Multiple sequence alignment - TraesCS3B01G244200

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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 TraesCS3B01G244200 chr3B 100.000 2564 0 0 1 2564 386376501 386373938 0.000000e+00 4735.0
1 TraesCS3B01G244200 chr3B 92.308 39 2 1 708 746 413809035 413809072 1.000000e-03 54.7
2 TraesCS3B01G244200 chr3B 96.875 32 0 1 2113 2143 361765906 361765937 5.000000e-03 52.8
3 TraesCS3B01G244200 chr3D 92.650 1347 53 18 737 2071 292373762 292375074 0.000000e+00 1897.0
4 TraesCS3B01G244200 chr3D 95.800 500 17 2 1 497 292373261 292373759 0.000000e+00 804.0
5 TraesCS3B01G244200 chr3D 92.723 481 33 2 2082 2561 292375026 292375505 0.000000e+00 693.0
6 TraesCS3B01G244200 chr3D 74.312 218 40 13 1803 2012 520649337 520649128 7.610000e-11 78.7
7 TraesCS3B01G244200 chr3A 93.231 916 36 13 737 1650 385524589 385523698 0.000000e+00 1325.0
8 TraesCS3B01G244200 chr3A 95.418 502 15 4 1 497 385525090 385524592 0.000000e+00 793.0
9 TraesCS3B01G244200 chr3A 87.680 487 46 10 2082 2564 385522256 385521780 2.880000e-154 555.0
10 TraesCS3B01G244200 chr3A 91.071 336 28 2 1749 2083 385522529 385522195 1.080000e-123 453.0
11 TraesCS3B01G244200 chr3A 96.226 106 4 0 1645 1750 385523671 385523566 9.430000e-40 174.0
12 TraesCS3B01G244200 chr3A 97.701 87 1 1 594 679 596769580 596769666 5.720000e-32 148.0
13 TraesCS3B01G244200 chr7B 89.516 124 10 2 595 717 114499633 114499754 1.230000e-33 154.0
14 TraesCS3B01G244200 chr7B 100.000 28 0 0 506 533 20054386 20054359 5.000000e-03 52.8
15 TraesCS3B01G244200 chr2B 89.516 124 10 2 594 716 519020849 519020728 1.230000e-33 154.0
16 TraesCS3B01G244200 chr2B 97.701 87 1 1 594 679 44414796 44414882 5.720000e-32 148.0
17 TraesCS3B01G244200 chr2B 100.000 36 0 0 682 717 793507291 793507256 1.650000e-07 67.6
18 TraesCS3B01G244200 chr2B 72.959 196 42 11 2109 2297 704289726 704289535 9.910000e-05 58.4
19 TraesCS3B01G244200 chr2B 92.308 39 1 2 704 741 655842008 655841971 1.000000e-03 54.7
20 TraesCS3B01G244200 chr5B 97.727 88 1 1 593 679 65189365 65189452 1.590000e-32 150.0
21 TraesCS3B01G244200 chr5B 95.122 41 2 0 682 722 539466160 539466120 5.920000e-07 65.8
22 TraesCS3B01G244200 chr5B 96.875 32 0 1 711 742 70795681 70795651 5.000000e-03 52.8
23 TraesCS3B01G244200 chr5B 100.000 28 0 0 506 533 303230859 303230886 5.000000e-03 52.8
24 TraesCS3B01G244200 chr5B 100.000 28 0 0 718 745 596547684 596547657 5.000000e-03 52.8
25 TraesCS3B01G244200 chr7A 97.701 87 1 1 594 679 719561638 719561552 5.720000e-32 148.0
26 TraesCS3B01G244200 chr4B 97.674 86 2 0 594 679 548610690 548610775 5.720000e-32 148.0
27 TraesCS3B01G244200 chr2A 97.674 86 2 0 594 679 753531324 753531409 5.720000e-32 148.0
28 TraesCS3B01G244200 chr6A 87.121 132 9 6 594 717 73067857 73067726 2.660000e-30 143.0
29 TraesCS3B01G244200 chrUn 98.361 61 1 0 534 594 216510166 216510226 9.700000e-20 108.0
30 TraesCS3B01G244200 chrUn 98.361 61 1 0 534 594 397078352 397078412 9.700000e-20 108.0
31 TraesCS3B01G244200 chrUn 98.361 61 1 0 534 594 424751203 424751263 9.700000e-20 108.0
32 TraesCS3B01G244200 chrUn 98.361 61 1 0 534 594 455551844 455551784 9.700000e-20 108.0
33 TraesCS3B01G244200 chrUn 100.000 28 0 0 716 743 70385210 70385237 5.000000e-03 52.8
34 TraesCS3B01G244200 chr6D 98.361 61 1 0 534 594 389248327 389248267 9.700000e-20 108.0
35 TraesCS3B01G244200 chr6D 98.361 61 1 0 534 594 389253122 389253062 9.700000e-20 108.0
36 TraesCS3B01G244200 chr6D 84.058 69 11 0 2187 2255 104576963 104576895 1.650000e-07 67.6
37 TraesCS3B01G244200 chr6D 94.286 35 1 1 708 742 336183899 336183932 5.000000e-03 52.8
38 TraesCS3B01G244200 chr4D 98.361 61 1 0 534 594 207361828 207361888 9.700000e-20 108.0
39 TraesCS3B01G244200 chr4D 98.361 61 1 0 534 594 393153647 393153587 9.700000e-20 108.0
40 TraesCS3B01G244200 chr4D 100.000 28 0 0 716 743 234179236 234179263 5.000000e-03 52.8
41 TraesCS3B01G244200 chr1D 98.361 61 1 0 534 594 176205693 176205633 9.700000e-20 108.0
42 TraesCS3B01G244200 chr1D 97.143 35 0 1 499 533 335031407 335031440 9.910000e-05 58.4
43 TraesCS3B01G244200 chr2D 87.500 72 9 0 2197 2268 512667493 512667422 1.630000e-12 84.2
44 TraesCS3B01G244200 chr2D 97.500 40 0 1 679 717 649832236 649832197 1.650000e-07 67.6
45 TraesCS3B01G244200 chr2D 95.000 40 1 1 677 716 160601002 160601040 7.660000e-06 62.1
46 TraesCS3B01G244200 chr2D 100.000 28 0 0 716 743 21925298 21925271 5.000000e-03 52.8
47 TraesCS3B01G244200 chr2D 90.244 41 2 2 704 743 158283374 158283413 5.000000e-03 52.8
48 TraesCS3B01G244200 chr7D 90.476 63 3 3 1803 1863 613056486 613056425 2.110000e-11 80.5
49 TraesCS3B01G244200 chr1B 97.619 42 1 0 676 717 659688416 659688375 3.540000e-09 73.1
50 TraesCS3B01G244200 chr1B 100.000 29 0 0 505 533 503812464 503812436 1.000000e-03 54.7
51 TraesCS3B01G244200 chr6B 100.000 36 0 0 682 717 574032330 574032365 1.650000e-07 67.6
52 TraesCS3B01G244200 chr5A 100.000 32 0 0 502 533 101414211 101414180 2.760000e-05 60.2
53 TraesCS3B01G244200 chr5D 100.000 29 0 0 505 533 110618035 110618007 1.000000e-03 54.7


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 TraesCS3B01G244200 chr3B 386373938 386376501 2563 True 4735.000000 4735 100.000000 1 2564 1 chr3B.!!$R1 2563
