Multiple sequence alignment - TraesCS1B01G424600

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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 TraesCS1B01G424600 chr1B 100.000 2549 0 0 1 2549 648816316 648813768 0 4708
1 TraesCS1B01G424600 chr1B 90.776 1984 130 27 616 2549 571670835 571672815 0 2601
2 TraesCS1B01G424600 chr1B 90.051 1950 135 17 615 2530 645321436 645323360 0 2471
3 TraesCS1B01G424600 chr1B 95.130 616 29 1 1 615 648825670 648825055 0 970
4 TraesCS1B01G424600 chr2D 92.167 1966 110 17 616 2549 16065486 16067439 0 2737
5 TraesCS1B01G424600 chr2D 90.206 1215 86 4 614 1798 435209597 435210808 0 1554
6 TraesCS1B01G424600 chr2D 94.481 616 33 1 1 615 584334887 584335502 0 948
7 TraesCS1B01G424600 chr7D 91.730 1983 112 10 611 2549 94497482 94495508 0 2706
8 TraesCS1B01G424600 chr3B 91.423 1982 116 19 616 2549 599079411 599077436 0 2669
9 TraesCS1B01G424600 chr3B 93.075 1574 77 13 1004 2549 548472452 548474021 0 2274
10 TraesCS1B01G424600 chr3B 93.887 1276 47 5 1302 2549 550862661 550863933 0 1895
11 TraesCS1B01G424600 chr3B 94.137 614 33 3 4 615 394909302 394908690 0 931
12 TraesCS1B01G424600 chr3B 94.127 613 35 1 4 615 394918868 394918256 0 931
13 TraesCS1B01G424600 chr4D 90.932 2007 108 23 613 2549 43272766 43270764 0 2630
14 TraesCS1B01G424600 chr3A 91.182 1962 132 12 616 2549 164803399 164801451 0 2627
15 TraesCS1B01G424600 chr7B 90.818 2004 105 22 616 2549 523525076 523523082 0 2608
16 TraesCS1B01G424600 chr5A 90.265 1962 132 21 616 2549 689409578 689407648 0 2510
17 TraesCS1B01G424600 chr5A 91.228 1083 83 6 613 1689 553455280 553454204 0 1463
18 TraesCS1B01G424600 chr6B 92.717 1730 86 8 854 2549 59433392 59431669 0 2460
19 TraesCS1B01G424600 chr5B 93.032 1636 80 12 942 2549 508124157 508122528 0 2359
20 TraesCS1B01G424600 chr5B 94.156 616 35 1 1 615 459317016 459317631 0 937
21 TraesCS1B01G424600 chr5D 90.728 1704 114 9 616 2278 357075968 357074268 0 2231
22 TraesCS1B01G424600 chr4B 90.183 1691 125 12 618 2272 251255863 251257548 0 2165
23 TraesCS1B01G424600 chr4B 94.003 617 34 3 1 615 270224546 270225161 0 931
24 TraesCS1B01G424600 chr4B 94.003 617 34 3 1 615 612071723 612071108 0 931
25 TraesCS1B01G424600 chr6D 89.548 1703 131 22 616 2278 329896761 329895066 0 2115
26 TraesCS1B01G424600 chr2B 94.003 617 34 3 1 615 643373572 643374187 0 931
27 TraesCS1B01G424600 chr2B 94.003 617 34 3 1 615 643383025 643383640 0 931


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 TraesCS1B01G424600 chr1B 648813768 648816316 2548 True 4708 4708 100.000 1 2549 1 chr1B.!!$R1 2548
1 TraesCS1B01G424600 chr1B 571670835 571672815 1980 False 2601 2601 90.776 616 2549 1 chr1B.!!$F1 1933
2 TraesCS1B01G424600 chr1B 645321436 645323360 1924 False 2471 2471 90.051 615 2530 1 chr1B.!!$F2 1915
3 TraesCS1B01G424600 chr1B 648825055 648825670 615 True 970 970 95.130 1 615 1 chr1B.!!$R2 614
4 TraesCS1B01G424600 chr2D 16065486 16067439 1953 False 2737 2737 92.167 616 2549 1 chr2D.!!$F1 1933
5 TraesCS1B01G424600 chr2D 435209597 435210808 1211 False 1554 1554 90.206 614 1798 1 chr2D.!!$F2 1184
6 TraesCS1B01G424600 chr2D 584334887 584335502 615 False 948 948 94.481 1 615 1 chr2D.!!$F3 614
7 TraesCS1B01G424600 chr7D 94495508 94497482 1974 True 2706 2706 91.730 611 2549 1 chr7D.!!$R1 1938
8 TraesCS1B01G424600 chr3B 599077436 599079411 1975 True 2669 2669 91.423 616 2549 1 chr3B.!!$R3 1933
9 TraesCS1B01G424600 chr3B 548472452 548474021 1569 False 2274 2274 93.075 1004 2549 1 chr3B.!!$F1 1545
10 TraesCS1B01G424600 chr3B 550862661 550863933 1272 False 1895 1895 93.887 1302 2549 1 chr3B.!!$F2 1247
11 TraesCS1B01G424600 chr3B 394908690 394909302 612 True 931 931 94.137 4 615 1 chr3B.!!$R1 611
12 TraesCS1B01G424600 chr3B 394918256 394918868 612 True 931 931 94.127 4 615 1 chr3B.!!$R2 611
13 TraesCS1B01G424600 chr4D 43270764 43272766 2002 True 2630 2630 90.932 613 2549 1 chr4D.!!$R1 1936
14 TraesCS1B01G424600 chr3A 164801451 164803399 1948 True 2627 2627 91.182 616 2549 1 chr3A.!!$R1 1933
15 TraesCS1B01G424600 chr7B 523523082 523525076 1994 True 2608 2608 90.818 616 2549 1 chr7B.!!$R1 1933
16 TraesCS1B01G424600 chr5A 689407648 689409578 1930 True 2510 2510 90.265 616 2549 1 chr5A.!!$R2 1933
17 TraesCS1B01G424600 chr5A 553454204 553455280 1076 True 1463 1463 91.228 613 1689 1 chr5A.!!$R1 1076
18 TraesCS1B01G424600 chr6B 59431669 59433392 1723 True 2460 2460 92.717 854 2549 1 chr6B.!!$R1 1695
19 TraesCS1B01G424600 chr5B 508122528 508124157 1629 True 2359 2359 93.032 942 2549 1 chr5B.!!$R1 1607
20 TraesCS1B01G424600 chr5B 459317016 459317631 615 False 937 937 94.156 1 615 1 chr5B.!!$F1 614
21 TraesCS1B01G424600 chr5D 357074268 357075968 1700 True 2231 2231 90.728 616 2278 1 chr5D.!!$R1 1662
22 TraesCS1B01G424600 chr4B 251255863 251257548 1685 False 2165 2165 90.183 618 2272 1 chr4B.!!$F1 1654
23 TraesCS1B01G424600 chr4B 270224546 270225161 615 False 931 931 94.003 1 615 1 chr4B.!!$F2 614
