Multiple sequence alignment - TraesCS4A01G240000

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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 TraesCS4A01G240000 chr4A 100.000 2801 0 0 1 2801 549801138 549798338 0.000000e+00 5173.0
1 TraesCS4A01G240000 chr4D 93.408 986 50 6 1826 2800 47992577 47993558 0.000000e+00 1447.0
2 TraesCS4A01G240000 chr4D 96.050 886 30 3 910 1793 47990885 47991767 0.000000e+00 1437.0
3 TraesCS4A01G240000 chr4D 89.474 285 23 6 1 280 47990159 47990441 1.230000e-93 353.0
4 TraesCS4A01G240000 chr4B 94.124 885 48 2 910 1793 70575739 70576620 0.000000e+00 1343.0
5 TraesCS4A01G240000 chr4B 91.701 482 26 5 2332 2801 70577835 70578314 0.000000e+00 656.0
6 TraesCS4A01G240000 chr4B 94.377 409 22 1 1826 2234 70577428 70577835 6.590000e-176 627.0
7 TraesCS4A01G240000 chr4B 91.489 47 3 1 858 903 70575343 70575389 2.330000e-06 63.9
8 TraesCS4A01G240000 chr3D 83.125 160 19 7 487 638 341490957 341490798 3.760000e-29 139.0
9 TraesCS4A01G240000 chr3D 100.000 36 0 0 1794 1829 372457809 372457774 1.800000e-07 67.6
10 TraesCS4A01G240000 chr3A 81.366 161 21 6 487 638 461843694 461843854 3.790000e-24 122.0
11 TraesCS4A01G240000 chr3A 80.870 115 15 7 677 787 688144446 688144335 1.790000e-12 84.2
12 TraesCS4A01G240000 chr5B 83.871 124 20 0 687 810 707437742 707437619 4.900000e-23 119.0
13 TraesCS4A01G240000 chr3B 85.393 89 9 2 722 810 65547018 65547102 3.840000e-14 89.8
14 TraesCS4A01G240000 chr7B 82.524 103 11 4 487 582 642750458 642750356 1.790000e-12 84.2
15 TraesCS4A01G240000 chr7B 94.286 35 2 0 484 518 642750434 642750468 1.000000e-03 54.7
16 TraesCS4A01G240000 chr5D 97.436 39 1 0 507 545 215139170 215139132 1.800000e-07 67.6
17 TraesCS4A01G240000 chr5D 100.000 33 0 0 753 785 410345683 410345715 8.380000e-06 62.1
18 TraesCS4A01G240000 chr7D 100.000 28 0 0 487 514 22523978 22524005 5.000000e-03 52.8


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 TraesCS4A01G240000 chr4A 549798338 549801138 2800 True 5173.000 5173 100.000000 1 2801 1 chr4A.!!$R1 2800
1 TraesCS4A01G240000 chr4D 47990159 47993558 3399 False 1079.000 1447 92.977333 1 2800 3 chr4D.!!$F1 2799
2 TraesCS4A01G240000 chr4B 70575343 70578314 2971 False 672.475 1343 92.922750 858 2801 4 chr4B.!!$F1 1943

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
991 1404 0.04109 TTTGCTCCTCCCCCAAATCC 59.959 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 3477 0.249073 GACCCTCGACATGATGTCCG 60.249 60.0 19.01 13.95 44.2 4.79 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
356 396 3.909732 ACAAATGACCTCCAACTCCAAA 58.090 40.909 0.00 0.00 0.00 3.28
357 397 4.482990 ACAAATGACCTCCAACTCCAAAT 58.517 39.130 0.00 0.00 0.00 2.32
359 399 3.814504 ATGACCTCCAACTCCAAATGT 57.185 42.857 0.00 0.00 0.00 2.71
360 400 4.927267 ATGACCTCCAACTCCAAATGTA 57.073 40.909 0.00 0.00 0.00 2.29
364 409 6.074648 TGACCTCCAACTCCAAATGTAAAAT 58.925 36.000 0.00 0.00 0.00 1.82
369 414 7.540745 CCTCCAACTCCAAATGTAAAATTTACG 59.459 37.037 10.81 0.00 0.00 3.18
374 419 7.364970 ACTCCAAATGTAAAATTTACGTCACC 58.635 34.615 10.62 0.00 0.00 4.02
377 422 3.436817 TGTAAAATTTACGTCACCGCG 57.563 42.857 10.81 0.00 37.70 6.46
399 444 4.720902 CGGCCATGGTGAGGTGCA 62.721 66.667 14.67 0.00 0.00 4.57
400 445 3.064324 GGCCATGGTGAGGTGCAC 61.064 66.667 14.67 8.80 46.98 4.57
421 466 2.173669 CAGCGGTGATTAGTGGCCG 61.174 63.158 9.50 0.00 46.17 6.13
423 468 2.895372 CGGTGATTAGTGGCCGCC 60.895 66.667 14.07 1.04 37.69 6.13
427 472 4.171103 GATTAGTGGCCGCCGGGT 62.171 66.667 14.07 0.00 34.97 5.28
428 473 4.171103 ATTAGTGGCCGCCGGGTC 62.171 66.667 14.07 0.00 38.88 4.46
440 485 3.827898 CGGGTCTGAGGAGGCGTC 61.828 72.222 0.00 0.00 0.00 5.19
441 486 3.462678 GGGTCTGAGGAGGCGTCC 61.463 72.222 17.88 17.88 44.33 4.79
442 487 2.680352 GGTCTGAGGAGGCGTCCA 60.680 66.667 26.40 6.76 46.80 4.02
443 488 2.060980 GGTCTGAGGAGGCGTCCAT 61.061 63.158 26.40 12.10 46.80 3.41
444 489 1.142748 GTCTGAGGAGGCGTCCATG 59.857 63.158 26.40 15.33 46.80 3.66
445 490 1.000359 TCTGAGGAGGCGTCCATGA 60.000 57.895 26.40 17.20 46.80 3.07
446 491 1.039785 TCTGAGGAGGCGTCCATGAG 61.040 60.000 26.40 17.55 46.80 2.90
447 492 2.025767 CTGAGGAGGCGTCCATGAGG 62.026 65.000 26.40 8.52 46.80 3.86
448 493 2.039624 AGGAGGCGTCCATGAGGT 59.960 61.111 26.40 2.39 46.80 3.85
449 494 2.022240 GAGGAGGCGTCCATGAGGTC 62.022 65.000 26.40 10.87 46.80 3.85