1 TraesCS3B01G244200 chr3D 292373261 292375505 2244 False 1131.333333 1897 93.724333 1 2561 3 chr3D.!!$F1 2560
2 TraesCS3B01G244200 chr3A 385521780 385525090 3310 True 660.000000 1325 92.725200 1 2564 5 chr3A.!!$R1 2563

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
734 738 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 3062 0.174617 TCATCCTATGCGCACGAACA 59.825 50.0 14.9 0.0 0.0 3.18 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
123 124 4.097892 AGTTGTGGTAAGCCTGTTTTTCAG 59.902 41.667 0.00 0.00 43.27 3.02
131 132 3.761481 CTGTTTTTCAGGAGCAGCG 57.239 52.632 0.00 0.00 40.23 5.18
132 133 1.229428 CTGTTTTTCAGGAGCAGCGA 58.771 50.000 0.00 0.00 40.23 4.93
211 215 1.335872 GGTGTTGCTTGGTCGAAATGG 60.336 52.381 0.00 0.00 0.00 3.16
302 306 8.587608 TGTTGATTGATAAAGAAAGGCAAGAAT 58.412 29.630 0.00 0.00 0.00 2.40
345 349 3.119919 AGTGACTCGAGTTTATGTCGGTC 60.120 47.826 21.08 3.27 38.02 4.79
365 369 5.506483 CGGTCTGAGTTCTGATGTACCTATG 60.506 48.000 0.00 0.00 0.00 2.23
483 487 0.961019 TTTTGTGCCTGATGAGTGCC 59.039 50.000 0.00 0.00 0.00 5.01
485 489 2.066700 TTGTGCCTGATGAGTGCCCA 62.067 55.000 0.00 0.00 0.00 5.36
486 490 1.303561 GTGCCTGATGAGTGCCCAA 60.304 57.895 0.00 0.00 0.00 4.12
487 491 0.682209 GTGCCTGATGAGTGCCCAAT 60.682 55.000 0.00 0.00 0.00 3.16
488 492 0.394762 TGCCTGATGAGTGCCCAATC 60.395 55.000 0.00 0.00 0.00 2.67
489 493 1.442526 GCCTGATGAGTGCCCAATCG 61.443 60.000 0.00 0.00 0.00 3.34
490 494 0.178767 CCTGATGAGTGCCCAATCGA 59.821 55.000 0.00 0.00 0.00 3.59
491 495 1.202734 CCTGATGAGTGCCCAATCGAT 60.203 52.381 0.00 0.00 0.00 3.59
492 496 2.569059 CTGATGAGTGCCCAATCGATT 58.431 47.619 4.39 4.39 0.00 3.34
493 497 2.289820 CTGATGAGTGCCCAATCGATTG 59.710 50.000 27.66 27.66 37.52 2.67
494 498 2.292267 GATGAGTGCCCAATCGATTGT 58.708 47.619 30.71 16.09 36.06 2.71
495 499 1.452110 TGAGTGCCCAATCGATTGTG 58.548 50.000 30.71 23.56 36.06 3.33
496 500 1.271325 TGAGTGCCCAATCGATTGTGT 60.271 47.619 30.71 14.05 36.06 3.72
509 513 3.314913 TCGATTGTGTTCAATTGTGTGCT 59.685 39.130 5.13 0.00 43.33 4.40
510 514 4.513318 TCGATTGTGTTCAATTGTGTGCTA 59.487 37.500 5.13 0.00 43.33 3.49
511 515 4.612614 CGATTGTGTTCAATTGTGTGCTAC 59.387 41.667 5.13 0.00 43.33 3.58
512 516 5.560760 CGATTGTGTTCAATTGTGTGCTACT 60.561 40.000 5.13 0.00 43.33 2.57
513 517 4.811555 TGTGTTCAATTGTGTGCTACTC 57.188 40.909 5.13 0.00 0.00 2.59
514 518 3.563808 TGTGTTCAATTGTGTGCTACTCC 59.436 43.478 5.13 0.00 0.00 3.85
515 519 3.058224 GTGTTCAATTGTGTGCTACTCCC 60.058 47.826 5.13 0.00 0.00 4.30
516 520 3.181445 TGTTCAATTGTGTGCTACTCCCT 60.181 43.478 5.13 0.00 0.00 4.20
517 521 3.334583 TCAATTGTGTGCTACTCCCTC 57.665 47.619 5.13 0.00 0.00 4.30
518 522 2.027192 TCAATTGTGTGCTACTCCCTCC 60.027 50.000 5.13 0.00 0.00 4.30
519 523 0.537188 ATTGTGTGCTACTCCCTCCG 59.463 55.000 0.00 0.00 0.00 4.63
520 524 0.830444 TTGTGTGCTACTCCCTCCGT 60.830 55.000 0.00 0.00 0.00 4.69
521 525 1.248785 TGTGTGCTACTCCCTCCGTC 61.249 60.000 0.00 0.00 0.00 4.79
522 526 1.681327 TGTGCTACTCCCTCCGTCC 60.681 63.158 0.00 0.00 0.00 4.79
523 527 2.439701 TGCTACTCCCTCCGTCCG 60.440 66.667 0.00 0.00 0.00 4.79
524 528 2.124403 GCTACTCCCTCCGTCCGA 60.124 66.667 0.00 0.00 0.00 4.55
525 529 1.751927 GCTACTCCCTCCGTCCGAA 60.752 63.158 0.00 0.00 0.00 4.30
526 530 1.318158 GCTACTCCCTCCGTCCGAAA 61.318 60.000 0.00 0.00 0.00 3.46
527 531 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
528 532 1.755380 CTACTCCCTCCGTCCGAAAAT 59.245 52.381 0.00 0.00 0.00 1.82
529 533 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
530 534 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
531 535 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
532 536 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
533 537 2.167075 TCCCTCCGTCCGAAAATACTTC 59.833 50.000 0.00 0.00 0.00 3.01
534 538 2.547826 CCTCCGTCCGAAAATACTTCC 58.452 52.381 0.00 0.00 0.00 3.46
535 539 2.093869 CCTCCGTCCGAAAATACTTCCA 60.094 50.000 0.00 0.00 0.00 3.53
536 540 3.187700 CTCCGTCCGAAAATACTTCCAG 58.812 50.000 0.00 0.00 0.00 3.86
537 541 2.827322 TCCGTCCGAAAATACTTCCAGA 59.173 45.455 0.00 0.00 0.00 3.86
538 542 3.449737 TCCGTCCGAAAATACTTCCAGAT 59.550 43.478 0.00 0.00 0.00 2.90
539 543 4.081309 TCCGTCCGAAAATACTTCCAGATT 60.081 41.667 0.00 0.00 0.00 2.40
540 544 4.270325 CCGTCCGAAAATACTTCCAGATTC 59.730 45.833 0.00 0.00 0.00 2.52
541 545 4.270325 CGTCCGAAAATACTTCCAGATTCC 59.730 45.833 0.00 0.00 0.00 3.01
542 546 5.183228 GTCCGAAAATACTTCCAGATTCCA 58.817 41.667 0.00 0.00 0.00 3.53
543 547 5.646360 GTCCGAAAATACTTCCAGATTCCAA 59.354 40.000 0.00 0.00 0.00 3.53
544 548 6.150474 GTCCGAAAATACTTCCAGATTCCAAA 59.850 38.462 0.00 0.00 0.00 3.28
545 549 6.889722 TCCGAAAATACTTCCAGATTCCAAAT 59.110 34.615 0.00 0.00 0.00 2.32
546 550 6.974622 CCGAAAATACTTCCAGATTCCAAATG 59.025 38.462 0.00 0.00 0.00 2.32
547 551 7.148086 CCGAAAATACTTCCAGATTCCAAATGA 60.148 37.037 0.00 0.00 0.00 2.57
548 552 8.243426 CGAAAATACTTCCAGATTCCAAATGAA 58.757 33.333 0.00 0.00 37.38 2.57
549 553 9.578439 GAAAATACTTCCAGATTCCAAATGAAG 57.422 33.333 0.00 0.00 36.14 3.02
550 554 8.884124 AAATACTTCCAGATTCCAAATGAAGA 57.116 30.769 0.00 0.00 36.14 2.87
551 555 8.884124 AATACTTCCAGATTCCAAATGAAGAA 57.116 30.769 0.00 0.00 36.14 2.52
552 556 8.884124 ATACTTCCAGATTCCAAATGAAGAAA 57.116 30.769 0.00 0.00 36.14 2.52