24 TraesCS1B01G424600 chr4B 612071108 612071723 615 True 931 931 94.003 1 615 1 chr4B.!!$R1 614
25 TraesCS1B01G424600 chr6D 329895066 329896761 1695 True 2115 2115 89.548 616 2278 1 chr6D.!!$R1 1662
26 TraesCS1B01G424600 chr2B 643373572 643374187 615 False 931 931 94.003 1 615 1 chr2B.!!$F1 614
27 TraesCS1B01G424600 chr2B 643383025 643383640 615 False 931 931 94.003 1 615 1 chr2B.!!$F2 614

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
749 753 0.175073 GGCGTCTCCGTTAGGTCAAT 59.825 55.0 0.0 0.0 39.05 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 2241 4.021916 GGTGTAAACCTCTACCAGAGCTA 58.978 47.826 0.0 0.0 40.98 3.32 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
26 27 3.308832 CCCACCTAAGGCCAAACTTCATA 60.309 47.826 5.01 0.00 32.02 2.15
222 223 5.948162 ACTAAGGTGATGATGCACAAGAAAT 59.052 36.000 0.00 0.00 40.52 2.17
240 241 3.931907 AATACCAGCTACAATGGAGCA 57.068 42.857 20.85 0.00 42.69 4.26
241 242 3.931907 ATACCAGCTACAATGGAGCAA 57.068 42.857 20.85 2.21 42.69 3.91
242 243 2.119801 ACCAGCTACAATGGAGCAAG 57.880 50.000 20.85 12.48 42.69 4.01
243 244 1.352352 ACCAGCTACAATGGAGCAAGT 59.648 47.619 20.85 13.17 42.69 3.16
244 245 1.741706 CCAGCTACAATGGAGCAAGTG 59.258 52.381 20.85 9.19 42.69 3.16
245 246 2.616256 CCAGCTACAATGGAGCAAGTGA 60.616 50.000 20.85 0.00 42.69 3.41
246 247 3.076621 CAGCTACAATGGAGCAAGTGAA 58.923 45.455 20.85 0.00 42.69 3.18
247 248 3.503363 CAGCTACAATGGAGCAAGTGAAA 59.497 43.478 20.85 0.00 42.69 2.69
248 249 4.157289 CAGCTACAATGGAGCAAGTGAAAT 59.843 41.667 20.85 0.00 42.69 2.17
249 250 4.157289 AGCTACAATGGAGCAAGTGAAATG 59.843 41.667 20.85 0.00 42.69 2.32
250 251 3.947910 ACAATGGAGCAAGTGAAATGG 57.052 42.857 0.00 0.00 0.00 3.16
251 252 3.233507 ACAATGGAGCAAGTGAAATGGT 58.766 40.909 0.00 0.00 0.00 3.55
252 253 4.406456 ACAATGGAGCAAGTGAAATGGTA 58.594 39.130 0.00 0.00 0.00 3.25
253 254 4.460382 ACAATGGAGCAAGTGAAATGGTAG 59.540 41.667 0.00 0.00 0.00 3.18
254 255 3.788227 TGGAGCAAGTGAAATGGTAGT 57.212 42.857 0.00 0.00 0.00 2.73
255 256 4.098914 TGGAGCAAGTGAAATGGTAGTT 57.901 40.909 0.00 0.00 0.00 2.24
256 257 3.820467 TGGAGCAAGTGAAATGGTAGTTG 59.180 43.478 0.00 0.00 0.00 3.16
258 259 3.923017 GCAAGTGAAATGGTAGTTGCT 57.077 42.857 8.96 0.00 45.29 3.91
260 261 5.567138 GCAAGTGAAATGGTAGTTGCTAT 57.433 39.130 8.96 0.00 45.29 2.97
261 262 6.677781 GCAAGTGAAATGGTAGTTGCTATA 57.322 37.500 8.96 0.00 45.29 1.31
262 263 6.719365 GCAAGTGAAATGGTAGTTGCTATAG 58.281 40.000 8.96 0.00 45.29 1.31
263 264 6.538742 GCAAGTGAAATGGTAGTTGCTATAGA 59.461 38.462 3.21 0.00 45.29 1.98
264 265 7.065803 GCAAGTGAAATGGTAGTTGCTATAGAA 59.934 37.037 3.21 0.00 45.29 2.10
265 266 8.946085 CAAGTGAAATGGTAGTTGCTATAGAAA 58.054 33.333 3.21 0.00 0.00 2.52
266 267 8.494016 AGTGAAATGGTAGTTGCTATAGAAAC 57.506 34.615 14.98 14.98 33.70 2.78
267 268 8.322091 AGTGAAATGGTAGTTGCTATAGAAACT 58.678 33.333 26.07 26.07 45.51 2.66
268 269 9.595823 GTGAAATGGTAGTTGCTATAGAAACTA 57.404 33.333 24.17 24.17 41.97 2.24
277 278 8.723942 AGTTGCTATAGAAACTACCATTTCTG 57.276 34.615 22.59 0.00 46.15 3.02
278 279 8.322091 AGTTGCTATAGAAACTACCATTTCTGT 58.678 33.333 22.59 6.83 46.15 3.41
279 280 8.604890 GTTGCTATAGAAACTACCATTTCTGTC 58.395 37.037 15.43 0.00 46.15 3.51
280 281 7.272978 TGCTATAGAAACTACCATTTCTGTCC 58.727 38.462 3.21 1.56 46.15 4.02
281 282 7.093068 TGCTATAGAAACTACCATTTCTGTCCA 60.093 37.037 3.21 3.65 46.15 4.02
282 283 7.439655 GCTATAGAAACTACCATTTCTGTCCAG 59.560 40.741 3.21 2.07 46.15 3.86
283 284 5.825593 AGAAACTACCATTTCTGTCCAGA 57.174 39.130 0.09 0.00 45.22 3.86
284 285 6.187727 AGAAACTACCATTTCTGTCCAGAA 57.812 37.500 5.64 5.64 45.22 3.02
322 323 9.474313 TTCTGTAGCCAAAATATTCCAATAAGT 57.526 29.630 0.00 0.00 0.00 2.24
323 324 8.902806 TCTGTAGCCAAAATATTCCAATAAGTG 58.097 33.333 0.00 0.00 0.00 3.16
324 325 8.815565 TGTAGCCAAAATATTCCAATAAGTGA 57.184 30.769 0.00 0.00 0.00 3.41
325 326 9.420118 TGTAGCCAAAATATTCCAATAAGTGAT 57.580 29.630 0.00 0.00 0.00 3.06
326 327 9.683069 GTAGCCAAAATATTCCAATAAGTGATG 57.317 33.333 0.00 0.00 0.00 3.07
327 328 8.537728 AGCCAAAATATTCCAATAAGTGATGA 57.462 30.769 0.00 0.00 0.00 2.92
328 329 8.980596 AGCCAAAATATTCCAATAAGTGATGAA 58.019 29.630 0.00 0.00 0.00 2.57
329 330 9.598517 GCCAAAATATTCCAATAAGTGATGAAA 57.401 29.630 0.00 0.00 0.00 2.69
352 353 3.625649 TTTTTGCTCAAAAAGTGCCCT 57.374 38.095 14.41 0.00 43.08 5.19
353 354 4.744795 TTTTTGCTCAAAAAGTGCCCTA 57.255 36.364 14.41 0.00 43.08 3.53
354 355 4.320608 TTTTGCTCAAAAAGTGCCCTAG 57.679 40.909 5.40 0.00 37.35 3.02
355 356 1.909700 TGCTCAAAAAGTGCCCTAGG 58.090 50.000 0.06 0.06 35.92 3.02
356 357 1.177401 GCTCAAAAAGTGCCCTAGGG 58.823 55.000 24.89 24.89 38.57 3.53
357 358 1.547901 GCTCAAAAAGTGCCCTAGGGT 60.548 52.381 28.96 6.64 37.65 4.34
358 359 2.876581 CTCAAAAAGTGCCCTAGGGTT 58.123 47.619 28.96 13.00 37.65 4.11
359 360 2.820197 CTCAAAAAGTGCCCTAGGGTTC 59.180 50.000 28.96 20.60 37.65 3.62
360 361 2.175931 TCAAAAAGTGCCCTAGGGTTCA 59.824 45.455 28.96 16.56 37.65 3.18
