Multiple sequence alignment - TraesCS6D01G213000

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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 TraesCS6D01G213000 chr6D 100.000 5159 0 0 1 5159 302061647 302056489 0.000000e+00 9527
1 TraesCS6D01G213000 chr6D 92.486 173 11 2 120 291 40409562 40409391 3.990000e-61 246
2 TraesCS6D01G213000 chr6D 92.486 173 11 2 120 291 40427934 40427763 3.990000e-61 246
3 TraesCS6D01G213000 chr6A 97.282 4195 82 10 285 4464 414864433 414868610 0.000000e+00 7086
4 TraesCS6D01G213000 chr6A 97.222 504 14 0 4625 5128 414868609 414869112 0.000000e+00 854
5 TraesCS6D01G213000 chr6A 98.387 124 1 1 1 123 414864311 414864434 3.130000e-52 217
6 TraesCS6D01G213000 chr6B 97.690 3940 77 8 530 4464 467461373 467457443 0.000000e+00 6759
7 TraesCS6D01G213000 chr6B 97.944 535 9 2 4623 5157 467457446 467456914 0.000000e+00 926
8 TraesCS6D01G213000 chr6B 92.344 209 13 1 285 490 467465158 467464950 1.400000e-75 294
9 TraesCS6D01G213000 chr6B 94.536 183 10 0 4444 4626 67539148 67538966 3.040000e-72 283
10 TraesCS6D01G213000 chr6B 94.872 117 4 2 1 115 467465268 467465152 1.140000e-41 182
11 TraesCS6D01G213000 chr2D 98.246 171 2 1 4462 4631 560959650 560959480 1.090000e-76 298
12 TraesCS6D01G213000 chr2D 92.571 175 12 1 113 286 593801770 593801596 3.080000e-62 250
13 TraesCS6D01G213000 chr4D 94.737 190 9 1 4442 4630 238640350 238640161 1.400000e-75 294
14 TraesCS6D01G213000 chr4D 97.661 171 2 2 4457 4626 75782222 75782053 5.050000e-75 292
15 TraesCS6D01G213000 chr4D 94.798 173 8 1 119 291 57386236 57386407 8.510000e-68 268
16 TraesCS6D01G213000 chr3B 97.674 172 3 1 4461 4631 120616911 120617082 1.400000e-75 294
17 TraesCS6D01G213000 chr5D 96.591 176 5 1 4455 4629 274578184 274578009 1.820000e-74 291
18 TraesCS6D01G213000 chr5D 96.067 178 6 1 4460 4636 61715385 61715208 6.540000e-74 289
19 TraesCS6D01G213000 chr5D 88.265 196 21 2 119 314 361648671 361648478 3.110000e-57 233
20 TraesCS6D01G213000 chr1B 93.617 188 11 1 4463 4649 606841317 606841130 3.930000e-71 279
21 TraesCS6D01G213000 chr1A 94.054 185 10 1 4443 4626 67697428 67697244 3.930000e-71 279
22 TraesCS6D01G213000 chr1D 93.103 174 12 0 114 287 140136973 140137146 6.630000e-64 255
23 TraesCS6D01G213000 chr1D 93.452 168 11 0 119 286 414878243 414878410 3.080000e-62 250
24 TraesCS6D01G213000 chr5A 93.064 173 12 0 121 293 519947335 519947507 2.380000e-63 254
25 TraesCS6D01G213000 chr5B 92.486 173 13 0 115 287 560393882 560393710 1.110000e-61 248


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 TraesCS6D01G213000 chr6D 302056489 302061647 5158 True 9527.00 9527 100.000000 1 5159 1 chr6D.!!$R3 5158
1 TraesCS6D01G213000 chr6A 414864311 414869112 4801 False 2719.00 7086 97.630333 1 5128 3 chr6A.!!$F1 5127
2 TraesCS6D01G213000 chr6B 467456914 467465268 8354 True 2040.25 6759 95.712500 1 5157 4 chr6B.!!$R2 5156

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
595 4161 0.546122 ATGCAGGCCGTATCCTTCAA 59.454 50.0 0.00 0.00 33.30 2.69 F
1159 4726 0.539518 GGAAGGCTTCCTGAGAGGTC 59.460 60.0 33.93 8.62 46.57 3.85 F
1296 4863 1.075601 ATGGCAGGAAACTCAAGGGA 58.924 50.0 0.00 0.00 40.21 4.20 F
3114 6681 0.390078 TTGGCATTGCAATTGGAGCG 60.390 50.0 9.83 0.00 33.85 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 5025 1.519455 CTCAATCACCGGGAGCGAC 60.519 63.158 6.32 0.0 0.00 5.19 R
3114 6681 1.866601 GCAACAGACAAAACCATTGCC 59.133 47.619 0.00 0.0 37.14 4.52 R
3259 6826 5.356190 CACTGATAGTCAATGCCTTGTCATT 59.644 40.000 1.49 0.0 37.16 2.57 R
4613 8185 0.252103 TGCCTTCTACTCCCTCCGTT 60.252 55.000 0.00 0.0 0.00 4.44 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
98 100 6.615088 CATCCTTCAGTTTTTGGATGTACAG 58.385 40.000 0.33 0.00 46.39 2.74
130 132 5.963176 GTAGTATAGCAACTACTCCCTCC 57.037 47.826 13.70 0.00 45.52 4.30
131 133 3.488363 AGTATAGCAACTACTCCCTCCG 58.512 50.000 0.00 0.00 0.00 4.63
132 134 2.456073 ATAGCAACTACTCCCTCCGT 57.544 50.000 0.00 0.00 0.00 4.69
133 135 2.226962 TAGCAACTACTCCCTCCGTT 57.773 50.000 0.00 0.00 0.00 4.44
134 136 1.349067 AGCAACTACTCCCTCCGTTT 58.651 50.000 0.00 0.00 0.00 3.60
