Multiple sequence alignment - TraesCS7A01G225200

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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 TraesCS7A01G225200 chr7A 100.000 2474 0 0 1 2474 194457587 194460060 0.000000e+00 4569.0
1 TraesCS7A01G225200 chr7B 90.925 1664 85 33 398 2030 334302111 334300483 0.000000e+00 2176.0
2 TraesCS7A01G225200 chr7B 91.061 179 16 0 2072 2250 334300141 334299963 2.460000e-60 243.0
3 TraesCS7A01G225200 chr7B 92.254 142 9 2 2235 2374 118126348 118126207 1.500000e-47 200.0
4 TraesCS7A01G225200 chr7B 92.029 138 10 1 2240 2376 635489335 635489472 2.510000e-45 193.0
5 TraesCS7A01G225200 chr7B 90.476 147 10 4 2239 2383 395246215 395246359 9.030000e-45 191.0
6 TraesCS7A01G225200 chr7B 96.341 82 3 0 2393 2474 334299955 334299874 4.290000e-28 135.0
7 TraesCS7A01G225200 chr7B 90.217 92 8 1 31 122 334304475 334304385 4.320000e-23 119.0
8 TraesCS7A01G225200 chr7D 92.324 1394 58 23 398 1756 189311719 189310340 0.000000e+00 1936.0
9 TraesCS7A01G225200 chr7D 95.122 82 4 0 2393 2474 189259569 189259488 2.000000e-26 130.0
10 TraesCS7A01G225200 chr7D 94.118 68 4 0 1 68 189320308 189320241 1.210000e-18 104.0
11 TraesCS7A01G225200 chr2A 93.431 137 8 1 2248 2384 172348834 172348699 4.170000e-48 202.0
12 TraesCS7A01G225200 chr4B 93.893 131 8 0 2245 2375 32425832 32425702 5.400000e-47 198.0
13 TraesCS7A01G225200 chr4B 93.798 129 8 0 2247 2375 653214419 653214291 6.980000e-46 195.0
14 TraesCS7A01G225200 chr2B 92.593 135 10 0 2240 2374 245013899 245013765 6.980000e-46 195.0
15 TraesCS7A01G225200 chr1B 89.865 148 11 4 2240 2385 653879238 653879093 1.170000e-43 187.0
16 TraesCS7A01G225200 chr5A 88.312 154 14 3 2241 2394 332786308 332786457 5.440000e-42 182.0
17 TraesCS7A01G225200 chr1D 81.197 117 15 6 1788 1901 285435777 285435665 1.220000e-13 87.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G225200 chr7A 194457587 194460060 2473 False 4569.00 4569 100.000 1 2474 1 chr7A.!!$F1 2473
1 TraesCS7A01G225200 chr7B 334299874 334304475 4601 True 668.25 2176 92.136 31 2474 4 chr7B.!!$R2 2443
2 TraesCS7A01G225200 chr7D 189310340 189311719 1379 True 1936.00 1936 92.324 398 1756 1 chr7D.!!$R2 1358

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
236 283 0.109153 GGTAACCGGGGTGTTTCTGT 59.891 55.0 6.32 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 3769 0.171007 ATTAAGTGGCACGTGCATGC 59.829 50.0 38.6 26.84 45.34 4.06 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
47 48 7.865706 ATATCATTAGCCGTTTTCTTGTCTT 57.134 32.000 0.00 0.00 0.00 3.01
83 84 0.699577 TTTCCACCCCCTGTTCCTCA 60.700 55.000 0.00 0.00 0.00 3.86
85 86 1.847968 CCACCCCCTGTTCCTCACT 60.848 63.158 0.00 0.00 0.00 3.41
94 95 3.578716 CCCTGTTCCTCACTTTCTCTGTA 59.421 47.826 0.00 0.00 0.00 2.74
101 102 4.041567 TCCTCACTTTCTCTGTATGCCAAA 59.958 41.667 0.00 0.00 0.00 3.28
102 103 4.946157 CCTCACTTTCTCTGTATGCCAAAT 59.054 41.667 0.00 0.00 0.00 2.32
109 110 4.033009 TCTCTGTATGCCAAATGAGGAGA 58.967 43.478 0.00 0.00 0.00 3.71
119 120 4.712476 CCAAATGAGGAGAGGTTGATAGG 58.288 47.826 0.00 0.00 0.00 2.57
122 123 6.284459 CAAATGAGGAGAGGTTGATAGGTAC 58.716 44.000 0.00 0.00 0.00 3.34
123 124 3.912248 TGAGGAGAGGTTGATAGGTACC 58.088 50.000 2.73 2.73 34.54 3.34
125 126 3.892588 GAGGAGAGGTTGATAGGTACCTG 59.107 52.174 25.33 0.00 44.65 4.00
126 127 2.966516 GGAGAGGTTGATAGGTACCTGG 59.033 54.545 25.33 0.00 44.65 4.45
131 178 2.706190 GGTTGATAGGTACCTGGATGCT 59.294 50.000 25.33 0.00 0.00 3.79
140 187 4.039124 AGGTACCTGGATGCTTTTTGTTTG 59.961 41.667 15.42 0.00 0.00 2.93
158 205 3.449746 TTGTGCTGGCTTAAACCCTAT 57.550 42.857 0.00 0.00 0.00 2.57
180 227 2.643933 GCCAACAGGCTTGAAATCTC 57.356 50.000 1.40 0.00 45.21 2.75
184 231 3.305608 CCAACAGGCTTGAAATCTCAACC 60.306 47.826 1.40 0.00 36.62 3.77
189 236 5.221322 ACAGGCTTGAAATCTCAACCTTTTC 60.221 40.000 1.40 0.00 39.26 2.29
190 237 4.895297 AGGCTTGAAATCTCAACCTTTTCA 59.105 37.500 0.00 0.00 38.70 2.69
194 241 6.469782 TTGAAATCTCAACCTTTTCAAGCT 57.530 33.333 6.08 0.00 41.75 3.74
196 243 6.275335 TGAAATCTCAACCTTTTCAAGCTTG 58.725 36.000 20.81 20.81 36.66 4.01
197 244 4.861102 ATCTCAACCTTTTCAAGCTTGG 57.139 40.909 25.73 12.24 0.00 3.61
198 245 3.897239 TCTCAACCTTTTCAAGCTTGGA 58.103 40.909 25.73 15.86 0.00 3.53
199 246 4.473444 TCTCAACCTTTTCAAGCTTGGAT 58.527 39.130 25.73 0.00 0.00 3.41
200 247 4.895297 TCTCAACCTTTTCAAGCTTGGATT 59.105 37.500 25.73 6.04 0.00 3.01
201 248 5.010012 TCTCAACCTTTTCAAGCTTGGATTC 59.990 40.000 25.73 0.00 0.00 2.52
202 249 4.039124 TCAACCTTTTCAAGCTTGGATTCC 59.961 41.667 25.73 0.00 0.00 3.01
203 250 3.575805 ACCTTTTCAAGCTTGGATTCCA 58.424 40.909 25.73 0.00 0.00 3.53
204 251 3.966665 ACCTTTTCAAGCTTGGATTCCAA 59.033 39.130 25.73 17.09 41.69 3.53
205 252 4.408596 ACCTTTTCAAGCTTGGATTCCAAA 59.591 37.500 25.73 14.53 43.44 3.28
