Multiple sequence alignment - TraesCS5D01G252800

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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 TraesCS5D01G252800 chr5D 100.000 2972 0 0 1 2972 358826589 358823618 0.000000e+00 5489
1 TraesCS5D01G252800 chr5D 82.485 982 140 25 1004 1970 403415468 403414504 0.000000e+00 832
2 TraesCS5D01G252800 chr5B 94.752 2477 66 20 531 2972 423902009 423899562 0.000000e+00 3795
3 TraesCS5D01G252800 chr5B 89.302 215 20 2 2 214 423902446 423902233 1.760000e-67 267
4 TraesCS5D01G252800 chr5A 94.858 2392 78 21 612 2972 459677486 459675109 0.000000e+00 3694
5 TraesCS5D01G252800 chr5A 81.680 988 143 27 1004 1970 510078692 510077722 0.000000e+00 787


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 TraesCS5D01G252800 chr5D 358823618 358826589 2971 True 5489 5489 100.000 1 2972 1 chr5D.!!$R1 2971
1 TraesCS5D01G252800 chr5D 403414504 403415468 964 True 832 832 82.485 1004 1970 1 chr5D.!!$R2 966
2 TraesCS5D01G252800 chr5B 423899562 423902446 2884 True 2031 3795 92.027 2 2972 2 chr5B.!!$R1 2970
3 TraesCS5D01G252800 chr5A 459675109 459677486 2377 True 3694 3694 94.858 612 2972 1 chr5A.!!$R1 2360
4 TraesCS5D01G252800 chr5A 510077722 510078692 970 True 787 787 81.680 1004 1970 1 chr5A.!!$R2 966

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
280 460 0.042131 ATACTGGTCCGTCCTTCCCA 59.958 55.0 0.0 0.0 37.07 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2235 2460 0.824109 CGGCTCTAGAACACCCATGA 59.176 55.0 0.0 0.0 0.0 3.07 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
73 74 5.445964 AGGAAAGCTAAGTTGACTCCAAAA 58.554 37.500 0.00 0.00 33.49 2.44
74 75 5.299531 AGGAAAGCTAAGTTGACTCCAAAAC 59.700 40.000 0.00 0.00 33.49 2.43
91 92 5.129815 TCCAAAACTATAGTACCAAGCGGAT 59.870 40.000 5.65 0.00 35.59 4.18
102 103 6.769512 AGTACCAAGCGGATTGATATATTGT 58.230 36.000 7.69 0.00 41.83 2.71
107 108 8.049117 ACCAAGCGGATTGATATATTGTGATAT 58.951 33.333 7.69 0.00 41.83 1.63
109 110 9.322773 CAAGCGGATTGATATATTGTGATATCT 57.677 33.333 0.00 0.00 41.83 1.98
133 134 8.319146 TCTTTAGTGTCCAGTTTCCCTTATTAG 58.681 37.037 0.00 0.00 0.00 1.73
136 137 3.589735 TGTCCAGTTTCCCTTATTAGCCA 59.410 43.478 0.00 0.00 0.00 4.75
144 145 6.378280 AGTTTCCCTTATTAGCCAGTCAATTG 59.622 38.462 0.00 0.00 0.00 2.32
148 149 6.723977 TCCCTTATTAGCCAGTCAATTGTTTT 59.276 34.615 5.13 0.00 0.00 2.43
149 150 7.035612 CCCTTATTAGCCAGTCAATTGTTTTC 58.964 38.462 5.13 0.00 0.00 2.29
156 157 7.054491 AGCCAGTCAATTGTTTTCATAGTTT 57.946 32.000 5.13 0.00 0.00 2.66
214 217 7.524717 AGTTATGTTGCAATTCTACTTGGTT 57.475 32.000 0.59 0.00 0.00 3.67
219 399 5.304101 TGTTGCAATTCTACTTGGTTCCAAT 59.696 36.000 0.59 0.00 0.00 3.16
233 413 5.063204 TGGTTCCAATAGAGTTTGTGACAG 58.937 41.667 0.00 0.00 0.00 3.51
234 414 5.163248 TGGTTCCAATAGAGTTTGTGACAGA 60.163 40.000 0.00 0.00 0.00 3.41
252 432 9.114952 TGTGACAGAGAAAATAACATTGTTGTA 57.885 29.630 12.30 0.00 34.06 2.41
253 433 9.944663 GTGACAGAGAAAATAACATTGTTGTAA 57.055 29.630 12.30 0.00 34.06 2.41
270 450 9.998106 ATTGTTGTAATAGACATATACTGGTCC 57.002 33.333 0.00 0.00 38.07 4.46
271 451 7.654568 TGTTGTAATAGACATATACTGGTCCG 58.345 38.462 0.00 0.00 38.07 4.79
272 452 7.286087 TGTTGTAATAGACATATACTGGTCCGT 59.714 37.037 0.00 0.00 38.07 4.69
273 453 7.444629 TGTAATAGACATATACTGGTCCGTC 57.555 40.000 0.00 0.00 34.58 4.79
274 454 5.979288 AATAGACATATACTGGTCCGTCC 57.021 43.478 0.00 0.00 34.58 4.79
275 455 3.596940 AGACATATACTGGTCCGTCCT 57.403 47.619 0.00 0.00 34.58 3.85
276 456 3.912248 AGACATATACTGGTCCGTCCTT 58.088 45.455 0.00 0.00 34.58 3.36
277 457 3.890147 AGACATATACTGGTCCGTCCTTC 59.110 47.826 0.00 0.00 34.58 3.46
278 458 2.963782 ACATATACTGGTCCGTCCTTCC 59.036 50.000 0.00 0.00 37.07 3.46
279 459 2.077687 TATACTGGTCCGTCCTTCCC 57.922 55.000 0.00 0.00 37.07 3.97
280 460 0.042131 ATACTGGTCCGTCCTTCCCA 59.958 55.000 0.00 0.00 37.07 4.37
281 461 0.178926 TACTGGTCCGTCCTTCCCAA 60.179 55.000 0.00 0.00 37.07 4.12
282 462 1.057851 ACTGGTCCGTCCTTCCCAAA 61.058 55.000 0.00 0.00 37.07 3.28
283 463 0.109723 CTGGTCCGTCCTTCCCAAAA 59.890 55.000 0.00 0.00 37.07 2.44
284 464 0.774908 TGGTCCGTCCTTCCCAAAAT 59.225 50.000 0.00 0.00 37.07 1.82
285 465 1.271707 TGGTCCGTCCTTCCCAAAATC 60.272 52.381 0.00 0.00 37.07 2.17
286 466 1.004394 GGTCCGTCCTTCCCAAAATCT 59.996 52.381 0.00 0.00 0.00 2.40
287 467 2.554564 GGTCCGTCCTTCCCAAAATCTT 60.555 50.000 0.00 0.00 0.00 2.40
288 468 3.307904 GGTCCGTCCTTCCCAAAATCTTA 60.308 47.826 0.00 0.00 0.00 2.10
289 469 3.939592 GTCCGTCCTTCCCAAAATCTTAG 59.060 47.826 0.00 0.00 0.00 2.18
290 470 3.054655 TCCGTCCTTCCCAAAATCTTAGG 60.055 47.826 0.00 0.00 0.00 2.69
291 471 2.683362 CGTCCTTCCCAAAATCTTAGGC 59.317 50.000 0.00 0.00 0.00 3.93
292 472 3.697166 GTCCTTCCCAAAATCTTAGGCA 58.303 45.455 0.00 0.00 0.00 4.75
293 473 3.444034 GTCCTTCCCAAAATCTTAGGCAC 59.556 47.826 0.00 0.00 0.00 5.01
294 474 2.760650 CCTTCCCAAAATCTTAGGCACC 59.239 50.000 0.00 0.00 0.00 5.01
295 475 3.564352 CCTTCCCAAAATCTTAGGCACCT 60.564 47.826 0.00 0.00 0.00 4.00
