Multiple sequence alignment - TraesCS4D01G173700

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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 TraesCS4D01G173700 chr4D 100.000 3173 0 0 1 3173 301533657 301536829 0.000000e+00 5860
1 TraesCS4D01G173700 chr4D 95.455 132 5 1 255 385 614522 614653 3.210000e-50 209
2 TraesCS4D01G173700 chr4D 97.590 83 1 1 1104 1185 301534700 301534782 1.190000e-29 141
3 TraesCS4D01G173700 chr4D 97.590 83 1 1 1044 1126 301534760 301534841 1.190000e-29 141
4 TraesCS4D01G173700 chr4B 95.208 1419 40 14 1094 2502 375790698 375792098 0.000000e+00 2218
5 TraesCS4D01G173700 chr4B 92.258 620 44 4 2557 3173 498933397 498934015 0.000000e+00 876
6 TraesCS4D01G173700 chr4B 91.558 616 44 8 2560 3172 661616989 661616379 0.000000e+00 843
7 TraesCS4D01G173700 chr4B 95.844 385 14 2 653 1036 375790337 375790720 3.480000e-174 621
8 TraesCS4D01G173700 chr4B 84.496 258 29 8 6 260 375788541 375788790 8.790000e-61 244
9 TraesCS4D01G173700 chr4B 83.212 137 10 3 395 531 375788803 375788926 2.590000e-21 113
10 TraesCS4D01G173700 chr4A 90.776 1095 68 17 1104 2186 179480466 179479393 0.000000e+00 1432
11 TraesCS4D01G173700 chr4A 89.070 613 34 10 531 1129 179480974 179480381 0.000000e+00 730
12 TraesCS4D01G173700 chr4A 92.121 165 12 1 2292 2456 179476201 179476038 6.840000e-57 231
13 TraesCS4D01G173700 chr4A 96.429 84 2 1 177 260 179481261 179481179 1.530000e-28 137
14 TraesCS4D01G173700 chr1D 93.881 621 34 2 2556 3173 17706054 17705435 0.000000e+00 933
15 TraesCS4D01G173700 chr1D 93.720 621 36 1 2556 3173 17729471 17728851 0.000000e+00 928
16 TraesCS4D01G173700 chr1D 75.506 494 103 17 1244 1728 110335420 110335904 3.180000e-55 226
17 TraesCS4D01G173700 chr1D 94.853 136 6 1 257 391 262705520 262705385 8.920000e-51 211
18 TraesCS4D01G173700 chr1D 92.958 142 7 3 250 390 445057536 445057675 1.490000e-48 204
19 TraesCS4D01G173700 chr5B 92.846 615 41 3 2561 3173 508773962 508773349 0.000000e+00 889
20 TraesCS4D01G173700 chr7D 91.748 618 47 4 2559 3173 20477328 20476712 0.000000e+00 856
21 TraesCS4D01G173700 chr5D 91.774 620 44 7 2559 3173 454721488 454720871 0.000000e+00 856
22 TraesCS4D01G173700 chr5D 97.778 135 2 1 258 391 354741250 354741116 6.840000e-57 231
23 TraesCS4D01G173700 chr5D 96.875 128 4 0 258 385 364050414 364050541 6.890000e-52 215
24 TraesCS4D01G173700 chr6D 91.640 622 43 8 2559 3173 471505247 471505866 0.000000e+00 852
25 TraesCS4D01G173700 chr6B 91.680 613 46 5 2562 3171 392585857 392586467 0.000000e+00 845
26 TraesCS4D01G173700 chr1B 75.709 494 102 17 1244 1728 167713500 167713984 6.840000e-57 231
27 TraesCS4D01G173700 chrUn 96.875 128 4 0 258 385 98153915 98153788 6.890000e-52 215
28 TraesCS4D01G173700 chr5A 94.245 139 7 1 247 385 521007330 521007467 8.920000e-51 211
29 TraesCS4D01G173700 chr2B 93.617 141 6 2 259 397 114324926 114324787 1.150000e-49 207
30 TraesCS4D01G173700 chr6A 93.525 139 8 1 247 385 2728074 2727937 4.150000e-49 206


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 TraesCS4D01G173700 chr4D 301533657 301536829 3172 False 2047.333333 5860 98.393333 1 3173 3 chr4D.!!$F2 3172
1 TraesCS4D01G173700 chr4B 498933397 498934015 618 False 876.000000 876 92.258000 2557 3173 1 chr4B.!!$F1 616
2 TraesCS4D01G173700 chr4B 661616379 661616989 610 True 843.000000 843 91.558000 2560 3172 1 chr4B.!!$R1 612
3 TraesCS4D01G173700 chr4B 375788541 375792098 3557 False 799.000000 2218 89.690000 6 2502 4 chr4B.!!$F2 2496
4 TraesCS4D01G173700 chr4A 179476038 179481261 5223 True 632.500000 1432 92.099000 177 2456 4 chr4A.!!$R1 2279
5 TraesCS4D01G173700 chr1D 17705435 17706054 619 True 933.000000 933 93.881000 2556 3173 1 chr1D.!!$R1 617
6 TraesCS4D01G173700 chr1D 17728851 17729471 620 True 928.000000 928 93.720000 2556 3173 1 chr1D.!!$R2 617
7 TraesCS4D01G173700 chr5B 508773349 508773962 613 True 889.000000 889 92.846000 2561 3173 1 chr5B.!!$R1 612
8 TraesCS4D01G173700 chr7D 20476712 20477328 616 True 856.000000 856 91.748000 2559 3173 1 chr7D.!!$R1 614
9 TraesCS4D01G173700 chr5D 454720871 454721488 617 True 856.000000 856 91.774000 2559 3173 1 chr5D.!!$R2 614
10 TraesCS4D01G173700 chr6D 471505247 471505866 619 False 852.000000 852 91.640000 2559 3173 1 chr6D.!!$F1 614
11 TraesCS4D01G173700 chr6B 392585857 392586467 610 False 845.000000 845 91.680000 2562 3171 1 chr6B.!!$F1 609

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
126 136 0.175760 GGACAGCAGATTAGCCGACA 59.824 55.0 0.00 0.0 34.23 4.35 F
182 192 0.179108 GCTAGCCTACAAGGTCACCG 60.179 60.0 2.29 0.0 37.80 4.94 F
2002 3326 0.251341 ACCAGCACTTCACATTCCCC 60.251 55.0 0.00 0.0 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 3307 0.251297 TGGGGAATGTGAAGTGCTGG 60.251 55.000 0.00 0.0 0.00 4.85 R
2078 3404 3.111098 GTCAGCAACTGCACAGAAAAAG 58.889 45.455 4.31 0.0 45.16 2.27 R
2820 7246 2.969821 TGGAGCATTTGGTTACTGGT 57.030 45.000 0.00 0.0 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 31 2.440796 CCAGCGCATCATGGGGTT 60.441 61.111 11.47 0.00 39.03 4.11
