Multiple sequence alignment - TraesCS2A01G092200

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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 TraesCS2A01G092200 chr2A 100.000 2306 0 0 1 2306 45086622 45084317 0.000000e+00 4259
1 TraesCS2A01G092200 chr2A 88.038 836 56 19 496 1305 45096589 45095772 0.000000e+00 950
2 TraesCS2A01G092200 chr2B 87.327 1736 87 41 496 2152 68202096 68200415 0.000000e+00 1864
3 TraesCS2A01G092200 chr2B 92.058 554 20 8 764 1305 68207221 68206680 0.000000e+00 758
4 TraesCS2A01G092200 chr2D 87.189 1366 64 38 501 1812 43295590 43294282 0.000000e+00 1450
5 TraesCS2A01G092200 chr2D 91.365 857 38 13 466 1305 43301254 43300417 0.000000e+00 1140
6 TraesCS2A01G092200 chr2D 84.528 265 38 3 4 267 43332507 43332245 2.270000e-65 259
7 TraesCS2A01G092200 chr2D 91.713 181 15 0 296 476 43332035 43331855 3.800000e-63 252
8 TraesCS2A01G092200 chr2D 91.241 137 7 3 2166 2302 43293954 43293823 5.060000e-42 182
9 TraesCS2A01G092200 chr2D 81.500 200 10 6 1867 2059 43294172 43293993 3.090000e-29 139
10 TraesCS2A01G092200 chr1A 93.455 275 18 0 747 1021 133999244 133999518 2.130000e-110 409
11 TraesCS2A01G092200 chr4D 83.967 368 44 12 863 1224 329311082 329311440 2.840000e-89 339
12 TraesCS2A01G092200 chr4A 83.641 379 40 11 863 1236 140756008 140755647 1.020000e-88 337
13 TraesCS2A01G092200 chr4B 83.200 375 48 13 869 1237 409339248 409339613 1.710000e-86 329


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 TraesCS2A01G092200 chr2A 45084317 45086622 2305 True 4259.000000 4259 100.000000 1 2306 1 chr2A.!!$R1 2305
1 TraesCS2A01G092200 chr2A 45095772 45096589 817 True 950.000000 950 88.038000 496 1305 1 chr2A.!!$R2 809
2 TraesCS2A01G092200 chr2B 68200415 68202096 1681 True 1864.000000 1864 87.327000 496 2152 1 chr2B.!!$R1 1656
3 TraesCS2A01G092200 chr2B 68206680 68207221 541 True 758.000000 758 92.058000 764 1305 1 chr2B.!!$R2 541
4 TraesCS2A01G092200 chr2D 43300417 43301254 837 True 1140.000000 1140 91.365000 466 1305 1 chr2D.!!$R1 839
5 TraesCS2A01G092200 chr2D 43293823 43295590 1767 True 590.333333 1450 86.643333 501 2302 3 chr2D.!!$R2 1801
6 TraesCS2A01G092200 chr2D 43331855 43332507 652 True 255.500000 259 88.120500 4 476 2 chr2D.!!$R3 472

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
726 934 0.171455 GACGATCTCGAGCACCAAGT 59.829 55.0 7.81 1.58 43.02 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 2535 1.079127 CTTGGGTTCTGCGGATCGT 60.079 57.895 0.0 0.0 0.0 3.73 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
24 25 2.507484 CCTCATCCAGCTTGTTGTCAA 58.493 47.619 0.00 0.00 0.00 3.18
28 29 1.032014 TCCAGCTTGTTGTCAAAGCC 58.968 50.000 5.77 0.00 32.87 4.35
38 39 0.884704 TGTCAAAGCCGGAGTTGAGC 60.885 55.000 17.71 13.51 34.52 4.26
70 71 3.106738 CCCATTGGCACTGGATCTC 57.893 57.895 24.04 0.00 35.70 2.75
71 72 0.816825 CCCATTGGCACTGGATCTCG 60.817 60.000 24.04 4.21 35.70 4.04
72 73 0.178767 CCATTGGCACTGGATCTCGA 59.821 55.000 18.34 0.00 35.70 4.04
73 74 1.293924 CATTGGCACTGGATCTCGAC 58.706 55.000 0.00 0.00 0.00 4.20
77 78 1.064946 GCACTGGATCTCGACCTCG 59.935 63.158 0.00 0.00 41.45 4.63
82 83 0.965866 TGGATCTCGACCTCGCACTT 60.966 55.000 0.00 0.00 39.60 3.16
84 85 0.526524 GATCTCGACCTCGCACTTGG 60.527 60.000 0.00 0.00 39.60 3.61
88 89 2.034879 CGACCTCGCACTTGGCATT 61.035 57.895 0.00 0.00 45.17 3.56
98 99 2.416431 GCACTTGGCATTCTCAATGGAC 60.416 50.000 0.00 0.00 43.97 4.02
126 127 1.005630 GCAAGTGACGAGCTCCAGT 60.006 57.895 8.47 0.15 0.00 4.00
135 136 1.337260 ACGAGCTCCAGTTGTTGCTAG 60.337 52.381 8.47 0.00 35.76 3.42
138 139 1.071605 GCTCCAGTTGTTGCTAGTCG 58.928 55.000 0.00 0.00 0.00 4.18
147 148 2.167662 TGTTGCTAGTCGTCCATCTCA 58.832 47.619 0.00 0.00 0.00 3.27
148 149 2.760650 TGTTGCTAGTCGTCCATCTCAT 59.239 45.455 0.00 0.00 0.00 2.90
150 151 1.604278 TGCTAGTCGTCCATCTCATCG 59.396 52.381 0.00 0.00 0.00 3.84
158 159 3.550431 CATCTCATCGGCGGGGGT 61.550 66.667 7.21 0.00 0.00 4.95