296 476 4.325030 CCTTCCCAAAATCTTAGGCACCTA 60.325 45.833 0.00 0.00 0.00 3.08
297 477 4.938575 TCCCAAAATCTTAGGCACCTAA 57.061 40.909 8.80 8.80 37.06 2.69
306 486 4.207891 CTTAGGCACCTAAGCTCTTTCA 57.792 45.455 20.57 0.00 45.76 2.69
307 487 2.777832 AGGCACCTAAGCTCTTTCAG 57.222 50.000 0.00 0.00 34.17 3.02
308 488 2.260822 AGGCACCTAAGCTCTTTCAGA 58.739 47.619 0.00 0.00 34.17 3.27
309 489 2.639839 AGGCACCTAAGCTCTTTCAGAA 59.360 45.455 0.00 0.00 34.17 3.02
310 490 3.073062 AGGCACCTAAGCTCTTTCAGAAA 59.927 43.478 0.00 0.00 34.17 2.52
311 491 3.821033 GGCACCTAAGCTCTTTCAGAAAA 59.179 43.478 0.00 0.00 34.17 2.29
312 492 4.460731 GGCACCTAAGCTCTTTCAGAAAAT 59.539 41.667 0.00 0.00 34.17 1.82
313 493 5.392487 GGCACCTAAGCTCTTTCAGAAAATC 60.392 44.000 0.00 0.00 34.17 2.17
314 494 5.392487 GCACCTAAGCTCTTTCAGAAAATCC 60.392 44.000 0.00 0.00 0.00 3.01
315 495 5.124617 CACCTAAGCTCTTTCAGAAAATCCC 59.875 44.000 0.00 0.00 0.00 3.85
316 496 5.222130 ACCTAAGCTCTTTCAGAAAATCCCA 60.222 40.000 0.00 0.00 0.00 4.37
317 497 5.711976 CCTAAGCTCTTTCAGAAAATCCCAA 59.288 40.000 0.00 0.00 0.00 4.12
318 498 6.209391 CCTAAGCTCTTTCAGAAAATCCCAAA 59.791 38.462 0.00 0.00 0.00 3.28
319 499 6.484364 AAGCTCTTTCAGAAAATCCCAAAA 57.516 33.333 0.00 0.00 0.00 2.44
320 500 6.676990 AGCTCTTTCAGAAAATCCCAAAAT 57.323 33.333 0.00 0.00 0.00 1.82
321 501 6.695429 AGCTCTTTCAGAAAATCCCAAAATC 58.305 36.000 0.00 0.00 0.00 2.17
322 502 6.496218 AGCTCTTTCAGAAAATCCCAAAATCT 59.504 34.615 0.00 0.00 0.00 2.40
323 503 7.671398 AGCTCTTTCAGAAAATCCCAAAATCTA 59.329 33.333 0.00 0.00 0.00 1.98
324 504 8.306761 GCTCTTTCAGAAAATCCCAAAATCTAA 58.693 33.333 0.00 0.00 0.00 2.10
325 505 9.631452 CTCTTTCAGAAAATCCCAAAATCTAAC 57.369 33.333 0.00 0.00 0.00 2.34
326 506 8.296713 TCTTTCAGAAAATCCCAAAATCTAACG 58.703 33.333 0.00 0.00 0.00 3.18
327 507 5.949735 TCAGAAAATCCCAAAATCTAACGC 58.050 37.500 0.00 0.00 0.00 4.84
328 508 4.793216 CAGAAAATCCCAAAATCTAACGCG 59.207 41.667 3.53 3.53 0.00 6.01
329 509 4.457949 AGAAAATCCCAAAATCTAACGCGT 59.542 37.500 5.58 5.58 0.00 6.01
330 510 3.757745 AATCCCAAAATCTAACGCGTG 57.242 42.857 14.98 0.00 0.00 5.34
331 511 2.172851 TCCCAAAATCTAACGCGTGT 57.827 45.000 14.98 5.77 0.00 4.49
332 512 2.496111 TCCCAAAATCTAACGCGTGTT 58.504 42.857 14.98 19.53 42.19 3.32
333 513 3.661944 TCCCAAAATCTAACGCGTGTTA 58.338 40.909 14.98 19.68 39.54 2.41
342 522 0.584876 AACGCGTGTTAGAAACCAGC 59.415 50.000 14.98 0.00 36.28 4.85
343 523 0.249741 ACGCGTGTTAGAAACCAGCT 60.250 50.000 12.93 0.00 32.83 4.24
344 524 0.438830 CGCGTGTTAGAAACCAGCTC 59.561 55.000 0.00 0.00 32.83 4.09
345 525 0.796927 GCGTGTTAGAAACCAGCTCC 59.203 55.000 0.00 0.00 32.45 4.70
346 526 1.068474 CGTGTTAGAAACCAGCTCCG 58.932 55.000 0.00 0.00 0.00 4.63
347 527 1.439679 GTGTTAGAAACCAGCTCCGG 58.560 55.000 0.00 0.00 0.00 5.14
348 528 1.001633 GTGTTAGAAACCAGCTCCGGA 59.998 52.381 2.93 2.93 0.00 5.14
349 529 1.906574 TGTTAGAAACCAGCTCCGGAT 59.093 47.619 3.57 0.00 0.00 4.18
350 530 3.101437 TGTTAGAAACCAGCTCCGGATA 58.899 45.455 3.57 0.00 0.00 2.59
351 531 3.709653 TGTTAGAAACCAGCTCCGGATAT 59.290 43.478 3.57 0.00 0.00 1.63
352 532 4.163458 TGTTAGAAACCAGCTCCGGATATT 59.837 41.667 3.57 0.00 0.00 1.28
353 533 3.477210 AGAAACCAGCTCCGGATATTC 57.523 47.619 3.57 3.87 0.00 1.75
354 534 3.041946 AGAAACCAGCTCCGGATATTCT 58.958 45.455 3.57 6.19 0.00 2.40
355 535 3.456277 AGAAACCAGCTCCGGATATTCTT 59.544 43.478 3.57 0.00 0.00 2.52
356 536 2.918712 ACCAGCTCCGGATATTCTTG 57.081 50.000 3.57 0.00 0.00 3.02
357 537 1.202698 ACCAGCTCCGGATATTCTTGC 60.203 52.381 3.57 2.34 0.00 4.01
358 538 1.071385 CCAGCTCCGGATATTCTTGCT 59.929 52.381 3.57 5.25 0.00 3.91
359 539 2.486191 CCAGCTCCGGATATTCTTGCTT 60.486 50.000 3.57 0.00 0.00 3.91
360 540 2.547211 CAGCTCCGGATATTCTTGCTTG 59.453 50.000 3.57 0.00 0.00 4.01
361 541 2.171448 AGCTCCGGATATTCTTGCTTGT 59.829 45.455 3.57 0.00 0.00 3.16
362 542 3.388024 AGCTCCGGATATTCTTGCTTGTA 59.612 43.478 3.57 0.00 0.00 2.41
363 543 3.495001 GCTCCGGATATTCTTGCTTGTAC 59.505 47.826 3.57 0.00 0.00 2.90
364 544 3.713288 TCCGGATATTCTTGCTTGTACG 58.287 45.455 0.00 0.00 0.00 3.67
365 545 2.800544 CCGGATATTCTTGCTTGTACGG 59.199 50.000 0.00 0.00 0.00 4.02
366 546 3.454375 CGGATATTCTTGCTTGTACGGT 58.546 45.455 0.00 0.00 0.00 4.83
367 547 3.489785 CGGATATTCTTGCTTGTACGGTC 59.510 47.826 0.00 0.00 0.00 4.79
368 548 4.439057 GGATATTCTTGCTTGTACGGTCA 58.561 43.478 0.00 0.00 0.00 4.02
369 549 4.873827 GGATATTCTTGCTTGTACGGTCAA 59.126 41.667 0.00 0.00 0.00 3.18
370 550 5.353123 GGATATTCTTGCTTGTACGGTCAAA 59.647 40.000 0.00 0.00 0.00 2.69
371 551 4.749245 ATTCTTGCTTGTACGGTCAAAG 57.251 40.909 0.00 0.00 0.00 2.77
372 552 3.188159 TCTTGCTTGTACGGTCAAAGT 57.812 42.857 5.08 0.00 0.00 2.66
373 553 4.325028 TCTTGCTTGTACGGTCAAAGTA 57.675 40.909 5.08 0.00 0.00 2.24
374 554 4.695396 TCTTGCTTGTACGGTCAAAGTAA 58.305 39.130 6.24 6.24 0.00 2.24
375 555 5.302360 TCTTGCTTGTACGGTCAAAGTAAT 58.698 37.500 6.68 0.00 0.00 1.89
376 556 5.407387 TCTTGCTTGTACGGTCAAAGTAATC 59.593 40.000 6.68 0.00 0.00 1.75
377 557 4.890088 TGCTTGTACGGTCAAAGTAATCT 58.110 39.130 5.08 0.00 0.00 2.40