361 362 2.962421 CAAAAAGTGCCCTAGGGTTCAA 59.038 45.455 28.96 9.94 37.65 2.69
362 363 3.322191 AAAAGTGCCCTAGGGTTCAAA 57.678 42.857 28.96 7.38 37.65 2.69
363 364 2.586648 AAGTGCCCTAGGGTTCAAAG 57.413 50.000 28.96 1.85 37.65 2.77
364 365 1.742308 AGTGCCCTAGGGTTCAAAGA 58.258 50.000 28.96 2.05 37.65 2.52
365 366 2.062636 AGTGCCCTAGGGTTCAAAGAA 58.937 47.619 28.96 2.42 37.65 2.52
366 367 2.649816 AGTGCCCTAGGGTTCAAAGAAT 59.350 45.455 28.96 2.70 37.65 2.40
367 368 3.850173 AGTGCCCTAGGGTTCAAAGAATA 59.150 43.478 28.96 0.67 37.65 1.75
368 369 4.291249 AGTGCCCTAGGGTTCAAAGAATAA 59.709 41.667 28.96 0.00 37.65 1.40
369 370 5.044105 AGTGCCCTAGGGTTCAAAGAATAAT 60.044 40.000 28.96 1.12 37.65 1.28
370 371 5.656859 GTGCCCTAGGGTTCAAAGAATAATT 59.343 40.000 28.96 0.00 37.65 1.40
371 372 5.656416 TGCCCTAGGGTTCAAAGAATAATTG 59.344 40.000 28.96 0.00 37.65 2.32
372 373 5.069119 GCCCTAGGGTTCAAAGAATAATTGG 59.931 44.000 28.96 0.00 37.65 3.16
373 374 5.598417 CCCTAGGGTTCAAAGAATAATTGGG 59.402 44.000 20.88 0.00 0.00 4.12
374 375 6.431722 CCTAGGGTTCAAAGAATAATTGGGA 58.568 40.000 0.00 0.00 0.00 4.37
375 376 7.069344 CCTAGGGTTCAAAGAATAATTGGGAT 58.931 38.462 0.00 0.00 0.00 3.85
376 377 7.565029 CCTAGGGTTCAAAGAATAATTGGGATT 59.435 37.037 0.00 0.00 0.00 3.01
377 378 7.813087 AGGGTTCAAAGAATAATTGGGATTT 57.187 32.000 0.00 0.00 0.00 2.17
378 379 8.218423 AGGGTTCAAAGAATAATTGGGATTTT 57.782 30.769 0.00 0.00 0.00 1.82
379 380 8.668653 AGGGTTCAAAGAATAATTGGGATTTTT 58.331 29.630 0.00 0.00 0.00 1.94
380 381 8.946085 GGGTTCAAAGAATAATTGGGATTTTTC 58.054 33.333 0.00 0.00 35.02 2.29
381 382 9.725019 GGTTCAAAGAATAATTGGGATTTTTCT 57.275 29.630 0.00 0.00 41.96 2.52
395 396 9.608718 TTGGGATTTTTCTTAGAATTTTAGGGA 57.391 29.630 0.00 0.00 0.00 4.20
396 397 9.031537 TGGGATTTTTCTTAGAATTTTAGGGAC 57.968 33.333 0.00 0.00 0.00 4.46
397 398 9.031537 GGGATTTTTCTTAGAATTTTAGGGACA 57.968 33.333 0.00 0.00 0.00 4.02
409 410 8.933653 AGAATTTTAGGGACAAGAAAAATTGGA 58.066 29.630 8.79 0.00 40.04 3.53
410 411 9.208022 GAATTTTAGGGACAAGAAAAATTGGAG 57.792 33.333 8.79 0.00 40.04 3.86
411 412 7.669089 TTTTAGGGACAAGAAAAATTGGAGT 57.331 32.000 0.00 0.00 34.36 3.85
412 413 7.669089 TTTAGGGACAAGAAAAATTGGAGTT 57.331 32.000 0.00 0.00 34.36 3.01
413 414 5.535753 AGGGACAAGAAAAATTGGAGTTG 57.464 39.130 0.00 0.00 34.36 3.16
414 415 4.058124 GGGACAAGAAAAATTGGAGTTGC 58.942 43.478 0.00 0.00 34.36 4.17
415 416 4.202253 GGGACAAGAAAAATTGGAGTTGCT 60.202 41.667 0.00 0.00 34.36 3.91
416 417 5.359756 GGACAAGAAAAATTGGAGTTGCTT 58.640 37.500 0.00 0.00 34.36 3.91
417 418 5.817296 GGACAAGAAAAATTGGAGTTGCTTT 59.183 36.000 0.00 0.00 34.36 3.51
418 419 6.238184 GGACAAGAAAAATTGGAGTTGCTTTG 60.238 38.462 0.00 0.00 34.36 2.77
419 420 5.585844 ACAAGAAAAATTGGAGTTGCTTTGG 59.414 36.000 0.00 0.00 34.36 3.28
420 421 5.612725 AGAAAAATTGGAGTTGCTTTGGA 57.387 34.783 0.00 0.00 0.00 3.53
421 422 5.604565 AGAAAAATTGGAGTTGCTTTGGAG 58.395 37.500 0.00 0.00 0.00 3.86
435 436 1.742761 TTGGAGCACATTGAGCTAGC 58.257 50.000 6.62 6.62 43.58 3.42
436 437 0.907486 TGGAGCACATTGAGCTAGCT 59.093 50.000 19.45 19.45 43.58 3.32
437 438 2.110578 TGGAGCACATTGAGCTAGCTA 58.889 47.619 19.38 2.78 43.58 3.32
438 439 2.102084 TGGAGCACATTGAGCTAGCTAG 59.898 50.000 19.38 16.84 43.58 3.42
439 440 2.547642 GGAGCACATTGAGCTAGCTAGG 60.548 54.545 19.38 7.49 43.58 3.02
440 441 1.415659 AGCACATTGAGCTAGCTAGGG 59.584 52.381 19.38 10.40 41.32 3.53
441 442 1.139853 GCACATTGAGCTAGCTAGGGT 59.860 52.381 19.38 10.93 0.00 4.34
442 443 2.420687 GCACATTGAGCTAGCTAGGGTT 60.421 50.000 19.38 0.00 0.00 4.11
443 444 3.878778 CACATTGAGCTAGCTAGGGTTT 58.121 45.455 19.38 0.00 0.00 3.27
444 445 4.683400 GCACATTGAGCTAGCTAGGGTTTA 60.683 45.833 19.38 0.00 0.00 2.01
445 446 5.053145 CACATTGAGCTAGCTAGGGTTTAG 58.947 45.833 19.38 5.18 0.00 1.85
446 447 4.101741 ACATTGAGCTAGCTAGGGTTTAGG 59.898 45.833 19.38 3.31 0.00 2.69
447 448 3.682592 TGAGCTAGCTAGGGTTTAGGA 57.317 47.619 19.38 0.00 0.00 2.94
448 449 3.567397 TGAGCTAGCTAGGGTTTAGGAG 58.433 50.000 19.38 0.00 0.00 3.69
449 450 2.894765 GAGCTAGCTAGGGTTTAGGAGG 59.105 54.545 19.38 0.00 0.00 4.30
450 451 1.972075 GCTAGCTAGGGTTTAGGAGGG 59.028 57.143 22.10 0.00 0.00 4.30
451 452 2.610873 CTAGCTAGGGTTTAGGAGGGG 58.389 57.143 13.32 0.00 0.00 4.79
452 453 1.024536 AGCTAGGGTTTAGGAGGGGA 58.975 55.000 0.00 0.00 0.00 4.81
453 454 1.368558 AGCTAGGGTTTAGGAGGGGAA 59.631 52.381 0.00 0.00 0.00 3.97
454 455 2.202707 GCTAGGGTTTAGGAGGGGAAA 58.797 52.381 0.00 0.00 0.00 3.13
455 456 2.579400 GCTAGGGTTTAGGAGGGGAAAA 59.421 50.000 0.00 0.00 0.00 2.29
456 457 3.204606 GCTAGGGTTTAGGAGGGGAAAAT 59.795 47.826 0.00 0.00 0.00 1.82
457 458 3.757947 AGGGTTTAGGAGGGGAAAATG 57.242 47.619 0.00 0.00 0.00 2.32
458 459 3.274383 AGGGTTTAGGAGGGGAAAATGA 58.726 45.455 0.00 0.00 0.00 2.57
459 460 3.665618 AGGGTTTAGGAGGGGAAAATGAA 59.334 43.478 0.00 0.00 0.00 2.57
460 461 4.297664 AGGGTTTAGGAGGGGAAAATGAAT 59.702 41.667 0.00 0.00 0.00 2.57
