Multiple sequence alignment - TraesCS3D01G239200

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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 TraesCS3D01G239200 chr3D 100.000 2918 0 0 1 2918 331014020 331016937 0.000000e+00 5389
1 TraesCS3D01G239200 chr3D 97.015 134 4 0 2566 2699 422517661 422517794 2.930000e-55 226
2 TraesCS3D01G239200 chr3A 98.458 2205 31 3 716 2918 447495135 447497338 0.000000e+00 3880
3 TraesCS3D01G239200 chr3A 85.821 134 17 2 588 720 447144294 447144426 1.090000e-29 141
4 TraesCS3D01G239200 chr3B 97.639 1906 41 4 663 2565 429970304 429972208 0.000000e+00 3267
5 TraesCS3D01G239200 chr3B 92.140 229 8 5 2699 2918 429972191 429972418 6.070000e-82 315
6 TraesCS3D01G239200 chr2D 94.854 583 30 0 2 584 536173810 536173228 0.000000e+00 911
7 TraesCS3D01G239200 chr7A 97.744 133 3 0 2566 2698 83784967 83784835 2.260000e-56 230
8 TraesCS3D01G239200 chr2B 97.744 133 3 0 2566 2698 660461555 660461423 2.260000e-56 230
9 TraesCS3D01G239200 chr7B 97.015 134 4 0 2566 2699 639088021 639087888 2.930000e-55 226
10 TraesCS3D01G239200 chr1B 97.015 134 4 0 2566 2699 415223991 415223858 2.930000e-55 226
11 TraesCS3D01G239200 chr4D 96.992 133 4 0 2566 2698 482703492 482703624 1.050000e-54 224
12 TraesCS3D01G239200 chr4A 96.350 137 3 2 2565 2699 200090435 200090571 1.050000e-54 224
13 TraesCS3D01G239200 chr2A 96.992 133 4 0 2566 2698 611937051 611937183 1.050000e-54 224


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 TraesCS3D01G239200 chr3D 331014020 331016937 2917 False 5389 5389 100.0000 1 2918 1 chr3D.!!$F1 2917
1 TraesCS3D01G239200 chr3A 447495135 447497338 2203 False 3880 3880 98.4580 716 2918 1 chr3A.!!$F2 2202
2 TraesCS3D01G239200 chr3B 429970304 429972418 2114 False 1791 3267 94.8895 663 2918 2 chr3B.!!$F1 2255
3 TraesCS3D01G239200 chr2D 536173228 536173810 582 True 911 911 94.8540 2 584 1 chr2D.!!$R1 582

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
645 646 0.024238 CGTTCTCTTGAATGAGCGCG 59.976 55.0 0.0 0.0 40.63 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2543 2614 0.250295 CCGACAAGCTGACCTTCCAA 60.25 55.0 0.0 0.0 0.0 3.53 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.954382 CATCGAGGAATAGGTGGACGA 59.046 52.381 0.00 0.00 0.00 4.20
132 133 3.911260 TGGGTACAACTCCAAATAGGTGA 59.089 43.478 0.00 0.00 36.19 4.02
133 134 4.538490 TGGGTACAACTCCAAATAGGTGAT 59.462 41.667 0.00 0.00 36.19 3.06
164 165 1.953017 CGCTATGGAGAGAGGGACG 59.047 63.158 0.00 0.00 0.00 4.79
165 166 0.820074 CGCTATGGAGAGAGGGACGT 60.820 60.000 0.00 0.00 0.00 4.34
178 179 1.204941 AGGGACGTTGTGTAGCAGATC 59.795 52.381 0.00 0.00 0.00 2.75
255 256 1.209504 TCAAACATCCCCCTCACGATC 59.790 52.381 0.00 0.00 0.00 3.69
284 285 2.494918 CCCCTCACATCGTCGTCC 59.505 66.667 0.00 0.00 0.00 4.79
311 312 2.586792 GCCTCGGCAGATCAAGGT 59.413 61.111 2.41 0.00 41.49 3.50
318 319 1.648467 GGCAGATCAAGGTGAACGGC 61.648 60.000 0.00 2.80 39.00 5.68
319 320 0.674895 GCAGATCAAGGTGAACGGCT 60.675 55.000 0.00 0.00 37.38 5.52
320 321 1.813513 CAGATCAAGGTGAACGGCTT 58.186 50.000 0.00 0.00 0.00 4.35
321 322 1.734465 CAGATCAAGGTGAACGGCTTC 59.266 52.381 0.00 0.00 0.00 3.86
322 323 1.347707 AGATCAAGGTGAACGGCTTCA 59.652 47.619 0.00 0.00 33.76 3.02
323 324 2.026822 AGATCAAGGTGAACGGCTTCAT 60.027 45.455 0.00 0.00 38.69 2.57
324 325 1.808411 TCAAGGTGAACGGCTTCATC 58.192 50.000 3.35 3.09 38.69 2.92
325 326 0.804989 CAAGGTGAACGGCTTCATCC 59.195 55.000 6.40 7.68 38.17 3.51
336 337 1.264288 GGCTTCATCCGAAATTAGCCG 59.736 52.381 0.00 0.00 31.42 5.52
337 338 1.264288 GCTTCATCCGAAATTAGCCGG 59.736 52.381 0.00 0.00 46.57 6.13
338 339 1.264288 CTTCATCCGAAATTAGCCGGC 59.736 52.381 21.89 21.89 44.96 6.13
339 340 0.878523 TCATCCGAAATTAGCCGGCG 60.879 55.000 23.20 4.23 44.96 6.46
340 341 2.251642 ATCCGAAATTAGCCGGCGC 61.252 57.895 23.20 0.00 44.96 6.53
342 343 2.626455 CGAAATTAGCCGGCGCTC 59.374 61.111 23.20 13.01 43.95 5.03
343 344 2.882366 CGAAATTAGCCGGCGCTCC 61.882 63.158 23.20 8.62 43.95 4.70
344 345 1.523938 GAAATTAGCCGGCGCTCCT 60.524 57.895 23.20 5.39 43.95 3.69
345 346 1.077716 AAATTAGCCGGCGCTCCTT 60.078 52.632 23.20 9.42 43.95 3.36
346 347 1.376609 AAATTAGCCGGCGCTCCTTG 61.377 55.000 23.20 0.00 43.95 3.61
347 348 2.536997 AATTAGCCGGCGCTCCTTGT 62.537 55.000 23.20 2.71 43.95 3.16
348 349 2.925162 ATTAGCCGGCGCTCCTTGTC 62.925 60.000 23.20 0.00 43.95 3.18
353 354 4.719369 GGCGCTCCTTGTCGACGT 62.719 66.667 11.62 0.00 0.00 4.34
354 355 2.177531 GCGCTCCTTGTCGACGTA 59.822 61.111 11.62 0.15 0.00 3.57
355 356 2.150837 GCGCTCCTTGTCGACGTAC 61.151 63.158 11.62 0.00 0.00 3.67
356 357 1.500844 CGCTCCTTGTCGACGTACT 59.499 57.895 11.62 0.00 0.00 2.73
357 358 0.520827 CGCTCCTTGTCGACGTACTC 60.521 60.000 11.62 0.00 0.00 2.59
358 359 0.520827 GCTCCTTGTCGACGTACTCG 60.521 60.000 11.62 8.00 44.44 4.18
359 360 0.520827 CTCCTTGTCGACGTACTCGC 60.521 60.000 11.62 6.21 42.62 5.03
360 361 1.513586 CCTTGTCGACGTACTCGCC 60.514 63.158 11.62 0.68 42.62 5.54
361 362 1.208358 CTTGTCGACGTACTCGCCA 59.792 57.895 11.62 2.97 42.62 5.69
362 363 0.386352 CTTGTCGACGTACTCGCCAA 60.386 55.000 11.62 9.59 42.62 4.52
363 364 0.661187 TTGTCGACGTACTCGCCAAC 60.661 55.000 11.62 3.84 42.62 3.77