378 558 6.028146 TGCTTGTACGGTCAAAGTAATCTA 57.972 37.500 5.08 0.00 0.00 1.98
379 559 6.457355 TGCTTGTACGGTCAAAGTAATCTAA 58.543 36.000 5.08 0.00 0.00 2.10
380 560 6.366877 TGCTTGTACGGTCAAAGTAATCTAAC 59.633 38.462 5.08 0.00 0.00 2.34
381 561 6.183360 GCTTGTACGGTCAAAGTAATCTAACC 60.183 42.308 5.08 0.00 0.00 2.85
382 562 6.343716 TGTACGGTCAAAGTAATCTAACCA 57.656 37.500 0.00 0.00 0.00 3.67
383 563 6.938507 TGTACGGTCAAAGTAATCTAACCAT 58.061 36.000 0.00 0.00 0.00 3.55
384 564 7.037438 TGTACGGTCAAAGTAATCTAACCATC 58.963 38.462 0.00 0.00 0.00 3.51
385 565 5.107133 ACGGTCAAAGTAATCTAACCATCG 58.893 41.667 0.00 0.00 0.00 3.84
386 566 4.025979 CGGTCAAAGTAATCTAACCATCGC 60.026 45.833 0.00 0.00 0.00 4.58
387 567 5.116882 GGTCAAAGTAATCTAACCATCGCT 58.883 41.667 0.00 0.00 0.00 4.93
388 568 6.278363 GGTCAAAGTAATCTAACCATCGCTA 58.722 40.000 0.00 0.00 0.00 4.26
389 569 6.759827 GGTCAAAGTAATCTAACCATCGCTAA 59.240 38.462 0.00 0.00 0.00 3.09
390 570 7.441458 GGTCAAAGTAATCTAACCATCGCTAAT 59.559 37.037 0.00 0.00 0.00 1.73
391 571 8.488764 GTCAAAGTAATCTAACCATCGCTAATC 58.511 37.037 0.00 0.00 0.00 1.75
392 572 7.381408 TCAAAGTAATCTAACCATCGCTAATCG 59.619 37.037 0.00 0.00 40.15 3.34
393 573 6.328641 AGTAATCTAACCATCGCTAATCGT 57.671 37.500 0.00 0.00 39.67 3.73
394 574 6.150318 AGTAATCTAACCATCGCTAATCGTG 58.850 40.000 0.00 0.00 39.67 4.35
395 575 3.364889 TCTAACCATCGCTAATCGTGG 57.635 47.619 0.00 0.00 41.69 4.94
396 576 2.953648 TCTAACCATCGCTAATCGTGGA 59.046 45.455 10.96 0.00 39.83 4.02
397 577 2.910688 AACCATCGCTAATCGTGGAT 57.089 45.000 10.96 0.26 39.83 3.41
398 578 2.440539 ACCATCGCTAATCGTGGATC 57.559 50.000 10.96 0.00 39.83 3.36
399 579 1.686587 ACCATCGCTAATCGTGGATCA 59.313 47.619 10.96 0.00 39.83 2.92
400 580 2.102420 ACCATCGCTAATCGTGGATCAA 59.898 45.455 10.96 0.00 39.83 2.57
401 581 2.476619 CCATCGCTAATCGTGGATCAAC 59.523 50.000 0.00 0.00 39.83 3.18
402 582 2.218953 TCGCTAATCGTGGATCAACC 57.781 50.000 0.00 0.00 39.67 3.77
403 583 1.478916 TCGCTAATCGTGGATCAACCA 59.521 47.619 0.00 0.00 40.95 3.67
417 597 7.782897 TGGATCAACCAACCATATTTGTTAA 57.217 32.000 0.00 0.00 46.75 2.01
418 598 8.195165 TGGATCAACCAACCATATTTGTTAAA 57.805 30.769 0.00 0.00 46.75 1.52
419 599 8.310382 TGGATCAACCAACCATATTTGTTAAAG 58.690 33.333 0.00 0.00 46.75 1.85
420 600 7.763985 GGATCAACCAACCATATTTGTTAAAGG 59.236 37.037 0.00 0.00 38.79 3.11
421 601 7.841282 TCAACCAACCATATTTGTTAAAGGA 57.159 32.000 0.00 0.00 0.00 3.36
422 602 8.429237 TCAACCAACCATATTTGTTAAAGGAT 57.571 30.769 0.00 0.00 0.00 3.24
423 603 9.535170 TCAACCAACCATATTTGTTAAAGGATA 57.465 29.630 0.00 0.00 0.00 2.59
426 606 9.707957 ACCAACCATATTTGTTAAAGGATATCA 57.292 29.630 4.83 0.00 0.00 2.15
438 618 9.753674 TGTTAAAGGATATCATGAAGGAAAACT 57.246 29.630 0.00 0.00 0.00 2.66
442 622 9.539194 AAAGGATATCATGAAGGAAAACTTTCT 57.461 29.630 0.00 0.00 40.21 2.52
443 623 8.517062 AGGATATCATGAAGGAAAACTTTCTG 57.483 34.615 0.00 0.00 40.21 3.02
444 624 8.112183 AGGATATCATGAAGGAAAACTTTCTGT 58.888 33.333 0.00 0.00 40.21 3.41
445 625 9.396022 GGATATCATGAAGGAAAACTTTCTGTA 57.604 33.333 0.00 0.00 40.21 2.74
448 628 7.272037 TCATGAAGGAAAACTTTCTGTAACC 57.728 36.000 0.00 0.00 40.21 2.85
449 629 6.831353 TCATGAAGGAAAACTTTCTGTAACCA 59.169 34.615 0.00 0.00 40.21 3.67
450 630 7.505585 TCATGAAGGAAAACTTTCTGTAACCAT 59.494 33.333 0.00 0.00 40.21 3.55
451 631 7.038154 TGAAGGAAAACTTTCTGTAACCATG 57.962 36.000 2.41 0.00 40.21 3.66
452 632 6.040391 TGAAGGAAAACTTTCTGTAACCATGG 59.960 38.462 11.19 11.19 40.21 3.66
453 633 4.280929 AGGAAAACTTTCTGTAACCATGGC 59.719 41.667 13.04 0.00 37.35 4.40
454 634 4.280929 GGAAAACTTTCTGTAACCATGGCT 59.719 41.667 13.04 0.95 37.35 4.75
455 635 5.221441 GGAAAACTTTCTGTAACCATGGCTT 60.221 40.000 13.04 8.20 37.35 4.35
456 636 6.015772 GGAAAACTTTCTGTAACCATGGCTTA 60.016 38.462 13.04 7.16 37.35 3.09
457 637 6.575162 AAACTTTCTGTAACCATGGCTTAG 57.425 37.500 13.04 5.60 0.00 2.18
458 638 5.242795 ACTTTCTGTAACCATGGCTTAGT 57.757 39.130 13.04 1.50 0.00 2.24
459 639 6.368779 ACTTTCTGTAACCATGGCTTAGTA 57.631 37.500 13.04 0.00 0.00 1.82
460 640 6.775708 ACTTTCTGTAACCATGGCTTAGTAA 58.224 36.000 13.04 4.91 0.00 2.24
461 641 7.402862 ACTTTCTGTAACCATGGCTTAGTAAT 58.597 34.615 13.04 0.00 0.00 1.89
462 642 7.888546 ACTTTCTGTAACCATGGCTTAGTAATT 59.111 33.333 13.04 0.00 0.00 1.40
463 643 8.644374 TTTCTGTAACCATGGCTTAGTAATTT 57.356 30.769 13.04 0.00 0.00 1.82
464 644 7.624360 TCTGTAACCATGGCTTAGTAATTTG 57.376 36.000 13.04 0.00 0.00 2.32
465 645 6.094881 TCTGTAACCATGGCTTAGTAATTTGC 59.905 38.462 13.04 0.00 0.00 3.68
466 646 5.712446 TGTAACCATGGCTTAGTAATTTGCA 59.288 36.000 13.04 2.00 0.00 4.08
467 647 5.937975 AACCATGGCTTAGTAATTTGCAT 57.062 34.783 13.04 0.00 0.00 3.96
468 648 5.937975 ACCATGGCTTAGTAATTTGCATT 57.062 34.783 13.04 0.00 0.00 3.56
469 649 6.298441 ACCATGGCTTAGTAATTTGCATTT 57.702 33.333 13.04 0.00 0.00 2.32
470 650 7.416964 ACCATGGCTTAGTAATTTGCATTTA 57.583 32.000 13.04 0.00 0.00 1.40
471 651 7.491682 ACCATGGCTTAGTAATTTGCATTTAG 58.508 34.615 13.04 0.00 0.00 1.85
