Multiple sequence alignment - TraesCS6A01G157600

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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 TraesCS6A01G157600 chr6A 100.000 2549 0 0 1 2549 147431425 147428877 0 4708
1 TraesCS6A01G157600 chr2B 98.940 1982 16 2 571 2549 776222962 776224941 0 3539
2 TraesCS6A01G157600 chr2B 98.788 1981 20 2 571 2549 776449258 776447280 0 3522
3 TraesCS6A01G157600 chr2B 98.690 1985 21 2 568 2549 781094238 781096220 0 3517
4 TraesCS6A01G157600 chr3B 98.889 1981 18 2 571 2549 702857654 702855676 0 3533
5 TraesCS6A01G157600 chrUn 98.790 1984 23 1 567 2549 175762108 175764091 0 3530
6 TraesCS6A01G157600 chr5B 98.790 1983 18 2 571 2549 641128779 641126799 0 3524
7 TraesCS6A01G157600 chr4A 98.789 1982 18 3 571 2549 690993564 690995542 0 3522
8 TraesCS6A01G157600 chr3A 98.691 1987 19 2 568 2549 9952655 9954639 0 3518
9 TraesCS6A01G157600 chr7B 98.691 1986 19 4 567 2549 202776911 202778892 0 3517
10 TraesCS6A01G157600 chr5D 93.728 574 29 7 1 570 57302029 57302599 0 854
11 TraesCS6A01G157600 chr6D 93.576 576 30 7 1 570 445326129 445326703 0 852
12 TraesCS6A01G157600 chr1D 93.588 577 28 8 1 570 62839517 62838943 0 852
13 TraesCS6A01G157600 chr1D 93.588 577 27 9 2 570 241150068 241149494 0 852
14 TraesCS6A01G157600 chr1D 93.241 577 30 9 1 570 475788170 475787596 0 841
15 TraesCS6A01G157600 chr2D 93.554 574 29 6 1 571 574551196 574550628 0 848
16 TraesCS6A01G157600 chr7D 93.380 574 32 5 1 570 435200495 435201066 0 845
17 TraesCS6A01G157600 chr4D 93.391 575 28 8 1 570 305778576 305778007 0 843
18 TraesCS6A01G157600 chr4D 93.357 572 34 3 1 570 486110502 486109933 0 843


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 TraesCS6A01G157600 chr6A 147428877 147431425 2548 True 4708 4708 100.000 1 2549 1 chr6A.!!$R1 2548
1 TraesCS6A01G157600 chr2B 776222962 776224941 1979 False 3539 3539 98.940 571 2549 1 chr2B.!!$F1 1978
2 TraesCS6A01G157600 chr2B 776447280 776449258 1978 True 3522 3522 98.788 571 2549 1 chr2B.!!$R1 1978
3 TraesCS6A01G157600 chr2B 781094238 781096220 1982 False 3517 3517 98.690 568 2549 1 chr2B.!!$F2 1981
4 TraesCS6A01G157600 chr3B 702855676 702857654 1978 True 3533 3533 98.889 571 2549 1 chr3B.!!$R1 1978
5 TraesCS6A01G157600 chrUn 175762108 175764091 1983 False 3530 3530 98.790 567 2549 1 chrUn.!!$F1 1982
6 TraesCS6A01G157600 chr5B 641126799 641128779 1980 True 3524 3524 98.790 571 2549 1 chr5B.!!$R1 1978
7 TraesCS6A01G157600 chr4A 690993564 690995542 1978 False 3522 3522 98.789 571 2549 1 chr4A.!!$F1 1978
8 TraesCS6A01G157600 chr3A 9952655 9954639 1984 False 3518 3518 98.691 568 2549 1 chr3A.!!$F1 1981
9 TraesCS6A01G157600 chr7B 202776911 202778892 1981 False 3517 3517 98.691 567 2549 1 chr7B.!!$F1 1982
10 TraesCS6A01G157600 chr5D 57302029 57302599 570 False 854 854 93.728 1 570 1 chr5D.!!$F1 569
11 TraesCS6A01G157600 chr6D 445326129 445326703 574 False 852 852 93.576 1 570 1 chr6D.!!$F1 569
12 TraesCS6A01G157600 chr1D 62838943 62839517 574 True 852 852 93.588 1 570 1 chr1D.!!$R1 569
13 TraesCS6A01G157600 chr1D 241149494 241150068 574 True 852 852 93.588 2 570 1 chr1D.!!$R2 568
14 TraesCS6A01G157600 chr1D 475787596 475788170 574 True 841 841 93.241 1 570 1 chr1D.!!$R3 569
15 TraesCS6A01G157600 chr2D 574550628 574551196 568 True 848 848 93.554 1 571 1 chr2D.!!$R1 570
16 TraesCS6A01G157600 chr7D 435200495 435201066 571 False 845 845 93.380 1 570 1 chr7D.!!$F1 569
17 TraesCS6A01G157600 chr4D 305778007 305778576 569 True 843 843 93.391 1 570 1 chr4D.!!$R1 569
18 TraesCS6A01G157600 chr4D 486109933 486110502 569 True 843 843 93.357 1 570 1 chr4D.!!$R2 569

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
372 380 0.034616 CCTCTCCGATGGCCATCTTC 59.965 60.0 36.51 18.4 35.72 2.87 F
381 389 0.109153 TGGCCATCTTCATCATCCCG 59.891 55.0 0.00 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1270 1278 3.009363 TCATTCATCAGAGTCTTGGCCAA 59.991 43.478 19.25 19.25 0.00 4.52 R
1739 1999 3.096092 AGAGCAACCTTTGTTTGGACAA 58.904 40.909 0.00 0.00 43.73 3.18 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
79 80 0.601841 GAAACCTTCGGGAGCGTGAA 60.602 55.000 0.00 0.00 38.77 3.18
226 231 1.005394 TGACCGACTTCTTTCGCCC 60.005 57.895 0.00 0.00 37.70 6.13
304 312 2.237393 CAGAAGCCTCTGTAGCCATC 57.763 55.000 4.01 0.00 43.64 3.51
305 313 0.749649 AGAAGCCTCTGTAGCCATCG 59.250 55.000 0.00 0.00 0.00 3.84
306 314 0.747255 GAAGCCTCTGTAGCCATCGA 59.253 55.000 0.00 0.00 0.00 3.59
307 315 1.137086 GAAGCCTCTGTAGCCATCGAA 59.863 52.381 0.00 0.00 0.00 3.71
