Multiple sequence alignment - TraesCS6A01G216000

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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 TraesCS6A01G216000 chr6A 100.000 2258 0 0 1 2258 397958454 397960711 0.000000e+00 4170.0
1 TraesCS6A01G216000 chr6A 95.760 566 23 1 1694 2258 204527694 204527129 0.000000e+00 911.0
2 TraesCS6A01G216000 chr6A 93.594 281 16 2 227 506 48508772 48508493 3.470000e-113 418.0
3 TraesCS6A01G216000 chr6D 93.174 1128 45 13 503 1611 277252541 277253655 0.000000e+00 1628.0
4 TraesCS6A01G216000 chr6D 94.872 234 4 1 5 230 277252310 277252543 2.130000e-95 359.0
5 TraesCS6A01G216000 chr6D 87.097 62 6 2 1438 1498 277253511 277253571 4.020000e-08 69.4
6 TraesCS6A01G216000 chr6B 92.343 1084 53 14 532 1611 439176328 439175271 0.000000e+00 1515.0
7 TraesCS6A01G216000 chr6B 93.286 283 17 2 228 509 518680052 518679771 1.250000e-112 416.0
8 TraesCS6A01G216000 chr6B 93.750 208 9 2 23 230 439176608 439176405 2.180000e-80 309.0
9 TraesCS6A01G216000 chr6B 96.970 33 1 0 1663 1695 573411806 573411774 3.130000e-04 56.5
10 TraesCS6A01G216000 chr3A 96.637 565 18 1 1694 2258 237367763 237368326 0.000000e+00 937.0
11 TraesCS6A01G216000 chr3A 95.915 563 21 1 1694 2256 551355606 551356166 0.000000e+00 911.0
12 TraesCS6A01G216000 chr3A 97.818 275 3 2 230 503 44720985 44720713 2.630000e-129 472.0
13 TraesCS6A01G216000 chr4A 96.466 566 19 1 1693 2258 590548262 590548826 0.000000e+00 933.0
14 TraesCS6A01G216000 chr4A 96.106 565 22 0 1694 2258 315774192 315773628 0.000000e+00 922.0
15 TraesCS6A01G216000 chr4A 95.760 566 23 1 1694 2258 56696319 56695754 0.000000e+00 911.0
16 TraesCS6A01G216000 chr4A 95.752 565 23 1 1694 2258 231094075 231093512 0.000000e+00 909.0
17 TraesCS6A01G216000 chr4A 97.818 275 5 1 228 501 26980185 26979911 7.300000e-130 473.0
18 TraesCS6A01G216000 chr7A 96.120 567 20 2 1693 2258 610653817 610654382 0.000000e+00 924.0
19 TraesCS6A01G216000 chr7A 95.760 566 22 2 1693 2258 698826550 698827113 0.000000e+00 911.0
20 TraesCS6A01G216000 chr7A 96.786 280 8 1 227 505 66781868 66782147 1.220000e-127 466.0
21 TraesCS6A01G216000 chr7A 94.737 38 1 1 1655 1692 667481048 667481084 8.710000e-05 58.4
22 TraesCS6A01G216000 chr2A 98.566 279 2 2 226 503 685044166 685044443 2.020000e-135 492.0
23 TraesCS6A01G216000 chr2A 94.265 279 14 2 228 505 722516002 722516279 2.070000e-115 425.0
24 TraesCS6A01G216000 chr2A 97.297 37 1 0 1656 1692 66460329 66460365 1.870000e-06 63.9
25 TraesCS6A01G216000 chr4B 97.455 275 4 2 230 503 158318784 158318512 1.220000e-127 466.0
26 TraesCS6A01G216000 chr3B 93.907 279 14 2 228 505 229575888 229575612 3.470000e-113 418.0
27 TraesCS6A01G216000 chr5D 97.297 37 1 0 1656 1692 399296991 399296955 1.870000e-06 63.9
28 TraesCS6A01G216000 chr5D 96.970 33 1 0 1663 1695 524593987 524593955 3.130000e-04 56.5
29 TraesCS6A01G216000 chr1D 93.023 43 3 0 1651 1693 236090072 236090114 1.870000e-06 63.9
30 TraesCS6A01G216000 chr1D 94.286 35 2 0 1661 1695 478235234 478235200 1.000000e-03 54.7
31 TraesCS6A01G216000 chr3D 97.222 36 1 0 1657 1692 545437454 545437489 6.730000e-06 62.1
32 TraesCS6A01G216000 chr3D 94.872 39 1 1 1654 1692 84888537 84888574 2.420000e-05 60.2
33 TraesCS6A01G216000 chr4D 97.143 35 1 0 1659 1693 370366952 370366986 2.420000e-05 60.2
34 TraesCS6A01G216000 chr4D 97.143 35 1 0 1658 1692 451681339 451681305 2.420000e-05 60.2
35 TraesCS6A01G216000 chr2D 97.143 35 1 0 1659 1693 15396468 15396502 2.420000e-05 60.2
36 TraesCS6A01G216000 chr2D 97.059 34 1 0 1663 1696 36380374 36380341 8.710000e-05 58.4
37 TraesCS6A01G216000 chr1A 97.143 35 1 0 1659 1693 504414840 504414874 2.420000e-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 TraesCS6A01G216000 chr6A 397958454 397960711 2257 False 4170.000000 4170 100.000000 1 2258 1 chr6A.!!$F1 2257
1 TraesCS6A01G216000 chr6A 204527129 204527694 565 True 911.000000 911 95.760000 1694 2258 1 chr6A.!!$R2 564
2 TraesCS6A01G216000 chr6D 277252310 277253655 1345 False 685.466667 1628 91.714333 5 1611 3 chr6D.!!$F1 1606
3 TraesCS6A01G216000 chr6B 439175271 439176608 1337 True 912.000000 1515 93.046500 23 1611 2 chr6B.!!$R3 1588
4 TraesCS6A01G216000 chr3A 237367763 237368326 563 False 937.000000 937 96.637000 1694 2258 1 chr3A.!!$F1 564
5 TraesCS6A01G216000 chr3A 551355606 551356166 560 False 911.000000 911 95.915000 1694 2256 1 chr3A.!!$F2 562
6 TraesCS6A01G216000 chr4A 590548262 590548826 564 False 933.000000 933 96.466000 1693 2258 1 chr4A.!!$F1 565
7 TraesCS6A01G216000 chr4A 315773628 315774192 564 True 922.000000 922 96.106000 1694 2258 1 chr4A.!!$R4 564
8 TraesCS6A01G216000 chr4A 56695754 56696319 565 True 911.000000 911 95.760000 1694 2258 1 chr4A.!!$R2 564
9 TraesCS6A01G216000 chr4A 231093512 231094075 563 True 909.000000 909 95.752000 1694 2258 1 chr4A.!!$R3 564
10 TraesCS6A01G216000 chr7A 610653817 610654382 565 False 924.000000 924 96.120000 1693 2258 1 chr7A.!!$F2 565
