Multiple sequence alignment - TraesCS1D01G177700

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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 TraesCS1D01G177700 chr1D 100.000 2318 0 0 1 2318 252911473 252913790 0.000000e+00 4281
1 TraesCS1D01G177700 chr1D 86.486 407 50 5 1 402 416449913 416449507 2.110000e-120 442
2 TraesCS1D01G177700 chr1D 86.454 251 30 4 1 248 140108006 140107757 2.930000e-69 272
3 TraesCS1D01G177700 chr1B 94.438 1798 72 10 529 2318 359910631 359908854 0.000000e+00 2741
4 TraesCS1D01G177700 chr1B 83.582 402 46 10 1 398 680785889 680785504 2.190000e-95 359
5 TraesCS1D01G177700 chr1B 80.211 475 59 18 1 440 583078296 583078770 7.990000e-85 324
6 TraesCS1D01G177700 chr1A 89.270 699 48 15 961 1655 324490301 324490976 0.000000e+00 850
7 TraesCS1D01G177700 chr1A 90.873 504 31 7 434 923 324489794 324490296 0.000000e+00 662
8 TraesCS1D01G177700 chr1A 79.832 357 39 14 1966 2318 324491381 324491708 1.790000e-56 230
9 TraesCS1D01G177700 chr5B 82.906 468 43 18 1 433 620310646 620311111 1.000000e-103 387
10 TraesCS1D01G177700 chr5B 86.475 244 29 4 120 359 376505909 376505666 4.910000e-67 265
11 TraesCS1D01G177700 chr3B 80.255 471 48 10 1 436 113912850 113913310 1.730000e-81 313
12 TraesCS1D01G177700 chr4A 79.873 472 56 14 1 434 729507322 729507792 2.240000e-80 309
13 TraesCS1D01G177700 chr7D 83.750 320 46 5 121 434 186333728 186334047 4.840000e-77 298
14 TraesCS1D01G177700 chr7D 91.146 192 15 2 1 191 251354639 251354829 2.280000e-65 259
15 TraesCS1D01G177700 chr2B 86.071 280 36 3 161 437 759264555 759264834 4.840000e-77 298
16 TraesCS1D01G177700 chrUn 79.075 454 75 14 1 436 18792114 18792565 6.260000e-76 294
17 TraesCS1D01G177700 chrUn 87.029 239 28 3 1 236 53429534 53429296 1.370000e-67 267
18 TraesCS1D01G177700 chr2A 85.609 271 36 3 1 268 192063952 192063682 4.880000e-72 281
19 TraesCS1D01G177700 chr6D 95.238 168 8 0 1 168 8159011 8158844 1.370000e-67 267
20 TraesCS1D01G177700 chr6B 84.058 276 35 8 1 273 41847481 41847750 8.220000e-65 257
21 TraesCS1D01G177700 chr6B 84.255 235 29 8 209 436 472714202 472714435 3.000000e-54 222


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 TraesCS1D01G177700 chr1D 252911473 252913790 2317 False 4281.000000 4281 100.000000 1 2318 1 chr1D.!!$F1 2317
1 TraesCS1D01G177700 chr1B 359908854 359910631 1777 True 2741.000000 2741 94.438000 529 2318 1 chr1B.!!$R1 1789
2 TraesCS1D01G177700 chr1A 324489794 324491708 1914 False 580.666667 850 86.658333 434 2318 3 chr1A.!!$F1 1884

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
108 109 0.039888 TGACTCGACGCGTGATGAAA 60.04 50.0 20.7 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2203 0.042188 CGTTTTCTGTGTGGCGTCAG 60.042 55.0 0.0 0.0 0.0 3.51 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
19 20 1.911057 ATATGCGTCAGGAGATCCGA 58.089 50.000 0.00 0.00 42.08 4.55
20 21 1.239347 TATGCGTCAGGAGATCCGAG 58.761 55.000 0.00 0.00 42.08 4.63
21 22 0.466372 ATGCGTCAGGAGATCCGAGA 60.466 55.000 0.00 0.00 42.08 4.04
22 23 1.357334 GCGTCAGGAGATCCGAGAC 59.643 63.158 14.02 14.02 42.08 3.36
23 24 2.026522 CGTCAGGAGATCCGAGACC 58.973 63.158 16.67 0.00 40.44 3.85
24 25 1.448922 CGTCAGGAGATCCGAGACCC 61.449 65.000 16.67 0.00 40.44 4.46
25 26 1.152943 TCAGGAGATCCGAGACCCG 60.153 63.158 0.00 0.00 42.08 5.28
26 27 2.519780 AGGAGATCCGAGACCCGC 60.520 66.667 0.00 0.00 42.08 6.13
27 28 2.833582 GGAGATCCGAGACCCGCA 60.834 66.667 0.00 0.00 36.84 5.69
28 29 2.725008 GAGATCCGAGACCCGCAG 59.275 66.667 0.00 0.00 36.84 5.18
41 42 4.539152 CGCAGGTGCATCAACAAC 57.461 55.556 0.00 0.00 42.21 3.32
42 43 1.951510 CGCAGGTGCATCAACAACT 59.048 52.632 0.00 0.00 38.42 3.16
45 46 3.114527 AGGTGCATCAACAACTGCA 57.885 47.368 0.00 0.00 45.60 4.41
48 49 2.416901 TGCATCAACAACTGCAGCA 58.583 47.368 15.27 0.00 43.11 4.41
49 50 0.312729 TGCATCAACAACTGCAGCAG 59.687 50.000 21.54 21.54 43.11 4.24
50 51 0.388134 GCATCAACAACTGCAGCAGG 60.388 55.000 26.38 12.00 38.28 4.85
51 52 1.241165 CATCAACAACTGCAGCAGGA 58.759 50.000 26.38 13.53 35.51 3.86
52 53 1.816835 CATCAACAACTGCAGCAGGAT 59.183 47.619 26.38 15.17 35.51 3.24
53 54 1.527034 TCAACAACTGCAGCAGGATC 58.473 50.000 26.38 0.00 35.51 3.36
54 55 1.072806 TCAACAACTGCAGCAGGATCT 59.927 47.619 26.38 2.01 35.51 2.75
55 56 1.199327 CAACAACTGCAGCAGGATCTG 59.801 52.381 26.38 18.20 35.51 2.90
56 57 0.322277 ACAACTGCAGCAGGATCTGG 60.322 55.000 26.38 5.47 35.51 3.86
57 58 0.322277 CAACTGCAGCAGGATCTGGT 60.322 55.000 26.38 0.98 43.33 4.00
62 63 3.318191 AGCAGGATCTGGTGGAGC 58.682 61.111 0.00 0.00 40.87 4.70
63 64 1.614525 AGCAGGATCTGGTGGAGCA 60.615 57.895 0.00 0.00 40.87 4.26
64 65 1.451028 GCAGGATCTGGTGGAGCAC 60.451 63.158 0.00 0.00 30.93 4.40
82 83 1.453669 CCTATGGAGGCTCAAGGGC 59.546 63.158 17.69 0.00 35.54 5.19
83 84 1.348008 CCTATGGAGGCTCAAGGGCA 61.348 60.000 17.69 4.77 43.56 5.36
84 85 0.548031 CTATGGAGGCTCAAGGGCAA 59.452 55.000 17.69 0.00 43.56 4.52
85 86 0.255890 TATGGAGGCTCAAGGGCAAC 59.744 55.000 17.69 0.00 43.56 4.17
86 87 2.747855 GGAGGCTCAAGGGCAACG 60.748 66.667 17.69 0.00 43.56 4.10
