Multiple sequence alignment - TraesCS4A01G084100

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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 TraesCS4A01G084100 chr4A 100.000 2642 0 0 1 2642 88542383 88539742 0.000000e+00 4879.0
1 TraesCS4A01G084100 chr4A 87.372 293 28 7 264 554 479901607 479901322 7.050000e-86 327.0
2 TraesCS4A01G084100 chr4A 77.257 576 89 29 1046 1613 88705013 88704472 1.540000e-77 300.0
3 TraesCS4A01G084100 chr4B 93.196 1411 54 16 555 1935 462696375 462697773 0.000000e+00 2036.0
4 TraesCS4A01G084100 chr4B 90.939 309 13 7 2214 2517 462698039 462698337 4.100000e-108 401.0
5 TraesCS4A01G084100 chr4B 89.310 290 23 6 266 553 116485836 116486119 8.990000e-95 357.0
6 TraesCS4A01G084100 chr4B 86.301 292 35 5 264 554 16529038 16528751 1.970000e-81 313.0
7 TraesCS4A01G084100 chr4B 77.661 573 87 29 1046 1613 462592291 462592827 7.100000e-81 311.0
8 TraesCS4A01G084100 chr4B 88.636 220 9 7 2 220 462696004 462696208 1.210000e-63 254.0
9 TraesCS4A01G084100 chr4B 93.711 159 8 1 1931 2089 462697799 462697955 1.220000e-58 237.0
10 TraesCS4A01G084100 chr4B 95.349 43 0 2 221 263 462696332 462696372 1.700000e-07 67.6
11 TraesCS4A01G084100 chr4D 92.716 1414 55 17 555 1935 375508362 375509760 0.000000e+00 1997.0
12 TraesCS4A01G084100 chr4D 93.445 717 34 5 1931 2642 375509786 375510494 0.000000e+00 1051.0
13 TraesCS4A01G084100 chr4D 87.783 221 10 8 2 220 375507992 375508197 2.630000e-60 243.0
14 TraesCS4A01G084100 chr4D 77.652 443 59 27 1060 1498 375445366 375445772 1.580000e-57 233.0
15 TraesCS4A01G084100 chr2B 88.699 292 28 5 261 552 61455310 61455596 4.180000e-93 351.0
16 TraesCS4A01G084100 chr1B 88.475 295 27 7 261 554 395308703 395308991 1.500000e-92 350.0
17 TraesCS4A01G084100 chr6B 88.014 292 31 4 264 554 48490706 48490418 2.520000e-90 342.0
18 TraesCS4A01G084100 chr5D 88.014 292 32 3 264 555 538028047 538027759 2.520000e-90 342.0
19 TraesCS4A01G084100 chr2D 87.671 292 31 5 264 554 513966033 513965746 4.210000e-88 335.0
20 TraesCS4A01G084100 chr3A 86.254 291 35 5 264 554 20295321 20295036 7.100000e-81 311.0


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 TraesCS4A01G084100 chr4A 88539742 88542383 2641 True 4879.00 4879 100.000000 1 2642 1 chr4A.!!$R1 2641
1 TraesCS4A01G084100 chr4A 88704472 88705013 541 True 300.00 300 77.257000 1046 1613 1 chr4A.!!$R2 567
2 TraesCS4A01G084100 chr4B 462696004 462698337 2333 False 599.12 2036 92.366200 2 2517 5 chr4B.!!$F3 2515
3 TraesCS4A01G084100 chr4B 462592291 462592827 536 False 311.00 311 77.661000 1046 1613 1 chr4B.!!$F2 567
4 TraesCS4A01G084100 chr4D 375507992 375510494 2502 False 1097.00 1997 91.314667 2 2642 3 chr4D.!!$F2 2640

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
551 679 0.108585 TGGGAGCGCCTGATATTTCC 59.891 55.0 2.29 0.69 0.0 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 2007 0.47008 TAGCGGGAGGAGGAAGATGG 60.47 60.0 0.0 0.0 0.0 3.51 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
131 133 7.709947 TGTACTCCTACATACAAAAGGTATCG 58.290 38.462 0.00 0.00 40.76 2.92
203 206 7.441157 TGTCTTTTGGAACAGTGTGAGTATTAG 59.559 37.037 0.00 0.00 42.39 1.73
263 391 7.439381 TCTAAAACGTAGAATCAACCTCAAGT 58.561 34.615 0.00 0.00 0.00 3.16
264 392 6.937436 AAAACGTAGAATCAACCTCAAGTT 57.063 33.333 0.00 0.00 40.16 2.66
265 393 6.541111 AAACGTAGAATCAACCTCAAGTTC 57.459 37.500 0.00 0.00 36.18 3.01
266 394 5.209818 ACGTAGAATCAACCTCAAGTTCA 57.790 39.130 0.00 0.00 36.18 3.18
267 395 5.230942 ACGTAGAATCAACCTCAAGTTCAG 58.769 41.667 0.00 0.00 36.18 3.02
268 396 4.627467 CGTAGAATCAACCTCAAGTTCAGG 59.373 45.833 0.00 0.00 36.18 3.86
270 398 4.646572 AGAATCAACCTCAAGTTCAGGTC 58.353 43.478 0.00 0.00 44.03 3.85
271 399 2.526304 TCAACCTCAAGTTCAGGTCG 57.474 50.000 0.00 0.00 44.03 4.79
272 400 2.036387 TCAACCTCAAGTTCAGGTCGA 58.964 47.619 0.00 0.00 44.03 4.20
273 401 2.432874 TCAACCTCAAGTTCAGGTCGAA 59.567 45.455 0.00 0.00 44.03 3.71
274 402 3.118555 TCAACCTCAAGTTCAGGTCGAAA 60.119 43.478 0.00 0.00 44.03 3.46
275 403 2.835027 ACCTCAAGTTCAGGTCGAAAC 58.165 47.619 0.00 0.00 40.54 2.78
276 404 2.434702 ACCTCAAGTTCAGGTCGAAACT 59.565 45.455 0.00 0.00 40.54 2.66
277 405 3.060602 CCTCAAGTTCAGGTCGAAACTC 58.939 50.000 0.91 0.00 34.69 3.01
278 406 2.726760 CTCAAGTTCAGGTCGAAACTCG 59.273 50.000 0.91 0.00 42.10 4.18
295 423 9.797556 TCGAAACTCGAAATTTATATTGAGAGA 57.202 29.630 13.69 2.44 46.90 3.10
296 424 9.836739 CGAAACTCGAAATTTATATTGAGAGAC 57.163 33.333 13.69 7.19 43.74 3.36
