Multiple sequence alignment - TraesCS2A01G069600

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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 TraesCS2A01G069600 chr2A 100.000 5284 0 0 1 5284 30560355 30565638 0.000000e+00 9758.0
1 TraesCS2A01G069600 chr2D 94.544 4637 168 23 1 4580 28755282 28759890 0.000000e+00 7083.0
2 TraesCS2A01G069600 chr2D 90.173 173 16 1 5112 5284 28760381 28760552 1.920000e-54 224.0
3 TraesCS2A01G069600 chr2D 92.913 127 9 0 4642 4768 28760016 28760142 9.040000e-43 185.0
4 TraesCS2A01G069600 chr2B 87.386 1863 160 37 2685 4512 46103483 46105305 0.000000e+00 2069.0
5 TraesCS2A01G069600 chr2B 92.904 1367 83 7 1284 2645 46101732 46103089 0.000000e+00 1975.0
6 TraesCS2A01G069600 chr2B 88.370 1264 125 11 1 1243 46100459 46101721 0.000000e+00 1500.0
7 TraesCS2A01G069600 chr3A 79.570 186 29 5 4770 4948 551411895 551412078 2.000000e-24 124.0
8 TraesCS2A01G069600 chr3A 82.609 115 11 9 4772 4882 278739813 278739922 5.630000e-15 93.5
9 TraesCS2A01G069600 chr1D 79.032 186 16 13 4770 4946 494305064 494304893 7.240000e-19 106.0
10 TraesCS2A01G069600 chr5B 77.540 187 24 13 4770 4948 406408713 406408889 4.360000e-16 97.1
11 TraesCS2A01G069600 chr5B 97.143 35 0 1 4896 4929 633906493 633906459 2.060000e-04 58.4
12 TraesCS2A01G069600 chr4B 86.517 89 6 5 4867 4949 476352754 476352666 5.630000e-15 93.5
13 TraesCS2A01G069600 chr4D 80.508 118 11 8 4839 4946 50230449 50230564 4.390000e-11 80.5


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 TraesCS2A01G069600 chr2A 30560355 30565638 5283 False 9758.000000 9758 100.000000 1 5284 1 chr2A.!!$F1 5283
1 TraesCS2A01G069600 chr2D 28755282 28760552 5270 False 2497.333333 7083 92.543333 1 5284 3 chr2D.!!$F1 5283
2 TraesCS2A01G069600 chr2B 46100459 46105305 4846 False 1848.000000 2069 89.553333 1 4512 3 chr2B.!!$F1 4511

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
253 255 0.031994 GCGTGCAAACCAACTTCCAT 59.968 50.000 0.00 0.00 0.00 3.41 F
268 270 0.404040 TCCATTTGACCAGACACCCC 59.596 55.000 0.00 0.00 0.00 4.95 F
479 483 0.671796 CCACGATCCACATACGGCTA 59.328 55.000 0.00 0.00 0.00 3.93 F
532 537 0.834687 AGGCAACCCGAAGTACCTGA 60.835 55.000 0.00 0.00 34.60 3.86 F
643 648 1.511464 GTGACTCGTCGCGGTGTAG 60.511 63.158 6.13 1.39 0.00 2.74 F
1272 1299 1.813178 GTTTTAGGCCTTCCTGTGCTC 59.187 52.381 12.58 0.00 44.08 4.26 F
1684 1714 2.168521 TGCTAAGGCGATTAGACAGCTT 59.831 45.455 10.59 0.00 43.17 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2129 2163 0.178992 AGGCCTTGTTAAGCACAGCA 60.179 50.000 0.00 0.0 36.48 4.41 R
2688 3076 4.037923 TGAAAAATGGAGTGAACTCTTGCC 59.962 41.667 10.17 0.0 42.48 4.52 R
3183 3572 4.732285 AACTGTGCTAAATCGTCAACAG 57.268 40.909 0.00 0.0 0.00 3.16 R
3285 3674 5.869344 TGTATTTCGTTCATGAAGACTCCTG 59.131 40.000 8.80 0.0 0.00 3.86 R
3509 3898 1.152943 AGGCCGCGAGAGAGATACA 60.153 57.895 8.23 0.0 0.00 2.29 R
3620 4009 7.331440 TGATGTTCAAATTGTTCATGCATTACC 59.669 33.333 0.00 0.0 0.00 2.85 R
4320 4730 0.383231 GATCAAAGAGCGGGGCATTG 59.617 55.000 0.00 0.0 0.00 2.82 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
18 19 4.101448 GCTGACATCCCACCGCCT 62.101 66.667 0.00 0.00 0.00 5.52
32 33 1.524393 CGCCTGCCTCACATATGCA 60.524 57.895 1.58 0.00 0.00 3.96
89 91 6.370994 TCCGACCAATACTCGATATTAGACTC 59.629 42.308 0.00 0.00 31.88 3.36
107 109 0.612174 TCTGCCCTAGCGAACACTCT 60.612 55.000 0.00 0.00 44.31 3.24
124 126 0.098200 TCTACCGCGACATCGAACAG 59.902 55.000 8.23 0.00 43.02 3.16
157 159 4.591929 TCATGAGGAACATCAATCTGCAA 58.408 39.130 0.00 0.00 37.07 4.08
162 164 2.494870 GGAACATCAATCTGCAAGCCTT 59.505 45.455 0.00 0.00 0.00 4.35
163 165 3.508762 GAACATCAATCTGCAAGCCTTG 58.491 45.455 0.00 0.00 0.00 3.61
246 248 1.448119 TTCATCGGCGTGCAAACCAA 61.448 50.000 6.85 0.00 0.00 3.67
253 255 0.031994 GCGTGCAAACCAACTTCCAT 59.968 50.000 0.00 0.00 0.00 3.41
265 267 3.004734 CCAACTTCCATTTGACCAGACAC 59.995 47.826 0.00 0.00 0.00 3.67
268 270 0.404040 TCCATTTGACCAGACACCCC 59.596 55.000 0.00 0.00 0.00 4.95
339 342 4.401022 TGTTGATGCAAGAGAGAAACCAT 58.599 39.130 0.00 0.00 0.00 3.55
341 344 6.182627 TGTTGATGCAAGAGAGAAACCATAT 58.817 36.000 0.00 0.00 0.00 1.78
349 353 5.523438 AGAGAGAAACCATATCGGAAGAC 57.477 43.478 0.00 0.00 46.97 3.01
479 483 0.671796 CCACGATCCACATACGGCTA 59.328 55.000 0.00 0.00 0.00 3.93
495 499 2.158900 CGGCTACAGGTGAATCTTGGAT 60.159 50.000 0.00 0.00 0.00 3.41
522 526 3.382832 ACGGAGAGAGGCAACCCG 61.383 66.667 0.00 0.00 45.09 5.28
532 537 0.834687 AGGCAACCCGAAGTACCTGA 60.835 55.000 0.00 0.00 34.60 3.86
550 555 3.378112 CCTGACAAGAAAGTTGAGCACAA 59.622 43.478 0.00 0.00 0.00 3.33
553 558 3.356290 ACAAGAAAGTTGAGCACAAGGT 58.644 40.909 0.00 0.00 36.64 3.50