87 88 3.435186 GAGGCTCAAGGGCAACGC 61.435 66.667 10.25 0.00 43.56 4.84
97 98 3.112709 GGCAACGCCTGACTCGAC 61.113 66.667 0.00 0.00 46.69 4.20
98 99 3.470567 GCAACGCCTGACTCGACG 61.471 66.667 0.00 0.00 0.00 5.12
99 100 3.470567 CAACGCCTGACTCGACGC 61.471 66.667 0.00 0.00 0.00 5.19
103 104 4.400109 GCCTGACTCGACGCGTGA 62.400 66.667 20.70 13.96 0.00 4.35
104 105 2.485582 CCTGACTCGACGCGTGAT 59.514 61.111 20.70 0.00 0.00 3.06
105 106 1.869574 CCTGACTCGACGCGTGATG 60.870 63.158 20.70 8.60 0.00 3.07
106 107 1.134694 CTGACTCGACGCGTGATGA 59.865 57.895 20.70 11.14 0.00 2.92
107 108 0.454452 CTGACTCGACGCGTGATGAA 60.454 55.000 20.70 0.00 0.00 2.57
108 109 0.039888 TGACTCGACGCGTGATGAAA 60.040 50.000 20.70 0.00 0.00 2.69
109 110 1.269166 GACTCGACGCGTGATGAAAT 58.731 50.000 20.70 2.58 0.00 2.17
110 111 2.159490 TGACTCGACGCGTGATGAAATA 60.159 45.455 20.70 0.00 0.00 1.40
111 112 3.043586 GACTCGACGCGTGATGAAATAT 58.956 45.455 20.70 0.00 0.00 1.28
112 113 2.789339 ACTCGACGCGTGATGAAATATG 59.211 45.455 20.70 1.96 0.00 1.78
113 114 3.042887 CTCGACGCGTGATGAAATATGA 58.957 45.455 20.70 0.00 0.00 2.15
114 115 3.042887 TCGACGCGTGATGAAATATGAG 58.957 45.455 20.70 0.00 0.00 2.90
115 116 2.789339 CGACGCGTGATGAAATATGAGT 59.211 45.455 20.70 0.00 0.00 3.41
116 117 3.242944 CGACGCGTGATGAAATATGAGTT 59.757 43.478 20.70 0.00 0.00 3.01
117 118 4.259810 CGACGCGTGATGAAATATGAGTTT 60.260 41.667 20.70 0.00 0.00 2.66
118 119 5.545658 ACGCGTGATGAAATATGAGTTTT 57.454 34.783 12.93 0.00 0.00 2.43
119 120 5.938322 ACGCGTGATGAAATATGAGTTTTT 58.062 33.333 12.93 0.00 0.00 1.94
120 121 7.067532 ACGCGTGATGAAATATGAGTTTTTA 57.932 32.000 12.93 0.00 0.00 1.52
121 122 7.693952 ACGCGTGATGAAATATGAGTTTTTAT 58.306 30.769 12.93 0.00 0.00 1.40
122 123 8.181573 ACGCGTGATGAAATATGAGTTTTTATT 58.818 29.630 12.93 0.00 0.00 1.40
123 124 9.009327 CGCGTGATGAAATATGAGTTTTTATTT 57.991 29.630 0.00 0.00 32.21 1.40
196 197 7.406799 AATAACTTCTTTTGAATTTGTGCCG 57.593 32.000 0.00 0.00 37.85 5.69
197 198 4.647424 ACTTCTTTTGAATTTGTGCCGA 57.353 36.364 0.00 0.00 37.85 5.54
198 199 5.004922 ACTTCTTTTGAATTTGTGCCGAA 57.995 34.783 0.00 0.00 37.85 4.30
199 200 5.415221 ACTTCTTTTGAATTTGTGCCGAAA 58.585 33.333 0.00 0.00 37.85 3.46
200 201 5.290885 ACTTCTTTTGAATTTGTGCCGAAAC 59.709 36.000 0.00 0.00 37.85 2.78
201 202 4.748892 TCTTTTGAATTTGTGCCGAAACA 58.251 34.783 0.00 0.00 0.00 2.83
202 203 4.564769 TCTTTTGAATTTGTGCCGAAACAC 59.435 37.500 0.00 0.00 41.10 3.32
203 204 2.112475 TGAATTTGTGCCGAAACACG 57.888 45.000 0.00 0.00 43.74 4.49
204 205 0.775861 GAATTTGTGCCGAAACACGC 59.224 50.000 0.00 0.00 43.74 5.34
205 206 0.101399 AATTTGTGCCGAAACACGCA 59.899 45.000 0.00 0.00 43.74 5.24
206 207 0.101399 ATTTGTGCCGAAACACGCAA 59.899 45.000 0.00 0.00 43.74 4.85
207 208 0.109272 TTTGTGCCGAAACACGCAAA 60.109 45.000 0.00 0.00 43.74 3.68
208 209 0.109272 TTGTGCCGAAACACGCAAAA 60.109 45.000 0.00 0.00 43.74 2.44
209 210 0.101399 TGTGCCGAAACACGCAAAAT 59.899 45.000 0.00 0.00 43.74 1.82
210 211 1.333931 TGTGCCGAAACACGCAAAATA 59.666 42.857 0.00 0.00 43.74 1.40
211 212 2.030717 TGTGCCGAAACACGCAAAATAT 60.031 40.909 0.00 0.00 43.74 1.28
212 213 2.341168 GTGCCGAAACACGCAAAATATG 59.659 45.455 0.00 0.00 41.07 1.78
213 214 1.917303 GCCGAAACACGCAAAATATGG 59.083 47.619 0.00 0.00 41.07 2.74
214 215 2.525055 CCGAAACACGCAAAATATGGG 58.475 47.619 0.00 0.00 46.83 4.00
215 216 1.917303 CGAAACACGCAAAATATGGGC 59.083 47.619 0.00 0.00 45.43 5.36
216 217 2.267426 GAAACACGCAAAATATGGGCC 58.733 47.619 0.00 0.00 45.43 5.80
217 218 0.172352 AACACGCAAAATATGGGCCG 59.828 50.000 0.00 0.00 45.43 6.13
218 219 0.678366 ACACGCAAAATATGGGCCGA 60.678 50.000 0.00 0.00 45.43 5.54
219 220 0.453793 CACGCAAAATATGGGCCGAA 59.546 50.000 0.00 0.00 45.43 4.30
220 221 1.135257 CACGCAAAATATGGGCCGAAA 60.135 47.619 0.00 0.00 45.43 3.46
221 222 1.754226 ACGCAAAATATGGGCCGAAAT 59.246 42.857 0.00 0.00 45.43 2.17
222 223 2.167487 ACGCAAAATATGGGCCGAAATT 59.833 40.909 0.00 0.00 45.43 1.82
223 224 2.539274 CGCAAAATATGGGCCGAAATTG 59.461 45.455 0.00 1.74 34.98 2.32
224 225 2.871633 GCAAAATATGGGCCGAAATTGG 59.128 45.455 0.00 0.00 0.00 3.16
225 226 3.681313 GCAAAATATGGGCCGAAATTGGT 60.681 43.478 0.00 0.00 0.00 3.67
226 227 4.119136 CAAAATATGGGCCGAAATTGGTC 58.881 43.478 0.00 0.00 0.00 4.02
227 228 2.746279 ATATGGGCCGAAATTGGTCA 57.254 45.000 0.00 0.00 34.42 4.02
228 229 2.516227 TATGGGCCGAAATTGGTCAA 57.484 45.000 0.00 0.00 34.42 3.18
229 230 1.864669 ATGGGCCGAAATTGGTCAAT 58.135 45.000 0.00 0.00 34.42 2.57
230 231 1.638529 TGGGCCGAAATTGGTCAATT 58.361 45.000 0.00 3.34 42.35 2.32
238 239 3.383620 AAATTGGTCAATTTGCGCTGA 57.616 38.095 17.63 0.00 45.99 4.26
239 240 3.598019 AATTGGTCAATTTGCGCTGAT 57.402 38.095 9.73 0.00 37.74 2.90
240 241 4.717233 AATTGGTCAATTTGCGCTGATA 57.283 36.364 9.73 0.00 37.74 2.15
241 242 3.763097 TTGGTCAATTTGCGCTGATAG 57.237 42.857 9.73 0.00 0.00 2.08
242 243 2.710377 TGGTCAATTTGCGCTGATAGT 58.290 42.857 9.73 0.00 0.00 2.12
243 244 3.867857 TGGTCAATTTGCGCTGATAGTA 58.132 40.909 9.73 0.00 0.00 1.82
