Multiple sequence alignment - TraesCS3A01G309500

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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 TraesCS3A01G309500 chr3A 100.000 2372 0 0 1 2372 547413493 547415864 0.000000e+00 4381.0
1 TraesCS3A01G309500 chr3A 84.735 1153 123 34 647 1764 547402776 547403910 0.000000e+00 1105.0
2 TraesCS3A01G309500 chr3A 92.717 508 26 9 1868 2372 466100627 466101126 0.000000e+00 723.0
3 TraesCS3A01G309500 chr3A 87.102 659 54 17 1 629 547472375 547473032 0.000000e+00 717.0
4 TraesCS3A01G309500 chr3A 93.239 355 16 4 1 347 547405615 547405969 1.260000e-142 516.0
5 TraesCS3A01G309500 chr3A 81.174 579 77 21 940 1514 547405997 547406547 1.010000e-118 436.0
6 TraesCS3A01G309500 chr3A 82.004 489 73 9 739 1220 547374854 547375334 3.670000e-108 401.0
7 TraesCS3A01G309500 chr3A 95.652 92 4 0 1763 1854 466100551 466100642 5.280000e-32 148.0
8 TraesCS3A01G309500 chr3B 89.672 1036 97 6 505 1535 144780705 144781735 0.000000e+00 1312.0
9 TraesCS3A01G309500 chr3B 90.516 949 80 8 824 1764 144799988 144800934 0.000000e+00 1245.0
10 TraesCS3A01G309500 chr3B 90.705 624 52 4 753 1371 144777030 144777652 0.000000e+00 826.0
11 TraesCS3A01G309500 chr3B 92.623 244 17 1 7 249 144780430 144780673 1.350000e-92 350.0
12 TraesCS3A01G309500 chr3B 89.916 119 11 1 1429 1546 144777894 144778012 4.080000e-33 152.0
13 TraesCS3A01G309500 chr3B 92.188 64 5 0 761 824 144787794 144787857 9.030000e-15 91.6
14 TraesCS3A01G309500 chr3B 97.143 35 0 1 670 703 144116751 144116717 9.160000e-05 58.4
15 TraesCS3A01G309500 chr2D 96.252 507 14 4 1867 2372 37499282 37498780 0.000000e+00 826.0
16 TraesCS3A01G309500 chr2D 95.858 507 17 4 1867 2372 522760938 522760435 0.000000e+00 817.0
17 TraesCS3A01G309500 chr2D 95.050 505 20 5 1869 2372 476031914 476032414 0.000000e+00 789.0
18 TraesCS3A01G309500 chr2D 90.373 509 23 9 1867 2372 600035015 600034530 0.000000e+00 645.0
19 TraesCS3A01G309500 chr2D 97.778 90 2 0 1765 1854 600035088 600034999 3.160000e-34 156.0
20 TraesCS3A01G309500 chr2D 96.703 91 3 0 1764 1854 522761012 522760922 4.080000e-33 152.0
21 TraesCS3A01G309500 chr2D 94.505 91 5 0 1764 1854 37499356 37499266 8.840000e-30 141.0
22 TraesCS3A01G309500 chr5B 95.874 509 16 5 1867 2372 589467503 589468009 0.000000e+00 819.0
23 TraesCS3A01G309500 chr5B 97.778 90 2 0 1765 1854 589467430 589467519 3.160000e-34 156.0
24 TraesCS3A01G309500 chr7D 95.842 505 16 3 1869 2372 610686973 610687473 0.000000e+00 811.0
25 TraesCS3A01G309500 chr7D 95.604 91 4 0 1764 1854 610686897 610686987 1.900000e-31 147.0
26 TraesCS3A01G309500 chr1D 95.661 507 19 3 1867 2372 462158849 462159353 0.000000e+00 811.0
27 TraesCS3A01G309500 chr1D 93.281 506 16 7 1869 2372 229047895 229048384 0.000000e+00 730.0
28 TraesCS3A01G309500 chr1D 95.699 93 4 0 1762 1854 462158773 462158865 1.470000e-32 150.0
29 TraesCS3A01G309500 chr1D 94.565 92 5 0 1763 1854 229047818 229047909 2.460000e-30 143.0
30 TraesCS3A01G309500 chr6A 94.094 508 22 6 1867 2372 184948088 184948589 0.000000e+00 765.0
31 TraesCS3A01G309500 chr6A 97.778 90 2 0 1765 1854 184948015 184948104 3.160000e-34 156.0
32 TraesCS3A01G309500 chr3D 85.863 481 57 8 907 1384 94245343 94245815 3.520000e-138 501.0
33 TraesCS3A01G309500 chr3D 85.069 288 17 14 647 911 94236353 94236637 1.080000e-68 270.0


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 TraesCS3A01G309500 chr3A 547413493 547415864 2371 False 4381.000000 4381 100.000000 1 2372 1 chr3A.!!$F2 2371
1 TraesCS3A01G309500 chr3A 547472375 547473032 657 False 717.000000 717 87.102000 1 629 1 chr3A.!!$F3 628
2 TraesCS3A01G309500 chr3A 547402776 547406547 3771 False 685.666667 1105 86.382667 1 1764 3 chr3A.!!$F5 1763
3 TraesCS3A01G309500 chr3A 466100551 466101126 575 False 435.500000 723 94.184500 1763 2372 2 chr3A.!!$F4 609
4 TraesCS3A01G309500 chr3B 144799988 144800934 946 False 1245.000000 1245 90.516000 824 1764 1 chr3B.!!$F2 940
5 TraesCS3A01G309500 chr3B 144777030 144781735 4705 False 660.000000 1312 90.729000 7 1546 4 chr3B.!!$F3 1539
6 TraesCS3A01G309500 chr2D 476031914 476032414 500 False 789.000000 789 95.050000 1869 2372 1 chr2D.!!$F1 503
7 TraesCS3A01G309500 chr2D 522760435 522761012 577 True 484.500000 817 96.280500 1764 2372 2 chr2D.!!$R2 608
8 TraesCS3A01G309500 chr2D 37498780 37499356 576 True 483.500000 826 95.378500 1764 2372 2 chr2D.!!$R1 608
9 TraesCS3A01G309500 chr2D 600034530 600035088 558 True 400.500000 645 94.075500 1765 2372 2 chr2D.!!$R3 607
10 TraesCS3A01G309500 chr5B 589467430 589468009 579 False 487.500000 819 96.826000 1765 2372 2 chr5B.!!$F1 607
11 TraesCS3A01G309500 chr7D 610686897 610687473 576 False 479.000000 811 95.723000 1764 2372 2 chr7D.!!$F1 608
12 TraesCS3A01G309500 chr1D 462158773 462159353 580 False 480.500000 811 95.680000 1762 2372 2 chr1D.!!$F2 610
13 TraesCS3A01G309500 chr1D 229047818 229048384 566 False 436.500000 730 93.923000 1763 2372 2 chr1D.!!$F1 609
14 TraesCS3A01G309500 chr6A 184948015 184948589 574 False 460.500000 765 95.936000 1765 2372 2 chr6A.!!$F1 607

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
286 287 0.032952 CGGGAGGAAGAACACGACAA 59.967 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1855 6705 0.674269 ATCGCGGCGTTTCCCTAAAA 60.674 50.0 22.9 0.0 0.0 1.52 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
29 30 3.141488 CGCAGCCTAGGACGAGGT 61.141 66.667 14.75 0.00 39.02 3.85
