Multiple sequence alignment - TraesCS5B01G066700

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 TraesCS5B01G066700 chr5B 100.000 5427 0 0 1 5427 74687875 74682449 0.000000e+00 10022.0
1 TraesCS5B01G066700 chr5D 96.869 3929 112 11 1458 5382 68904775 68900854 0.000000e+00 6564.0
2 TraesCS5B01G066700 chr5D 89.560 613 23 12 782 1356 68905446 68904837 0.000000e+00 739.0
3 TraesCS5B01G066700 chr5D 90.347 518 39 4 8 516 522481602 522481087 0.000000e+00 669.0
4 TraesCS5B01G066700 chr5D 90.890 472 28 3 57 513 382874937 382875408 2.150000e-173 619.0
5 TraesCS5B01G066700 chr5D 98.039 51 1 0 5377 5427 68900833 68900783 7.490000e-14 89.8
6 TraesCS5B01G066700 chr5A 89.967 2701 202 33 1349 4018 59646764 59644102 0.000000e+00 3422.0
7 TraesCS5B01G066700 chr5A 93.804 581 27 4 782 1356 59647371 59646794 0.000000e+00 865.0
8 TraesCS5B01G066700 chr5A 91.418 536 38 5 4658 5188 59643099 59642567 0.000000e+00 728.0
9 TraesCS5B01G066700 chr5A 90.772 531 34 3 1 516 521195703 521195173 0.000000e+00 695.0
10 TraesCS5B01G066700 chr5A 90.341 528 36 3 1 513 649235600 649236127 0.000000e+00 678.0
11 TraesCS5B01G066700 chr5A 86.179 615 66 17 4048 4655 59643869 59643267 0.000000e+00 647.0
12 TraesCS5B01G066700 chr5A 94.656 131 6 1 519 649 348073653 348073524 9.220000e-48 202.0
13 TraesCS5B01G066700 chr5A 89.655 58 6 0 5188 5245 59640963 59640906 2.100000e-09 75.0
14 TraesCS5B01G066700 chr3B 90.683 644 57 3 1350 1991 662437280 662437922 0.000000e+00 854.0
15 TraesCS5B01G066700 chr3B 94.776 134 7 0 516 649 755041802 755041669 5.510000e-50 209.0
16 TraesCS5B01G066700 chr3B 84.507 213 24 5 1153 1356 662437037 662437249 9.220000e-48 202.0
17 TraesCS5B01G066700 chr1D 89.720 642 64 1 1350 1991 458306804 458306165 0.000000e+00 819.0
18 TraesCS5B01G066700 chr1D 84.762 210 23 5 1156 1356 458307044 458306835 9.220000e-48 202.0
19 TraesCS5B01G066700 chr7D 90.720 528 34 3 1 513 140799980 140800507 0.000000e+00 689.0
20 TraesCS5B01G066700 chr6D 90.226 532 36 4 1 516 93881760 93881229 0.000000e+00 680.0
21 TraesCS5B01G066700 chr4D 90.226 532 36 6 1 516 300795660 300795129 0.000000e+00 680.0
22 TraesCS5B01G066700 chr4D 91.667 144 9 3 517 658 117644077 117643935 4.290000e-46 196.0
23 TraesCS5B01G066700 chr2D 89.749 517 40 6 10 516 293715302 293714789 0.000000e+00 649.0
24 TraesCS5B01G066700 chr2D 88.679 159 15 2 509 666 507841527 507841683 2.000000e-44 191.0
25 TraesCS5B01G066700 chr3D 90.020 511 35 7 1 495 40697317 40696807 0.000000e+00 647.0
26 TraesCS5B01G066700 chr2B 88.719 523 43 8 1 513 369504468 369503952 4.620000e-175 625.0
27 TraesCS5B01G066700 chr1B 89.384 471 34 4 59 513 670037917 670038387 3.640000e-161 579.0
28 TraesCS5B01G066700 chrUn 91.162 396 25 3 1 386 232154516 232154911 3.720000e-146 529.0
29 TraesCS5B01G066700 chrUn 91.162 396 25 3 1 386 237973555 237973950 3.720000e-146 529.0
30 TraesCS5B01G066700 chr2A 91.566 166 14 0 1539 1704 379297765 379297600 4.230000e-56 230.0
31 TraesCS5B01G066700 chr2A 85.388 219 31 1 1350 1568 379297993 379297776 5.470000e-55 226.0
32 TraesCS5B01G066700 chr7B 95.385 130 6 0 516 645 41302556 41302685 1.980000e-49 207.0
33 TraesCS5B01G066700 chr7B 92.806 139 10 0 515 653 450584204 450584066 9.220000e-48 202.0
34 TraesCS5B01G066700 chr6B 94.074 135 8 0 512 646 39206384 39206518 7.130000e-49 206.0
35 TraesCS5B01G066700 chr6B 91.608 143 11 1 517 659 599409474 599409333 4.290000e-46 196.0
36 TraesCS5B01G066700 chr4B 94.656 131 7 0 519 649 56414496 56414366 2.560000e-48 204.0


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 TraesCS5B01G066700 chr5B 74682449 74687875 5426 True 10022.000000 10022 100.000000 1 5427 1 chr5B.!!$R1 5426
1 TraesCS5B01G066700 chr5D 68900783 68905446 4663 True 2464.266667 6564 94.822667 782 5427 3 chr5D.!!$R2 4645
2 TraesCS5B01G066700 chr5D 522481087 522481602 515 True 669.000000 669 90.347000 8 516 1 chr5D.!!$R1 508
3 TraesCS5B01G066700 chr5A 59640906 59647371 6465 True 1147.400000 3422 90.204600 782 5245 5 chr5A.!!$R3 4463
4 TraesCS5B01G066700 chr5A 521195173 521195703 530 True 695.000000 695 90.772000 1 516 1 chr5A.!!$R2 515
5 TraesCS5B01G066700 chr5A 649235600 649236127 527 False 678.000000 678 90.341000 1 513 1 chr5A.!!$F1 512
6 TraesCS5B01G066700 chr3B 662437037 662437922 885 False 528.000000 854 87.595000 1153 1991 2 chr3B.!!$F1 838
7 TraesCS5B01G066700 chr1D 458306165 458307044 879 True 510.500000 819 87.241000 1156 1991 2 chr1D.!!$R1 835
8 TraesCS5B01G066700 chr7D 140799980 140800507 527 False 689.000000 689 90.720000 1 513 1 chr7D.!!$F1 512
9 TraesCS5B01G066700 chr6D 93881229 93881760 531 True 680.000000 680 90.226000 1 516 1 chr6D.!!$R1 515
10 TraesCS5B01G066700 chr4D 300795129 300795660 531 True 680.000000 680 90.226000 1 516 1 chr4D.!!$R2 515
11 TraesCS5B01G066700 chr2D 293714789 293715302 513 True 649.000000 649 89.749000 10 516 1 chr2D.!!$R1 506
12 TraesCS5B01G066700 chr3D 40696807 40697317 510 True 647.000000 647 90.020000 1 495 1 chr3D.!!$R1 494
13 TraesCS5B01G066700 chr2B 369503952 369504468 516 True 625.000000 625 88.719000 1 513 1 chr2B.!!$R1 512

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
327 337 0.030773 CGAGGCGATTGCTGCTAGTA 59.969 55.000 4.59 0.0 42.25 1.82 F
799 819 0.528924 TCGTACTCCCGTGTTCCATG 59.471 55.000 0.00 0.0 0.00 3.66 F
