Multiple sequence alignment - TraesCS6D01G162900

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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 TraesCS6D01G162900 chr6D 100.000 2894 0 0 1 2894 142140118 142137225 0.000000e+00 5345
1 TraesCS6D01G162900 chr6B 93.307 2510 123 23 401 2894 245986340 245983860 0.000000e+00 3663
2 TraesCS6D01G162900 chr6B 87.937 315 32 5 1 309 219219031 219219345 1.640000e-97 366
3 TraesCS6D01G162900 chr6B 86.084 309 38 5 4 309 394617211 394616905 7.730000e-86 327
4 TraesCS6D01G162900 chr6A 92.819 2270 106 26 425 2666 187272900 187270660 0.000000e+00 3236
5 TraesCS6D01G162900 chr7D 86.810 326 43 0 1012 1337 615765514 615765839 5.890000e-97 364
6 TraesCS6D01G162900 chr7D 81.153 451 65 12 1018 1464 615559438 615559004 7.680000e-91 344
7 TraesCS6D01G162900 chr7D 85.625 320 46 0 1018 1337 615774925 615775244 1.280000e-88 337
8 TraesCS6D01G162900 chr7D 86.424 302 32 8 12 309 198499129 198499425 3.600000e-84 322
9 TraesCS6D01G162900 chr7A 86.061 330 42 4 1012 1339 708326523 708326850 4.590000e-93 351
10 TraesCS6D01G162900 chr7A 84.969 326 49 0 1012 1337 708319099 708319424 5.980000e-87 331
11 TraesCS6D01G162900 chr7B 85.981 321 45 0 1019 1339 708552469 708552789 7.680000e-91 344
12 TraesCS6D01G162900 chr7B 84.049 326 52 0 1012 1337 708446071 708446396 6.020000e-82 315
13 TraesCS6D01G162900 chr5D 86.624 314 34 6 1 309 245715019 245715329 9.930000e-90 340
14 TraesCS6D01G162900 chr5D 86.495 311 35 7 6 311 447301244 447301552 4.620000e-88 335
15 TraesCS6D01G162900 chr5B 85.942 313 40 4 1 309 125262465 125262777 5.980000e-87 331
16 TraesCS6D01G162900 chr5B 83.951 324 46 6 1 320 518238746 518239067 3.620000e-79 305
17 TraesCS6D01G162900 chr5B 96.875 64 1 1 2033 2096 309666807 309666745 3.940000e-19 106
18 TraesCS6D01G162900 chr4D 85.623 313 37 7 5 312 319112359 319112668 3.600000e-84 322
19 TraesCS6D01G162900 chr3D 84.615 312 42 6 1 309 378533631 378533939 3.620000e-79 305


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 TraesCS6D01G162900 chr6D 142137225 142140118 2893 True 5345 5345 100.000 1 2894 1 chr6D.!!$R1 2893
1 TraesCS6D01G162900 chr6B 245983860 245986340 2480 True 3663 3663 93.307 401 2894 1 chr6B.!!$R1 2493
2 TraesCS6D01G162900 chr6A 187270660 187272900 2240 True 3236 3236 92.819 425 2666 1 chr6A.!!$R1 2241

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
203 204 0.033504 GTCTCCTGTTGGACGCTCAA 59.966 55.0 0.0 0.0 37.46 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2192 1.086696 ATTCCTGTGCCGAAATGACG 58.913 50.0 0.0 0.0 0.0 4.35 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
18 19 3.751767 ACATCAAGAGCAAGGGCAA 57.248 47.368 0.00 0.00 44.61 4.52
19 20 1.542492 ACATCAAGAGCAAGGGCAAG 58.458 50.000 0.00 0.00 44.61 4.01
20 21 0.815734 CATCAAGAGCAAGGGCAAGG 59.184 55.000 0.00 0.00 44.61 3.61
21 22 0.969409 ATCAAGAGCAAGGGCAAGGC 60.969 55.000 0.00 0.00 44.61 4.35
22 23 2.674380 AAGAGCAAGGGCAAGGCG 60.674 61.111 0.00 0.00 44.61 5.52
23 24 4.729918 AGAGCAAGGGCAAGGCGG 62.730 66.667 0.00 0.00 44.61 6.13
24 25 4.722700 GAGCAAGGGCAAGGCGGA 62.723 66.667 0.00 0.00 44.61 5.54
25 26 4.052518 AGCAAGGGCAAGGCGGAT 62.053 61.111 0.00 0.00 44.61 4.18
26 27 3.830192 GCAAGGGCAAGGCGGATG 61.830 66.667 0.00 0.00 40.72 3.51
27 28 2.045045 CAAGGGCAAGGCGGATGA 60.045 61.111 0.00 0.00 0.00 2.92
28 29 2.044946 AAGGGCAAGGCGGATGAC 60.045 61.111 0.00 0.00 0.00 3.06
30 31 4.778143 GGGCAAGGCGGATGACGT 62.778 66.667 0.00 0.00 46.52 4.34
31 32 2.746277 GGCAAGGCGGATGACGTT 60.746 61.111 0.00 0.00 46.52 3.99
32 33 2.332654 GGCAAGGCGGATGACGTTT 61.333 57.895 0.00 0.00 46.52 3.60
33 34 1.022451 GGCAAGGCGGATGACGTTTA 61.022 55.000 0.00 0.00 46.52 2.01
34 35 0.373716 GCAAGGCGGATGACGTTTAG 59.626 55.000 0.00 0.00 46.52 1.85
35 36 1.006832 CAAGGCGGATGACGTTTAGG 58.993 55.000 0.00 0.00 46.52 2.69
36 37 0.107848 AAGGCGGATGACGTTTAGGG 60.108 55.000 0.00 0.00 46.52 3.53
37 38 1.219935 GGCGGATGACGTTTAGGGT 59.780 57.895 0.00 0.00 46.52 4.34
38 39 0.461135 GGCGGATGACGTTTAGGGTA 59.539 55.000 0.00 0.00 46.52 3.69
39 40 1.537562 GGCGGATGACGTTTAGGGTAG 60.538 57.143 0.00 0.00 46.52 3.18
40 41 1.849097 CGGATGACGTTTAGGGTAGC 58.151 55.000 0.00 0.00 37.93 3.58
41 42 1.849097 GGATGACGTTTAGGGTAGCG 58.151 55.000 0.00 0.00 0.00 4.26
42 43 1.135721 GGATGACGTTTAGGGTAGCGT 59.864 52.381 0.00 0.00 40.44 5.07
43 44 2.190981 GATGACGTTTAGGGTAGCGTG 58.809 52.381 0.00 0.00 37.71 5.34
44 45 0.388907 TGACGTTTAGGGTAGCGTGC 60.389 55.000 0.00 0.00 37.71 5.34
45 46 1.079612 ACGTTTAGGGTAGCGTGCC 60.080 57.895 0.00 0.00 36.16 5.01
46 47 2.162754 CGTTTAGGGTAGCGTGCCG 61.163 63.158 0.00 0.00 0.00 5.69
47 48 1.812507 GTTTAGGGTAGCGTGCCGG 60.813 63.158 0.00 0.00 0.00 6.13
48 49 3.668980 TTTAGGGTAGCGTGCCGGC 62.669 63.158 22.73 22.73 0.00 6.13
53 54 4.183686 GTAGCGTGCCGGCGTAGA 62.184 66.667 23.90 0.00 38.18 2.59
54 55 4.183686 TAGCGTGCCGGCGTAGAC 62.184 66.667 23.90 13.61 38.18 2.59