461 462 5.498373 AGGGTTTAGGAGGGGAAAATGAATA 59.502 40.000 0.00 0.00 0.00 1.75
462 463 6.164042 AGGGTTTAGGAGGGGAAAATGAATAT 59.836 38.462 0.00 0.00 0.00 1.28
463 464 6.844388 GGGTTTAGGAGGGGAAAATGAATATT 59.156 38.462 0.00 0.00 0.00 1.28
464 465 7.347222 GGGTTTAGGAGGGGAAAATGAATATTT 59.653 37.037 0.00 0.00 38.11 1.40
465 466 8.768397 GGTTTAGGAGGGGAAAATGAATATTTT 58.232 33.333 0.00 0.00 46.35 1.82
468 469 9.554053 TTAGGAGGGGAAAATGAATATTTTTCA 57.446 29.630 11.38 0.00 44.35 2.69
469 470 8.628368 AGGAGGGGAAAATGAATATTTTTCAT 57.372 30.769 11.38 0.07 44.35 2.57
515 516 9.993454 TGATATTTTGAGATGAACTAGAGATGG 57.007 33.333 0.00 0.00 0.00 3.51
518 519 7.487822 TTTTGAGATGAACTAGAGATGGAGT 57.512 36.000 0.00 0.00 0.00 3.85
519 520 6.462552 TTGAGATGAACTAGAGATGGAGTG 57.537 41.667 0.00 0.00 0.00 3.51
520 521 5.760131 TGAGATGAACTAGAGATGGAGTGA 58.240 41.667 0.00 0.00 0.00 3.41
521 522 6.372104 TGAGATGAACTAGAGATGGAGTGAT 58.628 40.000 0.00 0.00 0.00 3.06
522 523 6.264970 TGAGATGAACTAGAGATGGAGTGATG 59.735 42.308 0.00 0.00 0.00 3.07
523 524 6.372104 AGATGAACTAGAGATGGAGTGATGA 58.628 40.000 0.00 0.00 0.00 2.92
524 525 7.011994 AGATGAACTAGAGATGGAGTGATGAT 58.988 38.462 0.00 0.00 0.00 2.45
525 526 7.510001 AGATGAACTAGAGATGGAGTGATGATT 59.490 37.037 0.00 0.00 0.00 2.57
526 527 8.718158 ATGAACTAGAGATGGAGTGATGATTA 57.282 34.615 0.00 0.00 0.00 1.75
527 528 8.175925 TGAACTAGAGATGGAGTGATGATTAG 57.824 38.462 0.00 0.00 0.00 1.73
528 529 8.001292 TGAACTAGAGATGGAGTGATGATTAGA 58.999 37.037 0.00 0.00 0.00 2.10
529 530 8.408043 AACTAGAGATGGAGTGATGATTAGAG 57.592 38.462 0.00 0.00 0.00 2.43
530 531 7.754624 ACTAGAGATGGAGTGATGATTAGAGA 58.245 38.462 0.00 0.00 0.00 3.10
531 532 7.884877 ACTAGAGATGGAGTGATGATTAGAGAG 59.115 40.741 0.00 0.00 0.00 3.20
532 533 6.012113 AGAGATGGAGTGATGATTAGAGAGG 58.988 44.000 0.00 0.00 0.00 3.69
533 534 5.085920 AGATGGAGTGATGATTAGAGAGGG 58.914 45.833 0.00 0.00 0.00 4.30
534 535 4.542906 TGGAGTGATGATTAGAGAGGGA 57.457 45.455 0.00 0.00 0.00 4.20
535 536 4.478203 TGGAGTGATGATTAGAGAGGGAG 58.522 47.826 0.00 0.00 0.00 4.30
536 537 4.168871 TGGAGTGATGATTAGAGAGGGAGA 59.831 45.833 0.00 0.00 0.00 3.71
537 538 5.162892 TGGAGTGATGATTAGAGAGGGAGAT 60.163 44.000 0.00 0.00 0.00 2.75
538 539 5.185635 GGAGTGATGATTAGAGAGGGAGATG 59.814 48.000 0.00 0.00 0.00 2.90
539 540 5.963092 AGTGATGATTAGAGAGGGAGATGA 58.037 41.667 0.00 0.00 0.00 2.92
540 541 6.380414 AGTGATGATTAGAGAGGGAGATGAA 58.620 40.000 0.00 0.00 0.00 2.57
541 542 6.494491 AGTGATGATTAGAGAGGGAGATGAAG 59.506 42.308 0.00 0.00 0.00 3.02
542 543 5.245751 TGATGATTAGAGAGGGAGATGAAGC 59.754 44.000 0.00 0.00 0.00 3.86
543 544 4.550669 TGATTAGAGAGGGAGATGAAGCA 58.449 43.478 0.00 0.00 0.00 3.91
544 545 4.343526 TGATTAGAGAGGGAGATGAAGCAC 59.656 45.833 0.00 0.00 0.00 4.40
545 546 2.548464 AGAGAGGGAGATGAAGCACT 57.452 50.000 0.00 0.00 0.00 4.40
546 547 2.831565 AGAGAGGGAGATGAAGCACTT 58.168 47.619 0.00 0.00 0.00 3.16
547 548 2.500910 AGAGAGGGAGATGAAGCACTTG 59.499 50.000 0.00 0.00 0.00 3.16
548 549 1.558756 AGAGGGAGATGAAGCACTTGG 59.441 52.381 0.00 0.00 0.00 3.61
549 550 0.622665 AGGGAGATGAAGCACTTGGG 59.377 55.000 0.00 0.00 0.00 4.12
550 551 0.329596 GGGAGATGAAGCACTTGGGT 59.670 55.000 0.00 0.00 0.00 4.51
551 552 1.457346 GGAGATGAAGCACTTGGGTG 58.543 55.000 0.00 0.00 45.53 4.61
552 553 1.003580 GGAGATGAAGCACTTGGGTGA 59.996 52.381 0.00 0.00 45.61 4.02
553 554 2.553028 GGAGATGAAGCACTTGGGTGAA 60.553 50.000 0.00 0.00 45.61 3.18
554 555 3.149196 GAGATGAAGCACTTGGGTGAAA 58.851 45.455 0.00 0.00 45.61 2.69
555 556 3.152341 AGATGAAGCACTTGGGTGAAAG 58.848 45.455 0.00 0.00 45.61 2.62
556 557 2.727123 TGAAGCACTTGGGTGAAAGA 57.273 45.000 0.00 0.00 45.61 2.52
557 558 2.575532 TGAAGCACTTGGGTGAAAGAG 58.424 47.619 0.00 0.00 45.61 2.85
558 559 2.172505 TGAAGCACTTGGGTGAAAGAGA 59.827 45.455 0.00 0.00 45.61 3.10
559 560 3.214328 GAAGCACTTGGGTGAAAGAGAA 58.786 45.455 0.00 0.00 45.61 2.87
560 561 2.856222 AGCACTTGGGTGAAAGAGAAG 58.144 47.619 0.00 0.00 45.61 2.85
561 562 1.882623 GCACTTGGGTGAAAGAGAAGG 59.117 52.381 0.00 0.00 45.61 3.46
562 563 2.508526 CACTTGGGTGAAAGAGAAGGG 58.491 52.381 0.00 0.00 45.61 3.95
563 564 2.136026 ACTTGGGTGAAAGAGAAGGGT 58.864 47.619 0.00 0.00 0.00 4.34
564 565 2.514160 ACTTGGGTGAAAGAGAAGGGTT 59.486 45.455 0.00 0.00 0.00 4.11
565 566 3.720002 ACTTGGGTGAAAGAGAAGGGTTA 59.280 43.478 0.00 0.00 0.00 2.85
566 567 3.782656 TGGGTGAAAGAGAAGGGTTAC 57.217 47.619 0.00 0.00 0.00 2.50
567 568 2.374170 TGGGTGAAAGAGAAGGGTTACC 59.626 50.000 0.00 0.00 0.00 2.85
568 569 2.290768 GGGTGAAAGAGAAGGGTTACCC 60.291 54.545 13.56 13.56 45.90 3.69
588 589 5.110814 CCCAAGTGGTTAAGTCCATATGA 57.889 43.478 3.65 0.00 39.81 2.15
589 590 5.505780 CCCAAGTGGTTAAGTCCATATGAA 58.494 41.667 3.65 0.00 39.81 2.57
590 591 5.949354 CCCAAGTGGTTAAGTCCATATGAAA 59.051 40.000 3.65 0.00 39.81 2.69
591 592 6.435904 CCCAAGTGGTTAAGTCCATATGAAAA 59.564 38.462 3.65 0.00 39.81 2.29
592 593 7.362920 CCCAAGTGGTTAAGTCCATATGAAAAG 60.363 40.741 3.65 0.00 39.81 2.27
