Multiple sequence alignment - TraesCS3B01G216200

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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 TraesCS3B01G216200 chr3B 100.000 5190 0 0 253 5442 257239901 257245090 0.000000e+00 9585.0
1 TraesCS3B01G216200 chr3B 100.000 41 0 0 1 41 257239649 257239689 5.850000e-10 76.8
2 TraesCS3B01G216200 chr3D 94.184 4952 189 31 540 5442 179163799 179168700 0.000000e+00 7457.0
3 TraesCS3B01G216200 chr3D 92.350 183 13 1 253 434 179158830 179159012 5.410000e-65 259.0
4 TraesCS3B01G216200 chr3A 92.840 2891 112 33 2587 5442 221928823 221931653 0.000000e+00 4104.0
5 TraesCS3B01G216200 chr3A 94.444 2052 89 10 557 2584 221923279 221925329 0.000000e+00 3134.0
6 TraesCS3B01G216200 chr3A 87.973 291 30 3 253 542 221916300 221916586 6.750000e-89 339.0
7 TraesCS3B01G216200 chr6B 82.390 159 12 10 424 577 376370729 376370582 2.060000e-24 124.0


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 TraesCS3B01G216200 chr3B 257239649 257245090 5441 False 4830.9 9585 100.000 1 5442 2 chr3B.!!$F1 5441
1 TraesCS3B01G216200 chr3D 179163799 179168700 4901 False 7457.0 7457 94.184 540 5442 1 chr3D.!!$F2 4902
2 TraesCS3B01G216200 chr3A 221923279 221931653 8374 False 3619.0 4104 93.642 557 5442 2 chr3A.!!$F2 4885

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
422 423 0.034059 ACTGAAGACGACCAGCAAGG 59.966 55.0 0.00 0.00 45.67 3.61 F
501 502 0.250124 TTGAATGTTCGGGCGTGACT 60.250 50.0 0.00 0.00 0.00 3.41 F
507 508 0.316689 GTTCGGGCGTGACTTTTGTG 60.317 55.0 0.00 0.00 0.00 3.33 F
623 630 0.457853 GTCGGTTGAGCGCATAGACA 60.458 55.0 11.47 0.00 0.00 3.41 F
1609 1622 1.091537 ACGGGCACATTTTGGTATCG 58.908 50.0 0.00 0.00 0.00 2.92 F
2524 2553 0.601046 GTTTGGCAGGCCTTTTCAGC 60.601 55.0 0.00 2.03 36.94 4.26 F
2525 2554 1.047596 TTTGGCAGGCCTTTTCAGCA 61.048 50.0 0.00 0.00 36.94 4.41 F
3123 6644 1.571919 GTAATGTAGGCGGCAGTCAG 58.428 55.0 13.08 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1294 1306 1.144716 GATGGCGATGCTGGTCTCA 59.855 57.895 0.00 0.0 0.00 3.27 R
2244 2272 1.230635 TTCAGCAAACCAGAGCGAGC 61.231 55.000 0.00 0.0 35.48 5.03 R
2320 2348 2.432874 TCAAGTCTCGTTCTGAAACCCA 59.567 45.455 0.00 0.0 31.27 4.51 R
2489 2517 7.120726 GCCTGCCAAACTCTAGTTTATTTTCTA 59.879 37.037 7.73 0.0 45.54 2.10 R
2664 6185 0.479378 TGTTACCTGGTTTGGGGGAC 59.521 55.000 3.84 0.0 0.00 4.46 R
3384 6905 1.346365 CACCACGTCGTCCTTGTATG 58.654 55.000 0.00 0.0 0.00 2.39 R
3828 7361 1.993369 GAGTGGCATTTACAGGCGGC 61.993 60.000 0.00 0.0 0.00 6.53 R
5051 8622 1.202279 CGAGCTCTGTGAGTCATCCAG 60.202 57.143 12.85 0.0 31.39 3.86 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
18 19 4.404098 CACCTTAACCGCCGGCCT 62.404 66.667 23.46 8.36 0.00 5.19
19 20 4.091939 ACCTTAACCGCCGGCCTC 62.092 66.667 23.46 0.00 0.00 4.70
21 22 4.446413 CTTAACCGCCGGCCTCGT 62.446 66.667 23.46 12.10 33.95 4.18
22 23 4.745751 TTAACCGCCGGCCTCGTG 62.746 66.667 23.46 5.99 33.95 4.35
33 34 4.033776 CCTCGTGGGTGGGCACAT 62.034 66.667 0.00 0.00 0.00 3.21
34 35 2.665089 CCTCGTGGGTGGGCACATA 61.665 63.158 0.00 0.00 0.00 2.29
35 36 1.153369 CTCGTGGGTGGGCACATAG 60.153 63.158 0.00 0.00 0.00 2.23
36 37 2.824041 CGTGGGTGGGCACATAGC 60.824 66.667 0.00 0.00 44.65 2.97
37 38 2.677228 GTGGGTGGGCACATAGCT 59.323 61.111 0.00 0.00 44.79 3.32
38 39 1.750399 GTGGGTGGGCACATAGCTG 60.750 63.158 0.00 0.00 44.79 4.24
39 40 2.230653 TGGGTGGGCACATAGCTGT 61.231 57.895 0.00 0.00 44.79 4.40
291 292 4.929807 CCTCTTTGGCAACCACCT 57.070 55.556 0.00 0.00 30.78 4.00
292 293 2.344535 CCTCTTTGGCAACCACCTG 58.655 57.895 0.00 0.00 30.78 4.00
293 294 0.178992 CCTCTTTGGCAACCACCTGA 60.179 55.000 0.00 0.00 30.78 3.86
294 295 1.242076 CTCTTTGGCAACCACCTGAG 58.758 55.000 0.00 0.00 30.78 3.35
295 296 0.178992 TCTTTGGCAACCACCTGAGG 60.179 55.000 0.00 0.00 30.78 3.86
296 297 1.809567 CTTTGGCAACCACCTGAGGC 61.810 60.000 0.00 0.00 30.78 4.70
297 298 4.641645 TGGCAACCACCTGAGGCG 62.642 66.667 0.00 0.00 0.00 5.52
298 299 4.643387 GGCAACCACCTGAGGCGT 62.643 66.667 0.00 0.00 0.00 5.68
299 300 2.594592 GCAACCACCTGAGGCGTT 60.595 61.111 0.00 0.00 0.00 4.84
300 301 2.908073 GCAACCACCTGAGGCGTTG 61.908 63.158 21.47 21.47 38.49 4.10
301 302 2.594592 AACCACCTGAGGCGTTGC 60.595 61.111 0.00 0.00 0.00 4.17
312 313 2.985847 GCGTTGCCTGCCCTTCTT 60.986 61.111 0.00 0.00 0.00 2.52
313 314 2.564721 GCGTTGCCTGCCCTTCTTT 61.565 57.895 0.00 0.00 0.00 2.52
314 315 1.286880 CGTTGCCTGCCCTTCTTTG 59.713 57.895 0.00 0.00 0.00 2.77
315 316 1.667722 GTTGCCTGCCCTTCTTTGG 59.332 57.895 0.00 0.00 0.00 3.28
322 323 3.369921 CCCTTCTTTGGCAGCCAC 58.630 61.111 15.89 0.00 30.78 5.01
323 324 2.278330 CCCTTCTTTGGCAGCCACC 61.278 63.158 15.89 0.00 30.78 4.61
324 325 1.531365 CCTTCTTTGGCAGCCACCA 60.531 57.895 15.89 2.42 38.16 4.17
329 330 4.100479 TTGGCAGCCACCAATGAG 57.900 55.556 15.89 0.00 44.80 2.90
330 331 1.607178 TTGGCAGCCACCAATGAGG 60.607 57.895 15.89 0.00 44.80 3.86
336 337 4.738998 CCACCAATGAGGCCGCCA 62.739 66.667 13.15 3.31 43.14 5.69
337 338 2.676121 CACCAATGAGGCCGCCAA 60.676 61.111 13.15 0.00 43.14 4.52
338 339 2.676471 ACCAATGAGGCCGCCAAC 60.676 61.111 13.15 5.92 43.14 3.77
