Multiple sequence alignment - TraesCS5D01G257900

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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 TraesCS5D01G257900 chr5D 100.000 6474 0 0 1 6474 364663165 364669638 0.000000e+00 11956
1 TraesCS5D01G257900 chr5D 89.652 1894 150 27 2080 3943 364766621 364764744 0.000000e+00 2370
2 TraesCS5D01G257900 chr5D 86.992 1476 122 35 116 1564 364768185 364766753 0.000000e+00 1598
3 TraesCS5D01G257900 chr5D 86.013 765 63 16 4616 5377 364764095 364763372 0.000000e+00 780
4 TraesCS5D01G257900 chr5D 81.763 817 117 17 711 1498 364563110 364563923 0.000000e+00 654
5 TraesCS5D01G257900 chr5D 86.964 560 51 11 4086 4624 364764742 364764184 1.540000e-170 610
6 TraesCS5D01G257900 chr5D 82.724 602 88 15 117 708 364558842 364559437 7.440000e-144 521
7 TraesCS5D01G257900 chr5D 87.991 433 49 3 4949 5379 30615835 30615404 5.790000e-140 508
8 TraesCS5D01G257900 chr5D 82.452 416 48 13 3413 3810 30673524 30673116 2.240000e-89 340
9 TraesCS5D01G257900 chr5D 85.938 192 21 3 3162 3347 30673731 30673540 3.960000e-47 200
10 TraesCS5D01G257900 chr5D 91.860 86 7 0 5367 5452 30615377 30615292 3.170000e-23 121
11 TraesCS5D01G257900 chr5B 93.116 2513 116 25 2911 5379 430670621 430673120 0.000000e+00 3629
12 TraesCS5D01G257900 chr5B 87.174 1536 139 33 116 1621 430754792 430753285 0.000000e+00 1692
13 TraesCS5D01G257900 chr5B 94.023 1121 37 13 5367 6474 430673147 430674250 0.000000e+00 1672
14 TraesCS5D01G257900 chr5B 89.713 1322 88 21 756 2058 430668371 430669663 0.000000e+00 1644
15 TraesCS5D01G257900 chr5B 87.927 1317 96 27 4086 5377 430751307 430750029 0.000000e+00 1493
16 TraesCS5D01G257900 chr5B 89.388 1046 86 8 2907 3943 430752338 430751309 0.000000e+00 1293
17 TraesCS5D01G257900 chr5B 90.499 842 45 15 2068 2903 430669760 430670572 0.000000e+00 1079
18 TraesCS5D01G257900 chr5B 88.035 794 54 24 2058 2820 430753222 430752439 0.000000e+00 902
19 TraesCS5D01G257900 chr5B 82.801 814 110 18 711 1497 430625638 430626448 0.000000e+00 701
20 TraesCS5D01G257900 chr5B 81.122 784 123 16 706 1468 430617007 430617786 7.180000e-169 604
21 TraesCS5D01G257900 chr5B 83.893 596 82 10 117 703 430618524 430619114 2.040000e-154 556
22 TraesCS5D01G257900 chr5B 83.893 596 80 13 117 703 430627755 430628343 7.330000e-154 555
23 TraesCS5D01G257900 chr5B 83.670 594 84 9 117 703 430634863 430635450 1.230000e-151 547
24 TraesCS5D01G257900 chr5B 82.886 596 88 12 117 703 430621752 430622342 2.070000e-144 523
25 TraesCS5D01G257900 chr5B 82.828 594 92 9 117 703 430632234 430632824 2.070000e-144 523
26 TraesCS5D01G257900 chr5A 93.117 2499 128 27 2910 5379 465992089 465994572 0.000000e+00 3622
27 TraesCS5D01G257900 chr5A 90.685 1503 103 14 479 1958 465987722 465989210 0.000000e+00 1965
28 TraesCS5D01G257900 chr5A 96.406 1113 30 4 5367 6474 465994599 465995706 0.000000e+00 1825
29 TraesCS5D01G257900 chr5A 89.928 1390 117 13 2564 3943 466038899 466037523 0.000000e+00 1770
30 TraesCS5D01G257900 chr5A 87.778 1530 145 26 116 1621 466041678 466040167 0.000000e+00 1751
31 TraesCS5D01G257900 chr5A 86.353 1319 109 30 4086 5379 466037521 466036249 0.000000e+00 1373
32 TraesCS5D01G257900 chr5A 90.498 863 50 13 2058 2911 465991146 465991985 0.000000e+00 1110
33 TraesCS5D01G257900 chr5A 87.666 754 58 22 2080 2821 466039737 466039007 0.000000e+00 845
34 TraesCS5D01G257900 chr5A 81.725 777 128 9 706 1469 465690088 465690863 2.550000e-178 636
35 TraesCS5D01G257900 chr5A 81.271 598 96 13 117 703 465647788 465648380 2.730000e-128 470
36 TraesCS5D01G257900 chr5A 84.964 419 44 13 5367 5779 466036222 466035817 2.170000e-109 407
37 TraesCS5D01G257900 chr5A 82.921 445 54 11 1622 2044 528290270 528289826 1.320000e-101 381
38 TraesCS5D01G257900 chr1D 83.407 452 38 22 1622 2042 384847663 384848108 1.020000e-102 385
39 TraesCS5D01G257900 chr1D 83.182 440 39 17 1622 2041 480010024 480009600 2.850000e-98 370
40 TraesCS5D01G257900 chr3A 83.960 399 39 12 1665 2041 683683681 683683286 6.170000e-95 359
41 TraesCS5D01G257900 chr3A 90.840 131 10 2 1915 2044 219341298 219341427 2.400000e-39 174
42 TraesCS5D01G257900 chr3B 81.473 448 50 15 1623 2041 53570330 53570773 2.890000e-88 337
