Multiple sequence alignment - TraesCS7D01G365700

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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 TraesCS7D01G365700 chr7D 100.000 3731 0 0 1 3731 472538786 472542516 0.000000e+00 6890.0
1 TraesCS7D01G365700 chr7D 98.469 196 3 0 3536 3731 11013177 11012982 2.760000e-91 346.0
2 TraesCS7D01G365700 chr7D 97.990 199 4 0 3533 3731 131725558 131725756 2.760000e-91 346.0
3 TraesCS7D01G365700 chr7D 97.970 197 4 0 3535 3731 12438601 12438797 3.570000e-90 342.0
4 TraesCS7D01G365700 chr7A 94.135 2728 134 17 812 3535 523148163 523145458 0.000000e+00 4128.0
5 TraesCS7D01G365700 chr7B 97.759 2142 44 4 816 2957 496656829 496658966 0.000000e+00 3687.0
6 TraesCS7D01G365700 chr7B 91.404 570 44 3 2967 3535 496659133 496659698 0.000000e+00 776.0
7 TraesCS7D01G365700 chr7B 81.671 742 84 39 1 711 540779072 540778352 1.500000e-158 569.0
8 TraesCS7D01G365700 chr5D 88.531 715 67 6 1 710 352819728 352820432 0.000000e+00 852.0
9 TraesCS7D01G365700 chr5D 85.894 716 61 16 1 711 499853393 499852713 0.000000e+00 726.0
10 TraesCS7D01G365700 chr5D 97.970 197 4 0 3535 3731 490581389 490581585 3.570000e-90 342.0
11 TraesCS7D01G365700 chr5D 87.059 85 9 2 733 816 287303568 287303651 1.100000e-15 95.3
12 TraesCS7D01G365700 chr1D 87.398 738 62 20 1 711 108839691 108838958 0.000000e+00 819.0
13 TraesCS7D01G365700 chr1D 87.137 482 52 6 210 689 79830415 79829942 4.240000e-149 538.0
14 TraesCS7D01G365700 chrUn 88.201 695 57 9 1 692 127125820 127125148 0.000000e+00 806.0
15 TraesCS7D01G365700 chrUn 96.117 206 5 2 3526 3731 299706018 299706220 2.150000e-87 333.0
16 TraesCS7D01G365700 chrUn 96.117 206 5 2 3526 3731 352730094 352730296 2.150000e-87 333.0
17 TraesCS7D01G365700 chr2D 86.901 710 68 13 1 689 512281046 512281751 0.000000e+00 773.0
18 TraesCS7D01G365700 chr2D 85.854 714 69 19 1 692 576276005 576276708 0.000000e+00 730.0
19 TraesCS7D01G365700 chr5A 87.013 693 63 11 5 692 47776400 47777070 0.000000e+00 756.0
20 TraesCS7D01G365700 chr5A 80.450 844 126 25 1 812 144776270 144775434 3.190000e-170 608.0
21 TraesCS7D01G365700 chr5A 91.250 80 7 0 735 814 640319694 640319615 3.940000e-20 110.0
22 TraesCS7D01G365700 chr5B 85.077 717 92 10 1 711 625040567 625041274 0.000000e+00 717.0
23 TraesCS7D01G365700 chr5B 82.845 717 96 15 1 711 628611639 628612334 5.290000e-173 617.0
24 TraesCS7D01G365700 chr5B 84.653 606 74 16 111 711 682403733 682403142 1.490000e-163 586.0
25 TraesCS7D01G365700 chr4D 80.118 850 123 25 5 812 415024279 415023434 3.210000e-165 592.0
26 TraesCS7D01G365700 chr4B 80.536 709 110 12 1 685 655760057 655759353 1.540000e-143 520.0
27 TraesCS7D01G365700 chr2A 87.556 450 38 12 256 689 606815533 606815980 4.300000e-139 505.0
28 TraesCS7D01G365700 chr2A 90.000 80 8 0 735 814 751480518 751480597 1.830000e-18 104.0
29 TraesCS7D01G365700 chr6D 97.015 201 6 0 3531 3731 432975088 432975288 4.620000e-89 339.0
30 TraesCS7D01G365700 chr3D 96.117 206 5 2 3526 3731 29509136 29508934 2.150000e-87 333.0
31 TraesCS7D01G365700 chr3D 96.117 206 5 2 3526 3731 29597112 29596910 2.150000e-87 333.0
32 TraesCS7D01G365700 chr3D 88.350 103 11 1 714 816 492673497 492673598 5.060000e-24 122.0
33 TraesCS7D01G365700 chr3A 83.929 112 13 5 721 830 624014036 624014144 6.590000e-18 102.0
34 TraesCS7D01G365700 chr2B 86.022 93 12 1 720 812 734646909 734646818 8.530000e-17 99.0
35 TraesCS7D01G365700 chr3B 84.848 99 12 3 721 817 447984693 447984596 3.070000e-16 97.1


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 TraesCS7D01G365700 chr7D 472538786 472542516 3730 False 6890.0 6890 100.0000 1 3731 1 chr7D.!!$F3 3730
1 TraesCS7D01G365700 chr7A 523145458 523148163 2705 True 4128.0 4128 94.1350 812 3535 1 chr7A.!!$R1 2723
2 TraesCS7D01G365700 chr7B 496656829 496659698 2869 False 2231.5 3687 94.5815 816 3535 2 chr7B.!!$F1 2719
3 TraesCS7D01G365700 chr7B 540778352 540779072 720 True 569.0 569 81.6710 1 711 1 chr7B.!!$R1 710
4 TraesCS7D01G365700 chr5D 352819728 352820432 704 False 852.0 852 88.5310 1 710 1 chr5D.!!$F2 709
5 TraesCS7D01G365700 chr5D 499852713 499853393 680 True 726.0 726 85.8940 1 711 1 chr5D.!!$R1 710
6 TraesCS7D01G365700 chr1D 108838958 108839691 733 True 819.0 819 87.3980 1 711 1 chr1D.!!$R2 710
7 TraesCS7D01G365700 chrUn 127125148 127125820 672 True 806.0 806 88.2010 1 692 1 chrUn.!!$R1 691
