Multiple sequence alignment - TraesCS6D01G347800

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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 TraesCS6D01G347800 chr6D 100.000 1913 0 0 1 1913 446228081 446229993 0.000000e+00 3533.0
1 TraesCS6D01G347800 chr6D 100.000 533 0 0 2201 2733 446230281 446230813 0.000000e+00 985.0
2 TraesCS6D01G347800 chr6D 91.008 367 29 3 447 809 470898284 470898650 2.450000e-135 492.0
3 TraesCS6D01G347800 chr6D 85.941 441 62 0 979 1419 446434845 446435285 3.190000e-129 472.0
4 TraesCS6D01G347800 chr6D 85.268 448 62 2 975 1418 445835054 445834607 2.480000e-125 459.0
5 TraesCS6D01G347800 chr6D 83.333 234 20 12 159 386 446092879 446092659 5.970000e-47 198.0
6 TraesCS6D01G347800 chr6D 92.941 85 2 2 1828 1912 446090436 446090356 1.330000e-23 121.0
7 TraesCS6D01G347800 chr6D 81.529 157 14 7 843 994 446092591 446092445 6.180000e-22 115.0
8 TraesCS6D01G347800 chr6D 87.755 49 6 0 102 150 114241829 114241781 1.060000e-04 58.4
9 TraesCS6D01G347800 chr6A 93.614 689 34 4 809 1497 592870232 592870910 0.000000e+00 1020.0
10 TraesCS6D01G347800 chr6A 83.841 1083 72 36 809 1847 592705483 592704460 0.000000e+00 935.0
11 TraesCS6D01G347800 chr6A 87.893 826 51 20 993 1816 592875731 592876509 0.000000e+00 926.0
12 TraesCS6D01G347800 chr6A 93.086 405 25 2 996 1397 593003129 593002725 8.430000e-165 590.0
13 TraesCS6D01G347800 chr6A 85.805 472 33 16 2272 2727 592876969 592877422 1.150000e-128 470.0
14 TraesCS6D01G347800 chr6A 82.796 279 28 13 146 417 592705752 592705487 5.890000e-57 231.0
15 TraesCS6D01G347800 chr6A 86.408 206 19 2 1707 1912 592871049 592871245 1.650000e-52 217.0
16 TraesCS6D01G347800 chr6A 89.344 122 6 1 1558 1672 592870932 592871053 2.190000e-31 147.0
17 TraesCS6D01G347800 chr6A 93.407 91 4 1 1825 1913 592876587 592876677 1.710000e-27 134.0
18 TraesCS6D01G347800 chr6A 93.750 64 4 0 1850 1913 592704068 592704005 2.240000e-16 97.1
19 TraesCS6D01G347800 chr6A 88.732 71 8 0 2203 2273 592876701 592876771 1.350000e-13 87.9
20 TraesCS6D01G347800 chr6A 100.000 46 0 0 400 445 592870194 592870239 4.850000e-13 86.1
21 TraesCS6D01G347800 chr6B 94.410 483 26 1 1028 1509 674407084 674407566 0.000000e+00 741.0
22 TraesCS6D01G347800 chr6B 90.994 533 35 9 991 1519 674380858 674381381 0.000000e+00 706.0
23 TraesCS6D01G347800 chr6B 93.719 398 24 1 996 1392 674558441 674558838 1.810000e-166 595.0
24 TraesCS6D01G347800 chr6B 93.315 359 22 2 1557 1913 674407566 674407924 1.860000e-146 529.0
25 TraesCS6D01G347800 chr6B 88.641 449 30 6 1 445 674404432 674404863 6.700000e-146 527.0
26 TraesCS6D01G347800 chr6B 87.339 466 36 11 2272 2733 674408218 674408664 1.880000e-141 512.0
27 TraesCS6D01G347800 chr6B 85.714 441 63 0 979 1419 674572947 674572507 1.480000e-127 466.0
28 TraesCS6D01G347800 chr6B 85.224 379 41 6 1517 1895 674381495 674381858 2.570000e-100 375.0
29 TraesCS6D01G347800 chr6B 89.167 240 17 5 1683 1913 674158931 674158692 9.570000e-75 291.0
30 TraesCS6D01G347800 chr6B 91.542 201 8 3 823 1019 674404874 674405069 4.490000e-68 268.0
31 TraesCS6D01G347800 chr6B 90.000 50 5 0 2222 2271 674158608 674158559 6.320000e-07 65.8
32 TraesCS6D01G347800 chr5B 93.923 362 18 2 447 808 532565770 532566127 6.660000e-151 544.0
33 TraesCS6D01G347800 chr7D 92.287 363 25 1 447 809 550885487 550885128 1.880000e-141 512.0
34 TraesCS6D01G347800 chr7D 91.160 362 28 2 447 808 106023144 106023501 3.160000e-134 488.0
35 TraesCS6D01G347800 chr7D 90.400 375 31 2 434 808 106311150 106311519 3.160000e-134 488.0
36 TraesCS6D01G347800 chr7D 91.525 354 27 1 456 809 532895872 532896222 4.090000e-133 484.0
37 TraesCS6D01G347800 chr3D 91.436 362 28 1 447 808 567114354 567114712 6.800000e-136 494.0
38 TraesCS6D01G347800 chrUn 91.111 360 28 2 450 809 27580936 27580581 4.090000e-133 484.0
39 TraesCS6D01G347800 chrUn 90.833 360 30 1 450 809 27572837 27572481 1.900000e-131 479.0
40 TraesCS6D01G347800 chr4D 97.436 39 1 0 99 137 503813730 503813692 1.760000e-07 67.6
41 TraesCS6D01G347800 chr2B 97.368 38 1 0 97 134 114505471 114505508 6.320000e-07 65.8
42 TraesCS6D01G347800 chr1D 91.304 46 4 0 97 142 383754699 383754654 2.270000e-06 63.9
43 TraesCS6D01G347800 chr1D 87.500 48 6 0 106 153 479748725 479748678 3.800000e-04 56.5
44 TraesCS6D01G347800 chr1A 89.583 48 5 0 106 153 576137065 576137018 8.170000e-06 62.1
45 TraesCS6D01G347800 chr1A 89.583 48 5 0 106 153 576201452 576201405 8.170000e-06 62.1
46 TraesCS6D01G347800 chr3A 82.812 64 9 2 97 158 702538863 702538926 3.800000e-04 56.5


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 TraesCS6D01G347800 chr6D 446228081 446230813 2732 False 2259.000000 3533 100.000000 1 2733 2 chr6D.!!$F3 2732
1 TraesCS6D01G347800 chr6A 592704005 592705752 1747 True 421.033333 935 86.795667 146 1913 3 chr6A.!!$R2 1767
2 TraesCS6D01G347800 chr6A 592875731 592877422 1691 False 404.475000 926 88.959250 993 2727 4 chr6A.!!$F2 1734
3 TraesCS6D01G347800 chr6A 592870194 592871245 1051 False 367.525000 1020 92.341500 400 1912 4 chr6A.!!$F1 1512
