Multiple sequence alignment - TraesCS3A01G338400

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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 TraesCS3A01G338400 chr3A 100.000 4937 0 0 1 4937 585025457 585020521 0.000000e+00 9118.0
1 TraesCS3A01G338400 chr3A 84.109 623 90 6 1 616 241766402 241767022 1.180000e-165 593.0
2 TraesCS3A01G338400 chr3A 98.387 62 1 0 3488 3549 585021910 585021849 5.220000e-20 110.0
3 TraesCS3A01G338400 chr3A 98.387 62 1 0 3548 3609 585021970 585021909 5.220000e-20 110.0
4 TraesCS3A01G338400 chr3A 95.833 48 2 0 4351 4398 585021072 585021025 1.470000e-10 78.7
5 TraesCS3A01G338400 chr3A 95.833 48 2 0 4386 4433 585021107 585021060 1.470000e-10 78.7
6 TraesCS3A01G338400 chr3D 90.533 3993 213 68 1040 4933 444061366 444057440 0.000000e+00 5127.0
7 TraesCS3A01G338400 chr3D 88.272 324 17 8 659 976 444062101 444061793 7.810000e-98 368.0
8 TraesCS3A01G338400 chr3D 100.000 62 0 0 3488 3549 444058799 444058738 1.120000e-21 115.0
9 TraesCS3A01G338400 chr3D 97.959 49 1 0 4348 4396 444057983 444057935 8.810000e-13 86.1
10 TraesCS3A01G338400 chr3B 91.104 2383 121 40 2599 4937 581965310 581962975 0.000000e+00 3142.0
11 TraesCS3A01G338400 chr3B 95.982 672 26 1 1876 2547 581965979 581965309 0.000000e+00 1090.0
12 TraesCS3A01G338400 chr3B 86.720 994 59 22 786 1719 581967333 581966353 0.000000e+00 1037.0
13 TraesCS3A01G338400 chr3B 89.815 108 10 1 659 766 581967699 581967593 2.400000e-28 137.0
14 TraesCS3A01G338400 chr3B 100.000 62 0 0 3488 3549 581964359 581964298 1.120000e-21 115.0
15 TraesCS3A01G338400 chr3B 95.745 47 2 0 4352 4398 581963522 581963476 5.300000e-10 76.8
16 TraesCS3A01G338400 chr5D 85.215 629 83 9 1 621 299394765 299394139 5.390000e-179 638.0
17 TraesCS3A01G338400 chr4B 84.098 610 83 12 15 616 636039816 636040419 1.190000e-160 577.0
18 TraesCS3A01G338400 chr4B 86.614 508 60 7 1 501 671841001 671841507 5.580000e-154 555.0
19 TraesCS3A01G338400 chr4B 81.525 590 96 12 29 611 549137539 549138122 1.610000e-129 473.0
20 TraesCS3A01G338400 chr5B 83.223 602 88 11 15 609 687108023 687107428 1.560000e-149 540.0
21 TraesCS3A01G338400 chr7A 86.420 486 59 6 30 509 726415961 726415477 4.380000e-145 525.0
22 TraesCS3A01G338400 chr7B 85.207 507 67 7 1 501 642506029 642505525 9.480000e-142 514.0
23 TraesCS3A01G338400 chr4D 84.825 514 71 6 93 599 486431131 486431644 1.230000e-140 510.0


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 TraesCS3A01G338400 chr3A 585020521 585025457 4936 True 9118.000000 9118 100.000000 1 4937 1 chr3A.!!$R1 4936
1 TraesCS3A01G338400 chr3A 241766402 241767022 620 False 593.000000 593 84.109000 1 616 1 chr3A.!!$F1 615
2 TraesCS3A01G338400 chr3D 444057440 444062101 4661 True 1424.025000 5127 94.191000 659 4933 4 chr3D.!!$R1 4274
3 TraesCS3A01G338400 chr3B 581962975 581967699 4724 True 932.966667 3142 93.227667 659 4937 6 chr3B.!!$R1 4278
4 TraesCS3A01G338400 chr5D 299394139 299394765 626 True 638.000000 638 85.215000 1 621 1 chr5D.!!$R1 620
5 TraesCS3A01G338400 chr4B 636039816 636040419 603 False 577.000000 577 84.098000 15 616 1 chr4B.!!$F2 601
6 TraesCS3A01G338400 chr4B 671841001 671841507 506 False 555.000000 555 86.614000 1 501 1 chr4B.!!$F3 500
7 TraesCS3A01G338400 chr4B 549137539 549138122 583 False 473.000000 473 81.525000 29 611 1 chr4B.!!$F1 582
8 TraesCS3A01G338400 chr5B 687107428 687108023 595 True 540.000000 540 83.223000 15 609 1 chr5B.!!$R1 594
9 TraesCS3A01G338400 chr7B 642505525 642506029 504 True 514.000000 514 85.207000 1 501 1 chr7B.!!$R1 500
10 TraesCS3A01G338400 chr4D 486431131 486431644 513 False 510.000000 510 84.825000 93 599 1 chr4D.!!$F1 506

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
641 659 0.033796 ACCCGTCCGAATGTAGGAGA 60.034 55.000 0.00 0.0 38.65 3.71 F
1074 1712 0.030092 TCCGATCCCCAAATCCCTCT 60.030 55.000 0.00 0.0 0.00 3.69 F
1485 2160 0.179097 GCTCGTCCTGAGGATTGTCC 60.179 60.000 3.65 0.0 45.38 4.02 F
1575 2250 0.385751 GATCAGCAGGTCCGATCGAA 59.614 55.000 18.66 0.0 0.00 3.71 F
1616 2291 1.002430 GTGGTGATTGCTGTCTCTCCA 59.998 52.381 0.00 0.0 33.78 3.86 F
2428 3334 1.067142 GTGGTCACATCGTCAGCCTTA 60.067 52.381 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 2236 0.456221 TCTCTTTCGATCGGACCTGC 59.544 55.000 16.41 0.00 0.00 4.85 R
2597 3506 1.301677 GAGCCGCATAGCTATTGGCC 61.302 60.000 30.12 21.84 46.92 5.36 R
3356 4316 0.250858 TGCCATATGCCTTCCGATGG 60.251 55.000 0.00 0.00 41.58 3.51 R
3485 4445 1.361204 TCTGTTCCATGGCCTTCAGA 58.639 50.000 6.96 14.09 0.00 3.27 R
3515 4475 1.745864 CTCCTTGCAGCAGCTGGAG 60.746 63.158 24.13 21.64 46.78 3.86 R
4336 5310 0.033504 GTCGTGGTCCAAAGCTCTCA 59.966 55.000 0.00 0.00 0.00 3.27 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
237 249 4.218578 CGGCGAGGCTGCAGATCT 62.219 66.667 20.43 13.99 36.28 2.75
348 361 2.268920 GGAGCTCGACATTGGCCA 59.731 61.111 0.00 0.00 0.00 5.36
391 405 3.894947 GAGGAGAGGACGGAGCGC 61.895 72.222 0.00 0.00 0.00 5.92
413 427 4.085733 CGAGAGGAGAATGGGTGAGATAT 58.914 47.826 0.00 0.00 0.00 1.63
421 435 6.078456 AGAATGGGTGAGATATGGTTTTGA 57.922 37.500 0.00 0.00 0.00 2.69
423 437 7.128077 AGAATGGGTGAGATATGGTTTTGAAT 58.872 34.615 0.00 0.00 0.00 2.57
434 448 1.886542 GGTTTTGAATCAACGAGGCCT 59.113 47.619 3.86 3.86 0.00 5.19
