Multiple sequence alignment - TraesCS7B01G216400

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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 TraesCS7B01G216400 chr7B 100.000 2309 0 0 1 2309 399259369 399261677 0.000000e+00 4265.0
1 TraesCS7B01G216400 chr7B 81.221 213 32 7 1061 1267 396044738 396044948 5.100000e-37 165.0
2 TraesCS7B01G216400 chr7B 90.698 86 7 1 1737 1822 702879295 702879211 1.870000e-21 113.0
3 TraesCS7B01G216400 chr7D 95.868 847 28 3 614 1453 396125254 396126100 0.000000e+00 1363.0
4 TraesCS7B01G216400 chr7D 92.348 379 19 6 2 373 396124668 396125043 4.370000e-147 531.0
5 TraesCS7B01G216400 chr7D 90.535 243 21 2 1450 1691 396126202 396126443 1.030000e-83 320.0
6 TraesCS7B01G216400 chr7D 86.182 275 29 8 2038 2309 396126858 396127126 2.900000e-74 289.0
7 TraesCS7B01G216400 chr7D 92.105 114 9 0 1814 1927 396126631 396126744 6.600000e-36 161.0
8 TraesCS7B01G216400 chr7D 77.941 272 41 13 1001 1267 396113405 396113662 3.970000e-33 152.0
9 TraesCS7B01G216400 chr7A 94.731 873 39 6 605 1476 449703931 449704797 0.000000e+00 1351.0
10 TraesCS7B01G216400 chr7A 94.408 304 13 3 1 303 449703626 449703926 4.490000e-127 464.0
11 TraesCS7B01G216400 chr7A 79.717 212 35 8 1061 1266 449641201 449641410 1.850000e-31 147.0
12 TraesCS7B01G216400 chr7A 93.506 77 4 1 1737 1813 135517726 135517801 1.870000e-21 113.0
13 TraesCS7B01G216400 chr3B 94.805 77 3 1 1737 1813 227028715 227028640 4.030000e-23 119.0
14 TraesCS7B01G216400 chr1D 94.805 77 3 1 1737 1813 6523333 6523408 4.030000e-23 119.0
15 TraesCS7B01G216400 chr1D 92.208 77 5 1 1737 1813 335345705 335345630 8.720000e-20 108.0
16 TraesCS7B01G216400 chr4D 93.506 77 4 1 1737 1813 501663676 501663751 1.870000e-21 113.0
17 TraesCS7B01G216400 chr4D 90.588 85 7 1 1731 1815 448165023 448165106 6.740000e-21 111.0
18 TraesCS7B01G216400 chr6B 92.308 78 5 1 1737 1814 3697093 3697017 2.430000e-20 110.0
19 TraesCS7B01G216400 chr6D 85.714 98 8 5 1737 1829 399654280 399654184 5.250000e-17 99.0
20 TraesCS7B01G216400 chrUn 90.000 70 4 3 480 546 300922152 300922083 1.140000e-13 87.9
21 TraesCS7B01G216400 chr2B 90.000 70 4 3 480 546 81551030 81550961 1.140000e-13 87.9
22 TraesCS7B01G216400 chr2B 91.803 61 4 1 487 546 797992259 797992199 1.470000e-12 84.2


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 TraesCS7B01G216400 chr7B 399259369 399261677 2308 False 4265.0 4265 100.0000 1 2309 1 chr7B.!!$F2 2308
1 TraesCS7B01G216400 chr7D 396124668 396127126 2458 False 532.8 1363 91.4076 2 2309 5 chr7D.!!$F2 2307
2 TraesCS7B01G216400 chr7A 449703626 449704797 1171 False 907.5 1351 94.5695 1 1476 2 chr7A.!!$F3 1475


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
313 321 0.098728 GTCGGGATGGCGATGTTTTG 59.901 55.0 0.0 0.0 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2381 0.035439 CGCACCTAACAATGGGAGGT 60.035 55.0 2.89 2.89 44.65 3.85 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
192 199 1.568612 ATTGTCCAGTTGTCGCTGCG 61.569 55.000 17.25 17.25 35.28 5.18
226 233 1.165907 CCGTGCAAGTTGGAGCAAGA 61.166 55.000 4.75 0.00 43.20 3.02
271 279 0.108329 CGACAGCCACCGGTTCTTAT 60.108 55.000 2.97 0.00 0.00 1.73
272 280 1.135527 CGACAGCCACCGGTTCTTATA 59.864 52.381 2.97 0.00 0.00 0.98
298 306 1.597663 GAAACGGGCTATTCATGTCGG 59.402 52.381 0.00 0.00 0.00 4.79
313 321 0.098728 GTCGGGATGGCGATGTTTTG 59.901 55.000 0.00 0.00 0.00 2.44
328 336 5.718649 ATGTTTTGTTCATCGGATAGACG 57.281 39.130 0.00 0.00 0.00 4.18
340 348 3.616821 TCGGATAGACGTTCAGCAAATTG 59.383 43.478 0.00 0.00 34.94 2.32
346 354 1.344114 ACGTTCAGCAAATTGCCCAAT 59.656 42.857 15.04 0.00 46.52 3.16
356 364 5.591067 AGCAAATTGCCCAATAATGAAATGG 59.409 36.000 15.04 0.00 46.52 3.16
357 365 5.357596 GCAAATTGCCCAATAATGAAATGGT 59.642 36.000 6.72 0.00 37.42 3.55
363 371 7.053316 TGCCCAATAATGAAATGGTCTATTG 57.947 36.000 0.00 0.00 32.13 1.90
369 377 9.752961 CAATAATGAAATGGTCTATTGCATCAA 57.247 29.630 3.00 0.00 43.02 2.57
386 416 7.712264 TGCATCAAAAACTACATTGAAAAGG 57.288 32.000 0.00 0.00 38.88 3.11
387 417 7.271511 TGCATCAAAAACTACATTGAAAAGGT 58.728 30.769 0.00 0.00 45.91 3.50
388 418 7.768120 TGCATCAAAAACTACATTGAAAAGGTT 59.232 29.630 0.00 0.00 37.74 3.50
389 419 9.255304 GCATCAAAAACTACATTGAAAAGGTTA 57.745 29.630 0.00 0.00 37.74 2.85
408 438 8.747538 AAGGTTACTTTTAGTTCACTGATTGT 57.252 30.769 0.00 0.00 31.39 2.71
409 439 8.747538 AGGTTACTTTTAGTTCACTGATTGTT 57.252 30.769 0.00 0.00 0.00 2.83
410 440 9.185680 AGGTTACTTTTAGTTCACTGATTGTTT 57.814 29.630 0.00 0.00 0.00 2.83
414 444 8.514330 ACTTTTAGTTCACTGATTGTTTACCA 57.486 30.769 0.00 0.00 0.00 3.25
415 445 9.131791 ACTTTTAGTTCACTGATTGTTTACCAT 57.868 29.630 0.00 0.00 0.00 3.55
416 446 9.398170 CTTTTAGTTCACTGATTGTTTACCATG 57.602 33.333 0.00 0.00 0.00 3.66
417 447 8.684386 TTTAGTTCACTGATTGTTTACCATGA 57.316 30.769 0.00 0.00 0.00 3.07
418 448 8.862325 TTAGTTCACTGATTGTTTACCATGAT 57.138 30.769 0.00 0.00 0.00 2.45
