Multiple sequence alignment - TraesCS2D01G286400

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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 TraesCS2D01G286400 chr2D 100.000 5320 0 0 2632 7951 366091119 366096438 0.000000e+00 9825.0
1 TraesCS2D01G286400 chr2D 100.000 2324 0 0 1 2324 366088488 366090811 0.000000e+00 4292.0
2 TraesCS2D01G286400 chr2D 93.139 583 26 10 1 580 619872840 619872269 0.000000e+00 843.0
3 TraesCS2D01G286400 chr2D 92.281 583 27 12 1 580 602575960 602576527 0.000000e+00 811.0
4 TraesCS2D01G286400 chr2D 90.492 589 38 12 1 580 435156441 435157020 0.000000e+00 761.0
5 TraesCS2D01G286400 chr2D 88.147 464 42 5 7200 7653 28854400 28854860 2.520000e-149 540.0
6 TraesCS2D01G286400 chr2A 97.505 4328 76 10 2632 6958 494956377 494960673 0.000000e+00 7365.0
7 TraesCS2D01G286400 chr2A 97.752 1112 19 5 883 1988 494955130 494956241 0.000000e+00 1910.0
8 TraesCS2D01G286400 chr2A 98.492 199 3 0 6992 7190 494960674 494960872 1.270000e-92 351.0
9 TraesCS2D01G286400 chr2A 88.889 144 13 3 6498 6639 744446300 744446442 2.950000e-39 174.0
10 TraesCS2D01G286400 chr2A 91.176 102 8 1 577 677 494951969 494952070 3.870000e-28 137.0
11 TraesCS2D01G286400 chr2B 95.626 4504 143 23 2698 7190 434691136 434695596 0.000000e+00 7177.0
12 TraesCS2D01G286400 chr2B 95.632 847 29 3 1473 2319 434689896 434690734 0.000000e+00 1352.0
13 TraesCS2D01G286400 chr2B 96.333 600 17 3 881 1476 434689263 434689861 0.000000e+00 981.0
14 TraesCS2D01G286400 chr2B 94.702 151 8 0 7699 7849 146778084 146777934 1.330000e-57 235.0
15 TraesCS2D01G286400 chr2B 93.069 101 7 0 577 677 434689114 434689214 1.790000e-31 148.0
16 TraesCS2D01G286400 chr2B 100.000 28 0 0 679 706 434689241 434689268 1.400000e-02 52.8
17 TraesCS2D01G286400 chr7D 88.129 775 62 12 7200 7950 161474851 161475619 0.000000e+00 894.0
18 TraesCS2D01G286400 chr7D 89.674 184 14 4 706 884 509584384 509584567 6.210000e-56 230.0
19 TraesCS2D01G286400 chr7D 89.362 141 13 2 6499 6637 246808015 246807875 8.200000e-40 176.0
20 TraesCS2D01G286400 chr4D 91.809 586 35 8 1 582 110190667 110191243 0.000000e+00 804.0
21 TraesCS2D01G286400 chr1D 91.092 595 31 10 2 586 318553342 318552760 0.000000e+00 785.0
22 TraesCS2D01G286400 chr5D 90.604 596 42 8 1 587 439601299 439601889 0.000000e+00 778.0
23 TraesCS2D01G286400 chr5D 84.940 498 48 17 7197 7681 389235315 389235798 5.580000e-131 479.0
24 TraesCS2D01G286400 chr3D 90.741 594 38 9 1 584 575771725 575771139 0.000000e+00 776.0
25 TraesCS2D01G286400 chr3D 89.799 598 41 9 1 586 605131291 605131880 0.000000e+00 749.0
26 TraesCS2D01G286400 chr3D 89.247 465 35 7 7200 7653 120884023 120883563 1.160000e-157 568.0
27 TraesCS2D01G286400 chr3D 90.000 190 14 4 702 886 459959595 459959406 2.870000e-59 241.0
28 TraesCS2D01G286400 chr3A 90.273 586 42 8 1 583 749816530 749815957 0.000000e+00 752.0
29 TraesCS2D01G286400 chr3A 88.235 425 41 7 7200 7621 468531363 468530945 4.280000e-137 499.0
30 TraesCS2D01G286400 chr6A 90.047 422 37 1 7200 7621 36083247 36083663 7.020000e-150 542.0
31 TraesCS2D01G286400 chr6A 90.845 142 12 1 6498 6638 412366252 412366393 1.050000e-43 189.0
32 TraesCS2D01G286400 chr7A 87.041 463 49 5 7200 7653 194005673 194005213 5.500000e-141 512.0
33 TraesCS2D01G286400 chr7A 86.792 265 12 3 7699 7947 288052262 288052005 2.830000e-69 274.0
34 TraesCS2D01G286400 chr6D 86.784 454 42 12 7200 7648 202982026 202981586 2.580000e-134 490.0
35 TraesCS2D01G286400 chr6D 91.549 142 9 3 6495 6634 304115557 304115697 8.140000e-45 193.0
36 TraesCS2D01G286400 chr6D 90.909 143 11 2 6498 6639 303623272 303623413 2.930000e-44 191.0
37 TraesCS2D01G286400 chr3B 84.538 498 55 14 7196 7682 506969760 506970246 2.600000e-129 473.0
38 TraesCS2D01G286400 chr3B 97.419 155 4 0 7699 7853 808662379 808662533 1.700000e-66 265.0
39 TraesCS2D01G286400 chr3B 90.000 190 13 4 703 887 647147629 647147441 2.870000e-59 241.0
40 TraesCS2D01G286400 chr7B 90.079 252 11 5 7699 7936 654134819 654134568 1.670000e-81 315.0
41 TraesCS2D01G286400 chr5B 95.431 197 8 1 7699 7895 548247433 548247238 5.990000e-81 313.0
42 TraesCS2D01G286400 chr5B 89.894 188 13 5 704 886 487329534 487329348 3.710000e-58 237.0
43 TraesCS2D01G286400 chr1B 91.005 189 11 4 703 886 90423889 90423702 4.760000e-62 250.0
44 TraesCS2D01G286400 chr1B 89.894 188 14 3 704 886 28519864 28519677 3.710000e-58 237.0
45 TraesCS2D01G286400 chr1A 91.398 186 11 3 705 885 360460147 360459962 4.760000e-62 250.0
46 TraesCS2D01G286400 chr4B 90.659 182 12 3 708 884 621703413 621703594 3.710000e-58 237.0
47 TraesCS2D01G286400 chr5A 89.474 190 15 4 704 888 448995672 448995861 1.330000e-57 235.0
48 TraesCS2D01G286400 chr6B 88.811 143 15 1 6498 6639 469288127 469288269 2.950000e-39 174.0
49 TraesCS2D01G286400 chr6B 88.276 145 15 2 6495 6637 469786868 469787012 1.060000e-38 172.0


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 TraesCS2D01G286400 chr2D 366088488 366096438 7950 False 7058.50 9825 100.00000 1 7951 2 chr2D.!!$F4 7950