43 TraesCS5D01G257900 chr3B 89.256 242 26 0 1740 1981 727786106 727786347 2.930000e-78 303
44 TraesCS5D01G257900 chr2D 82.834 367 39 10 1621 1965 567805505 567805869 2.270000e-79 307
45 TraesCS5D01G257900 chr4B 83.939 330 28 11 1638 1954 522698081 522698398 6.350000e-75 292
46 TraesCS5D01G257900 chr1A 96.552 174 5 1 2080 2252 439339836 439339663 2.950000e-73 287
47 TraesCS5D01G257900 chr4D 80.583 412 40 19 1647 2041 151981626 151981238 1.370000e-71 281
48 TraesCS5D01G257900 chr7A 83.137 255 33 7 1799 2044 509139217 509138964 2.350000e-54 224


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 TraesCS5D01G257900 chr5D 364663165 364669638 6473 False 11956.000000 11956 100.000000 1 6474 1 chr5D.!!$F1 6473
1 TraesCS5D01G257900 chr5D 364763372 364768185 4813 True 1339.500000 2370 87.405250 116 5377 4 chr5D.!!$R3 5261
2 TraesCS5D01G257900 chr5D 364558842 364563923 5081 False 587.500000 654 82.243500 117 1498 2 chr5D.!!$F2 1381
3 TraesCS5D01G257900 chr5D 30615292 30615835 543 True 314.500000 508 89.925500 4949 5452 2 chr5D.!!$R1 503
4 TraesCS5D01G257900 chr5D 30673116 30673731 615 True 270.000000 340 84.195000 3162 3810 2 chr5D.!!$R2 648
5 TraesCS5D01G257900 chr5B 430668371 430674250 5879 False 2006.000000 3629 91.837750 756 6474 4 chr5B.!!$F2 5718
6 TraesCS5D01G257900 chr5B 430750029 430754792 4763 True 1345.000000 1692 88.131000 116 5377 4 chr5B.!!$R1 5261
7 TraesCS5D01G257900 chr5B 430617007 430635450 18443 False 572.714286 701 83.013286 117 1497 7 chr5B.!!$F1 1380
8 TraesCS5D01G257900 chr5A 465987722 465995706 7984 False 2130.500000 3622 92.676500 479 6474 4 chr5A.!!$F3 5995
9 TraesCS5D01G257900 chr5A 466035817 466041678 5861 True 1229.200000 1770 87.337800 116 5779 5 chr5A.!!$R2 5663
10 TraesCS5D01G257900 chr5A 465690088 465690863 775 False 636.000000 636 81.725000 706 1469 1 chr5A.!!$F2 763
11 TraesCS5D01G257900 chr5A 465647788 465648380 592 False 470.000000 470 81.271000 117 703 1 chr5A.!!$F1 586

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
93 94 0.036875 CTTTCACTTCCCTTCGGCCT 59.963 55.0 0.00 0.0 0.00 5.19 F
842 8780 0.046242 AGATTCCCCCATCCTCCACA 59.954 55.0 0.00 0.0 0.00 4.17 F
1820 16844 0.308376 GGCGCACTGGACGTTTTTAA 59.692 50.0 10.83 0.0 0.00 1.52 F
2218 19257 0.814010 AACTGGCTCGCGTTCTGTTT 60.814 50.0 5.77 0.0 0.00 2.83 F
3993 22403 0.321653 AGAGGACAACGGGACATTGC 60.322 55.0 0.00 0.0 33.38 3.56 F
4239 22718 2.891191 AGAGGCGGGGTTGATTTAAA 57.109 45.0 0.00 0.0 0.00 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 16824 0.814410 TAAAAACGTCCAGTGCGCCA 60.814 50.000 4.18 0.0 0.00 5.69 R
2319 19371 0.251354 TGAGCATGGTTCCTCTCAGC 59.749 55.000 0.00 0.0 32.43 4.26 R
3407 21341 0.615331 GTGCTCTGTCAAGGATGGGA 59.385 55.000 0.00 0.0 0.00 4.37 R
4214 22686 2.097110 TCAACCCCGCCTCTACATAT 57.903 50.000 0.00 0.0 0.00 1.78 R
5350 24947 1.347378 GAATCCCTCCTCTCATGGCTC 59.653 57.143 0.00 0.0 0.00 4.70 R
6213 25864 0.954452 CCTGCAAAAGTGACCTGACC 59.046 55.000 0.00 0.0 0.00 4.02 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.082523 TGGTGCCGCCAGTCTAGC 62.083 66.667 0.00 0.00 43.61 3.42
23 24 4.840005 GGTGCCGCCAGTCTAGCC 62.840 72.222 0.00 0.00 37.17 3.93
24 25 4.840005 GTGCCGCCAGTCTAGCCC 62.840 72.222 0.00 0.00 0.00 5.19
26 27 4.840005 GCCGCCAGTCTAGCCCAC 62.840 72.222 0.00 0.00 0.00 4.61
27 28 4.162690 CCGCCAGTCTAGCCCACC 62.163 72.222 0.00 0.00 0.00 4.61
28 29 3.390521 CGCCAGTCTAGCCCACCA 61.391 66.667 0.00 0.00 0.00 4.17
29 30 2.954684 CGCCAGTCTAGCCCACCAA 61.955 63.158 0.00 0.00 0.00 3.67
32 33 1.616994 GCCAGTCTAGCCCACCAAATT 60.617 52.381 0.00 0.00 0.00 1.82
33 34 2.369394 CCAGTCTAGCCCACCAAATTC 58.631 52.381 0.00 0.00 0.00 2.17
34 35 2.290896 CCAGTCTAGCCCACCAAATTCA 60.291 50.000 0.00 0.00 0.00 2.57
35 36 3.624777 CAGTCTAGCCCACCAAATTCAT 58.375 45.455 0.00 0.00 0.00 2.57
36 37 4.385199 CCAGTCTAGCCCACCAAATTCATA 60.385 45.833 0.00 0.00 0.00 2.15
37 38 4.818546 CAGTCTAGCCCACCAAATTCATAG 59.181 45.833 0.00 0.00 0.00 2.23
39 40 5.059833 GTCTAGCCCACCAAATTCATAGAG 58.940 45.833 0.00 0.00 0.00 2.43
40 41 3.303351 AGCCCACCAAATTCATAGAGG 57.697 47.619 0.00 0.00 0.00 3.69
41 42 2.091665 AGCCCACCAAATTCATAGAGGG 60.092 50.000 0.00 0.00 38.10 4.30
42 43 2.358195 GCCCACCAAATTCATAGAGGGT 60.358 50.000 0.00 0.00 37.38 4.34
