Multiple sequence alignment - TraesCS2A01G027500

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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 TraesCS2A01G027500 chr2A 100.000 3287 0 0 1 3287 12703342 12700056 0.000000e+00 6071.0
1 TraesCS2A01G027500 chr2A 96.399 1222 40 4 2068 3287 12577893 12576674 0.000000e+00 2010.0
2 TraesCS2A01G027500 chr2A 84.420 1181 154 23 2093 3265 12589056 12587898 0.000000e+00 1134.0
3 TraesCS2A01G027500 chr2A 85.907 1036 130 12 921 1946 12590240 12589211 0.000000e+00 1090.0
4 TraesCS2A01G027500 chr2A 100.000 491 0 0 3477 3967 12699866 12699376 0.000000e+00 907.0
5 TraesCS2A01G027500 chr2A 80.844 924 159 13 994 1905 551721513 551722430 0.000000e+00 710.0
6 TraesCS2A01G027500 chr2A 84.908 709 98 4 2330 3038 551722702 551723401 0.000000e+00 708.0
7 TraesCS2A01G027500 chr2A 92.216 501 26 6 3477 3966 12576643 12576145 0.000000e+00 697.0
8 TraesCS2A01G027500 chr2D 97.017 2581 62 2 720 3287 11965006 11962428 0.000000e+00 4325.0
9 TraesCS2A01G027500 chr2D 81.343 938 157 13 980 1905 435072632 435071701 0.000000e+00 747.0
10 TraesCS2A01G027500 chr2D 84.146 738 108 4 2301 3038 435071112 435070384 0.000000e+00 706.0
11 TraesCS2A01G027500 chr2D 89.262 447 40 4 3477 3919 11962398 11961956 1.610000e-153 553.0
12 TraesCS2A01G027500 chr2D 94.030 134 6 2 561 693 11973988 11973856 6.720000e-48 202.0
13 TraesCS2A01G027500 chr2D 94.545 55 2 1 3913 3966 5040792 5040738 2.540000e-12 84.2
14 TraesCS2A01G027500 chr5D 80.472 1060 189 14 877 1928 522761752 522760703 0.000000e+00 795.0
15 TraesCS2A01G027500 chr5D 85.623 626 90 0 2325 2950 522759648 522759023 0.000000e+00 658.0
16 TraesCS2A01G027500 chr5D 82.540 315 52 3 163 476 225793965 225794277 1.400000e-69 274.0
17 TraesCS2A01G027500 chr3A 96.458 480 17 0 2 481 568022732 568022253 0.000000e+00 793.0
18 TraesCS2A01G027500 chr2B 81.520 974 157 13 944 1905 513481274 513480312 0.000000e+00 780.0
19 TraesCS2A01G027500 chr2B 84.345 741 107 4 2301 3041 513480110 513479379 0.000000e+00 717.0
20 TraesCS2A01G027500 chr1A 94.617 483 26 0 1 483 199538891 199539373 0.000000e+00 749.0
21 TraesCS2A01G027500 chr1A 83.758 314 50 1 163 476 30769080 30769392 3.000000e-76 296.0
22 TraesCS2A01G027500 chr7D 91.833 502 19 4 1 481 589263678 589263178 0.000000e+00 680.0
23 TraesCS2A01G027500 chr5A 77.885 624 129 6 2333 2954 626229007 626228391 2.890000e-101 379.0
24 TraesCS2A01G027500 chr6D 83.439 314 51 1 163 476 224424035 224424347 1.390000e-74 291.0
25 TraesCS2A01G027500 chr3D 74.295 638 144 18 2328 2954 73714317 73713689 6.580000e-63 252.0
26 TraesCS2A01G027500 chr7A 95.862 145 6 0 338 482 93499490 93499346 6.630000e-58 235.0
27 TraesCS2A01G027500 chr7A 92.982 57 4 0 3910 3966 653442289 653442345 2.540000e-12 84.2
28 TraesCS2A01G027500 chr7A 91.525 59 5 0 3908 3966 115744348 115744406 9.140000e-12 82.4
29 TraesCS2A01G027500 chr3B 73.899 636 145 17 2328 2951 118809060 118808434 6.630000e-58 235.0
30 TraesCS2A01G027500 chr6A 82.550 149 26 0 321 469 277563091 277563239 8.950000e-27 132.0
31 TraesCS2A01G027500 chr6A 93.220 59 2 2 3909 3966 998345 998402 7.060000e-13 86.1
32 TraesCS2A01G027500 chr6A 90.625 64 5 1 3904 3966 3110970 3110907 2.540000e-12 84.2
33 TraesCS2A01G027500 chr6A 94.545 55 2 1 3912 3966 574817654 574817601 2.540000e-12 84.2
34 TraesCS2A01G027500 chr4A 94.643 56 2 1 3912 3966 633707817 633707762 7.060000e-13 86.1
35 TraesCS2A01G027500 chr4A 94.545 55 2 1 3913 3966 633401287 633401233 2.540000e-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 TraesCS2A01G027500 chr2A 12699376 12703342 3966 True 3489.0 6071 100.0000 1 3967 2 chr2A.!!$R3 3966
1 TraesCS2A01G027500 chr2A 12576145 12577893 1748 True 1353.5 2010 94.3075 2068 3966 2 chr2A.!!$R1 1898
2 TraesCS2A01G027500 chr2A 12587898 12590240 2342 True 1112.0 1134 85.1635 921 3265 2 chr2A.!!$R2 2344
3 TraesCS2A01G027500 chr2A 551721513 551723401 1888 False 709.0 710 82.8760 994 3038 2 chr2A.!!$F1 2044
4 TraesCS2A01G027500 chr2D 11961956 11965006 3050 True 2439.0 4325 93.1395 720 3919 2 chr2D.!!$R3 3199
5 TraesCS2A01G027500 chr2D 435070384 435072632 2248 True 726.5 747 82.7445 980 3038 2 chr2D.!!$R4 2058
6 TraesCS2A01G027500 chr5D 522759023 522761752 2729 True 726.5 795 83.0475 877 2950 2 chr5D.!!$R1 2073
