Multiple sequence alignment - TraesCS1D01G173400

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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 TraesCS1D01G173400 chr1D 100.000 2570 0 0 1 2570 247293098 247295667 0.000000e+00 4747
1 TraesCS1D01G173400 chr1D 94.131 886 50 2 1658 2542 287621937 287622821 0.000000e+00 1347
2 TraesCS1D01G173400 chr1D 93.165 556 37 1 2 556 308351134 308350579 0.000000e+00 815
3 TraesCS1D01G173400 chr5A 93.137 918 55 4 1655 2570 616542817 616541906 0.000000e+00 1339
4 TraesCS1D01G173400 chr4A 92.904 916 53 6 1657 2570 468435768 468436673 0.000000e+00 1321
5 TraesCS1D01G173400 chr4A 83.852 1028 110 25 635 1657 684502821 684503797 0.000000e+00 928
6 TraesCS1D01G173400 chr2D 92.904 916 51 6 1658 2570 631414563 631413659 0.000000e+00 1319
7 TraesCS1D01G173400 chr2D 93.967 547 31 2 2 547 141780237 141779692 0.000000e+00 826
8 TraesCS1D01G173400 chr2D 93.478 552 36 0 1 552 337031292 337030741 0.000000e+00 821
9 TraesCS1D01G173400 chr6A 93.545 883 55 2 1661 2542 78227178 78226297 0.000000e+00 1314
10 TraesCS1D01G173400 chr6A 83.293 826 107 17 759 1568 9054063 9054873 0.000000e+00 732
11 TraesCS1D01G173400 chr5D 93.348 887 56 3 1655 2540 376912150 376911266 0.000000e+00 1308
12 TraesCS1D01G173400 chr5D 93.989 549 31 2 2 549 381130309 381129762 0.000000e+00 830
13 TraesCS1D01G173400 chr7A 92.275 932 55 6 1647 2570 62025028 62025950 0.000000e+00 1306
14 TraesCS1D01G173400 chr3A 92.000 925 61 5 1648 2570 229937609 229936696 0.000000e+00 1286
15 TraesCS1D01G173400 chr2A 92.232 914 58 7 1658 2569 56805340 56804438 0.000000e+00 1282
16 TraesCS1D01G173400 chr4B 84.608 1033 121 18 635 1657 603165880 603166884 0.000000e+00 992
17 TraesCS1D01G173400 chr4D 84.718 975 107 19 610 1580 477577139 477578075 0.000000e+00 937
18 TraesCS1D01G173400 chr4D 94.708 548 27 2 2 548 307500891 307500345 0.000000e+00 850
19 TraesCS1D01G173400 chr6D 94.343 548 30 1 2 548 88992155 88992702 0.000000e+00 839
20 TraesCS1D01G173400 chr6D 93.048 561 37 2 2 561 371050350 371049791 0.000000e+00 819
21 TraesCS1D01G173400 chr6D 85.675 733 89 11 882 1605 8743688 8742963 0.000000e+00 758
22 TraesCS1D01G173400 chr6D 85.402 733 91 11 882 1605 8733002 8732277 0.000000e+00 747
23 TraesCS1D01G173400 chr3D 94.150 547 30 2 2 547 170627161 170627706 0.000000e+00 832
24 TraesCS1D01G173400 chr3D 93.796 548 33 1 2 548 185384073 185383526 0.000000e+00 822
25 TraesCS1D01G173400 chr6B 82.353 918 116 26 747 1657 15890769 15889891 0.000000e+00 756
26 TraesCS1D01G173400 chr6B 83.413 832 111 14 747 1571 15919652 15918841 0.000000e+00 747
27 TraesCS1D01G173400 chrUn 85.402 733 91 11 882 1605 355457651 355456926 0.000000e+00 747
28 TraesCS1D01G173400 chr1B 85.593 354 43 2 553 906 330553950 330553605 5.230000e-97 364


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 TraesCS1D01G173400 chr1D 247293098 247295667 2569 False 4747 4747 100.000 1 2570 1 chr1D.!!$F1 2569
1 TraesCS1D01G173400 chr1D 287621937 287622821 884 False 1347 1347 94.131 1658 2542 1 chr1D.!!$F2 884
2 TraesCS1D01G173400 chr1D 308350579 308351134 555 True 815 815 93.165 2 556 1 chr1D.!!$R1 554
3 TraesCS1D01G173400 chr5A 616541906 616542817 911 True 1339 1339 93.137 1655 2570 1 chr5A.!!$R1 915
4 TraesCS1D01G173400 chr4A 468435768 468436673 905 False 1321 1321 92.904 1657 2570 1 chr4A.!!$F1 913
5 TraesCS1D01G173400 chr4A 684502821 684503797 976 False 928 928 83.852 635 1657 1 chr4A.!!$F2 1022
6 TraesCS1D01G173400 chr2D 631413659 631414563 904 True 1319 1319 92.904 1658 2570 1 chr2D.!!$R3 912
7 TraesCS1D01G173400 chr2D 141779692 141780237 545 True 826 826 93.967 2 547 1 chr2D.!!$R1 545
8 TraesCS1D01G173400 chr2D 337030741 337031292 551 True 821 821 93.478 1 552 1 chr2D.!!$R2 551
9 TraesCS1D01G173400 chr6A 78226297 78227178 881 True 1314 1314 93.545 1661 2542 1 chr6A.!!$R1 881