44 46 2.590092 GTTGGGCAGGGATAGCGT 59.410 61.111 0.00 0.00 0.00 5.07
48 50 2.279517 GGCAGGGATAGCGTGACG 60.280 66.667 0.00 0.00 0.00 4.35
73 83 2.818274 GGCCTTCCGTTACTGGCG 60.818 66.667 0.00 0.00 45.75 5.69
95 105 4.081030 GACGACGACGGCGACTCA 62.081 66.667 32.70 0.00 44.46 3.41
96 106 3.584250 GACGACGACGGCGACTCAA 62.584 63.158 32.70 0.00 44.46 3.02
97 107 2.427905 CGACGACGGCGACTCAAA 60.428 61.111 22.49 0.00 41.64 2.69
99 109 1.702299 GACGACGGCGACTCAAATG 59.298 57.895 22.49 0.00 41.64 2.32
121 131 1.889573 GCGGGGACAGCAGATTAGC 60.890 63.158 0.00 0.00 34.19 3.09
122 132 1.227674 CGGGGACAGCAGATTAGCC 60.228 63.158 0.00 0.00 34.23 3.93
125 135 0.530870 GGGACAGCAGATTAGCCGAC 60.531 60.000 0.00 0.00 34.23 4.79
126 136 0.175760 GGACAGCAGATTAGCCGACA 59.824 55.000 0.00 0.00 34.23 4.35
168 178 2.611012 GATGGCCTCGAAAGCTAGC 58.389 57.895 6.62 6.62 0.00 3.42
169 179 0.882484 GATGGCCTCGAAAGCTAGCC 60.882 60.000 12.13 0.00 44.13 3.93
170 180 1.341156 ATGGCCTCGAAAGCTAGCCT 61.341 55.000 12.13 0.00 44.19 4.58
171 181 0.686441 TGGCCTCGAAAGCTAGCCTA 60.686 55.000 12.13 0.00 44.19 3.93
172 182 0.249531 GGCCTCGAAAGCTAGCCTAC 60.250 60.000 12.13 1.71 40.57 3.18
174 184 1.134788 GCCTCGAAAGCTAGCCTACAA 60.135 52.381 12.13 0.00 0.00 2.41
175 185 2.815478 CCTCGAAAGCTAGCCTACAAG 58.185 52.381 12.13 4.10 0.00 3.16
176 186 2.482142 CCTCGAAAGCTAGCCTACAAGG 60.482 54.545 12.13 9.75 38.80 3.61
177 187 2.166664 CTCGAAAGCTAGCCTACAAGGT 59.833 50.000 12.13 0.00 37.80 3.50
180 190 3.263261 GAAAGCTAGCCTACAAGGTCAC 58.737 50.000 12.13 0.00 37.80 3.67
181 191 1.196012 AGCTAGCCTACAAGGTCACC 58.804 55.000 12.13 0.00 37.80 4.02
182 192 0.179108 GCTAGCCTACAAGGTCACCG 60.179 60.000 2.29 0.00 37.80 4.94
260 270 6.299023 TCAATATCGTCCATTTGCATGTAC 57.701 37.500 0.00 0.00 0.00 2.90
262 272 6.202762 TCAATATCGTCCATTTGCATGTACTC 59.797 38.462 0.00 0.00 0.00 2.59
264 274 1.670811 CGTCCATTTGCATGTACTCCC 59.329 52.381 0.00 0.00 0.00 4.30
267 277 2.092429 TCCATTTGCATGTACTCCCTCC 60.092 50.000 0.00 0.00 0.00 4.30
268 278 1.942657 CATTTGCATGTACTCCCTCCG 59.057 52.381 0.00 0.00 0.00 4.63
270 280 0.535335 TTGCATGTACTCCCTCCGTC 59.465 55.000 0.00 0.00 0.00 4.79
271 281 1.327690 TGCATGTACTCCCTCCGTCC 61.328 60.000 0.00 0.00 0.00 4.79
272 282 1.043673 GCATGTACTCCCTCCGTCCT 61.044 60.000 0.00 0.00 0.00 3.85
273 283 1.753141 GCATGTACTCCCTCCGTCCTA 60.753 57.143 0.00 0.00 0.00 2.94
274 284 2.662866 CATGTACTCCCTCCGTCCTAA 58.337 52.381 0.00 0.00 0.00 2.69
275 285 2.905415 TGTACTCCCTCCGTCCTAAA 57.095 50.000 0.00 0.00 0.00 1.85
276 286 3.173953 TGTACTCCCTCCGTCCTAAAA 57.826 47.619 0.00 0.00 0.00 1.52
277 287 3.716431 TGTACTCCCTCCGTCCTAAAAT 58.284 45.455 0.00 0.00 0.00 1.82
278 288 4.098894 TGTACTCCCTCCGTCCTAAAATT 58.901 43.478 0.00 0.00 0.00 1.82
279 289 3.908643 ACTCCCTCCGTCCTAAAATTC 57.091 47.619 0.00 0.00 0.00 2.17
280 290 3.451890 ACTCCCTCCGTCCTAAAATTCT 58.548 45.455 0.00 0.00 0.00 2.40
281 291 3.844804 ACTCCCTCCGTCCTAAAATTCTT 59.155 43.478 0.00 0.00 0.00 2.52
282 292 4.192317 CTCCCTCCGTCCTAAAATTCTTG 58.808 47.826 0.00 0.00 0.00 3.02
283 293 3.585732 TCCCTCCGTCCTAAAATTCTTGT 59.414 43.478 0.00 0.00 0.00 3.16
284 294 3.939592 CCCTCCGTCCTAAAATTCTTGTC 59.060 47.826 0.00 0.00 0.00 3.18
285 295 4.323562 CCCTCCGTCCTAAAATTCTTGTCT 60.324 45.833 0.00 0.00 0.00 3.41
286 296 5.246307 CCTCCGTCCTAAAATTCTTGTCTT 58.754 41.667 0.00 0.00 0.00 3.01
287 297 6.403878 CCTCCGTCCTAAAATTCTTGTCTTA 58.596 40.000 0.00 0.00 0.00 2.10
288 298 6.535508 CCTCCGTCCTAAAATTCTTGTCTTAG 59.464 42.308 0.00 0.00 0.00 2.18
289 299 7.235935 TCCGTCCTAAAATTCTTGTCTTAGA 57.764 36.000 0.00 0.00 0.00 2.10
290 300 7.848128 TCCGTCCTAAAATTCTTGTCTTAGAT 58.152 34.615 0.00 0.00 0.00 1.98
291 301 8.319146 TCCGTCCTAAAATTCTTGTCTTAGATT 58.681 33.333 0.00 0.00 0.00 2.40
292 302 8.947115 CCGTCCTAAAATTCTTGTCTTAGATTT 58.053 33.333 0.00 0.00 0.00 2.17
326 336 8.462143 ACAGATGTATCTAACACTAAAACGTG 57.538 34.615 0.00 0.00 42.09 4.49
327 337 8.301720 ACAGATGTATCTAACACTAAAACGTGA 58.698 33.333 0.00 0.00 42.09 4.35
328 338 9.135843 CAGATGTATCTAACACTAAAACGTGAA 57.864 33.333 0.00 0.00 42.09 3.18
329 339 9.871238 AGATGTATCTAACACTAAAACGTGAAT 57.129 29.630 0.00 0.00 42.09 2.57
336 346 9.494479 TCTAACACTAAAACGTGAATAGATACG 57.506 33.333 8.90 0.00 45.19 3.06
345 355 5.027206 CGTGAATAGATACGTCCGTATGT 57.973 43.478 16.33 14.57 40.93 2.29
346 356 6.156932 CGTGAATAGATACGTCCGTATGTA 57.843 41.667 16.33 16.14 40.93 2.29
347 357 6.239226 CGTGAATAGATACGTCCGTATGTAG 58.761 44.000 16.33 2.39 40.93 2.74
348 358 6.089954 CGTGAATAGATACGTCCGTATGTAGA 59.910 42.308 16.33 0.14 40.93 2.59
349 359 7.232994 GTGAATAGATACGTCCGTATGTAGAC 58.767 42.308 16.33 13.62 40.93 2.59
350 360 6.930722 TGAATAGATACGTCCGTATGTAGACA 59.069 38.462 16.33 15.48 40.93 3.41
351 361 7.442062 TGAATAGATACGTCCGTATGTAGACAA 59.558 37.037 16.33 0.00 40.93 3.18
352 362 7.734924 ATAGATACGTCCGTATGTAGACAAA 57.265 36.000 16.33 0.00 40.93 2.83
353 363 6.630444 AGATACGTCCGTATGTAGACAAAT 57.370 37.500 16.33 0.00 40.93 2.32