557 562 4.327680 AGAAAGTTGAGCACAAGGTATCC 58.672 43.478 0.00 0.00 36.64 2.59
558 563 2.789409 AGTTGAGCACAAGGTATCCC 57.211 50.000 0.00 0.00 36.64 3.85
569 574 2.684881 CAAGGTATCCCAGTGATTGCAC 59.315 50.000 0.00 0.00 45.49 4.57
643 648 1.511464 GTGACTCGTCGCGGTGTAG 60.511 63.158 6.13 1.39 0.00 2.74
673 679 4.827087 CGCCATCACCGCTGCTCT 62.827 66.667 0.00 0.00 0.00 4.09
680 686 4.074526 ACCGCTGCTCTGACGCAT 62.075 61.111 0.00 0.00 39.52 4.73
689 695 3.057548 CTGACGCATGGCAGCCAA 61.058 61.111 20.84 1.43 36.95 4.52
735 741 4.241555 ATCCCAGCCGTCGGATGC 62.242 66.667 23.99 3.75 37.84 3.91
753 759 2.892425 GGCAGGAACGCTGGATCG 60.892 66.667 0.00 0.00 0.00 3.69
1220 1244 3.709987 CTGCTAGTTGCCCAATTATTGC 58.290 45.455 0.00 0.00 42.00 3.56
1251 1275 6.145534 TCGTCTGTAAATCAAGTGCTTTGTAG 59.854 38.462 2.27 0.00 38.01 2.74
1252 1276 6.603095 GTCTGTAAATCAAGTGCTTTGTAGG 58.397 40.000 2.27 0.00 38.01 3.18
1272 1299 1.813178 GTTTTAGGCCTTCCTGTGCTC 59.187 52.381 12.58 0.00 44.08 4.26
1307 1334 8.756864 GTTTTAAGACTATTCGATGATCCACTC 58.243 37.037 0.00 0.00 0.00 3.51
1330 1357 2.644798 AGGCCTAGAAACTTGTGGTGAT 59.355 45.455 1.29 0.00 0.00 3.06
1349 1376 8.186821 GTGGTGATTAGAGATTGAAAATTGGAG 58.813 37.037 0.00 0.00 0.00 3.86
1357 1384 2.373540 TGAAAATTGGAGCTGCATGC 57.626 45.000 9.39 11.82 43.29 4.06
1381 1408 3.935371 TTTTTCCAAGAGCCCACCA 57.065 47.368 0.00 0.00 0.00 4.17
1460 1487 7.692460 TGAATTGCTTCTTCTCATGTTACAT 57.308 32.000 0.00 0.00 32.29 2.29
1541 1570 9.807649 ACATCATTGTTTTCTCAATTTATAGGC 57.192 29.630 0.00 0.00 36.10 3.93
1617 1646 7.040478 TGCCATGTTAATAGACCAATAGATTGC 60.040 37.037 0.00 0.00 36.48 3.56
1620 1649 9.276590 CATGTTAATAGACCAATAGATTGCTGA 57.723 33.333 0.00 0.00 36.48 4.26
1631 1660 6.595326 CCAATAGATTGCTGACTTTGTGTCTA 59.405 38.462 0.00 0.00 40.02 2.59
1640 1670 8.032952 TGCTGACTTTGTGTCTAAATTCATAG 57.967 34.615 0.00 0.00 45.54 2.23
1651 1681 9.587772 GTGTCTAAATTCATAGCTTCTGAAGTA 57.412 33.333 17.97 9.90 36.16 2.24
1684 1714 2.168521 TGCTAAGGCGATTAGACAGCTT 59.831 45.455 10.59 0.00 43.17 3.74
1695 1725 6.478588 CGATTAGACAGCTTTTACATGAACC 58.521 40.000 0.00 0.00 0.00 3.62
1699 1729 5.865085 AGACAGCTTTTACATGAACCTGTA 58.135 37.500 0.00 0.00 32.76 2.74
1717 1747 5.816777 ACCTGTATCTCTCAGTTACGAGTAC 59.183 44.000 0.00 0.00 34.46 2.73
1732 1762 5.086104 ACGAGTACAAAGCTGGATAACAT 57.914 39.130 0.00 0.00 0.00 2.71
1742 1772 9.905713 ACAAAGCTGGATAACATTCTAGATTTA 57.094 29.630 0.00 0.00 39.72 1.40
1786 1818 8.373048 CAAGTTATTTGTGTGTTCAGGTAGTA 57.627 34.615 0.00 0.00 31.92 1.82
1788 1820 8.547967 AGTTATTTGTGTGTTCAGGTAGTATG 57.452 34.615 0.00 0.00 0.00 2.39
1792 1824 3.070302 TGTGTGTTCAGGTAGTATGCACA 59.930 43.478 0.00 0.00 33.71 4.57
1915 1947 4.683832 AGAGATATTGTGACGTTACAGGC 58.316 43.478 13.22 4.85 0.00 4.85
2034 2067 5.987953 TCTGAAGTAGATCATAATGCTGTGC 59.012 40.000 0.00 0.00 0.00 4.57
2129 2163 5.634118 TCTCCCAGTGAGATGAAATTTTGT 58.366 37.500 0.00 0.00 45.29 2.83
2674 2709 9.294030 CATTGTTCTAATTGCTTTACTCCATTC 57.706 33.333 0.00 0.00 0.00 2.67
3285 3674 8.535335 TCTAACAGATCCCTATATGAATGAAGC 58.465 37.037 0.00 0.00 0.00 3.86
3509 3898 8.519526 TCAGTTGTAATGTTCTTTTCACAGTTT 58.480 29.630 0.00 0.00 0.00 2.66
3620 4009 2.250485 GCACGTCTGCAGCTGTTG 59.750 61.111 16.64 8.63 43.62 3.33
3713 4102 4.782156 TGCATCGCCGTAATAAATGAATG 58.218 39.130 0.00 0.00 0.00 2.67
4103 4513 0.322187 GGTGCCGTCCCTTGTTACAT 60.322 55.000 0.00 0.00 0.00 2.29
4145 4555 8.584063 TTTACAAGTCTGACCTTTTTACCTTT 57.416 30.769 3.76 0.00 0.00 3.11
4146 4556 6.451064 ACAAGTCTGACCTTTTTACCTTTG 57.549 37.500 3.76 1.28 0.00 2.77
4161 4571 1.246649 CTTTGTGCAGGCACCATACA 58.753 50.000 20.60 0.00 45.63 2.29
4320 4730 1.641577 CGTGCCTGTTCTTACTAGCC 58.358 55.000 0.00 0.00 0.00 3.93
4325 4735 2.356069 GCCTGTTCTTACTAGCCAATGC 59.644 50.000 0.00 0.00 37.95 3.56
4347 4757 3.397482 CCCGCTCTTTGATCTGAATAGG 58.603 50.000 0.00 0.00 0.00 2.57
4374 4784 1.281899 CTTTTCCTCCTGATCGCGTC 58.718 55.000 5.77 3.66 0.00 5.19
4469 4906 0.825010 CTTTTGTGCCACTCTGCCCT 60.825 55.000 0.00 0.00 0.00 5.19
4470 4907 1.108727 TTTTGTGCCACTCTGCCCTG 61.109 55.000 0.00 0.00 0.00 4.45
4471 4908 2.283143 TTTGTGCCACTCTGCCCTGT 62.283 55.000 0.00 0.00 0.00 4.00
4481 4918 2.290960 ACTCTGCCCTGTTGTTATTCCC 60.291 50.000 0.00 0.00 0.00 3.97
4513 4950 5.182001 GTGTGCTGAGAGTTGATGGTTAAAT 59.818 40.000 0.00 0.00 0.00 1.40
4514 4951 5.181811 TGTGCTGAGAGTTGATGGTTAAATG 59.818 40.000 0.00 0.00 0.00 2.32
4515 4952 4.156556 TGCTGAGAGTTGATGGTTAAATGC 59.843 41.667 0.00 0.00 0.00 3.56
4516 4953 4.156556 GCTGAGAGTTGATGGTTAAATGCA 59.843 41.667 0.00 0.00 0.00 3.96
4517 4954 5.675575 GCTGAGAGTTGATGGTTAAATGCAG 60.676 44.000 0.00 0.00 0.00 4.41
4523 4960 7.394359 AGAGTTGATGGTTAAATGCAGTATGTT 59.606 33.333 0.00 0.00 39.31 2.71
