Multiple sequence alignment - TraesCS1B01G132700

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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 TraesCS1B01G132700 chr1B 100.000 3676 0 0 1 3676 167711687 167715362 0.000000e+00 6789.0
1 TraesCS1B01G132700 chr1D 93.012 2347 84 22 556 2883 110334208 110336493 0.000000e+00 3352.0
2 TraesCS1B01G132700 chr1D 88.288 444 23 12 3236 3676 110336837 110337254 4.240000e-139 505.0
3 TraesCS1B01G132700 chr1D 93.151 146 8 2 318 462 434734670 434734814 2.880000e-51 213.0
4 TraesCS1B01G132700 chr1D 75.839 149 30 5 319 463 355170358 355170504 1.830000e-08 71.3
5 TraesCS1B01G132700 chr1A 90.754 2574 143 34 555 3099 114544315 114546822 0.000000e+00 3347.0
6 TraesCS1B01G132700 chr1A 89.342 319 24 5 3096 3409 114547158 114547471 3.440000e-105 392.0
7 TraesCS1B01G132700 chr1A 93.237 207 12 2 1 206 114543338 114543543 1.660000e-78 303.0
8 TraesCS1B01G132700 chr4B 86.434 516 68 2 1811 2325 119275144 119275658 6.890000e-157 564.0
9 TraesCS1B01G132700 chr4B 76.162 495 98 18 1814 2298 375790852 375791336 3.670000e-60 243.0
10 TraesCS1B01G132700 chr4B 92.857 154 9 2 310 463 71000020 70999869 4.780000e-54 222.0
11 TraesCS1B01G132700 chr4A 86.434 516 68 2 1811 2325 497011898 497012412 6.890000e-157 564.0
12 TraesCS1B01G132700 chr4D 85.853 516 71 2 1811 2325 84278112 84278626 6.940000e-152 547.0
13 TraesCS1B01G132700 chr4D 75.709 494 102 16 1814 2298 301534900 301535384 7.940000e-57 231.0
14 TraesCS1B01G132700 chr3A 90.972 144 13 0 317 460 596715643 596715500 1.040000e-45 195.0
15 TraesCS1B01G132700 chr5D 89.865 148 15 0 318 465 481480188 481480041 1.350000e-44 191.0
16 TraesCS1B01G132700 chr6B 89.796 147 11 4 318 462 473283 473427 6.270000e-43 185.0
17 TraesCS1B01G132700 chr2B 88.356 146 17 0 317 462 706566790 706566935 3.770000e-40 176.0
18 TraesCS1B01G132700 chr6D 86.986 146 15 4 318 462 448798439 448798297 1.060000e-35 161.0
19 TraesCS1B01G132700 chr6D 86.301 146 18 2 318 462 441677604 441677460 1.370000e-34 158.0


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 TraesCS1B01G132700 chr1B 167711687 167715362 3675 False 6789.000000 6789 100.000 1 3676 1 chr1B.!!$F1 3675
1 TraesCS1B01G132700 chr1D 110334208 110337254 3046 False 1928.500000 3352 90.650 556 3676 2 chr1D.!!$F3 3120
2 TraesCS1B01G132700 chr1A 114543338 114547471 4133 False 1347.333333 3347 91.111 1 3409 3 chr1A.!!$F1 3408
3 TraesCS1B01G132700 chr4B 119275144 119275658 514 False 564.000000 564 86.434 1811 2325 1 chr4B.!!$F1 514
4 TraesCS1B01G132700 chr4A 497011898 497012412 514 False 564.000000 564 86.434 1811 2325 1 chr4A.!!$F1 514
5 TraesCS1B01G132700 chr4D 84278112 84278626 514 False 547.000000 547 85.853 1811 2325 1 chr4D.!!$F1 514

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
441 523 0.040425 GTTTATGCGGGCTTATGCGG 60.040 55.0 0.00 0.0 40.82 5.69 F
516 598 0.043940 AGTGGAGAGAGGAAGGGCAT 59.956 55.0 0.00 0.0 0.00 4.40 F
1121 1701 0.596341 GTTTGAATTGGCGCGGTTGT 60.596 50.0 8.83 0.0 0.00 3.32 F
2502 3097 0.034896 ATGGAGTCAACGCGAAGGTT 59.965 50.0 15.93 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1547 2139 0.321346 TCAGAATGAGCAGTTGGCGA 59.679 50.000 0.00 0.00 42.56 5.54 R
1583 2175 4.702131 ACCATTGATAGGCAAACAAGAGAC 59.298 41.667 0.00 0.00 40.48 3.36 R
2601 3197 1.002868 ATCCGAGCAGCTGCAAAGT 60.003 52.632 38.24 19.88 45.16 2.66 R
3325 4328 0.912487 TCCCAACGTAGCCATCCCTT 60.912 55.000 0.00 0.00 0.00 3.95 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
33 34 9.685276 AGATGAGTAATCCAGATAGATAGTCTG 57.315 37.037 0.00 0.00 42.11 3.51
114 158 5.474876 AGAGTCCTAAAATTCAGCCAAACAG 59.525 40.000 0.00 0.00 0.00 3.16
140 184 8.999431 GGACATGTTTCAGTTAATTTAGAGTCA 58.001 33.333 0.00 0.00 0.00 3.41
214 259 7.439157 TCAGTCAAATAGGACAACAAGATTG 57.561 36.000 0.00 0.00 40.29 2.67
216 261 7.719193 TCAGTCAAATAGGACAACAAGATTGAA 59.281 33.333 0.00 0.00 40.29 2.69
228 296 8.776376 ACAACAAGATTGAATCAAACAAGTTT 57.224 26.923 8.03 0.00 0.00 2.66
233 301 8.667463 CAAGATTGAATCAAACAAGTTTTGGTT 58.333 29.630 8.03 0.00 42.35 3.67
240 308 8.558973 AATCAAACAAGTTTTGGTTCATTCAA 57.441 26.923 0.00 0.00 38.84 2.69
290 372 6.276847 ACAACGAAATTTGCTACAATTCCAA 58.723 32.000 0.00 0.00 0.00 3.53
300 382 6.266168 TGCTACAATTCCAACAAACCATAG 57.734 37.500 0.00 0.00 0.00 2.23
304 386 6.096673 ACAATTCCAACAAACCATAGTTCC 57.903 37.500 0.00 0.00 34.19 3.62
