Multiple sequence alignment - TraesCS5A01G534300

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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 TraesCS5A01G534300 chr5A 100.000 3591 0 0 1 3591 691672079 691668489 0.000000e+00 6632.0
1 TraesCS5A01G534300 chr5A 96.825 63 1 1 3312 3373 691668708 691668646 1.760000e-18 104.0
2 TraesCS5A01G534300 chr5A 96.825 63 1 1 3372 3434 691668768 691668707 1.760000e-18 104.0
3 TraesCS5A01G534300 chr5A 91.525 59 4 1 3368 3425 118664118 118664060 2.970000e-11 80.5
4 TraesCS5A01G534300 chrUn 93.242 2264 68 29 676 2914 126673653 126675856 0.000000e+00 3254.0
5 TraesCS5A01G534300 chrUn 85.336 491 34 18 2831 3302 126675854 126676325 1.170000e-129 473.0
6 TraesCS5A01G534300 chrUn 75.000 440 89 15 88 512 41530607 41530174 2.200000e-42 183.0
7 TraesCS5A01G534300 chrUn 82.234 197 13 5 3390 3586 126676447 126676621 2.230000e-32 150.0
8 TraesCS5A01G534300 chr4B 90.320 2314 108 58 654 2914 654038082 654035832 0.000000e+00 2926.0
9 TraesCS5A01G534300 chr4B 88.889 657 71 2 1909 2564 12230442 12231097 0.000000e+00 808.0
10 TraesCS5A01G534300 chr4B 90.175 285 27 1 1527 1811 12230096 12230379 1.570000e-98 370.0
11 TraesCS5A01G534300 chr4B 80.182 550 47 19 2831 3343 654035834 654035310 4.410000e-94 355.0
12 TraesCS5A01G534300 chr1A 90.356 674 59 2 1921 2591 500563579 500562909 0.000000e+00 880.0
13 TraesCS5A01G534300 chr1A 90.952 420 36 2 994 1411 452018569 452018988 6.730000e-157 564.0
14 TraesCS5A01G534300 chr1A 91.398 279 24 0 1529 1807 452019061 452019339 2.020000e-102 383.0
15 TraesCS5A01G534300 chr1A 85.333 75 7 4 3311 3382 571880982 571880909 1.380000e-09 75.0
16 TraesCS5A01G534300 chr1A 85.714 63 8 1 3361 3422 75096447 75096509 8.320000e-07 65.8
17 TraesCS5A01G534300 chr1D 90.208 674 60 2 1921 2591 405111093 405110423 0.000000e+00 874.0
18 TraesCS5A01G534300 chr1D 91.190 420 35 2 994 1411 351245574 351245993 1.450000e-158 569.0
19 TraesCS5A01G534300 chr1D 91.398 279 24 0 1529 1807 351246066 351246344 2.020000e-102 383.0
20 TraesCS5A01G534300 chr1D 91.667 60 2 3 3369 3425 105352525 105352466 2.970000e-11 80.5
21 TraesCS5A01G534300 chr4D 89.634 656 68 0 1909 2564 6898879 6899534 0.000000e+00 835.0
22 TraesCS5A01G534300 chr4D 90.370 270 25 1 1527 1795 6898535 6898804 1.590000e-93 353.0
23 TraesCS5A01G534300 chr1B 89.021 674 68 2 1921 2591 544997379 544996709 0.000000e+00 830.0
24 TraesCS5A01G534300 chr1B 87.764 662 75 4 1908 2566 473824101 473824759 0.000000e+00 769.0
25 TraesCS5A01G534300 chr1B 91.429 420 34 2 994 1411 473822300 473822719 3.110000e-160 575.0
26 TraesCS5A01G534300 chr1B 91.398 279 24 0 1529 1807 473822792 473823070 2.020000e-102 383.0
27 TraesCS5A01G534300 chr1B 90.164 61 3 3 3311 3370 678771326 678771384 3.840000e-10 76.8
28 TraesCS5A01G534300 chr4A 88.872 656 73 0 1909 2564 596625280 596624625 0.000000e+00 808.0
29 TraesCS5A01G534300 chr4A 90.370 270 25 1 1527 1795 596625635 596625366 1.590000e-93 353.0
30 TraesCS5A01G534300 chr4A 87.879 66 6 2 3309 3372 532693711 532693646 3.840000e-10 76.8
31 TraesCS5A01G534300 chr6A 92.893 394 28 0 1003 1396 115944849 115945242 1.120000e-159 573.0
32 TraesCS5A01G534300 chr6A 94.444 54 2 1 3366 3418 288406487 288406540 8.260000e-12 82.4
33 TraesCS5A01G534300 chr6D 92.677 396 29 0 1001 1396 97012775 97013170 4.020000e-159 571.0
34 TraesCS5A01G534300 chr6D 94.340 53 2 1 3366 3417 192109405 192109457 2.970000e-11 80.5
35 TraesCS5A01G534300 chr6B 92.424 396 30 0 1001 1396 180922095 180922490 1.870000e-157 566.0
36 TraesCS5A01G534300 chr6B 77.528 445 83 12 84 513 483376987 483376545 5.950000e-63 252.0
37 TraesCS5A01G534300 chr6B 90.000 60 5 1 3367 3425 715708461 715708402 3.840000e-10 76.8
38 TraesCS5A01G534300 chr5B 90.887 406 37 0 991 1396 594873406 594873811 2.440000e-151 545.0
39 TraesCS5A01G534300 chr5B 90.769 65 3 3 3304 3365 123753563 123753499 2.300000e-12 84.2
40 TraesCS5A01G534300 chr5B 94.340 53 1 1 3361 3413 549974047 549974097 2.970000e-11 80.5
41 TraesCS5A01G534300 chr7A 80.140 428 77 6 30 453 489174750 489174327 2.690000e-81 313.0
42 TraesCS5A01G534300 chr2A 77.973 513 100 11 10 514 525034467 525033960 3.480000e-80 309.0
43 TraesCS5A01G534300 chr2A 79.623 265 51 3 226 489 755993746 755994008 1.700000e-43 187.0
44 TraesCS5A01G534300 chr2A 90.000 60 5 1 3364 3422 417745639 417745698 3.840000e-10 76.8
45 TraesCS5A01G534300 chr2D 76.938 529 109 10 10 530 388518994 388518471 4.540000e-74 289.0
46 TraesCS5A01G534300 chr7B 93.443 61 2 2 3304 3362 123782858 123782918 4.940000e-14 89.8
47 TraesCS5A01G534300 chr7B 96.154 52 1 1 3372 3422 123782867 123782918 2.300000e-12 84.2
48 TraesCS5A01G534300 chr2B 91.045 67 4 2 3364 3429 210261411 210261476 4.940000e-14 89.8
49 TraesCS5A01G534300 chr2B 96.226 53 1 1 3311 3362 273740374 273740426 6.390000e-13 86.1
50 TraesCS5A01G534300 chr2B 96.154 52 1 1 3372 3422 273740375 273740426 2.300000e-12 84.2
51 TraesCS5A01G534300 chr2B 90.476 63 4 2 3311 3371 210261418 210261480 8.260000e-12 82.4
