Multiple sequence alignment - TraesCS7A01G126800

Loading Multiple Alignment...

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 TraesCS7A01G126800 chr7A 100.000 2312 0 0 1 2312 81608384 81606073 0.000000e+00 4270.0
1 TraesCS7A01G126800 chr7A 90.518 791 63 9 1419 2206 724116157 724115376 0.000000e+00 1035.0
2 TraesCS7A01G126800 chr6A 98.096 893 16 1 1420 2312 109779361 109778470 0.000000e+00 1554.0
3 TraesCS7A01G126800 chr6A 79.825 228 30 12 342 564 182491698 182491482 3.980000e-33 152.0
4 TraesCS7A01G126800 chr6A 84.848 66 7 3 165 228 376888787 376888723 1.920000e-06 63.9
5 TraesCS7A01G126800 chr2A 98.096 893 16 1 1420 2312 277160829 277159938 0.000000e+00 1554.0
6 TraesCS7A01G126800 chr2A 93.415 896 37 6 1420 2312 745006778 745005902 0.000000e+00 1308.0
7 TraesCS7A01G126800 chr5A 89.873 790 68 10 1420 2206 487272619 487271839 0.000000e+00 1005.0
8 TraesCS7A01G126800 chr7B 91.263 744 45 10 682 1419 25404463 25403734 0.000000e+00 996.0
9 TraesCS7A01G126800 chr7B 82.517 143 16 9 375 510 135979485 135979345 1.450000e-22 117.0
10 TraesCS7A01G126800 chr2B 91.828 673 45 9 1420 2092 761653973 761653311 0.000000e+00 929.0
11 TraesCS7A01G126800 chr2B 90.961 697 47 12 1420 2112 761684081 761683397 0.000000e+00 924.0
12 TraesCS7A01G126800 chr2B 91.382 673 48 8 1420 2092 761627972 761627310 0.000000e+00 913.0
13 TraesCS7A01G126800 chr2B 90.196 51 3 2 163 212 787232925 787232876 5.330000e-07 65.8
14 TraesCS7A01G126800 chr1B 89.154 544 49 8 1420 1962 578544365 578544899 0.000000e+00 669.0
15 TraesCS7A01G126800 chr7D 79.316 585 84 22 4 561 413689091 413689665 2.170000e-100 375.0
16 TraesCS7A01G126800 chr7D 79.024 205 38 3 364 567 526965153 526964953 4.010000e-28 135.0
17 TraesCS7A01G126800 chr5D 75.749 334 53 22 223 542 225638835 225638516 2.390000e-30 143.0
18 TraesCS7A01G126800 chr3A 81.657 169 17 10 363 518 131455285 131455118 6.700000e-26 128.0
19 TraesCS7A01G126800 chr3A 78.462 195 31 10 380 569 36136340 36136528 1.450000e-22 117.0
20 TraesCS7A01G126800 chr2D 78.804 184 33 6 341 520 50466391 50466210 4.040000e-23 119.0
21 TraesCS7A01G126800 chr2D 78.610 187 26 11 343 520 7968085 7967904 6.750000e-21 111.0
22 TraesCS7A01G126800 chr2D 87.755 49 6 0 164 212 345628504 345628456 8.920000e-05 58.4
23 TraesCS7A01G126800 chr4A 92.857 70 4 1 2031 2100 668371026 668370958 1.460000e-17 100.0
24 TraesCS7A01G126800 chr6B 75.743 202 30 15 319 510 589050460 589050652 1.470000e-12 84.2
25 TraesCS7A01G126800 chr1D 93.333 45 2 1 164 208 39682224 39682267 5.330000e-07 65.8


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 TraesCS7A01G126800 chr7A 81606073 81608384 2311 True 4270 4270 100.000 1 2312 1 chr7A.!!$R1 2311
1 TraesCS7A01G126800 chr7A 724115376 724116157 781 True 1035 1035 90.518 1419 2206 1 chr7A.!!$R2 787
2 TraesCS7A01G126800 chr6A 109778470 109779361 891 True 1554 1554 98.096 1420 2312 1 chr6A.!!$R1 892
3 TraesCS7A01G126800 chr2A 277159938 277160829 891 True 1554 1554 98.096 1420 2312 1 chr2A.!!$R1 892
4 TraesCS7A01G126800 chr2A 745005902 745006778 876 True 1308 1308 93.415 1420 2312 1 chr2A.!!$R2 892
5 TraesCS7A01G126800 chr5A 487271839 487272619 780 True 1005 1005 89.873 1420 2206 1 chr5A.!!$R1 786
6 TraesCS7A01G126800 chr7B 25403734 25404463 729 True 996 996 91.263 682 1419 1 chr7B.!!$R1 737
7 TraesCS7A01G126800 chr2B 761653311 761653973 662 True 929 929 91.828 1420 2092 1 chr2B.!!$R2 672
8 TraesCS7A01G126800 chr2B 761683397 761684081 684 True 924 924 90.961 1420 2112 1 chr2B.!!$R3 692
9 TraesCS7A01G126800 chr2B 761627310 761627972 662 True 913 913 91.382 1420 2092 1 chr2B.!!$R1 672
10 TraesCS7A01G126800 chr1B 578544365 578544899 534 False 669 669 89.154 1420 1962 1 chr1B.!!$F1 542
11 TraesCS7A01G126800 chr7D 413689091 413689665 574 False 375 375 79.316 4 561 1 chr7D.!!$F1 557

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
540 543 0.109319 CAACACGTTAATGGGCCAGC 60.109 55.0 13.78 1.01 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 1385 0.028902 GCAAGCACGAAACGGTCTTT 59.971 50.0 0.0 0.0 0.0 2.52 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
78 80 7.791949 TGTGAACAAGTTTTGAAAACATGAAC 58.208 30.769 26.48 20.60 0.00 3.18
129 131 9.695526 TTGACAATTTCTGATAACTTTGAATGG 57.304 29.630 0.00 0.00 0.00 3.16
130 132 9.076781 TGACAATTTCTGATAACTTTGAATGGA 57.923 29.630 0.00 0.00 0.00 3.41
150 152 9.922305 GAATGGAAATATTCAGAACTAGTTTCG 57.078 33.333 10.02 4.27 39.47 3.46
162 164 6.479001 CAGAACTAGTTTCGAAAAAGTCTCCA 59.521 38.462 21.11 0.00 39.47 3.86
218 221 9.617975 GAAATTCCTGAACATTTCTTAGAAGTG 57.382 33.333 14.54 14.54 36.73 3.16
225 228 7.542890 TGAACATTTCTTAGAAGTGCAAAACA 58.457 30.769 15.77 7.60 0.00 2.83
232 235 8.994429 TTCTTAGAAGTGCAAAACATTTTTCA 57.006 26.923 0.00 0.00 0.00 2.69
238 241 9.344309 AGAAGTGCAAAACATTTTTCAAATTTG 57.656 25.926 12.15 12.15 0.00 2.32
