Multiple sequence alignment - TraesCS7B01G026600

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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 TraesCS7B01G026600 chr7B 100.000 3862 0 0 1 3862 25638427 25634566 0.000000e+00 7132.0
1 TraesCS7B01G026600 chr7B 100.000 30 0 0 3833 3862 25657641 25657612 5.390000e-04 56.5
2 TraesCS7B01G026600 chr7D 95.150 2474 80 23 1203 3643 78214923 78212457 0.000000e+00 3868.0
3 TraesCS7B01G026600 chr7D 92.761 594 37 3 609 1201 78215557 78214969 0.000000e+00 854.0
4 TraesCS7B01G026600 chr7D 79.500 400 53 27 12 394 44583811 44583424 1.380000e-64 257.0
5 TraesCS7B01G026600 chr7D 76.382 398 51 23 3409 3772 58622547 58622935 1.430000e-39 174.0
6 TraesCS7B01G026600 chr7A 84.268 642 60 24 2682 3295 81644315 81643687 4.300000e-164 588.0
7 TraesCS7B01G026600 chr7A 88.889 252 14 8 3393 3643 81643627 81643389 8.110000e-77 298.0
8 TraesCS7B01G026600 chr7A 93.182 132 7 2 3645 3775 81643359 81643229 3.940000e-45 193.0
9 TraesCS7B01G026600 chr7A 89.600 125 11 2 3645 3768 62883630 62883753 1.440000e-34 158.0
10 TraesCS7B01G026600 chr7A 89.773 88 7 1 3774 3861 81642754 81642669 1.130000e-20 111.0
11 TraesCS7B01G026600 chr6B 89.831 354 33 2 174 524 561696403 561696050 5.880000e-123 451.0
12 TraesCS7B01G026600 chr6B 81.489 524 83 11 1 514 345847277 345846758 5.970000e-113 418.0
13 TraesCS7B01G026600 chr6B 79.146 398 62 17 12 394 88454500 88454109 4.950000e-64 255.0
14 TraesCS7B01G026600 chr3D 83.202 506 66 12 1 491 561413095 561413596 2.740000e-121 446.0
15 TraesCS7B01G026600 chr4D 83.164 493 63 18 1 482 144869377 144868894 2.130000e-117 433.0
16 TraesCS7B01G026600 chr4D 77.540 374 80 4 1968 2339 349563157 349562786 5.020000e-54 222.0
17 TraesCS7B01G026600 chr4D 75.676 370 87 3 2433 2801 349562675 349562308 8.520000e-42 182.0
18 TraesCS7B01G026600 chrUn 91.586 309 25 1 217 524 108616831 108616523 3.570000e-115 425.0
19 TraesCS7B01G026600 chrUn 80.682 440 61 19 9 428 15962565 15963000 1.730000e-83 320.0
20 TraesCS7B01G026600 chr3A 77.341 534 90 21 1 518 502909673 502910191 1.760000e-73 287.0
21 TraesCS7B01G026600 chr5A 78.391 435 73 14 9 426 4949515 4949945 2.960000e-66 263.0
22 TraesCS7B01G026600 chr5A 79.239 289 24 14 3510 3768 623929041 623928759 6.640000e-38 169.0
23 TraesCS7B01G026600 chr5A 89.764 127 10 3 3645 3769 645126180 645126055 3.990000e-35 159.0
24 TraesCS7B01G026600 chr5A 90.164 122 10 2 3645 3765 655997040 655996920 1.440000e-34 158.0
25 TraesCS7B01G026600 chr5A 87.050 139 14 4 3505 3642 540263006 540262871 1.860000e-33 154.0
26 TraesCS7B01G026600 chr5A 86.525 141 11 5 3504 3642 649710273 649710407 8.640000e-32 148.0
27 TraesCS7B01G026600 chr4B 78.310 355 69 7 1968 2318 432787705 432787355 5.020000e-54 222.0
28 TraesCS7B01G026600 chr4B 77.326 344 75 3 2430 2772 432787229 432786888 2.350000e-47 200.0
29 TraesCS7B01G026600 chr5B 92.000 125 8 2 3645 3768 650165507 650165384 1.430000e-39 174.0
30 TraesCS7B01G026600 chr5B 80.455 220 26 14 3432 3642 515382319 515382108 6.680000e-33 152.0
31 TraesCS7B01G026600 chr5B 85.612 139 14 3 3505 3642 657596030 657596163 1.450000e-29 141.0
32 TraesCS7B01G026600 chr3B 75.978 358 72 14 174 522 41965011 41964659 5.130000e-39 172.0
33 TraesCS7B01G026600 chr3B 78.125 192 36 5 312 498 736579477 736579667 2.440000e-22 117.0
34 TraesCS7B01G026600 chr2D 90.400 125 9 3 3645 3768 607641382 607641504 1.110000e-35 161.0
35 TraesCS7B01G026600 chr1D 90.244 123 10 2 3645 3766 295280952 295281073 3.990000e-35 159.0
36 TraesCS7B01G026600 chr5D 77.966 295 30 18 3505 3769 521373376 521373665 6.680000e-33 152.0
37 TraesCS7B01G026600 chr5D 85.714 140 14 6 3505 3642 425984776 425984641 4.020000e-30 143.0
38 TraesCS7B01G026600 chr1B 75.490 204 33 14 318 514 577956719 577956912 2.470000e-12 84.2
39 TraesCS7B01G026600 chr2B 100.000 29 0 0 455 483 278820382 278820410 2.000000e-03 54.7


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 TraesCS7B01G026600 chr7B 25634566 25638427 3861 True 7132.0 7132 100.0000 1 3862 1 chr7B.!!$R1 3861
1 TraesCS7B01G026600 chr7D 78212457 78215557 3100 True 2361.0 3868 93.9555 609 3643 2 chr7D.!!$R2 3034
2 TraesCS7B01G026600 chr7A 81642669 81644315 1646 True 297.5 588 89.0280 2682 3861 4 chr7A.!!$R1 1179
3 TraesCS7B01G026600 chr6B 345846758 345847277 519 True 418.0 418 81.4890 1 514 1 chr6B.!!$R2 513
4 TraesCS7B01G026600 chr3D 561413095 561413596 501 False 446.0 446 83.2020 1 491 1 chr3D.!!$F1 490
