Multiple sequence alignment - TraesCS6B01G361100

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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 TraesCS6B01G361100 chr6B 100.000 1932 0 0 1 1932 632877151 632879082 0.000000e+00 3568.0
1 TraesCS6B01G361100 chr6B 100.000 1616 0 0 2347 3962 632879497 632881112 0.000000e+00 2985.0
2 TraesCS6B01G361100 chr6B 98.276 58 0 1 3 59 632851708 632851765 2.520000e-17 100.0
3 TraesCS6B01G361100 chr6B 100.000 51 0 0 3224 3274 632880296 632880346 1.170000e-15 95.3
4 TraesCS6B01G361100 chr6B 100.000 51 0 0 3146 3196 632880374 632880424 1.170000e-15 95.3
5 TraesCS6B01G361100 chr6B 95.122 41 2 0 2716 2756 632879830 632879870 9.190000e-07 65.8
6 TraesCS6B01G361100 chr6B 95.122 41 2 0 2680 2720 632879866 632879906 9.190000e-07 65.8
7 TraesCS6B01G361100 chr6A 92.291 1349 61 16 614 1932 562933588 562934923 0.000000e+00 1875.0
8 TraesCS6B01G361100 chr6A 96.076 892 31 4 2977 3868 562935680 562936567 0.000000e+00 1450.0
9 TraesCS6B01G361100 chr6A 96.530 634 15 4 2349 2978 562935011 562935641 0.000000e+00 1042.0
10 TraesCS6B01G361100 chr6A 84.477 277 32 6 59 324 562933313 562933589 3.040000e-66 263.0
11 TraesCS6B01G361100 chr6A 93.103 58 4 0 3905 3962 562936569 562936626 7.050000e-13 86.1
12 TraesCS6B01G361100 chr6A 94.118 51 3 0 3224 3274 562935847 562935897 1.180000e-10 78.7
13 TraesCS6B01G361100 chr6A 95.122 41 2 0 2680 2720 562935376 562935416 9.190000e-07 65.8
14 TraesCS6B01G361100 chr6D 92.279 1334 64 11 627 1932 419882034 419883356 0.000000e+00 1857.0
15 TraesCS6B01G361100 chr6D 95.781 640 20 4 2347 2980 419883442 419884080 0.000000e+00 1026.0
16 TraesCS6B01G361100 chr6D 94.976 617 28 2 3204 3817 419884286 419884902 0.000000e+00 965.0
17 TraesCS6B01G361100 chr6D 88.947 380 30 5 59 429 419881628 419882004 3.610000e-125 459.0
18 TraesCS6B01G361100 chr6D 100.000 33 0 0 2688 2720 419883819 419883851 1.190000e-05 62.1
19 TraesCS6B01G361100 chr4A 85.813 289 37 3 323 609 556761896 556761610 1.790000e-78 303.0
20 TraesCS6B01G361100 chr5D 84.669 287 38 6 320 603 299406011 299406294 8.380000e-72 281.0
21 TraesCS6B01G361100 chr3B 83.849 291 39 8 319 603 341964895 341965183 1.810000e-68 270.0
22 TraesCS6B01G361100 chr3B 81.090 312 50 8 320 629 179670044 179670348 1.420000e-59 241.0
23 TraesCS6B01G361100 chr3B 78.523 298 50 12 314 603 62309756 62310047 2.430000e-42 183.0
24 TraesCS6B01G361100 chr4B 82.796 279 40 7 317 590 142519455 142519180 3.960000e-60 243.0
25 TraesCS6B01G361100 chr2B 82.206 281 39 9 319 591 195687550 195687827 8.560000e-57 231.0
26 TraesCS6B01G361100 chr1B 84.052 232 31 4 381 609 155735118 155734890 6.670000e-53 219.0
27 TraesCS6B01G361100 chr7D 81.641 256 42 5 356 609 463266766 463266514 1.440000e-49 207.0


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 TraesCS6B01G361100 chr6B 632877151 632881112 3961 False 1145.866667 3568 98.374000 1 3962 6 chr6B.!!$F2 3961
1 TraesCS6B01G361100 chr6A 562933313 562936626 3313 False 694.371429 1875 93.102429 59 3962 7 chr6A.!!$F1 3903
2 TraesCS6B01G361100 chr6D 419881628 419884902 3274 False 873.820000 1857 94.396600 59 3817 5 chr6D.!!$F1 3758

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
750 768 0.181350 CTATGCTGTCACCCTTCCCC 59.819 60.0 0.0 0.0 0.00 4.81 F
1171 1209 0.179062 CCTCTCGGCCTTCTTCATGG 60.179 60.0 0.0 0.0 0.00 3.66 F
1495 1542 0.320771 GCGGAACTCACTCCACATGT 60.321 55.0 0.0 0.0 34.91 3.21 F
2506 2559 0.326618 TTCCCTCTCCCCAGATGACC 60.327 60.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2506 2559 0.094046 ATTTCTTCGTAAACGCCGCG 59.906 50.000 12.14 12.14 39.60 6.46 R
2685 2738 0.776176 GAGGCATGGAAGGGGATGAT 59.224 55.000 0.00 0.00 0.00 2.45 R
2886 2940 1.434513 TTGTGCCCAGGTCCATTCCT 61.435 55.000 0.00 0.00 38.51 3.36 R
3892 3996 1.275010 TCTCTGTGTGTGTGTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72 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
22 23 5.931441 CCGATTGAACCTTGATAATCCTC 57.069 43.478 0.00 0.00 0.00 3.71
23 24 4.757149 CCGATTGAACCTTGATAATCCTCC 59.243 45.833 0.00 0.00 0.00 4.30
24 25 5.455326 CCGATTGAACCTTGATAATCCTCCT 60.455 44.000 0.00 0.00 0.00 3.69
25 26 6.058183 CGATTGAACCTTGATAATCCTCCTT 58.942 40.000 0.00 0.00 0.00 3.36
26 27 6.203723 CGATTGAACCTTGATAATCCTCCTTC 59.796 42.308 0.00 0.00 0.00 3.46
27 28 6.642733 TTGAACCTTGATAATCCTCCTTCT 57.357 37.500 0.00 0.00 0.00 2.85
28 29 5.994250 TGAACCTTGATAATCCTCCTTCTG 58.006 41.667 0.00 0.00 0.00 3.02
29 30 4.429854 ACCTTGATAATCCTCCTTCTGC 57.570 45.455 0.00 0.00 0.00 4.26
30 31 4.043596 ACCTTGATAATCCTCCTTCTGCT 58.956 43.478 0.00 0.00 0.00 4.24
31 32 5.219739 ACCTTGATAATCCTCCTTCTGCTA 58.780 41.667 0.00 0.00 0.00 3.49
32 33 5.848921 ACCTTGATAATCCTCCTTCTGCTAT 59.151 40.000 0.00 0.00 0.00 2.97
