Multiple sequence alignment - TraesCS2D01G350600

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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 TraesCS2D01G350600 chr2D 100.000 5997 0 0 1 5997 448526308 448520312 0.000000e+00 11075.0
1 TraesCS2D01G350600 chr2D 90.253 513 36 7 5477 5983 71440492 71440996 0.000000e+00 658.0
2 TraesCS2D01G350600 chr2D 87.617 533 45 8 5475 5997 50493831 50494352 3.090000e-167 599.0
3 TraesCS2D01G350600 chr2B 94.342 2881 109 20 712 3551 529693367 529696234 0.000000e+00 4368.0
4 TraesCS2D01G350600 chr2B 92.313 1522 81 15 3975 5478 529696681 529698184 0.000000e+00 2130.0
5 TraesCS2D01G350600 chr2B 90.734 518 36 4 5477 5990 547943712 547944221 0.000000e+00 680.0
6 TraesCS2D01G350600 chr2B 95.225 356 12 2 3592 3943 529696233 529696587 5.250000e-155 558.0
7 TraesCS2D01G350600 chr2A 92.272 1941 82 18 724 2637 594112921 594114820 0.000000e+00 2691.0
8 TraesCS2D01G350600 chr2A 96.006 1252 34 6 2696 3943 594115117 594116356 0.000000e+00 2021.0
9 TraesCS2D01G350600 chr2A 90.507 1538 65 23 3975 5476 594116451 594117943 0.000000e+00 1956.0
10 TraesCS2D01G350600 chr2A 88.040 694 73 10 23 712 7917170 7916483 0.000000e+00 813.0
11 TraesCS2D01G350600 chr7D 89.870 691 65 5 23 710 182612231 182612919 0.000000e+00 883.0
12 TraesCS2D01G350600 chr7D 88.484 686 74 5 26 709 99419037 99419719 0.000000e+00 824.0
13 TraesCS2D01G350600 chr7D 90.207 531 36 6 5475 5997 607550281 607549759 0.000000e+00 678.0
14 TraesCS2D01G350600 chr4A 88.133 691 75 6 23 710 609126107 609125421 0.000000e+00 815.0
15 TraesCS2D01G350600 chr3D 87.936 688 75 8 26 710 26442273 26441591 0.000000e+00 804.0
16 TraesCS2D01G350600 chr3D 87.590 693 70 12 23 710 13188755 13189436 0.000000e+00 789.0
17 TraesCS2D01G350600 chr3D 92.410 527 30 3 5470 5995 429313714 429313197 0.000000e+00 743.0
18 TraesCS2D01G350600 chr3D 86.187 695 82 11 23 710 47217140 47217827 0.000000e+00 739.0
19 TraesCS2D01G350600 chr3D 85.962 691 87 8 23 710 547930749 547930066 0.000000e+00 730.0
20 TraesCS2D01G350600 chr4D 87.013 693 82 8 23 710 315022493 315023182 0.000000e+00 774.0
21 TraesCS2D01G350600 chr4D 92.131 521 27 6 5479 5997 35486609 35487117 0.000000e+00 723.0
22 TraesCS2D01G350600 chr4D 91.445 526 34 5 5475 5997 23274152 23273635 0.000000e+00 712.0
23 TraesCS2D01G350600 chr4D 89.564 527 41 5 5475 5997 41719788 41720304 0.000000e+00 656.0
24 TraesCS2D01G350600 chr4D 89.098 532 38 6 5477 5997 476862153 476862675 1.410000e-180 643.0
25 TraesCS2D01G350600 chr4D 87.958 382 26 6 5628 5997 479012857 479013230 3.320000e-117 433.0
26 TraesCS2D01G350600 chr5D 91.794 524 31 5 5477 5997 430529772 430530286 0.000000e+00 719.0
27 TraesCS2D01G350600 chr1A 90.996 522 35 4 5477 5997 534310775 534311285 0.000000e+00 693.0
28 TraesCS2D01G350600 chr1D 89.583 528 41 5 5475 5997 257428852 257428334 0.000000e+00 658.0
29 TraesCS2D01G350600 chr1D 88.340 506 34 11 5494 5997 281370350 281370832 8.660000e-163 584.0
30 TraesCS2D01G350600 chrUn 87.218 532 40 10 5477 5997 359551137 359551651 1.120000e-161 580.0
31 TraesCS2D01G350600 chrUn 88.506 348 24 4 5658 5997 393406070 393406409 2.010000e-109 407.0
32 TraesCS2D01G350600 chr5A 85.448 536 50 17 5474 5997 610242287 610242806 3.180000e-147 532.0
33 TraesCS2D01G350600 chr3B 94.207 328 19 0 4603 4930 409599416 409599743 8.970000e-138 501.0
34 TraesCS2D01G350600 chr6B 83.213 417 51 16 4592 5002 440556063 440555660 1.230000e-96 364.0
35 TraesCS2D01G350600 chr6B 85.789 190 27 0 2982 3171 440556880 440556691 1.020000e-47 202.0
36 TraesCS2D01G350600 chr6B 94.118 68 3 1 3877 3943 141106408 141106475 1.060000e-17 102.0
37 TraesCS2D01G350600 chr6A 83.213 417 51 16 4592 5002 401886485 401886082 1.230000e-96 364.0
38 TraesCS2D01G350600 chr6A 87.368 190 24 0 2982 3171 401887441 401887252 1.010000e-52 219.0
39 TraesCS2D01G350600 chr6D 83.130 409 54 12 4592 4997 280905697 280906093 5.710000e-95 359.0
40 TraesCS2D01G350600 chr6D 94.118 68 3 1 3877 3943 65994322 65994389 1.060000e-17 102.0
41 TraesCS2D01G350600 chr7A 94.366 71 3 1 3877 3946 510625401 510625331 2.290000e-19 108.0
42 TraesCS2D01G350600 chr7B 91.549 71 5 1 3877 3946 419041473 419041403 4.950000e-16 97.1
43 TraesCS2D01G350600 chr4B 94.444 36 1 1 3910 3944 650885460 650885495 3.000000e-03 54.7
44 TraesCS2D01G350600 chr3A 94.444 36 1 1 3910 3944 692954367 692954402 3.000000e-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 TraesCS2D01G350600 chr2D 448520312 448526308 5996 True 11075.000000 11075 100.000000 1 5997 1 chr2D.!!$R1 5996