311 393 6.011981 TCCAACAAACCATAGTTCCCTTATCT 60.012 38.462 0.00 0.00 34.19 1.98
314 396 5.491078 ACAAACCATAGTTCCCTTATCTGGA 59.509 40.000 0.00 0.00 34.19 3.86
315 397 6.160459 ACAAACCATAGTTCCCTTATCTGGAT 59.840 38.462 0.00 0.00 34.19 3.41
316 398 6.441088 AACCATAGTTCCCTTATCTGGATC 57.559 41.667 0.00 0.00 0.00 3.36
317 399 5.731924 ACCATAGTTCCCTTATCTGGATCT 58.268 41.667 0.00 0.00 36.26 2.75
318 400 6.875469 ACCATAGTTCCCTTATCTGGATCTA 58.125 40.000 0.00 0.00 38.13 1.98
319 401 6.957020 ACCATAGTTCCCTTATCTGGATCTAG 59.043 42.308 0.00 0.00 37.52 2.43
320 402 6.382570 CCATAGTTCCCTTATCTGGATCTAGG 59.617 46.154 6.21 0.00 37.52 3.02
321 403 4.757692 AGTTCCCTTATCTGGATCTAGGG 58.242 47.826 17.61 17.61 41.07 3.53
322 404 4.423960 AGTTCCCTTATCTGGATCTAGGGA 59.576 45.833 20.30 20.30 44.00 4.20
323 405 5.078573 AGTTCCCTTATCTGGATCTAGGGAT 59.921 44.000 22.74 13.20 44.53 3.85
324 406 4.952845 TCCCTTATCTGGATCTAGGGATG 58.047 47.826 20.30 0.00 42.36 3.51
325 407 4.361367 TCCCTTATCTGGATCTAGGGATGT 59.639 45.833 20.30 0.00 42.36 3.06
326 408 5.559947 TCCCTTATCTGGATCTAGGGATGTA 59.440 44.000 20.30 7.19 42.36 2.29
327 409 5.896678 CCCTTATCTGGATCTAGGGATGTAG 59.103 48.000 18.35 0.00 41.71 2.74
328 410 6.297889 CCCTTATCTGGATCTAGGGATGTAGA 60.298 46.154 18.35 0.00 41.71 2.59
329 411 6.833416 CCTTATCTGGATCTAGGGATGTAGAG 59.167 46.154 6.21 0.00 32.49 2.43
330 412 4.040936 TCTGGATCTAGGGATGTAGAGC 57.959 50.000 6.21 0.00 35.15 4.09
331 413 2.752354 CTGGATCTAGGGATGTAGAGCG 59.248 54.545 0.00 0.00 36.48 5.03
332 414 2.096248 GGATCTAGGGATGTAGAGCGG 58.904 57.143 0.00 0.00 36.48 5.52
333 415 1.474879 GATCTAGGGATGTAGAGCGGC 59.525 57.143 0.00 0.00 32.49 6.53
334 416 0.889638 TCTAGGGATGTAGAGCGGCG 60.890 60.000 0.51 0.51 0.00 6.46
335 417 2.479412 CTAGGGATGTAGAGCGGCGC 62.479 65.000 26.86 26.86 0.00 6.53
336 418 2.978298 TAGGGATGTAGAGCGGCGCT 62.978 60.000 37.11 37.11 43.88 5.92
352 434 4.951963 CTCGATCCGCCCCGCTTC 62.952 72.222 0.00 0.00 0.00 3.86
355 437 4.483243 GATCCGCCCCGCTTCCAA 62.483 66.667 0.00 0.00 0.00 3.53
356 438 4.489771 ATCCGCCCCGCTTCCAAG 62.490 66.667 0.00 0.00 0.00 3.61
359 441 4.697756 CGCCCCGCTTCCAAGTCA 62.698 66.667 0.00 0.00 0.00 3.41
360 442 2.282180 GCCCCGCTTCCAAGTCAA 60.282 61.111 0.00 0.00 0.00 3.18
361 443 1.901464 GCCCCGCTTCCAAGTCAAA 60.901 57.895 0.00 0.00 0.00 2.69
362 444 1.460273 GCCCCGCTTCCAAGTCAAAA 61.460 55.000 0.00 0.00 0.00 2.44
363 445 1.256812 CCCCGCTTCCAAGTCAAAAT 58.743 50.000 0.00 0.00 0.00 1.82
364 446 1.067635 CCCCGCTTCCAAGTCAAAATG 60.068 52.381 0.00 0.00 0.00 2.32
365 447 1.669795 CCCGCTTCCAAGTCAAAATGC 60.670 52.381 0.00 0.00 0.00 3.56
366 448 1.000385 CCGCTTCCAAGTCAAAATGCA 60.000 47.619 0.00 0.00 0.00 3.96
367 449 2.353011 CCGCTTCCAAGTCAAAATGCAT 60.353 45.455 0.00 0.00 0.00 3.96
368 450 2.664568 CGCTTCCAAGTCAAAATGCATG 59.335 45.455 0.00 0.00 0.00 4.06
369 451 3.612241 CGCTTCCAAGTCAAAATGCATGA 60.612 43.478 0.00 0.00 0.00 3.07
370 452 3.924686 GCTTCCAAGTCAAAATGCATGAG 59.075 43.478 0.00 0.00 0.00 2.90
371 453 3.581024 TCCAAGTCAAAATGCATGAGC 57.419 42.857 0.00 0.00 42.57 4.26
372 454 3.159472 TCCAAGTCAAAATGCATGAGCT 58.841 40.909 0.00 0.00 42.74 4.09
373 455 3.575256 TCCAAGTCAAAATGCATGAGCTT 59.425 39.130 0.00 0.00 42.74 3.74
374 456 4.766373 TCCAAGTCAAAATGCATGAGCTTA 59.234 37.500 0.00 0.00 42.74 3.09
375 457 5.100259 CCAAGTCAAAATGCATGAGCTTAG 58.900 41.667 0.00 0.00 42.74 2.18
376 458 5.336213 CCAAGTCAAAATGCATGAGCTTAGT 60.336 40.000 0.00 0.00 42.74 2.24
377 459 5.972107 AGTCAAAATGCATGAGCTTAGTT 57.028 34.783 0.00 0.00 42.74 2.24
378 460 7.307694 CAAGTCAAAATGCATGAGCTTAGTTA 58.692 34.615 0.00 0.00 42.74 2.24
379 461 7.636150 AGTCAAAATGCATGAGCTTAGTTAT 57.364 32.000 0.00 0.00 42.74 1.89
380 462 8.737168 AGTCAAAATGCATGAGCTTAGTTATA 57.263 30.769 0.00 0.00 42.74 0.98
381 463 9.177608 AGTCAAAATGCATGAGCTTAGTTATAA 57.822 29.630 0.00 0.00 42.74 0.98
382 464 9.956720 GTCAAAATGCATGAGCTTAGTTATAAT 57.043 29.630 0.00 0.00 42.74 1.28
385 467 9.971922 AAAATGCATGAGCTTAGTTATAATTCC 57.028 29.630 0.00 0.00 42.74 3.01
386 468 8.930846 AATGCATGAGCTTAGTTATAATTCCT 57.069 30.769 0.00 0.00 42.74 3.36
387 469 7.969536 TGCATGAGCTTAGTTATAATTCCTC 57.030 36.000 0.00 0.00 42.74 3.71
388 470 7.739825 TGCATGAGCTTAGTTATAATTCCTCT 58.260 34.615 0.00 0.00 42.74 3.69
389 471 7.658982 TGCATGAGCTTAGTTATAATTCCTCTG 59.341 37.037 0.00 0.00 42.74 3.35