5 TraesCS7B01G026600 chr4D 349562308 349563157 849 True 202.0 222 76.6080 1968 2801 2 chr4D.!!$R2 833
6 TraesCS7B01G026600 chr3A 502909673 502910191 518 False 287.0 287 77.3410 1 518 1 chr3A.!!$F1 517
7 TraesCS7B01G026600 chr4B 432786888 432787705 817 True 211.0 222 77.8180 1968 2772 2 chr4B.!!$R1 804

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
839 863 0.034574 TTATGGGCCAGTGCGTGAAT 60.035 50.0 13.78 0.0 38.85 2.57 F
844 868 0.109597 GGCCAGTGCGTGAATCAAAG 60.110 55.0 0.00 0.0 38.85 2.77 F
994 1019 0.537143 AGACACCAATTGCTTCCGCA 60.537 50.0 0.00 0.0 46.24 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1821 1.269831 GGTAGCTACTCCCGAATGCAG 60.270 57.143 22.74 0.00 0.00 4.41 R
1777 1846 2.025510 CAGCTGGAAAATCTCCCTTCCT 60.026 50.000 5.57 0.00 44.69 3.36 R
2971 3058 0.320683 GAAGCCCCAAATGTGTTGGC 60.321 55.000 5.69 5.69 39.78 4.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.836072 TGGATCATGAGAGGCCCA 57.164 55.556 0.00 0.73 0.00 5.36
21 22 2.305009 GGATCATGAGAGGCCCAAAAG 58.695 52.381 0.00 0.00 0.00 2.27
22 23 2.092212 GGATCATGAGAGGCCCAAAAGA 60.092 50.000 0.00 0.00 0.00 2.52
23 24 3.624777 GATCATGAGAGGCCCAAAAGAA 58.375 45.455 0.00 0.00 0.00 2.52
25 26 3.157087 TCATGAGAGGCCCAAAAGAAAC 58.843 45.455 0.00 0.00 0.00 2.78
26 27 2.746279 TGAGAGGCCCAAAAGAAACA 57.254 45.000 0.00 0.00 0.00 2.83
27 28 3.243359 TGAGAGGCCCAAAAGAAACAT 57.757 42.857 0.00 0.00 0.00 2.71
28 29 4.380843 TGAGAGGCCCAAAAGAAACATA 57.619 40.909 0.00 0.00 0.00 2.29
79 82 2.035704 AGCTGTCTGATTCTATCGGCAG 59.964 50.000 11.93 11.93 40.05 4.85
189 202 3.181440 GGGGGATGTTAGATTGATCTGCA 60.181 47.826 3.79 3.74 37.76 4.41
193 206 3.998913 TGTTAGATTGATCTGCACCCA 57.001 42.857 3.79 0.00 37.76 4.51
199 212 3.698040 AGATTGATCTGCACCCATTTGAC 59.302 43.478 0.00 0.00 35.42 3.18
201 214 1.355381 TGATCTGCACCCATTTGACCT 59.645 47.619 0.00 0.00 0.00 3.85
211 224 1.522668 CATTTGACCTCAACGGCTCA 58.477 50.000 0.00 0.00 35.28 4.26
258 271 2.434774 GGACGCCCAACCCTCTTT 59.565 61.111 0.00 0.00 0.00 2.52
272 285 0.469892 CTCTTTTGGTTGGTGGGCCT 60.470 55.000 4.53 0.00 35.27 5.19
290 304 1.269309 CCTCTGTCGCCAGCACTATAC 60.269 57.143 0.00 0.00 38.66 1.47
299 315 2.035321 GCCAGCACTATACAGAGAGGTC 59.965 54.545 0.00 0.00 0.00 3.85
317 333 4.101448 GGGGCCAGACGCACAGAT 62.101 66.667 4.39 0.00 45.76 2.90
375 392 3.240302 CCCCAATCCGATCTAGGTTAGT 58.760 50.000 0.00 0.00 0.00 2.24
427 446 2.591753 CCCACTCGCCATCACCAT 59.408 61.111 0.00 0.00 0.00 3.55
428 447 1.077501 CCCACTCGCCATCACCATT 60.078 57.895 0.00 0.00 0.00 3.16
432 451 0.324614 ACTCGCCATCACCATTGTCA 59.675 50.000 0.00 0.00 0.00 3.58
439 462 0.253044 ATCACCATTGTCACCCTCCG 59.747 55.000 0.00 0.00 0.00 4.63
491 515 4.399934 CCAAGGAGAAGGTAGACTACTGTC 59.600 50.000 12.31 9.60 43.22 3.51
501 525 8.880991 AAGGTAGACTACTGTCAAATCTCTAA 57.119 34.615 12.31 0.00 45.20 2.10
502 526 9.482175 AAGGTAGACTACTGTCAAATCTCTAAT 57.518 33.333 12.31 0.00 45.20 1.73
514 538 6.209788 GTCAAATCTCTAATCTACCCGATCCT 59.790 42.308 0.00 0.00 0.00 3.24
518 542 5.817784 TCTCTAATCTACCCGATCCTAAGG 58.182 45.833 0.00 0.00 0.00 2.69
519 543 5.550796 TCTCTAATCTACCCGATCCTAAGGA 59.449 44.000 0.00 0.00 35.55 3.36
520 544 6.217900 TCTCTAATCTACCCGATCCTAAGGAT 59.782 42.308 0.00 0.00 46.28 3.24
540 564 8.928270 AAGGATCTAGTATCAGTTAAAACACG 57.072 34.615 0.00 0.00 0.00 4.49
541 565 8.289939 AGGATCTAGTATCAGTTAAAACACGA 57.710 34.615 0.00 0.00 0.00 4.35
542 566 8.746530 AGGATCTAGTATCAGTTAAAACACGAA 58.253 33.333 0.00 0.00 0.00 3.85
543 567 9.362539 GGATCTAGTATCAGTTAAAACACGAAA 57.637 33.333 0.00 0.00 0.00 3.46
545 569 9.701098 ATCTAGTATCAGTTAAAACACGAAACA 57.299 29.630 0.00 0.00 0.00 2.83
546 570 9.531942 TCTAGTATCAGTTAAAACACGAAACAA 57.468 29.630 0.00 0.00 0.00 2.83
549 573 8.885722 AGTATCAGTTAAAACACGAAACAAAGA 58.114 29.630 0.00 0.00 0.00 2.52
550 574 9.493206 GTATCAGTTAAAACACGAAACAAAGAA 57.507 29.630 0.00 0.00 0.00 2.52
551 575 7.784790 TCAGTTAAAACACGAAACAAAGAAC 57.215 32.000 0.00 0.00 0.00 3.01
552 576 7.361127 TCAGTTAAAACACGAAACAAAGAACA 58.639 30.769 0.00 0.00 0.00 3.18
553 577 7.324135 TCAGTTAAAACACGAAACAAAGAACAC 59.676 33.333 0.00 0.00 0.00 3.32
554 578 6.583427 AGTTAAAACACGAAACAAAGAACACC 59.417 34.615 0.00 0.00 0.00 4.16
555 579 4.506886 AAACACGAAACAAAGAACACCA 57.493 36.364 0.00 0.00 0.00 4.17
556 580 3.757745 ACACGAAACAAAGAACACCAG 57.242 42.857 0.00 0.00 0.00 4.00