313 441 8.746052 TTGAGAGACAGAAAAAGGTAAATTCA 57.254 30.769 0.00 0.00 0.00 2.57
314 442 8.383318 TGAGAGACAGAAAAAGGTAAATTCAG 57.617 34.615 0.00 0.00 0.00 3.02
315 443 8.210946 TGAGAGACAGAAAAAGGTAAATTCAGA 58.789 33.333 0.00 0.00 0.00 3.27
316 444 9.225436 GAGAGACAGAAAAAGGTAAATTCAGAT 57.775 33.333 0.00 0.00 0.00 2.90
317 445 9.007901 AGAGACAGAAAAAGGTAAATTCAGATG 57.992 33.333 0.00 0.00 0.00 2.90
318 446 8.697507 AGACAGAAAAAGGTAAATTCAGATGT 57.302 30.769 0.00 0.00 0.00 3.06
319 447 8.571336 AGACAGAAAAAGGTAAATTCAGATGTG 58.429 33.333 0.00 0.00 0.00 3.21
320 448 8.463930 ACAGAAAAAGGTAAATTCAGATGTGA 57.536 30.769 0.00 0.00 0.00 3.58
321 449 8.912988 ACAGAAAAAGGTAAATTCAGATGTGAA 58.087 29.630 7.86 7.86 46.81 3.18
334 462 7.984422 TTCAGATGTGAATAGTGTCAAATGT 57.016 32.000 0.23 0.00 37.79 2.71
335 463 7.984422 TCAGATGTGAATAGTGTCAAATGTT 57.016 32.000 0.00 0.00 0.00 2.71
336 464 7.809665 TCAGATGTGAATAGTGTCAAATGTTG 58.190 34.615 0.00 0.00 0.00 3.33
337 465 7.445096 TCAGATGTGAATAGTGTCAAATGTTGT 59.555 33.333 0.00 0.00 0.00 3.32
338 466 8.077991 CAGATGTGAATAGTGTCAAATGTTGTT 58.922 33.333 0.00 0.00 0.00 2.83
339 467 8.632679 AGATGTGAATAGTGTCAAATGTTGTTT 58.367 29.630 0.00 0.00 0.00 2.83
340 468 9.248291 GATGTGAATAGTGTCAAATGTTGTTTT 57.752 29.630 0.00 0.00 0.00 2.43
341 469 8.994429 TGTGAATAGTGTCAAATGTTGTTTTT 57.006 26.923 0.00 0.00 0.00 1.94
342 470 8.867935 TGTGAATAGTGTCAAATGTTGTTTTTG 58.132 29.630 0.00 0.00 35.79 2.44
343 471 8.327429 GTGAATAGTGTCAAATGTTGTTTTTGG 58.673 33.333 0.00 0.00 35.31 3.28
344 472 8.037758 TGAATAGTGTCAAATGTTGTTTTTGGT 58.962 29.630 0.00 0.00 35.31 3.67
345 473 8.419076 AATAGTGTCAAATGTTGTTTTTGGTC 57.581 30.769 0.00 0.00 35.31 4.02
346 474 6.036577 AGTGTCAAATGTTGTTTTTGGTCT 57.963 33.333 0.00 0.00 35.31 3.85
347 475 6.463360 AGTGTCAAATGTTGTTTTTGGTCTT 58.537 32.000 0.00 0.00 35.31 3.01
348 476 6.934083 AGTGTCAAATGTTGTTTTTGGTCTTT 59.066 30.769 0.00 0.00 35.31 2.52
349 477 7.443879 AGTGTCAAATGTTGTTTTTGGTCTTTT 59.556 29.630 0.00 0.00 35.31 2.27
350 478 8.073167 GTGTCAAATGTTGTTTTTGGTCTTTTT 58.927 29.630 0.00 0.00 35.31 1.94
351 479 9.273016 TGTCAAATGTTGTTTTTGGTCTTTTTA 57.727 25.926 0.00 0.00 35.31 1.52
356 484 9.442047 AATGTTGTTTTTGGTCTTTTTATGACA 57.558 25.926 0.00 0.00 36.26 3.58
357 485 8.245701 TGTTGTTTTTGGTCTTTTTATGACAC 57.754 30.769 0.00 0.00 36.26 3.67
358 486 8.091449 TGTTGTTTTTGGTCTTTTTATGACACT 58.909 29.630 0.00 0.00 36.26 3.55
359 487 9.575783 GTTGTTTTTGGTCTTTTTATGACACTA 57.424 29.630 0.00 0.00 36.26 2.74
361 489 9.959749 TGTTTTTGGTCTTTTTATGACACTATC 57.040 29.630 0.00 0.00 36.26 2.08
362 490 9.406828 GTTTTTGGTCTTTTTATGACACTATCC 57.593 33.333 0.00 0.00 36.26 2.59
363 491 8.698973 TTTTGGTCTTTTTATGACACTATCCA 57.301 30.769 0.00 0.00 36.26 3.41
364 492 8.877864 TTTGGTCTTTTTATGACACTATCCAT 57.122 30.769 0.00 0.00 36.26 3.41
365 493 7.864108 TGGTCTTTTTATGACACTATCCATG 57.136 36.000 0.00 0.00 36.26 3.66
366 494 6.318648 TGGTCTTTTTATGACACTATCCATGC 59.681 38.462 0.00 0.00 36.26 4.06
367 495 6.543831 GGTCTTTTTATGACACTATCCATGCT 59.456 38.462 0.00 0.00 36.26 3.79
368 496 7.715249 GGTCTTTTTATGACACTATCCATGCTA 59.285 37.037 0.00 0.00 36.26 3.49
369 497 8.768955 GTCTTTTTATGACACTATCCATGCTAG 58.231 37.037 0.00 0.00 34.80 3.42
370 498 8.704668 TCTTTTTATGACACTATCCATGCTAGA 58.295 33.333 0.00 0.00 0.00 2.43
371 499 9.499479 CTTTTTATGACACTATCCATGCTAGAT 57.501 33.333 0.00 0.00 0.00 1.98
372 500 9.851686 TTTTTATGACACTATCCATGCTAGATT 57.148 29.630 0.00 0.00 0.00 2.40
373 501 9.851686 TTTTATGACACTATCCATGCTAGATTT 57.148 29.630 0.00 0.00 0.00 2.17
374 502 9.494271 TTTATGACACTATCCATGCTAGATTTC 57.506 33.333 0.00 2.64 0.00 2.17
375 503 6.484364 TGACACTATCCATGCTAGATTTCA 57.516 37.500 0.00 4.52 0.00 2.69
376 504 6.283694 TGACACTATCCATGCTAGATTTCAC 58.716 40.000 0.00 0.00 0.00 3.18
377 505 6.127083 TGACACTATCCATGCTAGATTTCACA 60.127 38.462 0.00 0.00 0.00 3.58
378 506 6.835174 ACACTATCCATGCTAGATTTCACAT 58.165 36.000 0.00 0.00 0.00 3.21
379 507 7.285566 ACACTATCCATGCTAGATTTCACATT 58.714 34.615 0.00 0.00 0.00 2.71
380 508 7.776969 ACACTATCCATGCTAGATTTCACATTT 59.223 33.333 0.00 0.00 0.00 2.32
381 509 8.627403 CACTATCCATGCTAGATTTCACATTTT 58.373 33.333 0.00 0.00 0.00 1.82
382 510 9.193806 ACTATCCATGCTAGATTTCACATTTTT 57.806 29.630 0.00 0.00 0.00 1.94
383 511 9.459640 CTATCCATGCTAGATTTCACATTTTTG 57.540 33.333 0.00 0.00 0.00 2.44
384 512 7.230849 TCCATGCTAGATTTCACATTTTTGT 57.769 32.000 0.00 0.00 0.00 2.83
