Multiple sequence alignment - TraesCS2A01G131000

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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 TraesCS2A01G131000 chr2A 100.000 3239 0 0 1 3239 78743101 78739863 0.000000e+00 5982.0
1 TraesCS2A01G131000 chr2A 84.492 1251 106 44 829 2071 78262815 78263985 0.000000e+00 1155.0
2 TraesCS2A01G131000 chr2A 93.659 615 39 0 2625 3239 78722727 78722113 0.000000e+00 920.0
3 TraesCS2A01G131000 chr2A 84.673 796 75 23 834 1602 78773353 78772578 0.000000e+00 750.0
4 TraesCS2A01G131000 chr2A 87.678 633 47 14 1073 1674 78323386 78324018 0.000000e+00 708.0
5 TraesCS2A01G131000 chr2A 89.041 365 36 4 1217 1578 78255296 78255659 1.770000e-122 449.0
6 TraesCS2A01G131000 chr2A 83.721 301 44 5 5 303 78260558 78260855 2.460000e-71 279.0
7 TraesCS2A01G131000 chr2A 95.652 46 0 2 672 716 78773464 78773420 4.480000e-09 73.1
8 TraesCS2A01G131000 chr2A 97.500 40 1 0 677 716 78262677 78262716 5.800000e-08 69.4
9 TraesCS2A01G131000 chr2A 93.617 47 0 3 672 716 78762791 78762746 2.090000e-07 67.6
10 TraesCS2A01G131000 chr2B 90.017 1803 106 23 829 2579 121383424 121381644 0.000000e+00 2265.0
11 TraesCS2A01G131000 chr2B 92.611 812 56 3 1071 1878 121433011 121432200 0.000000e+00 1164.0
12 TraesCS2A01G131000 chr2B 82.416 927 93 40 834 1702 121483466 121482552 0.000000e+00 745.0
13 TraesCS2A01G131000 chr2B 87.969 640 53 10 1072 1691 121474977 121474342 0.000000e+00 734.0
14 TraesCS2A01G131000 chr2B 87.417 302 35 3 1932 2231 121384690 121384390 8.600000e-91 344.0
15 TraesCS2A01G131000 chr2B 80.351 285 50 3 27 306 121440844 121440561 9.100000e-51 211.0
16 TraesCS2A01G131000 chr2B 85.401 137 20 0 533 669 753014158 753014294 3.370000e-30 143.0
17 TraesCS2A01G131000 chr2B 97.778 45 0 1 2581 2624 121381615 121381571 3.470000e-10 76.8
18 TraesCS2A01G131000 chr2B 93.750 48 3 0 669 716 121438704 121438657 4.480000e-09 73.1
19 TraesCS2A01G131000 chr2B 97.561 41 1 0 669 709 121383574 121383534 1.610000e-08 71.3
20 TraesCS2A01G131000 chr2D 93.914 838 42 5 826 1657 78436342 78435508 0.000000e+00 1256.0
21 TraesCS2A01G131000 chr2D 83.886 875 89 15 850 1682 78502565 78501701 0.000000e+00 787.0
22 TraesCS2A01G131000 chr2D 81.382 1042 98 44 829 1806 78406628 78405619 0.000000e+00 761.0
23 TraesCS2A01G131000 chr2D 87.211 649 53 14 1076 1695 78508936 78508289 0.000000e+00 712.0
24 TraesCS2A01G131000 chr2D 87.437 597 56 10 1691 2269 78434226 78433631 0.000000e+00 669.0
25 TraesCS2A01G131000 chr2D 92.790 319 21 2 1 318 78437583 78437266 8.190000e-126 460.0
26 TraesCS2A01G131000 chr2D 87.580 314 21 9 2267 2579 78414822 78414526 6.650000e-92 348.0
27 TraesCS2A01G131000 chr2D 86.282 277 34 3 5 280 78504938 78504665 6.790000e-77 298.0
28 TraesCS2A01G131000 chr2D 93.846 65 3 1 829 893 78502629 78502566 2.660000e-16 97.1
29 TraesCS2A01G131000 chr2D 84.848 99 6 5 678 776 78502811 78502722 1.240000e-14 91.6
30 TraesCS2A01G131000 chr2D 82.278 79 13 1 2491 2569 621481541 621481464 2.090000e-07 67.6
31 TraesCS2A01G131000 chr4A 93.627 612 37 1 2627 3238 263709229 263709838 0.000000e+00 913.0
32 TraesCS2A01G131000 chr4A 93.506 616 37 2 2625 3239 291510923 291510310 0.000000e+00 913.0
33 TraesCS2A01G131000 chr4A 93.333 615 37 4 2625 3239 284492190 284492800 0.000000e+00 905.0
34 TraesCS2A01G131000 chr4A 83.041 171 24 4 2286 2454 628188046 628187879 2.010000e-32 150.0
35 TraesCS2A01G131000 chr4A 89.189 111 6 4 2181 2285 154501786 154501896 2.030000e-27 134.0
36 TraesCS2A01G131000 chr4A 78.125 192 29 5 2107 2285 464988555 464988746 3.420000e-20 110.0
37 TraesCS2A01G131000 chr1A 93.366 618 37 2 2625 3239 317771207 317770591 0.000000e+00 911.0
38 TraesCS2A01G131000 chr1A 92.846 615 40 4 2625 3239 152170337 152170947 0.000000e+00 889.0
39 TraesCS2A01G131000 chr1A 80.808 198 38 0 2286 2483 298724560 298724363 4.330000e-34 156.0
40 TraesCS2A01G131000 chr3A 93.008 615 43 0 2625 3239 612084228 612083614 0.000000e+00 898.0
41 TraesCS2A01G131000 chr3A 93.031 617 39 4 2625 3239 634249668 634250282 0.000000e+00 898.0
42 TraesCS2A01G131000 chr3A 80.905 199 38 0 2286 2484 423159566 423159368 1.200000e-34 158.0
43 TraesCS2A01G131000 chr3A 81.915 188 32 2 2286 2472 690714847 690715033 1.200000e-34 158.0
44 TraesCS2A01G131000 chr3A 84.397 141 22 0 533 673 727251135 727250995 4.360000e-29 139.0
45 TraesCS2A01G131000 chr5A 92.695 616 43 2 2624 3239 13364383 13364996 0.000000e+00 887.0
46 TraesCS2A01G131000 chr5A 81.159 207 24 9 2092 2285 616153234 616153030 5.600000e-33 152.0
47 TraesCS2A01G131000 chr5A 84.507 142 22 0 533 674 42097093 42097234 1.210000e-29 141.0
48 TraesCS2A01G131000 chr7A 83.262 233 29 4 2063 2285 341444291 341444523 4.240000e-49 206.0
49 TraesCS2A01G131000 chr7A 85.000 140 17 4 533 670 724037659 724037522 4.360000e-29 139.0
50 TraesCS2A01G131000 chr6D 81.974 233 32 7 2063 2285 434464517 434464285 4.270000e-44 189.0
51 TraesCS2A01G131000 chr6D 81.667 240 28 11 2062 2285 38894807 38895046 5.520000e-43 185.0
52 TraesCS2A01G131000 chr7D 81.197 234 24 5 2063 2285 312573841 312574065 1.550000e-38 171.0
53 TraesCS2A01G131000 chr6A 85.714 140 19 1 530 669 29213221 29213359 2.600000e-31 147.0