214 215 0.248377 GCATTCATCTGCTTCGTGGC 60.248 55.000 0.00 0.00 39.12 5.01
215 216 0.379669 CATTCATCTGCTTCGTGGCC 59.620 55.000 0.00 0.00 0.00 5.36
218 219 4.473520 ATCTGCTTCGTGGCCGGG 62.474 66.667 2.18 0.00 33.95 5.73
232 233 2.046892 CGGGGAGCTCAAGTGTGG 60.047 66.667 17.19 0.00 0.00 4.17
236 237 0.324943 GGGAGCTCAAGTGTGGCTAA 59.675 55.000 17.19 0.00 33.17 3.09
237 238 1.677217 GGGAGCTCAAGTGTGGCTAAG 60.677 57.143 17.19 0.00 33.17 2.18
249 250 3.125316 GTGTGGCTAAGATGTTTTCCTCG 59.875 47.826 0.00 0.00 0.00 4.63
253 254 2.919228 CTAAGATGTTTTCCTCGGGGG 58.081 52.381 0.00 0.00 0.00 5.40
256 257 1.173913 GATGTTTTCCTCGGGGGTTG 58.826 55.000 0.00 0.00 36.25 3.77
264 265 2.678934 TCGGGGGTTGGACTCGAG 60.679 66.667 11.84 11.84 0.00 4.04
267 268 1.916777 GGGGGTTGGACTCGAGGAA 60.917 63.158 18.41 3.48 0.00 3.36
268 269 1.272554 GGGGGTTGGACTCGAGGAAT 61.273 60.000 18.41 0.00 0.00 3.01
270 271 1.004394 GGGGTTGGACTCGAGGAATTT 59.996 52.381 18.41 0.00 0.00 1.82
273 455 3.610911 GGTTGGACTCGAGGAATTTCAT 58.389 45.455 18.41 0.00 0.00 2.57
276 458 5.646360 GGTTGGACTCGAGGAATTTCATAAA 59.354 40.000 18.41 0.00 0.00 1.40
285 467 7.699566 TCGAGGAATTTCATAAAATAAACCCG 58.300 34.615 0.00 0.00 33.93 5.28
286 468 7.553402 TCGAGGAATTTCATAAAATAAACCCGA 59.447 33.333 0.00 0.00 33.93 5.14
290 472 9.256477 GGAATTTCATAAAATAAACCCGATTCC 57.744 33.333 0.00 0.00 33.93 3.01
291 473 8.865590 AATTTCATAAAATAAACCCGATTCCG 57.134 30.769 0.00 0.00 33.93 4.30
293 475 7.627298 TTCATAAAATAAACCCGATTCCGAA 57.373 32.000 0.00 0.00 38.22 4.30
294 476 7.254227 TCATAAAATAAACCCGATTCCGAAG 57.746 36.000 0.00 0.00 38.22 3.79
307 489 6.092748 CCGATTCCGAAGAATTTCACAAAAT 58.907 36.000 0.00 0.00 42.93 1.82
310 492 5.782893 TCCGAAGAATTTCACAAAATGGT 57.217 34.783 0.00 0.00 35.27 3.55
323 505 4.152759 CACAAAATGGTCCATTTGCATGAC 59.847 41.667 26.94 0.00 42.32 3.06
329 511 2.098108 CATTTGCATGACGCGCGA 59.902 55.556 39.36 16.76 46.97 5.87
364 546 1.306148 CTAGATAGCACGACGACCCA 58.694 55.000 0.00 0.00 0.00 4.51
365 547 1.264557 CTAGATAGCACGACGACCCAG 59.735 57.143 0.00 0.00 0.00 4.45
366 548 1.589196 GATAGCACGACGACCCAGC 60.589 63.158 0.00 0.00 0.00 4.85
367 549 2.005960 GATAGCACGACGACCCAGCT 62.006 60.000 0.00 5.38 39.22 4.24
368 550 1.605058 ATAGCACGACGACCCAGCTT 61.605 55.000 0.00 0.00 36.80 3.74
369 551 2.486636 TAGCACGACGACCCAGCTTG 62.487 60.000 0.00 0.00 36.80 4.01
370 552 2.338620 CACGACGACCCAGCTTGA 59.661 61.111 0.00 0.00 0.00 3.02
371 553 1.734477 CACGACGACCCAGCTTGAG 60.734 63.158 0.00 0.00 0.00 3.02
372 554 2.125912 CGACGACCCAGCTTGAGG 60.126 66.667 0.00 0.00 0.00 3.86
373 555 2.435059 GACGACCCAGCTTGAGGC 60.435 66.667 0.00 0.00 42.19 4.70
383 565 3.688553 GCTTGAGGCGCCTTACTAT 57.311 52.632 33.34 6.93 0.00 2.12
384 566 1.954927 GCTTGAGGCGCCTTACTATT 58.045 50.000 33.34 5.97 0.00 1.73
385 567 2.289565 GCTTGAGGCGCCTTACTATTT 58.710 47.619 33.34 5.00 0.00 1.40
386 568 3.463944 GCTTGAGGCGCCTTACTATTTA 58.536 45.455 33.34 9.33 0.00 1.40
387 569 3.495001 GCTTGAGGCGCCTTACTATTTAG 59.505 47.826 33.34 19.98 0.00 1.85
388 570 3.107642 TGAGGCGCCTTACTATTTAGC 57.892 47.619 33.34 14.19 0.00 3.09
389 571 2.432874 TGAGGCGCCTTACTATTTAGCA 59.567 45.455 33.34 16.93 0.00 3.49
390 572 3.071023 TGAGGCGCCTTACTATTTAGCAT 59.929 43.478 33.34 1.58 0.00 3.79
391 573 3.403038 AGGCGCCTTACTATTTAGCATG 58.597 45.455 27.08 0.00 0.00 4.06
392 574 3.071023 AGGCGCCTTACTATTTAGCATGA 59.929 43.478 27.08 0.00 0.00 3.07
393 575 3.186613 GGCGCCTTACTATTTAGCATGAC 59.813 47.826 22.15 0.00 0.00 3.06
394 576 3.807622 GCGCCTTACTATTTAGCATGACA 59.192 43.478 0.00 0.00 0.00 3.58
395 577 4.318831 GCGCCTTACTATTTAGCATGACAC 60.319 45.833 0.00 0.00 0.00 3.67
396 578 4.211374 CGCCTTACTATTTAGCATGACACC 59.789 45.833 0.00 0.00 0.00 4.16
397 579 4.515567 GCCTTACTATTTAGCATGACACCC 59.484 45.833 0.00 0.00 0.00 4.61
398 580 5.063880 CCTTACTATTTAGCATGACACCCC 58.936 45.833 0.00 0.00 0.00 4.95
399 581 5.397447 CCTTACTATTTAGCATGACACCCCA 60.397 44.000 0.00 0.00 0.00 4.96
