Multiple sequence alignment - TraesCS7A01G281800

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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 TraesCS7A01G281800 chr7A 100.000 5739 0 0 1 5739 306349283 306343545 0.000000e+00 10599.0
1 TraesCS7A01G281800 chr7D 95.689 4083 88 22 647 4671 272602171 272598119 0.000000e+00 6484.0
2 TraesCS7A01G281800 chr7D 90.636 566 49 4 5175 5739 92727206 92727768 0.000000e+00 749.0
3 TraesCS7A01G281800 chr7D 95.329 471 20 2 4666 5134 272597665 272597195 0.000000e+00 747.0
4 TraesCS7A01G281800 chr7D 89.483 561 57 2 5180 5739 632888465 632887906 0.000000e+00 708.0
5 TraesCS7A01G281800 chr7D 89.104 569 57 5 5174 5739 68433494 68432928 0.000000e+00 702.0
6 TraesCS7A01G281800 chr7D 91.791 402 14 9 1 397 272602580 272602193 5.060000e-150 542.0
7 TraesCS7A01G281800 chr7D 83.468 248 38 1 405 652 200826696 200826452 1.610000e-55 228.0
8 TraesCS7A01G281800 chr7D 83.065 248 39 1 405 652 427170472 427170716 7.480000e-54 222.0
9 TraesCS7A01G281800 chr7D 81.298 262 43 4 395 654 143003939 143004196 2.100000e-49 207.0
10 TraesCS7A01G281800 chr7B 95.925 3828 87 19 647 4446 265429916 265433702 0.000000e+00 6141.0
11 TraesCS7A01G281800 chr7B 86.944 360 11 7 55 382 265429521 265429876 7.020000e-99 372.0
12 TraesCS7A01G281800 chr7B 94.760 229 9 2 4666 4894 265468144 265468369 2.540000e-93 353.0
13 TraesCS7A01G281800 chr7B 95.266 169 7 1 4826 4994 265468337 265468504 3.410000e-67 267.0
14 TraesCS7A01G281800 chr7B 88.742 151 7 4 4527 4668 265465264 265465413 5.910000e-40 176.0
15 TraesCS7A01G281800 chr7B 98.913 92 1 0 4438 4529 265433726 265433817 1.280000e-36 165.0
16 TraesCS7A01G281800 chr4B 90.476 567 51 3 5174 5739 455410022 455409458 0.000000e+00 745.0
17 TraesCS7A01G281800 chr4B 85.333 75 11 0 1344 1418 23822195 23822121 1.710000e-10 78.7
18 TraesCS7A01G281800 chr4B 85.714 49 7 0 4513 4561 654796489 654796441 1.000000e-02 52.8
19 TraesCS7A01G281800 chr6D 90.300 567 49 6 5175 5739 386895963 386896525 0.000000e+00 737.0
20 TraesCS7A01G281800 chr6D 90.265 565 49 4 5176 5739 296757735 296758294 0.000000e+00 734.0
21 TraesCS7A01G281800 chr3D 89.771 567 55 3 5174 5739 253572897 253573461 0.000000e+00 723.0
22 TraesCS7A01G281800 chr3D 89.474 570 54 6 5173 5739 605997820 605997254 0.000000e+00 715.0
23 TraesCS7A01G281800 chr3D 81.377 247 43 1 405 651 121171440 121171197 1.260000e-46 198.0
24 TraesCS7A01G281800 chr2D 89.261 568 56 5 5173 5739 399899463 399898900 0.000000e+00 706.0
25 TraesCS7A01G281800 chr1B 83.200 250 39 1 401 650 388625887 388625641 5.790000e-55 226.0
26 TraesCS7A01G281800 chr1B 82.927 246 39 1 405 650 118610476 118610234 9.680000e-53 219.0
27 TraesCS7A01G281800 chr3A 82.258 248 41 1 405 652 409426148 409426392 1.620000e-50 211.0
28 TraesCS7A01G281800 chr3A 81.781 247 42 1 405 651 499281335 499281578 2.710000e-48 204.0
29 TraesCS7A01G281800 chr6B 81.781 247 42 1 405 651 575488203 575488446 2.710000e-48 204.0
30 TraesCS7A01G281800 chr4D 85.333 75 11 0 1344 1418 13200255 13200181 1.710000e-10 78.7
31 TraesCS7A01G281800 chr4A 84.615 78 12 0 1341 1418 589108502 589108579 1.710000e-10 78.7
32 TraesCS7A01G281800 chr2B 84.615 78 12 0 1341 1418 17040286 17040363 1.710000e-10 78.7


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 TraesCS7A01G281800 chr7A 306343545 306349283 5738 True 10599.000000 10599 100.000000 1 5739 1 chr7A.!!$R1 5738
1 TraesCS7A01G281800 chr7D 272597195 272602580 5385 True 2591.000000 6484 94.269667 1 5134 3 chr7D.!!$R4 5133
2 TraesCS7A01G281800 chr7D 92727206 92727768 562 False 749.000000 749 90.636000 5175 5739 1 chr7D.!!$F1 564
3 TraesCS7A01G281800 chr7D 632887906 632888465 559 True 708.000000 708 89.483000 5180 5739 1 chr7D.!!$R3 559
4 TraesCS7A01G281800 chr7D 68432928 68433494 566 True 702.000000 702 89.104000 5174 5739 1 chr7D.!!$R1 565
5 TraesCS7A01G281800 chr7B 265429521 265433817 4296 False 2226.000000 6141 93.927333 55 4529 3 chr7B.!!$F1 4474
6 TraesCS7A01G281800 chr7B 265465264 265468504 3240 False 265.333333 353 92.922667 4527 4994 3 chr7B.!!$F2 467
7 TraesCS7A01G281800 chr4B 455409458 455410022 564 True 745.000000 745 90.476000 5174 5739 1 chr4B.!!$R2 565
8 TraesCS7A01G281800 chr6D 386895963 386896525 562 False 737.000000 737 90.300000 5175 5739 1 chr6D.!!$F2 564
9 TraesCS7A01G281800 chr6D 296757735 296758294 559 False 734.000000 734 90.265000 5176 5739 1 chr6D.!!$F1 563
10 TraesCS7A01G281800 chr3D 253572897 253573461 564 False 723.000000 723 89.771000 5174 5739 1 chr3D.!!$F1 565
11 TraesCS7A01G281800 chr3D 605997254 605997820 566 True 715.000000 715 89.474000 5173 5739 1 chr3D.!!$R2 566
12 TraesCS7A01G281800 chr2D 399898900 399899463 563 True 706.000000 706 89.261000 5173 5739 1 chr2D.!!$R1 566

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
150 153 0.037512 CTGCTGCTACTGTGCACTCT 60.038 55.000 19.41 5.21 38.12 3.24 F
433 494 0.246910 TGCCTATGCGTTGTACGGAA 59.753 50.000 0.00 0.00 46.78 4.30 F
1473 1564 0.251341 TTTCCTCTCTTTGGCTGGGC 60.251 55.000 0.00 0.00 0.00 5.36 F
2195 2305 0.953727 AAAGAAGCACGCAAGCATCA 59.046 45.000 5.57 0.00 45.62 3.07 F
2736 2846 1.067425 CATGTTGGCACCATGGACTTG 60.067 52.381 21.47 7.72 36.81 3.16 F
