Multiple sequence alignment - TraesCS3D01G074200

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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 TraesCS3D01G074200 chr3D 100.000 3278 0 0 1 3278 35042702 35045979 0.000000e+00 6054.0
1 TraesCS3D01G074200 chr3D 88.636 88 7 3 36 122 547986339 547986254 1.610000e-18 104.0
2 TraesCS3D01G074200 chr3B 97.668 1801 36 1 648 2442 58006499 58008299 0.000000e+00 3088.0
3 TraesCS3D01G074200 chr3B 92.345 614 24 5 2444 3039 58008340 58008948 0.000000e+00 852.0
4 TraesCS3D01G074200 chr3B 88.192 271 23 6 273 534 79291690 79291420 6.830000e-82 315.0
5 TraesCS3D01G074200 chr3B 93.333 120 8 0 532 651 58006120 58006239 9.350000e-41 178.0
6 TraesCS3D01G074200 chr3B 83.333 198 8 4 83 280 58005951 58006123 3.390000e-35 159.0
7 TraesCS3D01G074200 chr3B 92.453 106 7 1 118 223 478325953 478325849 2.040000e-32 150.0
8 TraesCS3D01G074200 chr3B 95.122 41 2 0 241 281 787109242 787109202 7.590000e-07 65.8
9 TraesCS3D01G074200 chr2A 89.334 1622 118 27 709 2309 32232146 32230559 0.000000e+00 1986.0
10 TraesCS3D01G074200 chr2A 86.504 1267 148 17 995 2251 32265147 32266400 0.000000e+00 1371.0
11 TraesCS3D01G074200 chr2A 87.778 270 21 9 278 537 703429097 703428830 4.110000e-79 305.0
12 TraesCS3D01G074200 chr2B 85.714 1372 168 14 911 2269 48815876 48817232 0.000000e+00 1423.0
13 TraesCS3D01G074200 chr2B 85.216 832 104 8 1430 2254 48804186 48803367 0.000000e+00 837.0
14 TraesCS3D01G074200 chr2D 85.327 1329 163 23 934 2251 30334248 30335555 0.000000e+00 1345.0
15 TraesCS3D01G074200 chr2D 86.957 276 23 9 269 534 371829342 371829614 6.880000e-77 298.0
16 TraesCS3D01G074200 chr4A 86.806 576 59 9 2465 3030 621730156 621730724 7.720000e-176 627.0
17 TraesCS3D01G074200 chr4A 88.931 262 20 6 278 530 54120259 54120520 6.830000e-82 315.0
18 TraesCS3D01G074200 chr4A 89.641 251 16 7 278 518 678553410 678553660 8.830000e-81 311.0
19 TraesCS3D01G074200 chr3A 80.454 793 102 25 2472 3245 713554843 713554085 1.030000e-154 556.0
20 TraesCS3D01G074200 chr3A 88.123 261 21 7 278 529 429797623 429797882 5.320000e-78 302.0
21 TraesCS3D01G074200 chr1B 88.931 262 19 7 278 529 593527726 593527987 6.830000e-82 315.0
22 TraesCS3D01G074200 chr1B 80.469 128 21 4 13 139 7162894 7163018 9.680000e-16 95.3
23 TraesCS3D01G074200 chr1B 80.315 127 21 4 14 139 7202892 7203015 3.480000e-15 93.5
24 TraesCS3D01G074200 chr7D 89.105 257 17 8 269 514 126245063 126244807 3.180000e-80 309.0
25 TraesCS3D01G074200 chr5A 88.934 244 21 4 277 517 476663376 476663136 2.470000e-76 296.0
26 TraesCS3D01G074200 chr5A 84.848 99 15 0 121 219 569066291 569066389 2.080000e-17 100.0
27 TraesCS3D01G074200 chr6B 86.869 99 12 1 122 220 141091468 141091565 3.460000e-20 110.0
28 TraesCS3D01G074200 chr1D 86.458 96 13 0 122 217 437684946 437684851 4.470000e-19 106.0
29 TraesCS3D01G074200 chr1D 87.500 72 9 0 47 118 288922860 288922789 2.100000e-12 84.2
30 TraesCS3D01G074200 chr7A 84.375 64 7 3 3177 3238 40719171 40719233 3.530000e-05 60.2


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 TraesCS3D01G074200 chr3D 35042702 35045979 3277 False 6054.00 6054 100.00000 1 3278 1 chr3D.!!$F1 3277
1 TraesCS3D01G074200 chr3B 58005951 58008948 2997 False 1069.25 3088 91.66975 83 3039 4 chr3B.!!$F1 2956
2 TraesCS3D01G074200 chr2A 32230559 32232146 1587 True 1986.00 1986 89.33400 709 2309 1 chr2A.!!$R1 1600
3 TraesCS3D01G074200 chr2A 32265147 32266400 1253 False 1371.00 1371 86.50400 995 2251 1 chr2A.!!$F1 1256
4 TraesCS3D01G074200 chr2B 48815876 48817232 1356 False 1423.00 1423 85.71400 911 2269 1 chr2B.!!$F1 1358
5 TraesCS3D01G074200 chr2B 48803367 48804186 819 True 837.00 837 85.21600 1430 2254 1 chr2B.!!$R1 824
6 TraesCS3D01G074200 chr2D 30334248 30335555 1307 False 1345.00 1345 85.32700 934 2251 1 chr2D.!!$F1 1317
7 TraesCS3D01G074200 chr4A 621730156 621730724 568 False 627.00 627 86.80600 2465 3030 1 chr4A.!!$F2 565
8 TraesCS3D01G074200 chr3A 713554085 713554843 758 True 556.00 556 80.45400 2472 3245 1 chr3A.!!$R1 773

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
