Multiple sequence alignment - TraesCS2D01G505300

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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 TraesCS2D01G505300 chr2D 100.000 5284 0 0 495 5778 599295575 599290292 0.000000e+00 9758.0
1 TraesCS2D01G505300 chr2D 85.852 622 61 18 2695 3301 80249965 80249356 2.270000e-178 636.0
2 TraesCS2D01G505300 chr2D 100.000 125 0 0 1 125 599296069 599295945 1.250000e-56 231.0
3 TraesCS2D01G505300 chr2D 91.463 164 13 1 1844 2007 599293545 599293383 2.100000e-54 224.0
4 TraesCS2D01G505300 chr2D 91.463 164 13 1 2525 2687 599294226 599294063 2.100000e-54 224.0
5 TraesCS2D01G505300 chr2D 94.505 91 5 0 2103 2193 599293372 599293282 2.170000e-29 141.0
6 TraesCS2D01G505300 chr2D 94.505 91 5 0 2698 2788 599293967 599293877 2.170000e-29 141.0
7 TraesCS2D01G505300 chr2D 86.538 104 8 3 2005 2102 367506396 367506499 6.120000e-20 110.0
8 TraesCS2D01G505300 chr2D 85.484 62 8 1 604 664 131303933 131303872 4.830000e-06 63.9
9 TraesCS2D01G505300 chr2D 86.207 58 4 4 3710 3766 246544361 246544415 6.250000e-05 60.2
10 TraesCS2D01G505300 chr2A 95.877 4632 129 24 712 5325 733399026 733394439 0.000000e+00 7439.0
11 TraesCS2D01G505300 chr2A 89.815 216 16 3 509 724 733399253 733399044 7.380000e-69 272.0
12 TraesCS2D01G505300 chr2A 92.025 163 13 0 2525 2687 733397910 733397748 4.500000e-56 230.0
13 TraesCS2D01G505300 chr2A 90.244 164 15 1 1844 2007 733397230 733397068 4.540000e-51 213.0
14 TraesCS2D01G505300 chr2A 79.630 324 27 15 5475 5778 733394397 733394093 4.570000e-46 196.0
15 TraesCS2D01G505300 chr2A 95.604 91 4 0 2103 2193 733397057 733396967 4.670000e-31 147.0
16 TraesCS2D01G505300 chr2A 94.505 91 5 0 2698 2788 733397652 733397562 2.170000e-29 141.0
17 TraesCS2D01G505300 chr2A 88.235 102 9 3 2000 2099 34324924 34324824 1.020000e-22 119.0
18 TraesCS2D01G505300 chr2B 94.344 4827 126 46 509 5265 728759892 728755143 0.000000e+00 7265.0
19 TraesCS2D01G505300 chr2B 87.344 640 51 19 677 1309 728762937 728762321 0.000000e+00 706.0
20 TraesCS2D01G505300 chr2B 85.938 448 18 15 5363 5777 728755123 728754688 2.470000e-118 436.0
21 TraesCS2D01G505300 chr2B 91.429 175 14 1 2514 2687 728758588 728758414 7.480000e-59 239.0
22 TraesCS2D01G505300 chr2B 90.854 164 14 1 1844 2007 728757886 728757724 9.750000e-53 219.0
