Multiple sequence alignment - TraesCS6D01G358000

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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 TraesCS6D01G358000 chr6D 100.000 4201 0 0 1 4201 451160719 451156519 0.000000e+00 7758.0
1 TraesCS6D01G358000 chr6D 85.507 69 9 1 126 193 77826413 77826345 2.100000e-08 71.3
2 TraesCS6D01G358000 chr6B 91.809 3333 179 25 914 4201 685308282 685304999 0.000000e+00 4556.0
3 TraesCS6D01G358000 chr6B 94.964 139 7 0 736 874 685308426 685308288 7.070000e-53 219.0
4 TraesCS6D01G358000 chr6B 83.951 162 9 6 591 740 685308721 685308565 5.660000e-29 139.0
5 TraesCS6D01G358000 chr6A 92.271 2109 109 21 599 2672 596893916 596891827 0.000000e+00 2942.0
6 TraesCS6D01G358000 chr6A 90.394 1572 82 13 2668 4201 596891572 596890032 0.000000e+00 2002.0
7 TraesCS6D01G358000 chrUn 86.957 69 8 1 126 193 332139898 332139966 4.500000e-10 76.8
8 TraesCS6D01G358000 chr2B 86.957 69 8 1 126 193 6884845 6884913 4.500000e-10 76.8
9 TraesCS6D01G358000 chr2B 86.957 69 8 1 126 193 6965255 6965323 4.500000e-10 76.8
10 TraesCS6D01G358000 chr1A 88.136 59 6 1 289 347 539979628 539979571 7.540000e-08 69.4
11 TraesCS6D01G358000 chr1A 88.462 52 3 3 297 347 539979538 539979587 4.540000e-05 60.2
12 TraesCS6D01G358000 chr3D 88.889 54 4 2 281 334 327838977 327839028 9.750000e-07 65.8
13 TraesCS6D01G358000 chr3D 84.286 70 8 3 126 193 483190994 483190926 9.750000e-07 65.8
14 TraesCS6D01G358000 chr7A 90.000 50 3 2 285 334 44739947 44739900 3.510000e-06 63.9
15 TraesCS6D01G358000 chr3A 85.938 64 3 4 284 344 696285066 696285006 3.510000e-06 63.9
16 TraesCS6D01G358000 chr7B 87.273 55 5 2 279 332 479780599 479780546 1.260000e-05 62.1
17 TraesCS6D01G358000 chr2D 87.273 55 5 2 292 344 53362761 53362707 1.260000e-05 62.1
18 TraesCS6D01G358000 chr1D 86.441 59 4 3 289 344 318090097 318090040 1.260000e-05 62.1
19 TraesCS6D01G358000 chr5A 87.500 56 2 4 290 341 663844209 663844263 4.540000e-05 60.2
20 TraesCS6D01G358000 chr3B 100.000 29 0 0 126 154 746798820 746798848 2.000000e-03 54.7


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 TraesCS6D01G358000 chr6D 451156519 451160719 4200 True 7758 7758 100.000000 1 4201 1 chr6D.!!$R2 4200
1 TraesCS6D01G358000 chr6B 685304999 685308721 3722 True 1638 4556 90.241333 591 4201 3 chr6B.!!$R1 3610
2 TraesCS6D01G358000 chr6A 596890032 596893916 3884 True 2472 2942 91.332500 599 4201 2 chr6A.!!$R1 3602

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
899 1078 0.109086 ATATCGGATCGAAGCAGCGG 60.109 55.0 0.00 0.0 39.99 5.52 F
2489 2691 0.174162 GGATGCAGCCATTGGTTCAC 59.826 55.0 18.08 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2889 3359 0.402121 AGAGGCTGGTTCCTGGAAAC 59.598 55.0 17.63 17.63 36.38 2.78 R
3703 4205 0.039256 GCAAGGAAACGCAAGCATCA 60.039 50.0 0.00 0.00 45.62 3.07 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
168 169 7.790782 ATAAATTTGGCCAAACTTTCCTAGA 57.209 32.000 32.62 12.65 32.51 2.43
169 170 6.686484 AAATTTGGCCAAACTTTCCTAGAT 57.314 33.333 32.62 10.42 32.51 1.98
170 171 6.686484 AATTTGGCCAAACTTTCCTAGATT 57.314 33.333 32.62 15.87 32.51 2.40
171 172 6.686484 ATTTGGCCAAACTTTCCTAGATTT 57.314 33.333 32.62 9.66 32.51 2.17
172 173 5.467035 TTGGCCAAACTTTCCTAGATTTG 57.533 39.130 17.98 0.00 32.89 2.32
173 174 4.735369 TGGCCAAACTTTCCTAGATTTGA 58.265 39.130 0.61 0.00 34.62 2.69
174 175 4.522789 TGGCCAAACTTTCCTAGATTTGAC 59.477 41.667 0.61 0.00 34.62 3.18
175 176 4.767409 GGCCAAACTTTCCTAGATTTGACT 59.233 41.667 0.00 0.00 34.62 3.41
176 177 5.243954 GGCCAAACTTTCCTAGATTTGACTT 59.756 40.000 0.00 0.00 34.62 3.01
177 178 6.433093 GGCCAAACTTTCCTAGATTTGACTTA 59.567 38.462 0.00 0.00 34.62 2.24
178 179 7.306213 GCCAAACTTTCCTAGATTTGACTTAC 58.694 38.462 0.00 0.00 34.62 2.34
179 180 7.519002 CCAAACTTTCCTAGATTTGACTTACG 58.481 38.462 0.00 0.00 34.62 3.18
180 181 7.386848 CCAAACTTTCCTAGATTTGACTTACGA 59.613 37.037 0.00 0.00 34.62 3.43
181 182 8.770828 CAAACTTTCCTAGATTTGACTTACGAA 58.229 33.333 0.00 0.00 34.62 3.85
182 183 8.897872 AACTTTCCTAGATTTGACTTACGAAA 57.102 30.769 0.00 0.00 0.00 3.46
183 184 8.897872 ACTTTCCTAGATTTGACTTACGAAAA 57.102 30.769 0.00 0.00 0.00 2.29
184 185 8.989980 ACTTTCCTAGATTTGACTTACGAAAAG 58.010 33.333 0.00 0.00 0.00 2.27
185 186 6.963049 TCCTAGATTTGACTTACGAAAAGC 57.037 37.500 0.00 0.00 0.00 3.51
186 187 6.698380 TCCTAGATTTGACTTACGAAAAGCT 58.302 36.000 0.00 0.00 34.26 3.74
187 188 7.833786 TCCTAGATTTGACTTACGAAAAGCTA 58.166 34.615 0.00 0.00 32.30 3.32
188 189 8.308931 TCCTAGATTTGACTTACGAAAAGCTAA 58.691 33.333 0.00 0.00 33.00 3.09
189 190 9.099454 CCTAGATTTGACTTACGAAAAGCTAAT 57.901 33.333 0.00 0.00 33.00 1.73
271 272 7.497925 AAGACAAACTTCATAAACTCTGACC 57.502 36.000 0.00 0.00 32.91 4.02
272 273 6.591935 AGACAAACTTCATAAACTCTGACCA 58.408 36.000 0.00 0.00 0.00 4.02
273 274 7.054124 AGACAAACTTCATAAACTCTGACCAA 58.946 34.615 0.00 0.00 0.00 3.67
274 275 7.721399 AGACAAACTTCATAAACTCTGACCAAT 59.279 33.333 0.00 0.00 0.00 3.16
275 276 8.918202 ACAAACTTCATAAACTCTGACCAATA 57.082 30.769 0.00 0.00 0.00 1.90
276 277 9.520515 ACAAACTTCATAAACTCTGACCAATAT 57.479 29.630 0.00 0.00 0.00 1.28
277 278 9.778993 CAAACTTCATAAACTCTGACCAATATG 57.221 33.333 0.00 0.00 0.00 1.78
278 279 9.739276 AAACTTCATAAACTCTGACCAATATGA 57.261 29.630 0.00 0.00 0.00 2.15