8 TraesCS7D01G365700 chr2D 512281046 512281751 705 False 773.0 773 86.9010 1 689 1 chr2D.!!$F1 688
9 TraesCS7D01G365700 chr2D 576276005 576276708 703 False 730.0 730 85.8540 1 692 1 chr2D.!!$F2 691
10 TraesCS7D01G365700 chr5A 47776400 47777070 670 False 756.0 756 87.0130 5 692 1 chr5A.!!$F1 687
11 TraesCS7D01G365700 chr5A 144775434 144776270 836 True 608.0 608 80.4500 1 812 1 chr5A.!!$R1 811
12 TraesCS7D01G365700 chr5B 625040567 625041274 707 False 717.0 717 85.0770 1 711 1 chr5B.!!$F1 710
13 TraesCS7D01G365700 chr5B 628611639 628612334 695 False 617.0 617 82.8450 1 711 1 chr5B.!!$F2 710
14 TraesCS7D01G365700 chr5B 682403142 682403733 591 True 586.0 586 84.6530 111 711 1 chr5B.!!$R1 600
15 TraesCS7D01G365700 chr4D 415023434 415024279 845 True 592.0 592 80.1180 5 812 1 chr4D.!!$R1 807
16 TraesCS7D01G365700 chr4B 655759353 655760057 704 True 520.0 520 80.5360 1 685 1 chr4B.!!$R1 684

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
709 899 0.030101 CTTTTCTTGCGCCGTCCAAA 59.970 50.0 4.18 0.0 0.00 3.28 F
720 941 0.236187 CCGTCCAAATCAAAACGCGA 59.764 50.0 15.93 0.0 33.95 5.87 F
813 1034 0.321298 GCCCGTTGGAGTTGCTCTTA 60.321 55.0 0.00 0.0 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 2375 0.466922 CATGGCCAAGAGTCCCATCC 60.467 60.000 10.96 0.00 37.25 3.51 R
2713 2935 0.181114 TCTCAAAGCACCTGCACTGT 59.819 50.000 0.00 0.00 45.16 3.55 R
2812 3034 8.571461 ACACATTAGCACAGTACTTAGTACTA 57.429 34.615 22.66 8.56 46.08 1.82 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
73 74 3.068691 CGGTGGCGGAGGAAGAGA 61.069 66.667 0.00 0.00 0.00 3.10
203 253 4.416738 GCTGGAGCTGTCCCCCAC 62.417 72.222 0.00 0.00 43.15 4.61
464 622 3.419759 GCGCCCGACATGAACGTT 61.420 61.111 0.00 0.00 0.00 3.99
471 629 0.716108 CGACATGAACGTTCTCTGGC 59.284 55.000 27.32 23.58 0.00 4.85
527 686 1.109920 CATCGATCTCACGGACCCCT 61.110 60.000 0.00 0.00 0.00 4.79
700 890 7.096106 TGCATGTATTCTTTTTCTTTTCTTGCG 60.096 33.333 0.00 0.00 0.00 4.85
701 891 6.747659 TGTATTCTTTTTCTTTTCTTGCGC 57.252 33.333 0.00 0.00 0.00 6.09
702 892 5.689961 TGTATTCTTTTTCTTTTCTTGCGCC 59.310 36.000 4.18 0.00 0.00 6.53
703 893 2.726633 TCTTTTTCTTTTCTTGCGCCG 58.273 42.857 4.18 0.00 0.00 6.46
704 894 2.098443 TCTTTTTCTTTTCTTGCGCCGT 59.902 40.909 4.18 0.00 0.00 5.68
705 895 2.113910 TTTTCTTTTCTTGCGCCGTC 57.886 45.000 4.18 0.00 0.00 4.79
706 896 0.309612 TTTCTTTTCTTGCGCCGTCC 59.690 50.000 4.18 0.00 0.00 4.79
709 899 0.030101 CTTTTCTTGCGCCGTCCAAA 59.970 50.000 4.18 0.00 0.00 3.28
710 900 0.671251 TTTTCTTGCGCCGTCCAAAT 59.329 45.000 4.18 0.00 0.00 2.32
711 901 0.239879 TTTCTTGCGCCGTCCAAATC 59.760 50.000 4.18 0.00 0.00 2.17
712 902 0.886938 TTCTTGCGCCGTCCAAATCA 60.887 50.000 4.18 0.00 0.00 2.57
720 941 0.236187 CCGTCCAAATCAAAACGCGA 59.764 50.000 15.93 0.00 33.95 5.87
744 965 0.904865 AGAGGTTCATGTCCGCCTGA 60.905 55.000 8.94 0.00 0.00 3.86
782 1003 2.559330 GCGGACAAAATCGCGGTT 59.441 55.556 6.13 0.56 42.48 4.44
783 1004 1.081708 GCGGACAAAATCGCGGTTT 60.082 52.632 12.49 12.49 42.48 3.27
792 1013 1.606903 AATCGCGGTTTGTTTGGGTA 58.393 45.000 6.13 0.00 0.00 3.69
812 1033 1.600916 GCCCGTTGGAGTTGCTCTT 60.601 57.895 0.00 0.00 0.00 2.85
813 1034 0.321298 GCCCGTTGGAGTTGCTCTTA 60.321 55.000 0.00 0.00 0.00 2.10
814 1035 1.880646 GCCCGTTGGAGTTGCTCTTAA 60.881 52.381 0.00 0.00 0.00 1.85
815 1036 1.804748 CCCGTTGGAGTTGCTCTTAAC 59.195 52.381 0.00 0.00 0.00 2.01
816 1037 1.459592 CCGTTGGAGTTGCTCTTAACG 59.540 52.381 20.58 20.58 43.24 3.18
817 1038 1.136336 CGTTGGAGTTGCTCTTAACGC 60.136 52.381 17.99 0.00 40.57 4.84
818 1039 1.871039 GTTGGAGTTGCTCTTAACGCA 59.129 47.619 0.00 0.00 35.73 5.24
819 1040 2.248280 TGGAGTTGCTCTTAACGCAA 57.752 45.000 3.89 3.89 44.36 4.85
820 1041 2.143122 TGGAGTTGCTCTTAACGCAAG 58.857 47.619 7.48 0.00 46.81 4.01
840 1061 2.296471 AGGCCGTCGTCATCCTTATAAG 59.704 50.000 5.43 5.43 0.00 1.73
860 1081 3.200593 CCCATGCACTCGCTCTGC 61.201 66.667 0.00 0.00 39.64 4.26
925 1146 2.616842 ACACCACCAAGCTTTAAACTCG 59.383 45.455 0.00 0.00 0.00 4.18
946 1167 1.961793 CTCTGCTACTAGTCTCGCCT 58.038 55.000 0.00 0.00 0.00 5.52
1158 1380 2.357836 CCCCAGCTCAAGTGCCAT 59.642 61.111 0.00 0.00 0.00 4.40
1193 1415 2.425592 CGTGCCCCTGACTGTGAA 59.574 61.111 0.00 0.00 0.00 3.18
1449 1671 4.070552 AACCAGCCGACGCTCCTC 62.071 66.667 0.00 0.00 43.95 3.71
2067 2289 4.051167 TCCCTGGGTCTCGGCGTA 62.051 66.667 13.56 0.00 0.00 4.42
2850 3072 8.351495 TGTGCTAATGTGTTCATTTCTTTTTC 57.649 30.769 0.00 0.00 43.12 2.29
