Multiple sequence alignment - TraesCS3D01G192000

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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 TraesCS3D01G192000 chr3D 100.000 6461 0 0 1 6461 182108095 182101635 0.000000e+00 11932.0
1 TraesCS3D01G192000 chr3D 92.007 538 23 9 1 521 182160297 182159763 0.000000e+00 737.0
2 TraesCS3D01G192000 chr3D 82.012 517 77 14 4 516 72259685 72260189 5.990000e-115 425.0
3 TraesCS3D01G192000 chr3D 80.303 264 45 6 5823 6082 528181375 528181115 6.610000e-45 193.0
4 TraesCS3D01G192000 chr3B 98.941 3115 25 6 2210 5322 260384269 260381161 0.000000e+00 5563.0
5 TraesCS3D01G192000 chr3B 95.475 1525 18 9 697 2174 260385788 260384268 0.000000e+00 2386.0
6 TraesCS3D01G192000 chr3B 94.306 720 20 8 5320 6037 260380649 260379949 0.000000e+00 1083.0
7 TraesCS3D01G192000 chr3B 90.640 203 10 5 6263 6461 260379754 260379557 1.790000e-65 261.0
8 TraesCS3D01G192000 chr3B 96.528 144 4 1 6319 6461 201482941 201482798 3.010000e-58 237.0
9 TraesCS3D01G192000 chr3B 84.722 216 31 1 5825 6040 689992895 689993108 1.410000e-51 215.0
10 TraesCS3D01G192000 chr3B 91.753 97 8 0 6103 6199 260379941 260379845 1.130000e-27 135.0
11 TraesCS3D01G192000 chr3B 100.000 29 0 0 6235 6263 260379845 260379817 3.000000e-03 54.7
12 TraesCS3D01G192000 chr3A 94.831 3366 89 33 686 4015 229182396 229179080 0.000000e+00 5173.0
13 TraesCS3D01G192000 chr3A 97.365 835 15 2 3987 4821 229179187 229178360 0.000000e+00 1413.0
14 TraesCS3D01G192000 chr3A 91.309 1024 25 22 4808 5787 229178346 229177343 0.000000e+00 1339.0
15 TraesCS3D01G192000 chr6D 91.076 762 55 9 3323 4078 444837105 444837859 0.000000e+00 1018.0
16 TraesCS3D01G192000 chr6D 96.528 144 4 1 6319 6461 87402175 87402032 3.010000e-58 237.0
17 TraesCS3D01G192000 chr5D 91.188 522 42 3 1 521 524418043 524417525 0.000000e+00 706.0
18 TraesCS3D01G192000 chr5D 88.824 340 34 4 10 348 136524590 136524254 1.300000e-111 414.0
19 TraesCS3D01G192000 chr5D 79.110 517 96 11 3 515 406175794 406176302 4.800000e-91 346.0
20 TraesCS3D01G192000 chr5D 96.503 143 5 0 6319 6461 6242809 6242951 3.010000e-58 237.0
21 TraesCS3D01G192000 chr1D 88.462 520 54 6 3 521 328672053 328671539 1.980000e-174 623.0
22 TraesCS3D01G192000 chr1D 83.254 418 55 14 1 409 265712362 265712773 2.850000e-98 370.0
23 TraesCS3D01G192000 chr1D 84.444 270 35 6 5826 6090 433916805 433917072 6.430000e-65 259.0
24 TraesCS3D01G192000 chr1D 97.222 144 3 1 6319 6461 254469893 254469750 6.470000e-60 243.0
25 TraesCS3D01G192000 chr7B 89.497 457 34 8 5819 6263 176742824 176742370 3.380000e-157 566.0
26 TraesCS3D01G192000 chr7B 96.552 145 3 1 6319 6461 662744546 662744690 8.370000e-59 239.0
27 TraesCS3D01G192000 chr2D 83.669 496 74 7 1 494 178954025 178954515 1.640000e-125 460.0
28 TraesCS3D01G192000 chr2D 81.474 529 68 19 1 521 207271430 207270924 2.170000e-109 407.0
29 TraesCS3D01G192000 chr4D 82.008 528 79 14 1 521 242738845 242739363 9.950000e-118 435.0
30 TraesCS3D01G192000 chr1B 97.203 143 4 0 6319 6461 217992804 217992662 6.470000e-60 243.0
31 TraesCS3D01G192000 chrUn 96.552 145 3 1 6319 6461 438111363 438111507 8.370000e-59 239.0
32 TraesCS3D01G192000 chrUn 96.528 144 4 1 6319 6461 298933433 298933576 3.010000e-58 237.0
33 TraesCS3D01G192000 chr6A 83.525 261 37 6 5826 6081 251556751 251556492 8.370000e-59 239.0
34 TraesCS3D01G192000 chr5B 82.692 260 40 4 5826 6081 440181236 440180978 6.520000e-55 226.0
35 TraesCS3D01G192000 chr4B 81.041 269 35 13 5824 6082 660341066 660340804 3.950000e-47 200.0
36 TraesCS3D01G192000 chr5A 80.843 261 42 7 5826 6082 84127385 84127129 1.420000e-46 198.0
37 TraesCS3D01G192000 chr5A 80.608 263 45 6 5823 6082 502610491 502610232 1.420000e-46 198.0
38 TraesCS3D01G192000 chr6B 80.460 261 45 5 5825 6082 591140367 591140110 1.840000e-45 195.0
39 TraesCS3D01G192000 chr7A 82.390 159 26 2 338 495 166618560 166618717 3.140000e-28 137.0


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 TraesCS3D01G192000 chr3D 182101635 182108095 6460 True 11932.000000 11932 100.000000 1 6461 1 chr3D.!!$R1 6460
1 TraesCS3D01G192000 chr3D 182159763 182160297 534 True 737.000000 737 92.007000 1 521 1 chr3D.!!$R2 520
2 TraesCS3D01G192000 chr3D 72259685 72260189 504 False 425.000000 425 82.012000 4 516 1 chr3D.!!$F1 512
3 TraesCS3D01G192000 chr3B 260379557 260385788 6231 True 1580.450000 5563 95.185833 697 6461 6 chr3B.!!$R2 5764
4 TraesCS3D01G192000 chr3A 229177343 229182396 5053 True 2641.666667 5173 94.501667 686 5787 3 chr3A.!!$R1 5101
5 TraesCS3D01G192000 chr6D 444837105 444837859 754 False 1018.000000 1018 91.076000 3323 4078 1 chr6D.!!$F1 755
6 TraesCS3D01G192000 chr5D 524417525 524418043 518 True 706.000000 706 91.188000 1 521 1 chr5D.!!$R2 520
7 TraesCS3D01G192000 chr5D 406175794 406176302 508 False 346.000000 346 79.110000 3 515 1 chr5D.!!$F2 512