10 TraesCS1D01G173400 chr6A 9054063 9054873 810 False 732 732 83.293 759 1568 1 chr6A.!!$F1 809
11 TraesCS1D01G173400 chr5D 376911266 376912150 884 True 1308 1308 93.348 1655 2540 1 chr5D.!!$R1 885
12 TraesCS1D01G173400 chr5D 381129762 381130309 547 True 830 830 93.989 2 549 1 chr5D.!!$R2 547
13 TraesCS1D01G173400 chr7A 62025028 62025950 922 False 1306 1306 92.275 1647 2570 1 chr7A.!!$F1 923
14 TraesCS1D01G173400 chr3A 229936696 229937609 913 True 1286 1286 92.000 1648 2570 1 chr3A.!!$R1 922
15 TraesCS1D01G173400 chr2A 56804438 56805340 902 True 1282 1282 92.232 1658 2569 1 chr2A.!!$R1 911
16 TraesCS1D01G173400 chr4B 603165880 603166884 1004 False 992 992 84.608 635 1657 1 chr4B.!!$F1 1022
17 TraesCS1D01G173400 chr4D 477577139 477578075 936 False 937 937 84.718 610 1580 1 chr4D.!!$F1 970
18 TraesCS1D01G173400 chr4D 307500345 307500891 546 True 850 850 94.708 2 548 1 chr4D.!!$R1 546
19 TraesCS1D01G173400 chr6D 88992155 88992702 547 False 839 839 94.343 2 548 1 chr6D.!!$F1 546
20 TraesCS1D01G173400 chr6D 371049791 371050350 559 True 819 819 93.048 2 561 1 chr6D.!!$R3 559
21 TraesCS1D01G173400 chr6D 8742963 8743688 725 True 758 758 85.675 882 1605 1 chr6D.!!$R2 723
22 TraesCS1D01G173400 chr6D 8732277 8733002 725 True 747 747 85.402 882 1605 1 chr6D.!!$R1 723
23 TraesCS1D01G173400 chr3D 170627161 170627706 545 False 832 832 94.150 2 547 1 chr3D.!!$F1 545
24 TraesCS1D01G173400 chr3D 185383526 185384073 547 True 822 822 93.796 2 548 1 chr3D.!!$R1 546
25 TraesCS1D01G173400 chr6B 15889891 15890769 878 True 756 756 82.353 747 1657 1 chr6B.!!$R1 910
26 TraesCS1D01G173400 chr6B 15918841 15919652 811 True 747 747 83.413 747 1571 1 chr6B.!!$R2 824
27 TraesCS1D01G173400 chrUn 355456926 355457651 725 True 747 747 85.402 882 1605 1 chrUn.!!$R1 723

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
872 887 0.109412 GAACTGGCAGATGCAGCAAC 60.109 55.0 23.66 0.0 44.36 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 1854 1.000843 GACAGGGGCAAAAATGTCCAC 59.999 52.381 1.48 0.0 36.83 4.02 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
26 27 6.419791 AGGAATAAACCGTGTTGGATCAATA 58.580 36.000 0.00 0.00 42.00 1.90
59 60 5.063438 CACACGACTTTCTCTTGAAAACTGA 59.937 40.000 0.00 0.00 41.09 3.41
97 98 1.049251 CGCAAACGTTTACCACATGC 58.951 50.000 14.20 10.89 33.53 4.06
223 225 4.701171 TGTACCTGTGAAGGAAACGTTTTT 59.299 37.500 15.89 6.31 0.00 1.94
227 229 5.648960 ACCTGTGAAGGAAACGTTTTTCTTA 59.351 36.000 22.00 12.71 40.98 2.10
258 260 2.754002 TGTGGGATGTACATACGAACGA 59.246 45.455 12.01 2.32 0.00 3.85
263 265 6.476380 GTGGGATGTACATACGAACGAAAATA 59.524 38.462 12.01 0.00 0.00 1.40
279 281 6.117488 ACGAAAATATTTAACGGGGACTGAT 58.883 36.000 22.32 5.57 38.67 2.90
300 302 1.337728 TGTGTGGGATGTACTTGCGAG 60.338 52.381 0.00 0.00 0.00 5.03
323 325 6.670233 AGCGGAAACAATTTTGTCGTATAAA 58.330 32.000 0.00 0.00 41.31 1.40
407 410 3.249799 CCTCATTTTGCTGAACGTGTGTA 59.750 43.478 0.00 0.00 0.00 2.90
408 411 4.083324 CCTCATTTTGCTGAACGTGTGTAT 60.083 41.667 0.00 0.00 0.00 2.29
420 423 1.134401 CGTGTGTATCAGGAGGGCATT 60.134 52.381 0.00 0.00 34.28 3.56
423 426 2.846206 TGTGTATCAGGAGGGCATTTCT 59.154 45.455 0.00 0.00 0.00 2.52
487 490 0.591170 CATTCACTTGGCGACGGTTT 59.409 50.000 0.00 0.00 0.00 3.27
541 544 4.387862 CGTTTGTTTAGGAGCTCGTTGTAT 59.612 41.667 15.09 0.00 0.00 2.29
558 561 9.737427 CTCGTTGTATTAGTGTTGATAGATCTT 57.263 33.333 0.00 0.00 0.00 2.40
566 569 9.829507 ATTAGTGTTGATAGATCTTTTGAGGAG 57.170 33.333 0.00 0.00 0.00 3.69
567 570 6.112058 AGTGTTGATAGATCTTTTGAGGAGC 58.888 40.000 0.00 0.00 0.00 4.70
568 571 6.070309 AGTGTTGATAGATCTTTTGAGGAGCT 60.070 38.462 0.00 0.00 33.81 4.09
569 572 6.257630 GTGTTGATAGATCTTTTGAGGAGCTC 59.742 42.308 4.71 4.71 31.63 4.09
570 573 6.070596 TGTTGATAGATCTTTTGAGGAGCTCA 60.071 38.462 17.19 0.00 38.87 4.26
571 574 6.159299 TGATAGATCTTTTGAGGAGCTCAG 57.841 41.667 17.19 2.87 41.75 3.35