57 58 2.431942 CGTGCCGGCGTAGACTTT 60.432 61.111 23.90 0.00 0.00 2.66
58 59 2.025418 CGTGCCGGCGTAGACTTTT 61.025 57.895 23.90 0.00 0.00 2.27
59 60 1.562575 CGTGCCGGCGTAGACTTTTT 61.563 55.000 23.90 0.00 0.00 1.94
99 100 9.596308 AATGTTTAATTAGGTTTAGGTGGACTT 57.404 29.630 0.00 0.00 0.00 3.01
100 101 8.999905 TGTTTAATTAGGTTTAGGTGGACTTT 57.000 30.769 0.00 0.00 0.00 2.66
101 102 8.852135 TGTTTAATTAGGTTTAGGTGGACTTTG 58.148 33.333 0.00 0.00 0.00 2.77
102 103 8.301720 GTTTAATTAGGTTTAGGTGGACTTTGG 58.698 37.037 0.00 0.00 0.00 3.28
103 104 2.287977 AGGTTTAGGTGGACTTTGGC 57.712 50.000 0.00 0.00 0.00 4.52
104 105 1.203013 AGGTTTAGGTGGACTTTGGCC 60.203 52.381 0.00 0.00 0.00 5.36
105 106 0.879090 GTTTAGGTGGACTTTGGCCG 59.121 55.000 0.00 0.00 0.00 6.13
106 107 0.766131 TTTAGGTGGACTTTGGCCGA 59.234 50.000 0.00 0.00 0.00 5.54
107 108 0.035739 TTAGGTGGACTTTGGCCGAC 59.964 55.000 0.00 0.00 0.00 4.79
108 109 2.162338 TAGGTGGACTTTGGCCGACG 62.162 60.000 0.00 0.00 0.00 5.12
109 110 3.047877 GTGGACTTTGGCCGACGG 61.048 66.667 10.29 10.29 0.00 4.79
110 111 3.552384 TGGACTTTGGCCGACGGT 61.552 61.111 16.73 0.00 0.00 4.83
111 112 2.281276 GGACTTTGGCCGACGGTT 60.281 61.111 16.73 0.00 0.00 4.44
112 113 2.613506 GGACTTTGGCCGACGGTTG 61.614 63.158 16.73 4.16 0.00 3.77
113 114 1.595929 GACTTTGGCCGACGGTTGA 60.596 57.895 16.73 0.00 0.00 3.18
114 115 1.838568 GACTTTGGCCGACGGTTGAC 61.839 60.000 16.73 4.48 0.00 3.18
115 116 2.592287 TTTGGCCGACGGTTGACC 60.592 61.111 16.73 8.57 0.00 4.02
128 129 3.824414 GGTTGACCGACCACTTTAATG 57.176 47.619 1.58 0.00 39.57 1.90
129 130 3.143728 GGTTGACCGACCACTTTAATGT 58.856 45.455 1.58 0.00 39.57 2.71
130 131 3.566742 GGTTGACCGACCACTTTAATGTT 59.433 43.478 1.58 0.00 39.57 2.71
131 132 4.037089 GGTTGACCGACCACTTTAATGTTT 59.963 41.667 1.58 0.00 39.57 2.83
132 133 5.239087 GGTTGACCGACCACTTTAATGTTTA 59.761 40.000 1.58 0.00 39.57 2.01
133 134 6.238703 GGTTGACCGACCACTTTAATGTTTAA 60.239 38.462 1.58 0.00 39.57 1.52
134 135 7.364970 GTTGACCGACCACTTTAATGTTTAAT 58.635 34.615 0.00 0.00 0.00 1.40
135 136 7.513371 TGACCGACCACTTTAATGTTTAATT 57.487 32.000 0.00 0.00 0.00 1.40
136 137 8.618702 TGACCGACCACTTTAATGTTTAATTA 57.381 30.769 0.00 0.00 0.00 1.40
137 138 9.233649 TGACCGACCACTTTAATGTTTAATTAT 57.766 29.630 0.00 0.00 0.00 1.28
138 139 9.498307 GACCGACCACTTTAATGTTTAATTATG 57.502 33.333 0.00 0.00 0.00 1.90
139 140 9.016438 ACCGACCACTTTAATGTTTAATTATGT 57.984 29.630 0.00 0.00 0.00 2.29
140 141 9.849166 CCGACCACTTTAATGTTTAATTATGTT 57.151 29.630 0.00 0.00 0.00 2.71
153 154 9.562583 TGTTTAATTATGTTTATTTCTGCGACC 57.437 29.630 0.00 0.00 0.00 4.79
154 155 9.783256 GTTTAATTATGTTTATTTCTGCGACCT 57.217 29.630 0.00 0.00 0.00 3.85
180 181 3.572604 TTTTACGCCGGTAAATTTGGG 57.427 42.857 1.90 0.76 45.36 4.12
181 182 2.197283 TTACGCCGGTAAATTTGGGT 57.803 45.000 1.90 1.23 35.74 4.51
182 183 1.736612 TACGCCGGTAAATTTGGGTC 58.263 50.000 1.90 0.00 0.00 4.46
183 184 0.961857 ACGCCGGTAAATTTGGGTCC 60.962 55.000 1.90 0.00 0.00 4.46
184 185 1.804598 GCCGGTAAATTTGGGTCCG 59.195 57.895 1.90 9.43 40.72 4.79
185 186 0.961857 GCCGGTAAATTTGGGTCCGT 60.962 55.000 1.90 0.00 39.62 4.69
186 187 1.089112 CCGGTAAATTTGGGTCCGTC 58.911 55.000 17.60 0.00 39.62 4.79
187 188 1.339342 CCGGTAAATTTGGGTCCGTCT 60.339 52.381 17.60 0.00 39.62 4.18
188 189 2.004733 CGGTAAATTTGGGTCCGTCTC 58.995 52.381 0.00 0.00 36.99 3.36
189 190 2.362736 GGTAAATTTGGGTCCGTCTCC 58.637 52.381 0.00 0.00 0.00 3.71
190 191 2.026542 GGTAAATTTGGGTCCGTCTCCT 60.027 50.000 0.00 0.00 0.00 3.69
191 192 2.200373 AAATTTGGGTCCGTCTCCTG 57.800 50.000 0.00 0.00 0.00 3.86
192 193 1.064825 AATTTGGGTCCGTCTCCTGT 58.935 50.000 0.00 0.00 0.00 4.00
193 194 1.064825 ATTTGGGTCCGTCTCCTGTT 58.935 50.000 0.00 0.00 0.00 3.16
194 195 0.107831 TTTGGGTCCGTCTCCTGTTG 59.892 55.000 0.00 0.00 0.00 3.33
195 196 1.764571 TTGGGTCCGTCTCCTGTTGG 61.765 60.000 0.00 0.00 0.00 3.77
196 197 1.911766 GGGTCCGTCTCCTGTTGGA 60.912 63.158 0.00 0.00 40.69 3.53
197 198 4.990288 GTCCGTCTCCTGTTGGAC 57.010 61.111 0.00 0.00 43.60 4.02
200 201 2.651361 CGTCTCCTGTTGGACGCT 59.349 61.111 2.72 0.00 46.23 5.07
201 202 1.444553 CGTCTCCTGTTGGACGCTC 60.445 63.158 2.72 0.00 46.23 5.03
202 203 1.666011 GTCTCCTGTTGGACGCTCA 59.334 57.895 0.00 0.00 37.46 4.26
203 204 0.033504 GTCTCCTGTTGGACGCTCAA 59.966 55.000 0.00 0.00 37.46 3.02
204 205 0.318441 TCTCCTGTTGGACGCTCAAG 59.682 55.000 0.00 0.00 37.46 3.02
205 206 1.294659 CTCCTGTTGGACGCTCAAGC 61.295 60.000 0.00 0.00 37.46 4.01
206 207 2.328099 CCTGTTGGACGCTCAAGCC 61.328 63.158 0.00 0.00 34.45 4.35
207 208 2.664851 TGTTGGACGCTCAAGCCG 60.665 61.111 0.00 0.00 37.91 5.52
208 209 2.357034 GTTGGACGCTCAAGCCGA 60.357 61.111 0.00 0.00 37.91 5.54
209 210 2.357034 TTGGACGCTCAAGCCGAC 60.357 61.111 0.00 0.00 37.91 4.79
210 211 3.876589 TTGGACGCTCAAGCCGACC 62.877 63.158 0.00 3.02 37.91 4.79
212 213 4.373116 GACGCTCAAGCCGACCCA 62.373 66.667 0.00 0.00 37.91 4.51