30 31 2.496817 GCAGCCTAGGACGAGGTG 59.503 66.667 14.75 1.52 39.02 4.00
31 32 3.082579 GCAGCCTAGGACGAGGTGG 62.083 68.421 14.75 0.00 39.02 4.61
32 33 2.760385 AGCCTAGGACGAGGTGGC 60.760 66.667 14.75 0.00 43.52 5.01
33 34 2.760385 GCCTAGGACGAGGTGGCT 60.760 66.667 14.75 0.00 40.36 4.75
34 35 2.787567 GCCTAGGACGAGGTGGCTC 61.788 68.421 14.75 0.00 40.36 4.70
35 36 1.076632 CCTAGGACGAGGTGGCTCT 60.077 63.158 1.05 0.00 0.00 4.09
36 37 1.104577 CCTAGGACGAGGTGGCTCTC 61.105 65.000 1.05 0.00 0.00 3.20
37 38 0.106918 CTAGGACGAGGTGGCTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
38 39 0.107116 TAGGACGAGGTGGCTCTCTC 60.107 60.000 0.00 2.21 0.00 3.20
39 40 1.379309 GGACGAGGTGGCTCTCTCT 60.379 63.158 0.00 0.00 0.00 3.10
40 41 0.968393 GGACGAGGTGGCTCTCTCTT 60.968 60.000 0.00 0.00 0.00 2.85
41 42 0.172352 GACGAGGTGGCTCTCTCTTG 59.828 60.000 0.00 0.00 0.00 3.02
42 43 1.153667 CGAGGTGGCTCTCTCTTGC 60.154 63.158 6.81 0.00 0.00 4.01
43 44 1.153667 GAGGTGGCTCTCTCTTGCG 60.154 63.158 2.08 0.00 0.00 4.85
44 45 2.125350 GGTGGCTCTCTCTTGCGG 60.125 66.667 0.00 0.00 0.00 5.69
45 46 2.817396 GTGGCTCTCTCTTGCGGC 60.817 66.667 0.00 0.00 0.00 6.53
46 47 4.087892 TGGCTCTCTCTTGCGGCC 62.088 66.667 0.00 0.00 42.73 6.13
47 48 4.087892 GGCTCTCTCTTGCGGCCA 62.088 66.667 2.24 0.00 42.08 5.36
48 49 2.817396 GCTCTCTCTTGCGGCCAC 60.817 66.667 2.24 0.00 0.00 5.01
49 50 2.125350 CTCTCTCTTGCGGCCACC 60.125 66.667 2.24 0.00 0.00 4.61
50 51 2.604686 TCTCTCTTGCGGCCACCT 60.605 61.111 2.24 0.00 0.00 4.00
51 52 2.125350 CTCTCTTGCGGCCACCTC 60.125 66.667 2.24 0.00 0.00 3.85
52 53 3.997064 CTCTCTTGCGGCCACCTCG 62.997 68.421 2.24 0.00 0.00 4.63
96 97 4.222847 GGCGACCTCCCCGACATC 62.223 72.222 0.00 0.00 34.67 3.06
97 98 3.148279 GCGACCTCCCCGACATCT 61.148 66.667 0.00 0.00 0.00 2.90
98 99 1.826921 GCGACCTCCCCGACATCTA 60.827 63.158 0.00 0.00 0.00 1.98
99 100 2.031360 CGACCTCCCCGACATCTAC 58.969 63.158 0.00 0.00 0.00 2.59
100 101 0.465824 CGACCTCCCCGACATCTACT 60.466 60.000 0.00 0.00 0.00 2.57
101 102 1.777941 GACCTCCCCGACATCTACTT 58.222 55.000 0.00 0.00 0.00 2.24
102 103 1.682323 GACCTCCCCGACATCTACTTC 59.318 57.143 0.00 0.00 0.00 3.01
103 104 1.041437 CCTCCCCGACATCTACTTCC 58.959 60.000 0.00 0.00 0.00 3.46
104 105 0.669077 CTCCCCGACATCTACTTCCG 59.331 60.000 0.00 0.00 0.00 4.30
105 106 1.067582 CCCCGACATCTACTTCCGC 59.932 63.158 0.00 0.00 0.00 5.54
106 107 1.299165 CCCGACATCTACTTCCGCG 60.299 63.158 0.00 0.00 0.00 6.46
107 108 1.944676 CCGACATCTACTTCCGCGC 60.945 63.158 0.00 0.00 0.00 6.86
108 109 1.944676 CGACATCTACTTCCGCGCC 60.945 63.158 0.00 0.00 0.00 6.53
109 110 1.141019 GACATCTACTTCCGCGCCA 59.859 57.895 0.00 0.00 0.00 5.69
110 111 0.459585 GACATCTACTTCCGCGCCAA 60.460 55.000 0.00 0.00 0.00 4.52
111 112 0.460284 ACATCTACTTCCGCGCCAAG 60.460 55.000 12.95 12.95 0.00 3.61
112 113 0.460284 CATCTACTTCCGCGCCAAGT 60.460 55.000 21.06 21.06 37.80 3.16
113 114 0.249398 ATCTACTTCCGCGCCAAGTT 59.751 50.000 22.08 6.53 35.63 2.66
114 115 0.034337 TCTACTTCCGCGCCAAGTTT 59.966 50.000 22.08 5.89 35.63 2.66
115 116 0.442699 CTACTTCCGCGCCAAGTTTC 59.557 55.000 22.08 0.00 35.63 2.78
116 117 0.034337 TACTTCCGCGCCAAGTTTCT 59.966 50.000 22.08 5.01 35.63 2.52
117 118 1.228657 ACTTCCGCGCCAAGTTTCTC 61.229 55.000 14.09 0.00 29.29 2.87
118 119 2.227968 CTTCCGCGCCAAGTTTCTCG 62.228 60.000 0.00 0.00 0.00 4.04
119 120 4.445545 CCGCGCCAAGTTTCTCGC 62.446 66.667 0.00 0.00 43.62 5.03
120 121 4.445545 CGCGCCAAGTTTCTCGCC 62.446 66.667 0.00 0.00 44.12 5.54
121 122 4.445545 GCGCCAAGTTTCTCGCCG 62.446 66.667 0.00 0.00 41.53 6.46
122 123 4.445545 CGCCAAGTTTCTCGCCGC 62.446 66.667 0.00 0.00 0.00 6.53
123 124 4.103103 GCCAAGTTTCTCGCCGCC 62.103 66.667 0.00 0.00 0.00 6.13
124 125 2.668212 CCAAGTTTCTCGCCGCCA 60.668 61.111 0.00 0.00 0.00 5.69
125 126 2.556287 CAAGTTTCTCGCCGCCAC 59.444 61.111 0.00 0.00 0.00 5.01
126 127 2.110213 AAGTTTCTCGCCGCCACA 59.890 55.556 0.00 0.00 0.00 4.17
127 128 1.961277 AAGTTTCTCGCCGCCACAG 60.961 57.895 0.00 0.00 0.00 3.66
128 129 2.357034 GTTTCTCGCCGCCACAGA 60.357 61.111 0.00 0.00 0.00 3.41
129 130 2.048222 TTTCTCGCCGCCACAGAG 60.048 61.111 0.00 0.00 0.00 3.35
130 131 4.742201 TTCTCGCCGCCACAGAGC 62.742 66.667 0.00 0.00 32.42 4.09
155 156 4.500116 GCGTCCTCGGAGCACCTC 62.500 72.222 0.00 0.00 37.56 3.85
156 157 3.827898 CGTCCTCGGAGCACCTCC 61.828 72.222 0.00 1.10 46.44 4.30
178 179 4.436998 GGTGGACGACGCCCTGAG 62.437 72.222 0.79 0.00 44.24 3.35
181 182 4.148825 GGACGACGCCCTGAGCAT 62.149 66.667 0.00 0.00 44.04 3.79
182 183 2.583593 GACGACGCCCTGAGCATC 60.584 66.667 0.00 0.00 44.04 3.91
183 184 4.148825 ACGACGCCCTGAGCATCC 62.149 66.667 0.00 0.00 44.04 3.51
206 207 4.070552 GACCTCGCGCCTCCACTT 62.071 66.667 0.00 0.00 0.00 3.16
207 208 3.991536 GACCTCGCGCCTCCACTTC 62.992 68.421 0.00 0.00 0.00 3.01
208 209 3.764466 CCTCGCGCCTCCACTTCT 61.764 66.667 0.00 0.00 0.00 2.85
209 210 2.262915 CTCGCGCCTCCACTTCTT 59.737 61.111 0.00 0.00 0.00 2.52
210 211 1.807573 CTCGCGCCTCCACTTCTTC 60.808 63.158 0.00 0.00 0.00 2.87
211 212 2.815647 CGCGCCTCCACTTCTTCC 60.816 66.667 0.00 0.00 0.00 3.46
212 213 2.436824 GCGCCTCCACTTCTTCCC 60.437 66.667 0.00 0.00 0.00 3.97
213 214 2.269241 CGCCTCCACTTCTTCCCC 59.731 66.667 0.00 0.00 0.00 4.81
214 215 2.294078 CGCCTCCACTTCTTCCCCT 61.294 63.158 0.00 0.00 0.00 4.79
215 216 1.301293 GCCTCCACTTCTTCCCCTG 59.699 63.158 0.00 0.00 0.00 4.45
216 217 1.994463 CCTCCACTTCTTCCCCTGG 59.006 63.158 0.00 0.00 0.00 4.45