241 244 8.295288 AGTGCAAAACATTTTTCAAATTTGTGA 58.705 25.926 17.47 5.60 32.03 3.58
242 245 8.364482 GTGCAAAACATTTTTCAAATTTGTGAC 58.636 29.630 17.47 0.00 32.03 3.67
294 297 8.830201 AATATTGAGCATGTTTTAAAAGCACA 57.170 26.923 11.77 9.18 0.00 4.57
417 420 9.656040 AAAACGAAACATAAAAACCTAAAACCT 57.344 25.926 0.00 0.00 0.00 3.50
429 432 8.598202 AAAACCTAAAACCTAAAGGAAACAGA 57.402 30.769 2.23 0.00 38.94 3.41
430 433 8.598202 AAACCTAAAACCTAAAGGAAACAGAA 57.402 30.769 2.23 0.00 38.94 3.02
431 434 8.598202 AACCTAAAACCTAAAGGAAACAGAAA 57.402 30.769 2.23 0.00 38.94 2.52
432 435 8.598202 ACCTAAAACCTAAAGGAAACAGAAAA 57.402 30.769 2.23 0.00 38.94 2.29
433 436 8.472413 ACCTAAAACCTAAAGGAAACAGAAAAC 58.528 33.333 2.23 0.00 38.94 2.43
434 437 7.924412 CCTAAAACCTAAAGGAAACAGAAAACC 59.076 37.037 2.23 0.00 38.94 3.27
435 438 5.509716 AACCTAAAGGAAACAGAAAACCG 57.490 39.130 2.23 0.00 38.94 4.44
436 439 3.887110 ACCTAAAGGAAACAGAAAACCGG 59.113 43.478 0.00 0.00 38.94 5.28
437 440 3.887110 CCTAAAGGAAACAGAAAACCGGT 59.113 43.478 0.00 0.00 37.39 5.28
438 441 4.340097 CCTAAAGGAAACAGAAAACCGGTT 59.660 41.667 15.86 15.86 37.39 4.44
439 442 4.380841 AAAGGAAACAGAAAACCGGTTC 57.619 40.909 22.53 9.57 32.01 3.62
440 443 1.944709 AGGAAACAGAAAACCGGTTCG 59.055 47.619 22.53 12.07 32.01 3.95
441 444 1.672363 GGAAACAGAAAACCGGTTCGT 59.328 47.619 22.53 12.09 32.01 3.85
442 445 2.540157 GGAAACAGAAAACCGGTTCGTG 60.540 50.000 22.53 19.46 32.01 4.35
443 446 1.018910 AACAGAAAACCGGTTCGTGG 58.981 50.000 22.53 13.40 32.50 4.94
444 447 0.178533 ACAGAAAACCGGTTCGTGGA 59.821 50.000 22.53 0.00 32.50 4.02
445 448 1.301423 CAGAAAACCGGTTCGTGGAA 58.699 50.000 22.53 0.00 32.50 3.53
446 449 1.003223 CAGAAAACCGGTTCGTGGAAC 60.003 52.381 22.53 7.18 41.32 3.62
470 473 6.319141 CTTCTAGAAGGTTTCCAAAACCAG 57.681 41.667 22.67 10.94 42.69 4.00
471 474 5.640158 TCTAGAAGGTTTCCAAAACCAGA 57.360 39.130 20.47 12.71 42.69 3.86
472 475 6.008696 TCTAGAAGGTTTCCAAAACCAGAA 57.991 37.500 20.47 5.46 42.69 3.02
473 476 6.428295 TCTAGAAGGTTTCCAAAACCAGAAA 58.572 36.000 20.47 5.75 42.69 2.52
474 477 6.893005 TCTAGAAGGTTTCCAAAACCAGAAAA 59.107 34.615 20.47 4.61 42.69 2.29
475 478 6.367374 AGAAGGTTTCCAAAACCAGAAAAA 57.633 33.333 20.47 0.00 42.69 1.94
476 479 6.170506 AGAAGGTTTCCAAAACCAGAAAAAC 58.829 36.000 20.47 6.50 42.69 2.43
477 480 4.839121 AGGTTTCCAAAACCAGAAAAACC 58.161 39.130 20.47 6.69 43.72 3.27
478 481 3.619483 GGTTTCCAAAACCAGAAAAACCG 59.381 43.478 15.06 0.00 40.03 4.44
479 482 3.528597 TTCCAAAACCAGAAAAACCGG 57.471 42.857 0.00 0.00 0.00 5.28
480 483 1.137282 TCCAAAACCAGAAAAACCGGC 59.863 47.619 0.00 0.00 0.00 6.13
481 484 1.138069 CCAAAACCAGAAAAACCGGCT 59.862 47.619 0.00 0.00 0.00 5.52
482 485 2.200899 CAAAACCAGAAAAACCGGCTG 58.799 47.619 0.00 0.00 0.00 4.85
483 486 1.770294 AAACCAGAAAAACCGGCTGA 58.230 45.000 0.00 0.00 0.00 4.26
484 487 1.318576 AACCAGAAAAACCGGCTGAG 58.681 50.000 0.00 0.00 0.00 3.35
485 488 0.472471 ACCAGAAAAACCGGCTGAGA 59.528 50.000 0.00 0.00 0.00 3.27
486 489 1.133915 ACCAGAAAAACCGGCTGAGAA 60.134 47.619 0.00 0.00 0.00 2.87
487 490 1.953686 CCAGAAAAACCGGCTGAGAAA 59.046 47.619 0.00 0.00 0.00 2.52
488 491 2.558359 CCAGAAAAACCGGCTGAGAAAT 59.442 45.455 0.00 0.00 0.00 2.17
489 492 3.568538 CAGAAAAACCGGCTGAGAAATG 58.431 45.455 0.00 0.00 0.00 2.32
490 493 3.004734 CAGAAAAACCGGCTGAGAAATGT 59.995 43.478 0.00 0.00 0.00 2.71
491 494 4.215399 CAGAAAAACCGGCTGAGAAATGTA 59.785 41.667 0.00 0.00 0.00 2.29
492 495 4.455877 AGAAAAACCGGCTGAGAAATGTAG 59.544 41.667 0.00 0.00 0.00 2.74
493 496 3.695830 AAACCGGCTGAGAAATGTAGA 57.304 42.857 0.00 0.00 0.00 2.59
494 497 3.695830 AACCGGCTGAGAAATGTAGAA 57.304 42.857 0.00 0.00 0.00 2.10
495 498 3.252974 ACCGGCTGAGAAATGTAGAAG 57.747 47.619 0.00 0.00 0.00 2.85
496 499 2.093447 ACCGGCTGAGAAATGTAGAAGG 60.093 50.000 0.00 0.00 0.00 3.46
497 500 2.093447 CCGGCTGAGAAATGTAGAAGGT 60.093 50.000 0.00 0.00 0.00 3.50
498 501 3.600388 CGGCTGAGAAATGTAGAAGGTT 58.400 45.455 0.00 0.00 0.00 3.50
499 502 3.619038 CGGCTGAGAAATGTAGAAGGTTC 59.381 47.826 0.00 0.00 0.00 3.62
500 503 3.942115 GGCTGAGAAATGTAGAAGGTTCC 59.058 47.826 0.00 0.00 0.00 3.62
501 504 3.942115 GCTGAGAAATGTAGAAGGTTCCC 59.058 47.826 0.00 0.00 0.00 3.97
502 505 4.565652 GCTGAGAAATGTAGAAGGTTCCCA 60.566 45.833 0.00 0.00 0.00 4.37
503 506 5.560724 CTGAGAAATGTAGAAGGTTCCCAA 58.439 41.667 0.00 0.00 0.00 4.12
504 507 5.947663 TGAGAAATGTAGAAGGTTCCCAAA 58.052 37.500 0.00 0.00 0.00 3.28
505 508 6.369629 TGAGAAATGTAGAAGGTTCCCAAAA 58.630 36.000 0.00 0.00 0.00 2.44
506 509 6.264518 TGAGAAATGTAGAAGGTTCCCAAAAC 59.735 38.462 0.00 0.00 0.00 2.43
507 510 5.538813 AGAAATGTAGAAGGTTCCCAAAACC 59.461 40.000 0.00 0.00 40.58 3.27
508 511 2.853705 TGTAGAAGGTTCCCAAAACCG 58.146 47.619 1.52 0.00 44.82 4.44
509 512 2.156917 GTAGAAGGTTCCCAAAACCGG 58.843 52.381 0.00 0.00 44.82 5.28
510 513 0.848053 AGAAGGTTCCCAAAACCGGA 59.152 50.000 9.46 0.00 44.82 5.14