11 TraesCS6A01G216000 chr7A 698826550 698827113 563 False 911.000000 911 95.760000 1693 2258 1 chr7A.!!$F4 565

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
234 243 0.034477 GCTTAGGGTGCTTAAGGGCA 60.034 55.0 4.29 0.0 40.15 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 1764 0.109781 ACAATTTCACGACATGCGGC 60.11 50.0 12.85 0.0 46.49 6.53 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
90 91 1.340399 ATCCAAGCGCATCTCCTCCA 61.340 55.000 11.47 0.00 0.00 3.86
102 103 1.770658 TCTCCTCCATGGCATACCTTG 59.229 52.381 6.96 0.00 40.12 3.61
227 236 0.108138 CGCAGTAGCTTAGGGTGCTT 60.108 55.000 0.00 0.00 41.46 3.91
228 237 1.136305 CGCAGTAGCTTAGGGTGCTTA 59.864 52.381 0.00 0.00 41.46 3.09
229 238 2.418197 CGCAGTAGCTTAGGGTGCTTAA 60.418 50.000 0.00 0.00 41.46 1.85
230 239 3.198872 GCAGTAGCTTAGGGTGCTTAAG 58.801 50.000 0.00 0.00 41.46 1.85
231 240 3.798202 CAGTAGCTTAGGGTGCTTAAGG 58.202 50.000 4.29 0.00 41.46 2.69
232 241 2.772515 AGTAGCTTAGGGTGCTTAAGGG 59.227 50.000 4.29 0.00 41.46 3.95
233 242 0.256177 AGCTTAGGGTGCTTAAGGGC 59.744 55.000 4.29 0.00 37.52 5.19
234 243 0.034477 GCTTAGGGTGCTTAAGGGCA 60.034 55.000 4.29 0.00 40.15 5.36
235 244 1.410224 GCTTAGGGTGCTTAAGGGCAT 60.410 52.381 4.29 0.00 44.34 4.40
236 245 2.301346 CTTAGGGTGCTTAAGGGCATG 58.699 52.381 4.29 0.00 44.34 4.06
237 246 1.295020 TAGGGTGCTTAAGGGCATGT 58.705 50.000 4.29 0.00 44.34 3.21
238 247 1.295020 AGGGTGCTTAAGGGCATGTA 58.705 50.000 4.29 0.00 44.34 2.29
239 248 1.064685 AGGGTGCTTAAGGGCATGTAC 60.065 52.381 4.29 0.00 44.34 2.90
240 249 1.340600 GGGTGCTTAAGGGCATGTACA 60.341 52.381 4.29 0.00 44.34 2.90
241 250 2.017049 GGTGCTTAAGGGCATGTACAG 58.983 52.381 4.29 0.00 44.34 2.74
242 251 2.618045 GGTGCTTAAGGGCATGTACAGT 60.618 50.000 4.29 0.00 44.34 3.55
243 252 2.420022 GTGCTTAAGGGCATGTACAGTG 59.580 50.000 4.29 1.44 44.34 3.66
244 253 2.017049 GCTTAAGGGCATGTACAGTGG 58.983 52.381 4.29 0.00 0.00 4.00
245 254 2.618045 GCTTAAGGGCATGTACAGTGGT 60.618 50.000 4.29 0.00 0.00 4.16
246 255 3.686016 CTTAAGGGCATGTACAGTGGTT 58.314 45.455 0.33 0.00 0.00 3.67
247 256 1.909700 AAGGGCATGTACAGTGGTTG 58.090 50.000 0.33 0.00 0.00 3.77
248 257 1.064003 AGGGCATGTACAGTGGTTGA 58.936 50.000 0.33 0.00 0.00 3.18
249 258 1.635487 AGGGCATGTACAGTGGTTGAT 59.365 47.619 0.33 0.00 0.00 2.57
250 259 2.843730 AGGGCATGTACAGTGGTTGATA 59.156 45.455 0.33 0.00 0.00 2.15
251 260 3.265737 AGGGCATGTACAGTGGTTGATAA 59.734 43.478 0.33 0.00 0.00 1.75
252 261 3.627577 GGGCATGTACAGTGGTTGATAAG 59.372 47.826 0.33 0.00 0.00 1.73
253 262 4.513442 GGCATGTACAGTGGTTGATAAGA 58.487 43.478 0.33 0.00 0.00 2.10
254 263 5.126067 GGCATGTACAGTGGTTGATAAGAT 58.874 41.667 0.33 0.00 0.00 2.40
255 264 6.288294 GGCATGTACAGTGGTTGATAAGATA 58.712 40.000 0.33 0.00 0.00 1.98
256 265 6.425114 GGCATGTACAGTGGTTGATAAGATAG 59.575 42.308 0.33 0.00 0.00 2.08
257 266 6.986817 GCATGTACAGTGGTTGATAAGATAGT 59.013 38.462 0.33 0.00 0.00 2.12
258 267 7.169982 GCATGTACAGTGGTTGATAAGATAGTC 59.830 40.741 0.33 0.00 0.00 2.59
259 268 7.956328 TGTACAGTGGTTGATAAGATAGTCT 57.044 36.000 0.00 0.00 0.00 3.24
260 269 8.362464 TGTACAGTGGTTGATAAGATAGTCTT 57.638 34.615 0.00 0.00 40.35 3.01
261 270 9.470399 TGTACAGTGGTTGATAAGATAGTCTTA 57.530 33.333 0.00 2.24 42.49 2.10
319 328 7.781324 AAAAAGAATGTCTACAATGGGTCAT 57.219 32.000 0.00 0.00 0.00 3.06
320 329 7.396540 AAAAGAATGTCTACAATGGGTCATC 57.603 36.000 0.00 0.00 0.00 2.92
321 330 5.965033 AGAATGTCTACAATGGGTCATCT 57.035 39.130 0.00 0.00 0.00 2.90
322 331 5.923204 AGAATGTCTACAATGGGTCATCTC 58.077 41.667 0.00 0.00 0.00 2.75
323 332 5.664908 AGAATGTCTACAATGGGTCATCTCT 59.335 40.000 0.00 0.00 0.00 3.10
324 333 5.965033 ATGTCTACAATGGGTCATCTCTT 57.035 39.130 0.00 0.00 0.00 2.85
325 334 7.345653 AGAATGTCTACAATGGGTCATCTCTTA 59.654 37.037 0.00 0.00 0.00 2.10
326 335 6.471233 TGTCTACAATGGGTCATCTCTTAG 57.529 41.667 0.00 0.00 0.00 2.18
327 336 5.958380 TGTCTACAATGGGTCATCTCTTAGT 59.042 40.000 0.00 0.00 0.00 2.24
328 337 6.096987 TGTCTACAATGGGTCATCTCTTAGTC 59.903 42.308 0.00 0.00 0.00 2.59
329 338 6.322712 GTCTACAATGGGTCATCTCTTAGTCT 59.677 42.308 0.00 0.00 0.00 3.24
330 339 6.897966 TCTACAATGGGTCATCTCTTAGTCTT 59.102 38.462 0.00 0.00 0.00 3.01
331 340 8.059461 TCTACAATGGGTCATCTCTTAGTCTTA 58.941 37.037 0.00 0.00 0.00 2.10
332 341 7.682787 ACAATGGGTCATCTCTTAGTCTTAT 57.317 36.000 0.00 0.00 0.00 1.73
333 342 7.731054 ACAATGGGTCATCTCTTAGTCTTATC 58.269 38.462 0.00 0.00 0.00 1.75
334 343 7.566879 ACAATGGGTCATCTCTTAGTCTTATCT 59.433 37.037 0.00 0.00 0.00 1.98
335 344 8.428063 CAATGGGTCATCTCTTAGTCTTATCTT 58.572 37.037 0.00 0.00 0.00 2.40
336 345 9.661954 AATGGGTCATCTCTTAGTCTTATCTTA 57.338 33.333 0.00 0.00 0.00 2.10
337 346 9.661954 ATGGGTCATCTCTTAGTCTTATCTTAA 57.338 33.333 0.00 0.00 0.00 1.85
338 347 9.488762 TGGGTCATCTCTTAGTCTTATCTTAAA 57.511 33.333 0.00 0.00 0.00 1.52
363 372 8.879427 AAACTAGCTATTCCTAAAAACATGGT 57.121 30.769 0.00 0.00 0.00 3.55
364 373 7.865706 ACTAGCTATTCCTAAAAACATGGTG 57.134 36.000 0.00 0.00 0.00 4.17
