Multiple sequence alignment - TraesCS4A01G429500

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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 TraesCS4A01G429500 chr4A 100.000 3578 0 0 1 3578 700430887 700427310 0.000000e+00 6608
1 TraesCS4A01G429500 chr4A 95.255 548 21 2 1 548 735074072 735074614 0.000000e+00 863
2 TraesCS4A01G429500 chr4A 95.255 548 21 2 1 548 735877246 735877788 0.000000e+00 863
3 TraesCS4A01G429500 chr4A 97.015 402 12 0 128 529 733350749 733351150 0.000000e+00 676
4 TraesCS4A01G429500 chr4A 96.377 138 5 0 1 138 733350561 733350698 9.990000e-56 228
5 TraesCS4A01G429500 chr7B 94.142 2219 86 12 660 2839 715155748 715153535 0.000000e+00 3338
6 TraesCS4A01G429500 chr7B 94.120 2211 87 12 660 2832 714901372 714899167 0.000000e+00 3323
7 TraesCS4A01G429500 chr7B 93.916 2219 91 12 660 2839 715123068 715120855 0.000000e+00 3310
8 TraesCS4A01G429500 chr7B 93.913 2218 86 20 660 2839 715083671 715081465 0.000000e+00 3302
9 TraesCS4A01G429500 chr7B 86.770 1799 149 41 816 2579 715322453 715320709 0.000000e+00 1921
10 TraesCS4A01G429500 chr7B 92.296 1298 66 16 547 1819 714950635 714949347 0.000000e+00 1812
11 TraesCS4A01G429500 chr7B 92.440 1045 50 6 1817 2839 714947476 714946439 0.000000e+00 1465
12 TraesCS4A01G429500 chr7B 86.500 600 65 8 2993 3578 714895432 714894835 0.000000e+00 645
13 TraesCS4A01G429500 chr7B 86.500 600 65 9 2993 3578 715115265 715114668 0.000000e+00 645
14 TraesCS4A01G429500 chr7B 86.144 599 67 7 2994 3578 714840926 714840330 1.810000e-177 632
15 TraesCS4A01G429500 chr7B 86.000 600 67 10 2993 3578 715076461 715075865 8.430000e-176 627
16 TraesCS4A01G429500 chr7B 85.358 601 71 11 2993 3578 714943103 714942505 1.100000e-169 606
17 TraesCS4A01G429500 chr7B 96.610 118 4 0 547 664 715084253 715084136 2.820000e-46 196
18 TraesCS4A01G429500 chr7B 95.763 118 4 1 547 664 715156329 715156213 4.720000e-44 189
19 TraesCS4A01G429500 chr7B 94.915 118 6 0 547 664 714901954 714901837 6.100000e-43 185
20 TraesCS4A01G429500 chr7B 88.636 132 14 1 2847 2977 715078302 715078171 3.700000e-35 159
21 TraesCS4A01G429500 chr7D 90.062 2093 119 27 1539 3578 619358579 619356523 0.000000e+00 2630
22 TraesCS4A01G429500 chr7D 86.063 1966 165 61 804 2700 619581977 619583902 0.000000e+00 2012
23 TraesCS4A01G429500 chr7D 85.598 1958 176 55 805 2700 620583046 620584959 0.000000e+00 1956
24 TraesCS4A01G429500 chr7D 93.818 550 24 8 1 548 107264186 107264727 0.000000e+00 819
25 TraesCS4A01G429500 chr7D 93.468 444 21 6 113 553 107262783 107263221 0.000000e+00 652
26 TraesCS4A01G429500 chr7D 92.208 462 24 6 1084 1545 619359201 619358752 0.000000e+00 643
27 TraesCS4A01G429500 chr7D 88.725 408 25 7 746 1136 619359590 619359187 2.500000e-131 479
28 TraesCS4A01G429500 chr7D 88.144 194 22 1 547 739 619384438 619384245 2.780000e-56 230
29 TraesCS4A01G429500 chr7A 84.838 2071 195 62 805 2794 713833383 713835415 0.000000e+00 1975
30 TraesCS4A01G429500 chr7A 83.085 739 81 32 804 1520 714031788 714032504 1.810000e-177 632
31 TraesCS4A01G429500 chrUn 86.409 1398 106 44 750 2100 93249919 93248559 0.000000e+00 1452
32 TraesCS4A01G429500 chr3B 82.773 238 25 7 15 237 804800654 804800890 7.840000e-47 198
33 TraesCS4A01G429500 chr2B 80.795 151 14 14 387 534 496360665 496360803 1.760000e-18 104


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 TraesCS4A01G429500 chr4A 700427310 700430887 3577 True 6608.000000 6608 100.000000 1 3578 1 chr4A.!!$R1 3577
1 TraesCS4A01G429500 chr4A 735074072 735074614 542 False 863.000000 863 95.255000 1 548 1 chr4A.!!$F1 547
2 TraesCS4A01G429500 chr4A 735877246 735877788 542 False 863.000000 863 95.255000 1 548 1 chr4A.!!$F2 547
3 TraesCS4A01G429500 chr4A 733350561 733351150 589 False 452.000000 676 96.696000 1 529 2 chr4A.!!$F3 528
4 TraesCS4A01G429500 chr7B 715120855 715123068 2213 True 3310.000000 3310 93.916000 660 2839 1 chr7B.!!$R3 2179
5 TraesCS4A01G429500 chr7B 715320709 715322453 1744 True 1921.000000 1921 86.770000 816 2579 1 chr7B.!!$R4 1763
6 TraesCS4A01G429500 chr7B 715153535 715156329 2794 True 1763.500000 3338 94.952500 547 2839 2 chr7B.!!$R8 2292
7 TraesCS4A01G429500 chr7B 714894835 714901954 7119 True 1384.333333 3323 91.845000 547 3578 3 chr7B.!!$R5 3031
8 TraesCS4A01G429500 chr7B 714942505 714950635 8130 True 1294.333333 1812 90.031333 547 3578 3 chr7B.!!$R6 3031
9 TraesCS4A01G429500 chr7B 715075865 715084253 8388 True 1071.000000 3302 91.289750 547 3578 4 chr7B.!!$R7 3031
10 TraesCS4A01G429500 chr7B 715114668 715115265 597 True 645.000000 645 86.500000 2993 3578 1 chr7B.!!$R2 585
11 TraesCS4A01G429500 chr7B 714840330 714840926 596 True 632.000000 632 86.144000 2994 3578 1 chr7B.!!$R1 584
