Multiple sequence alignment - TraesCS7D01G512100

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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 TraesCS7D01G512100 chr7D 100.000 4649 0 0 1 4649 613866773 613871421 0.000000e+00 8586.0
1 TraesCS7D01G512100 chr7D 94.565 92 5 0 2230 2321 626199969 626199878 4.850000e-30 143.0
2 TraesCS7D01G512100 chr7D 83.459 133 12 9 3850 3980 38641590 38641466 1.060000e-21 115.0
3 TraesCS7D01G512100 chr7B 92.175 1508 82 21 2315 3806 705252548 705254035 0.000000e+00 2098.0
4 TraesCS7D01G512100 chr7B 89.384 1413 95 13 843 2227 705251158 705252543 0.000000e+00 1727.0
5 TraesCS7D01G512100 chr7B 92.157 663 33 6 4000 4649 705254125 705254781 0.000000e+00 918.0
6 TraesCS7D01G512100 chr7B 92.857 98 6 1 2230 2327 208276708 208276804 1.740000e-29 141.0
7 TraesCS7D01G512100 chr7B 93.478 92 5 1 2230 2321 62852510 62852600 8.110000e-28 135.0
8 TraesCS7D01G512100 chr7B 91.089 101 7 2 2223 2322 739935357 739935258 8.110000e-28 135.0
9 TraesCS7D01G512100 chr7B 83.871 124 16 4 3859 3982 419527370 419527489 1.060000e-21 115.0
10 TraesCS7D01G512100 chr7B 83.898 118 15 4 3864 3981 419527488 419527375 4.920000e-20 110.0
11 TraesCS7D01G512100 chr7B 82.443 131 13 6 3864 3988 115523710 115523584 6.360000e-19 106.0
12 TraesCS7D01G512100 chr7A 94.517 1295 60 6 2315 3609 705686205 705687488 0.000000e+00 1988.0
13 TraesCS7D01G512100 chr7A 90.306 1403 84 23 859 2226 705684814 705686199 0.000000e+00 1790.0
14 TraesCS7D01G512100 chr7A 95.067 669 30 1 3984 4649 705687719 705688387 0.000000e+00 1050.0
15 TraesCS7D01G512100 chr7A 89.859 779 62 10 2822 3596 34788292 34789057 0.000000e+00 985.0
16 TraesCS7D01G512100 chr7A 94.304 316 16 2 2214 2528 34787523 34787837 2.520000e-132 483.0
17 TraesCS7D01G512100 chr7A 87.854 247 11 5 3634 3866 705687483 705687724 5.930000e-69 272.0
18 TraesCS7D01G512100 chr6A 85.695 748 85 17 105 843 555211263 555211997 0.000000e+00 769.0
19 TraesCS7D01G512100 chr6A 93.617 94 4 2 2229 2321 462268521 462268613 6.270000e-29 139.0
20 TraesCS7D01G512100 chr6A 93.407 91 6 0 2230 2320 142784310 142784220 8.110000e-28 135.0
21 TraesCS7D01G512100 chr6A 84.298 121 7 9 3862 3981 53117825 53117716 1.770000e-19 108.0
22 TraesCS7D01G512100 chr2B 90.070 574 41 13 29 591 794323021 794323589 0.000000e+00 730.0
23 TraesCS7D01G512100 chr2B 85.366 123 10 6 3864 3981 25018791 25018672 2.270000e-23 121.0
24 TraesCS7D01G512100 chr2B 82.857 140 13 9 3849 3981 25018656 25018791 1.060000e-21 115.0
25 TraesCS7D01G512100 chr1D 85.482 737 64 27 144 848 355673797 355673072 0.000000e+00 728.0
26 TraesCS7D01G512100 chr1D 95.294 85 4 0 2230 2314 104427170 104427254 8.110000e-28 135.0
27 TraesCS7D01G512100 chr1D 88.889 81 5 4 3906 3984 286378396 286378318 3.830000e-16 97.1
28 TraesCS7D01G512100 chr1D 87.179 78 6 4 3854 3929 389356904 389356979 8.290000e-13 86.1
29 TraesCS7D01G512100 chr6B 83.333 804 106 21 55 840 198913843 198914636 0.000000e+00 717.0
30 TraesCS7D01G512100 chr6B 91.837 98 7 1 2230 2326 8925439 8925536 8.110000e-28 135.0
31 TraesCS7D01G512100 chr6B 86.777 121 10 6 3862 3981 106468771 106468656 3.780000e-26 130.0
32 TraesCS7D01G512100 chr1B 86.870 655 61 22 143 786 47203403 47202763 0.000000e+00 710.0
33 TraesCS7D01G512100 chr1B 96.471 85 3 0 2230 2314 322104547 322104631 1.740000e-29 141.0
34 TraesCS7D01G512100 chr1B 90.099 101 8 2 2230 2328 53076308 53076208 3.780000e-26 130.0
35 TraesCS7D01G512100 chr1B 84.127 126 9 8 3864 3981 420362952 420363074 1.370000e-20 111.0
36 TraesCS7D01G512100 chr1B 83.333 126 10 7 3864 3981 420363074 420362952 6.360000e-19 106.0
37 TraesCS7D01G512100 chr1B 82.400 125 11 8 3863 3981 439843957 439844076 1.060000e-16 99.0
38 TraesCS7D01G512100 chr4D 88.966 580 48 13 278 846 434096311 434095737 0.000000e+00 702.0
39 TraesCS7D01G512100 chr4D 83.453 695 94 17 161 843 123092525 123093210 1.100000e-175 627.0
40 TraesCS7D01G512100 chr4D 95.349 86 4 0 2230 2315 64543014 64543099 2.260000e-28 137.0
41 TraesCS7D01G512100 chr4D 94.253 87 5 0 2230 2316 428390098 428390184 2.920000e-27 134.0
42 TraesCS7D01G512100 chr4D 94.118 85 5 0 2230 2314 24455801 24455885 3.780000e-26 130.0