450 495 2.501610 GAGGCGTCCATGAGGTCC 59.498 66.667 0.00 0.00 35.89 4.46
451 496 3.432051 GAGGCGTCCATGAGGTCCG 62.432 68.421 0.00 0.00 35.89 4.79
452 497 3.771160 GGCGTCCATGAGGTCCGT 61.771 66.667 0.00 0.00 34.41 4.69
453 498 2.264794 GCGTCCATGAGGTCCGTT 59.735 61.111 0.00 0.00 34.41 4.44
454 499 2.100631 GCGTCCATGAGGTCCGTTG 61.101 63.158 0.00 0.00 34.41 4.10
455 500 1.447838 CGTCCATGAGGTCCGTTGG 60.448 63.158 0.00 2.31 35.89 3.77
456 501 1.745489 GTCCATGAGGTCCGTTGGC 60.745 63.158 0.00 0.00 35.89 4.52
457 502 2.819595 CCATGAGGTCCGTTGGCG 60.820 66.667 0.00 0.00 37.95 5.69
467 512 3.124921 CGTTGGCGGCAGTTAGGG 61.125 66.667 12.87 0.00 0.00 3.53
468 513 3.440415 GTTGGCGGCAGTTAGGGC 61.440 66.667 12.87 0.00 0.00 5.19
469 514 3.646715 TTGGCGGCAGTTAGGGCT 61.647 61.111 12.87 0.00 0.00 5.19
470 515 3.918253 TTGGCGGCAGTTAGGGCTG 62.918 63.158 12.87 0.00 40.63 4.85
488 533 3.698463 CGCGCGTTTTGGTCGAGT 61.698 61.111 24.19 0.00 0.00 4.18
489 534 2.127758 GCGCGTTTTGGTCGAGTG 60.128 61.111 8.43 0.00 0.00 3.51
490 535 2.591311 GCGCGTTTTGGTCGAGTGA 61.591 57.895 8.43 0.00 0.00 3.41
491 536 1.897398 GCGCGTTTTGGTCGAGTGAT 61.897 55.000 8.43 0.00 0.00 3.06
492 537 0.179250 CGCGTTTTGGTCGAGTGATG 60.179 55.000 0.00 0.00 0.00 3.07
493 538 0.452784 GCGTTTTGGTCGAGTGATGC 60.453 55.000 0.00 0.00 0.00 3.91
494 539 0.865111 CGTTTTGGTCGAGTGATGCA 59.135 50.000 0.00 0.00 0.00 3.96
495 540 1.262950 CGTTTTGGTCGAGTGATGCAA 59.737 47.619 0.00 0.00 0.00 4.08
496 541 2.286713 CGTTTTGGTCGAGTGATGCAAA 60.287 45.455 0.00 0.00 0.00 3.68
497 542 3.609175 CGTTTTGGTCGAGTGATGCAAAT 60.609 43.478 0.00 0.00 0.00 2.32
498 543 4.298332 GTTTTGGTCGAGTGATGCAAATT 58.702 39.130 0.00 0.00 0.00 1.82
499 544 4.582701 TTTGGTCGAGTGATGCAAATTT 57.417 36.364 0.00 0.00 0.00 1.82
500 545 3.557577 TGGTCGAGTGATGCAAATTTG 57.442 42.857 14.03 14.03 0.00 2.32
524 569 6.698008 CATCACTTGATGCCCTATTTTACA 57.302 37.500 6.29 0.00 44.44 2.41
525 570 7.281040 CATCACTTGATGCCCTATTTTACAT 57.719 36.000 6.29 0.00 44.44 2.29
526 571 6.942532 TCACTTGATGCCCTATTTTACATC 57.057 37.500 0.00 0.00 39.47 3.06
527 572 6.422333 TCACTTGATGCCCTATTTTACATCA 58.578 36.000 0.00 0.00 45.25 3.07
528 573 6.318648 TCACTTGATGCCCTATTTTACATCAC 59.681 38.462 4.14 0.00 46.24 3.06
529 574 5.296780 ACTTGATGCCCTATTTTACATCACG 59.703 40.000 4.14 5.58 46.24 4.35
530 575 5.029807 TGATGCCCTATTTTACATCACGA 57.970 39.130 0.00 0.00 42.86 4.35
531 576 5.056480 TGATGCCCTATTTTACATCACGAG 58.944 41.667 0.00 0.00 42.86 4.18
532 577 3.202906 TGCCCTATTTTACATCACGAGC 58.797 45.455 0.00 0.00 0.00 5.03
533 578 3.202906 GCCCTATTTTACATCACGAGCA 58.797 45.455 0.00 0.00 0.00 4.26
534 579 3.625764 GCCCTATTTTACATCACGAGCAA 59.374 43.478 0.00 0.00 0.00 3.91
535 580 4.095782 GCCCTATTTTACATCACGAGCAAA 59.904 41.667 0.00 0.00 0.00 3.68
536 581 5.221048 GCCCTATTTTACATCACGAGCAAAT 60.221 40.000 0.00 0.00 0.00 2.32
537 582 6.430451 CCCTATTTTACATCACGAGCAAATC 58.570 40.000 0.00 0.00 0.00 2.17
538 583 6.260936 CCCTATTTTACATCACGAGCAAATCT 59.739 38.462 0.00 0.00 0.00 2.40
539 584 7.348201 CCTATTTTACATCACGAGCAAATCTC 58.652 38.462 0.00 0.00 38.47 2.75
572 617 5.649782 AAAATTACATCCTGTTGGAGCAG 57.350 39.130 0.00 0.00 46.91 4.24
573 618 2.113860 TTACATCCTGTTGGAGCAGC 57.886 50.000 0.00 0.00 46.91 5.25
574 619 0.108186 TACATCCTGTTGGAGCAGCG 60.108 55.000 0.00 0.00 46.91 5.18
575 620 1.376424 CATCCTGTTGGAGCAGCGT 60.376 57.895 0.00 0.00 46.91 5.07
576 621 0.957395 CATCCTGTTGGAGCAGCGTT 60.957 55.000 0.00 0.00 46.91 4.84
577 622 0.250901 ATCCTGTTGGAGCAGCGTTT 60.251 50.000 0.00 0.00 46.91 3.60
578 623 0.465460 TCCTGTTGGAGCAGCGTTTT 60.465 50.000 0.00 0.00 37.46 2.43
579 624 0.385390 CCTGTTGGAGCAGCGTTTTT 59.615 50.000 0.00 0.00 35.28 1.94
580 625 1.480205 CTGTTGGAGCAGCGTTTTTG 58.520 50.000 0.00 0.00 0.00 2.44
581 626 0.814457 TGTTGGAGCAGCGTTTTTGT 59.186 45.000 0.00 0.00 0.00 2.83
582 627 1.199624 GTTGGAGCAGCGTTTTTGTG 58.800 50.000 0.00 0.00 0.00 3.33
583 628 0.527385 TTGGAGCAGCGTTTTTGTGC 60.527 50.000 0.00 0.00 37.48 4.57
584 629 1.661509 GGAGCAGCGTTTTTGTGCC 60.662 57.895 0.00 0.00 37.98 5.01
585 630 1.360192 GAGCAGCGTTTTTGTGCCT 59.640 52.632 0.00 0.00 37.98 4.75
586 631 0.249031 GAGCAGCGTTTTTGTGCCTT 60.249 50.000 0.00 0.00 37.98 4.35
587 632 0.528249 AGCAGCGTTTTTGTGCCTTG 60.528 50.000 0.00 0.00 37.98 3.61
588 633 0.527385 GCAGCGTTTTTGTGCCTTGA 60.527 50.000 0.00 0.00 0.00 3.02
