Multiple sequence alignment - TraesCS3D01G436000

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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 TraesCS3D01G436000 chr3D 100.000 5677 0 0 1 5677 548241738 548247414 0.000000e+00 10484.0
1 TraesCS3D01G436000 chr3A 95.311 4308 143 29 653 4912 685115063 685119359 0.000000e+00 6782.0
2 TraesCS3D01G436000 chr3A 93.229 576 29 4 85 652 685114417 685114990 0.000000e+00 839.0
3 TraesCS3D01G436000 chr3A 86.221 733 52 26 4961 5677 685119361 685120060 0.000000e+00 749.0
4 TraesCS3D01G436000 chr3B 93.997 3848 148 34 414 4200 725702274 725706099 0.000000e+00 5749.0
5 TraesCS3D01G436000 chr3B 96.016 728 29 0 4185 4912 725706149 725706876 0.000000e+00 1184.0
6 TraesCS3D01G436000 chr3B 84.605 734 55 25 4961 5677 725706878 725707570 0.000000e+00 676.0
7 TraesCS3D01G436000 chr7B 96.380 442 15 1 3921 4361 603668317 603667876 0.000000e+00 726.0
8 TraesCS3D01G436000 chr7B 95.037 403 16 3 3199 3600 603669425 603669026 1.040000e-176 630.0
9 TraesCS3D01G436000 chr7B 97.153 281 5 2 3614 3892 603668590 603668311 6.660000e-129 472.0
10 TraesCS3D01G436000 chr7B 91.960 199 15 1 4422 4620 603667769 603667572 1.560000e-70 278.0
11 TraesCS3D01G436000 chr7B 96.875 32 1 0 4206 4237 603667845 603667814 3.000000e-03 54.7
12 TraesCS3D01G436000 chr6B 93.220 59 3 1 1 59 59145340 59145283 1.010000e-12 86.1
13 TraesCS3D01G436000 chr6A 94.545 55 2 1 1 55 256310431 256310378 3.640000e-12 84.2
14 TraesCS3D01G436000 chr6D 92.857 56 3 1 1 55 201799417 201799472 4.710000e-11 80.5
15 TraesCS3D01G436000 chr5A 90.476 63 3 3 1 62 593881273 593881213 4.710000e-11 80.5
16 TraesCS3D01G436000 chr2A 92.857 56 2 2 1 55 319067178 319067232 4.710000e-11 80.5
17 TraesCS3D01G436000 chr2A 90.000 60 4 2 1 58 552064979 552064920 6.100000e-10 76.8
18 TraesCS3D01G436000 chr2A 100.000 41 0 0 1 41 662859104 662859144 6.100000e-10 76.8
19 TraesCS3D01G436000 chr5D 91.379 58 4 1 1 58 290595260 290595204 1.700000e-10 78.7
20 TraesCS3D01G436000 chr5B 91.379 58 4 1 1 58 418150733 418150677 1.700000e-10 78.7


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 TraesCS3D01G436000 chr3D 548241738 548247414 5676 False 10484.000000 10484 100.000000 1 5677 1 chr3D.!!$F1 5676
1 TraesCS3D01G436000 chr3A 685114417 685120060 5643 False 2790.000000 6782 91.587000 85 5677 3 chr3A.!!$F1 5592
2 TraesCS3D01G436000 chr3B 725702274 725707570 5296 False 2536.333333 5749 91.539333 414 5677 3 chr3B.!!$F1 5263
3 TraesCS3D01G436000 chr7B 603667572 603669425 1853 True 432.140000 726 95.481000 3199 4620 5 chr7B.!!$R1 1421

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
29 30 0.396435 AAGGACATCTGCCGTGACAA 59.604 50.000 0.00 0.00 0.00 3.18 F
1162 1286 0.104304 CCCCTCTGTTATTCCGGTCG 59.896 60.000 0.00 0.00 0.00 4.79 F
1238 1362 1.202320 CACCGTACGGCGTTTGTTC 59.798 57.895 33.62 3.37 39.32 3.18 F
1688 1821 1.264288 GTGAGAACTTGGACGCCTTTG 59.736 52.381 0.00 0.00 0.00 2.77 F
3449 3588 0.472471 AGAAAAACCCGAGCCTCACA 59.528 50.000 0.00 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1652 0.322098 TGCACAGTCCCATAAACCCG 60.322 55.000 0.00 0.00 0.00 5.28 R
2516 2654 1.001378 AGGTTTGCACGCAGAACAATC 60.001 47.619 14.54 0.00 0.00 2.67 R
3024 3162 3.696051 TCAAATGTAGGCTCCTGAATTGC 59.304 43.478 0.00 0.00 0.00 3.56 R
3502 3641 5.922544 GGATCAAGTCAAACCAATTTCACTG 59.077 40.000 0.00 0.00 0.00 3.66 R
5189 5888 0.315251 TGACTGCAGTCTTCTGGTCG 59.685 55.000 38.81 4.01 44.99 4.79 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
21 22 2.497675 TCCTGACACTAAGGACATCTGC 59.502 50.000 0.00 0.00 38.96 4.26
22 23 2.419297 CCTGACACTAAGGACATCTGCC 60.419 54.545 0.00 0.00 36.91 4.85
23 24 1.204704 TGACACTAAGGACATCTGCCG 59.795 52.381 0.00 0.00 0.00 5.69
24 25 1.204941 GACACTAAGGACATCTGCCGT 59.795 52.381 0.00 0.00 0.00 5.68
25 26 1.066858 ACACTAAGGACATCTGCCGTG 60.067 52.381 0.00 0.00 0.00 4.94
26 27 1.204704 CACTAAGGACATCTGCCGTGA 59.795 52.381 0.00 0.00 0.00 4.35
27 28 1.204941 ACTAAGGACATCTGCCGTGAC 59.795 52.381 0.00 0.00 0.00 3.67
28 29 1.204704 CTAAGGACATCTGCCGTGACA 59.795 52.381 0.00 0.00 0.00 3.58
29 30 0.396435 AAGGACATCTGCCGTGACAA 59.604 50.000 0.00 0.00 0.00 3.18
30 31 0.615331 AGGACATCTGCCGTGACAAT 59.385 50.000 0.00 0.00 0.00 2.71
31 32 1.003580 AGGACATCTGCCGTGACAATT 59.996 47.619 0.00 0.00 0.00 2.32
32 33 1.398390 GGACATCTGCCGTGACAATTC 59.602 52.381 0.00 0.00 0.00 2.17
33 34 1.398390 GACATCTGCCGTGACAATTCC 59.602 52.381 0.00 0.00 0.00 3.01
34 35 1.271325 ACATCTGCCGTGACAATTCCA 60.271 47.619 0.00 0.00 0.00 3.53
35 36 1.131126 CATCTGCCGTGACAATTCCAC 59.869 52.381 0.00 0.00 0.00 4.02
43 44 2.210116 GTGACAATTCCACGACAGTGT 58.790 47.619 0.00 0.00 46.56 3.55