33 34 7.019388 ACCTTGATAATCCTCCTTCTGCTATA 58.981 38.462 0.00 0.00 0.00 1.31
34 35 7.038658 ACCTTGATAATCCTCCTTCTGCTATAC 60.039 40.741 0.00 0.00 0.00 1.47
35 36 7.038729 CCTTGATAATCCTCCTTCTGCTATACA 60.039 40.741 0.00 0.00 0.00 2.29
36 37 7.855784 TGATAATCCTCCTTCTGCTATACAA 57.144 36.000 0.00 0.00 0.00 2.41
37 38 8.441311 TGATAATCCTCCTTCTGCTATACAAT 57.559 34.615 0.00 0.00 0.00 2.71
38 39 8.535335 TGATAATCCTCCTTCTGCTATACAATC 58.465 37.037 0.00 0.00 0.00 2.67
39 40 5.753721 ATCCTCCTTCTGCTATACAATCC 57.246 43.478 0.00 0.00 0.00 3.01
40 41 3.574396 TCCTCCTTCTGCTATACAATCCG 59.426 47.826 0.00 0.00 0.00 4.18
41 42 3.574396 CCTCCTTCTGCTATACAATCCGA 59.426 47.826 0.00 0.00 0.00 4.55
42 43 4.221703 CCTCCTTCTGCTATACAATCCGAT 59.778 45.833 0.00 0.00 0.00 4.18
43 44 5.392767 TCCTTCTGCTATACAATCCGATC 57.607 43.478 0.00 0.00 0.00 3.69
44 45 4.220821 TCCTTCTGCTATACAATCCGATCC 59.779 45.833 0.00 0.00 0.00 3.36
45 46 4.499183 CTTCTGCTATACAATCCGATCCC 58.501 47.826 0.00 0.00 0.00 3.85
46 47 3.779444 TCTGCTATACAATCCGATCCCT 58.221 45.455 0.00 0.00 0.00 4.20
47 48 3.511540 TCTGCTATACAATCCGATCCCTG 59.488 47.826 0.00 0.00 0.00 4.45
48 49 2.028112 TGCTATACAATCCGATCCCTGC 60.028 50.000 0.00 0.00 0.00 4.85
49 50 2.234908 GCTATACAATCCGATCCCTGCT 59.765 50.000 0.00 0.00 0.00 4.24
50 51 3.677424 GCTATACAATCCGATCCCTGCTC 60.677 52.174 0.00 0.00 0.00 4.26
51 52 2.088104 TACAATCCGATCCCTGCTCT 57.912 50.000 0.00 0.00 0.00 4.09
52 53 1.207791 ACAATCCGATCCCTGCTCTT 58.792 50.000 0.00 0.00 0.00 2.85
53 54 2.398588 ACAATCCGATCCCTGCTCTTA 58.601 47.619 0.00 0.00 0.00 2.10
54 55 2.103263 ACAATCCGATCCCTGCTCTTAC 59.897 50.000 0.00 0.00 0.00 2.34
55 56 2.088104 ATCCGATCCCTGCTCTTACA 57.912 50.000 0.00 0.00 0.00 2.41
56 57 1.403814 TCCGATCCCTGCTCTTACAG 58.596 55.000 0.00 0.00 37.42 2.74
57 58 1.115467 CCGATCCCTGCTCTTACAGT 58.885 55.000 0.00 0.00 35.83 3.55
78 81 2.942376 TGAGCAAAGTGAAAGCGAAAGA 59.058 40.909 0.00 0.00 0.00 2.52
93 96 2.529632 GAAAGAGATGGCAAAACCCCT 58.470 47.619 0.00 0.00 37.83 4.79
167 171 4.489737 TCCACTATCAAGGGATAACGGAT 58.510 43.478 0.00 0.00 35.64 4.18
248 255 7.412853 AAGGTAAAAGTTCTAGCAAACCAAA 57.587 32.000 0.00 0.00 0.00 3.28
249 256 7.039313 AGGTAAAAGTTCTAGCAAACCAAAG 57.961 36.000 0.00 0.00 0.00 2.77
250 257 5.690409 GGTAAAAGTTCTAGCAAACCAAAGC 59.310 40.000 0.00 0.00 0.00 3.51
287 299 1.339610 CCTCGTCTAAGCTAGCAGCAT 59.660 52.381 18.83 2.46 45.56 3.79
288 300 2.606795 CCTCGTCTAAGCTAGCAGCATC 60.607 54.545 18.83 3.44 45.56 3.91
289 301 1.338337 TCGTCTAAGCTAGCAGCATCC 59.662 52.381 18.83 0.00 45.56 3.51
314 326 8.515414 CCGATAAAAGTTTTCCATCTCTTTCTT 58.485 33.333 3.60 0.00 31.12 2.52
347 364 3.036091 CCCTCCGTTCCTAAATACTCCA 58.964 50.000 0.00 0.00 0.00 3.86
354 372 8.660295 TCCGTTCCTAAATACTCCATATGTAT 57.340 34.615 1.24 0.00 32.60 2.29
392 410 6.908870 ACTACGTACGAATGTACATAGACA 57.091 37.500 24.41 0.00 45.60 3.41
429 447 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
431 449 2.677836 TCACTCATTTTGCTCCGTATGC 59.322 45.455 0.00 0.00 0.00 3.14
433 451 2.679837 ACTCATTTTGCTCCGTATGCAG 59.320 45.455 0.00 0.00 41.71 4.41
435 453 2.677836 TCATTTTGCTCCGTATGCAGTC 59.322 45.455 0.00 0.00 41.71 3.51
436 454 1.448985 TTTTGCTCCGTATGCAGTCC 58.551 50.000 0.00 0.00 41.71 3.85
437 455 0.323302 TTTGCTCCGTATGCAGTCCA 59.677 50.000 0.00 0.00 41.71 4.02
438 456 0.541392 TTGCTCCGTATGCAGTCCAT 59.459 50.000 0.00 0.00 41.71 3.41
440 458 1.970640 TGCTCCGTATGCAGTCCATAT 59.029 47.619 0.00 0.00 38.60 1.78
441 459 2.368548 TGCTCCGTATGCAGTCCATATT 59.631 45.455 0.00 0.00 38.60 1.28
442 460 3.576550 TGCTCCGTATGCAGTCCATATTA 59.423 43.478 0.00 0.00 38.60 0.98
443 461 4.177026 GCTCCGTATGCAGTCCATATTAG 58.823 47.826 0.00 0.00 38.60 1.73
444 462 4.322049 GCTCCGTATGCAGTCCATATTAGT 60.322 45.833 0.00 0.00 38.60 2.24
445 463 5.134202 TCCGTATGCAGTCCATATTAGTG 57.866 43.478 0.00 0.00 38.60 2.74
446 464 4.587262 TCCGTATGCAGTCCATATTAGTGT 59.413 41.667 0.00 0.00 38.60 3.55
447 465 4.923871 CCGTATGCAGTCCATATTAGTGTC 59.076 45.833 0.00 0.00 38.60 3.67
448 466 5.279006 CCGTATGCAGTCCATATTAGTGTCT 60.279 44.000 0.00 0.00 38.60 3.41
449 467 5.859114 CGTATGCAGTCCATATTAGTGTCTC 59.141 44.000 0.00 0.00 38.60 3.36
450 468 6.294231 CGTATGCAGTCCATATTAGTGTCTCT 60.294 42.308 0.00 0.00 38.60 3.10
451 469 7.094762 CGTATGCAGTCCATATTAGTGTCTCTA 60.095 40.741 0.00 0.00 38.60 2.43
452 470 7.603180 ATGCAGTCCATATTAGTGTCTCTAA 57.397 36.000 0.00 0.00 41.98 2.10
453 471 7.418337 TGCAGTCCATATTAGTGTCTCTAAA 57.582 36.000 0.00 0.00 41.25 1.85
454 472 7.847096 TGCAGTCCATATTAGTGTCTCTAAAA 58.153 34.615 0.00 0.00 41.25 1.52
455 473 8.318412 TGCAGTCCATATTAGTGTCTCTAAAAA 58.682 33.333 0.00 0.00 41.25 1.94
456 474 8.821894 GCAGTCCATATTAGTGTCTCTAAAAAG 58.178 37.037 0.00 0.00 41.25 2.27