279 280 9.739276 AACTTCATAAACTCTGACCAATATGAA 57.261 29.630 0.00 0.00 37.40 2.57
280 281 9.911788 ACTTCATAAACTCTGACCAATATGAAT 57.088 29.630 6.51 0.00 38.41 2.57
306 307 7.874252 AGATACATAAGATATACTCCCTCCGT 58.126 38.462 0.00 0.00 0.00 4.69
307 308 9.000978 AGATACATAAGATATACTCCCTCCGTA 57.999 37.037 0.00 0.00 0.00 4.02
308 309 9.624373 GATACATAAGATATACTCCCTCCGTAA 57.376 37.037 0.00 0.00 0.00 3.18
309 310 9.986157 ATACATAAGATATACTCCCTCCGTAAA 57.014 33.333 0.00 0.00 0.00 2.01
310 311 8.120140 ACATAAGATATACTCCCTCCGTAAAC 57.880 38.462 0.00 0.00 0.00 2.01
311 312 7.949006 ACATAAGATATACTCCCTCCGTAAACT 59.051 37.037 0.00 0.00 0.00 2.66
312 313 9.458727 CATAAGATATACTCCCTCCGTAAACTA 57.541 37.037 0.00 0.00 0.00 2.24
314 315 8.953223 AAGATATACTCCCTCCGTAAACTAAT 57.047 34.615 0.00 0.00 0.00 1.73
322 323 9.605275 ACTCCCTCCGTAAACTAATATAAAAAC 57.395 33.333 0.00 0.00 0.00 2.43
323 324 8.647143 TCCCTCCGTAAACTAATATAAAAACG 57.353 34.615 0.00 0.00 0.00 3.60
324 325 8.257306 TCCCTCCGTAAACTAATATAAAAACGT 58.743 33.333 0.00 0.00 0.00 3.99
325 326 8.542953 CCCTCCGTAAACTAATATAAAAACGTC 58.457 37.037 0.00 0.00 0.00 4.34
326 327 9.305925 CCTCCGTAAACTAATATAAAAACGTCT 57.694 33.333 0.00 0.00 0.00 4.18
409 410 8.836268 ATACTAATAGTTCTCAGTCGACTAGG 57.164 38.462 19.57 13.71 30.19 3.02
410 411 6.887013 ACTAATAGTTCTCAGTCGACTAGGA 58.113 40.000 19.57 15.84 30.19 2.94
411 412 7.511268 ACTAATAGTTCTCAGTCGACTAGGAT 58.489 38.462 19.57 7.83 30.19 3.24
412 413 7.994334 ACTAATAGTTCTCAGTCGACTAGGATT 59.006 37.037 19.57 12.59 30.19 3.01
413 414 7.648039 AATAGTTCTCAGTCGACTAGGATTT 57.352 36.000 19.57 11.84 30.19 2.17
414 415 8.749026 AATAGTTCTCAGTCGACTAGGATTTA 57.251 34.615 19.57 13.35 30.19 1.40
415 416 8.749026 ATAGTTCTCAGTCGACTAGGATTTAA 57.251 34.615 19.57 4.84 30.19 1.52
416 417 7.648039 AGTTCTCAGTCGACTAGGATTTAAT 57.352 36.000 19.57 1.50 0.00 1.40
417 418 7.708998 AGTTCTCAGTCGACTAGGATTTAATC 58.291 38.462 19.57 0.00 0.00 1.75
418 419 7.339721 AGTTCTCAGTCGACTAGGATTTAATCA 59.660 37.037 19.57 0.00 0.00 2.57
419 420 7.640597 TCTCAGTCGACTAGGATTTAATCAA 57.359 36.000 19.57 0.00 0.00 2.57
420 421 7.708051 TCTCAGTCGACTAGGATTTAATCAAG 58.292 38.462 19.57 6.20 0.00 3.02
421 422 7.339721 TCTCAGTCGACTAGGATTTAATCAAGT 59.660 37.037 19.57 9.18 32.00 3.16
422 423 7.481642 TCAGTCGACTAGGATTTAATCAAGTC 58.518 38.462 19.57 20.40 38.98 3.01
423 424 7.339721 TCAGTCGACTAGGATTTAATCAAGTCT 59.660 37.037 19.57 12.31 39.62 3.24
424 425 7.976734 CAGTCGACTAGGATTTAATCAAGTCTT 59.023 37.037 19.57 14.22 39.62 3.01
425 426 9.186837 AGTCGACTAGGATTTAATCAAGTCTTA 57.813 33.333 18.46 15.74 39.62 2.10
426 427 9.453325 GTCGACTAGGATTTAATCAAGTCTTAG 57.547 37.037 24.16 15.53 39.62 2.18
427 428 8.136165 TCGACTAGGATTTAATCAAGTCTTAGC 58.864 37.037 24.16 9.68 39.62 3.09
428 429 8.138712 CGACTAGGATTTAATCAAGTCTTAGCT 58.861 37.037 24.16 0.00 39.62 3.32
433 434 9.606631 AGGATTTAATCAAGTCTTAGCTAAGTG 57.393 33.333 28.31 20.68 34.93 3.16
434 435 9.601217 GGATTTAATCAAGTCTTAGCTAAGTGA 57.399 33.333 28.31 24.39 34.93 3.41
444 445 9.482627 AAGTCTTAGCTAAGTGATATAACATGC 57.517 33.333 28.31 7.89 34.93 4.06
445 446 8.642432 AGTCTTAGCTAAGTGATATAACATGCA 58.358 33.333 28.31 5.65 34.93 3.96
446 447 9.261180 GTCTTAGCTAAGTGATATAACATGCAA 57.739 33.333 28.31 5.05 34.93 4.08
447 448 9.481340 TCTTAGCTAAGTGATATAACATGCAAG 57.519 33.333 28.31 3.88 34.93 4.01
448 449 9.481340 CTTAGCTAAGTGATATAACATGCAAGA 57.519 33.333 23.01 0.00 0.00 3.02
449 450 7.959689 AGCTAAGTGATATAACATGCAAGAG 57.040 36.000 0.00 0.00 0.00 2.85
450 451 7.730084 AGCTAAGTGATATAACATGCAAGAGA 58.270 34.615 0.00 0.00 0.00 3.10
451 452 7.871973 AGCTAAGTGATATAACATGCAAGAGAG 59.128 37.037 0.00 0.00 0.00 3.20
452 453 7.869937 GCTAAGTGATATAACATGCAAGAGAGA 59.130 37.037 0.00 0.00 0.00 3.10
453 454 9.755804 CTAAGTGATATAACATGCAAGAGAGAA 57.244 33.333 0.00 0.00 0.00 2.87
455 456 9.453572 AAGTGATATAACATGCAAGAGAGAAAA 57.546 29.630 0.00 0.00 0.00 2.29
456 457 9.453572 AGTGATATAACATGCAAGAGAGAAAAA 57.546 29.630 0.00 0.00 0.00 1.94
457 458 9.713740 GTGATATAACATGCAAGAGAGAAAAAG 57.286 33.333 0.00 0.00 0.00 2.27
458 459 9.671279 TGATATAACATGCAAGAGAGAAAAAGA 57.329 29.630 0.00 0.00 0.00 2.52
462 463 7.998753 AACATGCAAGAGAGAAAAAGAAAAG 57.001 32.000 0.00 0.00 0.00 2.27
463 464 7.338800 ACATGCAAGAGAGAAAAAGAAAAGA 57.661 32.000 0.00 0.00 0.00 2.52
464 465 7.199078 ACATGCAAGAGAGAAAAAGAAAAGAC 58.801 34.615 0.00 0.00 0.00 3.01
465 466 7.067981 ACATGCAAGAGAGAAAAAGAAAAGACT 59.932 33.333 0.00 0.00 0.00 3.24
466 467 8.562892 CATGCAAGAGAGAAAAAGAAAAGACTA 58.437 33.333 0.00 0.00 0.00 2.59
467 468 8.506168 TGCAAGAGAGAAAAAGAAAAGACTAA 57.494 30.769 0.00 0.00 0.00 2.24
468 469 8.956426 TGCAAGAGAGAAAAAGAAAAGACTAAA 58.044 29.630 0.00 0.00 0.00 1.85
469 470 9.788960 GCAAGAGAGAAAAAGAAAAGACTAAAA 57.211 29.630 0.00 0.00 0.00 1.52
484 485 9.516314 AAAAGACTAAAAAGAAAATTCTGGACG 57.484 29.630 0.00 0.00 37.65 4.79
485 486 7.203255 AGACTAAAAAGAAAATTCTGGACGG 57.797 36.000 0.00 0.00 37.65 4.79
486 487 6.996282 AGACTAAAAAGAAAATTCTGGACGGA 59.004 34.615 0.00 0.00 37.65 4.69
487 488 7.665974 AGACTAAAAAGAAAATTCTGGACGGAT 59.334 33.333 0.00 0.00 37.65 4.18
488 489 7.817641 ACTAAAAAGAAAATTCTGGACGGATC 58.182 34.615 0.00 0.00 37.65 3.36
489 490 6.901081 AAAAAGAAAATTCTGGACGGATCT 57.099 33.333 0.00 0.00 37.65 2.75