400 582 4.584638 ACTATTTAGCATGACACCCCAA 57.415 40.909 0.00 0.00 0.00 4.12
401 583 4.526970 ACTATTTAGCATGACACCCCAAG 58.473 43.478 0.00 0.00 0.00 3.61
402 584 1.544724 TTTAGCATGACACCCCAAGC 58.455 50.000 0.00 0.00 0.00 4.01
403 585 0.323360 TTAGCATGACACCCCAAGCC 60.323 55.000 0.00 0.00 31.76 4.35
404 586 2.210144 TAGCATGACACCCCAAGCCC 62.210 60.000 0.00 0.00 31.76 5.19
405 587 2.440147 CATGACACCCCAAGCCCA 59.560 61.111 0.00 0.00 0.00 5.36
406 588 1.000739 CATGACACCCCAAGCCCAT 59.999 57.895 0.00 0.00 0.00 4.00
407 589 1.000739 ATGACACCCCAAGCCCATG 59.999 57.895 0.00 0.00 0.00 3.66
408 590 1.803453 ATGACACCCCAAGCCCATGT 61.803 55.000 0.00 0.00 0.00 3.21
409 591 1.678970 GACACCCCAAGCCCATGTC 60.679 63.158 0.00 0.00 33.50 3.06
410 592 2.751436 CACCCCAAGCCCATGTCG 60.751 66.667 0.00 0.00 0.00 4.35
411 593 2.933287 ACCCCAAGCCCATGTCGA 60.933 61.111 0.00 0.00 0.00 4.20
412 594 2.308722 ACCCCAAGCCCATGTCGAT 61.309 57.895 0.00 0.00 0.00 3.59
413 595 0.986019 ACCCCAAGCCCATGTCGATA 60.986 55.000 0.00 0.00 0.00 2.92
414 596 0.401738 CCCCAAGCCCATGTCGATAT 59.598 55.000 0.00 0.00 0.00 1.63
415 597 1.527034 CCCAAGCCCATGTCGATATG 58.473 55.000 14.67 14.67 0.00 1.78
416 598 1.527034 CCAAGCCCATGTCGATATGG 58.473 55.000 28.92 28.92 45.83 2.74
421 603 3.963733 CCATGTCGATATGGGCCAT 57.036 52.632 28.39 24.69 43.16 4.40
422 604 2.205022 CCATGTCGATATGGGCCATT 57.795 50.000 28.39 12.59 43.16 3.16
423 605 2.517959 CCATGTCGATATGGGCCATTT 58.482 47.619 28.39 17.78 43.16 2.32
424 606 2.892852 CCATGTCGATATGGGCCATTTT 59.107 45.455 28.39 13.05 43.16 1.82
425 607 3.321682 CCATGTCGATATGGGCCATTTTT 59.678 43.478 28.39 10.25 43.16 1.94
448 630 8.710835 TTTTGAATACCTTTTGAAACCTGTTC 57.289 30.769 0.00 0.00 0.00 3.18
449 631 7.411486 TTGAATACCTTTTGAAACCTGTTCA 57.589 32.000 0.00 0.00 0.00 3.18
450 632 7.595819 TGAATACCTTTTGAAACCTGTTCAT 57.404 32.000 0.00 0.00 0.00 2.57
451 633 8.017418 TGAATACCTTTTGAAACCTGTTCATT 57.983 30.769 0.00 0.00 0.00 2.57
452 634 8.482128 TGAATACCTTTTGAAACCTGTTCATTT 58.518 29.630 0.00 0.00 0.00 2.32
453 635 9.325198 GAATACCTTTTGAAACCTGTTCATTTT 57.675 29.630 0.00 0.00 0.00 1.82
454 636 6.983474 ACCTTTTGAAACCTGTTCATTTTG 57.017 33.333 0.00 0.00 0.00 2.44
455 637 6.472016 ACCTTTTGAAACCTGTTCATTTTGT 58.528 32.000 0.00 0.00 0.00 2.83
456 638 6.371271 ACCTTTTGAAACCTGTTCATTTTGTG 59.629 34.615 0.00 0.00 0.00 3.33
457 639 6.371271 CCTTTTGAAACCTGTTCATTTTGTGT 59.629 34.615 0.00 0.00 0.00 3.72
458 640 7.094848 CCTTTTGAAACCTGTTCATTTTGTGTT 60.095 33.333 0.00 0.00 0.00 3.32
459 641 8.833231 TTTTGAAACCTGTTCATTTTGTGTTA 57.167 26.923 0.00 0.00 0.00 2.41
460 642 8.833231 TTTGAAACCTGTTCATTTTGTGTTAA 57.167 26.923 0.00 0.00 0.00 2.01
461 643 8.833231 TTGAAACCTGTTCATTTTGTGTTAAA 57.167 26.923 0.00 0.00 0.00 1.52
462 644 8.472683 TGAAACCTGTTCATTTTGTGTTAAAG 57.527 30.769 0.00 0.00 0.00 1.85
463 645 8.307483 TGAAACCTGTTCATTTTGTGTTAAAGA 58.693 29.630 0.00 0.00 0.00 2.52
464 646 9.313118 GAAACCTGTTCATTTTGTGTTAAAGAT 57.687 29.630 0.00 0.00 0.00 2.40
510 692 4.453480 TTTTCACTCTGATTGGTTCCCT 57.547 40.909 0.00 0.00 0.00 4.20
512 694 2.338809 TCACTCTGATTGGTTCCCTGT 58.661 47.619 0.00 0.00 0.00 4.00
555 737 0.463204 CCATCATCCGACTCAGCAGT 59.537 55.000 0.00 0.00 34.57 4.40
649 843 2.174969 CGCTATAAAACGCGCCCCA 61.175 57.895 5.73 0.00 43.01 4.96
682 878 1.988293 CTCCAATCTCTCGGAGCCTA 58.012 55.000 0.00 0.00 42.30 3.93
714 919 2.018544 CTTCTCGCCGAGACGATCT 58.981 57.895 17.79 0.00 42.02 2.75
724 932 0.452184 GAGACGATCTCGAGCACCAA 59.548 55.000 7.81 0.00 43.02 3.67
725 933 0.453793 AGACGATCTCGAGCACCAAG 59.546 55.000 7.81 0.00 43.02 3.61
726 934 0.171455 GACGATCTCGAGCACCAAGT 59.829 55.000 7.81 1.58 43.02 3.16
737 945 3.673594 CGAGCACCAAGTAGTAGTTGAGG 60.674 52.174 17.69 10.62 30.18 3.86
740 948 3.834610 CACCAAGTAGTAGTTGAGGTCG 58.165 50.000 17.69 4.71 30.18 4.79
1349 1596 4.612412 TGGACGACGCCCACAACC 62.612 66.667 0.00 0.00 0.00 3.77
1350 1597 4.612412 GGACGACGCCCACAACCA 62.612 66.667 0.00 0.00 0.00 3.67