4549 4986 1.740296 CGGGAATCGGCTGTCGTTT 60.740 57.895 0.09 0.00 40.32 3.60
4558 4995 1.391485 CGGCTGTCGTTTCTGAATGAG 59.609 52.381 0.00 0.00 31.65 2.90
4561 4998 0.790207 TGTCGTTTCTGAATGAGCGC 59.210 50.000 0.00 0.00 31.65 5.92
4562 4999 0.246912 GTCGTTTCTGAATGAGCGCG 60.247 55.000 0.00 0.00 31.65 6.86
4599 5055 1.681264 CGATATTGGGGGAAAAGGCAC 59.319 52.381 0.00 0.00 0.00 5.01
4610 5066 0.035176 AAAAGGCACCCGCGTAGTTA 59.965 50.000 4.92 0.00 39.92 2.24
4615 5073 2.103601 AGGCACCCGCGTAGTTATTTAT 59.896 45.455 4.92 0.00 39.92 1.40
4616 5074 2.874086 GGCACCCGCGTAGTTATTTATT 59.126 45.455 4.92 0.00 39.92 1.40
4617 5075 3.313249 GGCACCCGCGTAGTTATTTATTT 59.687 43.478 4.92 0.00 39.92 1.40
4619 5077 5.179929 GGCACCCGCGTAGTTATTTATTTAT 59.820 40.000 4.92 0.00 39.92 1.40
4622 5080 7.321984 GCACCCGCGTAGTTATTTATTTATTTC 59.678 37.037 4.92 0.00 0.00 2.17
4624 5082 8.553696 ACCCGCGTAGTTATTTATTTATTTCTG 58.446 33.333 4.92 0.00 0.00 3.02
4635 5093 7.575414 TTTATTTATTTCTGCGAATAGGCCA 57.425 32.000 5.01 0.00 0.00 5.36
4636 5094 7.575414 TTATTTATTTCTGCGAATAGGCCAA 57.425 32.000 5.01 0.00 0.00 4.52
4637 5095 4.893424 TTATTTCTGCGAATAGGCCAAC 57.107 40.909 5.01 0.00 0.00 3.77
4638 5096 2.192664 TTTCTGCGAATAGGCCAACA 57.807 45.000 5.01 0.00 0.00 3.33
4639 5097 2.192664 TTCTGCGAATAGGCCAACAA 57.807 45.000 5.01 0.00 0.00 2.83
4640 5098 1.737838 TCTGCGAATAGGCCAACAAG 58.262 50.000 5.01 0.00 0.00 3.16
4643 5101 2.351726 CTGCGAATAGGCCAACAAGTAC 59.648 50.000 5.01 0.00 0.00 2.73
4644 5102 1.669265 GCGAATAGGCCAACAAGTACC 59.331 52.381 5.01 0.00 0.00 3.34
4647 5105 3.369052 CGAATAGGCCAACAAGTACCTGA 60.369 47.826 5.01 0.00 33.60 3.86
4650 5108 3.306472 AGGCCAACAAGTACCTGAAAA 57.694 42.857 5.01 0.00 0.00 2.29
4656 5157 3.832615 ACAAGTACCTGAAAACGGACT 57.167 42.857 0.00 0.00 0.00 3.85
4670 5171 3.059352 ACGGACTGAAGGAAGGAATTG 57.941 47.619 0.00 0.00 0.00 2.32
4697 5198 5.749596 AATCCGCATTCGTATTCAAATGA 57.250 34.783 0.00 0.00 35.35 2.57
4737 5238 7.701539 TTTACAGTCATACCAGCATTTTCAT 57.298 32.000 0.00 0.00 0.00 2.57
4746 5247 3.642848 ACCAGCATTTTCATGAGTTGGTT 59.357 39.130 13.34 1.82 37.64 3.67
4752 5253 4.669206 TTTTCATGAGTTGGTTGTGCAT 57.331 36.364 0.00 0.00 0.00 3.96
4853 5379 3.859386 GCCATCTAAACAGAAAATTGCCG 59.141 43.478 0.00 0.00 0.00 5.69
4869 5395 1.601903 TGCCGTGCTTCACAACTAAAG 59.398 47.619 0.00 0.00 33.40 1.85
4929 5463 0.593128 GAATTGCTTCGTGCCACACT 59.407 50.000 0.00 0.00 42.00 3.55
4930 5464 1.001378 GAATTGCTTCGTGCCACACTT 60.001 47.619 0.00 0.00 42.00 3.16
4931 5465 0.311790 ATTGCTTCGTGCCACACTTG 59.688 50.000 0.00 0.00 42.00 3.16
4932 5466 1.029408 TTGCTTCGTGCCACACTTGT 61.029 50.000 0.00 0.00 42.00 3.16
4933 5467 0.179070 TGCTTCGTGCCACACTTGTA 60.179 50.000 0.00 0.00 42.00 2.41
4934 5468 0.512952 GCTTCGTGCCACACTTGTAG 59.487 55.000 0.00 0.00 35.15 2.74
4935 5469 0.512952 CTTCGTGCCACACTTGTAGC 59.487 55.000 0.00 0.00 33.28 3.58
4936 5470 0.179070 TTCGTGCCACACTTGTAGCA 60.179 50.000 0.00 0.00 40.17 3.49
4939 5473 3.798794 TGCCACACTTGTAGCACTT 57.201 47.368 0.00 0.00 37.73 3.16
4940 5474 2.920724 TGCCACACTTGTAGCACTTA 57.079 45.000 0.00 0.00 37.73 2.24
4941 5475 3.417069 TGCCACACTTGTAGCACTTAT 57.583 42.857 0.00 0.00 37.73 1.73
4942 5476 3.334691 TGCCACACTTGTAGCACTTATC 58.665 45.455 0.00 0.00 37.73 1.75
4943 5477 3.244387 TGCCACACTTGTAGCACTTATCA 60.244 43.478 0.00 0.00 37.73 2.15
4944 5478 3.372206 GCCACACTTGTAGCACTTATCAG 59.628 47.826 0.00 0.00 32.91 2.90
4945 5479 3.935203 CCACACTTGTAGCACTTATCAGG 59.065 47.826 0.00 0.00 0.00 3.86
4946 5480 3.935203 CACACTTGTAGCACTTATCAGGG 59.065 47.826 0.00 0.00 0.00 4.45
4947 5481 3.583086 ACACTTGTAGCACTTATCAGGGT 59.417 43.478 0.00 0.00 0.00 4.34
4948 5482 3.935203 CACTTGTAGCACTTATCAGGGTG 59.065 47.826 0.00 0.00 36.62 4.61
4955 5489 3.340814 CACTTATCAGGGTGCTGAGTT 57.659 47.619 0.00 0.00 36.73 3.01
4956 5490 3.679389 CACTTATCAGGGTGCTGAGTTT 58.321 45.455 0.00 0.00 36.73 2.66
4957 5491 4.074970 CACTTATCAGGGTGCTGAGTTTT 58.925 43.478 0.00 0.00 36.73 2.43
4958 5492 4.520492 CACTTATCAGGGTGCTGAGTTTTT 59.480 41.667 0.00 0.00 36.73 1.94
4978 5512 5.549742 TTTTCCATTCTCCTGCAAAATGT 57.450 34.783 0.00 0.00 0.00 2.71
4979 5513 4.524316 TTCCATTCTCCTGCAAAATGTG 57.476 40.909 0.00 0.00 0.00 3.21
4980 5514 3.765381 TCCATTCTCCTGCAAAATGTGA 58.235 40.909 0.00 0.00 0.00 3.58
4981 5515 3.760151 TCCATTCTCCTGCAAAATGTGAG 59.240 43.478 0.00 0.00 0.00 3.51
4982 5516 3.508793 CCATTCTCCTGCAAAATGTGAGT 59.491 43.478 0.00 0.00 0.00 3.41
4983 5517 4.380233 CCATTCTCCTGCAAAATGTGAGTC 60.380 45.833 0.00 0.00 0.00 3.36
4984 5518 3.490439 TCTCCTGCAAAATGTGAGTCA 57.510 42.857 0.00 0.00 0.00 3.41
4985 5519 3.819368 TCTCCTGCAAAATGTGAGTCAA 58.181 40.909 0.00 0.00 0.00 3.18