364 365 2.142239 GTCGACGTACTCGCCAACG 61.142 63.158 0.00 2.40 42.62 4.10
376 377 2.145053 CGCCAACGAAATTCTTCTCG 57.855 50.000 0.00 0.00 43.93 4.04
382 383 2.864968 ACGAAATTCTTCTCGTCTCCG 58.135 47.619 0.00 0.00 44.64 4.63
383 384 1.584308 CGAAATTCTTCTCGTCTCCGC 59.416 52.381 0.00 0.00 0.00 5.54
384 385 2.732597 CGAAATTCTTCTCGTCTCCGCT 60.733 50.000 0.00 0.00 0.00 5.52
385 386 2.570442 AATTCTTCTCGTCTCCGCTC 57.430 50.000 0.00 0.00 0.00 5.03
386 387 0.741915 ATTCTTCTCGTCTCCGCTCC 59.258 55.000 0.00 0.00 0.00 4.70
387 388 0.322636 TTCTTCTCGTCTCCGCTCCT 60.323 55.000 0.00 0.00 0.00 3.69
388 389 0.745128 TCTTCTCGTCTCCGCTCCTC 60.745 60.000 0.00 0.00 0.00 3.71
389 390 1.002502 TTCTCGTCTCCGCTCCTCA 60.003 57.895 0.00 0.00 0.00 3.86
390 391 0.394488 TTCTCGTCTCCGCTCCTCAT 60.394 55.000 0.00 0.00 0.00 2.90
391 392 0.816018 TCTCGTCTCCGCTCCTCATC 60.816 60.000 0.00 0.00 0.00 2.92
392 393 2.111932 CTCGTCTCCGCTCCTCATCG 62.112 65.000 0.00 0.00 0.00 3.84
393 394 2.725008 GTCTCCGCTCCTCATCGG 59.275 66.667 0.00 0.00 46.52 4.18
394 395 3.219928 TCTCCGCTCCTCATCGGC 61.220 66.667 0.00 0.00 44.91 5.54
395 396 3.531207 CTCCGCTCCTCATCGGCA 61.531 66.667 0.00 0.00 44.91 5.69
396 397 2.839632 TCCGCTCCTCATCGGCAT 60.840 61.111 0.00 0.00 44.91 4.40
397 398 2.356793 CCGCTCCTCATCGGCATC 60.357 66.667 0.00 0.00 39.14 3.91
398 399 2.732468 CGCTCCTCATCGGCATCG 60.732 66.667 0.00 0.00 37.82 3.84
399 400 3.040763 GCTCCTCATCGGCATCGC 61.041 66.667 0.00 0.00 36.13 4.58
400 401 2.732468 CTCCTCATCGGCATCGCG 60.732 66.667 0.00 0.00 36.13 5.87
401 402 3.490793 CTCCTCATCGGCATCGCGT 62.491 63.158 5.77 0.00 36.13 6.01
402 403 2.130073 CTCCTCATCGGCATCGCGTA 62.130 60.000 5.77 0.00 36.13 4.42
403 404 2.016704 CCTCATCGGCATCGCGTAC 61.017 63.158 5.77 0.00 36.13 3.67
404 405 2.353030 TCATCGGCATCGCGTACG 60.353 61.111 11.84 11.84 42.01 3.67
405 406 2.654085 CATCGGCATCGCGTACGT 60.654 61.111 17.90 0.00 41.18 3.57
406 407 2.654085 ATCGGCATCGCGTACGTG 60.654 61.111 22.43 22.43 41.18 4.49
407 408 3.115910 ATCGGCATCGCGTACGTGA 62.116 57.895 31.25 31.25 41.18 4.35
408 409 2.601628 ATCGGCATCGCGTACGTGAA 62.602 55.000 32.50 17.92 41.18 3.18
409 410 2.438148 CGGCATCGCGTACGTGAAA 61.438 57.895 32.50 13.91 41.18 2.69
410 411 1.058284 GGCATCGCGTACGTGAAAC 59.942 57.895 32.50 25.57 41.18 2.78
411 412 1.349259 GGCATCGCGTACGTGAAACT 61.349 55.000 32.50 15.95 41.18 2.66
412 413 0.437295 GCATCGCGTACGTGAAACTT 59.563 50.000 32.50 15.58 41.18 2.66
413 414 1.136446 GCATCGCGTACGTGAAACTTT 60.136 47.619 32.50 15.21 41.18 2.66
414 415 2.090967 GCATCGCGTACGTGAAACTTTA 59.909 45.455 32.50 10.91 41.18 1.85
415 416 3.776795 GCATCGCGTACGTGAAACTTTAG 60.777 47.826 32.50 17.39 41.18 1.85
416 417 2.318578 TCGCGTACGTGAAACTTTAGG 58.681 47.619 27.87 0.00 41.18 2.69
417 418 1.387756 CGCGTACGTGAAACTTTAGGG 59.612 52.381 23.95 0.00 31.75 3.53
418 419 2.676076 GCGTACGTGAAACTTTAGGGA 58.324 47.619 17.90 0.00 31.75 4.20
419 420 3.256558 GCGTACGTGAAACTTTAGGGAT 58.743 45.455 17.90 0.00 31.75 3.85
420 421 3.061697 GCGTACGTGAAACTTTAGGGATG 59.938 47.826 17.90 0.00 31.75 3.51
421 422 3.615496 CGTACGTGAAACTTTAGGGATGG 59.385 47.826 7.22 0.00 31.75 3.51
422 423 2.433436 ACGTGAAACTTTAGGGATGGC 58.567 47.619 0.00 0.00 31.75 4.40
423 424 1.396996 CGTGAAACTTTAGGGATGGCG 59.603 52.381 0.00 0.00 31.75 5.69
424 425 1.743394 GTGAAACTTTAGGGATGGCGG 59.257 52.381 0.00 0.00 0.00 6.13
425 426 1.353022 TGAAACTTTAGGGATGGCGGT 59.647 47.619 0.00 0.00 0.00 5.68
426 427 2.224917 TGAAACTTTAGGGATGGCGGTT 60.225 45.455 0.00 0.00 0.00 4.44
427 428 1.834188 AACTTTAGGGATGGCGGTTG 58.166 50.000 0.00 0.00 0.00 3.77
428 429 0.696501 ACTTTAGGGATGGCGGTTGT 59.303 50.000 0.00 0.00 0.00 3.32
429 430 1.094785 CTTTAGGGATGGCGGTTGTG 58.905 55.000 0.00 0.00 0.00 3.33
430 431 0.322997 TTTAGGGATGGCGGTTGTGG 60.323 55.000 0.00 0.00 0.00 4.17
431 432 1.493854 TTAGGGATGGCGGTTGTGGT 61.494 55.000 0.00 0.00 0.00 4.16
432 433 2.191786 TAGGGATGGCGGTTGTGGTG 62.192 60.000 0.00 0.00 0.00 4.17
433 434 3.061848 GGATGGCGGTTGTGGTGG 61.062 66.667 0.00 0.00 0.00 4.61
434 435 2.282180 GATGGCGGTTGTGGTGGT 60.282 61.111 0.00 0.00 0.00 4.16
435 436 1.901464 GATGGCGGTTGTGGTGGTT 60.901 57.895 0.00 0.00 0.00 3.67
436 437 0.606944 GATGGCGGTTGTGGTGGTTA 60.607 55.000 0.00 0.00 0.00 2.85
437 438 0.891904 ATGGCGGTTGTGGTGGTTAC 60.892 55.000 0.00 0.00 0.00 2.50
439 440 2.263021 GCGGTTGTGGTGGTTACCC 61.263 63.158 0.00 0.00 46.96 3.69
440 441 1.452801 CGGTTGTGGTGGTTACCCT 59.547 57.895 0.00 0.00 46.96 4.34
441 442 0.686224 CGGTTGTGGTGGTTACCCTA 59.314 55.000 0.00 0.00 46.96 3.53
442 443 1.338389 CGGTTGTGGTGGTTACCCTAG 60.338 57.143 0.00 0.00 46.96 3.02
443 444 1.612462 GGTTGTGGTGGTTACCCTAGC 60.612 57.143 0.00 0.00 46.96 3.42
444 445 1.350019 GTTGTGGTGGTTACCCTAGCT 59.650 52.381 0.00 0.00 46.96 3.32
445 446 2.568509 GTTGTGGTGGTTACCCTAGCTA 59.431 50.000 0.00 0.00 46.96 3.32
446 447 2.463752 TGTGGTGGTTACCCTAGCTAG 58.536 52.381 14.20 14.20 46.96 3.42
447 448 1.761198 GTGGTGGTTACCCTAGCTAGG 59.239 57.143 30.05 30.05 46.96 3.02
455 456 2.444140 CCTAGCTAGGGCGTGGGT 60.444 66.667 29.47 0.16 44.37 4.51
456 457 2.797278 CCTAGCTAGGGCGTGGGTG 61.797 68.421 29.47 2.80 44.37 4.61