12 TraesCS4A01G429500 chr7D 619581977 619583902 1925 False 2012.000000 2012 86.063000 804 2700 1 chr7D.!!$F1 1896
13 TraesCS4A01G429500 chr7D 620583046 620584959 1913 False 1956.000000 1956 85.598000 805 2700 1 chr7D.!!$F2 1895
14 TraesCS4A01G429500 chr7D 619356523 619359590 3067 True 1250.666667 2630 90.331667 746 3578 3 chr7D.!!$R2 2832
15 TraesCS4A01G429500 chr7D 107262783 107264727 1944 False 735.500000 819 93.643000 1 553 2 chr7D.!!$F3 552
16 TraesCS4A01G429500 chr7A 713833383 713835415 2032 False 1975.000000 1975 84.838000 805 2794 1 chr7A.!!$F1 1989
17 TraesCS4A01G429500 chr7A 714031788 714032504 716 False 632.000000 632 83.085000 804 1520 1 chr7A.!!$F2 716
18 TraesCS4A01G429500 chrUn 93248559 93249919 1360 True 1452.000000 1452 86.409000 750 2100 1 chrUn.!!$R1 1350

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
439 440 0.032540 GAAAAGGGCTTGGCTGTGTG 59.967 55.0 0.0 0.0 0.0 3.82 F
443 444 0.035056 AGGGCTTGGCTGTGTGATAC 60.035 55.0 0.0 0.0 0.0 2.24 F
2238 5901 0.035820 TCAATCACGCCCCTGGTAAC 60.036 55.0 0.0 0.0 0.0 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1308 1872 1.202879 TCCCCGAAGACAAACATGCTT 60.203 47.619 0.00 0.0 0.00 3.91 R
2333 6009 1.638529 GGACTGATCCGATCCTCCAT 58.361 55.000 13.81 0.0 34.48 3.41 R
3156 11879 0.100503 ACACAGTTGCCTTTCGTTGC 59.899 50.000 0.00 0.0 0.00 4.17 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
34 35 5.356751 TGTTTGTTTCAGTCTTGCATGTAGT 59.643 36.000 0.00 0.00 0.00 2.73
35 36 5.673337 TTGTTTCAGTCTTGCATGTAGTC 57.327 39.130 0.00 0.00 0.00 2.59
64 65 1.880027 GACTGTTCCGGCAAAGTCATT 59.120 47.619 18.39 0.00 39.09 2.57
244 245 5.179045 AGCATGCATAAGTATTCAGTTGC 57.821 39.130 21.98 0.00 0.00 4.17
290 291 6.834168 GGAGAGATTCCAGGAGTAAGATAG 57.166 45.833 0.00 0.00 46.01 2.08
332 333 0.618458 TGCATGGGTTAGTGGGAGTC 59.382 55.000 0.00 0.00 0.00 3.36
347 348 1.133407 GGAGTCTGTTGCCGAGAGTAG 59.867 57.143 0.00 0.00 0.00 2.57
370 371 0.384230 CTGGTTAGTGCGTGCGTTTG 60.384 55.000 0.00 0.00 0.00 2.93
388 389 5.560183 GCGTTTGTGTACTTAAACAGAGCAT 60.560 40.000 18.76 0.00 36.77 3.79
389 390 6.347079 GCGTTTGTGTACTTAAACAGAGCATA 60.347 38.462 18.76 0.00 36.77 3.14
390 391 7.623506 GCGTTTGTGTACTTAAACAGAGCATAT 60.624 37.037 18.76 0.00 36.77 1.78
391 392 8.227791 CGTTTGTGTACTTAAACAGAGCATATT 58.772 33.333 18.76 0.00 36.77 1.28
392 393 9.893305 GTTTGTGTACTTAAACAGAGCATATTT 57.107 29.630 15.83 0.00 36.91 1.40
393 394 9.891828 TTTGTGTACTTAAACAGAGCATATTTG 57.108 29.630 0.00 0.00 0.00 2.32
394 395 8.615878 TGTGTACTTAAACAGAGCATATTTGT 57.384 30.769 0.00 0.00 0.00 2.83
395 396 9.062524 TGTGTACTTAAACAGAGCATATTTGTT 57.937 29.630 0.00 0.00 36.66 2.83
396 397 9.893305 GTGTACTTAAACAGAGCATATTTGTTT 57.107 29.630 6.98 6.98 44.54 2.83
400 401 8.792633 ACTTAAACAGAGCATATTTGTTTAGCA 58.207 29.630 8.47 0.00 43.82 3.49
401 402 9.282247 CTTAAACAGAGCATATTTGTTTAGCAG 57.718 33.333 8.47 2.90 43.82 4.24
402 403 6.824305 AACAGAGCATATTTGTTTAGCAGT 57.176 33.333 0.00 0.00 31.38 4.40
403 404 6.428385 ACAGAGCATATTTGTTTAGCAGTC 57.572 37.500 0.00 0.00 0.00 3.51
404 405 5.939883 ACAGAGCATATTTGTTTAGCAGTCA 59.060 36.000 0.00 0.00 0.00 3.41
405 406 6.430925 ACAGAGCATATTTGTTTAGCAGTCAA 59.569 34.615 0.00 0.00 0.00 3.18
406 407 6.965500 CAGAGCATATTTGTTTAGCAGTCAAG 59.035 38.462 0.00 0.00 0.00 3.02
407 408 6.881065 AGAGCATATTTGTTTAGCAGTCAAGA 59.119 34.615 0.00 0.00 0.00 3.02
408 409 7.065563 AGAGCATATTTGTTTAGCAGTCAAGAG 59.934 37.037 0.00 0.00 0.00 2.85
409 410 6.881065 AGCATATTTGTTTAGCAGTCAAGAGA 59.119 34.615 0.00 0.00 0.00 3.10
410 411 7.391554 AGCATATTTGTTTAGCAGTCAAGAGAA 59.608 33.333 0.00 0.00 0.00 2.87
411 412 8.186821 GCATATTTGTTTAGCAGTCAAGAGAAT 58.813 33.333 0.00 0.00 0.00 2.40
415 416 9.678260 ATTTGTTTAGCAGTCAAGAGAATAGAT 57.322 29.630 0.00 0.00 0.00 1.98
417 418 9.809096 TTGTTTAGCAGTCAAGAGAATAGATAG 57.191 33.333 0.00 0.00 0.00 2.08
418 419 9.190317 TGTTTAGCAGTCAAGAGAATAGATAGA 57.810 33.333 0.00 0.00 0.00 1.98
421 422 9.634021 TTAGCAGTCAAGAGAATAGATAGAAGA 57.366 33.333 0.00 0.00 0.00 2.87
422 423 8.532186 AGCAGTCAAGAGAATAGATAGAAGAA 57.468 34.615 0.00 0.00 0.00 2.52
423 424 8.976353 AGCAGTCAAGAGAATAGATAGAAGAAA 58.024 33.333 0.00 0.00 0.00 2.52
424 425 9.593134 GCAGTCAAGAGAATAGATAGAAGAAAA 57.407 33.333 0.00 0.00 0.00 2.29
427 428 9.541143 GTCAAGAGAATAGATAGAAGAAAAGGG 57.459 37.037 0.00 0.00 0.00 3.95
428 429 8.207545 TCAAGAGAATAGATAGAAGAAAAGGGC 58.792 37.037 0.00 0.00 0.00 5.19
429 430 7.929348 AGAGAATAGATAGAAGAAAAGGGCT 57.071 36.000 0.00 0.00 0.00 5.19
430 431 8.330638 AGAGAATAGATAGAAGAAAAGGGCTT 57.669 34.615 0.00 0.00 0.00 4.35
431 432 8.210265 AGAGAATAGATAGAAGAAAAGGGCTTG 58.790 37.037 0.00 0.00 0.00 4.01
432 433 7.286313 AGAATAGATAGAAGAAAAGGGCTTGG 58.714 38.462 0.00 0.00 0.00 3.61