354 364 6.666417 AGATACGTCCGTATGTAGACAAATC 58.334 40.000 16.33 1.16 40.93 2.17
355 365 4.978083 ACGTCCGTATGTAGACAAATCT 57.022 40.909 0.00 0.00 39.15 2.40
356 366 7.658982 AGATACGTCCGTATGTAGACAAATCTA 59.341 37.037 16.33 0.00 40.93 1.98
357 367 6.441093 ACGTCCGTATGTAGACAAATCTAA 57.559 37.500 0.00 0.00 39.20 2.10
358 368 6.493116 ACGTCCGTATGTAGACAAATCTAAG 58.507 40.000 0.00 0.00 39.20 2.18
359 369 6.317140 ACGTCCGTATGTAGACAAATCTAAGA 59.683 38.462 0.00 0.00 39.20 2.10
360 370 6.632035 CGTCCGTATGTAGACAAATCTAAGAC 59.368 42.308 0.00 0.00 39.20 3.01
361 371 7.478322 GTCCGTATGTAGACAAATCTAAGACA 58.522 38.462 0.00 0.00 39.20 3.41
362 372 7.972277 GTCCGTATGTAGACAAATCTAAGACAA 59.028 37.037 0.00 0.00 39.20 3.18
363 373 8.188799 TCCGTATGTAGACAAATCTAAGACAAG 58.811 37.037 0.00 0.00 39.20 3.16
364 374 8.188799 CCGTATGTAGACAAATCTAAGACAAGA 58.811 37.037 0.00 0.00 39.20 3.02
365 375 9.569167 CGTATGTAGACAAATCTAAGACAAGAA 57.431 33.333 0.00 0.00 39.20 2.52
375 385 9.322776 CAAATCTAAGACAAGAATTTTGAGACG 57.677 33.333 7.18 0.00 31.51 4.18
376 386 7.602517 ATCTAAGACAAGAATTTTGAGACGG 57.397 36.000 7.18 0.00 0.00 4.79
377 387 6.755206 TCTAAGACAAGAATTTTGAGACGGA 58.245 36.000 7.18 0.00 0.00 4.69
378 388 5.931441 AAGACAAGAATTTTGAGACGGAG 57.069 39.130 7.18 0.00 0.00 4.63
379 389 4.319177 AGACAAGAATTTTGAGACGGAGG 58.681 43.478 7.18 0.00 0.00 4.30
380 390 3.412386 ACAAGAATTTTGAGACGGAGGG 58.588 45.455 7.18 0.00 0.00 4.30
381 391 3.072476 ACAAGAATTTTGAGACGGAGGGA 59.928 43.478 7.18 0.00 0.00 4.20
382 392 3.618690 AGAATTTTGAGACGGAGGGAG 57.381 47.619 0.00 0.00 0.00 4.30
383 393 2.907042 AGAATTTTGAGACGGAGGGAGT 59.093 45.455 0.00 0.00 0.00 3.85
384 394 4.094476 AGAATTTTGAGACGGAGGGAGTA 58.906 43.478 0.00 0.00 0.00 2.59
385 395 4.530946 AGAATTTTGAGACGGAGGGAGTAA 59.469 41.667 0.00 0.00 0.00 2.24
386 396 5.189934 AGAATTTTGAGACGGAGGGAGTAAT 59.810 40.000 0.00 0.00 0.00 1.89
387 397 6.383147 AGAATTTTGAGACGGAGGGAGTAATA 59.617 38.462 0.00 0.00 0.00 0.98
388 398 6.749036 ATTTTGAGACGGAGGGAGTAATAT 57.251 37.500 0.00 0.00 0.00 1.28
389 399 6.555463 TTTTGAGACGGAGGGAGTAATATT 57.445 37.500 0.00 0.00 0.00 1.28
390 400 6.555463 TTTGAGACGGAGGGAGTAATATTT 57.445 37.500 0.00 0.00 0.00 1.40
391 401 7.664552 TTTGAGACGGAGGGAGTAATATTTA 57.335 36.000 0.00 0.00 0.00 1.40
392 402 7.850935 TTGAGACGGAGGGAGTAATATTTAT 57.149 36.000 0.00 0.00 0.00 1.40
393 403 7.228314 TGAGACGGAGGGAGTAATATTTATG 57.772 40.000 0.00 0.00 0.00 1.90
417 427 6.487331 TGAACTTGCTTTAATTTCCTCCGTTA 59.513 34.615 0.00 0.00 29.52 3.18
433 443 3.434299 TCCGTTAAGCTCAAATTTCGTCC 59.566 43.478 0.00 0.00 0.00 4.79
463 473 2.772077 TCGATCCGTTTGAAATGGGA 57.228 45.000 15.66 9.39 38.15 4.37
576 663 0.396811 AAAGCTAACACTCGGGCAGT 59.603 50.000 0.00 0.00 34.67 4.40
592 679 1.798813 GCAGTACGAGGACCAGTTTTG 59.201 52.381 0.00 0.00 0.00 2.44
593 680 2.547218 GCAGTACGAGGACCAGTTTTGA 60.547 50.000 0.00 0.00 0.00 2.69
681 1986 0.533978 TGCGGCTTCACTTGCTTACA 60.534 50.000 0.00 0.00 0.00 2.41
742 2047 4.019919 GCAAATGCTTAGATCGCTTTCA 57.980 40.909 0.00 0.00 38.21 2.69
812 2117 1.832167 GGCCTGCCTCAACCAAACA 60.832 57.895 0.00 0.00 0.00 2.83
971 2276 0.413832 AAGACTCCACAGCCTCCCTA 59.586 55.000 0.00 0.00 0.00 3.53
990 2302 1.901591 ATTGTCACCTCAGGTTGCAG 58.098 50.000 0.00 0.00 31.02 4.41
1038 2350 3.829026 AGCCATCACCTTTCTTTCCTTTC 59.171 43.478 0.00 0.00 0.00 2.62
1050 2362 4.480115 TCTTTCCTTTCCTTTCCTTTCCC 58.520 43.478 0.00 0.00 0.00 3.97
1051 2363 4.170053 TCTTTCCTTTCCTTTCCTTTCCCT 59.830 41.667 0.00 0.00 0.00 4.20
1052 2364 4.552883 TTCCTTTCCTTTCCTTTCCCTT 57.447 40.909 0.00 0.00 0.00 3.95
1053 2365 4.552883 TCCTTTCCTTTCCTTTCCCTTT 57.447 40.909 0.00 0.00 0.00 3.11
1108 2420 0.961019 TGTTGCAGCCATCACCTTTC 59.039 50.000 0.00 0.00 0.00 2.62
1109 2421 1.251251 GTTGCAGCCATCACCTTTCT 58.749 50.000 0.00 0.00 0.00 2.52
1110 2422 1.615392 GTTGCAGCCATCACCTTTCTT 59.385 47.619 0.00 0.00 0.00 2.52
1111 2423 1.999648 TGCAGCCATCACCTTTCTTT 58.000 45.000 0.00 0.00 0.00 2.52
1112 2424 2.318908 TGCAGCCATCACCTTTCTTTT 58.681 42.857 0.00 0.00 0.00 2.27
1113 2425 2.297033 TGCAGCCATCACCTTTCTTTTC 59.703 45.455 0.00 0.00 0.00 2.29
1114 2426 2.560105 GCAGCCATCACCTTTCTTTTCT 59.440 45.455 0.00 0.00 0.00 2.52
1115 2427 3.006217 GCAGCCATCACCTTTCTTTTCTT 59.994 43.478 0.00 0.00 0.00 2.52
1116 2428 4.502087 GCAGCCATCACCTTTCTTTTCTTT 60.502 41.667 0.00 0.00 0.00 2.52
1117 2429 5.225642 CAGCCATCACCTTTCTTTTCTTTC 58.774 41.667 0.00 0.00 0.00 2.62
1118 2430 4.281941 AGCCATCACCTTTCTTTTCTTTCC 59.718 41.667 0.00 0.00 0.00 3.13
1119 2431 4.281941 GCCATCACCTTTCTTTTCTTTCCT 59.718 41.667 0.00 0.00 0.00 3.36
1120 2432 5.565637 GCCATCACCTTTCTTTTCTTTCCTC 60.566 44.000 0.00 0.00 0.00 3.71
1121 2433 5.772169 CCATCACCTTTCTTTTCTTTCCTCT 59.228 40.000 0.00 0.00 0.00 3.69
1122 2434 6.942576 CCATCACCTTTCTTTTCTTTCCTCTA 59.057 38.462 0.00 0.00 0.00 2.43
1123 2435 7.120432 CCATCACCTTTCTTTTCTTTCCTCTAG 59.880 40.741 0.00 0.00 0.00 2.43
1124 2436 5.998363 TCACCTTTCTTTTCTTTCCTCTAGC 59.002 40.000 0.00 0.00 0.00 3.42
1125 2437 6.000840 CACCTTTCTTTTCTTTCCTCTAGCT 58.999 40.000 0.00 0.00 0.00 3.32