206 253 4.751600 CCTTTTCAAGCTTGGATTCCAAAC 59.248 41.667 25.73 14.35 43.44 2.93
207 254 5.453762 CCTTTTCAAGCTTGGATTCCAAACT 60.454 40.000 25.73 16.35 43.44 2.66
208 255 5.612725 TTTCAAGCTTGGATTCCAAACTT 57.387 34.783 25.73 22.66 46.72 2.66
209 256 5.612725 TTCAAGCTTGGATTCCAAACTTT 57.387 34.783 24.81 14.24 44.42 2.66
210 257 5.612725 TCAAGCTTGGATTCCAAACTTTT 57.387 34.783 24.81 8.76 44.42 2.27
211 258 6.723298 TCAAGCTTGGATTCCAAACTTTTA 57.277 33.333 24.81 16.15 44.42 1.52
212 259 7.301868 TCAAGCTTGGATTCCAAACTTTTAT 57.698 32.000 24.81 7.84 44.42 1.40
213 260 7.378181 TCAAGCTTGGATTCCAAACTTTTATC 58.622 34.615 24.81 6.83 44.42 1.75
214 261 7.233348 TCAAGCTTGGATTCCAAACTTTTATCT 59.767 33.333 24.81 6.92 44.42 1.98
215 262 7.544804 AGCTTGGATTCCAAACTTTTATCTT 57.455 32.000 18.49 0.00 43.44 2.40
216 263 7.606349 AGCTTGGATTCCAAACTTTTATCTTC 58.394 34.615 18.49 0.00 43.44 2.87
217 264 6.528072 GCTTGGATTCCAAACTTTTATCTTCG 59.472 38.462 18.49 4.22 43.44 3.79
218 265 6.509418 TGGATTCCAAACTTTTATCTTCGG 57.491 37.500 1.94 0.00 0.00 4.30
219 266 6.007703 TGGATTCCAAACTTTTATCTTCGGT 58.992 36.000 1.94 0.00 0.00 4.69
220 267 7.169591 TGGATTCCAAACTTTTATCTTCGGTA 58.830 34.615 1.94 0.00 0.00 4.02
221 268 7.666388 TGGATTCCAAACTTTTATCTTCGGTAA 59.334 33.333 1.94 0.00 0.00 2.85
222 269 7.966753 GGATTCCAAACTTTTATCTTCGGTAAC 59.033 37.037 0.00 0.00 0.00 2.50
223 270 6.806388 TCCAAACTTTTATCTTCGGTAACC 57.194 37.500 0.00 0.00 0.00 2.85
233 280 3.970721 CGGTAACCGGGGTGTTTC 58.029 61.111 6.32 0.00 44.15 2.78
234 281 1.372307 CGGTAACCGGGGTGTTTCT 59.628 57.895 6.32 0.00 44.15 2.52
235 282 0.952010 CGGTAACCGGGGTGTTTCTG 60.952 60.000 6.32 0.00 44.15 3.02
236 283 0.109153 GGTAACCGGGGTGTTTCTGT 59.891 55.000 6.32 0.00 0.00 3.41
237 284 1.516161 GTAACCGGGGTGTTTCTGTC 58.484 55.000 6.32 0.00 0.00 3.51
238 285 0.397564 TAACCGGGGTGTTTCTGTCC 59.602 55.000 6.32 0.00 0.00 4.02
239 286 1.637724 AACCGGGGTGTTTCTGTCCA 61.638 55.000 6.32 0.00 0.00 4.02
240 287 1.599797 CCGGGGTGTTTCTGTCCAC 60.600 63.158 0.00 0.00 0.00 4.02
241 288 1.147376 CGGGGTGTTTCTGTCCACA 59.853 57.895 0.00 0.00 33.19 4.17
251 298 4.455533 TGTTTCTGTCCACAGCATGAATAC 59.544 41.667 0.00 0.00 43.46 1.89
255 302 3.749226 TGTCCACAGCATGAATACAACA 58.251 40.909 0.00 0.00 39.69 3.33
256 303 4.140536 TGTCCACAGCATGAATACAACAA 58.859 39.130 0.00 0.00 39.69 2.83
261 308 5.336610 CCACAGCATGAATACAACAAATCCA 60.337 40.000 0.00 0.00 39.69 3.41
267 314 6.477688 GCATGAATACAACAAATCCATTCCTG 59.522 38.462 0.00 0.00 0.00 3.86
268 315 7.549839 CATGAATACAACAAATCCATTCCTGT 58.450 34.615 0.00 0.00 0.00 4.00
275 322 7.661040 ACAACAAATCCATTCCTGTTTCTAAG 58.339 34.615 0.00 0.00 29.70 2.18
277 324 6.314917 ACAAATCCATTCCTGTTTCTAAGGT 58.685 36.000 0.00 0.00 36.14 3.50
280 327 3.835978 TCCATTCCTGTTTCTAAGGTCGA 59.164 43.478 0.00 0.00 36.14 4.20
281 328 4.285003 TCCATTCCTGTTTCTAAGGTCGAA 59.715 41.667 0.00 0.00 36.14 3.71
287 2137 2.289195 TGTTTCTAAGGTCGAATGCCGT 60.289 45.455 0.00 0.00 39.75 5.68
288 2138 3.056678 TGTTTCTAAGGTCGAATGCCGTA 60.057 43.478 0.00 0.00 39.75 4.02
305 2155 1.950909 CGTAGGGTTGCCTGACAAAAA 59.049 47.619 0.00 0.00 40.82 1.94
308 2158 1.970640 AGGGTTGCCTGACAAAAATCC 59.029 47.619 0.00 0.00 40.82 3.01
310 2160 2.368548 GGGTTGCCTGACAAAAATCCTT 59.631 45.455 0.00 0.00 40.82 3.36
311 2161 3.392882 GGTTGCCTGACAAAAATCCTTG 58.607 45.455 0.00 0.00 40.82 3.61
312 2162 3.069443 GGTTGCCTGACAAAAATCCTTGA 59.931 43.478 0.00 0.00 40.82 3.02
313 2163 4.301628 GTTGCCTGACAAAAATCCTTGAG 58.698 43.478 0.00 0.00 40.82 3.02
318 2350 6.267471 TGCCTGACAAAAATCCTTGAGTAAAT 59.733 34.615 0.00 0.00 0.00 1.40
355 2396 1.158434 TGGATTTACGACGCAAACCC 58.842 50.000 0.00 0.00 0.00 4.11
361 2402 2.752322 TACGACGCAAACCCTCACCG 62.752 60.000 0.00 0.00 0.00 4.94
374 2415 0.464735 CTCACCGAACCCAACAACCA 60.465 55.000 0.00 0.00 0.00 3.67
375 2416 0.464735 TCACCGAACCCAACAACCAG 60.465 55.000 0.00 0.00 0.00 4.00
376 2417 1.152839 ACCGAACCCAACAACCAGG 60.153 57.895 0.00 0.00 0.00 4.45
377 2418 1.152839 CCGAACCCAACAACCAGGT 60.153 57.895 0.00 0.00 34.60 4.00
378 2419 1.452145 CCGAACCCAACAACCAGGTG 61.452 60.000 0.00 0.00 33.05 4.00
391 2432 2.348411 CCAGGTGGTGTTCAACTTCT 57.652 50.000 0.00 0.00 41.45 2.85
393 2434 2.618709 CCAGGTGGTGTTCAACTTCTTC 59.381 50.000 0.00 0.00 41.45 2.87
394 2435 3.278574 CAGGTGGTGTTCAACTTCTTCA 58.721 45.455 0.00 0.00 41.45 3.02
395 2436 3.694072 CAGGTGGTGTTCAACTTCTTCAA 59.306 43.478 0.00 0.00 41.45 2.69
396 2437 3.694566 AGGTGGTGTTCAACTTCTTCAAC 59.305 43.478 0.00 0.00 41.45 3.18
434 2475 2.836372 TGATCTGACCACATCTTCAGCT 59.164 45.455 0.00 0.00 39.36 4.24
435 2476 2.756840 TCTGACCACATCTTCAGCTG 57.243 50.000 7.63 7.63 39.36 4.24
494 2542 2.032528 CGCACCAAAGAGCCTCCA 59.967 61.111 0.00 0.00 0.00 3.86
495 2543 2.328099 CGCACCAAAGAGCCTCCAC 61.328 63.158 0.00 0.00 0.00 4.02