572 575 5.660417 TGATAGATCTTTTGAGGAGCTCAGT 59.340 40.000 17.19 0.97 41.75 3.41
573 576 4.906747 AGATCTTTTGAGGAGCTCAGTT 57.093 40.909 17.19 0.00 41.75 3.16
574 577 5.240013 AGATCTTTTGAGGAGCTCAGTTT 57.760 39.130 17.19 0.00 41.75 2.66
575 578 5.629125 AGATCTTTTGAGGAGCTCAGTTTT 58.371 37.500 17.19 0.00 41.75 2.43
576 579 6.773638 AGATCTTTTGAGGAGCTCAGTTTTA 58.226 36.000 17.19 0.00 41.75 1.52
577 580 6.878389 AGATCTTTTGAGGAGCTCAGTTTTAG 59.122 38.462 17.19 5.95 41.75 1.85
578 581 5.930135 TCTTTTGAGGAGCTCAGTTTTAGT 58.070 37.500 17.19 0.00 41.75 2.24
579 582 7.062749 TCTTTTGAGGAGCTCAGTTTTAGTA 57.937 36.000 17.19 0.00 41.75 1.82
580 583 7.155328 TCTTTTGAGGAGCTCAGTTTTAGTAG 58.845 38.462 17.19 1.71 41.75 2.57
581 584 6.665992 TTTGAGGAGCTCAGTTTTAGTAGA 57.334 37.500 17.19 0.00 41.75 2.59
582 585 6.665992 TTGAGGAGCTCAGTTTTAGTAGAA 57.334 37.500 17.19 0.00 41.75 2.10
583 586 6.274157 TGAGGAGCTCAGTTTTAGTAGAAG 57.726 41.667 17.19 0.00 35.39 2.85
584 587 5.186021 TGAGGAGCTCAGTTTTAGTAGAAGG 59.814 44.000 17.19 0.00 35.39 3.46
585 588 5.334421 AGGAGCTCAGTTTTAGTAGAAGGA 58.666 41.667 17.19 0.00 0.00 3.36
586 589 5.186215 AGGAGCTCAGTTTTAGTAGAAGGAC 59.814 44.000 17.19 0.00 0.00 3.85
587 590 5.408880 AGCTCAGTTTTAGTAGAAGGACC 57.591 43.478 0.00 0.00 0.00 4.46
588 591 4.838986 AGCTCAGTTTTAGTAGAAGGACCA 59.161 41.667 0.00 0.00 0.00 4.02
589 592 5.046950 AGCTCAGTTTTAGTAGAAGGACCAG 60.047 44.000 0.00 0.00 0.00 4.00
590 593 5.047235 GCTCAGTTTTAGTAGAAGGACCAGA 60.047 44.000 0.00 0.00 0.00 3.86
591 594 6.591750 TCAGTTTTAGTAGAAGGACCAGAG 57.408 41.667 0.00 0.00 0.00 3.35
592 595 6.312529 TCAGTTTTAGTAGAAGGACCAGAGA 58.687 40.000 0.00 0.00 0.00 3.10
593 596 6.954684 TCAGTTTTAGTAGAAGGACCAGAGAT 59.045 38.462 0.00 0.00 0.00 2.75
594 597 7.038659 CAGTTTTAGTAGAAGGACCAGAGATG 58.961 42.308 0.00 0.00 0.00 2.90
595 598 5.599999 TTTAGTAGAAGGACCAGAGATGC 57.400 43.478 0.00 0.00 0.00 3.91
596 599 3.396685 AGTAGAAGGACCAGAGATGCT 57.603 47.619 0.00 0.00 0.00 3.79
597 600 3.295973 AGTAGAAGGACCAGAGATGCTC 58.704 50.000 0.00 0.00 0.00 4.26
598 601 1.110442 AGAAGGACCAGAGATGCTCG 58.890 55.000 0.00 0.00 35.36 5.03
599 602 0.820871 GAAGGACCAGAGATGCTCGT 59.179 55.000 0.00 0.00 35.36 4.18
600 603 2.025155 GAAGGACCAGAGATGCTCGTA 58.975 52.381 0.00 0.00 35.36 3.43
601 604 1.394618 AGGACCAGAGATGCTCGTAC 58.605 55.000 0.00 0.00 35.36 3.67
602 605 1.064314 AGGACCAGAGATGCTCGTACT 60.064 52.381 0.00 0.00 35.36 2.73
603 606 1.066303 GGACCAGAGATGCTCGTACTG 59.934 57.143 0.00 0.00 35.36 2.74
604 607 1.746220 GACCAGAGATGCTCGTACTGT 59.254 52.381 0.00 0.00 35.36 3.55
605 608 2.164624 GACCAGAGATGCTCGTACTGTT 59.835 50.000 0.00 0.00 35.36 3.16
606 609 3.353557 ACCAGAGATGCTCGTACTGTTA 58.646 45.455 0.00 0.00 35.36 2.41
607 610 3.128938 ACCAGAGATGCTCGTACTGTTAC 59.871 47.826 0.00 0.00 35.36 2.50
608 611 3.378742 CCAGAGATGCTCGTACTGTTACT 59.621 47.826 0.00 0.00 35.36 2.24
614 617 5.646793 AGATGCTCGTACTGTTACTCTGTTA 59.353 40.000 0.00 0.00 0.00 2.41
618 621 5.122082 GCTCGTACTGTTACTCTGTTAGTCT 59.878 44.000 0.00 0.00 39.80 3.24
622 625 5.610235 ACTGTTACTCTGTTAGTCTCGAC 57.390 43.478 0.00 0.00 39.80 4.20
628 631 2.683867 CTCTGTTAGTCTCGACCGGAAT 59.316 50.000 9.46 0.00 0.00 3.01
631 634 2.163010 TGTTAGTCTCGACCGGAATCAC 59.837 50.000 9.46 0.00 0.00 3.06
633 636 0.611062 AGTCTCGACCGGAATCACCA 60.611 55.000 9.46 0.00 38.90 4.17
636 639 2.186903 CGACCGGAATCACCAGGG 59.813 66.667 9.46 0.00 38.90 4.45
659 662 3.073274 AGGGTGGAAGAATGTTGCTAC 57.927 47.619 0.00 0.00 0.00 3.58
667 670 5.048083 TGGAAGAATGTTGCTACCAATTCAC 60.048 40.000 11.80 6.90 32.75 3.18
672 675 2.813754 TGTTGCTACCAATTCACTCAGC 59.186 45.455 0.00 0.00 32.75 4.26
706 713 8.025445 CCTATTCTGCAGTATTTTATCATTGGC 58.975 37.037 14.67 0.00 0.00 4.52
707 714 5.772825 TCTGCAGTATTTTATCATTGGCC 57.227 39.130 14.67 0.00 0.00 5.36
714 721 7.673180 CAGTATTTTATCATTGGCCCAATCAT 58.327 34.615 5.84 1.12 31.05 2.45