217 218 0.547712 CCTCCACTTCTTCCCCTGGA 60.548 60.000 0.00 0.00 0.00 3.86
218 219 0.615850 CTCCACTTCTTCCCCTGGAC 59.384 60.000 0.00 0.00 0.00 4.02
219 220 0.840722 TCCACTTCTTCCCCTGGACC 60.841 60.000 0.00 0.00 0.00 4.46
220 221 1.296715 CACTTCTTCCCCTGGACCG 59.703 63.158 0.00 0.00 0.00 4.79
221 222 1.918800 ACTTCTTCCCCTGGACCGG 60.919 63.158 0.00 0.00 0.00 5.28
222 223 1.612442 CTTCTTCCCCTGGACCGGA 60.612 63.158 9.46 0.00 0.00 5.14
223 224 1.612442 TTCTTCCCCTGGACCGGAG 60.612 63.158 9.46 0.00 0.00 4.63
224 225 3.787001 CTTCCCCTGGACCGGAGC 61.787 72.222 9.46 0.00 0.00 4.70
228 229 4.452733 CCCTGGACCGGAGCGTTC 62.453 72.222 9.46 0.00 0.00 3.95
229 230 3.691342 CCTGGACCGGAGCGTTCA 61.691 66.667 9.46 0.00 0.00 3.18
230 231 2.432628 CTGGACCGGAGCGTTCAC 60.433 66.667 9.46 0.00 0.00 3.18
231 232 3.934391 CTGGACCGGAGCGTTCACC 62.934 68.421 9.46 0.00 0.00 4.02
232 233 4.754667 GGACCGGAGCGTTCACCC 62.755 72.222 9.46 0.00 0.00 4.61
233 234 4.754667 GACCGGAGCGTTCACCCC 62.755 72.222 9.46 0.00 0.00 4.95
237 238 3.998672 GGAGCGTTCACCCCGACA 61.999 66.667 0.53 0.00 0.00 4.35
238 239 2.737376 GAGCGTTCACCCCGACAC 60.737 66.667 0.00 0.00 0.00 3.67
239 240 4.657824 AGCGTTCACCCCGACACG 62.658 66.667 0.00 0.00 33.82 4.49
278 279 2.351276 GCCAAGCGGGAGGAAGAA 59.649 61.111 1.23 0.00 40.01 2.52
279 280 2.041115 GCCAAGCGGGAGGAAGAAC 61.041 63.158 1.23 0.00 40.01 3.01
280 281 1.374947 CCAAGCGGGAGGAAGAACA 59.625 57.895 0.00 0.00 40.01 3.18
281 282 0.955919 CCAAGCGGGAGGAAGAACAC 60.956 60.000 0.00 0.00 40.01 3.32
282 283 1.004918 AAGCGGGAGGAAGAACACG 60.005 57.895 0.00 0.00 0.00 4.49
283 284 1.469335 AAGCGGGAGGAAGAACACGA 61.469 55.000 0.00 0.00 0.00 4.35
284 285 1.737008 GCGGGAGGAAGAACACGAC 60.737 63.158 0.00 0.00 0.00 4.34
285 286 1.663739 CGGGAGGAAGAACACGACA 59.336 57.895 0.00 0.00 0.00 4.35
286 287 0.032952 CGGGAGGAAGAACACGACAA 59.967 55.000 0.00 0.00 0.00 3.18
287 288 1.797025 GGGAGGAAGAACACGACAAG 58.203 55.000 0.00 0.00 0.00 3.16
288 289 1.608283 GGGAGGAAGAACACGACAAGG 60.608 57.143 0.00 0.00 0.00 3.61
289 290 1.149148 GAGGAAGAACACGACAAGGC 58.851 55.000 0.00 0.00 0.00 4.35
290 291 0.600255 AGGAAGAACACGACAAGGCG 60.600 55.000 0.00 0.00 37.29 5.52
291 292 0.878961 GGAAGAACACGACAAGGCGT 60.879 55.000 0.00 0.00 46.88 5.68
297 298 2.030562 ACGACAAGGCGTGGAAGG 59.969 61.111 0.00 0.00 43.79 3.46
306 307 4.431131 CGTGGAAGGCCCTGGCAT 62.431 66.667 10.86 0.00 44.11 4.40
307 308 2.757099 GTGGAAGGCCCTGGCATG 60.757 66.667 10.86 0.00 44.11 4.06
308 309 4.764771 TGGAAGGCCCTGGCATGC 62.765 66.667 9.90 9.90 44.11 4.06
309 310 4.453892 GGAAGGCCCTGGCATGCT 62.454 66.667 18.92 0.00 44.11 3.79
310 311 2.832201 GAAGGCCCTGGCATGCTC 60.832 66.667 18.92 8.46 44.11 4.26
311 312 4.453892 AAGGCCCTGGCATGCTCC 62.454 66.667 18.92 10.94 44.11 4.70
314 315 4.437587 GCCCTGGCATGCTCCACT 62.438 66.667 18.92 0.00 41.49 4.00
315 316 2.124403 CCCTGGCATGCTCCACTC 60.124 66.667 18.92 0.00 31.74 3.51
316 317 2.124403 CCTGGCATGCTCCACTCC 60.124 66.667 18.92 0.00 31.74 3.85
317 318 2.672908 CTGGCATGCTCCACTCCA 59.327 61.111 18.92 3.92 31.74 3.86
318 319 1.451567 CTGGCATGCTCCACTCCAG 60.452 63.158 18.92 10.44 38.41 3.86
319 320 2.827642 GGCATGCTCCACTCCAGC 60.828 66.667 18.92 0.00 37.40 4.85
320 321 2.827642 GCATGCTCCACTCCAGCC 60.828 66.667 11.37 0.00 35.89 4.85
321 322 2.513204 CATGCTCCACTCCAGCCG 60.513 66.667 0.00 0.00 35.89 5.52
322 323 4.479993 ATGCTCCACTCCAGCCGC 62.480 66.667 0.00 0.00 35.89 6.53
361 362 3.215245 CTCCCGGAGCTCAAGGAG 58.785 66.667 27.51 27.51 40.00 3.69
387 388 3.482783 GAGCTCGGCAAGTGCGTC 61.483 66.667 0.00 0.00 43.54 5.19
388 389 4.299547 AGCTCGGCAAGTGCGTCA 62.300 61.111 0.00 0.00 43.54 4.35
389 390 3.345808 GCTCGGCAAGTGCGTCAA 61.346 61.111 0.00 0.00 43.26 3.18
390 391 2.551270 CTCGGCAAGTGCGTCAAC 59.449 61.111 0.00 0.00 43.26 3.18
391 392 3.281751 CTCGGCAAGTGCGTCAACG 62.282 63.158 0.00 0.00 43.26 4.10
401 402 2.844146 CGTCAACGCCGTGAAGTC 59.156 61.111 0.00 0.00 0.00 3.01
402 403 2.654912 CGTCAACGCCGTGAAGTCC 61.655 63.158 0.00 0.00 0.00 3.85
403 404 1.300697 GTCAACGCCGTGAAGTCCT 60.301 57.895 0.00 0.00 0.00 3.85
404 405 0.878961 GTCAACGCCGTGAAGTCCTT 60.879 55.000 0.00 0.00 0.00 3.36
405 406 0.599204 TCAACGCCGTGAAGTCCTTC 60.599 55.000 0.00 0.00 39.91 3.46
406 407 1.663702 AACGCCGTGAAGTCCTTCG 60.664 57.895 0.00 0.00 42.28 3.79
407 408 3.479269 CGCCGTGAAGTCCTTCGC 61.479 66.667 9.94 9.94 44.25 4.70
408 409 3.119096 GCCGTGAAGTCCTTCGCC 61.119 66.667 13.39 1.81 44.71 5.54
409 410 2.809601 CCGTGAAGTCCTTCGCCG 60.810 66.667 13.39 11.71 44.71 6.46
410 411 3.479269 CGTGAAGTCCTTCGCCGC 61.479 66.667 13.39 0.00 44.71 6.53
411 412 3.119096 GTGAAGTCCTTCGCCGCC 61.119 66.667 9.00 0.00 42.51 6.13
412 413 3.621805 TGAAGTCCTTCGCCGCCA 61.622 61.111 2.82 0.00 42.28 5.69
413 414 2.358247 GAAGTCCTTCGCCGCCAA 60.358 61.111 0.00 0.00 0.00 4.52
414 415 2.358737 AAGTCCTTCGCCGCCAAG 60.359 61.111 0.00 0.00 0.00 3.61
415 416 2.781595 GAAGTCCTTCGCCGCCAAGA 62.782 60.000 0.00 0.00 0.00 3.02
416 417 2.358247 GTCCTTCGCCGCCAAGAA 60.358 61.111 0.00 0.00 0.00 2.52
417 418 2.047274 TCCTTCGCCGCCAAGAAG 60.047 61.111 0.00 0.00 42.42 2.85
491 492 4.736896 GGTGTCCCGCGTCCTGAC 62.737 72.222 4.92 6.86 0.00 3.51
501 502 4.554163 GTCCTGACGACCAACGAG 57.446 61.111 0.00 0.00 45.77 4.18
502 503 1.658673 GTCCTGACGACCAACGAGT 59.341 57.895 0.00 0.00 45.77 4.18
503 504 0.663568 GTCCTGACGACCAACGAGTG 60.664 60.000 0.00 0.00 45.77 3.51
513 514 4.344865 AACGAGTGGGCGGCCAAT 62.345 61.111 34.51 33.33 35.12 3.16