43 44 3.555966 CCCACCAAATTCATAGAGGGTC 58.444 50.000 0.00 0.00 0.00 4.46
44 45 3.053693 CCCACCAAATTCATAGAGGGTCA 60.054 47.826 0.00 0.00 0.00 4.02
45 46 4.569653 CCCACCAAATTCATAGAGGGTCAA 60.570 45.833 0.00 0.00 0.00 3.18
46 47 4.641989 CCACCAAATTCATAGAGGGTCAAG 59.358 45.833 0.00 0.00 0.00 3.02
48 49 3.313526 CCAAATTCATAGAGGGTCAAGCG 59.686 47.826 0.00 0.00 0.00 4.68
49 50 4.191544 CAAATTCATAGAGGGTCAAGCGA 58.808 43.478 0.00 0.00 0.00 4.93
50 51 3.742433 ATTCATAGAGGGTCAAGCGAG 57.258 47.619 0.00 0.00 0.00 5.03
51 52 2.145397 TCATAGAGGGTCAAGCGAGT 57.855 50.000 0.00 0.00 0.00 4.18
52 53 2.457598 TCATAGAGGGTCAAGCGAGTT 58.542 47.619 0.00 0.00 0.00 3.01
53 54 2.427453 TCATAGAGGGTCAAGCGAGTTC 59.573 50.000 0.00 0.00 0.00 3.01
54 55 2.217510 TAGAGGGTCAAGCGAGTTCT 57.782 50.000 0.00 0.00 0.00 3.01
55 56 0.605589 AGAGGGTCAAGCGAGTTCTG 59.394 55.000 0.00 0.00 0.00 3.02
56 57 0.603569 GAGGGTCAAGCGAGTTCTGA 59.396 55.000 0.00 0.00 0.00 3.27
57 58 0.605589 AGGGTCAAGCGAGTTCTGAG 59.394 55.000 0.00 0.00 0.00 3.35
60 61 1.795286 GGTCAAGCGAGTTCTGAGTTG 59.205 52.381 0.00 0.00 0.00 3.16
61 62 2.545952 GGTCAAGCGAGTTCTGAGTTGA 60.546 50.000 0.00 0.00 0.00 3.18
62 63 2.473235 GTCAAGCGAGTTCTGAGTTGAC 59.527 50.000 0.00 0.00 37.65 3.18
64 65 2.715737 AGCGAGTTCTGAGTTGACTC 57.284 50.000 4.20 4.20 43.15 3.36
65 66 1.271102 AGCGAGTTCTGAGTTGACTCC 59.729 52.381 8.56 0.00 42.20 3.85
66 67 1.670380 GCGAGTTCTGAGTTGACTCCC 60.670 57.143 8.56 0.00 42.20 4.30
67 68 1.889829 CGAGTTCTGAGTTGACTCCCT 59.110 52.381 8.56 0.22 42.20 4.20
68 69 3.082548 CGAGTTCTGAGTTGACTCCCTA 58.917 50.000 8.56 0.00 42.20 3.53
69 70 3.506455 CGAGTTCTGAGTTGACTCCCTAA 59.494 47.826 8.56 0.00 42.20 2.69
70 71 4.616373 CGAGTTCTGAGTTGACTCCCTAAC 60.616 50.000 8.56 9.50 42.20 2.34
71 72 4.484912 AGTTCTGAGTTGACTCCCTAACT 58.515 43.478 8.56 11.23 42.20 2.24
75 76 1.819903 GAGTTGACTCCCTAACTCGCT 59.180 52.381 0.00 0.00 42.12 4.93
77 78 2.633481 AGTTGACTCCCTAACTCGCTTT 59.367 45.455 0.00 0.00 31.88 3.51
78 79 2.994578 GTTGACTCCCTAACTCGCTTTC 59.005 50.000 0.00 0.00 0.00 2.62
80 81 2.029290 TGACTCCCTAACTCGCTTTCAC 60.029 50.000 0.00 0.00 0.00 3.18
81 82 2.231721 GACTCCCTAACTCGCTTTCACT 59.768 50.000 0.00 0.00 0.00 3.41
82 83 2.633481 ACTCCCTAACTCGCTTTCACTT 59.367 45.455 0.00 0.00 0.00 3.16
83 84 3.254892 CTCCCTAACTCGCTTTCACTTC 58.745 50.000 0.00 0.00 0.00 3.01
84 85 2.028385 TCCCTAACTCGCTTTCACTTCC 60.028 50.000 0.00 0.00 0.00 3.46
85 86 2.347731 CCTAACTCGCTTTCACTTCCC 58.652 52.381 0.00 0.00 0.00 3.97
86 87 2.028020 CCTAACTCGCTTTCACTTCCCT 60.028 50.000 0.00 0.00 0.00 4.20
87 88 2.640316 AACTCGCTTTCACTTCCCTT 57.360 45.000 0.00 0.00 0.00 3.95
88 89 2.171341 ACTCGCTTTCACTTCCCTTC 57.829 50.000 0.00 0.00 0.00 3.46
89 90 1.071605 CTCGCTTTCACTTCCCTTCG 58.928 55.000 0.00 0.00 0.00 3.79
90 91 0.320421 TCGCTTTCACTTCCCTTCGG 60.320 55.000 0.00 0.00 0.00 4.30
92 93 1.587043 GCTTTCACTTCCCTTCGGCC 61.587 60.000 0.00 0.00 0.00 6.13
93 94 0.036875 CTTTCACTTCCCTTCGGCCT 59.963 55.000 0.00 0.00 0.00 5.19
94 95 0.476771 TTTCACTTCCCTTCGGCCTT 59.523 50.000 0.00 0.00 0.00 4.35
97 98 0.391793 CACTTCCCTTCGGCCTTCTC 60.392 60.000 0.00 0.00 0.00 2.87
98 99 1.222113 CTTCCCTTCGGCCTTCTCC 59.778 63.158 0.00 0.00 0.00 3.71
99 100 1.537889 TTCCCTTCGGCCTTCTCCA 60.538 57.895 0.00 0.00 0.00 3.86
100 101 1.838073 TTCCCTTCGGCCTTCTCCAC 61.838 60.000 0.00 0.00 0.00 4.02
101 102 2.269241 CCTTCGGCCTTCTCCACC 59.731 66.667 0.00 0.00 0.00 4.61
102 103 2.269241 CTTCGGCCTTCTCCACCC 59.731 66.667 0.00 0.00 0.00 4.61
103 104 3.327404 TTCGGCCTTCTCCACCCC 61.327 66.667 0.00 0.00 0.00 4.95
107 108 2.936032 GCCTTCTCCACCCCCACT 60.936 66.667 0.00 0.00 0.00 4.00
108 109 2.539081 GCCTTCTCCACCCCCACTT 61.539 63.158 0.00 0.00 0.00 3.16
109 110 2.081585 GCCTTCTCCACCCCCACTTT 62.082 60.000 0.00 0.00 0.00 2.66
111 112 1.620822 CTTCTCCACCCCCACTTTTG 58.379 55.000 0.00 0.00 0.00 2.44
113 114 0.771127 TCTCCACCCCCACTTTTGAG 59.229 55.000 0.00 0.00 0.00 3.02
114 115 0.478507 CTCCACCCCCACTTTTGAGT 59.521 55.000 0.00 0.00 0.00 3.41
121 1523 1.806542 CCCCACTTTTGAGTGTCATCG 59.193 52.381 5.89 0.00 38.07 3.84
129 1531 1.511850 TGAGTGTCATCGTGCTTTGG 58.488 50.000 0.00 0.00 0.00 3.28
181 1584 2.424667 CCCATGCATTACCATTCCCAGA 60.425 50.000 0.00 0.00 0.00 3.86