1 TraesCS2D01G286400 chr2D 619872269 619872840 571 True 843.00 843 93.13900 1 580 1 chr2D.!!$R1 579
2 TraesCS2D01G286400 chr2D 602575960 602576527 567 False 811.00 811 92.28100 1 580 1 chr2D.!!$F3 579
3 TraesCS2D01G286400 chr2D 435156441 435157020 579 False 761.00 761 90.49200 1 580 1 chr2D.!!$F2 579
4 TraesCS2D01G286400 chr2A 494951969 494960872 8903 False 2440.75 7365 96.23125 577 7190 4 chr2A.!!$F2 6613
5 TraesCS2D01G286400 chr2B 434689114 434695596 6482 False 1942.16 7177 96.13200 577 7190 5 chr2B.!!$F1 6613
6 TraesCS2D01G286400 chr7D 161474851 161475619 768 False 894.00 894 88.12900 7200 7950 1 chr7D.!!$F1 750
7 TraesCS2D01G286400 chr4D 110190667 110191243 576 False 804.00 804 91.80900 1 582 1 chr4D.!!$F1 581
8 TraesCS2D01G286400 chr1D 318552760 318553342 582 True 785.00 785 91.09200 2 586 1 chr1D.!!$R1 584
9 TraesCS2D01G286400 chr5D 439601299 439601889 590 False 778.00 778 90.60400 1 587 1 chr5D.!!$F2 586
10 TraesCS2D01G286400 chr3D 575771139 575771725 586 True 776.00 776 90.74100 1 584 1 chr3D.!!$R3 583
11 TraesCS2D01G286400 chr3D 605131291 605131880 589 False 749.00 749 89.79900 1 586 1 chr3D.!!$F1 585
12 TraesCS2D01G286400 chr3A 749815957 749816530 573 True 752.00 752 90.27300 1 583 1 chr3A.!!$R2 582

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
870 923 0.833287 GCATCTCTCTAAGCACCCCA 59.167 55.000 0.00 0.00 0.00 4.96 F
2094 5026 0.035317 TCAATGAGTCCACTTGCGCT 59.965 50.000 9.73 0.00 0.00 5.92 F
2257 5189 1.003580 CTCAGTATGCAACCCACACCT 59.996 52.381 0.00 0.00 34.76 4.00 F
2744 5702 2.886913 TGATTTTGTTGATGCCCTGGA 58.113 42.857 0.00 0.00 0.00 3.86 F
3883 6851 3.879892 GGATTCAACATACAAGGAGCTCC 59.120 47.826 26.22 26.22 0.00 4.70 F
5475 8444 0.767375 AGAAGGAGCTTGGTCTTGCA 59.233 50.000 0.00 0.00 0.00 4.08 F
6225 9196 1.270625 TGGTCGCTTGTAGGTCCAAAG 60.271 52.381 0.00 0.00 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 5029 1.269723 TGACTAGCAGTGAGTGGTTCG 59.730 52.381 0.00 0.0 38.14 3.95 R
3022 5981 6.043243 AGGAGGAGAAAAACACAAGTAGATGA 59.957 38.462 0.00 0.0 0.00 2.92 R
3931 6899 9.573133 GCAGCAAGATAAATAAGTACATTTTGT 57.427 29.630 0.00 0.0 30.84 2.83 R
4473 7441 0.037232 ACAGCTTCACCGAGCCTAAC 60.037 55.000 0.00 0.0 43.74 2.34 R
5587 8557 0.539438 GTTTCACCCATGGCCTGTCA 60.539 55.000 6.09 0.0 0.00 3.58 R
6584 9557 0.109735 GCTCGCCAACTAAACTTGCC 60.110 55.000 0.00 0.0 0.00 4.52 R
7500 10496 0.243636 ATCACACGAGCACGACATCA 59.756 50.000 11.40 0.0 42.66 3.07 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
69 70 2.753043 GGGACGACTACCTCCGCA 60.753 66.667 0.00 0.00 0.00 5.69
289 299 1.400113 CGACTACACGCGGTTCTACAA 60.400 52.381 12.47 0.00 0.00 2.41
413 430 7.542534 TTTTAAATATGTATGAACTCGCCGT 57.457 32.000 0.00 0.00 0.00 5.68
440 459 3.130516 TGGTTGAATTTGCCGTGTTTGTA 59.869 39.130 0.00 0.00 0.00 2.41
443 462 2.688446 TGAATTTGCCGTGTTTGTACCA 59.312 40.909 0.00 0.00 0.00 3.25
449 469 2.952978 TGCCGTGTTTGTACCAGAATTT 59.047 40.909 0.00 0.00 0.00 1.82
629 657 1.029681 CACGTGGATGGGTAGATCGA 58.970 55.000 7.95 0.00 0.00 3.59
632 660 1.599667 CGTGGATGGGTAGATCGAACG 60.600 57.143 0.00 0.00 31.16 3.95
655 683 1.669760 GCGTCCATCCAACGGTCAA 60.670 57.895 0.00 0.00 40.41 3.18
668 696 2.264794 GTCAACCAGGCGACGGAT 59.735 61.111 6.14 0.00 0.00 4.18
677 730 2.550978 CAGGCGACGGATGTTTTCTAT 58.449 47.619 0.00 0.00 0.00 1.98
712 765 5.371115 TTTTTCGACTTCATTAGGCCTTG 57.629 39.130 12.58 3.71 0.00 3.61
714 767 4.811969 TTCGACTTCATTAGGCCTTGTA 57.188 40.909 12.58 0.00 0.00 2.41
715 768 4.119442 TCGACTTCATTAGGCCTTGTAC 57.881 45.455 12.58 0.00 0.00 2.90
717 770 4.020928 TCGACTTCATTAGGCCTTGTACAA 60.021 41.667 12.58 8.28 0.00 2.41
718 771 4.876107 CGACTTCATTAGGCCTTGTACAAT 59.124 41.667 12.58 0.00 0.00 2.71
719 772 5.220662 CGACTTCATTAGGCCTTGTACAATG 60.221 44.000 12.58 14.94 0.00 2.82
720 773 5.570320 ACTTCATTAGGCCTTGTACAATGT 58.430 37.500 12.58 0.00 0.00 2.71
721 774 5.415701 ACTTCATTAGGCCTTGTACAATGTG 59.584 40.000 12.58 13.53 0.00 3.21
722 775 5.172687 TCATTAGGCCTTGTACAATGTGA 57.827 39.130 12.58 3.20 0.00 3.58
723 776 5.185454 TCATTAGGCCTTGTACAATGTGAG 58.815 41.667 12.58 0.00 0.00 3.51
724 777 2.496899 AGGCCTTGTACAATGTGAGG 57.503 50.000 9.13 7.48 0.00 3.86
725 778 1.705186 AGGCCTTGTACAATGTGAGGT 59.295 47.619 9.13 0.00 0.00 3.85
726 779 1.812571 GGCCTTGTACAATGTGAGGTG 59.187 52.381 9.13 0.00 0.00 4.00
728 781 2.783135 CCTTGTACAATGTGAGGTGCT 58.217 47.619 9.13 0.00 0.00 4.40
730 783 4.323417 CCTTGTACAATGTGAGGTGCTTA 58.677 43.478 9.13 0.00 0.00 3.09
731 784 4.393062 CCTTGTACAATGTGAGGTGCTTAG 59.607 45.833 9.13 0.00 0.00 2.18
732 785 4.882842 TGTACAATGTGAGGTGCTTAGA 57.117 40.909 0.00 0.00 0.00 2.10
733 786 4.820897 TGTACAATGTGAGGTGCTTAGAG 58.179 43.478 0.00 0.00 0.00 2.43
734 787 4.526650 TGTACAATGTGAGGTGCTTAGAGA 59.473 41.667 0.00 0.00 0.00 3.10
735 788 4.623932 ACAATGTGAGGTGCTTAGAGAA 57.376 40.909 0.00 0.00 0.00 2.87
736 789 4.973168 ACAATGTGAGGTGCTTAGAGAAA 58.027 39.130 0.00 0.00 0.00 2.52
737 790 5.564550 ACAATGTGAGGTGCTTAGAGAAAT 58.435 37.500 0.00 0.00 0.00 2.17