23 TraesCS2D01G505300 chr2B 95.604 91 4 0 2103 2193 728757713 728757623 4.670000e-31 147.0
24 TraesCS2D01G505300 chr2B 86.607 112 8 6 1997 2102 601206954 601206844 3.660000e-22 117.0
25 TraesCS2D01G505300 chr1B 93.353 331 20 2 2191 2520 440055242 440054913 6.730000e-134 488.0
26 TraesCS2D01G505300 chr1B 89.831 59 5 1 607 664 530999100 530999042 2.230000e-09 75.0
27 TraesCS2D01G505300 chr1B 82.667 75 9 4 594 664 653825211 653825285 4.830000e-06 63.9
28 TraesCS2D01G505300 chr6A 90.634 331 23 4 2191 2520 115322146 115322469 3.200000e-117 433.0
29 TraesCS2D01G505300 chr6A 87.324 71 5 4 597 664 562265169 562265238 1.730000e-10 78.7
30 TraesCS2D01G505300 chr3B 89.362 94 9 1 7 100 755234964 755234872 3.660000e-22 117.0
31 TraesCS2D01G505300 chr3D 85.321 109 11 2 1999 2102 320429034 320429142 2.200000e-19 108.0
32 TraesCS2D01G505300 chr3D 84.167 120 8 9 1997 2108 277764766 277764882 7.920000e-19 106.0
33 TraesCS2D01G505300 chr3D 87.719 57 6 1 607 662 497712593 497712649 1.340000e-06 65.8
34 TraesCS2D01G505300 chr5D 83.333 120 12 5 1987 2099 228447080 228446962 2.850000e-18 104.0
35 TraesCS2D01G505300 chrUn 83.495 103 15 2 2194 2295 17285868 17285969 1.710000e-15 95.3
36 TraesCS2D01G505300 chr5A 97.561 41 1 0 3732 3772 313311122 313311162 2.890000e-08 71.3
37 TraesCS2D01G505300 chr5A 92.000 50 2 2 3730 3778 269770297 269770249 1.040000e-07 69.4
38 TraesCS2D01G505300 chr5A 95.349 43 1 1 3730 3772 705592610 705592569 3.740000e-07 67.6
39 TraesCS2D01G505300 chr4D 90.909 55 2 3 3714 3766 237615866 237615813 2.890000e-08 71.3
40 TraesCS2D01G505300 chr4B 95.349 43 1 1 3730 3772 665610854 665610813 3.740000e-07 67.6
41 TraesCS2D01G505300 chr1A 95.238 42 2 0 3731 3772 171007971 171007930 3.740000e-07 67.6
42 TraesCS2D01G505300 chr4A 86.667 60 7 1 606 664 741064431 741064372 1.340000e-06 65.8
43 TraesCS2D01G505300 chr4A 86.667 60 7 1 606 664 741078463 741078404 1.340000e-06 65.8


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 TraesCS2D01G505300 chr2D 599290292 599296069 5777 True 1786.5 9758 95.322667 1 5778 6 chr2D.!!$R3 5777
1 TraesCS2D01G505300 chr2D 80249356 80249965 609 True 636.0 636 85.852000 2695 3301 1 chr2D.!!$R1 606
2 TraesCS2D01G505300 chr2A 733394093 733399253 5160 True 1234.0 7439 91.100000 509 5778 7 chr2A.!!$R2 5269