511 514 1.427753 AGAAGGTTCCCAAAACCGGAT 59.572 47.619 9.46 0.00 44.82 4.18
512 515 2.645797 AGAAGGTTCCCAAAACCGGATA 59.354 45.455 9.46 0.00 44.82 2.59
513 516 2.502142 AGGTTCCCAAAACCGGATAC 57.498 50.000 9.46 0.00 44.82 2.24
527 530 2.998668 GGATACGCTTCATCAACACG 57.001 50.000 0.00 0.00 0.00 4.49
528 531 2.268298 GGATACGCTTCATCAACACGT 58.732 47.619 0.00 0.00 40.53 4.49
529 532 2.671396 GGATACGCTTCATCAACACGTT 59.329 45.455 0.00 0.00 38.12 3.99
530 533 3.861113 GGATACGCTTCATCAACACGTTA 59.139 43.478 0.00 0.00 38.12 3.18
531 534 4.327898 GGATACGCTTCATCAACACGTTAA 59.672 41.667 0.00 0.00 38.12 2.01
532 535 5.006358 GGATACGCTTCATCAACACGTTAAT 59.994 40.000 0.00 0.00 38.12 1.40
533 536 4.065423 ACGCTTCATCAACACGTTAATG 57.935 40.909 0.00 0.00 32.09 1.90
534 537 3.120338 ACGCTTCATCAACACGTTAATGG 60.120 43.478 0.00 0.00 32.09 3.16
535 538 3.727673 CGCTTCATCAACACGTTAATGGG 60.728 47.826 0.00 0.00 0.00 4.00
536 539 3.758300 CTTCATCAACACGTTAATGGGC 58.242 45.455 0.00 0.00 0.00 5.36
537 540 2.088423 TCATCAACACGTTAATGGGCC 58.912 47.619 0.00 0.00 0.00 5.80
538 541 1.815613 CATCAACACGTTAATGGGCCA 59.184 47.619 9.61 9.61 0.00 5.36
539 542 1.529226 TCAACACGTTAATGGGCCAG 58.471 50.000 13.78 0.00 0.00 4.85
540 543 0.109319 CAACACGTTAATGGGCCAGC 60.109 55.000 13.78 1.01 0.00 4.85
541 544 1.248101 AACACGTTAATGGGCCAGCC 61.248 55.000 13.78 0.00 0.00 4.85
542 545 1.677300 CACGTTAATGGGCCAGCCA 60.677 57.895 13.78 0.00 37.98 4.75
543 546 1.037030 CACGTTAATGGGCCAGCCAT 61.037 55.000 13.78 0.31 37.98 4.40
544 547 1.037030 ACGTTAATGGGCCAGCCATG 61.037 55.000 13.78 5.83 37.98 3.66
559 562 1.527034 CCATGGTAATGGCTCCATCG 58.473 55.000 2.57 0.00 46.89 3.84
560 563 0.877071 CATGGTAATGGCTCCATCGC 59.123 55.000 1.31 0.00 41.79 4.58
568 571 2.202987 GCTCCATCGCCAGGTCAG 60.203 66.667 0.00 0.00 0.00 3.51
569 572 2.503061 CTCCATCGCCAGGTCAGG 59.497 66.667 0.00 0.00 0.00 3.86
570 573 2.038813 TCCATCGCCAGGTCAGGA 59.961 61.111 0.00 0.00 0.00 3.86
571 574 1.612146 TCCATCGCCAGGTCAGGAA 60.612 57.895 0.00 0.00 0.00 3.36
572 575 0.982852 TCCATCGCCAGGTCAGGAAT 60.983 55.000 0.00 0.00 0.00 3.01
573 576 0.533755 CCATCGCCAGGTCAGGAATC 60.534 60.000 0.00 0.00 0.00 2.52
574 577 0.467384 CATCGCCAGGTCAGGAATCT 59.533 55.000 0.00 0.00 0.00 2.40
575 578 1.134280 CATCGCCAGGTCAGGAATCTT 60.134 52.381 0.00 0.00 0.00 2.40
576 579 0.984230 TCGCCAGGTCAGGAATCTTT 59.016 50.000 0.00 0.00 0.00 2.52
577 580 1.066143 TCGCCAGGTCAGGAATCTTTC 60.066 52.381 0.00 0.00 0.00 2.62
578 581 1.373570 GCCAGGTCAGGAATCTTTCG 58.626 55.000 0.00 0.00 0.00 3.46
579 582 2.014068 GCCAGGTCAGGAATCTTTCGG 61.014 57.143 0.00 0.00 0.00 4.30
580 583 1.555075 CCAGGTCAGGAATCTTTCGGA 59.445 52.381 0.00 0.00 0.00 4.55
581 584 2.622436 CAGGTCAGGAATCTTTCGGAC 58.378 52.381 0.00 0.00 35.31 4.79
582 585 2.234908 CAGGTCAGGAATCTTTCGGACT 59.765 50.000 2.26 0.00 35.93 3.85
583 586 2.234908 AGGTCAGGAATCTTTCGGACTG 59.765 50.000 2.26 0.00 35.93 3.51
584 587 2.028020 GGTCAGGAATCTTTCGGACTGT 60.028 50.000 2.26 0.00 35.93 3.55
585 588 3.557264 GGTCAGGAATCTTTCGGACTGTT 60.557 47.826 2.26 0.00 35.93 3.16
586 589 3.680458 GTCAGGAATCTTTCGGACTGTTC 59.320 47.826 0.00 0.00 34.09 3.18
587 590 3.003480 CAGGAATCTTTCGGACTGTTCC 58.997 50.000 0.00 0.00 38.77 3.62
588 591 2.027100 AGGAATCTTTCGGACTGTTCCC 60.027 50.000 0.00 0.00 38.99 3.97
589 592 2.290071 GGAATCTTTCGGACTGTTCCCA 60.290 50.000 0.00 0.00 38.99 4.37
590 593 3.408634 GAATCTTTCGGACTGTTCCCAA 58.591 45.455 0.00 0.00 38.99 4.12
591 594 3.502123 ATCTTTCGGACTGTTCCCAAA 57.498 42.857 0.00 0.00 38.99 3.28
592 595 3.284793 TCTTTCGGACTGTTCCCAAAA 57.715 42.857 0.00 0.00 38.99 2.44
593 596 2.946990 TCTTTCGGACTGTTCCCAAAAC 59.053 45.455 0.00 0.00 38.99 2.43
594 597 1.682740 TTCGGACTGTTCCCAAAACC 58.317 50.000 0.00 0.00 38.99 3.27
595 598 0.841289 TCGGACTGTTCCCAAAACCT 59.159 50.000 0.00 0.00 38.99 3.50
596 599 0.951558 CGGACTGTTCCCAAAACCTG 59.048 55.000 0.00 0.00 38.99 4.00
597 600 1.328279 GGACTGTTCCCAAAACCTGG 58.672 55.000 0.00 0.00 45.97 4.45
608 611 3.991605 CAAAACCTGGATCGTAGAACG 57.008 47.619 0.00 0.00 43.58 3.95
609 612 2.005971 AAACCTGGATCGTAGAACGC 57.994 50.000 0.00 0.00 43.58 4.84
610 613 1.183549 AACCTGGATCGTAGAACGCT 58.816 50.000 0.00 0.00 43.58 5.07
611 614 2.048444 ACCTGGATCGTAGAACGCTA 57.952 50.000 0.00 0.00 43.58 4.26
612 615 2.372264 ACCTGGATCGTAGAACGCTAA 58.628 47.619 0.00 0.00 43.58 3.09
613 616 2.957006 ACCTGGATCGTAGAACGCTAAT 59.043 45.455 0.00 0.00 43.58 1.73
614 617 3.004524 ACCTGGATCGTAGAACGCTAATC 59.995 47.826 0.00 0.00 43.58 1.75
615 618 3.253677 CCTGGATCGTAGAACGCTAATCT 59.746 47.826 0.00 0.00 43.58 2.40
616 619 4.222886 CTGGATCGTAGAACGCTAATCTG 58.777 47.826 0.00 0.00 43.58 2.90
617 620 3.630769 TGGATCGTAGAACGCTAATCTGT 59.369 43.478 0.00 0.00 43.58 3.41
618 621 3.975670 GGATCGTAGAACGCTAATCTGTG 59.024 47.826 0.00 0.00 43.58 3.66