514 515 4.778143 ACGAGTGGGCGGCCAATC 62.778 66.667 39.24 39.24 35.12 2.67
515 516 4.473520 CGAGTGGGCGGCCAATCT 62.474 66.667 42.34 32.28 33.36 2.40
516 517 2.514824 GAGTGGGCGGCCAATCTC 60.515 66.667 40.74 33.34 32.87 2.75
517 518 4.115199 AGTGGGCGGCCAATCTCC 62.115 66.667 34.51 19.98 0.00 3.71
518 519 4.115199 GTGGGCGGCCAATCTCCT 62.115 66.667 34.51 0.00 0.00 3.69
519 520 3.797353 TGGGCGGCCAATCTCCTC 61.797 66.667 30.86 0.00 0.00 3.71
520 521 4.570874 GGGCGGCCAATCTCCTCC 62.571 72.222 25.33 0.00 0.00 4.30
521 522 3.483869 GGCGGCCAATCTCCTCCT 61.484 66.667 15.62 0.00 0.00 3.69
522 523 2.110006 GCGGCCAATCTCCTCCTC 59.890 66.667 2.24 0.00 0.00 3.71
523 524 2.825264 CGGCCAATCTCCTCCTCC 59.175 66.667 2.24 0.00 0.00 4.30
524 525 1.764054 CGGCCAATCTCCTCCTCCT 60.764 63.158 2.24 0.00 0.00 3.69
525 526 1.753368 CGGCCAATCTCCTCCTCCTC 61.753 65.000 2.24 0.00 0.00 3.71
526 527 1.745264 GCCAATCTCCTCCTCCTCG 59.255 63.158 0.00 0.00 0.00 4.63
527 528 1.745264 CCAATCTCCTCCTCCTCGC 59.255 63.158 0.00 0.00 0.00 5.03
528 529 1.745264 CAATCTCCTCCTCCTCGCC 59.255 63.158 0.00 0.00 0.00 5.54
529 530 1.045350 CAATCTCCTCCTCCTCGCCA 61.045 60.000 0.00 0.00 0.00 5.69
530 531 0.758685 AATCTCCTCCTCCTCGCCAG 60.759 60.000 0.00 0.00 0.00 4.85
531 532 3.535962 CTCCTCCTCCTCGCCAGC 61.536 72.222 0.00 0.00 0.00 4.85
534 535 3.535962 CTCCTCCTCGCCAGCCTC 61.536 72.222 0.00 0.00 0.00 4.70
537 538 3.847602 CTCCTCGCCAGCCTCCAG 61.848 72.222 0.00 0.00 0.00 3.86
548 549 4.479993 CCTCCAGCTTGGCCTCGG 62.480 72.222 3.32 0.00 37.47 4.63
549 550 4.479993 CTCCAGCTTGGCCTCGGG 62.480 72.222 3.32 3.60 37.47 5.14
570 571 4.087892 CGGTGGCAGTCCTGGGAG 62.088 72.222 0.00 0.00 0.00 4.30
571 572 3.721706 GGTGGCAGTCCTGGGAGG 61.722 72.222 0.00 0.00 36.46 4.30
572 573 3.721706 GTGGCAGTCCTGGGAGGG 61.722 72.222 0.00 0.00 35.59 4.30
573 574 3.940480 TGGCAGTCCTGGGAGGGA 61.940 66.667 0.00 0.00 35.59 4.20
574 575 2.367512 GGCAGTCCTGGGAGGGAT 60.368 66.667 0.00 0.00 37.73 3.85
575 576 2.447714 GGCAGTCCTGGGAGGGATC 61.448 68.421 0.00 0.00 37.73 3.36
576 577 2.801631 GCAGTCCTGGGAGGGATCG 61.802 68.421 0.00 0.00 37.73 3.69
577 578 2.444895 AGTCCTGGGAGGGATCGC 60.445 66.667 0.54 0.54 37.73 4.58
578 579 2.444895 GTCCTGGGAGGGATCGCT 60.445 66.667 12.81 12.81 37.73 4.93
579 580 2.444706 TCCTGGGAGGGATCGCTG 60.445 66.667 18.19 2.24 35.59 5.18
580 581 3.554342 CCTGGGAGGGATCGCTGG 61.554 72.222 18.19 8.24 35.91 4.85
581 582 4.247380 CTGGGAGGGATCGCTGGC 62.247 72.222 18.19 3.36 0.00 4.85
612 613 4.803426 GCTGCCCTCGACCTCGTG 62.803 72.222 0.00 0.00 40.80 4.35
613 614 3.374402 CTGCCCTCGACCTCGTGT 61.374 66.667 0.00 0.00 40.80 4.49
614 615 3.633094 CTGCCCTCGACCTCGTGTG 62.633 68.421 0.00 0.00 40.80 3.82
615 616 4.436998 GCCCTCGACCTCGTGTGG 62.437 72.222 0.00 0.00 40.80 4.17
616 617 2.989824 CCCTCGACCTCGTGTGGT 60.990 66.667 0.00 0.00 44.10 4.16
629 630 4.773117 GTGGTCGCCGTCCTCGTC 62.773 72.222 1.46 0.00 35.01 4.20
632 633 4.176851 GTCGCCGTCCTCGTCCTC 62.177 72.222 0.00 0.00 35.01 3.71
650 651 3.866582 GGCCCCCGACCTCATCTG 61.867 72.222 0.00 0.00 0.00 2.90
681 682 2.221299 TGTAGTGTGGGCTGGGACC 61.221 63.158 0.00 0.00 0.00 4.46
693 694 2.582498 GGGACCGAATCACGCTCG 60.582 66.667 0.00 0.00 41.07 5.03
694 695 2.181021 GGACCGAATCACGCTCGT 59.819 61.111 0.00 0.00 41.07 4.18
695 696 1.430632 GGACCGAATCACGCTCGTA 59.569 57.895 0.00 0.00 41.07 3.43
696 697 0.864797 GGACCGAATCACGCTCGTAC 60.865 60.000 0.00 0.00 41.07 3.67
697 698 0.179181 GACCGAATCACGCTCGTACA 60.179 55.000 0.00 0.00 41.07 2.90
698 699 0.179171 ACCGAATCACGCTCGTACAG 60.179 55.000 0.00 0.00 41.07 2.74
699 700 0.179171 CCGAATCACGCTCGTACAGT 60.179 55.000 0.00 0.00 41.07 3.55
702 706 2.222976 CGAATCACGCTCGTACAGTACT 60.223 50.000 9.10 0.00 34.51 2.73
705 709 2.964740 TCACGCTCGTACAGTACTACT 58.035 47.619 9.10 0.00 0.00 2.57
710 714 2.354199 GCTCGTACAGTACTACTCCACC 59.646 54.545 9.10 0.00 0.00 4.61
730 744 3.859386 ACCGCGTATACGTTCCTAAAAAG 59.141 43.478 25.04 6.01 42.22 2.27
734 748 6.400940 CCGCGTATACGTTCCTAAAAAGAAAA 60.401 38.462 25.04 0.00 42.22 2.29
735 749 7.008859 CGCGTATACGTTCCTAAAAAGAAAAA 58.991 34.615 25.04 0.00 42.22 1.94
759 773 1.003223 CCACTGCGTATACGTCGATCA 60.003 52.381 25.04 13.55 42.22 2.92
805 819 1.077858 ACCGTCTCCTACTCCCGTC 60.078 63.158 0.00 0.00 0.00 4.79
816 830 2.031465 TCCCGTCGGGCAACTTTC 59.969 61.111 26.42 0.00 43.94 2.62
868 893 3.249917 CAACACAACCAAAGAACCACAC 58.750 45.455 0.00 0.00 0.00 3.82
883 908 1.005630 ACACGAGCCAGCTTCACTC 60.006 57.895 0.00 0.00 0.00 3.51
894 919 1.209383 CTTCACTCTTCGCCGTCGA 59.791 57.895 0.00 0.00 43.89 4.20
905 931 1.197910 CGCCGTCGAAACTAGATTCC 58.802 55.000 7.12 0.00 38.10 3.01
945 4897 0.538584 AGTCAGCAATCGATCAGCCA 59.461 50.000 16.44 4.19 0.00 4.75
952 4904 1.071228 CAATCGATCAGCCATCTGGGA 59.929 52.381 0.00 0.00 40.69 4.37
991 4943 2.223876 TGTTTTCGTAGCGTGGAGAGTT 60.224 45.455 0.00 0.00 0.00 3.01
1065 5017 0.759959 TGGACGAGGTGCTAAAACCA 59.240 50.000 0.00 0.00 43.20 3.67
1066 5018 1.141254 TGGACGAGGTGCTAAAACCAA 59.859 47.619 0.00 0.00 43.20 3.67
1152 5104 1.469335 GGAAGGAGACGGTGTGTGGA 61.469 60.000 0.00 0.00 0.00 4.02
1179 5131 1.802069 TTCATGAACGATGCGTGGAA 58.198 45.000 3.38 0.00 39.99 3.53
1220 5172 3.965258 TTGCCCCATGTGTCGGCT 61.965 61.111 10.55 0.00 43.42 5.52
1224 5176 1.298340 CCCCATGTGTCGGCTACAA 59.702 57.895 0.00 0.00 40.63 2.41
1298 5250 4.155462 CCTCATCTTTATGGCGATGGAATG 59.845 45.833 0.00 0.00 38.02 2.67