44 45 2.612212 GTGACAATTCCACGACAGTGTT 59.388 45.455 0.00 0.00 46.56 3.32
45 46 2.869801 TGACAATTCCACGACAGTGTTC 59.130 45.455 0.00 0.00 46.56 3.18
46 47 3.131396 GACAATTCCACGACAGTGTTCT 58.869 45.455 0.00 0.00 46.56 3.01
47 48 4.202172 TGACAATTCCACGACAGTGTTCTA 60.202 41.667 0.00 0.00 46.56 2.10
48 49 4.699637 ACAATTCCACGACAGTGTTCTAA 58.300 39.130 0.00 0.00 46.56 2.10
49 50 5.120399 ACAATTCCACGACAGTGTTCTAAA 58.880 37.500 0.00 0.00 46.56 1.85
50 51 5.763204 ACAATTCCACGACAGTGTTCTAAAT 59.237 36.000 0.00 0.00 46.56 1.40
51 52 6.932400 ACAATTCCACGACAGTGTTCTAAATA 59.068 34.615 0.00 0.00 46.56 1.40
52 53 7.442969 ACAATTCCACGACAGTGTTCTAAATAA 59.557 33.333 0.00 0.00 46.56 1.40
53 54 7.972832 ATTCCACGACAGTGTTCTAAATAAA 57.027 32.000 0.00 0.00 46.56 1.40
54 55 7.789273 TTCCACGACAGTGTTCTAAATAAAA 57.211 32.000 0.00 0.00 46.56 1.52
55 56 7.972832 TCCACGACAGTGTTCTAAATAAAAT 57.027 32.000 0.00 0.00 46.56 1.82
56 57 9.491675 TTCCACGACAGTGTTCTAAATAAAATA 57.508 29.630 0.00 0.00 46.56 1.40
57 58 9.491675 TCCACGACAGTGTTCTAAATAAAATAA 57.508 29.630 0.00 0.00 46.56 1.40
79 80 9.553064 AATAAAAACTTTCAATATTGGTGTGCA 57.447 25.926 15.36 0.00 0.00 4.57
80 81 9.723601 ATAAAAACTTTCAATATTGGTGTGCAT 57.276 25.926 15.36 5.08 0.00 3.96
81 82 7.424227 AAAACTTTCAATATTGGTGTGCATG 57.576 32.000 15.36 0.00 0.00 4.06
82 83 5.981088 ACTTTCAATATTGGTGTGCATGA 57.019 34.783 15.36 0.00 0.00 3.07
83 84 5.957798 ACTTTCAATATTGGTGTGCATGAG 58.042 37.500 15.36 3.83 0.00 2.90
99 100 7.168637 GTGTGCATGAGCCATAAATAAAATGAG 59.831 37.037 0.00 0.00 41.13 2.90
107 108 7.290061 AGCCATAAATAAAATGAGCTCTACCA 58.710 34.615 16.19 0.00 30.13 3.25
161 162 2.485835 GCCCCGCACACATAATACCTAA 60.486 50.000 0.00 0.00 0.00 2.69
290 298 2.967887 AGGAATTTCTGGCAAACAAGCT 59.032 40.909 0.00 0.00 34.17 3.74
337 345 7.533900 CACCAAGAGTTTTTATATTGTCACACG 59.466 37.037 0.00 0.00 0.00 4.49
340 348 7.045725 AGAGTTTTTATATTGTCACACGTCG 57.954 36.000 0.00 0.00 0.00 5.12
362 370 0.846401 CGTATTGCGTCATCAGTCGG 59.154 55.000 0.00 0.00 35.54 4.79
363 371 0.577269 GTATTGCGTCATCAGTCGGC 59.423 55.000 0.00 0.00 0.00 5.54
371 379 2.202932 ATCAGTCGGCGACCATGC 60.203 61.111 34.04 11.50 32.18 4.06
394 402 3.140143 ACTAGGAGGGAGGAGGAACATA 58.860 50.000 0.00 0.00 0.00 2.29
407 415 4.290942 GAGGAACATAGGAGGAAGGAGAA 58.709 47.826 0.00 0.00 0.00 2.87
438 449 3.321950 AGAAGGGGATACATGAAGAGGG 58.678 50.000 0.00 0.00 39.74 4.30
481 494 2.188818 AGGGGATGAAGGAAGAGGAG 57.811 55.000 0.00 0.00 0.00 3.69
560 573 4.574828 TGAATCGACTCGATGTCATCACTA 59.425 41.667 14.62 0.00 46.30 2.74
561 574 5.239525 TGAATCGACTCGATGTCATCACTAT 59.760 40.000 14.62 0.00 46.30 2.12
568 581 2.919859 CGATGTCATCACTATCGATGGC 59.080 50.000 8.54 0.00 46.14 4.40
606 619 3.708195 GCGGTAGCGTAGTGAAAGA 57.292 52.632 16.63 0.00 0.00 2.52
612 625 0.460284 AGCGTAGTGAAAGATGCGGG 60.460 55.000 0.00 0.00 32.65 6.13
675 760 3.810941 GGCATCGAAACGGGACAATATAA 59.189 43.478 0.00 0.00 0.00 0.98
713 798 7.555554 AGTGTGACTTGTAACTACGTATCCTAT 59.444 37.037 0.00 0.00 0.00 2.57
854 945 3.323979 GCCATAACTAATCGAGGGAAGGA 59.676 47.826 0.00 0.00 0.00 3.36
855 946 4.202326 GCCATAACTAATCGAGGGAAGGAA 60.202 45.833 0.00 0.00 0.00 3.36
856 947 5.542779 CCATAACTAATCGAGGGAAGGAAG 58.457 45.833 0.00 0.00 0.00 3.46
857 948 5.511545 CCATAACTAATCGAGGGAAGGAAGG 60.512 48.000 0.00 0.00 0.00 3.46
858 949 3.399952 ACTAATCGAGGGAAGGAAGGA 57.600 47.619 0.00 0.00 0.00 3.36
1116 1223 0.464870 AGCTCATCATGAAGCTCGCT 59.535 50.000 14.87 9.12 29.31 4.93
1162 1286 0.104304 CCCCTCTGTTATTCCGGTCG 59.896 60.000 0.00 0.00 0.00 4.79
1238 1362 1.202320 CACCGTACGGCGTTTGTTC 59.798 57.895 33.62 3.37 39.32 3.18
1302 1426 2.483876 CTGTTCTGAAGGAAAGCACGA 58.516 47.619 0.00 0.00 35.51 4.35
1460 1590 7.907841 TTCCTAATGTGGCTATCAAGTAGTA 57.092 36.000 0.00 0.00 32.72 1.82
1535 1668 2.106857 TGTTTCGGGTTTATGGGACTGT 59.893 45.455 0.00 0.00 0.00 3.55
1536 1669 2.483014 TTCGGGTTTATGGGACTGTG 57.517 50.000 0.00 0.00 0.00 3.66
1556 1689 6.968937 TGTGCAACTGAAAGCAAACTCTGC 62.969 45.833 0.00 0.00 45.37 4.26
1579 1712 1.466167 CCTGTTTCATGAAGAGCACGG 59.534 52.381 8.41 8.81 0.00 4.94
1688 1821 1.264288 GTGAGAACTTGGACGCCTTTG 59.736 52.381 0.00 0.00 0.00 2.77
1690 1823 2.103432 TGAGAACTTGGACGCCTTTGTA 59.897 45.455 0.00 0.00 0.00 2.41
1691 1824 2.737252 GAGAACTTGGACGCCTTTGTAG 59.263 50.000 0.00 0.00 0.00 2.74
2067 2201 7.726216 ACATATTATCTGACGATGAGGTTGAA 58.274 34.615 0.00 0.00 0.00 2.69
2152 2286 1.277273 TCCACTCACTCCAGAATGCAG 59.723 52.381 0.00 0.00 31.97 4.41
2193 2329 7.944729 ACTAGATTTCAGTGCCATTACATTT 57.055 32.000 0.00 0.00 0.00 2.32
2234 2370 6.262049 TGCAGTTAGATAGCAAACTTTTGTCA 59.738 34.615 3.74 0.00 40.24 3.58
2374 2512 5.562307 GCTGTTCTTATATTCTGGCTGCATG 60.562 44.000 0.50 0.00 0.00 4.06