4986 5520 3.817084 TCTCCTGCAAAATGTGAGTCAAG 59.183 43.478 0.00 0.00 0.00 3.02
4987 5521 2.294233 TCCTGCAAAATGTGAGTCAAGC 59.706 45.455 0.00 0.00 0.00 4.01
4988 5522 2.034939 CCTGCAAAATGTGAGTCAAGCA 59.965 45.455 0.00 0.00 0.00 3.91
4989 5523 3.305813 CCTGCAAAATGTGAGTCAAGCAT 60.306 43.478 0.00 0.00 0.00 3.79
4990 5524 3.644823 TGCAAAATGTGAGTCAAGCATG 58.355 40.909 0.00 0.00 0.00 4.06
4991 5525 2.410730 GCAAAATGTGAGTCAAGCATGC 59.589 45.455 10.51 10.51 0.00 4.06
4992 5526 3.644823 CAAAATGTGAGTCAAGCATGCA 58.355 40.909 21.98 0.00 0.00 3.96
4993 5527 4.052608 CAAAATGTGAGTCAAGCATGCAA 58.947 39.130 21.98 1.35 0.00 4.08
4994 5528 3.293311 AATGTGAGTCAAGCATGCAAC 57.707 42.857 21.98 14.60 0.00 4.17
4995 5529 0.953727 TGTGAGTCAAGCATGCAACC 59.046 50.000 21.98 4.47 0.00 3.77
4996 5530 0.242017 GTGAGTCAAGCATGCAACCC 59.758 55.000 21.98 6.46 0.00 4.11
4997 5531 0.178995 TGAGTCAAGCATGCAACCCA 60.179 50.000 21.98 9.14 0.00 4.51
4998 5532 0.524862 GAGTCAAGCATGCAACCCAG 59.475 55.000 21.98 2.63 0.00 4.45
4999 5533 0.896940 AGTCAAGCATGCAACCCAGG 60.897 55.000 21.98 0.74 0.00 4.45
5003 5537 4.073200 GCATGCAACCCAGGCCAC 62.073 66.667 14.21 0.00 45.05 5.01
5004 5538 2.601067 CATGCAACCCAGGCCACA 60.601 61.111 5.01 0.00 0.00 4.17
5005 5539 1.985662 CATGCAACCCAGGCCACAT 60.986 57.895 5.01 0.00 0.00 3.21
5006 5540 0.683828 CATGCAACCCAGGCCACATA 60.684 55.000 5.01 0.00 0.00 2.29
5007 5541 0.684153 ATGCAACCCAGGCCACATAC 60.684 55.000 5.01 0.00 0.00 2.39
5008 5542 1.304052 GCAACCCAGGCCACATACA 60.304 57.895 5.01 0.00 0.00 2.29
5009 5543 0.684153 GCAACCCAGGCCACATACAT 60.684 55.000 5.01 0.00 0.00 2.29
5010 5544 1.409521 GCAACCCAGGCCACATACATA 60.410 52.381 5.01 0.00 0.00 2.29
5011 5545 2.948147 GCAACCCAGGCCACATACATAA 60.948 50.000 5.01 0.00 0.00 1.90
5012 5546 3.360867 CAACCCAGGCCACATACATAAA 58.639 45.455 5.01 0.00 0.00 1.40
5013 5547 3.748645 ACCCAGGCCACATACATAAAA 57.251 42.857 5.01 0.00 0.00 1.52
5014 5548 3.361786 ACCCAGGCCACATACATAAAAC 58.638 45.455 5.01 0.00 0.00 2.43
5018 5552 3.632145 CAGGCCACATACATAAAACCTCC 59.368 47.826 5.01 0.00 0.00 4.30
5027 5561 7.334921 CACATACATAAAACCTCCTTTTACCGA 59.665 37.037 0.00 0.00 37.19 4.69
5031 5565 6.943718 ACATAAAACCTCCTTTTACCGATTCA 59.056 34.615 0.00 0.00 37.19 2.57
5062 5596 4.071423 CCAGTACAACATCCATCACACAA 58.929 43.478 0.00 0.00 0.00 3.33
5070 5604 4.343231 ACATCCATCACACAATGCCTTTA 58.657 39.130 0.00 0.00 0.00 1.85
5073 5607 5.798125 TCCATCACACAATGCCTTTAAAA 57.202 34.783 0.00 0.00 0.00 1.52
5074 5608 6.357579 TCCATCACACAATGCCTTTAAAAT 57.642 33.333 0.00 0.00 0.00 1.82
5075 5609 6.397272 TCCATCACACAATGCCTTTAAAATC 58.603 36.000 0.00 0.00 0.00 2.17
5076 5610 6.211184 TCCATCACACAATGCCTTTAAAATCT 59.789 34.615 0.00 0.00 0.00 2.40
5077 5611 7.395772 TCCATCACACAATGCCTTTAAAATCTA 59.604 33.333 0.00 0.00 0.00 1.98
5078 5612 8.199449 CCATCACACAATGCCTTTAAAATCTAT 58.801 33.333 0.00 0.00 0.00 1.98
5079 5613 9.027129 CATCACACAATGCCTTTAAAATCTATG 57.973 33.333 0.00 0.00 0.00 2.23
5080 5614 7.035004 TCACACAATGCCTTTAAAATCTATGC 58.965 34.615 0.00 0.00 0.00 3.14
5081 5615 6.812656 CACACAATGCCTTTAAAATCTATGCA 59.187 34.615 0.00 0.00 0.00 3.96
5082 5616 6.813152 ACACAATGCCTTTAAAATCTATGCAC 59.187 34.615 0.00 0.00 0.00 4.57
5083 5617 7.037438 CACAATGCCTTTAAAATCTATGCACT 58.963 34.615 0.00 0.00 0.00 4.40
5084 5618 7.546667 CACAATGCCTTTAAAATCTATGCACTT 59.453 33.333 0.00 0.00 0.00 3.16
5085 5619 8.096414 ACAATGCCTTTAAAATCTATGCACTTT 58.904 29.630 0.00 0.00 0.00 2.66
5086 5620 8.385111 CAATGCCTTTAAAATCTATGCACTTTG 58.615 33.333 0.00 0.00 0.00 2.77
5087 5621 6.991938 TGCCTTTAAAATCTATGCACTTTGT 58.008 32.000 0.00 0.00 0.00 2.83
5088 5622 8.116651 TGCCTTTAAAATCTATGCACTTTGTA 57.883 30.769 0.00 0.00 0.00 2.41
5089 5623 8.243426 TGCCTTTAAAATCTATGCACTTTGTAG 58.757 33.333 0.00 0.00 0.00 2.74
5090 5624 8.458843 GCCTTTAAAATCTATGCACTTTGTAGA 58.541 33.333 0.00 0.00 0.00 2.59
5095 5629 7.413475 AAATCTATGCACTTTGTAGATAGCG 57.587 36.000 7.11 0.00 34.88 4.26
5096 5630 4.871513 TCTATGCACTTTGTAGATAGCGG 58.128 43.478 0.00 0.00 0.00 5.52
5097 5631 2.309528 TGCACTTTGTAGATAGCGGG 57.690 50.000 0.00 0.00 0.00 6.13
5098 5632 1.134521 TGCACTTTGTAGATAGCGGGG 60.135 52.381 0.00 0.00 0.00 5.73
5099 5633 1.810412 GCACTTTGTAGATAGCGGGGG 60.810 57.143 0.00 0.00 0.00 5.40
5100 5634 0.468648 ACTTTGTAGATAGCGGGGGC 59.531 55.000 0.00 0.00 0.00 5.80
5101 5635 0.468226 CTTTGTAGATAGCGGGGGCA 59.532 55.000 0.00 0.00 0.00 5.36
5102 5636 0.913205 TTTGTAGATAGCGGGGGCAA 59.087 50.000 0.00 0.00 0.00 4.52
5103 5637 0.913205 TTGTAGATAGCGGGGGCAAA 59.087 50.000 0.00 0.00 0.00 3.68
5104 5638 0.913205 TGTAGATAGCGGGGGCAAAA 59.087 50.000 0.00 0.00 0.00 2.44
5105 5639 1.493022 TGTAGATAGCGGGGGCAAAAT 59.507 47.619 0.00 0.00 0.00 1.82