8 TraesCS3D01G192000 chr1D 328671539 328672053 514 True 623.000000 623 88.462000 3 521 1 chr1D.!!$R2 518
9 TraesCS3D01G192000 chr2D 207270924 207271430 506 True 407.000000 407 81.474000 1 521 1 chr2D.!!$R1 520
10 TraesCS3D01G192000 chr4D 242738845 242739363 518 False 435.000000 435 82.008000 1 521 1 chr4D.!!$F1 520

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
590 629 0.179272 CGCACGAGAGAGAAAAACGC 60.179 55.000 0.00 0.0 0.00 4.84 F
591 630 1.140816 GCACGAGAGAGAAAAACGCT 58.859 50.000 0.00 0.0 0.00 5.07 F
809 872 1.272807 CAGGGGTAGAAAAGTCCGGA 58.727 55.000 0.00 0.0 0.00 5.14 F
1431 1523 1.730487 CTCGTAGCGATCTGGCTGT 59.270 57.895 5.46 0.0 44.50 4.40 F
2273 2368 3.003275 ACAAGTTACACGTGAATTGCTGG 59.997 43.478 25.01 12.0 31.96 4.85 F
3643 3742 2.715737 TTATGGCCGAAAAACTGCAC 57.284 45.000 0.00 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 1814 1.469703 CCTGAGCATTCATTTGTGCGA 59.530 47.619 0.00 0.0 45.69 5.10 R
2273 2368 4.158384 CAACATTAGAAACATCACACGGC 58.842 43.478 0.00 0.0 0.00 5.68 R
2692 2787 4.124851 AGTCGCAAAAGGTGGATACTAG 57.875 45.455 0.00 0.0 37.61 2.57 R
3643 3742 3.686241 TGATCAAGCGACAATTCCTCAAG 59.314 43.478 0.00 0.0 0.00 3.02 R
3946 4049 4.095782 GGAATTCACTTGGCGCAGTTATTA 59.904 41.667 10.83 0.0 0.00 0.98 R
5611 6282 1.140252 ACTGGAGCACGTAACCAAACT 59.860 47.619 8.46 0.0 33.14 2.66 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
126 128 5.527951 TCGTCTTAATGTGGTGCAAACTTTA 59.472 36.000 0.00 0.00 0.00 1.85
227 230 2.281761 CTGTGAACTGCCGCCCTT 60.282 61.111 0.00 0.00 0.00 3.95
305 342 1.818674 GCCCCGATGTCTTGAATTGTT 59.181 47.619 0.00 0.00 0.00 2.83
525 564 4.492160 GTCGCGGCGAGGACATCA 62.492 66.667 27.15 0.00 36.23 3.07
526 565 4.492160 TCGCGGCGAGGACATCAC 62.492 66.667 22.69 0.00 0.00 3.06
527 566 4.498520 CGCGGCGAGGACATCACT 62.499 66.667 19.16 0.00 0.00 3.41
528 567 2.805546 GCGGCGAGGACATCACTA 59.194 61.111 12.98 0.00 0.00 2.74
529 568 1.299468 GCGGCGAGGACATCACTAG 60.299 63.158 12.98 0.00 0.00 2.57
530 569 1.725557 GCGGCGAGGACATCACTAGA 61.726 60.000 12.98 0.00 0.00 2.43
531 570 0.738975 CGGCGAGGACATCACTAGAA 59.261 55.000 0.00 0.00 0.00 2.10
532 571 1.268794 CGGCGAGGACATCACTAGAAG 60.269 57.143 0.00 0.00 0.00 2.85
533 572 1.067821 GGCGAGGACATCACTAGAAGG 59.932 57.143 0.00 0.00 0.00 3.46
534 573 1.537135 GCGAGGACATCACTAGAAGGC 60.537 57.143 0.00 0.00 0.00 4.35
535 574 2.028130 CGAGGACATCACTAGAAGGCT 58.972 52.381 0.00 0.00 0.00 4.58
536 575 2.223688 CGAGGACATCACTAGAAGGCTG 60.224 54.545 0.00 0.00 0.00 4.85
537 576 2.102252 GAGGACATCACTAGAAGGCTGG 59.898 54.545 0.00 0.00 0.00 4.85
538 577 1.474143 GGACATCACTAGAAGGCTGGC 60.474 57.143 0.00 0.00 0.00 4.85
539 578 0.543749 ACATCACTAGAAGGCTGGCC 59.456 55.000 3.00 3.00 0.00 5.36
555 594 3.324930 CCTCTCCTGGCAGTGGCA 61.325 66.667 19.44 19.44 43.71 4.92
562 601 2.203480 TGGCAGTGGCAGGTTTCC 60.203 61.111 16.56 0.00 43.71 3.13
563 602 3.365265 GGCAGTGGCAGGTTTCCG 61.365 66.667 12.58 0.00 43.71 4.30
564 603 3.365265 GCAGTGGCAGGTTTCCGG 61.365 66.667 0.00 0.00 40.72 5.14
565 604 2.113139 CAGTGGCAGGTTTCCGGT 59.887 61.111 0.00 0.00 0.00 5.28
566 605 1.966451 CAGTGGCAGGTTTCCGGTC 60.966 63.158 0.00 0.00 0.00 4.79
567 606 3.047877 GTGGCAGGTTTCCGGTCG 61.048 66.667 0.00 0.00 0.00 4.79
571 610 3.047877 CAGGTTTCCGGTCGCCAC 61.048 66.667 0.00 0.00 0.00 5.01
572 611 4.675029 AGGTTTCCGGTCGCCACG 62.675 66.667 0.00 0.00 0.00 4.94
581 620 4.400109 GTCGCCACGCACGAGAGA 62.400 66.667 0.00 0.00 40.80 3.10
582 621 4.103103 TCGCCACGCACGAGAGAG 62.103 66.667 0.00 0.00 33.96 3.20
583 622 4.103103 CGCCACGCACGAGAGAGA 62.103 66.667 0.00 0.00 0.00 3.10
584 623 2.258591 GCCACGCACGAGAGAGAA 59.741 61.111 0.00 0.00 0.00 2.87
585 624 1.372997 GCCACGCACGAGAGAGAAA 60.373 57.895 0.00 0.00 0.00 2.52
586 625 0.944311 GCCACGCACGAGAGAGAAAA 60.944 55.000 0.00 0.00 0.00 2.29
587 626 1.497991 CCACGCACGAGAGAGAAAAA 58.502 50.000 0.00 0.00 0.00 1.94
588 627 1.192534 CCACGCACGAGAGAGAAAAAC 59.807 52.381 0.00 0.00 0.00 2.43
589 628 1.129326 ACGCACGAGAGAGAAAAACG 58.871 50.000 0.00 0.00 0.00 3.60
590 629 0.179272 CGCACGAGAGAGAAAAACGC 60.179 55.000 0.00 0.00 0.00 4.84
591 630 1.140816 GCACGAGAGAGAAAAACGCT 58.859 50.000 0.00 0.00 0.00 5.07
592 631 1.527311 GCACGAGAGAGAAAAACGCTT 59.473 47.619 0.00 0.00 0.00 4.68
593 632 2.410389 GCACGAGAGAGAAAAACGCTTC 60.410 50.000 0.00 0.00 0.00 3.86
594 633 2.794910 CACGAGAGAGAAAAACGCTTCA 59.205 45.455 0.00 0.00 0.00 3.02
595 634 3.245284 CACGAGAGAGAAAAACGCTTCAA 59.755 43.478 0.00 0.00 0.00 2.69
596 635 4.058817 ACGAGAGAGAAAAACGCTTCAAT 58.941 39.130 0.00 0.00 0.00 2.57
597 636 5.118664 CACGAGAGAGAAAAACGCTTCAATA 59.881 40.000 0.00 0.00 0.00 1.90
598 637 5.346281 ACGAGAGAGAAAAACGCTTCAATAG 59.654 40.000 0.00 0.00 0.00 1.73