2399 2537 6.917477 GCACTCACTGTTGTTTCATCAAATTA 59.083 34.615 0.00 0.00 0.00 1.40
2480 2618 4.426704 ACCTTTTCCTCTCTTAGTAGCCA 58.573 43.478 0.00 0.00 0.00 4.75
2715 2853 6.310941 TCCACCACTCATTTATTTTCCTTCA 58.689 36.000 0.00 0.00 0.00 3.02
2919 3057 4.335594 ACTTGAGGTTTGTGCTGTTCTTAC 59.664 41.667 0.00 0.00 0.00 2.34
3024 3162 3.424697 GCGCAATTTAATTGGCAAGGTTG 60.425 43.478 17.89 7.18 40.57 3.77
3305 3443 1.000506 GTTCTGGTTAGTGCTGGACGA 59.999 52.381 0.00 0.00 0.00 4.20
3449 3588 0.472471 AGAAAAACCCGAGCCTCACA 59.528 50.000 0.00 0.00 0.00 3.58
3763 4324 2.500098 TGTGTATGACCTAACCAGGAGC 59.500 50.000 0.00 0.00 45.91 4.70
4350 4980 4.730949 AATTTTGAGGTGATGGATGCTG 57.269 40.909 0.00 0.00 0.00 4.41
4678 5373 3.403038 TGAAAGCCAGACAAAGCTAGTC 58.597 45.455 10.41 10.41 38.74 2.59
4685 5380 3.993081 CCAGACAAAGCTAGTCAACTCAG 59.007 47.826 18.22 4.40 38.46 3.35
4728 5423 4.127171 TGTAAACTCTTGACCAGCTGTTC 58.873 43.478 13.81 8.93 0.00 3.18
4781 5476 3.005554 GTGCTGACATGCTGACACTAAT 58.994 45.455 0.00 0.00 0.00 1.73
4784 5479 4.083164 TGCTGACATGCTGACACTAATTTG 60.083 41.667 0.00 0.00 0.00 2.32
4789 5484 6.039159 TGACATGCTGACACTAATTTGTTTCA 59.961 34.615 8.29 8.29 0.00 2.69
4790 5485 6.985117 ACATGCTGACACTAATTTGTTTCAT 58.015 32.000 8.89 0.26 0.00 2.57
4793 5488 7.928908 TGCTGACACTAATTTGTTTCATTTC 57.071 32.000 8.89 3.89 0.00 2.17
4841 5537 1.000496 GCGGAATAGTTCTCCTACGGG 60.000 57.143 0.00 0.00 0.00 5.28
4873 5569 2.324330 CGCGGCTGTGATTTGGTCA 61.324 57.895 0.00 0.00 0.00 4.02
4912 5608 8.951787 ATTATGTAGTATTTTAAGTGCGGTGA 57.048 30.769 0.00 0.00 0.00 4.02
4913 5609 8.774890 TTATGTAGTATTTTAAGTGCGGTGAA 57.225 30.769 0.00 0.00 0.00 3.18
4915 5611 6.457355 TGTAGTATTTTAAGTGCGGTGAAGA 58.543 36.000 0.00 0.00 0.00 2.87
4917 5613 7.604927 TGTAGTATTTTAAGTGCGGTGAAGAAT 59.395 33.333 0.00 0.00 0.00 2.40
4918 5614 7.448748 AGTATTTTAAGTGCGGTGAAGAATT 57.551 32.000 0.00 0.00 0.00 2.17
4919 5615 8.556213 AGTATTTTAAGTGCGGTGAAGAATTA 57.444 30.769 0.00 0.00 0.00 1.40
4920 5616 9.174166 AGTATTTTAAGTGCGGTGAAGAATTAT 57.826 29.630 0.00 0.00 0.00 1.28
4921 5617 9.783256 GTATTTTAAGTGCGGTGAAGAATTATT 57.217 29.630 0.00 0.00 0.00 1.40
4923 5619 9.705290 ATTTTAAGTGCGGTGAAGAATTATTTT 57.295 25.926 0.00 0.00 0.00 1.82
4924 5620 9.535878 TTTTAAGTGCGGTGAAGAATTATTTTT 57.464 25.926 0.00 0.00 0.00 1.94
4925 5621 8.514136 TTAAGTGCGGTGAAGAATTATTTTTG 57.486 30.769 0.00 0.00 0.00 2.44
4926 5622 4.923281 AGTGCGGTGAAGAATTATTTTTGC 59.077 37.500 0.00 0.00 0.00 3.68
4927 5623 3.917380 TGCGGTGAAGAATTATTTTTGCG 59.083 39.130 0.00 0.00 0.00 4.85
4928 5624 3.917985 GCGGTGAAGAATTATTTTTGCGT 59.082 39.130 0.00 0.00 0.00 5.24
4929 5625 5.090083 GCGGTGAAGAATTATTTTTGCGTA 58.910 37.500 0.00 0.00 0.00 4.42
4930 5626 5.227184 GCGGTGAAGAATTATTTTTGCGTAG 59.773 40.000 0.00 0.00 0.00 3.51
4931 5627 6.539324 CGGTGAAGAATTATTTTTGCGTAGA 58.461 36.000 0.00 0.00 0.00 2.59
4932 5628 7.018826 CGGTGAAGAATTATTTTTGCGTAGAA 58.981 34.615 0.00 0.00 0.00 2.10
4933 5629 7.216317 CGGTGAAGAATTATTTTTGCGTAGAAG 59.784 37.037 0.00 0.00 0.00 2.85
4934 5630 8.021396 GGTGAAGAATTATTTTTGCGTAGAAGT 58.979 33.333 0.00 0.00 0.00 3.01
4935 5631 8.840867 GTGAAGAATTATTTTTGCGTAGAAGTG 58.159 33.333 0.00 0.00 0.00 3.16
4936 5632 8.564574 TGAAGAATTATTTTTGCGTAGAAGTGT 58.435 29.630 0.00 0.00 0.00 3.55
4937 5633 8.728088 AAGAATTATTTTTGCGTAGAAGTGTG 57.272 30.769 0.00 0.00 0.00 3.82
4938 5634 7.305474 AGAATTATTTTTGCGTAGAAGTGTGG 58.695 34.615 0.00 0.00 0.00 4.17
4939 5635 6.569179 ATTATTTTTGCGTAGAAGTGTGGT 57.431 33.333 0.00 0.00 0.00 4.16
4940 5636 3.684103 TTTTTGCGTAGAAGTGTGGTG 57.316 42.857 0.00 0.00 0.00 4.17
4941 5637 2.319136 TTTGCGTAGAAGTGTGGTGT 57.681 45.000 0.00 0.00 0.00 4.16
4942 5638 3.455990 TTTGCGTAGAAGTGTGGTGTA 57.544 42.857 0.00 0.00 0.00 2.90
4943 5639 3.455990 TTGCGTAGAAGTGTGGTGTAA 57.544 42.857 0.00 0.00 0.00 2.41
4944 5640 3.021269 TGCGTAGAAGTGTGGTGTAAG 57.979 47.619 0.00 0.00 0.00 2.34
4945 5641 2.624364 TGCGTAGAAGTGTGGTGTAAGA 59.376 45.455 0.00 0.00 0.00 2.10
4946 5642 3.068448 TGCGTAGAAGTGTGGTGTAAGAA 59.932 43.478 0.00 0.00 0.00 2.52
4947 5643 3.673809 GCGTAGAAGTGTGGTGTAAGAAG 59.326 47.826 0.00 0.00 0.00 2.85
4948 5644 4.795308 GCGTAGAAGTGTGGTGTAAGAAGT 60.795 45.833 0.00 0.00 0.00 3.01
4949 5645 5.287226 CGTAGAAGTGTGGTGTAAGAAGTT 58.713 41.667 0.00 0.00 0.00 2.66
4950 5646 5.751990 CGTAGAAGTGTGGTGTAAGAAGTTT 59.248 40.000 0.00 0.00 0.00 2.66
4951 5647 6.257193 CGTAGAAGTGTGGTGTAAGAAGTTTT 59.743 38.462 0.00 0.00 0.00 2.43
4952 5648 7.201582 CGTAGAAGTGTGGTGTAAGAAGTTTTT 60.202 37.037 0.00 0.00 0.00 1.94
4972 5668 1.745232 TCTTTTGCGTGGAAGTGTGT 58.255 45.000 0.00 0.00 0.00 3.72
