Multiple sequence alignment - TraesCS6A01G154500

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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 TraesCS6A01G154500 chr6A 100.000 4303 0 0 1 4303 143373227 143377529 0.000000e+00 7947
1 TraesCS6A01G154500 chr6B 93.701 3572 165 18 751 4303 204330572 204334102 0.000000e+00 5295
2 TraesCS6A01G154500 chr6B 80.893 717 78 26 1326 2040 88718767 88719426 1.070000e-140 510
3 TraesCS6A01G154500 chr6B 75.588 680 145 18 1 667 204481865 204481194 2.500000e-82 316
4 TraesCS6A01G154500 chr6D 93.713 2354 120 15 1956 4303 115018925 115021256 0.000000e+00 3502
5 TraesCS6A01G154500 chr6D 94.666 1256 51 8 682 1924 115017677 115018929 0.000000e+00 1934
6 TraesCS6A01G154500 chr6D 95.541 314 12 2 26 337 115016564 115016877 6.420000e-138 501
7 TraesCS6A01G154500 chr6D 93.617 235 13 1 430 664 115016876 115017108 2.460000e-92 350
8 TraesCS6A01G154500 chr1B 87.336 458 45 6 1326 1778 326790021 326789572 2.970000e-141 512
9 TraesCS6A01G154500 chr1B 80.000 285 44 6 2339 2621 633192287 633192014 9.440000e-47 198
10 TraesCS6A01G154500 chr1A 81.029 622 62 23 1424 2039 462129890 462129319 1.100000e-120 444
11 TraesCS6A01G154500 chr1A 79.318 440 66 13 2403 2832 548490025 548490449 7.040000e-73 285
12 TraesCS6A01G154500 chr7A 82.353 442 58 9 1326 1765 429870634 429870211 2.440000e-97 366
13 TraesCS6A01G154500 chr7A 78.711 512 90 11 2298 2806 579013494 579012999 1.490000e-84 324
14 TraesCS6A01G154500 chr5A 78.599 514 88 12 2298 2806 622374658 622375154 1.930000e-83 320
15 TraesCS6A01G154500 chr7B 78.363 513 91 11 2298 2806 113921602 113922098 8.980000e-82 315
16 TraesCS6A01G154500 chr3B 78.252 469 79 14 2339 2802 735245399 735245849 3.280000e-71 279
17 TraesCS6A01G154500 chr3A 81.061 264 35 9 2339 2600 40814553 40814303 3.390000e-46 196


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 TraesCS6A01G154500 chr6A 143373227 143377529 4302 False 7947.00 7947 100.00000 1 4303 1 chr6A.!!$F1 4302
1 TraesCS6A01G154500 chr6B 204330572 204334102 3530 False 5295.00 5295 93.70100 751 4303 1 chr6B.!!$F2 3552
2 TraesCS6A01G154500 chr6B 88718767 88719426 659 False 510.00 510 80.89300 1326 2040 1 chr6B.!!$F1 714
3 TraesCS6A01G154500 chr6B 204481194 204481865 671 True 316.00 316 75.58800 1 667 1 chr6B.!!$R1 666
4 TraesCS6A01G154500 chr6D 115016564 115021256 4692 False 1571.75 3502 94.38425 26 4303 4 chr6D.!!$F1 4277
5 TraesCS6A01G154500 chr1A 462129319 462129890 571 True 444.00 444 81.02900 1424 2039 1 chr1A.!!$R1 615

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
385 479 0.037303 AGCAGTGGGTCAATGGTGAG 59.963 55.000 0.00 0.0 38.69 3.51 F
409 503 0.318120 AAAAGCATGGGTGAAAGCGG 59.682 50.000 0.00 0.0 33.03 5.52 F
419 513 0.669318 GTGAAAGCGGGTCGACATGA 60.669 55.000 18.91 0.0 0.00 3.07 F
566 667 1.072489 TCAAACAGGTACGCCCAATCA 59.928 47.619 0.00 0.0 34.66 2.57 F
1855 2534 1.098050 CAAGGGCCATTTCTCGAAGG 58.902 55.000 6.18 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2651 0.118346 TCAGGCTTGAGGTAGGGGAA 59.882 55.000 0.0 0.0 0.00 3.97 R
1945 2653 0.253327 GTTCAGGCTTGAGGTAGGGG 59.747 60.000 0.0 0.0 34.15 4.79 R
1946 2654 1.280457 AGTTCAGGCTTGAGGTAGGG 58.720 55.000 0.0 0.0 34.15 3.53 R
1950 2658 2.050144 TCAGAAGTTCAGGCTTGAGGT 58.950 47.619 5.5 0.0 34.15 3.85 R
3578 4301 0.110056 CAAGTGAAGCCATGCACGTC 60.110 55.000 0.0 0.0 39.88 4.34 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
20 21 2.397549 GAATGTGAGCACCAAACTTGC 58.602 47.619 0.00 0.00 40.52 4.01
22 23 1.008538 GTGAGCACCAAACTTGCCG 60.009 57.895 0.00 0.00 41.18 5.69
28 29 1.522668 CACCAAACTTGCCGATGAGA 58.477 50.000 0.00 0.00 0.00 3.27
98 101 2.199613 TATTTGCCGGGGAAAGCGGA 62.200 55.000 18.68 2.27 0.00 5.54
118 121 3.553922 GGACATCTTAGCTGGGAAGATCG 60.554 52.174 7.17 6.48 40.83 3.69
194 197 2.826128 TGCTGATGGTCGTTCTTAGACT 59.174 45.455 0.00 0.00 38.58 3.24
196 199 4.461431 TGCTGATGGTCGTTCTTAGACTAA 59.539 41.667 0.00 0.00 38.58 2.24
269 272 1.139853 GTTTGGGTGGCAAACATTCCA 59.860 47.619 0.00 0.00 40.94 3.53
284 288 4.621991 ACATTCCAGCATCATCTACGTAC 58.378 43.478 0.00 0.00 0.00 3.67
337 431 3.542969 AACAAGCTTAAGAACCCCCAT 57.457 42.857 6.67 0.00 0.00 4.00
338 432 3.542969 ACAAGCTTAAGAACCCCCATT 57.457 42.857 6.67 0.00 0.00 3.16
339 433 3.856900 ACAAGCTTAAGAACCCCCATTT 58.143 40.909 6.67 0.00 0.00 2.32
340 434 3.832490 ACAAGCTTAAGAACCCCCATTTC 59.168 43.478 6.67 0.00 0.00 2.17
341 435 4.089361 CAAGCTTAAGAACCCCCATTTCT 58.911 43.478 6.67 0.00 34.66 2.52