619 622 2.793933 TCGTAGAACGCTAATCTGTGC 58.206 47.619 0.00 0.00 42.21 4.57
626 629 0.647410 CGCTAATCTGTGCGTCAAGG 59.353 55.000 0.00 0.00 46.09 3.61
627 630 0.375106 GCTAATCTGTGCGTCAAGGC 59.625 55.000 0.00 0.00 0.00 4.35
628 631 1.725641 CTAATCTGTGCGTCAAGGCA 58.274 50.000 0.00 0.00 41.45 4.75
629 632 2.076100 CTAATCTGTGCGTCAAGGCAA 58.924 47.619 0.00 0.00 45.93 4.52
630 633 0.593128 AATCTGTGCGTCAAGGCAAC 59.407 50.000 0.00 0.00 45.93 4.17
642 645 2.474712 GGCAACTACTTGACGCGC 59.525 61.111 5.73 0.00 0.00 6.86
643 646 2.093983 GCAACTACTTGACGCGCG 59.906 61.111 30.96 30.96 0.00 6.86
644 647 2.093983 CAACTACTTGACGCGCGC 59.906 61.111 32.58 23.91 0.00 6.86
645 648 2.355363 AACTACTTGACGCGCGCA 60.355 55.556 32.58 25.38 0.00 6.09
646 649 2.654912 AACTACTTGACGCGCGCAC 61.655 57.895 32.58 24.27 0.00 5.34
647 650 4.178255 CTACTTGACGCGCGCACG 62.178 66.667 32.58 26.01 44.07 5.34
657 660 4.178393 CGCGCACGCATCAAATAG 57.822 55.556 16.04 0.00 42.06 1.73
658 661 1.368019 CGCGCACGCATCAAATAGG 60.368 57.895 16.04 0.00 42.06 2.57
659 662 1.761244 CGCGCACGCATCAAATAGGA 61.761 55.000 16.04 0.00 42.06 2.94
660 663 0.376852 GCGCACGCATCAAATAGGAA 59.623 50.000 10.65 0.00 41.49 3.36
661 664 1.202132 GCGCACGCATCAAATAGGAAA 60.202 47.619 10.65 0.00 41.49 3.13
662 665 2.541588 GCGCACGCATCAAATAGGAAAT 60.542 45.455 10.65 0.00 41.49 2.17
663 666 3.291585 CGCACGCATCAAATAGGAAATC 58.708 45.455 0.00 0.00 0.00 2.17
664 667 3.632189 GCACGCATCAAATAGGAAATCC 58.368 45.455 0.00 0.00 0.00 3.01
665 668 3.849645 GCACGCATCAAATAGGAAATCCG 60.850 47.826 0.00 0.00 42.08 4.18
666 669 3.312421 CACGCATCAAATAGGAAATCCGT 59.688 43.478 0.00 0.00 42.08 4.69
667 670 3.560068 ACGCATCAAATAGGAAATCCGTC 59.440 43.478 0.00 0.00 42.08 4.79
668 671 3.058914 CGCATCAAATAGGAAATCCGTCC 60.059 47.826 0.00 0.00 42.08 4.79
669 672 3.253432 GCATCAAATAGGAAATCCGTCCC 59.747 47.826 0.00 0.00 42.08 4.46
670 673 3.570912 TCAAATAGGAAATCCGTCCCC 57.429 47.619 0.00 0.00 42.08 4.81
671 674 3.120108 TCAAATAGGAAATCCGTCCCCT 58.880 45.455 0.00 0.00 42.08 4.79
672 675 4.300345 TCAAATAGGAAATCCGTCCCCTA 58.700 43.478 0.00 0.00 42.08 3.53
673 676 4.722781 TCAAATAGGAAATCCGTCCCCTAA 59.277 41.667 0.00 0.00 42.08 2.69
674 677 5.192121 TCAAATAGGAAATCCGTCCCCTAAA 59.808 40.000 0.00 0.00 42.08 1.85
675 678 5.720486 AATAGGAAATCCGTCCCCTAAAA 57.280 39.130 0.00 0.00 42.08 1.52
676 679 5.720486 ATAGGAAATCCGTCCCCTAAAAA 57.280 39.130 0.00 0.00 42.08 1.94
702 705 6.830838 AGAATCAAATAGGAAATCCGAAGCTT 59.169 34.615 0.00 0.00 42.08 3.74
704 707 8.519799 AATCAAATAGGAAATCCGAAGCTTTA 57.480 30.769 0.00 0.00 42.08 1.85
710 714 4.626287 AGGAAATCCGAAGCTTTATGCTGA 60.626 41.667 0.00 0.00 46.55 4.26
748 752 2.224314 GTGAACCTGAGAAAAAGGAGCG 59.776 50.000 0.00 0.00 38.27 5.03
767 771 2.736890 GCCGAAAAATTTGGCCGAG 58.263 52.632 9.77 1.00 43.06 4.63
783 787 0.670706 CGAGCCCAATCGAGATCTCA 59.329 55.000 22.31 10.04 45.56 3.27
822 826 4.623595 CGTAGCTTTCTCCTCTTCACTTTC 59.376 45.833 0.00 0.00 0.00 2.62
828 832 6.147000 GCTTTCTCCTCTTCACTTTCTACAAG 59.853 42.308 0.00 0.00 0.00 3.16
855 859 5.172687 TCTATTTACTGGTGAACATGCCA 57.827 39.130 0.00 0.00 0.00 4.92
859 863 2.165380 CTGGTGAACATGCCAGTCG 58.835 57.895 8.51 0.00 45.28 4.18
875 879 2.669924 CAGTCGATGTCACAATCCACAG 59.330 50.000 0.00 0.00 0.00 3.66
876 880 2.300152 AGTCGATGTCACAATCCACAGT 59.700 45.455 0.00 0.00 0.00 3.55
886 890 6.545666 TGTCACAATCCACAGTCTTACAAAAT 59.454 34.615 0.00 0.00 0.00 1.82
906 910 7.502561 ACAAAATGAGGCCTATAAATACTCCAC 59.497 37.037 4.42 0.00 0.00 4.02
909 913 4.168883 GAGGCCTATAAATACTCCACCCT 58.831 47.826 4.42 0.00 0.00 4.34
910 914 5.162804 TGAGGCCTATAAATACTCCACCCTA 60.163 44.000 4.42 0.00 0.00 3.53
915 919 6.571925 GCCTATAAATACTCCACCCTAACGAG 60.572 46.154 0.00 0.00 0.00 4.18
933 940 2.537128 CGAGACGACATACTCAACCTCG 60.537 54.545 0.00 0.00 36.74 4.63
939 946 1.623811 ACATACTCAACCTCGCCACTT 59.376 47.619 0.00 0.00 0.00 3.16
942 949 0.687354 ACTCAACCTCGCCACTTCAT 59.313 50.000 0.00 0.00 0.00 2.57
943 950 1.338200 ACTCAACCTCGCCACTTCATC 60.338 52.381 0.00 0.00 0.00 2.92
952 959 0.170561 GCCACTTCATCAGCAAGCAG 59.829 55.000 0.00 0.00 0.00 4.24
955 962 2.095364 CCACTTCATCAGCAAGCAGAAC 60.095 50.000 0.00 0.00 0.00 3.01
961 968 1.311859 TCAGCAAGCAGAACCACAAG 58.688 50.000 0.00 0.00 0.00 3.16
963 970 1.370900 GCAAGCAGAACCACAAGCG 60.371 57.895 0.00 0.00 0.00 4.68
967 974 1.301716 GCAGAACCACAAGCGGAGA 60.302 57.895 0.00 0.00 0.00 3.71
968 975 0.884704 GCAGAACCACAAGCGGAGAA 60.885 55.000 0.00 0.00 0.00 2.87
972 979 1.264288 GAACCACAAGCGGAGAAACAG 59.736 52.381 0.00 0.00 0.00 3.16
976 983 0.250338 ACAAGCGGAGAAACAGTCCC 60.250 55.000 0.00 0.00 0.00 4.46
989 996 7.219484 AGAAACAGTCCCACAAAATTGATAG 57.781 36.000 0.00 0.00 0.00 2.08
990 997 5.391312 AACAGTCCCACAAAATTGATAGC 57.609 39.130 0.00 0.00 0.00 2.97
991 998 4.406456 ACAGTCCCACAAAATTGATAGCA 58.594 39.130 0.00 0.00 0.00 3.49