4983 5679 5.732247 GCGTGGAAGTGTGTTGTAAGAATTT 60.732 40.000 0.00 0.00 0.00 1.82
4984 5680 6.262601 CGTGGAAGTGTGTTGTAAGAATTTT 58.737 36.000 0.00 0.00 0.00 1.82
4986 5682 7.911205 CGTGGAAGTGTGTTGTAAGAATTTTAA 59.089 33.333 0.00 0.00 0.00 1.52
4993 5689 9.406828 GTGTGTTGTAAGAATTTTAAATCTCCC 57.593 33.333 0.00 0.00 0.00 4.30
4994 5690 9.362151 TGTGTTGTAAGAATTTTAAATCTCCCT 57.638 29.630 0.00 0.00 0.00 4.20
5007 5703 2.496899 TCTCCCTCTGGAACAAATGC 57.503 50.000 0.00 0.00 41.17 3.56
5009 5705 0.322456 TCCCTCTGGAACAAATGCGG 60.322 55.000 0.00 0.00 38.70 5.69
5010 5706 0.322456 CCCTCTGGAACAAATGCGGA 60.322 55.000 0.00 0.00 38.70 5.54
5013 5709 2.559698 TCTGGAACAAATGCGGAGAA 57.440 45.000 0.00 0.00 38.70 2.87
5026 5722 3.420893 TGCGGAGAAATGTTCAAGGAAT 58.579 40.909 0.00 0.00 0.00 3.01
5031 5727 5.405797 GGAGAAATGTTCAAGGAATTGCTC 58.594 41.667 0.00 0.00 35.87 4.26
5038 5734 4.402155 TGTTCAAGGAATTGCTCTGTTTGT 59.598 37.500 0.00 0.00 0.00 2.83
5045 5741 5.047802 AGGAATTGCTCTGTTTGTACATTGG 60.048 40.000 0.00 0.00 32.86 3.16
5047 5743 4.829064 TTGCTCTGTTTGTACATTGGTC 57.171 40.909 0.00 0.00 32.86 4.02
5075 5773 8.190784 AGTTAATAATGAAAAGAATTCCCTGCG 58.809 33.333 0.65 0.00 0.00 5.18
5079 5777 2.288152 TGAAAAGAATTCCCTGCGTTGC 60.288 45.455 0.65 0.00 0.00 4.17
5083 5781 1.270550 AGAATTCCCTGCGTTGCTTTG 59.729 47.619 0.65 0.00 0.00 2.77
5097 5795 0.449388 GCTTTGGCTGGATCTGTTCG 59.551 55.000 0.00 0.00 35.22 3.95
5107 5805 1.412710 GGATCTGTTCGGCTCCACATA 59.587 52.381 0.00 0.00 0.00 2.29
5108 5806 2.158957 GGATCTGTTCGGCTCCACATAA 60.159 50.000 0.00 0.00 0.00 1.90
5109 5807 3.531538 GATCTGTTCGGCTCCACATAAA 58.468 45.455 0.00 0.00 0.00 1.40
5110 5808 2.972625 TCTGTTCGGCTCCACATAAAG 58.027 47.619 0.00 0.00 0.00 1.85
5111 5809 2.565391 TCTGTTCGGCTCCACATAAAGA 59.435 45.455 0.00 0.00 0.00 2.52
5112 5810 2.673368 CTGTTCGGCTCCACATAAAGAC 59.327 50.000 0.00 0.00 0.00 3.01
5113 5811 2.007608 GTTCGGCTCCACATAAAGACC 58.992 52.381 0.00 0.00 0.00 3.85
5114 5812 0.539986 TCGGCTCCACATAAAGACCC 59.460 55.000 0.00 0.00 0.00 4.46
5119 5817 0.981183 TCCACATAAAGACCCGCTGT 59.019 50.000 0.00 0.00 0.00 4.40
5121 5819 0.447801 CACATAAAGACCCGCTGTGC 59.552 55.000 0.00 0.00 31.81 4.57
5143 5841 4.038042 GCTATTTTCCTTCCCCTTATGTGC 59.962 45.833 0.00 0.00 0.00 4.57
5153 5852 5.652994 TCCCCTTATGTGCAAACATAAAC 57.347 39.130 11.31 0.00 40.67 2.01
5163 5862 2.231235 GCAAACATAAACCCCTGTGAGG 59.769 50.000 0.00 0.00 34.30 3.86
5166 5865 3.652057 ACATAAACCCCTGTGAGGATG 57.348 47.619 0.00 0.00 37.67 3.51
5173 5872 1.492176 CCCCTGTGAGGATGCAGTAAT 59.508 52.381 0.00 0.00 37.67 1.89
5177 5876 4.818546 CCCTGTGAGGATGCAGTAATTTAG 59.181 45.833 0.00 0.00 37.67 1.85
5182 5881 3.217626 AGGATGCAGTAATTTAGCAGGC 58.782 45.455 0.00 0.00 42.14 4.85
5183 5882 2.951642 GGATGCAGTAATTTAGCAGGCA 59.048 45.455 0.00 0.00 42.14 4.75
5185 5884 3.071874 TGCAGTAATTTAGCAGGCAGT 57.928 42.857 0.00 0.00 33.75 4.40
5186 5885 3.009723 TGCAGTAATTTAGCAGGCAGTC 58.990 45.455 0.00 0.00 33.75 3.51
5187 5886 2.030946 GCAGTAATTTAGCAGGCAGTCG 59.969 50.000 0.00 0.00 0.00 4.18
5188 5887 3.521560 CAGTAATTTAGCAGGCAGTCGA 58.478 45.455 0.00 0.00 0.00 4.20
5189 5888 3.307242 CAGTAATTTAGCAGGCAGTCGAC 59.693 47.826 7.70 7.70 0.00 4.20
5190 5889 1.359848 AATTTAGCAGGCAGTCGACG 58.640 50.000 10.46 6.47 0.00 5.12
5191 5890 0.530744 ATTTAGCAGGCAGTCGACGA 59.469 50.000 10.46 0.00 0.00 4.20
5192 5891 0.388134 TTTAGCAGGCAGTCGACGAC 60.388 55.000 20.25 20.25 0.00 4.34
5193 5892 2.209064 TTAGCAGGCAGTCGACGACC 62.209 60.000 23.76 18.86 32.18 4.79
5194 5893 4.357947 GCAGGCAGTCGACGACCA 62.358 66.667 23.76 0.00 32.18 4.02
5195 5894 2.126307 CAGGCAGTCGACGACCAG 60.126 66.667 23.76 17.47 32.18 4.00
5197 5896 1.901948 AGGCAGTCGACGACCAGAA 60.902 57.895 23.76 0.00 32.18 3.02
5198 5897 1.444553 GGCAGTCGACGACCAGAAG 60.445 63.158 23.76 10.36 32.18 2.85
5200 5899 0.729816 GCAGTCGACGACCAGAAGAC 60.730 60.000 23.76 2.93 32.18 3.01
5201 5900 0.875728 CAGTCGACGACCAGAAGACT 59.124 55.000 23.76 0.07 39.31 3.24
5202 5901 0.875728 AGTCGACGACCAGAAGACTG 59.124 55.000 23.76 0.00 43.12 3.51
5203 5902 0.729816 GTCGACGACCAGAAGACTGC 60.730 60.000 17.25 0.00 42.25 4.40
5205 5904 0.730834 CGACGACCAGAAGACTGCAG 60.731 60.000 13.48 13.48 42.25 4.41
5206 5905 0.315568 GACGACCAGAAGACTGCAGT 59.684 55.000 21.88 21.88 42.25 4.40
5247 5957 6.704493 GTGAGTTGATTACTGGTGAGTTTACA 59.296 38.462 0.00 0.00 37.17 2.41
5248 5958 7.387948 GTGAGTTGATTACTGGTGAGTTTACAT 59.612 37.037 0.00 0.00 37.17 2.29
5249 5959 7.936847 TGAGTTGATTACTGGTGAGTTTACATT 59.063 33.333 0.00 0.00 37.17 2.71
5250 5960 8.324163 AGTTGATTACTGGTGAGTTTACATTC 57.676 34.615 0.00 0.00 35.19 2.67
5251 5961 6.961359 TGATTACTGGTGAGTTTACATTCG 57.039 37.500 0.00 0.00 33.21 3.34