1126 2438 6.000840 ACCTTTCTTTTCTTTCCTCTAGCTG 58.999 40.000 0.00 0.00 0.00 4.24
1127 2439 5.414144 CCTTTCTTTTCTTTCCTCTAGCTGG 59.586 44.000 0.00 0.00 0.00 4.85
1128 2440 3.944087 TCTTTTCTTTCCTCTAGCTGGC 58.056 45.455 0.00 0.00 0.00 4.85
1129 2441 2.789409 TTTCTTTCCTCTAGCTGGCC 57.211 50.000 0.00 0.00 0.00 5.36
1130 2442 0.537188 TTCTTTCCTCTAGCTGGCCG 59.463 55.000 0.00 0.00 0.00 6.13
1131 2443 1.144936 CTTTCCTCTAGCTGGCCGG 59.855 63.158 7.41 7.41 0.00 6.13
1132 2444 1.305802 TTTCCTCTAGCTGGCCGGA 60.306 57.895 18.31 1.61 0.00 5.14
1133 2445 0.691078 TTTCCTCTAGCTGGCCGGAT 60.691 55.000 18.31 13.10 0.00 4.18
1134 2446 1.115930 TTCCTCTAGCTGGCCGGATC 61.116 60.000 18.31 0.00 0.00 3.36
1135 2447 1.532794 CCTCTAGCTGGCCGGATCT 60.533 63.158 18.31 6.32 0.00 2.75
1136 2448 1.531739 CCTCTAGCTGGCCGGATCTC 61.532 65.000 18.31 0.00 0.00 2.75
1137 2449 1.531739 CTCTAGCTGGCCGGATCTCC 61.532 65.000 18.31 0.00 0.00 3.71
1138 2450 1.834378 CTAGCTGGCCGGATCTCCA 60.834 63.158 18.31 0.87 35.14 3.86
1139 2451 1.152247 TAGCTGGCCGGATCTCCAT 60.152 57.895 18.31 0.00 35.14 3.41
1140 2452 1.188219 TAGCTGGCCGGATCTCCATC 61.188 60.000 18.31 0.00 35.14 3.51
1141 2453 2.341543 CTGGCCGGATCTCCATCG 59.658 66.667 5.28 0.00 35.14 3.84
1142 2454 2.443952 TGGCCGGATCTCCATCGT 60.444 61.111 5.05 0.00 35.14 3.73
1143 2455 2.340443 GGCCGGATCTCCATCGTC 59.660 66.667 5.05 0.00 35.14 4.20
1144 2456 2.203771 GGCCGGATCTCCATCGTCT 61.204 63.158 5.05 0.00 35.14 4.18
1145 2457 1.287503 GCCGGATCTCCATCGTCTC 59.712 63.158 5.05 0.00 35.14 3.36
1146 2458 1.960612 CCGGATCTCCATCGTCTCC 59.039 63.158 0.00 0.00 35.14 3.71
1147 2459 0.823769 CCGGATCTCCATCGTCTCCA 60.824 60.000 0.00 0.00 35.14 3.86
1148 2460 1.252175 CGGATCTCCATCGTCTCCAT 58.748 55.000 0.00 0.00 35.14 3.41
1149 2461 1.067985 CGGATCTCCATCGTCTCCATG 60.068 57.143 0.00 0.00 35.14 3.66
1150 2462 1.967066 GGATCTCCATCGTCTCCATGT 59.033 52.381 0.00 0.00 35.64 3.21
1151 2463 2.366916 GGATCTCCATCGTCTCCATGTT 59.633 50.000 0.00 0.00 35.64 2.71
1152 2464 2.967599 TCTCCATCGTCTCCATGTTG 57.032 50.000 0.00 0.00 0.00 3.33
1153 2465 1.134699 TCTCCATCGTCTCCATGTTGC 60.135 52.381 0.00 0.00 0.00 4.17
1154 2466 0.612744 TCCATCGTCTCCATGTTGCA 59.387 50.000 0.00 0.00 0.00 4.08
1155 2467 1.012086 CCATCGTCTCCATGTTGCAG 58.988 55.000 0.00 0.00 0.00 4.41
1156 2468 0.376152 CATCGTCTCCATGTTGCAGC 59.624 55.000 0.00 0.00 0.00 5.25
1157 2469 0.745845 ATCGTCTCCATGTTGCAGCC 60.746 55.000 0.00 0.00 0.00 4.85
1158 2470 1.672030 CGTCTCCATGTTGCAGCCA 60.672 57.895 0.00 0.00 0.00 4.75
1159 2471 1.028330 CGTCTCCATGTTGCAGCCAT 61.028 55.000 0.00 0.00 0.00 4.40
1160 2472 0.737219 GTCTCCATGTTGCAGCCATC 59.263 55.000 0.00 0.00 0.00 3.51
1216 2528 2.127251 TCGATCATGCACGATGTTAGC 58.873 47.619 0.00 0.00 33.62 3.09
1467 2786 2.753055 TCGCCTGCAACAAGTACATA 57.247 45.000 0.00 0.00 0.00 2.29
1713 3032 3.291383 CGCCGGGCCAAGTTCAAA 61.291 61.111 14.55 0.00 0.00 2.69
1778 3101 7.639113 ACGCCATCTTAAATTCTTAAATCCA 57.361 32.000 0.00 0.00 0.00 3.41
1791 3114 4.473559 TCTTAAATCCATCGGTCTTCCCTT 59.526 41.667 0.00 0.00 0.00 3.95
1873 3196 2.883386 GGGTAGATCTCAACCGTACGAT 59.117 50.000 18.76 0.00 36.57 3.73
1874 3197 3.317430 GGGTAGATCTCAACCGTACGATT 59.683 47.826 18.76 1.52 36.57 3.34
1875 3198 4.288531 GGTAGATCTCAACCGTACGATTG 58.711 47.826 16.54 16.54 0.00 2.67
1876 3199 4.201990 GGTAGATCTCAACCGTACGATTGT 60.202 45.833 21.39 6.04 0.00 2.71
1877 3200 4.030134 AGATCTCAACCGTACGATTGTC 57.970 45.455 21.39 12.18 0.00 3.18
1984 3307 2.095919 GTGTCAACGCCAAGGTAATCAC 60.096 50.000 0.00 0.00 0.00 3.06
1998 3321 3.758554 GGTAATCACCAGCACTTCACATT 59.241 43.478 0.00 0.00 45.04 2.71
2002 3326 0.251341 ACCAGCACTTCACATTCCCC 60.251 55.000 0.00 0.00 0.00 4.81
2078 3404 8.134895 TGATGAACAAATAGTTGAAGTGTTTCC 58.865 33.333 10.35 0.00 41.51 3.13
2188 3518 3.561313 GGCTTGAAGATTACAACCTCCCA 60.561 47.826 0.00 0.00 0.00 4.37
2298 6714 6.088749 CAGCTAGCTTTATGTATGCGAGTAAG 59.911 42.308 16.46 0.00 33.85 2.34
2502 6918 0.889186 ACCCTCTTTCGCAAACGCAT 60.889 50.000 0.00 0.00 39.84 4.73
2503 6919 1.083489 CCCTCTTTCGCAAACGCATA 58.917 50.000 0.00 0.00 39.84 3.14
2504 6920 1.670811 CCCTCTTTCGCAAACGCATAT 59.329 47.619 0.00 0.00 39.84 1.78
2505 6921 2.539547 CCCTCTTTCGCAAACGCATATG 60.540 50.000 0.00 0.00 39.84 1.78
2506 6922 2.104144 CTCTTTCGCAAACGCATATGC 58.896 47.619 18.08 18.08 39.84 3.14
2507 6923 1.466558 TCTTTCGCAAACGCATATGCA 59.533 42.857 26.52 2.93 42.68 3.96
2508 6924 2.095516 TCTTTCGCAAACGCATATGCAA 60.096 40.909 26.52 9.21 42.68 4.08
2509 6925 2.338140 TTCGCAAACGCATATGCAAA 57.662 40.000 26.52 6.61 42.68 3.68
2510 6926 1.612156 TCGCAAACGCATATGCAAAC 58.388 45.000 26.52 10.23 42.68 2.93
2511 6927 0.639756 CGCAAACGCATATGCAAACC 59.360 50.000 26.52 9.84 42.68 3.27
2512 6928 0.639756 GCAAACGCATATGCAAACCG 59.360 50.000 26.52 12.64 42.12 4.44
2513 6929 1.975837 CAAACGCATATGCAAACCGT 58.024 45.000 26.52 13.29 42.21 4.83
2514 6930 1.910819 CAAACGCATATGCAAACCGTC 59.089 47.619 26.52 0.00 42.21 4.79
2515 6931 0.096281 AACGCATATGCAAACCGTCG 59.904 50.000 26.52 10.54 42.21 5.12