3 TraesCS2D01G505300 chr2B 728754688 728762937 8249 True 1502.0 7265 90.918833 509 5777 6 chr2B.!!$R2 5268

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
793 3366 0.321653 ACTCACGGATTGGAAGGCAC 60.322 55.000 0.0 0.0 0.00 5.01 F
1426 4010 0.821517 CCCCGCCCCTGTTTATTTTC 59.178 55.000 0.0 0.0 0.00 2.29 F
1771 4358 1.065854 AGCTTGCTGACATACTGGGTC 60.066 52.381 0.0 0.0 35.83 4.46 F
2932 5544 1.602311 CTGGTTATGGATGCTGGCTC 58.398 55.000 0.0 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2656 5266 0.250727 TCCAAAACAGGGAGGCGAAG 60.251 55.000 0.0 0.0 0.00 3.79 R
2932 5544 4.216902 TGAGTTGAAACATCAATGCCTGAG 59.783 41.667 0.0 0.0 37.52 3.35 R
3760 6383 1.140052 TCCCTCTGTCTTGCGAAAACA 59.860 47.619 0.0 0.0 0.00 2.83 R
4833 7489 2.642139 AAGTGATGAAATGGCTTGCG 57.358 45.000 0.0 0.0 0.00 4.85 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 2.837532 TCCTTTTGGGCTTGATTTGC 57.162 45.000 0.00 0.00 40.87 3.68
22 23 2.328319 TCCTTTTGGGCTTGATTTGCT 58.672 42.857 0.00 0.00 40.87 3.91
23 24 2.037511 TCCTTTTGGGCTTGATTTGCTG 59.962 45.455 0.00 0.00 40.87 4.41
24 25 1.802365 CTTTTGGGCTTGATTTGCTGC 59.198 47.619 0.00 0.00 0.00 5.25
25 26 1.050204 TTTGGGCTTGATTTGCTGCT 58.950 45.000 0.00 0.00 0.00 4.24
26 27 0.604578 TTGGGCTTGATTTGCTGCTC 59.395 50.000 0.00 0.00 0.00 4.26
29 30 1.515736 GCTTGATTTGCTGCTCGCC 60.516 57.895 0.00 0.00 38.05 5.54
30 31 1.138247 CTTGATTTGCTGCTCGCCC 59.862 57.895 0.00 0.00 38.05 6.13
31 32 2.275547 CTTGATTTGCTGCTCGCCCC 62.276 60.000 0.00 0.00 38.05 5.80
32 33 2.751436 GATTTGCTGCTCGCCCCA 60.751 61.111 0.00 0.00 38.05 4.96
33 34 2.753043 ATTTGCTGCTCGCCCCAG 60.753 61.111 0.00 0.00 38.05 4.45
39 40 4.349503 TGCTCGCCCCAGCATTGT 62.350 61.111 0.00 0.00 44.73 2.71
40 41 3.818787 GCTCGCCCCAGCATTGTG 61.819 66.667 0.00 0.00 39.43 3.33
41 42 2.360350 CTCGCCCCAGCATTGTGT 60.360 61.111 0.00 0.00 39.83 3.72
42 43 1.973281 CTCGCCCCAGCATTGTGTT 60.973 57.895 0.00 0.00 39.83 3.32
43 44 2.203972 CTCGCCCCAGCATTGTGTTG 62.204 60.000 0.00 0.00 39.83 3.33
44 45 2.563798 CGCCCCAGCATTGTGTTGT 61.564 57.895 0.00 0.00 39.83 3.32
45 46 1.005867 GCCCCAGCATTGTGTTGTG 60.006 57.895 0.00 0.00 39.53 3.33
46 47 1.747325 GCCCCAGCATTGTGTTGTGT 61.747 55.000 0.00 0.00 39.53 3.72
47 48 1.614996 CCCCAGCATTGTGTTGTGTA 58.385 50.000 0.00 0.00 0.00 2.90