420 450 6.716628 AGTTCACTGATTGTTTACCATGATGT 59.283 34.615 0.00 0.00 0.00 3.06
421 451 7.231317 AGTTCACTGATTGTTTACCATGATGTT 59.769 33.333 0.00 0.00 0.00 2.71
422 452 7.523293 TCACTGATTGTTTACCATGATGTTT 57.477 32.000 0.00 0.00 0.00 2.83
423 453 7.592938 TCACTGATTGTTTACCATGATGTTTC 58.407 34.615 0.00 0.00 0.00 2.78
425 455 6.721208 ACTGATTGTTTACCATGATGTTTCCT 59.279 34.615 0.00 0.00 0.00 3.36
426 456 7.888021 ACTGATTGTTTACCATGATGTTTCCTA 59.112 33.333 0.00 0.00 0.00 2.94
427 457 8.642935 TGATTGTTTACCATGATGTTTCCTAA 57.357 30.769 0.00 0.00 0.00 2.69
428 458 8.739039 TGATTGTTTACCATGATGTTTCCTAAG 58.261 33.333 0.00 0.00 0.00 2.18
429 459 8.877864 ATTGTTTACCATGATGTTTCCTAAGA 57.122 30.769 0.00 0.00 0.00 2.10
431 461 7.227873 TGTTTACCATGATGTTTCCTAAGACA 58.772 34.615 0.00 0.00 0.00 3.41
432 462 7.390440 TGTTTACCATGATGTTTCCTAAGACAG 59.610 37.037 0.00 0.00 0.00 3.51
435 465 4.264253 CATGATGTTTCCTAAGACAGGCA 58.736 43.478 0.00 0.00 45.10 4.75
436 466 4.574674 TGATGTTTCCTAAGACAGGCAT 57.425 40.909 0.00 0.00 45.10 4.40
437 467 4.922206 TGATGTTTCCTAAGACAGGCATT 58.078 39.130 0.00 0.00 45.10 3.56
438 468 4.701651 TGATGTTTCCTAAGACAGGCATTG 59.298 41.667 0.00 0.00 45.10 2.82
439 469 3.420893 TGTTTCCTAAGACAGGCATTGG 58.579 45.455 0.00 0.00 45.10 3.16
440 470 3.073798 TGTTTCCTAAGACAGGCATTGGA 59.926 43.478 0.00 0.00 45.10 3.53
441 471 4.263905 TGTTTCCTAAGACAGGCATTGGAT 60.264 41.667 0.00 0.00 45.10 3.41
442 472 5.045213 TGTTTCCTAAGACAGGCATTGGATA 60.045 40.000 0.00 0.00 45.10 2.59
443 473 4.963318 TCCTAAGACAGGCATTGGATAG 57.037 45.455 0.00 0.00 45.10 2.08
444 474 3.071602 TCCTAAGACAGGCATTGGATAGC 59.928 47.826 0.00 0.00 45.10 2.97
445 475 3.072184 CCTAAGACAGGCATTGGATAGCT 59.928 47.826 0.00 0.00 37.70 3.32
446 476 3.659183 AAGACAGGCATTGGATAGCTT 57.341 42.857 0.00 0.00 0.00 3.74
448 478 4.348863 AGACAGGCATTGGATAGCTTAG 57.651 45.455 0.00 0.00 0.00 2.18
449 479 3.713764 AGACAGGCATTGGATAGCTTAGT 59.286 43.478 0.00 0.00 0.00 2.24
450 480 4.164988 AGACAGGCATTGGATAGCTTAGTT 59.835 41.667 0.00 0.00 0.00 2.24
451 481 5.366768 AGACAGGCATTGGATAGCTTAGTTA 59.633 40.000 0.00 0.00 0.00 2.24
525 555 8.706492 TGAAAATATACCGTAGAACAATCGTT 57.294 30.769 0.00 0.00 38.33 3.85
538 568 3.839293 ACAATCGTTCTACAGTCTCTGC 58.161 45.455 0.00 0.00 34.37 4.26
539 569 3.182967 CAATCGTTCTACAGTCTCTGCC 58.817 50.000 0.00 0.00 34.37 4.85
540 570 2.201921 TCGTTCTACAGTCTCTGCCT 57.798 50.000 0.00 0.00 34.37 4.75
541 571 2.085320 TCGTTCTACAGTCTCTGCCTC 58.915 52.381 0.00 0.00 34.37 4.70
542 572 1.813178 CGTTCTACAGTCTCTGCCTCA 59.187 52.381 0.00 0.00 34.37 3.86
543 573 2.229062 CGTTCTACAGTCTCTGCCTCAA 59.771 50.000 0.00 0.00 34.37 3.02
544 574 3.305403 CGTTCTACAGTCTCTGCCTCAAA 60.305 47.826 0.00 0.00 34.37 2.69
545 575 4.632153 GTTCTACAGTCTCTGCCTCAAAA 58.368 43.478 0.00 0.00 34.37 2.44
547 577 4.152647 TCTACAGTCTCTGCCTCAAAAGA 58.847 43.478 0.00 0.00 34.37 2.52
548 578 3.845781 ACAGTCTCTGCCTCAAAAGAA 57.154 42.857 0.00 0.00 34.37 2.52
549 579 4.156455 ACAGTCTCTGCCTCAAAAGAAA 57.844 40.909 0.00 0.00 34.37 2.52
551 581 4.141620 ACAGTCTCTGCCTCAAAAGAAAGA 60.142 41.667 0.00 0.00 34.37 2.52
554 584 5.059833 GTCTCTGCCTCAAAAGAAAGAAGA 58.940 41.667 0.00 0.00 0.00 2.87
555 585 5.704978 GTCTCTGCCTCAAAAGAAAGAAGAT 59.295 40.000 0.00 0.00 0.00 2.40
556 586 5.936956 TCTCTGCCTCAAAAGAAAGAAGATC 59.063 40.000 0.00 0.00 0.00 2.75
557 587 5.006386 TCTGCCTCAAAAGAAAGAAGATCC 58.994 41.667 0.00 0.00 0.00 3.36
560 590 5.474876 TGCCTCAAAAGAAAGAAGATCCTTC 59.525 40.000 0.00 0.00 0.00 3.46
561 591 5.474876 GCCTCAAAAGAAAGAAGATCCTTCA 59.525 40.000 9.10 0.00 0.00 3.02
562 592 6.569418 GCCTCAAAAGAAAGAAGATCCTTCAC 60.569 42.308 9.10 1.44 0.00 3.18
563 593 6.714356 CCTCAAAAGAAAGAAGATCCTTCACT 59.286 38.462 9.10 3.36 0.00 3.41
564 594 7.880195 CCTCAAAAGAAAGAAGATCCTTCACTA 59.120 37.037 9.10 0.00 0.00 2.74
565 595 9.277783 CTCAAAAGAAAGAAGATCCTTCACTAA 57.722 33.333 9.10 0.00 0.00 2.24
566 596 9.277783 TCAAAAGAAAGAAGATCCTTCACTAAG 57.722 33.333 9.10 0.00 0.00 2.18
567 597 7.680442 AAAGAAAGAAGATCCTTCACTAAGC 57.320 36.000 9.10 0.00 0.00 3.09
568 598 6.619329 AGAAAGAAGATCCTTCACTAAGCT 57.381 37.500 9.10 0.00 0.00 3.74
569 599 7.014988 AGAAAGAAGATCCTTCACTAAGCTT 57.985 36.000 3.48 3.48 0.00 3.74
570 600 8.140112 AGAAAGAAGATCCTTCACTAAGCTTA 57.860 34.615 5.94 5.94 0.00 3.09
571 601 8.038351 AGAAAGAAGATCCTTCACTAAGCTTAC 58.962 37.037 0.86 0.00 0.00 2.34
572 602 6.228616 AGAAGATCCTTCACTAAGCTTACC 57.771 41.667 0.86 0.00 0.00 2.85
573 603 5.961421 AGAAGATCCTTCACTAAGCTTACCT 59.039 40.000 0.86 0.00 0.00 3.08
574 604 5.606348 AGATCCTTCACTAAGCTTACCTG 57.394 43.478 0.86 1.17 0.00 4.00
575 605 5.026790 AGATCCTTCACTAAGCTTACCTGT 58.973 41.667 0.86 0.00 0.00 4.00
576 606 5.485708 AGATCCTTCACTAAGCTTACCTGTT 59.514 40.000 0.86 0.00 0.00 3.16
577 607 5.562298 TCCTTCACTAAGCTTACCTGTTT 57.438 39.130 0.86 0.00 0.00 2.83
578 608 6.675413 TCCTTCACTAAGCTTACCTGTTTA 57.325 37.500 0.86 0.00 0.00 2.01