593 594 7.393234 CCAAGTGGTTAAGTCCATATGAAAAGA 59.607 37.037 3.65 0.00 39.81 2.52
594 595 8.960591 CAAGTGGTTAAGTCCATATGAAAAGAT 58.039 33.333 3.65 0.00 39.81 2.40
595 596 9.533831 AAGTGGTTAAGTCCATATGAAAAGATT 57.466 29.630 3.65 0.00 39.81 2.40
596 597 9.178758 AGTGGTTAAGTCCATATGAAAAGATTC 57.821 33.333 3.65 0.00 39.81 2.52
597 598 8.956426 GTGGTTAAGTCCATATGAAAAGATTCA 58.044 33.333 3.65 0.00 43.26 2.57
598 599 9.527157 TGGTTAAGTCCATATGAAAAGATTCAA 57.473 29.630 3.65 0.00 39.54 2.69
621 622 8.490311 TCAAAACTCCAAAAATTCAAGGGTTAT 58.510 29.630 0.00 0.00 0.00 1.89
647 648 0.550914 TTTTGCCCTCAGTGGTGTCT 59.449 50.000 0.00 0.00 0.00 3.41
662 663 5.246203 AGTGGTGTCTATCTGCTCAGTTTTA 59.754 40.000 0.00 0.00 0.00 1.52
667 668 5.955959 TGTCTATCTGCTCAGTTTTACCCTA 59.044 40.000 0.00 0.00 0.00 3.53
691 692 4.455533 AGATGCGAATTGTGCTCAGTTTTA 59.544 37.500 0.00 0.00 0.00 1.52
741 745 1.289380 GAACTCTGGCGTCTCCGTT 59.711 57.895 0.00 0.00 37.80 4.44
749 753 0.175073 GGCGTCTCCGTTAGGTCAAT 59.825 55.000 0.00 0.00 39.05 2.57
770 774 2.223745 GTTTTGACTCGGCCCTTACAA 58.776 47.619 0.00 0.00 0.00 2.41
773 777 1.053424 TGACTCGGCCCTTACAAGTT 58.947 50.000 0.00 0.00 0.00 2.66
817 821 9.950680 CGACTAATTTTATTTAGACCATTGCAT 57.049 29.630 0.00 0.00 34.08 3.96
821 825 5.826601 TTTATTTAGACCATTGCATGCGA 57.173 34.783 10.79 10.79 0.00 5.10
891 933 1.293498 GACAGCGATGGTGACCACT 59.707 57.895 6.40 0.00 35.80 4.00
928 982 2.282251 TGACCACGGCGAGAGAGT 60.282 61.111 16.62 2.46 0.00 3.24
982 1121 4.514577 CGGCGGCGTTGAGATCCT 62.515 66.667 24.74 0.00 0.00 3.24
1009 1148 0.614697 TCCGAGCTCCATGTCTTCCA 60.615 55.000 8.47 0.00 0.00 3.53
1029 1168 1.462238 AAGCTCCCACACCACCTCT 60.462 57.895 0.00 0.00 0.00 3.69
1139 1279 2.168521 TGAGGAACCAGAATCGTCCATC 59.831 50.000 0.00 0.00 32.21 3.51
1206 1346 2.088950 TTTCGTGGTCGGGATCTTTC 57.911 50.000 0.00 0.00 37.69 2.62
1225 1365 3.998913 TCAGCAATGGGTTGATCTGTA 57.001 42.857 0.00 0.00 37.53 2.74
1228 1368 4.080413 TCAGCAATGGGTTGATCTGTATCA 60.080 41.667 0.00 0.00 40.43 2.15
1245 1385 1.441738 TCATGTTCATGCAGGTGACG 58.558 50.000 7.80 0.00 0.00 4.35
1326 1468 2.883574 CATGAAGAATGGTTGCGCATT 58.116 42.857 12.75 0.99 32.10 3.56
1331 1473 0.171903 GAATGGTTGCGCATTCTGCT 59.828 50.000 12.75 0.00 42.25 4.24
1340 1482 1.741770 GCATTCTGCTCCGAACCGT 60.742 57.895 0.00 0.00 40.96 4.83
1349 1491 4.060038 CCGAACCGTAGTGGCCGT 62.060 66.667 0.00 0.00 43.94 5.68
2031 2241 4.895668 AATGTCATGGAAAATGTGCCTT 57.104 36.364 0.00 0.00 0.00 4.35
2074 2284 4.252878 CCTGGTGCCAAAATAAATGAACC 58.747 43.478 0.00 0.00 0.00 3.62
2356 2615 8.447053 GTTTTCCTTTGTTTTGCACTGAAATTA 58.553 29.630 0.00 0.00 0.00 1.40
2370 2629 6.096001 GCACTGAAATTATGGAGAGTTGGAAT 59.904 38.462 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.297776 CAGATATGAAGTTTGGCCTTAGGTG 59.702 44.000 3.32 0.00 0.00 4.00
26 27 1.667830 CACGGACAACACGCCAGAT 60.668 57.895 0.00 0.00 34.00 2.90
222 223 2.571653 ACTTGCTCCATTGTAGCTGGTA 59.428 45.455 0.00 0.00 40.73 3.25
240 241 8.947115 GTTTCTATAGCAACTACCATTTCACTT 58.053 33.333 7.88 0.00 0.00 3.16
241 242 8.322091 AGTTTCTATAGCAACTACCATTTCACT 58.678 33.333 15.05 0.00 30.05 3.41
242 243 8.494016 AGTTTCTATAGCAACTACCATTTCAC 57.506 34.615 15.05 0.00 30.05 3.18
243 244 9.595823 GTAGTTTCTATAGCAACTACCATTTCA 57.404 33.333 29.98 9.18 43.81 2.69
250 251 9.819267 AGAAATGGTAGTTTCTATAGCAACTAC 57.181 33.333 31.21 31.21 46.58 2.73
251 252 9.817809 CAGAAATGGTAGTTTCTATAGCAACTA 57.182 33.333 17.68 17.68 44.38 2.24
252 253 8.322091 ACAGAAATGGTAGTTTCTATAGCAACT 58.678 33.333 19.49 19.49 44.38 3.16
253 254 8.494016 ACAGAAATGGTAGTTTCTATAGCAAC 57.506 34.615 7.12 7.12 44.38 4.17
254 255 7.769044 GGACAGAAATGGTAGTTTCTATAGCAA 59.231 37.037 0.00 0.00 44.38 3.91
255 256 7.093068 TGGACAGAAATGGTAGTTTCTATAGCA 60.093 37.037 0.00 0.00 44.38 3.49
256 257 7.272978 TGGACAGAAATGGTAGTTTCTATAGC 58.727 38.462 0.00 0.00 44.38 2.97
257 258 8.696374 TCTGGACAGAAATGGTAGTTTCTATAG 58.304 37.037 0.00 0.00 44.38 1.31
258 259 8.603898 TCTGGACAGAAATGGTAGTTTCTATA 57.396 34.615 0.00 0.00 44.38 1.31
259 260 7.496346 TCTGGACAGAAATGGTAGTTTCTAT 57.504 36.000 0.00 0.00 44.38 1.98
260 261 6.928348 TCTGGACAGAAATGGTAGTTTCTA 57.072 37.500 0.00 0.00 44.38 2.10
261 262 5.825593 TCTGGACAGAAATGGTAGTTTCT 57.174 39.130 0.00 0.00 46.46 2.52
296 297 9.474313 ACTTATTGGAATATTTTGGCTACAGAA 57.526 29.630 0.00 0.00 0.00 3.02
297 298 8.902806 CACTTATTGGAATATTTTGGCTACAGA 58.097 33.333 0.00 0.00 0.00 3.41
298 299 8.902806 TCACTTATTGGAATATTTTGGCTACAG 58.097 33.333 0.00 0.00 0.00 2.74
299 300 8.815565 TCACTTATTGGAATATTTTGGCTACA 57.184 30.769 0.00 0.00 0.00 2.74
300 301 9.683069 CATCACTTATTGGAATATTTTGGCTAC 57.317 33.333 0.00 0.00 0.00 3.58
301 302 9.639563 TCATCACTTATTGGAATATTTTGGCTA 57.360 29.630 0.00 0.00 0.00 3.93
302 303 8.537728 TCATCACTTATTGGAATATTTTGGCT 57.462 30.769 0.00 0.00 0.00 4.75
303 304 9.598517 TTTCATCACTTATTGGAATATTTTGGC 57.401 29.630 0.00 0.00 0.00 4.52
