Multiple sequence alignment - TraesCS1A01G103300

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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 TraesCS1A01G103300 chr1A 100.000 2546 0 0 1 2546 99341591 99339046 0.000000e+00 4702
1 TraesCS1A01G103300 chr1A 80.102 196 36 3 1863 2056 12169783 12169977 2.640000e-30 143
2 TraesCS1A01G103300 chr1A 81.250 176 30 3 1883 2056 12110426 12110252 3.420000e-29 139
3 TraesCS1A01G103300 chr1B 90.298 1711 80 27 380 2056 134418012 134416354 0.000000e+00 2161
4 TraesCS1A01G103300 chr1B 88.800 500 45 9 2055 2546 134416306 134415810 1.010000e-168 603
5 TraesCS1A01G103300 chr1B 92.308 208 14 2 1 206 134418210 134418003 6.890000e-76 294
6 TraesCS1A01G103300 chr1D 95.973 1167 33 6 447 1611 81152625 81151471 0.000000e+00 1882
7 TraesCS1A01G103300 chr4D 84.855 449 58 6 2055 2499 128909374 128909816 6.460000e-121 444
8 TraesCS1A01G103300 chr4D 82.432 444 63 12 2055 2493 343092598 343093031 8.600000e-100 374
9 TraesCS1A01G103300 chr2D 83.409 440 64 7 2064 2499 383561382 383561816 1.420000e-107 399
10 TraesCS1A01G103300 chr2A 82.851 449 67 8 2055 2499 21147369 21146927 6.600000e-106 394
11 TraesCS1A01G103300 chr6D 82.955 440 64 7 2065 2499 147688695 147688262 1.100000e-103 387
12 TraesCS1A01G103300 chr6B 82.040 451 64 10 2055 2499 710142809 710142370 4.000000e-98 368
13 TraesCS1A01G103300 chr5B 82.090 402 59 9 2055 2451 594753841 594754234 5.250000e-87 331
14 TraesCS1A01G103300 chr4B 80.690 435 69 10 2055 2483 642374673 642374248 8.790000e-85 324
15 TraesCS1A01G103300 chr4B 85.714 105 14 1 1953 2056 610076625 610076729 2.680000e-20 110
16 TraesCS1A01G103300 chr7B 80.579 242 39 4 1823 2056 144300809 144300568 2.010000e-41 180
17 TraesCS1A01G103300 chr5D 78.977 176 31 6 1883 2055 62516978 62516806 5.760000e-22 115


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 TraesCS1A01G103300 chr1A 99339046 99341591 2545 True 4702.000000 4702 100.000000 1 2546 1 chr1A.!!$R2 2545
1 TraesCS1A01G103300 chr1B 134415810 134418210 2400 True 1019.333333 2161 90.468667 1 2546 3 chr1B.!!$R1 2545
2 TraesCS1A01G103300 chr1D 81151471 81152625 1154 True 1882.000000 1882 95.973000 447 1611 1 chr1D.!!$R1 1164

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
296 299 0.331616 TTTTTAGGGGAGGCTGAGGC 59.668 55.0 0.0 0.0 37.82 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2098 0.319211 TGTTGGTACTCTTGCCGACG 60.319 55.0 0.0 0.0 43.36 5.12 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
53 55 1.388547 TGTGTTCAACTTGGTCCTGC 58.611 50.000 0.00 0.00 0.00 4.85
67 69 6.719370 ACTTGGTCCTGCAAAATAAATAGACA 59.281 34.615 0.00 0.00 0.00 3.41
96 99 1.625315 TCGGGGCATCTATTCATCAGG 59.375 52.381 0.00 0.00 0.00 3.86
146 149 9.469807 GTCAATTGTGTTTTTACCATTACATCA 57.530 29.630 5.13 0.00 0.00 3.07
180 183 3.414700 CCTCGCGGTGCAGTGTTC 61.415 66.667 6.13 0.00 0.00 3.18
194 197 2.436824 GTTCTGCTTCCTCCCCGC 60.437 66.667 0.00 0.00 0.00 6.13
201 204 1.067582 CTTCCTCCCCGCGACATAC 59.932 63.158 8.23 0.00 0.00 2.39
202 205 2.679132 CTTCCTCCCCGCGACATACG 62.679 65.000 8.23 0.00 45.66 3.06
203 206 3.524606 CCTCCCCGCGACATACGT 61.525 66.667 8.23 0.00 44.60 3.57
204 207 2.493030 CTCCCCGCGACATACGTT 59.507 61.111 8.23 0.00 44.60 3.99
205 208 1.153706 CTCCCCGCGACATACGTTT 60.154 57.895 8.23 0.00 44.60 3.60
206 209 1.418342 CTCCCCGCGACATACGTTTG 61.418 60.000 8.23 4.33 44.60 2.93
207 210 2.457778 CCCCGCGACATACGTTTGG 61.458 63.158 8.23 0.00 44.60 3.28
208 211 1.446445 CCCGCGACATACGTTTGGA 60.446 57.895 8.23 0.00 44.60 3.53
209 212 1.689352 CCCGCGACATACGTTTGGAC 61.689 60.000 8.23 3.65 44.60 4.02
210 213 1.009903 CCGCGACATACGTTTGGACA 61.010 55.000 8.23 0.00 44.60 4.02
211 214 0.785378 CGCGACATACGTTTGGACAA 59.215 50.000 0.00 0.00 44.60 3.18
212 215 1.461237 CGCGACATACGTTTGGACAAC 60.461 52.381 0.00 0.00 44.60 3.32
213 216 1.136169 GCGACATACGTTTGGACAACC 60.136 52.381 10.79 0.00 44.60 3.77
214 217 1.461897 CGACATACGTTTGGACAACCC 59.538 52.381 10.79 0.00 37.22 4.11
215 218 2.774687 GACATACGTTTGGACAACCCT 58.225 47.619 10.79 0.00 35.38 4.34