244 245 3.871006 TGGTCAATTTGCGCTGATAGTAG 59.129 43.478 9.73 0.00 0.00 2.57
245 246 3.248602 GGTCAATTTGCGCTGATAGTAGG 59.751 47.826 9.73 0.00 0.00 3.18
246 247 2.872245 TCAATTTGCGCTGATAGTAGGC 59.128 45.455 9.73 0.00 0.00 3.93
247 248 1.884235 ATTTGCGCTGATAGTAGGCC 58.116 50.000 9.73 0.00 0.00 5.19
248 249 0.539518 TTTGCGCTGATAGTAGGCCA 59.460 50.000 9.73 0.00 0.00 5.36
249 250 0.539518 TTGCGCTGATAGTAGGCCAA 59.460 50.000 9.73 0.00 0.00 4.52
250 251 0.758734 TGCGCTGATAGTAGGCCAAT 59.241 50.000 9.73 0.00 0.00 3.16
251 252 1.140852 TGCGCTGATAGTAGGCCAATT 59.859 47.619 9.73 0.00 0.00 2.32
252 253 2.222027 GCGCTGATAGTAGGCCAATTT 58.778 47.619 5.01 0.00 0.00 1.82
253 254 2.031682 GCGCTGATAGTAGGCCAATTTG 60.032 50.000 5.01 0.00 0.00 2.32
254 255 2.031682 CGCTGATAGTAGGCCAATTTGC 60.032 50.000 5.01 0.00 0.00 3.68
255 256 2.031682 GCTGATAGTAGGCCAATTTGCG 60.032 50.000 5.01 0.00 0.00 4.85
256 257 1.946768 TGATAGTAGGCCAATTTGCGC 59.053 47.619 5.01 0.00 0.00 6.09
257 258 1.266989 GATAGTAGGCCAATTTGCGCC 59.733 52.381 5.01 16.61 46.09 6.53
261 262 2.048690 GGCCAATTTGCGCCGAAA 60.049 55.556 4.18 0.00 34.94 3.46
262 263 2.094066 GGCCAATTTGCGCCGAAAG 61.094 57.895 4.18 0.00 34.94 2.62
263 264 1.372872 GCCAATTTGCGCCGAAAGT 60.373 52.632 4.18 0.00 0.00 2.66
264 265 1.616872 GCCAATTTGCGCCGAAAGTG 61.617 55.000 4.18 9.37 32.09 3.16
265 266 1.008361 CCAATTTGCGCCGAAAGTGG 61.008 55.000 20.57 20.57 42.73 4.00
266 267 1.008361 CAATTTGCGCCGAAAGTGGG 61.008 55.000 4.18 0.00 29.36 4.61
275 276 1.318576 CCGAAAGTGGGCTGAAAAGT 58.681 50.000 0.00 0.00 0.00 2.66
276 277 1.001378 CCGAAAGTGGGCTGAAAAGTG 60.001 52.381 0.00 0.00 0.00 3.16
277 278 1.001378 CGAAAGTGGGCTGAAAAGTGG 60.001 52.381 0.00 0.00 0.00 4.00
278 279 1.341209 GAAAGTGGGCTGAAAAGTGGG 59.659 52.381 0.00 0.00 0.00 4.61
279 280 1.115326 AAGTGGGCTGAAAAGTGGGC 61.115 55.000 0.00 0.00 0.00 5.36
280 281 2.203625 TGGGCTGAAAAGTGGGCC 60.204 61.111 0.00 0.00 44.50 5.80
281 282 2.203625 GGGCTGAAAAGTGGGCCA 60.204 61.111 0.00 0.00 45.68 5.36
282 283 1.836604 GGGCTGAAAAGTGGGCCAA 60.837 57.895 8.40 0.00 45.68 4.52
283 284 1.194121 GGGCTGAAAAGTGGGCCAAT 61.194 55.000 8.40 3.05 45.68 3.16
284 285 0.686789 GGCTGAAAAGTGGGCCAATT 59.313 50.000 14.45 14.45 43.59 2.32
285 286 1.072173 GGCTGAAAAGTGGGCCAATTT 59.928 47.619 25.03 25.03 43.59 1.82
286 287 2.145536 GCTGAAAAGTGGGCCAATTTG 58.854 47.619 30.15 19.40 32.02 2.32
287 288 2.145536 CTGAAAAGTGGGCCAATTTGC 58.854 47.619 30.15 28.38 32.02 3.68
288 289 1.147473 GAAAAGTGGGCCAATTTGCG 58.853 50.000 30.15 0.00 32.02 4.85
289 290 0.884259 AAAAGTGGGCCAATTTGCGC 60.884 50.000 30.15 11.18 43.84 6.09
290 291 2.730066 AAAGTGGGCCAATTTGCGCC 62.730 55.000 29.12 16.24 42.99 6.53
294 295 2.434709 GGCCAATTTGCGCCAAGG 60.435 61.111 18.43 0.00 45.01 3.61
295 296 2.343387 GCCAATTTGCGCCAAGGT 59.657 55.556 4.18 0.00 0.00 3.50
296 297 1.301637 GCCAATTTGCGCCAAGGTT 60.302 52.632 4.18 0.00 0.00 3.50
297 298 1.567746 GCCAATTTGCGCCAAGGTTG 61.568 55.000 4.18 2.54 0.00 3.77
308 309 0.527565 CCAAGGTTGGCTGAAATCGG 59.472 55.000 0.00 0.00 42.21 4.18
315 316 3.880846 GCTGAAATCGGCGCCTGG 61.881 66.667 26.68 10.37 38.61 4.45
316 317 3.204827 CTGAAATCGGCGCCTGGG 61.205 66.667 26.68 9.50 0.00 4.45
317 318 4.794648 TGAAATCGGCGCCTGGGG 62.795 66.667 26.68 9.07 0.00 4.96
318 319 4.483243 GAAATCGGCGCCTGGGGA 62.483 66.667 26.68 15.03 0.00 4.81
319 320 4.796495 AAATCGGCGCCTGGGGAC 62.796 66.667 26.68 11.31 0.00 4.46
357 358 4.851179 GAACCCGATCGCCCCCAC 62.851 72.222 10.32 0.00 0.00 4.61
362 363 4.444838 CGATCGCCCCCACGTTGA 62.445 66.667 0.26 0.00 0.00 3.18
363 364 2.189521 GATCGCCCCCACGTTGAT 59.810 61.111 0.00 0.00 0.00 2.57
364 365 1.451387 GATCGCCCCCACGTTGATT 60.451 57.895 0.00 0.00 0.00 2.57
365 366 1.001393 ATCGCCCCCACGTTGATTT 60.001 52.632 0.00 0.00 0.00 2.17
366 367 0.610785 ATCGCCCCCACGTTGATTTT 60.611 50.000 0.00 0.00 0.00 1.82
367 368 0.824182 TCGCCCCCACGTTGATTTTT 60.824 50.000 0.00 0.00 0.00 1.94
368 369 0.388006 CGCCCCCACGTTGATTTTTC 60.388 55.000 0.00 0.00 0.00 2.29
369 370 0.388006 GCCCCCACGTTGATTTTTCG 60.388 55.000 0.00 0.00 0.00 3.46
370 371 0.242555 CCCCCACGTTGATTTTTCGG 59.757 55.000 0.00 0.00 0.00 4.30
371 372 0.388006 CCCCACGTTGATTTTTCGGC 60.388 55.000 0.00 0.00 0.00 5.54
372 373 0.388006 CCCACGTTGATTTTTCGGCC 60.388 55.000 0.00 0.00 0.00 6.13
373 374 0.727793 CCACGTTGATTTTTCGGCCG 60.728 55.000 22.12 22.12 0.00 6.13
374 375 0.727793 CACGTTGATTTTTCGGCCGG 60.728 55.000 27.83 7.29 0.00 6.13
375 376 1.799916 CGTTGATTTTTCGGCCGGC 60.800 57.895 27.83 21.18 0.00 6.13
376 377 1.799916 GTTGATTTTTCGGCCGGCG 60.800 57.895 27.83 16.23 0.00 6.46
377 378 3.618710 TTGATTTTTCGGCCGGCGC 62.619 57.895 27.83 12.82 0.00 6.53
397 398 4.910585 CCCGAGGCGGCGCTATTT 62.911 66.667 32.30 14.85 46.86 1.40
398 399 3.338676 CCGAGGCGGCGCTATTTC 61.339 66.667 32.30 21.04 41.17 2.17
399 400 2.584970 CGAGGCGGCGCTATTTCA 60.585 61.111 32.30 0.00 0.00 2.69
400 401 2.171079 CGAGGCGGCGCTATTTCAA 61.171 57.895 32.30 0.00 0.00 2.69
401 402 1.643832 GAGGCGGCGCTATTTCAAG 59.356 57.895 32.30 0.00 0.00 3.02
402 403 2.024729 GGCGGCGCTATTTCAAGC 59.975 61.111 32.30 7.60 39.21 4.01