213 214 3.665675 GACGCTCAAGCCGACCCAT 62.666 63.158 0.00 0.00 37.91 4.00
214 215 2.292794 GACGCTCAAGCCGACCCATA 62.293 60.000 0.00 0.00 37.91 2.74
215 216 1.069765 CGCTCAAGCCGACCCATAT 59.930 57.895 0.00 0.00 37.91 1.78
216 217 1.224069 CGCTCAAGCCGACCCATATG 61.224 60.000 0.00 0.00 37.91 1.78
217 218 0.106708 GCTCAAGCCGACCCATATGA 59.893 55.000 3.65 0.00 34.31 2.15
218 219 1.475034 GCTCAAGCCGACCCATATGAA 60.475 52.381 3.65 0.00 34.31 2.57
219 220 2.917933 CTCAAGCCGACCCATATGAAA 58.082 47.619 3.65 0.00 0.00 2.69
220 221 3.278574 CTCAAGCCGACCCATATGAAAA 58.721 45.455 3.65 0.00 0.00 2.29
221 222 3.885297 CTCAAGCCGACCCATATGAAAAT 59.115 43.478 3.65 0.00 0.00 1.82
222 223 3.631686 TCAAGCCGACCCATATGAAAATG 59.368 43.478 3.65 0.00 0.00 2.32
223 224 1.956477 AGCCGACCCATATGAAAATGC 59.044 47.619 3.65 1.48 0.00 3.56
224 225 1.334960 GCCGACCCATATGAAAATGCG 60.335 52.381 3.65 0.00 0.00 4.73
225 226 1.266718 CCGACCCATATGAAAATGCGG 59.733 52.381 3.65 4.84 0.00 5.69
226 227 2.217750 CGACCCATATGAAAATGCGGA 58.782 47.619 3.65 0.00 0.00 5.54
227 228 2.032030 CGACCCATATGAAAATGCGGAC 60.032 50.000 3.65 0.00 0.00 4.79
228 229 1.946768 ACCCATATGAAAATGCGGACG 59.053 47.619 3.65 0.00 0.00 4.79
229 230 1.334960 CCCATATGAAAATGCGGACGC 60.335 52.381 10.13 10.13 42.35 5.19
230 231 1.660052 CCATATGAAAATGCGGACGCG 60.660 52.381 3.53 3.53 45.51 6.01
231 232 0.041312 ATATGAAAATGCGGACGCGC 60.041 50.000 5.73 0.00 45.51 6.86
261 262 4.178861 CGATCCAAGCGGACGAAA 57.821 55.556 0.00 0.00 46.79 3.46
262 263 2.451693 CGATCCAAGCGGACGAAAA 58.548 52.632 0.00 0.00 46.79 2.29
263 264 0.370273 CGATCCAAGCGGACGAAAAG 59.630 55.000 0.00 0.00 46.79 2.27
264 265 0.097150 GATCCAAGCGGACGAAAAGC 59.903 55.000 0.00 0.00 46.79 3.51
265 266 1.635663 ATCCAAGCGGACGAAAAGCG 61.636 55.000 0.00 0.00 46.79 4.68
266 267 2.173382 CAAGCGGACGAAAAGCGG 59.827 61.111 0.00 0.00 46.49 5.52
267 268 2.029964 AAGCGGACGAAAAGCGGA 59.970 55.556 0.00 0.00 46.49 5.54
268 269 2.315386 AAGCGGACGAAAAGCGGAC 61.315 57.895 0.00 0.00 46.49 4.79
269 270 2.981977 AAGCGGACGAAAAGCGGACA 62.982 55.000 0.00 0.00 46.49 4.02
270 271 3.011760 GCGGACGAAAAGCGGACAG 62.012 63.158 0.00 0.00 46.49 3.51
271 272 1.372499 CGGACGAAAAGCGGACAGA 60.372 57.895 0.00 0.00 46.49 3.41
272 273 0.942410 CGGACGAAAAGCGGACAGAA 60.942 55.000 0.00 0.00 46.49 3.02
273 274 0.511653 GGACGAAAAGCGGACAGAAC 59.488 55.000 0.00 0.00 46.49 3.01
274 275 0.161024 GACGAAAAGCGGACAGAACG 59.839 55.000 0.00 0.00 46.49 3.95
291 292 3.554692 GCGCGTCCGTTGGATCTG 61.555 66.667 8.43 0.00 32.73 2.90
292 293 3.554692 CGCGTCCGTTGGATCTGC 61.555 66.667 0.00 0.00 32.73 4.26
293 294 3.195698 GCGTCCGTTGGATCTGCC 61.196 66.667 0.00 0.00 32.73 4.85
294 295 2.511600 CGTCCGTTGGATCTGCCC 60.512 66.667 0.00 0.00 32.73 5.36
295 296 2.511600 GTCCGTTGGATCTGCCCG 60.512 66.667 0.00 0.00 32.73 6.13
296 297 3.000819 TCCGTTGGATCTGCCCGT 61.001 61.111 0.00 0.00 34.97 5.28
297 298 2.046314 CCGTTGGATCTGCCCGTT 60.046 61.111 0.00 0.00 34.97 4.44
298 299 2.398554 CCGTTGGATCTGCCCGTTG 61.399 63.158 0.00 0.00 34.97 4.10
299 300 1.375396 CGTTGGATCTGCCCGTTGA 60.375 57.895 0.00 0.00 34.97 3.18
300 301 0.953471 CGTTGGATCTGCCCGTTGAA 60.953 55.000 0.00 0.00 34.97 2.69
301 302 0.804989 GTTGGATCTGCCCGTTGAAG 59.195 55.000 0.00 0.00 34.97 3.02
302 303 0.400213 TTGGATCTGCCCGTTGAAGT 59.600 50.000 0.00 0.00 34.97 3.01
303 304 0.400213 TGGATCTGCCCGTTGAAGTT 59.600 50.000 0.00 0.00 34.97 2.66
304 305 1.626321 TGGATCTGCCCGTTGAAGTTA 59.374 47.619 0.00 0.00 34.97 2.24
305 306 2.007608 GGATCTGCCCGTTGAAGTTAC 58.992 52.381 0.00 0.00 0.00 2.50
306 307 2.354805 GGATCTGCCCGTTGAAGTTACT 60.355 50.000 0.00 0.00 0.00 2.24
307 308 2.450609 TCTGCCCGTTGAAGTTACTC 57.549 50.000 0.00 0.00 0.00 2.59
308 309 1.968493 TCTGCCCGTTGAAGTTACTCT 59.032 47.619 0.00 0.00 0.00 3.24
309 310 3.159472 TCTGCCCGTTGAAGTTACTCTA 58.841 45.455 0.00 0.00 0.00 2.43
310 311 3.575256 TCTGCCCGTTGAAGTTACTCTAA 59.425 43.478 0.00 0.00 0.00 2.10
311 312 4.222145 TCTGCCCGTTGAAGTTACTCTAAT 59.778 41.667 0.00 0.00 0.00 1.73
312 313 5.419788 TCTGCCCGTTGAAGTTACTCTAATA 59.580 40.000 0.00 0.00 0.00 0.98
313 314 6.040209 TGCCCGTTGAAGTTACTCTAATAA 57.960 37.500 0.00 0.00 0.00 1.40
314 315 5.870978 TGCCCGTTGAAGTTACTCTAATAAC 59.129 40.000 0.00 0.00 35.62 1.89
315 316 5.292834 GCCCGTTGAAGTTACTCTAATAACC 59.707 44.000 0.00 0.00 35.95 2.85
316 317 5.814188 CCCGTTGAAGTTACTCTAATAACCC 59.186 44.000 0.00 0.00 35.95 4.11
317 318 6.351626 CCCGTTGAAGTTACTCTAATAACCCT 60.352 42.308 0.00 0.00 35.95 4.34
318 319 6.534079 CCGTTGAAGTTACTCTAATAACCCTG 59.466 42.308 0.00 0.00 35.95 4.45
319 320 7.318141 CGTTGAAGTTACTCTAATAACCCTGA 58.682 38.462 0.00 0.00 35.95 3.86
320 321 7.816031 CGTTGAAGTTACTCTAATAACCCTGAA 59.184 37.037 0.00 0.00 35.95 3.02
321 322 9.498176 GTTGAAGTTACTCTAATAACCCTGAAA 57.502 33.333 0.00 0.00 35.95 2.69
329 330 8.803397 ACTCTAATAACCCTGAAAAATACACC 57.197 34.615 0.00 0.00 0.00 4.16
330 331 7.832685 ACTCTAATAACCCTGAAAAATACACCC 59.167 37.037 0.00 0.00 0.00 4.61