589 634 1.869342 GCAGCGTTTTTGTGCCTTGAT 60.869 47.619 0.00 0.00 0.00 2.57
590 635 1.788308 CAGCGTTTTTGTGCCTTGATG 59.212 47.619 0.00 0.00 0.00 3.07
591 636 1.680735 AGCGTTTTTGTGCCTTGATGA 59.319 42.857 0.00 0.00 0.00 2.92
592 637 2.297033 AGCGTTTTTGTGCCTTGATGAT 59.703 40.909 0.00 0.00 0.00 2.45
593 638 2.409378 GCGTTTTTGTGCCTTGATGATG 59.591 45.455 0.00 0.00 0.00 3.07
594 639 3.641648 CGTTTTTGTGCCTTGATGATGT 58.358 40.909 0.00 0.00 0.00 3.06
595 640 3.426191 CGTTTTTGTGCCTTGATGATGTG 59.574 43.478 0.00 0.00 0.00 3.21
596 641 4.619973 GTTTTTGTGCCTTGATGATGTGA 58.380 39.130 0.00 0.00 0.00 3.58
597 642 4.933505 TTTTGTGCCTTGATGATGTGAA 57.066 36.364 0.00 0.00 0.00 3.18
598 643 4.933505 TTTGTGCCTTGATGATGTGAAA 57.066 36.364 0.00 0.00 0.00 2.69
599 644 5.471556 TTTGTGCCTTGATGATGTGAAAT 57.528 34.783 0.00 0.00 0.00 2.17
600 645 6.587206 TTTGTGCCTTGATGATGTGAAATA 57.413 33.333 0.00 0.00 0.00 1.40
601 646 6.587206 TTGTGCCTTGATGATGTGAAATAA 57.413 33.333 0.00 0.00 0.00 1.40
602 647 6.778834 TGTGCCTTGATGATGTGAAATAAT 57.221 33.333 0.00 0.00 0.00 1.28
603 648 7.878547 TGTGCCTTGATGATGTGAAATAATA 57.121 32.000 0.00 0.00 0.00 0.98
604 649 8.467963 TGTGCCTTGATGATGTGAAATAATAT 57.532 30.769 0.00 0.00 0.00 1.28
605 650 8.916062 TGTGCCTTGATGATGTGAAATAATATT 58.084 29.630 0.00 0.00 0.00 1.28
606 651 9.754382 GTGCCTTGATGATGTGAAATAATATTT 57.246 29.630 0.00 0.00 0.00 1.40
633 678 8.311650 ACATCTACATTATTAATCGGAGTTGC 57.688 34.615 0.00 0.00 0.00 4.17
634 679 8.150945 ACATCTACATTATTAATCGGAGTTGCT 58.849 33.333 0.00 0.00 0.00 3.91
635 680 8.651588 CATCTACATTATTAATCGGAGTTGCTC 58.348 37.037 0.00 0.00 0.00 4.26
636 681 7.952671 TCTACATTATTAATCGGAGTTGCTCT 58.047 34.615 0.00 0.00 0.00 4.09
637 682 8.421784 TCTACATTATTAATCGGAGTTGCTCTT 58.578 33.333 0.00 0.00 0.00 2.85
638 683 7.865706 ACATTATTAATCGGAGTTGCTCTTT 57.134 32.000 0.00 0.00 0.00 2.52
639 684 8.281212 ACATTATTAATCGGAGTTGCTCTTTT 57.719 30.769 0.00 0.00 0.00 2.27
640 685 8.739972 ACATTATTAATCGGAGTTGCTCTTTTT 58.260 29.630 0.00 0.00 0.00 1.94
661 706 7.823745 TTTTTAGGGATTATTGGAGATGCTC 57.176 36.000 0.00 0.00 0.00 4.26
662 707 6.770286 TTTAGGGATTATTGGAGATGCTCT 57.230 37.500 0.00 0.00 0.00 4.09
663 708 7.872061 TTTAGGGATTATTGGAGATGCTCTA 57.128 36.000 0.00 0.00 0.00 2.43
664 709 7.872061 TTAGGGATTATTGGAGATGCTCTAA 57.128 36.000 0.00 0.00 35.57 2.10
665 710 6.966637 AGGGATTATTGGAGATGCTCTAAT 57.033 37.500 10.24 10.24 42.66 1.73
666 711 7.340531 AGGGATTATTGGAGATGCTCTAATT 57.659 36.000 10.57 0.00 38.24 1.40
667 712 7.173722 AGGGATTATTGGAGATGCTCTAATTG 58.826 38.462 10.57 0.00 38.24 2.32
668 713 6.376581 GGGATTATTGGAGATGCTCTAATTGG 59.623 42.308 10.57 0.00 38.24 3.16
669 714 6.127786 GGATTATTGGAGATGCTCTAATTGGC 60.128 42.308 10.57 2.53 38.24 4.52
670 715 3.939740 TTGGAGATGCTCTAATTGGCT 57.060 42.857 0.00 0.00 0.00 4.75
671 716 3.939740 TGGAGATGCTCTAATTGGCTT 57.060 42.857 0.00 0.00 0.00 4.35
672 717 3.813443 TGGAGATGCTCTAATTGGCTTC 58.187 45.455 0.00 0.00 34.30 3.86
673 718 3.145286 GGAGATGCTCTAATTGGCTTCC 58.855 50.000 0.00 7.16 34.52 3.46
674 719 3.434167 GGAGATGCTCTAATTGGCTTCCA 60.434 47.826 0.00 0.00 34.52 3.53
675 720 4.396522 GAGATGCTCTAATTGGCTTCCAT 58.603 43.478 10.05 0.00 34.52 3.41
676 721 4.142790 AGATGCTCTAATTGGCTTCCATG 58.857 43.478 10.05 0.00 34.52 3.66
677 722 3.650281 TGCTCTAATTGGCTTCCATGA 57.350 42.857 0.00 0.00 31.53 3.07
678 723 3.548770 TGCTCTAATTGGCTTCCATGAG 58.451 45.455 0.00 0.00 31.53 2.90
679 724 2.883386 GCTCTAATTGGCTTCCATGAGG 59.117 50.000 0.00 0.00 31.53 3.86
680 725 3.484407 CTCTAATTGGCTTCCATGAGGG 58.516 50.000 0.00 0.00 31.53 4.30
681 726 3.122480 TCTAATTGGCTTCCATGAGGGA 58.878 45.455 0.00 0.00 46.61 4.20
690 735 2.988010 TCCATGAGGGAAGAACGATG 57.012 50.000 0.00 0.00 44.80 3.84
691 736 2.466846 TCCATGAGGGAAGAACGATGA 58.533 47.619 0.00 0.00 44.80 2.92
692 737 2.168521 TCCATGAGGGAAGAACGATGAC 59.831 50.000 0.00 0.00 44.80 3.06
693 738 2.093500 CCATGAGGGAAGAACGATGACA 60.093 50.000 0.00 0.00 40.01 3.58
694 739 3.193263 CATGAGGGAAGAACGATGACAG 58.807 50.000 0.00 0.00 0.00 3.51
695 740 1.066858 TGAGGGAAGAACGATGACAGC 60.067 52.381 0.00 0.00 0.00 4.40
696 741 0.108615 AGGGAAGAACGATGACAGCG 60.109 55.000 12.26 12.26 0.00 5.18
697 742 1.084370 GGGAAGAACGATGACAGCGG 61.084 60.000 18.40 0.00 0.00 5.52
698 743 1.696832 GGAAGAACGATGACAGCGGC 61.697 60.000 18.40 8.99 0.00 6.53