2967 3189 9.978044 ATGTAGTATTTTTATCCGTCCTAAGTC 57.022 33.333 0.00 0.00 0.00 3.01
3109 3489 2.570135 CCATAGCTGGCTTCTTCTTCC 58.430 52.381 0.00 0.00 35.23 3.46
3128 3508 0.250553 CTTGGCCCTGTTCGGTACAA 60.251 55.000 0.00 0.00 36.02 2.41
3133 3513 1.951602 GCCCTGTTCGGTACAACTTTT 59.048 47.619 0.00 0.00 36.02 2.27
3303 3684 9.350951 TGCGAGCCTATTTAGATAGCTAATATA 57.649 33.333 0.44 2.75 36.54 0.86
3326 3707 5.728637 AAGTCAAAGTGGATTGGATTTCC 57.271 39.130 0.00 0.00 0.00 3.13
3406 3787 6.696411 TGAAATTGTTTTGGTGAGTGTTCTT 58.304 32.000 0.00 0.00 0.00 2.52
3409 3790 7.639113 AATTGTTTTGGTGAGTGTTCTTCTA 57.361 32.000 0.00 0.00 0.00 2.10
3543 3928 2.949451 CAGACCACTGGCACTAGTAG 57.051 55.000 0.00 0.00 40.14 2.57
3544 3929 2.447443 CAGACCACTGGCACTAGTAGA 58.553 52.381 3.59 0.00 40.14 2.59
3545 3930 2.826128 CAGACCACTGGCACTAGTAGAA 59.174 50.000 3.59 0.00 40.14 2.10
3546 3931 3.258372 CAGACCACTGGCACTAGTAGAAA 59.742 47.826 3.59 0.00 40.14 2.52
3547 3932 3.901844 AGACCACTGGCACTAGTAGAAAA 59.098 43.478 3.59 0.00 0.00 2.29
3548 3933 4.347000 AGACCACTGGCACTAGTAGAAAAA 59.653 41.667 3.59 0.00 0.00 1.94
3549 3934 4.642429 ACCACTGGCACTAGTAGAAAAAG 58.358 43.478 3.59 0.00 0.00 2.27
3550 3935 4.003648 CCACTGGCACTAGTAGAAAAAGG 58.996 47.826 3.59 0.00 0.00 3.11
3551 3936 4.003648 CACTGGCACTAGTAGAAAAAGGG 58.996 47.826 3.59 0.00 0.00 3.95
3552 3937 3.651423 ACTGGCACTAGTAGAAAAAGGGT 59.349 43.478 3.59 0.00 0.00 4.34
3553 3938 4.254492 CTGGCACTAGTAGAAAAAGGGTC 58.746 47.826 3.59 0.00 0.00 4.46
3554 3939 3.649023 TGGCACTAGTAGAAAAAGGGTCA 59.351 43.478 3.59 0.00 0.00 4.02
3555 3940 4.288626 TGGCACTAGTAGAAAAAGGGTCAT 59.711 41.667 3.59 0.00 0.00 3.06
3556 3941 4.876679 GGCACTAGTAGAAAAAGGGTCATC 59.123 45.833 3.59 0.00 0.00 2.92
3557 3942 5.338463 GGCACTAGTAGAAAAAGGGTCATCT 60.338 44.000 3.59 0.00 0.00 2.90
3558 3943 5.582665 GCACTAGTAGAAAAAGGGTCATCTG 59.417 44.000 3.59 0.00 0.00 2.90
3559 3944 6.702329 CACTAGTAGAAAAAGGGTCATCTGT 58.298 40.000 3.59 0.00 0.00 3.41
3560 3945 6.814146 CACTAGTAGAAAAAGGGTCATCTGTC 59.186 42.308 3.59 0.00 0.00 3.51
3561 3946 5.167303 AGTAGAAAAAGGGTCATCTGTCC 57.833 43.478 0.00 0.00 0.00 4.02
3562 3947 3.441500 AGAAAAAGGGTCATCTGTCCC 57.558 47.619 4.52 4.52 42.66 4.46
3563 3948 2.084546 GAAAAAGGGTCATCTGTCCCG 58.915 52.381 6.82 0.00 46.13 5.14
3564 3949 0.328258 AAAAGGGTCATCTGTCCCGG 59.672 55.000 6.82 0.00 46.13 5.73
3565 3950 0.840722 AAAGGGTCATCTGTCCCGGT 60.841 55.000 0.00 0.00 46.13 5.28
3566 3951 0.840722 AAGGGTCATCTGTCCCGGTT 60.841 55.000 0.00 0.00 46.13 4.44
3567 3952 1.078426 GGGTCATCTGTCCCGGTTG 60.078 63.158 0.00 0.00 33.91 3.77
3568 3953 1.078426 GGTCATCTGTCCCGGTTGG 60.078 63.158 0.00 0.00 0.00 3.77
3569 3954 1.677552 GTCATCTGTCCCGGTTGGT 59.322 57.895 0.00 0.00 34.77 3.67
3570 3955 0.899720 GTCATCTGTCCCGGTTGGTA 59.100 55.000 0.00 0.00 34.77 3.25
3571 3956 1.276989 GTCATCTGTCCCGGTTGGTAA 59.723 52.381 0.00 0.00 34.77 2.85
3572 3957 1.553248 TCATCTGTCCCGGTTGGTAAG 59.447 52.381 0.00 0.00 34.77 2.34
3573 3958 0.909623 ATCTGTCCCGGTTGGTAAGG 59.090 55.000 0.00 0.00 34.77 2.69
3574 3959 1.196104 TCTGTCCCGGTTGGTAAGGG 61.196 60.000 0.00 0.00 46.40 3.95
3575 3960 1.461849 TGTCCCGGTTGGTAAGGGT 60.462 57.895 0.00 0.00 45.27 4.34
3576 3961 1.297689 GTCCCGGTTGGTAAGGGTC 59.702 63.158 0.00 0.00 45.27 4.46
3577 3962 1.159184 TCCCGGTTGGTAAGGGTCT 59.841 57.895 0.00 0.00 45.27 3.85
3578 3963 0.474273 TCCCGGTTGGTAAGGGTCTT 60.474 55.000 0.00 0.00 45.27 3.01
3579 3964 0.402887 CCCGGTTGGTAAGGGTCTTT 59.597 55.000 0.00 0.00 40.27 2.52
3580 3965 1.202964 CCCGGTTGGTAAGGGTCTTTT 60.203 52.381 0.00 0.00 40.27 2.27
3581 3966 1.883926 CCGGTTGGTAAGGGTCTTTTG 59.116 52.381 0.00 0.00 0.00 2.44
3582 3967 2.578786 CGGTTGGTAAGGGTCTTTTGT 58.421 47.619 0.00 0.00 0.00 2.83
3583 3968 2.551032 CGGTTGGTAAGGGTCTTTTGTC 59.449 50.000 0.00 0.00 0.00 3.18
3584 3969 2.889045 GGTTGGTAAGGGTCTTTTGTCC 59.111 50.000 0.00 0.00 0.00 4.02
3585 3970 2.889045 GTTGGTAAGGGTCTTTTGTCCC 59.111 50.000 0.00 0.00 46.27 4.46
3589 3974 4.914128 GGGTCTTTTGTCCCGGTT 57.086 55.556 0.00 0.00 37.99 4.44
3590 3975 3.120796 GGGTCTTTTGTCCCGGTTT 57.879 52.632 0.00 0.00 37.99 3.27
3591 3976 1.405872 GGGTCTTTTGTCCCGGTTTT 58.594 50.000 0.00 0.00 37.99 2.43
3592 3977 1.758280 GGGTCTTTTGTCCCGGTTTTT 59.242 47.619 0.00 0.00 37.99 1.94
3593 3978 2.482316 GGGTCTTTTGTCCCGGTTTTTG 60.482 50.000 0.00 0.00 37.99 2.44