1 TraesCS2D01G350600 chr2D 71440492 71440996 504 False 658.000000 658 90.253000 5477 5983 1 chr2D.!!$F2 506
2 TraesCS2D01G350600 chr2D 50493831 50494352 521 False 599.000000 599 87.617000 5475 5997 1 chr2D.!!$F1 522
3 TraesCS2D01G350600 chr2B 529693367 529698184 4817 False 2352.000000 4368 93.960000 712 5478 3 chr2B.!!$F2 4766
4 TraesCS2D01G350600 chr2B 547943712 547944221 509 False 680.000000 680 90.734000 5477 5990 1 chr2B.!!$F1 513
5 TraesCS2D01G350600 chr2A 594112921 594117943 5022 False 2222.666667 2691 92.928333 724 5476 3 chr2A.!!$F1 4752
6 TraesCS2D01G350600 chr2A 7916483 7917170 687 True 813.000000 813 88.040000 23 712 1 chr2A.!!$R1 689
7 TraesCS2D01G350600 chr7D 182612231 182612919 688 False 883.000000 883 89.870000 23 710 1 chr7D.!!$F2 687
8 TraesCS2D01G350600 chr7D 99419037 99419719 682 False 824.000000 824 88.484000 26 709 1 chr7D.!!$F1 683
9 TraesCS2D01G350600 chr7D 607549759 607550281 522 True 678.000000 678 90.207000 5475 5997 1 chr7D.!!$R1 522
10 TraesCS2D01G350600 chr4A 609125421 609126107 686 True 815.000000 815 88.133000 23 710 1 chr4A.!!$R1 687
11 TraesCS2D01G350600 chr3D 26441591 26442273 682 True 804.000000 804 87.936000 26 710 1 chr3D.!!$R1 684
12 TraesCS2D01G350600 chr3D 13188755 13189436 681 False 789.000000 789 87.590000 23 710 1 chr3D.!!$F1 687
13 TraesCS2D01G350600 chr3D 429313197 429313714 517 True 743.000000 743 92.410000 5470 5995 1 chr3D.!!$R2 525
14 TraesCS2D01G350600 chr3D 47217140 47217827 687 False 739.000000 739 86.187000 23 710 1 chr3D.!!$F2 687
15 TraesCS2D01G350600 chr3D 547930066 547930749 683 True 730.000000 730 85.962000 23 710 1 chr3D.!!$R3 687
16 TraesCS2D01G350600 chr4D 315022493 315023182 689 False 774.000000 774 87.013000 23 710 1 chr4D.!!$F3 687
17 TraesCS2D01G350600 chr4D 35486609 35487117 508 False 723.000000 723 92.131000 5479 5997 1 chr4D.!!$F1 518
18 TraesCS2D01G350600 chr4D 23273635 23274152 517 True 712.000000 712 91.445000 5475 5997 1 chr4D.!!$R1 522
19 TraesCS2D01G350600 chr4D 41719788 41720304 516 False 656.000000 656 89.564000 5475 5997 1 chr4D.!!$F2 522
20 TraesCS2D01G350600 chr4D 476862153 476862675 522 False 643.000000 643 89.098000 5477 5997 1 chr4D.!!$F4 520
21 TraesCS2D01G350600 chr5D 430529772 430530286 514 False 719.000000 719 91.794000 5477 5997 1 chr5D.!!$F1 520
22 TraesCS2D01G350600 chr1A 534310775 534311285 510 False 693.000000 693 90.996000 5477 5997 1 chr1A.!!$F1 520
23 TraesCS2D01G350600 chr1D 257428334 257428852 518 True 658.000000 658 89.583000 5475 5997 1 chr1D.!!$R1 522
24 TraesCS2D01G350600 chrUn 359551137 359551651 514 False 580.000000 580 87.218000 5477 5997 1 chrUn.!!$F1 520
25 TraesCS2D01G350600 chr5A 610242287 610242806 519 False 532.000000 532 85.448000 5474 5997 1 chr5A.!!$F1 523
26 TraesCS2D01G350600 chr6B 440555660 440556880 1220 True 283.000000 364 84.501000 2982 5002 2 chr6B.!!$R1 2020
27 TraesCS2D01G350600 chr6A 401886082 401887441 1359 True 291.500000 364 85.290500 2982 5002 2 chr6A.!!$R1 2020

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
719 732 0.108233 GAGTTGCTCTCAGAGGGCAG 60.108 60.000 24.28 2.61 42.34 4.85 F
1042 1076 0.179067 TCCCACGCGGTAATCAATCC 60.179 55.000 12.47 0.00 0.00 3.01 F
2514 2567 0.388649 AGCACACGCGTCTTCCTTAG 60.389 55.000 9.86 0.00 45.49 2.18 F
2806 3131 0.900647 ACTTGAGACCCGGAGAGTGG 60.901 60.000 0.73 0.00 0.00 4.00 F
4564 5477 1.002684 AGCGATCGACCGTATCTTGAC 60.003 52.381 21.57 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2061 0.320683 TGAGTGGTGCGGTTCATCAG 60.321 55.000 0.00 0.00 36.27 2.90 R
2788 3113 0.612174 TCCACTCTCCGGGTCTCAAG 60.612 60.000 0.00 0.00 0.00 3.02 R
3816 4620 1.151413 TCCTATGTACCCAGATCCCCC 59.849 57.143 0.00 0.00 0.00 5.40 R
4763 5676 2.447070 CGCGGGTGTAGGCGTTTAC 61.447 63.158 0.00 0.00 46.79 2.01 R
5934 6900 0.247736 CCCTTCCTCTTGGTCGACTG 59.752 60.000 16.46 6.47 34.23 3.51 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
48 49 4.101448 GTCGGGCAGCACCATCCT 62.101 66.667 0.00 0.00 42.05 3.24
49 50 3.785859 TCGGGCAGCACCATCCTC 61.786 66.667 0.00 0.00 42.05 3.71
150 151 4.070552 GAGCGCCTCCCTCGTTGT 62.071 66.667 2.29 0.00 0.00 3.32
266 267 1.627297 GGTCCTTCCTCTTGGCCGAT 61.627 60.000 0.00 0.00 0.00 4.18
308 309 1.211190 CAGCGGCTTCTTTGGCTTC 59.789 57.895 0.00 0.00 32.46 3.86
355 356 3.569200 GAGGCTTGCCTTTCCCGGT 62.569 63.158 15.92 0.00 0.00 5.28