579 609 6.461640 TCCTTCACTAAGCTTACCTGTTTAC 58.538 40.000 0.86 0.00 0.00 2.01
580 610 6.269307 TCCTTCACTAAGCTTACCTGTTTACT 59.731 38.462 0.86 0.00 0.00 2.24
581 611 6.369065 CCTTCACTAAGCTTACCTGTTTACTG 59.631 42.308 0.86 0.00 0.00 2.74
582 612 6.659745 TCACTAAGCTTACCTGTTTACTGA 57.340 37.500 0.86 0.00 0.00 3.41
583 613 7.058023 TCACTAAGCTTACCTGTTTACTGAA 57.942 36.000 0.86 0.00 0.00 3.02
584 614 7.152645 TCACTAAGCTTACCTGTTTACTGAAG 58.847 38.462 0.86 0.00 0.00 3.02
585 615 5.932883 ACTAAGCTTACCTGTTTACTGAAGC 59.067 40.000 0.86 0.00 39.63 3.86
586 616 4.351874 AGCTTACCTGTTTACTGAAGCA 57.648 40.909 7.13 0.00 41.34 3.91
587 617 4.065789 AGCTTACCTGTTTACTGAAGCAC 58.934 43.478 7.13 0.00 41.34 4.40
588 618 4.065789 GCTTACCTGTTTACTGAAGCACT 58.934 43.478 0.00 0.00 39.24 4.40
589 619 5.011738 AGCTTACCTGTTTACTGAAGCACTA 59.988 40.000 7.13 0.00 41.34 2.74
590 620 5.699458 GCTTACCTGTTTACTGAAGCACTAA 59.301 40.000 0.00 0.00 39.24 2.24
591 621 6.347483 GCTTACCTGTTTACTGAAGCACTAAC 60.347 42.308 0.00 0.00 39.24 2.34
592 622 5.291905 ACCTGTTTACTGAAGCACTAACT 57.708 39.130 0.00 0.00 0.00 2.24
593 623 5.681639 ACCTGTTTACTGAAGCACTAACTT 58.318 37.500 0.00 0.00 0.00 2.66
594 624 6.823497 ACCTGTTTACTGAAGCACTAACTTA 58.177 36.000 0.00 0.00 0.00 2.24
595 625 6.704937 ACCTGTTTACTGAAGCACTAACTTAC 59.295 38.462 0.00 0.00 0.00 2.34
596 626 6.929606 CCTGTTTACTGAAGCACTAACTTACT 59.070 38.462 0.00 0.00 0.00 2.24
597 627 7.441458 CCTGTTTACTGAAGCACTAACTTACTT 59.559 37.037 0.00 0.00 0.00 2.24
598 628 8.361592 TGTTTACTGAAGCACTAACTTACTTC 57.638 34.615 0.00 0.00 39.16 3.01
599 629 8.202137 TGTTTACTGAAGCACTAACTTACTTCT 58.798 33.333 0.00 0.00 39.39 2.85
600 630 9.043079 GTTTACTGAAGCACTAACTTACTTCTT 57.957 33.333 0.00 0.00 39.39 2.52
601 631 8.813643 TTACTGAAGCACTAACTTACTTCTTC 57.186 34.615 0.00 0.00 39.39 2.87
602 632 7.056844 ACTGAAGCACTAACTTACTTCTTCT 57.943 36.000 0.00 0.00 39.39 2.85
603 633 7.501844 ACTGAAGCACTAACTTACTTCTTCTT 58.498 34.615 0.00 0.00 39.39 2.52
606 636 7.868415 TGAAGCACTAACTTACTTCTTCTTCTC 59.132 37.037 0.00 0.00 39.39 2.87
631 661 8.935844 TCACATGTATAAACTCAACAGCTAAAG 58.064 33.333 0.00 0.00 0.00 1.85
786 816 1.619827 CATGTGGCAATGTTCCTTGGT 59.380 47.619 0.00 0.00 0.00 3.67
801 831 7.972301 TGTTCCTTGGTCAAATTAATTCCATT 58.028 30.769 0.10 0.00 0.00 3.16
803 833 9.283768 GTTCCTTGGTCAAATTAATTCCATTTT 57.716 29.630 0.10 0.00 0.00 1.82
830 860 3.350912 GTTTAACAACTGACAGCACACG 58.649 45.455 1.25 0.00 0.00 4.49
832 862 1.095228 AACAACTGACAGCACACGGG 61.095 55.000 1.25 0.00 0.00 5.28
893 924 2.437359 GAGCTCCCGCAACATGCT 60.437 61.111 0.87 0.00 42.25 3.79
933 967 4.427096 ACTACTGATGAACTCACTCACG 57.573 45.455 0.00 0.00 0.00 4.35
1149 1186 3.480225 GATCCCGACGGCGTACCTG 62.480 68.421 14.74 3.00 35.23 4.00
1266 1303 1.081376 CTTCGTTGAGCTCGTCGGT 60.081 57.895 23.17 0.00 0.00 4.69
1307 1344 4.409218 GTCGTCGTGGCGGCACTA 62.409 66.667 35.12 25.05 36.38 2.74
1354 1391 7.148407 TGCGAGGAGATCTTGTTAATTCTTTTC 60.148 37.037 0.00 0.00 0.00 2.29
1365 1402 7.780008 TGTTAATTCTTTTCTCAGTTCGTGA 57.220 32.000 0.00 0.00 0.00 4.35
1395 1432 4.212214 GCAGTATGTACATAGCAGCTTTCC 59.788 45.833 15.93 1.44 39.31 3.13
1493 1635 1.504359 GTGACGGTCCATGTTTTCGA 58.496 50.000 5.55 0.00 0.00 3.71
1535 1677 3.181774 CGGTGCGAATCTATAAAGGAACG 59.818 47.826 0.00 0.00 0.00 3.95
1552 1694 3.859386 GGAACGCATGGATTTCAAATGAC 59.141 43.478 0.00 0.00 0.00 3.06
1566 1708 5.720371 TCAAATGACATTCGGGTTGAAAT 57.280 34.783 0.05 0.00 40.71 2.17
1567 1709 6.095432 TCAAATGACATTCGGGTTGAAATT 57.905 33.333 0.05 0.00 40.71 1.82
1568 1710 6.520272 TCAAATGACATTCGGGTTGAAATTT 58.480 32.000 0.05 0.00 40.71 1.82
1570 1712 7.497249 TCAAATGACATTCGGGTTGAAATTTTT 59.503 29.630 0.05 0.00 40.71 1.94
1592 1734 5.637006 TTATCGTGGGGAACAAATGAAAG 57.363 39.130 0.00 0.00 0.00 2.62
1598 1740 3.888930 TGGGGAACAAATGAAAGTCTGTC 59.111 43.478 0.00 0.00 0.00 3.51
1624 1767 9.302345 CTTAATATTACTTTGCGAGAGAACTGA 57.698 33.333 0.00 0.00 0.00 3.41
1626 1769 8.723942 AATATTACTTTGCGAGAGAACTGAAT 57.276 30.769 0.00 0.00 0.00 2.57
1641 1784 5.645497 AGAACTGAATTTCTGTATGGCAGTC 59.355 40.000 9.06 2.66 45.23 3.51
1647 1790 3.334583 TTCTGTATGGCAGTCTGAACC 57.665 47.619 3.32 0.00 45.23 3.62
1649 1792 2.028112 TCTGTATGGCAGTCTGAACCAC 60.028 50.000 3.32 0.00 45.23 4.16
1654 1797 2.451490 TGGCAGTCTGAACCACAAAAA 58.549 42.857 3.32 0.00 0.00 1.94
1666 1809 6.047870 TGAACCACAAAAATGGAAATCACTG 58.952 36.000 0.00 0.00 43.02 3.66
1711 2014 7.534085 TGTACGTAGGATTTTAATCAGCTTG 57.466 36.000 0.00 0.00 37.15 4.01
1733 2036 8.229137 GCTTGTCAGCATTTGCAAAATAAATTA 58.771 29.630 17.19 0.00 46.49 1.40
1745 2048 9.823098 TTGCAAAATAAATTAAATGTGTGCATC 57.177 25.926 0.00 0.00 38.01 3.91
1746 2049 9.217278 TGCAAAATAAATTAAATGTGTGCATCT 57.783 25.926 0.00 0.00 33.64 2.90
1763 2066 2.890808 TCTTAACTATGCAGAGGCCG 57.109 50.000 13.85 0.00 40.13 6.13