135 137 1.275573 AGCAACTACTCCCTCCGTTTC 59.724 52.381 0.00 0.00 0.00 2.78
136 138 1.275573 GCAACTACTCCCTCCGTTTCT 59.724 52.381 0.00 0.00 0.00 2.52
137 139 2.494870 GCAACTACTCCCTCCGTTTCTA 59.505 50.000 0.00 0.00 0.00 2.10
138 140 3.056322 GCAACTACTCCCTCCGTTTCTAA 60.056 47.826 0.00 0.00 0.00 2.10
139 141 4.562143 GCAACTACTCCCTCCGTTTCTAAA 60.562 45.833 0.00 0.00 0.00 1.85
140 142 5.731591 CAACTACTCCCTCCGTTTCTAAAT 58.268 41.667 0.00 0.00 0.00 1.40
141 143 6.628844 GCAACTACTCCCTCCGTTTCTAAATA 60.629 42.308 0.00 0.00 0.00 1.40
142 144 7.498443 CAACTACTCCCTCCGTTTCTAAATAT 58.502 38.462 0.00 0.00 0.00 1.28
143 145 8.636213 CAACTACTCCCTCCGTTTCTAAATATA 58.364 37.037 0.00 0.00 0.00 0.86
144 146 8.773033 ACTACTCCCTCCGTTTCTAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
145 147 8.858094 ACTACTCCCTCCGTTTCTAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
146 148 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
147 149 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
148 150 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
149 151 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
150 152 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
151 153 9.043079 CCCTCCGTTTCTAAATATAAGTCTTTC 57.957 37.037 0.00 0.00 0.00 2.62
152 154 9.819267 CCTCCGTTTCTAAATATAAGTCTTTCT 57.181 33.333 0.00 0.00 0.00 2.52
184 186 9.478768 TTTCAATAAGTGACTACATACGAAACA 57.521 29.630 0.00 0.00 35.39 2.83
185 187 9.478768 TTCAATAAGTGACTACATACGAAACAA 57.521 29.630 0.00 0.00 35.39 2.83
186 188 9.478768 TCAATAAGTGACTACATACGAAACAAA 57.521 29.630 0.00 0.00 0.00 2.83
190 192 7.956420 AGTGACTACATACGAAACAAAATGA 57.044 32.000 0.00 0.00 0.00 2.57
191 193 8.373048 AGTGACTACATACGAAACAAAATGAA 57.627 30.769 0.00 0.00 0.00 2.57
192 194 8.999431 AGTGACTACATACGAAACAAAATGAAT 58.001 29.630 0.00 0.00 0.00 2.57
193 195 9.051027 GTGACTACATACGAAACAAAATGAATG 57.949 33.333 0.00 0.00 0.00 2.67
194 196 8.994170 TGACTACATACGAAACAAAATGAATGA 58.006 29.630 0.00 0.00 0.00 2.57
195 197 9.820229 GACTACATACGAAACAAAATGAATGAA 57.180 29.630 0.00 0.00 0.00 2.57
203 205 9.528018 ACGAAACAAAATGAATGAATTTACACT 57.472 25.926 0.00 0.00 0.00 3.55
204 206 9.993881 CGAAACAAAATGAATGAATTTACACTC 57.006 29.630 0.00 0.00 0.00 3.51
235 237 6.954487 TGTCTACATACATCCGTATCTTGT 57.046 37.500 0.00 0.00 36.11 3.16
236 238 8.631480 ATGTCTACATACATCCGTATCTTGTA 57.369 34.615 0.00 0.00 35.08 2.41
237 239 8.095937 TGTCTACATACATCCGTATCTTGTAG 57.904 38.462 0.00 0.00 38.71 2.74
238 240 7.718314 TGTCTACATACATCCGTATCTTGTAGT 59.282 37.037 0.00 0.00 38.60 2.73
239 241 8.229137 GTCTACATACATCCGTATCTTGTAGTC 58.771 40.741 0.00 0.00 38.60 2.59
240 242 6.328641 ACATACATCCGTATCTTGTAGTCC 57.671 41.667 0.00 0.00 36.11 3.85
241 243 5.831525 ACATACATCCGTATCTTGTAGTCCA 59.168 40.000 0.00 0.00 36.11 4.02
242 244 6.493802 ACATACATCCGTATCTTGTAGTCCAT 59.506 38.462 0.00 0.00 36.11 3.41
243 245 5.871396 ACATCCGTATCTTGTAGTCCATT 57.129 39.130 0.00 0.00 0.00 3.16
244 246 5.844004 ACATCCGTATCTTGTAGTCCATTC 58.156 41.667 0.00 0.00 0.00 2.67
245 247 5.362717 ACATCCGTATCTTGTAGTCCATTCA 59.637 40.000 0.00 0.00 0.00 2.57
246 248 5.925506 TCCGTATCTTGTAGTCCATTCAA 57.074 39.130 0.00 0.00 0.00 2.69
247 249 6.288941 TCCGTATCTTGTAGTCCATTCAAA 57.711 37.500 0.00 0.00 0.00 2.69
248 250 6.703319 TCCGTATCTTGTAGTCCATTCAAAA 58.297 36.000 0.00 0.00 0.00 2.44
249 251 7.335627 TCCGTATCTTGTAGTCCATTCAAAAT 58.664 34.615 0.00 0.00 0.00 1.82
250 252 7.279981 TCCGTATCTTGTAGTCCATTCAAAATG 59.720 37.037 0.00 0.00 0.00 2.32
251 253 7.065803 CCGTATCTTGTAGTCCATTCAAAATGT 59.934 37.037 0.00 0.00 0.00 2.71
252 254 8.116753 CGTATCTTGTAGTCCATTCAAAATGTC 58.883 37.037 0.00 0.00 0.00 3.06
253 255 9.167311 GTATCTTGTAGTCCATTCAAAATGTCT 57.833 33.333 0.00 1.05 0.00 3.41
255 257 9.739276 ATCTTGTAGTCCATTCAAAATGTCTAA 57.261 29.630 0.00 0.00 0.00 2.10
256 258 9.567776 TCTTGTAGTCCATTCAAAATGTCTAAA 57.432 29.630 0.00 0.00 0.00 1.85
262 264 9.136323 AGTCCATTCAAAATGTCTAAAAAGACT 57.864 29.630 7.04 0.00 39.41 3.24
263 265 9.750125 GTCCATTCAAAATGTCTAAAAAGACTT 57.250 29.630 7.04 0.00 39.41 3.01