4 TraesCS6D01G347800 chr6B 674380858 674381858 1000 False 540.500000 706 88.109000 991 1895 2 chr6B.!!$F2 904
5 TraesCS6D01G347800 chr6B 674404432 674408664 4232 False 515.400000 741 91.049400 1 2733 5 chr6B.!!$F3 2732

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
786 814 0.033503 CCCCCTCGGTAAAATTGCCT 60.034 55.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 5217 0.526662 AGTAGTGCTTTCCTCGACGG 59.473 55.0 0.0 0.0 0.0 4.79 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 1.865865 GAAGCACAAGTCACTTCGGA 58.134 50.000 0.00 0.00 31.35 4.55
53 54 0.834612 AACACTTCGGAGTTCCCACA 59.165 50.000 0.00 0.00 32.54 4.17
69 70 2.237143 CCCACATAGACCACATGACAGT 59.763 50.000 0.00 0.00 0.00 3.55
73 74 5.105063 CACATAGACCACATGACAGTACTG 58.895 45.833 21.44 21.44 0.00 2.74
74 75 5.016831 ACATAGACCACATGACAGTACTGA 58.983 41.667 29.30 8.39 0.00 3.41
77 78 4.152647 AGACCACATGACAGTACTGAAGA 58.847 43.478 29.30 12.19 0.00 2.87
117 118 9.698617 GGCTAACAACTTTATACTAAATCAACG 57.301 33.333 0.00 0.00 0.00 4.10
150 154 6.840780 ATGGATCGGAAAGAACAATTTTCT 57.159 33.333 0.00 0.00 35.42 2.52
153 157 8.172352 TGGATCGGAAAGAACAATTTTCTTTA 57.828 30.769 19.37 10.83 45.59 1.85
154 158 8.296713 TGGATCGGAAAGAACAATTTTCTTTAG 58.703 33.333 19.37 17.06 45.59 1.85
155 159 8.512138 GGATCGGAAAGAACAATTTTCTTTAGA 58.488 33.333 19.37 19.72 45.59 2.10
156 160 9.548208 GATCGGAAAGAACAATTTTCTTTAGAG 57.452 33.333 19.37 15.39 45.59 2.43
157 161 8.671384 TCGGAAAGAACAATTTTCTTTAGAGA 57.329 30.769 19.37 16.57 45.59 3.10
173 177 7.423199 TCTTTAGAGATGTATCATAAACGCGT 58.577 34.615 5.58 5.58 0.00 6.01
211 215 2.464459 CGAAGCCAACATCGCCCTC 61.464 63.158 0.00 0.00 29.43 4.30
212 216 2.436646 AAGCCAACATCGCCCTCG 60.437 61.111 0.00 0.00 0.00 4.63
226 230 2.437359 CTCGGCCAAAGCTCCTGG 60.437 66.667 2.24 9.93 39.73 4.45
227 231 3.984193 CTCGGCCAAAGCTCCTGGG 62.984 68.421 14.89 3.23 39.73 4.45
229 233 4.766632 GGCCAAAGCTCCTGGGGG 62.767 72.222 14.89 0.00 39.73 5.40
231 235 3.665971 CCAAAGCTCCTGGGGGCT 61.666 66.667 8.39 8.39 40.85 5.19
290 297 5.050091 CGCACTCGCAATTCCTTTTCTATAT 60.050 40.000 0.00 0.00 38.40 0.86
291 298 6.511767 CGCACTCGCAATTCCTTTTCTATATT 60.512 38.462 0.00 0.00 38.40 1.28
292 299 7.307160 CGCACTCGCAATTCCTTTTCTATATTA 60.307 37.037 0.00 0.00 38.40 0.98
305 313 9.285770 CCTTTTCTATATTACAAAAAGTTCGCC 57.714 33.333 0.00 0.00 37.13 5.54
314 322 4.765273 ACAAAAAGTTCGCCCATTTCTTT 58.235 34.783 0.00 0.00 0.00 2.52
432 460 2.821366 GCGGCCACACTGATGGAG 60.821 66.667 2.24 2.00 43.02 3.86
435 463 2.042831 GGCCACACTGATGGAGCAC 61.043 63.158 0.00 0.00 43.02 4.40
436 464 1.002868 GCCACACTGATGGAGCACT 60.003 57.895 6.86 0.00 43.02 4.40
441 469 1.066573 ACACTGATGGAGCACTGCTAC 60.067 52.381 6.27 6.27 39.88 3.58
447 475 2.857186 TGGAGCACTGCTACATGAAA 57.143 45.000 12.28 0.00 45.48 2.69
448 476 2.703416 TGGAGCACTGCTACATGAAAG 58.297 47.619 12.28 0.00 45.48 2.62
450 478 2.616510 GGAGCACTGCTACATGAAAGGT 60.617 50.000 8.52 0.00 39.71 3.50
451 479 3.077359 GAGCACTGCTACATGAAAGGTT 58.923 45.455 2.71 0.00 39.88 3.50
453 481 3.891366 AGCACTGCTACATGAAAGGTTTT 59.109 39.130 0.21 0.00 36.99 2.43
454 482 3.983344 GCACTGCTACATGAAAGGTTTTG 59.017 43.478 0.00 0.00 28.09 2.44
455 483 4.549458 CACTGCTACATGAAAGGTTTTGG 58.451 43.478 0.00 0.00 28.09 3.28
456 484 4.037923 CACTGCTACATGAAAGGTTTTGGT 59.962 41.667 0.00 0.00 28.09 3.67
457 485 4.649218 ACTGCTACATGAAAGGTTTTGGTT 59.351 37.500 0.00 0.00 28.09 3.67
458 486 5.830991 ACTGCTACATGAAAGGTTTTGGTTA 59.169 36.000 0.00 0.00 28.09 2.85
459 487 6.079424 TGCTACATGAAAGGTTTTGGTTAC 57.921 37.500 0.00 0.00 28.09 2.50
460 488 5.010213 TGCTACATGAAAGGTTTTGGTTACC 59.990 40.000 0.00 0.00 35.85 2.85
461 489 4.577834 ACATGAAAGGTTTTGGTTACCG 57.422 40.909 0.00 0.00 40.69 4.02
462 490 3.319689 ACATGAAAGGTTTTGGTTACCGG 59.680 43.478 0.00 0.00 40.69 5.28
463 491 3.015675 TGAAAGGTTTTGGTTACCGGT 57.984 42.857 13.98 13.98 40.69 5.28
464 492 2.950975 TGAAAGGTTTTGGTTACCGGTC 59.049 45.455 12.40 0.00 40.69 4.79
465 493 1.596603 AAGGTTTTGGTTACCGGTCG 58.403 50.000 12.40 0.00 40.69 4.79
466 494 0.758123 AGGTTTTGGTTACCGGTCGA 59.242 50.000 12.40 0.00 40.69 4.20
467 495 1.140652 AGGTTTTGGTTACCGGTCGAA 59.859 47.619 12.40 0.00 40.69 3.71
468 496 1.946081 GGTTTTGGTTACCGGTCGAAA 59.054 47.619 12.40 6.74 0.00 3.46
469 497 2.553602 GGTTTTGGTTACCGGTCGAAAT 59.446 45.455 12.40 0.00 0.00 2.17
470 498 3.004629 GGTTTTGGTTACCGGTCGAAATT 59.995 43.478 12.40 0.00 0.00 1.82
471 499 4.499526 GGTTTTGGTTACCGGTCGAAATTT 60.500 41.667 12.40 0.00 0.00 1.82
472 500 4.486574 TTTGGTTACCGGTCGAAATTTC 57.513 40.909 12.40 8.20 0.00 2.17
487 515 5.582689 GAAATTTCGAGATTTCCCATGGT 57.417 39.130 23.99 0.00 39.16 3.55
488 516 5.965922 GAAATTTCGAGATTTCCCATGGTT 58.034 37.500 23.99 0.00 39.16 3.67
489 517 7.095695 GAAATTTCGAGATTTCCCATGGTTA 57.904 36.000 23.99 0.00 39.16 2.85
490 518 6.451064 AATTTCGAGATTTCCCATGGTTAC 57.549 37.500 11.73 0.00 0.00 2.50
491 519 3.553828 TCGAGATTTCCCATGGTTACC 57.446 47.619 11.73 0.00 0.00 2.85
