Multiple sequence alignment - TraesCS5B01G497000

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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 TraesCS5B01G497000 chr5B 100.000 4692 0 0 1 4692 664017849 664022540 0.000000e+00 8665
1 TraesCS5B01G497000 chr5B 88.537 410 31 9 910 1308 678674102 678674506 2.540000e-132 483
2 TraesCS5B01G497000 chr5B 95.906 171 7 0 154 324 701551646 701551816 1.290000e-70 278
3 TraesCS5B01G497000 chr5D 92.737 4351 174 66 426 4692 527494631 527498923 0.000000e+00 6154
4 TraesCS5B01G497000 chr5D 93.678 174 10 1 147 319 199125 198952 4.660000e-65 259
5 TraesCS5B01G497000 chr5A 91.475 3519 197 35 536 4005 654613969 654617433 0.000000e+00 4741
6 TraesCS5B01G497000 chr5A 95.022 683 28 4 4010 4692 654617411 654618087 0.000000e+00 1068
7 TraesCS5B01G497000 chr5A 93.671 158 8 1 1 158 654613310 654613465 7.850000e-58 235
8 TraesCS5B01G497000 chr2A 87.669 519 34 13 910 1425 97847986 97848477 1.130000e-160 577
9 TraesCS5B01G497000 chr6B 92.732 399 17 3 1030 1425 173904640 173904251 2.450000e-157 566
10 TraesCS5B01G497000 chr7B 96.407 167 6 0 153 319 497576790 497576624 4.620000e-70 276
11 TraesCS5B01G497000 chr7B 95.294 170 6 2 157 324 191180403 191180234 7.740000e-68 268
12 TraesCS5B01G497000 chr2B 96.933 163 5 0 157 319 664125038 664125200 1.660000e-69 274
13 TraesCS5B01G497000 chr4B 95.808 167 7 0 153 319 431792150 431792316 2.150000e-68 270
14 TraesCS5B01G497000 chr7D 95.783 166 7 0 157 322 416628415 416628250 7.740000e-68 268
15 TraesCS5B01G497000 chr1B 94.675 169 9 0 154 322 561836563 561836395 3.600000e-66 263
16 TraesCS5B01G497000 chr6D 94.152 171 10 0 154 324 359354944 359354774 1.300000e-65 261


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 TraesCS5B01G497000 chr5B 664017849 664022540 4691 False 8665.000000 8665 100.000000 1 4692 1 chr5B.!!$F1 4691
1 TraesCS5B01G497000 chr5D 527494631 527498923 4292 False 6154.000000 6154 92.737000 426 4692 1 chr5D.!!$F1 4266
2 TraesCS5B01G497000 chr5A 654613310 654618087 4777 False 2014.666667 4741 93.389333 1 4692 3 chr5A.!!$F1 4691

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
855 1117 0.109272 TCTTCGGTGACTGACGATGC 60.109 55.0 0.00 0.00 39.06 3.91 F
1478 1755 0.988063 GCCAAGAGGAGGAAGAAGGT 59.012 55.0 0.00 0.00 36.89 3.50 F
1850 2130 0.249911 GTGACGGCTCAGTTGGAGTT 60.250 55.0 0.00 0.00 45.88 3.01 F
1986 2266 0.718904 TGAAATCGGTCGATGCAACG 59.281 50.0 10.48 10.48 34.70 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1954 0.999406 CGTCATACAGAAACCTGCCG 59.001 55.000 0.0 0.0 35.09 5.69 R
2289 2569 1.008938 ACTAGCAGATCCTTCCCCTGT 59.991 52.381 0.0 0.0 0.00 4.00 R
3518 3804 2.129555 ATCCAGTTTGGCTGCTCCGT 62.130 55.000 0.0 0.0 43.71 4.69 R
3985 4300 1.980765 TCCACAGATCAAGAAGCACCT 59.019 47.619 0.0 0.0 0.00 4.00 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
42 43 7.251704 CCAGATGTTGTAATTTAGCTGGTAG 57.748 40.000 0.00 0.00 37.48 3.18
57 58 1.221021 GTAGAGCTTTCCGGTGGGG 59.779 63.158 0.00 0.00 37.02 4.96
93 94 5.445806 GCGTTTTGCAGAATGTTTTTGTTCT 60.446 36.000 10.57 0.00 45.45 3.01
95 96 6.462323 CGTTTTGCAGAATGTTTTTGTTCTTG 59.538 34.615 1.05 0.00 39.31 3.02
118 119 1.345089 TCGTAGGGCTGCAGTTTGTTA 59.655 47.619 16.64 0.00 0.00 2.41
129 130 5.278463 GCTGCAGTTTGTTATGGAAAGAGAA 60.278 40.000 16.64 0.00 0.00 2.87
130 131 6.317789 TGCAGTTTGTTATGGAAAGAGAAG 57.682 37.500 0.00 0.00 0.00 2.85
162 354 1.404315 CGTGTGCTTCCTTCTACTCCC 60.404 57.143 0.00 0.00 0.00 4.30
168 360 2.458620 CTTCCTTCTACTCCCTCCGTT 58.541 52.381 0.00 0.00 0.00 4.44
170 362 1.112950 CCTTCTACTCCCTCCGTTCC 58.887 60.000 0.00 0.00 0.00 3.62
171 363 1.342175 CCTTCTACTCCCTCCGTTCCT 60.342 57.143 0.00 0.00 0.00 3.36
177 369 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
178 370 7.095183 TCTACTCCCTCCGTTCCTAAATATA 57.905 40.000 0.00 0.00 0.00 0.86
179 371 7.529555 TCTACTCCCTCCGTTCCTAAATATAA 58.470 38.462 0.00 0.00 0.00 0.98
182 374 6.041751 ACTCCCTCCGTTCCTAAATATAAGTG 59.958 42.308 0.00 0.00 0.00 3.16
185 377 7.052248 CCCTCCGTTCCTAAATATAAGTGTTT 58.948 38.462 0.00 0.00 0.00 2.83
187 379 7.551617 CCTCCGTTCCTAAATATAAGTGTTTGT 59.448 37.037 0.00 0.00 0.00 2.83
189 381 9.590451 TCCGTTCCTAAATATAAGTGTTTGTAG 57.410 33.333 0.00 0.00 0.00 2.74
190 382 9.590451 CCGTTCCTAAATATAAGTGTTTGTAGA 57.410 33.333 0.00 0.00 0.00 2.59
202 394 6.287589 AGTGTTTGTAGAGATTCCACTAGG 57.712 41.667 0.00 0.00 30.45 3.02
203 395 4.870991 GTGTTTGTAGAGATTCCACTAGGC 59.129 45.833 0.00 0.00 33.74 3.93
204 396 4.113354 GTTTGTAGAGATTCCACTAGGCG 58.887 47.826 0.00 0.00 33.74 5.52
205 397 2.307768 TGTAGAGATTCCACTAGGCGG 58.692 52.381 0.00 0.00 33.74 6.13
206 398 2.092049 TGTAGAGATTCCACTAGGCGGA 60.092 50.000 0.00 0.00 33.74 5.54
207 399 1.404843 AGAGATTCCACTAGGCGGAC 58.595 55.000 2.76 0.00 30.29 4.79
208 400 1.063567 AGAGATTCCACTAGGCGGACT 60.064 52.381 2.76 0.00 30.29 3.85
209 401 2.175069 AGAGATTCCACTAGGCGGACTA 59.825 50.000 2.76 0.00 30.29 2.59
210 402 2.293955 GAGATTCCACTAGGCGGACTAC 59.706 54.545 2.76 0.00 30.29 2.73
211 403 2.029623 GATTCCACTAGGCGGACTACA 58.970 52.381 2.76 0.00 30.29 2.74
212 404 2.154567 TTCCACTAGGCGGACTACAT 57.845 50.000 2.76 0.00 30.29 2.29