403 404 2.024729 GCGGCGCTATTTCAAGCC 59.975 61.111 26.86 0.00 45.67 4.35
404 405 2.715624 CGGCGCTATTTCAAGCCC 59.284 61.111 7.64 0.00 46.36 5.19
405 406 2.834618 CGGCGCTATTTCAAGCCCC 61.835 63.158 7.64 0.00 46.36 5.80
406 407 1.453928 GGCGCTATTTCAAGCCCCT 60.454 57.895 7.64 0.00 43.54 4.79
407 408 1.728490 GGCGCTATTTCAAGCCCCTG 61.728 60.000 7.64 0.00 43.54 4.45
408 409 1.728490 GCGCTATTTCAAGCCCCTGG 61.728 60.000 0.00 0.00 39.43 4.45
409 410 1.103398 CGCTATTTCAAGCCCCTGGG 61.103 60.000 5.50 5.50 39.43 4.45
426 427 4.222847 GGGGGCGAACGGCTAGAG 62.223 72.222 18.90 0.00 42.94 2.43
427 428 3.145551 GGGGCGAACGGCTAGAGA 61.146 66.667 18.90 0.00 42.94 3.10
428 429 2.499827 GGGGCGAACGGCTAGAGAT 61.500 63.158 18.90 0.00 42.94 2.75
429 430 1.300233 GGGCGAACGGCTAGAGATG 60.300 63.158 18.90 0.00 42.94 2.90
430 431 1.951631 GGCGAACGGCTAGAGATGC 60.952 63.158 13.15 0.00 42.94 3.91
431 432 1.066587 GCGAACGGCTAGAGATGCT 59.933 57.895 0.00 0.00 39.11 3.79
432 433 0.937231 GCGAACGGCTAGAGATGCTC 60.937 60.000 0.00 0.00 39.11 4.26
512 513 8.533569 ACCCTTTTTATAAGTTGTATCATGGG 57.466 34.615 0.00 0.00 0.00 4.00
517 518 8.995027 TTTTATAAGTTGTATCATGGGAGCAT 57.005 30.769 0.00 0.00 0.00 3.79
518 519 8.995027 TTTATAAGTTGTATCATGGGAGCATT 57.005 30.769 0.00 0.00 0.00 3.56
524 525 3.814842 TGTATCATGGGAGCATTTAAGCG 59.185 43.478 0.00 0.00 40.15 4.68
535 536 4.708177 AGCATTTAAGCGATGGTATCACT 58.292 39.130 0.00 0.00 40.15 3.41
537 538 4.511454 GCATTTAAGCGATGGTATCACTCA 59.489 41.667 0.00 0.00 0.00 3.41
550 551 5.665360 TGGTATCACTCAATATTCACCCTCA 59.335 40.000 0.00 0.00 0.00 3.86
577 578 1.689233 TCCAATCTCCACCCTCCGG 60.689 63.158 0.00 0.00 0.00 5.14
650 651 3.057969 TGCTGGTGTTTGACTATCCAG 57.942 47.619 0.00 0.00 45.68 3.86
674 675 0.319900 CCACCACGTTCACCTCTCAG 60.320 60.000 0.00 0.00 0.00 3.35
903 919 4.279808 GATCCAGATCCAACGAACTCGTG 61.280 52.174 5.38 0.66 40.68 4.35
930 946 4.025061 ACGTCTGTCTATAGTGTACGCATC 60.025 45.833 9.48 0.00 32.42 3.91
981 998 0.817654 CGCATACTCTCCCACTCACA 59.182 55.000 0.00 0.00 0.00 3.58
1332 1349 1.986378 CACTGACGAACCGAATCTCAC 59.014 52.381 0.00 0.00 0.00 3.51
1336 1353 2.194271 GACGAACCGAATCTCACCATC 58.806 52.381 0.00 0.00 0.00 3.51
1397 1414 0.108472 GGCTGTACCTGTACGGGTTC 60.108 60.000 30.93 25.32 41.52 3.62
1448 1467 4.602259 CTCGTGCGTGGTGGTGGT 62.602 66.667 0.00 0.00 0.00 4.16
1451 1470 4.555709 GTGCGTGGTGGTGGTGGA 62.556 66.667 0.00 0.00 0.00 4.02
1452 1471 4.248842 TGCGTGGTGGTGGTGGAG 62.249 66.667 0.00 0.00 0.00 3.86
1502 1523 8.783833 TTTTCTTCTTCTTGATGAGATGTAGG 57.216 34.615 0.00 0.00 33.49 3.18
1503 1524 7.724490 TTCTTCTTCTTGATGAGATGTAGGA 57.276 36.000 0.00 0.00 33.49 2.94
1504 1525 7.345422 TCTTCTTCTTGATGAGATGTAGGAG 57.655 40.000 0.00 0.00 33.49 3.69
1505 1526 6.894654 TCTTCTTCTTGATGAGATGTAGGAGT 59.105 38.462 0.00 0.00 33.49 3.85
1524 1545 8.965172 GTAGGAGTATATAATGTCGTTTGTGTG 58.035 37.037 0.00 0.00 0.00 3.82
1536 1557 5.153513 GTCGTTTGTGTGGTACTACGAATA 58.846 41.667 4.80 0.00 43.34 1.75
1541 1562 7.462331 CGTTTGTGTGGTACTACGAATATCTTG 60.462 40.741 4.80 0.00 39.03 3.02
1552 1573 3.005897 ACGAATATCTTGGGAGGACATCG 59.994 47.826 0.00 0.00 0.00 3.84
1617 1638 5.178067 TGCATTCATCTAATATCACACGCAG 59.822 40.000 0.00 0.00 0.00 5.18
1676 1697 0.383590 ACGAGATGATCACGAGCCAG 59.616 55.000 18.55 0.00 34.62 4.85
1790 1811 0.175760 TCACCATCCTTACGAGCAGC 59.824 55.000 0.00 0.00 0.00 5.25
1853 1874 2.282180 TGGTTTCTCCTTGCCGCC 60.282 61.111 0.00 0.00 37.07 6.13
1899 1926 2.480610 CCACGTTGCCAAGCTGTGT 61.481 57.895 0.00 0.00 0.00 3.72
1941 1968 3.003480 AGCAAGGAATTCTACTCGCAAC 58.997 45.455 5.23 0.00 0.00 4.17
1954 1981 4.536687 GCAACGCGTATGCCCTGC 62.537 66.667 25.74 21.03 37.83 4.85
1968 2157 0.895530 CCCTGCTACGGAGTTCTTCA 59.104 55.000 0.00 0.00 37.78 3.02
1979 2168 5.772521 ACGGAGTTCTTCAAATCAATTTGG 58.227 37.500 13.88 1.67 42.71 3.28
1985 2174 8.059798 AGTTCTTCAAATCAATTTGGATCGAT 57.940 30.769 13.88 0.00 45.39 3.59
2000 2189 4.021981 TGGATCGATTAGATGGCACTACTG 60.022 45.833 0.00 0.00 40.26 2.74
2014 2203 2.978489 CACTACTGGAAAACGAGACGTC 59.022 50.000 7.70 7.70 39.99 4.34
2041 2230 1.083657 CACAGAAAACGACCGCACG 60.084 57.895 0.00 0.00 39.31 5.34
2087 2277 2.951229 AGGAAACTTCGGACCAACAT 57.049 45.000 0.00 0.00 37.44 2.71
2096 2289 0.930310 CGGACCAACATCATACAGCG 59.070 55.000 0.00 0.00 0.00 5.18
2201 2394 8.884124 AATGAAAAAGAGAGGTATGAAATGGA 57.116 30.769 0.00 0.00 0.00 3.41
2215 2408 4.885413 TGAAATGGAGCATGGAACTTTTG 58.115 39.130 0.00 0.00 0.00 2.44
2217 2410 4.525912 AATGGAGCATGGAACTTTTGAC 57.474 40.909 0.00 0.00 0.00 3.18
2271 2464 1.638070 TGGAGGTGTGAAATGGCCATA 59.362 47.619 21.15 0.00 0.00 2.74
2275 2468 2.578021 AGGTGTGAAATGGCCATACTCT 59.422 45.455 21.15 12.25 0.00 3.24
2284 2477 1.207089 TGGCCATACTCTCCAGAAACG 59.793 52.381 0.00 0.00 0.00 3.60
2287 2480 3.596214 GCCATACTCTCCAGAAACGAAA 58.404 45.455 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.815613 CTCGGATCTCCTGACGCATAT 59.184 52.381 0.00 0.00 0.00 1.78
1 2 1.202770 TCTCGGATCTCCTGACGCATA 60.203 52.381 0.00 0.00 0.00 3.14