272 1678 2.066262 CGGCTCTTTTTCACGCTTCTA 58.934 47.619 0.00 0.00 0.00 2.10
277 1683 1.810755 CTTTTTCACGCTTCTACCCCC 59.189 52.381 0.00 0.00 0.00 5.40
283 1689 1.227556 CGCTTCTACCCCCAATCCG 60.228 63.158 0.00 0.00 0.00 4.18
284 1690 1.912971 GCTTCTACCCCCAATCCGT 59.087 57.895 0.00 0.00 0.00 4.69
312 1718 2.445983 AACCGAACCCGACCACCTT 61.446 57.895 0.00 0.00 38.22 3.50
382 1790 1.441729 GTTCCATCGGCGATGAGGA 59.558 57.895 42.19 31.66 42.09 3.71
390 1799 2.143419 GGCGATGAGGAGGGATGGT 61.143 63.158 0.00 0.00 0.00 3.55
490 1902 7.934665 TCAAACACTAGTACCTTTATTTGCTCA 59.065 33.333 0.00 0.00 0.00 4.26
543 1958 8.141268 TCCTCTACAAATGATGTTTTTGGTTTC 58.859 33.333 0.00 0.00 43.63 2.78
570 1985 7.176515 TGGTACAATCTAGCATGTTGATGTTTT 59.823 33.333 5.69 0.00 31.92 2.43
618 2035 8.415950 TGTTCTCAAAATGTTGGGTACATATT 57.584 30.769 3.93 0.00 46.75 1.28
693 2113 2.287103 GTCTCACACCCAAGAACGTTTC 59.713 50.000 0.46 0.00 0.00 2.78
842 8780 0.046242 AGATTCCCCCATCCTCCACA 59.954 55.000 0.00 0.00 0.00 4.17
895 8834 3.691342 CGAACCCGGGACTGCTCA 61.691 66.667 32.02 0.00 0.00 4.26
1134 15819 2.992847 TCTCCCACTACTCCACAAGA 57.007 50.000 0.00 0.00 0.00 3.02
1164 15849 0.733223 GAAGGAGCAAGGACGACGTC 60.733 60.000 19.70 19.70 0.00 4.34
1279 15974 3.220773 CATGCGCGTAATATGCTTCAAG 58.779 45.455 8.43 0.00 0.00 3.02
1375 16085 8.766000 TTTCAGAGTTTAACACGCATCTATAA 57.234 30.769 0.00 0.00 0.00 0.98
1472 16215 2.100916 AGAATAAGCGCATACACCTCGT 59.899 45.455 11.47 0.00 0.00 4.18
1505 16255 5.531634 ACTCTTTACCATTTACGTCGTTCA 58.468 37.500 1.78 0.00 0.00 3.18
1570 16382 0.319211 AAACGCGACCTCATTGACGA 60.319 50.000 15.93 0.00 0.00 4.20
1609 16421 2.938428 AGGGCCCACCAAATTCATAA 57.062 45.000 27.56 0.00 43.89 1.90
1706 16529 3.444916 CGCCGAGGCACGATTATTATAT 58.555 45.455 15.03 0.00 45.77 0.86
1710 16533 4.142026 CCGAGGCACGATTATTATATGGGA 60.142 45.833 5.74 0.00 45.77 4.37
1712 16535 5.623596 CGAGGCACGATTATTATATGGGACA 60.624 44.000 0.00 0.00 45.05 4.02
1747 16581 4.105553 CAGCCTGCAGCCCAGCTA 62.106 66.667 13.83 0.00 45.47 3.32
1800 16824 3.370953 CCCACTAGTCTGCCTGCTATTTT 60.371 47.826 0.00 0.00 0.00 1.82
1811 16835 0.607762 TGCTATTTTGGCGCACTGGA 60.608 50.000 10.83 0.00 0.00 3.86
1814 16838 0.604243 TATTTTGGCGCACTGGACGT 60.604 50.000 10.83 0.00 0.00 4.34
1819 16843 0.814410 TGGCGCACTGGACGTTTTTA 60.814 50.000 10.83 0.00 0.00 1.52
1820 16844 0.308376 GGCGCACTGGACGTTTTTAA 59.692 50.000 10.83 0.00 0.00 1.52
1916 17204 2.123982 GCCTAGCAGCCCAAGCAT 60.124 61.111 0.00 0.00 43.56 3.79
2150 19170 1.741770 CTTCTTCTCCCCCGTTGCG 60.742 63.158 0.00 0.00 0.00 4.85
2183 19221 2.564062 TGGAGTCGATTCGGTAGGTTTT 59.436 45.455 6.18 0.00 0.00 2.43
2218 19257 0.814010 AACTGGCTCGCGTTCTGTTT 60.814 50.000 5.77 0.00 0.00 2.83
2248 19289 3.064207 TCCGAGTGTTCATTTTTCTCCG 58.936 45.455 0.00 0.00 0.00 4.63
2303 19354 2.361230 CCTTCCAAGGGGTTCCGC 60.361 66.667 0.00 0.00 42.66 5.54
2339 19391 2.011046 GCTGAGAGGAACCATGCTCAC 61.011 57.143 0.26 0.00 45.74 3.51
2382 19434 1.000739 AATGGATGCAGTGGGGTGG 59.999 57.895 0.00 0.00 0.00 4.61
2413 19468 3.818210 TGCCTTTTAATGTCTGAAAGCGA 59.182 39.130 0.00 0.00 0.00 4.93
2433 19488 4.043750 CGACAATGTTCTTTGTGCACAAT 58.956 39.130 31.48 14.33 39.85 2.71
2434 19489 4.503734 CGACAATGTTCTTTGTGCACAATT 59.496 37.500 31.48 18.99 39.85 2.32
2438 19494 6.539464 ACAATGTTCTTTGTGCACAATTGAAT 59.461 30.769 32.33 22.20 38.37 2.57
2464 19525 4.533222 CACACCGTTCAGTTTTATGGTTC 58.467 43.478 0.00 0.00 31.31 3.62
2566 19975 5.512788 CCTATGCGCTTTATGTTTTGTTCAG 59.487 40.000 9.73 0.00 0.00 3.02
2700 20141 5.466819 AGAATGCATTTGATGTCAGTTGTG 58.533 37.500 14.33 0.00 0.00 3.33
2820 20261 4.014847 TCGAGACACAAGCTTTGTTTTG 57.985 40.909 13.21 11.81 43.23 2.44
2821 20262 3.687212 TCGAGACACAAGCTTTGTTTTGA 59.313 39.130 13.21 13.34 43.23 2.69
2825 20266 4.943705 AGACACAAGCTTTGTTTTGAGAGA 59.056 37.500 13.21 0.00 43.23 3.10
2834 20275 5.634859 GCTTTGTTTTGAGAGAGAGAGAGAG 59.365 44.000 0.00 0.00 0.00 3.20
2836 20277 6.573664 TTGTTTTGAGAGAGAGAGAGAGAG 57.426 41.667 0.00 0.00 0.00 3.20
2995 20542 1.344438 TGTAGGTCTGTGCTGGACTTG 59.656 52.381 0.00 0.00 34.47 3.16
3036 20583 8.893727 AGGATGTTACACTTTACTATCATTTGC 58.106 33.333 0.00 0.00 0.00 3.68