472 652 6.421801 CCATGGCTTAGTAATTTGCATTTAGC 59.578 38.462 0.00 0.00 45.96 3.09
490 670 2.911198 CGTTGCGCTAATTTCCGTG 58.089 52.632 9.73 0.00 0.00 4.94
491 671 1.125847 CGTTGCGCTAATTTCCGTGC 61.126 55.000 9.73 0.00 37.18 5.34
492 672 0.796870 GTTGCGCTAATTTCCGTGCC 60.797 55.000 9.73 0.00 35.89 5.01
493 673 1.237954 TTGCGCTAATTTCCGTGCCA 61.238 50.000 9.73 0.00 35.89 4.92
494 674 1.237954 TGCGCTAATTTCCGTGCCAA 61.238 50.000 9.73 0.00 35.89 4.52
495 675 0.109504 GCGCTAATTTCCGTGCCAAA 60.110 50.000 0.00 0.00 0.00 3.28
496 676 1.667467 GCGCTAATTTCCGTGCCAAAA 60.667 47.619 0.00 0.00 0.00 2.44
497 677 2.250188 CGCTAATTTCCGTGCCAAAAG 58.750 47.619 0.00 0.00 0.00 2.27
498 678 1.992667 GCTAATTTCCGTGCCAAAAGC 59.007 47.619 0.00 0.00 44.14 3.51
499 679 2.606108 CTAATTTCCGTGCCAAAAGCC 58.394 47.619 0.00 0.00 42.71 4.35
500 680 1.047801 AATTTCCGTGCCAAAAGCCT 58.952 45.000 0.00 0.00 42.71 4.58
501 681 1.047801 ATTTCCGTGCCAAAAGCCTT 58.952 45.000 0.00 0.00 42.71 4.35
502 682 0.387565 TTTCCGTGCCAAAAGCCTTC 59.612 50.000 0.00 0.00 42.71 3.46
503 683 0.753479 TTCCGTGCCAAAAGCCTTCA 60.753 50.000 0.00 0.00 42.71 3.02
504 684 1.007387 CCGTGCCAAAAGCCTTCAC 60.007 57.895 0.00 0.00 42.71 3.18
505 685 1.370414 CGTGCCAAAAGCCTTCACG 60.370 57.895 2.60 2.60 43.19 4.35
506 686 1.661509 GTGCCAAAAGCCTTCACGC 60.662 57.895 0.00 0.00 42.71 5.34
507 687 2.124060 TGCCAAAAGCCTTCACGCA 61.124 52.632 0.00 0.00 42.71 5.24
508 688 1.661509 GCCAAAAGCCTTCACGCAC 60.662 57.895 0.00 0.00 34.35 5.34
509 689 2.032981 CCAAAAGCCTTCACGCACT 58.967 52.632 0.00 0.00 0.00 4.40
510 690 0.318107 CCAAAAGCCTTCACGCACTG 60.318 55.000 0.00 0.00 0.00 3.66
511 691 0.381801 CAAAAGCCTTCACGCACTGT 59.618 50.000 0.00 0.00 0.00 3.55
512 692 1.601903 CAAAAGCCTTCACGCACTGTA 59.398 47.619 0.00 0.00 0.00 2.74
513 693 2.185004 AAAGCCTTCACGCACTGTAT 57.815 45.000 0.00 0.00 0.00 2.29
514 694 3.328382 AAAGCCTTCACGCACTGTATA 57.672 42.857 0.00 0.00 0.00 1.47
515 695 3.328382 AAGCCTTCACGCACTGTATAA 57.672 42.857 0.00 0.00 0.00 0.98
516 696 3.543680 AGCCTTCACGCACTGTATAAT 57.456 42.857 0.00 0.00 0.00 1.28
517 697 3.198068 AGCCTTCACGCACTGTATAATG 58.802 45.455 0.00 0.00 0.00 1.90
518 698 2.287915 GCCTTCACGCACTGTATAATGG 59.712 50.000 0.00 0.00 0.00 3.16
519 699 2.872245 CCTTCACGCACTGTATAATGGG 59.128 50.000 0.00 0.00 35.06 4.00
520 700 3.431626 CCTTCACGCACTGTATAATGGGA 60.432 47.826 0.00 0.00 33.28 4.37
521 701 3.897141 TCACGCACTGTATAATGGGAA 57.103 42.857 0.00 0.00 33.28 3.97
522 702 4.415881 TCACGCACTGTATAATGGGAAT 57.584 40.909 0.00 0.00 33.28 3.01
523 703 4.126437 TCACGCACTGTATAATGGGAATG 58.874 43.478 0.00 0.00 33.28 2.67
524 704 4.126437 CACGCACTGTATAATGGGAATGA 58.874 43.478 0.00 0.00 33.28 2.57
525 705 4.212004 CACGCACTGTATAATGGGAATGAG 59.788 45.833 0.00 0.00 33.28 2.90
526 706 3.748048 CGCACTGTATAATGGGAATGAGG 59.252 47.826 0.00 0.00 0.00 3.86
527 707 4.074970 GCACTGTATAATGGGAATGAGGG 58.925 47.826 0.00 0.00 0.00 4.30
528 708 4.202461 GCACTGTATAATGGGAATGAGGGA 60.202 45.833 0.00 0.00 0.00 4.20
529 709 5.555017 CACTGTATAATGGGAATGAGGGAG 58.445 45.833 0.00 0.00 0.00 4.30
571 751 8.992835 AATCTTTTTGTTTGGAATATGCTCTC 57.007 30.769 0.00 0.00 0.00 3.20
574 754 9.295825 TCTTTTTGTTTGGAATATGCTCTCTTA 57.704 29.630 0.00 0.00 0.00 2.10
580 760 9.147732 TGTTTGGAATATGCTCTCTTATCTCTA 57.852 33.333 0.00 0.00 0.00 2.43
586 766 9.855021 GAATATGCTCTCTTATCTCTAGGTTTC 57.145 37.037 0.00 0.00 0.00 2.78
590 770 6.041409 TGCTCTCTTATCTCTAGGTTTCCATG 59.959 42.308 0.00 0.00 0.00 3.66
591 771 6.412362 TCTCTTATCTCTAGGTTTCCATGC 57.588 41.667 0.00 0.00 0.00 4.06
592 772 5.899547 TCTCTTATCTCTAGGTTTCCATGCA 59.100 40.000 0.00 0.00 0.00 3.96
593 773 6.384015 TCTCTTATCTCTAGGTTTCCATGCAA 59.616 38.462 0.00 0.00 0.00 4.08
594 774 6.957631 TCTTATCTCTAGGTTTCCATGCAAA 58.042 36.000 0.00 0.00 0.00 3.68
595 775 7.402054 TCTTATCTCTAGGTTTCCATGCAAAA 58.598 34.615 0.00 0.00 0.00 2.44
596 776 7.888021 TCTTATCTCTAGGTTTCCATGCAAAAA 59.112 33.333 0.00 0.00 0.00 1.94
640 832 1.088306 CAATTGGCATGGCGCAAAAT 58.912 45.000 15.27 5.77 45.17 1.82
641 833 1.088306 AATTGGCATGGCGCAAAATG 58.912 45.000 15.27 11.18 45.17 2.32
671 867 5.050490 CACTATCACCACCAACTACATAGC 58.950 45.833 0.00 0.00 0.00 2.97
776 972 1.746991 GCCAGCAGCAACTAGGGTC 60.747 63.158 0.00 0.00 42.97 4.46
803 999 0.752658 GGCAGCTTCCACCAACTTTT 59.247 50.000 0.00 0.00 0.00 2.27
1353 1571 1.195115 CGATCAAGAGGAGGTGGGAA 58.805 55.000 0.00 0.00 0.00 3.97
2073 2295 1.342496 CTCTCCCATAGATCGCAAGCA 59.658 52.381 0.00 0.00 32.41 3.91
2101 2323 1.113517 ACACCGTAGTCTGTGCCTGT 61.114 55.000 0.00 0.00 35.90 4.00
2257 2482 0.606604 TGGGTGTTCTAGAGCCGAAC 59.393 55.000 3.94 0.00 40.79 3.95
2375 2602 4.641989 CAGACAAAGATGGGTAGGAAATGG 59.358 45.833 0.00 0.00 0.00 3.16
2376 2603 3.954258 GACAAAGATGGGTAGGAAATGGG 59.046 47.826 0.00 0.00 0.00 4.00
2377 2604 3.596046 ACAAAGATGGGTAGGAAATGGGA 59.404 43.478 0.00 0.00 0.00 4.37
2378 2605 4.045334 ACAAAGATGGGTAGGAAATGGGAA 59.955 41.667 0.00 0.00 0.00 3.97
2619 2854 2.426268 GCCAAATGATACCCCATTCCCT 60.426 50.000 0.00 0.00 35.86 4.20