5252 5962 6.460781 TGATTACTGGTGAGTTTACATTCGT 58.539 36.000 0.00 0.00 33.21 3.85
5253 5963 6.588756 TGATTACTGGTGAGTTTACATTCGTC 59.411 38.462 0.00 0.00 33.21 4.20
5254 5964 4.602340 ACTGGTGAGTTTACATTCGTCT 57.398 40.909 0.00 0.00 0.00 4.18
5255 5965 5.717078 ACTGGTGAGTTTACATTCGTCTA 57.283 39.130 0.00 0.00 0.00 2.59
5256 5966 6.092955 ACTGGTGAGTTTACATTCGTCTAA 57.907 37.500 0.00 0.00 0.00 2.10
5257 5967 6.698380 ACTGGTGAGTTTACATTCGTCTAAT 58.302 36.000 0.00 0.00 0.00 1.73
5258 5968 7.159372 ACTGGTGAGTTTACATTCGTCTAATT 58.841 34.615 0.00 0.00 0.00 1.40
5259 5969 7.660208 ACTGGTGAGTTTACATTCGTCTAATTT 59.340 33.333 0.00 0.00 0.00 1.82
5260 5970 7.802738 TGGTGAGTTTACATTCGTCTAATTTG 58.197 34.615 0.00 0.00 0.00 2.32
5261 5971 6.741358 GGTGAGTTTACATTCGTCTAATTTGC 59.259 38.462 0.00 0.00 0.00 3.68
5266 5976 8.730680 AGTTTACATTCGTCTAATTTGCAGATT 58.269 29.630 7.70 7.70 0.00 2.40
5288 5998 8.637099 AGATTTCAAGGAAAAGGAGAAAGAAAG 58.363 33.333 0.00 0.00 35.11 2.62
5289 5999 7.954666 TTTCAAGGAAAAGGAGAAAGAAAGA 57.045 32.000 0.00 0.00 0.00 2.52
5291 6001 5.527582 TCAAGGAAAAGGAGAAAGAAAGACG 59.472 40.000 0.00 0.00 0.00 4.18
5295 6005 2.464157 AGGAGAAAGAAAGACGGCAG 57.536 50.000 0.00 0.00 0.00 4.85
5411 6123 3.959991 GAAGAGGGGGCACAGCGTC 62.960 68.421 0.00 0.00 0.00 5.19
5573 6285 2.268280 CTGGGAGAGCAGTGGCAG 59.732 66.667 0.00 0.00 44.61 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.497675 GCAGATGTCCTTAGTGTCAGGA 59.502 50.000 0.00 0.00 38.18 3.86
1 2 2.419297 GGCAGATGTCCTTAGTGTCAGG 60.419 54.545 0.00 0.00 0.00 3.86
2 3 2.736719 CGGCAGATGTCCTTAGTGTCAG 60.737 54.545 0.00 0.00 0.00 3.51
3 4 1.204704 CGGCAGATGTCCTTAGTGTCA 59.795 52.381 0.00 0.00 0.00 3.58
4 5 1.204941 ACGGCAGATGTCCTTAGTGTC 59.795 52.381 0.00 0.00 0.00 3.67
5 6 1.066858 CACGGCAGATGTCCTTAGTGT 60.067 52.381 0.00 0.00 0.00 3.55
6 7 1.204704 TCACGGCAGATGTCCTTAGTG 59.795 52.381 0.00 0.00 0.00 2.74
7 8 1.204941 GTCACGGCAGATGTCCTTAGT 59.795 52.381 0.00 0.00 0.00 2.24
8 9 1.204704 TGTCACGGCAGATGTCCTTAG 59.795 52.381 0.00 0.00 0.00 2.18
9 10 1.262417 TGTCACGGCAGATGTCCTTA 58.738 50.000 0.00 0.00 0.00 2.69
10 11 0.396435 TTGTCACGGCAGATGTCCTT 59.604 50.000 0.00 0.00 0.00 3.36
11 12 0.615331 ATTGTCACGGCAGATGTCCT 59.385 50.000 0.00 0.00 0.00 3.85
12 13 1.398390 GAATTGTCACGGCAGATGTCC 59.602 52.381 0.00 0.00 0.00 4.02
13 14 1.398390 GGAATTGTCACGGCAGATGTC 59.602 52.381 0.00 0.00 0.00 3.06
14 15 1.271325 TGGAATTGTCACGGCAGATGT 60.271 47.619 0.00 0.00 0.00 3.06
15 16 1.131126 GTGGAATTGTCACGGCAGATG 59.869 52.381 0.00 0.00 0.00 2.90
16 17 1.453155 GTGGAATTGTCACGGCAGAT 58.547 50.000 0.00 0.00 0.00 2.90
17 18 2.927004 GTGGAATTGTCACGGCAGA 58.073 52.632 0.00 0.00 0.00 4.26
23 24 2.210116 ACACTGTCGTGGAATTGTCAC 58.790 47.619 0.00 0.00 45.50 3.67
24 25 2.613026 ACACTGTCGTGGAATTGTCA 57.387 45.000 0.00 0.00 45.50 3.58
25 26 3.131396 AGAACACTGTCGTGGAATTGTC 58.869 45.455 0.00 0.00 45.50 3.18
26 27 3.194005 AGAACACTGTCGTGGAATTGT 57.806 42.857 0.00 0.00 45.50 2.71
27 28 5.666969 TTTAGAACACTGTCGTGGAATTG 57.333 39.130 0.00 0.00 45.50 2.32
28 29 7.972832 TTATTTAGAACACTGTCGTGGAATT 57.027 32.000 0.00 0.00 45.50 2.17
29 30 7.972832 TTTATTTAGAACACTGTCGTGGAAT 57.027 32.000 0.00 0.00 45.50 3.01
30 31 7.789273 TTTTATTTAGAACACTGTCGTGGAA 57.211 32.000 0.00 0.00 45.50 3.53
31 32 7.972832 ATTTTATTTAGAACACTGTCGTGGA 57.027 32.000 0.00 0.00 45.50 4.02
53 54 9.553064 TGCACACCAATATTGAAAGTTTTTATT 57.447 25.926 17.23 0.00 0.00 1.40
54 55 9.723601 ATGCACACCAATATTGAAAGTTTTTAT 57.276 25.926 17.23 0.00 0.00 1.40
55 56 8.986847 CATGCACACCAATATTGAAAGTTTTTA 58.013 29.630 17.23 0.00 0.00 1.52
56 57 7.714377 TCATGCACACCAATATTGAAAGTTTTT 59.286 29.630 17.23 0.00 0.00 1.94
57 58 7.215789 TCATGCACACCAATATTGAAAGTTTT 58.784 30.769 17.23 0.00 0.00 2.43
58 59 6.757237 TCATGCACACCAATATTGAAAGTTT 58.243 32.000 17.23 0.00 0.00 2.66
59 60 6.343716 TCATGCACACCAATATTGAAAGTT 57.656 33.333 17.23 0.00 0.00 2.66
60 61 5.622914 GCTCATGCACACCAATATTGAAAGT 60.623 40.000 17.23 8.96 39.41 2.66
61 62 4.802039 GCTCATGCACACCAATATTGAAAG 59.198 41.667 17.23 8.35 39.41 2.62
62 63 4.381825 GGCTCATGCACACCAATATTGAAA 60.382 41.667 17.23 0.00 41.91 2.69
63 64 3.130869 GGCTCATGCACACCAATATTGAA 59.869 43.478 17.23 0.00 41.91 2.69
64 65 2.689471 GGCTCATGCACACCAATATTGA 59.311 45.455 17.23 0.00 41.91 2.57
65 66 2.427812 TGGCTCATGCACACCAATATTG 59.572 45.455 8.58 8.58 41.91 1.90
66 67 2.737544 TGGCTCATGCACACCAATATT 58.262 42.857 0.00 0.00 41.91 1.28
67 68 2.440517 TGGCTCATGCACACCAATAT 57.559 45.000 0.00 0.00 41.91 1.28
68 69 2.440517 ATGGCTCATGCACACCAATA 57.559 45.000 0.00 0.00 41.91 1.90
69 70 2.440517 TATGGCTCATGCACACCAAT 57.559 45.000 0.00 0.00 41.91 3.16