385 513 7.669427 TCCATGCTAGATTTCACATTTTTGTT 58.331 30.769 0.00 0.00 0.00 2.83
386 514 8.149647 TCCATGCTAGATTTCACATTTTTGTTT 58.850 29.630 0.00 0.00 0.00 2.83
387 515 8.437742 CCATGCTAGATTTCACATTTTTGTTTC 58.562 33.333 0.00 0.00 0.00 2.78
388 516 9.199982 CATGCTAGATTTCACATTTTTGTTTCT 57.800 29.630 0.00 0.00 0.00 2.52
389 517 9.768662 ATGCTAGATTTCACATTTTTGTTTCTT 57.231 25.926 0.00 0.00 0.00 2.52
412 540 9.444600 TCTTAATGTACATTTAGAGTTTGGACC 57.555 33.333 25.80 0.00 33.22 4.46
413 541 9.449719 CTTAATGTACATTTAGAGTTTGGACCT 57.550 33.333 25.31 0.00 31.20 3.85
414 542 7.687941 AATGTACATTTAGAGTTTGGACCTG 57.312 36.000 15.47 0.00 0.00 4.00
415 543 5.556915 TGTACATTTAGAGTTTGGACCTGG 58.443 41.667 0.00 0.00 0.00 4.45
416 544 4.993705 ACATTTAGAGTTTGGACCTGGA 57.006 40.909 0.00 0.00 0.00 3.86
417 545 5.319043 ACATTTAGAGTTTGGACCTGGAA 57.681 39.130 0.00 0.00 0.00 3.53
418 546 5.892348 ACATTTAGAGTTTGGACCTGGAAT 58.108 37.500 0.00 0.00 0.00 3.01
419 547 6.314917 ACATTTAGAGTTTGGACCTGGAATT 58.685 36.000 0.00 0.00 0.00 2.17
420 548 6.782494 ACATTTAGAGTTTGGACCTGGAATTT 59.218 34.615 0.00 0.00 0.00 1.82
421 549 7.290014 ACATTTAGAGTTTGGACCTGGAATTTT 59.710 33.333 0.00 0.00 0.00 1.82
422 550 7.669089 TTTAGAGTTTGGACCTGGAATTTTT 57.331 32.000 0.00 0.00 0.00 1.94
423 551 8.770010 TTTAGAGTTTGGACCTGGAATTTTTA 57.230 30.769 0.00 0.00 0.00 1.52
424 552 6.901081 AGAGTTTGGACCTGGAATTTTTAG 57.099 37.500 0.00 0.00 0.00 1.85
425 553 6.610830 AGAGTTTGGACCTGGAATTTTTAGA 58.389 36.000 0.00 0.00 0.00 2.10
426 554 7.066781 AGAGTTTGGACCTGGAATTTTTAGAA 58.933 34.615 0.00 0.00 0.00 2.10
427 555 7.231519 AGAGTTTGGACCTGGAATTTTTAGAAG 59.768 37.037 0.00 0.00 0.00 2.85
428 556 6.839134 AGTTTGGACCTGGAATTTTTAGAAGT 59.161 34.615 0.00 0.00 0.00 3.01
429 557 7.344612 AGTTTGGACCTGGAATTTTTAGAAGTT 59.655 33.333 0.00 0.00 0.00 2.66
430 558 6.648879 TGGACCTGGAATTTTTAGAAGTTG 57.351 37.500 0.00 0.00 0.00 3.16
431 559 6.133356 TGGACCTGGAATTTTTAGAAGTTGT 58.867 36.000 0.00 0.00 0.00 3.32
432 560 7.291566 TGGACCTGGAATTTTTAGAAGTTGTA 58.708 34.615 0.00 0.00 0.00 2.41
433 561 7.447238 TGGACCTGGAATTTTTAGAAGTTGTAG 59.553 37.037 0.00 0.00 0.00 2.74
434 562 7.447545 GGACCTGGAATTTTTAGAAGTTGTAGT 59.552 37.037 0.00 0.00 0.00 2.73
435 563 8.392372 ACCTGGAATTTTTAGAAGTTGTAGTC 57.608 34.615 0.00 0.00 0.00 2.59
436 564 7.996644 ACCTGGAATTTTTAGAAGTTGTAGTCA 59.003 33.333 0.00 0.00 0.00 3.41
437 565 8.290325 CCTGGAATTTTTAGAAGTTGTAGTCAC 58.710 37.037 0.00 0.00 0.00 3.67
438 566 8.740123 TGGAATTTTTAGAAGTTGTAGTCACA 57.260 30.769 0.00 0.00 0.00 3.58
439 567 9.349713 TGGAATTTTTAGAAGTTGTAGTCACAT 57.650 29.630 0.00 0.00 33.76 3.21
443 571 8.974060 TTTTTAGAAGTTGTAGTCACATTCCT 57.026 30.769 0.00 0.00 33.76 3.36
444 572 8.974060 TTTTAGAAGTTGTAGTCACATTCCTT 57.026 30.769 0.00 0.00 33.76 3.36
445 573 7.962964 TTAGAAGTTGTAGTCACATTCCTTG 57.037 36.000 0.00 0.00 33.76 3.61
446 574 5.930135 AGAAGTTGTAGTCACATTCCTTGT 58.070 37.500 0.00 0.00 39.91 3.16
447 575 7.062749 AGAAGTTGTAGTCACATTCCTTGTA 57.937 36.000 0.00 0.00 36.57 2.41
448 576 7.506114 AGAAGTTGTAGTCACATTCCTTGTAA 58.494 34.615 0.00 0.00 36.57 2.41
449 577 7.990886 AGAAGTTGTAGTCACATTCCTTGTAAA 59.009 33.333 0.00 0.00 36.57 2.01
450 578 7.492352 AGTTGTAGTCACATTCCTTGTAAAC 57.508 36.000 0.00 0.00 36.57 2.01
451 579 7.051623 AGTTGTAGTCACATTCCTTGTAAACA 58.948 34.615 0.00 0.00 36.57 2.83
452 580 7.719633 AGTTGTAGTCACATTCCTTGTAAACAT 59.280 33.333 0.00 0.00 36.57 2.71
453 581 8.349983 GTTGTAGTCACATTCCTTGTAAACATT 58.650 33.333 0.00 0.00 36.57 2.71
454 582 8.094798 TGTAGTCACATTCCTTGTAAACATTC 57.905 34.615 0.00 0.00 36.57 2.67
455 583 7.717436 TGTAGTCACATTCCTTGTAAACATTCA 59.283 33.333 0.00 0.00 36.57 2.57
456 584 7.765695 AGTCACATTCCTTGTAAACATTCAT 57.234 32.000 0.00 0.00 36.57 2.57
457 585 8.862325 AGTCACATTCCTTGTAAACATTCATA 57.138 30.769 0.00 0.00 36.57 2.15
458 586 9.466497 AGTCACATTCCTTGTAAACATTCATAT 57.534 29.630 0.00 0.00 36.57 1.78
520 648 5.452078 TTTTTAAGTTGGAGCATGTGGAG 57.548 39.130 0.00 0.00 0.00 3.86
521 649 2.113860 TAAGTTGGAGCATGTGGAGC 57.886 50.000 0.00 0.00 0.00 4.70
522 650 0.111061 AAGTTGGAGCATGTGGAGCA 59.889 50.000 0.00 0.00 0.00 4.26
523 651 0.607489 AGTTGGAGCATGTGGAGCAC 60.607 55.000 0.00 0.00 34.56 4.40
524 652 1.303561 TTGGAGCATGTGGAGCACC 60.304 57.895 0.00 0.00 42.19 5.01
525 653 2.439156 GGAGCATGTGGAGCACCC 60.439 66.667 0.00 0.00 36.84 4.61
526 654 2.439156 GAGCATGTGGAGCACCCC 60.439 66.667 0.00 0.00 32.73 4.95
527 655 3.259314 AGCATGTGGAGCACCCCA 61.259 61.111 0.00 0.00 32.73 4.96