365 374 7.630082 ACTAGCTATTCCTAAAAACATGGTGA 58.370 34.615 0.00 0.00 0.00 4.02
366 375 7.770897 ACTAGCTATTCCTAAAAACATGGTGAG 59.229 37.037 0.00 0.00 0.00 3.51
367 376 6.721318 AGCTATTCCTAAAAACATGGTGAGA 58.279 36.000 0.00 0.00 0.00 3.27
368 377 6.599638 AGCTATTCCTAAAAACATGGTGAGAC 59.400 38.462 0.00 0.00 0.00 3.36
369 378 6.374333 GCTATTCCTAAAAACATGGTGAGACA 59.626 38.462 0.00 0.00 0.00 3.41
370 379 7.094377 GCTATTCCTAAAAACATGGTGAGACAA 60.094 37.037 0.00 0.00 0.00 3.18
371 380 7.595819 ATTCCTAAAAACATGGTGAGACAAA 57.404 32.000 0.00 0.00 0.00 2.83
372 381 7.595819 TTCCTAAAAACATGGTGAGACAAAT 57.404 32.000 0.00 0.00 0.00 2.32
373 382 7.595819 TCCTAAAAACATGGTGAGACAAATT 57.404 32.000 0.00 0.00 0.00 1.82
374 383 7.432869 TCCTAAAAACATGGTGAGACAAATTG 58.567 34.615 0.00 0.00 0.00 2.32
375 384 7.069331 TCCTAAAAACATGGTGAGACAAATTGT 59.931 33.333 0.00 0.00 0.00 2.71
376 385 6.907206 AAAAACATGGTGAGACAAATTGTG 57.093 33.333 2.20 0.00 0.00 3.33
377 386 3.648339 ACATGGTGAGACAAATTGTGC 57.352 42.857 2.20 0.00 0.00 4.57
378 387 3.225104 ACATGGTGAGACAAATTGTGCT 58.775 40.909 2.20 0.36 0.00 4.40
379 388 4.397420 ACATGGTGAGACAAATTGTGCTA 58.603 39.130 2.20 0.00 0.00 3.49
380 389 4.826733 ACATGGTGAGACAAATTGTGCTAA 59.173 37.500 2.20 0.00 0.00 3.09
381 390 5.048504 ACATGGTGAGACAAATTGTGCTAAG 60.049 40.000 2.20 0.00 0.00 2.18
382 391 4.713553 TGGTGAGACAAATTGTGCTAAGA 58.286 39.130 2.20 0.00 0.00 2.10
383 392 4.756642 TGGTGAGACAAATTGTGCTAAGAG 59.243 41.667 2.20 0.00 0.00 2.85
384 393 4.997395 GGTGAGACAAATTGTGCTAAGAGA 59.003 41.667 2.20 0.00 0.00 3.10
385 394 5.645497 GGTGAGACAAATTGTGCTAAGAGAT 59.355 40.000 2.20 0.00 0.00 2.75
386 395 6.183360 GGTGAGACAAATTGTGCTAAGAGATC 60.183 42.308 2.20 0.00 0.00 2.75
387 396 6.369890 GTGAGACAAATTGTGCTAAGAGATCA 59.630 38.462 2.20 0.00 0.00 2.92
388 397 7.065563 GTGAGACAAATTGTGCTAAGAGATCAT 59.934 37.037 2.20 0.00 0.00 2.45
389 398 7.279536 TGAGACAAATTGTGCTAAGAGATCATC 59.720 37.037 2.20 0.00 0.00 2.92
390 399 7.337167 AGACAAATTGTGCTAAGAGATCATCT 58.663 34.615 2.20 0.00 41.27 2.90
391 400 7.495279 AGACAAATTGTGCTAAGAGATCATCTC 59.505 37.037 6.55 6.55 43.70 2.75
402 411 4.942761 GAGATCATCTCTTGCCTTCTCT 57.057 45.455 7.48 0.00 40.30 3.10
403 412 5.280654 GAGATCATCTCTTGCCTTCTCTT 57.719 43.478 7.48 0.00 40.30 2.85
404 413 6.403866 GAGATCATCTCTTGCCTTCTCTTA 57.596 41.667 7.48 0.00 40.30 2.10
405 414 6.805016 AGATCATCTCTTGCCTTCTCTTAA 57.195 37.500 0.00 0.00 0.00 1.85
406 415 7.192852 AGATCATCTCTTGCCTTCTCTTAAA 57.807 36.000 0.00 0.00 0.00 1.52
407 416 7.804147 AGATCATCTCTTGCCTTCTCTTAAAT 58.196 34.615 0.00 0.00 0.00 1.40
408 417 8.932610 AGATCATCTCTTGCCTTCTCTTAAATA 58.067 33.333 0.00 0.00 0.00 1.40
409 418 9.553064 GATCATCTCTTGCCTTCTCTTAAATAA 57.447 33.333 0.00 0.00 0.00 1.40
410 419 8.954950 TCATCTCTTGCCTTCTCTTAAATAAG 57.045 34.615 0.00 0.00 34.65 1.73
411 420 8.762645 TCATCTCTTGCCTTCTCTTAAATAAGA 58.237 33.333 3.08 3.08 39.82 2.10
439 448 8.825667 AGACAAGTCTTTTCTTATGAGTTCTC 57.174 34.615 0.00 0.00 36.31 2.87
440 449 8.646900 AGACAAGTCTTTTCTTATGAGTTCTCT 58.353 33.333 0.00 0.00 36.31 3.10
441 450 8.825667 ACAAGTCTTTTCTTATGAGTTCTCTC 57.174 34.615 1.53 0.00 40.79 3.20
442 451 8.646900 ACAAGTCTTTTCTTATGAGTTCTCTCT 58.353 33.333 1.53 0.00 40.98 3.10
443 452 9.139174 CAAGTCTTTTCTTATGAGTTCTCTCTC 57.861 37.037 1.53 0.00 40.98 3.20
444 453 7.836842 AGTCTTTTCTTATGAGTTCTCTCTCC 58.163 38.462 1.53 0.00 40.98 3.71
445 454 7.673926 AGTCTTTTCTTATGAGTTCTCTCTCCT 59.326 37.037 1.53 0.00 40.98 3.69
446 455 7.973944 GTCTTTTCTTATGAGTTCTCTCTCCTC 59.026 40.741 1.53 0.00 40.98 3.71
447 456 6.783708 TTTCTTATGAGTTCTCTCTCCTCC 57.216 41.667 1.53 0.00 40.98 4.30
448 457 5.458451 TCTTATGAGTTCTCTCTCCTCCA 57.542 43.478 1.53 0.00 40.98 3.86
449 458 5.197451 TCTTATGAGTTCTCTCTCCTCCAC 58.803 45.833 1.53 0.00 40.98 4.02
450 459 2.223803 TGAGTTCTCTCTCCTCCACC 57.776 55.000 1.53 0.00 40.98 4.61
451 460 1.713647 TGAGTTCTCTCTCCTCCACCT 59.286 52.381 1.53 0.00 40.98 4.00
452 461 2.291282 TGAGTTCTCTCTCCTCCACCTC 60.291 54.545 1.53 0.00 40.98 3.85
453 462 1.713647 AGTTCTCTCTCCTCCACCTCA 59.286 52.381 0.00 0.00 0.00 3.86
454 463 2.314549 AGTTCTCTCTCCTCCACCTCAT 59.685 50.000 0.00 0.00 0.00 2.90
455 464 2.693074 GTTCTCTCTCCTCCACCTCATC 59.307 54.545 0.00 0.00 0.00 2.92
456 465 1.925959 TCTCTCTCCTCCACCTCATCA 59.074 52.381 0.00 0.00 0.00 3.07
457 466 2.517553 TCTCTCTCCTCCACCTCATCAT 59.482 50.000 0.00 0.00 0.00 2.45
458 467 3.052262 TCTCTCTCCTCCACCTCATCATT 60.052 47.826 0.00 0.00 0.00 2.57
459 468 3.710677 CTCTCTCCTCCACCTCATCATTT 59.289 47.826 0.00 0.00 0.00 2.32
460 469 4.883759 TCTCTCCTCCACCTCATCATTTA 58.116 43.478 0.00 0.00 0.00 1.40
461 470 5.471424 TCTCTCCTCCACCTCATCATTTAT 58.529 41.667 0.00 0.00 0.00 1.40
462 471 5.541868 TCTCTCCTCCACCTCATCATTTATC 59.458 44.000 0.00 0.00 0.00 1.75
463 472 5.471424 TCTCCTCCACCTCATCATTTATCT 58.529 41.667 0.00 0.00 0.00 1.98
464 473 5.907662 TCTCCTCCACCTCATCATTTATCTT 59.092 40.000 0.00 0.00 0.00 2.40
