Multiple sequence alignment - TraesCS7A01G230600

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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 TraesCS7A01G230600 chr7A 100.000 2411 0 0 1 2411 201365975 201368385 0.000000e+00 4453
1 TraesCS7A01G230600 chr2D 98.417 1200 11 3 820 2015 272798636 272799831 0.000000e+00 2104
2 TraesCS7A01G230600 chr2D 90.179 784 63 13 48 821 639600956 639601735 0.000000e+00 1009
3 TraesCS7A01G230600 chr2D 94.878 410 12 5 2010 2411 272799885 272800293 1.220000e-177 632
4 TraesCS7A01G230600 chrUn 98.336 1202 12 6 820 2015 93416748 93417947 0.000000e+00 2102
5 TraesCS7A01G230600 chrUn 95.343 408 12 4 2010 2411 93418001 93418407 2.020000e-180 641
6 TraesCS7A01G230600 chrUn 95.343 408 12 4 2010 2411 407707068 407707474 2.020000e-180 641
7 TraesCS7A01G230600 chrUn 94.878 410 12 5 2010 2411 327661531 327661939 1.220000e-177 632
8 TraesCS7A01G230600 chr5D 98.336 1202 11 4 820 2015 560880067 560878869 0.000000e+00 2100
9 TraesCS7A01G230600 chr5D 90.525 781 57 17 48 822 526890964 526891733 0.000000e+00 1016
10 TraesCS7A01G230600 chr5D 95.343 408 12 4 2010 2411 560878815 560878409 2.020000e-180 641
11 TraesCS7A01G230600 chr5D 95.098 408 12 5 2010 2411 503212254 503211849 9.400000e-179 636
12 TraesCS7A01G230600 chr1D 97.757 1204 12 6 820 2015 144238301 144237105 0.000000e+00 2060
13 TraesCS7A01G230600 chr1D 95.343 408 12 4 2010 2411 144237051 144236645 2.020000e-180 641
14 TraesCS7A01G230600 chr3B 97.257 1203 21 9 820 2015 201522272 201521075 0.000000e+00 2028
15 TraesCS7A01G230600 chr3B 95.098 408 12 5 2010 2411 201521022 201520617 9.400000e-179 636
16 TraesCS7A01G230600 chr3B 83.913 230 22 7 600 823 777833096 777832876 3.140000e-49 206
17 TraesCS7A01G230600 chr6A 97.248 1199 19 3 820 2015 271185037 271183850 0.000000e+00 2019
18 TraesCS7A01G230600 chr3A 97.081 1199 20 6 820 2015 672914743 672915929 0.000000e+00 2006
19 TraesCS7A01G230600 chr3A 94.840 407 14 4 2010 2411 672915983 672916387 1.570000e-176 628
20 TraesCS7A01G230600 chr3A 90.598 117 9 2 707 823 354845977 354846091 1.150000e-33 154
21 TraesCS7A01G230600 chr4A 96.919 1201 20 7 820 2015 722779299 722780487 0.000000e+00 1997
22 TraesCS7A01G230600 chr4A 91.909 791 40 14 47 825 193120689 193119911 0.000000e+00 1085
23 TraesCS7A01G230600 chr4A 91.710 193 15 1 831 1022 114912381 114912189 1.420000e-67 267
24 TraesCS7A01G230600 chr1A 95.830 1199 32 7 820 2015 168443032 168444215 0.000000e+00 1921
25 TraesCS7A01G230600 chr1A 93.617 705 33 8 46 747 219307396 219308091 0.000000e+00 1042
26 TraesCS7A01G230600 chr5A 93.878 784 38 10 46 825 152958578 152957801 0.000000e+00 1173
27 TraesCS7A01G230600 chr5A 92.593 783 40 13 46 822 19895568 19896338 0.000000e+00 1109
28 TraesCS7A01G230600 chr2A 91.750 800 35 15 46 830 247054669 247053886 0.000000e+00 1083
29 TraesCS7A01G230600 chr7D 90.525 781 58 16 48 822 360949039 360949809 0.000000e+00 1018
30 TraesCS7A01G230600 chr7D 90.446 785 55 16 48 825 582910118 582909347 0.000000e+00 1016
31 TraesCS7A01G230600 chr2B 97.209 215 2 1 830 1044 83489112 83488902 6.340000e-96 361


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 TraesCS7A01G230600 chr7A 201365975 201368385 2410 False 4453.0 4453 100.0000 1 2411 1 chr7A.!!$F1 2410
1 TraesCS7A01G230600 chr2D 272798636 272800293 1657 False 1368.0 2104 96.6475 820 2411 2 chr2D.!!$F2 1591
2 TraesCS7A01G230600 chr2D 639600956 639601735 779 False 1009.0 1009 90.1790 48 821 1 chr2D.!!$F1 773
3 TraesCS7A01G230600 chrUn 93416748 93418407 1659 False 1371.5 2102 96.8395 820 2411 2 chrUn.!!$F3 1591
4 TraesCS7A01G230600 chr5D 560878409 560880067 1658 True 1370.5 2100 96.8395 820 2411 2 chr5D.!!$R2 1591
5 TraesCS7A01G230600 chr5D 526890964 526891733 769 False 1016.0 1016 90.5250 48 822 1 chr5D.!!$F1 774
6 TraesCS7A01G230600 chr1D 144236645 144238301 1656 True 1350.5 2060 96.5500 820 2411 2 chr1D.!!$R1 1591
7 TraesCS7A01G230600 chr3B 201520617 201522272 1655 True 1332.0 2028 96.1775 820 2411 2 chr3B.!!$R2 1591
8 TraesCS7A01G230600 chr6A 271183850 271185037 1187 True 2019.0 2019 97.2480 820 2015 1 chr6A.!!$R1 1195
9 TraesCS7A01G230600 chr3A 672914743 672916387 1644 False 1317.0 2006 95.9605 820 2411 2 chr3A.!!$F2 1591
10 TraesCS7A01G230600 chr4A 722779299 722780487 1188 False 1997.0 1997 96.9190 820 2015 1 chr4A.!!$F1 1195
11 TraesCS7A01G230600 chr4A 193119911 193120689 778 True 1085.0 1085 91.9090 47 825 1 chr4A.!!$R2 778
12 TraesCS7A01G230600 chr1A 168443032 168444215 1183 False 1921.0 1921 95.8300 820 2015 1 chr1A.!!$F1 1195