528 656 2.283101 GCATGTGGAGCACCCCAA 60.283 61.111 0.00 0.00 38.06 4.12
529 657 2.345760 GCATGTGGAGCACCCCAAG 61.346 63.158 0.00 0.00 38.06 3.61
530 658 1.679977 CATGTGGAGCACCCCAAGG 60.680 63.158 0.00 0.00 38.06 3.61
531 659 1.852157 ATGTGGAGCACCCCAAGGA 60.852 57.895 0.00 0.00 38.06 3.36
532 660 1.217057 ATGTGGAGCACCCCAAGGAT 61.217 55.000 0.00 0.00 38.06 3.24
533 661 1.379044 GTGGAGCACCCCAAGGATG 60.379 63.158 0.00 0.00 38.06 3.51
542 670 3.801997 CCAAGGATGGGAGCGCCT 61.802 66.667 2.29 0.00 43.51 5.52
543 671 2.515523 CAAGGATGGGAGCGCCTG 60.516 66.667 2.29 0.00 31.06 4.85
544 672 2.688666 AAGGATGGGAGCGCCTGA 60.689 61.111 2.29 0.00 31.06 3.86
545 673 2.074948 AAGGATGGGAGCGCCTGAT 61.075 57.895 2.29 0.00 31.06 2.90
546 674 0.764369 AAGGATGGGAGCGCCTGATA 60.764 55.000 2.29 0.00 31.06 2.15
547 675 0.546267 AGGATGGGAGCGCCTGATAT 60.546 55.000 2.29 0.00 0.00 1.63
548 676 0.326264 GGATGGGAGCGCCTGATATT 59.674 55.000 2.29 0.00 0.00 1.28
549 677 1.271597 GGATGGGAGCGCCTGATATTT 60.272 52.381 2.29 0.00 0.00 1.40
550 678 2.079925 GATGGGAGCGCCTGATATTTC 58.920 52.381 2.29 0.00 0.00 2.17
551 679 0.108585 TGGGAGCGCCTGATATTTCC 59.891 55.000 2.29 0.69 0.00 3.13
552 680 0.606673 GGGAGCGCCTGATATTTCCC 60.607 60.000 10.89 10.89 37.68 3.97
553 681 0.606673 GGAGCGCCTGATATTTCCCC 60.607 60.000 2.29 0.00 0.00 4.81
558 686 2.230660 CGCCTGATATTTCCCCCTTTC 58.769 52.381 0.00 0.00 0.00 2.62
563 691 5.163088 GCCTGATATTTCCCCCTTTCTTAGA 60.163 44.000 0.00 0.00 0.00 2.10
576 704 6.609616 CCCCTTTCTTAGATCACTCTTACTCT 59.390 42.308 0.00 0.00 32.66 3.24
581 710 9.961264 TTTCTTAGATCACTCTTACTCTGAGTA 57.039 33.333 13.34 13.34 42.21 2.59
631 760 2.205022 TTCCTGTCAAATCAGCCAGG 57.795 50.000 0.00 0.00 44.74 4.45
639 768 2.964464 TCAAATCAGCCAGGCAGAAAAA 59.036 40.909 15.80 0.00 0.00 1.94
644 773 1.682854 CAGCCAGGCAGAAAAAGTTGA 59.317 47.619 15.80 0.00 0.00 3.18
680 809 4.804608 TTTAATGGCGTACATCCGAATG 57.195 40.909 0.00 0.00 39.40 2.67
696 825 2.478370 CGAATGTGCTGGCACCATTAAG 60.478 50.000 20.80 13.49 45.63 1.85
916 1047 0.928229 CGTCCTATAAACACAGCCGC 59.072 55.000 0.00 0.00 0.00 6.53
949 1080 0.538287 ACCAGACCAAAGCCTTCTGC 60.538 55.000 0.00 0.00 36.26 4.26
967 1098 1.007271 CCAGTCGCTCGTTGTCACT 60.007 57.895 0.00 0.00 0.00 3.41
968 1099 1.004277 CCAGTCGCTCGTTGTCACTC 61.004 60.000 0.00 0.00 0.00 3.51
969 1100 1.082038 AGTCGCTCGTTGTCACTCG 60.082 57.895 0.00 0.00 0.00 4.18
970 1101 1.082300 GTCGCTCGTTGTCACTCGA 60.082 57.895 0.00 0.00 34.88 4.04
971 1102 1.082300 TCGCTCGTTGTCACTCGAC 60.082 57.895 0.00 0.00 42.93 4.20
1266 1397 2.038269 CCCGCAAAGGTACGCACAT 61.038 57.895 0.00 0.00 38.74 3.21
1332 1467 3.310860 ATGCGGACGTCCCTTGACC 62.311 63.158 28.52 10.46 38.32 4.02
1340 1475 1.745489 GTCCCTTGACCGATGGCAC 60.745 63.158 0.00 0.00 35.34 5.01
1528 1663 1.364626 GGCCAAGACGCACATCTCAG 61.365 60.000 0.00 0.00 0.00 3.35
1627 1762 1.630244 CCTCCGTTTCTTCTGCTGCG 61.630 60.000 0.00 0.00 0.00 5.18
1734 1870 9.153721 TCGTCTAAAAAGTTCAGAAGTTGTAAA 57.846 29.630 3.87 0.00 0.00 2.01
1767 1904 5.482878 AGACTCGGAGTAATAACAAAAGGGA 59.517 40.000 11.27 0.00 0.00 4.20
1775 1912 6.240145 AGTAATAACAAAAGGGAACGCCTAA 58.760 36.000 0.00 0.00 0.00 2.69
1842 2007 1.227674 CCTTCCGCCAGCCACTATC 60.228 63.158 0.00 0.00 0.00 2.08
1964 2159 0.254178 GAGCTTCTGATTGGCCTCCA 59.746 55.000 3.32 0.00 0.00 3.86
1967 2162 1.747709 CTTCTGATTGGCCTCCACAG 58.252 55.000 3.32 8.77 30.78 3.66
2055 2250 2.364579 TCGGCCTCGGGGTTACAT 60.365 61.111 1.62 0.00 36.95 2.29
2057 2252 2.516225 GGCCTCGGGGTTACATGC 60.516 66.667 1.62 0.00 34.45 4.06
2073 2268 2.737376 GCACACGAGAACCGACCC 60.737 66.667 0.00 0.00 41.76 4.46
2191 2446 3.122850 CGCCATTGCTGGGATTCC 58.877 61.111 0.00 0.00 43.36 3.01
2274 2529 6.295249 TGAGAATGATGGTTGACAACTAACA 58.705 36.000 17.52 16.30 0.00 2.41
2296 2551 5.010922 ACAGACAAATCCTTGCAGCAAATAA 59.989 36.000 9.65 0.00 35.84 1.40
2328 2584 3.801997 CCCTGATCTTGGCCGGCT 61.802 66.667 28.56 5.35 0.00 5.52
2542 2802 6.256321 GGATGCCACATGACAATGAAAATTAC 59.744 38.462 0.00 0.00 37.24 1.89
2595 2855 3.673594 CGTGTTCACACATACTCCCTCTC 60.674 52.174 10.61 0.00 46.75 3.20
2610 2870 6.257586 ACTCCCTCTCTCTACAATTGTAAGT 58.742 40.000 18.55 12.51 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 102 9.886132 CCTTTTGTATGTAGGAGTACAAGTTAT 57.114 33.333 0.00 0.00 42.54 1.89
102 104 7.742767 ACCTTTTGTATGTAGGAGTACAAGTT 58.257 34.615 0.00 0.00 42.54 2.66
103 105 7.312415 ACCTTTTGTATGTAGGAGTACAAGT 57.688 36.000 0.00 0.00 42.54 3.16