281 283 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
282 284 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
283 285 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
284 286 7.564292 AGACTTATATTTAGAAACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
285 287 8.773033 ACTTATATTTAGAAACGGAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
339 347 5.866633 GCATTCCAAATTGATCACGGTTTTA 59.133 36.000 0.00 0.00 0.00 1.52
348 356 8.706492 AATTGATCACGGTTTTAGTATTACGA 57.294 30.769 0.00 0.00 0.00 3.43
359 367 1.484653 AGTATTACGACCATGCCAGCA 59.515 47.619 0.00 0.00 0.00 4.41
481 492 6.255887 GCGCAGTAGTATCTTCAACAGTAATT 59.744 38.462 0.30 0.00 0.00 1.40
490 501 9.614792 GTATCTTCAACAGTAATTGATTACCCT 57.385 33.333 9.62 0.00 42.71 4.34
492 503 8.561738 TCTTCAACAGTAATTGATTACCCTTC 57.438 34.615 9.62 0.00 42.71 3.46
493 504 7.610305 TCTTCAACAGTAATTGATTACCCTTCC 59.390 37.037 9.62 0.00 42.71 3.46
494 505 5.878116 TCAACAGTAATTGATTACCCTTCCG 59.122 40.000 9.62 0.00 42.71 4.30
495 506 4.196971 ACAGTAATTGATTACCCTTCCGC 58.803 43.478 9.62 0.00 42.71 5.54
496 507 4.196193 CAGTAATTGATTACCCTTCCGCA 58.804 43.478 9.62 0.00 42.71 5.69
497 508 4.638421 CAGTAATTGATTACCCTTCCGCAA 59.362 41.667 9.62 0.00 42.71 4.85
498 509 5.124776 CAGTAATTGATTACCCTTCCGCAAA 59.875 40.000 9.62 0.00 42.71 3.68
499 510 4.718940 AATTGATTACCCTTCCGCAAAG 57.281 40.909 0.00 0.00 34.52 2.77
500 511 2.871096 TGATTACCCTTCCGCAAAGT 57.129 45.000 0.00 0.00 32.69 2.66
501 512 3.985019 TGATTACCCTTCCGCAAAGTA 57.015 42.857 0.00 0.00 32.69 2.24
502 513 4.289238 TGATTACCCTTCCGCAAAGTAA 57.711 40.909 0.00 0.00 32.69 2.24
503 514 4.653868 TGATTACCCTTCCGCAAAGTAAA 58.346 39.130 0.00 0.00 32.69 2.01
504 515 5.258051 TGATTACCCTTCCGCAAAGTAAAT 58.742 37.500 0.00 0.00 32.69 1.40
505 516 5.712917 TGATTACCCTTCCGCAAAGTAAATT 59.287 36.000 0.00 0.00 32.69 1.82
543 4109 6.116680 GAAGCATAATCAGTCTGGTTCTTG 57.883 41.667 0.37 3.22 41.68 3.02
556 4122 4.225942 TCTGGTTCTTGGAACATCTAGCAT 59.774 41.667 11.67 0.00 39.30 3.79
566 4132 7.912056 TGGAACATCTAGCATTAGCAATATC 57.088 36.000 0.00 0.00 45.49 1.63
595 4161 0.546122 ATGCAGGCCGTATCCTTCAA 59.454 50.000 0.00 0.00 33.30 2.69
987 4554 2.406596 TCAACAGCATCAGCATAGCA 57.593 45.000 0.00 0.00 45.49 3.49
1122 4689 2.629656 CCAAAGCTCCTGCAACCCG 61.630 63.158 0.00 0.00 42.74 5.28
1159 4726 0.539518 GGAAGGCTTCCTGAGAGGTC 59.460 60.000 33.93 8.62 46.57 3.85
1203 4770 1.337817 CGCTCTCAAACACGACCTCG 61.338 60.000 0.00 0.00 46.33 4.63
1245 4812 2.124570 GTGGGCCTCACATGCGAT 60.125 61.111 16.71 0.00 45.39 4.58
1251 4818 3.274586 CTCACATGCGATGCCGGG 61.275 66.667 2.18 0.00 36.06 5.73
1296 4863 1.075601 ATGGCAGGAAACTCAAGGGA 58.924 50.000 0.00 0.00 40.21 4.20
1353 4920 1.079750 GTGGCTCAACCTCTCCGAC 60.080 63.158 0.00 0.00 40.22 4.79
1376 4943 3.402681 CCTCCGTGGTGCCATCCT 61.403 66.667 0.00 0.00 0.00 3.24
1377 4944 2.124983 CTCCGTGGTGCCATCCTG 60.125 66.667 0.00 0.00 0.00 3.86
1404 4971 1.767681 CTCCTTCAGCTCCATAGGCTT 59.232 52.381 0.00 0.00 38.03 4.35
1458 5025 2.671619 ACATTCCCGGCCAACGTG 60.672 61.111 2.24 0.00 42.24 4.49
1738 5305 4.020617 CCGGGAGCTTGCCAGACA 62.021 66.667 0.00 0.00 0.00 3.41
1835 5402 1.318158 GGCAATCTGTCCAGCCTTGG 61.318 60.000 0.00 0.00 46.49 3.61
2016 5583 4.455533 CGGAACAATTCACTGAATGGAAGA 59.544 41.667 12.44 0.00 32.14 2.87
3114 6681 0.390078 TTGGCATTGCAATTGGAGCG 60.390 50.000 9.83 0.00 33.85 5.03
3259 6826 7.088905 GGTACTTCTGTTTCAGAACGAAGATA 58.911 38.462 20.00 11.70 44.27 1.98
3402 6969 5.282055 AGATCGCCATCAAAAGACTATCA 57.718 39.130 0.00 0.00 0.00 2.15
3909 7476 7.792364 TCTGGAGTTATTAACAGGAAAGAGA 57.208 36.000 9.15 0.00 0.00 3.10
4054 7621 8.642432 AGATGCAAATGATGAAGATGATTGATT 58.358 29.630 0.00 0.00 0.00 2.57
4141 7708 3.304928 GCTTGACAACATTTGTGCTAGCT 60.305 43.478 17.23 0.00 45.52 3.32
4429 8001 7.414436 CGTCCAAAACTTTGAAGTCATCTTTA 58.586 34.615 3.72 0.00 40.55 1.85
4467 8039 6.880942 ACTCTCTACGTTCCATAATACTCC 57.119 41.667 0.00 0.00 0.00 3.85
4468 8040 5.769162 ACTCTCTACGTTCCATAATACTCCC 59.231 44.000 0.00 0.00 0.00 4.30