390 472 7.659390 GCATGAGCTTAGTTATAATTCCTCTGT 59.341 37.037 0.00 0.00 37.91 3.41
393 475 9.197306 TGAGCTTAGTTATAATTCCTCTGTACA 57.803 33.333 0.00 0.00 0.00 2.90
394 476 9.685828 GAGCTTAGTTATAATTCCTCTGTACAG 57.314 37.037 17.17 17.17 0.00 2.74
395 477 9.422681 AGCTTAGTTATAATTCCTCTGTACAGA 57.577 33.333 23.80 23.80 35.85 3.41
406 488 7.719871 TTCCTCTGTACAGATTTAGCTTAGT 57.280 36.000 25.35 0.00 36.76 2.24
407 489 7.719871 TCCTCTGTACAGATTTAGCTTAGTT 57.280 36.000 25.35 0.00 36.76 2.24
408 490 8.135382 TCCTCTGTACAGATTTAGCTTAGTTT 57.865 34.615 25.35 0.00 36.76 2.66
409 491 8.035394 TCCTCTGTACAGATTTAGCTTAGTTTG 58.965 37.037 25.35 8.75 36.76 2.93
410 492 8.035394 CCTCTGTACAGATTTAGCTTAGTTTGA 58.965 37.037 25.35 0.00 36.76 2.69
411 493 9.424319 CTCTGTACAGATTTAGCTTAGTTTGAA 57.576 33.333 25.35 0.00 36.76 2.69
412 494 9.204570 TCTGTACAGATTTAGCTTAGTTTGAAC 57.795 33.333 21.74 0.00 31.41 3.18
413 495 9.209175 CTGTACAGATTTAGCTTAGTTTGAACT 57.791 33.333 18.45 1.60 42.91 3.01
417 499 9.000486 ACAGATTTAGCTTAGTTTGAACTAACC 58.000 33.333 11.28 6.55 44.23 2.85
418 500 9.220767 CAGATTTAGCTTAGTTTGAACTAACCT 57.779 33.333 11.28 12.36 44.23 3.50
419 501 9.438228 AGATTTAGCTTAGTTTGAACTAACCTC 57.562 33.333 12.41 6.34 44.23 3.85
420 502 9.216117 GATTTAGCTTAGTTTGAACTAACCTCA 57.784 33.333 12.41 3.07 44.23 3.86
421 503 9.740710 ATTTAGCTTAGTTTGAACTAACCTCAT 57.259 29.630 12.41 6.37 44.23 2.90
422 504 8.547967 TTAGCTTAGTTTGAACTAACCTCATG 57.452 34.615 12.41 5.01 44.23 3.07
423 505 6.534634 AGCTTAGTTTGAACTAACCTCATGT 58.465 36.000 11.28 0.00 44.23 3.21
424 506 6.998673 AGCTTAGTTTGAACTAACCTCATGTT 59.001 34.615 11.28 0.00 44.23 2.71
425 507 7.502561 AGCTTAGTTTGAACTAACCTCATGTTT 59.497 33.333 11.28 0.00 44.23 2.83
426 508 8.780249 GCTTAGTTTGAACTAACCTCATGTTTA 58.220 33.333 11.28 0.00 44.23 2.01
429 511 7.593825 AGTTTGAACTAACCTCATGTTTATGC 58.406 34.615 0.00 0.00 37.52 3.14
430 512 5.794687 TGAACTAACCTCATGTTTATGCG 57.205 39.130 0.00 0.00 38.42 4.73
431 513 4.634004 TGAACTAACCTCATGTTTATGCGG 59.366 41.667 0.00 0.00 43.36 5.69
432 514 3.541632 ACTAACCTCATGTTTATGCGGG 58.458 45.455 0.00 0.00 42.29 6.13
433 515 1.102978 AACCTCATGTTTATGCGGGC 58.897 50.000 0.00 0.00 42.29 6.13
434 516 0.255890 ACCTCATGTTTATGCGGGCT 59.744 50.000 0.00 0.00 42.29 5.19
435 517 1.340991 ACCTCATGTTTATGCGGGCTT 60.341 47.619 0.00 0.00 42.29 4.35
436 518 2.092646 ACCTCATGTTTATGCGGGCTTA 60.093 45.455 0.00 0.00 42.29 3.09
437 519 3.149196 CCTCATGTTTATGCGGGCTTAT 58.851 45.455 0.00 0.00 35.88 1.73
438 520 3.058016 CCTCATGTTTATGCGGGCTTATG 60.058 47.826 0.00 0.00 35.88 1.90
439 521 2.293122 TCATGTTTATGCGGGCTTATGC 59.707 45.455 0.00 0.00 34.21 3.14
440 522 0.660488 TGTTTATGCGGGCTTATGCG 59.340 50.000 0.00 0.00 40.82 4.73
441 523 0.040425 GTTTATGCGGGCTTATGCGG 60.040 55.000 0.00 0.00 40.82 5.69
442 524 1.169661 TTTATGCGGGCTTATGCGGG 61.170 55.000 0.00 0.00 40.82 6.13
443 525 2.046009 TTATGCGGGCTTATGCGGGA 62.046 55.000 0.00 0.00 40.82 5.14
444 526 1.836999 TATGCGGGCTTATGCGGGAT 61.837 55.000 0.00 0.00 40.82 3.85
445 527 3.357079 GCGGGCTTATGCGGGATG 61.357 66.667 0.00 0.00 40.82 3.51
446 528 3.357079 CGGGCTTATGCGGGATGC 61.357 66.667 0.00 0.00 46.70 3.91
447 529 2.985847 GGGCTTATGCGGGATGCC 60.986 66.667 2.70 2.70 45.60 4.40
448 530 2.985847 GGCTTATGCGGGATGCCC 60.986 66.667 0.00 0.00 45.60 5.36
462 544 3.958860 GCCCGCCTGCATCCCTAT 61.959 66.667 0.00 0.00 0.00 2.57
463 545 2.033141 CCCGCCTGCATCCCTATG 59.967 66.667 0.00 0.00 36.09 2.23
464 546 2.822637 CCCGCCTGCATCCCTATGT 61.823 63.158 0.00 0.00 35.38 2.29
465 547 1.598962 CCGCCTGCATCCCTATGTG 60.599 63.158 0.00 0.00 35.38 3.21
466 548 1.447217 CGCCTGCATCCCTATGTGA 59.553 57.895 0.00 0.00 35.38 3.58
474 556 3.980022 TGCATCCCTATGTGAATCCCTAA 59.020 43.478 0.00 0.00 35.38 2.69
486 568 5.721000 TGTGAATCCCTAAAATTCCAGCAAT 59.279 36.000 0.00 0.00 33.13 3.56
505 587 4.201891 GCAATGACATTTGCTAGTGGAGAG 60.202 45.833 0.00 0.00 46.66 3.20
511 593 4.081198 ACATTTGCTAGTGGAGAGAGGAAG 60.081 45.833 0.00 0.00 0.00 3.46
516 598 0.043940 AGTGGAGAGAGGAAGGGCAT 59.956 55.000 0.00 0.00 0.00 4.40
537 619 1.987855 CACCTAGGGGCTCGACCAA 60.988 63.158 14.81 0.00 42.05 3.67
538 620 1.988406 ACCTAGGGGCTCGACCAAC 60.988 63.158 14.81 0.00 42.05 3.77
655 1234 6.269077 TCCAAGTCCAATATATATGACACGGT 59.731 38.462 13.05 0.00 0.00 4.83
659 1238 9.706691 AAGTCCAATATATATGACACGGTTTAG 57.293 33.333 13.05 0.00 0.00 1.85