457 458 2.038329 TAGCTAGGGCGTGGGTGT 59.962 61.111 5.49 0.00 44.37 4.16
458 459 2.298158 CTAGCTAGGGCGTGGGTGTG 62.298 65.000 13.32 0.00 44.37 3.82
459 460 2.791613 TAGCTAGGGCGTGGGTGTGA 62.792 60.000 5.49 0.00 44.37 3.58
460 461 2.579201 CTAGGGCGTGGGTGTGAG 59.421 66.667 0.00 0.00 0.00 3.51
461 462 1.982395 CTAGGGCGTGGGTGTGAGA 60.982 63.158 0.00 0.00 0.00 3.27
462 463 1.534476 TAGGGCGTGGGTGTGAGAA 60.534 57.895 0.00 0.00 0.00 2.87
463 464 1.823169 TAGGGCGTGGGTGTGAGAAC 61.823 60.000 0.00 0.00 0.00 3.01
464 465 2.110213 GGCGTGGGTGTGAGAACA 59.890 61.111 0.00 0.00 0.00 3.18
465 466 1.302511 GGCGTGGGTGTGAGAACAT 60.303 57.895 0.00 0.00 0.00 2.71
466 467 1.577328 GGCGTGGGTGTGAGAACATG 61.577 60.000 0.00 0.00 0.00 3.21
467 468 1.577328 GCGTGGGTGTGAGAACATGG 61.577 60.000 0.00 0.00 0.00 3.66
468 469 0.955428 CGTGGGTGTGAGAACATGGG 60.955 60.000 0.00 0.00 0.00 4.00
469 470 0.609131 GTGGGTGTGAGAACATGGGG 60.609 60.000 0.00 0.00 0.00 4.96
470 471 1.000896 GGGTGTGAGAACATGGGGG 60.001 63.158 0.00 0.00 0.00 5.40
471 472 1.767692 GGTGTGAGAACATGGGGGT 59.232 57.895 0.00 0.00 0.00 4.95
472 473 0.112412 GGTGTGAGAACATGGGGGTT 59.888 55.000 0.00 0.00 0.00 4.11
473 474 1.480498 GGTGTGAGAACATGGGGGTTT 60.480 52.381 0.00 0.00 0.00 3.27
474 475 1.613437 GTGTGAGAACATGGGGGTTTG 59.387 52.381 0.00 0.00 0.00 2.93
475 476 1.216678 TGTGAGAACATGGGGGTTTGT 59.783 47.619 0.00 0.00 0.00 2.83
476 477 2.443632 TGTGAGAACATGGGGGTTTGTA 59.556 45.455 0.00 0.00 0.00 2.41
477 478 3.081804 GTGAGAACATGGGGGTTTGTAG 58.918 50.000 0.00 0.00 0.00 2.74
478 479 2.041081 TGAGAACATGGGGGTTTGTAGG 59.959 50.000 0.00 0.00 0.00 3.18
479 480 2.307686 GAGAACATGGGGGTTTGTAGGA 59.692 50.000 0.00 0.00 0.00 2.94
480 481 2.926329 AGAACATGGGGGTTTGTAGGAT 59.074 45.455 0.00 0.00 0.00 3.24
481 482 3.336694 AGAACATGGGGGTTTGTAGGATT 59.663 43.478 0.00 0.00 0.00 3.01
482 483 4.542525 AGAACATGGGGGTTTGTAGGATTA 59.457 41.667 0.00 0.00 0.00 1.75
483 484 5.195756 AGAACATGGGGGTTTGTAGGATTAT 59.804 40.000 0.00 0.00 0.00 1.28
484 485 6.391649 AGAACATGGGGGTTTGTAGGATTATA 59.608 38.462 0.00 0.00 0.00 0.98
485 486 6.796867 ACATGGGGGTTTGTAGGATTATAT 57.203 37.500 0.00 0.00 0.00 0.86
486 487 7.898470 ACATGGGGGTTTGTAGGATTATATA 57.102 36.000 0.00 0.00 0.00 0.86
487 488 7.928873 ACATGGGGGTTTGTAGGATTATATAG 58.071 38.462 0.00 0.00 0.00 1.31
488 489 6.382919 TGGGGGTTTGTAGGATTATATAGC 57.617 41.667 0.00 0.00 0.00 2.97
489 490 5.252164 TGGGGGTTTGTAGGATTATATAGCC 59.748 44.000 0.00 0.00 0.00 3.93
490 491 5.339778 GGGGGTTTGTAGGATTATATAGCCC 60.340 48.000 0.00 0.00 38.24 5.19
491 492 5.252164 GGGGTTTGTAGGATTATATAGCCCA 59.748 44.000 0.00 0.00 38.57 5.36
492 493 6.069029 GGGGTTTGTAGGATTATATAGCCCAT 60.069 42.308 0.00 0.00 38.57 4.00
493 494 7.054751 GGGTTTGTAGGATTATATAGCCCATC 58.945 42.308 0.00 0.00 0.00 3.51
494 495 7.092399 GGGTTTGTAGGATTATATAGCCCATCT 60.092 40.741 0.00 0.00 0.00 2.90
495 496 7.770897 GGTTTGTAGGATTATATAGCCCATCTG 59.229 40.741 5.59 0.00 0.00 2.90
496 497 8.322091 GTTTGTAGGATTATATAGCCCATCTGT 58.678 37.037 5.59 0.00 0.00 3.41
497 498 9.555411 TTTGTAGGATTATATAGCCCATCTGTA 57.445 33.333 5.59 0.00 0.00 2.74
498 499 9.555411 TTGTAGGATTATATAGCCCATCTGTAA 57.445 33.333 5.59 0.00 0.00 2.41
499 500 9.201989 TGTAGGATTATATAGCCCATCTGTAAG 57.798 37.037 5.59 0.00 0.00 2.34
500 501 7.682787 AGGATTATATAGCCCATCTGTAAGG 57.317 40.000 5.59 0.00 0.00 2.69
504 505 4.637771 GCCCATCTGTAAGGCGTT 57.362 55.556 0.00 0.00 36.84 4.84
505 506 2.098293 GCCCATCTGTAAGGCGTTG 58.902 57.895 0.97 0.00 36.84 4.10
506 507 1.376609 GCCCATCTGTAAGGCGTTGG 61.377 60.000 0.97 0.00 36.84 3.77
507 508 0.251916 CCCATCTGTAAGGCGTTGGA 59.748 55.000 0.97 0.00 0.00 3.53
508 509 1.134098 CCCATCTGTAAGGCGTTGGAT 60.134 52.381 0.97 0.70 0.00 3.41
509 510 2.213499 CCATCTGTAAGGCGTTGGATC 58.787 52.381 0.97 0.00 0.00 3.36
510 511 2.158900 CCATCTGTAAGGCGTTGGATCT 60.159 50.000 0.97 0.00 0.00 2.75
511 512 3.535561 CATCTGTAAGGCGTTGGATCTT 58.464 45.455 0.97 0.00 0.00 2.40
512 513 3.695830 TCTGTAAGGCGTTGGATCTTT 57.304 42.857 0.97 0.00 0.00 2.52
513 514 4.015872 TCTGTAAGGCGTTGGATCTTTT 57.984 40.909 0.97 0.00 0.00 2.27
514 515 4.394729 TCTGTAAGGCGTTGGATCTTTTT 58.605 39.130 0.97 0.00 0.00 1.94
515 516 4.215399 TCTGTAAGGCGTTGGATCTTTTTG 59.785 41.667 0.97 0.00 0.00 2.44
516 517 2.438868 AAGGCGTTGGATCTTTTTGC 57.561 45.000 0.00 0.00 0.00 3.68
517 518 1.327303 AGGCGTTGGATCTTTTTGCA 58.673 45.000 0.00 0.00 0.00 4.08
518 519 1.686052 AGGCGTTGGATCTTTTTGCAA 59.314 42.857 0.00 0.00 0.00 4.08
519 520 2.102252 AGGCGTTGGATCTTTTTGCAAA 59.898 40.909 8.05 8.05 0.00 3.68
520 521 2.869192 GGCGTTGGATCTTTTTGCAAAA 59.131 40.909 20.46 20.46 0.00 2.44
521 522 3.498018 GGCGTTGGATCTTTTTGCAAAAT 59.502 39.130 24.39 10.72 0.00 1.82
522 523 4.377328 GGCGTTGGATCTTTTTGCAAAATC 60.377 41.667 24.39 18.23 0.00 2.17
523 524 4.377328 GCGTTGGATCTTTTTGCAAAATCC 60.377 41.667 25.99 25.99 33.96 3.01
524 525 4.749099 CGTTGGATCTTTTTGCAAAATCCA 59.251 37.500 29.30 29.30 37.55 3.41
525 526 5.236047 CGTTGGATCTTTTTGCAAAATCCAA 59.764 36.000 34.10 34.10 41.36 3.53
526 527 6.429624 GTTGGATCTTTTTGCAAAATCCAAC 58.570 36.000 40.03 40.03 46.54 3.77
527 528 5.678583 TGGATCTTTTTGCAAAATCCAACA 58.321 33.333 30.21 21.40 37.03 3.33
