Multiple sequence alignment - TraesCS5D01G319000

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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 TraesCS5D01G319000 chr5D 100.000 3575 0 0 1 3575 412075819 412079393 0.000000e+00 6602
1 TraesCS5D01G319000 chr5D 86.641 262 29 4 224 480 243093442 243093702 5.840000e-73 285
2 TraesCS5D01G319000 chr5D 87.302 252 28 2 233 480 399931131 399931382 5.840000e-73 285
3 TraesCS5D01G319000 chr5B 94.914 3028 82 17 493 3492 495019221 495022204 0.000000e+00 4673
4 TraesCS5D01G319000 chr5B 93.860 114 6 1 1 114 495017558 495017670 1.710000e-38 171
5 TraesCS5D01G319000 chr5B 97.590 83 2 0 3493 3575 495022245 495022327 3.720000e-30 143
6 TraesCS5D01G319000 chr5A 93.417 2947 90 29 601 3492 523815108 523818005 0.000000e+00 4272
7 TraesCS5D01G319000 chr5A 94.828 116 6 0 493 608 523814762 523814877 7.880000e-42 182
8 TraesCS5D01G319000 chr5A 93.396 106 6 1 128 233 523814672 523814776 4.780000e-34 156
9 TraesCS5D01G319000 chr5A 90.351 114 11 0 1 114 523814573 523814686 2.220000e-32 150
10 TraesCS5D01G319000 chr5A 96.386 83 3 0 3493 3575 523818049 523818131 1.730000e-28 137
11 TraesCS5D01G319000 chr7A 81.273 1367 242 12 1118 2474 274662814 274661452 0.000000e+00 1094
12 TraesCS5D01G319000 chr7D 81.053 1367 245 11 1118 2474 255059163 255057801 0.000000e+00 1077
13 TraesCS5D01G319000 chr7D 88.845 251 25 3 233 480 540241727 540241477 4.480000e-79 305
14 TraesCS5D01G319000 chr7B 81.053 1367 245 11 1118 2474 233027603 233026241 0.000000e+00 1077
15 TraesCS5D01G319000 chr1B 87.600 250 29 2 233 480 466944116 466943867 4.520000e-74 289
16 TraesCS5D01G319000 chr3B 87.302 252 29 2 232 480 380510347 380510598 5.840000e-73 285
17 TraesCS5D01G319000 chr3B 87.251 251 29 2 233 480 52345348 52345098 2.100000e-72 283
18 TraesCS5D01G319000 chr6B 87.805 246 24 5 241 480 708040670 708040425 2.100000e-72 283
19 TraesCS5D01G319000 chr6B 73.922 487 103 21 1164 1638 484100845 484100371 1.320000e-39 174
20 TraesCS5D01G319000 chr4A 87.251 251 28 4 233 480 625264000 625263751 2.100000e-72 283
21 TraesCS5D01G319000 chr4D 87.603 242 28 2 241 480 4665117 4665358 2.720000e-71 279
22 TraesCS5D01G319000 chr2D 75.794 504 110 12 1838 2335 509230197 509230694 9.910000e-61 244
23 TraesCS5D01G319000 chr2A 75.746 503 112 10 1838 2335 653001035 653001532 9.910000e-61 244
24 TraesCS5D01G319000 chr6D 74.263 509 107 21 1164 1660 336366560 336367056 3.640000e-45 193
25 TraesCS5D01G319000 chr6A 73.665 543 119 21 1130 1660 476000196 476000726 4.710000e-44 189


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 TraesCS5D01G319000 chr5D 412075819 412079393 3574 False 6602.000000 6602 100.000000 1 3575 1 chr5D.!!$F3 3574
1 TraesCS5D01G319000 chr5B 495017558 495022327 4769 False 1662.333333 4673 95.454667 1 3575 3 chr5B.!!$F1 3574
2 TraesCS5D01G319000 chr5A 523814573 523818131 3558 False 979.400000 4272 93.675600 1 3575 5 chr5A.!!$F1 3574
3 TraesCS5D01G319000 chr7A 274661452 274662814 1362 True 1094.000000 1094 81.273000 1118 2474 1 chr7A.!!$R1 1356
4 TraesCS5D01G319000 chr7D 255057801 255059163 1362 True 1077.000000 1077 81.053000 1118 2474 1 chr7D.!!$R1 1356
5 TraesCS5D01G319000 chr7B 233026241 233027603 1362 True 1077.000000 1077 81.053000 1118 2474 1 chr7B.!!$R1 1356

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
410 507 0.036388 GCCACTCTCCGAATCCACAA 60.036 55.0 0.0 0.0 0.0 3.33 F
450 547 0.102663 GCTACTACGCCAAGAGACCC 59.897 60.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2499 3967 0.179171 CTGCATGCTTTCTCTTGCCG 60.179 55.0 20.33 0.00 36.61 5.69 R
2577 4056 0.527817 AAGAATCGATGCCCGTCGTC 60.528 55.0 0.00 1.93 42.07 4.20 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
82 83 9.912634 CCACATTAGTATCACTGTTTGATTTTT 57.087 29.630 0.00 0.00 42.87 1.94
113 114 4.019860 ACAGCTCACATAATGAACACCTCT 60.020 41.667 0.00 0.00 36.69 3.69
114 115 4.940046 CAGCTCACATAATGAACACCTCTT 59.060 41.667 0.00 0.00 36.69 2.85
115 116 5.064452 CAGCTCACATAATGAACACCTCTTC 59.936 44.000 0.00 0.00 36.69 2.87
116 117 5.046014 AGCTCACATAATGAACACCTCTTCT 60.046 40.000 0.00 0.00 36.69 2.85
117 118 5.293079 GCTCACATAATGAACACCTCTTCTC 59.707 44.000 0.00 0.00 36.69 2.87
118 119 5.410924 TCACATAATGAACACCTCTTCTCG 58.589 41.667 0.00 0.00 33.02 4.04
119 120 4.033358 CACATAATGAACACCTCTTCTCGC 59.967 45.833 0.00 0.00 0.00 5.03
120 121 2.839486 AATGAACACCTCTTCTCGCA 57.161 45.000 0.00 0.00 0.00 5.10
121 122 2.839486 ATGAACACCTCTTCTCGCAA 57.161 45.000 0.00 0.00 0.00 4.85
122 123 2.613026 TGAACACCTCTTCTCGCAAA 57.387 45.000 0.00 0.00 0.00 3.68
123 124 2.912771 TGAACACCTCTTCTCGCAAAA 58.087 42.857 0.00 0.00 0.00 2.44
124 125 3.275143 TGAACACCTCTTCTCGCAAAAA 58.725 40.909 0.00 0.00 0.00 1.94
178 179 3.127030 GGGTGAATCTCGTGTTTGAATCC 59.873 47.826 0.00 0.00 0.00 3.01
182 279 4.083324 TGAATCTCGTGTTTGAATCCTTGC 60.083 41.667 0.00 0.00 0.00 4.01
184 281 1.531149 CTCGTGTTTGAATCCTTGCGT 59.469 47.619 0.00 0.00 0.00 5.24