3594 3979 2.427812 GGTCTTTTGTCCCGGTTTTTGA 59.572 45.455 0.00 0.00 0.00 2.69
3595 3980 3.119065 GGTCTTTTGTCCCGGTTTTTGAA 60.119 43.478 0.00 0.00 0.00 2.69
3596 3981 3.861113 GTCTTTTGTCCCGGTTTTTGAAC 59.139 43.478 0.00 0.00 0.00 3.18
3597 3982 3.510360 TCTTTTGTCCCGGTTTTTGAACA 59.490 39.130 0.00 0.00 0.00 3.18
3598 3983 3.512033 TTTGTCCCGGTTTTTGAACAG 57.488 42.857 0.00 0.00 0.00 3.16
3599 3984 1.394618 TGTCCCGGTTTTTGAACAGG 58.605 50.000 0.00 2.10 37.69 4.00
3603 3988 1.687563 CCGGTTTTTGAACAGGGACT 58.312 50.000 0.00 0.00 43.88 3.85
3604 3989 2.853705 CCGGTTTTTGAACAGGGACTA 58.146 47.619 0.00 0.00 36.02 2.59
3605 3990 3.215975 CCGGTTTTTGAACAGGGACTAA 58.784 45.455 0.00 0.00 36.02 2.24
3606 3991 3.633065 CCGGTTTTTGAACAGGGACTAAA 59.367 43.478 0.00 0.00 36.02 1.85
3607 3992 4.261447 CCGGTTTTTGAACAGGGACTAAAG 60.261 45.833 0.00 0.00 36.02 1.85
3608 3993 4.261447 CGGTTTTTGAACAGGGACTAAAGG 60.261 45.833 0.00 0.00 36.02 3.11
3609 3994 4.038763 GGTTTTTGAACAGGGACTAAAGGG 59.961 45.833 0.00 0.00 36.02 3.95
3610 3995 4.529716 TTTTGAACAGGGACTAAAGGGT 57.470 40.909 0.00 0.00 36.02 4.34
3611 3996 3.782656 TTGAACAGGGACTAAAGGGTC 57.217 47.619 0.00 0.00 36.02 4.46
3612 3997 1.621814 TGAACAGGGACTAAAGGGTCG 59.378 52.381 0.00 0.00 36.02 4.79
3613 3998 1.622312 GAACAGGGACTAAAGGGTCGT 59.378 52.381 0.00 0.00 36.02 4.34
3614 3999 1.725803 ACAGGGACTAAAGGGTCGTT 58.274 50.000 0.00 0.00 36.02 3.85
3615 4000 2.893424 ACAGGGACTAAAGGGTCGTTA 58.107 47.619 0.00 0.00 36.02 3.18
3616 4001 2.564504 ACAGGGACTAAAGGGTCGTTAC 59.435 50.000 0.00 0.00 36.02 2.50
3617 4002 2.830321 CAGGGACTAAAGGGTCGTTACT 59.170 50.000 0.00 0.00 36.02 2.24
3618 4003 4.019174 CAGGGACTAAAGGGTCGTTACTA 58.981 47.826 0.00 0.00 36.02 1.82
3619 4004 4.463891 CAGGGACTAAAGGGTCGTTACTAA 59.536 45.833 0.00 0.00 36.02 2.24
3620 4005 5.128335 CAGGGACTAAAGGGTCGTTACTAAT 59.872 44.000 0.00 0.00 36.02 1.73
3621 4006 5.128335 AGGGACTAAAGGGTCGTTACTAATG 59.872 44.000 0.00 0.00 36.02 1.90
3622 4007 4.807834 GGACTAAAGGGTCGTTACTAATGC 59.192 45.833 0.00 0.00 37.12 3.56
3623 4008 4.763073 ACTAAAGGGTCGTTACTAATGCC 58.237 43.478 0.00 0.00 0.00 4.40
3624 4009 2.704464 AAGGGTCGTTACTAATGCCC 57.296 50.000 10.40 10.40 35.35 5.36
3625 4010 1.875488 AGGGTCGTTACTAATGCCCT 58.125 50.000 13.37 13.37 38.46 5.19
3626 4011 3.036452 AGGGTCGTTACTAATGCCCTA 57.964 47.619 15.90 0.00 40.21 3.53
3627 4012 2.963782 AGGGTCGTTACTAATGCCCTAG 59.036 50.000 15.90 0.00 40.21 3.02
3628 4013 2.547430 GGGTCGTTACTAATGCCCTAGC 60.547 54.545 10.85 0.00 40.48 3.42
3629 4014 2.547430 GGTCGTTACTAATGCCCTAGCC 60.547 54.545 0.00 0.00 38.69 3.93
3630 4015 1.690352 TCGTTACTAATGCCCTAGCCC 59.310 52.381 0.00 0.00 38.69 5.19
3631 4016 1.692519 CGTTACTAATGCCCTAGCCCT 59.307 52.381 0.00 0.00 38.69 5.19
3632 4017 2.104281 CGTTACTAATGCCCTAGCCCTT 59.896 50.000 0.00 0.00 38.69 3.95
3633 4018 3.433173 CGTTACTAATGCCCTAGCCCTTT 60.433 47.826 0.00 0.00 38.69 3.11
3634 4019 4.202284 CGTTACTAATGCCCTAGCCCTTTA 60.202 45.833 0.00 0.00 38.69 1.85
3635 4020 5.306394 GTTACTAATGCCCTAGCCCTTTAG 58.694 45.833 9.81 9.81 38.69 1.85
3636 4021 3.394645 ACTAATGCCCTAGCCCTTTAGT 58.605 45.455 10.64 10.64 38.69 2.24
3637 4022 3.391626 ACTAATGCCCTAGCCCTTTAGTC 59.608 47.826 10.64 0.00 35.19 2.59
3638 4023 1.141185 ATGCCCTAGCCCTTTAGTCC 58.859 55.000 0.00 0.00 38.69 3.85
3639 4024 0.986550 TGCCCTAGCCCTTTAGTCCC 60.987 60.000 0.00 0.00 38.69 4.46
3640 4025 2.041206 GCCCTAGCCCTTTAGTCCCG 62.041 65.000 0.00 0.00 0.00 5.14
3641 4026 1.408453 CCCTAGCCCTTTAGTCCCGG 61.408 65.000 0.00 0.00 0.00 5.73
3642 4027 0.690077 CCTAGCCCTTTAGTCCCGGT 60.690 60.000 0.00 0.00 0.00 5.28
3643 4028 1.201424 CTAGCCCTTTAGTCCCGGTT 58.799 55.000 0.00 0.00 0.00 4.44
3644 4029 1.138464 CTAGCCCTTTAGTCCCGGTTC 59.862 57.143 0.00 0.00 0.00 3.62
3645 4030 0.546988 AGCCCTTTAGTCCCGGTTCT 60.547 55.000 0.00 0.15 0.00 3.01
3646 4031 0.327259 GCCCTTTAGTCCCGGTTCTT 59.673 55.000 0.00 0.00 0.00 2.52
3647 4032 1.556451 GCCCTTTAGTCCCGGTTCTTA 59.444 52.381 0.00 0.00 0.00 2.10
3648 4033 2.679059 GCCCTTTAGTCCCGGTTCTTAC 60.679 54.545 0.00 0.00 0.00 2.34
3649 4034 2.568509 CCCTTTAGTCCCGGTTCTTACA 59.431 50.000 0.00 0.00 0.00 2.41
3650 4035 3.593096 CCTTTAGTCCCGGTTCTTACAC 58.407 50.000 0.00 0.00 0.00 2.90
3651 4036 3.248266 CTTTAGTCCCGGTTCTTACACG 58.752 50.000 0.00 0.00 0.00 4.49
3652 4037 2.198827 TAGTCCCGGTTCTTACACGA 57.801 50.000 0.00 0.00 0.00 4.35