528 529 5.759273 TGGATCTTTTTGCAAAATCCAACAG 59.241 36.000 30.21 21.47 37.03 3.16
529 530 5.990996 GGATCTTTTTGCAAAATCCAACAGA 59.009 36.000 27.05 23.13 33.77 3.41
530 531 6.146673 GGATCTTTTTGCAAAATCCAACAGAG 59.853 38.462 27.05 18.63 33.77 3.35
531 532 6.219417 TCTTTTTGCAAAATCCAACAGAGA 57.781 33.333 24.39 17.61 0.00 3.10
532 533 6.042143 TCTTTTTGCAAAATCCAACAGAGAC 58.958 36.000 24.39 0.00 0.00 3.36
533 534 4.320608 TTTGCAAAATCCAACAGAGACC 57.679 40.909 10.02 0.00 0.00 3.85
534 535 1.879380 TGCAAAATCCAACAGAGACCG 59.121 47.619 0.00 0.00 0.00 4.79
535 536 2.151202 GCAAAATCCAACAGAGACCGA 58.849 47.619 0.00 0.00 0.00 4.69
536 537 2.160417 GCAAAATCCAACAGAGACCGAG 59.840 50.000 0.00 0.00 0.00 4.63
537 538 3.403038 CAAAATCCAACAGAGACCGAGT 58.597 45.455 0.00 0.00 0.00 4.18
538 539 2.751166 AATCCAACAGAGACCGAGTG 57.249 50.000 0.00 0.00 0.00 3.51
539 540 0.898320 ATCCAACAGAGACCGAGTGG 59.102 55.000 0.00 0.00 42.84 4.00
549 550 3.351450 CCGAGTGGTCTGACGTGA 58.649 61.111 0.00 0.00 0.00 4.35
550 551 1.210413 CCGAGTGGTCTGACGTGAG 59.790 63.158 0.00 0.00 0.00 3.51
551 552 1.442857 CGAGTGGTCTGACGTGAGC 60.443 63.158 0.00 0.00 35.28 4.26
552 553 1.442857 GAGTGGTCTGACGTGAGCG 60.443 63.158 0.00 0.00 44.93 5.03
562 563 2.885113 CGTGAGCGTGGGATCAGA 59.115 61.111 0.00 0.00 39.65 3.27
563 564 1.517257 CGTGAGCGTGGGATCAGAC 60.517 63.158 0.00 0.00 39.65 3.51
564 565 1.893786 GTGAGCGTGGGATCAGACT 59.106 57.895 0.00 0.00 39.65 3.24
565 566 0.179124 GTGAGCGTGGGATCAGACTC 60.179 60.000 0.00 0.00 39.65 3.36
566 567 1.323271 TGAGCGTGGGATCAGACTCC 61.323 60.000 0.00 0.00 32.73 3.85
567 568 1.000993 AGCGTGGGATCAGACTCCT 59.999 57.895 0.00 0.00 35.50 3.69
568 569 1.142748 GCGTGGGATCAGACTCCTG 59.857 63.158 0.00 0.00 41.74 3.86
579 580 3.821748 TCAGACTCCTGATACATAGCGT 58.178 45.455 0.00 0.00 44.01 5.07
580 581 4.207955 TCAGACTCCTGATACATAGCGTT 58.792 43.478 0.00 0.00 44.01 4.84
581 582 4.645136 TCAGACTCCTGATACATAGCGTTT 59.355 41.667 0.00 0.00 44.01 3.60
582 583 4.979197 CAGACTCCTGATACATAGCGTTTC 59.021 45.833 0.00 0.00 43.02 2.78
583 584 4.038162 AGACTCCTGATACATAGCGTTTCC 59.962 45.833 0.00 0.00 0.00 3.13
584 585 3.961408 ACTCCTGATACATAGCGTTTCCT 59.039 43.478 0.00 0.00 0.00 3.36
585 586 4.038162 ACTCCTGATACATAGCGTTTCCTC 59.962 45.833 0.00 0.00 0.00 3.71
586 587 3.321111 TCCTGATACATAGCGTTTCCTCC 59.679 47.826 0.00 0.00 0.00 4.30
587 588 3.069586 CCTGATACATAGCGTTTCCTCCA 59.930 47.826 0.00 0.00 0.00 3.86
588 589 4.442893 CCTGATACATAGCGTTTCCTCCAA 60.443 45.833 0.00 0.00 0.00 3.53
589 590 5.092554 TGATACATAGCGTTTCCTCCAAA 57.907 39.130 0.00 0.00 0.00 3.28
590 591 5.680619 TGATACATAGCGTTTCCTCCAAAT 58.319 37.500 0.00 0.00 0.00 2.32
591 592 6.822442 TGATACATAGCGTTTCCTCCAAATA 58.178 36.000 0.00 0.00 0.00 1.40
592 593 7.276658 TGATACATAGCGTTTCCTCCAAATAA 58.723 34.615 0.00 0.00 0.00 1.40
593 594 7.771361 TGATACATAGCGTTTCCTCCAAATAAA 59.229 33.333 0.00 0.00 0.00 1.40
594 595 6.827586 ACATAGCGTTTCCTCCAAATAAAA 57.172 33.333 0.00 0.00 0.00 1.52
595 596 6.852664 ACATAGCGTTTCCTCCAAATAAAAG 58.147 36.000 0.00 0.00 0.00 2.27
596 597 6.433093 ACATAGCGTTTCCTCCAAATAAAAGT 59.567 34.615 0.00 0.00 0.00 2.66
597 598 7.608761 ACATAGCGTTTCCTCCAAATAAAAGTA 59.391 33.333 0.00 0.00 0.00 2.24
598 599 6.250344 AGCGTTTCCTCCAAATAAAAGTAC 57.750 37.500 0.00 0.00 0.00 2.73
599 600 5.766174 AGCGTTTCCTCCAAATAAAAGTACA 59.234 36.000 0.00 0.00 0.00 2.90
600 601 6.433093 AGCGTTTCCTCCAAATAAAAGTACAT 59.567 34.615 0.00 0.00 0.00 2.29
601 602 7.608761 AGCGTTTCCTCCAAATAAAAGTACATA 59.391 33.333 0.00 0.00 0.00 2.29
602 603 8.403236 GCGTTTCCTCCAAATAAAAGTACATAT 58.597 33.333 0.00 0.00 0.00 1.78
603 604 9.716507 CGTTTCCTCCAAATAAAAGTACATATG 57.283 33.333 0.00 0.00 0.00 1.78
604 605 9.516314 GTTTCCTCCAAATAAAAGTACATATGC 57.484 33.333 1.58 0.00 0.00 3.14
605 606 8.815565 TTCCTCCAAATAAAAGTACATATGCA 57.184 30.769 1.58 0.00 0.00 3.96
606 607 8.995027 TCCTCCAAATAAAAGTACATATGCAT 57.005 30.769 3.79 3.79 0.00 3.96
620 621 2.839486 ATGCATATGTGGTAGACCGG 57.161 50.000 0.00 0.00 39.43 5.28
621 622 1.783071 TGCATATGTGGTAGACCGGA 58.217 50.000 9.46 0.00 39.43 5.14
622 623 1.411246 TGCATATGTGGTAGACCGGAC 59.589 52.381 9.46 0.10 39.43 4.79
623 624 1.602165 GCATATGTGGTAGACCGGACG 60.602 57.143 9.46 0.00 39.43 4.79
624 625 0.672342 ATATGTGGTAGACCGGACGC 59.328 55.000 9.46 0.00 39.43 5.19
625 626 0.394762 TATGTGGTAGACCGGACGCT 60.395 55.000 9.46 4.80 39.43 5.07
626 627 1.664321 ATGTGGTAGACCGGACGCTC 61.664 60.000 9.46 0.00 39.43 5.03
627 628 3.129502 TGGTAGACCGGACGCTCG 61.130 66.667 9.46 0.00 39.43 5.03
628 629 3.130160 GGTAGACCGGACGCTCGT 61.130 66.667 9.46 0.00 0.00 4.18
629 630 2.694760 GGTAGACCGGACGCTCGTT 61.695 63.158 9.46 0.00 0.00 3.85
630 631 1.226239 GTAGACCGGACGCTCGTTC 60.226 63.158 9.46 0.00 0.00 3.95
631 632 1.376424 TAGACCGGACGCTCGTTCT 60.376 57.895 9.46 0.00 36.04 3.01
632 633 1.364626 TAGACCGGACGCTCGTTCTC 61.365 60.000 9.46 0.00 34.00 2.87
633 634 2.672307 ACCGGACGCTCGTTCTCT 60.672 61.111 9.46 0.00 0.00 3.10
634 635 2.197643 GACCGGACGCTCGTTCTCTT 62.198 60.000 9.46 0.00 0.00 2.85
635 636 1.801913 CCGGACGCTCGTTCTCTTG 60.802 63.158 0.00 0.00 0.00 3.02