557 581 3.078837 ACACGAAACAAAGAACACCAGT 58.921 40.909 0.00 0.00 0.00 4.00
558 582 3.119990 ACACGAAACAAAGAACACCAGTG 60.120 43.478 0.00 0.00 0.00 3.66
560 584 4.093703 CACGAAACAAAGAACACCAGTGTA 59.906 41.667 3.43 0.00 44.13 2.90
561 585 4.331717 ACGAAACAAAGAACACCAGTGTAG 59.668 41.667 3.43 0.00 44.13 2.74
562 586 4.569162 CGAAACAAAGAACACCAGTGTAGA 59.431 41.667 3.43 0.00 44.13 2.59
563 587 5.501897 CGAAACAAAGAACACCAGTGTAGAC 60.502 44.000 3.43 0.00 44.13 2.59
564 588 3.454375 ACAAAGAACACCAGTGTAGACG 58.546 45.455 3.43 0.00 44.13 4.18
565 589 3.131577 ACAAAGAACACCAGTGTAGACGA 59.868 43.478 3.43 0.00 44.13 4.20
566 590 4.116961 CAAAGAACACCAGTGTAGACGAA 58.883 43.478 3.43 0.00 44.13 3.85
567 591 4.602340 AAGAACACCAGTGTAGACGAAT 57.398 40.909 3.43 0.00 44.13 3.34
568 592 3.914312 AGAACACCAGTGTAGACGAATG 58.086 45.455 3.43 0.00 44.13 2.67
569 593 2.743636 ACACCAGTGTAGACGAATGG 57.256 50.000 0.54 0.00 42.90 3.16
570 594 2.244695 ACACCAGTGTAGACGAATGGA 58.755 47.619 0.54 0.00 42.90 3.41
571 595 2.231478 ACACCAGTGTAGACGAATGGAG 59.769 50.000 0.54 0.00 42.90 3.86
572 596 1.204941 ACCAGTGTAGACGAATGGAGC 59.795 52.381 4.05 0.00 34.99 4.70
573 597 1.204704 CCAGTGTAGACGAATGGAGCA 59.795 52.381 0.00 0.00 32.55 4.26
574 598 2.534298 CAGTGTAGACGAATGGAGCAG 58.466 52.381 0.00 0.00 0.00 4.24
575 599 1.134965 AGTGTAGACGAATGGAGCAGC 60.135 52.381 0.00 0.00 0.00 5.25
576 600 1.134965 GTGTAGACGAATGGAGCAGCT 60.135 52.381 0.00 0.00 0.00 4.24
577 601 1.135139 TGTAGACGAATGGAGCAGCTC 59.865 52.381 14.69 14.69 0.00 4.09
578 602 0.382158 TAGACGAATGGAGCAGCTCG 59.618 55.000 16.47 7.87 37.33 5.03
579 603 2.510238 ACGAATGGAGCAGCTCGC 60.510 61.111 16.47 9.83 42.91 5.03
580 604 2.510012 CGAATGGAGCAGCTCGCA 60.510 61.111 16.47 15.02 46.13 5.10
581 605 2.523507 CGAATGGAGCAGCTCGCAG 61.524 63.158 16.47 2.30 46.13 5.18
582 606 2.124819 AATGGAGCAGCTCGCAGG 60.125 61.111 16.47 0.00 46.13 4.85
583 607 4.853050 ATGGAGCAGCTCGCAGGC 62.853 66.667 16.47 2.51 46.13 4.85
585 609 4.853050 GGAGCAGCTCGCAGGCAT 62.853 66.667 16.47 0.00 46.13 4.40
586 610 3.574445 GAGCAGCTCGCAGGCATG 61.574 66.667 6.67 0.00 46.13 4.06
587 611 4.405671 AGCAGCTCGCAGGCATGT 62.406 61.111 0.00 0.00 46.13 3.21
588 612 3.873883 GCAGCTCGCAGGCATGTC 61.874 66.667 0.00 0.00 41.79 3.06
589 613 2.435410 CAGCTCGCAGGCATGTCA 60.435 61.111 0.00 0.00 34.17 3.58
590 614 1.818363 CAGCTCGCAGGCATGTCAT 60.818 57.895 0.00 0.00 34.17 3.06
591 615 1.523258 AGCTCGCAGGCATGTCATC 60.523 57.895 0.00 0.00 34.17 2.92
592 616 2.879070 GCTCGCAGGCATGTCATCG 61.879 63.158 0.00 2.11 0.00 3.84
593 617 2.879070 CTCGCAGGCATGTCATCGC 61.879 63.158 0.00 0.00 0.00 4.58
594 618 2.893895 CGCAGGCATGTCATCGCT 60.894 61.111 0.00 0.00 0.00 4.93
595 619 2.713770 GCAGGCATGTCATCGCTG 59.286 61.111 0.00 0.00 0.00 5.18
596 620 2.110967 GCAGGCATGTCATCGCTGT 61.111 57.895 0.00 0.00 0.00 4.40
597 621 1.651240 GCAGGCATGTCATCGCTGTT 61.651 55.000 0.00 0.00 0.00 3.16
598 622 0.098200 CAGGCATGTCATCGCTGTTG 59.902 55.000 0.00 0.00 0.00 3.33
599 623 1.028330 AGGCATGTCATCGCTGTTGG 61.028 55.000 0.00 0.00 0.00 3.77
600 624 1.226491 GCATGTCATCGCTGTTGGC 60.226 57.895 0.00 0.00 37.64 4.52
601 625 1.651240 GCATGTCATCGCTGTTGGCT 61.651 55.000 0.00 0.00 39.13 4.75
602 626 0.376152 CATGTCATCGCTGTTGGCTC 59.624 55.000 0.00 0.00 39.13 4.70
603 627 1.086067 ATGTCATCGCTGTTGGCTCG 61.086 55.000 0.00 0.00 39.13 5.03
604 628 1.738099 GTCATCGCTGTTGGCTCGT 60.738 57.895 0.00 0.00 39.13 4.18
605 629 1.005037 TCATCGCTGTTGGCTCGTT 60.005 52.632 0.00 0.00 39.13 3.85
606 630 1.133253 CATCGCTGTTGGCTCGTTG 59.867 57.895 0.00 0.00 39.13 4.10
607 631 2.034879 ATCGCTGTTGGCTCGTTGG 61.035 57.895 0.00 0.00 39.13 3.77
616 640 4.643463 TGTTGGCTCGTTGGACTAAATTA 58.357 39.130 0.00 0.00 0.00 1.40
622 646 6.759827 TGGCTCGTTGGACTAAATTAATACTC 59.240 38.462 0.00 0.00 0.00 2.59
647 671 5.516696 CAGTGTACACCAATGTAAGAGATCG 59.483 44.000 22.28 0.00 42.99 3.69
685 709 1.871077 CTTGAGCTGTGCGCATTGA 59.129 52.632 15.91 0.00 38.27 2.57
722 746 3.199946 TCACCTAACCAATCAGATCACCC 59.800 47.826 0.00 0.00 0.00 4.61
818 842 9.696572 ATAGTACTACCACTCTCTCATGTTTAA 57.303 33.333 4.31 0.00 0.00 1.52
819 843 8.596781 AGTACTACCACTCTCTCATGTTTAAT 57.403 34.615 0.00 0.00 0.00 1.40
820 844 9.036980 AGTACTACCACTCTCTCATGTTTAATT 57.963 33.333 0.00 0.00 0.00 1.40
830 854 6.547141 TCTCTCATGTTTAATTTATGGGCCAG 59.453 38.462 13.78 0.00 0.00 4.85
839 863 0.034574 TTATGGGCCAGTGCGTGAAT 60.035 50.000 13.78 0.00 38.85 2.57