342 436 3.701664 AGCTTAAGAACCCCCATTTCTG 58.298 45.455 6.67 0.00 33.46 3.02
343 437 3.076032 AGCTTAAGAACCCCCATTTCTGT 59.924 43.478 6.67 0.00 33.46 3.41
344 438 4.291249 AGCTTAAGAACCCCCATTTCTGTA 59.709 41.667 6.67 0.00 33.46 2.74
345 439 4.640647 GCTTAAGAACCCCCATTTCTGTAG 59.359 45.833 6.67 0.00 33.46 2.74
346 440 2.808906 AGAACCCCCATTTCTGTAGC 57.191 50.000 0.00 0.00 31.88 3.58
347 441 1.285078 AGAACCCCCATTTCTGTAGCC 59.715 52.381 0.00 0.00 31.88 3.93
348 442 1.005450 GAACCCCCATTTCTGTAGCCA 59.995 52.381 0.00 0.00 0.00 4.75
349 443 1.308877 ACCCCCATTTCTGTAGCCAT 58.691 50.000 0.00 0.00 0.00 4.40
350 444 1.063717 ACCCCCATTTCTGTAGCCATG 60.064 52.381 0.00 0.00 0.00 3.66
351 445 1.063717 CCCCCATTTCTGTAGCCATGT 60.064 52.381 0.00 0.00 0.00 3.21
352 446 2.624029 CCCCCATTTCTGTAGCCATGTT 60.624 50.000 0.00 0.00 0.00 2.71
353 447 2.428171 CCCCATTTCTGTAGCCATGTTG 59.572 50.000 0.00 0.00 0.00 3.33
354 448 3.091545 CCCATTTCTGTAGCCATGTTGT 58.908 45.455 0.00 0.00 0.00 3.32
355 449 3.119388 CCCATTTCTGTAGCCATGTTGTG 60.119 47.826 0.00 0.00 0.00 3.33
356 450 3.507233 CCATTTCTGTAGCCATGTTGTGT 59.493 43.478 0.00 0.00 0.00 3.72
357 451 4.699735 CCATTTCTGTAGCCATGTTGTGTA 59.300 41.667 0.00 0.00 0.00 2.90
358 452 5.357878 CCATTTCTGTAGCCATGTTGTGTAT 59.642 40.000 0.00 0.00 0.00 2.29
359 453 6.458751 CCATTTCTGTAGCCATGTTGTGTATC 60.459 42.308 0.00 0.00 0.00 2.24
360 454 5.420725 TTCTGTAGCCATGTTGTGTATCT 57.579 39.130 0.00 0.00 0.00 1.98
361 455 4.758688 TCTGTAGCCATGTTGTGTATCTG 58.241 43.478 0.00 0.00 0.00 2.90
362 456 4.222810 TCTGTAGCCATGTTGTGTATCTGT 59.777 41.667 0.00 0.00 0.00 3.41
363 457 4.905429 TGTAGCCATGTTGTGTATCTGTT 58.095 39.130 0.00 0.00 0.00 3.16
364 458 4.694982 TGTAGCCATGTTGTGTATCTGTTG 59.305 41.667 0.00 0.00 0.00 3.33
365 459 2.489329 AGCCATGTTGTGTATCTGTTGC 59.511 45.455 0.00 0.00 0.00 4.17
366 460 2.228582 GCCATGTTGTGTATCTGTTGCA 59.771 45.455 0.00 0.00 0.00 4.08
367 461 3.671433 GCCATGTTGTGTATCTGTTGCAG 60.671 47.826 0.00 0.00 0.00 4.41
368 462 3.495193 CATGTTGTGTATCTGTTGCAGC 58.505 45.455 0.00 0.00 0.00 5.25
369 463 2.570135 TGTTGTGTATCTGTTGCAGCA 58.430 42.857 2.37 2.37 0.00 4.41
370 464 2.549329 TGTTGTGTATCTGTTGCAGCAG 59.451 45.455 23.26 23.26 37.81 4.24
371 465 2.549064 TGTGTATCTGTTGCAGCAGT 57.451 45.000 27.01 17.64 37.70 4.40
372 466 2.145536 TGTGTATCTGTTGCAGCAGTG 58.854 47.619 27.01 6.94 37.70 3.66
373 467 1.466167 GTGTATCTGTTGCAGCAGTGG 59.534 52.381 27.01 6.21 37.70 4.00
374 468 1.089920 GTATCTGTTGCAGCAGTGGG 58.910 55.000 27.01 5.85 37.70 4.61
375 469 0.692476 TATCTGTTGCAGCAGTGGGT 59.308 50.000 27.01 15.30 37.70 4.51
376 470 0.607489 ATCTGTTGCAGCAGTGGGTC 60.607 55.000 27.01 0.00 37.70 4.46
377 471 1.526686 CTGTTGCAGCAGTGGGTCA 60.527 57.895 21.28 0.00 0.00 4.02
378 472 1.077140 TGTTGCAGCAGTGGGTCAA 60.077 52.632 0.00 0.00 0.00 3.18
379 473 0.467844 TGTTGCAGCAGTGGGTCAAT 60.468 50.000 0.00 0.00 0.00 2.57
380 474 0.038892 GTTGCAGCAGTGGGTCAATG 60.039 55.000 0.00 0.00 32.29 2.82
381 475 1.180456 TTGCAGCAGTGGGTCAATGG 61.180 55.000 0.00 0.00 29.66 3.16
382 476 1.604593 GCAGCAGTGGGTCAATGGT 60.605 57.895 0.00 0.00 40.72 3.55
383 477 4.828409 AGCAGTGGGTCAATGGTG 57.172 55.556 0.00 0.00 38.69 4.17
384 478 2.154139 AGCAGTGGGTCAATGGTGA 58.846 52.632 0.00 0.00 38.69 4.02
385 479 0.037303 AGCAGTGGGTCAATGGTGAG 59.963 55.000 0.00 0.00 38.69 3.51
386 480 0.962356 GCAGTGGGTCAATGGTGAGG 60.962 60.000 0.00 0.00 33.27 3.86
387 481 0.692476 CAGTGGGTCAATGGTGAGGA 59.308 55.000 0.00 0.00 33.27 3.71
388 482 1.283029 CAGTGGGTCAATGGTGAGGAT 59.717 52.381 0.00 0.00 33.27 3.24
389 483 1.283029 AGTGGGTCAATGGTGAGGATG 59.717 52.381 0.00 0.00 33.27 3.51
390 484 1.281867 GTGGGTCAATGGTGAGGATGA 59.718 52.381 0.00 0.00 33.27 2.92
391 485 1.991813 TGGGTCAATGGTGAGGATGAA 59.008 47.619 0.00 0.00 33.27 2.57
392 486 2.378208 TGGGTCAATGGTGAGGATGAAA 59.622 45.455 0.00 0.00 33.27 2.69
393 487 3.181424 TGGGTCAATGGTGAGGATGAAAA 60.181 43.478 0.00 0.00 33.27 2.29
394 488 3.445096 GGGTCAATGGTGAGGATGAAAAG 59.555 47.826 0.00 0.00 33.27 2.27
395 489 3.119352 GGTCAATGGTGAGGATGAAAAGC 60.119 47.826 0.00 0.00 33.27 3.51
396 490 3.507233 GTCAATGGTGAGGATGAAAAGCA 59.493 43.478 0.00 0.00 33.27 3.91
397 491 4.159135 GTCAATGGTGAGGATGAAAAGCAT 59.841 41.667 0.00 0.00 35.37 3.79
398 492 4.158949 TCAATGGTGAGGATGAAAAGCATG 59.841 41.667 0.00 0.00 37.34 4.06
399 493 2.449464 TGGTGAGGATGAAAAGCATGG 58.551 47.619 0.00 0.00 37.34 3.66
400 494 1.753073 GGTGAGGATGAAAAGCATGGG 59.247 52.381 0.00 0.00 37.34 4.00