492 520 2.159014 TCGAGATTTCCCATGGTTACCG 60.159 50.000 11.73 5.01 0.00 4.02
493 521 1.947456 GAGATTTCCCATGGTTACCGC 59.053 52.381 11.73 0.00 0.00 5.68
494 522 1.283613 AGATTTCCCATGGTTACCGCA 59.716 47.619 11.73 0.00 0.00 5.69
495 523 2.091885 AGATTTCCCATGGTTACCGCAT 60.092 45.455 11.73 0.00 0.00 4.73
496 524 3.137544 AGATTTCCCATGGTTACCGCATA 59.862 43.478 11.73 0.00 0.00 3.14
497 525 3.586470 TTTCCCATGGTTACCGCATAT 57.414 42.857 11.73 0.00 0.00 1.78
498 526 3.586470 TTCCCATGGTTACCGCATATT 57.414 42.857 11.73 0.00 0.00 1.28
499 527 3.586470 TCCCATGGTTACCGCATATTT 57.414 42.857 11.73 0.00 0.00 1.40
500 528 3.482436 TCCCATGGTTACCGCATATTTC 58.518 45.455 11.73 0.00 0.00 2.17
501 529 2.556622 CCCATGGTTACCGCATATTTCC 59.443 50.000 11.73 0.00 0.00 3.13
502 530 2.225491 CCATGGTTACCGCATATTTCCG 59.775 50.000 2.57 0.00 0.00 4.30
503 531 2.695127 TGGTTACCGCATATTTCCGT 57.305 45.000 0.00 0.00 0.00 4.69
504 532 2.281517 TGGTTACCGCATATTTCCGTG 58.718 47.619 0.00 0.00 0.00 4.94
505 533 1.003223 GGTTACCGCATATTTCCGTGC 60.003 52.381 0.00 0.00 37.97 5.34
506 534 1.003223 GTTACCGCATATTTCCGTGCC 60.003 52.381 0.00 0.00 38.08 5.01
507 535 0.533308 TACCGCATATTTCCGTGCCC 60.533 55.000 0.00 0.00 38.08 5.36
508 536 2.551912 CCGCATATTTCCGTGCCCC 61.552 63.158 0.00 0.00 38.08 5.80
509 537 1.525995 CGCATATTTCCGTGCCCCT 60.526 57.895 0.00 0.00 38.08 4.79
510 538 1.507141 CGCATATTTCCGTGCCCCTC 61.507 60.000 0.00 0.00 38.08 4.30
511 539 1.507141 GCATATTTCCGTGCCCCTCG 61.507 60.000 0.00 0.00 35.35 4.63
513 541 1.342672 ATATTTCCGTGCCCCTCGGT 61.343 55.000 4.36 0.00 46.86 4.69
514 542 0.687098 TATTTCCGTGCCCCTCGGTA 60.687 55.000 4.36 0.00 46.86 4.02
515 543 1.555477 ATTTCCGTGCCCCTCGGTAA 61.555 55.000 4.36 1.98 46.86 2.85
516 544 1.766625 TTTCCGTGCCCCTCGGTAAA 61.767 55.000 4.36 2.21 46.86 2.01
517 545 1.555477 TTCCGTGCCCCTCGGTAAAT 61.555 55.000 4.36 0.00 46.86 1.40
518 546 1.523032 CCGTGCCCCTCGGTAAATC 60.523 63.158 0.00 0.00 42.62 2.17
519 547 1.523032 CGTGCCCCTCGGTAAATCC 60.523 63.158 0.00 0.00 0.00 3.01
520 548 1.153025 GTGCCCCTCGGTAAATCCC 60.153 63.158 0.00 0.00 0.00 3.85
521 549 2.380285 TGCCCCTCGGTAAATCCCC 61.380 63.158 0.00 0.00 0.00 4.81
522 550 2.380285 GCCCCTCGGTAAATCCCCA 61.380 63.158 0.00 0.00 0.00 4.96
523 551 1.716028 GCCCCTCGGTAAATCCCCAT 61.716 60.000 0.00 0.00 0.00 4.00
524 552 1.737199 CCCCTCGGTAAATCCCCATA 58.263 55.000 0.00 0.00 0.00 2.74
525 553 1.350019 CCCCTCGGTAAATCCCCATAC 59.650 57.143 0.00 0.00 0.00 2.39
526 554 1.350019 CCCTCGGTAAATCCCCATACC 59.650 57.143 0.00 0.00 38.55 2.73
527 555 2.051692 CCTCGGTAAATCCCCATACCA 58.948 52.381 3.19 0.00 41.37 3.25
528 556 2.440253 CCTCGGTAAATCCCCATACCAA 59.560 50.000 3.19 0.00 41.37 3.67
529 557 3.496160 CCTCGGTAAATCCCCATACCAAG 60.496 52.174 3.19 0.00 41.37 3.61
530 558 2.158726 TCGGTAAATCCCCATACCAAGC 60.159 50.000 3.19 0.00 41.37 4.01
531 559 2.422235 CGGTAAATCCCCATACCAAGCA 60.422 50.000 3.19 0.00 41.37 3.91
532 560 3.637769 GGTAAATCCCCATACCAAGCAA 58.362 45.455 0.00 0.00 41.05 3.91
533 561 4.027437 GGTAAATCCCCATACCAAGCAAA 58.973 43.478 0.00 0.00 41.05 3.68
534 562 4.468153 GGTAAATCCCCATACCAAGCAAAA 59.532 41.667 0.00 0.00 41.05 2.44
535 563 5.046231 GGTAAATCCCCATACCAAGCAAAAA 60.046 40.000 0.00 0.00 41.05 1.94
613 641 9.911788 AATCTAATTAATGTCATGAGAGTTGGT 57.088 29.630 0.00 0.00 0.00 3.67
614 642 9.911788 ATCTAATTAATGTCATGAGAGTTGGTT 57.088 29.630 0.00 0.00 0.00 3.67
615 643 9.383519 TCTAATTAATGTCATGAGAGTTGGTTC 57.616 33.333 0.00 0.00 0.00 3.62
616 644 9.388506 CTAATTAATGTCATGAGAGTTGGTTCT 57.611 33.333 0.00 0.00 0.00 3.01
617 645 7.621428 ATTAATGTCATGAGAGTTGGTTCTG 57.379 36.000 0.00 0.00 0.00 3.02
618 646 4.897509 ATGTCATGAGAGTTGGTTCTGA 57.102 40.909 0.00 0.00 0.00 3.27
619 647 4.897509 TGTCATGAGAGTTGGTTCTGAT 57.102 40.909 0.00 0.00 0.00 2.90
620 648 4.572909 TGTCATGAGAGTTGGTTCTGATG 58.427 43.478 0.00 0.00 39.32 3.07
621 649 4.040829 TGTCATGAGAGTTGGTTCTGATGT 59.959 41.667 0.00 0.00 39.10 3.06
622 650 4.391216 GTCATGAGAGTTGGTTCTGATGTG 59.609 45.833 0.00 0.00 39.10 3.21
623 651 4.040829 TCATGAGAGTTGGTTCTGATGTGT 59.959 41.667 0.00 0.00 39.10 3.72
624 652 4.422073 TGAGAGTTGGTTCTGATGTGTT 57.578 40.909 0.00 0.00 0.00 3.32
625 653 4.129380 TGAGAGTTGGTTCTGATGTGTTG 58.871 43.478 0.00 0.00 0.00 3.33
626 654 3.480470 AGAGTTGGTTCTGATGTGTTGG 58.520 45.455 0.00 0.00 0.00 3.77
627 655 3.117888 AGAGTTGGTTCTGATGTGTTGGT 60.118 43.478 0.00 0.00 0.00 3.67
628 656 4.102524 AGAGTTGGTTCTGATGTGTTGGTA 59.897 41.667 0.00 0.00 0.00 3.25
629 657 4.389374 AGTTGGTTCTGATGTGTTGGTAG 58.611 43.478 0.00 0.00 0.00 3.18
630 658 2.778299 TGGTTCTGATGTGTTGGTAGC 58.222 47.619 0.00 0.00 0.00 3.58
631 659 2.105649 TGGTTCTGATGTGTTGGTAGCA 59.894 45.455 0.00 0.00 0.00 3.49
632 660 3.146066 GGTTCTGATGTGTTGGTAGCAA 58.854 45.455 2.54 2.54 0.00 3.91
633 661 3.058224 GGTTCTGATGTGTTGGTAGCAAC 60.058 47.826 26.90 26.90 35.75 4.17
634 662 2.778299 TCTGATGTGTTGGTAGCAACC 58.222 47.619 29.46 21.76 46.98 3.77
635 663 2.371841 TCTGATGTGTTGGTAGCAACCT 59.628 45.455 29.46 17.06 46.91 3.50