339 340 3.451894 CCAATGAGGCCGCCAACC 61.452 66.667 13.15 0.63 0.00 3.77
340 341 3.451894 CAATGAGGCCGCCAACCC 61.452 66.667 13.15 0.00 0.00 4.11
341 342 3.978193 AATGAGGCCGCCAACCCA 61.978 61.111 13.15 4.26 0.00 4.51
342 343 4.740822 ATGAGGCCGCCAACCCAC 62.741 66.667 13.15 0.00 0.00 4.61
347 348 3.989787 GCCGCCAACCCACCTTTG 61.990 66.667 0.00 0.00 0.00 2.77
348 349 3.302344 CCGCCAACCCACCTTTGG 61.302 66.667 0.00 0.00 45.60 3.28
351 352 3.458653 CCAACCCACCTTTGGCAG 58.541 61.111 0.00 0.00 42.35 4.85
352 353 2.736531 CAACCCACCTTTGGCAGC 59.263 61.111 0.00 0.00 42.35 5.25
353 354 2.524148 AACCCACCTTTGGCAGCC 60.524 61.111 3.66 3.66 42.35 4.85
354 355 3.387609 AACCCACCTTTGGCAGCCA 62.388 57.895 11.22 11.22 42.35 4.75
355 356 3.305516 CCCACCTTTGGCAGCCAC 61.306 66.667 15.89 0.00 42.35 5.01
356 357 3.673484 CCACCTTTGGCAGCCACG 61.673 66.667 15.89 8.40 35.56 4.94
357 358 4.347453 CACCTTTGGCAGCCACGC 62.347 66.667 15.89 0.00 30.78 5.34
365 366 3.124921 GCAGCCACGCCGTACATT 61.125 61.111 0.00 0.00 0.00 2.71
366 367 2.784596 CAGCCACGCCGTACATTG 59.215 61.111 0.00 0.00 0.00 2.82
367 368 1.739929 CAGCCACGCCGTACATTGA 60.740 57.895 0.00 0.00 0.00 2.57
368 369 1.740296 AGCCACGCCGTACATTGAC 60.740 57.895 0.00 0.00 0.00 3.18
369 370 2.746803 GCCACGCCGTACATTGACC 61.747 63.158 0.00 0.00 0.00 4.02
370 371 1.079405 CCACGCCGTACATTGACCT 60.079 57.895 0.00 0.00 0.00 3.85
371 372 1.082117 CCACGCCGTACATTGACCTC 61.082 60.000 0.00 0.00 0.00 3.85
372 373 0.389296 CACGCCGTACATTGACCTCA 60.389 55.000 0.00 0.00 0.00 3.86
373 374 0.389426 ACGCCGTACATTGACCTCAC 60.389 55.000 0.00 0.00 0.00 3.51
374 375 1.082117 CGCCGTACATTGACCTCACC 61.082 60.000 0.00 0.00 0.00 4.02
375 376 0.036765 GCCGTACATTGACCTCACCA 60.037 55.000 0.00 0.00 0.00 4.17
376 377 1.406887 GCCGTACATTGACCTCACCAT 60.407 52.381 0.00 0.00 0.00 3.55
377 378 2.279741 CCGTACATTGACCTCACCATG 58.720 52.381 0.00 0.00 0.00 3.66
378 379 2.279741 CGTACATTGACCTCACCATGG 58.720 52.381 11.19 11.19 0.00 3.66
379 380 2.093711 CGTACATTGACCTCACCATGGA 60.094 50.000 21.47 0.00 0.00 3.41
380 381 3.432186 CGTACATTGACCTCACCATGGAT 60.432 47.826 21.47 0.00 0.00 3.41
381 382 3.008835 ACATTGACCTCACCATGGATG 57.991 47.619 21.47 13.20 0.00 3.51
382 383 2.577563 ACATTGACCTCACCATGGATGA 59.422 45.455 21.47 16.76 0.00 2.92
383 384 3.203710 ACATTGACCTCACCATGGATGAT 59.796 43.478 21.47 4.52 0.00 2.45
384 385 3.286329 TTGACCTCACCATGGATGATG 57.714 47.619 21.47 16.47 0.00 3.07
385 386 2.480390 TGACCTCACCATGGATGATGA 58.520 47.619 21.47 10.81 33.31 2.92
386 387 3.050835 TGACCTCACCATGGATGATGAT 58.949 45.455 21.47 6.76 33.31 2.45
387 388 3.181448 TGACCTCACCATGGATGATGATG 60.181 47.826 21.47 11.01 33.31 3.07
388 389 3.050835 ACCTCACCATGGATGATGATGA 58.949 45.455 21.47 8.83 33.31 2.92
389 390 3.181447 ACCTCACCATGGATGATGATGAC 60.181 47.826 21.47 0.00 33.31 3.06
390 391 3.064931 CTCACCATGGATGATGATGACG 58.935 50.000 21.47 1.44 33.31 4.35
391 392 2.699846 TCACCATGGATGATGATGACGA 59.300 45.455 21.47 0.00 33.31 4.20
392 393 3.064931 CACCATGGATGATGATGACGAG 58.935 50.000 21.47 0.00 33.31 4.18
393 394 2.038164 ACCATGGATGATGATGACGAGG 59.962 50.000 21.47 0.00 33.31 4.63
394 395 2.301009 CCATGGATGATGATGACGAGGA 59.699 50.000 5.56 0.00 33.31 3.71
395 396 3.324117 CATGGATGATGATGACGAGGAC 58.676 50.000 0.00 0.00 33.31 3.85
396 397 2.387757 TGGATGATGATGACGAGGACA 58.612 47.619 0.00 0.00 0.00 4.02
397 398 2.765699 TGGATGATGATGACGAGGACAA 59.234 45.455 0.00 0.00 0.00 3.18
398 399 3.126831 GGATGATGATGACGAGGACAAC 58.873 50.000 0.00 0.00 0.00 3.32
399 400 2.278026 TGATGATGACGAGGACAACG 57.722 50.000 0.00 0.00 0.00 4.10
400 401 1.816224 TGATGATGACGAGGACAACGA 59.184 47.619 0.00 0.00 34.70 3.85
401 402 2.186076 GATGATGACGAGGACAACGAC 58.814 52.381 0.00 0.00 34.70 4.34
402 403 0.109919 TGATGACGAGGACAACGACG 60.110 55.000 0.00 0.00 34.70 5.12
403 404 0.167470 GATGACGAGGACAACGACGA 59.833 55.000 0.00 0.00 34.70 4.20
404 405 0.109873 ATGACGAGGACAACGACGAC 60.110 55.000 0.00 0.00 34.70 4.34
405 406 1.162181 TGACGAGGACAACGACGACT 61.162 55.000 0.00 0.00 34.70 4.18
406 407 0.725118 GACGAGGACAACGACGACTG 60.725 60.000 0.00 0.54 34.70 3.51
407 408 1.162181 ACGAGGACAACGACGACTGA 61.162 55.000 0.00 0.00 34.70 3.41
408 409 0.040692 CGAGGACAACGACGACTGAA 60.041 55.000 0.00 0.00 0.00 3.02
409 410 1.687628 GAGGACAACGACGACTGAAG 58.312 55.000 0.00 0.00 0.00 3.02
410 411 1.266175 GAGGACAACGACGACTGAAGA 59.734 52.381 0.00 0.00 0.00 2.87
411 412 1.001597 AGGACAACGACGACTGAAGAC 60.002 52.381 0.00 0.00 0.00 3.01
412 413 1.043224 GACAACGACGACTGAAGACG 58.957 55.000 0.00 0.73 38.99 4.18
413 414 0.659427 ACAACGACGACTGAAGACGA 59.341 50.000 0.00 0.00 37.02 4.20
414 415 1.043224 CAACGACGACTGAAGACGAC 58.957 55.000 0.00 2.30 37.02 4.34
415 416 0.040603 AACGACGACTGAAGACGACC 60.041 55.000 0.00 0.53 37.02 4.79
416 417 1.162181 ACGACGACTGAAGACGACCA 61.162 55.000 0.00 0.00 37.02 4.02
417 418 0.452950 CGACGACTGAAGACGACCAG 60.453 60.000 9.07 0.00 37.02 4.00
418 419 0.729816 GACGACTGAAGACGACCAGC 60.730 60.000 9.07 0.00 37.02 4.85
419 420 1.285950 CGACTGAAGACGACCAGCA 59.714 57.895 0.00 0.00 35.37 4.41
420 421 0.318699 CGACTGAAGACGACCAGCAA 60.319 55.000 0.00 0.00 35.37 3.91