496 2544 1.973812 GCACCAAAGAGCCTCCACC 60.974 63.158 0.00 0.00 0.00 4.61
497 2545 1.672356 CACCAAAGAGCCTCCACCG 60.672 63.158 0.00 0.00 0.00 4.94
499 2547 2.032528 CAAAGAGCCTCCACCGCA 59.967 61.111 0.00 0.00 0.00 5.69
737 2792 1.386525 CGCCATGTCCCCAAATCTGG 61.387 60.000 0.00 0.00 43.10 3.86
750 2805 3.612247 ATCTGGCGCCACACTCCAC 62.612 63.158 29.03 0.00 0.00 4.02
905 2960 3.414464 CAGCTCACAAGTACTACGTACG 58.586 50.000 15.01 15.01 43.05 3.67
924 2979 1.515631 CGTGTATACGTGTTGATCGGC 59.484 52.381 3.56 0.00 44.99 5.54
1024 3079 1.834263 GTGCCCAGGAGATCAAGTACT 59.166 52.381 0.00 0.00 0.00 2.73
1025 3080 2.237392 GTGCCCAGGAGATCAAGTACTT 59.763 50.000 1.12 1.12 0.00 2.24
1026 3081 2.237143 TGCCCAGGAGATCAAGTACTTG 59.763 50.000 26.60 26.60 41.71 3.16
1027 3082 2.237392 GCCCAGGAGATCAAGTACTTGT 59.763 50.000 29.83 19.45 41.16 3.16
1028 3083 3.451178 GCCCAGGAGATCAAGTACTTGTA 59.549 47.826 29.83 19.13 41.16 2.41
1029 3084 4.680975 GCCCAGGAGATCAAGTACTTGTAC 60.681 50.000 29.83 23.82 41.16 2.90
1161 3216 2.512515 CTGCTGGGCCGCTACTTC 60.513 66.667 18.47 0.00 0.00 3.01
1277 3335 0.884259 CCGGCAGTGTCACAATCACA 60.884 55.000 5.62 0.00 38.16 3.58
1288 3346 3.395702 AATCACAGGCGGCCGGTA 61.396 61.111 29.38 13.07 29.37 4.02
1455 3516 1.964891 CGGCTATGGGCAGCATCAG 60.965 63.158 2.96 0.00 43.67 2.90
1459 3520 0.536687 CTATGGGCAGCATCAGGTGG 60.537 60.000 0.00 0.00 43.34 4.61
1498 3559 2.036217 TCCACCCGTTGTGTACTGTAAG 59.964 50.000 0.00 0.00 43.85 2.34
1521 3582 3.414343 TAAATACGACGCGGCGCCT 62.414 57.895 37.74 20.29 33.86 5.52
1605 3677 1.757118 TGGTCGATCTGGATGTCCTTC 59.243 52.381 0.00 0.00 36.82 3.46
1611 3683 3.624861 CGATCTGGATGTCCTTCCTTTTG 59.375 47.826 0.09 0.00 36.68 2.44
1662 3739 1.678970 GGGGTTAGCTGGTGCAAGG 60.679 63.158 0.00 0.00 42.74 3.61
1672 3749 0.968405 TGGTGCAAGGAAAAGATGGC 59.032 50.000 0.00 0.00 0.00 4.40
1684 3761 4.354587 GAAAAGATGGCGGATTGATTGAC 58.645 43.478 0.00 0.00 0.00 3.18
1692 3769 0.734889 GGATTGATTGACCGGCACAG 59.265 55.000 0.00 0.00 0.00 3.66
1709 3786 1.302431 AGCATGCACGTGCCACTTA 60.302 52.632 35.72 18.87 46.19 2.24
1719 3796 5.047847 GCACGTGCCACTTAATCTATCTTA 58.952 41.667 30.12 0.00 34.31 2.10
1772 3849 4.320023 TCTGTTGAAAGCTGGCGTATTAA 58.680 39.130 0.00 0.00 0.00 1.40
1793 3870 1.126488 ATGATGGCCGATGAGACTGT 58.874 50.000 0.00 0.00 0.00 3.55
1826 3903 9.465985 GAGAGTAATTTAGCTAGTAACATGTCC 57.534 37.037 0.00 0.00 0.00 4.02
1827 3904 8.422566 AGAGTAATTTAGCTAGTAACATGTCCC 58.577 37.037 0.00 0.00 0.00 4.46
1828 3905 8.086143 AGTAATTTAGCTAGTAACATGTCCCA 57.914 34.615 0.00 0.00 0.00 4.37
1829 3906 8.545472 AGTAATTTAGCTAGTAACATGTCCCAA 58.455 33.333 0.00 0.00 0.00 4.12
1835 3912 7.380423 AGCTAGTAACATGTCCCAAATATCT 57.620 36.000 0.00 0.00 0.00 1.98
1836 3913 7.445945 AGCTAGTAACATGTCCCAAATATCTC 58.554 38.462 0.00 0.00 0.00 2.75
1844 3921 6.947733 ACATGTCCCAAATATCTCAAGACAAA 59.052 34.615 0.00 0.00 36.46 2.83
1850 3927 8.869109 TCCCAAATATCTCAAGACAAATTTGTT 58.131 29.630 24.02 11.79 42.43 2.83
1857 3934 6.491394 TCTCAAGACAAATTTGTTTACGTGG 58.509 36.000 24.02 13.12 42.43 4.94
1869 3946 6.615264 TTGTTTACGTGGCAAGTGTTAATA 57.385 33.333 16.47 3.77 0.00 0.98
1890 3967 9.653287 TTAATAAGAAGAGAGTTGTGTATGGTG 57.347 33.333 0.00 0.00 0.00 4.17
1892 3969 5.140747 AGAAGAGAGTTGTGTATGGTGAC 57.859 43.478 0.00 0.00 0.00 3.67
1948 4025 2.279741 GCAGTTTCGATGAGGTGCATA 58.720 47.619 0.00 0.00 37.34 3.14
1949 4026 2.677836 GCAGTTTCGATGAGGTGCATAA 59.322 45.455 0.00 0.00 37.34 1.90
1950 4027 3.126858 GCAGTTTCGATGAGGTGCATAAA 59.873 43.478 0.00 0.00 37.34 1.40
1951 4028 4.201950 GCAGTTTCGATGAGGTGCATAAAT 60.202 41.667 0.00 0.00 37.34 1.40
1952 4029 5.268544 CAGTTTCGATGAGGTGCATAAATG 58.731 41.667 0.00 0.00 37.34 2.32
1954 4043 5.647658 AGTTTCGATGAGGTGCATAAATGAA 59.352 36.000 0.00 0.00 37.34 2.57
1981 4070 8.840200 AAAAAGGACTGAGTATCCTACTATCA 57.160 34.615 0.00 0.00 46.36 2.15
1983 4072 9.440761 AAAAGGACTGAGTATCCTACTATCATT 57.559 33.333 0.00 0.00 46.36 2.57
1984 4073 8.415950 AAGGACTGAGTATCCTACTATCATTG 57.584 38.462 0.00 0.00 46.36 2.82
1985 4074 7.531317 AGGACTGAGTATCCTACTATCATTGT 58.469 38.462 0.00 0.00 45.18 2.71
1987 4076 9.469097 GGACTGAGTATCCTACTATCATTGTAT 57.531 37.037 0.00 0.00 39.59 2.29
1989 4078 9.168451 ACTGAGTATCCTACTATCATTGTATCG 57.832 37.037 0.00 0.00 39.59 2.92
2121 4510 3.945640 AAGTTACCTTCCACACCAGTT 57.054 42.857 0.00 0.00 0.00 3.16
2122 4511 3.487120 AGTTACCTTCCACACCAGTTC 57.513 47.619 0.00 0.00 0.00 3.01
2123 4512 2.775384 AGTTACCTTCCACACCAGTTCA 59.225 45.455 0.00 0.00 0.00 3.18
2133 4522 3.535561 CACACCAGTTCAAGAGTTCTGT 58.464 45.455 0.00 0.00 0.00 3.41
2135 4524 3.055094 ACACCAGTTCAAGAGTTCTGTGT 60.055 43.478 0.00 0.00 0.00 3.72
2138 4527 3.310774 CCAGTTCAAGAGTTCTGTGTGTG 59.689 47.826 0.00 0.00 0.00 3.82
2151 4540 7.141363 AGTTCTGTGTGTGAGAATATTTTTGC 58.859 34.615 0.00 0.00 32.18 3.68