7 TraesCS2A01G027500 chr2B 513479379 513481274 1895 True 748.5 780 82.9325 944 3041 2 chr2B.!!$R1 2097
8 TraesCS2A01G027500 chr7D 589263178 589263678 500 True 680.0 680 91.8330 1 481 1 chr7D.!!$R1 480
9 TraesCS2A01G027500 chr5A 626228391 626229007 616 True 379.0 379 77.8850 2333 2954 1 chr5A.!!$R1 621
10 TraesCS2A01G027500 chr3D 73713689 73714317 628 True 252.0 252 74.2950 2328 2954 1 chr3D.!!$R1 626
11 TraesCS2A01G027500 chr3B 118808434 118809060 626 True 235.0 235 73.8990 2328 2951 1 chr3B.!!$R1 623

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
542 564 0.177604 GGGAGGTCATGACTGCTCAG 59.822 60.0 24.5 0.0 0.00 3.35 F
1303 1358 0.108329 CGCCCTGTCGAACCATAGTT 60.108 55.0 0.0 0.0 39.54 2.24 F
2046 2755 0.112412 TCAAGGTTTTCAGGAGGGCC 59.888 55.0 0.0 0.0 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 1841 0.738975 TCTTCATCGTCGCTGTAGGG 59.261 55.000 3.38 0.0 0.00 3.53 R
2170 2901 1.572085 CTCTCACGCCTGTTGCCAAG 61.572 60.000 0.00 0.0 36.24 3.61 R
3631 4698 1.078497 TTGGTGGCTATCGTGCTGG 60.078 57.895 0.00 0.0 0.00 4.85 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
88 89 4.595538 ACAGCGACGCCGAACCAA 62.596 61.111 17.79 0.00 38.22 3.67
165 187 4.549516 GACCCTAGCGACGACGGC 62.550 72.222 9.67 0.00 40.15 5.68
184 206 1.226030 CGACCGGTGTTCCCAGAAAC 61.226 60.000 14.63 0.00 0.00 2.78
192 214 1.347707 TGTTCCCAGAAACGAGATGCT 59.652 47.619 0.00 0.00 31.58 3.79
285 307 3.948719 GTGTTCCACTCCCCGCCA 61.949 66.667 0.00 0.00 0.00 5.69
316 338 2.115910 CAAGCACCTCAAGGGCCA 59.884 61.111 6.18 0.00 40.27 5.36
317 339 1.975407 CAAGCACCTCAAGGGCCAG 60.975 63.158 6.18 0.00 40.27 4.85
320 342 2.360852 CACCTCAAGGGCCAGCTG 60.361 66.667 6.78 6.78 40.27 4.24
351 373 4.933064 GGCGCATCCTCCTCGTCG 62.933 72.222 10.83 0.00 0.00 5.12
397 419 2.662006 TGAGAATCTTGAGCCAGACG 57.338 50.000 0.00 0.00 34.92 4.18
406 428 3.708220 GAGCCAGACGAGCTTCCCG 62.708 68.421 0.00 0.00 41.75 5.14
488 510 3.643398 GGTACCCATCCCTCGCTT 58.357 61.111 0.00 0.00 0.00 4.68
489 511 1.146263 GGTACCCATCCCTCGCTTG 59.854 63.158 0.00 0.00 0.00 4.01
490 512 1.146263 GTACCCATCCCTCGCTTGG 59.854 63.158 0.00 0.00 0.00 3.61
491 513 1.306654 TACCCATCCCTCGCTTGGT 60.307 57.895 0.00 0.00 0.00 3.67
492 514 0.912487 TACCCATCCCTCGCTTGGTT 60.912 55.000 0.00 0.00 0.00 3.67
493 515 1.000896 CCCATCCCTCGCTTGGTTT 60.001 57.895 0.00 0.00 0.00 3.27
494 516 1.315257 CCCATCCCTCGCTTGGTTTG 61.315 60.000 0.00 0.00 0.00 2.93
495 517 0.609131 CCATCCCTCGCTTGGTTTGT 60.609 55.000 0.00 0.00 0.00 2.83
496 518 1.247567 CATCCCTCGCTTGGTTTGTT 58.752 50.000 0.00 0.00 0.00 2.83
497 519 1.613437 CATCCCTCGCTTGGTTTGTTT 59.387 47.619 0.00 0.00 0.00 2.83
498 520 2.642154 TCCCTCGCTTGGTTTGTTTA 57.358 45.000 0.00 0.00 0.00 2.01
499 521 3.149005 TCCCTCGCTTGGTTTGTTTAT 57.851 42.857 0.00 0.00 0.00 1.40
500 522 3.078837 TCCCTCGCTTGGTTTGTTTATC 58.921 45.455 0.00 0.00 0.00 1.75
501 523 3.081804 CCCTCGCTTGGTTTGTTTATCT 58.918 45.455 0.00 0.00 0.00 1.98
502 524 3.506067 CCCTCGCTTGGTTTGTTTATCTT 59.494 43.478 0.00 0.00 0.00 2.40
503 525 4.698304 CCCTCGCTTGGTTTGTTTATCTTA 59.302 41.667 0.00 0.00 0.00 2.10
504 526 5.163754 CCCTCGCTTGGTTTGTTTATCTTAG 60.164 44.000 0.00 0.00 0.00 2.18
505 527 5.291293 TCGCTTGGTTTGTTTATCTTAGC 57.709 39.130 0.00 0.00 0.00 3.09
506 528 4.155280 TCGCTTGGTTTGTTTATCTTAGCC 59.845 41.667 0.00 0.00 0.00 3.93
507 529 4.156008 CGCTTGGTTTGTTTATCTTAGCCT 59.844 41.667 0.00 0.00 0.00 4.58
508 530 5.641709 GCTTGGTTTGTTTATCTTAGCCTC 58.358 41.667 0.00 0.00 0.00 4.70
509 531 5.673818 GCTTGGTTTGTTTATCTTAGCCTCG 60.674 44.000 0.00 0.00 0.00 4.63
510 532 4.901868 TGGTTTGTTTATCTTAGCCTCGT 58.098 39.130 0.00 0.00 0.00 4.18
511 533 4.693566 TGGTTTGTTTATCTTAGCCTCGTG 59.306 41.667 0.00 0.00 0.00 4.35
512 534 4.094442 GGTTTGTTTATCTTAGCCTCGTGG 59.906 45.833 0.00 0.00 0.00 4.94
513 535 3.536956 TGTTTATCTTAGCCTCGTGGG 57.463 47.619 5.54 0.00 38.36 4.61
514 536 3.101437 TGTTTATCTTAGCCTCGTGGGA 58.899 45.455 5.54 0.00 37.23 4.37
515 537 3.709653 TGTTTATCTTAGCCTCGTGGGAT 59.290 43.478 5.54 2.27 37.23 3.85
516 538 4.202223 TGTTTATCTTAGCCTCGTGGGATC 60.202 45.833 5.54 0.00 37.23 3.36
517 539 1.343069 ATCTTAGCCTCGTGGGATCC 58.657 55.000 1.92 1.92 37.23 3.36
518 540 0.759436 TCTTAGCCTCGTGGGATCCC 60.759 60.000 25.22 25.22 37.23 3.85