43 TraesCS7D01G512100 chr4D 94.828 58 1 2 3863 3920 117421190 117421245 6.410000e-14 89.8
44 TraesCS7D01G512100 chr4D 87.500 80 6 4 3906 3983 335890661 335890584 6.410000e-14 89.8
45 TraesCS7D01G512100 chr4D 89.706 68 5 2 3913 3980 130853264 130853329 8.290000e-13 86.1
46 TraesCS7D01G512100 chr4D 89.706 68 6 1 3913 3980 178015139 178015073 8.290000e-13 86.1
47 TraesCS7D01G512100 chr4D 86.667 75 7 3 3864 3938 48062530 48062459 3.860000e-11 80.5
48 TraesCS7D01G512100 chr3D 83.979 749 94 21 105 841 580344382 580345116 0.000000e+00 695.0
49 TraesCS7D01G512100 chr5B 84.150 694 83 20 166 844 349089128 349088447 0.000000e+00 647.0
50 TraesCS7D01G512100 chr5B 93.684 95 6 0 2230 2324 406172763 406172669 4.850000e-30 143.0
51 TraesCS7D01G512100 chr5B 89.076 119 6 4 3864 3982 344615819 344615930 1.740000e-29 141.0
52 TraesCS7D01G512100 chr5B 88.073 109 11 2 2212 2318 206473002 206473110 1.360000e-25 128.0
53 TraesCS7D01G512100 chr5B 85.593 118 10 6 3864 3981 344615929 344615819 2.940000e-22 117.0
54 TraesCS7D01G512100 chr5A 81.884 828 83 22 48 842 435701980 435702773 1.820000e-178 636.0
55 TraesCS7D01G512100 chr5A 94.792 96 5 0 2229 2324 536863616 536863521 2.900000e-32 150.0
56 TraesCS7D01G512100 chr2D 85.745 463 50 13 1 456 450874518 450874971 4.210000e-130 475.0
57 TraesCS7D01G512100 chr2D 88.235 119 8 5 3863 3979 627911301 627911187 2.260000e-28 137.0
58 TraesCS7D01G512100 chr2D 88.136 118 8 6 3866 3981 627911187 627911300 8.110000e-28 135.0
59 TraesCS7D01G512100 chr4A 97.647 85 2 0 2230 2314 464687364 464687280 3.750000e-31 147.0
60 TraesCS7D01G512100 chr6D 87.500 128 8 8 3860 3984 462028362 462028484 1.740000e-29 141.0
61 TraesCS7D01G512100 chr6D 87.931 116 10 4 3863 3978 382346981 382346870 2.920000e-27 134.0
62 TraesCS7D01G512100 chr6D 85.950 121 10 7 3864 3982 462028481 462028366 6.320000e-24 122.0
63 TraesCS7D01G512100 chr6D 94.286 70 3 1 3913 3982 427220921 427220989 6.360000e-19 106.0
64 TraesCS7D01G512100 chr6D 85.437 103 6 7 3865 3962 11053443 11053541 1.060000e-16 99.0
65 TraesCS7D01G512100 chr6D 92.754 69 3 2 3914 3982 11717557 11717491 1.060000e-16 99.0
66 TraesCS7D01G512100 chr6D 91.176 68 2 4 3854 3918 355860387 355860453 6.410000e-14 89.8
67 TraesCS7D01G512100 chr6D 94.737 57 1 2 3864 3920 48457973 48458027 2.300000e-13 87.9
68 TraesCS7D01G512100 chr6D 91.667 60 3 2 3913 3971 76835897 76835955 1.070000e-11 82.4
69 TraesCS7D01G512100 chr6D 88.235 68 7 1 3913 3980 198777727 198777661 3.860000e-11 80.5
70 TraesCS7D01G512100 chr3B 93.617 94 6 0 2230 2323 237977332 237977239 1.740000e-29 141.0
71 TraesCS7D01G512100 chr5D 92.632 95 7 0 2229 2323 267842763 267842669 2.260000e-28 137.0
72 TraesCS7D01G512100 chr5D 95.349 86 4 0 2230 2315 522111513 522111428 2.260000e-28 137.0
73 TraesCS7D01G512100 chr5D 91.000 100 6 3 2230 2326 342696382 342696481 1.050000e-26 132.0
74 TraesCS7D01G512100 chr5D 84.921 126 9 7 3864 3982 13912948 13913070 8.170000e-23 119.0
75 TraesCS7D01G512100 chr5D 90.789 76 3 4 3908 3981 542971152 542971225 1.060000e-16 99.0
76 TraesCS7D01G512100 chr5D 87.356 87 7 4 3864 3949 483521555 483521638 3.830000e-16 97.1
77 TraesCS7D01G512100 chr4B 95.349 86 4 0 2229 2314 616769097 616769012 2.260000e-28 137.0
78 TraesCS7D01G512100 chr4B 95.294 85 4 0 2230 2314 18440919 18440835 8.110000e-28 135.0
79 TraesCS7D01G512100 chr4B 93.407 91 6 0 2230 2320 187091067 187091157 8.110000e-28 135.0
80 TraesCS7D01G512100 chr4B 90.625 96 8 1 2230 2325 70561774 70561868 4.880000e-25 126.0
81 TraesCS7D01G512100 chr4B 89.474 76 3 4 3908 3981 59479012 59479084 1.780000e-14 91.6
82 TraesCS7D01G512100 chr4B 85.227 88 4 6 3856 3938 446769103 446769186 1.070000e-11 82.4
83 TraesCS7D01G512100 chrUn 92.308 91 7 0 2231 2321 343556711 343556801 3.780000e-26 130.0
84 TraesCS7D01G512100 chrUn 92.308 91 7 0 2231 2321 376516785 376516875 3.780000e-26 130.0
85 TraesCS7D01G512100 chrUn 91.304 92 8 0 2230 2321 333321179 333321270 4.880000e-25 126.0
86 TraesCS7D01G512100 chrUn 91.304 92 8 0 2230 2321 336906437 336906346 4.880000e-25 126.0