444 460 0.255033 AACGAGGCCTATGGGGTTTC 59.745 55.000 4.42 0.00 37.43 2.78
471 488 1.451927 CATCCATGGGTCGGTGGTG 60.452 63.158 13.02 0.00 36.84 4.17
519 537 3.889692 CATGCCCGGGCCACCTAT 61.890 66.667 41.75 25.74 41.09 2.57
520 538 2.122144 ATGCCCGGGCCACCTATA 60.122 61.111 41.75 22.88 41.09 1.31
521 539 1.541368 ATGCCCGGGCCACCTATAT 60.541 57.895 41.75 24.17 41.09 0.86
522 540 1.562672 ATGCCCGGGCCACCTATATC 61.563 60.000 41.75 11.96 41.09 1.63
524 542 2.656069 CCCGGGCCACCTATATCCG 61.656 68.421 8.08 0.00 40.32 4.18
525 543 2.264794 CGGGCCACCTATATCCGC 59.735 66.667 4.39 0.00 34.17 5.54
526 544 2.669240 GGGCCACCTATATCCGCC 59.331 66.667 4.39 0.00 38.96 6.13
527 545 1.918800 GGGCCACCTATATCCGCCT 60.919 63.158 4.39 0.00 39.64 5.52
528 546 1.597461 GGCCACCTATATCCGCCTC 59.403 63.158 0.00 0.00 36.65 4.70
529 547 1.192146 GGCCACCTATATCCGCCTCA 61.192 60.000 0.00 0.00 36.65 3.86
530 548 0.905357 GCCACCTATATCCGCCTCAT 59.095 55.000 0.00 0.00 0.00 2.90
531 549 2.108168 GCCACCTATATCCGCCTCATA 58.892 52.381 0.00 0.00 0.00 2.15
532 550 2.700897 GCCACCTATATCCGCCTCATAT 59.299 50.000 0.00 0.00 0.00 1.78
533 551 3.134804 GCCACCTATATCCGCCTCATATT 59.865 47.826 0.00 0.00 0.00 1.28
534 552 4.384208 GCCACCTATATCCGCCTCATATTT 60.384 45.833 0.00 0.00 0.00 1.40
535 553 5.163343 GCCACCTATATCCGCCTCATATTTA 60.163 44.000 0.00 0.00 0.00 1.40
536 554 6.516718 CCACCTATATCCGCCTCATATTTAG 58.483 44.000 0.00 0.00 0.00 1.85
537 555 6.463049 CCACCTATATCCGCCTCATATTTAGG 60.463 46.154 0.00 0.00 37.17 2.69
538 556 6.098409 CACCTATATCCGCCTCATATTTAGGT 59.902 42.308 0.00 0.00 37.76 3.08
539 557 6.672657 ACCTATATCCGCCTCATATTTAGGTT 59.327 38.462 0.00 0.00 35.36 3.50
540 558 6.986817 CCTATATCCGCCTCATATTTAGGTTG 59.013 42.308 3.39 0.00 36.43 3.77
541 559 4.974645 ATCCGCCTCATATTTAGGTTGA 57.025 40.909 3.39 1.56 36.43 3.18
542 560 4.764050 TCCGCCTCATATTTAGGTTGAA 57.236 40.909 3.39 0.00 36.43 2.69
543 561 5.304686 TCCGCCTCATATTTAGGTTGAAT 57.695 39.130 3.39 0.00 36.43 2.57
544 562 6.428083 TCCGCCTCATATTTAGGTTGAATA 57.572 37.500 3.39 0.00 36.43 1.75
545 563 7.016153 TCCGCCTCATATTTAGGTTGAATAT 57.984 36.000 3.39 0.00 36.43 1.28
546 564 8.141298 TCCGCCTCATATTTAGGTTGAATATA 57.859 34.615 3.39 0.00 36.43 0.86
547 565 8.598916 TCCGCCTCATATTTAGGTTGAATATAA 58.401 33.333 3.39 0.00 36.43 0.98
548 566 9.226606 CCGCCTCATATTTAGGTTGAATATAAA 57.773 33.333 3.39 0.00 36.43 1.40
566 584 2.107950 AAAAATGCCGGTCAGATCGA 57.892 45.000 4.08 0.00 0.00 3.59
567 585 2.107950 AAAATGCCGGTCAGATCGAA 57.892 45.000 4.08 0.00 0.00 3.71
568 586 1.369625 AAATGCCGGTCAGATCGAAC 58.630 50.000 4.08 0.00 0.00 3.95
569 587 0.249120 AATGCCGGTCAGATCGAACA 59.751 50.000 4.08 2.72 0.00 3.18
570 588 0.465705 ATGCCGGTCAGATCGAACAT 59.534 50.000 4.08 5.20 0.00 2.71
571 589 0.249120 TGCCGGTCAGATCGAACATT 59.751 50.000 4.08 0.00 0.00 2.71
572 590 1.338674 TGCCGGTCAGATCGAACATTT 60.339 47.619 4.08 0.00 0.00 2.32
573 591 1.062587 GCCGGTCAGATCGAACATTTG 59.937 52.381 4.08 0.00 0.00 2.32
574 592 2.616960 CCGGTCAGATCGAACATTTGA 58.383 47.619 4.08 0.00 0.00 2.69
575 593 2.604914 CCGGTCAGATCGAACATTTGAG 59.395 50.000 4.08 0.00 0.00 3.02
576 594 3.511699 CGGTCAGATCGAACATTTGAGA 58.488 45.455 0.00 0.00 0.00 3.27
577 595 3.304559 CGGTCAGATCGAACATTTGAGAC 59.695 47.826 0.00 0.00 0.00 3.36
578 596 4.499183 GGTCAGATCGAACATTTGAGACT 58.501 43.478 0.00 0.00 0.00 3.24
579 597 4.932200 GGTCAGATCGAACATTTGAGACTT 59.068 41.667 0.00 0.00 0.00 3.01
580 598 5.163913 GGTCAGATCGAACATTTGAGACTTG 60.164 44.000 0.00 0.00 0.00 3.16
581 599 5.406780 GTCAGATCGAACATTTGAGACTTGT 59.593 40.000 0.00 0.00 0.00 3.16
582 600 5.991606 TCAGATCGAACATTTGAGACTTGTT 59.008 36.000 0.00 0.00 36.34 2.83
583 601 6.483307 TCAGATCGAACATTTGAGACTTGTTT 59.517 34.615 0.00 0.00 33.92 2.83
584 602 7.655732 TCAGATCGAACATTTGAGACTTGTTTA 59.344 33.333 0.00 0.00 33.92 2.01
585 603 8.282592 CAGATCGAACATTTGAGACTTGTTTAA 58.717 33.333 0.00 0.00 33.92 1.52
586 604 8.499162 AGATCGAACATTTGAGACTTGTTTAAG 58.501 33.333 0.00 0.00 39.86 1.85
587 605 7.780008 TCGAACATTTGAGACTTGTTTAAGA 57.220 32.000 0.00 0.00 37.36 2.10
588 606 7.627340 TCGAACATTTGAGACTTGTTTAAGAC 58.373 34.615 0.00 0.00 37.36 3.01
589 607 6.570058 CGAACATTTGAGACTTGTTTAAGACG 59.430 38.462 0.00 0.00 37.36 4.18
590 608 6.920569 ACATTTGAGACTTGTTTAAGACGT 57.079 33.333 0.00 0.00 37.36 4.34
591 609 6.945072 ACATTTGAGACTTGTTTAAGACGTC 58.055 36.000 7.70 7.70 37.36 4.34
592 610 5.978934 TTTGAGACTTGTTTAAGACGTCC 57.021 39.130 13.01 0.00 37.36 4.79
593 611 3.635331 TGAGACTTGTTTAAGACGTCCG 58.365 45.455 13.01 0.00 37.36 4.79
594 612 3.067180 TGAGACTTGTTTAAGACGTCCGT 59.933 43.478 13.01 2.93 37.36 4.69
595 613 4.047142 GAGACTTGTTTAAGACGTCCGTT 58.953 43.478 13.01 3.36 37.36 4.44
596 614 4.436332 AGACTTGTTTAAGACGTCCGTTT 58.564 39.130 13.01 2.56 37.36 3.60
597 615 4.269363 AGACTTGTTTAAGACGTCCGTTTG 59.731 41.667 13.01 0.00 37.36 2.93
598 616 4.183101 ACTTGTTTAAGACGTCCGTTTGA 58.817 39.130 13.01 0.00 37.36 2.69
599 617 4.269363 ACTTGTTTAAGACGTCCGTTTGAG 59.731 41.667 13.01 5.44 37.36 3.02
600 618 4.044336 TGTTTAAGACGTCCGTTTGAGA 57.956 40.909 13.01 0.00 0.00 3.27
601 619 4.624015 TGTTTAAGACGTCCGTTTGAGAT 58.376 39.130 13.01 0.00 0.00 2.75