465 474 7.075797 TCTCCTCCACCTCATCATTTATCTTA 58.924 38.462 0.00 0.00 0.00 2.10
466 475 7.736691 TCTCCTCCACCTCATCATTTATCTTAT 59.263 37.037 0.00 0.00 0.00 1.73
467 476 7.683578 TCCTCCACCTCATCATTTATCTTATG 58.316 38.462 0.00 0.00 0.00 1.90
468 477 7.293299 TCCTCCACCTCATCATTTATCTTATGT 59.707 37.037 0.00 0.00 0.00 2.29
469 478 7.389884 CCTCCACCTCATCATTTATCTTATGTG 59.610 40.741 0.00 0.00 0.00 3.21
470 479 7.226441 TCCACCTCATCATTTATCTTATGTGG 58.774 38.462 0.00 0.00 39.68 4.17
471 480 6.072286 CCACCTCATCATTTATCTTATGTGGC 60.072 42.308 0.00 0.00 36.78 5.01
472 481 6.487668 CACCTCATCATTTATCTTATGTGGCA 59.512 38.462 0.00 0.00 36.78 4.92
473 482 6.488006 ACCTCATCATTTATCTTATGTGGCAC 59.512 38.462 11.55 11.55 36.78 5.01
474 483 6.713903 CCTCATCATTTATCTTATGTGGCACT 59.286 38.462 19.83 6.99 0.00 4.40
475 484 7.094890 CCTCATCATTTATCTTATGTGGCACTC 60.095 40.741 19.83 0.00 0.00 3.51
476 485 6.712095 TCATCATTTATCTTATGTGGCACTCC 59.288 38.462 19.83 0.00 0.00 3.85
477 486 6.252599 TCATTTATCTTATGTGGCACTCCT 57.747 37.500 19.83 6.19 0.00 3.69
478 487 7.373617 TCATTTATCTTATGTGGCACTCCTA 57.626 36.000 19.83 5.19 0.00 2.94
479 488 7.801104 TCATTTATCTTATGTGGCACTCCTAA 58.199 34.615 19.83 12.29 0.00 2.69
480 489 7.933577 TCATTTATCTTATGTGGCACTCCTAAG 59.066 37.037 19.83 19.84 33.51 2.18
481 490 7.432148 TTTATCTTATGTGGCACTCCTAAGA 57.568 36.000 25.49 25.49 40.93 2.10
482 491 7.618019 TTATCTTATGTGGCACTCCTAAGAT 57.382 36.000 30.42 30.42 44.97 2.40
483 492 8.721133 TTATCTTATGTGGCACTCCTAAGATA 57.279 34.615 29.22 29.22 42.97 1.98
484 493 6.656632 TCTTATGTGGCACTCCTAAGATAG 57.343 41.667 19.83 3.72 35.37 2.08
485 494 3.760580 ATGTGGCACTCCTAAGATAGC 57.239 47.619 19.83 0.00 0.00 2.97
486 495 2.466846 TGTGGCACTCCTAAGATAGCA 58.533 47.619 19.83 0.00 0.00 3.49
487 496 2.168521 TGTGGCACTCCTAAGATAGCAC 59.831 50.000 19.83 0.00 0.00 4.40
488 497 1.762957 TGGCACTCCTAAGATAGCACC 59.237 52.381 0.00 0.00 0.00 5.01
489 498 1.762957 GGCACTCCTAAGATAGCACCA 59.237 52.381 0.00 0.00 0.00 4.17
490 499 2.370189 GGCACTCCTAAGATAGCACCAT 59.630 50.000 0.00 0.00 0.00 3.55
491 500 3.181450 GGCACTCCTAAGATAGCACCATT 60.181 47.826 0.00 0.00 0.00 3.16
492 501 3.812053 GCACTCCTAAGATAGCACCATTG 59.188 47.826 0.00 0.00 0.00 2.82
493 502 4.684485 GCACTCCTAAGATAGCACCATTGT 60.684 45.833 0.00 0.00 0.00 2.71
494 503 5.453339 GCACTCCTAAGATAGCACCATTGTA 60.453 44.000 0.00 0.00 0.00 2.41
495 504 5.986135 CACTCCTAAGATAGCACCATTGTAC 59.014 44.000 0.00 0.00 0.00 2.90
496 505 5.661312 ACTCCTAAGATAGCACCATTGTACA 59.339 40.000 0.00 0.00 0.00 2.90
497 506 6.327626 ACTCCTAAGATAGCACCATTGTACAT 59.672 38.462 0.00 0.00 0.00 2.29
498 507 6.524734 TCCTAAGATAGCACCATTGTACATG 58.475 40.000 0.00 0.00 0.00 3.21
499 508 5.180117 CCTAAGATAGCACCATTGTACATGC 59.820 44.000 10.53 10.53 38.39 4.06
500 509 3.480470 AGATAGCACCATTGTACATGCC 58.520 45.455 14.08 1.71 38.92 4.40
501 510 2.051334 TAGCACCATTGTACATGCCC 57.949 50.000 14.08 0.00 38.92 5.36
596 655 6.590292 CAGTTTTCTCGGTAACATGACAGTAT 59.410 38.462 0.00 0.00 0.00 2.12
679 738 0.453950 GCATGCAGAAGACAAGCGTG 60.454 55.000 14.21 0.00 45.53 5.34
787 846 3.655276 AGGAACCGTTGTACACACTAG 57.345 47.619 0.00 0.00 0.00 2.57
840 899 3.963428 TTTCTCTAGTCCAGGAACAGC 57.037 47.619 0.00 0.00 0.00 4.40
872 931 3.329520 TCCAGCGCCTTGGGTTTATATAT 59.670 43.478 15.05 0.00 38.81 0.86
873 932 4.532916 TCCAGCGCCTTGGGTTTATATATA 59.467 41.667 15.05 0.00 38.81 0.86
874 933 5.190925 TCCAGCGCCTTGGGTTTATATATAT 59.809 40.000 15.05 0.00 38.81 0.86
875 934 5.296780 CCAGCGCCTTGGGTTTATATATATG 59.703 44.000 2.29 0.00 34.46 1.78
876 935 5.296780 CAGCGCCTTGGGTTTATATATATGG 59.703 44.000 2.29 0.00 0.00 2.74
969 1034 1.749334 ATGCTGCTAGGCTACGTCCC 61.749 60.000 0.00 0.00 0.00 4.46
1194 1259 2.915659 AGGTCCAAGACGGCGTCA 60.916 61.111 37.71 17.81 34.60 4.35
1296 1369 6.462768 GCTTAGCTAGATATATGGCAGCAGAT 60.463 42.308 8.48 0.00 34.65 2.90
1338 1411 0.753111 CTGCCCTGCCCTGATAAACC 60.753 60.000 0.00 0.00 0.00 3.27
1400 1473 2.270352 TCCGTGCATTTGGAAGAAGT 57.730 45.000 3.10 0.00 0.00 3.01
1409 1482 4.319177 CATTTGGAAGAAGTTCGGTCTCT 58.681 43.478 8.83 0.00 32.92 3.10
1410 1483 4.417426 TTTGGAAGAAGTTCGGTCTCTT 57.583 40.909 8.83 0.00 32.92 2.85
1468 1545 6.883744 AGTCTTCCCTCTTGATCTATGTTTC 58.116 40.000 0.00 0.00 0.00 2.78
1591 1668 1.883275 CAAGGTTGTATTCGTTGCCCA 59.117 47.619 0.00 0.00 0.00 5.36
1611 1688 5.704053 GCCCAGTGTTGTATAGTTTGTTAGT 59.296 40.000 0.00 0.00 0.00 2.24
1612 1689 6.875195 GCCCAGTGTTGTATAGTTTGTTAGTA 59.125 38.462 0.00 0.00 0.00 1.82
1613 1690 7.148523 GCCCAGTGTTGTATAGTTTGTTAGTAC 60.149 40.741 0.00 0.00 0.00 2.73
1614 1691 7.332678 CCCAGTGTTGTATAGTTTGTTAGTACC 59.667 40.741 0.00 0.00 0.00 3.34
1615 1692 8.092687 CCAGTGTTGTATAGTTTGTTAGTACCT 58.907 37.037 0.00 0.00 0.00 3.08
1632 1709 2.787473 CCTATTCAGGTGGTCAGCAA 57.213 50.000 2.96 0.00 37.15 3.91
1633 1710 2.359900 CCTATTCAGGTGGTCAGCAAC 58.640 52.381 2.96 0.00 37.15 4.17