54 TraesCS2A01G131000 chr6B 85.401 137 20 0 533 669 634640461 634640325 3.370000e-30 143.0
55 TraesCS2A01G131000 chr4B 85.401 137 20 0 533 669 211658989 211659125 3.370000e-30 143.0
56 TraesCS2A01G131000 chr4B 78.723 188 34 5 2286 2472 617868132 617868314 1.580000e-23 121.0
57 TraesCS2A01G131000 chr1B 85.401 137 20 0 533 669 430028659 430028795 3.370000e-30 143.0
58 TraesCS2A01G131000 chr3B 84.672 137 19 2 533 669 171514732 171514866 5.640000e-28 135.0
59 TraesCS2A01G131000 chr3B 79.570 186 36 2 2286 2469 416511301 416511486 7.290000e-27 132.0
60 TraesCS2A01G131000 chr3D 79.104 201 37 5 2287 2484 174883911 174884109 2.030000e-27 134.0
61 TraesCS2A01G131000 chr5B 88.525 61 7 0 2502 2562 134733157 134733217 1.250000e-09 75.0


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 TraesCS2A01G131000 chr2A 78739863 78743101 3238 True 5982.000000 5982 100.000000 1 3239 1 chr2A.!!$R2 3238
1 TraesCS2A01G131000 chr2A 78722113 78722727 614 True 920.000000 920 93.659000 2625 3239 1 chr2A.!!$R1 614
2 TraesCS2A01G131000 chr2A 78323386 78324018 632 False 708.000000 708 87.678000 1073 1674 1 chr2A.!!$F2 601
3 TraesCS2A01G131000 chr2A 78260558 78263985 3427 False 501.133333 1155 88.571000 5 2071 3 chr2A.!!$F3 2066
4 TraesCS2A01G131000 chr2A 78772578 78773464 886 True 411.550000 750 90.162500 672 1602 2 chr2A.!!$R4 930
5 TraesCS2A01G131000 chr2B 121432200 121433011 811 True 1164.000000 1164 92.611000 1071 1878 1 chr2B.!!$R1 807
6 TraesCS2A01G131000 chr2B 121482552 121483466 914 True 745.000000 745 82.416000 834 1702 1 chr2B.!!$R3 868
7 TraesCS2A01G131000 chr2B 121474342 121474977 635 True 734.000000 734 87.969000 1072 1691 1 chr2B.!!$R2 619
8 TraesCS2A01G131000 chr2B 121381571 121384690 3119 True 689.275000 2265 93.193250 669 2624 4 chr2B.!!$R4 1955
9 TraesCS2A01G131000 chr2D 78433631 78437583 3952 True 795.000000 1256 91.380333 1 2269 3 chr2D.!!$R4 2268
10 TraesCS2A01G131000 chr2D 78405619 78406628 1009 True 761.000000 761 81.382000 829 1806 1 chr2D.!!$R1 977
11 TraesCS2A01G131000 chr2D 78501701 78508936 7235 True 397.140000 787 87.214600 5 1695 5 chr2D.!!$R5 1690
12 TraesCS2A01G131000 chr4A 263709229 263709838 609 False 913.000000 913 93.627000 2627 3238 1 chr4A.!!$F2 611
13 TraesCS2A01G131000 chr4A 291510310 291510923 613 True 913.000000 913 93.506000 2625 3239 1 chr4A.!!$R1 614
14 TraesCS2A01G131000 chr4A 284492190 284492800 610 False 905.000000 905 93.333000 2625 3239 1 chr4A.!!$F3 614
15 TraesCS2A01G131000 chr1A 317770591 317771207 616 True 911.000000 911 93.366000 2625 3239 1 chr1A.!!$R2 614
16 TraesCS2A01G131000 chr1A 152170337 152170947 610 False 889.000000 889 92.846000 2625 3239 1 chr1A.!!$F1 614
17 TraesCS2A01G131000 chr3A 612083614 612084228 614 True 898.000000 898 93.008000 2625 3239 1 chr3A.!!$R2 614
18 TraesCS2A01G131000 chr3A 634249668 634250282 614 False 898.000000 898 93.031000 2625 3239 1 chr3A.!!$F1 614
19 TraesCS2A01G131000 chr5A 13364383 13364996 613 False 887.000000 887 92.695000 2624 3239 1 chr5A.!!$F1 615

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
429 5614 0.095589 GCGTGTGTTTGTCGTTGTGA 59.904 50.0 0.00 0.0 0.0 3.58 F
461 5646 0.107165 GGGGAAAAGGTAGCGCTCAT 60.107 55.0 16.34 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 9053 1.202639 TGATAGCCACCTTGTATGCCG 60.203 52.381 0.00 0.0 0.00 5.69 R
2441 9714 1.734465 CACTTCCCGAAGCAAGATGTC 59.266 52.381 4.34 0.0 41.99 3.06 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
96 4091 2.421775 ACAACAACAAGCATCAACACGA 59.578 40.909 0.00 0.00 0.00 4.35
183 4178 4.501198 CGCAACTCCGTTAAATTGTTTTGT 59.499 37.500 0.00 0.00 0.00 2.83
230 4225 4.209307 TGACTTTGTCCAGTGTTACACA 57.791 40.909 18.19 0.00 36.74 3.72
242 4237 3.182341 TGTTACACACAGCTAACCGTT 57.818 42.857 0.00 0.00 0.00 4.44
248 4243 2.750237 CAGCTAACCGTTGGGGGC 60.750 66.667 0.00 0.00 41.60 5.80
249 4244 3.253838 AGCTAACCGTTGGGGGCA 61.254 61.111 0.00 0.00 41.60 5.36
292 4287 5.245531 TGAGTTTGAATCTTTGCCGAGTAT 58.754 37.500 0.00 0.00 0.00 2.12
296 4291 5.344743 TTGAATCTTTGCCGAGTATCTCT 57.655 39.130 0.00 0.00 0.00 3.10
298 4293 6.465439 TGAATCTTTGCCGAGTATCTCTAA 57.535 37.500 0.00 0.00 0.00 2.10
339 4754 9.507329 AAGCTAAGACATTTATTTTGAGACAGA 57.493 29.630 0.00 0.00 0.00 3.41
340 4755 9.160496 AGCTAAGACATTTATTTTGAGACAGAG 57.840 33.333 0.00 0.00 0.00 3.35
341 4756 8.394121 GCTAAGACATTTATTTTGAGACAGAGG 58.606 37.037 0.00 0.00 0.00 3.69
342 4757 7.693969 AAGACATTTATTTTGAGACAGAGGG 57.306 36.000 0.00 0.00 0.00 4.30
343 4758 7.020827 AGACATTTATTTTGAGACAGAGGGA 57.979 36.000 0.00 0.00 0.00 4.20
344 4759 7.461749 AGACATTTATTTTGAGACAGAGGGAA 58.538 34.615 0.00 0.00 0.00 3.97
346 4761 9.396022 GACATTTATTTTGAGACAGAGGGAATA 57.604 33.333 0.00 0.00 0.00 1.75
347 4762 9.927081 ACATTTATTTTGAGACAGAGGGAATAT 57.073 29.630 0.00 0.00 0.00 1.28
377 5562 2.503920 ATAATAAGCTTCGTCGGCGT 57.496 45.000 10.18 0.00 39.49 5.68
378 5563 1.831343 TAATAAGCTTCGTCGGCGTC 58.169 50.000 10.18 0.00 39.49 5.19
402 5587 2.432444 CGCCATTTTGTAGTTCCCTGA 58.568 47.619 0.00 0.00 0.00 3.86
403 5588 2.817258 CGCCATTTTGTAGTTCCCTGAA 59.183 45.455 0.00 0.00 0.00 3.02
404 5589 3.119849 CGCCATTTTGTAGTTCCCTGAAG 60.120 47.826 0.00 0.00 0.00 3.02