602 620 5.051816 TGTTTAAGACGTCCGTTTGAGATT 58.948 37.500 13.01 0.00 0.00 2.40
603 621 5.050634 TGTTTAAGACGTCCGTTTGAGATTG 60.051 40.000 13.01 0.00 0.00 2.67
604 622 3.380479 AAGACGTCCGTTTGAGATTGA 57.620 42.857 13.01 0.00 0.00 2.57
605 623 3.380479 AGACGTCCGTTTGAGATTGAA 57.620 42.857 13.01 0.00 0.00 2.69
606 624 3.724374 AGACGTCCGTTTGAGATTGAAA 58.276 40.909 13.01 0.00 0.00 2.69
607 625 4.124238 AGACGTCCGTTTGAGATTGAAAA 58.876 39.130 13.01 0.00 0.00 2.29
608 626 4.573201 AGACGTCCGTTTGAGATTGAAAAA 59.427 37.500 13.01 0.00 0.00 1.94
624 642 1.292992 AAAAACGTGACTGGACGACC 58.707 50.000 8.25 0.00 42.10 4.79
625 643 0.531311 AAAACGTGACTGGACGACCC 60.531 55.000 0.34 0.00 42.10 4.46
626 644 2.688526 AAACGTGACTGGACGACCCG 62.689 60.000 0.34 0.00 42.10 5.28
627 645 3.667282 CGTGACTGGACGACCCGT 61.667 66.667 0.00 0.00 45.10 5.28
636 654 4.001248 ACGACCCGTCCGAATGTA 57.999 55.556 0.00 0.00 33.69 2.29
637 655 1.805254 ACGACCCGTCCGAATGTAG 59.195 57.895 0.00 0.00 33.69 2.74
638 656 1.065273 CGACCCGTCCGAATGTAGG 59.935 63.158 0.00 0.00 0.00 3.18
639 657 1.378882 CGACCCGTCCGAATGTAGGA 61.379 60.000 0.00 0.00 34.99 2.94
640 658 0.384669 GACCCGTCCGAATGTAGGAG 59.615 60.000 0.00 0.00 38.65 3.69
641 659 0.033796 ACCCGTCCGAATGTAGGAGA 60.034 55.000 0.00 0.00 38.65 3.71
642 660 0.384669 CCCGTCCGAATGTAGGAGAC 59.615 60.000 0.00 0.00 38.65 3.36
643 661 1.100510 CCGTCCGAATGTAGGAGACA 58.899 55.000 0.00 0.00 43.97 3.41
644 662 1.065701 CCGTCCGAATGTAGGAGACAG 59.934 57.143 0.00 0.00 42.79 3.51
645 663 2.014857 CGTCCGAATGTAGGAGACAGA 58.985 52.381 0.00 0.00 42.79 3.41
646 664 2.619177 CGTCCGAATGTAGGAGACAGAT 59.381 50.000 0.00 0.00 42.79 2.90
647 665 3.066900 CGTCCGAATGTAGGAGACAGATT 59.933 47.826 0.00 0.00 42.79 2.40
648 666 4.440250 CGTCCGAATGTAGGAGACAGATTT 60.440 45.833 0.00 0.00 42.79 2.17
649 667 4.806247 GTCCGAATGTAGGAGACAGATTTG 59.194 45.833 0.00 0.00 42.79 2.32
650 668 4.709886 TCCGAATGTAGGAGACAGATTTGA 59.290 41.667 0.00 0.00 42.79 2.69
651 669 5.046529 CCGAATGTAGGAGACAGATTTGAG 58.953 45.833 0.00 0.00 42.79 3.02
652 670 4.505922 CGAATGTAGGAGACAGATTTGAGC 59.494 45.833 0.00 0.00 42.79 4.26
653 671 3.510388 TGTAGGAGACAGATTTGAGCG 57.490 47.619 0.00 0.00 32.86 5.03
654 672 2.166459 TGTAGGAGACAGATTTGAGCGG 59.834 50.000 0.00 0.00 32.86 5.52
655 673 1.270907 AGGAGACAGATTTGAGCGGT 58.729 50.000 0.00 0.00 0.00 5.68
656 674 1.066573 AGGAGACAGATTTGAGCGGTG 60.067 52.381 0.00 0.00 0.00 4.94
657 675 1.066858 GGAGACAGATTTGAGCGGTGA 60.067 52.381 0.00 0.00 0.00 4.02
666 684 0.821711 TTGAGCGGTGACCCCAAAAG 60.822 55.000 0.00 0.00 0.00 2.27
667 685 1.072505 GAGCGGTGACCCCAAAAGA 59.927 57.895 0.00 0.00 0.00 2.52
723 741 4.524318 ATCGTACCCGCCGGCTTG 62.524 66.667 26.68 17.71 0.00 4.01
735 753 1.144936 CGGCTTGATCACTCCCCTC 59.855 63.158 0.00 0.00 0.00 4.30
759 777 3.580904 TCCAAAACAGGACGAGTCG 57.419 52.632 11.85 11.85 31.23 4.18
778 802 1.153881 GAGTACGACAACCGCCTCC 60.154 63.158 0.00 0.00 43.32 4.30
811 1069 0.683179 CCCCCGTCTGAATTTTCCCC 60.683 60.000 0.00 0.00 0.00 4.81
812 1070 1.029947 CCCCGTCTGAATTTTCCCCG 61.030 60.000 0.00 0.00 0.00 5.73
813 1071 1.029947 CCCGTCTGAATTTTCCCCGG 61.030 60.000 0.00 0.00 33.35 5.73
814 1072 1.029947 CCGTCTGAATTTTCCCCGGG 61.030 60.000 15.80 15.80 31.36 5.73
815 1073 1.654023 CGTCTGAATTTTCCCCGGGC 61.654 60.000 17.73 0.00 0.00 6.13
816 1074 1.377987 TCTGAATTTTCCCCGGGCG 60.378 57.895 17.73 9.08 0.00 6.13
817 1075 1.677633 CTGAATTTTCCCCGGGCGT 60.678 57.895 17.73 0.00 0.00 5.68
818 1076 1.654023 CTGAATTTTCCCCGGGCGTC 61.654 60.000 17.73 5.66 0.00 5.19
819 1077 2.361992 AATTTTCCCCGGGCGTCC 60.362 61.111 17.73 0.00 0.00 4.79
940 1213 0.393537 CAGCCTGTCATCCACTTCCC 60.394 60.000 0.00 0.00 0.00 3.97
943 1216 1.680249 GCCTGTCATCCACTTCCCTTC 60.680 57.143 0.00 0.00 0.00 3.46
1072 1710 1.068121 GATCCGATCCCCAAATCCCT 58.932 55.000 0.00 0.00 0.00 4.20
1073 1711 1.003696 GATCCGATCCCCAAATCCCTC 59.996 57.143 0.00 0.00 0.00 4.30
1074 1712 0.030092 TCCGATCCCCAAATCCCTCT 60.030 55.000 0.00 0.00 0.00 3.69
1357 2032 4.314440 TCGCACCGCCTCAAGCTT 62.314 61.111 0.00 0.00 40.39 3.74
1393 2068 9.178427 CATCGTTTTAGTAGTAGTAGTATTGGC 57.822 37.037 0.00 0.00 0.00 4.52
1456 2131 0.801067 CACGACCTTCGGTTCGATCC 60.801 60.000 2.15 2.15 45.59 3.36
1485 2160 0.179097 GCTCGTCCTGAGGATTGTCC 60.179 60.000 3.65 0.00 45.38 4.02
1519 2194 1.484240 AGGTGCTACATCTCTGCCTTC 59.516 52.381 0.00 0.00 0.00 3.46
1548 2223 1.381165 GCGGGTTTGGTGTCTGTGTT 61.381 55.000 0.00 0.00 0.00 3.32
1549 2224 0.661020 CGGGTTTGGTGTCTGTGTTC 59.339 55.000 0.00 0.00 0.00 3.18
1551 2226 1.658994 GGTTTGGTGTCTGTGTTCGA 58.341 50.000 0.00 0.00 0.00 3.71
1552 2227 2.218603 GGTTTGGTGTCTGTGTTCGAT 58.781 47.619 0.00 0.00 0.00 3.59
1573 2248 4.643733 GATCAGCAGGTCCGATCG 57.356 61.111 8.51 8.51 0.00 3.69
1575 2250 0.385751 GATCAGCAGGTCCGATCGAA 59.614 55.000 18.66 0.00 0.00 3.71
1616 2291 1.002430 GTGGTGATTGCTGTCTCTCCA 59.998 52.381 0.00 0.00 33.78 3.86
1815 2650 5.312895 TGGAGTGAATGCTTTAGTTGCTTA 58.687 37.500 0.00 0.00 0.00 3.09
1832 2667 8.943909 AGTTGCTTAATAAAATACTACTCGCT 57.056 30.769 0.00 0.00 0.00 4.93
1855 2697 6.088616 GCTTGATCCATATTAATTTTCGCTGC 59.911 38.462 0.00 0.00 0.00 5.25
1862 2704 9.332502 TCCATATTAATTTTCGCTGCTTTAGTA 57.667 29.630 0.00 0.00 0.00 1.82