490 491 6.502136 AAAAGAAAATTCTGGACGGATCTC 57.498 37.500 0.00 0.00 37.65 2.75
491 492 4.826274 AGAAAATTCTGGACGGATCTCA 57.174 40.909 0.00 0.00 35.89 3.27
492 493 5.165961 AGAAAATTCTGGACGGATCTCAA 57.834 39.130 0.00 0.00 35.89 3.02
493 494 5.749462 AGAAAATTCTGGACGGATCTCAAT 58.251 37.500 0.00 0.00 35.89 2.57
494 495 5.587844 AGAAAATTCTGGACGGATCTCAATG 59.412 40.000 0.00 0.00 35.89 2.82
495 496 4.494091 AATTCTGGACGGATCTCAATGT 57.506 40.909 0.00 0.00 0.00 2.71
496 497 5.614324 AATTCTGGACGGATCTCAATGTA 57.386 39.130 0.00 0.00 0.00 2.29
497 498 5.614324 ATTCTGGACGGATCTCAATGTAA 57.386 39.130 0.00 0.00 0.00 2.41
498 499 4.655762 TCTGGACGGATCTCAATGTAAG 57.344 45.455 0.00 0.00 0.00 2.34
499 500 4.278310 TCTGGACGGATCTCAATGTAAGA 58.722 43.478 0.00 0.00 0.00 2.10
500 501 4.895889 TCTGGACGGATCTCAATGTAAGAT 59.104 41.667 0.00 0.00 36.19 2.40
501 502 5.010112 TCTGGACGGATCTCAATGTAAGATC 59.990 44.000 4.85 4.85 45.54 2.75
502 503 4.895889 TGGACGGATCTCAATGTAAGATCT 59.104 41.667 11.66 0.00 45.56 2.75
503 504 5.010112 TGGACGGATCTCAATGTAAGATCTC 59.990 44.000 11.66 4.23 45.56 2.75
504 505 5.010112 GGACGGATCTCAATGTAAGATCTCA 59.990 44.000 11.66 0.00 45.56 3.27
505 506 6.295011 GGACGGATCTCAATGTAAGATCTCAT 60.295 42.308 11.66 0.00 45.56 2.90
506 507 6.453943 ACGGATCTCAATGTAAGATCTCATG 58.546 40.000 11.66 0.00 45.56 3.07
507 508 5.868258 CGGATCTCAATGTAAGATCTCATGG 59.132 44.000 11.66 0.00 45.56 3.66
508 509 6.171921 GGATCTCAATGTAAGATCTCATGGG 58.828 44.000 11.66 0.00 45.56 4.00
509 510 6.239829 GGATCTCAATGTAAGATCTCATGGGT 60.240 42.308 11.66 0.00 45.56 4.51
510 511 7.038729 GGATCTCAATGTAAGATCTCATGGGTA 60.039 40.741 11.66 0.00 45.56 3.69
511 512 7.862274 TCTCAATGTAAGATCTCATGGGTAT 57.138 36.000 0.00 0.00 0.00 2.73
512 513 8.956446 TCTCAATGTAAGATCTCATGGGTATA 57.044 34.615 0.00 0.00 0.00 1.47
513 514 9.029368 TCTCAATGTAAGATCTCATGGGTATAG 57.971 37.037 0.00 0.00 0.00 1.31
514 515 8.727100 TCAATGTAAGATCTCATGGGTATAGT 57.273 34.615 0.00 0.00 0.00 2.12
515 516 9.822727 TCAATGTAAGATCTCATGGGTATAGTA 57.177 33.333 0.00 0.00 0.00 1.82
518 519 8.507524 TGTAAGATCTCATGGGTATAGTATCG 57.492 38.462 0.00 0.00 0.00 2.92
519 520 8.326529 TGTAAGATCTCATGGGTATAGTATCGA 58.673 37.037 0.00 0.00 0.00 3.59
520 521 7.633193 AAGATCTCATGGGTATAGTATCGAC 57.367 40.000 0.00 0.00 0.00 4.20
521 522 6.964464 AGATCTCATGGGTATAGTATCGACT 58.036 40.000 0.00 0.00 39.92 4.18
522 523 6.826231 AGATCTCATGGGTATAGTATCGACTG 59.174 42.308 0.00 0.00 36.28 3.51
523 524 6.123045 TCTCATGGGTATAGTATCGACTGA 57.877 41.667 0.00 0.00 36.28 3.41
524 525 6.174049 TCTCATGGGTATAGTATCGACTGAG 58.826 44.000 0.00 0.00 36.28 3.35
525 526 6.013639 TCTCATGGGTATAGTATCGACTGAGA 60.014 42.308 0.00 0.00 36.28 3.27
526 527 6.722328 TCATGGGTATAGTATCGACTGAGAT 58.278 40.000 0.00 0.00 36.28 2.75
527 528 7.175797 TCATGGGTATAGTATCGACTGAGATT 58.824 38.462 0.00 0.00 36.28 2.40
528 529 7.670140 TCATGGGTATAGTATCGACTGAGATTT 59.330 37.037 0.00 0.00 36.28 2.17
529 530 7.450124 TGGGTATAGTATCGACTGAGATTTC 57.550 40.000 0.00 0.00 36.28 2.17
530 531 6.148976 TGGGTATAGTATCGACTGAGATTTCG 59.851 42.308 0.00 0.00 36.28 3.46
532 533 7.235777 GGTATAGTATCGACTGAGATTTCGAC 58.764 42.308 0.00 0.00 46.41 4.20
533 534 7.118101 GGTATAGTATCGACTGAGATTTCGACT 59.882 40.741 0.00 0.00 46.41 4.18
534 535 9.138062 GTATAGTATCGACTGAGATTTCGACTA 57.862 37.037 0.00 0.00 46.41 2.59
535 536 6.922247 AGTATCGACTGAGATTTCGACTAA 57.078 37.500 0.00 0.00 46.41 2.24
536 537 6.950545 AGTATCGACTGAGATTTCGACTAAG 58.049 40.000 0.00 0.00 46.41 2.18
537 538 6.762187 AGTATCGACTGAGATTTCGACTAAGA 59.238 38.462 0.00 0.00 46.41 2.10
538 539 5.219226 TCGACTGAGATTTCGACTAAGAC 57.781 43.478 0.00 0.00 39.29 3.01
539 540 4.936411 TCGACTGAGATTTCGACTAAGACT 59.064 41.667 0.00 0.00 39.29 3.24
540 541 5.411977 TCGACTGAGATTTCGACTAAGACTT 59.588 40.000 0.00 0.00 39.29 3.01
541 542 6.592994 TCGACTGAGATTTCGACTAAGACTTA 59.407 38.462 0.00 0.00 39.29 2.24
542 543 6.902948 CGACTGAGATTTCGACTAAGACTTAG 59.097 42.308 18.80 18.80 37.43 2.18
543 544 6.557110 ACTGAGATTTCGACTAAGACTTAGC 58.443 40.000 20.05 12.60 36.71 3.09
544 545 6.151312 ACTGAGATTTCGACTAAGACTTAGCA 59.849 38.462 20.05 7.46 36.71 3.49
545 546 6.920817 TGAGATTTCGACTAAGACTTAGCAA 58.079 36.000 20.05 9.29 36.71 3.91
546 547 7.030165 TGAGATTTCGACTAAGACTTAGCAAG 58.970 38.462 20.05 12.35 36.71 4.01
547 548 7.094334 TGAGATTTCGACTAAGACTTAGCAAGA 60.094 37.037 20.05 14.15 36.71 3.02
548 549 7.777095 AGATTTCGACTAAGACTTAGCAAGAT 58.223 34.615 20.05 9.44 36.71 2.40
549 550 7.918562 AGATTTCGACTAAGACTTAGCAAGATC 59.081 37.037 20.05 15.88 36.71 2.75
550 551 5.502153 TCGACTAAGACTTAGCAAGATCC 57.498 43.478 20.05 2.95 36.71 3.36
551 552 5.194432 TCGACTAAGACTTAGCAAGATCCT 58.806 41.667 20.05 0.33 36.71 3.24
552 553 6.354938 TCGACTAAGACTTAGCAAGATCCTA 58.645 40.000 20.05 0.43 36.71 2.94
553 554 6.483974 TCGACTAAGACTTAGCAAGATCCTAG 59.516 42.308 20.05 1.62 36.71 3.02
554 555 6.261381 CGACTAAGACTTAGCAAGATCCTAGT 59.739 42.308 20.05 0.76 36.71 2.57
555 556 7.201750 CGACTAAGACTTAGCAAGATCCTAGTT 60.202 40.741 20.05 0.00 36.71 2.24
556 557 8.368962 ACTAAGACTTAGCAAGATCCTAGTTT 57.631 34.615 20.05 0.00 36.71 2.66
557 558 8.817876 ACTAAGACTTAGCAAGATCCTAGTTTT 58.182 33.333 20.05 0.00 36.71 2.43