1764 2067 1.412710 TCTTAACTATGCAGAGGCCGG 59.587 52.381 13.85 0.00 40.13 6.13
1765 2068 0.468226 TTAACTATGCAGAGGCCGGG 59.532 55.000 13.85 0.00 40.13 5.73
1766 2069 0.689745 TAACTATGCAGAGGCCGGGT 60.690 55.000 13.85 0.00 40.13 5.28
1767 2070 2.109799 CTATGCAGAGGCCGGGTG 59.890 66.667 2.18 0.00 40.13 4.61
1768 2071 2.687200 TATGCAGAGGCCGGGTGT 60.687 61.111 2.18 0.00 40.13 4.16
1769 2072 1.382009 TATGCAGAGGCCGGGTGTA 60.382 57.895 2.18 0.00 40.13 2.90
1770 2073 0.978667 TATGCAGAGGCCGGGTGTAA 60.979 55.000 2.18 0.00 40.13 2.41
1771 2074 1.635817 ATGCAGAGGCCGGGTGTAAT 61.636 55.000 2.18 0.00 40.13 1.89
1772 2075 0.978667 TGCAGAGGCCGGGTGTAATA 60.979 55.000 2.18 0.00 40.13 0.98
1773 2076 0.532196 GCAGAGGCCGGGTGTAATAC 60.532 60.000 2.18 0.00 0.00 1.89
1774 2077 1.120530 CAGAGGCCGGGTGTAATACT 58.879 55.000 2.18 0.00 0.00 2.12
1775 2078 1.485066 CAGAGGCCGGGTGTAATACTT 59.515 52.381 2.18 0.00 0.00 2.24
1776 2079 2.696707 CAGAGGCCGGGTGTAATACTTA 59.303 50.000 2.18 0.00 0.00 2.24
1777 2080 3.133362 CAGAGGCCGGGTGTAATACTTAA 59.867 47.826 2.18 0.00 0.00 1.85
1778 2081 3.776417 AGAGGCCGGGTGTAATACTTAAA 59.224 43.478 2.18 0.00 0.00 1.52
1779 2082 3.873361 GAGGCCGGGTGTAATACTTAAAC 59.127 47.826 2.18 0.00 0.00 2.01
1780 2083 2.945008 GGCCGGGTGTAATACTTAAACC 59.055 50.000 2.18 0.00 41.91 3.27
1781 2084 3.370846 GGCCGGGTGTAATACTTAAACCT 60.371 47.826 2.18 0.00 42.23 3.50
1782 2085 4.264253 GCCGGGTGTAATACTTAAACCTT 58.736 43.478 2.18 0.00 42.23 3.50
1783 2086 4.701651 GCCGGGTGTAATACTTAAACCTTT 59.298 41.667 2.18 0.00 42.23 3.11
1784 2087 5.183713 GCCGGGTGTAATACTTAAACCTTTT 59.816 40.000 2.18 0.00 42.23 2.27
1785 2088 6.374053 GCCGGGTGTAATACTTAAACCTTTTA 59.626 38.462 2.18 0.00 42.23 1.52
1786 2089 7.094420 GCCGGGTGTAATACTTAAACCTTTTAA 60.094 37.037 2.18 0.00 42.23 1.52
1787 2090 8.453320 CCGGGTGTAATACTTAAACCTTTTAAG 58.547 37.037 14.21 14.21 42.23 1.85
1788 2091 9.002600 CGGGTGTAATACTTAAACCTTTTAAGT 57.997 33.333 21.61 21.61 42.23 2.24
1850 2153 3.213506 TCATTTTATCGGCCCAGATGTG 58.786 45.455 0.00 0.00 32.39 3.21
1862 2165 2.625737 CCAGATGTGAGCCTGTAACTG 58.374 52.381 0.00 0.00 0.00 3.16
1871 2174 2.642254 CCTGTAACTGTCGGCCCGA 61.642 63.158 0.00 0.00 0.00 5.14
1922 2225 1.888512 CAACCTGTGGATTCAACCCTG 59.111 52.381 0.00 0.00 0.00 4.45
1927 2230 0.698818 GTGGATTCAACCCTGGGAGT 59.301 55.000 22.23 3.44 0.00 3.85
1928 2231 0.991920 TGGATTCAACCCTGGGAGTC 59.008 55.000 22.23 9.12 0.00 3.36
1929 2232 0.991920 GGATTCAACCCTGGGAGTCA 59.008 55.000 22.23 0.34 0.00 3.41
1930 2233 1.340114 GGATTCAACCCTGGGAGTCAC 60.340 57.143 22.23 5.93 0.00 3.67
1931 2234 0.698818 ATTCAACCCTGGGAGTCACC 59.301 55.000 22.23 0.00 38.08 4.02
1932 2235 0.696143 TTCAACCCTGGGAGTCACCA 60.696 55.000 22.23 0.00 41.20 4.17
1933 2236 0.696143 TCAACCCTGGGAGTCACCAA 60.696 55.000 22.23 0.00 40.68 3.67
1934 2237 0.250901 CAACCCTGGGAGTCACCAAG 60.251 60.000 22.23 0.00 40.68 3.61
1939 2242 1.897560 CTGGGAGTCACCAAGGAAAC 58.102 55.000 0.00 0.00 40.68 2.78
1940 2243 0.476771 TGGGAGTCACCAAGGAAACC 59.523 55.000 0.00 0.00 41.20 3.27
1941 2244 0.771755 GGGAGTCACCAAGGAAACCT 59.228 55.000 0.00 0.00 41.20 3.50
1942 2245 1.271434 GGGAGTCACCAAGGAAACCTC 60.271 57.143 0.00 0.00 41.20 3.85
1943 2246 1.271434 GGAGTCACCAAGGAAACCTCC 60.271 57.143 0.00 0.00 39.27 4.30
1960 2263 5.036117 ACCTCCTATATGTCGCATTTTGT 57.964 39.130 0.00 0.00 0.00 2.83
1995 2340 5.241378 GTGATTCGCACAACAATTGAAAG 57.759 39.130 13.59 3.78 46.91 2.62
1997 2342 4.975502 TGATTCGCACAACAATTGAAAGTC 59.024 37.500 13.59 0.00 0.00 3.01
2003 2348 4.270808 GCACAACAATTGAAAGTCCCAAAG 59.729 41.667 13.59 0.00 0.00 2.77
2004 2349 4.810491 CACAACAATTGAAAGTCCCAAAGG 59.190 41.667 13.59 0.00 0.00 3.11
2014 2359 2.714259 TCCCAAAGGACTTTGTGCG 58.286 52.632 19.89 9.63 46.19 5.34
2015 2360 1.007387 CCCAAAGGACTTTGTGCGC 60.007 57.895 19.89 0.00 46.19 6.09
2016 2361 1.007387 CCAAAGGACTTTGTGCGCC 60.007 57.895 19.89 0.00 46.19 6.53
2017 2362 1.007387 CAAAGGACTTTGTGCGCCC 60.007 57.895 14.92 0.00 43.52 6.13
2018 2363 1.152756 AAAGGACTTTGTGCGCCCT 60.153 52.632 4.18 0.00 0.00 5.19
2019 2364 1.455383 AAAGGACTTTGTGCGCCCTG 61.455 55.000 4.18 0.00 0.00 4.45
2020 2365 3.365265 GGACTTTGTGCGCCCTGG 61.365 66.667 4.18 0.00 0.00 4.45
2021 2366 3.365265 GACTTTGTGCGCCCTGGG 61.365 66.667 8.86 8.86 0.00 4.45
2022 2367 4.974721 ACTTTGTGCGCCCTGGGG 62.975 66.667 16.03 4.75 38.57 4.96
2023 2368 4.659172 CTTTGTGCGCCCTGGGGA 62.659 66.667 16.03 0.00 37.50 4.81
2024 2369 3.944250 CTTTGTGCGCCCTGGGGAT 62.944 63.158 16.03 0.00 37.50 3.85
2025 2370 3.521765 TTTGTGCGCCCTGGGGATT 62.522 57.895 16.03 0.00 37.50 3.01
2026 2371 3.936772 TTGTGCGCCCTGGGGATTC 62.937 63.158 16.03 0.00 37.50 2.52
2029 2374 4.483243 GCGCCCTGGGGATTCGAA 62.483 66.667 16.03 0.00 37.50 3.71
2030 2375 2.513897 CGCCCTGGGGATTCGAAC 60.514 66.667 16.03 0.00 37.50 3.95
2031 2376 2.674754 GCCCTGGGGATTCGAACA 59.325 61.111 16.03 0.00 37.50 3.18
2032 2377 1.749258 GCCCTGGGGATTCGAACAC 60.749 63.158 16.03 0.00 37.50 3.32