104 106 9.530633 GATACCTTTTGTATGTAGGAGTACAAG 57.469 37.037 0.00 0.00 42.54 3.16
105 107 8.192774 CGATACCTTTTGTATGTAGGAGTACAA 58.807 37.037 0.00 0.00 42.54 2.41
106 108 7.201848 CCGATACCTTTTGTATGTAGGAGTACA 60.202 40.741 0.00 0.00 43.43 2.90
107 109 7.144000 CCGATACCTTTTGTATGTAGGAGTAC 58.856 42.308 0.00 0.00 40.31 2.73
108 110 6.239120 GCCGATACCTTTTGTATGTAGGAGTA 60.239 42.308 0.00 0.00 40.31 2.59
109 111 5.452917 GCCGATACCTTTTGTATGTAGGAGT 60.453 44.000 0.00 0.00 40.31 3.85
110 112 4.989168 GCCGATACCTTTTGTATGTAGGAG 59.011 45.833 0.00 0.00 40.31 3.69
111 113 4.202284 GGCCGATACCTTTTGTATGTAGGA 60.202 45.833 0.00 0.00 40.31 2.94
112 114 4.062991 GGCCGATACCTTTTGTATGTAGG 58.937 47.826 0.00 0.00 40.31 3.18
113 115 4.699637 TGGCCGATACCTTTTGTATGTAG 58.300 43.478 0.00 0.00 40.31 2.74
166 168 8.357402 ACTGTTCCAAAAGACAATATGGTTTAC 58.643 33.333 0.00 0.00 34.50 2.01
179 181 7.506114 ACTAATACTCACACTGTTCCAAAAGA 58.494 34.615 0.00 0.00 0.00 2.52
180 182 7.730364 ACTAATACTCACACTGTTCCAAAAG 57.270 36.000 0.00 0.00 0.00 2.27
185 187 9.431887 TGAATAAACTAATACTCACACTGTTCC 57.568 33.333 0.00 0.00 0.00 3.62
220 223 7.305474 GTTTTAGATTTTGACACGGTCATCAT 58.695 34.615 7.43 3.77 42.40 2.45
222 225 5.788531 CGTTTTAGATTTTGACACGGTCATC 59.211 40.000 7.43 3.65 42.40 2.92
223 226 5.237779 ACGTTTTAGATTTTGACACGGTCAT 59.762 36.000 7.43 0.00 42.40 3.06
225 228 5.086888 ACGTTTTAGATTTTGACACGGTC 57.913 39.130 0.00 0.00 0.00 4.79
226 229 5.984926 TCTACGTTTTAGATTTTGACACGGT 59.015 36.000 0.00 0.00 0.00 4.83
227 230 6.456447 TCTACGTTTTAGATTTTGACACGG 57.544 37.500 0.00 0.00 0.00 4.94
228 231 8.218441 TGATTCTACGTTTTAGATTTTGACACG 58.782 33.333 0.00 0.00 0.00 4.49
229 232 9.872757 TTGATTCTACGTTTTAGATTTTGACAC 57.127 29.630 0.00 0.00 0.00 3.67
270 398 9.836739 GTCTCTCAATATAAATTTCGAGTTTCG 57.163 33.333 0.00 0.00 42.10 3.46
287 415 9.354673 TGAATTTACCTTTTTCTGTCTCTCAAT 57.645 29.630 0.00 0.00 0.00 2.57
288 416 8.746052 TGAATTTACCTTTTTCTGTCTCTCAA 57.254 30.769 0.00 0.00 0.00 3.02
289 417 8.210946 TCTGAATTTACCTTTTTCTGTCTCTCA 58.789 33.333 0.00 0.00 0.00 3.27
290 418 8.608844 TCTGAATTTACCTTTTTCTGTCTCTC 57.391 34.615 0.00 0.00 0.00 3.20
291 419 9.007901 CATCTGAATTTACCTTTTTCTGTCTCT 57.992 33.333 0.00 0.00 0.00 3.10
292 420 8.787852 ACATCTGAATTTACCTTTTTCTGTCTC 58.212 33.333 0.00 0.00 0.00 3.36
293 421 8.571336 CACATCTGAATTTACCTTTTTCTGTCT 58.429 33.333 0.00 0.00 0.00 3.41
294 422 8.567948 TCACATCTGAATTTACCTTTTTCTGTC 58.432 33.333 0.00 0.00 0.00 3.51
295 423 8.463930 TCACATCTGAATTTACCTTTTTCTGT 57.536 30.769 0.00 0.00 0.00 3.41
296 424 9.918630 ATTCACATCTGAATTTACCTTTTTCTG 57.081 29.630 0.00 0.00 43.48 3.02
301 429 9.520515 ACACTATTCACATCTGAATTTACCTTT 57.479 29.630 1.29 0.00 43.48 3.11
302 430 9.167311 GACACTATTCACATCTGAATTTACCTT 57.833 33.333 1.29 0.00 43.48 3.50
303 431 8.321353 TGACACTATTCACATCTGAATTTACCT 58.679 33.333 1.29 0.00 43.48 3.08
304 432 8.492673 TGACACTATTCACATCTGAATTTACC 57.507 34.615 1.29 0.00 43.48 2.85
307 435 9.850628 CATTTGACACTATTCACATCTGAATTT 57.149 29.630 1.29 0.00 43.48 1.82
308 436 9.017509 ACATTTGACACTATTCACATCTGAATT 57.982 29.630 1.29 0.00 43.48 2.17
309 437 8.571461 ACATTTGACACTATTCACATCTGAAT 57.429 30.769 1.66 1.66 46.84 2.57
310 438 7.984422 ACATTTGACACTATTCACATCTGAA 57.016 32.000 0.00 0.00 40.77 3.02
311 439 7.445096 ACAACATTTGACACTATTCACATCTGA 59.555 33.333 0.00 0.00 0.00 3.27
312 440 7.587629 ACAACATTTGACACTATTCACATCTG 58.412 34.615 0.00 0.00 0.00 2.90
313 441 7.750229 ACAACATTTGACACTATTCACATCT 57.250 32.000 0.00 0.00 0.00 2.90
314 442 8.801715 AAACAACATTTGACACTATTCACATC 57.198 30.769 0.00 0.00 0.00 3.06
315 443 9.598517 AAAAACAACATTTGACACTATTCACAT 57.401 25.926 0.00 0.00 0.00 3.21
316 444 8.867935 CAAAAACAACATTTGACACTATTCACA 58.132 29.630 0.00 0.00 39.56 3.58
317 445 8.327429 CCAAAAACAACATTTGACACTATTCAC 58.673 33.333 0.83 0.00 39.56 3.18
318 446 8.037758 ACCAAAAACAACATTTGACACTATTCA 58.962 29.630 0.83 0.00 39.56 2.57
319 447 8.419076 ACCAAAAACAACATTTGACACTATTC 57.581 30.769 0.83 0.00 39.56 1.75
320 448 8.257306 AGACCAAAAACAACATTTGACACTATT 58.743 29.630 0.83 0.00 39.56 1.73
321 449 7.781056 AGACCAAAAACAACATTTGACACTAT 58.219 30.769 0.83 0.00 39.56 2.12
322 450 7.164230 AGACCAAAAACAACATTTGACACTA 57.836 32.000 0.83 0.00 39.56 2.74
323 451 6.036577 AGACCAAAAACAACATTTGACACT 57.963 33.333 0.83 0.00 39.56 3.55
324 452 6.720012 AAGACCAAAAACAACATTTGACAC 57.280 33.333 0.83 0.00 39.56 3.67