13 TraesCS7A01G230600 chr1A 219307396 219308091 695 False 1042.0 1042 93.6170 46 747 1 chr1A.!!$F2 701
14 TraesCS7A01G230600 chr5A 152957801 152958578 777 True 1173.0 1173 93.8780 46 825 1 chr5A.!!$R1 779
15 TraesCS7A01G230600 chr5A 19895568 19896338 770 False 1109.0 1109 92.5930 46 822 1 chr5A.!!$F1 776
16 TraesCS7A01G230600 chr2A 247053886 247054669 783 True 1083.0 1083 91.7500 46 830 1 chr2A.!!$R1 784
17 TraesCS7A01G230600 chr7D 360949039 360949809 770 False 1018.0 1018 90.5250 48 822 1 chr7D.!!$F1 774
18 TraesCS7A01G230600 chr7D 582909347 582910118 771 True 1016.0 1016 90.4460 48 825 1 chr7D.!!$R1 777

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
798 802 0.037697 TTACTAGTGGCGCACTGTGG 60.038 55.0 18.7 12.34 45.01 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 2778 4.219944 AGTTATTCTACGTGCACTCTTCCA 59.78 41.667 16.19 0.0 0.0 3.53 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
61 62 4.025145 GTCACTACAAGCACGCTTAACTTT 60.025 41.667 3.53 0.00 34.50 2.66
297 300 0.387929 TAGTGGCGCACCTAGCATAC 59.612 55.000 10.83 0.00 46.13 2.39
360 364 2.427095 CCTCCAAATCTTAAAAGCCCCG 59.573 50.000 0.00 0.00 0.00 5.73
364 368 5.078256 TCCAAATCTTAAAAGCCCCGTAAA 58.922 37.500 0.00 0.00 0.00 2.01
412 416 6.073494 GGATTTTGAAAATGTTTAACGGGGTG 60.073 38.462 8.03 0.00 0.00 4.61
414 418 2.693591 TGAAAATGTTTAACGGGGTGCA 59.306 40.909 0.00 0.00 0.00 4.57
415 419 2.804697 AAATGTTTAACGGGGTGCAC 57.195 45.000 8.80 8.80 0.00 4.57
416 420 0.963225 AATGTTTAACGGGGTGCACC 59.037 50.000 28.57 28.57 39.11 5.01
430 434 4.450082 GGTGCACCCTAGTTAAATTTGG 57.550 45.455 26.31 0.00 0.00 3.28
431 435 4.083565 GGTGCACCCTAGTTAAATTTGGA 58.916 43.478 26.31 0.00 0.00 3.53
432 436 4.709886 GGTGCACCCTAGTTAAATTTGGAT 59.290 41.667 26.31 0.00 0.00 3.41
433 437 5.394115 GGTGCACCCTAGTTAAATTTGGATG 60.394 44.000 26.31 0.00 0.00 3.51
434 438 5.185056 GTGCACCCTAGTTAAATTTGGATGT 59.815 40.000 5.22 0.00 0.00 3.06
435 439 6.376018 GTGCACCCTAGTTAAATTTGGATGTA 59.624 38.462 5.22 0.00 0.00 2.29
436 440 6.948886 TGCACCCTAGTTAAATTTGGATGTAA 59.051 34.615 0.00 0.00 0.00 2.41
437 441 7.094118 TGCACCCTAGTTAAATTTGGATGTAAC 60.094 37.037 0.00 0.00 36.57 2.50
438 442 7.122204 GCACCCTAGTTAAATTTGGATGTAACT 59.878 37.037 0.00 4.12 44.66 2.24
439 443 9.020731 CACCCTAGTTAAATTTGGATGTAACTT 57.979 33.333 0.00 0.00 41.47 2.66
440 444 9.596308 ACCCTAGTTAAATTTGGATGTAACTTT 57.404 29.630 0.00 0.00 41.47 2.66
445 449 9.893305 AGTTAAATTTGGATGTAACTTTTCGAG 57.107 29.630 0.00 0.00 41.47 4.04
446 450 9.673454 GTTAAATTTGGATGTAACTTTTCGAGT 57.327 29.630 0.00 0.00 41.47 4.18
449 453 8.842358 AATTTGGATGTAACTTTTCGAGTAGA 57.158 30.769 3.22 0.00 37.72 2.59
450 454 9.449719 AATTTGGATGTAACTTTTCGAGTAGAT 57.550 29.630 3.22 0.00 37.72 1.98
451 455 7.827819 TTGGATGTAACTTTTCGAGTAGATG 57.172 36.000 3.22 0.00 37.72 2.90
452 456 7.165460 TGGATGTAACTTTTCGAGTAGATGA 57.835 36.000 3.22 0.00 37.72 2.92
453 457 7.782049 TGGATGTAACTTTTCGAGTAGATGAT 58.218 34.615 3.22 0.00 37.72 2.45
454 458 8.258007 TGGATGTAACTTTTCGAGTAGATGATT 58.742 33.333 3.22 0.00 37.72 2.57
455 459 9.099454 GGATGTAACTTTTCGAGTAGATGATTT 57.901 33.333 3.22 0.00 37.72 2.17
487 491 9.813446 ATAGAAAACTATTTAATCCGAGTTCGT 57.187 29.630 0.48 0.00 37.74 3.85
489 493 9.813446 AGAAAACTATTTAATCCGAGTTCGTAT 57.187 29.630 0.48 0.00 37.74 3.06
490 494 9.845305 GAAAACTATTTAATCCGAGTTCGTATG 57.155 33.333 0.48 0.00 37.74 2.39
491 495 7.404139 AACTATTTAATCCGAGTTCGTATGC 57.596 36.000 0.48 0.00 37.74 3.14
492 496 6.509656 ACTATTTAATCCGAGTTCGTATGCA 58.490 36.000 0.00 0.00 37.74 3.96
493 497 6.982141 ACTATTTAATCCGAGTTCGTATGCAA 59.018 34.615 0.00 0.00 37.74 4.08
494 498 6.671614 ATTTAATCCGAGTTCGTATGCAAA 57.328 33.333 0.00 0.00 37.74 3.68
495 499 6.483385 TTTAATCCGAGTTCGTATGCAAAA 57.517 33.333 0.00 0.00 37.74 2.44
496 500 4.600012 AATCCGAGTTCGTATGCAAAAG 57.400 40.909 0.00 0.00 37.74 2.27
497 501 3.034721 TCCGAGTTCGTATGCAAAAGT 57.965 42.857 0.00 0.00 37.74 2.66
498 502 3.395639 TCCGAGTTCGTATGCAAAAGTT 58.604 40.909 0.00 0.00 37.74 2.66
499 503 4.558178 TCCGAGTTCGTATGCAAAAGTTA 58.442 39.130 0.00 0.00 37.74 2.24
500 504 5.172934 TCCGAGTTCGTATGCAAAAGTTAT 58.827 37.500 0.00 0.00 37.74 1.89
501 505 5.062934 TCCGAGTTCGTATGCAAAAGTTATG 59.937 40.000 0.00 0.00 37.74 1.90
502 506 4.723862 CGAGTTCGTATGCAAAAGTTATGC 59.276 41.667 0.00 0.00 38.20 3.14
503 507 4.981794 AGTTCGTATGCAAAAGTTATGCC 58.018 39.130 0.00 0.00 43.16 4.40
504 508 4.102649 GTTCGTATGCAAAAGTTATGCCC 58.897 43.478 0.00 0.00 43.16 5.36