87 TraesCS7D01G512100 chrUn 91.304 92 8 0 2230 2321 336908069 336907978 4.880000e-25 126.0
88 TraesCS7D01G512100 chrUn 91.304 92 8 0 2230 2321 336908613 336908522 4.880000e-25 126.0
89 TraesCS7D01G512100 chrUn 91.304 92 8 0 2230 2321 361682635 361682726 4.880000e-25 126.0
90 TraesCS7D01G512100 chrUn 91.304 92 8 0 2230 2321 361735424 361735333 4.880000e-25 126.0
91 TraesCS7D01G512100 chrUn 91.304 92 8 0 2230 2321 363221950 363221859 4.880000e-25 126.0
92 TraesCS7D01G512100 chrUn 90.526 95 8 1 2230 2324 23609562 23609469 1.760000e-24 124.0
93 TraesCS7D01G512100 chrUn 93.103 58 2 2 3864 3920 74677078 74677134 2.980000e-12 84.2
94 TraesCS7D01G512100 chrUn 94.545 55 2 1 3854 3908 96464982 96464929 2.980000e-12 84.2
95 TraesCS7D01G512100 chrUn 89.706 68 4 3 3913 3980 98021790 98021726 2.980000e-12 84.2
96 TraesCS7D01G512100 chrUn 87.179 78 5 4 3864 3938 323779663 323779588 2.980000e-12 84.2
97 TraesCS7D01G512100 chrUn 92.982 57 2 2 3864 3920 41734215 41734269 1.070000e-11 82.4
98 TraesCS7D01G512100 chrUn 96.078 51 0 2 3861 3911 86671314 86671362 1.070000e-11 82.4
99 TraesCS7D01G512100 chrUn 91.667 60 3 2 3861 3920 271159154 271159211 1.070000e-11 82.4
100 TraesCS7D01G512100 chrUn 91.667 60 3 2 3861 3920 289933968 289934025 1.070000e-11 82.4
101 TraesCS7D01G512100 chrUn 94.231 52 3 0 3857 3908 363525687 363525636 3.860000e-11 80.5
102 TraesCS7D01G512100 chrUn 88.060 67 6 2 3863 3929 21367989 21367925 1.390000e-10 78.7
103 TraesCS7D01G512100 chrUn 92.857 56 1 3 3864 3919 43287793 43287845 1.390000e-10 78.7
104 TraesCS7D01G512100 chrUn 92.857 56 1 3 3864 3919 70231880 70231828 1.390000e-10 78.7
105 TraesCS7D01G512100 chrUn 86.957 69 7 2 3913 3981 468628807 468628741 4.990000e-10 76.8
106 TraesCS7D01G512100 chrUn 82.927 82 8 4 3864 3941 115107902 115107981 8.350000e-08 69.4
107 TraesCS7D01G512100 chrUn 86.364 66 5 2 3920 3985 132151496 132151557 8.350000e-08 69.4
108 TraesCS7D01G512100 chrUn 83.951 81 4 7 3864 3938 272972332 272972255 8.350000e-08 69.4
109 TraesCS7D01G512100 chrUn 82.143 84 10 3 3859 3938 298877557 298877639 3.000000e-07 67.6
110 TraesCS7D01G512100 chr1A 93.182 88 6 0 2227 2314 48977162 48977249 3.780000e-26 130.0
111 TraesCS7D01G512100 chr1A 88.158 76 5 3 3857 3929 532768404 532768330 2.300000e-13 87.9


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 TraesCS7D01G512100 chr7D 613866773 613871421 4648 False 8586 8586 100.000000 1 4649 1 chr7D.!!$F1 4648
1 TraesCS7D01G512100 chr7B 705251158 705254781 3623 False 1581 2098 91.238667 843 4649 3 chr7B.!!$F4 3806
2 TraesCS7D01G512100 chr7A 705684814 705688387 3573 False 1275 1988 91.936000 859 4649 4 chr7A.!!$F2 3790
3 TraesCS7D01G512100 chr7A 34787523 34789057 1534 False 734 985 92.081500 2214 3596 2 chr7A.!!$F1 1382
4 TraesCS7D01G512100 chr6A 555211263 555211997 734 False 769 769 85.695000 105 843 1 chr6A.!!$F2 738
5 TraesCS7D01G512100 chr2B 794323021 794323589 568 False 730 730 90.070000 29 591 1 chr2B.!!$F2 562
6 TraesCS7D01G512100 chr1D 355673072 355673797 725 True 728 728 85.482000 144 848 1 chr1D.!!$R2 704
7 TraesCS7D01G512100 chr6B 198913843 198914636 793 False 717 717 83.333000 55 840 1 chr6B.!!$F2 785
8 TraesCS7D01G512100 chr1B 47202763 47203403 640 True 710 710 86.870000 143 786 1 chr1B.!!$R1 643
9 TraesCS7D01G512100 chr4D 434095737 434096311 574 True 702 702 88.966000 278 846 1 chr4D.!!$R4 568
10 TraesCS7D01G512100 chr4D 123092525 123093210 685 False 627 627 83.453000 161 843 1 chr4D.!!$F4 682
11 TraesCS7D01G512100 chr3D 580344382 580345116 734 False 695 695 83.979000 105 841 1 chr3D.!!$F1 736
12 TraesCS7D01G512100 chr5B 349088447 349089128 681 True 647 647 84.150000 166 844 1 chr5B.!!$R2 678
13 TraesCS7D01G512100 chr5A 435701980 435702773 793 False 636 636 81.884000 48 842 1 chr5A.!!$F1 794

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
26 27 0.028505 CGGCCATGCATCTCGAAAAG 59.971 55.0 2.24 0.00 0.0 2.27 F
928 1195 0.321653 ATCCACGAAGCCCAGACAAC 60.322 55.0 0.00 0.00 0.0 3.32 F
1245 1541 1.043116 TGTCCCTGCTCATACCCTCG 61.043 60.0 0.00 0.00 0.0 4.63 F
2939 3439 0.735978 TGGTGCACTCATCTAACGCG 60.736 55.0 17.98 3.53 0.0 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 1798 0.252197 ACCAACCGAGCCACCTAATC 59.748 55.000 0.00 0.0 0.00 1.75 R