1603 1886 4.010667 TGGCTTGTACTGGACGTAATTT 57.989 40.909 0.00 0.00 0.00 1.82
1625 1908 3.170791 TCTTCACCGCAATTTGCAAAA 57.829 38.095 17.19 8.02 45.36 2.44
1628 1911 4.574013 TCTTCACCGCAATTTGCAAAATTT 59.426 33.333 17.19 3.89 45.36 1.82
1726 2017 5.402270 CGGTTGACCACAATTTTCATCTTTC 59.598 40.000 0.51 0.00 38.32 2.62
1750 2041 1.827315 GCGTGCGCAGTAAACAGTCA 61.827 55.000 12.22 0.00 41.49 3.41
1753 2044 0.105964 TGCGCAGTAAACAGTCAGGT 59.894 50.000 5.66 0.00 0.00 4.00
1756 2047 2.803956 GCGCAGTAAACAGTCAGGTTTA 59.196 45.455 0.30 0.00 41.07 2.01
1758 2049 4.610680 GCGCAGTAAACAGTCAGGTTTAAG 60.611 45.833 0.30 0.00 42.87 1.85
1760 2051 5.007332 CGCAGTAAACAGTCAGGTTTAAGTT 59.993 40.000 0.00 0.00 42.87 2.66
1761 2052 6.427974 GCAGTAAACAGTCAGGTTTAAGTTC 58.572 40.000 0.00 0.00 42.87 3.01
1762 2053 6.260271 GCAGTAAACAGTCAGGTTTAAGTTCT 59.740 38.462 0.00 0.00 42.87 3.01
1763 2054 7.630924 CAGTAAACAGTCAGGTTTAAGTTCTG 58.369 38.462 0.00 0.00 42.87 3.02
1764 2055 7.494625 CAGTAAACAGTCAGGTTTAAGTTCTGA 59.505 37.037 0.00 0.00 42.87 3.27
1793 2084 6.993079 TGAGCATACTCTAACAGAAGAACAA 58.007 36.000 0.00 0.00 43.85 2.83
1801 2092 8.649973 ACTCTAACAGAAGAACAACTTTACAG 57.350 34.615 0.00 0.00 39.13 2.74
1851 2213 0.183014 TTCACCGGCCTACCAAAACA 59.817 50.000 0.00 0.00 34.57 2.83
1856 2218 2.167662 CCGGCCTACCAAAACATCTTT 58.832 47.619 0.00 0.00 34.57 2.52
1857 2219 3.244981 ACCGGCCTACCAAAACATCTTTA 60.245 43.478 0.00 0.00 34.57 1.85
1858 2220 3.128068 CCGGCCTACCAAAACATCTTTAC 59.872 47.826 0.00 0.00 34.57 2.01
1859 2221 3.754323 CGGCCTACCAAAACATCTTTACA 59.246 43.478 0.00 0.00 34.57 2.41
1861 2223 5.587043 CGGCCTACCAAAACATCTTTACATA 59.413 40.000 0.00 0.00 34.57 2.29
1865 2227 7.425606 CCTACCAAAACATCTTTACATATGGC 58.574 38.462 7.80 0.00 0.00 4.40
1936 2316 2.433868 TACACTGCCGAAGTTCAGAC 57.566 50.000 3.32 0.00 36.83 3.51
1943 2323 2.224281 TGCCGAAGTTCAGACTGATGTT 60.224 45.455 5.87 2.75 35.91 2.71
1947 2327 4.692625 CCGAAGTTCAGACTGATGTTGAAT 59.307 41.667 5.87 0.00 35.91 2.57
1962 2342 8.105097 TGATGTTGAATAATTCCAACGAAAGA 57.895 30.769 11.27 0.00 43.96 2.52
1963 2343 8.572185 TGATGTTGAATAATTCCAACGAAAGAA 58.428 29.630 11.27 0.00 43.96 2.52
1964 2344 8.970691 ATGTTGAATAATTCCAACGAAAGAAG 57.029 30.769 11.27 0.00 43.96 2.85
1965 2345 8.160521 TGTTGAATAATTCCAACGAAAGAAGA 57.839 30.769 11.27 0.00 43.96 2.87
1966 2346 8.625651 TGTTGAATAATTCCAACGAAAGAAGAA 58.374 29.630 11.27 0.00 43.96 2.52
1967 2347 9.458374 GTTGAATAATTCCAACGAAAGAAGAAA 57.542 29.630 0.00 0.00 34.20 2.52
1968 2348 9.677567 TTGAATAATTCCAACGAAAGAAGAAAG 57.322 29.630 0.00 0.00 0.00 2.62
1969 2349 9.062524 TGAATAATTCCAACGAAAGAAGAAAGA 57.937 29.630 0.00 0.00 0.00 2.52
2003 2383 1.572415 AGATTCCCATGGCACCTGATT 59.428 47.619 6.09 0.00 0.00 2.57
2004 2384 2.023695 AGATTCCCATGGCACCTGATTT 60.024 45.455 6.09 0.00 0.00 2.17
2005 2385 1.559368 TTCCCATGGCACCTGATTTG 58.441 50.000 6.09 0.00 0.00 2.32
2006 2386 0.703488 TCCCATGGCACCTGATTTGA 59.297 50.000 6.09 0.00 0.00 2.69
2007 2387 1.288633 TCCCATGGCACCTGATTTGAT 59.711 47.619 6.09 0.00 0.00 2.57
2008 2388 2.112998 CCCATGGCACCTGATTTGATT 58.887 47.619 6.09 0.00 0.00 2.57
2009 2389 2.502538 CCCATGGCACCTGATTTGATTT 59.497 45.455 6.09 0.00 0.00 2.17
2010 2390 3.527533 CCATGGCACCTGATTTGATTTG 58.472 45.455 0.00 0.00 0.00 2.32
2011 2391 3.196039 CCATGGCACCTGATTTGATTTGA 59.804 43.478 0.00 0.00 0.00 2.69
2012 2392 4.141801 CCATGGCACCTGATTTGATTTGAT 60.142 41.667 0.00 0.00 0.00 2.57
2053 2433 2.602257 AAAGCAAACAAGAGTTGCCC 57.398 45.000 5.56 0.00 38.17 5.36
2054 2434 1.780503 AAGCAAACAAGAGTTGCCCT 58.219 45.000 5.56 0.00 38.17 5.19
2055 2435 1.035139 AGCAAACAAGAGTTGCCCTG 58.965 50.000 5.56 0.00 38.17 4.45
2056 2436 1.032014 GCAAACAAGAGTTGCCCTGA 58.968 50.000 0.00 0.00 38.17 3.86
2057 2437 1.408702 GCAAACAAGAGTTGCCCTGAA 59.591 47.619 0.00 0.00 38.17 3.02
2058 2438 2.159114 GCAAACAAGAGTTGCCCTGAAA 60.159 45.455 0.00 0.00 38.17 2.69
2059 2439 3.447742 CAAACAAGAGTTGCCCTGAAAC 58.552 45.455 0.00 0.00 38.17 2.78