308 316 1.195115 AGCCTCTGTAGCCATCGAAA 58.805 50.000 0.00 0.00 0.00 3.46
309 317 1.555075 AGCCTCTGTAGCCATCGAAAA 59.445 47.619 0.00 0.00 0.00 2.29
310 318 1.666189 GCCTCTGTAGCCATCGAAAAC 59.334 52.381 0.00 0.00 0.00 2.43
311 319 2.280628 CCTCTGTAGCCATCGAAAACC 58.719 52.381 0.00 0.00 0.00 3.27
312 320 2.354704 CCTCTGTAGCCATCGAAAACCA 60.355 50.000 0.00 0.00 0.00 3.67
313 321 3.334691 CTCTGTAGCCATCGAAAACCAA 58.665 45.455 0.00 0.00 0.00 3.67
314 322 3.941483 CTCTGTAGCCATCGAAAACCAAT 59.059 43.478 0.00 0.00 0.00 3.16
315 323 3.938963 TCTGTAGCCATCGAAAACCAATC 59.061 43.478 0.00 0.00 0.00 2.67
316 324 3.941483 CTGTAGCCATCGAAAACCAATCT 59.059 43.478 0.00 0.00 0.00 2.40
317 325 5.092554 TGTAGCCATCGAAAACCAATCTA 57.907 39.130 0.00 0.00 0.00 1.98
318 326 5.116180 TGTAGCCATCGAAAACCAATCTAG 58.884 41.667 0.00 0.00 0.00 2.43
319 327 4.487714 AGCCATCGAAAACCAATCTAGA 57.512 40.909 0.00 0.00 0.00 2.43
320 328 5.041191 AGCCATCGAAAACCAATCTAGAT 57.959 39.130 0.00 0.00 0.00 1.98
321 329 5.059833 AGCCATCGAAAACCAATCTAGATC 58.940 41.667 5.51 0.00 0.00 2.75
322 330 4.214332 GCCATCGAAAACCAATCTAGATCC 59.786 45.833 5.51 0.00 0.00 3.36
323 331 4.449068 CCATCGAAAACCAATCTAGATCCG 59.551 45.833 5.51 1.59 0.00 4.18
324 332 4.730949 TCGAAAACCAATCTAGATCCGT 57.269 40.909 5.51 2.25 0.00 4.69
325 333 5.080969 TCGAAAACCAATCTAGATCCGTT 57.919 39.130 5.51 8.45 0.00 4.44
326 334 5.107133 TCGAAAACCAATCTAGATCCGTTC 58.893 41.667 5.51 5.35 0.00 3.95
327 335 4.270325 CGAAAACCAATCTAGATCCGTTCC 59.730 45.833 5.51 6.47 0.00 3.62
328 336 4.837093 AAACCAATCTAGATCCGTTCCA 57.163 40.909 5.51 0.00 0.00 3.53
329 337 4.408182 AACCAATCTAGATCCGTTCCAG 57.592 45.455 5.51 0.00 0.00 3.86
330 338 2.103263 ACCAATCTAGATCCGTTCCAGC 59.897 50.000 5.51 0.00 0.00 4.85
331 339 2.103094 CCAATCTAGATCCGTTCCAGCA 59.897 50.000 5.51 0.00 0.00 4.41
332 340 3.126831 CAATCTAGATCCGTTCCAGCAC 58.873 50.000 5.51 0.00 0.00 4.40
333 341 1.112113 TCTAGATCCGTTCCAGCACC 58.888 55.000 0.00 0.00 0.00 5.01
334 342 0.105039 CTAGATCCGTTCCAGCACCC 59.895 60.000 0.00 0.00 0.00 4.61
335 343 0.325296 TAGATCCGTTCCAGCACCCT 60.325 55.000 0.00 0.00 0.00 4.34
336 344 1.450312 GATCCGTTCCAGCACCCTG 60.450 63.158 0.00 0.00 38.85 4.45
337 345 3.628646 ATCCGTTCCAGCACCCTGC 62.629 63.158 0.00 0.00 45.46 4.85
339 347 4.641645 CGTTCCAGCACCCTGCCA 62.642 66.667 0.00 0.00 46.52 4.92
340 348 2.674380 GTTCCAGCACCCTGCCAG 60.674 66.667 0.00 0.00 46.52 4.85
341 349 2.853542 TTCCAGCACCCTGCCAGA 60.854 61.111 0.00 0.00 46.52 3.86
342 350 2.898933 TTCCAGCACCCTGCCAGAG 61.899 63.158 0.00 0.00 46.52 3.35
343 351 4.421515 CCAGCACCCTGCCAGAGG 62.422 72.222 0.00 0.00 46.52 3.69
364 372 2.062070 GGGAATCCCTCTCCGATGG 58.938 63.158 11.95 0.00 41.34 3.51
365 373 1.373059 GGAATCCCTCTCCGATGGC 59.627 63.158 0.00 0.00 0.00 4.40
366 374 1.373059 GAATCCCTCTCCGATGGCC 59.627 63.158 0.00 0.00 0.00 5.36
367 375 1.384502 AATCCCTCTCCGATGGCCA 60.385 57.895 8.56 8.56 0.00 5.36
368 376 0.769776 AATCCCTCTCCGATGGCCAT 60.770 55.000 20.96 20.96 0.00 4.40
369 377 1.197430 ATCCCTCTCCGATGGCCATC 61.197 60.000 32.34 32.34 34.56 3.51
370 378 1.840650 CCCTCTCCGATGGCCATCT 60.841 63.158 36.51 11.79 35.72 2.90
371 379 1.414061 CCCTCTCCGATGGCCATCTT 61.414 60.000 36.51 10.95 35.72 2.40
372 380 0.034616 CCTCTCCGATGGCCATCTTC 59.965 60.000 36.51 18.40 35.72 2.87
373 381 0.755079 CTCTCCGATGGCCATCTTCA 59.245 55.000 36.51 21.81 35.72 3.02
374 382 1.347050 CTCTCCGATGGCCATCTTCAT 59.653 52.381 36.51 9.27 35.72 2.57
375 383 1.345741 TCTCCGATGGCCATCTTCATC 59.654 52.381 36.51 16.95 37.12 2.92
376 384 1.071228 CTCCGATGGCCATCTTCATCA 59.929 52.381 36.51 16.55 39.60 3.07
377 385 1.701292 TCCGATGGCCATCTTCATCAT 59.299 47.619 36.51 6.80 39.60 2.45
378 386 2.082231 CCGATGGCCATCTTCATCATC 58.918 52.381 36.51 14.80 39.60 2.92
379 387 2.082231 CGATGGCCATCTTCATCATCC 58.918 52.381 36.51 13.09 39.60 3.51
380 388 2.444421 GATGGCCATCTTCATCATCCC 58.556 52.381 34.20 7.66 39.47 3.85
381 389 0.109153 TGGCCATCTTCATCATCCCG 59.891 55.000 0.00 0.00 0.00 5.14
382 390 0.607489 GGCCATCTTCATCATCCCGG 60.607 60.000 0.00 0.00 0.00 5.73
383 391 1.239968 GCCATCTTCATCATCCCGGC 61.240 60.000 0.00 0.00 0.00 6.13
384 392 0.952497 CCATCTTCATCATCCCGGCG 60.952 60.000 0.00 0.00 0.00 6.46
385 393 1.302033 ATCTTCATCATCCCGGCGC 60.302 57.895 0.00 0.00 0.00 6.53
386 394 1.762522 ATCTTCATCATCCCGGCGCT 61.763 55.000 7.64 0.00 0.00 5.92
387 395 1.958205 CTTCATCATCCCGGCGCTC 60.958 63.158 7.64 0.00 0.00 5.03