466 484 9.962783 TTAGTGTCTCTAAAAAGACTTGTACTC 57.037 33.333 5.71 0.00 44.90 2.59
467 485 7.435305 AGTGTCTCTAAAAAGACTTGTACTCC 58.565 38.462 5.71 0.00 44.90 3.85
468 486 7.069578 AGTGTCTCTAAAAAGACTTGTACTCCA 59.930 37.037 5.71 0.00 44.90 3.86
469 487 7.873505 GTGTCTCTAAAAAGACTTGTACTCCAT 59.126 37.037 5.71 0.00 44.90 3.41
470 488 8.088981 TGTCTCTAAAAAGACTTGTACTCCATC 58.911 37.037 5.71 0.00 44.90 3.51
471 489 7.546316 GTCTCTAAAAAGACTTGTACTCCATCC 59.454 40.741 0.00 0.00 42.01 3.51
472 490 6.395629 TCTAAAAAGACTTGTACTCCATCCG 58.604 40.000 0.00 0.00 0.00 4.18
473 491 4.618920 AAAAGACTTGTACTCCATCCGT 57.381 40.909 0.00 0.00 0.00 4.69
474 492 3.870633 AAGACTTGTACTCCATCCGTC 57.129 47.619 0.00 0.00 0.00 4.79
475 493 2.100989 AGACTTGTACTCCATCCGTCC 58.899 52.381 0.00 0.00 0.00 4.79
476 494 1.136500 GACTTGTACTCCATCCGTCCC 59.864 57.143 0.00 0.00 0.00 4.46
477 495 1.191535 CTTGTACTCCATCCGTCCCA 58.808 55.000 0.00 0.00 0.00 4.37
478 496 1.553248 CTTGTACTCCATCCGTCCCAA 59.447 52.381 0.00 0.00 0.00 4.12
479 497 1.646912 TGTACTCCATCCGTCCCAAA 58.353 50.000 0.00 0.00 0.00 3.28
480 498 1.979308 TGTACTCCATCCGTCCCAAAA 59.021 47.619 0.00 0.00 0.00 2.44
481 499 2.574369 TGTACTCCATCCGTCCCAAAAT 59.426 45.455 0.00 0.00 0.00 1.82
482 500 2.899303 ACTCCATCCGTCCCAAAATT 57.101 45.000 0.00 0.00 0.00 1.82
483 501 2.723273 ACTCCATCCGTCCCAAAATTC 58.277 47.619 0.00 0.00 0.00 2.17
484 502 2.308866 ACTCCATCCGTCCCAAAATTCT 59.691 45.455 0.00 0.00 0.00 2.40
485 503 3.245264 ACTCCATCCGTCCCAAAATTCTT 60.245 43.478 0.00 0.00 0.00 2.52
486 504 3.088532 TCCATCCGTCCCAAAATTCTTG 58.911 45.455 0.00 0.00 0.00 3.02
487 505 2.825532 CCATCCGTCCCAAAATTCTTGT 59.174 45.455 0.00 0.00 0.00 3.16
488 506 3.119495 CCATCCGTCCCAAAATTCTTGTC 60.119 47.826 0.00 0.00 0.00 3.18
489 507 3.502123 TCCGTCCCAAAATTCTTGTCT 57.498 42.857 0.00 0.00 0.00 3.41
490 508 3.827722 TCCGTCCCAAAATTCTTGTCTT 58.172 40.909 0.00 0.00 0.00 3.01
491 509 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
492 510 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
493 511 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
494 512 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
495 513 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
496 514 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
497 515 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
498 516 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
499 517 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
500 518 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
532 550 9.628500 TGTATGTATCTAGTCACATCTTAGTGT 57.372 33.333 13.03 0.00 40.37 3.55
536 554 9.901172 TGTATCTAGTCACATCTTAGTGTTAGA 57.099 33.333 0.00 0.00 40.37 2.10
540 558 9.901172 TCTAGTCACATCTTAGTGTTAGATACA 57.099 33.333 0.00 0.00 40.37 2.29
544 562 8.959058 GTCACATCTTAGTGTTAGATACATTCG 58.041 37.037 0.00 0.00 39.39 3.34
545 563 8.683615 TCACATCTTAGTGTTAGATACATTCGT 58.316 33.333 0.00 0.00 39.39 3.85
546 564 9.946165 CACATCTTAGTGTTAGATACATTCGTA 57.054 33.333 0.00 0.00 39.39 3.43
591 609 4.376225 TTTTTGGAACGGAGGGAGTATT 57.624 40.909 0.00 0.00 0.00 1.89
592 610 4.376225 TTTTGGAACGGAGGGAGTATTT 57.624 40.909 0.00 0.00 0.00 1.40
593 611 5.502089 TTTTGGAACGGAGGGAGTATTTA 57.498 39.130 0.00 0.00 0.00 1.40
595 613 3.036091 TGGAACGGAGGGAGTATTTAGG 58.964 50.000 0.00 0.00 0.00 2.69
596 614 3.303049 GGAACGGAGGGAGTATTTAGGA 58.697 50.000 0.00 0.00 0.00 2.94
597 615 3.708121 GGAACGGAGGGAGTATTTAGGAA 59.292 47.826 0.00 0.00 0.00 3.36
598 616 4.442612 GGAACGGAGGGAGTATTTAGGAAC 60.443 50.000 0.00 0.00 0.00 3.62
599 617 2.692041 ACGGAGGGAGTATTTAGGAACG 59.308 50.000 0.00 0.00 0.00 3.95
600 618 2.035576 CGGAGGGAGTATTTAGGAACGG 59.964 54.545 0.00 0.00 0.00 4.44
601 619 3.303049 GGAGGGAGTATTTAGGAACGGA 58.697 50.000 0.00 0.00 0.00 4.69
602 620 3.321396 GGAGGGAGTATTTAGGAACGGAG 59.679 52.174 0.00 0.00 0.00 4.63
604 622 5.134725 AGGGAGTATTTAGGAACGGAGTA 57.865 43.478 0.00 0.00 45.00 2.59
605 623 5.522641 AGGGAGTATTTAGGAACGGAGTAA 58.477 41.667 0.00 0.00 45.00 2.24
606 624 5.597594 AGGGAGTATTTAGGAACGGAGTAAG 59.402 44.000 0.00 0.00 45.00 2.34
607 625 5.362143 GGGAGTATTTAGGAACGGAGTAAGT 59.638 44.000 0.00 0.00 45.00 2.24
608 626 6.547510 GGGAGTATTTAGGAACGGAGTAAGTA 59.452 42.308 0.00 0.00 45.00 2.24
609 627 7.255416 GGGAGTATTTAGGAACGGAGTAAGTAG 60.255 44.444 0.00 0.00 45.00 2.57
610 628 7.255416 GGAGTATTTAGGAACGGAGTAAGTAGG 60.255 44.444 0.00 0.00 45.00 3.18
611 629 7.349598 AGTATTTAGGAACGGAGTAAGTAGGA 58.650 38.462 0.00 0.00 45.00 2.94
612 630 6.712179 ATTTAGGAACGGAGTAAGTAGGAG 57.288 41.667 0.00 0.00 45.00 3.69
613 631 3.735720 AGGAACGGAGTAAGTAGGAGT 57.264 47.619 0.00 0.00 45.00 3.85
614 632 4.851639 AGGAACGGAGTAAGTAGGAGTA 57.148 45.455 0.00 0.00 45.00 2.59
