Multiple sequence alignment - TraesCS2D01G116300

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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 TraesCS2D01G116300 chr2D 100.000 4454 0 0 1 4454 65267984 65263531 0.000000e+00 8226.0
1 TraesCS2D01G116300 chr2D 93.550 1597 79 8 2055 3651 64732334 64733906 0.000000e+00 2357.0
2 TraesCS2D01G116300 chr2D 87.278 1407 122 23 2069 3454 69148936 69150306 0.000000e+00 1554.0
3 TraesCS2D01G116300 chr2D 86.839 1003 96 15 2049 3032 68903119 68902134 0.000000e+00 1088.0
4 TraesCS2D01G116300 chr2D 92.235 425 33 0 3030 3454 68888185 68887761 1.770000e-168 603.0
5 TraesCS2D01G116300 chr2B 96.423 3411 65 13 510 3906 101237273 101233906 0.000000e+00 5570.0
6 TraesCS2D01G116300 chr2B 93.287 1594 83 11 2055 3648 101072890 101074459 0.000000e+00 2329.0
7 TraesCS2D01G116300 chr2B 90.458 765 72 1 2691 3454 101418970 101418206 0.000000e+00 1007.0
8 TraesCS2D01G116300 chr2B 90.196 765 74 1 2691 3454 101451888 101451124 0.000000e+00 996.0
9 TraesCS2D01G116300 chr2B 89.935 765 75 2 2691 3454 101432871 101432108 0.000000e+00 985.0
10 TraesCS2D01G116300 chr2B 90.592 574 10 5 3904 4440 101231804 101231238 0.000000e+00 721.0
11 TraesCS2D01G116300 chr2B 86.312 526 52 8 2049 2571 101452475 101451967 5.030000e-154 555.0
12 TraesCS2D01G116300 chr2B 84.130 523 43 18 2049 2571 101433432 101432950 1.880000e-128 470.0
13 TraesCS2D01G116300 chr2B 83.939 523 45 18 2049 2571 101419532 101419049 8.730000e-127 464.0
14 TraesCS2D01G116300 chr2B 94.389 303 9 2 1 296 101237570 101237269 4.060000e-125 459.0
15 TraesCS2D01G116300 chr2A 92.652 626 46 0 2829 3454 65702505 65701880 0.000000e+00 902.0
16 TraesCS2D01G116300 chr2A 82.454 929 91 39 1940 2831 65703673 65702780 0.000000e+00 747.0
17 TraesCS2D01G116300 chr5B 92.308 52 4 0 277 328 439263231 439263282 1.720000e-09 75.0
18 TraesCS2D01G116300 chr5B 100.000 29 0 0 286 314 687334575 687334547 2.000000e-03 54.7
19 TraesCS2D01G116300 chr7A 87.500 56 6 1 277 331 21849186 21849131 3.720000e-06 63.9
20 TraesCS2D01G116300 chr6A 72.768 224 45 12 263 473 29148358 29148578 1.340000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G116300 chr2D 65263531 65267984 4453 True 8226.0 8226 100.000000 1 4454 1 chr2D.!!$R1 4453
1 TraesCS2D01G116300 chr2D 64732334 64733906 1572 False 2357.0 2357 93.550000 2055 3651 1 chr2D.!!$F1 1596
2 TraesCS2D01G116300 chr2D 69148936 69150306 1370 False 1554.0 1554 87.278000 2069 3454 1 chr2D.!!$F2 1385
3 TraesCS2D01G116300 chr2D 68902134 68903119 985 True 1088.0 1088 86.839000 2049 3032 1 chr2D.!!$R3 983
4 TraesCS2D01G116300 chr2B 101072890 101074459 1569 False 2329.0 2329 93.287000 2055 3648 1 chr2B.!!$F1 1593
5 TraesCS2D01G116300 chr2B 101231238 101237570 6332 True 2250.0 5570 93.801333 1 4440 3 chr2B.!!$R1 4439
6 TraesCS2D01G116300 chr2B 101451124 101452475 1351 True 775.5 996 88.254000 2049 3454 2 chr2B.!!$R4 1405
7 TraesCS2D01G116300 chr2B 101418206 101419532 1326 True 735.5 1007 87.198500 2049 3454 2 chr2B.!!$R2 1405
8 TraesCS2D01G116300 chr2B 101432108 101433432 1324 True 727.5 985 87.032500 2049 3454 2 chr2B.!!$R3 1405
9 TraesCS2D01G116300 chr2A 65701880 65703673 1793 True 824.5 902 87.553000 1940 3454 2 chr2A.!!$R1 1514

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
334 342 0.179108 GGCTTTCTGGCGACGTCTAT 60.179 55.0 14.7 0.00 0.0 1.98 F
1418 1435 0.038166 TTCGAAGCCATGGAAGCCTT 59.962 50.0 18.4 9.17 0.0 4.35 F
2159 2200 0.455005 GCCTCGTACCGTAGAAGCTT 59.545 55.0 0.0 0.00 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1925 0.177141 CGCGGTTCCCCTTCTTATGA 59.823 55.0 0.00 0.0 0.00 2.15 R
2304 2377 1.165907 TCGCTGCAAAGACCAACCAG 61.166 55.0 0.00 0.0 0.00 4.00 R
4018 6541 0.331278 TCCATGGTGGATTGGTGGAC 59.669 55.0 12.58 0.0 42.67 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 5.730296 ATTAGTTAGTGCTCTGTGTCAGT 57.270 39.130 0.00 0.00 32.61 3.41
251 259 3.719871 TGAATAGCCAGGAGGACAGTAA 58.280 45.455 0.00 0.00 36.89 2.24
256 264 4.965200 AGCCAGGAGGACAGTAATATTC 57.035 45.455 0.00 0.00 36.89 1.75
258 266 3.244596 GCCAGGAGGACAGTAATATTCCC 60.245 52.174 0.00 0.00 36.89 3.97
277 285 1.394917 CCTGCAGTTCAAGTCGCATAC 59.605 52.381 13.81 0.00 33.15 2.39
296 304 2.522185 ACTTGAGATTGGTGCTTGCAT 58.478 42.857 0.00 0.00 0.00 3.96
297 305 2.895404 ACTTGAGATTGGTGCTTGCATT 59.105 40.909 0.00 0.00 0.00 3.56
298 306 3.322828 ACTTGAGATTGGTGCTTGCATTT 59.677 39.130 0.00 0.00 0.00 2.32
299 307 4.202284 ACTTGAGATTGGTGCTTGCATTTT 60.202 37.500 0.00 0.00 0.00 1.82
300 308 4.339872 TGAGATTGGTGCTTGCATTTTT 57.660 36.364 0.00 0.00 0.00 1.94
301 309 4.309099 TGAGATTGGTGCTTGCATTTTTC 58.691 39.130 0.00 0.00 0.00 2.29
302 310 4.039488 TGAGATTGGTGCTTGCATTTTTCT 59.961 37.500 0.00 0.29 0.00 2.52
303 311 5.243507 TGAGATTGGTGCTTGCATTTTTCTA 59.756 36.000 0.00 0.00 0.00 2.10
304 312 5.717119 AGATTGGTGCTTGCATTTTTCTAG 58.283 37.500 0.00 0.00 0.00 2.43
305 313 5.477984 AGATTGGTGCTTGCATTTTTCTAGA 59.522 36.000 0.00 0.00 0.00 2.43
306 314 5.726980 TTGGTGCTTGCATTTTTCTAGAT 57.273 34.783 0.00 0.00 0.00 1.98