599 638 5.573282 CGAGAGAGAAAAACGCTTCAATAGA 59.427 40.000 0.00 0.00 0.00 1.98
600 639 6.453134 CGAGAGAGAAAAACGCTTCAATAGAC 60.453 42.308 0.00 0.00 0.00 2.59
601 640 6.223852 AGAGAGAAAAACGCTTCAATAGACA 58.776 36.000 0.00 0.00 0.00 3.41
602 641 6.876257 AGAGAGAAAAACGCTTCAATAGACAT 59.124 34.615 0.00 0.00 0.00 3.06
603 642 7.389053 AGAGAGAAAAACGCTTCAATAGACATT 59.611 33.333 0.00 0.00 0.00 2.71
604 643 7.522374 AGAGAAAAACGCTTCAATAGACATTC 58.478 34.615 0.00 0.00 0.00 2.67
605 644 7.173218 AGAGAAAAACGCTTCAATAGACATTCA 59.827 33.333 0.00 0.00 0.00 2.57
606 645 7.301054 AGAAAAACGCTTCAATAGACATTCAG 58.699 34.615 0.00 0.00 0.00 3.02
607 646 6.560253 AAAACGCTTCAATAGACATTCAGT 57.440 33.333 0.00 0.00 0.00 3.41
608 647 6.560253 AAACGCTTCAATAGACATTCAGTT 57.440 33.333 0.00 0.00 0.00 3.16
609 648 6.560253 AACGCTTCAATAGACATTCAGTTT 57.440 33.333 0.00 0.00 0.00 2.66
610 649 6.560253 ACGCTTCAATAGACATTCAGTTTT 57.440 33.333 0.00 0.00 0.00 2.43
611 650 6.373779 ACGCTTCAATAGACATTCAGTTTTG 58.626 36.000 0.00 0.00 0.00 2.44
612 651 6.017109 ACGCTTCAATAGACATTCAGTTTTGT 60.017 34.615 0.00 0.00 0.00 2.83
613 652 7.172532 ACGCTTCAATAGACATTCAGTTTTGTA 59.827 33.333 0.00 0.00 0.00 2.41
614 653 8.177663 CGCTTCAATAGACATTCAGTTTTGTAT 58.822 33.333 0.00 0.00 0.00 2.29
615 654 9.282247 GCTTCAATAGACATTCAGTTTTGTATG 57.718 33.333 0.00 0.00 37.89 2.39
623 662 9.950680 AGACATTCAGTTTTGTATGTTAAACAG 57.049 29.630 0.00 0.00 42.93 3.16
624 663 9.730420 GACATTCAGTTTTGTATGTTAAACAGT 57.270 29.630 0.00 0.00 42.93 3.55
625 664 9.515020 ACATTCAGTTTTGTATGTTAAACAGTG 57.485 29.630 0.00 0.00 40.95 3.66
626 665 9.515020 CATTCAGTTTTGTATGTTAAACAGTGT 57.485 29.630 0.00 0.00 36.85 3.55
627 666 9.730420 ATTCAGTTTTGTATGTTAAACAGTGTC 57.270 29.630 0.00 0.00 36.85 3.67
628 667 7.699566 TCAGTTTTGTATGTTAAACAGTGTCC 58.300 34.615 0.00 0.00 36.85 4.02
629 668 7.337184 TCAGTTTTGTATGTTAAACAGTGTCCA 59.663 33.333 0.00 0.00 36.85 4.02
630 669 8.134895 CAGTTTTGTATGTTAAACAGTGTCCAT 58.865 33.333 0.00 0.00 36.85 3.41
631 670 8.349983 AGTTTTGTATGTTAAACAGTGTCCATC 58.650 33.333 0.00 0.00 36.85 3.51
632 671 8.349983 GTTTTGTATGTTAAACAGTGTCCATCT 58.650 33.333 0.00 0.00 35.02 2.90
633 672 7.433708 TTGTATGTTAAACAGTGTCCATCTG 57.566 36.000 0.00 0.00 38.68 2.90
634 673 6.530120 TGTATGTTAAACAGTGTCCATCTGT 58.470 36.000 0.00 0.00 46.30 3.41
635 674 7.672240 TGTATGTTAAACAGTGTCCATCTGTA 58.328 34.615 0.00 0.00 44.03 2.74
636 675 8.318412 TGTATGTTAAACAGTGTCCATCTGTAT 58.682 33.333 0.00 0.00 44.03 2.29
637 676 9.162764 GTATGTTAAACAGTGTCCATCTGTATT 57.837 33.333 0.00 0.00 44.03 1.89
638 677 7.667043 TGTTAAACAGTGTCCATCTGTATTC 57.333 36.000 0.00 0.00 44.03 1.75
639 678 6.653320 TGTTAAACAGTGTCCATCTGTATTCC 59.347 38.462 0.00 0.00 44.03 3.01
640 679 4.908601 AACAGTGTCCATCTGTATTCCA 57.091 40.909 0.00 0.00 44.03 3.53
641 680 5.441718 AACAGTGTCCATCTGTATTCCAT 57.558 39.130 0.00 0.00 44.03 3.41
642 681 6.560003 AACAGTGTCCATCTGTATTCCATA 57.440 37.500 0.00 0.00 44.03 2.74
643 682 6.166984 ACAGTGTCCATCTGTATTCCATAG 57.833 41.667 0.00 0.00 43.17 2.23
644 683 5.663106 ACAGTGTCCATCTGTATTCCATAGT 59.337 40.000 0.00 0.00 43.17 2.12
645 684 6.183360 ACAGTGTCCATCTGTATTCCATAGTC 60.183 42.308 0.00 0.00 43.17 2.59
646 685 5.899547 AGTGTCCATCTGTATTCCATAGTCA 59.100 40.000 0.00 0.00 0.00 3.41
647 686 6.384015 AGTGTCCATCTGTATTCCATAGTCAA 59.616 38.462 0.00 0.00 0.00 3.18
648 687 6.480320 GTGTCCATCTGTATTCCATAGTCAAC 59.520 42.308 0.00 0.00 0.00 3.18
649 688 6.156083 TGTCCATCTGTATTCCATAGTCAACA 59.844 38.462 0.00 0.00 0.00 3.33
650 689 7.047891 GTCCATCTGTATTCCATAGTCAACAA 58.952 38.462 0.00 0.00 0.00 2.83
651 690 7.552687 GTCCATCTGTATTCCATAGTCAACAAA 59.447 37.037 0.00 0.00 0.00 2.83
652 691 8.106462 TCCATCTGTATTCCATAGTCAACAAAA 58.894 33.333 0.00 0.00 0.00 2.44
653 692 8.906867 CCATCTGTATTCCATAGTCAACAAAAT 58.093 33.333 0.00 0.00 0.00 1.82
654 693 9.941664 CATCTGTATTCCATAGTCAACAAAATC 57.058 33.333 0.00 0.00 0.00 2.17
655 694 9.911788 ATCTGTATTCCATAGTCAACAAAATCT 57.088 29.630 0.00 0.00 0.00 2.40
656 695 9.383519 TCTGTATTCCATAGTCAACAAAATCTC 57.616 33.333 0.00 0.00 0.00 2.75
657 696 9.388506 CTGTATTCCATAGTCAACAAAATCTCT 57.611 33.333 0.00 0.00 0.00 3.10
660 699 7.827819 TTCCATAGTCAACAAAATCTCTACG 57.172 36.000 0.00 0.00 0.00 3.51
661 700 6.931838 TCCATAGTCAACAAAATCTCTACGT 58.068 36.000 0.00 0.00 0.00 3.57
662 701 8.058667 TCCATAGTCAACAAAATCTCTACGTA 57.941 34.615 0.00 0.00 0.00 3.57
663 702 7.972277 TCCATAGTCAACAAAATCTCTACGTAC 59.028 37.037 0.00 0.00 0.00 3.67
664 703 7.758076 CCATAGTCAACAAAATCTCTACGTACA 59.242 37.037 0.00 0.00 0.00 2.90
665 704 9.135843 CATAGTCAACAAAATCTCTACGTACAA 57.864 33.333 0.00 0.00 0.00 2.41
666 705 9.871238 ATAGTCAACAAAATCTCTACGTACAAT 57.129 29.630 0.00 0.00 0.00 2.71
668 707 9.871238 AGTCAACAAAATCTCTACGTACAATAT 57.129 29.630 0.00 0.00 0.00 1.28