331 332 5.907866 AATAACCCTGAAAAATACACCCG 57.092 39.130 0.00 0.00 0.00 5.28
332 333 1.541379 ACCCTGAAAAATACACCCGC 58.459 50.000 0.00 0.00 0.00 6.13
333 334 1.202952 ACCCTGAAAAATACACCCGCA 60.203 47.619 0.00 0.00 0.00 5.69
334 335 1.889829 CCCTGAAAAATACACCCGCAA 59.110 47.619 0.00 0.00 0.00 4.85
335 336 2.297597 CCCTGAAAAATACACCCGCAAA 59.702 45.455 0.00 0.00 0.00 3.68
336 337 3.243907 CCCTGAAAAATACACCCGCAAAA 60.244 43.478 0.00 0.00 0.00 2.44
337 338 4.372656 CCTGAAAAATACACCCGCAAAAA 58.627 39.130 0.00 0.00 0.00 1.94
361 362 6.857437 AAATTCCCCTGAAAAATACAGAGG 57.143 37.500 0.00 0.00 37.54 3.69
362 363 5.536497 ATTCCCCTGAAAAATACAGAGGT 57.464 39.130 0.00 0.00 35.30 3.85
363 364 5.333566 TTCCCCTGAAAAATACAGAGGTT 57.666 39.130 0.00 0.00 35.30 3.50
364 365 4.918588 TCCCCTGAAAAATACAGAGGTTC 58.081 43.478 0.00 0.00 35.30 3.62
365 366 4.352595 TCCCCTGAAAAATACAGAGGTTCA 59.647 41.667 0.00 0.00 35.30 3.18
366 367 5.015178 TCCCCTGAAAAATACAGAGGTTCAT 59.985 40.000 0.00 0.00 35.30 2.57
367 368 5.126061 CCCCTGAAAAATACAGAGGTTCATG 59.874 44.000 0.00 0.00 37.54 3.07
368 369 5.711976 CCCTGAAAAATACAGAGGTTCATGT 59.288 40.000 0.00 0.00 37.54 3.21
369 370 6.349611 CCCTGAAAAATACAGAGGTTCATGTG 60.350 42.308 0.00 0.00 37.54 3.21
370 371 6.430925 CCTGAAAAATACAGAGGTTCATGTGA 59.569 38.462 0.00 0.00 37.54 3.58
371 372 7.040478 CCTGAAAAATACAGAGGTTCATGTGAA 60.040 37.037 0.00 0.00 37.54 3.18
372 373 7.874940 TGAAAAATACAGAGGTTCATGTGAAG 58.125 34.615 0.00 0.00 34.27 3.02
383 384 5.725110 GTTCATGTGAAGCATACGATCTT 57.275 39.130 0.00 0.00 35.74 2.40
384 385 6.111768 GTTCATGTGAAGCATACGATCTTT 57.888 37.500 0.00 0.00 35.74 2.52
385 386 6.546395 GTTCATGTGAAGCATACGATCTTTT 58.454 36.000 0.00 0.00 35.74 2.27
386 387 6.741992 TCATGTGAAGCATACGATCTTTTT 57.258 33.333 0.00 0.00 35.74 1.94
409 410 7.517614 TTTTTAGTGGAATGTGAAGCATACA 57.482 32.000 0.00 0.00 36.67 2.29
444 445 3.066190 CCGGTGAGGGCTCGTACA 61.066 66.667 0.00 0.00 35.97 2.90
454 455 2.045131 GCTCGTACAGGGTCGGAGT 61.045 63.158 0.00 0.00 0.00 3.85
466 467 1.219646 GTCGGAGTTGTTTTGGCGTA 58.780 50.000 0.00 0.00 0.00 4.42
947 953 2.807045 GCGTCTGCTCGTGAGGTG 60.807 66.667 0.00 0.00 38.39 4.00
953 959 1.533033 TGCTCGTGAGGTGAAGGGA 60.533 57.895 0.00 0.00 0.00 4.20
990 1001 4.427096 TTTTGGTTGTAGTGTGTGTGTG 57.573 40.909 0.00 0.00 0.00 3.82
1581 1595 0.326595 TCACCTCTCTGTCGCTCTCT 59.673 55.000 0.00 0.00 0.00 3.10
1596 1610 1.755008 CTCTCTCCCCGGACTGGAC 60.755 68.421 0.73 0.00 42.00 4.02
1647 1661 3.423162 CTTCCAGGAGCTCTCGCCG 62.423 68.421 14.64 0.00 37.24 6.46
1906 1923 4.231439 CCGCCAGTAAAAATAAAAACGCT 58.769 39.130 0.00 0.00 0.00 5.07
2043 2061 0.657368 CTGGTTCGTTCTGTTTGCGC 60.657 55.000 0.00 0.00 0.00 6.09
2114 2132 3.702048 CGAAGTCGGCAAGGGGGA 61.702 66.667 0.00 0.00 35.37 4.81
2128 2146 4.263462 GCAAGGGGGAAAATGGAAAGAAAT 60.263 41.667 0.00 0.00 0.00 2.17
2155 2175 9.997482 GAGAACGGAAATTGTTAATTATTGCTA 57.003 29.630 0.00 0.00 0.00 3.49
2157 2177 8.920509 AACGGAAATTGTTAATTATTGCTACC 57.079 30.769 0.00 0.00 0.00 3.18
2163 2183 8.823220 AATTGTTAATTATTGCTACCACTCCT 57.177 30.769 0.00 0.00 0.00 3.69
2164 2184 9.914834 AATTGTTAATTATTGCTACCACTCCTA 57.085 29.630 0.00 0.00 0.00 2.94
2170 2190 1.035932 TGCTACCACTCCTACCGAGC 61.036 60.000 0.00 0.00 43.01 5.03
2172 2192 1.076485 TACCACTCCTACCGAGCCC 60.076 63.158 0.00 0.00 43.01 5.19
2199 2219 1.134699 TCGGCACAGGAATGAGATGAC 60.135 52.381 0.00 0.00 0.00 3.06
2206 2226 2.770802 CAGGAATGAGATGACTGGGACT 59.229 50.000 0.00 0.00 0.00 3.85
2239 2259 3.598019 ATTTGGCAAATCATGTTCGCT 57.402 38.095 19.39 0.00 0.00 4.93
2293 2313 2.621055 CAGGTTCCGTTGATGGTTTGAA 59.379 45.455 0.00 0.00 0.00 2.69
2294 2314 2.621526 AGGTTCCGTTGATGGTTTGAAC 59.378 45.455 0.00 0.00 33.20 3.18
2295 2315 2.621526 GGTTCCGTTGATGGTTTGAACT 59.378 45.455 0.00 0.00 34.15 3.01
2360 2387 7.675619 TGGTCATCTCTGAATCCTGCTATAATA 59.324 37.037 0.00 0.00 31.85 0.98
2362 2389 9.585099 GTCATCTCTGAATCCTGCTATAATAAG 57.415 37.037 0.00 0.00 31.85 1.73
2381 2408 6.689663 ATAAGATCTAGTAAGCCCTTTCCC 57.310 41.667 0.00 0.00 0.00 3.97
2387 2414 1.553704 AGTAAGCCCTTTCCCGTGTAG 59.446 52.381 0.00 0.00 0.00 2.74
2393 2423 2.100418 GCCCTTTCCCGTGTAGTACTAG 59.900 54.545 1.87 0.00 0.00 2.57
2394 2424 3.359950 CCCTTTCCCGTGTAGTACTAGT 58.640 50.000 1.87 0.00 0.00 2.57
2398 2428 5.184671 CCTTTCCCGTGTAGTACTAGTTCTT 59.815 44.000 7.37 0.00 0.00 2.52
2399 2429 5.633830 TTCCCGTGTAGTACTAGTTCTTG 57.366 43.478 7.37 0.00 0.00 3.02
2400 2430 4.012374 TCCCGTGTAGTACTAGTTCTTGG 58.988 47.826 7.37 5.35 0.00 3.61
2401 2431 3.760684 CCCGTGTAGTACTAGTTCTTGGT 59.239 47.826 7.37 0.00 0.00 3.67
2402 2432 4.142513 CCCGTGTAGTACTAGTTCTTGGTC 60.143 50.000 7.37 0.00 0.00 4.02
2409 2439 6.197364 AGTACTAGTTCTTGGTCGATCAAG 57.803 41.667 28.87 28.87 43.91 3.02
2428 2458 2.475200 GCCAAACATGGCGTCTAATC 57.525 50.000 3.80 0.00 45.79 1.75
2494 2525 0.884704 GGAGCAGAAACGACAAGCCA 60.885 55.000 0.00 0.00 0.00 4.75