1676 1770 0.460284 CCTTGACCGAGCGCTGTAAT 60.460 55.000 18.48 0.0 0.00 1.89 F
2215 2310 1.553706 ATCCTTTTTCTGCTGCCAGG 58.446 50.000 0.00 0.0 39.61 4.45 F
2761 2858 2.177950 GCCAGGTGCATGTTCTCTG 58.822 57.895 0.00 0.0 40.77 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1395 0.108138 AAGGCTCGTCTCCAAATCGG 60.108 55.000 0.00 0.0 0.00 4.18 R
1910 2005 0.324943 TCGGGAGCTTCTTGGAAAGG 59.675 55.000 0.00 0.0 46.24 3.11 R
3421 3542 1.924731 ATCTCAGACCGAAGACACCA 58.075 50.000 0.00 0.0 0.00 4.17 R
3451 3572 5.595885 AGCATAGCGCATATAATAGTCCTG 58.404 41.667 11.47 0.0 46.13 3.86 R
4621 4953 3.142174 AGTGTTTAAGAGGAAGCAGCAC 58.858 45.455 0.00 0.0 0.00 4.40 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
22 23 1.202806 ACACACACCAGTTGGGAGATG 60.203 52.381 2.79 0.00 41.15 2.90
55 56 3.411446 ACCATCGACATTCTTCTTTGCA 58.589 40.909 0.00 0.00 0.00 4.08
63 64 6.132353 GACATTCTTCTTTGCAAAATGTCG 57.868 37.500 26.17 11.97 43.41 4.35
159 169 1.669265 AGATGATTGTCACTGCATGCG 59.331 47.619 14.09 10.50 0.00 4.73
167 177 0.532640 TCACTGCATGCGTGTGTCTT 60.533 50.000 29.77 4.69 34.14 3.01
203 213 5.474825 TGTGATAGCAAGTTACGTGATGAA 58.525 37.500 1.88 0.00 0.00 2.57
227 237 7.524294 ACATTTTGACAAGTTTGACAATGAC 57.476 32.000 11.56 0.00 41.09 3.06
257 267 1.135803 CAACCTCCATTGCCGTTTACG 60.136 52.381 0.00 0.00 39.44 3.18
275 285 2.663196 GGTGCCAACGCTCTACCT 59.337 61.111 0.00 0.00 35.36 3.08
304 314 2.784347 TGATGGTACCATGAACGCAAA 58.216 42.857 32.07 4.33 36.70 3.68
327 337 0.030773 CGAGGCGATTGCTGCTAGTA 59.969 55.000 4.59 0.00 42.25 1.82
445 465 8.969121 TTCGTAAATCACTTTCGTACTCATAA 57.031 30.769 0.00 0.00 0.00 1.90
455 475 7.583401 CACTTTCGTACTCATAATCGACTAGAC 59.417 40.741 0.00 0.00 32.14 2.59
459 479 7.428826 TCGTACTCATAATCGACTAGACACTA 58.571 38.462 0.00 0.00 0.00 2.74
527 547 7.522249 TCTAAGGGTAGTATATACTCCCTCC 57.478 44.000 31.89 23.15 45.22 4.30
528 548 4.858965 AGGGTAGTATATACTCCCTCCG 57.141 50.000 29.22 0.00 43.93 4.63
529 549 4.182318 AGGGTAGTATATACTCCCTCCGT 58.818 47.826 29.22 20.74 43.93 4.69
530 550 4.605371 AGGGTAGTATATACTCCCTCCGTT 59.395 45.833 29.22 17.43 43.93 4.44
531 551 4.946772 GGGTAGTATATACTCCCTCCGTTC 59.053 50.000 27.00 10.10 39.01 3.95
532 552 4.946772 GGTAGTATATACTCCCTCCGTTCC 59.053 50.000 18.68 5.73 37.73 3.62
533 553 4.736611 AGTATATACTCCCTCCGTTCCA 57.263 45.455 9.71 0.00 0.00 3.53
534 554 5.070823 AGTATATACTCCCTCCGTTCCAA 57.929 43.478 9.71 0.00 0.00 3.53
535 555 5.461327 AGTATATACTCCCTCCGTTCCAAA 58.539 41.667 9.71 0.00 0.00 3.28
536 556 5.901276 AGTATATACTCCCTCCGTTCCAAAA 59.099 40.000 9.71 0.00 0.00 2.44
537 557 5.906772 ATATACTCCCTCCGTTCCAAAAT 57.093 39.130 0.00 0.00 0.00 1.82
538 558 2.971901 ACTCCCTCCGTTCCAAAATT 57.028 45.000 0.00 0.00 0.00 1.82
539 559 2.791655 ACTCCCTCCGTTCCAAAATTC 58.208 47.619 0.00 0.00 0.00 2.17
540 560 2.375509 ACTCCCTCCGTTCCAAAATTCT 59.624 45.455 0.00 0.00 0.00 2.40
541 561 3.181433 ACTCCCTCCGTTCCAAAATTCTT 60.181 43.478 0.00 0.00 0.00 2.52
542 562 3.153919 TCCCTCCGTTCCAAAATTCTTG 58.846 45.455 0.00 0.00 0.00 3.02
543 563 2.890945 CCCTCCGTTCCAAAATTCTTGT 59.109 45.455 0.00 0.00 0.00 3.16
544 564 3.057526 CCCTCCGTTCCAAAATTCTTGTC 60.058 47.826 0.00 0.00 0.00 3.18
545 565 3.821033 CCTCCGTTCCAAAATTCTTGTCT 59.179 43.478 0.00 0.00 0.00 3.41
546 566 4.278419 CCTCCGTTCCAAAATTCTTGTCTT 59.722 41.667 0.00 0.00 0.00 3.01
547 567 5.472137 CCTCCGTTCCAAAATTCTTGTCTTA 59.528 40.000 0.00 0.00 0.00 2.10
548 568 6.308371 TCCGTTCCAAAATTCTTGTCTTAC 57.692 37.500 0.00 0.00 0.00 2.34
549 569 5.823570 TCCGTTCCAAAATTCTTGTCTTACA 59.176 36.000 0.00 0.00 0.00 2.41
550 570 6.488683 TCCGTTCCAAAATTCTTGTCTTACAT 59.511 34.615 0.00 0.00 0.00 2.29
551 571 7.013846 TCCGTTCCAAAATTCTTGTCTTACATT 59.986 33.333 0.00 0.00 0.00 2.71
552 572 7.651704 CCGTTCCAAAATTCTTGTCTTACATTT 59.348 33.333 0.00 0.00 0.00 2.32
553 573 8.479280 CGTTCCAAAATTCTTGTCTTACATTTG 58.521 33.333 0.00 0.00 0.00 2.32
554 574 9.313118 GTTCCAAAATTCTTGTCTTACATTTGT 57.687 29.630 0.00 0.00 27.14 2.83
555 575 9.528018 TTCCAAAATTCTTGTCTTACATTTGTC 57.472 29.630 0.00 0.00 27.14 3.18
556 576 8.912988 TCCAAAATTCTTGTCTTACATTTGTCT 58.087 29.630 0.00 0.00 27.14 3.41
563 583 9.569167 TTCTTGTCTTACATTTGTCTAGATACG 57.431 33.333 0.00 0.00 0.00 3.06
564 584 8.188799 TCTTGTCTTACATTTGTCTAGATACGG 58.811 37.037 0.00 0.00 0.00 4.02
565 585 7.634671 TGTCTTACATTTGTCTAGATACGGA 57.365 36.000 0.00 0.00 0.00 4.69
566 586 8.234136 TGTCTTACATTTGTCTAGATACGGAT 57.766 34.615 0.00 0.00 0.00 4.18
567 587 8.135529 TGTCTTACATTTGTCTAGATACGGATG 58.864 37.037 0.00 0.85 0.00 3.51
568 588 8.136165 GTCTTACATTTGTCTAGATACGGATGT 58.864 37.037 13.29 13.29 34.19 3.06
569 589 9.346005 TCTTACATTTGTCTAGATACGGATGTA 57.654 33.333 11.94 11.94 32.86 2.29
570 590 9.395707 CTTACATTTGTCTAGATACGGATGTAC 57.604 37.037 14.05 0.00 33.35 2.90
571 591 6.746120 ACATTTGTCTAGATACGGATGTACC 58.254 40.000 0.00 0.00 32.26 3.34
572 592 6.550108 ACATTTGTCTAGATACGGATGTACCT 59.450 38.462 0.00 0.00 36.31 3.08
573 593 7.722728 ACATTTGTCTAGATACGGATGTACCTA 59.277 37.037 0.00 0.00 36.31 3.08
574 594 8.573885 CATTTGTCTAGATACGGATGTACCTAA 58.426 37.037 0.00 0.00 36.31 2.69
575 595 8.701908 TTTGTCTAGATACGGATGTACCTAAT 57.298 34.615 0.00 0.00 36.31 1.73
576 596 9.797642 TTTGTCTAGATACGGATGTACCTAATA 57.202 33.333 0.00 0.00 36.31 0.98