52 TraesCS5A01G534300 chr2B 86.667 60 4 4 3367 3422 604992908 604992967 2.990000e-06 63.9
53 TraesCS5A01G534300 chr3A 94.643 56 2 1 3311 3365 599863802 599863747 6.390000e-13 86.1
54 TraesCS5A01G534300 chr3A 94.545 55 2 1 3372 3425 599863801 599863747 2.300000e-12 84.2
55 TraesCS5A01G534300 chr3B 92.982 57 3 1 3367 3422 637088489 637088545 8.260000e-12 82.4
56 TraesCS5A01G534300 chr3B 88.235 68 6 2 3308 3373 45828458 45828391 2.970000e-11 80.5
57 TraesCS5A01G534300 chr3B 88.235 68 6 2 3308 3373 45923684 45923617 2.970000e-11 80.5
58 TraesCS5A01G534300 chr3B 88.235 68 6 2 3308 3373 45973977 45973910 2.970000e-11 80.5
59 TraesCS5A01G534300 chr3B 86.765 68 7 2 3308 3373 45758445 45758378 1.380000e-09 75.0


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 TraesCS5A01G534300 chr5A 691668489 691672079 3590 True 2280.000000 6632 97.883333 1 3591 3 chr5A.!!$R2 3590
1 TraesCS5A01G534300 chrUn 126673653 126676621 2968 False 1292.333333 3254 86.937333 676 3586 3 chrUn.!!$F1 2910
2 TraesCS5A01G534300 chr4B 654035310 654038082 2772 True 1640.500000 2926 85.251000 654 3343 2 chr4B.!!$R1 2689
3 TraesCS5A01G534300 chr4B 12230096 12231097 1001 False 589.000000 808 89.532000 1527 2564 2 chr4B.!!$F1 1037
4 TraesCS5A01G534300 chr1A 500562909 500563579 670 True 880.000000 880 90.356000 1921 2591 1 chr1A.!!$R1 670
5 TraesCS5A01G534300 chr1A 452018569 452019339 770 False 473.500000 564 91.175000 994 1807 2 chr1A.!!$F2 813
6 TraesCS5A01G534300 chr1D 405110423 405111093 670 True 874.000000 874 90.208000 1921 2591 1 chr1D.!!$R2 670
7 TraesCS5A01G534300 chr1D 351245574 351246344 770 False 476.000000 569 91.294000 994 1807 2 chr1D.!!$F1 813
8 TraesCS5A01G534300 chr4D 6898535 6899534 999 False 594.000000 835 90.002000 1527 2564 2 chr4D.!!$F1 1037
9 TraesCS5A01G534300 chr1B 544996709 544997379 670 True 830.000000 830 89.021000 1921 2591 1 chr1B.!!$R1 670
10 TraesCS5A01G534300 chr1B 473822300 473824759 2459 False 575.666667 769 90.197000 994 2566 3 chr1B.!!$F2 1572
11 TraesCS5A01G534300 chr4A 596624625 596625635 1010 True 580.500000 808 89.621000 1527 2564 2 chr4A.!!$R2 1037
12 TraesCS5A01G534300 chr2A 525033960 525034467 507 True 309.000000 309 77.973000 10 514 1 chr2A.!!$R1 504
13 TraesCS5A01G534300 chr2D 388518471 388518994 523 True 289.000000 289 76.938000 10 530 1 chr2D.!!$R1 520

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
19 20 0.031857 CAACTGCGGGATGTGCAAAA 59.968 50.000 0.0 0.0 42.70 2.44 F
555 560 0.099259 ATGCGATCACAACAATGGCG 59.901 50.000 0.0 0.0 31.27 5.69 F
642 647 0.381089 CGTAGGAGTACGCAAGAGGG 59.619 60.000 0.0 0.0 45.22 4.30 F
848 864 0.390735 ACTAACGATCCACCAACGCC 60.391 55.000 0.0 0.0 0.00 5.68 F
1446 1519 1.000060 CCCGTTCCTCTGTTACGTTCA 60.000 52.381 0.0 0.0 33.68 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 1473 1.071857 ACAGAGGAACGGGGAAGAAAC 59.928 52.381 0.00 0.00 0.0 2.78 R
1478 1557 1.338136 TTCCCTTCCGCTCCAGATCC 61.338 60.000 0.00 0.00 0.0 3.36 R
1703 1789 1.444553 GTTCTCGACGAGCTGGTGG 60.445 63.158 20.11 5.11 0.0 4.61 R
1808 1894 2.225017 GGAGGAATTGGGTCTGTTTGGA 60.225 50.000 0.00 0.00 0.0 3.53 R
2980 4114 0.179240 GCAGATCGACAGCAACAACG 60.179 55.000 0.00 0.00 0.0 4.10 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
19 20 0.031857 CAACTGCGGGATGTGCAAAA 59.968 50.000 0.00 0.00 42.70 2.44
28 29 1.483415 GGATGTGCAAAATCATGGGCT 59.517 47.619 11.61 0.00 29.78 5.19
29 30 2.093341 GGATGTGCAAAATCATGGGCTT 60.093 45.455 11.61 0.00 29.78 4.35
33 34 0.532115 GCAAAATCATGGGCTTCGGT 59.468 50.000 0.00 0.00 0.00 4.69
78 79 4.147449 CTCCAGCGGATCGTGGCA 62.147 66.667 5.08 0.00 33.43 4.92
162 164 5.050126 AGATTGTCATCTCATCCAGCAAT 57.950 39.130 0.00 0.00 34.26 3.56
164 166 3.639672 TGTCATCTCATCCAGCAATGT 57.360 42.857 0.00 0.00 0.00 2.71
200 205 2.432628 GCAACAGTCCGCGCTAGT 60.433 61.111 5.56 0.00 0.00 2.57
219 224 2.585247 GCGACGGGCCTGATGTAC 60.585 66.667 21.41 3.13 34.80 2.90
221 226 2.585247 GACGGGCCTGATGTACGC 60.585 66.667 21.41 0.00 0.00 4.42
224 229 2.203070 GGGCCTGATGTACGCTGG 60.203 66.667 0.84 6.99 0.00 4.85
231 236 1.227263 GATGTACGCTGGCACCGAT 60.227 57.895 9.51 0.00 0.00 4.18
256 261 3.685756 GGAGTACGAGGAATAGATCGAGG 59.314 52.174 1.13 0.00 41.40 4.63
291 296 3.050275 GTGCTCCACCTGAACGGC 61.050 66.667 0.00 0.00 35.61 5.68
294 299 3.322466 CTCCACCTGAACGGCCCT 61.322 66.667 0.00 0.00 35.61 5.19
333 338 4.020617 CTCCCCGTGCAGCAGGAA 62.021 66.667 16.85 1.11 0.00 3.36
341 346 3.064324 GCAGCAGGAACCGGCATT 61.064 61.111 17.00 0.00 39.53 3.56
343 348 2.436646 AGCAGGAACCGGCATTCG 60.437 61.111 17.00 0.00 39.53 3.34
347 352 2.125106 GGAACCGGCATTCGCTCT 60.125 61.111 0.00 0.00 38.60 4.09
381 386 3.428282 GACCGCGGCGTCCAAATT 61.428 61.111 28.58 0.57 0.00 1.82
386 391 1.443702 GCGGCGTCCAAATTGAACC 60.444 57.895 9.37 0.00 0.00 3.62
405 410 3.843240 CGCGTGAAGGAAGAGCGC 61.843 66.667 0.00 0.00 44.19 5.92
432 437 3.767230 CTGCGCCGACGTGTCAAG 61.767 66.667 4.18 0.00 42.83 3.02
