACGGG 61.343 66.667 0.00 0.00 0.00 5.28
914 2384 2.044352 GTGGGGATTGGGGAACGG 60.044 66.667 0.00 0.00 0.00 4.44
915 2385 2.437716 CGTGGGGATTGGGGAACG 60.438 66.667 0.00 0.00 0.00 3.95
916 2386 2.754254 GCGTGGGGATTGGGGAAC 60.754 66.667 0.00 0.00 0.00 3.62
995 2465 0.670706 CTCGGAGATCTTCATGGCGA 59.329 55.000 0.96 0.00 33.89 5.54
1827 3336 1.807573 CTTGGCTTCGAGACGCTCC 60.808 63.158 1.73 0.00 0.00 4.70
1950 3459 4.323477 TCCGCCAAGTTCCCGGTG 62.323 66.667 0.00 0.00 42.48 4.94
1984 3493 1.098050 GCGTTGGCCATGATTCTCTT 58.902 50.000 6.09 0.00 0.00 2.85
2146 3655 1.208535 GATACCACCATCAACCACCGA 59.791 52.381 0.00 0.00 0.00 4.69
2411 3920 0.453282 CTCAAACAAGTCCGCGCATG 60.453 55.000 8.75 0.00 0.00 4.06
2415 3924 1.126846 GATGTCTCAAACAAGTCCGCG 59.873 52.381 0.00 0.00 42.37 6.46
2610 4119 5.403897 TTTGAGTCAAACGTAAGAAGCAG 57.596 39.130 14.35 0.00 43.62 4.24
2622 4131 9.349713 ACCTACAGATACAAATTTTGAGTCAAA 57.650 29.630 14.35 14.35 0.00 2.69
2626 4135 7.458397 TCCACCTACAGATACAAATTTTGAGT 58.542 34.615 15.81 3.75 0.00 3.41
2635 4144 5.554437 TTGTGTTCCACCTACAGATACAA 57.446 39.130 0.00 0.00 32.73 2.41
2749 4258 9.552114 CTGAAGATGAATTTTGATCTACACAAC 57.448 33.333 0.00 0.00 29.63 3.32
2782 4291 1.405821 CTTGATAGCCTCGTCCTCGTT 59.594 52.381 0.00 0.00 38.33 3.85
2842 4351 4.910195 TGAGTTGTGAGCATTAGGAATGT 58.090 39.130 1.47 0.00 41.01 2.71
2844 4353 5.748402 TCATGAGTTGTGAGCATTAGGAAT 58.252 37.500 0.00 0.00 0.00 3.01
3071 4580 0.890683 ATTGCCAAAGAAGCCTTCCG 59.109 50.000 0.00 0.00 0.00 4.30
3081 4590 0.604578 CACCAGGTCCATTGCCAAAG 59.395 55.000 0.00 0.00 0.00 2.77
3098 4607 4.980805 TCAGTTCACGCGCCCCAC 62.981 66.667 5.73 0.00 0.00 4.61
3152 4661 0.251077 CTTCTGCTCCTTTGCCACCT 60.251 55.000 0.00 0.00 0.00 4.00
3221 4730 3.877559 TCACCCTCATCATTACTTGCAG 58.122 45.455 0.00 0.00 0.00 4.41
3399 4908 6.717997 ACACAAGGGGTAGTAAATTTTGGTAG 59.282 38.462 0.00 0.00 0.00 3.18
3477 4987 6.039047 CAGATTGAAGGTAATAGCTGCACATT 59.961 38.462 0.00 3.58 29.44 2.71
3542 5052 7.509546 AGAAGGTATGAAGAAACAGAAAGTCA 58.490 34.615 0.00 0.00 0.00 3.41
3543 5053 7.971183 AGAAGGTATGAAGAAACAGAAAGTC 57.029 36.000 0.00 0.00 0.00 3.01
3623 5133 2.668945 GGAAGCGAAGTTCTTGACTAGC 59.331 50.000 0.56 0.00 37.72 3.42
3687 5197 1.073897 GGGTGCCTTCAGAAGCAGT 59.926 57.895 4.41 0.00 40.28 4.40
3894 5404 2.038952 CACCATCTCTCAGTCCAACCAA 59.961 50.000 0.00 0.00 0.00 3.67
4038 5548 2.089201 CTTCATGCTCTCAACATGCCA 58.911 47.619 0.00 0.00 43.71 4.92
4142 5652 6.623767 GCTGACTACATTCATCAGGGTTTTTC 60.624 42.308 2.90 0.00 40.23 2.29
4234 5744 1.678970 GCCCCGTTCAGGAGCATTT 60.679 57.895 0.00 0.00 45.00 2.32
4235 5745 2.044946 GCCCCGTTCAGGAGCATT 60.045 61.111 0.00 0.00 45.00 3.56
4236 5746 3.329889 TGCCCCGTTCAGGAGCAT 61.330 61.111 0.00 0.00 45.00 3.79
4237 5747 4.020617 CTGCCCCGTTCAGGAGCA 62.021 66.667 0.00 0.00 45.00 4.26
4241 5751 2.429930 TGAACTGCCCCGTTCAGG 59.570 61.111 8.65 0.00 45.92 3.86
4244 5754 1.652563 GTTGTGAACTGCCCCGTTC 59.347 57.895 4.29 4.29 42.73 3.95
4351 5861 6.703319 TGGTTACTATCGACAAAGAATCCAA 58.297 36.000 0.00 0.00 0.00 3.53