699 744 2.014093 GAAGAACGATGACAGCGGCG 62.014 60.000 18.40 0.51 0.00 6.46
700 745 4.210304 GAACGATGACAGCGGCGC 62.210 66.667 26.86 26.86 0.00 6.53
718 763 3.267974 GCCTTTGGCTCGTTCCAG 58.732 61.111 0.73 0.00 46.69 3.86
719 764 1.600916 GCCTTTGGCTCGTTCCAGT 60.601 57.895 0.73 0.00 46.69 4.00
720 765 1.172812 GCCTTTGGCTCGTTCCAGTT 61.173 55.000 0.73 0.00 46.69 3.16
723 768 2.678336 CCTTTGGCTCGTTCCAGTTATC 59.322 50.000 0.00 0.00 37.44 1.75
732 777 3.436704 TCGTTCCAGTTATCGTAGTCGTT 59.563 43.478 0.00 0.00 38.33 3.85
733 778 4.629634 TCGTTCCAGTTATCGTAGTCGTTA 59.370 41.667 0.00 0.00 38.33 3.18
734 779 5.294306 TCGTTCCAGTTATCGTAGTCGTTAT 59.706 40.000 0.00 0.00 38.33 1.89
749 794 4.643784 AGTCGTTATTAGGTGGTCTACAGG 59.356 45.833 0.00 0.00 0.00 4.00
750 795 3.382546 TCGTTATTAGGTGGTCTACAGGC 59.617 47.826 0.00 0.00 0.00 4.85
758 803 1.279271 GTGGTCTACAGGCTTGGATGT 59.721 52.381 0.00 0.00 0.00 3.06
790 835 8.032952 TGTTACTTCTCATGTTCTTTATGCTG 57.967 34.615 0.00 0.00 0.00 4.41
794 839 4.529897 TCTCATGTTCTTTATGCTGCCAT 58.470 39.130 0.00 0.00 35.44 4.40
798 843 6.063404 TCATGTTCTTTATGCTGCCATGATA 58.937 36.000 9.01 0.00 34.08 2.15
811 856 6.071784 TGCTGCCATGATATTTGATGAATACC 60.072 38.462 0.00 0.00 33.20 2.73
817 862 9.682465 CCATGATATTTGATGAATACCAGATCT 57.318 33.333 0.00 0.00 33.20 2.75
820 865 9.939802 TGATATTTGATGAATACCAGATCTGAG 57.060 33.333 24.62 15.81 33.20 3.35
825 874 8.868522 TTGATGAATACCAGATCTGAGTTTTT 57.131 30.769 24.62 15.18 0.00 1.94
903 966 2.184579 GACCGAGCCAGTGCCTAC 59.815 66.667 0.00 0.00 38.69 3.18
904 967 2.603473 ACCGAGCCAGTGCCTACA 60.603 61.111 0.00 0.00 38.69 2.74
905 968 2.167398 GACCGAGCCAGTGCCTACAA 62.167 60.000 0.00 0.00 38.69 2.41
906 969 1.003839 CCGAGCCAGTGCCTACAAA 60.004 57.895 0.00 0.00 38.69 2.83
908 971 1.298859 CGAGCCAGTGCCTACAAACC 61.299 60.000 0.00 0.00 38.69 3.27
909 972 0.250727 GAGCCAGTGCCTACAAACCA 60.251 55.000 0.00 0.00 38.69 3.67
911 974 1.036707 GCCAGTGCCTACAAACCAAA 58.963 50.000 0.00 0.00 0.00 3.28
912 975 1.000274 GCCAGTGCCTACAAACCAAAG 60.000 52.381 0.00 0.00 0.00 2.77
913 976 1.613437 CCAGTGCCTACAAACCAAAGG 59.387 52.381 0.00 0.00 0.00 3.11
950 1362 1.950630 GCACGCAAGCAACCCAAAG 60.951 57.895 0.00 0.00 45.62 2.77
958 1370 2.919494 GCAACCCAAAGCCCTGACG 61.919 63.158 0.00 0.00 0.00 4.35
979 1392 2.772287 CCGAGGATAGGATTTTGCTCC 58.228 52.381 0.00 0.00 29.15 4.70
991 1404 0.041090 TTTGCTCCTCCCCCAAATCC 59.959 55.000 0.00 0.00 0.00 3.01
1197 1610 4.849329 GCCGCGGAGACCTACGTG 62.849 72.222 33.48 8.14 46.22 4.49
1253 1666 0.951040 GTGAAGAAGGTGTCGGCCAG 60.951 60.000 2.24 0.00 0.00 4.85
1428 1841 1.296722 CGAGGAGTACGAGTTCGCG 60.297 63.158 0.00 0.00 44.43 5.87
1561 1974 2.546778 TCGAAAACGAGCTGTGAGTTT 58.453 42.857 0.00 0.00 39.45 2.66
1567 1980 2.205074 ACGAGCTGTGAGTTTTGTCTG 58.795 47.619 0.00 0.00 0.00 3.51
1574 1987 1.021202 TGAGTTTTGTCTGGGCAACG 58.979 50.000 0.00 0.00 37.60 4.10
1621 2034 7.704578 ATTTAGCTGAGTCTTGTAGTAGTGA 57.295 36.000 0.00 0.00 0.00 3.41
1676 2089 1.378531 TTCGAGCTTTGTGTTGCTGT 58.621 45.000 0.00 0.00 39.91 4.40
1733 2146 3.019564 GCAGAATGTAGCATCAGGGTTT 58.980 45.455 0.00 0.00 39.31 3.27
1769 2182 6.655078 AACAAATTGGTTCTCTATTGCACT 57.345 33.333 0.00 0.00 0.00 4.40
1793 2206 4.556942 TCTTGTGTGCTTTGTCATTGAG 57.443 40.909 0.00 0.00 0.00 3.02
1795 2208 4.274214 TCTTGTGTGCTTTGTCATTGAGAG 59.726 41.667 0.00 0.00 0.00 3.20
1797 2210 2.291465 GTGTGCTTTGTCATTGAGAGCA 59.709 45.455 12.66 12.66 40.70 4.26
1799 2212 3.057806 TGTGCTTTGTCATTGAGAGCATG 60.058 43.478 17.26 0.00 44.19 4.06
1800 2213 3.189910 GTGCTTTGTCATTGAGAGCATGA 59.810 43.478 17.26 0.00 44.19 3.07
1803 2216 4.798907 GCTTTGTCATTGAGAGCATGATTG 59.201 41.667 0.00 0.00 33.68 2.67
1805 2218 2.686405 TGTCATTGAGAGCATGATTGGC 59.314 45.455 0.00 0.00 0.00 4.52
1809 2222 1.100510 TGAGAGCATGATTGGCTTGC 58.899 50.000 0.00 0.00 42.78 4.01
1812 2225 4.104143 GCATGATTGGCTTGCTGC 57.896 55.556 0.00 0.00 42.58 5.25
1860 3050 1.943968 GCGGTTGTGCTGATAGGTTCA 60.944 52.381 0.00 0.00 0.00 3.18
1892 3082 6.235664 TCTATTTCCTGGTGGTTAAACAGTC 58.764 40.000 0.00 0.00 34.23 3.51
1942 3132 1.685302 CATTTTCCAGTTCGTTGGCG 58.315 50.000 0.00 0.00 38.16 5.69
1962 3152 2.223249 CGGTTGTTCTATGCGGATTTGG 60.223 50.000 0.00 0.00 0.00 3.28
1984 3174 3.143807 TGGTTTATATGCTTTGCACGC 57.856 42.857 0.32 0.32 43.04 5.34