2060 2440 2.736670 ACAAGAGTTGCCCTGAAACT 57.263 45.000 0.00 0.00 40.54 2.66
2061 2441 2.301346 ACAAGAGTTGCCCTGAAACTG 58.699 47.619 0.00 0.00 37.98 3.16
2062 2442 2.092429 ACAAGAGTTGCCCTGAAACTGA 60.092 45.455 0.00 0.00 37.98 3.41
2063 2443 2.951642 CAAGAGTTGCCCTGAAACTGAA 59.048 45.455 0.00 0.00 37.98 3.02
2064 2444 3.297134 AGAGTTGCCCTGAAACTGAAA 57.703 42.857 0.00 0.00 37.98 2.69
2065 2445 2.952310 AGAGTTGCCCTGAAACTGAAAC 59.048 45.455 0.00 0.00 37.98 2.78
2066 2446 2.952310 GAGTTGCCCTGAAACTGAAACT 59.048 45.455 0.00 0.00 37.98 2.66
2102 2482 0.538287 AGCTGGGCTGGAACTGAAAC 60.538 55.000 0.00 0.00 37.57 2.78
2180 2569 0.889186 GCAGAACCCAAGCGAGGAAA 60.889 55.000 0.00 0.00 0.00 3.13
2210 2599 3.386402 ACATGTTCCCCAAATCAAACGTT 59.614 39.130 0.00 0.00 0.00 3.99
2221 2610 1.064946 CAAACGTTGCTTTCCGGCA 59.935 52.632 0.00 0.00 40.74 5.69
2229 2618 0.539438 TGCTTTCCGGCATCCAAACT 60.539 50.000 0.00 0.00 37.29 2.66
2296 2685 3.897122 GGAACCACAGGGCCACCA 61.897 66.667 6.18 0.00 40.13 4.17
2299 2688 4.684134 ACCACAGGGCCACCATGC 62.684 66.667 6.18 0.00 40.13 4.06
2304 2693 4.753662 AGGGCCACCATGCTGCAG 62.754 66.667 10.11 10.11 40.13 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.111061 AACAAGCTGGATGAGGCACA 59.889 50.000 0.00 0.00 0.00 4.57
1 2 0.524862 CAACAAGCTGGATGAGGCAC 59.475 55.000 0.00 0.00 0.00 5.01
2 3 0.111061 ACAACAAGCTGGATGAGGCA 59.889 50.000 5.20 0.00 0.00 4.75
8 9 1.615392 GGCTTTGACAACAAGCTGGAT 59.385 47.619 10.82 0.00 37.32 3.41
11 12 0.318107 CCGGCTTTGACAACAAGCTG 60.318 55.000 12.08 12.08 37.32 4.24
14 15 1.308998 ACTCCGGCTTTGACAACAAG 58.691 50.000 0.00 0.00 37.32 3.16
16 17 1.021202 CAACTCCGGCTTTGACAACA 58.979 50.000 8.75 0.00 0.00 3.33
56 57 0.904865 AGGTCGAGATCCAGTGCCAA 60.905 55.000 0.00 0.00 0.00 4.52
62 63 1.064946 GTGCGAGGTCGAGATCCAG 59.935 63.158 2.94 0.00 43.02 3.86
70 71 1.970917 GAATGCCAAGTGCGAGGTCG 61.971 60.000 0.00 0.00 45.60 4.79
71 72 0.674895 AGAATGCCAAGTGCGAGGTC 60.675 55.000 0.00 0.00 45.60 3.85
72 73 0.674895 GAGAATGCCAAGTGCGAGGT 60.675 55.000 0.00 0.00 45.60 3.85
73 74 0.674581 TGAGAATGCCAAGTGCGAGG 60.675 55.000 0.00 0.00 45.60 4.63
77 78 1.820519 TCCATTGAGAATGCCAAGTGC 59.179 47.619 0.00 0.00 37.57 4.40
82 83 3.548770 GAGATGTCCATTGAGAATGCCA 58.451 45.455 0.00 0.00 37.57 4.92
84 85 3.201290 ACGAGATGTCCATTGAGAATGC 58.799 45.455 0.00 0.00 37.57 3.56
107 108 1.291588 CTGGAGCTCGTCACTTGCT 59.708 57.895 7.83 0.00 40.02 3.91
113 114 0.880278 GCAACAACTGGAGCTCGTCA 60.880 55.000 7.83 0.00 0.00 4.35
126 127 2.560981 TGAGATGGACGACTAGCAACAA 59.439 45.455 0.00 0.00 0.00 2.83
135 136 1.658717 CGCCGATGAGATGGACGAC 60.659 63.158 0.00 0.00 0.00 4.34
138 139 2.029666 CCCGCCGATGAGATGGAC 59.970 66.667 0.00 0.00 0.00 4.02
170 171 2.470362 CGAGAAGAGGAGCGCCGTA 61.470 63.158 2.29 0.00 39.96 4.02
171 172 3.816524 CGAGAAGAGGAGCGCCGT 61.817 66.667 2.29 0.00 39.96 5.68
175 176 0.730834 CACACACGAGAAGAGGAGCG 60.731 60.000 0.00 0.00 0.00 5.03
214 215 2.046892 CACACTTGAGCTCCCCGG 60.047 66.667 12.15 0.00 0.00 5.73
215 216 2.046892 CCACACTTGAGCTCCCCG 60.047 66.667 12.15 1.68 0.00 5.73
218 219 1.276421 TCTTAGCCACACTTGAGCTCC 59.724 52.381 12.15 0.00 38.06 4.70
228 229 3.334691 CGAGGAAAACATCTTAGCCACA 58.665 45.455 0.00 0.00 0.00 4.17
232 233 2.289565 CCCCGAGGAAAACATCTTAGC 58.710 52.381 0.00 0.00 33.47 3.09
236 237 1.073098 AACCCCCGAGGAAAACATCT 58.927 50.000 0.00 0.00 39.89 2.90
237 238 1.173913 CAACCCCCGAGGAAAACATC 58.826 55.000 0.00 0.00 39.89 3.06
249 250 1.272554 ATTCCTCGAGTCCAACCCCC 61.273 60.000 12.31 0.00 0.00 5.40
253 254 6.737254 TTTATGAAATTCCTCGAGTCCAAC 57.263 37.500 12.31 0.00 0.00 3.77
256 257 9.717892 GTTTATTTTATGAAATTCCTCGAGTCC 57.282 33.333 12.31 0.00 36.82 3.85
264 265 9.256477 GGAATCGGGTTTATTTTATGAAATTCC 57.744 33.333 0.26 2.75 36.82 3.01
267 268 8.228035 TCGGAATCGGGTTTATTTTATGAAAT 57.772 30.769 0.74 0.74 36.87 2.17
268 269 7.627298 TCGGAATCGGGTTTATTTTATGAAA 57.373 32.000 0.00 0.00 36.95 2.69