577 597 8.783833 TGTCTAGATACGGATGTACCTAATAC 57.216 38.462 0.00 0.00 36.31 1.89
578 598 8.600668 TGTCTAGATACGGATGTACCTAATACT 58.399 37.037 0.00 0.00 34.56 2.12
584 604 9.334693 GATACGGATGTACCTAATACTAAAACG 57.665 37.037 0.00 0.00 34.56 3.60
585 605 7.100458 ACGGATGTACCTAATACTAAAACGT 57.900 36.000 0.00 0.00 34.56 3.99
586 606 6.974622 ACGGATGTACCTAATACTAAAACGTG 59.025 38.462 0.00 0.00 34.56 4.49
587 607 7.148086 ACGGATGTACCTAATACTAAAACGTGA 60.148 37.037 0.00 0.00 34.56 4.35
588 608 7.166473 CGGATGTACCTAATACTAAAACGTGAC 59.834 40.741 0.00 0.00 34.56 3.67
589 609 8.193438 GGATGTACCTAATACTAAAACGTGACT 58.807 37.037 0.00 0.00 34.56 3.41
590 610 9.578439 GATGTACCTAATACTAAAACGTGACTT 57.422 33.333 0.00 0.00 34.56 3.01
591 611 8.746922 TGTACCTAATACTAAAACGTGACTTG 57.253 34.615 0.00 0.00 34.56 3.16
592 612 8.575589 TGTACCTAATACTAAAACGTGACTTGA 58.424 33.333 0.00 0.00 34.56 3.02
593 613 9.578439 GTACCTAATACTAAAACGTGACTTGAT 57.422 33.333 0.00 0.00 0.00 2.57
595 615 9.578439 ACCTAATACTAAAACGTGACTTGATAC 57.422 33.333 0.00 0.00 0.00 2.24
596 616 9.577110 CCTAATACTAAAACGTGACTTGATACA 57.423 33.333 0.00 0.00 0.00 2.29
599 619 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
600 620 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
601 621 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
602 622 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
603 623 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
604 624 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
605 625 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
606 626 5.518847 ACGTGACTTGATACATCCGTATTTG 59.481 40.000 0.00 0.00 38.48 2.32
607 627 5.051039 CGTGACTTGATACATCCGTATTTGG 60.051 44.000 0.00 0.00 38.48 3.28
608 628 6.046593 GTGACTTGATACATCCGTATTTGGA 58.953 40.000 0.00 0.00 43.58 3.53
636 656 9.463443 AAATTTAAGACAAGAATTTTGAGACGG 57.537 29.630 0.00 0.00 31.00 4.79
637 657 7.795482 TTTAAGACAAGAATTTTGAGACGGA 57.205 32.000 7.18 0.00 0.00 4.69
638 658 5.931441 AAGACAAGAATTTTGAGACGGAG 57.069 39.130 7.18 0.00 0.00 4.63
639 659 3.748568 AGACAAGAATTTTGAGACGGAGC 59.251 43.478 7.18 0.00 0.00 4.70
640 660 2.480419 ACAAGAATTTTGAGACGGAGCG 59.520 45.455 7.18 0.00 0.00 5.03
641 661 2.736721 CAAGAATTTTGAGACGGAGCGA 59.263 45.455 0.00 0.00 0.00 4.93
642 662 2.611518 AGAATTTTGAGACGGAGCGAG 58.388 47.619 0.00 0.00 0.00 5.03
643 663 2.028930 AGAATTTTGAGACGGAGCGAGT 60.029 45.455 0.00 0.00 0.00 4.18
644 664 3.192844 AGAATTTTGAGACGGAGCGAGTA 59.807 43.478 0.00 0.00 0.00 2.59
645 665 2.342910 TTTTGAGACGGAGCGAGTAC 57.657 50.000 0.00 0.00 0.00 2.73
646 666 1.241165 TTTGAGACGGAGCGAGTACA 58.759 50.000 0.00 0.00 0.00 2.90
647 667 1.460504 TTGAGACGGAGCGAGTACAT 58.539 50.000 0.00 0.00 0.00 2.29
648 668 1.460504 TGAGACGGAGCGAGTACATT 58.539 50.000 0.00 0.00 0.00 2.71
649 669 1.816835 TGAGACGGAGCGAGTACATTT 59.183 47.619 0.00 0.00 0.00 2.32
650 670 2.159421 TGAGACGGAGCGAGTACATTTC 60.159 50.000 0.00 0.00 0.00 2.17
651 671 1.816835 AGACGGAGCGAGTACATTTCA 59.183 47.619 0.00 0.00 0.00 2.69
652 672 2.230508 AGACGGAGCGAGTACATTTCAA 59.769 45.455 0.00 0.00 0.00 2.69
653 673 2.334838 ACGGAGCGAGTACATTTCAAC 58.665 47.619 0.00 0.00 0.00 3.18
654 674 2.288579 ACGGAGCGAGTACATTTCAACA 60.289 45.455 0.00 0.00 0.00 3.33
655 675 2.092211 CGGAGCGAGTACATTTCAACAC 59.908 50.000 0.00 0.00 0.00 3.32
656 676 3.064207 GGAGCGAGTACATTTCAACACA 58.936 45.455 0.00 0.00 0.00 3.72
657 677 3.496884 GGAGCGAGTACATTTCAACACAA 59.503 43.478 0.00 0.00 0.00 3.33
658 678 4.024387 GGAGCGAGTACATTTCAACACAAA 60.024 41.667 0.00 0.00 0.00 2.83
659 679 5.493133 AGCGAGTACATTTCAACACAAAA 57.507 34.783 0.00 0.00 0.00 2.44
660 680 5.270853 AGCGAGTACATTTCAACACAAAAC 58.729 37.500 0.00 0.00 0.00 2.43
661 681 5.065988 AGCGAGTACATTTCAACACAAAACT 59.934 36.000 0.00 0.00 0.00 2.66
662 682 5.395486 GCGAGTACATTTCAACACAAAACTC 59.605 40.000 0.00 0.00 0.00 3.01
663 683 6.715464 CGAGTACATTTCAACACAAAACTCT 58.285 36.000 0.00 0.00 31.00 3.24
664 684 7.186804 CGAGTACATTTCAACACAAAACTCTT 58.813 34.615 0.00 0.00 31.00 2.85
665 685 7.696453 CGAGTACATTTCAACACAAAACTCTTT 59.304 33.333 0.00 0.00 31.00 2.52
666 686 9.353999 GAGTACATTTCAACACAAAACTCTTTT 57.646 29.630 0.00 0.00 0.00 2.27
667 687 9.353999 AGTACATTTCAACACAAAACTCTTTTC 57.646 29.630 0.00 0.00 0.00 2.29
668 688 9.134734 GTACATTTCAACACAAAACTCTTTTCA 57.865 29.630 0.00 0.00 0.00 2.69
669 689 8.243289 ACATTTCAACACAAAACTCTTTTCAG 57.757 30.769 0.00 0.00 0.00 3.02
670 690 8.087750 ACATTTCAACACAAAACTCTTTTCAGA 58.912 29.630 0.00 0.00 0.00 3.27
671 691 9.090692 CATTTCAACACAAAACTCTTTTCAGAT 57.909 29.630 0.00 0.00 0.00 2.90
672 692 8.687824 TTTCAACACAAAACTCTTTTCAGATC 57.312 30.769 0.00 0.00 0.00 2.75
673 693 7.630242 TCAACACAAAACTCTTTTCAGATCT 57.370 32.000 0.00 0.00 0.00 2.75
674 694 7.697691 TCAACACAAAACTCTTTTCAGATCTC 58.302 34.615 0.00 0.00 0.00 2.75
675 695 7.336679 TCAACACAAAACTCTTTTCAGATCTCA 59.663 33.333 0.00 0.00 0.00 3.27
676 696 7.630242 ACACAAAACTCTTTTCAGATCTCAA 57.370 32.000 0.00 0.00 0.00 3.02
677 697 7.475840 ACACAAAACTCTTTTCAGATCTCAAC 58.524 34.615 0.00 0.00 0.00 3.18
678 698 7.121168 ACACAAAACTCTTTTCAGATCTCAACA 59.879 33.333 0.00 0.00 0.00 3.33
679 699 8.133627 CACAAAACTCTTTTCAGATCTCAACAT 58.866 33.333 0.00 0.00 0.00 2.71
680 700 9.342308 ACAAAACTCTTTTCAGATCTCAACATA 57.658 29.630 0.00 0.00 0.00 2.29