519 541 1.002403 TTAGCCTCGTGGGATCCCA 59.998 57.895 30.62 30.62 45.02 4.37
534 556 3.387716 CCACACGGGAGGTCATGA 58.612 61.111 0.00 0.00 40.01 3.07
535 557 1.079127 CCACACGGGAGGTCATGAC 60.079 63.158 17.91 17.91 40.01 3.06
536 558 1.544825 CCACACGGGAGGTCATGACT 61.545 60.000 24.50 11.25 40.01 3.41
537 559 0.390340 CACACGGGAGGTCATGACTG 60.390 60.000 24.50 15.93 0.00 3.51
538 560 1.448540 CACGGGAGGTCATGACTGC 60.449 63.158 24.50 16.09 0.00 4.40
539 561 1.610673 ACGGGAGGTCATGACTGCT 60.611 57.895 24.50 14.47 0.00 4.24
540 562 1.142748 CGGGAGGTCATGACTGCTC 59.857 63.158 24.50 21.18 0.00 4.26
541 563 1.607801 CGGGAGGTCATGACTGCTCA 61.608 60.000 24.50 0.00 0.00 4.26
542 564 0.177604 GGGAGGTCATGACTGCTCAG 59.822 60.000 24.50 0.00 0.00 3.35
543 565 1.189752 GGAGGTCATGACTGCTCAGA 58.810 55.000 24.50 0.00 0.00 3.27
544 566 1.552337 GGAGGTCATGACTGCTCAGAA 59.448 52.381 24.50 0.00 0.00 3.02
545 567 2.027745 GGAGGTCATGACTGCTCAGAAA 60.028 50.000 24.50 0.00 0.00 2.52
546 568 3.557898 GGAGGTCATGACTGCTCAGAAAA 60.558 47.826 24.50 0.00 0.00 2.29
547 569 3.406764 AGGTCATGACTGCTCAGAAAAC 58.593 45.455 24.50 4.18 0.00 2.43
548 570 2.485814 GGTCATGACTGCTCAGAAAACC 59.514 50.000 24.50 0.64 0.00 3.27
549 571 3.141398 GTCATGACTGCTCAGAAAACCA 58.859 45.455 18.83 0.00 0.00 3.67
550 572 3.188048 GTCATGACTGCTCAGAAAACCAG 59.812 47.826 18.83 0.00 0.00 4.00
551 573 3.144506 CATGACTGCTCAGAAAACCAGT 58.855 45.455 3.60 0.00 40.92 4.00
552 574 2.564771 TGACTGCTCAGAAAACCAGTG 58.435 47.619 3.60 0.00 38.55 3.66
553 575 2.170397 TGACTGCTCAGAAAACCAGTGA 59.830 45.455 3.60 0.00 38.55 3.41
554 576 3.206150 GACTGCTCAGAAAACCAGTGAA 58.794 45.455 3.60 0.00 38.55 3.18
555 577 2.945668 ACTGCTCAGAAAACCAGTGAAC 59.054 45.455 3.60 0.00 37.18 3.18
556 578 2.291741 CTGCTCAGAAAACCAGTGAACC 59.708 50.000 0.00 0.00 0.00 3.62
557 579 2.092429 TGCTCAGAAAACCAGTGAACCT 60.092 45.455 0.00 0.00 0.00 3.50
558 580 3.135712 TGCTCAGAAAACCAGTGAACCTA 59.864 43.478 0.00 0.00 0.00 3.08
559 581 4.134563 GCTCAGAAAACCAGTGAACCTAA 58.865 43.478 0.00 0.00 0.00 2.69
560 582 4.762251 GCTCAGAAAACCAGTGAACCTAAT 59.238 41.667 0.00 0.00 0.00 1.73
561 583 5.335191 GCTCAGAAAACCAGTGAACCTAATG 60.335 44.000 0.00 0.00 0.00 1.90
562 584 5.935945 TCAGAAAACCAGTGAACCTAATGA 58.064 37.500 0.00 0.00 0.00 2.57
563 585 5.997746 TCAGAAAACCAGTGAACCTAATGAG 59.002 40.000 0.00 0.00 0.00 2.90
564 586 5.765182 CAGAAAACCAGTGAACCTAATGAGT 59.235 40.000 0.00 0.00 0.00 3.41
565 587 5.765182 AGAAAACCAGTGAACCTAATGAGTG 59.235 40.000 0.00 0.00 0.00 3.51
566 588 3.059352 ACCAGTGAACCTAATGAGTGC 57.941 47.619 0.00 0.00 0.00 4.40
567 589 2.371841 ACCAGTGAACCTAATGAGTGCA 59.628 45.455 0.00 0.00 0.00 4.57
568 590 3.009473 ACCAGTGAACCTAATGAGTGCAT 59.991 43.478 0.00 0.00 35.92 3.96
569 591 4.225042 ACCAGTGAACCTAATGAGTGCATA 59.775 41.667 0.00 0.00 33.44 3.14
570 592 5.185454 CCAGTGAACCTAATGAGTGCATAA 58.815 41.667 0.00 0.00 33.44 1.90
571 593 5.065218 CCAGTGAACCTAATGAGTGCATAAC 59.935 44.000 0.00 0.00 33.44 1.89
572 594 5.065218 CAGTGAACCTAATGAGTGCATAACC 59.935 44.000 0.00 0.00 33.44 2.85
573 595 5.045578 AGTGAACCTAATGAGTGCATAACCT 60.046 40.000 0.00 0.00 33.44 3.50
574 596 5.648092 GTGAACCTAATGAGTGCATAACCTT 59.352 40.000 0.00 0.00 33.44 3.50
575 597 5.647658 TGAACCTAATGAGTGCATAACCTTG 59.352 40.000 0.00 0.00 33.44 3.61
576 598 5.435686 ACCTAATGAGTGCATAACCTTGA 57.564 39.130 0.00 0.00 33.44 3.02
577 599 5.431765 ACCTAATGAGTGCATAACCTTGAG 58.568 41.667 0.00 0.00 33.44 3.02
578 600 4.274459 CCTAATGAGTGCATAACCTTGAGC 59.726 45.833 0.00 0.00 33.44 4.26
579 601 2.857186 TGAGTGCATAACCTTGAGCA 57.143 45.000 0.00 0.00 34.10 4.26
580 602 3.354948 TGAGTGCATAACCTTGAGCAT 57.645 42.857 0.00 0.00 39.43 3.79
581 603 3.011818 TGAGTGCATAACCTTGAGCATG 58.988 45.455 0.00 0.00 39.43 4.06
582 604 3.012518 GAGTGCATAACCTTGAGCATGT 58.987 45.455 0.00 0.00 39.43 3.21
583 605 3.424703 AGTGCATAACCTTGAGCATGTT 58.575 40.909 0.00 0.00 39.43 2.71
584 606 3.828451 AGTGCATAACCTTGAGCATGTTT 59.172 39.130 0.00 0.00 39.43 2.83
585 607 5.009631 AGTGCATAACCTTGAGCATGTTTA 58.990 37.500 0.00 0.00 39.43 2.01
586 608 5.124457 AGTGCATAACCTTGAGCATGTTTAG 59.876 40.000 0.00 0.00 39.43 1.85
587 609 5.123820 GTGCATAACCTTGAGCATGTTTAGA 59.876 40.000 0.00 0.00 39.43 2.10
588 610 5.355071 TGCATAACCTTGAGCATGTTTAGAG 59.645 40.000 0.00 0.00 31.05 2.43