323 324 9.321590 GCACTTTTTGAGCAAAAATATTTCATC 57.678 29.630 18.20 0.00 45.69 2.92
324 325 8.291740 GGCACTTTTTGAGCAAAAATATTTCAT 58.708 29.630 18.20 0.00 45.69 2.57
325 326 7.255070 GGGCACTTTTTGAGCAAAAATATTTCA 60.255 33.333 18.20 0.00 45.69 2.69
326 327 7.041167 AGGGCACTTTTTGAGCAAAAATATTTC 60.041 33.333 18.20 10.43 45.69 2.17
327 328 6.772233 AGGGCACTTTTTGAGCAAAAATATTT 59.228 30.769 18.20 0.00 45.69 1.40
328 329 6.298361 AGGGCACTTTTTGAGCAAAAATATT 58.702 32.000 18.20 6.56 45.69 1.28
329 330 5.868454 AGGGCACTTTTTGAGCAAAAATAT 58.132 33.333 18.20 9.51 45.69 1.28
330 331 5.289083 AGGGCACTTTTTGAGCAAAAATA 57.711 34.783 18.20 1.75 45.69 1.40
331 332 4.155063 AGGGCACTTTTTGAGCAAAAAT 57.845 36.364 18.20 8.71 45.69 1.82
332 333 3.625649 AGGGCACTTTTTGAGCAAAAA 57.374 38.095 17.25 17.25 44.98 1.94
333 334 3.069443 CCTAGGGCACTTTTTGAGCAAAA 59.931 43.478 0.00 4.39 38.40 2.44
334 335 2.627699 CCTAGGGCACTTTTTGAGCAAA 59.372 45.455 0.00 0.00 33.86 3.68
335 336 2.238521 CCTAGGGCACTTTTTGAGCAA 58.761 47.619 0.00 0.00 33.86 3.91
336 337 1.547675 CCCTAGGGCACTTTTTGAGCA 60.548 52.381 16.90 0.00 33.86 4.26
337 338 1.177401 CCCTAGGGCACTTTTTGAGC 58.823 55.000 16.90 0.00 0.00 4.26
338 339 2.586648 ACCCTAGGGCACTTTTTGAG 57.413 50.000 28.88 0.00 39.32 3.02
339 340 2.175931 TGAACCCTAGGGCACTTTTTGA 59.824 45.455 28.88 4.55 39.32 2.69
340 341 2.593026 TGAACCCTAGGGCACTTTTTG 58.407 47.619 28.88 0.54 39.32 2.44
341 342 3.322191 TTGAACCCTAGGGCACTTTTT 57.678 42.857 28.88 13.46 39.32 1.94
342 343 3.117284 TCTTTGAACCCTAGGGCACTTTT 60.117 43.478 28.88 14.26 39.32 2.27
343 344 2.445525 TCTTTGAACCCTAGGGCACTTT 59.554 45.455 28.88 14.68 39.32 2.66
344 345 2.062636 TCTTTGAACCCTAGGGCACTT 58.937 47.619 28.88 15.08 39.32 3.16
345 346 1.742308 TCTTTGAACCCTAGGGCACT 58.258 50.000 28.88 12.79 39.32 4.40
346 347 2.579410 TTCTTTGAACCCTAGGGCAC 57.421 50.000 28.88 21.18 39.32 5.01
347 348 4.938575 TTATTCTTTGAACCCTAGGGCA 57.061 40.909 28.88 15.99 39.32 5.36
348 349 5.069119 CCAATTATTCTTTGAACCCTAGGGC 59.931 44.000 28.88 13.26 39.32 5.19
349 350 5.598417 CCCAATTATTCTTTGAACCCTAGGG 59.402 44.000 27.36 27.36 42.03 3.53
350 351 6.431722 TCCCAATTATTCTTTGAACCCTAGG 58.568 40.000 0.06 0.06 0.00 3.02
351 352 8.539117 AATCCCAATTATTCTTTGAACCCTAG 57.461 34.615 0.00 0.00 0.00 3.02
352 353 8.909423 AAATCCCAATTATTCTTTGAACCCTA 57.091 30.769 0.00 0.00 0.00 3.53
353 354 7.813087 AAATCCCAATTATTCTTTGAACCCT 57.187 32.000 0.00 0.00 0.00 4.34
354 355 8.862325 AAAAATCCCAATTATTCTTTGAACCC 57.138 30.769 0.00 0.00 0.00 4.11
355 356 9.725019 AGAAAAATCCCAATTATTCTTTGAACC 57.275 29.630 0.00 0.00 0.00 3.62
369 370 9.608718 TCCCTAAAATTCTAAGAAAAATCCCAA 57.391 29.630 0.00 0.00 0.00 4.12
370 371 9.031537 GTCCCTAAAATTCTAAGAAAAATCCCA 57.968 33.333 0.00 0.00 0.00 4.37
371 372 9.031537 TGTCCCTAAAATTCTAAGAAAAATCCC 57.968 33.333 0.00 0.00 0.00 3.85
383 384 8.933653 TCCAATTTTTCTTGTCCCTAAAATTCT 58.066 29.630 0.00 0.00 37.82 2.40
384 385 9.208022 CTCCAATTTTTCTTGTCCCTAAAATTC 57.792 33.333 0.00 0.00 37.82 2.17
385 386 8.713971 ACTCCAATTTTTCTTGTCCCTAAAATT 58.286 29.630 0.00 0.00 39.47 1.82
386 387 8.262601 ACTCCAATTTTTCTTGTCCCTAAAAT 57.737 30.769 0.00 0.00 33.05 1.82
387 388 7.669089 ACTCCAATTTTTCTTGTCCCTAAAA 57.331 32.000 0.00 0.00 0.00 1.52
388 389 7.496747 CAACTCCAATTTTTCTTGTCCCTAAA 58.503 34.615 0.00 0.00 0.00 1.85
389 390 6.462347 GCAACTCCAATTTTTCTTGTCCCTAA 60.462 38.462 0.00 0.00 0.00 2.69
390 391 5.010617 GCAACTCCAATTTTTCTTGTCCCTA 59.989 40.000 0.00 0.00 0.00 3.53
391 392 4.202253 GCAACTCCAATTTTTCTTGTCCCT 60.202 41.667 0.00 0.00 0.00 4.20
392 393 4.058124 GCAACTCCAATTTTTCTTGTCCC 58.942 43.478 0.00 0.00 0.00 4.46
393 394 4.948847 AGCAACTCCAATTTTTCTTGTCC 58.051 39.130 0.00 0.00 0.00 4.02
394 395 6.238184 CCAAAGCAACTCCAATTTTTCTTGTC 60.238 38.462 0.00 0.00 0.00 3.18
395 396 5.585844 CCAAAGCAACTCCAATTTTTCTTGT 59.414 36.000 0.00 0.00 0.00 3.16
396 397 5.816777 TCCAAAGCAACTCCAATTTTTCTTG 59.183 36.000 0.00 0.00 0.00 3.02
397 398 5.988287 TCCAAAGCAACTCCAATTTTTCTT 58.012 33.333 0.00 0.00 0.00 2.52
398 399 5.604565 CTCCAAAGCAACTCCAATTTTTCT 58.395 37.500 0.00 0.00 0.00 2.52
399 400 5.912360 CTCCAAAGCAACTCCAATTTTTC 57.088 39.130 0.00 0.00 0.00 2.29
414 415 2.097142 GCTAGCTCAATGTGCTCCAAAG 59.903 50.000 13.38 6.75 41.46 2.77
415 416 2.086869 GCTAGCTCAATGTGCTCCAAA 58.913 47.619 13.38 0.00 41.46 3.28
416 417 1.280133 AGCTAGCTCAATGTGCTCCAA 59.720 47.619 12.68 0.00 41.46 3.53
417 418 0.907486 AGCTAGCTCAATGTGCTCCA 59.093 50.000 12.68 0.00 41.46 3.86
418 419 2.547642 CCTAGCTAGCTCAATGTGCTCC 60.548 54.545 23.26 6.45 41.46 4.70
419 420 2.547642 CCCTAGCTAGCTCAATGTGCTC 60.548 54.545 23.26 0.60 41.46 4.26
420 421 1.415659 CCCTAGCTAGCTCAATGTGCT 59.584 52.381 23.26 14.41 43.79 4.40
421 422 1.139853 ACCCTAGCTAGCTCAATGTGC 59.860 52.381 23.26 0.00 0.00 4.57
422 423 3.550437 AACCCTAGCTAGCTCAATGTG 57.450 47.619 23.26 7.72 0.00 3.21
423 424 4.101741 CCTAAACCCTAGCTAGCTCAATGT 59.898 45.833 23.26 11.69 0.00 2.71