388 396 2.374830 CTTCATCATCCCGGCGCTCT 62.375 60.000 7.64 0.00 0.00 4.09
389 397 2.356793 CATCATCCCGGCGCTCTC 60.357 66.667 7.64 0.00 0.00 3.20
390 398 3.620785 ATCATCCCGGCGCTCTCC 61.621 66.667 7.64 0.00 0.00 3.71
392 400 3.933722 CATCCCGGCGCTCTCCAT 61.934 66.667 7.64 0.00 0.00 3.41
393 401 3.933722 ATCCCGGCGCTCTCCATG 61.934 66.667 7.64 0.00 0.00 3.66
395 403 4.899239 CCCGGCGCTCTCCATGAC 62.899 72.222 7.64 0.00 0.00 3.06
397 405 4.193334 CGGCGCTCTCCATGACGA 62.193 66.667 7.64 0.00 0.00 4.20
398 406 2.279120 GGCGCTCTCCATGACGAG 60.279 66.667 7.64 0.17 0.00 4.18
399 407 2.279120 GCGCTCTCCATGACGAGG 60.279 66.667 0.00 5.06 0.00 4.63
400 408 2.775856 GCGCTCTCCATGACGAGGA 61.776 63.158 0.00 0.00 0.00 3.71
405 413 4.686695 TCCATGACGAGGAGGGAG 57.313 61.111 0.00 0.00 0.00 4.30
406 414 1.697910 TCCATGACGAGGAGGGAGT 59.302 57.895 0.00 0.00 0.00 3.85
407 415 0.924090 TCCATGACGAGGAGGGAGTA 59.076 55.000 0.00 0.00 0.00 2.59
408 416 1.133761 TCCATGACGAGGAGGGAGTAG 60.134 57.143 0.00 0.00 0.00 2.57
409 417 1.410365 CCATGACGAGGAGGGAGTAGT 60.410 57.143 0.00 0.00 0.00 2.73
410 418 2.379972 CATGACGAGGAGGGAGTAGTT 58.620 52.381 0.00 0.00 0.00 2.24
411 419 2.125773 TGACGAGGAGGGAGTAGTTC 57.874 55.000 0.00 0.00 0.00 3.01
412 420 1.353358 TGACGAGGAGGGAGTAGTTCA 59.647 52.381 0.00 0.00 0.00 3.18
413 421 1.744522 GACGAGGAGGGAGTAGTTCAC 59.255 57.143 0.00 0.00 0.00 3.18
414 422 1.104630 CGAGGAGGGAGTAGTTCACC 58.895 60.000 0.00 0.00 0.00 4.02
415 423 1.487300 GAGGAGGGAGTAGTTCACCC 58.513 60.000 0.00 0.00 45.50 4.61
419 427 2.200052 GGGAGTAGTTCACCCTCGG 58.800 63.158 0.00 0.00 42.53 4.63
420 428 1.328430 GGGAGTAGTTCACCCTCGGG 61.328 65.000 0.00 0.00 42.53 5.14
430 438 2.284493 CCCTCGGGGCTAAGGGTA 59.716 66.667 0.00 0.00 46.21 3.69
431 439 1.152096 CCCTCGGGGCTAAGGGTAT 60.152 63.158 0.00 0.00 46.21 2.73
432 440 1.481056 CCCTCGGGGCTAAGGGTATG 61.481 65.000 0.00 0.00 46.21 2.39
433 441 0.763223 CCTCGGGGCTAAGGGTATGT 60.763 60.000 0.00 0.00 0.00 2.29
434 442 1.481802 CCTCGGGGCTAAGGGTATGTA 60.482 57.143 0.00 0.00 0.00 2.29
435 443 1.617357 CTCGGGGCTAAGGGTATGTAC 59.383 57.143 0.00 0.00 0.00 2.90
436 444 0.683412 CGGGGCTAAGGGTATGTACC 59.317 60.000 0.40 0.40 45.71 3.34
443 451 5.485209 GCTAAGGGTATGTACCAATAGCT 57.515 43.478 23.94 0.00 46.90 3.32
444 452 6.600882 GCTAAGGGTATGTACCAATAGCTA 57.399 41.667 23.94 0.00 46.90 3.32
445 453 7.184067 GCTAAGGGTATGTACCAATAGCTAT 57.816 40.000 23.94 0.00 46.90 2.97
446 454 7.042335 GCTAAGGGTATGTACCAATAGCTATG 58.958 42.308 23.94 0.00 46.90 2.23
447 455 7.310485 GCTAAGGGTATGTACCAATAGCTATGT 60.310 40.741 23.94 4.46 46.90 2.29
452 460 7.861630 GGTATGTACCAATAGCTATGTGTTTG 58.138 38.462 7.09 1.91 45.73 2.93
453 461 7.713507 GGTATGTACCAATAGCTATGTGTTTGA 59.286 37.037 7.09 0.00 45.73 2.69
454 462 9.273016 GTATGTACCAATAGCTATGTGTTTGAT 57.727 33.333 7.09 0.00 0.00 2.57
455 463 8.752005 ATGTACCAATAGCTATGTGTTTGATT 57.248 30.769 7.09 0.00 0.00 2.57
456 464 8.574251 TGTACCAATAGCTATGTGTTTGATTT 57.426 30.769 7.09 0.00 0.00 2.17
457 465 9.019656 TGTACCAATAGCTATGTGTTTGATTTT 57.980 29.630 7.09 0.00 0.00 1.82
458 466 9.855021 GTACCAATAGCTATGTGTTTGATTTTT 57.145 29.630 7.09 0.00 0.00 1.94
459 467 8.986477 ACCAATAGCTATGTGTTTGATTTTTC 57.014 30.769 7.09 0.00 0.00 2.29
460 468 8.806146 ACCAATAGCTATGTGTTTGATTTTTCT 58.194 29.630 7.09 0.00 0.00 2.52
461 469 9.294030 CCAATAGCTATGTGTTTGATTTTTCTC 57.706 33.333 7.09 0.00 0.00 2.87
464 472 7.992754 AGCTATGTGTTTGATTTTTCTCTCT 57.007 32.000 0.00 0.00 0.00 3.10
465 473 8.038492 AGCTATGTGTTTGATTTTTCTCTCTC 57.962 34.615 0.00 0.00 0.00 3.20
466 474 6.958193 GCTATGTGTTTGATTTTTCTCTCTCG 59.042 38.462 0.00 0.00 0.00 4.04
467 475 6.867662 ATGTGTTTGATTTTTCTCTCTCGT 57.132 33.333 0.00 0.00 0.00 4.18
468 476 6.048073 TGTGTTTGATTTTTCTCTCTCGTG 57.952 37.500 0.00 0.00 0.00 4.35
469 477 5.584649 TGTGTTTGATTTTTCTCTCTCGTGT 59.415 36.000 0.00 0.00 0.00 4.49
470 478 6.093495 TGTGTTTGATTTTTCTCTCTCGTGTT 59.907 34.615 0.00 0.00 0.00 3.32
471 479 6.629252 GTGTTTGATTTTTCTCTCTCGTGTTC 59.371 38.462 0.00 0.00 0.00 3.18
472 480 6.538742 TGTTTGATTTTTCTCTCTCGTGTTCT 59.461 34.615 0.00 0.00 0.00 3.01
473 481 7.065803 TGTTTGATTTTTCTCTCTCGTGTTCTT 59.934 33.333 0.00 0.00 0.00 2.52
474 482 6.530913 TGATTTTTCTCTCTCGTGTTCTTG 57.469 37.500 0.00 0.00 0.00 3.02
475 483 6.280643 TGATTTTTCTCTCTCGTGTTCTTGA 58.719 36.000 0.00 0.00 0.00 3.02
476 484 6.422100 TGATTTTTCTCTCTCGTGTTCTTGAG 59.578 38.462 0.00 0.00 0.00 3.02
477 485 3.924918 TTCTCTCTCGTGTTCTTGAGG 57.075 47.619 0.00 0.00 33.00 3.86