325 453 7.736447 AAAAGACCAAAAACAACATTTGACA 57.264 28.000 0.83 0.00 39.56 3.58
330 458 9.442047 TGTCATAAAAAGACCAAAAACAACATT 57.558 25.926 0.00 0.00 35.15 2.71
331 459 8.878769 GTGTCATAAAAAGACCAAAAACAACAT 58.121 29.630 0.00 0.00 35.15 2.71
332 460 8.091449 AGTGTCATAAAAAGACCAAAAACAACA 58.909 29.630 0.00 0.00 35.15 3.33
333 461 8.474006 AGTGTCATAAAAAGACCAAAAACAAC 57.526 30.769 0.00 0.00 35.15 3.32
335 463 9.959749 GATAGTGTCATAAAAAGACCAAAAACA 57.040 29.630 0.00 0.00 35.15 2.83
336 464 9.406828 GGATAGTGTCATAAAAAGACCAAAAAC 57.593 33.333 0.00 0.00 35.15 2.43
337 465 9.137459 TGGATAGTGTCATAAAAAGACCAAAAA 57.863 29.630 0.00 0.00 35.15 1.94
338 466 8.698973 TGGATAGTGTCATAAAAAGACCAAAA 57.301 30.769 0.00 0.00 35.15 2.44
339 467 8.739039 CATGGATAGTGTCATAAAAAGACCAAA 58.261 33.333 0.00 0.00 35.15 3.28
340 468 7.148086 GCATGGATAGTGTCATAAAAAGACCAA 60.148 37.037 0.00 0.00 35.15 3.67
341 469 6.318648 GCATGGATAGTGTCATAAAAAGACCA 59.681 38.462 0.00 0.00 35.15 4.02
342 470 6.543831 AGCATGGATAGTGTCATAAAAAGACC 59.456 38.462 0.00 0.00 35.15 3.85
343 471 7.559590 AGCATGGATAGTGTCATAAAAAGAC 57.440 36.000 0.00 0.00 36.55 3.01
344 472 8.704668 TCTAGCATGGATAGTGTCATAAAAAGA 58.295 33.333 0.00 0.00 0.00 2.52
345 473 8.893219 TCTAGCATGGATAGTGTCATAAAAAG 57.107 34.615 0.00 0.00 0.00 2.27
346 474 9.851686 AATCTAGCATGGATAGTGTCATAAAAA 57.148 29.630 0.00 0.00 34.06 1.94
347 475 9.851686 AAATCTAGCATGGATAGTGTCATAAAA 57.148 29.630 0.00 0.00 34.06 1.52
348 476 9.494271 GAAATCTAGCATGGATAGTGTCATAAA 57.506 33.333 0.00 0.00 34.06 1.40
349 477 8.650490 TGAAATCTAGCATGGATAGTGTCATAA 58.350 33.333 0.00 0.00 34.06 1.90
350 478 8.090831 GTGAAATCTAGCATGGATAGTGTCATA 58.909 37.037 0.00 0.00 34.06 2.15
351 479 6.933521 GTGAAATCTAGCATGGATAGTGTCAT 59.066 38.462 0.00 0.00 34.06 3.06
352 480 6.127083 TGTGAAATCTAGCATGGATAGTGTCA 60.127 38.462 0.00 0.00 34.06 3.58
353 481 6.283694 TGTGAAATCTAGCATGGATAGTGTC 58.716 40.000 0.00 0.00 34.06 3.67
354 482 6.239217 TGTGAAATCTAGCATGGATAGTGT 57.761 37.500 0.00 0.00 34.06 3.55
355 483 7.741027 AATGTGAAATCTAGCATGGATAGTG 57.259 36.000 0.00 0.00 34.06 2.74
356 484 8.757982 AAAATGTGAAATCTAGCATGGATAGT 57.242 30.769 0.00 0.00 34.06 2.12
357 485 9.459640 CAAAAATGTGAAATCTAGCATGGATAG 57.540 33.333 0.00 0.00 34.06 2.08
358 486 8.970020 ACAAAAATGTGAAATCTAGCATGGATA 58.030 29.630 0.00 0.00 34.06 2.59
359 487 7.844009 ACAAAAATGTGAAATCTAGCATGGAT 58.156 30.769 0.00 0.00 38.25 3.41
360 488 7.230849 ACAAAAATGTGAAATCTAGCATGGA 57.769 32.000 0.00 0.00 0.00 3.41
361 489 7.894376 AACAAAAATGTGAAATCTAGCATGG 57.106 32.000 0.00 0.00 0.00 3.66
362 490 9.199982 AGAAACAAAAATGTGAAATCTAGCATG 57.800 29.630 0.00 0.00 0.00 4.06
363 491 9.768662 AAGAAACAAAAATGTGAAATCTAGCAT 57.231 25.926 0.00 0.00 0.00 3.79
386 514 9.444600 GGTCCAAACTCTAAATGTACATTAAGA 57.555 33.333 21.07 9.14 0.00 2.10
387 515 9.449719 AGGTCCAAACTCTAAATGTACATTAAG 57.550 33.333 21.07 18.90 0.00 1.85
388 516 9.226606 CAGGTCCAAACTCTAAATGTACATTAA 57.773 33.333 21.07 9.32 0.00 1.40
389 517 7.827236 CCAGGTCCAAACTCTAAATGTACATTA 59.173 37.037 21.07 5.50 0.00 1.90
390 518 6.659242 CCAGGTCCAAACTCTAAATGTACATT 59.341 38.462 15.47 15.47 0.00 2.71
391 519 6.012858 TCCAGGTCCAAACTCTAAATGTACAT 60.013 38.462 1.41 1.41 0.00 2.29
392 520 5.308497 TCCAGGTCCAAACTCTAAATGTACA 59.692 40.000 0.00 0.00 0.00 2.90
393 521 5.801380 TCCAGGTCCAAACTCTAAATGTAC 58.199 41.667 0.00 0.00 0.00 2.90
394 522 6.442541 TTCCAGGTCCAAACTCTAAATGTA 57.557 37.500 0.00 0.00 0.00 2.29
395 523 4.993705 TCCAGGTCCAAACTCTAAATGT 57.006 40.909 0.00 0.00 0.00 2.71
396 524 6.840780 AATTCCAGGTCCAAACTCTAAATG 57.159 37.500 0.00 0.00 0.00 2.32
397 525 7.855784 AAAATTCCAGGTCCAAACTCTAAAT 57.144 32.000 0.00 0.00 0.00 1.40
398 526 7.669089 AAAAATTCCAGGTCCAAACTCTAAA 57.331 32.000 0.00 0.00 0.00 1.85
399 527 8.221944 TCTAAAAATTCCAGGTCCAAACTCTAA 58.778 33.333 0.00 0.00 0.00 2.10
400 528 7.751646 TCTAAAAATTCCAGGTCCAAACTCTA 58.248 34.615 0.00 0.00 0.00 2.43
401 529 6.610830 TCTAAAAATTCCAGGTCCAAACTCT 58.389 36.000 0.00 0.00 0.00 3.24
402 530 6.894339 TCTAAAAATTCCAGGTCCAAACTC 57.106 37.500 0.00 0.00 0.00 3.01
403 531 6.839134 ACTTCTAAAAATTCCAGGTCCAAACT 59.161 34.615 0.00 0.00 0.00 2.66
404 532 7.050970 ACTTCTAAAAATTCCAGGTCCAAAC 57.949 36.000 0.00 0.00 0.00 2.93
405 533 7.125053 ACAACTTCTAAAAATTCCAGGTCCAAA 59.875 33.333 0.00 0.00 0.00 3.28
406 534 6.609616 ACAACTTCTAAAAATTCCAGGTCCAA 59.390 34.615 0.00 0.00 0.00 3.53
407 535 6.133356 ACAACTTCTAAAAATTCCAGGTCCA 58.867 36.000 0.00 0.00 0.00 4.02