505 509 3.348119 TCGTATGCAAAAGTTATGCCCA 58.652 40.909 0.00 0.00 43.16 5.36
506 510 3.951037 TCGTATGCAAAAGTTATGCCCAT 59.049 39.130 0.00 0.00 43.16 4.00
507 511 4.400884 TCGTATGCAAAAGTTATGCCCATT 59.599 37.500 0.00 0.00 43.16 3.16
508 512 5.105554 TCGTATGCAAAAGTTATGCCCATTT 60.106 36.000 0.00 0.00 43.16 2.32
509 513 5.580297 CGTATGCAAAAGTTATGCCCATTTT 59.420 36.000 0.00 0.00 43.16 1.82
510 514 6.754209 CGTATGCAAAAGTTATGCCCATTTTA 59.246 34.615 0.00 0.00 43.16 1.52
511 515 6.983474 ATGCAAAAGTTATGCCCATTTTAC 57.017 33.333 0.00 0.00 43.16 2.01
512 516 5.858381 TGCAAAAGTTATGCCCATTTTACA 58.142 33.333 0.00 0.00 43.16 2.41
513 517 6.291377 TGCAAAAGTTATGCCCATTTTACAA 58.709 32.000 0.00 0.00 43.16 2.41
514 518 6.767902 TGCAAAAGTTATGCCCATTTTACAAA 59.232 30.769 0.00 0.00 43.16 2.83
515 519 7.446625 TGCAAAAGTTATGCCCATTTTACAAAT 59.553 29.630 0.00 0.00 43.16 2.32
516 520 8.296000 GCAAAAGTTATGCCCATTTTACAAATT 58.704 29.630 0.00 0.00 37.85 1.82
517 521 9.824534 CAAAAGTTATGCCCATTTTACAAATTC 57.175 29.630 0.00 0.00 0.00 2.17
518 522 8.560355 AAAGTTATGCCCATTTTACAAATTCC 57.440 30.769 0.00 0.00 0.00 3.01
519 523 7.251321 AGTTATGCCCATTTTACAAATTCCA 57.749 32.000 0.00 0.00 0.00 3.53
520 524 7.330262 AGTTATGCCCATTTTACAAATTCCAG 58.670 34.615 0.00 0.00 0.00 3.86
521 525 7.180051 AGTTATGCCCATTTTACAAATTCCAGA 59.820 33.333 0.00 0.00 0.00 3.86
522 526 5.404466 TGCCCATTTTACAAATTCCAGAG 57.596 39.130 0.00 0.00 0.00 3.35
523 527 5.083122 TGCCCATTTTACAAATTCCAGAGA 58.917 37.500 0.00 0.00 0.00 3.10
524 528 5.185635 TGCCCATTTTACAAATTCCAGAGAG 59.814 40.000 0.00 0.00 0.00 3.20
525 529 5.418840 GCCCATTTTACAAATTCCAGAGAGA 59.581 40.000 0.00 0.00 0.00 3.10
526 530 6.097412 GCCCATTTTACAAATTCCAGAGAGAT 59.903 38.462 0.00 0.00 0.00 2.75
527 531 7.364144 GCCCATTTTACAAATTCCAGAGAGATT 60.364 37.037 0.00 0.00 0.00 2.40
528 532 8.534496 CCCATTTTACAAATTCCAGAGAGATTT 58.466 33.333 0.00 0.00 0.00 2.17
529 533 9.933723 CCATTTTACAAATTCCAGAGAGATTTT 57.066 29.630 0.00 0.00 0.00 1.82
531 535 8.816640 TTTTACAAATTCCAGAGAGATTTTGC 57.183 30.769 8.17 0.00 39.22 3.68
532 536 7.523293 TTACAAATTCCAGAGAGATTTTGCA 57.477 32.000 8.17 0.00 39.22 4.08
533 537 6.409524 ACAAATTCCAGAGAGATTTTGCAA 57.590 33.333 0.00 0.00 39.22 4.08
534 538 6.819284 ACAAATTCCAGAGAGATTTTGCAAA 58.181 32.000 8.05 8.05 39.22 3.68
535 539 7.447594 ACAAATTCCAGAGAGATTTTGCAAAT 58.552 30.769 13.65 3.23 39.22 2.32
536 540 8.587608 ACAAATTCCAGAGAGATTTTGCAAATA 58.412 29.630 13.65 4.65 39.22 1.40
537 541 9.426837 CAAATTCCAGAGAGATTTTGCAAATAA 57.573 29.630 13.65 0.00 33.11 1.40
539 543 9.649167 AATTCCAGAGAGATTTTGCAAATAAAG 57.351 29.630 13.65 0.00 0.00 1.85
540 544 7.765695 TCCAGAGAGATTTTGCAAATAAAGT 57.234 32.000 13.65 0.00 0.00 2.66
541 545 7.820648 TCCAGAGAGATTTTGCAAATAAAGTC 58.179 34.615 13.65 7.84 0.00 3.01
542 546 7.448161 TCCAGAGAGATTTTGCAAATAAAGTCA 59.552 33.333 13.65 0.00 31.13 3.41
543 547 8.084073 CCAGAGAGATTTTGCAAATAAAGTCAA 58.916 33.333 13.65 0.00 31.13 3.18
544 548 9.467258 CAGAGAGATTTTGCAAATAAAGTCAAA 57.533 29.630 13.65 0.00 31.13 2.69
577 581 9.758651 ATTTGTAAATTTTCCCAACAACTAGAC 57.241 29.630 0.00 0.00 30.28 2.59
578 582 7.279750 TGTAAATTTTCCCAACAACTAGACC 57.720 36.000 0.00 0.00 0.00 3.85
579 583 6.834451 TGTAAATTTTCCCAACAACTAGACCA 59.166 34.615 0.00 0.00 0.00 4.02
580 584 5.784578 AATTTTCCCAACAACTAGACCAC 57.215 39.130 0.00 0.00 0.00 4.16
581 585 3.935818 TTTCCCAACAACTAGACCACA 57.064 42.857 0.00 0.00 0.00 4.17
582 586 4.447138 TTTCCCAACAACTAGACCACAT 57.553 40.909 0.00 0.00 0.00 3.21
583 587 5.570205 TTTCCCAACAACTAGACCACATA 57.430 39.130 0.00 0.00 0.00 2.29
584 588 5.772393 TTCCCAACAACTAGACCACATAT 57.228 39.130 0.00 0.00 0.00 1.78
585 589 5.353394 TCCCAACAACTAGACCACATATC 57.647 43.478 0.00 0.00 0.00 1.63
586 590 4.780554 TCCCAACAACTAGACCACATATCA 59.219 41.667 0.00 0.00 0.00 2.15
587 591 4.876107 CCCAACAACTAGACCACATATCAC 59.124 45.833 0.00 0.00 0.00 3.06
588 592 5.487433 CCAACAACTAGACCACATATCACA 58.513 41.667 0.00 0.00 0.00 3.58
589 593 6.115446 CCAACAACTAGACCACATATCACAT 58.885 40.000 0.00 0.00 0.00 3.21
590 594 6.037500 CCAACAACTAGACCACATATCACATG 59.962 42.308 0.00 0.00 0.00 3.21
591 595 5.674525 ACAACTAGACCACATATCACATGG 58.325 41.667 0.00 0.00 39.57 3.66
592 596 4.963318 ACTAGACCACATATCACATGGG 57.037 45.455 0.00 0.00 37.86 4.00
593 597 4.556697 ACTAGACCACATATCACATGGGA 58.443 43.478 0.00 0.00 37.86 4.37
594 598 4.968719 ACTAGACCACATATCACATGGGAA 59.031 41.667 0.00 0.00 37.86 3.97
595 599 4.860802 AGACCACATATCACATGGGAAA 57.139 40.909 0.00 0.00 37.86 3.13