478 486 2.865079 TCTCTCTCGTGTTCTTGAGGT 58.135 47.619 0.00 0.00 33.00 3.85
479 487 2.554462 TCTCTCTCGTGTTCTTGAGGTG 59.446 50.000 0.00 0.00 33.00 4.00
480 488 1.613925 TCTCTCGTGTTCTTGAGGTGG 59.386 52.381 0.00 0.00 33.00 4.61
481 489 1.341531 CTCTCGTGTTCTTGAGGTGGT 59.658 52.381 0.00 0.00 33.00 4.16
482 490 2.557056 CTCTCGTGTTCTTGAGGTGGTA 59.443 50.000 0.00 0.00 33.00 3.25
483 491 2.295349 TCTCGTGTTCTTGAGGTGGTAC 59.705 50.000 0.00 0.00 33.00 3.34
484 492 2.033372 TCGTGTTCTTGAGGTGGTACA 58.967 47.619 0.00 0.00 0.00 2.90
485 493 2.431419 TCGTGTTCTTGAGGTGGTACAA 59.569 45.455 0.00 0.00 44.16 2.41
486 494 3.070446 TCGTGTTCTTGAGGTGGTACAAT 59.930 43.478 0.00 0.00 44.16 2.71
487 495 3.432252 CGTGTTCTTGAGGTGGTACAATC 59.568 47.826 0.00 0.00 44.16 2.67
488 496 4.642429 GTGTTCTTGAGGTGGTACAATCT 58.358 43.478 0.00 0.00 44.16 2.40
489 497 5.063880 GTGTTCTTGAGGTGGTACAATCTT 58.936 41.667 0.00 0.00 44.16 2.40
490 498 5.049405 GTGTTCTTGAGGTGGTACAATCTTG 60.049 44.000 0.00 0.00 44.16 3.02
491 499 5.163248 TGTTCTTGAGGTGGTACAATCTTGA 60.163 40.000 0.00 0.00 44.16 3.02
492 500 5.762179 TCTTGAGGTGGTACAATCTTGAT 57.238 39.130 0.00 0.00 44.16 2.57
493 501 5.491070 TCTTGAGGTGGTACAATCTTGATG 58.509 41.667 0.00 0.00 44.16 3.07
494 502 4.908601 TGAGGTGGTACAATCTTGATGT 57.091 40.909 0.00 0.00 44.16 3.06
495 503 6.212589 TCTTGAGGTGGTACAATCTTGATGTA 59.787 38.462 0.00 0.00 44.16 2.29
496 504 6.560003 TGAGGTGGTACAATCTTGATGTAT 57.440 37.500 0.00 0.00 44.16 2.29
497 505 6.582636 TGAGGTGGTACAATCTTGATGTATC 58.417 40.000 0.00 0.00 44.16 2.24
498 506 5.601662 AGGTGGTACAATCTTGATGTATCG 58.398 41.667 0.00 0.00 44.16 2.92
499 507 4.211374 GGTGGTACAATCTTGATGTATCGC 59.789 45.833 0.00 2.69 44.16 4.58
500 508 4.048504 TGGTACAATCTTGATGTATCGCG 58.951 43.478 0.00 0.00 37.22 5.87
501 509 4.202070 TGGTACAATCTTGATGTATCGCGA 60.202 41.667 13.09 13.09 37.22 5.87
502 510 4.383052 GGTACAATCTTGATGTATCGCGAG 59.617 45.833 16.66 0.00 35.84 5.03
503 511 2.797156 ACAATCTTGATGTATCGCGAGC 59.203 45.455 16.66 10.85 0.00 5.03
504 512 3.055591 CAATCTTGATGTATCGCGAGCT 58.944 45.455 16.66 0.00 0.00 4.09
505 513 2.871182 TCTTGATGTATCGCGAGCTT 57.129 45.000 16.66 8.25 0.00 3.74
506 514 3.165058 TCTTGATGTATCGCGAGCTTT 57.835 42.857 16.66 0.00 0.00 3.51
507 515 2.860136 TCTTGATGTATCGCGAGCTTTG 59.140 45.455 16.66 0.00 0.00 2.77
508 516 0.930310 TGATGTATCGCGAGCTTTGC 59.070 50.000 16.66 1.11 0.00 3.68
509 517 1.212616 GATGTATCGCGAGCTTTGCT 58.787 50.000 16.66 0.00 43.88 3.91
510 518 2.223711 TGATGTATCGCGAGCTTTGCTA 60.224 45.455 16.66 0.00 39.88 3.49
511 519 2.509052 TGTATCGCGAGCTTTGCTAT 57.491 45.000 16.66 7.12 39.88 2.97
512 520 2.821546 TGTATCGCGAGCTTTGCTATT 58.178 42.857 16.66 0.00 39.88 1.73
513 521 3.972403 TGTATCGCGAGCTTTGCTATTA 58.028 40.909 16.66 0.00 39.88 0.98
514 522 4.556233 TGTATCGCGAGCTTTGCTATTAT 58.444 39.130 16.66 0.00 39.88 1.28
515 523 5.705902 TGTATCGCGAGCTTTGCTATTATA 58.294 37.500 16.66 0.00 39.88 0.98
516 524 5.800438 TGTATCGCGAGCTTTGCTATTATAG 59.200 40.000 16.66 0.00 39.88 1.31
517 525 4.238761 TCGCGAGCTTTGCTATTATAGT 57.761 40.909 3.71 0.00 39.88 2.12
518 526 4.617959 TCGCGAGCTTTGCTATTATAGTT 58.382 39.130 3.71 0.00 39.88 2.24
519 527 4.444388 TCGCGAGCTTTGCTATTATAGTTG 59.556 41.667 3.71 0.00 39.88 3.16
520 528 4.376413 CGCGAGCTTTGCTATTATAGTTGG 60.376 45.833 0.00 0.00 39.88 3.77
521 529 4.750098 GCGAGCTTTGCTATTATAGTTGGA 59.250 41.667 4.76 0.00 39.88 3.53
522 530 5.409826 GCGAGCTTTGCTATTATAGTTGGAT 59.590 40.000 4.76 0.00 39.88 3.41
523 531 6.590292 GCGAGCTTTGCTATTATAGTTGGATA 59.410 38.462 4.76 0.00 39.88 2.59
524 532 7.278868 GCGAGCTTTGCTATTATAGTTGGATAT 59.721 37.037 4.76 0.00 39.88 1.63
525 533 9.155975 CGAGCTTTGCTATTATAGTTGGATATT 57.844 33.333 0.94 0.00 39.88 1.28
539 547 9.965902 ATAGTTGGATATTATGATGTTTCTCCC 57.034 33.333 0.00 0.00 0.00 4.30
540 548 7.234355 AGTTGGATATTATGATGTTTCTCCCC 58.766 38.462 0.00 0.00 0.00 4.81
541 549 6.139679 TGGATATTATGATGTTTCTCCCCC 57.860 41.667 0.00 0.00 0.00 5.40
542 550 5.857283 TGGATATTATGATGTTTCTCCCCCT 59.143 40.000 0.00 0.00 0.00 4.79
543 551 6.012508 TGGATATTATGATGTTTCTCCCCCTC 60.013 42.308 0.00 0.00 0.00 4.30
544 552 6.216456 GGATATTATGATGTTTCTCCCCCTCT 59.784 42.308 0.00 0.00 0.00 3.69
545 553 7.403231 GGATATTATGATGTTTCTCCCCCTCTA 59.597 40.741 0.00 0.00 0.00 2.43
546 554 5.888982 TTATGATGTTTCTCCCCCTCTAC 57.111 43.478 0.00 0.00 0.00 2.59
547 555 3.491766 TGATGTTTCTCCCCCTCTACT 57.508 47.619 0.00 0.00 0.00 2.57
548 556 3.375699 TGATGTTTCTCCCCCTCTACTC 58.624 50.000 0.00 0.00 0.00 2.59