636 664 2.744202 CTGATGTGTTGGTAGCAACCTC 59.256 50.000 29.46 22.99 46.91 3.85
637 665 1.732259 GATGTGTTGGTAGCAACCTCG 59.268 52.381 29.46 0.00 46.91 4.63
638 666 0.466543 TGTGTTGGTAGCAACCTCGT 59.533 50.000 29.46 0.00 46.91 4.18
639 667 1.134340 TGTGTTGGTAGCAACCTCGTT 60.134 47.619 29.46 0.00 46.91 3.85
640 668 1.529865 GTGTTGGTAGCAACCTCGTTC 59.470 52.381 29.46 12.62 46.91 3.95
641 669 1.154197 GTTGGTAGCAACCTCGTTCC 58.846 55.000 24.08 0.00 46.91 3.62
642 670 1.053424 TTGGTAGCAACCTCGTTCCT 58.947 50.000 2.54 0.00 46.91 3.36
643 671 0.320374 TGGTAGCAACCTCGTTCCTG 59.680 55.000 0.00 0.00 46.91 3.86
644 672 0.320697 GGTAGCAACCTCGTTCCTGT 59.679 55.000 0.00 0.00 43.08 4.00
645 673 1.270678 GGTAGCAACCTCGTTCCTGTT 60.271 52.381 0.00 0.00 43.08 3.16
646 674 2.490991 GTAGCAACCTCGTTCCTGTTT 58.509 47.619 0.00 0.00 0.00 2.83
647 675 2.052782 AGCAACCTCGTTCCTGTTTT 57.947 45.000 0.00 0.00 0.00 2.43
648 676 1.676006 AGCAACCTCGTTCCTGTTTTG 59.324 47.619 0.00 0.00 0.00 2.44
649 677 1.673920 GCAACCTCGTTCCTGTTTTGA 59.326 47.619 0.00 0.00 0.00 2.69
650 678 2.287009 GCAACCTCGTTCCTGTTTTGAG 60.287 50.000 0.00 0.00 0.00 3.02
651 679 3.202906 CAACCTCGTTCCTGTTTTGAGA 58.797 45.455 0.00 0.00 0.00 3.27
652 680 3.113260 ACCTCGTTCCTGTTTTGAGAG 57.887 47.619 0.00 0.00 0.00 3.20
653 681 2.224305 ACCTCGTTCCTGTTTTGAGAGG 60.224 50.000 7.01 7.01 46.59 3.69
654 682 2.224305 CCTCGTTCCTGTTTTGAGAGGT 60.224 50.000 0.79 0.00 39.02 3.85
655 683 3.060602 CTCGTTCCTGTTTTGAGAGGTC 58.939 50.000 0.00 0.00 0.00 3.85
656 684 2.698797 TCGTTCCTGTTTTGAGAGGTCT 59.301 45.455 0.00 0.00 0.00 3.85
657 685 3.060602 CGTTCCTGTTTTGAGAGGTCTC 58.939 50.000 0.00 0.00 43.15 3.36
658 686 3.243907 CGTTCCTGTTTTGAGAGGTCTCT 60.244 47.826 8.44 0.00 43.25 3.10
659 687 4.061596 GTTCCTGTTTTGAGAGGTCTCTG 58.938 47.826 5.09 0.00 43.25 3.35
660 688 2.634940 TCCTGTTTTGAGAGGTCTCTGG 59.365 50.000 5.09 0.00 43.25 3.86
661 689 2.370189 CCTGTTTTGAGAGGTCTCTGGT 59.630 50.000 5.09 0.00 43.25 4.00
662 690 3.181450 CCTGTTTTGAGAGGTCTCTGGTT 60.181 47.826 5.09 0.00 43.25 3.67
663 691 4.061596 CTGTTTTGAGAGGTCTCTGGTTC 58.938 47.826 5.09 0.00 43.25 3.62
664 692 3.060602 GTTTTGAGAGGTCTCTGGTTCG 58.939 50.000 5.09 0.00 43.25 3.95
665 693 2.287977 TTGAGAGGTCTCTGGTTCGA 57.712 50.000 5.09 0.00 43.25 3.71
666 694 2.287977 TGAGAGGTCTCTGGTTCGAA 57.712 50.000 5.09 0.00 43.25 3.71
667 695 2.808919 TGAGAGGTCTCTGGTTCGAAT 58.191 47.619 0.00 0.00 43.25 3.34
668 696 2.493675 TGAGAGGTCTCTGGTTCGAATG 59.506 50.000 0.00 0.00 43.25 2.67
669 697 2.494073 GAGAGGTCTCTGGTTCGAATGT 59.506 50.000 0.00 0.00 40.61 2.71
670 698 2.900546 AGAGGTCTCTGGTTCGAATGTT 59.099 45.455 0.00 0.00 38.75 2.71
671 699 3.056465 AGAGGTCTCTGGTTCGAATGTTC 60.056 47.826 0.00 0.00 38.75 3.18
672 700 2.632996 AGGTCTCTGGTTCGAATGTTCA 59.367 45.455 0.00 0.00 0.00 3.18
673 701 3.261897 AGGTCTCTGGTTCGAATGTTCAT 59.738 43.478 0.00 0.00 0.00 2.57
674 702 4.003648 GGTCTCTGGTTCGAATGTTCATT 58.996 43.478 0.00 0.00 0.00 2.57
675 703 4.093556 GGTCTCTGGTTCGAATGTTCATTC 59.906 45.833 13.56 13.56 0.00 2.67
676 704 4.690748 GTCTCTGGTTCGAATGTTCATTCA 59.309 41.667 20.57 8.97 0.00 2.57
677 705 5.352569 GTCTCTGGTTCGAATGTTCATTCAT 59.647 40.000 20.57 0.00 0.00 2.57
678 706 5.939883 TCTCTGGTTCGAATGTTCATTCATT 59.060 36.000 20.57 3.51 40.20 2.57
679 707 6.092670 TCTCTGGTTCGAATGTTCATTCATTC 59.907 38.462 20.57 8.72 45.70 2.67
746 774 9.204570 AATATTCTTGATATTTCTCGGTAACCG 57.795 33.333 0.00 0.00 41.70 4.44
769 797 2.416747 GTAACCACGTTTACCAGTCCC 58.583 52.381 0.00 0.00 0.00 4.46
770 798 0.109153 AACCACGTTTACCAGTCCCC 59.891 55.000 0.00 0.00 0.00 4.81
771 799 1.002990 CCACGTTTACCAGTCCCCC 60.003 63.158 0.00 0.00 0.00 5.40
772 800 1.486145 CCACGTTTACCAGTCCCCCT 61.486 60.000 0.00 0.00 0.00 4.79
773 801 0.036671 CACGTTTACCAGTCCCCCTC 60.037 60.000 0.00 0.00 0.00 4.30
774 802 1.217244 CGTTTACCAGTCCCCCTCG 59.783 63.158 0.00 0.00 0.00 4.63
775 803 1.600638 GTTTACCAGTCCCCCTCGG 59.399 63.158 0.00 0.00 0.00 4.63
776 804 1.159184 TTTACCAGTCCCCCTCGGT 59.841 57.895 0.00 0.00 35.46 4.69
777 805 0.413037 TTTACCAGTCCCCCTCGGTA 59.587 55.000 0.00 0.00 32.81 4.02
778 806 0.413037 TTACCAGTCCCCCTCGGTAA 59.587 55.000 0.00 0.00 40.74 2.85
779 807 0.413037 TACCAGTCCCCCTCGGTAAA 59.587 55.000 0.00 0.00 31.10 2.01
780 808 0.474273 ACCAGTCCCCCTCGGTAAAA 60.474 55.000 0.00 0.00 0.00 1.52
781 809 0.916809 CCAGTCCCCCTCGGTAAAAT 59.083 55.000 0.00 0.00 0.00 1.82
782 810 1.283905 CCAGTCCCCCTCGGTAAAATT 59.716 52.381 0.00 0.00 0.00 1.82
783 811 2.365582 CAGTCCCCCTCGGTAAAATTG 58.634 52.381 0.00 0.00 0.00 2.32
784 812 1.100510 GTCCCCCTCGGTAAAATTGC 58.899 55.000 0.00 0.00 0.00 3.56
785 813 0.033894 TCCCCCTCGGTAAAATTGCC 60.034 55.000 0.00 0.00 0.00 4.52
786 814 0.033503 CCCCCTCGGTAAAATTGCCT 60.034 55.000 0.00 0.00 0.00 4.75
787 815 1.618616 CCCCCTCGGTAAAATTGCCTT 60.619 52.381 0.00 0.00 0.00 4.35
788 816 2.357361 CCCCCTCGGTAAAATTGCCTTA 60.357 50.000 0.00 0.00 0.00 2.69
789 817 3.562182 CCCCTCGGTAAAATTGCCTTAT 58.438 45.455 0.00 0.00 0.00 1.73