589 611 5.586243 GCATAACCTTGAGCATGTTTAGAGA 59.414 40.000 0.00 0.00 0.00 3.10
590 612 6.094048 GCATAACCTTGAGCATGTTTAGAGAA 59.906 38.462 0.00 0.00 0.00 2.87
591 613 7.362056 GCATAACCTTGAGCATGTTTAGAGAAA 60.362 37.037 0.00 0.00 0.00 2.52
592 614 8.680903 CATAACCTTGAGCATGTTTAGAGAAAT 58.319 33.333 0.00 0.00 0.00 2.17
593 615 6.506500 ACCTTGAGCATGTTTAGAGAAATG 57.493 37.500 0.00 0.00 0.00 2.32
594 616 5.416952 ACCTTGAGCATGTTTAGAGAAATGG 59.583 40.000 0.00 0.00 0.00 3.16
595 617 5.163581 CCTTGAGCATGTTTAGAGAAATGGG 60.164 44.000 0.00 0.00 0.00 4.00
596 618 5.178096 TGAGCATGTTTAGAGAAATGGGA 57.822 39.130 0.00 0.00 0.00 4.37
597 619 5.759059 TGAGCATGTTTAGAGAAATGGGAT 58.241 37.500 0.00 0.00 0.00 3.85
598 620 6.899089 TGAGCATGTTTAGAGAAATGGGATA 58.101 36.000 0.00 0.00 0.00 2.59
599 621 6.767902 TGAGCATGTTTAGAGAAATGGGATAC 59.232 38.462 0.00 0.00 0.00 2.24
600 622 6.904626 AGCATGTTTAGAGAAATGGGATACT 58.095 36.000 0.00 0.00 0.00 2.12
601 623 6.769822 AGCATGTTTAGAGAAATGGGATACTG 59.230 38.462 0.00 0.00 0.00 2.74
602 624 6.767902 GCATGTTTAGAGAAATGGGATACTGA 59.232 38.462 0.00 0.00 0.00 3.41
603 625 7.041508 GCATGTTTAGAGAAATGGGATACTGAG 60.042 40.741 0.00 0.00 0.00 3.35
604 626 6.349300 TGTTTAGAGAAATGGGATACTGAGC 58.651 40.000 0.00 0.00 0.00 4.26
605 627 6.070251 TGTTTAGAGAAATGGGATACTGAGCA 60.070 38.462 0.00 0.00 0.00 4.26
606 628 6.560003 TTAGAGAAATGGGATACTGAGCAA 57.440 37.500 0.00 0.00 0.00 3.91
607 629 5.643421 AGAGAAATGGGATACTGAGCAAT 57.357 39.130 0.00 0.00 0.00 3.56
608 630 5.374921 AGAGAAATGGGATACTGAGCAATG 58.625 41.667 0.00 0.00 0.00 2.82
609 631 4.467769 AGAAATGGGATACTGAGCAATGG 58.532 43.478 0.00 0.00 0.00 3.16
610 632 2.283145 ATGGGATACTGAGCAATGGC 57.717 50.000 0.00 0.00 41.61 4.40
611 633 0.918258 TGGGATACTGAGCAATGGCA 59.082 50.000 0.00 0.00 44.61 4.92
612 634 1.284491 TGGGATACTGAGCAATGGCAA 59.716 47.619 0.00 0.00 44.61 4.52
613 635 2.091720 TGGGATACTGAGCAATGGCAAT 60.092 45.455 0.00 0.00 44.61 3.56
614 636 2.295349 GGGATACTGAGCAATGGCAATG 59.705 50.000 0.00 0.00 44.61 2.82
615 637 3.216800 GGATACTGAGCAATGGCAATGA 58.783 45.455 6.76 0.00 44.61 2.57
616 638 3.004106 GGATACTGAGCAATGGCAATGAC 59.996 47.826 6.76 0.07 44.61 3.06
617 639 1.913778 ACTGAGCAATGGCAATGACA 58.086 45.000 6.76 0.00 44.61 3.58
618 640 2.241160 ACTGAGCAATGGCAATGACAA 58.759 42.857 6.76 0.00 44.61 3.18
619 641 2.829720 ACTGAGCAATGGCAATGACAAT 59.170 40.909 6.76 0.00 44.61 2.71
620 642 3.186909 CTGAGCAATGGCAATGACAATG 58.813 45.455 6.76 0.00 44.61 2.82
621 643 2.826725 TGAGCAATGGCAATGACAATGA 59.173 40.909 8.58 0.00 44.61 2.57
622 644 3.184541 GAGCAATGGCAATGACAATGAC 58.815 45.455 8.58 0.00 44.61 3.06
623 645 2.563620 AGCAATGGCAATGACAATGACA 59.436 40.909 8.58 0.44 44.61 3.58
625 647 3.308595 GCAATGGCAATGACAATGACATG 59.691 43.478 12.67 8.18 45.72 3.21
626 648 4.749976 CAATGGCAATGACAATGACATGA 58.250 39.130 12.67 0.00 45.72 3.07
627 649 3.853831 TGGCAATGACAATGACATGAC 57.146 42.857 0.00 0.00 28.68 3.06
628 650 2.492881 TGGCAATGACAATGACATGACC 59.507 45.455 0.00 4.91 28.68 4.02
629 651 2.492881 GGCAATGACAATGACATGACCA 59.507 45.455 0.00 0.00 0.00 4.02
630 652 3.056678 GGCAATGACAATGACATGACCAA 60.057 43.478 0.00 0.00 0.00 3.67
631 653 4.171005 GCAATGACAATGACATGACCAAG 58.829 43.478 0.00 0.00 0.00 3.61
632 654 4.082625 GCAATGACAATGACATGACCAAGA 60.083 41.667 0.00 0.00 0.00 3.02
633 655 5.565242 GCAATGACAATGACATGACCAAGAA 60.565 40.000 0.00 0.00 0.00 2.52
634 656 6.448852 CAATGACAATGACATGACCAAGAAA 58.551 36.000 0.00 0.00 0.00 2.52
635 657 6.653526 ATGACAATGACATGACCAAGAAAA 57.346 33.333 0.00 0.00 0.00 2.29
636 658 5.830912 TGACAATGACATGACCAAGAAAAC 58.169 37.500 0.00 0.00 0.00 2.43
637 659 5.359292 TGACAATGACATGACCAAGAAAACA 59.641 36.000 0.00 0.00 0.00 2.83
638 660 6.040729 TGACAATGACATGACCAAGAAAACAT 59.959 34.615 0.00 0.00 0.00 2.71
639 661 7.230309 TGACAATGACATGACCAAGAAAACATA 59.770 33.333 0.00 0.00 0.00 2.29
640 662 7.596494 ACAATGACATGACCAAGAAAACATAG 58.404 34.615 0.00 0.00 0.00 2.23
641 663 7.231317 ACAATGACATGACCAAGAAAACATAGT 59.769 33.333 0.00 0.00 0.00 2.12
642 664 8.729756 CAATGACATGACCAAGAAAACATAGTA 58.270 33.333 0.00 0.00 0.00 1.82
643 665 7.905604 TGACATGACCAAGAAAACATAGTAG 57.094 36.000 0.00 0.00 0.00 2.57
644 666 6.878923 TGACATGACCAAGAAAACATAGTAGG 59.121 38.462 0.00 0.00 0.00 3.18