406 5591 4.706962 GCCATTTTGTAGTTCCCTGAAGAT 59.293 41.667 0.00 0.00 0.00 2.40
407 5592 5.163612 GCCATTTTGTAGTTCCCTGAAGATC 60.164 44.000 0.00 0.00 0.00 2.75
408 5593 5.945784 CCATTTTGTAGTTCCCTGAAGATCA 59.054 40.000 0.00 0.00 0.00 2.92
409 5594 6.604795 CCATTTTGTAGTTCCCTGAAGATCAT 59.395 38.462 0.00 0.00 0.00 2.45
410 5595 7.415989 CCATTTTGTAGTTCCCTGAAGATCATG 60.416 40.741 0.00 0.00 0.00 3.07
411 5596 4.142609 TGTAGTTCCCTGAAGATCATGC 57.857 45.455 0.00 0.00 0.00 4.06
412 5597 2.322355 AGTTCCCTGAAGATCATGCG 57.678 50.000 0.00 0.00 0.00 4.73
413 5598 1.556911 AGTTCCCTGAAGATCATGCGT 59.443 47.619 0.00 0.00 0.00 5.24
415 5600 0.904649 TCCCTGAAGATCATGCGTGT 59.095 50.000 5.68 0.00 0.00 4.49
416 5601 1.012086 CCCTGAAGATCATGCGTGTG 58.988 55.000 5.68 0.00 0.00 3.82
417 5602 1.676916 CCCTGAAGATCATGCGTGTGT 60.677 52.381 5.68 0.00 0.00 3.72
420 5605 3.485633 CTGAAGATCATGCGTGTGTTTG 58.514 45.455 5.68 0.00 0.00 2.93
424 5609 1.194547 GATCATGCGTGTGTTTGTCGT 59.805 47.619 5.68 0.00 0.00 4.34
426 5611 1.111667 CATGCGTGTGTTTGTCGTTG 58.888 50.000 0.00 0.00 0.00 4.10
427 5612 0.730265 ATGCGTGTGTTTGTCGTTGT 59.270 45.000 0.00 0.00 0.00 3.32
428 5613 0.179212 TGCGTGTGTTTGTCGTTGTG 60.179 50.000 0.00 0.00 0.00 3.33
429 5614 0.095589 GCGTGTGTTTGTCGTTGTGA 59.904 50.000 0.00 0.00 0.00 3.58
431 5616 2.427169 CGTGTGTTTGTCGTTGTGAAG 58.573 47.619 0.00 0.00 0.00 3.02
432 5617 2.092995 CGTGTGTTTGTCGTTGTGAAGA 59.907 45.455 0.00 0.00 0.00 2.87
435 5620 4.912766 GTGTGTTTGTCGTTGTGAAGAAAA 59.087 37.500 0.00 0.00 0.00 2.29
437 5622 5.627367 TGTGTTTGTCGTTGTGAAGAAAAAG 59.373 36.000 0.00 0.00 0.00 2.27
441 5626 6.921332 TTGTCGTTGTGAAGAAAAAGAAAC 57.079 33.333 0.00 0.00 0.00 2.78
442 5627 5.083389 TGTCGTTGTGAAGAAAAAGAAACG 58.917 37.500 0.00 0.00 40.02 3.60
443 5628 4.494410 GTCGTTGTGAAGAAAAAGAAACGG 59.506 41.667 0.00 0.00 39.36 4.44
453 5638 5.202765 AGAAAAAGAAACGGGGAAAAGGTA 58.797 37.500 0.00 0.00 0.00 3.08
454 5639 5.301045 AGAAAAAGAAACGGGGAAAAGGTAG 59.699 40.000 0.00 0.00 0.00 3.18
455 5640 2.195741 AGAAACGGGGAAAAGGTAGC 57.804 50.000 0.00 0.00 0.00 3.58
459 5644 1.814169 CGGGGAAAAGGTAGCGCTC 60.814 63.158 16.34 5.63 0.00 5.03
461 5646 0.107165 GGGGAAAAGGTAGCGCTCAT 60.107 55.000 16.34 0.00 0.00 2.90
462 5647 1.140252 GGGGAAAAGGTAGCGCTCATA 59.860 52.381 16.34 0.00 0.00 2.15
464 5649 2.419574 GGGAAAAGGTAGCGCTCATACA 60.420 50.000 16.34 0.00 0.00 2.29
465 5650 3.267483 GGAAAAGGTAGCGCTCATACAA 58.733 45.455 16.34 0.00 0.00 2.41
467 5652 4.335594 GGAAAAGGTAGCGCTCATACAAAT 59.664 41.667 16.34 0.00 0.00 2.32
468 5653 5.526111 GGAAAAGGTAGCGCTCATACAAATA 59.474 40.000 16.34 0.00 0.00 1.40
471 5656 2.155155 GGTAGCGCTCATACAAATACGC 59.845 50.000 16.34 0.00 46.20 4.42
475 5660 3.722123 GCGCTCATACAAATACGCATAC 58.278 45.455 0.00 0.00 45.25 2.39
476 5661 3.183574 GCGCTCATACAAATACGCATACA 59.816 43.478 0.00 0.00 45.25 2.29
477 5662 4.688063 CGCTCATACAAATACGCATACAC 58.312 43.478 0.00 0.00 0.00 2.90
479 5664 5.387444 CGCTCATACAAATACGCATACACTC 60.387 44.000 0.00 0.00 0.00 3.51
480 5665 5.462068 GCTCATACAAATACGCATACACTCA 59.538 40.000 0.00 0.00 0.00 3.41
482 5667 7.620188 GCTCATACAAATACGCATACACTCATC 60.620 40.741 0.00 0.00 0.00 2.92
484 5669 7.595130 TCATACAAATACGCATACACTCATCTC 59.405 37.037 0.00 0.00 0.00 2.75
485 5670 5.907207 ACAAATACGCATACACTCATCTCT 58.093 37.500 0.00 0.00 0.00 3.10
486 5671 7.039313 ACAAATACGCATACACTCATCTCTA 57.961 36.000 0.00 0.00 0.00 2.43
487 5672 7.661968 ACAAATACGCATACACTCATCTCTAT 58.338 34.615 0.00 0.00 0.00 1.98
488 5673 7.596621 ACAAATACGCATACACTCATCTCTATG 59.403 37.037 0.00 0.00 0.00 2.23
489 5674 7.454260 AATACGCATACACTCATCTCTATGA 57.546 36.000 0.00 0.00 39.87 2.15
490 5675 5.774498 ACGCATACACTCATCTCTATGAA 57.226 39.130 0.00 0.00 41.57 2.57
491 5676 6.338214 ACGCATACACTCATCTCTATGAAT 57.662 37.500 0.00 0.00 41.57 2.57
492 5677 6.155136 ACGCATACACTCATCTCTATGAATG 58.845 40.000 0.00 0.00 43.41 2.67
493 5678 5.061933 CGCATACACTCATCTCTATGAATGC 59.938 44.000 10.56 10.56 41.91 3.56
494 5679 5.930569 GCATACACTCATCTCTATGAATGCA 59.069 40.000 13.77 0.00 44.61 3.96
495 5680 6.594547 GCATACACTCATCTCTATGAATGCAT 59.405 38.462 13.77 0.00 44.61 3.96
497 5682 5.926663 ACACTCATCTCTATGAATGCATGT 58.073 37.500 0.00 0.00 41.91 3.21
498 5683 5.758784 ACACTCATCTCTATGAATGCATGTG 59.241 40.000 0.00 1.48 41.91 3.21
499 5684 4.755629 ACTCATCTCTATGAATGCATGTGC 59.244 41.667 0.00 0.00 41.57 4.57
500 5685 3.744426 TCATCTCTATGAATGCATGTGCG 59.256 43.478 0.00 0.00 40.62 5.34
501 5686 1.869132 TCTCTATGAATGCATGTGCGC 59.131 47.619 0.00 0.00 45.83 6.09
503 5688 1.331447 TCTATGAATGCATGTGCGCAC 59.669 47.619 33.11 33.11 46.56 5.34
504 5689 1.064357 CTATGAATGCATGTGCGCACA 59.936 47.619 41.97 41.97 46.56 4.57
505 5690 0.457166 ATGAATGCATGTGCGCACAC 60.457 50.000 42.74 30.95 46.56 3.82
506 5691 1.802715 GAATGCATGTGCGCACACC 60.803 57.895 42.74 33.77 46.56 4.16
508 5693 4.953010 TGCATGTGCGCACACCCT 62.953 61.111 42.74 26.47 46.86 4.34
510 5695 3.039202 GCATGTGCGCACACCCTAC 62.039 63.158 42.74 25.82 46.86 3.18
511 5696 2.046314 ATGTGCGCACACCCTACC 60.046 61.111 42.74 14.60 46.86 3.18
512 5697 3.622060 ATGTGCGCACACCCTACCC 62.622 63.158 42.74 13.81 46.86 3.69
515 5700 4.338710 GCGCACACCCTACCCCAA 62.339 66.667 0.30 0.00 0.00 4.12