408 536 6.650427 ACAACTTCTAAAAATTCCAGGTCC 57.350 37.500 0.00 0.00 0.00 4.46
409 537 8.392372 ACTACAACTTCTAAAAATTCCAGGTC 57.608 34.615 0.00 0.00 0.00 3.85
410 538 7.996644 TGACTACAACTTCTAAAAATTCCAGGT 59.003 33.333 0.00 0.00 0.00 4.00
411 539 8.290325 GTGACTACAACTTCTAAAAATTCCAGG 58.710 37.037 0.00 0.00 0.00 4.45
412 540 8.836413 TGTGACTACAACTTCTAAAAATTCCAG 58.164 33.333 0.00 0.00 32.88 3.86
413 541 8.740123 TGTGACTACAACTTCTAAAAATTCCA 57.260 30.769 0.00 0.00 32.88 3.53
417 545 9.574516 AGGAATGTGACTACAACTTCTAAAAAT 57.425 29.630 0.00 0.00 40.84 1.82
418 546 8.974060 AGGAATGTGACTACAACTTCTAAAAA 57.026 30.769 0.00 0.00 40.84 1.94
419 547 8.836413 CAAGGAATGTGACTACAACTTCTAAAA 58.164 33.333 0.00 0.00 40.84 1.52
420 548 7.990886 ACAAGGAATGTGACTACAACTTCTAAA 59.009 33.333 0.00 0.00 41.93 1.85
421 549 7.506114 ACAAGGAATGTGACTACAACTTCTAA 58.494 34.615 0.00 0.00 41.93 2.10
422 550 7.062749 ACAAGGAATGTGACTACAACTTCTA 57.937 36.000 0.00 0.00 41.93 2.10
423 551 5.930135 ACAAGGAATGTGACTACAACTTCT 58.070 37.500 0.00 0.00 41.93 2.85
424 552 7.724305 TTACAAGGAATGTGACTACAACTTC 57.276 36.000 0.00 0.00 43.77 3.01
425 553 7.554835 TGTTTACAAGGAATGTGACTACAACTT 59.445 33.333 0.00 0.00 43.77 2.66
426 554 7.051623 TGTTTACAAGGAATGTGACTACAACT 58.948 34.615 0.00 0.00 43.77 3.16
427 555 7.254227 TGTTTACAAGGAATGTGACTACAAC 57.746 36.000 0.00 0.00 43.77 3.32
428 556 8.458573 AATGTTTACAAGGAATGTGACTACAA 57.541 30.769 0.00 0.00 43.77 2.41
429 557 7.717436 TGAATGTTTACAAGGAATGTGACTACA 59.283 33.333 0.00 0.00 43.77 2.74
430 558 8.094798 TGAATGTTTACAAGGAATGTGACTAC 57.905 34.615 0.00 0.00 43.77 2.73
431 559 8.862325 ATGAATGTTTACAAGGAATGTGACTA 57.138 30.769 0.00 0.00 43.77 2.59
432 560 7.765695 ATGAATGTTTACAAGGAATGTGACT 57.234 32.000 0.00 0.00 43.77 3.41
498 626 4.261994 GCTCCACATGCTCCAACTTAAAAA 60.262 41.667 0.00 0.00 0.00 1.94
499 627 3.255642 GCTCCACATGCTCCAACTTAAAA 59.744 43.478 0.00 0.00 0.00 1.52
500 628 2.819608 GCTCCACATGCTCCAACTTAAA 59.180 45.455 0.00 0.00 0.00 1.52
501 629 2.224744 TGCTCCACATGCTCCAACTTAA 60.225 45.455 0.00 0.00 0.00 1.85
502 630 1.350684 TGCTCCACATGCTCCAACTTA 59.649 47.619 0.00 0.00 0.00 2.24
503 631 0.111061 TGCTCCACATGCTCCAACTT 59.889 50.000 0.00 0.00 0.00 2.66
504 632 0.607489 GTGCTCCACATGCTCCAACT 60.607 55.000 0.00 0.00 34.08 3.16
505 633 1.589716 GGTGCTCCACATGCTCCAAC 61.590 60.000 0.00 0.00 41.91 3.77
506 634 1.303561 GGTGCTCCACATGCTCCAA 60.304 57.895 0.00 0.00 41.91 3.53
507 635 2.352422 GGTGCTCCACATGCTCCA 59.648 61.111 0.00 0.00 41.91 3.86
508 636 2.439156 GGGTGCTCCACATGCTCC 60.439 66.667 7.20 0.00 41.68 4.70
509 637 2.439156 GGGGTGCTCCACATGCTC 60.439 66.667 7.20 0.00 37.04 4.26
510 638 3.259314 TGGGGTGCTCCACATGCT 61.259 61.111 5.43 0.00 42.97 3.79
514 642 1.852157 ATCCTTGGGGTGCTCCACA 60.852 57.895 5.43 5.43 46.62 4.17
515 643 1.379044 CATCCTTGGGGTGCTCCAC 60.379 63.158 7.20 3.07 36.38 4.02
516 644 2.615465 CCATCCTTGGGGTGCTCCA 61.615 63.158 7.20 0.00 39.56 3.86
517 645 2.276740 CCATCCTTGGGGTGCTCC 59.723 66.667 0.00 0.00 39.56 4.70
525 653 3.801997 AGGCGCTCCCATCCTTGG 61.802 66.667 7.64 0.00 43.23 3.61
526 654 2.335092 ATCAGGCGCTCCCATCCTTG 62.335 60.000 7.64 0.00 35.39 3.61
527 655 0.764369 TATCAGGCGCTCCCATCCTT 60.764 55.000 7.64 0.00 35.39 3.36
528 656 0.546267 ATATCAGGCGCTCCCATCCT 60.546 55.000 7.64 0.00 35.39 3.24
529 657 0.326264 AATATCAGGCGCTCCCATCC 59.674 55.000 7.64 0.00 35.39 3.51
530 658 2.079925 GAAATATCAGGCGCTCCCATC 58.920 52.381 7.64 0.00 35.39 3.51
531 659 1.271597 GGAAATATCAGGCGCTCCCAT 60.272 52.381 7.64 0.00 35.39 4.00
532 660 0.108585 GGAAATATCAGGCGCTCCCA 59.891 55.000 7.64 0.00 35.39 4.37
533 661 0.606673 GGGAAATATCAGGCGCTCCC 60.607 60.000 7.64 9.60 36.01 4.30
534 662 0.606673 GGGGAAATATCAGGCGCTCC 60.607 60.000 7.64 2.98 0.00 4.70
535 663 0.606673 GGGGGAAATATCAGGCGCTC 60.607 60.000 7.64 0.00 0.00 5.03
536 664 1.062488 AGGGGGAAATATCAGGCGCT 61.062 55.000 7.64 0.00 0.00 5.92
537 665 0.178990 AAGGGGGAAATATCAGGCGC 60.179 55.000 0.00 0.00 0.00 6.53
538 666 2.158608 AGAAAGGGGGAAATATCAGGCG 60.159 50.000 0.00 0.00 0.00 5.52
539 667 3.602205 AGAAAGGGGGAAATATCAGGC 57.398 47.619 0.00 0.00 0.00 4.85
540 668 6.515512 TCTAAGAAAGGGGGAAATATCAGG 57.484 41.667 0.00 0.00 0.00 3.86
541 669 7.663493 GTGATCTAAGAAAGGGGGAAATATCAG 59.337 40.741 0.00 0.00 0.00 2.90
542 670 7.350921 AGTGATCTAAGAAAGGGGGAAATATCA 59.649 37.037 0.00 0.00 0.00 2.15
543 671 7.750655 AGTGATCTAAGAAAGGGGGAAATATC 58.249 38.462 0.00 0.00 0.00 1.63