270 271 7.049133 TCTTCGGAATCGGGTTTATTTTATGA 58.951 34.615 0.00 0.00 36.95 2.15
273 455 7.868906 ATTCTTCGGAATCGGGTTTATTTTA 57.131 32.000 0.00 0.00 40.28 1.52
276 458 6.376018 TGAAATTCTTCGGAATCGGGTTTATT 59.624 34.615 0.00 0.00 43.14 1.40
285 467 6.868339 ACCATTTTGTGAAATTCTTCGGAATC 59.132 34.615 0.00 0.00 43.14 2.52
286 468 6.758254 ACCATTTTGTGAAATTCTTCGGAAT 58.242 32.000 0.00 0.00 45.57 3.01
290 472 5.527951 TGGACCATTTTGTGAAATTCTTCG 58.472 37.500 0.00 0.00 33.25 3.79
291 473 7.967890 AATGGACCATTTTGTGAAATTCTTC 57.032 32.000 14.28 0.00 33.25 2.87
293 475 6.205270 GCAAATGGACCATTTTGTGAAATTCT 59.795 34.615 26.65 2.02 40.60 2.40
294 476 6.017275 TGCAAATGGACCATTTTGTGAAATTC 60.017 34.615 26.65 7.19 40.60 2.17
307 489 1.882311 GCGTCATGCAAATGGACCA 59.118 52.632 0.00 0.00 45.45 4.02
310 492 2.484662 GCGCGTCATGCAAATGGA 59.515 55.556 8.43 0.00 46.97 3.41
361 543 3.329542 TAAGGCGCCTCAAGCTGGG 62.330 63.158 32.93 0.00 40.39 4.45
362 544 2.109126 GTAAGGCGCCTCAAGCTGG 61.109 63.158 32.93 0.00 40.39 4.85
363 545 0.175760 TAGTAAGGCGCCTCAAGCTG 59.824 55.000 32.93 0.00 40.39 4.24
364 546 1.123928 ATAGTAAGGCGCCTCAAGCT 58.876 50.000 32.93 24.99 40.39 3.74
365 547 1.954927 AATAGTAAGGCGCCTCAAGC 58.045 50.000 32.93 19.42 38.52 4.01
366 548 3.495001 GCTAAATAGTAAGGCGCCTCAAG 59.505 47.826 32.93 17.80 0.00 3.02
367 549 3.118555 TGCTAAATAGTAAGGCGCCTCAA 60.119 43.478 32.93 19.09 0.00 3.02
368 550 2.432874 TGCTAAATAGTAAGGCGCCTCA 59.567 45.455 32.93 14.52 0.00 3.86
369 551 3.107642 TGCTAAATAGTAAGGCGCCTC 57.892 47.619 32.93 19.21 0.00 4.70
370 552 3.071023 TCATGCTAAATAGTAAGGCGCCT 59.929 43.478 27.08 27.08 0.00 5.52
371 553 3.186613 GTCATGCTAAATAGTAAGGCGCC 59.813 47.826 21.89 21.89 0.00 6.53
372 554 3.807622 TGTCATGCTAAATAGTAAGGCGC 59.192 43.478 0.00 0.00 0.00 6.53
373 555 4.211374 GGTGTCATGCTAAATAGTAAGGCG 59.789 45.833 0.00 0.00 0.00 5.52
374 556 4.515567 GGGTGTCATGCTAAATAGTAAGGC 59.484 45.833 0.00 0.00 0.00 4.35
375 557 5.063880 GGGGTGTCATGCTAAATAGTAAGG 58.936 45.833 0.00 0.00 0.00 2.69
376 558 5.680619 TGGGGTGTCATGCTAAATAGTAAG 58.319 41.667 0.00 0.00 0.00 2.34
377 559 5.702065 TGGGGTGTCATGCTAAATAGTAA 57.298 39.130 0.00 0.00 0.00 2.24
378 560 5.680619 CTTGGGGTGTCATGCTAAATAGTA 58.319 41.667 0.00 0.00 0.00 1.82
379 561 4.526970 CTTGGGGTGTCATGCTAAATAGT 58.473 43.478 0.00 0.00 0.00 2.12
380 562 3.316308 GCTTGGGGTGTCATGCTAAATAG 59.684 47.826 0.00 0.00 35.67 1.73
381 563 3.287222 GCTTGGGGTGTCATGCTAAATA 58.713 45.455 0.00 0.00 35.67 1.40
382 564 2.102578 GCTTGGGGTGTCATGCTAAAT 58.897 47.619 0.00 0.00 35.67 1.40
383 565 1.544724 GCTTGGGGTGTCATGCTAAA 58.455 50.000 0.00 0.00 35.67 1.85
384 566 0.323360 GGCTTGGGGTGTCATGCTAA 60.323 55.000 0.00 0.00 37.76 3.09
385 567 1.302949 GGCTTGGGGTGTCATGCTA 59.697 57.895 0.00 0.00 37.76 3.49
386 568 2.036256 GGCTTGGGGTGTCATGCT 59.964 61.111 0.00 0.00 37.76 3.79
387 569 3.070576 GGGCTTGGGGTGTCATGC 61.071 66.667 0.00 0.00 37.17 4.06
388 570 1.000739 ATGGGCTTGGGGTGTCATG 59.999 57.895 0.00 0.00 0.00 3.07
389 571 1.000739 CATGGGCTTGGGGTGTCAT 59.999 57.895 0.00 0.00 0.00 3.06
390 572 2.424842 GACATGGGCTTGGGGTGTCA 62.425 60.000 0.00 0.00 39.10 3.58
391 573 1.678970 GACATGGGCTTGGGGTGTC 60.679 63.158 0.00 0.00 33.32 3.67
392 574 2.440599 GACATGGGCTTGGGGTGT 59.559 61.111 0.00 0.00 0.00 4.16
393 575 2.556840 ATCGACATGGGCTTGGGGTG 62.557 60.000 0.00 0.00 0.00 4.61
394 576 0.986019 TATCGACATGGGCTTGGGGT 60.986 55.000 0.00 0.00 0.00 4.95
395 577 0.401738 ATATCGACATGGGCTTGGGG 59.598 55.000 0.00 0.00 0.00 4.96
396 578 1.527034 CATATCGACATGGGCTTGGG 58.473 55.000 0.00 0.00 0.00 4.12
397 579 1.527034 CCATATCGACATGGGCTTGG 58.473 55.000 15.26 0.00 41.63 3.61
403 585 2.205022 AATGGCCCATATCGACATGG 57.795 50.000 16.11 16.11 44.44 3.66
404 586 4.589216 AAAAATGGCCCATATCGACATG 57.411 40.909 0.00 0.00 0.00 3.21
422 604 9.157104 GAACAGGTTTCAAAAGGTATTCAAAAA 57.843 29.630 0.00 0.00 0.00 1.94
423 605 8.314751 TGAACAGGTTTCAAAAGGTATTCAAAA 58.685 29.630 0.00 0.00 0.00 2.44