636 637 1.209383 CGGACGCTCGTTCTCTTGA 59.791 57.895 0.00 0.00 0.00 3.02
637 638 0.386858 CGGACGCTCGTTCTCTTGAA 60.387 55.000 0.00 0.00 0.00 2.69
638 639 1.732732 CGGACGCTCGTTCTCTTGAAT 60.733 52.381 0.00 0.00 34.40 2.57
639 640 1.656095 GGACGCTCGTTCTCTTGAATG 59.344 52.381 0.00 0.00 39.79 2.67
640 641 2.596452 GACGCTCGTTCTCTTGAATGA 58.404 47.619 0.00 0.00 43.57 2.57
644 645 1.350193 TCGTTCTCTTGAATGAGCGC 58.650 50.000 0.00 0.00 41.66 5.92
645 646 0.024238 CGTTCTCTTGAATGAGCGCG 59.976 55.000 0.00 0.00 40.63 6.86
646 647 1.350193 GTTCTCTTGAATGAGCGCGA 58.650 50.000 12.10 0.00 34.40 5.87
647 648 1.726791 GTTCTCTTGAATGAGCGCGAA 59.273 47.619 12.10 0.00 34.40 4.70
648 649 1.350193 TCTCTTGAATGAGCGCGAAC 58.650 50.000 12.10 2.54 34.29 3.95
649 650 1.070821 CTCTTGAATGAGCGCGAACA 58.929 50.000 12.10 9.52 0.00 3.18
650 651 0.790207 TCTTGAATGAGCGCGAACAC 59.210 50.000 12.10 0.00 0.00 3.32
651 652 0.512518 CTTGAATGAGCGCGAACACA 59.487 50.000 12.10 3.59 0.00 3.72
652 653 0.234625 TTGAATGAGCGCGAACACAC 59.765 50.000 12.10 7.22 0.00 3.82
653 654 0.599991 TGAATGAGCGCGAACACACT 60.600 50.000 12.10 0.00 0.00 3.55
654 655 0.512952 GAATGAGCGCGAACACACTT 59.487 50.000 12.10 0.00 0.00 3.16
655 656 0.944386 AATGAGCGCGAACACACTTT 59.056 45.000 12.10 0.00 0.00 2.66
656 657 0.944386 ATGAGCGCGAACACACTTTT 59.056 45.000 12.10 0.00 0.00 2.27
657 658 1.573026 TGAGCGCGAACACACTTTTA 58.427 45.000 12.10 0.00 0.00 1.52
658 659 1.934525 TGAGCGCGAACACACTTTTAA 59.065 42.857 12.10 0.00 0.00 1.52
659 660 2.033236 TGAGCGCGAACACACTTTTAAG 60.033 45.455 12.10 0.00 0.00 1.85
660 661 2.206750 AGCGCGAACACACTTTTAAGA 58.793 42.857 12.10 0.00 0.00 2.10
661 662 2.806244 AGCGCGAACACACTTTTAAGAT 59.194 40.909 12.10 0.00 0.00 2.40
666 667 6.183359 GCGCGAACACACTTTTAAGATTTTAG 60.183 38.462 12.10 0.00 0.00 1.85
756 758 2.751259 GGAATTGCAGATGCTCTCACAA 59.249 45.455 6.35 0.00 42.66 3.33
830 832 4.003788 ACCCGTTGGCAGGACTCG 62.004 66.667 0.00 0.00 33.59 4.18
2015 2085 6.874664 TGTGGATAATTAGTTTGTTGACGCTA 59.125 34.615 0.00 0.00 0.00 4.26
2143 2213 1.321474 TCTGCAAAAAGTGAGCCAGG 58.679 50.000 0.00 0.00 0.00 4.45
2543 2614 9.883142 TGATTTATGTTCCTTCTGTTTTTGTTT 57.117 25.926 0.00 0.00 0.00 2.83
2621 2692 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2641 2712 2.752121 GTACTATAGACCCAAAGCGGC 58.248 52.381 6.78 0.00 0.00 6.53
2717 2788 2.617274 GGTCAAGCTTGTCGGCCAC 61.617 63.158 25.19 14.73 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.767409 TCCACCTATTCCTCGATGTATCTG 59.233 45.833 0.00 0.00 0.00 2.90
17 18 1.671742 GACACACCATCGTCCACCT 59.328 57.895 0.00 0.00 0.00 4.00
26 27 0.324614 TCTTGCCATCGACACACCAT 59.675 50.000 0.00 0.00 0.00 3.55
52 53 1.001120 TGTCGGAGCCACCCATCTA 59.999 57.895 0.00 0.00 34.64 1.98
81 82 2.114670 CGTTCCAATCCGGCTGCAT 61.115 57.895 0.50 0.00 33.14 3.96
82 83 2.745884 CGTTCCAATCCGGCTGCA 60.746 61.111 0.50 0.00 33.14 4.41
89 90 1.173043 TCATGTTGCCGTTCCAATCC 58.827 50.000 0.00 0.00 0.00 3.01
102 103 4.380843 TGGAGTTGTACCCATTCATGTT 57.619 40.909 0.00 0.00 0.00 2.71
103 104 4.380843 TTGGAGTTGTACCCATTCATGT 57.619 40.909 0.00 0.00 31.66 3.21
132 133 3.141398 CCATAGCGCATCCAACTACAAT 58.859 45.455 11.47 0.00 0.00 2.71
133 134 2.169561 TCCATAGCGCATCCAACTACAA 59.830 45.455 11.47 0.00 0.00 2.41
164 165 4.725556 TTGTTTCGATCTGCTACACAAC 57.274 40.909 0.00 0.00 0.00 3.32
165 166 4.994217 TCATTGTTTCGATCTGCTACACAA 59.006 37.500 0.00 0.00 0.00 3.33
178 179 5.289434 TGAGATCGATCAACTCATTGTTTCG 59.711 40.000 26.47 8.04 40.59 3.46
336 337 3.332493 TACGTCGACAAGGAGCGCC 62.332 63.158 17.16 0.00 0.00 6.53
337 338 2.150837 GTACGTCGACAAGGAGCGC 61.151 63.158 17.16 0.00 0.00 5.92
338 339 0.520827 GAGTACGTCGACAAGGAGCG 60.521 60.000 17.16 1.70 0.00 5.03
339 340 3.309453 GAGTACGTCGACAAGGAGC 57.691 57.895 17.16 0.00 0.00 4.70
353 354 7.778512 ACGAGAAGAATTTCGTTGGCGAGTA 62.779 44.000 0.00 0.00 46.87 2.59
355 356 4.701364 ACGAGAAGAATTTCGTTGGCGAG 61.701 47.826 0.00 0.00 46.87 5.03
356 357 1.724623 CGAGAAGAATTTCGTTGGCGA 59.275 47.619 0.00 0.00 46.36 5.54
357 358 1.459592 ACGAGAAGAATTTCGTTGGCG 59.540 47.619 0.00 0.00 46.87 5.69
381 382 2.732468 CGATGCCGATGAGGAGCG 60.732 66.667 0.00 0.00 45.00 5.03
382 383 3.040763 GCGATGCCGATGAGGAGC 61.041 66.667 0.00 0.00 45.00 4.70
383 384 2.130073 TACGCGATGCCGATGAGGAG 62.130 60.000 15.93 0.00 45.00 3.69
384 385 2.190841 TACGCGATGCCGATGAGGA 61.191 57.895 15.93 0.00 45.00 3.71
385 386 2.016704 GTACGCGATGCCGATGAGG 61.017 63.158 15.93 0.00 44.97 3.86
386 387 2.357543 CGTACGCGATGCCGATGAG 61.358 63.158 15.93 0.00 41.33 2.90
387 388 2.353030 CGTACGCGATGCCGATGA 60.353 61.111 15.93 0.00 41.33 2.92
388 389 2.654085 ACGTACGCGATGCCGATG 60.654 61.111 15.93 0.00 42.00 3.84
389 390 2.601628 TTCACGTACGCGATGCCGAT 62.602 55.000 15.93 0.00 42.00 4.18
390 391 2.799488 TTTCACGTACGCGATGCCGA 62.799 55.000 15.93 0.00 42.00 5.54
391 392 2.438148 TTTCACGTACGCGATGCCG 61.438 57.895 15.93 11.53 42.00 5.69
392 393 1.058284 GTTTCACGTACGCGATGCC 59.942 57.895 15.93 0.00 42.00 4.40
393 394 0.437295 AAGTTTCACGTACGCGATGC 59.563 50.000 15.93 7.29 42.00 3.91
394 395 2.848562 AAAGTTTCACGTACGCGATG 57.151 45.000 15.93 6.60 42.00 3.84
395 396 2.919229 CCTAAAGTTTCACGTACGCGAT 59.081 45.455 15.93 0.00 42.00 4.58