553 557 7.787623 ACTTCCAGATTCCAAATGAAGAAAT 57.212 32.000 0.00 0.00 36.14 2.17
554 558 7.609056 ACTTCCAGATTCCAAATGAAGAAATG 58.391 34.615 0.00 0.00 36.14 2.32
555 559 6.534475 TCCAGATTCCAAATGAAGAAATGG 57.466 37.500 0.00 0.00 36.14 3.16
556 560 6.255287 TCCAGATTCCAAATGAAGAAATGGA 58.745 36.000 0.00 0.00 38.55 3.41
562 566 6.012658 TCCAAATGAAGAAATGGAAACTCG 57.987 37.500 0.00 0.00 38.95 4.18
563 567 5.767665 TCCAAATGAAGAAATGGAAACTCGA 59.232 36.000 0.00 0.00 38.95 4.04
564 568 6.264292 TCCAAATGAAGAAATGGAAACTCGAA 59.736 34.615 0.00 0.00 38.95 3.71
565 569 6.922957 CCAAATGAAGAAATGGAAACTCGAAA 59.077 34.615 0.00 0.00 34.82 3.46
566 570 7.437862 CCAAATGAAGAAATGGAAACTCGAAAA 59.562 33.333 0.00 0.00 34.82 2.29
567 571 8.482429 CAAATGAAGAAATGGAAACTCGAAAAG 58.518 33.333 0.00 0.00 0.00 2.27
568 572 6.072112 TGAAGAAATGGAAACTCGAAAAGG 57.928 37.500 0.00 0.00 0.00 3.11
569 573 5.825679 TGAAGAAATGGAAACTCGAAAAGGA 59.174 36.000 0.00 0.00 0.00 3.36
570 574 6.490040 TGAAGAAATGGAAACTCGAAAAGGAT 59.510 34.615 0.00 0.00 0.00 3.24
571 575 6.502136 AGAAATGGAAACTCGAAAAGGATC 57.498 37.500 0.00 0.00 0.00 3.36
572 576 5.416013 AGAAATGGAAACTCGAAAAGGATCC 59.584 40.000 2.48 2.48 35.48 3.36
573 577 4.576330 ATGGAAACTCGAAAAGGATCCT 57.424 40.909 9.02 9.02 35.77 3.24
574 578 4.367039 TGGAAACTCGAAAAGGATCCTT 57.633 40.909 21.89 21.89 35.77 3.36
575 579 4.324267 TGGAAACTCGAAAAGGATCCTTC 58.676 43.478 27.20 15.03 35.77 3.46
576 580 4.041691 TGGAAACTCGAAAAGGATCCTTCT 59.958 41.667 27.20 14.65 35.77 2.85
577 581 4.393371 GGAAACTCGAAAAGGATCCTTCTG 59.607 45.833 27.20 18.60 34.84 3.02
578 582 4.891992 AACTCGAAAAGGATCCTTCTGA 57.108 40.909 27.20 21.38 34.84 3.27
579 583 5.428184 AACTCGAAAAGGATCCTTCTGAT 57.572 39.130 27.20 13.74 34.84 2.90
580 584 5.428184 ACTCGAAAAGGATCCTTCTGATT 57.572 39.130 27.20 17.36 34.84 2.57
581 585 5.423886 ACTCGAAAAGGATCCTTCTGATTC 58.576 41.667 27.20 23.01 34.84 2.52
582 586 5.188751 ACTCGAAAAGGATCCTTCTGATTCT 59.811 40.000 27.20 7.13 41.42 2.40
584 588 7.093289 ACTCGAAAAGGATCCTTCTGATTCTTA 60.093 37.037 27.20 15.04 46.74 2.10
585 589 7.620880 TCGAAAAGGATCCTTCTGATTCTTAA 58.379 34.615 27.20 11.76 46.74 1.85
586 590 8.100791 TCGAAAAGGATCCTTCTGATTCTTAAA 58.899 33.333 27.20 9.68 46.74 1.52
587 591 8.394121 CGAAAAGGATCCTTCTGATTCTTAAAG 58.606 37.037 27.20 9.97 46.74 1.85
588 592 9.454859 GAAAAGGATCCTTCTGATTCTTAAAGA 57.545 33.333 27.20 0.00 46.74 2.52
589 593 9.813826 AAAAGGATCCTTCTGATTCTTAAAGAA 57.186 29.630 27.20 0.00 46.74 2.52
590 594 9.987726 AAAGGATCCTTCTGATTCTTAAAGAAT 57.012 29.630 27.20 2.49 46.74 2.40
591 595 8.977267 AGGATCCTTCTGATTCTTAAAGAATG 57.023 34.615 9.02 0.00 44.41 2.67
592 596 8.776119 AGGATCCTTCTGATTCTTAAAGAATGA 58.224 33.333 9.02 0.00 44.41 2.57
593 597 9.054922 GGATCCTTCTGATTCTTAAAGAATGAG 57.945 37.037 3.84 0.00 44.41 2.90
594 598 9.612066 GATCCTTCTGATTCTTAAAGAATGAGT 57.388 33.333 0.00 0.00 44.41 3.41
595 599 9.612066 ATCCTTCTGATTCTTAAAGAATGAGTC 57.388 33.333 0.00 1.04 44.41 3.36
596 600 8.597167 TCCTTCTGATTCTTAAAGAATGAGTCA 58.403 33.333 0.00 0.00 44.41 3.41
597 601 9.393512 CCTTCTGATTCTTAAAGAATGAGTCAT 57.606 33.333 0.00 0.00 44.41 3.06
599 603 9.948964 TTCTGATTCTTAAAGAATGAGTCATCA 57.051 29.630 5.98 0.00 44.41 3.07
600 604 9.948964 TCTGATTCTTAAAGAATGAGTCATCAA 57.051 29.630 5.98 0.00 44.41 2.57
606 610 9.519191 TCTTAAAGAATGAGTCATCAAAATGGA 57.481 29.630 5.98 0.00 39.39 3.41
607 611 9.565213 CTTAAAGAATGAGTCATCAAAATGGAC 57.435 33.333 5.98 0.00 39.39 4.02
608 612 7.528996 AAAGAATGAGTCATCAAAATGGACA 57.471 32.000 5.98 0.00 39.39 4.02
609 613 7.528996 AAGAATGAGTCATCAAAATGGACAA 57.471 32.000 5.98 0.00 39.39 3.18
610 614 7.528996 AGAATGAGTCATCAAAATGGACAAA 57.471 32.000 5.98 0.00 39.39 2.83
611 615 7.954835 AGAATGAGTCATCAAAATGGACAAAA 58.045 30.769 5.98 0.00 39.39 2.44
612 616 8.423349 AGAATGAGTCATCAAAATGGACAAAAA 58.577 29.630 5.98 0.00 39.39 1.94
613 617 8.597662 AATGAGTCATCAAAATGGACAAAAAG 57.402 30.769 5.98 0.00 39.39 2.27
614 618 6.514947 TGAGTCATCAAAATGGACAAAAAGG 58.485 36.000 0.00 0.00 33.42 3.11
615 619 6.323482 TGAGTCATCAAAATGGACAAAAAGGA 59.677 34.615 0.00 0.00 33.42 3.36
616 620 7.015487 TGAGTCATCAAAATGGACAAAAAGGAT 59.985 33.333 0.00 0.00 33.42 3.24
617 621 7.156673 AGTCATCAAAATGGACAAAAAGGATG 58.843 34.615 0.00 0.00 33.42 3.51
618 622 6.930722 GTCATCAAAATGGACAAAAAGGATGT 59.069 34.615 0.00 0.00 33.29 3.06
619 623 8.087750 GTCATCAAAATGGACAAAAAGGATGTA 58.912 33.333 0.00 0.00 33.29 2.29
620 624 8.814931 TCATCAAAATGGACAAAAAGGATGTAT 58.185 29.630 0.00 0.00 33.29 2.29
621 625 9.090692 CATCAAAATGGACAAAAAGGATGTATC 57.909 33.333 0.00 0.00 0.00 2.24
622 626 8.421249 TCAAAATGGACAAAAAGGATGTATCT 57.579 30.769 0.00 0.00 0.00 1.98
623 627 9.527157 TCAAAATGGACAAAAAGGATGTATCTA 57.473 29.630 0.00 0.00 0.00 1.98
624 628 9.793252 CAAAATGGACAAAAAGGATGTATCTAG 57.207 33.333 0.00 0.00 0.00 2.43
625 629 9.753674 AAAATGGACAAAAAGGATGTATCTAGA 57.246 29.630 0.00 0.00 0.00 2.43
626 630 9.753674 AAATGGACAAAAAGGATGTATCTAGAA 57.246 29.630 0.00 0.00 0.00 2.10
627 631 8.738645 ATGGACAAAAAGGATGTATCTAGAAC 57.261 34.615 0.00 0.00 0.00 3.01
628 632 7.918076 TGGACAAAAAGGATGTATCTAGAACT 58.082 34.615 0.00 0.00 0.00 3.01
629 633 9.042450 TGGACAAAAAGGATGTATCTAGAACTA 57.958 33.333 0.00 0.00 0.00 2.24