673 712 9.622004 ACAAAATCTCTACGTACAATATATCCG 57.378 33.333 0.00 0.00 0.00 4.18
674 713 9.073368 CAAAATCTCTACGTACAATATATCCGG 57.927 37.037 0.00 0.00 0.00 5.14
675 714 7.934855 AATCTCTACGTACAATATATCCGGT 57.065 36.000 0.00 0.00 0.00 5.28
676 715 7.934855 ATCTCTACGTACAATATATCCGGTT 57.065 36.000 0.00 0.00 0.00 4.44
677 716 9.453572 AATCTCTACGTACAATATATCCGGTTA 57.546 33.333 0.00 0.00 0.00 2.85
678 717 8.846943 TCTCTACGTACAATATATCCGGTTAA 57.153 34.615 0.00 0.00 0.00 2.01
679 718 9.283768 TCTCTACGTACAATATATCCGGTTAAA 57.716 33.333 0.00 0.00 0.00 1.52
680 719 9.334693 CTCTACGTACAATATATCCGGTTAAAC 57.665 37.037 0.00 0.00 0.00 2.01
681 720 8.845227 TCTACGTACAATATATCCGGTTAAACA 58.155 33.333 0.00 0.00 0.00 2.83
682 721 9.630098 CTACGTACAATATATCCGGTTAAACAT 57.370 33.333 0.00 0.00 0.00 2.71
684 723 9.630098 ACGTACAATATATCCGGTTAAACATAG 57.370 33.333 0.00 0.00 0.00 2.23
734 773 3.560068 CGAATCCGTTTCCAATTCTAGGG 59.440 47.826 0.00 0.00 0.00 3.53
809 872 1.272807 CAGGGGTAGAAAAGTCCGGA 58.727 55.000 0.00 0.00 0.00 5.14
852 915 4.590918 TCTAGCGACCCAGATAAGATAGG 58.409 47.826 0.00 0.00 0.00 2.57
1415 1507 4.906437 CGTTTCTTTTCAGCTAAACTGCTC 59.094 41.667 6.10 0.00 46.76 4.26
1431 1523 1.730487 CTCGTAGCGATCTGGCTGT 59.270 57.895 5.46 0.00 44.50 4.40
1720 1814 7.787725 AGTACGAAGTCACAGAAAATCTTTT 57.212 32.000 0.00 0.00 43.93 2.27
2192 2287 8.118976 TCTTACGAGTTATCTCTTTCCTCAAA 57.881 34.615 0.00 0.00 38.45 2.69
2273 2368 3.003275 ACAAGTTACACGTGAATTGCTGG 59.997 43.478 25.01 12.00 31.96 4.85
3643 3742 2.715737 TTATGGCCGAAAAACTGCAC 57.284 45.000 0.00 0.00 0.00 4.57
3737 3836 5.576384 ACACACTGTTACAAAGCAACATTTG 59.424 36.000 0.00 0.00 44.14 2.32
3799 3898 8.746052 TTATGGGATTCTAATCGTGAATTGTT 57.254 30.769 0.00 0.00 36.27 2.83
3866 3965 8.234546 CACAAAGTATCCACCTTGTGTTAATAC 58.765 37.037 9.91 0.00 45.76 1.89
3946 4049 8.375506 TGATGAAATCTAACTACCAGTCAGTTT 58.624 33.333 0.00 0.00 45.81 2.66
5274 5404 5.240623 TGTGTTATTGTACTGCCTTTCCTTG 59.759 40.000 0.00 0.00 0.00 3.61
5607 6278 1.399714 ATGCCCTCGTCGTCATTAGA 58.600 50.000 0.00 0.00 0.00 2.10
5611 6282 3.382227 TGCCCTCGTCGTCATTAGATTAA 59.618 43.478 0.00 0.00 0.00 1.40
5691 6362 5.853936 TGCGAGCAGATAAGTATAAATGGT 58.146 37.500 0.00 0.00 0.00 3.55
5857 6546 3.951663 ACCATAGGTGCCTTAACTTGTC 58.048 45.455 0.00 0.00 32.98 3.18
5858 6547 3.279434 CCATAGGTGCCTTAACTTGTCC 58.721 50.000 0.00 0.00 0.00 4.02
5859 6548 3.308117 CCATAGGTGCCTTAACTTGTCCA 60.308 47.826 0.00 0.00 0.00 4.02
5860 6549 4.526970 CATAGGTGCCTTAACTTGTCCAT 58.473 43.478 0.00 0.00 0.00 3.41
5861 6550 3.525800 AGGTGCCTTAACTTGTCCATT 57.474 42.857 0.00 0.00 0.00 3.16
5862 6551 3.157087 AGGTGCCTTAACTTGTCCATTG 58.843 45.455 0.00 0.00 0.00 2.82
5863 6552 2.890945 GGTGCCTTAACTTGTCCATTGT 59.109 45.455 0.00 0.00 0.00 2.71
5864 6553 3.305335 GGTGCCTTAACTTGTCCATTGTG 60.305 47.826 0.00 0.00 0.00 3.33
5865 6554 2.295909 TGCCTTAACTTGTCCATTGTGC 59.704 45.455 0.00 0.00 0.00 4.57
5866 6555 2.558359 GCCTTAACTTGTCCATTGTGCT 59.442 45.455 0.00 0.00 0.00 4.40
5867 6556 3.366374 GCCTTAACTTGTCCATTGTGCTC 60.366 47.826 0.00 0.00 0.00 4.26
5868 6557 3.820467 CCTTAACTTGTCCATTGTGCTCA 59.180 43.478 0.00 0.00 0.00 4.26
5869 6558 4.083110 CCTTAACTTGTCCATTGTGCTCAG 60.083 45.833 0.00 0.00 0.00 3.35
5870 6559 2.645838 ACTTGTCCATTGTGCTCAGT 57.354 45.000 0.00 0.00 0.00 3.41
5871 6560 2.936202 ACTTGTCCATTGTGCTCAGTT 58.064 42.857 0.00 0.00 0.00 3.16
5872 6561 3.290710 ACTTGTCCATTGTGCTCAGTTT 58.709 40.909 0.00 0.00 0.00 2.66
5873 6562 4.460263 ACTTGTCCATTGTGCTCAGTTTA 58.540 39.130 0.00 0.00 0.00 2.01
5874 6563 4.887071 ACTTGTCCATTGTGCTCAGTTTAA 59.113 37.500 0.00 0.00 0.00 1.52
5875 6564 5.536161 ACTTGTCCATTGTGCTCAGTTTAAT 59.464 36.000 0.00 0.00 0.00 1.40
5876 6565 5.375417 TGTCCATTGTGCTCAGTTTAATG 57.625 39.130 0.00 0.00 0.00 1.90
5942 6635 2.057140 TGGTGCATATATGGTGCCTCT 58.943 47.619 14.51 0.00 41.83 3.69
5946 6639 1.952367 GCATATATGGTGCCTCTGCCC 60.952 57.143 14.51 0.00 36.61 5.36
5950 6643 0.762842 TATGGTGCCTCTGCCCGTAT 60.763 55.000 0.00 0.00 36.33 3.06
5956 6649 4.227134 CTCTGCCCGTATGCCGCT 62.227 66.667 0.00 0.00 34.38 5.52
6039 6732 4.746361 CCTGCGCTAGGTGAGATG 57.254 61.111 9.73 0.00 42.00 2.90
6041 6734 1.068753 CTGCGCTAGGTGAGATGGG 59.931 63.158 9.73 0.00 0.00 4.00
6042 6735 2.280457 GCGCTAGGTGAGATGGGC 60.280 66.667 0.00 0.00 0.00 5.36
6043 6736 3.094062 GCGCTAGGTGAGATGGGCA 62.094 63.158 0.00 0.00 38.10 5.36
6044 6737 1.227380 CGCTAGGTGAGATGGGCAC 60.227 63.158 0.00 0.00 35.56 5.01
6045 6738 1.227380 GCTAGGTGAGATGGGCACG 60.227 63.158 0.00 0.00 37.13 5.34
6046 6739 1.227380 CTAGGTGAGATGGGCACGC 60.227 63.158 0.00 0.00 37.13 5.34
6047 6740 1.960040 CTAGGTGAGATGGGCACGCA 61.960 60.000 0.00 0.00 37.13 5.24
6048 6741 1.337384 TAGGTGAGATGGGCACGCAT 61.337 55.000 0.00 0.00 37.13 4.73