2154 4543 6.012658 TGTGTGTGAGAATATTTTTGCCTC 57.987 37.500 0.00 0.00 0.00 4.70
2156 4545 6.088824 GTGTGTGAGAATATTTTTGCCTCTG 58.911 40.000 0.00 0.00 0.00 3.35
2190 4579 3.985877 GCACTGCATGTAGTGGCA 58.014 55.556 35.22 9.32 46.32 4.92
2216 4605 0.879090 GCCCGACGTTTCCAGAAAAT 59.121 50.000 0.00 0.00 31.33 1.82
2250 4639 0.314302 CGGCGTGGCTAGCTAATACT 59.686 55.000 15.72 0.00 34.52 2.12
2251 4640 1.666311 CGGCGTGGCTAGCTAATACTC 60.666 57.143 15.72 4.31 34.52 2.59
2252 4641 1.336980 GGCGTGGCTAGCTAATACTCC 60.337 57.143 15.72 9.49 34.52 3.85
2253 4642 1.336980 GCGTGGCTAGCTAATACTCCC 60.337 57.143 15.72 0.00 0.00 4.30
2254 4643 2.240279 CGTGGCTAGCTAATACTCCCT 58.760 52.381 15.72 0.00 0.00 4.20
2255 4644 2.628657 CGTGGCTAGCTAATACTCCCTT 59.371 50.000 15.72 0.00 0.00 3.95
2257 4646 3.641906 GTGGCTAGCTAATACTCCCTTCA 59.358 47.826 15.72 0.00 0.00 3.02
2258 4647 4.284746 GTGGCTAGCTAATACTCCCTTCAT 59.715 45.833 15.72 0.00 0.00 2.57
2259 4648 4.907875 TGGCTAGCTAATACTCCCTTCATT 59.092 41.667 15.72 0.00 0.00 2.57
2260 4649 5.012148 TGGCTAGCTAATACTCCCTTCATTC 59.988 44.000 15.72 0.00 0.00 2.67
2261 4650 5.164954 GCTAGCTAATACTCCCTTCATTCG 58.835 45.833 7.70 0.00 0.00 3.34
2262 4651 5.047943 GCTAGCTAATACTCCCTTCATTCGA 60.048 44.000 7.70 0.00 0.00 3.71
2263 4652 5.871396 AGCTAATACTCCCTTCATTCGAA 57.129 39.130 0.00 0.00 0.00 3.71
2264 4653 6.235231 AGCTAATACTCCCTTCATTCGAAA 57.765 37.500 0.00 0.00 0.00 3.46
2265 4654 6.650120 AGCTAATACTCCCTTCATTCGAAAA 58.350 36.000 0.00 0.00 0.00 2.29
2266 4655 7.283329 AGCTAATACTCCCTTCATTCGAAAAT 58.717 34.615 0.00 0.00 0.00 1.82
2267 4656 8.429641 AGCTAATACTCCCTTCATTCGAAAATA 58.570 33.333 0.00 0.00 0.00 1.40
2268 4657 8.496751 GCTAATACTCCCTTCATTCGAAAATAC 58.503 37.037 0.00 0.00 0.00 1.89
2269 4658 9.765795 CTAATACTCCCTTCATTCGAAAATACT 57.234 33.333 0.00 0.00 0.00 2.12
2271 4660 6.743575 ACTCCCTTCATTCGAAAATACTTG 57.256 37.500 0.00 0.00 0.00 3.16
2272 4661 6.238648 ACTCCCTTCATTCGAAAATACTTGT 58.761 36.000 0.00 0.00 0.00 3.16
2273 4662 6.371825 ACTCCCTTCATTCGAAAATACTTGTC 59.628 38.462 0.00 0.00 0.00 3.18
2274 4663 6.234920 TCCCTTCATTCGAAAATACTTGTCA 58.765 36.000 0.00 0.00 0.00 3.58
2275 4664 6.884295 TCCCTTCATTCGAAAATACTTGTCAT 59.116 34.615 0.00 0.00 0.00 3.06
2276 4665 7.065803 TCCCTTCATTCGAAAATACTTGTCATC 59.934 37.037 0.00 0.00 0.00 2.92
2277 4666 7.148255 CCCTTCATTCGAAAATACTTGTCATCA 60.148 37.037 0.00 0.00 0.00 3.07
2278 4667 8.236586 CCTTCATTCGAAAATACTTGTCATCAA 58.763 33.333 0.00 0.00 0.00 2.57
2279 4668 9.611284 CTTCATTCGAAAATACTTGTCATCAAA 57.389 29.630 0.00 0.00 32.87 2.69
2280 4669 9.958234 TTCATTCGAAAATACTTGTCATCAAAA 57.042 25.926 0.00 0.00 32.87 2.44
2283 4672 8.741101 TTCGAAAATACTTGTCATCAAAATGG 57.259 30.769 0.00 0.00 33.42 3.16
2284 4673 8.105097 TCGAAAATACTTGTCATCAAAATGGA 57.895 30.769 0.00 0.00 33.42 3.41
2285 4674 8.020819 TCGAAAATACTTGTCATCAAAATGGAC 58.979 33.333 0.00 0.00 33.42 4.02
2286 4675 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
2287 4676 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
2288 4677 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
2289 4678 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
2290 4679 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
2292 4681 8.145316 ACTTGTCATCAAAATGGACAAAAATG 57.855 30.769 7.70 0.11 34.98 2.32
2293 4682 7.986320 ACTTGTCATCAAAATGGACAAAAATGA 59.014 29.630 7.70 0.00 34.98 2.57
2294 4683 8.728337 TTGTCATCAAAATGGACAAAAATGAA 57.272 26.923 4.15 0.00 33.71 2.57
2295 4684 8.905660 TGTCATCAAAATGGACAAAAATGAAT 57.094 26.923 0.00 0.00 33.42 2.57
2296 4685 8.775527 TGTCATCAAAATGGACAAAAATGAATG 58.224 29.630 0.00 0.00 33.42 2.67
2297 4686 8.776470 GTCATCAAAATGGACAAAAATGAATGT 58.224 29.630 0.00 0.00 33.42 2.71
2298 4687 9.993454 TCATCAAAATGGACAAAAATGAATGTA 57.007 25.926 0.00 0.00 33.42 2.29
2353 4742 9.942850 CCCCTTTTATTTATTTTGATGACAAGT 57.057 29.630 0.00 0.00 37.32 3.16
2363 4752 9.834628 TTATTTTGATGACAAGTATTTTCGGAC 57.165 29.630 0.00 0.00 37.32 4.79
2364 4753 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2365 4754 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2366 4755 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2367 4756 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2368 4757 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2369 4758 2.564062 ACAAGTATTTTCGGACGGAGGA 59.436 45.455 0.00 0.00 0.00 3.71
2370 4759 3.007182 ACAAGTATTTTCGGACGGAGGAA 59.993 43.478 0.00 0.00 0.00 3.36
2371 4760 3.521947 AGTATTTTCGGACGGAGGAAG 57.478 47.619 0.00 0.00 0.00 3.46
2372 4761 2.830321 AGTATTTTCGGACGGAGGAAGT 59.170 45.455 0.00 0.00 0.00 3.01
2373 4762 4.019174 AGTATTTTCGGACGGAGGAAGTA 58.981 43.478 0.00 0.00 0.00 2.24
2374 4763 4.648307 AGTATTTTCGGACGGAGGAAGTAT 59.352 41.667 0.00 0.00 0.00 2.12