738 791 6.711277 ACAATGTGAGGTGCTTAGAGAAATA 58.289 36.000 0.00 0.00 0.00 1.40
739 792 7.168219 ACAATGTGAGGTGCTTAGAGAAATAA 58.832 34.615 0.00 0.00 0.00 1.40
740 793 7.665559 ACAATGTGAGGTGCTTAGAGAAATAAA 59.334 33.333 0.00 0.00 0.00 1.40
741 794 7.617041 ATGTGAGGTGCTTAGAGAAATAAAC 57.383 36.000 0.00 0.00 0.00 2.01
744 797 6.092807 GTGAGGTGCTTAGAGAAATAAACCAG 59.907 42.308 0.00 0.00 0.00 4.00
745 798 6.128138 AGGTGCTTAGAGAAATAAACCAGT 57.872 37.500 0.00 0.00 0.00 4.00
746 799 6.543735 AGGTGCTTAGAGAAATAAACCAGTT 58.456 36.000 0.00 0.00 0.00 3.16
747 800 7.004691 AGGTGCTTAGAGAAATAAACCAGTTT 58.995 34.615 0.86 0.86 36.63 2.66
748 801 7.505923 AGGTGCTTAGAGAAATAAACCAGTTTT 59.494 33.333 0.37 0.00 34.23 2.43
778 831 4.014847 CACCGGTGCTTATTTGTACATG 57.985 45.455 24.02 0.00 0.00 3.21
779 832 3.687212 CACCGGTGCTTATTTGTACATGA 59.313 43.478 24.02 0.00 0.00 3.07
780 833 4.335315 CACCGGTGCTTATTTGTACATGAT 59.665 41.667 24.02 0.00 0.00 2.45
781 834 5.525745 CACCGGTGCTTATTTGTACATGATA 59.474 40.000 24.02 0.00 0.00 2.15
782 835 6.204688 CACCGGTGCTTATTTGTACATGATAT 59.795 38.462 24.02 0.00 0.00 1.63
783 836 7.386573 CACCGGTGCTTATTTGTACATGATATA 59.613 37.037 24.02 0.00 0.00 0.86
784 837 7.386848 ACCGGTGCTTATTTGTACATGATATAC 59.613 37.037 6.12 0.00 0.00 1.47
787 840 7.117812 GGTGCTTATTTGTACATGATATACGCT 59.882 37.037 0.00 0.00 0.00 5.07
789 842 8.708742 TGCTTATTTGTACATGATATACGCTTC 58.291 33.333 0.00 0.00 0.00 3.86
790 843 8.708742 GCTTATTTGTACATGATATACGCTTCA 58.291 33.333 0.00 0.00 0.00 3.02
794 847 9.758651 ATTTGTACATGATATACGCTTCACTAA 57.241 29.630 0.00 0.00 0.00 2.24
795 848 8.797266 TTGTACATGATATACGCTTCACTAAG 57.203 34.615 0.00 0.00 35.68 2.18
807 860 4.167554 CTTCACTAAGCGTCTCTTCTGT 57.832 45.455 0.00 0.00 36.25 3.41
808 861 5.298197 CTTCACTAAGCGTCTCTTCTGTA 57.702 43.478 0.00 0.00 36.25 2.74
809 862 4.948608 TCACTAAGCGTCTCTTCTGTAG 57.051 45.455 0.00 0.00 36.25 2.74
810 863 4.576879 TCACTAAGCGTCTCTTCTGTAGA 58.423 43.478 0.00 0.00 36.25 2.59
811 864 5.001874 TCACTAAGCGTCTCTTCTGTAGAA 58.998 41.667 0.00 0.00 36.25 2.10
812 865 5.472478 TCACTAAGCGTCTCTTCTGTAGAAA 59.528 40.000 0.00 0.00 36.25 2.52
813 866 6.151312 TCACTAAGCGTCTCTTCTGTAGAAAT 59.849 38.462 0.00 0.00 36.25 2.17
815 868 7.642194 CACTAAGCGTCTCTTCTGTAGAAATAG 59.358 40.741 0.00 0.00 36.25 1.73
816 869 5.508200 AGCGTCTCTTCTGTAGAAATAGG 57.492 43.478 0.00 0.00 33.07 2.57
817 870 4.045783 GCGTCTCTTCTGTAGAAATAGGC 58.954 47.826 0.00 0.00 33.07 3.93
818 871 4.440250 GCGTCTCTTCTGTAGAAATAGGCA 60.440 45.833 8.22 0.00 33.07 4.75
819 872 5.038033 CGTCTCTTCTGTAGAAATAGGCAC 58.962 45.833 8.22 0.58 33.07 5.01
820 873 5.353111 GTCTCTTCTGTAGAAATAGGCACC 58.647 45.833 0.00 0.00 33.07 5.01
821 874 4.098044 TCTCTTCTGTAGAAATAGGCACCG 59.902 45.833 0.00 0.00 33.07 4.94
822 875 3.132289 TCTTCTGTAGAAATAGGCACCGG 59.868 47.826 0.00 0.00 33.07 5.28
823 876 2.463752 TCTGTAGAAATAGGCACCGGT 58.536 47.619 0.00 0.00 0.00 5.28
824 877 2.167693 TCTGTAGAAATAGGCACCGGTG 59.832 50.000 30.66 30.66 0.00 4.94
835 888 1.569493 CACCGGTGCTTCAGAAACG 59.431 57.895 24.02 0.00 0.00 3.60
836 889 2.251642 ACCGGTGCTTCAGAAACGC 61.252 57.895 6.12 0.00 0.00 4.84
837 890 2.556287 CGGTGCTTCAGAAACGCC 59.444 61.111 6.12 6.12 0.00 5.68
838 891 2.954611 GGTGCTTCAGAAACGCCC 59.045 61.111 4.96 0.00 0.00 6.13
839 892 2.556287 GTGCTTCAGAAACGCCCG 59.444 61.111 0.00 0.00 0.00 6.13
840 893 2.668212 TGCTTCAGAAACGCCCGG 60.668 61.111 0.00 0.00 0.00 5.73
841 894 2.668550 GCTTCAGAAACGCCCGGT 60.669 61.111 0.00 0.00 0.00 5.28
842 895 2.258726 GCTTCAGAAACGCCCGGTT 61.259 57.895 0.00 0.00 41.76 4.44
867 920 6.743575 TTTTTAAGCATCTCTCTAAGCACC 57.256 37.500 0.00 0.00 0.00 5.01
868 921 2.998316 AAGCATCTCTCTAAGCACCC 57.002 50.000 0.00 0.00 0.00 4.61
869 922 1.127343 AGCATCTCTCTAAGCACCCC 58.873 55.000 0.00 0.00 0.00 4.95
870 923 0.833287 GCATCTCTCTAAGCACCCCA 59.167 55.000 0.00 0.00 0.00 4.96
871 924 1.419387 GCATCTCTCTAAGCACCCCAT 59.581 52.381 0.00 0.00 0.00 4.00
872 925 2.158696 GCATCTCTCTAAGCACCCCATT 60.159 50.000 0.00 0.00 0.00 3.16
874 927 2.551270 TCTCTCTAAGCACCCCATTGT 58.449 47.619 0.00 0.00 0.00 2.71
875 928 3.719871 TCTCTCTAAGCACCCCATTGTA 58.280 45.455 0.00 0.00 0.00 2.41
876 929 3.451178 TCTCTCTAAGCACCCCATTGTAC 59.549 47.826 0.00 0.00 0.00 2.90
877 930 3.178046 TCTCTAAGCACCCCATTGTACA 58.822 45.455 0.00 0.00 0.00 2.90
878 931 3.585289 TCTCTAAGCACCCCATTGTACAA 59.415 43.478 11.41 11.41 0.00 2.41
880 933 2.675658 AAGCACCCCATTGTACAAGT 57.324 45.000 14.65 3.43 0.00 3.16
881 934 2.200373 AGCACCCCATTGTACAAGTC 57.800 50.000 14.65 1.82 0.00 3.01
884 937 2.817839 GCACCCCATTGTACAAGTCCTT 60.818 50.000 14.65 0.00 0.00 3.36
885 938 3.560453 GCACCCCATTGTACAAGTCCTTA 60.560 47.826 14.65 0.00 0.00 2.69
900 3785 7.023120 ACAAGTCCTTATTATCCAGGCCTATA 58.977 38.462 3.98 0.00 0.00 1.31
1071 3957 2.543797 CCCACCCCAAACCCTAGCA 61.544 63.158 0.00 0.00 0.00 3.49
1434 4323 2.757508 TGGCGAGAGAGGCTCCAG 60.758 66.667 11.71 1.25 40.70 3.86