401 495 2.450476 GTGAGGATGAAAAGCATGGGT 58.550 47.619 0.00 0.00 37.34 4.51
402 496 2.165030 GTGAGGATGAAAAGCATGGGTG 59.835 50.000 0.00 0.00 37.34 4.61
403 497 2.041485 TGAGGATGAAAAGCATGGGTGA 59.959 45.455 0.00 0.00 37.34 4.02
404 498 3.091545 GAGGATGAAAAGCATGGGTGAA 58.908 45.455 0.00 0.00 37.34 3.18
405 499 3.509442 AGGATGAAAAGCATGGGTGAAA 58.491 40.909 0.00 0.00 37.34 2.69
406 500 3.512724 AGGATGAAAAGCATGGGTGAAAG 59.487 43.478 0.00 0.00 37.34 2.62
407 501 2.818130 TGAAAAGCATGGGTGAAAGC 57.182 45.000 0.00 0.00 0.00 3.51
408 502 1.000385 TGAAAAGCATGGGTGAAAGCG 60.000 47.619 0.00 0.00 33.03 4.68
409 503 0.318120 AAAAGCATGGGTGAAAGCGG 59.682 50.000 0.00 0.00 33.03 5.52
410 504 1.535204 AAAGCATGGGTGAAAGCGGG 61.535 55.000 0.00 0.00 33.03 6.13
411 505 2.676471 GCATGGGTGAAAGCGGGT 60.676 61.111 0.00 0.00 33.03 5.28
412 506 2.700773 GCATGGGTGAAAGCGGGTC 61.701 63.158 0.00 0.00 33.03 4.46
413 507 2.046314 ATGGGTGAAAGCGGGTCG 60.046 61.111 0.00 0.00 33.03 4.79
414 508 2.589157 ATGGGTGAAAGCGGGTCGA 61.589 57.895 0.00 0.00 33.03 4.20
415 509 2.741211 GGGTGAAAGCGGGTCGAC 60.741 66.667 7.13 7.13 33.03 4.20
416 510 2.029964 GGTGAAAGCGGGTCGACA 59.970 61.111 18.91 0.00 0.00 4.35
417 511 1.375523 GGTGAAAGCGGGTCGACAT 60.376 57.895 18.91 0.00 0.00 3.06
418 512 1.635663 GGTGAAAGCGGGTCGACATG 61.636 60.000 18.91 9.93 0.00 3.21
419 513 0.669318 GTGAAAGCGGGTCGACATGA 60.669 55.000 18.91 0.00 0.00 3.07
428 522 3.704381 GTCGACATGACGAAGCTCT 57.296 52.632 21.19 0.00 43.75 4.09
429 523 1.540407 GTCGACATGACGAAGCTCTC 58.460 55.000 21.19 4.98 43.75 3.20
430 524 1.135660 GTCGACATGACGAAGCTCTCA 60.136 52.381 21.19 0.00 43.75 3.27
456 555 3.178611 GGGATGGGGGCGGAATCT 61.179 66.667 0.00 0.00 0.00 2.40
464 563 1.158484 GGGGCGGAATCTCGTTAAGC 61.158 60.000 0.00 0.00 0.00 3.09
510 611 3.815401 CAGGAACAAAGAAATCCAGTCGT 59.185 43.478 0.00 0.00 35.62 4.34
515 616 4.323417 ACAAAGAAATCCAGTCGTGCATA 58.677 39.130 0.00 0.00 0.00 3.14
566 667 1.072489 TCAAACAGGTACGCCCAATCA 59.928 47.619 0.00 0.00 34.66 2.57
613 714 3.070446 TCGAGCTTTAAGAAGTGGTTGGA 59.930 43.478 0.00 0.00 35.25 3.53
616 717 5.048713 CGAGCTTTAAGAAGTGGTTGGATTT 60.049 40.000 0.00 0.00 35.25 2.17
658 761 8.756864 GTTTCGATAAGATTCTAGACATGGAAC 58.243 37.037 0.00 0.00 0.00 3.62
675 778 9.071276 GACATGGAACATTATTGTATCTCCATT 57.929 33.333 15.22 9.84 43.65 3.16
677 780 7.822161 TGGAACATTATTGTATCTCCATTGG 57.178 36.000 0.00 0.00 36.03 3.16
678 781 7.581814 TGGAACATTATTGTATCTCCATTGGA 58.418 34.615 5.05 5.05 36.03 3.53
679 782 7.720957 TGGAACATTATTGTATCTCCATTGGAG 59.279 37.037 24.35 24.35 42.41 3.86
698 1352 4.123506 GGAGATTCTTCCTTTCATCGGTC 58.876 47.826 0.00 0.00 34.27 4.79
703 1357 2.093973 TCTTCCTTTCATCGGTCTGAGC 60.094 50.000 0.00 0.00 0.00 4.26
736 1390 2.476854 GCTAAGATGCAACTTTCGCCAG 60.477 50.000 14.90 6.79 0.00 4.85
743 1397 2.028112 TGCAACTTTCGCCAGTCTATCT 60.028 45.455 0.00 0.00 0.00 1.98
747 1401 5.592054 CAACTTTCGCCAGTCTATCTATCA 58.408 41.667 0.00 0.00 0.00 2.15
749 1403 6.412362 ACTTTCGCCAGTCTATCTATCAAT 57.588 37.500 0.00 0.00 0.00 2.57
775 1431 4.742274 ACAGCGTGTGAAGCGTTA 57.258 50.000 0.00 0.00 40.04 3.18
876 1532 3.253432 AGGGAATTCTTCGTTTCTTGCAC 59.747 43.478 5.23 0.00 0.00 4.57
912 1568 3.369147 CCAAAGCATCTCAAGACGTACTG 59.631 47.826 0.00 0.00 0.00 2.74
976 1634 2.513204 CCGCCTCTCGTCCTCGTA 60.513 66.667 0.00 0.00 38.33 3.43
1072 1733 2.685380 AGGAGGAGGCCGTGAAGG 60.685 66.667 0.00 0.00 44.97 3.46
1401 2062 1.814169 GTTCTTCGGCGTGGATCCC 60.814 63.158 9.90 0.00 0.00 3.85
1544 2218 3.665675 ATCACGGCGTCCAAGAGGC 62.666 63.158 10.85 0.76 41.88 4.70
1661 2338 1.818785 GTCATGAGCAGGCAGAGGC 60.819 63.158 0.00 0.00 40.13 4.70
1704 2381 4.202111 CCAAGGGAGCGAAAAGAAAAGAAA 60.202 41.667 0.00 0.00 0.00 2.52
1855 2534 1.098050 CAAGGGCCATTTCTCGAAGG 58.902 55.000 6.18 0.00 0.00 3.46
1919 2627 3.197333 GTCCCCTACCAGAAGAAAGGTAC 59.803 52.174 0.00 0.00 39.31 3.34
1924 2632 4.527038 CCTACCAGAAGAAAGGTACAGTCA 59.473 45.833 0.00 0.00 39.31 3.41
1925 2633 5.187967 CCTACCAGAAGAAAGGTACAGTCAT 59.812 44.000 0.00 0.00 39.31 3.06
1926 2634 5.153950 ACCAGAAGAAAGGTACAGTCATC 57.846 43.478 0.00 0.00 36.07 2.92
1927 2635 4.593206 ACCAGAAGAAAGGTACAGTCATCA 59.407 41.667 0.00 0.00 36.07 3.07
1928 2636 5.174395 CCAGAAGAAAGGTACAGTCATCAG 58.826 45.833 0.00 0.00 0.00 2.90
1929 2637 5.279708 CCAGAAGAAAGGTACAGTCATCAGT 60.280 44.000 0.00 0.00 0.00 3.41
1930 2638 5.866633 CAGAAGAAAGGTACAGTCATCAGTC 59.133 44.000 0.00 0.00 0.00 3.51
1931 2639 5.540337 AGAAGAAAGGTACAGTCATCAGTCA 59.460 40.000 0.00 0.00 0.00 3.41