216 219 3.614630 CGACATACGTTTGGACAACCCTA 60.615 47.826 10.79 0.00 37.22 3.53
217 220 3.930848 GACATACGTTTGGACAACCCTAG 59.069 47.826 10.79 0.00 35.38 3.02
218 221 3.579586 ACATACGTTTGGACAACCCTAGA 59.420 43.478 10.79 0.00 35.38 2.43
219 222 2.538512 ACGTTTGGACAACCCTAGAC 57.461 50.000 0.00 0.00 35.38 2.59
220 223 2.044758 ACGTTTGGACAACCCTAGACT 58.955 47.619 0.00 0.00 35.38 3.24
221 224 2.436911 ACGTTTGGACAACCCTAGACTT 59.563 45.455 0.00 0.00 35.38 3.01
222 225 3.642848 ACGTTTGGACAACCCTAGACTTA 59.357 43.478 0.00 0.00 35.38 2.24
223 226 3.992427 CGTTTGGACAACCCTAGACTTAC 59.008 47.826 0.00 0.00 35.38 2.34
224 227 3.947910 TTGGACAACCCTAGACTTACG 57.052 47.619 0.00 0.00 35.38 3.18
225 228 2.880443 TGGACAACCCTAGACTTACGT 58.120 47.619 0.00 0.00 35.38 3.57
226 229 4.032960 TGGACAACCCTAGACTTACGTA 57.967 45.455 0.00 0.00 35.38 3.57
227 230 4.406456 TGGACAACCCTAGACTTACGTAA 58.594 43.478 7.94 7.94 35.38 3.18
228 231 4.460382 TGGACAACCCTAGACTTACGTAAG 59.540 45.833 29.27 29.27 38.80 2.34
229 232 4.142293 GGACAACCCTAGACTTACGTAAGG 60.142 50.000 32.63 20.28 46.39 2.69
230 233 4.666512 ACAACCCTAGACTTACGTAAGGA 58.333 43.478 32.63 19.30 46.39 3.36
231 234 5.079643 ACAACCCTAGACTTACGTAAGGAA 58.920 41.667 32.63 19.11 46.39 3.36
263 266 6.779385 CGTTTACGTAATAGTCATCGTGAA 57.221 37.500 9.18 0.00 37.66 3.18
264 267 7.196282 CGTTTACGTAATAGTCATCGTGAAA 57.804 36.000 9.18 0.00 34.70 2.69
265 268 7.317901 CGTTTACGTAATAGTCATCGTGAAAG 58.682 38.462 9.18 0.00 34.70 2.62
266 269 7.216881 CGTTTACGTAATAGTCATCGTGAAAGA 59.783 37.037 9.18 0.00 35.08 2.52
267 270 9.017669 GTTTACGTAATAGTCATCGTGAAAGAT 57.982 33.333 9.18 0.00 34.70 2.40
268 271 9.577110 TTTACGTAATAGTCATCGTGAAAGATT 57.423 29.630 9.18 0.00 37.66 2.40
270 273 8.783999 ACGTAATAGTCATCGTGAAAGATTAG 57.216 34.615 0.00 0.00 35.24 1.73
271 274 7.861372 ACGTAATAGTCATCGTGAAAGATTAGG 59.139 37.037 0.00 0.00 35.24 2.69
272 275 8.074370 CGTAATAGTCATCGTGAAAGATTAGGA 58.926 37.037 0.00 0.00 0.00 2.94
273 276 9.915629 GTAATAGTCATCGTGAAAGATTAGGAT 57.084 33.333 0.00 0.00 0.00 3.24
275 278 8.824159 ATAGTCATCGTGAAAGATTAGGATTG 57.176 34.615 0.00 0.00 0.00 2.67
276 279 6.051717 AGTCATCGTGAAAGATTAGGATTGG 58.948 40.000 0.00 0.00 0.00 3.16
277 280 5.817816 GTCATCGTGAAAGATTAGGATTGGT 59.182 40.000 0.00 0.00 0.00 3.67
278 281 6.316390 GTCATCGTGAAAGATTAGGATTGGTT 59.684 38.462 0.00 0.00 0.00 3.67
279 282 6.884295 TCATCGTGAAAGATTAGGATTGGTTT 59.116 34.615 0.00 0.00 0.00 3.27
280 283 7.393234 TCATCGTGAAAGATTAGGATTGGTTTT 59.607 33.333 0.00 0.00 0.00 2.43
281 284 7.519032 TCGTGAAAGATTAGGATTGGTTTTT 57.481 32.000 0.00 0.00 0.00 1.94
282 285 8.624367 TCGTGAAAGATTAGGATTGGTTTTTA 57.376 30.769 0.00 0.00 0.00 1.52
283 286 8.726988 TCGTGAAAGATTAGGATTGGTTTTTAG 58.273 33.333 0.00 0.00 0.00 1.85
284 287 7.968405 CGTGAAAGATTAGGATTGGTTTTTAGG 59.032 37.037 0.00 0.00 0.00 2.69
285 288 8.251026 GTGAAAGATTAGGATTGGTTTTTAGGG 58.749 37.037 0.00 0.00 0.00 3.53
286 289 7.398904 TGAAAGATTAGGATTGGTTTTTAGGGG 59.601 37.037 0.00 0.00 0.00 4.79
287 290 6.668133 AGATTAGGATTGGTTTTTAGGGGA 57.332 37.500 0.00 0.00 0.00 4.81
288 291 6.673583 AGATTAGGATTGGTTTTTAGGGGAG 58.326 40.000 0.00 0.00 0.00 4.30
289 292 3.757947 AGGATTGGTTTTTAGGGGAGG 57.242 47.619 0.00 0.00 0.00 4.30
290 293 2.108168 GGATTGGTTTTTAGGGGAGGC 58.892 52.381 0.00 0.00 0.00 4.70
291 294 2.292257 GGATTGGTTTTTAGGGGAGGCT 60.292 50.000 0.00 0.00 0.00 4.58
292 295 2.302587 TTGGTTTTTAGGGGAGGCTG 57.697 50.000 0.00 0.00 0.00 4.85
293 296 1.451449 TGGTTTTTAGGGGAGGCTGA 58.549 50.000 0.00 0.00 0.00 4.26
294 297 1.354368 TGGTTTTTAGGGGAGGCTGAG 59.646 52.381 0.00 0.00 0.00 3.35
295 298 1.341089 GGTTTTTAGGGGAGGCTGAGG 60.341 57.143 0.00 0.00 0.00 3.86
296 299 0.331616 TTTTTAGGGGAGGCTGAGGC 59.668 55.000 0.00 0.00 37.82 4.70
313 316 3.032265 AGGCCCACCTCCATAAAAATC 57.968 47.619 0.00 0.00 46.34 2.17
314 317 2.314549 AGGCCCACCTCCATAAAAATCA 59.685 45.455 0.00 0.00 46.34 2.57
315 318 2.695147 GGCCCACCTCCATAAAAATCAG 59.305 50.000 0.00 0.00 0.00 2.90
316 319 2.695147 GCCCACCTCCATAAAAATCAGG 59.305 50.000 0.00 0.00 0.00 3.86