681 701 9.604626 CAAAACTCTTTTCAGATCTCAACATAC 57.395 33.333 0.00 0.00 0.00 2.39
682 702 8.908786 AAACTCTTTTCAGATCTCAACATACA 57.091 30.769 0.00 0.00 0.00 2.29
683 703 8.908786 AACTCTTTTCAGATCTCAACATACAA 57.091 30.769 0.00 0.00 0.00 2.41
684 704 9.512588 AACTCTTTTCAGATCTCAACATACAAT 57.487 29.630 0.00 0.00 0.00 2.71
715 735 9.487790 AAAAACTCAACAACAGATTTTGAAAGA 57.512 25.926 0.00 0.00 28.02 2.52
716 736 9.487790 AAAACTCAACAACAGATTTTGAAAGAA 57.512 25.926 0.00 0.00 0.00 2.52
717 737 8.693542 AACTCAACAACAGATTTTGAAAGAAG 57.306 30.769 0.00 0.00 0.00 2.85
718 738 6.753744 ACTCAACAACAGATTTTGAAAGAAGC 59.246 34.615 0.00 0.00 0.00 3.86
719 739 6.629128 TCAACAACAGATTTTGAAAGAAGCA 58.371 32.000 0.00 0.00 0.00 3.91
720 740 6.753279 TCAACAACAGATTTTGAAAGAAGCAG 59.247 34.615 0.00 0.00 0.00 4.24
721 741 6.455360 ACAACAGATTTTGAAAGAAGCAGA 57.545 33.333 0.00 0.00 0.00 4.26
722 742 7.047460 ACAACAGATTTTGAAAGAAGCAGAT 57.953 32.000 0.00 0.00 0.00 2.90
723 743 7.495055 ACAACAGATTTTGAAAGAAGCAGATT 58.505 30.769 0.00 0.00 0.00 2.40
724 744 7.650903 ACAACAGATTTTGAAAGAAGCAGATTC 59.349 33.333 0.00 0.00 38.28 2.52
747 767 7.369803 TCTGGAAGAATTTTCGAGAATCTTG 57.630 36.000 13.93 0.00 42.31 3.02
748 768 7.161404 TCTGGAAGAATTTTCGAGAATCTTGA 58.839 34.615 13.93 0.00 42.31 3.02
749 769 7.826252 TCTGGAAGAATTTTCGAGAATCTTGAT 59.174 33.333 13.93 0.00 42.31 2.57
750 770 8.340618 TGGAAGAATTTTCGAGAATCTTGATT 57.659 30.769 13.93 0.00 0.00 2.57
751 771 8.454106 TGGAAGAATTTTCGAGAATCTTGATTC 58.546 33.333 13.71 13.71 0.00 2.52
752 772 8.672815 GGAAGAATTTTCGAGAATCTTGATTCT 58.327 33.333 21.53 21.53 43.04 2.40
753 773 9.488124 GAAGAATTTTCGAGAATCTTGATTCTG 57.512 33.333 25.04 17.83 40.67 3.02
754 774 7.470900 AGAATTTTCGAGAATCTTGATTCTGC 58.529 34.615 25.04 16.58 40.67 4.26
755 775 6.748333 ATTTTCGAGAATCTTGATTCTGCA 57.252 33.333 25.04 11.85 40.67 4.41
756 776 5.791367 TTTCGAGAATCTTGATTCTGCAG 57.209 39.130 25.04 7.63 40.67 4.41
757 777 4.725790 TCGAGAATCTTGATTCTGCAGA 57.274 40.909 25.04 13.74 40.67 4.26
758 778 5.077134 TCGAGAATCTTGATTCTGCAGAA 57.923 39.130 30.23 30.23 40.67 3.02
759 779 5.668471 TCGAGAATCTTGATTCTGCAGAAT 58.332 37.500 36.15 36.15 46.54 2.40
760 780 6.111382 TCGAGAATCTTGATTCTGCAGAATT 58.889 36.000 35.91 23.24 44.14 2.17
761 781 6.257411 TCGAGAATCTTGATTCTGCAGAATTC 59.743 38.462 35.91 28.42 44.14 2.17
762 782 6.258287 CGAGAATCTTGATTCTGCAGAATTCT 59.742 38.462 35.91 31.66 44.14 2.40
763 783 7.323049 AGAATCTTGATTCTGCAGAATTCTG 57.677 36.000 35.91 27.82 44.14 3.02
778 798 6.266323 CAGAATTCTGCATGAAAAGATCTGG 58.734 40.000 21.96 0.00 38.29 3.86
779 799 5.360144 AGAATTCTGCATGAAAAGATCTGGG 59.640 40.000 7.30 0.00 38.29 4.45
780 800 3.726557 TCTGCATGAAAAGATCTGGGT 57.273 42.857 0.00 0.00 0.00 4.51
799 819 0.528924 TCGTACTCCCGTGTTCCATG 59.471 55.000 0.00 0.00 0.00 3.66
887 912 8.517062 AATCAAATCTATCCTGTTCCTTTCAG 57.483 34.615 0.00 0.00 0.00 3.02
895 920 5.779241 TCCTGTTCCTTTCAGTGGAATAT 57.221 39.130 0.00 0.00 44.27 1.28
906 937 3.646162 TCAGTGGAATATGGGTAAGCGAT 59.354 43.478 0.00 0.00 0.00 4.58
986 1017 2.511600 CCGGTCAATCGCCTCACC 60.512 66.667 0.00 0.00 0.00 4.02
987 1018 2.264480 CGGTCAATCGCCTCACCA 59.736 61.111 0.00 0.00 0.00 4.17
1032 1063 1.908793 CTCCCACGTGACCTCCACT 60.909 63.158 19.30 0.00 43.53 4.00
1309 1356 2.783609 AGACCCGCGCTCTATCTATA 57.216 50.000 5.56 0.00 0.00 1.31
1318 1373 3.249080 GCGCTCTATCTATACCCTCGATC 59.751 52.174 0.00 0.00 0.00 3.69
1320 1375 3.249080 GCTCTATCTATACCCTCGATCGC 59.751 52.174 11.09 0.00 0.00 4.58
1339 1395 4.953269 TCGCGCGGATATATTTTCAATTC 58.047 39.130 31.69 0.00 0.00 2.17
1414 1507 2.299297 TCGAGAAAACCAAGTCTCCTCC 59.701 50.000 0.00 0.00 37.57 4.30
1424 1517 2.439701 TCTCCTCCCGTACCAGCG 60.440 66.667 0.00 0.00 0.00 5.18
1426 1519 2.283388 TCCTCCCGTACCAGCGTT 60.283 61.111 0.00 0.00 0.00 4.84
1434 1527 2.159626 CCCGTACCAGCGTTTATGTTTG 60.160 50.000 0.00 0.00 0.00 2.93
1510 1604 1.115930 AGTCTGACCAGCACTTCCGT 61.116 55.000 3.76 0.00 0.00 4.69
1524 1618 1.792949 CTTCCGTTTCAACCAGAGTCG 59.207 52.381 0.00 0.00 0.00 4.18
1535 1629 1.153745 CAGAGTCGCCTACAGCCAC 60.154 63.158 0.00 0.00 38.78 5.01
1569 1663 1.014352 ATATTCGACTTGTTGCGCCC 58.986 50.000 4.18 0.00 0.00 6.13
1584 1678 1.302511 GCCCCAAAGCGAGAAGTGA 60.303 57.895 0.00 0.00 0.00 3.41
1676 1770 0.460284 CCTTGACCGAGCGCTGTAAT 60.460 55.000 18.48 0.00 0.00 1.89
1780 1874 6.696411 TCCGAATTGCCAATCTTTTTGTTAT 58.304 32.000 0.00 0.00 0.00 1.89
1790 1884 7.095649 GCCAATCTTTTTGTTATTTCTGGTGTC 60.096 37.037 0.00 0.00 0.00 3.67
1838 1932 3.473625 ACCAACCGTTAGAAAAGACCTG 58.526 45.455 0.00 0.00 0.00 4.00
1850 1944 9.232473 GTTAGAAAAGACCTGGAAGATATTTGT 57.768 33.333 0.00 0.00 34.07 2.83
1997 2092 5.404366 CACATTGATTCCTGCAAAGTTTGAG 59.596 40.000 19.82 12.62 0.00 3.02
2124 2219 9.691362 TGCTAAATTATTTCAGTCCTTTGTTTC 57.309 29.630 0.00 0.00 0.00 2.78
2127 2222 5.699097 TTATTTCAGTCCTTTGTTTCCGG 57.301 39.130 0.00 0.00 0.00 5.14
2143 2238 9.717942 TTTGTTTCCGGATATCATTTCAAAAAT 57.282 25.926 4.15 0.00 0.00 1.82
2215 2310 1.553706 ATCCTTTTTCTGCTGCCAGG 58.446 50.000 0.00 0.00 39.61 4.45
2448 2543 5.794726 TCCATCCTCCAATATGCATTTTG 57.205 39.130 19.45 19.45 0.00 2.44
2461 2556 8.908678 CAATATGCATTTTGTGTGCTGTATATC 58.091 33.333 18.48 0.00 42.92 1.63
2589 2684 3.530265 TTTCAAGATTGATGGGCATGC 57.470 42.857 9.90 9.90 37.00 4.06