435 440 2.805353 CGCCGACGTGTCAAGGAG 60.805 66.667 0.00 0.00 33.53 3.69
436 441 2.432628 GCCGACGTGTCAAGGAGG 60.433 66.667 0.00 0.00 0.00 4.30
437 442 2.927580 GCCGACGTGTCAAGGAGGA 61.928 63.158 0.00 0.00 0.00 3.71
438 443 1.213013 CCGACGTGTCAAGGAGGAG 59.787 63.158 0.00 0.00 0.00 3.69
439 444 1.444553 CGACGTGTCAAGGAGGAGC 60.445 63.158 0.00 0.00 0.00 4.70
440 445 1.444553 GACGTGTCAAGGAGGAGCG 60.445 63.158 0.00 0.00 0.00 5.03
441 446 2.811317 CGTGTCAAGGAGGAGCGC 60.811 66.667 0.00 0.00 0.00 5.92
442 447 2.435059 GTGTCAAGGAGGAGCGCC 60.435 66.667 2.29 0.00 0.00 6.53
467 472 4.612412 GCCACCCCGACACGTCAA 62.612 66.667 0.00 0.00 0.00 3.18
468 473 2.357034 CCACCCCGACACGTCAAG 60.357 66.667 0.00 0.00 0.00 3.02
469 474 2.357034 CACCCCGACACGTCAAGG 60.357 66.667 0.00 0.00 0.00 3.61
470 475 2.522436 ACCCCGACACGTCAAGGA 60.522 61.111 8.96 0.00 0.00 3.36
471 476 2.135581 ACCCCGACACGTCAAGGAA 61.136 57.895 8.96 0.00 0.00 3.36
472 477 1.374252 CCCCGACACGTCAAGGAAG 60.374 63.158 5.10 0.00 0.00 3.46
473 478 1.663739 CCCGACACGTCAAGGAAGA 59.336 57.895 1.64 0.00 0.00 2.87
474 479 0.388649 CCCGACACGTCAAGGAAGAG 60.389 60.000 1.64 0.00 0.00 2.85
475 480 1.009389 CCGACACGTCAAGGAAGAGC 61.009 60.000 0.00 0.00 0.00 4.09
476 481 1.337817 CGACACGTCAAGGAAGAGCG 61.338 60.000 0.00 0.00 0.00 5.03
477 482 1.006102 ACACGTCAAGGAAGAGCGG 60.006 57.895 0.00 0.00 0.00 5.52
478 483 1.006102 CACGTCAAGGAAGAGCGGT 60.006 57.895 0.00 0.00 0.00 5.68
479 484 0.600255 CACGTCAAGGAAGAGCGGTT 60.600 55.000 0.00 0.00 0.00 4.44
480 485 0.600255 ACGTCAAGGAAGAGCGGTTG 60.600 55.000 0.00 0.00 0.00 3.77
481 486 1.869690 GTCAAGGAAGAGCGGTTGC 59.130 57.895 0.00 0.00 43.24 4.17
482 487 1.302511 TCAAGGAAGAGCGGTTGCC 60.303 57.895 0.00 0.00 44.31 4.52
483 488 1.302832 CAAGGAAGAGCGGTTGCCT 60.303 57.895 0.00 0.00 44.31 4.75
484 489 1.003233 AAGGAAGAGCGGTTGCCTC 60.003 57.895 4.66 0.00 44.31 4.70
485 490 2.436824 GGAAGAGCGGTTGCCTCC 60.437 66.667 0.00 0.00 44.31 4.30
515 520 2.895865 CGTCGAGGAGGAGCGCTA 60.896 66.667 11.50 0.00 0.00 4.26
516 521 2.716864 GTCGAGGAGGAGCGCTAC 59.283 66.667 13.18 13.18 0.00 3.58
517 522 2.113433 GTCGAGGAGGAGCGCTACA 61.113 63.158 24.39 0.00 0.00 2.74
518 523 2.113433 TCGAGGAGGAGCGCTACAC 61.113 63.158 24.39 16.62 0.00 2.90
536 541 4.235762 GCCGCCGCTCCTATCCAA 62.236 66.667 0.00 0.00 0.00 3.53
537 542 2.743718 CCGCCGCTCCTATCCAAT 59.256 61.111 0.00 0.00 0.00 3.16
538 543 1.669115 CCGCCGCTCCTATCCAATG 60.669 63.158 0.00 0.00 0.00 2.82
539 544 2.320587 CGCCGCTCCTATCCAATGC 61.321 63.158 0.00 0.00 0.00 3.56
540 545 2.320587 GCCGCTCCTATCCAATGCG 61.321 63.158 0.00 0.00 45.22 4.73
544 549 2.462456 GCTCCTATCCAATGCGATCA 57.538 50.000 0.00 0.00 0.00 2.92
545 550 2.072298 GCTCCTATCCAATGCGATCAC 58.928 52.381 0.00 0.00 0.00 3.06
546 551 2.548707 GCTCCTATCCAATGCGATCACA 60.549 50.000 0.00 0.00 0.00 3.58
547 552 3.732212 CTCCTATCCAATGCGATCACAA 58.268 45.455 0.00 0.00 0.00 3.33
548 553 3.466836 TCCTATCCAATGCGATCACAAC 58.533 45.455 0.00 0.00 0.00 3.32
549 554 3.118445 TCCTATCCAATGCGATCACAACA 60.118 43.478 0.00 0.00 0.00 3.33
550 555 3.627123 CCTATCCAATGCGATCACAACAA 59.373 43.478 0.00 0.00 0.00 2.83
551 556 4.276678 CCTATCCAATGCGATCACAACAAT 59.723 41.667 0.00 0.00 0.00 2.71
552 557 3.490800 TCCAATGCGATCACAACAATG 57.509 42.857 0.00 0.00 0.00 2.82
553 558 2.164017 TCCAATGCGATCACAACAATGG 59.836 45.455 0.00 0.00 0.00 3.16
554 559 1.921887 CAATGCGATCACAACAATGGC 59.078 47.619 0.00 0.00 0.00 4.40
555 560 0.099259 ATGCGATCACAACAATGGCG 59.901 50.000 0.00 0.00 31.27 5.69
556 561 1.869132 GCGATCACAACAATGGCGC 60.869 57.895 0.00 0.00 36.91 6.53
557 562 1.580893 CGATCACAACAATGGCGCG 60.581 57.895 0.00 0.00 0.00 6.86
558 563 1.869132 GATCACAACAATGGCGCGC 60.869 57.895 25.94 25.94 0.00 6.86
559 564 3.665825 ATCACAACAATGGCGCGCG 62.666 57.895 28.44 28.44 0.00 6.86
566 571 4.884257 AATGGCGCGCGGTCGTAT 62.884 61.111 33.06 10.60 38.14 3.06
567 572 4.884257 ATGGCGCGCGGTCGTATT 62.884 61.111 33.06 0.00 38.14 1.89
570 575 3.679326 GCGCGCGGTCGTATTCTC 61.679 66.667 33.06 6.44 38.14 2.87
571 576 3.022914 CGCGCGGTCGTATTCTCC 61.023 66.667 24.84 0.00 38.14 3.71
572 577 2.103538 GCGCGGTCGTATTCTCCA 59.896 61.111 8.83 0.00 38.14 3.86
573 578 1.944676 GCGCGGTCGTATTCTCCAG 60.945 63.158 8.83 0.00 38.14 3.86
574 579 1.432251 CGCGGTCGTATTCTCCAGT 59.568 57.895 0.00 0.00 0.00 4.00
575 580 0.659427 CGCGGTCGTATTCTCCAGTA 59.341 55.000 0.00 0.00 0.00 2.74
576 581 1.596464 CGCGGTCGTATTCTCCAGTAC 60.596 57.143 0.00 0.00 0.00 2.73
577 582 1.268948 GCGGTCGTATTCTCCAGTACC 60.269 57.143 0.00 0.00 0.00 3.34
578 583 2.295885 CGGTCGTATTCTCCAGTACCT 58.704 52.381 0.00 0.00 0.00 3.08
579 584 2.686915 CGGTCGTATTCTCCAGTACCTT 59.313 50.000 0.00 0.00 0.00 3.50
580 585 3.488721 CGGTCGTATTCTCCAGTACCTTG 60.489 52.174 0.00 0.00 0.00 3.61
581 586 3.181478 GGTCGTATTCTCCAGTACCTTGG 60.181 52.174 0.00 0.00 39.70 3.61
582 587 2.429610 TCGTATTCTCCAGTACCTTGGC 59.570 50.000 0.00 0.00 38.16 4.52
583 588 2.167693 CGTATTCTCCAGTACCTTGGCA 59.832 50.000 0.00 0.00 38.16 4.92