200 297 0.868406 GCGTGGTTTCTTGTCCTCAG 59.132 55.000 0.00 0.00 0.00 3.35
220 317 4.080582 TCAGACCAAAGAACTTGTTCTCCA 60.081 41.667 15.27 0.00 34.75 3.86
221 318 4.823989 CAGACCAAAGAACTTGTTCTCCAT 59.176 41.667 15.27 4.12 34.75 3.41
223 320 5.053978 ACCAAAGAACTTGTTCTCCATCT 57.946 39.130 15.27 0.00 32.65 2.90
224 321 5.066593 ACCAAAGAACTTGTTCTCCATCTC 58.933 41.667 15.27 0.00 32.65 2.75
226 323 5.767168 CCAAAGAACTTGTTCTCCATCTCTT 59.233 40.000 15.27 3.19 32.65 2.85
227 324 6.072783 CCAAAGAACTTGTTCTCCATCTCTTC 60.073 42.308 15.27 0.00 32.65 2.87
229 326 6.371595 AGAACTTGTTCTCCATCTCTTCAT 57.628 37.500 9.93 0.00 0.00 2.57
231 328 7.327214 AGAACTTGTTCTCCATCTCTTCATAC 58.673 38.462 9.93 0.00 0.00 2.39
232 329 6.865834 ACTTGTTCTCCATCTCTTCATACT 57.134 37.500 0.00 0.00 0.00 2.12
233 330 7.251321 ACTTGTTCTCCATCTCTTCATACTT 57.749 36.000 0.00 0.00 0.00 2.24
235 332 8.160106 ACTTGTTCTCCATCTCTTCATACTTTT 58.840 33.333 0.00 0.00 0.00 2.27
260 357 6.370433 TTTAAATGGAGGCAAAAGTTTTGC 57.630 33.333 34.99 34.99 44.22 3.68
270 367 3.989817 GCAAAAGTTTTGCCTCATCGATT 59.010 39.130 33.57 0.00 39.38 3.34
271 368 5.160641 GCAAAAGTTTTGCCTCATCGATTA 58.839 37.500 33.57 0.00 39.38 1.75
272 369 5.633182 GCAAAAGTTTTGCCTCATCGATTAA 59.367 36.000 33.57 0.00 39.38 1.40
273 370 6.311200 GCAAAAGTTTTGCCTCATCGATTAAT 59.689 34.615 33.57 0.00 39.38 1.40
274 371 7.148590 GCAAAAGTTTTGCCTCATCGATTAATT 60.149 33.333 33.57 0.00 39.38 1.40
275 372 9.352784 CAAAAGTTTTGCCTCATCGATTAATTA 57.647 29.630 15.06 0.00 0.00 1.40
276 373 9.921637 AAAAGTTTTGCCTCATCGATTAATTAA 57.078 25.926 0.00 0.00 0.00 1.40
277 374 9.573133 AAAGTTTTGCCTCATCGATTAATTAAG 57.427 29.630 3.94 0.00 0.00 1.85
278 375 7.707104 AGTTTTGCCTCATCGATTAATTAAGG 58.293 34.615 3.94 0.00 0.00 2.69
279 376 7.556275 AGTTTTGCCTCATCGATTAATTAAGGA 59.444 33.333 3.94 4.38 0.00 3.36
280 377 7.496529 TTTGCCTCATCGATTAATTAAGGAG 57.503 36.000 3.94 0.00 0.00 3.69
281 378 6.419484 TGCCTCATCGATTAATTAAGGAGA 57.581 37.500 11.88 3.72 0.00 3.71
282 379 6.826668 TGCCTCATCGATTAATTAAGGAGAA 58.173 36.000 11.88 1.55 0.00 2.87
283 380 6.931281 TGCCTCATCGATTAATTAAGGAGAAG 59.069 38.462 11.88 5.63 0.00 2.85
284 381 7.155328 GCCTCATCGATTAATTAAGGAGAAGA 58.845 38.462 11.88 5.03 0.00 2.87
285 382 7.330700 GCCTCATCGATTAATTAAGGAGAAGAG 59.669 40.741 16.89 16.89 0.00 2.85
286 383 8.580720 CCTCATCGATTAATTAAGGAGAAGAGA 58.419 37.037 21.25 12.30 0.00 3.10
287 384 9.973450 CTCATCGATTAATTAAGGAGAAGAGAA 57.027 33.333 17.95 0.00 0.00 2.87
291 388 9.046296 TCGATTAATTAAGGAGAAGAGAATTGC 57.954 33.333 3.94 0.00 0.00 3.56
292 389 8.286097 CGATTAATTAAGGAGAAGAGAATTGCC 58.714 37.037 3.94 0.00 0.00 4.52
293 390 7.881775 TTAATTAAGGAGAAGAGAATTGCCC 57.118 36.000 0.00 0.00 0.00 5.36
295 392 3.362870 AAGGAGAAGAGAATTGCCCAG 57.637 47.619 0.00 0.00 0.00 4.45
296 393 2.273619 AGGAGAAGAGAATTGCCCAGT 58.726 47.619 0.00 0.00 0.00 4.00
297 394 2.646798 AGGAGAAGAGAATTGCCCAGTT 59.353 45.455 0.00 0.00 0.00 3.16
299 396 4.289672 AGGAGAAGAGAATTGCCCAGTTAA 59.710 41.667 0.00 0.00 0.00 2.01
300 397 5.044550 AGGAGAAGAGAATTGCCCAGTTAAT 60.045 40.000 0.00 0.00 0.00 1.40
301 398 5.654209 GGAGAAGAGAATTGCCCAGTTAATT 59.346 40.000 0.00 0.00 0.00 1.40
303 400 7.339466 GGAGAAGAGAATTGCCCAGTTAATTTA 59.661 37.037 0.00 0.00 0.00 1.40
304 401 8.056407 AGAAGAGAATTGCCCAGTTAATTTAC 57.944 34.615 0.00 0.00 0.00 2.01
305 402 6.436843 AGAGAATTGCCCAGTTAATTTACG 57.563 37.500 0.00 0.00 0.00 3.18
307 404 5.258051 AGAATTGCCCAGTTAATTTACGGA 58.742 37.500 6.93 0.00 0.00 4.69
308 405 5.712917 AGAATTGCCCAGTTAATTTACGGAA 59.287 36.000 6.93 0.00 0.00 4.30
309 406 5.986501 ATTGCCCAGTTAATTTACGGAAA 57.013 34.783 0.00 0.00 0.00 3.13
310 407 5.786264 TTGCCCAGTTAATTTACGGAAAA 57.214 34.783 0.00 0.00 0.00 2.29
311 408 5.986501 TGCCCAGTTAATTTACGGAAAAT 57.013 34.783 0.00 0.00 39.56 1.82
312 409 5.956642 TGCCCAGTTAATTTACGGAAAATC 58.043 37.500 0.00 0.00 36.76 2.17
313 410 5.477291 TGCCCAGTTAATTTACGGAAAATCA 59.523 36.000 0.00 0.00 36.76 2.57
315 412 6.127842 GCCCAGTTAATTTACGGAAAATCAGA 60.128 38.462 0.00 0.00 36.76 3.27
316 413 7.248437 CCCAGTTAATTTACGGAAAATCAGAC 58.752 38.462 0.00 0.00 36.76 3.51
318 415 7.148540 CCAGTTAATTTACGGAAAATCAGACGA 60.149 37.037 0.00 0.00 36.76 4.20
321 418 9.384682 GTTAATTTACGGAAAATCAGACGAAAA 57.615 29.630 0.00 0.00 36.76 2.29
322 419 7.847166 AATTTACGGAAAATCAGACGAAAAC 57.153 32.000 0.00 0.00 36.76 2.43
323 420 3.891056 ACGGAAAATCAGACGAAAACC 57.109 42.857 0.00 0.00 0.00 3.27
325 422 3.628487 ACGGAAAATCAGACGAAAACCAA 59.372 39.130 0.00 0.00 0.00 3.67
326 423 4.277423 ACGGAAAATCAGACGAAAACCAAT 59.723 37.500 0.00 0.00 0.00 3.16
328 425 5.793457 CGGAAAATCAGACGAAAACCAATAC 59.207 40.000 0.00 0.00 0.00 1.89
330 427 7.142680 GGAAAATCAGACGAAAACCAATACAA 58.857 34.615 0.00 0.00 0.00 2.41
333 430 6.627395 ATCAGACGAAAACCAATACAAACA 57.373 33.333 0.00 0.00 0.00 2.83
334 431 6.438259 TCAGACGAAAACCAATACAAACAA 57.562 33.333 0.00 0.00 0.00 2.83