70 71 2.212812 TTATGGCTCATGCACACCAA 57.787 45.000 0.00 0.00 41.91 3.67
71 72 2.212812 TTTATGGCTCATGCACACCA 57.787 45.000 0.00 0.00 41.91 4.17
72 73 4.916983 TTATTTATGGCTCATGCACACC 57.083 40.909 0.00 0.00 41.91 4.16
73 74 6.979817 TCATTTTATTTATGGCTCATGCACAC 59.020 34.615 0.00 0.00 41.91 3.82
74 75 7.110043 TCATTTTATTTATGGCTCATGCACA 57.890 32.000 0.00 0.00 41.91 4.57
75 76 6.145048 GCTCATTTTATTTATGGCTCATGCAC 59.855 38.462 0.00 0.00 41.91 4.57
76 77 6.041182 AGCTCATTTTATTTATGGCTCATGCA 59.959 34.615 0.00 0.00 41.91 3.96
77 78 6.453092 AGCTCATTTTATTTATGGCTCATGC 58.547 36.000 0.00 0.00 38.76 4.06
78 79 7.883217 AGAGCTCATTTTATTTATGGCTCATG 58.117 34.615 17.77 0.00 42.42 3.07
79 80 9.007901 GTAGAGCTCATTTTATTTATGGCTCAT 57.992 33.333 17.77 11.73 42.42 2.90
80 81 7.445402 GGTAGAGCTCATTTTATTTATGGCTCA 59.555 37.037 17.77 9.42 42.42 4.26
81 82 7.445402 TGGTAGAGCTCATTTTATTTATGGCTC 59.555 37.037 17.77 13.58 41.48 4.70
82 83 7.290061 TGGTAGAGCTCATTTTATTTATGGCT 58.710 34.615 17.77 0.00 34.45 4.75
83 84 7.510549 TGGTAGAGCTCATTTTATTTATGGC 57.489 36.000 17.77 0.00 0.00 4.40
129 130 1.071814 TGCGGGGCGGATTAATACC 59.928 57.895 0.00 0.00 0.00 2.73
290 298 7.724287 TGGTGAGATTGTTGATTCAAAATTGA 58.276 30.769 0.00 0.00 34.92 2.57
362 370 1.299468 CTCCTAGTCGCATGGTCGC 60.299 63.158 0.00 0.00 0.00 5.19
363 371 1.360551 CCTCCTAGTCGCATGGTCG 59.639 63.158 0.00 0.00 0.00 4.79
371 379 0.551879 TTCCTCCTCCCTCCTAGTCG 59.448 60.000 0.00 0.00 0.00 4.18
394 402 3.579742 TTAACCCTTCTCCTTCCTCCT 57.420 47.619 0.00 0.00 0.00 3.69
407 415 4.641868 TGTATCCCCTTCTCATTAACCCT 58.358 43.478 0.00 0.00 0.00 4.34
438 449 3.951680 CTCACTAACTCTTCTCTCCTCCC 59.048 52.174 0.00 0.00 0.00 4.30
481 494 4.097361 GGTCCGCCCCTTCACTCC 62.097 72.222 0.00 0.00 0.00 3.85
560 573 0.897621 TGATATCCGCTGCCATCGAT 59.102 50.000 0.00 0.00 0.00 3.59
561 574 0.897621 ATGATATCCGCTGCCATCGA 59.102 50.000 0.00 0.00 0.00 3.59
568 581 2.348872 GCGTTGACAATGATATCCGCTG 60.349 50.000 11.67 3.66 37.14 5.18
606 619 1.078072 TGTTCATTACCGCCCGCAT 60.078 52.632 0.00 0.00 0.00 4.73
612 625 4.759516 TCCTTTTTCTGTTCATTACCGC 57.240 40.909 0.00 0.00 0.00 5.68
656 741 6.092533 ACGTTTTTATATTGTCCCGTTTCGAT 59.907 34.615 0.00 0.00 0.00 3.59
675 760 5.850614 ACAAGTCACACTAGGATACGTTTT 58.149 37.500 0.00 0.00 46.39 2.43
696 781 7.557358 TCTTCCACAATAGGATACGTAGTTACA 59.443 37.037 0.08 0.00 46.39 2.41
713 798 3.071892 ACTTGGGAATACGTCTTCCACAA 59.928 43.478 27.88 25.00 45.51 3.33
854 945 0.741221 GAACGGCTCGATGCTTCCTT 60.741 55.000 1.50 0.00 42.39 3.36
855 946 1.153549 GAACGGCTCGATGCTTCCT 60.154 57.895 1.50 0.00 42.39 3.36
856 947 2.174319 GGAACGGCTCGATGCTTCC 61.174 63.158 10.10 10.10 42.39 3.46
857 948 1.019278 TTGGAACGGCTCGATGCTTC 61.019 55.000 1.50 4.36 42.39 3.86
858 949 0.392998 ATTGGAACGGCTCGATGCTT 60.393 50.000 1.50 0.00 42.39 3.91
965 1060 3.300667 GAGCAAACGCAGACGCCAG 62.301 63.158 0.00 0.00 45.53 4.85
1116 1223 5.071788 AGTCAGAGACAAACCAATGAGGTAA 59.928 40.000 0.00 0.00 42.09 2.85
1183 1307 2.225491 CGAAAGGGAATCAAGAAACGCA 59.775 45.455 0.00 0.00 0.00 5.24
1302 1426 7.722949 AACATGGATCAGTCAAACCAATATT 57.277 32.000 0.00 0.00 36.00 1.28
1341 1469 7.967303 GGATTTCTTTGAGCACAATCTTTCTAG 59.033 37.037 0.00 0.00 35.85 2.43
1514 1644 2.106857 ACAGTCCCATAAACCCGAAACA 59.893 45.455 0.00 0.00 0.00 2.83
1519 1652 0.322098 TGCACAGTCCCATAAACCCG 60.322 55.000 0.00 0.00 0.00 5.28
1535 1668 3.425577 CAGAGTTTGCTTTCAGTTGCA 57.574 42.857 0.00 0.00 37.42 4.08
1556 1689 3.369147 CGTGCTCTTCATGAAACAGGTAG 59.631 47.826 9.88 0.00 33.49 3.18
1558 1691 2.146342 CGTGCTCTTCATGAAACAGGT 58.854 47.619 9.88 0.00 33.49 4.00
1579 1712 2.027100 AGGAATTCCTCCCTGTCGTTTC 60.027 50.000 21.89 0.00 44.77 2.78
1690 1823 8.908786 TGAAAATGTATGAAGAACAAGTCTCT 57.091 30.769 0.00 0.00 34.56 3.10
1691 1824 9.552114 CATGAAAATGTATGAAGAACAAGTCTC 57.448 33.333 0.00 0.00 34.56 3.36
1746 1879 2.636830 TGAGCAGCTCTTTAAGATGGC 58.363 47.619 23.15 0.00 41.84 4.40
1778 1911 7.663827 ACATCAAATCTGCTTCAATTTCAAGA 58.336 30.769 0.00 0.00 0.00 3.02
2067 2201 4.018960 AGGTATTGTCCAGAATGAGCAAGT 60.019 41.667 0.00 0.00 39.69 3.16
2115 2249 4.469657 AGTGGACATTAACCTTTGCTTCA 58.530 39.130 0.00 0.00 0.00 3.02
2234 2370 5.324409 TGATGGTGCTCCTTGAAATACTTT 58.676 37.500 6.34 0.00 34.23 2.66
2374 2512 3.969117 TGATGAAACAACAGTGAGTGC 57.031 42.857 0.00 0.00 0.00 4.40
2480 2618 3.864789 ATATGAGGAAAACCGAGCCAT 57.135 42.857 0.00 0.00 0.00 4.40
2516 2654 1.001378 AGGTTTGCACGCAGAACAATC 60.001 47.619 14.54 0.00 0.00 2.67
2715 2853 6.899393 TGTGGAATGAGCAAGATAAACTTT 57.101 33.333 0.00 0.00 36.61 2.66
2919 3057 4.080582 TGGGATTGTGATAGTGTAACAGGG 60.081 45.833 0.00 0.00 41.43 4.45