596 600 4.526970 AGACCACATATCACATGGGAAAC 58.473 43.478 0.00 0.00 37.86 2.78
597 601 4.228210 AGACCACATATCACATGGGAAACT 59.772 41.667 0.00 0.00 37.86 2.66
598 602 4.934356 ACCACATATCACATGGGAAACTT 58.066 39.130 0.00 0.00 37.86 2.66
599 603 6.069673 AGACCACATATCACATGGGAAACTTA 60.070 38.462 0.00 0.00 37.86 2.24
600 604 6.672593 ACCACATATCACATGGGAAACTTAT 58.327 36.000 0.00 0.00 37.86 1.73
601 605 7.125391 ACCACATATCACATGGGAAACTTATT 58.875 34.615 0.00 0.00 37.86 1.40
602 606 7.619302 ACCACATATCACATGGGAAACTTATTT 59.381 33.333 0.00 0.00 37.86 1.40
603 607 8.477256 CCACATATCACATGGGAAACTTATTTT 58.523 33.333 0.00 0.00 0.00 1.82
604 608 9.520204 CACATATCACATGGGAAACTTATTTTC 57.480 33.333 0.00 0.00 42.74 2.29
605 609 9.479549 ACATATCACATGGGAAACTTATTTTCT 57.520 29.630 0.00 0.00 43.00 2.52
664 668 2.882927 AAAAACTGAAAAGGCGGTCC 57.117 45.000 0.00 0.00 0.00 4.46
665 669 1.770294 AAAACTGAAAAGGCGGTCCA 58.230 45.000 0.00 0.00 33.74 4.02
666 670 1.029681 AAACTGAAAAGGCGGTCCAC 58.970 50.000 0.00 0.00 33.74 4.02
667 671 0.106918 AACTGAAAAGGCGGTCCACA 60.107 50.000 0.00 0.00 33.74 4.17
668 672 0.535102 ACTGAAAAGGCGGTCCACAG 60.535 55.000 0.00 0.00 33.74 3.66
669 673 0.535102 CTGAAAAGGCGGTCCACAGT 60.535 55.000 0.00 0.00 33.74 3.55
670 674 0.817634 TGAAAAGGCGGTCCACAGTG 60.818 55.000 0.00 0.00 33.74 3.66
671 675 1.515521 GAAAAGGCGGTCCACAGTGG 61.516 60.000 14.19 14.19 39.43 4.00
672 676 2.976494 AAAAGGCGGTCCACAGTGGG 62.976 60.000 20.14 4.82 38.32 4.61
689 693 2.362889 GGGGGTTGCATGTGAGGG 60.363 66.667 0.00 0.00 0.00 4.30
690 694 2.763215 GGGGTTGCATGTGAGGGA 59.237 61.111 0.00 0.00 0.00 4.20
691 695 1.076549 GGGGTTGCATGTGAGGGAA 59.923 57.895 0.00 0.00 0.00 3.97
692 696 0.324645 GGGGTTGCATGTGAGGGAAT 60.325 55.000 0.00 0.00 0.00 3.01
693 697 1.560505 GGGTTGCATGTGAGGGAATT 58.439 50.000 0.00 0.00 0.00 2.17
694 698 1.901833 GGGTTGCATGTGAGGGAATTT 59.098 47.619 0.00 0.00 0.00 1.82
695 699 2.302733 GGGTTGCATGTGAGGGAATTTT 59.697 45.455 0.00 0.00 0.00 1.82
696 700 3.244526 GGGTTGCATGTGAGGGAATTTTT 60.245 43.478 0.00 0.00 0.00 1.94
697 701 4.020662 GGGTTGCATGTGAGGGAATTTTTA 60.021 41.667 0.00 0.00 0.00 1.52
698 702 5.170748 GGTTGCATGTGAGGGAATTTTTAG 58.829 41.667 0.00 0.00 0.00 1.85
699 703 5.170748 GTTGCATGTGAGGGAATTTTTAGG 58.829 41.667 0.00 0.00 0.00 2.69
700 704 3.195396 TGCATGTGAGGGAATTTTTAGGC 59.805 43.478 0.00 0.00 0.00 3.93
701 705 3.430790 GCATGTGAGGGAATTTTTAGGCC 60.431 47.826 0.00 0.00 0.00 5.19
702 706 3.534357 TGTGAGGGAATTTTTAGGCCA 57.466 42.857 5.01 0.00 0.00 5.36
703 707 3.850752 TGTGAGGGAATTTTTAGGCCAA 58.149 40.909 5.01 0.00 0.00 4.52
704 708 3.831911 TGTGAGGGAATTTTTAGGCCAAG 59.168 43.478 5.01 0.00 0.00 3.61
705 709 3.832490 GTGAGGGAATTTTTAGGCCAAGT 59.168 43.478 5.01 0.00 0.00 3.16
706 710 4.283467 GTGAGGGAATTTTTAGGCCAAGTT 59.717 41.667 5.01 0.00 0.00 2.66
707 711 5.479027 GTGAGGGAATTTTTAGGCCAAGTTA 59.521 40.000 5.01 0.00 0.00 2.24
708 712 5.714806 TGAGGGAATTTTTAGGCCAAGTTAG 59.285 40.000 5.01 0.00 0.00 2.34
709 713 5.651303 AGGGAATTTTTAGGCCAAGTTAGT 58.349 37.500 5.01 0.00 0.00 2.24
710 714 6.796648 AGGGAATTTTTAGGCCAAGTTAGTA 58.203 36.000 5.01 0.00 0.00 1.82
711 715 7.243091 AGGGAATTTTTAGGCCAAGTTAGTAA 58.757 34.615 5.01 0.00 0.00 2.24
712 716 7.899172 AGGGAATTTTTAGGCCAAGTTAGTAAT 59.101 33.333 5.01 0.00 0.00 1.89
713 717 7.979537 GGGAATTTTTAGGCCAAGTTAGTAATG 59.020 37.037 5.01 0.00 0.00 1.90
714 718 7.979537 GGAATTTTTAGGCCAAGTTAGTAATGG 59.020 37.037 5.01 0.00 37.29 3.16
715 719 6.844097 TTTTTAGGCCAAGTTAGTAATGGG 57.156 37.500 5.01 0.19 34.71 4.00
716 720 4.513406 TTAGGCCAAGTTAGTAATGGGG 57.487 45.455 5.01 0.00 34.71 4.96
717 721 1.063942 AGGCCAAGTTAGTAATGGGGC 60.064 52.381 5.01 12.98 40.89 5.80
718 722 1.341581 GGCCAAGTTAGTAATGGGGCA 60.342 52.381 17.85 0.00 41.61 5.36
719 723 1.749063 GCCAAGTTAGTAATGGGGCAC 59.251 52.381 13.61 0.00 39.66 5.01
747 751 2.483014 TGGTGCGCCATTACTAGTTT 57.517 45.000 16.89 0.00 40.46 2.66
748 752 2.785562 TGGTGCGCCATTACTAGTTTT 58.214 42.857 16.89 0.00 40.46 2.43
749 753 2.745281 TGGTGCGCCATTACTAGTTTTC 59.255 45.455 16.89 0.00 40.46 2.29
750 754 2.745281 GGTGCGCCATTACTAGTTTTCA 59.255 45.455 12.58 0.00 34.09 2.69
751 755 3.189702 GGTGCGCCATTACTAGTTTTCAA 59.810 43.478 12.58 0.00 34.09 2.69
752 756 4.320641 GGTGCGCCATTACTAGTTTTCAAA 60.321 41.667 12.58 0.00 34.09 2.69
753 757 5.216648 GTGCGCCATTACTAGTTTTCAAAA 58.783 37.500 4.18 0.00 0.00 2.44
754 758 5.688176 GTGCGCCATTACTAGTTTTCAAAAA 59.312 36.000 4.18 0.00 0.00 1.94
795 799 4.419522 AAAATTTACTAGTGGCGCACTG 57.580 40.909 18.70 12.45 45.01 3.66