213 405 3.301794 TTCCACTAGGCGGACTACATA 57.698 47.619 2.76 0.00 30.29 2.29
214 406 2.579873 TCCACTAGGCGGACTACATAC 58.420 52.381 0.00 0.00 33.74 2.39
215 407 1.266175 CCACTAGGCGGACTACATACG 59.734 57.143 0.00 0.00 0.00 3.06
216 408 1.266175 CACTAGGCGGACTACATACGG 59.734 57.143 0.00 0.00 0.00 4.02
217 409 1.141657 ACTAGGCGGACTACATACGGA 59.858 52.381 0.00 0.00 0.00 4.69
218 410 1.805345 CTAGGCGGACTACATACGGAG 59.195 57.143 0.00 0.00 0.00 4.63
219 411 1.007618 GGCGGACTACATACGGAGC 60.008 63.158 0.00 0.00 0.00 4.70
226 418 4.439057 GGACTACATACGGAGCAAAATGA 58.561 43.478 0.00 0.00 0.00 2.57
230 422 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
233 425 7.566760 ACATACGGAGCAAAATGAATGAATA 57.433 32.000 0.00 0.00 0.00 1.75
238 430 8.856490 ACGGAGCAAAATGAATGAATATAAAC 57.144 30.769 0.00 0.00 0.00 2.01
239 431 8.686334 ACGGAGCAAAATGAATGAATATAAACT 58.314 29.630 0.00 0.00 0.00 2.66
263 455 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
266 458 7.987268 AAATGCATCTATATACATCCGTACG 57.013 36.000 8.69 8.69 0.00 3.67
267 459 4.916870 TGCATCTATATACATCCGTACGC 58.083 43.478 10.49 0.00 0.00 4.42
268 460 3.966844 GCATCTATATACATCCGTACGCG 59.033 47.826 10.49 3.53 37.95 6.01
280 472 2.473530 CGTACGCGGTTTATAGTGGA 57.526 50.000 12.47 0.00 0.00 4.02
284 476 3.814005 ACGCGGTTTATAGTGGAATCT 57.186 42.857 12.47 0.00 0.00 2.40
287 479 5.663456 ACGCGGTTTATAGTGGAATCTTTA 58.337 37.500 12.47 0.00 0.00 1.85
291 483 7.413219 CGCGGTTTATAGTGGAATCTTTACAAA 60.413 37.037 0.00 0.00 0.00 2.83
322 514 2.433662 AGGAACGGAGGGAGTAGTAC 57.566 55.000 0.00 0.00 0.00 2.73
323 515 1.637553 AGGAACGGAGGGAGTAGTACA 59.362 52.381 2.52 0.00 0.00 2.90
324 516 2.022934 GGAACGGAGGGAGTAGTACAG 58.977 57.143 2.52 0.00 0.00 2.74
325 517 2.620108 GGAACGGAGGGAGTAGTACAGT 60.620 54.545 2.52 0.00 0.00 3.55
327 519 3.166560 ACGGAGGGAGTAGTACAGTTT 57.833 47.619 2.52 0.00 0.00 2.66
328 520 3.504375 ACGGAGGGAGTAGTACAGTTTT 58.496 45.455 2.52 0.00 0.00 2.43
330 522 4.460731 ACGGAGGGAGTAGTACAGTTTTAC 59.539 45.833 2.52 0.00 0.00 2.01
331 523 4.704057 CGGAGGGAGTAGTACAGTTTTACT 59.296 45.833 2.52 0.00 36.28 2.24
332 524 5.184671 CGGAGGGAGTAGTACAGTTTTACTT 59.815 44.000 2.52 0.00 34.10 2.24
333 525 6.624642 CGGAGGGAGTAGTACAGTTTTACTTC 60.625 46.154 2.52 0.00 34.10 3.01
336 528 7.668492 AGGGAGTAGTACAGTTTTACTTCAAG 58.332 38.462 2.52 0.00 34.10 3.02
337 529 7.289549 AGGGAGTAGTACAGTTTTACTTCAAGT 59.710 37.037 2.52 0.00 34.10 3.16
338 530 7.930325 GGGAGTAGTACAGTTTTACTTCAAGTT 59.070 37.037 0.00 0.00 34.10 2.66
339 531 9.322773 GGAGTAGTACAGTTTTACTTCAAGTTT 57.677 33.333 0.00 0.00 34.10 2.66
344 536 8.248253 AGTACAGTTTTACTTCAAGTTTTTGGG 58.752 33.333 0.00 0.00 34.97 4.12
345 537 6.403049 ACAGTTTTACTTCAAGTTTTTGGGG 58.597 36.000 0.00 0.00 34.97 4.96
346 538 6.014070 ACAGTTTTACTTCAAGTTTTTGGGGT 60.014 34.615 0.00 0.00 34.97 4.95
347 539 6.876789 CAGTTTTACTTCAAGTTTTTGGGGTT 59.123 34.615 0.00 0.00 34.97 4.11
348 540 6.876789 AGTTTTACTTCAAGTTTTTGGGGTTG 59.123 34.615 0.00 0.00 34.97 3.77
349 541 6.607004 TTTACTTCAAGTTTTTGGGGTTGA 57.393 33.333 0.00 0.00 34.97 3.18
351 543 5.491323 ACTTCAAGTTTTTGGGGTTGAAA 57.509 34.783 0.00 0.00 38.19 2.69
353 545 5.247337 ACTTCAAGTTTTTGGGGTTGAAAGA 59.753 36.000 0.00 0.00 38.19 2.52
354 546 5.948742 TCAAGTTTTTGGGGTTGAAAGAT 57.051 34.783 0.00 0.00 34.97 2.40
355 547 7.125053 ACTTCAAGTTTTTGGGGTTGAAAGATA 59.875 33.333 0.00 0.00 38.19 1.98
356 548 6.811954 TCAAGTTTTTGGGGTTGAAAGATAC 58.188 36.000 0.00 0.00 34.97 2.24
357 549 6.609616 TCAAGTTTTTGGGGTTGAAAGATACT 59.390 34.615 0.00 0.00 34.97 2.12
358 550 6.405278 AGTTTTTGGGGTTGAAAGATACTG 57.595 37.500 0.00 0.00 0.00 2.74
359 551 6.133356 AGTTTTTGGGGTTGAAAGATACTGA 58.867 36.000 0.00 0.00 0.00 3.41
360 552 6.609616 AGTTTTTGGGGTTGAAAGATACTGAA 59.390 34.615 0.00 0.00 0.00 3.02
361 553 6.399639 TTTTGGGGTTGAAAGATACTGAAC 57.600 37.500 0.00 0.00 0.00 3.18
362 554 4.715534 TGGGGTTGAAAGATACTGAACA 57.284 40.909 0.00 0.00 0.00 3.18
363 555 5.255397 TGGGGTTGAAAGATACTGAACAT 57.745 39.130 0.00 0.00 0.00 2.71
364 556 5.009631 TGGGGTTGAAAGATACTGAACATG 58.990 41.667 0.00 0.00 0.00 3.21
365 557 5.010282 GGGGTTGAAAGATACTGAACATGT 58.990 41.667 0.00 0.00 0.00 3.21
366 558 5.123979 GGGGTTGAAAGATACTGAACATGTC 59.876 44.000 0.00 0.00 0.00 3.06
367 559 5.940470 GGGTTGAAAGATACTGAACATGTCT 59.060 40.000 0.00 0.00 0.00 3.41
368 560 6.128172 GGGTTGAAAGATACTGAACATGTCTG 60.128 42.308 0.00 0.00 0.00 3.51
369 561 6.650807 GGTTGAAAGATACTGAACATGTCTGA 59.349 38.462 0.00 0.00 0.00 3.27
370 562 7.173218 GGTTGAAAGATACTGAACATGTCTGAA 59.827 37.037 0.00 0.00 0.00 3.02
371 563 8.725148 GTTGAAAGATACTGAACATGTCTGAAT 58.275 33.333 0.00 0.00 0.00 2.57
372 564 8.853077 TGAAAGATACTGAACATGTCTGAATT 57.147 30.769 0.00 0.00 0.00 2.17
373 565 8.939929 TGAAAGATACTGAACATGTCTGAATTC 58.060 33.333 0.00 0.00 0.00 2.17
374 566 9.160496 GAAAGATACTGAACATGTCTGAATTCT 57.840 33.333 7.05 0.00 0.00 2.40
375 567 9.512588 AAAGATACTGAACATGTCTGAATTCTT 57.487 29.630 7.05 2.21 0.00 2.52
376 568 9.512588 AAGATACTGAACATGTCTGAATTCTTT 57.487 29.630 7.05 0.00 0.00 2.52