1308 5260 2.301346 GCGATGGAATGGGAAGACAAT 58.699 47.619 0.00 0.00 0.00 2.71
1387 5339 2.544685 GGTGATGAGACAATGTCGAGG 58.455 52.381 7.83 0.00 37.67 4.63
1440 5393 5.049198 CAGACTGTCGGTTGTACTTACTGTA 60.049 44.000 1.52 0.00 0.00 2.74
1554 5507 3.876309 ATCCATTTGTTATAGCCGGGT 57.124 42.857 12.58 12.58 0.00 5.28
1566 5519 0.609662 AGCCGGGTAAGCGTCTTTTA 59.390 50.000 3.10 0.00 34.64 1.52
1567 5520 1.002315 AGCCGGGTAAGCGTCTTTTAA 59.998 47.619 3.10 0.00 34.64 1.52
1568 5521 1.805943 GCCGGGTAAGCGTCTTTTAAA 59.194 47.619 2.18 0.00 0.00 1.52
1641 5599 6.885735 ACAAACAGTTGCAATTCAAACTAC 57.114 33.333 0.59 0.00 38.39 2.73
1646 5604 3.255642 AGTTGCAATTCAAACTACGGCAT 59.744 39.130 0.59 0.00 36.26 4.40
1663 5621 3.609604 ATGTGATTTCGCATGCACG 57.390 47.368 19.57 1.83 44.53 5.34
1670 5628 0.957888 TTTCGCATGCACGGGAATGA 60.958 50.000 19.57 0.55 37.63 2.57
1681 5639 4.202202 TGCACGGGAATGATTTGTCTTTTT 60.202 37.500 0.00 0.00 0.00 1.94
1682 5640 4.385748 GCACGGGAATGATTTGTCTTTTTC 59.614 41.667 0.00 0.00 0.00 2.29
1700 5658 9.191995 GTCTTTTTCAGTTTTCTCTCAAAACAA 57.808 29.630 11.47 0.00 41.29 2.83
1712 5670 6.906659 TCTCTCAAAACAAGCTTTCATCATC 58.093 36.000 0.00 0.00 0.00 2.92
1755 5718 1.542915 GGTTTCCCGCCCTAACTTTTC 59.457 52.381 0.00 0.00 0.00 2.29
1839 6689 4.521062 AGTCGGATCCAGCTGCGC 62.521 66.667 13.41 0.00 0.00 6.09
1850 6700 4.950974 GCTGCGCCGCGATTCATG 62.951 66.667 18.91 0.03 0.00 3.07
1851 6701 3.566853 CTGCGCCGCGATTCATGT 61.567 61.111 18.91 0.00 0.00 3.21
1852 6702 3.099619 CTGCGCCGCGATTCATGTT 62.100 57.895 18.91 0.00 0.00 2.71
1853 6703 2.100216 GCGCCGCGATTCATGTTT 59.900 55.556 18.91 0.00 0.00 2.83
1854 6704 1.514014 GCGCCGCGATTCATGTTTT 60.514 52.632 18.91 0.00 0.00 2.43
1855 6705 1.070471 GCGCCGCGATTCATGTTTTT 61.070 50.000 18.91 0.00 0.00 1.94
1892 6742 2.034423 CGATTCGTGTTTGTCAACGTGA 60.034 45.455 0.00 0.00 35.40 4.35
1976 7127 4.699522 GTCTTTGCGGTCCGGCCT 62.700 66.667 14.38 0.00 34.25 5.19
2009 7160 2.602568 CAAAAGCCCAGGCCTGCT 60.603 61.111 28.39 19.81 43.17 4.24
2147 8085 1.113517 TATCAGCGGCCTCCAGTACC 61.114 60.000 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.577246 CCTCGTCCTAGGCTGCGC 62.577 72.222 2.96 0.00 0.00 6.09
12 13 3.141488 ACCTCGTCCTAGGCTGCG 61.141 66.667 2.96 8.82 40.62 5.18
13 14 2.496817 CACCTCGTCCTAGGCTGC 59.503 66.667 2.96 0.00 40.62 5.25
14 15 3.082579 GCCACCTCGTCCTAGGCTG 62.083 68.421 2.96 0.00 42.01 4.85
15 16 2.760385 GCCACCTCGTCCTAGGCT 60.760 66.667 2.96 0.00 42.01 4.58
16 17 2.760385 AGCCACCTCGTCCTAGGC 60.760 66.667 2.96 0.00 45.54 3.93
17 18 1.076632 AGAGCCACCTCGTCCTAGG 60.077 63.158 0.82 0.82 43.05 3.02
18 19 0.106918 AGAGAGCCACCTCGTCCTAG 60.107 60.000 0.00 0.00 43.05 3.02
19 20 0.107116 GAGAGAGCCACCTCGTCCTA 60.107 60.000 0.00 0.00 43.05 2.94
20 21 1.379309 GAGAGAGCCACCTCGTCCT 60.379 63.158 0.00 0.00 43.05 3.85
21 22 0.968393 AAGAGAGAGCCACCTCGTCC 60.968 60.000 0.00 0.00 43.05 4.79
22 23 0.172352 CAAGAGAGAGCCACCTCGTC 59.828 60.000 0.00 0.00 43.05 4.20
23 24 1.882989 GCAAGAGAGAGCCACCTCGT 61.883 60.000 0.00 0.00 43.05 4.18
24 25 1.153667 GCAAGAGAGAGCCACCTCG 60.154 63.158 0.00 0.00 43.05 4.63
25 26 1.153667 CGCAAGAGAGAGCCACCTC 60.154 63.158 0.00 0.00 43.02 3.85
26 27 2.654079 CCGCAAGAGAGAGCCACCT 61.654 63.158 0.00 0.00 43.02 4.00
27 28 2.125350 CCGCAAGAGAGAGCCACC 60.125 66.667 0.00 0.00 43.02 4.61
28 29 2.817396 GCCGCAAGAGAGAGCCAC 60.817 66.667 0.00 0.00 43.02 5.01
29 30 4.087892 GGCCGCAAGAGAGAGCCA 62.088 66.667 0.00 0.00 43.32 4.75
30 31 4.087892 TGGCCGCAAGAGAGAGCC 62.088 66.667 0.00 0.00 44.13 4.70
31 32 2.817396 GTGGCCGCAAGAGAGAGC 60.817 66.667 12.58 0.00 43.02 4.09
32 33 2.125350 GGTGGCCGCAAGAGAGAG 60.125 66.667 19.98 0.00 43.02 3.20
33 34 2.604686 AGGTGGCCGCAAGAGAGA 60.605 61.111 19.98 0.00 43.02 3.10
34 35 2.125350 GAGGTGGCCGCAAGAGAG 60.125 66.667 19.98 0.00 43.02 3.20
35 36 4.069232 CGAGGTGGCCGCAAGAGA 62.069 66.667 19.98 0.00 43.02 3.10
79 80 4.222847 GATGTCGGGGAGGTCGCC 62.223 72.222 2.95 2.95 44.62 5.54
80 81 1.826921 TAGATGTCGGGGAGGTCGC 60.827 63.158 0.00 0.00 0.00 5.19
81 82 0.465824 AGTAGATGTCGGGGAGGTCG 60.466 60.000 0.00 0.00 0.00 4.79
82 83 1.682323 GAAGTAGATGTCGGGGAGGTC 59.318 57.143 0.00 0.00 0.00 3.85
83 84 1.688627 GGAAGTAGATGTCGGGGAGGT 60.689 57.143 0.00 0.00 0.00 3.85
84 85 1.041437 GGAAGTAGATGTCGGGGAGG 58.959 60.000 0.00 0.00 0.00 4.30
85 86 0.669077 CGGAAGTAGATGTCGGGGAG 59.331 60.000 0.00 0.00 0.00 4.30
86 87 1.389609 GCGGAAGTAGATGTCGGGGA 61.390 60.000 0.00 0.00 0.00 4.81
87 88 1.067582 GCGGAAGTAGATGTCGGGG 59.932 63.158 0.00 0.00 0.00 5.73
88 89 1.299165 CGCGGAAGTAGATGTCGGG 60.299 63.158 0.00 0.00 0.00 5.14
89 90 1.944676 GCGCGGAAGTAGATGTCGG 60.945 63.158 8.83 0.00 0.00 4.79
90 91 1.944676 GGCGCGGAAGTAGATGTCG 60.945 63.158 8.83 0.00 0.00 4.35
91 92 0.459585 TTGGCGCGGAAGTAGATGTC 60.460 55.000 8.83 0.00 0.00 3.06
92 93 0.460284 CTTGGCGCGGAAGTAGATGT 60.460 55.000 8.83 0.00 0.00 3.06
93 94 0.460284 ACTTGGCGCGGAAGTAGATG 60.460 55.000 18.81 0.00 31.72 2.90
94 95 0.249398 AACTTGGCGCGGAAGTAGAT 59.751 50.000 20.09 5.98 33.20 1.98
95 96 0.034337 AAACTTGGCGCGGAAGTAGA 59.966 50.000 20.09 0.00 33.20 2.59
96 97 0.442699 GAAACTTGGCGCGGAAGTAG 59.557 55.000 20.09 5.85 33.20 2.57
97 98 0.034337 AGAAACTTGGCGCGGAAGTA 59.966 50.000 20.09 0.00 33.20 2.24
98 99 1.227853 AGAAACTTGGCGCGGAAGT 60.228 52.632 15.58 15.58 35.08 3.01
99 100 1.497722 GAGAAACTTGGCGCGGAAG 59.502 57.895 8.83 14.42 0.00 3.46
100 101 2.314647 CGAGAAACTTGGCGCGGAA 61.315 57.895 8.83 0.00 0.00 4.30