317 320 3.627237 GCCCACCTCCATAAAAATCAGGA 60.627 47.826 0.00 0.00 0.00 3.86
318 321 3.954258 CCCACCTCCATAAAAATCAGGAC 59.046 47.826 0.00 0.00 0.00 3.85
319 322 3.627577 CCACCTCCATAAAAATCAGGACG 59.372 47.826 0.00 0.00 0.00 4.79
320 323 4.513442 CACCTCCATAAAAATCAGGACGA 58.487 43.478 0.00 0.00 0.00 4.20
321 324 4.941263 CACCTCCATAAAAATCAGGACGAA 59.059 41.667 0.00 0.00 0.00 3.85
322 325 5.590259 CACCTCCATAAAAATCAGGACGAAT 59.410 40.000 0.00 0.00 0.00 3.34
323 326 5.590259 ACCTCCATAAAAATCAGGACGAATG 59.410 40.000 0.00 0.00 0.00 2.67
324 327 5.590259 CCTCCATAAAAATCAGGACGAATGT 59.410 40.000 0.00 0.00 0.00 2.71
325 328 6.095440 CCTCCATAAAAATCAGGACGAATGTT 59.905 38.462 0.00 0.00 0.00 2.71
326 329 7.362920 CCTCCATAAAAATCAGGACGAATGTTT 60.363 37.037 0.00 0.00 0.00 2.83
327 330 8.568676 TCCATAAAAATCAGGACGAATGTTTA 57.431 30.769 0.00 0.00 0.00 2.01
328 331 8.673711 TCCATAAAAATCAGGACGAATGTTTAG 58.326 33.333 0.00 0.00 0.00 1.85
329 332 8.673711 CCATAAAAATCAGGACGAATGTTTAGA 58.326 33.333 0.00 0.00 0.00 2.10
334 337 9.449719 AAAATCAGGACGAATGTTTAGATAAGT 57.550 29.630 0.00 0.00 0.00 2.24
335 338 9.449719 AAATCAGGACGAATGTTTAGATAAGTT 57.550 29.630 0.00 0.00 0.00 2.66
336 339 9.449719 AATCAGGACGAATGTTTAGATAAGTTT 57.550 29.630 0.00 0.00 0.00 2.66
337 340 8.251750 TCAGGACGAATGTTTAGATAAGTTTG 57.748 34.615 0.00 0.00 0.00 2.93
338 341 8.092068 TCAGGACGAATGTTTAGATAAGTTTGA 58.908 33.333 0.00 0.00 0.00 2.69
339 342 8.169268 CAGGACGAATGTTTAGATAAGTTTGAC 58.831 37.037 0.00 0.00 0.00 3.18
340 343 7.876068 AGGACGAATGTTTAGATAAGTTTGACA 59.124 33.333 0.00 0.00 0.00 3.58
341 344 8.665685 GGACGAATGTTTAGATAAGTTTGACAT 58.334 33.333 0.00 0.00 0.00 3.06
342 345 9.478019 GACGAATGTTTAGATAAGTTTGACATG 57.522 33.333 0.00 0.00 0.00 3.21
343 346 8.999431 ACGAATGTTTAGATAAGTTTGACATGT 58.001 29.630 0.00 0.00 0.00 3.21
344 347 9.825972 CGAATGTTTAGATAAGTTTGACATGTT 57.174 29.630 0.00 0.00 0.00 2.71
358 361 9.959749 AGTTTGACATGTTTCATAAATTTACGT 57.040 25.926 0.00 0.00 0.00 3.57
362 365 8.178964 TGACATGTTTCATAAATTTACGTAGGC 58.821 33.333 0.00 0.00 0.00 3.93
363 366 8.276252 ACATGTTTCATAAATTTACGTAGGCT 57.724 30.769 0.00 0.00 0.00 4.58
364 367 8.736244 ACATGTTTCATAAATTTACGTAGGCTT 58.264 29.630 0.00 0.00 0.00 4.35
365 368 9.567848 CATGTTTCATAAATTTACGTAGGCTTT 57.432 29.630 0.00 0.35 0.00 3.51
367 370 9.615295 TGTTTCATAAATTTACGTAGGCTTTTC 57.385 29.630 0.00 0.00 0.00 2.29
368 371 8.782327 GTTTCATAAATTTACGTAGGCTTTTCG 58.218 33.333 0.00 0.00 0.00 3.46
369 372 7.599630 TCATAAATTTACGTAGGCTTTTCGT 57.400 32.000 14.17 14.17 40.78 3.85
370 373 8.700722 TCATAAATTTACGTAGGCTTTTCGTA 57.299 30.769 0.00 12.60 38.69 3.43
371 374 8.810427 TCATAAATTTACGTAGGCTTTTCGTAG 58.190 33.333 14.87 6.48 40.26 3.51
372 375 6.413018 AAATTTACGTAGGCTTTTCGTAGG 57.587 37.500 14.87 0.00 40.26 3.18
373 376 4.519540 TTTACGTAGGCTTTTCGTAGGT 57.480 40.909 14.87 2.48 40.26 3.08
374 377 4.519540 TTACGTAGGCTTTTCGTAGGTT 57.480 40.909 14.87 0.00 40.26 3.50
375 378 3.391506 ACGTAGGCTTTTCGTAGGTTT 57.608 42.857 9.55 0.00 36.05 3.27
376 379 4.519540 ACGTAGGCTTTTCGTAGGTTTA 57.480 40.909 9.55 0.00 36.05 2.01
377 380 5.077134 ACGTAGGCTTTTCGTAGGTTTAT 57.923 39.130 9.55 0.00 36.05 1.40
378 381 5.105063 ACGTAGGCTTTTCGTAGGTTTATC 58.895 41.667 9.55 0.00 36.05 1.75
379 382 5.104374 CGTAGGCTTTTCGTAGGTTTATCA 58.896 41.667 0.00 0.00 0.00 2.15
380 383 5.005107 CGTAGGCTTTTCGTAGGTTTATCAC 59.995 44.000 0.00 0.00 0.00 3.06
381 384 4.901868 AGGCTTTTCGTAGGTTTATCACA 58.098 39.130 0.00 0.00 0.00 3.58
382 385 5.497474 AGGCTTTTCGTAGGTTTATCACAT 58.503 37.500 0.00 0.00 0.00 3.21
383 386 5.354234 AGGCTTTTCGTAGGTTTATCACATG 59.646 40.000 0.00 0.00 0.00 3.21
415 418 1.371758 CACACGCTATCGATCCCCG 60.372 63.158 0.00 5.94 39.41 5.73
439 442 0.808755 CCTAACCGCAACCCATTGTC 59.191 55.000 0.00 0.00 38.17 3.18
443 446 1.963855 CCGCAACCCATTGTCGTGA 60.964 57.895 0.00 0.00 38.17 4.35
444 447 1.206578 CGCAACCCATTGTCGTGAC 59.793 57.895 0.00 0.00 38.17 3.67
445 448 1.502990 CGCAACCCATTGTCGTGACA 61.503 55.000 0.00 0.00 38.17 3.58