2594 2625 3.550974 AGTTGTGGACTGGCTCGT 58.449 55.556 0.00 0.00 37.17 4.18
2615 2646 0.172803 GTTACGCGACTGGAGGACAT 59.827 55.000 15.93 0.00 0.00 3.06
2721 2753 1.630878 GTATTGATAGAGGGGCAGGGG 59.369 57.143 0.00 0.00 0.00 4.79
2728 2760 1.519498 AGAGGGGCAGGGGTAAATAC 58.481 55.000 0.00 0.00 0.00 1.89
2759 2791 6.682113 GCTGTTCACCGTAGAGTAAATATCCA 60.682 42.308 0.00 0.00 0.00 3.41
2803 2835 1.808799 CGAGAGCTGCGCAATCTGT 60.809 57.895 24.88 17.01 0.00 3.41
2808 2840 3.056313 GCTGCGCAATCTGTTCCCC 62.056 63.158 13.05 0.00 0.00 4.81
2812 2844 1.937546 GCGCAATCTGTTCCCCCAAG 61.938 60.000 0.30 0.00 0.00 3.61
2821 2853 7.320399 CAATCTGTTCCCCCAAGTTTTAATAC 58.680 38.462 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.542492 CTTGCCCTTGCTCTTGATGT 58.458 50.000 0.00 0.00 38.71 3.06
1 2 0.815734 CCTTGCCCTTGCTCTTGATG 59.184 55.000 0.00 0.00 38.71 3.07
2 3 0.969409 GCCTTGCCCTTGCTCTTGAT 60.969 55.000 0.00 0.00 38.71 2.57
3 4 1.604593 GCCTTGCCCTTGCTCTTGA 60.605 57.895 0.00 0.00 38.71 3.02
4 5 2.968206 GCCTTGCCCTTGCTCTTG 59.032 61.111 0.00 0.00 38.71 3.02
5 6 2.674380 CGCCTTGCCCTTGCTCTT 60.674 61.111 0.00 0.00 38.71 2.85
6 7 4.729918 CCGCCTTGCCCTTGCTCT 62.730 66.667 0.00 0.00 38.71 4.09
7 8 4.722700 TCCGCCTTGCCCTTGCTC 62.723 66.667 0.00 0.00 38.71 4.26
8 9 4.052518 ATCCGCCTTGCCCTTGCT 62.053 61.111 0.00 0.00 38.71 3.91
9 10 3.830192 CATCCGCCTTGCCCTTGC 61.830 66.667 0.00 0.00 38.26 4.01
10 11 2.045045 TCATCCGCCTTGCCCTTG 60.045 61.111 0.00 0.00 0.00 3.61
11 12 2.044946 GTCATCCGCCTTGCCCTT 60.045 61.111 0.00 0.00 0.00 3.95
12 13 4.473520 CGTCATCCGCCTTGCCCT 62.474 66.667 0.00 0.00 0.00 5.19
13 14 4.778143 ACGTCATCCGCCTTGCCC 62.778 66.667 0.00 0.00 41.42 5.36
14 15 1.022451 TAAACGTCATCCGCCTTGCC 61.022 55.000 0.00 0.00 41.42 4.52
15 16 0.373716 CTAAACGTCATCCGCCTTGC 59.626 55.000 0.00 0.00 41.42 4.01
16 17 1.006832 CCTAAACGTCATCCGCCTTG 58.993 55.000 0.00 0.00 41.42 3.61
17 18 0.107848 CCCTAAACGTCATCCGCCTT 60.108 55.000 0.00 0.00 41.42 4.35
18 19 1.262640 ACCCTAAACGTCATCCGCCT 61.263 55.000 0.00 0.00 41.42 5.52
19 20 0.461135 TACCCTAAACGTCATCCGCC 59.539 55.000 0.00 0.00 41.42 6.13
20 21 1.849097 CTACCCTAAACGTCATCCGC 58.151 55.000 0.00 0.00 41.42 5.54
21 22 1.849097 GCTACCCTAAACGTCATCCG 58.151 55.000 0.00 0.00 44.03 4.18
22 23 1.135721 ACGCTACCCTAAACGTCATCC 59.864 52.381 0.00 0.00 32.37 3.51
23 24 2.190981 CACGCTACCCTAAACGTCATC 58.809 52.381 0.00 0.00 36.45 2.92
24 25 1.738030 GCACGCTACCCTAAACGTCAT 60.738 52.381 0.00 0.00 36.45 3.06
25 26 0.388907 GCACGCTACCCTAAACGTCA 60.389 55.000 0.00 0.00 36.45 4.35
26 27 1.080435 GGCACGCTACCCTAAACGTC 61.080 60.000 0.00 0.00 36.45 4.34
27 28 1.079612 GGCACGCTACCCTAAACGT 60.080 57.895 0.00 0.00 39.78 3.99
28 29 3.790177 GGCACGCTACCCTAAACG 58.210 61.111 0.00 0.00 0.00 3.60
41 42 2.241171 AAAAAGTCTACGCCGGCAC 58.759 52.632 28.98 17.32 0.00 5.01
42 43 4.783667 AAAAAGTCTACGCCGGCA 57.216 50.000 28.98 6.80 0.00 5.69
73 74 9.596308 AAGTCCACCTAAACCTAATTAAACATT 57.404 29.630 0.00 0.00 0.00 2.71
74 75 9.596308 AAAGTCCACCTAAACCTAATTAAACAT 57.404 29.630 0.00 0.00 0.00 2.71
75 76 8.852135 CAAAGTCCACCTAAACCTAATTAAACA 58.148 33.333 0.00 0.00 0.00 2.83
76 77 8.301720 CCAAAGTCCACCTAAACCTAATTAAAC 58.698 37.037 0.00 0.00 0.00 2.01
77 78 7.039574 GCCAAAGTCCACCTAAACCTAATTAAA 60.040 37.037 0.00 0.00 0.00 1.52
78 79 6.434965 GCCAAAGTCCACCTAAACCTAATTAA 59.565 38.462 0.00 0.00 0.00 1.40
79 80 5.947566 GCCAAAGTCCACCTAAACCTAATTA 59.052 40.000 0.00 0.00 0.00 1.40
80 81 4.770531 GCCAAAGTCCACCTAAACCTAATT 59.229 41.667 0.00 0.00 0.00 1.40
81 82 4.341487 GCCAAAGTCCACCTAAACCTAAT 58.659 43.478 0.00 0.00 0.00 1.73
82 83 3.499021 GGCCAAAGTCCACCTAAACCTAA 60.499 47.826 0.00 0.00 0.00 2.69
83 84 2.040679 GGCCAAAGTCCACCTAAACCTA 59.959 50.000 0.00 0.00 0.00 3.08
84 85 1.203013 GGCCAAAGTCCACCTAAACCT 60.203 52.381 0.00 0.00 0.00 3.50
85 86 1.254026 GGCCAAAGTCCACCTAAACC 58.746 55.000 0.00 0.00 0.00 3.27
86 87 0.879090 CGGCCAAAGTCCACCTAAAC 59.121 55.000 2.24 0.00 0.00 2.01
87 88 0.766131 TCGGCCAAAGTCCACCTAAA 59.234 50.000 2.24 0.00 0.00 1.85
88 89 0.035739 GTCGGCCAAAGTCCACCTAA 59.964 55.000 2.24 0.00 0.00 2.69
89 90 1.675219 GTCGGCCAAAGTCCACCTA 59.325 57.895 2.24 0.00 0.00 3.08
90 91 2.430367 GTCGGCCAAAGTCCACCT 59.570 61.111 2.24 0.00 0.00 4.00
91 92 3.047877 CGTCGGCCAAAGTCCACC 61.048 66.667 2.24 0.00 0.00 4.61
92 93 3.047877 CCGTCGGCCAAAGTCCAC 61.048 66.667 2.24 0.00 0.00 4.02
93 94 3.109592 AACCGTCGGCCAAAGTCCA 62.110 57.895 12.28 0.00 0.00 4.02
94 95 2.281276 AACCGTCGGCCAAAGTCC 60.281 61.111 12.28 0.00 0.00 3.85
95 96 1.595929 TCAACCGTCGGCCAAAGTC 60.596 57.895 12.28 0.00 0.00 3.01
96 97 1.890510 GTCAACCGTCGGCCAAAGT 60.891 57.895 12.28 0.00 0.00 2.66
97 98 2.613506 GGTCAACCGTCGGCCAAAG 61.614 63.158 12.28 0.00 0.00 2.77
98 99 2.592287 GGTCAACCGTCGGCCAAA 60.592 61.111 12.28 0.00 0.00 3.28
108 109 3.143728 ACATTAAAGTGGTCGGTCAACC 58.856 45.455 0.00 0.00 39.94 3.77