584 589 3.738281 CGTATTCTCCAGTACCTTGGCAG 60.738 52.174 0.00 0.00 38.16 4.85
585 590 2.024176 TTCTCCAGTACCTTGGCAGA 57.976 50.000 0.00 0.00 38.16 4.26
586 591 1.561643 TCTCCAGTACCTTGGCAGAG 58.438 55.000 0.00 0.00 38.16 3.35
587 592 0.539051 CTCCAGTACCTTGGCAGAGG 59.461 60.000 12.35 12.35 42.75 3.69
588 593 1.078143 CCAGTACCTTGGCAGAGGC 60.078 63.158 13.45 1.97 40.65 4.70
589 594 1.448540 CAGTACCTTGGCAGAGGCG 60.449 63.158 13.45 0.00 40.65 5.52
590 595 2.125106 GTACCTTGGCAGAGGCGG 60.125 66.667 13.45 2.45 40.65 6.13
591 596 4.096003 TACCTTGGCAGAGGCGGC 62.096 66.667 0.00 0.00 40.65 6.53
610 615 4.629523 GGTGTTGGTCGCCCCGAA 62.630 66.667 0.00 0.00 40.57 4.30
611 616 3.047877 GTGTTGGTCGCCCCGAAG 61.048 66.667 0.00 0.00 37.72 3.79
620 625 2.967615 GCCCCGAAGCGCTATGAC 60.968 66.667 12.05 1.71 0.00 3.06
621 626 2.658593 CCCCGAAGCGCTATGACG 60.659 66.667 12.05 14.39 0.00 4.35
622 627 2.658593 CCCGAAGCGCTATGACGG 60.659 66.667 26.50 26.50 42.67 4.79
623 628 3.330853 CCGAAGCGCTATGACGGC 61.331 66.667 23.91 4.90 37.32 5.68
629 634 3.028130 CGCTATGACGGCGTAGGA 58.972 61.111 19.13 0.00 46.37 2.94
630 635 1.082038 CGCTATGACGGCGTAGGAG 60.082 63.158 19.13 11.40 46.37 3.69
631 636 1.783031 CGCTATGACGGCGTAGGAGT 61.783 60.000 19.13 0.00 46.37 3.85
632 637 1.233019 GCTATGACGGCGTAGGAGTA 58.767 55.000 19.13 0.80 34.77 2.59
633 638 1.069364 GCTATGACGGCGTAGGAGTAC 60.069 57.143 19.13 0.00 34.77 2.73
641 646 3.920144 CGTAGGAGTACGCAAGAGG 57.080 57.895 0.00 0.00 45.22 3.69
642 647 0.381089 CGTAGGAGTACGCAAGAGGG 59.619 60.000 0.00 0.00 45.22 4.30
643 648 1.472188 GTAGGAGTACGCAAGAGGGT 58.528 55.000 0.00 0.00 43.95 4.34
644 649 1.134560 GTAGGAGTACGCAAGAGGGTG 59.865 57.143 0.00 0.00 41.48 4.61
645 650 1.218316 GGAGTACGCAAGAGGGTGG 59.782 63.158 0.00 0.00 41.48 4.61
646 651 1.448013 GAGTACGCAAGAGGGTGGC 60.448 63.158 0.00 0.00 41.48 5.01
652 657 3.322466 CAAGAGGGTGGCGGACCT 61.322 66.667 3.71 0.00 45.33 3.85
685 690 3.084039 TGAGTTTCACCATGATGAAGCC 58.916 45.455 12.66 5.77 39.79 4.35
791 806 3.121362 CCACGCAAAAATCGCTTCTTTTC 60.121 43.478 0.00 0.00 0.00 2.29
836 852 2.019807 ACTCCCCCTCAAACTAACGA 57.980 50.000 0.00 0.00 0.00 3.85
837 853 2.547990 ACTCCCCCTCAAACTAACGAT 58.452 47.619 0.00 0.00 0.00 3.73
838 854 2.500504 ACTCCCCCTCAAACTAACGATC 59.499 50.000 0.00 0.00 0.00 3.69
839 855 1.835531 TCCCCCTCAAACTAACGATCC 59.164 52.381 0.00 0.00 0.00 3.36
840 856 1.557832 CCCCCTCAAACTAACGATCCA 59.442 52.381 0.00 0.00 0.00 3.41
841 857 2.629051 CCCCTCAAACTAACGATCCAC 58.371 52.381 0.00 0.00 0.00 4.02
842 858 2.629051 CCCTCAAACTAACGATCCACC 58.371 52.381 0.00 0.00 0.00 4.61
843 859 2.027561 CCCTCAAACTAACGATCCACCA 60.028 50.000 0.00 0.00 0.00 4.17
844 860 3.558321 CCCTCAAACTAACGATCCACCAA 60.558 47.826 0.00 0.00 0.00 3.67
845 861 3.435671 CCTCAAACTAACGATCCACCAAC 59.564 47.826 0.00 0.00 0.00 3.77
846 862 3.061322 TCAAACTAACGATCCACCAACG 58.939 45.455 0.00 0.00 0.00 4.10
847 863 1.435577 AACTAACGATCCACCAACGC 58.564 50.000 0.00 0.00 0.00 4.84
848 864 0.390735 ACTAACGATCCACCAACGCC 60.391 55.000 0.00 0.00 0.00 5.68
849 865 1.418342 CTAACGATCCACCAACGCCG 61.418 60.000 0.00 0.00 0.00 6.46
850 866 2.157305 TAACGATCCACCAACGCCGT 62.157 55.000 0.00 0.00 0.00 5.68
851 867 3.186047 CGATCCACCAACGCCGTC 61.186 66.667 0.00 0.00 0.00 4.79
852 868 2.047655 GATCCACCAACGCCGTCA 60.048 61.111 0.00 0.00 0.00 4.35
853 869 2.047274 ATCCACCAACGCCGTCAG 60.047 61.111 0.00 0.00 0.00 3.51
854 870 4.980805 TCCACCAACGCCGTCAGC 62.981 66.667 0.00 0.00 38.52 4.26
930 955 1.075301 CCATCCCCCAATTCCCCAC 60.075 63.158 0.00 0.00 0.00 4.61
934 966 3.280151 CCCCAATTCCCCACCCCA 61.280 66.667 0.00 0.00 0.00 4.96
1377 1429 2.187946 CGCAAGGAGGCCGAGAAT 59.812 61.111 0.00 0.00 0.00 2.40
1412 1467 4.215185 CCAAGGTCTCTGCTTTTTCTTCTC 59.785 45.833 0.00 0.00 0.00 2.87
1418 1473 2.165998 CTGCTTTTTCTTCTCCCCCTG 58.834 52.381 0.00 0.00 0.00 4.45
1419 1474 1.499007 TGCTTTTTCTTCTCCCCCTGT 59.501 47.619 0.00 0.00 0.00 4.00
1440 1513 2.314071 TCTTCCCCGTTCCTCTGTTA 57.686 50.000 0.00 0.00 0.00 2.41
1446 1519 1.000060 CCCGTTCCTCTGTTACGTTCA 60.000 52.381 0.00 0.00 33.68 3.18
1447 1520 2.056577 CCGTTCCTCTGTTACGTTCAC 58.943 52.381 0.00 0.00 33.68 3.18
1455 1528 2.049248 TTACGTTCACCCGTCCGC 60.049 61.111 0.00 0.00 42.00 5.54
1703 1789 3.692406 AACGCCACCCTCTCCGTC 61.692 66.667 0.00 0.00 32.89 4.79
1790 1876 2.031012 CGCACCCTCAAGCTCACA 59.969 61.111 0.00 0.00 0.00 3.58
1819 1905 1.798813 CTGTAAGCGTCCAAACAGACC 59.201 52.381 0.00 0.00 41.47 3.85
2664 3695 4.455533 TGATTGCTTTAGGCTTGTGTAGTG 59.544 41.667 0.00 0.00 42.39 2.74
2665 3696 2.151202 TGCTTTAGGCTTGTGTAGTGC 58.849 47.619 0.00 0.00 42.39 4.40
2668 3699 3.403038 CTTTAGGCTTGTGTAGTGCTGT 58.597 45.455 0.00 0.00 0.00 4.40
2873 3922 8.693542 ATCTAATGTAATTTGAAGTTGCTTGC 57.306 30.769 0.00 0.00 41.15 4.01
2948 4082 5.710513 TGCTGTGAAATGAAATGTTAGCT 57.289 34.783 0.00 0.00 0.00 3.32
2954 4088 6.430925 TGTGAAATGAAATGTTAGCTAGCACT 59.569 34.615 18.83 0.00 0.00 4.40