338 435 5.411781 ACGAAAACCAATACAAACAAAGCA 58.588 33.333 0.00 0.00 0.00 3.91
339 436 5.289917 ACGAAAACCAATACAAACAAAGCAC 59.710 36.000 0.00 0.00 0.00 4.40
340 437 5.553581 CGAAAACCAATACAAACAAAGCACG 60.554 40.000 0.00 0.00 0.00 5.34
341 438 4.640789 AACCAATACAAACAAAGCACGA 57.359 36.364 0.00 0.00 0.00 4.35
342 439 4.640789 ACCAATACAAACAAAGCACGAA 57.359 36.364 0.00 0.00 0.00 3.85
344 441 4.097286 ACCAATACAAACAAAGCACGAACT 59.903 37.500 0.00 0.00 0.00 3.01
345 442 5.297278 ACCAATACAAACAAAGCACGAACTA 59.703 36.000 0.00 0.00 0.00 2.24
346 443 6.183360 ACCAATACAAACAAAGCACGAACTAA 60.183 34.615 0.00 0.00 0.00 2.24
347 444 6.141685 CCAATACAAACAAAGCACGAACTAAC 59.858 38.462 0.00 0.00 0.00 2.34
348 445 4.957759 ACAAACAAAGCACGAACTAACT 57.042 36.364 0.00 0.00 0.00 2.24
349 446 7.718272 ATACAAACAAAGCACGAACTAACTA 57.282 32.000 0.00 0.00 0.00 2.24
350 447 5.803118 ACAAACAAAGCACGAACTAACTAC 58.197 37.500 0.00 0.00 0.00 2.73
351 448 5.583457 ACAAACAAAGCACGAACTAACTACT 59.417 36.000 0.00 0.00 0.00 2.57
354 451 4.743644 ACAAAGCACGAACTAACTACTCAC 59.256 41.667 0.00 0.00 0.00 3.51
357 454 4.486090 AGCACGAACTAACTACTCACATG 58.514 43.478 0.00 0.00 0.00 3.21
360 457 3.257375 ACGAACTAACTACTCACATGGCA 59.743 43.478 0.00 0.00 0.00 4.92
361 458 4.242475 CGAACTAACTACTCACATGGCAA 58.758 43.478 0.00 0.00 0.00 4.52
362 459 4.327357 CGAACTAACTACTCACATGGCAAG 59.673 45.833 0.00 0.00 0.00 4.01
363 460 5.479306 GAACTAACTACTCACATGGCAAGA 58.521 41.667 0.00 0.00 0.00 3.02
364 461 5.483685 ACTAACTACTCACATGGCAAGAA 57.516 39.130 0.00 0.00 0.00 2.52
365 462 5.865085 ACTAACTACTCACATGGCAAGAAA 58.135 37.500 0.00 0.00 0.00 2.52
366 463 5.701290 ACTAACTACTCACATGGCAAGAAAC 59.299 40.000 0.00 0.00 0.00 2.78
367 464 3.412386 ACTACTCACATGGCAAGAAACC 58.588 45.455 0.00 0.00 0.00 3.27
368 465 2.363306 ACTCACATGGCAAGAAACCA 57.637 45.000 0.00 0.00 42.61 3.67
369 466 1.956477 ACTCACATGGCAAGAAACCAC 59.044 47.619 0.00 0.00 40.82 4.16
371 468 2.559668 CTCACATGGCAAGAAACCACAT 59.440 45.455 0.00 0.00 40.82 3.21
372 469 3.758023 CTCACATGGCAAGAAACCACATA 59.242 43.478 0.00 0.00 40.82 2.29
374 471 3.507233 CACATGGCAAGAAACCACATAGT 59.493 43.478 0.00 0.00 40.82 2.12
375 472 4.699735 CACATGGCAAGAAACCACATAGTA 59.300 41.667 0.00 0.00 40.82 1.82
376 473 4.943705 ACATGGCAAGAAACCACATAGTAG 59.056 41.667 0.00 0.00 40.82 2.57
377 474 3.343617 TGGCAAGAAACCACATAGTAGC 58.656 45.455 0.00 0.00 30.29 3.58
378 475 3.244735 TGGCAAGAAACCACATAGTAGCA 60.245 43.478 0.00 0.00 30.29 3.49
379 476 3.127030 GGCAAGAAACCACATAGTAGCAC 59.873 47.826 0.00 0.00 0.00 4.40
380 477 3.751175 GCAAGAAACCACATAGTAGCACA 59.249 43.478 0.00 0.00 0.00 4.57
383 480 2.403252 AACCACATAGTAGCACAGGC 57.597 50.000 0.00 0.00 41.61 4.85
384 481 1.275666 ACCACATAGTAGCACAGGCA 58.724 50.000 0.00 0.00 44.61 4.75
385 482 1.208052 ACCACATAGTAGCACAGGCAG 59.792 52.381 0.00 0.00 44.61 4.85
386 483 1.293924 CACATAGTAGCACAGGCAGC 58.706 55.000 0.00 0.00 44.61 5.25
387 484 0.179000 ACATAGTAGCACAGGCAGCC 59.821 55.000 1.84 1.84 44.61 4.85
388 485 0.533755 CATAGTAGCACAGGCAGCCC 60.534 60.000 8.22 0.00 44.61 5.19
389 486 1.700042 ATAGTAGCACAGGCAGCCCC 61.700 60.000 8.22 0.00 44.61 5.80
390 487 4.803908 GTAGCACAGGCAGCCCCC 62.804 72.222 8.22 0.00 44.61 5.40
405 502 2.107141 CCCGCCACTCTCCGAATC 59.893 66.667 0.00 0.00 0.00 2.52
406 503 2.107141 CCGCCACTCTCCGAATCC 59.893 66.667 0.00 0.00 0.00 3.01
407 504 2.721167 CCGCCACTCTCCGAATCCA 61.721 63.158 0.00 0.00 0.00 3.41
408 505 1.519455 CGCCACTCTCCGAATCCAC 60.519 63.158 0.00 0.00 0.00 4.02
409 506 1.596934 GCCACTCTCCGAATCCACA 59.403 57.895 0.00 0.00 0.00 4.17
410 507 0.036388 GCCACTCTCCGAATCCACAA 60.036 55.000 0.00 0.00 0.00 3.33
411 508 1.726853 CCACTCTCCGAATCCACAAC 58.273 55.000 0.00 0.00 0.00 3.32
412 509 1.001974 CCACTCTCCGAATCCACAACA 59.998 52.381 0.00 0.00 0.00 3.33
413 510 2.355108 CCACTCTCCGAATCCACAACAT 60.355 50.000 0.00 0.00 0.00 2.71
414 511 3.118775 CCACTCTCCGAATCCACAACATA 60.119 47.826 0.00 0.00 0.00 2.29
415 512 3.865745 CACTCTCCGAATCCACAACATAC 59.134 47.826 0.00 0.00 0.00 2.39
416 513 3.513912 ACTCTCCGAATCCACAACATACA 59.486 43.478 0.00 0.00 0.00 2.29
417 514 3.857052 TCTCCGAATCCACAACATACAC 58.143 45.455 0.00 0.00 0.00 2.90
418 515 3.259625 TCTCCGAATCCACAACATACACA 59.740 43.478 0.00 0.00 0.00 3.72
420 517 4.390264 TCCGAATCCACAACATACACAAA 58.610 39.130 0.00 0.00 0.00 2.83
422 519 4.472286 CGAATCCACAACATACACAAACC 58.528 43.478 0.00 0.00 0.00 3.27
423 520 4.614993 CGAATCCACAACATACACAAACCC 60.615 45.833 0.00 0.00 0.00 4.11
424 521 3.586470 TCCACAACATACACAAACCCT 57.414 42.857 0.00 0.00 0.00 4.34
425 522 3.218453 TCCACAACATACACAAACCCTG 58.782 45.455 0.00 0.00 0.00 4.45
426 523 3.117851 TCCACAACATACACAAACCCTGA 60.118 43.478 0.00 0.00 0.00 3.86
428 525 3.629855 CACAACATACACAAACCCTGACA 59.370 43.478 0.00 0.00 0.00 3.58
429 526 4.278170 CACAACATACACAAACCCTGACAT 59.722 41.667 0.00 0.00 0.00 3.06
430 527 4.892934 ACAACATACACAAACCCTGACATT 59.107 37.500 0.00 0.00 0.00 2.71