1932 2640 6.212388 AGAAGAAAGGTACAGTCATCAGTCAT 59.788 38.462 0.00 0.00 0.00 3.06
1933 2641 5.728471 AGAAAGGTACAGTCATCAGTCATG 58.272 41.667 0.00 0.00 0.00 3.07
1934 2642 3.533606 AGGTACAGTCATCAGTCATGC 57.466 47.619 0.00 0.00 31.70 4.06
1935 2643 2.833943 AGGTACAGTCATCAGTCATGCA 59.166 45.455 0.00 0.00 31.70 3.96
1936 2644 3.261643 AGGTACAGTCATCAGTCATGCAA 59.738 43.478 0.00 0.00 31.70 4.08
1937 2645 4.002982 GGTACAGTCATCAGTCATGCAAA 58.997 43.478 0.00 0.00 31.70 3.68
1938 2646 4.455533 GGTACAGTCATCAGTCATGCAAAA 59.544 41.667 0.00 0.00 31.70 2.44
1939 2647 4.494350 ACAGTCATCAGTCATGCAAAAC 57.506 40.909 0.00 0.00 31.70 2.43
1940 2648 3.254166 ACAGTCATCAGTCATGCAAAACC 59.746 43.478 0.00 0.00 31.70 3.27
1941 2649 3.504906 CAGTCATCAGTCATGCAAAACCT 59.495 43.478 0.00 0.00 31.70 3.50
1942 2650 3.755378 AGTCATCAGTCATGCAAAACCTC 59.245 43.478 0.00 0.00 31.70 3.85
1943 2651 3.755378 GTCATCAGTCATGCAAAACCTCT 59.245 43.478 0.00 0.00 31.70 3.69
1944 2652 4.217118 GTCATCAGTCATGCAAAACCTCTT 59.783 41.667 0.00 0.00 31.70 2.85
1945 2653 4.456911 TCATCAGTCATGCAAAACCTCTTC 59.543 41.667 0.00 0.00 31.70 2.87
1946 2654 3.149196 TCAGTCATGCAAAACCTCTTCC 58.851 45.455 0.00 0.00 0.00 3.46
1947 2655 2.229784 CAGTCATGCAAAACCTCTTCCC 59.770 50.000 0.00 0.00 0.00 3.97
1948 2656 1.546029 GTCATGCAAAACCTCTTCCCC 59.454 52.381 0.00 0.00 0.00 4.81
1949 2657 1.428912 TCATGCAAAACCTCTTCCCCT 59.571 47.619 0.00 0.00 0.00 4.79
1950 2658 2.647299 TCATGCAAAACCTCTTCCCCTA 59.353 45.455 0.00 0.00 0.00 3.53
1951 2659 2.579410 TGCAAAACCTCTTCCCCTAC 57.421 50.000 0.00 0.00 0.00 3.18
1952 2660 1.074889 TGCAAAACCTCTTCCCCTACC 59.925 52.381 0.00 0.00 0.00 3.18
1953 2661 1.354705 GCAAAACCTCTTCCCCTACCT 59.645 52.381 0.00 0.00 0.00 3.08
1954 2662 2.618302 GCAAAACCTCTTCCCCTACCTC 60.618 54.545 0.00 0.00 0.00 3.85
1955 2663 2.642807 CAAAACCTCTTCCCCTACCTCA 59.357 50.000 0.00 0.00 0.00 3.86
1956 2664 2.735259 AACCTCTTCCCCTACCTCAA 57.265 50.000 0.00 0.00 0.00 3.02
1957 2665 2.255770 ACCTCTTCCCCTACCTCAAG 57.744 55.000 0.00 0.00 0.00 3.02
1958 2666 0.833949 CCTCTTCCCCTACCTCAAGC 59.166 60.000 0.00 0.00 0.00 4.01
1959 2667 0.833949 CTCTTCCCCTACCTCAAGCC 59.166 60.000 0.00 0.00 0.00 4.35
2001 2709 5.183713 CCCTGTCATGTCAATTGCTTTTCTA 59.816 40.000 0.00 0.00 0.00 2.10
2027 2735 7.531857 TCTTCAGACTAGAACAGAGTGAATT 57.468 36.000 0.00 0.00 32.63 2.17
2068 2776 2.603892 GCTGTAGCATTGATCATTGCCG 60.604 50.000 29.64 19.73 41.59 5.69
2276 2984 1.073216 CGATCACACGCGCTTCTCTT 61.073 55.000 5.73 0.00 0.00 2.85
2292 3000 5.615764 GCTTCTCTTCGAATTCAACTCCAAC 60.616 44.000 6.22 0.00 0.00 3.77
2300 3008 4.559251 CGAATTCAACTCCAACTCTCGTAG 59.441 45.833 6.22 0.00 0.00 3.51
2304 3012 5.060662 TCAACTCCAACTCTCGTAGAATG 57.939 43.478 0.00 0.00 34.09 2.67
2305 3013 4.765339 TCAACTCCAACTCTCGTAGAATGA 59.235 41.667 0.00 0.00 34.09 2.57
2309 3017 5.596361 ACTCCAACTCTCGTAGAATGATCAT 59.404 40.000 1.18 1.18 34.09 2.45
2591 3299 0.100682 CTCATCCGAGGGTACGTGTG 59.899 60.000 0.00 0.00 35.44 3.82
2640 3348 2.593148 ACAATGGTGACGCCGCAA 60.593 55.556 0.00 0.00 41.21 4.85
2650 3358 0.452784 GACGCCGCAAGTGTTTGATC 60.453 55.000 0.00 0.00 40.03 2.92
2657 3370 3.554524 CGCAAGTGTTTGATCGATGTTT 58.445 40.909 0.54 0.00 36.36 2.83
2663 3376 4.386049 AGTGTTTGATCGATGTTTCTCGTC 59.614 41.667 0.54 0.00 39.62 4.20
2668 3381 4.164252 GATGTTTCTCGTCGGCGT 57.836 55.556 10.18 0.00 39.49 5.68
2702 3415 3.818787 CTGGCAAGGATGTGGCGC 61.819 66.667 0.00 0.00 46.67 6.53
2738 3451 3.853330 CGGGTGATGAAGCGCACG 61.853 66.667 11.47 0.00 38.93 5.34
3239 3952 0.687427 TGGCCGAGATGGATGACAGA 60.687 55.000 0.00 0.00 42.00 3.41
3242 3955 1.410517 GCCGAGATGGATGACAGAGAA 59.589 52.381 0.00 0.00 42.00 2.87
3293 4006 0.958822 AGCCGTCCATCCAAAACAAC 59.041 50.000 0.00 0.00 0.00 3.32
3302 4015 2.431954 TCCAAAACAACCCACCGTAA 57.568 45.000 0.00 0.00 0.00 3.18
3356 4070 5.064707 GCACCGTGTGTAATCTGTAAATGAT 59.935 40.000 0.00 0.00 35.75 2.45
3357 4071 6.477742 CACCGTGTGTAATCTGTAAATGATG 58.522 40.000 0.00 0.00 0.00 3.07
3358 4072 6.312672 CACCGTGTGTAATCTGTAAATGATGA 59.687 38.462 0.00 0.00 0.00 2.92
3367 4081 6.851222 ATCTGTAAATGATGAAGCTTACCG 57.149 37.500 0.00 0.00 0.00 4.02
3369 4083 3.625764 TGTAAATGATGAAGCTTACCGCC 59.374 43.478 0.00 0.00 40.39 6.13
3402 4116 4.883083 TCACAGTTAACTGACATGGTCTC 58.117 43.478 36.14 0.00 46.59 3.36
3453 4176 5.324784 TCCATTACATAGCTATAGGCACG 57.675 43.478 5.77 0.00 44.79 5.34
3545 4268 6.096001 AGAGTTTTCATCAGCTCAAACACTTT 59.904 34.615 0.00 0.00 29.19 2.66