796 800 2.762535 ATTTACTAGTGGCGCACTGT 57.237 45.000 18.70 16.10 45.01 3.55
797 801 1.790755 TTTACTAGTGGCGCACTGTG 58.209 50.000 18.70 2.76 45.01 3.66
798 802 0.037697 TTACTAGTGGCGCACTGTGG 60.038 55.000 18.70 12.34 45.01 4.17
799 803 0.896479 TACTAGTGGCGCACTGTGGA 60.896 55.000 18.70 8.47 45.01 4.02
800 804 1.219124 CTAGTGGCGCACTGTGGAT 59.781 57.895 18.70 0.00 45.01 3.41
801 805 1.079197 TAGTGGCGCACTGTGGATG 60.079 57.895 18.70 0.00 45.01 3.51
802 806 1.826340 TAGTGGCGCACTGTGGATGT 61.826 55.000 18.70 0.00 45.01 3.06
803 807 2.669229 TGGCGCACTGTGGATGTG 60.669 61.111 10.83 0.00 38.36 3.21
804 808 3.434319 GGCGCACTGTGGATGTGG 61.434 66.667 10.83 0.00 36.08 4.17
805 809 2.669569 GCGCACTGTGGATGTGGT 60.670 61.111 10.21 0.00 36.08 4.16
806 810 2.969806 GCGCACTGTGGATGTGGTG 61.970 63.158 10.21 0.00 36.08 4.17
807 811 2.956987 GCACTGTGGATGTGGTGC 59.043 61.111 10.21 0.00 45.93 5.01
808 812 2.969806 GCACTGTGGATGTGGTGCG 61.970 63.158 10.21 0.00 43.91 5.34
809 813 2.669569 ACTGTGGATGTGGTGCGC 60.670 61.111 0.00 0.00 0.00 6.09
810 814 3.434319 CTGTGGATGTGGTGCGCC 61.434 66.667 10.11 10.11 0.00 6.53
811 815 4.262089 TGTGGATGTGGTGCGCCA 62.262 61.111 16.89 16.89 43.73 5.69
882 886 6.963083 ATACTAGTAGGCGAAATTGAGACT 57.037 37.500 8.85 0.00 0.00 3.24
1313 1379 6.183361 GGAATTCCTAAAGTTTTGGGTGGAAA 60.183 38.462 17.73 3.51 39.55 3.13
1788 2245 6.268847 AGGATAGCGAAGATTTGAAGGATAGT 59.731 38.462 0.00 0.00 0.00 2.12
2017 2540 7.011482 GTGGACGAATTAGAGTCATTTGCTAAT 59.989 37.037 9.46 0.00 39.01 1.73
2236 2767 3.404224 TGGTTTACGTAGGAATGCACA 57.596 42.857 0.00 0.00 0.00 4.57
2247 2778 8.276252 ACGTAGGAATGCACATTTTAGTTTAT 57.724 30.769 0.00 0.00 0.00 1.40
2270 2801 4.219944 TGGAAGAGTGCACGTAGAATAACT 59.780 41.667 12.01 0.00 0.00 2.24
2300 2831 7.309805 GGGGTTATTCATGTTCAAGCTAGTTTT 60.310 37.037 0.00 0.00 0.00 2.43
2404 2935 4.922206 TCAAGAAAAGCATCACCCTATGT 58.078 39.130 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.761312 TGTAGTGACCCGAGATTAAGAAAAA 58.239 36.000 0.00 0.00 0.00 1.94
23 24 6.349243 TGTAGTGACCCGAGATTAAGAAAA 57.651 37.500 0.00 0.00 0.00 2.29
24 25 5.988310 TGTAGTGACCCGAGATTAAGAAA 57.012 39.130 0.00 0.00 0.00 2.52
25 26 5.623824 GCTTGTAGTGACCCGAGATTAAGAA 60.624 44.000 0.00 0.00 0.00 2.52
26 27 4.142227 GCTTGTAGTGACCCGAGATTAAGA 60.142 45.833 0.00 0.00 0.00 2.10
27 28 4.113354 GCTTGTAGTGACCCGAGATTAAG 58.887 47.826 0.00 0.00 0.00 1.85
28 29 3.512329 TGCTTGTAGTGACCCGAGATTAA 59.488 43.478 0.00 0.00 0.00 1.40
29 30 3.093814 TGCTTGTAGTGACCCGAGATTA 58.906 45.455 0.00 0.00 0.00 1.75
30 31 1.899814 TGCTTGTAGTGACCCGAGATT 59.100 47.619 0.00 0.00 0.00 2.40
31 32 1.204941 GTGCTTGTAGTGACCCGAGAT 59.795 52.381 0.00 0.00 0.00 2.75
32 33 0.601558 GTGCTTGTAGTGACCCGAGA 59.398 55.000 0.00 0.00 0.00 4.04
33 34 0.732880 CGTGCTTGTAGTGACCCGAG 60.733 60.000 0.00 0.00 0.00 4.63
34 35 1.287815 CGTGCTTGTAGTGACCCGA 59.712 57.895 0.00 0.00 0.00 5.14
35 36 2.380410 GCGTGCTTGTAGTGACCCG 61.380 63.158 0.00 0.00 0.00 5.28
36 37 0.602905 AAGCGTGCTTGTAGTGACCC 60.603 55.000 6.25 0.00 34.60 4.46
37 38 2.074547 TAAGCGTGCTTGTAGTGACC 57.925 50.000 16.98 0.00 37.47 4.02
38 39 3.057734 AGTTAAGCGTGCTTGTAGTGAC 58.942 45.455 16.98 6.25 37.47 3.67
39 40 3.380479 AGTTAAGCGTGCTTGTAGTGA 57.620 42.857 16.98 0.00 37.47 3.41
40 41 4.468095 AAAGTTAAGCGTGCTTGTAGTG 57.532 40.909 16.98 0.00 37.47 2.74
41 42 5.535333 TCTAAAGTTAAGCGTGCTTGTAGT 58.465 37.500 16.98 5.39 37.47 2.73
42 43 5.634020 ACTCTAAAGTTAAGCGTGCTTGTAG 59.366 40.000 16.98 9.93 37.47 2.74
43 44 5.535333 ACTCTAAAGTTAAGCGTGCTTGTA 58.465 37.500 16.98 2.53 37.47 2.41
44 45 4.377897 ACTCTAAAGTTAAGCGTGCTTGT 58.622 39.130 16.98 0.38 37.47 3.16
61 62 4.224370 GTGTTGGGGTTGGATAGAACTCTA 59.776 45.833 0.00 0.00 0.00 2.43
140 141 7.831753 TGAACAAAGTCCTAAACATCAACAAA 58.168 30.769 0.00 0.00 0.00 2.83
297 300 0.389426 AACTTACTAGTGGCGCACCG 60.389 55.000 10.83 2.80 39.70 4.94
371 375 7.889873 TCAAAATCCTCAAAAACCTAACAGA 57.110 32.000 0.00 0.00 0.00 3.41
372 376 8.940768 TTTCAAAATCCTCAAAAACCTAACAG 57.059 30.769 0.00 0.00 0.00 3.16
373 377 9.898152 ATTTTCAAAATCCTCAAAAACCTAACA 57.102 25.926 0.00 0.00 0.00 2.41
412 416 5.914898 ACATCCAAATTTAACTAGGGTGC 57.085 39.130 4.99 0.00 33.78 5.01
414 418 9.596308 AAAGTTACATCCAAATTTAACTAGGGT 57.404 29.630 2.95 0.00 37.38 4.34
419 423 9.893305 CTCGAAAAGTTACATCCAAATTTAACT 57.107 29.630 0.00 0.00 39.12 2.24
420 424 9.673454 ACTCGAAAAGTTACATCCAAATTTAAC 57.327 29.630 0.00 0.00 33.03 2.01
423 427 9.280174 TCTACTCGAAAAGTTACATCCAAATTT 57.720 29.630 0.00 0.00 39.55 1.82