1639 4566 7.203910 AGCGATCGTCTTTCTAGTTAAATCAT 58.796 34.615 17.81 0.00 0.00 2.45
1765 4697 6.113411 GCTGCCTTAAATTCTACTACTTCCA 58.887 40.000 0.00 0.00 0.00 3.53
1792 4724 2.972348 ACTGTAGGTCTCCAAGGTGAA 58.028 47.619 0.00 0.00 0.00 3.18
1992 4924 1.043816 CACACTGTGACTCAGAGGGT 58.956 55.000 15.86 5.25 42.18 4.34
2054 4986 6.463190 CCCCTCTTAGTTACAGAAGGAATAGC 60.463 46.154 0.00 0.00 0.00 2.97
2055 4987 6.098409 CCCTCTTAGTTACAGAAGGAATAGCA 59.902 42.308 0.00 0.00 0.00 3.49
2056 4988 7.364762 CCCTCTTAGTTACAGAAGGAATAGCAA 60.365 40.741 0.00 0.00 0.00 3.91
2057 4989 7.492994 CCTCTTAGTTACAGAAGGAATAGCAAC 59.507 40.741 0.00 0.00 0.00 4.17
2094 5026 0.035317 TCAATGAGTCCACTTGCGCT 59.965 50.000 9.73 0.00 0.00 5.92
2097 5029 3.426568 GAGTCCACTTGCGCTGCC 61.427 66.667 9.73 0.00 0.00 4.85
2185 5117 7.435068 GCCTATGGCGATAAATAAGAAAGAA 57.565 36.000 0.00 0.00 39.62 2.52
2193 5125 8.626526 GGCGATAAATAAGAAAGAAAATGGGTA 58.373 33.333 0.00 0.00 0.00 3.69
2222 5154 5.705609 AAGCAAAATGATGGTAGACGTTT 57.294 34.783 0.00 0.00 0.00 3.60
2257 5189 1.003580 CTCAGTATGCAACCCACACCT 59.996 52.381 0.00 0.00 34.76 4.00
2301 5234 5.247110 AGTCAACCAACTCAGACACTCATAT 59.753 40.000 0.00 0.00 33.56 1.78
2744 5702 2.886913 TGATTTTGTTGATGCCCTGGA 58.113 42.857 0.00 0.00 0.00 3.86
2907 5866 6.506147 TCCAAATCCATGCATTTAAATCTCG 58.494 36.000 0.00 0.00 0.00 4.04
3259 6218 4.908601 ATACATTGTCACCACAGAAGGA 57.091 40.909 0.00 0.00 32.71 3.36
3815 6783 8.538409 ACATATGAAAAACTCTTTTTGATGGC 57.462 30.769 10.38 0.00 42.51 4.40
3816 6784 8.149647 ACATATGAAAAACTCTTTTTGATGGCA 58.850 29.630 10.38 0.00 42.51 4.92
3817 6785 9.158233 CATATGAAAAACTCTTTTTGATGGCAT 57.842 29.630 0.00 0.00 42.51 4.40
3818 6786 9.729281 ATATGAAAAACTCTTTTTGATGGCATT 57.271 25.926 0.00 0.00 42.51 3.56
3819 6787 7.249186 TGAAAAACTCTTTTTGATGGCATTG 57.751 32.000 0.00 0.00 42.51 2.82
3883 6851 3.879892 GGATTCAACATACAAGGAGCTCC 59.120 47.826 26.22 26.22 0.00 4.70
3931 6899 4.934797 ATCTTCTCCTTTCCACCATCAA 57.065 40.909 0.00 0.00 0.00 2.57
4473 7441 1.339610 CAGGAAGATCCGCCACTAGAG 59.660 57.143 0.00 0.00 42.75 2.43
4733 7701 3.952323 CTGATTGTTGGGATGCAGAGATT 59.048 43.478 0.00 0.00 0.00 2.40
4827 7795 5.708697 TCGGTATGTATCATCATTCGGTAGT 59.291 40.000 0.00 0.00 0.00 2.73
4928 7896 2.683867 TGTTGGAAAACCACTTGTACGG 59.316 45.455 0.00 0.00 0.00 4.02
5184 8152 5.280164 TGTGTGAAGTGTATTTTGCACATG 58.720 37.500 0.00 0.00 38.35 3.21
5301 8269 2.769095 GAGAAGTGGAGGTGAGGCTTAT 59.231 50.000 0.00 0.00 0.00 1.73
5397 8366 7.361286 GCTTTGGTGAGTTTCTCGAATTATCTT 60.361 37.037 0.00 0.00 32.35 2.40
5475 8444 0.767375 AGAAGGAGCTTGGTCTTGCA 59.233 50.000 0.00 0.00 0.00 4.08
5566 8536 3.641437 TCTTATTGCTGTTGTGTTGGC 57.359 42.857 0.00 0.00 0.00 4.52
5587 8557 3.139077 CCAACACTTAAGTTTCTCCGCT 58.861 45.455 5.07 0.00 0.00 5.52
6225 9196 1.270625 TGGTCGCTTGTAGGTCCAAAG 60.271 52.381 0.00 0.00 0.00 2.77
6310 9283 8.477256 TGATATTTACCGCATGAGATATCATCA 58.523 33.333 11.84 6.43 33.77 3.07
6397 9370 7.341769 TCAGTGGATTATTTTATTGGAACCTGG 59.658 37.037 0.00 0.00 0.00 4.45
6440 9413 8.867112 ACATGTTTCTATTGAATGAATCATGC 57.133 30.769 23.09 0.00 45.09 4.06
6579 9552 3.935828 TCATGGCAATTTATGTTCGTCGA 59.064 39.130 0.00 0.00 0.00 4.20
6580 9553 4.033932 TCATGGCAATTTATGTTCGTCGAG 59.966 41.667 0.00 0.00 0.00 4.04
6581 9554 2.675844 TGGCAATTTATGTTCGTCGAGG 59.324 45.455 0.00 0.00 0.00 4.63
6582 9555 2.933906 GGCAATTTATGTTCGTCGAGGA 59.066 45.455 3.17 3.17 0.00 3.71
6583 9556 3.560068 GGCAATTTATGTTCGTCGAGGAT 59.440 43.478 8.88 0.00 0.00 3.24
6584 9557 4.518217 GCAATTTATGTTCGTCGAGGATG 58.482 43.478 8.88 2.88 0.00 3.51
6585 9558 4.552767 GCAATTTATGTTCGTCGAGGATGG 60.553 45.833 8.88 0.00 0.00 3.51
6586 9559 2.218953 TTATGTTCGTCGAGGATGGC 57.781 50.000 8.88 3.61 0.00 4.40
6587 9560 1.107945 TATGTTCGTCGAGGATGGCA 58.892 50.000 8.88 8.96 0.00 4.92
6588 9561 0.249120 ATGTTCGTCGAGGATGGCAA 59.751 50.000 8.88 0.00 0.00 4.52
6589 9562 0.389817 TGTTCGTCGAGGATGGCAAG 60.390 55.000 8.88 0.00 0.00 4.01
6590 9563 0.389948 GTTCGTCGAGGATGGCAAGT 60.390 55.000 8.88 0.00 0.00 3.16
6591 9564 0.320374 TTCGTCGAGGATGGCAAGTT 59.680 50.000 8.88 0.00 0.00 2.66
6592 9565 0.320374 TCGTCGAGGATGGCAAGTTT 59.680 50.000 3.17 0.00 0.00 2.66
6788 9775 5.086104 ACTCAACTACAAGTGTGACTGTT 57.914 39.130 0.00 0.00 0.00 3.16
6976 9963 3.584406 ACAGTCGAAGAGTCTTCCATG 57.416 47.619 24.01 20.73 38.70 3.66
6987 9974 4.229123 AGAGTCTTCCATGGGTTGAATGAT 59.771 41.667 13.02 0.00 0.00 2.45
6988 9975 4.275810 AGTCTTCCATGGGTTGAATGATG 58.724 43.478 13.02 0.00 0.00 3.07
6989 9976 4.019174 GTCTTCCATGGGTTGAATGATGT 58.981 43.478 13.02 0.00 0.00 3.06
6990 9977 4.463891 GTCTTCCATGGGTTGAATGATGTT 59.536 41.667 13.02 0.00 0.00 2.71
7007 9994 2.306847 TGTTTGGCTTCCTGAGTTTCC 58.693 47.619 0.00 0.00 0.00 3.13
7103 10091 2.500229 GTTTTCATCCGTTCCCTGTCA 58.500 47.619 0.00 0.00 0.00 3.58
7161 10149 1.730501 ATGGAAGAGACGTGTGCATG 58.269 50.000 0.00 0.00 0.00 4.06
7190 10178 7.461182 TCTTTTGGTCGGATTGATATTGTTT 57.539 32.000 0.00 0.00 0.00 2.83