3547 4270 5.833406 TTTCATCAGCTCAAACACTTTGA 57.167 34.783 0.00 0.00 46.68 2.69
3569 4292 3.025619 CGTAGGTAGGTACGCGGG 58.974 66.667 12.47 0.00 39.40 6.13
3693 4420 2.493973 CTGTGCTCGAGGCTCTCC 59.506 66.667 15.58 1.04 42.39 3.71
4029 4756 2.038813 TCACCCCGGAGCTGATCA 59.961 61.111 0.73 0.00 0.00 2.92
4038 4765 0.035630 GGAGCTGATCAACCTGCAGT 60.036 55.000 13.81 0.00 34.07 4.40
4039 4766 1.367659 GAGCTGATCAACCTGCAGTC 58.632 55.000 13.81 3.48 34.07 3.51
4043 4770 1.002888 CTGATCAACCTGCAGTCCAGT 59.997 52.381 13.81 0.00 40.06 4.00
4046 4773 0.106708 TCAACCTGCAGTCCAGTCAC 59.893 55.000 13.81 0.00 40.06 3.67
4047 4774 0.886490 CAACCTGCAGTCCAGTCACC 60.886 60.000 13.81 0.00 40.06 4.02
4054 4781 0.886490 CAGTCCAGTCACCCACAAGC 60.886 60.000 0.00 0.00 0.00 4.01
4057 4784 1.075482 CCAGTCACCCACAAGCCAT 59.925 57.895 0.00 0.00 0.00 4.40
4107 4834 1.582937 CTAGTCAGTACGCACGCCG 60.583 63.158 0.00 0.00 44.21 6.46
4169 4896 1.596895 GCTTCCTCTTCCTCGACCGT 61.597 60.000 0.00 0.00 0.00 4.83
4172 4899 2.762234 CCTCTTCCTCGACCGTCGG 61.762 68.421 20.35 10.48 40.88 4.79
4226 4953 5.559148 AATTGGCAAACAAGGGTTTATGA 57.441 34.783 3.01 0.00 45.18 2.15
4249 4976 4.818534 TTGAGCAGTGAATGAAGAACAC 57.181 40.909 0.00 0.00 35.15 3.32
4283 5010 4.741321 AAGGCATAATGGTTCATGGTTG 57.259 40.909 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.537143 ATCGGCAAGTTTGGTGCTCA 60.537 50.000 0.00 0.00 41.88 4.26
13 14 2.154462 CAACCTCTCATCGGCAAGTTT 58.846 47.619 0.00 0.00 0.00 2.66
19 20 1.064654 GAATTGCAACCTCTCATCGGC 59.935 52.381 0.00 0.00 0.00 5.54
20 21 1.672881 GGAATTGCAACCTCTCATCGG 59.327 52.381 0.00 0.00 0.00 4.18
22 23 2.424956 GGTGGAATTGCAACCTCTCATC 59.575 50.000 3.13 0.00 0.00 2.92
28 29 1.632589 GGAAGGTGGAATTGCAACCT 58.367 50.000 11.83 12.49 46.40 3.50
98 101 3.300388 TCGATCTTCCCAGCTAAGATGT 58.700 45.455 13.70 0.00 42.38 3.06
118 121 1.107945 GACCTAGCTGACACCCTCTC 58.892 60.000 0.00 0.00 0.00 3.20
194 197 1.454201 TGTTTTCGCCGATGCCATTA 58.546 45.000 0.00 0.00 0.00 1.90
196 199 0.381801 GATGTTTTCGCCGATGCCAT 59.618 50.000 0.00 0.00 0.00 4.40
269 272 3.818210 CTCCTCTGTACGTAGATGATGCT 59.182 47.826 0.00 0.00 0.00 3.79
284 288 6.463995 AATGCTAGACTAAGAACTCCTCTG 57.536 41.667 0.00 0.00 33.37 3.35
337 431 5.643348 CAGATACACAACATGGCTACAGAAA 59.357 40.000 0.00 0.00 0.00 2.52
338 432 5.178061 CAGATACACAACATGGCTACAGAA 58.822 41.667 0.00 0.00 0.00 3.02
339 433 4.222810 ACAGATACACAACATGGCTACAGA 59.777 41.667 0.00 0.00 0.00 3.41
340 434 4.507710 ACAGATACACAACATGGCTACAG 58.492 43.478 0.00 0.00 0.00 2.74
341 435 4.551702 ACAGATACACAACATGGCTACA 57.448 40.909 0.00 0.00 0.00 2.74
342 436 4.437390 GCAACAGATACACAACATGGCTAC 60.437 45.833 0.00 0.00 0.00 3.58
343 437 3.689161 GCAACAGATACACAACATGGCTA 59.311 43.478 0.00 0.00 0.00 3.93
344 438 2.489329 GCAACAGATACACAACATGGCT 59.511 45.455 0.00 0.00 0.00 4.75
345 439 2.228582 TGCAACAGATACACAACATGGC 59.771 45.455 0.00 0.00 0.00 4.40
346 440 3.671433 GCTGCAACAGATACACAACATGG 60.671 47.826 0.00 0.00 32.44 3.66
347 441 3.058085 TGCTGCAACAGATACACAACATG 60.058 43.478 0.00 0.00 32.44 3.21
348 442 3.148412 TGCTGCAACAGATACACAACAT 58.852 40.909 0.00 0.00 32.44 2.71
349 443 2.549329 CTGCTGCAACAGATACACAACA 59.451 45.455 11.82 0.00 40.25 3.33
350 444 2.549754 ACTGCTGCAACAGATACACAAC 59.450 45.455 23.44 0.00 40.25 3.32
351 445 2.549329 CACTGCTGCAACAGATACACAA 59.451 45.455 23.44 0.00 40.25 3.33
352 446 2.145536 CACTGCTGCAACAGATACACA 58.854 47.619 23.44 0.00 40.25 3.72
353 447 1.466167 CCACTGCTGCAACAGATACAC 59.534 52.381 23.44 0.00 40.25 2.90
354 448 1.611410 CCCACTGCTGCAACAGATACA 60.611 52.381 23.44 0.00 40.25 2.29
355 449 1.089920 CCCACTGCTGCAACAGATAC 58.910 55.000 23.44 0.00 40.25 2.24
356 450 0.692476 ACCCACTGCTGCAACAGATA 59.308 50.000 23.44 0.00 40.25 1.98
357 451 0.607489 GACCCACTGCTGCAACAGAT 60.607 55.000 23.44 5.34 40.25 2.90
358 452 1.227943 GACCCACTGCTGCAACAGA 60.228 57.895 23.44 0.00 40.25 3.41
359 453 1.102809 TTGACCCACTGCTGCAACAG 61.103 55.000 15.51 15.51 43.59 3.16
360 454 0.467844 ATTGACCCACTGCTGCAACA 60.468 50.000 3.02 0.00 0.00 3.33
361 455 0.038892 CATTGACCCACTGCTGCAAC 60.039 55.000 3.02 0.00 0.00 4.17
362 456 1.180456 CCATTGACCCACTGCTGCAA 61.180 55.000 3.02 0.00 0.00 4.08
363 457 1.604308 CCATTGACCCACTGCTGCA 60.604 57.895 0.88 0.88 0.00 4.41
364 458 1.604593 ACCATTGACCCACTGCTGC 60.605 57.895 0.00 0.00 0.00 5.25
365 459 0.250858 TCACCATTGACCCACTGCTG 60.251 55.000 0.00 0.00 0.00 4.41
366 460 0.037303 CTCACCATTGACCCACTGCT 59.963 55.000 0.00 0.00 0.00 4.24