424 428 8.842358 TCTACTCGAAAAGTTACATCCAAATT 57.158 30.769 0.00 0.00 39.55 1.82
425 429 8.883731 CATCTACTCGAAAAGTTACATCCAAAT 58.116 33.333 0.00 0.00 39.55 2.32
426 430 8.092068 TCATCTACTCGAAAAGTTACATCCAAA 58.908 33.333 0.00 0.00 39.55 3.28
427 431 7.608153 TCATCTACTCGAAAAGTTACATCCAA 58.392 34.615 0.00 0.00 39.55 3.53
428 432 7.165460 TCATCTACTCGAAAAGTTACATCCA 57.835 36.000 0.00 0.00 39.55 3.41
429 433 8.649973 AATCATCTACTCGAAAAGTTACATCC 57.350 34.615 0.00 0.00 39.55 3.51
461 465 9.813446 ACGAACTCGGATTAAATAGTTTTCTAT 57.187 29.630 3.88 0.00 43.10 1.98
463 467 9.813446 ATACGAACTCGGATTAAATAGTTTTCT 57.187 29.630 3.88 0.00 40.60 2.52
464 468 9.845305 CATACGAACTCGGATTAAATAGTTTTC 57.155 33.333 3.88 0.00 40.60 2.29
465 469 8.333186 GCATACGAACTCGGATTAAATAGTTTT 58.667 33.333 3.88 0.00 40.60 2.43
466 470 7.493320 TGCATACGAACTCGGATTAAATAGTTT 59.507 33.333 3.88 0.00 40.60 2.66
467 471 6.982141 TGCATACGAACTCGGATTAAATAGTT 59.018 34.615 3.88 0.00 40.60 2.24
468 472 6.509656 TGCATACGAACTCGGATTAAATAGT 58.490 36.000 3.88 0.00 40.60 2.12
469 473 7.402811 TTGCATACGAACTCGGATTAAATAG 57.597 36.000 3.88 0.00 40.60 1.73
470 474 7.773864 TTTGCATACGAACTCGGATTAAATA 57.226 32.000 3.88 0.00 40.60 1.40
471 475 6.671614 TTTGCATACGAACTCGGATTAAAT 57.328 33.333 3.88 0.00 40.60 1.40
472 476 6.148150 ACTTTTGCATACGAACTCGGATTAAA 59.852 34.615 3.88 2.39 40.60 1.52
473 477 5.640357 ACTTTTGCATACGAACTCGGATTAA 59.360 36.000 3.88 0.00 40.60 1.40
474 478 5.172934 ACTTTTGCATACGAACTCGGATTA 58.827 37.500 3.88 0.00 40.60 1.75
475 479 4.000988 ACTTTTGCATACGAACTCGGATT 58.999 39.130 3.88 0.00 40.60 3.01
476 480 3.596214 ACTTTTGCATACGAACTCGGAT 58.404 40.909 3.88 0.00 45.12 4.18
477 481 3.034721 ACTTTTGCATACGAACTCGGA 57.965 42.857 3.88 0.00 44.95 4.55
478 482 3.806316 AACTTTTGCATACGAACTCGG 57.194 42.857 3.88 0.00 44.95 4.63
479 483 4.723862 GCATAACTTTTGCATACGAACTCG 59.276 41.667 0.00 0.00 41.50 4.18
480 484 5.028375 GGCATAACTTTTGCATACGAACTC 58.972 41.667 6.55 0.00 41.95 3.01
481 485 4.142469 GGGCATAACTTTTGCATACGAACT 60.142 41.667 6.55 0.00 41.95 3.01
482 486 4.102649 GGGCATAACTTTTGCATACGAAC 58.897 43.478 6.55 0.00 41.95 3.95
483 487 3.759086 TGGGCATAACTTTTGCATACGAA 59.241 39.130 6.55 0.00 41.95 3.85
484 488 3.348119 TGGGCATAACTTTTGCATACGA 58.652 40.909 6.55 0.00 41.95 3.43
485 489 3.773860 TGGGCATAACTTTTGCATACG 57.226 42.857 6.55 0.00 41.95 3.06
486 490 6.983474 AAAATGGGCATAACTTTTGCATAC 57.017 33.333 6.55 0.00 41.95 2.39
487 491 7.615403 TGTAAAATGGGCATAACTTTTGCATA 58.385 30.769 6.55 0.00 41.95 3.14
488 492 6.471146 TGTAAAATGGGCATAACTTTTGCAT 58.529 32.000 6.55 0.00 41.95 3.96
489 493 5.858381 TGTAAAATGGGCATAACTTTTGCA 58.142 33.333 6.55 0.00 41.95 4.08
490 494 6.793492 TTGTAAAATGGGCATAACTTTTGC 57.207 33.333 0.00 0.00 39.41 3.68
491 495 9.824534 GAATTTGTAAAATGGGCATAACTTTTG 57.175 29.630 0.00 0.00 0.00 2.44
492 496 9.008965 GGAATTTGTAAAATGGGCATAACTTTT 57.991 29.630 0.00 0.00 0.00 2.27
493 497 8.160106 TGGAATTTGTAAAATGGGCATAACTTT 58.840 29.630 0.00 0.00 0.00 2.66
494 498 7.684529 TGGAATTTGTAAAATGGGCATAACTT 58.315 30.769 0.00 0.00 0.00 2.66
495 499 7.180051 TCTGGAATTTGTAAAATGGGCATAACT 59.820 33.333 0.00 0.00 0.00 2.24
496 500 7.327214 TCTGGAATTTGTAAAATGGGCATAAC 58.673 34.615 0.00 0.00 0.00 1.89
497 501 7.398618 TCTCTGGAATTTGTAAAATGGGCATAA 59.601 33.333 0.00 0.00 0.00 1.90
498 502 6.894654 TCTCTGGAATTTGTAAAATGGGCATA 59.105 34.615 0.00 0.00 0.00 3.14
499 503 5.721000 TCTCTGGAATTTGTAAAATGGGCAT 59.279 36.000 0.00 0.00 0.00 4.40
500 504 5.083122 TCTCTGGAATTTGTAAAATGGGCA 58.917 37.500 0.00 0.00 0.00 5.36
501 505 5.418840 TCTCTCTGGAATTTGTAAAATGGGC 59.581 40.000 0.00 0.00 0.00 5.36
502 506 7.651027 ATCTCTCTGGAATTTGTAAAATGGG 57.349 36.000 0.00 0.00 0.00 4.00
503 507 9.933723 AAAATCTCTCTGGAATTTGTAAAATGG 57.066 29.630 0.00 0.00 0.00 3.16
505 509 9.428097 GCAAAATCTCTCTGGAATTTGTAAAAT 57.572 29.630 0.00 0.00 32.03 1.82
506 510 8.420222 TGCAAAATCTCTCTGGAATTTGTAAAA 58.580 29.630 0.00 0.00 32.03 1.52
507 511 7.950512 TGCAAAATCTCTCTGGAATTTGTAAA 58.049 30.769 0.00 0.00 32.03 2.01
508 512 7.523293 TGCAAAATCTCTCTGGAATTTGTAA 57.477 32.000 0.00 0.00 32.03 2.41
509 513 7.523293 TTGCAAAATCTCTCTGGAATTTGTA 57.477 32.000 0.00 0.00 32.03 2.41
510 514 6.409524 TTGCAAAATCTCTCTGGAATTTGT 57.590 33.333 0.00 0.00 32.03 2.83
511 515 7.900782 ATTTGCAAAATCTCTCTGGAATTTG 57.099 32.000 17.19 0.00 0.00 2.32
513 517 9.649167 CTTTATTTGCAAAATCTCTCTGGAATT 57.351 29.630 17.19 0.00 0.00 2.17