2761 2858 2.177950 GCCAGGTGCATGTTCTCTG 58.822 57.895 0.00 0.00 40.77 3.35
2815 2914 9.512435 CAAGAATGGTAATAGCATTTCTCTTTG 57.488 33.333 17.35 12.86 45.23 2.77
2870 2969 3.477530 GTCAGTATGCCAAATAGGTCCC 58.522 50.000 0.00 0.00 40.61 4.46
3135 3254 8.276325 GTCTATGATGTTGCTATCGGTTTTAAG 58.724 37.037 0.00 0.00 0.00 1.85
3309 3430 7.547019 TCAGACATGCTAACTTTCTTCTGTATG 59.453 37.037 0.00 0.00 32.71 2.39
3353 3474 5.425630 CATGACACAGATGAGAGATTGGAA 58.574 41.667 0.00 0.00 0.00 3.53
3412 3533 8.373256 GCTTTTGAAGTTTACTTTGTCAAAGAC 58.627 33.333 28.07 17.13 41.02 3.01
3421 3542 8.403236 GTTTACTTTGTCAAAGACCAAGTATGT 58.597 33.333 28.07 8.21 44.41 2.29
3451 3572 2.670414 CGGTCTGAGATTGCAAGAAGTC 59.330 50.000 4.94 0.00 0.00 3.01
3508 3629 9.659830 CTAGGTTTATTGTGTTGTTACAACTTC 57.340 33.333 25.61 18.89 42.74 3.01
3597 3718 4.460382 TGTGAAATTCAATCTTCCTCTGCC 59.540 41.667 0.00 0.00 0.00 4.85
3601 3722 2.099141 TCAATCTTCCTCTGCCGTTG 57.901 50.000 0.00 0.00 0.00 4.10
3688 3809 9.562583 AAATGAAATTGAAATAAATGCACATGC 57.437 25.926 0.00 0.00 36.10 4.06
3831 3952 9.881773 ATATGAAAGAATTATGCCCTTCCTTTA 57.118 29.630 0.00 0.00 0.00 1.85
3836 3957 9.890629 AAAGAATTATGCCCTTCCTTTATTTTC 57.109 29.630 0.00 0.00 0.00 2.29
3837 3958 8.844865 AGAATTATGCCCTTCCTTTATTTTCT 57.155 30.769 0.00 0.00 0.00 2.52
3841 3962 5.982890 TGCCCTTCCTTTATTTTCTTCTG 57.017 39.130 0.00 0.00 0.00 3.02
3897 4021 5.482006 GCCACTCATTTCCTTAAGCAAAAT 58.518 37.500 0.00 2.46 0.00 1.82
4057 4384 3.620821 TGCATGTACCGTACATCACATTG 59.379 43.478 19.33 11.21 45.83 2.82
4059 4386 4.806775 GCATGTACCGTACATCACATTGTA 59.193 41.667 19.33 0.00 45.83 2.41
4068 4395 9.168451 ACCGTACATCACATTGTAATTAATTCA 57.832 29.630 3.39 0.41 34.05 2.57
4113 4440 7.028962 TGAGAAACAAATATCATGGAAAAGCG 58.971 34.615 0.00 0.00 0.00 4.68
4116 4443 5.266733 ACAAATATCATGGAAAAGCGCAT 57.733 34.783 11.47 0.00 0.00 4.73
4440 4771 2.366916 GTGGCTGAGGTATGCTCTATGT 59.633 50.000 0.00 0.00 0.00 2.29
4621 4953 8.971321 CAAATTTTGTATTCTGACAGAACCAAG 58.029 33.333 19.96 9.63 37.00 3.61
4633 4966 0.877743 GAACCAAGTGCTGCTTCCTC 59.122 55.000 0.00 0.00 34.69 3.71
4820 5318 5.064707 CACTTATTGGTCACAAAGGTATCCG 59.935 44.000 0.00 0.00 40.55 4.18
4953 5456 6.381481 TGCATGACAGCTAAGATAAATTGG 57.619 37.500 0.00 0.00 34.99 3.16
4971 5474 3.216187 TGGTAGCTGGCTGTTGTTTTA 57.784 42.857 5.25 0.00 0.00 1.52
5002 5505 4.479619 GTTGCACAATTTAGCTCCAGAAG 58.520 43.478 0.00 0.00 0.00 2.85
5028 5531 4.217550 GGCAACTCAAAGGCAATACAGTTA 59.782 41.667 0.00 0.00 0.00 2.24
5289 7396 5.389516 CGTGTTATTCTCTACAAGGCAACAC 60.390 44.000 0.00 0.00 37.63 3.32
5299 7406 3.620488 ACAAGGCAACACTTTCTTCTCA 58.380 40.909 0.00 0.00 41.41 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.349026 CTCACATCTCCCAACTGGTGT 59.651 52.381 0.00 0.00 34.77 4.16
22 23 3.325870 TGTCGATGGTTGAATGTCTCAC 58.674 45.455 0.00 0.00 32.21 3.51
55 56 5.685511 CCAAATGTTCTTTCGACGACATTTT 59.314 36.000 17.14 5.56 45.37 1.82
63 64 4.545823 TGACACCAAATGTTCTTTCGAC 57.454 40.909 0.00 0.00 43.56 4.20
123 133 2.084546 CATCTTTTGGGTCTCCGGTTC 58.915 52.381 0.00 0.00 35.24 3.62
180 190 5.066968 TCATCACGTAACTTGCTATCACA 57.933 39.130 0.00 0.00 0.00 3.58
203 213 6.253298 CGTCATTGTCAAACTTGTCAAAATGT 59.747 34.615 6.28 0.00 39.07 2.71
257 267 2.436115 GGTAGAGCGTTGGCACCC 60.436 66.667 0.00 0.00 43.41 4.61
275 285 4.297768 TCATGGTACCATCATCTTCTGGA 58.702 43.478 24.99 12.52 36.35 3.86
327 337 7.396540 AAAAAGAATAATCTCAAGGTGCGAT 57.603 32.000 0.00 0.00 33.77 4.58
445 465 8.737175 TGTTGTTTCTAATAGTGTCTAGTCGAT 58.263 33.333 0.00 0.00 0.00 3.59
516 536 5.427481 AGAATTTTGGAACGGAGGGAGTATA 59.573 40.000 0.00 0.00 0.00 1.47
517 537 4.227527 AGAATTTTGGAACGGAGGGAGTAT 59.772 41.667 0.00 0.00 0.00 2.12
518 538 3.585732 AGAATTTTGGAACGGAGGGAGTA 59.414 43.478 0.00 0.00 0.00 2.59
519 539 2.375509 AGAATTTTGGAACGGAGGGAGT 59.624 45.455 0.00 0.00 0.00 3.85
520 540 3.073274 AGAATTTTGGAACGGAGGGAG 57.927 47.619 0.00 0.00 0.00 4.30
521 541 3.153919 CAAGAATTTTGGAACGGAGGGA 58.846 45.455 0.00 0.00 0.00 4.20
522 542 2.890945 ACAAGAATTTTGGAACGGAGGG 59.109 45.455 0.00 0.00 0.00 4.30
523 543 3.821033 AGACAAGAATTTTGGAACGGAGG 59.179 43.478 0.00 0.00 0.00 4.30
524 544 5.438761 AAGACAAGAATTTTGGAACGGAG 57.561 39.130 0.00 0.00 0.00 4.63
525 545 5.823570 TGTAAGACAAGAATTTTGGAACGGA 59.176 36.000 0.00 0.00 0.00 4.69
526 546 6.067263 TGTAAGACAAGAATTTTGGAACGG 57.933 37.500 0.00 0.00 0.00 4.44
527 547 8.479280 CAAATGTAAGACAAGAATTTTGGAACG 58.521 33.333 5.68 0.00 0.00 3.95
528 548 9.313118 ACAAATGTAAGACAAGAATTTTGGAAC 57.687 29.630 7.26 0.00 31.16 3.62
529 549 9.528018 GACAAATGTAAGACAAGAATTTTGGAA 57.472 29.630 7.26 0.00 31.16 3.53
530 550 8.912988 AGACAAATGTAAGACAAGAATTTTGGA 58.087 29.630 7.26 0.00 31.16 3.53
537 557 9.569167 CGTATCTAGACAAATGTAAGACAAGAA 57.431 33.333 0.00 0.00 0.00 2.52
538 558 8.188799 CCGTATCTAGACAAATGTAAGACAAGA 58.811 37.037 0.00 0.00 0.00 3.02
539 559 8.188799 TCCGTATCTAGACAAATGTAAGACAAG 58.811 37.037 0.00 0.00 0.00 3.16
540 560 8.058667 TCCGTATCTAGACAAATGTAAGACAA 57.941 34.615 0.00 0.00 0.00 3.18
541 561 7.634671 TCCGTATCTAGACAAATGTAAGACA 57.365 36.000 0.00 0.00 0.00 3.41
542 562 8.136165 ACATCCGTATCTAGACAAATGTAAGAC 58.864 37.037 0.00 0.00 0.00 3.01
543 563 8.234136 ACATCCGTATCTAGACAAATGTAAGA 57.766 34.615 0.00 1.82 0.00 2.10