679 943 0.106894 CTCCCCCGAGGTATTTGCTC 59.893 60.0 0.0 0.0 36.75 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 2633 1.079405 GCTCATTCGGTCGAACCCA 60.079 57.895 8.0 0.0 36.91 4.51 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.907917 TTTTTCCGCCACCACCGG 60.908 61.111 0.00 0.00 46.88 5.28
100 101 1.407329 CGCGACGCTAATATCGTGC 59.593 57.895 19.02 0.00 41.37 5.34
168 169 9.918630 AAAGACAAATAAGATCCAACAATTCTG 57.081 29.630 0.00 0.00 0.00 3.02
170 171 9.300681 AGACAAATAAGATCCAACAATTCTGAA 57.699 29.630 0.00 0.00 0.00 3.02
195 196 7.763172 CTCAGATGTGAGGTAAGTATTTCAC 57.237 40.000 12.01 0.00 45.85 3.18
200 201 5.931294 TGTGAGGTAAGTATTTCACAACCA 58.069 37.500 3.89 0.00 44.81 3.67
201 202 5.995282 TGTGAGGTAAGTATTTCACAACCAG 59.005 40.000 3.89 0.00 44.81 4.00
202 203 6.183361 TGTGAGGTAAGTATTTCACAACCAGA 60.183 38.462 3.89 0.00 44.81 3.86
203 204 6.879458 GTGAGGTAAGTATTTCACAACCAGAT 59.121 38.462 0.00 0.00 39.67 2.90
204 205 6.878923 TGAGGTAAGTATTTCACAACCAGATG 59.121 38.462 0.00 0.00 37.72 2.90
205 206 6.779860 AGGTAAGTATTTCACAACCAGATGT 58.220 36.000 0.00 0.00 37.72 3.06
227 228 3.188873 TGAAATAGCAAACCCGTTTACCG 59.811 43.478 0.00 0.00 0.00 4.02
233 234 1.192090 CAAACCCGTTTACCGTACACG 59.808 52.381 9.76 9.76 39.44 4.49
280 281 3.081804 GGCCACACTGCTTGTTTATACT 58.918 45.455 0.00 0.00 35.67 2.12
281 282 3.127030 GGCCACACTGCTTGTTTATACTC 59.873 47.826 0.00 0.00 35.67 2.59
282 283 4.003648 GCCACACTGCTTGTTTATACTCT 58.996 43.478 0.00 0.00 35.67 3.24
283 284 4.093556 GCCACACTGCTTGTTTATACTCTC 59.906 45.833 0.00 0.00 35.67 3.20
284 285 5.482908 CCACACTGCTTGTTTATACTCTCT 58.517 41.667 0.00 0.00 35.67 3.10
285 286 5.934625 CCACACTGCTTGTTTATACTCTCTT 59.065 40.000 0.00 0.00 35.67 2.85
286 287 6.091441 CCACACTGCTTGTTTATACTCTCTTC 59.909 42.308 0.00 0.00 35.67 2.87
287 288 5.864474 ACACTGCTTGTTTATACTCTCTTCG 59.136 40.000 0.00 0.00 33.09 3.79
288 289 5.864474 CACTGCTTGTTTATACTCTCTTCGT 59.136 40.000 0.00 0.00 0.00 3.85
289 290 6.366332 CACTGCTTGTTTATACTCTCTTCGTT 59.634 38.462 0.00 0.00 0.00 3.85
290 291 6.929606 ACTGCTTGTTTATACTCTCTTCGTTT 59.070 34.615 0.00 0.00 0.00 3.60
291 292 7.116519 ACTGCTTGTTTATACTCTCTTCGTTTC 59.883 37.037 0.00 0.00 0.00 2.78
292 293 7.152645 TGCTTGTTTATACTCTCTTCGTTTCT 58.847 34.615 0.00 0.00 0.00 2.52
293 294 7.656137 TGCTTGTTTATACTCTCTTCGTTTCTT 59.344 33.333 0.00 0.00 0.00 2.52
294 295 8.496751 GCTTGTTTATACTCTCTTCGTTTCTTT 58.503 33.333 0.00 0.00 0.00 2.52
301 302 8.760103 ATACTCTCTTCGTTTCTTTTTAGTCC 57.240 34.615 0.00 0.00 0.00 3.85
302 303 5.690857 ACTCTCTTCGTTTCTTTTTAGTCCG 59.309 40.000 0.00 0.00 0.00 4.79
303 304 4.446719 TCTCTTCGTTTCTTTTTAGTCCGC 59.553 41.667 0.00 0.00 0.00 5.54
304 305 4.121317 TCTTCGTTTCTTTTTAGTCCGCA 58.879 39.130 0.00 0.00 0.00 5.69
305 306 4.753107 TCTTCGTTTCTTTTTAGTCCGCAT 59.247 37.500 0.00 0.00 0.00 4.73
306 307 5.927689 TCTTCGTTTCTTTTTAGTCCGCATA 59.072 36.000 0.00 0.00 0.00 3.14
307 308 6.592607 TCTTCGTTTCTTTTTAGTCCGCATAT 59.407 34.615 0.00 0.00 0.00 1.78
308 309 7.760794 TCTTCGTTTCTTTTTAGTCCGCATATA 59.239 33.333 0.00 0.00 0.00 0.86
309 310 7.830940 TCGTTTCTTTTTAGTCCGCATATAA 57.169 32.000 0.00 0.00 0.00 0.98
310 311 7.902032 TCGTTTCTTTTTAGTCCGCATATAAG 58.098 34.615 0.00 0.00 0.00 1.73
311 312 7.010738 TCGTTTCTTTTTAGTCCGCATATAAGG 59.989 37.037 0.00 0.00 0.00 2.69
312 313 7.201582 CGTTTCTTTTTAGTCCGCATATAAGGT 60.202 37.037 0.00 0.00 0.00 3.50
313 314 8.456471 GTTTCTTTTTAGTCCGCATATAAGGTT 58.544 33.333 0.00 0.00 0.00 3.50
314 315 8.570068 TTCTTTTTAGTCCGCATATAAGGTTT 57.430 30.769 0.00 0.00 0.00 3.27
315 316 7.981142 TCTTTTTAGTCCGCATATAAGGTTTG 58.019 34.615 0.00 0.00 0.00 2.93
316 317 6.687081 TTTTAGTCCGCATATAAGGTTTGG 57.313 37.500 0.00 0.00 0.00 3.28
317 318 3.926058 AGTCCGCATATAAGGTTTGGT 57.074 42.857 0.00 0.00 0.00 3.67
318 319 3.805207 AGTCCGCATATAAGGTTTGGTC 58.195 45.455 0.00 0.00 0.00 4.02
319 320 3.199071 AGTCCGCATATAAGGTTTGGTCA 59.801 43.478 0.00 0.00 0.00 4.02
320 321 3.942748 GTCCGCATATAAGGTTTGGTCAA 59.057 43.478 0.00 0.00 0.00 3.18