844 868 0.109597 GGCCAGTGCGTGAATCAAAG 60.110 55.000 0.00 0.00 38.85 2.77
845 869 0.109597 GCCAGTGCGTGAATCAAAGG 60.110 55.000 0.00 0.00 0.00 3.11
850 874 1.067635 GTGCGTGAATCAAAGGGCAAT 60.068 47.619 2.04 0.00 31.53 3.56
857 881 6.735694 GCGTGAATCAAAGGGCAATACATAAT 60.736 38.462 0.00 0.00 0.00 1.28
870 895 7.872483 GGGCAATACATAATTTAGACAAATGGG 59.128 37.037 0.00 0.00 34.53 4.00
883 908 5.950023 AGACAAATGGGCATATGAATCTCT 58.050 37.500 6.97 0.00 0.00 3.10
888 913 9.404848 ACAAATGGGCATATGAATCTCTATATG 57.595 33.333 6.97 0.00 39.26 1.78
892 917 8.844865 TGGGCATATGAATCTCTATATGTACT 57.155 34.615 6.97 0.00 38.76 2.73
898 923 7.789202 ATGAATCTCTATATGTACTGTGGCT 57.211 36.000 0.00 0.00 0.00 4.75
903 928 2.082140 ATATGTACTGTGGCTCCCGA 57.918 50.000 0.00 0.00 0.00 5.14
905 930 0.614979 ATGTACTGTGGCTCCCGACT 60.615 55.000 0.00 0.00 0.00 4.18
910 935 2.181021 GTGGCTCCCGACTGTACG 59.819 66.667 0.00 0.00 0.00 3.67
916 941 0.592148 CTCCCGACTGTACGATAGCC 59.408 60.000 0.00 0.00 42.67 3.93
925 950 4.827692 ACTGTACGATAGCCATCAAAACA 58.172 39.130 0.00 0.00 42.67 2.83
929 954 5.703592 TGTACGATAGCCATCAAAACAAAGT 59.296 36.000 0.00 0.00 42.67 2.66
940 965 4.241681 TCAAAACAAAGTTCCACTTGCAC 58.758 39.130 0.00 0.00 38.66 4.57
983 1008 1.843851 ACCTCTCAACCAAGACACCAA 59.156 47.619 0.00 0.00 0.00 3.67
990 1015 3.068024 TCAACCAAGACACCAATTGCTTC 59.932 43.478 0.00 0.00 0.00 3.86
994 1019 0.537143 AGACACCAATTGCTTCCGCA 60.537 50.000 0.00 0.00 46.24 5.69
1030 1055 1.546323 CCTCAATTCCATGGGGATCCG 60.546 57.143 13.02 2.53 44.28 4.18
1103 1128 2.195683 CTGGTTGTGGTGGTGCCT 59.804 61.111 0.00 0.00 38.35 4.75
1186 1211 1.588674 CGGCGACATTATTAAGGCCA 58.411 50.000 5.01 0.00 40.52 5.36
1187 1212 1.944024 CGGCGACATTATTAAGGCCAA 59.056 47.619 5.01 0.00 40.52 4.52
1190 1215 2.286772 GCGACATTATTAAGGCCAACCG 60.287 50.000 5.01 0.00 42.76 4.44
1201 1226 2.613506 GCCAACCGACGAAACAGGG 61.614 63.158 0.00 0.00 0.00 4.45
1248 1317 1.338769 GGTTGCCACGACATTAGTCCT 60.339 52.381 0.00 0.00 41.87 3.85
1258 1327 3.786635 GACATTAGTCCTCATGTCGCTT 58.213 45.455 6.00 0.00 39.88 4.68
1295 1364 1.475751 CCTACGGAAGCATGGCAAGAT 60.476 52.381 0.00 0.00 0.00 2.40
1352 1421 2.900546 CCATTGTAGACCCTAGCCTAGG 59.099 54.545 11.08 11.08 45.81 3.02
1377 1446 3.117512 AGGAGGTGATGTCCAACAAGTTT 60.118 43.478 0.00 0.00 36.43 2.66
1610 1679 3.048600 TGTGGGCTATGGCTAAATCTCT 58.951 45.455 0.00 0.00 38.73 3.10
1611 1680 3.071602 TGTGGGCTATGGCTAAATCTCTC 59.928 47.826 0.00 0.00 38.73 3.20
1615 1684 3.393800 GCTATGGCTAAATCTCTCGCAA 58.606 45.455 0.00 0.00 35.22 4.85
1752 1821 1.590238 CGGAGATGTCATTTCTCGCAC 59.410 52.381 3.57 0.00 40.46 5.34
1777 1846 2.519771 TCGGGAGTAGCTACCTTGAA 57.480 50.000 20.31 1.12 30.74 2.69
1849 1918 8.089625 TGACCAACCTGAAGAAGATTATCATA 57.910 34.615 0.00 0.00 0.00 2.15
1956 2025 9.434559 GTATAAGCGTGTAAATTTTCAGATTCC 57.565 33.333 0.00 0.00 0.00 3.01
1990 2059 4.361451 ACAATCGAAGGATGCATCAAAC 57.639 40.909 27.25 15.62 31.83 2.93
2020 2089 7.541783 CAGAAAGATTGAATCCATTTTGCGTAA 59.458 33.333 0.75 0.00 0.00 3.18
2090 2159 7.042335 CCAAAGATGACTTACTCGGTCTAATT 58.958 38.462 0.00 0.00 35.05 1.40
2138 2207 6.983906 AATGAAAATAGTCAATCCATCCCC 57.016 37.500 0.00 0.00 0.00 4.81
2407 2476 9.349713 TGTGAAAGTGATTTGGACTTATAAAGT 57.650 29.630 0.00 0.00 46.38 2.66
2541 2627 2.546494 GCATCACATACCCAGCCGC 61.546 63.158 0.00 0.00 0.00 6.53
2561 2647 2.320781 CCATCCTCATCGAACTACCCT 58.679 52.381 0.00 0.00 0.00 4.34
2583 2669 3.244249 TGTGTTGTTCATCCACCACGATA 60.244 43.478 0.00 0.00 0.00 2.92
2805 2892 1.083806 ATACACTCATGCACCGCACG 61.084 55.000 0.00 0.00 43.04 5.34
2851 2938 4.336433 GCATGGTGCTCAAATTAAGCTCTA 59.664 41.667 12.47 8.25 40.96 2.43
2870 2957 5.515548 TCTACGCGATTTGATCATTATGC 57.484 39.130 15.93 0.00 0.00 3.14
2878 2965 4.801147 TTTGATCATTATGCTCGCTCAC 57.199 40.909 0.00 0.00 0.00 3.51
2881 2968 0.875908 TCATTATGCTCGCTCACGCC 60.876 55.000 0.00 0.00 39.84 5.68
2910 2997 0.109458 GCCATGTGTGCACTCATGTG 60.109 55.000 39.07 33.11 42.86 3.21
3090 3183 3.641437 TCCAGCAACAAAGCACAATAC 57.359 42.857 0.00 0.00 36.85 1.89
3229 3330 9.734984 CTCTCCTGGTTTATCCTTTTAAGTAAA 57.265 33.333 0.00 0.00 37.07 2.01
3262 3397 5.230942 TCAAATTTCGTGTGTTTTTGGTGT 58.769 33.333 0.00 0.00 0.00 4.16
3281 3417 1.951602 GTAGCGTCAAACACCCCTTTT 59.048 47.619 0.00 0.00 0.00 2.27
3291 3427 6.317642 GTCAAACACCCCTTTTAAGCAATTTT 59.682 34.615 0.00 0.00 0.00 1.82
3295 3431 6.184068 ACACCCCTTTTAAGCAATTTTTGTT 58.816 32.000 0.00 0.00 0.00 2.83