101 102 2.736995 CGAGAAACTTGGCGCGGA 60.737 61.111 8.83 0.00 0.00 5.54
102 103 4.445545 GCGAGAAACTTGGCGCGG 62.446 66.667 8.83 0.00 40.06 6.46
106 107 4.103103 GGCGGCGAGAAACTTGGC 62.103 66.667 12.98 0.00 37.12 4.52
107 108 2.668212 TGGCGGCGAGAAACTTGG 60.668 61.111 12.98 0.00 0.00 3.61
108 109 2.175184 CTGTGGCGGCGAGAAACTTG 62.175 60.000 12.98 0.00 0.00 3.16
109 110 1.961277 CTGTGGCGGCGAGAAACTT 60.961 57.895 12.98 0.00 0.00 2.66
110 111 2.357517 CTGTGGCGGCGAGAAACT 60.358 61.111 12.98 0.00 0.00 2.66
111 112 2.357034 TCTGTGGCGGCGAGAAAC 60.357 61.111 12.98 2.61 0.00 2.78
112 113 2.048222 CTCTGTGGCGGCGAGAAA 60.048 61.111 12.98 0.00 0.00 2.52
113 114 4.742201 GCTCTGTGGCGGCGAGAA 62.742 66.667 12.98 0.00 0.00 2.87
138 139 4.500116 GAGGTGCTCCGAGGACGC 62.500 72.222 13.27 7.10 37.44 5.19
139 140 3.827898 GGAGGTGCTCCGAGGACG 61.828 72.222 13.27 0.00 41.08 4.79
161 162 4.436998 CTCAGGGCGTCGTCCACC 62.437 72.222 19.87 4.01 0.00 4.61
164 165 4.148825 ATGCTCAGGGCGTCGTCC 62.149 66.667 8.12 8.12 45.43 4.79
165 166 2.583593 GATGCTCAGGGCGTCGTC 60.584 66.667 0.00 0.00 45.42 4.20
189 190 3.991536 GAAGTGGAGGCGCGAGGTC 62.992 68.421 12.10 1.54 0.00 3.85
190 191 4.070552 GAAGTGGAGGCGCGAGGT 62.071 66.667 12.10 0.00 0.00 3.85
191 192 3.302347 AAGAAGTGGAGGCGCGAGG 62.302 63.158 12.10 0.00 0.00 4.63
192 193 1.807573 GAAGAAGTGGAGGCGCGAG 60.808 63.158 12.10 0.00 0.00 5.03
193 194 2.261671 GAAGAAGTGGAGGCGCGA 59.738 61.111 12.10 0.00 0.00 5.87
194 195 2.815647 GGAAGAAGTGGAGGCGCG 60.816 66.667 0.00 0.00 0.00 6.86
195 196 2.436824 GGGAAGAAGTGGAGGCGC 60.437 66.667 0.00 0.00 0.00 6.53
196 197 2.269241 GGGGAAGAAGTGGAGGCG 59.731 66.667 0.00 0.00 0.00 5.52
197 198 1.301293 CAGGGGAAGAAGTGGAGGC 59.699 63.158 0.00 0.00 0.00 4.70
198 199 0.547712 TCCAGGGGAAGAAGTGGAGG 60.548 60.000 0.00 0.00 34.03 4.30
199 200 0.615850 GTCCAGGGGAAGAAGTGGAG 59.384 60.000 0.00 0.00 39.80 3.86
200 201 0.840722 GGTCCAGGGGAAGAAGTGGA 60.841 60.000 0.00 0.00 36.72 4.02
201 202 1.685820 GGTCCAGGGGAAGAAGTGG 59.314 63.158 0.00 0.00 31.38 4.00
202 203 1.296715 CGGTCCAGGGGAAGAAGTG 59.703 63.158 0.00 0.00 31.38 3.16
203 204 1.918800 CCGGTCCAGGGGAAGAAGT 60.919 63.158 0.00 0.00 31.38 3.01
204 205 1.612442 TCCGGTCCAGGGGAAGAAG 60.612 63.158 0.00 0.00 31.38 2.85
205 206 1.612442 CTCCGGTCCAGGGGAAGAA 60.612 63.158 0.00 0.00 32.01 2.52
206 207 2.038975 CTCCGGTCCAGGGGAAGA 59.961 66.667 0.00 0.00 32.01 2.87
207 208 3.787001 GCTCCGGTCCAGGGGAAG 61.787 72.222 0.00 0.00 32.01 3.46
211 212 4.452733 GAACGCTCCGGTCCAGGG 62.453 72.222 0.00 2.26 37.65 4.45
212 213 3.691342 TGAACGCTCCGGTCCAGG 61.691 66.667 0.00 0.00 43.57 4.45
213 214 2.432628 GTGAACGCTCCGGTCCAG 60.433 66.667 0.00 0.00 43.57 3.86
214 215 3.998672 GGTGAACGCTCCGGTCCA 61.999 66.667 0.00 0.00 43.57 4.02
215 216 4.754667 GGGTGAACGCTCCGGTCC 62.755 72.222 0.00 0.00 43.57 4.46
216 217 4.754667 GGGGTGAACGCTCCGGTC 62.755 72.222 0.00 0.00 44.56 4.79
220 221 3.998672 TGTCGGGGTGAACGCTCC 61.999 66.667 0.00 0.00 0.00 4.70
221 222 2.737376 GTGTCGGGGTGAACGCTC 60.737 66.667 0.00 0.00 0.00 5.03
222 223 4.657824 CGTGTCGGGGTGAACGCT 62.658 66.667 0.00 0.00 0.00 5.07
261 262 2.041115 GTTCTTCCTCCCGCTTGGC 61.041 63.158 0.00 0.00 0.00 4.52
262 263 0.955919 GTGTTCTTCCTCCCGCTTGG 60.956 60.000 0.00 0.00 0.00 3.61
263 264 1.291877 CGTGTTCTTCCTCCCGCTTG 61.292 60.000 0.00 0.00 0.00 4.01
264 265 1.004918 CGTGTTCTTCCTCCCGCTT 60.005 57.895 0.00 0.00 0.00 4.68
265 266 1.906824 TCGTGTTCTTCCTCCCGCT 60.907 57.895 0.00 0.00 0.00 5.52
266 267 1.737008 GTCGTGTTCTTCCTCCCGC 60.737 63.158 0.00 0.00 0.00 6.13
267 268 0.032952 TTGTCGTGTTCTTCCTCCCG 59.967 55.000 0.00 0.00 0.00 5.14
268 269 1.608283 CCTTGTCGTGTTCTTCCTCCC 60.608 57.143 0.00 0.00 0.00 4.30
269 270 1.797025 CCTTGTCGTGTTCTTCCTCC 58.203 55.000 0.00 0.00 0.00 4.30
270 271 1.149148 GCCTTGTCGTGTTCTTCCTC 58.851 55.000 0.00 0.00 0.00 3.71
271 272 0.600255 CGCCTTGTCGTGTTCTTCCT 60.600 55.000 0.00 0.00 0.00 3.36
272 273 0.878961 ACGCCTTGTCGTGTTCTTCC 60.879 55.000 0.00 0.00 41.62 3.46
273 274 2.601562 ACGCCTTGTCGTGTTCTTC 58.398 52.632 0.00 0.00 41.62 2.87
274 275 4.848685 ACGCCTTGTCGTGTTCTT 57.151 50.000 0.00 0.00 41.62 2.52
280 281 2.030562 CCTTCCACGCCTTGTCGT 59.969 61.111 0.00 0.00 44.35 4.34
281 282 3.423154 GCCTTCCACGCCTTGTCG 61.423 66.667 0.00 0.00 0.00 4.35
282 283 3.056328 GGCCTTCCACGCCTTGTC 61.056 66.667 0.00 0.00 43.48 3.18
283 284 4.660938 GGGCCTTCCACGCCTTGT 62.661 66.667 0.84 0.00 46.24 3.16
284 285 4.351054 AGGGCCTTCCACGCCTTG 62.351 66.667 0.00 0.00 46.24 3.61
285 286 4.351054 CAGGGCCTTCCACGCCTT 62.351 66.667 1.32 0.00 46.24 4.35
289 290 4.431131 ATGCCAGGGCCTTCCACG 62.431 66.667 1.32 0.00 41.09 4.94
290 291 2.757099 CATGCCAGGGCCTTCCAC 60.757 66.667 1.32 0.00 41.09 4.02
291 292 4.764771 GCATGCCAGGGCCTTCCA 62.765 66.667 1.32 3.93 41.09 3.53
292 293 4.453892 AGCATGCCAGGGCCTTCC 62.454 66.667 15.66 0.00 41.09 3.46
293 294 2.832201 GAGCATGCCAGGGCCTTC 60.832 66.667 15.66 0.00 41.09 3.46
294 295 4.453892 GGAGCATGCCAGGGCCTT 62.454 66.667 15.66 0.00 41.09 4.35
297 298 4.437587 AGTGGAGCATGCCAGGGC 62.438 66.667 15.66 2.62 38.95 5.19
298 299 2.124403 GAGTGGAGCATGCCAGGG 60.124 66.667 15.66 0.00 38.95 4.45
299 300 2.124403 GGAGTGGAGCATGCCAGG 60.124 66.667 15.66 0.00 38.95 4.45
300 301 1.451567 CTGGAGTGGAGCATGCCAG 60.452 63.158 15.66 8.78 38.95 4.85
301 302 2.672908 CTGGAGTGGAGCATGCCA 59.327 61.111 15.66 2.78 35.02 4.92