2639 2874 5.046304 TCCCTTGTTCATCTGGTAAGAAGAG 60.046 44.000 0.00 0.00 35.59 2.85
2686 2935 1.605165 GGACGGATGGCCCAACAAA 60.605 57.895 0.00 0.00 34.14 2.83
2687 2936 1.584495 GACGGATGGCCCAACAAAC 59.416 57.895 0.00 0.00 34.14 2.93
2688 2937 1.152652 ACGGATGGCCCAACAAACA 60.153 52.632 0.00 0.00 34.14 2.83
2689 2938 0.541764 ACGGATGGCCCAACAAACAT 60.542 50.000 0.00 0.00 34.14 2.71
2690 2939 1.272203 ACGGATGGCCCAACAAACATA 60.272 47.619 0.00 0.00 34.14 2.29
2691 2940 2.031120 CGGATGGCCCAACAAACATAT 58.969 47.619 0.00 0.00 34.14 1.78
2692 2941 2.223782 CGGATGGCCCAACAAACATATG 60.224 50.000 0.00 0.00 34.14 1.78
2693 2942 3.030291 GGATGGCCCAACAAACATATGA 58.970 45.455 10.38 0.00 34.14 2.15
2694 2943 3.181476 GGATGGCCCAACAAACATATGAC 60.181 47.826 10.38 0.00 34.14 3.06
2695 2944 2.881734 TGGCCCAACAAACATATGACA 58.118 42.857 10.38 0.00 0.00 3.58
2696 2945 3.234353 TGGCCCAACAAACATATGACAA 58.766 40.909 10.38 0.00 0.00 3.18
2697 2946 3.006323 TGGCCCAACAAACATATGACAAC 59.994 43.478 10.38 0.00 0.00 3.32
2698 2947 3.006323 GGCCCAACAAACATATGACAACA 59.994 43.478 10.38 0.00 0.00 3.33
2699 2948 4.502259 GGCCCAACAAACATATGACAACAA 60.502 41.667 10.38 0.00 0.00 2.83
2728 2977 2.293677 GCCATGCTCATTCAAGATCTGG 59.706 50.000 0.00 0.00 0.00 3.86
2764 3013 4.398988 TCAGCATCGCCAATGTTTATTTCT 59.601 37.500 0.00 0.00 37.71 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.884639 TCAACTTAGCTTTCCTTGCACC 59.115 45.455 0.00 0.00 0.00 5.01
50 51 4.706842 TTGGAGTCAACTTAGCTTTCCT 57.293 40.909 0.00 0.00 0.00 3.36
56 57 9.085250 GTACTATAGTTTTGGAGTCAACTTAGC 57.915 37.037 11.40 0.00 34.92 3.09
73 74 7.719871 ATATCAATCCGCTTGGTACTATAGT 57.280 36.000 10.87 10.87 33.29 2.12
102 103 6.443849 AGGGAAACTGGACACTAAAGATATCA 59.556 38.462 5.32 0.00 0.00 2.15
107 108 6.697641 ATAAGGGAAACTGGACACTAAAGA 57.302 37.500 0.00 0.00 0.00 2.52
109 110 6.882678 GCTAATAAGGGAAACTGGACACTAAA 59.117 38.462 0.00 0.00 0.00 1.85
133 134 8.986477 ATAAACTATGAAAACAATTGACTGGC 57.014 30.769 13.59 0.00 0.00 4.85
168 169 5.525378 ACTTCTCACGATTGGCAGAAATATC 59.475 40.000 0.00 0.00 0.00 1.63
176 177 3.937814 ACATAACTTCTCACGATTGGCA 58.062 40.909 0.00 0.00 0.00 4.92
178 179 4.154015 TGCAACATAACTTCTCACGATTGG 59.846 41.667 0.00 0.00 0.00 3.16
183 184 5.931532 AGAATTGCAACATAACTTCTCACG 58.068 37.500 0.00 0.00 0.00 4.35
214 217 6.419484 TTCTCTGTCACAAACTCTATTGGA 57.581 37.500 0.00 0.00 34.56 3.53
219 399 9.778741 ATGTTATTTTCTCTGTCACAAACTCTA 57.221 29.630 0.00 0.00 0.00 2.43
252 432 5.642165 AGGACGGACCAGTATATGTCTATT 58.358 41.667 0.00 0.00 42.04 1.73
253 433 5.258216 AGGACGGACCAGTATATGTCTAT 57.742 43.478 0.00 0.00 42.04 1.98
258 438 2.299297 GGGAAGGACGGACCAGTATATG 59.701 54.545 0.00 0.00 42.04 1.78
260 440 1.288633 TGGGAAGGACGGACCAGTATA 59.711 52.381 0.00 0.00 42.04 1.47
262 442 0.178926 TTGGGAAGGACGGACCAGTA 60.179 55.000 0.00 0.00 42.04 2.74
263 443 1.057851 TTTGGGAAGGACGGACCAGT 61.058 55.000 0.00 0.00 42.04 4.00
264 444 0.109723 TTTTGGGAAGGACGGACCAG 59.890 55.000 0.00 0.00 42.04 4.00
265 445 0.774908 ATTTTGGGAAGGACGGACCA 59.225 50.000 0.00 0.00 42.04 4.02
266 446 1.004394 AGATTTTGGGAAGGACGGACC 59.996 52.381 0.00 0.00 39.35 4.46
267 447 2.491675 AGATTTTGGGAAGGACGGAC 57.508 50.000 0.00 0.00 0.00 4.79
268 448 3.054655 CCTAAGATTTTGGGAAGGACGGA 60.055 47.826 0.00 0.00 37.11 4.69
269 449 3.279434 CCTAAGATTTTGGGAAGGACGG 58.721 50.000 0.00 0.00 37.11 4.79
270 450 2.683362 GCCTAAGATTTTGGGAAGGACG 59.317 50.000 2.20 0.00 37.11 4.79
271 451 3.444034 GTGCCTAAGATTTTGGGAAGGAC 59.556 47.826 2.20 0.00 37.11 3.85
272 452 3.563479 GGTGCCTAAGATTTTGGGAAGGA 60.563 47.826 2.20 0.00 37.11 3.36
273 453 2.760650 GGTGCCTAAGATTTTGGGAAGG 59.239 50.000 2.20 0.00 37.11 3.46
274 454 3.701664 AGGTGCCTAAGATTTTGGGAAG 58.298 45.455 2.20 0.00 37.11 3.46
275 455 3.825908 AGGTGCCTAAGATTTTGGGAA 57.174 42.857 2.20 0.00 37.11 3.97
276 456 4.938575 TTAGGTGCCTAAGATTTTGGGA 57.061 40.909 6.60 0.00 37.11 4.37
284 464 4.081420 CTGAAAGAGCTTAGGTGCCTAAGA 60.081 45.833 31.34 14.43 46.58 2.10
285 465 4.081420 TCTGAAAGAGCTTAGGTGCCTAAG 60.081 45.833 25.84 25.84 46.73 2.18
286 466 3.838317 TCTGAAAGAGCTTAGGTGCCTAA 59.162 43.478 9.99 9.99 38.67 2.69
287 467 3.441101 TCTGAAAGAGCTTAGGTGCCTA 58.559 45.455 0.00 0.00 38.67 3.93
288 468 2.260822 TCTGAAAGAGCTTAGGTGCCT 58.739 47.619 0.00 0.00 38.67 4.75
289 469 2.770164 TCTGAAAGAGCTTAGGTGCC 57.230 50.000 0.00 0.00 38.67 5.01
300 480 8.296713 CGTTAGATTTTGGGATTTTCTGAAAGA 58.703 33.333 2.75 0.00 44.68 2.52
301 481 7.062255 GCGTTAGATTTTGGGATTTTCTGAAAG 59.938 37.037 2.75 0.00 0.00 2.62
302 482 6.866248 GCGTTAGATTTTGGGATTTTCTGAAA 59.134 34.615 0.00 0.00 0.00 2.69
303 483 6.386654 GCGTTAGATTTTGGGATTTTCTGAA 58.613 36.000 0.00 0.00 0.00 3.02
304 484 5.391523 CGCGTTAGATTTTGGGATTTTCTGA 60.392 40.000 0.00 0.00 0.00 3.27
305 485 4.793216 CGCGTTAGATTTTGGGATTTTCTG 59.207 41.667 0.00 0.00 0.00 3.02
306 486 4.457949 ACGCGTTAGATTTTGGGATTTTCT 59.542 37.500 5.58 0.00 0.00 2.52
307 487 4.557301 CACGCGTTAGATTTTGGGATTTTC 59.443 41.667 10.22 0.00 0.00 2.29