3296 3432 6.094742 ACACCCCTTTTAAGCAATTTTTGTTG 59.905 34.615 0.00 0.00 0.00 3.33
3297 3433 5.592282 ACCCCTTTTAAGCAATTTTTGTTGG 59.408 36.000 0.00 0.00 0.00 3.77
3298 3434 5.825151 CCCCTTTTAAGCAATTTTTGTTGGA 59.175 36.000 0.00 0.00 0.00 3.53
3301 3437 7.861872 CCCTTTTAAGCAATTTTTGTTGGATTG 59.138 33.333 0.00 0.00 34.67 2.67
3309 3445 7.244166 CAATTTTTGTTGGATTGCACTGTAA 57.756 32.000 0.00 0.00 0.00 2.41
3310 3446 6.843069 ATTTTTGTTGGATTGCACTGTAAC 57.157 33.333 0.00 0.00 0.00 2.50
3314 3450 3.242903 TGTTGGATTGCACTGTAACGTTG 60.243 43.478 11.99 0.00 0.00 4.10
3315 3451 1.265635 TGGATTGCACTGTAACGTTGC 59.734 47.619 11.99 10.76 0.00 4.17
3316 3452 1.591248 GATTGCACTGTAACGTTGCG 58.409 50.000 11.99 8.73 0.00 4.85
3412 3572 2.597510 GGCCCAAGTCCAACGCTT 60.598 61.111 0.00 0.00 0.00 4.68
3416 3576 1.569493 CCAAGTCCAACGCTTGTCG 59.431 57.895 0.00 0.00 41.08 4.35
3441 3601 0.034059 CGAGGCCCAGATAAAGCGAT 59.966 55.000 0.00 0.00 0.00 4.58
3457 3617 0.028505 CGATCGCAAAGCCCATGAAG 59.971 55.000 0.26 0.00 0.00 3.02
3499 3659 4.719369 GTTCCGCTCGCTCGTGGT 62.719 66.667 2.26 0.00 36.01 4.16
3500 3660 3.057548 TTCCGCTCGCTCGTGGTA 61.058 61.111 2.26 0.00 36.01 3.25
3504 3664 2.202623 GCTCGCTCGTGGTAGTGG 60.203 66.667 0.00 0.00 0.00 4.00
3505 3665 2.202623 CTCGCTCGTGGTAGTGGC 60.203 66.667 0.00 0.00 0.00 5.01
3506 3666 2.675423 TCGCTCGTGGTAGTGGCT 60.675 61.111 0.00 0.00 0.00 4.75
3556 3716 4.785453 CGCCCAGCCAAGGAGGAC 62.785 72.222 0.00 0.00 41.22 3.85
3557 3717 4.785453 GCCCAGCCAAGGAGGACG 62.785 72.222 0.00 0.00 41.22 4.79
3597 3758 3.695606 GGAGAGGCAGGTGCGACA 61.696 66.667 0.00 0.00 43.26 4.35
3643 3804 0.747255 CGACGGGTGATCAGGAAGAT 59.253 55.000 0.00 0.00 40.48 2.40
3659 3848 1.377202 GATCACATGGTGGGTGCGT 60.377 57.895 0.00 0.00 36.22 5.24
3680 3869 3.085952 TGGCTTACCATCTTCCCAAAG 57.914 47.619 0.00 0.00 42.67 2.77
3681 3870 2.378547 TGGCTTACCATCTTCCCAAAGT 59.621 45.455 0.00 0.00 42.67 2.66
3765 3955 6.478512 TCTGCAAAATTAAACTTTGGTCCT 57.521 33.333 12.70 0.00 34.89 3.85
3768 3958 6.410540 TGCAAAATTAAACTTTGGTCCTTGT 58.589 32.000 12.70 0.00 34.89 3.16
3771 3961 5.447624 AATTAAACTTTGGTCCTTGTCCG 57.552 39.130 0.00 0.00 0.00 4.79
3784 4450 2.550208 CCTTGTCCGAGCTTAAACCACT 60.550 50.000 0.00 0.00 0.00 4.00
3790 4456 3.081804 CCGAGCTTAAACCACTTCCAAT 58.918 45.455 0.00 0.00 0.00 3.16
3791 4457 3.506067 CCGAGCTTAAACCACTTCCAATT 59.494 43.478 0.00 0.00 0.00 2.32
3792 4458 4.022329 CCGAGCTTAAACCACTTCCAATTT 60.022 41.667 0.00 0.00 0.00 1.82
3793 4459 5.154222 CGAGCTTAAACCACTTCCAATTTC 58.846 41.667 0.00 0.00 0.00 2.17
3827 4493 3.432517 AGAGCAACTGAAGCTAGCG 57.567 52.632 9.55 0.00 43.58 4.26
3861 4527 1.080025 GTGCTACACGGACTGGACC 60.080 63.158 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 45 7.492524 TCAGACAGCTACAATATACCTTTCTG 58.507 38.462 0.00 0.00 33.74 3.02
46 49 8.256356 AGAATCAGACAGCTACAATATACCTT 57.744 34.615 0.00 0.00 0.00 3.50
53 56 5.777802 CCGATAGAATCAGACAGCTACAAT 58.222 41.667 0.00 0.00 39.76 2.71
79 82 2.543848 TGTTTCATCGTCACAGCTCAAC 59.456 45.455 0.00 0.00 0.00 3.18
112 115 5.621197 TTACAAGTTTCATCACCGATTGG 57.379 39.130 0.00 0.00 42.84 3.16
113 116 6.668323 ACTTTACAAGTTTCATCACCGATTG 58.332 36.000 0.00 0.00 39.04 2.67
114 117 6.877611 ACTTTACAAGTTTCATCACCGATT 57.122 33.333 0.00 0.00 39.04 3.34
171 184 4.454678 TGGGTGCAGATCAATCTAACATC 58.545 43.478 0.00 0.00 34.85 3.06
179 192 2.762327 GGTCAAATGGGTGCAGATCAAT 59.238 45.455 0.00 0.00 0.00 2.57
187 200 0.240945 CGTTGAGGTCAAATGGGTGC 59.759 55.000 0.00 0.00 37.63 5.01
189 202 0.893727 GCCGTTGAGGTCAAATGGGT 60.894 55.000 12.03 0.00 43.70 4.51
193 206 1.880027 GTTGAGCCGTTGAGGTCAAAT 59.120 47.619 7.65 0.00 43.70 2.32
199 212 2.742372 CCCGTTGAGCCGTTGAGG 60.742 66.667 0.00 0.00 44.97 3.86
243 256 1.530655 CCAAAAGAGGGTTGGGCGT 60.531 57.895 0.00 0.00 41.64 5.68
258 271 2.351924 GACAGAGGCCCACCAACCAA 62.352 60.000 0.00 0.00 39.06 3.67
284 297 1.479021 GCCCCGACCTCTCTGTATAGT 60.479 57.143 0.00 0.00 0.00 2.12
290 304 3.465403 CTGGCCCCGACCTCTCTG 61.465 72.222 0.00 0.00 0.00 3.35
336 352 3.867783 TGTCGGTGGGGTGTGTGG 61.868 66.667 0.00 0.00 0.00 4.17
375 392 3.019003 GCTTCCCGTCAGCCTAGCA 62.019 63.158 0.00 0.00 0.00 3.49
427 446 2.350895 CATGGCGGAGGGTGACAA 59.649 61.111 0.00 0.00 0.00 3.18
428 447 3.716195 CCATGGCGGAGGGTGACA 61.716 66.667 0.00 0.00 36.56 3.58
491 515 6.597832 AGGATCGGGTAGATTAGAGATTTG 57.402 41.667 0.00 0.00 40.26 2.32