4690 7978 0.119155 ACCCCCATTCTCTCTCACCA 59.881 55.000 0.00 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1479 1570 0.978146 AAGCTACACGGATCAGCCCT 60.978 55.000 0.00 0.00 35.88 5.19 R
1717 1827 1.003839 TCGGCCTTGGTGTTGCTAG 60.004 57.895 0.00 0.00 0.00 3.42 R
2459 2569 2.215196 TCAACTTGAGTAAACCGTGGC 58.785 47.619 0.00 0.00 0.00 5.01 R
3702 3816 0.035881 CTCCAGAAGCAAGCCTGTGA 59.964 55.000 0.00 0.00 0.00 3.58 R
4708 7996 0.727398 GTGGAGCGTTAGCAACCATC 59.273 55.000 11.08 4.31 46.89 3.51 R
5633 8962 1.745489 GGACGTGGCTTGATGGGAC 60.745 63.158 0.00 0.00 0.00 4.46 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
75 78 3.083997 AGAGCAAGGTAGGGCGGG 61.084 66.667 0.00 0.00 34.54 6.13
150 153 0.037512 CTGCTGCTACTGTGCACTCT 60.038 55.000 19.41 5.21 38.12 3.24
159 162 2.383855 ACTGTGCACTCTAGATCCCTC 58.616 52.381 19.41 0.00 0.00 4.30
254 288 2.161410 TCATGGTAATTTGCGTCTGTGC 59.839 45.455 0.00 0.00 0.00 4.57
416 477 9.617975 GGAATTAATTATTGACTAGCAAGATGC 57.382 33.333 0.00 0.00 45.46 3.91
417 478 9.617975 GAATTAATTATTGACTAGCAAGATGCC 57.382 33.333 0.00 0.00 46.52 4.40
418 479 8.930846 ATTAATTATTGACTAGCAAGATGCCT 57.069 30.769 0.00 0.00 46.52 4.75
421 482 7.918536 ATTATTGACTAGCAAGATGCCTATG 57.081 36.000 0.00 0.00 46.52 2.23
422 483 3.117491 TGACTAGCAAGATGCCTATGC 57.883 47.619 0.00 0.00 46.52 3.14
423 484 2.064762 GACTAGCAAGATGCCTATGCG 58.935 52.381 0.00 0.00 46.52 4.73
424 485 1.414181 ACTAGCAAGATGCCTATGCGT 59.586 47.619 0.00 0.00 46.52 5.24
425 486 2.158900 ACTAGCAAGATGCCTATGCGTT 60.159 45.455 0.00 0.00 46.52 4.84
426 487 1.019673 AGCAAGATGCCTATGCGTTG 58.980 50.000 0.00 0.00 46.52 4.10
427 488 0.734889 GCAAGATGCCTATGCGTTGT 59.265 50.000 0.00 0.00 41.78 3.32
428 489 1.939934 GCAAGATGCCTATGCGTTGTA 59.060 47.619 0.00 0.00 41.78 2.41
429 490 2.286418 GCAAGATGCCTATGCGTTGTAC 60.286 50.000 0.00 0.00 41.78 2.90
430 491 1.852942 AGATGCCTATGCGTTGTACG 58.147 50.000 0.00 0.00 45.88 3.67
431 492 0.859232 GATGCCTATGCGTTGTACGG 59.141 55.000 1.14 0.00 42.82 4.02
433 494 0.246910 TGCCTATGCGTTGTACGGAA 59.753 50.000 0.00 0.00 46.78 4.30
434 495 0.648958 GCCTATGCGTTGTACGGAAC 59.351 55.000 0.00 0.00 46.78 3.62
435 496 1.999048 CCTATGCGTTGTACGGAACA 58.001 50.000 0.00 0.00 46.78 3.18
436 497 2.546778 CCTATGCGTTGTACGGAACAT 58.453 47.619 0.00 0.00 46.78 2.71
437 498 2.933906 CCTATGCGTTGTACGGAACATT 59.066 45.455 0.00 0.00 46.78 2.71
438 499 4.114073 CCTATGCGTTGTACGGAACATTA 58.886 43.478 0.00 0.00 46.78 1.90
439 500 4.567558 CCTATGCGTTGTACGGAACATTAA 59.432 41.667 0.00 0.00 46.78 1.40
440 501 3.791993 TGCGTTGTACGGAACATTAAC 57.208 42.857 1.14 0.00 39.47 2.01
441 502 3.129109 TGCGTTGTACGGAACATTAACA 58.871 40.909 1.14 0.00 39.47 2.41
442 503 3.747010 TGCGTTGTACGGAACATTAACAT 59.253 39.130 1.14 0.00 39.47 2.71
443 504 4.085884 GCGTTGTACGGAACATTAACATG 58.914 43.478 1.14 0.00 42.82 3.21
444 505 4.085884 CGTTGTACGGAACATTAACATGC 58.914 43.478 0.00 0.00 38.10 4.06
445 506 4.377533 CGTTGTACGGAACATTAACATGCA 60.378 41.667 0.00 0.00 38.10 3.96
446 507 5.636837 GTTGTACGGAACATTAACATGCAT 58.363 37.500 0.00 0.00 38.10 3.96
447 508 5.888691 TGTACGGAACATTAACATGCATT 57.111 34.783 0.00 0.00 33.05 3.56
448 509 6.260870 TGTACGGAACATTAACATGCATTT 57.739 33.333 0.00 0.00 33.05 2.32
449 510 6.089476 TGTACGGAACATTAACATGCATTTG 58.911 36.000 0.00 0.00 33.05 2.32
450 511 5.132897 ACGGAACATTAACATGCATTTGT 57.867 34.783 0.00 0.00 33.05 2.83
451 512 6.260870 ACGGAACATTAACATGCATTTGTA 57.739 33.333 0.00 0.00 33.05 2.41
452 513 6.862209 ACGGAACATTAACATGCATTTGTAT 58.138 32.000 0.00 0.00 33.05 2.29
453 514 7.990917 ACGGAACATTAACATGCATTTGTATA 58.009 30.769 0.00 0.00 33.05 1.47
454 515 8.462811 ACGGAACATTAACATGCATTTGTATAA 58.537 29.630 0.00 0.00 33.05 0.98
455 516 8.957028 CGGAACATTAACATGCATTTGTATAAG 58.043 33.333 0.00 0.00 33.05 1.73
456 517 9.801873 GGAACATTAACATGCATTTGTATAAGT 57.198 29.630 0.00 0.00 33.05 2.24
495 556 8.940397 ATGAGAGAAAAGAATAAACAAGGGAA 57.060 30.769 0.00 0.00 0.00 3.97
496 557 8.940397 TGAGAGAAAAGAATAAACAAGGGAAT 57.060 30.769 0.00 0.00 0.00 3.01
497 558 8.796475 TGAGAGAAAAGAATAAACAAGGGAATG 58.204 33.333 0.00 0.00 0.00 2.67
498 559 7.606349 AGAGAAAAGAATAAACAAGGGAATGC 58.394 34.615 0.00 0.00 0.00 3.56
499 560 7.452813 AGAGAAAAGAATAAACAAGGGAATGCT 59.547 33.333 0.00 0.00 0.00 3.79
500 561 7.966812 AGAAAAGAATAAACAAGGGAATGCTT 58.033 30.769 0.00 0.00 0.00 3.91
501 562 8.432013 AGAAAAGAATAAACAAGGGAATGCTTT 58.568 29.630 0.00 0.00 0.00 3.51
502 563 9.705290 GAAAAGAATAAACAAGGGAATGCTTTA 57.295 29.630 0.00 0.00 0.00 1.85
508 569 9.581099 AATAAACAAGGGAATGCTTTATTTACG 57.419 29.630 0.00 0.00 30.85 3.18
509 570 6.584185 AACAAGGGAATGCTTTATTTACGT 57.416 33.333 0.00 0.00 0.00 3.57
510 571 7.690952 AACAAGGGAATGCTTTATTTACGTA 57.309 32.000 0.00 0.00 0.00 3.57
511 572 7.875327 ACAAGGGAATGCTTTATTTACGTAT 57.125 32.000 0.00 0.00 0.00 3.06
512 573 7.703328 ACAAGGGAATGCTTTATTTACGTATG 58.297 34.615 0.00 0.00 0.00 2.39
513 574 7.338449 ACAAGGGAATGCTTTATTTACGTATGT 59.662 33.333 0.00 0.00 0.00 2.29
514 575 7.259290 AGGGAATGCTTTATTTACGTATGTG 57.741 36.000 0.00 0.00 0.00 3.21