2516 6932 1.651132 CGCATATGCAAACCGTCGC 60.651 57.895 26.52 0.00 42.21 5.19
2517 6933 1.298339 GCATATGCAAACCGTCGCC 60.298 57.895 22.84 0.00 41.59 5.54
2518 6934 1.714899 GCATATGCAAACCGTCGCCT 61.715 55.000 22.84 0.00 41.59 5.52
2519 6935 0.732571 CATATGCAAACCGTCGCCTT 59.267 50.000 0.00 0.00 0.00 4.35
2520 6936 0.732571 ATATGCAAACCGTCGCCTTG 59.267 50.000 0.00 0.00 0.00 3.61
2521 6937 1.917782 TATGCAAACCGTCGCCTTGC 61.918 55.000 17.72 17.72 44.54 4.01
2532 6948 4.980903 GCCTTGCGTTGGTGTGCG 62.981 66.667 0.00 0.00 0.00 5.34
2533 6949 3.276091 CCTTGCGTTGGTGTGCGA 61.276 61.111 0.00 0.00 0.00 5.10
2534 6950 2.616330 CCTTGCGTTGGTGTGCGAT 61.616 57.895 0.00 0.00 0.00 4.58
2535 6951 1.440850 CTTGCGTTGGTGTGCGATG 60.441 57.895 0.00 0.00 0.00 3.84
2536 6952 1.840630 CTTGCGTTGGTGTGCGATGA 61.841 55.000 0.00 0.00 0.00 2.92
2537 6953 2.111932 TTGCGTTGGTGTGCGATGAC 62.112 55.000 0.00 0.00 0.00 3.06
2538 6954 2.603247 GCGTTGGTGTGCGATGACA 61.603 57.895 0.00 0.00 0.00 3.58
2539 6955 1.938125 CGTTGGTGTGCGATGACAA 59.062 52.632 0.00 0.00 0.00 3.18
2540 6956 0.384230 CGTTGGTGTGCGATGACAAC 60.384 55.000 0.00 0.00 38.36 3.32
2541 6957 0.384230 GTTGGTGTGCGATGACAACG 60.384 55.000 0.02 0.02 36.23 4.10
2542 6958 0.812014 TTGGTGTGCGATGACAACGT 60.812 50.000 6.98 0.00 36.23 3.99
2543 6959 0.032267 TGGTGTGCGATGACAACGTA 59.968 50.000 6.98 0.00 36.23 3.57
2544 6960 1.337354 TGGTGTGCGATGACAACGTAT 60.337 47.619 6.98 0.00 36.23 3.06
2545 6961 1.060553 GGTGTGCGATGACAACGTATG 59.939 52.381 6.98 0.00 0.00 2.39
2546 6962 1.989864 GTGTGCGATGACAACGTATGA 59.010 47.619 6.98 0.00 0.00 2.15
2547 6963 2.410392 GTGTGCGATGACAACGTATGAA 59.590 45.455 6.98 0.00 0.00 2.57
2548 6964 3.060602 TGTGCGATGACAACGTATGAAA 58.939 40.909 6.98 0.00 0.00 2.69
2549 6965 3.495001 TGTGCGATGACAACGTATGAAAA 59.505 39.130 6.98 0.00 0.00 2.29
2550 6966 4.153296 TGTGCGATGACAACGTATGAAAAT 59.847 37.500 6.98 0.00 0.00 1.82
2551 6967 4.491942 GTGCGATGACAACGTATGAAAATG 59.508 41.667 6.98 0.00 0.00 2.32
2552 6968 3.478516 GCGATGACAACGTATGAAAATGC 59.521 43.478 6.98 0.00 0.00 3.56
2553 6969 4.646960 CGATGACAACGTATGAAAATGCA 58.353 39.130 0.00 0.00 0.00 3.96
2554 6970 4.725280 CGATGACAACGTATGAAAATGCAG 59.275 41.667 0.00 0.00 0.00 4.41
2555 6971 5.445806 CGATGACAACGTATGAAAATGCAGA 60.446 40.000 0.00 0.00 0.00 4.26
2556 6972 5.878332 TGACAACGTATGAAAATGCAGAT 57.122 34.783 0.00 0.00 0.00 2.90
2557 6973 5.630061 TGACAACGTATGAAAATGCAGATG 58.370 37.500 0.00 0.00 0.00 2.90
2648 7066 6.644347 TGATAAGCAAAAGGTCCAACAAAAA 58.356 32.000 0.00 0.00 0.00 1.94
2650 7068 7.772757 TGATAAGCAAAAGGTCCAACAAAAATT 59.227 29.630 0.00 0.00 0.00 1.82
2687 7107 6.815089 ACAAAGGAACATATGCTCAACAAAA 58.185 32.000 8.33 0.00 0.00 2.44
2818 7244 3.093057 GCTACTGTCTCCCATCGGATAT 58.907 50.000 0.00 0.00 37.60 1.63
2820 7246 4.705507 GCTACTGTCTCCCATCGGATATAA 59.294 45.833 0.00 0.00 37.60 0.98
2839 7265 2.969821 ACCAGTAACCAAATGCTCCA 57.030 45.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.691732 CCTGCCCAACCCCATGAT 59.308 61.111 0.00 0.00 0.00 2.45
23 24 2.006415 CTATCCCTGCCCAACCCCA 61.006 63.158 0.00 0.00 0.00 4.96
29 31 2.364973 TCACGCTATCCCTGCCCA 60.365 61.111 0.00 0.00 0.00 5.36
57 59 3.497031 GCGCCAGTAACGGAAGGC 61.497 66.667 0.00 0.00 43.61 4.35
66 68 2.260434 GTCGTCTTGGCGCCAGTA 59.740 61.111 30.75 19.03 0.00 2.74
86 96 3.864686 CCGCCATTTGAGTCGCCG 61.865 66.667 0.00 0.00 0.00 6.46
87 97 4.179579 GCCGCCATTTGAGTCGCC 62.180 66.667 0.00 0.00 0.00 5.54
89 99 3.864686 CCGCCGCCATTTGAGTCG 61.865 66.667 0.00 0.00 0.00 4.18
90 100 3.508840 CCCGCCGCCATTTGAGTC 61.509 66.667 0.00 0.00 0.00 3.36
92 102 4.794648 TCCCCGCCGCCATTTGAG 62.795 66.667 0.00 0.00 0.00 3.02
102 112 1.227674 CTAATCTGCTGTCCCCGCC 60.228 63.158 0.00 0.00 0.00 6.13
112 122 1.076332 AACGTTGTCGGCTAATCTGC 58.924 50.000 0.00 0.00 41.85 4.26
114 124 2.334838 GTCAACGTTGTCGGCTAATCT 58.665 47.619 26.47 0.00 41.85 2.40
121 131 1.124297 CATCTTCGTCAACGTTGTCGG 59.876 52.381 35.14 24.80 39.53 4.79
122 132 1.124297 CCATCTTCGTCAACGTTGTCG 59.876 52.381 32.35 32.35 40.22 4.35
125 135 2.800544 ACTTCCATCTTCGTCAACGTTG 59.199 45.455 22.35 22.35 40.80 4.10
126 136 2.800544 CACTTCCATCTTCGTCAACGTT 59.199 45.455 0.00 0.00 40.80 3.99
164 174 1.134560 GACGGTGACCTTGTAGGCTAG 59.865 57.143 0.00 0.00 39.63 3.42
165 175 1.180029 GACGGTGACCTTGTAGGCTA 58.820 55.000 0.00 0.00 39.63 3.93
166 176 0.542232 AGACGGTGACCTTGTAGGCT 60.542 55.000 0.00 0.00 39.63 4.58
167 177 1.134560 CTAGACGGTGACCTTGTAGGC 59.865 57.143 4.59 0.00 39.63 3.93
168 178 2.163815 CACTAGACGGTGACCTTGTAGG 59.836 54.545 15.18 2.81 42.49 3.18
169 179 2.415625 GCACTAGACGGTGACCTTGTAG 60.416 54.545 10.22 10.22 39.34 2.74
170 180 1.542915 GCACTAGACGGTGACCTTGTA 59.457 52.381 0.00 0.00 39.34 2.41
171 181 0.317479 GCACTAGACGGTGACCTTGT 59.683 55.000 0.00 0.00 39.34 3.16
172 182 0.389948 GGCACTAGACGGTGACCTTG 60.390 60.000 0.00 0.00 39.18 3.61
174 184 0.330604 TAGGCACTAGACGGTGACCT 59.669 55.000 0.00 15.43 45.69 3.85
175 185 2.877975 TAGGCACTAGACGGTGACC 58.122 57.895 0.00 0.00 45.69 4.02