476 484 2.684943 GGGAGGGTTTTTGAGGGAAAA 58.315 47.619 0.00 0.00 0.00 2.29
477 485 3.248024 GGGAGGGTTTTTGAGGGAAAAT 58.752 45.455 0.00 0.00 33.46 1.82
479 487 3.007940 GGAGGGTTTTTGAGGGAAAATGG 59.992 47.826 0.00 0.00 33.46 3.16
617 630 2.593436 CCAAGCGGACGGGTGTTT 60.593 61.111 0.00 0.00 0.00 2.83
618 631 2.190841 CCAAGCGGACGGGTGTTTT 61.191 57.895 0.00 0.00 0.00 2.43
619 632 1.730451 CCAAGCGGACGGGTGTTTTT 61.730 55.000 0.00 0.00 0.00 1.94
635 648 3.855630 TTTTTGGGTCGACGCATTG 57.144 47.368 32.33 0.00 38.62 2.82
636 649 0.312416 TTTTTGGGTCGACGCATTGG 59.688 50.000 32.33 0.00 38.62 3.16
637 650 1.519751 TTTTGGGTCGACGCATTGGG 61.520 55.000 32.33 0.00 38.62 4.12
644 657 2.746277 GACGCATTGGGCCGACTT 60.746 61.111 0.00 0.00 40.31 3.01
645 658 2.282180 ACGCATTGGGCCGACTTT 60.282 55.556 0.00 0.00 40.31 2.66
646 659 1.862602 GACGCATTGGGCCGACTTTT 61.863 55.000 0.00 0.00 40.31 2.27
647 660 1.444212 CGCATTGGGCCGACTTTTG 60.444 57.895 0.00 0.00 40.31 2.44
648 661 1.665442 GCATTGGGCCGACTTTTGT 59.335 52.632 0.00 0.00 36.11 2.83
649 662 0.667184 GCATTGGGCCGACTTTTGTG 60.667 55.000 0.00 0.00 36.11 3.33
650 663 0.673437 CATTGGGCCGACTTTTGTGT 59.327 50.000 0.00 0.00 0.00 3.72
651 664 0.958822 ATTGGGCCGACTTTTGTGTC 59.041 50.000 0.00 0.00 0.00 3.67
652 665 1.104577 TTGGGCCGACTTTTGTGTCC 61.105 55.000 0.00 0.00 33.70 4.02
653 666 2.613506 GGGCCGACTTTTGTGTCCG 61.614 63.158 0.00 0.00 33.70 4.79
654 667 2.251371 GCCGACTTTTGTGTCCGC 59.749 61.111 0.00 0.00 35.04 5.54
655 668 2.549282 CCGACTTTTGTGTCCGCG 59.451 61.111 0.00 0.00 33.70 6.46
656 669 2.127758 CGACTTTTGTGTCCGCGC 60.128 61.111 0.00 0.00 33.70 6.86
657 670 2.251371 GACTTTTGTGTCCGCGCC 59.749 61.111 0.00 0.00 0.00 6.53
658 671 3.573489 GACTTTTGTGTCCGCGCCG 62.573 63.158 0.00 0.00 0.00 6.46
659 672 3.342627 CTTTTGTGTCCGCGCCGA 61.343 61.111 0.00 0.00 0.00 5.54
660 673 2.666862 TTTTGTGTCCGCGCCGAT 60.667 55.556 0.00 0.00 0.00 4.18
661 674 2.182614 CTTTTGTGTCCGCGCCGATT 62.183 55.000 0.00 0.00 0.00 3.34
662 675 2.177654 TTTTGTGTCCGCGCCGATTC 62.178 55.000 0.00 0.00 0.00 2.52
663 676 3.867700 TTGTGTCCGCGCCGATTCA 62.868 57.895 0.00 1.78 0.00 2.57
664 677 3.115892 GTGTCCGCGCCGATTCAA 61.116 61.111 0.00 0.00 0.00 2.69
665 678 2.357638 TGTCCGCGCCGATTCAAA 60.358 55.556 0.00 0.00 0.00 2.69
666 679 2.097728 GTCCGCGCCGATTCAAAC 59.902 61.111 0.00 0.00 0.00 2.93
667 680 3.483665 TCCGCGCCGATTCAAACG 61.484 61.111 0.00 0.00 0.00 3.60
674 687 3.556625 CGATTCAAACGGACGGCA 58.443 55.556 0.00 0.00 0.00 5.69
675 688 1.419922 CGATTCAAACGGACGGCAG 59.580 57.895 0.00 0.00 0.00 4.85
676 689 1.134694 GATTCAAACGGACGGCAGC 59.865 57.895 0.00 0.00 0.00 5.25
677 690 2.563086 GATTCAAACGGACGGCAGCG 62.563 60.000 0.00 0.00 0.00 5.18
678 691 3.793775 TTCAAACGGACGGCAGCGA 62.794 57.895 0.00 0.00 0.00 4.93
679 692 3.342627 CAAACGGACGGCAGCGAA 61.343 61.111 0.00 0.00 0.00 4.70
680 693 3.343421 AAACGGACGGCAGCGAAC 61.343 61.111 0.00 0.00 0.00 3.95
684 697 3.039588 GGACGGCAGCGAACGAAA 61.040 61.111 0.00 0.00 0.00 3.46
685 698 2.388232 GGACGGCAGCGAACGAAAT 61.388 57.895 0.00 0.00 0.00 2.17
686 699 1.225745 GACGGCAGCGAACGAAATG 60.226 57.895 0.00 0.00 0.00 2.32
687 700 2.098298 CGGCAGCGAACGAAATGG 59.902 61.111 0.00 0.00 0.00 3.16
688 701 2.485122 GGCAGCGAACGAAATGGG 59.515 61.111 0.00 0.00 0.00 4.00
689 702 2.332654 GGCAGCGAACGAAATGGGT 61.333 57.895 0.00 0.00 0.00 4.51
690 703 1.134694 GCAGCGAACGAAATGGGTC 59.865 57.895 0.00 0.00 0.00 4.46
691 704 1.419922 CAGCGAACGAAATGGGTCG 59.580 57.895 0.00 0.00 46.54 4.79
692 705 2.097728 GCGAACGAAATGGGTCGC 59.902 61.111 11.88 11.88 45.00 5.19
693 706 2.388232 GCGAACGAAATGGGTCGCT 61.388 57.895 18.59 0.00 45.00 4.93
694 707 1.708027 CGAACGAAATGGGTCGCTC 59.292 57.895 0.00 0.00 45.00 5.03
695 708 1.693083 CGAACGAAATGGGTCGCTCC 61.693 60.000 0.00 0.00 45.00 4.70
696 709 0.672401 GAACGAAATGGGTCGCTCCA 60.672 55.000 0.00 0.00 45.00 3.86
703 716 1.794714 ATGGGTCGCTCCATTAGAGT 58.205 50.000 3.91 0.00 44.55 3.24
704 717 1.568504 TGGGTCGCTCCATTAGAGTT 58.431 50.000 0.00 0.00 45.21 3.01
705 718 1.207089 TGGGTCGCTCCATTAGAGTTG 59.793 52.381 0.00 0.00 45.21 3.16
706 719 1.291132 GGTCGCTCCATTAGAGTTGC 58.709 55.000 0.00 0.00 45.21 4.17
707 720 1.134670 GGTCGCTCCATTAGAGTTGCT 60.135 52.381 0.00 0.00 45.21 3.91
708 721 2.197577 GTCGCTCCATTAGAGTTGCTC 58.802 52.381 0.00 0.00 45.21 4.26
709 722 2.103373 TCGCTCCATTAGAGTTGCTCT 58.897 47.619 4.02 4.02 45.21 4.09