4469 8041 5.950023 TCTCTACGTTCCATAATACTCCCT 58.050 41.667 0.00 0.00 0.00 4.20
4470 8042 6.002704 TCTCTACGTTCCATAATACTCCCTC 58.997 44.000 0.00 0.00 0.00 4.30
4471 8043 5.075493 TCTACGTTCCATAATACTCCCTCC 58.925 45.833 0.00 0.00 0.00 4.30
4472 8044 2.626743 ACGTTCCATAATACTCCCTCCG 59.373 50.000 0.00 0.00 0.00 4.63
4473 8045 2.626743 CGTTCCATAATACTCCCTCCGT 59.373 50.000 0.00 0.00 0.00 4.69
4474 8046 3.069158 CGTTCCATAATACTCCCTCCGTT 59.931 47.826 0.00 0.00 0.00 4.44
4475 8047 4.629092 GTTCCATAATACTCCCTCCGTTC 58.371 47.826 0.00 0.00 0.00 3.95
4476 8048 3.236896 TCCATAATACTCCCTCCGTTCC 58.763 50.000 0.00 0.00 0.00 3.62
4477 8049 3.116862 TCCATAATACTCCCTCCGTTCCT 60.117 47.826 0.00 0.00 0.00 3.36
4478 8050 4.106825 TCCATAATACTCCCTCCGTTCCTA 59.893 45.833 0.00 0.00 0.00 2.94
4479 8051 4.836736 CCATAATACTCCCTCCGTTCCTAA 59.163 45.833 0.00 0.00 0.00 2.69
4480 8052 5.306160 CCATAATACTCCCTCCGTTCCTAAA 59.694 44.000 0.00 0.00 0.00 1.85
4481 8053 6.013639 CCATAATACTCCCTCCGTTCCTAAAT 60.014 42.308 0.00 0.00 0.00 1.40
4482 8054 7.179694 CCATAATACTCCCTCCGTTCCTAAATA 59.820 40.741 0.00 0.00 0.00 1.40
4483 8055 8.759782 CATAATACTCCCTCCGTTCCTAAATAT 58.240 37.037 0.00 0.00 0.00 1.28
4484 8056 7.628501 AATACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
4485 8057 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4486 8058 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4487 8059 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4488 8060 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4489 8061 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4490 8062 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4491 8063 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4492 8064 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
4493 8065 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
4494 8066 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
4495 8067 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
4496 8068 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
4509 8081 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
4510 8082 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
4511 8083 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
4512 8084 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
4513 8085 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
4514 8086 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
4515 8087 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
4516 8088 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
4517 8089 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
4519 8091 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
4520 8092 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
4521 8093 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
4522 8094 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
4523 8095 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
4524 8096 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
4525 8097 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
4526 8098 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
4527 8099 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
4528 8100 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
4529 8101 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
4530 8102 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
4531 8103 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
4532 8104 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
4533 8105 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
4534 8106 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
4535 8107 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
4536 8108 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
4537 8109 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
4538 8110 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
4539 8111 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
4540 8112 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
4541 8113 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