3041 20588 8.726988 GTTACACTTTACTATCATTTGCAAGGA 58.273 33.333 0.00 1.98 0.00 3.36
3095 20643 5.294552 GCCATACTACTTCTTTTGCGAGAAT 59.705 40.000 0.00 0.00 35.27 2.40
3161 20731 4.262164 GGCAAACAATGACAGAATGAAGGT 60.262 41.667 0.00 0.00 39.69 3.50
3295 21122 1.617322 TATATCGGGAAGCTCGCACT 58.383 50.000 0.00 0.00 0.00 4.40
3300 21230 1.961394 TCGGGAAGCTCGCACTATTAT 59.039 47.619 0.00 0.00 0.00 1.28
3310 21240 6.915349 AGCTCGCACTATTATAAGTCTTAGG 58.085 40.000 0.00 0.00 0.00 2.69
3348 21282 3.634448 TGGGCTTCGAAAAAGACAAATCA 59.366 39.130 0.00 0.00 0.00 2.57
3432 21366 4.318332 CATCCTTGACAGAGCACAGTTAA 58.682 43.478 0.00 0.00 0.00 2.01
3445 21379 8.239314 CAGAGCACAGTTAATCATTTGTTACAT 58.761 33.333 0.00 0.00 0.00 2.29
3475 21409 6.751514 TCTTCTTCTTGTTGTTGCTGTAAA 57.248 33.333 0.00 0.00 0.00 2.01
3513 21455 7.977789 TGTAAGTTCTTTGCATTCTCATGTA 57.022 32.000 0.00 0.00 32.28 2.29
3658 21604 7.854916 GTCTTCAGCTTCATGCATTAAATAGAC 59.145 37.037 0.00 1.27 45.94 2.59
3790 22192 6.760298 TCACAATGCATCAAGTTGCTTTAAAA 59.240 30.769 0.00 0.00 43.18 1.52
3872 22281 1.562008 TCAGTGTGGGTCAGGACAAAA 59.438 47.619 1.41 0.00 0.00 2.44
3873 22282 2.025793 TCAGTGTGGGTCAGGACAAAAA 60.026 45.455 1.41 0.00 0.00 1.94
3874 22283 2.358898 CAGTGTGGGTCAGGACAAAAAG 59.641 50.000 1.41 0.00 0.00 2.27
3875 22284 1.067060 GTGTGGGTCAGGACAAAAAGC 59.933 52.381 1.41 0.00 0.00 3.51
3876 22285 1.341482 TGTGGGTCAGGACAAAAAGCA 60.341 47.619 1.41 0.00 0.00 3.91
3993 22403 0.321653 AGAGGACAACGGGACATTGC 60.322 55.000 0.00 0.00 33.38 3.56
4226 22705 3.736252 CGACTTCCAAATATGTAGAGGCG 59.264 47.826 0.00 0.00 0.00 5.52
4239 22718 2.891191 AGAGGCGGGGTTGATTTAAA 57.109 45.000 0.00 0.00 0.00 1.52
4254 22733 7.698130 GGTTGATTTAAACTCATCTGATTTCGG 59.302 37.037 0.00 0.00 0.00 4.30
4256 22735 5.560966 TTTAAACTCATCTGATTTCGGGC 57.439 39.130 0.00 0.00 0.00 6.13
4266 22745 3.000727 CTGATTTCGGGCGAGTTACTTT 58.999 45.455 0.00 0.00 0.00 2.66
4309 22788 5.438761 AATACAGCCTGTCTTGTTGTTTC 57.561 39.130 0.00 0.00 0.00 2.78
4472 22962 6.059484 CCAGTAACCCTAAGTTTCAACAAGA 58.941 40.000 0.00 0.00 40.05 3.02
4473 22963 6.544564 CCAGTAACCCTAAGTTTCAACAAGAA 59.455 38.462 0.00 0.00 40.05 2.52
4483 22973 4.966965 TTTCAACAAGAAACACGGCTAA 57.033 36.364 0.00 0.00 41.17 3.09
4485 22975 5.508200 TTCAACAAGAAACACGGCTAATT 57.492 34.783 0.00 0.00 32.05 1.40
4518 23020 6.150641 CCAATGAATGATATCTCCCACATGAC 59.849 42.308 0.00 0.00 0.00 3.06
4531 23641 6.998074 TCTCCCACATGACATTTTCCATATAC 59.002 38.462 0.00 0.00 0.00 1.47
4532 23642 6.910191 TCCCACATGACATTTTCCATATACT 58.090 36.000 0.00 0.00 0.00 2.12
4927 24145 6.217487 TGAATTCTCAGGGGAAAAGAGGATAA 59.783 38.462 7.05 0.00 27.68 1.75
4928 24146 6.658555 ATTCTCAGGGGAAAAGAGGATAAA 57.341 37.500 0.00 0.00 0.00 1.40
4929 24147 6.463053 TTCTCAGGGGAAAAGAGGATAAAA 57.537 37.500 0.00 0.00 0.00 1.52
4930 24148 6.463053 TCTCAGGGGAAAAGAGGATAAAAA 57.537 37.500 0.00 0.00 0.00 1.94
5030 24250 4.647853 ACTCAGTAGTGAACACTGGTACAA 59.352 41.667 16.37 0.00 42.98 2.41
5243 24840 3.612423 GGTGTGTTTTCTGTGTGCTTTTC 59.388 43.478 0.00 0.00 0.00 2.29
5284 24881 6.829229 TGAATATGGCATTCATCTCCATTC 57.171 37.500 4.78 6.84 40.71 2.67
5340 24937 3.075884 CGAACCCGGTAAATTTTCTCCA 58.924 45.455 0.00 0.00 0.00 3.86
5455 25091 2.703536 TCTAACACCTGGCAAGAGACAA 59.296 45.455 0.00 0.00 27.50 3.18
5509 25145 3.439129 GGCTAGTGGGTTGTTGTATGTTC 59.561 47.826 0.00 0.00 0.00 3.18
5538 25177 2.233271 CCTGAAGACATGCAACAACCT 58.767 47.619 0.00 0.00 0.00 3.50
5591 25238 3.374764 TGTCCAGCAGATGTATGTAGGT 58.625 45.455 0.00 0.00 0.00 3.08
5641 25288 2.022934 TCAGCAGCATGTGTTGTGAAA 58.977 42.857 0.00 0.00 38.48 2.69
5662 25309 8.116136 GTGAAAAATTTGTTGCCTTAAGTCTTG 58.884 33.333 0.97 0.00 0.00 3.02
5717 25364 3.859411 TTAAAAATAACCTGCCCTGCG 57.141 42.857 0.00 0.00 0.00 5.18
5958 25609 5.806654 TTCCTTTTCCTTTCCCTGATTTG 57.193 39.130 0.00 0.00 0.00 2.32
6021 25672 7.901029 ACCATAGACAGAACTGGATATACATG 58.099 38.462 6.76 0.00 32.92 3.21
6250 25901 2.430921 GTCCCTGTGACGTGAGCG 60.431 66.667 0.00 0.00 44.93 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.840005 GGCTAGACTGGCGGCACC 62.840 72.222 7.97 2.26 39.84 5.01
7 8 4.840005 GGGCTAGACTGGCGGCAC 62.840 72.222 7.97 0.00 0.00 5.01
9 10 4.840005 GTGGGCTAGACTGGCGGC 62.840 72.222 0.00 0.00 0.00 6.53