431 528 5.221224 ACAACATACACAAACCCTGACATTG 60.221 40.000 0.00 0.00 0.00 2.82
433 530 2.071778 ACACAAACCCTGACATTGCT 57.928 45.000 0.00 0.00 0.00 3.91
438 535 4.154195 CACAAACCCTGACATTGCTACTAC 59.846 45.833 0.00 0.00 0.00 2.73
439 536 2.961526 ACCCTGACATTGCTACTACG 57.038 50.000 0.00 0.00 0.00 3.51
442 539 1.134818 CCTGACATTGCTACTACGCCA 60.135 52.381 0.00 0.00 0.00 5.69
443 540 2.616960 CTGACATTGCTACTACGCCAA 58.383 47.619 0.00 0.00 0.00 4.52
446 543 2.860735 GACATTGCTACTACGCCAAGAG 59.139 50.000 0.00 0.00 0.00 2.85
447 544 2.496070 ACATTGCTACTACGCCAAGAGA 59.504 45.455 0.00 0.00 0.00 3.10
448 545 2.649331 TTGCTACTACGCCAAGAGAC 57.351 50.000 0.00 0.00 0.00 3.36
449 546 0.815734 TGCTACTACGCCAAGAGACC 59.184 55.000 0.00 0.00 0.00 3.85
450 547 0.102663 GCTACTACGCCAAGAGACCC 59.897 60.000 0.00 0.00 0.00 4.46
451 548 0.745468 CTACTACGCCAAGAGACCCC 59.255 60.000 0.00 0.00 0.00 4.95
452 549 0.685458 TACTACGCCAAGAGACCCCC 60.685 60.000 0.00 0.00 0.00 5.40
454 551 3.588817 TACGCCAAGAGACCCCCGA 62.589 63.158 0.00 0.00 0.00 5.14
456 553 3.319198 GCCAAGAGACCCCCGACA 61.319 66.667 0.00 0.00 0.00 4.35
457 554 2.890766 GCCAAGAGACCCCCGACAA 61.891 63.158 0.00 0.00 0.00 3.18
458 555 1.296715 CCAAGAGACCCCCGACAAG 59.703 63.158 0.00 0.00 0.00 3.16
460 557 0.685097 CAAGAGACCCCCGACAAGAA 59.315 55.000 0.00 0.00 0.00 2.52
461 558 0.685660 AAGAGACCCCCGACAAGAAC 59.314 55.000 0.00 0.00 0.00 3.01
462 559 0.471211 AGAGACCCCCGACAAGAACA 60.471 55.000 0.00 0.00 0.00 3.18
463 560 0.320508 GAGACCCCCGACAAGAACAC 60.321 60.000 0.00 0.00 0.00 3.32
464 561 1.302271 GACCCCCGACAAGAACACC 60.302 63.158 0.00 0.00 0.00 4.16
465 562 1.765597 GACCCCCGACAAGAACACCT 61.766 60.000 0.00 0.00 0.00 4.00
466 563 1.350310 ACCCCCGACAAGAACACCTT 61.350 55.000 0.00 0.00 34.91 3.50
477 574 3.627395 AGAACACCTTGACACAAGACA 57.373 42.857 12.25 0.00 0.00 3.41
478 575 4.156455 AGAACACCTTGACACAAGACAT 57.844 40.909 12.25 0.00 0.00 3.06
479 576 4.130118 AGAACACCTTGACACAAGACATC 58.870 43.478 12.25 5.99 0.00 3.06
482 579 3.070018 CACCTTGACACAAGACATCTCC 58.930 50.000 12.25 0.00 0.00 3.71
484 581 2.029020 CCTTGACACAAGACATCTCCGA 60.029 50.000 12.25 0.00 0.00 4.55
485 582 2.724977 TGACACAAGACATCTCCGAC 57.275 50.000 0.00 0.00 0.00 4.79
486 583 1.960689 TGACACAAGACATCTCCGACA 59.039 47.619 0.00 0.00 0.00 4.35
487 584 2.364002 TGACACAAGACATCTCCGACAA 59.636 45.455 0.00 0.00 0.00 3.18
488 585 2.989840 GACACAAGACATCTCCGACAAG 59.010 50.000 0.00 0.00 0.00 3.16
490 587 3.069586 ACACAAGACATCTCCGACAAGAA 59.930 43.478 0.00 0.00 0.00 2.52
491 588 3.430218 CACAAGACATCTCCGACAAGAAC 59.570 47.826 0.00 0.00 0.00 3.01
492 589 2.996621 CAAGACATCTCCGACAAGAACC 59.003 50.000 0.00 0.00 0.00 3.62
493 590 1.550976 AGACATCTCCGACAAGAACCC 59.449 52.381 0.00 0.00 0.00 4.11
506 1708 3.576982 ACAAGAACCCGTCTCTTCATACA 59.423 43.478 0.00 0.00 34.56 2.29
507 1709 3.870633 AGAACCCGTCTCTTCATACAC 57.129 47.619 0.00 0.00 0.00 2.90
608 1810 3.135225 TGTCACGTGGACCAAATACAAG 58.865 45.455 17.00 0.00 46.38 3.16
721 2161 2.002586 CTGAGCACCATACGTTTCAGG 58.997 52.381 0.00 0.00 33.12 3.86
761 2201 2.029073 CAGTCCCTCGTTGTGCGT 59.971 61.111 0.00 0.00 42.13 5.24
764 2204 4.351938 TCCCTCGTTGTGCGTCCG 62.352 66.667 0.00 0.00 42.13 4.79
768 2208 4.224274 TCGTTGTGCGTCCGGGTT 62.224 61.111 0.00 0.00 42.13 4.11
781 2221 0.165079 CCGGGTTTTCATCGTGAACG 59.835 55.000 0.00 0.00 35.89 3.95
951 2404 0.733150 GAACAGGCGGATTAACCAGC 59.267 55.000 0.00 0.00 38.90 4.85
1530 2992 2.034879 CCTCGCCGTGCAGTCATTT 61.035 57.895 0.00 0.00 0.00 2.32
2499 3967 3.799755 GGCGATGTTGTGGACGGC 61.800 66.667 0.00 0.00 42.98 5.68
2576 4055 2.809601 GGCCGACTGTGTGTAGCG 60.810 66.667 0.00 0.00 0.00 4.26
2577 4056 2.809601 GCCGACTGTGTGTAGCGG 60.810 66.667 0.00 0.00 39.05 5.52
2578 4057 2.959372 CCGACTGTGTGTAGCGGA 59.041 61.111 0.00 0.00 38.65 5.54
2579 4058 1.443872 CCGACTGTGTGTAGCGGAC 60.444 63.158 0.00 0.00 38.65 4.79
2580 4059 1.796355 CGACTGTGTGTAGCGGACG 60.796 63.158 0.00 0.00 0.00 4.79
2581 4060 1.577922 GACTGTGTGTAGCGGACGA 59.422 57.895 0.00 0.00 0.00 4.20
2582 4061 0.728466 GACTGTGTGTAGCGGACGAC 60.728 60.000 0.00 0.00 0.00 4.34
2584 4063 2.503375 GTGTGTAGCGGACGACGG 60.503 66.667 0.00 0.00 44.51 4.79
2585 4064 3.740397 TGTGTAGCGGACGACGGG 61.740 66.667 0.00 0.00 44.51 5.28
2898 4381 1.887198 CCCGCGGTGATCTCTAATAGT 59.113 52.381 26.12 0.00 0.00 2.12
2908 4391 6.657541 GGTGATCTCTAATAGTAGGACCTGAG 59.342 46.154 3.53 0.01 0.00 3.35
2910 4393 7.389607 GTGATCTCTAATAGTAGGACCTGAGTC 59.610 44.444 3.53 2.25 42.73 3.36
3043 4529 3.398406 CAAAGGTTTGTTATTGTGGGGC 58.602 45.455 0.00 0.00 33.59 5.80
3162 4649 2.165437 GTCAAGCTCTCTGTGTCCCTAG 59.835 54.545 0.00 0.00 0.00 3.02
3203 4690 1.815408 GCTTCTCTGTTGGCACCTTCA 60.815 52.381 0.00 0.00 0.00 3.02
3204 4691 2.787994 CTTCTCTGTTGGCACCTTCAT 58.212 47.619 0.00 0.00 0.00 2.57
3205 4692 2.957402 TCTCTGTTGGCACCTTCATT 57.043 45.000 0.00 0.00 0.00 2.57