514 518 8.810041 ACTTTATTTGCAAAATCTCTCTGGAAT 58.190 29.630 17.19 0.00 0.00 3.01
515 519 8.181904 ACTTTATTTGCAAAATCTCTCTGGAA 57.818 30.769 17.19 0.00 0.00 3.53
516 520 7.448161 TGACTTTATTTGCAAAATCTCTCTGGA 59.552 33.333 17.19 0.00 0.00 3.86
517 521 7.596494 TGACTTTATTTGCAAAATCTCTCTGG 58.404 34.615 17.19 2.86 0.00 3.86
518 522 9.467258 TTTGACTTTATTTGCAAAATCTCTCTG 57.533 29.630 17.19 4.24 0.00 3.35
551 555 9.758651 GTCTAGTTGTTGGGAAAATTTACAAAT 57.241 29.630 8.32 8.32 32.64 2.32
552 556 8.198778 GGTCTAGTTGTTGGGAAAATTTACAAA 58.801 33.333 5.30 0.00 31.29 2.83
553 557 7.342284 TGGTCTAGTTGTTGGGAAAATTTACAA 59.658 33.333 0.00 0.00 0.00 2.41
554 558 6.834451 TGGTCTAGTTGTTGGGAAAATTTACA 59.166 34.615 0.00 0.00 0.00 2.41
555 559 7.143340 GTGGTCTAGTTGTTGGGAAAATTTAC 58.857 38.462 0.00 0.00 0.00 2.01
556 560 6.834451 TGTGGTCTAGTTGTTGGGAAAATTTA 59.166 34.615 0.00 0.00 0.00 1.40
557 561 5.659079 TGTGGTCTAGTTGTTGGGAAAATTT 59.341 36.000 0.00 0.00 0.00 1.82
558 562 5.205056 TGTGGTCTAGTTGTTGGGAAAATT 58.795 37.500 0.00 0.00 0.00 1.82
559 563 4.798882 TGTGGTCTAGTTGTTGGGAAAAT 58.201 39.130 0.00 0.00 0.00 1.82
560 564 4.237976 TGTGGTCTAGTTGTTGGGAAAA 57.762 40.909 0.00 0.00 0.00 2.29
561 565 3.935818 TGTGGTCTAGTTGTTGGGAAA 57.064 42.857 0.00 0.00 0.00 3.13
562 566 5.249622 TGATATGTGGTCTAGTTGTTGGGAA 59.750 40.000 0.00 0.00 0.00 3.97
563 567 4.780554 TGATATGTGGTCTAGTTGTTGGGA 59.219 41.667 0.00 0.00 0.00 4.37
564 568 4.876107 GTGATATGTGGTCTAGTTGTTGGG 59.124 45.833 0.00 0.00 0.00 4.12
565 569 5.487433 TGTGATATGTGGTCTAGTTGTTGG 58.513 41.667 0.00 0.00 0.00 3.77
566 570 6.037500 CCATGTGATATGTGGTCTAGTTGTTG 59.962 42.308 0.00 0.00 0.00 3.33
567 571 6.115446 CCATGTGATATGTGGTCTAGTTGTT 58.885 40.000 0.00 0.00 0.00 2.83
568 572 5.396772 CCCATGTGATATGTGGTCTAGTTGT 60.397 44.000 0.00 0.00 0.00 3.32
569 573 5.059161 CCCATGTGATATGTGGTCTAGTTG 58.941 45.833 0.00 0.00 0.00 3.16
570 574 4.968719 TCCCATGTGATATGTGGTCTAGTT 59.031 41.667 0.00 0.00 0.00 2.24
571 575 4.556697 TCCCATGTGATATGTGGTCTAGT 58.443 43.478 0.00 0.00 0.00 2.57
572 576 5.551305 TTCCCATGTGATATGTGGTCTAG 57.449 43.478 0.00 0.00 0.00 2.43
573 577 5.428457 AGTTTCCCATGTGATATGTGGTCTA 59.572 40.000 0.00 0.00 0.00 2.59
574 578 4.228210 AGTTTCCCATGTGATATGTGGTCT 59.772 41.667 0.00 0.00 0.00 3.85
575 579 4.526970 AGTTTCCCATGTGATATGTGGTC 58.473 43.478 0.00 0.00 0.00 4.02
576 580 4.591321 AGTTTCCCATGTGATATGTGGT 57.409 40.909 0.00 0.00 0.00 4.16
577 581 7.587037 AATAAGTTTCCCATGTGATATGTGG 57.413 36.000 0.00 0.00 0.00 4.17
578 582 9.520204 GAAAATAAGTTTCCCATGTGATATGTG 57.480 33.333 0.00 0.00 39.91 3.21
579 583 9.479549 AGAAAATAAGTTTCCCATGTGATATGT 57.520 29.630 0.00 0.00 45.91 2.29
645 649 2.104170 TGGACCGCCTTTTCAGTTTTT 58.896 42.857 0.00 0.00 34.31 1.94
646 650 1.407618 GTGGACCGCCTTTTCAGTTTT 59.592 47.619 0.00 0.00 34.31 2.43
647 651 1.029681 GTGGACCGCCTTTTCAGTTT 58.970 50.000 0.00 0.00 34.31 2.66
648 652 0.106918 TGTGGACCGCCTTTTCAGTT 60.107 50.000 1.74 0.00 34.31 3.16
649 653 0.535102 CTGTGGACCGCCTTTTCAGT 60.535 55.000 1.74 0.00 34.31 3.41
650 654 0.535102 ACTGTGGACCGCCTTTTCAG 60.535 55.000 1.74 0.00 34.31 3.02
651 655 0.817634 CACTGTGGACCGCCTTTTCA 60.818 55.000 1.74 0.00 34.31 2.69
652 656 1.515521 CCACTGTGGACCGCCTTTTC 61.516 60.000 22.33 0.00 40.96 2.29
653 657 1.528309 CCACTGTGGACCGCCTTTT 60.528 57.895 22.33 0.00 40.96 2.27
654 658 2.113139 CCACTGTGGACCGCCTTT 59.887 61.111 22.33 0.00 40.96 3.11
655 659 3.953775 CCCACTGTGGACCGCCTT 61.954 66.667 27.94 0.00 40.96 4.35
672 676 2.362889 CCCTCACATGCAACCCCC 60.363 66.667 0.00 0.00 0.00 5.40
673 677 0.324645 ATTCCCTCACATGCAACCCC 60.325 55.000 0.00 0.00 0.00 4.95
674 678 1.560505 AATTCCCTCACATGCAACCC 58.439 50.000 0.00 0.00 0.00 4.11
675 679 3.683365 AAAATTCCCTCACATGCAACC 57.317 42.857 0.00 0.00 0.00 3.77
676 680 5.170748 CCTAAAAATTCCCTCACATGCAAC 58.829 41.667 0.00 0.00 0.00 4.17
677 681 4.322650 GCCTAAAAATTCCCTCACATGCAA 60.323 41.667 0.00 0.00 0.00 4.08
678 682 3.195396 GCCTAAAAATTCCCTCACATGCA 59.805 43.478 0.00 0.00 0.00 3.96
679 683 3.430790 GGCCTAAAAATTCCCTCACATGC 60.431 47.826 0.00 0.00 0.00 4.06
680 684 3.768757 TGGCCTAAAAATTCCCTCACATG 59.231 43.478 3.32 0.00 0.00 3.21
681 685 4.059773 TGGCCTAAAAATTCCCTCACAT 57.940 40.909 3.32 0.00 0.00 3.21
682 686 3.534357 TGGCCTAAAAATTCCCTCACA 57.466 42.857 3.32 0.00 0.00 3.58
683 687 3.832490 ACTTGGCCTAAAAATTCCCTCAC 59.168 43.478 3.32 0.00 0.00 3.51
684 688 4.126520 ACTTGGCCTAAAAATTCCCTCA 57.873 40.909 3.32 0.00 0.00 3.86
685 689 5.715279 ACTAACTTGGCCTAAAAATTCCCTC 59.285 40.000 3.32 0.00 0.00 4.30