5106 5640 2.152016 GTAGATAGCGGGGGCAAAATC 58.848 52.381 0.00 0.00 0.00 2.17
5107 5641 0.178990 AGATAGCGGGGGCAAAATCC 60.179 55.000 0.00 0.00 0.00 3.01
5108 5642 0.178990 GATAGCGGGGGCAAAATCCT 60.179 55.000 0.00 0.00 0.00 3.24
5109 5643 0.261696 ATAGCGGGGGCAAAATCCTT 59.738 50.000 0.00 0.00 0.00 3.36
5110 5644 0.040499 TAGCGGGGGCAAAATCCTTT 59.960 50.000 0.00 0.00 0.00 3.11
5111 5645 0.835971 AGCGGGGGCAAAATCCTTTT 60.836 50.000 0.00 0.00 0.00 2.27
5112 5646 0.036164 GCGGGGGCAAAATCCTTTTT 59.964 50.000 0.00 0.00 35.41 1.94
5143 5677 0.685097 TGCACTTGTGGTCCTACTCC 59.315 55.000 2.81 0.00 0.00 3.85
5152 5686 6.479972 TTGTGGTCCTACTCCATAAGTATG 57.520 41.667 0.00 0.00 39.73 2.39
5158 5692 6.778559 GGTCCTACTCCATAAGTATGTCTCTT 59.221 42.308 0.00 0.00 39.73 2.85
5215 5749 7.989741 CACTTAAGTCAAATAGTGATCCCATCT 59.010 37.037 4.77 0.00 40.24 2.90
5218 5752 3.496130 GTCAAATAGTGATCCCATCTGCG 59.504 47.826 0.00 0.00 38.90 5.18
5222 5756 1.051008 AGTGATCCCATCTGCGCATA 58.949 50.000 12.24 3.38 0.00 3.14
5223 5757 1.151668 GTGATCCCATCTGCGCATAC 58.848 55.000 12.24 0.00 0.00 2.39
5247 5781 5.136068 TGACACATATTCTCTCTCCTCCT 57.864 43.478 0.00 0.00 0.00 3.69
5255 5789 7.786943 ACATATTCTCTCTCCTCCTAACAATGA 59.213 37.037 0.00 0.00 0.00 2.57
5261 5795 2.233922 CTCCTCCTAACAATGACACGGT 59.766 50.000 0.00 0.00 0.00 4.83
5264 5798 2.993899 CTCCTAACAATGACACGGTCAC 59.006 50.000 8.60 0.00 45.65 3.67
5268 5802 4.932799 CCTAACAATGACACGGTCACAATA 59.067 41.667 8.60 1.63 45.65 1.90
5273 5807 1.893137 TGACACGGTCACAATAGCTCT 59.107 47.619 0.00 0.00 37.67 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.329539 ATATGTGAGGCAGGCGGTGG 62.330 60.000 0.00 0.00 0.00 4.61
32 33 2.660064 GGCAGGAGTGTGGGACGAT 61.660 63.158 0.00 0.00 0.00 3.73
89 91 1.103803 TAGAGTGTTCGCTAGGGCAG 58.896 55.000 1.02 0.00 38.60 4.85
107 109 0.098200 CTCTGTTCGATGTCGCGGTA 59.902 55.000 6.13 0.00 39.60 4.02
124 126 1.812922 CCTCATGAGGCGTGTGCTC 60.813 63.158 28.45 0.00 42.44 4.26
162 164 1.372683 GAGTGGACAAGCCTCTGCA 59.627 57.895 0.00 0.00 40.48 4.41
163 165 0.035630 ATGAGTGGACAAGCCTCTGC 60.036 55.000 0.00 0.00 40.48 4.26
165 167 0.035630 GCATGAGTGGACAAGCCTCT 60.036 55.000 0.00 0.00 43.00 3.69
246 248 2.489073 GGGTGTCTGGTCAAATGGAAGT 60.489 50.000 0.00 0.00 0.00 3.01
304 307 0.324943 ATCAACAAGGTCTGTCGGGG 59.675 55.000 0.00 0.00 37.23 5.73
349 353 0.744874 TTCCCTATGCTCGTTCTCGG 59.255 55.000 0.00 0.00 37.69 4.63
479 483 4.023980 TCGTCTATCCAAGATTCACCTGT 58.976 43.478 0.00 0.00 36.36 4.00
495 499 1.134759 CCTCTCTCCGTGACTCGTCTA 60.135 57.143 0.00 0.00 37.94 2.59
507 511 1.219393 CTTCGGGTTGCCTCTCTCC 59.781 63.158 0.00 0.00 0.00 3.71
522 526 5.050023 GCTCAACTTTCTTGTCAGGTACTTC 60.050 44.000 0.00 0.00 34.60 3.01
532 537 3.356290 ACCTTGTGCTCAACTTTCTTGT 58.644 40.909 0.00 0.00 0.00 3.16
550 555 2.717639 GTGCAATCACTGGGATACCT 57.282 50.000 0.00 0.00 46.58 3.08
553 558 1.406751 CGTGGTGCAATCACTGGGATA 60.407 52.381 16.25 0.00 42.72 2.59
557 562 2.562912 GCGTGGTGCAATCACTGG 59.437 61.111 16.25 6.11 45.45 4.00
606 611 1.658686 CCGCTGCGAGTTCTACCTCT 61.659 60.000 25.45 0.00 0.00 3.69
611 616 1.211969 GTCACCGCTGCGAGTTCTA 59.788 57.895 25.45 5.03 0.00 2.10
673 679 3.057548 CTTGGCTGCCATGCGTCA 61.058 61.111 24.03 5.13 31.53 4.35
712 718 2.506472 GACGGCTGGGATCCTTCC 59.494 66.667 12.58 9.34 41.77 3.46
735 741 2.892425 GATCCAGCGTTCCTGCCG 60.892 66.667 0.00 0.00 40.36 5.69
740 746 2.582498 CGGTCGATCCAGCGTTCC 60.582 66.667 3.63 0.00 35.57 3.62
922 944 1.838073 CTTAGGGTTGGAGGCGGTGT 61.838 60.000 0.00 0.00 0.00 4.16
975 997 4.214327 CTCCCTCCCGCTTCGAGC 62.214 72.222 0.00 0.00 38.02 5.03
1233 1257 8.573035 CCTAAAACCTACAAAGCACTTGATTTA 58.427 33.333 5.64 3.44 38.50 1.40
1251 1275 0.888619 GCACAGGAAGGCCTAAAACC 59.111 55.000 5.16 7.95 44.80 3.27
1252 1276 1.813178 GAGCACAGGAAGGCCTAAAAC 59.187 52.381 5.16 0.00 44.80 2.43
1272 1299 6.364165 TCGAATAGTCTTAAAACACCTCAACG 59.636 38.462 0.00 0.00 0.00 4.10
1307 1334 3.260884 TCACCACAAGTTTCTAGGCCTAG 59.739 47.826 30.94 30.94 34.56 3.02
1330 1357 5.711506 TGCAGCTCCAATTTTCAATCTCTAA 59.288 36.000 0.00 0.00 0.00 2.10
1368 1395 1.304713 AGCATTGGTGGGCTCTTGG 60.305 57.895 0.00 0.00 34.76 3.61
1369 1396 1.601419 CCAGCATTGGTGGGCTCTTG 61.601 60.000 24.23 0.00 46.19 3.02
1381 1408 0.613853 ATGTGCAAGCTCCCAGCATT 60.614 50.000 6.41 0.00 45.56 3.56
1434 1461 7.362662 TGTAACATGAGAAGAAGCAATTCAAC 58.637 34.615 0.00 0.00 0.00 3.18
1551 1580 8.762481 AGTTTGGAACCAACTTTTATTCTACT 57.238 30.769 5.73 0.83 35.46 2.57
1572 1601 3.375299 GGCATTCTATCAAGCACGAGTTT 59.625 43.478 0.00 0.00 0.00 2.66
1573 1602 2.939103 GGCATTCTATCAAGCACGAGTT 59.061 45.455 0.00 0.00 0.00 3.01