517 5702 1.748879 CGCACACCCTACCCCAATG 60.749 63.158 0.00 0.00 0.00 2.82
518 5703 1.688811 GCACACCCTACCCCAATGA 59.311 57.895 0.00 0.00 0.00 2.57
521 5706 0.844661 ACACCCTACCCCAATGAGCA 60.845 55.000 0.00 0.00 0.00 4.26
522 5707 0.552848 CACCCTACCCCAATGAGCAT 59.447 55.000 0.00 0.00 0.00 3.79
523 5708 0.846693 ACCCTACCCCAATGAGCATC 59.153 55.000 0.00 0.00 0.00 3.91
525 5710 1.072965 CCCTACCCCAATGAGCATCTC 59.927 57.143 0.00 0.00 34.92 2.75
527 5712 2.224475 CCTACCCCAATGAGCATCTCTG 60.224 54.545 0.00 0.00 34.92 3.35
528 5713 1.588239 ACCCCAATGAGCATCTCTGA 58.412 50.000 0.00 0.00 34.92 3.27
529 5714 1.489649 ACCCCAATGAGCATCTCTGAG 59.510 52.381 0.00 0.00 34.92 3.35
530 5715 1.767088 CCCCAATGAGCATCTCTGAGA 59.233 52.381 10.23 10.23 34.92 3.27
534 5719 4.096081 CCCAATGAGCATCTCTGAGAAAAC 59.904 45.833 12.00 4.29 34.92 2.43
535 5720 4.201792 CCAATGAGCATCTCTGAGAAAACG 60.202 45.833 12.00 2.27 34.92 3.60
536 5721 3.667497 TGAGCATCTCTGAGAAAACGT 57.333 42.857 12.00 0.00 34.92 3.99
538 5723 3.256879 TGAGCATCTCTGAGAAAACGTCT 59.743 43.478 12.00 2.94 35.74 4.18
539 5724 4.617067 TGAGCATCTCTGAGAAAACGTCTC 60.617 45.833 12.00 11.36 44.55 3.36
546 5731 2.081725 GAGAAAACGTCTCCTCCCAC 57.918 55.000 0.00 0.00 46.32 4.61
547 5732 0.685660 AGAAAACGTCTCCTCCCACC 59.314 55.000 0.00 0.00 0.00 4.61
548 5733 0.669625 GAAAACGTCTCCTCCCACCG 60.670 60.000 0.00 0.00 0.00 4.94
549 5734 1.117142 AAAACGTCTCCTCCCACCGA 61.117 55.000 0.00 0.00 0.00 4.69
550 5735 1.117142 AAACGTCTCCTCCCACCGAA 61.117 55.000 0.00 0.00 0.00 4.30
551 5736 1.117142 AACGTCTCCTCCCACCGAAA 61.117 55.000 0.00 0.00 0.00 3.46
552 5737 1.215647 CGTCTCCTCCCACCGAAAG 59.784 63.158 0.00 0.00 0.00 2.62
553 5738 1.079057 GTCTCCTCCCACCGAAAGC 60.079 63.158 0.00 0.00 0.00 3.51
554 5739 2.125512 CTCCTCCCACCGAAAGCG 60.126 66.667 0.00 0.00 37.24 4.68
555 5740 2.920912 TCCTCCCACCGAAAGCGT 60.921 61.111 0.00 0.00 35.23 5.07
556 5741 1.601419 CTCCTCCCACCGAAAGCGTA 61.601 60.000 0.00 0.00 35.23 4.42
557 5742 0.974010 TCCTCCCACCGAAAGCGTAT 60.974 55.000 0.00 0.00 35.23 3.06
559 5744 1.006832 CTCCCACCGAAAGCGTATTG 58.993 55.000 0.00 0.00 35.23 1.90
561 5746 0.725117 CCCACCGAAAGCGTATTGTC 59.275 55.000 0.00 0.00 35.23 3.18
562 5747 0.368907 CCACCGAAAGCGTATTGTCG 59.631 55.000 0.00 0.00 35.23 4.35
568 5753 3.998522 CGAAAGCGTATTGTCGGAAATT 58.001 40.909 0.00 0.00 0.00 1.82
569 5754 4.019867 CGAAAGCGTATTGTCGGAAATTC 58.980 43.478 0.00 0.00 0.00 2.17
570 5755 4.201685 CGAAAGCGTATTGTCGGAAATTCT 60.202 41.667 0.00 0.00 0.00 2.40
571 5756 5.005012 CGAAAGCGTATTGTCGGAAATTCTA 59.995 40.000 0.00 0.00 0.00 2.10
572 5757 6.454583 CGAAAGCGTATTGTCGGAAATTCTAA 60.455 38.462 0.00 0.00 0.00 2.10
573 5758 6.730960 AAGCGTATTGTCGGAAATTCTAAA 57.269 33.333 0.00 0.00 0.00 1.85
574 5759 6.730960 AGCGTATTGTCGGAAATTCTAAAA 57.269 33.333 0.00 0.00 0.00 1.52
576 5761 8.428186 AGCGTATTGTCGGAAATTCTAAAATA 57.572 30.769 0.00 0.00 0.00 1.40
577 5762 8.885722 AGCGTATTGTCGGAAATTCTAAAATAA 58.114 29.630 0.00 0.00 0.00 1.40
584 5769 8.682710 TGTCGGAAATTCTAAAATAAATCCAGG 58.317 33.333 0.00 0.00 0.00 4.45
586 5771 9.640952 TCGGAAATTCTAAAATAAATCCAGGAT 57.359 29.630 0.00 0.00 0.00 3.24
597 5782 8.537728 AAATAAATCCAGGATAAATGTGAGCA 57.462 30.769 1.02 0.00 0.00 4.26
598 5783 5.841957 AAATCCAGGATAAATGTGAGCAC 57.158 39.130 1.02 0.00 0.00 4.40
599 5784 3.281727 TCCAGGATAAATGTGAGCACC 57.718 47.619 0.00 0.00 0.00 5.01
600 5785 2.575735 TCCAGGATAAATGTGAGCACCA 59.424 45.455 0.00 0.00 0.00 4.17
601 5786 2.947652 CCAGGATAAATGTGAGCACCAG 59.052 50.000 0.00 0.00 0.00 4.00
602 5787 2.947652 CAGGATAAATGTGAGCACCAGG 59.052 50.000 0.00 0.00 0.00 4.45
603 5788 2.846206 AGGATAAATGTGAGCACCAGGA 59.154 45.455 0.00 0.00 0.00 3.86
604 5789 3.461085 AGGATAAATGTGAGCACCAGGAT 59.539 43.478 0.00 0.00 0.00 3.24
605 5790 4.079558 AGGATAAATGTGAGCACCAGGATT 60.080 41.667 0.00 0.00 0.00 3.01
606 5791 4.646492 GGATAAATGTGAGCACCAGGATTT 59.354 41.667 0.00 0.94 0.00 2.17
607 5792 3.947910 AAATGTGAGCACCAGGATTTG 57.052 42.857 0.00 0.00 0.00 2.32
608 5793 2.885135 ATGTGAGCACCAGGATTTGA 57.115 45.000 0.00 0.00 0.00 2.69
609 5794 2.655090 TGTGAGCACCAGGATTTGAA 57.345 45.000 0.00 0.00 0.00 2.69
611 5796 3.084039 TGTGAGCACCAGGATTTGAATC 58.916 45.455 0.00 0.00 34.66 2.52
622 5807 3.874392 GATTTGAATCCTGGTGGGTTG 57.126 47.619 0.00 0.00 36.67 3.77
624 5809 2.584835 TTGAATCCTGGTGGGTTGAG 57.415 50.000 0.00 0.00 36.67 3.02
627 5812 1.566231 GAATCCTGGTGGGTTGAGGAT 59.434 52.381 0.00 0.00 46.65 3.24
628 5813 2.587060 ATCCTGGTGGGTTGAGGATA 57.413 50.000 0.00 0.00 43.52 2.59
629 5814 2.587060 TCCTGGTGGGTTGAGGATAT 57.413 50.000 0.00 0.00 36.25 1.63
630 5815 2.408565 TCCTGGTGGGTTGAGGATATC 58.591 52.381 0.00 0.00 36.25 1.63
633 5818 2.774234 CTGGTGGGTTGAGGATATCACT 59.226 50.000 4.83 0.00 37.77 3.41
636 5821 4.975147 TGGTGGGTTGAGGATATCACTATT 59.025 41.667 4.83 0.00 37.77 1.73
637 5822 5.071788 TGGTGGGTTGAGGATATCACTATTC 59.928 44.000 4.83 0.00 37.77 1.75
638 5823 5.071788 GGTGGGTTGAGGATATCACTATTCA 59.928 44.000 4.83 0.00 37.77 2.57
639 5824 5.992217 GTGGGTTGAGGATATCACTATTCAC 59.008 44.000 4.83 1.49 37.77 3.18
640 5825 5.665360 TGGGTTGAGGATATCACTATTCACA 59.335 40.000 4.83 0.00 37.77 3.58