710 723 2.099921 TCGCTCCATTAGAGTTGCTCTC 59.900 50.000 1.54 2.14 45.21 3.20
711 724 2.159184 CGCTCCATTAGAGTTGCTCTCA 60.159 50.000 1.54 0.00 45.21 3.27
712 725 3.456280 GCTCCATTAGAGTTGCTCTCAG 58.544 50.000 1.54 0.00 45.21 3.35
713 726 3.131933 GCTCCATTAGAGTTGCTCTCAGA 59.868 47.826 1.54 0.00 45.21 3.27
714 727 4.737352 GCTCCATTAGAGTTGCTCTCAGAG 60.737 50.000 0.00 0.00 45.21 3.35
715 728 3.703556 TCCATTAGAGTTGCTCTCAGAGG 59.296 47.826 3.18 2.14 44.98 3.69
716 729 3.181467 CCATTAGAGTTGCTCTCAGAGGG 60.181 52.174 3.18 0.00 44.98 4.30
717 730 1.479709 TAGAGTTGCTCTCAGAGGGC 58.520 55.000 16.23 16.23 44.98 5.19
718 731 0.543883 AGAGTTGCTCTCAGAGGGCA 60.544 55.000 21.95 21.95 44.98 5.36
719 732 0.108233 GAGTTGCTCTCAGAGGGCAG 60.108 60.000 24.28 2.61 42.34 4.85
1042 1076 0.179067 TCCCACGCGGTAATCAATCC 60.179 55.000 12.47 0.00 0.00 3.01
1622 1662 0.580578 CTCTCGCTTTGCATCGGATG 59.419 55.000 13.63 13.63 0.00 3.51
1729 1769 3.728600 CGTCGACCAACGGAATAAAAAG 58.271 45.455 10.58 0.00 42.82 2.27
1756 1796 0.795085 CACTCTCAGAAAAGCCGCAG 59.205 55.000 0.00 0.00 0.00 5.18
1844 1884 1.595357 GTTCCCCGTTCGTCATCCT 59.405 57.895 0.00 0.00 0.00 3.24
1961 2001 1.335145 ACAGTACGCACCTACACCTT 58.665 50.000 0.00 0.00 0.00 3.50
1962 2002 2.517959 ACAGTACGCACCTACACCTTA 58.482 47.619 0.00 0.00 0.00 2.69
2068 2118 1.270094 CCAAGTGTGCCTCGTTGACTA 60.270 52.381 0.00 0.00 0.00 2.59
2109 2159 4.159693 TGTGCATCATCTACCGAGTTTACT 59.840 41.667 0.00 0.00 0.00 2.24
2118 2168 3.938289 ACCGAGTTTACTGGAGTTCTC 57.062 47.619 5.69 0.00 0.00 2.87
2176 2228 8.873830 AGATTCTAGTATCGTGTCAATTTTGTG 58.126 33.333 3.94 0.00 0.00 3.33
2235 2287 7.283127 TCAGACATTTCTAGTTTCAACTGCTTT 59.717 33.333 2.26 0.00 40.07 3.51
2282 2334 7.020914 TGAAAATTTACAAAAACACATGGGC 57.979 32.000 0.00 0.00 0.00 5.36
2325 2378 1.537202 GCAAACGGATGCTTTCTGAGT 59.463 47.619 7.37 0.00 43.06 3.41
2514 2567 0.388649 AGCACACGCGTCTTCCTTAG 60.389 55.000 9.86 0.00 45.49 2.18
2519 2572 1.459592 CACGCGTCTTCCTTAGTTTGG 59.540 52.381 9.86 0.00 0.00 3.28
2580 2639 5.833082 TCATATAGGAGAAGAAACGAGCAC 58.167 41.667 0.00 0.00 0.00 4.40
2585 2644 2.288518 GGAGAAGAAACGAGCACACTCT 60.289 50.000 0.00 0.00 41.09 3.24
2613 2672 1.080638 ATGGTGGCCCCTAACAGAAA 58.919 50.000 0.00 0.00 0.00 2.52
2620 2681 3.850173 TGGCCCCTAACAGAAAGTATTCT 59.150 43.478 0.00 0.00 46.91 2.40
2653 2805 2.758979 ACATAGTTCACTACCCCACTCG 59.241 50.000 0.00 0.00 0.00 4.18
2788 3113 6.955963 CGAAAGCATACTTTGATAGTTGTGAC 59.044 38.462 0.00 0.00 46.20 3.67
2795 3120 8.651588 CATACTTTGATAGTTGTGACTTGAGAC 58.348 37.037 0.00 0.00 38.33 3.36
2806 3131 0.900647 ACTTGAGACCCGGAGAGTGG 60.901 60.000 0.73 0.00 0.00 4.00
2973 3302 8.579850 AATTAATGAAGTTGCATTCCTGTCTA 57.420 30.769 0.00 0.00 39.15 2.59
3190 3519 2.056577 GTGCAAGCATGTTCTTTCAGC 58.943 47.619 0.00 0.00 0.00 4.26
3214 3543 6.238593 GCTCAGATGGATGGTATTTCAAAGTC 60.239 42.308 0.00 0.00 0.00 3.01
3436 4200 7.391275 CCAAATTAAGCCACTCCATTTGAAATT 59.609 33.333 10.71 0.00 37.11 1.82
3551 4355 9.454859 CTTCTGTTTAAAGATTCTCCAACCTAT 57.545 33.333 0.00 0.00 0.00 2.57
3562 4366 9.482175 AGATTCTCCAACCTATATCTGTATACC 57.518 37.037 0.00 0.00 0.00 2.73
3563 4367 9.256228 GATTCTCCAACCTATATCTGTATACCA 57.744 37.037 0.00 0.00 0.00 3.25
3564 4368 9.790297 ATTCTCCAACCTATATCTGTATACCAT 57.210 33.333 0.00 0.00 0.00 3.55
3565 4369 9.615660 TTCTCCAACCTATATCTGTATACCATT 57.384 33.333 0.00 0.00 0.00 3.16
3566 4370 9.256228 TCTCCAACCTATATCTGTATACCATTC 57.744 37.037 0.00 0.00 0.00 2.67
3567 4371 8.966155 TCCAACCTATATCTGTATACCATTCA 57.034 34.615 0.00 0.00 0.00 2.57
3568 4372 9.387397 TCCAACCTATATCTGTATACCATTCAA 57.613 33.333 0.00 0.00 0.00 2.69
3579 4383 9.642343 TCTGTATACCATTCAATAGTACAGAGT 57.358 33.333 7.91 0.00 40.66 3.24
3782 4586 5.890110 AGTCTATAAAACGATCATGCACG 57.110 39.130 9.17 9.17 0.00 5.34
3816 4620 2.091166 TGGATGAATGGGAGGGGATTTG 60.091 50.000 0.00 0.00 0.00 2.32
3817 4621 2.601905 GATGAATGGGAGGGGATTTGG 58.398 52.381 0.00 0.00 0.00 3.28
3832 4636 1.994399 TTTGGGGGATCTGGGTACAT 58.006 50.000 0.00 0.00 0.00 2.29
3910 4717 8.851416 CAAAATAACTGTCTCAACTCTAGTACG 58.149 37.037 0.00 0.00 0.00 3.67
3947 4754 7.730364 AGTTAGTACAAAGTGAGACATTTGG 57.270 36.000 0.00 0.00 40.05 3.28
3948 4755 6.204882 AGTTAGTACAAAGTGAGACATTTGGC 59.795 38.462 0.00 0.00 40.05 4.52
3950 4757 5.865085 AGTACAAAGTGAGACATTTGGCTA 58.135 37.500 0.00 0.00 40.05 3.93
3953 4760 4.022849 ACAAAGTGAGACATTTGGCTAAGC 60.023 41.667 3.08 0.00 40.05 3.09