48 49 1.269448 CCCCAGCATTGTGTTGTGTAC 59.731 52.381 0.00 0.00 0.00 2.90
49 50 1.952990 CCCAGCATTGTGTTGTGTACA 59.047 47.619 0.00 0.00 0.00 2.90
50 51 2.360483 CCCAGCATTGTGTTGTGTACAA 59.640 45.455 0.00 0.00 41.72 2.41
51 52 3.005684 CCCAGCATTGTGTTGTGTACAAT 59.994 43.478 0.00 0.00 46.54 2.71
59 60 5.843673 TGTGTTGTGTACAATGATGGTTT 57.156 34.783 0.00 0.00 38.80 3.27
60 61 5.586339 TGTGTTGTGTACAATGATGGTTTG 58.414 37.500 0.00 0.00 38.80 2.93
61 62 4.444056 GTGTTGTGTACAATGATGGTTTGC 59.556 41.667 0.00 0.00 38.80 3.68
62 63 4.340666 TGTTGTGTACAATGATGGTTTGCT 59.659 37.500 0.00 0.00 38.24 3.91
63 64 5.163468 TGTTGTGTACAATGATGGTTTGCTT 60.163 36.000 0.00 0.00 38.24 3.91
64 65 5.528043 TGTGTACAATGATGGTTTGCTTT 57.472 34.783 0.00 0.00 0.00 3.51
65 66 5.527951 TGTGTACAATGATGGTTTGCTTTC 58.472 37.500 0.00 0.00 0.00 2.62
66 67 4.616802 GTGTACAATGATGGTTTGCTTTCG 59.383 41.667 0.00 0.00 0.00 3.46
67 68 4.517075 TGTACAATGATGGTTTGCTTTCGA 59.483 37.500 0.00 0.00 0.00 3.71
69 70 5.138125 ACAATGATGGTTTGCTTTCGAAT 57.862 34.783 0.00 0.00 0.00 3.34
70 71 6.266168 ACAATGATGGTTTGCTTTCGAATA 57.734 33.333 0.00 0.00 0.00 1.75
71 72 6.092748 ACAATGATGGTTTGCTTTCGAATAC 58.907 36.000 0.00 0.00 0.00 1.89
72 73 5.895636 ATGATGGTTTGCTTTCGAATACA 57.104 34.783 0.00 0.00 0.00 2.29
74 75 6.078202 TGATGGTTTGCTTTCGAATACAAA 57.922 33.333 17.38 17.38 0.00 2.83
75 76 6.148948 TGATGGTTTGCTTTCGAATACAAAG 58.851 36.000 20.25 7.67 33.02 2.77
76 77 5.508200 TGGTTTGCTTTCGAATACAAAGT 57.492 34.783 20.25 0.00 33.96 2.66
77 78 5.277825 TGGTTTGCTTTCGAATACAAAGTG 58.722 37.500 20.25 0.00 33.96 3.16
78 79 4.679654 GGTTTGCTTTCGAATACAAAGTGG 59.320 41.667 20.25 0.00 33.96 4.00
79 80 4.497473 TTGCTTTCGAATACAAAGTGGG 57.503 40.909 10.05 0.00 33.96 4.61
80 81 2.817258 TGCTTTCGAATACAAAGTGGGG 59.183 45.455 0.00 0.00 33.96 4.96
81 82 2.163613 GCTTTCGAATACAAAGTGGGGG 59.836 50.000 0.00 0.00 33.96 5.40
101 102 0.892755 GGGGGCCTTTTTCGGTAAAG 59.107 55.000 0.84 3.96 35.39 1.85
102 103 1.548355 GGGGGCCTTTTTCGGTAAAGA 60.548 52.381 0.84 0.00 37.31 2.52
103 104 2.453521 GGGGCCTTTTTCGGTAAAGAT 58.546 47.619 0.84 0.00 37.31 2.40
104 105 2.165641 GGGGCCTTTTTCGGTAAAGATG 59.834 50.000 0.84 0.00 37.31 2.90
105 106 3.086282 GGGCCTTTTTCGGTAAAGATGA 58.914 45.455 0.84 0.00 37.31 2.92