558 559 9.660180 CTAAGACTTAGCAAGATCCTAGTTTTT 57.340 33.333 9.27 0.00 0.00 1.94
679 697 1.825090 AGTGATTCCAGAAATGCGCA 58.175 45.000 14.96 14.96 0.00 6.09
723 745 4.974721 GGCCAGTGGTGGTGGTGG 62.975 72.222 11.74 0.00 46.96 4.61
727 749 3.570212 AGTGGTGGTGGTGGGAGC 61.570 66.667 0.00 0.00 0.00 4.70
729 751 3.569210 TGGTGGTGGTGGGAGCAG 61.569 66.667 0.00 0.00 0.00 4.24
785 946 2.910199 CATCATGGAGTTCGTCACCAT 58.090 47.619 0.00 0.00 45.82 3.55
853 1014 2.890371 GGCTAACGGAAGGCGAGA 59.110 61.111 0.00 0.00 31.82 4.04
894 1073 4.344448 GCTAGTACATATCGGATCGAAGC 58.656 47.826 0.00 0.00 39.99 3.86
895 1074 4.142665 GCTAGTACATATCGGATCGAAGCA 60.143 45.833 0.00 0.00 39.99 3.91
896 1075 4.427096 AGTACATATCGGATCGAAGCAG 57.573 45.455 0.00 0.00 39.99 4.24
897 1076 2.071688 ACATATCGGATCGAAGCAGC 57.928 50.000 0.00 0.00 39.99 5.25
898 1077 0.987715 CATATCGGATCGAAGCAGCG 59.012 55.000 0.00 0.00 39.99 5.18
899 1078 0.109086 ATATCGGATCGAAGCAGCGG 60.109 55.000 0.00 0.00 39.99 5.52
900 1079 2.142357 TATCGGATCGAAGCAGCGGG 62.142 60.000 0.00 0.00 39.99 6.13
1451 1653 7.425224 ACTGCCACTCTGAGTATTATTACTT 57.575 36.000 10.47 0.00 38.81 2.24
1452 1654 7.268586 ACTGCCACTCTGAGTATTATTACTTG 58.731 38.462 10.47 0.00 38.81 3.16
1455 1657 8.195436 TGCCACTCTGAGTATTATTACTTGTAC 58.805 37.037 10.47 0.00 38.81 2.90
1474 1676 9.672673 ACTTGTACTAGCATTCAGTATTCAAAT 57.327 29.630 4.10 0.00 31.46 2.32
1476 1678 8.662781 TGTACTAGCATTCAGTATTCAAATCC 57.337 34.615 0.00 0.00 31.46 3.01
1477 1679 8.264347 TGTACTAGCATTCAGTATTCAAATCCA 58.736 33.333 0.00 0.00 31.46 3.41
1481 1683 6.732154 AGCATTCAGTATTCAAATCCATTCG 58.268 36.000 0.00 0.00 0.00 3.34
1484 1686 7.166473 GCATTCAGTATTCAAATCCATTCGTTC 59.834 37.037 0.00 0.00 0.00 3.95
1491 1693 2.819608 CAAATCCATTCGTTCCACACCT 59.180 45.455 0.00 0.00 0.00 4.00
1496 1698 2.031157 CCATTCGTTCCACACCTTGAAC 60.031 50.000 0.00 0.00 37.97 3.18
1497 1699 1.670791 TTCGTTCCACACCTTGAACC 58.329 50.000 0.00 0.00 38.05 3.62
1584 1786 3.258372 AGTGAGTCTCAATGCCTAAACGA 59.742 43.478 3.51 0.00 0.00 3.85
1609 1811 7.428826 AGATGCTGCTTAGTTAAATTATTGGC 58.571 34.615 0.00 0.00 0.00 4.52
1679 1881 4.152402 CCCATTCGATAAATAAGACTGCGG 59.848 45.833 0.00 0.00 0.00 5.69
1762 1964 1.578423 GCTTTGCAGCCTCACAGTC 59.422 57.895 0.00 0.00 40.61 3.51
1803 2005 5.357878 TCAAGTTCCAACATATCAGGAATGC 59.642 40.000 0.00 0.00 42.82 3.56
1856 2058 3.030668 TGTCTACTCGTGACGTCACTA 57.969 47.619 37.63 29.39 44.34 2.74
1933 2135 6.544931 GTGGTGGTTAGTTCCTAATAAATCCC 59.455 42.308 0.00 0.00 0.00 3.85
1940 2142 9.274206 GTTAGTTCCTAATAAATCCCATCTGTC 57.726 37.037 0.00 0.00 0.00 3.51
1995 2197 2.034558 GTGAGCTGGCTACTCTCAGATC 59.965 54.545 0.00 0.00 44.04 2.75
2036 2238 1.941294 TCGATCGTAGCAGAGGAAGAC 59.059 52.381 15.94 0.00 0.00 3.01
2040 2242 1.671328 TCGTAGCAGAGGAAGACGATG 59.329 52.381 0.00 0.00 37.60 3.84
2084 2286 0.514691 CGGCTTTGCTTGAGTCTGTC 59.485 55.000 0.00 0.00 0.00 3.51
2099 2301 1.880601 CTGTCGTCGCTGCAGTCAAC 61.881 60.000 16.64 10.08 0.00 3.18
2282 2484 2.256117 GGGACCAATACGCTATTGCT 57.744 50.000 10.44 0.87 43.19 3.91
2489 2691 0.174162 GGATGCAGCCATTGGTTCAC 59.826 55.000 18.08 0.00 0.00 3.18
2537 2739 3.195825 ACTCAAGGGAGGTTCAAGTATCG 59.804 47.826 0.00 0.00 45.81 2.92
2552 2754 1.948145 GTATCGTCCGTCAGTGATCCT 59.052 52.381 0.00 0.00 0.00 3.24
2594 2796 1.882623 CCTGTTGAGAAAGCCAACTCC 59.117 52.381 0.00 0.00 43.05 3.85
2648 2852 4.021016 AGTGTAGGCTTAAGGTCAGTTCTG 60.021 45.833 4.29 0.00 0.00 3.02
2663 2867 6.146347 GGTCAGTTCTGAATTTCACTGTCTAC 59.854 42.308 12.57 6.43 38.26 2.59
2664 2868 6.701841 GTCAGTTCTGAATTTCACTGTCTACA 59.298 38.462 12.57 0.00 38.26 2.74
2665 2869 6.701841 TCAGTTCTGAATTTCACTGTCTACAC 59.298 38.462 12.57 0.00 38.26 2.90
2688 3151 9.841295 ACACGGTACTTTTATTAACCATGATAT 57.159 29.630 0.00 0.00 30.10 1.63
2768 3231 8.517878 GCATATGGTATTGCTGAATAGTGAATT 58.482 33.333 4.56 0.00 35.95 2.17
2780 3250 7.403312 TGAATAGTGAATTGGTTTACATGGG 57.597 36.000 0.00 0.00 0.00 4.00
2793 3263 6.610830 TGGTTTACATGGGCATTAGAATGAAT 59.389 34.615 6.43 0.00 38.70 2.57
2837 3307 1.810853 CGTGTCATCTGCATGCGGA 60.811 57.895 30.50 30.50 35.60 5.54
2858 3328 2.777832 TGCAAGTTTTGGCTTTTGGT 57.222 40.000 0.00 0.00 0.00 3.67
2861 3331 2.746904 GCAAGTTTTGGCTTTTGGTTGT 59.253 40.909 0.00 0.00 0.00 3.32
2863 3333 4.320861 GCAAGTTTTGGCTTTTGGTTGTTT 60.321 37.500 0.00 0.00 0.00 2.83
2864 3334 5.767269 CAAGTTTTGGCTTTTGGTTGTTTT 58.233 33.333 0.00 0.00 0.00 2.43
2897 3367 6.229733 TGATTTATTTTGCTTGGTTTCCAGG 58.770 36.000 0.00 0.00 33.81 4.45
3017 3487 0.254178 AGATATGGGATCATGCCGCC 59.746 55.000 0.00 0.00 34.96 6.13
3053 3523 1.484444 AAGAGGCTGGTGGAGTGGTC 61.484 60.000 0.00 0.00 0.00 4.02
3062 3532 0.322975 GTGGAGTGGTCACAGATGCT 59.677 55.000 3.82 0.00 35.39 3.79
3065 3535 0.392193 GAGTGGTCACAGATGCTGGG 60.392 60.000 3.82 0.00 36.00 4.45
3134 3604 5.363939 GACAGAGGCATAATAGCTTGTTCT 58.636 41.667 0.00 0.00 34.17 3.01
3137 3607 3.817647 GAGGCATAATAGCTTGTTCTGGG 59.182 47.826 0.00 0.00 34.17 4.45
3162 3632 4.168760 GTTGCTTCATCGGAGAATTTTGG 58.831 43.478 0.00 0.00 43.58 3.28
3170 3640 3.074412 TCGGAGAATTTTGGAAGCTGTC 58.926 45.455 0.00 0.00 0.00 3.51
3238 3708 3.305676 CCCTTACAGTCAGATAGATGGCG 60.306 52.174 0.00 0.00 0.00 5.69
3246 3716 3.057245 GTCAGATAGATGGCGTGATGCTA 60.057 47.826 0.00 0.00 45.43 3.49