7191 10179 7.312154 TCTTTTGGTCGGATTGATATTGTTTG 58.688 34.615 0.00 0.00 0.00 2.93
7192 10180 6.582677 TTTGGTCGGATTGATATTGTTTGT 57.417 33.333 0.00 0.00 0.00 2.83
7193 10181 5.811399 TGGTCGGATTGATATTGTTTGTC 57.189 39.130 0.00 0.00 0.00 3.18
7194 10182 5.249420 TGGTCGGATTGATATTGTTTGTCA 58.751 37.500 0.00 0.00 0.00 3.58
7195 10183 5.885352 TGGTCGGATTGATATTGTTTGTCAT 59.115 36.000 0.00 0.00 0.00 3.06
7196 10184 6.183360 TGGTCGGATTGATATTGTTTGTCATG 60.183 38.462 0.00 0.00 0.00 3.07
7197 10185 6.183360 GGTCGGATTGATATTGTTTGTCATGT 60.183 38.462 0.00 0.00 0.00 3.21
7198 10186 6.688385 GTCGGATTGATATTGTTTGTCATGTG 59.312 38.462 0.00 0.00 0.00 3.21
7199 10187 6.374053 TCGGATTGATATTGTTTGTCATGTGT 59.626 34.615 0.00 0.00 0.00 3.72
7200 10188 6.469915 CGGATTGATATTGTTTGTCATGTGTG 59.530 38.462 0.00 0.00 0.00 3.82
7201 10189 7.315142 GGATTGATATTGTTTGTCATGTGTGT 58.685 34.615 0.00 0.00 0.00 3.72
7202 10190 7.814107 GGATTGATATTGTTTGTCATGTGTGTT 59.186 33.333 0.00 0.00 0.00 3.32
7203 10191 9.838975 GATTGATATTGTTTGTCATGTGTGTTA 57.161 29.630 0.00 0.00 0.00 2.41
7220 10208 6.926826 TGTGTGTTAGAGTTGTGTCGAATATT 59.073 34.615 0.00 0.00 0.00 1.28
7227 10215 6.452242 AGAGTTGTGTCGAATATTGTGTACA 58.548 36.000 0.00 0.00 0.00 2.90
7230 10218 6.147164 AGTTGTGTCGAATATTGTGTACAAGG 59.853 38.462 0.00 0.00 39.47 3.61
7243 10231 6.975196 TGTGTACAAGGTAGGTTACAGTTA 57.025 37.500 0.00 0.00 0.00 2.24
7248 10236 8.163408 TGTACAAGGTAGGTTACAGTTAGACTA 58.837 37.037 0.00 0.00 0.00 2.59
7249 10237 9.183368 GTACAAGGTAGGTTACAGTTAGACTAT 57.817 37.037 0.00 0.00 0.00 2.12
7250 10238 8.064336 ACAAGGTAGGTTACAGTTAGACTATG 57.936 38.462 0.00 0.00 0.00 2.23
7254 10242 8.114743 AGGTAGGTTACAGTTAGACTATGAGTT 58.885 37.037 0.00 0.00 0.00 3.01
7257 10245 8.874744 AGGTTACAGTTAGACTATGAGTTGTA 57.125 34.615 0.00 0.00 0.00 2.41
7281 10269 9.998106 GTATTGTGTTTACATAGGATATGGAGT 57.002 33.333 2.15 0.00 36.53 3.85
7283 10271 6.745116 TGTGTTTACATAGGATATGGAGTCG 58.255 40.000 2.15 0.00 0.00 4.18
7284 10272 6.322969 TGTGTTTACATAGGATATGGAGTCGT 59.677 38.462 2.15 0.00 0.00 4.34
7285 10273 6.641314 GTGTTTACATAGGATATGGAGTCGTG 59.359 42.308 2.15 0.00 0.00 4.35
7291 10279 3.757270 AGGATATGGAGTCGTGTCCTAG 58.243 50.000 9.72 0.00 45.13 3.02
7328 10316 9.504708 GTATTCTAGGCCTCTTATATATAGCGA 57.495 37.037 9.68 0.00 0.00 4.93
7331 10319 4.475345 AGGCCTCTTATATATAGCGAGGG 58.525 47.826 25.93 15.87 41.17 4.30
7344 10332 1.019673 GCGAGGGTAGACACACGATA 58.980 55.000 5.92 0.00 31.29 2.92
7349 10337 4.514441 CGAGGGTAGACACACGATATAACT 59.486 45.833 0.00 0.00 31.29 2.24
7350 10338 5.008415 CGAGGGTAGACACACGATATAACTT 59.992 44.000 0.00 0.00 31.29 2.66
7371 10359 6.356556 ACTTATGCCAACATAATAGCACAGA 58.643 36.000 0.00 0.00 45.41 3.41
7372 10360 7.000472 ACTTATGCCAACATAATAGCACAGAT 59.000 34.615 0.00 0.00 45.41 2.90
7373 10361 5.700722 ATGCCAACATAATAGCACAGATG 57.299 39.130 0.00 0.00 38.21 2.90
7382 10370 2.747460 GCACAGATGCGCAAGGGA 60.747 61.111 17.11 0.00 43.33 4.20
7383 10371 2.758089 GCACAGATGCGCAAGGGAG 61.758 63.158 17.11 6.13 43.33 4.30
7388 10376 4.845580 ATGCGCAAGGGAGAGCCG 62.846 66.667 17.11 0.00 33.05 5.52
7423 10419 3.034370 GCCGGTGTGCGGTATTGTG 62.034 63.158 1.90 0.00 0.00 3.33
7424 10420 1.374885 CCGGTGTGCGGTATTGTGA 60.375 57.895 0.00 0.00 0.00 3.58
7425 10421 0.742990 CCGGTGTGCGGTATTGTGAT 60.743 55.000 0.00 0.00 0.00 3.06
7484 10480 5.482908 GAAGATGTAGCCATATCGGTGAAT 58.517 41.667 0.00 0.00 36.97 2.57
7500 10496 5.929992 TCGGTGAATCTCGTTAACAAATCTT 59.070 36.000 6.39 0.00 0.00 2.40
7539 10535 0.465705 TGCTTGGTCCTCGGATGATC 59.534 55.000 0.00 0.00 0.00 2.92
7560 10556 2.401351 GACGGTATGCCTCGGATTTAC 58.599 52.381 0.00 0.00 0.00 2.01
7562 10558 2.433239 ACGGTATGCCTCGGATTTACTT 59.567 45.455 0.00 0.00 0.00 2.24
7572 10568 5.410439 GCCTCGGATTTACTTTAACAAGTGA 59.590 40.000 0.00 0.00 43.54 3.41
7590 10586 6.127814 ACAAGTGATATCATGAGCAAGGTTTG 60.128 38.462 9.02 3.64 0.00 2.93
7598 10594 3.616956 TGAGCAAGGTTTGAGATCGAT 57.383 42.857 0.00 0.00 0.00 3.59
7599 10595 3.264947 TGAGCAAGGTTTGAGATCGATG 58.735 45.455 0.54 0.00 0.00 3.84
7638 10634 5.570234 AGAGGAAGTATCGAGTTTGAGAC 57.430 43.478 0.00 0.00 0.00 3.36
7640 10636 3.757493 AGGAAGTATCGAGTTTGAGACGT 59.243 43.478 0.00 0.00 35.31 4.34
7646 10642 1.199327 TCGAGTTTGAGACGTAGCTGG 59.801 52.381 0.00 0.00 0.00 4.85
7675 10671 1.008194 CGGTGTGGTTCTCGACGAA 60.008 57.895 0.00 0.00 0.00 3.85
7950 10961 0.108138 GCTTGGCATACACGGAGAGT 60.108 55.000 0.00 0.00 34.44 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 2.579201 CTGCCGGACCATCTCGTT 59.421 61.111 5.05 0.00 0.00 3.85
160 161 4.495939 CGTCCTCGTCGTCGTCGG 62.496 72.222 11.74 4.59 38.33 4.79
289 299 1.395826 GCTCTACATGCCGAGGAGGT 61.396 60.000 12.24 0.00 43.70 3.85
413 430 3.381908 ACACGGCAAATTCAACCAAACTA 59.618 39.130 0.00 0.00 0.00 2.24
655 683 0.953960 GAAAACATCCGTCGCCTGGT 60.954 55.000 0.00 0.00 0.00 4.00
668 696 2.304761 AGAAGGACGGCCATAGAAAACA 59.695 45.455 11.69 0.00 36.29 2.83
707 760 1.200020 GCACCTCACATTGTACAAGGC 59.800 52.381 19.55 6.40 0.00 4.35