4542 8114 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
4543 8115 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
4576 8148 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
4578 8150 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
4579 8151 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
4580 8152 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
4581 8153 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
4582 8154 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
4583 8155 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
4584 8156 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
4585 8157 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
4586 8158 4.395959 TCCGTATGTGGTAGTCCATTTC 57.604 45.455 0.00 0.00 46.20 2.17
4587 8159 3.770388 TCCGTATGTGGTAGTCCATTTCA 59.230 43.478 0.00 0.00 46.20 2.69
4588 8160 4.223255 TCCGTATGTGGTAGTCCATTTCAA 59.777 41.667 0.00 0.00 46.20 2.69
4589 8161 5.104693 TCCGTATGTGGTAGTCCATTTCAAT 60.105 40.000 0.00 0.00 46.20 2.57
4590 8162 5.236478 CCGTATGTGGTAGTCCATTTCAATC 59.764 44.000 0.00 0.00 46.20 2.67
4591 8163 6.049149 CGTATGTGGTAGTCCATTTCAATCT 58.951 40.000 0.00 0.00 46.20 2.40
4592 8164 6.538742 CGTATGTGGTAGTCCATTTCAATCTT 59.461 38.462 0.00 0.00 46.20 2.40
4593 8165 7.065803 CGTATGTGGTAGTCCATTTCAATCTTT 59.934 37.037 0.00 0.00 46.20 2.52
4594 8166 9.391006 GTATGTGGTAGTCCATTTCAATCTTTA 57.609 33.333 0.00 0.00 46.20 1.85
4595 8167 8.877864 ATGTGGTAGTCCATTTCAATCTTTAA 57.122 30.769 0.00 0.00 46.20 1.52
4596 8168 8.698973 TGTGGTAGTCCATTTCAATCTTTAAA 57.301 30.769 0.00 0.00 46.20 1.52
4597 8169 9.137459 TGTGGTAGTCCATTTCAATCTTTAAAA 57.863 29.630 0.00 0.00 46.20 1.52
4598 8170 9.974980 GTGGTAGTCCATTTCAATCTTTAAAAA 57.025 29.630 0.00 0.00 46.20 1.94
4620 8192 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
4621 8193 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
5158 8730 8.507524 AGTCTTGCTAAAAGAAAAAGTACACT 57.492 30.769 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 100 1.416401 TGCTATACTACTTGCCAGGCC 59.584 52.381 9.64 0.00 0.00 5.19
123 125 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
124 126 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
125 127 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
126 128 9.819267 AGAAAGACTTATATTTAGAAACGGAGG 57.181 33.333 0.00 0.00 0.00 4.30
158 160 9.478768 TGTTTCGTATGTAGTCACTTATTGAAA 57.521 29.630 0.00 0.00 35.39 2.69
159 161 9.478768 TTGTTTCGTATGTAGTCACTTATTGAA 57.521 29.630 0.00 0.00 35.39 2.69
160 162 9.478768 TTTGTTTCGTATGTAGTCACTTATTGA 57.521 29.630 0.00 0.00 0.00 2.57
164 166 9.478768 TCATTTTGTTTCGTATGTAGTCACTTA 57.521 29.630 0.00 0.00 0.00 2.24
165 167 8.373048 TCATTTTGTTTCGTATGTAGTCACTT 57.627 30.769 0.00 0.00 0.00 3.16
166 168 7.956420 TCATTTTGTTTCGTATGTAGTCACT 57.044 32.000 0.00 0.00 0.00 3.41
167 169 9.051027 CATTCATTTTGTTTCGTATGTAGTCAC 57.949 33.333 0.00 0.00 0.00 3.67
168 170 8.994170 TCATTCATTTTGTTTCGTATGTAGTCA 58.006 29.630 0.00 0.00 0.00 3.41
169 171 9.820229 TTCATTCATTTTGTTTCGTATGTAGTC 57.180 29.630 0.00 0.00 0.00 2.59
177 179 9.528018 AGTGTAAATTCATTCATTTTGTTTCGT 57.472 25.926 0.00 0.00 0.00 3.85
178 180 9.993881 GAGTGTAAATTCATTCATTTTGTTTCG 57.006 29.630 0.00 0.00 0.00 3.46
209 211 9.244292 ACAAGATACGGATGTATGTAGACATAT 57.756 33.333 5.69 0.00 41.37 1.78
210 212 8.631480 ACAAGATACGGATGTATGTAGACATA 57.369 34.615 0.00 0.00 41.37 2.29
211 213 7.526142 ACAAGATACGGATGTATGTAGACAT 57.474 36.000 0.08 0.08 41.37 3.06
212 214 6.954487 ACAAGATACGGATGTATGTAGACA 57.046 37.500 0.00 0.00 41.37 3.41
213 215 8.097078 ACTACAAGATACGGATGTATGTAGAC 57.903 38.462 22.37 0.00 40.69 2.59
214 216 7.389884 GGACTACAAGATACGGATGTATGTAGA 59.610 40.741 22.37 0.97 40.69 2.59
215 217 7.174426 TGGACTACAAGATACGGATGTATGTAG 59.826 40.741 17.68 17.68 42.27 2.74
216 218 6.999871 TGGACTACAAGATACGGATGTATGTA 59.000 38.462 0.00 0.00 41.37 2.29
217 219 5.831525 TGGACTACAAGATACGGATGTATGT 59.168 40.000 0.00 0.00 41.37 2.29
218 220 6.327279 TGGACTACAAGATACGGATGTATG 57.673 41.667 0.00 0.00 41.37 2.39