321 322 4.396790 GTCCGCATATAAGGTTTGGTCAAA 59.603 41.667 0.00 0.00 0.00 2.69
322 323 4.638421 TCCGCATATAAGGTTTGGTCAAAG 59.362 41.667 0.00 0.00 0.00 2.77
323 324 4.398044 CCGCATATAAGGTTTGGTCAAAGT 59.602 41.667 0.00 0.00 0.00 2.66
324 325 5.448632 CCGCATATAAGGTTTGGTCAAAGTC 60.449 44.000 0.00 0.00 0.00 3.01
325 326 5.123186 CGCATATAAGGTTTGGTCAAAGTCA 59.877 40.000 0.00 0.00 0.00 3.41
326 327 6.348950 CGCATATAAGGTTTGGTCAAAGTCAA 60.349 38.462 0.00 0.00 0.00 3.18
327 328 7.029563 GCATATAAGGTTTGGTCAAAGTCAAG 58.970 38.462 0.00 0.00 0.00 3.02
328 329 3.801114 AAGGTTTGGTCAAAGTCAAGC 57.199 42.857 0.00 0.00 0.00 4.01
329 330 3.018423 AGGTTTGGTCAAAGTCAAGCT 57.982 42.857 0.00 0.00 0.00 3.74
330 331 3.365472 AGGTTTGGTCAAAGTCAAGCTT 58.635 40.909 0.00 0.00 39.52 3.74
347 348 7.478520 TCAAGCTTTGTAGAGTTTGACTAAC 57.521 36.000 0.00 0.00 40.46 2.34
349 350 7.769044 TCAAGCTTTGTAGAGTTTGACTAACTT 59.231 33.333 0.00 0.00 47.00 2.66
350 351 8.398665 CAAGCTTTGTAGAGTTTGACTAACTTT 58.601 33.333 0.00 1.31 47.00 2.66
351 352 9.609346 AAGCTTTGTAGAGTTTGACTAACTTTA 57.391 29.630 3.78 0.37 47.00 1.85
352 353 9.780186 AGCTTTGTAGAGTTTGACTAACTTTAT 57.220 29.630 3.78 0.00 47.00 1.40
404 405 9.743581 ATGAAATCAGTATTATCATATGCACCA 57.256 29.630 0.00 0.00 0.00 4.17
405 406 9.743581 TGAAATCAGTATTATCATATGCACCAT 57.256 29.630 0.00 0.00 0.00 3.55
407 408 8.429493 AATCAGTATTATCATATGCACCATCG 57.571 34.615 0.00 0.00 0.00 3.84
408 409 7.169158 TCAGTATTATCATATGCACCATCGA 57.831 36.000 0.00 0.00 0.00 3.59
409 410 7.610865 TCAGTATTATCATATGCACCATCGAA 58.389 34.615 0.00 0.00 0.00 3.71
410 411 8.260114 TCAGTATTATCATATGCACCATCGAAT 58.740 33.333 0.00 0.00 0.00 3.34
411 412 8.333186 CAGTATTATCATATGCACCATCGAATG 58.667 37.037 0.00 0.00 0.00 2.67
412 413 8.043113 AGTATTATCATATGCACCATCGAATGT 58.957 33.333 0.00 0.00 0.00 2.71
413 414 9.313118 GTATTATCATATGCACCATCGAATGTA 57.687 33.333 0.00 0.00 0.00 2.29
414 415 8.969260 ATTATCATATGCACCATCGAATGTAT 57.031 30.769 0.00 0.00 0.00 2.29
415 416 8.791327 TTATCATATGCACCATCGAATGTATT 57.209 30.769 0.00 0.00 0.00 1.89
416 417 7.692460 ATCATATGCACCATCGAATGTATTT 57.308 32.000 0.00 0.00 0.00 1.40
417 418 7.509141 TCATATGCACCATCGAATGTATTTT 57.491 32.000 0.00 0.00 0.00 1.82
418 419 7.584108 TCATATGCACCATCGAATGTATTTTC 58.416 34.615 0.00 0.00 0.00 2.29
419 420 5.833406 ATGCACCATCGAATGTATTTTCA 57.167 34.783 0.00 0.00 0.00 2.69
420 421 5.833406 TGCACCATCGAATGTATTTTCAT 57.167 34.783 0.00 0.00 0.00 2.57
421 422 6.934048 TGCACCATCGAATGTATTTTCATA 57.066 33.333 0.00 0.00 0.00 2.15
422 423 6.724263 TGCACCATCGAATGTATTTTCATAC 58.276 36.000 0.00 0.00 36.52 2.39
423 424 6.542005 TGCACCATCGAATGTATTTTCATACT 59.458 34.615 0.00 0.00 36.87 2.12
424 425 7.713073 TGCACCATCGAATGTATTTTCATACTA 59.287 33.333 0.00 0.00 36.87 1.82
425 426 8.721478 GCACCATCGAATGTATTTTCATACTAT 58.279 33.333 0.00 0.00 36.87 2.12
489 490 9.783256 AAATTTACTGTGTAGTTTGACTTTGAC 57.217 29.630 0.00 0.00 38.36 3.18
490 491 8.732746 ATTTACTGTGTAGTTTGACTTTGACT 57.267 30.769 0.00 0.00 38.36 3.41
491 492 9.826574 ATTTACTGTGTAGTTTGACTTTGACTA 57.173 29.630 0.00 0.00 38.36 2.59
492 493 9.656040 TTTACTGTGTAGTTTGACTTTGACTAA 57.344 29.630 0.00 0.00 38.36 2.24
493 494 9.656040 TTACTGTGTAGTTTGACTTTGACTAAA 57.344 29.630 0.00 0.00 38.36 1.85
494 495 8.732746 ACTGTGTAGTTTGACTTTGACTAAAT 57.267 30.769 0.00 0.00 31.66 1.40
495 496 8.827677 ACTGTGTAGTTTGACTTTGACTAAATC 58.172 33.333 0.00 0.00 31.66 2.17
496 497 8.958119 TGTGTAGTTTGACTTTGACTAAATCT 57.042 30.769 0.00 0.00 0.00 2.40
497 498 9.391006 TGTGTAGTTTGACTTTGACTAAATCTT 57.609 29.630 0.00 0.00 0.00 2.40
505 506 8.322906 TGACTTTGACTAAATCTTATGTGTGG 57.677 34.615 0.00 0.00 0.00 4.17
506 507 8.154203 TGACTTTGACTAAATCTTATGTGTGGA 58.846 33.333 0.00 0.00 0.00 4.02
507 508 8.553459 ACTTTGACTAAATCTTATGTGTGGAG 57.447 34.615 0.00 0.00 0.00 3.86
508 509 8.157476 ACTTTGACTAAATCTTATGTGTGGAGT 58.843 33.333 0.00 0.00 0.00 3.85
509 510 9.653287 CTTTGACTAAATCTTATGTGTGGAGTA 57.347 33.333 0.00 0.00 0.00 2.59
520 521 8.792633 TCTTATGTGTGGAGTAAAAAGAAATGG 58.207 33.333 0.00 0.00 0.00 3.16