708 761 2.783135 AGCACCTCACATTGTACAAGG 58.217 47.619 18.17 18.17 0.00 3.61
710 763 5.011635 TCTCTAAGCACCTCACATTGTACAA 59.988 40.000 11.41 11.41 0.00 2.41
711 764 4.526650 TCTCTAAGCACCTCACATTGTACA 59.473 41.667 0.00 0.00 0.00 2.90
712 765 5.073311 TCTCTAAGCACCTCACATTGTAC 57.927 43.478 0.00 0.00 0.00 2.90
714 767 4.623932 TTCTCTAAGCACCTCACATTGT 57.376 40.909 0.00 0.00 0.00 2.71
715 768 7.615582 TTATTTCTCTAAGCACCTCACATTG 57.384 36.000 0.00 0.00 0.00 2.82
717 770 6.599638 GGTTTATTTCTCTAAGCACCTCACAT 59.400 38.462 0.00 0.00 0.00 3.21
718 771 5.938125 GGTTTATTTCTCTAAGCACCTCACA 59.062 40.000 0.00 0.00 0.00 3.58
719 772 5.938125 TGGTTTATTTCTCTAAGCACCTCAC 59.062 40.000 0.00 0.00 0.00 3.51
720 773 6.121776 TGGTTTATTTCTCTAAGCACCTCA 57.878 37.500 0.00 0.00 0.00 3.86
721 774 6.174049 ACTGGTTTATTTCTCTAAGCACCTC 58.826 40.000 0.00 0.00 0.00 3.85
722 775 6.128138 ACTGGTTTATTTCTCTAAGCACCT 57.872 37.500 0.00 0.00 0.00 4.00
723 776 6.819397 AACTGGTTTATTTCTCTAAGCACC 57.181 37.500 0.00 0.00 0.00 5.01
757 810 3.687212 TCATGTACAAATAAGCACCGGTG 59.313 43.478 30.66 30.66 0.00 4.94
758 811 3.945346 TCATGTACAAATAAGCACCGGT 58.055 40.909 0.00 0.00 0.00 5.28
759 812 6.801539 ATATCATGTACAAATAAGCACCGG 57.198 37.500 0.00 0.00 0.00 5.28
762 815 8.018677 AGCGTATATCATGTACAAATAAGCAC 57.981 34.615 20.02 12.00 32.29 4.40
763 816 8.601845 AAGCGTATATCATGTACAAATAAGCA 57.398 30.769 20.02 5.15 32.29 3.91
766 819 9.758651 AGTGAAGCGTATATCATGTACAAATAA 57.241 29.630 0.00 0.00 0.00 1.40
769 822 9.244799 CTTAGTGAAGCGTATATCATGTACAAA 57.755 33.333 0.00 0.00 0.00 2.83
787 840 5.001874 TCTACAGAAGAGACGCTTAGTGAA 58.998 41.667 0.00 0.00 36.83 3.18
789 842 4.948608 TCTACAGAAGAGACGCTTAGTG 57.051 45.455 6.73 0.00 36.83 2.74
790 843 5.961396 TTTCTACAGAAGAGACGCTTAGT 57.039 39.130 0.00 0.00 36.83 2.24
791 844 7.136119 CCTATTTCTACAGAAGAGACGCTTAG 58.864 42.308 0.00 0.00 36.83 2.18
793 846 5.680151 GCCTATTTCTACAGAAGAGACGCTT 60.680 44.000 0.00 0.00 40.25 4.68
794 847 4.202070 GCCTATTTCTACAGAAGAGACGCT 60.202 45.833 5.12 0.00 35.05 5.07
795 848 4.045783 GCCTATTTCTACAGAAGAGACGC 58.954 47.826 5.12 0.00 35.05 5.19
798 851 4.098044 CGGTGCCTATTTCTACAGAAGAGA 59.902 45.833 5.12 0.00 35.05 3.10
799 852 4.363999 CGGTGCCTATTTCTACAGAAGAG 58.636 47.826 0.00 0.00 35.05 2.85
800 853 3.132289 CCGGTGCCTATTTCTACAGAAGA 59.868 47.826 0.00 0.00 35.21 2.87
801 854 3.118738 ACCGGTGCCTATTTCTACAGAAG 60.119 47.826 6.12 0.00 35.21 2.85
803 856 2.167693 CACCGGTGCCTATTTCTACAGA 59.832 50.000 24.02 0.00 0.00 3.41
805 858 2.684001 CACCGGTGCCTATTTCTACA 57.316 50.000 24.02 0.00 0.00 2.74
817 870 1.569493 CGTTTCTGAAGCACCGGTG 59.431 57.895 30.66 30.66 0.00 4.94
818 871 2.251642 GCGTTTCTGAAGCACCGGT 61.252 57.895 0.00 0.00 0.00 5.28
819 872 2.556287 GCGTTTCTGAAGCACCGG 59.444 61.111 0.00 0.00 0.00 5.28
820 873 2.556287 GGCGTTTCTGAAGCACCG 59.444 61.111 5.12 1.70 0.00 4.94
821 874 2.954611 GGGCGTTTCTGAAGCACC 59.045 61.111 3.03 3.03 0.00 5.01
822 875 2.556287 CGGGCGTTTCTGAAGCAC 59.444 61.111 5.12 0.00 0.00 4.40
823 876 2.668212 CCGGGCGTTTCTGAAGCA 60.668 61.111 5.12 0.00 0.00 3.91
824 877 1.792118 AAACCGGGCGTTTCTGAAGC 61.792 55.000 6.32 0.00 40.86 3.86
825 878 0.666374 AAAACCGGGCGTTTCTGAAG 59.334 50.000 6.32 0.00 44.09 3.02
827 880 2.796500 AAAAACCGGGCGTTTCTGA 58.204 47.368 6.32 0.00 44.09 3.27
845 898 5.186198 GGGTGCTTAGAGAGATGCTTAAAA 58.814 41.667 0.00 0.00 0.00 1.52
847 900 3.134804 GGGGTGCTTAGAGAGATGCTTAA 59.865 47.826 0.00 0.00 0.00 1.85
849 902 1.488393 GGGGTGCTTAGAGAGATGCTT 59.512 52.381 0.00 0.00 0.00 3.91
850 903 1.127343 GGGGTGCTTAGAGAGATGCT 58.873 55.000 0.00 0.00 0.00 3.79
851 904 0.833287 TGGGGTGCTTAGAGAGATGC 59.167 55.000 0.00 0.00 0.00 3.91
852 905 3.118112 ACAATGGGGTGCTTAGAGAGATG 60.118 47.826 0.00 0.00 0.00 2.90
853 906 3.118531 ACAATGGGGTGCTTAGAGAGAT 58.881 45.455 0.00 0.00 0.00 2.75
855 908 3.197766 TGTACAATGGGGTGCTTAGAGAG 59.802 47.826 0.00 0.00 0.00 3.20
857 910 3.627395 TGTACAATGGGGTGCTTAGAG 57.373 47.619 0.00 0.00 0.00 2.43
858 911 3.329520 ACTTGTACAATGGGGTGCTTAGA 59.670 43.478 9.13 0.00 0.00 2.10
859 912 3.686016 ACTTGTACAATGGGGTGCTTAG 58.314 45.455 9.13 0.00 0.00 2.18
860 913 3.560453 GGACTTGTACAATGGGGTGCTTA 60.560 47.826 9.13 0.00 0.00 3.09
861 914 2.514803 GACTTGTACAATGGGGTGCTT 58.485 47.619 9.13 0.00 0.00 3.91
862 915 1.271926 GGACTTGTACAATGGGGTGCT 60.272 52.381 9.13 0.00 0.00 4.40
863 916 1.173913 GGACTTGTACAATGGGGTGC 58.826 55.000 9.13 5.15 0.00 5.01
864 917 2.879103 AGGACTTGTACAATGGGGTG 57.121 50.000 9.13 0.00 0.00 4.61
865 918 5.530176 AATAAGGACTTGTACAATGGGGT 57.470 39.130 9.13 3.16 0.00 4.95
866 919 6.715264 GGATAATAAGGACTTGTACAATGGGG 59.285 42.308 9.13 0.00 0.00 4.96
867 920 7.287061 TGGATAATAAGGACTTGTACAATGGG 58.713 38.462 9.13 0.00 0.00 4.00
868 921 7.445402 CCTGGATAATAAGGACTTGTACAATGG 59.555 40.741 9.13 0.68 35.40 3.16
869 922 7.041098 GCCTGGATAATAAGGACTTGTACAATG 60.041 40.741 9.13 6.16 35.40 2.82
870 923 6.998673 GCCTGGATAATAAGGACTTGTACAAT 59.001 38.462 9.13 0.00 35.40 2.71