615 633 5.385628 AGGAACGGAGTAAGTAGGAGTAT 57.614 43.478 0.00 0.00 45.00 2.12
616 634 6.506538 AGGAACGGAGTAAGTAGGAGTATA 57.493 41.667 0.00 0.00 45.00 1.47
617 635 7.089106 AGGAACGGAGTAAGTAGGAGTATAT 57.911 40.000 0.00 0.00 45.00 0.86
618 636 6.941436 AGGAACGGAGTAAGTAGGAGTATATG 59.059 42.308 0.00 0.00 45.00 1.78
619 637 6.150809 GGAACGGAGTAAGTAGGAGTATATGG 59.849 46.154 0.00 0.00 45.00 2.74
620 638 5.008980 ACGGAGTAAGTAGGAGTATATGGC 58.991 45.833 0.00 0.00 41.94 4.40
621 639 5.008331 CGGAGTAAGTAGGAGTATATGGCA 58.992 45.833 0.00 0.00 0.00 4.92
622 640 5.475909 CGGAGTAAGTAGGAGTATATGGCAA 59.524 44.000 0.00 0.00 0.00 4.52
632 650 7.158099 AGGAGTATATGGCAAAAAGACAAAC 57.842 36.000 0.00 0.00 39.98 2.93
750 768 0.181350 CTATGCTGTCACCCTTCCCC 59.819 60.000 0.00 0.00 0.00 4.81
753 791 1.384191 GCTGTCACCCTTCCCCATT 59.616 57.895 0.00 0.00 0.00 3.16
784 822 0.883833 GTGTTCACAAGGCCTGATGG 59.116 55.000 5.69 0.00 0.00 3.51
799 837 3.279434 CTGATGGTTTTACTACTGCCCC 58.721 50.000 0.00 0.00 0.00 5.80
821 859 6.113411 CCCCCAGTTTTGATTGTACTAGTAG 58.887 44.000 1.87 0.00 0.00 2.57
822 860 6.296259 CCCCCAGTTTTGATTGTACTAGTAGT 60.296 42.308 8.14 8.14 0.00 2.73
823 861 6.817140 CCCCAGTTTTGATTGTACTAGTAGTC 59.183 42.308 5.96 3.16 0.00 2.59
824 862 7.310485 CCCCAGTTTTGATTGTACTAGTAGTCT 60.310 40.741 5.96 0.00 0.00 3.24
825 863 7.545965 CCCAGTTTTGATTGTACTAGTAGTCTG 59.454 40.741 5.96 3.96 0.00 3.51
826 864 7.545965 CCAGTTTTGATTGTACTAGTAGTCTGG 59.454 40.741 5.96 9.19 0.00 3.86
827 865 8.088981 CAGTTTTGATTGTACTAGTAGTCTGGT 58.911 37.037 5.96 0.00 38.81 4.00
828 866 8.648693 AGTTTTGATTGTACTAGTAGTCTGGTT 58.351 33.333 5.96 0.00 36.75 3.67
829 867 9.918630 GTTTTGATTGTACTAGTAGTCTGGTTA 57.081 33.333 5.96 0.00 36.75 2.85
831 869 8.874744 TTGATTGTACTAGTAGTCTGGTTAGT 57.125 34.615 5.96 0.00 36.75 2.24
832 870 9.964354 TTGATTGTACTAGTAGTCTGGTTAGTA 57.036 33.333 5.96 0.00 36.75 1.82
929 967 1.692042 CTCAGCAGTCCCCCTCCAT 60.692 63.158 0.00 0.00 0.00 3.41
930 968 1.229951 TCAGCAGTCCCCCTCCATT 60.230 57.895 0.00 0.00 0.00 3.16
931 969 1.225704 CAGCAGTCCCCCTCCATTC 59.774 63.158 0.00 0.00 0.00 2.67
949 987 5.720371 CATTCCTGATGGTCTCTACCTAG 57.280 47.826 0.00 0.00 46.91 3.02
1051 1089 4.500116 GACGCCTCCCTGAGACGC 62.500 72.222 0.00 0.00 39.03 5.19
1065 1103 4.868116 ACGCCAACCAGCAACGGT 62.868 61.111 0.00 0.00 42.71 4.83
1096 1134 1.215382 CGATGGACCGCTCAAGTGA 59.785 57.895 0.00 0.00 0.00 3.41
1171 1209 0.179062 CCTCTCGGCCTTCTTCATGG 60.179 60.000 0.00 0.00 0.00 3.66
1201 1239 2.668632 GATCACCGGGGAACAGCA 59.331 61.111 12.35 0.00 0.00 4.41
1367 1411 6.980051 AATACAAGAACATCCTTCGGTAAC 57.020 37.500 0.00 0.00 0.00 2.50
1389 1433 3.567164 CCAACCATAGTCATCAATCTGCC 59.433 47.826 0.00 0.00 0.00 4.85
1392 1436 2.804527 CCATAGTCATCAATCTGCCACG 59.195 50.000 0.00 0.00 0.00 4.94
1495 1542 0.320771 GCGGAACTCACTCCACATGT 60.321 55.000 0.00 0.00 34.91 3.21
1751 1801 4.767409 AGGAAAAACTTGATCCAGCTTACC 59.233 41.667 0.00 0.00 35.62 2.85
1863 1913 9.101325 CAATAGAATTAGAACCCCTACAGGATA 57.899 37.037 0.00 0.00 38.24 2.59
1890 1940 2.169832 TCTACAAGTTGCACAGCCTC 57.830 50.000 1.81 0.00 0.00 4.70
2506 2559 0.326618 TTCCCTCTCCCCAGATGACC 60.327 60.000 0.00 0.00 0.00 4.02
2507 2560 2.136878 CCCTCTCCCCAGATGACCG 61.137 68.421 0.00 0.00 0.00 4.79
2508 2561 2.801631 CCTCTCCCCAGATGACCGC 61.802 68.421 0.00 0.00 0.00 5.68
2623 2676 5.028549 TGGTAGAATCAAGGATCTCAAGC 57.971 43.478 0.00 0.00 0.00 4.01
2627 2680 3.522750 AGAATCAAGGATCTCAAGCTGGT 59.477 43.478 0.00 0.00 0.00 4.00
2634 2687 1.888436 ATCTCAAGCTGGTTCCGCGA 61.888 55.000 8.23 0.00 0.00 5.87
2685 2738 3.266510 AGCTCATCTCCAACGCAAATA 57.733 42.857 0.00 0.00 0.00 1.40
2692 2745 3.476552 TCTCCAACGCAAATATCATCCC 58.523 45.455 0.00 0.00 0.00 3.85
2765 2818 2.839486 TCACAGCCAAGTAGAACCAG 57.161 50.000 0.00 0.00 0.00 4.00
2820 2873 6.034898 GGATGAAACTAAATGCAACCAATTCG 59.965 38.462 0.00 0.00 0.00 3.34
2886 2940 0.034756 ACCAACACAGCGTCATAGCA 59.965 50.000 0.00 0.00 40.15 3.49
3109 3210 9.719355 CAATGCCTTTACCTAACCTTTTAAAAT 57.281 29.630 0.09 0.00 0.00 1.82
3149 3250 9.754382 AAATGCATGATATAAACAAAGATGGTC 57.246 29.630 0.00 0.00 0.00 4.02
3163 3264 7.785033 ACAAAGATGGTCTGAATTTTGTTTCT 58.215 30.769 0.00 0.00 35.83 2.52
3192 3293 6.833041 TGAATTTTCTCCAGGTACTTGTACA 58.167 36.000 12.23 0.00 34.60 2.90
3240 3341 8.336801 AGGTATACTGGTCTGAATTTTGTTTC 57.663 34.615 2.25 0.00 0.00 2.78
3279 3382 3.090037 AGGTACTTGTACAGTCGAGCAT 58.910 45.455 12.23 0.00 36.88 3.79
3387 3490 7.530010 CAGCTTATATTACAGTGCAACACTTT 58.470 34.615 0.00 0.00 42.59 2.66
3482 3585 7.993183 TCCTATTTTGTAAGAAATCTAGGCCAG 59.007 37.037 5.01 0.00 30.17 4.85
3733 3837 3.950395 GGCCTGAATCTTGCTTATGAGTT 59.050 43.478 0.00 0.00 0.00 3.01
3811 3915 8.504812 AAACCAAGAATTGTAAGTTTTGCAAT 57.495 26.923 0.00 0.22 46.99 3.56