641 5826 6.329986 TGGGTTGAGGATATCACTATTCACAT 59.670 38.462 4.83 0.00 37.77 3.21
643 5828 8.375506 GGGTTGAGGATATCACTATTCACATAA 58.624 37.037 4.83 0.00 37.77 1.90
659 5844 8.806429 ATTCACATAATCATCTTAACCACACA 57.194 30.769 0.00 0.00 0.00 3.72
661 5846 8.806429 TCACATAATCATCTTAACCACACAAT 57.194 30.769 0.00 0.00 0.00 2.71
662 5847 8.676401 TCACATAATCATCTTAACCACACAATG 58.324 33.333 0.00 0.00 0.00 2.82
663 5848 8.676401 CACATAATCATCTTAACCACACAATGA 58.324 33.333 0.00 0.00 0.00 2.57
664 5849 9.412460 ACATAATCATCTTAACCACACAATGAT 57.588 29.630 0.00 0.00 35.85 2.45
667 5852 6.421377 TCATCTTAACCACACAATGATTCG 57.579 37.500 0.00 0.00 0.00 3.34
668 5853 4.678509 TCTTAACCACACAATGATTCGC 57.321 40.909 0.00 0.00 0.00 4.70
669 5854 3.124466 TCTTAACCACACAATGATTCGCG 59.876 43.478 0.00 0.00 0.00 5.87
670 5855 1.234821 AACCACACAATGATTCGCGT 58.765 45.000 5.77 0.00 0.00 6.01
716 6451 6.456988 CCAAAATTGAGCTAACGAGATGTACC 60.457 42.308 0.00 0.00 0.00 3.34
717 6452 3.416119 TTGAGCTAACGAGATGTACCG 57.584 47.619 0.00 0.00 0.00 4.02
718 6453 2.362736 TGAGCTAACGAGATGTACCGT 58.637 47.619 0.00 0.00 41.14 4.83
719 6454 2.096980 TGAGCTAACGAGATGTACCGTG 59.903 50.000 0.00 0.00 39.14 4.94
722 6457 3.064545 AGCTAACGAGATGTACCGTGTAC 59.935 47.826 7.11 7.11 39.14 2.90
769 6505 8.644318 AAAATGTAACAGAGATGTACGTATCC 57.356 34.615 6.09 0.00 0.00 2.59
771 6507 7.584122 ATGTAACAGAGATGTACGTATCCTT 57.416 36.000 6.09 1.58 0.00 3.36
772 6508 6.792326 TGTAACAGAGATGTACGTATCCTTG 58.208 40.000 6.09 2.24 0.00 3.61
773 6509 6.600427 TGTAACAGAGATGTACGTATCCTTGA 59.400 38.462 6.09 0.00 0.00 3.02
774 6510 6.716934 AACAGAGATGTACGTATCCTTGAT 57.283 37.500 6.09 0.00 0.00 2.57
775 6511 6.320494 ACAGAGATGTACGTATCCTTGATC 57.680 41.667 6.09 0.00 0.00 2.92
776 6512 5.049336 ACAGAGATGTACGTATCCTTGATCG 60.049 44.000 6.09 0.00 0.00 3.69
777 6513 5.049336 CAGAGATGTACGTATCCTTGATCGT 60.049 44.000 6.09 0.00 39.74 3.73
778 6514 5.179742 AGAGATGTACGTATCCTTGATCGTC 59.820 44.000 6.09 0.00 37.66 4.20
779 6515 3.976793 TGTACGTATCCTTGATCGTCC 57.023 47.619 0.00 0.00 37.66 4.79
780 6516 3.548770 TGTACGTATCCTTGATCGTCCT 58.451 45.455 0.00 0.00 37.66 3.85
781 6517 3.949754 TGTACGTATCCTTGATCGTCCTT 59.050 43.478 0.00 0.00 37.66 3.36
782 6518 4.400251 TGTACGTATCCTTGATCGTCCTTT 59.600 41.667 0.00 0.00 37.66 3.11
783 6519 4.467198 ACGTATCCTTGATCGTCCTTTT 57.533 40.909 0.00 0.00 30.71 2.27
784 6520 4.430908 ACGTATCCTTGATCGTCCTTTTC 58.569 43.478 0.00 0.00 30.71 2.29
785 6521 3.486108 CGTATCCTTGATCGTCCTTTTCG 59.514 47.826 0.00 0.00 0.00 3.46
786 6522 3.887621 ATCCTTGATCGTCCTTTTCGA 57.112 42.857 0.00 0.00 41.45 3.71
787 6523 3.671008 TCCTTGATCGTCCTTTTCGAA 57.329 42.857 0.00 0.00 40.61 3.71
788 6524 3.997762 TCCTTGATCGTCCTTTTCGAAA 58.002 40.909 6.47 6.47 40.61 3.46
789 6525 4.382291 TCCTTGATCGTCCTTTTCGAAAA 58.618 39.130 21.35 21.35 40.61 2.29
790 6526 4.817464 TCCTTGATCGTCCTTTTCGAAAAA 59.183 37.500 22.67 9.34 40.61 1.94
942 6806 0.674534 AGCACGACTCGGAGTTCTTT 59.325 50.000 12.67 0.00 0.00 2.52
1032 6914 2.512745 ACGACGCAAGCACCAACA 60.513 55.556 0.00 0.00 45.62 3.33
1060 6942 2.498078 TCACACACTCCCATAATACGCA 59.502 45.455 0.00 0.00 0.00 5.24
1088 6997 1.730902 CGATCGATCAGCGGCGATT 60.731 57.895 24.40 0.00 46.13 3.34
1245 7154 3.415087 GGAGATGTGGCTGCCCCT 61.415 66.667 17.53 7.93 0.00 4.79
1311 7223 0.829333 AGAAGTCGATGAGCCTGCAT 59.171 50.000 0.00 0.00 0.00 3.96
1603 7545 8.339714 TGTGTACAGTTTTAGTTTACTCATTGC 58.660 33.333 0.00 0.00 0.00 3.56
1609 7551 9.612620 CAGTTTTAGTTTACTCATTGCCTTTAG 57.387 33.333 0.00 0.00 0.00 1.85
1707 7669 6.466885 AGTGACCTATTACTGTGTACCATC 57.533 41.667 0.00 0.00 0.00 3.51
1708 7670 6.195700 AGTGACCTATTACTGTGTACCATCT 58.804 40.000 0.00 0.00 0.00 2.90
1839 9086 4.441634 GGTGGCTATCATACACGAGACTTT 60.442 45.833 0.00 0.00 36.02 2.66
1853 9100 6.183360 ACACGAGACTTTGCAGTTTTCATAAA 60.183 34.615 0.00 0.00 31.22 1.40
1892 9139 0.466372 GGCAAATCTGTCCCCCTAGC 60.466 60.000 0.00 0.00 0.00 3.42
2080 9333 8.730680 CATAGTTTAACTCAAATGGTAAGTGCT 58.269 33.333 0.00 0.00 0.00 4.40
2090 9343 0.387622 GGTAAGTGCTACGCGTGTGA 60.388 55.000 24.59 0.00 0.00 3.58
2193 9449 3.953712 TCCGAGAAAGTTGTCATGCTA 57.046 42.857 0.00 0.00 0.00 3.49
2291 9552 7.101054 GTGTGACACTTATCAGGGTAAACATA 58.899 38.462 8.76 0.00 36.47 2.29
2331 9604 6.922957 TGCACAATTCAAACATTAAACTCCTC 59.077 34.615 0.00 0.00 0.00 3.71
2338 9611 7.102847 TCAAACATTAAACTCCTCGGTTTTT 57.897 32.000 0.00 0.00 39.66 1.94
2349 9622 6.296803 ACTCCTCGGTTTTTATTATGGATCC 58.703 40.000 4.20 4.20 0.00 3.36
2399 9672 2.870372 GCGTGCACCTGTTCATCC 59.130 61.111 12.15 0.00 0.00 3.51
2400 9673 3.027170 GCGTGCACCTGTTCATCCG 62.027 63.158 12.15 0.00 0.00 4.18
2401 9674 2.390599 CGTGCACCTGTTCATCCGG 61.391 63.158 12.15 0.00 0.00 5.14
2417 9690 5.375773 TCATCCGGAAGATTTTGATGCATA 58.624 37.500 9.01 0.00 34.29 3.14
2473 9746 3.827722 TCGGGAAGTGGATTTGTTCTTT 58.172 40.909 0.00 0.00 0.00 2.52
2499 9772 6.507958 GCTTCTCAGAGCCTAAAAGAATTT 57.492 37.500 0.00 0.00 36.87 1.82
2512 9790 6.873605 CCTAAAAGAATTTCTCGGGCAATTTT 59.126 34.615 0.00 0.00 37.28 1.82
2514 9792 6.785488 AAAGAATTTCTCGGGCAATTTTTC 57.215 33.333 0.00 0.00 27.08 2.29
2551 9829 0.036022 GGTGCAGTTCCAGAAGAGCT 59.964 55.000 0.00 0.00 36.29 4.09