544 672 7.574372 AGAGTGATCTAAGAAAGGGGGAAATAT 59.426 37.037 0.00 0.00 0.00 1.28
545 673 6.909158 AGAGTGATCTAAGAAAGGGGGAAATA 59.091 38.462 0.00 0.00 0.00 1.40
546 674 5.733647 AGAGTGATCTAAGAAAGGGGGAAAT 59.266 40.000 0.00 0.00 0.00 2.17
547 675 5.101529 AGAGTGATCTAAGAAAGGGGGAAA 58.898 41.667 0.00 0.00 0.00 3.13
548 676 4.699994 AGAGTGATCTAAGAAAGGGGGAA 58.300 43.478 0.00 0.00 0.00 3.97
549 677 4.354208 AGAGTGATCTAAGAAAGGGGGA 57.646 45.455 0.00 0.00 0.00 4.81
550 678 5.663556 AGTAAGAGTGATCTAAGAAAGGGGG 59.336 44.000 0.00 0.00 0.00 5.40
551 679 6.609616 AGAGTAAGAGTGATCTAAGAAAGGGG 59.390 42.308 0.00 0.00 0.00 4.79
552 680 7.340743 TCAGAGTAAGAGTGATCTAAGAAAGGG 59.659 40.741 0.00 0.00 0.00 3.95
553 681 8.287439 TCAGAGTAAGAGTGATCTAAGAAAGG 57.713 38.462 0.00 0.00 0.00 3.11
631 760 7.639945 AGTACACATAGTTCAACTTTTTCTGC 58.360 34.615 0.00 0.00 0.00 4.26
644 773 6.821665 ACGCCATTAAATGAGTACACATAGTT 59.178 34.615 6.20 1.36 0.00 2.24
680 809 1.470098 CTCACTTAATGGTGCCAGCAC 59.530 52.381 14.39 14.39 45.49 4.40
696 825 3.124297 GCTGTCATTTAGAGTGTGCTCAC 59.876 47.826 10.92 10.92 44.00 3.51
791 920 3.251479 TGCAGCCATACAGTCAGTTAG 57.749 47.619 0.00 0.00 0.00 2.34
792 921 3.197549 TGATGCAGCCATACAGTCAGTTA 59.802 43.478 0.00 0.00 0.00 2.24
793 922 2.026915 TGATGCAGCCATACAGTCAGTT 60.027 45.455 0.00 0.00 0.00 3.16
800 929 1.003464 ACAGTGTGATGCAGCCATACA 59.997 47.619 16.85 5.68 0.00 2.29
806 937 0.668706 ACTCGACAGTGTGATGCAGC 60.669 55.000 0.00 0.00 0.00 5.25
916 1047 1.403679 GTCTGGTCGACTCTGATGGAG 59.596 57.143 16.46 0.00 46.87 3.86
936 1067 1.580845 CGACTGGCAGAAGGCTTTGG 61.581 60.000 23.66 0.00 44.01 3.28
949 1080 1.004277 GAGTGACAACGAGCGACTGG 61.004 60.000 0.00 0.00 0.00 4.00
968 1099 1.008875 CCACATGGTGTCGACTGTCG 61.009 60.000 23.33 23.33 42.10 4.35
969 1100 0.317160 TCCACATGGTGTCGACTGTC 59.683 55.000 17.92 7.22 36.34 3.51
970 1101 0.756294 TTCCACATGGTGTCGACTGT 59.244 50.000 17.92 9.76 36.34 3.55
971 1102 1.148310 GTTCCACATGGTGTCGACTG 58.852 55.000 17.92 9.06 36.34 3.51
972 1103 0.756294 TGTTCCACATGGTGTCGACT 59.244 50.000 17.92 0.00 36.34 4.18
973 1104 1.263217 GTTGTTCCACATGGTGTCGAC 59.737 52.381 9.11 9.11 36.34 4.20
1266 1397 2.874648 CTAACCAGGAGCATGCGCCA 62.875 60.000 37.09 18.64 39.83 5.69
1324 1459 2.819595 CGTGCCATCGGTCAAGGG 60.820 66.667 0.00 0.00 0.00 3.95
1627 1762 3.173240 GCGTCAGTTCTCGCGGTC 61.173 66.667 6.13 0.00 42.79 4.79
1734 1870 8.362639 TGTTATTACTCCGAGTCTAAACAAAGT 58.637 33.333 3.74 0.00 0.00 2.66
1767 1904 3.587797 TCGACTGAAAGATTAGGCGTT 57.412 42.857 0.00 0.00 45.37 4.84
1775 1912 6.145535 GCTTTGACAAAATCGACTGAAAGAT 58.854 36.000 1.62 0.00 37.43 2.40
1842 2007 0.470080 TAGCGGGAGGAGGAAGATGG 60.470 60.000 0.00 0.00 0.00 3.51
1964 2159 4.760047 GGCCGCGATGTCACCTGT 62.760 66.667 8.23 0.00 0.00 4.00
2050 2245 1.000052 TCGGTTCTCGTGTGCATGTAA 60.000 47.619 0.00 0.00 40.32 2.41
2055 2250 2.028484 GGTCGGTTCTCGTGTGCA 59.972 61.111 0.00 0.00 40.32 4.57
2057 2252 1.014044 CATGGGTCGGTTCTCGTGTG 61.014 60.000 0.00 0.00 40.32 3.82
2073 2268 4.035324 TGCAATTGAGGTTTTGTTTGCATG 59.965 37.500 10.34 0.00 43.02 4.06
2126 2381 4.276926 GTCTCCATCAGCAACTTGAAGTTT 59.723 41.667 8.03 0.00 36.03 2.66
2133 2388 3.341823 GACATGTCTCCATCAGCAACTT 58.658 45.455 18.83 0.00 0.00 2.66
2138 2393 1.156645 GCCGACATGTCTCCATCAGC 61.157 60.000 22.95 10.39 0.00 4.26
2186 2441 1.521681 CGCGTGGGGAAGAGGAATC 60.522 63.158 0.00 0.00 0.00 2.52
2246 2501 6.742109 AGTTGTCAACCATCATTCTCAAAAG 58.258 36.000 12.17 0.00 0.00 2.27
2247 2502 6.713762 AGTTGTCAACCATCATTCTCAAAA 57.286 33.333 12.17 0.00 0.00 2.44
2248 2503 7.284261 TGTTAGTTGTCAACCATCATTCTCAAA 59.716 33.333 12.17 0.00 0.00 2.69
2249 2504 6.770303 TGTTAGTTGTCAACCATCATTCTCAA 59.230 34.615 12.17 0.00 0.00 3.02
2250 2505 6.295249 TGTTAGTTGTCAACCATCATTCTCA 58.705 36.000 12.17 0.00 0.00 3.27
2274 2529 5.477984 TCTTATTTGCTGCAAGGATTTGTCT 59.522 36.000 15.39 0.00 36.65 3.41
2296 2551 2.511600 GGGTACGCAGCGCATTCT 60.512 61.111 16.61 0.00 0.00 2.40
2409 2665 6.785337 AACTAGGTGTAGGCAAAAGTTTTT 57.215 33.333 0.00 0.00 0.00 1.94
2412 2668 4.583073 CCAAACTAGGTGTAGGCAAAAGTT 59.417 41.667 0.00 0.00 0.00 2.66
2419 2675 1.407025 GGAGCCAAACTAGGTGTAGGC 60.407 57.143 10.36 10.36 45.03 3.93
2556 2816 9.232082 TGTGAACACGAAATTCAAATTCTTAAG 57.768 29.630 0.00 0.00 37.80 1.85
2610 2870 8.517056 TGTAAGACGTATAGTGTCAAGAAATGA 58.483 33.333 7.57 0.00 38.83 2.57


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

AutoCloner maintained by Alex Coulton.