424 606 7.841956 TGAACAGGTTTCAAAAGGTATTCAAA 58.158 30.769 0.00 0.00 0.00 2.69
425 607 7.411486 TGAACAGGTTTCAAAAGGTATTCAA 57.589 32.000 0.00 0.00 0.00 2.69
426 608 7.595819 ATGAACAGGTTTCAAAAGGTATTCA 57.404 32.000 0.00 0.00 31.55 2.57
427 609 8.887036 AAATGAACAGGTTTCAAAAGGTATTC 57.113 30.769 0.00 0.00 31.55 1.75
428 610 9.108284 CAAAATGAACAGGTTTCAAAAGGTATT 57.892 29.630 0.00 0.00 31.55 1.89
429 611 8.264347 ACAAAATGAACAGGTTTCAAAAGGTAT 58.736 29.630 0.00 0.00 31.55 2.73
430 612 7.547370 CACAAAATGAACAGGTTTCAAAAGGTA 59.453 33.333 0.00 0.00 31.55 3.08
431 613 6.371271 CACAAAATGAACAGGTTTCAAAAGGT 59.629 34.615 0.00 0.00 31.55 3.50
432 614 6.371271 ACACAAAATGAACAGGTTTCAAAAGG 59.629 34.615 0.00 0.00 31.55 3.11
433 615 7.363205 ACACAAAATGAACAGGTTTCAAAAG 57.637 32.000 0.00 0.00 31.55 2.27
434 616 7.736447 AACACAAAATGAACAGGTTTCAAAA 57.264 28.000 0.00 0.00 31.55 2.44
435 617 8.833231 TTAACACAAAATGAACAGGTTTCAAA 57.167 26.923 0.00 0.00 31.55 2.69
436 618 8.833231 TTTAACACAAAATGAACAGGTTTCAA 57.167 26.923 0.00 0.00 31.55 2.69
437 619 8.307483 TCTTTAACACAAAATGAACAGGTTTCA 58.693 29.630 0.00 0.00 0.00 2.69
438 620 8.696410 TCTTTAACACAAAATGAACAGGTTTC 57.304 30.769 0.00 0.00 0.00 2.78
439 621 9.665719 AATCTTTAACACAAAATGAACAGGTTT 57.334 25.926 0.00 0.00 0.00 3.27
440 622 9.665719 AAATCTTTAACACAAAATGAACAGGTT 57.334 25.926 0.00 0.00 0.00 3.50
472 654 1.937191 AAATTGACGGATTTGCCCCT 58.063 45.000 0.00 0.00 0.00 4.79
526 708 2.123428 GGATGATGGGTGCTGGTGC 61.123 63.158 0.00 0.00 40.20 5.01
530 712 0.531532 GAGTCGGATGATGGGTGCTG 60.532 60.000 0.00 0.00 0.00 4.41
532 714 0.531532 CTGAGTCGGATGATGGGTGC 60.532 60.000 0.00 0.00 0.00 5.01
573 761 3.953775 CCAGGGTGGACGGCAACT 61.954 66.667 0.00 0.00 40.96 3.16
612 800 3.993234 GTGCGCGCGATGATGGAG 61.993 66.667 37.18 0.23 0.00 3.86
682 878 1.069568 CGAGAAGCAGCGAGATACGAT 60.070 52.381 0.00 0.00 45.77 3.73
714 919 3.151554 TCAACTACTACTTGGTGCTCGA 58.848 45.455 0.00 0.00 0.00 4.04
721 929 3.427773 GCTCGACCTCAACTACTACTTGG 60.428 52.174 0.00 0.00 0.00 3.61
724 932 2.367486 GGCTCGACCTCAACTACTACT 58.633 52.381 0.00 0.00 34.51 2.57
725 933 1.063764 CGGCTCGACCTCAACTACTAC 59.936 57.143 3.15 0.00 35.61 2.73
726 934 1.376543 CGGCTCGACCTCAACTACTA 58.623 55.000 3.15 0.00 35.61 1.82
758 978 0.458716 GGAGACGAAGAAGAAGGCGG 60.459 60.000 0.00 0.00 0.00 6.13
759 979 3.037485 GGAGACGAAGAAGAAGGCG 57.963 57.895 0.00 0.00 0.00 5.52
1125 1372 2.434884 CAGGCGTGCACCCAGTAG 60.435 66.667 21.71 5.15 0.00 2.57
1346 1593 2.667199 GCGTACGCCCAAGTGGTT 60.667 61.111 29.51 0.00 36.04 3.67
1349 1596 2.749865 CCATGCGTACGCCCAAGTG 61.750 63.158 35.11 23.52 41.09 3.16
1350 1597 2.435938 CCATGCGTACGCCCAAGT 60.436 61.111 35.11 14.56 41.09 3.16
1458 1720 3.284197 CCGGTTCGATCGGCTATTT 57.716 52.632 16.41 0.00 41.07 1.40
1625 1908 4.832248 TCAACAGAGCGACCAGATAAAAT 58.168 39.130 0.00 0.00 0.00 1.82
1628 1911 4.471904 AATCAACAGAGCGACCAGATAA 57.528 40.909 0.00 0.00 0.00 1.75
1750 2041 5.163301 TGCTCAGAAGTCAGAACTTAAACCT 60.163 40.000 0.00 0.00 45.80 3.50
1753 2044 7.671302 AGTATGCTCAGAAGTCAGAACTTAAA 58.329 34.615 0.00 0.00 45.80 1.52
1756 2047 5.480073 AGAGTATGCTCAGAAGTCAGAACTT 59.520 40.000 13.64 0.00 44.89 2.66
1758 2049 5.323371 AGAGTATGCTCAGAAGTCAGAAC 57.677 43.478 13.64 0.00 44.00 3.01
1760 2051 5.946377 TGTTAGAGTATGCTCAGAAGTCAGA 59.054 40.000 13.64 0.00 44.00 3.27
1761 2052 6.094742 TCTGTTAGAGTATGCTCAGAAGTCAG 59.905 42.308 13.64 10.38 44.00 3.51
1762 2053 5.946377 TCTGTTAGAGTATGCTCAGAAGTCA 59.054 40.000 13.64 2.13 44.00 3.41
1763 2054 6.443934 TCTGTTAGAGTATGCTCAGAAGTC 57.556 41.667 13.64 0.00 44.00 3.01
1764 2055 6.661377 TCTTCTGTTAGAGTATGCTCAGAAGT 59.339 38.462 25.46 7.13 42.56 3.01
1765 2056 7.094508 TCTTCTGTTAGAGTATGCTCAGAAG 57.905 40.000 22.96 22.96 42.91 2.85
1793 2084 7.889873 ATACTGCTCTATGTCTCTGTAAAGT 57.110 36.000 0.00 0.00 0.00 2.66
1856 2218 9.250246 TGCACTAGTAATATACTGCCATATGTA 57.750 33.333 1.24 0.00 39.81 2.29
1857 2219 8.134202 TGCACTAGTAATATACTGCCATATGT 57.866 34.615 1.24 0.00 39.81 2.29