2 3 0.466372 TCTCGGATCTCCTGACGCAT 60.466 55.000 0.00 0.00 0.00 4.73
3 4 1.077716 TCTCGGATCTCCTGACGCA 60.078 57.895 0.00 0.00 0.00 5.24
4 5 1.357334 GTCTCGGATCTCCTGACGC 59.643 63.158 0.00 0.00 31.38 5.19
5 6 1.448922 GGGTCTCGGATCTCCTGACG 61.449 65.000 10.82 0.00 37.73 4.35
6 7 1.448922 CGGGTCTCGGATCTCCTGAC 61.449 65.000 9.40 9.40 36.84 3.51
7 8 1.152943 CGGGTCTCGGATCTCCTGA 60.153 63.158 0.00 0.00 34.75 3.86
8 9 2.851071 GCGGGTCTCGGATCTCCTG 61.851 68.421 0.00 0.00 39.69 3.86
9 10 2.519780 GCGGGTCTCGGATCTCCT 60.520 66.667 0.00 0.00 39.69 3.69
10 11 2.833582 TGCGGGTCTCGGATCTCC 60.834 66.667 0.00 0.00 39.69 3.71
11 12 2.725008 CTGCGGGTCTCGGATCTC 59.275 66.667 0.00 0.00 38.83 2.75
12 13 2.835431 CCTGCGGGTCTCGGATCT 60.835 66.667 2.29 0.00 38.83 2.75
13 14 3.148279 ACCTGCGGGTCTCGGATC 61.148 66.667 12.85 0.00 43.38 3.36
14 15 3.461773 CACCTGCGGGTCTCGGAT 61.462 66.667 16.42 0.00 45.41 4.18
17 18 4.457496 ATGCACCTGCGGGTCTCG 62.457 66.667 16.42 5.01 45.41 4.04
18 19 2.512515 GATGCACCTGCGGGTCTC 60.513 66.667 16.42 10.50 45.41 3.36
19 20 2.894257 TTGATGCACCTGCGGGTCT 61.894 57.895 16.42 1.84 45.41 3.85
20 21 2.359850 TTGATGCACCTGCGGGTC 60.360 61.111 16.42 10.68 45.41 4.46
22 23 2.267351 TTGTTGATGCACCTGCGGG 61.267 57.895 11.02 11.02 45.83 6.13
23 24 1.081242 GTTGTTGATGCACCTGCGG 60.081 57.895 0.00 0.00 45.83 5.69
24 25 0.386352 CAGTTGTTGATGCACCTGCG 60.386 55.000 0.00 0.00 45.83 5.18
25 26 0.665369 GCAGTTGTTGATGCACCTGC 60.665 55.000 0.00 0.29 45.00 4.85
26 27 0.669619 TGCAGTTGTTGATGCACCTG 59.330 50.000 0.00 0.00 46.97 4.00
27 28 0.956633 CTGCAGTTGTTGATGCACCT 59.043 50.000 5.25 0.00 46.97 4.00
28 29 0.665369 GCTGCAGTTGTTGATGCACC 60.665 55.000 16.64 0.00 46.97 5.01
29 30 0.031043 TGCTGCAGTTGTTGATGCAC 59.969 50.000 16.64 0.00 46.97 4.57
31 32 0.388134 CCTGCTGCAGTTGTTGATGC 60.388 55.000 26.41 0.00 42.86 3.91
32 33 1.241165 TCCTGCTGCAGTTGTTGATG 58.759 50.000 26.41 10.01 0.00 3.07
33 34 2.089980 GATCCTGCTGCAGTTGTTGAT 58.910 47.619 26.41 20.34 0.00 2.57
34 35 1.072806 AGATCCTGCTGCAGTTGTTGA 59.927 47.619 26.41 16.78 0.00 3.18
35 36 1.199327 CAGATCCTGCTGCAGTTGTTG 59.801 52.381 26.41 15.68 0.00 3.33
36 37 1.531423 CAGATCCTGCTGCAGTTGTT 58.469 50.000 26.41 8.78 0.00 2.83
37 38 0.322277 CCAGATCCTGCTGCAGTTGT 60.322 55.000 26.41 12.84 34.56 3.32
38 39 0.322277 ACCAGATCCTGCTGCAGTTG 60.322 55.000 26.41 17.84 34.56 3.16
39 40 0.322277 CACCAGATCCTGCTGCAGTT 60.322 55.000 26.41 14.63 34.56 3.16
40 41 1.298993 CACCAGATCCTGCTGCAGT 59.701 57.895 26.41 10.66 34.56 4.40
41 42 1.451567 CCACCAGATCCTGCTGCAG 60.452 63.158 22.44 22.44 34.56 4.41
42 43 1.907222 CTCCACCAGATCCTGCTGCA 61.907 60.000 0.88 0.88 34.56 4.41
43 44 1.153208 CTCCACCAGATCCTGCTGC 60.153 63.158 0.00 0.00 34.56 5.25
44 45 1.153208 GCTCCACCAGATCCTGCTG 60.153 63.158 0.00 0.00 35.66 4.41
45 46 1.614525 TGCTCCACCAGATCCTGCT 60.615 57.895 0.00 0.00 0.00 4.24
46 47 1.451028 GTGCTCCACCAGATCCTGC 60.451 63.158 0.00 0.00 0.00 4.85
47 48 4.950479 GTGCTCCACCAGATCCTG 57.050 61.111 0.00 0.00 0.00 3.86
56 57 1.147153 GCCTCCATAGGTGCTCCAC 59.853 63.158 7.70 0.00 45.64 4.02
57 58 1.003442 AGCCTCCATAGGTGCTCCA 59.997 57.895 7.70 0.00 45.64 3.86
58 59 1.050988 TGAGCCTCCATAGGTGCTCC 61.051 60.000 19.71 0.00 45.64 4.70
59 60 0.833287 TTGAGCCTCCATAGGTGCTC 59.167 55.000 17.36 17.36 45.64 4.26
60 61 0.835941 CTTGAGCCTCCATAGGTGCT 59.164 55.000 3.23 3.23 45.64 4.40
61 62 0.179034 CCTTGAGCCTCCATAGGTGC 60.179 60.000 0.00 0.00 45.64 5.01
62 63 0.471617 CCCTTGAGCCTCCATAGGTG 59.528 60.000 0.00 0.00 45.64 4.00
63 64 1.348775 GCCCTTGAGCCTCCATAGGT 61.349 60.000 0.00 0.00 45.64 3.08
64 65 1.348008 TGCCCTTGAGCCTCCATAGG 61.348 60.000 0.00 0.00 46.76 2.57
65 66 0.548031 TTGCCCTTGAGCCTCCATAG 59.452 55.000 0.00 0.00 0.00 2.23
66 67 0.255890 GTTGCCCTTGAGCCTCCATA 59.744 55.000 0.00 0.00 0.00 2.74
67 68 1.000396 GTTGCCCTTGAGCCTCCAT 60.000 57.895 0.00 0.00 0.00 3.41
68 69 2.436109 GTTGCCCTTGAGCCTCCA 59.564 61.111 0.00 0.00 0.00 3.86
69 70 2.747855 CGTTGCCCTTGAGCCTCC 60.748 66.667 0.00 0.00 0.00 4.30
70 71 3.435186 GCGTTGCCCTTGAGCCTC 61.435 66.667 0.00 0.00 0.00 4.70
81 82 3.470567 CGTCGAGTCAGGCGTTGC 61.471 66.667 0.00 0.00 34.13 4.17
82 83 3.470567 GCGTCGAGTCAGGCGTTG 61.471 66.667 0.00 0.00 41.85 4.10
86 87 3.685214 ATCACGCGTCGAGTCAGGC 62.685 63.158 9.86 0.00 0.00 4.85
87 88 1.869574 CATCACGCGTCGAGTCAGG 60.870 63.158 9.86 0.00 0.00 3.86
88 89 0.454452 TTCATCACGCGTCGAGTCAG 60.454 55.000 9.86 0.00 0.00 3.51
89 90 0.039888 TTTCATCACGCGTCGAGTCA 60.040 50.000 9.86 0.00 0.00 3.41
90 91 1.269166 ATTTCATCACGCGTCGAGTC 58.731 50.000 9.86 0.00 0.00 3.36
91 92 2.554806 TATTTCATCACGCGTCGAGT 57.445 45.000 9.86 0.00 0.00 4.18
92 93 3.042887 TCATATTTCATCACGCGTCGAG 58.957 45.455 9.86 1.07 0.00 4.04
93 94 3.042887 CTCATATTTCATCACGCGTCGA 58.957 45.455 9.86 11.59 0.00 4.20
94 95 2.789339 ACTCATATTTCATCACGCGTCG 59.211 45.455 9.86 5.44 0.00 5.12
95 96 4.778842 AACTCATATTTCATCACGCGTC 57.221 40.909 9.86 0.00 0.00 5.19
96 97 5.545658 AAAACTCATATTTCATCACGCGT 57.454 34.783 5.58 5.58 0.00 6.01