871 924 6.354130 GCCTGGATAATAAGGACTTGTACAA 58.646 40.000 8.28 8.28 35.40 2.41
872 925 5.163237 GGCCTGGATAATAAGGACTTGTACA 60.163 44.000 0.00 0.00 38.70 2.90
874 927 5.562298 GGCCTGGATAATAAGGACTTGTA 57.438 43.478 0.00 0.00 38.70 2.41
875 928 4.439253 GGCCTGGATAATAAGGACTTGT 57.561 45.455 0.00 0.00 38.70 3.16
880 933 5.854843 AGCTATAGGCCTGGATAATAAGGA 58.145 41.667 17.99 0.00 43.05 3.36
881 934 6.069963 ACAAGCTATAGGCCTGGATAATAAGG 60.070 42.308 17.99 0.00 43.05 2.69
884 937 6.022958 TCACAAGCTATAGGCCTGGATAATA 58.977 40.000 17.99 3.48 43.05 0.98
885 938 4.846367 TCACAAGCTATAGGCCTGGATAAT 59.154 41.667 17.99 2.18 43.05 1.28
900 3785 3.244665 TGGTGACAGATGATTCACAAGCT 60.245 43.478 4.27 0.00 43.40 3.74
1434 4323 4.081309 TCACCCAGTATAAGTAGCACCAAC 60.081 45.833 0.00 0.00 0.00 3.77
1446 4335 5.487488 AGACCAAAACTGATCACCCAGTATA 59.513 40.000 0.00 0.00 45.82 1.47
1639 4566 4.389890 AGTTTGCTGCTGATCAACAAAA 57.610 36.364 11.98 3.96 40.97 2.44
1765 4697 3.116096 TGGAGACCTACAGTATGGCTT 57.884 47.619 0.00 0.00 43.62 4.35
1941 4873 5.619625 AGAATTTCTGCTAGTCAAACAGC 57.380 39.130 0.00 0.00 38.31 4.40
2024 4956 4.961440 TCTGTAACTAAGAGGGGGTAGT 57.039 45.455 0.00 0.00 31.81 2.73
2028 4960 3.721021 TCCTTCTGTAACTAAGAGGGGG 58.279 50.000 2.22 0.00 40.44 5.40
2054 4986 1.898574 AGAGCGCCCAAGTTGGTTG 60.899 57.895 20.54 12.96 35.17 3.77
2055 4987 1.898574 CAGAGCGCCCAAGTTGGTT 60.899 57.895 20.54 3.33 35.17 3.67
2056 4988 2.281761 CAGAGCGCCCAAGTTGGT 60.282 61.111 20.54 1.44 35.17 3.67
2057 4989 3.058160 CCAGAGCGCCCAAGTTGG 61.058 66.667 15.52 15.52 37.25 3.77
2094 5026 1.468506 TAGCAGTGAGTGGTTCGGCA 61.469 55.000 0.00 0.00 38.14 5.69
2097 5029 1.269723 TGACTAGCAGTGAGTGGTTCG 59.730 52.381 0.00 0.00 38.14 3.95
2185 5117 5.606348 TTTTGCTTTCTGTGTACCCATTT 57.394 34.783 0.00 0.00 0.00 2.32
2193 5125 4.942761 ACCATCATTTTGCTTTCTGTGT 57.057 36.364 0.00 0.00 0.00 3.72
2196 5128 5.106555 ACGTCTACCATCATTTTGCTTTCTG 60.107 40.000 0.00 0.00 0.00 3.02
2197 5129 5.003804 ACGTCTACCATCATTTTGCTTTCT 58.996 37.500 0.00 0.00 0.00 2.52
2222 5154 5.125417 GCATACTGAGGAAGCCAACAAAATA 59.875 40.000 0.00 0.00 0.00 1.40
3022 5981 6.043243 AGGAGGAGAAAAACACAAGTAGATGA 59.957 38.462 0.00 0.00 0.00 2.92
3931 6899 9.573133 GCAGCAAGATAAATAAGTACATTTTGT 57.427 29.630 0.00 0.00 30.84 2.83
4473 7441 0.037232 ACAGCTTCACCGAGCCTAAC 60.037 55.000 0.00 0.00 43.74 2.34
4733 7701 4.284234 TCGATCCATCCATAAGAGCATTCA 59.716 41.667 0.00 0.00 0.00 2.57
4827 7795 5.779922 ACAGAAAACATTCTACTCGCAGTA 58.220 37.500 0.00 0.00 0.00 2.74
4928 7896 1.463674 ATGGTGAAGGGTTGCGATTC 58.536 50.000 0.00 0.00 0.00 2.52
5418 8387 5.564550 ACTAACTTCTGAATGTGCCAAGAT 58.435 37.500 0.00 0.00 0.00 2.40
5475 8444 3.840078 CCATCTTTTGGTCCCCTTTGAAT 59.160 43.478 0.00 0.00 40.99 2.57
5566 8536 3.058914 CAGCGGAGAAACTTAAGTGTTGG 60.059 47.826 9.34 0.00 0.00 3.77
5577 8547 2.035442 GGCCTGTCAGCGGAGAAAC 61.035 63.158 0.00 0.00 0.00 2.78
5587 8557 0.539438 GTTTCACCCATGGCCTGTCA 60.539 55.000 6.09 0.00 0.00 3.58
6225 9196 3.421844 ACCAAAGAATGCCTAGTGGAAC 58.578 45.455 0.00 0.00 35.33 3.62
6310 9283 7.706607 GCAAACTGGACAGAAGTTTAAGAAATT 59.293 33.333 6.29 0.00 44.11 1.82
6397 9370 9.528847 GAAACATGTTGAAAAGAAAACAGAAAC 57.471 29.630 12.82 0.00 39.50 2.78
6440 9413 7.061094 GCCTATTTTGAAGAACGAATTCTGTTG 59.939 37.037 16.65 0.00 44.82 3.33
6569 9542 0.249120 TTGCCATCCTCGACGAACAT 59.751 50.000 0.00 0.00 0.00 2.71
6579 9552 2.171003 GCCAACTAAACTTGCCATCCT 58.829 47.619 0.00 0.00 0.00 3.24
6580 9553 1.135402 CGCCAACTAAACTTGCCATCC 60.135 52.381 0.00 0.00 0.00 3.51
6581 9554 1.810151 TCGCCAACTAAACTTGCCATC 59.190 47.619 0.00 0.00 0.00 3.51
6582 9555 1.812571 CTCGCCAACTAAACTTGCCAT 59.187 47.619 0.00 0.00 0.00 4.40
6583 9556 1.234821 CTCGCCAACTAAACTTGCCA 58.765 50.000 0.00 0.00 0.00 4.92
6584 9557 0.109735 GCTCGCCAACTAAACTTGCC 60.110 55.000 0.00 0.00 0.00 4.52
6585 9558 0.591170 TGCTCGCCAACTAAACTTGC 59.409 50.000 0.00 0.00 0.00 4.01
6586 9559 2.474526 CGATGCTCGCCAACTAAACTTG 60.475 50.000 0.00 0.00 31.14 3.16
6587 9560 1.732259 CGATGCTCGCCAACTAAACTT 59.268 47.619 0.00 0.00 31.14 2.66
6588 9561 1.359848 CGATGCTCGCCAACTAAACT 58.640 50.000 0.00 0.00 31.14 2.66
6589 9562 3.877801 CGATGCTCGCCAACTAAAC 57.122 52.632 0.00 0.00 31.14 2.01
6649 9636 9.853555 CAAATTACTTGCCAAATGTACAAGATA 57.146 29.630 15.98 7.21 42.71 1.98
6650 9637 8.367156 ACAAATTACTTGCCAAATGTACAAGAT 58.633 29.630 15.98 6.91 42.71 2.40
6788 9775 3.220999 CTTGCTGTCCCGGTCACGA 62.221 63.158 0.00 0.00 44.60 4.35
6976 9963 3.588955 GAAGCCAAACATCATTCAACCC 58.411 45.455 0.00 0.00 0.00 4.11
6987 9974 2.306847 GGAAACTCAGGAAGCCAAACA 58.693 47.619 0.00 0.00 0.00 2.83
6988 9975 1.266989 CGGAAACTCAGGAAGCCAAAC 59.733 52.381 0.00 0.00 0.00 2.93
6989 9976 1.142060 TCGGAAACTCAGGAAGCCAAA 59.858 47.619 0.00 0.00 0.00 3.28
6990 9977 0.762418 TCGGAAACTCAGGAAGCCAA 59.238 50.000 0.00 0.00 0.00 4.52
7007 9994 3.649073 TCTGTTAACAGGACACACATCG 58.351 45.455 30.35 6.29 43.91 3.84
7161 10149 9.023967 CAATATCAATCCGACCAAAAGAAAATC 57.976 33.333 0.00 0.00 0.00 2.17