521 522 8.698973 TTATGTGTGGAGTAAAAAGAAATGGA 57.301 30.769 0.00 0.00 0.00 3.41
522 523 7.595819 ATGTGTGGAGTAAAAAGAAATGGAA 57.404 32.000 0.00 0.00 0.00 3.53
523 524 7.595819 TGTGTGGAGTAAAAAGAAATGGAAT 57.404 32.000 0.00 0.00 0.00 3.01
524 525 7.432869 TGTGTGGAGTAAAAAGAAATGGAATG 58.567 34.615 0.00 0.00 0.00 2.67
525 526 7.286546 TGTGTGGAGTAAAAAGAAATGGAATGA 59.713 33.333 0.00 0.00 0.00 2.57
526 527 7.809806 GTGTGGAGTAAAAAGAAATGGAATGAG 59.190 37.037 0.00 0.00 0.00 2.90
527 528 7.505585 TGTGGAGTAAAAAGAAATGGAATGAGT 59.494 33.333 0.00 0.00 0.00 3.41
528 529 9.010029 GTGGAGTAAAAAGAAATGGAATGAGTA 57.990 33.333 0.00 0.00 0.00 2.59
529 530 9.010029 TGGAGTAAAAAGAAATGGAATGAGTAC 57.990 33.333 0.00 0.00 0.00 2.73
530 531 9.010029 GGAGTAAAAAGAAATGGAATGAGTACA 57.990 33.333 0.00 0.00 0.00 2.90
556 557 5.869579 ACAATGAATACAGAGGTGAACAGT 58.130 37.500 0.00 0.00 0.00 3.55
564 565 5.312120 ACAGAGGTGAACAGTTCTATACG 57.688 43.478 14.51 2.01 0.00 3.06
565 566 4.106197 CAGAGGTGAACAGTTCTATACGC 58.894 47.826 14.51 4.29 0.00 4.42
665 929 0.242825 GCTAAAACGCCAAACTCCCC 59.757 55.000 0.00 0.00 0.00 4.81
679 943 0.106894 CTCCCCCGAGGTATTTGCTC 59.893 60.000 0.00 0.00 36.75 4.26
927 1192 2.079170 TCCCACATGCAACAAGGAAA 57.921 45.000 0.00 0.00 0.00 3.13
940 1209 6.094881 TGCAACAAGGAAAGGCTTATATACAC 59.905 38.462 0.00 0.00 0.00 2.90
1027 1306 2.732016 CGGTGGTGACCAAGTCGA 59.268 61.111 5.57 0.00 43.33 4.20
1104 1383 2.599281 TCCTTCGACAGGTCCGCA 60.599 61.111 11.73 0.00 44.37 5.69
1180 1459 1.142748 GAGACCATCAGGACGGCAG 59.857 63.158 0.00 0.00 38.69 4.85
1623 1905 2.262603 CAGGCACTCAGCTGCGTA 59.737 61.111 9.41 0.00 44.79 4.42
1659 1941 1.642037 CGCTCCTCGACTTCACCGTA 61.642 60.000 0.00 0.00 41.67 4.02
1998 2289 1.903877 CGGATCTGCTTGTCCCCAGT 61.904 60.000 0.00 0.00 0.00 4.00
2478 2837 1.915769 AAAGAGCAGGGCCGTCTCT 60.916 57.895 20.16 20.16 38.72 3.10
2488 2847 1.407979 GGGCCGTCTCTAGAAATTCGA 59.592 52.381 0.00 0.00 0.00 3.71
2491 2850 2.099427 GCCGTCTCTAGAAATTCGAGGT 59.901 50.000 3.39 0.00 0.00 3.85
2550 2909 5.358298 AAGTTCCTTACAACGAAAGCATC 57.642 39.130 0.00 0.00 0.00 3.91
2551 2910 4.385825 AGTTCCTTACAACGAAAGCATCA 58.614 39.130 0.00 0.00 0.00 3.07
2885 3263 0.455633 CTCTGCTTTGCGGCATGTTC 60.456 55.000 2.28 0.00 41.63 3.18
3059 3437 6.525578 TTTTTGAGAGAGATAGCGAGGTAA 57.474 37.500 0.00 0.00 0.00 2.85
3060 3438 5.502153 TTTGAGAGAGATAGCGAGGTAAC 57.498 43.478 0.00 0.00 0.00 2.50
3089 3467 2.108168 CCTAATCGGGGACAGAGTTCA 58.892 52.381 0.00 0.00 0.00 3.18
3094 3472 0.944311 CGGGGACAGAGTTCAACACG 60.944 60.000 0.00 0.00 0.00 4.49
3099 3477 1.071471 CAGAGTTCAACACGGCCCT 59.929 57.895 0.00 0.00 0.00 5.19
3116 3520 1.817099 CTTGCGATCAGACCAGGCC 60.817 63.158 0.00 0.00 0.00 5.19
3147 3551 4.820716 CCAAATCCATGCAAACAAAGGAAA 59.179 37.500 0.00 0.00 37.53 3.13
3149 3553 6.016108 CCAAATCCATGCAAACAAAGGAAAAT 60.016 34.615 0.00 0.00 37.53 1.82
3150 3554 7.174599 CCAAATCCATGCAAACAAAGGAAAATA 59.825 33.333 0.00 0.00 37.53 1.40
3151 3555 8.566260 CAAATCCATGCAAACAAAGGAAAATAA 58.434 29.630 0.00 0.00 37.53 1.40
3152 3556 8.688747 AATCCATGCAAACAAAGGAAAATAAA 57.311 26.923 0.00 0.00 37.53 1.40
3153 3557 8.688747 ATCCATGCAAACAAAGGAAAATAAAA 57.311 26.923 0.00 0.00 37.53 1.52
3157 3561 9.947669 CATGCAAACAAAGGAAAATAAAAATCA 57.052 25.926 0.00 0.00 0.00 2.57
3187 3591 3.688049 ATATAGCCTTGGCCCAAAACT 57.312 42.857 8.17 0.04 0.00 2.66
3188 3592 4.806952 ATATAGCCTTGGCCCAAAACTA 57.193 40.909 8.17 2.56 0.00 2.24
3191 3595 0.541998 GCCTTGGCCCAAAACTAGGT 60.542 55.000 0.00 0.00 33.08 3.08
3203 3609 6.239772 GCCCAAAACTAGGTCCCTAAAATTTT 60.240 38.462 8.75 8.75 0.00 1.82
3204 3610 7.690797 GCCCAAAACTAGGTCCCTAAAATTTTT 60.691 37.037 9.06 0.00 0.00 1.94
3205 3611 7.659799 CCCAAAACTAGGTCCCTAAAATTTTTG 59.340 37.037 9.06 7.07 31.94 2.44
3216 3622 0.842635 AAATTTTTGGGCCCTGTGCA 59.157 45.000 25.70 0.00 43.89 4.57
3245 3651 2.491152 CGCACATGGCATTGGACC 59.509 61.111 0.00 0.00 45.17 4.46
3246 3652 2.894919 GCACATGGCATTGGACCC 59.105 61.111 0.00 0.00 43.97 4.46
3247 3653 2.724273 GCACATGGCATTGGACCCC 61.724 63.158 0.00 0.00 43.97 4.95