3954 4761 3.710209 AGTGAGACATTTGGCTAAGCT 57.290 42.857 0.00 0.00 30.09 3.74
3955 4762 4.026356 AGTGAGACATTTGGCTAAGCTT 57.974 40.909 3.48 3.48 30.09 3.74
3956 4763 4.401925 AGTGAGACATTTGGCTAAGCTTT 58.598 39.130 3.20 0.00 30.09 3.51
3957 4764 5.560724 AGTGAGACATTTGGCTAAGCTTTA 58.439 37.500 3.20 0.00 30.09 1.85
3958 4765 5.645497 AGTGAGACATTTGGCTAAGCTTTAG 59.355 40.000 3.20 1.27 30.09 1.85
3959 4766 5.643777 GTGAGACATTTGGCTAAGCTTTAGA 59.356 40.000 3.20 0.00 30.09 2.10
3960 4767 6.149474 GTGAGACATTTGGCTAAGCTTTAGAA 59.851 38.462 3.20 0.00 30.09 2.10
3961 4768 6.714810 TGAGACATTTGGCTAAGCTTTAGAAA 59.285 34.615 3.20 0.00 30.09 2.52
3962 4769 7.094634 TGAGACATTTGGCTAAGCTTTAGAAAG 60.095 37.037 3.20 0.00 34.36 2.62
4065 4961 6.669154 AGTCCATCACCATTCCAATATTTTGT 59.331 34.615 0.00 0.00 0.00 2.83
4132 5028 4.346709 TGTGTCAGAGGAACCACAATAGAA 59.653 41.667 0.00 0.00 35.07 2.10
4250 5147 1.173043 TGAAACATGGCGGGAACATC 58.827 50.000 0.00 0.00 0.00 3.06
4251 5148 1.271871 TGAAACATGGCGGGAACATCT 60.272 47.619 0.00 0.00 0.00 2.90
4261 5158 1.760613 CGGGAACATCTACAAGGGCTA 59.239 52.381 0.00 0.00 0.00 3.93
4278 5175 1.409427 GCTAGTCTGCCCAACGACTAT 59.591 52.381 0.00 0.00 40.72 2.12
4498 5396 1.676529 TCATAGAGGTAGAGTGTGCGC 59.323 52.381 0.00 0.00 0.00 6.09
4564 5477 1.002684 AGCGATCGACCGTATCTTGAC 60.003 52.381 21.57 0.00 0.00 3.18
4765 5678 2.978824 GTCTCCAAGCTGGCGGTA 59.021 61.111 0.00 0.00 37.47 4.02
5009 5922 0.102120 GCTGTGAGAGACGGAGGATG 59.898 60.000 0.00 0.00 31.77 3.51
5034 5947 2.288729 CGTATCCGATGGTGTTCGTCTA 59.711 50.000 0.00 0.00 37.42 2.59
5071 5984 2.749621 GTCGATGGTTGCTGGAATTCTT 59.250 45.455 5.23 0.00 0.00 2.52
5075 5988 0.968405 GGTTGCTGGAATTCTTGGCA 59.032 50.000 5.23 10.33 0.00 4.92
5078 5991 1.243342 TGCTGGAATTCTTGGCACCG 61.243 55.000 5.23 0.00 0.00 4.94
5132 6045 5.057819 TGTTTCAGTTTAGCCATCGTTGTA 58.942 37.500 0.00 0.00 0.00 2.41
5137 6050 4.868171 CAGTTTAGCCATCGTTGTAGCTAA 59.132 41.667 11.04 11.04 43.96 3.09
5138 6051 5.005779 CAGTTTAGCCATCGTTGTAGCTAAG 59.994 44.000 13.37 4.02 45.61 2.18
5142 6058 3.056107 AGCCATCGTTGTAGCTAAGTTGA 60.056 43.478 0.00 0.00 32.73 3.18
5147 6063 4.566004 TCGTTGTAGCTAAGTTGATGCTT 58.434 39.130 0.00 0.00 38.15 3.91
5231 6147 0.527565 AACACGGCATGGATTCAAGC 59.472 50.000 0.00 0.00 36.92 4.01
5233 6149 0.742505 CACGGCATGGATTCAAGCAT 59.257 50.000 3.20 0.00 39.15 3.79
5256 6180 1.550524 TCTCATTGCTTAGCCGTCACT 59.449 47.619 0.29 0.00 0.00 3.41
5269 6193 3.992260 CCGTCACTAAGATGGTAGAGG 57.008 52.381 0.00 0.00 46.53 3.69
5270 6194 2.623889 CCGTCACTAAGATGGTAGAGGG 59.376 54.545 0.00 0.00 46.53 4.30
5291 6215 4.624364 TGTGAGCCCGTGCAGTGG 62.624 66.667 0.00 0.00 41.13 4.00
5319 6251 1.747355 CGGGAAATCAAGCAGAAGCAT 59.253 47.619 0.00 0.00 45.49 3.79
5320 6252 2.945008 CGGGAAATCAAGCAGAAGCATA 59.055 45.455 0.00 0.00 45.49 3.14
5349 6283 1.671379 GTGGCAACGTCCCCTCTTC 60.671 63.158 6.08 0.00 42.51 2.87
5379 6313 9.244292 AGATGGAGAATAATTTGGATGATCATG 57.756 33.333 14.30 0.00 0.00 3.07
5425 6361 2.332063 AAGTAGGGCATCATGTTCGG 57.668 50.000 0.00 0.00 0.00 4.30
5619 6556 2.043252 ACCCATTCCCGACCCAATTTTA 59.957 45.455 0.00 0.00 0.00 1.52
5637 6574 2.510064 TAAGCCGGATTTGCGTCGGT 62.510 55.000 11.69 0.00 44.97 4.69
5936 6902 4.785453 GGCAAGGGAGTCGGGCAG 62.785 72.222 0.00 0.00 0.00 4.85
5937 6903 4.021925 GCAAGGGAGTCGGGCAGT 62.022 66.667 0.00 0.00 0.00 4.40
5938 6904 2.266055 CAAGGGAGTCGGGCAGTC 59.734 66.667 0.00 0.00 0.00 3.51
5939 6905 3.382832 AAGGGAGTCGGGCAGTCG 61.383 66.667 0.00 0.00 0.00 4.18
5940 6906 3.881019 AAGGGAGTCGGGCAGTCGA 62.881 63.158 0.00 0.00 36.76 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 3.011517 ATGGCCTCCTCAACGCCT 61.012 61.111 3.32 0.00 43.42 5.52
103 104 0.614697 GGTTAAACCCTGGCCAGCAT 60.615 55.000 28.39 14.38 30.04 3.79
166 167 1.757306 CAGCAGGAGGTCACCAACT 59.243 57.895 0.00 0.00 0.00 3.16
266 267 2.909965 GCACAACGGGCAAGGGAA 60.910 61.111 0.00 0.00 0.00 3.97
571 584 2.510906 CGATCCATTCCCGGCCTT 59.489 61.111 0.00 0.00 0.00 4.35
617 630 0.312416 CCAATGCGTCGACCCAAAAA 59.688 50.000 10.58 0.00 0.00 1.94
618 631 1.519751 CCCAATGCGTCGACCCAAAA 61.520 55.000 10.58 0.00 0.00 2.44
619 632 1.969064 CCCAATGCGTCGACCCAAA 60.969 57.895 10.58 0.00 0.00 3.28
620 633 2.359354 CCCAATGCGTCGACCCAA 60.359 61.111 10.58 0.00 0.00 4.12
627 640 1.862602 AAAAGTCGGCCCAATGCGTC 61.863 55.000 0.00 0.00 42.61 5.19
628 641 1.901464 AAAAGTCGGCCCAATGCGT 60.901 52.632 0.00 0.00 42.61 5.24