97 98 8.547091 AATAAAAACTCATATTTCATCACGCG 57.453 30.769 3.53 3.53 0.00 6.01
170 171 8.334632 CGGCACAAATTCAAAAGAAGTTATTTT 58.665 29.630 2.38 2.38 0.00 1.82
171 172 7.708752 TCGGCACAAATTCAAAAGAAGTTATTT 59.291 29.630 0.00 0.00 0.00 1.40
172 173 7.206687 TCGGCACAAATTCAAAAGAAGTTATT 58.793 30.769 0.00 0.00 0.00 1.40
173 174 6.744112 TCGGCACAAATTCAAAAGAAGTTAT 58.256 32.000 0.00 0.00 0.00 1.89
174 175 6.137794 TCGGCACAAATTCAAAAGAAGTTA 57.862 33.333 0.00 0.00 0.00 2.24
175 176 5.004922 TCGGCACAAATTCAAAAGAAGTT 57.995 34.783 0.00 0.00 0.00 2.66
176 177 4.647424 TCGGCACAAATTCAAAAGAAGT 57.353 36.364 0.00 0.00 0.00 3.01
177 178 5.290643 TGTTTCGGCACAAATTCAAAAGAAG 59.709 36.000 0.00 0.00 0.00 2.85
178 179 5.062809 GTGTTTCGGCACAAATTCAAAAGAA 59.937 36.000 0.00 0.00 39.07 2.52
179 180 4.564769 GTGTTTCGGCACAAATTCAAAAGA 59.435 37.500 0.00 0.00 39.07 2.52
180 181 4.547966 CGTGTTTCGGCACAAATTCAAAAG 60.548 41.667 6.52 0.00 39.19 2.27
181 182 3.304559 CGTGTTTCGGCACAAATTCAAAA 59.695 39.130 6.52 0.00 39.19 2.44
182 183 2.854777 CGTGTTTCGGCACAAATTCAAA 59.145 40.909 6.52 0.00 39.19 2.69
183 184 2.455032 CGTGTTTCGGCACAAATTCAA 58.545 42.857 6.52 0.00 39.19 2.69
184 185 1.862008 GCGTGTTTCGGCACAAATTCA 60.862 47.619 6.52 0.00 39.19 2.57
185 186 0.775861 GCGTGTTTCGGCACAAATTC 59.224 50.000 6.52 0.00 39.19 2.17
186 187 0.101399 TGCGTGTTTCGGCACAAATT 59.899 45.000 6.52 0.00 39.19 1.82
187 188 0.101399 TTGCGTGTTTCGGCACAAAT 59.899 45.000 6.52 0.00 39.19 2.32
188 189 0.109272 TTTGCGTGTTTCGGCACAAA 60.109 45.000 6.52 0.00 39.19 2.83
189 190 0.109272 TTTTGCGTGTTTCGGCACAA 60.109 45.000 6.52 0.00 39.19 3.33
190 191 0.101399 ATTTTGCGTGTTTCGGCACA 59.899 45.000 6.52 0.00 39.19 4.57
191 192 2.039327 TATTTTGCGTGTTTCGGCAC 57.961 45.000 0.00 0.00 40.26 5.01
192 193 2.590073 CATATTTTGCGTGTTTCGGCA 58.410 42.857 0.00 0.00 40.26 5.69
193 194 1.917303 CCATATTTTGCGTGTTTCGGC 59.083 47.619 0.00 0.00 40.26 5.54
194 195 2.525055 CCCATATTTTGCGTGTTTCGG 58.475 47.619 0.00 0.00 40.26 4.30
195 196 1.917303 GCCCATATTTTGCGTGTTTCG 59.083 47.619 0.00 0.00 43.12 3.46
196 197 2.267426 GGCCCATATTTTGCGTGTTTC 58.733 47.619 0.00 0.00 0.00 2.78
197 198 1.403514 CGGCCCATATTTTGCGTGTTT 60.404 47.619 0.00 0.00 0.00 2.83
198 199 0.172352 CGGCCCATATTTTGCGTGTT 59.828 50.000 0.00 0.00 0.00 3.32
199 200 0.678366 TCGGCCCATATTTTGCGTGT 60.678 50.000 0.00 0.00 0.00 4.49
200 201 0.453793 TTCGGCCCATATTTTGCGTG 59.546 50.000 0.00 0.00 0.00 5.34
201 202 1.178276 TTTCGGCCCATATTTTGCGT 58.822 45.000 0.00 0.00 0.00 5.24
202 203 2.507339 ATTTCGGCCCATATTTTGCG 57.493 45.000 0.00 0.00 0.00 4.85
203 204 2.871633 CCAATTTCGGCCCATATTTTGC 59.128 45.455 0.00 0.00 0.00 3.68
204 205 4.119136 GACCAATTTCGGCCCATATTTTG 58.881 43.478 0.00 0.00 0.00 2.44
205 206 3.772025 TGACCAATTTCGGCCCATATTTT 59.228 39.130 0.00 0.00 0.00 1.82
206 207 3.370104 TGACCAATTTCGGCCCATATTT 58.630 40.909 0.00 0.00 0.00 1.40
207 208 3.025322 TGACCAATTTCGGCCCATATT 57.975 42.857 0.00 0.00 0.00 1.28
208 209 2.746279 TGACCAATTTCGGCCCATAT 57.254 45.000 0.00 0.00 0.00 1.78
209 210 2.516227 TTGACCAATTTCGGCCCATA 57.484 45.000 0.00 0.00 0.00 2.74
210 211 1.864669 ATTGACCAATTTCGGCCCAT 58.135 45.000 0.00 0.00 0.00 4.00
211 212 1.638529 AATTGACCAATTTCGGCCCA 58.361 45.000 0.00 0.00 37.74 5.36
212 213 2.345876 CAAATTGACCAATTTCGGCCC 58.654 47.619 15.47 0.00 46.01 5.80
213 214 1.731709 GCAAATTGACCAATTTCGGCC 59.268 47.619 15.47 0.00 46.01 6.13
214 215 1.389784 CGCAAATTGACCAATTTCGGC 59.610 47.619 15.47 15.22 46.01 5.54
215 216 1.389784 GCGCAAATTGACCAATTTCGG 59.610 47.619 23.91 17.39 46.01 4.30
216 217 2.090967 CAGCGCAAATTGACCAATTTCG 59.909 45.455 11.47 21.43 46.01 3.46
217 218 3.316283 TCAGCGCAAATTGACCAATTTC 58.684 40.909 11.47 10.69 46.01 2.17
219 220 3.598019 ATCAGCGCAAATTGACCAATT 57.402 38.095 11.47 2.38 42.35 2.32
220 221 3.696051 ACTATCAGCGCAAATTGACCAAT 59.304 39.130 11.47 0.00 0.00 3.16
221 222 3.081061 ACTATCAGCGCAAATTGACCAA 58.919 40.909 11.47 0.00 0.00 3.67
222 223 2.710377 ACTATCAGCGCAAATTGACCA 58.290 42.857 11.47 0.00 0.00 4.02
223 224 3.248602 CCTACTATCAGCGCAAATTGACC 59.751 47.826 11.47 0.00 0.00 4.02
224 225 3.303395 GCCTACTATCAGCGCAAATTGAC 60.303 47.826 11.47 0.00 0.00 3.18
225 226 2.872245 GCCTACTATCAGCGCAAATTGA 59.128 45.455 11.47 4.51 0.00 2.57
226 227 2.031682 GGCCTACTATCAGCGCAAATTG 60.032 50.000 11.47 6.04 0.00 2.32
227 228 2.222027 GGCCTACTATCAGCGCAAATT 58.778 47.619 11.47 0.00 0.00 1.82
228 229 1.140852 TGGCCTACTATCAGCGCAAAT 59.859 47.619 11.47 4.77 0.00 2.32
229 230 0.539518 TGGCCTACTATCAGCGCAAA 59.460 50.000 11.47 0.00 0.00 3.68
230 231 0.539518 TTGGCCTACTATCAGCGCAA 59.460 50.000 11.47 0.00 0.00 4.85
231 232 0.758734 ATTGGCCTACTATCAGCGCA 59.241 50.000 11.47 0.00 0.00 6.09
232 233 1.884235 AATTGGCCTACTATCAGCGC 58.116 50.000 3.32 0.00 0.00 5.92
233 234 2.031682 GCAAATTGGCCTACTATCAGCG 60.032 50.000 3.32 0.00 0.00 5.18
234 235 2.031682 CGCAAATTGGCCTACTATCAGC 60.032 50.000 3.32 0.00 0.00 4.26
235 236 2.031682 GCGCAAATTGGCCTACTATCAG 60.032 50.000 3.32 0.00 0.00 2.90