544 564 9.395707 GTACATCCGTATCTAGACAAATGTAAG 57.604 37.037 12.89 0.00 32.51 2.34
545 565 8.355169 GGTACATCCGTATCTAGACAAATGTAA 58.645 37.037 12.89 1.88 32.51 2.41
546 566 7.722728 AGGTACATCCGTATCTAGACAAATGTA 59.277 37.037 0.00 3.24 37.29 2.29
547 567 6.550108 AGGTACATCCGTATCTAGACAAATGT 59.450 38.462 0.00 4.18 37.29 2.71
548 568 6.982852 AGGTACATCCGTATCTAGACAAATG 58.017 40.000 0.00 0.00 37.29 2.32
549 569 8.701908 TTAGGTACATCCGTATCTAGACAAAT 57.298 34.615 0.00 0.00 41.33 2.32
550 570 8.701908 ATTAGGTACATCCGTATCTAGACAAA 57.298 34.615 0.00 0.00 41.33 2.83
551 571 9.224267 GTATTAGGTACATCCGTATCTAGACAA 57.776 37.037 0.00 0.00 41.33 3.18
552 572 8.600668 AGTATTAGGTACATCCGTATCTAGACA 58.399 37.037 0.00 0.00 41.33 3.41
558 578 9.334693 CGTTTTAGTATTAGGTACATCCGTATC 57.665 37.037 0.00 0.00 41.99 2.24
559 579 8.850156 ACGTTTTAGTATTAGGTACATCCGTAT 58.150 33.333 0.00 0.00 41.99 3.06
560 580 8.128582 CACGTTTTAGTATTAGGTACATCCGTA 58.871 37.037 0.00 0.00 41.99 4.02
561 581 6.974622 CACGTTTTAGTATTAGGTACATCCGT 59.025 38.462 0.00 0.00 41.99 4.69
562 582 7.166473 GTCACGTTTTAGTATTAGGTACATCCG 59.834 40.741 0.00 0.00 41.99 4.18
563 583 8.193438 AGTCACGTTTTAGTATTAGGTACATCC 58.807 37.037 0.00 0.00 35.67 3.51
564 584 9.578439 AAGTCACGTTTTAGTATTAGGTACATC 57.422 33.333 0.00 0.00 35.67 3.06
565 585 9.362539 CAAGTCACGTTTTAGTATTAGGTACAT 57.637 33.333 0.00 0.00 35.67 2.29
566 586 8.575589 TCAAGTCACGTTTTAGTATTAGGTACA 58.424 33.333 0.00 0.00 35.67 2.90
567 587 8.970691 TCAAGTCACGTTTTAGTATTAGGTAC 57.029 34.615 0.00 0.00 0.00 3.34
569 589 9.578439 GTATCAAGTCACGTTTTAGTATTAGGT 57.422 33.333 0.00 0.00 0.00 3.08
570 590 9.577110 TGTATCAAGTCACGTTTTAGTATTAGG 57.423 33.333 0.00 0.00 0.00 2.69
573 593 9.095065 GGATGTATCAAGTCACGTTTTAGTATT 57.905 33.333 0.00 0.00 0.00 1.89
574 594 7.434307 CGGATGTATCAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
575 595 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
576 596 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
577 597 5.575606 ACGGATGTATCAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
578 598 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
579 599 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
580 600 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
581 601 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
582 602 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
583 603 5.051039 CCAAATACGGATGTATCAAGTCACG 60.051 44.000 0.00 0.00 40.42 4.35
584 604 6.046593 TCCAAATACGGATGTATCAAGTCAC 58.953 40.000 0.00 0.00 40.42 3.67
585 605 6.228616 TCCAAATACGGATGTATCAAGTCA 57.771 37.500 0.00 0.00 40.42 3.41
586 606 8.827177 TTATCCAAATACGGATGTATCAAGTC 57.173 34.615 2.67 0.00 45.65 3.01
587 607 9.793259 ATTTATCCAAATACGGATGTATCAAGT 57.207 29.630 2.67 0.00 45.65 3.16
610 630 9.463443 CCGTCTCAAAATTCTTGTCTTAAATTT 57.537 29.630 0.00 0.00 34.86 1.82
611 631 8.846211 TCCGTCTCAAAATTCTTGTCTTAAATT 58.154 29.630 0.00 0.00 0.00 1.82
612 632 8.391075 TCCGTCTCAAAATTCTTGTCTTAAAT 57.609 30.769 0.00 0.00 0.00 1.40
613 633 7.519970 GCTCCGTCTCAAAATTCTTGTCTTAAA 60.520 37.037 0.00 0.00 0.00 1.52
614 634 6.073222 GCTCCGTCTCAAAATTCTTGTCTTAA 60.073 38.462 0.00 0.00 0.00 1.85
615 635 5.408604 GCTCCGTCTCAAAATTCTTGTCTTA 59.591 40.000 0.00 0.00 0.00 2.10
616 636 4.214332 GCTCCGTCTCAAAATTCTTGTCTT 59.786 41.667 0.00 0.00 0.00 3.01
617 637 3.748568 GCTCCGTCTCAAAATTCTTGTCT 59.251 43.478 0.00 0.00 0.00 3.41
618 638 3.423645 CGCTCCGTCTCAAAATTCTTGTC 60.424 47.826 0.00 0.00 0.00 3.18
619 639 2.480419 CGCTCCGTCTCAAAATTCTTGT 59.520 45.455 0.00 0.00 0.00 3.16
620 640 2.736721 TCGCTCCGTCTCAAAATTCTTG 59.263 45.455 0.00 0.00 0.00 3.02
621 641 2.996621 CTCGCTCCGTCTCAAAATTCTT 59.003 45.455 0.00 0.00 0.00 2.52
622 642 2.028930 ACTCGCTCCGTCTCAAAATTCT 60.029 45.455 0.00 0.00 0.00 2.40
623 643 2.338500 ACTCGCTCCGTCTCAAAATTC 58.662 47.619 0.00 0.00 0.00 2.17
624 644 2.457366 ACTCGCTCCGTCTCAAAATT 57.543 45.000 0.00 0.00 0.00 1.82
625 645 2.230508 TGTACTCGCTCCGTCTCAAAAT 59.769 45.455 0.00 0.00 0.00 1.82
626 646 1.610038 TGTACTCGCTCCGTCTCAAAA 59.390 47.619 0.00 0.00 0.00 2.44
627 647 1.241165 TGTACTCGCTCCGTCTCAAA 58.759 50.000 0.00 0.00 0.00 2.69
628 648 1.460504 ATGTACTCGCTCCGTCTCAA 58.539 50.000 0.00 0.00 0.00 3.02
629 649 1.460504 AATGTACTCGCTCCGTCTCA 58.539 50.000 0.00 0.00 0.00 3.27
630 650 2.159421 TGAAATGTACTCGCTCCGTCTC 60.159 50.000 0.00 0.00 0.00 3.36
631 651 1.816835 TGAAATGTACTCGCTCCGTCT 59.183 47.619 0.00 0.00 0.00 4.18
632 652 2.273370 TGAAATGTACTCGCTCCGTC 57.727 50.000 0.00 0.00 0.00 4.79
633 653 2.288579 TGTTGAAATGTACTCGCTCCGT 60.289 45.455 0.00 0.00 0.00 4.69
634 654 2.092211 GTGTTGAAATGTACTCGCTCCG 59.908 50.000 0.00 0.00 0.00 4.63
635 655 3.064207 TGTGTTGAAATGTACTCGCTCC 58.936 45.455 0.00 0.00 0.00 4.70
636 656 4.725556 TTGTGTTGAAATGTACTCGCTC 57.274 40.909 0.00 0.00 0.00 5.03
637 657 5.065988 AGTTTTGTGTTGAAATGTACTCGCT 59.934 36.000 0.00 0.00 0.00 4.93
638 658 5.270853 AGTTTTGTGTTGAAATGTACTCGC 58.729 37.500 0.00 0.00 0.00 5.03
639 659 6.715464 AGAGTTTTGTGTTGAAATGTACTCG 58.285 36.000 0.00 0.00 0.00 4.18
640 660 8.911247 AAAGAGTTTTGTGTTGAAATGTACTC 57.089 30.769 0.00 0.00 0.00 2.59
641 661 9.353999 GAAAAGAGTTTTGTGTTGAAATGTACT 57.646 29.630 0.00 0.00 31.94 2.73
642 662 9.134734 TGAAAAGAGTTTTGTGTTGAAATGTAC 57.865 29.630 0.00 0.00 31.94 2.90