377 569 9.512588 AGATACTGAACATGTCTGAATTCTTTT 57.487 29.630 7.05 0.00 0.00 2.27
378 570 9.766277 GATACTGAACATGTCTGAATTCTTTTC 57.234 33.333 7.05 0.00 0.00 2.29
379 571 7.814264 ACTGAACATGTCTGAATTCTTTTCT 57.186 32.000 7.05 0.00 0.00 2.52
380 572 7.869800 ACTGAACATGTCTGAATTCTTTTCTC 58.130 34.615 7.05 0.00 0.00 2.87
381 573 7.718753 ACTGAACATGTCTGAATTCTTTTCTCT 59.281 33.333 7.05 0.00 0.00 3.10
382 574 8.455903 TGAACATGTCTGAATTCTTTTCTCTT 57.544 30.769 7.05 0.00 0.00 2.85
383 575 8.347771 TGAACATGTCTGAATTCTTTTCTCTTG 58.652 33.333 7.05 3.46 0.00 3.02
384 576 8.455903 AACATGTCTGAATTCTTTTCTCTTGA 57.544 30.769 7.05 0.00 0.00 3.02
385 577 8.097078 ACATGTCTGAATTCTTTTCTCTTGAG 57.903 34.615 7.05 0.00 0.00 3.02
386 578 7.935755 ACATGTCTGAATTCTTTTCTCTTGAGA 59.064 33.333 7.05 0.00 0.00 3.27
387 579 7.721286 TGTCTGAATTCTTTTCTCTTGAGAC 57.279 36.000 7.05 7.51 0.00 3.36
388 580 7.275183 TGTCTGAATTCTTTTCTCTTGAGACA 58.725 34.615 7.05 9.88 35.06 3.41
389 581 7.935755 TGTCTGAATTCTTTTCTCTTGAGACAT 59.064 33.333 7.05 0.00 33.08 3.06
390 582 8.782144 GTCTGAATTCTTTTCTCTTGAGACATT 58.218 33.333 7.05 0.00 0.00 2.71
391 583 8.781196 TCTGAATTCTTTTCTCTTGAGACATTG 58.219 33.333 7.05 0.00 0.00 2.82
392 584 7.879070 TGAATTCTTTTCTCTTGAGACATTGG 58.121 34.615 7.05 0.00 0.00 3.16
393 585 7.720957 TGAATTCTTTTCTCTTGAGACATTGGA 59.279 33.333 7.05 0.00 0.00 3.53
394 586 6.867662 TTCTTTTCTCTTGAGACATTGGAC 57.132 37.500 0.00 0.00 0.00 4.02
395 587 5.928976 TCTTTTCTCTTGAGACATTGGACA 58.071 37.500 0.00 0.00 0.00 4.02
396 588 6.537355 TCTTTTCTCTTGAGACATTGGACAT 58.463 36.000 0.00 0.00 0.00 3.06
397 589 6.429078 TCTTTTCTCTTGAGACATTGGACATG 59.571 38.462 0.00 0.00 0.00 3.21
398 590 3.603532 TCTCTTGAGACATTGGACATGC 58.396 45.455 0.00 0.00 0.00 4.06
399 591 2.681848 CTCTTGAGACATTGGACATGCC 59.318 50.000 0.00 0.00 37.10 4.40
400 592 2.306805 TCTTGAGACATTGGACATGCCT 59.693 45.455 7.54 0.00 37.63 4.75
401 593 2.118313 TGAGACATTGGACATGCCTG 57.882 50.000 7.54 2.02 37.63 4.85
402 594 1.629861 TGAGACATTGGACATGCCTGA 59.370 47.619 0.00 0.00 37.63 3.86
410 602 2.942804 TGGACATGCCTGAAACTGAAA 58.057 42.857 0.00 0.00 37.63 2.69
413 605 3.190118 GGACATGCCTGAAACTGAAAGAG 59.810 47.826 0.00 0.00 37.43 2.85
435 639 3.759086 GAGAGGGAAGGATTTTGTTCACC 59.241 47.826 0.00 0.00 0.00 4.02
452 656 2.696759 CCAACGAACCGGCCCAATC 61.697 63.158 0.00 0.00 0.00 2.67
508 716 3.741476 GCCGAGCCAACCAAGCAG 61.741 66.667 0.00 0.00 0.00 4.24
509 719 3.741476 CCGAGCCAACCAAGCAGC 61.741 66.667 0.00 0.00 0.00 5.25
540 773 6.059484 CGAGAAGAGAGAGATTAACCCTAGT 58.941 44.000 0.00 0.00 0.00 2.57
543 776 5.735733 AGAGAGAGATTAACCCTAGTCCA 57.264 43.478 0.00 0.00 0.00 4.02
545 778 6.311735 AGAGAGAGATTAACCCTAGTCCATC 58.688 44.000 0.00 0.00 0.00 3.51
572 805 2.434359 GGAACCGAACCGCTCCTG 60.434 66.667 0.00 0.00 0.00 3.86
574 807 1.301479 GAACCGAACCGCTCCTGTT 60.301 57.895 0.00 0.00 0.00 3.16
575 808 1.289800 GAACCGAACCGCTCCTGTTC 61.290 60.000 0.00 0.00 38.95 3.18
576 809 1.755393 AACCGAACCGCTCCTGTTCT 61.755 55.000 0.00 0.00 39.92 3.01
577 810 1.738099 CCGAACCGCTCCTGTTCTG 60.738 63.158 0.00 0.00 39.92 3.02
578 811 1.006102 CGAACCGCTCCTGTTCTGT 60.006 57.895 0.00 0.00 39.92 3.41
579 812 1.009389 CGAACCGCTCCTGTTCTGTC 61.009 60.000 0.00 0.00 39.92 3.51
580 813 0.318762 GAACCGCTCCTGTTCTGTCT 59.681 55.000 0.00 0.00 39.18 3.41
581 814 0.318762 AACCGCTCCTGTTCTGTCTC 59.681 55.000 0.00 0.00 0.00 3.36
582 815 1.216710 CCGCTCCTGTTCTGTCTCC 59.783 63.158 0.00 0.00 0.00 3.71
583 816 1.153939 CGCTCCTGTTCTGTCTCCG 60.154 63.158 0.00 0.00 0.00 4.63
585 818 1.216710 CTCCTGTTCTGTCTCCGCC 59.783 63.158 0.00 0.00 0.00 6.13
628 877 1.072159 CCCATCTCGCCCCAGATTC 59.928 63.158 0.00 0.00 30.07 2.52
683 940 1.666011 GCCGACAGACCACAGAGAA 59.334 57.895 0.00 0.00 0.00 2.87
684 941 0.667792 GCCGACAGACCACAGAGAAC 60.668 60.000 0.00 0.00 0.00 3.01
709 967 6.474140 AAAATAAACCCGGTGAGTTTTCTT 57.526 33.333 11.77 5.07 38.37 2.52
710 968 5.700722 AATAAACCCGGTGAGTTTTCTTC 57.299 39.130 11.77 0.00 38.37 2.87
711 969 1.977056 AACCCGGTGAGTTTTCTTCC 58.023 50.000 0.00 0.00 0.00 3.46
714 972 0.953960 CCGGTGAGTTTTCTTCCCCG 60.954 60.000 0.00 0.00 35.78 5.73
730 988 1.687493 CCGCTCTTCTTCTCCCCCT 60.687 63.158 0.00 0.00 0.00 4.79
734 992 0.692756 CTCTTCTTCTCCCCCTCCCC 60.693 65.000 0.00 0.00 0.00 4.81
736 994 4.798682 TCTTCTCCCCCTCCCCGC 62.799 72.222 0.00 0.00 0.00 6.13
815 1077 1.660917 GGGATTAGCTCGTCCGGAG 59.339 63.158 3.06 0.00 46.06 4.63
825 1087 0.249573 TCGTCCGGAGCGAAGTTTTT 60.250 50.000 21.48 0.00 35.28 1.94
838 1100 5.480422 AGCGAAGTTTTTGGGGATTAATTCT 59.520 36.000 0.00 0.00 0.00 2.40
855 1117 0.109272 TCTTCGGTGACTGACGATGC 60.109 55.000 0.00 0.00 39.06 3.91
975 1237 1.231928 GGAGGAGGAGGAGGAGGAC 59.768 68.421 0.00 0.00 0.00 3.85
1227 1495 2.749044 CTCATGCACCGCAGCCTT 60.749 61.111 0.00 0.00 43.65 4.35
1233 1501 3.414700 CACCGCAGCCTTGACGAC 61.415 66.667 0.00 0.00 0.00 4.34
1397 1665 4.135153 CCACGTCCTCCCGCTCAG 62.135 72.222 0.00 0.00 0.00 3.35
1478 1755 0.988063 GCCAAGAGGAGGAAGAAGGT 59.012 55.000 0.00 0.00 36.89 3.50
1483 1760 1.203237 AGAGGAGGAAGAAGGTGCTGA 60.203 52.381 0.00 0.00 0.00 4.26
1551 1831 2.188994 CAGCCTGCTACTCCTGCC 59.811 66.667 0.00 0.00 0.00 4.85