421 422 1.423395 GACTGAAGACGACCAGCAAG 58.577 55.000 0.00 0.00 33.90 4.01
422 423 0.034059 ACTGAAGACGACCAGCAAGG 59.966 55.000 0.00 0.00 45.67 3.61
423 424 1.294659 CTGAAGACGACCAGCAAGGC 61.295 60.000 0.00 0.00 43.14 4.35
424 425 2.357517 AAGACGACCAGCAAGGCG 60.358 61.111 0.00 0.00 43.14 5.52
425 426 3.883744 AAGACGACCAGCAAGGCGG 62.884 63.158 6.19 0.00 43.14 6.13
426 427 4.681978 GACGACCAGCAAGGCGGT 62.682 66.667 6.19 4.81 43.14 5.68
427 428 4.988598 ACGACCAGCAAGGCGGTG 62.989 66.667 6.19 0.00 43.14 4.94
428 429 4.680237 CGACCAGCAAGGCGGTGA 62.680 66.667 8.92 0.00 46.47 4.02
429 430 2.045926 GACCAGCAAGGCGGTGAT 60.046 61.111 8.92 0.00 46.47 3.06
430 431 2.360350 ACCAGCAAGGCGGTGATG 60.360 61.111 2.94 2.94 46.47 3.07
432 433 3.818787 CAGCAAGGCGGTGATGGC 61.819 66.667 2.07 0.00 46.47 4.40
442 443 1.674057 GGTGATGGCCCGATCTAGG 59.326 63.158 0.00 0.00 0.00 3.02
454 455 5.354842 CCCGATCTAGGGTTTCTAGTTTT 57.645 43.478 0.00 0.00 46.38 2.43
455 456 5.742063 CCCGATCTAGGGTTTCTAGTTTTT 58.258 41.667 0.00 0.00 46.38 1.94
456 457 6.881570 CCCGATCTAGGGTTTCTAGTTTTTA 58.118 40.000 0.00 0.00 46.38 1.52
457 458 6.760298 CCCGATCTAGGGTTTCTAGTTTTTAC 59.240 42.308 0.00 0.00 46.38 2.01
458 459 7.325694 CCGATCTAGGGTTTCTAGTTTTTACA 58.674 38.462 0.00 0.00 44.45 2.41
459 460 7.985752 CCGATCTAGGGTTTCTAGTTTTTACAT 59.014 37.037 0.00 0.00 44.45 2.29
460 461 9.379791 CGATCTAGGGTTTCTAGTTTTTACATT 57.620 33.333 0.00 0.00 44.45 2.71
493 494 7.938563 TTCCAAGTTTAATTTGAATGTTCGG 57.061 32.000 1.70 0.00 0.00 4.30
494 495 6.451393 TCCAAGTTTAATTTGAATGTTCGGG 58.549 36.000 1.70 0.00 0.00 5.14
495 496 5.120053 CCAAGTTTAATTTGAATGTTCGGGC 59.880 40.000 1.70 0.00 0.00 6.13
496 497 4.481463 AGTTTAATTTGAATGTTCGGGCG 58.519 39.130 0.00 0.00 0.00 6.13
497 498 4.022676 AGTTTAATTTGAATGTTCGGGCGT 60.023 37.500 0.00 0.00 0.00 5.68
498 499 2.346099 AATTTGAATGTTCGGGCGTG 57.654 45.000 0.00 0.00 0.00 5.34
499 500 1.529226 ATTTGAATGTTCGGGCGTGA 58.471 45.000 0.00 0.00 0.00 4.35
500 501 0.589223 TTTGAATGTTCGGGCGTGAC 59.411 50.000 0.00 0.00 0.00 3.67
501 502 0.250124 TTGAATGTTCGGGCGTGACT 60.250 50.000 0.00 0.00 0.00 3.41
502 503 0.250124 TGAATGTTCGGGCGTGACTT 60.250 50.000 0.00 0.00 0.00 3.01
503 504 0.872388 GAATGTTCGGGCGTGACTTT 59.128 50.000 0.00 0.00 0.00 2.66
504 505 1.265905 GAATGTTCGGGCGTGACTTTT 59.734 47.619 0.00 0.00 0.00 2.27
505 506 0.591170 ATGTTCGGGCGTGACTTTTG 59.409 50.000 0.00 0.00 0.00 2.44
506 507 0.745128 TGTTCGGGCGTGACTTTTGT 60.745 50.000 0.00 0.00 0.00 2.83
507 508 0.316689 GTTCGGGCGTGACTTTTGTG 60.317 55.000 0.00 0.00 0.00 3.33
508 509 1.440938 TTCGGGCGTGACTTTTGTGG 61.441 55.000 0.00 0.00 0.00 4.17
509 510 1.890041 CGGGCGTGACTTTTGTGGA 60.890 57.895 0.00 0.00 0.00 4.02
510 511 1.652563 GGGCGTGACTTTTGTGGAC 59.347 57.895 0.00 0.00 0.00 4.02
511 512 0.818040 GGGCGTGACTTTTGTGGACT 60.818 55.000 0.00 0.00 0.00 3.85
512 513 1.021968 GGCGTGACTTTTGTGGACTT 58.978 50.000 0.00 0.00 0.00 3.01
513 514 1.404035 GGCGTGACTTTTGTGGACTTT 59.596 47.619 0.00 0.00 0.00 2.66
514 515 2.540973 GGCGTGACTTTTGTGGACTTTC 60.541 50.000 0.00 0.00 0.00 2.62
515 516 2.354821 GCGTGACTTTTGTGGACTTTCT 59.645 45.455 0.00 0.00 0.00 2.52
516 517 3.558418 GCGTGACTTTTGTGGACTTTCTA 59.442 43.478 0.00 0.00 0.00 2.10
517 518 4.034742 GCGTGACTTTTGTGGACTTTCTAA 59.965 41.667 0.00 0.00 0.00 2.10
518 519 5.738370 CGTGACTTTTGTGGACTTTCTAAG 58.262 41.667 0.00 0.00 0.00 2.18
519 520 5.293569 CGTGACTTTTGTGGACTTTCTAAGT 59.706 40.000 0.00 0.00 46.38 2.24
520 521 6.183360 CGTGACTTTTGTGGACTTTCTAAGTT 60.183 38.462 0.00 0.00 43.03 2.66
521 522 7.010738 CGTGACTTTTGTGGACTTTCTAAGTTA 59.989 37.037 0.00 0.00 43.03 2.24
522 523 8.671028 GTGACTTTTGTGGACTTTCTAAGTTAA 58.329 33.333 0.00 0.00 43.03 2.01
523 524 9.403583 TGACTTTTGTGGACTTTCTAAGTTAAT 57.596 29.630 0.00 0.00 43.03 1.40
524 525 9.665264 GACTTTTGTGGACTTTCTAAGTTAATG 57.335 33.333 0.00 0.00 43.03 1.90
525 526 9.185680 ACTTTTGTGGACTTTCTAAGTTAATGT 57.814 29.630 0.00 0.00 43.03 2.71
623 630 0.457853 GTCGGTTGAGCGCATAGACA 60.458 55.000 11.47 0.00 0.00 3.41
671 678 1.195222 GTCCGTTTTACCGACGCAAAT 59.805 47.619 0.00 0.00 39.09 2.32
681 688 1.468520 CCGACGCAAATGGACAGAAAT 59.531 47.619 0.00 0.00 0.00 2.17
688 695 4.925054 CGCAAATGGACAGAAATCAAACAT 59.075 37.500 0.00 0.00 0.00 2.71
717 724 2.248135 ATTTGCGGTCGTGCGTTGA 61.248 52.632 0.00 0.00 37.81 3.18
719 726 1.978712 TTTGCGGTCGTGCGTTGAAA 61.979 50.000 0.00 0.00 37.81 2.69
741 748 6.699575 AATTGGCCTTATAGCTACTTTGTG 57.300 37.500 3.32 0.00 0.00 3.33
746 753 5.414765 GGCCTTATAGCTACTTTGTGTTTGT 59.585 40.000 0.00 0.00 0.00 2.83
808 815 5.010719 CGTTTTAGGGAGGCTGTCATATAGA 59.989 44.000 0.00 0.00 0.00 1.98
825 832 2.806945 AGAGACTCTGCTAGAGCTGT 57.193 50.000 3.56 0.00 46.12 4.40
827 834 3.430453 AGAGACTCTGCTAGAGCTGTTT 58.570 45.455 3.56 0.00 46.12 2.83
835 842 4.997395 TCTGCTAGAGCTGTTTTAAACCAG 59.003 41.667 8.31 8.31 42.66 4.00
839 846 6.768861 TGCTAGAGCTGTTTTAAACCAGTTTA 59.231 34.615 13.52 0.00 42.66 2.01
840 847 7.283580 TGCTAGAGCTGTTTTAAACCAGTTTAA 59.716 33.333 13.52 10.84 40.86 1.52
841 848 7.803659 GCTAGAGCTGTTTTAAACCAGTTTAAG 59.196 37.037 13.52 9.97 40.39 1.85