2926 3426 0.739813 GGCAACCGCGTTAGATGAGT 60.740 55.000 4.92 0.0 39.92 3.41 R
3087 3587 4.103627 ACAATCAGGCCATGTATGATCAGA 59.896 41.667 5.01 0.0 32.59 3.27 R
4432 4994 0.036010 CGGTGAGGCCTCTGTTCATT 60.036 55.000 32.28 0.0 34.25 2.57 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
17 18 2.993008 AGAGTCACGGCCATGCAT 59.007 55.556 2.24 0.00 0.00 3.96
18 19 1.153289 AGAGTCACGGCCATGCATC 60.153 57.895 2.24 0.00 0.00 3.91
19 20 1.153289 GAGTCACGGCCATGCATCT 60.153 57.895 2.24 0.00 0.00 2.90
20 21 1.153289 AGTCACGGCCATGCATCTC 60.153 57.895 2.24 0.00 0.00 2.75
21 22 2.202919 TCACGGCCATGCATCTCG 60.203 61.111 2.24 3.65 0.00 4.04
22 23 2.202919 CACGGCCATGCATCTCGA 60.203 61.111 16.47 0.00 0.00 4.04
23 24 1.815003 CACGGCCATGCATCTCGAA 60.815 57.895 16.47 0.00 0.00 3.71
24 25 1.078497 ACGGCCATGCATCTCGAAA 60.078 52.632 16.47 0.00 0.00 3.46
25 26 0.676466 ACGGCCATGCATCTCGAAAA 60.676 50.000 16.47 0.00 0.00 2.29
26 27 0.028505 CGGCCATGCATCTCGAAAAG 59.971 55.000 2.24 0.00 0.00 2.27
27 28 1.382522 GGCCATGCATCTCGAAAAGA 58.617 50.000 0.00 0.00 38.72 2.52
113 114 2.174969 ACGGTTGTGCTTTCGCGAA 61.175 52.632 19.38 19.38 39.65 4.70
115 116 0.385473 CGGTTGTGCTTTCGCGAAAT 60.385 50.000 32.28 0.00 39.65 2.17
140 143 1.019278 GCCGTGCCTCTCGAAAATGA 61.019 55.000 0.00 0.00 0.00 2.57
141 144 1.438651 CCGTGCCTCTCGAAAATGAA 58.561 50.000 0.00 0.00 0.00 2.57
189 195 2.551032 TCTTTCGCGAGAGTCACAGTTA 59.449 45.455 24.05 1.63 43.69 2.24
321 375 1.372997 GCTTCCGCAAGAGTCACGA 60.373 57.895 0.00 0.00 43.02 4.35
328 382 1.299850 CAAGAGTCACGACCGTGCA 60.300 57.895 16.76 4.47 45.04 4.57
340 480 4.910956 CGTGCATCTCGGAAAGGA 57.089 55.556 0.00 0.00 0.00 3.36
630 890 7.283127 TCAAAACCTATCAACATGGAATCTAGC 59.717 37.037 0.00 0.00 0.00 3.42
910 1177 2.037208 CCCCAGTTTTCGGCCCAT 59.963 61.111 0.00 0.00 0.00 4.00
911 1178 2.052104 CCCCAGTTTTCGGCCCATC 61.052 63.158 0.00 0.00 0.00 3.51
928 1195 0.321653 ATCCACGAAGCCCAGACAAC 60.322 55.000 0.00 0.00 0.00 3.32
1229 1525 2.531206 GACCTCGACAGTAAGCATGTC 58.469 52.381 0.00 0.00 42.94 3.06
1245 1541 1.043116 TGTCCCTGCTCATACCCTCG 61.043 60.000 0.00 0.00 0.00 4.63
1261 1557 2.005451 CCTCGGTTCAGATCAAGCAAG 58.995 52.381 0.00 0.00 0.00 4.01
1263 1559 3.368427 CCTCGGTTCAGATCAAGCAAGTA 60.368 47.826 0.00 0.00 0.00 2.24
1396 1705 7.868922 GCCTGCAATATGTATGATGAAAATTGA 59.131 33.333 0.00 0.00 0.00 2.57
1397 1706 9.752961 CCTGCAATATGTATGATGAAAATTGAA 57.247 29.630 0.00 0.00 0.00 2.69
1432 1744 5.342017 TGAGGTCAGGAGAAGGAAAGATTA 58.658 41.667 0.00 0.00 0.00 1.75
1438 1750 7.106239 GTCAGGAGAAGGAAAGATTATGAACA 58.894 38.462 0.00 0.00 0.00 3.18
1486 1798 3.204827 GGCTATGTGCACTGGCCG 61.205 66.667 24.03 9.29 45.15 6.13
1495 1807 1.819632 GCACTGGCCGATTAGGTGG 60.820 63.158 0.00 0.00 43.70 4.61
1520 1832 2.821366 GGTGCTCATCAGGCCGTG 60.821 66.667 0.00 0.00 0.00 4.94
1523 1835 1.987306 TGCTCATCAGGCCGTGGTA 60.987 57.895 0.00 0.00 0.00 3.25
1543 1855 5.600908 GTAATTTACCAGCGTTTCTGTCA 57.399 39.130 0.00 0.00 41.25 3.58
1692 2004 2.125472 TTCGCCGCGCCTATGAAA 60.125 55.556 8.21 0.00 0.00 2.69
1841 2153 7.147828 TGGAAGAAATGTGTTTTGTGGTGAATA 60.148 33.333 0.00 0.00 0.00 1.75
1852 2164 6.951062 TTTGTGGTGAATATGTGTTCTGAA 57.049 33.333 0.00 0.00 0.00 3.02
1861 2173 8.292448 GTGAATATGTGTTCTGAACATGTTTCT 58.708 33.333 24.44 9.48 44.35 2.52
1930 2242 3.462021 GATAGCTTGGCAGTACAGGAAG 58.538 50.000 0.00 0.00 0.00 3.46
1955 2267 1.327690 TGGGGACGAGAGGAATTCCG 61.328 60.000 18.82 9.38 42.08 4.30
1994 2307 3.772572 TGATGTCGAATACTTCCCTTCCA 59.227 43.478 0.00 0.00 32.55 3.53
2020 2336 7.867305 TTGTTTACTTGATGGTTAGTTGTCA 57.133 32.000 0.00 0.00 0.00 3.58
2041 2360 5.293079 GTCATAAAGAGCCATTGTCTCTGTC 59.707 44.000 0.00 0.00 40.51 3.51
2052 2374 6.211515 CCATTGTCTCTGTCAAAAAGGAAAG 58.788 40.000 0.00 0.00 0.00 2.62
2059 2381 9.490379 GTCTCTGTCAAAAAGGAAAGTTAGATA 57.510 33.333 0.00 0.00 0.00 1.98
2105 2427 8.853077 ATGAAAAGAAGTATCACATTGTCAGA 57.147 30.769 0.00 0.00 0.00 3.27
2108 2430 8.682936 AAAAGAAGTATCACATTGTCAGAGTT 57.317 30.769 0.00 0.00 0.00 3.01