698 1277 3.917985 CCGAACGATTGAAAAATCCAACC 59.082 43.478 0.00 0.00 0.00 3.77
702 1281 3.171277 CGATTGAAAAATCCAACCGCTC 58.829 45.455 0.00 0.00 0.00 5.03
703 1282 3.511699 GATTGAAAAATCCAACCGCTCC 58.488 45.455 0.00 0.00 0.00 4.70
704 1283 1.988293 TGAAAAATCCAACCGCTCCA 58.012 45.000 0.00 0.00 0.00 3.86
705 1284 1.611491 TGAAAAATCCAACCGCTCCAC 59.389 47.619 0.00 0.00 0.00 4.02
706 1285 0.966179 AAAAATCCAACCGCTCCACC 59.034 50.000 0.00 0.00 0.00 4.61
707 1286 1.241315 AAAATCCAACCGCTCCACCG 61.241 55.000 0.00 0.00 0.00 4.94
758 1337 2.574018 GGTGTTTTCTGGGCCTGGC 61.574 63.158 11.05 11.05 0.00 4.85
792 1371 4.722700 CCCAACAGCTCCACCGGG 62.723 72.222 6.32 0.00 0.00 5.73
793 1372 3.953775 CCAACAGCTCCACCGGGT 61.954 66.667 6.32 0.00 34.93 5.28
794 1373 2.358737 CAACAGCTCCACCGGGTC 60.359 66.667 6.32 0.00 34.93 4.46
1019 1598 1.207089 CATGGGGAGAAGTAAGCACGA 59.793 52.381 0.00 0.00 0.00 4.35
1088 1668 1.854227 GTTCATCTGGCCGTAGCTAC 58.146 55.000 14.19 14.19 39.73 3.58
1121 1701 0.596341 GTTTGAATTGGCGCGGTTGT 60.596 50.000 8.83 0.00 0.00 3.32
1170 1750 1.151777 CGCGCGGAACCTGTGATATT 61.152 55.000 24.84 0.00 0.00 1.28
1216 1808 7.771927 AGTTTCTGTCTGGATGATTTTCATT 57.228 32.000 0.00 0.00 37.20 2.57
1230 1822 3.410631 TTTCATTCCCGTAGCTGTTCA 57.589 42.857 0.00 0.00 0.00 3.18
1281 1873 1.073025 ACAAGCTGCGGGTTCATCA 59.927 52.632 7.09 0.00 0.00 3.07
1294 1886 4.003648 GGGTTCATCATCTGTTCGTTTCT 58.996 43.478 0.00 0.00 0.00 2.52
1298 1890 7.308348 GGGTTCATCATCTGTTCGTTTCTTTTA 60.308 37.037 0.00 0.00 0.00 1.52
1301 1893 7.298122 TCATCATCTGTTCGTTTCTTTTAAGC 58.702 34.615 0.00 0.00 0.00 3.09
1315 1907 9.016623 GTTTCTTTTAAGCGTCTGTTTGTTTAT 57.983 29.630 0.00 0.00 0.00 1.40
1325 1917 1.341531 TGTTTGTTTATTGGTGCCCGG 59.658 47.619 0.00 0.00 0.00 5.73
1411 2003 6.289834 AGGAAATGAAGAGATGTATGCTCTG 58.710 40.000 0.00 0.00 41.66 3.35
1423 2015 3.503363 TGTATGCTCTGGCTTGAAAGTTG 59.497 43.478 0.00 0.00 39.59 3.16
1447 2039 7.217200 TGTTCTAATCACTCTTAACACTGCTT 58.783 34.615 0.00 0.00 0.00 3.91
1454 2046 4.811024 CACTCTTAACACTGCTTCTGTTGA 59.189 41.667 4.95 0.00 33.79 3.18
1456 2048 6.017605 CACTCTTAACACTGCTTCTGTTGATT 60.018 38.462 4.95 0.00 33.79 2.57
1458 2050 7.715249 ACTCTTAACACTGCTTCTGTTGATTTA 59.285 33.333 4.95 0.00 33.79 1.40
1505 2097 4.154737 TGAATGTGAATGAGTAGTTGCTGC 59.845 41.667 0.00 0.00 0.00 5.25
1538 2130 4.024302 GGTATGCGTTCCCTGTTAATAAGC 60.024 45.833 0.00 0.00 0.00 3.09
1539 2131 3.343941 TGCGTTCCCTGTTAATAAGCT 57.656 42.857 0.00 0.00 0.00 3.74
1543 2135 4.082949 GCGTTCCCTGTTAATAAGCTGTTT 60.083 41.667 0.00 0.00 0.00 2.83
1547 2139 7.094933 CGTTCCCTGTTAATAAGCTGTTTAACT 60.095 37.037 22.45 0.00 38.51 2.24
1578 2170 6.098838 ACTGCTCATTCTGAATCATGGTAGTA 59.901 38.462 0.00 0.00 0.00 1.82
1583 2175 9.689976 CTCATTCTGAATCATGGTAGTAAGTAG 57.310 37.037 0.00 0.00 0.00 2.57
1598 2190 6.912951 AGTAAGTAGTCTCTTGTTTGCCTA 57.087 37.500 0.00 0.00 0.00 3.93
1666 2259 6.946340 TCATATCTAGTGTTGAATGTGGTGT 58.054 36.000 0.00 0.00 0.00 4.16
1734 2327 5.964758 TGAACTGAGTTGCACATTCTTTTT 58.035 33.333 0.90 0.00 0.00 1.94
1763 2357 8.816144 TGTTCACTGCATTTTGTTATTTTCTTC 58.184 29.630 0.00 0.00 0.00 2.87
1806 2400 7.257722 AGTTGTTTTGTTCTGGTAATGACAAG 58.742 34.615 0.00 0.00 0.00 3.16
2124 2718 2.686558 TCAACAAGATGCTTTCGTGC 57.313 45.000 3.80 0.00 37.34 5.34
2372 2966 9.216117 TGCTGAGATGATATGATATTCTTGTTG 57.784 33.333 0.00 0.00 0.00 3.33
2385 2979 7.814107 TGATATTCTTGTTGAAATTTCTGTGCC 59.186 33.333 18.64 3.60 38.29 5.01
2388 2982 1.406898 TGTTGAAATTTCTGTGCCGCA 59.593 42.857 18.64 0.00 0.00 5.69
2496 3091 2.456119 GCCTGATGGAGTCAACGCG 61.456 63.158 3.53 3.53 36.14 6.01
2502 3097 0.034896 ATGGAGTCAACGCGAAGGTT 59.965 50.000 15.93 0.00 0.00 3.50
2596 3192 6.869913 CCTGCATCAACTAATTGTTTCATGTT 59.130 34.615 0.00 0.00 36.63 2.71
2597 3193 7.385752 CCTGCATCAACTAATTGTTTCATGTTT 59.614 33.333 0.00 0.00 36.63 2.83
2687 3283 2.103094 TGCCGCATAATCTAGCAGAAGT 59.897 45.455 0.00 0.00 0.00 3.01
2688 3284 2.734079 GCCGCATAATCTAGCAGAAGTC 59.266 50.000 0.00 0.00 0.00 3.01
2701 3302 2.722071 CAGAAGTCTCCGTTCTATCGC 58.278 52.381 0.00 0.00 32.81 4.58
2895 3496 1.024271 CTGTGGTTGTTGTCCTGTGG 58.976 55.000 0.00 0.00 0.00 4.17
2916 3517 6.203145 TGTGGTTGAATTTGATGCTTCATTTG 59.797 34.615 2.75 0.00 31.83 2.32
2942 3543 9.937175 GATGAAGCTACATAAGGAAAATGTTAC 57.063 33.333 0.00 0.00 38.49 2.50