1634 1711 2.026822 CCTATTCAGGTGGTCAGCAACT 60.027 50.000 0.00 0.00 37.15 3.16
1635 1712 2.191128 ATTCAGGTGGTCAGCAACTC 57.809 50.000 0.00 0.00 0.00 3.01
1636 1713 0.249868 TTCAGGTGGTCAGCAACTCG 60.250 55.000 0.00 0.00 0.00 4.18
1637 1714 1.069765 CAGGTGGTCAGCAACTCGT 59.930 57.895 0.00 0.00 0.00 4.18
1638 1715 0.532862 CAGGTGGTCAGCAACTCGTT 60.533 55.000 0.00 0.00 0.00 3.85
1639 1716 0.532862 AGGTGGTCAGCAACTCGTTG 60.533 55.000 5.45 5.45 43.14 4.10
1653 1730 4.657075 ACTCGTTGCTATAACAAAACCG 57.343 40.909 0.00 0.00 0.00 4.44
1654 1731 4.060205 ACTCGTTGCTATAACAAAACCGT 58.940 39.130 0.00 0.00 0.00 4.83
1655 1732 4.512571 ACTCGTTGCTATAACAAAACCGTT 59.487 37.500 0.00 0.00 0.00 4.44
1656 1733 4.774586 TCGTTGCTATAACAAAACCGTTG 58.225 39.130 0.00 0.00 0.00 4.10
1657 1734 3.359580 CGTTGCTATAACAAAACCGTTGC 59.640 43.478 0.00 0.00 0.00 4.17
1658 1735 4.542735 GTTGCTATAACAAAACCGTTGCT 58.457 39.130 0.00 0.00 0.00 3.91
1659 1736 5.615106 CGTTGCTATAACAAAACCGTTGCTA 60.615 40.000 0.00 0.00 0.00 3.49
1660 1737 5.943706 TGCTATAACAAAACCGTTGCTAA 57.056 34.783 0.00 0.00 0.00 3.09
1661 1738 6.315091 TGCTATAACAAAACCGTTGCTAAA 57.685 33.333 0.00 0.00 0.00 1.85
1662 1739 6.736123 TGCTATAACAAAACCGTTGCTAAAA 58.264 32.000 0.00 0.00 0.00 1.52
1663 1740 6.858993 TGCTATAACAAAACCGTTGCTAAAAG 59.141 34.615 0.00 0.00 0.00 2.27
1664 1741 6.183359 GCTATAACAAAACCGTTGCTAAAAGC 60.183 38.462 0.00 0.00 42.82 3.51
1676 1753 3.142404 GCTAAAAGCATCTCCAACAGC 57.858 47.619 0.00 0.00 41.89 4.40
1677 1754 2.159324 GCTAAAAGCATCTCCAACAGCC 60.159 50.000 0.00 0.00 41.89 4.85
1678 1755 0.883833 AAAAGCATCTCCAACAGCCG 59.116 50.000 0.00 0.00 0.00 5.52
1679 1756 1.589716 AAAGCATCTCCAACAGCCGC 61.590 55.000 0.00 0.00 0.00 6.53
1680 1757 3.869272 GCATCTCCAACAGCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
1681 1758 3.869272 CATCTCCAACAGCCGCGC 61.869 66.667 0.00 0.00 0.00 6.86
1682 1759 4.393155 ATCTCCAACAGCCGCGCA 62.393 61.111 8.75 0.00 0.00 6.09
1683 1760 3.899981 ATCTCCAACAGCCGCGCAA 62.900 57.895 8.75 0.00 0.00 4.85
1684 1761 4.389576 CTCCAACAGCCGCGCAAC 62.390 66.667 8.75 0.00 0.00 4.17
1730 1807 3.244422 ACGGCAGATGTCCTTTTGTAAGA 60.244 43.478 0.00 0.00 32.92 2.10
1775 1852 5.695424 ACTAGGAAGCTTAAAGGGGTTAG 57.305 43.478 0.00 0.00 0.00 2.34
1910 1987 1.549620 CTATGCCTGGCTCTCGATCAT 59.450 52.381 21.03 4.66 0.00 2.45
2027 2105 0.669077 CCGGCTCAGCGACTAGTTAT 59.331 55.000 0.00 0.00 0.00 1.89
2034 2112 5.221087 GGCTCAGCGACTAGTTATTTCTACT 60.221 44.000 0.00 0.00 0.00 2.57
2184 2262 1.684734 GTAACCCGGCCTCTCCTGA 60.685 63.158 0.00 0.00 0.00 3.86
2230 2308 2.176798 CCCAACATTAGGCCCCAGATTA 59.823 50.000 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.832135 TCGGAGCTTTGTGAGGGAGT 60.832 55.000 0.00 0.00 0.00 3.85
1 2 0.539051 ATCGGAGCTTTGTGAGGGAG 59.461 55.000 0.00 0.00 0.00 4.30
2 3 0.250234 CATCGGAGCTTTGTGAGGGA 59.750 55.000 0.00 0.00 0.00 4.20
3 4 0.036010 ACATCGGAGCTTTGTGAGGG 60.036 55.000 0.00 0.00 0.00 4.30
90 91 0.779997 GGGGATCCAAGGTATGCCAT 59.220 55.000 15.23 0.00 36.61 4.40
227 236 2.640332 TCAACCACTGTACATGCCCTTA 59.360 45.455 0.00 0.00 0.00 2.69
228 237 1.423541 TCAACCACTGTACATGCCCTT 59.576 47.619 0.00 0.00 0.00 3.95
229 238 1.064003 TCAACCACTGTACATGCCCT 58.936 50.000 0.00 0.00 0.00 5.19
230 239 2.128771 ATCAACCACTGTACATGCCC 57.871 50.000 0.00 0.00 0.00 5.36
231 240 4.513442 TCTTATCAACCACTGTACATGCC 58.487 43.478 0.00 0.00 0.00 4.40
232 241 6.986817 ACTATCTTATCAACCACTGTACATGC 59.013 38.462 0.00 0.00 0.00 4.06
233 242 8.417106 AGACTATCTTATCAACCACTGTACATG 58.583 37.037 0.00 0.00 0.00 3.21
234 243 8.540507 AGACTATCTTATCAACCACTGTACAT 57.459 34.615 0.00 0.00 0.00 2.29
235 244 7.956328 AGACTATCTTATCAACCACTGTACA 57.044 36.000 0.00 0.00 0.00 2.90
295 304 7.671398 AGATGACCCATTGTAGACATTCTTTTT 59.329 33.333 0.00 0.00 0.00 1.94
296 305 7.177878 AGATGACCCATTGTAGACATTCTTTT 58.822 34.615 0.00 0.00 0.00 2.27
297 306 6.725364 AGATGACCCATTGTAGACATTCTTT 58.275 36.000 0.00 0.00 0.00 2.52
298 307 6.157645 AGAGATGACCCATTGTAGACATTCTT 59.842 38.462 0.00 0.00 0.00 2.52
299 308 5.664908 AGAGATGACCCATTGTAGACATTCT 59.335 40.000 0.00 0.00 0.00 2.40
300 309 5.923204 AGAGATGACCCATTGTAGACATTC 58.077 41.667 0.00 0.00 0.00 2.67
301 310 5.965033 AGAGATGACCCATTGTAGACATT 57.035 39.130 0.00 0.00 0.00 2.71
302 311 5.965033 AAGAGATGACCCATTGTAGACAT 57.035 39.130 0.00 0.00 0.00 3.06
303 312 5.958380 ACTAAGAGATGACCCATTGTAGACA 59.042 40.000 0.00 0.00 0.00 3.41
304 313 6.322712 AGACTAAGAGATGACCCATTGTAGAC 59.677 42.308 0.00 0.00 0.00 2.59
305 314 6.436027 AGACTAAGAGATGACCCATTGTAGA 58.564 40.000 0.00 0.00 0.00 2.59
306 315 6.723298 AGACTAAGAGATGACCCATTGTAG 57.277 41.667 0.00 0.00 0.00 2.74
307 316 8.783660 ATAAGACTAAGAGATGACCCATTGTA 57.216 34.615 0.00 0.00 0.00 2.41
308 317 7.566879 AGATAAGACTAAGAGATGACCCATTGT 59.433 37.037 0.00 0.00 0.00 2.71
309 318 7.961351 AGATAAGACTAAGAGATGACCCATTG 58.039 38.462 0.00 0.00 0.00 2.82
310 319 8.560124 AAGATAAGACTAAGAGATGACCCATT 57.440 34.615 0.00 0.00 0.00 3.16