1620 1649 8.725148 CAGAAGCTATGAATTTAGACACAAAGT 58.275 33.333 0.00 0.00 0.00 2.66
1631 1660 9.844257 AGCTAATACTTCAGAAGCTATGAATTT 57.156 29.630 10.33 10.33 41.56 1.82
1640 1670 5.293079 CAGTGGAAGCTAATACTTCAGAAGC 59.707 44.000 10.33 0.00 46.48 3.86
1684 1714 7.482169 ACTGAGAGATACAGGTTCATGTAAA 57.518 36.000 1.65 0.00 39.04 2.01
1695 1725 6.905544 TGTACTCGTAACTGAGAGATACAG 57.094 41.667 0.00 0.00 39.35 2.74
1699 1729 5.416326 AGCTTTGTACTCGTAACTGAGAGAT 59.584 40.000 0.00 0.00 39.35 2.75
1742 1772 9.691362 ATAACTTGTTTCGCTAATGTCAAAAAT 57.309 25.926 0.00 0.00 0.00 1.82
1807 1839 8.770438 AACATTATATTCGCCACAACAATTTT 57.230 26.923 0.00 0.00 0.00 1.82
2081 2114 3.651206 TGCAACCAATTAACACTGCATG 58.349 40.909 0.00 0.00 35.02 4.06
2129 2163 0.178992 AGGCCTTGTTAAGCACAGCA 60.179 50.000 0.00 0.00 36.48 4.41
2688 3076 4.037923 TGAAAAATGGAGTGAACTCTTGCC 59.962 41.667 10.17 0.00 42.48 4.52
3183 3572 4.732285 AACTGTGCTAAATCGTCAACAG 57.268 40.909 0.00 0.00 0.00 3.16
3285 3674 5.869344 TGTATTTCGTTCATGAAGACTCCTG 59.131 40.000 8.80 0.00 0.00 3.86
3509 3898 1.152943 AGGCCGCGAGAGAGATACA 60.153 57.895 8.23 0.00 0.00 2.29
3620 4009 7.331440 TGATGTTCAAATTGTTCATGCATTACC 59.669 33.333 0.00 0.00 0.00 2.85
3713 4102 9.436957 AATACGATTGTCATATCATTAGGGTTC 57.563 33.333 0.00 0.00 0.00 3.62
4103 4513 8.026396 ACTTGTAAAAAGTACTCCCTAACAGA 57.974 34.615 0.00 0.00 0.00 3.41
4146 4556 2.109431 CCATGTATGGTGCCTGCAC 58.891 57.895 13.75 13.75 43.05 4.57
4161 4571 0.757188 AGCTTCGTCCTCGGATCCAT 60.757 55.000 13.41 0.00 37.69 3.41
4253 4663 3.454587 AACCGCTGCGTTCCTCACA 62.455 57.895 21.59 0.00 0.00 3.58
4320 4730 0.383231 GATCAAAGAGCGGGGCATTG 59.617 55.000 0.00 0.00 0.00 2.82
4325 4735 2.338577 ATTCAGATCAAAGAGCGGGG 57.661 50.000 0.00 0.00 0.00 5.73
4347 4757 3.287867 TCAGGAGGAAAAGGATGATGC 57.712 47.619 0.00 0.00 0.00 3.91
4374 4784 1.265635 CAGTAGCCTAGTGAGCTAGCG 59.734 57.143 9.55 0.00 43.26 4.26
4469 4906 1.883275 CCAGCAACGGGAATAACAACA 59.117 47.619 0.00 0.00 0.00 3.33
4470 4907 1.883926 ACCAGCAACGGGAATAACAAC 59.116 47.619 0.00 0.00 0.00 3.32
4471 4908 1.883275 CACCAGCAACGGGAATAACAA 59.117 47.619 0.00 0.00 0.00 2.83
4481 4918 1.563435 CTCTCAGCACACCAGCAACG 61.563 60.000 0.00 0.00 36.85 4.10
4513 4950 2.354303 CCCGGACTAACAACATACTGCA 60.354 50.000 0.73 0.00 0.00 4.41
4514 4951 2.093869 TCCCGGACTAACAACATACTGC 60.094 50.000 0.73 0.00 0.00 4.40
4515 4952 3.880047 TCCCGGACTAACAACATACTG 57.120 47.619 0.73 0.00 0.00 2.74
4516 4953 4.441079 CGATTCCCGGACTAACAACATACT 60.441 45.833 0.73 0.00 33.91 2.12
4517 4954 3.800506 CGATTCCCGGACTAACAACATAC 59.199 47.826 0.73 0.00 33.91 2.39
4549 4986 1.032794 AGTATCCGCGCTCATTCAGA 58.967 50.000 5.56 0.00 0.00 3.27
4558 4995 2.511600 AAGTGCCAGTATCCGCGC 60.512 61.111 0.00 0.00 35.72 6.86
4561 4998 1.819632 GCCCAAGTGCCAGTATCCG 60.820 63.158 0.00 0.00 0.00 4.18
4562 4999 1.819632 CGCCCAAGTGCCAGTATCC 60.820 63.158 0.00 0.00 0.00 2.59
4580 5017 2.039418 GGTGCCTTTTCCCCCAATATC 58.961 52.381 0.00 0.00 0.00 1.63
4599 5055 7.532884 GCAGAAATAAATAAATAACTACGCGGG 59.467 37.037 12.47 5.29 0.00 6.13
4610 5066 8.177119 TGGCCTATTCGCAGAAATAAATAAAT 57.823 30.769 3.32 0.00 45.90 1.40
4615 5073 4.702612 TGTTGGCCTATTCGCAGAAATAAA 59.297 37.500 3.32 0.00 45.90 1.40
4616 5074 4.265893 TGTTGGCCTATTCGCAGAAATAA 58.734 39.130 3.32 0.00 45.90 1.40
4617 5075 3.879998 TGTTGGCCTATTCGCAGAAATA 58.120 40.909 3.32 0.00 45.90 1.40
4619 5077 2.192664 TGTTGGCCTATTCGCAGAAA 57.807 45.000 3.32 0.00 45.90 2.52
4622 5080 1.453155 ACTTGTTGGCCTATTCGCAG 58.547 50.000 3.32 0.00 0.00 5.18
4624 5082 1.669265 GGTACTTGTTGGCCTATTCGC 59.331 52.381 3.32 0.00 0.00 4.70
4634 5092 3.875134 AGTCCGTTTTCAGGTACTTGTTG 59.125 43.478 4.75 0.00 34.60 3.33
4635 5093 3.875134 CAGTCCGTTTTCAGGTACTTGTT 59.125 43.478 4.75 0.00 34.60 2.83
4636 5094 3.133362 TCAGTCCGTTTTCAGGTACTTGT 59.867 43.478 4.75 0.00 34.60 3.16
4637 5095 3.724374 TCAGTCCGTTTTCAGGTACTTG 58.276 45.455 0.00 0.00 34.60 3.16
4638 5096 4.377897 CTTCAGTCCGTTTTCAGGTACTT 58.622 43.478 0.00 0.00 34.60 2.24
4639 5097 3.244112 CCTTCAGTCCGTTTTCAGGTACT 60.244 47.826 0.00 0.00 43.88 2.73
4640 5098 3.064931 CCTTCAGTCCGTTTTCAGGTAC 58.935 50.000 0.00 0.00 0.00 3.34
4643 5101 2.543777 TCCTTCAGTCCGTTTTCAGG 57.456 50.000 0.00 0.00 0.00 3.86
4644 5102 2.808543 CCTTCCTTCAGTCCGTTTTCAG 59.191 50.000 0.00 0.00 0.00 3.02
4647 5105 3.570912 TTCCTTCCTTCAGTCCGTTTT 57.429 42.857 0.00 0.00 0.00 2.43
4650 5108 2.876079 GCAATTCCTTCCTTCAGTCCGT 60.876 50.000 0.00 0.00 0.00 4.69
4656 5157 4.895297 GGATTATGGCAATTCCTTCCTTCA 59.105 41.667 0.00 0.00 35.26 3.02
4726 5227 4.446385 CACAACCAACTCATGAAAATGCTG 59.554 41.667 0.00 0.05 0.00 4.41
4737 5238 6.403866 AAGAAAATATGCACAACCAACTCA 57.596 33.333 0.00 0.00 0.00 3.41