6049 6742 1.750399 GGTGAGATGGGCACGCATT 60.750 57.895 1.44 0.00 37.13 3.56
6050 6743 1.315257 GGTGAGATGGGCACGCATTT 61.315 55.000 1.44 0.00 37.13 2.32
6051 6744 0.527565 GTGAGATGGGCACGCATTTT 59.472 50.000 1.44 0.00 0.00 1.82
6052 6745 1.067635 GTGAGATGGGCACGCATTTTT 60.068 47.619 1.44 0.00 0.00 1.94
6096 6789 9.469807 TTTTTATTAAATCTCGCAAAAGCTTCA 57.530 25.926 0.00 0.00 0.00 3.02
6097 6790 8.447787 TTTATTAAATCTCGCAAAAGCTTCAC 57.552 30.769 0.00 0.00 0.00 3.18
6098 6791 5.689383 TTAAATCTCGCAAAAGCTTCACT 57.311 34.783 0.00 0.00 0.00 3.41
6099 6792 3.820777 AATCTCGCAAAAGCTTCACTC 57.179 42.857 0.00 0.00 0.00 3.51
6100 6793 2.533266 TCTCGCAAAAGCTTCACTCT 57.467 45.000 0.00 0.00 0.00 3.24
6101 6794 2.838736 TCTCGCAAAAGCTTCACTCTT 58.161 42.857 0.00 0.00 0.00 2.85
6167 6860 1.612676 AAAGCAAACCGGGTTACTCC 58.387 50.000 13.79 2.13 0.00 3.85
6180 6873 2.092592 GGTTACTCCGTGGGATTCCAAT 60.093 50.000 4.80 0.00 46.04 3.16
6181 6874 3.617284 GTTACTCCGTGGGATTCCAATT 58.383 45.455 4.80 0.00 46.04 2.32
6193 6886 1.533625 TTCCAATTTGCGACCTCCAG 58.466 50.000 0.00 0.00 0.00 3.86
6194 6887 0.322456 TCCAATTTGCGACCTCCAGG 60.322 55.000 0.00 0.00 42.17 4.45
6198 6891 3.278574 CAATTTGCGACCTCCAGGATAA 58.721 45.455 0.00 0.00 38.94 1.75
6199 6892 3.644966 ATTTGCGACCTCCAGGATAAA 57.355 42.857 0.00 0.00 38.94 1.40
6200 6893 3.644966 TTTGCGACCTCCAGGATAAAT 57.355 42.857 0.00 0.00 38.94 1.40
6201 6894 4.764050 TTTGCGACCTCCAGGATAAATA 57.236 40.909 0.00 0.00 38.94 1.40
6202 6895 4.336889 TTGCGACCTCCAGGATAAATAG 57.663 45.455 0.00 0.00 38.94 1.73
6203 6896 2.037251 TGCGACCTCCAGGATAAATAGC 59.963 50.000 0.00 0.00 38.94 2.97
6204 6897 2.037251 GCGACCTCCAGGATAAATAGCA 59.963 50.000 0.00 0.00 38.94 3.49
6205 6898 3.307059 GCGACCTCCAGGATAAATAGCAT 60.307 47.826 0.00 0.00 38.94 3.79
6206 6899 4.248859 CGACCTCCAGGATAAATAGCATG 58.751 47.826 0.00 0.00 38.94 4.06
6207 6900 4.006319 GACCTCCAGGATAAATAGCATGC 58.994 47.826 10.51 10.51 38.94 4.06
6208 6901 3.395607 ACCTCCAGGATAAATAGCATGCA 59.604 43.478 21.98 6.36 38.94 3.96
6209 6902 4.043812 ACCTCCAGGATAAATAGCATGCAT 59.956 41.667 21.98 8.63 38.94 3.96
6210 6903 4.398358 CCTCCAGGATAAATAGCATGCATG 59.602 45.833 22.70 22.70 37.39 4.06
6211 6904 4.338012 TCCAGGATAAATAGCATGCATGG 58.662 43.478 27.34 8.28 0.00 3.66
6212 6905 4.084287 CCAGGATAAATAGCATGCATGGT 58.916 43.478 31.85 31.85 41.93 3.55
6213 6906 5.014018 TCCAGGATAAATAGCATGCATGGTA 59.986 40.000 33.74 33.74 43.86 3.25
6214 6907 5.711506 CCAGGATAAATAGCATGCATGGTAA 59.288 40.000 34.81 22.75 43.09 2.85
6215 6908 6.349611 CCAGGATAAATAGCATGCATGGTAAC 60.350 42.308 34.81 23.43 43.09 2.50
6216 6909 5.711976 AGGATAAATAGCATGCATGGTAACC 59.288 40.000 34.81 28.62 43.09 2.85
6217 6910 5.476599 GGATAAATAGCATGCATGGTAACCA 59.523 40.000 34.81 24.03 43.09 3.67
6218 6911 4.654091 AAATAGCATGCATGGTAACCAC 57.346 40.909 34.81 15.02 43.09 4.16
6219 6912 2.051334 TAGCATGCATGGTAACCACC 57.949 50.000 30.91 11.67 46.00 4.61
6230 6923 2.081462 GGTAACCACCAGGACAATTCG 58.919 52.381 0.00 0.00 45.04 3.34
6231 6924 2.551504 GGTAACCACCAGGACAATTCGT 60.552 50.000 0.00 0.00 45.04 3.85
6232 6925 1.604604 AACCACCAGGACAATTCGTG 58.395 50.000 0.00 0.00 38.69 4.35
6233 6926 0.472471 ACCACCAGGACAATTCGTGT 59.528 50.000 0.00 0.00 45.74 4.49
6280 7037 4.467198 AGATTCCAAGGTTACAGGTACG 57.533 45.455 0.00 0.00 0.00 3.67
6312 7069 7.497925 AATTAATCTTCCCAAATCTAGACGC 57.502 36.000 0.00 0.00 0.00 5.19
6314 7071 2.467880 TCTTCCCAAATCTAGACGCCT 58.532 47.619 0.00 0.00 0.00 5.52
6374 7134 1.810755 GAAACCCCTTCTTACCGCAAG 59.189 52.381 0.00 0.00 35.38 4.01
6391 7151 4.616802 CCGCAAGCTTTTAATAATATGGCG 59.383 41.667 11.13 11.13 39.33 5.69
6400 7160 7.308589 GCTTTTAATAATATGGCGGTGATCTGT 60.309 37.037 0.00 0.00 0.00 3.41
6432 7192 5.608676 CGACTATCGCCACTATAGAAAGA 57.391 43.478 6.78 0.91 31.14 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.209812 CGGACATCTCTCGCCCGA 61.210 66.667 0.00 0.00 42.49 5.14
56 57 3.406595 CTGCCACCCTCGAATCCCC 62.407 68.421 0.00 0.00 0.00 4.81
305 342 2.217038 GCCTCATCCGCTCCCCATA 61.217 63.158 0.00 0.00 0.00 2.74
410 448 1.676529 GATCGATCAGACCACTCGGAA 59.323 52.381 20.52 0.00 35.59 4.30
517 556 2.114616 CCAGCCTTCTAGTGATGTCCT 58.885 52.381 0.00 0.00 0.00 3.85
519 558 1.474143 GGCCAGCCTTCTAGTGATGTC 60.474 57.143 0.00 0.00 0.00 3.06
520 559 0.543749 GGCCAGCCTTCTAGTGATGT 59.456 55.000 0.00 0.00 0.00 3.06
521 560 0.835941 AGGCCAGCCTTCTAGTGATG 59.164 55.000 5.04 0.00 45.70 3.07
522 561 3.331252 AGGCCAGCCTTCTAGTGAT 57.669 52.632 5.04 0.00 45.70 3.06
523 562 4.896979 AGGCCAGCCTTCTAGTGA 57.103 55.556 5.04 0.00 45.70 3.41
538 577 3.324930 TGCCACTGCCAGGAGAGG 61.325 66.667 0.00 0.00 36.33 3.69
539 578 2.268280 CTGCCACTGCCAGGAGAG 59.732 66.667 0.00 0.00 36.33 3.20
540 579 3.324930 CCTGCCACTGCCAGGAGA 61.325 66.667 0.00 0.00 37.74 3.71