716 723 5.954153 TTTTATCATTGGCCCAATCATGT 57.046 34.783 5.84 0.00 31.05 3.21
720 727 3.025978 TCATTGGCCCAATCATGTCTTC 58.974 45.455 5.84 0.00 31.05 2.87
725 732 1.668419 CCCAATCATGTCTTCCCGAC 58.332 55.000 0.00 0.00 43.14 4.79
728 735 0.178068 AATCATGTCTTCCCGACGGG 59.822 55.000 27.86 27.86 45.87 5.28
730 737 0.323633 TCATGTCTTCCCGACGGGTA 60.324 55.000 31.54 22.13 45.87 3.69
733 740 0.827089 TGTCTTCCCGACGGGTAACA 60.827 55.000 31.54 27.13 45.87 2.41
734 741 0.533951 GTCTTCCCGACGGGTAACAT 59.466 55.000 31.54 0.00 44.74 2.71
768 775 8.926710 CAGAATATGTCCGTCCTATTTATCAAC 58.073 37.037 0.00 0.00 0.00 3.18
769 776 8.871125 AGAATATGTCCGTCCTATTTATCAACT 58.129 33.333 0.00 0.00 0.00 3.16
776 783 6.260050 TCCGTCCTATTTATCAACTCATTTGC 59.740 38.462 0.00 0.00 34.88 3.68
780 787 9.109393 GTCCTATTTATCAACTCATTTGCTACA 57.891 33.333 0.00 0.00 34.88 2.74
785 792 5.648178 ATCAACTCATTTGCTACATTGCA 57.352 34.783 0.00 0.00 41.65 4.08
790 797 4.155462 ACTCATTTGCTACATTGCAGACTG 59.845 41.667 0.00 0.00 44.27 3.51
791 801 4.325972 TCATTTGCTACATTGCAGACTGA 58.674 39.130 6.65 0.00 44.27 3.41
818 832 7.609760 TGTATGAACTTATCAACGATTTGCT 57.390 32.000 0.00 0.00 42.54 3.91
833 847 1.241165 TTGCTGTGGAGAACATGCAG 58.759 50.000 0.00 0.00 41.09 4.41
837 851 2.915349 CTGTGGAGAACATGCAGCTAT 58.085 47.619 0.00 0.00 38.39 2.97
840 854 4.081406 TGTGGAGAACATGCAGCTATTTT 58.919 39.130 0.00 0.00 32.36 1.82
843 857 5.123820 GTGGAGAACATGCAGCTATTTTGTA 59.876 40.000 0.00 0.00 0.00 2.41
864 879 6.653020 TGTATTCATAACTGAACTGGCAGAT 58.347 36.000 23.66 9.90 43.92 2.90
867 882 2.857186 TAACTGAACTGGCAGATGCA 57.143 45.000 23.66 14.16 44.36 3.96
869 884 0.959372 ACTGAACTGGCAGATGCAGC 60.959 55.000 23.66 0.00 44.36 5.25
870 885 0.958876 CTGAACTGGCAGATGCAGCA 60.959 55.000 23.66 0.00 44.36 4.41
871 886 0.537828 TGAACTGGCAGATGCAGCAA 60.538 50.000 23.66 0.00 44.36 3.91
872 887 0.109412 GAACTGGCAGATGCAGCAAC 60.109 55.000 23.66 0.00 44.36 4.17
873 888 0.824595 AACTGGCAGATGCAGCAACA 60.825 50.000 23.66 0.00 44.36 3.33
874 889 1.241990 ACTGGCAGATGCAGCAACAG 61.242 55.000 23.66 15.79 44.36 3.16
875 890 1.934220 CTGGCAGATGCAGCAACAGG 61.934 60.000 9.42 0.00 44.36 4.00
876 891 2.707849 GGCAGATGCAGCAACAGGG 61.708 63.158 4.07 0.00 44.36 4.45
921 936 2.009042 GCAGCTCTCTAACCACGCAAT 61.009 52.381 0.00 0.00 0.00 3.56
922 937 1.929836 CAGCTCTCTAACCACGCAATC 59.070 52.381 0.00 0.00 0.00 2.67
923 938 1.550524 AGCTCTCTAACCACGCAATCA 59.449 47.619 0.00 0.00 0.00 2.57
925 940 2.939103 GCTCTCTAACCACGCAATCAAT 59.061 45.455 0.00 0.00 0.00 2.57
926 941 3.001736 GCTCTCTAACCACGCAATCAATC 59.998 47.826 0.00 0.00 0.00 2.67
927 942 4.183865 CTCTCTAACCACGCAATCAATCA 58.816 43.478 0.00 0.00 0.00 2.57
945 963 1.408702 TCAAGAGGCAAACAAACCAGC 59.591 47.619 0.00 0.00 0.00 4.85
957 978 1.126113 CAAACCAGCGTAGTAGCAACG 59.874 52.381 0.00 0.00 43.12 4.10
958 979 0.389426 AACCAGCGTAGTAGCAACGG 60.389 55.000 0.00 0.00 40.64 4.44
986 1013 5.632034 AAGAGGGTTACAGTTCAAGAGTT 57.368 39.130 0.00 0.00 0.00 3.01
1004 1031 6.613153 AGAGTTTTCAGTAGCTAAGATGGT 57.387 37.500 0.00 0.00 0.00 3.55
1014 1041 1.330829 GCTAAGATGGTTACCGCAAGC 59.669 52.381 0.00 1.87 35.11 4.01
1050 1077 1.000396 AATCTTCCTGCTGGTGGCC 60.000 57.895 9.73 0.00 40.92 5.36
1070 1097 1.481428 CCTCTCCACCTCCCATATCGT 60.481 57.143 0.00 0.00 0.00 3.73
1090 1117 4.135153 CCTCACTCCGCTCGGGTG 62.135 72.222 17.76 17.76 37.61 4.61
1109 1136 3.276091 CGGTGTCTGCCGTGCAAA 61.276 61.111 0.00 0.00 46.11 3.68
1152 1179 1.949525 GGCAACTGTGAGAAGAGCAAA 59.050 47.619 0.00 0.00 0.00 3.68
1153 1180 2.358898 GGCAACTGTGAGAAGAGCAAAA 59.641 45.455 0.00 0.00 0.00 2.44
1238 1265 1.616921 CCACCAAGGCCATCCTGAT 59.383 57.895 5.01 0.00 43.40 2.90
1242 1269 1.107538 CCAAGGCCATCCTGATGCTG 61.108 60.000 5.01 0.00 43.40 4.41
1263 1290 0.108585 ACAGCTTCGAGAAGGGCAAA 59.891 50.000 13.92 0.00 38.80 3.68
1266 1293 1.280421 AGCTTCGAGAAGGGCAAAGAT 59.720 47.619 13.92 0.00 38.80 2.40