1869 2711 5.682943 TTTCGCTGCTTTAGTACAACAAT 57.317 34.783 0.00 0.00 0.00 2.71
1905 2810 4.469657 ACCTACTTTGCCAGAAATGTTGA 58.530 39.130 0.00 0.00 0.00 3.18
1958 2863 8.331022 GCAATATATGTGCACCTATTTCTATCG 58.669 37.037 18.11 6.27 41.80 2.92
1964 2869 4.929808 GTGCACCTATTTCTATCGTATGGG 59.070 45.833 5.22 0.00 0.00 4.00
1968 2873 5.869888 CACCTATTTCTATCGTATGGGCTTC 59.130 44.000 0.00 0.00 0.00 3.86
1976 2881 6.746120 TCTATCGTATGGGCTTCTTAACTTC 58.254 40.000 0.00 0.00 0.00 3.01
2014 2920 4.445879 GGTGTGGTCCTTAAGAAGTCCTTT 60.446 45.833 3.36 0.00 36.34 3.11
2119 3025 1.160137 CTTTGGTAGACTGCAGTGCC 58.840 55.000 27.27 22.25 0.00 5.01
2214 3120 5.350091 GTGCTCTACCTGAAGATGAAAAGTC 59.650 44.000 0.00 0.00 0.00 3.01
2407 3313 7.381766 TGATTTGGTTGATATTGACACTGAG 57.618 36.000 0.00 0.00 0.00 3.35
2428 3334 1.067142 GTGGTCACATCGTCAGCCTTA 60.067 52.381 0.00 0.00 0.00 2.69
2447 3353 1.895020 AACTGCCGGGAATGCGTCTA 61.895 55.000 2.18 0.00 0.00 2.59
2472 3378 8.591114 AAATCATCAACTGGAAATTCAGAGAT 57.409 30.769 1.40 2.39 38.11 2.75
2549 3455 8.855110 TCTTCCTAATCTGTCTTATCTTGCTAG 58.145 37.037 0.00 0.00 0.00 3.42
2550 3456 6.987386 TCCTAATCTGTCTTATCTTGCTAGC 58.013 40.000 8.10 8.10 0.00 3.42
2551 3457 6.015010 TCCTAATCTGTCTTATCTTGCTAGCC 60.015 42.308 13.29 0.00 0.00 3.93
2552 3458 5.620738 AATCTGTCTTATCTTGCTAGCCA 57.379 39.130 13.29 0.00 0.00 4.75
2553 3459 5.620738 ATCTGTCTTATCTTGCTAGCCAA 57.379 39.130 13.29 5.87 0.00 4.52
2554 3460 5.420725 TCTGTCTTATCTTGCTAGCCAAA 57.579 39.130 13.29 0.00 31.94 3.28
2555 3461 5.423015 TCTGTCTTATCTTGCTAGCCAAAG 58.577 41.667 13.29 10.35 31.94 2.77
2556 3462 3.941483 TGTCTTATCTTGCTAGCCAAAGC 59.059 43.478 13.29 5.90 43.08 3.51
2558 3464 2.691409 TATCTTGCTAGCCAAAGCGT 57.309 45.000 13.29 5.24 45.85 5.07
2559 3465 1.826385 ATCTTGCTAGCCAAAGCGTT 58.174 45.000 13.29 0.00 45.85 4.84
2561 3467 1.535462 TCTTGCTAGCCAAAGCGTTTC 59.465 47.619 13.29 0.00 45.85 2.78
2564 3473 1.535462 TGCTAGCCAAAGCGTTTCTTC 59.465 47.619 13.29 0.00 45.85 2.87
2569 3478 2.033424 AGCCAAAGCGTTTCTTCTTGTC 59.967 45.455 0.00 0.00 46.67 3.18
2576 3485 5.757850 AGCGTTTCTTCTTGTCATCTTTT 57.242 34.783 0.00 0.00 0.00 2.27
2578 3487 5.973565 AGCGTTTCTTCTTGTCATCTTTTTG 59.026 36.000 0.00 0.00 0.00 2.44
2585 3494 7.102346 TCTTCTTGTCATCTTTTTGCCAAAAA 58.898 30.769 14.19 14.19 37.99 1.94
2617 3526 1.301677 GCCAATAGCTATGCGGCTCC 61.302 60.000 28.33 10.04 42.97 4.70
2635 3544 5.009010 CGGCTCCTCATATAAAAATGTGCTT 59.991 40.000 0.00 0.00 0.00 3.91
2766 3678 4.154375 GCTGCTCCTTTTTCTACCTGTTAC 59.846 45.833 0.00 0.00 0.00 2.50
2820 3732 9.988350 GTAAATTGATTGTGTTGATACGATCTT 57.012 29.630 8.85 0.00 40.57 2.40
2851 3767 6.825944 TCGATATTTGTTTGAATTGACCCA 57.174 33.333 0.00 0.00 0.00 4.51
2863 3779 6.028146 TGAATTGACCCAAGAATGATGTTG 57.972 37.500 0.00 0.00 0.00 3.33
2864 3780 5.539574 TGAATTGACCCAAGAATGATGTTGT 59.460 36.000 0.00 0.00 0.00 3.32
2865 3781 6.041865 TGAATTGACCCAAGAATGATGTTGTT 59.958 34.615 0.00 0.00 0.00 2.83
2866 3782 7.232330 TGAATTGACCCAAGAATGATGTTGTTA 59.768 33.333 0.00 0.00 0.00 2.41
2867 3783 7.722949 ATTGACCCAAGAATGATGTTGTTAT 57.277 32.000 0.00 0.00 0.00 1.89
2950 3867 8.102676 TCTGAATTCTGAAAATGAGTATGACCA 58.897 33.333 12.17 0.00 0.00 4.02
2954 3871 9.685276 AATTCTGAAAATGAGTATGACCACATA 57.315 29.630 0.00 0.00 37.87 2.29
2983 3922 8.690840 GTTATTGCTTGTGTTAAATGTTCTGTC 58.309 33.333 0.00 0.00 0.00 3.51
3008 3955 6.316390 CCTCTACTTGGATGGTGATTTGTAAC 59.684 42.308 0.00 0.00 0.00 2.50
3476 4436 2.685999 GAAGAAGCCATGCCCCCT 59.314 61.111 0.00 0.00 0.00 4.79
3485 4445 1.691219 CATGCCCCCTGTACCTGTT 59.309 57.895 0.00 0.00 0.00 3.16
3739 4699 1.468520 GCGCTTCTGGTTATCAGCAAA 59.531 47.619 0.00 0.00 43.06 3.68
3761 4721 3.642848 AGCTTTCATGTTGGATGGTGTTT 59.357 39.130 0.00 0.00 0.00 2.83
3768 4728 4.852134 TGTTGGATGGTGTTTTGATCTG 57.148 40.909 0.00 0.00 0.00 2.90
3846 4807 4.742438 TGCACGACCTTGAGATTTTAAC 57.258 40.909 0.00 0.00 0.00 2.01
3941 4903 7.967854 TGTGTGTAATTTCTGTAATAAGCATGC 59.032 33.333 10.51 10.51 0.00 4.06
4015 4977 0.924823 AGCTGATTCCTTCATGCCCT 59.075 50.000 0.00 0.00 32.72 5.19
4018 4980 0.332293 TGATTCCTTCATGCCCTGCA 59.668 50.000 0.00 0.00 44.86 4.41
4062 5024 7.215085 TCATGGATCAGATAATGACTGAAGTG 58.785 38.462 0.00 0.00 45.44 3.16
4085 5047 5.428457 TGAAGTAACACATGGAGGGATGTAT 59.572 40.000 0.00 0.00 34.69 2.29
4086 5048 5.296151 AGTAACACATGGAGGGATGTATG 57.704 43.478 0.00 0.00 34.69 2.39
4087 5049 4.721776 AGTAACACATGGAGGGATGTATGT 59.278 41.667 0.00 0.00 34.69 2.29
4089 5051 5.708736 AACACATGGAGGGATGTATGTAA 57.291 39.130 0.00 0.00 34.69 2.41
4090 5052 5.036117 ACACATGGAGGGATGTATGTAAC 57.964 43.478 0.00 0.00 34.69 2.50
4091 5053 4.141482 ACACATGGAGGGATGTATGTAACC 60.141 45.833 0.00 0.00 34.69 2.85
4092 5054 3.394606 ACATGGAGGGATGTATGTAACCC 59.605 47.826 0.00 0.00 42.36 4.11
4224 5198 1.339610 CATCTCTGACCGTCTCCATCC 59.660 57.143 0.00 0.00 0.00 3.51
4225 5199 0.331616 TCTCTGACCGTCTCCATCCA 59.668 55.000 0.00 0.00 0.00 3.41
4226 5200 0.457851 CTCTGACCGTCTCCATCCAC 59.542 60.000 0.00 0.00 0.00 4.02
4227 5201 0.251608 TCTGACCGTCTCCATCCACA 60.252 55.000 0.00 0.00 0.00 4.17
4228 5202 0.826715 CTGACCGTCTCCATCCACAT 59.173 55.000 0.00 0.00 0.00 3.21
4229 5203 0.536724 TGACCGTCTCCATCCACATG 59.463 55.000 0.00 0.00 0.00 3.21