519 543 9.701098 TGTTTCGTGTTTTAACTGATACTAGAT 57.299 29.630 0.00 0.00 0.00 1.98
520 544 9.531942 TTGTTTCGTGTTTTAACTGATACTAGA 57.468 29.630 0.00 0.00 0.00 2.43
523 547 8.885722 TCTTTGTTTCGTGTTTTAACTGATACT 58.114 29.630 0.00 0.00 0.00 2.12
524 548 9.493206 TTCTTTGTTTCGTGTTTTAACTGATAC 57.507 29.630 0.00 0.00 0.00 2.24
525 549 9.493206 GTTCTTTGTTTCGTGTTTTAACTGATA 57.507 29.630 0.00 0.00 0.00 2.15
526 550 8.024285 TGTTCTTTGTTTCGTGTTTTAACTGAT 58.976 29.630 0.00 0.00 0.00 2.90
527 551 7.324135 GTGTTCTTTGTTTCGTGTTTTAACTGA 59.676 33.333 0.00 0.00 0.00 3.41
528 552 7.409980 GGTGTTCTTTGTTTCGTGTTTTAACTG 60.410 37.037 0.00 0.00 0.00 3.16
529 553 6.583427 GGTGTTCTTTGTTTCGTGTTTTAACT 59.417 34.615 0.00 0.00 0.00 2.24
530 554 6.362820 TGGTGTTCTTTGTTTCGTGTTTTAAC 59.637 34.615 0.00 0.00 0.00 2.01
531 555 6.444633 TGGTGTTCTTTGTTTCGTGTTTTAA 58.555 32.000 0.00 0.00 0.00 1.52
532 556 6.010294 TGGTGTTCTTTGTTTCGTGTTTTA 57.990 33.333 0.00 0.00 0.00 1.52
533 557 4.872664 TGGTGTTCTTTGTTTCGTGTTTT 58.127 34.783 0.00 0.00 0.00 2.43
534 558 4.022676 ACTGGTGTTCTTTGTTTCGTGTTT 60.023 37.500 0.00 0.00 0.00 2.83
535 559 3.504520 ACTGGTGTTCTTTGTTTCGTGTT 59.495 39.130 0.00 0.00 0.00 3.32
536 560 3.078837 ACTGGTGTTCTTTGTTTCGTGT 58.921 40.909 0.00 0.00 0.00 4.49
537 561 3.119990 ACACTGGTGTTCTTTGTTTCGTG 60.120 43.478 0.01 0.00 41.83 4.35
538 562 3.078837 ACACTGGTGTTCTTTGTTTCGT 58.921 40.909 0.01 0.00 41.83 3.85
539 563 3.757745 ACACTGGTGTTCTTTGTTTCG 57.242 42.857 0.01 0.00 41.83 3.46
540 564 5.501897 CGTCTACACTGGTGTTCTTTGTTTC 60.502 44.000 11.69 0.00 41.83 2.78
541 565 4.331717 CGTCTACACTGGTGTTCTTTGTTT 59.668 41.667 11.69 0.00 41.83 2.83
542 566 3.869246 CGTCTACACTGGTGTTCTTTGTT 59.131 43.478 11.69 0.00 41.83 2.83
543 567 3.131577 TCGTCTACACTGGTGTTCTTTGT 59.868 43.478 11.69 0.00 41.83 2.83
544 568 3.713288 TCGTCTACACTGGTGTTCTTTG 58.287 45.455 11.69 0.25 41.83 2.77
545 569 4.395959 TTCGTCTACACTGGTGTTCTTT 57.604 40.909 11.69 0.00 41.83 2.52
546 570 4.307432 CATTCGTCTACACTGGTGTTCTT 58.693 43.478 11.69 0.00 41.83 2.52
547 571 3.306088 CCATTCGTCTACACTGGTGTTCT 60.306 47.826 11.69 0.00 41.83 3.01
548 572 2.993899 CCATTCGTCTACACTGGTGTTC 59.006 50.000 11.69 3.26 41.83 3.18
549 573 2.631062 TCCATTCGTCTACACTGGTGTT 59.369 45.455 11.69 0.00 41.83 3.32
550 574 2.231478 CTCCATTCGTCTACACTGGTGT 59.769 50.000 11.20 11.20 46.87 4.16
551 575 2.881074 CTCCATTCGTCTACACTGGTG 58.119 52.381 0.00 0.00 0.00 4.17
552 576 1.204941 GCTCCATTCGTCTACACTGGT 59.795 52.381 0.00 0.00 0.00 4.00
553 577 1.204704 TGCTCCATTCGTCTACACTGG 59.795 52.381 0.00 0.00 0.00 4.00
554 578 2.534298 CTGCTCCATTCGTCTACACTG 58.466 52.381 0.00 0.00 0.00 3.66
555 579 1.134965 GCTGCTCCATTCGTCTACACT 60.135 52.381 0.00 0.00 0.00 3.55
556 580 1.134965 AGCTGCTCCATTCGTCTACAC 60.135 52.381 0.00 0.00 0.00 2.90
557 581 1.135139 GAGCTGCTCCATTCGTCTACA 59.865 52.381 18.80 0.00 0.00 2.74
558 582 1.846541 GAGCTGCTCCATTCGTCTAC 58.153 55.000 18.80 0.00 0.00 2.59
559 583 0.382158 CGAGCTGCTCCATTCGTCTA 59.618 55.000 22.97 0.00 0.00 2.59
560 584 1.140589 CGAGCTGCTCCATTCGTCT 59.859 57.895 22.97 0.00 0.00 4.18
561 585 2.520904 GCGAGCTGCTCCATTCGTC 61.521 63.158 22.97 5.67 41.73 4.20
562 586 2.510238 GCGAGCTGCTCCATTCGT 60.510 61.111 22.97 0.00 41.73 3.85
563 587 2.510012 TGCGAGCTGCTCCATTCG 60.510 61.111 22.97 13.37 46.63 3.34
564 588 2.178890 CCTGCGAGCTGCTCCATTC 61.179 63.158 22.97 10.71 46.63 2.67
565 589 2.124819 CCTGCGAGCTGCTCCATT 60.125 61.111 22.97 0.00 46.63 3.16
566 590 4.853050 GCCTGCGAGCTGCTCCAT 62.853 66.667 22.97 0.00 46.63 3.41
568 592 4.853050 ATGCCTGCGAGCTGCTCC 62.853 66.667 22.97 15.91 46.63 4.70
569 593 3.574445 CATGCCTGCGAGCTGCTC 61.574 66.667 19.53 19.53 46.63 4.26
570 594 4.405671 ACATGCCTGCGAGCTGCT 62.406 61.111 0.00 0.00 46.63 4.24
571 595 3.873883 GACATGCCTGCGAGCTGC 61.874 66.667 0.00 0.00 46.70 5.25
572 596 1.773054 GATGACATGCCTGCGAGCTG 61.773 60.000 0.00 0.00 0.00 4.24
573 597 1.523258 GATGACATGCCTGCGAGCT 60.523 57.895 0.00 0.00 0.00 4.09
574 598 2.879070 CGATGACATGCCTGCGAGC 61.879 63.158 0.00 0.00 0.00 5.03
575 599 2.879070 GCGATGACATGCCTGCGAG 61.879 63.158 0.00 0.00 0.00 5.03
576 600 2.891936 GCGATGACATGCCTGCGA 60.892 61.111 0.00 0.00 0.00 5.10
577 601 2.893895 AGCGATGACATGCCTGCG 60.894 61.111 0.00 0.00 0.00 5.18
578 602 1.651240 AACAGCGATGACATGCCTGC 61.651 55.000 8.12 2.34 0.00 4.85
579 603 0.098200 CAACAGCGATGACATGCCTG 59.902 55.000 8.12 1.55 0.00 4.85