307 315 5.726980 TGGTGCTTGCATTTTTCTAGATT 57.273 34.783 0.00 0.00 0.00 2.40
308 316 6.100404 TGGTGCTTGCATTTTTCTAGATTT 57.900 33.333 0.00 0.00 0.00 2.17
309 317 7.225784 TGGTGCTTGCATTTTTCTAGATTTA 57.774 32.000 0.00 0.00 0.00 1.40
310 318 7.839907 TGGTGCTTGCATTTTTCTAGATTTAT 58.160 30.769 0.00 0.00 0.00 1.40
311 319 8.313292 TGGTGCTTGCATTTTTCTAGATTTATT 58.687 29.630 0.00 0.00 0.00 1.40
312 320 9.154847 GGTGCTTGCATTTTTCTAGATTTATTT 57.845 29.630 0.00 0.00 0.00 1.40
314 322 9.075519 TGCTTGCATTTTTCTAGATTTATTTCG 57.924 29.630 0.00 0.00 0.00 3.46
315 323 8.534778 GCTTGCATTTTTCTAGATTTATTTCGG 58.465 33.333 0.00 0.00 0.00 4.30
316 324 8.925161 TTGCATTTTTCTAGATTTATTTCGGG 57.075 30.769 0.00 0.00 0.00 5.14
317 325 6.978080 TGCATTTTTCTAGATTTATTTCGGGC 59.022 34.615 0.00 0.00 0.00 6.13
318 326 7.147915 TGCATTTTTCTAGATTTATTTCGGGCT 60.148 33.333 0.00 0.00 0.00 5.19
319 327 7.706607 GCATTTTTCTAGATTTATTTCGGGCTT 59.293 33.333 0.00 0.00 0.00 4.35
320 328 9.586435 CATTTTTCTAGATTTATTTCGGGCTTT 57.414 29.630 0.00 0.00 0.00 3.51
321 329 9.803315 ATTTTTCTAGATTTATTTCGGGCTTTC 57.197 29.630 0.00 0.00 0.00 2.62
322 330 8.575649 TTTTCTAGATTTATTTCGGGCTTTCT 57.424 30.769 0.00 0.00 0.00 2.52
323 331 7.553881 TTCTAGATTTATTTCGGGCTTTCTG 57.446 36.000 0.00 0.00 0.00 3.02
324 332 6.055588 TCTAGATTTATTTCGGGCTTTCTGG 58.944 40.000 0.00 0.00 0.00 3.86
325 333 3.381590 AGATTTATTTCGGGCTTTCTGGC 59.618 43.478 0.00 0.00 40.96 4.85
326 334 1.091537 TTATTTCGGGCTTTCTGGCG 58.908 50.000 0.00 0.00 42.84 5.69
327 335 0.250793 TATTTCGGGCTTTCTGGCGA 59.749 50.000 0.00 0.00 42.84 5.54
328 336 1.305930 ATTTCGGGCTTTCTGGCGAC 61.306 55.000 0.00 0.00 42.84 5.19
329 337 4.735132 TCGGGCTTTCTGGCGACG 62.735 66.667 0.00 0.00 42.84 5.12
331 339 3.119096 GGGCTTTCTGGCGACGTC 61.119 66.667 5.18 5.18 42.84 4.34
332 340 2.048127 GGCTTTCTGGCGACGTCT 60.048 61.111 14.70 0.00 0.00 4.18
333 341 1.214589 GGCTTTCTGGCGACGTCTA 59.785 57.895 14.70 0.00 0.00 2.59
334 342 0.179108 GGCTTTCTGGCGACGTCTAT 60.179 55.000 14.70 0.00 0.00 1.98
335 343 1.641577 GCTTTCTGGCGACGTCTATT 58.358 50.000 14.70 0.00 0.00 1.73
336 344 2.000447 GCTTTCTGGCGACGTCTATTT 59.000 47.619 14.70 0.00 0.00 1.40
337 345 3.184541 GCTTTCTGGCGACGTCTATTTA 58.815 45.455 14.70 0.00 0.00 1.40
338 346 3.243177 GCTTTCTGGCGACGTCTATTTAG 59.757 47.826 14.70 5.07 0.00 1.85
339 347 4.421948 CTTTCTGGCGACGTCTATTTAGT 58.578 43.478 14.70 0.00 0.00 2.24
340 348 3.416119 TCTGGCGACGTCTATTTAGTG 57.584 47.619 14.70 0.00 0.00 2.74
341 349 2.098607 TCTGGCGACGTCTATTTAGTGG 59.901 50.000 14.70 0.00 0.00 4.00
342 350 1.135527 TGGCGACGTCTATTTAGTGGG 59.864 52.381 14.70 0.00 0.00 4.61
343 351 1.406539 GGCGACGTCTATTTAGTGGGA 59.593 52.381 14.70 0.00 0.00 4.37
344 352 2.159198 GGCGACGTCTATTTAGTGGGAA 60.159 50.000 14.70 0.00 0.00 3.97
345 353 3.114065 GCGACGTCTATTTAGTGGGAAG 58.886 50.000 14.70 0.00 0.00 3.46
346 354 3.181493 GCGACGTCTATTTAGTGGGAAGA 60.181 47.826 14.70 0.00 0.00 2.87
347 355 4.599047 CGACGTCTATTTAGTGGGAAGAG 58.401 47.826 14.70 0.00 0.00 2.85
348 356 4.334759 CGACGTCTATTTAGTGGGAAGAGA 59.665 45.833 14.70 0.00 0.00 3.10
349 357 5.008811 CGACGTCTATTTAGTGGGAAGAGAT 59.991 44.000 14.70 0.00 28.41 2.75
350 358 6.150396 ACGTCTATTTAGTGGGAAGAGATG 57.850 41.667 0.00 0.00 37.37 2.90
351 359 5.657302 ACGTCTATTTAGTGGGAAGAGATGT 59.343 40.000 1.70 1.70 38.85 3.06
352 360 6.154706 ACGTCTATTTAGTGGGAAGAGATGTT 59.845 38.462 1.70 0.00 39.99 2.71
353 361 6.697892 CGTCTATTTAGTGGGAAGAGATGTTC 59.302 42.308 0.00 0.00 30.55 3.18
354 362 7.416890 CGTCTATTTAGTGGGAAGAGATGTTCT 60.417 40.741 0.00 0.00 37.93 3.01
355 363 7.923878 GTCTATTTAGTGGGAAGAGATGTTCTC 59.076 40.741 0.00 0.00 43.70 2.87
356 364 6.627087 ATTTAGTGGGAAGAGATGTTCTCA 57.373 37.500 7.24 0.00 45.73 3.27
357 365 6.627087 TTTAGTGGGAAGAGATGTTCTCAT 57.373 37.500 7.24 0.00 45.73 2.90
358 366 4.751767 AGTGGGAAGAGATGTTCTCATC 57.248 45.455 7.24 4.53 45.73 2.92
370 378 5.786401 ATGTTCTCATCAACTACGAAAGC 57.214 39.130 0.00 0.00 0.00 3.51
371 379 4.627058 TGTTCTCATCAACTACGAAAGCA 58.373 39.130 0.00 0.00 0.00 3.91
372 380 5.237815 TGTTCTCATCAACTACGAAAGCAT 58.762 37.500 0.00 0.00 0.00 3.79
373 381 5.348724 TGTTCTCATCAACTACGAAAGCATC 59.651 40.000 0.00 0.00 0.00 3.91
374 382 5.330455 TCTCATCAACTACGAAAGCATCT 57.670 39.130 0.00 0.00 0.00 2.90
375 383 5.724328 TCTCATCAACTACGAAAGCATCTT 58.276 37.500 0.00 0.00 0.00 2.40
376 384 6.166279 TCTCATCAACTACGAAAGCATCTTT 58.834 36.000 0.00 0.00 0.00 2.52
377 385 7.320399 TCTCATCAACTACGAAAGCATCTTTA 58.680 34.615 0.00 0.00 0.00 1.85
378 386 7.981789 TCTCATCAACTACGAAAGCATCTTTAT 59.018 33.333 0.00 0.00 0.00 1.40
379 387 7.909267 TCATCAACTACGAAAGCATCTTTATG 58.091 34.615 0.00 0.00 36.09 1.90
380 388 7.549134 TCATCAACTACGAAAGCATCTTTATGT 59.451 33.333 0.00 0.00 35.38 2.29
381 389 8.817100 CATCAACTACGAAAGCATCTTTATGTA 58.183 33.333 0.00 0.00 35.38 2.29
382 390 8.942338 TCAACTACGAAAGCATCTTTATGTAT 57.058 30.769 0.00 0.00 35.38 2.29
383 391 9.031360 TCAACTACGAAAGCATCTTTATGTATC 57.969 33.333 0.00 0.00 35.38 2.24
384 392 9.035607 CAACTACGAAAGCATCTTTATGTATCT 57.964 33.333 0.00 0.00 35.38 1.98
385 393 8.804688 ACTACGAAAGCATCTTTATGTATCTC 57.195 34.615 0.00 0.00 35.38 2.75