2943 3544 9.686683 ATGAAGCTACATAAGGAAAATGTTACT 57.313 29.630 0.00 0.00 38.49 2.24
2951 3552 8.718734 ACATAAGGAAAATGTTACTCGTTCTTC 58.281 33.333 0.00 0.00 33.83 2.87
2955 3556 6.018180 AGGAAAATGTTACTCGTTCTTCACAC 60.018 38.462 0.00 0.00 0.00 3.82
2973 3574 4.876679 TCACACGGTTTGAAACATTCTGTA 59.123 37.500 10.53 0.00 0.00 2.74
2980 3581 7.148137 ACGGTTTGAAACATTCTGTAAAGAGTT 60.148 33.333 10.53 0.00 0.00 3.01
2981 3582 7.165812 CGGTTTGAAACATTCTGTAAAGAGTTG 59.834 37.037 10.53 0.00 0.00 3.16
2992 3593 6.658831 TCTGTAAAGAGTTGAGCAAAATTCG 58.341 36.000 0.00 0.00 0.00 3.34
2997 3598 0.732538 GTTGAGCAAAATTCGGGCCG 60.733 55.000 22.51 22.51 0.00 6.13
2999 3600 1.154035 GAGCAAAATTCGGGCCGTG 60.154 57.895 27.32 17.44 0.00 4.94
3015 3616 2.937873 GCCGTGGCACCTTTCAGTAATA 60.938 50.000 12.86 0.00 41.49 0.98
3018 3628 4.201910 CCGTGGCACCTTTCAGTAATATTG 60.202 45.833 12.86 0.00 0.00 1.90
3048 3665 6.041637 AGCAGTATACAATTTCCGGATGTCTA 59.958 38.462 12.37 5.22 0.00 2.59
3054 3671 5.671493 ACAATTTCCGGATGTCTAGTTAGG 58.329 41.667 4.15 0.00 0.00 2.69
3060 3677 4.105217 TCCGGATGTCTAGTTAGGGTATCA 59.895 45.833 0.00 0.00 0.00 2.15
3086 3703 1.269517 TGGTCAATTTTGCTGGCGTTC 60.270 47.619 0.00 0.00 0.00 3.95
3117 4073 2.413310 ATACAATTTCCGGACGCCTT 57.587 45.000 1.83 0.00 0.00 4.35
3229 4189 4.365514 TCATGTCAGTTTGCCTTCCTTA 57.634 40.909 0.00 0.00 0.00 2.69
3232 4192 5.774690 TCATGTCAGTTTGCCTTCCTTATTT 59.225 36.000 0.00 0.00 0.00 1.40
3239 4239 2.000048 TGCCTTCCTTATTTCCCCTGT 59.000 47.619 0.00 0.00 0.00 4.00
3272 4275 6.407752 GGTTCGAAATCCCTAGAATTACCAGA 60.408 42.308 0.00 0.00 0.00 3.86
3320 4323 6.573664 AATTGAGAATTGACCGAACATGAA 57.426 33.333 0.00 0.00 0.00 2.57
3325 4328 5.009631 AGAATTGACCGAACATGAAATCCA 58.990 37.500 0.00 0.00 0.00 3.41
3332 4335 3.067180 CCGAACATGAAATCCAAGGGATG 59.933 47.826 0.00 0.00 42.27 3.51
3454 4457 1.609580 CGGGGAGACGAACAAAATCCA 60.610 52.381 0.00 0.00 35.47 3.41
3482 4485 4.986587 CGTCGCCCACACGAACGA 62.987 66.667 0.14 0.00 44.93 3.85
3483 4486 3.103911 GTCGCCCACACGAACGAG 61.104 66.667 0.14 0.00 44.93 4.18
3484 4487 3.598715 TCGCCCACACGAACGAGT 61.599 61.111 0.14 0.00 39.54 4.18
3485 4488 2.660552 CGCCCACACGAACGAGTT 60.661 61.111 0.14 0.00 34.06 3.01
3486 4489 2.654912 CGCCCACACGAACGAGTTC 61.655 63.158 5.93 5.93 36.29 3.01
3536 4539 2.503356 TGTTGCCCACAAAATCCAAACT 59.497 40.909 0.00 0.00 37.58 2.66
3572 4575 2.581246 ACATAAACCCCCTTCCTTCCTC 59.419 50.000 0.00 0.00 0.00 3.71
3575 4578 2.696504 CCCCCTTCCTTCCTCCCC 60.697 72.222 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 158 8.999431 TGACTCTAAATTAACTGAAACATGTCC 58.001 33.333 0.00 0.00 0.00 4.02
190 235 7.223584 TCAATCTTGTTGTCCTATTTGACTGA 58.776 34.615 0.00 0.00 36.21 3.41
199 244 7.815840 TGTTTGATTCAATCTTGTTGTCCTA 57.184 32.000 0.00 0.00 0.00 2.94
214 259 8.195617 TGAATGAACCAAAACTTGTTTGATTC 57.804 30.769 0.00 0.14 33.57 2.52
216 261 8.735692 ATTGAATGAACCAAAACTTGTTTGAT 57.264 26.923 0.00 0.00 0.00 2.57
228 296 6.401394 TGTTGTTTGTGATTGAATGAACCAA 58.599 32.000 0.00 0.00 0.00 3.67
233 301 6.870439 TGTTGTTGTTGTTTGTGATTGAATGA 59.130 30.769 0.00 0.00 0.00 2.57
240 308 6.042143 GGATCTTGTTGTTGTTGTTTGTGAT 58.958 36.000 0.00 0.00 0.00 3.06
290 372 5.491078 TCCAGATAAGGGAACTATGGTTTGT 59.509 40.000 0.00 0.00 42.68 2.83
300 382 4.753186 TCCCTAGATCCAGATAAGGGAAC 58.247 47.826 20.51 0.00 44.20 3.62
304 386 6.736581 TCTACATCCCTAGATCCAGATAAGG 58.263 44.000 0.00 2.74 0.00 2.69
311 393 2.555448 CCGCTCTACATCCCTAGATCCA 60.555 54.545 0.00 0.00 0.00 3.41
314 396 1.551452 GCCGCTCTACATCCCTAGAT 58.449 55.000 0.00 0.00 0.00 1.98
315 397 0.889638 CGCCGCTCTACATCCCTAGA 60.890 60.000 0.00 0.00 0.00 2.43
316 398 1.581954 CGCCGCTCTACATCCCTAG 59.418 63.158 0.00 0.00 0.00 3.02
317 399 2.561956 GCGCCGCTCTACATCCCTA 61.562 63.158 0.00 0.00 0.00 3.53
318 400 3.917760 GCGCCGCTCTACATCCCT 61.918 66.667 0.00 0.00 0.00 4.20
319 401 3.917760 AGCGCCGCTCTACATCCC 61.918 66.667 5.39 0.00 30.62 3.85
335 417 4.951963 GAAGCGGGGCGGATCGAG 62.952 72.222 0.00 0.00 0.00 4.04
338 420 4.483243 TTGGAAGCGGGGCGGATC 62.483 66.667 0.00 0.00 0.00 3.36
339 421 4.489771 CTTGGAAGCGGGGCGGAT 62.490 66.667 0.00 0.00 0.00 4.18
342 424 4.697756 TGACTTGGAAGCGGGGCG 62.698 66.667 0.00 0.00 0.00 6.13
343 425 1.460273 TTTTGACTTGGAAGCGGGGC 61.460 55.000 0.00 0.00 0.00 5.80
344 426 1.067635 CATTTTGACTTGGAAGCGGGG 60.068 52.381 0.00 0.00 0.00 5.73