645 667 6.779860 ACATGACCAAGAAAACATAGTAGGT 58.220 36.000 0.00 0.00 0.00 3.08
646 668 7.231467 ACATGACCAAGAAAACATAGTAGGTT 58.769 34.615 0.00 0.00 0.00 3.50
647 669 7.724061 ACATGACCAAGAAAACATAGTAGGTTT 59.276 33.333 7.10 7.10 39.99 3.27
649 671 8.528044 TGACCAAGAAAACATAGTAGGTTTTT 57.472 30.769 22.48 9.78 45.56 1.94
676 698 9.924650 TTTTAAGTGTGGTTCTTCTAGTATCTC 57.075 33.333 0.00 0.00 0.00 2.75
677 699 8.880991 TTAAGTGTGGTTCTTCTAGTATCTCT 57.119 34.615 0.00 0.00 0.00 3.10
678 700 7.784470 AAGTGTGGTTCTTCTAGTATCTCTT 57.216 36.000 0.00 0.00 0.00 2.85
679 701 7.784470 AGTGTGGTTCTTCTAGTATCTCTTT 57.216 36.000 0.00 0.00 0.00 2.52
680 702 8.880991 AGTGTGGTTCTTCTAGTATCTCTTTA 57.119 34.615 0.00 0.00 0.00 1.85
681 703 9.482175 AGTGTGGTTCTTCTAGTATCTCTTTAT 57.518 33.333 0.00 0.00 0.00 1.40
717 739 8.410912 ACTTTGTACTCCAATTTAACAGTTTCC 58.589 33.333 0.00 0.00 31.81 3.13
718 740 8.528044 TTTGTACTCCAATTTAACAGTTTCCT 57.472 30.769 0.00 0.00 31.81 3.36
742 764 4.266502 GTGAATGTGTCTGTCGCTATCTTC 59.733 45.833 0.00 0.00 0.00 2.87
786 808 5.353400 GTGCATGAATGTCAATCTCTGAGAA 59.647 40.000 12.00 0.00 33.60 2.87
820 842 6.348786 CCATCAGGCAACCATATATTTCTTCG 60.349 42.308 0.00 0.00 37.17 3.79
977 1017 0.599991 TGACAACGCACGAGCTGATT 60.600 50.000 2.73 0.00 39.10 2.57
1188 1243 0.681887 TTACTGATCTGGGTCGCCGA 60.682 55.000 4.49 0.00 0.00 5.54
1243 1298 1.068083 CCCATCGTGGTGATCTCCG 59.932 63.158 9.20 0.00 35.17 4.63
1303 1358 0.108329 CGCCCTGTCGAACCATAGTT 60.108 55.000 0.00 0.00 39.54 2.24
1659 1714 2.359967 CCTCGTGGACCTCTTCCCC 61.360 68.421 0.00 0.00 45.17 4.81
1786 1841 2.514824 GAGCTTCCCGTCATGGCC 60.515 66.667 0.00 0.00 35.87 5.36
1997 2154 5.514500 AAAATCCTTGCTAGGTTACTCCA 57.486 39.130 14.12 0.00 42.60 3.86
2046 2755 0.112412 TCAAGGTTTTCAGGAGGGCC 59.888 55.000 0.00 0.00 0.00 5.80
2065 2774 1.064685 CCCGGGGTGCTCTTTCTATTT 60.065 52.381 14.71 0.00 0.00 1.40
2066 2775 2.171870 CCCGGGGTGCTCTTTCTATTTA 59.828 50.000 14.71 0.00 0.00 1.40
2070 2779 5.643777 CCGGGGTGCTCTTTCTATTTATATG 59.356 44.000 0.00 0.00 0.00 1.78
2118 2848 1.217942 GGGATATGGGGCCAGAAAACT 59.782 52.381 4.39 0.00 0.00 2.66
2170 2901 4.928661 AGACAAATAGCGAACACACATC 57.071 40.909 0.00 0.00 0.00 3.06
2978 4033 7.326454 CAACACATATATAGATCCACCTCAGG 58.674 42.308 0.00 0.00 0.00 3.86
3013 4068 5.617609 CCCATATTTGTCGCATATTGTACG 58.382 41.667 0.00 0.00 0.00 3.67
3091 4146 3.803778 GCGATTATGGGCCAAAATGAAAG 59.196 43.478 11.89 0.00 0.00 2.62
3129 4184 3.683822 GCATGATATCAGGTTAGCAGCTC 59.316 47.826 17.94 0.00 0.00 4.09
3249 4305 4.473477 AGTAGTCTACCAATGCAACTCC 57.527 45.455 6.38 0.00 0.00 3.85
3259 4315 3.495753 CCAATGCAACTCCTTCTTTTTGC 59.504 43.478 0.00 0.00 43.80 3.68
3515 4571 5.502089 TGAATGGCCATGGAAATTTCTTT 57.498 34.783 21.63 0.00 0.00 2.52
3531 4587 7.941795 AATTTCTTTCTTCTGATGTTTGCAG 57.058 32.000 0.00 0.00 34.71 4.41
3631 4698 5.086058 CGACATACAACACAAACTATTGGC 58.914 41.667 0.00 0.00 41.01 4.52
3654 4721 1.078709 CACGATAGCCACCAACACAG 58.921 55.000 0.00 0.00 42.67 3.66
3672 4739 2.263077 CAGTACTCATCGGCTTGACAC 58.737 52.381 0.00 0.00 0.00 3.67
3699 4766 2.691409 ACCCGTGAATTCATCGTCAT 57.309 45.000 12.12 2.78 0.00 3.06
3727 4794 6.007076 TGTTGGCAATTCCATCTACTTACAA 58.993 36.000 1.92 0.00 46.04 2.41
3790 4857 8.296713 TGAATGCCTGAGTACAATTTTCTAAAC 58.703 33.333 0.00 0.00 0.00 2.01
3826 4893 4.514781 ACAGCACGTTGACTATTCACTA 57.485 40.909 0.00 0.00 0.00 2.74
3848 4915 1.407437 GCACCTCCTTACATGTGGGAG 60.407 57.143 28.27 28.27 44.36 4.30
3851 4918 0.179073 CTCCTTACATGTGGGAGCCG 60.179 60.000 25.92 12.19 39.87 5.52
3886 4953 7.755618 ACTTATCTATCCTCTCACTCTAGCTT 58.244 38.462 0.00 0.00 0.00 3.74
3921 4988 5.716228 TCCTTGACCTCATGCAAAATAACAT 59.284 36.000 0.00 0.00 0.00 2.71
3937 5004 9.353999 CAAAATAACATTAGTAGAAAACAGGGC 57.646 33.333 0.00 0.00 0.00 5.19
3947 5014 1.341209 GAAAACAGGGCTTTGGTCCAG 59.659 52.381 0.00 0.00 40.27 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.047877 CGGCCCGAAACCTGTGTC 61.048 66.667 0.00 0.00 0.00 3.67
165 187 1.070105 TTTCTGGGAACACCGGTCG 59.930 57.895 2.59 2.80 46.44 4.79
285 307 1.384191 GCTTGGGGAGGATGTTGGT 59.616 57.895 0.00 0.00 0.00 3.67
351 373 2.630592 GATCGGACGTTGGCTCCTCC 62.631 65.000 0.00 0.00 0.00 4.30
387 409 2.650116 GGGAAGCTCGTCTGGCTCA 61.650 63.158 0.00 0.00 39.30 4.26