260 270 4.192317 CAAGAATTTTAGGACGGAGGGAG 58.808 47.826 0.00 0.00 0.00 4.30
262 272 3.939592 GACAAGAATTTTAGGACGGAGGG 59.060 47.826 0.00 0.00 0.00 4.30
264 274 7.321153 TCTAAGACAAGAATTTTAGGACGGAG 58.679 38.462 0.00 0.00 0.00 4.63
300 310 9.563898 CACGTTTTAGTGTTAGATACATCTGTA 57.436 33.333 1.88 0.00 39.39 2.74
301 311 8.301720 TCACGTTTTAGTGTTAGATACATCTGT 58.698 33.333 1.88 0.00 42.40 3.41
302 312 8.683550 TCACGTTTTAGTGTTAGATACATCTG 57.316 34.615 1.88 0.00 42.40 2.90
303 313 9.871238 ATTCACGTTTTAGTGTTAGATACATCT 57.129 29.630 0.00 0.00 42.40 2.90
310 320 9.494479 CGTATCTATTCACGTTTTAGTGTTAGA 57.506 33.333 11.61 11.61 42.40 2.10
323 333 5.027206 ACATACGGACGTATCTATTCACG 57.973 43.478 13.86 4.19 39.07 4.35
324 334 7.095481 TGTCTACATACGGACGTATCTATTCAC 60.095 40.741 13.86 7.51 39.07 3.18
325 335 6.930722 TGTCTACATACGGACGTATCTATTCA 59.069 38.462 13.86 8.73 39.07 2.57
326 336 7.356641 TGTCTACATACGGACGTATCTATTC 57.643 40.000 13.86 6.65 39.07 1.75
327 337 7.734924 TTGTCTACATACGGACGTATCTATT 57.265 36.000 13.86 3.06 39.07 1.73
328 338 7.734924 TTTGTCTACATACGGACGTATCTAT 57.265 36.000 13.86 6.29 39.07 1.98
329 339 7.658982 AGATTTGTCTACATACGGACGTATCTA 59.341 37.037 13.86 6.97 39.07 1.98
330 340 6.485984 AGATTTGTCTACATACGGACGTATCT 59.514 38.462 13.86 6.18 39.07 1.98
331 341 6.666417 AGATTTGTCTACATACGGACGTATC 58.334 40.000 13.86 4.37 39.07 2.24
332 342 6.630444 AGATTTGTCTACATACGGACGTAT 57.370 37.500 11.25 11.25 41.49 3.06
333 343 7.495606 TCTTAGATTTGTCTACATACGGACGTA 59.504 37.037 7.05 7.05 35.45 3.57
334 344 4.978083 AGATTTGTCTACATACGGACGT 57.022 40.909 1.98 1.98 35.45 4.34
335 345 6.632035 GTCTTAGATTTGTCTACATACGGACG 59.368 42.308 0.00 0.00 35.45 4.79
336 346 7.478322 TGTCTTAGATTTGTCTACATACGGAC 58.522 38.462 0.00 0.00 0.00 4.79
337 347 7.634671 TGTCTTAGATTTGTCTACATACGGA 57.365 36.000 0.00 0.00 0.00 4.69
338 348 8.188799 TCTTGTCTTAGATTTGTCTACATACGG 58.811 37.037 0.00 0.00 0.00 4.02
339 349 9.569167 TTCTTGTCTTAGATTTGTCTACATACG 57.431 33.333 0.00 0.00 0.00 3.06
349 359 9.322776 CGTCTCAAAATTCTTGTCTTAGATTTG 57.677 33.333 0.00 0.00 30.65 2.32
350 360 8.507249 CCGTCTCAAAATTCTTGTCTTAGATTT 58.493 33.333 0.00 0.00 0.00 2.17
351 361 7.878127 TCCGTCTCAAAATTCTTGTCTTAGATT 59.122 33.333 0.00 0.00 0.00 2.40
352 362 7.386851 TCCGTCTCAAAATTCTTGTCTTAGAT 58.613 34.615 0.00 0.00 0.00 1.98
353 363 6.755206 TCCGTCTCAAAATTCTTGTCTTAGA 58.245 36.000 0.00 0.00 0.00 2.10
354 364 6.091441 CCTCCGTCTCAAAATTCTTGTCTTAG 59.909 42.308 0.00 0.00 0.00 2.18
355 365 5.932303 CCTCCGTCTCAAAATTCTTGTCTTA 59.068 40.000 0.00 0.00 0.00 2.10
356 366 4.757149 CCTCCGTCTCAAAATTCTTGTCTT 59.243 41.667 0.00 0.00 0.00 3.01
357 367 4.319177 CCTCCGTCTCAAAATTCTTGTCT 58.681 43.478 0.00 0.00 0.00 3.41
358 368 3.437049 CCCTCCGTCTCAAAATTCTTGTC 59.563 47.826 0.00 0.00 0.00 3.18
359 369 3.072476 TCCCTCCGTCTCAAAATTCTTGT 59.928 43.478 0.00 0.00 0.00 3.16
360 370 3.674997 TCCCTCCGTCTCAAAATTCTTG 58.325 45.455 0.00 0.00 0.00 3.02
361 371 3.328050 ACTCCCTCCGTCTCAAAATTCTT 59.672 43.478 0.00 0.00 0.00 2.52
362 372 2.907042 ACTCCCTCCGTCTCAAAATTCT 59.093 45.455 0.00 0.00 0.00 2.40
363 373 3.336138 ACTCCCTCCGTCTCAAAATTC 57.664 47.619 0.00 0.00 0.00 2.17
364 374 4.903045 TTACTCCCTCCGTCTCAAAATT 57.097 40.909 0.00 0.00 0.00 1.82
365 375 6.749036 ATATTACTCCCTCCGTCTCAAAAT 57.251 37.500 0.00 0.00 0.00 1.82
366 376 6.555463 AATATTACTCCCTCCGTCTCAAAA 57.445 37.500 0.00 0.00 0.00 2.44
367 377 6.555463 AAATATTACTCCCTCCGTCTCAAA 57.445 37.500 0.00 0.00 0.00 2.69
368 378 7.507956 TCATAAATATTACTCCCTCCGTCTCAA 59.492 37.037 0.00 0.00 0.00 3.02
369 379 7.008332 TCATAAATATTACTCCCTCCGTCTCA 58.992 38.462 0.00 0.00 0.00 3.27
370 380 7.463961 TCATAAATATTACTCCCTCCGTCTC 57.536 40.000 0.00 0.00 0.00 3.36
371 381 7.509659 AGTTCATAAATATTACTCCCTCCGTCT 59.490 37.037 0.00 0.00 0.00 4.18
372 382 7.668492 AGTTCATAAATATTACTCCCTCCGTC 58.332 38.462 0.00 0.00 0.00 4.79
373 383 7.613551 AGTTCATAAATATTACTCCCTCCGT 57.386 36.000 0.00 0.00 0.00 4.69
374 384 7.095187 GCAAGTTCATAAATATTACTCCCTCCG 60.095 40.741 0.00 0.00 0.00 4.63
375 385 7.939588 AGCAAGTTCATAAATATTACTCCCTCC 59.060 37.037 0.00 0.00 0.00 4.30
376 386 8.910351 AGCAAGTTCATAAATATTACTCCCTC 57.090 34.615 0.00 0.00 0.00 4.30
377 387 9.700831 AAAGCAAGTTCATAAATATTACTCCCT 57.299 29.630 0.00 0.00 0.00 4.20
387 397 9.875691 GGAGGAAATTAAAGCAAGTTCATAAAT 57.124 29.630 0.47 0.00 41.84 1.40
388 398 8.026607 CGGAGGAAATTAAAGCAAGTTCATAAA 58.973 33.333 0.47 0.00 41.84 1.40
389 399 7.175990 ACGGAGGAAATTAAAGCAAGTTCATAA 59.824 33.333 0.47 0.00 41.84 1.90
390 400 6.657541 ACGGAGGAAATTAAAGCAAGTTCATA 59.342 34.615 0.47 0.00 41.84 2.15
391 401 5.476945 ACGGAGGAAATTAAAGCAAGTTCAT 59.523 36.000 0.47 0.00 41.84 2.57
392 402 4.825085 ACGGAGGAAATTAAAGCAAGTTCA 59.175 37.500 0.47 0.00 41.84 3.18
393 403 5.372547 ACGGAGGAAATTAAAGCAAGTTC 57.627 39.130 0.00 0.00 39.86 3.01
417 427 2.218603 ACACGGACGAAATTTGAGCTT 58.781 42.857 0.00 0.00 0.00 3.74
433 443 3.984018 AACGGATCGAATACAAACACG 57.016 42.857 0.00 0.00 0.00 4.49