541 580 2.703675 AAACCTGCCACTGCCAGGAG 62.704 60.000 13.03 0.00 38.43 3.69
542 581 2.697147 GAAACCTGCCACTGCCAGGA 62.697 60.000 13.03 0.00 38.43 3.86
543 582 2.203538 AAACCTGCCACTGCCAGG 60.204 61.111 4.44 4.44 39.92 4.45
544 583 2.270986 GGAAACCTGCCACTGCCAG 61.271 63.158 0.00 0.00 36.33 4.85
545 584 2.203480 GGAAACCTGCCACTGCCA 60.203 61.111 0.00 0.00 36.33 4.92
546 585 3.365265 CGGAAACCTGCCACTGCC 61.365 66.667 0.00 0.00 36.33 4.85
547 586 3.365265 CCGGAAACCTGCCACTGC 61.365 66.667 0.00 0.00 38.26 4.40
548 587 1.966451 GACCGGAAACCTGCCACTG 60.966 63.158 9.46 0.00 0.00 3.66
549 588 2.430367 GACCGGAAACCTGCCACT 59.570 61.111 9.46 0.00 0.00 4.00
550 589 3.047877 CGACCGGAAACCTGCCAC 61.048 66.667 9.46 0.00 0.00 5.01
554 593 3.047877 GTGGCGACCGGAAACCTG 61.048 66.667 9.46 0.00 0.00 4.00
555 594 4.675029 CGTGGCGACCGGAAACCT 62.675 66.667 9.46 0.00 0.00 3.50
564 603 4.400109 TCTCTCGTGCGTGGCGAC 62.400 66.667 0.00 0.00 34.47 5.19
565 604 4.103103 CTCTCTCGTGCGTGGCGA 62.103 66.667 0.00 0.00 36.85 5.54
566 605 3.610791 TTCTCTCTCGTGCGTGGCG 62.611 63.158 0.00 0.00 0.00 5.69
567 606 0.944311 TTTTCTCTCTCGTGCGTGGC 60.944 55.000 0.00 0.00 0.00 5.01
568 607 1.192534 GTTTTTCTCTCTCGTGCGTGG 59.807 52.381 0.00 0.00 0.00 4.94
569 608 1.136884 CGTTTTTCTCTCTCGTGCGTG 60.137 52.381 0.00 0.00 0.00 5.34
570 609 1.129326 CGTTTTTCTCTCTCGTGCGT 58.871 50.000 0.00 0.00 0.00 5.24
571 610 0.179272 GCGTTTTTCTCTCTCGTGCG 60.179 55.000 0.00 0.00 0.00 5.34
572 611 1.140816 AGCGTTTTTCTCTCTCGTGC 58.859 50.000 0.00 0.00 0.00 5.34
573 612 2.794910 TGAAGCGTTTTTCTCTCTCGTG 59.205 45.455 0.00 0.00 0.00 4.35
574 613 3.093717 TGAAGCGTTTTTCTCTCTCGT 57.906 42.857 0.00 0.00 0.00 4.18
575 614 4.653806 ATTGAAGCGTTTTTCTCTCTCG 57.346 40.909 0.00 0.00 0.00 4.04
576 615 6.366332 TGTCTATTGAAGCGTTTTTCTCTCTC 59.634 38.462 0.00 0.00 0.00 3.20
577 616 6.223852 TGTCTATTGAAGCGTTTTTCTCTCT 58.776 36.000 0.00 0.00 0.00 3.10
578 617 6.467723 TGTCTATTGAAGCGTTTTTCTCTC 57.532 37.500 0.00 0.00 0.00 3.20
579 618 7.173218 TGAATGTCTATTGAAGCGTTTTTCTCT 59.827 33.333 0.00 0.00 0.00 3.10
580 619 7.298122 TGAATGTCTATTGAAGCGTTTTTCTC 58.702 34.615 0.00 0.00 0.00 2.87
581 620 7.041098 ACTGAATGTCTATTGAAGCGTTTTTCT 60.041 33.333 0.00 0.00 0.00 2.52
582 621 7.078228 ACTGAATGTCTATTGAAGCGTTTTTC 58.922 34.615 0.00 0.00 0.00 2.29
583 622 6.970484 ACTGAATGTCTATTGAAGCGTTTTT 58.030 32.000 0.00 0.00 0.00 1.94
584 623 6.560253 ACTGAATGTCTATTGAAGCGTTTT 57.440 33.333 0.00 0.00 0.00 2.43
585 624 6.560253 AACTGAATGTCTATTGAAGCGTTT 57.440 33.333 0.00 0.00 0.00 3.60
586 625 6.560253 AAACTGAATGTCTATTGAAGCGTT 57.440 33.333 0.00 0.00 0.00 4.84
587 626 6.017109 ACAAAACTGAATGTCTATTGAAGCGT 60.017 34.615 0.00 0.00 0.00 5.07
588 627 6.373779 ACAAAACTGAATGTCTATTGAAGCG 58.626 36.000 0.00 0.00 0.00 4.68
589 628 9.282247 CATACAAAACTGAATGTCTATTGAAGC 57.718 33.333 0.00 0.00 0.00 3.86
597 636 9.950680 CTGTTTAACATACAAAACTGAATGTCT 57.049 29.630 0.00 0.00 36.95 3.41
598 637 9.730420 ACTGTTTAACATACAAAACTGAATGTC 57.270 29.630 0.00 0.00 37.72 3.06
599 638 9.515020 CACTGTTTAACATACAAAACTGAATGT 57.485 29.630 0.00 0.00 37.72 2.71
600 639 9.515020 ACACTGTTTAACATACAAAACTGAATG 57.485 29.630 0.00 4.00 37.72 2.67
601 640 9.730420 GACACTGTTTAACATACAAAACTGAAT 57.270 29.630 0.00 0.84 37.72 2.57
602 641 8.185505 GGACACTGTTTAACATACAAAACTGAA 58.814 33.333 0.00 0.00 37.72 3.02
603 642 7.337184 TGGACACTGTTTAACATACAAAACTGA 59.663 33.333 0.00 0.00 37.72 3.41
604 643 7.476667 TGGACACTGTTTAACATACAAAACTG 58.523 34.615 0.00 0.00 39.22 3.16
605 644 7.633193 TGGACACTGTTTAACATACAAAACT 57.367 32.000 0.00 0.00 36.70 2.66
606 645 8.349983 AGATGGACACTGTTTAACATACAAAAC 58.650 33.333 0.00 0.00 36.38 2.43
607 646 8.349245 CAGATGGACACTGTTTAACATACAAAA 58.651 33.333 0.00 0.00 0.00 2.44
608 647 7.500892 ACAGATGGACACTGTTTAACATACAAA 59.499 33.333 0.00 0.00 44.69 2.83
609 648 6.995686 ACAGATGGACACTGTTTAACATACAA 59.004 34.615 0.00 0.00 44.69 2.41
610 649 6.530120 ACAGATGGACACTGTTTAACATACA 58.470 36.000 0.00 0.00 44.69 2.29
611 650 8.718102 ATACAGATGGACACTGTTTAACATAC 57.282 34.615 0.00 0.00 44.69 2.39
612 651 9.378551 GAATACAGATGGACACTGTTTAACATA 57.621 33.333 0.00 0.00 44.69 2.29
613 652 7.336931 GGAATACAGATGGACACTGTTTAACAT 59.663 37.037 0.00 0.00 44.69 2.71
614 653 6.653320 GGAATACAGATGGACACTGTTTAACA 59.347 38.462 0.00 0.00 44.69 2.41
615 654 6.653320 TGGAATACAGATGGACACTGTTTAAC 59.347 38.462 0.00 0.00 44.69 2.01
616 655 6.774673 TGGAATACAGATGGACACTGTTTAA 58.225 36.000 0.00 0.00 44.69 1.52
617 656 6.367374 TGGAATACAGATGGACACTGTTTA 57.633 37.500 0.00 0.00 44.69 2.01
618 657 5.241403 TGGAATACAGATGGACACTGTTT 57.759 39.130 0.00 0.00 44.69 2.83
619 658 4.908601 TGGAATACAGATGGACACTGTT 57.091 40.909 0.00 0.00 44.69 3.16
621 660 6.166984 ACTATGGAATACAGATGGACACTG 57.833 41.667 0.00 0.00 40.68 3.66