4230 5204 0.824109 GACCGTCTCCATCCACATGA 59.176 55.000 0.00 0.00 30.57 3.07
4231 5205 0.826715 ACCGTCTCCATCCACATGAG 59.173 55.000 0.00 0.00 30.57 2.90
4232 5206 1.114627 CCGTCTCCATCCACATGAGA 58.885 55.000 0.00 0.00 30.57 3.27
4233 5207 1.482182 CCGTCTCCATCCACATGAGAA 59.518 52.381 0.00 0.00 30.57 2.87
4234 5208 2.482664 CCGTCTCCATCCACATGAGAAG 60.483 54.545 0.00 0.00 30.57 2.85
4235 5209 2.559440 GTCTCCATCCACATGAGAAGC 58.441 52.381 0.00 0.00 30.57 3.86
4236 5210 2.170187 GTCTCCATCCACATGAGAAGCT 59.830 50.000 0.00 0.00 30.57 3.74
4237 5211 2.433604 TCTCCATCCACATGAGAAGCTC 59.566 50.000 0.00 0.00 30.57 4.09
4238 5212 2.169978 CTCCATCCACATGAGAAGCTCA 59.830 50.000 0.00 0.00 44.99 4.26
4239 5213 2.573009 TCCATCCACATGAGAAGCTCAA 59.427 45.455 0.00 0.00 44.04 3.02
4240 5214 3.201487 TCCATCCACATGAGAAGCTCAAT 59.799 43.478 0.00 0.00 44.04 2.57
4241 5215 3.564644 CCATCCACATGAGAAGCTCAATC 59.435 47.826 0.00 0.00 44.04 2.67
4242 5216 2.897436 TCCACATGAGAAGCTCAATCG 58.103 47.619 0.00 0.00 44.04 3.34
4243 5217 2.234661 TCCACATGAGAAGCTCAATCGT 59.765 45.455 0.00 0.00 44.04 3.73
4244 5218 2.350804 CCACATGAGAAGCTCAATCGTG 59.649 50.000 0.00 11.45 44.04 4.35
4245 5219 2.005451 ACATGAGAAGCTCAATCGTGC 58.995 47.619 0.00 0.00 44.04 5.34
4246 5220 1.329906 CATGAGAAGCTCAATCGTGCC 59.670 52.381 0.78 0.00 44.04 5.01
4251 5225 0.391661 AAGCTCAATCGTGCCGACAT 60.392 50.000 0.00 0.00 39.18 3.06
4277 5251 0.443869 CTCAATCGTGCCGTCAAAGG 59.556 55.000 0.00 0.00 0.00 3.11
4300 5274 6.938596 AGGCAAGTAATAAGGTTACGAACTTT 59.061 34.615 0.00 0.00 34.81 2.66
4301 5275 7.446319 AGGCAAGTAATAAGGTTACGAACTTTT 59.554 33.333 0.00 0.00 32.56 2.27
4402 5389 2.046938 ACACGACATGTTCCTCGGT 58.953 52.632 0.00 0.00 38.98 4.69
4455 5445 4.484872 GCCGACCTTGGGTAGCCC 62.485 72.222 8.85 0.62 45.71 5.19
4496 5486 0.826256 GTGTTGGACCTTTGGGACCC 60.826 60.000 2.45 2.45 44.83 4.46
4578 5575 1.215173 CCCCTGAAGTGGCCATATTGA 59.785 52.381 9.72 0.00 0.00 2.57
4642 5639 4.201657 TGTGCATCCAATGATAGTTCCAG 58.798 43.478 0.00 0.00 0.00 3.86
4733 5732 0.245266 CAAGCCATGACAGCAATGCA 59.755 50.000 8.35 0.00 0.00 3.96
4741 5740 1.580845 GACAGCAATGCAGTCGCCTT 61.581 55.000 14.67 0.00 35.58 4.35
4742 5741 1.136147 CAGCAATGCAGTCGCCTTC 59.864 57.895 8.35 0.00 37.32 3.46
4743 5742 1.002868 AGCAATGCAGTCGCCTTCT 60.003 52.632 8.35 0.00 37.32 2.85
4744 5743 1.023513 AGCAATGCAGTCGCCTTCTC 61.024 55.000 8.35 0.00 37.32 2.87
4750 5749 0.100503 GCAGTCGCCTTCTCTCTCTC 59.899 60.000 0.00 0.00 0.00 3.20
4772 5771 7.313646 TCTCTCTCTTTTAGGTTGATACAACG 58.686 38.462 8.22 0.00 0.00 4.10
4837 5836 0.829333 AGGCACTAGCACTGGAGATG 59.171 55.000 0.00 0.00 44.61 2.90
4846 5845 0.244721 CACTGGAGATGCAGACGACA 59.755 55.000 8.45 0.00 0.00 4.35
4869 5868 1.464608 ACGCAACATCGAATTCTGGTG 59.535 47.619 8.08 8.08 33.13 4.17
4876 5875 4.753233 ACATCGAATTCTGGTGAGAAGAG 58.247 43.478 14.64 0.00 41.62 2.85
4893 5892 3.877951 AGGAGTACCTCGACGATGT 57.122 52.632 10.63 10.63 44.13 3.06
4894 5893 2.996249 AGGAGTACCTCGACGATGTA 57.004 50.000 8.66 8.66 44.13 2.29
4898 5897 4.643784 AGGAGTACCTCGACGATGTAAAAT 59.356 41.667 13.53 4.59 44.13 1.82
4900 5899 6.489361 AGGAGTACCTCGACGATGTAAAATAT 59.511 38.462 13.53 0.37 44.13 1.28
4901 5900 6.581542 GGAGTACCTCGACGATGTAAAATATG 59.418 42.308 13.53 0.00 0.00 1.78
4902 5901 7.035840 AGTACCTCGACGATGTAAAATATGT 57.964 36.000 13.53 0.00 0.00 2.29
4906 5905 6.020121 ACCTCGACGATGTAAAATATGTTTCG 60.020 38.462 3.80 0.00 0.00 3.46
4926 5925 1.170442 GTAACATTGGAACCCCCGTG 58.830 55.000 0.00 0.00 37.93 4.94
4929 5928 1.291109 ACATTGGAACCCCCGTGATA 58.709 50.000 0.00 0.00 37.93 2.15
4934 5933 1.444250 GAACCCCCGTGATATGCGA 59.556 57.895 0.00 0.00 0.00 5.10
4936 5935 0.179056 AACCCCCGTGATATGCGAAG 60.179 55.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 114 4.835891 CCTCCCCTACGCCGTCCT 62.836 72.222 0.00 0.00 0.00 3.85
237 249 2.203877 ACACCGGGGGCAACTCTA 60.204 61.111 9.50 0.00 37.10 2.43
295 307 0.750911 ACGAGGTGGATCCGGAGTAC 60.751 60.000 11.34 8.64 41.99 2.73
391 405 1.769026 TCTCACCCATTCTCCTCTCG 58.231 55.000 0.00 0.00 0.00 4.04
413 427 1.611491 GGCCTCGTTGATTCAAAACCA 59.389 47.619 0.00 0.00 0.00 3.67
421 435 0.474184 CCCCATAGGCCTCGTTGATT 59.526 55.000 9.68 0.00 0.00 2.57
423 437 0.912487 AACCCCATAGGCCTCGTTGA 60.912 55.000 9.68 0.00 40.58 3.18
434 448 2.066592 TGTCCCACAAGAAACCCCATA 58.933 47.619 0.00 0.00 0.00 2.74
474 491 3.691342 TCCGTCTGACAAGCCCGG 61.691 66.667 8.73 0.00 38.36 5.73
517 535 7.727578 TCAACCTAAATATGAGGCGGATATA 57.272 36.000 4.19 0.00 37.63 0.86
518 536 6.620877 TCAACCTAAATATGAGGCGGATAT 57.379 37.500 4.19 0.00 37.63 1.63
519 537 6.428083 TTCAACCTAAATATGAGGCGGATA 57.572 37.500 4.19 0.00 37.63 2.59
520 538 4.974645 TCAACCTAAATATGAGGCGGAT 57.025 40.909 4.19 0.00 37.63 4.18
521 539 4.764050 TTCAACCTAAATATGAGGCGGA 57.236 40.909 4.19 0.52 37.63 5.54
522 540 8.786826 TTATATTCAACCTAAATATGAGGCGG 57.213 34.615 4.19 0.00 37.63 6.13
547 565 2.107950 TCGATCTGACCGGCATTTTT 57.892 45.000 0.00 0.00 0.00 1.94
548 566 1.737793 GTTCGATCTGACCGGCATTTT 59.262 47.619 0.00 0.00 0.00 1.82
549 567 1.338674 TGTTCGATCTGACCGGCATTT 60.339 47.619 0.00 0.00 0.00 2.32
550 568 0.249120 TGTTCGATCTGACCGGCATT 59.751 50.000 0.00 0.00 0.00 3.56