3206 4693 3.228188 TCTCTGTTGGCACCTTCATTT 57.772 42.857 0.00 0.00 0.00 2.32
3207 4694 3.149196 TCTCTGTTGGCACCTTCATTTC 58.851 45.455 0.00 0.00 0.00 2.17
3208 4695 3.152341 CTCTGTTGGCACCTTCATTTCT 58.848 45.455 0.00 0.00 0.00 2.52
3209 4696 3.565307 TCTGTTGGCACCTTCATTTCTT 58.435 40.909 0.00 0.00 0.00 2.52
3210 4697 3.318839 TCTGTTGGCACCTTCATTTCTTG 59.681 43.478 0.00 0.00 0.00 3.02
3211 4698 2.364970 TGTTGGCACCTTCATTTCTTGG 59.635 45.455 0.00 0.00 0.00 3.61
3212 4699 2.627699 GTTGGCACCTTCATTTCTTGGA 59.372 45.455 0.00 0.00 0.00 3.53
3213 4700 2.956132 TGGCACCTTCATTTCTTGGAA 58.044 42.857 0.00 0.00 0.00 3.53
3221 4708 5.012046 ACCTTCATTTCTTGGAAAATCACCC 59.988 40.000 0.00 0.00 0.00 4.61
3315 4802 0.183492 TATGCAATGCCACTCCCCTC 59.817 55.000 1.53 0.00 0.00 4.30
3328 4815 4.087892 CCCTCGGGTGGCAGTCAG 62.088 72.222 0.00 0.00 0.00 3.51
3339 4829 1.195115 GGCAGTCAGGTGATGGAGTA 58.805 55.000 0.00 0.00 0.00 2.59
3400 4896 1.116308 TGGAGTTTGGTGACGTCTGA 58.884 50.000 17.92 0.00 0.00 3.27
3424 4936 1.719117 GCGCCTAATTAGCACGCAA 59.281 52.632 30.35 0.00 42.81 4.85
3444 4956 2.029743 GCCAGTTTTCAAGGCGTGA 58.970 52.632 0.00 0.00 38.86 4.35
3457 4969 1.202533 AGGCGTGATATTCGGGAGTTG 60.203 52.381 4.05 0.00 0.00 3.16
3492 5007 6.487331 GTGCTAGTAGTACTGTACTCCATCAT 59.513 42.308 22.79 7.51 40.14 2.45
3493 5008 7.013464 GTGCTAGTAGTACTGTACTCCATCATT 59.987 40.741 22.79 5.94 40.14 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.554982 AGAACATGTGTCTGCTATATCCCTTA 59.445 38.462 0.00 0.00 0.00 2.69
82 83 0.983467 TATGTGAGCTGTGAGGGCAA 59.017 50.000 0.00 0.00 0.00 4.52
136 137 2.224621 CCAGTCCAACACATCAAGAGGT 60.225 50.000 0.00 0.00 0.00 3.85
137 138 2.430465 CCAGTCCAACACATCAAGAGG 58.570 52.381 0.00 0.00 0.00 3.69
138 139 2.224621 ACCCAGTCCAACACATCAAGAG 60.225 50.000 0.00 0.00 0.00 2.85
139 140 1.774254 ACCCAGTCCAACACATCAAGA 59.226 47.619 0.00 0.00 0.00 3.02
140 141 1.881973 CACCCAGTCCAACACATCAAG 59.118 52.381 0.00 0.00 0.00 3.02
141 142 1.492599 TCACCCAGTCCAACACATCAA 59.507 47.619 0.00 0.00 0.00 2.57
182 279 2.135933 GTCTGAGGACAAGAAACCACG 58.864 52.381 0.00 0.00 41.75 4.94
184 281 2.123589 TGGTCTGAGGACAAGAAACCA 58.876 47.619 0.00 0.00 43.77 3.67
235 332 7.254137 GCAAAACTTTTGCCTCCATTTAAAAA 58.746 30.769 23.40 0.00 39.38 1.94
248 345 3.011949 TCGATGAGGCAAAACTTTTGC 57.988 42.857 25.11 25.11 44.22 3.68
249 346 7.816945 ATTAATCGATGAGGCAAAACTTTTG 57.183 32.000 9.54 9.54 0.00 2.44
251 348 9.573133 CTTAATTAATCGATGAGGCAAAACTTT 57.427 29.630 0.00 0.00 0.00 2.66
252 349 8.190784 CCTTAATTAATCGATGAGGCAAAACTT 58.809 33.333 0.00 0.00 0.00 2.66
253 350 7.556275 TCCTTAATTAATCGATGAGGCAAAACT 59.444 33.333 0.00 0.00 0.00 2.66
254 351 7.703328 TCCTTAATTAATCGATGAGGCAAAAC 58.297 34.615 0.00 0.00 0.00 2.43
255 352 7.773224 TCTCCTTAATTAATCGATGAGGCAAAA 59.227 33.333 0.00 0.00 0.00 2.44
256 353 7.279615 TCTCCTTAATTAATCGATGAGGCAAA 58.720 34.615 0.00 0.00 0.00 3.68
258 355 6.419484 TCTCCTTAATTAATCGATGAGGCA 57.581 37.500 0.00 0.00 0.00 4.75
259 356 7.155328 TCTTCTCCTTAATTAATCGATGAGGC 58.845 38.462 0.00 0.00 0.00 4.70
260 357 8.580720 TCTCTTCTCCTTAATTAATCGATGAGG 58.419 37.037 19.96 10.43 0.00 3.86
261 358 9.973450 TTCTCTTCTCCTTAATTAATCGATGAG 57.027 33.333 0.00 17.35 0.00 2.90
265 362 9.046296 GCAATTCTCTTCTCCTTAATTAATCGA 57.954 33.333 0.00 0.00 0.00 3.59
266 363 8.286097 GGCAATTCTCTTCTCCTTAATTAATCG 58.714 37.037 0.00 0.00 0.00 3.34
267 364 8.572185 GGGCAATTCTCTTCTCCTTAATTAATC 58.428 37.037 0.00 0.00 0.00 1.75
270 367 6.969043 TGGGCAATTCTCTTCTCCTTAATTA 58.031 36.000 0.00 0.00 0.00 1.40
271 368 5.831103 TGGGCAATTCTCTTCTCCTTAATT 58.169 37.500 0.00 0.00 0.00 1.40
272 369 5.044550 ACTGGGCAATTCTCTTCTCCTTAAT 60.045 40.000 0.00 0.00 0.00 1.40
273 370 4.289672 ACTGGGCAATTCTCTTCTCCTTAA 59.710 41.667 0.00 0.00 0.00 1.85
274 371 3.846588 ACTGGGCAATTCTCTTCTCCTTA 59.153 43.478 0.00 0.00 0.00 2.69
275 372 2.646798 ACTGGGCAATTCTCTTCTCCTT 59.353 45.455 0.00 0.00 0.00 3.36
276 373 2.273619 ACTGGGCAATTCTCTTCTCCT 58.726 47.619 0.00 0.00 0.00 3.69
277 374 2.797177 ACTGGGCAATTCTCTTCTCC 57.203 50.000 0.00 0.00 0.00 3.71
278 375 6.765915 AATTAACTGGGCAATTCTCTTCTC 57.234 37.500 0.00 0.00 0.00 2.87
279 376 7.148239 CGTAAATTAACTGGGCAATTCTCTTCT 60.148 37.037 0.00 0.00 0.00 2.85
280 377 6.967199 CGTAAATTAACTGGGCAATTCTCTTC 59.033 38.462 0.00 0.00 0.00 2.87
281 378 6.127730 CCGTAAATTAACTGGGCAATTCTCTT 60.128 38.462 0.00 0.00 0.00 2.85
282 379 5.357032 CCGTAAATTAACTGGGCAATTCTCT 59.643 40.000 0.00 0.00 0.00 3.10
283 380 5.355910 TCCGTAAATTAACTGGGCAATTCTC 59.644 40.000 0.00 0.00 0.00 2.87
284 381 5.258051 TCCGTAAATTAACTGGGCAATTCT 58.742 37.500 0.00 0.00 0.00 2.40
285 382 5.570234 TCCGTAAATTAACTGGGCAATTC 57.430 39.130 0.00 0.00 0.00 2.17
286 383 5.986501 TTCCGTAAATTAACTGGGCAATT 57.013 34.783 0.00 0.00 0.00 2.32
287 384 5.986501 TTTCCGTAAATTAACTGGGCAAT 57.013 34.783 0.00 0.00 0.00 3.56
288 385 5.786264 TTTTCCGTAAATTAACTGGGCAA 57.214 34.783 0.00 0.00 0.00 4.52