2579 9857 2.202987 CGGTGGCATCCAGAGCTC 60.203 66.667 5.27 5.27 32.34 4.09
2700 10007 4.518249 GAAGTCTTTCCCTCCTACCAATG 58.482 47.826 0.00 0.00 0.00 2.82
2711 10018 3.311091 TCCTACCAATGTACGCCCTAAT 58.689 45.455 0.00 0.00 0.00 1.73
2971 10290 5.202004 GGCTAGCTCTACTTATATAGGCCA 58.798 45.833 15.72 0.00 35.37 5.36
3003 10322 2.422803 CCCAAATATTGAGCGGGAAGGA 60.423 50.000 6.65 0.00 39.44 3.36
3083 10402 0.756294 TGGTCTTCGCCTGTGAAAGA 59.244 50.000 0.00 0.00 0.00 2.52
3092 10411 1.070758 GCCTGTGAAAGACTCTGGTGA 59.929 52.381 0.00 0.00 34.88 4.02
3175 10494 2.294074 GCACCGATATGGCAACCTTTA 58.706 47.619 0.00 0.00 43.94 1.85
3198 10517 0.739561 GATGCCTCGGTACTCTTCGT 59.260 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 4039 0.605050 TTGCCGCTATGTGTTGCTGA 60.605 50.000 0.00 0.00 0.00 4.26
230 4225 2.754375 CCCCCAACGGTTAGCTGT 59.246 61.111 0.00 0.00 35.32 4.40
235 4230 1.202099 TCAGATGCCCCCAACGGTTA 61.202 55.000 0.00 0.00 0.00 2.85
242 4237 5.779771 GGAAAATAAATATCAGATGCCCCCA 59.220 40.000 0.00 0.00 0.00 4.96
349 4764 9.132521 GCCGACGAAGCTTATTATAAAATACTA 57.867 33.333 0.00 0.00 0.00 1.82
361 5546 1.585521 CGACGCCGACGAAGCTTAT 60.586 57.895 2.16 0.00 43.93 1.73
377 5562 0.606944 AACTACAAAATGGCGGGCGA 60.607 50.000 0.00 0.00 0.00 5.54
378 5563 0.179174 GAACTACAAAATGGCGGGCG 60.179 55.000 0.00 0.00 0.00 6.13
381 5566 1.472480 CAGGGAACTACAAAATGGCGG 59.528 52.381 0.00 0.00 40.21 6.13
382 5567 2.432444 TCAGGGAACTACAAAATGGCG 58.568 47.619 0.00 0.00 40.21 5.69
383 5568 4.079253 TCTTCAGGGAACTACAAAATGGC 58.921 43.478 0.00 0.00 40.21 4.40
384 5569 5.945784 TGATCTTCAGGGAACTACAAAATGG 59.054 40.000 0.00 0.00 40.21 3.16
385 5570 7.478322 CATGATCTTCAGGGAACTACAAAATG 58.522 38.462 0.00 0.00 40.21 2.32
402 5587 2.096268 CGACAAACACACGCATGATCTT 60.096 45.455 0.00 0.00 0.00 2.40
403 5588 1.460743 CGACAAACACACGCATGATCT 59.539 47.619 0.00 0.00 0.00 2.75
404 5589 1.194547 ACGACAAACACACGCATGATC 59.805 47.619 0.00 0.00 0.00 2.92
406 5591 1.010580 AACGACAAACACACGCATGA 58.989 45.000 0.00 0.00 0.00 3.07
407 5592 1.111667 CAACGACAAACACACGCATG 58.888 50.000 0.00 0.00 0.00 4.06
408 5593 0.730265 ACAACGACAAACACACGCAT 59.270 45.000 0.00 0.00 0.00 4.73
409 5594 0.179212 CACAACGACAAACACACGCA 60.179 50.000 0.00 0.00 0.00 5.24
410 5595 0.095589 TCACAACGACAAACACACGC 59.904 50.000 0.00 0.00 0.00 5.34
411 5596 2.092995 TCTTCACAACGACAAACACACG 59.907 45.455 0.00 0.00 0.00 4.49
412 5597 3.733024 TCTTCACAACGACAAACACAC 57.267 42.857 0.00 0.00 0.00 3.82
413 5598 4.750952 TTTCTTCACAACGACAAACACA 57.249 36.364 0.00 0.00 0.00 3.72
415 5600 6.003234 TCTTTTTCTTCACAACGACAAACA 57.997 33.333 0.00 0.00 0.00 2.83
416 5601 6.921332 TTCTTTTTCTTCACAACGACAAAC 57.079 33.333 0.00 0.00 0.00 2.93
417 5602 6.087028 CGTTTCTTTTTCTTCACAACGACAAA 59.913 34.615 0.00 0.00 38.18 2.83
420 5605 4.494410 CCGTTTCTTTTTCTTCACAACGAC 59.506 41.667 3.25 0.00 38.18 4.34
424 5609 4.017808 TCCCCGTTTCTTTTTCTTCACAA 58.982 39.130 0.00 0.00 0.00 3.33
426 5611 4.642445 TTCCCCGTTTCTTTTTCTTCAC 57.358 40.909 0.00 0.00 0.00 3.18
427 5612 5.394773 CCTTTTCCCCGTTTCTTTTTCTTCA 60.395 40.000 0.00 0.00 0.00 3.02
428 5613 5.047847 CCTTTTCCCCGTTTCTTTTTCTTC 58.952 41.667 0.00 0.00 0.00 2.87
429 5614 4.468510 ACCTTTTCCCCGTTTCTTTTTCTT 59.531 37.500 0.00 0.00 0.00 2.52
431 5616 4.395959 ACCTTTTCCCCGTTTCTTTTTC 57.604 40.909 0.00 0.00 0.00 2.29
432 5617 4.202182 GCTACCTTTTCCCCGTTTCTTTTT 60.202 41.667 0.00 0.00 0.00 1.94
435 5620 2.511659 GCTACCTTTTCCCCGTTTCTT 58.488 47.619 0.00 0.00 0.00 2.52
437 5622 0.800631 CGCTACCTTTTCCCCGTTTC 59.199 55.000 0.00 0.00 0.00 2.78
441 5626 1.814169 GAGCGCTACCTTTTCCCCG 60.814 63.158 11.50 0.00 0.00 5.73
442 5627 0.107165 ATGAGCGCTACCTTTTCCCC 60.107 55.000 11.50 0.00 0.00 4.81
443 5628 2.210961 GTATGAGCGCTACCTTTTCCC 58.789 52.381 11.50 0.00 0.00 3.97
453 5638 1.934589 TGCGTATTTGTATGAGCGCT 58.065 45.000 11.27 11.27 44.34 5.92
454 5639 2.949714 ATGCGTATTTGTATGAGCGC 57.050 45.000 0.00 0.00 44.29 5.92
455 5640 4.444388 AGTGTATGCGTATTTGTATGAGCG 59.556 41.667 0.00 0.00 0.00 5.03
459 5644 7.596621 AGAGATGAGTGTATGCGTATTTGTATG 59.403 37.037 0.00 0.00 0.00 2.39
461 5646 7.039313 AGAGATGAGTGTATGCGTATTTGTA 57.961 36.000 0.00 0.00 0.00 2.41
462 5647 5.907207 AGAGATGAGTGTATGCGTATTTGT 58.093 37.500 0.00 0.00 0.00 2.83
464 5649 7.886338 TCATAGAGATGAGTGTATGCGTATTT 58.114 34.615 0.00 0.00 37.15 1.40
465 5650 7.454260 TCATAGAGATGAGTGTATGCGTATT 57.546 36.000 0.00 0.00 37.15 1.89
467 5652 6.877611 TTCATAGAGATGAGTGTATGCGTA 57.122 37.500 0.00 0.00 43.03 4.42
468 5653 5.774498 TTCATAGAGATGAGTGTATGCGT 57.226 39.130 0.00 0.00 43.03 5.24
476 5661 4.755629 GCACATGCATTCATAGAGATGAGT 59.244 41.667 0.00 0.00 41.03 3.41
477 5662 4.143094 CGCACATGCATTCATAGAGATGAG 60.143 45.833 0.00 0.00 41.24 2.90
479 5664 3.667166 GCGCACATGCATTCATAGAGATG 60.667 47.826 0.30 0.00 42.21 2.90
480 5665 2.483106 GCGCACATGCATTCATAGAGAT 59.517 45.455 0.30 0.00 42.21 2.75
482 5667 1.600485 TGCGCACATGCATTCATAGAG 59.400 47.619 5.66 0.00 40.62 2.43
491 5676 3.543536 TAGGGTGTGCGCACATGCA 62.544 57.895 42.22 25.65 46.95 3.96
492 5677 2.745884 TAGGGTGTGCGCACATGC 60.746 61.111 42.22 30.51 46.95 4.06
493 5678 2.398554 GGTAGGGTGTGCGCACATG 61.399 63.158 42.22 0.00 46.95 3.21