622 661 5.899547 TGACTATGGAATACAGATGGACACT 59.100 40.000 0.00 0.00 0.00 3.55
623 662 6.161855 TGACTATGGAATACAGATGGACAC 57.838 41.667 0.00 0.00 0.00 3.67
624 663 6.156083 TGTTGACTATGGAATACAGATGGACA 59.844 38.462 0.00 0.00 0.00 4.02
625 664 6.582636 TGTTGACTATGGAATACAGATGGAC 58.417 40.000 0.00 0.00 0.00 4.02
626 665 6.806668 TGTTGACTATGGAATACAGATGGA 57.193 37.500 0.00 0.00 0.00 3.41
627 666 7.864108 TTTGTTGACTATGGAATACAGATGG 57.136 36.000 0.00 0.00 0.00 3.51
628 667 9.941664 GATTTTGTTGACTATGGAATACAGATG 57.058 33.333 0.00 0.00 0.00 2.90
629 668 9.911788 AGATTTTGTTGACTATGGAATACAGAT 57.088 29.630 0.00 0.00 0.00 2.90
630 669 9.383519 GAGATTTTGTTGACTATGGAATACAGA 57.616 33.333 0.00 0.00 0.00 3.41
631 670 9.388506 AGAGATTTTGTTGACTATGGAATACAG 57.611 33.333 0.00 0.00 0.00 2.74
634 673 9.529325 CGTAGAGATTTTGTTGACTATGGAATA 57.471 33.333 0.00 0.00 0.00 1.75
635 674 8.041323 ACGTAGAGATTTTGTTGACTATGGAAT 58.959 33.333 0.00 0.00 0.00 3.01
636 675 7.383687 ACGTAGAGATTTTGTTGACTATGGAA 58.616 34.615 0.00 0.00 0.00 3.53
637 676 6.931838 ACGTAGAGATTTTGTTGACTATGGA 58.068 36.000 0.00 0.00 0.00 3.41
638 677 7.758076 TGTACGTAGAGATTTTGTTGACTATGG 59.242 37.037 0.00 0.00 0.00 2.74
639 678 8.683550 TGTACGTAGAGATTTTGTTGACTATG 57.316 34.615 0.00 0.00 0.00 2.23
640 679 9.871238 ATTGTACGTAGAGATTTTGTTGACTAT 57.129 29.630 0.00 0.00 0.00 2.12
642 681 9.871238 ATATTGTACGTAGAGATTTTGTTGACT 57.129 29.630 0.00 0.00 0.00 3.41
647 686 9.622004 CGGATATATTGTACGTAGAGATTTTGT 57.378 33.333 0.00 0.00 0.00 2.83
648 687 9.073368 CCGGATATATTGTACGTAGAGATTTTG 57.927 37.037 0.00 0.00 0.00 2.44
649 688 8.800332 ACCGGATATATTGTACGTAGAGATTTT 58.200 33.333 9.46 0.00 0.00 1.82
650 689 8.345724 ACCGGATATATTGTACGTAGAGATTT 57.654 34.615 9.46 0.00 0.00 2.17
651 690 7.934855 ACCGGATATATTGTACGTAGAGATT 57.065 36.000 9.46 0.00 0.00 2.40
652 691 7.934855 AACCGGATATATTGTACGTAGAGAT 57.065 36.000 9.46 0.00 0.00 2.75
653 692 8.846943 TTAACCGGATATATTGTACGTAGAGA 57.153 34.615 9.46 0.00 0.00 3.10
654 693 9.334693 GTTTAACCGGATATATTGTACGTAGAG 57.665 37.037 9.46 0.00 0.00 2.43
655 694 8.845227 TGTTTAACCGGATATATTGTACGTAGA 58.155 33.333 9.46 0.00 0.00 2.59
656 695 9.630098 ATGTTTAACCGGATATATTGTACGTAG 57.370 33.333 9.46 0.00 0.00 3.51
658 697 9.630098 CTATGTTTAACCGGATATATTGTACGT 57.370 33.333 9.46 0.00 0.00 3.57
659 698 9.079833 CCTATGTTTAACCGGATATATTGTACG 57.920 37.037 9.46 0.00 0.00 3.67
667 706 7.869429 CGTAGTTTCCTATGTTTAACCGGATAT 59.131 37.037 9.46 0.00 0.00 1.63
668 707 7.202526 CGTAGTTTCCTATGTTTAACCGGATA 58.797 38.462 9.46 0.00 0.00 2.59
669 708 6.044682 CGTAGTTTCCTATGTTTAACCGGAT 58.955 40.000 9.46 0.00 0.00 4.18
670 709 5.410067 CGTAGTTTCCTATGTTTAACCGGA 58.590 41.667 9.46 0.00 0.00 5.14
671 710 4.567959 CCGTAGTTTCCTATGTTTAACCGG 59.432 45.833 0.00 0.00 0.00 5.28
672 711 4.567959 CCCGTAGTTTCCTATGTTTAACCG 59.432 45.833 0.00 0.00 0.00 4.44
673 712 5.491070 ACCCGTAGTTTCCTATGTTTAACC 58.509 41.667 0.00 0.00 0.00 2.85
674 713 6.621380 GCAACCCGTAGTTTCCTATGTTTAAC 60.621 42.308 0.00 0.00 36.18 2.01
675 714 5.412286 GCAACCCGTAGTTTCCTATGTTTAA 59.588 40.000 0.00 0.00 36.18 1.52
676 715 4.937015 GCAACCCGTAGTTTCCTATGTTTA 59.063 41.667 0.00 0.00 36.18 2.01
677 716 3.754850 GCAACCCGTAGTTTCCTATGTTT 59.245 43.478 0.00 0.00 36.18 2.83
678 717 3.244630 TGCAACCCGTAGTTTCCTATGTT 60.245 43.478 0.00 0.00 36.18 2.71
679 718 2.303600 TGCAACCCGTAGTTTCCTATGT 59.696 45.455 0.00 0.00 36.18 2.29
680 719 2.980568 TGCAACCCGTAGTTTCCTATG 58.019 47.619 0.00 0.00 36.18 2.23
681 720 3.262405 TCTTGCAACCCGTAGTTTCCTAT 59.738 43.478 0.00 0.00 36.18 2.57
682 721 2.633967 TCTTGCAACCCGTAGTTTCCTA 59.366 45.455 0.00 0.00 36.18 2.94
683 722 1.418637 TCTTGCAACCCGTAGTTTCCT 59.581 47.619 0.00 0.00 36.18 3.36
684 723 1.804748 CTCTTGCAACCCGTAGTTTCC 59.195 52.381 0.00 0.00 36.18 3.13
693 732 3.071479 TCGACAAATACTCTTGCAACCC 58.929 45.455 0.00 0.00 0.00 4.11
699 738 5.779806 AACGGATTCGACAAATACTCTTG 57.220 39.130 0.00 0.00 40.11 3.02
734 773 0.108424 AGAGTCCGATGCAAGCTGTC 60.108 55.000 0.00 0.00 0.00 3.51
809 872 0.736325 CGGCCTCGAGATTCGTGTTT 60.736 55.000 15.71 0.00 41.35 2.83
1415 1507 2.054363 CATTACAGCCAGATCGCTACG 58.946 52.381 0.00 0.00 36.82 3.51
1720 1814 1.469703 CCTGAGCATTCATTTGTGCGA 59.530 47.619 0.00 0.00 45.69 5.10
2273 2368 4.158384 CAACATTAGAAACATCACACGGC 58.842 43.478 0.00 0.00 0.00 5.68
2458 2553 8.184848 CAGATCGTCAGACAGATAAACTAAGAA 58.815 37.037 0.41 0.00 0.00 2.52
2692 2787 4.124851 AGTCGCAAAAGGTGGATACTAG 57.875 45.455 0.00 0.00 37.61 2.57
3643 3742 3.686241 TGATCAAGCGACAATTCCTCAAG 59.314 43.478 0.00 0.00 0.00 3.02
3737 3836 6.715347 ATTCCAATATTAGCAACCTGAACC 57.285 37.500 0.00 0.00 0.00 3.62
3799 3898 9.549078 ACAAGTTTTTGTTTTCTTAGTTTCCAA 57.451 25.926 0.00 0.00 45.01 3.53
3866 3965 6.421801 CCAGTTTCCTGCACTTAATTTTTCAG 59.578 38.462 0.00 0.00 37.38 3.02