311 320 9.661954 TTAAGATAAGACTAAGAGATGACCCAT 57.338 33.333 0.00 0.00 0.00 4.00
312 321 9.488762 TTTAAGATAAGACTAAGAGATGACCCA 57.511 33.333 0.00 0.00 0.00 4.51
337 346 9.309224 ACCATGTTTTTAGGAATAGCTAGTTTT 57.691 29.630 0.00 0.00 0.00 2.43
338 347 8.739972 CACCATGTTTTTAGGAATAGCTAGTTT 58.260 33.333 0.00 0.00 0.00 2.66
339 348 8.107095 TCACCATGTTTTTAGGAATAGCTAGTT 58.893 33.333 0.00 0.00 0.00 2.24
340 349 7.630082 TCACCATGTTTTTAGGAATAGCTAGT 58.370 34.615 0.00 0.00 0.00 2.57
341 350 7.987458 TCTCACCATGTTTTTAGGAATAGCTAG 59.013 37.037 0.00 0.00 0.00 3.42
342 351 7.769044 GTCTCACCATGTTTTTAGGAATAGCTA 59.231 37.037 0.00 0.00 0.00 3.32
343 352 6.599638 GTCTCACCATGTTTTTAGGAATAGCT 59.400 38.462 0.00 0.00 0.00 3.32
344 353 6.374333 TGTCTCACCATGTTTTTAGGAATAGC 59.626 38.462 0.00 0.00 0.00 2.97
345 354 7.921786 TGTCTCACCATGTTTTTAGGAATAG 57.078 36.000 0.00 0.00 0.00 1.73
346 355 8.698973 TTTGTCTCACCATGTTTTTAGGAATA 57.301 30.769 0.00 0.00 0.00 1.75
347 356 7.595819 TTTGTCTCACCATGTTTTTAGGAAT 57.404 32.000 0.00 0.00 0.00 3.01
348 357 7.595819 ATTTGTCTCACCATGTTTTTAGGAA 57.404 32.000 0.00 0.00 0.00 3.36
349 358 7.069331 ACAATTTGTCTCACCATGTTTTTAGGA 59.931 33.333 0.00 0.00 0.00 2.94
350 359 7.169645 CACAATTTGTCTCACCATGTTTTTAGG 59.830 37.037 0.00 0.00 0.00 2.69
351 360 7.306749 GCACAATTTGTCTCACCATGTTTTTAG 60.307 37.037 0.00 0.00 0.00 1.85
352 361 6.478344 GCACAATTTGTCTCACCATGTTTTTA 59.522 34.615 0.00 0.00 0.00 1.52
353 362 5.294060 GCACAATTTGTCTCACCATGTTTTT 59.706 36.000 0.00 0.00 0.00 1.94
354 363 4.810491 GCACAATTTGTCTCACCATGTTTT 59.190 37.500 0.00 0.00 0.00 2.43
355 364 4.099881 AGCACAATTTGTCTCACCATGTTT 59.900 37.500 0.00 0.00 0.00 2.83
356 365 3.638160 AGCACAATTTGTCTCACCATGTT 59.362 39.130 0.00 0.00 0.00 2.71
357 366 3.225104 AGCACAATTTGTCTCACCATGT 58.775 40.909 0.00 0.00 0.00 3.21
358 367 3.928727 AGCACAATTTGTCTCACCATG 57.071 42.857 0.00 0.00 0.00 3.66
359 368 5.316167 TCTTAGCACAATTTGTCTCACCAT 58.684 37.500 0.00 0.00 0.00 3.55
360 369 4.713553 TCTTAGCACAATTTGTCTCACCA 58.286 39.130 0.00 0.00 0.00 4.17
361 370 4.997395 TCTCTTAGCACAATTTGTCTCACC 59.003 41.667 0.00 0.00 0.00 4.02
362 371 6.369890 TGATCTCTTAGCACAATTTGTCTCAC 59.630 38.462 0.00 0.00 0.00 3.51
363 372 6.466812 TGATCTCTTAGCACAATTTGTCTCA 58.533 36.000 0.00 0.00 0.00 3.27
364 373 6.974932 TGATCTCTTAGCACAATTTGTCTC 57.025 37.500 0.00 0.00 0.00 3.36
365 374 7.337167 AGATGATCTCTTAGCACAATTTGTCT 58.663 34.615 0.00 3.34 0.00 3.41
366 375 7.551035 AGATGATCTCTTAGCACAATTTGTC 57.449 36.000 0.00 0.00 0.00 3.18
367 376 7.551035 GAGATGATCTCTTAGCACAATTTGT 57.449 36.000 14.98 0.00 40.30 2.83
381 390 4.942761 AGAGAAGGCAAGAGATGATCTC 57.057 45.455 14.47 14.47 43.70 2.75
382 391 6.805016 TTAAGAGAAGGCAAGAGATGATCT 57.195 37.500 0.00 0.00 41.27 2.75
383 392 9.553064 TTATTTAAGAGAAGGCAAGAGATGATC 57.447 33.333 0.00 0.00 0.00 2.92
384 393 9.558396 CTTATTTAAGAGAAGGCAAGAGATGAT 57.442 33.333 0.00 0.00 35.33 2.45
385 394 8.762645 TCTTATTTAAGAGAAGGCAAGAGATGA 58.237 33.333 0.00 0.00 37.40 2.92
386 395 8.954950 TCTTATTTAAGAGAAGGCAAGAGATG 57.045 34.615 0.00 0.00 37.40 2.90
408 417 9.487790 CTCATAAGAAAAGACTTGTCTTCTCTT 57.512 33.333 25.61 25.61 39.50 2.85
409 418 8.646900 ACTCATAAGAAAAGACTTGTCTTCTCT 58.353 33.333 21.53 13.63 33.70 3.10
410 419 8.825667 ACTCATAAGAAAAGACTTGTCTTCTC 57.174 34.615 21.53 11.71 33.70 2.87
411 420 9.267084 GAACTCATAAGAAAAGACTTGTCTTCT 57.733 33.333 21.53 11.28 33.70 2.85
412 421 9.267084 AGAACTCATAAGAAAAGACTTGTCTTC 57.733 33.333 21.53 8.09 33.70 2.87
413 422 9.267084 GAGAACTCATAAGAAAAGACTTGTCTT 57.733 33.333 21.59 21.59 35.77 3.01
414 423 8.646900 AGAGAACTCATAAGAAAAGACTTGTCT 58.353 33.333 1.69 1.69 0.00 3.41
415 424 8.825667 AGAGAACTCATAAGAAAAGACTTGTC 57.174 34.615 0.00 0.00 0.00 3.18
416 425 8.646900 AGAGAGAACTCATAAGAAAAGACTTGT 58.353 33.333 4.64 0.00 44.79 3.16
417 426 9.139174 GAGAGAGAACTCATAAGAAAAGACTTG 57.861 37.037 4.64 0.00 44.79 3.16
418 427 8.311109 GGAGAGAGAACTCATAAGAAAAGACTT 58.689 37.037 4.64 0.00 44.79 3.01
419 428 7.673926 AGGAGAGAGAACTCATAAGAAAAGACT 59.326 37.037 4.64 0.00 44.79 3.24
420 429 7.836842 AGGAGAGAGAACTCATAAGAAAAGAC 58.163 38.462 4.64 0.00 44.79 3.01
421 430 7.123547 GGAGGAGAGAGAACTCATAAGAAAAGA 59.876 40.741 4.64 0.00 44.79 2.52
422 431 7.093552 TGGAGGAGAGAGAACTCATAAGAAAAG 60.094 40.741 4.64 0.00 44.79 2.27
423 432 6.726299 TGGAGGAGAGAGAACTCATAAGAAAA 59.274 38.462 4.64 0.00 44.79 2.29
424 433 6.153680 GTGGAGGAGAGAGAACTCATAAGAAA 59.846 42.308 4.64 0.00 44.79 2.52
425 434 5.654650 GTGGAGGAGAGAGAACTCATAAGAA 59.345 44.000 4.64 0.00 44.79 2.52
426 435 5.197451 GTGGAGGAGAGAGAACTCATAAGA 58.803 45.833 4.64 0.00 44.79 2.10
427 436 4.340950 GGTGGAGGAGAGAGAACTCATAAG 59.659 50.000 4.64 0.00 44.79 1.73
428 437 4.017037 AGGTGGAGGAGAGAGAACTCATAA 60.017 45.833 4.64 0.00 44.79 1.90
429 438 3.529734 AGGTGGAGGAGAGAGAACTCATA 59.470 47.826 4.64 0.00 44.79 2.15
430 439 2.314549 AGGTGGAGGAGAGAGAACTCAT 59.685 50.000 4.64 0.00 44.79 2.90