367 461 0.962356 CCTCACCATTGACCCACTGC 60.962 60.000 0.00 0.00 0.00 4.40
368 462 0.692476 TCCTCACCATTGACCCACTG 59.308 55.000 0.00 0.00 0.00 3.66
369 463 1.283029 CATCCTCACCATTGACCCACT 59.717 52.381 0.00 0.00 0.00 4.00
370 464 1.281867 TCATCCTCACCATTGACCCAC 59.718 52.381 0.00 0.00 0.00 4.61
371 465 1.667595 TCATCCTCACCATTGACCCA 58.332 50.000 0.00 0.00 0.00 4.51
372 466 2.806945 TTCATCCTCACCATTGACCC 57.193 50.000 0.00 0.00 0.00 4.46
373 467 3.119352 GCTTTTCATCCTCACCATTGACC 60.119 47.826 0.00 0.00 0.00 4.02
374 468 3.507233 TGCTTTTCATCCTCACCATTGAC 59.493 43.478 0.00 0.00 0.00 3.18
375 469 3.765381 TGCTTTTCATCCTCACCATTGA 58.235 40.909 0.00 0.00 0.00 2.57
376 470 4.430007 CATGCTTTTCATCCTCACCATTG 58.570 43.478 0.00 0.00 31.79 2.82
377 471 3.449737 CCATGCTTTTCATCCTCACCATT 59.550 43.478 0.00 0.00 31.79 3.16
378 472 3.028850 CCATGCTTTTCATCCTCACCAT 58.971 45.455 0.00 0.00 31.79 3.55
379 473 2.449464 CCATGCTTTTCATCCTCACCA 58.551 47.619 0.00 0.00 31.79 4.17
380 474 1.753073 CCCATGCTTTTCATCCTCACC 59.247 52.381 0.00 0.00 31.79 4.02
381 475 2.165030 CACCCATGCTTTTCATCCTCAC 59.835 50.000 0.00 0.00 31.79 3.51
382 476 2.041485 TCACCCATGCTTTTCATCCTCA 59.959 45.455 0.00 0.00 31.79 3.86
383 477 2.726821 TCACCCATGCTTTTCATCCTC 58.273 47.619 0.00 0.00 31.79 3.71
384 478 2.905415 TCACCCATGCTTTTCATCCT 57.095 45.000 0.00 0.00 31.79 3.24
385 479 3.853475 CTTTCACCCATGCTTTTCATCC 58.147 45.455 0.00 0.00 31.79 3.51
386 480 3.256558 GCTTTCACCCATGCTTTTCATC 58.743 45.455 0.00 0.00 31.79 2.92
387 481 2.353011 CGCTTTCACCCATGCTTTTCAT 60.353 45.455 0.00 0.00 35.31 2.57
388 482 1.000385 CGCTTTCACCCATGCTTTTCA 60.000 47.619 0.00 0.00 0.00 2.69
389 483 1.669795 CCGCTTTCACCCATGCTTTTC 60.670 52.381 0.00 0.00 0.00 2.29
390 484 0.318120 CCGCTTTCACCCATGCTTTT 59.682 50.000 0.00 0.00 0.00 2.27
391 485 1.535204 CCCGCTTTCACCCATGCTTT 61.535 55.000 0.00 0.00 0.00 3.51
392 486 1.978617 CCCGCTTTCACCCATGCTT 60.979 57.895 0.00 0.00 0.00 3.91
393 487 2.361610 CCCGCTTTCACCCATGCT 60.362 61.111 0.00 0.00 0.00 3.79
394 488 2.676471 ACCCGCTTTCACCCATGC 60.676 61.111 0.00 0.00 0.00 4.06
395 489 2.398554 CGACCCGCTTTCACCCATG 61.399 63.158 0.00 0.00 0.00 3.66
396 490 2.046314 CGACCCGCTTTCACCCAT 60.046 61.111 0.00 0.00 0.00 4.00
397 491 3.235481 TCGACCCGCTTTCACCCA 61.235 61.111 0.00 0.00 0.00 4.51
398 492 2.741211 GTCGACCCGCTTTCACCC 60.741 66.667 3.51 0.00 0.00 4.61
399 493 1.375523 ATGTCGACCCGCTTTCACC 60.376 57.895 14.12 0.00 0.00 4.02
400 494 0.669318 TCATGTCGACCCGCTTTCAC 60.669 55.000 14.12 0.00 0.00 3.18
401 495 0.669318 GTCATGTCGACCCGCTTTCA 60.669 55.000 14.12 0.00 38.85 2.69
402 496 1.683790 CGTCATGTCGACCCGCTTTC 61.684 60.000 14.12 0.00 42.07 2.62
403 497 1.736645 CGTCATGTCGACCCGCTTT 60.737 57.895 14.12 0.00 42.07 3.51
404 498 2.126071 CGTCATGTCGACCCGCTT 60.126 61.111 14.12 0.00 42.07 4.68
405 499 2.543687 CTTCGTCATGTCGACCCGCT 62.544 60.000 14.56 0.00 42.07 5.52
406 500 2.126228 TTCGTCATGTCGACCCGC 60.126 61.111 14.56 0.00 42.07 6.13
407 501 2.158959 GCTTCGTCATGTCGACCCG 61.159 63.158 14.56 10.13 42.07 5.28
408 502 0.802607 GAGCTTCGTCATGTCGACCC 60.803 60.000 14.56 8.60 42.07 4.46
409 503 0.171455 AGAGCTTCGTCATGTCGACC 59.829 55.000 14.56 8.93 42.07 4.79
410 504 1.135660 TGAGAGCTTCGTCATGTCGAC 60.136 52.381 14.56 9.11 39.58 4.20
411 505 1.165270 TGAGAGCTTCGTCATGTCGA 58.835 50.000 11.02 11.02 38.08 4.20
412 506 1.916651 CTTGAGAGCTTCGTCATGTCG 59.083 52.381 5.98 5.98 0.00 4.35
413 507 1.658095 GCTTGAGAGCTTCGTCATGTC 59.342 52.381 0.00 0.00 45.65 3.06
414 508 1.719600 GCTTGAGAGCTTCGTCATGT 58.280 50.000 0.00 0.00 45.65 3.21
425 519 1.676746 CATCCCACCATGCTTGAGAG 58.323 55.000 0.22 0.00 0.00 3.20
426 520 0.256752 CCATCCCACCATGCTTGAGA 59.743 55.000 0.22 0.00 0.00 3.27
427 521 0.754217 CCCATCCCACCATGCTTGAG 60.754 60.000 0.22 0.00 0.00 3.02
428 522 1.307309 CCCATCCCACCATGCTTGA 59.693 57.895 0.22 0.00 0.00 3.02
429 523 1.759299 CCCCATCCCACCATGCTTG 60.759 63.158 0.00 0.00 0.00 4.01
430 524 2.691732 CCCCATCCCACCATGCTT 59.308 61.111 0.00 0.00 0.00 3.91
464 563 4.215399 TCATCCTTGACCTTTAGCGTTTTG 59.785 41.667 0.00 0.00 0.00 2.44
510 611 1.830477 GGGTTTTGGCCAGAATATGCA 59.170 47.619 12.49 0.00 0.00 3.96
515 616 1.928868 CTCTGGGTTTTGGCCAGAAT 58.071 50.000 12.49 0.00 39.61 2.40
566 667 2.526432 TCTAAGGCCTTCGACTCAGTT 58.474 47.619 24.49 0.00 0.00 3.16
633 734 8.474831 TGTTCCATGTCTAGAATCTTATCGAAA 58.525 33.333 0.00 0.00 0.00 3.46
636 737 8.824159 AATGTTCCATGTCTAGAATCTTATCG 57.176 34.615 0.00 0.00 0.00 2.92