4380 5891 5.793457 CACATCAGCATGCATTATATTCACG 59.207 40.000 21.98 0.00 34.76 4.35
4387 5898 4.976864 TCCTACACATCAGCATGCATTAT 58.023 39.130 21.98 7.05 34.76 1.28
4433 5944 5.245977 CCAGTAGGTTCCCAAATTCAATGTT 59.754 40.000 0.00 0.00 0.00 2.71
4435 5946 5.016173 TCCAGTAGGTTCCCAAATTCAATG 58.984 41.667 0.00 0.00 35.89 2.82
4436 5947 5.269554 TCCAGTAGGTTCCCAAATTCAAT 57.730 39.130 0.00 0.00 35.89 2.57
4437 5948 4.733077 TCCAGTAGGTTCCCAAATTCAA 57.267 40.909 0.00 0.00 35.89 2.69
4438 5949 4.946160 ATCCAGTAGGTTCCCAAATTCA 57.054 40.909 0.00 0.00 35.89 2.57
4439 5950 5.480422 ACAAATCCAGTAGGTTCCCAAATTC 59.520 40.000 0.00 0.00 35.89 2.17
4480 5999 9.696917 GATTAGTTGAATTTGACAGAAAATGGT 57.303 29.630 0.00 0.00 30.21 3.55
4494 6013 5.136105 GGGCATCAGGAGATTAGTTGAATT 58.864 41.667 0.00 0.00 30.20 2.17
4498 6017 2.441001 AGGGGCATCAGGAGATTAGTTG 59.559 50.000 0.00 0.00 30.20 3.16
4499 6018 2.781667 AGGGGCATCAGGAGATTAGTT 58.218 47.619 0.00 0.00 30.20 2.24
4543 6062 9.071276 CTAGAATAGTTTGAATGGTAATGCCAT 57.929 33.333 0.00 0.00 46.38 4.40
4544 6063 8.450578 CTAGAATAGTTTGAATGGTAATGCCA 57.549 34.615 0.00 0.00 42.36 4.92
4566 6085 3.696548 GCCCCTCTCCAATTTTCAACTAG 59.303 47.826 0.00 0.00 0.00 2.57
4571 6090 1.710244 TCTGCCCCTCTCCAATTTTCA 59.290 47.619 0.00 0.00 0.00 2.69
4577 6096 2.274542 TGTATTTCTGCCCCTCTCCAA 58.725 47.619 0.00 0.00 0.00 3.53
4604 6123 1.281287 GGTTTCAGGGAGTCCTTACCC 59.719 57.143 9.58 0.00 42.67 3.69
4616 6138 7.406031 TGTGTAGACTATAGAAGGTTTCAGG 57.594 40.000 6.78 0.00 0.00 3.86
4655 8372 7.281774 AGTGTTAGTTCAGCATTATGAATCTGG 59.718 37.037 0.00 0.00 41.05 3.86
4873 8591 2.373169 TGGAGTCCACTTGAGCAGATTT 59.627 45.455 8.12 0.00 0.00 2.17
5003 8747 9.586435 CTGATATTACTTTCTGTACATGTCACA 57.414 33.333 0.00 4.84 0.00 3.58
5004 8748 9.803315 TCTGATATTACTTTCTGTACATGTCAC 57.197 33.333 0.00 0.00 0.00 3.67
5020 8764 8.076714 TGCAATCTTGTCGATTCTGATATTAC 57.923 34.615 0.00 0.00 40.33 1.89
5021 8765 8.837788 ATGCAATCTTGTCGATTCTGATATTA 57.162 30.769 0.00 0.00 40.33 0.98
5110 9038 3.672241 GCTCACAACAAAAACCGTCTTGT 60.672 43.478 0.00 0.00 37.36 3.16
5116 9044 3.443037 TGAATGCTCACAACAAAAACCG 58.557 40.909 0.00 0.00 0.00 4.44
5118 9046 5.176223 CCTCATGAATGCTCACAACAAAAAC 59.824 40.000 0.00 0.00 33.30 2.43
5127 9055 5.371526 TCCTAATTCCTCATGAATGCTCAC 58.628 41.667 0.00 0.00 42.97 3.51
5235 9163 0.827507 AAAACCCAAGCACGGCATCT 60.828 50.000 0.00 0.00 0.00 2.90
5333 9261 2.864343 AGCACACTCAGAAACGTGTAAC 59.136 45.455 0.00 0.00 42.05 2.50
5379 9307 4.136796 TCCTTTCTGTATATGCACATGCC 58.863 43.478 0.49 0.00 41.18 4.40
5397 9325 7.072454 TGGTATACTTGGAATGATAGCTTCCTT 59.928 37.037 2.25 0.00 42.27 3.36
5446 9374 7.761409 TGTTGCCTGATTAGACATATTCAAAC 58.239 34.615 0.00 0.00 0.00 2.93
5478 9406 4.855340 TCCTTCATGATTAAAGGGACACC 58.145 43.478 10.61 0.00 42.00 4.16
5606 9542 4.384056 CAGCAGCTGCAGGTAAGTAATAT 58.616 43.478 38.24 11.97 45.16 1.28


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

AutoCloner maintained by Alex Coulton.