289 386 5.477291 TGATTTTCCGTAAATTAACTGGGCA 59.523 36.000 0.00 0.00 36.59 5.36
290 387 5.956642 TGATTTTCCGTAAATTAACTGGGC 58.043 37.500 0.00 0.00 36.59 5.36
291 388 7.248437 GTCTGATTTTCCGTAAATTAACTGGG 58.752 38.462 0.00 0.00 36.59 4.45
292 389 6.959311 CGTCTGATTTTCCGTAAATTAACTGG 59.041 38.462 0.00 0.00 36.59 4.00
293 390 7.735500 TCGTCTGATTTTCCGTAAATTAACTG 58.264 34.615 0.00 0.00 36.59 3.16
295 392 8.938047 TTTCGTCTGATTTTCCGTAAATTAAC 57.062 30.769 0.00 0.00 36.59 2.01
296 393 9.384682 GTTTTCGTCTGATTTTCCGTAAATTAA 57.615 29.630 0.00 0.00 36.59 1.40
297 394 8.016801 GGTTTTCGTCTGATTTTCCGTAAATTA 58.983 33.333 0.00 0.00 36.59 1.40
299 396 6.016943 TGGTTTTCGTCTGATTTTCCGTAAAT 60.017 34.615 0.00 0.00 39.15 1.40
300 397 5.296283 TGGTTTTCGTCTGATTTTCCGTAAA 59.704 36.000 0.00 0.00 0.00 2.01
301 398 4.815308 TGGTTTTCGTCTGATTTTCCGTAA 59.185 37.500 0.00 0.00 0.00 3.18
303 400 3.207778 TGGTTTTCGTCTGATTTTCCGT 58.792 40.909 0.00 0.00 0.00 4.69
304 401 3.889196 TGGTTTTCGTCTGATTTTCCG 57.111 42.857 0.00 0.00 0.00 4.30
305 402 6.674066 TGTATTGGTTTTCGTCTGATTTTCC 58.326 36.000 0.00 0.00 0.00 3.13
307 404 7.976734 TGTTTGTATTGGTTTTCGTCTGATTTT 59.023 29.630 0.00 0.00 0.00 1.82
308 405 7.484975 TGTTTGTATTGGTTTTCGTCTGATTT 58.515 30.769 0.00 0.00 0.00 2.17
309 406 7.033530 TGTTTGTATTGGTTTTCGTCTGATT 57.966 32.000 0.00 0.00 0.00 2.57
310 407 6.627395 TGTTTGTATTGGTTTTCGTCTGAT 57.373 33.333 0.00 0.00 0.00 2.90
311 408 6.438259 TTGTTTGTATTGGTTTTCGTCTGA 57.562 33.333 0.00 0.00 0.00 3.27
312 409 6.291585 GCTTTGTTTGTATTGGTTTTCGTCTG 60.292 38.462 0.00 0.00 0.00 3.51
313 410 5.746721 GCTTTGTTTGTATTGGTTTTCGTCT 59.253 36.000 0.00 0.00 0.00 4.18
315 412 5.289917 GTGCTTTGTTTGTATTGGTTTTCGT 59.710 36.000 0.00 0.00 0.00 3.85
316 413 5.553581 CGTGCTTTGTTTGTATTGGTTTTCG 60.554 40.000 0.00 0.00 0.00 3.46
318 415 5.411781 TCGTGCTTTGTTTGTATTGGTTTT 58.588 33.333 0.00 0.00 0.00 2.43
321 418 4.097286 AGTTCGTGCTTTGTTTGTATTGGT 59.903 37.500 0.00 0.00 0.00 3.67
322 419 4.606961 AGTTCGTGCTTTGTTTGTATTGG 58.393 39.130 0.00 0.00 0.00 3.16
323 420 6.910433 AGTTAGTTCGTGCTTTGTTTGTATTG 59.090 34.615 0.00 0.00 0.00 1.90
325 422 6.613755 AGTTAGTTCGTGCTTTGTTTGTAT 57.386 33.333 0.00 0.00 0.00 2.29
326 423 6.757947 AGTAGTTAGTTCGTGCTTTGTTTGTA 59.242 34.615 0.00 0.00 0.00 2.41
328 425 6.044512 AGTAGTTAGTTCGTGCTTTGTTTG 57.955 37.500 0.00 0.00 0.00 2.93
330 427 5.233689 GTGAGTAGTTAGTTCGTGCTTTGTT 59.766 40.000 0.00 0.00 0.00 2.83
333 430 4.940463 TGTGAGTAGTTAGTTCGTGCTTT 58.060 39.130 0.00 0.00 0.00 3.51
334 431 4.579454 TGTGAGTAGTTAGTTCGTGCTT 57.421 40.909 0.00 0.00 0.00 3.91
338 435 3.257375 TGCCATGTGAGTAGTTAGTTCGT 59.743 43.478 0.00 0.00 0.00 3.85
339 436 3.845178 TGCCATGTGAGTAGTTAGTTCG 58.155 45.455 0.00 0.00 0.00 3.95
340 437 5.479306 TCTTGCCATGTGAGTAGTTAGTTC 58.521 41.667 0.00 0.00 0.00 3.01
341 438 5.483685 TCTTGCCATGTGAGTAGTTAGTT 57.516 39.130 0.00 0.00 0.00 2.24
342 439 5.483685 TTCTTGCCATGTGAGTAGTTAGT 57.516 39.130 0.00 0.00 0.00 2.24
344 441 5.001232 GGTTTCTTGCCATGTGAGTAGTTA 58.999 41.667 0.00 0.00 0.00 2.24
345 442 3.821033 GGTTTCTTGCCATGTGAGTAGTT 59.179 43.478 0.00 0.00 0.00 2.24
346 443 3.181445 TGGTTTCTTGCCATGTGAGTAGT 60.181 43.478 0.00 0.00 0.00 2.73
347 444 3.189287 GTGGTTTCTTGCCATGTGAGTAG 59.811 47.826 0.00 0.00 38.40 2.57
348 445 3.146066 GTGGTTTCTTGCCATGTGAGTA 58.854 45.455 0.00 0.00 38.40 2.59
349 446 1.956477 GTGGTTTCTTGCCATGTGAGT 59.044 47.619 0.00 0.00 38.40 3.41
350 447 1.955778 TGTGGTTTCTTGCCATGTGAG 59.044 47.619 0.00 0.00 38.40 3.51
351 448 2.064434 TGTGGTTTCTTGCCATGTGA 57.936 45.000 0.00 0.00 38.40 3.58
354 451 4.201950 GCTACTATGTGGTTTCTTGCCATG 60.202 45.833 0.00 0.00 38.40 3.66
357 454 3.127030 GTGCTACTATGTGGTTTCTTGCC 59.873 47.826 0.00 0.00 0.00 4.52
360 457 4.579869 CCTGTGCTACTATGTGGTTTCTT 58.420 43.478 0.00 0.00 0.00 2.52
361 458 3.619979 GCCTGTGCTACTATGTGGTTTCT 60.620 47.826 0.00 0.00 33.53 2.52
362 459 2.678336 GCCTGTGCTACTATGTGGTTTC 59.322 50.000 0.00 0.00 33.53 2.78
363 460 2.039746 TGCCTGTGCTACTATGTGGTTT 59.960 45.455 0.00 0.00 38.71 3.27
364 461 1.628340 TGCCTGTGCTACTATGTGGTT 59.372 47.619 0.00 0.00 38.71 3.67
365 462 1.208052 CTGCCTGTGCTACTATGTGGT 59.792 52.381 0.00 0.00 38.71 4.16
366 463 1.945387 CTGCCTGTGCTACTATGTGG 58.055 55.000 0.00 0.00 38.71 4.17
367 464 1.293924 GCTGCCTGTGCTACTATGTG 58.706 55.000 0.00 0.00 38.71 3.21
368 465 0.179000 GGCTGCCTGTGCTACTATGT 59.821 55.000 12.43 0.00 38.71 2.29
369 466 0.533755 GGGCTGCCTGTGCTACTATG 60.534 60.000 19.68 0.00 38.71 2.23
371 468 2.367202 GGGGCTGCCTGTGCTACTA 61.367 63.158 19.68 0.00 38.71 1.82
372 469 3.721706 GGGGCTGCCTGTGCTACT 61.722 66.667 19.68 0.00 38.71 2.57
387 484 3.447025 GATTCGGAGAGTGGCGGGG 62.447 68.421 0.00 0.00 38.43 5.73
388 485 2.107141 GATTCGGAGAGTGGCGGG 59.893 66.667 0.00 0.00 38.43 6.13
389 486 2.107141 GGATTCGGAGAGTGGCGG 59.893 66.667 0.00 0.00 38.43 6.13
390 487 1.519455 GTGGATTCGGAGAGTGGCG 60.519 63.158 0.00 0.00 38.43 5.69