2033 2378 1.077716 CCCTGGGGATTCGAACACC 60.078 63.158 4.27 7.36 37.50 4.16
2034 2379 1.682849 CCTGGGGATTCGAACACCA 59.317 57.895 20.01 18.61 38.61 4.17
2035 2380 0.676782 CCTGGGGATTCGAACACCAC 60.677 60.000 20.01 17.99 35.76 4.16
2036 2381 0.036164 CTGGGGATTCGAACACCACA 59.964 55.000 21.57 21.57 35.76 4.17
2043 2388 1.338890 TTCGAACACCACACCTCCCA 61.339 55.000 0.00 0.00 0.00 4.37
2059 2404 0.741574 CCCATTGTTAGGTGCGCGTA 60.742 55.000 8.43 0.00 0.00 4.42
2101 2446 6.531503 TGAACTTTGGTGACCAATAAACAA 57.468 33.333 19.03 0.49 43.55 2.83
2102 2447 7.118496 TGAACTTTGGTGACCAATAAACAAT 57.882 32.000 19.03 0.65 43.55 2.71
2105 2450 7.589958 ACTTTGGTGACCAATAAACAATACA 57.410 32.000 19.03 0.00 43.55 2.29
2107 2452 7.504238 ACTTTGGTGACCAATAAACAATACAGA 59.496 33.333 19.03 0.00 43.55 3.41
2114 2459 8.995220 TGACCAATAAACAATACAGAGTTGTAC 58.005 33.333 0.00 0.00 42.29 2.90
2131 2476 1.089920 TACGAACTACCAGGAGCGAC 58.910 55.000 0.00 0.00 0.00 5.19
2138 2483 4.060038 ACTACCAGGAGCGACATATTTG 57.940 45.455 0.00 0.00 0.00 2.32
2146 2491 6.381801 CAGGAGCGACATATTTGAAGTTTTT 58.618 36.000 0.00 0.00 0.00 1.94
2152 2497 9.522804 AGCGACATATTTGAAGTTTTTACAAAA 57.477 25.926 0.00 0.00 37.14 2.44
2210 2556 9.218440 ACACAGAAACTTTTCAAAATTGTGAAT 57.782 25.926 19.74 0.00 39.07 2.57
2283 2630 6.106877 AGATCACGTACATTTTTGGAATCG 57.893 37.500 0.00 0.00 0.00 3.34
2284 2631 5.872617 AGATCACGTACATTTTTGGAATCGA 59.127 36.000 0.00 0.00 0.00 3.59
2288 2635 6.147985 TCACGTACATTTTTGGAATCGATGAA 59.852 34.615 0.00 0.00 0.00 2.57
2289 2636 6.248420 CACGTACATTTTTGGAATCGATGAAC 59.752 38.462 0.00 0.00 0.00 3.18
2292 2639 7.484641 CGTACATTTTTGGAATCGATGAACAAT 59.515 33.333 0.00 0.00 0.00 2.71
2293 2640 9.139174 GTACATTTTTGGAATCGATGAACAATT 57.861 29.630 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 145 1.221566 CCACGAGTGGCATCCATCA 59.778 57.895 9.54 0.00 44.73 3.07
226 233 1.160329 GGCGTCACAGCAGTTCAACT 61.160 55.000 0.00 0.00 39.27 3.16
271 279 6.119536 ACATGAATAGCCCGTTTCAAGATTA 58.880 36.000 0.00 0.00 35.63 1.75
272 280 4.949856 ACATGAATAGCCCGTTTCAAGATT 59.050 37.500 0.00 0.00 35.63 2.40
298 306 3.438360 GATGAACAAAACATCGCCATCC 58.562 45.455 0.00 0.00 35.55 3.51
313 321 2.789893 GCTGAACGTCTATCCGATGAAC 59.210 50.000 0.00 0.00 32.79 3.18
325 333 0.313672 TGGGCAATTTGCTGAACGTC 59.686 50.000 20.06 2.52 44.28 4.34
326 334 0.749649 TTGGGCAATTTGCTGAACGT 59.250 45.000 20.06 0.00 44.28 3.99
328 336 5.177326 TCATTATTGGGCAATTTGCTGAAC 58.823 37.500 20.06 9.46 44.28 3.18
340 348 5.928264 GCAATAGACCATTTCATTATTGGGC 59.072 40.000 5.12 0.00 38.96 5.36
356 364 9.624697 TTCAATGTAGTTTTTGATGCAATAGAC 57.375 29.630 0.00 0.00 32.27 2.59
363 371 7.713764 ACCTTTTCAATGTAGTTTTTGATGC 57.286 32.000 0.00 0.00 32.27 3.91
384 414 8.747538 AACAATCAGTGAACTAAAAGTAACCT 57.252 30.769 0.00 0.00 0.00 3.50
388 418 9.616156 TGGTAAACAATCAGTGAACTAAAAGTA 57.384 29.630 0.00 0.00 0.00 2.24
389 419 8.514330 TGGTAAACAATCAGTGAACTAAAAGT 57.486 30.769 0.00 0.00 0.00 2.66
390 420 9.398170 CATGGTAAACAATCAGTGAACTAAAAG 57.602 33.333 0.00 0.00 0.00 2.27
391 421 9.126151 TCATGGTAAACAATCAGTGAACTAAAA 57.874 29.630 0.00 0.00 0.00 1.52
392 422 8.684386 TCATGGTAAACAATCAGTGAACTAAA 57.316 30.769 0.00 0.00 0.00 1.85
393 423 8.729756 CATCATGGTAAACAATCAGTGAACTAA 58.270 33.333 0.00 0.00 0.00 2.24
394 424 7.882791 ACATCATGGTAAACAATCAGTGAACTA 59.117 33.333 0.00 0.00 0.00 2.24
395 425 6.716628 ACATCATGGTAAACAATCAGTGAACT 59.283 34.615 0.00 0.00 0.00 3.01
396 426 6.913170 ACATCATGGTAAACAATCAGTGAAC 58.087 36.000 0.00 0.00 0.00 3.18
400 430 6.721208 AGGAAACATCATGGTAAACAATCAGT 59.279 34.615 0.00 0.00 0.00 3.41
401 431 7.161773 AGGAAACATCATGGTAAACAATCAG 57.838 36.000 0.00 0.00 0.00 2.90
402 432 8.642935 TTAGGAAACATCATGGTAAACAATCA 57.357 30.769 0.00 0.00 0.00 2.57
403 433 8.956426 TCTTAGGAAACATCATGGTAAACAATC 58.044 33.333 0.00 0.00 0.00 2.67
404 434 8.739972 GTCTTAGGAAACATCATGGTAAACAAT 58.260 33.333 0.00 0.00 0.00 2.71
405 435 7.721842 TGTCTTAGGAAACATCATGGTAAACAA 59.278 33.333 0.00 0.00 0.00 2.83
406 436 7.227873 TGTCTTAGGAAACATCATGGTAAACA 58.772 34.615 0.00 0.00 0.00 2.83
407 437 7.681939 TGTCTTAGGAAACATCATGGTAAAC 57.318 36.000 0.00 0.00 0.00 2.01
408 438 7.921786 CTGTCTTAGGAAACATCATGGTAAA 57.078 36.000 0.00 0.00 0.00 2.01
425 455 4.778213 AAGCTATCCAATGCCTGTCTTA 57.222 40.909 0.00 0.00 0.00 2.10
426 456 3.659183 AAGCTATCCAATGCCTGTCTT 57.341 42.857 0.00 0.00 0.00 3.01
427 457 3.713764 ACTAAGCTATCCAATGCCTGTCT 59.286 43.478 0.00 0.00 0.00 3.41
428 458 4.078639 ACTAAGCTATCCAATGCCTGTC 57.921 45.455 0.00 0.00 0.00 3.51
429 459 4.510167 AACTAAGCTATCCAATGCCTGT 57.490 40.909 0.00 0.00 0.00 4.00
499 529 8.706492 ACGATTGTTCTACGGTATATTTTCAA 57.294 30.769 0.00 0.00 0.00 2.69
500 530 8.706492 AACGATTGTTCTACGGTATATTTTCA 57.294 30.769 0.00 0.00 30.83 2.69
516 546 4.238514 GCAGAGACTGTAGAACGATTGTT 58.761 43.478 0.00 0.00 35.87 2.83