308 488 4.022676 ACACGCGTTAGATTTTGGGATTTT 60.023 37.500 10.22 0.00 0.00 1.82
309 489 3.504520 ACACGCGTTAGATTTTGGGATTT 59.495 39.130 10.22 0.00 0.00 2.17
310 490 3.078837 ACACGCGTTAGATTTTGGGATT 58.921 40.909 10.22 0.00 0.00 3.01
311 491 2.706890 ACACGCGTTAGATTTTGGGAT 58.293 42.857 10.22 0.00 0.00 3.85
312 492 2.172851 ACACGCGTTAGATTTTGGGA 57.827 45.000 10.22 0.00 0.00 4.37
313 493 2.981400 AACACGCGTTAGATTTTGGG 57.019 45.000 10.22 0.00 32.05 4.12
322 502 1.794116 GCTGGTTTCTAACACGCGTTA 59.206 47.619 10.22 0.00 36.52 3.18
323 503 0.584876 GCTGGTTTCTAACACGCGTT 59.415 50.000 10.22 0.00 39.24 4.84
324 504 0.249741 AGCTGGTTTCTAACACGCGT 60.250 50.000 5.58 5.58 34.58 6.01
325 505 0.438830 GAGCTGGTTTCTAACACGCG 59.561 55.000 3.53 3.53 34.58 6.01
326 506 0.796927 GGAGCTGGTTTCTAACACGC 59.203 55.000 0.00 0.00 0.00 5.34
327 507 1.068474 CGGAGCTGGTTTCTAACACG 58.932 55.000 0.00 0.00 0.00 4.49
328 508 1.001633 TCCGGAGCTGGTTTCTAACAC 59.998 52.381 0.00 0.00 0.00 3.32
329 509 1.344065 TCCGGAGCTGGTTTCTAACA 58.656 50.000 0.00 0.00 0.00 2.41
330 510 2.693267 ATCCGGAGCTGGTTTCTAAC 57.307 50.000 11.34 0.00 0.00 2.34
331 511 4.654262 AGAATATCCGGAGCTGGTTTCTAA 59.346 41.667 11.34 0.00 0.00 2.10
332 512 4.223953 AGAATATCCGGAGCTGGTTTCTA 58.776 43.478 11.34 0.00 0.00 2.10
333 513 3.041946 AGAATATCCGGAGCTGGTTTCT 58.958 45.455 11.34 8.67 0.00 2.52
334 514 3.477210 AGAATATCCGGAGCTGGTTTC 57.523 47.619 11.34 6.51 0.00 2.78
335 515 3.545703 CAAGAATATCCGGAGCTGGTTT 58.454 45.455 11.34 0.00 0.00 3.27
336 516 2.746472 GCAAGAATATCCGGAGCTGGTT 60.746 50.000 11.34 0.00 0.00 3.67
337 517 1.202698 GCAAGAATATCCGGAGCTGGT 60.203 52.381 11.34 0.00 0.00 4.00
338 518 1.071385 AGCAAGAATATCCGGAGCTGG 59.929 52.381 11.34 3.35 0.00 4.85
339 519 2.540265 AGCAAGAATATCCGGAGCTG 57.460 50.000 11.34 1.61 0.00 4.24
340 520 2.171448 ACAAGCAAGAATATCCGGAGCT 59.829 45.455 11.34 8.45 0.00 4.09
341 521 2.565841 ACAAGCAAGAATATCCGGAGC 58.434 47.619 11.34 5.81 0.00 4.70
342 522 3.736252 CGTACAAGCAAGAATATCCGGAG 59.264 47.826 11.34 0.00 0.00 4.63
343 523 3.491964 CCGTACAAGCAAGAATATCCGGA 60.492 47.826 6.61 6.61 33.80 5.14
344 524 2.800544 CCGTACAAGCAAGAATATCCGG 59.199 50.000 0.00 0.00 0.00 5.14
345 525 3.454375 ACCGTACAAGCAAGAATATCCG 58.546 45.455 0.00 0.00 0.00 4.18
346 526 4.439057 TGACCGTACAAGCAAGAATATCC 58.561 43.478 0.00 0.00 0.00 2.59
347 527 6.092259 ACTTTGACCGTACAAGCAAGAATATC 59.908 38.462 0.00 0.00 0.00 1.63
348 528 5.938125 ACTTTGACCGTACAAGCAAGAATAT 59.062 36.000 0.00 0.00 0.00 1.28
349 529 5.302360 ACTTTGACCGTACAAGCAAGAATA 58.698 37.500 0.00 0.00 0.00 1.75
350 530 4.134563 ACTTTGACCGTACAAGCAAGAAT 58.865 39.130 0.00 0.00 0.00 2.40
351 531 3.537580 ACTTTGACCGTACAAGCAAGAA 58.462 40.909 0.00 0.00 0.00 2.52
352 532 3.188159 ACTTTGACCGTACAAGCAAGA 57.812 42.857 0.00 0.00 0.00 3.02
353 533 5.408604 AGATTACTTTGACCGTACAAGCAAG 59.591 40.000 0.00 0.00 0.00 4.01
354 534 5.302360 AGATTACTTTGACCGTACAAGCAA 58.698 37.500 0.00 0.00 0.00 3.91
355 535 4.890088 AGATTACTTTGACCGTACAAGCA 58.110 39.130 0.00 0.00 0.00 3.91
356 536 6.183360 GGTTAGATTACTTTGACCGTACAAGC 60.183 42.308 0.00 0.00 0.00 4.01
357 537 6.869913 TGGTTAGATTACTTTGACCGTACAAG 59.130 38.462 0.00 0.00 0.00 3.16
358 538 6.757237 TGGTTAGATTACTTTGACCGTACAA 58.243 36.000 0.00 0.00 0.00 2.41
359 539 6.343716 TGGTTAGATTACTTTGACCGTACA 57.656 37.500 0.00 0.00 0.00 2.90
360 540 6.197842 CGATGGTTAGATTACTTTGACCGTAC 59.802 42.308 0.00 0.00 0.00 3.67
361 541 6.267817 CGATGGTTAGATTACTTTGACCGTA 58.732 40.000 0.00 0.00 0.00 4.02
362 542 5.107133 CGATGGTTAGATTACTTTGACCGT 58.893 41.667 0.00 0.00 0.00 4.83
363 543 4.025979 GCGATGGTTAGATTACTTTGACCG 60.026 45.833 0.00 0.00 0.00 4.79
364 544 5.116882 AGCGATGGTTAGATTACTTTGACC 58.883 41.667 0.00 0.00 0.00 4.02
365 545 7.766219 TTAGCGATGGTTAGATTACTTTGAC 57.234 36.000 0.00 0.00 0.00 3.18
366 546 7.381408 CGATTAGCGATGGTTAGATTACTTTGA 59.619 37.037 0.00 0.00 44.57 2.69
367 547 7.169308 ACGATTAGCGATGGTTAGATTACTTTG 59.831 37.037 0.00 0.00 44.57 2.77
368 548 7.169308 CACGATTAGCGATGGTTAGATTACTTT 59.831 37.037 0.00 0.00 44.57 2.66
369 549 6.641314 CACGATTAGCGATGGTTAGATTACTT 59.359 38.462 0.00 0.00 44.57 2.24
370 550 6.150318 CACGATTAGCGATGGTTAGATTACT 58.850 40.000 0.00 0.00 44.57 2.24
371 551 5.345202 CCACGATTAGCGATGGTTAGATTAC 59.655 44.000 0.00 0.00 44.57 1.89
372 552 5.242171 TCCACGATTAGCGATGGTTAGATTA 59.758 40.000 0.00 0.00 44.57 1.75
373 553 4.038763 TCCACGATTAGCGATGGTTAGATT 59.961 41.667 0.00 0.00 44.57 2.40
374 554 3.572682 TCCACGATTAGCGATGGTTAGAT 59.427 43.478 0.00 0.00 44.57 1.98
375 555 2.953648 TCCACGATTAGCGATGGTTAGA 59.046 45.455 0.00 0.00 44.57 2.10
376 556 3.364889 TCCACGATTAGCGATGGTTAG 57.635 47.619 0.00 0.00 44.57 2.34
377 557 3.319689 TGATCCACGATTAGCGATGGTTA 59.680 43.478 0.00 0.00 44.57 2.85
378 558 2.102420 TGATCCACGATTAGCGATGGTT 59.898 45.455 0.00 0.00 44.57 3.67
379 559 1.686587 TGATCCACGATTAGCGATGGT 59.313 47.619 0.00 0.00 44.57 3.55
380 560 2.438868 TGATCCACGATTAGCGATGG 57.561 50.000 0.00 0.63 44.57 3.51
381 561 2.476619 GGTTGATCCACGATTAGCGATG 59.523 50.000 0.00 0.00 44.66 3.84