790 818 3.958147 CCCCTCGGTAAAATTGCCTTATT 59.042 43.478 0.00 0.00 0.00 1.40
791 819 4.037565 CCCCTCGGTAAAATTGCCTTATTC 59.962 45.833 0.00 0.00 0.00 1.75
792 820 4.261031 CCCTCGGTAAAATTGCCTTATTCG 60.261 45.833 0.00 0.00 0.00 3.34
793 821 4.261031 CCTCGGTAAAATTGCCTTATTCGG 60.261 45.833 0.00 0.00 0.00 4.30
794 822 4.263435 TCGGTAAAATTGCCTTATTCGGT 58.737 39.130 0.00 0.00 0.00 4.69
795 823 5.426504 TCGGTAAAATTGCCTTATTCGGTA 58.573 37.500 0.00 0.00 0.00 4.02
796 824 5.879223 TCGGTAAAATTGCCTTATTCGGTAA 59.121 36.000 0.00 0.00 33.14 2.85
797 825 5.967088 CGGTAAAATTGCCTTATTCGGTAAC 59.033 40.000 0.00 0.00 31.36 2.50
798 826 6.267817 GGTAAAATTGCCTTATTCGGTAACC 58.732 40.000 0.00 0.00 31.36 2.85
799 827 5.986501 AAAATTGCCTTATTCGGTAACCA 57.013 34.783 0.00 0.00 31.36 3.67
800 828 5.986501 AAATTGCCTTATTCGGTAACCAA 57.013 34.783 0.00 0.00 31.36 3.67
801 829 5.986501 AATTGCCTTATTCGGTAACCAAA 57.013 34.783 0.00 0.00 31.36 3.28
802 830 5.986501 ATTGCCTTATTCGGTAACCAAAA 57.013 34.783 0.00 0.00 31.36 2.44
803 831 4.769859 TGCCTTATTCGGTAACCAAAAC 57.230 40.909 0.00 0.00 0.00 2.43
804 832 3.506844 TGCCTTATTCGGTAACCAAAACC 59.493 43.478 0.00 0.00 0.00 3.27
805 833 3.760151 GCCTTATTCGGTAACCAAAACCT 59.240 43.478 0.00 0.00 34.66 3.50
806 834 4.219070 GCCTTATTCGGTAACCAAAACCTT 59.781 41.667 0.00 0.00 34.66 3.50
807 835 5.705902 CCTTATTCGGTAACCAAAACCTTG 58.294 41.667 0.00 0.00 34.66 3.61
1012 1044 3.072468 GGACGATGGGGACGGTGA 61.072 66.667 0.00 0.00 34.93 4.02
1474 3571 3.619233 ACGTTAATGTGAGGTGCAAAC 57.381 42.857 0.00 0.00 0.00 2.93
1509 3616 2.479560 CGATGTAACTCTGTCGGATGCA 60.480 50.000 0.00 0.00 0.00 3.96
1511 3618 2.167662 TGTAACTCTGTCGGATGCAGA 58.832 47.619 0.00 0.00 40.28 4.26
1548 3771 1.661112 GCCTAATTGCGTCTCTGACAC 59.339 52.381 0.00 0.00 32.09 3.67
1549 3772 2.675317 GCCTAATTGCGTCTCTGACACT 60.675 50.000 0.00 0.00 32.09 3.55
1550 3773 3.428999 GCCTAATTGCGTCTCTGACACTA 60.429 47.826 0.00 0.00 32.09 2.74
1551 3774 4.737946 GCCTAATTGCGTCTCTGACACTAT 60.738 45.833 0.00 0.00 32.09 2.12
1552 3775 5.507482 GCCTAATTGCGTCTCTGACACTATA 60.507 44.000 0.00 0.00 32.09 1.31
1553 3776 6.504398 CCTAATTGCGTCTCTGACACTATAA 58.496 40.000 0.00 0.00 32.09 0.98
1554 3777 6.638873 CCTAATTGCGTCTCTGACACTATAAG 59.361 42.308 0.00 0.00 32.09 1.73
1555 3778 5.584253 ATTGCGTCTCTGACACTATAAGT 57.416 39.130 0.00 0.00 32.09 2.24
1604 3827 3.497640 CAGGATTCAAGAGGCGAATGATC 59.502 47.826 0.00 0.00 33.26 2.92
1649 3882 0.681175 AGTGAGCAATTGCCCCAAAC 59.319 50.000 26.45 16.52 43.38 2.93
1668 3901 2.616960 ACTCGCAGCAATTCGTGATAA 58.383 42.857 0.00 0.00 0.00 1.75
1724 3957 1.372251 AGTCAGACAGAAGCGTGCG 60.372 57.895 2.66 0.00 0.00 5.34
1821 4062 1.837439 TGGTAATGGATTCTCAGGCGT 59.163 47.619 0.00 0.00 0.00 5.68
1887 4590 5.241285 TGCAAAGTGAAGAATGCAACATCTA 59.759 36.000 0.00 0.00 45.04 1.98
2253 4956 2.352960 GGAAGTTGATTCGCCATCTGAC 59.647 50.000 0.00 0.00 38.95 3.51
2254 4957 2.768253 AGTTGATTCGCCATCTGACA 57.232 45.000 0.00 0.00 32.34 3.58
2256 4959 2.744202 AGTTGATTCGCCATCTGACAAC 59.256 45.455 0.00 0.00 37.14 3.32
2287 5189 9.847706 AGATTAATCATACAACTATGTCTAGCG 57.152 33.333 17.56 0.00 41.05 4.26
2296 5198 6.626441 ACAACTATGTCTAGCGTAACGCAAC 61.626 44.000 0.00 0.00 46.24 4.17
2315 5217 1.435515 CGAGACTAGTGCAGCCTCC 59.564 63.158 0.00 0.00 0.00 4.30
2389 5291 1.735571 CGATTTCCCGTTCATCCGTTT 59.264 47.619 0.00 0.00 0.00 3.60
2396 5298 2.550978 CCGTTCATCCGTTTGCTCTAT 58.449 47.619 0.00 0.00 0.00 1.98
2397 5299 2.936498 CCGTTCATCCGTTTGCTCTATT 59.064 45.455 0.00 0.00 0.00 1.73
2398 5300 3.242413 CCGTTCATCCGTTTGCTCTATTG 60.242 47.826 0.00 0.00 0.00 1.90
2399 5301 3.685058 GTTCATCCGTTTGCTCTATTGC 58.315 45.455 0.00 0.00 0.00 3.56
2400 5302 3.266510 TCATCCGTTTGCTCTATTGCT 57.733 42.857 0.00 0.00 0.00 3.91
2401 5303 3.198068 TCATCCGTTTGCTCTATTGCTC 58.802 45.455 0.00 0.00 0.00 4.26
2402 5304 3.118629 TCATCCGTTTGCTCTATTGCTCT 60.119 43.478 0.00 0.00 0.00 4.09
2403 5305 4.099419 TCATCCGTTTGCTCTATTGCTCTA 59.901 41.667 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.056660 ATGTGGGAACTCCGAAGTGT 58.943 50.000 0.00 0.00 38.76 3.55
43 44 3.197766 TCATGTGGTCTATGTGGGAACTC 59.802 47.826 0.00 0.00 0.00 3.01
53 54 5.952347 TCTTCAGTACTGTCATGTGGTCTAT 59.048 40.000 21.99 0.00 0.00 1.98
69 70 7.934313 AGCCCTAGAGTATATGATCTTCAGTA 58.066 38.462 0.00 0.00 0.00 2.74
73 74 8.582657 TGTTAGCCCTAGAGTATATGATCTTC 57.417 38.462 0.00 0.00 0.00 2.87
74 75 8.808092 GTTGTTAGCCCTAGAGTATATGATCTT 58.192 37.037 0.00 0.00 0.00 2.40
77 78 8.728596 AAGTTGTTAGCCCTAGAGTATATGAT 57.271 34.615 0.00 0.00 0.00 2.45
114 115 7.713507 TCTTTCCGATCCATATTAATTGTCGTT 59.286 33.333 0.00 0.00 0.00 3.85
117 118 8.836413 TGTTCTTTCCGATCCATATTAATTGTC 58.164 33.333 0.00 0.00 0.00 3.18
133 134 9.334693 CATCTCTAAAGAAAATTGTTCTTTCCG 57.665 33.333 16.15 10.14 44.75 4.30
150 154 8.961092 GTTACGCGTTTATGATACATCTCTAAA 58.039 33.333 20.78 0.00 0.00 1.85
152 156 7.641760 TGTTACGCGTTTATGATACATCTCTA 58.358 34.615 20.78 0.00 0.00 2.43