844 851 8.188799 AGAGCTGTTTTAAACCAGTTTAAGTTC 58.811 33.333 13.52 10.43 43.36 3.01
886 898 3.086282 TGGCCCTTTCTCCGTAAAATTC 58.914 45.455 0.00 0.00 0.00 2.17
925 937 4.929707 GGTGGATTAGCCGGCCGG 62.930 72.222 40.26 40.26 40.66 6.13
1108 1120 1.138883 GACTGTATGCAGGCGACGA 59.861 57.895 15.65 0.00 46.62 4.20
1204 1216 2.046892 ATGGTGCTGCACGACTCC 60.047 61.111 24.86 12.53 34.83 3.85
1210 1222 3.069980 GCTGCACGACTCCCTCGAT 62.070 63.158 0.00 0.00 46.14 3.59
1294 1306 2.259818 CTCACGAGGCTCAACGCT 59.740 61.111 15.95 0.00 39.13 5.07
1387 1399 1.379309 GCTCGTCTCCCACTCCTCT 60.379 63.158 0.00 0.00 0.00 3.69
1609 1622 1.091537 ACGGGCACATTTTGGTATCG 58.908 50.000 0.00 0.00 0.00 2.92
1612 1625 3.135225 CGGGCACATTTTGGTATCGATA 58.865 45.455 0.00 0.00 0.00 2.92
1621 1634 7.116948 CACATTTTGGTATCGATATGAGACTCC 59.883 40.741 8.66 3.82 38.86 3.85
1658 1671 4.853924 AGCCCTTCATTAAATTATGCGG 57.146 40.909 0.00 0.00 0.00 5.69
1711 1728 5.882000 TCAATTGATGTGCTAGCATGTTACT 59.118 36.000 22.51 2.26 0.00 2.24
1996 2013 6.428083 ACTAGACTTCGATGAGGAGATCTA 57.572 41.667 5.16 0.46 0.00 1.98
2081 2098 6.852853 GTGATGAACCAAATATTATGACAGCG 59.147 38.462 0.00 0.00 0.00 5.18
2177 2205 6.061022 TGTGGAAGTATCAGGCAAGAATAA 57.939 37.500 0.00 0.00 0.00 1.40
2244 2272 8.674263 AGTATCCTGCAATTGAGAAATCTTAG 57.326 34.615 10.34 0.00 0.00 2.18
2265 2293 2.621338 CTCGCTCTGGTTTGCTGAATA 58.379 47.619 0.00 0.00 0.00 1.75
2320 2348 4.573021 AAATGGCTGCCATATTGGTTTT 57.427 36.364 32.71 19.59 44.40 2.43
2362 2390 3.573967 GAGTTCAATCCCTTCTTGGCAAA 59.426 43.478 0.00 0.00 0.00 3.68
2394 2422 5.126222 TGCAAATACTGTCAAAGGTGTTTCA 59.874 36.000 0.00 0.00 0.00 2.69
2426 2454 6.169094 AGACAATTCATTCTCACGACATTCT 58.831 36.000 0.00 0.00 0.00 2.40
2489 2517 8.529476 ACTTATCCGTATACAAGTCTTCTGTTT 58.471 33.333 3.32 0.00 0.00 2.83
2524 2553 0.601046 GTTTGGCAGGCCTTTTCAGC 60.601 55.000 0.00 2.03 36.94 4.26
2525 2554 1.047596 TTTGGCAGGCCTTTTCAGCA 61.048 50.000 0.00 0.00 36.94 4.41
2638 6159 5.042463 TCATGTTTGAGACCCAACAGTTA 57.958 39.130 0.00 0.00 33.85 2.24
2646 6167 6.182507 TGAGACCCAACAGTTAAGTTACAT 57.817 37.500 0.00 0.00 0.00 2.29
2664 6185 8.722342 AGTTACATTTGCAAAGTTATTACGTG 57.278 30.769 18.19 9.74 0.00 4.49
2688 6209 2.750712 CCCCAAACCAGGTAACATTACG 59.249 50.000 0.00 0.00 41.41 3.18
2713 6234 4.156739 GGTTTTCACCTGATGATTCTGGAC 59.843 45.833 5.98 0.00 42.12 4.02
2720 6241 4.162320 ACCTGATGATTCTGGACGTTACAT 59.838 41.667 5.98 0.00 42.12 2.29
2803 6324 9.920946 TCTGAATAATATCTTAACTGGGCTTTT 57.079 29.630 0.00 0.00 0.00 2.27
2913 6434 5.818136 TGTTAGCTATCATGCTTTGGTTC 57.182 39.130 0.15 0.00 43.74 3.62
2947 6468 6.715347 ATGGTGATTTTATAAGGCTCCAAC 57.285 37.500 0.00 0.00 0.00 3.77
2982 6503 2.302157 TGAATGCAATGACATTTGGGCA 59.698 40.909 12.47 12.47 40.31 5.36
3123 6644 1.571919 GTAATGTAGGCGGCAGTCAG 58.428 55.000 13.08 0.00 0.00 3.51
3241 6762 9.010029 ACTGGAGTGACGTGATTTTATTTTTAT 57.990 29.630 0.00 0.00 0.00 1.40
3370 6891 7.964559 ACAACACTTTTCCGTTTAGTTTCTTAC 59.035 33.333 0.00 0.00 0.00 2.34
3384 6905 6.819397 AGTTTCTTACTAATTTGGAGGTGC 57.181 37.500 0.00 0.00 34.56 5.01
3437 6958 9.627123 TGGATCTTCCGTTAAAATGATTAGAAT 57.373 29.630 0.00 0.00 40.17 2.40
3477 6998 9.807649 GATAATTCACAATAGTGCCTTTGATTT 57.192 29.630 0.00 0.00 45.49 2.17
3583 7107 5.391312 GCCATTGCCTTTCTTTTCTCTAA 57.609 39.130 0.00 0.00 0.00 2.10
3584 7108 5.405797 GCCATTGCCTTTCTTTTCTCTAAG 58.594 41.667 0.00 0.00 0.00 2.18
3586 7110 6.616017 CCATTGCCTTTCTTTTCTCTAAGTC 58.384 40.000 0.00 0.00 0.00 3.01
3589 7113 4.351111 TGCCTTTCTTTTCTCTAAGTCCCT 59.649 41.667 0.00 0.00 0.00 4.20
3828 7361 6.136071 GCATTCAGCCATTGTAAATACTACG 58.864 40.000 0.00 0.00 37.23 3.51
3835 7368 2.212869 TGTAAATACTACGCCGCCTG 57.787 50.000 0.00 0.00 0.00 4.85
3871 7404 5.373812 ACATCTATTCCTTACAGGTTGGG 57.626 43.478 0.00 0.00 36.53 4.12
4045 7578 7.284716 ACACTCTTGACCGATCAGTGTATATAA 59.715 37.037 10.15 0.00 39.00 0.98
4164 7713 4.212004 CGTTCTCACTTTGCATCTTTCTCA 59.788 41.667 0.00 0.00 0.00 3.27
4181 7730 5.384063 TTCTCAACTTGTGCAGTCAAAAA 57.616 34.783 0.00 0.00 32.94 1.94
4204 7753 6.612247 ACAATCACGACAAATGTAAACTCA 57.388 33.333 0.00 0.00 0.00 3.41
4208 7757 9.773328 CAATCACGACAAATGTAAACTCATATT 57.227 29.630 0.00 0.00 0.00 1.28
4256 7807 6.034591 CACCGAAGAACTTGTACGAGATATT 58.965 40.000 17.37 8.52 0.00 1.28
4257 7808 7.066163 TCACCGAAGAACTTGTACGAGATATTA 59.934 37.037 17.37 0.00 0.00 0.98
4273 7824 9.052759 ACGAGATATTAACCATTGATGTAAACC 57.947 33.333 0.00 0.00 0.00 3.27
4306 7857 1.481240 CACGGATCACAGTATCGCAG 58.519 55.000 0.00 0.00 0.00 5.18
4325 7876 4.993584 CGCAGTAGCATAAGATTCAAGGAT 59.006 41.667 0.00 0.00 42.27 3.24
4454 8005 8.035165 ACTAGCATATCACGAATGACTAGTAG 57.965 38.462 0.00 0.00 39.60 2.57
4948 8499 7.645058 ACTTGAAGTCTGGAATCAAAAGAAA 57.355 32.000 0.00 0.00 33.08 2.52
4975 8526 1.442769 GTTGCAGGACACACGATCAT 58.557 50.000 0.00 0.00 0.00 2.45
4977 8528 0.321346 TGCAGGACACACGATCATGT 59.679 50.000 0.00 0.00 30.60 3.21
5030 8600 2.711542 GTTGGTGACATGGTAAGGGAG 58.288 52.381 0.00 0.00 42.32 4.30
5051 8622 4.567971 AGATGGAAGAATGATGAGATCGC 58.432 43.478 0.00 0.00 0.00 4.58