391 488 0.036388 TTGTGGATTCGGAGAGTGGC 60.036 55.000 0.00 0.00 38.43 5.01
393 490 2.455674 TGTTGTGGATTCGGAGAGTG 57.544 50.000 0.00 0.00 38.43 3.51
394 491 3.513912 TGTATGTTGTGGATTCGGAGAGT 59.486 43.478 0.00 0.00 38.43 3.24
395 492 3.865745 GTGTATGTTGTGGATTCGGAGAG 59.134 47.826 0.00 0.00 38.43 3.20
398 495 3.686916 TGTGTATGTTGTGGATTCGGA 57.313 42.857 0.00 0.00 0.00 4.55
399 496 4.472286 GTTTGTGTATGTTGTGGATTCGG 58.528 43.478 0.00 0.00 0.00 4.30
400 497 4.472286 GGTTTGTGTATGTTGTGGATTCG 58.528 43.478 0.00 0.00 0.00 3.34
403 500 3.826157 CAGGGTTTGTGTATGTTGTGGAT 59.174 43.478 0.00 0.00 0.00 3.41
405 502 3.004315 GTCAGGGTTTGTGTATGTTGTGG 59.996 47.826 0.00 0.00 0.00 4.17
406 503 3.629855 TGTCAGGGTTTGTGTATGTTGTG 59.370 43.478 0.00 0.00 0.00 3.33
407 504 3.892284 TGTCAGGGTTTGTGTATGTTGT 58.108 40.909 0.00 0.00 0.00 3.32
408 505 5.221880 CAATGTCAGGGTTTGTGTATGTTG 58.778 41.667 0.00 0.00 0.00 3.33
409 506 4.261994 GCAATGTCAGGGTTTGTGTATGTT 60.262 41.667 0.00 0.00 0.00 2.71
410 507 3.255642 GCAATGTCAGGGTTTGTGTATGT 59.744 43.478 0.00 0.00 0.00 2.29
411 508 3.507233 AGCAATGTCAGGGTTTGTGTATG 59.493 43.478 0.00 0.00 0.00 2.39
412 509 3.766545 AGCAATGTCAGGGTTTGTGTAT 58.233 40.909 0.00 0.00 0.00 2.29
413 510 3.222173 AGCAATGTCAGGGTTTGTGTA 57.778 42.857 0.00 0.00 0.00 2.90
414 511 2.071778 AGCAATGTCAGGGTTTGTGT 57.928 45.000 0.00 0.00 0.00 3.72
415 512 3.149196 AGTAGCAATGTCAGGGTTTGTG 58.851 45.455 0.00 0.00 0.00 3.33
416 513 3.508845 AGTAGCAATGTCAGGGTTTGT 57.491 42.857 0.00 0.00 0.00 2.83
417 514 3.370978 CGTAGTAGCAATGTCAGGGTTTG 59.629 47.826 0.00 0.00 0.00 2.93
418 515 3.596214 CGTAGTAGCAATGTCAGGGTTT 58.404 45.455 0.00 0.00 0.00 3.27
420 517 1.134788 GCGTAGTAGCAATGTCAGGGT 60.135 52.381 0.00 0.00 37.05 4.34
422 519 1.134818 TGGCGTAGTAGCAATGTCAGG 60.135 52.381 0.00 0.00 39.27 3.86
423 520 2.293677 TGGCGTAGTAGCAATGTCAG 57.706 50.000 0.00 0.00 39.27 3.51
424 521 2.232696 TCTTGGCGTAGTAGCAATGTCA 59.767 45.455 0.00 0.00 39.27 3.58
425 522 2.860735 CTCTTGGCGTAGTAGCAATGTC 59.139 50.000 0.00 0.00 39.27 3.06
426 523 2.496070 TCTCTTGGCGTAGTAGCAATGT 59.504 45.455 0.00 0.00 39.27 2.71
428 525 2.159085 GGTCTCTTGGCGTAGTAGCAAT 60.159 50.000 0.00 0.00 39.27 3.56
429 526 1.203994 GGTCTCTTGGCGTAGTAGCAA 59.796 52.381 0.00 0.00 39.27 3.91
430 527 0.815734 GGTCTCTTGGCGTAGTAGCA 59.184 55.000 0.00 0.00 39.27 3.49
431 528 0.102663 GGGTCTCTTGGCGTAGTAGC 59.897 60.000 0.00 0.00 0.00 3.58
433 530 0.685458 GGGGGTCTCTTGGCGTAGTA 60.685 60.000 0.00 0.00 0.00 1.82
438 535 4.452733 GTCGGGGGTCTCTTGGCG 62.453 72.222 0.00 0.00 0.00 5.69
439 536 2.804828 CTTGTCGGGGGTCTCTTGGC 62.805 65.000 0.00 0.00 0.00 4.52
442 539 0.685660 GTTCTTGTCGGGGGTCTCTT 59.314 55.000 0.00 0.00 0.00 2.85
443 540 0.471211 TGTTCTTGTCGGGGGTCTCT 60.471 55.000 0.00 0.00 0.00 3.10
446 543 1.302271 GGTGTTCTTGTCGGGGGTC 60.302 63.158 0.00 0.00 0.00 4.46
447 544 1.350310 AAGGTGTTCTTGTCGGGGGT 61.350 55.000 0.00 0.00 33.76 4.95
448 545 0.889186 CAAGGTGTTCTTGTCGGGGG 60.889 60.000 0.00 0.00 45.81 5.40
449 546 2.629002 CAAGGTGTTCTTGTCGGGG 58.371 57.895 0.00 0.00 45.81 5.73
456 553 3.950397 TGTCTTGTGTCAAGGTGTTCTT 58.050 40.909 9.18 0.00 35.79 2.52
457 554 3.627395 TGTCTTGTGTCAAGGTGTTCT 57.373 42.857 9.18 0.00 0.00 3.01
458 555 4.130118 AGATGTCTTGTGTCAAGGTGTTC 58.870 43.478 9.18 3.37 0.00 3.18
460 557 3.495100 GGAGATGTCTTGTGTCAAGGTGT 60.495 47.826 9.18 0.00 0.00 4.16
461 558 3.070018 GGAGATGTCTTGTGTCAAGGTG 58.930 50.000 9.18 0.00 0.00 4.00
462 559 2.289072 CGGAGATGTCTTGTGTCAAGGT 60.289 50.000 9.18 0.00 0.00 3.50
463 560 2.029020 TCGGAGATGTCTTGTGTCAAGG 60.029 50.000 9.18 0.00 0.00 3.61
464 561 2.989840 GTCGGAGATGTCTTGTGTCAAG 59.010 50.000 3.44 3.44 40.67 3.02
465 562 2.364002 TGTCGGAGATGTCTTGTGTCAA 59.636 45.455 0.00 0.00 40.67 3.18
466 563 1.960689 TGTCGGAGATGTCTTGTGTCA 59.039 47.619 0.00 0.00 40.67 3.58
467 564 2.724977 TGTCGGAGATGTCTTGTGTC 57.275 50.000 0.00 0.00 40.67 3.67
468 565 2.628178 TCTTGTCGGAGATGTCTTGTGT 59.372 45.455 0.00 0.00 40.67 3.72
469 566 3.303881 TCTTGTCGGAGATGTCTTGTG 57.696 47.619 0.00 0.00 40.67 3.33
470 567 3.555168 GGTTCTTGTCGGAGATGTCTTGT 60.555 47.826 0.00 0.00 40.67 3.16
471 568 2.996621 GGTTCTTGTCGGAGATGTCTTG 59.003 50.000 0.00 0.00 40.67 3.02
472 569 2.028020 GGGTTCTTGTCGGAGATGTCTT 60.028 50.000 0.00 0.00 40.67 3.01
473 570 1.550976 GGGTTCTTGTCGGAGATGTCT 59.449 52.381 0.00 0.00 40.67 3.41
474 571 1.736032 CGGGTTCTTGTCGGAGATGTC 60.736 57.143 0.00 0.00 40.67 3.06
475 572 0.246635 CGGGTTCTTGTCGGAGATGT 59.753 55.000 0.00 0.00 40.67 3.06
477 574 0.531200 GACGGGTTCTTGTCGGAGAT 59.469 55.000 0.00 0.00 40.67 2.75
478 575 0.538977 AGACGGGTTCTTGTCGGAGA 60.539 55.000 0.00 0.00 40.05 3.71
479 576 0.109226 GAGACGGGTTCTTGTCGGAG 60.109 60.000 0.00 0.00 40.05 4.63
482 579 1.000607 TGAAGAGACGGGTTCTTGTCG 60.001 52.381 3.51 0.00 40.05 4.35
484 581 3.576982 TGTATGAAGAGACGGGTTCTTGT 59.423 43.478 3.51 0.00 35.14 3.16