463 473 8.641498 ATTCAACCAGAGTCTCAATTATTTGT 57.359 30.769 1.94 0.00 34.32 2.83
473 483 4.438148 GAAGGCTATTCAACCAGAGTCTC 58.562 47.826 0.00 0.00 0.00 3.36
474 484 3.118956 CGAAGGCTATTCAACCAGAGTCT 60.119 47.826 0.00 0.00 0.00 3.24
510 520 3.061429 GCGTCACTCTCAAATGTCTAAGC 59.939 47.826 0.00 0.00 0.00 3.09
599 693 3.089284 TGAACTGATCCTCGTGCTTCTA 58.911 45.455 0.00 0.00 0.00 2.10
640 739 0.037882 CCATGATCTCCGGGATGACG 60.038 60.000 0.00 0.00 34.33 4.35
651 750 2.955022 GAAGCCGCAGCCCATGATCT 62.955 60.000 0.00 0.00 41.25 2.75
681 1986 3.905249 GGCCGAGCCGAATTCTTT 58.095 55.556 3.52 0.00 39.62 2.52
708 2013 2.559440 GCATTTGCTTGGGTTTGAACA 58.441 42.857 0.00 0.00 38.21 3.18
742 2047 3.083848 TTGACACGTCGTGGGCTGT 62.084 57.895 27.77 7.74 37.94 4.40
882 2187 4.897051 AGTGGTGGGTTTATAGAGGAGAT 58.103 43.478 0.00 0.00 0.00 2.75
922 2227 2.101415 TGGCTAGGATGTGTGATTCGAG 59.899 50.000 0.00 0.00 0.00 4.04
971 2276 1.901591 CTGCAACCTGAGGTGACAAT 58.098 50.000 4.15 0.00 35.34 2.71
1038 2350 4.483950 AGGAAAGAAAGGGAAAGGAAAGG 58.516 43.478 0.00 0.00 0.00 3.11
1050 2362 2.637947 GGCCAGCTAGAGGAAAGAAAG 58.362 52.381 0.00 0.00 0.00 2.62
1051 2363 1.066143 CGGCCAGCTAGAGGAAAGAAA 60.066 52.381 2.24 0.00 0.00 2.52
1052 2364 0.537188 CGGCCAGCTAGAGGAAAGAA 59.463 55.000 2.24 0.00 0.00 2.52
1053 2365 1.330655 CCGGCCAGCTAGAGGAAAGA 61.331 60.000 2.24 0.00 0.00 2.52
1108 2420 3.013219 GGCCAGCTAGAGGAAAGAAAAG 58.987 50.000 0.00 0.00 0.00 2.27
1109 2421 2.615493 CGGCCAGCTAGAGGAAAGAAAA 60.615 50.000 2.24 0.00 0.00 2.29
1110 2422 1.066143 CGGCCAGCTAGAGGAAAGAAA 60.066 52.381 2.24 0.00 0.00 2.52
1111 2423 0.537188 CGGCCAGCTAGAGGAAAGAA 59.463 55.000 2.24 0.00 0.00 2.52
1112 2424 1.330655 CCGGCCAGCTAGAGGAAAGA 61.331 60.000 2.24 0.00 0.00 2.52
1113 2425 1.144936 CCGGCCAGCTAGAGGAAAG 59.855 63.158 2.24 0.00 0.00 2.62
1114 2426 0.691078 ATCCGGCCAGCTAGAGGAAA 60.691 55.000 2.24 0.00 34.35 3.13
1115 2427 1.075226 ATCCGGCCAGCTAGAGGAA 60.075 57.895 2.24 0.00 34.35 3.36
1116 2428 1.531840 GATCCGGCCAGCTAGAGGA 60.532 63.158 2.24 0.00 35.24 3.71
1117 2429 1.531739 GAGATCCGGCCAGCTAGAGG 61.532 65.000 2.24 0.00 0.00 3.69
1118 2430 1.531739 GGAGATCCGGCCAGCTAGAG 61.532 65.000 2.24 0.00 0.00 2.43
1119 2431 1.531840 GGAGATCCGGCCAGCTAGA 60.532 63.158 2.24 0.00 0.00 2.43
1120 2432 1.190833 ATGGAGATCCGGCCAGCTAG 61.191 60.000 2.24 0.00 37.64 3.42
1121 2433 1.152247 ATGGAGATCCGGCCAGCTA 60.152 57.895 2.24 0.00 37.64 3.32
1122 2434 2.447379 ATGGAGATCCGGCCAGCT 60.447 61.111 2.24 0.00 37.64 4.24
1123 2435 2.031768 GATGGAGATCCGGCCAGC 59.968 66.667 2.24 0.00 37.64 4.85
1124 2436 2.341543 CGATGGAGATCCGGCCAG 59.658 66.667 2.24 0.00 37.64 4.85
1125 2437 2.443952 ACGATGGAGATCCGGCCA 60.444 61.111 2.24 0.00 39.43 5.36
1126 2438 2.148558 GAGACGATGGAGATCCGGCC 62.149 65.000 0.00 0.00 39.43 6.13
1127 2439 1.287503 GAGACGATGGAGATCCGGC 59.712 63.158 0.00 0.00 39.43 6.13
1128 2440 0.823769 TGGAGACGATGGAGATCCGG 60.824 60.000 0.00 0.00 39.43 5.14
1129 2441 1.067985 CATGGAGACGATGGAGATCCG 60.068 57.143 0.00 0.00 39.43 4.18
1130 2442 1.967066 ACATGGAGACGATGGAGATCC 59.033 52.381 0.00 0.00 0.00 3.36
1131 2443 3.388308 CAACATGGAGACGATGGAGATC 58.612 50.000 0.00 0.00 0.00 2.75
1132 2444 2.484417 GCAACATGGAGACGATGGAGAT 60.484 50.000 0.00 0.00 0.00 2.75
1133 2445 1.134699 GCAACATGGAGACGATGGAGA 60.135 52.381 0.00 0.00 0.00 3.71
1134 2446 1.293924 GCAACATGGAGACGATGGAG 58.706 55.000 0.00 0.00 0.00 3.86
1135 2447 0.612744 TGCAACATGGAGACGATGGA 59.387 50.000 0.00 0.00 0.00 3.41
1136 2448 1.012086 CTGCAACATGGAGACGATGG 58.988 55.000 0.00 0.00 38.14 3.51
1137 2449 0.376152 GCTGCAACATGGAGACGATG 59.624 55.000 2.86 0.00 38.14 3.84
1138 2450 0.745845 GGCTGCAACATGGAGACGAT 60.746 55.000 0.50 0.00 38.14 3.73
1139 2451 1.375908 GGCTGCAACATGGAGACGA 60.376 57.895 0.50 0.00 38.14 4.20
1140 2452 3.181367 GGCTGCAACATGGAGACG 58.819 61.111 0.50 0.00 38.14 4.18
1141 2453 0.737219 GATGGCTGCAACATGGAGAC 59.263 55.000 8.17 0.00 44.95 3.36
1142 2454 0.328926 TGATGGCTGCAACATGGAGA 59.671 50.000 8.17 0.00 38.14 3.71
1143 2455 0.454600 GTGATGGCTGCAACATGGAG 59.545 55.000 8.17 0.00 38.97 3.86
1144 2456 0.966875 GGTGATGGCTGCAACATGGA 60.967 55.000 8.17 0.00 0.00 3.41
1145 2457 0.968901 AGGTGATGGCTGCAACATGG 60.969 55.000 8.17 0.00 0.00 3.66
1146 2458 0.892755 AAGGTGATGGCTGCAACATG 59.107 50.000 8.17 0.00 0.00 3.21
1147 2459 1.547372 GAAAGGTGATGGCTGCAACAT 59.453 47.619 0.50 3.40 0.00 2.71
1148 2460 0.961019 GAAAGGTGATGGCTGCAACA 59.039 50.000 0.50 0.00 0.00 3.33
1149 2461 1.251251 AGAAAGGTGATGGCTGCAAC 58.749 50.000 0.50 0.00 0.00 4.17
1150 2462 1.999648 AAGAAAGGTGATGGCTGCAA 58.000 45.000 0.50 0.00 0.00 4.08
1151 2463 1.999648 AAAGAAAGGTGATGGCTGCA 58.000 45.000 0.50 0.00 0.00 4.41
1152 2464 2.560105 AGAAAAGAAAGGTGATGGCTGC 59.440 45.455 0.00 0.00 0.00 5.25
1153 2465 4.861102 AAGAAAAGAAAGGTGATGGCTG 57.139 40.909 0.00 0.00 0.00 4.85
1154 2466 4.281941 GGAAAGAAAAGAAAGGTGATGGCT 59.718 41.667 0.00 0.00 0.00 4.75
1155 2467 4.281941 AGGAAAGAAAAGAAAGGTGATGGC 59.718 41.667 0.00 0.00 0.00 4.40