671 774 5.008415 CGATGAAAGGAAGAATCTCCAATGG 59.992 44.000 0.00 0.00 38.02 3.16
675 778 3.519510 ACCGATGAAAGGAAGAATCTCCA 59.480 43.478 0.00 0.00 38.02 3.86
677 780 4.808364 CAGACCGATGAAAGGAAGAATCTC 59.192 45.833 0.00 0.00 0.00 2.75
678 781 4.467795 TCAGACCGATGAAAGGAAGAATCT 59.532 41.667 0.00 0.00 0.00 2.40
679 782 4.759782 TCAGACCGATGAAAGGAAGAATC 58.240 43.478 0.00 0.00 0.00 2.52
680 783 4.764172 CTCAGACCGATGAAAGGAAGAAT 58.236 43.478 0.00 0.00 0.00 2.40
698 1352 1.174783 AGCATTGCTTCTTGGCTCAG 58.825 50.000 5.03 0.00 33.89 3.35
703 1357 3.129813 TGCATCTTAGCATTGCTTCTTGG 59.870 43.478 17.71 5.78 40.11 3.61
736 1390 8.707839 GCTGTGCTTCTTTATTGATAGATAGAC 58.292 37.037 0.00 0.00 0.00 2.59
743 1397 4.935205 ACACGCTGTGCTTCTTTATTGATA 59.065 37.500 8.31 0.00 36.98 2.15
747 1401 3.542712 CACACGCTGTGCTTCTTTATT 57.457 42.857 8.31 0.00 41.89 1.40
773 1429 2.734606 CGCTGACAAGAAATGGTCGTAA 59.265 45.455 0.00 0.00 36.83 3.18
775 1431 1.148310 CGCTGACAAGAAATGGTCGT 58.852 50.000 0.00 0.00 36.83 4.34
876 1532 0.030638 CTTTGGTTGCGTTGGGTCTG 59.969 55.000 0.00 0.00 0.00 3.51
912 1568 4.715527 ACGTGTTCTTGTAGTAGGGATC 57.284 45.455 0.00 0.00 0.00 3.36
1380 2041 3.659089 ATCCACGCCGAAGAACCCG 62.659 63.158 0.00 0.00 0.00 5.28
1544 2218 3.875727 ACCATCTTCTTGATCAGCATTCG 59.124 43.478 0.00 0.00 32.05 3.34
1661 2338 2.434884 CCACTACCACCTGCGCTG 60.435 66.667 9.73 8.47 0.00 5.18
1704 2381 2.113139 CTCACACCCGCCACCTTT 59.887 61.111 0.00 0.00 0.00 3.11
1785 2464 2.604174 CGGCCTGTCGACAAACACC 61.604 63.158 20.49 16.12 0.00 4.16
1919 2627 3.504906 AGGTTTTGCATGACTGATGACTG 59.495 43.478 0.00 0.00 33.31 3.51
1924 2632 3.760684 GGAAGAGGTTTTGCATGACTGAT 59.239 43.478 0.00 0.00 0.00 2.90
1925 2633 3.149196 GGAAGAGGTTTTGCATGACTGA 58.851 45.455 0.00 0.00 0.00 3.41
1926 2634 2.229784 GGGAAGAGGTTTTGCATGACTG 59.770 50.000 0.00 0.00 0.00 3.51
1927 2635 2.519013 GGGAAGAGGTTTTGCATGACT 58.481 47.619 0.00 0.00 0.00 3.41
1928 2636 1.546029 GGGGAAGAGGTTTTGCATGAC 59.454 52.381 0.00 0.00 0.00 3.06
1929 2637 1.428912 AGGGGAAGAGGTTTTGCATGA 59.571 47.619 0.00 0.00 0.00 3.07
1930 2638 1.928868 AGGGGAAGAGGTTTTGCATG 58.071 50.000 0.00 0.00 0.00 4.06
1931 2639 2.291605 GGTAGGGGAAGAGGTTTTGCAT 60.292 50.000 0.00 0.00 0.00 3.96
1932 2640 1.074889 GGTAGGGGAAGAGGTTTTGCA 59.925 52.381 0.00 0.00 0.00 4.08
1933 2641 1.354705 AGGTAGGGGAAGAGGTTTTGC 59.645 52.381 0.00 0.00 0.00 3.68
1934 2642 2.642807 TGAGGTAGGGGAAGAGGTTTTG 59.357 50.000 0.00 0.00 0.00 2.44
1935 2643 2.999928 TGAGGTAGGGGAAGAGGTTTT 58.000 47.619 0.00 0.00 0.00 2.43
1936 2644 2.735259 TGAGGTAGGGGAAGAGGTTT 57.265 50.000 0.00 0.00 0.00 3.27
1937 2645 2.552367 CTTGAGGTAGGGGAAGAGGTT 58.448 52.381 0.00 0.00 0.00 3.50
1938 2646 1.902141 GCTTGAGGTAGGGGAAGAGGT 60.902 57.143 0.00 0.00 0.00 3.85
1939 2647 0.833949 GCTTGAGGTAGGGGAAGAGG 59.166 60.000 0.00 0.00 0.00 3.69
1940 2648 0.833949 GGCTTGAGGTAGGGGAAGAG 59.166 60.000 0.00 0.00 0.00 2.85
1941 2649 0.417841 AGGCTTGAGGTAGGGGAAGA 59.582 55.000 0.00 0.00 0.00 2.87
1942 2650 0.543749 CAGGCTTGAGGTAGGGGAAG 59.456 60.000 0.00 0.00 0.00 3.46
1943 2651 0.118346 TCAGGCTTGAGGTAGGGGAA 59.882 55.000 0.00 0.00 0.00 3.97
1944 2652 0.118346 TTCAGGCTTGAGGTAGGGGA 59.882 55.000 0.00 0.00 34.15 4.81
1945 2653 0.253327 GTTCAGGCTTGAGGTAGGGG 59.747 60.000 0.00 0.00 34.15 4.79
1946 2654 1.280457 AGTTCAGGCTTGAGGTAGGG 58.720 55.000 0.00 0.00 34.15 3.53
1947 2655 2.569404 AGAAGTTCAGGCTTGAGGTAGG 59.431 50.000 5.50 0.00 34.15 3.18
1948 2656 3.259374 TCAGAAGTTCAGGCTTGAGGTAG 59.741 47.826 5.50 0.00 34.15 3.18
1949 2657 3.239449 TCAGAAGTTCAGGCTTGAGGTA 58.761 45.455 5.50 0.00 34.15 3.08
1950 2658 2.050144 TCAGAAGTTCAGGCTTGAGGT 58.950 47.619 5.50 0.00 34.15 3.85
1951 2659 2.847327 TCAGAAGTTCAGGCTTGAGG 57.153 50.000 5.50 0.00 34.15 3.86
1952 2660 6.998968 ATAATTCAGAAGTTCAGGCTTGAG 57.001 37.500 5.50 0.00 34.15 3.02
1953 2661 6.823689 GGTATAATTCAGAAGTTCAGGCTTGA 59.176 38.462 5.50 0.00 0.00 3.02
1954 2662 6.038714 GGGTATAATTCAGAAGTTCAGGCTTG 59.961 42.308 5.50 0.00 0.00 4.01
1955 2663 6.069381 AGGGTATAATTCAGAAGTTCAGGCTT 60.069 38.462 5.50 0.00 0.00 4.35
1956 2664 5.430089 AGGGTATAATTCAGAAGTTCAGGCT 59.570 40.000 5.50 0.00 0.00 4.58
1957 2665 5.529060 CAGGGTATAATTCAGAAGTTCAGGC 59.471 44.000 5.50 0.00 0.00 4.85
1958 2666 6.653989 ACAGGGTATAATTCAGAAGTTCAGG 58.346 40.000 5.50 0.00 0.00 3.86
1959 2667 7.331026 TGACAGGGTATAATTCAGAAGTTCAG 58.669 38.462 5.50 0.00 0.00 3.02
2001 2709 7.531857 TTCACTCTGTTCTAGTCTGAAGAAT 57.468 36.000 0.00 0.00 35.53 2.40