2955 4089 6.744537 GTGAAATGAAATGTTAGCTAGCACTG 59.255 38.462 18.83 0.00 0.00 3.66
2981 4115 2.874849 GAGCTTCTTCTCCTCTCAACG 58.125 52.381 0.00 0.00 0.00 4.10
2982 4116 2.230266 GAGCTTCTTCTCCTCTCAACGT 59.770 50.000 0.00 0.00 0.00 3.99
2983 4117 2.630580 AGCTTCTTCTCCTCTCAACGTT 59.369 45.455 0.00 0.00 0.00 3.99
3006 4141 0.248377 GCTGTCGATCTGCAAATGGC 60.248 55.000 10.40 0.00 45.13 4.40
3019 4179 2.159338 GCAAATGGCGATGACAGATTGT 60.159 45.455 0.00 0.00 0.00 2.71
3024 4185 1.933853 GGCGATGACAGATTGTACACC 59.066 52.381 0.00 0.00 0.00 4.16
3064 4231 8.243426 AGTGTTTACATATTATTGGTTGCAGTG 58.757 33.333 0.00 0.00 0.00 3.66
3339 4506 5.484715 CTCCGTCCCAAATTACTTGTCTTA 58.515 41.667 0.00 0.00 32.65 2.10
3340 4507 5.484715 TCCGTCCCAAATTACTTGTCTTAG 58.515 41.667 0.00 0.00 32.65 2.18
3342 4509 6.070424 TCCGTCCCAAATTACTTGTCTTAGAT 60.070 38.462 0.00 0.00 32.65 1.98
3343 4510 6.598064 CCGTCCCAAATTACTTGTCTTAGATT 59.402 38.462 0.00 0.00 32.65 2.40
3346 4513 8.793592 GTCCCAAATTACTTGTCTTAGATTTGT 58.206 33.333 0.00 0.00 34.40 2.83
3347 4514 9.010029 TCCCAAATTACTTGTCTTAGATTTGTC 57.990 33.333 0.00 0.00 34.40 3.18
3356 4523 7.339721 ACTTGTCTTAGATTTGTCTAGATCGGA 59.660 37.037 0.00 0.00 0.00 4.55
3358 4563 8.919777 TGTCTTAGATTTGTCTAGATCGGATA 57.080 34.615 0.00 0.00 0.00 2.59
3418 4626 8.919777 TGTCTTAGATTTGTCTAGATCGGATA 57.080 34.615 0.00 0.00 0.00 2.59
3462 4670 4.957759 ATAAATTGTGCTACGTTGGACC 57.042 40.909 17.77 2.31 0.00 4.46
3482 4690 3.008049 ACCGGTCTTATCTCAAGTTGCTT 59.992 43.478 0.00 0.00 0.00 3.91
3483 4691 3.372206 CCGGTCTTATCTCAAGTTGCTTG 59.628 47.826 0.00 2.71 42.25 4.01
3484 4692 3.997021 CGGTCTTATCTCAAGTTGCTTGT 59.003 43.478 8.48 0.00 41.66 3.16
3485 4693 4.143030 CGGTCTTATCTCAAGTTGCTTGTG 60.143 45.833 8.48 6.67 41.66 3.33
3486 4694 4.997395 GGTCTTATCTCAAGTTGCTTGTGA 59.003 41.667 13.57 13.57 44.32 3.58
3487 4695 5.121454 GGTCTTATCTCAAGTTGCTTGTGAG 59.879 44.000 15.55 5.88 43.75 3.51
3492 4700 4.965814 TCTCAAGTTGCTTGTGAGATTCT 58.034 39.130 8.48 0.00 42.14 2.40
3493 4701 4.753610 TCTCAAGTTGCTTGTGAGATTCTG 59.246 41.667 8.48 0.00 42.14 3.02
3494 4702 4.454678 TCAAGTTGCTTGTGAGATTCTGT 58.545 39.130 8.48 0.00 41.66 3.41
3495 4703 4.512944 TCAAGTTGCTTGTGAGATTCTGTC 59.487 41.667 8.48 0.00 41.66 3.51
3496 4704 4.348863 AGTTGCTTGTGAGATTCTGTCT 57.651 40.909 0.00 0.00 40.81 3.41
3508 4716 2.234300 TTCTGTCTGTTTGACCGGTC 57.766 50.000 28.17 28.17 44.75 4.79
3527 4735 2.863137 GTCATCATCTTGTTCCTCTCGC 59.137 50.000 0.00 0.00 0.00 5.03
3577 4785 3.802948 ATCTACCTTGCGATTCGTCTT 57.197 42.857 8.03 0.00 0.00 3.01
3578 4786 4.913335 ATCTACCTTGCGATTCGTCTTA 57.087 40.909 8.03 0.00 0.00 2.10
3579 4787 4.913335 TCTACCTTGCGATTCGTCTTAT 57.087 40.909 8.03 0.00 0.00 1.73
3580 4788 4.856664 TCTACCTTGCGATTCGTCTTATC 58.143 43.478 8.03 0.00 0.00 1.75
3582 4790 4.124851 ACCTTGCGATTCGTCTTATCTT 57.875 40.909 8.03 0.00 0.00 2.40
3583 4791 5.258456 ACCTTGCGATTCGTCTTATCTTA 57.742 39.130 8.03 0.00 0.00 2.10
3584 4792 5.844004 ACCTTGCGATTCGTCTTATCTTAT 58.156 37.500 8.03 0.00 0.00 1.73
3585 4793 5.921408 ACCTTGCGATTCGTCTTATCTTATC 59.079 40.000 8.03 0.00 0.00 1.75
3586 4794 6.153067 CCTTGCGATTCGTCTTATCTTATCT 58.847 40.000 8.03 0.00 0.00 1.98
3587 4795 6.306837 CCTTGCGATTCGTCTTATCTTATCTC 59.693 42.308 8.03 0.00 0.00 2.75
3588 4796 6.313744 TGCGATTCGTCTTATCTTATCTCA 57.686 37.500 8.03 0.00 0.00 3.27
3589 4797 6.735130 TGCGATTCGTCTTATCTTATCTCAA 58.265 36.000 8.03 0.00 0.00 3.02
3590 4798 6.858478 TGCGATTCGTCTTATCTTATCTCAAG 59.142 38.462 8.03 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.031857 TTTTGCACATCCCGCAGTTG 59.968 50.000 0.00 0.00 41.18 3.16
2 3 0.527565 GATTTTGCACATCCCGCAGT 59.472 50.000 0.00 0.00 41.18 4.40
4 5 1.135053 CATGATTTTGCACATCCCGCA 60.135 47.619 3.16 0.00 37.68 5.69
7 8 1.473788 GCCCATGATTTTGCACATCCC 60.474 52.381 0.00 0.00 0.00 3.85
8 9 1.483415 AGCCCATGATTTTGCACATCC 59.517 47.619 0.00 0.00 0.00 3.51
9 10 2.973694 AGCCCATGATTTTGCACATC 57.026 45.000 0.00 0.00 0.00 3.06
10 11 2.417651 CGAAGCCCATGATTTTGCACAT 60.418 45.455 0.00 0.00 0.00 3.21
11 12 1.067706 CGAAGCCCATGATTTTGCACA 60.068 47.619 0.00 0.00 0.00 4.57
12 13 1.632422 CGAAGCCCATGATTTTGCAC 58.368 50.000 0.00 0.00 0.00 4.57
13 14 0.531657 CCGAAGCCCATGATTTTGCA 59.468 50.000 0.00 0.00 0.00 4.08
14 15 0.532115 ACCGAAGCCCATGATTTTGC 59.468 50.000 0.00 0.00 0.00 3.68
15 16 1.736696 GCACCGAAGCCCATGATTTTG 60.737 52.381 0.00 0.00 0.00 2.44
16 17 0.532115 GCACCGAAGCCCATGATTTT 59.468 50.000 0.00 0.00 0.00 1.82
61 62 3.664025 TTGCCACGATCCGCTGGAG 62.664 63.158 10.51 0.00 34.05 3.86
63 64 3.499737 GTTGCCACGATCCGCTGG 61.500 66.667 0.00 0.00 33.57 4.85
64 65 2.040213 GATGTTGCCACGATCCGCTG 62.040 60.000 0.00 0.00 0.00 5.18
65 66 1.815421 GATGTTGCCACGATCCGCT 60.815 57.895 0.00 0.00 0.00 5.52
67 68 3.005898 CGATGTTGCCACGATCCG 58.994 61.111 0.00 0.00 0.00 4.18
102 103 4.899239 CCCGCCGATGAGGACAGC 62.899 72.222 0.00 0.00 45.00 4.40
103 104 4.899239 GCCCGCCGATGAGGACAG 62.899 72.222 0.00 0.00 45.00 3.51