302 303 2.827642 GCTGGAGTGGAGCATGCC 60.828 66.667 15.66 5.80 36.40 4.40
303 304 2.827642 GGCTGGAGTGGAGCATGC 60.828 66.667 10.51 10.51 38.27 4.06
304 305 2.513204 CGGCTGGAGTGGAGCATG 60.513 66.667 0.00 0.00 38.27 4.06
305 306 4.479993 GCGGCTGGAGTGGAGCAT 62.480 66.667 0.00 0.00 38.27 3.79
344 345 3.215245 CTCCTTGAGCTCCGGGAG 58.785 66.667 26.75 26.75 39.22 4.30
370 371 3.482783 GACGCACTTGCCGAGCTC 61.483 66.667 2.73 2.73 37.91 4.09
371 372 3.807631 TTGACGCACTTGCCGAGCT 62.808 57.895 0.00 0.00 37.91 4.09
372 373 3.345808 TTGACGCACTTGCCGAGC 61.346 61.111 0.00 0.00 37.91 5.03
373 374 2.551270 GTTGACGCACTTGCCGAG 59.449 61.111 0.00 0.00 37.91 4.63
374 375 3.334751 CGTTGACGCACTTGCCGA 61.335 61.111 0.00 0.00 37.91 5.54
384 385 2.654912 GGACTTCACGGCGTTGACG 61.655 63.158 11.19 11.74 41.40 4.35
385 386 0.878961 AAGGACTTCACGGCGTTGAC 60.879 55.000 11.19 4.06 0.00 3.18
386 387 0.599204 GAAGGACTTCACGGCGTTGA 60.599 55.000 11.19 9.08 39.31 3.18
387 388 1.860078 GAAGGACTTCACGGCGTTG 59.140 57.895 11.19 6.46 39.31 4.10
388 389 1.663702 CGAAGGACTTCACGGCGTT 60.664 57.895 11.19 0.00 39.46 4.84
389 390 2.049433 CGAAGGACTTCACGGCGT 60.049 61.111 6.77 6.77 39.46 5.68
390 391 3.479269 GCGAAGGACTTCACGGCG 61.479 66.667 4.80 4.80 39.46 6.46
391 392 3.119096 GGCGAAGGACTTCACGGC 61.119 66.667 12.12 8.13 42.98 5.68
392 393 2.809601 CGGCGAAGGACTTCACGG 60.810 66.667 0.00 3.53 39.46 4.94
393 394 3.479269 GCGGCGAAGGACTTCACG 61.479 66.667 12.98 16.73 39.46 4.35
394 395 3.119096 GGCGGCGAAGGACTTCAC 61.119 66.667 12.98 2.48 39.46 3.18
395 396 3.171828 TTGGCGGCGAAGGACTTCA 62.172 57.895 12.98 0.00 39.46 3.02
396 397 2.358247 TTGGCGGCGAAGGACTTC 60.358 61.111 12.98 1.98 36.29 3.01
397 398 2.358737 CTTGGCGGCGAAGGACTT 60.359 61.111 12.98 0.00 0.00 3.01
398 399 2.788191 CTTCTTGGCGGCGAAGGACT 62.788 60.000 21.96 0.00 34.45 3.85
399 400 2.358247 TTCTTGGCGGCGAAGGAC 60.358 61.111 21.96 0.00 0.00 3.85
400 401 2.047274 CTTCTTGGCGGCGAAGGA 60.047 61.111 21.96 14.41 34.45 3.36
474 475 4.736896 GTCAGGACGCGGGACACC 62.737 72.222 12.47 5.74 0.00 4.16
484 485 0.663568 CACTCGTTGGTCGTCAGGAC 60.664 60.000 0.00 0.00 45.31 3.85
485 486 1.658114 CACTCGTTGGTCGTCAGGA 59.342 57.895 0.00 0.00 40.80 3.86
486 487 1.372997 CCACTCGTTGGTCGTCAGG 60.373 63.158 0.00 0.00 41.10 3.86
487 488 1.372997 CCCACTCGTTGGTCGTCAG 60.373 63.158 5.31 0.00 45.25 3.51
488 489 2.732016 CCCACTCGTTGGTCGTCA 59.268 61.111 5.31 0.00 45.25 4.35
489 490 2.737376 GCCCACTCGTTGGTCGTC 60.737 66.667 5.31 0.00 45.25 4.20
490 491 4.657824 CGCCCACTCGTTGGTCGT 62.658 66.667 1.84 0.00 42.03 4.34
496 497 4.344865 ATTGGCCGCCCACTCGTT 62.345 61.111 7.03 0.00 41.97 3.85
497 498 4.778143 GATTGGCCGCCCACTCGT 62.778 66.667 7.03 0.00 41.97 4.18
498 499 4.473520 AGATTGGCCGCCCACTCG 62.474 66.667 7.03 0.00 43.52 4.18
499 500 2.514824 GAGATTGGCCGCCCACTC 60.515 66.667 7.03 9.15 41.97 3.51
500 501 4.115199 GGAGATTGGCCGCCCACT 62.115 66.667 7.03 3.30 41.97 4.00
501 502 4.115199 AGGAGATTGGCCGCCCAC 62.115 66.667 7.03 0.00 41.97 4.61
502 503 3.797353 GAGGAGATTGGCCGCCCA 61.797 66.667 7.03 0.00 40.06 5.36
503 504 4.570874 GGAGGAGATTGGCCGCCC 62.571 72.222 7.03 0.00 39.22 6.13
504 505 3.468326 GAGGAGGAGATTGGCCGCC 62.468 68.421 1.04 1.04 44.73 6.13
505 506 2.110006 GAGGAGGAGATTGGCCGC 59.890 66.667 0.00 0.00 0.00 6.53
506 507 1.753368 GAGGAGGAGGAGATTGGCCG 61.753 65.000 0.00 0.00 0.00 6.13
507 508 1.753368 CGAGGAGGAGGAGATTGGCC 61.753 65.000 0.00 0.00 0.00 5.36
508 509 1.745264 CGAGGAGGAGGAGATTGGC 59.255 63.158 0.00 0.00 0.00 4.52
509 510 1.745264 GCGAGGAGGAGGAGATTGG 59.255 63.158 0.00 0.00 0.00 3.16
510 511 1.045350 TGGCGAGGAGGAGGAGATTG 61.045 60.000 0.00 0.00 0.00 2.67
511 512 0.758685 CTGGCGAGGAGGAGGAGATT 60.759 60.000 0.00 0.00 0.00 2.40
512 513 1.152567 CTGGCGAGGAGGAGGAGAT 60.153 63.158 0.00 0.00 0.00 2.75
513 514 2.277072 CTGGCGAGGAGGAGGAGA 59.723 66.667 0.00 0.00 0.00 3.71
514 515 3.535962 GCTGGCGAGGAGGAGGAG 61.536 72.222 0.00 0.00 0.00 3.69
517 518 3.535962 GAGGCTGGCGAGGAGGAG 61.536 72.222 0.00 0.00 0.00 3.69
520 521 3.847602 CTGGAGGCTGGCGAGGAG 61.848 72.222 0.00 0.00 0.00 3.69
531 532 4.479993 CCGAGGCCAAGCTGGAGG 62.480 72.222 5.01 1.38 40.96 4.30
532 533 4.479993 CCCGAGGCCAAGCTGGAG 62.480 72.222 5.01 0.00 40.96 3.86
553 554 4.087892 CTCCCAGGACTGCCACCG 62.088 72.222 0.00 0.00 36.29 4.94
554 555 3.721706 CCTCCCAGGACTGCCACC 61.722 72.222 0.00 0.00 37.67 4.61
555 556 3.721706 CCCTCCCAGGACTGCCAC 61.722 72.222 0.00 0.00 37.67 5.01
556 557 3.273071 ATCCCTCCCAGGACTGCCA 62.273 63.158 0.00 0.00 39.24 4.92
557 558 2.367512 ATCCCTCCCAGGACTGCC 60.368 66.667 0.00 0.00 39.24 4.85
558 559 2.801631 CGATCCCTCCCAGGACTGC 61.802 68.421 0.00 0.00 39.24 4.40
559 560 2.801631 GCGATCCCTCCCAGGACTG 61.802 68.421 0.00 0.00 39.24 3.51
560 561 2.444895 GCGATCCCTCCCAGGACT 60.445 66.667 0.00 0.00 39.24 3.85
561 562 2.444895 AGCGATCCCTCCCAGGAC 60.445 66.667 0.00 0.00 39.24 3.85
562 563 2.444706 CAGCGATCCCTCCCAGGA 60.445 66.667 0.00 0.00 37.67 3.86
563 564 3.554342 CCAGCGATCCCTCCCAGG 61.554 72.222 0.00 0.00 34.30 4.45
564 565 4.247380 GCCAGCGATCCCTCCCAG 62.247 72.222 0.00 0.00 0.00 4.45
568 569 4.593864 GTCGGCCAGCGATCCCTC 62.594 72.222 2.24 0.00 0.00 4.30
595 596 4.803426 CACGAGGTCGAGGGCAGC 62.803 72.222 6.35 0.00 43.02 5.25
596 597 3.374402 ACACGAGGTCGAGGGCAG 61.374 66.667 6.35 0.00 43.02 4.85
597 598 3.680786 CACACGAGGTCGAGGGCA 61.681 66.667 6.35 0.00 43.02 5.36
598 599 4.436998 CCACACGAGGTCGAGGGC 62.437 72.222 6.35 0.00 43.02 5.19