2109 2431 7.664082 AAGAAGTATCACATTGTCAGAGTTG 57.336 36.000 0.00 0.00 0.00 3.16
2145 2467 5.878116 TGCTAACGGAACAACAGCTATATTT 59.122 36.000 0.00 0.00 33.38 1.40
2200 2522 7.446625 AGCATCATTTCTAGGGCTGTTATTTAG 59.553 37.037 0.00 0.00 0.00 1.85
2227 2549 5.758570 AGCTATCGTTACTGTTTTTCGAC 57.241 39.130 0.00 0.00 33.55 4.20
2303 2625 8.333186 GTCAAATAACGTCTTACATTATGGGAC 58.667 37.037 0.00 1.75 0.00 4.46
2808 3307 2.666508 GCTTGATGCAGCACATTCAAAG 59.333 45.455 2.94 0.00 39.84 2.77
2847 3346 2.109834 TGCTTCCTCCCTTCCAAATCAA 59.890 45.455 0.00 0.00 0.00 2.57
2852 3352 6.358974 TTCCTCCCTTCCAAATCAATTTTC 57.641 37.500 0.00 0.00 0.00 2.29
2926 3426 1.604308 CACTGAAGGCCATGGTGCA 60.604 57.895 14.67 5.76 0.00 4.57
2939 3439 0.735978 TGGTGCACTCATCTAACGCG 60.736 55.000 17.98 3.53 0.00 6.01
3069 3569 6.205658 GCCTAACACTTCAGAATCTGTTTTCT 59.794 38.462 10.36 0.00 36.38 2.52
3087 3587 5.499139 TTTCTTGATTGCAACTTCGACTT 57.501 34.783 0.00 0.00 0.00 3.01
3089 3589 4.380531 TCTTGATTGCAACTTCGACTTCT 58.619 39.130 0.00 0.00 0.00 2.85
3296 3796 3.764434 TGTTGTGCCCTTCTGTTTTAACA 59.236 39.130 0.00 0.00 37.37 2.41
3298 3798 5.105146 TGTTGTGCCCTTCTGTTTTAACAAT 60.105 36.000 0.00 0.00 38.66 2.71
3300 3800 4.202202 TGTGCCCTTCTGTTTTAACAATGG 60.202 41.667 0.00 0.33 38.66 3.16
3454 3954 1.078918 TGGATCAGGCAGTTGCTCG 60.079 57.895 3.88 0.00 41.70 5.03
3481 3981 3.184683 CAAGGCTCGCAGCTCGAC 61.185 66.667 7.85 3.16 43.16 4.20
3493 3994 1.403679 CAGCTCGACTTCTAGTGGGAG 59.596 57.143 0.00 0.00 31.91 4.30
3520 4021 3.385111 GGAGCTTCCCTTCGAGAATAGAA 59.615 47.826 0.00 0.00 0.00 2.10
3589 4092 3.390175 AGTAGCTGAGAAAGGCTCCTA 57.610 47.619 0.00 0.00 43.26 2.94
3634 4137 7.555965 ACTGAAAATGCAACTTTTAGAGGTTT 58.444 30.769 17.85 0.00 0.00 3.27
3687 4190 4.225942 GCCTATCCATTCCCATCTCATGTA 59.774 45.833 0.00 0.00 0.00 2.29
3690 4193 4.541973 TCCATTCCCATCTCATGTATCG 57.458 45.455 0.00 0.00 0.00 2.92
3723 4228 6.978343 TGGTGTATACAACTTTCAGCATAC 57.022 37.500 21.18 0.00 33.92 2.39
3758 4263 9.668497 ATTCTGAAAGGTTTAGATTGTACTACC 57.332 33.333 0.00 0.00 0.00 3.18
3759 4264 8.197592 TCTGAAAGGTTTAGATTGTACTACCA 57.802 34.615 0.00 0.00 0.00 3.25
3760 4265 8.822805 TCTGAAAGGTTTAGATTGTACTACCAT 58.177 33.333 0.00 0.00 0.00 3.55
3761 4266 8.786826 TGAAAGGTTTAGATTGTACTACCATG 57.213 34.615 0.00 0.00 0.00 3.66
3762 4267 8.598916 TGAAAGGTTTAGATTGTACTACCATGA 58.401 33.333 0.00 0.00 0.00 3.07
3763 4268 9.614792 GAAAGGTTTAGATTGTACTACCATGAT 57.385 33.333 0.00 0.00 0.00 2.45
3838 4372 7.562454 CTTCTTGTGAAGGTTGGTAAGTTTA 57.438 36.000 0.00 0.00 44.33 2.01
3872 4418 4.279982 AGTAGCTGTAAACTACTCCCTCC 58.720 47.826 0.00 0.00 45.65 4.30
3873 4419 2.100989 AGCTGTAAACTACTCCCTCCG 58.899 52.381 0.00 0.00 0.00 4.63
3874 4420 1.823610 GCTGTAAACTACTCCCTCCGT 59.176 52.381 0.00 0.00 0.00 4.69
3875 4421 2.233186 GCTGTAAACTACTCCCTCCGTT 59.767 50.000 0.00 0.00 0.00 4.44
3876 4422 3.675502 GCTGTAAACTACTCCCTCCGTTC 60.676 52.174 0.00 0.00 0.00 3.95
3877 4423 2.827921 TGTAAACTACTCCCTCCGTTCC 59.172 50.000 0.00 0.00 0.00 3.62
3878 4424 2.322339 AAACTACTCCCTCCGTTCCT 57.678 50.000 0.00 0.00 0.00 3.36
3879 4425 3.463048 AAACTACTCCCTCCGTTCCTA 57.537 47.619 0.00 0.00 0.00 2.94
3880 4426 3.463048 AACTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
3881 4427 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3882 4428 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3883 4429 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3884 4430 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
3885 4431 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
3886 4432 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
3887 4433 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3888 4434 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3889 4435 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3890 4436 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3891 4437 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3892 4438 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3893 4439 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
3894 4440 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3976 4522 8.515695 AAAAACTTATATTTAGGAACGGAGGG 57.484 34.615 0.00 0.00 0.00 4.30