140 142 4.498894 TTGCTGGATGAGATGACAATCT 57.501 40.909 0.00 0.00 46.23 2.40
143 145 3.692593 CACATTGCTGGATGAGATGACAA 59.307 43.478 2.97 0.00 0.00 3.18
144 146 3.275999 CACATTGCTGGATGAGATGACA 58.724 45.455 2.97 0.00 0.00 3.58
157 159 0.682209 GGCTGGTCATCCACATTGCT 60.682 55.000 0.00 0.00 39.03 3.91
160 162 1.750399 GCGGCTGGTCATCCACATT 60.750 57.895 0.00 0.00 39.03 2.71
162 164 4.408821 GGCGGCTGGTCATCCACA 62.409 66.667 0.00 0.00 39.03 4.17
203 208 2.278596 CGTACATCAGGCCCGTCG 60.279 66.667 0.00 0.00 0.00 5.12
205 210 3.075005 AGCGTACATCAGGCCCGT 61.075 61.111 0.00 0.00 38.87 5.28
207 212 2.203070 CCAGCGTACATCAGGCCC 60.203 66.667 0.00 0.00 38.87 5.80
212 217 1.955495 ATCGGTGCCAGCGTACATCA 61.955 55.000 16.56 0.00 40.41 3.07
214 219 1.521457 CATCGGTGCCAGCGTACAT 60.521 57.895 16.56 0.00 40.41 2.29
231 236 2.336945 TCTATTCCTCGTACTCCGCA 57.663 50.000 0.00 0.00 36.19 5.69
246 251 1.815613 CGGAGCATCACCTCGATCTAT 59.184 52.381 0.00 0.00 36.25 1.98
247 252 1.239347 CGGAGCATCACCTCGATCTA 58.761 55.000 0.00 0.00 36.25 1.98
252 257 2.278206 CGACGGAGCATCACCTCG 60.278 66.667 0.00 0.00 36.25 4.63
254 259 3.069980 GAGCGACGGAGCATCACCT 62.070 63.158 7.12 0.00 40.15 4.00
256 261 2.583593 GGAGCGACGGAGCATCAC 60.584 66.667 7.12 0.00 40.15 3.06
325 330 2.753966 CGAATGCCGGTTCCTGCTG 61.754 63.158 1.90 0.00 33.91 4.41
364 369 3.428282 AATTTGGACGCCGCGGTC 61.428 61.111 28.70 17.49 36.18 4.79
371 376 0.454452 GCGAGGTTCAATTTGGACGC 60.454 55.000 1.75 0.00 38.23 5.19
372 377 0.179225 CGCGAGGTTCAATTTGGACG 60.179 55.000 0.00 0.00 0.00 4.79
375 380 0.871722 TCACGCGAGGTTCAATTTGG 59.128 50.000 15.93 0.00 0.00 3.28
376 381 2.574322 CTTCACGCGAGGTTCAATTTG 58.426 47.619 15.93 0.00 0.00 2.32
381 386 0.319555 CTTCCTTCACGCGAGGTTCA 60.320 55.000 15.93 0.00 35.71 3.18
386 391 2.155194 CGCTCTTCCTTCACGCGAG 61.155 63.158 15.93 4.59 45.99 5.03
415 420 3.767230 CTTGACACGTCGGCGCAG 61.767 66.667 10.50 5.07 42.83 5.18
418 423 2.805353 CTCCTTGACACGTCGGCG 60.805 66.667 8.42 8.42 44.93 6.46
419 424 2.432628 CCTCCTTGACACGTCGGC 60.433 66.667 0.00 0.00 0.00 5.54
422 427 1.444553 CGCTCCTCCTTGACACGTC 60.445 63.158 0.00 0.00 0.00 4.34
423 428 2.651361 CGCTCCTCCTTGACACGT 59.349 61.111 0.00 0.00 0.00 4.49
450 455 4.612412 TTGACGTGTCGGGGTGGC 62.612 66.667 0.00 0.00 0.00 5.01
451 456 2.357034 CTTGACGTGTCGGGGTGG 60.357 66.667 0.00 0.00 0.00 4.61
452 457 2.357034 CCTTGACGTGTCGGGGTG 60.357 66.667 0.00 0.00 0.00 4.61
453 458 2.095978 CTTCCTTGACGTGTCGGGGT 62.096 60.000 0.00 0.00 0.00 4.95
454 459 1.374252 CTTCCTTGACGTGTCGGGG 60.374 63.158 0.00 7.91 0.00 5.73
455 460 0.388649 CTCTTCCTTGACGTGTCGGG 60.389 60.000 0.00 5.75 0.00 5.14
456 461 1.009389 GCTCTTCCTTGACGTGTCGG 61.009 60.000 0.00 0.00 0.00 4.79
457 462 1.337817 CGCTCTTCCTTGACGTGTCG 61.338 60.000 0.00 0.00 0.00 4.35
458 463 1.009389 CCGCTCTTCCTTGACGTGTC 61.009 60.000 0.00 0.00 0.00 3.67
459 464 1.006102 CCGCTCTTCCTTGACGTGT 60.006 57.895 0.00 0.00 0.00 4.49
460 465 0.600255 AACCGCTCTTCCTTGACGTG 60.600 55.000 0.00 0.00 0.00 4.49
461 466 0.600255 CAACCGCTCTTCCTTGACGT 60.600 55.000 0.00 0.00 0.00 4.34
462 467 1.901650 GCAACCGCTCTTCCTTGACG 61.902 60.000 0.00 0.00 34.30 4.35
463 468 1.578206 GGCAACCGCTCTTCCTTGAC 61.578 60.000 0.00 0.00 38.60 3.18
464 469 1.302511 GGCAACCGCTCTTCCTTGA 60.303 57.895 0.00 0.00 38.60 3.02
465 470 1.301677 GAGGCAACCGCTCTTCCTTG 61.302 60.000 0.00 0.00 38.60 3.61
466 471 1.003233 GAGGCAACCGCTCTTCCTT 60.003 57.895 0.00 0.00 38.60 3.36
467 472 2.665603 GAGGCAACCGCTCTTCCT 59.334 61.111 0.00 0.00 38.60 3.36
468 473 2.436824 GGAGGCAACCGCTCTTCC 60.437 66.667 0.00 0.00 38.60 3.46
469 474 2.815647 CGGAGGCAACCGCTCTTC 60.816 66.667 9.86 0.00 46.20 2.87
498 503 2.895865 TAGCGCTCCTCCTCGACG 60.896 66.667 16.34 0.00 0.00 5.12
499 504 2.113433 TGTAGCGCTCCTCCTCGAC 61.113 63.158 16.34 4.05 0.00 4.20
500 505 2.113433 GTGTAGCGCTCCTCCTCGA 61.113 63.158 16.34 0.00 0.00 4.04
501 506 2.409651 GTGTAGCGCTCCTCCTCG 59.590 66.667 16.34 0.00 0.00 4.63
502 507 2.409651 CGTGTAGCGCTCCTCCTC 59.590 66.667 16.34 0.55 0.00 3.71
519 524 3.537206 ATTGGATAGGAGCGGCGGC 62.537 63.158 9.78 8.43 40.37 6.53
520 525 1.669115 CATTGGATAGGAGCGGCGG 60.669 63.158 9.78 0.00 0.00 6.13
521 526 2.320587 GCATTGGATAGGAGCGGCG 61.321 63.158 0.51 0.51 0.00 6.46
522 527 2.320587 CGCATTGGATAGGAGCGGC 61.321 63.158 0.00 0.00 44.20 6.53
523 528 3.957260 CGCATTGGATAGGAGCGG 58.043 61.111 0.00 0.00 44.20 5.52
525 530 2.072298 GTGATCGCATTGGATAGGAGC 58.928 52.381 0.16 0.00 0.00 4.70
526 531 3.391506 TGTGATCGCATTGGATAGGAG 57.608 47.619 4.45 0.00 0.00 3.69
527 532 3.118445 TGTTGTGATCGCATTGGATAGGA 60.118 43.478 10.29 0.00 0.00 2.94
528 533 3.205338 TGTTGTGATCGCATTGGATAGG 58.795 45.455 10.29 0.00 0.00 2.57
529 534 4.880886 TTGTTGTGATCGCATTGGATAG 57.119 40.909 10.29 0.00 0.00 2.08
530 535 4.036616 CCATTGTTGTGATCGCATTGGATA 59.963 41.667 10.29 0.00 36.37 2.59
531 536 3.181484 CCATTGTTGTGATCGCATTGGAT 60.181 43.478 10.29 0.00 36.37 3.41