153 157 6.500910 TGTTACGCGTTTATGATACATCTCT 58.499 36.000 20.78 0.00 0.00 3.10
154 158 6.635641 TCTGTTACGCGTTTATGATACATCTC 59.364 38.462 20.78 0.00 0.00 2.75
155 159 6.500910 TCTGTTACGCGTTTATGATACATCT 58.499 36.000 20.78 0.00 0.00 2.90
156 160 6.742999 TCTGTTACGCGTTTATGATACATC 57.257 37.500 20.78 0.00 0.00 3.06
157 161 7.095774 GGAATCTGTTACGCGTTTATGATACAT 60.096 37.037 20.78 2.45 0.00 2.29
162 166 3.866910 GGGAATCTGTTACGCGTTTATGA 59.133 43.478 20.78 12.09 0.00 2.15
171 175 4.917998 CGTCTCATATGGGAATCTGTTACG 59.082 45.833 6.92 0.59 0.00 3.18
173 177 6.724893 TTCGTCTCATATGGGAATCTGTTA 57.275 37.500 6.92 0.00 0.00 2.41
212 216 4.766632 CCCCCAGGAGCTTTGGCC 62.767 72.222 11.65 0.00 39.73 5.36
226 230 3.721706 CAGTGTCCCTCCAGCCCC 61.722 72.222 0.00 0.00 0.00 5.80
227 231 2.069165 AAACAGTGTCCCTCCAGCCC 62.069 60.000 0.00 0.00 0.00 5.19
228 232 0.178990 AAAACAGTGTCCCTCCAGCC 60.179 55.000 0.00 0.00 0.00 4.85
229 233 1.239347 GAAAACAGTGTCCCTCCAGC 58.761 55.000 0.00 0.00 0.00 4.85
230 234 1.202651 ACGAAAACAGTGTCCCTCCAG 60.203 52.381 0.00 0.00 0.00 3.86
231 235 0.834612 ACGAAAACAGTGTCCCTCCA 59.165 50.000 0.00 0.00 0.00 3.86
290 297 5.523438 AGAAATGGGCGAACTTTTTGTAA 57.477 34.783 0.00 0.00 0.00 2.41
291 298 5.523438 AAGAAATGGGCGAACTTTTTGTA 57.477 34.783 0.00 0.00 0.00 2.41
292 299 4.400529 AAGAAATGGGCGAACTTTTTGT 57.599 36.364 0.00 0.00 0.00 2.83
420 447 0.321387 AGCAGTGCTCCATCAGTGTG 60.321 55.000 13.14 0.00 39.10 3.82
425 453 1.832998 TCATGTAGCAGTGCTCCATCA 59.167 47.619 23.64 16.46 33.04 3.07
432 460 3.923017 AAACCTTTCATGTAGCAGTGC 57.077 42.857 7.13 7.13 0.00 4.40
435 463 4.853924 ACCAAAACCTTTCATGTAGCAG 57.146 40.909 0.00 0.00 0.00 4.24
436 464 5.010213 GGTAACCAAAACCTTTCATGTAGCA 59.990 40.000 0.00 0.00 33.97 3.49
441 469 3.319689 ACCGGTAACCAAAACCTTTCATG 59.680 43.478 4.49 0.00 34.66 3.07
445 473 1.948834 CGACCGGTAACCAAAACCTTT 59.051 47.619 7.34 0.00 34.66 3.11
446 474 1.140652 TCGACCGGTAACCAAAACCTT 59.859 47.619 7.34 0.00 34.66 3.50
447 475 0.758123 TCGACCGGTAACCAAAACCT 59.242 50.000 7.34 0.00 34.66 3.50
448 476 1.592064 TTCGACCGGTAACCAAAACC 58.408 50.000 7.34 0.00 0.00 3.27
450 478 4.857799 GAAATTTCGACCGGTAACCAAAA 58.142 39.130 7.34 4.39 0.00 2.44
451 479 4.486574 GAAATTTCGACCGGTAACCAAA 57.513 40.909 7.34 4.53 0.00 3.28
465 493 5.582689 ACCATGGGAAATCTCGAAATTTC 57.417 39.130 18.09 14.57 42.41 2.17
466 494 6.127451 GGTAACCATGGGAAATCTCGAAATTT 60.127 38.462 18.09 0.00 0.00 1.82
467 495 5.359860 GGTAACCATGGGAAATCTCGAAATT 59.640 40.000 18.09 0.00 0.00 1.82
468 496 4.887655 GGTAACCATGGGAAATCTCGAAAT 59.112 41.667 18.09 0.00 0.00 2.17
469 497 4.266714 GGTAACCATGGGAAATCTCGAAA 58.733 43.478 18.09 0.00 0.00 3.46
470 498 3.680475 CGGTAACCATGGGAAATCTCGAA 60.680 47.826 18.09 0.00 0.00 3.71
471 499 2.159014 CGGTAACCATGGGAAATCTCGA 60.159 50.000 18.09 0.00 0.00 4.04
472 500 2.210116 CGGTAACCATGGGAAATCTCG 58.790 52.381 18.09 6.68 0.00 4.04
473 501 1.947456 GCGGTAACCATGGGAAATCTC 59.053 52.381 18.09 0.00 0.00 2.75
474 502 1.283613 TGCGGTAACCATGGGAAATCT 59.716 47.619 18.09 0.00 0.00 2.40
475 503 1.757682 TGCGGTAACCATGGGAAATC 58.242 50.000 18.09 0.00 0.00 2.17
476 504 2.452600 ATGCGGTAACCATGGGAAAT 57.547 45.000 18.09 1.59 0.00 2.17
477 505 3.586470 ATATGCGGTAACCATGGGAAA 57.414 42.857 18.09 0.00 0.00 3.13
478 506 3.586470 AATATGCGGTAACCATGGGAA 57.414 42.857 18.09 0.00 0.00 3.97
479 507 3.482436 GAAATATGCGGTAACCATGGGA 58.518 45.455 18.09 0.00 0.00 4.37
480 508 2.556622 GGAAATATGCGGTAACCATGGG 59.443 50.000 18.09 0.00 0.00 4.00
481 509 2.225491 CGGAAATATGCGGTAACCATGG 59.775 50.000 11.19 11.19 36.66 3.66
482 510 2.875933 ACGGAAATATGCGGTAACCATG 59.124 45.455 0.00 0.00 45.62 3.66
483 511 2.875933 CACGGAAATATGCGGTAACCAT 59.124 45.455 0.00 0.00 45.62 3.55
484 512 2.281517 CACGGAAATATGCGGTAACCA 58.718 47.619 0.00 0.00 45.62 3.67
485 513 1.003223 GCACGGAAATATGCGGTAACC 60.003 52.381 0.00 0.00 45.62 2.85
486 514 1.003223 GGCACGGAAATATGCGGTAAC 60.003 52.381 0.00 0.00 45.62 2.50
487 515 1.301423 GGCACGGAAATATGCGGTAA 58.699 50.000 0.00 0.00 45.62 2.85
488 516 0.533308 GGGCACGGAAATATGCGGTA 60.533 55.000 0.00 0.00 45.62 4.02
489 517 1.822186 GGGCACGGAAATATGCGGT 60.822 57.895 0.00 0.00 45.62 5.68
490 518 2.551912 GGGGCACGGAAATATGCGG 61.552 63.158 0.00 0.00 45.62 5.69
491 519 1.507141 GAGGGGCACGGAAATATGCG 61.507 60.000 0.00 0.00 46.87 4.73
492 520 1.507141 CGAGGGGCACGGAAATATGC 61.507 60.000 0.00 0.00 41.29 3.14
493 521 2.616969 CGAGGGGCACGGAAATATG 58.383 57.895 0.00 0.00 0.00 1.78
501 529 1.523032 GGATTTACCGAGGGGCACG 60.523 63.158 0.00 0.00 36.48 5.34
502 530 1.153025 GGGATTTACCGAGGGGCAC 60.153 63.158 0.00 0.00 40.11 5.01
503 531 2.380285 GGGGATTTACCGAGGGGCA 61.380 63.158 0.00 0.00 40.11 5.36
504 532 1.716028 ATGGGGATTTACCGAGGGGC 61.716 60.000 0.00 0.00 40.11 5.80
505 533 1.350019 GTATGGGGATTTACCGAGGGG 59.650 57.143 0.00 0.00 40.11 4.79
506 534 1.350019 GGTATGGGGATTTACCGAGGG 59.650 57.143 0.00 0.00 40.11 4.30
507 535 2.051692 TGGTATGGGGATTTACCGAGG 58.948 52.381 0.00 0.00 40.11 4.63