517 547 3.367498 GGCAGAGACTGTAGAACGATTGT 60.367 47.826 0.00 0.00 33.43 2.71
519 549 3.093057 AGGCAGAGACTGTAGAACGATT 58.907 45.455 0.00 0.00 33.43 3.34
520 550 2.685897 GAGGCAGAGACTGTAGAACGAT 59.314 50.000 0.00 0.00 33.43 3.73
522 552 1.813178 TGAGGCAGAGACTGTAGAACG 59.187 52.381 0.00 0.00 33.43 3.95
523 553 3.944055 TTGAGGCAGAGACTGTAGAAC 57.056 47.619 0.00 0.00 33.43 3.01
525 555 4.152647 TCTTTTGAGGCAGAGACTGTAGA 58.847 43.478 0.00 0.00 33.43 2.59
527 557 4.955811 TTCTTTTGAGGCAGAGACTGTA 57.044 40.909 0.00 0.00 33.43 2.74
528 558 3.845781 TTCTTTTGAGGCAGAGACTGT 57.154 42.857 0.00 0.00 33.43 3.55
529 559 4.384056 TCTTTCTTTTGAGGCAGAGACTG 58.616 43.478 0.00 0.00 34.12 3.51
530 560 4.696479 TCTTTCTTTTGAGGCAGAGACT 57.304 40.909 0.00 0.00 0.00 3.24
532 562 5.296151 TCTTCTTTCTTTTGAGGCAGAGA 57.704 39.130 0.00 0.00 0.00 3.10
533 563 5.123661 GGATCTTCTTTCTTTTGAGGCAGAG 59.876 44.000 0.00 0.00 0.00 3.35
534 564 5.006386 GGATCTTCTTTCTTTTGAGGCAGA 58.994 41.667 0.00 0.00 0.00 4.26
536 566 4.990526 AGGATCTTCTTTCTTTTGAGGCA 58.009 39.130 0.00 0.00 0.00 4.75
538 568 6.714356 AGTGAAGGATCTTCTTTCTTTTGAGG 59.286 38.462 8.80 0.00 34.09 3.86
539 569 7.742556 AGTGAAGGATCTTCTTTCTTTTGAG 57.257 36.000 8.80 0.00 34.09 3.02
540 570 9.277783 CTTAGTGAAGGATCTTCTTTCTTTTGA 57.722 33.333 8.80 0.00 34.09 2.69
541 571 8.020244 GCTTAGTGAAGGATCTTCTTTCTTTTG 58.980 37.037 8.80 2.36 34.09 2.44
542 572 7.941790 AGCTTAGTGAAGGATCTTCTTTCTTTT 59.058 33.333 8.80 0.00 34.09 2.27
543 573 7.457561 AGCTTAGTGAAGGATCTTCTTTCTTT 58.542 34.615 8.80 0.00 34.09 2.52
544 574 7.014988 AGCTTAGTGAAGGATCTTCTTTCTT 57.985 36.000 8.80 0.00 34.09 2.52
545 575 6.619329 AGCTTAGTGAAGGATCTTCTTTCT 57.381 37.500 8.80 7.24 34.09 2.52
547 577 7.037945 AGGTAAGCTTAGTGAAGGATCTTCTTT 60.038 37.037 6.38 1.05 32.84 2.52
548 578 6.442244 AGGTAAGCTTAGTGAAGGATCTTCTT 59.558 38.462 6.38 0.00 32.84 2.52
549 579 5.961421 AGGTAAGCTTAGTGAAGGATCTTCT 59.039 40.000 6.38 0.00 32.84 2.85
551 581 5.485708 ACAGGTAAGCTTAGTGAAGGATCTT 59.514 40.000 18.49 0.00 32.84 2.40
554 584 5.763876 AACAGGTAAGCTTAGTGAAGGAT 57.236 39.130 18.49 0.00 32.84 3.24
555 585 5.562298 AAACAGGTAAGCTTAGTGAAGGA 57.438 39.130 18.49 0.00 32.84 3.36
556 586 6.369065 CAGTAAACAGGTAAGCTTAGTGAAGG 59.631 42.308 18.49 4.89 32.84 3.46
557 587 7.152645 TCAGTAAACAGGTAAGCTTAGTGAAG 58.847 38.462 18.49 6.36 33.09 3.02
560 590 6.128526 GCTTCAGTAAACAGGTAAGCTTAGTG 60.129 42.308 6.38 10.09 37.08 2.74
561 591 5.932883 GCTTCAGTAAACAGGTAAGCTTAGT 59.067 40.000 6.38 0.00 37.08 2.24
562 592 5.932303 TGCTTCAGTAAACAGGTAAGCTTAG 59.068 40.000 6.38 0.00 39.93 2.18
563 593 5.699458 GTGCTTCAGTAAACAGGTAAGCTTA 59.301 40.000 0.86 0.86 39.93 3.09
564 594 4.515567 GTGCTTCAGTAAACAGGTAAGCTT 59.484 41.667 3.48 3.48 39.93 3.74
565 595 4.065789 GTGCTTCAGTAAACAGGTAAGCT 58.934 43.478 0.00 0.00 39.93 3.74
566 596 4.065789 AGTGCTTCAGTAAACAGGTAAGC 58.934 43.478 0.00 0.00 39.73 3.09
567 597 6.929606 AGTTAGTGCTTCAGTAAACAGGTAAG 59.070 38.462 0.00 0.00 32.10 2.34
568 598 6.823497 AGTTAGTGCTTCAGTAAACAGGTAA 58.177 36.000 0.00 0.00 32.10 2.85
569 599 6.415206 AGTTAGTGCTTCAGTAAACAGGTA 57.585 37.500 0.00 0.00 32.10 3.08
570 600 5.291905 AGTTAGTGCTTCAGTAAACAGGT 57.708 39.130 0.00 0.00 32.10 4.00
571 601 6.929606 AGTAAGTTAGTGCTTCAGTAAACAGG 59.070 38.462 0.00 0.00 32.10 4.00
572 602 7.948278 AGTAAGTTAGTGCTTCAGTAAACAG 57.052 36.000 0.00 0.00 32.10 3.16
573 603 8.202137 AGAAGTAAGTTAGTGCTTCAGTAAACA 58.798 33.333 11.99 0.00 39.62 2.83
574 604 8.590719 AGAAGTAAGTTAGTGCTTCAGTAAAC 57.409 34.615 11.99 0.00 39.62 2.01
575 605 9.257651 GAAGAAGTAAGTTAGTGCTTCAGTAAA 57.742 33.333 24.96 0.00 41.52 2.01
576 606 8.639761 AGAAGAAGTAAGTTAGTGCTTCAGTAA 58.360 33.333 28.88 0.00 43.45 2.24
577 607 8.179509 AGAAGAAGTAAGTTAGTGCTTCAGTA 57.820 34.615 28.88 0.00 43.45 2.74
578 608 7.056844 AGAAGAAGTAAGTTAGTGCTTCAGT 57.943 36.000 28.88 14.46 43.45 3.41
579 609 7.870445 AGAAGAAGAAGTAAGTTAGTGCTTCAG 59.130 37.037 28.88 0.00 43.45 3.02
580 610 7.727181 AGAAGAAGAAGTAAGTTAGTGCTTCA 58.273 34.615 28.88 0.00 43.45 3.02
581 611 7.868415 TGAGAAGAAGAAGTAAGTTAGTGCTTC 59.132 37.037 23.39 23.39 41.99 3.86
582 612 7.654116 GTGAGAAGAAGAAGTAAGTTAGTGCTT 59.346 37.037 10.33 10.33 29.42 3.91
583 613 7.149307 GTGAGAAGAAGAAGTAAGTTAGTGCT 58.851 38.462 0.00 0.00 0.00 4.40
584 614 6.924060 TGTGAGAAGAAGAAGTAAGTTAGTGC 59.076 38.462 0.00 0.00 0.00 4.40
585 615 8.920665 CATGTGAGAAGAAGAAGTAAGTTAGTG 58.079 37.037 0.00 0.00 0.00 2.74
586 616 8.643324 ACATGTGAGAAGAAGAAGTAAGTTAGT 58.357 33.333 0.00 0.00 0.00 2.24
594 624 9.646427 GAGTTTATACATGTGAGAAGAAGAAGT 57.354 33.333 9.11 0.00 0.00 3.01
595 625 9.645059 TGAGTTTATACATGTGAGAAGAAGAAG 57.355 33.333 9.11 0.00 0.00 2.85
596 626 9.996554 TTGAGTTTATACATGTGAGAAGAAGAA 57.003 29.630 9.11 0.00 0.00 2.52
597 627 9.424319 GTTGAGTTTATACATGTGAGAAGAAGA 57.576 33.333 9.11 0.00 0.00 2.87