3977 4523 7.441903 AAACTTATATTTAGGAACGGAGGGA 57.558 36.000 0.00 0.00 0.00 4.20
3978 4524 6.667558 ACTTATATTTAGGAACGGAGGGAG 57.332 41.667 0.00 0.00 0.00 4.30
3979 4525 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
3980 4526 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
3981 4527 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
3982 4528 2.149973 TTAGGAACGGAGGGAGTACC 57.850 55.000 0.00 0.00 40.67 3.34
3983 4529 1.002069 TAGGAACGGAGGGAGTACCA 58.998 55.000 0.00 0.00 43.89 3.25
3984 4530 0.115745 AGGAACGGAGGGAGTACCAA 59.884 55.000 0.00 0.00 43.89 3.67
3985 4531 0.248565 GGAACGGAGGGAGTACCAAC 59.751 60.000 0.00 0.00 43.89 3.77
3986 4532 1.264295 GAACGGAGGGAGTACCAACT 58.736 55.000 0.00 0.00 43.89 3.16
3987 4533 2.450476 GAACGGAGGGAGTACCAACTA 58.550 52.381 0.00 0.00 43.89 2.24
3988 4534 1.844687 ACGGAGGGAGTACCAACTAC 58.155 55.000 0.00 0.00 43.89 2.73
3996 4542 4.120792 GGAGTACCAACTACCAACTAGC 57.879 50.000 0.00 0.00 35.56 3.42
4007 4553 2.806434 ACCAACTAGCCATGCATGAAA 58.194 42.857 28.31 11.36 0.00 2.69
4080 4634 1.303888 CAGTTGGGCTCAGGCATGT 60.304 57.895 0.00 0.00 40.87 3.21
4193 4750 4.803088 GCATGATCGAGATATACTTCAGGC 59.197 45.833 0.00 2.78 34.94 4.85
4195 4752 5.888691 TGATCGAGATATACTTCAGGCTC 57.111 43.478 0.00 0.00 0.00 4.70
4197 4759 3.075148 TCGAGATATACTTCAGGCTCCG 58.925 50.000 0.00 0.00 0.00 4.63
4342 4904 1.383109 AGGATCGGCACCCTGATCA 60.383 57.895 12.91 0.00 42.19 2.92
4390 4952 0.322816 GCCTTGTGATGCTCTTCCCA 60.323 55.000 0.00 0.00 0.00 4.37
4432 4994 4.301072 AGCAGTAAAGAAACCTATGGCA 57.699 40.909 0.00 0.00 0.00 4.92
4492 5054 3.123621 GGTGCTCATACTTCTTCACAACG 59.876 47.826 0.00 0.00 0.00 4.10
4589 5151 0.178992 TTTGCCAGGGAAGGTCACAG 60.179 55.000 0.00 0.00 0.00 3.66
4628 5190 5.449107 GAGTATCTGTGAAATACGGCCTA 57.551 43.478 0.00 0.00 35.26 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.153289 GATGCATGGCCGTGACTCT 60.153 57.895 29.54 8.86 0.00 3.24
1 2 1.153289 AGATGCATGGCCGTGACTC 60.153 57.895 29.54 21.55 0.00 3.36
3 4 2.528743 CGAGATGCATGGCCGTGAC 61.529 63.158 29.54 19.20 0.00 3.67
5 6 1.368345 TTTCGAGATGCATGGCCGTG 61.368 55.000 21.33 21.33 0.00 4.94
6 7 0.676466 TTTTCGAGATGCATGGCCGT 60.676 50.000 2.46 0.00 0.00 5.68
7 8 0.028505 CTTTTCGAGATGCATGGCCG 59.971 55.000 2.46 4.68 0.00 6.13
8 9 1.332997 CTCTTTTCGAGATGCATGGCC 59.667 52.381 2.46 0.00 42.62 5.36
9 10 2.283298 TCTCTTTTCGAGATGCATGGC 58.717 47.619 2.46 0.00 43.72 4.40
30 31 7.514573 AAGAAAACAGAAAACGCGTATTTTT 57.485 28.000 14.46 10.09 31.90 1.94
31 32 7.514573 AAAGAAAACAGAAAACGCGTATTTT 57.485 28.000 14.46 10.98 34.46 1.82
32 33 7.514573 AAAAGAAAACAGAAAACGCGTATTT 57.485 28.000 14.46 15.34 0.00 1.40
33 34 7.486870 AGAAAAAGAAAACAGAAAACGCGTATT 59.513 29.630 14.46 6.51 0.00 1.89
35 36 6.316319 AGAAAAAGAAAACAGAAAACGCGTA 58.684 32.000 14.46 0.00 0.00 4.42
45 46 5.263185 TCTCGCGAAAGAAAAAGAAAACAG 58.737 37.500 11.33 0.00 0.00 3.16
52 53 3.788941 GTGACTCTCGCGAAAGAAAAAG 58.211 45.455 17.91 0.00 0.00 2.27
189 195 2.846371 GTGCCTCTCACGAAAGCAT 58.154 52.632 0.00 0.00 35.76 3.79
244 252 3.183754 CGCGTTTTGTTTTTCCCTTTCT 58.816 40.909 0.00 0.00 0.00 2.52
287 295 2.210116 GAAGCAAAACGGTGACTCTCA 58.790 47.619 0.00 0.00 0.00 3.27
362 509 4.318121 CCGTGACTCTCGTGAAAGAAAAAG 60.318 45.833 0.24 0.00 0.00 2.27
492 741 0.036732 TGCCTCTCGTGGAAGCAAAT 59.963 50.000 2.93 0.00 38.32 2.32
601 859 7.835682 AGATTCCATGTTGATAGGTTTTGATGA 59.164 33.333 0.00 0.00 0.00 2.92
630 890 1.923204 CCTCGCGTGAGATCTTCAAAG 59.077 52.381 27.11 3.16 45.57 2.77
898 1165 1.238625 TTCGTGGATGGGCCGAAAAC 61.239 55.000 0.00 0.00 40.66 2.43
910 1177 1.070786 GTTGTCTGGGCTTCGTGGA 59.929 57.895 0.00 0.00 0.00 4.02
911 1178 2.317609 CGTTGTCTGGGCTTCGTGG 61.318 63.158 0.00 0.00 0.00 4.94
962 1229 2.442188 GCTGCTGCGCTTTCATTGC 61.442 57.895 9.73 0.00 0.00 3.56
1229 1525 1.338136 AACCGAGGGTATGAGCAGGG 61.338 60.000 0.00 0.00 33.12 4.45
1245 1541 7.370383 TCAAAAATACTTGCTTGATCTGAACC 58.630 34.615 0.00 0.00 0.00 3.62
1261 1557 7.757097 TGAGACTAAGCTCGATCAAAAATAC 57.243 36.000 0.00 0.00 37.73 1.89