1628 1908 4.492160 TCCGTCGTCGAGGCATGC 62.492 66.667 9.90 9.90 39.71 4.06
1674 1954 2.568090 CAGGTTTGCATGGCGGTC 59.432 61.111 0.00 0.00 0.00 4.79
1677 1957 4.776647 GTTTGCATGGCGGTCGGC 62.777 66.667 10.01 10.01 42.51 5.54
1827 2107 0.320771 TTCTGAAGAAGTCGCTGGGC 60.321 55.000 0.00 0.00 0.00 5.36
1850 2130 0.249911 GTGACGGCTCAGTTGGAGTT 60.250 55.000 0.00 0.00 45.88 3.01
1867 2147 1.916181 AGTTCTACAAGGGGTCATGGG 59.084 52.381 0.00 0.00 0.00 4.00
1914 2194 2.607038 CGATGAGTGGACGACTGACAAA 60.607 50.000 0.00 0.00 33.83 2.83
1938 2218 3.812167 GCAGGACCTTGATGACCTTTTCT 60.812 47.826 0.00 0.00 0.00 2.52
1986 2266 0.718904 TGAAATCGGTCGATGCAACG 59.281 50.000 10.48 10.48 34.70 4.10
2067 2347 3.664107 TGGAGAGAAAAATGTCGTCCAG 58.336 45.455 0.00 0.00 33.19 3.86
2197 2477 1.167851 TGAAGATTTCAGCAAGGCGG 58.832 50.000 0.00 0.00 34.08 6.13
2198 2478 1.168714 GAAGATTTCAGCAAGGCGGT 58.831 50.000 0.00 0.00 0.00 5.68
2217 2497 3.679917 CGGTGGCAGTTAGTGAGATCATT 60.680 47.826 0.00 0.00 0.00 2.57
2223 2503 5.762218 GGCAGTTAGTGAGATCATTAGCAAT 59.238 40.000 0.00 0.00 0.00 3.56
2265 2545 0.945743 TGTACAGCAGTGCTCTTGCG 60.946 55.000 16.58 6.23 43.34 4.85
2283 2563 4.891627 TGCGTTGAGTTTGATGAAGAAA 57.108 36.364 0.00 0.00 0.00 2.52
2289 2569 7.571244 GCGTTGAGTTTGATGAAGAAACATCTA 60.571 37.037 0.00 0.00 44.61 1.98
2322 2602 1.930251 TGCTAGTTCCTGCAGAGACT 58.070 50.000 17.39 19.53 34.84 3.24
2340 2620 2.996621 GACTCGTGCTGCTATGAACTTT 59.003 45.455 0.00 0.00 0.00 2.66
2373 2653 6.826231 TGAAAAACATGTACAGTCTGAAGGAA 59.174 34.615 6.91 0.00 0.00 3.36
2617 2897 3.688673 AGCAGCAATCAAGAAAGAGCTAC 59.311 43.478 0.00 0.00 0.00 3.58
2682 2962 4.084265 TGGGACAAGCACATGCAG 57.916 55.556 6.64 0.70 45.16 4.41
2920 3200 5.649831 CGTACTTTACCTCCTGGTTAGTACT 59.350 44.000 22.69 0.00 46.78 2.73
2921 3201 6.823689 CGTACTTTACCTCCTGGTTAGTACTA 59.176 42.308 22.69 0.00 46.78 1.82
2922 3202 7.201652 CGTACTTTACCTCCTGGTTAGTACTAC 60.202 44.444 22.69 0.00 46.78 2.73
3350 3633 9.816354 TTAATCGATGACATGTTATTCTGAGAA 57.184 29.630 4.41 0.00 0.00 2.87
3351 3634 8.899427 AATCGATGACATGTTATTCTGAGAAT 57.101 30.769 12.86 12.86 0.00 2.40
3398 3681 5.063180 TGGATGCAACAAGTGATTTGATC 57.937 39.130 0.00 0.00 39.21 2.92
3401 3684 6.604396 TGGATGCAACAAGTGATTTGATCTAT 59.396 34.615 0.00 0.00 39.21 1.98
3402 3685 6.916387 GGATGCAACAAGTGATTTGATCTATG 59.084 38.462 0.00 0.00 39.21 2.23
3405 3688 8.510243 TGCAACAAGTGATTTGATCTATGTAT 57.490 30.769 0.00 0.00 39.21 2.29
3436 3722 2.446435 AGGCAACAATACAAGGCGAAT 58.554 42.857 0.00 0.00 41.41 3.34
3518 3804 1.112916 TGCACTGTTCTCTGGACCGA 61.113 55.000 0.00 0.00 0.00 4.69
3628 3914 5.903010 TGAAGGTACATATCCTCCTTGCTTA 59.097 40.000 0.00 0.00 39.91 3.09
3668 3954 7.312899 GGTAATGTTGAGGGTTAAACATGAAG 58.687 38.462 0.00 0.00 44.24 3.02
3756 4042 5.801350 TGACGACAAAGATGATTCCAATC 57.199 39.130 0.00 0.00 35.97 2.67
3984 4299 2.551459 GCAAGCAGCATACAAGGGATAG 59.449 50.000 0.00 0.00 44.79 2.08
3985 4300 3.745480 GCAAGCAGCATACAAGGGATAGA 60.745 47.826 0.00 0.00 44.79 1.98
3986 4301 4.063689 CAAGCAGCATACAAGGGATAGAG 58.936 47.826 0.00 0.00 0.00 2.43
3987 4302 2.636893 AGCAGCATACAAGGGATAGAGG 59.363 50.000 0.00 0.00 0.00 3.69
3988 4303 2.370189 GCAGCATACAAGGGATAGAGGT 59.630 50.000 0.00 0.00 0.00 3.85
3989 4304 3.805108 GCAGCATACAAGGGATAGAGGTG 60.805 52.174 0.00 0.00 0.00 4.00
3990 4305 2.370189 AGCATACAAGGGATAGAGGTGC 59.630 50.000 0.00 0.00 0.00 5.01
3991 4306 2.370189 GCATACAAGGGATAGAGGTGCT 59.630 50.000 0.00 0.00 0.00 4.40
3992 4307 3.181450 GCATACAAGGGATAGAGGTGCTT 60.181 47.826 0.00 0.00 0.00 3.91
3993 4308 4.636249 CATACAAGGGATAGAGGTGCTTC 58.364 47.826 0.00 0.00 0.00 3.86
3994 4309 2.839228 ACAAGGGATAGAGGTGCTTCT 58.161 47.619 0.00 0.00 0.00 2.85
3995 4310 3.185455 ACAAGGGATAGAGGTGCTTCTT 58.815 45.455 0.00 0.00 0.00 2.52
3996 4311 3.054802 ACAAGGGATAGAGGTGCTTCTTG 60.055 47.826 0.00 0.00 0.00 3.02
3997 4312 3.121929 AGGGATAGAGGTGCTTCTTGA 57.878 47.619 0.00 0.00 0.00 3.02
3998 4313 3.663198 AGGGATAGAGGTGCTTCTTGAT 58.337 45.455 0.00 0.00 0.00 2.57
3999 4314 3.645687 AGGGATAGAGGTGCTTCTTGATC 59.354 47.826 0.00 0.00 0.00 2.92
4000 4315 3.645687 GGGATAGAGGTGCTTCTTGATCT 59.354 47.826 0.00 0.00 0.00 2.75
4001 4316 4.502950 GGGATAGAGGTGCTTCTTGATCTG 60.503 50.000 0.00 0.00 0.00 2.90
4002 4317 4.100808 GGATAGAGGTGCTTCTTGATCTGT 59.899 45.833 0.00 0.00 0.00 3.41
4003 4318 3.331478 AGAGGTGCTTCTTGATCTGTG 57.669 47.619 0.00 0.00 0.00 3.66
4004 4319 2.027377 AGAGGTGCTTCTTGATCTGTGG 60.027 50.000 0.00 0.00 0.00 4.17
4005 4320 1.980765 AGGTGCTTCTTGATCTGTGGA 59.019 47.619 0.00 0.00 0.00 4.02
4006 4321 2.373169 AGGTGCTTCTTGATCTGTGGAA 59.627 45.455 0.00 0.00 0.00 3.53
4007 4322 3.149196 GGTGCTTCTTGATCTGTGGAAA 58.851 45.455 0.00 0.00 0.00 3.13
4008 4323 3.190118 GGTGCTTCTTGATCTGTGGAAAG 59.810 47.826 0.00 0.00 0.00 2.62
4009 4324 3.817647 GTGCTTCTTGATCTGTGGAAAGT 59.182 43.478 0.00 0.00 0.00 2.66
4010 4325 4.997395 GTGCTTCTTGATCTGTGGAAAGTA 59.003 41.667 0.00 0.00 0.00 2.24
4011 4326 4.997395 TGCTTCTTGATCTGTGGAAAGTAC 59.003 41.667 0.00 0.00 0.00 2.73
4046 4361 8.514330 TTGTTCTGTGGTTTAGACTTTAATGT 57.486 30.769 0.00 0.00 0.00 2.71