549 557 3.012959 TGATGTTTCTCCCCCTCTACTCT 59.987 47.826 0.00 0.00 0.00 3.24
550 558 3.103080 TGTTTCTCCCCCTCTACTCTC 57.897 52.381 0.00 0.00 0.00 3.20
551 559 2.655407 TGTTTCTCCCCCTCTACTCTCT 59.345 50.000 0.00 0.00 0.00 3.10
552 560 3.077695 TGTTTCTCCCCCTCTACTCTCTT 59.922 47.826 0.00 0.00 0.00 2.85
553 561 3.390175 TTCTCCCCCTCTACTCTCTTG 57.610 52.381 0.00 0.00 0.00 3.02
554 562 2.289467 TCTCCCCCTCTACTCTCTTGT 58.711 52.381 0.00 0.00 0.00 3.16
555 563 3.471879 TCTCCCCCTCTACTCTCTTGTA 58.528 50.000 0.00 0.00 0.00 2.41
556 564 3.856813 TCTCCCCCTCTACTCTCTTGTAA 59.143 47.826 0.00 0.00 0.00 2.41
557 565 4.482772 TCTCCCCCTCTACTCTCTTGTAAT 59.517 45.833 0.00 0.00 0.00 1.89
558 566 4.547671 TCCCCCTCTACTCTCTTGTAATG 58.452 47.826 0.00 0.00 0.00 1.90
559 567 3.643792 CCCCCTCTACTCTCTTGTAATGG 59.356 52.174 0.00 0.00 0.00 3.16
560 568 4.547671 CCCCTCTACTCTCTTGTAATGGA 58.452 47.826 0.00 0.00 0.00 3.41
561 569 5.151454 CCCCTCTACTCTCTTGTAATGGAT 58.849 45.833 0.00 0.00 0.00 3.41
562 570 5.604650 CCCCTCTACTCTCTTGTAATGGATT 59.395 44.000 0.00 0.00 0.00 3.01
563 571 6.463614 CCCCTCTACTCTCTTGTAATGGATTG 60.464 46.154 0.00 0.00 0.00 2.67
564 572 6.325028 CCCTCTACTCTCTTGTAATGGATTGA 59.675 42.308 0.00 0.00 0.00 2.57
565 573 7.432869 CCTCTACTCTCTTGTAATGGATTGAG 58.567 42.308 0.00 0.00 0.00 3.02
566 574 7.069331 CCTCTACTCTCTTGTAATGGATTGAGT 59.931 40.741 0.00 0.00 37.33 3.41
610 618 0.473755 TCAGTGGTGTCCATGTGCTT 59.526 50.000 0.00 0.00 35.28 3.91
1270 1278 3.140325 TCTTTCTTTGGGTCGATGCTT 57.860 42.857 0.00 0.00 0.00 3.91
1739 1999 3.246403 GCTCTCTGCTCTGCCTTTT 57.754 52.632 0.00 0.00 38.95 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 3.142951 TGGATCACGTTCGTTCCAAAAT 58.857 40.909 13.92 0.00 35.38 1.82
300 308 4.449068 CGGATCTAGATTGGTTTTCGATGG 59.551 45.833 6.70 0.00 0.00 3.51
301 309 5.050490 ACGGATCTAGATTGGTTTTCGATG 58.950 41.667 6.70 0.00 0.00 3.84
302 310 5.277857 ACGGATCTAGATTGGTTTTCGAT 57.722 39.130 6.70 0.00 0.00 3.59
303 311 4.730949 ACGGATCTAGATTGGTTTTCGA 57.269 40.909 6.70 0.00 0.00 3.71
304 312 4.270325 GGAACGGATCTAGATTGGTTTTCG 59.730 45.833 18.01 6.00 0.00 3.46
305 313 5.183228 TGGAACGGATCTAGATTGGTTTTC 58.817 41.667 18.01 14.71 0.00 2.29
306 314 5.174037 TGGAACGGATCTAGATTGGTTTT 57.826 39.130 18.01 5.25 0.00 2.43
307 315 4.770795 CTGGAACGGATCTAGATTGGTTT 58.229 43.478 18.01 6.65 38.88 3.27
308 316 3.432326 GCTGGAACGGATCTAGATTGGTT 60.432 47.826 17.35 17.35 38.88 3.67
309 317 2.103263 GCTGGAACGGATCTAGATTGGT 59.897 50.000 6.70 5.29 38.88 3.67
310 318 2.103094 TGCTGGAACGGATCTAGATTGG 59.897 50.000 6.70 4.64 38.88 3.16
311 319 3.126831 GTGCTGGAACGGATCTAGATTG 58.873 50.000 6.70 5.57 38.88 2.67
312 320 2.103263 GGTGCTGGAACGGATCTAGATT 59.897 50.000 6.70 0.00 38.88 2.40
313 321 1.689273 GGTGCTGGAACGGATCTAGAT 59.311 52.381 4.47 4.47 38.88 1.98
314 322 1.112113 GGTGCTGGAACGGATCTAGA 58.888 55.000 2.83 0.00 38.88 2.43
315 323 0.105039 GGGTGCTGGAACGGATCTAG 59.895 60.000 0.00 0.00 39.53 2.43
316 324 0.325296 AGGGTGCTGGAACGGATCTA 60.325 55.000 0.00 0.00 36.31 1.98
317 325 1.613630 AGGGTGCTGGAACGGATCT 60.614 57.895 0.00 0.00 36.31 2.75
318 326 1.450312 CAGGGTGCTGGAACGGATC 60.450 63.158 0.00 0.00 36.31 3.36
319 327 2.671070 CAGGGTGCTGGAACGGAT 59.329 61.111 0.00 0.00 36.31 4.18
320 328 4.329545 GCAGGGTGCTGGAACGGA 62.330 66.667 0.00 0.00 40.96 4.69
322 330 4.641645 TGGCAGGGTGCTGGAACG 62.642 66.667 0.00 0.00 44.28 3.95
323 331 2.674380 CTGGCAGGGTGCTGGAAC 60.674 66.667 6.61 0.00 44.28 3.62
324 332 2.853542 TCTGGCAGGGTGCTGGAA 60.854 61.111 15.73 0.00 44.28 3.53
325 333 3.324930 CTCTGGCAGGGTGCTGGA 61.325 66.667 15.73 0.00 44.28 3.86
326 334 4.421515 CCTCTGGCAGGGTGCTGG 62.422 72.222 14.42 3.72 44.28 4.85
353 361 0.034616 GAAGATGGCCATCGGAGAGG 59.965 60.000 34.48 0.00 43.63 3.69
354 362 0.755079 TGAAGATGGCCATCGGAGAG 59.245 55.000 34.48 0.00 43.63 3.20
355 363 1.345741 GATGAAGATGGCCATCGGAGA 59.654 52.381 34.48 22.08 42.48 3.71
356 364 1.071228 TGATGAAGATGGCCATCGGAG 59.929 52.381 34.48 0.00 41.40 4.63
357 365 1.130777 TGATGAAGATGGCCATCGGA 58.869 50.000 34.48 24.01 41.40 4.55
358 366 2.082231 GATGATGAAGATGGCCATCGG 58.918 52.381 34.48 0.00 41.40 4.18
359 367 2.082231 GGATGATGAAGATGGCCATCG 58.918 52.381 34.48 0.00 41.40 3.84
360 368 2.444421 GGGATGATGAAGATGGCCATC 58.556 52.381 34.48 34.48 39.55 3.51
361 369 1.271762 CGGGATGATGAAGATGGCCAT 60.272 52.381 20.96 20.96 0.00 4.40
362 370 0.109153 CGGGATGATGAAGATGGCCA 59.891 55.000 8.56 8.56 0.00 5.36
363 371 0.607489 CCGGGATGATGAAGATGGCC 60.607 60.000 0.00 0.00 0.00 5.36