3248 3654 1.000739 CACATGGCATTGGACCCCT 59.999 57.895 0.00 0.00 0.00 4.79
3249 3655 1.000739 ACATGGCATTGGACCCCTG 59.999 57.895 0.00 0.00 0.00 4.45
3250 3656 1.307309 CATGGCATTGGACCCCTGA 59.693 57.895 0.00 0.00 0.00 3.86
3251 3657 1.039233 CATGGCATTGGACCCCTGAC 61.039 60.000 0.00 0.00 0.00 3.51
3252 3658 1.508667 ATGGCATTGGACCCCTGACA 61.509 55.000 0.00 1.65 31.25 3.58
3253 3659 1.076549 GGCATTGGACCCCTGACAA 59.923 57.895 0.00 0.00 0.00 3.18
3254 3660 0.541764 GGCATTGGACCCCTGACAAA 60.542 55.000 0.00 0.00 0.00 2.83
3255 3661 0.890683 GCATTGGACCCCTGACAAAG 59.109 55.000 0.00 0.00 0.00 2.77
3256 3662 1.547675 GCATTGGACCCCTGACAAAGA 60.548 52.381 0.00 0.00 0.00 2.52
3257 3663 2.440409 CATTGGACCCCTGACAAAGAG 58.560 52.381 0.00 0.00 0.00 2.85
3258 3664 0.771127 TTGGACCCCTGACAAAGAGG 59.229 55.000 0.00 0.00 0.00 3.69
3259 3665 0.104672 TGGACCCCTGACAAAGAGGA 60.105 55.000 0.00 0.00 31.48 3.71
3260 3666 1.290134 GGACCCCTGACAAAGAGGAT 58.710 55.000 0.00 0.00 31.48 3.24
3261 3667 2.225779 TGGACCCCTGACAAAGAGGATA 60.226 50.000 0.00 0.00 31.48 2.59
3262 3668 3.049344 GGACCCCTGACAAAGAGGATAT 58.951 50.000 0.00 0.00 31.48 1.63
3263 3669 3.071747 GGACCCCTGACAAAGAGGATATC 59.928 52.174 0.00 0.00 31.48 1.63
3264 3670 2.700897 ACCCCTGACAAAGAGGATATCG 59.299 50.000 0.00 0.00 31.48 2.92
3265 3671 2.700897 CCCCTGACAAAGAGGATATCGT 59.299 50.000 0.00 0.00 31.48 3.73
3266 3672 3.493350 CCCCTGACAAAGAGGATATCGTG 60.493 52.174 1.92 0.00 31.48 4.35
3267 3673 3.384789 CCCTGACAAAGAGGATATCGTGA 59.615 47.826 1.92 0.00 31.48 4.35
3268 3674 4.363999 CCTGACAAAGAGGATATCGTGAC 58.636 47.826 1.92 0.00 31.48 3.67
3269 3675 4.098654 CCTGACAAAGAGGATATCGTGACT 59.901 45.833 1.92 0.00 31.48 3.41
3270 3676 5.299531 CCTGACAAAGAGGATATCGTGACTA 59.700 44.000 1.92 0.00 31.48 2.59
3271 3677 6.015856 CCTGACAAAGAGGATATCGTGACTAT 60.016 42.308 1.92 0.00 31.48 2.12
3272 3678 6.971602 TGACAAAGAGGATATCGTGACTATC 58.028 40.000 1.92 0.00 0.00 2.08
3273 3679 6.546034 TGACAAAGAGGATATCGTGACTATCA 59.454 38.462 1.92 0.00 0.00 2.15
3274 3680 7.068226 TGACAAAGAGGATATCGTGACTATCAA 59.932 37.037 1.92 0.00 0.00 2.57
3275 3681 7.957002 ACAAAGAGGATATCGTGACTATCAAT 58.043 34.615 1.92 0.00 0.00 2.57
3276 3682 8.424918 ACAAAGAGGATATCGTGACTATCAATT 58.575 33.333 1.92 0.00 0.00 2.32
3277 3683 9.914131 CAAAGAGGATATCGTGACTATCAATTA 57.086 33.333 1.92 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.907917 CCGGTGGTGGCGGAAAAA 60.908 61.111 0.00 0.00 0.00 1.94
20 21 3.835790 CTCCGGTGGTGGCGGAAAA 62.836 63.158 0.00 0.00 0.00 2.29
21 22 4.323477 CTCCGGTGGTGGCGGAAA 62.323 66.667 0.00 0.00 0.00 3.13
98 99 2.747460 GCATCTCCAACAGGCGCA 60.747 61.111 10.83 0.00 0.00 6.09
100 101 3.805267 GAGCATCTCCAACAGGCG 58.195 61.111 0.00 0.00 0.00 5.52
168 169 8.035394 TGAAATACTTACCTCACATCTGAGTTC 58.965 37.037 0.00 0.00 42.36 3.01
170 171 7.039011 TGTGAAATACTTACCTCACATCTGAGT 60.039 37.037 0.00 0.00 42.36 3.41
193 194 5.375417 TTGCTATTTCACATCTGGTTGTG 57.625 39.130 5.68 5.68 46.70 3.33
194 195 5.278957 GGTTTGCTATTTCACATCTGGTTGT 60.279 40.000 0.00 0.00 0.00 3.32
195 196 5.163513 GGTTTGCTATTTCACATCTGGTTG 58.836 41.667 0.00 0.00 0.00 3.77
196 197 4.220602 GGGTTTGCTATTTCACATCTGGTT 59.779 41.667 0.00 0.00 0.00 3.67
197 198 3.763897 GGGTTTGCTATTTCACATCTGGT 59.236 43.478 0.00 0.00 0.00 4.00
198 199 3.181497 CGGGTTTGCTATTTCACATCTGG 60.181 47.826 0.00 0.00 0.00 3.86
199 200 3.440173 ACGGGTTTGCTATTTCACATCTG 59.560 43.478 0.00 0.00 0.00 2.90
200 201 3.686016 ACGGGTTTGCTATTTCACATCT 58.314 40.909 0.00 0.00 0.00 2.90
201 202 4.434713 AACGGGTTTGCTATTTCACATC 57.565 40.909 0.00 0.00 0.00 3.06
202 203 4.864704 AAACGGGTTTGCTATTTCACAT 57.135 36.364 0.00 0.00 0.00 3.21
203 204 4.023021 GGTAAACGGGTTTGCTATTTCACA 60.023 41.667 11.24 0.00 35.84 3.58
204 205 4.478699 GGTAAACGGGTTTGCTATTTCAC 58.521 43.478 11.24 0.00 35.84 3.18
205 206 3.188873 CGGTAAACGGGTTTGCTATTTCA 59.811 43.478 11.24 0.00 39.42 2.69
206 207 3.750512 CGGTAAACGGGTTTGCTATTTC 58.249 45.455 11.24 0.00 39.42 2.17
207 208 3.835378 CGGTAAACGGGTTTGCTATTT 57.165 42.857 11.24 0.00 39.42 1.40