5075 8646 1.513160 GACTCACAGAGCTCGTCGC 60.513 63.158 8.37 0.00 39.57 5.19
5125 8696 4.740922 CCATAGCTGGTGTTGGCA 57.259 55.556 0.00 0.00 37.79 4.92
5378 8949 3.795041 CCCTAGGCTGCTGCTGCT 61.795 66.667 26.79 16.79 40.48 4.24
5379 8950 2.203042 CCTAGGCTGCTGCTGCTC 60.203 66.667 26.79 18.15 40.48 4.26
5380 8951 2.733669 CCTAGGCTGCTGCTGCTCT 61.734 63.158 26.79 22.91 40.48 4.09
5381 8952 1.227321 CTAGGCTGCTGCTGCTCTC 60.227 63.158 26.79 13.39 40.48 3.20
5382 8953 1.678598 CTAGGCTGCTGCTGCTCTCT 61.679 60.000 26.79 18.88 40.48 3.10
5383 8954 1.674764 TAGGCTGCTGCTGCTCTCTC 61.675 60.000 26.79 12.74 40.48 3.20
5384 8955 2.580276 GCTGCTGCTGCTCTCTCT 59.420 61.111 22.10 0.00 40.48 3.10
5385 8956 1.519898 GCTGCTGCTGCTCTCTCTC 60.520 63.158 22.10 0.00 40.48 3.20
5386 8957 1.952102 GCTGCTGCTGCTCTCTCTCT 61.952 60.000 22.10 0.00 40.48 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.404098 AGGCCGGCGGTTAAGGTG 62.404 66.667 28.82 0.00 0.00 4.00
2 3 4.091939 GAGGCCGGCGGTTAAGGT 62.092 66.667 28.82 5.64 0.00 3.50
4 5 4.446413 ACGAGGCCGGCGGTTAAG 62.446 66.667 28.82 18.57 40.78 1.85
5 6 4.745751 CACGAGGCCGGCGGTTAA 62.746 66.667 28.82 0.00 40.78 2.01
16 17 2.593468 CTATGTGCCCACCCACGAGG 62.593 65.000 0.00 0.00 38.55 4.63
17 18 1.153369 CTATGTGCCCACCCACGAG 60.153 63.158 0.00 0.00 38.55 4.18
18 19 2.986290 CTATGTGCCCACCCACGA 59.014 61.111 0.00 0.00 38.55 4.35
19 20 2.824041 GCTATGTGCCCACCCACG 60.824 66.667 0.00 0.00 38.55 4.94
20 21 1.750399 CAGCTATGTGCCCACCCAC 60.750 63.158 0.00 0.00 44.23 4.61
21 22 2.230653 ACAGCTATGTGCCCACCCA 61.231 57.895 0.00 0.00 44.23 4.51
22 23 2.677228 ACAGCTATGTGCCCACCC 59.323 61.111 0.00 0.00 44.23 4.61
274 275 0.178992 TCAGGTGGTTGCCAAAGAGG 60.179 55.000 0.00 0.00 34.18 3.69
275 276 1.242076 CTCAGGTGGTTGCCAAAGAG 58.758 55.000 0.00 0.00 34.18 2.85
276 277 0.178992 CCTCAGGTGGTTGCCAAAGA 60.179 55.000 0.00 0.00 34.18 2.52
277 278 1.809567 GCCTCAGGTGGTTGCCAAAG 61.810 60.000 0.00 0.00 34.18 2.77
278 279 1.832167 GCCTCAGGTGGTTGCCAAA 60.832 57.895 0.00 0.00 34.18 3.28
279 280 2.203480 GCCTCAGGTGGTTGCCAA 60.203 61.111 0.00 0.00 34.18 4.52
280 281 4.641645 CGCCTCAGGTGGTTGCCA 62.642 66.667 0.00 0.00 0.00 4.92
281 282 4.643387 ACGCCTCAGGTGGTTGCC 62.643 66.667 9.68 0.00 37.55 4.52
282 283 2.594592 AACGCCTCAGGTGGTTGC 60.595 61.111 9.68 0.00 37.55 4.17
283 284 2.908073 GCAACGCCTCAGGTGGTTG 61.908 63.158 19.82 19.82 39.97 3.77
284 285 2.594592 GCAACGCCTCAGGTGGTT 60.595 61.111 9.68 2.63 37.55 3.67
285 286 4.643387 GGCAACGCCTCAGGTGGT 62.643 66.667 9.68 0.00 46.69 4.16
295 296 2.564721 AAAGAAGGGCAGGCAACGC 61.565 57.895 0.00 0.00 46.39 4.84
296 297 1.286880 CAAAGAAGGGCAGGCAACG 59.713 57.895 0.00 0.00 46.39 4.10
297 298 1.667722 CCAAAGAAGGGCAGGCAAC 59.332 57.895 0.00 0.00 0.00 4.17
298 299 4.196372 CCAAAGAAGGGCAGGCAA 57.804 55.556 0.00 0.00 0.00 4.52
305 306 2.278330 GGTGGCTGCCAAAGAAGGG 61.278 63.158 25.23 0.00 34.18 3.95
306 307 1.114722 TTGGTGGCTGCCAAAGAAGG 61.115 55.000 25.23 0.00 44.67 3.46
307 308 2.428834 TTGGTGGCTGCCAAAGAAG 58.571 52.632 25.23 0.00 44.67 2.85
308 309 4.695014 TTGGTGGCTGCCAAAGAA 57.305 50.000 25.23 13.25 44.67 2.52
313 314 2.036098 CCTCATTGGTGGCTGCCA 59.964 61.111 19.30 19.30 36.62 4.92
319 320 4.738998 TGGCGGCCTCATTGGTGG 62.739 66.667 21.46 0.00 38.35 4.61
320 321 2.676121 TTGGCGGCCTCATTGGTG 60.676 61.111 21.46 0.00 38.35 4.17
321 322 2.676471 GTTGGCGGCCTCATTGGT 60.676 61.111 21.46 0.00 38.35 3.67
322 323 3.451894 GGTTGGCGGCCTCATTGG 61.452 66.667 21.46 0.00 39.35 3.16
323 324 3.451894 GGGTTGGCGGCCTCATTG 61.452 66.667 21.46 0.00 0.00 2.82
324 325 3.978193 TGGGTTGGCGGCCTCATT 61.978 61.111 21.46 0.00 0.00 2.57
325 326 4.740822 GTGGGTTGGCGGCCTCAT 62.741 66.667 21.46 0.00 0.00 2.90
330 331 3.989787 CAAAGGTGGGTTGGCGGC 61.990 66.667 0.00 0.00 0.00 6.53
331 332 3.302344 CCAAAGGTGGGTTGGCGG 61.302 66.667 0.00 0.00 41.77 6.13
334 335 2.871253 GCTGCCAAAGGTGGGTTGG 61.871 63.158 0.00 0.00 46.09 3.77
335 336 2.736531 GCTGCCAAAGGTGGGTTG 59.263 61.111 0.00 0.00 46.09 3.77
336 337 2.524148 GGCTGCCAAAGGTGGGTT 60.524 61.111 15.17 0.00 46.09 4.11
337 338 3.831637 TGGCTGCCAAAGGTGGGT 61.832 61.111 21.08 0.00 46.09 4.51
338 339 3.305516 GTGGCTGCCAAAGGTGGG 61.306 66.667 25.23 0.00 46.09 4.61
340 341 4.347453 GCGTGGCTGCCAAAGGTG 62.347 66.667 25.23 11.91 34.18 4.00
348 349 3.124921 AATGTACGGCGTGGCTGC 61.125 61.111 24.86 8.02 38.71 5.25
349 350 1.739929 TCAATGTACGGCGTGGCTG 60.740 57.895 24.86 14.15 41.29 4.85
350 351 1.740296 GTCAATGTACGGCGTGGCT 60.740 57.895 24.86 3.25 0.00 4.75
351 352 2.746803 GGTCAATGTACGGCGTGGC 61.747 63.158 24.86 15.79 0.00 5.01
352 353 1.079405 AGGTCAATGTACGGCGTGG 60.079 57.895 24.86 6.96 0.00 4.94
353 354 0.389296 TGAGGTCAATGTACGGCGTG 60.389 55.000 24.86 5.30 0.00 5.34
354 355 0.389426 GTGAGGTCAATGTACGGCGT 60.389 55.000 19.64 19.64 0.00 5.68
355 356 1.082117 GGTGAGGTCAATGTACGGCG 61.082 60.000 4.80 4.80 0.00 6.46
356 357 0.036765 TGGTGAGGTCAATGTACGGC 60.037 55.000 0.00 0.00 0.00 5.68
357 358 2.279741 CATGGTGAGGTCAATGTACGG 58.720 52.381 0.00 0.00 0.00 4.02
358 359 2.093711 TCCATGGTGAGGTCAATGTACG 60.094 50.000 12.58 0.00 0.00 3.67