643 663 9.352784 CTGAAAAGAGTTTTGTGTTGAAATGTA 57.647 29.630 0.00 0.00 31.94 2.29
644 664 8.087750 TCTGAAAAGAGTTTTGTGTTGAAATGT 58.912 29.630 0.00 0.00 31.94 2.71
645 665 8.464770 TCTGAAAAGAGTTTTGTGTTGAAATG 57.535 30.769 0.00 0.00 31.94 2.32
646 666 9.305925 GATCTGAAAAGAGTTTTGTGTTGAAAT 57.694 29.630 0.00 0.00 31.94 2.17
647 667 8.522830 AGATCTGAAAAGAGTTTTGTGTTGAAA 58.477 29.630 0.00 0.00 31.94 2.69
648 668 8.055279 AGATCTGAAAAGAGTTTTGTGTTGAA 57.945 30.769 0.00 0.00 31.94 2.69
649 669 7.336679 TGAGATCTGAAAAGAGTTTTGTGTTGA 59.663 33.333 0.00 0.00 31.94 3.18
650 670 7.475015 TGAGATCTGAAAAGAGTTTTGTGTTG 58.525 34.615 0.00 0.00 31.94 3.33
651 671 7.630242 TGAGATCTGAAAAGAGTTTTGTGTT 57.370 32.000 0.00 0.00 31.94 3.32
652 672 7.121168 TGTTGAGATCTGAAAAGAGTTTTGTGT 59.879 33.333 0.00 0.00 31.94 3.72
653 673 7.475015 TGTTGAGATCTGAAAAGAGTTTTGTG 58.525 34.615 0.00 0.00 31.94 3.33
654 674 7.630242 TGTTGAGATCTGAAAAGAGTTTTGT 57.370 32.000 0.00 0.00 31.94 2.83
655 675 9.604626 GTATGTTGAGATCTGAAAAGAGTTTTG 57.395 33.333 0.00 0.00 31.94 2.44
656 676 9.342308 TGTATGTTGAGATCTGAAAAGAGTTTT 57.658 29.630 0.00 0.00 35.12 2.43
657 677 8.908786 TGTATGTTGAGATCTGAAAAGAGTTT 57.091 30.769 0.00 0.00 0.00 2.66
658 678 8.908786 TTGTATGTTGAGATCTGAAAAGAGTT 57.091 30.769 0.00 0.00 0.00 3.01
689 709 9.487790 TCTTTCAAAATCTGTTGTTGAGTTTTT 57.512 25.926 0.00 0.00 33.10 1.94
690 710 9.487790 TTCTTTCAAAATCTGTTGTTGAGTTTT 57.512 25.926 0.00 0.00 33.10 2.43
691 711 9.143631 CTTCTTTCAAAATCTGTTGTTGAGTTT 57.856 29.630 0.00 0.00 33.10 2.66
692 712 7.276438 GCTTCTTTCAAAATCTGTTGTTGAGTT 59.724 33.333 0.00 0.00 33.10 3.01
693 713 6.753744 GCTTCTTTCAAAATCTGTTGTTGAGT 59.246 34.615 0.00 0.00 33.10 3.41
694 714 6.753279 TGCTTCTTTCAAAATCTGTTGTTGAG 59.247 34.615 0.00 0.00 33.10 3.02
695 715 6.629128 TGCTTCTTTCAAAATCTGTTGTTGA 58.371 32.000 0.00 0.00 0.00 3.18
696 716 6.753279 TCTGCTTCTTTCAAAATCTGTTGTTG 59.247 34.615 0.00 0.00 0.00 3.33
697 717 6.866480 TCTGCTTCTTTCAAAATCTGTTGTT 58.134 32.000 0.00 0.00 0.00 2.83
698 718 6.455360 TCTGCTTCTTTCAAAATCTGTTGT 57.545 33.333 0.00 0.00 0.00 3.32
699 719 7.866393 AGAATCTGCTTCTTTCAAAATCTGTTG 59.134 33.333 0.00 0.00 41.60 3.33
700 720 7.866393 CAGAATCTGCTTCTTTCAAAATCTGTT 59.134 33.333 0.00 0.00 41.60 3.16
701 721 7.368833 CAGAATCTGCTTCTTTCAAAATCTGT 58.631 34.615 0.00 0.00 41.60 3.41
702 722 6.807230 CCAGAATCTGCTTCTTTCAAAATCTG 59.193 38.462 4.40 0.00 41.60 2.90
703 723 6.718454 TCCAGAATCTGCTTCTTTCAAAATCT 59.282 34.615 4.40 0.00 41.60 2.40
704 724 6.917533 TCCAGAATCTGCTTCTTTCAAAATC 58.082 36.000 4.40 0.00 41.60 2.17
705 725 6.906157 TCCAGAATCTGCTTCTTTCAAAAT 57.094 33.333 4.40 0.00 41.60 1.82
706 726 6.547141 TCTTCCAGAATCTGCTTCTTTCAAAA 59.453 34.615 4.40 0.00 41.60 2.44
707 727 6.064060 TCTTCCAGAATCTGCTTCTTTCAAA 58.936 36.000 4.40 0.00 41.60 2.69
708 728 5.624159 TCTTCCAGAATCTGCTTCTTTCAA 58.376 37.500 4.40 0.00 41.60 2.69
709 729 5.233083 TCTTCCAGAATCTGCTTCTTTCA 57.767 39.130 4.40 0.00 41.60 2.69
710 730 6.756299 ATTCTTCCAGAATCTGCTTCTTTC 57.244 37.500 4.40 0.00 40.75 2.62
711 731 7.536159 AAATTCTTCCAGAATCTGCTTCTTT 57.464 32.000 4.40 0.00 43.67 2.52
712 732 7.536159 AAAATTCTTCCAGAATCTGCTTCTT 57.464 32.000 4.40 0.00 43.67 2.52
713 733 6.128063 CGAAAATTCTTCCAGAATCTGCTTCT 60.128 38.462 4.40 0.00 43.67 2.85
714 734 6.026513 CGAAAATTCTTCCAGAATCTGCTTC 58.973 40.000 4.40 1.74 43.67 3.86
715 735 5.707298 TCGAAAATTCTTCCAGAATCTGCTT 59.293 36.000 4.40 0.00 43.67 3.91
716 736 5.248640 TCGAAAATTCTTCCAGAATCTGCT 58.751 37.500 4.40 0.00 43.67 4.24
717 737 5.352569 TCTCGAAAATTCTTCCAGAATCTGC 59.647 40.000 4.40 0.00 43.67 4.26
718 738 6.974932 TCTCGAAAATTCTTCCAGAATCTG 57.025 37.500 2.68 2.68 43.67 2.90
719 739 8.046107 AGATTCTCGAAAATTCTTCCAGAATCT 58.954 33.333 25.62 25.62 43.67 2.40
720 740 8.207521 AGATTCTCGAAAATTCTTCCAGAATC 57.792 34.615 23.70 23.70 43.67 2.52
721 741 8.457261 CAAGATTCTCGAAAATTCTTCCAGAAT 58.543 33.333 15.76 15.76 46.22 2.40
722 742 7.661437 TCAAGATTCTCGAAAATTCTTCCAGAA 59.339 33.333 10.40 10.40 38.78 3.02
723 743 7.161404 TCAAGATTCTCGAAAATTCTTCCAGA 58.839 34.615 0.00 0.00 0.00 3.86
724 744 7.369803 TCAAGATTCTCGAAAATTCTTCCAG 57.630 36.000 0.00 0.00 0.00 3.86
725 745 7.928307 ATCAAGATTCTCGAAAATTCTTCCA 57.072 32.000 0.00 0.00 0.00 3.53
726 746 8.833976 GAATCAAGATTCTCGAAAATTCTTCC 57.166 34.615 14.02 0.00 42.85 3.46
737 757 7.727121 CAGAATTCTGCAGAATCAAGATTCTCG 60.727 40.741 35.67 23.28 43.80 4.04
738 758 7.411274 CAGAATTCTGCAGAATCAAGATTCTC 58.589 38.462 35.67 26.55 43.80 2.87
739 759 7.323049 CAGAATTCTGCAGAATCAAGATTCT 57.677 36.000 35.67 29.66 44.73 2.40
754 774 6.266323 CCAGATCTTTTCATGCAGAATTCTG 58.734 40.000 27.82 27.82 46.40 3.02
755 775 5.360144 CCCAGATCTTTTCATGCAGAATTCT 59.640 40.000 0.88 0.88 35.83 2.40
756 776 5.126707 ACCCAGATCTTTTCATGCAGAATTC 59.873 40.000 0.00 0.00 35.83 2.17
757 777 5.021458 ACCCAGATCTTTTCATGCAGAATT 58.979 37.500 0.00 0.00 35.83 2.17
758 778 4.607239 ACCCAGATCTTTTCATGCAGAAT 58.393 39.130 0.00 0.00 35.83 2.40
759 779 4.012374 GACCCAGATCTTTTCATGCAGAA 58.988 43.478 0.00 0.00 0.00 3.02
760 780 3.614092 GACCCAGATCTTTTCATGCAGA 58.386 45.455 0.00 0.00 0.00 4.26
761 781 2.353889 CGACCCAGATCTTTTCATGCAG 59.646 50.000 0.00 0.00 0.00 4.41
762 782 2.290260 ACGACCCAGATCTTTTCATGCA 60.290 45.455 0.00 0.00 0.00 3.96