364 372 1.239968 GCCGGGATGATGAAGATGGC 61.240 60.000 2.18 0.00 0.00 4.40
365 373 0.952497 CGCCGGGATGATGAAGATGG 60.952 60.000 2.18 0.00 0.00 3.51
366 374 1.572085 GCGCCGGGATGATGAAGATG 61.572 60.000 2.18 0.00 0.00 2.90
367 375 1.302033 GCGCCGGGATGATGAAGAT 60.302 57.895 2.18 0.00 0.00 2.40
368 376 2.108976 GCGCCGGGATGATGAAGA 59.891 61.111 2.18 0.00 0.00 2.87
369 377 1.958205 GAGCGCCGGGATGATGAAG 60.958 63.158 2.29 0.00 0.00 3.02
370 378 2.108976 GAGCGCCGGGATGATGAA 59.891 61.111 2.29 0.00 0.00 2.57
371 379 2.839632 AGAGCGCCGGGATGATGA 60.840 61.111 2.29 0.00 0.00 2.92
372 380 2.356793 GAGAGCGCCGGGATGATG 60.357 66.667 2.29 0.00 0.00 3.07
373 381 3.620785 GGAGAGCGCCGGGATGAT 61.621 66.667 2.29 0.00 0.00 2.45
375 383 3.933722 ATGGAGAGCGCCGGGATG 61.934 66.667 2.29 0.00 0.00 3.51
376 384 3.933722 CATGGAGAGCGCCGGGAT 61.934 66.667 2.29 0.00 0.00 3.85
378 386 4.899239 GTCATGGAGAGCGCCGGG 62.899 72.222 2.29 0.00 0.00 5.73
380 388 4.193334 TCGTCATGGAGAGCGCCG 62.193 66.667 2.29 0.00 0.00 6.46
381 389 2.279120 CTCGTCATGGAGAGCGCC 60.279 66.667 2.29 0.00 36.08 6.53
382 390 2.279120 CCTCGTCATGGAGAGCGC 60.279 66.667 0.00 0.00 36.08 5.92
383 391 3.514417 TCCTCGTCATGGAGAGCG 58.486 61.111 11.32 6.64 36.08 5.03
388 396 0.924090 TACTCCCTCCTCGTCATGGA 59.076 55.000 0.00 0.00 0.00 3.41
389 397 1.323412 CTACTCCCTCCTCGTCATGG 58.677 60.000 0.00 0.00 0.00 3.66
390 398 2.060050 ACTACTCCCTCCTCGTCATG 57.940 55.000 0.00 0.00 0.00 3.07
391 399 2.025226 TGAACTACTCCCTCCTCGTCAT 60.025 50.000 0.00 0.00 0.00 3.06
392 400 1.353358 TGAACTACTCCCTCCTCGTCA 59.647 52.381 0.00 0.00 0.00 4.35
393 401 1.744522 GTGAACTACTCCCTCCTCGTC 59.255 57.143 0.00 0.00 0.00 4.20
394 402 1.616456 GGTGAACTACTCCCTCCTCGT 60.616 57.143 0.00 0.00 0.00 4.18
395 403 1.104630 GGTGAACTACTCCCTCCTCG 58.895 60.000 0.00 0.00 0.00 4.63
396 404 1.487300 GGGTGAACTACTCCCTCCTC 58.513 60.000 0.00 0.00 45.77 3.71
397 405 3.713867 GGGTGAACTACTCCCTCCT 57.286 57.895 0.00 0.00 45.77 3.69
402 410 1.328430 CCCCGAGGGTGAACTACTCC 61.328 65.000 7.48 0.00 38.25 3.85
403 411 1.957765 GCCCCGAGGGTGAACTACTC 61.958 65.000 7.48 0.00 46.51 2.59
404 412 1.988406 GCCCCGAGGGTGAACTACT 60.988 63.158 7.48 0.00 46.51 2.57
405 413 0.685458 TAGCCCCGAGGGTGAACTAC 60.685 60.000 7.48 0.00 46.51 2.73
406 414 0.041535 TTAGCCCCGAGGGTGAACTA 59.958 55.000 7.48 0.99 46.51 2.24
407 415 1.229400 TTAGCCCCGAGGGTGAACT 60.229 57.895 7.48 1.91 46.51 3.01
408 416 1.221021 CTTAGCCCCGAGGGTGAAC 59.779 63.158 7.48 0.00 46.51 3.18
409 417 1.993391 CCTTAGCCCCGAGGGTGAA 60.993 63.158 7.48 0.00 46.51 3.18
410 418 2.365105 CCTTAGCCCCGAGGGTGA 60.365 66.667 7.48 0.00 46.51 4.02
411 419 3.480133 CCCTTAGCCCCGAGGGTG 61.480 72.222 7.48 0.00 46.51 4.61
414 422 0.763223 ACATACCCTTAGCCCCGAGG 60.763 60.000 0.00 0.00 0.00 4.63
415 423 1.617357 GTACATACCCTTAGCCCCGAG 59.383 57.143 0.00 0.00 0.00 4.63
416 424 1.708341 GTACATACCCTTAGCCCCGA 58.292 55.000 0.00 0.00 0.00 5.14
417 425 0.683412 GGTACATACCCTTAGCCCCG 59.317 60.000 0.00 0.00 40.53 5.73
418 426 1.810455 TGGTACATACCCTTAGCCCC 58.190 55.000 5.62 0.00 45.87 5.80
419 427 4.565028 GCTATTGGTACATACCCTTAGCCC 60.565 50.000 19.34 3.83 45.87 5.19
420 428 4.286291 AGCTATTGGTACATACCCTTAGCC 59.714 45.833 23.04 13.08 46.36 3.93
421 429 5.485209 AGCTATTGGTACATACCCTTAGC 57.515 43.478 21.02 21.02 45.98 3.09
422 430 8.035394 CACATAGCTATTGGTACATACCCTTAG 58.965 40.741 2.64 7.57 45.87 2.18
423 431 7.511371 ACACATAGCTATTGGTACATACCCTTA 59.489 37.037 2.64 0.00 45.87 2.69
424 432 6.329197 ACACATAGCTATTGGTACATACCCTT 59.671 38.462 2.64 0.00 45.87 3.95
425 433 5.844516 ACACATAGCTATTGGTACATACCCT 59.155 40.000 2.64 0.00 45.87 4.34
426 434 6.110411 ACACATAGCTATTGGTACATACCC 57.890 41.667 2.64 0.00 45.87 3.69
427 435 7.713507 TCAAACACATAGCTATTGGTACATACC 59.286 37.037 2.64 0.75 46.62 2.73
428 436 8.657074 TCAAACACATAGCTATTGGTACATAC 57.343 34.615 2.64 0.00 39.30 2.39
429 437 9.845740 AATCAAACACATAGCTATTGGTACATA 57.154 29.630 2.64 0.00 39.30 2.29
430 438 8.752005 AATCAAACACATAGCTATTGGTACAT 57.248 30.769 2.64 0.00 39.30 2.29
431 439 8.574251 AAATCAAACACATAGCTATTGGTACA 57.426 30.769 2.64 0.00 0.00 2.90
432 440 9.855021 AAAAATCAAACACATAGCTATTGGTAC 57.145 29.630 2.64 0.00 0.00 3.34
434 442 8.806146 AGAAAAATCAAACACATAGCTATTGGT 58.194 29.630 2.64 2.24 0.00 3.67
435 443 9.294030 GAGAAAAATCAAACACATAGCTATTGG 57.706 33.333 2.64 1.56 0.00 3.16
438 446 9.678260 AGAGAGAAAAATCAAACACATAGCTAT 57.322 29.630 0.00 0.00 0.00 2.97
439 447 9.155975 GAGAGAGAAAAATCAAACACATAGCTA 57.844 33.333 0.00 0.00 0.00 3.32