386 394 8.414003 ACTACGAAAGCATCTTTATGTATCTCA 58.586 33.333 0.00 0.00 35.38 3.27
387 395 9.249457 CTACGAAAGCATCTTTATGTATCTCAA 57.751 33.333 0.00 0.00 35.38 3.02
388 396 7.910304 ACGAAAGCATCTTTATGTATCTCAAC 58.090 34.615 0.00 0.00 35.38 3.18
389 397 7.549134 ACGAAAGCATCTTTATGTATCTCAACA 59.451 33.333 0.00 0.00 35.38 3.33
390 398 8.554528 CGAAAGCATCTTTATGTATCTCAACAT 58.445 33.333 0.00 0.00 42.62 2.71
391 399 9.661187 GAAAGCATCTTTATGTATCTCAACATG 57.339 33.333 0.00 0.00 40.29 3.21
392 400 8.969260 AAGCATCTTTATGTATCTCAACATGA 57.031 30.769 0.00 0.00 40.29 3.07
393 401 8.375608 AGCATCTTTATGTATCTCAACATGAC 57.624 34.615 0.00 0.00 40.29 3.06
394 402 7.989170 AGCATCTTTATGTATCTCAACATGACA 59.011 33.333 0.00 0.00 40.29 3.58
395 403 8.066595 GCATCTTTATGTATCTCAACATGACAC 58.933 37.037 0.00 0.00 40.29 3.67
396 404 7.755582 TCTTTATGTATCTCAACATGACACG 57.244 36.000 0.00 0.00 40.29 4.49
397 405 6.756542 TCTTTATGTATCTCAACATGACACGG 59.243 38.462 0.00 0.00 40.29 4.94
398 406 2.616960 TGTATCTCAACATGACACGGC 58.383 47.619 0.00 0.00 0.00 5.68
399 407 2.028567 TGTATCTCAACATGACACGGCA 60.029 45.455 0.00 0.00 0.00 5.69
400 408 1.730501 ATCTCAACATGACACGGCAG 58.269 50.000 0.00 0.00 0.00 4.85
401 409 0.392706 TCTCAACATGACACGGCAGT 59.607 50.000 0.00 0.00 0.00 4.40
402 410 1.202639 TCTCAACATGACACGGCAGTT 60.203 47.619 0.00 0.00 0.00 3.16
403 411 1.195448 CTCAACATGACACGGCAGTTC 59.805 52.381 0.00 0.00 0.00 3.01
404 412 0.943673 CAACATGACACGGCAGTTCA 59.056 50.000 0.00 4.87 0.00 3.18
405 413 1.333308 CAACATGACACGGCAGTTCAA 59.667 47.619 0.00 0.00 0.00 2.69
406 414 1.896220 ACATGACACGGCAGTTCAAT 58.104 45.000 0.00 0.00 0.00 2.57
407 415 3.052455 ACATGACACGGCAGTTCAATA 57.948 42.857 0.00 0.00 0.00 1.90
408 416 3.609853 ACATGACACGGCAGTTCAATAT 58.390 40.909 0.00 0.00 0.00 1.28
409 417 4.009675 ACATGACACGGCAGTTCAATATT 58.990 39.130 0.00 0.00 0.00 1.28
410 418 4.458989 ACATGACACGGCAGTTCAATATTT 59.541 37.500 0.00 0.00 0.00 1.40
411 419 4.678509 TGACACGGCAGTTCAATATTTC 57.321 40.909 0.00 0.00 0.00 2.17
412 420 3.124466 TGACACGGCAGTTCAATATTTCG 59.876 43.478 0.00 0.00 0.00 3.46
413 421 2.418628 ACACGGCAGTTCAATATTTCGG 59.581 45.455 0.00 0.00 0.00 4.30
414 422 2.675844 CACGGCAGTTCAATATTTCGGA 59.324 45.455 0.00 0.00 0.00 4.55
415 423 2.936498 ACGGCAGTTCAATATTTCGGAG 59.064 45.455 0.00 0.00 0.00 4.63
416 424 3.194861 CGGCAGTTCAATATTTCGGAGA 58.805 45.455 0.00 0.00 0.00 3.71
417 425 3.001330 CGGCAGTTCAATATTTCGGAGAC 59.999 47.826 0.00 0.00 34.32 3.36
432 440 2.213499 GGAGACGCTCATAACATTGGG 58.787 52.381 8.71 0.00 31.08 4.12
433 441 2.420129 GGAGACGCTCATAACATTGGGT 60.420 50.000 8.71 0.00 31.08 4.51
434 442 3.181469 GGAGACGCTCATAACATTGGGTA 60.181 47.826 8.71 0.00 31.08 3.69
435 443 4.439057 GAGACGCTCATAACATTGGGTAA 58.561 43.478 2.53 0.00 0.00 2.85
436 444 4.442706 AGACGCTCATAACATTGGGTAAG 58.557 43.478 0.00 0.00 0.00 2.34
437 445 4.081087 AGACGCTCATAACATTGGGTAAGT 60.081 41.667 0.00 0.00 0.00 2.24
438 446 4.585879 ACGCTCATAACATTGGGTAAGTT 58.414 39.130 0.00 0.00 0.00 2.66
439 447 5.007682 ACGCTCATAACATTGGGTAAGTTT 58.992 37.500 0.00 0.00 0.00 2.66
440 448 5.475564 ACGCTCATAACATTGGGTAAGTTTT 59.524 36.000 0.00 0.00 0.00 2.43
441 449 6.015772 ACGCTCATAACATTGGGTAAGTTTTT 60.016 34.615 0.00 0.00 0.00 1.94
442 450 6.307800 CGCTCATAACATTGGGTAAGTTTTTG 59.692 38.462 0.00 0.00 0.00 2.44
443 451 6.090763 GCTCATAACATTGGGTAAGTTTTTGC 59.909 38.462 0.00 0.00 0.00 3.68
444 452 6.153067 TCATAACATTGGGTAAGTTTTTGCG 58.847 36.000 0.00 0.00 0.00 4.85
445 453 2.749776 ACATTGGGTAAGTTTTTGCGC 58.250 42.857 0.00 0.00 33.46 6.09
446 454 1.718711 CATTGGGTAAGTTTTTGCGCG 59.281 47.619 0.00 0.00 35.16 6.86
447 455 0.739561 TTGGGTAAGTTTTTGCGCGT 59.260 45.000 8.43 0.00 35.16 6.01
448 456 0.739561 TGGGTAAGTTTTTGCGCGTT 59.260 45.000 8.43 0.00 35.16 4.84
449 457 1.134560 TGGGTAAGTTTTTGCGCGTTT 59.865 42.857 8.43 0.00 35.16 3.60
450 458 2.357009 TGGGTAAGTTTTTGCGCGTTTA 59.643 40.909 8.43 0.00 35.16 2.01
451 459 3.004524 TGGGTAAGTTTTTGCGCGTTTAT 59.995 39.130 8.43 0.00 35.16 1.40
452 460 4.214971 TGGGTAAGTTTTTGCGCGTTTATA 59.785 37.500 8.43 0.00 35.16 0.98
453 461 4.789629 GGGTAAGTTTTTGCGCGTTTATAG 59.210 41.667 8.43 0.00 0.00 1.31
454 462 5.390779 GGGTAAGTTTTTGCGCGTTTATAGA 60.391 40.000 8.43 0.00 0.00 1.98
455 463 6.079120 GGTAAGTTTTTGCGCGTTTATAGAA 58.921 36.000 8.43 0.00 0.00 2.10
456 464 6.578172 GGTAAGTTTTTGCGCGTTTATAGAAA 59.422 34.615 8.43 0.00 0.00 2.52
457 465 7.271868 GGTAAGTTTTTGCGCGTTTATAGAAAT 59.728 33.333 8.43 0.00 0.00 2.17
458 466 6.611380 AGTTTTTGCGCGTTTATAGAAATG 57.389 33.333 8.43 0.00 35.07 2.32
459 467 6.375377 AGTTTTTGCGCGTTTATAGAAATGA 58.625 32.000 8.43 0.00 34.00 2.57
460 468 6.523201 AGTTTTTGCGCGTTTATAGAAATGAG 59.477 34.615 8.43 3.96 34.00 2.90
461 469 5.539582 TTTGCGCGTTTATAGAAATGAGT 57.460 34.783 8.43 0.00 34.77 3.41
462 470 4.514545 TGCGCGTTTATAGAAATGAGTG 57.485 40.909 8.43 0.25 34.77 3.51
463 471 3.930229 TGCGCGTTTATAGAAATGAGTGT 59.070 39.130 8.43 0.00 34.77 3.55
464 472 5.103687 TGCGCGTTTATAGAAATGAGTGTA 58.896 37.500 8.43 0.00 34.77 2.90