106 107 3.508402 GGGCCTTTTTCGGTAAAGATGAA 59.492 43.478 0.84 0.00 37.31 2.57
107 108 4.021807 GGGCCTTTTTCGGTAAAGATGAAA 60.022 41.667 0.84 0.00 37.31 2.69
108 109 5.161358 GGCCTTTTTCGGTAAAGATGAAAG 58.839 41.667 0.00 0.00 37.31 2.62
109 110 4.621460 GCCTTTTTCGGTAAAGATGAAAGC 59.379 41.667 10.50 2.92 37.31 3.51
111 112 5.427036 TTTTTCGGTAAAGATGAAAGCGT 57.573 34.783 0.00 0.00 33.57 5.07
112 113 4.398549 TTTCGGTAAAGATGAAAGCGTG 57.601 40.909 0.00 0.00 35.73 5.34
113 114 2.343101 TCGGTAAAGATGAAAGCGTGG 58.657 47.619 0.00 0.00 35.73 4.94
115 116 2.706890 GGTAAAGATGAAAGCGTGGGA 58.293 47.619 0.00 0.00 0.00 4.37
116 117 2.678336 GGTAAAGATGAAAGCGTGGGAG 59.322 50.000 0.00 0.00 0.00 4.30
117 118 1.826385 AAAGATGAAAGCGTGGGAGG 58.174 50.000 0.00 0.00 0.00 4.30
119 120 1.452108 GATGAAAGCGTGGGAGGGG 60.452 63.158 0.00 0.00 0.00 4.79
121 122 4.035102 GAAAGCGTGGGAGGGGCT 62.035 66.667 0.00 0.00 39.01 5.19
123 124 2.193087 GAAAGCGTGGGAGGGGCTTA 62.193 60.000 0.00 0.00 45.58 3.09
124 125 2.479820 AAAGCGTGGGAGGGGCTTAC 62.480 60.000 0.00 0.00 45.58 2.34
537 3075 4.759693 TGATTACCAAAGATGAAAGCGTGT 59.240 37.500 0.00 0.00 0.00 4.49
597 3135 1.136500 GGTTGTACGAGGAGGATGGAC 59.864 57.143 0.00 0.00 0.00 4.02
599 3137 0.750546 TGTACGAGGAGGATGGACGG 60.751 60.000 0.00 0.00 0.00 4.79
666 3207 9.476928 AGGTAGTAGAGATAGAGATAGAGAGAC 57.523 40.741 0.00 0.00 0.00 3.36
667 3208 8.404000 GGTAGTAGAGATAGAGATAGAGAGACG 58.596 44.444 0.00 0.00 0.00 4.18
668 3209 7.406031 AGTAGAGATAGAGATAGAGAGACGG 57.594 44.000 0.00 0.00 0.00 4.79
669 3210 7.179966 AGTAGAGATAGAGATAGAGAGACGGA 58.820 42.308 0.00 0.00 0.00 4.69
670 3211 6.531503 AGAGATAGAGATAGAGAGACGGAG 57.468 45.833 0.00 0.00 0.00 4.63
746 3319 4.083802 GCCAAGGATATATTCGCAACACTC 60.084 45.833 0.00 0.00 0.00 3.51
778 3351 5.450818 AAGCCCAATAGATTACCAACTCA 57.549 39.130 0.00 0.00 0.00 3.41
781 3354 4.127171 CCCAATAGATTACCAACTCACGG 58.873 47.826 0.00 0.00 0.00 4.94
792 3365 0.400213 AACTCACGGATTGGAAGGCA 59.600 50.000 0.00 0.00 0.00 4.75
793 3366 0.321653 ACTCACGGATTGGAAGGCAC 60.322 55.000 0.00 0.00 0.00 5.01
794 3367 1.361668 CTCACGGATTGGAAGGCACG 61.362 60.000 0.00 0.00 0.00 5.34
795 3368 1.375396 CACGGATTGGAAGGCACGA 60.375 57.895 0.00 0.00 0.00 4.35
825 3398 3.502164 CGGAGGAATCAGCCCAAAT 57.498 52.632 0.00 0.00 0.00 2.32