359 360 3.627395 TCCATGGTGAGGTCAATGTAC 57.373 47.619 12.58 0.00 0.00 2.90
360 361 3.779738 TCATCCATGGTGAGGTCAATGTA 59.220 43.478 12.58 0.00 0.00 2.29
361 362 2.577563 TCATCCATGGTGAGGTCAATGT 59.422 45.455 12.58 0.00 0.00 2.71
362 363 3.286329 TCATCCATGGTGAGGTCAATG 57.714 47.619 12.58 5.55 0.00 2.82
363 364 3.460712 TCATCATCCATGGTGAGGTCAAT 59.539 43.478 20.67 1.66 42.61 2.57
364 365 2.845586 TCATCATCCATGGTGAGGTCAA 59.154 45.455 20.67 6.75 42.61 3.18
365 366 2.480390 TCATCATCCATGGTGAGGTCA 58.520 47.619 20.67 7.27 42.61 4.02
371 372 3.064931 CTCGTCATCATCATCCATGGTG 58.935 50.000 12.58 9.69 44.23 4.17
372 373 2.038164 CCTCGTCATCATCATCCATGGT 59.962 50.000 12.58 0.00 32.64 3.55
373 374 2.301009 TCCTCGTCATCATCATCCATGG 59.699 50.000 4.97 4.97 32.64 3.66
374 375 3.243975 TGTCCTCGTCATCATCATCCATG 60.244 47.826 0.00 0.00 0.00 3.66
375 376 2.967887 TGTCCTCGTCATCATCATCCAT 59.032 45.455 0.00 0.00 0.00 3.41
376 377 2.387757 TGTCCTCGTCATCATCATCCA 58.612 47.619 0.00 0.00 0.00 3.41
377 378 3.126831 GTTGTCCTCGTCATCATCATCC 58.873 50.000 0.00 0.00 0.00 3.51
378 379 2.791560 CGTTGTCCTCGTCATCATCATC 59.208 50.000 0.00 0.00 0.00 2.92
379 380 2.427095 TCGTTGTCCTCGTCATCATCAT 59.573 45.455 0.00 0.00 0.00 2.45
380 381 1.816224 TCGTTGTCCTCGTCATCATCA 59.184 47.619 0.00 0.00 0.00 3.07
381 382 2.186076 GTCGTTGTCCTCGTCATCATC 58.814 52.381 0.00 0.00 0.00 2.92
382 383 1.467543 CGTCGTTGTCCTCGTCATCAT 60.468 52.381 0.00 0.00 0.00 2.45
383 384 0.109919 CGTCGTTGTCCTCGTCATCA 60.110 55.000 0.00 0.00 0.00 3.07
384 385 0.167470 TCGTCGTTGTCCTCGTCATC 59.833 55.000 0.00 0.00 0.00 2.92
385 386 0.109873 GTCGTCGTTGTCCTCGTCAT 60.110 55.000 0.00 0.00 0.00 3.06
386 387 1.162181 AGTCGTCGTTGTCCTCGTCA 61.162 55.000 0.00 0.00 0.00 4.35
387 388 0.725118 CAGTCGTCGTTGTCCTCGTC 60.725 60.000 0.00 0.00 0.00 4.20
388 389 1.162181 TCAGTCGTCGTTGTCCTCGT 61.162 55.000 0.00 0.00 0.00 4.18
389 390 0.040692 TTCAGTCGTCGTTGTCCTCG 60.041 55.000 0.00 0.00 0.00 4.63
390 391 1.266175 TCTTCAGTCGTCGTTGTCCTC 59.734 52.381 0.00 0.00 0.00 3.71
391 392 1.001597 GTCTTCAGTCGTCGTTGTCCT 60.002 52.381 0.00 0.00 0.00 3.85
392 393 1.406447 GTCTTCAGTCGTCGTTGTCC 58.594 55.000 0.00 0.00 0.00 4.02
393 394 1.043224 CGTCTTCAGTCGTCGTTGTC 58.957 55.000 0.00 0.00 0.00 3.18
394 395 0.659427 TCGTCTTCAGTCGTCGTTGT 59.341 50.000 0.00 0.00 0.00 3.32
395 396 1.043224 GTCGTCTTCAGTCGTCGTTG 58.957 55.000 0.00 0.00 0.00 4.10
396 397 0.040603 GGTCGTCTTCAGTCGTCGTT 60.041 55.000 0.00 0.00 0.00 3.85
397 398 1.162181 TGGTCGTCTTCAGTCGTCGT 61.162 55.000 0.00 0.00 0.00 4.34
398 399 0.452950 CTGGTCGTCTTCAGTCGTCG 60.453 60.000 0.00 0.00 0.00 5.12
399 400 0.729816 GCTGGTCGTCTTCAGTCGTC 60.730 60.000 0.00 0.00 33.81 4.20
400 401 1.286260 GCTGGTCGTCTTCAGTCGT 59.714 57.895 0.00 0.00 33.81 4.34
401 402 0.318699 TTGCTGGTCGTCTTCAGTCG 60.319 55.000 0.00 0.00 33.81 4.18
402 403 1.423395 CTTGCTGGTCGTCTTCAGTC 58.577 55.000 0.00 0.00 33.81 3.51
403 404 0.034059 CCTTGCTGGTCGTCTTCAGT 59.966 55.000 0.00 0.00 33.81 3.41
404 405 1.294659 GCCTTGCTGGTCGTCTTCAG 61.295 60.000 0.00 0.00 38.35 3.02
405 406 1.301716 GCCTTGCTGGTCGTCTTCA 60.302 57.895 0.00 0.00 38.35 3.02
406 407 2.383527 CGCCTTGCTGGTCGTCTTC 61.384 63.158 0.00 0.00 38.35 2.87
407 408 2.357517 CGCCTTGCTGGTCGTCTT 60.358 61.111 0.00 0.00 38.35 3.01
408 409 4.379243 CCGCCTTGCTGGTCGTCT 62.379 66.667 10.18 0.00 38.35 4.18
409 410 4.681978 ACCGCCTTGCTGGTCGTC 62.682 66.667 10.18 0.00 38.35 4.20
410 411 4.988598 CACCGCCTTGCTGGTCGT 62.989 66.667 0.73 0.99 34.45 4.34
411 412 3.958147 ATCACCGCCTTGCTGGTCG 62.958 63.158 0.73 0.00 34.45 4.79
412 413 2.045926 ATCACCGCCTTGCTGGTC 60.046 61.111 0.73 0.00 34.45 4.02
413 414 2.360350 CATCACCGCCTTGCTGGT 60.360 61.111 0.00 0.00 36.32 4.00
414 415 3.136123 CCATCACCGCCTTGCTGG 61.136 66.667 0.00 0.00 39.35 4.85
415 416 3.818787 GCCATCACCGCCTTGCTG 61.819 66.667 0.00 0.00 0.00 4.41
424 425 1.674057 CCTAGATCGGGCCATCACC 59.326 63.158 4.39 0.00 0.00 4.02
425 426 1.674057 CCCTAGATCGGGCCATCAC 59.326 63.158 4.39 0.00 37.41 3.06
426 427 4.215370 CCCTAGATCGGGCCATCA 57.785 61.111 4.39 0.00 37.41 3.07
432 433 5.354842 AAAACTAGAAACCCTAGATCGGG 57.645 43.478 4.23 4.23 46.17 5.14
433 434 7.325694 TGTAAAAACTAGAAACCCTAGATCGG 58.674 38.462 0.00 0.00 46.17 4.18
434 435 8.943909 ATGTAAAAACTAGAAACCCTAGATCG 57.056 34.615 0.00 0.00 46.17 3.69
467 468 8.987890 CCGAACATTCAAATTAAACTTGGAATT 58.012 29.630 0.00 0.00 0.00 2.17
468 469 7.602265 CCCGAACATTCAAATTAAACTTGGAAT 59.398 33.333 0.00 0.00 0.00 3.01
469 470 6.926272 CCCGAACATTCAAATTAAACTTGGAA 59.074 34.615 0.00 0.00 0.00 3.53
470 471 6.451393 CCCGAACATTCAAATTAAACTTGGA 58.549 36.000 0.00 0.00 0.00 3.53
471 472 5.120053 GCCCGAACATTCAAATTAAACTTGG 59.880 40.000 0.00 0.00 0.00 3.61
472 473 5.164100 CGCCCGAACATTCAAATTAAACTTG 60.164 40.000 0.00 0.00 0.00 3.16
473 474 4.920927 CGCCCGAACATTCAAATTAAACTT 59.079 37.500 0.00 0.00 0.00 2.66
474 475 4.022676 ACGCCCGAACATTCAAATTAAACT 60.023 37.500 0.00 0.00 0.00 2.66
475 476 4.089351 CACGCCCGAACATTCAAATTAAAC 59.911 41.667 0.00 0.00 0.00 2.01
476 477 4.023107 TCACGCCCGAACATTCAAATTAAA 60.023 37.500 0.00 0.00 0.00 1.52