1302 1329 2.350522 GAGTGTGACAATGCCTACCAG 58.649 52.381 0.00 0.00 0.00 4.00
1329 1356 1.957177 GAGGAGATGGTCGTCATGCTA 59.043 52.381 0.00 0.00 39.48 3.49
1360 1387 1.377202 TTCAAGAGCATGGCCCGTC 60.377 57.895 0.00 0.00 0.00 4.79
1405 1432 1.610624 CCAATGGCAACTCCGTGTACT 60.611 52.381 0.00 0.00 37.80 2.73
1427 1454 3.124921 GGTGGTGGACGAATGCGG 61.125 66.667 0.00 0.00 43.17 5.69
1444 1471 1.820581 GGCTCCGTGTATGGCTGTA 59.179 57.895 0.00 0.00 0.00 2.74
1450 1477 1.135199 CCGTGTATGGCTGTAACGACT 60.135 52.381 0.00 0.00 36.38 4.18
1452 1479 3.243301 CCGTGTATGGCTGTAACGACTAT 60.243 47.826 0.00 0.00 36.38 2.12
1458 1485 4.465632 TGGCTGTAACGACTATCACAAT 57.534 40.909 0.00 0.00 0.00 2.71
1470 1497 2.779755 ATCACAATTACGAGCCACCA 57.220 45.000 0.00 0.00 0.00 4.17
1485 1512 1.891811 CCACCATGTGCCAACAACATA 59.108 47.619 0.00 0.00 40.46 2.29
1489 1516 2.819019 CCATGTGCCAACAACATAGTCA 59.181 45.455 0.00 0.00 40.46 3.41
1499 1526 2.563179 ACAACATAGTCAACGCCTCTCT 59.437 45.455 0.00 0.00 0.00 3.10
1500 1527 3.762288 ACAACATAGTCAACGCCTCTCTA 59.238 43.478 0.00 0.00 0.00 2.43
1502 1529 2.952978 ACATAGTCAACGCCTCTCTAGG 59.047 50.000 0.00 0.00 46.76 3.02
1514 1541 2.438411 CTCTCTAGGAGTGTGGAACGT 58.562 52.381 0.00 0.00 37.30 3.99
1537 1564 2.649034 GGCTCGACCAGAACGTCA 59.351 61.111 0.00 0.00 38.86 4.35
1574 1601 0.823769 TGGTCTGACGAGTGAGCACT 60.824 55.000 2.20 2.20 45.84 4.40
1576 1603 1.667467 GGTCTGACGAGTGAGCACTTC 60.667 57.143 4.42 0.31 42.66 3.01
1577 1604 0.238553 TCTGACGAGTGAGCACTTCG 59.761 55.000 4.42 11.51 42.66 3.79
1578 1605 0.039978 CTGACGAGTGAGCACTTCGT 60.040 55.000 19.95 19.95 42.66 3.85
1580 1607 1.053811 GACGAGTGAGCACTTCGTTC 58.946 55.000 20.45 13.74 42.66 3.95
1591 1622 4.412207 AGCACTTCGTTCTCAAAACAAAC 58.588 39.130 0.00 0.00 0.00 2.93
1592 1623 4.083003 AGCACTTCGTTCTCAAAACAAACA 60.083 37.500 0.00 0.00 0.00 2.83
1595 1626 5.229887 CACTTCGTTCTCAAAACAAACATGG 59.770 40.000 0.00 0.00 0.00 3.66
1629 1660 1.071605 CTGAGCTCGTACCACTTTGC 58.928 55.000 9.64 0.00 0.00 3.68
1652 1684 5.765176 CCGGTCGAGTGTCATGTAATATAA 58.235 41.667 0.00 0.00 0.00 0.98
1816 1848 2.461945 TTTGACCGCAAACGACGCA 61.462 52.632 0.00 0.00 43.93 5.24
1822 1854 0.518355 CCGCAAACGACGCATTACTG 60.518 55.000 0.00 0.00 43.93 2.74
1846 1878 0.678950 CATTTTTGCCCCTGTCGGTT 59.321 50.000 0.00 0.00 0.00 4.44
1853 1885 1.342674 TGCCCCTGTCGGTTCTATACT 60.343 52.381 0.00 0.00 0.00 2.12
1909 1941 4.759183 AGGAAACAGAGCAGAATGAGAAAC 59.241 41.667 0.00 0.00 39.69 2.78
1996 2028 1.068921 GCTCGGGCTCTTCCATCTC 59.931 63.158 0.00 0.00 36.21 2.75
2072 2112 5.690865 CCCTAATGCATTCTAGGGTTTGTA 58.309 41.667 28.80 4.87 46.58 2.41
2153 2193 8.316497 TCTGAGTTCTATCTTCCAGATGAAAT 57.684 34.615 0.00 0.00 35.37 2.17
2410 2450 1.203300 TCCTCCTCCTCCATTGTGTGA 60.203 52.381 0.00 0.00 0.00 3.58
2419 2459 3.355378 CTCCATTGTGTGATGCCCTTAA 58.645 45.455 0.00 0.00 0.00 1.85
2447 2487 1.226916 CCTGCACGCAGAGCTAGAG 60.227 63.158 20.42 0.00 46.38 2.43
2453 2493 0.891373 ACGCAGAGCTAGAGCAAAGA 59.109 50.000 4.01 0.00 45.16 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.876107 AGAGAAAGTCGTGTGTGATTGTTT 59.124 37.500 0.00 0.00 0.00 2.83
59 60 1.595093 GCAAGGTGGCCTAACGCAAT 61.595 55.000 3.32 0.00 40.31 3.56
97 98 2.287188 GCTGTCCATCACACACAGTTTG 60.287 50.000 0.00 0.00 39.86 2.93
223 225 0.888619 CCCACACAGTCGCTCTAAGA 59.111 55.000 0.00 0.00 0.00 2.10
227 229 1.188219 ACATCCCACACAGTCGCTCT 61.188 55.000 0.00 0.00 0.00 4.09
258 260 7.177744 ACACAATCAGTCCCCGTTAAATATTTT 59.822 33.333 5.91 0.00 0.00 1.82
263 265 3.756434 CACACAATCAGTCCCCGTTAAAT 59.244 43.478 0.00 0.00 0.00 1.40
279 281 1.070914 TCGCAAGTACATCCCACACAA 59.929 47.619 0.00 0.00 39.48 3.33
300 302 6.914760 TTTATACGACAAAATTGTTTCCGC 57.085 33.333 0.00 0.00 42.43 5.54
407 410 0.471617 CGGAGAAATGCCCTCCTGAT 59.528 55.000 0.00 0.00 46.15 2.90
408 411 0.617535 TCGGAGAAATGCCCTCCTGA 60.618 55.000 0.00 0.00 46.15 3.86