109 110 4.823790 AACATTAAAGTGGTCGGTCAAC 57.176 40.909 0.00 0.00 0.00 3.18
110 111 6.939132 TTAAACATTAAAGTGGTCGGTCAA 57.061 33.333 0.00 0.00 0.00 3.18
111 112 7.513371 AATTAAACATTAAAGTGGTCGGTCA 57.487 32.000 0.00 0.00 0.00 4.02
112 113 9.498307 CATAATTAAACATTAAAGTGGTCGGTC 57.502 33.333 0.00 0.00 0.00 4.79
113 114 9.016438 ACATAATTAAACATTAAAGTGGTCGGT 57.984 29.630 0.00 0.00 0.00 4.69
114 115 9.849166 AACATAATTAAACATTAAAGTGGTCGG 57.151 29.630 0.00 0.00 0.00 4.79
127 128 9.562583 GGTCGCAGAAATAAACATAATTAAACA 57.437 29.630 0.00 0.00 39.69 2.83
128 129 9.783256 AGGTCGCAGAAATAAACATAATTAAAC 57.217 29.630 0.00 0.00 39.69 2.01
159 160 3.320256 ACCCAAATTTACCGGCGTAAAAA 59.680 39.130 6.01 3.50 45.24 1.94
160 161 2.889678 ACCCAAATTTACCGGCGTAAAA 59.110 40.909 6.01 6.24 45.24 1.52
161 162 2.487372 GACCCAAATTTACCGGCGTAAA 59.513 45.455 6.01 11.18 45.95 2.01
162 163 2.083002 GACCCAAATTTACCGGCGTAA 58.917 47.619 6.01 1.86 32.50 3.18
163 164 1.678425 GGACCCAAATTTACCGGCGTA 60.678 52.381 6.01 0.00 0.00 4.42
164 165 0.961857 GGACCCAAATTTACCGGCGT 60.962 55.000 6.01 0.00 0.00 5.68
165 166 1.804598 GGACCCAAATTTACCGGCG 59.195 57.895 0.00 0.00 0.00 6.46
166 167 0.961857 ACGGACCCAAATTTACCGGC 60.962 55.000 20.64 3.82 46.45 6.13
167 168 1.089112 GACGGACCCAAATTTACCGG 58.911 55.000 20.64 0.00 46.45 5.28
169 170 2.026542 AGGAGACGGACCCAAATTTACC 60.027 50.000 0.00 0.00 0.00 2.85
170 171 3.007635 CAGGAGACGGACCCAAATTTAC 58.992 50.000 0.00 0.00 0.00 2.01
171 172 2.640826 ACAGGAGACGGACCCAAATTTA 59.359 45.455 0.00 0.00 0.00 1.40
172 173 1.423921 ACAGGAGACGGACCCAAATTT 59.576 47.619 0.00 0.00 0.00 1.82
173 174 1.064825 ACAGGAGACGGACCCAAATT 58.935 50.000 0.00 0.00 0.00 1.82
174 175 1.064825 AACAGGAGACGGACCCAAAT 58.935 50.000 0.00 0.00 0.00 2.32
175 176 0.107831 CAACAGGAGACGGACCCAAA 59.892 55.000 0.00 0.00 0.00 3.28
176 177 1.752198 CAACAGGAGACGGACCCAA 59.248 57.895 0.00 0.00 0.00 4.12
177 178 2.214216 CCAACAGGAGACGGACCCA 61.214 63.158 0.00 0.00 0.00 4.51
178 179 1.911766 TCCAACAGGAGACGGACCC 60.912 63.158 0.00 0.00 0.00 4.46
179 180 1.292541 GTCCAACAGGAGACGGACC 59.707 63.158 0.00 0.00 41.77 4.46
180 181 4.990288 GTCCAACAGGAGACGGAC 57.010 61.111 0.00 0.00 41.08 4.79
184 185 0.033504 TTGAGCGTCCAACAGGAGAC 59.966 55.000 0.00 0.00 30.42 3.36
185 186 0.318441 CTTGAGCGTCCAACAGGAGA 59.682 55.000 0.00 0.00 30.42 3.71
186 187 1.294659 GCTTGAGCGTCCAACAGGAG 61.295 60.000 0.00 0.00 30.42 3.69
187 188 1.301716 GCTTGAGCGTCCAACAGGA 60.302 57.895 0.00 0.00 0.00 3.86
188 189 2.328099 GGCTTGAGCGTCCAACAGG 61.328 63.158 0.00 0.00 43.26 4.00
189 190 2.671177 CGGCTTGAGCGTCCAACAG 61.671 63.158 0.00 0.00 43.26 3.16
190 191 2.664851 CGGCTTGAGCGTCCAACA 60.665 61.111 0.00 0.00 43.26 3.33
191 192 2.357034 TCGGCTTGAGCGTCCAAC 60.357 61.111 0.00 0.00 43.26 3.77
192 193 2.357034 GTCGGCTTGAGCGTCCAA 60.357 61.111 0.00 0.00 43.26 3.53
193 194 4.373116 GGTCGGCTTGAGCGTCCA 62.373 66.667 0.00 0.00 43.26 4.02
195 196 2.292794 TATGGGTCGGCTTGAGCGTC 62.293 60.000 0.00 0.00 46.20 5.19
196 197 1.686325 ATATGGGTCGGCTTGAGCGT 61.686 55.000 0.00 0.00 46.20 5.07
197 198 1.069765 ATATGGGTCGGCTTGAGCG 59.930 57.895 0.00 0.00 46.20 5.03
198 199 0.106708 TCATATGGGTCGGCTTGAGC 59.893 55.000 2.13 0.00 44.49 4.26
199 200 2.620251 TTCATATGGGTCGGCTTGAG 57.380 50.000 2.13 0.00 0.00 3.02
200 201 3.358111 TTTTCATATGGGTCGGCTTGA 57.642 42.857 2.13 0.00 0.00 3.02
201 202 3.796504 GCATTTTCATATGGGTCGGCTTG 60.797 47.826 2.13 0.00 0.00 4.01
202 203 2.362077 GCATTTTCATATGGGTCGGCTT 59.638 45.455 2.13 0.00 0.00 4.35
203 204 1.956477 GCATTTTCATATGGGTCGGCT 59.044 47.619 2.13 0.00 0.00 5.52
204 205 1.334960 CGCATTTTCATATGGGTCGGC 60.335 52.381 2.13 1.57 34.72 5.54
205 206 1.266718 CCGCATTTTCATATGGGTCGG 59.733 52.381 2.13 4.44 36.91 4.79
206 207 2.032030 GTCCGCATTTTCATATGGGTCG 60.032 50.000 2.13 0.00 36.91 4.79
207 208 2.032030 CGTCCGCATTTTCATATGGGTC 60.032 50.000 2.13 0.00 36.91 4.46
208 209 1.946768 CGTCCGCATTTTCATATGGGT 59.053 47.619 2.13 0.00 36.91 4.51
209 210 1.334960 GCGTCCGCATTTTCATATGGG 60.335 52.381 6.82 0.00 41.49 4.00
210 211 1.660052 CGCGTCCGCATTTTCATATGG 60.660 52.381 12.58 0.00 42.06 2.74
211 212 1.662360 CGCGTCCGCATTTTCATATG 58.338 50.000 12.58 0.00 42.06 1.78
242 243 4.508128 TCGTCCGCTTGGATCGGC 62.508 66.667 0.00 0.00 45.53 5.54
243 244 1.017177 TTTTCGTCCGCTTGGATCGG 61.017 55.000 0.00 0.00 45.53 4.18
244 245 0.370273 CTTTTCGTCCGCTTGGATCG 59.630 55.000 0.00 0.00 45.53 3.69
245 246 0.097150 GCTTTTCGTCCGCTTGGATC 59.903 55.000 0.00 0.00 45.53 3.36
246 247 1.635663 CGCTTTTCGTCCGCTTGGAT 61.636 55.000 0.00 0.00 45.53 3.41
247 248 2.314647 CGCTTTTCGTCCGCTTGGA 61.315 57.895 0.00 0.00 40.32 3.53
248 249 2.173382 CGCTTTTCGTCCGCTTGG 59.827 61.111 0.00 0.00 0.00 3.61
249 250 2.173382 CCGCTTTTCGTCCGCTTG 59.827 61.111 0.00 0.00 36.19 4.01
250 251 2.029964 TCCGCTTTTCGTCCGCTT 59.970 55.556 0.00 0.00 36.19 4.68
251 252 2.737376 GTCCGCTTTTCGTCCGCT 60.737 61.111 0.00 0.00 36.19 5.52