431 440 1.713647 AGGTGGAGGAGAGAGAACTCA 59.286 52.381 4.64 0.00 44.79 3.41
432 441 2.291282 TGAGGTGGAGGAGAGAGAACTC 60.291 54.545 0.00 0.00 42.90 3.01
433 442 1.713647 TGAGGTGGAGGAGAGAGAACT 59.286 52.381 0.00 0.00 0.00 3.01
434 443 2.223803 TGAGGTGGAGGAGAGAGAAC 57.776 55.000 0.00 0.00 0.00 3.01
435 444 2.313041 TGATGAGGTGGAGGAGAGAGAA 59.687 50.000 0.00 0.00 0.00 2.87
436 445 1.925959 TGATGAGGTGGAGGAGAGAGA 59.074 52.381 0.00 0.00 0.00 3.10
437 446 2.450867 TGATGAGGTGGAGGAGAGAG 57.549 55.000 0.00 0.00 0.00 3.20
438 447 3.411454 AATGATGAGGTGGAGGAGAGA 57.589 47.619 0.00 0.00 0.00 3.10
439 448 5.543405 AGATAAATGATGAGGTGGAGGAGAG 59.457 44.000 0.00 0.00 0.00 3.20
440 449 5.471424 AGATAAATGATGAGGTGGAGGAGA 58.529 41.667 0.00 0.00 0.00 3.71
441 450 5.822132 AGATAAATGATGAGGTGGAGGAG 57.178 43.478 0.00 0.00 0.00 3.69
442 451 7.293299 ACATAAGATAAATGATGAGGTGGAGGA 59.707 37.037 0.00 0.00 0.00 3.71
443 452 7.389884 CACATAAGATAAATGATGAGGTGGAGG 59.610 40.741 0.00 0.00 0.00 4.30
444 453 7.389884 CCACATAAGATAAATGATGAGGTGGAG 59.610 40.741 0.00 0.00 42.55 3.86
445 454 7.226441 CCACATAAGATAAATGATGAGGTGGA 58.774 38.462 0.00 0.00 42.55 4.02
446 455 6.072286 GCCACATAAGATAAATGATGAGGTGG 60.072 42.308 0.00 0.00 42.75 4.61
447 456 6.487668 TGCCACATAAGATAAATGATGAGGTG 59.512 38.462 0.00 0.00 33.89 4.00
448 457 6.488006 GTGCCACATAAGATAAATGATGAGGT 59.512 38.462 0.00 0.00 33.89 3.85
449 458 6.713903 AGTGCCACATAAGATAAATGATGAGG 59.286 38.462 0.00 0.00 34.33 3.86
450 459 7.094890 GGAGTGCCACATAAGATAAATGATGAG 60.095 40.741 0.00 0.00 0.00 2.90
451 460 6.712095 GGAGTGCCACATAAGATAAATGATGA 59.288 38.462 0.00 0.00 0.00 2.92
452 461 6.713903 AGGAGTGCCACATAAGATAAATGATG 59.286 38.462 0.00 0.00 36.29 3.07
453 462 6.845908 AGGAGTGCCACATAAGATAAATGAT 58.154 36.000 0.00 0.00 36.29 2.45
454 463 6.252599 AGGAGTGCCACATAAGATAAATGA 57.747 37.500 0.00 0.00 36.29 2.57
455 464 7.933577 TCTTAGGAGTGCCACATAAGATAAATG 59.066 37.037 11.06 0.00 36.30 2.32
456 465 8.034313 TCTTAGGAGTGCCACATAAGATAAAT 57.966 34.615 11.06 0.00 36.30 1.40
457 466 7.432148 TCTTAGGAGTGCCACATAAGATAAA 57.568 36.000 11.06 0.00 36.30 1.40
458 467 7.618019 ATCTTAGGAGTGCCACATAAGATAA 57.382 36.000 19.75 3.88 44.08 1.75
459 468 7.093727 GCTATCTTAGGAGTGCCACATAAGATA 60.094 40.741 22.35 22.35 44.08 1.98
460 469 6.295575 GCTATCTTAGGAGTGCCACATAAGAT 60.296 42.308 22.45 22.45 46.03 2.40
461 470 5.011125 GCTATCTTAGGAGTGCCACATAAGA 59.989 44.000 15.18 15.18 42.07 2.10
462 471 5.221521 TGCTATCTTAGGAGTGCCACATAAG 60.222 44.000 0.00 3.12 36.29 1.73
463 472 4.653801 TGCTATCTTAGGAGTGCCACATAA 59.346 41.667 0.00 0.00 36.29 1.90
464 473 4.039245 GTGCTATCTTAGGAGTGCCACATA 59.961 45.833 0.00 0.00 36.29 2.29
465 474 3.041211 TGCTATCTTAGGAGTGCCACAT 58.959 45.455 0.00 0.00 36.29 3.21
466 475 2.168521 GTGCTATCTTAGGAGTGCCACA 59.831 50.000 0.00 0.00 36.29 4.17
467 476 2.483889 GGTGCTATCTTAGGAGTGCCAC 60.484 54.545 0.00 0.00 36.29 5.01
468 477 1.762957 GGTGCTATCTTAGGAGTGCCA 59.237 52.381 0.00 0.00 36.29 4.92
469 478 1.762957 TGGTGCTATCTTAGGAGTGCC 59.237 52.381 0.70 0.00 0.00 5.01
470 479 3.760580 ATGGTGCTATCTTAGGAGTGC 57.239 47.619 0.00 0.00 0.00 4.40
471 480 5.028549 ACAATGGTGCTATCTTAGGAGTG 57.971 43.478 0.00 0.00 0.00 3.51
472 481 5.661312 TGTACAATGGTGCTATCTTAGGAGT 59.339 40.000 0.00 0.00 0.00 3.85
473 482 6.161855 TGTACAATGGTGCTATCTTAGGAG 57.838 41.667 0.00 0.00 0.00 3.69
474 483 6.524734 CATGTACAATGGTGCTATCTTAGGA 58.475 40.000 0.00 0.00 0.00 2.94
475 484 5.180117 GCATGTACAATGGTGCTATCTTAGG 59.820 44.000 11.12 0.00 34.85 2.69
476 485 5.180117 GGCATGTACAATGGTGCTATCTTAG 59.820 44.000 16.47 0.00 37.70 2.18
477 486 5.063204 GGCATGTACAATGGTGCTATCTTA 58.937 41.667 16.47 0.00 37.70 2.10
478 487 3.885297 GGCATGTACAATGGTGCTATCTT 59.115 43.478 16.47 0.00 37.70 2.40
479 488 3.480470 GGCATGTACAATGGTGCTATCT 58.520 45.455 16.47 0.00 37.70 1.98
480 489 2.554032 GGGCATGTACAATGGTGCTATC 59.446 50.000 16.47 3.12 37.70 2.08
481 490 2.175499 AGGGCATGTACAATGGTGCTAT 59.825 45.455 16.47 5.35 37.70 2.97
482 491 1.563879 AGGGCATGTACAATGGTGCTA 59.436 47.619 16.47 0.00 37.70 3.49
483 492 0.332632 AGGGCATGTACAATGGTGCT 59.667 50.000 16.47 0.00 37.70 4.40
484 493 2.051334 TAGGGCATGTACAATGGTGC 57.949 50.000 10.12 10.12 36.88 5.01
485 494 5.278463 GCTAATTAGGGCATGTACAATGGTG 60.278 44.000 14.28 0.00 0.00 4.17
486 495 4.827284 GCTAATTAGGGCATGTACAATGGT 59.173 41.667 14.28 0.00 0.00 3.55
487 496 5.072741 AGCTAATTAGGGCATGTACAATGG 58.927 41.667 14.28 0.00 0.00 3.16
488 497 6.000219 AGAGCTAATTAGGGCATGTACAATG 59.000 40.000 14.28 0.12 0.00 2.82
489 498 6.000219 CAGAGCTAATTAGGGCATGTACAAT 59.000 40.000 14.28 0.00 0.00 2.71
490 499 5.104527 ACAGAGCTAATTAGGGCATGTACAA 60.105 40.000 14.28 0.00 31.99 2.41
491 500 4.408921 ACAGAGCTAATTAGGGCATGTACA 59.591 41.667 14.28 0.00 31.99 2.90
492 501 4.962155 ACAGAGCTAATTAGGGCATGTAC 58.038 43.478 14.28 0.00 31.99 2.90
493 502 5.130311 TCAACAGAGCTAATTAGGGCATGTA 59.870 40.000 14.28 0.00 32.91 2.29