3653 4038 1.331214 AGTCCCGGTTCTTACACGAA 58.669 50.000 0.00 0.00 0.00 3.85
3654 4039 1.000171 AGTCCCGGTTCTTACACGAAC 60.000 52.381 0.00 0.00 41.91 3.95
3659 4044 3.892200 GTTCTTACACGAACCGGGA 57.108 52.632 6.32 0.00 37.82 5.14
3660 4045 2.375173 GTTCTTACACGAACCGGGAT 57.625 50.000 6.32 0.00 37.82 3.85
3661 4046 3.508744 GTTCTTACACGAACCGGGATA 57.491 47.619 6.32 0.00 37.82 2.59
3662 4047 3.442100 GTTCTTACACGAACCGGGATAG 58.558 50.000 6.32 0.00 37.82 2.08
3663 4048 3.003394 TCTTACACGAACCGGGATAGA 57.997 47.619 6.32 0.00 32.98 1.98
3664 4049 3.559069 TCTTACACGAACCGGGATAGAT 58.441 45.455 6.32 0.00 32.98 1.98
3665 4050 3.317149 TCTTACACGAACCGGGATAGATG 59.683 47.826 6.32 0.00 32.98 2.90
3666 4051 0.750850 ACACGAACCGGGATAGATGG 59.249 55.000 6.32 0.00 32.98 3.51
3667 4052 0.033504 CACGAACCGGGATAGATGGG 59.966 60.000 6.32 0.00 28.17 4.00
3668 4053 1.004918 CGAACCGGGATAGATGGGC 60.005 63.158 6.32 0.00 0.00 5.36
3669 4054 1.375326 GAACCGGGATAGATGGGCC 59.625 63.158 6.32 0.00 0.00 5.80
3670 4055 1.073706 AACCGGGATAGATGGGCCT 60.074 57.895 6.32 0.00 0.00 5.19
3671 4056 1.128188 AACCGGGATAGATGGGCCTC 61.128 60.000 6.32 0.00 0.00 4.70
3672 4057 2.294078 CCGGGATAGATGGGCCTCC 61.294 68.421 4.53 2.00 0.00 4.30
3714 4099 2.361737 GCAGGAGGGCCTTTGGTC 60.362 66.667 7.89 0.00 43.90 4.02
3720 4105 4.295199 GGGCCTTTGGTCCCGGTT 62.295 66.667 0.84 0.00 42.67 4.44
3721 4106 2.989253 GGCCTTTGGTCCCGGTTG 60.989 66.667 0.00 0.00 0.00 3.77
3722 4107 2.989253 GCCTTTGGTCCCGGTTGG 60.989 66.667 0.00 0.00 0.00 3.77
3723 4108 2.518933 CCTTTGGTCCCGGTTGGT 59.481 61.111 0.00 0.00 34.77 3.67
3724 4109 1.901464 CCTTTGGTCCCGGTTGGTG 60.901 63.158 0.00 0.00 34.77 4.17
3725 4110 1.901464 CTTTGGTCCCGGTTGGTGG 60.901 63.158 0.00 0.00 34.77 4.61
3726 4111 4.589675 TTGGTCCCGGTTGGTGGC 62.590 66.667 0.00 0.00 34.77 5.01
3729 4114 4.265056 GTCCCGGTTGGTGGCACT 62.265 66.667 18.45 0.00 34.77 4.40
3730 4115 2.527123 TCCCGGTTGGTGGCACTA 60.527 61.111 18.45 8.99 34.77 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
194 244 3.533079 TAGCACTCGGTGGGGGACA 62.533 63.158 6.23 0.00 33.64 4.02
195 245 2.682494 TAGCACTCGGTGGGGGAC 60.682 66.667 6.23 0.00 33.64 4.46
196 246 2.682494 GTAGCACTCGGTGGGGGA 60.682 66.667 6.23 0.00 33.64 4.81
197 247 2.683933 AGTAGCACTCGGTGGGGG 60.684 66.667 6.23 0.00 33.64 5.40
198 248 2.722201 GGAGTAGCACTCGGTGGGG 61.722 68.421 9.29 0.00 45.96 4.96
199 249 1.682684 AGGAGTAGCACTCGGTGGG 60.683 63.158 9.29 0.00 45.96 4.61
203 253 1.810532 GTCCAGGAGTAGCACTCGG 59.189 63.158 0.00 6.92 45.96 4.63
287 338 1.378531 GCCAATGTTCGAGGTATGCA 58.621 50.000 0.00 0.00 0.00 3.96
290 341 0.814010 GGCGCCAATGTTCGAGGTAT 60.814 55.000 24.80 0.00 0.00 2.73
464 622 2.355837 GAACGCGTGTGCCAGAGA 60.356 61.111 14.98 0.00 38.08 3.10
527 686 2.557059 TAGGCGTCGTCGTCGTCCTA 62.557 60.000 21.13 21.13 46.96 2.94
629 818 4.810191 ATTAAACATTAAAGCCGGCCAA 57.190 36.364 26.15 15.81 0.00 4.52
690 879 0.030101 TTTGGACGGCGCAAGAAAAG 59.970 50.000 10.83 0.00 43.02 2.27
700 890 1.334288 CGCGTTTTGATTTGGACGGC 61.334 55.000 0.00 0.00 36.14 5.68
701 891 0.236187 TCGCGTTTTGATTTGGACGG 59.764 50.000 5.77 0.00 36.14 4.79
702 892 2.025544 TTCGCGTTTTGATTTGGACG 57.974 45.000 5.77 0.00 38.45 4.79
703 893 2.153057 GCTTTCGCGTTTTGATTTGGAC 59.847 45.455 5.77 0.00 0.00 4.02
704 894 2.223595 TGCTTTCGCGTTTTGATTTGGA 60.224 40.909 5.77 0.00 39.65 3.53
705 895 2.123342 TGCTTTCGCGTTTTGATTTGG 58.877 42.857 5.77 0.00 39.65 3.28
706 896 3.042189 TCTGCTTTCGCGTTTTGATTTG 58.958 40.909 5.77 0.00 39.65 2.32
709 899 1.197721 CCTCTGCTTTCGCGTTTTGAT 59.802 47.619 5.77 0.00 39.65 2.57
710 900 0.586319 CCTCTGCTTTCGCGTTTTGA 59.414 50.000 5.77 0.00 39.65 2.69
711 901 0.307760 ACCTCTGCTTTCGCGTTTTG 59.692 50.000 5.77 0.00 39.65 2.44
712 902 1.002792 GAACCTCTGCTTTCGCGTTTT 60.003 47.619 5.77 0.00 39.65 2.43
720 941 1.813513 CGGACATGAACCTCTGCTTT 58.186 50.000 0.00 0.00 0.00 3.51
725 946 0.904865 TCAGGCGGACATGAACCTCT 60.905 55.000 0.00 0.78 0.00 3.69
728 949 3.890674 GTCAGGCGGACATGAACC 58.109 61.111 13.03 1.31 46.19 3.62
744 965 2.074729 TTTTGTCCATTTGGGTCGGT 57.925 45.000 0.00 0.00 38.11 4.69
792 1013 3.553095 GAGCAACTCCAACGGGCCT 62.553 63.158 0.84 0.00 0.00 5.19
812 1033 2.431260 GACGACGGCCTTGCGTTA 60.431 61.111 14.18 0.00 38.51 3.18
813 1034 3.876589 ATGACGACGGCCTTGCGTT 62.877 57.895 14.18 0.00 38.51 4.84
814 1035 4.373116 ATGACGACGGCCTTGCGT 62.373 61.111 13.12 13.12 41.45 5.24