465 473 5.751509 TGCGCGTTTATAGAAATGAGTGTAT 59.248 36.000 8.43 0.00 34.77 2.29
466 474 6.065153 GCGCGTTTATAGAAATGAGTGTATG 58.935 40.000 8.43 0.00 34.77 2.39
467 475 6.292168 GCGCGTTTATAGAAATGAGTGTATGT 60.292 38.462 8.43 0.00 34.77 2.29
468 476 7.057402 CGCGTTTATAGAAATGAGTGTATGTG 58.943 38.462 6.23 0.00 34.00 3.21
469 477 6.846283 GCGTTTATAGAAATGAGTGTATGTGC 59.154 38.462 6.23 0.00 34.00 4.57
470 478 7.057402 CGTTTATAGAAATGAGTGTATGTGCG 58.943 38.462 0.00 0.00 34.00 5.34
471 479 7.253983 CGTTTATAGAAATGAGTGTATGTGCGT 60.254 37.037 0.00 0.00 34.00 5.24
472 480 9.027129 GTTTATAGAAATGAGTGTATGTGCGTA 57.973 33.333 0.00 0.00 0.00 4.42
473 481 8.570096 TTATAGAAATGAGTGTATGTGCGTAC 57.430 34.615 0.00 0.00 0.00 3.67
474 482 3.857665 AGAAATGAGTGTATGTGCGTACG 59.142 43.478 11.84 11.84 0.00 3.67
475 483 2.933495 ATGAGTGTATGTGCGTACGT 57.067 45.000 17.90 3.27 0.00 3.57
476 484 1.971792 TGAGTGTATGTGCGTACGTG 58.028 50.000 17.90 0.00 0.00 4.49
477 485 1.267533 TGAGTGTATGTGCGTACGTGT 59.732 47.619 17.90 3.27 0.00 4.49
478 486 1.909532 GAGTGTATGTGCGTACGTGTC 59.090 52.381 17.90 8.18 0.00 3.67
479 487 1.538512 AGTGTATGTGCGTACGTGTCT 59.461 47.619 17.90 2.60 0.00 3.41
480 488 2.743664 AGTGTATGTGCGTACGTGTCTA 59.256 45.455 17.90 1.62 0.00 2.59
481 489 3.376234 AGTGTATGTGCGTACGTGTCTAT 59.624 43.478 17.90 7.38 0.00 1.98
482 490 4.571984 AGTGTATGTGCGTACGTGTCTATA 59.428 41.667 17.90 6.46 0.00 1.31
483 491 5.237996 AGTGTATGTGCGTACGTGTCTATAT 59.762 40.000 17.90 5.07 0.00 0.86
484 492 5.911280 GTGTATGTGCGTACGTGTCTATATT 59.089 40.000 17.90 0.00 0.00 1.28
485 493 5.910723 TGTATGTGCGTACGTGTCTATATTG 59.089 40.000 17.90 0.00 0.00 1.90
486 494 4.359971 TGTGCGTACGTGTCTATATTGT 57.640 40.909 17.90 0.00 0.00 2.71
487 495 4.099824 TGTGCGTACGTGTCTATATTGTG 58.900 43.478 17.90 0.00 0.00 3.33
488 496 4.100529 GTGCGTACGTGTCTATATTGTGT 58.899 43.478 17.90 0.00 0.00 3.72
489 497 4.560035 GTGCGTACGTGTCTATATTGTGTT 59.440 41.667 17.90 0.00 0.00 3.32
490 498 5.738693 GTGCGTACGTGTCTATATTGTGTTA 59.261 40.000 17.90 0.00 0.00 2.41
491 499 6.251163 GTGCGTACGTGTCTATATTGTGTTAA 59.749 38.462 17.90 0.00 0.00 2.01
492 500 6.805760 TGCGTACGTGTCTATATTGTGTTAAA 59.194 34.615 17.90 0.00 0.00 1.52
493 501 7.328005 TGCGTACGTGTCTATATTGTGTTAAAA 59.672 33.333 17.90 0.00 0.00 1.52
494 502 8.161610 GCGTACGTGTCTATATTGTGTTAAAAA 58.838 33.333 17.90 0.00 0.00 1.94
594 602 6.594159 CGGGATATATGAGTGGTCATTTTACC 59.406 42.308 0.00 0.00 40.84 2.85
687 699 2.404923 GGAGGAACCCTAAGTTGAGC 57.595 55.000 0.00 0.00 39.40 4.26
695 707 2.979678 ACCCTAAGTTGAGCTCTTTCCA 59.020 45.455 16.19 0.00 0.00 3.53
1015 1030 2.516930 GGATGGTGGTGGCGATGG 60.517 66.667 0.00 0.00 0.00 3.51
1016 1031 3.211963 GATGGTGGTGGCGATGGC 61.212 66.667 0.00 0.00 38.90 4.40
1035 1050 1.953138 GCAGAGGATGCGATGGACG 60.953 63.158 0.00 0.00 46.99 4.79
1123 1140 0.978667 GGTTCCAGTCCCTCCTCCTC 60.979 65.000 0.00 0.00 0.00 3.71
1145 1162 1.923395 ACGGCATGAAGAAGGGGGA 60.923 57.895 0.00 0.00 0.00 4.81
1340 1357 6.258727 GTGGAATATGTATCAGTTGTGAGTGG 59.741 42.308 0.00 0.00 35.66 4.00
1359 1376 3.621715 GTGGTATTTTGGATGACCTCGAC 59.378 47.826 0.00 0.00 37.04 4.20
1418 1435 0.038166 TTCGAAGCCATGGAAGCCTT 59.962 50.000 18.40 9.17 0.00 4.35
1625 1642 1.527844 GTGCCCATGAGGATGAGGC 60.528 63.158 0.00 0.00 44.13 4.70
1640 1657 3.134127 GGCGACAACCATGGAGGC 61.134 66.667 21.47 11.94 43.14 4.70
1695 1712 0.890683 TAGACGACGGGGAAAAGGTC 59.109 55.000 0.00 0.00 0.00 3.85
1701 1718 2.436115 GGGGAAAAGGTCGAGGCG 60.436 66.667 0.00 0.00 0.00 5.52
1819 1836 2.165030 CAGTTGATTGGTCCATTGCCTC 59.835 50.000 0.00 0.00 0.00 4.70
1916 1933 2.904905 CCGCGGGGGTCATAAGAA 59.095 61.111 20.10 0.00 0.00 2.52
1917 1934 1.227556 CCGCGGGGGTCATAAGAAG 60.228 63.158 20.10 0.00 0.00 2.85
1918 1935 1.227556 CGCGGGGGTCATAAGAAGG 60.228 63.158 0.00 0.00 0.00 3.46
1919 1936 1.148498 GCGGGGGTCATAAGAAGGG 59.852 63.158 0.00 0.00 0.00 3.95
1920 1937 1.837090 CGGGGGTCATAAGAAGGGG 59.163 63.158 0.00 0.00 0.00 4.79
1921 1938 0.693092 CGGGGGTCATAAGAAGGGGA 60.693 60.000 0.00 0.00 0.00 4.81
1922 1939 1.603634 GGGGGTCATAAGAAGGGGAA 58.396 55.000 0.00 0.00 0.00 3.97
1923 1940 1.214673 GGGGGTCATAAGAAGGGGAAC 59.785 57.143 0.00 0.00 0.00 3.62
1949 1966 1.564348 GGGTCATAAGAAGGGGAAGCA 59.436 52.381 0.00 0.00 0.00 3.91
2159 2200 0.455005 GCCTCGTACCGTAGAAGCTT 59.545 55.000 0.00 0.00 0.00 3.74
2212 2253 1.069159 TCTTCGAAGACACGAGTGAGC 60.069 52.381 23.74 1.86 43.04 4.26
2304 2377 5.128827 TCTGTAACACCCATGGTCTTCTATC 59.871 44.000 11.73 0.00 31.02 2.08
2486 2559 2.507324 GGTTGCCGCTCGAGACTC 60.507 66.667 18.75 3.88 0.00 3.36
2487 2560 2.569134 GTTGCCGCTCGAGACTCT 59.431 61.111 18.75 0.00 0.00 3.24
2967 3381 3.820467 TGGAGCGAATTCATGAAACTGTT 59.180 39.130 13.09 1.59 0.00 3.16
3130 3544 3.057033 GGAAGTTGTGATGCTTGCTTCAT 60.057 43.478 13.00 0.00 35.41 2.57
3185 3599 2.766263 ACCTTCGTCTATCAAGGCATGA 59.234 45.455 0.00 0.00 42.80 3.07
3276 3690 1.402787 CACAGGGTGAGGTTTGCTTT 58.597 50.000 0.00 0.00 35.23 3.51
3374 3788 0.793250 GTCGCTTGGTCTCTTCTTGC 59.207 55.000 0.00 0.00 0.00 4.01
3619 4033 2.013400 TGCATGTTATGTAGGCAACCG 58.987 47.619 0.00 0.00 37.17 4.44