252 253 3.011760 CTGTCCGCTTTTCGTCCGC 62.012 63.158 0.00 0.00 36.19 5.54
253 254 0.942410 TTCTGTCCGCTTTTCGTCCG 60.942 55.000 0.00 0.00 36.19 4.79
254 255 0.511653 GTTCTGTCCGCTTTTCGTCC 59.488 55.000 0.00 0.00 36.19 4.79
255 256 0.161024 CGTTCTGTCCGCTTTTCGTC 59.839 55.000 0.00 0.00 36.19 4.20
256 257 2.222592 CGTTCTGTCCGCTTTTCGT 58.777 52.632 0.00 0.00 36.19 3.85
267 268 4.936823 AACGGACGCGCGTTCTGT 62.937 61.111 38.03 32.33 0.00 3.41
268 269 4.409588 CAACGGACGCGCGTTCTG 62.410 66.667 38.03 31.71 0.00 3.02
274 275 3.554692 CAGATCCAACGGACGCGC 61.555 66.667 5.73 0.00 32.98 6.86
275 276 3.554692 GCAGATCCAACGGACGCG 61.555 66.667 3.53 3.53 32.98 6.01
276 277 3.195698 GGCAGATCCAACGGACGC 61.196 66.667 0.00 0.00 32.98 5.19
277 278 2.511600 GGGCAGATCCAACGGACG 60.512 66.667 0.00 0.00 32.98 4.79
278 279 2.511600 CGGGCAGATCCAACGGAC 60.512 66.667 0.00 0.00 32.98 4.79
279 280 2.589157 AACGGGCAGATCCAACGGA 61.589 57.895 0.00 0.00 36.21 4.69
280 281 2.046314 AACGGGCAGATCCAACGG 60.046 61.111 0.00 0.00 36.21 4.44
281 282 0.953471 TTCAACGGGCAGATCCAACG 60.953 55.000 0.00 0.00 36.21 4.10
282 283 0.804989 CTTCAACGGGCAGATCCAAC 59.195 55.000 0.00 0.00 36.21 3.77
283 284 0.400213 ACTTCAACGGGCAGATCCAA 59.600 50.000 0.00 0.00 36.21 3.53
284 285 0.400213 AACTTCAACGGGCAGATCCA 59.600 50.000 0.00 0.00 36.21 3.41
285 286 2.007608 GTAACTTCAACGGGCAGATCC 58.992 52.381 0.00 0.00 0.00 3.36
286 287 2.930682 GAGTAACTTCAACGGGCAGATC 59.069 50.000 0.00 0.00 0.00 2.75
287 288 2.567615 AGAGTAACTTCAACGGGCAGAT 59.432 45.455 0.00 0.00 0.00 2.90
288 289 1.968493 AGAGTAACTTCAACGGGCAGA 59.032 47.619 0.00 0.00 0.00 4.26
289 290 2.457366 AGAGTAACTTCAACGGGCAG 57.543 50.000 0.00 0.00 0.00 4.85
290 291 4.546829 ATTAGAGTAACTTCAACGGGCA 57.453 40.909 0.00 0.00 0.00 5.36
291 292 5.292834 GGTTATTAGAGTAACTTCAACGGGC 59.707 44.000 0.00 0.00 35.43 6.13
292 293 5.814188 GGGTTATTAGAGTAACTTCAACGGG 59.186 44.000 0.00 0.00 35.43 5.28
293 294 6.534079 CAGGGTTATTAGAGTAACTTCAACGG 59.466 42.308 0.00 0.00 35.43 4.44
294 295 7.318141 TCAGGGTTATTAGAGTAACTTCAACG 58.682 38.462 0.00 0.00 35.43 4.10
295 296 9.498176 TTTCAGGGTTATTAGAGTAACTTCAAC 57.502 33.333 0.00 0.00 35.43 3.18
303 304 9.895138 GGTGTATTTTTCAGGGTTATTAGAGTA 57.105 33.333 0.00 0.00 0.00 2.59
304 305 7.832685 GGGTGTATTTTTCAGGGTTATTAGAGT 59.167 37.037 0.00 0.00 0.00 3.24
305 306 7.012044 CGGGTGTATTTTTCAGGGTTATTAGAG 59.988 40.741 0.00 0.00 0.00 2.43
306 307 6.824704 CGGGTGTATTTTTCAGGGTTATTAGA 59.175 38.462 0.00 0.00 0.00 2.10
307 308 6.459161 GCGGGTGTATTTTTCAGGGTTATTAG 60.459 42.308 0.00 0.00 0.00 1.73
308 309 5.357596 GCGGGTGTATTTTTCAGGGTTATTA 59.642 40.000 0.00 0.00 0.00 0.98
309 310 4.158949 GCGGGTGTATTTTTCAGGGTTATT 59.841 41.667 0.00 0.00 0.00 1.40
310 311 3.697542 GCGGGTGTATTTTTCAGGGTTAT 59.302 43.478 0.00 0.00 0.00 1.89
311 312 3.083293 GCGGGTGTATTTTTCAGGGTTA 58.917 45.455 0.00 0.00 0.00 2.85
312 313 1.890489 GCGGGTGTATTTTTCAGGGTT 59.110 47.619 0.00 0.00 0.00 4.11
313 314 1.202952 TGCGGGTGTATTTTTCAGGGT 60.203 47.619 0.00 0.00 0.00 4.34
314 315 1.540267 TGCGGGTGTATTTTTCAGGG 58.460 50.000 0.00 0.00 0.00 4.45
315 316 3.651803 TTTGCGGGTGTATTTTTCAGG 57.348 42.857 0.00 0.00 0.00 3.86
344 345 5.711976 ACATGAACCTCTGTATTTTTCAGGG 59.288 40.000 0.00 0.00 33.41 4.45
345 346 6.430925 TCACATGAACCTCTGTATTTTTCAGG 59.569 38.462 0.00 0.00 34.86 3.86
346 347 7.439157 TCACATGAACCTCTGTATTTTTCAG 57.561 36.000 0.00 0.00 30.07 3.02
347 348 7.522073 GCTTCACATGAACCTCTGTATTTTTCA 60.522 37.037 0.00 0.00 0.00 2.69
348 349 6.803807 GCTTCACATGAACCTCTGTATTTTTC 59.196 38.462 0.00 0.00 0.00 2.29
349 350 6.265196 TGCTTCACATGAACCTCTGTATTTTT 59.735 34.615 0.00 0.00 0.00 1.94
350 351 5.769662 TGCTTCACATGAACCTCTGTATTTT 59.230 36.000 0.00 0.00 0.00 1.82
351 352 5.316167 TGCTTCACATGAACCTCTGTATTT 58.684 37.500 0.00 0.00 0.00 1.40
352 353 4.910195 TGCTTCACATGAACCTCTGTATT 58.090 39.130 0.00 0.00 0.00 1.89
353 354 4.558226 TGCTTCACATGAACCTCTGTAT 57.442 40.909 0.00 0.00 0.00 2.29
354 355 4.558226 ATGCTTCACATGAACCTCTGTA 57.442 40.909 0.00 0.00 37.70 2.74
355 356 2.936919 TGCTTCACATGAACCTCTGT 57.063 45.000 0.00 0.00 0.00 3.41
356 357 3.308053 CGTATGCTTCACATGAACCTCTG 59.692 47.826 0.00 0.00 40.06 3.35
357 358 3.195610 TCGTATGCTTCACATGAACCTCT 59.804 43.478 0.00 0.00 40.06 3.69
358 359 3.521560 TCGTATGCTTCACATGAACCTC 58.478 45.455 0.00 0.00 40.06 3.85
359 360 3.610040 TCGTATGCTTCACATGAACCT 57.390 42.857 0.00 0.00 40.06 3.50
360 361 4.122776 AGATCGTATGCTTCACATGAACC 58.877 43.478 0.00 0.00 40.06 3.62
361 362 5.725110 AAGATCGTATGCTTCACATGAAC 57.275 39.130 0.00 0.00 40.06 3.18
362 363 6.741992 AAAAGATCGTATGCTTCACATGAA 57.258 33.333 0.00 0.00 40.06 2.57
363 364 6.741992 AAAAAGATCGTATGCTTCACATGA 57.258 33.333 0.00 0.00 40.06 3.07
385 386 7.517614 TGTATGCTTCACATTCCACTAAAAA 57.482 32.000 0.00 0.00 40.38 1.94
386 387 7.517614 TTGTATGCTTCACATTCCACTAAAA 57.482 32.000 0.00 0.00 40.38 1.52
387 388 7.611467 AGATTGTATGCTTCACATTCCACTAAA 59.389 33.333 0.00 0.00 40.38 1.85