1990 3180 1.646189 TATGCTTTGCACGCGATGTA 58.354 45.000 15.93 3.96 43.04 2.29
2101 3291 2.504367 GTTCTCTGCTGGCCTTTGTTA 58.496 47.619 3.32 0.00 0.00 2.41
2102 3292 2.884639 GTTCTCTGCTGGCCTTTGTTAA 59.115 45.455 3.32 0.00 0.00 2.01
2133 3323 0.895530 TCTTCTGGGTGATCGTGGTC 59.104 55.000 0.00 0.00 0.00 4.02
2142 3332 3.583276 GATCGTGGTCGGTGGTGCA 62.583 63.158 0.00 0.00 37.69 4.57
2152 3342 4.722855 GTGGTGCATTGCCACGGC 62.723 66.667 9.02 0.00 45.57 5.68
2215 3405 0.773644 TTTCCTGCTTCTGCCTCCTT 59.226 50.000 0.00 0.00 38.71 3.36
2246 3436 1.432270 CGCTCAGAAATTCCTCGGGC 61.432 60.000 0.00 0.00 0.00 6.13
2262 3452 1.153289 GGCGAGATGTGGCTGTGAT 60.153 57.895 0.00 0.00 0.00 3.06
2268 3458 1.002430 AGATGTGGCTGTGATGACGTT 59.998 47.619 0.00 0.00 0.00 3.99
2287 3477 1.407258 TTGTTGGTTACCAGCAGCAAC 59.593 47.619 19.51 7.76 44.89 4.17
2289 3479 1.169661 TTGGTTACCAGCAGCAACGG 61.170 55.000 3.65 0.00 33.81 4.44
2308 3498 2.215907 GACATCATGTCGAGGGTCAG 57.784 55.000 0.93 0.00 37.67 3.51
2459 3649 8.854117 GGCAAGATCACATCCTAGATTATTTTT 58.146 33.333 0.00 0.00 0.00 1.94
2460 3650 9.674824 GCAAGATCACATCCTAGATTATTTTTG 57.325 33.333 0.00 0.00 0.00 2.44
2506 3696 2.065899 TGGTCCCTTGGTTTGTTCTG 57.934 50.000 0.00 0.00 0.00 3.02
2536 3730 6.576662 GAAGTATTCCAGATGATCGTCCTA 57.423 41.667 11.42 0.00 39.83 2.94
2610 3806 5.802956 GCCGTTTTGTTTGCTGCTAATTATA 59.197 36.000 0.00 0.00 0.00 0.98
2611 3807 6.237463 GCCGTTTTGTTTGCTGCTAATTATAC 60.237 38.462 0.00 0.00 0.00 1.47
2694 3890 5.661056 TTTCCGAGAGATTTCTTCAGCTA 57.339 39.130 0.00 0.00 32.53 3.32
2700 3896 5.659463 GAGAGATTTCTTCAGCTAGAGCAA 58.341 41.667 4.01 0.00 37.36 3.91
2708 3904 5.114780 TCTTCAGCTAGAGCAAGCATAAAG 58.885 41.667 4.01 7.90 45.30 1.85
2733 3934 6.038050 GTGGTCAATGGAATCATTCTCTTCTC 59.962 42.308 0.00 0.00 41.29 2.87
2734 3935 6.069789 TGGTCAATGGAATCATTCTCTTCTCT 60.070 38.462 0.00 0.00 41.29 3.10
2758 3959 1.917273 ACCAATGTATCGTTCGGTCG 58.083 50.000 0.00 0.00 0.00 4.79
2776 3978 4.032900 CGGTCGAAGAATTATGTGTCTTGG 59.967 45.833 0.00 0.00 39.69 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
318 334 9.750125 GGTCATTTGTTGAAGTTAGAGATTTTT 57.250 29.630 0.00 0.00 35.70 1.94
319 335 9.136323 AGGTCATTTGTTGAAGTTAGAGATTTT 57.864 29.630 0.00 0.00 35.70 1.82
320 336 8.697507 AGGTCATTTGTTGAAGTTAGAGATTT 57.302 30.769 0.00 0.00 35.70 2.17
321 337 7.391833 GGAGGTCATTTGTTGAAGTTAGAGATT 59.608 37.037 0.00 0.00 35.70 2.40
327 343 6.126409 AGTTGGAGGTCATTTGTTGAAGTTA 58.874 36.000 0.00 0.00 35.70 2.24
338 354 4.118168 ACATTTGGAGTTGGAGGTCATT 57.882 40.909 0.00 0.00 0.00 2.57
377 422 4.864334 CTCACCATGGCCGCCTCC 62.864 72.222 13.04 0.00 0.00 4.30
401 446 0.811616 GGCCACTAATCACCGCTGAG 60.812 60.000 0.00 0.00 0.00 3.35
402 447 1.220749 GGCCACTAATCACCGCTGA 59.779 57.895 0.00 0.00 0.00 4.26
408 453 2.895372 CCGGCGGCCACTAATCAC 60.895 66.667 20.71 0.00 0.00 3.06
409 454 4.169696 CCCGGCGGCCACTAATCA 62.170 66.667 23.20 0.00 0.00 2.57
411 456 4.171103 GACCCGGCGGCCACTAAT 62.171 66.667 23.20 0.00 0.00 1.73
423 468 3.827898 GACGCCTCCTCAGACCCG 61.828 72.222 0.00 0.00 0.00 5.28
427 472 1.000359 TCATGGACGCCTCCTCAGA 60.000 57.895 3.30 0.00 37.48 3.27
428 473 1.440893 CTCATGGACGCCTCCTCAG 59.559 63.158 3.30 0.00 37.48 3.35
429 474 2.060383 CCTCATGGACGCCTCCTCA 61.060 63.158 3.30 0.00 37.48 3.86
430 475 2.022240 GACCTCATGGACGCCTCCTC 62.022 65.000 3.30 0.00 37.48 3.71
431 476 2.039624 ACCTCATGGACGCCTCCT 59.960 61.111 3.30 0.00 37.48 3.69
432 477 2.501610 GACCTCATGGACGCCTCC 59.498 66.667 0.00 0.00 37.04 4.30
434 479 3.461773 CGGACCTCATGGACGCCT 61.462 66.667 0.00 0.00 37.04 5.52
435 480 3.310860 AACGGACCTCATGGACGCC 62.311 63.158 0.00 0.00 39.46 5.68
436 481 2.100631 CAACGGACCTCATGGACGC 61.101 63.158 0.00 0.00 39.46 5.19
437 482 1.447838 CCAACGGACCTCATGGACG 60.448 63.158 0.00 0.00 40.77 4.79
438 483 1.745489 GCCAACGGACCTCATGGAC 60.745 63.158 10.35 0.49 34.82 4.02
439 484 2.668632 GCCAACGGACCTCATGGA 59.331 61.111 10.35 0.00 34.82 3.41
440 485 2.819595 CGCCAACGGACCTCATGG 60.820 66.667 0.00 3.37 35.87 3.66
450 495 3.124921 CCCTAACTGCCGCCAACG 61.125 66.667 0.00 0.00 39.67 4.10
451 496 3.440415 GCCCTAACTGCCGCCAAC 61.440 66.667 0.00 0.00 0.00 3.77
452 497 3.646715 AGCCCTAACTGCCGCCAA 61.647 61.111 0.00 0.00 0.00 4.52
453 498 4.408821 CAGCCCTAACTGCCGCCA 62.409 66.667 0.00 0.00 0.00 5.69
471 516 3.698463 ACTCGACCAAAACGCGCG 61.698 61.111 30.96 30.96 0.00 6.86