3692 4106 4.639334 AGAGAATTGCGCTGTCATATCAT 58.361 39.130 9.73 0.00 0.00 2.45
3693 4107 4.689812 AGAGAATTGCGCTGTCATATCATC 59.310 41.667 9.73 0.00 0.00 2.92
3694 4108 4.383173 AGAATTGCGCTGTCATATCATCA 58.617 39.130 9.73 0.00 0.00 3.07
3773 4187 2.282887 ACCCAAATCCACCGGCAC 60.283 61.111 0.00 0.00 0.00 5.01
3774 4188 2.282816 CCCAAATCCACCGGCACA 60.283 61.111 0.00 0.00 0.00 4.57
3921 6444 2.773487 TGTTATCGAACACCAACCCTG 58.227 47.619 0.00 0.00 40.72 4.45
4018 6541 4.988598 AGGTGCTGGCGTTGGTCG 62.989 66.667 0.00 0.00 43.12 4.79
4020 6543 3.712881 GTGCTGGCGTTGGTCGTC 61.713 66.667 0.00 0.00 45.13 4.20
4034 6557 0.035439 GTCGTCCACCAATCCACCAT 60.035 55.000 0.00 0.00 0.00 3.55
4125 6648 2.430465 GAGAAAGAGCATTGCACCAGA 58.570 47.619 11.91 0.00 0.00 3.86
4141 6664 5.238432 TGCACCAGAAGTTATGTTGTGTTAG 59.762 40.000 8.16 0.00 0.00 2.34
4177 6700 7.872113 TTTTTGCAGGGAAAATTATGTTGTT 57.128 28.000 0.00 0.00 0.00 2.83
4239 6762 8.196771 TGTGCATATAGGTTGATTGGAAAATTC 58.803 33.333 0.00 0.00 0.00 2.17
4241 6764 7.068103 TGCATATAGGTTGATTGGAAAATTCGT 59.932 33.333 0.00 0.00 0.00 3.85
4301 6824 9.522804 TCGTTTACAAGTAAAATCAAATTTGCT 57.477 25.926 13.54 0.29 36.90 3.91
4380 6940 5.238583 CGTGATGGACCTCTTTTCTTTACT 58.761 41.667 0.00 0.00 0.00 2.24
4449 7009 7.531857 TTTTTAACAGATTAACAGGGCATGA 57.468 32.000 5.99 0.00 29.77 3.07
4450 7010 7.531857 TTTTAACAGATTAACAGGGCATGAA 57.468 32.000 5.99 0.00 29.77 2.57
4451 7011 7.531857 TTTAACAGATTAACAGGGCATGAAA 57.468 32.000 5.99 0.00 29.77 2.69
4452 7012 7.716799 TTAACAGATTAACAGGGCATGAAAT 57.283 32.000 5.99 5.15 0.00 2.17
4453 7013 8.815565 TTAACAGATTAACAGGGCATGAAATA 57.184 30.769 5.99 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 5.070685 GGGTCTGTTACAGTCCAGAAAAAT 58.929 41.667 25.01 0.00 40.48 1.82
251 259 3.535561 CGACTTGAACTGCAGGGAATAT 58.464 45.455 19.93 0.00 0.00 1.28
256 264 0.957395 ATGCGACTTGAACTGCAGGG 60.957 55.000 19.93 5.11 41.19 4.45
258 266 2.341257 AGTATGCGACTTGAACTGCAG 58.659 47.619 13.48 13.48 41.19 4.41
277 285 3.587797 AATGCAAGCACCAATCTCAAG 57.412 42.857 0.00 0.00 0.00 3.02
296 304 9.020731 AGAAAGCCCGAAATAAATCTAGAAAAA 57.979 29.630 0.00 0.00 0.00 1.94
297 305 8.458843 CAGAAAGCCCGAAATAAATCTAGAAAA 58.541 33.333 0.00 0.00 0.00 2.29
298 306 7.067008 CCAGAAAGCCCGAAATAAATCTAGAAA 59.933 37.037 0.00 0.00 0.00 2.52
299 307 6.542370 CCAGAAAGCCCGAAATAAATCTAGAA 59.458 38.462 0.00 0.00 0.00 2.10
300 308 6.055588 CCAGAAAGCCCGAAATAAATCTAGA 58.944 40.000 0.00 0.00 0.00 2.43
301 309 5.278022 GCCAGAAAGCCCGAAATAAATCTAG 60.278 44.000 0.00 0.00 0.00 2.43
302 310 4.578928 GCCAGAAAGCCCGAAATAAATCTA 59.421 41.667 0.00 0.00 0.00 1.98
303 311 3.381590 GCCAGAAAGCCCGAAATAAATCT 59.618 43.478 0.00 0.00 0.00 2.40
304 312 3.706698 GCCAGAAAGCCCGAAATAAATC 58.293 45.455 0.00 0.00 0.00 2.17
305 313 2.099098 CGCCAGAAAGCCCGAAATAAAT 59.901 45.455 0.00 0.00 0.00 1.40
306 314 1.470890 CGCCAGAAAGCCCGAAATAAA 59.529 47.619 0.00 0.00 0.00 1.40
307 315 1.091537 CGCCAGAAAGCCCGAAATAA 58.908 50.000 0.00 0.00 0.00 1.40
308 316 0.250793 TCGCCAGAAAGCCCGAAATA 59.749 50.000 0.00 0.00 0.00 1.40
309 317 1.002624 TCGCCAGAAAGCCCGAAAT 60.003 52.632 0.00 0.00 0.00 2.17
310 318 1.964373 GTCGCCAGAAAGCCCGAAA 60.964 57.895 0.00 0.00 0.00 3.46
311 319 2.358247 GTCGCCAGAAAGCCCGAA 60.358 61.111 0.00 0.00 0.00 4.30
312 320 4.735132 CGTCGCCAGAAAGCCCGA 62.735 66.667 0.00 0.00 0.00 5.14
314 322 2.221906 TAGACGTCGCCAGAAAGCCC 62.222 60.000 10.46 0.00 0.00 5.19
315 323 0.179108 ATAGACGTCGCCAGAAAGCC 60.179 55.000 10.46 0.00 0.00 4.35
316 324 1.641577 AATAGACGTCGCCAGAAAGC 58.358 50.000 10.46 0.00 0.00 3.51
317 325 4.265556 CACTAAATAGACGTCGCCAGAAAG 59.734 45.833 10.46 5.95 0.00 2.62
318 326 4.171005 CACTAAATAGACGTCGCCAGAAA 58.829 43.478 10.46 0.00 0.00 2.52
319 327 3.428452 CCACTAAATAGACGTCGCCAGAA 60.428 47.826 10.46 0.00 0.00 3.02
320 328 2.098607 CCACTAAATAGACGTCGCCAGA 59.901 50.000 10.46 0.00 0.00 3.86
321 329 2.460918 CCACTAAATAGACGTCGCCAG 58.539 52.381 10.46 6.99 0.00 4.85
322 330 1.135527 CCCACTAAATAGACGTCGCCA 59.864 52.381 10.46 0.00 0.00 5.69
323 331 1.406539 TCCCACTAAATAGACGTCGCC 59.593 52.381 10.46 0.00 0.00 5.54
324 332 2.857592 TCCCACTAAATAGACGTCGC 57.142 50.000 10.46 0.00 0.00 5.19
325 333 4.334759 TCTCTTCCCACTAAATAGACGTCG 59.665 45.833 10.46 0.00 0.00 5.12
326 334 5.831702 TCTCTTCCCACTAAATAGACGTC 57.168 43.478 7.70 7.70 0.00 4.34
327 335 5.657302 ACATCTCTTCCCACTAAATAGACGT 59.343 40.000 0.00 0.00 0.00 4.34
328 336 6.150396 ACATCTCTTCCCACTAAATAGACG 57.850 41.667 0.00 0.00 0.00 4.18
329 337 7.787028 AGAACATCTCTTCCCACTAAATAGAC 58.213 38.462 0.00 0.00 0.00 2.59
330 338 7.619698 TGAGAACATCTCTTCCCACTAAATAGA 59.380 37.037 8.68 0.00 43.73 1.98
331 339 7.786030 TGAGAACATCTCTTCCCACTAAATAG 58.214 38.462 8.68 0.00 43.73 1.73
332 340 7.733773 TGAGAACATCTCTTCCCACTAAATA 57.266 36.000 8.68 0.00 43.73 1.40
333 341 6.627087 TGAGAACATCTCTTCCCACTAAAT 57.373 37.500 8.68 0.00 43.73 1.40
334 342 6.627087 ATGAGAACATCTCTTCCCACTAAA 57.373 37.500 8.68 0.00 43.73 1.85
335 343 6.227298 GATGAGAACATCTCTTCCCACTAA 57.773 41.667 8.68 0.00 46.47 2.24