826 3399 2.638480 CGGAGGAATCAGCCCAAATA 57.362 50.000 0.00 0.00 0.00 1.40
829 3402 4.003648 CGGAGGAATCAGCCCAAATATAC 58.996 47.826 0.00 0.00 0.00 1.47
835 3408 5.009010 GGAATCAGCCCAAATATACACACAG 59.991 44.000 0.00 0.00 0.00 3.66
836 3409 3.884895 TCAGCCCAAATATACACACAGG 58.115 45.455 0.00 0.00 0.00 4.00
837 3410 3.521531 TCAGCCCAAATATACACACAGGA 59.478 43.478 0.00 0.00 0.00 3.86
838 3411 3.879295 CAGCCCAAATATACACACAGGAG 59.121 47.826 0.00 0.00 0.00 3.69
843 3416 5.163301 CCCAAATATACACACAGGAGTAGCT 60.163 44.000 0.00 0.00 0.00 3.32
907 3484 1.128188 ACCGAGCAGAGAAACCCCTT 61.128 55.000 0.00 0.00 0.00 3.95
1305 3889 3.195698 GTCATGGACGCCTTCGCC 61.196 66.667 0.00 0.00 39.84 5.54
1426 4010 0.821517 CCCCGCCCCTGTTTATTTTC 59.178 55.000 0.00 0.00 0.00 2.29
1580 4164 2.669434 GCAATGCTGCTAATTTGGTGTG 59.331 45.455 0.00 0.00 45.74 3.82
1771 4358 1.065854 AGCTTGCTGACATACTGGGTC 60.066 52.381 0.00 0.00 35.83 4.46
1810 4410 6.484288 AGTGGAAACATGATTAGTGGATTCA 58.516 36.000 0.00 0.00 46.14 2.57
1812 4412 7.284034 AGTGGAAACATGATTAGTGGATTCATC 59.716 37.037 0.00 0.00 46.14 2.92
1886 4486 7.985184 GGTGTCATAGTATTTAGTGTTGGATCA 59.015 37.037 0.00 0.00 0.00 2.92
2016 4616 8.554490 TTTGAAAGCTTAGATATACTCCCTCT 57.446 34.615 0.00 0.00 0.00 3.69
2038 4638 3.751175 TGTCCCAAAATAAGCGTCTCAAG 59.249 43.478 0.00 0.00 0.00 3.02
2296 4906 3.299503 CCAATATTTTGGCTAGCCCAGT 58.700 45.455 30.81 16.24 45.71 4.00
2516 5126 4.801516 CGTGGTTGTTTCGATTTCCTTTTT 59.198 37.500 0.00 0.00 0.00 1.94
2729 5339 4.989797 TGCATTTGTGCTTGTTTAATCTGG 59.010 37.500 1.86 0.00 35.49 3.86
2932 5544 1.602311 CTGGTTATGGATGCTGGCTC 58.398 55.000 0.00 0.00 0.00 4.70
3453 6074 5.067805 GGTTATATCTTGTTTGGCCTTCCAG 59.932 44.000 3.32 0.00 44.53 3.86
3607 6228 3.255642 TGTTCATGCCCTTTAAACTCTGC 59.744 43.478 0.00 0.00 0.00 4.26
3760 6383 5.850278 TCCCTCCGTCCCATAATATAAGAT 58.150 41.667 0.00 0.00 0.00 2.40
3802 6425 8.548877 AGGGAGTAGTTATTATGATGTTGTGTT 58.451 33.333 0.00 0.00 0.00 3.32
3868 6491 4.944962 TTTGTCTGACTGTCACTTGTTG 57.055 40.909 6.36 0.00 0.00 3.33
3877 6500 2.088423 TGTCACTTGTTGGCTTTTCGT 58.912 42.857 0.00 0.00 0.00 3.85
4114 6746 6.374333 TCCACTTCAATTCCATGCTTAGTTAC 59.626 38.462 0.00 0.00 0.00 2.50
4119 6751 8.856153 TTCAATTCCATGCTTAGTTACTTGTA 57.144 30.769 0.00 0.00 0.00 2.41
4239 6871 9.802039 TTTAGTTTTGTAATATGTTCCTCCTGT 57.198 29.630 0.00 0.00 0.00 4.00