424 425 4.345257 TCCTAAACCCTAGCTAGCTCAATG 59.655 45.833 23.26 11.02 0.00 2.82
425 426 4.557705 TCCTAAACCCTAGCTAGCTCAAT 58.442 43.478 23.26 2.38 0.00 2.57
426 427 3.961408 CTCCTAAACCCTAGCTAGCTCAA 59.039 47.826 23.26 3.28 0.00 3.02
427 428 3.567397 CTCCTAAACCCTAGCTAGCTCA 58.433 50.000 23.26 7.11 0.00 4.26
428 429 2.894765 CCTCCTAAACCCTAGCTAGCTC 59.105 54.545 23.26 0.00 0.00 4.09
429 430 2.426561 CCCTCCTAAACCCTAGCTAGCT 60.427 54.545 23.12 23.12 0.00 3.32
430 431 1.972075 CCCTCCTAAACCCTAGCTAGC 59.028 57.143 15.74 6.62 0.00 3.42
431 432 2.179424 TCCCCTCCTAAACCCTAGCTAG 59.821 54.545 14.20 14.20 0.00 3.42
432 433 2.229523 TCCCCTCCTAAACCCTAGCTA 58.770 52.381 0.00 0.00 0.00 3.32
433 434 1.024536 TCCCCTCCTAAACCCTAGCT 58.975 55.000 0.00 0.00 0.00 3.32
434 435 1.889174 TTCCCCTCCTAAACCCTAGC 58.111 55.000 0.00 0.00 0.00 3.42
435 436 4.477213 TCATTTTCCCCTCCTAAACCCTAG 59.523 45.833 0.00 0.00 0.00 3.02
436 437 4.450348 TCATTTTCCCCTCCTAAACCCTA 58.550 43.478 0.00 0.00 0.00 3.53
437 438 3.274383 TCATTTTCCCCTCCTAAACCCT 58.726 45.455 0.00 0.00 0.00 4.34
438 439 3.750501 TCATTTTCCCCTCCTAAACCC 57.249 47.619 0.00 0.00 0.00 4.11
439 440 7.914427 AATATTCATTTTCCCCTCCTAAACC 57.086 36.000 0.00 0.00 0.00 3.27
442 443 9.554053 TGAAAAATATTCATTTTCCCCTCCTAA 57.446 29.630 8.71 0.00 42.29 2.69
443 444 9.728100 ATGAAAAATATTCATTTTCCCCTCCTA 57.272 29.630 8.71 0.00 42.29 2.94
444 445 8.628368 ATGAAAAATATTCATTTTCCCCTCCT 57.372 30.769 8.71 0.00 42.29 3.69
489 490 9.993454 CCATCTCTAGTTCATCTCAAAATATCA 57.007 33.333 0.00 0.00 0.00 2.15
492 493 9.206690 ACTCCATCTCTAGTTCATCTCAAAATA 57.793 33.333 0.00 0.00 0.00 1.40
493 494 7.986320 CACTCCATCTCTAGTTCATCTCAAAAT 59.014 37.037 0.00 0.00 0.00 1.82
494 495 7.179160 TCACTCCATCTCTAGTTCATCTCAAAA 59.821 37.037 0.00 0.00 0.00 2.44
495 496 6.665248 TCACTCCATCTCTAGTTCATCTCAAA 59.335 38.462 0.00 0.00 0.00 2.69
496 497 6.190587 TCACTCCATCTCTAGTTCATCTCAA 58.809 40.000 0.00 0.00 0.00 3.02
497 498 5.760131 TCACTCCATCTCTAGTTCATCTCA 58.240 41.667 0.00 0.00 0.00 3.27
498 499 6.489700 TCATCACTCCATCTCTAGTTCATCTC 59.510 42.308 0.00 0.00 0.00 2.75
499 500 6.372104 TCATCACTCCATCTCTAGTTCATCT 58.628 40.000 0.00 0.00 0.00 2.90
500 501 6.647334 TCATCACTCCATCTCTAGTTCATC 57.353 41.667 0.00 0.00 0.00 2.92
501 502 7.615039 AATCATCACTCCATCTCTAGTTCAT 57.385 36.000 0.00 0.00 0.00 2.57
502 503 8.001292 TCTAATCATCACTCCATCTCTAGTTCA 58.999 37.037 0.00 0.00 0.00 3.18
503 504 8.402798 TCTAATCATCACTCCATCTCTAGTTC 57.597 38.462 0.00 0.00 0.00 3.01
504 505 8.224025 TCTCTAATCATCACTCCATCTCTAGTT 58.776 37.037 0.00 0.00 0.00 2.24
505 506 7.754624 TCTCTAATCATCACTCCATCTCTAGT 58.245 38.462 0.00 0.00 0.00 2.57
506 507 7.337689 CCTCTCTAATCATCACTCCATCTCTAG 59.662 44.444 0.00 0.00 0.00 2.43
507 508 7.174413 CCTCTCTAATCATCACTCCATCTCTA 58.826 42.308 0.00 0.00 0.00 2.43
508 509 6.012113 CCTCTCTAATCATCACTCCATCTCT 58.988 44.000 0.00 0.00 0.00 3.10
509 510 5.185635 CCCTCTCTAATCATCACTCCATCTC 59.814 48.000 0.00 0.00 0.00 2.75
510 511 5.085920 CCCTCTCTAATCATCACTCCATCT 58.914 45.833 0.00 0.00 0.00 2.90
511 512 5.083122 TCCCTCTCTAATCATCACTCCATC 58.917 45.833 0.00 0.00 0.00 3.51
512 513 5.085275 TCCCTCTCTAATCATCACTCCAT 57.915 43.478 0.00 0.00 0.00 3.41
513 514 4.168871 TCTCCCTCTCTAATCATCACTCCA 59.831 45.833 0.00 0.00 0.00 3.86
514 515 4.735369 TCTCCCTCTCTAATCATCACTCC 58.265 47.826 0.00 0.00 0.00 3.85
515 516 6.009589 TCATCTCCCTCTCTAATCATCACTC 58.990 44.000 0.00 0.00 0.00 3.51
516 517 5.963092 TCATCTCCCTCTCTAATCATCACT 58.037 41.667 0.00 0.00 0.00 3.41
517 518 6.662865 TTCATCTCCCTCTCTAATCATCAC 57.337 41.667 0.00 0.00 0.00 3.06
518 519 5.245751 GCTTCATCTCCCTCTCTAATCATCA 59.754 44.000 0.00 0.00 0.00 3.07
519 520 5.245751 TGCTTCATCTCCCTCTCTAATCATC 59.754 44.000 0.00 0.00 0.00 2.92
520 521 5.011943 GTGCTTCATCTCCCTCTCTAATCAT 59.988 44.000 0.00 0.00 0.00 2.45
521 522 4.343526 GTGCTTCATCTCCCTCTCTAATCA 59.656 45.833 0.00 0.00 0.00 2.57
522 523 4.588528 AGTGCTTCATCTCCCTCTCTAATC 59.411 45.833 0.00 0.00 0.00 1.75
523 524 4.555689 AGTGCTTCATCTCCCTCTCTAAT 58.444 43.478 0.00 0.00 0.00 1.73
524 525 3.987745 AGTGCTTCATCTCCCTCTCTAA 58.012 45.455 0.00 0.00 0.00 2.10
525 526 3.678965 AGTGCTTCATCTCCCTCTCTA 57.321 47.619 0.00 0.00 0.00 2.43
526 527 2.500910 CAAGTGCTTCATCTCCCTCTCT 59.499 50.000 0.00 0.00 0.00 3.10
527 528 2.419851 CCAAGTGCTTCATCTCCCTCTC 60.420 54.545 0.00 0.00 0.00 3.20
528 529 1.558756 CCAAGTGCTTCATCTCCCTCT 59.441 52.381 0.00 0.00 0.00 3.69
529 530 1.407989 CCCAAGTGCTTCATCTCCCTC 60.408 57.143 0.00 0.00 0.00 4.30
530 531 0.622665 CCCAAGTGCTTCATCTCCCT 59.377 55.000 0.00 0.00 0.00 4.20
531 532 0.329596 ACCCAAGTGCTTCATCTCCC 59.670 55.000 0.00 0.00 0.00 4.30
532 533 1.003580 TCACCCAAGTGCTTCATCTCC 59.996 52.381 0.00 0.00 44.16 3.71
533 534 2.479566 TCACCCAAGTGCTTCATCTC 57.520 50.000 0.00 0.00 44.16 2.75
534 535 2.957402 TTCACCCAAGTGCTTCATCT 57.043 45.000 0.00 0.00 44.16 2.90
535 536 3.149196 TCTTTCACCCAAGTGCTTCATC 58.851 45.455 0.00 0.00 44.16 2.92