382 562 2.102420 TGGTTGATCCACGATTAGCGAT 59.898 45.455 0.00 0.00 41.38 4.58
383 563 1.478916 TGGTTGATCCACGATTAGCGA 59.521 47.619 0.00 0.00 41.38 4.93
384 564 1.934589 TGGTTGATCCACGATTAGCG 58.065 50.000 0.00 0.00 41.93 4.26
393 573 7.782897 TTAACAAATATGGTTGGTTGATCCA 57.217 32.000 3.86 0.00 45.60 3.41
394 574 7.763985 CCTTTAACAAATATGGTTGGTTGATCC 59.236 37.037 3.86 0.00 32.50 3.36
395 575 8.527810 TCCTTTAACAAATATGGTTGGTTGATC 58.472 33.333 3.86 0.00 32.50 2.92
396 576 8.429237 TCCTTTAACAAATATGGTTGGTTGAT 57.571 30.769 3.86 0.00 32.50 2.57
397 577 7.841282 TCCTTTAACAAATATGGTTGGTTGA 57.159 32.000 3.86 0.00 32.50 3.18
400 580 9.707957 TGATATCCTTTAACAAATATGGTTGGT 57.292 29.630 0.00 0.00 32.50 3.67
412 592 9.753674 AGTTTTCCTTCATGATATCCTTTAACA 57.246 29.630 0.00 0.00 0.00 2.41
416 596 9.539194 AGAAAGTTTTCCTTCATGATATCCTTT 57.461 29.630 0.00 0.00 37.92 3.11
417 597 8.964772 CAGAAAGTTTTCCTTCATGATATCCTT 58.035 33.333 0.00 0.00 37.92 3.36
418 598 8.112183 ACAGAAAGTTTTCCTTCATGATATCCT 58.888 33.333 0.00 0.00 37.92 3.24
419 599 8.286191 ACAGAAAGTTTTCCTTCATGATATCC 57.714 34.615 0.00 0.00 37.92 2.59
422 602 9.010029 GGTTACAGAAAGTTTTCCTTCATGATA 57.990 33.333 0.00 0.00 37.92 2.15
423 603 7.505585 TGGTTACAGAAAGTTTTCCTTCATGAT 59.494 33.333 0.00 0.00 37.92 2.45
424 604 6.831353 TGGTTACAGAAAGTTTTCCTTCATGA 59.169 34.615 0.00 0.00 37.92 3.07
425 605 7.038154 TGGTTACAGAAAGTTTTCCTTCATG 57.962 36.000 1.16 0.00 37.92 3.07
426 606 7.255942 CCATGGTTACAGAAAGTTTTCCTTCAT 60.256 37.037 2.57 0.00 37.92 2.57
427 607 6.040391 CCATGGTTACAGAAAGTTTTCCTTCA 59.960 38.462 2.57 0.00 37.92 3.02
428 608 6.447162 CCATGGTTACAGAAAGTTTTCCTTC 58.553 40.000 2.57 0.00 37.92 3.46
429 609 5.221441 GCCATGGTTACAGAAAGTTTTCCTT 60.221 40.000 14.67 0.00 37.92 3.36
430 610 4.280929 GCCATGGTTACAGAAAGTTTTCCT 59.719 41.667 14.67 0.00 37.92 3.36
431 611 4.280929 AGCCATGGTTACAGAAAGTTTTCC 59.719 41.667 14.67 0.00 37.92 3.13
432 612 5.453567 AGCCATGGTTACAGAAAGTTTTC 57.546 39.130 14.67 0.00 37.45 2.29
433 613 5.869649 AAGCCATGGTTACAGAAAGTTTT 57.130 34.783 14.67 0.00 0.00 2.43
434 614 6.068670 ACTAAGCCATGGTTACAGAAAGTTT 58.931 36.000 14.67 0.00 0.00 2.66
435 615 5.631119 ACTAAGCCATGGTTACAGAAAGTT 58.369 37.500 14.67 0.00 0.00 2.66
436 616 5.242795 ACTAAGCCATGGTTACAGAAAGT 57.757 39.130 14.67 3.51 0.00 2.66
437 617 7.865706 ATTACTAAGCCATGGTTACAGAAAG 57.134 36.000 14.67 2.90 0.00 2.62
438 618 8.519526 CAAATTACTAAGCCATGGTTACAGAAA 58.480 33.333 14.67 0.92 0.00 2.52
439 619 7.362574 GCAAATTACTAAGCCATGGTTACAGAA 60.363 37.037 14.67 2.22 0.00 3.02
440 620 6.094881 GCAAATTACTAAGCCATGGTTACAGA 59.905 38.462 14.67 0.00 0.00 3.41
441 621 6.127758 TGCAAATTACTAAGCCATGGTTACAG 60.128 38.462 14.67 10.80 0.00 2.74
442 622 5.712446 TGCAAATTACTAAGCCATGGTTACA 59.288 36.000 14.67 0.00 0.00 2.41
443 623 6.202516 TGCAAATTACTAAGCCATGGTTAC 57.797 37.500 14.67 0.00 0.00 2.50
444 624 7.416964 AATGCAAATTACTAAGCCATGGTTA 57.583 32.000 14.67 9.73 0.00 2.85
445 625 5.937975 ATGCAAATTACTAAGCCATGGTT 57.062 34.783 14.67 3.81 0.00 3.67
446 626 5.937975 AATGCAAATTACTAAGCCATGGT 57.062 34.783 14.67 0.00 0.00 3.55
447 627 6.421801 GCTAAATGCAAATTACTAAGCCATGG 59.578 38.462 7.63 7.63 42.31 3.66
448 628 6.142798 CGCTAAATGCAAATTACTAAGCCATG 59.857 38.462 0.00 0.00 43.06 3.66
449 629 6.183360 ACGCTAAATGCAAATTACTAAGCCAT 60.183 34.615 0.00 0.00 43.06 4.40
450 630 5.124776 ACGCTAAATGCAAATTACTAAGCCA 59.875 36.000 0.00 0.00 43.06 4.75
451 631 5.578776 ACGCTAAATGCAAATTACTAAGCC 58.421 37.500 0.00 0.00 43.06 4.35
452 632 6.506357 GCAACGCTAAATGCAAATTACTAAGC 60.506 38.462 0.00 0.00 42.12 3.09
453 633 6.290540 CGCAACGCTAAATGCAAATTACTAAG 60.291 38.462 0.00 0.00 42.68 2.18
454 634 5.509972 CGCAACGCTAAATGCAAATTACTAA 59.490 36.000 0.00 0.00 42.68 2.24
455 635 5.025190 CGCAACGCTAAATGCAAATTACTA 58.975 37.500 0.00 0.00 42.68 1.82
456 636 3.851403 CGCAACGCTAAATGCAAATTACT 59.149 39.130 0.00 0.00 42.68 2.24
457 637 4.150287 CGCAACGCTAAATGCAAATTAC 57.850 40.909 0.00 0.00 42.68 1.89
472 652 1.125847 GCACGGAAATTAGCGCAACG 61.126 55.000 11.47 5.48 0.00 4.10
473 653 0.796870 GGCACGGAAATTAGCGCAAC 60.797 55.000 11.47 0.00 0.00 4.17
474 654 1.237954 TGGCACGGAAATTAGCGCAA 61.238 50.000 11.47 1.85 0.00 4.85
475 655 1.237954 TTGGCACGGAAATTAGCGCA 61.238 50.000 11.47 0.00 0.00 6.09
476 656 0.109504 TTTGGCACGGAAATTAGCGC 60.110 50.000 0.00 0.00 0.00 5.92
477 657 2.250188 CTTTTGGCACGGAAATTAGCG 58.750 47.619 0.00 0.00 0.00 4.26
478 658 1.992667 GCTTTTGGCACGGAAATTAGC 59.007 47.619 0.00 0.00 41.35 3.09
479 659 2.606108 GGCTTTTGGCACGGAAATTAG 58.394 47.619 0.00 0.00 45.26 1.73
480 660 2.734276 GGCTTTTGGCACGGAAATTA 57.266 45.000 0.00 0.00 45.26 1.40
481 661 3.605013 GGCTTTTGGCACGGAAATT 57.395 47.368 0.00 0.00 45.26 1.82
490 670 1.661509 GTGCGTGAAGGCTTTTGGC 60.662 57.895 0.00 5.81 46.43 4.52
491 671 0.318107 CAGTGCGTGAAGGCTTTTGG 60.318 55.000 0.00 0.00 0.00 3.28
492 672 0.381801 ACAGTGCGTGAAGGCTTTTG 59.618 50.000 0.00 0.00 0.00 2.44
493 673 1.961793 TACAGTGCGTGAAGGCTTTT 58.038 45.000 0.00 0.00 0.00 2.27