629 642 1.444212 CAAAAGTCGGCCCAATGCG 60.444 57.895 0.00 0.00 42.61 4.73
630 643 0.667184 CACAAAAGTCGGCCCAATGC 60.667 55.000 0.00 0.00 40.16 3.56
631 644 0.673437 ACACAAAAGTCGGCCCAATG 59.327 50.000 0.00 0.00 0.00 2.82
632 645 0.958822 GACACAAAAGTCGGCCCAAT 59.041 50.000 0.00 0.00 0.00 3.16
633 646 1.104577 GGACACAAAAGTCGGCCCAA 61.105 55.000 0.00 0.00 39.42 4.12
634 647 1.527380 GGACACAAAAGTCGGCCCA 60.527 57.895 0.00 0.00 39.42 5.36
635 648 2.613506 CGGACACAAAAGTCGGCCC 61.614 63.158 0.00 0.00 39.42 5.80
636 649 2.943653 CGGACACAAAAGTCGGCC 59.056 61.111 0.00 0.00 39.42 6.13
638 651 2.549282 CGCGGACACAAAAGTCGG 59.451 61.111 0.00 0.00 39.42 4.79
639 652 2.127758 GCGCGGACACAAAAGTCG 60.128 61.111 8.83 0.00 39.42 4.18
640 653 2.251371 GGCGCGGACACAAAAGTC 59.749 61.111 8.83 0.00 37.80 3.01
641 654 3.645975 CGGCGCGGACACAAAAGT 61.646 61.111 9.72 0.00 0.00 2.66
642 655 2.182614 AATCGGCGCGGACACAAAAG 62.183 55.000 20.65 0.00 0.00 2.27
643 656 2.177654 GAATCGGCGCGGACACAAAA 62.178 55.000 20.65 0.00 0.00 2.44
644 657 2.666862 AATCGGCGCGGACACAAA 60.667 55.556 20.65 0.00 0.00 2.83
645 658 3.115892 GAATCGGCGCGGACACAA 61.116 61.111 20.65 0.00 0.00 3.33
646 659 3.867700 TTGAATCGGCGCGGACACA 62.868 57.895 20.65 18.58 0.00 3.72
647 660 2.673114 TTTGAATCGGCGCGGACAC 61.673 57.895 20.65 16.34 0.00 3.67
648 661 2.357638 TTTGAATCGGCGCGGACA 60.358 55.556 20.65 11.80 0.00 4.02
649 662 2.097728 GTTTGAATCGGCGCGGAC 59.902 61.111 20.65 9.15 0.00 4.79
650 663 3.483665 CGTTTGAATCGGCGCGGA 61.484 61.111 20.50 20.50 0.00 5.54
651 664 4.514569 CCGTTTGAATCGGCGCGG 62.515 66.667 8.83 8.94 41.48 6.46
652 665 3.483665 TCCGTTTGAATCGGCGCG 61.484 61.111 9.70 0.00 46.49 6.86
653 666 2.097728 GTCCGTTTGAATCGGCGC 59.902 61.111 9.70 0.00 46.49 6.53
654 667 2.394136 CGTCCGTTTGAATCGGCG 59.606 61.111 9.70 12.06 46.49 6.46
655 668 2.782615 CCGTCCGTTTGAATCGGC 59.217 61.111 9.70 4.78 46.49 5.54
657 670 1.419922 CTGCCGTCCGTTTGAATCG 59.580 57.895 0.00 0.00 0.00 3.34
658 671 1.134694 GCTGCCGTCCGTTTGAATC 59.865 57.895 0.00 0.00 0.00 2.52
659 672 2.677003 CGCTGCCGTCCGTTTGAAT 61.677 57.895 0.00 0.00 0.00 2.57
660 673 3.342627 CGCTGCCGTCCGTTTGAA 61.343 61.111 0.00 0.00 0.00 2.69
661 674 3.793775 TTCGCTGCCGTCCGTTTGA 62.794 57.895 0.00 0.00 35.54 2.69
662 675 3.342627 TTCGCTGCCGTCCGTTTG 61.343 61.111 0.00 0.00 35.54 2.93
663 676 3.343421 GTTCGCTGCCGTCCGTTT 61.343 61.111 0.00 0.00 35.54 3.60
667 680 2.388232 ATTTCGTTCGCTGCCGTCC 61.388 57.895 0.00 0.00 35.54 4.79
668 681 1.225745 CATTTCGTTCGCTGCCGTC 60.226 57.895 0.00 0.00 35.54 4.79
669 682 2.677003 CCATTTCGTTCGCTGCCGT 61.677 57.895 0.00 0.00 35.54 5.68
670 683 2.098298 CCATTTCGTTCGCTGCCG 59.902 61.111 0.00 0.00 0.00 5.69
671 684 2.253414 GACCCATTTCGTTCGCTGCC 62.253 60.000 0.00 0.00 0.00 4.85
672 685 1.134694 GACCCATTTCGTTCGCTGC 59.865 57.895 0.00 0.00 0.00 5.25
673 686 1.419922 CGACCCATTTCGTTCGCTG 59.580 57.895 0.00 0.00 34.16 5.18
674 687 2.388232 GCGACCCATTTCGTTCGCT 61.388 57.895 7.53 0.00 42.37 4.93
675 688 2.097728 GCGACCCATTTCGTTCGC 59.902 61.111 0.00 0.00 41.26 4.70
676 689 1.693083 GGAGCGACCCATTTCGTTCG 61.693 60.000 3.77 0.00 46.66 3.95
677 690 0.672401 TGGAGCGACCCATTTCGTTC 60.672 55.000 1.27 1.27 45.44 3.95
678 691 0.035439 ATGGAGCGACCCATTTCGTT 60.035 50.000 3.50 0.00 44.11 3.85
679 692 1.602237 ATGGAGCGACCCATTTCGT 59.398 52.632 3.50 0.00 44.11 3.85
680 693 4.540153 ATGGAGCGACCCATTTCG 57.460 55.556 3.50 0.00 44.11 3.46
685 698 1.207089 CAACTCTAATGGAGCGACCCA 59.793 52.381 0.00 0.00 45.48 4.51
686 699 1.941325 CAACTCTAATGGAGCGACCC 58.059 55.000 0.00 0.00 45.48 4.46
687 700 1.134670 AGCAACTCTAATGGAGCGACC 60.135 52.381 0.00 0.00 45.48 4.79
688 701 2.159170 AGAGCAACTCTAATGGAGCGAC 60.159 50.000 0.00 0.00 45.48 5.19
689 702 2.099921 GAGAGCAACTCTAATGGAGCGA 59.900 50.000 0.00 0.00 45.48 4.93
690 703 2.159184 TGAGAGCAACTCTAATGGAGCG 60.159 50.000 11.18 0.00 45.48 5.03
691 704 3.131933 TCTGAGAGCAACTCTAATGGAGC 59.868 47.826 11.18 0.00 45.48 4.70
692 705 4.202141 CCTCTGAGAGCAACTCTAATGGAG 60.202 50.000 6.17 0.00 41.35 3.86
693 706 3.703556 CCTCTGAGAGCAACTCTAATGGA 59.296 47.826 6.17 0.00 41.35 3.41
694 707 3.181467 CCCTCTGAGAGCAACTCTAATGG 60.181 52.174 6.17 0.00 41.35 3.16
695 708 3.740764 GCCCTCTGAGAGCAACTCTAATG 60.741 52.174 6.27 0.00 41.35 1.90
696 709 2.433970 GCCCTCTGAGAGCAACTCTAAT 59.566 50.000 6.27 0.00 41.35 1.73
697 710 1.827969 GCCCTCTGAGAGCAACTCTAA 59.172 52.381 6.27 0.00 41.35 2.10