481 503 4.766404 AAGATAAACAAACCAAGCGAGG 57.234 40.909 0.00 0.00 0.00 4.63
482 504 5.324697 GCTAAGATAAACAAACCAAGCGAG 58.675 41.667 0.00 0.00 0.00 5.03
483 505 4.155280 GGCTAAGATAAACAAACCAAGCGA 59.845 41.667 0.00 0.00 0.00 4.93
484 506 4.156008 AGGCTAAGATAAACAAACCAAGCG 59.844 41.667 0.00 0.00 0.00 4.68
485 507 5.641709 GAGGCTAAGATAAACAAACCAAGC 58.358 41.667 0.00 0.00 0.00 4.01
486 508 5.411669 ACGAGGCTAAGATAAACAAACCAAG 59.588 40.000 0.00 0.00 0.00 3.61
487 509 5.180492 CACGAGGCTAAGATAAACAAACCAA 59.820 40.000 0.00 0.00 0.00 3.67
488 510 4.693566 CACGAGGCTAAGATAAACAAACCA 59.306 41.667 0.00 0.00 0.00 3.67
489 511 4.094442 CCACGAGGCTAAGATAAACAAACC 59.906 45.833 0.00 0.00 0.00 3.27
490 512 4.094442 CCCACGAGGCTAAGATAAACAAAC 59.906 45.833 0.00 0.00 0.00 2.93
491 513 4.020039 TCCCACGAGGCTAAGATAAACAAA 60.020 41.667 0.00 0.00 34.51 2.83
492 514 3.516300 TCCCACGAGGCTAAGATAAACAA 59.484 43.478 0.00 0.00 34.51 2.83
493 515 3.101437 TCCCACGAGGCTAAGATAAACA 58.899 45.455 0.00 0.00 34.51 2.83
494 516 3.814005 TCCCACGAGGCTAAGATAAAC 57.186 47.619 0.00 0.00 34.51 2.01
495 517 3.323979 GGATCCCACGAGGCTAAGATAAA 59.676 47.826 0.00 0.00 34.51 1.40
496 518 2.897969 GGATCCCACGAGGCTAAGATAA 59.102 50.000 0.00 0.00 34.51 1.75
497 519 2.526432 GGATCCCACGAGGCTAAGATA 58.474 52.381 0.00 0.00 34.51 1.98
498 520 1.343069 GGATCCCACGAGGCTAAGAT 58.657 55.000 0.00 0.00 34.51 2.40
499 521 0.759436 GGGATCCCACGAGGCTAAGA 60.759 60.000 26.95 0.00 35.81 2.10
500 522 1.048724 TGGGATCCCACGAGGCTAAG 61.049 60.000 30.62 0.00 41.89 2.18
501 523 1.002403 TGGGATCCCACGAGGCTAA 59.998 57.895 30.62 3.04 41.89 3.09
502 524 2.693660 TGGGATCCCACGAGGCTA 59.306 61.111 30.62 3.90 41.89 3.93
517 539 1.079127 GTCATGACCTCCCGTGTGG 60.079 63.158 15.31 0.00 0.00 4.17
518 540 0.390340 CAGTCATGACCTCCCGTGTG 60.390 60.000 22.21 7.60 0.00 3.82
519 541 1.975327 CAGTCATGACCTCCCGTGT 59.025 57.895 22.21 0.00 0.00 4.49
520 542 1.448540 GCAGTCATGACCTCCCGTG 60.449 63.158 22.21 13.46 0.00 4.94
521 543 1.608717 GAGCAGTCATGACCTCCCGT 61.609 60.000 22.21 0.00 0.00 5.28
522 544 1.142748 GAGCAGTCATGACCTCCCG 59.857 63.158 22.21 7.27 0.00 5.14
523 545 0.177604 CTGAGCAGTCATGACCTCCC 59.822 60.000 22.21 10.11 30.18 4.30
524 546 1.189752 TCTGAGCAGTCATGACCTCC 58.810 55.000 22.21 10.65 30.18 4.30
525 547 3.325293 TTTCTGAGCAGTCATGACCTC 57.675 47.619 22.21 20.65 30.18 3.85
526 548 3.406764 GTTTTCTGAGCAGTCATGACCT 58.593 45.455 22.21 13.03 30.18 3.85
527 549 2.485814 GGTTTTCTGAGCAGTCATGACC 59.514 50.000 22.21 8.10 30.18 4.02
528 550 3.141398 TGGTTTTCTGAGCAGTCATGAC 58.859 45.455 18.47 18.47 30.18 3.06
529 551 3.405831 CTGGTTTTCTGAGCAGTCATGA 58.594 45.455 0.00 0.00 39.62 3.07
530 552 3.826236 CTGGTTTTCTGAGCAGTCATG 57.174 47.619 0.00 0.00 39.62 3.07
536 558 2.092429 AGGTTCACTGGTTTTCTGAGCA 60.092 45.455 0.00 0.00 0.00 4.26
537 559 2.576615 AGGTTCACTGGTTTTCTGAGC 58.423 47.619 0.00 0.00 0.00 4.26
538 560 5.997746 TCATTAGGTTCACTGGTTTTCTGAG 59.002 40.000 0.00 0.00 0.00 3.35
539 561 5.935945 TCATTAGGTTCACTGGTTTTCTGA 58.064 37.500 0.00 0.00 0.00 3.27
540 562 5.765182 ACTCATTAGGTTCACTGGTTTTCTG 59.235 40.000 0.00 0.00 0.00 3.02
541 563 5.765182 CACTCATTAGGTTCACTGGTTTTCT 59.235 40.000 0.00 0.00 0.00 2.52
542 564 5.562890 GCACTCATTAGGTTCACTGGTTTTC 60.563 44.000 0.00 0.00 0.00 2.29
543 565 4.278419 GCACTCATTAGGTTCACTGGTTTT 59.722 41.667 0.00 0.00 0.00 2.43
544 566 3.821033 GCACTCATTAGGTTCACTGGTTT 59.179 43.478 0.00 0.00 0.00 3.27
545 567 3.181445 TGCACTCATTAGGTTCACTGGTT 60.181 43.478 0.00 0.00 0.00 3.67
546 568 2.371841 TGCACTCATTAGGTTCACTGGT 59.628 45.455 0.00 0.00 0.00 4.00
547 569 3.057969 TGCACTCATTAGGTTCACTGG 57.942 47.619 0.00 0.00 0.00 4.00
548 570 5.065218 GGTTATGCACTCATTAGGTTCACTG 59.935 44.000 0.00 0.00 34.22 3.66
549 571 5.045578 AGGTTATGCACTCATTAGGTTCACT 60.046 40.000 0.00 0.00 34.22 3.41
550 572 5.186198 AGGTTATGCACTCATTAGGTTCAC 58.814 41.667 0.00 0.00 34.22 3.18
551 573 5.435686 AGGTTATGCACTCATTAGGTTCA 57.564 39.130 0.00 0.00 34.22 3.18
552 574 5.880332 TCAAGGTTATGCACTCATTAGGTTC 59.120 40.000 0.00 0.00 34.22 3.62
553 575 5.815581 TCAAGGTTATGCACTCATTAGGTT 58.184 37.500 0.00 0.00 34.22 3.50
554 576 5.431765 CTCAAGGTTATGCACTCATTAGGT 58.568 41.667 0.00 0.00 34.22 3.08
555 577 4.274459 GCTCAAGGTTATGCACTCATTAGG 59.726 45.833 0.00 0.00 34.22 2.69