336 344 5.860941 GATGAGAACATCTCTTCCCACTA 57.139 43.478 8.68 0.00 46.47 2.74
337 345 4.751767 GATGAGAACATCTCTTCCCACT 57.248 45.455 8.68 0.00 46.47 4.00
348 356 5.237815 TGCTTTCGTAGTTGATGAGAACAT 58.762 37.500 0.00 0.00 39.67 2.71
349 357 4.627058 TGCTTTCGTAGTTGATGAGAACA 58.373 39.130 0.00 0.00 0.00 3.18
350 358 5.578727 AGATGCTTTCGTAGTTGATGAGAAC 59.421 40.000 0.00 0.00 0.00 3.01
351 359 5.724328 AGATGCTTTCGTAGTTGATGAGAA 58.276 37.500 0.00 0.00 0.00 2.87
352 360 5.330455 AGATGCTTTCGTAGTTGATGAGA 57.670 39.130 0.00 0.00 0.00 3.27
353 361 6.414408 AAAGATGCTTTCGTAGTTGATGAG 57.586 37.500 0.00 0.00 0.00 2.90
354 362 7.549134 ACATAAAGATGCTTTCGTAGTTGATGA 59.451 33.333 0.00 0.00 36.43 2.92
355 363 7.688372 ACATAAAGATGCTTTCGTAGTTGATG 58.312 34.615 0.00 0.00 36.43 3.07
356 364 7.849804 ACATAAAGATGCTTTCGTAGTTGAT 57.150 32.000 0.00 0.00 36.43 2.57
357 365 8.942338 ATACATAAAGATGCTTTCGTAGTTGA 57.058 30.769 0.00 0.00 36.43 3.18
358 366 9.035607 AGATACATAAAGATGCTTTCGTAGTTG 57.964 33.333 0.00 0.00 36.43 3.16
359 367 9.250624 GAGATACATAAAGATGCTTTCGTAGTT 57.749 33.333 0.00 0.00 36.43 2.24
360 368 8.414003 TGAGATACATAAAGATGCTTTCGTAGT 58.586 33.333 0.00 0.00 36.43 2.73
361 369 8.803201 TGAGATACATAAAGATGCTTTCGTAG 57.197 34.615 0.00 0.00 36.43 3.51
362 370 9.031360 GTTGAGATACATAAAGATGCTTTCGTA 57.969 33.333 0.00 0.00 36.43 3.43
363 371 7.549134 TGTTGAGATACATAAAGATGCTTTCGT 59.451 33.333 0.00 0.00 36.43 3.85
364 372 7.909267 TGTTGAGATACATAAAGATGCTTTCG 58.091 34.615 0.00 0.00 36.43 3.46
365 373 9.661187 CATGTTGAGATACATAAAGATGCTTTC 57.339 33.333 0.00 0.00 36.64 2.62
366 374 9.399797 TCATGTTGAGATACATAAAGATGCTTT 57.600 29.630 0.00 0.00 36.64 3.51
367 375 8.834465 GTCATGTTGAGATACATAAAGATGCTT 58.166 33.333 0.00 0.00 36.64 3.91
368 376 7.989170 TGTCATGTTGAGATACATAAAGATGCT 59.011 33.333 0.00 0.00 36.64 3.79
369 377 8.066595 GTGTCATGTTGAGATACATAAAGATGC 58.933 37.037 0.00 0.00 36.64 3.91
370 378 8.271487 CGTGTCATGTTGAGATACATAAAGATG 58.729 37.037 0.00 0.00 36.64 2.90
371 379 7.439356 CCGTGTCATGTTGAGATACATAAAGAT 59.561 37.037 0.00 0.00 36.64 2.40
372 380 6.756542 CCGTGTCATGTTGAGATACATAAAGA 59.243 38.462 0.00 0.00 36.64 2.52
373 381 6.510157 GCCGTGTCATGTTGAGATACATAAAG 60.510 42.308 0.00 0.00 36.64 1.85
374 382 5.293324 GCCGTGTCATGTTGAGATACATAAA 59.707 40.000 0.00 0.00 36.64 1.40
375 383 4.808895 GCCGTGTCATGTTGAGATACATAA 59.191 41.667 0.00 0.00 36.64 1.90
376 384 4.142049 TGCCGTGTCATGTTGAGATACATA 60.142 41.667 0.00 0.00 36.64 2.29
377 385 3.198068 GCCGTGTCATGTTGAGATACAT 58.802 45.455 0.00 0.00 39.27 2.29
378 386 2.028567 TGCCGTGTCATGTTGAGATACA 60.029 45.455 0.00 0.00 0.00 2.29
379 387 2.604914 CTGCCGTGTCATGTTGAGATAC 59.395 50.000 0.00 0.00 0.00 2.24
380 388 2.233676 ACTGCCGTGTCATGTTGAGATA 59.766 45.455 0.00 0.00 0.00 1.98
381 389 1.002430 ACTGCCGTGTCATGTTGAGAT 59.998 47.619 0.00 0.00 0.00 2.75
382 390 0.392706 ACTGCCGTGTCATGTTGAGA 59.607 50.000 0.00 0.00 0.00 3.27
383 391 1.195448 GAACTGCCGTGTCATGTTGAG 59.805 52.381 0.00 0.00 0.00 3.02
384 392 1.225855 GAACTGCCGTGTCATGTTGA 58.774 50.000 0.00 0.00 0.00 3.18
385 393 0.943673 TGAACTGCCGTGTCATGTTG 59.056 50.000 0.00 0.00 0.00 3.33
386 394 1.674359 TTGAACTGCCGTGTCATGTT 58.326 45.000 0.00 0.00 0.00 2.71
387 395 1.896220 ATTGAACTGCCGTGTCATGT 58.104 45.000 0.00 0.00 0.00 3.21
388 396 4.621068 AATATTGAACTGCCGTGTCATG 57.379 40.909 0.00 0.00 0.00 3.07
389 397 4.201812 CGAAATATTGAACTGCCGTGTCAT 60.202 41.667 0.00 0.00 0.00 3.06
390 398 3.124466 CGAAATATTGAACTGCCGTGTCA 59.876 43.478 0.00 0.00 0.00 3.58
391 399 3.485216 CCGAAATATTGAACTGCCGTGTC 60.485 47.826 0.00 0.00 0.00 3.67
392 400 2.418628 CCGAAATATTGAACTGCCGTGT 59.581 45.455 0.00 0.00 0.00 4.49
393 401 2.675844 TCCGAAATATTGAACTGCCGTG 59.324 45.455 0.00 0.00 0.00 4.94
394 402 2.936498 CTCCGAAATATTGAACTGCCGT 59.064 45.455 0.00 0.00 0.00 5.68
395 403 3.001330 GTCTCCGAAATATTGAACTGCCG 59.999 47.826 0.00 0.00 0.00 5.69
396 404 3.001330 CGTCTCCGAAATATTGAACTGCC 59.999 47.826 0.00 0.00 35.63 4.85
397 405 3.544244 GCGTCTCCGAAATATTGAACTGC 60.544 47.826 0.00 0.00 35.63 4.40
398 406 3.865745 AGCGTCTCCGAAATATTGAACTG 59.134 43.478 0.00 0.00 35.63 3.16
399 407 4.113354 GAGCGTCTCCGAAATATTGAACT 58.887 43.478 0.00 0.00 35.63 3.01
400 408 3.863424 TGAGCGTCTCCGAAATATTGAAC 59.137 43.478 4.73 0.00 35.63 3.18
401 409 4.118093 TGAGCGTCTCCGAAATATTGAA 57.882 40.909 4.73 0.00 35.63 2.69
402 410 3.793797 TGAGCGTCTCCGAAATATTGA 57.206 42.857 4.73 0.00 35.63 2.57
403 411 5.462068 TGTTATGAGCGTCTCCGAAATATTG 59.538 40.000 4.73 0.00 35.63 1.90
404 412 5.597806 TGTTATGAGCGTCTCCGAAATATT 58.402 37.500 4.73 0.00 35.63 1.28
405 413 5.196341 TGTTATGAGCGTCTCCGAAATAT 57.804 39.130 4.73 0.00 35.63 1.28
406 414 4.642445 TGTTATGAGCGTCTCCGAAATA 57.358 40.909 4.73 0.00 35.63 1.40
407 415 3.520290 TGTTATGAGCGTCTCCGAAAT 57.480 42.857 4.73 0.00 35.63 2.17
408 416 3.520290 ATGTTATGAGCGTCTCCGAAA 57.480 42.857 4.73 0.00 35.63 3.46
409 417 3.186909 CAATGTTATGAGCGTCTCCGAA 58.813 45.455 4.73 0.00 35.63 4.30
410 418 2.481276 CCAATGTTATGAGCGTCTCCGA 60.481 50.000 4.73 0.00 35.63 4.55