630 634 9.886132 GGACAAAAAGGATGTATCTAGAACTAA 57.114 33.333 0.00 0.00 0.00 2.24
670 674 9.118300 ACATCTCCTTTTATTCATTCTGATGAC 57.882 33.333 0.00 0.00 41.84 3.06
671 675 9.117183 CATCTCCTTTTATTCATTCTGATGACA 57.883 33.333 0.00 0.00 41.84 3.58
672 676 9.690913 ATCTCCTTTTATTCATTCTGATGACAA 57.309 29.630 0.00 0.00 41.84 3.18
673 677 9.170734 TCTCCTTTTATTCATTCTGATGACAAG 57.829 33.333 0.00 0.00 41.84 3.16
674 678 8.868522 TCCTTTTATTCATTCTGATGACAAGT 57.131 30.769 0.00 0.00 41.84 3.16
675 679 9.958180 TCCTTTTATTCATTCTGATGACAAGTA 57.042 29.630 0.00 0.00 41.84 2.24
710 714 7.307493 TCATTCTGATGACAAGTATTTTCGG 57.693 36.000 0.00 0.00 37.37 4.30
711 715 7.102993 TCATTCTGATGACAAGTATTTTCGGA 58.897 34.615 0.00 0.00 37.37 4.55
712 716 6.721571 TTCTGATGACAAGTATTTTCGGAC 57.278 37.500 0.00 0.00 0.00 4.79
713 717 4.862574 TCTGATGACAAGTATTTTCGGACG 59.137 41.667 0.00 0.00 0.00 4.79
714 718 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
715 719 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
716 720 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
731 735 3.961576 GGAGTATTTCCGGACGGAG 57.038 57.895 13.64 0.00 46.06 4.63
732 736 0.388294 GGAGTATTTCCGGACGGAGG 59.612 60.000 13.64 0.00 46.06 4.30
733 737 0.388294 GAGTATTTCCGGACGGAGGG 59.612 60.000 13.64 0.00 46.06 4.30
734 738 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
735 739 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
752 756 4.213513 AGGGAGTACTTCGGTTCGATATT 58.786 43.478 0.00 0.00 35.23 1.28
784 789 4.578928 ACTAAATTGACGGCAGTTTGTCTT 59.421 37.500 20.89 0.00 35.16 3.01
797 803 5.392595 GCAGTTTGTCTTAGTCACAACCAAA 60.393 40.000 0.00 0.00 33.42 3.28
801 807 7.285401 AGTTTGTCTTAGTCACAACCAAATCAT 59.715 33.333 0.00 0.00 33.42 2.45
818 824 2.346803 TCATTCAACTGCTCGCCTAAC 58.653 47.619 0.00 0.00 0.00 2.34
868 875 3.594134 CGACTTGCTGAGGATCTTTTCT 58.406 45.455 0.00 0.00 34.92 2.52
889 896 5.338632 TCTTCTAGGTTGGTGGTTGATCTA 58.661 41.667 0.00 0.00 0.00 1.98
890 897 5.783360 TCTTCTAGGTTGGTGGTTGATCTAA 59.217 40.000 0.00 0.00 0.00 2.10
899 909 4.408921 TGGTGGTTGATCTAAGTATCCCTG 59.591 45.833 0.00 0.00 0.00 4.45
933 943 3.405831 GCCTGATGCATGTAGATTAGCA 58.594 45.455 2.46 0.00 41.73 3.49
935 945 4.383173 CCTGATGCATGTAGATTAGCACA 58.617 43.478 2.46 0.00 40.14 4.57
936 946 5.001874 CCTGATGCATGTAGATTAGCACAT 58.998 41.667 2.46 0.00 40.14 3.21
942 952 2.459934 TGTAGATTAGCACATGACGCG 58.540 47.619 3.53 3.53 0.00 6.01
943 953 1.190323 GTAGATTAGCACATGACGCGC 59.810 52.381 5.73 0.00 0.00 6.86
944 954 1.154205 AGATTAGCACATGACGCGCC 61.154 55.000 5.73 0.00 0.00 6.53
945 955 1.153369 ATTAGCACATGACGCGCCT 60.153 52.632 5.73 0.00 0.00 5.52
946 956 1.431488 ATTAGCACATGACGCGCCTG 61.431 55.000 5.73 3.44 0.00 4.85
949 959 4.156622 CACATGACGCGCCTGCAG 62.157 66.667 5.73 6.78 42.97 4.41
950 960 4.687215 ACATGACGCGCCTGCAGT 62.687 61.111 13.81 0.00 42.97 4.40
951 961 2.509111 CATGACGCGCCTGCAGTA 60.509 61.111 13.81 0.00 42.97 2.74
952 962 2.509336 ATGACGCGCCTGCAGTAC 60.509 61.111 13.81 3.23 42.97 2.73
953 963 4.735132 TGACGCGCCTGCAGTACC 62.735 66.667 13.81 0.00 42.97 3.34
954 964 4.436998 GACGCGCCTGCAGTACCT 62.437 66.667 13.81 0.00 42.97 3.08
955 965 4.436998 ACGCGCCTGCAGTACCTC 62.437 66.667 13.81 0.00 42.97 3.85
1011 1021 2.607038 GGCTTCAACGATGGGTTTGAAC 60.607 50.000 0.00 0.00 36.49 3.18
1047 1057 2.743718 CCACGTTCCTCTGCCAGT 59.256 61.111 0.00 0.00 0.00 4.00
1053 1063 3.846405 TTCCTCTGCCAGTCCCCGT 62.846 63.158 0.00 0.00 0.00 5.28
1122 1132 2.186903 CGGGATCAGAACCGGGTG 59.813 66.667 6.32 0.00 46.08 4.61
1211 1221 2.213499 CTAGCGCTTGATTCCGGAAAT 58.787 47.619 23.08 9.95 0.00 2.17
1231 1247 2.509569 TGCAAGCGGAAATTTACCTCA 58.490 42.857 0.00 0.00 0.00 3.86
1235 1251 4.723248 CAAGCGGAAATTTACCTCAAGAC 58.277 43.478 0.00 0.00 0.00 3.01
1497 1513 2.177580 CGTGGTTGGCAACGTGACT 61.178 57.895 22.95 0.00 37.28 3.41
1585 1601 2.671963 GCTGTTTCCCGGTCCACC 60.672 66.667 0.00 0.00 0.00 4.61
1603 1619 1.359848 CCGTGTGGTGATAGCACTTC 58.640 55.000 11.48 5.23 46.03 3.01
1755 2840 4.221926 ACTCGATCGTCTCATCAATCTG 57.778 45.455 15.94 0.00 0.00 2.90
1782 2878 2.100584 TGTTGTTTGTGGTGGAATCAGC 59.899 45.455 0.00 0.00 41.42 4.26
1783 2879 1.327303 TGTTTGTGGTGGAATCAGCC 58.673 50.000 0.00 0.00 40.42 4.85
1784 2880 0.603065 GTTTGTGGTGGAATCAGCCC 59.397 55.000 0.00 0.00 40.42 5.19
1785 2881 0.187117 TTTGTGGTGGAATCAGCCCA 59.813 50.000 0.00 0.00 40.42 5.36
1790 2886 2.799176 GTGGAATCAGCCCACCATC 58.201 57.895 0.00 0.00 46.30 3.51
1791 2887 0.034186 GTGGAATCAGCCCACCATCA 60.034 55.000 0.00 0.00 46.30 3.07
1792 2888 0.256752 TGGAATCAGCCCACCATCAG 59.743 55.000 0.00 0.00 0.00 2.90
1811 2907 1.352352 AGGGTCTACTTGTGCTTGCAT 59.648 47.619 0.00 0.00 0.00 3.96
1889 2985 5.255710 ACATTTCTGTCGACTATGGAGAG 57.744 43.478 17.92 3.70 0.00 3.20
1921 3017 5.164233 TGACTTCGTCAATCTCAAGATGAC 58.836 41.667 0.00 3.61 39.78 3.06
1957 3053 0.255890 TCAAAGGTGCTCATAGGGGC 59.744 55.000 0.00 0.00 0.00 5.80
1960 3056 2.203266 GGTGCTCATAGGGGCAGC 60.203 66.667 16.36 16.36 46.73 5.25
1966 3062 2.159819 CTCATAGGGGCAGCGCGTAT 62.160 60.000 16.65 16.65 0.00 3.06
1986 3082 1.286501 GTTCGTGCGCATAGGATGAA 58.713 50.000 15.91 4.01 42.68 2.57
2071 3168 1.417890 CCGTCTTAGGGCATCTCCAAT 59.582 52.381 0.00 0.00 36.21 3.16
2077 3174 0.851469 AGGGCATCTCCAATGCTGAT 59.149 50.000 9.62 0.00 44.02 2.90