433 434 3.625853 AGATAGAAGAAAAGGGCTTGGC 58.374 45.455 0.00 0.00 0.00 4.52
434 435 3.268072 AGATAGAAGAAAAGGGCTTGGCT 59.732 43.478 0.00 0.00 0.00 4.75
435 436 1.625511 AGAAGAAAAGGGCTTGGCTG 58.374 50.000 0.00 0.00 0.00 4.85
436 437 1.133356 AGAAGAAAAGGGCTTGGCTGT 60.133 47.619 0.00 0.00 0.00 4.40
437 438 1.000171 GAAGAAAAGGGCTTGGCTGTG 60.000 52.381 0.00 0.00 0.00 3.66
438 439 0.106015 AGAAAAGGGCTTGGCTGTGT 60.106 50.000 0.00 0.00 0.00 3.72
439 440 0.032540 GAAAAGGGCTTGGCTGTGTG 59.967 55.000 0.00 0.00 0.00 3.82
440 441 0.396974 AAAAGGGCTTGGCTGTGTGA 60.397 50.000 0.00 0.00 0.00 3.58
441 442 0.178953 AAAGGGCTTGGCTGTGTGAT 60.179 50.000 0.00 0.00 0.00 3.06
442 443 0.698238 AAGGGCTTGGCTGTGTGATA 59.302 50.000 0.00 0.00 0.00 2.15
443 444 0.035056 AGGGCTTGGCTGTGTGATAC 60.035 55.000 0.00 0.00 0.00 2.24
444 445 1.369091 GGGCTTGGCTGTGTGATACG 61.369 60.000 0.00 0.00 0.00 3.06
445 446 1.369091 GGCTTGGCTGTGTGATACGG 61.369 60.000 0.00 0.00 38.77 4.02
450 451 4.919653 CTGTGTGATACGGCAGCT 57.080 55.556 0.00 0.00 0.00 4.24
451 452 2.670635 CTGTGTGATACGGCAGCTC 58.329 57.895 0.00 0.00 0.00 4.09
452 453 0.108662 CTGTGTGATACGGCAGCTCA 60.109 55.000 0.00 0.00 0.00 4.26
453 454 0.389817 TGTGTGATACGGCAGCTCAC 60.390 55.000 11.53 11.53 39.74 3.51
454 455 1.084370 GTGTGATACGGCAGCTCACC 61.084 60.000 14.52 0.00 38.79 4.02
455 456 1.218047 GTGATACGGCAGCTCACCA 59.782 57.895 8.38 0.00 34.55 4.17
456 457 0.391130 GTGATACGGCAGCTCACCAA 60.391 55.000 8.38 0.00 34.55 3.67
457 458 0.323302 TGATACGGCAGCTCACCAAA 59.677 50.000 3.29 0.00 0.00 3.28
458 459 1.065491 TGATACGGCAGCTCACCAAAT 60.065 47.619 3.29 0.00 0.00 2.32
459 460 2.169561 TGATACGGCAGCTCACCAAATA 59.830 45.455 3.29 0.00 0.00 1.40
460 461 3.181455 TGATACGGCAGCTCACCAAATAT 60.181 43.478 3.29 0.00 0.00 1.28
461 462 1.668419 ACGGCAGCTCACCAAATATC 58.332 50.000 3.29 0.00 0.00 1.63
462 463 0.583438 CGGCAGCTCACCAAATATCG 59.417 55.000 3.29 0.00 0.00 2.92
463 464 1.668419 GGCAGCTCACCAAATATCGT 58.332 50.000 0.00 0.00 0.00 3.73
464 465 1.599542 GGCAGCTCACCAAATATCGTC 59.400 52.381 0.00 0.00 0.00 4.20
465 466 2.555199 GCAGCTCACCAAATATCGTCT 58.445 47.619 0.00 0.00 0.00 4.18
466 467 2.939103 GCAGCTCACCAAATATCGTCTT 59.061 45.455 0.00 0.00 0.00 3.01
467 468 3.001736 GCAGCTCACCAAATATCGTCTTC 59.998 47.826 0.00 0.00 0.00 2.87
468 469 4.437239 CAGCTCACCAAATATCGTCTTCT 58.563 43.478 0.00 0.00 0.00 2.85
469 470 4.505922 CAGCTCACCAAATATCGTCTTCTC 59.494 45.833 0.00 0.00 0.00 2.87
470 471 3.804873 GCTCACCAAATATCGTCTTCTCC 59.195 47.826 0.00 0.00 0.00 3.71
471 472 4.680708 GCTCACCAAATATCGTCTTCTCCA 60.681 45.833 0.00 0.00 0.00 3.86
472 473 5.605534 CTCACCAAATATCGTCTTCTCCAT 58.394 41.667 0.00 0.00 0.00 3.41
473 474 5.989477 TCACCAAATATCGTCTTCTCCATT 58.011 37.500 0.00 0.00 0.00 3.16
474 475 7.119709 TCACCAAATATCGTCTTCTCCATTA 57.880 36.000 0.00 0.00 0.00 1.90
475 476 7.735917 TCACCAAATATCGTCTTCTCCATTAT 58.264 34.615 0.00 0.00 0.00 1.28
476 477 7.872993 TCACCAAATATCGTCTTCTCCATTATC 59.127 37.037 0.00 0.00 0.00 1.75
477 478 7.875041 CACCAAATATCGTCTTCTCCATTATCT 59.125 37.037 0.00 0.00 0.00 1.98
478 479 8.091449 ACCAAATATCGTCTTCTCCATTATCTC 58.909 37.037 0.00 0.00 0.00 2.75
479 480 7.274468 CCAAATATCGTCTTCTCCATTATCTCG 59.726 40.741 0.00 0.00 0.00 4.04
480 481 7.455641 AATATCGTCTTCTCCATTATCTCGT 57.544 36.000 0.00 0.00 0.00 4.18
481 482 4.553756 TCGTCTTCTCCATTATCTCGTG 57.446 45.455 0.00 0.00 0.00 4.35
482 483 3.945921 TCGTCTTCTCCATTATCTCGTGT 59.054 43.478 0.00 0.00 0.00 4.49
483 484 4.038361 CGTCTTCTCCATTATCTCGTGTG 58.962 47.826 0.00 0.00 0.00 3.82
484 485 4.438880 CGTCTTCTCCATTATCTCGTGTGT 60.439 45.833 0.00 0.00 0.00 3.72
485 486 4.800993 GTCTTCTCCATTATCTCGTGTGTG 59.199 45.833 0.00 0.00 0.00 3.82
486 487 4.462834 TCTTCTCCATTATCTCGTGTGTGT 59.537 41.667 0.00 0.00 0.00 3.72
487 488 4.110036 TCTCCATTATCTCGTGTGTGTG 57.890 45.455 0.00 0.00 0.00 3.82
488 489 3.509967 TCTCCATTATCTCGTGTGTGTGT 59.490 43.478 0.00 0.00 0.00 3.72
489 490 3.584834 TCCATTATCTCGTGTGTGTGTG 58.415 45.455 0.00 0.00 0.00 3.82
490 491 3.006430 TCCATTATCTCGTGTGTGTGTGT 59.994 43.478 0.00 0.00 0.00 3.72
491 492 3.123453 CCATTATCTCGTGTGTGTGTGTG 59.877 47.826 0.00 0.00 0.00 3.82
492 493 2.432206 TATCTCGTGTGTGTGTGTGG 57.568 50.000 0.00 0.00 0.00 4.17
493 494 0.249868 ATCTCGTGTGTGTGTGTGGG 60.250 55.000 0.00 0.00 0.00 4.61
494 495 1.153449 CTCGTGTGTGTGTGTGGGT 60.153 57.895 0.00 0.00 0.00 4.51
495 496 0.742990 CTCGTGTGTGTGTGTGGGTT 60.743 55.000 0.00 0.00 0.00 4.11
496 497 1.021920 TCGTGTGTGTGTGTGGGTTG 61.022 55.000 0.00 0.00 0.00 3.77
497 498 1.302383 CGTGTGTGTGTGTGGGTTGT 61.302 55.000 0.00 0.00 0.00 3.32
498 499 0.170116 GTGTGTGTGTGTGGGTTGTG 59.830 55.000 0.00 0.00 0.00 3.33