2375 4764 3.515330 TTTTCGGACGGAGGAAGTATC 57.485 47.619 0.00 0.00 0.00 2.24
2376 4765 2.431954 TTCGGACGGAGGAAGTATCT 57.568 50.000 0.00 0.00 0.00 1.98
2377 4766 3.565764 TTCGGACGGAGGAAGTATCTA 57.434 47.619 0.00 0.00 0.00 1.98
2378 4767 3.784511 TCGGACGGAGGAAGTATCTAT 57.215 47.619 0.00 0.00 0.00 1.98
2379 4768 3.672808 TCGGACGGAGGAAGTATCTATC 58.327 50.000 0.00 0.00 0.00 2.08
2380 4769 3.072038 TCGGACGGAGGAAGTATCTATCA 59.928 47.826 0.00 0.00 0.00 2.15
2381 4770 4.011023 CGGACGGAGGAAGTATCTATCAT 58.989 47.826 0.00 0.00 0.00 2.45
2382 4771 5.046087 TCGGACGGAGGAAGTATCTATCATA 60.046 44.000 0.00 0.00 0.00 2.15
2383 4772 5.294799 CGGACGGAGGAAGTATCTATCATAG 59.705 48.000 0.00 0.00 0.00 2.23
2384 4773 6.416415 GGACGGAGGAAGTATCTATCATAGA 58.584 44.000 0.00 0.00 39.50 1.98
2385 4774 6.316890 GGACGGAGGAAGTATCTATCATAGAC 59.683 46.154 0.00 0.00 37.69 2.59
2386 4775 5.875910 ACGGAGGAAGTATCTATCATAGACG 59.124 44.000 0.00 0.00 37.69 4.18
2387 4776 6.107343 CGGAGGAAGTATCTATCATAGACGA 58.893 44.000 0.00 0.00 37.69 4.20
2388 4777 6.594547 CGGAGGAAGTATCTATCATAGACGAA 59.405 42.308 0.00 0.00 37.69 3.85
2389 4778 7.413219 CGGAGGAAGTATCTATCATAGACGAAC 60.413 44.444 0.00 0.00 37.69 3.95
2390 4779 7.390996 GGAGGAAGTATCTATCATAGACGAACA 59.609 40.741 0.00 0.00 37.69 3.18
2391 4780 8.871629 AGGAAGTATCTATCATAGACGAACAT 57.128 34.615 0.00 0.00 37.69 2.71
2410 4799 9.049523 ACGAACATAGACGAACAGTATAATCTA 57.950 33.333 0.00 0.00 29.53 1.98
2461 4850 3.497118 TCACACTTGTTTTTGCTTGTCG 58.503 40.909 0.00 0.00 0.00 4.35
2468 4857 6.306837 CACTTGTTTTTGCTTGTCGTTCTTAA 59.693 34.615 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.998106 AGAAAACGGCTAATGATATAACAGTAT 57.002 29.630 0.00 0.00 0.00 2.12
16 17 9.826574 AAGAAAACGGCTAATGATATAACAGTA 57.173 29.630 0.00 0.00 0.00 2.74
17 18 8.612619 CAAGAAAACGGCTAATGATATAACAGT 58.387 33.333 0.00 0.00 0.00 3.55
18 19 8.612619 ACAAGAAAACGGCTAATGATATAACAG 58.387 33.333 0.00 0.00 0.00 3.16
19 20 8.500753 ACAAGAAAACGGCTAATGATATAACA 57.499 30.769 0.00 0.00 0.00 2.41
20 21 8.827677 AGACAAGAAAACGGCTAATGATATAAC 58.172 33.333 0.00 0.00 0.00 1.89
21 22 8.958119 AGACAAGAAAACGGCTAATGATATAA 57.042 30.769 0.00 0.00 0.00 0.98
22 23 8.958119 AAGACAAGAAAACGGCTAATGATATA 57.042 30.769 0.00 0.00 0.00 0.86
23 24 7.552687 TGAAGACAAGAAAACGGCTAATGATAT 59.447 33.333 0.00 0.00 0.00 1.63
24 25 6.876789 TGAAGACAAGAAAACGGCTAATGATA 59.123 34.615 0.00 0.00 0.00 2.15
25 26 5.705441 TGAAGACAAGAAAACGGCTAATGAT 59.295 36.000 0.00 0.00 0.00 2.45
26 27 5.060506 TGAAGACAAGAAAACGGCTAATGA 58.939 37.500 0.00 0.00 0.00 2.57
27 28 5.356882 TGAAGACAAGAAAACGGCTAATG 57.643 39.130 0.00 0.00 0.00 1.90
28 29 5.298276 TGTTGAAGACAAGAAAACGGCTAAT 59.702 36.000 0.00 0.00 36.64 1.73
29 30 4.636648 TGTTGAAGACAAGAAAACGGCTAA 59.363 37.500 0.00 0.00 36.64 3.09
47 48 4.633565 GTGGAAATTGGTTTGCTTTGTTGA 59.366 37.500 0.00 0.00 36.70 3.18
83 84 4.946157 CCTCATTTGGCATACAGAGAAAGT 59.054 41.667 9.69 0.00 0.00 2.66
85 86 5.045651 TCTCCTCATTTGGCATACAGAGAAA 60.046 40.000 9.69 0.00 0.00 2.52
94 95 2.309755 TCAACCTCTCCTCATTTGGCAT 59.690 45.455 0.00 0.00 0.00 4.40
101 102 4.171044 AGGTACCTATCAACCTCTCCTCAT 59.829 45.833 14.41 0.00 42.60 2.90
102 103 3.532232 AGGTACCTATCAACCTCTCCTCA 59.468 47.826 14.41 0.00 42.60 3.86
119 120 4.744631 CACAAACAAAAAGCATCCAGGTAC 59.255 41.667 0.00 0.00 0.00 3.34
122 123 2.545106 GCACAAACAAAAAGCATCCAGG 59.455 45.455 0.00 0.00 0.00 4.45
123 124 3.246699 CAGCACAAACAAAAAGCATCCAG 59.753 43.478 0.00 0.00 0.00 3.86
125 126 2.545106 CCAGCACAAACAAAAAGCATCC 59.455 45.455 0.00 0.00 0.00 3.51
126 127 2.032636 GCCAGCACAAACAAAAAGCATC 60.033 45.455 0.00 0.00 0.00 3.91
131 178 4.393371 GGTTTAAGCCAGCACAAACAAAAA 59.607 37.500 16.16 0.00 33.53 1.94
140 187 3.315470 GCTAATAGGGTTTAAGCCAGCAC 59.685 47.826 15.91 0.00 38.48 4.40
184 231 5.912360 GTTTGGAATCCAAGCTTGAAAAG 57.088 39.130 28.05 10.97 44.84 2.27
192 239 6.528072 CGAAGATAAAAGTTTGGAATCCAAGC 59.472 38.462 19.33 19.33 44.84 4.01
193 240 7.029563 CCGAAGATAAAAGTTTGGAATCCAAG 58.970 38.462 14.96 0.00 44.84 3.61
194 241 6.492087 ACCGAAGATAAAAGTTTGGAATCCAA 59.508 34.615 11.23 11.23 42.29 3.53
196 243 6.510879 ACCGAAGATAAAAGTTTGGAATCC 57.489 37.500 0.00 0.00 32.20 3.01
197 244 7.966753 GGTTACCGAAGATAAAAGTTTGGAATC 59.033 37.037 0.00 0.00 32.20 2.52
198 245 7.823665 GGTTACCGAAGATAAAAGTTTGGAAT 58.176 34.615 0.00 0.00 32.20 3.01
199 246 7.205737 GGTTACCGAAGATAAAAGTTTGGAA 57.794 36.000 0.00 0.00 32.20 3.53
200 247 6.806388 GGTTACCGAAGATAAAAGTTTGGA 57.194 37.500 0.00 0.00 32.20 3.53
217 264 0.109153 ACAGAAACACCCCGGTTACC 59.891 55.000 0.00 0.00 0.00 2.85
218 265 1.516161 GACAGAAACACCCCGGTTAC 58.484 55.000 0.00 0.00 0.00 2.50
219 266 0.397564 GGACAGAAACACCCCGGTTA 59.602 55.000 0.00 0.00 0.00 2.85
220 267 1.149854 GGACAGAAACACCCCGGTT 59.850 57.895 0.00 0.00 0.00 4.44