556 578 4.877823 TGCTCAAGGTTATGCACTCATTAG 59.122 41.667 0.00 0.00 34.22 1.73
557 579 4.842574 TGCTCAAGGTTATGCACTCATTA 58.157 39.130 0.00 0.00 34.22 1.90
558 580 3.689347 TGCTCAAGGTTATGCACTCATT 58.311 40.909 0.00 0.00 34.22 2.57
559 581 3.354948 TGCTCAAGGTTATGCACTCAT 57.645 42.857 0.00 0.00 36.73 2.90
560 582 2.857186 TGCTCAAGGTTATGCACTCA 57.143 45.000 0.00 0.00 0.00 3.41
561 583 3.012518 ACATGCTCAAGGTTATGCACTC 58.987 45.455 0.00 0.00 38.29 3.51
562 584 3.077484 ACATGCTCAAGGTTATGCACT 57.923 42.857 0.00 0.00 38.29 4.40
563 585 3.855689 AACATGCTCAAGGTTATGCAC 57.144 42.857 0.00 0.00 38.29 4.57
564 586 5.252547 TCTAAACATGCTCAAGGTTATGCA 58.747 37.500 0.00 0.00 39.83 3.96
565 587 5.586243 TCTCTAAACATGCTCAAGGTTATGC 59.414 40.000 0.00 0.00 0.00 3.14
566 588 7.615582 TTCTCTAAACATGCTCAAGGTTATG 57.384 36.000 0.00 0.00 0.00 1.90
567 589 8.680903 CATTTCTCTAAACATGCTCAAGGTTAT 58.319 33.333 0.00 0.00 0.00 1.89
568 590 7.121168 CCATTTCTCTAAACATGCTCAAGGTTA 59.879 37.037 0.00 0.00 0.00 2.85
569 591 6.071728 CCATTTCTCTAAACATGCTCAAGGTT 60.072 38.462 0.00 0.00 0.00 3.50
570 592 5.416952 CCATTTCTCTAAACATGCTCAAGGT 59.583 40.000 0.00 0.00 0.00 3.50
571 593 5.163581 CCCATTTCTCTAAACATGCTCAAGG 60.164 44.000 0.00 0.00 0.00 3.61
572 594 5.649395 TCCCATTTCTCTAAACATGCTCAAG 59.351 40.000 0.00 0.00 0.00 3.02
573 595 5.569355 TCCCATTTCTCTAAACATGCTCAA 58.431 37.500 0.00 0.00 0.00 3.02
574 596 5.178096 TCCCATTTCTCTAAACATGCTCA 57.822 39.130 0.00 0.00 0.00 4.26
575 597 6.995091 AGTATCCCATTTCTCTAAACATGCTC 59.005 38.462 0.00 0.00 0.00 4.26
576 598 6.769822 CAGTATCCCATTTCTCTAAACATGCT 59.230 38.462 0.00 0.00 0.00 3.79
577 599 6.767902 TCAGTATCCCATTTCTCTAAACATGC 59.232 38.462 0.00 0.00 0.00 4.06
578 600 7.041508 GCTCAGTATCCCATTTCTCTAAACATG 60.042 40.741 0.00 0.00 0.00 3.21
579 601 6.995091 GCTCAGTATCCCATTTCTCTAAACAT 59.005 38.462 0.00 0.00 0.00 2.71
580 602 6.070251 TGCTCAGTATCCCATTTCTCTAAACA 60.070 38.462 0.00 0.00 0.00 2.83
581 603 6.349300 TGCTCAGTATCCCATTTCTCTAAAC 58.651 40.000 0.00 0.00 0.00 2.01
582 604 6.560003 TGCTCAGTATCCCATTTCTCTAAA 57.440 37.500 0.00 0.00 0.00 1.85
583 605 6.560003 TTGCTCAGTATCCCATTTCTCTAA 57.440 37.500 0.00 0.00 0.00 2.10
584 606 6.464892 CCATTGCTCAGTATCCCATTTCTCTA 60.465 42.308 0.00 0.00 0.00 2.43
585 607 5.374921 CATTGCTCAGTATCCCATTTCTCT 58.625 41.667 0.00 0.00 0.00 3.10
586 608 4.518211 CCATTGCTCAGTATCCCATTTCTC 59.482 45.833 0.00 0.00 0.00 2.87
587 609 4.467769 CCATTGCTCAGTATCCCATTTCT 58.532 43.478 0.00 0.00 0.00 2.52
588 610 3.005155 GCCATTGCTCAGTATCCCATTTC 59.995 47.826 0.00 0.00 33.53 2.17
589 611 2.961062 GCCATTGCTCAGTATCCCATTT 59.039 45.455 0.00 0.00 33.53 2.32
590 612 2.091720 TGCCATTGCTCAGTATCCCATT 60.092 45.455 0.00 0.00 38.71 3.16
591 613 1.496001 TGCCATTGCTCAGTATCCCAT 59.504 47.619 0.00 0.00 38.71 4.00
592 614 0.918258 TGCCATTGCTCAGTATCCCA 59.082 50.000 0.00 0.00 38.71 4.37
593 615 2.057137 TTGCCATTGCTCAGTATCCC 57.943 50.000 0.00 0.00 38.71 3.85
594 616 3.004106 GTCATTGCCATTGCTCAGTATCC 59.996 47.826 0.00 0.00 38.71 2.59
595 617 3.628942 TGTCATTGCCATTGCTCAGTATC 59.371 43.478 0.00 0.00 38.71 2.24
596 618 3.623703 TGTCATTGCCATTGCTCAGTAT 58.376 40.909 0.00 0.00 38.71 2.12
597 619 3.070476 TGTCATTGCCATTGCTCAGTA 57.930 42.857 0.00 0.00 38.71 2.74
598 620 1.913778 TGTCATTGCCATTGCTCAGT 58.086 45.000 0.00 0.00 38.71 3.41
599 621 3.119280 TCATTGTCATTGCCATTGCTCAG 60.119 43.478 0.00 0.00 38.71 3.35
600 622 2.826725 TCATTGTCATTGCCATTGCTCA 59.173 40.909 0.00 0.00 38.71 4.26
601 623 3.184541 GTCATTGTCATTGCCATTGCTC 58.815 45.455 0.00 0.00 38.71 4.26
602 624 2.563620 TGTCATTGTCATTGCCATTGCT 59.436 40.909 0.00 0.00 38.71 3.91
603 625 2.962125 TGTCATTGTCATTGCCATTGC 58.038 42.857 0.00 0.00 38.26 3.56
604 626 4.565166 GTCATGTCATTGTCATTGCCATTG 59.435 41.667 0.00 0.00 0.00 2.82
605 627 4.382254 GGTCATGTCATTGTCATTGCCATT 60.382 41.667 0.00 0.00 0.00 3.16
606 628 3.131577 GGTCATGTCATTGTCATTGCCAT 59.868 43.478 0.00 0.00 0.00 4.40
607 629 2.492881 GGTCATGTCATTGTCATTGCCA 59.507 45.455 0.00 0.00 0.00 4.92
608 630 2.492881 TGGTCATGTCATTGTCATTGCC 59.507 45.455 0.00 1.36 0.00 4.52
609 631 3.853831 TGGTCATGTCATTGTCATTGC 57.146 42.857 0.00 0.00 0.00 3.56
610 632 5.632244 TCTTGGTCATGTCATTGTCATTG 57.368 39.130 0.00 0.00 0.00 2.82
611 633 6.653526 TTTCTTGGTCATGTCATTGTCATT 57.346 33.333 0.00 0.00 0.00 2.57