4072 4398 6.763355 TCTTTCAGTGCTTGAGATAGTTTCT 58.237 36.000 0.00 0.00 37.07 2.52
4191 4519 4.326504 AGTATGCAGCAGCTTTGTTTTT 57.673 36.364 0.00 0.00 42.74 1.94
4204 4532 8.910666 GCAGCTTTGTTTTTGTTTTGTTTTATT 58.089 25.926 0.00 0.00 0.00 1.40
4298 4626 5.581975 AGAAGGTAGTTGGACTAGTAGCTT 58.418 41.667 11.06 11.06 41.81 3.74
4338 4666 2.969628 AGAACACTAATCTGGAGCCG 57.030 50.000 0.00 0.00 0.00 5.52
4371 4699 0.030101 TTGTAACAAGTTGCAGCCGC 59.970 50.000 1.81 0.00 36.59 6.53
4534 4862 4.640201 CGAGGCAAAATAATCTCCTTGGAA 59.360 41.667 0.00 0.00 0.00 3.53
4599 4927 1.286570 CAGCGCCTGCATTTTGTCA 59.713 52.632 2.29 0.00 46.23 3.58
4608 4936 1.686052 TGCATTTTGTCACCTGGGAAC 59.314 47.619 0.00 0.00 0.00 3.62
4652 4980 1.482182 TCATCAGAGAATCACCCACCG 59.518 52.381 0.00 0.00 37.82 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.254590 GCTCTACCAGCTAAATTACAACATCTG 60.255 40.741 0.00 0.00 45.83 2.90
93 94 1.003839 CTGCAGCCCTACGAACCAA 60.004 57.895 0.00 0.00 0.00 3.67
95 96 0.605589 AAACTGCAGCCCTACGAACC 60.606 55.000 15.27 0.00 0.00 3.62
118 119 5.338300 GCCTTCTCTTCTCTTCTCTTTCCAT 60.338 44.000 0.00 0.00 0.00 3.41
129 130 0.037790 GCACACGCCTTCTCTTCTCT 60.038 55.000 0.00 0.00 0.00 3.10
130 131 0.037790 AGCACACGCCTTCTCTTCTC 60.038 55.000 0.00 0.00 39.83 2.87
162 354 8.488651 ACAAACACTTATATTTAGGAACGGAG 57.511 34.615 0.00 0.00 0.00 4.63
177 369 7.578955 GCCTAGTGGAATCTCTACAAACACTTA 60.579 40.741 0.00 0.00 38.50 2.24
178 370 6.702329 CCTAGTGGAATCTCTACAAACACTT 58.298 40.000 0.00 0.00 38.50 3.16
179 371 5.337652 GCCTAGTGGAATCTCTACAAACACT 60.338 44.000 0.00 0.00 40.41 3.55
182 374 4.113354 CGCCTAGTGGAATCTCTACAAAC 58.887 47.826 0.00 0.00 34.57 2.93
185 377 2.092049 TCCGCCTAGTGGAATCTCTACA 60.092 50.000 0.00 0.00 39.45 2.74
187 379 2.175069 AGTCCGCCTAGTGGAATCTCTA 59.825 50.000 0.00 0.00 44.24 2.43
189 381 1.404843 AGTCCGCCTAGTGGAATCTC 58.595 55.000 0.00 0.00 44.24 2.75
190 382 2.308690 GTAGTCCGCCTAGTGGAATCT 58.691 52.381 0.00 0.00 44.24 2.40
193 385 2.154567 ATGTAGTCCGCCTAGTGGAA 57.845 50.000 0.00 0.00 44.24 3.53
195 387 1.266175 CGTATGTAGTCCGCCTAGTGG 59.734 57.143 0.00 0.00 33.99 4.00
196 388 1.266175 CCGTATGTAGTCCGCCTAGTG 59.734 57.143 0.00 0.00 0.00 2.74
197 389 1.141657 TCCGTATGTAGTCCGCCTAGT 59.858 52.381 0.00 0.00 0.00 2.57
198 390 1.805345 CTCCGTATGTAGTCCGCCTAG 59.195 57.143 0.00 0.00 0.00 3.02
199 391 1.888215 CTCCGTATGTAGTCCGCCTA 58.112 55.000 0.00 0.00 0.00 3.93
200 392 1.453762 GCTCCGTATGTAGTCCGCCT 61.454 60.000 0.00 0.00 0.00 5.52
201 393 1.007618 GCTCCGTATGTAGTCCGCC 60.008 63.158 0.00 0.00 0.00 6.13
202 394 0.101759 TTGCTCCGTATGTAGTCCGC 59.898 55.000 0.00 0.00 0.00 5.54
203 395 2.572191 TTTGCTCCGTATGTAGTCCG 57.428 50.000 0.00 0.00 0.00 4.79
204 396 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
205 397 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
206 398 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
207 399 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
208 400 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
209 401 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
212 404 9.944663 GTTTATATTCATTCATTTTGCTCCGTA 57.055 29.630 0.00 0.00 0.00 4.02
213 405 8.686334 AGTTTATATTCATTCATTTTGCTCCGT 58.314 29.630 0.00 0.00 0.00 4.69
214 406 9.520204 AAGTTTATATTCATTCATTTTGCTCCG 57.480 29.630 0.00 0.00 0.00 4.63
246 438 3.966844 CGCGTACGGATGTATATAGATGC 59.033 47.826 18.39 0.00 34.97 3.91
261 453 2.473530 TCCACTATAAACCGCGTACG 57.526 50.000 11.84 11.84 39.67 3.67
262 454 4.614946 AGATTCCACTATAAACCGCGTAC 58.385 43.478 4.92 0.00 0.00 3.67
263 455 4.924305 AGATTCCACTATAAACCGCGTA 57.076 40.909 4.92 0.00 0.00 4.42
264 456 3.814005 AGATTCCACTATAAACCGCGT 57.186 42.857 4.92 0.00 0.00 6.01
265 457 5.521010 TGTAAAGATTCCACTATAAACCGCG 59.479 40.000 0.00 0.00 0.00 6.46
266 458 6.913873 TGTAAAGATTCCACTATAAACCGC 57.086 37.500 0.00 0.00 0.00 5.68
267 459 9.158233 TCTTTGTAAAGATTCCACTATAAACCG 57.842 33.333 3.05 0.00 39.95 4.44
275 467 9.574516 AATGTAAGTCTTTGTAAAGATTCCACT 57.425 29.630 9.98 1.06 45.83 4.00
284 476 8.776470 CCGTTCCTAAATGTAAGTCTTTGTAAA 58.224 33.333 0.00 0.00 0.00 2.01
287 479 6.527423 TCCGTTCCTAAATGTAAGTCTTTGT 58.473 36.000 0.00 0.00 0.00 2.83
291 483 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
295 487 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
296 488 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
297 489 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
298 490 3.705072 ACTACTCCCTCCGTTCCTAAATG 59.295 47.826 0.00 0.00 0.00 2.32
303 495 1.637553 TGTACTACTCCCTCCGTTCCT 59.362 52.381 0.00 0.00 0.00 3.36
304 496 2.022934 CTGTACTACTCCCTCCGTTCC 58.977 57.143 0.00 0.00 0.00 3.62
306 498 2.895242 ACTGTACTACTCCCTCCGTT 57.105 50.000 0.00 0.00 0.00 4.44
322 514 6.403049 ACCCCAAAAACTTGAAGTAAAACTG 58.597 36.000 0.00 0.00 0.00 3.16
323 515 6.614694 ACCCCAAAAACTTGAAGTAAAACT 57.385 33.333 0.00 0.00 0.00 2.66
324 516 6.874664 TCAACCCCAAAAACTTGAAGTAAAAC 59.125 34.615 0.00 0.00 0.00 2.43
325 517 7.005709 TCAACCCCAAAAACTTGAAGTAAAA 57.994 32.000 0.00 0.00 0.00 1.52