396 397 2.318578 CCTAAAGTTTCACGTACGCGA 58.681 47.619 15.93 8.88 42.00 5.87
397 398 1.387756 CCCTAAAGTTTCACGTACGCG 59.612 52.381 16.72 3.53 44.93 6.01
398 399 2.676076 TCCCTAAAGTTTCACGTACGC 58.324 47.619 16.72 0.00 0.00 4.42
399 400 3.615496 CCATCCCTAAAGTTTCACGTACG 59.385 47.826 15.01 15.01 0.00 3.67
400 401 3.373130 GCCATCCCTAAAGTTTCACGTAC 59.627 47.826 0.00 0.00 0.00 3.67
401 402 3.602483 GCCATCCCTAAAGTTTCACGTA 58.398 45.455 0.00 0.00 0.00 3.57
402 403 2.433436 GCCATCCCTAAAGTTTCACGT 58.567 47.619 0.00 0.00 0.00 4.49
403 404 1.396996 CGCCATCCCTAAAGTTTCACG 59.603 52.381 0.00 0.00 0.00 4.35
404 405 1.743394 CCGCCATCCCTAAAGTTTCAC 59.257 52.381 0.00 0.00 0.00 3.18
405 406 1.353022 ACCGCCATCCCTAAAGTTTCA 59.647 47.619 0.00 0.00 0.00 2.69
406 407 2.124277 ACCGCCATCCCTAAAGTTTC 57.876 50.000 0.00 0.00 0.00 2.78
407 408 2.167662 CAACCGCCATCCCTAAAGTTT 58.832 47.619 0.00 0.00 0.00 2.66
408 409 1.074889 ACAACCGCCATCCCTAAAGTT 59.925 47.619 0.00 0.00 0.00 2.66
409 410 0.696501 ACAACCGCCATCCCTAAAGT 59.303 50.000 0.00 0.00 0.00 2.66
410 411 1.094785 CACAACCGCCATCCCTAAAG 58.905 55.000 0.00 0.00 0.00 1.85
411 412 0.322997 CCACAACCGCCATCCCTAAA 60.323 55.000 0.00 0.00 0.00 1.85
412 413 1.301623 CCACAACCGCCATCCCTAA 59.698 57.895 0.00 0.00 0.00 2.69
413 414 1.921346 ACCACAACCGCCATCCCTA 60.921 57.895 0.00 0.00 0.00 3.53
414 415 3.256960 ACCACAACCGCCATCCCT 61.257 61.111 0.00 0.00 0.00 4.20
415 416 3.061848 CACCACAACCGCCATCCC 61.062 66.667 0.00 0.00 0.00 3.85
416 417 3.061848 CCACCACAACCGCCATCC 61.062 66.667 0.00 0.00 0.00 3.51
417 418 0.606944 TAACCACCACAACCGCCATC 60.607 55.000 0.00 0.00 0.00 3.51
418 419 0.891904 GTAACCACCACAACCGCCAT 60.892 55.000 0.00 0.00 0.00 4.40
419 420 1.526455 GTAACCACCACAACCGCCA 60.526 57.895 0.00 0.00 0.00 5.69
420 421 2.263021 GGTAACCACCACAACCGCC 61.263 63.158 0.00 0.00 45.04 6.13
421 422 3.347168 GGTAACCACCACAACCGC 58.653 61.111 0.00 0.00 45.04 5.68
438 439 2.444140 ACCCACGCCCTAGCTAGG 60.444 66.667 30.05 30.05 43.25 3.02
439 440 2.058595 ACACCCACGCCCTAGCTAG 61.059 63.158 14.20 14.20 36.60 3.42
440 441 2.038329 ACACCCACGCCCTAGCTA 59.962 61.111 0.00 0.00 36.60 3.32
441 442 3.706373 CACACCCACGCCCTAGCT 61.706 66.667 0.00 0.00 36.60 3.32
442 443 3.665675 CTCACACCCACGCCCTAGC 62.666 68.421 0.00 0.00 0.00 3.42
443 444 1.541310 TTCTCACACCCACGCCCTAG 61.541 60.000 0.00 0.00 0.00 3.02
444 445 1.534476 TTCTCACACCCACGCCCTA 60.534 57.895 0.00 0.00 0.00 3.53
445 446 2.847234 TTCTCACACCCACGCCCT 60.847 61.111 0.00 0.00 0.00 5.19
446 447 2.668550 GTTCTCACACCCACGCCC 60.669 66.667 0.00 0.00 0.00 6.13
447 448 1.302511 ATGTTCTCACACCCACGCC 60.303 57.895 0.00 0.00 35.03 5.68
448 449 1.577328 CCATGTTCTCACACCCACGC 61.577 60.000 0.00 0.00 35.03 5.34
449 450 0.955428 CCCATGTTCTCACACCCACG 60.955 60.000 0.00 0.00 35.03 4.94
450 451 0.609131 CCCCATGTTCTCACACCCAC 60.609 60.000 0.00 0.00 35.03 4.61
451 452 1.767036 CCCCATGTTCTCACACCCA 59.233 57.895 0.00 0.00 35.03 4.51
452 453 1.000896 CCCCCATGTTCTCACACCC 60.001 63.158 0.00 0.00 35.03 4.61
453 454 0.112412 AACCCCCATGTTCTCACACC 59.888 55.000 0.00 0.00 35.03 4.16
454 455 1.613437 CAAACCCCCATGTTCTCACAC 59.387 52.381 0.00 0.00 35.03 3.82
455 456 1.216678 ACAAACCCCCATGTTCTCACA 59.783 47.619 0.00 0.00 37.31 3.58
456 457 1.995376 ACAAACCCCCATGTTCTCAC 58.005 50.000 0.00 0.00 0.00 3.51
457 458 2.041081 CCTACAAACCCCCATGTTCTCA 59.959 50.000 0.00 0.00 0.00 3.27
458 459 2.307686 TCCTACAAACCCCCATGTTCTC 59.692 50.000 0.00 0.00 0.00 2.87
459 460 2.354328 TCCTACAAACCCCCATGTTCT 58.646 47.619 0.00 0.00 0.00 3.01
460 461 2.891191 TCCTACAAACCCCCATGTTC 57.109 50.000 0.00 0.00 0.00 3.18
461 462 3.845109 AATCCTACAAACCCCCATGTT 57.155 42.857 0.00 0.00 0.00 2.71
462 463 6.796867 ATATAATCCTACAAACCCCCATGT 57.203 37.500 0.00 0.00 0.00 3.21
463 464 6.828785 GCTATATAATCCTACAAACCCCCATG 59.171 42.308 0.00 0.00 0.00 3.66
464 465 6.069029 GGCTATATAATCCTACAAACCCCCAT 60.069 42.308 0.00 0.00 0.00 4.00
465 466 5.252164 GGCTATATAATCCTACAAACCCCCA 59.748 44.000 0.00 0.00 0.00 4.96
466 467 5.339778 GGGCTATATAATCCTACAAACCCCC 60.340 48.000 0.00 0.00 0.00 5.40
467 468 5.252164 TGGGCTATATAATCCTACAAACCCC 59.748 44.000 0.00 0.00 0.00 4.95
468 469 6.382919 TGGGCTATATAATCCTACAAACCC 57.617 41.667 0.00 0.00 0.00 4.11
469 470 7.770897 CAGATGGGCTATATAATCCTACAAACC 59.229 40.741 0.00 0.00 0.00 3.27
470 471 8.322091 ACAGATGGGCTATATAATCCTACAAAC 58.678 37.037 0.00 0.00 0.00 2.93
471 472 8.449423 ACAGATGGGCTATATAATCCTACAAA 57.551 34.615 0.00 0.00 0.00 2.83
472 473 9.555411 TTACAGATGGGCTATATAATCCTACAA 57.445 33.333 0.00 0.00 0.00 2.41
473 474 9.201989 CTTACAGATGGGCTATATAATCCTACA 57.798 37.037 0.00 0.00 0.00 2.74
474 475 8.643324 CCTTACAGATGGGCTATATAATCCTAC 58.357 40.741 0.00 0.00 0.00 3.18
475 476 7.290248 GCCTTACAGATGGGCTATATAATCCTA 59.710 40.741 0.00 0.00 42.31 2.94
476 477 6.100424 GCCTTACAGATGGGCTATATAATCCT 59.900 42.308 0.00 0.00 42.31 3.24
477 478 6.292150 GCCTTACAGATGGGCTATATAATCC 58.708 44.000 0.00 0.00 42.31 3.01
478 479 5.986135 CGCCTTACAGATGGGCTATATAATC 59.014 44.000 0.00 0.00 43.29 1.75
479 480 5.425539 ACGCCTTACAGATGGGCTATATAAT 59.574 40.000 0.00 0.00 43.29 1.28