7190 10178 4.765273 ACACAACTCTAACACACATGACA 58.235 39.130 0.00 0.00 0.00 3.58
7191 10179 4.085055 CGACACAACTCTAACACACATGAC 60.085 45.833 0.00 0.00 0.00 3.06
7192 10180 4.048504 CGACACAACTCTAACACACATGA 58.951 43.478 0.00 0.00 0.00 3.07
7193 10181 4.048504 TCGACACAACTCTAACACACATG 58.951 43.478 0.00 0.00 0.00 3.21
7194 10182 4.316205 TCGACACAACTCTAACACACAT 57.684 40.909 0.00 0.00 0.00 3.21
7195 10183 3.786516 TCGACACAACTCTAACACACA 57.213 42.857 0.00 0.00 0.00 3.72
7196 10184 6.946229 ATATTCGACACAACTCTAACACAC 57.054 37.500 0.00 0.00 0.00 3.82
7197 10185 6.926826 ACAATATTCGACACAACTCTAACACA 59.073 34.615 0.00 0.00 0.00 3.72
7198 10186 7.095774 ACACAATATTCGACACAACTCTAACAC 60.096 37.037 0.00 0.00 0.00 3.32
7199 10187 6.926826 ACACAATATTCGACACAACTCTAACA 59.073 34.615 0.00 0.00 0.00 2.41
7200 10188 7.347508 ACACAATATTCGACACAACTCTAAC 57.652 36.000 0.00 0.00 0.00 2.34
7201 10189 8.083462 TGTACACAATATTCGACACAACTCTAA 58.917 33.333 0.00 0.00 0.00 2.10
7202 10190 7.595604 TGTACACAATATTCGACACAACTCTA 58.404 34.615 0.00 0.00 0.00 2.43
7203 10191 6.452242 TGTACACAATATTCGACACAACTCT 58.548 36.000 0.00 0.00 0.00 3.24
7220 10208 5.874897 AACTGTAACCTACCTTGTACACA 57.125 39.130 0.00 0.00 0.00 3.72
7227 10215 8.114743 ACTCATAGTCTAACTGTAACCTACCTT 58.885 37.037 0.00 0.00 0.00 3.50
7230 10218 8.738106 ACAACTCATAGTCTAACTGTAACCTAC 58.262 37.037 0.00 0.00 0.00 3.18
7243 10231 9.944376 ATGTAAACACAATACAACTCATAGTCT 57.056 29.630 0.00 0.00 36.88 3.24
7248 10236 9.905713 ATCCTATGTAAACACAATACAACTCAT 57.094 29.630 0.00 0.00 36.88 2.90
7254 10242 9.996554 CTCCATATCCTATGTAAACACAATACA 57.003 33.333 0.00 0.00 37.64 2.29
7257 10245 7.872993 CGACTCCATATCCTATGTAAACACAAT 59.127 37.037 0.00 0.00 0.00 2.71
7267 10255 4.082845 AGGACACGACTCCATATCCTATG 58.917 47.826 6.01 0.00 34.77 2.23
7272 10260 4.696402 CCTACTAGGACACGACTCCATATC 59.304 50.000 0.00 0.00 37.67 1.63
7291 10279 4.650131 AGGCCTAGAATACAAGTGTCCTAC 59.350 45.833 1.29 0.00 0.00 3.18
7302 10290 9.504708 TCGCTATATATAAGAGGCCTAGAATAC 57.495 37.037 4.42 0.00 0.00 1.89
7306 10294 6.466038 CCCTCGCTATATATAAGAGGCCTAGA 60.466 46.154 24.86 0.00 45.20 2.43
7328 10316 7.523380 GCATAAGTTATATCGTGTGTCTACCCT 60.523 40.741 0.00 0.00 0.00 4.34
7331 10319 7.143340 TGGCATAAGTTATATCGTGTGTCTAC 58.857 38.462 0.00 0.00 0.00 2.59
7344 10332 8.690203 TGTGCTATTATGTTGGCATAAGTTAT 57.310 30.769 6.27 0.00 46.80 1.89
7350 10338 6.806388 CATCTGTGCTATTATGTTGGCATA 57.194 37.500 0.00 0.00 37.05 3.14
7371 10359 4.845580 CGGCTCTCCCTTGCGCAT 62.846 66.667 12.75 0.00 0.00 4.73
7408 10396 0.732571 CCATCACAATACCGCACACC 59.267 55.000 0.00 0.00 0.00 4.16
7410 10398 1.271108 ACACCATCACAATACCGCACA 60.271 47.619 0.00 0.00 0.00 4.57
7423 10419 1.961180 CTCCTCCCCGTGACACCATC 61.961 65.000 0.00 0.00 0.00 3.51
7424 10420 1.990060 CTCCTCCCCGTGACACCAT 60.990 63.158 0.00 0.00 0.00 3.55
7425 10421 2.603473 CTCCTCCCCGTGACACCA 60.603 66.667 0.00 0.00 0.00 4.17
7446 10442 3.692101 ACATCTTCGAGACCTGACTACAG 59.308 47.826 0.00 0.00 43.12 2.74
7447 10443 3.687125 ACATCTTCGAGACCTGACTACA 58.313 45.455 0.00 0.00 0.00 2.74
7448 10444 4.260866 GCTACATCTTCGAGACCTGACTAC 60.261 50.000 0.00 0.00 0.00 2.73
7457 10453 3.440522 CCGATATGGCTACATCTTCGAGA 59.559 47.826 11.91 0.00 41.56 4.04
7459 10455 3.057526 CACCGATATGGCTACATCTTCGA 60.058 47.826 11.91 0.00 41.56 3.71
7461 10457 4.521130 TCACCGATATGGCTACATCTTC 57.479 45.455 0.00 0.00 43.94 2.87
7462 10458 4.955811 TTCACCGATATGGCTACATCTT 57.044 40.909 0.00 0.00 43.94 2.40
7463 10459 4.774726 AGATTCACCGATATGGCTACATCT 59.225 41.667 0.00 0.00 43.94 2.90
7484 10480 5.924254 ACGACATCAAGATTTGTTAACGAGA 59.076 36.000 0.26 0.00 0.00 4.04
7500 10496 0.243636 ATCACACGAGCACGACATCA 59.756 50.000 11.40 0.00 42.66 3.07
7539 10535 0.249322 AAATCCGAGGCATACCGTCG 60.249 55.000 0.00 0.00 42.76 5.12
7560 10556 8.127327 CCTTGCTCATGATATCACTTGTTAAAG 58.873 37.037 7.78 8.49 39.49 1.85
7562 10558 7.112122 ACCTTGCTCATGATATCACTTGTTAA 58.888 34.615 7.78 0.00 0.00 2.01
7572 10568 5.699915 CGATCTCAAACCTTGCTCATGATAT 59.300 40.000 0.00 0.00 0.00 1.63
7578 10574 3.264947 CATCGATCTCAAACCTTGCTCA 58.735 45.455 0.00 0.00 0.00 4.26
7579 10575 2.031437 GCATCGATCTCAAACCTTGCTC 59.969 50.000 0.00 0.00 0.00 4.26
7582 10578 1.328680 CCGCATCGATCTCAAACCTTG 59.671 52.381 0.00 0.00 0.00 3.61
7606 10602 6.261381 ACTCGATACTTCCTCTAGATCAACAC 59.739 42.308 0.00 0.00 0.00 3.32
7610 10606 7.054751 TCAAACTCGATACTTCCTCTAGATCA 58.945 38.462 0.00 0.00 0.00 2.92
7614 10610 6.510478 CGTCTCAAACTCGATACTTCCTCTAG 60.510 46.154 0.00 0.00 0.00 2.43
7617 10613 4.142643 ACGTCTCAAACTCGATACTTCCTC 60.143 45.833 0.00 0.00 0.00 3.71
7652 10648 2.668550 GAGAACCACACCGGCCAC 60.669 66.667 0.00 0.00 39.03 5.01
7656 10652 2.410638 TTCGTCGAGAACCACACCGG 62.411 60.000 0.00 0.00 42.50 5.28
7675 10671 1.091771 CACGCTCCGCTGATCCAATT 61.092 55.000 0.00 0.00 0.00 2.32
7930 10941 0.811616 CTCTCCGTGTATGCCAAGCC 60.812 60.000 0.00 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.