3024 3162 3.696051 TCAAATGTAGGCTCCTGAATTGC 59.304 43.478 0.00 0.00 0.00 3.56
3326 3464 6.976934 AACTTTTGGACATAACCACATCTT 57.023 33.333 0.00 0.00 39.85 2.40
3449 3588 6.293765 ATGAACTGAACCCAGTCCATTGGT 62.294 45.833 1.86 0.00 44.50 3.67
3502 3641 5.922544 GGATCAAGTCAAACCAATTTCACTG 59.077 40.000 0.00 0.00 0.00 3.66
4396 5091 3.582714 AGCAATACAAGAAAAGGCTGC 57.417 42.857 0.00 0.00 0.00 5.25
4678 5373 5.765182 AGATTACCTGGTTCAAACTGAGTTG 59.235 40.000 3.84 0.00 0.00 3.16
4685 5380 6.635030 ACAAGAAGATTACCTGGTTCAAAC 57.365 37.500 3.84 0.00 0.00 2.93
4728 5423 7.251704 AGTAATCCAGAAACATTAGAATGCG 57.748 36.000 2.09 0.00 40.04 4.73
4781 5476 2.774234 TGCCCCCTTGAAATGAAACAAA 59.226 40.909 0.00 0.00 0.00 2.83
4784 5479 2.368548 ACTTGCCCCCTTGAAATGAAAC 59.631 45.455 0.00 0.00 0.00 2.78
4789 5484 2.990740 TGTACTTGCCCCCTTGAAAT 57.009 45.000 0.00 0.00 0.00 2.17
4790 5485 2.556559 GGATGTACTTGCCCCCTTGAAA 60.557 50.000 0.00 0.00 0.00 2.69
4793 5488 0.625849 AGGATGTACTTGCCCCCTTG 59.374 55.000 0.00 0.00 0.00 3.61
4841 5537 2.704616 CGCGTCTCTCCTCGACTC 59.295 66.667 0.00 0.00 0.00 3.36
4845 5541 4.544689 CAGCCGCGTCTCTCCTCG 62.545 72.222 4.92 0.00 0.00 4.63
4901 5597 6.584563 GCAAAAATAATTCTTCACCGCACTTA 59.415 34.615 0.00 0.00 0.00 2.24
4912 5608 7.807907 CCACACTTCTACGCAAAAATAATTCTT 59.192 33.333 0.00 0.00 0.00 2.52
4913 5609 7.040686 ACCACACTTCTACGCAAAAATAATTCT 60.041 33.333 0.00 0.00 0.00 2.40
4915 5611 6.861055 CACCACACTTCTACGCAAAAATAATT 59.139 34.615 0.00 0.00 0.00 1.40
4917 5613 5.297278 ACACCACACTTCTACGCAAAAATAA 59.703 36.000 0.00 0.00 0.00 1.40
4918 5614 4.817464 ACACCACACTTCTACGCAAAAATA 59.183 37.500 0.00 0.00 0.00 1.40
4919 5615 3.630312 ACACCACACTTCTACGCAAAAAT 59.370 39.130 0.00 0.00 0.00 1.82
4920 5616 3.011119 ACACCACACTTCTACGCAAAAA 58.989 40.909 0.00 0.00 0.00 1.94
4921 5617 2.634600 ACACCACACTTCTACGCAAAA 58.365 42.857 0.00 0.00 0.00 2.44
4922 5618 2.319136 ACACCACACTTCTACGCAAA 57.681 45.000 0.00 0.00 0.00 3.68
4923 5619 3.068448 TCTTACACCACACTTCTACGCAA 59.932 43.478 0.00 0.00 0.00 4.85
4924 5620 2.624364 TCTTACACCACACTTCTACGCA 59.376 45.455 0.00 0.00 0.00 5.24
4925 5621 3.293311 TCTTACACCACACTTCTACGC 57.707 47.619 0.00 0.00 0.00 4.42
4926 5622 4.868067 ACTTCTTACACCACACTTCTACG 58.132 43.478 0.00 0.00 0.00 3.51
4927 5623 7.549615 AAAACTTCTTACACCACACTTCTAC 57.450 36.000 0.00 0.00 0.00 2.59
4949 5645 3.923461 CACACTTCCACGCAAAAGAAAAA 59.077 39.130 0.00 0.00 0.00 1.94
4950 5646 3.057174 ACACACTTCCACGCAAAAGAAAA 60.057 39.130 0.00 0.00 0.00 2.29
4951 5647 2.490115 ACACACTTCCACGCAAAAGAAA 59.510 40.909 0.00 0.00 0.00 2.52
4952 5648 2.088423 ACACACTTCCACGCAAAAGAA 58.912 42.857 0.00 0.00 0.00 2.52
4953 5649 1.745232 ACACACTTCCACGCAAAAGA 58.255 45.000 0.00 0.00 0.00 2.52
4954 5650 2.184448 CAACACACTTCCACGCAAAAG 58.816 47.619 0.00 0.00 0.00 2.27
4955 5651 1.542030 ACAACACACTTCCACGCAAAA 59.458 42.857 0.00 0.00 0.00 2.44
4956 5652 1.169577 ACAACACACTTCCACGCAAA 58.830 45.000 0.00 0.00 0.00 3.68
4957 5653 2.025589 TACAACACACTTCCACGCAA 57.974 45.000 0.00 0.00 0.00 4.85
4958 5654 1.937223 CTTACAACACACTTCCACGCA 59.063 47.619 0.00 0.00 0.00 5.24
4959 5655 2.206750 TCTTACAACACACTTCCACGC 58.793 47.619 0.00 0.00 0.00 5.34
4960 5656 5.418310 AATTCTTACAACACACTTCCACG 57.582 39.130 0.00 0.00 0.00 4.94
4961 5657 9.575783 TTTAAAATTCTTACAACACACTTCCAC 57.424 29.630 0.00 0.00 0.00 4.02
4972 5668 9.243105 CCAGAGGGAGATTTAAAATTCTTACAA 57.757 33.333 0.00 0.00 35.59 2.41
4983 5679 5.418840 GCATTTGTTCCAGAGGGAGATTTAA 59.581 40.000 0.00 0.00 46.01 1.52
4984 5680 4.949856 GCATTTGTTCCAGAGGGAGATTTA 59.050 41.667 0.00 0.00 46.01 1.40
4986 5682 3.359950 GCATTTGTTCCAGAGGGAGATT 58.640 45.455 0.00 0.00 46.01 2.40
4993 5689 2.099141 TCTCCGCATTTGTTCCAGAG 57.901 50.000 0.00 0.00 0.00 3.35
4994 5690 2.559698 TTCTCCGCATTTGTTCCAGA 57.440 45.000 0.00 0.00 0.00 3.86
5007 5703 4.082571 AGCAATTCCTTGAACATTTCTCCG 60.083 41.667 0.00 0.00 34.04 4.63
5009 5705 6.091437 CAGAGCAATTCCTTGAACATTTCTC 58.909 40.000 0.00 0.00 34.04 2.87
5010 5706 5.537674 ACAGAGCAATTCCTTGAACATTTCT 59.462 36.000 0.00 0.00 34.04 2.52
5013 5709 5.796424 AACAGAGCAATTCCTTGAACATT 57.204 34.783 0.00 0.00 34.04 2.71
5026 5722 4.203226 TGACCAATGTACAAACAGAGCAA 58.797 39.130 0.00 0.00 39.49 3.91
5058 5755 2.288152 GCAACGCAGGGAATTCTTTTCA 60.288 45.455 5.23 0.00 0.00 2.69
5075 5773 1.251251 ACAGATCCAGCCAAAGCAAC 58.749 50.000 0.00 0.00 43.56 4.17
5079 5777 1.089920 CCGAACAGATCCAGCCAAAG 58.910 55.000 0.00 0.00 0.00 2.77
5083 5781 1.522580 GAGCCGAACAGATCCAGCC 60.523 63.158 0.00 0.00 0.00 4.85
5097 5795 1.095807 GCGGGTCTTTATGTGGAGCC 61.096 60.000 0.00 0.00 44.01 4.70
5107 5805 2.200373 AAATAGCACAGCGGGTCTTT 57.800 45.000 0.00 0.00 0.00 2.52