4824 5350 9.474920 CAATTTTCTGTTTAGATGGCAAGTTTA 57.525 29.630 0.00 0.00 31.81 2.01
4828 5354 5.349543 GGCAATTTTCTGTTTAGATGGCAAG 59.650 40.000 0.00 0.00 35.81 4.01
4833 5359 4.324402 GCACGGCAATTTTCTGTTTAGATG 59.676 41.667 0.00 0.00 31.81 2.90
4837 5363 4.202060 TGAAGCACGGCAATTTTCTGTTTA 60.202 37.500 0.00 0.00 0.00 2.01
4847 5373 1.890876 TAGTTGTGAAGCACGGCAAT 58.109 45.000 0.00 0.00 37.14 3.56
4869 5395 4.319694 GCAAGTTTCAATTTGGATGGCAAC 60.320 41.667 0.00 0.00 0.00 4.17
4872 5398 3.401182 TGCAAGTTTCAATTTGGATGGC 58.599 40.909 0.00 0.00 0.00 4.40
4901 5431 0.179189 CGAAGCAATTCCGCCTTGAC 60.179 55.000 0.00 0.00 0.00 3.18
4902 5432 0.605319 ACGAAGCAATTCCGCCTTGA 60.605 50.000 0.00 0.00 0.00 3.02
4903 5433 0.454957 CACGAAGCAATTCCGCCTTG 60.455 55.000 0.00 0.00 0.00 3.61
4904 5434 1.875963 CACGAAGCAATTCCGCCTT 59.124 52.632 0.00 0.00 0.00 4.35
4906 5436 2.202479 GCACGAAGCAATTCCGCC 60.202 61.111 0.00 0.00 44.79 6.13
4935 5469 3.340814 AACTCAGCACCCTGATAAGTG 57.659 47.619 0.00 0.00 46.44 3.16
4936 5470 4.373156 AAAACTCAGCACCCTGATAAGT 57.627 40.909 0.00 0.00 46.44 2.24
4957 5491 4.588106 TCACATTTTGCAGGAGAATGGAAA 59.412 37.500 9.60 0.00 38.53 3.13
4958 5492 4.151121 TCACATTTTGCAGGAGAATGGAA 58.849 39.130 9.60 0.00 35.60 3.53
4959 5493 3.760151 CTCACATTTTGCAGGAGAATGGA 59.240 43.478 9.60 4.00 35.60 3.41
4960 5494 3.508793 ACTCACATTTTGCAGGAGAATGG 59.491 43.478 9.60 0.28 35.60 3.16
4961 5495 4.216902 TGACTCACATTTTGCAGGAGAATG 59.783 41.667 3.86 3.86 36.95 2.67
4962 5496 4.401022 TGACTCACATTTTGCAGGAGAAT 58.599 39.130 0.00 0.00 0.00 2.40
4963 5497 3.819368 TGACTCACATTTTGCAGGAGAA 58.181 40.909 0.00 0.00 0.00 2.87
4964 5498 3.490439 TGACTCACATTTTGCAGGAGA 57.510 42.857 0.00 0.00 0.00 3.71
4965 5499 3.611057 GCTTGACTCACATTTTGCAGGAG 60.611 47.826 0.00 0.00 0.00 3.69
4966 5500 2.294233 GCTTGACTCACATTTTGCAGGA 59.706 45.455 0.00 0.00 0.00 3.86
4967 5501 2.034939 TGCTTGACTCACATTTTGCAGG 59.965 45.455 0.00 0.00 0.00 4.85
4968 5502 3.358707 TGCTTGACTCACATTTTGCAG 57.641 42.857 0.00 0.00 0.00 4.41
4969 5503 3.644823 CATGCTTGACTCACATTTTGCA 58.355 40.909 0.00 0.00 0.00 4.08
4970 5504 2.410730 GCATGCTTGACTCACATTTTGC 59.589 45.455 11.37 0.00 0.00 3.68
4971 5505 3.644823 TGCATGCTTGACTCACATTTTG 58.355 40.909 20.33 0.00 0.00 2.44
4972 5506 4.053295 GTTGCATGCTTGACTCACATTTT 58.947 39.130 20.33 0.00 0.00 1.82
4973 5507 3.553508 GGTTGCATGCTTGACTCACATTT 60.554 43.478 20.33 0.00 0.00 2.32
4974 5508 2.029649 GGTTGCATGCTTGACTCACATT 60.030 45.455 20.33 0.00 0.00 2.71
4975 5509 1.542915 GGTTGCATGCTTGACTCACAT 59.457 47.619 20.33 0.00 0.00 3.21
4976 5510 0.953727 GGTTGCATGCTTGACTCACA 59.046 50.000 20.33 0.00 0.00 3.58
4977 5511 0.242017 GGGTTGCATGCTTGACTCAC 59.758 55.000 20.33 4.08 0.00 3.51
4978 5512 0.178995 TGGGTTGCATGCTTGACTCA 60.179 50.000 20.33 17.17 0.00 3.41
4979 5513 0.524862 CTGGGTTGCATGCTTGACTC 59.475 55.000 20.33 14.81 0.00 3.36
4980 5514 0.896940 CCTGGGTTGCATGCTTGACT 60.897 55.000 20.33 0.00 0.00 3.41
4981 5515 1.588082 CCTGGGTTGCATGCTTGAC 59.412 57.895 20.33 14.18 0.00 3.18
4982 5516 2.277591 GCCTGGGTTGCATGCTTGA 61.278 57.895 20.33 1.79 0.00 3.02
4983 5517 2.263540 GCCTGGGTTGCATGCTTG 59.736 61.111 20.33 2.54 0.00 4.01
4984 5518 2.999063 GGCCTGGGTTGCATGCTT 60.999 61.111 20.33 0.00 0.00 3.91
4985 5519 4.304413 TGGCCTGGGTTGCATGCT 62.304 61.111 20.33 0.00 0.00 3.79
4986 5520 4.073200 GTGGCCTGGGTTGCATGC 62.073 66.667 11.82 11.82 0.00 4.06
4987 5521 0.683828 TATGTGGCCTGGGTTGCATG 60.684 55.000 3.32 0.00 0.00 4.06
4988 5522 0.684153 GTATGTGGCCTGGGTTGCAT 60.684 55.000 3.32 0.00 0.00 3.96
4989 5523 1.304052 GTATGTGGCCTGGGTTGCA 60.304 57.895 3.32 0.00 0.00 4.08
4990 5524 0.684153 ATGTATGTGGCCTGGGTTGC 60.684 55.000 3.32 0.00 0.00 4.17
4991 5525 2.727123 TATGTATGTGGCCTGGGTTG 57.273 50.000 3.32 0.00 0.00 3.77
4992 5526 3.748645 TTTATGTATGTGGCCTGGGTT 57.251 42.857 3.32 0.00 0.00 4.11
4993 5527 3.361786 GTTTTATGTATGTGGCCTGGGT 58.638 45.455 3.32 0.00 0.00 4.51
4994 5528 2.693074 GGTTTTATGTATGTGGCCTGGG 59.307 50.000 3.32 0.00 0.00 4.45
4995 5529 3.631250 AGGTTTTATGTATGTGGCCTGG 58.369 45.455 3.32 0.00 0.00 4.45
4996 5530 3.632145 GGAGGTTTTATGTATGTGGCCTG 59.368 47.826 3.32 0.00 0.00 4.85
4997 5531 3.527665 AGGAGGTTTTATGTATGTGGCCT 59.472 43.478 3.32 0.00 0.00 5.19
4998 5532 3.898482 AGGAGGTTTTATGTATGTGGCC 58.102 45.455 0.00 0.00 0.00 5.36
4999 5533 5.914898 AAAGGAGGTTTTATGTATGTGGC 57.085 39.130 0.00 0.00 0.00 5.01
5000 5534 7.414762 CGGTAAAAGGAGGTTTTATGTATGTGG 60.415 40.741 0.00 0.00 41.59 4.17
5001 5535 7.334921 TCGGTAAAAGGAGGTTTTATGTATGTG 59.665 37.037 0.00 0.00 41.59 3.21
5002 5536 7.396418 TCGGTAAAAGGAGGTTTTATGTATGT 58.604 34.615 0.00 0.00 41.59 2.29