698 711 1.272704 TGCCCTCTGAGAGCAACTCTA 60.273 52.381 11.69 0.00 41.35 2.43
699 712 0.543883 TGCCCTCTGAGAGCAACTCT 60.544 55.000 11.69 0.00 44.28 3.24
700 713 0.108233 CTGCCCTCTGAGAGCAACTC 60.108 60.000 14.88 4.35 45.11 3.01
701 714 1.551908 CCTGCCCTCTGAGAGCAACT 61.552 60.000 14.88 0.00 35.79 3.16
702 715 1.078567 CCTGCCCTCTGAGAGCAAC 60.079 63.158 14.88 0.00 35.79 4.17
703 716 2.296365 CCCTGCCCTCTGAGAGCAA 61.296 63.158 14.88 0.00 35.79 3.91
704 717 2.686470 CCCTGCCCTCTGAGAGCA 60.686 66.667 13.39 13.39 34.79 4.26
705 718 4.173924 GCCCTGCCCTCTGAGAGC 62.174 72.222 6.17 5.03 0.00 4.09
706 719 2.365370 AGCCCTGCCCTCTGAGAG 60.365 66.667 6.17 1.57 0.00 3.20
707 720 2.168272 TACAGCCCTGCCCTCTGAGA 62.168 60.000 6.17 0.00 0.00 3.27
708 721 1.684386 CTACAGCCCTGCCCTCTGAG 61.684 65.000 0.00 0.00 0.00 3.35
709 722 1.687146 CTACAGCCCTGCCCTCTGA 60.687 63.158 0.00 0.00 0.00 3.27
710 723 1.053264 ATCTACAGCCCTGCCCTCTG 61.053 60.000 0.00 0.00 0.00 3.35
711 724 1.053264 CATCTACAGCCCTGCCCTCT 61.053 60.000 0.00 0.00 0.00 3.69
712 725 1.449353 CATCTACAGCCCTGCCCTC 59.551 63.158 0.00 0.00 0.00 4.30
713 726 2.750657 GCATCTACAGCCCTGCCCT 61.751 63.158 0.00 0.00 0.00 5.19
714 727 2.203266 GCATCTACAGCCCTGCCC 60.203 66.667 0.00 0.00 0.00 5.36
715 728 1.227793 GAGCATCTACAGCCCTGCC 60.228 63.158 0.00 0.00 35.21 4.85
716 729 4.453093 GAGCATCTACAGCCCTGC 57.547 61.111 0.00 0.00 34.85 4.85
878 896 2.046507 GACTGACTGGCTGGGCTG 60.047 66.667 0.00 0.02 0.00 4.85
879 897 3.325753 GGACTGACTGGCTGGGCT 61.326 66.667 0.00 0.00 0.00 5.19
882 900 4.087892 CGGGGACTGACTGGCTGG 62.088 72.222 0.00 0.00 36.31 4.85
883 901 2.788191 GAACGGGGACTGACTGGCTG 62.788 65.000 0.00 0.00 38.67 4.85
884 902 2.526873 AACGGGGACTGACTGGCT 60.527 61.111 0.00 0.00 38.67 4.75
885 903 2.047179 GAACGGGGACTGACTGGC 60.047 66.667 0.00 0.00 38.67 4.85
886 904 2.663196 GGAACGGGGACTGACTGG 59.337 66.667 0.00 0.00 38.67 4.00
1042 1076 1.312815 GAAGGCGGGAAGGATTGATG 58.687 55.000 0.00 0.00 0.00 3.07
1078 1112 1.154413 AGAAACAAGAATGCGCGCG 60.154 52.632 28.44 28.44 0.00 6.86
1426 1460 0.763223 GGAGGATAAAGGGGAGGCGA 60.763 60.000 0.00 0.00 0.00 5.54
1428 1462 1.060729 GAGGAGGATAAAGGGGAGGC 58.939 60.000 0.00 0.00 0.00 4.70
1551 1591 1.429148 GGTGCGTGGAATCGTGGATC 61.429 60.000 0.00 0.00 0.00 3.36
1605 1645 0.580578 CTCATCCGATGCAAAGCGAG 59.419 55.000 3.25 0.00 0.00 5.03
1606 1646 0.811219 CCTCATCCGATGCAAAGCGA 60.811 55.000 3.25 0.00 0.00 4.93
1607 1647 1.645455 CCTCATCCGATGCAAAGCG 59.355 57.895 3.25 0.00 0.00 4.68
1608 1648 1.358046 GCCTCATCCGATGCAAAGC 59.642 57.895 3.25 0.53 33.38 3.51
1609 1649 2.028130 GGCCTCATCCGATGCAAAG 58.972 57.895 3.25 0.00 34.71 2.77
1610 1650 4.240881 GGCCTCATCCGATGCAAA 57.759 55.556 3.25 0.00 34.71 3.68
1729 1769 3.434984 GCTTTTCTGAGAGTGACATGACC 59.565 47.826 0.00 0.00 0.00 4.02
1808 1848 4.125695 GGAAGGTCGTCGGACGGG 62.126 72.222 28.07 3.70 44.39 5.28
1809 1849 4.471726 CGGAAGGTCGTCGGACGG 62.472 72.222 28.07 11.53 44.39 4.79
1961 2001 2.047655 CCCGGACGCAAGCAACTA 60.048 61.111 0.73 0.00 45.62 2.24
2012 2061 0.320683 TGAGTGGTGCGGTTCATCAG 60.321 55.000 0.00 0.00 36.27 2.90
2068 2118 6.747414 TGCACATTATTATCACCTACTCCT 57.253 37.500 0.00 0.00 0.00 3.69
2109 2159 7.609146 TCTGTAGAATTAAGTACGAGAACTCCA 59.391 37.037 0.00 0.00 0.00 3.86
2163 2215 3.000177 GCAAACGTCCACAAAATTGACAC 60.000 43.478 0.00 0.00 0.00 3.67
2197 2249 9.646427 ACTAGAAATGTCTGAAACTCTGAATAC 57.354 33.333 0.00 0.00 35.12 1.89
2282 2334 2.369394 CAACTAAGGCTAAGGGCAAGG 58.631 52.381 0.00 0.00 44.01 3.61
2325 2378 0.991146 TGTATCCTTGGCTTGGCTCA 59.009 50.000 0.00 0.00 0.00 4.26
2369 2422 3.876309 TCTTCCTTAGCTTGGTTTGGT 57.124 42.857 0.00 0.00 0.00 3.67
2435 2488 9.178758 AGTTCAAAGTAGAAATGTCTGAAACTT 57.821 29.630 0.00 0.00 33.47 2.66
2556 2609 5.918011 GTGCTCGTTTCTTCTCCTATATGAG 59.082 44.000 0.00 0.00 0.00 2.90
2580 2639 4.306600 GGCCACCATTTTGTTTAAGAGTG 58.693 43.478 0.00 0.00 0.00 3.51
2585 2644 2.695585 AGGGGCCACCATTTTGTTTAA 58.304 42.857 0.00 0.00 43.89 1.52
2788 3113 0.612174 TCCACTCTCCGGGTCTCAAG 60.612 60.000 0.00 0.00 0.00 3.02
2795 3120 2.317149 GATGCCTTCCACTCTCCGGG 62.317 65.000 0.00 0.00 0.00 5.73
2806 3131 3.201290 CTGACTGGTGTATGATGCCTTC 58.799 50.000 0.00 0.00 0.00 3.46
2973 3302 3.206150 GGCATTGTTCACCTACATCGAT 58.794 45.455 0.00 0.00 0.00 3.59
3132 3461 0.738762 GCTGCGAGCTGATGTTGAGA 60.739 55.000 6.15 0.00 38.45 3.27
3190 3519 7.012138 CAGACTTTGAAATACCATCCATCTGAG 59.988 40.741 0.00 0.00 32.30 3.35