5108 5806 2.084546 GAAAATAGCACAGCGGGTCTT 58.915 47.619 0.00 0.00 0.00 3.01
5109 5807 1.679032 GGAAAATAGCACAGCGGGTCT 60.679 52.381 0.00 0.00 0.00 3.85
5110 5808 0.733150 GGAAAATAGCACAGCGGGTC 59.267 55.000 0.00 0.00 0.00 4.46
5111 5809 0.328258 AGGAAAATAGCACAGCGGGT 59.672 50.000 0.00 0.00 0.00 5.28
5112 5810 1.401905 GAAGGAAAATAGCACAGCGGG 59.598 52.381 0.00 0.00 0.00 6.13
5113 5811 1.401905 GGAAGGAAAATAGCACAGCGG 59.598 52.381 0.00 0.00 0.00 5.52
5114 5812 1.401905 GGGAAGGAAAATAGCACAGCG 59.598 52.381 0.00 0.00 0.00 5.18
5119 5817 5.200483 CACATAAGGGGAAGGAAAATAGCA 58.800 41.667 0.00 0.00 0.00 3.49
5121 5819 5.200483 TGCACATAAGGGGAAGGAAAATAG 58.800 41.667 0.00 0.00 0.00 1.73
5143 5841 3.761897 TCCTCACAGGGGTTTATGTTTG 58.238 45.455 0.00 0.00 35.59 2.93
5153 5852 0.911769 TTACTGCATCCTCACAGGGG 59.088 55.000 0.00 0.00 38.25 4.79
5163 5862 3.629398 ACTGCCTGCTAAATTACTGCATC 59.371 43.478 0.00 0.00 36.07 3.91
5166 5865 2.030946 CGACTGCCTGCTAAATTACTGC 59.969 50.000 0.00 0.00 0.00 4.40
5173 5872 0.388134 GTCGTCGACTGCCTGCTAAA 60.388 55.000 18.09 0.00 0.00 1.85
5177 5876 4.357947 TGGTCGTCGACTGCCTGC 62.358 66.667 23.69 7.63 32.47 4.85
5182 5881 0.875728 AGTCTTCTGGTCGTCGACTG 59.124 55.000 23.69 16.62 33.99 3.51
5183 5882 0.875728 CAGTCTTCTGGTCGTCGACT 59.124 55.000 23.69 0.00 37.97 4.18
5185 5884 1.170290 TGCAGTCTTCTGGTCGTCGA 61.170 55.000 0.00 0.00 41.57 4.20
5186 5885 0.730834 CTGCAGTCTTCTGGTCGTCG 60.731 60.000 5.25 0.00 41.57 5.12
5187 5886 0.315568 ACTGCAGTCTTCTGGTCGTC 59.684 55.000 15.25 0.00 41.57 4.20
5188 5887 0.315568 GACTGCAGTCTTCTGGTCGT 59.684 55.000 34.54 2.84 41.65 4.34
5189 5888 0.315251 TGACTGCAGTCTTCTGGTCG 59.685 55.000 38.81 4.01 44.99 4.79
5190 5889 2.289320 ACATGACTGCAGTCTTCTGGTC 60.289 50.000 38.81 18.02 44.99 4.02
5191 5890 1.696336 ACATGACTGCAGTCTTCTGGT 59.304 47.619 38.81 26.07 44.99 4.00
5192 5891 2.469274 ACATGACTGCAGTCTTCTGG 57.531 50.000 38.81 25.52 44.99 3.86
5193 5892 4.309933 TGTTACATGACTGCAGTCTTCTG 58.690 43.478 38.81 32.60 44.99 3.02
5194 5893 4.039730 ACTGTTACATGACTGCAGTCTTCT 59.960 41.667 38.81 26.21 44.99 2.85
5195 5894 4.310769 ACTGTTACATGACTGCAGTCTTC 58.689 43.478 38.81 23.94 44.99 2.87
5197 5896 4.342862 AACTGTTACATGACTGCAGTCT 57.657 40.909 38.81 25.65 44.99 3.24
5198 5897 4.752101 AGAAACTGTTACATGACTGCAGTC 59.248 41.667 35.04 35.04 44.97 3.51
5200 5899 4.512944 ACAGAAACTGTTACATGACTGCAG 59.487 41.667 13.48 13.48 42.59 4.41
5201 5900 4.273235 CACAGAAACTGTTACATGACTGCA 59.727 41.667 0.00 0.00 42.59 4.41
5202 5901 4.511454 TCACAGAAACTGTTACATGACTGC 59.489 41.667 0.00 0.00 42.59 4.40
5203 5902 5.755375 ACTCACAGAAACTGTTACATGACTG 59.245 40.000 0.00 0.00 42.59 3.51
5205 5904 6.257849 TCAACTCACAGAAACTGTTACATGAC 59.742 38.462 0.00 0.00 42.59 3.06
5206 5905 6.345298 TCAACTCACAGAAACTGTTACATGA 58.655 36.000 0.00 3.25 42.59 3.07
5247 5957 7.121168 TCCTTGAAATCTGCAAATTAGACGAAT 59.879 33.333 0.00 0.00 0.00 3.34
5248 5958 6.429692 TCCTTGAAATCTGCAAATTAGACGAA 59.570 34.615 0.00 0.00 0.00 3.85
5249 5959 5.937540 TCCTTGAAATCTGCAAATTAGACGA 59.062 36.000 0.00 0.00 0.00 4.20
5250 5960 6.182039 TCCTTGAAATCTGCAAATTAGACG 57.818 37.500 0.00 0.00 0.00 4.18
5251 5961 8.816640 TTTTCCTTGAAATCTGCAAATTAGAC 57.183 30.769 0.00 0.00 31.34 2.59
5252 5962 8.090214 CCTTTTCCTTGAAATCTGCAAATTAGA 58.910 33.333 0.00 0.00 31.34 2.10
5253 5963 8.090214 TCCTTTTCCTTGAAATCTGCAAATTAG 58.910 33.333 0.00 0.00 31.34 1.73
5254 5964 7.961351 TCCTTTTCCTTGAAATCTGCAAATTA 58.039 30.769 0.00 0.00 31.34 1.40
5255 5965 6.829849 TCCTTTTCCTTGAAATCTGCAAATT 58.170 32.000 0.00 0.00 31.34 1.82
5256 5966 6.268387 TCTCCTTTTCCTTGAAATCTGCAAAT 59.732 34.615 0.00 0.00 31.34 2.32
5257 5967 5.598005 TCTCCTTTTCCTTGAAATCTGCAAA 59.402 36.000 0.00 0.00 31.34 3.68
5258 5968 5.139727 TCTCCTTTTCCTTGAAATCTGCAA 58.860 37.500 0.00 0.00 31.34 4.08
5259 5969 4.728772 TCTCCTTTTCCTTGAAATCTGCA 58.271 39.130 0.00 0.00 31.34 4.41
5260 5970 5.712152 TTCTCCTTTTCCTTGAAATCTGC 57.288 39.130 0.00 0.00 31.34 4.26
5261 5971 7.516198 TCTTTCTCCTTTTCCTTGAAATCTG 57.484 36.000 0.00 0.00 31.34 2.90
5266 5976 6.038271 CGTCTTTCTTTCTCCTTTTCCTTGAA 59.962 38.462 0.00 0.00 0.00 2.69
5295 6005 5.217895 GACATGTACCGTCCAGAAAATTC 57.782 43.478 0.00 0.00 0.00 2.17
5411 6123 1.770658 TGCTCATTATCTCACCCCCAG 59.229 52.381 0.00 0.00 0.00 4.45
5443 6155 1.228552 AAATGGTGGACGCCAAGCT 60.229 52.632 8.86 0.00 42.48 3.74
5444 6156 1.212751 GAAATGGTGGACGCCAAGC 59.787 57.895 8.86 0.00 42.48 4.01
5445 6157 0.523072 CAGAAATGGTGGACGCCAAG 59.477 55.000 8.86 0.00 42.48 3.61
5518 6230 4.303257 GTGTGGCTTCACCCTAGC 57.697 61.111 2.86 0.00 40.53 3.42


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

AutoCloner maintained by Alex Coulton.