580 604 1.028330 CCAACAGCGATGACATGCCT 61.028 55.000 8.12 0.00 0.00 4.75
581 605 1.430632 CCAACAGCGATGACATGCC 59.569 57.895 8.12 0.00 0.00 4.40
582 606 1.226491 GCCAACAGCGATGACATGC 60.226 57.895 8.12 0.06 0.00 4.06
592 616 0.320421 TAGTCCAACGAGCCAACAGC 60.320 55.000 0.00 0.00 44.25 4.40
593 617 2.163818 TTAGTCCAACGAGCCAACAG 57.836 50.000 0.00 0.00 0.00 3.16
594 618 2.623878 TTTAGTCCAACGAGCCAACA 57.376 45.000 0.00 0.00 0.00 3.33
595 619 5.616488 TTAATTTAGTCCAACGAGCCAAC 57.384 39.130 0.00 0.00 0.00 3.77
596 620 7.107542 AGTATTAATTTAGTCCAACGAGCCAA 58.892 34.615 0.00 0.00 0.00 4.52
597 621 6.646267 AGTATTAATTTAGTCCAACGAGCCA 58.354 36.000 0.00 0.00 0.00 4.75
598 622 6.202379 GGAGTATTAATTTAGTCCAACGAGCC 59.798 42.308 7.09 0.00 40.20 4.70
599 623 6.759827 TGGAGTATTAATTTAGTCCAACGAGC 59.240 38.462 11.02 0.00 44.84 5.03
600 624 7.980099 ACTGGAGTATTAATTTAGTCCAACGAG 59.020 37.037 13.47 6.80 46.26 4.18
601 625 7.762615 CACTGGAGTATTAATTTAGTCCAACGA 59.237 37.037 13.47 0.00 46.26 3.85
602 626 7.548075 ACACTGGAGTATTAATTTAGTCCAACG 59.452 37.037 13.47 10.47 46.26 4.10
603 627 8.788325 ACACTGGAGTATTAATTTAGTCCAAC 57.212 34.615 13.47 0.00 46.26 3.77
604 628 9.880157 GTACACTGGAGTATTAATTTAGTCCAA 57.120 33.333 13.47 0.28 46.26 3.53
605 629 9.038072 TGTACACTGGAGTATTAATTTAGTCCA 57.962 33.333 12.35 12.35 45.35 4.02
606 630 9.310716 GTGTACACTGGAGTATTAATTTAGTCC 57.689 37.037 18.92 5.45 40.66 3.85
607 631 9.310716 GGTGTACACTGGAGTATTAATTTAGTC 57.689 37.037 24.55 0.00 0.00 2.59
616 640 5.499004 ACATTGGTGTACACTGGAGTATT 57.501 39.130 24.55 0.68 36.63 1.89
622 646 5.147330 TCTCTTACATTGGTGTACACTGG 57.853 43.478 24.55 13.89 40.40 4.00
647 671 1.810412 GCCGGGGTCATATCTGTTGAC 60.810 57.143 2.18 0.00 42.20 3.18
685 709 1.227556 GTGAAGTGCAGGGACGTGT 60.228 57.895 0.00 0.00 0.00 4.49
722 746 1.523154 CCATTGGTTGGGTGACACGG 61.523 60.000 0.00 0.00 42.33 4.94
744 768 3.070446 TGGAGAAGAAACTGCGGTAGAAA 59.930 43.478 0.00 0.00 0.00 2.52
748 772 1.001633 GGTGGAGAAGAAACTGCGGTA 59.998 52.381 0.00 0.00 0.00 4.02
795 819 9.654663 AAATTAAACATGAGAGAGTGGTAGTAC 57.345 33.333 0.00 0.00 0.00 2.73
817 841 0.817013 CACGCACTGGCCCATAAATT 59.183 50.000 0.00 0.00 36.38 1.82
818 842 0.034574 TCACGCACTGGCCCATAAAT 60.035 50.000 0.00 0.00 36.38 1.40
819 843 0.250945 TTCACGCACTGGCCCATAAA 60.251 50.000 0.00 0.00 36.38 1.40
820 844 0.034574 ATTCACGCACTGGCCCATAA 60.035 50.000 0.00 0.00 36.38 1.90
830 854 0.313672 TTGCCCTTTGATTCACGCAC 59.686 50.000 0.00 0.00 0.00 5.34
839 863 8.815565 TGTCTAAATTATGTATTGCCCTTTGA 57.184 30.769 0.00 0.00 0.00 2.69
844 868 7.872483 CCCATTTGTCTAAATTATGTATTGCCC 59.128 37.037 0.00 0.00 34.34 5.36
845 869 7.384932 GCCCATTTGTCTAAATTATGTATTGCC 59.615 37.037 0.00 0.00 34.34 4.52
857 881 8.000709 AGAGATTCATATGCCCATTTGTCTAAA 58.999 33.333 0.00 0.00 0.00 1.85
861 886 7.934855 ATAGAGATTCATATGCCCATTTGTC 57.065 36.000 0.00 0.00 0.00 3.18
870 895 9.526713 CCACAGTACATATAGAGATTCATATGC 57.473 37.037 0.00 0.00 38.25 3.14
883 908 2.889045 GTCGGGAGCCACAGTACATATA 59.111 50.000 0.00 0.00 0.00 0.86
888 913 1.215647 CAGTCGGGAGCCACAGTAC 59.784 63.158 0.00 0.00 0.00 2.73
892 917 2.632544 CGTACAGTCGGGAGCCACA 61.633 63.158 0.00 0.00 0.00 4.17
898 923 0.107066 TGGCTATCGTACAGTCGGGA 60.107 55.000 0.00 0.00 0.00 5.14
903 928 4.827692 TGTTTTGATGGCTATCGTACAGT 58.172 39.130 5.52 0.00 36.04 3.55
905 930 5.703592 ACTTTGTTTTGATGGCTATCGTACA 59.296 36.000 5.52 6.59 36.04 2.90
910 935 5.863935 GTGGAACTTTGTTTTGATGGCTATC 59.136 40.000 2.55 2.55 0.00 2.08
929 954 2.284754 TTATGGCAGTGCAAGTGGAA 57.715 45.000 18.61 0.00 37.87 3.53
940 965 5.121454 GTGAGAGAAGACAAGTTTATGGCAG 59.879 44.000 0.00 0.00 0.00 4.85
990 1015 3.673956 TAGGTTCATGGCCGTGCGG 62.674 63.158 20.86 6.22 38.57 5.69
994 1019 2.590092 GGCTAGGTTCATGGCCGT 59.410 61.111 0.00 0.00 35.08 5.68
1030 1055 1.373497 CTAGGATGCCGCGGATCAC 60.373 63.158 33.48 19.80 0.00 3.06
1076 1101 2.247790 CACAACCAGTGTAGCAGCC 58.752 57.895 0.00 0.00 43.40 4.85
1186 1211 2.428622 CCCCCTGTTTCGTCGGTT 59.571 61.111 0.00 0.00 0.00 4.44
1207 1276 1.080569 GCAACATGGGCTTTGACCG 60.081 57.895 0.00 0.00 29.56 4.79
1248 1317 0.108804 GGAGGAACGAAGCGACATGA 60.109 55.000 0.00 0.00 0.00 3.07
1258 1327 0.611062 AGGACGTCATGGAGGAACGA 60.611 55.000 18.91 0.00 0.00 3.85
1295 1364 1.817520 CCAAGCCACGACACACACA 60.818 57.895 0.00 0.00 0.00 3.72
1320 1389 3.196254 GGTCTACAATGGTTACCTTCGGA 59.804 47.826 2.07 0.00 32.12 4.55