494 5679 2.046314 GGTAGGGTGTGCGCACAT 60.046 61.111 42.22 29.89 46.95 3.21
495 5680 4.323477 GGGTAGGGTGTGCGCACA 62.323 66.667 37.86 37.86 46.95 4.57
498 5683 3.638592 ATTGGGGTAGGGTGTGCGC 62.639 63.158 0.00 0.00 0.00 6.09
499 5684 1.748879 CATTGGGGTAGGGTGTGCG 60.749 63.158 0.00 0.00 0.00 5.34
500 5685 0.394352 CTCATTGGGGTAGGGTGTGC 60.394 60.000 0.00 0.00 0.00 4.57
501 5686 0.394352 GCTCATTGGGGTAGGGTGTG 60.394 60.000 0.00 0.00 0.00 3.82
503 5688 0.552848 ATGCTCATTGGGGTAGGGTG 59.447 55.000 0.00 0.00 0.00 4.61
504 5689 0.846693 GATGCTCATTGGGGTAGGGT 59.153 55.000 0.00 0.00 0.00 4.34
505 5690 1.072965 GAGATGCTCATTGGGGTAGGG 59.927 57.143 0.00 0.00 0.00 3.53
506 5691 2.053244 AGAGATGCTCATTGGGGTAGG 58.947 52.381 0.00 0.00 32.06 3.18
508 5693 2.702478 CTCAGAGATGCTCATTGGGGTA 59.298 50.000 0.00 0.00 32.06 3.69
510 5695 1.767088 TCTCAGAGATGCTCATTGGGG 59.233 52.381 0.00 0.00 32.06 4.96
511 5696 3.555527 TTCTCAGAGATGCTCATTGGG 57.444 47.619 0.00 0.00 32.06 4.12
512 5697 4.201792 CGTTTTCTCAGAGATGCTCATTGG 60.202 45.833 0.00 0.00 32.06 3.16
514 5699 4.573900 ACGTTTTCTCAGAGATGCTCATT 58.426 39.130 0.00 0.00 32.06 2.57
515 5700 4.081752 AGACGTTTTCTCAGAGATGCTCAT 60.082 41.667 0.00 0.00 32.06 2.90
517 5702 3.843999 AGACGTTTTCTCAGAGATGCTC 58.156 45.455 0.00 0.00 0.00 4.26
518 5703 3.951775 AGACGTTTTCTCAGAGATGCT 57.048 42.857 0.00 0.00 0.00 3.79
528 5713 0.685660 GGTGGGAGGAGACGTTTTCT 59.314 55.000 0.00 0.00 37.23 2.52
529 5714 0.669625 CGGTGGGAGGAGACGTTTTC 60.670 60.000 0.00 0.00 0.00 2.29
530 5715 1.117142 TCGGTGGGAGGAGACGTTTT 61.117 55.000 0.00 0.00 0.00 2.43
534 5719 1.215647 CTTTCGGTGGGAGGAGACG 59.784 63.158 0.00 0.00 0.00 4.18
535 5720 1.079057 GCTTTCGGTGGGAGGAGAC 60.079 63.158 0.00 0.00 0.00 3.36
536 5721 2.646175 CGCTTTCGGTGGGAGGAGA 61.646 63.158 0.00 0.00 0.00 3.71
538 5723 0.974010 ATACGCTTTCGGTGGGAGGA 60.974 55.000 0.00 0.00 40.69 3.71
539 5724 0.107848 AATACGCTTTCGGTGGGAGG 60.108 55.000 0.00 0.00 40.69 4.30
542 5727 0.725117 GACAATACGCTTTCGGTGGG 59.275 55.000 0.00 0.00 40.69 4.61
547 5732 3.651562 ATTTCCGACAATACGCTTTCG 57.348 42.857 0.00 0.00 42.43 3.46
548 5733 5.217895 AGAATTTCCGACAATACGCTTTC 57.782 39.130 0.00 0.00 0.00 2.62
549 5734 6.730960 TTAGAATTTCCGACAATACGCTTT 57.269 33.333 0.00 0.00 0.00 3.51
550 5735 6.730960 TTTAGAATTTCCGACAATACGCTT 57.269 33.333 0.00 0.00 0.00 4.68
551 5736 6.730960 TTTTAGAATTTCCGACAATACGCT 57.269 33.333 0.00 0.00 0.00 5.07
552 5737 9.493206 TTTATTTTAGAATTTCCGACAATACGC 57.507 29.630 0.00 0.00 0.00 4.42
559 5744 8.899771 TCCTGGATTTATTTTAGAATTTCCGAC 58.100 33.333 0.00 0.00 0.00 4.79
571 5756 8.980596 TGCTCACATTTATCCTGGATTTATTTT 58.019 29.630 15.55 0.00 0.00 1.82
572 5757 8.416329 GTGCTCACATTTATCCTGGATTTATTT 58.584 33.333 15.55 0.00 0.00 1.40
573 5758 7.014615 GGTGCTCACATTTATCCTGGATTTATT 59.985 37.037 15.55 0.00 0.00 1.40
574 5759 6.491403 GGTGCTCACATTTATCCTGGATTTAT 59.509 38.462 15.55 5.99 0.00 1.40
576 5761 4.646492 GGTGCTCACATTTATCCTGGATTT 59.354 41.667 15.55 0.00 0.00 2.17
577 5762 4.210331 GGTGCTCACATTTATCCTGGATT 58.790 43.478 15.55 0.00 0.00 3.01
579 5764 2.575735 TGGTGCTCACATTTATCCTGGA 59.424 45.455 0.00 0.00 0.00 3.86
580 5765 2.947652 CTGGTGCTCACATTTATCCTGG 59.052 50.000 2.21 0.00 0.00 4.45
581 5766 2.947652 CCTGGTGCTCACATTTATCCTG 59.052 50.000 2.21 0.00 0.00 3.86
582 5767 2.846206 TCCTGGTGCTCACATTTATCCT 59.154 45.455 2.21 0.00 0.00 3.24
583 5768 3.281727 TCCTGGTGCTCACATTTATCC 57.718 47.619 2.21 0.00 0.00 2.59
584 5769 5.357878 TCAAATCCTGGTGCTCACATTTATC 59.642 40.000 2.21 0.00 0.00 1.75
586 5771 4.661222 TCAAATCCTGGTGCTCACATTTA 58.339 39.130 2.21 0.00 0.00 1.40
587 5772 3.499338 TCAAATCCTGGTGCTCACATTT 58.501 40.909 2.21 0.00 0.00 2.32
588 5773 3.159213 TCAAATCCTGGTGCTCACATT 57.841 42.857 2.21 0.00 0.00 2.71
589 5774 2.885135 TCAAATCCTGGTGCTCACAT 57.115 45.000 2.21 0.00 0.00 3.21
602 5787 3.430453 TCAACCCACCAGGATTCAAATC 58.570 45.455 0.00 0.00 39.89 2.17
603 5788 3.434309 CTCAACCCACCAGGATTCAAAT 58.566 45.455 0.00 0.00 39.89 2.32
604 5789 2.490718 CCTCAACCCACCAGGATTCAAA 60.491 50.000 0.00 0.00 39.89 2.69
605 5790 1.075374 CCTCAACCCACCAGGATTCAA 59.925 52.381 0.00 0.00 39.89 2.69
606 5791 0.698238 CCTCAACCCACCAGGATTCA 59.302 55.000 0.00 0.00 39.89 2.57
607 5792 0.991920 TCCTCAACCCACCAGGATTC 59.008 55.000 0.00 0.00 39.89 2.52
608 5793 1.686236 ATCCTCAACCCACCAGGATT 58.314 50.000 0.00 0.00 43.40 3.01
609 5794 2.587060 TATCCTCAACCCACCAGGAT 57.413 50.000 5.10 5.10 46.79 3.24
611 5796 2.126882 TGATATCCTCAACCCACCAGG 58.873 52.381 0.00 0.00 43.78 4.45
612 5797 2.774234 AGTGATATCCTCAACCCACCAG 59.226 50.000 0.00 0.00 35.07 4.00
614 5799 5.071788 TGAATAGTGATATCCTCAACCCACC 59.928 44.000 0.00 0.00 35.07 4.61
616 5801 5.665360 TGTGAATAGTGATATCCTCAACCCA 59.335 40.000 0.00 0.00 35.07 4.51
617 5802 6.174720 TGTGAATAGTGATATCCTCAACCC 57.825 41.667 0.00 0.00 35.07 4.11
618 5803 9.950496 ATTATGTGAATAGTGATATCCTCAACC 57.050 33.333 0.00 0.00 35.07 3.77
633 5818 9.898152 TGTGTGGTTAAGATGATTATGTGAATA 57.102 29.630 0.00 0.00 0.00 1.75
636 5821 8.676401 CATTGTGTGGTTAAGATGATTATGTGA 58.324 33.333 0.00 0.00 0.00 3.58
637 5822 8.676401 TCATTGTGTGGTTAAGATGATTATGTG 58.324 33.333 0.00 0.00 0.00 3.21