2078 3175 1.202903 AGGGCATCTCCAATGCTGATC 60.203 52.381 9.62 0.00 44.02 2.92
2079 3176 1.245732 GGCATCTCCAATGCTGATCC 58.754 55.000 9.62 0.00 44.02 3.36
2080 3177 1.202903 GGCATCTCCAATGCTGATCCT 60.203 52.381 9.62 0.00 44.02 3.24
2081 3178 2.152830 GCATCTCCAATGCTGATCCTC 58.847 52.381 2.84 0.00 41.52 3.71
2082 3179 2.414806 CATCTCCAATGCTGATCCTCG 58.585 52.381 0.00 0.00 0.00 4.63
2083 3180 1.489481 TCTCCAATGCTGATCCTCGT 58.511 50.000 0.00 0.00 0.00 4.18
2084 3181 1.137675 TCTCCAATGCTGATCCTCGTG 59.862 52.381 0.00 0.00 0.00 4.35
2085 3182 0.904649 TCCAATGCTGATCCTCGTGT 59.095 50.000 0.00 0.00 0.00 4.49
2086 3183 1.278985 TCCAATGCTGATCCTCGTGTT 59.721 47.619 0.00 0.00 0.00 3.32
2087 3184 2.499693 TCCAATGCTGATCCTCGTGTTA 59.500 45.455 0.00 0.00 0.00 2.41
2088 3185 3.055458 TCCAATGCTGATCCTCGTGTTAA 60.055 43.478 0.00 0.00 0.00 2.01
2089 3186 3.689161 CCAATGCTGATCCTCGTGTTAAA 59.311 43.478 0.00 0.00 0.00 1.52
2090 3187 4.155826 CCAATGCTGATCCTCGTGTTAAAA 59.844 41.667 0.00 0.00 0.00 1.52
2091 3188 5.335583 CCAATGCTGATCCTCGTGTTAAAAA 60.336 40.000 0.00 0.00 0.00 1.94
2092 3189 6.324819 CAATGCTGATCCTCGTGTTAAAAAT 58.675 36.000 0.00 0.00 0.00 1.82
2093 3190 7.415095 CCAATGCTGATCCTCGTGTTAAAAATA 60.415 37.037 0.00 0.00 0.00 1.40
2094 3191 7.624360 ATGCTGATCCTCGTGTTAAAAATAA 57.376 32.000 0.00 0.00 0.00 1.40
2095 3192 7.624360 TGCTGATCCTCGTGTTAAAAATAAT 57.376 32.000 0.00 0.00 0.00 1.28
2096 3193 7.693952 TGCTGATCCTCGTGTTAAAAATAATC 58.306 34.615 0.00 0.00 0.00 1.75
2097 3194 7.552687 TGCTGATCCTCGTGTTAAAAATAATCT 59.447 33.333 0.00 0.00 0.00 2.40
2098 3195 9.042008 GCTGATCCTCGTGTTAAAAATAATCTA 57.958 33.333 0.00 0.00 0.00 1.98
2123 3220 6.619801 AAAATGTATTCGTCTTAGGGCATC 57.380 37.500 0.00 0.00 0.00 3.91
2124 3221 5.552870 AATGTATTCGTCTTAGGGCATCT 57.447 39.130 0.00 0.00 0.00 2.90
2125 3222 4.585955 TGTATTCGTCTTAGGGCATCTC 57.414 45.455 0.00 0.00 0.00 2.75
2126 3223 3.321111 TGTATTCGTCTTAGGGCATCTCC 59.679 47.826 0.00 0.00 0.00 3.71
2127 3224 1.860641 TTCGTCTTAGGGCATCTCCA 58.139 50.000 0.00 0.00 36.21 3.86
2128 3225 1.860641 TCGTCTTAGGGCATCTCCAA 58.139 50.000 0.00 0.00 36.21 3.53
2129 3226 2.398588 TCGTCTTAGGGCATCTCCAAT 58.601 47.619 0.00 0.00 36.21 3.16
2130 3227 2.103094 TCGTCTTAGGGCATCTCCAATG 59.897 50.000 0.00 0.00 36.21 2.82
2131 3228 2.225467 GTCTTAGGGCATCTCCAATGC 58.775 52.381 1.40 1.40 43.85 3.56
2174 3271 1.030488 GTCTGGATCGAGTGGTCCGA 61.030 60.000 4.53 0.00 40.53 4.55
2248 3345 1.035932 TCCGTTTTCCCGCAAACCAA 61.036 50.000 0.00 0.00 33.71 3.67
2282 3379 1.290955 CTTTACGGGCGTCTGGACA 59.709 57.895 0.00 0.00 0.00 4.02
2295 3392 2.674033 GGACAGCTGCCATGCACA 60.674 61.111 15.27 0.00 33.79 4.57
2341 3438 4.008330 CCATCCCAGTCATGATAGCAATC 58.992 47.826 0.00 0.00 0.00 2.67
2377 3474 0.249615 CCGCACACCTCATCGATCAT 60.250 55.000 0.00 0.00 0.00 2.45
2471 3568 2.223525 GGAGATACCGACGACTTCCTTG 60.224 54.545 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 124 0.179179 GTGCATTTCTTCGCTGCTCC 60.179 55.000 0.00 0.00 36.84 4.70
131 132 7.168135 CACCAAAACTCTAAAGTGCATTTCTTC 59.832 37.037 0.00 0.00 35.36 2.87
132 133 6.980397 CACCAAAACTCTAAAGTGCATTTCTT 59.020 34.615 0.00 0.00 35.36 2.52
175 179 6.996509 AGCAACACCTAAAATTTCATGATGT 58.003 32.000 0.00 0.00 0.00 3.06
211 215 3.193267 TCAGATGCCACCAACAAATTAGC 59.807 43.478 0.00 0.00 0.00 3.09
302 306 8.347035 GTCACTAACAAAATGTACTAAAAGCCA 58.653 33.333 0.00 0.00 0.00 4.75
345 349 8.402798 AGATACATAGGTACATCAGAACTCAG 57.597 38.462 0.00 0.00 30.94 3.35
485 489 4.681025 GCACACAATTGAACACAATCGATT 59.319 37.500 13.59 4.39 34.42 3.34
486 490 4.022935 AGCACACAATTGAACACAATCGAT 60.023 37.500 13.59 0.00 33.78 3.59
487 491 3.314913 AGCACACAATTGAACACAATCGA 59.685 39.130 13.59 0.00 33.78 3.59
488 492 3.631144 AGCACACAATTGAACACAATCG 58.369 40.909 13.59 0.00 33.78 3.34
489 493 5.762045 AGTAGCACACAATTGAACACAATC 58.238 37.500 13.59 0.00 33.78 2.67
490 494 5.278463 GGAGTAGCACACAATTGAACACAAT 60.278 40.000 13.59 0.00 36.02 2.71
491 495 4.036262 GGAGTAGCACACAATTGAACACAA 59.964 41.667 13.59 0.00 0.00 3.33
492 496 3.563808 GGAGTAGCACACAATTGAACACA 59.436 43.478 13.59 0.00 0.00 3.72
493 497 3.058224 GGGAGTAGCACACAATTGAACAC 60.058 47.826 13.59 0.00 0.00 3.32
494 498 3.146066 GGGAGTAGCACACAATTGAACA 58.854 45.455 13.59 0.00 0.00 3.18
495 499 3.412386 AGGGAGTAGCACACAATTGAAC 58.588 45.455 13.59 0.00 0.00 3.18
496 500 3.559171 GGAGGGAGTAGCACACAATTGAA 60.559 47.826 13.59 0.00 0.00 2.69
509 513 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
510 514 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
511 515 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
512 516 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
513 517 2.547826 GAAGTATTTTCGGACGGAGGG 58.452 52.381 0.00 0.00 0.00 4.30
514 518 2.093869 TGGAAGTATTTTCGGACGGAGG 60.094 50.000 0.00 0.00 0.00 4.30
515 519 3.119245 TCTGGAAGTATTTTCGGACGGAG 60.119 47.826 0.00 0.00 33.76 4.63
516 520 2.827322 TCTGGAAGTATTTTCGGACGGA 59.173 45.455 0.00 0.00 33.76 4.69
517 521 3.241067 TCTGGAAGTATTTTCGGACGG 57.759 47.619 0.00 0.00 33.76 4.79
518 522 4.270325 GGAATCTGGAAGTATTTTCGGACG 59.730 45.833 0.00 0.00 33.76 4.79
519 523 5.183228 TGGAATCTGGAAGTATTTTCGGAC 58.817 41.667 0.00 0.00 33.76 4.79
520 524 5.429681 TGGAATCTGGAAGTATTTTCGGA 57.570 39.130 0.00 0.00 33.76 4.55