532 537 2.164017 CCATTGTTGTGATCGCATTGGA 59.836 45.455 10.29 0.00 36.37 3.53
533 538 2.532235 CCATTGTTGTGATCGCATTGG 58.468 47.619 10.29 10.96 0.00 3.16
534 539 1.921887 GCCATTGTTGTGATCGCATTG 59.078 47.619 10.29 6.00 0.00 2.82
535 540 1.467883 CGCCATTGTTGTGATCGCATT 60.468 47.619 10.29 0.00 0.00 3.56
536 541 0.099259 CGCCATTGTTGTGATCGCAT 59.901 50.000 10.29 0.00 0.00 4.73
537 542 1.501292 CGCCATTGTTGTGATCGCA 59.499 52.632 4.45 4.45 0.00 5.10
538 543 1.869132 GCGCCATTGTTGTGATCGC 60.869 57.895 0.00 0.00 35.24 4.58
539 544 1.580893 CGCGCCATTGTTGTGATCG 60.581 57.895 0.00 0.00 0.00 3.69
540 545 1.869132 GCGCGCCATTGTTGTGATC 60.869 57.895 23.24 0.00 0.00 2.92
541 546 2.179018 GCGCGCCATTGTTGTGAT 59.821 55.556 23.24 0.00 0.00 3.06
542 547 4.382114 CGCGCGCCATTGTTGTGA 62.382 61.111 27.72 0.00 0.00 3.58
549 554 4.884257 ATACGACCGCGCGCCATT 62.884 61.111 27.36 9.87 42.48 3.16
550 555 4.884257 AATACGACCGCGCGCCAT 62.884 61.111 27.36 14.41 42.48 4.40
553 558 3.679326 GAGAATACGACCGCGCGC 61.679 66.667 27.36 23.91 42.48 6.86
554 559 3.022914 GGAGAATACGACCGCGCG 61.023 66.667 25.67 25.67 42.48 6.86
555 560 1.944676 CTGGAGAATACGACCGCGC 60.945 63.158 0.00 0.00 42.48 6.86
556 561 0.659427 TACTGGAGAATACGACCGCG 59.341 55.000 0.00 0.00 44.79 6.46
557 562 1.268948 GGTACTGGAGAATACGACCGC 60.269 57.143 0.00 0.00 0.00 5.68
558 563 2.295885 AGGTACTGGAGAATACGACCG 58.704 52.381 0.00 0.00 37.18 4.79
559 564 3.181478 CCAAGGTACTGGAGAATACGACC 60.181 52.174 0.00 0.00 40.86 4.79
560 565 3.737355 GCCAAGGTACTGGAGAATACGAC 60.737 52.174 5.35 0.00 40.86 4.34
561 566 2.429610 GCCAAGGTACTGGAGAATACGA 59.570 50.000 5.35 0.00 40.86 3.43
562 567 2.167693 TGCCAAGGTACTGGAGAATACG 59.832 50.000 5.35 0.00 40.86 3.06
563 568 3.451178 TCTGCCAAGGTACTGGAGAATAC 59.549 47.826 5.35 0.00 40.86 1.89
564 569 3.706594 CTCTGCCAAGGTACTGGAGAATA 59.293 47.826 5.35 0.00 40.86 1.75
565 570 2.503356 CTCTGCCAAGGTACTGGAGAAT 59.497 50.000 5.35 0.00 40.86 2.40
566 571 1.902508 CTCTGCCAAGGTACTGGAGAA 59.097 52.381 5.35 0.00 40.86 2.87
567 572 1.561643 CTCTGCCAAGGTACTGGAGA 58.438 55.000 5.35 4.79 40.86 3.71
568 573 0.539051 CCTCTGCCAAGGTACTGGAG 59.461 60.000 5.35 1.07 40.86 3.86
569 574 1.553690 GCCTCTGCCAAGGTACTGGA 61.554 60.000 5.35 0.00 40.86 3.86
570 575 1.078143 GCCTCTGCCAAGGTACTGG 60.078 63.158 3.64 0.00 40.86 4.00
571 576 1.448540 CGCCTCTGCCAAGGTACTG 60.449 63.158 3.64 0.00 40.86 2.74
573 578 2.125106 CCGCCTCTGCCAAGGTAC 60.125 66.667 3.64 0.00 38.79 3.34
574 579 4.096003 GCCGCCTCTGCCAAGGTA 62.096 66.667 3.64 0.00 38.79 3.08
604 609 2.658593 CGTCATAGCGCTTCGGGG 60.659 66.667 18.68 0.61 0.00 5.73
605 610 2.658593 CCGTCATAGCGCTTCGGG 60.659 66.667 18.68 6.76 37.92 5.14
606 611 3.330853 GCCGTCATAGCGCTTCGG 61.331 66.667 26.46 26.46 43.37 4.30
613 618 1.069364 GTACTCCTACGCCGTCATAGC 60.069 57.143 0.00 0.00 0.00 2.97
614 619 1.194098 CGTACTCCTACGCCGTCATAG 59.806 57.143 0.00 0.00 39.43 2.23
615 620 1.220529 CGTACTCCTACGCCGTCATA 58.779 55.000 0.00 0.00 39.43 2.15
616 621 2.020131 CGTACTCCTACGCCGTCAT 58.980 57.895 0.00 0.00 39.43 3.06
617 622 3.489731 CGTACTCCTACGCCGTCA 58.510 61.111 0.00 0.00 39.43 4.35
624 629 1.134560 CACCCTCTTGCGTACTCCTAC 59.865 57.143 0.00 0.00 0.00 3.18
625 630 1.471119 CACCCTCTTGCGTACTCCTA 58.529 55.000 0.00 0.00 0.00 2.94
626 631 1.258445 CCACCCTCTTGCGTACTCCT 61.258 60.000 0.00 0.00 0.00 3.69
627 632 1.218316 CCACCCTCTTGCGTACTCC 59.782 63.158 0.00 0.00 0.00 3.85
628 633 1.448013 GCCACCCTCTTGCGTACTC 60.448 63.158 0.00 0.00 0.00 2.59
629 634 2.663196 GCCACCCTCTTGCGTACT 59.337 61.111 0.00 0.00 0.00 2.73
630 635 2.813908 CGCCACCCTCTTGCGTAC 60.814 66.667 0.00 0.00 43.12 3.67
631 636 4.077184 CCGCCACCCTCTTGCGTA 62.077 66.667 0.00 0.00 46.44 4.42
642 647 0.250338 AAAGTCAAGAGGTCCGCCAC 60.250 55.000 0.00 0.00 37.19 5.01
643 648 0.250295 CAAAGTCAAGAGGTCCGCCA 60.250 55.000 0.00 0.00 37.19 5.69
644 649 0.250338 ACAAAGTCAAGAGGTCCGCC 60.250 55.000 0.00 0.00 0.00 6.13
645 650 1.264288 CAACAAAGTCAAGAGGTCCGC 59.736 52.381 0.00 0.00 0.00 5.54
646 651 2.802816 CTCAACAAAGTCAAGAGGTCCG 59.197 50.000 0.00 0.00 0.00 4.79
647 652 3.809905 ACTCAACAAAGTCAAGAGGTCC 58.190 45.455 0.00 0.00 0.00 4.46
648 653 5.354234 TGAAACTCAACAAAGTCAAGAGGTC 59.646 40.000 0.00 0.00 0.00 3.85
649 654 5.123979 GTGAAACTCAACAAAGTCAAGAGGT 59.876 40.000 0.00 0.00 0.00 3.85
650 655 5.449177 GGTGAAACTCAACAAAGTCAAGAGG 60.449 44.000 0.00 0.00 33.38 3.69
651 656 5.123820 TGGTGAAACTCAACAAAGTCAAGAG 59.876 40.000 0.00 0.00 41.82 2.85
652 657 5.007034 TGGTGAAACTCAACAAAGTCAAGA 58.993 37.500 0.00 0.00 41.82 3.02
685 690 2.030274 GGGGAGGTGAATTTTGTTGACG 60.030 50.000 0.00 0.00 0.00 4.35
725 739 4.635961 CGTGGTAACGGTTACTTCTTTC 57.364 45.455 25.36 11.82 46.25 2.62
779 794 3.884226 GGGGGAGAAAAGAAGCGAT 57.116 52.632 0.00 0.00 0.00 4.58
836 852 2.047274 CTGACGGCGTTGGTGGAT 60.047 61.111 16.19 0.00 0.00 3.41
837 853 4.980805 GCTGACGGCGTTGGTGGA 62.981 66.667 16.19 0.00 0.00 4.02
865 881 0.618981 GGCGGGATTTATAGAGGGGG 59.381 60.000 0.00 0.00 0.00 5.40