10 11 4.162690 GGTGGGCTAGACTGGCGG 62.163 72.222 4.57 0.00 0.00 6.13
11 12 2.463589 TTTGGTGGGCTAGACTGGCG 62.464 60.000 4.57 0.00 0.00 5.69
12 13 0.034089 ATTTGGTGGGCTAGACTGGC 60.034 55.000 1.43 1.43 0.00 4.85
13 14 2.290896 TGAATTTGGTGGGCTAGACTGG 60.291 50.000 0.00 0.00 0.00 4.00
14 15 3.071874 TGAATTTGGTGGGCTAGACTG 57.928 47.619 0.00 0.00 0.00 3.51
16 17 5.036117 TCTATGAATTTGGTGGGCTAGAC 57.964 43.478 0.00 0.00 0.00 2.59
17 18 4.103153 CCTCTATGAATTTGGTGGGCTAGA 59.897 45.833 0.00 0.00 0.00 2.43
18 19 4.392940 CCTCTATGAATTTGGTGGGCTAG 58.607 47.826 0.00 0.00 0.00 3.42
19 20 3.138283 CCCTCTATGAATTTGGTGGGCTA 59.862 47.826 0.00 0.00 0.00 3.93
20 21 2.091665 CCCTCTATGAATTTGGTGGGCT 60.092 50.000 0.00 0.00 0.00 5.19
21 22 2.310538 CCCTCTATGAATTTGGTGGGC 58.689 52.381 0.00 0.00 0.00 5.36
22 23 3.053693 TGACCCTCTATGAATTTGGTGGG 60.054 47.826 0.00 0.00 38.16 4.61
23 24 4.235079 TGACCCTCTATGAATTTGGTGG 57.765 45.455 0.00 0.00 0.00 4.61
24 25 4.096984 GCTTGACCCTCTATGAATTTGGTG 59.903 45.833 0.00 0.00 0.00 4.17
25 26 4.273318 GCTTGACCCTCTATGAATTTGGT 58.727 43.478 0.00 0.00 0.00 3.67
26 27 3.313526 CGCTTGACCCTCTATGAATTTGG 59.686 47.826 0.00 0.00 0.00 3.28
27 28 4.191544 TCGCTTGACCCTCTATGAATTTG 58.808 43.478 0.00 0.00 0.00 2.32
28 29 4.080863 ACTCGCTTGACCCTCTATGAATTT 60.081 41.667 0.00 0.00 0.00 1.82
29 30 3.452627 ACTCGCTTGACCCTCTATGAATT 59.547 43.478 0.00 0.00 0.00 2.17
32 33 2.145397 ACTCGCTTGACCCTCTATGA 57.855 50.000 0.00 0.00 0.00 2.15
33 34 2.428890 AGAACTCGCTTGACCCTCTATG 59.571 50.000 0.00 0.00 0.00 2.23
34 35 2.428890 CAGAACTCGCTTGACCCTCTAT 59.571 50.000 0.00 0.00 0.00 1.98
35 36 1.819288 CAGAACTCGCTTGACCCTCTA 59.181 52.381 0.00 0.00 0.00 2.43
36 37 0.605589 CAGAACTCGCTTGACCCTCT 59.394 55.000 0.00 0.00 0.00 3.69
37 38 0.603569 TCAGAACTCGCTTGACCCTC 59.396 55.000 0.00 0.00 0.00 4.30
39 40 0.318762 ACTCAGAACTCGCTTGACCC 59.681 55.000 0.00 0.00 0.00 4.46
40 41 1.795286 CAACTCAGAACTCGCTTGACC 59.205 52.381 0.00 0.00 0.00 4.02
41 42 2.473235 GTCAACTCAGAACTCGCTTGAC 59.527 50.000 0.00 0.00 33.00 3.18
42 43 2.362397 AGTCAACTCAGAACTCGCTTGA 59.638 45.455 0.00 0.00 0.00 3.02
43 44 2.728839 GAGTCAACTCAGAACTCGCTTG 59.271 50.000 5.28 0.00 42.42 4.01
44 45 2.288518 GGAGTCAACTCAGAACTCGCTT 60.289 50.000 11.99 0.00 44.60 4.68
45 46 1.271102 GGAGTCAACTCAGAACTCGCT 59.729 52.381 11.99 0.00 44.60 4.93
46 47 1.670380 GGGAGTCAACTCAGAACTCGC 60.670 57.143 11.99 3.54 44.60 5.03
48 49 4.525100 AGTTAGGGAGTCAACTCAGAACTC 59.475 45.833 11.99 0.00 44.60 3.01
49 50 4.484912 AGTTAGGGAGTCAACTCAGAACT 58.515 43.478 11.99 12.88 44.60 3.01
50 51 4.811908 GAGTTAGGGAGTCAACTCAGAAC 58.188 47.826 14.05 11.18 46.45 3.01
55 56 1.819903 AGCGAGTTAGGGAGTCAACTC 59.180 52.381 10.42 10.42 44.66 3.01
56 57 1.926108 AGCGAGTTAGGGAGTCAACT 58.074 50.000 0.00 0.00 37.69 3.16
57 58 2.745515 AAGCGAGTTAGGGAGTCAAC 57.254 50.000 0.00 0.00 0.00 3.18
60 61 2.231721 AGTGAAAGCGAGTTAGGGAGTC 59.768 50.000 0.00 0.00 0.00 3.36
61 62 2.249139 AGTGAAAGCGAGTTAGGGAGT 58.751 47.619 0.00 0.00 0.00 3.85
62 63 3.254892 GAAGTGAAAGCGAGTTAGGGAG 58.745 50.000 0.00 0.00 0.00 4.30
64 65 2.347731 GGAAGTGAAAGCGAGTTAGGG 58.652 52.381 0.00 0.00 0.00 3.53
65 66 2.028020 AGGGAAGTGAAAGCGAGTTAGG 60.028 50.000 0.00 0.00 0.00 2.69
66 67 3.320673 AGGGAAGTGAAAGCGAGTTAG 57.679 47.619 0.00 0.00 0.00 2.34
67 68 3.660865 GAAGGGAAGTGAAAGCGAGTTA 58.339 45.455 0.00 0.00 0.00 2.24
68 69 2.495084 GAAGGGAAGTGAAAGCGAGTT 58.505 47.619 0.00 0.00 0.00 3.01
69 70 1.605712 CGAAGGGAAGTGAAAGCGAGT 60.606 52.381 0.00 0.00 0.00 4.18
70 71 1.071605 CGAAGGGAAGTGAAAGCGAG 58.928 55.000 0.00 0.00 0.00 5.03
71 72 3.210857 CGAAGGGAAGTGAAAGCGA 57.789 52.632 0.00 0.00 0.00 4.93
85 86 2.269241 GGGTGGAGAAGGCCGAAG 59.731 66.667 0.00 0.00 0.00 3.79
86 87 3.327404 GGGGTGGAGAAGGCCGAA 61.327 66.667 0.00 0.00 0.00 4.30
89 90 4.048470 GTGGGGGTGGAGAAGGCC 62.048 72.222 0.00 0.00 0.00 5.19
90 91 2.081585 AAAGTGGGGGTGGAGAAGGC 62.082 60.000 0.00 0.00 0.00 4.35
92 93 1.144913 TCAAAAGTGGGGGTGGAGAAG 59.855 52.381 0.00 0.00 0.00 2.85
93 94 1.144913 CTCAAAAGTGGGGGTGGAGAA 59.855 52.381 0.00 0.00 0.00 2.87
94 95 0.771127 CTCAAAAGTGGGGGTGGAGA 59.229 55.000 0.00 0.00 0.00 3.71
105 106 2.838736 AGCACGATGACACTCAAAAGT 58.161 42.857 0.00 0.00 35.60 2.66