1263 1559 7.604164 TCTTTGAGACTAAGCTCGATCAAAAAT 59.396 33.333 7.67 0.00 36.53 1.82
1396 1705 4.348168 TCCTGACCTCAAGAACTTAGCTTT 59.652 41.667 0.00 0.00 0.00 3.51
1397 1706 3.904339 TCCTGACCTCAAGAACTTAGCTT 59.096 43.478 0.00 0.00 0.00 3.74
1432 1744 3.454082 GACCATTCTCTCTCCCTGTTCAT 59.546 47.826 0.00 0.00 0.00 2.57
1438 1750 1.008206 AGCAGACCATTCTCTCTCCCT 59.992 52.381 0.00 0.00 0.00 4.20
1486 1798 0.252197 ACCAACCGAGCCACCTAATC 59.748 55.000 0.00 0.00 0.00 1.75
1495 1807 1.364626 CTGATGAGCACCAACCGAGC 61.365 60.000 0.00 0.00 0.00 5.03
1498 1810 2.401766 GCCTGATGAGCACCAACCG 61.402 63.158 0.00 0.00 0.00 4.44
1680 1992 2.247437 GGGCTCTTTCATAGGCGCG 61.247 63.158 0.00 0.00 40.28 6.86
1683 1995 1.894282 GCGGGGCTCTTTCATAGGC 60.894 63.158 0.00 0.00 38.73 3.93
1788 2100 3.261951 CATACGCTTGCCCGTCCG 61.262 66.667 0.00 0.00 42.20 4.79
1800 2112 2.418976 TCTTCCACGAGACAGACATACG 59.581 50.000 0.00 0.00 0.00 3.06
1841 2153 9.467258 CAATAAAGAAACATGTTCAGAACACAT 57.533 29.630 18.49 6.71 45.50 3.21
1930 2242 1.553706 TCCTCTCGTCCCCAAAGTAC 58.446 55.000 0.00 0.00 0.00 2.73
1933 2245 2.633488 GAATTCCTCTCGTCCCCAAAG 58.367 52.381 0.00 0.00 0.00 2.77
1994 2307 8.908903 TGACAACTAACCATCAAGTAAACAAAT 58.091 29.630 0.00 0.00 0.00 2.32
2020 2336 5.426689 TGACAGAGACAATGGCTCTTTAT 57.573 39.130 17.35 4.85 40.60 1.40
2076 2398 9.766277 GACAATGTGATACTTCTTTTCATCTTC 57.234 33.333 0.00 0.00 0.00 2.87
2082 2404 8.316640 ACTCTGACAATGTGATACTTCTTTTC 57.683 34.615 0.00 0.00 0.00 2.29
2105 2427 2.629656 GCATCAGGCGGCAACAACT 61.630 57.895 13.08 0.00 0.00 3.16
2145 2467 7.221450 ACAAGAAAACTATAACAGGTAGCACA 58.779 34.615 0.00 0.00 0.00 4.57
2165 2487 6.936900 GCCCTAGAAATGATGCTTATACAAGA 59.063 38.462 0.00 0.00 33.20 3.02
2200 2522 8.216453 TCGAAAAACAGTAACGATAGCTTAAAC 58.784 33.333 0.00 0.00 42.67 2.01
2220 2542 2.165030 GACGGAGGGAGTATGTCGAAAA 59.835 50.000 0.00 0.00 0.00 2.29
2227 2549 2.304221 TATGGGACGGAGGGAGTATG 57.696 55.000 0.00 0.00 0.00 2.39
2283 2605 6.183360 CCTCTGTCCCATAATGTAAGACGTTA 60.183 42.308 0.00 0.00 34.45 3.18
2287 2609 4.654262 TCCCTCTGTCCCATAATGTAAGAC 59.346 45.833 0.00 0.00 0.00 3.01
2553 2924 0.749649 GTCGTCTGGAGGCAGATCAT 59.250 55.000 0.00 0.00 33.34 2.45
2565 2936 9.093970 TGGTAATTAAACAATCATAGTCGTCTG 57.906 33.333 0.00 0.00 0.00 3.51
2926 3426 0.739813 GGCAACCGCGTTAGATGAGT 60.740 55.000 4.92 0.00 39.92 3.41
2939 3439 5.810074 GTGTGGAAATGTTATAATGGCAACC 59.190 40.000 0.00 0.00 0.00 3.77
3069 3569 4.126437 TCAGAAGTCGAAGTTGCAATCAA 58.874 39.130 0.59 0.00 0.00 2.57
3087 3587 4.103627 ACAATCAGGCCATGTATGATCAGA 59.896 41.667 5.01 0.00 32.59 3.27
3089 3589 4.442401 ACAATCAGGCCATGTATGATCA 57.558 40.909 5.01 0.00 32.59 2.92
3296 3796 5.106038 CCTGCATATCGATGTAAATGCCATT 60.106 40.000 22.05 0.00 43.19 3.16
3298 3798 3.752747 CCTGCATATCGATGTAAATGCCA 59.247 43.478 22.05 12.61 43.19 4.92
3300 3800 5.362556 AACCTGCATATCGATGTAAATGC 57.637 39.130 19.44 19.44 43.92 3.56
3454 3954 2.507324 GAGCCTTGCGTCGAGGAC 60.507 66.667 9.75 0.95 37.20 3.85
3481 3981 2.383855 CTCCAGGACTCCCACTAGAAG 58.616 57.143 0.00 0.00 33.88 2.85
3493 3994 1.219393 CGAAGGGAAGCTCCAGGAC 59.781 63.158 0.00 0.00 38.64 3.85
3520 4021 2.373169 TGAAGAACAGTGGATGCTTCCT 59.627 45.455 18.67 0.00 43.07 3.36
3548 4049 8.639761 GCTACTTTCTGTTTCCAGTATCCTATA 58.360 37.037 0.00 0.00 39.82 1.31
3549 4050 7.345914 AGCTACTTTCTGTTTCCAGTATCCTAT 59.654 37.037 0.00 0.00 39.82 2.57
3567 4068 3.342377 GGAGCCTTTCTCAGCTACTTT 57.658 47.619 0.00 0.00 43.70 2.66
3589 4092 5.820423 TCAGTAACAAATACACACAGCAACT 59.180 36.000 0.00 0.00 36.94 3.16
3634 4137 3.944015 CCTCCATTGCAAAACCAAAACAA 59.056 39.130 1.71 0.00 0.00 2.83
3687 4190 7.227910 AGTTGTATACACCAAAAACTGAACGAT 59.772 33.333 4.68 0.00 0.00 3.73
3690 4193 8.920509 AAAGTTGTATACACCAAAAACTGAAC 57.079 30.769 4.68 0.00 0.00 3.18
3723 4228 9.838339 ATCTAAACCTTTCAGAATACAGGTATG 57.162 33.333 5.57 1.06 38.80 2.39
3756 4261 9.547279 TCTGTTATCACCAGTATATATCATGGT 57.453 33.333 13.54 13.54 46.91 3.55
3826 4360 8.403236 ACTTCATGTTTCTGTAAACTTACCAAC 58.597 33.333 0.00 0.13 44.44 3.77
3838 4372 6.992715 AGTTTACAGCTACTTCATGTTTCTGT 59.007 34.615 0.00 0.00 40.48 3.41