515 576 6.262273 AGGGAATGCTTTATTTACGTATGTGG 59.738 38.462 0.00 0.00 0.00 4.17
516 577 6.261381 GGGAATGCTTTATTTACGTATGTGGA 59.739 38.462 0.00 0.00 0.00 4.02
517 578 7.352739 GGAATGCTTTATTTACGTATGTGGAG 58.647 38.462 0.00 0.00 0.00 3.86
518 579 7.225931 GGAATGCTTTATTTACGTATGTGGAGA 59.774 37.037 0.00 0.00 0.00 3.71
519 580 8.500753 AATGCTTTATTTACGTATGTGGAGAA 57.499 30.769 0.00 0.00 0.00 2.87
520 581 7.534085 TGCTTTATTTACGTATGTGGAGAAG 57.466 36.000 0.00 0.00 0.00 2.85
521 582 6.537301 TGCTTTATTTACGTATGTGGAGAAGG 59.463 38.462 0.00 0.00 0.00 3.46
522 583 6.018180 GCTTTATTTACGTATGTGGAGAAGGG 60.018 42.308 0.00 0.00 0.00 3.95
523 584 6.549433 TTATTTACGTATGTGGAGAAGGGT 57.451 37.500 0.00 0.00 0.00 4.34
524 585 7.658525 TTATTTACGTATGTGGAGAAGGGTA 57.341 36.000 0.00 0.00 0.00 3.69
525 586 6.742559 ATTTACGTATGTGGAGAAGGGTAT 57.257 37.500 0.00 0.00 0.00 2.73
526 587 5.524971 TTACGTATGTGGAGAAGGGTATG 57.475 43.478 0.00 0.00 0.00 2.39
527 588 2.698797 ACGTATGTGGAGAAGGGTATGG 59.301 50.000 0.00 0.00 0.00 2.74
528 589 2.963101 CGTATGTGGAGAAGGGTATGGA 59.037 50.000 0.00 0.00 0.00 3.41
529 590 3.578716 CGTATGTGGAGAAGGGTATGGAT 59.421 47.826 0.00 0.00 0.00 3.41
530 591 4.770531 CGTATGTGGAGAAGGGTATGGATA 59.229 45.833 0.00 0.00 0.00 2.59
531 592 5.422331 CGTATGTGGAGAAGGGTATGGATAT 59.578 44.000 0.00 0.00 0.00 1.63
532 593 6.605995 CGTATGTGGAGAAGGGTATGGATATA 59.394 42.308 0.00 0.00 0.00 0.86
533 594 7.287927 CGTATGTGGAGAAGGGTATGGATATAT 59.712 40.741 0.00 0.00 0.00 0.86
534 595 8.993424 GTATGTGGAGAAGGGTATGGATATATT 58.007 37.037 0.00 0.00 0.00 1.28
535 596 7.888514 TGTGGAGAAGGGTATGGATATATTT 57.111 36.000 0.00 0.00 0.00 1.40
536 597 8.287904 TGTGGAGAAGGGTATGGATATATTTT 57.712 34.615 0.00 0.00 0.00 1.82
537 598 8.732854 TGTGGAGAAGGGTATGGATATATTTTT 58.267 33.333 0.00 0.00 0.00 1.94
568 629 9.981460 AATTGTCATAGTTTTCTTTCTATCCCT 57.019 29.630 0.00 0.00 0.00 4.20
569 630 9.620259 ATTGTCATAGTTTTCTTTCTATCCCTC 57.380 33.333 0.00 0.00 0.00 4.30
570 631 8.146053 TGTCATAGTTTTCTTTCTATCCCTCA 57.854 34.615 0.00 0.00 0.00 3.86
571 632 8.602424 TGTCATAGTTTTCTTTCTATCCCTCAA 58.398 33.333 0.00 0.00 0.00 3.02
572 633 9.449719 GTCATAGTTTTCTTTCTATCCCTCAAA 57.550 33.333 0.00 0.00 0.00 2.69
582 643 9.944376 TCTTTCTATCCCTCAAATATAAATCGG 57.056 33.333 0.00 0.00 0.00 4.18
583 644 9.944376 CTTTCTATCCCTCAAATATAAATCGGA 57.056 33.333 0.00 0.00 0.00 4.55
585 646 9.890629 TTCTATCCCTCAAATATAAATCGGATG 57.109 33.333 0.00 0.00 31.48 3.51
586 647 9.267071 TCTATCCCTCAAATATAAATCGGATGA 57.733 33.333 0.00 0.00 31.48 2.92
587 648 9.319143 CTATCCCTCAAATATAAATCGGATGAC 57.681 37.037 0.00 0.00 31.48 3.06
588 649 7.316393 TCCCTCAAATATAAATCGGATGACT 57.684 36.000 0.00 0.00 0.00 3.41
589 650 7.745717 TCCCTCAAATATAAATCGGATGACTT 58.254 34.615 0.00 0.00 0.00 3.01
590 651 8.876181 TCCCTCAAATATAAATCGGATGACTTA 58.124 33.333 0.00 0.00 0.00 2.24
591 652 9.672673 CCCTCAAATATAAATCGGATGACTTAT 57.327 33.333 0.00 0.00 31.87 1.73
600 661 6.918067 AATCGGATGACTTATATCACAGGA 57.082 37.500 0.00 0.00 0.00 3.86
601 662 7.487822 AATCGGATGACTTATATCACAGGAT 57.512 36.000 0.00 0.00 37.55 3.24
602 663 6.272822 TCGGATGACTTATATCACAGGATG 57.727 41.667 0.00 0.00 46.00 3.51
603 664 6.010219 TCGGATGACTTATATCACAGGATGA 58.990 40.000 0.00 0.00 43.13 2.92
604 665 6.071896 TCGGATGACTTATATCACAGGATGAC 60.072 42.308 0.00 0.00 41.24 3.06
605 666 6.294731 CGGATGACTTATATCACAGGATGACA 60.295 42.308 0.00 0.00 41.24 3.58
606 667 7.095910 GGATGACTTATATCACAGGATGACAG 58.904 42.308 0.00 0.00 41.24 3.51
607 668 7.039434 GGATGACTTATATCACAGGATGACAGA 60.039 40.741 0.00 0.00 41.24 3.41
608 669 7.660030 TGACTTATATCACAGGATGACAGAA 57.340 36.000 0.00 0.00 41.24 3.02
609 670 8.078060 TGACTTATATCACAGGATGACAGAAA 57.922 34.615 0.00 0.00 41.24 2.52
610 671 7.981789 TGACTTATATCACAGGATGACAGAAAC 59.018 37.037 0.00 0.00 41.24 2.78
611 672 7.851228 ACTTATATCACAGGATGACAGAAACA 58.149 34.615 0.00 0.00 41.24 2.83
612 673 7.766278 ACTTATATCACAGGATGACAGAAACAC 59.234 37.037 0.00 0.00 41.24 3.32
613 674 3.126001 TCACAGGATGACAGAAACACC 57.874 47.619 0.00 0.00 39.69 4.16
614 675 2.437651 TCACAGGATGACAGAAACACCA 59.562 45.455 0.00 0.00 39.69 4.17
615 676 3.072915 TCACAGGATGACAGAAACACCAT 59.927 43.478 0.00 0.00 39.69 3.55
616 677 3.822735 CACAGGATGACAGAAACACCATT 59.177 43.478 0.00 0.00 39.69 3.16
617 678 5.003160 CACAGGATGACAGAAACACCATTA 58.997 41.667 0.00 0.00 39.69 1.90
618 679 5.649395 CACAGGATGACAGAAACACCATTAT 59.351 40.000 0.00 0.00 39.69 1.28
619 680 5.882557 ACAGGATGACAGAAACACCATTATC 59.117 40.000 0.00 0.00 39.69 1.75
620 681 5.882000 CAGGATGACAGAAACACCATTATCA 59.118 40.000 0.00 0.00 39.69 2.15
621 682 6.544931 CAGGATGACAGAAACACCATTATCAT 59.455 38.462 0.00 0.00 39.69 2.45
622 683 7.067859 CAGGATGACAGAAACACCATTATCATT 59.932 37.037 0.00 0.00 39.69 2.57
623 684 8.274322 AGGATGACAGAAACACCATTATCATTA 58.726 33.333 0.00 0.00 0.00 1.90
624 685 8.902806 GGATGACAGAAACACCATTATCATTAA 58.097 33.333 0.00 0.00 0.00 1.40
625 686 9.722056 GATGACAGAAACACCATTATCATTAAC 57.278 33.333 0.00 0.00 0.00 2.01
626 687 8.862325 TGACAGAAACACCATTATCATTAACT 57.138 30.769 0.00 0.00 0.00 2.24
627 688 8.946085 TGACAGAAACACCATTATCATTAACTC 58.054 33.333 0.00 0.00 0.00 3.01