5003 5537 7.852971 TCGGTAAAAGGAGGTTTTATGTATG 57.147 36.000 0.00 0.00 41.59 2.39
5004 5538 9.117183 GAATCGGTAAAAGGAGGTTTTATGTAT 57.883 33.333 0.00 0.00 41.59 2.29
5005 5539 8.102047 TGAATCGGTAAAAGGAGGTTTTATGTA 58.898 33.333 0.00 0.00 41.59 2.29
5006 5540 6.943718 TGAATCGGTAAAAGGAGGTTTTATGT 59.056 34.615 0.00 0.00 41.59 2.29
5007 5541 7.385778 TGAATCGGTAAAAGGAGGTTTTATG 57.614 36.000 0.00 0.00 41.59 1.90
5008 5542 6.602009 CCTGAATCGGTAAAAGGAGGTTTTAT 59.398 38.462 0.00 0.00 41.59 1.40
5009 5543 5.941647 CCTGAATCGGTAAAAGGAGGTTTTA 59.058 40.000 0.00 0.00 39.23 1.52
5010 5544 4.765339 CCTGAATCGGTAAAAGGAGGTTTT 59.235 41.667 0.00 0.00 41.45 2.43
5011 5545 4.202535 ACCTGAATCGGTAAAAGGAGGTTT 60.203 41.667 0.00 0.00 34.94 3.27
5012 5546 3.329814 ACCTGAATCGGTAAAAGGAGGTT 59.670 43.478 0.00 0.00 34.94 3.50
5013 5547 2.910977 ACCTGAATCGGTAAAAGGAGGT 59.089 45.455 0.00 0.00 34.94 3.85
5014 5548 3.629142 ACCTGAATCGGTAAAAGGAGG 57.371 47.619 0.00 0.00 34.94 4.30
5018 5552 6.342906 TGGTACATACCTGAATCGGTAAAAG 58.657 40.000 9.46 4.94 46.58 2.27
5027 5561 6.614694 TGTTGTACTGGTACATACCTGAAT 57.385 37.500 18.72 3.43 46.58 2.57
5031 5565 5.027460 TGGATGTTGTACTGGTACATACCT 58.973 41.667 13.34 8.32 46.58 3.08
5042 5576 4.156556 GCATTGTGTGATGGATGTTGTACT 59.843 41.667 0.00 0.00 0.00 2.73
5055 5589 7.035004 GCATAGATTTTAAAGGCATTGTGTGA 58.965 34.615 0.00 0.00 0.00 3.58
5062 5596 7.614494 ACAAAGTGCATAGATTTTAAAGGCAT 58.386 30.769 0.00 0.00 31.92 4.40
5070 5604 7.041780 CCGCTATCTACAAAGTGCATAGATTTT 60.042 37.037 11.09 0.00 37.03 1.82
5073 5607 5.473931 CCGCTATCTACAAAGTGCATAGAT 58.526 41.667 10.72 10.72 38.78 1.98
5074 5608 4.262036 CCCGCTATCTACAAAGTGCATAGA 60.262 45.833 0.00 0.00 0.00 1.98
5075 5609 3.990469 CCCGCTATCTACAAAGTGCATAG 59.010 47.826 0.00 0.00 0.00 2.23
5076 5610 3.244078 CCCCGCTATCTACAAAGTGCATA 60.244 47.826 0.00 0.00 0.00 3.14
5077 5611 2.485479 CCCCGCTATCTACAAAGTGCAT 60.485 50.000 0.00 0.00 0.00 3.96
5078 5612 1.134521 CCCCGCTATCTACAAAGTGCA 60.135 52.381 0.00 0.00 0.00 4.57
5079 5613 1.583054 CCCCGCTATCTACAAAGTGC 58.417 55.000 0.00 0.00 0.00 4.40
5080 5614 1.810412 GCCCCCGCTATCTACAAAGTG 60.810 57.143 0.00 0.00 0.00 3.16
5081 5615 0.468648 GCCCCCGCTATCTACAAAGT 59.531 55.000 0.00 0.00 0.00 2.66
5082 5616 0.468226 TGCCCCCGCTATCTACAAAG 59.532 55.000 0.00 0.00 35.36 2.77
5083 5617 0.913205 TTGCCCCCGCTATCTACAAA 59.087 50.000 0.00 0.00 35.36 2.83
5084 5618 0.913205 TTTGCCCCCGCTATCTACAA 59.087 50.000 0.00 0.00 35.36 2.41
5085 5619 0.913205 TTTTGCCCCCGCTATCTACA 59.087 50.000 0.00 0.00 35.36 2.74
5086 5620 2.152016 GATTTTGCCCCCGCTATCTAC 58.848 52.381 0.00 0.00 35.36 2.59
5087 5621 1.073284 GGATTTTGCCCCCGCTATCTA 59.927 52.381 0.00 0.00 35.36 1.98
5088 5622 0.178990 GGATTTTGCCCCCGCTATCT 60.179 55.000 0.00 0.00 35.36 1.98
5089 5623 0.178990 AGGATTTTGCCCCCGCTATC 60.179 55.000 0.00 0.00 35.36 2.08
5090 5624 0.261696 AAGGATTTTGCCCCCGCTAT 59.738 50.000 0.00 0.00 35.36 2.97
5091 5625 0.040499 AAAGGATTTTGCCCCCGCTA 59.960 50.000 0.00 0.00 31.62 4.26
5092 5626 1.229177 AAAGGATTTTGCCCCCGCT 60.229 52.632 0.00 0.00 31.62 5.52
5093 5627 3.387716 AAAGGATTTTGCCCCCGC 58.612 55.556 0.00 0.00 31.62 6.13
5109 5643 8.200792 ACCACAAGTGCATAGATTTTACAAAAA 58.799 29.630 0.00 0.00 0.00 1.94
5110 5644 7.721402 ACCACAAGTGCATAGATTTTACAAAA 58.279 30.769 0.00 0.00 0.00 2.44
5111 5645 7.283625 ACCACAAGTGCATAGATTTTACAAA 57.716 32.000 0.00 0.00 0.00 2.83
5112 5646 6.072175 GGACCACAAGTGCATAGATTTTACAA 60.072 38.462 0.00 0.00 36.67 2.41
5113 5647 5.414454 GGACCACAAGTGCATAGATTTTACA 59.586 40.000 0.00 0.00 36.67 2.41
5114 5648 5.648092 AGGACCACAAGTGCATAGATTTTAC 59.352 40.000 0.00 0.00 39.79 2.01
5115 5649 5.815581 AGGACCACAAGTGCATAGATTTTA 58.184 37.500 0.00 0.00 39.79 1.52
5116 5650 4.666512 AGGACCACAAGTGCATAGATTTT 58.333 39.130 0.00 0.00 39.79 1.82
5117 5651 4.307032 AGGACCACAAGTGCATAGATTT 57.693 40.909 0.00 0.00 39.79 2.17
5118 5652 4.471386 AGTAGGACCACAAGTGCATAGATT 59.529 41.667 0.00 0.00 39.79 2.40
5128 5662 6.098409 ACATACTTATGGAGTAGGACCACAAG 59.902 42.308 0.00 0.00 43.56 3.16
5132 5666 6.027025 AGACATACTTATGGAGTAGGACCA 57.973 41.667 8.97 0.00 43.56 4.02
5215 5749 4.379652 AGAATATGTGTCATGTATGCGCA 58.620 39.130 14.96 14.96 0.00 6.09
5218 5752 6.589523 GGAGAGAGAATATGTGTCATGTATGC 59.410 42.308 0.00 0.00 0.00 3.14
5222 5756 5.304101 GGAGGAGAGAGAATATGTGTCATGT 59.696 44.000 0.00 0.00 0.00 3.21
5223 5757 5.539574 AGGAGGAGAGAGAATATGTGTCATG 59.460 44.000 0.00 0.00 0.00 3.07
5247 5781 4.390603 GCTATTGTGACCGTGTCATTGTTA 59.609 41.667 9.47 1.57 44.63 2.41
5255 5789 1.893137 TGAGAGCTATTGTGACCGTGT 59.107 47.619 0.00 0.00 0.00 4.49
5261 5795 3.894427 GGGAGAGATGAGAGCTATTGTGA 59.106 47.826 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.