485 582 3.927142 GTGTATGAAGAGACGGGTTCTTG 59.073 47.826 3.51 0.00 35.14 3.02
486 583 3.576982 TGTGTATGAAGAGACGGGTTCTT 59.423 43.478 0.00 0.00 37.59 2.52
487 584 3.162666 TGTGTATGAAGAGACGGGTTCT 58.837 45.455 0.00 0.00 37.23 3.01
488 585 3.587797 TGTGTATGAAGAGACGGGTTC 57.412 47.619 0.00 0.00 0.00 3.62
490 587 4.893524 TGATATGTGTATGAAGAGACGGGT 59.106 41.667 0.00 0.00 0.00 5.28
491 588 5.453567 TGATATGTGTATGAAGAGACGGG 57.546 43.478 0.00 0.00 0.00 5.28
492 589 7.953158 AATTGATATGTGTATGAAGAGACGG 57.047 36.000 0.00 0.00 0.00 4.79
536 1738 6.074648 TGGTTTTACTTTGGGAATGATCTGT 58.925 36.000 0.00 0.00 0.00 3.41
608 1810 8.453238 TCCTAGTATCACACAAACTCTCTATC 57.547 38.462 0.00 0.00 0.00 2.08
721 2161 1.641577 GGCACTTGTCCTCGTATGAC 58.358 55.000 0.00 0.00 0.00 3.06
761 2201 1.515081 GTTCACGATGAAAACCCGGA 58.485 50.000 0.73 0.00 38.22 5.14
764 2204 0.109919 GCCGTTCACGATGAAAACCC 60.110 55.000 0.00 0.00 38.22 4.11
768 2208 0.672401 GGGAGCCGTTCACGATGAAA 60.672 55.000 0.00 0.00 38.22 2.69
781 2221 0.106967 CCAGCTAGGAAAAGGGAGCC 60.107 60.000 0.00 0.00 41.22 4.70
951 2404 4.659172 TTTGTGCCGGGCCTCTGG 62.659 66.667 17.97 3.43 42.40 3.86
952 2405 3.365265 GTTTGTGCCGGGCCTCTG 61.365 66.667 17.97 0.00 0.00 3.35
953 2406 3.884774 TGTTTGTGCCGGGCCTCT 61.885 61.111 17.97 0.00 0.00 3.69
954 2407 3.670377 GTGTTTGTGCCGGGCCTC 61.670 66.667 17.97 10.39 0.00 4.70
2499 3967 0.179171 CTGCATGCTTTCTCTTGCCG 60.179 55.000 20.33 0.00 36.61 5.69
2576 4055 1.949631 GAATCGATGCCCGTCGTCC 60.950 63.158 0.00 0.00 42.07 4.79
2577 4056 0.527817 AAGAATCGATGCCCGTCGTC 60.528 55.000 0.00 1.93 42.07 4.20
2578 4057 0.806102 CAAGAATCGATGCCCGTCGT 60.806 55.000 0.00 0.00 42.07 4.34
2579 4058 1.490693 CCAAGAATCGATGCCCGTCG 61.491 60.000 0.00 3.61 42.74 5.12
2580 4059 0.179084 TCCAAGAATCGATGCCCGTC 60.179 55.000 0.00 0.00 39.75 4.79
2581 4060 0.469917 ATCCAAGAATCGATGCCCGT 59.530 50.000 0.00 0.00 39.75 5.28
2582 4061 1.151668 GATCCAAGAATCGATGCCCG 58.848 55.000 0.00 0.00 40.25 6.13
2583 4062 2.260844 TGATCCAAGAATCGATGCCC 57.739 50.000 0.00 0.00 0.00 5.36
2584 4063 4.276678 TCAAATGATCCAAGAATCGATGCC 59.723 41.667 0.00 0.00 0.00 4.40
2585 4064 5.428496 TCAAATGATCCAAGAATCGATGC 57.572 39.130 0.00 0.00 0.00 3.91
2586 4065 7.040617 AGGATTCAAATGATCCAAGAATCGATG 60.041 37.037 0.00 0.00 43.26 3.84
2898 4381 2.243478 AGATCAGCAGACTCAGGTCCTA 59.757 50.000 0.00 0.00 43.05 2.94
2908 4391 9.717942 ATCCATTAATAACTAAGATCAGCAGAC 57.282 33.333 0.00 0.00 0.00 3.51
2943 4426 1.327303 AGAAATTCGGCTTGCACCAA 58.673 45.000 0.00 0.00 0.00 3.67
2949 4432 6.648725 TCCCAAAATTAAAGAAATTCGGCTTG 59.351 34.615 0.00 0.00 36.76 4.01
3056 4542 7.432350 TTTGGCTCATTCGCAAAATAAAAAT 57.568 28.000 0.00 0.00 28.23 1.82
3059 4545 6.851222 TTTTTGGCTCATTCGCAAAATAAA 57.149 29.167 0.00 0.00 33.16 1.40
3162 4649 2.429739 GCGCCTTGTTTCTGCTGC 60.430 61.111 0.00 0.00 0.00 5.25
3203 4690 5.846164 AGAAAGGGGTGATTTTCCAAGAAAT 59.154 36.000 0.00 0.00 34.60 2.17
3204 4691 5.215845 AGAAAGGGGTGATTTTCCAAGAAA 58.784 37.500 0.00 0.00 34.60 2.52
3205 4692 4.814967 AGAAAGGGGTGATTTTCCAAGAA 58.185 39.130 0.00 0.00 34.60 2.52
3206 4693 4.469469 AGAAAGGGGTGATTTTCCAAGA 57.531 40.909 0.00 0.00 34.60 3.02
3207 4694 5.299949 CAAAGAAAGGGGTGATTTTCCAAG 58.700 41.667 0.00 0.00 34.60 3.61
3208 4695 4.102367 CCAAAGAAAGGGGTGATTTTCCAA 59.898 41.667 0.00 0.00 34.60 3.53
3209 4696 3.645687 CCAAAGAAAGGGGTGATTTTCCA 59.354 43.478 0.00 0.00 34.60 3.53
3210 4697 3.901222 TCCAAAGAAAGGGGTGATTTTCC 59.099 43.478 0.00 0.00 34.60 3.13
3211 4698 4.343814 TGTCCAAAGAAAGGGGTGATTTTC 59.656 41.667 0.00 0.00 34.34 2.29
3212 4699 4.294347 TGTCCAAAGAAAGGGGTGATTTT 58.706 39.130 0.00 0.00 0.00 1.82
3213 4700 3.922375 TGTCCAAAGAAAGGGGTGATTT 58.078 40.909 0.00 0.00 0.00 2.17
3221 4708 3.905784 GACAGCATTGTCCAAAGAAAGG 58.094 45.455 0.00 0.00 46.47 3.11
3315 4802 2.959484 ATCACCTGACTGCCACCCG 61.959 63.158 0.00 0.00 0.00 5.28
3324 4811 2.180276 ACCACTACTCCATCACCTGAC 58.820 52.381 0.00 0.00 0.00 3.51
3325 4812 2.623418 ACCACTACTCCATCACCTGA 57.377 50.000 0.00 0.00 0.00 3.86
3326 4813 3.004839 CGATACCACTACTCCATCACCTG 59.995 52.174 0.00 0.00 0.00 4.00
3327 4814 3.223435 CGATACCACTACTCCATCACCT 58.777 50.000 0.00 0.00 0.00 4.00
3328 4815 2.296471 CCGATACCACTACTCCATCACC 59.704 54.545 0.00 0.00 0.00 4.02
3339 4829 1.195115 ATCTGTGTGCCGATACCACT 58.805 50.000 0.00 0.00 34.38 4.00
3400 4896 0.105964 TGCTAATTAGGCGCGTGGAT 59.894 50.000 13.84 3.89 0.00 3.41
3424 4936 0.314935 CACGCCTTGAAAACTGGCAT 59.685 50.000 0.00 0.00 46.39 4.40
3444 4956 2.092592 GGTTCCCACAACTCCCGAATAT 60.093 50.000 0.00 0.00 0.00 1.28
3457 4969 1.900486 ACTACTAGCACTGGTTCCCAC 59.100 52.381 0.00 0.00 0.00 4.61
3469 4981 7.513371 AATGATGGAGTACAGTACTACTAGC 57.487 40.000 21.61 12.37 40.41 3.42
3492 5007 8.331931 AGGATTTACTGGGATCAAGTGTATAA 57.668 34.615 9.86 1.68 0.00 0.98
3493 5008 7.931015 AGGATTTACTGGGATCAAGTGTATA 57.069 36.000 9.86 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.