521 525 6.509418 TTTGGAATCTGGAAGTATTTTCGG 57.491 37.500 0.00 0.00 33.76 4.30
522 526 7.761409 TCATTTGGAATCTGGAAGTATTTTCG 58.239 34.615 0.00 0.00 33.76 3.46
523 527 9.578439 CTTCATTTGGAATCTGGAAGTATTTTC 57.422 33.333 0.00 0.00 34.32 2.29
524 528 9.312904 TCTTCATTTGGAATCTGGAAGTATTTT 57.687 29.630 0.00 0.00 34.32 1.82
525 529 8.884124 TCTTCATTTGGAATCTGGAAGTATTT 57.116 30.769 0.00 0.00 34.32 1.40
526 530 8.884124 TTCTTCATTTGGAATCTGGAAGTATT 57.116 30.769 0.00 0.00 34.32 1.89
527 531 8.884124 TTTCTTCATTTGGAATCTGGAAGTAT 57.116 30.769 0.00 0.00 34.32 2.12
528 532 8.742777 CATTTCTTCATTTGGAATCTGGAAGTA 58.257 33.333 0.00 0.00 34.32 2.24
529 533 7.310237 CCATTTCTTCATTTGGAATCTGGAAGT 60.310 37.037 0.00 0.00 34.32 3.01
530 534 7.039882 CCATTTCTTCATTTGGAATCTGGAAG 58.960 38.462 0.00 0.00 34.32 3.46
531 535 6.725369 TCCATTTCTTCATTTGGAATCTGGAA 59.275 34.615 0.00 0.00 35.38 3.53
532 536 6.255287 TCCATTTCTTCATTTGGAATCTGGA 58.745 36.000 0.00 0.00 35.38 3.86
533 537 6.534475 TCCATTTCTTCATTTGGAATCTGG 57.466 37.500 0.00 0.00 35.38 3.86
534 538 8.092687 AGTTTCCATTTCTTCATTTGGAATCTG 58.907 33.333 11.41 0.00 45.14 2.90
535 539 8.198807 AGTTTCCATTTCTTCATTTGGAATCT 57.801 30.769 4.24 6.26 45.14 2.40
536 540 7.274250 CGAGTTTCCATTTCTTCATTTGGAATC 59.726 37.037 4.24 4.26 45.14 2.52
537 541 7.039784 TCGAGTTTCCATTTCTTCATTTGGAAT 60.040 33.333 4.24 0.00 45.14 3.01
538 542 6.264292 TCGAGTTTCCATTTCTTCATTTGGAA 59.736 34.615 0.00 0.00 44.38 3.53
539 543 5.767665 TCGAGTTTCCATTTCTTCATTTGGA 59.232 36.000 0.00 0.00 36.49 3.53
540 544 6.012658 TCGAGTTTCCATTTCTTCATTTGG 57.987 37.500 0.00 0.00 0.00 3.28
541 545 7.928908 TTTCGAGTTTCCATTTCTTCATTTG 57.071 32.000 0.00 0.00 0.00 2.32
542 546 7.653311 CCTTTTCGAGTTTCCATTTCTTCATTT 59.347 33.333 0.00 0.00 0.00 2.32
543 547 7.014230 TCCTTTTCGAGTTTCCATTTCTTCATT 59.986 33.333 0.00 0.00 0.00 2.57
544 548 6.490040 TCCTTTTCGAGTTTCCATTTCTTCAT 59.510 34.615 0.00 0.00 0.00 2.57
545 549 5.825679 TCCTTTTCGAGTTTCCATTTCTTCA 59.174 36.000 0.00 0.00 0.00 3.02
546 550 6.313744 TCCTTTTCGAGTTTCCATTTCTTC 57.686 37.500 0.00 0.00 0.00 2.87
547 551 6.071896 GGATCCTTTTCGAGTTTCCATTTCTT 60.072 38.462 3.84 0.00 0.00 2.52
548 552 5.416013 GGATCCTTTTCGAGTTTCCATTTCT 59.584 40.000 3.84 0.00 0.00 2.52
549 553 5.416013 AGGATCCTTTTCGAGTTTCCATTTC 59.584 40.000 9.02 0.00 30.59 2.17
550 554 5.325239 AGGATCCTTTTCGAGTTTCCATTT 58.675 37.500 9.02 0.00 30.59 2.32
551 555 4.923415 AGGATCCTTTTCGAGTTTCCATT 58.077 39.130 9.02 0.00 30.59 3.16
552 556 4.576330 AGGATCCTTTTCGAGTTTCCAT 57.424 40.909 9.02 0.00 30.59 3.41
553 557 4.041691 AGAAGGATCCTTTTCGAGTTTCCA 59.958 41.667 27.68 0.00 36.26 3.53
554 558 4.393371 CAGAAGGATCCTTTTCGAGTTTCC 59.607 45.833 27.68 10.99 36.26 3.13
555 559 5.238583 TCAGAAGGATCCTTTTCGAGTTTC 58.761 41.667 27.68 11.96 36.26 2.78
556 560 5.228945 TCAGAAGGATCCTTTTCGAGTTT 57.771 39.130 27.68 2.05 36.26 2.66
557 561 4.891992 TCAGAAGGATCCTTTTCGAGTT 57.108 40.909 27.68 2.88 36.26 3.01
558 562 5.188751 AGAATCAGAAGGATCCTTTTCGAGT 59.811 40.000 27.68 21.28 36.26 4.18
559 563 5.669477 AGAATCAGAAGGATCCTTTTCGAG 58.331 41.667 27.68 15.31 36.26 4.04
560 564 5.683876 AGAATCAGAAGGATCCTTTTCGA 57.316 39.130 27.68 22.24 36.26 3.71
561 565 7.849804 TTAAGAATCAGAAGGATCCTTTTCG 57.150 36.000 27.68 18.14 32.29 3.46
562 566 9.454859 TCTTTAAGAATCAGAAGGATCCTTTTC 57.545 33.333 27.68 24.14 32.29 2.29
563 567 9.813826 TTCTTTAAGAATCAGAAGGATCCTTTT 57.186 29.630 27.68 19.87 32.29 2.27
564 568 9.987726 ATTCTTTAAGAATCAGAAGGATCCTTT 57.012 29.630 27.68 11.94 40.75 3.11
565 569 9.406113 CATTCTTTAAGAATCAGAAGGATCCTT 57.594 33.333 27.39 27.39 42.67 3.36
566 570 8.776119 TCATTCTTTAAGAATCAGAAGGATCCT 58.224 33.333 16.36 9.02 42.67 3.24
567 571 8.970859 TCATTCTTTAAGAATCAGAAGGATCC 57.029 34.615 16.36 2.48 42.67 3.36
568 572 9.612066 ACTCATTCTTTAAGAATCAGAAGGATC 57.388 33.333 22.10 0.00 42.67 3.36
569 573 9.612066 GACTCATTCTTTAAGAATCAGAAGGAT 57.388 33.333 22.10 2.52 42.67 3.24
570 574 8.597167 TGACTCATTCTTTAAGAATCAGAAGGA 58.403 33.333 22.10 12.40 42.67 3.36
571 575 8.783833 TGACTCATTCTTTAAGAATCAGAAGG 57.216 34.615 22.10 9.21 42.67 3.46
573 577 9.948964 TGATGACTCATTCTTTAAGAATCAGAA 57.051 29.630 22.10 11.79 42.67 3.02
574 578 9.948964 TTGATGACTCATTCTTTAAGAATCAGA 57.051 29.630 22.10 14.18 42.67 3.27
580 584 9.519191 TCCATTTTGATGACTCATTCTTTAAGA 57.481 29.630 0.00 0.00 0.00 2.10
581 585 9.565213 GTCCATTTTGATGACTCATTCTTTAAG 57.435 33.333 0.00 0.00 0.00 1.85
582 586 9.076781 TGTCCATTTTGATGACTCATTCTTTAA 57.923 29.630 0.00 0.00 0.00 1.52
583 587 8.634335 TGTCCATTTTGATGACTCATTCTTTA 57.366 30.769 0.00 0.00 0.00 1.85
584 588 7.528996 TGTCCATTTTGATGACTCATTCTTT 57.471 32.000 0.00 0.00 0.00 2.52
585 589 7.528996 TTGTCCATTTTGATGACTCATTCTT 57.471 32.000 0.00 0.00 0.00 2.52
586 590 7.528996 TTTGTCCATTTTGATGACTCATTCT 57.471 32.000 0.00 0.00 0.00 2.40
587 591 8.592105 TTTTTGTCCATTTTGATGACTCATTC 57.408 30.769 0.00 0.00 0.00 2.67
588 592 7.658575 CCTTTTTGTCCATTTTGATGACTCATT 59.341 33.333 0.00 0.00 0.00 2.57
589 593 7.015487 TCCTTTTTGTCCATTTTGATGACTCAT 59.985 33.333 0.00 0.00 0.00 2.90
590 594 6.323482 TCCTTTTTGTCCATTTTGATGACTCA 59.677 34.615 0.00 0.00 0.00 3.41
591 595 6.748132 TCCTTTTTGTCCATTTTGATGACTC 58.252 36.000 0.00 0.00 0.00 3.36