236 237 1.946768 GCGCAAATTGGCCTACTATCA 59.053 47.619 3.32 0.00 0.00 2.15
237 238 1.266989 GGCGCAAATTGGCCTACTATC 59.733 52.381 10.83 0.00 45.93 2.08
238 239 1.318576 GGCGCAAATTGGCCTACTAT 58.681 50.000 10.83 0.00 45.93 2.12
239 240 2.788515 GGCGCAAATTGGCCTACTA 58.211 52.632 10.83 0.00 45.93 1.82
240 241 3.603365 GGCGCAAATTGGCCTACT 58.397 55.556 10.83 0.00 45.93 2.57
244 245 2.048690 TTTCGGCGCAAATTGGCC 60.049 55.556 10.83 13.23 45.95 5.36
245 246 1.372872 ACTTTCGGCGCAAATTGGC 60.373 52.632 10.83 0.00 0.00 4.52
246 247 1.008361 CCACTTTCGGCGCAAATTGG 61.008 55.000 10.83 18.71 31.80 3.16
247 248 1.008361 CCCACTTTCGGCGCAAATTG 61.008 55.000 10.83 6.66 0.00 2.32
248 249 1.288752 CCCACTTTCGGCGCAAATT 59.711 52.632 10.83 0.00 0.00 1.82
249 250 2.961768 CCCACTTTCGGCGCAAAT 59.038 55.556 10.83 0.00 0.00 2.32
250 251 3.972276 GCCCACTTTCGGCGCAAA 61.972 61.111 10.83 0.33 36.47 3.68
256 257 1.001378 CACTTTTCAGCCCACTTTCGG 60.001 52.381 0.00 0.00 0.00 4.30
257 258 1.001378 CCACTTTTCAGCCCACTTTCG 60.001 52.381 0.00 0.00 0.00 3.46
258 259 1.341209 CCCACTTTTCAGCCCACTTTC 59.659 52.381 0.00 0.00 0.00 2.62
259 260 1.413118 CCCACTTTTCAGCCCACTTT 58.587 50.000 0.00 0.00 0.00 2.66
260 261 1.115326 GCCCACTTTTCAGCCCACTT 61.115 55.000 0.00 0.00 0.00 3.16
261 262 1.531602 GCCCACTTTTCAGCCCACT 60.532 57.895 0.00 0.00 0.00 4.00
262 263 2.574018 GGCCCACTTTTCAGCCCAC 61.574 63.158 0.00 0.00 39.60 4.61
263 264 2.203625 GGCCCACTTTTCAGCCCA 60.204 61.111 0.00 0.00 39.60 5.36
264 265 1.194121 ATTGGCCCACTTTTCAGCCC 61.194 55.000 0.00 0.00 45.14 5.19
265 266 0.686789 AATTGGCCCACTTTTCAGCC 59.313 50.000 0.00 0.00 45.96 4.85
266 267 2.145536 CAAATTGGCCCACTTTTCAGC 58.854 47.619 0.00 0.00 0.00 4.26
267 268 2.145536 GCAAATTGGCCCACTTTTCAG 58.854 47.619 0.00 0.00 0.00 3.02
268 269 1.539929 CGCAAATTGGCCCACTTTTCA 60.540 47.619 0.00 0.00 0.00 2.69
269 270 1.147473 CGCAAATTGGCCCACTTTTC 58.853 50.000 0.00 0.00 0.00 2.29
270 271 0.884259 GCGCAAATTGGCCCACTTTT 60.884 50.000 0.30 0.00 0.00 2.27
271 272 1.301637 GCGCAAATTGGCCCACTTT 60.302 52.632 0.30 0.00 0.00 2.66
272 273 2.343387 GCGCAAATTGGCCCACTT 59.657 55.556 0.30 0.00 0.00 3.16
273 274 3.694538 GGCGCAAATTGGCCCACT 61.695 61.111 10.83 0.00 43.64 4.00
278 279 1.301637 AACCTTGGCGCAAATTGGC 60.302 52.632 10.83 0.00 0.00 4.52
279 280 0.950071 CCAACCTTGGCGCAAATTGG 60.950 55.000 14.03 14.03 42.21 3.16
280 281 2.531055 CCAACCTTGGCGCAAATTG 58.469 52.632 10.83 6.82 42.21 2.32
290 291 0.109132 GCCGATTTCAGCCAACCTTG 60.109 55.000 0.00 0.00 0.00 3.61
291 292 1.586154 CGCCGATTTCAGCCAACCTT 61.586 55.000 0.00 0.00 0.00 3.50
292 293 2.040544 CGCCGATTTCAGCCAACCT 61.041 57.895 0.00 0.00 0.00 3.50
293 294 2.485122 CGCCGATTTCAGCCAACC 59.515 61.111 0.00 0.00 0.00 3.77
294 295 2.202479 GCGCCGATTTCAGCCAAC 60.202 61.111 0.00 0.00 0.00 3.77
298 299 3.880846 CCAGGCGCCGATTTCAGC 61.881 66.667 23.20 0.00 0.00 4.26
299 300 3.204827 CCCAGGCGCCGATTTCAG 61.205 66.667 23.20 5.59 0.00 3.02
300 301 4.794648 CCCCAGGCGCCGATTTCA 62.795 66.667 23.20 0.00 0.00 2.69
301 302 4.483243 TCCCCAGGCGCCGATTTC 62.483 66.667 23.20 0.00 0.00 2.17
302 303 4.796495 GTCCCCAGGCGCCGATTT 62.796 66.667 23.20 0.00 0.00 2.17
336 337 4.547367 GGGCGATCGGGTTCCCAG 62.547 72.222 19.95 1.53 38.62 4.45
340 341 4.851179 GTGGGGGCGATCGGGTTC 62.851 72.222 18.30 0.00 0.00 3.62
345 346 3.733344 ATCAACGTGGGGGCGATCG 62.733 63.158 11.69 11.69 35.59 3.69
346 347 1.029947 AAATCAACGTGGGGGCGATC 61.030 55.000 0.00 0.00 35.59 3.69
347 348 0.610785 AAAATCAACGTGGGGGCGAT 60.611 50.000 0.00 0.00 35.59 4.58
348 349 0.824182 AAAAATCAACGTGGGGGCGA 60.824 50.000 0.00 0.00 35.59 5.54
349 350 0.388006 GAAAAATCAACGTGGGGGCG 60.388 55.000 0.00 0.00 37.94 6.13
350 351 0.388006 CGAAAAATCAACGTGGGGGC 60.388 55.000 0.00 0.00 0.00 5.80
351 352 0.242555 CCGAAAAATCAACGTGGGGG 59.757 55.000 0.00 0.00 0.00 5.40
352 353 0.388006 GCCGAAAAATCAACGTGGGG 60.388 55.000 0.00 0.00 0.00 4.96
353 354 0.388006 GGCCGAAAAATCAACGTGGG 60.388 55.000 0.00 0.00 0.00 4.61
354 355 0.727793 CGGCCGAAAAATCAACGTGG 60.728 55.000 24.07 0.00 0.00 4.94
355 356 0.727793 CCGGCCGAAAAATCAACGTG 60.728 55.000 30.73 0.00 0.00 4.49
356 357 1.577421 CCGGCCGAAAAATCAACGT 59.423 52.632 30.73 0.00 0.00 3.99
357 358 1.799916 GCCGGCCGAAAAATCAACG 60.800 57.895 30.73 6.52 0.00 4.10
358 359 1.799916 CGCCGGCCGAAAAATCAAC 60.800 57.895 30.73 2.89 40.02 3.18
359 360 2.563942 CGCCGGCCGAAAAATCAA 59.436 55.556 30.73 0.00 40.02 2.57
360 361 4.109693 GCGCCGGCCGAAAAATCA 62.110 61.111 30.73 0.00 40.02 2.57
382 383 2.094126 CTTGAAATAGCGCCGCCTCG 62.094 60.000 4.98 0.00 0.00 4.63
383 384 1.643832 CTTGAAATAGCGCCGCCTC 59.356 57.895 4.98 0.00 0.00 4.70
384 385 2.472909 GCTTGAAATAGCGCCGCCT 61.473 57.895 4.98 0.00 0.00 5.52
385 386 2.024729 GCTTGAAATAGCGCCGCC 59.975 61.111 4.98 0.00 0.00 6.13
386 387 2.024729 GGCTTGAAATAGCGCCGC 59.975 61.111 2.29 0.00 42.15 6.53
387 388 2.715624 GGGCTTGAAATAGCGCCG 59.284 61.111 2.29 0.00 45.37 6.46
390 391 1.103398 CCCAGGGGCTTGAAATAGCG 61.103 60.000 0.00 0.00 42.15 4.26
391 392 0.756815 CCCCAGGGGCTTGAAATAGC 60.757 60.000 13.35 0.00 35.35 2.97