345 427 1.669795 GCATTTTGACTTGGAAGCGGG 60.670 52.381 0.00 0.00 0.00 6.13
346 428 1.000385 TGCATTTTGACTTGGAAGCGG 60.000 47.619 0.00 0.00 0.00 5.52
347 429 2.420628 TGCATTTTGACTTGGAAGCG 57.579 45.000 0.00 0.00 0.00 4.68
348 430 3.916761 TCATGCATTTTGACTTGGAAGC 58.083 40.909 0.00 0.00 0.00 3.86
349 431 3.924686 GCTCATGCATTTTGACTTGGAAG 59.075 43.478 0.00 0.00 39.41 3.46
350 432 3.575256 AGCTCATGCATTTTGACTTGGAA 59.425 39.130 0.00 0.00 42.74 3.53
351 433 3.159472 AGCTCATGCATTTTGACTTGGA 58.841 40.909 0.00 0.00 42.74 3.53
352 434 3.587797 AGCTCATGCATTTTGACTTGG 57.412 42.857 0.00 0.00 42.74 3.61
353 435 5.706916 ACTAAGCTCATGCATTTTGACTTG 58.293 37.500 0.00 0.00 42.74 3.16
354 436 5.972107 ACTAAGCTCATGCATTTTGACTT 57.028 34.783 0.00 3.10 42.74 3.01
355 437 5.972107 AACTAAGCTCATGCATTTTGACT 57.028 34.783 0.00 0.00 42.74 3.41
356 438 9.956720 ATTATAACTAAGCTCATGCATTTTGAC 57.043 29.630 0.00 0.00 42.74 3.18
359 441 9.971922 GGAATTATAACTAAGCTCATGCATTTT 57.028 29.630 0.00 0.00 42.74 1.82
360 442 9.359653 AGGAATTATAACTAAGCTCATGCATTT 57.640 29.630 0.00 0.00 42.74 2.32
361 443 8.930846 AGGAATTATAACTAAGCTCATGCATT 57.069 30.769 0.00 0.00 42.74 3.56
362 444 8.381636 AGAGGAATTATAACTAAGCTCATGCAT 58.618 33.333 0.00 0.00 42.74 3.96
363 445 7.658982 CAGAGGAATTATAACTAAGCTCATGCA 59.341 37.037 0.00 0.00 42.74 3.96
364 446 7.659390 ACAGAGGAATTATAACTAAGCTCATGC 59.341 37.037 0.00 0.00 40.05 4.06
367 449 9.197306 TGTACAGAGGAATTATAACTAAGCTCA 57.803 33.333 0.00 0.00 0.00 4.26
368 450 9.685828 CTGTACAGAGGAATTATAACTAAGCTC 57.314 37.037 18.45 0.00 0.00 4.09
369 451 9.422681 TCTGTACAGAGGAATTATAACTAAGCT 57.577 33.333 21.74 0.00 32.82 3.74
380 462 8.763601 ACTAAGCTAAATCTGTACAGAGGAATT 58.236 33.333 28.29 21.01 41.33 2.17
381 463 8.312669 ACTAAGCTAAATCTGTACAGAGGAAT 57.687 34.615 28.29 16.82 41.33 3.01
382 464 7.719871 ACTAAGCTAAATCTGTACAGAGGAA 57.280 36.000 28.29 15.54 41.33 3.36
383 465 7.719871 AACTAAGCTAAATCTGTACAGAGGA 57.280 36.000 28.29 15.73 41.33 3.71
384 466 8.035394 TCAAACTAAGCTAAATCTGTACAGAGG 58.965 37.037 28.29 18.64 41.33 3.69
385 467 8.988064 TCAAACTAAGCTAAATCTGTACAGAG 57.012 34.615 28.29 16.81 41.33 3.35
386 468 9.204570 GTTCAAACTAAGCTAAATCTGTACAGA 57.795 33.333 27.07 27.07 42.37 3.41
387 469 9.209175 AGTTCAAACTAAGCTAAATCTGTACAG 57.791 33.333 17.17 17.17 37.52 2.74
403 485 8.726988 GCATAAACATGAGGTTAGTTCAAACTA 58.273 33.333 0.00 0.00 39.29 2.24
404 486 7.573096 CGCATAAACATGAGGTTAGTTCAAACT 60.573 37.037 0.00 0.46 39.29 2.66
405 487 6.523201 CGCATAAACATGAGGTTAGTTCAAAC 59.477 38.462 0.00 0.00 39.29 2.93
406 488 6.348950 CCGCATAAACATGAGGTTAGTTCAAA 60.349 38.462 0.00 0.00 39.29 2.69
407 489 5.123186 CCGCATAAACATGAGGTTAGTTCAA 59.877 40.000 0.00 0.00 39.29 2.69
408 490 4.634004 CCGCATAAACATGAGGTTAGTTCA 59.366 41.667 0.00 0.00 39.29 3.18
409 491 4.035208 CCCGCATAAACATGAGGTTAGTTC 59.965 45.833 0.00 0.00 39.29 3.01
410 492 3.945285 CCCGCATAAACATGAGGTTAGTT 59.055 43.478 0.00 0.00 39.29 2.24
411 493 3.541632 CCCGCATAAACATGAGGTTAGT 58.458 45.455 0.00 0.00 39.29 2.24
412 494 2.290641 GCCCGCATAAACATGAGGTTAG 59.709 50.000 0.00 0.00 39.29 2.34
413 495 2.092646 AGCCCGCATAAACATGAGGTTA 60.093 45.455 0.00 0.00 39.29 2.85
414 496 1.102978 GCCCGCATAAACATGAGGTT 58.897 50.000 0.00 0.00 42.98 3.50
415 497 0.255890 AGCCCGCATAAACATGAGGT 59.744 50.000 0.00 0.00 39.46 3.85
416 498 1.392589 AAGCCCGCATAAACATGAGG 58.607 50.000 0.00 0.87 40.57 3.86
417 499 3.610114 GCATAAGCCCGCATAAACATGAG 60.610 47.826 0.00 0.00 33.58 2.90
418 500 2.293122 GCATAAGCCCGCATAAACATGA 59.707 45.455 0.00 0.00 33.58 3.07
419 501 2.664916 GCATAAGCCCGCATAAACATG 58.335 47.619 0.00 0.00 33.58 3.21
420 502 1.266718 CGCATAAGCCCGCATAAACAT 59.733 47.619 0.00 0.00 37.52 2.71
421 503 0.660488 CGCATAAGCCCGCATAAACA 59.340 50.000 0.00 0.00 37.52 2.83
422 504 0.040425 CCGCATAAGCCCGCATAAAC 60.040 55.000 0.00 0.00 37.52 2.01
423 505 1.169661 CCCGCATAAGCCCGCATAAA 61.170 55.000 0.00 0.00 37.52 1.40
424 506 1.599518 CCCGCATAAGCCCGCATAA 60.600 57.895 0.00 0.00 37.52 1.90
425 507 1.836999 ATCCCGCATAAGCCCGCATA 61.837 55.000 0.00 0.00 37.52 3.14
426 508 3.196207 ATCCCGCATAAGCCCGCAT 62.196 57.895 0.00 0.00 37.52 4.73
427 509 3.872603 ATCCCGCATAAGCCCGCA 61.873 61.111 0.00 0.00 37.52 5.69
428 510 3.357079 CATCCCGCATAAGCCCGC 61.357 66.667 0.00 0.00 37.52 6.13
429 511 3.357079 GCATCCCGCATAAGCCCG 61.357 66.667 0.00 0.00 41.79 6.13