327 519 6.607004 TTCAACCCCAAAAACTTGAAGTAA 57.393 33.333 0.00 0.00 30.83 2.24
328 520 6.437793 TCTTTCAACCCCAAAAACTTGAAGTA 59.562 34.615 0.00 0.00 34.85 2.24
330 522 5.729510 TCTTTCAACCCCAAAAACTTGAAG 58.270 37.500 0.00 0.00 34.85 3.02
331 523 5.746990 TCTTTCAACCCCAAAAACTTGAA 57.253 34.783 0.00 0.00 32.16 2.69
332 524 5.948742 ATCTTTCAACCCCAAAAACTTGA 57.051 34.783 0.00 0.00 0.00 3.02
333 525 6.701400 CAGTATCTTTCAACCCCAAAAACTTG 59.299 38.462 0.00 0.00 0.00 3.16
336 528 6.399639 TCAGTATCTTTCAACCCCAAAAAC 57.600 37.500 0.00 0.00 0.00 2.43
337 529 6.381420 TGTTCAGTATCTTTCAACCCCAAAAA 59.619 34.615 0.00 0.00 0.00 1.94
338 530 5.894393 TGTTCAGTATCTTTCAACCCCAAAA 59.106 36.000 0.00 0.00 0.00 2.44
339 531 5.450453 TGTTCAGTATCTTTCAACCCCAAA 58.550 37.500 0.00 0.00 0.00 3.28
340 532 5.055265 TGTTCAGTATCTTTCAACCCCAA 57.945 39.130 0.00 0.00 0.00 4.12
343 535 5.940470 AGACATGTTCAGTATCTTTCAACCC 59.060 40.000 0.00 0.00 0.00 4.11
344 536 6.650807 TCAGACATGTTCAGTATCTTTCAACC 59.349 38.462 0.00 0.00 0.00 3.77
345 537 7.658179 TCAGACATGTTCAGTATCTTTCAAC 57.342 36.000 0.00 0.00 0.00 3.18
346 538 8.853077 ATTCAGACATGTTCAGTATCTTTCAA 57.147 30.769 0.00 0.00 0.00 2.69
347 539 8.853077 AATTCAGACATGTTCAGTATCTTTCA 57.147 30.769 0.00 0.00 0.00 2.69
348 540 9.160496 AGAATTCAGACATGTTCAGTATCTTTC 57.840 33.333 8.44 0.00 0.00 2.62
349 541 9.512588 AAGAATTCAGACATGTTCAGTATCTTT 57.487 29.630 8.44 0.00 0.00 2.52
351 543 9.512588 AAAAGAATTCAGACATGTTCAGTATCT 57.487 29.630 8.44 0.00 0.00 1.98
353 545 9.512588 AGAAAAGAATTCAGACATGTTCAGTAT 57.487 29.630 8.44 0.00 0.00 2.12
354 546 8.908786 AGAAAAGAATTCAGACATGTTCAGTA 57.091 30.769 8.44 0.00 0.00 2.74
355 547 7.718753 AGAGAAAAGAATTCAGACATGTTCAGT 59.281 33.333 8.44 0.00 0.00 3.41
356 548 8.097078 AGAGAAAAGAATTCAGACATGTTCAG 57.903 34.615 8.44 0.00 0.00 3.02
357 549 8.347771 CAAGAGAAAAGAATTCAGACATGTTCA 58.652 33.333 8.44 0.00 0.00 3.18
358 550 8.562892 TCAAGAGAAAAGAATTCAGACATGTTC 58.437 33.333 8.44 0.00 0.00 3.18
359 551 8.455903 TCAAGAGAAAAGAATTCAGACATGTT 57.544 30.769 8.44 0.00 0.00 2.71
360 552 7.935755 TCTCAAGAGAAAAGAATTCAGACATGT 59.064 33.333 8.44 0.00 33.91 3.21
361 553 8.229137 GTCTCAAGAGAAAAGAATTCAGACATG 58.771 37.037 8.44 0.00 39.48 3.21
362 554 7.935755 TGTCTCAAGAGAAAAGAATTCAGACAT 59.064 33.333 8.44 0.00 39.48 3.06
363 555 7.275183 TGTCTCAAGAGAAAAGAATTCAGACA 58.725 34.615 8.44 10.44 39.48 3.41
364 556 7.721286 TGTCTCAAGAGAAAAGAATTCAGAC 57.279 36.000 8.44 8.05 39.48 3.51
365 557 8.781196 CAATGTCTCAAGAGAAAAGAATTCAGA 58.219 33.333 8.44 0.00 39.48 3.27
366 558 8.021973 CCAATGTCTCAAGAGAAAAGAATTCAG 58.978 37.037 8.44 0.00 39.48 3.02
367 559 7.720957 TCCAATGTCTCAAGAGAAAAGAATTCA 59.279 33.333 8.44 0.00 39.48 2.57
368 560 8.020244 GTCCAATGTCTCAAGAGAAAAGAATTC 58.980 37.037 0.57 0.00 39.48 2.17
369 561 7.503566 TGTCCAATGTCTCAAGAGAAAAGAATT 59.496 33.333 0.57 0.00 39.48 2.17
370 562 7.000472 TGTCCAATGTCTCAAGAGAAAAGAAT 59.000 34.615 0.57 0.00 39.48 2.40
371 563 6.356556 TGTCCAATGTCTCAAGAGAAAAGAA 58.643 36.000 0.57 0.00 39.48 2.52
372 564 5.928976 TGTCCAATGTCTCAAGAGAAAAGA 58.071 37.500 0.57 0.00 39.48 2.52
373 565 6.609533 CATGTCCAATGTCTCAAGAGAAAAG 58.390 40.000 0.57 0.00 39.48 2.27
374 566 5.048504 GCATGTCCAATGTCTCAAGAGAAAA 60.049 40.000 0.57 0.00 39.48 2.29
375 567 4.456911 GCATGTCCAATGTCTCAAGAGAAA 59.543 41.667 0.57 0.00 39.48 2.52
376 568 4.005650 GCATGTCCAATGTCTCAAGAGAA 58.994 43.478 0.57 0.00 39.48 2.87
377 569 3.603532 GCATGTCCAATGTCTCAAGAGA 58.396 45.455 0.00 0.00 34.56 3.10
378 570 2.681848 GGCATGTCCAATGTCTCAAGAG 59.318 50.000 0.00 0.00 34.01 2.85
379 571 2.306805 AGGCATGTCCAATGTCTCAAGA 59.693 45.455 8.58 0.00 37.29 3.02
380 572 2.422479 CAGGCATGTCCAATGTCTCAAG 59.578 50.000 8.58 0.00 37.29 3.02
381 573 2.040145 TCAGGCATGTCCAATGTCTCAA 59.960 45.455 0.00 0.00 37.29 3.02
382 574 1.629861 TCAGGCATGTCCAATGTCTCA 59.370 47.619 0.00 0.00 37.29 3.27
383 575 2.408271 TCAGGCATGTCCAATGTCTC 57.592 50.000 0.00 0.00 37.29 3.36
384 576 2.821969 GTTTCAGGCATGTCCAATGTCT 59.178 45.455 0.00 0.00 37.29 3.41
385 577 2.821969 AGTTTCAGGCATGTCCAATGTC 59.178 45.455 0.00 0.00 37.29 3.06
386 578 2.559668 CAGTTTCAGGCATGTCCAATGT 59.440 45.455 0.00 0.00 37.29 2.71
387 579 2.821378 TCAGTTTCAGGCATGTCCAATG 59.179 45.455 0.00 0.00 37.29 2.82
388 580 3.159213 TCAGTTTCAGGCATGTCCAAT 57.841 42.857 0.00 0.00 37.29 3.16
389 581 2.655090 TCAGTTTCAGGCATGTCCAA 57.345 45.000 0.00 0.00 37.29 3.53
390 582 2.655090 TTCAGTTTCAGGCATGTCCA 57.345 45.000 0.00 0.00 37.29 4.02
391 583 3.149196 TCTTTCAGTTTCAGGCATGTCC 58.851 45.455 0.00 0.00 0.00 4.02
392 584 4.067896 TCTCTTTCAGTTTCAGGCATGTC 58.932 43.478 0.00 0.00 0.00 3.06
393 585 4.070716 CTCTCTTTCAGTTTCAGGCATGT 58.929 43.478 0.00 0.00 0.00 3.21
394 586 4.321718 TCTCTCTTTCAGTTTCAGGCATG 58.678 43.478 0.00 0.00 0.00 4.06
395 587 4.565236 CCTCTCTCTTTCAGTTTCAGGCAT 60.565 45.833 0.00 0.00 0.00 4.40
396 588 3.244353 CCTCTCTCTTTCAGTTTCAGGCA 60.244 47.826 0.00 0.00 0.00 4.75
397 589 3.333804 CCTCTCTCTTTCAGTTTCAGGC 58.666 50.000 0.00 0.00 0.00 4.85
398 590 3.580458 TCCCTCTCTCTTTCAGTTTCAGG 59.420 47.826 0.00 0.00 0.00 3.86
399 591 4.881019 TCCCTCTCTCTTTCAGTTTCAG 57.119 45.455 0.00 0.00 0.00 3.02