3301 3771 7.432252 AGAACTTTTGCTCTGTTTTTATCAACG 59.568 33.333 0.00 0.00 0.00 4.10
3436 3932 2.938451 CTGCTCATAAACAATCTGCGGA 59.062 45.455 0.00 0.00 0.00 5.54
3518 4014 6.165577 GGCTGTTTTGATGGTTTGTATCATT 58.834 36.000 0.00 0.00 34.76 2.57
3520 4016 6.311200 GCTGTTTTGATGGTTTGTATCATTCC 59.689 38.462 0.00 0.00 34.76 3.01
3534 4030 1.708551 TCATTCCTTTTTCCCTCGGGT 59.291 47.619 1.18 0.00 36.47 5.28
3536 4032 2.865119 TTCCTTTTTCCCTCGGGTAC 57.135 50.000 1.18 0.00 36.47 3.34
3571 4067 1.449601 GGGTTGATGGCACGTCGAT 60.450 57.895 0.00 0.00 0.00 3.59
3628 4124 6.936279 TGATAACTCGAATCTCTGAACCTTT 58.064 36.000 0.00 0.00 0.00 3.11
3702 4204 5.809001 TGCCTTCAGTTATTCTCATTGTCT 58.191 37.500 0.00 0.00 0.00 3.41
3703 4205 6.240894 TGCCTTCAGTTATTCTCATTGTCTT 58.759 36.000 0.00 0.00 0.00 3.01
3789 4291 8.555896 TTGGGTATAAAGTATCACTCCATGTA 57.444 34.615 0.00 0.00 0.00 2.29
3848 4353 8.504005 AGGAAAAATACAGTCACACGAATTTAG 58.496 33.333 0.00 0.00 0.00 1.85
3874 4381 5.519927 ACAACAGCACAAGTAGCAATTTTTC 59.480 36.000 0.00 0.00 0.00 2.29
3875 4382 5.261209 ACAGCACAAGTAGCAATTTTTCA 57.739 34.783 0.00 0.00 0.00 2.69
4090 4600 1.006102 GTCGTAGCTGTGCACCAGT 60.006 57.895 15.69 0.32 43.55 4.00
4183 4693 1.153369 CACGGCCATGGTGAGGTAG 60.153 63.158 14.67 0.00 37.60 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 9.487442 TCTAGGAAAGTTTGGCCAAATTTATAT 57.513 29.630 31.82 23.12 31.37 0.86
143 144 8.887264 TCTAGGAAAGTTTGGCCAAATTTATA 57.113 30.769 31.82 23.55 31.37 0.98
144 145 7.790782 TCTAGGAAAGTTTGGCCAAATTTAT 57.209 32.000 31.82 23.67 31.37 1.40
145 146 7.790782 ATCTAGGAAAGTTTGGCCAAATTTA 57.209 32.000 31.82 19.32 31.37 1.40
146 147 6.686484 ATCTAGGAAAGTTTGGCCAAATTT 57.314 33.333 32.52 30.02 32.66 1.82
147 148 6.686484 AATCTAGGAAAGTTTGGCCAAATT 57.314 33.333 32.52 26.15 32.36 1.82
148 149 6.269769 TCAAATCTAGGAAAGTTTGGCCAAAT 59.730 34.615 32.52 18.14 32.07 2.32
149 150 5.600484 TCAAATCTAGGAAAGTTTGGCCAAA 59.400 36.000 27.13 27.13 32.07 3.28
150 151 5.010617 GTCAAATCTAGGAAAGTTTGGCCAA 59.989 40.000 16.05 16.05 30.84 4.52
151 152 4.522789 GTCAAATCTAGGAAAGTTTGGCCA 59.477 41.667 0.00 0.00 30.84 5.36
152 153 4.767409 AGTCAAATCTAGGAAAGTTTGGCC 59.233 41.667 0.00 0.00 34.29 5.36
153 154 5.966742 AGTCAAATCTAGGAAAGTTTGGC 57.033 39.130 0.00 0.00 34.13 4.52
154 155 7.386848 TCGTAAGTCAAATCTAGGAAAGTTTGG 59.613 37.037 0.00 0.00 39.48 3.28
155 156 8.306680 TCGTAAGTCAAATCTAGGAAAGTTTG 57.693 34.615 0.00 0.00 39.48 2.93
156 157 8.897872 TTCGTAAGTCAAATCTAGGAAAGTTT 57.102 30.769 0.00 0.00 39.48 2.66
157 158 8.897872 TTTCGTAAGTCAAATCTAGGAAAGTT 57.102 30.769 0.00 0.00 39.48 2.66
158 159 8.897872 TTTTCGTAAGTCAAATCTAGGAAAGT 57.102 30.769 0.00 0.00 39.48 2.66
159 160 7.958025 GCTTTTCGTAAGTCAAATCTAGGAAAG 59.042 37.037 0.00 0.00 39.48 2.62
160 161 7.660208 AGCTTTTCGTAAGTCAAATCTAGGAAA 59.340 33.333 0.00 0.00 39.48 3.13
161 162 7.159372 AGCTTTTCGTAAGTCAAATCTAGGAA 58.841 34.615 0.00 0.00 39.48 3.36
162 163 6.698380 AGCTTTTCGTAAGTCAAATCTAGGA 58.302 36.000 0.00 0.00 39.48 2.94
163 164 6.969828 AGCTTTTCGTAAGTCAAATCTAGG 57.030 37.500 0.00 0.00 39.48 3.02
247 248 7.054124 TGGTCAGAGTTTATGAAGTTTGTCTT 58.946 34.615 0.00 0.00 39.32 3.01
248 249 6.591935 TGGTCAGAGTTTATGAAGTTTGTCT 58.408 36.000 0.00 0.00 0.00 3.41
249 250 6.861065 TGGTCAGAGTTTATGAAGTTTGTC 57.139 37.500 0.00 0.00 0.00 3.18
250 251 7.823745 ATTGGTCAGAGTTTATGAAGTTTGT 57.176 32.000 0.00 0.00 0.00 2.83
251 252 9.778993 CATATTGGTCAGAGTTTATGAAGTTTG 57.221 33.333 0.00 0.00 0.00 2.93
252 253 9.739276 TCATATTGGTCAGAGTTTATGAAGTTT 57.261 29.630 0.00 0.00 0.00 2.66
253 254 9.739276 TTCATATTGGTCAGAGTTTATGAAGTT 57.261 29.630 0.00 0.00 33.46 2.66
254 255 9.911788 ATTCATATTGGTCAGAGTTTATGAAGT 57.088 29.630 8.56 0.00 38.63 3.01
280 281 9.000978 ACGGAGGGAGTATATCTTATGTATCTA 57.999 37.037 0.00 0.00 0.00 1.98
281 282 7.874252 ACGGAGGGAGTATATCTTATGTATCT 58.126 38.462 0.00 0.00 0.00 1.98
282 283 9.624373 TTACGGAGGGAGTATATCTTATGTATC 57.376 37.037 0.00 0.00 0.00 2.24
283 284 9.986157 TTTACGGAGGGAGTATATCTTATGTAT 57.014 33.333 0.00 0.00 0.00 2.29
284 285 9.236006 GTTTACGGAGGGAGTATATCTTATGTA 57.764 37.037 0.00 0.00 0.00 2.29
285 286 7.949006 AGTTTACGGAGGGAGTATATCTTATGT 59.051 37.037 0.00 0.00 0.00 2.29
286 287 8.350852 AGTTTACGGAGGGAGTATATCTTATG 57.649 38.462 0.00 0.00 0.00 1.90
289 290 8.953223 ATTAGTTTACGGAGGGAGTATATCTT 57.047 34.615 0.00 0.00 0.00 2.40
296 297 9.605275 GTTTTTATATTAGTTTACGGAGGGAGT 57.395 33.333 0.00 0.00 0.00 3.85
297 298 8.758715 CGTTTTTATATTAGTTTACGGAGGGAG 58.241 37.037 0.00 0.00 0.00 4.30
298 299 8.257306 ACGTTTTTATATTAGTTTACGGAGGGA 58.743 33.333 0.00 0.00 32.54 4.20
299 300 8.424274 ACGTTTTTATATTAGTTTACGGAGGG 57.576 34.615 0.00 0.00 32.54 4.30
300 301 9.305925 AGACGTTTTTATATTAGTTTACGGAGG 57.694 33.333 0.00 0.00 32.54 4.30
383 384 9.926158 CCTAGTCGACTGAGAACTATTAGTATA 57.074 37.037 28.12 0.29 0.00 1.47
384 385 8.649591 TCCTAGTCGACTGAGAACTATTAGTAT 58.350 37.037 28.12 0.00 0.00 2.12
385 386 8.016301 TCCTAGTCGACTGAGAACTATTAGTA 57.984 38.462 28.12 1.39 0.00 1.82
386 387 6.887013 TCCTAGTCGACTGAGAACTATTAGT 58.113 40.000 28.12 0.00 0.00 2.24
387 388 7.972832 ATCCTAGTCGACTGAGAACTATTAG 57.027 40.000 28.12 12.49 0.00 1.73
388 389 8.749026 AAATCCTAGTCGACTGAGAACTATTA 57.251 34.615 28.12 2.62 0.00 0.98