440 448 7.148507 CGAGAGAGAAAAATCAAACACATAGCT 60.149 37.037 0.00 0.00 0.00 3.32
441 449 6.958193 CGAGAGAGAAAAATCAAACACATAGC 59.042 38.462 0.00 0.00 0.00 2.97
442 450 7.954248 CACGAGAGAGAAAAATCAAACACATAG 59.046 37.037 0.00 0.00 0.00 2.23
443 451 7.441157 ACACGAGAGAGAAAAATCAAACACATA 59.559 33.333 0.00 0.00 0.00 2.29
444 452 6.260936 ACACGAGAGAGAAAAATCAAACACAT 59.739 34.615 0.00 0.00 0.00 3.21
445 453 5.584649 ACACGAGAGAGAAAAATCAAACACA 59.415 36.000 0.00 0.00 0.00 3.72
446 454 6.049263 ACACGAGAGAGAAAAATCAAACAC 57.951 37.500 0.00 0.00 0.00 3.32
447 455 6.538742 AGAACACGAGAGAGAAAAATCAAACA 59.461 34.615 0.00 0.00 0.00 2.83
448 456 6.949449 AGAACACGAGAGAGAAAAATCAAAC 58.051 36.000 0.00 0.00 0.00 2.93
449 457 7.279981 TCAAGAACACGAGAGAGAAAAATCAAA 59.720 33.333 0.00 0.00 0.00 2.69
450 458 6.761242 TCAAGAACACGAGAGAGAAAAATCAA 59.239 34.615 0.00 0.00 0.00 2.57
451 459 6.280643 TCAAGAACACGAGAGAGAAAAATCA 58.719 36.000 0.00 0.00 0.00 2.57
452 460 6.128688 CCTCAAGAACACGAGAGAGAAAAATC 60.129 42.308 0.00 0.00 0.00 2.17
453 461 5.698545 CCTCAAGAACACGAGAGAGAAAAAT 59.301 40.000 0.00 0.00 0.00 1.82
454 462 5.050490 CCTCAAGAACACGAGAGAGAAAAA 58.950 41.667 0.00 0.00 0.00 1.94
455 463 4.099573 ACCTCAAGAACACGAGAGAGAAAA 59.900 41.667 0.00 0.00 0.00 2.29
456 464 3.637229 ACCTCAAGAACACGAGAGAGAAA 59.363 43.478 0.00 0.00 0.00 2.52
457 465 3.004839 CACCTCAAGAACACGAGAGAGAA 59.995 47.826 0.00 0.00 0.00 2.87
458 466 2.554462 CACCTCAAGAACACGAGAGAGA 59.446 50.000 0.00 0.00 0.00 3.10
459 467 2.352225 CCACCTCAAGAACACGAGAGAG 60.352 54.545 0.00 0.00 0.00 3.20
460 468 1.613925 CCACCTCAAGAACACGAGAGA 59.386 52.381 0.00 0.00 0.00 3.10
461 469 1.341531 ACCACCTCAAGAACACGAGAG 59.658 52.381 0.00 0.00 0.00 3.20
462 470 1.410004 ACCACCTCAAGAACACGAGA 58.590 50.000 0.00 0.00 0.00 4.04
463 471 2.035449 TGTACCACCTCAAGAACACGAG 59.965 50.000 0.00 0.00 0.00 4.18
464 472 2.033372 TGTACCACCTCAAGAACACGA 58.967 47.619 0.00 0.00 0.00 4.35
465 473 2.519377 TGTACCACCTCAAGAACACG 57.481 50.000 0.00 0.00 0.00 4.49
466 474 4.642429 AGATTGTACCACCTCAAGAACAC 58.358 43.478 0.00 0.00 0.00 3.32
467 475 4.974645 AGATTGTACCACCTCAAGAACA 57.025 40.909 0.00 0.00 0.00 3.18
468 476 5.305585 TCAAGATTGTACCACCTCAAGAAC 58.694 41.667 0.00 0.00 0.00 3.01
469 477 5.560722 TCAAGATTGTACCACCTCAAGAA 57.439 39.130 0.00 0.00 0.00 2.52
470 478 5.013079 ACATCAAGATTGTACCACCTCAAGA 59.987 40.000 0.00 0.00 0.00 3.02
471 479 5.248640 ACATCAAGATTGTACCACCTCAAG 58.751 41.667 0.00 0.00 0.00 3.02
472 480 5.241403 ACATCAAGATTGTACCACCTCAA 57.759 39.130 0.00 0.00 0.00 3.02
473 481 4.908601 ACATCAAGATTGTACCACCTCA 57.091 40.909 0.00 0.00 0.00 3.86
474 482 5.692204 CGATACATCAAGATTGTACCACCTC 59.308 44.000 0.00 0.00 0.00 3.85
475 483 5.601662 CGATACATCAAGATTGTACCACCT 58.398 41.667 0.00 0.00 0.00 4.00
476 484 4.211374 GCGATACATCAAGATTGTACCACC 59.789 45.833 0.00 0.00 0.00 4.61
477 485 4.085055 CGCGATACATCAAGATTGTACCAC 60.085 45.833 0.00 0.00 0.00 4.16
478 486 4.048504 CGCGATACATCAAGATTGTACCA 58.951 43.478 0.00 0.00 0.00 3.25
479 487 4.295870 TCGCGATACATCAAGATTGTACC 58.704 43.478 3.71 0.00 0.00 3.34
480 488 4.143514 GCTCGCGATACATCAAGATTGTAC 60.144 45.833 10.36 0.00 0.00 2.90
481 489 3.981416 GCTCGCGATACATCAAGATTGTA 59.019 43.478 10.36 0.00 0.00 2.41
482 490 2.797156 GCTCGCGATACATCAAGATTGT 59.203 45.455 10.36 0.00 0.00 2.71
483 491 3.055591 AGCTCGCGATACATCAAGATTG 58.944 45.455 10.36 0.00 0.00 2.67
484 492 3.377346 AGCTCGCGATACATCAAGATT 57.623 42.857 10.36 0.00 0.00 2.40
485 493 3.377346 AAGCTCGCGATACATCAAGAT 57.623 42.857 10.36 0.00 0.00 2.40
486 494 2.860136 CAAAGCTCGCGATACATCAAGA 59.140 45.455 10.36 0.00 0.00 3.02
487 495 2.598439 GCAAAGCTCGCGATACATCAAG 60.598 50.000 10.36 0.00 0.00 3.02
488 496 1.327460 GCAAAGCTCGCGATACATCAA 59.673 47.619 10.36 0.00 0.00 2.57
489 497 0.930310 GCAAAGCTCGCGATACATCA 59.070 50.000 10.36 0.00 0.00 3.07
490 498 1.212616 AGCAAAGCTCGCGATACATC 58.787 50.000 10.36 0.00 30.62 3.06
491 499 2.509052 TAGCAAAGCTCGCGATACAT 57.491 45.000 10.36 0.00 40.44 2.29
492 500 2.509052 ATAGCAAAGCTCGCGATACA 57.491 45.000 10.36 0.00 40.44 2.29
493 501 5.800941 ACTATAATAGCAAAGCTCGCGATAC 59.199 40.000 10.36 4.99 40.44 2.24
494 502 5.950883 ACTATAATAGCAAAGCTCGCGATA 58.049 37.500 10.36 0.00 40.44 2.92
495 503 4.810790 ACTATAATAGCAAAGCTCGCGAT 58.189 39.130 10.36 0.00 40.44 4.58
496 504 4.238761 ACTATAATAGCAAAGCTCGCGA 57.761 40.909 9.26 9.26 40.44 5.87
497 505 4.376413 CCAACTATAATAGCAAAGCTCGCG 60.376 45.833 0.00 0.00 40.44 5.87