536 547 1.652563 GCACCCGAACTTGTCAACC 59.347 57.895 0.00 0.00 0.00 3.77
783 795 1.996191 GGAGCACAGTCGAGTTGAATC 59.004 52.381 4.01 3.03 0.00 2.52
989 1001 2.103941 AGGATTTCGGAGCAGATCTTCC 59.896 50.000 3.62 3.62 0.00 3.46
1550 1562 1.195448 CAACCTCGTCAAGTGATGCAC 59.805 52.381 0.00 0.00 34.10 4.57
1611 1623 9.197694 GTGATAAAGCTCCAATAGTGTATAGTG 57.802 37.037 0.00 0.00 0.00 2.74
1618 1654 6.490721 GCTCCAATAGTGTATAGTGTCCTAGT 59.509 42.308 0.00 0.00 0.00 2.57
1660 1696 8.528044 AATCTAATAAAAAGGGGCAATTCGTA 57.472 30.769 0.00 0.00 0.00 3.43
1672 1708 4.381079 GGGCAATTCGTATGCTTGGTTAAA 60.381 41.667 9.07 0.00 43.34 1.52
1675 1711 6.312672 GGCAATTCGTATGCTTGGTTAAATTT 59.687 34.615 0.00 0.00 43.34 1.82
1686 1722 7.172342 TGCTTGGTTAAATTTAGAGCCTTAGA 58.828 34.615 15.89 2.61 0.00 2.10
1699 1735 6.120507 AGAGCCTTAGACTGTCAATTTTCT 57.879 37.500 10.88 3.20 0.00 2.52
1728 1764 9.349713 TCTTCAAATGGTTATATAATGTCCACC 57.650 33.333 5.65 0.00 0.00 4.61
1729 1765 8.472007 TTCAAATGGTTATATAATGTCCACCC 57.528 34.615 5.65 0.00 0.00 4.61
1730 1766 6.712998 TCAAATGGTTATATAATGTCCACCCG 59.287 38.462 5.65 0.00 0.00 5.28
1731 1767 4.010667 TGGTTATATAATGTCCACCCGC 57.989 45.455 0.00 0.00 0.00 6.13
1732 1768 3.391626 TGGTTATATAATGTCCACCCGCA 59.608 43.478 0.00 0.00 0.00 5.69
1733 1769 4.141459 TGGTTATATAATGTCCACCCGCAA 60.141 41.667 0.00 0.00 0.00 4.85
1734 1770 4.822896 GGTTATATAATGTCCACCCGCAAA 59.177 41.667 0.00 0.00 0.00 3.68
1735 1771 5.299782 GGTTATATAATGTCCACCCGCAAAA 59.700 40.000 0.00 0.00 0.00 2.44
1736 1772 6.183360 GGTTATATAATGTCCACCCGCAAAAA 60.183 38.462 0.00 0.00 0.00 1.94
1876 1916 5.648178 TTTACAACATGCATGAGCTGATT 57.352 34.783 32.75 12.70 42.74 2.57
1892 1932 3.100817 CTGATTGCGGCGATTACAAAAG 58.899 45.455 12.98 4.04 0.00 2.27
1893 1933 2.744741 TGATTGCGGCGATTACAAAAGA 59.255 40.909 12.98 0.00 0.00 2.52
1896 1936 3.196007 TGCGGCGATTACAAAAGAAAG 57.804 42.857 12.98 0.00 0.00 2.62
1932 1972 7.804843 AAAGCATATCTTTGAGATCTTCAGG 57.195 36.000 0.00 0.00 43.04 3.86
1933 1973 5.307204 AGCATATCTTTGAGATCTTCAGGC 58.693 41.667 0.00 0.00 36.20 4.85
2014 2054 5.354234 ACAAAGATATTAAACCGTGGAGCTG 59.646 40.000 0.00 0.00 0.00 4.24
2023 2063 3.975168 ACCGTGGAGCTGTAAATACTT 57.025 42.857 0.00 0.00 0.00 2.24
2026 2066 6.720112 ACCGTGGAGCTGTAAATACTTATA 57.280 37.500 0.00 0.00 0.00 0.98
2036 2076 8.430431 AGCTGTAAATACTTATAAGGGTTCTCC 58.570 37.037 16.73 0.40 0.00 3.71
2056 2096 4.865905 TCCCATAGCTTTAATTTGAGCCA 58.134 39.130 0.00 0.00 39.71 4.75
2057 2097 5.268387 TCCCATAGCTTTAATTTGAGCCAA 58.732 37.500 0.00 0.35 39.71 4.52
2058 2098 5.127031 TCCCATAGCTTTAATTTGAGCCAAC 59.873 40.000 0.00 0.00 39.71 3.77
2119 2209 1.272490 ACACAACCAGATCGATGTCGT 59.728 47.619 0.54 0.00 40.80 4.34
2122 2212 2.288825 ACAACCAGATCGATGTCGTTGT 60.289 45.455 25.70 25.70 40.80 3.32
2128 2218 0.802222 ATCGATGTCGTTGTGAGCCG 60.802 55.000 0.00 0.00 40.80 5.52
2142 2232 1.400846 TGAGCCGAGAGTACGAATCAC 59.599 52.381 0.00 0.00 35.09 3.06
2150 2240 4.674362 CGAGAGTACGAATCACCATTGTCA 60.674 45.833 0.00 0.00 35.09 3.58
2171 2261 1.136984 GACGTAGCAGTCGGGACAG 59.863 63.158 1.17 0.00 0.00 3.51
2185 2275 2.419990 CGGGACAGATATTGCAAGGACA 60.420 50.000 4.94 0.00 0.00 4.02
2240 2331 4.551702 TCCAAAATCGATCTGGTGAAGA 57.448 40.909 20.36 4.30 39.94 2.87
2254 2345 5.486775 TCTGGTGAAGAAAGATCTGAAGGAT 59.513 40.000 0.00 0.00 35.59 3.24
2287 2378 7.433680 AGACAAATTTAATCTTCCAACACCAC 58.566 34.615 0.00 0.00 0.00 4.16
2289 2380 6.098982 ACAAATTTAATCTTCCAACACCACCA 59.901 34.615 0.00 0.00 0.00 4.17
2292 2383 8.429237 AATTTAATCTTCCAACACCACCATTA 57.571 30.769 0.00 0.00 0.00 1.90
2297 2388 4.582656 TCTTCCAACACCACCATTAACTTG 59.417 41.667 0.00 0.00 0.00 3.16
2298 2389 2.625790 TCCAACACCACCATTAACTTGC 59.374 45.455 0.00 0.00 0.00 4.01
2315 2406 0.679960 TGCGGAAGGAGATCTCGTCA 60.680 55.000 17.78 9.07 0.00 4.35
2318 2409 1.950216 CGGAAGGAGATCTCGTCATGA 59.050 52.381 17.78 0.00 0.00 3.07
2321 2412 4.116238 GGAAGGAGATCTCGTCATGAAAC 58.884 47.826 17.78 0.35 0.00 2.78
2385 2476 5.923733 AAGAAGATGAAGACGACTACCAT 57.076 39.130 0.00 0.00 0.00 3.55