992 999 5.018809 ACAGTCCCACAAAATTGATAGCAT 58.981 37.500 0.00 0.00 0.00 3.79
997 1004 6.974622 GTCCCACAAAATTGATAGCATTACAG 59.025 38.462 0.00 0.00 0.00 2.74
1012 1019 0.322456 TACAGTCATGGCCAAGGCAC 60.322 55.000 16.01 6.97 41.84 5.01
1324 1331 1.759293 CTGCTGATGGATGCGTCACG 61.759 60.000 4.82 0.00 0.00 4.35
1332 1339 5.478407 TGATGGATGCGTCACGAAATATAT 58.522 37.500 0.00 0.00 0.00 0.86
1333 1340 5.348451 TGATGGATGCGTCACGAAATATATG 59.652 40.000 0.00 0.00 0.00 1.78
1376 1384 7.715265 ATACCTAGAATAAATGAAGCACGTG 57.285 36.000 12.28 12.28 0.00 4.49
1377 1385 5.730550 ACCTAGAATAAATGAAGCACGTGA 58.269 37.500 22.23 0.00 0.00 4.35
1395 1403 1.329292 TGAAAGACCGTTTCGTGCTTG 59.671 47.619 0.00 0.00 0.00 4.01
1396 1404 0.028902 AAAGACCGTTTCGTGCTTGC 59.971 50.000 0.00 0.00 0.00 4.01
1397 1405 0.814010 AAGACCGTTTCGTGCTTGCT 60.814 50.000 0.00 0.00 0.00 3.91
1410 1418 2.875933 GTGCTTGCTTTGGTGTGTACTA 59.124 45.455 0.00 0.00 0.00 1.82
1568 1576 5.414765 CGTTTTTATGCCCTAAAGAACTCCT 59.585 40.000 0.00 0.00 31.12 3.69
1716 1728 9.748708 TTTGTCAGTGGAAAAATAGAAGAAATG 57.251 29.630 0.00 0.00 0.00 2.32
1898 1942 2.702270 AGGCCTTTGACCCAAGAAAT 57.298 45.000 0.00 0.00 0.00 2.17
2014 2058 3.142579 AGGGGAGTGAGATGGAGAAAT 57.857 47.619 0.00 0.00 0.00 2.17
2218 2262 0.341961 ACCTACTGGGATGGTGGCTA 59.658 55.000 0.00 0.00 38.76 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 37 8.600449 TGTTCACAAATTCAAAAAGTGTTCTT 57.400 26.923 0.00 0.00 35.14 2.52
40 42 9.662545 AAAACTTGTTCACAAATTCAAAAAGTG 57.337 25.926 0.00 0.00 35.15 3.16
41 43 9.662545 CAAAACTTGTTCACAAATTCAAAAAGT 57.337 25.926 0.00 0.00 35.15 2.66
48 50 9.824534 ATGTTTTCAAAACTTGTTCACAAATTC 57.175 25.926 14.10 0.00 35.15 2.17
103 105 9.695526 CCATTCAAAGTTATCAGAAATTGTCAA 57.304 29.630 0.00 0.00 0.00 3.18
125 127 9.667107 TCGAAACTAGTTCTGAATATTTCCATT 57.333 29.630 8.95 0.00 33.70 3.16
126 128 9.667107 TTCGAAACTAGTTCTGAATATTTCCAT 57.333 29.630 8.95 0.00 33.70 3.41
127 129 9.496873 TTTCGAAACTAGTTCTGAATATTTCCA 57.503 29.630 18.00 4.54 32.59 3.53
138 140 6.579865 TGGAGACTTTTTCGAAACTAGTTCT 58.420 36.000 19.99 17.65 33.70 3.01
143 145 6.988622 TGTTTGGAGACTTTTTCGAAACTA 57.011 33.333 10.79 0.76 41.17 2.24
145 147 6.090783 ACTTGTTTGGAGACTTTTTCGAAAC 58.909 36.000 10.79 0.00 41.05 2.78
149 151 6.584563 TCAAAACTTGTTTGGAGACTTTTTCG 59.415 34.615 0.00 0.00 0.00 3.46
150 152 7.883229 TCAAAACTTGTTTGGAGACTTTTTC 57.117 32.000 0.00 0.00 0.00 2.29
156 158 8.194769 TCCTATTTTCAAAACTTGTTTGGAGAC 58.805 33.333 3.88 0.00 0.00 3.36
157 159 8.299990 TCCTATTTTCAAAACTTGTTTGGAGA 57.700 30.769 3.88 0.00 0.00 3.71
192 194 9.617975 CACTTCTAAGAAATGTTCAGGAATTTC 57.382 33.333 0.00 0.00 41.20 2.17
208 211 8.994429 TTGAAAAATGTTTTGCACTTCTAAGA 57.006 26.923 0.00 0.00 35.50 2.10
213 216 9.127006 ACAAATTTGAAAAATGTTTTGCACTTC 57.873 25.926 24.64 0.00 35.50 3.01
216 219 8.364482 GTCACAAATTTGAAAAATGTTTTGCAC 58.636 29.630 24.64 2.03 35.50 4.57
218 221 8.672214 AGTCACAAATTTGAAAAATGTTTTGC 57.328 26.923 24.64 5.19 0.00 3.68
391 394 9.656040 AGGTTTTAGGTTTTTATGTTTCGTTTT 57.344 25.926 0.00 0.00 0.00 2.43
403 406 9.038072 TCTGTTTCCTTTAGGTTTTAGGTTTTT 57.962 29.630 0.00 0.00 36.34 1.94
404 407 8.598202 TCTGTTTCCTTTAGGTTTTAGGTTTT 57.402 30.769 0.00 0.00 36.34 2.43
405 408 8.598202 TTCTGTTTCCTTTAGGTTTTAGGTTT 57.402 30.769 0.00 0.00 36.34 3.27
406 409 8.598202 TTTCTGTTTCCTTTAGGTTTTAGGTT 57.402 30.769 0.00 0.00 36.34 3.50
407 410 8.472413 GTTTTCTGTTTCCTTTAGGTTTTAGGT 58.528 33.333 0.00 0.00 36.34 3.08
408 411 7.924412 GGTTTTCTGTTTCCTTTAGGTTTTAGG 59.076 37.037 0.00 0.00 36.34 2.69
409 412 7.646526 CGGTTTTCTGTTTCCTTTAGGTTTTAG 59.353 37.037 0.00 0.00 36.34 1.85
410 413 7.416551 CCGGTTTTCTGTTTCCTTTAGGTTTTA 60.417 37.037 0.00 0.00 36.34 1.52
411 414 6.334989 CGGTTTTCTGTTTCCTTTAGGTTTT 58.665 36.000 0.00 0.00 36.34 2.43
412 415 5.163488 CCGGTTTTCTGTTTCCTTTAGGTTT 60.163 40.000 0.00 0.00 36.34 3.27
413 416 4.340097 CCGGTTTTCTGTTTCCTTTAGGTT 59.660 41.667 0.00 0.00 36.34 3.50
414 417 3.887110 CCGGTTTTCTGTTTCCTTTAGGT 59.113 43.478 0.00 0.00 36.34 3.08
415 418 3.887110 ACCGGTTTTCTGTTTCCTTTAGG 59.113 43.478 0.00 0.00 0.00 2.69
416 419 5.509716 AACCGGTTTTCTGTTTCCTTTAG 57.490 39.130 15.86 0.00 0.00 1.85
417 420 4.035441 CGAACCGGTTTTCTGTTTCCTTTA 59.965 41.667 23.22 0.00 0.00 1.85
418 421 3.181494 CGAACCGGTTTTCTGTTTCCTTT 60.181 43.478 23.22 0.00 0.00 3.11
419 422 2.356695 CGAACCGGTTTTCTGTTTCCTT 59.643 45.455 23.22 0.00 0.00 3.36
420 423 1.944709 CGAACCGGTTTTCTGTTTCCT 59.055 47.619 23.22 0.00 0.00 3.36
421 424 1.672363 ACGAACCGGTTTTCTGTTTCC 59.328 47.619 23.22 3.91 0.00 3.13
422 425 2.540157 CCACGAACCGGTTTTCTGTTTC 60.540 50.000 23.22 4.78 0.00 2.78
423 426 1.402613 CCACGAACCGGTTTTCTGTTT 59.597 47.619 23.22 0.00 0.00 2.83
424 427 1.018910 CCACGAACCGGTTTTCTGTT 58.981 50.000 23.22 0.00 0.00 3.16
425 428 0.178533 TCCACGAACCGGTTTTCTGT 59.821 50.000 23.22 14.74 0.00 3.41