472 517 1.897398 ATCACTCGACCAAAACGCGC 61.897 55.000 5.73 0.00 0.00 6.86
473 518 0.179250 CATCACTCGACCAAAACGCG 60.179 55.000 3.53 3.53 0.00 6.01
474 519 0.452784 GCATCACTCGACCAAAACGC 60.453 55.000 0.00 0.00 0.00 4.84
475 520 0.865111 TGCATCACTCGACCAAAACG 59.135 50.000 0.00 0.00 0.00 3.60
476 521 3.347958 TTTGCATCACTCGACCAAAAC 57.652 42.857 0.00 0.00 0.00 2.43
477 522 4.582701 AATTTGCATCACTCGACCAAAA 57.417 36.364 0.00 0.00 32.60 2.44
478 523 4.297510 CAAATTTGCATCACTCGACCAAA 58.702 39.130 5.01 0.00 33.08 3.28
479 524 3.899734 CAAATTTGCATCACTCGACCAA 58.100 40.909 5.01 0.00 0.00 3.67
480 525 3.557577 CAAATTTGCATCACTCGACCA 57.442 42.857 5.01 0.00 0.00 4.02
502 547 7.013655 GTGATGTAAAATAGGGCATCAAGTGAT 59.986 37.037 7.51 0.00 45.93 3.06
503 548 6.318648 GTGATGTAAAATAGGGCATCAAGTGA 59.681 38.462 7.51 0.00 45.93 3.41
504 549 6.498304 GTGATGTAAAATAGGGCATCAAGTG 58.502 40.000 7.51 0.00 45.93 3.16
505 550 5.296780 CGTGATGTAAAATAGGGCATCAAGT 59.703 40.000 7.51 0.00 45.93 3.16
506 551 5.527214 TCGTGATGTAAAATAGGGCATCAAG 59.473 40.000 7.51 9.52 45.93 3.02
507 552 5.432645 TCGTGATGTAAAATAGGGCATCAA 58.567 37.500 7.51 0.00 45.93 2.57
508 553 5.029807 TCGTGATGTAAAATAGGGCATCA 57.970 39.130 0.00 0.00 43.44 3.07
509 554 4.083802 GCTCGTGATGTAAAATAGGGCATC 60.084 45.833 0.00 0.00 38.45 3.91
510 555 3.815401 GCTCGTGATGTAAAATAGGGCAT 59.185 43.478 0.00 0.00 0.00 4.40
511 556 3.202906 GCTCGTGATGTAAAATAGGGCA 58.797 45.455 0.00 0.00 0.00 5.36
512 557 3.202906 TGCTCGTGATGTAAAATAGGGC 58.797 45.455 0.00 0.00 0.00 5.19
513 558 5.811399 TTTGCTCGTGATGTAAAATAGGG 57.189 39.130 0.00 0.00 0.00 3.53
514 559 7.251704 AGATTTGCTCGTGATGTAAAATAGG 57.748 36.000 0.00 0.00 0.00 2.57
557 602 0.957395 AACGCTGCTCCAACAGGATG 60.957 55.000 0.00 0.00 46.00 3.51
558 603 0.250901 AAACGCTGCTCCAACAGGAT 60.251 50.000 0.00 0.00 38.16 3.24
559 604 0.465460 AAAACGCTGCTCCAACAGGA 60.465 50.000 0.00 0.00 38.16 3.86
560 605 0.385390 AAAAACGCTGCTCCAACAGG 59.615 50.000 0.00 0.00 38.16 4.00
561 606 1.202290 ACAAAAACGCTGCTCCAACAG 60.202 47.619 0.00 0.00 40.80 3.16
562 607 0.814457 ACAAAAACGCTGCTCCAACA 59.186 45.000 0.00 0.00 0.00 3.33
563 608 1.199624 CACAAAAACGCTGCTCCAAC 58.800 50.000 0.00 0.00 0.00 3.77
564 609 0.527385 GCACAAAAACGCTGCTCCAA 60.527 50.000 0.00 0.00 0.00 3.53
565 610 1.065600 GCACAAAAACGCTGCTCCA 59.934 52.632 0.00 0.00 0.00 3.86
566 611 1.661509 GGCACAAAAACGCTGCTCC 60.662 57.895 0.00 0.00 0.00 4.70
567 612 0.249031 AAGGCACAAAAACGCTGCTC 60.249 50.000 0.00 0.00 0.00 4.26
568 613 0.528249 CAAGGCACAAAAACGCTGCT 60.528 50.000 0.00 0.00 0.00 4.24
569 614 0.527385 TCAAGGCACAAAAACGCTGC 60.527 50.000 0.00 0.00 0.00 5.25
570 615 1.788308 CATCAAGGCACAAAAACGCTG 59.212 47.619 0.00 0.00 0.00 5.18
571 616 1.680735 TCATCAAGGCACAAAAACGCT 59.319 42.857 0.00 0.00 0.00 5.07
572 617 2.132740 TCATCAAGGCACAAAAACGC 57.867 45.000 0.00 0.00 0.00 4.84
573 618 3.426191 CACATCATCAAGGCACAAAAACG 59.574 43.478 0.00 0.00 0.00 3.60
574 619 4.619973 TCACATCATCAAGGCACAAAAAC 58.380 39.130 0.00 0.00 0.00 2.43
575 620 4.933505 TCACATCATCAAGGCACAAAAA 57.066 36.364 0.00 0.00 0.00 1.94
576 621 4.933505 TTCACATCATCAAGGCACAAAA 57.066 36.364 0.00 0.00 0.00 2.44
577 622 4.933505 TTTCACATCATCAAGGCACAAA 57.066 36.364 0.00 0.00 0.00 2.83
578 623 6.587206 TTATTTCACATCATCAAGGCACAA 57.413 33.333 0.00 0.00 0.00 3.33
579 624 6.778834 ATTATTTCACATCATCAAGGCACA 57.221 33.333 0.00 0.00 0.00 4.57
580 625 9.754382 AAATATTATTTCACATCATCAAGGCAC 57.246 29.630 0.00 0.00 0.00 5.01
607 652 9.419297 GCAACTCCGATTAATAATGTAGATGTA 57.581 33.333 0.00 0.00 0.00 2.29
608 653 8.150945 AGCAACTCCGATTAATAATGTAGATGT 58.849 33.333 0.00 0.00 0.00 3.06
609 654 8.539770 AGCAACTCCGATTAATAATGTAGATG 57.460 34.615 0.00 0.00 0.00 2.90
610 655 8.589338 AGAGCAACTCCGATTAATAATGTAGAT 58.411 33.333 0.00 0.00 0.00 1.98
611 656 7.952671 AGAGCAACTCCGATTAATAATGTAGA 58.047 34.615 0.00 0.00 0.00 2.59
612 657 8.594881 AAGAGCAACTCCGATTAATAATGTAG 57.405 34.615 0.00 0.00 0.00 2.74
613 658 8.958119 AAAGAGCAACTCCGATTAATAATGTA 57.042 30.769 0.00 0.00 0.00 2.29
614 659 7.865706 AAAGAGCAACTCCGATTAATAATGT 57.134 32.000 0.00 0.00 0.00 2.71
637 682 7.823745 GAGCATCTCCAATAATCCCTAAAAA 57.176 36.000 0.00 0.00 0.00 1.94
649 694 9.774401 ATGGAAGCCAATTAGAGCATCTCCAAT 62.774 40.741 12.57 0.00 40.87 3.16
650 695 8.564313 ATGGAAGCCAATTAGAGCATCTCCAA 62.564 42.308 12.57 0.00 40.87 3.53