612 634 6.040729 TGTTTTCTTGGTCATGTCATTGTCAT 59.959 34.615 0.00 0.00 0.00 3.06
613 635 5.359292 TGTTTTCTTGGTCATGTCATTGTCA 59.641 36.000 0.00 0.00 0.00 3.58
614 636 5.830912 TGTTTTCTTGGTCATGTCATTGTC 58.169 37.500 0.00 0.00 0.00 3.18
615 637 5.850557 TGTTTTCTTGGTCATGTCATTGT 57.149 34.783 0.00 0.00 0.00 2.71
616 638 7.596494 ACTATGTTTTCTTGGTCATGTCATTG 58.404 34.615 0.00 0.00 0.00 2.82
617 639 7.765695 ACTATGTTTTCTTGGTCATGTCATT 57.234 32.000 0.00 0.00 0.00 2.57
618 640 7.554118 CCTACTATGTTTTCTTGGTCATGTCAT 59.446 37.037 0.00 0.00 0.00 3.06
619 641 6.878923 CCTACTATGTTTTCTTGGTCATGTCA 59.121 38.462 0.00 0.00 0.00 3.58
620 642 6.879458 ACCTACTATGTTTTCTTGGTCATGTC 59.121 38.462 0.00 0.00 0.00 3.06
621 643 6.779860 ACCTACTATGTTTTCTTGGTCATGT 58.220 36.000 0.00 0.00 0.00 3.21
622 644 7.687941 AACCTACTATGTTTTCTTGGTCATG 57.312 36.000 0.00 0.00 0.00 3.07
623 645 8.706322 AAAACCTACTATGTTTTCTTGGTCAT 57.294 30.769 0.00 0.00 40.85 3.06
624 646 8.528044 AAAAACCTACTATGTTTTCTTGGTCA 57.472 30.769 2.03 0.00 43.19 4.02
650 672 9.924650 GAGATACTAGAAGAACCACACTTAAAA 57.075 33.333 0.00 0.00 0.00 1.52
651 673 9.310449 AGAGATACTAGAAGAACCACACTTAAA 57.690 33.333 0.00 0.00 0.00 1.52
652 674 8.880991 AGAGATACTAGAAGAACCACACTTAA 57.119 34.615 0.00 0.00 0.00 1.85
653 675 8.880991 AAGAGATACTAGAAGAACCACACTTA 57.119 34.615 0.00 0.00 0.00 2.24
654 676 7.784470 AAGAGATACTAGAAGAACCACACTT 57.216 36.000 0.00 0.00 0.00 3.16
655 677 7.784470 AAAGAGATACTAGAAGAACCACACT 57.216 36.000 0.00 0.00 0.00 3.55
691 713 8.410912 GGAAACTGTTAAATTGGAGTACAAAGT 58.589 33.333 0.00 0.00 43.46 2.66
692 714 8.630037 AGGAAACTGTTAAATTGGAGTACAAAG 58.370 33.333 0.00 0.00 40.70 2.77
693 715 8.528044 AGGAAACTGTTAAATTGGAGTACAAA 57.472 30.769 0.00 0.00 40.70 2.83
711 733 4.130118 GACAGACACATTCACAGGAAACT 58.870 43.478 0.00 0.00 46.44 2.66
712 734 3.059597 CGACAGACACATTCACAGGAAAC 60.060 47.826 0.00 0.00 36.43 2.78
713 735 3.130633 CGACAGACACATTCACAGGAAA 58.869 45.455 0.00 0.00 36.43 3.13
714 736 2.754472 CGACAGACACATTCACAGGAA 58.246 47.619 0.00 0.00 37.45 3.36
715 737 1.605457 GCGACAGACACATTCACAGGA 60.605 52.381 0.00 0.00 0.00 3.86
716 738 0.792640 GCGACAGACACATTCACAGG 59.207 55.000 0.00 0.00 0.00 4.00
717 739 1.788258 AGCGACAGACACATTCACAG 58.212 50.000 0.00 0.00 0.00 3.66
718 740 3.193479 AGATAGCGACAGACACATTCACA 59.807 43.478 0.00 0.00 0.00 3.58
786 808 2.450476 GTTGCCTGATGGACCATCTTT 58.550 47.619 30.11 0.00 41.06 2.52
820 842 1.398451 CGTTTTCAGCACGTGTGGATC 60.398 52.381 18.38 0.00 32.80 3.36
977 1017 0.677731 AGGCAGCTTATTTGCGAGCA 60.678 50.000 0.00 0.00 42.42 4.26
1107 1159 1.817209 GATGACCGGGAGAGTCCAC 59.183 63.158 6.32 0.00 38.64 4.02
1188 1243 1.077212 GAGCATCACTGGCCCATGT 60.077 57.895 0.00 0.00 33.17 3.21
1659 1714 2.031012 TGCACCAGCCAAGACGAG 59.969 61.111 0.00 0.00 41.13 4.18
1786 1841 0.738975 TCTTCATCGTCGCTGTAGGG 59.261 55.000 3.38 0.00 0.00 3.53
2046 2755 2.420058 AAATAGAAAGAGCACCCCGG 57.580 50.000 0.00 0.00 0.00 5.73
2066 2775 9.444600 ACGTGGTTAATTTCTTGTACTTCATAT 57.555 29.630 0.00 0.00 0.00 1.78
2096 2811 1.313889 TTTCTGGCCCCATATCCCAA 58.686 50.000 0.00 0.00 0.00 4.12
2118 2848 5.074804 TGAGCAGTGTACCTACTAAGAACA 58.925 41.667 0.00 0.00 0.00 3.18
2170 2901 1.572085 CTCTCACGCCTGTTGCCAAG 61.572 60.000 0.00 0.00 36.24 3.61
2570 3624 6.529220 ACCCATAATATTGCAGTTCTCTCTC 58.471 40.000 0.00 0.00 0.00 3.20
3046 4101 6.700960 CGCATCCTATTTTTGCAAATTATCCA 59.299 34.615 13.65 0.00 36.15 3.41
3091 4146 7.756272 TGATATCATGCATTCACAACTTTGAAC 59.244 33.333 0.00 0.00 38.31 3.18
3498 4554 5.047092 TCAGAAGAAAGAAATTTCCATGGCC 60.047 40.000 14.61 0.00 0.00 5.36
3504 4560 7.439056 TGCAAACATCAGAAGAAAGAAATTTCC 59.561 33.333 14.61 0.00 0.00 3.13
3631 4698 1.078497 TTGGTGGCTATCGTGCTGG 60.078 57.895 0.00 0.00 0.00 4.85
3654 4721 1.204941 AGGTGTCAAGCCGATGAGTAC 59.795 52.381 0.00 0.00 0.00 2.73
3672 4739 2.778299 TGAATTCACGGGTTTCTGAGG 58.222 47.619 3.38 0.00 0.00 3.86
3727 4794 2.216046 GTGATGACGGACATGATGCAT 58.784 47.619 0.00 0.00 39.56 3.96
3790 4857 3.974401 CGTGCTGTTGTAATGGACTTTTG 59.026 43.478 0.00 0.00 0.00 2.44
3886 4953 6.351711 CATGAGGTCAAGGATGAGTTAATGA 58.648 40.000 0.00 0.00 35.88 2.57
3921 4988 5.056553 ACCAAAGCCCTGTTTTCTACTAA 57.943 39.130 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.