2400 2491 5.696724 CGACTACCATCATCCTAAACCAATC 59.303 44.000 0.00 0.00 0.00 2.67
2405 2496 9.224267 CTACCATCATCCTAAACCAATCTAATG 57.776 37.037 0.00 0.00 0.00 1.90
2411 2502 8.673711 TCATCCTAAACCAATCTAATGAAAACG 58.326 33.333 0.00 0.00 0.00 3.60
2414 2505 7.825270 TCCTAAACCAATCTAATGAAAACGCTA 59.175 33.333 0.00 0.00 0.00 4.26
2452 2543 3.134081 TCACTCATAAATCGGGTTCCCTC 59.866 47.826 6.31 0.00 0.00 4.30
2454 2545 1.772453 TCATAAATCGGGTTCCCTCCC 59.228 52.381 6.31 0.00 43.78 4.30
2460 2555 2.204090 GGGTTCCCTCCCACTCCA 60.204 66.667 0.00 0.00 46.30 3.86
2461 2556 2.301738 GGGTTCCCTCCCACTCCAG 61.302 68.421 0.00 0.00 46.30 3.86
2463 2558 2.206900 TTCCCTCCCACTCCAGCA 59.793 61.111 0.00 0.00 0.00 4.41
2464 2559 1.229951 TTCCCTCCCACTCCAGCAT 60.230 57.895 0.00 0.00 0.00 3.79
2485 2580 4.752879 CGAGGCCCGCCGAAGAAA 62.753 66.667 0.00 0.00 41.95 2.52
2493 2588 1.003718 CGCCGAAGAAAGGGGAACT 60.004 57.895 0.00 0.00 43.49 3.01
2494 2589 1.298859 CGCCGAAGAAAGGGGAACTG 61.299 60.000 0.00 0.00 43.49 3.16
2517 2612 4.292186 TCTTCTTCCCTGATGAAGGTTG 57.708 45.455 15.52 0.00 45.78 3.77
2518 2613 2.496899 TCTTCCCTGATGAAGGTTGC 57.503 50.000 0.00 0.00 45.78 4.17
2520 2615 0.322456 TTCCCTGATGAAGGTTGCCG 60.322 55.000 0.00 0.00 45.78 5.69
2528 2623 1.234821 TGAAGGTTGCCGTGTTCATC 58.765 50.000 0.00 0.00 0.00 2.92
2533 2628 0.240678 GTTGCCGTGTTCATCATGCA 59.759 50.000 0.00 0.00 35.79 3.96
2539 2634 1.730121 CGTGTTCATCATGCAAGCCAC 60.730 52.381 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.381590 AGTTGAACACAAGCCTCCTTTTC 59.618 43.478 0.00 0.00 0.00 2.29
35 37 1.388547 TGCAGGACCAAGTTGAACAC 58.611 50.000 3.87 0.00 0.00 3.32
67 69 6.068010 TGAATAGATGCCCCGAAACATTTAT 58.932 36.000 0.00 0.00 0.00 1.40
96 99 7.658261 ACTGGAACTTAAATTCTTTTAGCCAC 58.342 34.615 0.00 0.00 0.00 5.01
180 183 4.821589 GTCGCGGGGAGGAAGCAG 62.822 72.222 6.13 0.00 0.00 4.24
186 189 2.567564 AAACGTATGTCGCGGGGAGG 62.568 60.000 6.13 0.00 44.19 4.30
189 192 2.457778 CCAAACGTATGTCGCGGGG 61.458 63.158 6.13 0.00 44.19 5.73
194 197 1.461897 GGGTTGTCCAAACGTATGTCG 59.538 52.381 0.00 0.00 39.50 4.35
201 204 2.833631 AGTCTAGGGTTGTCCAAACG 57.166 50.000 0.00 0.00 38.24 3.60
202 205 3.992427 CGTAAGTCTAGGGTTGTCCAAAC 59.008 47.826 0.00 0.00 38.24 2.93
203 206 4.261578 CGTAAGTCTAGGGTTGTCCAAA 57.738 45.455 0.00 0.00 38.24 3.28
204 207 3.947910 CGTAAGTCTAGGGTTGTCCAA 57.052 47.619 0.00 0.00 38.24 3.53
240 243 6.779385 TTCACGATGACTATTACGTAAACG 57.221 37.500 12.81 8.71 46.33 3.60
241 244 8.385789 TCTTTCACGATGACTATTACGTAAAC 57.614 34.615 12.81 5.33 37.22 2.01
242 245 9.577110 AATCTTTCACGATGACTATTACGTAAA 57.423 29.630 12.81 0.00 37.22 2.01
244 247 9.874215 CTAATCTTTCACGATGACTATTACGTA 57.126 33.333 0.00 0.00 37.22 3.57
245 248 7.861372 CCTAATCTTTCACGATGACTATTACGT 59.139 37.037 0.00 0.00 39.53 3.57
246 249 8.074370 TCCTAATCTTTCACGATGACTATTACG 58.926 37.037 0.00 0.00 0.00 3.18
247 250 9.915629 ATCCTAATCTTTCACGATGACTATTAC 57.084 33.333 0.00 0.00 0.00 1.89
249 252 9.265901 CAATCCTAATCTTTCACGATGACTATT 57.734 33.333 0.00 0.00 0.00 1.73
250 253 7.875041 CCAATCCTAATCTTTCACGATGACTAT 59.125 37.037 0.00 0.00 0.00 2.12
251 254 7.147724 ACCAATCCTAATCTTTCACGATGACTA 60.148 37.037 0.00 0.00 0.00 2.59
252 255 6.051717 CCAATCCTAATCTTTCACGATGACT 58.948 40.000 0.00 0.00 0.00 3.41
253 256 5.817816 ACCAATCCTAATCTTTCACGATGAC 59.182 40.000 0.00 0.00 0.00 3.06
254 257 5.989477 ACCAATCCTAATCTTTCACGATGA 58.011 37.500 0.00 0.00 0.00 2.92
255 258 6.683974 AACCAATCCTAATCTTTCACGATG 57.316 37.500 0.00 0.00 0.00 3.84
256 259 7.703058 AAAACCAATCCTAATCTTTCACGAT 57.297 32.000 0.00 0.00 0.00 3.73
257 260 7.519032 AAAAACCAATCCTAATCTTTCACGA 57.481 32.000 0.00 0.00 0.00 4.35
258 261 7.968405 CCTAAAAACCAATCCTAATCTTTCACG 59.032 37.037 0.00 0.00 0.00 4.35
259 262 8.251026 CCCTAAAAACCAATCCTAATCTTTCAC 58.749 37.037 0.00 0.00 0.00 3.18
260 263 7.398904 CCCCTAAAAACCAATCCTAATCTTTCA 59.601 37.037 0.00 0.00 0.00 2.69
261 264 7.618117 TCCCCTAAAAACCAATCCTAATCTTTC 59.382 37.037 0.00 0.00 0.00 2.62
262 265 7.483881 TCCCCTAAAAACCAATCCTAATCTTT 58.516 34.615 0.00 0.00 0.00 2.52