536 537 3.152341 CTCTTTCACCCAAGTGCTTCAT 58.848 45.455 0.00 0.00 44.16 2.57
537 538 2.172505 TCTCTTTCACCCAAGTGCTTCA 59.827 45.455 0.00 0.00 44.16 3.02
538 539 2.851195 TCTCTTTCACCCAAGTGCTTC 58.149 47.619 0.00 0.00 44.16 3.86
539 540 3.217626 CTTCTCTTTCACCCAAGTGCTT 58.782 45.455 0.00 0.00 44.16 3.91
540 541 2.487986 CCTTCTCTTTCACCCAAGTGCT 60.488 50.000 0.00 0.00 44.16 4.40
541 542 1.882623 CCTTCTCTTTCACCCAAGTGC 59.117 52.381 0.00 0.00 44.16 4.40
542 543 2.158608 ACCCTTCTCTTTCACCCAAGTG 60.159 50.000 0.00 0.00 46.00 3.16
543 544 2.136026 ACCCTTCTCTTTCACCCAAGT 58.864 47.619 0.00 0.00 0.00 3.16
544 545 2.959465 ACCCTTCTCTTTCACCCAAG 57.041 50.000 0.00 0.00 0.00 3.61
545 546 3.181437 GGTAACCCTTCTCTTTCACCCAA 60.181 47.826 0.00 0.00 0.00 4.12
546 547 2.374170 GGTAACCCTTCTCTTTCACCCA 59.626 50.000 0.00 0.00 0.00 4.51
547 548 3.069079 GGTAACCCTTCTCTTTCACCC 57.931 52.381 0.00 0.00 0.00 4.61
566 567 5.110814 TCATATGGACTTAACCACTTGGG 57.889 43.478 2.13 0.00 43.03 4.12
567 568 7.393234 TCTTTTCATATGGACTTAACCACTTGG 59.607 37.037 2.13 0.00 43.03 3.61
568 569 8.335532 TCTTTTCATATGGACTTAACCACTTG 57.664 34.615 2.13 0.00 43.03 3.16
569 570 9.533831 AATCTTTTCATATGGACTTAACCACTT 57.466 29.630 2.13 0.00 43.03 3.16
570 571 9.178758 GAATCTTTTCATATGGACTTAACCACT 57.821 33.333 2.13 0.00 43.03 4.00
571 572 8.956426 TGAATCTTTTCATATGGACTTAACCAC 58.044 33.333 2.13 0.00 38.59 4.16
572 573 9.527157 TTGAATCTTTTCATATGGACTTAACCA 57.473 29.630 2.13 0.00 41.38 3.67
578 579 8.743714 GGAGTTTTGAATCTTTTCATATGGACT 58.256 33.333 2.13 0.00 41.38 3.85
579 580 8.522830 TGGAGTTTTGAATCTTTTCATATGGAC 58.477 33.333 2.13 0.00 41.38 4.02
580 581 8.648698 TGGAGTTTTGAATCTTTTCATATGGA 57.351 30.769 2.13 0.00 41.38 3.41
581 582 9.709495 TTTGGAGTTTTGAATCTTTTCATATGG 57.291 29.630 2.13 0.00 41.38 2.74
590 591 9.112725 CCTTGAATTTTTGGAGTTTTGAATCTT 57.887 29.630 0.00 0.00 0.00 2.40
591 592 7.716560 CCCTTGAATTTTTGGAGTTTTGAATCT 59.283 33.333 0.00 0.00 0.00 2.40
592 593 7.498900 ACCCTTGAATTTTTGGAGTTTTGAATC 59.501 33.333 0.00 0.00 0.00 2.52
593 594 7.345691 ACCCTTGAATTTTTGGAGTTTTGAAT 58.654 30.769 0.00 0.00 0.00 2.57
594 595 6.716284 ACCCTTGAATTTTTGGAGTTTTGAA 58.284 32.000 0.00 0.00 0.00 2.69
595 596 6.306643 ACCCTTGAATTTTTGGAGTTTTGA 57.693 33.333 0.00 0.00 0.00 2.69
596 597 8.675705 ATAACCCTTGAATTTTTGGAGTTTTG 57.324 30.769 0.00 0.00 0.00 2.44
597 598 9.693739 AAATAACCCTTGAATTTTTGGAGTTTT 57.306 25.926 0.00 0.00 0.00 2.43
601 602 9.599866 GGATAAATAACCCTTGAATTTTTGGAG 57.400 33.333 0.00 0.00 0.00 3.86
602 603 9.332713 AGGATAAATAACCCTTGAATTTTTGGA 57.667 29.630 0.00 0.00 0.00 3.53
603 604 9.958180 AAGGATAAATAACCCTTGAATTTTTGG 57.042 29.630 0.00 0.00 38.74 3.28
607 608 9.448438 GCAAAAGGATAAATAACCCTTGAATTT 57.552 29.630 0.00 0.00 39.97 1.82
608 609 8.046708 GGCAAAAGGATAAATAACCCTTGAATT 58.953 33.333 0.00 0.00 39.97 2.17
609 610 7.365563 GGGCAAAAGGATAAATAACCCTTGAAT 60.366 37.037 0.00 0.00 39.97 2.57
621 622 3.181423 ACCACTGAGGGCAAAAGGATAAA 60.181 43.478 0.00 0.00 43.89 1.40
647 648 7.500992 CATCTTAGGGTAAAACTGAGCAGATA 58.499 38.462 4.21 0.00 0.00 1.98
662 663 2.017049 GCACAATTCGCATCTTAGGGT 58.983 47.619 0.00 0.00 0.00 4.34
667 668 2.430465 ACTGAGCACAATTCGCATCTT 58.570 42.857 0.00 0.00 0.00 2.40
691 692 2.203728 TGCACACGGACTAGGGGT 60.204 61.111 0.00 0.00 0.00 4.95
749 753 1.141254 TGTAAGGGCCGAGTCAAAACA 59.859 47.619 0.00 0.00 0.00 2.83
770 774 4.335647 CTGCCGCCTGGTCCAACT 62.336 66.667 0.00 0.00 37.67 3.16
891 933 4.724602 GCCGTGCTCTCTGTCGCA 62.725 66.667 0.00 0.00 0.00 5.10
928 982 3.625897 CCCACCACCGTGCTCTCA 61.626 66.667 0.00 0.00 38.79 3.27
1009 1148 2.056906 GAGGTGGTGTGGGAGCTTGT 62.057 60.000 0.00 0.00 0.00 3.16
1029 1168 2.268920 GCCCGACTCTGCATCCAA 59.731 61.111 0.00 0.00 0.00 3.53
1139 1279 0.458543 ATTCTCGCTGCACACGTAGG 60.459 55.000 0.00 0.00 0.00 3.18
1206 1346 4.201657 TGATACAGATCAACCCATTGCTG 58.798 43.478 0.00 0.00 39.20 4.41
1225 1365 2.011947 CGTCACCTGCATGAACATGAT 58.988 47.619 17.40 0.00 41.20 2.45
1228 1368 1.159285 CACGTCACCTGCATGAACAT 58.841 50.000 0.00 0.00 0.00 2.71
1245 1385 2.218603 TCGACCCAAAGAAAGAAGCAC 58.781 47.619 0.00 0.00 0.00 4.40
1326 1468 1.592400 CCACTACGGTTCGGAGCAGA 61.592 60.000 0.00 0.00 42.26 4.26
1331 1473 3.751246 CGGCCACTACGGTTCGGA 61.751 66.667 2.24 0.00 36.97 4.55
1340 1482 3.060020 GCTCGTGCTACGGCCACTA 62.060 63.158 2.24 0.00 42.81 2.74
1634 1784 7.410120 AAATGTTGGTCACTTCTTCTCTTTT 57.590 32.000 0.00 0.00 0.00 2.27
1869 2058 5.532557 AGCTTCCATAAAAAGTTTCAGCAC 58.467 37.500 0.00 0.00 0.00 4.40
2031 2241 4.021916 GGTGTAAACCTCTACCAGAGCTA 58.978 47.826 0.00 0.00 40.98 3.32
2115 2326 4.452114 GTGCATTTTCCACCCTTCATTTTC 59.548 41.667 0.00 0.00 0.00 2.29
2356 2615 5.278463 CGTTTTCAACATTCCAACTCTCCAT 60.278 40.000 0.00 0.00 0.00 3.41
2370 2629 4.795795 CAGTGCAAACATACGTTTTCAACA 59.204 37.500 0.00 0.00 42.82 3.33


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

AutoCloner maintained by Alex Coulton.