219 221 7.232737 TGAATGGACTACAAGATACGGATGTAT 59.767 37.037 0.00 0.00 43.97 2.29
220 222 6.548251 TGAATGGACTACAAGATACGGATGTA 59.452 38.462 0.00 0.00 34.45 2.29
221 223 5.362717 TGAATGGACTACAAGATACGGATGT 59.637 40.000 0.00 0.00 0.00 3.06
222 224 5.842907 TGAATGGACTACAAGATACGGATG 58.157 41.667 0.00 0.00 0.00 3.51
223 225 6.479972 TTGAATGGACTACAAGATACGGAT 57.520 37.500 0.00 0.00 0.00 4.18
224 226 5.925506 TTGAATGGACTACAAGATACGGA 57.074 39.130 0.00 0.00 0.00 4.69
225 227 6.978343 TTTTGAATGGACTACAAGATACGG 57.022 37.500 0.00 0.00 0.00 4.02
226 228 7.974675 ACATTTTGAATGGACTACAAGATACG 58.025 34.615 5.73 0.00 0.00 3.06
227 229 9.167311 AGACATTTTGAATGGACTACAAGATAC 57.833 33.333 5.73 0.00 0.00 2.24
229 231 9.739276 TTAGACATTTTGAATGGACTACAAGAT 57.261 29.630 5.73 0.00 0.00 2.40
230 232 9.567776 TTTAGACATTTTGAATGGACTACAAGA 57.432 29.630 5.73 0.00 0.00 3.02
236 238 9.136323 AGTCTTTTTAGACATTTTGAATGGACT 57.864 29.630 7.92 6.70 41.02 3.85
237 239 9.750125 AAGTCTTTTTAGACATTTTGAATGGAC 57.250 29.630 7.92 0.00 41.02 4.02
255 257 9.392259 CCCTCCGTTTCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
256 258 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
257 259 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
258 260 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
259 261 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
260 262 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
261 263 7.813627 GCTACTCCCTCCGTTTCTAAATATAAG 59.186 40.741 0.00 0.00 0.00 1.73
262 264 7.508296 AGCTACTCCCTCCGTTTCTAAATATAA 59.492 37.037 0.00 0.00 0.00 0.98
263 265 7.008941 AGCTACTCCCTCCGTTTCTAAATATA 58.991 38.462 0.00 0.00 0.00 0.86
264 266 5.839606 AGCTACTCCCTCCGTTTCTAAATAT 59.160 40.000 0.00 0.00 0.00 1.28
265 267 5.206587 AGCTACTCCCTCCGTTTCTAAATA 58.793 41.667 0.00 0.00 0.00 1.40
266 268 4.031611 AGCTACTCCCTCCGTTTCTAAAT 58.968 43.478 0.00 0.00 0.00 1.40
267 269 3.438183 AGCTACTCCCTCCGTTTCTAAA 58.562 45.455 0.00 0.00 0.00 1.85
268 270 3.097342 AGCTACTCCCTCCGTTTCTAA 57.903 47.619 0.00 0.00 0.00 2.10
269 271 2.822707 AGCTACTCCCTCCGTTTCTA 57.177 50.000 0.00 0.00 0.00 2.10
270 272 2.822707 TAGCTACTCCCTCCGTTTCT 57.177 50.000 0.00 0.00 0.00 2.52
271 273 3.224269 AGATAGCTACTCCCTCCGTTTC 58.776 50.000 0.00 0.00 0.00 2.78
272 274 3.315880 AGATAGCTACTCCCTCCGTTT 57.684 47.619 0.00 0.00 0.00 3.60
273 275 3.224269 GAAGATAGCTACTCCCTCCGTT 58.776 50.000 0.00 0.00 0.00 4.44
274 276 2.811136 CGAAGATAGCTACTCCCTCCGT 60.811 54.545 0.00 0.00 0.00 4.69
275 277 1.807742 CGAAGATAGCTACTCCCTCCG 59.192 57.143 0.00 0.00 0.00 4.63
276 278 2.866351 ACGAAGATAGCTACTCCCTCC 58.134 52.381 0.00 0.00 0.00 4.30
277 279 7.684937 TTTATACGAAGATAGCTACTCCCTC 57.315 40.000 0.00 0.00 0.00 4.30
278 280 9.924010 ATATTTATACGAAGATAGCTACTCCCT 57.076 33.333 0.00 0.00 0.00 4.20
339 347 1.484653 TGCTGGCATGGTCGTAATACT 59.515 47.619 0.00 0.00 0.00 2.12
348 356 0.625316 TTAGTGGATGCTGGCATGGT 59.375 50.000 13.04 0.00 36.70 3.55
481 492 2.871096 ACTTTGCGGAAGGGTAATCA 57.129 45.000 3.43 0.00 39.79 2.57
487 498 4.676986 GCCTTAATTTACTTTGCGGAAGGG 60.677 45.833 3.43 0.00 39.79 3.95
490 501 4.278669 TGTGCCTTAATTTACTTTGCGGAA 59.721 37.500 0.00 0.00 0.00 4.30
491 502 3.821600 TGTGCCTTAATTTACTTTGCGGA 59.178 39.130 0.00 0.00 0.00 5.54
492 503 4.167554 TGTGCCTTAATTTACTTTGCGG 57.832 40.909 0.00 0.00 0.00 5.69
493 504 6.400940 CCATTTGTGCCTTAATTTACTTTGCG 60.401 38.462 0.00 0.00 0.00 4.85
494 505 6.648725 TCCATTTGTGCCTTAATTTACTTTGC 59.351 34.615 0.00 0.00 0.00 3.68
495 506 8.087750 TCTCCATTTGTGCCTTAATTTACTTTG 58.912 33.333 0.00 0.00 0.00 2.77
496 507 8.189119 TCTCCATTTGTGCCTTAATTTACTTT 57.811 30.769 0.00 0.00 0.00 2.66
497 508 7.775053 TCTCCATTTGTGCCTTAATTTACTT 57.225 32.000 0.00 0.00 0.00 2.24
498 509 7.577616 GCTTCTCCATTTGTGCCTTAATTTACT 60.578 37.037 0.00 0.00 0.00 2.24
499 510 6.531594 GCTTCTCCATTTGTGCCTTAATTTAC 59.468 38.462 0.00 0.00 0.00 2.01
500 511 6.210385 TGCTTCTCCATTTGTGCCTTAATTTA 59.790 34.615 0.00 0.00 0.00 1.40
501 512 5.011943 TGCTTCTCCATTTGTGCCTTAATTT 59.988 36.000 0.00 0.00 0.00 1.82