686 690 5.651303 ACTAACTTGGCCTAAAAATTCCCT 58.349 37.500 3.32 0.00 0.00 4.20
687 691 5.995565 ACTAACTTGGCCTAAAAATTCCC 57.004 39.130 3.32 0.00 0.00 3.97
688 692 7.979537 CCATTACTAACTTGGCCTAAAAATTCC 59.020 37.037 3.32 0.00 0.00 3.01
689 693 7.979537 CCCATTACTAACTTGGCCTAAAAATTC 59.020 37.037 3.32 0.00 0.00 2.17
690 694 7.093068 CCCCATTACTAACTTGGCCTAAAAATT 60.093 37.037 3.32 0.00 0.00 1.82
691 695 6.382859 CCCCATTACTAACTTGGCCTAAAAAT 59.617 38.462 3.32 0.00 0.00 1.82
692 696 5.717654 CCCCATTACTAACTTGGCCTAAAAA 59.282 40.000 3.32 0.00 0.00 1.94
693 697 5.265989 CCCCATTACTAACTTGGCCTAAAA 58.734 41.667 3.32 0.00 0.00 1.52
694 698 4.862371 CCCCATTACTAACTTGGCCTAAA 58.138 43.478 3.32 0.00 0.00 1.85
695 699 3.372241 GCCCCATTACTAACTTGGCCTAA 60.372 47.826 3.32 0.00 0.00 2.69
696 700 2.173996 GCCCCATTACTAACTTGGCCTA 59.826 50.000 3.32 0.00 0.00 3.93
697 701 1.063942 GCCCCATTACTAACTTGGCCT 60.064 52.381 3.32 0.00 0.00 5.19
698 702 1.341581 TGCCCCATTACTAACTTGGCC 60.342 52.381 0.00 0.00 36.58 5.36
699 703 1.749063 GTGCCCCATTACTAACTTGGC 59.251 52.381 0.00 0.00 37.90 4.52
700 704 2.375146 GGTGCCCCATTACTAACTTGG 58.625 52.381 0.00 0.00 0.00 3.61
701 705 2.014128 CGGTGCCCCATTACTAACTTG 58.986 52.381 0.00 0.00 0.00 3.16
702 706 1.631898 ACGGTGCCCCATTACTAACTT 59.368 47.619 0.00 0.00 0.00 2.66
703 707 1.065709 CACGGTGCCCCATTACTAACT 60.066 52.381 0.00 0.00 0.00 2.24
704 708 1.375551 CACGGTGCCCCATTACTAAC 58.624 55.000 0.00 0.00 0.00 2.34
705 709 0.253610 CCACGGTGCCCCATTACTAA 59.746 55.000 1.68 0.00 0.00 2.24
706 710 1.628238 CCCACGGTGCCCCATTACTA 61.628 60.000 1.68 0.00 0.00 1.82
707 711 2.674754 CCACGGTGCCCCATTACT 59.325 61.111 1.68 0.00 0.00 2.24
708 712 2.439519 CCCACGGTGCCCCATTAC 60.440 66.667 1.68 0.00 0.00 1.89
709 713 2.611172 TCCCACGGTGCCCCATTA 60.611 61.111 1.68 0.00 0.00 1.90
710 714 4.047125 CTCCCACGGTGCCCCATT 62.047 66.667 1.68 0.00 0.00 3.16
729 733 2.745281 TGAAAACTAGTAATGGCGCACC 59.255 45.455 10.83 0.00 0.00 5.01
730 734 4.413495 TTGAAAACTAGTAATGGCGCAC 57.587 40.909 10.83 0.00 0.00 5.34
731 735 5.440234 TTTTGAAAACTAGTAATGGCGCA 57.560 34.783 10.83 0.00 0.00 6.09
773 777 4.277423 ACAGTGCGCCACTAGTAAATTTTT 59.723 37.500 4.18 0.00 43.43 1.94
774 778 3.818773 ACAGTGCGCCACTAGTAAATTTT 59.181 39.130 4.18 0.00 43.43 1.82
775 779 3.188460 CACAGTGCGCCACTAGTAAATTT 59.812 43.478 4.18 0.00 43.43 1.82
776 780 2.742053 CACAGTGCGCCACTAGTAAATT 59.258 45.455 4.18 0.00 43.43 1.82
777 781 2.346803 CACAGTGCGCCACTAGTAAAT 58.653 47.619 4.18 0.00 43.43 1.40
778 782 1.606994 CCACAGTGCGCCACTAGTAAA 60.607 52.381 4.18 0.00 43.43 2.01
779 783 0.037697 CCACAGTGCGCCACTAGTAA 60.038 55.000 4.18 0.00 43.43 2.24
780 784 0.896479 TCCACAGTGCGCCACTAGTA 60.896 55.000 4.18 0.00 43.43 1.82
781 785 1.544825 ATCCACAGTGCGCCACTAGT 61.545 55.000 4.18 7.03 43.43 2.57
782 786 1.086067 CATCCACAGTGCGCCACTAG 61.086 60.000 4.18 6.44 43.43 2.57
783 787 1.079197 CATCCACAGTGCGCCACTA 60.079 57.895 4.18 0.00 43.43 2.74
784 788 2.359107 CATCCACAGTGCGCCACT 60.359 61.111 4.18 5.73 46.51 4.00
785 789 2.669569 ACATCCACAGTGCGCCAC 60.670 61.111 4.18 3.02 34.10 5.01
786 790 2.669229 CACATCCACAGTGCGCCA 60.669 61.111 4.18 0.00 0.00 5.69
787 791 3.434319 CCACATCCACAGTGCGCC 61.434 66.667 4.18 0.00 35.69 6.53
788 792 2.669569 ACCACATCCACAGTGCGC 60.670 61.111 0.00 0.00 35.69 6.09
789 793 2.969806 GCACCACATCCACAGTGCG 61.970 63.158 0.00 0.00 45.28 5.34
791 795 2.969806 GCGCACCACATCCACAGTG 61.970 63.158 0.30 0.00 36.76 3.66
792 796 2.669569 GCGCACCACATCCACAGT 60.670 61.111 0.30 0.00 0.00 3.55
793 797 3.434319 GGCGCACCACATCCACAG 61.434 66.667 10.83 0.00 35.26 3.66
794 798 4.262089 TGGCGCACCACATCCACA 62.262 61.111 10.83 0.00 42.67 4.17
803 807 3.064408 GGTAAAACTAGTAATGGCGCACC 59.936 47.826 10.83 0.00 0.00 5.01
804 808 3.685756 TGGTAAAACTAGTAATGGCGCAC 59.314 43.478 10.83 0.00 0.00 5.34
805 809 3.940319 TGGTAAAACTAGTAATGGCGCA 58.060 40.909 10.83 0.00 0.00 6.09
806 810 4.950434 TTGGTAAAACTAGTAATGGCGC 57.050 40.909 0.00 0.00 0.00 6.53
807 811 8.671028 ACTATTTTGGTAAAACTAGTAATGGCG 58.329 33.333 0.00 0.00 38.98 5.69
1313 1379 7.866870 AGAAGTAGAAAGAATAGCAATTCCCT 58.133 34.615 0.00 0.00 42.20 4.20
1788 2245 8.884124 AATCTTTGGTATCCTTCAAATCTTCA 57.116 30.769 0.00 0.00 33.19 3.02
2236 2767 6.430000 ACGTGCACTCTTCCATAAACTAAAAT 59.570 34.615 16.19 0.00 0.00 1.82
2247 2778 4.219944 AGTTATTCTACGTGCACTCTTCCA 59.780 41.667 16.19 0.00 0.00 3.53
2270 2801 6.252995 AGCTTGAACATGAATAACCCCTTTA 58.747 36.000 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.