2027 2735 5.163269 ACAGCTCTATGGCATGTTCTGAATA 60.163 40.000 10.98 0.00 34.17 1.75
2068 2776 5.094134 GGTCGAACTGTCTATGTACAAGAC 58.906 45.833 21.48 21.48 43.04 3.01
2276 2984 3.005472 ACGAGAGTTGGAGTTGAATTCGA 59.995 43.478 0.04 0.00 46.40 3.71
2292 3000 8.563732 TCTGAACTTATGATCATTCTACGAGAG 58.436 37.037 14.65 1.81 0.00 3.20
2300 3008 7.856145 ACTGGTTCTGAACTTATGATCATTC 57.144 36.000 14.65 6.67 0.00 2.67
2304 3012 7.556844 TCCTAACTGGTTCTGAACTTATGATC 58.443 38.462 19.05 2.60 37.07 2.92
2305 3013 7.496346 TCCTAACTGGTTCTGAACTTATGAT 57.504 36.000 19.05 5.26 37.07 2.45
2309 3017 6.928348 TCATCCTAACTGGTTCTGAACTTA 57.072 37.500 19.05 9.77 37.07 2.24
2442 3150 2.503382 GGCCCTGGTCCTCTCGATC 61.503 68.421 0.00 0.00 0.00 3.69
2568 3276 1.655329 GTACCCTCGGATGAGCTCG 59.345 63.158 9.64 0.00 41.13 5.03
2591 3299 3.421826 CGATCGAGCACGCCATAATAAAC 60.422 47.826 10.26 0.00 39.58 2.01
2621 3329 3.799755 GCGGCGTCACCATTGTCC 61.800 66.667 9.37 0.00 39.03 4.02
2640 3348 4.307432 ACGAGAAACATCGATCAAACACT 58.693 39.130 0.00 0.00 45.56 3.55
2664 3377 4.077188 GAACAGCACAGCGACGCC 62.077 66.667 17.79 0.15 0.00 5.68
2665 3378 3.287121 CTGAACAGCACAGCGACGC 62.287 63.158 13.03 13.03 0.00 5.19
2666 3379 2.661566 CCTGAACAGCACAGCGACG 61.662 63.158 0.00 0.00 34.47 5.12
2667 3380 2.959357 GCCTGAACAGCACAGCGAC 61.959 63.158 0.00 0.00 34.47 5.19
2668 3381 2.666190 GCCTGAACAGCACAGCGA 60.666 61.111 0.00 0.00 34.47 4.93
3239 3952 1.021390 CCATTTCTGCCTCGCGTTCT 61.021 55.000 5.77 0.00 0.00 3.01
3242 3955 3.127533 GCCATTTCTGCCTCGCGT 61.128 61.111 5.77 0.00 0.00 6.01
3293 4006 3.337694 TCATTTACAGGTTACGGTGGG 57.662 47.619 0.00 0.00 0.00 4.61
3302 4015 2.099405 CCCGCCATTTCATTTACAGGT 58.901 47.619 0.00 0.00 0.00 4.00
3367 4081 0.244994 ACTGTGATCTGTCAGTCGGC 59.755 55.000 11.07 0.00 40.28 5.54
3369 4083 4.618912 CAGTTAACTGTGATCTGTCAGTCG 59.381 45.833 24.70 0.00 42.95 4.18
3402 4116 6.127168 TTCTACCCAGAGTACATGTAATGGTG 60.127 42.308 22.22 17.76 39.58 4.17
3453 4176 4.286101 GGTAATAACTCTACGTCTTCGCC 58.714 47.826 0.00 0.00 41.18 5.54
3463 4186 3.001634 CGCGTCAGTCGGTAATAACTCTA 59.998 47.826 0.00 0.00 40.26 2.43
3545 4268 2.872245 GCGTACCTACCTACGTACATCA 59.128 50.000 0.00 0.00 41.34 3.07
3547 4270 1.867233 CGCGTACCTACCTACGTACAT 59.133 52.381 0.00 0.00 41.34 2.29
3548 4271 1.286501 CGCGTACCTACCTACGTACA 58.713 55.000 0.00 0.00 41.34 2.90
3549 4272 0.582005 CCGCGTACCTACCTACGTAC 59.418 60.000 4.92 0.00 41.34 3.67
3550 4273 0.531974 CCCGCGTACCTACCTACGTA 60.532 60.000 4.92 0.00 41.34 3.57
3553 4276 2.068277 CTGCCCGCGTACCTACCTAC 62.068 65.000 4.92 0.00 0.00 3.18
3569 4292 4.101448 ATGCACGTCCCTCCCTGC 62.101 66.667 0.00 0.00 0.00 4.85
3578 4301 0.110056 CAAGTGAAGCCATGCACGTC 60.110 55.000 0.00 0.00 39.88 4.34
3693 4420 2.829003 CAGAGCATGGCCAGCCTG 60.829 66.667 13.05 18.02 36.94 4.85
4029 4756 1.451936 GGTGACTGGACTGCAGGTT 59.548 57.895 19.93 0.00 0.00 3.50
4038 4765 1.426251 ATGGCTTGTGGGTGACTGGA 61.426 55.000 0.00 0.00 0.00 3.86
4039 4766 0.327924 TATGGCTTGTGGGTGACTGG 59.672 55.000 0.00 0.00 0.00 4.00
4043 4770 3.088532 GTTCATTATGGCTTGTGGGTGA 58.911 45.455 0.00 0.00 0.00 4.02
4046 4773 3.355378 TGAGTTCATTATGGCTTGTGGG 58.645 45.455 0.00 0.00 0.00 4.61
4047 4774 4.460382 AGTTGAGTTCATTATGGCTTGTGG 59.540 41.667 0.00 0.00 0.00 4.17
4054 4781 6.430925 TCAAGGTTCAGTTGAGTTCATTATGG 59.569 38.462 0.00 0.00 30.36 2.74
4057 4784 7.873719 TTTCAAGGTTCAGTTGAGTTCATTA 57.126 32.000 0.00 0.00 35.39 1.90
4107 4834 2.885894 AGACGCAGGTAAGATAGGCTAC 59.114 50.000 0.00 0.00 0.00 3.58
4111 4838 2.294791 CTGGAGACGCAGGTAAGATAGG 59.705 54.545 0.00 0.00 0.00 2.57
4112 4839 2.287909 GCTGGAGACGCAGGTAAGATAG 60.288 54.545 0.00 0.00 0.00 2.08
4115 4842 0.612174 AGCTGGAGACGCAGGTAAGA 60.612 55.000 0.00 0.00 33.30 2.10
4226 4953 5.300034 TGTGTTCTTCATTCACTGCTCAAAT 59.700 36.000 0.00 0.00 33.82 2.32
4261 4988 4.531732 ACAACCATGAACCATTATGCCTTT 59.468 37.500 0.00 0.00 0.00 3.11
4262 4989 4.095946 ACAACCATGAACCATTATGCCTT 58.904 39.130 0.00 0.00 0.00 4.35
4263 4990 3.711863 ACAACCATGAACCATTATGCCT 58.288 40.909 0.00 0.00 0.00 4.75
4269 4996 5.047377 GGTACATCAACAACCATGAACCATT 60.047 40.000 0.00 0.00 33.28 3.16
4274 5001 3.745799 ACGGTACATCAACAACCATGAA 58.254 40.909 0.00 0.00 32.55 2.57
4277 5004 3.007506 TGAGACGGTACATCAACAACCAT 59.992 43.478 0.00 0.00 32.55 3.55
4280 5007 3.617263 GGATGAGACGGTACATCAACAAC 59.383 47.826 20.95 7.29 32.44 3.32


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

AutoCloner maintained by Alex Coulton.