815 1036 3.554692 GATGACGACGGCCTTGCG 61.555 66.667 0.00 3.98 0.00 4.85
816 1037 3.195698 GGATGACGACGGCCTTGC 61.196 66.667 0.00 0.00 0.00 4.01
817 1038 0.174845 TAAGGATGACGACGGCCTTG 59.825 55.000 16.88 0.00 40.71 3.61
818 1039 1.120530 ATAAGGATGACGACGGCCTT 58.879 50.000 13.53 13.53 42.91 4.35
819 1040 1.991121 TATAAGGATGACGACGGCCT 58.009 50.000 0.00 0.00 0.00 5.19
820 1041 2.295349 TCTTATAAGGATGACGACGGCC 59.705 50.000 12.54 0.00 0.00 6.13
840 1061 2.512515 GAGCGAGTGCATGGGGTC 60.513 66.667 0.00 0.00 46.23 4.46
925 1146 0.309612 GCGAGACTAGTAGCAGAGCC 59.690 60.000 11.23 0.00 0.00 4.70
946 1167 6.481976 CAGCTTAGAGATCGAGAAGAAGAGTA 59.518 42.308 7.47 0.00 0.00 2.59
1181 1403 0.962356 GCCACCATTCACAGTCAGGG 60.962 60.000 0.00 0.00 0.00 4.45
1193 1415 1.079127 CGGAAAGTCTCGCCACCAT 60.079 57.895 0.00 0.00 0.00 3.55
1449 1671 3.528370 CGGTAGAGGGTGAGGCCG 61.528 72.222 0.00 0.00 38.44 6.13
1707 1929 1.596752 CACGTAGTTGGCCAGCACA 60.597 57.895 22.64 6.07 41.61 4.57
2067 2289 3.697747 TTTCCCACCCGCGTCGAT 61.698 61.111 4.92 0.00 0.00 3.59
2153 2375 0.466922 CATGGCCAAGAGTCCCATCC 60.467 60.000 10.96 0.00 37.25 3.51
2233 2455 2.190578 GGCTGCAGTTAGGCGGAT 59.809 61.111 16.64 0.00 42.91 4.18
2713 2935 0.181114 TCTCAAAGCACCTGCACTGT 59.819 50.000 0.00 0.00 45.16 3.55
2812 3034 8.571461 ACACATTAGCACAGTACTTAGTACTA 57.429 34.615 22.66 8.56 46.08 1.82
2850 3072 5.292101 GTGATAAGAACCGGAGAACATCTTG 59.708 44.000 9.46 0.00 32.87 3.02
2944 3166 8.537728 TGGACTTAGGACGGATAAAAATACTA 57.462 34.615 0.00 0.00 0.00 1.82
2965 3187 6.502136 AAACAAGAGCTTAGCTAATTGGAC 57.498 37.500 25.41 7.45 39.88 4.02
2967 3189 6.095377 CCAAAACAAGAGCTTAGCTAATTGG 58.905 40.000 25.41 19.43 39.88 3.16
3016 3395 8.358148 GTGAGCCATCATATTTCATGAAGAATT 58.642 33.333 8.41 0.00 37.87 2.17
3023 3403 7.381408 GTCAATTGTGAGCCATCATATTTCATG 59.619 37.037 5.13 0.00 37.87 3.07
3109 3489 0.250553 TTGTACCGAACAGGGCCAAG 60.251 55.000 6.18 0.00 46.96 3.61
3144 3524 9.399403 TCGAAATCTAGATTTACATTCGATGAG 57.601 33.333 26.76 5.47 40.77 2.90
3252 3633 4.229876 GTTTAGCTCTGAACCAAACATGC 58.770 43.478 0.00 0.00 0.00 4.06
3303 3684 5.012046 GGGAAATCCAATCCACTTTGACTTT 59.988 40.000 1.22 0.00 38.80 2.66
3306 3687 3.831911 TGGGAAATCCAATCCACTTTGAC 59.168 43.478 1.22 0.00 43.84 3.18
3326 3707 3.845781 AGTGGTTATCTAGGTGCATGG 57.154 47.619 0.00 0.00 0.00 3.66
3376 3757 8.791675 ACACTCACCAAAACAATTTCAATTTTT 58.208 25.926 0.00 0.00 0.00 1.94
3378 3759 7.920160 ACACTCACCAAAACAATTTCAATTT 57.080 28.000 0.00 0.00 0.00 1.82
3379 3760 7.823799 AGAACACTCACCAAAACAATTTCAATT 59.176 29.630 0.00 0.00 0.00 2.32
3380 3761 7.330262 AGAACACTCACCAAAACAATTTCAAT 58.670 30.769 0.00 0.00 0.00 2.57
3406 3787 3.316029 TCCACGAAACTTCAGACGTTAGA 59.684 43.478 0.00 0.00 36.86 2.10
3409 3790 2.100252 TCTCCACGAAACTTCAGACGTT 59.900 45.455 0.00 0.00 36.86 3.99
3535 3920 6.702329 ACAGATGACCCTTTTTCTACTAGTG 58.298 40.000 5.39 0.00 0.00 2.74
3536 3921 6.070710 GGACAGATGACCCTTTTTCTACTAGT 60.071 42.308 0.00 0.00 0.00 2.57
3537 3922 6.342111 GGACAGATGACCCTTTTTCTACTAG 58.658 44.000 0.00 0.00 0.00 2.57
3538 3923 5.189145 GGGACAGATGACCCTTTTTCTACTA 59.811 44.000 12.40 0.00 44.84 1.82
3539 3924 4.019231 GGGACAGATGACCCTTTTTCTACT 60.019 45.833 12.40 0.00 44.84 2.57
3540 3925 4.262617 GGGACAGATGACCCTTTTTCTAC 58.737 47.826 12.40 0.00 44.84 2.59
3541 3926 3.055385 CGGGACAGATGACCCTTTTTCTA 60.055 47.826 16.56 0.00 45.84 2.10
3542 3927 2.290323 CGGGACAGATGACCCTTTTTCT 60.290 50.000 16.56 0.00 45.84 2.52
3543 3928 2.084546 CGGGACAGATGACCCTTTTTC 58.915 52.381 16.56 0.00 45.84 2.29
3544 3929 1.271926 CCGGGACAGATGACCCTTTTT 60.272 52.381 16.56 0.00 45.84 1.94
3545 3930 0.328258 CCGGGACAGATGACCCTTTT 59.672 55.000 16.56 0.00 45.84 2.27
3546 3931 0.840722 ACCGGGACAGATGACCCTTT 60.841 55.000 16.56 2.55 45.84 3.11
3547 3932 0.840722 AACCGGGACAGATGACCCTT 60.841 55.000 16.56 4.36 45.84 3.95
3548 3933 1.229529 AACCGGGACAGATGACCCT 60.230 57.895 16.56 0.00 45.84 4.34
3549 3934 1.078426 CAACCGGGACAGATGACCC 60.078 63.158 6.32 9.97 44.81 4.46
3550 3935 1.078426 CCAACCGGGACAGATGACC 60.078 63.158 6.32 0.00 40.01 4.02
3551 3936 0.899720 TACCAACCGGGACAGATGAC 59.100 55.000 6.32 0.00 41.15 3.06
3552 3937 1.553248 CTTACCAACCGGGACAGATGA 59.447 52.381 6.32 0.00 41.15 2.92
3553 3938 1.406887 CCTTACCAACCGGGACAGATG 60.407 57.143 6.32 0.00 41.15 2.90
3554 3939 0.909623 CCTTACCAACCGGGACAGAT 59.090 55.000 6.32 0.00 41.15 2.90