502 513 4.527816 TGCTTCTCCATTTGTGCCTTAATT 59.472 37.500 0.00 0.00 0.00 1.40
503 514 4.088634 TGCTTCTCCATTTGTGCCTTAAT 58.911 39.130 0.00 0.00 0.00 1.40
504 515 3.495331 TGCTTCTCCATTTGTGCCTTAA 58.505 40.909 0.00 0.00 0.00 1.85
505 516 3.153369 TGCTTCTCCATTTGTGCCTTA 57.847 42.857 0.00 0.00 0.00 2.69
543 4109 6.317391 GGGATATTGCTAATGCTAGATGTTCC 59.683 42.308 0.00 0.00 40.48 3.62
556 4122 7.255906 CCTGCATACAAAATGGGATATTGCTAA 60.256 37.037 0.00 0.00 0.00 3.09
566 4132 0.102844 CGGCCTGCATACAAAATGGG 59.897 55.000 0.00 0.00 0.00 4.00
595 4161 1.956170 CAGCGTGAAAGCAGACCGT 60.956 57.895 0.00 0.00 40.15 4.83
987 4554 0.685458 GCCCCATTGATGCAGGAAGT 60.685 55.000 0.00 0.00 0.00 3.01
1040 4607 3.287867 AGCACCATAGGATGAAACAGG 57.712 47.619 0.00 0.00 0.00 4.00
1122 4689 3.213206 TCCAGTGCACCATAATCATCC 57.787 47.619 14.63 0.00 0.00 3.51
1159 4726 2.202987 GCTGATGCCTCCGGTGAG 60.203 66.667 4.76 0.00 38.42 3.51
1203 4770 1.529244 ACAGCAGTTGGCCACTTCC 60.529 57.895 3.88 0.00 46.50 3.46
1234 4801 3.274586 CCCGGCATCGCATGTGAG 61.275 66.667 15.24 8.04 34.56 3.51
1251 4818 3.083997 AGCCTGATGACCCGACCC 61.084 66.667 0.00 0.00 0.00 4.46
1254 4821 2.038813 TCCAGCCTGATGACCCGA 59.961 61.111 0.00 0.00 0.00 5.14
1296 4863 3.317571 AGCGAAGGTGCCAGCTCT 61.318 61.111 0.00 0.00 36.17 4.09
1325 4892 0.326264 GTTGAGCCACTGGAGATGGT 59.674 55.000 0.00 0.00 39.63 3.55
1376 4943 3.650950 GCTGAAGGAGGGGTGCCA 61.651 66.667 0.00 0.00 0.00 4.92
1377 4944 3.334054 AGCTGAAGGAGGGGTGCC 61.334 66.667 0.00 0.00 0.00 5.01
1404 4971 2.483745 CTTACGTCGAGCCGCTGA 59.516 61.111 0.00 0.00 0.00 4.26
1458 5025 1.519455 CTCAATCACCGGGAGCGAC 60.519 63.158 6.32 0.00 0.00 5.19
1582 5149 4.453478 TGACTCACAGATGCTTGAATCAAC 59.547 41.667 0.00 0.00 0.00 3.18
1738 5305 9.199982 CTTCAGAAATTGCAACTTGAATATGTT 57.800 29.630 0.00 0.00 0.00 2.71
1835 5402 6.808704 GGAATTAAAAGAAATGTCCAGCTGAC 59.191 38.462 17.39 12.09 44.72 3.51
3114 6681 1.866601 GCAACAGACAAAACCATTGCC 59.133 47.619 0.00 0.00 37.14 4.52
3259 6826 5.356190 CACTGATAGTCAATGCCTTGTCATT 59.644 40.000 1.49 0.00 37.16 2.57
3402 6969 1.358787 TCCATCTGGCCAAAATCACCT 59.641 47.619 7.01 0.00 34.44 4.00
3909 7476 3.264193 TCCTCTTGCACATATCAACAGGT 59.736 43.478 0.00 0.00 33.23 4.00
4141 7708 2.754552 AGCTTCACTTTGTTGCTTCACA 59.245 40.909 0.00 0.00 0.00 3.58
4290 7857 3.942115 GAGGGGAGAAATTGAGTACAAGC 59.058 47.826 0.00 0.00 39.46 4.01
4464 8036 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4465 8037 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
4466 8038 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
4467 8039 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
4468 8040 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
4469 8041 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
4470 8042 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
4483 8055 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
4484 8056 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
4485 8057 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
4486 8058 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
4487 8059 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
4488 8060 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
4489 8061 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
4490 8062 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
4491 8063 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
4492 8064 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
4493 8065 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
4494 8066 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
4495 8067 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
4496 8068 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
4497 8069 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
4498 8070 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
4499 8071 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
4500 8072 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
4501 8073 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
4502 8074 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