107 108 3.243035 CCAAAGCACGATGACACTCAAAA 60.243 43.478 0.00 0.00 0.00 2.44
108 109 2.290367 CCAAAGCACGATGACACTCAAA 59.710 45.455 0.00 0.00 0.00 2.69
109 110 1.872952 CCAAAGCACGATGACACTCAA 59.127 47.619 0.00 0.00 0.00 3.02
111 112 1.728971 CTCCAAAGCACGATGACACTC 59.271 52.381 0.00 0.00 0.00 3.51
113 114 1.195448 CACTCCAAAGCACGATGACAC 59.805 52.381 0.00 0.00 0.00 3.67
114 115 1.069978 TCACTCCAAAGCACGATGACA 59.930 47.619 0.00 0.00 0.00 3.58
121 1523 1.815003 CCATCCTTCACTCCAAAGCAC 59.185 52.381 0.00 0.00 0.00 4.40
129 1531 1.340405 ACACATGGCCATCCTTCACTC 60.340 52.381 17.61 0.00 0.00 3.51
181 1584 2.637165 ACCAGAGAGGAATTTCCCAGT 58.363 47.619 11.92 0.00 41.22 4.00
272 1678 0.251608 CCTGAAAACGGATTGGGGGT 60.252 55.000 0.00 0.00 0.00 4.95
277 1683 1.336795 GGTTGGCCTGAAAACGGATTG 60.337 52.381 3.32 0.00 0.00 2.67
283 1689 0.031585 GGTTCGGTTGGCCTGAAAAC 59.968 55.000 3.32 0.00 32.31 2.43
284 1690 1.110518 GGGTTCGGTTGGCCTGAAAA 61.111 55.000 3.32 0.00 32.31 2.29
382 1790 2.320781 CGAAGTATCCTGACCATCCCT 58.679 52.381 0.00 0.00 0.00 4.20
390 1799 2.219458 CGAGCTACCGAAGTATCCTGA 58.781 52.381 0.00 0.00 0.00 3.86
490 1902 6.078456 TCATTTGGATACCTCACAGGAAAT 57.922 37.500 0.00 0.00 37.67 2.17
543 1958 5.819379 ACATCAACATGCTAGATTGTACCAG 59.181 40.000 0.00 0.00 32.57 4.00
584 2001 6.047870 CAACATTTTGAGAACATGGGAACAA 58.952 36.000 0.00 0.00 38.44 2.83
617 2034 5.054477 CCAAGAGTAACGAAGGAACTCAAA 58.946 41.667 4.69 0.00 41.69 2.69
618 2035 4.502604 CCCAAGAGTAACGAAGGAACTCAA 60.503 45.833 4.69 0.00 41.69 3.02
693 2113 3.651562 AGTTTGAACAGAACACGTTCG 57.348 42.857 4.35 2.95 44.63 3.95
895 8834 2.985847 GCGGCAGAGGGTTTGCTT 60.986 61.111 0.00 0.00 41.27 3.91
1134 15819 1.600916 GCTCCTTCGTGGCAGGTTT 60.601 57.895 7.12 0.00 35.26 3.27
1279 15974 5.222631 AGCAAAAATCTCAACATTCGGAAC 58.777 37.500 0.00 0.00 0.00 3.62
1375 16085 4.255510 ACAGCTTTCATCCCCATTGTAT 57.744 40.909 0.00 0.00 0.00 2.29
1457 16193 1.447838 CCAACGAGGTGTATGCGCT 60.448 57.895 9.73 0.00 0.00 5.92
1472 16215 6.969993 AAATGGTAAAGAGTAAAGTGCCAA 57.030 33.333 0.00 0.00 0.00 4.52
1609 16421 4.225497 GCTATGCGCTTGACCCTT 57.775 55.556 9.73 0.00 35.14 3.95
1800 16824 0.814410 TAAAAACGTCCAGTGCGCCA 60.814 50.000 4.18 0.00 0.00 5.69
1814 16838 9.713713 GCCCAACAGGTAAAAATAGATTAAAAA 57.286 29.630 0.00 0.00 38.26 1.94
1819 16843 5.337788 TGGCCCAACAGGTAAAAATAGATT 58.662 37.500 0.00 0.00 38.26 2.40
1820 16844 4.941713 TGGCCCAACAGGTAAAAATAGAT 58.058 39.130 0.00 0.00 38.26 1.98
2150 19170 3.941657 GACTCCACGCCAGTCCAGC 62.942 68.421 0.00 0.00 35.19 4.85
2224 19263 5.393962 GGAGAAAAATGAACACTCGGATTG 58.606 41.667 0.00 0.00 0.00 2.67
2248 19289 0.718220 CGCAAGAAACTGAACGCGTC 60.718 55.000 14.44 7.01 43.02 5.19
2280 19326 1.068352 AACCCCTTGGAAGGTCAGCT 61.068 55.000 4.72 0.00 44.98 4.24
2319 19371 0.251354 TGAGCATGGTTCCTCTCAGC 59.749 55.000 0.00 0.00 32.43 4.26
2322 19374 0.460987 CGGTGAGCATGGTTCCTCTC 60.461 60.000 14.81 4.26 0.00 3.20
2323 19375 1.194781 ACGGTGAGCATGGTTCCTCT 61.195 55.000 14.81 0.00 0.00 3.69
2339 19391 2.027625 GCAGGTTCGGACTTGACGG 61.028 63.158 10.68 0.00 35.02 4.79
2382 19434 6.928492 TCAGACATTAAAAGGCAAAATTGACC 59.072 34.615 0.00 0.00 36.67 4.02
2413 19468 5.417811 TCAATTGTGCACAAAGAACATTGT 58.582 33.333 34.06 13.22 44.08 2.71
2433 19488 1.872952 CTGAACGGTGTGCTCATTCAA 59.127 47.619 5.19 0.00 0.00 2.69
2434 19489 1.202639 ACTGAACGGTGTGCTCATTCA 60.203 47.619 3.93 3.93 0.00 2.57
2438 19494 1.745232 AAAACTGAACGGTGTGCTCA 58.255 45.000 0.00 0.00 0.00 4.26
2464 19525 3.324556 TGGAAAAGGCAAAATTGGAGGAG 59.675 43.478 0.00 0.00 0.00 3.69
2566 19975 7.824672 ACATCTGAATTCTGAAGGATCAAAAC 58.175 34.615 17.62 0.00 34.49 2.43
2700 20141 1.442857 CGGCTGACAGACACTCGTC 60.443 63.158 9.48 0.00 42.95 4.20
2820 20261 6.410540 ACTCTTTTCTCTCTCTCTCTCTCTC 58.589 44.000 0.00 0.00 0.00 3.20
2821 20262 6.380079 ACTCTTTTCTCTCTCTCTCTCTCT 57.620 41.667 0.00 0.00 0.00 3.10
2825 20266 5.123344 GCGTTACTCTTTTCTCTCTCTCTCT 59.877 44.000 0.00 0.00 0.00 3.10
2834 20275 5.774878 ATTTACCGCGTTACTCTTTTCTC 57.225 39.130 4.92 0.00 0.00 2.87
2836 20277 5.682869 ACAATTTACCGCGTTACTCTTTTC 58.317 37.500 4.92 0.00 0.00 2.29
2995 20542 2.028930 ACATCCTGAGTGACTCGAAACC 60.029 50.000 8.23 0.00 32.35 3.27