3946 4049 4.095782 GGAATTCACTTGGCGCAGTTATTA 59.904 41.667 10.83 0.00 0.00 0.98
4778 4881 7.279981 TGGTTACAACTACTGTCATATCATTGC 59.720 37.037 0.00 0.00 39.64 3.56
5274 5404 4.855388 CAGTGCTTGATTCAACATGCTAAC 59.145 41.667 9.63 2.59 40.16 2.34
5516 6186 6.819284 ACACAAAATCATCACAATCCTTGTT 58.181 32.000 0.00 0.00 43.23 2.83
5607 6278 4.391155 TGGAGCACGTAACCAAACTTAAT 58.609 39.130 5.30 0.00 0.00 1.40
5611 6282 1.140252 ACTGGAGCACGTAACCAAACT 59.860 47.619 8.46 0.00 33.14 2.66
5702 6373 4.627741 GCTGTCCCAGGTATACCAAAATGA 60.628 45.833 23.87 9.63 38.89 2.57
5856 6545 3.193267 GGCATTAAACTGAGCACAATGGA 59.807 43.478 0.00 0.00 0.00 3.41
5857 6546 3.194116 AGGCATTAAACTGAGCACAATGG 59.806 43.478 0.00 0.00 0.00 3.16
5858 6547 4.445452 AGGCATTAAACTGAGCACAATG 57.555 40.909 0.00 0.00 0.00 2.82
5859 6548 6.389906 GTTTAGGCATTAAACTGAGCACAAT 58.610 36.000 13.04 0.00 44.99 2.71
5860 6549 5.768317 GTTTAGGCATTAAACTGAGCACAA 58.232 37.500 13.04 0.00 44.99 3.33
5861 6550 5.371115 GTTTAGGCATTAAACTGAGCACA 57.629 39.130 13.04 0.00 44.99 4.57
5901 6592 3.260475 TGCGACAAGTTATAGCACCAT 57.740 42.857 0.00 0.00 32.43 3.55
5904 6595 2.936498 ACCATGCGACAAGTTATAGCAC 59.064 45.455 0.00 0.00 40.82 4.40
5942 6635 2.802724 ATACAGCGGCATACGGGCA 61.803 57.895 1.45 0.00 44.51 5.36
5998 6691 1.327690 ACTCACACCCACTGACGTGT 61.328 55.000 0.00 0.00 43.90 4.49
6003 6696 0.463654 GCAACACTCACACCCACTGA 60.464 55.000 0.00 0.00 0.00 3.41
6162 6855 3.616219 CAAATTGGAATCCCACGGAGTA 58.384 45.455 0.00 0.00 41.61 2.59
6167 6860 0.808125 TCGCAAATTGGAATCCCACG 59.192 50.000 0.00 0.00 43.41 4.94
6180 6873 3.644966 ATTTATCCTGGAGGTCGCAAA 57.355 42.857 1.52 0.00 36.34 3.68
6181 6874 3.494398 GCTATTTATCCTGGAGGTCGCAA 60.494 47.826 1.52 0.00 36.34 4.85
6193 6886 5.476599 TGGTTACCATGCATGCTATTTATCC 59.523 40.000 21.69 13.81 0.00 2.59
6194 6887 6.381801 GTGGTTACCATGCATGCTATTTATC 58.618 40.000 21.69 5.96 35.28 1.75
6198 6891 2.958355 GGTGGTTACCATGCATGCTATT 59.042 45.455 21.69 7.31 46.71 1.73
6199 6892 2.586425 GGTGGTTACCATGCATGCTAT 58.414 47.619 21.69 10.98 46.71 2.97
6200 6893 2.051334 GGTGGTTACCATGCATGCTA 57.949 50.000 21.69 9.51 46.71 3.49
6201 6894 2.886382 GGTGGTTACCATGCATGCT 58.114 52.632 21.69 10.65 46.71 3.79
6210 6903 7.759450 TACACGAATTGTCCTGGTGGTTACC 62.759 48.000 0.00 0.00 42.57 2.85
6211 6904 2.482721 CACGAATTGTCCTGGTGGTTAC 59.517 50.000 0.00 0.00 34.23 2.50
6212 6905 2.105134 ACACGAATTGTCCTGGTGGTTA 59.895 45.455 0.00 0.00 29.79 2.85
6213 6906 1.133915 ACACGAATTGTCCTGGTGGTT 60.134 47.619 0.00 0.00 29.79 3.67
6214 6907 0.472471 ACACGAATTGTCCTGGTGGT 59.528 50.000 0.00 0.00 29.79 4.16
6215 6908 2.073816 GTACACGAATTGTCCTGGTGG 58.926 52.381 0.00 0.00 39.91 4.61
6216 6909 2.761559 TGTACACGAATTGTCCTGGTG 58.238 47.619 0.00 0.00 39.91 4.17
6217 6910 3.135994 GTTGTACACGAATTGTCCTGGT 58.864 45.455 0.00 0.00 39.91 4.00
6218 6911 3.399330 AGTTGTACACGAATTGTCCTGG 58.601 45.455 0.00 0.00 39.91 4.45
6219 6912 6.721571 ATAAGTTGTACACGAATTGTCCTG 57.278 37.500 0.00 0.00 39.91 3.86
6220 6913 6.534079 GCTATAAGTTGTACACGAATTGTCCT 59.466 38.462 0.00 0.00 39.91 3.85
6221 6914 6.534079 AGCTATAAGTTGTACACGAATTGTCC 59.466 38.462 0.00 0.00 39.91 4.02
6222 6915 7.391786 CAGCTATAAGTTGTACACGAATTGTC 58.608 38.462 0.00 0.00 39.91 3.18
6223 6916 6.312918 CCAGCTATAAGTTGTACACGAATTGT 59.687 38.462 0.00 0.00 42.84 2.71
6224 6917 6.533723 TCCAGCTATAAGTTGTACACGAATTG 59.466 38.462 0.00 0.00 0.00 2.32
6225 6918 6.636705 TCCAGCTATAAGTTGTACACGAATT 58.363 36.000 0.00 0.00 0.00 2.17
6226 6919 6.216801 TCCAGCTATAAGTTGTACACGAAT 57.783 37.500 0.00 0.00 0.00 3.34
6227 6920 5.648178 TCCAGCTATAAGTTGTACACGAA 57.352 39.130 0.00 0.00 0.00 3.85
6228 6921 5.648178 TTCCAGCTATAAGTTGTACACGA 57.352 39.130 0.00 0.00 0.00 4.35
6229 6922 5.867716 AGTTTCCAGCTATAAGTTGTACACG 59.132 40.000 0.00 0.00 0.00 4.49
6230 6923 7.386848 TGAAGTTTCCAGCTATAAGTTGTACAC 59.613 37.037 0.00 0.00 0.00 2.90
6231 6924 7.446769 TGAAGTTTCCAGCTATAAGTTGTACA 58.553 34.615 0.00 0.00 0.00 2.90
6232 6925 7.900782 TGAAGTTTCCAGCTATAAGTTGTAC 57.099 36.000 0.00 0.00 0.00 2.90
6263 6956 3.833650 TCAATCGTACCTGTAACCTTGGA 59.166 43.478 0.00 0.00 0.00 3.53
6264 6957 4.196626 TCAATCGTACCTGTAACCTTGG 57.803 45.455 0.00 0.00 0.00 3.61
6265 6958 7.837202 TTAATCAATCGTACCTGTAACCTTG 57.163 36.000 0.00 0.00 0.00 3.61
6298 7055 0.106894 GGGAGGCGTCTAGATTTGGG 59.893 60.000 6.34 0.00 0.00 4.12
6299 7056 0.106894 GGGGAGGCGTCTAGATTTGG 59.893 60.000 6.34 0.00 0.00 3.28
6340 7100 1.017701 GGTTTCGTTCTAGTGCCCGG 61.018 60.000 0.00 0.00 0.00 5.73
6374 7134 7.023575 CAGATCACCGCCATATTATTAAAAGC 58.976 38.462 0.00 0.00 0.00 3.51
6391 7151 1.588404 CGCACGTAATGACAGATCACC 59.412 52.381 0.00 0.00 37.79 4.02


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

AutoCloner maintained by Alex Coulton.