420 423 1.117142 ACCCAGAAACCGTCGGAGAA 61.117 55.000 20.51 0.00 39.69 2.87
423 426 2.922950 CGACCCAGAAACCGTCGGA 61.923 63.158 20.51 0.00 44.26 4.55
470 473 0.462225 TGAAACCGTCGCCAAGTGAA 60.462 50.000 0.00 0.00 0.00 3.18
541 544 7.766278 GCTCCTCAAAAGATCTATCAACACTAA 59.234 37.037 0.00 0.00 0.00 2.24
558 561 6.665992 TCTACTAAAACTGAGCTCCTCAAA 57.334 37.500 12.15 0.00 40.18 2.69
561 564 5.419471 TCCTTCTACTAAAACTGAGCTCCTC 59.581 44.000 12.15 0.00 0.00 3.71
562 565 5.186215 GTCCTTCTACTAAAACTGAGCTCCT 59.814 44.000 12.15 0.00 0.00 3.69
563 566 5.412640 GTCCTTCTACTAAAACTGAGCTCC 58.587 45.833 12.15 0.00 0.00 4.70
564 567 5.047235 TGGTCCTTCTACTAAAACTGAGCTC 60.047 44.000 6.82 6.82 0.00 4.09
565 568 4.838986 TGGTCCTTCTACTAAAACTGAGCT 59.161 41.667 0.00 0.00 0.00 4.09
566 569 5.047235 TCTGGTCCTTCTACTAAAACTGAGC 60.047 44.000 0.00 0.00 0.00 4.26
567 570 6.434652 TCTCTGGTCCTTCTACTAAAACTGAG 59.565 42.308 0.00 0.00 0.00 3.35
568 571 6.312529 TCTCTGGTCCTTCTACTAAAACTGA 58.687 40.000 0.00 0.00 0.00 3.41
569 572 6.591750 TCTCTGGTCCTTCTACTAAAACTG 57.408 41.667 0.00 0.00 0.00 3.16
570 573 6.351456 GCATCTCTGGTCCTTCTACTAAAACT 60.351 42.308 0.00 0.00 0.00 2.66
571 574 5.813157 GCATCTCTGGTCCTTCTACTAAAAC 59.187 44.000 0.00 0.00 0.00 2.43
572 575 5.721960 AGCATCTCTGGTCCTTCTACTAAAA 59.278 40.000 0.00 0.00 0.00 1.52
573 576 5.273208 AGCATCTCTGGTCCTTCTACTAAA 58.727 41.667 0.00 0.00 0.00 1.85
574 577 4.873010 AGCATCTCTGGTCCTTCTACTAA 58.127 43.478 0.00 0.00 0.00 2.24
575 578 4.465886 GAGCATCTCTGGTCCTTCTACTA 58.534 47.826 0.00 0.00 42.77 1.82
576 579 3.295973 GAGCATCTCTGGTCCTTCTACT 58.704 50.000 0.00 0.00 42.77 2.57
577 580 2.034053 CGAGCATCTCTGGTCCTTCTAC 59.966 54.545 0.00 0.00 45.16 2.59
578 581 2.302260 CGAGCATCTCTGGTCCTTCTA 58.698 52.381 0.00 0.00 45.16 2.10
579 582 1.110442 CGAGCATCTCTGGTCCTTCT 58.890 55.000 0.00 0.00 45.16 2.85
580 583 0.820871 ACGAGCATCTCTGGTCCTTC 59.179 55.000 0.00 0.00 45.16 3.46
581 584 1.751924 GTACGAGCATCTCTGGTCCTT 59.248 52.381 0.00 0.00 45.16 3.36
582 585 1.064314 AGTACGAGCATCTCTGGTCCT 60.064 52.381 0.00 0.00 45.16 3.85
583 586 1.066303 CAGTACGAGCATCTCTGGTCC 59.934 57.143 0.00 0.00 45.16 4.46
584 587 1.746220 ACAGTACGAGCATCTCTGGTC 59.254 52.381 0.00 0.00 44.64 4.02
585 588 1.840737 ACAGTACGAGCATCTCTGGT 58.159 50.000 0.00 0.00 37.51 4.00
586 589 2.949451 AACAGTACGAGCATCTCTGG 57.051 50.000 0.00 0.00 32.99 3.86
587 590 4.334203 AGAGTAACAGTACGAGCATCTCTG 59.666 45.833 0.00 0.00 35.20 3.35
588 591 4.334203 CAGAGTAACAGTACGAGCATCTCT 59.666 45.833 0.00 0.00 35.20 3.10
589 592 4.095185 ACAGAGTAACAGTACGAGCATCTC 59.905 45.833 0.00 0.00 35.20 2.75
590 593 4.011023 ACAGAGTAACAGTACGAGCATCT 58.989 43.478 0.00 0.00 35.20 2.90
591 594 4.358494 ACAGAGTAACAGTACGAGCATC 57.642 45.455 0.00 0.00 35.20 3.91
592 595 4.785511 AACAGAGTAACAGTACGAGCAT 57.214 40.909 0.00 0.00 35.20 3.79
593 596 4.758674 ACTAACAGAGTAACAGTACGAGCA 59.241 41.667 0.00 0.00 36.27 4.26
594 597 5.122082 AGACTAACAGAGTAACAGTACGAGC 59.878 44.000 0.00 0.00 39.06 5.03
595 598 6.454054 CGAGACTAACAGAGTAACAGTACGAG 60.454 46.154 0.00 0.00 39.06 4.18
596 599 5.347093 CGAGACTAACAGAGTAACAGTACGA 59.653 44.000 0.00 0.00 39.06 3.43
597 600 5.347093 TCGAGACTAACAGAGTAACAGTACG 59.653 44.000 0.00 0.00 39.06 3.67
598 601 6.402011 GGTCGAGACTAACAGAGTAACAGTAC 60.402 46.154 3.09 0.00 39.06 2.73
599 602 5.641209 GGTCGAGACTAACAGAGTAACAGTA 59.359 44.000 3.09 0.00 39.06 2.74
600 603 4.455190 GGTCGAGACTAACAGAGTAACAGT 59.545 45.833 3.09 0.00 39.06 3.55
601 604 4.435784 CGGTCGAGACTAACAGAGTAACAG 60.436 50.000 3.09 0.00 39.06 3.16
602 605 3.434641 CGGTCGAGACTAACAGAGTAACA 59.565 47.826 3.09 0.00 39.06 2.41
603 606 3.181512 CCGGTCGAGACTAACAGAGTAAC 60.182 52.174 0.00 0.00 39.06 2.50
604 607 3.005554 CCGGTCGAGACTAACAGAGTAA 58.994 50.000 0.00 0.00 39.06 2.24
605 608 2.234661 TCCGGTCGAGACTAACAGAGTA 59.765 50.000 0.00 0.00 39.06 2.59