494 674 2.185004 ATACAGTGCGTGAAGGCTTT 57.815 45.000 0.00 0.00 0.00 3.51
495 675 3.328382 TTATACAGTGCGTGAAGGCTT 57.672 42.857 0.00 0.00 0.00 4.35
496 676 3.198068 CATTATACAGTGCGTGAAGGCT 58.802 45.455 0.00 0.00 0.00 4.58
497 677 2.287915 CCATTATACAGTGCGTGAAGGC 59.712 50.000 0.00 0.00 0.00 4.35
498 678 2.872245 CCCATTATACAGTGCGTGAAGG 59.128 50.000 0.00 0.00 0.00 3.46
499 679 3.792401 TCCCATTATACAGTGCGTGAAG 58.208 45.455 0.00 0.00 0.00 3.02
500 680 3.897141 TCCCATTATACAGTGCGTGAA 57.103 42.857 0.00 0.00 0.00 3.18
501 681 3.897141 TTCCCATTATACAGTGCGTGA 57.103 42.857 0.00 0.00 0.00 4.35
502 682 4.126437 TCATTCCCATTATACAGTGCGTG 58.874 43.478 0.00 0.00 0.00 5.34
503 683 4.380531 CTCATTCCCATTATACAGTGCGT 58.619 43.478 0.00 0.00 0.00 5.24
504 684 3.748048 CCTCATTCCCATTATACAGTGCG 59.252 47.826 0.00 0.00 0.00 5.34
505 685 4.074970 CCCTCATTCCCATTATACAGTGC 58.925 47.826 0.00 0.00 0.00 4.40
506 686 5.072329 ACTCCCTCATTCCCATTATACAGTG 59.928 44.000 0.00 0.00 0.00 3.66
507 687 5.227593 ACTCCCTCATTCCCATTATACAGT 58.772 41.667 0.00 0.00 0.00 3.55
508 688 5.832539 ACTCCCTCATTCCCATTATACAG 57.167 43.478 0.00 0.00 0.00 2.74
509 689 7.888514 ATTACTCCCTCATTCCCATTATACA 57.111 36.000 0.00 0.00 0.00 2.29
510 690 8.164070 ACAATTACTCCCTCATTCCCATTATAC 58.836 37.037 0.00 0.00 0.00 1.47
511 691 8.287904 ACAATTACTCCCTCATTCCCATTATA 57.712 34.615 0.00 0.00 0.00 0.98
512 692 7.166758 ACAATTACTCCCTCATTCCCATTAT 57.833 36.000 0.00 0.00 0.00 1.28
513 693 6.590656 ACAATTACTCCCTCATTCCCATTA 57.409 37.500 0.00 0.00 0.00 1.90
514 694 5.472301 ACAATTACTCCCTCATTCCCATT 57.528 39.130 0.00 0.00 0.00 3.16
515 695 5.472301 AACAATTACTCCCTCATTCCCAT 57.528 39.130 0.00 0.00 0.00 4.00
516 696 4.946160 AACAATTACTCCCTCATTCCCA 57.054 40.909 0.00 0.00 0.00 4.37
517 697 6.659824 TCTTAACAATTACTCCCTCATTCCC 58.340 40.000 0.00 0.00 0.00 3.97
518 698 7.829706 ACTTCTTAACAATTACTCCCTCATTCC 59.170 37.037 0.00 0.00 0.00 3.01
519 699 8.794335 ACTTCTTAACAATTACTCCCTCATTC 57.206 34.615 0.00 0.00 0.00 2.67
564 744 6.139671 TGGAAACCTAGAGATAAGAGAGCAT 58.860 40.000 0.00 0.00 0.00 3.79
570 750 6.560003 TTGCATGGAAACCTAGAGATAAGA 57.440 37.500 0.00 0.00 0.00 2.10
571 751 7.630242 TTTTGCATGGAAACCTAGAGATAAG 57.370 36.000 12.36 0.00 0.00 1.73
595 775 5.770162 CACTTCCACCTTCCATCTACTTTTT 59.230 40.000 0.00 0.00 0.00 1.94
596 776 5.316987 CACTTCCACCTTCCATCTACTTTT 58.683 41.667 0.00 0.00 0.00 2.27
597 777 4.263506 CCACTTCCACCTTCCATCTACTTT 60.264 45.833 0.00 0.00 0.00 2.66
656 852 4.331968 TCTTTTGGCTATGTAGTTGGTGG 58.668 43.478 0.00 0.00 0.00 4.61
776 972 1.073722 TGGAAGCTGCCAAGTGGAG 59.926 57.895 12.48 0.00 37.39 3.86
982 1191 1.135257 CATGTCTCCGTCTCTGGTGTC 60.135 57.143 0.00 0.00 0.00 3.67
1291 1509 2.760385 GGAGTAGACCGCCTGCCT 60.760 66.667 0.00 0.00 0.00 4.75
1857 2075 2.347490 CCCTTGTACAGCGCCAGT 59.653 61.111 2.29 5.96 0.00 4.00
2073 2295 1.878656 GACTACGGTGTGGAGCTGCT 61.879 60.000 6.82 0.00 0.00 4.24
2101 2323 5.830457 TCCACCATAATTTATCAAATCCGCA 59.170 36.000 0.00 0.00 0.00 5.69
2235 2460 0.824109 CGGCTCTAGAACACCCATGA 59.176 55.000 0.00 0.00 0.00 3.07
2236 2461 0.824109 TCGGCTCTAGAACACCCATG 59.176 55.000 0.00 0.00 0.00 3.66
2257 2482 2.403252 ATTGGTAAGCCTGAACCGAG 57.597 50.000 0.00 0.00 38.70 4.63
2375 2602 3.674410 GCTAAGCCTGCTGATTTGTTTCC 60.674 47.826 0.00 0.00 0.00 3.13
2376 2603 3.057315 TGCTAAGCCTGCTGATTTGTTTC 60.057 43.478 0.00 0.00 0.00 2.78
2377 2604 2.892852 TGCTAAGCCTGCTGATTTGTTT 59.107 40.909 0.00 0.00 0.00 2.83
2378 2605 2.517959 TGCTAAGCCTGCTGATTTGTT 58.482 42.857 0.00 0.00 0.00 2.83
2639 2874 8.996988 TGACTGTTCGTTCATTTGTTTATAAC 57.003 30.769 0.00 0.00 0.00 1.89
2652 2887 1.071698 CGTCCGTTTGACTGTTCGTTC 60.072 52.381 0.00 0.00 42.13 3.95
2686 2935 4.279169 GGCCATATGCTTGTTGTCATATGT 59.721 41.667 16.34 0.00 45.37 2.29
2687 2936 4.278919 TGGCCATATGCTTGTTGTCATATG 59.721 41.667 0.00 12.71 45.92 1.78
2688 2937 4.472496 TGGCCATATGCTTGTTGTCATAT 58.528 39.130 0.00 0.00 40.92 1.78
2689 2938 3.895998 TGGCCATATGCTTGTTGTCATA 58.104 40.909 0.00 0.00 40.92 2.15
2690 2939 2.737544 TGGCCATATGCTTGTTGTCAT 58.262 42.857 0.00 0.00 40.92 3.06
2691 2940 2.212812 TGGCCATATGCTTGTTGTCA 57.787 45.000 0.00 0.00 40.92 3.58
2692 2941 3.088194 CATGGCCATATGCTTGTTGTC 57.912 47.619 20.30 0.00 40.92 3.18
2740 2989 4.924305 AATAAACATTGGCGATGCTGAT 57.076 36.364 14.75 0.00 39.47 2.90
2741 2990 4.398988 AGAAATAAACATTGGCGATGCTGA 59.601 37.500 14.75 0.00 39.47 4.26
2742 2991 4.675510 AGAAATAAACATTGGCGATGCTG 58.324 39.130 14.75 0.00 39.47 4.41
2743 2992 4.989279 AGAAATAAACATTGGCGATGCT 57.011 36.364 14.75 0.00 39.47 3.79
2744 2993 6.697019 ACATAAGAAATAAACATTGGCGATGC 59.303 34.615 14.75 0.00 39.47 3.91
2745 2994 7.112009 CGACATAAGAAATAAACATTGGCGATG 59.888 37.037 13.27 13.27 36.50 3.84
2790 3042 0.249031 GGCATGCGGTCTATTTTGCC 60.249 55.000 12.44 0.00 42.40 4.52
2793 3045 5.852282 AAATTAGGCATGCGGTCTATTTT 57.148 34.783 12.44 12.54 34.26 1.82


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

AutoCloner maintained by Alex Coulton.