598 628 9.208022 TGTTGAGTTTATACATGTGAGAAGAAG 57.792 33.333 9.11 0.00 0.00 2.85
599 629 9.208022 CTGTTGAGTTTATACATGTGAGAAGAA 57.792 33.333 9.11 0.00 0.00 2.52
600 630 7.331934 GCTGTTGAGTTTATACATGTGAGAAGA 59.668 37.037 9.11 0.00 0.00 2.87
601 631 7.332926 AGCTGTTGAGTTTATACATGTGAGAAG 59.667 37.037 9.11 0.00 0.00 2.85
602 632 7.161404 AGCTGTTGAGTTTATACATGTGAGAA 58.839 34.615 9.11 0.00 0.00 2.87
603 633 6.701340 AGCTGTTGAGTTTATACATGTGAGA 58.299 36.000 9.11 0.00 0.00 3.27
606 636 8.177663 CCTTTAGCTGTTGAGTTTATACATGTG 58.822 37.037 9.11 0.00 0.00 3.21
704 734 2.462456 TTGAGATGAGATATGCCGCC 57.538 50.000 0.00 0.00 0.00 6.13
801 831 5.529800 GCTGTCAGTTGTTAAACCTCCTAAA 59.470 40.000 0.93 0.00 36.94 1.85
803 833 4.101898 TGCTGTCAGTTGTTAAACCTCCTA 59.898 41.667 0.93 0.00 36.94 2.94
830 860 6.990798 AGTAGCGGAGTACTATATTTTTCCC 58.009 40.000 0.00 0.00 31.14 3.97
893 924 1.066908 GTTGCTTGCTTGCTTGGTGTA 59.933 47.619 3.47 0.00 0.00 2.90
907 938 5.220710 AGTGAGTTCATCAGTAGTTGCTT 57.779 39.130 0.00 0.00 39.94 3.91
933 967 4.815040 TCGATAGCTAACTAGTGTCAGC 57.185 45.455 13.77 13.77 0.00 4.26
1307 1344 1.461127 GTGAAGAAACGAGCAGCGATT 59.539 47.619 5.99 0.14 44.57 3.34
1354 1391 1.872952 TGCCAAATGTCACGAACTGAG 59.127 47.619 0.00 0.00 0.00 3.35
1365 1402 5.436175 TGCTATGTACATACTGCCAAATGT 58.564 37.500 19.08 0.00 39.56 2.71
1448 1590 6.648879 TTAAAAAGCATTCACCAGCTACTT 57.351 33.333 0.00 0.00 40.90 2.24
1493 1635 3.078097 CGAGTCAGATCGACCATAGGAT 58.922 50.000 12.17 0.00 46.69 3.24
1535 1677 4.505191 CCGAATGTCATTTGAAATCCATGC 59.495 41.667 13.60 0.00 0.00 4.06
1567 1709 6.406692 TTCATTTGTTCCCCACGATAAAAA 57.593 33.333 0.00 0.00 0.00 1.94
1568 1710 6.041069 ACTTTCATTTGTTCCCCACGATAAAA 59.959 34.615 0.00 0.00 0.00 1.52
1570 1712 5.074115 ACTTTCATTTGTTCCCCACGATAA 58.926 37.500 0.00 0.00 0.00 1.75
1571 1713 4.658063 ACTTTCATTTGTTCCCCACGATA 58.342 39.130 0.00 0.00 0.00 2.92
1592 1734 8.630278 TCTCGCAAAGTAATATTAAGACAGAC 57.370 34.615 0.00 0.00 0.00 3.51
1598 1740 9.302345 TCAGTTCTCTCGCAAAGTAATATTAAG 57.698 33.333 0.00 0.00 0.00 1.85
1607 1749 5.049818 CAGAAATTCAGTTCTCTCGCAAAGT 60.050 40.000 0.00 0.00 35.63 2.66
1608 1750 5.049818 ACAGAAATTCAGTTCTCTCGCAAAG 60.050 40.000 0.00 0.00 35.63 2.77
1613 1756 5.006165 GCCATACAGAAATTCAGTTCTCTCG 59.994 44.000 0.00 0.00 35.63 4.04
1641 1784 6.201425 CAGTGATTTCCATTTTTGTGGTTCAG 59.799 38.462 0.00 0.00 40.27 3.02
1647 1790 4.990426 GGGACAGTGATTTCCATTTTTGTG 59.010 41.667 0.00 0.00 33.01 3.33
1649 1792 5.212532 TGGGACAGTGATTTCCATTTTTG 57.787 39.130 0.00 0.00 33.01 2.44
1654 1797 3.828451 CAGTTTGGGACAGTGATTTCCAT 59.172 43.478 0.00 0.00 42.39 3.41
1742 2045 3.062763 CGGCCTCTGCATAGTTAAGATG 58.937 50.000 0.00 0.00 40.13 2.90
1743 2046 2.037772 CCGGCCTCTGCATAGTTAAGAT 59.962 50.000 0.00 0.00 40.13 2.40
1744 2047 1.412710 CCGGCCTCTGCATAGTTAAGA 59.587 52.381 0.00 0.00 40.13 2.10
1745 2048 1.541233 CCCGGCCTCTGCATAGTTAAG 60.541 57.143 0.00 0.00 40.13 1.85
1746 2049 0.468226 CCCGGCCTCTGCATAGTTAA 59.532 55.000 0.00 0.00 40.13 2.01
1747 2050 0.689745 ACCCGGCCTCTGCATAGTTA 60.690 55.000 0.00 0.00 40.13 2.24
1748 2051 1.995626 ACCCGGCCTCTGCATAGTT 60.996 57.895 0.00 0.00 40.13 2.24
1749 2052 2.365635 ACCCGGCCTCTGCATAGT 60.366 61.111 0.00 0.00 40.13 2.12
1750 2053 1.399744 TACACCCGGCCTCTGCATAG 61.400 60.000 0.00 0.00 40.13 2.23
1751 2054 0.978667 TTACACCCGGCCTCTGCATA 60.979 55.000 0.00 0.00 40.13 3.14
1752 2055 1.635817 ATTACACCCGGCCTCTGCAT 61.636 55.000 0.00 0.00 40.13 3.96
1753 2056 0.978667 TATTACACCCGGCCTCTGCA 60.979 55.000 0.00 0.00 40.13 4.41
1754 2057 0.532196 GTATTACACCCGGCCTCTGC 60.532 60.000 0.00 0.00 0.00 4.26
1755 2058 1.120530 AGTATTACACCCGGCCTCTG 58.879 55.000 0.00 0.00 0.00 3.35
1756 2059 1.875488 AAGTATTACACCCGGCCTCT 58.125 50.000 0.00 0.00 0.00 3.69
1757 2060 3.825143 TTAAGTATTACACCCGGCCTC 57.175 47.619 0.00 0.00 0.00 4.70
1758 2061 3.370846 GGTTTAAGTATTACACCCGGCCT 60.371 47.826 0.00 0.00 43.82 5.19
1759 2062 2.945008 GGTTTAAGTATTACACCCGGCC 59.055 50.000 0.00 0.00 43.82 6.13
1818 2121 8.482128 TGGGCCGATAAAATGAAGAATTTATTT 58.518 29.630 0.00 0.00 44.79 1.40
1819 2122 8.017418 TGGGCCGATAAAATGAAGAATTTATT 57.983 30.769 0.00 0.00 37.51 1.40
1820 2123 7.505585 TCTGGGCCGATAAAATGAAGAATTTAT 59.494 33.333 0.00 0.00 37.51 1.40
1821 2124 6.831353 TCTGGGCCGATAAAATGAAGAATTTA 59.169 34.615 0.00 0.00 37.51 1.40
1822 2125 5.656416 TCTGGGCCGATAAAATGAAGAATTT 59.344 36.000 0.00 0.00 40.32 1.82
1823 2126 5.200483 TCTGGGCCGATAAAATGAAGAATT 58.800 37.500 0.00 0.00 0.00 2.17
1824 2127 4.792068 TCTGGGCCGATAAAATGAAGAAT 58.208 39.130 0.00 0.00 0.00 2.40
1825 2128 4.229304 TCTGGGCCGATAAAATGAAGAA 57.771 40.909 0.00 0.00 0.00 2.52
1826 2129 3.924114 TCTGGGCCGATAAAATGAAGA 57.076 42.857 0.00 0.00 0.00 2.87
1827 2130 3.885297 ACATCTGGGCCGATAAAATGAAG 59.115 43.478 9.90 0.00 0.00 3.02
1828 2131 3.631686 CACATCTGGGCCGATAAAATGAA 59.368 43.478 9.90 0.00 0.00 2.57
1829 2132 3.118075 TCACATCTGGGCCGATAAAATGA 60.118 43.478 9.90 8.99 0.00 2.57