606 609 1.002888 TCCGGTCGAGACTAACAGAGT 59.997 52.381 0.00 0.00 42.90 3.24
607 610 1.735386 TCCGGTCGAGACTAACAGAG 58.265 55.000 0.00 0.00 0.00 3.35
608 611 2.189594 TTCCGGTCGAGACTAACAGA 57.810 50.000 0.00 0.00 0.00 3.41
614 617 0.611062 TGGTGATTCCGGTCGAGACT 60.611 55.000 0.00 0.00 39.52 3.24
618 621 2.355986 CCCTGGTGATTCCGGTCGA 61.356 63.158 0.00 0.00 40.86 4.20
622 625 0.394352 CCTTTCCCTGGTGATTCCGG 60.394 60.000 0.00 0.00 42.06 5.14
631 634 0.777446 TTCTTCCACCCTTTCCCTGG 59.223 55.000 0.00 0.00 0.00 4.45
633 636 2.073776 ACATTCTTCCACCCTTTCCCT 58.926 47.619 0.00 0.00 0.00 4.20
636 639 2.893489 AGCAACATTCTTCCACCCTTTC 59.107 45.455 0.00 0.00 0.00 2.62
646 649 5.769662 TGAGTGAATTGGTAGCAACATTCTT 59.230 36.000 9.99 0.00 0.00 2.52
659 662 3.691609 GGTTAAGGAGCTGAGTGAATTGG 59.308 47.826 0.00 0.00 0.00 3.16
667 670 4.141846 TGCAGAATAGGTTAAGGAGCTGAG 60.142 45.833 0.00 0.00 37.30 3.35
672 675 8.738645 AAAATACTGCAGAATAGGTTAAGGAG 57.261 34.615 23.35 0.00 0.00 3.69
703 710 0.033208 GGGAAGACATGATTGGGCCA 60.033 55.000 0.00 0.00 0.00 5.36
725 732 3.313012 TCTGTGTCTCAATGTTACCCG 57.687 47.619 0.00 0.00 0.00 5.28
728 735 7.254117 CGGACATATTCTGTGTCTCAATGTTAC 60.254 40.741 6.27 0.00 44.15 2.50
730 737 5.582269 CGGACATATTCTGTGTCTCAATGTT 59.418 40.000 6.27 0.00 44.15 2.71
733 740 5.344743 ACGGACATATTCTGTGTCTCAAT 57.655 39.130 6.27 0.00 42.76 2.57
734 741 4.381612 GGACGGACATATTCTGTGTCTCAA 60.382 45.833 6.27 0.00 44.56 3.02
768 775 4.393990 TCAGTCTGCAATGTAGCAAATGAG 59.606 41.667 0.00 0.00 45.13 2.90
769 776 4.154737 GTCAGTCTGCAATGTAGCAAATGA 59.845 41.667 0.00 0.00 45.13 2.57
776 783 6.044682 TCATACATGTCAGTCTGCAATGTAG 58.955 40.000 21.80 16.62 0.00 2.74
780 787 5.494724 AGTTCATACATGTCAGTCTGCAAT 58.505 37.500 0.00 0.00 0.00 3.56
783 790 6.758416 TGATAAGTTCATACATGTCAGTCTGC 59.242 38.462 0.00 0.00 0.00 4.26
785 792 7.489435 CGTTGATAAGTTCATACATGTCAGTCT 59.511 37.037 0.00 0.00 33.34 3.24
790 797 9.425893 CAAATCGTTGATAAGTTCATACATGTC 57.574 33.333 0.00 0.00 36.83 3.06
791 801 7.910162 GCAAATCGTTGATAAGTTCATACATGT 59.090 33.333 2.69 2.69 36.83 3.21
818 832 3.354948 AATAGCTGCATGTTCTCCACA 57.645 42.857 1.02 0.00 40.71 4.17
833 847 9.722056 CCAGTTCAGTTATGAATACAAAATAGC 57.278 33.333 0.00 0.00 46.75 2.97
837 851 7.446931 TCTGCCAGTTCAGTTATGAATACAAAA 59.553 33.333 0.00 0.00 46.75 2.44
840 854 6.048732 TCTGCCAGTTCAGTTATGAATACA 57.951 37.500 0.00 0.00 46.75 2.29
843 857 4.337555 GCATCTGCCAGTTCAGTTATGAAT 59.662 41.667 0.00 0.00 40.34 2.57
858 872 2.707849 CCCTGTTGCTGCATCTGCC 61.708 63.158 1.84 0.00 41.18 4.85
864 879 0.321919 GTGATCTCCCTGTTGCTGCA 60.322 55.000 0.00 0.00 0.00 4.41
867 882 7.291182 ACTTTATATAGTGATCTCCCTGTTGCT 59.709 37.037 0.00 0.00 0.00 3.91
869 884 7.810282 CGACTTTATATAGTGATCTCCCTGTTG 59.190 40.741 0.09 0.00 0.00 3.33
870 885 7.724506 TCGACTTTATATAGTGATCTCCCTGTT 59.275 37.037 0.09 0.00 0.00 3.16
871 886 7.175293 GTCGACTTTATATAGTGATCTCCCTGT 59.825 40.741 8.70 0.00 0.00 4.00
872 887 7.362229 GGTCGACTTTATATAGTGATCTCCCTG 60.362 44.444 16.46 0.00 0.00 4.45
873 888 6.660094 GGTCGACTTTATATAGTGATCTCCCT 59.340 42.308 16.46 0.00 0.00 4.20
874 889 6.127675 GGGTCGACTTTATATAGTGATCTCCC 60.128 46.154 16.46 0.00 0.00 4.30
875 890 6.660094 AGGGTCGACTTTATATAGTGATCTCC 59.340 42.308 16.46 1.44 0.00 3.71
876 891 7.531716 CAGGGTCGACTTTATATAGTGATCTC 58.468 42.308 16.46 0.00 0.00 2.75
921 936 3.703556 TGGTTTGTTTGCCTCTTGATTGA 59.296 39.130 0.00 0.00 0.00 2.57
922 937 4.053295 CTGGTTTGTTTGCCTCTTGATTG 58.947 43.478 0.00 0.00 0.00 2.67
923 938 3.493176 GCTGGTTTGTTTGCCTCTTGATT 60.493 43.478 0.00 0.00 0.00 2.57
925 940 1.408702 GCTGGTTTGTTTGCCTCTTGA 59.591 47.619 0.00 0.00 0.00 3.02
926 941 1.856802 GCTGGTTTGTTTGCCTCTTG 58.143 50.000 0.00 0.00 0.00 3.02
927 942 0.385390 CGCTGGTTTGTTTGCCTCTT 59.615 50.000 0.00 0.00 0.00 2.85
945 963 5.165911 TCTTATTCTCCGTTGCTACTACG 57.834 43.478 0.00 0.00 38.67 3.51