3555 3940 1.196104 CCCTTACCAACCGGGACAGA 61.196 60.000 6.32 0.00 40.55 3.41
3556 3941 1.298667 CCCTTACCAACCGGGACAG 59.701 63.158 6.32 0.00 40.55 3.51
3557 3942 1.461849 ACCCTTACCAACCGGGACA 60.462 57.895 6.32 0.00 40.55 4.02
3558 3943 1.196766 AGACCCTTACCAACCGGGAC 61.197 60.000 6.32 0.00 40.55 4.46
3559 3944 0.474273 AAGACCCTTACCAACCGGGA 60.474 55.000 6.32 0.00 40.55 5.14
3560 3945 0.402887 AAAGACCCTTACCAACCGGG 59.597 55.000 6.32 0.00 43.79 5.73
3561 3946 1.883926 CAAAAGACCCTTACCAACCGG 59.116 52.381 0.00 0.00 38.77 5.28
3562 3947 2.551032 GACAAAAGACCCTTACCAACCG 59.449 50.000 0.00 0.00 0.00 4.44
3563 3948 2.889045 GGACAAAAGACCCTTACCAACC 59.111 50.000 0.00 0.00 0.00 3.77
3564 3949 2.889045 GGGACAAAAGACCCTTACCAAC 59.111 50.000 0.00 0.00 42.56 3.77
3565 3950 2.487625 CGGGACAAAAGACCCTTACCAA 60.488 50.000 0.00 0.00 43.57 3.67
3566 3951 1.072648 CGGGACAAAAGACCCTTACCA 59.927 52.381 0.00 0.00 43.57 3.25
3567 3952 1.612462 CCGGGACAAAAGACCCTTACC 60.612 57.143 0.00 0.00 43.57 2.85
3568 3953 1.072806 ACCGGGACAAAAGACCCTTAC 59.927 52.381 6.32 0.00 43.57 2.34
3569 3954 1.437397 ACCGGGACAAAAGACCCTTA 58.563 50.000 6.32 0.00 43.57 2.69
3570 3955 0.554305 AACCGGGACAAAAGACCCTT 59.446 50.000 6.32 0.00 43.57 3.95
3571 3956 0.554305 AAACCGGGACAAAAGACCCT 59.446 50.000 6.32 0.00 43.57 4.34
3572 3957 1.405872 AAAACCGGGACAAAAGACCC 58.594 50.000 6.32 0.00 42.43 4.46
3573 3958 2.427812 TCAAAAACCGGGACAAAAGACC 59.572 45.455 6.32 0.00 0.00 3.85
3574 3959 3.786516 TCAAAAACCGGGACAAAAGAC 57.213 42.857 6.32 0.00 0.00 3.01
3575 3960 3.510360 TGTTCAAAAACCGGGACAAAAGA 59.490 39.130 6.32 0.00 34.28 2.52
3576 3961 3.851098 TGTTCAAAAACCGGGACAAAAG 58.149 40.909 6.32 0.00 34.28 2.27
3577 3962 3.368531 CCTGTTCAAAAACCGGGACAAAA 60.369 43.478 6.32 0.00 36.43 2.44
3578 3963 2.166664 CCTGTTCAAAAACCGGGACAAA 59.833 45.455 6.32 0.00 36.43 2.83
3579 3964 1.751924 CCTGTTCAAAAACCGGGACAA 59.248 47.619 6.32 0.00 36.43 3.18
3580 3965 1.394618 CCTGTTCAAAAACCGGGACA 58.605 50.000 6.32 0.00 36.43 4.02
3584 3969 1.687563 AGTCCCTGTTCAAAAACCGG 58.312 50.000 0.00 0.00 38.95 5.28
3585 3970 4.261447 CCTTTAGTCCCTGTTCAAAAACCG 60.261 45.833 0.00 0.00 34.28 4.44
3586 3971 4.038763 CCCTTTAGTCCCTGTTCAAAAACC 59.961 45.833 0.00 0.00 34.28 3.27
3587 3972 4.647853 ACCCTTTAGTCCCTGTTCAAAAAC 59.352 41.667 0.00 0.00 35.85 2.43
3588 3973 4.874199 ACCCTTTAGTCCCTGTTCAAAAA 58.126 39.130 0.00 0.00 0.00 1.94
3589 3974 4.466827 GACCCTTTAGTCCCTGTTCAAAA 58.533 43.478 0.00 0.00 0.00 2.44
3590 3975 3.495453 CGACCCTTTAGTCCCTGTTCAAA 60.495 47.826 0.00 0.00 32.91 2.69
3591 3976 2.038033 CGACCCTTTAGTCCCTGTTCAA 59.962 50.000 0.00 0.00 32.91 2.69
3592 3977 1.621814 CGACCCTTTAGTCCCTGTTCA 59.378 52.381 0.00 0.00 32.91 3.18
3593 3978 1.622312 ACGACCCTTTAGTCCCTGTTC 59.378 52.381 0.00 0.00 32.91 3.18
3594 3979 1.725803 ACGACCCTTTAGTCCCTGTT 58.274 50.000 0.00 0.00 32.91 3.16
3595 3980 1.725803 AACGACCCTTTAGTCCCTGT 58.274 50.000 0.00 0.00 32.91 4.00
3596 3981 2.830321 AGTAACGACCCTTTAGTCCCTG 59.170 50.000 0.00 0.00 32.91 4.45
3597 3982 3.181393 AGTAACGACCCTTTAGTCCCT 57.819 47.619 0.00 0.00 32.91 4.20
3598 3983 5.354767 CATTAGTAACGACCCTTTAGTCCC 58.645 45.833 0.00 0.00 32.91 4.46
3599 3984 4.807834 GCATTAGTAACGACCCTTTAGTCC 59.192 45.833 0.00 0.00 32.91 3.85
3600 3985 4.807834 GGCATTAGTAACGACCCTTTAGTC 59.192 45.833 0.00 0.00 0.00 2.59
3601 3986 4.383444 GGGCATTAGTAACGACCCTTTAGT 60.383 45.833 8.75 0.00 34.34 2.24
3602 3987 4.124970 GGGCATTAGTAACGACCCTTTAG 58.875 47.826 8.75 0.00 34.34 1.85
3603 3988 3.776417 AGGGCATTAGTAACGACCCTTTA 59.224 43.478 11.72 0.00 45.55 1.85
3604 3989 2.574824 AGGGCATTAGTAACGACCCTTT 59.425 45.455 11.72 0.00 45.55 3.11
3605 3990 2.193993 AGGGCATTAGTAACGACCCTT 58.806 47.619 11.72 0.48 45.55 3.95
3606 3991 1.875488 AGGGCATTAGTAACGACCCT 58.125 50.000 11.72 11.72 42.97 4.34
3607 3992 2.547430 GCTAGGGCATTAGTAACGACCC 60.547 54.545 0.00 3.07 38.54 4.46
3608 3993 2.547430 GGCTAGGGCATTAGTAACGACC 60.547 54.545 0.00 0.00 40.87 4.79
3609 3994 2.547430 GGGCTAGGGCATTAGTAACGAC 60.547 54.545 0.00 0.00 40.87 4.34
3610 3995 1.690352 GGGCTAGGGCATTAGTAACGA 59.310 52.381 0.00 0.00 40.87 3.85
3611 3996 1.692519 AGGGCTAGGGCATTAGTAACG 59.307 52.381 0.00 0.00 40.87 3.18
3612 3997 3.859061 AAGGGCTAGGGCATTAGTAAC 57.141 47.619 0.00 0.00 40.87 2.50
3613 3998 4.973211 ACTAAAGGGCTAGGGCATTAGTAA 59.027 41.667 14.68 0.00 39.59 2.24