3857 3961 8.271231 CTGACTATCAGCTAAACGTGTATAAC 57.729 38.462 0.00 0.00 37.72 1.89
3858 3962 7.764331 TGACTATCAGCTAAACGTGTATAACA 58.236 34.615 0.00 0.00 0.00 2.41
3859 3963 7.699391 TGACTATCAGCTAAACGTGTATAACAC 59.301 37.037 0.00 0.01 45.26 3.32
3860 3964 6.976925 ACTATCAGCTAAACGTGTATAACACC 59.023 38.462 4.69 0.00 45.93 4.16
3861 3965 5.136816 TCAGCTAAACGTGTATAACACCA 57.863 39.130 4.69 0.00 45.93 4.17
3862 3966 4.925054 TCAGCTAAACGTGTATAACACCAC 59.075 41.667 4.69 0.00 45.93 4.16
3863 3967 4.092383 CAGCTAAACGTGTATAACACCACC 59.908 45.833 4.69 0.00 45.93 4.61
3864 3968 3.371898 GCTAAACGTGTATAACACCACCC 59.628 47.826 4.69 0.00 45.93 4.61
3865 3969 2.477845 AACGTGTATAACACCACCCC 57.522 50.000 4.69 0.00 45.93 4.95
3866 3970 0.614812 ACGTGTATAACACCACCCCC 59.385 55.000 4.69 0.00 45.93 5.40
3891 3995 2.177580 CACCCCGACACACACACAC 61.178 63.158 0.00 0.00 0.00 3.82
3892 3996 2.188207 CCCCGACACACACACACA 59.812 61.111 0.00 0.00 0.00 3.72
3893 3997 2.177580 CCCCGACACACACACACAC 61.178 63.158 0.00 0.00 0.00 3.82
3894 3998 1.448717 CCCGACACACACACACACA 60.449 57.895 0.00 0.00 0.00 3.72
3895 3999 1.701545 CCCGACACACACACACACAC 61.702 60.000 0.00 0.00 0.00 3.82
3896 4000 1.016653 CCGACACACACACACACACA 61.017 55.000 0.00 0.00 0.00 3.72
3897 4001 0.094558 CGACACACACACACACACAC 59.905 55.000 0.00 0.00 0.00 3.82
3898 4002 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
3899 4003 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3900 4004 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3901 4005 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3902 4006 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3903 4007 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3904 4008 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3905 4009 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3906 4010 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3907 4011 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3908 4012 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3909 4013 1.136000 CACACACACACACACACACAG 60.136 52.381 0.00 0.00 0.00 3.66
3910 4014 1.270571 ACACACACACACACACACAGA 60.271 47.619 0.00 0.00 0.00 3.41
3911 4015 1.394572 CACACACACACACACACAGAG 59.605 52.381 0.00 0.00 0.00 3.35
3912 4016 1.275010 ACACACACACACACACAGAGA 59.725 47.619 0.00 0.00 0.00 3.10
3913 4017 1.929169 CACACACACACACACAGAGAG 59.071 52.381 0.00 0.00 0.00 3.20
3914 4018 1.824852 ACACACACACACACAGAGAGA 59.175 47.619 0.00 0.00 0.00 3.10
3950 4054 8.621286 ACATTTTAGATCTTTCTCGTGTTTTGT 58.379 29.630 0.00 0.00 33.17 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.757149 GGAGGATTATCAAGGTTCAATCGG 59.243 45.833 0.00 0.00 0.00 4.18
1 2 5.615289 AGGAGGATTATCAAGGTTCAATCG 58.385 41.667 0.00 0.00 0.00 3.34
2 3 7.228308 CAGAAGGAGGATTATCAAGGTTCAATC 59.772 40.741 0.00 0.00 0.00 2.67
3 4 7.059156 CAGAAGGAGGATTATCAAGGTTCAAT 58.941 38.462 0.00 0.00 0.00 2.57
4 5 6.418101 CAGAAGGAGGATTATCAAGGTTCAA 58.582 40.000 0.00 0.00 0.00 2.69
5 6 5.630069 GCAGAAGGAGGATTATCAAGGTTCA 60.630 44.000 0.00 0.00 0.00 3.18
6 7 4.819088 GCAGAAGGAGGATTATCAAGGTTC 59.181 45.833 0.00 0.00 0.00 3.62
7 8 4.476479 AGCAGAAGGAGGATTATCAAGGTT 59.524 41.667 0.00 0.00 0.00 3.50
8 9 4.043596 AGCAGAAGGAGGATTATCAAGGT 58.956 43.478 0.00 0.00 0.00 3.50
9 10 4.703379 AGCAGAAGGAGGATTATCAAGG 57.297 45.455 0.00 0.00 0.00 3.61
10 11 7.901029 TGTATAGCAGAAGGAGGATTATCAAG 58.099 38.462 0.00 0.00 0.00 3.02
11 12 7.855784 TGTATAGCAGAAGGAGGATTATCAA 57.144 36.000 0.00 0.00 0.00 2.57
12 13 7.855784 TTGTATAGCAGAAGGAGGATTATCA 57.144 36.000 0.00 0.00 0.00 2.15
13 14 7.984617 GGATTGTATAGCAGAAGGAGGATTATC 59.015 40.741 0.00 0.00 0.00 1.75
14 15 7.364232 CGGATTGTATAGCAGAAGGAGGATTAT 60.364 40.741 0.00 0.00 0.00 1.28
15 16 6.071334 CGGATTGTATAGCAGAAGGAGGATTA 60.071 42.308 0.00 0.00 0.00 1.75
16 17 5.279708 CGGATTGTATAGCAGAAGGAGGATT 60.280 44.000 0.00 0.00 0.00 3.01
17 18 4.221703 CGGATTGTATAGCAGAAGGAGGAT 59.778 45.833 0.00 0.00 0.00 3.24
18 19 3.574396 CGGATTGTATAGCAGAAGGAGGA 59.426 47.826 0.00 0.00 0.00 3.71
19 20 3.574396 TCGGATTGTATAGCAGAAGGAGG 59.426 47.826 0.00 0.00 0.00 4.30
20 21 4.855715 TCGGATTGTATAGCAGAAGGAG 57.144 45.455 0.00 0.00 0.00 3.69
21 22 4.220821 GGATCGGATTGTATAGCAGAAGGA 59.779 45.833 0.00 0.00 0.00 3.36
22 23 4.499183 GGATCGGATTGTATAGCAGAAGG 58.501 47.826 0.00 0.00 0.00 3.46
23 24 4.221703 AGGGATCGGATTGTATAGCAGAAG 59.778 45.833 0.00 0.00 0.00 2.85
24 25 4.021104 CAGGGATCGGATTGTATAGCAGAA 60.021 45.833 0.00 0.00 0.00 3.02
25 26 3.511540 CAGGGATCGGATTGTATAGCAGA 59.488 47.826 0.00 0.00 0.00 4.26
26 27 3.854666 CAGGGATCGGATTGTATAGCAG 58.145 50.000 0.00 0.00 0.00 4.24
27 28 2.028112 GCAGGGATCGGATTGTATAGCA 60.028 50.000 0.00 0.00 0.00 3.49