480 481 4.775780 ACGCCTTACAGATGGGCTATATAA 59.224 41.667 0.00 0.00 43.29 0.98
481 482 4.350245 ACGCCTTACAGATGGGCTATATA 58.650 43.478 0.00 0.00 43.29 0.86
482 483 3.173965 ACGCCTTACAGATGGGCTATAT 58.826 45.455 0.00 0.00 43.29 0.86
483 484 2.605257 ACGCCTTACAGATGGGCTATA 58.395 47.619 0.00 0.00 43.29 1.31
484 485 1.424638 ACGCCTTACAGATGGGCTAT 58.575 50.000 0.00 0.00 43.29 2.97
485 486 1.134521 CAACGCCTTACAGATGGGCTA 60.135 52.381 0.00 0.00 43.29 3.93
486 487 0.392998 CAACGCCTTACAGATGGGCT 60.393 55.000 0.00 0.00 43.29 5.19
487 488 1.376609 CCAACGCCTTACAGATGGGC 61.377 60.000 0.00 0.00 42.18 5.36
488 489 0.251916 TCCAACGCCTTACAGATGGG 59.748 55.000 0.00 0.00 0.00 4.00
489 490 2.158900 AGATCCAACGCCTTACAGATGG 60.159 50.000 0.00 0.00 0.00 3.51
490 491 3.185246 AGATCCAACGCCTTACAGATG 57.815 47.619 0.00 0.00 0.00 2.90
491 492 3.914426 AAGATCCAACGCCTTACAGAT 57.086 42.857 0.00 0.00 0.00 2.90
492 493 3.695830 AAAGATCCAACGCCTTACAGA 57.304 42.857 0.00 0.00 0.00 3.41
493 494 4.475944 CAAAAAGATCCAACGCCTTACAG 58.524 43.478 0.00 0.00 0.00 2.74
494 495 3.305064 GCAAAAAGATCCAACGCCTTACA 60.305 43.478 0.00 0.00 0.00 2.41
495 496 3.242518 GCAAAAAGATCCAACGCCTTAC 58.757 45.455 0.00 0.00 0.00 2.34
496 497 2.887783 TGCAAAAAGATCCAACGCCTTA 59.112 40.909 0.00 0.00 0.00 2.69
497 498 1.686052 TGCAAAAAGATCCAACGCCTT 59.314 42.857 0.00 0.00 0.00 4.35
498 499 1.327303 TGCAAAAAGATCCAACGCCT 58.673 45.000 0.00 0.00 0.00 5.52
499 500 2.147436 TTGCAAAAAGATCCAACGCC 57.853 45.000 0.00 0.00 0.00 5.68
500 501 4.377328 GGATTTTGCAAAAAGATCCAACGC 60.377 41.667 27.05 8.84 29.29 4.84
501 502 4.749099 TGGATTTTGCAAAAAGATCCAACG 59.251 37.500 30.21 0.00 33.79 4.10
502 503 6.429624 GTTGGATTTTGCAAAAAGATCCAAC 58.570 36.000 40.03 40.03 46.75 3.77
503 504 6.118170 TGTTGGATTTTGCAAAAAGATCCAA 58.882 32.000 34.10 34.10 39.97 3.53
504 505 5.678583 TGTTGGATTTTGCAAAAAGATCCA 58.321 33.333 29.30 29.30 34.49 3.41
505 506 5.990996 TCTGTTGGATTTTGCAAAAAGATCC 59.009 36.000 27.10 26.45 26.96 3.36
506 507 6.925165 TCTCTGTTGGATTTTGCAAAAAGATC 59.075 34.615 27.10 19.50 27.89 2.75
507 508 6.703165 GTCTCTGTTGGATTTTGCAAAAAGAT 59.297 34.615 27.10 12.26 27.89 2.40
508 509 6.042143 GTCTCTGTTGGATTTTGCAAAAAGA 58.958 36.000 27.10 21.11 26.96 2.52
509 510 5.234972 GGTCTCTGTTGGATTTTGCAAAAAG 59.765 40.000 27.10 18.35 26.96 2.27
510 511 5.115480 GGTCTCTGTTGGATTTTGCAAAAA 58.885 37.500 27.10 9.61 26.96 1.94
511 512 4.692228 GGTCTCTGTTGGATTTTGCAAAA 58.308 39.130 25.76 25.76 26.96 2.44
512 513 3.243367 CGGTCTCTGTTGGATTTTGCAAA 60.243 43.478 8.05 8.05 26.96 3.68
513 514 2.293122 CGGTCTCTGTTGGATTTTGCAA 59.707 45.455 0.00 0.00 0.00 4.08
514 515 1.879380 CGGTCTCTGTTGGATTTTGCA 59.121 47.619 0.00 0.00 0.00 4.08
515 516 2.151202 TCGGTCTCTGTTGGATTTTGC 58.849 47.619 0.00 0.00 0.00 3.68
516 517 3.187227 CACTCGGTCTCTGTTGGATTTTG 59.813 47.826 0.00 0.00 0.00 2.44
517 518 3.403038 CACTCGGTCTCTGTTGGATTTT 58.597 45.455 0.00 0.00 0.00 1.82
518 519 2.289694 CCACTCGGTCTCTGTTGGATTT 60.290 50.000 0.00 0.00 0.00 2.17
519 520 1.276421 CCACTCGGTCTCTGTTGGATT 59.724 52.381 0.00 0.00 0.00 3.01
520 521 0.898320 CCACTCGGTCTCTGTTGGAT 59.102 55.000 0.00 0.00 0.00 3.41
521 522 0.469331 ACCACTCGGTCTCTGTTGGA 60.469 55.000 0.00 0.00 44.71 3.53
522 523 2.050269 ACCACTCGGTCTCTGTTGG 58.950 57.895 0.00 0.00 44.71 3.77
532 533 1.210413 CTCACGTCAGACCACTCGG 59.790 63.158 0.00 0.00 38.77 4.63
533 534 1.442857 GCTCACGTCAGACCACTCG 60.443 63.158 0.00 0.00 0.00 4.18
534 535 1.442857 CGCTCACGTCAGACCACTC 60.443 63.158 0.00 0.00 33.53 3.51
535 536 2.645567 CGCTCACGTCAGACCACT 59.354 61.111 0.00 0.00 33.53 4.00
546 547 0.179124 GAGTCTGATCCCACGCTCAC 60.179 60.000 0.00 0.00 0.00 3.51
547 548 1.323271 GGAGTCTGATCCCACGCTCA 61.323 60.000 0.00 0.00 32.79 4.26
548 549 1.040339 AGGAGTCTGATCCCACGCTC 61.040 60.000 0.00 0.00 40.53 5.03
549 550 1.000993 AGGAGTCTGATCCCACGCT 59.999 57.895 0.00 0.00 40.53 5.07
550 551 1.142748 CAGGAGTCTGATCCCACGC 59.857 63.158 0.00 0.00 43.49 5.34
551 552 2.887790 TCAGGAGTCTGATCCCACG 58.112 57.895 0.00 0.00 44.39 4.94
559 560 4.576216 AACGCTATGTATCAGGAGTCTG 57.424 45.455 0.00 0.00 42.21 3.51
560 561 4.038162 GGAAACGCTATGTATCAGGAGTCT 59.962 45.833 0.00 0.00 0.00 3.24
561 562 4.038162 AGGAAACGCTATGTATCAGGAGTC 59.962 45.833 0.00 0.00 0.00 3.36
562 563 3.961408 AGGAAACGCTATGTATCAGGAGT 59.039 43.478 0.00 0.00 0.00 3.85
563 564 4.551388 GAGGAAACGCTATGTATCAGGAG 58.449 47.826 0.00 0.00 0.00 3.69
564 565 3.321111 GGAGGAAACGCTATGTATCAGGA 59.679 47.826 0.00 0.00 0.00 3.86
565 566 3.069586 TGGAGGAAACGCTATGTATCAGG 59.930 47.826 0.00 0.00 0.00 3.86
566 567 4.322080 TGGAGGAAACGCTATGTATCAG 57.678 45.455 0.00 0.00 0.00 2.90
567 568 4.746535 TTGGAGGAAACGCTATGTATCA 57.253 40.909 0.00 0.00 0.00 2.15
568 569 7.724305 TTATTTGGAGGAAACGCTATGTATC 57.276 36.000 0.00 0.00 0.00 2.24
569 570 8.514330 TTTTATTTGGAGGAAACGCTATGTAT 57.486 30.769 0.00 0.00 0.00 2.29
570 571 7.608761 ACTTTTATTTGGAGGAAACGCTATGTA 59.391 33.333 0.00 0.00 0.00 2.29
571 572 6.433093 ACTTTTATTTGGAGGAAACGCTATGT 59.567 34.615 0.00 0.00 0.00 2.29
572 573 6.852664 ACTTTTATTTGGAGGAAACGCTATG 58.147 36.000 0.00 0.00 0.00 2.23