508 536 3.740115 CTTGGTATGGGGATTTACCGAG 58.260 50.000 2.75 2.75 40.11 4.63
509 537 2.158726 GCTTGGTATGGGGATTTACCGA 60.159 50.000 0.00 0.00 40.11 4.69
510 538 2.227194 GCTTGGTATGGGGATTTACCG 58.773 52.381 0.00 0.00 40.11 4.02
511 539 3.306472 TGCTTGGTATGGGGATTTACC 57.694 47.619 0.00 0.00 38.08 2.85
512 540 5.669164 TTTTGCTTGGTATGGGGATTTAC 57.331 39.130 0.00 0.00 0.00 2.01
587 615 9.911788 ACCAACTCTCATGACATTAATTAGATT 57.088 29.630 0.00 0.00 0.00 2.40
588 616 9.911788 AACCAACTCTCATGACATTAATTAGAT 57.088 29.630 0.00 0.00 0.00 1.98
589 617 9.383519 GAACCAACTCTCATGACATTAATTAGA 57.616 33.333 0.00 0.00 0.00 2.10
590 618 9.388506 AGAACCAACTCTCATGACATTAATTAG 57.611 33.333 0.00 0.00 0.00 1.73
591 619 9.166173 CAGAACCAACTCTCATGACATTAATTA 57.834 33.333 0.00 0.00 0.00 1.40
592 620 7.884877 TCAGAACCAACTCTCATGACATTAATT 59.115 33.333 0.00 0.00 0.00 1.40
593 621 7.397221 TCAGAACCAACTCTCATGACATTAAT 58.603 34.615 0.00 0.00 0.00 1.40
594 622 6.768483 TCAGAACCAACTCTCATGACATTAA 58.232 36.000 0.00 0.00 0.00 1.40
595 623 6.358974 TCAGAACCAACTCTCATGACATTA 57.641 37.500 0.00 0.00 0.00 1.90
596 624 5.233083 TCAGAACCAACTCTCATGACATT 57.767 39.130 0.00 0.00 0.00 2.71
597 625 4.897509 TCAGAACCAACTCTCATGACAT 57.102 40.909 0.00 0.00 0.00 3.06
598 626 4.040829 ACATCAGAACCAACTCTCATGACA 59.959 41.667 0.00 0.00 0.00 3.58
599 627 4.391216 CACATCAGAACCAACTCTCATGAC 59.609 45.833 0.00 0.00 0.00 3.06
600 628 4.040829 ACACATCAGAACCAACTCTCATGA 59.959 41.667 0.00 0.00 0.00 3.07
601 629 4.321718 ACACATCAGAACCAACTCTCATG 58.678 43.478 0.00 0.00 0.00 3.07
602 630 4.630644 ACACATCAGAACCAACTCTCAT 57.369 40.909 0.00 0.00 0.00 2.90
603 631 4.129380 CAACACATCAGAACCAACTCTCA 58.871 43.478 0.00 0.00 0.00 3.27
604 632 3.499918 CCAACACATCAGAACCAACTCTC 59.500 47.826 0.00 0.00 0.00 3.20
605 633 3.117888 ACCAACACATCAGAACCAACTCT 60.118 43.478 0.00 0.00 0.00 3.24
606 634 3.214328 ACCAACACATCAGAACCAACTC 58.786 45.455 0.00 0.00 0.00 3.01
607 635 3.297134 ACCAACACATCAGAACCAACT 57.703 42.857 0.00 0.00 0.00 3.16
608 636 3.058224 GCTACCAACACATCAGAACCAAC 60.058 47.826 0.00 0.00 0.00 3.77
609 637 3.146066 GCTACCAACACATCAGAACCAA 58.854 45.455 0.00 0.00 0.00 3.67
610 638 2.105649 TGCTACCAACACATCAGAACCA 59.894 45.455 0.00 0.00 0.00 3.67
611 639 2.778299 TGCTACCAACACATCAGAACC 58.222 47.619 0.00 0.00 0.00 3.62
625 653 0.320697 ACAGGAACGAGGTTGCTACC 59.679 55.000 9.54 9.54 42.02 3.18
626 654 2.165319 AACAGGAACGAGGTTGCTAC 57.835 50.000 2.17 0.00 42.02 3.58
627 655 2.875933 CAAAACAGGAACGAGGTTGCTA 59.124 45.455 2.17 0.00 42.02 3.49
628 656 1.676006 CAAAACAGGAACGAGGTTGCT 59.324 47.619 0.00 0.00 44.62 3.91
629 657 1.673920 TCAAAACAGGAACGAGGTTGC 59.326 47.619 0.00 0.00 34.11 4.17
630 658 3.202906 TCTCAAAACAGGAACGAGGTTG 58.797 45.455 0.00 0.00 0.00 3.77
631 659 3.467803 CTCTCAAAACAGGAACGAGGTT 58.532 45.455 0.00 0.00 0.00 3.50
632 660 2.224305 CCTCTCAAAACAGGAACGAGGT 60.224 50.000 0.00 0.00 33.60 3.85
633 661 2.224305 ACCTCTCAAAACAGGAACGAGG 60.224 50.000 0.00 0.00 41.68 4.63
634 662 3.060602 GACCTCTCAAAACAGGAACGAG 58.939 50.000 0.00 0.00 33.52 4.18
635 663 2.698797 AGACCTCTCAAAACAGGAACGA 59.301 45.455 0.00 0.00 33.52 3.85
636 664 3.060602 GAGACCTCTCAAAACAGGAACG 58.939 50.000 0.00 0.00 42.42 3.95
637 665 4.061596 CAGAGACCTCTCAAAACAGGAAC 58.938 47.826 5.13 0.00 45.21 3.62
638 666 3.071602 CCAGAGACCTCTCAAAACAGGAA 59.928 47.826 5.13 0.00 45.21 3.36
639 667 2.634940 CCAGAGACCTCTCAAAACAGGA 59.365 50.000 5.13 0.00 45.21 3.86
640 668 2.370189 ACCAGAGACCTCTCAAAACAGG 59.630 50.000 5.13 0.00 45.21 4.00
641 669 3.760580 ACCAGAGACCTCTCAAAACAG 57.239 47.619 5.13 0.00 45.21 3.16
642 670 3.492656 CGAACCAGAGACCTCTCAAAACA 60.493 47.826 5.13 0.00 45.21 2.83
643 671 3.060602 CGAACCAGAGACCTCTCAAAAC 58.939 50.000 5.13 0.00 45.21 2.43
644 672 2.963101 TCGAACCAGAGACCTCTCAAAA 59.037 45.455 5.13 0.00 45.21 2.44
645 673 2.594131 TCGAACCAGAGACCTCTCAAA 58.406 47.619 5.13 0.00 45.21 2.69
646 674 2.287977 TCGAACCAGAGACCTCTCAA 57.712 50.000 5.13 0.00 45.21 3.02
647 675 2.287977 TTCGAACCAGAGACCTCTCA 57.712 50.000 5.13 0.00 45.21 3.27
648 676 2.494073 ACATTCGAACCAGAGACCTCTC 59.506 50.000 0.00 0.00 43.17 3.20
649 677 2.530701 ACATTCGAACCAGAGACCTCT 58.469 47.619 0.00 0.00 41.37 3.69
650 678 3.254892 GAACATTCGAACCAGAGACCTC 58.745 50.000 0.00 0.00 0.00 3.85
651 679 2.632996 TGAACATTCGAACCAGAGACCT 59.367 45.455 0.00 0.00 0.00 3.85
652 680 3.040147 TGAACATTCGAACCAGAGACC 57.960 47.619 0.00 0.00 0.00 3.85
653 681 5.209944 GAATGAACATTCGAACCAGAGAC 57.790 43.478 0.00 0.00 37.97 3.36
749 777 2.416747 GGGACTGGTAAACGTGGTTAC 58.583 52.381 0.00 0.00 33.91 2.50
750 778 1.347378 GGGGACTGGTAAACGTGGTTA 59.653 52.381 0.00 0.00 0.00 2.85
751 779 0.109153 GGGGACTGGTAAACGTGGTT 59.891 55.000 0.00 0.00 0.00 3.67
752 780 1.756665 GGGGACTGGTAAACGTGGT 59.243 57.895 0.00 0.00 0.00 4.16
753 781 1.002990 GGGGGACTGGTAAACGTGG 60.003 63.158 0.00 0.00 0.00 4.94
754 782 0.036671 GAGGGGGACTGGTAAACGTG 60.037 60.000 0.00 0.00 0.00 4.49
755 783 1.538687 CGAGGGGGACTGGTAAACGT 61.539 60.000 0.00 0.00 0.00 3.99