628 689 9.167311 GACAGAAACACCATTATCATTAACTCT 57.833 33.333 0.00 0.00 0.00 3.24
629 690 8.950210 ACAGAAACACCATTATCATTAACTCTG 58.050 33.333 0.00 0.00 0.00 3.35
630 691 8.950210 CAGAAACACCATTATCATTAACTCTGT 58.050 33.333 0.00 0.00 0.00 3.41
631 692 9.520515 AGAAACACCATTATCATTAACTCTGTT 57.479 29.630 0.00 0.00 0.00 3.16
663 724 1.686325 GAGATACTTGGGGCCGAGCA 61.686 60.000 0.00 0.00 0.00 4.26
674 735 2.103042 GCCGAGCAGACACATGGAC 61.103 63.158 0.00 0.00 0.00 4.02
877 951 1.159713 CGAGCTGCGGCCATTAATGA 61.160 55.000 15.55 0.00 39.73 2.57
955 1034 3.741476 GGCCACTTTGCTGCTCCG 61.741 66.667 0.00 0.00 0.00 4.63
956 1035 4.410743 GCCACTTTGCTGCTCCGC 62.411 66.667 0.00 0.00 0.00 5.54
957 1036 2.670934 CCACTTTGCTGCTCCGCT 60.671 61.111 0.00 0.00 0.00 5.52
958 1037 2.684843 CCACTTTGCTGCTCCGCTC 61.685 63.158 0.00 0.00 0.00 5.03
959 1038 2.359230 ACTTTGCTGCTCCGCTCC 60.359 61.111 0.00 0.00 0.00 4.70
1270 1361 3.050275 GTGAGCCCGCCAACAGAC 61.050 66.667 0.00 0.00 0.00 3.51
1447 1538 1.442769 TTGATTGCTCTTGTCGAGGC 58.557 50.000 0.00 0.00 40.25 4.70
1462 1553 2.028930 TCGAGGCTTCAACTTTCCTCTC 60.029 50.000 0.00 0.00 42.15 3.20
1464 1555 3.556004 CGAGGCTTCAACTTTCCTCTCTT 60.556 47.826 0.00 0.00 42.15 2.85
1465 1556 4.393834 GAGGCTTCAACTTTCCTCTCTTT 58.606 43.478 0.00 0.00 41.35 2.52
1466 1557 4.140536 AGGCTTCAACTTTCCTCTCTTTG 58.859 43.478 0.00 0.00 0.00 2.77
1467 1558 3.254411 GGCTTCAACTTTCCTCTCTTTGG 59.746 47.826 0.00 0.00 0.00 3.28
1468 1559 3.304996 GCTTCAACTTTCCTCTCTTTGGC 60.305 47.826 0.00 0.00 0.00 4.52
1469 1560 3.864789 TCAACTTTCCTCTCTTTGGCT 57.135 42.857 0.00 0.00 0.00 4.75
1470 1561 3.480470 TCAACTTTCCTCTCTTTGGCTG 58.520 45.455 0.00 0.00 0.00 4.85
1471 1562 2.555757 CAACTTTCCTCTCTTTGGCTGG 59.444 50.000 0.00 0.00 0.00 4.85
1472 1563 1.074566 ACTTTCCTCTCTTTGGCTGGG 59.925 52.381 0.00 0.00 0.00 4.45
1473 1564 0.251341 TTTCCTCTCTTTGGCTGGGC 60.251 55.000 0.00 0.00 0.00 5.36
1474 1565 1.426251 TTCCTCTCTTTGGCTGGGCA 61.426 55.000 0.00 0.00 0.00 5.36
1475 1566 1.378250 CCTCTCTTTGGCTGGGCAG 60.378 63.158 0.00 0.00 0.00 4.85
1717 1827 4.802051 TCGGCAGCAGAATGGCCC 62.802 66.667 0.00 0.00 39.87 5.80
2195 2305 0.953727 AAAGAAGCACGCAAGCATCA 59.046 45.000 5.57 0.00 45.62 3.07
2214 2324 4.136341 TCACCAAAGGTCCCTCTACTTA 57.864 45.455 0.00 0.00 31.02 2.24
2459 2569 2.505407 TGGACTCATCCCAACATACAGG 59.495 50.000 0.00 0.00 45.59 4.00
2544 2654 3.820467 CCTTGACAATGTTCCTTGTAGCA 59.180 43.478 0.00 0.00 39.40 3.49
2736 2846 1.067425 CATGTTGGCACCATGGACTTG 60.067 52.381 21.47 7.72 36.81 3.16
2767 2877 6.106003 TGATTGTCTTGATAGCGAGCTTTTA 58.894 36.000 1.86 0.00 0.00 1.52
2874 2986 4.435386 TTTTTGAGAAAACGCAAAGCTTGC 60.435 37.500 0.00 5.22 40.16 4.01
2948 3060 5.437191 AGAAGGGGTAGGATACAACAAAG 57.563 43.478 0.00 0.00 45.43 2.77
3029 3141 7.328249 TGGTCAATTCATTTCTTTTCGCATTAC 59.672 33.333 0.00 0.00 0.00 1.89
3478 3592 5.482175 AGGTACAGCTCTAGTCAACAAGAAT 59.518 40.000 0.00 0.00 0.00 2.40
3654 3768 8.621286 CATTATTCTTATTCGTTGGCCTAGTTT 58.379 33.333 3.32 0.00 0.00 2.66
3702 3816 8.511321 ACGACATACACACACAAAAATCATAAT 58.489 29.630 0.00 0.00 0.00 1.28
3805 3919 6.381707 ACTGTAAGGGGTTGTGTTACATTTTT 59.618 34.615 0.00 0.00 39.30 1.94
3823 3937 7.931275 ACATTTTTCTGTGAACTTACCTTCTC 58.069 34.615 0.00 0.00 0.00 2.87
3847 3961 3.304659 GGAATTTGCTGCTTGTCTCGAAA 60.305 43.478 0.00 0.00 0.00 3.46
3870 3984 2.165437 TGTTGGGTTGAAAGTGCAGTTC 59.835 45.455 7.36 5.17 0.00 3.01
3875 3989 3.243401 GGGTTGAAAGTGCAGTTCGATTT 60.243 43.478 7.36 0.00 0.00 2.17
3910 4029 7.437862 GCTGAGTTTGATTCATTTTGTAACCAA 59.562 33.333 0.00 0.00 0.00 3.67
3964 4083 4.153117 CCTTCAGGAAGAATTTGTCACTCG 59.847 45.833 10.52 0.00 40.79 4.18
4021 4140 1.751351 TCTCCTGCGTCTTGTATCAGG 59.249 52.381 0.92 0.92 45.59 3.86
4147 4267 1.459348 TGTGGCTCAGGACCAGTCA 60.459 57.895 0.00 0.00 38.04 3.41
4358 4478 6.199393 GCTTTTGTTCGTATATAAAGCCTGG 58.801 40.000 0.00 0.00 42.84 4.45
4395 4515 5.102020 TGACATAATGACGTGTTTGGTTG 57.898 39.130 0.00 0.00 0.00 3.77
4539 4691 8.736244 ACGTGGTGATTGCTTTATTTATAAAGT 58.264 29.630 18.51 4.54 46.78 2.66
4553 4709 5.511234 TTATAAAGTACGGTGAGAGCCTC 57.489 43.478 0.00 0.00 0.00 4.70
4627 4792 1.515521 GGCCTGGTTGTGGAGAAACG 61.516 60.000 0.00 0.00 0.00 3.60
4655 4820 3.517296 TGACCATTTCTAGCAACCCAA 57.483 42.857 0.00 0.00 0.00 4.12
4690 7978 0.119155 ACCCCCATTCTCTCTCACCA 59.881 55.000 0.00 0.00 0.00 4.17
4708 7996 2.301009 ACCACCTCTTAAGTTACCACCG 59.699 50.000 1.63 0.00 0.00 4.94
4747 8035 1.202463 CCGTCAGGCTGAGATACAAGG 60.202 57.143 19.38 8.87 0.00 3.61
4748 8036 1.478510 CGTCAGGCTGAGATACAAGGT 59.521 52.381 19.38 0.00 0.00 3.50
4775 8065 3.641437 TTGGCTCTTGTTGCATGTTAC 57.359 42.857 0.00 0.00 0.00 2.50
4787 8077 9.329913 CTTGTTGCATGTTACATTAGAGTAAAC 57.670 33.333 0.00 0.00 35.88 2.01
4858 8182 5.807520 ACTGTGTTCTGTAATGAGAATAGCG 59.192 40.000 0.00 0.00 34.50 4.26
4888 8212 5.588246 TGCAACTGTGTTTTCTGTAATGAGA 59.412 36.000 0.00 0.00 0.00 3.27
4894 8218 7.661437 ACTGTGTTTTCTGTAATGAGAATAGCA 59.339 33.333 0.00 0.00 31.98 3.49
4956 8280 6.912591 GGTTCAATGCTTATGGAACTTTATCG 59.087 38.462 7.30 0.00 39.55 2.92
4966 8290 6.727824 ATGGAACTTTATCGTTCTCAACAG 57.272 37.500 4.01 0.00 42.20 3.16