263 266 7.051696 TCCCCTAAAAACCAATCCTAATCTT 57.948 36.000 0.00 0.00 0.00 2.40
264 267 6.354829 CCTCCCCTAAAAACCAATCCTAATCT 60.355 42.308 0.00 0.00 0.00 2.40
265 268 5.833667 CCTCCCCTAAAAACCAATCCTAATC 59.166 44.000 0.00 0.00 0.00 1.75
266 269 5.777449 CCTCCCCTAAAAACCAATCCTAAT 58.223 41.667 0.00 0.00 0.00 1.73
267 270 4.571148 GCCTCCCCTAAAAACCAATCCTAA 60.571 45.833 0.00 0.00 0.00 2.69
268 271 3.053170 GCCTCCCCTAAAAACCAATCCTA 60.053 47.826 0.00 0.00 0.00 2.94
269 272 2.292257 GCCTCCCCTAAAAACCAATCCT 60.292 50.000 0.00 0.00 0.00 3.24
270 273 2.108168 GCCTCCCCTAAAAACCAATCC 58.892 52.381 0.00 0.00 0.00 3.01
271 274 2.760650 CAGCCTCCCCTAAAAACCAATC 59.239 50.000 0.00 0.00 0.00 2.67
272 275 2.381961 TCAGCCTCCCCTAAAAACCAAT 59.618 45.455 0.00 0.00 0.00 3.16
273 276 1.783979 TCAGCCTCCCCTAAAAACCAA 59.216 47.619 0.00 0.00 0.00 3.67
274 277 1.354368 CTCAGCCTCCCCTAAAAACCA 59.646 52.381 0.00 0.00 0.00 3.67
275 278 1.341089 CCTCAGCCTCCCCTAAAAACC 60.341 57.143 0.00 0.00 0.00 3.27
276 279 1.955683 GCCTCAGCCTCCCCTAAAAAC 60.956 57.143 0.00 0.00 0.00 2.43
277 280 0.331616 GCCTCAGCCTCCCCTAAAAA 59.668 55.000 0.00 0.00 0.00 1.94
278 281 1.999346 GCCTCAGCCTCCCCTAAAA 59.001 57.895 0.00 0.00 0.00 1.52
279 282 3.741325 GCCTCAGCCTCCCCTAAA 58.259 61.111 0.00 0.00 0.00 1.85
294 297 2.695147 CTGATTTTTATGGAGGTGGGCC 59.305 50.000 0.00 0.00 0.00 5.80
295 298 2.695147 CCTGATTTTTATGGAGGTGGGC 59.305 50.000 0.00 0.00 0.00 5.36
296 299 3.954258 GTCCTGATTTTTATGGAGGTGGG 59.046 47.826 0.00 0.00 0.00 4.61
297 300 3.627577 CGTCCTGATTTTTATGGAGGTGG 59.372 47.826 0.00 0.00 31.97 4.61
298 301 4.513442 TCGTCCTGATTTTTATGGAGGTG 58.487 43.478 0.00 0.00 36.31 4.00
299 302 4.837093 TCGTCCTGATTTTTATGGAGGT 57.163 40.909 0.00 0.00 36.31 3.85
300 303 5.590259 ACATTCGTCCTGATTTTTATGGAGG 59.410 40.000 0.00 0.00 36.25 4.30
301 304 6.683974 ACATTCGTCCTGATTTTTATGGAG 57.316 37.500 0.00 0.00 0.00 3.86
302 305 7.461182 AAACATTCGTCCTGATTTTTATGGA 57.539 32.000 0.00 0.00 0.00 3.41
303 306 8.673711 TCTAAACATTCGTCCTGATTTTTATGG 58.326 33.333 0.00 0.00 0.00 2.74
308 311 9.449719 ACTTATCTAAACATTCGTCCTGATTTT 57.550 29.630 0.00 0.00 0.00 1.82
309 312 9.449719 AACTTATCTAAACATTCGTCCTGATTT 57.550 29.630 0.00 0.00 0.00 2.17
310 313 9.449719 AAACTTATCTAAACATTCGTCCTGATT 57.550 29.630 0.00 0.00 0.00 2.57
311 314 8.883731 CAAACTTATCTAAACATTCGTCCTGAT 58.116 33.333 0.00 0.00 0.00 2.90
312 315 8.092068 TCAAACTTATCTAAACATTCGTCCTGA 58.908 33.333 0.00 0.00 0.00 3.86
313 316 8.169268 GTCAAACTTATCTAAACATTCGTCCTG 58.831 37.037 0.00 0.00 0.00 3.86
314 317 7.876068 TGTCAAACTTATCTAAACATTCGTCCT 59.124 33.333 0.00 0.00 0.00 3.85
315 318 8.025243 TGTCAAACTTATCTAAACATTCGTCC 57.975 34.615 0.00 0.00 0.00 4.79
316 319 9.478019 CATGTCAAACTTATCTAAACATTCGTC 57.522 33.333 0.00 0.00 0.00 4.20
317 320 8.999431 ACATGTCAAACTTATCTAAACATTCGT 58.001 29.630 0.00 0.00 0.00 3.85
318 321 9.825972 AACATGTCAAACTTATCTAAACATTCG 57.174 29.630 0.00 0.00 0.00 3.34
332 335 9.959749 ACGTAAATTTATGAAACATGTCAAACT 57.040 25.926 21.54 0.00 0.00 2.66
336 339 8.178964 GCCTACGTAAATTTATGAAACATGTCA 58.821 33.333 21.54 0.00 0.00 3.58
337 340 8.395633 AGCCTACGTAAATTTATGAAACATGTC 58.604 33.333 21.54 0.00 0.00 3.06
338 341 8.276252 AGCCTACGTAAATTTATGAAACATGT 57.724 30.769 21.54 0.00 0.00 3.21
339 342 9.567848 AAAGCCTACGTAAATTTATGAAACATG 57.432 29.630 21.54 0.00 0.00 3.21
341 344 9.615295 GAAAAGCCTACGTAAATTTATGAAACA 57.385 29.630 21.54 5.40 0.00 2.83
342 345 8.782327 CGAAAAGCCTACGTAAATTTATGAAAC 58.218 33.333 21.54 9.44 0.00 2.78
343 346 8.505625 ACGAAAAGCCTACGTAAATTTATGAAA 58.494 29.630 21.54 9.78 38.47 2.69
344 347 8.031848 ACGAAAAGCCTACGTAAATTTATGAA 57.968 30.769 21.54 1.22 38.47 2.57
345 348 7.599630 ACGAAAAGCCTACGTAAATTTATGA 57.400 32.000 21.54 6.84 38.47 2.15
346 349 8.060090 CCTACGAAAAGCCTACGTAAATTTATG 58.940 37.037 14.60 14.60 40.88 1.90
347 350 7.765819 ACCTACGAAAAGCCTACGTAAATTTAT 59.234 33.333 0.31 0.00 40.88 1.40
348 351 7.096551 ACCTACGAAAAGCCTACGTAAATTTA 58.903 34.615 0.00 0.00 40.88 1.40