389 390 7.648039 AAATCCTAGTCGACTGAGAACTATT 57.352 36.000 28.12 13.55 0.00 1.73
390 391 8.749026 TTAAATCCTAGTCGACTGAGAACTAT 57.251 34.615 28.12 12.98 0.00 2.12
391 392 8.749026 ATTAAATCCTAGTCGACTGAGAACTA 57.251 34.615 28.12 14.96 0.00 2.24
392 393 7.339721 TGATTAAATCCTAGTCGACTGAGAACT 59.660 37.037 28.12 15.81 0.00 3.01
393 394 7.481642 TGATTAAATCCTAGTCGACTGAGAAC 58.518 38.462 28.12 12.03 0.00 3.01
394 395 7.640597 TGATTAAATCCTAGTCGACTGAGAA 57.359 36.000 28.12 12.69 0.00 2.87
395 396 7.339721 ACTTGATTAAATCCTAGTCGACTGAGA 59.660 37.037 28.12 22.52 0.00 3.27
396 397 7.484975 ACTTGATTAAATCCTAGTCGACTGAG 58.515 38.462 28.12 18.10 0.00 3.35
397 398 7.339721 AGACTTGATTAAATCCTAGTCGACTGA 59.660 37.037 28.12 17.62 41.23 3.41
398 399 7.484975 AGACTTGATTAAATCCTAGTCGACTG 58.515 38.462 28.12 16.71 41.23 3.51
399 400 7.648039 AGACTTGATTAAATCCTAGTCGACT 57.352 36.000 23.66 23.66 41.23 4.18
400 401 9.453325 CTAAGACTTGATTAAATCCTAGTCGAC 57.547 37.037 7.70 7.70 41.23 4.20
401 402 8.136165 GCTAAGACTTGATTAAATCCTAGTCGA 58.864 37.037 0.00 0.00 41.23 4.20
402 403 8.138712 AGCTAAGACTTGATTAAATCCTAGTCG 58.861 37.037 0.00 0.00 41.23 4.18
407 408 9.606631 CACTTAGCTAAGACTTGATTAAATCCT 57.393 33.333 34.65 8.18 37.08 3.24
408 409 9.601217 TCACTTAGCTAAGACTTGATTAAATCC 57.399 33.333 34.65 0.00 37.08 3.01
418 419 9.482627 GCATGTTATATCACTTAGCTAAGACTT 57.517 33.333 34.65 21.06 37.08 3.01
419 420 8.642432 TGCATGTTATATCACTTAGCTAAGACT 58.358 33.333 34.65 21.23 37.08 3.24
420 421 8.818141 TGCATGTTATATCACTTAGCTAAGAC 57.182 34.615 34.65 21.83 37.08 3.01
421 422 9.481340 CTTGCATGTTATATCACTTAGCTAAGA 57.519 33.333 34.65 17.64 37.08 2.10
422 423 9.481340 TCTTGCATGTTATATCACTTAGCTAAG 57.519 33.333 28.16 28.16 39.18 2.18
423 424 9.481340 CTCTTGCATGTTATATCACTTAGCTAA 57.519 33.333 5.94 5.94 0.00 3.09
424 425 8.860088 TCTCTTGCATGTTATATCACTTAGCTA 58.140 33.333 0.00 0.00 0.00 3.32
425 426 7.730084 TCTCTTGCATGTTATATCACTTAGCT 58.270 34.615 0.00 0.00 0.00 3.32
426 427 7.869937 TCTCTCTTGCATGTTATATCACTTAGC 59.130 37.037 0.00 0.00 0.00 3.09
427 428 9.755804 TTCTCTCTTGCATGTTATATCACTTAG 57.244 33.333 0.00 0.00 0.00 2.18
429 430 9.453572 TTTTCTCTCTTGCATGTTATATCACTT 57.546 29.630 0.00 0.00 0.00 3.16
430 431 9.453572 TTTTTCTCTCTTGCATGTTATATCACT 57.546 29.630 0.00 0.00 0.00 3.41
431 432 9.713740 CTTTTTCTCTCTTGCATGTTATATCAC 57.286 33.333 0.00 0.00 0.00 3.06
432 433 9.671279 TCTTTTTCTCTCTTGCATGTTATATCA 57.329 29.630 0.00 0.00 0.00 2.15
436 437 9.688592 CTTTTCTTTTTCTCTCTTGCATGTTAT 57.311 29.630 0.00 0.00 0.00 1.89
437 438 8.902806 TCTTTTCTTTTTCTCTCTTGCATGTTA 58.097 29.630 0.00 0.00 0.00 2.41
438 439 7.704047 GTCTTTTCTTTTTCTCTCTTGCATGTT 59.296 33.333 0.00 0.00 0.00 2.71
439 440 7.067981 AGTCTTTTCTTTTTCTCTCTTGCATGT 59.932 33.333 0.00 0.00 0.00 3.21
440 441 7.424001 AGTCTTTTCTTTTTCTCTCTTGCATG 58.576 34.615 0.00 0.00 0.00 4.06
441 442 7.579761 AGTCTTTTCTTTTTCTCTCTTGCAT 57.420 32.000 0.00 0.00 0.00 3.96
442 443 8.506168 TTAGTCTTTTCTTTTTCTCTCTTGCA 57.494 30.769 0.00 0.00 0.00 4.08
443 444 9.788960 TTTTAGTCTTTTCTTTTTCTCTCTTGC 57.211 29.630 0.00 0.00 0.00 4.01
458 459 9.516314 CGTCCAGAATTTTCTTTTTAGTCTTTT 57.484 29.630 0.00 0.00 34.74 2.27
459 460 8.135529 CCGTCCAGAATTTTCTTTTTAGTCTTT 58.864 33.333 0.00 0.00 34.74 2.52
460 461 7.501225 TCCGTCCAGAATTTTCTTTTTAGTCTT 59.499 33.333 0.00 0.00 34.74 3.01
461 462 6.996282 TCCGTCCAGAATTTTCTTTTTAGTCT 59.004 34.615 0.00 0.00 34.74 3.24
462 463 7.198306 TCCGTCCAGAATTTTCTTTTTAGTC 57.802 36.000 0.00 0.00 34.74 2.59
463 464 7.665974 AGATCCGTCCAGAATTTTCTTTTTAGT 59.334 33.333 0.00 0.00 34.74 2.24
464 465 8.045176 AGATCCGTCCAGAATTTTCTTTTTAG 57.955 34.615 0.00 0.00 34.74 1.85
465 466 7.663905 TGAGATCCGTCCAGAATTTTCTTTTTA 59.336 33.333 0.00 0.00 34.74 1.52
466 467 6.490040 TGAGATCCGTCCAGAATTTTCTTTTT 59.510 34.615 0.00 0.00 34.74 1.94
467 468 6.003950 TGAGATCCGTCCAGAATTTTCTTTT 58.996 36.000 0.00 0.00 34.74 2.27
468 469 5.560724 TGAGATCCGTCCAGAATTTTCTTT 58.439 37.500 0.00 0.00 34.74 2.52
469 470 5.165961 TGAGATCCGTCCAGAATTTTCTT 57.834 39.130 0.00 0.00 34.74 2.52
470 471 4.826274 TGAGATCCGTCCAGAATTTTCT 57.174 40.909 0.00 0.00 38.25 2.52
471 472 5.355350 ACATTGAGATCCGTCCAGAATTTTC 59.645 40.000 0.00 0.00 0.00 2.29
472 473 5.256474 ACATTGAGATCCGTCCAGAATTTT 58.744 37.500 0.00 0.00 0.00 1.82
473 474 4.848357 ACATTGAGATCCGTCCAGAATTT 58.152 39.130 0.00 0.00 0.00 1.82
474 475 4.494091 ACATTGAGATCCGTCCAGAATT 57.506 40.909 0.00 0.00 0.00 2.17
475 476 5.363868 TCTTACATTGAGATCCGTCCAGAAT 59.636 40.000 0.00 0.00 0.00 2.40
476 477 4.709886 TCTTACATTGAGATCCGTCCAGAA 59.290 41.667 0.00 0.00 0.00 3.02
477 478 4.278310 TCTTACATTGAGATCCGTCCAGA 58.722 43.478 0.00 0.00 0.00 3.86
478 479 4.655762 TCTTACATTGAGATCCGTCCAG 57.344 45.455 0.00 0.00 0.00 3.86
479 480 4.895889 AGATCTTACATTGAGATCCGTCCA 59.104 41.667 9.76 0.00 46.88 4.02
480 481 5.010112 TGAGATCTTACATTGAGATCCGTCC 59.990 44.000 9.76 0.68 46.88 4.79
481 482 6.078202 TGAGATCTTACATTGAGATCCGTC 57.922 41.667 9.76 4.23 46.88 4.79
482 483 6.453943 CATGAGATCTTACATTGAGATCCGT 58.546 40.000 9.76 2.48 46.88 4.69
483 484 5.868258 CCATGAGATCTTACATTGAGATCCG 59.132 44.000 9.76 0.00 46.88 4.18
484 485 6.171921 CCCATGAGATCTTACATTGAGATCC 58.828 44.000 9.76 4.01 46.88 3.36