957 978 6.295719 TGAACTGTAACCCTCTTATTCTCC 57.704 41.667 0.00 0.00 0.00 3.71
958 979 7.612677 TCTTGAACTGTAACCCTCTTATTCTC 58.387 38.462 0.00 0.00 0.00 2.87
986 1013 5.657474 CGGTAACCATCTTAGCTACTGAAA 58.343 41.667 0.00 0.00 0.00 2.69
1004 1031 2.434185 CCAGAGCGCTTGCGGTAA 60.434 61.111 19.41 0.00 45.69 2.85
1050 1077 1.261480 CGATATGGGAGGTGGAGAGG 58.739 60.000 0.00 0.00 0.00 3.69
1070 1097 3.062466 CCGAGCGGAGTGAGGACA 61.062 66.667 2.00 0.00 37.50 4.02
1109 1136 3.181461 CGACTTTCCTGGAAGATAGCCAT 60.181 47.826 9.42 0.00 34.07 4.40
1152 1179 0.179029 CCTCACAACAGTCCGGGTTT 60.179 55.000 0.00 0.00 0.00 3.27
1153 1180 1.052124 TCCTCACAACAGTCCGGGTT 61.052 55.000 0.00 0.00 0.00 4.11
1231 1258 2.641305 GAAGCTGTTCAGCATCAGGAT 58.359 47.619 23.69 1.65 37.25 3.24
1234 1261 1.659601 CTCGAAGCTGTTCAGCATCAG 59.340 52.381 23.69 16.96 37.25 2.90
1238 1265 1.606480 CCTTCTCGAAGCTGTTCAGCA 60.606 52.381 23.69 5.20 37.11 4.41
1242 1269 0.320771 TGCCCTTCTCGAAGCTGTTC 60.321 55.000 1.13 0.00 37.11 3.18
1302 1329 0.039617 CGACCATCTCCTCATCGCTC 60.040 60.000 0.00 0.00 0.00 5.03
1405 1432 0.036164 CATTCGTCCACCACCTTGGA 59.964 55.000 0.00 0.00 43.83 3.53
1427 1454 1.287425 GTTACAGCCATACACGGAGC 58.713 55.000 0.00 0.00 0.00 4.70
1444 1471 4.110482 GGCTCGTAATTGTGATAGTCGTT 58.890 43.478 0.00 0.00 0.00 3.85
1450 1477 3.897141 TGGTGGCTCGTAATTGTGATA 57.103 42.857 0.00 0.00 0.00 2.15
1452 1479 2.290008 ACATGGTGGCTCGTAATTGTGA 60.290 45.455 0.00 0.00 0.00 3.58
1458 1485 4.294523 GCACATGGTGGCTCGTAA 57.705 55.556 0.00 0.00 33.64 3.18
1470 1497 3.058293 CGTTGACTATGTTGTTGGCACAT 60.058 43.478 0.00 0.00 39.30 3.21
1485 1512 1.757682 CTCCTAGAGAGGCGTTGACT 58.242 55.000 0.00 0.00 43.40 3.41
1499 1526 1.069513 CCAACACGTTCCACACTCCTA 59.930 52.381 0.00 0.00 0.00 2.94
1500 1527 0.179056 CCAACACGTTCCACACTCCT 60.179 55.000 0.00 0.00 0.00 3.69
1502 1529 1.164041 CCCCAACACGTTCCACACTC 61.164 60.000 0.00 0.00 0.00 3.51
1503 1530 1.153046 CCCCAACACGTTCCACACT 60.153 57.895 0.00 0.00 0.00 3.55
1514 1541 2.144078 TTCTGGTCGAGCCCCAACA 61.144 57.895 12.85 0.00 36.04 3.33
1537 1564 2.005266 AGGTGATGCCCTCCATGCT 61.005 57.895 0.00 0.00 38.26 3.79
1574 1601 4.677584 CCCATGTTTGTTTTGAGAACGAA 58.322 39.130 0.00 0.00 0.00 3.85
1576 1603 2.794350 GCCCATGTTTGTTTTGAGAACG 59.206 45.455 0.00 0.00 0.00 3.95
1577 1604 2.794350 CGCCCATGTTTGTTTTGAGAAC 59.206 45.455 0.00 0.00 0.00 3.01
1578 1605 2.801342 GCGCCCATGTTTGTTTTGAGAA 60.801 45.455 0.00 0.00 0.00 2.87
1580 1607 1.139163 GCGCCCATGTTTGTTTTGAG 58.861 50.000 0.00 0.00 0.00 3.02
1613 1644 1.374252 CGGCAAAGTGGTACGAGCT 60.374 57.895 0.00 0.00 0.00 4.09
1629 1660 2.579207 ATTACATGACACTCGACCGG 57.421 50.000 0.00 0.00 0.00 5.28
1777 1809 3.069980 GCGCTGACTGGACGGAGAT 62.070 63.158 0.00 0.00 0.00 2.75
1816 1848 3.260632 GGGGCAAAAATGTCCACAGTAAT 59.739 43.478 1.48 0.00 34.69 1.89
1822 1854 1.000843 GACAGGGGCAAAAATGTCCAC 59.999 52.381 1.48 0.00 36.83 4.02
1846 1878 6.856757 AGGACGAAGGGGTATTAAGTATAGA 58.143 40.000 0.00 0.00 0.00 1.98
1853 1885 4.472108 ACATTGAGGACGAAGGGGTATTAA 59.528 41.667 0.00 0.00 0.00 1.40
1909 1941 1.745489 CTCCTTTTTCCTCGCCGGG 60.745 63.158 2.18 0.00 0.00 5.73
1945 1977 2.579201 GCTCCTTGCTCTACCGCA 59.421 61.111 0.00 0.00 38.95 5.69
2153 2193 4.734398 AAATGCTCCAATCCGCAATAAA 57.266 36.364 0.00 0.00 39.89 1.40
2196 2236 1.607467 GGCAGGAACAAGGCCATGT 60.607 57.895 8.06 8.06 46.92 3.21
2299 2339 9.193806 AGAGATTGCATAAACACCATCTAAAAT 57.806 29.630 0.00 0.00 0.00 1.82
2410 2450 4.081476 GCAGGTCTTCAAAATTAAGGGCAT 60.081 41.667 0.00 0.00 0.00 4.40
2419 2459 1.267806 CTGCGTGCAGGTCTTCAAAAT 59.732 47.619 14.00 0.00 40.17 1.82
2447 2487 2.098770 GTGGCTTCTGATCCATCTTTGC 59.901 50.000 3.05 0.00 34.47 3.68
2453 2493 3.118884 GCATTTTGTGGCTTCTGATCCAT 60.119 43.478 3.05 0.00 34.47 3.41
2486 2526 7.867403 GCAAGATTTTTCTTTGACAACTCCATA 59.133 33.333 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.