1858 2220 9.435688 TTTGCACTAGTAATATACTGCCATATG 57.564 33.333 0.00 0.00 39.81 1.78
1859 2221 9.436957 GTTTGCACTAGTAATATACTGCCATAT 57.563 33.333 0.00 0.00 39.81 1.78
1861 2223 7.279615 TGTTTGCACTAGTAATATACTGCCAT 58.720 34.615 0.00 0.00 39.81 4.40
1865 2227 7.279981 TGCCTTGTTTGCACTAGTAATATACTG 59.720 37.037 0.00 0.00 35.09 2.74
1924 2304 3.653344 TCAACATCAGTCTGAACTTCGG 58.347 45.455 6.64 0.00 31.71 4.30
1925 2305 5.852738 ATTCAACATCAGTCTGAACTTCG 57.147 39.130 6.64 0.00 31.71 3.79
1936 2316 8.236586 TCTTTCGTTGGAATTATTCAACATCAG 58.763 33.333 7.29 5.68 42.22 2.90
1943 2323 9.062524 TCTTTCTTCTTTCGTTGGAATTATTCA 57.937 29.630 7.29 0.00 30.88 2.57
1947 2327 9.116067 TCTTTCTTTCTTCTTTCGTTGGAATTA 57.884 29.630 0.00 0.00 30.88 1.40
1963 2343 9.283768 GGAATCTCTCTTTCTTTCTTTCTTTCT 57.716 33.333 0.00 0.00 0.00 2.52
1964 2344 8.511321 GGGAATCTCTCTTTCTTTCTTTCTTTC 58.489 37.037 0.00 0.00 0.00 2.62
1965 2345 8.001292 TGGGAATCTCTCTTTCTTTCTTTCTTT 58.999 33.333 0.00 0.00 0.00 2.52
1966 2346 7.521669 TGGGAATCTCTCTTTCTTTCTTTCTT 58.478 34.615 0.00 0.00 0.00 2.52
1967 2347 7.084268 TGGGAATCTCTCTTTCTTTCTTTCT 57.916 36.000 0.00 0.00 0.00 2.52
1968 2348 7.148103 CCATGGGAATCTCTCTTTCTTTCTTTC 60.148 40.741 2.85 0.00 0.00 2.62
1969 2349 6.662663 CCATGGGAATCTCTCTTTCTTTCTTT 59.337 38.462 2.85 0.00 0.00 2.52
2047 2427 2.952310 AGAGTTTCAGTTTCAGGGCAAC 59.048 45.455 0.00 0.00 0.00 4.17
2053 2433 5.490139 TGCTTTCAGAGTTTCAGTTTCAG 57.510 39.130 0.00 0.00 0.00 3.02
2054 2434 5.163622 CCTTGCTTTCAGAGTTTCAGTTTCA 60.164 40.000 0.00 0.00 0.00 2.69
2055 2435 5.066505 TCCTTGCTTTCAGAGTTTCAGTTTC 59.933 40.000 0.00 0.00 0.00 2.78
2056 2436 4.949856 TCCTTGCTTTCAGAGTTTCAGTTT 59.050 37.500 0.00 0.00 0.00 2.66
2057 2437 4.526970 TCCTTGCTTTCAGAGTTTCAGTT 58.473 39.130 0.00 0.00 0.00 3.16
2058 2438 4.156455 TCCTTGCTTTCAGAGTTTCAGT 57.844 40.909 0.00 0.00 0.00 3.41
2059 2439 4.142945 CGATCCTTGCTTTCAGAGTTTCAG 60.143 45.833 0.00 0.00 0.00 3.02
2060 2440 3.748048 CGATCCTTGCTTTCAGAGTTTCA 59.252 43.478 0.00 0.00 0.00 2.69
2061 2441 3.997021 TCGATCCTTGCTTTCAGAGTTTC 59.003 43.478 0.00 0.00 0.00 2.78
2062 2442 3.999663 CTCGATCCTTGCTTTCAGAGTTT 59.000 43.478 0.00 0.00 0.00 2.66
2063 2443 3.594134 CTCGATCCTTGCTTTCAGAGTT 58.406 45.455 0.00 0.00 0.00 3.01
2064 2444 2.676463 GCTCGATCCTTGCTTTCAGAGT 60.676 50.000 0.00 0.00 0.00 3.24
2065 2445 1.932511 GCTCGATCCTTGCTTTCAGAG 59.067 52.381 0.00 0.00 0.00 3.35
2066 2446 1.552337 AGCTCGATCCTTGCTTTCAGA 59.448 47.619 0.00 0.00 32.61 3.27
2102 2482 2.498167 CCCTTTCAGTCCTGTCTTGTG 58.502 52.381 0.00 0.00 0.00 3.33
2152 2533 1.822114 TTGGGTTCTGCGGATCGTCA 61.822 55.000 0.00 0.00 0.00 4.35
2153 2534 1.079405 TTGGGTTCTGCGGATCGTC 60.079 57.895 0.00 0.00 0.00 4.20
2154 2535 1.079127 CTTGGGTTCTGCGGATCGT 60.079 57.895 0.00 0.00 0.00 3.73
2155 2536 2.464459 GCTTGGGTTCTGCGGATCG 61.464 63.158 0.00 0.00 0.00 3.69
2180 2569 5.602145 TGATTTGGGGAACATGTCTCTTTTT 59.398 36.000 0.00 0.00 0.00 1.94
2184 2573 4.387026 TTGATTTGGGGAACATGTCTCT 57.613 40.909 0.00 0.00 0.00 3.10
2185 2574 4.615912 CGTTTGATTTGGGGAACATGTCTC 60.616 45.833 0.00 0.00 0.00 3.36
2186 2575 3.255642 CGTTTGATTTGGGGAACATGTCT 59.744 43.478 0.00 0.00 0.00 3.41
2187 2576 3.005367 ACGTTTGATTTGGGGAACATGTC 59.995 43.478 0.00 0.00 0.00 3.06
2188 2577 2.962421 ACGTTTGATTTGGGGAACATGT 59.038 40.909 0.00 0.00 0.00 3.21
2189 2578 3.658757 ACGTTTGATTTGGGGAACATG 57.341 42.857 0.00 0.00 0.00 3.21
2190 2579 3.801983 GCAACGTTTGATTTGGGGAACAT 60.802 43.478 0.00 0.00 0.00 2.71
2191 2580 2.482142 GCAACGTTTGATTTGGGGAACA 60.482 45.455 0.00 0.00 0.00 3.18
2192 2581 2.131972 GCAACGTTTGATTTGGGGAAC 58.868 47.619 0.00 0.00 0.00 3.62
2221 2610 6.214412 AGAAGATGGACTAGTTCAGTTTGGAT 59.786 38.462 10.27 0.00 37.72 3.41
2229 2618 4.223032 GGGTTCAGAAGATGGACTAGTTCA 59.777 45.833 6.25 6.25 37.58 3.18
2283 2672 4.371417 AGCATGGTGGCCCTGTGG 62.371 66.667 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.