1830 2133 3.213506 TCACATCTGGGCCGATAAAATG 58.786 45.455 9.90 4.78 0.00 2.32
1831 2134 3.480470 CTCACATCTGGGCCGATAAAAT 58.520 45.455 9.90 0.00 0.00 1.82
1832 2135 2.917933 CTCACATCTGGGCCGATAAAA 58.082 47.619 9.90 0.25 0.00 1.52
1841 2144 1.556911 AGTTACAGGCTCACATCTGGG 59.443 52.381 0.00 0.00 35.47 4.45
1850 2153 4.187056 GCCGACAGTTACAGGCTC 57.813 61.111 0.00 0.00 45.67 4.70
1871 2174 2.104281 GGTAGACACTGTTGTTCCTGGT 59.896 50.000 0.00 0.00 35.47 4.00
1909 2212 0.991920 GACTCCCAGGGTTGAATCCA 59.008 55.000 5.01 0.00 0.00 3.41
1922 2225 0.771755 AGGTTTCCTTGGTGACTCCC 59.228 55.000 0.00 0.00 34.77 4.30
1934 2237 3.746045 TGCGACATATAGGAGGTTTCC 57.254 47.619 0.00 0.00 44.39 3.13
1935 2238 6.038271 ACAAAATGCGACATATAGGAGGTTTC 59.962 38.462 0.00 0.00 0.00 2.78
1936 2239 5.885912 ACAAAATGCGACATATAGGAGGTTT 59.114 36.000 0.00 0.00 0.00 3.27
1937 2240 5.296780 CACAAAATGCGACATATAGGAGGTT 59.703 40.000 0.00 0.00 0.00 3.50
1938 2241 4.816385 CACAAAATGCGACATATAGGAGGT 59.184 41.667 0.00 0.00 0.00 3.85
1939 2242 5.050091 GTCACAAAATGCGACATATAGGAGG 60.050 44.000 0.00 0.00 30.34 4.30
1940 2243 5.523552 TGTCACAAAATGCGACATATAGGAG 59.476 40.000 0.00 0.00 34.85 3.69
1941 2244 5.423886 TGTCACAAAATGCGACATATAGGA 58.576 37.500 0.00 0.00 34.85 2.94
1942 2245 5.733226 TGTCACAAAATGCGACATATAGG 57.267 39.130 0.00 0.00 34.85 2.57
1943 2246 8.446489 TTTTTGTCACAAAATGCGACATATAG 57.554 30.769 16.41 0.00 38.94 1.31
1944 2247 8.079203 ACTTTTTGTCACAAAATGCGACATATA 58.921 29.630 22.55 3.41 38.94 0.86
1945 2248 6.922957 ACTTTTTGTCACAAAATGCGACATAT 59.077 30.769 22.55 4.97 38.94 1.78
1960 2263 2.032377 GCGAATCACCGACTTTTTGTCA 60.032 45.455 0.00 0.00 45.60 3.58
1967 2270 0.865769 GTTGTGCGAATCACCGACTT 59.134 50.000 0.00 0.00 45.03 3.01
1971 2274 1.978097 CAATTGTTGTGCGAATCACCG 59.022 47.619 0.00 0.00 45.03 4.94
1974 2277 4.930963 ACTTTCAATTGTTGTGCGAATCA 58.069 34.783 5.13 0.00 0.00 2.57
2003 2348 3.365265 CCAGGGCGCACAAAGTCC 61.365 66.667 14.57 0.00 0.00 3.85
2004 2349 3.365265 CCCAGGGCGCACAAAGTC 61.365 66.667 14.57 0.00 0.00 3.01
2006 2351 3.944250 ATCCCCAGGGCGCACAAAG 62.944 63.158 14.57 0.00 34.68 2.77
2008 2353 3.936772 GAATCCCCAGGGCGCACAA 62.937 63.158 14.57 0.00 34.68 3.33
2014 2359 1.749258 GTGTTCGAATCCCCAGGGC 60.749 63.158 0.00 0.00 34.68 5.19
2015 2360 1.077716 GGTGTTCGAATCCCCAGGG 60.078 63.158 0.00 0.00 0.00 4.45
2016 2361 0.676782 GTGGTGTTCGAATCCCCAGG 60.677 60.000 16.11 0.00 0.00 4.45
2017 2362 0.036164 TGTGGTGTTCGAATCCCCAG 59.964 55.000 16.11 0.00 0.00 4.45
2018 2363 0.250553 GTGTGGTGTTCGAATCCCCA 60.251 55.000 16.11 12.61 0.00 4.96
2019 2364 0.958876 GGTGTGGTGTTCGAATCCCC 60.959 60.000 16.11 10.56 0.00 4.81
2020 2365 0.036306 AGGTGTGGTGTTCGAATCCC 59.964 55.000 16.11 12.63 0.00 3.85
2021 2366 1.439679 GAGGTGTGGTGTTCGAATCC 58.560 55.000 0.00 8.23 0.00 3.01
2022 2367 1.439679 GGAGGTGTGGTGTTCGAATC 58.560 55.000 0.00 0.00 0.00 2.52
2023 2368 0.036306 GGGAGGTGTGGTGTTCGAAT 59.964 55.000 0.00 0.00 0.00 3.34
2024 2369 1.338890 TGGGAGGTGTGGTGTTCGAA 61.339 55.000 0.00 0.00 0.00 3.71
2025 2370 1.125093 ATGGGAGGTGTGGTGTTCGA 61.125 55.000 0.00 0.00 0.00 3.71
2026 2371 0.250727 AATGGGAGGTGTGGTGTTCG 60.251 55.000 0.00 0.00 0.00 3.95
2027 2372 1.247567 CAATGGGAGGTGTGGTGTTC 58.752 55.000 0.00 0.00 0.00 3.18
2028 2373 0.555769 ACAATGGGAGGTGTGGTGTT 59.444 50.000 0.00 0.00 0.00 3.32
2029 2374 0.555769 AACAATGGGAGGTGTGGTGT 59.444 50.000 0.00 0.00 0.00 4.16
2030 2375 2.436417 CTAACAATGGGAGGTGTGGTG 58.564 52.381 0.00 0.00 0.00 4.17
2031 2376 1.354368 CCTAACAATGGGAGGTGTGGT 59.646 52.381 0.00 0.00 0.00 4.16
2032 2377 1.354368 ACCTAACAATGGGAGGTGTGG 59.646 52.381 7.44 0.00 42.13 4.17
2033 2378 2.879103 ACCTAACAATGGGAGGTGTG 57.121 50.000 7.44 0.00 42.13 3.82
2036 2381 0.035439 CGCACCTAACAATGGGAGGT 60.035 55.000 2.89 2.89 44.65 3.85
2043 2388 2.596904 AGATACGCGCACCTAACAAT 57.403 45.000 5.73 0.00 0.00 2.71
2101 2446 5.125097 CCTGGTAGTTCGTACAACTCTGTAT 59.875 44.000 12.14 0.00 40.16 2.29
2102 2447 4.456911 CCTGGTAGTTCGTACAACTCTGTA 59.543 45.833 12.14 0.00 36.96 2.74
2105 2450 3.757493 CTCCTGGTAGTTCGTACAACTCT 59.243 47.826 12.14 0.00 32.62 3.24
2107 2452 2.230750 GCTCCTGGTAGTTCGTACAACT 59.769 50.000 13.01 13.01 32.62 3.16
2114 2459 0.456221 ATGTCGCTCCTGGTAGTTCG 59.544 55.000 0.00 0.00 0.00 3.95
2245 2591 6.254281 ACGTGATCTTCCAAAATGTTTAGG 57.746 37.500 0.00 0.00 0.00 2.69
2246 2592 7.802738 TGTACGTGATCTTCCAAAATGTTTAG 58.197 34.615 0.00 0.00 0.00 1.85
2247 2593 7.731882 TGTACGTGATCTTCCAAAATGTTTA 57.268 32.000 0.00 0.00 0.00 2.01
2252 2598 7.598493 CCAAAAATGTACGTGATCTTCCAAAAT 59.402 33.333 0.00 0.00 0.00 1.82
2261 2608 6.102006 TCGATTCCAAAAATGTACGTGATC 57.898 37.500 0.00 0.00 0.00 2.92
2263 2610 5.639931 TCATCGATTCCAAAAATGTACGTGA 59.360 36.000 0.00 0.00 0.00 4.35



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

AutoCloner maintained by Alex Coulton.