227 228 0.860618 CGGCTAGCTTCGTCGTGTAC 60.861 60.000 15.72 0.00 0.00 2.90
280 281 4.446719 GCGGACTAAAAAGAAACGAAGAGA 59.553 41.667 0.00 0.00 0.00 3.10
281 282 4.210537 TGCGGACTAAAAAGAAACGAAGAG 59.789 41.667 0.00 0.00 0.00 2.85
282 283 4.121317 TGCGGACTAAAAAGAAACGAAGA 58.879 39.130 0.00 0.00 0.00 2.87
283 284 4.461992 TGCGGACTAAAAAGAAACGAAG 57.538 40.909 0.00 0.00 0.00 3.79
284 285 6.730960 ATATGCGGACTAAAAAGAAACGAA 57.269 33.333 0.00 0.00 0.00 3.85
285 286 7.010738 CCTTATATGCGGACTAAAAAGAAACGA 59.989 37.037 0.00 0.00 0.00 3.85
286 287 7.123830 CCTTATATGCGGACTAAAAAGAAACG 58.876 38.462 0.00 0.00 0.00 3.60
287 288 7.982224 ACCTTATATGCGGACTAAAAAGAAAC 58.018 34.615 0.00 0.00 0.00 2.78
288 289 8.570068 AACCTTATATGCGGACTAAAAAGAAA 57.430 30.769 0.00 0.00 0.00 2.52
289 290 8.455682 CAAACCTTATATGCGGACTAAAAAGAA 58.544 33.333 0.00 0.00 0.00 2.52
290 291 7.066525 CCAAACCTTATATGCGGACTAAAAAGA 59.933 37.037 0.00 0.00 0.00 2.52
291 292 7.148137 ACCAAACCTTATATGCGGACTAAAAAG 60.148 37.037 0.00 0.00 0.00 2.27
292 293 6.660094 ACCAAACCTTATATGCGGACTAAAAA 59.340 34.615 0.00 0.00 0.00 1.94
293 294 6.181908 ACCAAACCTTATATGCGGACTAAAA 58.818 36.000 0.00 0.00 0.00 1.52
294 295 5.747342 ACCAAACCTTATATGCGGACTAAA 58.253 37.500 0.00 0.00 0.00 1.85
295 296 5.104859 TGACCAAACCTTATATGCGGACTAA 60.105 40.000 0.00 0.00 0.00 2.24
296 297 4.406326 TGACCAAACCTTATATGCGGACTA 59.594 41.667 0.00 0.00 0.00 2.59
297 298 3.199071 TGACCAAACCTTATATGCGGACT 59.801 43.478 0.00 0.00 0.00 3.85
298 299 3.537580 TGACCAAACCTTATATGCGGAC 58.462 45.455 0.00 0.00 0.00 4.79
299 300 3.916359 TGACCAAACCTTATATGCGGA 57.084 42.857 0.00 0.00 0.00 5.54
300 301 4.398044 ACTTTGACCAAACCTTATATGCGG 59.602 41.667 0.00 0.00 0.00 5.69
301 302 5.123186 TGACTTTGACCAAACCTTATATGCG 59.877 40.000 0.00 0.00 0.00 4.73
302 303 6.509418 TGACTTTGACCAAACCTTATATGC 57.491 37.500 0.00 0.00 0.00 3.14
303 304 7.029563 GCTTGACTTTGACCAAACCTTATATG 58.970 38.462 0.00 0.00 0.00 1.78
304 305 6.948309 AGCTTGACTTTGACCAAACCTTATAT 59.052 34.615 0.00 0.00 0.00 0.86
305 306 6.303839 AGCTTGACTTTGACCAAACCTTATA 58.696 36.000 0.00 0.00 0.00 0.98
306 307 5.140454 AGCTTGACTTTGACCAAACCTTAT 58.860 37.500 0.00 0.00 0.00 1.73
307 308 4.532834 AGCTTGACTTTGACCAAACCTTA 58.467 39.130 0.00 0.00 0.00 2.69
308 309 3.365472 AGCTTGACTTTGACCAAACCTT 58.635 40.909 0.00 0.00 0.00 3.50
309 310 3.018423 AGCTTGACTTTGACCAAACCT 57.982 42.857 0.00 0.00 0.00 3.50
310 311 3.801114 AAGCTTGACTTTGACCAAACC 57.199 42.857 0.00 0.00 33.71 3.27
320 321 6.116126 AGTCAAACTCTACAAAGCTTGACTT 58.884 36.000 13.94 3.16 41.70 3.01
321 322 5.675538 AGTCAAACTCTACAAAGCTTGACT 58.324 37.500 13.94 13.94 0.00 3.41
322 323 5.993106 AGTCAAACTCTACAAAGCTTGAC 57.007 39.130 0.00 10.63 0.00 3.18
323 324 7.272978 AGTTAGTCAAACTCTACAAAGCTTGA 58.727 34.615 0.00 0.00 45.64 3.02
324 325 7.484035 AGTTAGTCAAACTCTACAAAGCTTG 57.516 36.000 0.00 0.00 45.64 4.01
378 379 9.743581 TGGTGCATATGATAATACTGATTTCAT 57.256 29.630 6.97 0.00 32.44 2.57
379 380 9.743581 ATGGTGCATATGATAATACTGATTTCA 57.256 29.630 6.97 0.00 0.00 2.69
381 382 8.886719 CGATGGTGCATATGATAATACTGATTT 58.113 33.333 6.97 0.00 0.00 2.17
382 383 8.260114 TCGATGGTGCATATGATAATACTGATT 58.740 33.333 6.97 0.00 0.00 2.57
383 384 7.785033 TCGATGGTGCATATGATAATACTGAT 58.215 34.615 6.97 0.00 0.00 2.90
384 385 7.169158 TCGATGGTGCATATGATAATACTGA 57.831 36.000 6.97 0.00 0.00 3.41
385 386 7.832503 TTCGATGGTGCATATGATAATACTG 57.167 36.000 6.97 0.00 0.00 2.74
386 387 8.043113 ACATTCGATGGTGCATATGATAATACT 58.957 33.333 6.97 0.00 33.60 2.12
387 388 8.201554 ACATTCGATGGTGCATATGATAATAC 57.798 34.615 6.97 0.00 33.60 1.89
389 390 8.969260 ATACATTCGATGGTGCATATGATAAT 57.031 30.769 6.97 0.00 33.60 1.28
390 391 8.791327 AATACATTCGATGGTGCATATGATAA 57.209 30.769 6.97 0.00 33.60 1.75
391 392 8.791327 AAATACATTCGATGGTGCATATGATA 57.209 30.769 6.97 0.00 33.60 2.15
392 393 7.692460 AAATACATTCGATGGTGCATATGAT 57.308 32.000 6.97 0.00 33.60 2.45
393 394 7.228308 TGAAAATACATTCGATGGTGCATATGA 59.772 33.333 6.97 0.00 31.80 2.15
394 395 7.361894 TGAAAATACATTCGATGGTGCATATG 58.638 34.615 0.00 0.00 31.80 1.78