400 592 4.040952 CCTTCCCTCTCTCTTTCAGTTTCA 59.959 45.833 0.00 0.00 0.00 2.69
401 593 4.284746 TCCTTCCCTCTCTCTTTCAGTTTC 59.715 45.833 0.00 0.00 0.00 2.78
402 594 4.235372 TCCTTCCCTCTCTCTTTCAGTTT 58.765 43.478 0.00 0.00 0.00 2.66
410 602 4.599241 TGAACAAAATCCTTCCCTCTCTCT 59.401 41.667 0.00 0.00 0.00 3.10
413 605 3.759086 GGTGAACAAAATCCTTCCCTCTC 59.241 47.826 0.00 0.00 0.00 3.20
435 639 1.969064 TGATTGGGCCGGTTCGTTG 60.969 57.895 1.90 0.00 0.00 4.10
505 713 3.793144 CTTCTCGCGTTGGGCTGC 61.793 66.667 5.77 0.00 40.44 5.25
508 716 1.807573 CTCTCTTCTCGCGTTGGGC 60.808 63.158 5.77 0.00 38.69 5.36
509 719 0.179150 CTCTCTCTTCTCGCGTTGGG 60.179 60.000 5.77 0.00 0.00 4.12
572 805 2.266055 CAGGGGCGGAGACAGAAC 59.734 66.667 0.00 0.00 37.00 3.01
574 807 3.846405 AACCAGGGGCGGAGACAGA 62.846 63.158 0.00 0.00 37.00 3.41
575 808 2.411765 AAAACCAGGGGCGGAGACAG 62.412 60.000 0.00 0.00 37.00 3.51
576 809 2.406002 GAAAACCAGGGGCGGAGACA 62.406 60.000 0.00 0.00 37.00 3.41
577 810 1.674651 GAAAACCAGGGGCGGAGAC 60.675 63.158 0.00 0.00 0.00 3.36
578 811 1.423794 AAGAAAACCAGGGGCGGAGA 61.424 55.000 0.00 0.00 0.00 3.71
579 812 0.960861 GAAGAAAACCAGGGGCGGAG 60.961 60.000 0.00 0.00 0.00 4.63
580 813 1.074248 GAAGAAAACCAGGGGCGGA 59.926 57.895 0.00 0.00 0.00 5.54
581 814 0.960861 GAGAAGAAAACCAGGGGCGG 60.961 60.000 0.00 0.00 0.00 6.13
582 815 0.960861 GGAGAAGAAAACCAGGGGCG 60.961 60.000 0.00 0.00 0.00 6.13
583 816 0.612174 GGGAGAAGAAAACCAGGGGC 60.612 60.000 0.00 0.00 0.00 5.80
585 818 0.039764 GGGGGAGAAGAAAACCAGGG 59.960 60.000 0.00 0.00 0.00 4.45
611 850 1.072159 GGAATCTGGGGCGAGATGG 59.928 63.158 0.00 0.00 32.77 3.51
628 877 2.890474 CACGGAATCGGCGGAAGG 60.890 66.667 7.21 0.00 41.39 3.46
658 915 2.582498 GGTCTGTCGGCGAATCGG 60.582 66.667 12.92 5.44 0.00 4.18
659 916 2.158959 GTGGTCTGTCGGCGAATCG 61.159 63.158 12.92 0.00 0.00 3.34
660 917 1.078759 CTGTGGTCTGTCGGCGAATC 61.079 60.000 12.92 0.00 0.00 2.52
665 922 0.667792 GTTCTCTGTGGTCTGTCGGC 60.668 60.000 0.00 0.00 0.00 5.54
683 940 5.601583 AAACTCACCGGGTTTATTTTTGT 57.398 34.783 6.32 0.00 35.48 2.83
684 941 6.277605 AGAAAACTCACCGGGTTTATTTTTG 58.722 36.000 6.32 0.00 36.09 2.44
709 967 1.686110 GGGAGAAGAAGAGCGGGGA 60.686 63.158 0.00 0.00 0.00 4.81
710 968 2.736826 GGGGAGAAGAAGAGCGGGG 61.737 68.421 0.00 0.00 0.00 5.73
711 969 2.736826 GGGGGAGAAGAAGAGCGGG 61.737 68.421 0.00 0.00 0.00 6.13
714 972 1.341913 GGGAGGGGGAGAAGAAGAGC 61.342 65.000 0.00 0.00 0.00 4.09
741 999 4.824515 AGGGAGAGGACGAGCCGG 62.825 72.222 0.00 0.00 43.43 6.13
742 1000 3.522731 CAGGGAGAGGACGAGCCG 61.523 72.222 0.00 0.00 43.43 5.52
815 1077 5.720202 AGAATTAATCCCCAAAAACTTCGC 58.280 37.500 0.00 0.00 0.00 4.70
817 1079 6.811665 CCGAAGAATTAATCCCCAAAAACTTC 59.188 38.462 0.00 0.00 0.00 3.01
818 1080 6.269077 ACCGAAGAATTAATCCCCAAAAACTT 59.731 34.615 0.00 0.00 0.00 2.66
825 1087 3.521937 AGTCACCGAAGAATTAATCCCCA 59.478 43.478 0.00 0.00 0.00 4.96
838 1100 1.080093 GGCATCGTCAGTCACCGAA 60.080 57.895 0.00 0.00 36.57 4.30
989 1251 4.888325 CCTCCATCCCCTCGCCCT 62.888 72.222 0.00 0.00 0.00 5.19
992 1254 3.866582 CCACCTCCATCCCCTCGC 61.867 72.222 0.00 0.00 0.00 5.03
993 1255 2.365635 ACCACCTCCATCCCCTCG 60.366 66.667 0.00 0.00 0.00 4.63
995 1257 2.286425 CCACCACCTCCATCCCCT 60.286 66.667 0.00 0.00 0.00 4.79
1000 1268 4.033776 CGGCACCACCACCTCCAT 62.034 66.667 0.00 0.00 39.03 3.41
1455 1732 0.837691 TCTTCCTCCTCTTGGCAGCA 60.838 55.000 0.00 0.00 0.00 4.41
1458 1735 0.987294 CCTTCTTCCTCCTCTTGGCA 59.013 55.000 0.00 0.00 0.00 4.92
1459 1736 0.988063 ACCTTCTTCCTCCTCTTGGC 59.012 55.000 0.00 0.00 0.00 4.52
1530 1810 1.382420 AGGAGTAGCAGGCTGGAGG 60.382 63.158 17.64 0.00 0.00 4.30
1611 1891 4.492160 GCATGCCTCGACGACGGA 62.492 66.667 6.36 4.28 40.21 4.69
1615 1895 3.484742 GATCGGCATGCCTCGACGA 62.485 63.158 33.07 24.27 38.25 4.20
1674 1954 0.999406 CGTCATACAGAAACCTGCCG 59.001 55.000 0.00 0.00 35.09 5.69
1677 1957 0.999406 CGGCGTCATACAGAAACCTG 59.001 55.000 0.00 0.00 37.67 4.00
1683 1963 1.214325 CACACCGGCGTCATACAGA 59.786 57.895 6.01 0.00 0.00 3.41
1827 2107 1.284982 CCAACTGAGCCGTCACTTCG 61.285 60.000 0.00 0.00 0.00 3.79
1850 2130 1.279025 GGCCCATGACCCCTTGTAGA 61.279 60.000 0.00 0.00 0.00 2.59
1875 2155 1.451936 GGACAACACTGAGCACCCT 59.548 57.895 0.00 0.00 0.00 4.34
1938 2218 2.026636 GGTACCTTCAGGGCAATACACA 60.027 50.000 4.06 0.00 40.27 3.72
2067 2347 4.887748 TCTCAGAGTTCTTTGTGATCACC 58.112 43.478 22.85 6.41 0.00 4.02
2113 2393 4.693566 CAGCGTAGGAAATGTTTCACCTAA 59.306 41.667 7.69 0.00 38.92 2.69
2197 2477 4.509600 GCTAATGATCTCACTAACTGCCAC 59.490 45.833 0.00 0.00 0.00 5.01
2198 2478 4.162131 TGCTAATGATCTCACTAACTGCCA 59.838 41.667 0.00 0.00 0.00 4.92
2217 2497 3.441222 CAGTGATGGTCTTTGCATTGCTA 59.559 43.478 10.49 0.00 0.00 3.49
2223 2503 2.885135 ATCCAGTGATGGTCTTTGCA 57.115 45.000 0.00 0.00 0.00 4.08
2265 2545 8.559536 TGTAGATGTTTCTTCATCAAACTCAAC 58.440 33.333 8.93 0.00 44.46 3.18
2283 2563 3.312890 CAGATCCTTCCCCTGTAGATGT 58.687 50.000 0.00 0.00 0.00 3.06
2289 2569 1.008938 ACTAGCAGATCCTTCCCCTGT 59.991 52.381 0.00 0.00 0.00 4.00
2322 2602 2.480037 CACAAAGTTCATAGCAGCACGA 59.520 45.455 0.00 0.00 0.00 4.35