499 500 0.250945 TGTGTGTGTGTGGGTTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
500 501 0.170116 GTGTGTGTGTGGGTTGTGTG 59.830 55.000 0.00 0.00 0.00 3.82
501 502 0.036875 TGTGTGTGTGGGTTGTGTGA 59.963 50.000 0.00 0.00 0.00 3.58
502 503 1.169577 GTGTGTGTGGGTTGTGTGAA 58.830 50.000 0.00 0.00 0.00 3.18
503 504 1.542030 GTGTGTGTGGGTTGTGTGAAA 59.458 47.619 0.00 0.00 0.00 2.69
504 505 1.542030 TGTGTGTGGGTTGTGTGAAAC 59.458 47.619 0.00 0.00 37.35 2.78
515 516 3.289128 TGTGAAACAGCCGTGAGAG 57.711 52.632 0.00 0.00 45.67 3.20
516 517 0.750249 TGTGAAACAGCCGTGAGAGA 59.250 50.000 0.00 0.00 45.67 3.10
517 518 1.138069 TGTGAAACAGCCGTGAGAGAA 59.862 47.619 0.00 0.00 45.67 2.87
518 519 1.795286 GTGAAACAGCCGTGAGAGAAG 59.205 52.381 0.00 0.00 36.32 2.85
519 520 1.686587 TGAAACAGCCGTGAGAGAAGA 59.313 47.619 0.00 0.00 0.00 2.87
520 521 2.102420 TGAAACAGCCGTGAGAGAAGAA 59.898 45.455 0.00 0.00 0.00 2.52
521 522 2.447244 AACAGCCGTGAGAGAAGAAG 57.553 50.000 0.00 0.00 0.00 2.85
522 523 0.605589 ACAGCCGTGAGAGAAGAAGG 59.394 55.000 0.00 0.00 0.00 3.46
523 524 0.108424 CAGCCGTGAGAGAAGAAGGG 60.108 60.000 0.00 0.00 0.00 3.95
524 525 0.251832 AGCCGTGAGAGAAGAAGGGA 60.252 55.000 0.00 0.00 0.00 4.20
525 526 0.174617 GCCGTGAGAGAAGAAGGGAG 59.825 60.000 0.00 0.00 0.00 4.30
526 527 1.551452 CCGTGAGAGAAGAAGGGAGT 58.449 55.000 0.00 0.00 0.00 3.85
527 528 1.896465 CCGTGAGAGAAGAAGGGAGTT 59.104 52.381 0.00 0.00 0.00 3.01
528 529 2.353208 CCGTGAGAGAAGAAGGGAGTTG 60.353 54.545 0.00 0.00 0.00 3.16
529 530 2.353208 CGTGAGAGAAGAAGGGAGTTGG 60.353 54.545 0.00 0.00 0.00 3.77
530 531 2.900546 GTGAGAGAAGAAGGGAGTTGGA 59.099 50.000 0.00 0.00 0.00 3.53
531 532 3.056179 GTGAGAGAAGAAGGGAGTTGGAG 60.056 52.174 0.00 0.00 0.00 3.86
532 533 3.181417 TGAGAGAAGAAGGGAGTTGGAGA 60.181 47.826 0.00 0.00 0.00 3.71
533 534 3.440127 AGAGAAGAAGGGAGTTGGAGAG 58.560 50.000 0.00 0.00 0.00 3.20
534 535 3.076785 AGAGAAGAAGGGAGTTGGAGAGA 59.923 47.826 0.00 0.00 0.00 3.10
535 536 3.440127 AGAAGAAGGGAGTTGGAGAGAG 58.560 50.000 0.00 0.00 0.00 3.20
536 537 3.169908 GAAGAAGGGAGTTGGAGAGAGT 58.830 50.000 0.00 0.00 0.00 3.24
537 538 2.815158 AGAAGGGAGTTGGAGAGAGTC 58.185 52.381 0.00 0.00 0.00 3.36
538 539 2.110899 AGAAGGGAGTTGGAGAGAGTCA 59.889 50.000 0.00 0.00 0.00 3.41
539 540 2.230130 AGGGAGTTGGAGAGAGTCAG 57.770 55.000 0.00 0.00 0.00 3.51
540 541 0.534873 GGGAGTTGGAGAGAGTCAGC 59.465 60.000 0.00 0.00 0.00 4.26
541 542 1.555967 GGAGTTGGAGAGAGTCAGCT 58.444 55.000 0.00 0.00 0.00 4.24
542 543 1.476488 GGAGTTGGAGAGAGTCAGCTC 59.524 57.143 4.85 4.85 39.46 4.09
695 1167 3.782992 AGAAGGAACAATGGGCAGAAAT 58.217 40.909 0.00 0.00 0.00 2.17
801 1278 4.466370 AGATTAGGTCGGTGAAAGACATGA 59.534 41.667 0.00 0.00 40.20 3.07
875 1367 2.933492 GCAGGAAAGGTACACGTGCATA 60.933 50.000 17.22 0.00 42.40 3.14
942 1446 0.402566 CATCCCCATCTCCCTCCCTT 60.403 60.000 0.00 0.00 0.00 3.95
943 1447 0.104197 ATCCCCATCTCCCTCCCTTC 60.104 60.000 0.00 0.00 0.00 3.46
1013 1519 2.176273 CGGCCATGAAGCTTCCTCG 61.176 63.158 23.42 14.82 0.00 4.63
1140 1688 3.621715 CCGCCATGTCTTCCTTTTAGTAC 59.378 47.826 0.00 0.00 0.00 2.73
1174 1730 3.056536 TGCTAGCGATCACTTCAAGTTCT 60.057 43.478 10.77 0.00 0.00 3.01
1198 1754 0.608035 TGCCCGGTTCTTCATGTTCC 60.608 55.000 0.00 0.00 0.00 3.62
1201 1765 2.084546 CCCGGTTCTTCATGTTCCTTC 58.915 52.381 0.00 0.00 0.00 3.46
1203 1767 2.552155 CCGGTTCTTCATGTTCCTTCCA 60.552 50.000 0.00 0.00 0.00 3.53
1204 1768 2.744202 CGGTTCTTCATGTTCCTTCCAG 59.256 50.000 0.00 0.00 0.00 3.86
1271 1835 4.988716 TCGTGTGGAGGCCCGAGT 62.989 66.667 0.00 0.00 34.29 4.18
1281 1845 2.047179 GCCCGAGTCACACCTTCC 60.047 66.667 0.00 0.00 0.00 3.46
1286 1850 0.387367 CGAGTCACACCTTCCTCACG 60.387 60.000 0.00 0.00 0.00 4.35
1308 1872 0.541764 GGCCCAAGAACCAATGGTCA 60.542 55.000 4.95 0.00 33.12 4.02
1326 1890 1.879380 TCAAGCATGTTTGTCTTCGGG 59.121 47.619 20.01 0.00 0.00 5.14
2161 5824 7.083858 GCACAACAAGTATCTAAAGCAAATGA 58.916 34.615 0.00 0.00 0.00 2.57
2166 5829 8.668510 ACAAGTATCTAAAGCAAATGATCGAT 57.331 30.769 0.00 0.00 0.00 3.59
2168 5831 8.554528 CAAGTATCTAAAGCAAATGATCGATGT 58.445 33.333 0.54 0.00 0.00 3.06
2238 5901 0.035820 TCAATCACGCCCCTGGTAAC 60.036 55.000 0.00 0.00 0.00 2.50
2275 5938 4.266029 GCATTGATGTTGTAAGCCAAATCG 59.734 41.667 0.00 0.00 34.07 3.34
2276 5939 5.401550 CATTGATGTTGTAAGCCAAATCGT 58.598 37.500 0.00 0.00 34.07 3.73
2291 5957 5.505654 GCCAAATCGTGTTCCTTATGTATGG 60.506 44.000 0.00 0.00 0.00 2.74
2333 6009 7.216973 TGCATATATATTTTGTGCATGCAGA 57.783 32.000 23.41 18.82 41.53 4.26
2442 6138 1.821332 CCATTCAGGGAAGCGCCTC 60.821 63.158 2.29 0.00 36.66 4.70
2609 6335 2.962253 GGCTAGCTAGTTGGCGCG 60.962 66.667 21.62 0.00 37.29 6.86
2732 6478 3.848272 ACATGAACGGGTGCTAATTTG 57.152 42.857 0.00 0.00 0.00 2.32