411 419 1.860950 CCAATGTTATGAGCGTCTCCG 59.139 52.381 4.73 0.00 37.07 4.63
412 420 2.213499 CCCAATGTTATGAGCGTCTCC 58.787 52.381 4.73 0.00 0.00 3.71
413 421 2.906354 ACCCAATGTTATGAGCGTCTC 58.094 47.619 0.58 0.58 0.00 3.36
414 422 4.081087 ACTTACCCAATGTTATGAGCGTCT 60.081 41.667 0.00 0.00 0.00 4.18
415 423 4.189231 ACTTACCCAATGTTATGAGCGTC 58.811 43.478 0.00 0.00 0.00 5.19
416 424 4.216411 ACTTACCCAATGTTATGAGCGT 57.784 40.909 0.00 0.00 0.00 5.07
417 425 5.560966 AAACTTACCCAATGTTATGAGCG 57.439 39.130 0.00 0.00 0.00 5.03
418 426 6.090763 GCAAAAACTTACCCAATGTTATGAGC 59.909 38.462 0.00 0.00 0.00 4.26
419 427 6.307800 CGCAAAAACTTACCCAATGTTATGAG 59.692 38.462 0.00 0.00 0.00 2.90
420 428 6.153067 CGCAAAAACTTACCCAATGTTATGA 58.847 36.000 0.00 0.00 0.00 2.15
421 429 5.164002 GCGCAAAAACTTACCCAATGTTATG 60.164 40.000 0.30 0.00 0.00 1.90
422 430 4.926832 GCGCAAAAACTTACCCAATGTTAT 59.073 37.500 0.30 0.00 0.00 1.89
423 431 4.299978 GCGCAAAAACTTACCCAATGTTA 58.700 39.130 0.30 0.00 0.00 2.41
424 432 3.127589 GCGCAAAAACTTACCCAATGTT 58.872 40.909 0.30 0.00 0.00 2.71
425 433 2.749776 GCGCAAAAACTTACCCAATGT 58.250 42.857 0.30 0.00 0.00 2.71
426 434 1.718711 CGCGCAAAAACTTACCCAATG 59.281 47.619 8.75 0.00 0.00 2.82
427 435 1.338655 ACGCGCAAAAACTTACCCAAT 59.661 42.857 5.73 0.00 0.00 3.16
428 436 0.739561 ACGCGCAAAAACTTACCCAA 59.260 45.000 5.73 0.00 0.00 4.12
429 437 0.739561 AACGCGCAAAAACTTACCCA 59.260 45.000 5.73 0.00 0.00 4.51
430 438 1.842720 AAACGCGCAAAAACTTACCC 58.157 45.000 5.73 0.00 0.00 3.69
431 439 5.620467 TCTATAAACGCGCAAAAACTTACC 58.380 37.500 5.73 0.00 0.00 2.85
432 440 7.537602 TTTCTATAAACGCGCAAAAACTTAC 57.462 32.000 5.73 0.00 0.00 2.34
433 441 8.016229 TCATTTCTATAAACGCGCAAAAACTTA 58.984 29.630 5.73 0.00 0.00 2.24
434 442 6.858993 TCATTTCTATAAACGCGCAAAAACTT 59.141 30.769 5.73 0.00 0.00 2.66
435 443 6.375377 TCATTTCTATAAACGCGCAAAAACT 58.625 32.000 5.73 0.00 0.00 2.66
436 444 6.304683 ACTCATTTCTATAAACGCGCAAAAAC 59.695 34.615 5.73 0.00 0.00 2.43
437 445 6.304445 CACTCATTTCTATAAACGCGCAAAAA 59.696 34.615 5.73 0.00 0.00 1.94
438 446 5.792962 CACTCATTTCTATAAACGCGCAAAA 59.207 36.000 5.73 0.00 0.00 2.44
439 447 5.106869 ACACTCATTTCTATAAACGCGCAAA 60.107 36.000 5.73 0.00 0.00 3.68
440 448 4.390603 ACACTCATTTCTATAAACGCGCAA 59.609 37.500 5.73 0.00 0.00 4.85
441 449 3.930229 ACACTCATTTCTATAAACGCGCA 59.070 39.130 5.73 0.00 0.00 6.09
442 450 4.516092 ACACTCATTTCTATAAACGCGC 57.484 40.909 5.73 0.00 0.00 6.86
443 451 7.057402 CACATACACTCATTTCTATAAACGCG 58.943 38.462 3.53 3.53 0.00 6.01
444 452 6.846283 GCACATACACTCATTTCTATAAACGC 59.154 38.462 0.00 0.00 0.00 4.84
445 453 7.057402 CGCACATACACTCATTTCTATAAACG 58.943 38.462 0.00 0.00 0.00 3.60
446 454 7.906160 ACGCACATACACTCATTTCTATAAAC 58.094 34.615 0.00 0.00 0.00 2.01
447 455 9.027129 GTACGCACATACACTCATTTCTATAAA 57.973 33.333 0.00 0.00 0.00 1.40
448 456 7.377662 CGTACGCACATACACTCATTTCTATAA 59.622 37.037 0.52 0.00 0.00 0.98
449 457 6.854381 CGTACGCACATACACTCATTTCTATA 59.146 38.462 0.52 0.00 0.00 1.31
450 458 5.685954 CGTACGCACATACACTCATTTCTAT 59.314 40.000 0.52 0.00 0.00 1.98
451 459 5.032220 CGTACGCACATACACTCATTTCTA 58.968 41.667 0.52 0.00 0.00 2.10
452 460 3.857665 CGTACGCACATACACTCATTTCT 59.142 43.478 0.52 0.00 0.00 2.52
453 461 3.611113 ACGTACGCACATACACTCATTTC 59.389 43.478 16.72 0.00 0.00 2.17
454 462 3.366724 CACGTACGCACATACACTCATTT 59.633 43.478 16.72 0.00 0.00 2.32
455 463 2.921121 CACGTACGCACATACACTCATT 59.079 45.455 16.72 0.00 0.00 2.57
456 464 2.094906 ACACGTACGCACATACACTCAT 60.095 45.455 16.72 0.00 0.00 2.90
457 465 1.267533 ACACGTACGCACATACACTCA 59.732 47.619 16.72 0.00 0.00 3.41
458 466 1.909532 GACACGTACGCACATACACTC 59.090 52.381 16.72 0.00 0.00 3.51
459 467 1.538512 AGACACGTACGCACATACACT 59.461 47.619 16.72 1.13 0.00 3.55
460 468 1.973138 AGACACGTACGCACATACAC 58.027 50.000 16.72 0.00 0.00 2.90
461 469 5.678132 ATATAGACACGTACGCACATACA 57.322 39.130 16.72 0.00 0.00 2.29
462 470 5.911280 ACAATATAGACACGTACGCACATAC 59.089 40.000 16.72 1.40 0.00 2.39
463 471 5.910723 CACAATATAGACACGTACGCACATA 59.089 40.000 16.72 6.64 0.00 2.29
464 472 4.738252 CACAATATAGACACGTACGCACAT 59.262 41.667 16.72 4.53 0.00 3.21
465 473 4.099824 CACAATATAGACACGTACGCACA 58.900 43.478 16.72 0.00 0.00 4.57
466 474 4.100529 ACACAATATAGACACGTACGCAC 58.899 43.478 16.72 7.00 0.00 5.34
467 475 4.359971 ACACAATATAGACACGTACGCA 57.640 40.909 16.72 0.00 0.00 5.24
468 476 6.795053 TTAACACAATATAGACACGTACGC 57.205 37.500 16.72 0.00 0.00 4.42
501 509 1.094785 AGTCCGGTGCAATTACATGC 58.905 50.000 0.00 0.00 46.58 4.06
502 510 4.955925 TTAAGTCCGGTGCAATTACATG 57.044 40.909 0.00 0.00 0.00 3.21
503 511 4.157105 GGTTTAAGTCCGGTGCAATTACAT 59.843 41.667 0.00 0.00 0.00 2.29
504 512 3.502979 GGTTTAAGTCCGGTGCAATTACA 59.497 43.478 0.00 0.00 0.00 2.41
505 513 3.425227 CGGTTTAAGTCCGGTGCAATTAC 60.425 47.826 0.00 0.00 43.68 1.89
506 514 2.743126 CGGTTTAAGTCCGGTGCAATTA 59.257 45.455 0.00 0.00 43.68 1.40
507 515 1.538075 CGGTTTAAGTCCGGTGCAATT 59.462 47.619 0.00 0.00 43.68 2.32
508 516 1.161843 CGGTTTAAGTCCGGTGCAAT 58.838 50.000 0.00 0.00 43.68 3.56