349 352 5.934043 ACCTACGAAAAGCCTACGTAAATTT 59.066 36.000 0.00 0.00 40.88 1.82
350 353 5.482006 ACCTACGAAAAGCCTACGTAAATT 58.518 37.500 0.00 0.00 40.88 1.82
351 354 5.077134 ACCTACGAAAAGCCTACGTAAAT 57.923 39.130 0.00 0.00 40.88 1.40
352 355 4.519540 ACCTACGAAAAGCCTACGTAAA 57.480 40.909 0.00 0.00 40.88 2.01
353 356 4.519540 AACCTACGAAAAGCCTACGTAA 57.480 40.909 0.00 0.00 40.88 3.18
354 357 4.519540 AAACCTACGAAAAGCCTACGTA 57.480 40.909 0.00 0.00 40.61 3.57
355 358 3.391506 AAACCTACGAAAAGCCTACGT 57.608 42.857 0.00 0.00 42.70 3.57
356 359 5.005107 GTGATAAACCTACGAAAAGCCTACG 59.995 44.000 0.00 0.00 0.00 3.51
357 360 5.870978 TGTGATAAACCTACGAAAAGCCTAC 59.129 40.000 0.00 0.00 0.00 3.18
358 361 6.040209 TGTGATAAACCTACGAAAAGCCTA 57.960 37.500 0.00 0.00 0.00 3.93
359 362 4.901868 TGTGATAAACCTACGAAAAGCCT 58.098 39.130 0.00 0.00 0.00 4.58
360 363 5.569413 CATGTGATAAACCTACGAAAAGCC 58.431 41.667 0.00 0.00 0.00 4.35
361 364 5.028375 GCATGTGATAAACCTACGAAAAGC 58.972 41.667 0.00 0.00 0.00 3.51
362 365 5.163893 ACGCATGTGATAAACCTACGAAAAG 60.164 40.000 14.43 0.00 0.00 2.27
363 366 4.691685 ACGCATGTGATAAACCTACGAAAA 59.308 37.500 14.43 0.00 0.00 2.29
364 367 4.247258 ACGCATGTGATAAACCTACGAAA 58.753 39.130 14.43 0.00 0.00 3.46
365 368 3.852286 ACGCATGTGATAAACCTACGAA 58.148 40.909 14.43 0.00 0.00 3.85
366 369 3.513680 ACGCATGTGATAAACCTACGA 57.486 42.857 14.43 0.00 0.00 3.43
367 370 4.593597 AAACGCATGTGATAAACCTACG 57.406 40.909 14.43 0.00 0.00 3.51
368 371 5.695818 ACAAAACGCATGTGATAAACCTAC 58.304 37.500 14.43 0.00 0.00 3.18
369 372 5.950758 ACAAAACGCATGTGATAAACCTA 57.049 34.783 14.43 0.00 0.00 3.08
370 373 4.846779 ACAAAACGCATGTGATAAACCT 57.153 36.364 14.43 0.00 0.00 3.50
371 374 5.689961 AGAAACAAAACGCATGTGATAAACC 59.310 36.000 14.43 0.00 0.00 3.27
372 375 6.129194 GGAGAAACAAAACGCATGTGATAAAC 60.129 38.462 14.43 0.00 0.00 2.01
373 376 5.918011 GGAGAAACAAAACGCATGTGATAAA 59.082 36.000 14.43 0.00 0.00 1.40
374 377 5.009110 TGGAGAAACAAAACGCATGTGATAA 59.991 36.000 14.43 0.00 0.00 1.75
375 378 4.517075 TGGAGAAACAAAACGCATGTGATA 59.483 37.500 14.43 0.00 0.00 2.15
376 379 3.317711 TGGAGAAACAAAACGCATGTGAT 59.682 39.130 14.43 0.00 0.00 3.06
377 380 2.685388 TGGAGAAACAAAACGCATGTGA 59.315 40.909 14.43 0.00 0.00 3.58
378 381 2.788786 GTGGAGAAACAAAACGCATGTG 59.211 45.455 4.30 4.30 0.00 3.21
379 382 2.425312 TGTGGAGAAACAAAACGCATGT 59.575 40.909 0.00 0.00 0.00 3.21
380 383 2.788786 GTGTGGAGAAACAAAACGCATG 59.211 45.455 0.00 0.00 0.00 4.06
381 384 2.540769 CGTGTGGAGAAACAAAACGCAT 60.541 45.455 0.00 0.00 0.00 4.73
382 385 1.202087 CGTGTGGAGAAACAAAACGCA 60.202 47.619 0.00 0.00 0.00 5.24
383 386 1.462791 CGTGTGGAGAAACAAAACGC 58.537 50.000 0.00 0.00 0.00 4.84
429 432 2.151202 GATGTGTCACGACAATGGGTT 58.849 47.619 0.50 0.00 43.77 4.11
430 433 1.808411 GATGTGTCACGACAATGGGT 58.192 50.000 0.50 0.00 43.77 4.51
439 442 2.815211 CCTGGGCGATGTGTCACG 60.815 66.667 0.00 0.00 0.00 4.35
459 470 0.910338 GGTGGGAAGGTTAGAGGGAC 59.090 60.000 0.00 0.00 0.00 4.46
615 626 4.778025 CGCAATCGATTTATATGAAGCACG 59.222 41.667 8.21 0.00 38.10 5.34
760 772 0.888619 CAACTCGACTGTGCTCCCTA 59.111 55.000 0.00 0.00 0.00 3.53
761 773 0.827925 TCAACTCGACTGTGCTCCCT 60.828 55.000 0.00 0.00 0.00 4.20
762 774 0.033504 TTCAACTCGACTGTGCTCCC 59.966 55.000 0.00 0.00 0.00 4.30
765 777 2.820059 TGATTCAACTCGACTGTGCT 57.180 45.000 0.00 0.00 0.00 4.40
766 778 4.388773 TGTAATGATTCAACTCGACTGTGC 59.611 41.667 0.00 0.00 0.00 4.57
767 779 5.443301 CGTGTAATGATTCAACTCGACTGTG 60.443 44.000 6.99 0.00 33.33 3.66
768 780 4.621460 CGTGTAATGATTCAACTCGACTGT 59.379 41.667 6.99 0.00 33.33 3.55
989 1001 3.801050 CGCCTTGATCATCTGTACTCTTG 59.199 47.826 0.00 0.00 0.00 3.02
1550 1562 2.778026 ATGTGTTCGACGCATGCG 59.222 55.556 36.79 36.79 46.45 4.73
1566 1578 1.148310 CACGCGAAGAAGAACCACAT 58.852 50.000 15.93 0.00 0.00 3.21
1660 1696 6.857437 AAGGCTCTAAATTTAACCAAGCAT 57.143 33.333 16.76 10.90 0.00 3.79
1672 1708 8.870075 AAAATTGACAGTCTAAGGCTCTAAAT 57.130 30.769 1.31 0.00 0.00 1.40
1675 1711 7.246171 AGAAAATTGACAGTCTAAGGCTCTA 57.754 36.000 1.31 0.00 0.00 2.43