2736 6482 2.030363 TGAACGGGTGCTAATTTGCTTG 60.030 45.455 12.99 3.23 0.00 4.01
2738 6486 1.960689 ACGGGTGCTAATTTGCTTGTT 59.039 42.857 12.99 0.00 0.00 2.83
2743 6491 4.574421 GGGTGCTAATTTGCTTGTTGTTTT 59.426 37.500 12.99 0.00 0.00 2.43
2744 6492 5.755861 GGGTGCTAATTTGCTTGTTGTTTTA 59.244 36.000 12.99 0.00 0.00 1.52
2745 6493 6.258947 GGGTGCTAATTTGCTTGTTGTTTTAA 59.741 34.615 12.99 0.00 0.00 1.52
2777 6530 6.961576 TGTTGAGATTAAAAATTCGGTCGTT 58.038 32.000 0.00 0.00 0.00 3.85
2839 6598 6.691508 TCTAATCAGTACGCTTGCATATGAT 58.308 36.000 6.97 0.00 0.00 2.45
2840 6599 5.602458 AATCAGTACGCTTGCATATGATG 57.398 39.130 6.97 0.00 0.00 3.07
2881 9804 5.548406 GCGTGGTCCCAGAAATTATATAGT 58.452 41.667 0.00 0.00 0.00 2.12
2901 9824 5.474578 AGTTCTATGTCTCAAAGACTGCA 57.525 39.130 8.44 0.00 45.27 4.41
2902 9825 5.477510 AGTTCTATGTCTCAAAGACTGCAG 58.522 41.667 13.48 13.48 45.27 4.41
2903 9826 5.244851 AGTTCTATGTCTCAAAGACTGCAGA 59.755 40.000 23.35 0.00 45.27 4.26
2933 9856 4.593864 GGGAGATCGGCAGCGACC 62.594 72.222 0.00 0.00 0.00 4.79
2959 9882 1.320507 CCCTTACGCTACTCTCCTCC 58.679 60.000 0.00 0.00 0.00 4.30
3060 11770 2.615912 GGCCTGATTTCATAGTGCACTC 59.384 50.000 25.56 7.92 0.00 3.51
3075 11785 1.536072 GCACTCGCCGAGATGATTGTA 60.536 52.381 22.80 0.00 33.32 2.41
3156 11879 5.050091 GGAATGAATAGCATAACACAGGACG 60.050 44.000 0.00 0.00 35.78 4.79
3183 11906 3.145228 GGCAACTGTGTAGAGGAGC 57.855 57.895 0.00 0.00 0.00 4.70
3195 11918 2.685380 AGGAGCGGGAGGACAAGG 60.685 66.667 0.00 0.00 0.00 3.61
3231 11954 1.885887 CCCAAAAGCGATCCAACTTCA 59.114 47.619 0.00 0.00 0.00 3.02
3233 11956 3.056607 CCCAAAAGCGATCCAACTTCAAT 60.057 43.478 0.00 0.00 0.00 2.57
3242 11966 5.988561 GCGATCCAACTTCAATCTCTATCTT 59.011 40.000 0.00 0.00 0.00 2.40
3287 12011 3.195182 GGGAGACTAGGTTACAAGTCCAC 59.805 52.174 11.72 7.82 42.56 4.02
3290 12014 4.220724 AGACTAGGTTACAAGTCCACACA 58.779 43.478 11.72 0.00 42.56 3.72
3368 12092 4.324267 TGAAAGCTAAGGTTAAGGAGTGC 58.676 43.478 0.00 0.00 0.00 4.40
3379 12103 7.380423 AGGTTAAGGAGTGCAGATAATATGT 57.620 36.000 0.00 0.00 0.00 2.29
3419 12143 2.806244 GCTTGCGAGACAAACTTAAGGA 59.194 45.455 4.70 0.00 37.96 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.062809 GCTAGACTACATGCAAGACTGAAAC 59.937 44.000 0.00 0.00 0.00 2.78
34 35 2.376109 CCGGAACAGTCCTAAGCTAGA 58.624 52.381 0.00 0.00 42.44 2.43
35 36 1.202428 GCCGGAACAGTCCTAAGCTAG 60.202 57.143 5.05 0.00 42.44 3.42
64 65 3.692370 ATGGCATCTCGCTGCAGCA 62.692 57.895 36.03 22.30 44.12 4.41
190 191 0.469070 ATGACTCAGCCAGATCAGCC 59.531 55.000 4.28 0.00 0.00 4.85
238 239 2.743752 CGACTCGGCCATGCAACTG 61.744 63.158 2.24 0.00 0.00 3.16
244 245 2.815211 CCACACGACTCGGCCATG 60.815 66.667 2.24 0.00 0.00 3.66
267 268 6.311735 ACTATCTTACTCCTGGAATCTCTCC 58.688 44.000 0.00 0.00 45.64 3.71
290 291 2.268298 CACTAACGCACTACCCATGAC 58.732 52.381 0.00 0.00 0.00 3.06
332 333 1.517257 CCGCTACTCTCGGCAACAG 60.517 63.158 0.00 0.00 40.46 3.16
347 348 3.788766 CACGCACTAACCAGCCGC 61.789 66.667 0.00 0.00 0.00 6.53
370 371 9.893305 AAACAAATATGCTCTGTTTAAGTACAC 57.107 29.630 0.00 0.00 40.54 2.90
389 390 9.678260 ATCTATTCTCTTGACTGCTAAACAAAT 57.322 29.630 0.00 0.00 0.00 2.32
391 392 9.809096 CTATCTATTCTCTTGACTGCTAAACAA 57.191 33.333 0.00 0.00 0.00 2.83
392 393 9.190317 TCTATCTATTCTCTTGACTGCTAAACA 57.810 33.333 0.00 0.00 0.00 2.83
395 396 9.634021 TCTTCTATCTATTCTCTTGACTGCTAA 57.366 33.333 0.00 0.00 0.00 3.09
396 397 9.634021 TTCTTCTATCTATTCTCTTGACTGCTA 57.366 33.333 0.00 0.00 0.00 3.49
397 398 8.532186 TTCTTCTATCTATTCTCTTGACTGCT 57.468 34.615 0.00 0.00 0.00 4.24
398 399 9.593134 TTTTCTTCTATCTATTCTCTTGACTGC 57.407 33.333 0.00 0.00 0.00 4.40
401 402 9.541143 CCCTTTTCTTCTATCTATTCTCTTGAC 57.459 37.037 0.00 0.00 0.00 3.18
402 403 8.207545 GCCCTTTTCTTCTATCTATTCTCTTGA 58.792 37.037 0.00 0.00 0.00 3.02
403 404 8.210265 AGCCCTTTTCTTCTATCTATTCTCTTG 58.790 37.037 0.00 0.00 0.00 3.02
404 405 8.330638 AGCCCTTTTCTTCTATCTATTCTCTT 57.669 34.615 0.00 0.00 0.00 2.85
405 406 7.929348 AGCCCTTTTCTTCTATCTATTCTCT 57.071 36.000 0.00 0.00 0.00 3.10
406 407 7.443879 CCAAGCCCTTTTCTTCTATCTATTCTC 59.556 40.741 0.00 0.00 0.00 2.87
407 408 7.286313 CCAAGCCCTTTTCTTCTATCTATTCT 58.714 38.462 0.00 0.00 0.00 2.40
408 409 6.016693 GCCAAGCCCTTTTCTTCTATCTATTC 60.017 42.308 0.00 0.00 0.00 1.75
409 410 5.830457 GCCAAGCCCTTTTCTTCTATCTATT 59.170 40.000 0.00 0.00 0.00 1.73
410 411 5.133491 AGCCAAGCCCTTTTCTTCTATCTAT 59.867 40.000 0.00 0.00 0.00 1.98
411 412 4.475016 AGCCAAGCCCTTTTCTTCTATCTA 59.525 41.667 0.00 0.00 0.00 1.98
412 413 3.268072 AGCCAAGCCCTTTTCTTCTATCT 59.732 43.478 0.00 0.00 0.00 1.98
413 414 3.379688 CAGCCAAGCCCTTTTCTTCTATC 59.620 47.826 0.00 0.00 0.00 2.08
414 415 3.245407 ACAGCCAAGCCCTTTTCTTCTAT 60.245 43.478 0.00 0.00 0.00 1.98