3866 4412 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3867 4413 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3868 4414 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
3951 4497 8.330993 TCCCTCCGTTCCTAAATATAAGTTTTT 58.669 33.333 0.00 0.00 0.00 1.94
3952 4498 7.864770 TCCCTCCGTTCCTAAATATAAGTTTT 58.135 34.615 0.00 0.00 0.00 2.43
3953 4499 7.126879 ACTCCCTCCGTTCCTAAATATAAGTTT 59.873 37.037 0.00 0.00 0.00 2.66
3954 4500 6.614496 ACTCCCTCCGTTCCTAAATATAAGTT 59.386 38.462 0.00 0.00 0.00 2.66
3955 4501 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3956 4502 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3957 4503 6.494835 GGTACTCCCTCCGTTCCTAAATATAA 59.505 42.308 0.00 0.00 0.00 0.98
3958 4504 6.012745 GGTACTCCCTCCGTTCCTAAATATA 58.987 44.000 0.00 0.00 0.00 0.86
3959 4505 4.837298 GGTACTCCCTCCGTTCCTAAATAT 59.163 45.833 0.00 0.00 0.00 1.28
3960 4506 4.218312 GGTACTCCCTCCGTTCCTAAATA 58.782 47.826 0.00 0.00 0.00 1.40
3961 4507 3.036819 GGTACTCCCTCCGTTCCTAAAT 58.963 50.000 0.00 0.00 0.00 1.40
3962 4508 2.225343 TGGTACTCCCTCCGTTCCTAAA 60.225 50.000 0.00 0.00 0.00 1.85
3963 4509 1.358787 TGGTACTCCCTCCGTTCCTAA 59.641 52.381 0.00 0.00 0.00 2.69
3964 4510 1.002069 TGGTACTCCCTCCGTTCCTA 58.998 55.000 0.00 0.00 0.00 2.94
3965 4511 0.115745 TTGGTACTCCCTCCGTTCCT 59.884 55.000 0.00 0.00 0.00 3.36
3966 4512 0.248565 GTTGGTACTCCCTCCGTTCC 59.751 60.000 0.00 0.00 0.00 3.62
3967 4513 1.264295 AGTTGGTACTCCCTCCGTTC 58.736 55.000 0.00 0.00 0.00 3.95
3968 4514 2.174360 GTAGTTGGTACTCCCTCCGTT 58.826 52.381 0.00 0.00 35.78 4.44
3969 4515 1.618074 GGTAGTTGGTACTCCCTCCGT 60.618 57.143 0.00 0.00 35.78 4.69
3970 4516 1.109609 GGTAGTTGGTACTCCCTCCG 58.890 60.000 0.00 0.00 35.78 4.63
3971 4517 2.235650 GTTGGTAGTTGGTACTCCCTCC 59.764 54.545 0.00 0.00 31.88 4.30
3972 4518 3.171528 AGTTGGTAGTTGGTACTCCCTC 58.828 50.000 0.00 0.00 31.88 4.30
3973 4519 3.271153 AGTTGGTAGTTGGTACTCCCT 57.729 47.619 0.00 0.00 31.88 4.20
3974 4520 3.118847 GCTAGTTGGTAGTTGGTACTCCC 60.119 52.174 0.00 0.00 35.78 4.30
3975 4521 3.118847 GGCTAGTTGGTAGTTGGTACTCC 60.119 52.174 0.00 0.00 35.78 3.85
3976 4522 3.512724 TGGCTAGTTGGTAGTTGGTACTC 59.487 47.826 0.00 0.00 35.78 2.59
3977 4523 3.513517 TGGCTAGTTGGTAGTTGGTACT 58.486 45.455 0.00 0.00 38.44 2.73
3978 4524 3.967332 TGGCTAGTTGGTAGTTGGTAC 57.033 47.619 0.00 0.00 0.00 3.34
3979 4525 3.370103 GCATGGCTAGTTGGTAGTTGGTA 60.370 47.826 0.00 0.00 0.00 3.25
3980 4526 2.618045 GCATGGCTAGTTGGTAGTTGGT 60.618 50.000 0.00 0.00 0.00 3.67
3981 4527 2.017049 GCATGGCTAGTTGGTAGTTGG 58.983 52.381 0.00 0.00 0.00 3.77
3982 4528 2.710377 TGCATGGCTAGTTGGTAGTTG 58.290 47.619 0.00 0.00 0.00 3.16
3983 4529 3.054434 TCATGCATGGCTAGTTGGTAGTT 60.054 43.478 25.97 0.00 0.00 2.24
3984 4530 2.505407 TCATGCATGGCTAGTTGGTAGT 59.495 45.455 25.97 0.00 0.00 2.73
3985 4531 3.198409 TCATGCATGGCTAGTTGGTAG 57.802 47.619 25.97 0.00 0.00 3.18
3986 4532 3.643199 TTCATGCATGGCTAGTTGGTA 57.357 42.857 25.97 0.00 0.00 3.25
3987 4533 2.512692 TTCATGCATGGCTAGTTGGT 57.487 45.000 25.97 0.00 0.00 3.67
3988 4534 3.444742 TCTTTTCATGCATGGCTAGTTGG 59.555 43.478 25.97 8.92 0.00 3.77
3996 4542 3.760151 TGAGGTTCTCTTTTCATGCATGG 59.240 43.478 25.97 10.42 0.00 3.66
4007 4553 4.623932 TGCAACTACATGAGGTTCTCTT 57.376 40.909 0.00 0.00 0.00 2.85
4193 4750 0.240945 AAAAGCAATGTTCGGCGGAG 59.759 50.000 7.21 0.00 34.54 4.63
4195 4752 1.616872 GCAAAAGCAATGTTCGGCGG 61.617 55.000 7.21 0.00 34.54 6.13
4197 4759 0.785979 CTGCAAAAGCAATGTTCGGC 59.214 50.000 0.00 0.00 0.00 5.54
4200 4762 5.277297 GGGTAAAACTGCAAAAGCAATGTTC 60.277 40.000 0.00 0.00 0.00 3.18
4245 4807 0.697010 CGTCGCAAACATGCTTTTCG 59.303 50.000 0.00 0.00 0.00 3.46
4287 4849 2.401583 AGAAGTGCACAACAGTGTCA 57.598 45.000 21.04 0.00 35.07 3.58
4342 4904 2.493907 GAAAGGTCGCCAGCGTCTCT 62.494 60.000 12.32 5.45 40.74 3.10
4390 4952 4.938226 GCTATGAAGCTAGGTGTCTTTGTT 59.062 41.667 0.00 0.00 45.85 2.83
4432 4994 0.036010 CGGTGAGGCCTCTGTTCATT 60.036 55.000 32.28 0.00 34.25 2.57
4492 5054 2.357034 TTCGACAAGTGCGAGGGC 60.357 61.111 0.00 0.00 39.14 5.19
4589 5151 0.942962 CTCTCGAATGGATGCCTTGC 59.057 55.000 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.