28 29 2.234908 AGCAGGGATCGGATTGTATAGC 59.765 50.000 0.00 0.00 0.00 2.97
29 30 3.766591 AGAGCAGGGATCGGATTGTATAG 59.233 47.826 0.00 0.00 0.00 1.31
30 31 3.779444 AGAGCAGGGATCGGATTGTATA 58.221 45.455 0.00 0.00 0.00 1.47
31 32 2.614259 AGAGCAGGGATCGGATTGTAT 58.386 47.619 0.00 0.00 0.00 2.29
32 33 2.088104 AGAGCAGGGATCGGATTGTA 57.912 50.000 0.00 0.00 0.00 2.41
33 34 1.207791 AAGAGCAGGGATCGGATTGT 58.792 50.000 0.00 0.00 0.00 2.71
34 35 2.103094 TGTAAGAGCAGGGATCGGATTG 59.897 50.000 0.00 0.00 0.00 2.67
35 36 2.366916 CTGTAAGAGCAGGGATCGGATT 59.633 50.000 0.00 0.00 34.07 3.01
36 37 1.967066 CTGTAAGAGCAGGGATCGGAT 59.033 52.381 0.00 0.00 34.07 4.18
37 38 1.342076 ACTGTAAGAGCAGGGATCGGA 60.342 52.381 0.00 0.00 40.59 4.55
38 39 1.115467 ACTGTAAGAGCAGGGATCGG 58.885 55.000 0.00 0.00 40.59 4.18
39 40 1.751351 TCACTGTAAGAGCAGGGATCG 59.249 52.381 0.00 0.00 43.28 3.69
40 41 3.451141 CTCACTGTAAGAGCAGGGATC 57.549 52.381 0.00 0.00 46.47 3.36
48 49 5.559799 GCTTTCACTTTGCTCACTGTAAGAG 60.560 44.000 0.00 0.00 37.43 2.85
49 50 4.273480 GCTTTCACTTTGCTCACTGTAAGA 59.727 41.667 0.00 0.00 37.43 2.10
50 51 4.531332 GCTTTCACTTTGCTCACTGTAAG 58.469 43.478 0.00 0.00 42.29 2.34
51 52 3.002246 CGCTTTCACTTTGCTCACTGTAA 59.998 43.478 0.00 0.00 0.00 2.41
52 53 2.543848 CGCTTTCACTTTGCTCACTGTA 59.456 45.455 0.00 0.00 0.00 2.74
53 54 1.331756 CGCTTTCACTTTGCTCACTGT 59.668 47.619 0.00 0.00 0.00 3.55
54 55 1.599071 TCGCTTTCACTTTGCTCACTG 59.401 47.619 0.00 0.00 0.00 3.66
55 56 1.953559 TCGCTTTCACTTTGCTCACT 58.046 45.000 0.00 0.00 0.00 3.41
56 57 2.755836 TTCGCTTTCACTTTGCTCAC 57.244 45.000 0.00 0.00 0.00 3.51
57 58 2.942376 TCTTTCGCTTTCACTTTGCTCA 59.058 40.909 0.00 0.00 0.00 4.26
78 81 2.158325 TCTTGAAGGGGTTTTGCCATCT 60.158 45.455 0.00 0.00 39.65 2.90
93 96 7.510549 AAATGGAAACTCTTTCGATCTTGAA 57.489 32.000 0.00 0.00 37.15 2.69
117 120 7.870445 CCCATTTTTGGATCTTACGAAAAAGAA 59.130 33.333 0.00 0.00 39.40 2.52
118 121 7.014808 ACCCATTTTTGGATCTTACGAAAAAGA 59.985 33.333 0.00 0.00 39.40 2.52
119 122 7.151976 ACCCATTTTTGGATCTTACGAAAAAG 58.848 34.615 0.00 0.00 39.40 2.27
167 171 4.159321 TGGATGCTCTGTTTTGTTGTTTGA 59.841 37.500 0.00 0.00 0.00 2.69
248 255 2.039613 AGGCAGTCTTCTAGCAAAAGCT 59.960 45.455 0.00 0.00 0.00 3.74
249 256 2.418280 GAGGCAGTCTTCTAGCAAAAGC 59.582 50.000 0.00 0.00 0.00 3.51
250 257 2.670414 CGAGGCAGTCTTCTAGCAAAAG 59.330 50.000 0.00 0.00 0.00 2.27
262 269 1.268845 GCTAGCTTAGACGAGGCAGTC 60.269 57.143 7.70 5.18 41.23 3.51
263 270 0.741915 GCTAGCTTAGACGAGGCAGT 59.258 55.000 7.70 0.00 0.00 4.40
287 299 7.883311 AGAAAGAGATGGAAAACTTTTATCGGA 59.117 33.333 0.00 0.00 33.61 4.55
288 300 8.045176 AGAAAGAGATGGAAAACTTTTATCGG 57.955 34.615 0.00 0.00 33.61 4.18
289 301 9.548208 GAAGAAAGAGATGGAAAACTTTTATCG 57.452 33.333 0.00 0.00 33.61 2.92
314 326 3.703052 GGAACGGAGGGAGTAGTTAATGA 59.297 47.826 0.00 0.00 0.00 2.57
429 447 7.418337 TTTAGAGACACTAATATGGACTGCA 57.582 36.000 0.00 0.00 40.24 4.41
440 458 9.962783 GAGTACAAGTCTTTTTAGAGACACTAA 57.037 33.333 7.66 0.00 46.69 2.24
441 459 8.574737 GGAGTACAAGTCTTTTTAGAGACACTA 58.425 37.037 7.66 0.00 46.69 2.74
442 460 7.069578 TGGAGTACAAGTCTTTTTAGAGACACT 59.930 37.037 7.66 2.47 46.69 3.55
443 461 7.208080 TGGAGTACAAGTCTTTTTAGAGACAC 58.792 38.462 7.66 0.00 46.69 3.67
444 462 7.356089 TGGAGTACAAGTCTTTTTAGAGACA 57.644 36.000 7.66 0.00 46.69 3.41
445 463 7.546316 GGATGGAGTACAAGTCTTTTTAGAGAC 59.454 40.741 0.00 0.00 45.05 3.36
446 464 7.577046 CGGATGGAGTACAAGTCTTTTTAGAGA 60.577 40.741 0.00 0.00 0.00 3.10
447 465 6.531948 CGGATGGAGTACAAGTCTTTTTAGAG 59.468 42.308 0.00 0.00 0.00 2.43
448 466 6.014840 ACGGATGGAGTACAAGTCTTTTTAGA 60.015 38.462 0.00 0.00 0.00 2.10
449 467 6.164176 ACGGATGGAGTACAAGTCTTTTTAG 58.836 40.000 0.00 0.00 0.00 1.85
450 468 6.105397 ACGGATGGAGTACAAGTCTTTTTA 57.895 37.500 0.00 0.00 0.00 1.52
451 469 4.969484 ACGGATGGAGTACAAGTCTTTTT 58.031 39.130 0.00 0.00 0.00 1.94
452 470 4.562963 GGACGGATGGAGTACAAGTCTTTT 60.563 45.833 8.33 0.00 34.57 2.27
453 471 3.056035 GGACGGATGGAGTACAAGTCTTT 60.056 47.826 8.33 0.00 34.57 2.52
454 472 2.496470 GGACGGATGGAGTACAAGTCTT 59.504 50.000 8.33 0.00 34.57 3.01
455 473 2.100989 GGACGGATGGAGTACAAGTCT 58.899 52.381 8.33 0.00 34.57 3.24
456 474 1.136500 GGGACGGATGGAGTACAAGTC 59.864 57.143 0.00 1.59 33.89 3.01
457 475 1.192428 GGGACGGATGGAGTACAAGT 58.808 55.000 0.00 0.00 0.00 3.16
458 476 1.191535 TGGGACGGATGGAGTACAAG 58.808 55.000 0.00 0.00 0.00 3.16
459 477 1.646912 TTGGGACGGATGGAGTACAA 58.353 50.000 0.00 0.00 0.00 2.41
460 478 1.646912 TTTGGGACGGATGGAGTACA 58.353 50.000 0.00 0.00 0.00 2.90
461 479 2.773993 TTTTGGGACGGATGGAGTAC 57.226 50.000 0.00 0.00 0.00 2.73
462 480 3.521937 AGAATTTTGGGACGGATGGAGTA 59.478 43.478 0.00 0.00 0.00 2.59