599 600 2.989824 ACCACACGAGGTCGAGGG 60.990 66.667 6.35 6.77 37.28 4.30
612 613 4.773117 GACGAGGACGGCGACCAC 62.773 72.222 28.53 21.65 44.46 4.16
633 634 3.866582 CAGATGAGGTCGGGGGCC 61.867 72.222 0.00 0.00 0.00 5.80
634 635 3.866582 CCAGATGAGGTCGGGGGC 61.867 72.222 0.00 0.00 38.40 5.80
637 638 3.866582 GGCCCAGATGAGGTCGGG 61.867 72.222 0.00 0.00 41.36 5.14
638 639 3.866582 GGGCCCAGATGAGGTCGG 61.867 72.222 19.95 0.00 0.00 4.79
639 640 4.227134 CGGGCCCAGATGAGGTCG 62.227 72.222 24.92 0.00 0.00 4.79
640 641 3.866582 CCGGGCCCAGATGAGGTC 61.867 72.222 24.92 0.00 0.00 3.85
659 660 1.672356 CCAGCCCACACTACACTGC 60.672 63.158 0.00 0.00 0.00 4.40
681 682 2.099621 GTACTGTACGAGCGTGATTCG 58.900 52.381 5.69 0.00 43.38 3.34
693 694 1.063174 CGCGGTGGAGTAGTACTGTAC 59.937 57.143 7.76 9.93 0.00 2.90
694 695 1.339055 ACGCGGTGGAGTAGTACTGTA 60.339 52.381 12.47 0.00 0.00 2.74
695 696 0.607489 ACGCGGTGGAGTAGTACTGT 60.607 55.000 12.47 0.00 0.00 3.55
696 697 1.372582 TACGCGGTGGAGTAGTACTG 58.627 55.000 12.47 0.00 0.00 2.74
697 698 2.338577 ATACGCGGTGGAGTAGTACT 57.661 50.000 12.47 1.37 31.83 2.73
698 699 2.096713 CGTATACGCGGTGGAGTAGTAC 60.097 54.545 13.08 0.00 31.83 2.73
699 700 2.135139 CGTATACGCGGTGGAGTAGTA 58.865 52.381 13.08 0.00 31.83 1.82
702 706 1.330521 GAACGTATACGCGGTGGAGTA 59.669 52.381 24.64 0.00 44.43 2.59
705 709 1.031571 AGGAACGTATACGCGGTGGA 61.032 55.000 24.64 0.00 44.43 4.02
710 714 5.685195 TTCTTTTTAGGAACGTATACGCG 57.315 39.130 24.64 3.53 44.43 6.01
734 748 2.730090 CGACGTATACGCAGTGGAGTTT 60.730 50.000 24.64 1.11 45.73 2.66
735 749 1.202110 CGACGTATACGCAGTGGAGTT 60.202 52.381 24.64 1.90 45.73 3.01
738 752 1.262417 GATCGACGTATACGCAGTGGA 59.738 52.381 24.64 12.61 45.73 4.02
759 773 2.091278 TCCACGAGTAGGATTCAGGGAT 60.091 50.000 0.00 0.00 0.00 3.85
805 819 0.035056 ATGGAGAGGAAAGTTGCCCG 60.035 55.000 0.00 0.00 0.00 6.13
816 830 4.371624 TTGGGTTGCATATATGGAGAGG 57.628 45.455 14.51 0.00 0.00 3.69
868 893 1.075425 CGAAGAGTGAAGCTGGCTCG 61.075 60.000 0.00 0.00 34.69 5.03
894 919 3.842436 AGTGTTACCGGGGAATCTAGTTT 59.158 43.478 6.32 0.00 0.00 2.66
905 931 1.241165 GGGTTTTCAGTGTTACCGGG 58.759 55.000 6.32 0.00 0.00 5.73
945 4897 0.108329 CTACGGCGTGTTTCCCAGAT 60.108 55.000 24.86 0.00 0.00 2.90
991 4943 1.697432 ACGTGGTTCCATGGAAGAAGA 59.303 47.619 27.73 8.84 34.49 2.87
1022 4974 2.125753 CAGTGCTGGACTCCTCGC 60.126 66.667 0.00 0.07 29.75 5.03
1130 5082 1.372997 CACACCGTCTCCTTCCACG 60.373 63.158 0.00 0.00 35.72 4.94
1161 5113 1.731709 CTTTCCACGCATCGTTCATGA 59.268 47.619 0.00 0.00 38.32 3.07
1166 5118 1.234615 CCACCTTTCCACGCATCGTT 61.235 55.000 0.00 0.00 38.32 3.85
1179 5131 3.249189 TTCGCCTGGAGCCACCTT 61.249 61.111 0.00 0.00 38.78 3.50
1220 5172 2.096174 GCACGTGGTTGTTGAAGTTGTA 59.904 45.455 18.88 0.00 0.00 2.41
1224 5176 1.014352 GAGCACGTGGTTGTTGAAGT 58.986 50.000 22.78 0.00 0.00 3.01
1298 5250 4.911390 TGAAAGAGGAGAATTGTCTTCCC 58.089 43.478 10.63 2.71 32.80 3.97
1308 5260 7.893658 AGTTAGTACGATTTGAAAGAGGAGAA 58.106 34.615 0.00 0.00 0.00 2.87
1347 5299 2.642807 CCCAACAAAAGTCTCCTCCCTA 59.357 50.000 0.00 0.00 0.00 3.53
1416 5369 4.227538 CAGTAAGTACAACCGACAGTCTG 58.772 47.826 0.00 0.00 0.00 3.51
1422 5375 5.947443 ACATCTACAGTAAGTACAACCGAC 58.053 41.667 0.00 0.00 0.00 4.79
1427 5380 9.382275 TCGTATGTACATCTACAGTAAGTACAA 57.618 33.333 12.68 9.36 45.39 2.41
1440 5393 6.701145 ACTGATGTTCTCGTATGTACATCT 57.299 37.500 12.68 0.00 44.43 2.90
1641 5599 2.862700 CATGCGAAATCACATGCCG 58.137 52.632 0.00 0.00 37.46 5.69
1646 5604 1.501292 CCGTGCATGCGAAATCACA 59.499 52.632 14.09 0.00 0.00 3.58
1663 5621 8.437360 AAAACTGAAAAAGACAAATCATTCCC 57.563 30.769 0.00 0.00 0.00 3.97
1670 5628 9.927668 TTTGAGAGAAAACTGAAAAAGACAAAT 57.072 25.926 0.00 0.00 0.00 2.32
1681 5639 6.515272 AAGCTTGTTTTGAGAGAAAACTGA 57.485 33.333 0.00 1.04 39.97 3.41
1682 5640 6.808212 TGAAAGCTTGTTTTGAGAGAAAACTG 59.192 34.615 0.00 5.77 39.97 3.16
1747 5710 7.332182 AGCAAAACCGTTTTCAATGAAAAGTTA 59.668 29.630 20.08 0.00 41.32 2.24
1854 6704 0.883814 TCGCGGCGTTTCCCTAAAAA 60.884 50.000 22.90 0.00 0.00 1.94
1855 6705 0.674269 ATCGCGGCGTTTCCCTAAAA 60.674 50.000 22.90 0.00 0.00 1.52
1856 6706 0.674269 AATCGCGGCGTTTCCCTAAA 60.674 50.000 22.90 0.00 0.00 1.85
1857 6707 1.078988 AATCGCGGCGTTTCCCTAA 60.079 52.632 22.90 0.00 0.00 2.69
1858 6708 1.519898 GAATCGCGGCGTTTCCCTA 60.520 57.895 27.17 7.45 31.82 3.53
1859 6709 2.818274 GAATCGCGGCGTTTCCCT 60.818 61.111 27.17 5.17 31.82 4.20
1860 6710 4.218478 CGAATCGCGGCGTTTCCC 62.218 66.667 29.62 14.75 33.65 3.97
1861 6711 3.484547 ACGAATCGCGGCGTTTCC 61.485 61.111 29.62 17.59 46.49 3.13
1862 6712 2.275812 CACGAATCGCGGCGTTTC 60.276 61.111 27.46 27.46 46.49 2.78
1863 6713 2.108344 AAACACGAATCGCGGCGTTT 62.108 50.000 22.90 20.08 46.49 3.60
1864 6714 2.600475 AAACACGAATCGCGGCGTT 61.600 52.632 22.90 15.34 46.49 4.84
1865 6715 3.039588 AAACACGAATCGCGGCGT 61.040 55.556 22.90 11.64 46.49 5.68
1866 6716 2.570581 CAAACACGAATCGCGGCG 60.571 61.111 17.70 17.70 46.49 6.46
1867 6717 1.509162 GACAAACACGAATCGCGGC 60.509 57.895 6.13 0.00 46.49 6.53
1976 7127 3.506810 CTTTTGCGTCAAAAACAGTCCA 58.493 40.909 15.25 0.00 41.77 4.02
2147 8085 0.957395 AGAAAGGGCATGACACTGCG 60.957 55.000 0.00 0.00 43.23 5.18
2229 8173 3.303229 GGTATTACACAAAAATGCGCTGC 59.697 43.478 9.73 0.00 0.00 5.25
2234 8178 8.495148 CAAGGAAAAGGTATTACACAAAAATGC 58.505 33.333 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.