426 429 1.003223 GTTCCACGAACCGGTTTTCTG 60.003 52.381 23.22 15.88 36.65 3.02
427 430 1.302366 GTTCCACGAACCGGTTTTCT 58.698 50.000 23.22 0.00 36.65 2.52
428 431 3.831729 GTTCCACGAACCGGTTTTC 57.168 52.632 23.22 8.97 36.65 2.29
447 450 6.062095 TCTGGTTTTGGAAACCTTCTAGAAG 58.938 40.000 23.31 23.31 40.88 2.85
448 451 6.008696 TCTGGTTTTGGAAACCTTCTAGAA 57.991 37.500 19.85 4.81 40.88 2.10
449 452 5.640158 TCTGGTTTTGGAAACCTTCTAGA 57.360 39.130 19.85 12.84 40.88 2.43
450 453 6.709018 TTTCTGGTTTTGGAAACCTTCTAG 57.291 37.500 19.85 11.12 40.88 2.43
451 454 7.324935 GTTTTTCTGGTTTTGGAAACCTTCTA 58.675 34.615 19.85 3.03 40.88 2.10
452 455 6.170506 GTTTTTCTGGTTTTGGAAACCTTCT 58.829 36.000 19.85 0.00 40.88 2.85
453 456 5.353123 GGTTTTTCTGGTTTTGGAAACCTTC 59.647 40.000 19.85 6.13 41.55 3.46
454 457 5.250200 GGTTTTTCTGGTTTTGGAAACCTT 58.750 37.500 19.85 0.00 41.55 3.50
455 458 4.621983 CGGTTTTTCTGGTTTTGGAAACCT 60.622 41.667 19.85 0.00 42.22 3.50
456 459 3.619483 CGGTTTTTCTGGTTTTGGAAACC 59.381 43.478 14.15 14.15 41.43 3.27
457 460 3.619483 CCGGTTTTTCTGGTTTTGGAAAC 59.381 43.478 0.00 0.00 37.78 2.78
458 461 3.863041 CCGGTTTTTCTGGTTTTGGAAA 58.137 40.909 0.00 0.00 37.78 3.13
459 462 2.418884 GCCGGTTTTTCTGGTTTTGGAA 60.419 45.455 1.90 0.00 44.16 3.53
460 463 1.137282 GCCGGTTTTTCTGGTTTTGGA 59.863 47.619 1.90 0.00 44.16 3.53
461 464 1.138069 AGCCGGTTTTTCTGGTTTTGG 59.862 47.619 1.90 0.00 44.16 3.28
462 465 2.159170 TCAGCCGGTTTTTCTGGTTTTG 60.159 45.455 1.90 0.00 44.16 2.44
463 466 2.100749 CTCAGCCGGTTTTTCTGGTTTT 59.899 45.455 1.90 0.00 44.16 2.43
464 467 1.681264 CTCAGCCGGTTTTTCTGGTTT 59.319 47.619 1.90 0.00 44.16 3.27
465 468 1.133915 TCTCAGCCGGTTTTTCTGGTT 60.134 47.619 1.90 0.00 44.16 3.67
466 469 0.472471 TCTCAGCCGGTTTTTCTGGT 59.528 50.000 1.90 0.00 44.16 4.00
467 470 1.604604 TTCTCAGCCGGTTTTTCTGG 58.395 50.000 1.90 0.00 45.06 3.86
468 471 3.004734 ACATTTCTCAGCCGGTTTTTCTG 59.995 43.478 1.90 0.73 0.00 3.02
469 472 3.222603 ACATTTCTCAGCCGGTTTTTCT 58.777 40.909 1.90 0.00 0.00 2.52
470 473 3.643159 ACATTTCTCAGCCGGTTTTTC 57.357 42.857 1.90 0.00 0.00 2.29
471 474 4.394729 TCTACATTTCTCAGCCGGTTTTT 58.605 39.130 1.90 0.00 0.00 1.94
472 475 4.015872 TCTACATTTCTCAGCCGGTTTT 57.984 40.909 1.90 0.00 0.00 2.43
473 476 3.695830 TCTACATTTCTCAGCCGGTTT 57.304 42.857 1.90 0.00 0.00 3.27
474 477 3.600388 CTTCTACATTTCTCAGCCGGTT 58.400 45.455 1.90 0.00 0.00 4.44
475 478 2.093447 CCTTCTACATTTCTCAGCCGGT 60.093 50.000 1.90 0.00 0.00 5.28
476 479 2.093447 ACCTTCTACATTTCTCAGCCGG 60.093 50.000 0.00 0.00 0.00 6.13
477 480 3.252974 ACCTTCTACATTTCTCAGCCG 57.747 47.619 0.00 0.00 0.00 5.52
478 481 3.942115 GGAACCTTCTACATTTCTCAGCC 59.058 47.826 0.00 0.00 0.00 4.85
495 498 2.875078 GCGTATCCGGTTTTGGGAACC 61.875 57.143 0.00 0.00 42.07 3.62
496 499 0.448990 GCGTATCCGGTTTTGGGAAC 59.551 55.000 0.00 0.00 37.07 3.62
497 500 0.325602 AGCGTATCCGGTTTTGGGAA 59.674 50.000 0.00 0.00 43.33 3.97
498 501 1.984817 AGCGTATCCGGTTTTGGGA 59.015 52.632 0.00 0.00 43.33 4.37
499 502 4.629779 AGCGTATCCGGTTTTGGG 57.370 55.556 0.00 0.00 43.33 4.12
506 509 1.593006 GTGTTGATGAAGCGTATCCGG 59.407 52.381 0.00 0.00 33.68 5.14
507 510 1.255342 CGTGTTGATGAAGCGTATCCG 59.745 52.381 0.00 0.00 37.07 4.18
508 511 2.268298 ACGTGTTGATGAAGCGTATCC 58.732 47.619 0.00 0.00 33.85 2.59
509 512 3.991605 AACGTGTTGATGAAGCGTATC 57.008 42.857 0.00 0.00 35.22 2.24
510 513 5.220586 CCATTAACGTGTTGATGAAGCGTAT 60.221 40.000 16.37 0.00 38.40 3.06
511 514 4.092237 CCATTAACGTGTTGATGAAGCGTA 59.908 41.667 16.37 0.00 38.40 4.42
512 515 3.120338 CCATTAACGTGTTGATGAAGCGT 60.120 43.478 16.37 0.00 38.40 5.07
513 516 3.416277 CCATTAACGTGTTGATGAAGCG 58.584 45.455 16.37 0.00 38.40 4.68
514 517 3.758300 CCCATTAACGTGTTGATGAAGC 58.242 45.455 16.37 0.00 38.40 3.86
515 518 3.427503 GGCCCATTAACGTGTTGATGAAG 60.428 47.826 16.37 9.82 38.40 3.02
516 519 2.490115 GGCCCATTAACGTGTTGATGAA 59.510 45.455 16.37 0.00 38.40 2.57
517 520 2.088423 GGCCCATTAACGTGTTGATGA 58.912 47.619 16.37 0.00 38.40 2.92
518 521 1.815613 TGGCCCATTAACGTGTTGATG 59.184 47.619 0.00 9.76 36.62 3.07
519 522 2.091541 CTGGCCCATTAACGTGTTGAT 58.908 47.619 0.00 0.00 0.00 2.57
520 523 1.529226 CTGGCCCATTAACGTGTTGA 58.471 50.000 0.00 0.00 0.00 3.18
521 524 0.109319 GCTGGCCCATTAACGTGTTG 60.109 55.000 0.00 0.00 0.00 3.33
522 525 1.248101 GGCTGGCCCATTAACGTGTT 61.248 55.000 0.00 0.00 0.00 3.32
523 526 1.677633 GGCTGGCCCATTAACGTGT 60.678 57.895 0.00 0.00 0.00 4.49
524 527 1.677300 TGGCTGGCCCATTAACGTG 60.677 57.895 9.28 0.00 39.18 4.49
525 528 2.760477 TGGCTGGCCCATTAACGT 59.240 55.556 9.28 0.00 39.18 3.99
541 544 0.877071 GCGATGGAGCCATTACCATG 59.123 55.000 3.11 0.00 45.41 3.66
543 546 4.876701 GCGATGGAGCCATTACCA 57.123 55.556 3.11 0.00 40.57 3.25
551 554 2.202987 CTGACCTGGCGATGGAGC 60.203 66.667 0.00 0.00 0.00 4.70
552 555 1.617018 TTCCTGACCTGGCGATGGAG 61.617 60.000 0.00 0.00 0.00 3.86