592 596 6.729690 TCCTTTTTGTCCATTTTGATGACT 57.270 33.333 0.00 0.00 0.00 3.41
593 597 6.930722 ACATCCTTTTTGTCCATTTTGATGAC 59.069 34.615 0.00 0.00 33.22 3.06
594 598 7.065120 ACATCCTTTTTGTCCATTTTGATGA 57.935 32.000 0.00 0.00 33.22 2.92
595 599 9.090692 GATACATCCTTTTTGTCCATTTTGATG 57.909 33.333 0.00 0.00 34.68 3.07
596 600 9.039165 AGATACATCCTTTTTGTCCATTTTGAT 57.961 29.630 0.00 0.00 0.00 2.57
597 601 8.421249 AGATACATCCTTTTTGTCCATTTTGA 57.579 30.769 0.00 0.00 0.00 2.69
598 602 9.793252 CTAGATACATCCTTTTTGTCCATTTTG 57.207 33.333 0.00 0.00 0.00 2.44
599 603 9.753674 TCTAGATACATCCTTTTTGTCCATTTT 57.246 29.630 0.00 0.00 0.00 1.82
600 604 9.753674 TTCTAGATACATCCTTTTTGTCCATTT 57.246 29.630 0.00 0.00 0.00 2.32
601 605 9.178758 GTTCTAGATACATCCTTTTTGTCCATT 57.821 33.333 0.00 0.00 0.00 3.16
602 606 8.552296 AGTTCTAGATACATCCTTTTTGTCCAT 58.448 33.333 0.00 0.00 0.00 3.41
603 607 7.918076 AGTTCTAGATACATCCTTTTTGTCCA 58.082 34.615 0.00 0.00 0.00 4.02
604 608 9.886132 TTAGTTCTAGATACATCCTTTTTGTCC 57.114 33.333 0.00 0.00 0.00 4.02
687 691 7.182761 GTCCGAAAATACTTGTCATCAGAATG 58.817 38.462 0.00 0.00 37.54 2.67
688 692 6.036083 CGTCCGAAAATACTTGTCATCAGAAT 59.964 38.462 0.00 0.00 0.00 2.40
689 693 5.347635 CGTCCGAAAATACTTGTCATCAGAA 59.652 40.000 0.00 0.00 0.00 3.02
690 694 4.862574 CGTCCGAAAATACTTGTCATCAGA 59.137 41.667 0.00 0.00 0.00 3.27
691 695 4.032900 CCGTCCGAAAATACTTGTCATCAG 59.967 45.833 0.00 0.00 0.00 2.90
692 696 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
693 697 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
694 698 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
695 699 3.006110 ACTCCGTCCGAAAATACTTGTCA 59.994 43.478 0.00 0.00 0.00 3.58
696 700 3.582780 ACTCCGTCCGAAAATACTTGTC 58.417 45.455 0.00 0.00 0.00 3.18
697 701 3.672767 ACTCCGTCCGAAAATACTTGT 57.327 42.857 0.00 0.00 0.00 3.16
698 702 6.238022 GGAAATACTCCGTCCGAAAATACTTG 60.238 42.308 0.00 0.00 33.37 3.16
699 703 5.814188 GGAAATACTCCGTCCGAAAATACTT 59.186 40.000 0.00 0.00 33.37 2.24
700 704 5.354767 GGAAATACTCCGTCCGAAAATACT 58.645 41.667 0.00 0.00 33.37 2.12
701 705 5.648033 GGAAATACTCCGTCCGAAAATAC 57.352 43.478 0.00 0.00 33.37 1.89
713 717 0.388294 CCTCCGTCCGGAAATACTCC 59.612 60.000 5.23 0.00 44.66 3.85
714 718 0.388294 CCCTCCGTCCGGAAATACTC 59.612 60.000 5.23 0.00 44.66 2.59
715 719 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
716 720 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
717 721 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
718 722 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
719 723 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
720 724 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
721 725 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
722 726 1.379576 AAGTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
723 727 1.712977 CGAAGTACTCCCTCCGTCCG 61.713 65.000 0.00 0.00 0.00 4.79
724 728 1.382692 CCGAAGTACTCCCTCCGTCC 61.383 65.000 0.00 0.00 0.00 4.79
725 729 0.679321 ACCGAAGTACTCCCTCCGTC 60.679 60.000 0.00 0.00 0.00 4.79
726 730 0.251519 AACCGAAGTACTCCCTCCGT 60.252 55.000 0.00 0.00 0.00 4.69
727 731 0.455005 GAACCGAAGTACTCCCTCCG 59.545 60.000 0.00 0.00 0.00 4.63
728 732 0.455005 CGAACCGAAGTACTCCCTCC 59.545 60.000 0.00 0.00 0.00 4.30
729 733 1.457346 TCGAACCGAAGTACTCCCTC 58.543 55.000 0.00 0.00 31.06 4.30
730 734 2.140839 ATCGAACCGAAGTACTCCCT 57.859 50.000 0.00 0.00 39.99 4.20
731 735 4.581077 AATATCGAACCGAAGTACTCCC 57.419 45.455 0.00 0.00 39.99 4.30
732 736 6.800892 GTGATAATATCGAACCGAAGTACTCC 59.199 42.308 0.00 0.00 39.99 3.85
733 737 7.358066 TGTGATAATATCGAACCGAAGTACTC 58.642 38.462 0.00 0.00 39.99 2.59
734 738 7.268199 TGTGATAATATCGAACCGAAGTACT 57.732 36.000 0.00 0.00 39.99 2.73
735 739 8.516811 AATGTGATAATATCGAACCGAAGTAC 57.483 34.615 0.00 0.00 39.99 2.73
752 756 7.045416 ACTGCCGTCAATTTAGTAATGTGATA 58.955 34.615 0.76 0.00 0.00 2.15
766 770 3.740115 ACTAAGACAAACTGCCGTCAAT 58.260 40.909 0.00 0.00 34.48 2.57
784 789 6.514870 GCAGTTGAATGATTTGGTTGTGACTA 60.515 38.462 0.00 0.00 0.00 2.59
797 803 2.939103 GTTAGGCGAGCAGTTGAATGAT 59.061 45.455 0.00 0.00 0.00 2.45
801 807 0.669318 CGGTTAGGCGAGCAGTTGAA 60.669 55.000 0.00 0.00 0.00 2.69
836 842 2.979130 GCAAGTCGCTGGTAGATCC 58.021 57.895 0.00 0.00 37.77 3.36
856 863 5.877564 CACCAACCTAGAAGAAAAGATCCTC 59.122 44.000 0.00 0.00 0.00 3.71
868 875 5.546499 ACTTAGATCAACCACCAACCTAGAA 59.454 40.000 0.00 0.00 0.00 2.10
889 896 6.948309 GGCAACCAATATTATCAGGGATACTT 59.052 38.462 0.00 0.00 0.00 2.24
890 897 6.275618 AGGCAACCAATATTATCAGGGATACT 59.724 38.462 0.00 0.00 37.17 2.12
932 942 4.156622 CTGCAGGCGCGTCATGTG 62.157 66.667 15.58 3.19 42.97 3.21
933 943 3.295304 TACTGCAGGCGCGTCATGT 62.295 57.895 19.93 8.32 42.97 3.21
935 945 2.509336 GTACTGCAGGCGCGTCAT 60.509 61.111 19.93 0.00 42.97 3.06
936 946 4.735132 GGTACTGCAGGCGCGTCA 62.735 66.667 19.93 2.76 42.97 4.35
937 947 4.436998 AGGTACTGCAGGCGCGTC 62.437 66.667 19.93 0.21 42.97 5.19
939 949 2.076622 ATAGAGGTACTGCAGGCGCG 62.077 60.000 19.93 0.00 41.55 6.86
940 950 0.959553 TATAGAGGTACTGCAGGCGC 59.040 55.000 19.93 0.00 41.55 6.53
941 951 2.558795 ACATATAGAGGTACTGCAGGCG 59.441 50.000 19.93 0.00 41.55 5.52
942 952 3.574396 TCACATATAGAGGTACTGCAGGC 59.426 47.826 19.93 10.34 41.55 4.85