485 486 6.767456 ACCCATGAGATCTTACATTGAGATC 58.233 40.000 0.00 6.09 46.32 2.75
486 487 6.760440 ACCCATGAGATCTTACATTGAGAT 57.240 37.500 0.00 0.00 36.60 2.75
487 488 7.862274 ATACCCATGAGATCTTACATTGAGA 57.138 36.000 0.00 0.00 0.00 3.27
488 489 8.811017 ACTATACCCATGAGATCTTACATTGAG 58.189 37.037 0.00 0.00 0.00 3.02
489 490 8.727100 ACTATACCCATGAGATCTTACATTGA 57.273 34.615 0.00 0.00 0.00 2.57
492 493 9.126151 CGATACTATACCCATGAGATCTTACAT 57.874 37.037 0.00 0.00 0.00 2.29
493 494 8.326529 TCGATACTATACCCATGAGATCTTACA 58.673 37.037 0.00 0.00 0.00 2.41
494 495 8.614346 GTCGATACTATACCCATGAGATCTTAC 58.386 40.741 0.00 0.00 0.00 2.34
495 496 8.549731 AGTCGATACTATACCCATGAGATCTTA 58.450 37.037 0.00 0.00 32.84 2.10
496 497 7.338196 CAGTCGATACTATACCCATGAGATCTT 59.662 40.741 0.00 0.00 33.48 2.40
497 498 6.826231 CAGTCGATACTATACCCATGAGATCT 59.174 42.308 0.00 0.00 33.48 2.75
498 499 6.824196 TCAGTCGATACTATACCCATGAGATC 59.176 42.308 0.00 0.00 33.48 2.75
499 500 6.722328 TCAGTCGATACTATACCCATGAGAT 58.278 40.000 0.00 0.00 33.48 2.75
500 501 6.013639 TCTCAGTCGATACTATACCCATGAGA 60.014 42.308 0.00 0.00 33.48 3.27
501 502 6.174049 TCTCAGTCGATACTATACCCATGAG 58.826 44.000 0.00 0.00 33.48 2.90
502 503 6.123045 TCTCAGTCGATACTATACCCATGA 57.877 41.667 0.00 0.00 33.48 3.07
503 504 7.397892 AATCTCAGTCGATACTATACCCATG 57.602 40.000 0.00 0.00 33.48 3.66
504 505 7.148222 CGAAATCTCAGTCGATACTATACCCAT 60.148 40.741 0.00 0.00 39.64 4.00
505 506 6.148976 CGAAATCTCAGTCGATACTATACCCA 59.851 42.308 0.00 0.00 39.64 4.51
506 507 6.370994 TCGAAATCTCAGTCGATACTATACCC 59.629 42.308 0.00 0.00 41.13 3.69
507 508 7.118101 AGTCGAAATCTCAGTCGATACTATACC 59.882 40.741 0.00 0.00 46.91 2.73
508 509 8.020861 AGTCGAAATCTCAGTCGATACTATAC 57.979 38.462 0.00 0.00 46.91 1.47
509 510 9.702494 TTAGTCGAAATCTCAGTCGATACTATA 57.298 33.333 0.00 0.00 46.91 1.31
510 511 8.604640 TTAGTCGAAATCTCAGTCGATACTAT 57.395 34.615 0.00 0.00 46.91 2.12
511 512 7.924947 TCTTAGTCGAAATCTCAGTCGATACTA 59.075 37.037 0.00 0.00 46.91 1.82
512 513 6.762187 TCTTAGTCGAAATCTCAGTCGATACT 59.238 38.462 0.00 0.00 46.91 2.12
513 514 6.847289 GTCTTAGTCGAAATCTCAGTCGATAC 59.153 42.308 0.00 0.00 46.91 2.24
514 515 6.762187 AGTCTTAGTCGAAATCTCAGTCGATA 59.238 38.462 0.00 0.00 46.91 2.92
515 516 5.587043 AGTCTTAGTCGAAATCTCAGTCGAT 59.413 40.000 0.00 0.00 46.91 3.59
516 517 4.936411 AGTCTTAGTCGAAATCTCAGTCGA 59.064 41.667 0.00 0.00 43.61 4.20
517 518 5.224562 AGTCTTAGTCGAAATCTCAGTCG 57.775 43.478 0.00 0.00 38.62 4.18
518 519 6.689669 GCTAAGTCTTAGTCGAAATCTCAGTC 59.310 42.308 18.72 0.00 35.66 3.51
519 520 6.151312 TGCTAAGTCTTAGTCGAAATCTCAGT 59.849 38.462 18.72 0.00 35.66 3.41
520 521 6.556212 TGCTAAGTCTTAGTCGAAATCTCAG 58.444 40.000 18.72 0.00 35.66 3.35
521 522 6.510879 TGCTAAGTCTTAGTCGAAATCTCA 57.489 37.500 18.72 4.58 35.66 3.27
522 523 7.251994 TCTTGCTAAGTCTTAGTCGAAATCTC 58.748 38.462 18.72 2.30 35.66 2.75
523 524 7.159322 TCTTGCTAAGTCTTAGTCGAAATCT 57.841 36.000 18.72 0.00 35.66 2.40
524 525 7.168469 GGATCTTGCTAAGTCTTAGTCGAAATC 59.832 40.741 18.72 14.47 35.66 2.17
525 526 6.981559 GGATCTTGCTAAGTCTTAGTCGAAAT 59.018 38.462 18.72 8.32 35.66 2.17
526 527 6.153000 AGGATCTTGCTAAGTCTTAGTCGAAA 59.847 38.462 18.72 9.21 35.66 3.46
527 528 5.652891 AGGATCTTGCTAAGTCTTAGTCGAA 59.347 40.000 18.72 9.86 35.66 3.71
528 529 5.194432 AGGATCTTGCTAAGTCTTAGTCGA 58.806 41.667 18.72 13.23 35.66 4.20
529 530 5.508200 AGGATCTTGCTAAGTCTTAGTCG 57.492 43.478 18.72 9.18 35.66 4.18
530 531 7.576861 ACTAGGATCTTGCTAAGTCTTAGTC 57.423 40.000 18.72 12.37 32.02 2.59
531 532 7.964666 AACTAGGATCTTGCTAAGTCTTAGT 57.035 36.000 18.72 1.04 35.32 2.24
532 533 9.660180 AAAAACTAGGATCTTGCTAAGTCTTAG 57.340 33.333 14.35 14.35 36.32 2.18
607 608 7.565680 TCAACTACTCCTTTCCTTCCATAATC 58.434 38.462 0.00 0.00 0.00 1.75
621 628 2.269940 ACAGCCCAATCAACTACTCCT 58.730 47.619 0.00 0.00 0.00 3.69
679 697 1.286880 GAGCACCGCAAAACAGCAT 59.713 52.632 0.00 0.00 0.00 3.79
721 743 0.339859 ACTCTGTATCCCTGCTCCCA 59.660 55.000 0.00 0.00 0.00 4.37
723 745 1.139853 CCAACTCTGTATCCCTGCTCC 59.860 57.143 0.00 0.00 0.00 4.70
727 749 1.879575 TCCCCAACTCTGTATCCCTG 58.120 55.000 0.00 0.00 0.00 4.45
729 751 2.092375 CCTTTCCCCAACTCTGTATCCC 60.092 54.545 0.00 0.00 0.00 3.85
775 936 2.047655 GCCGTGGATGGTGACGAA 60.048 61.111 0.00 0.00 37.81 3.85
862 1023 4.084171 CGATATGTACTAGCGTTCCGAGAA 60.084 45.833 0.00 0.00 34.59 2.87
901 1080 4.399395 TGGCTGGCTGGCTCTTCG 62.399 66.667 18.27 0.00 42.34 3.79
902 1081 2.438075 CTGGCTGGCTGGCTCTTC 60.438 66.667 18.27 0.00 42.34 2.87
903 1082 4.737177 GCTGGCTGGCTGGCTCTT 62.737 66.667 18.27 0.00 42.34 2.85
1251 1453 2.614013 TCCTTCTTGCCCCCTCCC 60.614 66.667 0.00 0.00 0.00 4.30
1377 1579 3.959991 GAGCTTGGAGTGGACGCCC 62.960 68.421 0.00 0.00 34.71 6.13
1451 1653 8.264347 TGGATTTGAATACTGAATGCTAGTACA 58.736 33.333 0.00 0.00 33.80 2.90
1452 1654 8.662781 TGGATTTGAATACTGAATGCTAGTAC 57.337 34.615 0.00 0.00 33.80 2.73
1455 1657 8.013947 CGAATGGATTTGAATACTGAATGCTAG 58.986 37.037 0.00 0.00 0.00 3.42
1474 1676 1.418264 TCAAGGTGTGGAACGAATGGA 59.582 47.619 0.00 0.00 42.39 3.41
1476 1678 2.031157 GGTTCAAGGTGTGGAACGAATG 60.031 50.000 0.00 0.00 43.29 2.67
1477 1679 2.227194 GGTTCAAGGTGTGGAACGAAT 58.773 47.619 0.00 0.00 43.29 3.34
1481 1683 1.318576 CTGGGTTCAAGGTGTGGAAC 58.681 55.000 0.00 0.00 42.00 3.62