221 268 2.073716 TGGACAGAAACACCCCGGT 61.074 57.895 0.00 0.00 0.00 5.28
222 269 1.599797 GTGGACAGAAACACCCCGG 60.600 63.158 0.00 0.00 0.00 5.73
223 270 0.884704 CTGTGGACAGAAACACCCCG 60.885 60.000 0.04 0.00 46.59 5.73
224 271 1.172812 GCTGTGGACAGAAACACCCC 61.173 60.000 11.06 0.00 46.59 4.95
225 272 0.465460 TGCTGTGGACAGAAACACCC 60.465 55.000 11.06 0.00 46.59 4.61
226 273 1.267806 CATGCTGTGGACAGAAACACC 59.732 52.381 11.06 0.00 46.59 4.16
227 274 2.221169 TCATGCTGTGGACAGAAACAC 58.779 47.619 11.06 0.00 46.59 3.32
228 275 2.636647 TCATGCTGTGGACAGAAACA 57.363 45.000 11.06 0.00 46.59 2.83
229 276 4.455533 TGTATTCATGCTGTGGACAGAAAC 59.544 41.667 11.06 0.00 46.59 2.78
230 277 4.650734 TGTATTCATGCTGTGGACAGAAA 58.349 39.130 11.06 0.00 46.59 2.52
231 278 4.284829 TGTATTCATGCTGTGGACAGAA 57.715 40.909 11.06 0.00 46.59 3.02
232 279 3.979101 TGTATTCATGCTGTGGACAGA 57.021 42.857 11.06 0.00 46.59 3.41
233 280 3.752747 TGTTGTATTCATGCTGTGGACAG 59.247 43.478 2.19 2.19 46.40 3.51
234 281 3.749226 TGTTGTATTCATGCTGTGGACA 58.251 40.909 0.00 0.00 0.00 4.02
235 282 4.764679 TTGTTGTATTCATGCTGTGGAC 57.235 40.909 0.00 0.00 0.00 4.02
236 283 5.105797 GGATTTGTTGTATTCATGCTGTGGA 60.106 40.000 0.00 0.00 0.00 4.02
237 284 5.104374 GGATTTGTTGTATTCATGCTGTGG 58.896 41.667 0.00 0.00 0.00 4.17
238 285 5.712004 TGGATTTGTTGTATTCATGCTGTG 58.288 37.500 0.00 0.00 0.00 3.66
239 286 5.981088 TGGATTTGTTGTATTCATGCTGT 57.019 34.783 0.00 0.00 0.00 4.40
240 287 6.477688 GGAATGGATTTGTTGTATTCATGCTG 59.522 38.462 0.00 0.00 31.19 4.41
241 288 6.381994 AGGAATGGATTTGTTGTATTCATGCT 59.618 34.615 0.00 0.00 31.19 3.79
251 298 7.092716 CCTTAGAAACAGGAATGGATTTGTTG 58.907 38.462 0.00 0.00 34.28 3.33
255 302 5.648092 CGACCTTAGAAACAGGAATGGATTT 59.352 40.000 0.00 0.00 35.14 2.17
256 303 5.045869 TCGACCTTAGAAACAGGAATGGATT 60.046 40.000 0.00 0.00 35.14 3.01
261 308 4.636206 GCATTCGACCTTAGAAACAGGAAT 59.364 41.667 0.00 0.00 35.14 3.01
267 314 2.344025 ACGGCATTCGACCTTAGAAAC 58.656 47.619 0.00 0.00 42.43 2.78
268 315 2.754946 ACGGCATTCGACCTTAGAAA 57.245 45.000 0.00 0.00 42.43 2.52
275 322 1.087771 CAACCCTACGGCATTCGACC 61.088 60.000 0.00 0.00 42.43 4.79
277 324 1.448893 GCAACCCTACGGCATTCGA 60.449 57.895 0.00 0.00 42.43 3.71
280 327 1.378514 CAGGCAACCCTACGGCATT 60.379 57.895 0.00 0.00 40.33 3.56
281 328 2.272146 CAGGCAACCCTACGGCAT 59.728 61.111 0.00 0.00 40.33 4.40
287 2137 3.161866 GGATTTTTGTCAGGCAACCCTA 58.838 45.455 0.00 0.00 40.33 3.53
288 2138 1.970640 GGATTTTTGTCAGGCAACCCT 59.029 47.619 0.00 0.00 44.25 4.34
324 2356 6.183360 GCGTCGTAAATCCAAGTCAAGAATAA 60.183 38.462 0.00 0.00 0.00 1.40
327 2359 3.430895 GCGTCGTAAATCCAAGTCAAGAA 59.569 43.478 0.00 0.00 0.00 2.52
330 2362 2.756829 TGCGTCGTAAATCCAAGTCAA 58.243 42.857 0.00 0.00 0.00 3.18
333 2365 2.224784 GGTTTGCGTCGTAAATCCAAGT 59.775 45.455 11.67 0.00 0.00 3.16
339 2371 1.802365 GTGAGGGTTTGCGTCGTAAAT 59.198 47.619 11.67 0.00 0.00 1.40
355 2396 0.464735 TGGTTGTTGGGTTCGGTGAG 60.465 55.000 0.00 0.00 0.00 3.51
361 2402 2.425562 CCACCTGGTTGTTGGGTTC 58.574 57.895 0.00 0.00 0.00 3.62
374 2415 3.644966 TGAAGAAGTTGAACACCACCT 57.355 42.857 0.00 0.00 0.00 4.00
375 2416 3.181490 GGTTGAAGAAGTTGAACACCACC 60.181 47.826 0.00 0.00 31.86 4.61
376 2417 3.181490 GGGTTGAAGAAGTTGAACACCAC 60.181 47.826 0.00 0.00 31.86 4.16
377 2418 3.020984 GGGTTGAAGAAGTTGAACACCA 58.979 45.455 0.00 0.00 31.86 4.17
378 2419 3.020984 TGGGTTGAAGAAGTTGAACACC 58.979 45.455 0.00 0.00 32.58 4.16
379 2420 3.489229 GCTGGGTTGAAGAAGTTGAACAC 60.489 47.826 0.00 0.00 34.05 3.32
380 2421 2.687935 GCTGGGTTGAAGAAGTTGAACA 59.312 45.455 0.00 0.00 31.86 3.18
383 2424 2.575532 CAGCTGGGTTGAAGAAGTTGA 58.424 47.619 5.57 0.00 0.00 3.18
384 2425 1.000938 GCAGCTGGGTTGAAGAAGTTG 60.001 52.381 17.12 0.00 0.00 3.16
385 2426 1.133668 AGCAGCTGGGTTGAAGAAGTT 60.134 47.619 17.12 0.00 0.00 2.66
386 2427 0.475906 AGCAGCTGGGTTGAAGAAGT 59.524 50.000 17.12 0.00 0.00 3.01
387 2428 0.879765 CAGCAGCTGGGTTGAAGAAG 59.120 55.000 17.12 0.00 0.00 2.85
390 2431 1.572085 CGACAGCAGCTGGGTTGAAG 61.572 60.000 26.38 5.61 35.51 3.02
391 2432 1.597854 CGACAGCAGCTGGGTTGAA 60.598 57.895 26.38 0.00 35.51 2.69
393 2434 1.447317 AAACGACAGCAGCTGGGTTG 61.447 55.000 25.87 14.45 34.35 3.77
394 2435 0.751643 AAAACGACAGCAGCTGGGTT 60.752 50.000 26.38 23.80 35.11 4.11
395 2436 1.152963 AAAACGACAGCAGCTGGGT 60.153 52.632 26.38 19.66 35.51 4.51
396 2437 1.165907 TCAAAACGACAGCAGCTGGG 61.166 55.000 26.38 19.02 35.51 4.45
434 2475 2.632996 AGATTCCACTTCGAGTTCACCA 59.367 45.455 0.00 0.00 0.00 4.17
435 2476 3.320673 AGATTCCACTTCGAGTTCACC 57.679 47.619 0.00 0.00 0.00 4.02
737 2792 4.996434 AGCAGTGGAGTGTGGCGC 62.996 66.667 0.00 0.00 0.00 6.53
776 2831 2.283173 GCAGGAAGGTTGGTGGGG 60.283 66.667 0.00 0.00 0.00 4.96
813 2868 1.761735 CGATATATAGGGGGAGGGGCC 60.762 61.905 0.00 0.00 0.00 5.80