5071 8395 9.972106 AATTTTGGGATGCTAAAATATTTGGAA 57.028 25.926 19.01 0.00 35.94 3.53
5110 8435 9.520204 CAAGATTTTTAAAAAGAAGCTCTCACA 57.480 29.630 17.72 0.00 0.00 3.58
5122 8447 2.432146 AGCTCTCACACTCAACACTTGA 59.568 45.455 0.00 0.00 38.17 3.02
5134 8459 9.131791 ACACTCAACACTTGAAAATACCTATTT 57.868 29.630 0.00 0.00 39.58 1.40
5135 8460 9.965824 CACTCAACACTTGAAAATACCTATTTT 57.034 29.630 3.19 3.19 45.60 1.82
5154 8479 2.765689 TTTTGAAAAGGGGGAGCTCA 57.234 45.000 17.19 0.00 0.00 4.26
5155 8480 2.765689 TTTGAAAAGGGGGAGCTCAA 57.234 45.000 17.19 0.00 0.00 3.02
5156 8481 1.995376 TTGAAAAGGGGGAGCTCAAC 58.005 50.000 17.19 7.62 0.00 3.18
5157 8482 0.850100 TGAAAAGGGGGAGCTCAACA 59.150 50.000 17.19 0.63 0.00 3.33
5158 8483 1.248486 GAAAAGGGGGAGCTCAACAC 58.752 55.000 17.19 9.03 0.00 3.32
5159 8484 0.853530 AAAAGGGGGAGCTCAACACT 59.146 50.000 17.19 11.43 0.00 3.55
5160 8485 0.853530 AAAGGGGGAGCTCAACACTT 59.146 50.000 17.19 16.92 0.00 3.16
5161 8486 0.111253 AAGGGGGAGCTCAACACTTG 59.889 55.000 20.40 0.00 0.00 3.16
5162 8487 1.303643 GGGGGAGCTCAACACTTGG 60.304 63.158 17.19 0.00 0.00 3.61
5163 8488 1.761174 GGGGAGCTCAACACTTGGA 59.239 57.895 17.19 0.00 0.00 3.53
5164 8489 0.110486 GGGGAGCTCAACACTTGGAA 59.890 55.000 17.19 0.00 0.00 3.53
5165 8490 1.478654 GGGGAGCTCAACACTTGGAAA 60.479 52.381 17.19 0.00 0.00 3.13
5166 8491 2.519013 GGGAGCTCAACACTTGGAAAT 58.481 47.619 17.19 0.00 0.00 2.17
5167 8492 3.561313 GGGGAGCTCAACACTTGGAAATA 60.561 47.826 17.19 0.00 0.00 1.40
5168 8493 3.440522 GGGAGCTCAACACTTGGAAATAC 59.559 47.826 17.19 0.00 0.00 1.89
5169 8494 3.440522 GGAGCTCAACACTTGGAAATACC 59.559 47.826 17.19 0.00 39.54 2.73
5170 8495 4.327680 GAGCTCAACACTTGGAAATACCT 58.672 43.478 9.40 0.00 39.86 3.08
5171 8496 5.488341 GAGCTCAACACTTGGAAATACCTA 58.512 41.667 9.40 0.00 39.86 3.08
5199 8524 1.584724 TCTAAAAGGGGGAGCTCCTG 58.415 55.000 31.36 11.74 34.34 3.86
5359 8687 5.772169 GGCTGGCATAGAAAGATAGGAAAAT 59.228 40.000 0.00 0.00 0.00 1.82
5390 8718 6.650120 CCTATCCTATTACATAACCGCCATT 58.350 40.000 0.00 0.00 0.00 3.16
5398 8726 1.740585 CATAACCGCCATTCAAACCGA 59.259 47.619 0.00 0.00 0.00 4.69
5451 8780 8.914011 CCATCGGATAGATTCAGTAACCATATA 58.086 37.037 0.00 0.00 37.52 0.86
5460 8789 8.457757 AGATTCAGTAACCATATACTCCCTAGT 58.542 37.037 0.00 0.00 39.91 2.57
5497 8826 1.412710 AGCGACCACATACGGATCAAT 59.587 47.619 0.00 0.00 0.00 2.57
5595 8924 3.002656 CAGACTGCCCATAATAAAGCACG 59.997 47.826 0.00 0.00 0.00 5.34
5633 8962 1.656095 GTCTCGCTGTTTCGGAATCTG 59.344 52.381 0.00 0.00 0.00 2.90
5659 8988 3.080300 TCAAGCCACGTCCCAAATAAT 57.920 42.857 0.00 0.00 0.00 1.28
5695 9024 7.653767 ATTCGAAGGAGTAATATTAAAGGCG 57.346 36.000 3.35 0.00 0.00 5.52
5698 9027 7.439381 TCGAAGGAGTAATATTAAAGGCGATT 58.561 34.615 0.00 0.00 0.00 3.34
5711 9040 2.388232 GCGATTTGAACCGTCCGCT 61.388 57.895 0.00 0.00 39.57 5.52
5717 9046 4.143389 CGATTTGAACCGTCCGCTATAATC 60.143 45.833 0.00 0.00 0.00 1.75
5728 9057 5.505654 CGTCCGCTATAATCTTTTTGCCAAT 60.506 40.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.539051 CTCTCCACCGCAAGAGGAAT 59.461 55.000 0.00 0.00 40.09 3.01
75 78 0.251354 TCATGCTCCTCCTGTTCTGC 59.749 55.000 0.00 0.00 0.00 4.26
150 153 3.057245 CGAAATGAGATGCGAGGGATCTA 60.057 47.826 0.00 0.00 29.97 1.98
159 162 2.220363 CCAGATCACGAAATGAGATGCG 59.780 50.000 0.00 0.00 41.91 4.73
215 249 5.654650 ACCATGAACTTGTGAGGTTTGTTTA 59.345 36.000 0.00 0.00 0.00 2.01
216 250 4.466015 ACCATGAACTTGTGAGGTTTGTTT 59.534 37.500 0.00 0.00 0.00 2.83
217 251 4.023291 ACCATGAACTTGTGAGGTTTGTT 58.977 39.130 0.00 0.00 0.00 2.83
218 252 3.631250 ACCATGAACTTGTGAGGTTTGT 58.369 40.909 0.00 0.00 0.00 2.83
219 253 5.766150 TTACCATGAACTTGTGAGGTTTG 57.234 39.130 0.00 0.00 0.00 2.93
220 254 6.976934 AATTACCATGAACTTGTGAGGTTT 57.023 33.333 0.00 0.00 0.00 3.27
221 255 6.738453 GCAAATTACCATGAACTTGTGAGGTT 60.738 38.462 0.00 0.00 0.00 3.50
222 256 5.278957 GCAAATTACCATGAACTTGTGAGGT 60.279 40.000 0.00 0.00 0.00 3.85
254 288 0.035317 TGAGCGCATATTAGCCTGGG 59.965 55.000 11.47 0.00 0.00 4.45
333 376 0.674895 ACTGAGCATCTTTGACGCCC 60.675 55.000 0.00 0.00 34.92 6.13
392 453 9.359653 AGGCATCTTGCTAGTCAATAATTAATT 57.640 29.630 5.89 5.89 44.28 1.40
399 460 5.240891 GCATAGGCATCTTGCTAGTCAATA 58.759 41.667 0.00 0.00 44.28 1.90
403 464 2.064762 CGCATAGGCATCTTGCTAGTC 58.935 52.381 0.00 0.00 44.28 2.59
404 465 1.414181 ACGCATAGGCATCTTGCTAGT 59.586 47.619 0.00 0.00 44.28 2.57
405 466 2.160822 ACGCATAGGCATCTTGCTAG 57.839 50.000 0.00 0.00 44.28 3.42
406 467 2.212652 CAACGCATAGGCATCTTGCTA 58.787 47.619 0.00 0.00 44.28 3.49
407 468 1.019673 CAACGCATAGGCATCTTGCT 58.980 50.000 0.00 0.00 44.28 3.91
408 469 0.734889 ACAACGCATAGGCATCTTGC 59.265 50.000 0.00 0.00 44.08 4.01
409 470 2.033747 CGTACAACGCATAGGCATCTTG 60.034 50.000 0.00 0.05 41.24 3.02
410 471 2.201732 CGTACAACGCATAGGCATCTT 58.798 47.619 0.00 0.00 41.24 2.40
411 472 1.538204 CCGTACAACGCATAGGCATCT 60.538 52.381 0.00 0.00 40.91 2.90
412 473 0.859232 CCGTACAACGCATAGGCATC 59.141 55.000 0.00 0.00 40.91 3.91
413 474 0.462375 TCCGTACAACGCATAGGCAT 59.538 50.000 0.00 0.00 40.91 4.40
414 475 0.246910 TTCCGTACAACGCATAGGCA 59.753 50.000 0.00 0.00 40.91 4.75