1686 1722 8.571336 CCATTTGAAGAGTAGAAAATTGACAGT 58.429 33.333 0.00 0.00 0.00 3.55
1849 1889 5.062934 CAGCTCATGCATGTTGTAAATTTGG 59.937 40.000 25.43 0.00 42.74 3.28
1851 1891 6.028146 TCAGCTCATGCATGTTGTAAATTT 57.972 33.333 25.43 0.00 42.74 1.82
1864 1904 2.025727 GCCGCAATCAGCTCATGC 59.974 61.111 5.10 5.10 42.61 4.06
1876 1916 2.550606 ACTTTCTTTTGTAATCGCCGCA 59.449 40.909 0.00 0.00 0.00 5.69
1879 1919 8.287503 TCTTTTAGACTTTCTTTTGTAATCGCC 58.712 33.333 0.00 0.00 0.00 5.54
1909 1949 5.764192 GCCTGAAGATCTCAAAGATATGCTT 59.236 40.000 0.00 0.00 34.53 3.91
1914 1954 6.805016 AAGAGCCTGAAGATCTCAAAGATA 57.195 37.500 0.00 0.00 34.53 1.98
1931 1971 4.516698 TGTGTCATGAAAGAAGAAAGAGCC 59.483 41.667 0.00 0.00 0.00 4.70
1932 1972 5.679734 TGTGTCATGAAAGAAGAAAGAGC 57.320 39.130 0.00 0.00 0.00 4.09
1933 1973 8.097078 AGATTGTGTCATGAAAGAAGAAAGAG 57.903 34.615 0.00 0.00 0.00 2.85
1967 2007 8.128322 TGTTATTTTTCTATGGCTGCCTTAAA 57.872 30.769 21.03 10.93 0.00 1.52
1969 2009 7.710676 TTGTTATTTTTCTATGGCTGCCTTA 57.289 32.000 21.03 16.60 0.00 2.69
2006 2046 7.506971 ACCCTTATAAGTATTTACAGCTCCAC 58.493 38.462 11.50 0.00 0.00 4.02
2007 2047 7.685849 ACCCTTATAAGTATTTACAGCTCCA 57.314 36.000 11.50 0.00 0.00 3.86
2011 2051 8.604640 GGAGAACCCTTATAAGTATTTACAGC 57.395 38.462 11.50 0.00 0.00 4.40
2036 2076 5.036737 CGTTGGCTCAAATTAAAGCTATGG 58.963 41.667 10.74 0.00 38.58 2.74
2056 2096 0.390124 TTGGTACTCTTGCCGACGTT 59.610 50.000 0.00 0.00 0.00 3.99
2057 2097 0.319297 GTTGGTACTCTTGCCGACGT 60.319 55.000 0.00 0.00 32.67 4.34
2058 2098 0.319211 TGTTGGTACTCTTGCCGACG 60.319 55.000 0.00 0.00 43.36 5.12
2104 2194 1.544246 TCACAACGACATCGATCTGGT 59.456 47.619 8.54 0.00 43.02 4.00
2109 2199 0.802222 CGGCTCACAACGACATCGAT 60.802 55.000 8.54 0.00 43.02 3.59
2119 2209 1.241165 TTCGTACTCTCGGCTCACAA 58.759 50.000 0.00 0.00 0.00 3.33
2122 2212 1.400846 GTGATTCGTACTCTCGGCTCA 59.599 52.381 0.00 0.00 0.00 4.26
2128 2218 4.744570 TGACAATGGTGATTCGTACTCTC 58.255 43.478 0.00 0.00 0.00 3.20
2142 2232 2.002586 CTGCTACGTCCTTGACAATGG 58.997 52.381 0.00 0.00 32.09 3.16
2150 2240 1.303888 TCCCGACTGCTACGTCCTT 60.304 57.895 0.00 0.00 0.00 3.36
2185 2275 0.544357 TGGTCACCACGAGGAGGATT 60.544 55.000 5.68 0.00 38.69 3.01
2228 2319 5.816777 CCTTCAGATCTTTCTTCACCAGATC 59.183 44.000 0.00 0.00 42.28 2.75
2254 2345 9.878667 TGGAAGATTAAATTTGTCTACGTATGA 57.121 29.630 0.00 0.00 0.00 2.15
2260 2351 8.573035 TGGTGTTGGAAGATTAAATTTGTCTAC 58.427 33.333 0.00 1.09 0.00 2.59
2275 2366 4.795962 GCAAGTTAATGGTGGTGTTGGAAG 60.796 45.833 0.00 0.00 0.00 3.46
2287 2378 2.985896 TCTCCTTCCGCAAGTTAATGG 58.014 47.619 0.00 0.00 0.00 3.16
2289 2380 4.698575 GAGATCTCCTTCCGCAAGTTAAT 58.301 43.478 12.00 0.00 0.00 1.40
2292 2383 1.134965 CGAGATCTCCTTCCGCAAGTT 60.135 52.381 17.13 0.00 0.00 2.66
2297 2388 0.671251 ATGACGAGATCTCCTTCCGC 59.329 55.000 17.13 3.29 0.00 5.54
2298 2389 1.950216 TCATGACGAGATCTCCTTCCG 59.050 52.381 17.13 8.13 0.00 4.30
2315 2406 3.611766 ATCTTCGTCCCTTCGTTTCAT 57.388 42.857 0.00 0.00 0.00 2.57
2318 2409 4.532314 AGTAATCTTCGTCCCTTCGTTT 57.468 40.909 0.00 0.00 0.00 3.60
2321 2412 9.557338 CTATAATAAGTAATCTTCGTCCCTTCG 57.443 37.037 0.00 0.00 35.36 3.79
2349 2440 5.830000 CATCTTCTTTGAAGATGGCATCA 57.170 39.130 28.71 7.76 46.03 3.07
2365 2456 5.250235 TGATGGTAGTCGTCTTCATCTTC 57.750 43.478 18.39 1.63 35.84 2.87
2385 2476 8.673711 CGTTTTCATTAGATTGGTTTAGGATGA 58.326 33.333 0.00 0.00 0.00 2.92
2452 2543 2.513204 CGCTGATGCTGGAGTGGG 60.513 66.667 0.00 0.00 36.97 4.61
2454 2545 1.521010 CCTCGCTGATGCTGGAGTG 60.521 63.158 0.00 0.00 36.97 3.51
2475 2570 1.003718 AGTTCCCCTTTCTTCGGCG 60.004 57.895 0.00 0.00 0.00 6.46
2476 2571 0.036306 TCAGTTCCCCTTTCTTCGGC 59.964 55.000 0.00 0.00 0.00 5.54
2493 2588 4.767578 CCTTCATCAGGGAAGAAGATCA 57.232 45.455 11.54 0.00 45.66 2.92
2517 2612 0.799534 GCTTGCATGATGAACACGGC 60.800 55.000 3.33 0.00 34.23 5.68
2518 2613 0.179156 GGCTTGCATGATGAACACGG 60.179 55.000 3.33 0.00 0.00 4.94
2520 2615 1.403249 GGTGGCTTGCATGATGAACAC 60.403 52.381 3.33 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.