814 2869 1.718280 CGATATATAGGGGGAGGGGC 58.282 60.000 0.00 0.00 0.00 5.80
815 2870 1.718280 GCGATATATAGGGGGAGGGG 58.282 60.000 0.00 0.00 0.00 4.79
881 2936 1.135083 CGTAGTACTTGTGAGCTGGGG 60.135 57.143 0.00 0.00 0.00 4.96
905 2960 1.515631 CGCCGATCAACACGTATACAC 59.484 52.381 3.32 0.00 0.00 2.90
1024 3079 1.961378 TCGCCTGCGAGAAGTACAA 59.039 52.632 10.61 0.00 44.01 2.41
1025 3080 3.676216 TCGCCTGCGAGAAGTACA 58.324 55.556 10.61 0.00 44.01 2.90
1070 3125 4.649705 TGAGCCGGAACCCCCTCA 62.650 66.667 5.05 3.99 32.35 3.86
1441 3499 1.281199 ACCACCTGATGCTGCCCATA 61.281 55.000 0.00 0.00 33.29 2.74
1459 3520 1.079503 GATCTTCACGTGGCCTTCAC 58.920 55.000 17.00 0.00 42.74 3.18
1498 3559 0.569349 GCCGCGTCGTATTTACACTC 59.431 55.000 4.92 0.00 0.00 3.51
1521 3582 1.445410 CCCACGCGAGAAACGATGA 60.445 57.895 15.93 0.00 45.77 2.92
1605 3677 6.367969 ACGTACTTGCTAGAACATACAAAAGG 59.632 38.462 1.04 0.00 0.00 3.11
1611 3683 8.136057 TCTACTACGTACTTGCTAGAACATAC 57.864 38.462 1.04 0.00 0.00 2.39
1647 3724 2.884639 TCTTTTCCTTGCACCAGCTAAC 59.115 45.455 0.00 0.00 42.74 2.34
1662 3739 4.354587 GTCAATCAATCCGCCATCTTTTC 58.645 43.478 0.00 0.00 0.00 2.29
1672 3749 1.024046 TGTGCCGGTCAATCAATCCG 61.024 55.000 1.90 0.00 43.30 4.18
1692 3769 0.171007 ATTAAGTGGCACGTGCATGC 59.829 50.000 38.60 26.84 45.34 4.06
1719 3796 9.057089 AGATTCGACTCAACTAAAAGAAAACAT 57.943 29.630 5.50 0.00 0.00 2.71
1739 3816 6.238049 CCAGCTTTCAACAGAAGATAGATTCG 60.238 42.308 0.00 0.00 34.27 3.34
1772 3849 2.092753 ACAGTCTCATCGGCCATCATTT 60.093 45.455 2.24 0.00 0.00 2.32
1816 3893 7.552687 TGTCTTGAGATATTTGGGACATGTTAC 59.447 37.037 0.00 0.00 39.30 2.50
1820 3897 7.395190 TTTGTCTTGAGATATTTGGGACATG 57.605 36.000 0.00 0.00 39.30 3.21
1821 3898 8.599624 AATTTGTCTTGAGATATTTGGGACAT 57.400 30.769 0.00 0.00 39.30 3.06
1822 3899 8.306038 CAAATTTGTCTTGAGATATTTGGGACA 58.694 33.333 10.15 0.00 32.65 4.02
1823 3900 8.306761 ACAAATTTGTCTTGAGATATTTGGGAC 58.693 33.333 18.13 0.00 36.50 4.46
1824 3901 8.421249 ACAAATTTGTCTTGAGATATTTGGGA 57.579 30.769 18.13 0.00 36.50 4.37
1825 3902 9.492973 AAACAAATTTGTCTTGAGATATTTGGG 57.507 29.630 23.47 0.00 41.31 4.12
1835 3912 5.038033 GCCACGTAAACAAATTTGTCTTGA 58.962 37.500 23.47 7.22 41.31 3.02
1836 3913 4.800993 TGCCACGTAAACAAATTTGTCTTG 59.199 37.500 23.47 14.28 41.31 3.02
1844 3921 4.379339 AACACTTGCCACGTAAACAAAT 57.621 36.364 0.00 0.00 0.00 2.32
1850 3927 6.930164 TCTTCTTATTAACACTTGCCACGTAA 59.070 34.615 0.00 0.00 0.00 3.18
1857 3934 8.012241 CACAACTCTCTTCTTATTAACACTTGC 58.988 37.037 0.00 0.00 0.00 4.01
1869 3946 5.070446 TGTCACCATACACAACTCTCTTCTT 59.930 40.000 0.00 0.00 0.00 2.52
1924 4001 2.544685 CACCTCATCGAAACTGCCTAG 58.455 52.381 0.00 0.00 0.00 3.02
1931 4008 5.484173 TCATTTATGCACCTCATCGAAAC 57.516 39.130 0.00 0.00 36.63 2.78
2121 4510 4.736126 TTCTCACACACAGAACTCTTGA 57.264 40.909 0.00 0.00 0.00 3.02
2122 4511 7.664082 AATATTCTCACACACAGAACTCTTG 57.336 36.000 0.00 0.00 32.65 3.02
2123 4512 8.682936 AAAATATTCTCACACACAGAACTCTT 57.317 30.769 0.00 0.00 32.65 2.85
2133 4522 5.335897 GCAGAGGCAAAAATATTCTCACACA 60.336 40.000 4.48 0.00 40.72 3.72
2135 4524 4.158394 GGCAGAGGCAAAAATATTCTCACA 59.842 41.667 4.48 0.00 43.71 3.58
2138 4527 4.641989 TCTGGCAGAGGCAAAAATATTCTC 59.358 41.667 14.43 0.00 43.71 2.87
2151 4540 1.748122 GGCATGTGTCTGGCAGAGG 60.748 63.158 19.38 6.57 41.12 3.69
2156 4545 2.753043 CCCTGGCATGTGTCTGGC 60.753 66.667 5.13 0.00 37.42 4.85
2201 4590 9.543018 CTATTTGTTCTATTTTCTGGAAACGTC 57.457 33.333 0.00 0.00 0.00 4.34
2212 4601 4.438200 CGCCGGTGCTATTTGTTCTATTTT 60.438 41.667 0.00 0.00 34.43 1.82
2216 4605 1.066716 ACGCCGGTGCTATTTGTTCTA 60.067 47.619 16.69 0.00 34.43 2.10
2250 4639 6.234920 TGACAAGTATTTTCGAATGAAGGGA 58.765 36.000 0.00 0.00 35.06 4.20
2251 4640 6.494893 TGACAAGTATTTTCGAATGAAGGG 57.505 37.500 0.00 0.00 35.06 3.95
2252 4641 7.751732 TGATGACAAGTATTTTCGAATGAAGG 58.248 34.615 0.00 0.00 35.06 3.46
2253 4642 9.611284 TTTGATGACAAGTATTTTCGAATGAAG 57.389 29.630 0.00 0.00 37.32 3.02
2254 4643 9.958234 TTTTGATGACAAGTATTTTCGAATGAA 57.042 25.926 0.00 0.00 37.32 2.57
2257 4646 9.357652 CCATTTTGATGACAAGTATTTTCGAAT 57.642 29.630 0.00 0.00 37.32 3.34
2258 4647 8.572185 TCCATTTTGATGACAAGTATTTTCGAA 58.428 29.630 0.00 0.00 37.32 3.71
2259 4648 8.020819 GTCCATTTTGATGACAAGTATTTTCGA 58.979 33.333 0.00 0.00 37.32 3.71
2260 4649 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
2261 4650 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
2262 4651 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
2263 4652 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
2264 4653 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
2266 4655 9.258826 CATTTTTGTCCATTTTGATGACAAGTA 57.741 29.630 0.00 0.00 37.13 2.24