763 783 2.359900 ACGACCCAGATCTTTTCATGC 58.640 47.619 0.00 0.00 0.00 4.06
764 784 4.759782 AGTACGACCCAGATCTTTTCATG 58.240 43.478 0.00 0.00 0.00 3.07
765 785 4.141914 GGAGTACGACCCAGATCTTTTCAT 60.142 45.833 0.00 0.00 0.00 2.57
766 786 3.194968 GGAGTACGACCCAGATCTTTTCA 59.805 47.826 0.00 0.00 0.00 2.69
767 787 3.430513 GGGAGTACGACCCAGATCTTTTC 60.431 52.174 20.91 0.00 46.05 2.29
768 788 2.500504 GGGAGTACGACCCAGATCTTTT 59.499 50.000 20.91 0.00 46.05 2.27
769 789 2.108970 GGGAGTACGACCCAGATCTTT 58.891 52.381 20.91 0.00 46.05 2.52
770 790 1.777941 GGGAGTACGACCCAGATCTT 58.222 55.000 20.91 0.00 46.05 2.40
771 791 3.516911 GGGAGTACGACCCAGATCT 57.483 57.895 20.91 0.00 46.05 2.75
777 797 1.213799 GAACACGGGAGTACGACCC 59.786 63.158 17.44 17.44 44.67 4.46
778 798 1.213799 GGAACACGGGAGTACGACC 59.786 63.158 0.00 4.00 44.67 4.79
779 799 1.959085 TGGAACACGGGAGTACGAC 59.041 57.895 0.00 0.00 44.67 4.34
780 800 4.498346 TGGAACACGGGAGTACGA 57.502 55.556 0.00 0.00 44.67 3.43
887 912 3.997021 CTGATCGCTTACCCATATTCCAC 59.003 47.826 0.00 0.00 0.00 4.02
895 920 1.141019 GTCGCTGATCGCTTACCCA 59.859 57.895 7.71 0.00 38.27 4.51
986 1017 2.187946 GCATCGAGGAGGTGGGTG 59.812 66.667 0.00 0.00 0.00 4.61
987 1018 2.284625 TGCATCGAGGAGGTGGGT 60.285 61.111 0.00 0.00 0.00 4.51
1318 1373 4.088648 GGAATTGAAAATATATCCGCGCG 58.911 43.478 25.67 25.67 0.00 6.86
1320 1375 5.524511 TCGGAATTGAAAATATATCCGCG 57.475 39.130 0.00 0.00 46.95 6.46
1339 1395 0.108138 AAGGCTCGTCTCCAAATCGG 60.108 55.000 0.00 0.00 0.00 4.18
1414 1507 2.481185 ACAAACATAAACGCTGGTACGG 59.519 45.455 0.00 0.00 37.37 4.02
1434 1527 9.487635 CAAAGTTTTGGCGAATGTGTTACACAC 62.488 40.741 21.00 8.14 39.56 3.82
1510 1604 1.689813 TGTAGGCGACTCTGGTTGAAA 59.310 47.619 0.00 0.00 43.67 2.69
1524 1618 2.747855 GCACCTGTGGCTGTAGGC 60.748 66.667 0.00 0.00 37.61 3.93
1569 1663 2.932614 CTGGTATCACTTCTCGCTTTGG 59.067 50.000 0.00 0.00 0.00 3.28
1576 1670 4.691216 GTGTTTCCACTGGTATCACTTCTC 59.309 45.833 8.10 0.00 38.61 2.87
1584 1678 2.344592 TGAGGGTGTTTCCACTGGTAT 58.655 47.619 0.00 0.00 41.53 2.73
1676 1770 3.429960 GCATGCAGTACTGACATCTCAGA 60.430 47.826 27.08 1.00 46.32 3.27
1780 1874 3.554960 CCTGATCTTGTCGACACCAGAAA 60.555 47.826 25.36 16.27 28.45 2.52
1790 1884 3.679980 CACCAGTTAACCTGATCTTGTCG 59.320 47.826 0.88 0.00 44.49 4.35
1838 1932 7.490402 CCAGAAAGATGCAAACAAATATCTTCC 59.510 37.037 0.00 0.00 38.54 3.46
1850 1944 2.291209 TGAGGCCAGAAAGATGCAAA 57.709 45.000 5.01 0.00 0.00 3.68
1910 2005 0.324943 TCGGGAGCTTCTTGGAAAGG 59.675 55.000 0.00 0.00 46.24 3.11
1997 2092 1.659098 CCTTTACGCCTCGTCATGAAC 59.341 52.381 0.00 0.00 41.54 3.18
2093 2188 7.408756 AGGACTGAAATAATTTAGCATGCAA 57.591 32.000 21.98 6.70 0.00 4.08
2192 2287 3.495331 TGGCAGCAGAAAAAGGATAACA 58.505 40.909 0.00 0.00 0.00 2.41
2195 2290 2.041620 ACCTGGCAGCAGAAAAAGGATA 59.958 45.455 9.56 0.00 0.00 2.59
2215 2310 4.390603 TCCACGCATGATAACACAGTTAAC 59.609 41.667 0.00 0.00 0.00 2.01
2448 2543 9.862371 AGCTTACATAATAGATATACAGCACAC 57.138 33.333 0.00 0.00 0.00 3.82
2747 2844 2.119801 ATCCACAGAGAACATGCACC 57.880 50.000 0.00 0.00 0.00 5.01
2761 2858 7.542130 GTGAACATTCCAAGAAAACATATCCAC 59.458 37.037 0.00 0.00 0.00 4.02
2815 2914 2.502142 AGTCCGTTCATTAAACCCCC 57.498 50.000 0.00 0.00 34.11 5.40
2870 2969 5.869753 ATTCAGGAAAAGAACAGTGATCG 57.130 39.130 0.00 0.00 0.00 3.69
3292 3413 9.809096 TGATCTTAGCATACAGAAGAAAGTTAG 57.191 33.333 0.00 0.00 33.15 2.34
3353 3474 4.655963 ACAAAGCACATGAGTAAGGTCAT 58.344 39.130 0.00 0.00 37.68 3.06
3412 3533 2.289444 ACCGAAGACACCACATACTTGG 60.289 50.000 0.00 0.00 43.04 3.61
3421 3542 1.924731 ATCTCAGACCGAAGACACCA 58.075 50.000 0.00 0.00 0.00 4.17
3451 3572 5.595885 AGCATAGCGCATATAATAGTCCTG 58.404 41.667 11.47 0.00 46.13 3.86
3508 3629 5.639506 AGTACATTGAACGAATGAGACTTGG 59.360 40.000 2.62 0.00 43.87 3.61
3597 3718 9.472995 GTCAATACATATACAGAAAACACAACG 57.527 33.333 0.00 0.00 0.00 4.10
3831 3952 7.763985 ACCAAAATTCGACAAACAGAAGAAAAT 59.236 29.630 0.00 0.00 0.00 1.82
3836 3957 7.860373 TCAATACCAAAATTCGACAAACAGAAG 59.140 33.333 0.00 0.00 0.00 2.85
3837 3958 7.708051 TCAATACCAAAATTCGACAAACAGAA 58.292 30.769 0.00 0.00 0.00 3.02
3841 3962 7.220108 GCCTATCAATACCAAAATTCGACAAAC 59.780 37.037 0.00 0.00 0.00 2.93
4011 4135 6.875972 ATAGTACAGGTCCAAGATTGTTCT 57.124 37.500 0.00 0.00 0.00 3.01
4440 4771 5.766150 TTTTCATCGAAGGCAAAAGAAGA 57.234 34.783 0.00 0.00 0.00 2.87
4621 4953 3.142174 AGTGTTTAAGAGGAAGCAGCAC 58.858 45.455 0.00 0.00 0.00 4.40
4665 5163 5.034200 TGCTTCCCTAGGTTCCTAATACAA 58.966 41.667 8.29 0.00 0.00 2.41
4820 5318 6.176183 ACATATCCAGCCTAATTCAGCATAC 58.824 40.000 2.79 0.00 0.00 2.39
4882 5385 5.009631 TCCTGGTATGACAAAAGTGAATGG 58.990 41.667 0.00 0.00 0.00 3.16
4953 5456 4.215399 TGTCATAAAACAACAGCCAGCTAC 59.785 41.667 0.00 0.00 0.00 3.58
4971 5474 4.990426 GCTAAATTGTGCAACCTTTGTCAT 59.010 37.500 0.00 0.00 34.36 3.06
5002 5505 0.681175 ATTGCCTTTGAGTTGCCCAC 59.319 50.000 0.00 0.00 0.00 4.61
5289 7396 6.162079 TCTGTGCAGAATACTGAGAAGAAAG 58.838 40.000 0.00 0.00 46.03 2.62
5299 7406 6.936900 ACACAAGTATTTCTGTGCAGAATACT 59.063 34.615 14.43 17.54 45.78 2.12
5395 7528 7.273815 GGTGTCGTCTTTTAAACACAATTGAAA 59.726 33.333 13.59 0.00 42.92 2.69


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

AutoCloner maintained by Alex Coulton.