430 512 2.985847 GGCATCCCGCATAAGCCC 60.986 66.667 0.00 0.00 45.17 5.19
431 513 2.985847 GGGCATCCCGCATAAGCC 60.986 66.667 0.00 0.00 45.17 4.35
445 527 3.958860 ATAGGGATGCAGGCGGGC 61.959 66.667 0.00 0.00 0.00 6.13
446 528 2.033141 CATAGGGATGCAGGCGGG 59.967 66.667 0.00 0.00 0.00 6.13
447 529 1.598962 CACATAGGGATGCAGGCGG 60.599 63.158 0.00 0.00 36.43 6.13
448 530 0.179048 TTCACATAGGGATGCAGGCG 60.179 55.000 0.00 0.00 36.43 5.52
449 531 2.157738 GATTCACATAGGGATGCAGGC 58.842 52.381 0.00 0.00 36.43 4.85
450 532 2.553904 GGGATTCACATAGGGATGCAGG 60.554 54.545 0.00 0.00 36.43 4.85
451 533 2.374504 AGGGATTCACATAGGGATGCAG 59.625 50.000 0.00 0.00 36.43 4.41
452 534 2.421725 AGGGATTCACATAGGGATGCA 58.578 47.619 0.00 0.00 36.43 3.96
453 535 4.640771 TTAGGGATTCACATAGGGATGC 57.359 45.455 0.00 0.00 36.43 3.91
454 536 7.177392 GGAATTTTAGGGATTCACATAGGGATG 59.823 40.741 0.00 0.00 35.66 3.51
455 537 7.146960 TGGAATTTTAGGGATTCACATAGGGAT 60.147 37.037 0.00 0.00 35.66 3.85
456 538 6.161348 TGGAATTTTAGGGATTCACATAGGGA 59.839 38.462 0.00 0.00 35.66 4.20
457 539 6.372931 TGGAATTTTAGGGATTCACATAGGG 58.627 40.000 0.00 0.00 35.66 3.53
458 540 6.015940 GCTGGAATTTTAGGGATTCACATAGG 60.016 42.308 0.00 0.00 35.66 2.57
459 541 6.547141 TGCTGGAATTTTAGGGATTCACATAG 59.453 38.462 0.00 0.00 35.66 2.23
460 542 6.430864 TGCTGGAATTTTAGGGATTCACATA 58.569 36.000 0.00 0.00 35.66 2.29
461 543 5.271598 TGCTGGAATTTTAGGGATTCACAT 58.728 37.500 0.00 0.00 35.66 3.21
462 544 4.671831 TGCTGGAATTTTAGGGATTCACA 58.328 39.130 0.00 0.00 35.66 3.58
463 545 5.659440 TTGCTGGAATTTTAGGGATTCAC 57.341 39.130 0.00 0.00 35.66 3.18
464 546 5.957168 TCATTGCTGGAATTTTAGGGATTCA 59.043 36.000 0.00 0.00 35.66 2.57
465 547 6.127366 TGTCATTGCTGGAATTTTAGGGATTC 60.127 38.462 0.00 0.00 33.71 2.52
466 548 5.721000 TGTCATTGCTGGAATTTTAGGGATT 59.279 36.000 0.00 0.00 0.00 3.01
486 568 3.196469 CCTCTCTCCACTAGCAAATGTCA 59.804 47.826 0.00 0.00 0.00 3.58
505 587 1.691434 CTAGGTGAGATGCCCTTCCTC 59.309 57.143 0.00 0.00 33.68 3.71
511 593 2.823758 GCCCCTAGGTGAGATGCCC 61.824 68.421 8.29 0.00 34.57 5.36
516 598 1.076923 GTCGAGCCCCTAGGTGAGA 60.077 63.158 8.29 0.00 34.57 3.27
551 633 1.672854 GGAAATGGTTTAGGCCCGGC 61.673 60.000 0.00 0.00 0.00 6.13
552 634 0.033503 AGGAAATGGTTTAGGCCCGG 60.034 55.000 0.00 0.00 0.00 5.73
553 635 1.389555 GAGGAAATGGTTTAGGCCCG 58.610 55.000 0.00 0.00 0.00 6.13
655 1234 3.190535 GGCTCAAATCGGTTTGCTCTAAA 59.809 43.478 16.44 0.00 43.47 1.85
659 1238 0.179189 CGGCTCAAATCGGTTTGCTC 60.179 55.000 16.44 9.67 43.47 4.26
702 1281 1.196104 TTTACTCCCAGACCCGGTGG 61.196 60.000 0.00 0.67 37.80 4.61
703 1282 0.249398 CTTTACTCCCAGACCCGGTG 59.751 60.000 0.00 0.00 0.00 4.94
704 1283 0.178912 ACTTTACTCCCAGACCCGGT 60.179 55.000 0.00 0.00 0.00 5.28
705 1284 0.249398 CACTTTACTCCCAGACCCGG 59.751 60.000 0.00 0.00 0.00 5.73
706 1285 0.974383 ACACTTTACTCCCAGACCCG 59.026 55.000 0.00 0.00 0.00 5.28
707 1286 1.003233 CCACACTTTACTCCCAGACCC 59.997 57.143 0.00 0.00 0.00 4.46
708 1287 1.610886 GCCACACTTTACTCCCAGACC 60.611 57.143 0.00 0.00 0.00 3.85
709 1288 1.610886 GGCCACACTTTACTCCCAGAC 60.611 57.143 0.00 0.00 0.00 3.51
710 1289 0.690762 GGCCACACTTTACTCCCAGA 59.309 55.000 0.00 0.00 0.00 3.86
758 1337 0.396278 GGGCCTGAGGAGAAATTGGG 60.396 60.000 0.65 0.00 0.00 4.12
760 1339 1.821136 GTTGGGCCTGAGGAGAAATTG 59.179 52.381 0.65 0.00 0.00 2.32
1019 1598 0.326713 GAGAGGGGGAGGGTAAAGCT 60.327 60.000 0.00 0.00 0.00 3.74
1054 1633 5.178623 CCAGATGAACGCTAGACTAGAGTAG 59.821 48.000 17.82 6.30 37.87 2.57
1088 1668 0.233590 TCAAACGATTGCACGAACCG 59.766 50.000 3.48 0.00 36.45 4.44
1121 1701 2.435805 GGATCTAGGCCAGATTCACACA 59.564 50.000 15.93 0.00 44.41 3.72
1170 1750 5.708230 ACTAAATAAACATCGGGAGCAACAA 59.292 36.000 0.00 0.00 0.00 2.83
1216 1808 1.045407 ACAAGTGAACAGCTACGGGA 58.955 50.000 0.00 0.00 0.00 5.14
1230 1822 4.196193 TGTTCTTTCGAATCACCACAAGT 58.804 39.130 0.00 0.00 0.00 3.16
1262 1854 1.236616 TGATGAACCCGCAGCTTGTG 61.237 55.000 0.00 0.00 0.00 3.33
1281 1873 5.465724 AGACGCTTAAAAGAAACGAACAGAT 59.534 36.000 0.00 0.00 0.00 2.90
1294 1886 7.221067 CACCAATAAACAAACAGACGCTTAAAA 59.779 33.333 0.00 0.00 0.00 1.52
1298 1890 4.606961 CACCAATAAACAAACAGACGCTT 58.393 39.130 0.00 0.00 0.00 4.68
1301 1893 3.305110 GGCACCAATAAACAAACAGACG 58.695 45.455 0.00 0.00 0.00 4.18
1411 2003 6.205658 AGAGTGATTAGAACAACTTTCAAGCC 59.794 38.462 0.00 0.00 0.00 4.35