756 784 1.217244 CGAGGGGGACTGGTAAACG 59.783 63.158 0.00 0.00 0.00 3.60
757 785 1.196766 ACCGAGGGGGACTGGTAAAC 61.197 60.000 0.00 0.00 39.97 2.01
758 786 0.413037 TACCGAGGGGGACTGGTAAA 59.587 55.000 0.00 0.00 39.97 2.01
759 787 0.413037 TTACCGAGGGGGACTGGTAA 59.587 55.000 0.00 0.00 38.93 2.85
760 788 0.413037 TTTACCGAGGGGGACTGGTA 59.587 55.000 0.00 0.00 39.97 3.25
761 789 0.474273 TTTTACCGAGGGGGACTGGT 60.474 55.000 0.00 0.00 39.97 4.00
762 790 0.916809 ATTTTACCGAGGGGGACTGG 59.083 55.000 0.00 0.00 39.97 4.00
763 791 2.365582 CAATTTTACCGAGGGGGACTG 58.634 52.381 0.00 0.00 39.97 3.51
764 792 1.340697 GCAATTTTACCGAGGGGGACT 60.341 52.381 0.00 0.00 39.97 3.85
765 793 1.100510 GCAATTTTACCGAGGGGGAC 58.899 55.000 0.00 0.00 39.97 4.46
766 794 0.033894 GGCAATTTTACCGAGGGGGA 60.034 55.000 0.00 0.00 39.97 4.81
767 795 0.033503 AGGCAATTTTACCGAGGGGG 60.034 55.000 0.00 0.00 43.62 5.40
768 796 1.847328 AAGGCAATTTTACCGAGGGG 58.153 50.000 0.00 0.00 40.11 4.79
769 797 4.261031 CGAATAAGGCAATTTTACCGAGGG 60.261 45.833 0.00 0.00 0.00 4.30
770 798 4.261031 CCGAATAAGGCAATTTTACCGAGG 60.261 45.833 0.00 0.00 0.00 4.63
771 799 4.334481 ACCGAATAAGGCAATTTTACCGAG 59.666 41.667 0.00 0.00 33.69 4.63
772 800 4.263435 ACCGAATAAGGCAATTTTACCGA 58.737 39.130 0.00 0.00 33.69 4.69
773 801 4.625972 ACCGAATAAGGCAATTTTACCG 57.374 40.909 0.00 0.00 33.69 4.02
774 802 6.127675 TGGTTACCGAATAAGGCAATTTTACC 60.128 38.462 0.00 0.00 33.69 2.85
775 803 6.854778 TGGTTACCGAATAAGGCAATTTTAC 58.145 36.000 0.00 0.00 33.69 2.01
776 804 7.463961 TTGGTTACCGAATAAGGCAATTTTA 57.536 32.000 0.00 0.00 33.69 1.52
777 805 5.986501 TGGTTACCGAATAAGGCAATTTT 57.013 34.783 0.00 0.00 33.69 1.82
778 806 5.986501 TTGGTTACCGAATAAGGCAATTT 57.013 34.783 0.00 0.00 33.69 1.82
779 807 5.986501 TTTGGTTACCGAATAAGGCAATT 57.013 34.783 0.00 0.00 33.69 2.32
780 808 5.336929 GGTTTTGGTTACCGAATAAGGCAAT 60.337 40.000 4.72 0.00 33.69 3.56
781 809 4.022155 GGTTTTGGTTACCGAATAAGGCAA 60.022 41.667 4.72 0.00 33.69 4.52
782 810 3.506844 GGTTTTGGTTACCGAATAAGGCA 59.493 43.478 4.72 0.00 33.69 4.75
783 811 3.760151 AGGTTTTGGTTACCGAATAAGGC 59.240 43.478 4.72 0.00 40.69 4.35
784 812 5.705902 CAAGGTTTTGGTTACCGAATAAGG 58.294 41.667 4.72 0.00 40.69 2.69
798 826 3.317711 TGTGACATGTAGCCAAGGTTTTG 59.682 43.478 0.00 0.00 0.00 2.44
799 827 3.561143 TGTGACATGTAGCCAAGGTTTT 58.439 40.909 0.00 0.00 0.00 2.43
800 828 3.222173 TGTGACATGTAGCCAAGGTTT 57.778 42.857 0.00 0.00 0.00 3.27
801 829 2.949177 TGTGACATGTAGCCAAGGTT 57.051 45.000 0.00 0.00 0.00 3.50
802 830 2.949177 TTGTGACATGTAGCCAAGGT 57.051 45.000 0.00 0.00 0.00 3.50
803 831 4.460382 AGAAATTGTGACATGTAGCCAAGG 59.540 41.667 0.00 0.00 0.00 3.61
804 832 5.633830 AGAAATTGTGACATGTAGCCAAG 57.366 39.130 0.00 0.00 0.00 3.61
805 833 7.826744 TGTATAGAAATTGTGACATGTAGCCAA 59.173 33.333 0.00 2.40 0.00 4.52
806 834 7.334858 TGTATAGAAATTGTGACATGTAGCCA 58.665 34.615 0.00 0.00 0.00 4.75
807 835 7.786178 TGTATAGAAATTGTGACATGTAGCC 57.214 36.000 0.00 0.00 0.00 3.93
910 938 3.512680 CGGTCCTGTGAAAGAGTGATAC 58.487 50.000 0.00 0.00 0.00 2.24
911 939 2.496070 CCGGTCCTGTGAAAGAGTGATA 59.504 50.000 0.00 0.00 0.00 2.15
912 940 1.276421 CCGGTCCTGTGAAAGAGTGAT 59.724 52.381 0.00 0.00 0.00 3.06
913 941 0.679505 CCGGTCCTGTGAAAGAGTGA 59.320 55.000 0.00 0.00 0.00 3.41
1044 3082 2.109126 GGACATCTGCGCCAGGTTC 61.109 63.158 4.18 0.00 31.51 3.62
1259 3297 1.676635 TGGTAGGTGTCGACGAGGG 60.677 63.158 11.62 0.00 0.00 4.30
1270 3326 3.379445 CGTGCTCCGGTGGTAGGT 61.379 66.667 0.00 0.00 0.00 3.08
1474 3571 5.520632 AGTTACATCGACGGATCAACATAG 58.479 41.667 0.00 0.00 31.51 2.23
1509 3616 3.118592 AGGCGTAAGTAGGTACGTAGTCT 60.119 47.826 0.00 0.00 46.74 3.24
1511 3618 3.268023 AGGCGTAAGTAGGTACGTAGT 57.732 47.619 0.00 0.00 46.74 2.73
1536 3759 4.886247 AGACTTATAGTGTCAGAGACGC 57.114 45.455 2.65 2.65 42.60 5.19
1551 3774 8.623903 GCCAATCAAATCAACATGATAGACTTA 58.376 33.333 0.00 0.00 35.76 2.24
1552 3775 7.123098 TGCCAATCAAATCAACATGATAGACTT 59.877 33.333 0.00 0.00 35.76 3.01
1553 3776 6.604396 TGCCAATCAAATCAACATGATAGACT 59.396 34.615 0.00 0.00 35.76 3.24
1554 3777 6.798482 TGCCAATCAAATCAACATGATAGAC 58.202 36.000 0.00 0.00 35.76 2.59
1555 3778 7.259882 GTTGCCAATCAAATCAACATGATAGA 58.740 34.615 0.00 0.00 35.76 1.98
1604 3827 1.238439 ACACTTTGACCTTGCGATGG 58.762 50.000 0.00 0.00 0.00 3.51
1649 3882 3.245990 TGATTATCACGAATTGCTGCGAG 59.754 43.478 0.00 0.00 0.00 5.03
1668 3901 2.643551 CAGTATCGTTGGCCCTTTGAT 58.356 47.619 0.00 0.79 0.00 2.57
1724 3957 4.142609 TGGGAAATCATCACTAGAGCAC 57.857 45.455 0.00 0.00 30.45 4.40
2204 4907 9.914131 AGCTTATGACCTTTTGAATTAGAAAAC 57.086 29.630 0.00 0.00 0.00 2.43
2215 4918 5.712152 ACTTCCAAGCTTATGACCTTTTG 57.288 39.130 0.00 0.00 0.00 2.44
2287 5189 2.248487 CACTAGTCTCGGTTGCGTTAC 58.752 52.381 0.00 0.00 0.00 2.50
2296 5198 3.609703 AGGCTGCACTAGTCTCGG 58.390 61.111 0.50 0.00 36.33 4.63
2315 5217 0.526662 AGTAGTGCTTTCCTCGACGG 59.473 55.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.