415 416 2.108250 ACAGCCAAGCCCTTTTCTTCTA 59.892 45.455 0.00 0.00 0.00 2.10
416 417 1.133356 ACAGCCAAGCCCTTTTCTTCT 60.133 47.619 0.00 0.00 0.00 2.85
417 418 1.000171 CACAGCCAAGCCCTTTTCTTC 60.000 52.381 0.00 0.00 0.00 2.87
418 419 1.043022 CACAGCCAAGCCCTTTTCTT 58.957 50.000 0.00 0.00 0.00 2.52
419 420 0.106015 ACACAGCCAAGCCCTTTTCT 60.106 50.000 0.00 0.00 0.00 2.52
420 421 0.032540 CACACAGCCAAGCCCTTTTC 59.967 55.000 0.00 0.00 0.00 2.29
421 422 0.396974 TCACACAGCCAAGCCCTTTT 60.397 50.000 0.00 0.00 0.00 2.27
422 423 0.178953 ATCACACAGCCAAGCCCTTT 60.179 50.000 0.00 0.00 0.00 3.11
423 424 0.698238 TATCACACAGCCAAGCCCTT 59.302 50.000 0.00 0.00 0.00 3.95
424 425 0.035056 GTATCACACAGCCAAGCCCT 60.035 55.000 0.00 0.00 0.00 5.19
425 426 1.369091 CGTATCACACAGCCAAGCCC 61.369 60.000 0.00 0.00 0.00 5.19
426 427 1.369091 CCGTATCACACAGCCAAGCC 61.369 60.000 0.00 0.00 0.00 4.35
427 428 1.982073 GCCGTATCACACAGCCAAGC 61.982 60.000 0.00 0.00 0.00 4.01
428 429 0.673333 TGCCGTATCACACAGCCAAG 60.673 55.000 0.00 0.00 28.69 3.61
429 430 0.673333 CTGCCGTATCACACAGCCAA 60.673 55.000 0.00 0.00 28.69 4.52
430 431 1.079197 CTGCCGTATCACACAGCCA 60.079 57.895 0.00 0.00 28.69 4.75
431 432 3.799753 CTGCCGTATCACACAGCC 58.200 61.111 0.00 0.00 28.69 4.85
433 434 0.108662 TGAGCTGCCGTATCACACAG 60.109 55.000 0.00 0.00 0.00 3.66
434 435 0.389817 GTGAGCTGCCGTATCACACA 60.390 55.000 13.03 0.00 42.30 3.72
435 436 1.084370 GGTGAGCTGCCGTATCACAC 61.084 60.000 17.82 7.09 44.08 3.82
436 437 1.218047 GGTGAGCTGCCGTATCACA 59.782 57.895 17.82 0.00 44.08 3.58
437 438 0.391130 TTGGTGAGCTGCCGTATCAC 60.391 55.000 10.32 10.32 42.07 3.06
438 439 0.323302 TTTGGTGAGCTGCCGTATCA 59.677 50.000 0.00 0.00 0.00 2.15
439 440 1.668419 ATTTGGTGAGCTGCCGTATC 58.332 50.000 0.00 0.00 0.00 2.24
440 441 3.403038 GATATTTGGTGAGCTGCCGTAT 58.597 45.455 0.00 0.00 0.00 3.06
441 442 2.801699 CGATATTTGGTGAGCTGCCGTA 60.802 50.000 0.00 0.00 0.00 4.02
442 443 1.668419 GATATTTGGTGAGCTGCCGT 58.332 50.000 0.00 0.00 0.00 5.68
443 444 0.583438 CGATATTTGGTGAGCTGCCG 59.417 55.000 0.00 0.00 0.00 5.69
444 445 1.599542 GACGATATTTGGTGAGCTGCC 59.400 52.381 0.00 0.00 0.00 4.85
445 446 2.555199 AGACGATATTTGGTGAGCTGC 58.445 47.619 0.00 0.00 0.00 5.25
446 447 4.437239 AGAAGACGATATTTGGTGAGCTG 58.563 43.478 0.00 0.00 0.00 4.24
447 448 4.442192 GGAGAAGACGATATTTGGTGAGCT 60.442 45.833 0.00 0.00 0.00 4.09
448 449 3.804873 GGAGAAGACGATATTTGGTGAGC 59.195 47.826 0.00 0.00 0.00 4.26
449 450 5.011090 TGGAGAAGACGATATTTGGTGAG 57.989 43.478 0.00 0.00 0.00 3.51
450 451 5.614324 ATGGAGAAGACGATATTTGGTGA 57.386 39.130 0.00 0.00 0.00 4.02
451 452 7.875041 AGATAATGGAGAAGACGATATTTGGTG 59.125 37.037 0.00 0.00 0.00 4.17
452 453 7.967908 AGATAATGGAGAAGACGATATTTGGT 58.032 34.615 0.00 0.00 0.00 3.67
453 454 7.274468 CGAGATAATGGAGAAGACGATATTTGG 59.726 40.741 0.00 0.00 0.00 3.28
454 455 7.810282 ACGAGATAATGGAGAAGACGATATTTG 59.190 37.037 0.00 0.00 0.00 2.32
455 456 7.810282 CACGAGATAATGGAGAAGACGATATTT 59.190 37.037 0.00 0.00 0.00 1.40
456 457 7.040340 ACACGAGATAATGGAGAAGACGATATT 60.040 37.037 0.00 0.00 0.00 1.28
457 458 6.431543 ACACGAGATAATGGAGAAGACGATAT 59.568 38.462 0.00 0.00 0.00 1.63
458 459 5.763698 ACACGAGATAATGGAGAAGACGATA 59.236 40.000 0.00 0.00 0.00 2.92
459 460 4.580995 ACACGAGATAATGGAGAAGACGAT 59.419 41.667 0.00 0.00 0.00 3.73
460 461 3.945921 ACACGAGATAATGGAGAAGACGA 59.054 43.478 0.00 0.00 0.00 4.20
461 462 4.038361 CACACGAGATAATGGAGAAGACG 58.962 47.826 0.00 0.00 0.00 4.18
462 463 4.800993 CACACACGAGATAATGGAGAAGAC 59.199 45.833 0.00 0.00 0.00 3.01
463 464 4.462834 ACACACACGAGATAATGGAGAAGA 59.537 41.667 0.00 0.00 0.00 2.87
464 465 4.564372 CACACACACGAGATAATGGAGAAG 59.436 45.833 0.00 0.00 0.00 2.85
465 466 4.021456 ACACACACACGAGATAATGGAGAA 60.021 41.667 0.00 0.00 0.00 2.87
466 467 3.509967 ACACACACACGAGATAATGGAGA 59.490 43.478 0.00 0.00 0.00 3.71
467 468 3.614176 CACACACACACGAGATAATGGAG 59.386 47.826 0.00 0.00 0.00 3.86
468 469 3.006430 ACACACACACACGAGATAATGGA 59.994 43.478 0.00 0.00 0.00 3.41
469 470 3.123453 CACACACACACACGAGATAATGG 59.877 47.826 0.00 0.00 0.00 3.16
470 471 3.123453 CCACACACACACACGAGATAATG 59.877 47.826 0.00 0.00 0.00 1.90
471 472 3.325870 CCACACACACACACGAGATAAT 58.674 45.455 0.00 0.00 0.00 1.28
472 473 2.547007 CCCACACACACACACGAGATAA 60.547 50.000 0.00 0.00 0.00 1.75
473 474 1.000394 CCCACACACACACACGAGATA 60.000 52.381 0.00 0.00 0.00 1.98
474 475 0.249868 CCCACACACACACACGAGAT 60.250 55.000 0.00 0.00 0.00 2.75
475 476 1.142965 CCCACACACACACACGAGA 59.857 57.895 0.00 0.00 0.00 4.04
476 477 0.742990 AACCCACACACACACACGAG 60.743 55.000 0.00 0.00 0.00 4.18
477 478 1.021920 CAACCCACACACACACACGA 61.022 55.000 0.00 0.00 0.00 4.35
478 479 1.302383 ACAACCCACACACACACACG 61.302 55.000 0.00 0.00 0.00 4.49