463 481 2.308866 AGAATTTTGGGACGGATGGAGT 59.691 45.455 0.00 0.00 0.00 3.85
464 482 3.004752 AGAATTTTGGGACGGATGGAG 57.995 47.619 0.00 0.00 0.00 3.86
465 483 3.088532 CAAGAATTTTGGGACGGATGGA 58.911 45.455 0.00 0.00 0.00 3.41
466 484 2.825532 ACAAGAATTTTGGGACGGATGG 59.174 45.455 0.00 0.00 0.00 3.51
467 485 3.758554 AGACAAGAATTTTGGGACGGATG 59.241 43.478 0.00 0.00 0.00 3.51
468 486 4.034285 AGACAAGAATTTTGGGACGGAT 57.966 40.909 0.00 0.00 0.00 4.18
469 487 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
470 488 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
471 489 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
472 490 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
473 491 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
474 492 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
506 524 9.628500 ACACTAAGATGTGACTAGATACATACA 57.372 33.333 13.80 3.39 40.12 2.29
510 528 9.901172 TCTAACACTAAGATGTGACTAGATACA 57.099 33.333 0.00 1.16 40.12 2.29
514 532 9.901172 TGTATCTAACACTAAGATGTGACTAGA 57.099 33.333 0.00 7.41 40.12 2.43
518 536 8.959058 CGAATGTATCTAACACTAAGATGTGAC 58.041 37.037 1.47 0.00 42.09 3.67
519 537 8.683615 ACGAATGTATCTAACACTAAGATGTGA 58.316 33.333 1.47 0.00 42.09 3.58
520 538 8.858003 ACGAATGTATCTAACACTAAGATGTG 57.142 34.615 0.00 0.00 42.09 3.21
570 588 4.376225 AATACTCCCTCCGTTCCAAAAA 57.624 40.909 0.00 0.00 0.00 1.94
571 589 4.376225 AAATACTCCCTCCGTTCCAAAA 57.624 40.909 0.00 0.00 0.00 2.44
572 590 4.080751 CCTAAATACTCCCTCCGTTCCAAA 60.081 45.833 0.00 0.00 0.00 3.28
573 591 3.453353 CCTAAATACTCCCTCCGTTCCAA 59.547 47.826 0.00 0.00 0.00 3.53
574 592 3.036091 CCTAAATACTCCCTCCGTTCCA 58.964 50.000 0.00 0.00 0.00 3.53
575 593 3.303049 TCCTAAATACTCCCTCCGTTCC 58.697 50.000 0.00 0.00 0.00 3.62
576 594 4.691175 GTTCCTAAATACTCCCTCCGTTC 58.309 47.826 0.00 0.00 0.00 3.95
577 595 3.131755 CGTTCCTAAATACTCCCTCCGTT 59.868 47.826 0.00 0.00 0.00 4.44
578 596 2.692041 CGTTCCTAAATACTCCCTCCGT 59.308 50.000 0.00 0.00 0.00 4.69
591 609 5.184892 ACTCCTACTTACTCCGTTCCTAA 57.815 43.478 0.00 0.00 0.00 2.69
592 610 4.851639 ACTCCTACTTACTCCGTTCCTA 57.148 45.455 0.00 0.00 0.00 2.94
593 611 3.735720 ACTCCTACTTACTCCGTTCCT 57.264 47.619 0.00 0.00 0.00 3.36
595 613 6.349197 GCCATATACTCCTACTTACTCCGTTC 60.349 46.154 0.00 0.00 0.00 3.95
596 614 5.476254 GCCATATACTCCTACTTACTCCGTT 59.524 44.000 0.00 0.00 0.00 4.44
597 615 5.008980 GCCATATACTCCTACTTACTCCGT 58.991 45.833 0.00 0.00 0.00 4.69
598 616 5.008331 TGCCATATACTCCTACTTACTCCG 58.992 45.833 0.00 0.00 0.00 4.63
599 617 6.912951 TTGCCATATACTCCTACTTACTCC 57.087 41.667 0.00 0.00 0.00 3.85
600 618 9.262358 CTTTTTGCCATATACTCCTACTTACTC 57.738 37.037 0.00 0.00 0.00 2.59
601 619 8.989131 TCTTTTTGCCATATACTCCTACTTACT 58.011 33.333 0.00 0.00 0.00 2.24
602 620 9.043079 GTCTTTTTGCCATATACTCCTACTTAC 57.957 37.037 0.00 0.00 0.00 2.34
603 621 8.764558 TGTCTTTTTGCCATATACTCCTACTTA 58.235 33.333 0.00 0.00 0.00 2.24
604 622 7.630082 TGTCTTTTTGCCATATACTCCTACTT 58.370 34.615 0.00 0.00 0.00 2.24
605 623 7.195374 TGTCTTTTTGCCATATACTCCTACT 57.805 36.000 0.00 0.00 0.00 2.57
606 624 7.859325 TTGTCTTTTTGCCATATACTCCTAC 57.141 36.000 0.00 0.00 0.00 3.18
607 625 7.065324 CGTTTGTCTTTTTGCCATATACTCCTA 59.935 37.037 0.00 0.00 0.00 2.94
608 626 6.128007 CGTTTGTCTTTTTGCCATATACTCCT 60.128 38.462 0.00 0.00 0.00 3.69
609 627 6.027749 CGTTTGTCTTTTTGCCATATACTCC 58.972 40.000 0.00 0.00 0.00 3.85
610 628 6.837992 TCGTTTGTCTTTTTGCCATATACTC 58.162 36.000 0.00 0.00 0.00 2.59
611 629 6.811253 TCGTTTGTCTTTTTGCCATATACT 57.189 33.333 0.00 0.00 0.00 2.12
612 630 7.247728 TCATCGTTTGTCTTTTTGCCATATAC 58.752 34.615 0.00 0.00 0.00 1.47
613 631 7.384439 TCATCGTTTGTCTTTTTGCCATATA 57.616 32.000 0.00 0.00 0.00 0.86
614 632 6.266168 TCATCGTTTGTCTTTTTGCCATAT 57.734 33.333 0.00 0.00 0.00 1.78
615 633 5.697473 TCATCGTTTGTCTTTTTGCCATA 57.303 34.783 0.00 0.00 0.00 2.74
616 634 4.582701 TCATCGTTTGTCTTTTTGCCAT 57.417 36.364 0.00 0.00 0.00 4.40
617 635 4.037327 TCATCATCGTTTGTCTTTTTGCCA 59.963 37.500 0.00 0.00 0.00 4.92
618 636 4.545610 TCATCATCGTTTGTCTTTTTGCC 58.454 39.130 0.00 0.00 0.00 4.52
619 637 6.695292 AATCATCATCGTTTGTCTTTTTGC 57.305 33.333 0.00 0.00 0.00 3.68
632 650 6.309712 ACTGGCATCTAAAAATCATCATCG 57.690 37.500 0.00 0.00 0.00 3.84
769 807 2.380064 AAAACCATCAGGCCTTGTGA 57.620 45.000 0.00 0.00 39.06 3.58
770 808 3.157087 AGTAAAACCATCAGGCCTTGTG 58.843 45.455 0.00 4.57 39.06 3.33
799 837 7.545965 CAGACTACTAGTACAATCAAAACTGGG 59.454 40.741 0.00 0.00 0.00 4.45
814 852 5.192176 GGCAGTACTAACCAGACTACTAGT 58.808 45.833 0.00 0.00 0.00 2.57
818 856 3.130693 CAGGGCAGTACTAACCAGACTAC 59.869 52.174 15.22 0.00 0.00 2.73
821 859 1.900486 ACAGGGCAGTACTAACCAGAC 59.100 52.381 15.22 0.00 0.00 3.51