1323 1392 4.838904 AGGGTCTACAATGGTTACCTTC 57.161 45.455 2.07 0.00 34.15 3.46
1352 1421 1.168714 GTTGGACATCACCTCCTTGC 58.831 55.000 0.00 0.00 0.00 4.01
1377 1446 0.324614 TGAGCTTCTCGAAATGGCCA 59.675 50.000 8.56 8.56 32.35 5.36
1445 1514 2.843912 CTTGGCCCATTTCTCGCCCT 62.844 60.000 0.00 0.00 42.29 5.19
1450 1519 1.959282 CCTATGCTTGGCCCATTTCTC 59.041 52.381 0.00 0.00 0.00 2.87
1578 1647 4.269183 CCATAGCCCACACTTAATCACAA 58.731 43.478 0.00 0.00 0.00 3.33
1615 1684 2.076863 GAAAACGCAGGTAGCATGAGT 58.923 47.619 0.00 0.00 46.13 3.41
1690 1759 2.768253 AGACATCCAACTCGCATGAA 57.232 45.000 0.00 0.00 0.00 2.57
1752 1821 1.269831 GGTAGCTACTCCCGAATGCAG 60.270 57.143 22.74 0.00 0.00 4.41
1777 1846 2.025510 CAGCTGGAAAATCTCCCTTCCT 60.026 50.000 5.57 0.00 44.69 3.36
1849 1918 2.288640 GCTAACTCACGTGTAACCAGGT 60.289 50.000 16.51 6.20 40.16 4.00
1930 1999 9.434559 GGAATCTGAAAATTTACACGCTTATAC 57.565 33.333 0.00 0.00 0.00 1.47
1938 2007 6.272822 AGGCAGGAATCTGAAAATTTACAC 57.727 37.500 0.00 0.00 43.49 2.90
1956 2025 4.142816 CCTTCGATTGTTTCTTGTAGGCAG 60.143 45.833 0.00 0.00 0.00 4.85
1990 2059 8.866956 GCAAAATGGATTCAATCTTTCTGTTAG 58.133 33.333 0.00 0.00 0.00 2.34
2020 2089 9.458727 TTGCTTTCATTCTCTTCTCAATTAGAT 57.541 29.630 0.00 0.00 33.05 1.98
2138 2207 4.002982 TGACCTCTTCAATTGTCATTCCG 58.997 43.478 5.13 0.00 33.09 4.30
2407 2476 8.463607 TGCATCGGTCGTAGATTGATATATAAA 58.536 33.333 0.00 0.00 40.67 1.40
2541 2627 2.036475 CAGGGTAGTTCGATGAGGATGG 59.964 54.545 0.00 0.00 0.00 3.51
2583 2669 3.598299 CATCGTTGCCCCAAATTTCAAT 58.402 40.909 0.00 0.00 0.00 2.57
2606 2692 2.234908 CCTCTCCGGATTGAACTCAAGT 59.765 50.000 3.57 0.00 39.47 3.16
2805 2892 2.095969 TCGGACGCAAAAATGTCACATC 60.096 45.455 0.00 0.00 36.83 3.06
2851 2938 3.120889 CGAGCATAATGATCAAATCGCGT 60.121 43.478 5.77 0.00 31.10 6.01
2878 2965 0.742505 ACATGGCAATGAATGAGGCG 59.257 50.000 8.45 0.00 37.24 5.52
2881 2968 2.094442 TGCACACATGGCAATGAATGAG 60.094 45.455 8.45 0.00 38.54 2.90
2971 3058 0.320683 GAAGCCCCAAATGTGTTGGC 60.321 55.000 5.69 5.69 39.78 4.52
3062 3155 2.825205 CTTTGTTGCTGGAACTTTGGG 58.175 47.619 13.23 0.00 35.37 4.12
3090 3183 0.389166 GTCAGAGAGCCCTCACAACG 60.389 60.000 0.00 0.00 41.87 4.10
3189 3282 3.455910 CCAGGAGAGAGAGAGAGAGAGAA 59.544 52.174 0.00 0.00 0.00 2.87
3229 3330 7.202016 ACACACGAAATTTGAGATTATGTGT 57.798 32.000 0.00 3.90 42.34 3.72
3262 3397 2.351706 AAAAGGGGTGTTTGACGCTA 57.648 45.000 0.00 0.00 37.65 4.26
3291 3427 2.946329 ACGTTACAGTGCAATCCAACAA 59.054 40.909 7.81 0.00 0.00 2.83
3295 3431 1.265635 GCAACGTTACAGTGCAATCCA 59.734 47.619 0.00 0.00 0.00 3.41
3296 3432 1.724654 CGCAACGTTACAGTGCAATCC 60.725 52.381 0.00 0.00 0.00 3.01
3297 3433 1.070175 ACGCAACGTTACAGTGCAATC 60.070 47.619 0.00 0.00 36.35 2.67
3298 3434 0.941542 ACGCAACGTTACAGTGCAAT 59.058 45.000 0.00 0.00 36.35 3.56
3309 3445 1.202557 TCTTCCCTTACAACGCAACGT 60.203 47.619 0.00 0.00 43.97 3.99
3310 3446 1.193874 GTCTTCCCTTACAACGCAACG 59.806 52.381 0.00 0.00 0.00 4.10
3314 3450 3.193056 AGAGTAGTCTTCCCTTACAACGC 59.807 47.826 0.00 0.00 0.00 4.84
3315 3451 5.879223 TCTAGAGTAGTCTTCCCTTACAACG 59.121 44.000 5.16 0.00 33.84 4.10
3316 3452 7.394077 ACTTCTAGAGTAGTCTTCCCTTACAAC 59.606 40.741 5.16 0.00 36.65 3.32
3318 3454 7.030234 ACTTCTAGAGTAGTCTTCCCTTACA 57.970 40.000 5.16 0.00 36.65 2.41
3441 3601 0.035534 TAGCTTCATGGGCTTTGCGA 60.036 50.000 16.63 0.00 40.74 5.10
3467 3627 2.995574 AACGGGAGTCACGGGAGG 60.996 66.667 20.75 0.00 46.69 4.30
3548 3708 1.684049 CTCCTGCTCCGTCCTCCTT 60.684 63.158 0.00 0.00 0.00 3.36
3557 3717 0.896019 TATAGCGGCTCTCCTGCTCC 60.896 60.000 5.39 0.00 40.69 4.70
3597 3758 3.181465 CGTCCAGGTAAGTATGGAGCAAT 60.181 47.826 0.00 0.00 46.09 3.56
3643 3804 1.896183 CAACGCACCCACCATGTGA 60.896 57.895 0.00 0.00 35.23 3.58
3659 3848 3.181423 ACTTTGGGAAGATGGTAAGCCAA 60.181 43.478 0.00 0.00 41.14 4.52
3679 3868 0.251832 ATGACGTCCACTCTCCCACT 60.252 55.000 14.12 0.00 0.00 4.00
3680 3869 1.471119 TATGACGTCCACTCTCCCAC 58.529 55.000 14.12 0.00 0.00 4.61
3681 3870 2.225382 TTATGACGTCCACTCTCCCA 57.775 50.000 14.12 0.00 0.00 4.37
3741 3931 7.066307 AGGACCAAAGTTTAATTTTGCAGAT 57.934 32.000 7.31 0.00 34.88 2.90
3765 3955 2.922740 AGTGGTTTAAGCTCGGACAA 57.077 45.000 0.00 0.00 0.00 3.18
3768 3958 1.695242 TGGAAGTGGTTTAAGCTCGGA 59.305 47.619 0.00 0.00 0.00 4.55
3771 3961 5.154222 CGAAATTGGAAGTGGTTTAAGCTC 58.846 41.667 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.