551 569 0.465705 ATGTTCGATCTGACCGGCAT 59.534 50.000 0.00 0.00 0.00 4.40
552 570 0.249120 AATGTTCGATCTGACCGGCA 59.751 50.000 0.00 0.00 0.00 5.69
553 571 1.062587 CAAATGTTCGATCTGACCGGC 59.937 52.381 0.00 0.00 0.00 6.13
554 572 2.604914 CTCAAATGTTCGATCTGACCGG 59.395 50.000 0.00 0.00 0.00 5.28
555 573 3.304559 GTCTCAAATGTTCGATCTGACCG 59.695 47.826 0.00 0.00 0.00 4.79
556 574 4.499183 AGTCTCAAATGTTCGATCTGACC 58.501 43.478 0.00 0.00 0.00 4.02
557 575 5.406780 ACAAGTCTCAAATGTTCGATCTGAC 59.593 40.000 0.00 0.00 0.00 3.51
558 576 5.541845 ACAAGTCTCAAATGTTCGATCTGA 58.458 37.500 0.00 0.00 0.00 3.27
559 577 5.852738 ACAAGTCTCAAATGTTCGATCTG 57.147 39.130 0.00 0.00 0.00 2.90
560 578 6.867662 AAACAAGTCTCAAATGTTCGATCT 57.132 33.333 0.00 0.00 36.33 2.75
561 579 8.495949 TCTTAAACAAGTCTCAAATGTTCGATC 58.504 33.333 0.00 0.00 36.33 3.69
562 580 8.283291 GTCTTAAACAAGTCTCAAATGTTCGAT 58.717 33.333 0.00 0.00 36.33 3.59
563 581 7.516155 CGTCTTAAACAAGTCTCAAATGTTCGA 60.516 37.037 0.00 0.00 36.33 3.71
564 582 6.570058 CGTCTTAAACAAGTCTCAAATGTTCG 59.430 38.462 0.00 0.00 36.33 3.95
565 583 7.407337 ACGTCTTAAACAAGTCTCAAATGTTC 58.593 34.615 0.00 0.00 36.33 3.18
566 584 7.316544 ACGTCTTAAACAAGTCTCAAATGTT 57.683 32.000 0.00 0.00 38.85 2.71
567 585 6.018180 GGACGTCTTAAACAAGTCTCAAATGT 60.018 38.462 16.46 0.00 32.86 2.71
568 586 6.363473 GGACGTCTTAAACAAGTCTCAAATG 58.637 40.000 16.46 0.00 32.86 2.32
569 587 5.176958 CGGACGTCTTAAACAAGTCTCAAAT 59.823 40.000 16.46 0.00 32.86 2.32
570 588 4.505191 CGGACGTCTTAAACAAGTCTCAAA 59.495 41.667 16.46 0.00 32.86 2.69
571 589 4.046462 CGGACGTCTTAAACAAGTCTCAA 58.954 43.478 16.46 0.00 32.86 3.02
572 590 3.067180 ACGGACGTCTTAAACAAGTCTCA 59.933 43.478 16.46 0.00 32.86 3.27
573 591 3.636381 ACGGACGTCTTAAACAAGTCTC 58.364 45.455 16.46 0.00 32.86 3.36
574 592 3.722728 ACGGACGTCTTAAACAAGTCT 57.277 42.857 16.46 0.00 32.86 3.24
575 593 4.268405 TCAAACGGACGTCTTAAACAAGTC 59.732 41.667 16.46 0.00 0.00 3.01
576 594 4.183101 TCAAACGGACGTCTTAAACAAGT 58.817 39.130 16.46 0.71 0.00 3.16
577 595 4.505191 TCTCAAACGGACGTCTTAAACAAG 59.495 41.667 16.46 5.83 0.00 3.16
578 596 4.431809 TCTCAAACGGACGTCTTAAACAA 58.568 39.130 16.46 0.00 0.00 2.83
579 597 4.044336 TCTCAAACGGACGTCTTAAACA 57.956 40.909 16.46 0.00 0.00 2.83
580 598 5.176223 TCAATCTCAAACGGACGTCTTAAAC 59.824 40.000 16.46 0.00 0.00 2.01
581 599 5.291178 TCAATCTCAAACGGACGTCTTAAA 58.709 37.500 16.46 0.00 0.00 1.52
582 600 4.873817 TCAATCTCAAACGGACGTCTTAA 58.126 39.130 16.46 0.00 0.00 1.85
583 601 4.508461 TCAATCTCAAACGGACGTCTTA 57.492 40.909 16.46 0.00 0.00 2.10
584 602 3.380479 TCAATCTCAAACGGACGTCTT 57.620 42.857 16.46 0.00 0.00 3.01
585 603 3.380479 TTCAATCTCAAACGGACGTCT 57.620 42.857 16.46 0.00 0.00 4.18
586 604 4.461992 TTTTCAATCTCAAACGGACGTC 57.538 40.909 7.13 7.13 0.00 4.34
587 605 4.886247 TTTTTCAATCTCAAACGGACGT 57.114 36.364 0.00 0.00 0.00 4.34
605 623 1.292992 GGTCGTCCAGTCACGTTTTT 58.707 50.000 0.00 0.00 40.79 1.94
606 624 0.531311 GGGTCGTCCAGTCACGTTTT 60.531 55.000 0.04 0.00 40.79 2.43
607 625 1.068585 GGGTCGTCCAGTCACGTTT 59.931 57.895 0.04 0.00 40.79 3.60
608 626 2.732658 GGGTCGTCCAGTCACGTT 59.267 61.111 0.04 0.00 40.79 3.99
609 627 3.667282 CGGGTCGTCCAGTCACGT 61.667 66.667 0.04 0.00 40.79 4.49
610 628 3.667282 ACGGGTCGTCCAGTCACG 61.667 66.667 0.04 0.00 37.59 4.35
619 637 1.660560 CCTACATTCGGACGGGTCGT 61.661 60.000 0.00 0.00 45.10 4.34
620 638 1.065273 CCTACATTCGGACGGGTCG 59.935 63.158 0.00 0.00 0.00 4.79
621 639 0.384669 CTCCTACATTCGGACGGGTC 59.615 60.000 0.00 0.00 0.00 4.46
622 640 0.033796 TCTCCTACATTCGGACGGGT 60.034 55.000 0.00 0.00 0.00 5.28
623 641 0.384669 GTCTCCTACATTCGGACGGG 59.615 60.000 0.00 0.00 0.00 5.28
624 642 1.065701 CTGTCTCCTACATTCGGACGG 59.934 57.143 0.00 0.00 37.50 4.79
625 643 2.014857 TCTGTCTCCTACATTCGGACG 58.985 52.381 0.00 0.00 37.50 4.79
626 644 4.657436 AATCTGTCTCCTACATTCGGAC 57.343 45.455 0.00 0.00 37.50 4.79
627 645 4.709886 TCAAATCTGTCTCCTACATTCGGA 59.290 41.667 0.00 0.00 37.50 4.55
628 646 5.011090 TCAAATCTGTCTCCTACATTCGG 57.989 43.478 0.00 0.00 37.50 4.30
629 647 4.505922 GCTCAAATCTGTCTCCTACATTCG 59.494 45.833 0.00 0.00 37.50 3.34
630 648 4.505922 CGCTCAAATCTGTCTCCTACATTC 59.494 45.833 0.00 0.00 37.50 2.67
631 649 4.437239 CGCTCAAATCTGTCTCCTACATT 58.563 43.478 0.00 0.00 37.50 2.71
632 650 3.181471 CCGCTCAAATCTGTCTCCTACAT 60.181 47.826 0.00 0.00 37.50 2.29
633 651 2.166459 CCGCTCAAATCTGTCTCCTACA 59.834 50.000 0.00 0.00 36.42 2.74
634 652 2.166664 ACCGCTCAAATCTGTCTCCTAC 59.833 50.000 0.00 0.00 0.00 3.18
635 653 2.166459 CACCGCTCAAATCTGTCTCCTA 59.834 50.000 0.00 0.00 0.00 2.94
636 654 1.066573 CACCGCTCAAATCTGTCTCCT 60.067 52.381 0.00 0.00 0.00 3.69
637 655 1.066858 TCACCGCTCAAATCTGTCTCC 60.067 52.381 0.00 0.00 0.00 3.71
638 656 1.996191 GTCACCGCTCAAATCTGTCTC 59.004 52.381 0.00 0.00 0.00 3.36
639 657 1.338200 GGTCACCGCTCAAATCTGTCT 60.338 52.381 0.00 0.00 0.00 3.41
640 658 1.079503 GGTCACCGCTCAAATCTGTC 58.920 55.000 0.00 0.00 0.00 3.51
641 659 0.321653 GGGTCACCGCTCAAATCTGT 60.322 55.000 0.00 0.00 0.00 3.41
642 660 1.026718 GGGGTCACCGCTCAAATCTG 61.027 60.000 2.93 0.00 37.78 2.90
643 661 1.299976 GGGGTCACCGCTCAAATCT 59.700 57.895 2.93 0.00 37.78 2.40
644 662 0.608035 TTGGGGTCACCGCTCAAATC 60.608 55.000 12.93 0.00 44.64 2.17