822 860 2.320681 ACAGGGCAGTACTAACCAGA 57.679 50.000 15.22 0.00 0.00 3.86
823 861 2.301870 TGAACAGGGCAGTACTAACCAG 59.698 50.000 15.22 10.63 0.00 4.00
824 862 2.038033 GTGAACAGGGCAGTACTAACCA 59.962 50.000 15.22 0.00 0.00 3.67
825 863 2.696506 GTGAACAGGGCAGTACTAACC 58.303 52.381 0.00 0.36 0.00 2.85
826 864 2.288640 ACGTGAACAGGGCAGTACTAAC 60.289 50.000 0.00 0.00 0.00 2.34
827 865 1.965643 ACGTGAACAGGGCAGTACTAA 59.034 47.619 0.00 0.00 0.00 2.24
828 866 1.542915 GACGTGAACAGGGCAGTACTA 59.457 52.381 0.00 0.00 0.00 1.82
829 867 0.317479 GACGTGAACAGGGCAGTACT 59.683 55.000 0.00 0.00 0.00 2.73
830 868 0.032952 TGACGTGAACAGGGCAGTAC 59.967 55.000 0.00 0.00 29.78 2.73
831 869 0.032952 GTGACGTGAACAGGGCAGTA 59.967 55.000 3.22 0.00 34.53 2.74
832 870 1.227556 GTGACGTGAACAGGGCAGT 60.228 57.895 3.22 0.00 34.53 4.40
949 987 2.355444 GCTCCGAGGTTACTAGTCAGTC 59.645 54.545 0.00 0.00 36.14 3.51
1014 1052 4.687215 GCCTGCTCAGCGTCACCA 62.687 66.667 0.00 0.00 0.00 4.17
1072 1110 4.514577 AGCGGTCCATCGGCGAAG 62.515 66.667 15.93 10.04 45.16 3.79
1077 1115 1.811266 CACTTGAGCGGTCCATCGG 60.811 63.158 12.85 0.39 0.00 4.18
1096 1134 4.756458 GGCACTGAGAGCTGCGCT 62.756 66.667 9.73 5.34 43.88 5.92
1101 1139 1.302351 GCACTTGGCACTGAGAGCT 60.302 57.895 1.24 0.00 43.97 4.09
1171 1209 1.933853 CGGTGATCGGAATTGAAGGAC 59.066 52.381 0.00 0.00 34.75 3.85
1227 1265 1.275291 CTGAAGAAGCCGTCCTTACCA 59.725 52.381 0.00 0.00 32.78 3.25
1367 1411 3.567164 GGCAGATTGATGACTATGGTTGG 59.433 47.826 0.00 0.00 0.00 3.77
1389 1433 2.320587 GGAACTGCTGACTGCCGTG 61.321 63.158 2.28 0.00 39.07 4.94
1392 1436 1.001641 ATGGGAACTGCTGACTGCC 60.002 57.895 1.50 0.00 42.00 4.85
1424 1471 6.432162 CCTGAATTTCATCTGGAGAAGTGAAA 59.568 38.462 0.00 7.53 39.95 2.69
1479 1526 1.071605 GCGACATGTGGAGTGAGTTC 58.928 55.000 12.54 0.00 0.00 3.01
1495 1542 0.109272 CTCTTGTTGTAGCTCGGCGA 60.109 55.000 10.14 10.14 0.00 5.54
1863 1913 5.565439 GCTGTGCAACTTGTAGAATGGAATT 60.565 40.000 0.00 0.00 37.07 2.17
1890 1940 6.142139 TCATGTCAAGCGTTACATTGAAAAG 58.858 36.000 0.00 0.00 37.19 2.27
2506 2559 0.094046 ATTTCTTCGTAAACGCCGCG 59.906 50.000 12.14 12.14 39.60 6.46
2507 2560 1.520368 CATTTCTTCGTAAACGCCGC 58.480 50.000 0.00 0.00 39.60 6.53
2508 2561 1.201987 CCCATTTCTTCGTAAACGCCG 60.202 52.381 0.00 0.00 39.60 6.46
2623 2676 2.664851 TTGCAGTCGCGGAACCAG 60.665 61.111 6.13 0.00 42.97 4.00
2634 2687 2.032681 GGAACGAGGGCTTGCAGT 59.967 61.111 0.00 0.00 0.00 4.40
2685 2738 0.776176 GAGGCATGGAAGGGGATGAT 59.224 55.000 0.00 0.00 0.00 2.45
2692 2745 3.152341 GTGAATATGGAGGCATGGAAGG 58.848 50.000 0.00 0.00 0.00 3.46
2765 2818 3.182972 GCATGAACAATGTGCACAAAGAC 59.817 43.478 25.72 17.01 38.65 3.01
2843 2896 8.522830 GGTAATTGAAAGAGATTGTCATTGGAA 58.477 33.333 0.00 0.00 0.00 3.53
2886 2940 1.434513 TTGTGCCCAGGTCCATTCCT 61.435 55.000 0.00 0.00 38.51 3.36
3028 3129 2.855209 AAGAGATGAACTGCAGTGCT 57.145 45.000 25.34 17.16 0.00 4.40
3029 3130 2.675348 GGTAAGAGATGAACTGCAGTGC 59.325 50.000 22.49 20.54 0.00 4.40
3163 3264 7.942341 ACAAGTACCTGGAGAAAATTCAACATA 59.058 33.333 0.00 0.00 0.00 2.29
3240 3341 8.454106 CAAGTACCTGGAGAAAATTCAACATAG 58.546 37.037 0.00 0.00 0.00 2.23
3387 3490 3.489416 GTGCAACTCGCGATATGTTATCA 59.511 43.478 10.36 9.19 46.97 2.15
3665 3769 4.655649 TCTTGGAGATAAGAGCAATGCCTA 59.344 41.667 0.00 0.00 33.08 3.93
3733 3837 4.574674 AGGAGCATTTACAGAACATCCA 57.425 40.909 0.00 0.00 0.00 3.41
3811 3915 3.577848 AGCCATGCCACAAGAAAATACAA 59.422 39.130 0.00 0.00 0.00 2.41
3872 3976 2.590575 GTGTGTGTGTCGGGGTGG 60.591 66.667 0.00 0.00 0.00 4.61
3874 3978 2.188469 GTGTGTGTGTGTCGGGGT 59.812 61.111 0.00 0.00 0.00 4.95
3891 3995 1.394572 CTCTGTGTGTGTGTGTGTGTG 59.605 52.381 0.00 0.00 0.00 3.82
3892 3996 1.275010 TCTCTGTGTGTGTGTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
3893 3997 1.929169 CTCTCTGTGTGTGTGTGTGTG 59.071 52.381 0.00 0.00 0.00 3.82
3894 3998 1.824852 TCTCTCTGTGTGTGTGTGTGT 59.175 47.619 0.00 0.00 0.00 3.72
3895 3999 2.099756 TCTCTCTCTGTGTGTGTGTGTG 59.900 50.000 0.00 0.00 0.00 3.82
3896 4000 2.360483 CTCTCTCTCTGTGTGTGTGTGT 59.640 50.000 0.00 0.00 0.00 3.72
3897 4001 2.620585 TCTCTCTCTCTGTGTGTGTGTG 59.379 50.000 0.00 0.00 0.00 3.82
3898 4002 2.937519 TCTCTCTCTCTGTGTGTGTGT 58.062 47.619 0.00 0.00 0.00 3.72
3899 4003 3.998099 TTCTCTCTCTCTGTGTGTGTG 57.002 47.619 0.00 0.00 0.00 3.82
3900 4004 5.543507 ATTTTCTCTCTCTCTGTGTGTGT 57.456 39.130 0.00 0.00 0.00 3.72
3901 4005 6.925718 TGTTATTTTCTCTCTCTCTGTGTGTG 59.074 38.462 0.00 0.00 0.00 3.82
3902 4006 7.055667 TGTTATTTTCTCTCTCTCTGTGTGT 57.944 36.000 0.00 0.00 0.00 3.72
3903 4007 8.545229 AATGTTATTTTCTCTCTCTCTGTGTG 57.455 34.615 0.00 0.00 0.00 3.82
3904 4008 9.566432 AAAATGTTATTTTCTCTCTCTCTGTGT 57.434 29.630 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.