395 396 7.509141 TGAAAATACATTCGATGGTGCATAT 57.491 32.000 0.00 0.00 31.80 1.78
396 397 6.934048 TGAAAATACATTCGATGGTGCATA 57.066 33.333 0.00 0.00 31.80 3.14
397 398 5.833406 TGAAAATACATTCGATGGTGCAT 57.167 34.783 0.00 0.00 31.80 3.96
398 399 5.833406 ATGAAAATACATTCGATGGTGCA 57.167 34.783 0.00 0.00 31.80 4.57
399 400 6.959361 AGTATGAAAATACATTCGATGGTGC 58.041 36.000 0.00 0.00 31.80 5.01
463 464 9.783256 GTCAAAGTCAAACTACACAGTAAATTT 57.217 29.630 0.00 0.00 33.48 1.82
464 465 9.174166 AGTCAAAGTCAAACTACACAGTAAATT 57.826 29.630 0.00 0.00 33.48 1.82
465 466 8.732746 AGTCAAAGTCAAACTACACAGTAAAT 57.267 30.769 0.00 0.00 33.48 1.40
466 467 9.656040 TTAGTCAAAGTCAAACTACACAGTAAA 57.344 29.630 0.00 0.00 33.48 2.01
467 468 9.656040 TTTAGTCAAAGTCAAACTACACAGTAA 57.344 29.630 0.00 0.00 33.48 2.24
468 469 9.826574 ATTTAGTCAAAGTCAAACTACACAGTA 57.173 29.630 0.00 0.00 33.48 2.74
469 470 8.732746 ATTTAGTCAAAGTCAAACTACACAGT 57.267 30.769 0.00 0.00 36.19 3.55
470 471 9.046296 AGATTTAGTCAAAGTCAAACTACACAG 57.954 33.333 0.00 0.00 0.00 3.66
471 472 8.958119 AGATTTAGTCAAAGTCAAACTACACA 57.042 30.769 0.00 0.00 0.00 3.72
479 480 8.783093 CCACACATAAGATTTAGTCAAAGTCAA 58.217 33.333 0.00 0.00 0.00 3.18
480 481 8.154203 TCCACACATAAGATTTAGTCAAAGTCA 58.846 33.333 0.00 0.00 0.00 3.41
481 482 8.547967 TCCACACATAAGATTTAGTCAAAGTC 57.452 34.615 0.00 0.00 0.00 3.01
482 483 8.157476 ACTCCACACATAAGATTTAGTCAAAGT 58.843 33.333 0.00 0.00 0.00 2.66
483 484 8.553459 ACTCCACACATAAGATTTAGTCAAAG 57.447 34.615 0.00 0.00 0.00 2.77
494 495 8.792633 CCATTTCTTTTTACTCCACACATAAGA 58.207 33.333 0.00 0.00 0.00 2.10
495 496 8.792633 TCCATTTCTTTTTACTCCACACATAAG 58.207 33.333 0.00 0.00 0.00 1.73
496 497 8.698973 TCCATTTCTTTTTACTCCACACATAA 57.301 30.769 0.00 0.00 0.00 1.90
497 498 8.698973 TTCCATTTCTTTTTACTCCACACATA 57.301 30.769 0.00 0.00 0.00 2.29
498 499 7.595819 TTCCATTTCTTTTTACTCCACACAT 57.404 32.000 0.00 0.00 0.00 3.21
499 500 7.286546 TCATTCCATTTCTTTTTACTCCACACA 59.713 33.333 0.00 0.00 0.00 3.72
500 501 7.657336 TCATTCCATTTCTTTTTACTCCACAC 58.343 34.615 0.00 0.00 0.00 3.82
501 502 7.505585 ACTCATTCCATTTCTTTTTACTCCACA 59.494 33.333 0.00 0.00 0.00 4.17
502 503 7.886338 ACTCATTCCATTTCTTTTTACTCCAC 58.114 34.615 0.00 0.00 0.00 4.02
503 504 9.010029 GTACTCATTCCATTTCTTTTTACTCCA 57.990 33.333 0.00 0.00 0.00 3.86
504 505 9.010029 TGTACTCATTCCATTTCTTTTTACTCC 57.990 33.333 0.00 0.00 0.00 3.85
513 514 9.685276 TCATTGTATTGTACTCATTCCATTTCT 57.315 29.630 0.00 0.00 0.00 2.52
518 519 9.898152 TGTATTCATTGTATTGTACTCATTCCA 57.102 29.630 0.00 0.00 0.00 3.53
522 523 9.770097 CCTCTGTATTCATTGTATTGTACTCAT 57.230 33.333 0.00 0.00 0.00 2.90
523 524 8.758829 ACCTCTGTATTCATTGTATTGTACTCA 58.241 33.333 0.00 0.00 0.00 3.41
524 525 9.035607 CACCTCTGTATTCATTGTATTGTACTC 57.964 37.037 0.00 0.00 0.00 2.59
525 526 8.758829 TCACCTCTGTATTCATTGTATTGTACT 58.241 33.333 0.00 0.00 0.00 2.73
526 527 8.942338 TCACCTCTGTATTCATTGTATTGTAC 57.058 34.615 0.00 0.00 0.00 2.90
527 528 9.378551 GTTCACCTCTGTATTCATTGTATTGTA 57.621 33.333 0.00 0.00 0.00 2.41
528 529 7.882791 TGTTCACCTCTGTATTCATTGTATTGT 59.117 33.333 0.00 0.00 0.00 2.71
529 530 8.267620 TGTTCACCTCTGTATTCATTGTATTG 57.732 34.615 0.00 0.00 0.00 1.90
530 531 8.103305 ACTGTTCACCTCTGTATTCATTGTATT 58.897 33.333 0.00 0.00 0.00 1.89
531 532 7.624549 ACTGTTCACCTCTGTATTCATTGTAT 58.375 34.615 0.00 0.00 0.00 2.29
532 533 7.004555 ACTGTTCACCTCTGTATTCATTGTA 57.995 36.000 0.00 0.00 0.00 2.41
533 534 5.869579 ACTGTTCACCTCTGTATTCATTGT 58.130 37.500 0.00 0.00 0.00 2.71
534 535 6.652481 AGAACTGTTCACCTCTGTATTCATTG 59.348 38.462 21.50 0.00 0.00 2.82
541 542 5.163683 GCGTATAGAACTGTTCACCTCTGTA 60.164 44.000 21.50 4.82 0.00 2.74
546 547 2.167900 GGGCGTATAGAACTGTTCACCT 59.832 50.000 21.50 8.63 0.00 4.00
556 557 0.683828 TGGACCGTGGGCGTATAGAA 60.684 55.000 0.00 0.00 36.15 2.10
597 598 2.915659 AGGTCGTTGGGCTGTCGA 60.916 61.111 0.00 0.00 0.00 4.20
665 929 4.003648 AGTTTTGAGAGCAAATACCTCGG 58.996 43.478 0.00 0.00 43.07 4.63