392 393 3.520623 CCCCAGGGGCTTGAAATAG 57.479 57.895 13.35 0.00 35.35 1.73
409 410 4.222847 CTCTAGCCGTTCGCCCCC 62.223 72.222 0.00 0.00 38.78 5.40
410 411 2.499827 ATCTCTAGCCGTTCGCCCC 61.500 63.158 0.00 0.00 38.78 5.80
411 412 1.300233 CATCTCTAGCCGTTCGCCC 60.300 63.158 0.00 0.00 38.78 6.13
412 413 1.951631 GCATCTCTAGCCGTTCGCC 60.952 63.158 0.00 0.00 38.78 5.54
413 414 0.937231 GAGCATCTCTAGCCGTTCGC 60.937 60.000 0.00 0.00 37.98 4.70
414 415 3.171705 GAGCATCTCTAGCCGTTCG 57.828 57.895 0.00 0.00 0.00 3.95
422 423 7.362660 ACACGTGTGTTTATAAGAGCATCTCTA 60.363 37.037 22.71 0.00 43.71 2.43
423 424 6.572509 ACACGTGTGTTTATAAGAGCATCTCT 60.573 38.462 22.71 0.00 43.71 3.10
424 425 5.577164 ACACGTGTGTTTATAAGAGCATCTC 59.423 40.000 22.71 0.00 43.71 2.75
425 426 5.479306 ACACGTGTGTTTATAAGAGCATCT 58.521 37.500 22.71 0.00 45.90 2.90
426 427 5.779806 ACACGTGTGTTTATAAGAGCATC 57.220 39.130 22.71 0.00 41.83 3.91
485 486 9.801873 CCATGATACAACTTATAAAAAGGGTTG 57.198 33.333 11.11 11.11 41.75 3.77
490 491 8.902806 TGCTCCCATGATACAACTTATAAAAAG 58.097 33.333 0.00 0.00 0.00 2.27
493 494 8.995027 AATGCTCCCATGATACAACTTATAAA 57.005 30.769 0.00 0.00 0.00 1.40
496 497 8.995027 TTAAATGCTCCCATGATACAACTTAT 57.005 30.769 0.00 0.00 0.00 1.73
503 504 4.065088 TCGCTTAAATGCTCCCATGATAC 58.935 43.478 0.00 0.00 0.00 2.24
512 513 5.023551 GTGATACCATCGCTTAAATGCTC 57.976 43.478 0.00 0.00 36.86 4.26
524 525 6.773638 AGGGTGAATATTGAGTGATACCATC 58.226 40.000 0.00 0.00 0.00 3.51
535 536 9.206690 GGAGAGATATATGAGGGTGAATATTGA 57.793 37.037 0.00 0.00 0.00 2.57
537 538 9.566331 TTGGAGAGATATATGAGGGTGAATATT 57.434 33.333 0.00 0.00 0.00 1.28
550 551 6.177663 AGGGTGGAGATTGGAGAGATATAT 57.822 41.667 0.00 0.00 0.00 0.86
554 555 2.688477 GAGGGTGGAGATTGGAGAGAT 58.312 52.381 0.00 0.00 0.00 2.75
674 675 3.290710 TCTTATTGCATTTCCTCCTGGC 58.709 45.455 0.00 0.00 0.00 4.85
903 919 5.254088 CGTACACTATAGACAGACGTGTTC 58.746 45.833 6.78 0.00 39.33 3.18
981 998 0.252103 TGCCTCCTAACTTCTCGGGT 60.252 55.000 0.00 0.00 0.00 5.28
1332 1349 4.881850 AGTAATAAGCAAGGAAACGGATGG 59.118 41.667 0.00 0.00 0.00 3.51
1336 1353 8.658499 AATAGTAGTAATAAGCAAGGAAACGG 57.342 34.615 0.00 0.00 0.00 4.44
1397 1414 1.063488 CGCCGGCGGAAAATTTAGG 59.937 57.895 40.50 8.19 35.56 2.69
1448 1467 0.750546 ACATCCTACGCTACGCTCCA 60.751 55.000 0.00 0.00 0.00 3.86
1450 1469 1.872313 AGTACATCCTACGCTACGCTC 59.128 52.381 0.00 0.00 0.00 5.03
1451 1470 1.602851 CAGTACATCCTACGCTACGCT 59.397 52.381 0.00 0.00 0.00 5.07
1452 1471 1.332997 ACAGTACATCCTACGCTACGC 59.667 52.381 0.00 0.00 0.00 4.42
1453 1472 3.557185 TGTACAGTACATCCTACGCTACG 59.443 47.826 9.51 0.00 32.89 3.51
1500 1521 6.984474 CCACACAAACGACATTATATACTCCT 59.016 38.462 0.00 0.00 0.00 3.69
1501 1522 6.759827 ACCACACAAACGACATTATATACTCC 59.240 38.462 0.00 0.00 0.00 3.85
1502 1523 7.766219 ACCACACAAACGACATTATATACTC 57.234 36.000 0.00 0.00 0.00 2.59
1503 1524 8.472413 AGTACCACACAAACGACATTATATACT 58.528 33.333 0.00 0.00 0.00 2.12
1504 1525 8.638685 AGTACCACACAAACGACATTATATAC 57.361 34.615 0.00 0.00 0.00 1.47
1505 1526 9.734620 GTAGTACCACACAAACGACATTATATA 57.265 33.333 0.00 0.00 0.00 0.86
1524 1545 5.048154 GTCCTCCCAAGATATTCGTAGTACC 60.048 48.000 0.00 0.00 0.00 3.34
1536 1557 3.200825 ACATTTCGATGTCCTCCCAAGAT 59.799 43.478 0.00 0.00 0.00 2.40
1541 1562 1.401905 GCAACATTTCGATGTCCTCCC 59.598 52.381 0.00 0.00 32.87 4.30
1552 1573 0.740737 CAGATCGGGGGCAACATTTC 59.259 55.000 0.00 0.00 39.74 2.17
1617 1638 1.327764 GATCGTTGTCAAGGAATCCGC 59.672 52.381 11.71 0.00 0.00 5.54
1676 1697 2.020131 CACTCTGCGCCAATGGATC 58.980 57.895 2.05 0.00 0.00 3.36
1853 1874 5.050499 GCAATCTCTCGACCAGAATATGTTG 60.050 44.000 0.00 0.00 0.00 3.33
1899 1926 5.163353 TGCTATAGTATAACTGTTGGCAGCA 60.163 40.000 3.43 3.43 46.30 4.41
1941 1968 3.030308 CGTAGCAGGGCATACGCG 61.030 66.667 3.53 3.53 38.42 6.01
1944 1971 0.464452 AACTCCGTAGCAGGGCATAC 59.536 55.000 0.00 0.00 0.00 2.39
1947 1974 1.192146 AAGAACTCCGTAGCAGGGCA 61.192 55.000 0.00 0.00 0.00 5.36
1950 1977 2.743636 TTGAAGAACTCCGTAGCAGG 57.256 50.000 0.00 0.00 0.00 4.85
1968 2157 7.014518 TGCCATCTAATCGATCCAAATTGATTT 59.985 33.333 0.00 0.00 41.38 2.17
1979 2168 4.218635 TCCAGTAGTGCCATCTAATCGATC 59.781 45.833 0.00 0.00 0.00 3.69
1985 2174 4.020928 TCGTTTTCCAGTAGTGCCATCTAA 60.021 41.667 0.00 0.00 0.00 2.10
2000 2189 1.050767 CGTCAGACGTCTCGTTTTCC 58.949 55.000 16.96 0.00 41.37 3.13
2014 2203 0.042188 CGTTTTCTGTGTGGCGTCAG 60.042 55.000 0.00 0.00 0.00 3.51
2087 2277 2.480037 CAGTCAACTTTGCGCTGTATGA 59.520 45.455 9.73 4.10 0.00 2.15
2096 2289 8.537223 CAATTGCATTATATCAGTCAACTTTGC 58.463 33.333 0.00 0.00 0.00 3.68
2201 2394 2.158475 TCAGGGTCAAAAGTTCCATGCT 60.158 45.455 0.00 0.00 33.77 3.79
2215 2408 6.159293 GGAAGATTGACAATTTTTCAGGGTC 58.841 40.000 19.52 0.00 0.00 4.46
2217 2410 6.015180 TCTGGAAGATTGACAATTTTTCAGGG 60.015 38.462 27.40 13.16 38.67 4.45
2271 2464 5.008712 GGAATTGTTTTCGTTTCTGGAGAGT 59.991 40.000 0.00 0.00 0.00 3.24
2275 2468 4.496673 CGTGGAATTGTTTTCGTTTCTGGA 60.497 41.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.