498 506 4.750098 TCCAACTATAATAGCAAAGCTCGC 59.250 41.667 0.00 0.00 40.44 5.03
499 507 8.709386 ATATCCAACTATAATAGCAAAGCTCG 57.291 34.615 0.00 0.00 40.44 5.03
513 521 9.965902 GGGAGAAACATCATAATATCCAACTAT 57.034 33.333 0.00 0.00 0.00 2.12
514 522 8.383175 GGGGAGAAACATCATAATATCCAACTA 58.617 37.037 0.00 0.00 0.00 2.24
515 523 7.234355 GGGGAGAAACATCATAATATCCAACT 58.766 38.462 0.00 0.00 0.00 3.16
516 524 6.434340 GGGGGAGAAACATCATAATATCCAAC 59.566 42.308 0.00 0.00 0.00 3.77
517 525 6.335311 AGGGGGAGAAACATCATAATATCCAA 59.665 38.462 0.00 0.00 0.00 3.53
518 526 5.857283 AGGGGGAGAAACATCATAATATCCA 59.143 40.000 0.00 0.00 0.00 3.41
519 527 6.216456 AGAGGGGGAGAAACATCATAATATCC 59.784 42.308 0.00 0.00 0.00 2.59
520 528 7.264294 AGAGGGGGAGAAACATCATAATATC 57.736 40.000 0.00 0.00 0.00 1.63
521 529 7.964293 AGTAGAGGGGGAGAAACATCATAATAT 59.036 37.037 0.00 0.00 0.00 1.28
522 530 7.313731 AGTAGAGGGGGAGAAACATCATAATA 58.686 38.462 0.00 0.00 0.00 0.98
523 531 6.153924 AGTAGAGGGGGAGAAACATCATAAT 58.846 40.000 0.00 0.00 0.00 1.28
524 532 5.538877 AGTAGAGGGGGAGAAACATCATAA 58.461 41.667 0.00 0.00 0.00 1.90
525 533 5.103043 AGAGTAGAGGGGGAGAAACATCATA 60.103 44.000 0.00 0.00 0.00 2.15
526 534 3.970640 GAGTAGAGGGGGAGAAACATCAT 59.029 47.826 0.00 0.00 0.00 2.45
527 535 3.012959 AGAGTAGAGGGGGAGAAACATCA 59.987 47.826 0.00 0.00 0.00 3.07
528 536 3.639561 GAGAGTAGAGGGGGAGAAACATC 59.360 52.174 0.00 0.00 0.00 3.06
529 537 3.273618 AGAGAGTAGAGGGGGAGAAACAT 59.726 47.826 0.00 0.00 0.00 2.71
530 538 2.655407 AGAGAGTAGAGGGGGAGAAACA 59.345 50.000 0.00 0.00 0.00 2.83
531 539 3.391799 AGAGAGTAGAGGGGGAGAAAC 57.608 52.381 0.00 0.00 0.00 2.78
532 540 3.077695 ACAAGAGAGTAGAGGGGGAGAAA 59.922 47.826 0.00 0.00 0.00 2.52
533 541 2.655407 ACAAGAGAGTAGAGGGGGAGAA 59.345 50.000 0.00 0.00 0.00 2.87
534 542 2.289467 ACAAGAGAGTAGAGGGGGAGA 58.711 52.381 0.00 0.00 0.00 3.71
535 543 2.838637 ACAAGAGAGTAGAGGGGGAG 57.161 55.000 0.00 0.00 0.00 4.30
536 544 4.547671 CATTACAAGAGAGTAGAGGGGGA 58.452 47.826 0.00 0.00 0.00 4.81
537 545 3.643792 CCATTACAAGAGAGTAGAGGGGG 59.356 52.174 0.00 0.00 0.00 5.40
538 546 4.547671 TCCATTACAAGAGAGTAGAGGGG 58.452 47.826 0.00 0.00 0.00 4.79
539 547 6.325028 TCAATCCATTACAAGAGAGTAGAGGG 59.675 42.308 0.00 0.00 0.00 4.30
540 548 7.069331 ACTCAATCCATTACAAGAGAGTAGAGG 59.931 40.741 0.00 0.00 33.72 3.69
541 549 8.006298 ACTCAATCCATTACAAGAGAGTAGAG 57.994 38.462 0.00 0.00 33.72 2.43
542 550 7.962995 ACTCAATCCATTACAAGAGAGTAGA 57.037 36.000 0.00 0.00 33.72 2.59
543 551 9.442047 AAAACTCAATCCATTACAAGAGAGTAG 57.558 33.333 0.00 0.00 34.32 2.57
544 552 9.219603 CAAAACTCAATCCATTACAAGAGAGTA 57.780 33.333 0.00 0.00 34.32 2.59
545 553 7.175641 CCAAAACTCAATCCATTACAAGAGAGT 59.824 37.037 0.00 0.00 36.73 3.24
546 554 7.362401 CCCAAAACTCAATCCATTACAAGAGAG 60.362 40.741 0.00 0.00 0.00 3.20
547 555 6.434028 CCCAAAACTCAATCCATTACAAGAGA 59.566 38.462 0.00 0.00 0.00 3.10
548 556 6.209391 ACCCAAAACTCAATCCATTACAAGAG 59.791 38.462 0.00 0.00 0.00 2.85
549 557 6.074648 ACCCAAAACTCAATCCATTACAAGA 58.925 36.000 0.00 0.00 0.00 3.02
550 558 6.345096 ACCCAAAACTCAATCCATTACAAG 57.655 37.500 0.00 0.00 0.00 3.16
551 559 6.739331 AACCCAAAACTCAATCCATTACAA 57.261 33.333 0.00 0.00 0.00 2.41
552 560 7.841282 TTAACCCAAAACTCAATCCATTACA 57.159 32.000 0.00 0.00 0.00 2.41
556 564 8.704668 GGATAATTAACCCAAAACTCAATCCAT 58.295 33.333 0.24 0.00 0.00 3.41
557 565 7.898636 AGGATAATTAACCCAAAACTCAATCCA 59.101 33.333 8.09 0.00 32.28 3.41
558 566 8.306313 AGGATAATTAACCCAAAACTCAATCC 57.694 34.615 8.09 0.00 0.00 3.01
561 569 9.771534 CAAAAGGATAATTAACCCAAAACTCAA 57.228 29.630 8.09 0.00 0.00 3.02
562 570 7.875554 GCAAAAGGATAATTAACCCAAAACTCA 59.124 33.333 8.09 0.00 0.00 3.41
563 571 7.333423 GGCAAAAGGATAATTAACCCAAAACTC 59.667 37.037 8.09 0.00 0.00 3.01
564 572 7.165485 GGCAAAAGGATAATTAACCCAAAACT 58.835 34.615 8.09 0.00 0.00 2.66
565 573 6.373216 GGGCAAAAGGATAATTAACCCAAAAC 59.627 38.462 8.09 0.00 34.82 2.43
566 574 6.273495 AGGGCAAAAGGATAATTAACCCAAAA 59.727 34.615 8.09 0.00 37.28 2.44
610 618 1.277842 TCGCATCTGAGGGCAAAACTA 59.722 47.619 5.18 0.00 0.00 2.24
969 977 1.517832 CGAAGGGGATCTCAACGCT 59.482 57.895 0.00 0.00 0.00 5.07
1270 1278 3.009363 TCATTCATCAGAGTCTTGGCCAA 59.991 43.478 19.25 19.25 0.00 4.52
1701 1961 5.867716 AGAGCTGCATTTCATTGATCAAAAC 59.132 36.000 13.09 0.00 0.00 2.43
1739 1999 3.096092 AGAGCAACCTTTGTTTGGACAA 58.904 40.909 0.00 0.00 43.73 3.18


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

AutoCloner maintained by Alex Coulton.