509 517 0.106335 TCGGTTTAAGTCCGGTGCAA 59.894 50.000 17.00 0.00 46.82 4.08
510 518 0.106335 TTCGGTTTAAGTCCGGTGCA 59.894 50.000 17.00 0.00 46.82 4.57
511 519 0.794473 CTTCGGTTTAAGTCCGGTGC 59.206 55.000 17.00 0.00 46.82 5.01
512 520 1.001181 TCCTTCGGTTTAAGTCCGGTG 59.999 52.381 17.00 11.54 46.82 4.94
513 521 1.341080 TCCTTCGGTTTAAGTCCGGT 58.659 50.000 17.00 0.00 46.82 5.28
569 577 6.594159 GGTAAAATGACCACTCATATATCCCG 59.406 42.308 0.00 0.00 35.96 5.14
603 615 6.276832 ACGAGTAAAATGACCACTAGCTTA 57.723 37.500 0.00 0.00 0.00 3.09
677 689 4.453819 CCAGTTGGAAAGAGCTCAACTTAG 59.546 45.833 17.77 7.00 45.89 2.18
687 699 2.335712 GCCGCCCAGTTGGAAAGAG 61.336 63.158 0.00 0.00 37.39 2.85
714 726 7.444183 TCTCTTTTTGTGTTCTAATAGGTGGTG 59.556 37.037 0.00 0.00 0.00 4.17
762 774 2.269241 CCTCGCCTCACTTTCCCC 59.731 66.667 0.00 0.00 0.00 4.81
1019 1034 2.502492 CCCGTCCATCGCATCCTCT 61.502 63.158 0.00 0.00 38.35 3.69
1035 1050 2.229784 CTCCAAGACAACAGATTTGCCC 59.770 50.000 0.00 0.00 0.00 5.36
1145 1162 0.541863 GATGACCGGACCCTTGTGAT 59.458 55.000 9.46 0.00 0.00 3.06
1340 1357 2.864343 CGGTCGAGGTCATCCAAAATAC 59.136 50.000 0.00 0.00 35.89 1.89
1359 1376 3.743396 CCTTCTGTTTCTCTCTGTTTCGG 59.257 47.826 0.00 0.00 0.00 4.30
1418 1435 4.329545 GCCCCACTTCAGCCGACA 62.330 66.667 0.00 0.00 0.00 4.35
1625 1642 3.499737 GCGCCTCCATGGTTGTCG 61.500 66.667 12.58 12.12 38.35 4.35
1640 1657 6.018832 AGACAAGTCCAAATTTTTGAAATGCG 60.019 34.615 7.21 0.00 40.55 4.73
1701 1718 3.596066 TTCAGGCTGCTGCGTCCTC 62.596 63.158 10.34 0.00 40.82 3.71
1714 1731 6.037098 CAGGTCGACTAGAAATAACTTCAGG 58.963 44.000 16.46 0.00 36.40 3.86
1836 1853 1.014564 CGCGGGAAGGAAGTTGAGAC 61.015 60.000 0.00 0.00 0.00 3.36
1908 1925 0.177141 CGCGGTTCCCCTTCTTATGA 59.823 55.000 0.00 0.00 0.00 2.15
1909 1926 0.814010 CCGCGGTTCCCCTTCTTATG 60.814 60.000 19.50 0.00 0.00 1.90
1910 1927 1.525442 CCGCGGTTCCCCTTCTTAT 59.475 57.895 19.50 0.00 0.00 1.73
1911 1928 2.662070 CCCGCGGTTCCCCTTCTTA 61.662 63.158 26.12 0.00 0.00 2.10
1912 1929 4.029809 CCCGCGGTTCCCCTTCTT 62.030 66.667 26.12 0.00 0.00 2.52
1923 1940 1.227556 CTTCTTATGACCCCCGCGG 60.228 63.158 21.04 21.04 37.81 6.46
1924 1941 1.227556 CCTTCTTATGACCCCCGCG 60.228 63.158 0.00 0.00 0.00 6.46
1925 1942 1.148498 CCCTTCTTATGACCCCCGC 59.852 63.158 0.00 0.00 0.00 6.13
1926 1943 0.693092 TCCCCTTCTTATGACCCCCG 60.693 60.000 0.00 0.00 0.00 5.73
1927 1944 1.495148 CTTCCCCTTCTTATGACCCCC 59.505 57.143 0.00 0.00 0.00 5.40
1928 1945 1.133761 GCTTCCCCTTCTTATGACCCC 60.134 57.143 0.00 0.00 0.00 4.95
1929 1946 1.564348 TGCTTCCCCTTCTTATGACCC 59.436 52.381 0.00 0.00 0.00 4.46
1930 1947 2.644676 GTGCTTCCCCTTCTTATGACC 58.355 52.381 0.00 0.00 0.00 4.02
1931 1948 2.280628 CGTGCTTCCCCTTCTTATGAC 58.719 52.381 0.00 0.00 0.00 3.06
1949 1966 4.988598 CCGCAGCACAACCTCCGT 62.989 66.667 0.00 0.00 0.00 4.69
2159 2200 0.830648 CGCTCCCCAGTTAGATTCCA 59.169 55.000 0.00 0.00 0.00 3.53
2185 2226 1.299544 TGTCTTCGAAGAACGCGCA 60.300 52.632 28.58 18.71 45.90 6.09
2212 2253 7.652300 TGTGTTAACTTGCTAGTATTCAGTG 57.348 36.000 7.22 0.00 33.17 3.66
2304 2377 1.165907 TCGCTGCAAAGACCAACCAG 61.166 55.000 0.00 0.00 0.00 4.00
2454 2527 2.436417 GCAACCACACCATACACAGAT 58.564 47.619 0.00 0.00 0.00 2.90
2487 2560 1.965930 GTTGCGGCTGTGATCCACA 60.966 57.895 0.00 0.00 42.45 4.17
2603 2714 7.972832 CACCACATGTGCATTAAATAACATACA 59.027 33.333 20.81 0.00 38.34 2.29
2604 2715 8.338985 CACCACATGTGCATTAAATAACATAC 57.661 34.615 20.81 0.00 38.34 2.39
2683 2818 7.991084 ACAAAACATACCTACTTCTAAACCC 57.009 36.000 0.00 0.00 0.00 4.11
2967 3381 2.438021 GACACCCAATATAGTGGCCTGA 59.562 50.000 13.86 0.00 35.90 3.86
3130 3544 2.627945 CTTAGGCATTGTTCTACCGCA 58.372 47.619 0.00 0.00 0.00 5.69
3185 3599 6.207614 GCTTCCTTCCAATTCTACAGAAACTT 59.792 38.462 0.00 0.00 37.61 2.66
3374 3788 1.798223 TCAAATGACGCCTGTTCGAAG 59.202 47.619 0.00 0.00 0.00 3.79
3773 4187 2.032799 CGAGTAGTTAGGCAGAGCTCTG 59.967 54.545 34.82 34.82 46.40 3.35
3774 4188 2.294074 CGAGTAGTTAGGCAGAGCTCT 58.706 52.381 11.45 11.45 0.00 4.09
3921 6444 1.597742 TCTGAAAGGAGTGCAACAGC 58.402 50.000 0.00 0.00 41.43 4.40
3929 6452 2.457598 TGCGTAGGATCTGAAAGGAGT 58.542 47.619 0.00 0.00 0.00 3.85
4018 6541 0.331278 TCCATGGTGGATTGGTGGAC 59.669 55.000 12.58 0.00 42.67 4.02
4019 6542 2.798184 TCCATGGTGGATTGGTGGA 58.202 52.632 12.58 0.00 42.67 4.02
4034 6557 1.993653 CCTTCCCAGCATGACTCCA 59.006 57.895 0.00 0.00 39.69 3.86
4192 6715 6.035650 GCACACGTTATAAGTCAGCTGATTAA 59.964 38.462 21.47 12.50 0.00 1.40
4203 6726 7.494211 TCAACCTATATGCACACGTTATAAGT 58.506 34.615 0.00 0.00 0.00 2.24
4239 6762 5.173854 GCTGATTGAAACAAAAGGAAGAACG 59.826 40.000 0.00 0.00 0.00 3.95
4241 6764 5.600696 GGCTGATTGAAACAAAAGGAAGAA 58.399 37.500 0.00 0.00 0.00 2.52
4301 6824 6.045072 ACATTGAAACCACGAGAGGTATTA 57.955 37.500 0.00 0.00 42.25 0.98
4302 6825 4.906618 ACATTGAAACCACGAGAGGTATT 58.093 39.130 0.00 0.00 42.25 1.89
4303 6826 4.553330 ACATTGAAACCACGAGAGGTAT 57.447 40.909 0.00 0.00 42.25 2.73


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

AutoCloner maintained by Alex Coulton.