553 556 0.982852 ATTCCTGACCTGGCGATGGA 60.983 55.000 0.00 0.00 0.00 3.41
554 557 0.533755 GATTCCTGACCTGGCGATGG 60.534 60.000 0.00 0.00 0.00 3.51
555 558 0.467384 AGATTCCTGACCTGGCGATG 59.533 55.000 0.00 0.00 0.00 3.84
556 559 1.207791 AAGATTCCTGACCTGGCGAT 58.792 50.000 0.00 0.00 0.00 4.58
557 560 0.984230 AAAGATTCCTGACCTGGCGA 59.016 50.000 0.00 0.00 0.00 5.54
558 561 1.373570 GAAAGATTCCTGACCTGGCG 58.626 55.000 0.00 0.00 0.00 5.69
559 562 1.373570 CGAAAGATTCCTGACCTGGC 58.626 55.000 0.00 0.00 0.00 4.85
560 563 1.555075 TCCGAAAGATTCCTGACCTGG 59.445 52.381 0.00 0.00 0.00 4.45
561 564 2.234908 AGTCCGAAAGATTCCTGACCTG 59.765 50.000 0.00 0.00 31.74 4.00
562 565 2.234908 CAGTCCGAAAGATTCCTGACCT 59.765 50.000 0.00 0.00 31.74 3.85
563 566 2.028020 ACAGTCCGAAAGATTCCTGACC 60.028 50.000 0.00 0.00 31.74 4.02
564 567 3.320673 ACAGTCCGAAAGATTCCTGAC 57.679 47.619 0.00 0.00 0.00 3.51
565 568 3.306780 GGAACAGTCCGAAAGATTCCTGA 60.307 47.826 0.00 0.00 34.11 3.86
566 569 3.003480 GGAACAGTCCGAAAGATTCCTG 58.997 50.000 0.00 0.00 34.11 3.86
567 570 2.027100 GGGAACAGTCCGAAAGATTCCT 60.027 50.000 0.00 0.00 46.04 3.36
568 571 2.290071 TGGGAACAGTCCGAAAGATTCC 60.290 50.000 0.00 0.00 46.04 3.01
569 572 3.053831 TGGGAACAGTCCGAAAGATTC 57.946 47.619 0.00 0.00 46.04 2.52
570 573 3.502123 TTGGGAACAGTCCGAAAGATT 57.498 42.857 0.00 0.00 46.04 2.40
571 574 3.502123 TTTGGGAACAGTCCGAAAGAT 57.498 42.857 0.00 0.00 44.14 2.40
574 577 2.025898 GGTTTTGGGAACAGTCCGAAA 58.974 47.619 0.00 0.00 46.44 3.46
575 578 1.213430 AGGTTTTGGGAACAGTCCGAA 59.787 47.619 0.00 0.00 46.04 4.30
576 579 0.841289 AGGTTTTGGGAACAGTCCGA 59.159 50.000 0.00 0.00 46.04 4.55
577 580 0.951558 CAGGTTTTGGGAACAGTCCG 59.048 55.000 0.00 0.00 46.04 4.79
578 581 1.328279 CCAGGTTTTGGGAACAGTCC 58.672 55.000 0.00 0.00 43.75 3.85
585 588 6.650989 CGTTCTACGATCCAGGTTTTGGGA 62.651 50.000 0.00 0.00 46.05 4.37
586 589 4.472770 CGTTCTACGATCCAGGTTTTGGG 61.473 52.174 0.00 0.00 46.05 4.12
587 590 2.671396 CGTTCTACGATCCAGGTTTTGG 59.329 50.000 0.00 0.00 46.05 3.28
588 591 2.093783 GCGTTCTACGATCCAGGTTTTG 59.906 50.000 3.04 0.00 46.05 2.44
589 592 2.028385 AGCGTTCTACGATCCAGGTTTT 60.028 45.455 3.04 0.00 46.05 2.43
590 593 1.549170 AGCGTTCTACGATCCAGGTTT 59.451 47.619 3.04 0.00 46.05 3.27
591 594 1.183549 AGCGTTCTACGATCCAGGTT 58.816 50.000 3.04 0.00 46.05 3.50
592 595 2.048444 TAGCGTTCTACGATCCAGGT 57.952 50.000 3.04 0.00 46.05 4.00
593 596 3.253677 AGATTAGCGTTCTACGATCCAGG 59.746 47.826 3.04 0.00 46.05 4.45
594 597 4.222886 CAGATTAGCGTTCTACGATCCAG 58.777 47.826 3.04 0.00 46.05 3.86
595 598 3.630769 ACAGATTAGCGTTCTACGATCCA 59.369 43.478 3.04 0.00 46.05 3.41
596 599 3.975670 CACAGATTAGCGTTCTACGATCC 59.024 47.826 3.04 0.00 46.05 3.36
597 600 3.422546 GCACAGATTAGCGTTCTACGATC 59.577 47.826 3.04 0.00 46.05 3.69
598 601 3.372954 GCACAGATTAGCGTTCTACGAT 58.627 45.455 3.04 0.00 46.05 3.73
599 602 2.790123 CGCACAGATTAGCGTTCTACGA 60.790 50.000 3.04 0.00 46.05 3.43
608 611 0.375106 GCCTTGACGCACAGATTAGC 59.625 55.000 0.00 0.00 0.00 3.09
609 612 1.725641 TGCCTTGACGCACAGATTAG 58.274 50.000 0.00 0.00 32.62 1.73
610 613 1.804151 GTTGCCTTGACGCACAGATTA 59.196 47.619 0.00 0.00 38.83 1.75
611 614 0.593128 GTTGCCTTGACGCACAGATT 59.407 50.000 0.00 0.00 38.83 2.40
612 615 0.250467 AGTTGCCTTGACGCACAGAT 60.250 50.000 0.00 0.00 38.83 2.90
613 616 0.391228 TAGTTGCCTTGACGCACAGA 59.609 50.000 0.00 0.00 38.83 3.41
614 617 0.512952 GTAGTTGCCTTGACGCACAG 59.487 55.000 0.00 0.00 38.83 3.66
615 618 0.105964 AGTAGTTGCCTTGACGCACA 59.894 50.000 0.00 0.00 38.83 4.57
616 619 1.069906 CAAGTAGTTGCCTTGACGCAC 60.070 52.381 0.00 0.00 41.44 5.34
617 620 1.202592 TCAAGTAGTTGCCTTGACGCA 60.203 47.619 5.35 0.00 42.43 5.24
618 621 1.508632 TCAAGTAGTTGCCTTGACGC 58.491 50.000 5.35 0.00 42.43 5.19
621 624 1.508632 GCGTCAAGTAGTTGCCTTGA 58.491 50.000 5.35 0.00 44.44 3.02
622 625 0.163788 CGCGTCAAGTAGTTGCCTTG 59.836 55.000 5.35 0.00 40.51 3.61
623 626 1.566018 GCGCGTCAAGTAGTTGCCTT 61.566 55.000 8.43 0.00 33.23 4.35
624 627 2.027625 GCGCGTCAAGTAGTTGCCT 61.028 57.895 8.43 0.00 33.23 4.75
625 628 2.474712 GCGCGTCAAGTAGTTGCC 59.525 61.111 8.43 0.00 33.23 4.52
626 629 2.093983 CGCGCGTCAAGTAGTTGC 59.906 61.111 24.19 0.62 33.23 4.17
627 630 2.093983 GCGCGCGTCAAGTAGTTG 59.906 61.111 32.35 3.73 34.67 3.16
628 631 2.355363 TGCGCGCGTCAAGTAGTT 60.355 55.556 32.35 0.00 0.00 2.24
629 632 3.103911 GTGCGCGCGTCAAGTAGT 61.104 61.111 32.35 0.00 0.00 2.73
630 633 4.178255 CGTGCGCGCGTCAAGTAG 62.178 66.667 33.47 16.16 0.00 2.57
640 643 1.368019 CCTATTTGATGCGTGCGCG 60.368 57.895 16.86 16.86 45.51 6.86
641 644 0.376852 TTCCTATTTGATGCGTGCGC 59.623 50.000 9.85 9.85 42.35 6.09
642 645 2.823196 TTTCCTATTTGATGCGTGCG 57.177 45.000 0.00 0.00 0.00 5.34
643 646 3.632189 GGATTTCCTATTTGATGCGTGC 58.368 45.455 0.00 0.00 0.00 5.34
644 647 3.312421 ACGGATTTCCTATTTGATGCGTG 59.688 43.478 1.13 0.00 43.26 5.34