943 953 4.830046 ACTCACATATAGAGGTACTGCAGG 59.170 45.833 19.93 0.00 41.55 4.85
944 954 5.532779 TCACTCACATATAGAGGTACTGCAG 59.467 44.000 13.48 13.48 41.55 4.41
945 955 5.299531 GTCACTCACATATAGAGGTACTGCA 59.700 44.000 8.67 0.00 41.55 4.41
946 956 5.299531 TGTCACTCACATATAGAGGTACTGC 59.700 44.000 8.67 0.00 41.55 4.40
947 957 6.944234 TGTCACTCACATATAGAGGTACTG 57.056 41.667 8.67 0.11 41.55 2.74
948 958 7.780271 TGAATGTCACTCACATATAGAGGTACT 59.220 37.037 8.67 0.00 45.77 2.73
949 959 7.941919 TGAATGTCACTCACATATAGAGGTAC 58.058 38.462 8.67 6.77 45.77 3.34
950 960 8.712228 ATGAATGTCACTCACATATAGAGGTA 57.288 34.615 8.67 0.00 45.77 3.08
951 961 7.609097 ATGAATGTCACTCACATATAGAGGT 57.391 36.000 8.67 0.00 45.77 3.85
952 962 9.800433 GATATGAATGTCACTCACATATAGAGG 57.200 37.037 8.67 0.28 45.77 3.69
953 963 9.800433 GGATATGAATGTCACTCACATATAGAG 57.200 37.037 0.00 3.48 45.77 2.43
954 964 8.753133 GGGATATGAATGTCACTCACATATAGA 58.247 37.037 0.00 0.00 45.77 1.98
955 965 8.534496 TGGGATATGAATGTCACTCACATATAG 58.466 37.037 0.00 0.00 45.77 1.31
1011 1021 1.081641 CAGCCAACGCAGAGCTTTG 60.082 57.895 0.00 0.00 37.50 2.77
1027 1037 2.743928 GGCAGAGGAACGTGGCAG 60.744 66.667 0.00 0.00 39.03 4.85
1047 1057 1.305046 GTCTTCCTCCAGACGGGGA 60.305 63.158 0.00 0.00 32.53 4.81
1053 1063 2.287977 TGTCTTCGTCTTCCTCCAGA 57.712 50.000 0.00 0.00 0.00 3.86
1136 1146 1.795768 TTGCTCGTCAACATGGAGAC 58.204 50.000 9.11 9.11 0.00 3.36
1159 1169 3.807538 CACATGCGCACCTGCCTC 61.808 66.667 14.90 0.00 37.91 4.70
1198 1208 1.135431 CGCTTGCATTTCCGGAATCAA 60.135 47.619 19.62 19.45 0.00 2.57
1211 1221 2.509569 TGAGGTAAATTTCCGCTTGCA 58.490 42.857 0.00 0.00 0.00 4.08
1585 1601 2.094494 AGAGAAGTGCTATCACCACACG 60.094 50.000 0.00 0.00 44.16 4.49
1596 1612 4.816385 TCGTTTTCATCAAAGAGAAGTGCT 59.184 37.500 0.00 0.00 0.00 4.40
1603 1619 4.329489 CGCTCATCGTTTTCATCAAAGAG 58.671 43.478 0.00 0.00 0.00 2.85
1755 2840 7.151308 TGATTCCACCACAAACAACATATTTC 58.849 34.615 0.00 0.00 0.00 2.17
1786 2882 1.556911 AGCACAAGTAGACCCTGATGG 59.443 52.381 0.00 0.00 41.37 3.51
1787 2883 3.005554 CAAGCACAAGTAGACCCTGATG 58.994 50.000 0.00 0.00 0.00 3.07
1788 2884 2.616510 GCAAGCACAAGTAGACCCTGAT 60.617 50.000 0.00 0.00 0.00 2.90
1789 2885 1.270839 GCAAGCACAAGTAGACCCTGA 60.271 52.381 0.00 0.00 0.00 3.86
1790 2886 1.160137 GCAAGCACAAGTAGACCCTG 58.840 55.000 0.00 0.00 0.00 4.45
1791 2887 0.764890 TGCAAGCACAAGTAGACCCT 59.235 50.000 0.00 0.00 0.00 4.34
1792 2888 1.826385 ATGCAAGCACAAGTAGACCC 58.174 50.000 0.00 0.00 0.00 4.46
1825 2921 3.485463 ACATCACCGGAAGTCTGAAAA 57.515 42.857 9.46 0.00 0.00 2.29
1921 3017 2.561733 TGAGAGATAAAGCCGACACG 57.438 50.000 0.00 0.00 0.00 4.49
1957 3053 2.020016 GCACGAACATACGCGCTG 59.980 61.111 5.73 6.91 38.13 5.18
1966 3062 0.174617 TCATCCTATGCGCACGAACA 59.825 50.000 14.90 0.00 0.00 3.18
1986 3082 5.977725 GGCGCTCATATATACGAACATACAT 59.022 40.000 7.64 0.00 0.00 2.29
2048 3145 1.485066 GGAGATGCCCTAAGACGGAAA 59.515 52.381 0.00 0.00 0.00 3.13
2071 3168 7.552687 AGATTATTTTTAACACGAGGATCAGCA 59.447 33.333 0.00 0.00 33.17 4.41
2099 3196 6.828785 AGATGCCCTAAGACGAATACATTTTT 59.171 34.615 0.00 0.00 0.00 1.94
2100 3197 6.357367 AGATGCCCTAAGACGAATACATTTT 58.643 36.000 0.00 0.00 0.00 1.82
2101 3198 5.930135 AGATGCCCTAAGACGAATACATTT 58.070 37.500 0.00 0.00 0.00 2.32
2102 3199 5.511545 GGAGATGCCCTAAGACGAATACATT 60.512 44.000 0.00 0.00 0.00 2.71
2103 3200 4.021016 GGAGATGCCCTAAGACGAATACAT 60.021 45.833 0.00 0.00 0.00 2.29
2104 3201 3.321111 GGAGATGCCCTAAGACGAATACA 59.679 47.826 0.00 0.00 0.00 2.29
2105 3202 3.321111 TGGAGATGCCCTAAGACGAATAC 59.679 47.826 0.00 0.00 34.97 1.89
2106 3203 3.572642 TGGAGATGCCCTAAGACGAATA 58.427 45.455 0.00 0.00 34.97 1.75
2107 3204 2.398588 TGGAGATGCCCTAAGACGAAT 58.601 47.619 0.00 0.00 34.97 3.34
2108 3205 1.860641 TGGAGATGCCCTAAGACGAA 58.139 50.000 0.00 0.00 34.97 3.85
2109 3206 1.860641 TTGGAGATGCCCTAAGACGA 58.139 50.000 0.00 0.00 34.97 4.20
2110 3207 2.487934 CATTGGAGATGCCCTAAGACG 58.512 52.381 0.00 0.00 34.97 4.18
2111 3208 2.225467 GCATTGGAGATGCCCTAAGAC 58.775 52.381 0.00 0.00 39.01 3.01
2112 3209 2.645838 GCATTGGAGATGCCCTAAGA 57.354 50.000 0.00 0.00 39.01 2.10
2119 3216 0.250640 AGGATCGGCATTGGAGATGC 60.251 55.000 2.50 2.50 43.85 3.91
2120 3217 1.805869 GAGGATCGGCATTGGAGATG 58.194 55.000 0.00 0.00 0.00 2.90
2133 3230 0.941463 ATGCGCGTGATTCGAGGATC 60.941 55.000 8.43 0.00 45.18 3.36
2134 3231 1.068083 ATGCGCGTGATTCGAGGAT 59.932 52.632 8.43 0.00 43.88 3.24
2135 3232 1.588932 GATGCGCGTGATTCGAGGA 60.589 57.895 6.97 0.00 43.53 3.71
2162 3259 2.149803 AATGCGTTCGGACCACTCGA 62.150 55.000 0.00 0.00 34.62 4.04
2174 3271 3.380142 GTGTTGGATGTCAAAATGCGTT 58.620 40.909 0.00 0.00 37.08 4.84
2295 3392 2.248835 CCGTCCGAGTTTTTGGCGT 61.249 57.895 0.00 0.00 0.00 5.68
2320 3417 4.648651 TGATTGCTATCATGACTGGGATG 58.351 43.478 6.75 0.00 35.87 3.51
2327 3424 6.593382 GGAGTTATCCTGATTGCTATCATGAC 59.407 42.308 15.79 7.41 42.94 3.06
2358 3455 0.249615 ATGATCGATGAGGTGTGCGG 60.250 55.000 0.54 0.00 0.00 5.69
2369 3466 4.344968 TGGTTCCACTATGTGATGATCGAT 59.655 41.667 0.00 0.00 35.23 3.59
2377 3474 2.617788 GGCATGTGGTTCCACTATGTGA 60.618 50.000 20.48 2.25 37.78 3.58
2471 3568 5.880054 ATGCATATAATGGCGTAAAGTCC 57.120 39.130 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.