2340 2620 5.645929 ACTGTACATGTTTTTCAGTGTCACA 59.354 36.000 18.00 7.03 37.85 3.58
2373 2653 1.822990 CTGACCATGGCTTGCAAATCT 59.177 47.619 13.04 0.00 0.00 2.40
2617 2897 4.022416 AGGCATATAGTCGCTCTTCTTCAG 60.022 45.833 0.00 0.00 0.00 3.02
2682 2962 2.401195 GCTGAATGAAGCGGTCGC 59.599 61.111 7.32 7.32 42.33 5.19
2730 3010 9.788960 TCATTCGATATGTTATCTCTAATTCCG 57.211 33.333 0.00 0.00 0.00 4.30
2978 3261 6.412362 ACCTCATGCTTACAGGAATACTAG 57.588 41.667 4.48 0.00 35.91 2.57
2979 3262 6.808321 AACCTCATGCTTACAGGAATACTA 57.192 37.500 4.48 0.00 35.91 1.82
2981 3264 6.037610 CAGAAACCTCATGCTTACAGGAATAC 59.962 42.308 4.48 0.00 35.91 1.89
2983 3266 4.946157 CAGAAACCTCATGCTTACAGGAAT 59.054 41.667 4.48 0.00 35.91 3.01
2985 3268 3.582647 TCAGAAACCTCATGCTTACAGGA 59.417 43.478 4.48 0.00 34.90 3.86
2986 3269 3.942829 TCAGAAACCTCATGCTTACAGG 58.057 45.455 0.00 0.00 0.00 4.00
2987 3270 5.288543 GTTCAGAAACCTCATGCTTACAG 57.711 43.478 0.00 0.00 0.00 2.74
3355 3638 7.466746 TCCATGCTTTGCTAGTTTTTCTATT 57.533 32.000 0.00 0.00 0.00 1.73
3357 3640 6.855836 CATCCATGCTTTGCTAGTTTTTCTA 58.144 36.000 0.00 0.00 0.00 2.10
3398 3681 8.887036 TGTTGCCTATGAACAGTTATACATAG 57.113 34.615 11.24 11.24 40.70 2.23
3401 3684 9.104965 GTATTGTTGCCTATGAACAGTTATACA 57.895 33.333 0.00 0.00 34.85 2.29
3402 3685 9.104965 TGTATTGTTGCCTATGAACAGTTATAC 57.895 33.333 0.00 0.00 34.85 1.47
3405 3688 7.120579 CCTTGTATTGTTGCCTATGAACAGTTA 59.879 37.037 0.00 0.00 34.85 2.24
3436 3722 3.003394 ACCGAGATTGGATCAAATGCA 57.997 42.857 0.00 0.00 0.00 3.96
3518 3804 2.129555 ATCCAGTTTGGCTGCTCCGT 62.130 55.000 0.00 0.00 43.71 4.69
3668 3954 3.896648 TCGACTCCTGCAAACAAAATC 57.103 42.857 0.00 0.00 0.00 2.17
3756 4042 5.336150 TCCAAGTTAGAGCTCTCTTCATG 57.664 43.478 22.17 13.63 40.93 3.07
3984 4299 2.027745 TCCACAGATCAAGAAGCACCTC 60.028 50.000 0.00 0.00 0.00 3.85
3985 4300 1.980765 TCCACAGATCAAGAAGCACCT 59.019 47.619 0.00 0.00 0.00 4.00
3986 4301 2.479566 TCCACAGATCAAGAAGCACC 57.520 50.000 0.00 0.00 0.00 5.01
3987 4302 3.817647 ACTTTCCACAGATCAAGAAGCAC 59.182 43.478 0.00 0.00 0.00 4.40
3988 4303 4.090761 ACTTTCCACAGATCAAGAAGCA 57.909 40.909 0.00 0.00 0.00 3.91
3989 4304 4.997395 TGTACTTTCCACAGATCAAGAAGC 59.003 41.667 0.00 0.00 0.00 3.86
3990 4305 5.641209 CCTGTACTTTCCACAGATCAAGAAG 59.359 44.000 4.11 0.00 45.10 2.85
3991 4306 5.071788 ACCTGTACTTTCCACAGATCAAGAA 59.928 40.000 4.11 0.00 45.10 2.52
3992 4307 4.593206 ACCTGTACTTTCCACAGATCAAGA 59.407 41.667 4.11 0.00 45.10 3.02
3993 4308 4.692625 CACCTGTACTTTCCACAGATCAAG 59.307 45.833 4.11 0.00 45.10 3.02
3994 4309 4.641396 CACCTGTACTTTCCACAGATCAA 58.359 43.478 4.11 0.00 45.10 2.57
3995 4310 3.557054 GCACCTGTACTTTCCACAGATCA 60.557 47.826 4.11 0.00 45.10 2.92
3996 4311 3.003480 GCACCTGTACTTTCCACAGATC 58.997 50.000 4.11 0.00 45.10 2.75
3997 4312 2.639839 AGCACCTGTACTTTCCACAGAT 59.360 45.455 4.11 0.00 45.10 2.90
3998 4313 2.047061 AGCACCTGTACTTTCCACAGA 58.953 47.619 4.11 0.00 45.10 3.41
3999 4314 2.550830 AGCACCTGTACTTTCCACAG 57.449 50.000 0.00 0.00 42.52 3.66
4000 4315 2.438021 AGAAGCACCTGTACTTTCCACA 59.562 45.455 0.00 0.00 0.00 4.17
4001 4316 3.127425 AGAAGCACCTGTACTTTCCAC 57.873 47.619 0.00 0.00 0.00 4.02
4002 4317 3.118038 ACAAGAAGCACCTGTACTTTCCA 60.118 43.478 0.00 0.00 0.00 3.53
4003 4318 3.477530 ACAAGAAGCACCTGTACTTTCC 58.522 45.455 0.00 0.00 0.00 3.13
4004 4319 4.816925 AGAACAAGAAGCACCTGTACTTTC 59.183 41.667 0.00 0.00 0.00 2.62
4005 4320 4.576463 CAGAACAAGAAGCACCTGTACTTT 59.424 41.667 0.00 0.00 0.00 2.66
4006 4321 4.130118 CAGAACAAGAAGCACCTGTACTT 58.870 43.478 0.00 0.00 0.00 2.24
4007 4322 3.134804 ACAGAACAAGAAGCACCTGTACT 59.865 43.478 0.00 0.00 33.65 2.73
4008 4323 3.248602 CACAGAACAAGAAGCACCTGTAC 59.751 47.826 0.00 0.00 34.01 2.90
4009 4324 3.466836 CACAGAACAAGAAGCACCTGTA 58.533 45.455 0.00 0.00 34.01 2.74
4010 4325 2.292267 CACAGAACAAGAAGCACCTGT 58.708 47.619 0.00 0.00 35.51 4.00
4011 4326 1.605710 CCACAGAACAAGAAGCACCTG 59.394 52.381 0.00 0.00 0.00 4.00
4046 4361 8.535335 AGAAACTATCTCAAGCACTGAAAGATA 58.465 33.333 0.00 0.00 32.22 1.98
4072 4398 9.219603 CTCTAAATACCTCAATCACAAAGACAA 57.780 33.333 0.00 0.00 0.00 3.18
4112 4440 2.341257 CATGACCGGACAAAGACAGAG 58.659 52.381 9.46 0.00 0.00 3.35
4204 4532 6.066054 TGTTGATTATGTCGTGCAGAAAAA 57.934 33.333 0.00 0.00 31.56 1.94
4239 4567 4.160439 GGGAGGCCCTTCAGATTTAAAAAG 59.840 45.833 0.00 0.00 41.34 2.27
4244 4572 1.979809 TGGGAGGCCCTTCAGATTTA 58.020 50.000 0.00 0.00 45.70 1.40
4245 4573 1.312884 ATGGGAGGCCCTTCAGATTT 58.687 50.000 0.00 0.00 45.70 2.17
4246 4574 1.312884 AATGGGAGGCCCTTCAGATT 58.687 50.000 0.00 0.00 45.70 2.40
4409 4737 4.259770 CGCTGGTGTTTGCAACTTTTAAAG 60.260 41.667 0.00 2.81 32.44 1.85
4414 4742 0.814457 TCGCTGGTGTTTGCAACTTT 59.186 45.000 0.00 0.00 32.44 2.66
4534 4862 1.566298 ATCTGGCTTCTTTCGGGGCT 61.566 55.000 0.00 0.00 0.00 5.19
4599 4927 5.148502 CCTATGATGTACTAGTTCCCAGGT 58.851 45.833 0.00 0.00 0.00 4.00
4608 4936 6.242396 AGTAGTCCTGCCTATGATGTACTAG 58.758 44.000 0.00 0.00 0.00 2.57
4652 4980 5.694910 TGTTGACTACTTGAACCGAGAAATC 59.305 40.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.