2267 4656 7.986320 TCATTTTTGTCCATTTTGATGACAAGT 59.014 29.630 0.00 0.00 37.13 3.16
2268 4657 8.367943 TCATTTTTGTCCATTTTGATGACAAG 57.632 30.769 0.00 0.00 37.13 3.16
2269 4658 8.728337 TTCATTTTTGTCCATTTTGATGACAA 57.272 26.923 0.00 0.00 34.47 3.18
2270 4659 8.775527 CATTCATTTTTGTCCATTTTGATGACA 58.224 29.630 0.00 0.00 0.00 3.58
2271 4660 8.776470 ACATTCATTTTTGTCCATTTTGATGAC 58.224 29.630 0.00 0.00 0.00 3.06
2272 4661 8.905660 ACATTCATTTTTGTCCATTTTGATGA 57.094 26.923 0.00 0.00 0.00 2.92
2327 4716 9.942850 ACTTGTCATCAAAATAAATAAAAGGGG 57.057 29.630 0.00 0.00 32.87 4.79
2337 4726 9.834628 GTCCGAAAATACTTGTCATCAAAATAA 57.165 29.630 0.00 0.00 32.87 1.40
2338 4727 8.172484 CGTCCGAAAATACTTGTCATCAAAATA 58.828 33.333 0.00 0.00 32.87 1.40
2339 4728 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2340 4729 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2341 4730 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2342 4731 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2343 4732 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2344 4733 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2345 4734 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2346 4735 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2347 4736 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2348 4737 2.564062 TCCTCCGTCCGAAAATACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
2349 4738 3.241067 TCCTCCGTCCGAAAATACTTG 57.759 47.619 0.00 0.00 0.00 3.16
2350 4739 3.260128 ACTTCCTCCGTCCGAAAATACTT 59.740 43.478 0.00 0.00 0.00 2.24
2351 4740 2.830321 ACTTCCTCCGTCCGAAAATACT 59.170 45.455 0.00 0.00 0.00 2.12
2352 4741 3.242549 ACTTCCTCCGTCCGAAAATAC 57.757 47.619 0.00 0.00 0.00 1.89
2353 4742 4.891756 AGATACTTCCTCCGTCCGAAAATA 59.108 41.667 0.00 0.00 0.00 1.40
2354 4743 3.705072 AGATACTTCCTCCGTCCGAAAAT 59.295 43.478 0.00 0.00 0.00 1.82
2355 4744 3.094572 AGATACTTCCTCCGTCCGAAAA 58.905 45.455 0.00 0.00 0.00 2.29
2356 4745 2.731572 AGATACTTCCTCCGTCCGAAA 58.268 47.619 0.00 0.00 0.00 3.46
2357 4746 2.431954 AGATACTTCCTCCGTCCGAA 57.568 50.000 0.00 0.00 0.00 4.30
2358 4747 3.072038 TGATAGATACTTCCTCCGTCCGA 59.928 47.826 0.00 0.00 0.00 4.55
2359 4748 3.409570 TGATAGATACTTCCTCCGTCCG 58.590 50.000 0.00 0.00 0.00 4.79
2360 4749 6.316890 GTCTATGATAGATACTTCCTCCGTCC 59.683 46.154 5.33 0.00 37.13 4.79
2361 4750 6.036300 CGTCTATGATAGATACTTCCTCCGTC 59.964 46.154 5.33 0.00 37.13 4.79
2362 4751 5.875910 CGTCTATGATAGATACTTCCTCCGT 59.124 44.000 5.33 0.00 37.13 4.69
2363 4752 6.107343 TCGTCTATGATAGATACTTCCTCCG 58.893 44.000 5.33 1.69 37.13 4.63
2364 4753 7.390996 TGTTCGTCTATGATAGATACTTCCTCC 59.609 40.741 5.33 0.00 37.13 4.30
2365 4754 8.325421 TGTTCGTCTATGATAGATACTTCCTC 57.675 38.462 5.33 0.00 37.13 3.71
2366 4755 8.871629 ATGTTCGTCTATGATAGATACTTCCT 57.128 34.615 5.33 0.00 37.13 3.36
2370 4759 9.089601 CGTCTATGTTCGTCTATGATAGATACT 57.910 37.037 5.33 0.00 37.13 2.12
2371 4760 9.085250 TCGTCTATGTTCGTCTATGATAGATAC 57.915 37.037 5.33 5.61 37.13 2.24
2372 4761 9.649167 TTCGTCTATGTTCGTCTATGATAGATA 57.351 33.333 5.33 0.00 37.13 1.98
2373 4762 8.444715 GTTCGTCTATGTTCGTCTATGATAGAT 58.555 37.037 5.33 0.00 37.13 1.98
2374 4763 7.440255 TGTTCGTCTATGTTCGTCTATGATAGA 59.560 37.037 0.00 0.00 0.00 1.98
2375 4764 7.573627 TGTTCGTCTATGTTCGTCTATGATAG 58.426 38.462 0.00 0.00 0.00 2.08
2376 4765 7.226128 ACTGTTCGTCTATGTTCGTCTATGATA 59.774 37.037 0.00 0.00 0.00 2.15
2377 4766 6.038382 ACTGTTCGTCTATGTTCGTCTATGAT 59.962 38.462 0.00 0.00 0.00 2.45
2378 4767 5.353400 ACTGTTCGTCTATGTTCGTCTATGA 59.647 40.000 0.00 0.00 0.00 2.15
2379 4768 5.570344 ACTGTTCGTCTATGTTCGTCTATG 58.430 41.667 0.00 0.00 0.00 2.23
2380 4769 5.814764 ACTGTTCGTCTATGTTCGTCTAT 57.185 39.130 0.00 0.00 0.00 1.98
2381 4770 6.915544 ATACTGTTCGTCTATGTTCGTCTA 57.084 37.500 0.00 0.00 0.00 2.59
2382 4771 5.814764 ATACTGTTCGTCTATGTTCGTCT 57.185 39.130 0.00 0.00 0.00 4.18
2383 4772 8.068977 AGATTATACTGTTCGTCTATGTTCGTC 58.931 37.037 0.00 0.00 0.00 4.20
2384 4773 7.928103 AGATTATACTGTTCGTCTATGTTCGT 58.072 34.615 0.00 0.00 0.00 3.85
2385 4774 9.531412 CTAGATTATACTGTTCGTCTATGTTCG 57.469 37.037 0.00 0.00 0.00 3.95
2386 4775 9.332301 GCTAGATTATACTGTTCGTCTATGTTC 57.668 37.037 0.00 0.00 0.00 3.18
2387 4776 8.016229 CGCTAGATTATACTGTTCGTCTATGTT 58.984 37.037 0.00 0.00 0.00 2.71
2388 4777 7.172875 ACGCTAGATTATACTGTTCGTCTATGT 59.827 37.037 0.00 0.00 0.00 2.29
2389 4778 7.519843 ACGCTAGATTATACTGTTCGTCTATG 58.480 38.462 0.00 0.00 0.00 2.23
2390 4779 7.387122 TGACGCTAGATTATACTGTTCGTCTAT 59.613 37.037 11.31 0.00 42.64 1.98
2391 4780 6.703165 TGACGCTAGATTATACTGTTCGTCTA 59.297 38.462 11.31 0.00 42.64 2.59
2410 4799 4.352039 CGTACTTATCAACTGATGACGCT 58.648 43.478 2.36 0.00 41.93 5.07


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

AutoCloner maintained by Alex Coulton.