638 5823 8.806429 TCATTGTGTGGTTAAGATGATTATGT 57.194 30.769 0.00 0.00 0.00 2.29
641 5826 8.611757 CGAATCATTGTGTGGTTAAGATGATTA 58.388 33.333 8.77 0.00 41.61 1.75
643 5828 6.458751 GCGAATCATTGTGTGGTTAAGATGAT 60.459 38.462 0.00 0.00 36.19 2.45
645 5830 5.030295 GCGAATCATTGTGTGGTTAAGATG 58.970 41.667 0.00 0.00 29.18 2.90
646 5831 4.201812 CGCGAATCATTGTGTGGTTAAGAT 60.202 41.667 0.00 0.00 29.18 2.40
647 5832 3.124466 CGCGAATCATTGTGTGGTTAAGA 59.876 43.478 0.00 0.00 29.18 2.10
648 5833 3.120338 ACGCGAATCATTGTGTGGTTAAG 60.120 43.478 15.93 0.00 32.36 1.85
649 5834 2.809119 ACGCGAATCATTGTGTGGTTAA 59.191 40.909 15.93 0.00 32.36 2.01
650 5835 2.418692 ACGCGAATCATTGTGTGGTTA 58.581 42.857 15.93 0.00 32.36 2.85
651 5836 1.234821 ACGCGAATCATTGTGTGGTT 58.765 45.000 15.93 0.00 32.36 3.67
652 5837 1.234821 AACGCGAATCATTGTGTGGT 58.765 45.000 15.93 0.00 33.89 4.16
654 5839 2.241722 GGAAACGCGAATCATTGTGTG 58.758 47.619 15.93 0.00 33.89 3.82
655 5840 2.611974 GGAAACGCGAATCATTGTGT 57.388 45.000 15.93 0.00 35.11 3.72
669 5854 2.875933 TCATCCAACTCAACACGGAAAC 59.124 45.455 0.00 0.00 0.00 2.78
670 5855 2.875933 GTCATCCAACTCAACACGGAAA 59.124 45.455 0.00 0.00 0.00 3.13
739 6475 7.277981 ACGTACATCTCTGTTACATTTTCATCC 59.722 37.037 0.00 0.00 36.79 3.51
740 6476 8.186178 ACGTACATCTCTGTTACATTTTCATC 57.814 34.615 0.00 0.00 36.79 2.92
741 6477 9.817809 ATACGTACATCTCTGTTACATTTTCAT 57.182 29.630 0.00 0.00 36.79 2.57
743 6479 8.753175 GGATACGTACATCTCTGTTACATTTTC 58.247 37.037 0.00 0.00 36.79 2.29
744 6480 8.475639 AGGATACGTACATCTCTGTTACATTTT 58.524 33.333 0.00 0.00 46.39 1.82
745 6481 8.008513 AGGATACGTACATCTCTGTTACATTT 57.991 34.615 0.00 0.00 46.39 2.32
746 6482 7.584122 AGGATACGTACATCTCTGTTACATT 57.416 36.000 0.00 0.00 46.39 2.71
750 6486 7.307811 CGATCAAGGATACGTACATCTCTGTTA 60.308 40.741 0.00 0.00 46.39 2.41
790 6526 3.749088 TGCACGATCAAGGATACGTTTTT 59.251 39.130 0.00 0.00 46.39 1.94
791 6527 3.331150 TGCACGATCAAGGATACGTTTT 58.669 40.909 0.00 0.00 46.39 2.43
792 6528 2.967362 TGCACGATCAAGGATACGTTT 58.033 42.857 0.00 0.00 46.39 3.60
793 6529 2.665649 TGCACGATCAAGGATACGTT 57.334 45.000 0.00 0.00 46.39 3.99
794 6530 2.268298 GTTGCACGATCAAGGATACGT 58.732 47.619 0.00 0.00 46.39 3.57
795 6531 1.255342 CGTTGCACGATCAAGGATACG 59.745 52.381 3.04 0.00 46.05 3.06
796 6532 2.268298 ACGTTGCACGATCAAGGATAC 58.732 47.619 14.18 0.00 46.05 2.24
797 6533 2.665649 ACGTTGCACGATCAAGGATA 57.334 45.000 14.18 0.00 46.05 2.59
798 6534 2.665649 TACGTTGCACGATCAAGGAT 57.334 45.000 14.18 0.00 46.05 3.24
799 6535 2.442212 TTACGTTGCACGATCAAGGA 57.558 45.000 14.18 0.00 46.05 3.36
800 6536 2.724839 GCTTTACGTTGCACGATCAAGG 60.725 50.000 14.18 10.69 46.05 3.61
1032 6914 1.338107 TGGGAGTGTGTGAATCTCGT 58.662 50.000 0.00 0.00 0.00 4.18
1245 7154 3.249189 AGCTTCCCCTCAACGGCA 61.249 61.111 0.00 0.00 0.00 5.69
1251 7163 1.671742 GAACGTGAGCTTCCCCTCA 59.328 57.895 0.00 0.00 39.42 3.86
1311 7223 3.755628 GGTGCCGCGGTAGAGTCA 61.756 66.667 28.70 12.30 0.00 3.41
1507 7439 1.654954 GCGACGAGAGGGTTCTGCTA 61.655 60.000 0.00 0.00 32.53 3.49
1603 7545 6.605594 AGATCAAGTAGGAGAGACACTAAAGG 59.394 42.308 0.00 0.00 0.00 3.11
1609 7551 6.274157 TGAAAGATCAAGTAGGAGAGACAC 57.726 41.667 0.00 0.00 30.99 3.67
1707 7669 8.455903 ACATGGATGACTAATGGAATAACAAG 57.544 34.615 0.00 0.00 0.00 3.16
1806 9053 1.202639 TGATAGCCACCTTGTATGCCG 60.203 52.381 0.00 0.00 0.00 5.69
1853 9100 4.647853 TGCCACGTCCTGTTATAGATACTT 59.352 41.667 0.00 0.00 0.00 2.24
1949 9196 7.099120 GCATTTTTGAGTTTTGGTATGAGGAT 58.901 34.615 0.00 0.00 0.00 3.24
2090 9343 4.681978 GGCCGGAGTGCTTCGTGT 62.682 66.667 5.05 0.00 0.00 4.49
2119 9372 7.562454 TCTTTTCGGATGACAACTTTAGTTT 57.438 32.000 0.00 0.00 35.83 2.66
2157 9411 7.718314 ACTTTCTCGGATGGTAAGTTTAGTTTT 59.282 33.333 0.00 0.00 0.00 2.43
2193 9449 3.421844 GGGATGGCAAGTTTAGTTGTCT 58.578 45.455 0.00 0.00 32.97 3.41
2331 9604 8.792633 ACATATGTGGATCCATAATAAAAACCG 58.207 33.333 19.62 7.81 31.44 4.44
2338 9611 7.983363 TGTGGAACATATGTGGATCCATAATA 58.017 34.615 24.02 18.44 45.67 0.98
2428 9701 6.581171 AGCAAGATGTCGATCATACTATGA 57.419 37.500 1.10 1.10 44.55 2.15
2441 9714 1.734465 CACTTCCCGAAGCAAGATGTC 59.266 52.381 4.34 0.00 41.99 3.06
2499 9772 3.131223 TGTGTTTGAAAAATTGCCCGAGA 59.869 39.130 0.00 0.00 0.00 4.04
2512 9790 3.181434 ACCTTGCCCTCTATGTGTTTGAA 60.181 43.478 0.00 0.00 0.00 2.69
2514 9792 2.489329 CACCTTGCCCTCTATGTGTTTG 59.511 50.000 0.00 0.00 0.00 2.93
2537 9815 1.689273 ACGTTCAGCTCTTCTGGAACT 59.311 47.619 9.77 0.00 43.06 3.01
2579 9857 4.699257 CCAACAATTTTCCTCTCCTCTCTG 59.301 45.833 0.00 0.00 0.00 3.35
2667 9974 0.250901 AAAGACTTCGCATGCACCCT 60.251 50.000 19.57 3.93 0.00 4.34
2700 10007 5.298347 AGATCTTAGCAAATTAGGGCGTAC 58.702 41.667 0.00 0.00 34.54 3.67
2711 10018 1.797713 CGTCCGCGAGATCTTAGCAAA 60.798 52.381 8.23 7.73 41.33 3.68
2971 10290 5.699143 CTCAATATTTGGGAAGAGGACCAT 58.301 41.667 0.00 0.00 36.48 3.55
3017 10336 0.323451 GTCCCCCTTCGAATTTGCCT 60.323 55.000 0.00 0.00 0.00 4.75
3083 10402 2.214181 GACGGCGTCATCACCAGAGT 62.214 60.000 33.07 0.00 32.09 3.24
3175 10494 0.033011 AGAGTACCGAGGCATCAGGT 60.033 55.000 16.64 16.64 41.73 4.00


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

AutoCloner maintained by Alex Coulton.