479 480 0.170116 CACAACCCACACACACACAC 59.830 55.000 0.00 0.00 0.00 3.82
480 481 0.250945 ACACAACCCACACACACACA 60.251 50.000 0.00 0.00 0.00 3.72
481 482 0.170116 CACACAACCCACACACACAC 59.830 55.000 0.00 0.00 0.00 3.82
482 483 0.036875 TCACACAACCCACACACACA 59.963 50.000 0.00 0.00 0.00 3.72
483 484 1.169577 TTCACACAACCCACACACAC 58.830 50.000 0.00 0.00 0.00 3.82
484 485 1.542030 GTTTCACACAACCCACACACA 59.458 47.619 0.00 0.00 0.00 3.72
485 486 1.542030 TGTTTCACACAACCCACACAC 59.458 47.619 0.00 0.00 29.87 3.82
486 487 1.815613 CTGTTTCACACAACCCACACA 59.184 47.619 0.00 0.00 33.87 3.72
487 488 1.469079 GCTGTTTCACACAACCCACAC 60.469 52.381 0.00 0.00 33.87 3.82
488 489 0.814457 GCTGTTTCACACAACCCACA 59.186 50.000 0.00 0.00 33.87 4.17
489 490 0.102300 GGCTGTTTCACACAACCCAC 59.898 55.000 0.00 0.00 35.78 4.61
490 491 1.380403 CGGCTGTTTCACACAACCCA 61.380 55.000 0.00 0.00 38.30 4.51
491 492 1.358759 CGGCTGTTTCACACAACCC 59.641 57.895 0.00 0.00 38.30 4.11
492 493 0.248458 CACGGCTGTTTCACACAACC 60.248 55.000 0.00 0.00 38.18 3.77
493 494 0.730265 TCACGGCTGTTTCACACAAC 59.270 50.000 0.00 0.00 33.87 3.32
494 495 1.013596 CTCACGGCTGTTTCACACAA 58.986 50.000 0.00 0.00 33.87 3.33
495 496 0.176910 TCTCACGGCTGTTTCACACA 59.823 50.000 0.00 0.00 0.00 3.72
496 497 0.861837 CTCTCACGGCTGTTTCACAC 59.138 55.000 0.00 0.00 0.00 3.82
497 498 0.750249 TCTCTCACGGCTGTTTCACA 59.250 50.000 0.00 0.00 0.00 3.58
498 499 1.795286 CTTCTCTCACGGCTGTTTCAC 59.205 52.381 0.00 0.00 0.00 3.18
499 500 1.686587 TCTTCTCTCACGGCTGTTTCA 59.313 47.619 0.00 0.00 0.00 2.69
500 501 2.440539 TCTTCTCTCACGGCTGTTTC 57.559 50.000 0.00 0.00 0.00 2.78
501 502 2.548920 CCTTCTTCTCTCACGGCTGTTT 60.549 50.000 0.00 0.00 0.00 2.83
502 503 1.001406 CCTTCTTCTCTCACGGCTGTT 59.999 52.381 0.00 0.00 0.00 3.16
503 504 0.605589 CCTTCTTCTCTCACGGCTGT 59.394 55.000 0.00 0.00 0.00 4.40
504 505 0.108424 CCCTTCTTCTCTCACGGCTG 60.108 60.000 0.00 0.00 0.00 4.85
505 506 0.251832 TCCCTTCTTCTCTCACGGCT 60.252 55.000 0.00 0.00 0.00 5.52
506 507 0.174617 CTCCCTTCTTCTCTCACGGC 59.825 60.000 0.00 0.00 0.00 5.68
507 508 1.551452 ACTCCCTTCTTCTCTCACGG 58.449 55.000 0.00 0.00 0.00 4.94
508 509 2.353208 CCAACTCCCTTCTTCTCTCACG 60.353 54.545 0.00 0.00 0.00 4.35
509 510 2.900546 TCCAACTCCCTTCTTCTCTCAC 59.099 50.000 0.00 0.00 0.00 3.51
510 511 3.169099 CTCCAACTCCCTTCTTCTCTCA 58.831 50.000 0.00 0.00 0.00 3.27
511 512 3.436243 TCTCCAACTCCCTTCTTCTCTC 58.564 50.000 0.00 0.00 0.00 3.20
512 513 3.076785 TCTCTCCAACTCCCTTCTTCTCT 59.923 47.826 0.00 0.00 0.00 3.10
513 514 3.436243 TCTCTCCAACTCCCTTCTTCTC 58.564 50.000 0.00 0.00 0.00 2.87
514 515 3.181412 ACTCTCTCCAACTCCCTTCTTCT 60.181 47.826 0.00 0.00 0.00 2.85
515 516 3.169908 ACTCTCTCCAACTCCCTTCTTC 58.830 50.000 0.00 0.00 0.00 2.87
516 517 3.169908 GACTCTCTCCAACTCCCTTCTT 58.830 50.000 0.00 0.00 0.00 2.52
517 518 2.110899 TGACTCTCTCCAACTCCCTTCT 59.889 50.000 0.00 0.00 0.00 2.85
518 519 2.495669 CTGACTCTCTCCAACTCCCTTC 59.504 54.545 0.00 0.00 0.00 3.46
519 520 2.534990 CTGACTCTCTCCAACTCCCTT 58.465 52.381 0.00 0.00 0.00 3.95
520 521 1.894978 GCTGACTCTCTCCAACTCCCT 60.895 57.143 0.00 0.00 0.00 4.20
521 522 0.534873 GCTGACTCTCTCCAACTCCC 59.465 60.000 0.00 0.00 0.00 4.30
522 523 1.476488 GAGCTGACTCTCTCCAACTCC 59.524 57.143 0.00 0.00 40.03 3.85
523 524 1.476488 GGAGCTGACTCTCTCCAACTC 59.524 57.143 0.00 0.00 46.24 3.01
524 525 1.555967 GGAGCTGACTCTCTCCAACT 58.444 55.000 0.00 0.00 46.24 3.16
528 529 1.204467 CTGTTGGAGCTGACTCTCTCC 59.796 57.143 0.00 9.65 46.95 3.71
529 530 1.892474 ACTGTTGGAGCTGACTCTCTC 59.108 52.381 0.00 0.00 42.98 3.20
530 531 2.008242 ACTGTTGGAGCTGACTCTCT 57.992 50.000 0.00 0.00 42.98 3.10
531 532 2.036475 TCAACTGTTGGAGCTGACTCTC 59.964 50.000 19.55 0.00 42.98 3.20
532 533 2.042464 TCAACTGTTGGAGCTGACTCT 58.958 47.619 19.55 0.00 42.98 3.24
533 534 2.139118 GTCAACTGTTGGAGCTGACTC 58.861 52.381 19.55 0.00 42.66 3.36
534 535 1.539065 CGTCAACTGTTGGAGCTGACT 60.539 52.381 19.55 0.00 0.00 3.41
535 536 0.861837 CGTCAACTGTTGGAGCTGAC 59.138 55.000 19.55 9.01 0.00 3.51
536 537 0.249868 CCGTCAACTGTTGGAGCTGA 60.250 55.000 19.55 0.00 0.00 4.26
537 538 0.532862 ACCGTCAACTGTTGGAGCTG 60.533 55.000 19.55 9.67 0.00 4.24
538 539 0.532862 CACCGTCAACTGTTGGAGCT 60.533 55.000 19.55 0.00 0.00 4.09
539 540 1.507141 CCACCGTCAACTGTTGGAGC 61.507 60.000 19.55 9.86 0.00 4.70
540 541 0.105964 TCCACCGTCAACTGTTGGAG 59.894 55.000 19.55 13.36 0.00 3.86
541 542 0.105964 CTCCACCGTCAACTGTTGGA 59.894 55.000 19.55 8.40 0.00 3.53
542 543 0.884704 CCTCCACCGTCAACTGTTGG 60.885 60.000 19.55 7.22 0.00 3.77
543 544 0.884704 CCCTCCACCGTCAACTGTTG 60.885 60.000 14.24 14.24 0.00 3.33
544 545 1.450211 CCCTCCACCGTCAACTGTT 59.550 57.895 0.00 0.00 0.00 3.16