415 476 0.648958 GTTCCGTACAACGCATAGGC 59.351 55.000 0.00 0.00 40.91 3.93
416 477 1.999048 TGTTCCGTACAACGCATAGG 58.001 50.000 0.00 0.00 40.91 2.57
417 478 5.062433 TGTTAATGTTCCGTACAACGCATAG 59.938 40.000 0.00 0.00 40.91 2.23
418 479 4.928020 TGTTAATGTTCCGTACAACGCATA 59.072 37.500 0.00 0.00 40.91 3.14
419 480 3.747010 TGTTAATGTTCCGTACAACGCAT 59.253 39.130 0.00 0.00 40.91 4.73
420 481 3.129109 TGTTAATGTTCCGTACAACGCA 58.871 40.909 0.00 0.00 40.91 5.24
421 482 3.791993 TGTTAATGTTCCGTACAACGC 57.208 42.857 0.00 0.00 40.91 4.84
422 483 4.085884 GCATGTTAATGTTCCGTACAACG 58.914 43.478 0.00 0.00 40.89 4.10
423 484 5.037015 TGCATGTTAATGTTCCGTACAAC 57.963 39.130 0.00 0.00 40.89 3.32
424 485 5.888691 ATGCATGTTAATGTTCCGTACAA 57.111 34.783 0.00 0.00 40.89 2.41
425 486 5.888691 AATGCATGTTAATGTTCCGTACA 57.111 34.783 0.00 0.00 41.97 2.90
426 487 6.090129 ACAAATGCATGTTAATGTTCCGTAC 58.910 36.000 0.00 0.00 36.08 3.67
427 488 6.260870 ACAAATGCATGTTAATGTTCCGTA 57.739 33.333 0.00 0.00 36.08 4.02
428 489 5.132897 ACAAATGCATGTTAATGTTCCGT 57.867 34.783 0.00 0.00 36.08 4.69
429 490 8.848948 TTATACAAATGCATGTTAATGTTCCG 57.151 30.769 0.00 0.00 36.08 4.30
430 491 9.801873 ACTTATACAAATGCATGTTAATGTTCC 57.198 29.630 0.00 0.00 36.08 3.62
470 531 8.940397 TTCCCTTGTTTATTCTTTTCTCTCAT 57.060 30.769 0.00 0.00 0.00 2.90
471 532 8.796475 CATTCCCTTGTTTATTCTTTTCTCTCA 58.204 33.333 0.00 0.00 0.00 3.27
472 533 7.757173 GCATTCCCTTGTTTATTCTTTTCTCTC 59.243 37.037 0.00 0.00 0.00 3.20
473 534 7.452813 AGCATTCCCTTGTTTATTCTTTTCTCT 59.547 33.333 0.00 0.00 0.00 3.10
474 535 7.606349 AGCATTCCCTTGTTTATTCTTTTCTC 58.394 34.615 0.00 0.00 0.00 2.87
475 536 7.544804 AGCATTCCCTTGTTTATTCTTTTCT 57.455 32.000 0.00 0.00 0.00 2.52
476 537 8.607441 AAAGCATTCCCTTGTTTATTCTTTTC 57.393 30.769 0.00 0.00 0.00 2.29
482 543 9.581099 CGTAAATAAAGCATTCCCTTGTTTATT 57.419 29.630 0.00 0.00 35.70 1.40
483 544 8.745590 ACGTAAATAAAGCATTCCCTTGTTTAT 58.254 29.630 0.00 0.00 0.00 1.40
484 545 8.113173 ACGTAAATAAAGCATTCCCTTGTTTA 57.887 30.769 0.00 0.00 0.00 2.01
485 546 6.988522 ACGTAAATAAAGCATTCCCTTGTTT 58.011 32.000 0.00 0.00 0.00 2.83
486 547 6.584185 ACGTAAATAAAGCATTCCCTTGTT 57.416 33.333 0.00 0.00 0.00 2.83
487 548 7.338449 ACATACGTAAATAAAGCATTCCCTTGT 59.662 33.333 0.00 0.00 0.00 3.16
488 549 7.643764 CACATACGTAAATAAAGCATTCCCTTG 59.356 37.037 0.00 0.00 0.00 3.61
489 550 7.201785 CCACATACGTAAATAAAGCATTCCCTT 60.202 37.037 0.00 0.00 0.00 3.95
490 551 6.262273 CCACATACGTAAATAAAGCATTCCCT 59.738 38.462 0.00 0.00 0.00 4.20
491 552 6.261381 TCCACATACGTAAATAAAGCATTCCC 59.739 38.462 0.00 0.00 0.00 3.97
492 553 7.225931 TCTCCACATACGTAAATAAAGCATTCC 59.774 37.037 0.00 0.00 0.00 3.01
493 554 8.138365 TCTCCACATACGTAAATAAAGCATTC 57.862 34.615 0.00 0.00 0.00 2.67
494 555 8.500753 TTCTCCACATACGTAAATAAAGCATT 57.499 30.769 0.00 0.00 0.00 3.56
495 556 7.226720 CCTTCTCCACATACGTAAATAAAGCAT 59.773 37.037 0.00 0.00 0.00 3.79
496 557 6.537301 CCTTCTCCACATACGTAAATAAAGCA 59.463 38.462 0.00 0.00 0.00 3.91
497 558 6.018180 CCCTTCTCCACATACGTAAATAAAGC 60.018 42.308 0.00 0.00 0.00 3.51
498 559 7.046033 ACCCTTCTCCACATACGTAAATAAAG 58.954 38.462 0.00 0.00 0.00 1.85
499 560 6.949715 ACCCTTCTCCACATACGTAAATAAA 58.050 36.000 0.00 0.00 0.00 1.40
500 561 6.549433 ACCCTTCTCCACATACGTAAATAA 57.451 37.500 0.00 0.00 0.00 1.40
501 562 7.256048 CCATACCCTTCTCCACATACGTAAATA 60.256 40.741 0.00 0.00 0.00 1.40
502 563 6.463897 CCATACCCTTCTCCACATACGTAAAT 60.464 42.308 0.00 0.00 0.00 1.40
503 564 5.163385 CCATACCCTTCTCCACATACGTAAA 60.163 44.000 0.00 0.00 0.00 2.01
504 565 4.342951 CCATACCCTTCTCCACATACGTAA 59.657 45.833 0.00 0.00 0.00 3.18
505 566 3.893200 CCATACCCTTCTCCACATACGTA 59.107 47.826 0.00 0.00 0.00 3.57
506 567 2.698797 CCATACCCTTCTCCACATACGT 59.301 50.000 0.00 0.00 0.00 3.57
507 568 2.963101 TCCATACCCTTCTCCACATACG 59.037 50.000 0.00 0.00 0.00 3.06
508 569 6.875972 ATATCCATACCCTTCTCCACATAC 57.124 41.667 0.00 0.00 0.00 2.39
509 570 9.574577 AAATATATCCATACCCTTCTCCACATA 57.425 33.333 0.00 0.00 0.00 2.29
510 571 8.468547 AAATATATCCATACCCTTCTCCACAT 57.531 34.615 0.00 0.00 0.00 3.21
511 572 7.888514 AAATATATCCATACCCTTCTCCACA 57.111 36.000 0.00 0.00 0.00 4.17
542 603 9.981460 AGGGATAGAAAGAAAACTATGACAATT 57.019 29.630 0.00 0.00 30.74 2.32
543 604 9.620259 GAGGGATAGAAAGAAAACTATGACAAT 57.380 33.333 0.00 0.00 30.74 2.71
544 605 8.602424 TGAGGGATAGAAAGAAAACTATGACAA 58.398 33.333 0.00 0.00 30.74 3.18
545 606 8.146053 TGAGGGATAGAAAGAAAACTATGACA 57.854 34.615 0.00 0.00 30.74 3.58
546 607 9.449719 TTTGAGGGATAGAAAGAAAACTATGAC 57.550 33.333 0.00 0.00 30.74 3.06
556 617 9.944376 CCGATTTATATTTGAGGGATAGAAAGA 57.056 33.333 0.00 0.00 0.00 2.52
557 618 9.944376 TCCGATTTATATTTGAGGGATAGAAAG 57.056 33.333 0.00 0.00 0.00 2.62
559 620 9.890629 CATCCGATTTATATTTGAGGGATAGAA 57.109 33.333 0.00 0.00 32.09 2.10
560 621 9.267071 TCATCCGATTTATATTTGAGGGATAGA 57.733 33.333 0.00 0.00 32.09 1.98
561 622 9.319143 GTCATCCGATTTATATTTGAGGGATAG 57.681 37.037 0.00 0.00 32.09 2.08
562 623 9.046846 AGTCATCCGATTTATATTTGAGGGATA 57.953 33.333 0.00 0.00 32.09 2.59
563 624 7.922382 AGTCATCCGATTTATATTTGAGGGAT 58.078 34.615 0.00 0.00 33.49 3.85