645 663 0.178975 TTTGGGGTCACCGCTCAAAT 60.179 50.000 12.93 0.00 44.64 2.32
646 664 0.395862 TTTTGGGGTCACCGCTCAAA 60.396 50.000 12.93 8.42 44.64 2.69
647 665 0.821711 CTTTTGGGGTCACCGCTCAA 60.822 55.000 12.93 2.21 44.64 3.02
648 666 1.228124 CTTTTGGGGTCACCGCTCA 60.228 57.895 12.93 0.00 44.64 4.26
649 667 0.955919 CTCTTTTGGGGTCACCGCTC 60.956 60.000 12.93 0.00 44.64 5.03
650 668 1.073199 CTCTTTTGGGGTCACCGCT 59.927 57.895 12.93 0.00 44.64 5.52
651 669 1.971695 CCTCTTTTGGGGTCACCGC 60.972 63.158 3.27 3.27 44.64 5.68
652 670 1.303317 CCCTCTTTTGGGGTCACCG 60.303 63.158 0.00 0.00 44.64 4.94
653 671 4.843624 CCCTCTTTTGGGGTCACC 57.156 61.111 0.00 0.00 43.45 4.02
666 684 0.464554 CGGGATCTTTTCCTGCCCTC 60.465 60.000 0.00 0.00 43.99 4.30
667 685 1.609783 CGGGATCTTTTCCTGCCCT 59.390 57.895 0.00 0.00 43.99 5.19
723 741 2.844839 CCGGGGAGGGGAGTGATC 60.845 72.222 0.00 0.00 35.97 2.92
735 753 2.840576 TCCTGTTTTGGACCGGGG 59.159 61.111 6.32 0.00 33.74 5.73
758 776 2.505557 GGCGGTTGTCGTACTCCG 60.506 66.667 0.00 0.00 44.86 4.63
759 777 1.153881 GAGGCGGTTGTCGTACTCC 60.154 63.158 0.00 0.00 41.72 3.85
931 1204 3.702048 CGGGCGAAGGGAAGTGGA 61.702 66.667 0.00 0.00 0.00 4.02
1039 1334 4.959596 GATCAGGGCGAGCGAGGC 62.960 72.222 0.00 0.00 0.00 4.70
1041 1336 4.637489 CGGATCAGGGCGAGCGAG 62.637 72.222 0.00 0.00 0.00 5.03
1043 1338 3.905705 GATCGGATCAGGGCGAGCG 62.906 68.421 13.02 0.00 0.00 5.03
1357 2032 2.232941 ACTAAAACGATGCGAGGAGGAA 59.767 45.455 0.00 0.00 0.00 3.36
1393 2068 4.207224 CGTCAGAGGCAATTACTACGATTG 59.793 45.833 0.00 0.00 37.51 2.67
1456 2131 2.811317 GGACGAGCACAAGGAGCG 60.811 66.667 0.00 0.00 37.01 5.03
1485 2160 1.079127 CACCTAGCCCTCACAACCG 60.079 63.158 0.00 0.00 0.00 4.44
1549 2224 1.212616 GGACCTGCTGATCGAAATCG 58.787 55.000 0.00 0.00 41.45 3.34
1551 2226 0.824109 TCGGACCTGCTGATCGAAAT 59.176 50.000 0.00 0.00 0.00 2.17
1552 2227 0.824109 ATCGGACCTGCTGATCGAAA 59.176 50.000 0.00 0.00 38.20 3.46
1561 2236 0.456221 TCTCTTTCGATCGGACCTGC 59.544 55.000 16.41 0.00 0.00 4.85
1573 2248 4.457257 CCTCCAACAGACCAAATCTCTTTC 59.543 45.833 0.00 0.00 34.41 2.62
1575 2250 3.395941 ACCTCCAACAGACCAAATCTCTT 59.604 43.478 0.00 0.00 34.41 2.85
1578 2253 2.224867 CCACCTCCAACAGACCAAATCT 60.225 50.000 0.00 0.00 38.66 2.40
1586 2261 1.545428 GCAATCACCACCTCCAACAGA 60.545 52.381 0.00 0.00 0.00 3.41
1616 2291 5.187772 GCAAATTTCCCATACCTCTTTCCTT 59.812 40.000 0.00 0.00 0.00 3.36
1719 2402 9.170734 AGAATCGTAATTCCATCATTGATATGG 57.829 33.333 0.00 0.00 41.97 2.74
1724 2407 7.630026 CGAAAGAATCGTAATTCCATCATTGA 58.370 34.615 0.00 0.00 46.52 2.57
1725 2408 7.827156 CGAAAGAATCGTAATTCCATCATTG 57.173 36.000 0.00 0.00 46.52 2.82
1832 2667 7.275888 AGCAGCGAAAATTAATATGGATCAA 57.724 32.000 0.00 0.00 0.00 2.57
1845 2684 5.682943 TGTTGTACTAAAGCAGCGAAAAT 57.317 34.783 0.00 0.00 0.00 1.82
1848 2687 5.682943 AATTGTTGTACTAAAGCAGCGAA 57.317 34.783 0.00 0.00 0.00 4.70
1869 2711 9.310449 TGGCAAAGTAGGTAAACCAAATATTAA 57.690 29.630 1.26 0.00 38.89 1.40
1888 2793 6.317789 TCTAAGTCAACATTTCTGGCAAAG 57.682 37.500 0.00 0.00 0.00 2.77
1894 2799 8.189709 TCATTCGATCTAAGTCAACATTTCTG 57.810 34.615 0.00 0.00 0.00 3.02
1958 2863 7.501844 ACTAGATGAAGTTAAGAAGCCCATAC 58.498 38.462 0.00 0.00 0.00 2.39
1976 2881 5.244178 GGACCACACCCTAGATTACTAGATG 59.756 48.000 0.00 0.00 46.34 2.90
2061 2967 5.172205 AGCTAAATCCGAAGTTCAGAAGAC 58.828 41.667 3.32 0.00 0.00 3.01
2119 3025 2.675056 GCTGCTGCTCACACCTTCG 61.675 63.158 8.53 0.00 36.03 3.79
2163 3069 3.524541 CTGTGCTCAAAACCTGCTTTTT 58.475 40.909 0.00 0.00 28.85 1.94
2197 3103 4.759183 GCTTCAGACTTTTCATCTTCAGGT 59.241 41.667 0.00 0.00 0.00 4.00
2232 3138 6.075762 TGACAACCAAATCATCTTTCACAG 57.924 37.500 0.00 0.00 0.00 3.66
2407 3313 1.741770 GGCTGACGATGTGACCACC 60.742 63.158 0.00 0.00 0.00 4.61
2428 3334 1.895020 TAGACGCATTCCCGGCAGTT 61.895 55.000 0.00 0.00 39.14 3.16
2447 3353 8.591114 ATCTCTGAATTTCCAGTTGATGATTT 57.409 30.769 0.00 0.00 35.71 2.17
2472 3378 6.553100 ACTTACATTGGTTGAGGAATTTCCAA 59.447 34.615 17.57 3.07 39.61 3.53
2549 3455 2.223479 TGACAAGAAGAAACGCTTTGGC 60.223 45.455 0.00 0.00 36.83 4.52
2550 3456 3.691049 TGACAAGAAGAAACGCTTTGG 57.309 42.857 0.00 0.00 36.83 3.28
2551 3457 5.100751 AGATGACAAGAAGAAACGCTTTG 57.899 39.130 0.00 0.00 36.83 2.77
2552 3458 5.757850 AAGATGACAAGAAGAAACGCTTT 57.242 34.783 0.00 0.00 36.83 3.51
2553 3459 5.757850 AAAGATGACAAGAAGAAACGCTT 57.242 34.783 0.00 0.00 40.25 4.68
2554 3460 5.757850 AAAAGATGACAAGAAGAAACGCT 57.242 34.783 0.00 0.00 0.00 5.07
2555 3461 5.331830 GCAAAAAGATGACAAGAAGAAACGC 60.332 40.000 0.00 0.00 0.00 4.84
2556 3462 5.173854 GGCAAAAAGATGACAAGAAGAAACG 59.826 40.000 0.00 0.00 0.00 3.60
2558 3464 6.219417 TGGCAAAAAGATGACAAGAAGAAA 57.781 33.333 0.00 0.00 34.74 2.52
2559 3465 5.850557 TGGCAAAAAGATGACAAGAAGAA 57.149 34.783 0.00 0.00 34.74 2.52
2591 3500 2.096496 CGCATAGCTATTGGCCTATTGC 59.904 50.000 21.87 21.87 43.05 3.56
2594 3503 1.407437 GCCGCATAGCTATTGGCCTAT 60.407 52.381 26.27 4.11 43.05 2.57
2597 3506 1.301677 GAGCCGCATAGCTATTGGCC 61.302 60.000 30.12 21.84 46.92 5.36
2635 3544 6.439675 AAAAACTAAGCGTCCAACACTTAA 57.560 33.333 0.00 0.00 0.00 1.85
2659 3568 8.940952 GTTCTAAGAAGCAAGAGTCAATATGTT 58.059 33.333 0.00 0.00 0.00 2.71