477 478 3.502595 TCACGCCCGAACATTCAAATTAA 59.497 39.130 0.00 0.00 0.00 1.40
478 479 3.075148 TCACGCCCGAACATTCAAATTA 58.925 40.909 0.00 0.00 0.00 1.40
479 480 1.883275 TCACGCCCGAACATTCAAATT 59.117 42.857 0.00 0.00 0.00 1.82
480 481 1.199097 GTCACGCCCGAACATTCAAAT 59.801 47.619 0.00 0.00 0.00 2.32
481 482 0.589223 GTCACGCCCGAACATTCAAA 59.411 50.000 0.00 0.00 0.00 2.69
482 483 0.250124 AGTCACGCCCGAACATTCAA 60.250 50.000 0.00 0.00 0.00 2.69
483 484 0.250124 AAGTCACGCCCGAACATTCA 60.250 50.000 0.00 0.00 0.00 2.57
484 485 0.872388 AAAGTCACGCCCGAACATTC 59.128 50.000 0.00 0.00 0.00 2.67
485 486 1.001815 CAAAAGTCACGCCCGAACATT 60.002 47.619 0.00 0.00 0.00 2.71
486 487 0.591170 CAAAAGTCACGCCCGAACAT 59.409 50.000 0.00 0.00 0.00 2.71
487 488 0.745128 ACAAAAGTCACGCCCGAACA 60.745 50.000 0.00 0.00 0.00 3.18
488 489 0.316689 CACAAAAGTCACGCCCGAAC 60.317 55.000 0.00 0.00 0.00 3.95
489 490 1.440938 CCACAAAAGTCACGCCCGAA 61.441 55.000 0.00 0.00 0.00 4.30
490 491 1.890041 CCACAAAAGTCACGCCCGA 60.890 57.895 0.00 0.00 0.00 5.14
491 492 1.890041 TCCACAAAAGTCACGCCCG 60.890 57.895 0.00 0.00 0.00 6.13
492 493 0.818040 AGTCCACAAAAGTCACGCCC 60.818 55.000 0.00 0.00 0.00 6.13
493 494 1.021968 AAGTCCACAAAAGTCACGCC 58.978 50.000 0.00 0.00 0.00 5.68
494 495 2.354821 AGAAAGTCCACAAAAGTCACGC 59.645 45.455 0.00 0.00 0.00 5.34
495 496 5.293569 ACTTAGAAAGTCCACAAAAGTCACG 59.706 40.000 0.00 0.00 37.02 4.35
496 497 6.679327 ACTTAGAAAGTCCACAAAAGTCAC 57.321 37.500 0.00 0.00 37.02 3.67
497 498 8.795842 TTAACTTAGAAAGTCCACAAAAGTCA 57.204 30.769 0.00 0.00 41.91 3.41
498 499 9.665264 CATTAACTTAGAAAGTCCACAAAAGTC 57.335 33.333 0.00 0.00 41.91 3.01
499 500 9.185680 ACATTAACTTAGAAAGTCCACAAAAGT 57.814 29.630 0.00 0.00 41.91 2.66
588 595 0.375454 CGACCGCCGCATTTCAAATA 59.625 50.000 0.00 0.00 0.00 1.40
619 626 0.969149 TTGCGGTCACTCATCTGTCT 59.031 50.000 0.00 0.00 0.00 3.41
623 630 2.827604 CGTTTGCGGTCACTCATCT 58.172 52.632 0.00 0.00 0.00 2.90
671 678 7.959658 ATGGATTATGTTTGATTTCTGTCCA 57.040 32.000 0.00 0.00 36.57 4.02
681 688 7.014134 ACCGCAAATGATATGGATTATGTTTGA 59.986 33.333 0.00 0.00 30.90 2.69
688 695 4.450757 CACGACCGCAAATGATATGGATTA 59.549 41.667 0.00 0.00 0.00 1.75
717 724 6.663523 ACACAAAGTAGCTATAAGGCCAATTT 59.336 34.615 5.01 0.00 0.00 1.82
719 726 5.755849 ACACAAAGTAGCTATAAGGCCAAT 58.244 37.500 5.01 0.00 0.00 3.16
741 748 2.989166 GCTTATGAGGCAAAGCACAAAC 59.011 45.455 2.35 0.00 45.89 2.93
808 815 5.730296 TTAAAACAGCTCTAGCAGAGTCT 57.270 39.130 4.54 8.66 44.12 3.24
825 832 9.473640 AAAACGTGAACTTAAACTGGTTTAAAA 57.526 25.926 16.18 2.04 42.39 1.52
827 834 9.127006 GAAAAACGTGAACTTAAACTGGTTTAA 57.873 29.630 15.08 15.08 41.23 1.52
835 842 6.748198 TGGATGTGAAAAACGTGAACTTAAAC 59.252 34.615 0.00 0.00 0.00 2.01
839 846 4.974368 TGGATGTGAAAAACGTGAACTT 57.026 36.364 0.00 0.00 0.00 2.66
840 847 4.974368 TTGGATGTGAAAAACGTGAACT 57.026 36.364 0.00 0.00 0.00 3.01
841 848 6.582437 AATTTGGATGTGAAAAACGTGAAC 57.418 33.333 0.00 0.00 0.00 3.18
870 882 7.290857 TCAGAATCGAATTTTACGGAGAAAG 57.709 36.000 0.00 0.00 0.00 2.62
886 898 5.406175 ACCACAATTTGCAATTTCAGAATCG 59.594 36.000 0.00 0.00 0.00 3.34
925 937 0.962855 GGCCTTTCACCTGCTTCCTC 60.963 60.000 0.00 0.00 0.00 3.71
926 938 1.075659 GGCCTTTCACCTGCTTCCT 59.924 57.895 0.00 0.00 0.00 3.36
927 939 2.335712 CGGCCTTTCACCTGCTTCC 61.336 63.158 0.00 0.00 0.00 3.46
1077 1089 0.917821 TACAGTCGAGGGGGAGGAGA 60.918 60.000 0.00 0.00 0.00 3.71
1108 1120 3.437344 GGATAGTGTAGGAAGCTCTCCCT 60.437 52.174 10.27 8.84 46.81 4.20
1262 1274 2.107953 GAGCCTCCCGATCTGCAC 59.892 66.667 0.00 0.00 0.00 4.57
1263 1275 2.364186 TGAGCCTCCCGATCTGCA 60.364 61.111 0.00 0.00 0.00 4.41
1294 1306 1.144716 GATGGCGATGCTGGTCTCA 59.855 57.895 0.00 0.00 0.00 3.27
1591 1604 1.374560 TCGATACCAAAATGTGCCCG 58.625 50.000 0.00 0.00 0.00 6.13
1609 1622 7.840342 AATTGCATATTCGGAGTCTCATATC 57.160 36.000 1.47 0.00 0.00 1.63
1612 1625 6.057533 TGAAATTGCATATTCGGAGTCTCAT 58.942 36.000 1.47 0.00 0.00 2.90
1621 1634 4.311816 AGGGCTTGAAATTGCATATTCG 57.688 40.909 7.30 0.00 0.00 3.34
1711 1728 5.226396 CCCTGAATGAAAAATTGCAACGTA 58.774 37.500 0.00 0.00 0.00 3.57
1996 2013 3.698040 GCCATTGAGATCATGTGGAAAGT 59.302 43.478 15.24 0.00 35.35 2.66
2081 2098 3.945285 TCACCTCAACCAAAAGTGACTTC 59.055 43.478 0.00 0.00 32.75 3.01
2244 2272 1.230635 TTCAGCAAACCAGAGCGAGC 61.231 55.000 0.00 0.00 35.48 5.03
2265 2293 8.266473 AGTGAAGAAGCTGATGAAAATATCTCT 58.734 33.333 0.00 0.00 0.00 3.10
2307 2335 4.020662 TCTGAAACCCAAAACCAATATGGC 60.021 41.667 0.00 0.00 42.67 4.40
2320 2348 2.432874 TCAAGTCTCGTTCTGAAACCCA 59.567 45.455 0.00 0.00 31.27 4.51
2394 2422 9.653287 TCGTGAGAATGAATTGTCTAAAGTTAT 57.347 29.630 2.35 0.00 37.03 1.89
2426 2454 8.554011 ACCAAATAATAAGTTTAGGCTAGTCCA 58.446 33.333 6.07 0.00 37.29 4.02
2489 2517 7.120726 GCCTGCCAAACTCTAGTTTATTTTCTA 59.879 37.037 7.73 0.00 45.54 2.10
2584 2613 8.635328 TGAAACAAAAGACCCTAAGGAAAATAC 58.365 33.333 0.00 0.00 36.73 1.89
2631 6152 8.996024 AACTTTGCAAATGTAACTTAACTGTT 57.004 26.923 13.23 5.62 32.51 3.16
2638 6159 9.176181 CACGTAATAACTTTGCAAATGTAACTT 57.824 29.630 13.23 9.42 32.51 2.66
2646 6167 4.023021 GGGGACACGTAATAACTTTGCAAA 60.023 41.667 12.14 12.14 0.00 3.68