564 625 7.316393 AGTCATCCGATTTATATTTGAGGGA 57.684 36.000 0.00 0.00 0.00 4.20
565 626 7.986085 AAGTCATCCGATTTATATTTGAGGG 57.014 36.000 0.00 0.00 0.00 4.30
574 635 9.035890 TCCTGTGATATAAGTCATCCGATTTAT 57.964 33.333 0.00 0.00 37.66 1.40
575 636 8.417273 TCCTGTGATATAAGTCATCCGATTTA 57.583 34.615 0.00 0.00 0.00 1.40
576 637 7.303182 TCCTGTGATATAAGTCATCCGATTT 57.697 36.000 0.00 0.00 0.00 2.17
577 638 6.918067 TCCTGTGATATAAGTCATCCGATT 57.082 37.500 0.00 0.00 0.00 3.34
578 639 6.665248 TCATCCTGTGATATAAGTCATCCGAT 59.335 38.462 0.00 0.00 0.00 4.18
579 640 6.010219 TCATCCTGTGATATAAGTCATCCGA 58.990 40.000 0.00 0.00 0.00 4.55
580 641 6.096036 GTCATCCTGTGATATAAGTCATCCG 58.904 44.000 0.00 0.00 39.48 4.18
581 642 6.997655 TGTCATCCTGTGATATAAGTCATCC 58.002 40.000 0.00 0.00 39.48 3.51
582 643 7.890515 TCTGTCATCCTGTGATATAAGTCATC 58.109 38.462 0.00 0.00 39.48 2.92
583 644 7.846101 TCTGTCATCCTGTGATATAAGTCAT 57.154 36.000 0.00 0.00 39.48 3.06
584 645 7.660030 TTCTGTCATCCTGTGATATAAGTCA 57.340 36.000 0.00 0.00 39.48 3.41
585 646 7.981789 TGTTTCTGTCATCCTGTGATATAAGTC 59.018 37.037 0.00 0.00 39.48 3.01
586 647 7.766278 GTGTTTCTGTCATCCTGTGATATAAGT 59.234 37.037 0.00 0.00 39.48 2.24
587 648 7.225538 GGTGTTTCTGTCATCCTGTGATATAAG 59.774 40.741 0.00 0.00 39.48 1.73
588 649 7.047891 GGTGTTTCTGTCATCCTGTGATATAA 58.952 38.462 0.00 0.00 39.48 0.98
589 650 6.156083 TGGTGTTTCTGTCATCCTGTGATATA 59.844 38.462 0.00 0.00 39.48 0.86
590 651 5.045651 TGGTGTTTCTGTCATCCTGTGATAT 60.046 40.000 0.00 0.00 39.48 1.63
591 652 4.285775 TGGTGTTTCTGTCATCCTGTGATA 59.714 41.667 0.00 0.00 39.48 2.15
592 653 3.072915 TGGTGTTTCTGTCATCCTGTGAT 59.927 43.478 0.00 0.00 39.48 3.06
593 654 2.437651 TGGTGTTTCTGTCATCCTGTGA 59.562 45.455 0.00 0.00 0.00 3.58
594 655 2.849942 TGGTGTTTCTGTCATCCTGTG 58.150 47.619 0.00 0.00 0.00 3.66
595 656 3.795688 ATGGTGTTTCTGTCATCCTGT 57.204 42.857 0.00 0.00 0.00 4.00
596 657 5.882000 TGATAATGGTGTTTCTGTCATCCTG 59.118 40.000 0.00 0.00 0.00 3.86
597 658 6.065976 TGATAATGGTGTTTCTGTCATCCT 57.934 37.500 0.00 0.00 0.00 3.24
598 659 6.949352 ATGATAATGGTGTTTCTGTCATCC 57.051 37.500 0.00 0.00 0.00 3.51
599 660 9.722056 GTTAATGATAATGGTGTTTCTGTCATC 57.278 33.333 0.00 0.00 0.00 2.92
600 661 9.466497 AGTTAATGATAATGGTGTTTCTGTCAT 57.534 29.630 0.00 0.00 0.00 3.06
601 662 8.862325 AGTTAATGATAATGGTGTTTCTGTCA 57.138 30.769 0.00 0.00 0.00 3.58
602 663 9.167311 AGAGTTAATGATAATGGTGTTTCTGTC 57.833 33.333 0.00 0.00 0.00 3.51
603 664 8.950210 CAGAGTTAATGATAATGGTGTTTCTGT 58.050 33.333 0.00 0.00 0.00 3.41
604 665 8.950210 ACAGAGTTAATGATAATGGTGTTTCTG 58.050 33.333 0.00 0.00 33.82 3.02
605 666 9.520515 AACAGAGTTAATGATAATGGTGTTTCT 57.479 29.630 0.00 0.00 0.00 2.52
631 692 8.648693 GCCCCAAGTATCTCTACTCTTATAAAA 58.351 37.037 0.00 0.00 37.20 1.52
632 693 7.234988 GGCCCCAAGTATCTCTACTCTTATAAA 59.765 40.741 0.00 0.00 37.20 1.40
633 694 6.724905 GGCCCCAAGTATCTCTACTCTTATAA 59.275 42.308 0.00 0.00 37.20 0.98
634 695 6.254522 GGCCCCAAGTATCTCTACTCTTATA 58.745 44.000 0.00 0.00 37.20 0.98
635 696 5.088026 GGCCCCAAGTATCTCTACTCTTAT 58.912 45.833 0.00 0.00 37.20 1.73
636 697 4.481072 GGCCCCAAGTATCTCTACTCTTA 58.519 47.826 0.00 0.00 37.20 2.10
637 698 3.310193 GGCCCCAAGTATCTCTACTCTT 58.690 50.000 0.00 0.00 37.20 2.85
638 699 2.753507 CGGCCCCAAGTATCTCTACTCT 60.754 54.545 0.00 0.00 37.20 3.24
639 700 1.614413 CGGCCCCAAGTATCTCTACTC 59.386 57.143 0.00 0.00 37.20 2.59
640 701 1.217183 TCGGCCCCAAGTATCTCTACT 59.783 52.381 0.00 0.00 39.97 2.57
641 702 1.614413 CTCGGCCCCAAGTATCTCTAC 59.386 57.143 0.00 0.00 0.00 2.59
642 703 1.996798 CTCGGCCCCAAGTATCTCTA 58.003 55.000 0.00 0.00 0.00 2.43
643 704 1.403687 GCTCGGCCCCAAGTATCTCT 61.404 60.000 0.00 0.00 0.00 3.10
644 705 1.069935 GCTCGGCCCCAAGTATCTC 59.930 63.158 0.00 0.00 0.00 2.75
645 706 1.689233 TGCTCGGCCCCAAGTATCT 60.689 57.895 0.00 0.00 0.00 1.98
649 710 4.021925 GTCTGCTCGGCCCCAAGT 62.022 66.667 0.00 0.00 0.00 3.16
663 724 2.569853 TGGATTAACGGTCCATGTGTCT 59.430 45.455 0.00 0.00 40.72 3.41
674 735 4.737765 CACTGTTTGTGTTTGGATTAACGG 59.262 41.667 0.00 0.00 41.53 4.44
955 1034 0.034896 TTCTGAAACAGTCGGGGAGC 59.965 55.000 0.00 0.00 32.90 4.70
956 1035 1.608283 GGTTCTGAAACAGTCGGGGAG 60.608 57.143 0.00 0.00 37.10 4.30
957 1036 0.395312 GGTTCTGAAACAGTCGGGGA 59.605 55.000 0.00 0.00 37.10 4.81
958 1037 0.107831 TGGTTCTGAAACAGTCGGGG 59.892 55.000 3.54 0.00 37.10 5.73
959 1038 1.512926 CTGGTTCTGAAACAGTCGGG 58.487 55.000 23.95 2.52 37.10 5.14
1447 1538 4.023365 CAGCCAAAGAGAGGAAAGTTGAAG 60.023 45.833 0.00 0.00 0.00 3.02
1471 1562 4.891037 GATCAGCCCTGCCCTGCC 62.891 72.222 0.00 0.00 0.00 4.85
1472 1563 4.891037 GGATCAGCCCTGCCCTGC 62.891 72.222 0.00 0.00 0.00 4.85
1473 1564 4.559063 CGGATCAGCCCTGCCCTG 62.559 72.222 0.00 0.00 0.00 4.45
1475 1566 4.864334 CACGGATCAGCCCTGCCC 62.864 72.222 0.00 0.00 0.00 5.36
1479 1570 0.978146 AAGCTACACGGATCAGCCCT 60.978 55.000 0.00 0.00 35.88 5.19
1717 1827 1.003839 TCGGCCTTGGTGTTGCTAG 60.004 57.895 0.00 0.00 0.00 3.42
2195 2305 4.161754 CGAATAAGTAGAGGGACCTTTGGT 59.838 45.833 0.00 0.00 39.44 3.67
2459 2569 2.215196 TCAACTTGAGTAAACCGTGGC 58.785 47.619 0.00 0.00 0.00 5.01