545 546 3.148084 CCCTCCACCGTCAACTGT 58.852 61.111 0.00 0.00 0.00 3.55
573 574 7.671302 TCATCGAGAATCTAAATCCCCTTAAG 58.329 38.462 0.00 0.00 0.00 1.85
695 1167 6.882140 TCTTCTTTTATCTGCCCATAACGAAA 59.118 34.615 0.00 0.00 0.00 3.46
801 1278 1.486726 GGACGATCAACTTGGAGGGAT 59.513 52.381 0.00 0.00 0.00 3.85
875 1367 7.560626 CGTAGGGCTATATTTATAGGAGGAAGT 59.439 40.741 6.72 0.00 36.90 3.01
914 1406 2.455122 ATGGGGATGGGGATGGGG 60.455 66.667 0.00 0.00 0.00 4.96
942 1446 1.709578 CGAGGAAGGAGATGATGGGA 58.290 55.000 0.00 0.00 0.00 4.37
943 1447 0.034616 GCGAGGAAGGAGATGATGGG 59.965 60.000 0.00 0.00 0.00 4.00
994 1500 1.078143 GAGGAAGCTTCATGGCCGT 60.078 57.895 27.02 0.00 0.00 5.68
1013 1519 1.569479 GAGAAGACACGCAACAGCCC 61.569 60.000 0.00 0.00 0.00 5.19
1140 1688 5.061933 GTGATCGCTAGCAACAGATATGATG 59.938 44.000 16.45 0.00 0.00 3.07
1174 1730 2.238646 ACATGAAGAACCGGGCAAGATA 59.761 45.455 6.32 0.00 0.00 1.98
1198 1754 2.483745 CGTGCATGCTGCTGGAAG 59.516 61.111 20.33 0.00 45.31 3.46
1201 1765 4.476410 CTGCGTGCATGCTGCTGG 62.476 66.667 29.83 19.16 45.31 4.85
1203 1767 4.710167 TCCTGCGTGCATGCTGCT 62.710 61.111 29.83 0.00 45.31 4.24
1204 1768 4.471726 GTCCTGCGTGCATGCTGC 62.472 66.667 29.83 23.14 45.29 5.25
1218 1782 3.251245 AGATCGATCATGTCAGTACGTCC 59.749 47.826 26.47 0.00 0.00 4.79
1281 1845 4.697756 TTCTTGGGCCGCCGTGAG 62.698 66.667 2.55 1.14 0.00 3.51
1286 1850 2.679996 ATTGGTTCTTGGGCCGCC 60.680 61.111 0.00 0.00 0.00 6.13
1291 1855 1.273327 GCTTGACCATTGGTTCTTGGG 59.727 52.381 10.29 0.00 35.25 4.12
1293 1857 3.006110 ACATGCTTGACCATTGGTTCTTG 59.994 43.478 10.29 10.15 35.25 3.02
1308 1872 1.202879 TCCCCGAAGACAAACATGCTT 60.203 47.619 0.00 0.00 0.00 3.91
2079 5742 4.443394 GTGGTGTAGTTGTTCGAACTAGTG 59.557 45.833 27.32 0.00 33.81 2.74
2166 5829 2.983907 TGTGAACGTTGTCCCTTACA 57.016 45.000 5.00 0.00 35.88 2.41
2168 5831 4.062293 CAGAATGTGAACGTTGTCCCTTA 58.938 43.478 5.00 0.00 0.00 2.69
2238 5901 6.413018 ACATCAATGCGCATATATGTGTAG 57.587 37.500 32.91 21.65 40.29 2.74
2275 5938 7.730364 AATCGAATCCATACATAAGGAACAC 57.270 36.000 0.00 0.00 37.48 3.32
2276 5939 9.435688 CATAATCGAATCCATACATAAGGAACA 57.564 33.333 0.00 0.00 37.48 3.18
2333 6009 1.638529 GGACTGATCCGATCCTCCAT 58.361 55.000 13.81 0.00 34.48 3.41
2442 6138 3.057734 GGGATTTTCGCATAGGTCGTAG 58.942 50.000 0.00 0.00 0.00 3.51
2587 6310 1.270518 CGCCAACTAGCTAGCCATCAT 60.271 52.381 20.91 0.00 0.00 2.45
2732 6478 7.492994 TCAACAAATAGGGTTAAAACAACAAGC 59.507 33.333 0.00 0.00 0.00 4.01
2736 6482 9.758651 AATCTCAACAAATAGGGTTAAAACAAC 57.241 29.630 0.00 0.00 0.00 3.32
2745 6493 9.855021 CGAATTTTTAATCTCAACAAATAGGGT 57.145 29.630 0.00 0.00 0.00 4.34
2763 6515 7.419204 TCACTCAAATAAACGACCGAATTTTT 58.581 30.769 0.00 0.00 0.00 1.94
2764 6516 6.961576 TCACTCAAATAAACGACCGAATTTT 58.038 32.000 0.00 0.00 0.00 1.82
2777 6530 5.629435 CGCACGCTATATCTCACTCAAATAA 59.371 40.000 0.00 0.00 0.00 1.40
2840 6599 1.566563 CGCGGTTCTAGCATGATGC 59.433 57.895 9.89 9.89 45.46 3.91
2841 6600 1.566563 GCGCGGTTCTAGCATGATG 59.433 57.895 8.83 0.00 34.19 3.07
2842 6601 1.951130 CGCGCGGTTCTAGCATGAT 60.951 57.895 24.84 0.00 34.19 2.45
2843 6602 2.582226 CGCGCGGTTCTAGCATGA 60.582 61.111 24.84 0.00 34.19 3.07
2844 6603 2.885644 ACGCGCGGTTCTAGCATG 60.886 61.111 35.22 1.22 34.19 4.06
2845 6604 2.885644 CACGCGCGGTTCTAGCAT 60.886 61.111 35.22 6.31 34.19 3.79
2901 9824 2.360350 CCCTTGCGTGCACCATCT 60.360 61.111 12.15 0.00 0.00 2.90
2902 9825 2.359850 TCCCTTGCGTGCACCATC 60.360 61.111 12.15 1.12 0.00 3.51
2903 9826 2.202236 ATCTCCCTTGCGTGCACCAT 62.202 55.000 12.15 0.00 0.00 3.55
2912 9835 2.899339 GCTGCCGATCTCCCTTGC 60.899 66.667 0.00 0.00 0.00 4.01
2933 9856 0.389426 AGTAGCGTAAGGGTGTTGCG 60.389 55.000 0.00 0.00 38.28 4.85
3060 11770 6.653273 AAATATGATACAATCATCTCGGCG 57.347 37.500 0.00 0.00 46.62 6.46
3156 11879 0.100503 ACACAGTTGCCTTTCGTTGC 59.899 50.000 0.00 0.00 0.00 4.17
3171 11894 1.379977 CCTCCCGCTCCTCTACACA 60.380 63.158 0.00 0.00 0.00 3.72
3183 11906 2.045926 CCTTGCCTTGTCCTCCCG 60.046 66.667 0.00 0.00 0.00 5.14
3231 11954 9.753674 CTCTTCCTCCTGTATAAGATAGAGATT 57.246 37.037 0.00 0.00 0.00 2.40
3233 11956 8.513139 TCTCTTCCTCCTGTATAAGATAGAGA 57.487 38.462 0.00 0.00 33.89 3.10
3242 11966 5.425539 CCCACTTTTCTCTTCCTCCTGTATA 59.574 44.000 0.00 0.00 0.00 1.47
3287 12011 7.530010 ACGTGATCCTTCTCAAAATTTATGTG 58.470 34.615 0.00 0.00 0.00 3.21
3290 12014 8.110860 ACAACGTGATCCTTCTCAAAATTTAT 57.889 30.769 0.00 0.00 0.00 1.40
3379 12103 8.030692 TCGCAAGCTACAACTTAAGATACTAAA 58.969 33.333 10.09 0.00 37.18 1.85
3398 12122 2.806244 TCCTTAAGTTTGTCTCGCAAGC 59.194 45.455 0.97 0.00 38.47 4.01


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

AutoCloner maintained by Alex Coulton.