866 882 0.618981 GGGCGGGATTTATAGAGGGG 59.381 60.000 0.00 0.00 0.00 4.79
975 1007 3.578515 TTCGTTTCGGAGGACGGGC 62.579 63.158 13.52 0.00 44.45 6.13
976 1008 1.445582 CTTCGTTTCGGAGGACGGG 60.446 63.158 13.52 6.08 44.45 5.28
989 1021 1.007238 TCTCCCTCATCTTCCCTTCGT 59.993 52.381 0.00 0.00 0.00 3.85
990 1022 1.781786 TCTCCCTCATCTTCCCTTCG 58.218 55.000 0.00 0.00 0.00 3.79
1191 1243 2.818132 GGCTCGAGGTCCATGAGG 59.182 66.667 15.58 0.00 0.00 3.86
1377 1429 2.032528 CCTTGGAGGCAGTCGCAA 59.967 61.111 0.00 0.00 41.24 4.85
1412 1467 2.076597 AACGGGGAAGAAACAGGGGG 62.077 60.000 0.00 0.00 0.00 5.40
1418 1473 1.071857 ACAGAGGAACGGGGAAGAAAC 59.928 52.381 0.00 0.00 0.00 2.78
1419 1474 1.430992 ACAGAGGAACGGGGAAGAAA 58.569 50.000 0.00 0.00 0.00 2.52
1478 1557 1.338136 TTCCCTTCCGCTCCAGATCC 61.338 60.000 0.00 0.00 0.00 3.36
1703 1789 1.444553 GTTCTCGACGAGCTGGTGG 60.445 63.158 20.11 5.11 0.00 4.61
1790 1876 2.264794 CGCTTACAGCTCGGGGTT 59.735 61.111 0.00 0.00 39.60 4.11
1807 1893 2.820197 GAGGAATTGGGTCTGTTTGGAC 59.180 50.000 0.00 0.00 35.66 4.02
1808 1894 2.225017 GGAGGAATTGGGTCTGTTTGGA 60.225 50.000 0.00 0.00 0.00 3.53
1812 1898 2.649312 TGATGGAGGAATTGGGTCTGTT 59.351 45.455 0.00 0.00 0.00 3.16
1813 1899 2.278245 TGATGGAGGAATTGGGTCTGT 58.722 47.619 0.00 0.00 0.00 3.41
1815 1901 3.393941 GAGATGATGGAGGAATTGGGTCT 59.606 47.826 0.00 0.00 0.00 3.85
1816 1902 3.393941 AGAGATGATGGAGGAATTGGGTC 59.606 47.826 0.00 0.00 0.00 4.46
1817 1903 3.137913 CAGAGATGATGGAGGAATTGGGT 59.862 47.826 0.00 0.00 0.00 4.51
1818 1904 3.752665 CAGAGATGATGGAGGAATTGGG 58.247 50.000 0.00 0.00 0.00 4.12
1819 1905 3.147629 GCAGAGATGATGGAGGAATTGG 58.852 50.000 0.00 0.00 0.00 3.16
2664 3695 3.243201 CCACCAAGAAAGACAGAAACAGC 60.243 47.826 0.00 0.00 0.00 4.40
2665 3696 3.316308 CCCACCAAGAAAGACAGAAACAG 59.684 47.826 0.00 0.00 0.00 3.16
2668 3699 3.287222 CACCCACCAAGAAAGACAGAAA 58.713 45.455 0.00 0.00 0.00 2.52
2873 3922 6.522165 CACAAATCATGAACTGAAATCAGACG 59.478 38.462 16.93 1.29 46.59 4.18
2961 4095 2.230266 ACGTTGAGAGGAGAAGAAGCTC 59.770 50.000 0.00 0.00 0.00 4.09
2962 4096 2.243810 ACGTTGAGAGGAGAAGAAGCT 58.756 47.619 0.00 0.00 0.00 3.74
2963 4097 2.734079 CAACGTTGAGAGGAGAAGAAGC 59.266 50.000 23.90 0.00 0.00 3.86
2964 4098 3.983741 ACAACGTTGAGAGGAGAAGAAG 58.016 45.455 33.66 3.06 0.00 2.85
2972 4106 1.261619 GACAGCAACAACGTTGAGAGG 59.738 52.381 33.66 19.47 0.00 3.69
2975 4109 0.927537 TCGACAGCAACAACGTTGAG 59.072 50.000 33.66 24.29 0.00 3.02
2979 4113 1.139989 CAGATCGACAGCAACAACGT 58.860 50.000 0.00 0.00 0.00 3.99
2980 4114 0.179240 GCAGATCGACAGCAACAACG 60.179 55.000 0.00 0.00 0.00 4.10
2981 4115 0.867746 TGCAGATCGACAGCAACAAC 59.132 50.000 5.86 0.00 38.04 3.32
2982 4116 1.592064 TTGCAGATCGACAGCAACAA 58.408 45.000 14.64 1.08 43.92 2.83
2983 4117 3.304041 TTGCAGATCGACAGCAACA 57.696 47.368 14.64 0.00 43.92 3.33
3006 4141 4.686972 AGATGGTGTACAATCTGTCATCG 58.313 43.478 8.89 0.00 35.89 3.84
3249 4416 3.772387 TGTAAACCAATGCAGAATGGGA 58.228 40.909 17.37 3.21 41.17 4.37
3314 4481 2.374170 ACAAGTAATTTGGGACGGAGGT 59.626 45.455 0.00 0.00 41.25 3.85
3366 4571 8.057011 AGTAATTTGGGACGGAGGTAATTTATT 58.943 33.333 0.00 0.00 0.00 1.40
3369 4574 5.823312 AGTAATTTGGGACGGAGGTAATTT 58.177 37.500 0.00 0.00 0.00 1.82
3370 4575 5.446260 AGTAATTTGGGACGGAGGTAATT 57.554 39.130 0.00 0.00 0.00 1.40
3372 4577 4.041938 ACAAGTAATTTGGGACGGAGGTAA 59.958 41.667 0.00 0.00 41.25 2.85
3378 4583 5.484715 TCTAAGACAAGTAATTTGGGACGG 58.515 41.667 0.00 0.00 41.25 4.79
3382 4587 9.014297 AGACAAATCTAAGACAAGTAATTTGGG 57.986 33.333 9.60 0.00 38.04 4.12
3436 4644 8.780249 GGTCCAACGTAGCACAATTTATTATAT 58.220 33.333 0.00 0.00 0.00 0.86
3437 4645 7.042590 CGGTCCAACGTAGCACAATTTATTATA 60.043 37.037 0.00 0.00 0.00 0.98
3438 4646 6.238266 CGGTCCAACGTAGCACAATTTATTAT 60.238 38.462 0.00 0.00 0.00 1.28
3439 4647 5.063691 CGGTCCAACGTAGCACAATTTATTA 59.936 40.000 0.00 0.00 0.00 0.98
3440 4648 4.142773 CGGTCCAACGTAGCACAATTTATT 60.143 41.667 0.00 0.00 0.00 1.40
3445 4653 0.672401 CCGGTCCAACGTAGCACAAT 60.672 55.000 0.00 0.00 0.00 2.71
3450 4658 0.527565 TAAGACCGGTCCAACGTAGC 59.472 55.000 30.82 3.19 0.00 3.58
3454 4662 1.475280 TGAGATAAGACCGGTCCAACG 59.525 52.381 30.82 0.00 0.00 4.10
3458 4666 3.522553 CAACTTGAGATAAGACCGGTCC 58.477 50.000 30.82 15.53 0.00 4.46
3462 4670 3.997021 ACAAGCAACTTGAGATAAGACCG 59.003 43.478 13.94 0.00 43.42 4.79
3493 4701 2.163818 TGATGACCGGTCAAACAGAC 57.836 50.000 39.04 23.98 46.83 3.51
3494 4702 2.567169 AGATGATGACCGGTCAAACAGA 59.433 45.455 39.04 21.31 43.58 3.41
3495 4703 2.977914 AGATGATGACCGGTCAAACAG 58.022 47.619 39.04 0.00 43.58 3.16
3496 4704 3.073678 CAAGATGATGACCGGTCAAACA 58.926 45.455 39.04 35.77 43.58 2.83
3508 4716 2.864946 CAGCGAGAGGAACAAGATGATG 59.135 50.000 0.00 0.00 0.00 3.07
3556 4764 4.913335 AAGACGAATCGCAAGGTAGATA 57.087 40.909 1.15 0.00 38.47 1.98
3564 4772 6.735130 TGAGATAAGATAAGACGAATCGCAA 58.265 36.000 1.15 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.