388 389 7.066163 CAGATTGTATGCTTCACATTCCACTAA 59.934 37.037 0.00 0.00 40.38 2.24
389 390 6.539826 CAGATTGTATGCTTCACATTCCACTA 59.460 38.462 0.00 0.00 40.38 2.74
390 391 5.356190 CAGATTGTATGCTTCACATTCCACT 59.644 40.000 0.00 0.00 40.38 4.00
391 392 5.449588 CCAGATTGTATGCTTCACATTCCAC 60.450 44.000 0.00 0.00 40.38 4.02
392 393 4.641541 CCAGATTGTATGCTTCACATTCCA 59.358 41.667 0.00 0.00 40.38 3.53
393 394 4.037208 CCCAGATTGTATGCTTCACATTCC 59.963 45.833 0.00 0.00 40.38 3.01
394 395 4.883585 TCCCAGATTGTATGCTTCACATTC 59.116 41.667 0.00 0.00 40.38 2.67
395 396 4.641989 GTCCCAGATTGTATGCTTCACATT 59.358 41.667 0.00 0.00 40.38 2.71
396 397 4.202441 GTCCCAGATTGTATGCTTCACAT 58.798 43.478 0.00 0.00 43.18 3.21
397 398 3.008923 TGTCCCAGATTGTATGCTTCACA 59.991 43.478 0.00 0.00 0.00 3.58
398 399 3.375299 GTGTCCCAGATTGTATGCTTCAC 59.625 47.826 0.00 0.00 0.00 3.18
399 400 3.008923 TGTGTCCCAGATTGTATGCTTCA 59.991 43.478 0.00 0.00 0.00 3.02
409 410 0.251341 GGGCAGTTGTGTCCCAGATT 60.251 55.000 0.00 0.00 43.45 2.40
444 445 0.822121 GCCAAAACAACTCCGACCCT 60.822 55.000 0.00 0.00 0.00 4.34
483 484 3.810896 GAACCGGCCGTTCCATGC 61.811 66.667 26.12 1.86 44.46 4.06
730 732 2.440501 GTTTGCGATAACAGAATGGCG 58.559 47.619 0.00 0.00 43.62 5.69
931 937 0.730834 CTTCACCTCACGAGCAGACG 60.731 60.000 0.00 0.00 39.31 4.18
946 952 0.496382 TTCTCCTCCCCTTCCCTTCA 59.504 55.000 0.00 0.00 0.00 3.02
947 953 1.208706 CTTCTCCTCCCCTTCCCTTC 58.791 60.000 0.00 0.00 0.00 3.46
953 959 2.158310 CCAAAAACCTTCTCCTCCCCTT 60.158 50.000 0.00 0.00 0.00 3.95
1370 1384 3.973267 GAGTCGCCGGAGTCACTGC 62.973 68.421 5.05 0.00 41.43 4.40
1559 1573 1.098869 GAGCGACAGAGAGGTGATCA 58.901 55.000 0.00 0.00 0.00 2.92
1581 1595 3.596799 TGGTCCAGTCCGGGGAGA 61.597 66.667 0.00 0.00 34.44 3.71
1906 1923 3.195396 ACGGCCGATGGTTTTTACTACTA 59.805 43.478 35.90 0.00 0.00 1.82
2043 2061 2.557920 ACAGACTCCAAAGCAGGAAG 57.442 50.000 0.00 0.00 37.20 3.46
2114 2132 6.648879 TCCGTTCTCATTTCTTTCCATTTT 57.351 33.333 0.00 0.00 0.00 1.82
2128 2146 8.519526 AGCAATAATTAACAATTTCCGTTCTCA 58.480 29.630 0.00 0.00 32.38 3.27
2155 2175 2.363925 GGGCTCGGTAGGAGTGGT 60.364 66.667 0.00 0.00 45.03 4.16
2157 2177 2.754658 ACGGGCTCGGTAGGAGTG 60.755 66.667 12.42 0.00 45.03 3.51
2163 2183 1.140161 CGAAATGACGGGCTCGGTA 59.860 57.895 12.42 0.00 41.39 4.02
2164 2184 2.125673 CGAAATGACGGGCTCGGT 60.126 61.111 12.42 0.00 41.39 4.69
2172 2192 1.086696 ATTCCTGTGCCGAAATGACG 58.913 50.000 0.00 0.00 0.00 4.35
2199 2219 1.207488 TTCCCCATCACCAGTCCCAG 61.207 60.000 0.00 0.00 0.00 4.45
2206 2226 1.274712 GCCAAATTTCCCCATCACCA 58.725 50.000 0.00 0.00 0.00 4.17
2239 2259 1.769098 CGTAGATCGACCGCGGAGAA 61.769 60.000 35.90 16.62 42.86 2.87
2293 2313 1.377202 CCGGTGCTACATGCCAAGT 60.377 57.895 0.00 0.00 42.00 3.16
2294 2314 2.764314 GCCGGTGCTACATGCCAAG 61.764 63.158 1.90 0.00 42.00 3.61
2295 2315 2.749839 GCCGGTGCTACATGCCAA 60.750 61.111 1.90 0.00 42.00 4.52
2360 2387 3.388350 CGGGAAAGGGCTTACTAGATCTT 59.612 47.826 0.00 0.00 0.00 2.40
2362 2389 2.699321 ACGGGAAAGGGCTTACTAGATC 59.301 50.000 0.00 0.00 0.00 2.75
2378 2405 4.012374 CCAAGAACTAGTACTACACGGGA 58.988 47.826 0.00 0.00 0.00 5.14
2380 2407 4.436584 CGACCAAGAACTAGTACTACACGG 60.437 50.000 0.00 0.00 0.00 4.94
2381 2408 4.389992 TCGACCAAGAACTAGTACTACACG 59.610 45.833 0.00 0.00 0.00 4.49
2387 2414 4.799428 GCTTGATCGACCAAGAACTAGTAC 59.201 45.833 24.10 0.00 44.66 2.73
2393 2423 1.808411 TGGCTTGATCGACCAAGAAC 58.192 50.000 24.10 14.83 44.66 3.01
2394 2424 2.552315 GTTTGGCTTGATCGACCAAGAA 59.448 45.455 24.10 6.63 44.66 2.52
2398 2428 1.811965 CATGTTTGGCTTGATCGACCA 59.188 47.619 0.00 0.00 0.00 4.02
2399 2429 1.133025 CCATGTTTGGCTTGATCGACC 59.867 52.381 0.00 0.00 35.85 4.79
2400 2430 2.549633 CCATGTTTGGCTTGATCGAC 57.450 50.000 0.00 0.00 35.85 4.20
2424 2454 6.399639 TCCGTAGTACATGCATTCTGATTA 57.600 37.500 0.00 0.00 0.00 1.75
2428 2458 3.242944 CGTTCCGTAGTACATGCATTCTG 59.757 47.826 0.00 0.00 0.00 3.02
2581 2612 2.274920 GTAACTACGAGCCAGTCCAC 57.725 55.000 0.00 0.00 0.00 4.02
2594 2625 1.089920 GTCCTCCAGTCGCGTAACTA 58.910 55.000 5.77 0.00 0.00 2.24
2608 2639 3.093057 ACACACTAGTCCTGATGTCCTC 58.907 50.000 0.00 0.00 0.00 3.71
2615 2646 0.826256 ACGCCACACACTAGTCCTGA 60.826 55.000 0.00 0.00 0.00 3.86
2680 2711 0.387239 GCCAACTGTGAAATGTCGCC 60.387 55.000 0.00 0.00 32.98 5.54
2721 2753 3.014623 GTGAACAGCCAGGGGTATTTAC 58.985 50.000 0.00 0.00 0.00 2.01
2728 2760 2.521958 CTACGGTGAACAGCCAGGGG 62.522 65.000 0.00 0.00 0.00 4.79
2759 2791 2.312722 TGCTTTGCTGTTTTGCACAT 57.687 40.000 0.00 0.00 43.20 3.21
2803 2835 3.506844 GCGTGTATTAAAACTTGGGGGAA 59.493 43.478 0.00 0.00 0.00 3.97
2808 2840 3.754323 TCCCTGCGTGTATTAAAACTTGG 59.246 43.478 0.00 0.00 0.00 3.61
2812 2844 3.692593 ACCATCCCTGCGTGTATTAAAAC 59.307 43.478 0.00 0.00 0.00 2.43
2821 2853 2.981560 GCACAACCATCCCTGCGTG 61.982 63.158 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.