651 696 7.168529 ATGGAAGCCAATTAGAGCATCTCCA 62.169 44.000 11.65 11.65 40.87 3.86
652 697 4.749166 ATGGAAGCCAATTAGAGCATCTCC 60.749 45.833 0.00 0.00 40.87 3.71
653 698 4.215827 CATGGAAGCCAATTAGAGCATCTC 59.784 45.833 0.00 0.00 40.87 2.75
654 699 4.141321 TCATGGAAGCCAATTAGAGCATCT 60.141 41.667 0.00 0.00 43.47 2.90
655 700 4.139786 TCATGGAAGCCAATTAGAGCATC 58.860 43.478 0.00 0.00 36.95 3.91
656 701 4.142790 CTCATGGAAGCCAATTAGAGCAT 58.857 43.478 0.00 0.00 36.95 3.79
657 702 3.548770 CTCATGGAAGCCAATTAGAGCA 58.451 45.455 0.00 0.00 36.95 4.26
658 703 2.883386 CCTCATGGAAGCCAATTAGAGC 59.117 50.000 0.00 0.00 36.95 4.09
659 704 3.137176 TCCCTCATGGAAGCCAATTAGAG 59.863 47.826 0.00 0.00 41.40 2.43
660 705 3.122480 TCCCTCATGGAAGCCAATTAGA 58.878 45.455 0.00 0.00 41.40 2.10
661 706 3.582998 TCCCTCATGGAAGCCAATTAG 57.417 47.619 0.00 0.00 41.40 1.73
671 716 2.168521 GTCATCGTTCTTCCCTCATGGA 59.831 50.000 0.00 0.00 43.18 3.41
672 717 2.093500 TGTCATCGTTCTTCCCTCATGG 60.093 50.000 0.00 0.00 0.00 3.66
673 718 3.193263 CTGTCATCGTTCTTCCCTCATG 58.807 50.000 0.00 0.00 0.00 3.07
674 719 2.419297 GCTGTCATCGTTCTTCCCTCAT 60.419 50.000 0.00 0.00 0.00 2.90
675 720 1.066858 GCTGTCATCGTTCTTCCCTCA 60.067 52.381 0.00 0.00 0.00 3.86
676 721 1.646189 GCTGTCATCGTTCTTCCCTC 58.354 55.000 0.00 0.00 0.00 4.30
677 722 0.108615 CGCTGTCATCGTTCTTCCCT 60.109 55.000 0.00 0.00 0.00 4.20
678 723 1.084370 CCGCTGTCATCGTTCTTCCC 61.084 60.000 0.00 0.00 0.00 3.97
679 724 1.696832 GCCGCTGTCATCGTTCTTCC 61.697 60.000 0.00 0.00 0.00 3.46
680 725 1.710339 GCCGCTGTCATCGTTCTTC 59.290 57.895 0.00 0.00 0.00 2.87
681 726 2.094659 CGCCGCTGTCATCGTTCTT 61.095 57.895 0.00 0.00 0.00 2.52
682 727 2.507102 CGCCGCTGTCATCGTTCT 60.507 61.111 0.00 0.00 0.00 3.01
683 728 4.210304 GCGCCGCTGTCATCGTTC 62.210 66.667 0.00 0.00 0.00 3.95
702 747 2.178912 TAACTGGAACGAGCCAAAGG 57.821 50.000 0.00 0.00 37.52 3.11
703 748 2.348666 CGATAACTGGAACGAGCCAAAG 59.651 50.000 0.00 0.00 37.52 2.77
704 749 2.289195 ACGATAACTGGAACGAGCCAAA 60.289 45.455 0.00 0.00 37.52 3.28
705 750 1.274167 ACGATAACTGGAACGAGCCAA 59.726 47.619 0.00 0.00 37.52 4.52
706 751 0.892755 ACGATAACTGGAACGAGCCA 59.107 50.000 0.00 0.00 36.30 4.75
707 752 2.098770 ACTACGATAACTGGAACGAGCC 59.901 50.000 0.00 0.00 0.00 4.70
708 753 3.361414 GACTACGATAACTGGAACGAGC 58.639 50.000 0.00 0.00 0.00 5.03
709 754 3.063180 ACGACTACGATAACTGGAACGAG 59.937 47.826 0.00 0.00 42.66 4.18
710 755 3.002791 ACGACTACGATAACTGGAACGA 58.997 45.455 0.00 0.00 42.66 3.85
711 756 3.395858 ACGACTACGATAACTGGAACG 57.604 47.619 0.00 0.00 42.66 3.95
712 757 7.589221 CCTAATAACGACTACGATAACTGGAAC 59.411 40.741 0.00 0.00 42.66 3.62
713 758 7.283127 ACCTAATAACGACTACGATAACTGGAA 59.717 37.037 0.00 0.00 42.66 3.53
714 759 6.767902 ACCTAATAACGACTACGATAACTGGA 59.232 38.462 0.00 0.00 42.66 3.86
715 760 6.854892 CACCTAATAACGACTACGATAACTGG 59.145 42.308 0.00 0.00 42.66 4.00
716 761 6.854892 CCACCTAATAACGACTACGATAACTG 59.145 42.308 0.00 0.00 42.66 3.16
717 762 6.543831 ACCACCTAATAACGACTACGATAACT 59.456 38.462 0.00 0.00 42.66 2.24
718 763 6.729187 ACCACCTAATAACGACTACGATAAC 58.271 40.000 0.00 0.00 42.66 1.89
719 764 6.767902 AGACCACCTAATAACGACTACGATAA 59.232 38.462 0.00 0.00 42.66 1.75
720 765 6.291377 AGACCACCTAATAACGACTACGATA 58.709 40.000 0.00 0.00 42.66 2.92
723 768 4.889832 AGACCACCTAATAACGACTACG 57.110 45.455 0.00 0.00 45.75 3.51
732 777 3.709653 CCAAGCCTGTAGACCACCTAATA 59.290 47.826 0.00 0.00 0.00 0.98
733 778 2.505819 CCAAGCCTGTAGACCACCTAAT 59.494 50.000 0.00 0.00 0.00 1.73
734 779 1.906574 CCAAGCCTGTAGACCACCTAA 59.093 52.381 0.00 0.00 0.00 2.69
749 794 9.129209 GAGAAGTAACAAAAATTACATCCAAGC 57.871 33.333 0.00 0.00 37.49 4.01
781 826 7.599171 TCATCAAATATCATGGCAGCATAAAG 58.401 34.615 0.00 0.00 0.00 1.85
784 829 7.712204 ATTCATCAAATATCATGGCAGCATA 57.288 32.000 0.00 0.00 0.00 3.14
785 830 6.605471 ATTCATCAAATATCATGGCAGCAT 57.395 33.333 0.00 0.00 0.00 3.79
790 835 7.692460 TCTGGTATTCATCAAATATCATGGC 57.308 36.000 0.00 0.00 39.62 4.40
794 839 9.939802 CTCAGATCTGGTATTCATCAAATATCA 57.060 33.333 22.42 0.00 38.38 2.15
798 843 9.471702 AAAACTCAGATCTGGTATTCATCAAAT 57.528 29.630 22.42 0.00 0.00 2.32
852 901 1.550072 TCGCTCCATCACTGTTCATGA 59.450 47.619 0.00 0.00 0.00 3.07
854 903 2.350522 GTTCGCTCCATCACTGTTCAT 58.649 47.619 0.00 0.00 0.00 2.57