1423 2015 7.600752 AGAAGCAGTGTTAAGAGTGATTAGAAC 59.399 37.037 10.55 0.00 0.00 3.01
1447 2039 8.729756 CATTGACCATACAACTAAATCAACAGA 58.270 33.333 0.00 0.00 32.50 3.41
1458 2050 9.147732 TCATAGAGTATCATTGACCATACAACT 57.852 33.333 0.00 0.00 37.82 3.16
1505 2097 2.031191 GGAACGCATACCATTGTAACCG 59.969 50.000 0.00 0.17 33.43 4.44
1538 2130 2.316119 GCAGTTGGCGAGTTAAACAG 57.684 50.000 0.00 0.00 0.00 3.16
1543 2135 6.360924 TCAGAATGAGCAGTTGGCGAGTTA 62.361 45.833 0.00 0.00 42.56 2.24
1547 2139 0.321346 TCAGAATGAGCAGTTGGCGA 59.679 50.000 0.00 0.00 42.56 5.54
1578 2170 6.360370 TGATAGGCAAACAAGAGACTACTT 57.640 37.500 0.00 0.00 0.00 2.24
1583 2175 4.702131 ACCATTGATAGGCAAACAAGAGAC 59.298 41.667 0.00 0.00 40.48 3.36
2372 2966 4.925068 AGATATTGCGGCACAGAAATTTC 58.075 39.130 10.33 10.33 0.00 2.17
2385 2979 6.952743 AGAAGCACAAATTAGAGATATTGCG 58.047 36.000 0.00 0.00 0.00 4.85
2496 3091 6.072452 GCCCAGCATCAAGTATATTAACCTTC 60.072 42.308 0.00 0.00 0.00 3.46
2502 3097 6.777091 ACAATTGCCCAGCATCAAGTATATTA 59.223 34.615 5.05 0.00 38.76 0.98
2596 3192 1.800586 CGAGCAGCTGCAAAGTAAGAA 59.199 47.619 38.24 0.00 45.16 2.52
2597 3193 1.432514 CGAGCAGCTGCAAAGTAAGA 58.567 50.000 38.24 0.00 45.16 2.10
2601 3197 1.002868 ATCCGAGCAGCTGCAAAGT 60.003 52.632 38.24 19.88 45.16 2.66
2687 3283 4.913335 ATAAGTTGCGATAGAACGGAGA 57.087 40.909 0.00 0.00 34.85 3.71
2688 3284 5.968387 AAATAAGTTGCGATAGAACGGAG 57.032 39.130 0.00 0.00 34.85 4.63
2701 3302 6.308371 AGTTCCACACGGTAAAATAAGTTG 57.692 37.500 0.00 0.00 0.00 3.16
2895 3496 8.246908 TCATCAAATGAAGCATCAAATTCAAC 57.753 30.769 0.00 0.00 38.80 3.18
2916 3517 9.937175 GTAACATTTTCCTTATGTAGCTTCATC 57.063 33.333 9.33 0.00 35.26 2.92
2942 3543 2.198406 TCAAACCGTGTGAAGAACGAG 58.802 47.619 0.00 0.00 43.68 4.18
2943 3544 2.296831 TCAAACCGTGTGAAGAACGA 57.703 45.000 0.00 0.00 43.68 3.85
2973 3574 3.552890 GCCCGAATTTTGCTCAACTCTTT 60.553 43.478 0.00 0.00 0.00 2.52
2980 3581 1.602323 ACGGCCCGAATTTTGCTCA 60.602 52.632 11.71 0.00 0.00 4.26
2981 3582 1.154035 CACGGCCCGAATTTTGCTC 60.154 57.895 11.71 0.00 0.00 4.26
2992 3593 4.966787 TGAAAGGTGCCACGGCCC 62.967 66.667 5.42 6.54 41.09 5.80
2997 3598 5.897377 ACAATATTACTGAAAGGTGCCAC 57.103 39.130 0.00 0.00 39.30 5.01
2999 3600 6.509418 TCAACAATATTACTGAAAGGTGCC 57.491 37.500 0.00 0.00 39.30 5.01
3015 3616 7.250569 CGGAAATTGTATACTGCTTCAACAAT 58.749 34.615 4.17 0.00 41.29 2.71
3018 3628 5.353123 TCCGGAAATTGTATACTGCTTCAAC 59.647 40.000 0.00 0.00 0.00 3.18
3048 3665 3.643792 GACCAGCAGATGATACCCTAACT 59.356 47.826 0.00 0.00 0.00 2.24
3054 3671 5.585390 CAAAATTGACCAGCAGATGATACC 58.415 41.667 0.00 0.00 0.00 2.73
3060 3677 2.232941 CCAGCAAAATTGACCAGCAGAT 59.767 45.455 0.00 0.00 0.00 2.90
3086 3703 8.074972 GTCCGGAAATTGTATACTACTCTACTG 58.925 40.741 5.23 0.00 0.00 2.74
3117 4073 3.425094 CGAAACAACCAACTGAACGAACA 60.425 43.478 0.00 0.00 0.00 3.18
3195 4155 9.571810 GCAAACTGACATGAATGTTATATTTCA 57.428 29.630 0.00 0.00 41.95 2.69
3196 4156 9.023967 GGCAAACTGACATGAATGTTATATTTC 57.976 33.333 0.00 0.00 41.95 2.17
3205 4165 3.508793 AGGAAGGCAAACTGACATGAATG 59.491 43.478 0.00 0.00 0.00 2.67
3229 4189 4.600062 GAACCATCAACTACAGGGGAAAT 58.400 43.478 0.00 0.00 0.00 2.17
3232 4192 1.553248 CGAACCATCAACTACAGGGGA 59.447 52.381 0.00 0.00 0.00 4.81
3239 4239 4.837093 AGGGATTTCGAACCATCAACTA 57.163 40.909 11.04 0.00 0.00 2.24
3272 4275 2.243221 CTCCCAAATCCAGATCACCCTT 59.757 50.000 0.00 0.00 0.00 3.95
3284 4287 4.789012 TTCTCAATTGTGCTCCCAAATC 57.211 40.909 5.13 0.00 0.00 2.17
3312 4315 5.418576 AGCCATCCCTTGGATTTCATGTTC 61.419 45.833 0.00 0.00 43.17 3.18
3320 4323 1.213296 ACGTAGCCATCCCTTGGATT 58.787 50.000 0.00 0.00 43.17 3.01
3325 4328 0.912487 TCCCAACGTAGCCATCCCTT 60.912 55.000 0.00 0.00 0.00 3.95
3332 4335 1.227176 GACCGATCCCAACGTAGCC 60.227 63.158 0.00 0.00 0.00 3.93
3335 4338 1.067425 CAACAGACCGATCCCAACGTA 60.067 52.381 0.00 0.00 0.00 3.57
3397 4400 2.863401 TCGATGGTCGTCTATTGGTG 57.137 50.000 0.00 0.00 41.35 4.17
3428 4431 2.362120 TTCGTCTCCCCGGGTCTC 60.362 66.667 21.85 5.94 0.00 3.36
3437 4440 3.551551 CGTTTGGATTTTGTTCGTCTCC 58.448 45.455 0.00 0.00 0.00 3.71
3466 4469 3.103911 CTCGTTCGTGTGGGCGAC 61.104 66.667 0.00 0.00 40.85 5.19
3536 4539 1.746470 TATGTCCTCGTCGCTCTTGA 58.254 50.000 0.00 0.00 0.00 3.02
3572 4575 2.317378 GGGGAAAGGGGAAGAGGGG 61.317 68.421 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.