4503 8075 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
4504 8076 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
4505 8077 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
4506 8078 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
4507 8079 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
4508 8080 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
4509 8081 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
4510 8082 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
4511 8083 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
4512 8084 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
4513 8085 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
4514 8086 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
4515 8087 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
4516 8088 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
4517 8089 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
4518 8090 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
4519 8091 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
4520 8092 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
4521 8093 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
4550 8122 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
4552 8124 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
4553 8125 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
4554 8126 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
4555 8127 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
4556 8128 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
4557 8129 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
4558 8130 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
4559 8131 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
4560 8132 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
4561 8133 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
4594 8166 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
4595 8167 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
4596 8168 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4597 8169 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4598 8170 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4599 8171 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4600 8172 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4601 8173 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4602 8174 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4603 8175 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
4604 8176 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
4605 8177 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
4606 8178 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
4607 8179 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
4608 8180 3.626729 CCTTCTACTCCCTCCGTTCCTAA 60.627 52.174 0.00 0.00 0.00 2.69
4609 8181 2.091994 CCTTCTACTCCCTCCGTTCCTA 60.092 54.545 0.00 0.00 0.00 2.94
4610 8182 1.342175 CCTTCTACTCCCTCCGTTCCT 60.342 57.143 0.00 0.00 0.00 3.36
4611 8183 1.112950 CCTTCTACTCCCTCCGTTCC 58.887 60.000 0.00 0.00 0.00 3.62
4612 8184 0.460722 GCCTTCTACTCCCTCCGTTC 59.539 60.000 0.00 0.00 0.00 3.95
4613 8185 0.252103 TGCCTTCTACTCCCTCCGTT 60.252 55.000 0.00 0.00 0.00 4.44
4614 8186 0.971447 GTGCCTTCTACTCCCTCCGT 60.971 60.000 0.00 0.00 0.00 4.69
4615 8187 0.970937 TGTGCCTTCTACTCCCTCCG 60.971 60.000 0.00 0.00 0.00 4.63
4616 8188 1.501582 ATGTGCCTTCTACTCCCTCC 58.498 55.000 0.00 0.00 0.00 4.30
4617 8189 4.755266 TTTATGTGCCTTCTACTCCCTC 57.245 45.455 0.00 0.00 0.00 4.30
4618 8190 5.717119 AATTTATGTGCCTTCTACTCCCT 57.283 39.130 0.00 0.00 0.00 4.20
4619 8191 5.652452 ACAAATTTATGTGCCTTCTACTCCC 59.348 40.000 0.00 0.00 30.82 4.30
4620 8192 6.555315 CACAAATTTATGTGCCTTCTACTCC 58.445 40.000 0.00 0.00 43.67 3.85
4815 8387 3.757493 ACGTTTGACTTCTACGATCTCCT 59.243 43.478 0.00 0.00 38.56 3.69
4959 8531 9.905713 TTAAAACATCTTCCATAGCTTCATACT 57.094 29.630 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.