927 1192 3.573110 GTGACGGAGGTGTATATAAGCCT 59.427 47.826 6.16 6.16 0.00 4.58
1623 1905 1.298859 GCGCGAAGTCCCTGTTGAAT 61.299 55.000 12.10 0.00 0.00 2.57
1998 2289 1.380403 CCTGTTCCGTTGTTGTGCCA 61.380 55.000 0.00 0.00 0.00 4.92
2313 2633 1.079405 GCTCATTCGGTCGAACCCA 60.079 57.895 8.00 0.00 36.91 4.51
2368 2688 5.414144 TCATTCAGAATGTGCGGAAATACAA 59.586 36.000 20.49 0.00 39.87 2.41
2442 2762 5.683770 GCTCTTTGTGGTGGGTAAACAAATT 60.684 40.000 1.12 0.00 41.52 1.82
2443 2763 4.202212 GCTCTTTGTGGTGGGTAAACAAAT 60.202 41.667 1.12 0.00 41.52 2.32
2447 2767 2.293399 CTGCTCTTTGTGGTGGGTAAAC 59.707 50.000 0.00 0.00 0.00 2.01
2451 2810 1.151450 CCTGCTCTTTGTGGTGGGT 59.849 57.895 0.00 0.00 0.00 4.51
2478 2837 1.479323 CACCGGGACCTCGAATTTCTA 59.521 52.381 6.32 0.00 0.00 2.10
2488 2847 1.376812 GAATTTCGCACCGGGACCT 60.377 57.895 6.32 0.00 0.00 3.85
2491 2850 1.201181 CATTTGAATTTCGCACCGGGA 59.799 47.619 6.32 0.00 0.00 5.14
3037 3415 5.652891 AGTTACCTCGCTATCTCTCTCAAAA 59.347 40.000 0.00 0.00 0.00 2.44
3038 3416 5.066634 CAGTTACCTCGCTATCTCTCTCAAA 59.933 44.000 0.00 0.00 0.00 2.69
3040 3418 4.130857 CAGTTACCTCGCTATCTCTCTCA 58.869 47.826 0.00 0.00 0.00 3.27
3044 3422 5.182380 GCTAATCAGTTACCTCGCTATCTCT 59.818 44.000 0.00 0.00 0.00 3.10
3045 3423 5.395642 GCTAATCAGTTACCTCGCTATCTC 58.604 45.833 0.00 0.00 0.00 2.75
3046 3424 4.218852 GGCTAATCAGTTACCTCGCTATCT 59.781 45.833 0.00 0.00 0.00 1.98
3047 3425 4.487019 GGCTAATCAGTTACCTCGCTATC 58.513 47.826 0.00 0.00 0.00 2.08
3050 3428 1.413077 GGGCTAATCAGTTACCTCGCT 59.587 52.381 0.00 0.00 0.00 4.93
3051 3429 1.413077 AGGGCTAATCAGTTACCTCGC 59.587 52.381 0.00 0.00 0.00 5.03
3052 3430 4.931661 TTAGGGCTAATCAGTTACCTCG 57.068 45.455 0.00 0.00 0.00 4.63
3069 3447 2.108168 TGAACTCTGTCCCCGATTAGG 58.892 52.381 0.00 0.00 40.63 2.69
3070 3448 3.056107 TGTTGAACTCTGTCCCCGATTAG 60.056 47.826 0.00 0.00 0.00 1.73
3071 3449 2.901192 TGTTGAACTCTGTCCCCGATTA 59.099 45.455 0.00 0.00 0.00 1.75
3072 3450 1.697432 TGTTGAACTCTGTCCCCGATT 59.303 47.619 0.00 0.00 0.00 3.34
3073 3451 1.002087 GTGTTGAACTCTGTCCCCGAT 59.998 52.381 0.00 0.00 0.00 4.18
3074 3452 0.391597 GTGTTGAACTCTGTCCCCGA 59.608 55.000 0.00 0.00 0.00 5.14
3075 3453 0.944311 CGTGTTGAACTCTGTCCCCG 60.944 60.000 0.00 0.00 0.00 5.73
3076 3454 0.602905 CCGTGTTGAACTCTGTCCCC 60.603 60.000 0.00 0.00 0.00 4.81
3077 3455 1.228657 GCCGTGTTGAACTCTGTCCC 61.229 60.000 0.00 0.00 0.00 4.46
3084 3462 2.193536 GCAAGGGCCGTGTTGAACT 61.194 57.895 20.59 0.00 0.00 3.01
3089 3467 2.746277 GATCGCAAGGGCCGTGTT 60.746 61.111 20.59 6.38 36.38 3.32
3094 3472 2.514824 GGTCTGATCGCAAGGGCC 60.515 66.667 0.00 0.00 36.38 5.80
3099 3477 2.268920 GGCCTGGTCTGATCGCAA 59.731 61.111 0.00 0.00 0.00 4.85
3116 3520 1.455383 GCATGGATTTGGGCCTACCG 61.455 60.000 4.53 0.00 44.64 4.02
3119 3523 1.830477 GTTTGCATGGATTTGGGCCTA 59.170 47.619 4.53 0.00 0.00 3.93
3157 3561 8.170121 TGGGCCAAGGCTATATTTACTATTAT 57.830 34.615 2.13 0.00 41.60 1.28
3166 3570 3.994317 AGTTTTGGGCCAAGGCTATATT 58.006 40.909 19.90 0.00 41.60 1.28
3172 3576 0.541998 ACCTAGTTTTGGGCCAAGGC 60.542 55.000 19.90 15.58 41.06 4.35
3187 3591 4.098155 GGCCCAAAAATTTTAGGGACCTA 58.902 43.478 21.76 0.00 43.97 3.08
3188 3592 2.910319 GGCCCAAAAATTTTAGGGACCT 59.090 45.455 21.76 0.00 43.97 3.85
3191 3595 2.909662 CAGGGCCCAAAAATTTTAGGGA 59.090 45.455 27.56 0.00 44.30 4.20
3203 3609 4.641645 CGACTGCACAGGGCCCAA 62.642 66.667 27.56 2.42 43.89 4.12
3238 3644 1.355720 CCTCTTTGTCAGGGGTCCAAT 59.644 52.381 0.00 0.00 38.60 3.16
3245 3651 3.384789 TCACGATATCCTCTTTGTCAGGG 59.615 47.826 0.00 0.00 0.00 4.45
3246 3652 4.098654 AGTCACGATATCCTCTTTGTCAGG 59.901 45.833 0.00 0.00 0.00 3.86
3247 3653 5.255710 AGTCACGATATCCTCTTTGTCAG 57.744 43.478 0.00 0.00 0.00 3.51
3248 3654 6.546034 TGATAGTCACGATATCCTCTTTGTCA 59.454 38.462 0.00 0.00 0.00 3.58
3249 3655 6.971602 TGATAGTCACGATATCCTCTTTGTC 58.028 40.000 0.00 0.00 0.00 3.18
3250 3656 6.961360 TGATAGTCACGATATCCTCTTTGT 57.039 37.500 0.00 0.00 0.00 2.83
3251 3657 8.824159 AATTGATAGTCACGATATCCTCTTTG 57.176 34.615 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.