4413 7045 4.398358 GGCAGGTTCTCCAGTTTATTTACC 59.602 45.833 0.00 0.00 35.89 2.85
4647 7303 8.674607 CAAATTTCTGATGTTACCCCTAACTAC 58.325 37.037 0.00 0.00 34.38 2.73
4792 7448 3.672808 AGCATGAGAGTTCCAGTGAAAG 58.327 45.455 0.00 0.00 30.79 2.62
4793 7449 3.072184 AGCATGAGAGTTCCAGTGAAAGT 59.928 43.478 0.00 0.00 30.79 2.66
4794 7450 3.817647 GCATGAGAGTTCCAGTGAAAGTT 59.182 43.478 0.00 0.00 30.79 2.66
4833 7489 1.202615 GGATTAACCTACACCGGGCTC 60.203 57.143 6.32 0.00 35.41 4.70
4979 7636 1.446907 GTGATGCCACTGAGAGGTTG 58.553 55.000 0.00 0.00 40.10 3.77
5070 7729 4.240096 GTTGATTGCCTTTCTGATTGGTG 58.760 43.478 0.00 0.00 0.00 4.17
5117 7777 2.602211 CTCTATCAAACAGTGCGCTCAG 59.398 50.000 9.73 4.28 0.00 3.35
5150 7810 6.147328 CCCATAGTTTAAGACTTATAAGCGGC 59.853 42.308 12.54 2.76 39.86 6.53
5265 7926 5.048643 TGTTCTCCGTTTGTTTGACTTTGAA 60.049 36.000 0.00 0.00 0.00 2.69
5266 7927 5.828299 TCTCCGTTTGTTTGACTTTGAAT 57.172 34.783 0.00 0.00 0.00 2.57
5267 7928 5.816919 TCTCCGTTTGTTTGACTTTGAATC 58.183 37.500 0.00 0.00 0.00 2.52
5270 7931 5.008217 TCCGTTTGTTTGACTTTGAATCGAT 59.992 36.000 0.00 0.00 0.00 3.59
5272 7933 5.386323 CGTTTGTTTGACTTTGAATCGATGC 60.386 40.000 0.00 0.00 0.00 3.91
5273 7934 5.437289 TTGTTTGACTTTGAATCGATGCT 57.563 34.783 4.68 0.00 0.00 3.79
5274 7935 4.786507 TGTTTGACTTTGAATCGATGCTG 58.213 39.130 4.68 0.00 0.00 4.41
5275 7936 3.476295 TTGACTTTGAATCGATGCTGC 57.524 42.857 4.68 0.00 0.00 5.25
5316 7982 3.885777 GCTAGTAGCGTTACGTCGT 57.114 52.632 6.36 2.21 34.88 4.34
5322 7988 0.721154 TAGCGTTACGTCGTCATCGT 59.279 50.000 0.00 0.00 43.86 3.73
5323 7989 0.110056 AGCGTTACGTCGTCATCGTT 60.110 50.000 0.00 0.69 41.72 3.85
5324 7990 0.704551 GCGTTACGTCGTCATCGTTT 59.295 50.000 0.00 0.00 41.72 3.60
5325 7991 1.265590 GCGTTACGTCGTCATCGTTTC 60.266 52.381 0.00 0.00 41.72 2.78
5326 7992 1.971284 CGTTACGTCGTCATCGTTTCA 59.029 47.619 0.00 0.00 41.72 2.69
5327 7993 2.591148 CGTTACGTCGTCATCGTTTCAT 59.409 45.455 0.00 0.00 41.72 2.57
5328 7994 3.536934 CGTTACGTCGTCATCGTTTCATG 60.537 47.826 0.00 0.00 41.72 3.07
5329 7995 2.060326 ACGTCGTCATCGTTTCATGT 57.940 45.000 0.00 0.00 38.38 3.21
5330 7996 2.400399 ACGTCGTCATCGTTTCATGTT 58.600 42.857 0.00 0.00 38.38 2.71
5331 7997 2.798283 ACGTCGTCATCGTTTCATGTTT 59.202 40.909 0.00 0.00 38.38 2.83