3036 20583 3.904136 AAAAGAAGCGACATGTCCTTG 57.096 42.857 25.07 12.83 0.00 3.61
3095 20643 9.430399 AGGTCTAGTAAAGTTATATGCCACTTA 57.570 33.333 0.00 0.00 32.74 2.24
3161 20731 3.254657 CGGAAACATAAGAACCAAAGCCA 59.745 43.478 0.00 0.00 0.00 4.75
3287 21114 5.573669 GCCTAAGACTTATAATAGTGCGAGC 59.426 44.000 0.00 0.00 0.00 5.03
3300 21230 9.953565 ATGTGTATTTAGTTTGCCTAAGACTTA 57.046 29.630 0.00 0.00 36.98 2.24
3310 21240 4.718940 AGCCCATGTGTATTTAGTTTGC 57.281 40.909 0.00 0.00 0.00 3.68
3348 21282 2.233922 CCTGAGGTGACGTGGAAGTATT 59.766 50.000 0.00 0.00 0.00 1.89
3407 21341 0.615331 GTGCTCTGTCAAGGATGGGA 59.385 55.000 0.00 0.00 0.00 4.37
3445 21379 9.897744 CAGCAACAACAAGAAGAAGATAAAATA 57.102 29.630 0.00 0.00 0.00 1.40
3447 21381 7.771183 ACAGCAACAACAAGAAGAAGATAAAA 58.229 30.769 0.00 0.00 0.00 1.52
3513 21455 3.087031 TCCTCGATTTCCGACTTACTGT 58.913 45.455 0.00 0.00 43.23 3.55
3587 21529 9.975218 AAAAGCCTTATTAGAGAAGTATTTGGA 57.025 29.630 0.00 0.00 0.00 3.53
3712 22109 5.378230 AAAGAATGGCCTATCTGACATCA 57.622 39.130 3.32 0.00 0.00 3.07
3872 22281 8.820831 AGATAGCAACTAATATGTAGGATGCTT 58.179 33.333 19.69 13.44 40.14 3.91
3873 22282 8.256605 CAGATAGCAACTAATATGTAGGATGCT 58.743 37.037 19.10 19.10 41.42 3.79
3874 22283 7.010923 GCAGATAGCAACTAATATGTAGGATGC 59.989 40.741 12.06 12.06 44.79 3.91
3875 22284 8.417780 GCAGATAGCAACTAATATGTAGGATG 57.582 38.462 0.00 0.00 44.79 3.51
3984 22394 4.881273 TCAACATGTACTATGCAATGTCCC 59.119 41.667 0.00 0.00 0.00 4.46
4023 22433 5.753744 TGTTTTTATTGACGCGATGAAACT 58.246 33.333 15.93 0.00 0.00 2.66
4214 22686 2.097110 TCAACCCCGCCTCTACATAT 57.903 50.000 0.00 0.00 0.00 1.78
4226 22705 7.410120 AATCAGATGAGTTTAAATCAACCCC 57.590 36.000 0.00 0.00 0.00 4.95
4239 22718 0.824109 TCGCCCGAAATCAGATGAGT 59.176 50.000 0.00 0.00 0.00 3.41
4254 22733 6.178239 ACAATATGAACAAAGTAACTCGCC 57.822 37.500 0.00 0.00 0.00 5.54
4309 22788 4.836125 ATTTCCTTATTACCATGCAGCG 57.164 40.909 0.00 0.00 0.00 5.18
4438 22924 5.015603 ACTTAGGGTTACTGGTAGTAGGTCA 59.984 44.000 0.00 0.00 31.47 4.02
4439 22925 5.514169 ACTTAGGGTTACTGGTAGTAGGTC 58.486 45.833 0.00 0.00 31.47 3.85
4442 22929 7.472334 TGAAACTTAGGGTTACTGGTAGTAG 57.528 40.000 0.00 0.00 37.12 2.57
4590 23700 6.867519 TCAATATGGAGTGACAAACTAGGA 57.132 37.500 0.00 0.00 40.07 2.94
4928 24146 6.553100 TGTCCCATTCCATAAAGTCACTTTTT 59.447 34.615 8.41 0.00 35.21 1.94
4929 24147 6.074648 TGTCCCATTCCATAAAGTCACTTTT 58.925 36.000 8.41 0.00 35.21 2.27
4930 24148 5.640147 TGTCCCATTCCATAAAGTCACTTT 58.360 37.500 8.15 8.15 37.46 2.66
4961 24179 2.038557 TGACCTAAAAGACCACCTCAGC 59.961 50.000 0.00 0.00 0.00 4.26
5030 24250 2.874701 CACAAGTTTGCAGACTAGCTGT 59.125 45.455 10.74 8.73 46.62 4.40
5103 24323 1.474330 ATAGCAAAAAGAAGGGGCCG 58.526 50.000 0.00 0.00 0.00 6.13
5268 24865 3.209410 ACGAAGAATGGAGATGAATGCC 58.791 45.455 0.00 0.00 0.00 4.40
5284 24881 1.468520 CATGGCCACCTACAAACGAAG 59.531 52.381 8.16 0.00 0.00 3.79
5340 24937 3.451902 CCTCTCATGGCTCTTCTTCTCTT 59.548 47.826 0.00 0.00 0.00 2.85
5350 24947 1.347378 GAATCCCTCCTCTCATGGCTC 59.653 57.143 0.00 0.00 0.00 4.70
5455 25091 1.489649 CATCAGGTCTCCTTGGATGCT 59.510 52.381 4.12 0.00 30.82 3.79
5509 25145 2.419324 GCATGTCTTCAGGCTTGAGAAG 59.581 50.000 0.00 6.71 46.09 2.85
5538 25177 9.341078 TCATTATATGATAACTTGCAAGCTTCA 57.659 29.630 26.27 23.48 33.59 3.02
5591 25238 5.625921 TCAACGAAATGAATCAAGCATCA 57.374 34.783 0.00 0.00 0.00 3.07
5641 25288 6.098266 ACCTCAAGACTTAAGGCAACAAATTT 59.902 34.615 11.83 0.00 41.41 1.82
5662 25309 3.165875 TGCCTCAGGTAGCATATACCTC 58.834 50.000 3.58 0.00 45.55 3.85
5717 25364 3.717707 TGAATCTAGCATCGCCTAACAC 58.282 45.455 0.00 0.00 0.00 3.32
5875 25526 1.649171 CAACGAAGAACCGAGATGACG 59.351 52.381 0.00 0.00 0.00 4.35
5937 25588 3.578282 GCAAATCAGGGAAAGGAAAAGGA 59.422 43.478 0.00 0.00 0.00 3.36
6021 25672 2.817844 AGTTAACTTTCGGATGTTGCCC 59.182 45.455 1.12 0.00 0.00 5.36
6052 25703 5.183140 GGAACTGCATTACCTCAAAAAGCTA 59.817 40.000 0.00 0.00 0.00 3.32
6213 25864 0.954452 CCTGCAAAAGTGACCTGACC 59.046 55.000 0.00 0.00 0.00 4.02
6214 25865 0.954452 CCCTGCAAAAGTGACCTGAC 59.046 55.000 0.00 0.00 0.00 3.51
6250 25901 2.821366 CATGGACCAGTGCGAGGC 60.821 66.667 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.