856 905 0.716108 CGTTCGCTCCATCACTGTTC 59.284 55.000 0.00 0.00 0.00 3.18
857 906 0.317160 TCGTTCGCTCCATCACTGTT 59.683 50.000 0.00 0.00 0.00 3.16
858 907 0.109086 CTCGTTCGCTCCATCACTGT 60.109 55.000 0.00 0.00 0.00 3.55
859 908 0.109086 ACTCGTTCGCTCCATCACTG 60.109 55.000 0.00 0.00 0.00 3.66
908 971 1.528129 GCACTGAAGAGGACCCTTTG 58.472 55.000 0.00 0.00 0.00 2.77
909 972 0.035458 CGCACTGAAGAGGACCCTTT 59.965 55.000 0.00 0.00 0.00 3.11
911 974 2.948720 GCGCACTGAAGAGGACCCT 61.949 63.158 0.30 0.00 0.00 4.34
912 975 2.435059 GCGCACTGAAGAGGACCC 60.435 66.667 0.30 0.00 0.00 4.46
913 976 2.029844 GTGCGCACTGAAGAGGACC 61.030 63.158 32.55 1.36 0.00 4.46
950 1362 3.214250 CTATCCTCGGCGTCAGGGC 62.214 68.421 13.91 0.00 37.98 5.19
958 1370 2.147150 GAGCAAAATCCTATCCTCGGC 58.853 52.381 0.00 0.00 0.00 5.54
979 1392 2.919043 CGGAGGGATTTGGGGGAG 59.081 66.667 0.00 0.00 0.00 4.30
1428 1841 0.608640 CCCGTACCTGCATATCCCTC 59.391 60.000 0.00 0.00 0.00 4.30
1561 1974 0.466543 ACACTACGTTGCCCAGACAA 59.533 50.000 0.00 0.00 0.00 3.18
1567 1980 1.271656 ACTACAGACACTACGTTGCCC 59.728 52.381 0.00 0.00 0.00 5.36
1620 2033 6.960468 GGCTGCACCTAAAGAAATACTAATC 58.040 40.000 0.50 0.00 34.51 1.75
1621 2034 6.944234 GGCTGCACCTAAAGAAATACTAAT 57.056 37.500 0.50 0.00 34.51 1.73
1733 2146 4.202461 ACCAATTTGTTAGTCTCAGGCTCA 60.202 41.667 0.00 0.00 0.00 4.26
1769 2182 6.486320 TCTCAATGACAAAGCACACAAGAATA 59.514 34.615 0.00 0.00 0.00 1.75
1793 2206 0.527817 GCAGCAAGCCAATCATGCTC 60.528 55.000 0.00 0.00 45.62 4.26
1795 2208 4.104143 GCAGCAAGCCAATCATGC 57.896 55.556 0.00 0.00 39.53 4.06
1813 2226 3.491447 GGTGCAAGGCTAGCCAAATATTG 60.491 47.826 34.70 27.65 38.92 1.90
1814 2227 2.695147 GGTGCAAGGCTAGCCAAATATT 59.305 45.455 34.70 17.52 38.92 1.28
1815 2228 2.310538 GGTGCAAGGCTAGCCAAATAT 58.689 47.619 34.70 11.89 38.92 1.28
1817 2230 1.315257 CGGTGCAAGGCTAGCCAAAT 61.315 55.000 34.70 18.01 38.92 2.32
1819 2232 2.359850 CGGTGCAAGGCTAGCCAA 60.360 61.111 34.70 14.92 38.92 4.52
1822 2235 3.188786 CGACGGTGCAAGGCTAGC 61.189 66.667 6.04 6.04 0.00 3.42
1823 2236 2.509336 CCGACGGTGCAAGGCTAG 60.509 66.667 5.48 0.00 0.00 3.42
1824 2237 4.752879 GCCGACGGTGCAAGGCTA 62.753 66.667 16.73 0.00 45.67 3.93
1860 3050 3.639094 CCACCAGGAAATAGAGACGAGAT 59.361 47.826 0.00 0.00 36.89 2.75
1892 3082 1.825474 AGGTAATGGGAGACGTGACTG 59.175 52.381 0.00 0.00 0.00 3.51
1942 3132 2.752903 ACCAAATCCGCATAGAACAACC 59.247 45.455 0.00 0.00 0.00 3.77
1962 3152 3.303229 GCGTGCAAAGCATATAAACCAAC 59.697 43.478 10.18 0.00 42.41 3.77
1984 3174 7.594758 ACATTTGGAAGAACAACAAATACATCG 59.405 33.333 0.00 0.00 41.41 3.84
2101 3291 2.158505 CCCAGAAGATGAGGCATCCATT 60.159 50.000 0.00 0.00 41.36 3.16
2102 3292 1.424302 CCCAGAAGATGAGGCATCCAT 59.576 52.381 0.00 0.00 41.36 3.41
2142 3332 3.254024 AAGACTCGGCCGTGGCAAT 62.254 57.895 32.79 19.37 44.11 3.56
2215 3405 0.898326 TCTGAGCGGGCTAGAACACA 60.898 55.000 0.00 0.00 0.00 3.72
2246 3436 1.284657 GTCATCACAGCCACATCTCG 58.715 55.000 0.00 0.00 0.00 4.04
2262 3452 1.301423 GCTGGTAACCAACAACGTCA 58.699 50.000 0.00 0.00 30.80 4.35
2268 3458 1.028905 GTTGCTGCTGGTAACCAACA 58.971 50.000 0.00 0.00 36.64 3.33
2287 3477 0.249073 GACCCTCGACATGATGTCCG 60.249 60.000 19.01 13.95 44.20 4.79
2289 3479 1.478510 ACTGACCCTCGACATGATGTC 59.521 52.381 15.36 15.36 43.65 3.06
2308 3498 1.599576 GAGAACAGCCCAGGGAGAC 59.400 63.158 10.89 0.00 0.00 3.36
2459 3649 5.865085 AGCTACCAGATAAAACAGTGAACA 58.135 37.500 0.00 0.00 0.00 3.18
2460 3650 5.351740 GGAGCTACCAGATAAAACAGTGAAC 59.648 44.000 0.00 0.00 38.79 3.18
2506 3696 6.640499 CGATCATCTGGAATACTTCTCTGAAC 59.360 42.308 0.00 0.00 0.00 3.18
2670 3866 5.308825 AGCTGAAGAAATCTCTCGGAAAAA 58.691 37.500 0.00 0.00 0.00 1.94
2694 3890 3.423539 TGACCACTTTATGCTTGCTCT 57.576 42.857 0.00 0.00 0.00 4.09
2700 3896 5.263599 TGATTCCATTGACCACTTTATGCT 58.736 37.500 0.00 0.00 0.00 3.79
2708 3904 5.884792 AGAAGAGAATGATTCCATTGACCAC 59.115 40.000 0.75 0.00 42.66 4.16
2733 3934 5.047847 ACCGAACGATACATTGGTTATCAG 58.952 41.667 0.00 0.00 0.00 2.90
2734 3935 5.013568 ACCGAACGATACATTGGTTATCA 57.986 39.130 0.00 0.00 0.00 2.15
2758 3959 8.391106 GTGATGTACCAAGACACATAATTCTTC 58.609 37.037 0.00 0.00 35.55 2.87
2776 3978 7.961325 AAATTTTGGTCAAATGGTGATGTAC 57.039 32.000 0.00 0.00 38.90 2.90


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

AutoCloner maintained by Alex Coulton.