573 574 7.608761 TGTACTTTTATTTGGAGGAAACGCTAT 59.391 33.333 0.00 0.00 0.00 2.97
574 575 6.935771 TGTACTTTTATTTGGAGGAAACGCTA 59.064 34.615 0.00 0.00 0.00 4.26
575 576 5.766174 TGTACTTTTATTTGGAGGAAACGCT 59.234 36.000 0.00 0.00 0.00 5.07
576 577 6.004408 TGTACTTTTATTTGGAGGAAACGC 57.996 37.500 0.00 0.00 0.00 4.84
577 578 9.716507 CATATGTACTTTTATTTGGAGGAAACG 57.283 33.333 0.00 0.00 0.00 3.60
578 579 9.516314 GCATATGTACTTTTATTTGGAGGAAAC 57.484 33.333 4.29 0.00 0.00 2.78
579 580 9.249053 TGCATATGTACTTTTATTTGGAGGAAA 57.751 29.630 4.29 0.00 0.00 3.13
580 581 8.815565 TGCATATGTACTTTTATTTGGAGGAA 57.184 30.769 4.29 0.00 0.00 3.36
581 582 8.995027 ATGCATATGTACTTTTATTTGGAGGA 57.005 30.769 0.00 0.00 0.00 3.71
598 599 4.081697 TCCGGTCTACCACATATGCATATG 60.082 45.833 34.80 34.80 44.37 1.78
599 600 4.081642 GTCCGGTCTACCACATATGCATAT 60.082 45.833 13.63 13.63 35.14 1.78
600 601 3.257375 GTCCGGTCTACCACATATGCATA 59.743 47.826 9.27 9.27 35.14 3.14
601 602 2.037251 GTCCGGTCTACCACATATGCAT 59.963 50.000 3.79 3.79 35.14 3.96
602 603 1.411246 GTCCGGTCTACCACATATGCA 59.589 52.381 0.00 0.00 35.14 3.96
603 604 1.602165 CGTCCGGTCTACCACATATGC 60.602 57.143 0.00 0.00 35.14 3.14
604 605 1.602165 GCGTCCGGTCTACCACATATG 60.602 57.143 0.00 0.00 35.14 1.78
605 606 0.672342 GCGTCCGGTCTACCACATAT 59.328 55.000 0.00 0.00 35.14 1.78
606 607 0.394762 AGCGTCCGGTCTACCACATA 60.395 55.000 0.00 0.00 35.14 2.29
607 608 1.664321 GAGCGTCCGGTCTACCACAT 61.664 60.000 11.30 0.00 39.31 3.21
608 609 2.282674 AGCGTCCGGTCTACCACA 60.283 61.111 0.00 0.00 35.14 4.17
609 610 2.488820 GAGCGTCCGGTCTACCAC 59.511 66.667 11.30 0.00 39.31 4.16
610 611 3.129502 CGAGCGTCCGGTCTACCA 61.130 66.667 15.74 0.00 40.14 3.25
611 612 2.589636 GAACGAGCGTCCGGTCTACC 62.590 65.000 15.74 2.37 42.51 3.18
612 613 1.226239 GAACGAGCGTCCGGTCTAC 60.226 63.158 15.74 0.00 42.51 2.59
613 614 3.181367 GAACGAGCGTCCGGTCTA 58.819 61.111 15.74 0.00 42.51 2.59
615 616 2.197643 AAGAGAACGAGCGTCCGGTC 62.198 60.000 0.00 8.72 45.85 4.79
616 617 2.266627 AAGAGAACGAGCGTCCGGT 61.267 57.895 0.00 0.00 0.00 5.28
617 618 1.801913 CAAGAGAACGAGCGTCCGG 60.802 63.158 0.00 0.00 0.00 5.14
618 619 0.386858 TTCAAGAGAACGAGCGTCCG 60.387 55.000 0.00 0.00 0.00 4.79
619 620 1.656095 CATTCAAGAGAACGAGCGTCC 59.344 52.381 0.00 0.00 36.39 4.79
620 621 2.596419 CTCATTCAAGAGAACGAGCGTC 59.404 50.000 0.00 0.00 37.28 5.19
621 622 2.600731 CTCATTCAAGAGAACGAGCGT 58.399 47.619 0.00 0.00 37.28 5.07
624 625 1.322936 GCGCTCATTCAAGAGAACGAG 59.677 52.381 0.00 0.00 44.61 4.18
625 626 1.350193 GCGCTCATTCAAGAGAACGA 58.650 50.000 0.00 0.00 37.87 3.85
626 627 0.024238 CGCGCTCATTCAAGAGAACG 59.976 55.000 5.56 0.00 37.87 3.95
627 628 1.350193 TCGCGCTCATTCAAGAGAAC 58.650 50.000 5.56 0.00 37.87 3.01
628 629 1.726791 GTTCGCGCTCATTCAAGAGAA 59.273 47.619 5.56 0.00 37.87 2.87
629 630 1.336795 TGTTCGCGCTCATTCAAGAGA 60.337 47.619 5.56 0.00 37.87 3.10
630 631 1.070821 TGTTCGCGCTCATTCAAGAG 58.929 50.000 5.56 0.00 38.68 2.85
631 632 0.790207 GTGTTCGCGCTCATTCAAGA 59.210 50.000 5.56 0.00 0.00 3.02
632 633 0.512518 TGTGTTCGCGCTCATTCAAG 59.487 50.000 5.56 0.00 0.00 3.02
633 634 0.234625 GTGTGTTCGCGCTCATTCAA 59.765 50.000 5.56 0.00 0.00 2.69
634 635 0.599991 AGTGTGTTCGCGCTCATTCA 60.600 50.000 5.56 0.00 0.00 2.57
635 636 0.512952 AAGTGTGTTCGCGCTCATTC 59.487 50.000 5.56 0.99 0.00 2.67
636 637 0.944386 AAAGTGTGTTCGCGCTCATT 59.056 45.000 5.56 0.00 0.00 2.57
637 638 0.944386 AAAAGTGTGTTCGCGCTCAT 59.056 45.000 5.56 0.00 0.00 2.90
638 639 1.573026 TAAAAGTGTGTTCGCGCTCA 58.427 45.000 5.56 0.00 0.00 4.26
639 640 2.220133 TCTTAAAAGTGTGTTCGCGCTC 59.780 45.455 5.56 0.00 0.00 5.03
640 641 2.206750 TCTTAAAAGTGTGTTCGCGCT 58.793 42.857 5.56 0.00 0.00 5.92
641 642 2.656192 TCTTAAAAGTGTGTTCGCGC 57.344 45.000 0.00 0.00 0.00 6.86
642 643 7.067116 TCTAAAATCTTAAAAGTGTGTTCGCG 58.933 34.615 0.00 0.00 0.00 5.87
643 644 8.950403 ATCTAAAATCTTAAAAGTGTGTTCGC 57.050 30.769 0.00 0.00 0.00 4.70
700 702 4.160439 TGAGCACATCTTTCTAACCGATCT 59.840 41.667 0.00 0.00 0.00 2.75
756 758 4.379813 GCGGTTTGAGATGTGATTGACAAT 60.380 41.667 0.00 0.00 38.36 2.71
830 832 2.221055 GTGCGATCCGATGGTTATGAAC 59.779 50.000 0.00 0.00 0.00 3.18
1566 1568 4.827087 AGCACGCGGCCTGAGATG 62.827 66.667 12.47 0.00 46.50 2.90
1605 1607 1.386772 AGAAGGTGGGGGTGTTGGA 60.387 57.895 0.00 0.00 0.00 3.53
1668 1670 3.377172 GGTTGTCCGATCCCTTATTGTTG 59.623 47.826 0.00 0.00 0.00 3.33
1698 1700 1.225376 TGTTACTTGGCTTCACCGCG 61.225 55.000 0.00 0.00 43.94 6.46
2098 2168 5.913137 AACACTCAACAATTCCACTGAAA 57.087 34.783 0.00 0.00 33.32 2.69
2143 2213 1.202818 ACTCCACACTTCCTTGAAGGC 60.203 52.381 6.30 0.00 43.25 4.35
2319 2389 3.062639 GGCAGTGATGTAATTGACGACTG 59.937 47.826 0.00 0.00 36.31 3.51
2543 2614 0.250295 CCGACAAGCTGACCTTCCAA 60.250 55.000 0.00 0.00 0.00 3.53
2621 2692 2.547430 GGCCGCTTTGGGTCTATAGTAC 60.547 54.545 0.00 0.00 38.63 2.73
2641 2712 3.400054 GTCCGGGGAAGGGTCTGG 61.400 72.222 0.00 0.00 0.00 3.86
2717 2788 0.664761 CCAATTGGCCATGTAGCGAG 59.335 55.000 12.53 0.00 0.00 5.03
2823 2902 1.536922 CGATGCTATCAACGCCAGACT 60.537 52.381 0.00 0.00 32.00 3.24


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

AutoCloner maintained by Alex Coulton.