645 648 3.541632 ACGGATTTCCTATTTGATGCGT 58.458 40.909 0.00 0.00 40.80 5.24
646 649 3.058914 GGACGGATTTCCTATTTGATGCG 60.059 47.826 0.00 0.00 38.92 4.73
647 650 3.253432 GGGACGGATTTCCTATTTGATGC 59.747 47.826 0.00 0.00 35.76 3.91
648 651 3.821033 GGGGACGGATTTCCTATTTGATG 59.179 47.826 0.00 0.00 35.76 3.07
649 652 3.722101 AGGGGACGGATTTCCTATTTGAT 59.278 43.478 0.00 0.00 35.76 2.57
650 653 3.120108 AGGGGACGGATTTCCTATTTGA 58.880 45.455 0.00 0.00 35.76 2.69
651 654 3.577805 AGGGGACGGATTTCCTATTTG 57.422 47.619 0.00 0.00 35.76 2.32
652 655 5.720486 TTTAGGGGACGGATTTCCTATTT 57.280 39.130 0.00 0.00 35.76 1.40
653 656 5.720486 TTTTAGGGGACGGATTTCCTATT 57.280 39.130 0.00 0.00 35.76 1.73
654 657 5.720486 TTTTTAGGGGACGGATTTCCTAT 57.280 39.130 0.00 0.00 35.76 2.57
673 676 9.860898 CTTCGGATTTCCTATTTGATTCTTTTT 57.139 29.630 0.00 0.00 0.00 1.94
674 677 7.976175 GCTTCGGATTTCCTATTTGATTCTTTT 59.024 33.333 0.00 0.00 0.00 2.27
675 678 7.340487 AGCTTCGGATTTCCTATTTGATTCTTT 59.660 33.333 0.00 0.00 0.00 2.52
676 679 6.830838 AGCTTCGGATTTCCTATTTGATTCTT 59.169 34.615 0.00 0.00 0.00 2.52
677 680 6.360618 AGCTTCGGATTTCCTATTTGATTCT 58.639 36.000 0.00 0.00 0.00 2.40
678 681 6.625873 AGCTTCGGATTTCCTATTTGATTC 57.374 37.500 0.00 0.00 0.00 2.52
679 682 7.410120 AAAGCTTCGGATTTCCTATTTGATT 57.590 32.000 0.00 0.00 0.00 2.57
680 683 8.571336 CATAAAGCTTCGGATTTCCTATTTGAT 58.429 33.333 0.00 0.00 35.12 2.57
702 705 8.196771 ACACTTTTCTTTGAAACATCAGCATAA 58.803 29.630 0.00 0.00 0.00 1.90
704 707 6.477688 CACACTTTTCTTTGAAACATCAGCAT 59.522 34.615 0.00 0.00 0.00 3.79
710 714 6.813152 CAGGTTCACACTTTTCTTTGAAACAT 59.187 34.615 1.42 0.00 38.01 2.71
715 719 5.496556 TCTCAGGTTCACACTTTTCTTTGA 58.503 37.500 0.00 0.00 0.00 2.69
767 771 1.212616 CGTTGAGATCTCGATTGGGC 58.787 55.000 15.86 2.00 0.00 5.36
783 787 2.268298 CTACGCCTCTATTTGCACGTT 58.732 47.619 0.00 0.00 35.15 3.99
828 832 7.702348 GGCATGTTCACCAGTAAATAGATTTTC 59.298 37.037 0.00 0.00 0.00 2.29
855 859 2.300152 ACTGTGGATTGTGACATCGACT 59.700 45.455 0.00 0.00 0.00 4.18
859 863 5.237815 TGTAAGACTGTGGATTGTGACATC 58.762 41.667 0.00 0.00 0.00 3.06
886 890 3.908103 GGGTGGAGTATTTATAGGCCTCA 59.092 47.826 9.68 0.00 0.00 3.86
906 910 2.941064 TGAGTATGTCGTCTCGTTAGGG 59.059 50.000 0.00 0.00 33.88 3.53
909 913 4.005650 AGGTTGAGTATGTCGTCTCGTTA 58.994 43.478 0.00 0.00 33.88 3.18
910 914 2.818432 AGGTTGAGTATGTCGTCTCGTT 59.182 45.455 0.00 0.00 33.88 3.85
915 919 1.546834 GCGAGGTTGAGTATGTCGTC 58.453 55.000 0.00 0.00 33.19 4.20
933 940 0.170561 CTGCTTGCTGATGAAGTGGC 59.829 55.000 0.00 0.00 0.00 5.01
939 946 1.202794 TGTGGTTCTGCTTGCTGATGA 60.203 47.619 3.19 0.00 0.00 2.92
942 949 1.311859 CTTGTGGTTCTGCTTGCTGA 58.688 50.000 0.00 0.00 0.00 4.26
943 950 0.318445 GCTTGTGGTTCTGCTTGCTG 60.318 55.000 0.00 0.00 0.00 4.41
952 959 1.264288 CTGTTTCTCCGCTTGTGGTTC 59.736 52.381 0.00 0.00 0.00 3.62
955 962 0.868406 GACTGTTTCTCCGCTTGTGG 59.132 55.000 0.00 0.00 0.00 4.17
961 968 0.534203 TTGTGGGACTGTTTCTCCGC 60.534 55.000 0.00 0.00 0.00 5.54
963 970 4.340950 TCAATTTTGTGGGACTGTTTCTCC 59.659 41.667 0.00 0.00 0.00 3.71
967 974 5.304101 TGCTATCAATTTTGTGGGACTGTTT 59.696 36.000 0.00 0.00 0.00 2.83
968 975 4.832266 TGCTATCAATTTTGTGGGACTGTT 59.168 37.500 0.00 0.00 0.00 3.16
972 979 6.862209 TGTAATGCTATCAATTTTGTGGGAC 58.138 36.000 0.00 0.00 0.00 4.46
976 983 9.016623 CATGACTGTAATGCTATCAATTTTGTG 57.983 33.333 0.00 0.00 0.00 3.33
989 996 1.406539 CCTTGGCCATGACTGTAATGC 59.593 52.381 19.85 0.00 0.00 3.56
990 997 1.406539 GCCTTGGCCATGACTGTAATG 59.593 52.381 19.85 0.00 0.00 1.90
991 998 1.005805 TGCCTTGGCCATGACTGTAAT 59.994 47.619 19.85 0.00 0.00 1.89
992 999 0.403655 TGCCTTGGCCATGACTGTAA 59.596 50.000 19.85 0.00 0.00 2.41
997 1004 1.589716 GACTGTGCCTTGGCCATGAC 61.590 60.000 19.85 9.16 0.00 3.06
1125 1132 4.778143 GTCGGGTTGCGGATGGCT 62.778 66.667 0.00 0.00 44.05 4.75
1350 1358 9.424319 CACGTGCTTCATTTATTCTAGGTATAT 57.576 33.333 0.82 0.00 0.00 0.86
1351 1359 8.635328 TCACGTGCTTCATTTATTCTAGGTATA 58.365 33.333 11.67 0.00 0.00 1.47
1352 1360 7.497595 TCACGTGCTTCATTTATTCTAGGTAT 58.502 34.615 11.67 0.00 0.00 2.73
1353 1361 6.869695 TCACGTGCTTCATTTATTCTAGGTA 58.130 36.000 11.67 0.00 0.00 3.08
1354 1362 5.730550 TCACGTGCTTCATTTATTCTAGGT 58.269 37.500 11.67 0.00 0.00 3.08
1376 1384 1.920272 GCAAGCACGAAACGGTCTTTC 60.920 52.381 0.00 0.00 0.00 2.62
1377 1385 0.028902 GCAAGCACGAAACGGTCTTT 59.971 50.000 0.00 0.00 0.00 2.52
1395 1403 5.235516 ACAGTACATAGTACACACCAAAGC 58.764 41.667 9.68 0.00 0.00 3.51
1396 1404 6.452242 TGACAGTACATAGTACACACCAAAG 58.548 40.000 9.68 0.00 0.00 2.77
1397 1405 6.408107 TGACAGTACATAGTACACACCAAA 57.592 37.500 9.68 0.00 0.00 3.28
1410 1418 1.612442 ACCGGCCCTGACAGTACAT 60.612 57.895 0.00 0.00 0.00 2.29
1716 1728 1.387295 GCTTGGGATTGGGTAGCTGC 61.387 60.000 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.