494 503 4.080356 TCAACAGAGCTAATTAGGGCATGT 60.080 41.667 14.28 7.87 34.02 3.21
495 504 4.454678 TCAACAGAGCTAATTAGGGCATG 58.545 43.478 14.28 7.32 0.00 4.06
496 505 4.778213 TCAACAGAGCTAATTAGGGCAT 57.222 40.909 14.28 0.00 0.00 4.40
497 506 4.454678 CATCAACAGAGCTAATTAGGGCA 58.545 43.478 14.28 0.00 0.00 5.36
498 507 3.251972 GCATCAACAGAGCTAATTAGGGC 59.748 47.826 14.28 1.64 0.00 5.19
499 508 4.514441 CAGCATCAACAGAGCTAATTAGGG 59.486 45.833 14.28 0.00 36.73 3.53
500 509 5.363101 TCAGCATCAACAGAGCTAATTAGG 58.637 41.667 14.28 0.13 36.73 2.69
501 510 6.538021 AGTTCAGCATCAACAGAGCTAATTAG 59.462 38.462 8.20 8.20 36.73 1.73
679 738 2.680577 CCACTAACTTGTACACGGTCC 58.319 52.381 4.21 0.00 0.00 4.46
852 911 5.296780 CCATATATATAAACCCAAGGCGCTG 59.703 44.000 7.64 0.00 0.00 5.18
969 1034 3.573538 TGTTGGGATCAATGGTGAAAGTG 59.426 43.478 0.00 0.00 37.30 3.16
1128 1193 3.712881 GCGGTGTCGTGGCTGTTC 61.713 66.667 0.00 0.00 38.89 3.18
1152 1217 1.665544 CTTCGTGCAGCGTCGTGTAG 61.666 60.000 9.13 3.55 42.13 2.74
1189 1254 4.147322 CGCCATGACCGTTGACGC 62.147 66.667 0.00 0.00 38.18 5.19
1194 1259 2.358247 GTCCACGCCATGACCGTT 60.358 61.111 8.37 0.00 36.69 4.44
1296 1369 1.950216 CAGCCTCGATGCTACTACTGA 59.050 52.381 15.11 0.00 40.32 3.41
1327 1400 2.102578 CTTGGCCTTGGTTTATCAGGG 58.897 52.381 3.32 0.00 37.01 4.45
1328 1401 3.019564 CTCTTGGCCTTGGTTTATCAGG 58.980 50.000 3.32 0.00 0.00 3.86
1329 1402 2.424956 GCTCTTGGCCTTGGTTTATCAG 59.575 50.000 3.32 0.00 34.27 2.90
1330 1403 2.041620 AGCTCTTGGCCTTGGTTTATCA 59.958 45.455 3.32 0.00 43.05 2.15
1338 1411 0.251519 AAAGGGAGCTCTTGGCCTTG 60.252 55.000 19.07 0.00 43.05 3.61
1468 1545 3.292460 AGATCAAGAGGGAAGACTACCG 58.708 50.000 0.00 0.00 0.00 4.02
1614 1691 3.265791 GAGTTGCTGACCACCTGAATAG 58.734 50.000 0.00 0.00 0.00 1.73
1615 1692 2.353704 CGAGTTGCTGACCACCTGAATA 60.354 50.000 0.00 0.00 0.00 1.75
1616 1693 1.609061 CGAGTTGCTGACCACCTGAAT 60.609 52.381 0.00 0.00 0.00 2.57
1617 1694 0.249868 CGAGTTGCTGACCACCTGAA 60.250 55.000 0.00 0.00 0.00 3.02
1618 1695 1.367471 CGAGTTGCTGACCACCTGA 59.633 57.895 0.00 0.00 0.00 3.86
1619 1696 0.532862 AACGAGTTGCTGACCACCTG 60.533 55.000 0.00 0.00 0.00 4.00
1620 1697 0.532862 CAACGAGTTGCTGACCACCT 60.533 55.000 2.84 0.00 33.45 4.00
1621 1698 1.941812 CAACGAGTTGCTGACCACC 59.058 57.895 2.84 0.00 33.45 4.61
1630 1707 4.843984 CGGTTTTGTTATAGCAACGAGTTG 59.156 41.667 11.29 11.29 43.14 3.16
1631 1708 4.512571 ACGGTTTTGTTATAGCAACGAGTT 59.487 37.500 14.65 0.00 0.00 3.01
1632 1709 4.060205 ACGGTTTTGTTATAGCAACGAGT 58.940 39.130 14.65 5.77 0.00 4.18
1633 1710 4.657075 ACGGTTTTGTTATAGCAACGAG 57.343 40.909 14.65 5.28 0.00 4.18
1634 1711 4.774586 CAACGGTTTTGTTATAGCAACGA 58.225 39.130 14.65 0.59 0.00 3.85
1635 1712 3.359580 GCAACGGTTTTGTTATAGCAACG 59.640 43.478 0.96 5.53 0.00 4.10
1636 1713 4.542735 AGCAACGGTTTTGTTATAGCAAC 58.457 39.130 0.96 0.00 0.00 4.17
1637 1714 4.839668 AGCAACGGTTTTGTTATAGCAA 57.160 36.364 0.00 0.00 0.00 3.91
1638 1715 5.943706 TTAGCAACGGTTTTGTTATAGCA 57.056 34.783 0.00 0.00 0.00 3.49
1639 1716 6.183359 GCTTTTAGCAACGGTTTTGTTATAGC 60.183 38.462 0.00 0.00 41.89 2.97
1640 1717 7.260722 GCTTTTAGCAACGGTTTTGTTATAG 57.739 36.000 0.00 0.00 41.89 1.31
1656 1733 2.159324 GGCTGTTGGAGATGCTTTTAGC 60.159 50.000 0.00 0.00 42.82 3.09
1657 1734 2.096496 CGGCTGTTGGAGATGCTTTTAG 59.904 50.000 0.00 0.00 0.00 1.85
1658 1735 2.083774 CGGCTGTTGGAGATGCTTTTA 58.916 47.619 0.00 0.00 0.00 1.52
1659 1736 0.883833 CGGCTGTTGGAGATGCTTTT 59.116 50.000 0.00 0.00 0.00 2.27
1660 1737 1.589716 GCGGCTGTTGGAGATGCTTT 61.590 55.000 0.00 0.00 0.00 3.51
1661 1738 2.042831 GCGGCTGTTGGAGATGCTT 61.043 57.895 0.00 0.00 0.00 3.91
1662 1739 2.437359 GCGGCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 0.00 3.79
1663 1740 3.869272 CGCGGCTGTTGGAGATGC 61.869 66.667 0.00 0.00 0.00 3.91
1664 1741 3.869272 GCGCGGCTGTTGGAGATG 61.869 66.667 8.83 0.00 0.00 2.90
1665 1742 3.899981 TTGCGCGGCTGTTGGAGAT 62.900 57.895 8.83 0.00 0.00 2.75
1666 1743 4.617520 TTGCGCGGCTGTTGGAGA 62.618 61.111 8.83 0.00 0.00 3.71
1667 1744 4.389576 GTTGCGCGGCTGTTGGAG 62.390 66.667 8.83 0.00 0.00 3.86
1685 1762 2.849142 AATTTCACGACATGCGGCGC 62.849 55.000 27.44 27.44 46.49 6.53
1686 1763 1.127571 CAATTTCACGACATGCGGCG 61.128 55.000 0.51 0.51 46.49 6.46
1687 1764 0.109781 ACAATTTCACGACATGCGGC 60.110 50.000 12.85 0.00 46.49 6.53
1688 1765 1.196581 TGACAATTTCACGACATGCGG 59.803 47.619 12.85 0.00 46.49 5.69
1689 1766 2.233355 GTGACAATTTCACGACATGCG 58.767 47.619 7.79 7.79 45.33 4.73
1730 1807 1.135083 CGATGGCTCCACGACTAAGTT 60.135 52.381 0.00 0.00 0.00 2.66
1775 1852 2.737376 GCGTGTCCTTGTCCCGAC 60.737 66.667 0.00 0.00 0.00 4.79
1830 1907 1.274167 CAACCCAACTAGACGTAGGCA 59.726 52.381 0.00 0.00 0.00 4.75
2143 2221 4.272018 CGCAAATAGAGGTTCATCAGAAGG 59.728 45.833 0.00 0.00 33.63 3.46
2184 2262 7.448469 GGGATATGACTATTTGTGTAAGCCATT 59.552 37.037 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.