1156 2468 5.772169 AGAGGAAAGAAAAGAAAGGTGATGG 59.228 40.000 0.00 0.00 0.00 3.51
1157 2469 6.890979 AGAGGAAAGAAAAGAAAGGTGATG 57.109 37.500 0.00 0.00 0.00 3.07
1158 2470 6.657117 GCTAGAGGAAAGAAAAGAAAGGTGAT 59.343 38.462 0.00 0.00 0.00 3.06
1159 2471 5.998363 GCTAGAGGAAAGAAAAGAAAGGTGA 59.002 40.000 0.00 0.00 0.00 4.02
1160 2472 6.000840 AGCTAGAGGAAAGAAAAGAAAGGTG 58.999 40.000 0.00 0.00 0.00 4.00
1216 2528 3.483574 CGCGTTGGTTCAAGTAGCTATTG 60.484 47.826 0.00 3.31 0.00 1.90
1324 2643 0.530650 TCGAAGATGCGGATCTTGGC 60.531 55.000 33.19 19.81 47.00 4.52
1713 3032 3.470888 CTCTGGCGTCCGGGGAAT 61.471 66.667 0.00 0.00 30.29 3.01
1764 3087 6.321435 GGGAAGACCGATGGATTTAAGAATTT 59.679 38.462 0.00 0.00 36.97 1.82
1765 3088 5.828328 GGGAAGACCGATGGATTTAAGAATT 59.172 40.000 0.00 0.00 36.97 2.17
1766 3089 5.132816 AGGGAAGACCGATGGATTTAAGAAT 59.867 40.000 0.00 0.00 46.96 2.40
1767 3090 4.473559 AGGGAAGACCGATGGATTTAAGAA 59.526 41.667 0.00 0.00 46.96 2.52
1768 3091 4.037927 AGGGAAGACCGATGGATTTAAGA 58.962 43.478 0.00 0.00 46.96 2.10
1769 3092 4.423625 AGGGAAGACCGATGGATTTAAG 57.576 45.455 0.00 0.00 46.96 1.85
1770 3093 4.018779 ACAAGGGAAGACCGATGGATTTAA 60.019 41.667 0.00 0.00 46.96 1.52
1771 3094 3.521937 ACAAGGGAAGACCGATGGATTTA 59.478 43.478 0.00 0.00 46.96 1.40
1772 3095 2.308866 ACAAGGGAAGACCGATGGATTT 59.691 45.455 0.00 0.00 46.96 2.17
1778 3101 3.502123 TTCAAACAAGGGAAGACCGAT 57.498 42.857 0.00 0.00 46.96 4.18
1791 3114 1.403814 TTGGCCGTCCAATTCAAACA 58.596 45.000 0.00 0.00 46.89 2.83
1873 3196 3.064207 CTGGAAGAAACGATTCGGACAA 58.936 45.455 11.29 0.00 40.63 3.18
1874 3197 2.611971 CCTGGAAGAAACGATTCGGACA 60.612 50.000 11.29 0.22 40.63 4.02
1875 3198 2.000447 CCTGGAAGAAACGATTCGGAC 59.000 52.381 11.29 1.51 40.63 4.79
1876 3199 1.066430 CCCTGGAAGAAACGATTCGGA 60.066 52.381 11.29 0.00 40.63 4.55
1877 3200 1.369625 CCCTGGAAGAAACGATTCGG 58.630 55.000 11.29 0.00 40.63 4.30
1984 3307 0.251297 TGGGGAATGTGAAGTGCTGG 60.251 55.000 0.00 0.00 0.00 4.85
2078 3404 3.111098 GTCAGCAACTGCACAGAAAAAG 58.889 45.455 4.31 0.00 45.16 2.27
2188 3518 1.731424 CGACGAAGGCTGACACGTAAT 60.731 52.381 5.82 0.00 39.04 1.89
2298 6714 2.812011 GTCCCCACATGTTTATATCCGC 59.188 50.000 0.00 0.00 0.00 5.54
2457 6873 1.082117 CGTGTGCCCGATGGTCTTAC 61.082 60.000 0.00 0.00 0.00 2.34
2502 6918 1.917782 GCAAGGCGACGGTTTGCATA 61.918 55.000 8.72 0.00 44.88 3.14
2503 6919 2.953821 CAAGGCGACGGTTTGCAT 59.046 55.556 8.29 0.00 33.08 3.96
2504 6920 3.959975 GCAAGGCGACGGTTTGCA 61.960 61.111 8.72 0.00 44.88 4.08
2515 6931 4.980903 CGCACACCAACGCAAGGC 62.981 66.667 0.00 0.00 46.39 4.35
2516 6932 2.616330 ATCGCACACCAACGCAAGG 61.616 57.895 0.00 0.00 46.39 3.61
2518 6934 1.889573 TCATCGCACACCAACGCAA 60.890 52.632 0.00 0.00 0.00 4.85
2519 6935 2.280457 TCATCGCACACCAACGCA 60.280 55.556 0.00 0.00 0.00 5.24
2520 6936 2.111932 TTGTCATCGCACACCAACGC 62.112 55.000 0.00 0.00 0.00 4.84
2521 6937 0.384230 GTTGTCATCGCACACCAACG 60.384 55.000 0.00 0.00 0.00 4.10
2522 6938 0.384230 CGTTGTCATCGCACACCAAC 60.384 55.000 0.00 0.00 33.74 3.77
2523 6939 0.812014 ACGTTGTCATCGCACACCAA 60.812 50.000 3.21 0.00 0.00 3.67
2524 6940 0.032267 TACGTTGTCATCGCACACCA 59.968 50.000 0.00 0.00 0.00 4.17
2525 6941 1.060553 CATACGTTGTCATCGCACACC 59.939 52.381 0.00 0.00 0.00 4.16
2526 6942 1.989864 TCATACGTTGTCATCGCACAC 59.010 47.619 0.00 0.00 0.00 3.82
2527 6943 2.355717 TCATACGTTGTCATCGCACA 57.644 45.000 0.00 0.00 0.00 4.57
2528 6944 3.715618 TTTCATACGTTGTCATCGCAC 57.284 42.857 0.00 0.00 0.00 5.34
2529 6945 4.646960 CATTTTCATACGTTGTCATCGCA 58.353 39.130 0.00 0.00 0.00 5.10
2530 6946 3.478516 GCATTTTCATACGTTGTCATCGC 59.521 43.478 0.00 0.00 0.00 4.58
2531 6947 4.646960 TGCATTTTCATACGTTGTCATCG 58.353 39.130 0.00 1.75 0.00 3.84
2532 6948 5.868257 TCTGCATTTTCATACGTTGTCATC 58.132 37.500 0.00 0.00 0.00 2.92
2533 6949 5.878332 TCTGCATTTTCATACGTTGTCAT 57.122 34.783 0.00 0.00 0.00 3.06
2534 6950 5.181056 ACATCTGCATTTTCATACGTTGTCA 59.819 36.000 0.00 0.00 0.00 3.58
2535 6951 5.631026 ACATCTGCATTTTCATACGTTGTC 58.369 37.500 0.00 0.00 0.00 3.18
2536 6952 5.627499 ACATCTGCATTTTCATACGTTGT 57.373 34.783 0.00 0.00 0.00 3.32
2537 6953 6.932901 AAACATCTGCATTTTCATACGTTG 57.067 33.333 0.00 0.00 0.00 4.10
2538 6954 7.945033 AAAAACATCTGCATTTTCATACGTT 57.055 28.000 0.00 0.00 0.00 3.99
2585 7002 0.964700 CTATCTGATGCAGAGGCCGA 59.035 55.000 0.00 0.00 44.08 5.54
2612 7029 9.586732 ACCTTTTGCTTATCAATAATATGGCTA 57.413 29.630 0.00 0.00 34.12 3.93
2648 7066 8.062065 TGTTCCTTTGTTTGAGACTACAAAAT 57.938 30.769 4.13 0.00 41.96 1.82
2650 7068 7.639113 ATGTTCCTTTGTTTGAGACTACAAA 57.361 32.000 0.00 0.00 40.76 2.83
2760 7186 1.139520 GTTTGGATGGCGGTCATGC 59.860 57.895 7.18 7.18 43.44 4.06
2818 7244 4.374689 TGGAGCATTTGGTTACTGGTTA 57.625 40.909 0.00 0.00 0.00 2.85
2820 7246 2.969821 TGGAGCATTTGGTTACTGGT 57.030 45.000 0.00 0.00 0.00 4.00
2940 7366 4.317348 GCAATTTGAAACTGCAGAAACGAC 60.317 41.667 23.35 5.99 36.09 4.34


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

AutoCloner maintained by Alex Coulton.