1484 1686 2.504367 CTAACTGGGTTCAAGGTGTGG 58.496 52.381 0.00 0.00 0.00 4.17
1491 1693 0.476338 TGGCTGCTAACTGGGTTCAA 59.524 50.000 0.00 0.00 0.00 2.69
1496 1698 2.290323 ACTAACTTGGCTGCTAACTGGG 60.290 50.000 0.00 0.00 0.00 4.45
1497 1699 3.003480 GACTAACTTGGCTGCTAACTGG 58.997 50.000 0.00 0.00 0.00 4.00
1524 1726 7.524717 AAATTTACCAATACAGCAGAGTTGT 57.475 32.000 0.00 0.00 0.00 3.32
1584 1786 7.428826 GCCAATAATTTAACTAAGCAGCATCT 58.571 34.615 0.00 0.00 0.00 2.90
1609 1811 5.799936 ACAATTCAAAAGTCAACACTCAACG 59.200 36.000 0.00 0.00 29.93 4.10
1679 1881 5.180117 CAGCCAGTATATATCAGTGCAAACC 59.820 44.000 0.00 0.00 0.00 3.27
1746 1948 1.761449 TTTGACTGTGAGGCTGCAAA 58.239 45.000 0.50 0.00 0.00 3.68
1760 1962 7.448748 ACTTGAAACACCCACTATATTTGAC 57.551 36.000 0.00 0.00 0.00 3.18
1762 1964 7.040062 TGGAACTTGAAACACCCACTATATTTG 60.040 37.037 0.00 0.00 0.00 2.32
1933 2135 4.412796 TCTGGCATAAGGAAGACAGATG 57.587 45.455 0.00 0.00 30.75 2.90
1940 2142 2.590821 CCCCAATCTGGCATAAGGAAG 58.409 52.381 0.00 0.00 35.79 3.46
1995 2197 2.033299 ACACACTTTCATCACCAAAGCG 59.967 45.455 0.00 0.00 34.67 4.68
2036 2238 3.302805 CGCTACTAGACAGTGTCTCATCG 60.303 52.174 28.70 19.96 42.40 3.84
2040 2242 2.029486 CGTCGCTACTAGACAGTGTCTC 59.971 54.545 28.70 13.33 42.40 3.36
2099 2301 1.856265 GAGCTTCAACCAGGCAACCG 61.856 60.000 0.00 0.00 37.17 4.44
2418 2620 1.528309 CGCAACCCTTGTTCCAGGT 60.528 57.895 0.00 0.00 34.60 4.00
2489 2691 3.181510 GCCAACTAAGCATACCAAAGTCG 60.182 47.826 0.00 0.00 0.00 4.18
2594 2796 0.809385 CTGCAGTGAAGGAATGGCTG 59.191 55.000 5.25 0.00 0.00 4.85
2648 2852 5.467705 AGTACCGTGTAGACAGTGAAATTC 58.532 41.667 0.00 0.00 0.00 2.17
2719 3182 6.127925 TGCCAACTAGCACAAGAAAATCTATG 60.128 38.462 0.00 0.00 38.00 2.23
2768 3231 5.514169 TCATTCTAATGCCCATGTAAACCA 58.486 37.500 0.00 0.00 36.36 3.67
2780 3250 5.218139 GCTAGCACCAATTCATTCTAATGC 58.782 41.667 10.63 0.00 36.36 3.56
2793 3263 5.070001 ACAAGAGTAAAATGCTAGCACCAA 58.930 37.500 22.07 2.93 0.00 3.67
2837 3307 3.619419 ACCAAAAGCCAAAACTTGCAAT 58.381 36.364 0.00 0.00 0.00 3.56
2874 3344 6.463360 TCCTGGAAACCAAGCAAAATAAATC 58.537 36.000 0.00 0.00 30.80 2.17
2875 3345 6.432403 TCCTGGAAACCAAGCAAAATAAAT 57.568 33.333 0.00 0.00 30.80 1.40
2879 3349 3.181455 GGTTCCTGGAAACCAAGCAAAAT 60.181 43.478 13.66 0.00 46.62 1.82
2882 3352 1.408969 GGTTCCTGGAAACCAAGCAA 58.591 50.000 13.66 0.00 46.62 3.91
2889 3359 0.402121 AGAGGCTGGTTCCTGGAAAC 59.598 55.000 17.63 17.63 36.38 2.78
2897 3367 2.031163 ACACGCAGAGGCTGGTTC 59.969 61.111 0.00 0.00 38.10 3.62
3017 3487 1.065491 TCTTGAATGATGACCACCCCG 60.065 52.381 0.00 0.00 0.00 5.73
3053 3523 2.345760 GCAACCCCCAGCATCTGTG 61.346 63.158 0.00 0.00 0.00 3.66
3134 3604 2.745884 CGATGAAGCAACGCCCCA 60.746 61.111 0.00 0.00 0.00 4.96
3137 3607 1.019278 TTCTCCGATGAAGCAACGCC 61.019 55.000 0.00 0.00 0.00 5.68
3162 3632 1.135859 CCAACTTGCATCGACAGCTTC 60.136 52.381 12.28 0.00 0.00 3.86
3170 3640 2.743664 TGATGAGTTCCAACTTGCATCG 59.256 45.455 12.83 0.00 40.43 3.84
3246 3716 3.197333 ACTCACTCTTGCATGCTATGACT 59.803 43.478 20.33 0.00 0.00 3.41
3301 3771 3.367395 GGCAGGCCAATTTTAGTTCAGAC 60.367 47.826 5.01 0.00 35.81 3.51
3436 3932 0.453950 CGGTGTTCGTCGATCTCGTT 60.454 55.000 0.00 0.00 40.80 3.85
3492 3988 2.028130 ACAAACCATCAAAACAGCCGA 58.972 42.857 0.00 0.00 0.00 5.54
3493 3989 2.507339 ACAAACCATCAAAACAGCCG 57.493 45.000 0.00 0.00 0.00 5.52
3518 4014 1.732117 TGTACCCGAGGGAAAAAGGA 58.268 50.000 16.26 0.00 38.96 3.36
3520 4016 3.072211 GAGTTGTACCCGAGGGAAAAAG 58.928 50.000 16.26 0.00 38.96 2.27
3534 4030 2.167693 CCCAAGGAGCGTATGAGTTGTA 59.832 50.000 0.00 0.00 0.00 2.41
3536 4032 1.066143 ACCCAAGGAGCGTATGAGTTG 60.066 52.381 0.00 0.00 0.00 3.16
3571 4067 7.532571 CAAACTGCTCATGACTGATGATTTAA 58.467 34.615 0.00 0.00 40.46 1.52
3628 4124 8.856103 ACAATGCATCATGAGATCATTTTATCA 58.144 29.630 0.00 0.00 33.59 2.15
3699 4201 1.537202 AGGAAACGCAAGCATCAAGAC 59.463 47.619 0.00 0.00 45.62 3.01
3702 4204 1.602668 GCAAGGAAACGCAAGCATCAA 60.603 47.619 0.00 0.00 45.62 2.57
3703 4205 0.039256 GCAAGGAAACGCAAGCATCA 60.039 50.000 0.00 0.00 45.62 3.07
3743 4245 8.710239 ACCCAAATGTTAAAATGTTTCCTACTT 58.290 29.630 0.00 0.00 0.00 2.24
3744 4246 8.257602 ACCCAAATGTTAAAATGTTTCCTACT 57.742 30.769 0.00 0.00 0.00 2.57
3758 4260 9.841295 GGAGTGATACTTTATACCCAAATGTTA 57.159 33.333 0.00 0.00 0.00 2.41
3759 4261 8.333235 TGGAGTGATACTTTATACCCAAATGTT 58.667 33.333 0.00 0.00 0.00 2.71
3760 4262 7.867921 TGGAGTGATACTTTATACCCAAATGT 58.132 34.615 0.00 0.00 0.00 2.71
3761 4263 8.786898 CATGGAGTGATACTTTATACCCAAATG 58.213 37.037 0.00 0.00 0.00 2.32
3762 4264 8.502738 ACATGGAGTGATACTTTATACCCAAAT 58.497 33.333 0.00 0.00 0.00 2.32
3763 4265 7.867921 ACATGGAGTGATACTTTATACCCAAA 58.132 34.615 0.00 0.00 0.00 3.28
3764 4266 7.446106 ACATGGAGTGATACTTTATACCCAA 57.554 36.000 0.00 0.00 0.00 4.12
3765 4267 8.736097 ATACATGGAGTGATACTTTATACCCA 57.264 34.615 0.00 0.00 0.00 4.51
3789 4291 8.543774 GTGGAGTGGACAATGGAGAATATATAT 58.456 37.037 0.00 0.00 0.00 0.86
3848 4353 0.662619 TGCTACTTGTGCTGTTGTGC 59.337 50.000 0.00 0.00 0.00 4.57
4090 4600 0.251386 AGAGCTTCAGGACGGTCTCA 60.251 55.000 8.23 0.00 33.04 3.27


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

AutoCloner maintained by Alex Coulton.