2664 6185 0.479378 TGTTACCTGGTTTGGGGGAC 59.521 55.000 3.84 0.00 0.00 4.46
2688 6209 4.082571 CCAGAATCATCAGGTGAAAACCAC 60.083 45.833 0.00 0.00 44.95 4.16
2713 6234 5.682869 TGAGTATACGAATCGGATGTAACG 58.317 41.667 11.13 0.00 30.80 3.18
2720 6241 4.201657 TGGTTCTGAGTATACGAATCGGA 58.798 43.478 7.80 0.00 0.00 4.55
2798 6319 3.945921 GGGATACAGTTCCAGGTAAAAGC 59.054 47.826 4.71 0.00 37.53 3.51
2803 6324 2.841881 GGTTGGGATACAGTTCCAGGTA 59.158 50.000 4.71 0.00 37.53 3.08
2805 6326 1.064685 GGGTTGGGATACAGTTCCAGG 60.065 57.143 4.71 0.00 37.53 4.45
2947 6468 4.492791 TGCATTCAACAGATGTCAACTG 57.507 40.909 8.47 8.47 40.68 3.16
2982 6503 8.801882 TCTGGAAAACGGATTAATCAAAGTAT 57.198 30.769 17.07 6.78 0.00 2.12
3123 6644 1.473258 TATTGCCATGTGACCTTGCC 58.527 50.000 0.00 0.00 0.00 4.52
3370 6891 5.066505 GTCCTTGTATGCACCTCCAAATTAG 59.933 44.000 0.00 0.00 0.00 1.73
3384 6905 1.346365 CACCACGTCGTCCTTGTATG 58.654 55.000 0.00 0.00 0.00 2.39
3437 6958 9.685276 ATTGTGAATTATCAATGAGGTGACTTA 57.315 29.630 6.74 0.00 38.00 2.24
3494 7015 6.813649 CAGGTGTGGATAGTTTGGATATATCG 59.186 42.308 6.64 0.00 0.00 2.92
3509 7030 3.330701 ACAAGGAATGTACAGGTGTGGAT 59.669 43.478 0.33 0.00 41.63 3.41
3580 7104 5.645497 CAGATTTGGAGAAACAGGGACTTAG 59.355 44.000 0.00 0.00 34.60 2.18
3583 7107 3.812167 GCAGATTTGGAGAAACAGGGACT 60.812 47.826 0.00 0.00 43.88 3.85
3584 7108 2.489722 GCAGATTTGGAGAAACAGGGAC 59.510 50.000 0.00 0.00 0.00 4.46
3586 7110 2.517959 TGCAGATTTGGAGAAACAGGG 58.482 47.619 0.00 0.00 0.00 4.45
3589 7113 6.409524 AGAAAATGCAGATTTGGAGAAACA 57.590 33.333 5.10 0.00 31.83 2.83
3828 7361 1.993369 GAGTGGCATTTACAGGCGGC 61.993 60.000 0.00 0.00 0.00 6.53
3835 7368 7.445945 AGGAATAGATGTAGAGTGGCATTTAC 58.554 38.462 0.00 0.00 0.00 2.01
4045 7578 6.111382 CACATCCATGTCTCAGTTAGTGAAT 58.889 40.000 0.00 0.00 39.39 2.57
4164 7713 5.348451 GTGATTGTTTTTGACTGCACAAGTT 59.652 36.000 0.00 0.00 40.07 2.66
4181 7730 6.612247 TGAGTTTACATTTGTCGTGATTGT 57.388 33.333 0.00 0.00 0.00 2.71
4256 7807 7.446013 ACTTTTCGAGGTTTACATCAATGGTTA 59.554 33.333 0.00 0.00 0.00 2.85
4257 7808 6.264518 ACTTTTCGAGGTTTACATCAATGGTT 59.735 34.615 0.00 0.00 0.00 3.67
4273 7824 3.991773 TGATCCGTGGTAAACTTTTCGAG 59.008 43.478 0.00 0.00 0.00 4.04
4426 7977 6.885952 AGTCATTCGTGATATGCTAGTACT 57.114 37.500 0.00 0.00 0.00 2.73
4427 7978 7.808672 ACTAGTCATTCGTGATATGCTAGTAC 58.191 38.462 13.31 0.00 39.00 2.73
4428 7979 7.981102 ACTAGTCATTCGTGATATGCTAGTA 57.019 36.000 13.31 0.00 39.00 1.82
4429 7980 6.885952 ACTAGTCATTCGTGATATGCTAGT 57.114 37.500 0.00 0.00 37.69 2.57
4430 7981 6.964370 GCTACTAGTCATTCGTGATATGCTAG 59.036 42.308 0.00 0.00 36.67 3.42
4431 7982 6.430000 TGCTACTAGTCATTCGTGATATGCTA 59.570 38.462 0.00 0.00 0.00 3.49
4432 7983 5.241728 TGCTACTAGTCATTCGTGATATGCT 59.758 40.000 0.00 0.00 0.00 3.79
4433 7984 5.343593 GTGCTACTAGTCATTCGTGATATGC 59.656 44.000 0.00 0.00 0.00 3.14
4446 7997 2.688958 AGTTCATCCGGTGCTACTAGTC 59.311 50.000 0.00 0.00 0.00 2.59
4454 8005 4.278669 TCTCTATTAGAGTTCATCCGGTGC 59.721 45.833 18.06 0.00 42.83 5.01
4514 8065 6.435904 AGTGATCAGTTTGCTCTTCTAGTAGT 59.564 38.462 0.00 0.00 0.00 2.73
4625 8176 3.998672 TCTTCACCGGGCACGTCC 61.999 66.667 7.97 0.00 38.78 4.79
4948 8499 1.421268 TGTGTCCTGCAACCTGATCTT 59.579 47.619 0.00 0.00 0.00 2.40
4975 8526 6.486320 ACTTGTGTTGTGTATGATTCATCACA 59.514 34.615 19.25 19.25 40.03 3.58
4977 8528 7.148656 CGTACTTGTGTTGTGTATGATTCATCA 60.149 37.037 1.55 0.00 41.70 3.07
4982 8533 4.752604 TGCGTACTTGTGTTGTGTATGATT 59.247 37.500 0.00 0.00 0.00 2.57
4987 8542 1.853510 CGTGCGTACTTGTGTTGTGTA 59.146 47.619 1.24 0.00 0.00 2.90
5030 8600 4.389382 CAGCGATCTCATCATTCTTCCATC 59.611 45.833 0.00 0.00 0.00 3.51
5051 8622 1.202279 CGAGCTCTGTGAGTCATCCAG 60.202 57.143 12.85 0.00 31.39 3.86
5363 8934 1.227321 GAGAGCAGCAGCAGCCTAG 60.227 63.158 6.10 0.00 45.49 3.02
5371 8942 1.945394 GAGAGAGAGAGAGAGCAGCAG 59.055 57.143 0.00 0.00 0.00 4.24
5372 8943 1.561076 AGAGAGAGAGAGAGAGCAGCA 59.439 52.381 0.00 0.00 0.00 4.41
5373 8944 2.158842 AGAGAGAGAGAGAGAGAGCAGC 60.159 54.545 0.00 0.00 0.00 5.25
5374 8945 3.387374 AGAGAGAGAGAGAGAGAGAGCAG 59.613 52.174 0.00 0.00 0.00 4.24
5375 8946 3.378512 AGAGAGAGAGAGAGAGAGAGCA 58.621 50.000 0.00 0.00 0.00 4.26
5376 8947 3.551863 CGAGAGAGAGAGAGAGAGAGAGC 60.552 56.522 0.00 0.00 0.00 4.09
5377 8948 3.634448 ACGAGAGAGAGAGAGAGAGAGAG 59.366 52.174 0.00 0.00 0.00 3.20
5378 8949 3.632333 ACGAGAGAGAGAGAGAGAGAGA 58.368 50.000 0.00 0.00 0.00 3.10
5379 8950 4.115516 CAACGAGAGAGAGAGAGAGAGAG 58.884 52.174 0.00 0.00 0.00 3.20
5380 8951 3.678806 GCAACGAGAGAGAGAGAGAGAGA 60.679 52.174 0.00 0.00 0.00 3.10
5381 8952 2.609459 GCAACGAGAGAGAGAGAGAGAG 59.391 54.545 0.00 0.00 0.00 3.20
5382 8953 2.236146 AGCAACGAGAGAGAGAGAGAGA 59.764 50.000 0.00 0.00 0.00 3.10
5383 8954 2.609459 GAGCAACGAGAGAGAGAGAGAG 59.391 54.545 0.00 0.00 0.00 3.20
5384 8955 2.627945 GAGCAACGAGAGAGAGAGAGA 58.372 52.381 0.00 0.00 0.00 3.10
5385 8956 1.670811 GGAGCAACGAGAGAGAGAGAG 59.329 57.143 0.00 0.00 0.00 3.20
5386 8957 1.745232 GGAGCAACGAGAGAGAGAGA 58.255 55.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.