3436 4200 6.531021 ACGATAAGGAAAGAAAAGACTTGGA 58.469 36.000 0.00 0.00 0.00 3.53
3553 4357 9.642343 ACTCTGTACTATTGAATGGTATACAGA 57.358 33.333 19.46 19.46 37.16 3.41
3584 4388 8.570068 TTGAACACCTAACTCTGTAACTTTTT 57.430 30.769 0.00 0.00 0.00 1.94
3585 4389 8.747538 ATTGAACACCTAACTCTGTAACTTTT 57.252 30.769 0.00 0.00 0.00 2.27
3586 4390 7.444487 GGATTGAACACCTAACTCTGTAACTTT 59.556 37.037 0.00 0.00 0.00 2.66
3587 4391 6.935208 GGATTGAACACCTAACTCTGTAACTT 59.065 38.462 0.00 0.00 0.00 2.66
3588 4392 6.270231 AGGATTGAACACCTAACTCTGTAACT 59.730 38.462 0.00 0.00 34.47 2.24
3589 4393 6.369065 CAGGATTGAACACCTAACTCTGTAAC 59.631 42.308 0.00 0.00 34.87 2.50
3590 4394 6.464222 CAGGATTGAACACCTAACTCTGTAA 58.536 40.000 0.00 0.00 34.87 2.41
3591 4395 5.568825 GCAGGATTGAACACCTAACTCTGTA 60.569 44.000 0.00 0.00 34.87 2.74
3592 4396 4.804261 GCAGGATTGAACACCTAACTCTGT 60.804 45.833 0.00 0.00 34.87 3.41
3765 4569 3.309682 CCAGACGTGCATGATCGTTTTAT 59.690 43.478 14.17 0.00 40.39 1.40
3782 4586 2.408271 TCATCCATGCTTGTCCAGAC 57.592 50.000 0.00 0.00 0.00 3.51
3816 4620 1.151413 TCCTATGTACCCAGATCCCCC 59.849 57.143 0.00 0.00 0.00 5.40
3817 4621 2.638363 GTTCCTATGTACCCAGATCCCC 59.362 54.545 0.00 0.00 0.00 4.81
3832 4636 8.171400 TGGTAAATTTTATCAAGTGGGTTCCTA 58.829 33.333 0.00 0.00 0.00 2.94
3943 4750 4.522789 CCCACTTTCTAAAGCTTAGCCAAA 59.477 41.667 0.00 0.00 39.63 3.28
3946 4753 3.687125 ACCCACTTTCTAAAGCTTAGCC 58.313 45.455 0.00 0.00 39.63 3.93
3947 4754 6.812879 TTTACCCACTTTCTAAAGCTTAGC 57.187 37.500 0.00 0.00 39.63 3.09
4065 4961 5.670485 ACACTATATTTGCTCGTCATCCAA 58.330 37.500 0.00 0.00 0.00 3.53
4132 5028 3.555966 GCTTACCATTACCAGATTGGCT 58.444 45.455 0.00 0.00 42.67 4.75
4268 5165 4.213270 TGTCTCTGCAAAAATAGTCGTTGG 59.787 41.667 0.00 0.00 0.00 3.77
4269 5166 5.177511 TCTGTCTCTGCAAAAATAGTCGTTG 59.822 40.000 0.00 0.00 0.00 4.10
4270 5167 5.297547 TCTGTCTCTGCAAAAATAGTCGTT 58.702 37.500 0.00 0.00 0.00 3.85
4278 5175 4.512944 CACTAGCTTCTGTCTCTGCAAAAA 59.487 41.667 0.00 0.00 0.00 1.94
4454 5352 3.562176 CCCTTCTTTCTTGGCATGGTAGT 60.562 47.826 0.00 0.00 0.00 2.73
4514 5424 7.924103 TTAACACAGTACATACGCTCATATG 57.076 36.000 0.00 0.00 38.34 1.78
4515 5425 8.936070 TTTTAACACAGTACATACGCTCATAT 57.064 30.769 0.00 0.00 0.00 1.78
4763 5676 2.447070 CGCGGGTGTAGGCGTTTAC 61.447 63.158 0.00 0.00 46.79 2.01
5078 5991 2.019951 CACCACGGACGTACAGCAC 61.020 63.158 0.00 0.00 0.00 4.40
5109 6022 3.880490 ACAACGATGGCTAAACTGAAACA 59.120 39.130 0.00 0.00 0.00 2.83
5132 6045 6.155393 ACTTAGGTAGAAGCATCAACTTAGCT 59.845 38.462 0.00 0.00 41.03 3.32
5137 6050 5.746990 ACACTTAGGTAGAAGCATCAACT 57.253 39.130 0.00 0.00 0.00 3.16
5138 6051 6.395629 TGTACACTTAGGTAGAAGCATCAAC 58.604 40.000 0.00 0.00 0.00 3.18
5142 6058 7.070074 AGCTATTGTACACTTAGGTAGAAGCAT 59.930 37.037 12.68 0.00 31.17 3.79
5147 6063 9.636789 TTATCAGCTATTGTACACTTAGGTAGA 57.363 33.333 13.53 13.19 0.00 2.59
5256 6180 2.766263 CACACTGCCCTCTACCATCTTA 59.234 50.000 0.00 0.00 0.00 2.10
5262 6186 1.219393 GCTCACACTGCCCTCTACC 59.781 63.158 0.00 0.00 0.00 3.18
5286 6210 0.322456 TTTCCCGGAAGATGCCACTG 60.322 55.000 0.73 0.00 0.00 3.66
5291 6215 1.066152 GCTTGATTTCCCGGAAGATGC 59.934 52.381 0.73 0.05 0.00 3.91
5349 6283 4.136796 TCCAAATTATTCTCCATCTGGCG 58.863 43.478 0.00 0.00 34.44 5.69
5379 6313 4.937431 GGCGGCCCCTGCTATGAC 62.937 72.222 8.12 0.00 37.74 3.06
5405 6341 2.026262 ACCGAACATGATGCCCTACTTT 60.026 45.455 0.00 0.00 0.00 2.66
5445 6381 2.485903 TGTCAAACGGAATACAAGCGT 58.514 42.857 0.00 0.00 0.00 5.07
5619 6556 3.124921 CCGACGCAAATCCGGCTT 61.125 61.111 0.00 0.00 36.62 4.35
5637 6574 4.034258 GTCCGTCTCGTGTCCGCA 62.034 66.667 0.00 0.00 0.00 5.69
5694 6637 2.036256 GAATGGTGGTGGCTGCCT 59.964 61.111 21.03 0.00 0.00 4.75
5933 6899 0.390472 CCTTCCTCTTGGTCGACTGC 60.390 60.000 16.46 0.00 34.23 4.40
5934 6900 0.247736 CCCTTCCTCTTGGTCGACTG 59.752 60.000 16.46 6.47 34.23 3.51
5935 6901 1.545706 GCCCTTCCTCTTGGTCGACT 61.546 60.000 16.46 0.00 34.23 4.18
5936 6902 1.079057 GCCCTTCCTCTTGGTCGAC 60.079 63.158 7.13 7.13 34.23 4.20
5937 6903 2.291043 GGCCCTTCCTCTTGGTCGA 61.291 63.158 0.00 0.00 34.23 4.20
5938 6904 2.269241 GGCCCTTCCTCTTGGTCG 59.731 66.667 0.00 0.00 34.23 4.79
5939 6905 2.269241 CGGCCCTTCCTCTTGGTC 59.731 66.667 0.00 0.00 34.23 4.02
5940 6906 3.330720 CCGGCCCTTCCTCTTGGT 61.331 66.667 0.00 0.00 34.23 3.67
5969 6935 3.838271 GCCTCATCCCTCGCGTCA 61.838 66.667 5.77 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.