3614 3999 4.563782 ACTAAAGGGCTAGGGCATTAGTA 58.436 43.478 14.68 0.00 39.59 1.82
3615 4000 3.391626 GACTAAAGGGCTAGGGCATTAGT 59.608 47.826 15.56 15.56 41.69 2.24
3616 4001 3.244596 GGACTAAAGGGCTAGGGCATTAG 60.245 52.174 11.36 11.36 40.87 1.73
3617 4002 2.709397 GGACTAAAGGGCTAGGGCATTA 59.291 50.000 0.00 0.00 40.87 1.90
3618 4003 1.495148 GGACTAAAGGGCTAGGGCATT 59.505 52.381 0.00 0.00 40.87 3.56
3619 4004 1.141185 GGACTAAAGGGCTAGGGCAT 58.859 55.000 0.00 0.00 40.87 4.40
3620 4005 0.986550 GGGACTAAAGGGCTAGGGCA 60.987 60.000 0.00 0.00 40.87 5.36
3621 4006 1.837789 GGGACTAAAGGGCTAGGGC 59.162 63.158 0.00 0.00 37.82 5.19
3622 4007 1.408453 CCGGGACTAAAGGGCTAGGG 61.408 65.000 0.00 0.00 0.00 3.53
3623 4008 0.690077 ACCGGGACTAAAGGGCTAGG 60.690 60.000 6.32 0.00 0.00 3.02
3624 4009 1.138464 GAACCGGGACTAAAGGGCTAG 59.862 57.143 6.32 0.00 0.00 3.42
3625 4010 1.197812 GAACCGGGACTAAAGGGCTA 58.802 55.000 6.32 0.00 0.00 3.93
3626 4011 0.546988 AGAACCGGGACTAAAGGGCT 60.547 55.000 6.32 0.00 0.00 5.19
3627 4012 0.327259 AAGAACCGGGACTAAAGGGC 59.673 55.000 6.32 0.00 0.00 5.19
3628 4013 2.568509 TGTAAGAACCGGGACTAAAGGG 59.431 50.000 6.32 0.00 0.00 3.95
3629 4014 3.593096 GTGTAAGAACCGGGACTAAAGG 58.407 50.000 6.32 0.00 0.00 3.11
3630 4015 3.057315 TCGTGTAAGAACCGGGACTAAAG 60.057 47.826 6.32 0.00 0.00 1.85
3631 4016 2.890311 TCGTGTAAGAACCGGGACTAAA 59.110 45.455 6.32 0.00 0.00 1.85
3632 4017 2.513753 TCGTGTAAGAACCGGGACTAA 58.486 47.619 6.32 0.00 0.00 2.24
3633 4018 2.198827 TCGTGTAAGAACCGGGACTA 57.801 50.000 6.32 0.00 0.00 2.59
3634 4019 1.000171 GTTCGTGTAAGAACCGGGACT 60.000 52.381 6.32 0.73 43.33 3.85
3635 4020 1.422388 GTTCGTGTAAGAACCGGGAC 58.578 55.000 6.32 0.00 43.33 4.46
3636 4021 3.892200 GTTCGTGTAAGAACCGGGA 57.108 52.632 6.32 0.00 43.33 5.14
3642 4027 3.355378 TCTATCCCGGTTCGTGTAAGAA 58.645 45.455 0.00 0.00 0.00 2.52
3643 4028 3.003394 TCTATCCCGGTTCGTGTAAGA 57.997 47.619 0.00 0.00 0.00 2.10
3644 4029 3.552273 CCATCTATCCCGGTTCGTGTAAG 60.552 52.174 0.00 0.00 0.00 2.34
3645 4030 2.363038 CCATCTATCCCGGTTCGTGTAA 59.637 50.000 0.00 0.00 0.00 2.41
3646 4031 1.958579 CCATCTATCCCGGTTCGTGTA 59.041 52.381 0.00 0.00 0.00 2.90
3647 4032 0.750850 CCATCTATCCCGGTTCGTGT 59.249 55.000 0.00 0.00 0.00 4.49
3648 4033 0.033504 CCCATCTATCCCGGTTCGTG 59.966 60.000 0.00 0.00 0.00 4.35
3649 4034 1.755393 GCCCATCTATCCCGGTTCGT 61.755 60.000 0.00 0.00 0.00 3.85
3650 4035 1.004918 GCCCATCTATCCCGGTTCG 60.005 63.158 0.00 0.00 0.00 3.95
3651 4036 1.128188 AGGCCCATCTATCCCGGTTC 61.128 60.000 0.00 0.00 0.00 3.62
3652 4037 1.073706 AGGCCCATCTATCCCGGTT 60.074 57.895 0.00 0.00 0.00 4.44
3653 4038 1.536662 GAGGCCCATCTATCCCGGT 60.537 63.158 0.00 0.00 0.00 5.28
3654 4039 2.294078 GGAGGCCCATCTATCCCGG 61.294 68.421 0.00 0.00 0.00 5.73
3655 4040 1.536418 TGGAGGCCCATCTATCCCG 60.536 63.158 0.00 0.00 37.58 5.14
3656 4041 1.831652 CGTGGAGGCCCATCTATCCC 61.832 65.000 0.00 0.00 45.68 3.85
3657 4042 1.122019 ACGTGGAGGCCCATCTATCC 61.122 60.000 0.00 0.00 45.68 2.59
3658 4043 0.034059 CACGTGGAGGCCCATCTATC 59.966 60.000 7.95 0.00 45.68 2.08
3659 4044 1.410850 CCACGTGGAGGCCCATCTAT 61.411 60.000 31.31 0.00 45.68 1.98
3660 4045 2.063979 CCACGTGGAGGCCCATCTA 61.064 63.158 31.31 0.00 45.68 1.98
3661 4046 3.402681 CCACGTGGAGGCCCATCT 61.403 66.667 31.31 0.00 45.68 2.90
3697 4082 2.361737 GACCAAAGGCCCTCCTGC 60.362 66.667 0.00 0.00 43.40 4.85
3698 4083 2.356667 GGACCAAAGGCCCTCCTG 59.643 66.667 0.00 0.00 43.40 3.86
3700 4085 4.426313 CGGGACCAAAGGCCCTCC 62.426 72.222 0.00 0.00 37.05 4.30
3701 4086 4.426313 CCGGGACCAAAGGCCCTC 62.426 72.222 0.00 0.00 37.05 4.30
3703 4088 4.295199 AACCGGGACCAAAGGCCC 62.295 66.667 6.32 0.00 36.26 5.80
3704 4089 2.989253 CAACCGGGACCAAAGGCC 60.989 66.667 6.32 0.00 0.00 5.19
3705 4090 2.989253 CCAACCGGGACCAAAGGC 60.989 66.667 6.32 0.00 40.01 4.35
3706 4091 1.901464 CACCAACCGGGACCAAAGG 60.901 63.158 6.32 0.00 41.15 3.11
3707 4092 1.901464 CCACCAACCGGGACCAAAG 60.901 63.158 6.32 0.00 41.15 2.77
3708 4093 2.196229 CCACCAACCGGGACCAAA 59.804 61.111 6.32 0.00 41.15 3.28
3709 4094 4.589675 GCCACCAACCGGGACCAA 62.590 66.667 6.32 0.00 41.15 3.67
3712 4097 2.886134 TAGTGCCACCAACCGGGAC 61.886 63.158 6.32 0.00 44.66 4.46
3713 4098 2.527123 TAGTGCCACCAACCGGGA 60.527 61.111 6.32 0.00 41.15 5.14


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

AutoCloner maintained by Alex Coulton.