2544 2654 9.136323 AGAAACTCTTATTCCAATTGTTCTTGT 57.864 29.630 4.43 0.00 0.00 3.16
2703 2813 2.223876 GCCAACATGATAGCCCACAATG 60.224 50.000 0.00 0.00 0.00 2.82
2736 2846 4.378149 CGCTATCAAGACAATCATGCATCC 60.378 45.833 0.00 0.00 0.00 3.51
2874 2986 7.351414 TCAGTCTTTTCAATATGTTGAGACG 57.649 36.000 13.65 5.52 44.62 4.18
3004 3116 6.710692 AATGCGAAAAGAAATGAATTGACC 57.289 33.333 0.00 0.00 0.00 4.02
3478 3592 3.011369 AGTGGTGAGGATCCAGTACTACA 59.989 47.826 22.28 8.58 36.92 2.74
3654 3768 8.399425 GTCGTCAATCTCTAGAAACAGATAGAA 58.601 37.037 0.00 0.00 0.00 2.10
3702 3816 0.035881 CTCCAGAAGCAAGCCTGTGA 59.964 55.000 0.00 0.00 0.00 3.58
3805 3919 4.480115 TCCAGAGAAGGTAAGTTCACAGA 58.520 43.478 0.00 0.00 0.00 3.41
3823 3937 2.413765 CGAGACAAGCAGCAAATTCCAG 60.414 50.000 0.00 0.00 0.00 3.86
3847 3961 2.765699 ACTGCACTTTCAACCCAACAAT 59.234 40.909 0.00 0.00 0.00 2.71
3882 3996 7.115378 GGTTACAAAATGAATCAAACTCAGCTG 59.885 37.037 7.63 7.63 0.00 4.24
3964 4083 7.658575 AGAGTAAGATATTGTACGGACTCTCTC 59.341 40.741 0.00 0.00 38.35 3.20
4029 4148 7.755373 GGTAAGCTCTTTCATGGTTGTTTATTC 59.245 37.037 0.00 0.00 0.00 1.75
4031 4150 6.128007 CGGTAAGCTCTTTCATGGTTGTTTAT 60.128 38.462 0.00 0.00 0.00 1.40
4032 4151 5.180492 CGGTAAGCTCTTTCATGGTTGTTTA 59.820 40.000 0.00 0.00 0.00 2.01
4273 4393 7.181569 TGACAGGTGATGTATCTAATGTGAA 57.818 36.000 0.00 0.00 44.17 3.18
4358 4478 0.968405 TGTCAATTGGAAAGCAGGCC 59.032 50.000 5.42 0.00 0.00 5.19
4538 4690 1.467713 CGAAAGAGGCTCTCACCGTAC 60.468 57.143 19.03 3.85 32.06 3.67
4539 4691 0.809385 CGAAAGAGGCTCTCACCGTA 59.191 55.000 19.03 0.00 32.06 4.02
4553 4709 1.151668 CAGTGCAACCCTCTCGAAAG 58.848 55.000 0.00 0.00 37.80 2.62
4589 4754 4.079787 AGGCCCATGTCTGCTTTAAGATTA 60.080 41.667 0.00 0.00 0.00 1.75
4627 4792 5.991328 TGCTAGAAATGGTCAATTCGATC 57.009 39.130 0.00 0.00 0.00 3.69
4690 7978 3.197116 CCATCGGTGGTAACTTAAGAGGT 59.803 47.826 6.53 0.00 40.83 3.85
4708 7996 0.727398 GTGGAGCGTTAGCAACCATC 59.273 55.000 11.08 4.31 46.89 3.51
4775 8065 8.725148 AGCAGATTTCTTGTGTTTACTCTAATG 58.275 33.333 0.00 0.00 0.00 1.90
4787 8077 4.321718 TCCTCTTGAGCAGATTTCTTGTG 58.678 43.478 0.00 0.00 0.00 3.33
4858 8182 4.864247 ACAGAAAACACAGTTGCAACAATC 59.136 37.500 30.11 16.01 0.00 2.67
4888 8212 8.059798 AGATGCAATGTAGTTTCTTTGCTATT 57.940 30.769 14.72 4.42 43.80 1.73
4894 8218 7.442062 CCCAAAAAGATGCAATGTAGTTTCTTT 59.558 33.333 0.00 0.00 35.54 2.52
4911 8235 4.285863 ACCAAATCACAGTCCCAAAAAGA 58.714 39.130 0.00 0.00 0.00 2.52
4956 8280 4.771590 TGCATTTCATCCTGTTGAGAAC 57.228 40.909 0.00 0.00 0.00 3.01
5081 8405 8.788409 AGAGCTTCTTTTTAAAAATCTTGTCG 57.212 30.769 13.55 1.27 0.00 4.35
5098 8422 2.697751 AGTGTTGAGTGTGAGAGCTTCT 59.302 45.455 0.00 0.00 0.00 2.85
5099 8423 3.104843 AGTGTTGAGTGTGAGAGCTTC 57.895 47.619 0.00 0.00 0.00 3.86
5134 8459 3.039252 TGAGCTCCCCCTTTTCAAAAA 57.961 42.857 12.15 0.00 0.00 1.94
5135 8460 2.698274 GTTGAGCTCCCCCTTTTCAAAA 59.302 45.455 12.15 0.00 30.43 2.44
5136 8461 2.316108 GTTGAGCTCCCCCTTTTCAAA 58.684 47.619 12.15 0.00 30.43 2.69
5137 8462 1.216678 TGTTGAGCTCCCCCTTTTCAA 59.783 47.619 12.15 0.00 0.00 2.69
5138 8463 0.850100 TGTTGAGCTCCCCCTTTTCA 59.150 50.000 12.15 0.00 0.00 2.69
5139 8464 1.202940 AGTGTTGAGCTCCCCCTTTTC 60.203 52.381 12.15 0.00 0.00 2.29
5140 8465 0.853530 AGTGTTGAGCTCCCCCTTTT 59.146 50.000 12.15 0.00 0.00 2.27
5141 8466 0.853530 AAGTGTTGAGCTCCCCCTTT 59.146 50.000 12.15 0.00 0.00 3.11
5142 8467 0.111253 CAAGTGTTGAGCTCCCCCTT 59.889 55.000 12.15 5.30 0.00 3.95
5143 8468 1.763770 CAAGTGTTGAGCTCCCCCT 59.236 57.895 12.15 0.00 0.00 4.79
5144 8469 1.303643 CCAAGTGTTGAGCTCCCCC 60.304 63.158 12.15 0.00 0.00 5.40
5145 8470 0.110486 TTCCAAGTGTTGAGCTCCCC 59.890 55.000 12.15 1.67 0.00 4.81
5146 8471 1.981256 TTTCCAAGTGTTGAGCTCCC 58.019 50.000 12.15 2.07 0.00 4.30
5147 8472 3.440522 GGTATTTCCAAGTGTTGAGCTCC 59.559 47.826 12.15 0.00 35.97 4.70
5148 8473 4.327680 AGGTATTTCCAAGTGTTGAGCTC 58.672 43.478 6.82 6.82 39.02 4.09
5149 8474 4.373156 AGGTATTTCCAAGTGTTGAGCT 57.627 40.909 0.00 0.00 39.02 4.09
5150 8475 6.759497 ATTAGGTATTTCCAAGTGTTGAGC 57.241 37.500 0.00 0.00 39.02 4.26
5151 8476 9.981114 AAAAATTAGGTATTTCCAAGTGTTGAG 57.019 29.630 0.00 0.00 35.39 3.02
5182 8507 0.919289 CCCAGGAGCTCCCCCTTTTA 60.919 60.000 29.54 0.00 36.42 1.52
5305 8631 6.978659 GTGGCTTTACTTTTACTTTTCTGCTT 59.021 34.615 0.00 0.00 0.00 3.91
5315 8641 3.892522 CCGGTTGTGGCTTTACTTTTAC 58.107 45.455 0.00 0.00 0.00 2.01
5359 8687 9.661563 CGGTTATGTAATAGGATAGGCAATTAA 57.338 33.333 0.00 0.00 0.00 1.40
5390 8718 4.693566 ACGAGCTATTTTCAATCGGTTTGA 59.306 37.500 0.00 0.00 42.62 2.69
5451 8780 1.223501 TCCGATGGAGACTAGGGAGT 58.776 55.000 0.00 0.00 39.20 3.85
5497 8826 2.436417 GTTATCTTCCAAGCCACTGCA 58.564 47.619 0.00 0.00 41.13 4.41
5595 8924 5.274718 CGAGACACATTCATGTAGGAGTAC 58.725 45.833 0.00 0.00 39.39 2.73
5633 8962 1.745489 GGACGTGGCTTGATGGGAC 60.745 63.158 0.00 0.00 0.00 4.46
5659 8988 6.525578 ACTCCTTCGAATACTATCAACACA 57.474 37.500 0.00 0.00 0.00 3.72
5695 9024 4.989168 AGATTATAGCGGACGGTTCAAATC 59.011 41.667 0.55 9.00 0.00 2.17
5698 9027 4.395959 AAGATTATAGCGGACGGTTCAA 57.604 40.909 0.55 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.