2709 3621 5.057149 AGCAGAATTACATTTAGCTACCCG 58.943 41.667 0.00 0.00 33.07 5.28
2742 3654 2.087646 CAGGTAGAAAAAGGAGCAGCC 58.912 52.381 0.00 0.00 0.00 4.85
2766 3678 5.292765 ACAATGACAAGCTATGATACCTCG 58.707 41.667 0.00 0.00 0.00 4.63
2820 3732 9.558648 CAATTCAAACAAATATCGAAGATGACA 57.441 29.630 0.00 0.00 45.12 3.58
2894 3810 8.522830 ACAGTCGGACAATAATGAATGAAAAAT 58.477 29.630 11.27 0.00 31.47 1.82
2950 3867 9.624697 CATTTAACACAAGCAATAACACTATGT 57.375 29.630 0.00 0.00 0.00 2.29
2954 3871 8.413229 AGAACATTTAACACAAGCAATAACACT 58.587 29.630 0.00 0.00 0.00 3.55
2983 3922 4.848357 ACAAATCACCATCCAAGTAGAGG 58.152 43.478 0.00 0.00 0.00 3.69
3008 3955 4.528206 TCAGTCCCCTGCATATACAGTATG 59.472 45.833 3.03 0.00 39.61 2.39
3030 3984 4.305989 TCATTGCAGAAACCAACAGTTC 57.694 40.909 0.00 0.00 37.88 3.01
3284 4244 7.173032 GGTGGGAAGGTTTCTTATCTCTTTTA 58.827 38.462 0.00 0.00 32.52 1.52
3356 4316 0.250858 TGCCATATGCCTTCCGATGG 60.251 55.000 0.00 0.00 41.58 3.51
3476 4436 1.429930 TGGCCTTCAGAACAGGTACA 58.570 50.000 3.32 0.00 33.40 2.90
3485 4445 1.361204 TCTGTTCCATGGCCTTCAGA 58.639 50.000 6.96 14.09 0.00 3.27
3515 4475 1.745864 CTCCTTGCAGCAGCTGGAG 60.746 63.158 24.13 21.64 46.78 3.86
3596 4556 2.677199 CGTGATAGCATGCTTATCGGT 58.323 47.619 28.02 1.31 0.00 4.69
3695 4655 2.281139 GAATAGCGCAGGAGGCCC 60.281 66.667 11.47 0.00 40.31 5.80
3697 4657 1.153369 TGTGAATAGCGCAGGAGGC 60.153 57.895 11.47 0.00 39.90 4.70
3720 4680 2.476854 GCTTTGCTGATAACCAGAAGCG 60.477 50.000 0.00 0.00 45.78 4.68
3739 4699 2.880443 ACACCATCCAACATGAAAGCT 58.120 42.857 0.00 0.00 0.00 3.74
3761 4721 6.071672 TGTCCAAACAAAAGTTCACAGATCAA 60.072 34.615 0.00 0.00 30.70 2.57
3768 4728 5.516339 CACTGATGTCCAAACAAAAGTTCAC 59.484 40.000 0.00 0.00 39.30 3.18
4062 5024 4.222124 ACATCCCTCCATGTGTTACTTC 57.778 45.455 0.00 0.00 35.57 3.01
4085 5047 6.826231 CAGATACATTGTTACCATGGGTTACA 59.174 38.462 18.09 13.70 42.34 2.41
4086 5048 6.826741 ACAGATACATTGTTACCATGGGTTAC 59.173 38.462 18.09 11.16 37.09 2.50
4087 5049 6.826231 CACAGATACATTGTTACCATGGGTTA 59.174 38.462 18.09 0.00 37.09 2.85
4089 5051 5.192927 CACAGATACATTGTTACCATGGGT 58.807 41.667 18.09 4.67 40.16 4.51
4090 5052 4.580167 CCACAGATACATTGTTACCATGGG 59.420 45.833 18.09 0.00 0.00 4.00
4091 5053 5.436175 TCCACAGATACATTGTTACCATGG 58.564 41.667 11.19 11.19 0.00 3.66
4092 5054 6.543465 ACATCCACAGATACATTGTTACCATG 59.457 38.462 0.00 0.00 0.00 3.66
4203 5177 2.302260 GATGGAGACGGTCAGAGATGA 58.698 52.381 11.27 0.00 0.00 2.92
4214 5188 2.819115 CTTCTCATGTGGATGGAGACG 58.181 52.381 0.00 0.00 0.00 4.18
4224 5198 2.222976 GCACGATTGAGCTTCTCATGTG 60.223 50.000 14.52 14.52 40.39 3.21
4225 5199 2.005451 GCACGATTGAGCTTCTCATGT 58.995 47.619 0.00 0.00 40.39 3.21
4226 5200 1.329906 GGCACGATTGAGCTTCTCATG 59.670 52.381 2.21 0.00 40.39 3.07
4227 5201 1.661341 GGCACGATTGAGCTTCTCAT 58.339 50.000 2.21 0.00 40.39 2.90
4228 5202 3.143675 GGCACGATTGAGCTTCTCA 57.856 52.632 2.21 0.00 38.87 3.27
4241 5215 4.253546 TTGAGCTTTTCATGTCGGCACG 62.254 50.000 0.00 0.00 45.38 5.34
4242 5216 0.874390 TGAGCTTTTCATGTCGGCAC 59.126 50.000 0.00 0.00 0.00 5.01
4243 5217 1.603456 TTGAGCTTTTCATGTCGGCA 58.397 45.000 0.00 0.00 35.27 5.69
4244 5218 2.789092 CGATTGAGCTTTTCATGTCGGC 60.789 50.000 0.00 0.00 39.06 5.54
4245 5219 2.416547 ACGATTGAGCTTTTCATGTCGG 59.583 45.455 13.29 0.00 43.16 4.79
4246 5220 3.410850 CACGATTGAGCTTTTCATGTCG 58.589 45.455 0.00 0.00 43.83 4.35
4277 5251 8.284693 TCAAAAGTTCGTAACCTTATTACTTGC 58.715 33.333 0.00 0.00 0.00 4.01
4300 5274 2.151202 GGAACTGGAAGCAACGATCAA 58.849 47.619 0.00 0.00 37.60 2.57
4301 5275 1.808411 GGAACTGGAAGCAACGATCA 58.192 50.000 0.00 0.00 37.60 2.92
4330 5304 0.674895 GTCCAAAGCTCTCATGCCGT 60.675 55.000 0.00 0.00 0.00 5.68
4336 5310 0.033504 GTCGTGGTCCAAAGCTCTCA 59.966 55.000 0.00 0.00 0.00 3.27
4400 5387 1.832167 TTGCCAGGCAAAGGTGACC 60.832 57.895 25.43 0.00 45.96 4.02
4455 5445 2.863153 CAAGAGCGGGCTTGTTCG 59.137 61.111 0.00 0.00 40.22 3.95
4659 5656 2.093152 CCGGTTGCGTTACTCATTACAC 59.907 50.000 0.00 0.00 0.00 2.90
4660 5657 2.339418 CCGGTTGCGTTACTCATTACA 58.661 47.619 0.00 0.00 0.00 2.41
4741 5740 6.785076 TCAACCTAAAAGAGAGAGAGAGAGA 58.215 40.000 0.00 0.00 0.00 3.10
4742 5741 7.645058 ATCAACCTAAAAGAGAGAGAGAGAG 57.355 40.000 0.00 0.00 0.00 3.20
4743 5742 8.110271 TGTATCAACCTAAAAGAGAGAGAGAGA 58.890 37.037 0.00 0.00 0.00 3.10
4744 5743 8.287439 TGTATCAACCTAAAAGAGAGAGAGAG 57.713 38.462 0.00 0.00 0.00 3.20
4750 5749 6.310711 GGACGTTGTATCAACCTAAAAGAGAG 59.689 42.308 6.98 0.00 0.00 3.20
4772 5771 6.642707 AGCTACATTAGTGATAGACTGGAC 57.357 41.667 0.00 0.00 35.96 4.02
4819 5818 0.813210 GCATCTCCAGTGCTAGTGCC 60.813 60.000 0.00 0.00 39.45 5.01
4837 5836 2.355837 TTGCGTCCTGTCGTCTGC 60.356 61.111 0.00 0.00 0.00 4.26
4846 5845 2.002586 CAGAATTCGATGTTGCGTCCT 58.997 47.619 0.00 0.00 0.00 3.85
4901 5900 2.229543 GGGGTTCCAATGTTACCGAAAC 59.770 50.000 0.00 0.00 38.67 2.78
4902 5901 2.516906 GGGGTTCCAATGTTACCGAAA 58.483 47.619 0.00 0.00 32.61 3.46
4906 5905 0.038599 ACGGGGGTTCCAATGTTACC 59.961 55.000 0.00 0.00 34.36 2.85
4913 5912 0.106918 GCATATCACGGGGGTTCCAA 60.107 55.000 0.00 0.00 34.36 3.53


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

AutoCloner maintained by Alex Coulton.