5332 7998 3.982701 ACGTCGTCATCGTTTCATGTTTA 59.017 39.130 0.00 0.00 38.38 2.01
5333 7999 4.089493 ACGTCGTCATCGTTTCATGTTTAG 59.911 41.667 0.00 0.00 38.38 1.85
5334 8000 4.322539 CGTCGTCATCGTTTCATGTTTAGA 59.677 41.667 0.00 0.00 38.33 2.10
5335 8001 5.004440 CGTCGTCATCGTTTCATGTTTAGAT 59.996 40.000 0.00 0.00 38.33 1.98
5336 8002 6.178507 GTCGTCATCGTTTCATGTTTAGATG 58.821 40.000 13.62 13.62 37.43 2.90
5337 8003 4.957967 CGTCATCGTTTCATGTTTAGATGC 59.042 41.667 14.44 10.68 36.41 3.91
5338 8004 5.445806 CGTCATCGTTTCATGTTTAGATGCA 60.446 40.000 14.44 0.00 36.41 3.96
5339 8005 6.314018 GTCATCGTTTCATGTTTAGATGCAA 58.686 36.000 14.44 2.40 36.41 4.08
5340 8006 6.968904 GTCATCGTTTCATGTTTAGATGCAAT 59.031 34.615 14.44 0.00 36.41 3.56
5341 8007 7.485913 GTCATCGTTTCATGTTTAGATGCAATT 59.514 33.333 14.44 0.00 36.41 2.32
5342 8008 8.672815 TCATCGTTTCATGTTTAGATGCAATTA 58.327 29.630 14.44 0.00 36.41 1.40
5343 8009 9.454585 CATCGTTTCATGTTTAGATGCAATTAT 57.545 29.630 0.00 0.00 30.84 1.28
5357 8023 7.614494 AGATGCAATTATATTAAATGCCCACC 58.386 34.615 0.00 0.00 0.00 4.61
5358 8024 6.737720 TGCAATTATATTAAATGCCCACCA 57.262 33.333 5.19 0.00 0.00 4.17
5359 8025 6.757237 TGCAATTATATTAAATGCCCACCAG 58.243 36.000 5.19 0.00 0.00 4.00
5360 8026 6.326064 TGCAATTATATTAAATGCCCACCAGT 59.674 34.615 5.19 0.00 0.00 4.00
5361 8027 6.868339 GCAATTATATTAAATGCCCACCAGTC 59.132 38.462 0.00 0.00 0.00 3.51
5375 8041 5.745227 CCCACCAGTCAATATCTTAGTGTT 58.255 41.667 0.00 0.00 0.00 3.32
5402 8068 5.945155 TGCGATTGGTGAGGTAAAATAAAC 58.055 37.500 0.00 0.00 0.00 2.01
5437 8103 3.620488 TCCAATCAACATAACTCTGGGC 58.380 45.455 0.00 0.00 0.00 5.36
5441 8107 3.719268 TCAACATAACTCTGGGCACAT 57.281 42.857 0.00 0.00 0.00 3.21
5443 8109 5.372343 TCAACATAACTCTGGGCACATAT 57.628 39.130 0.00 0.00 0.00 1.78
5444 8110 5.754782 TCAACATAACTCTGGGCACATATT 58.245 37.500 0.00 0.00 0.00 1.28
5445 8111 6.186957 TCAACATAACTCTGGGCACATATTT 58.813 36.000 0.00 0.00 0.00 1.40
5446 8112 6.663093 TCAACATAACTCTGGGCACATATTTT 59.337 34.615 0.00 0.00 0.00 1.82
5447 8113 7.178274 TCAACATAACTCTGGGCACATATTTTT 59.822 33.333 0.00 0.00 0.00 1.94
5495 8179 5.507315 CCAAGTTATGGTTCTGTGGTTTGAC 60.507 44.000 0.00 0.00 44.85 3.18
5502 8188 3.624410 GGTTCTGTGGTTTGACGTTTACT 59.376 43.478 0.00 0.00 0.00 2.24
5599 8299 4.961438 ATGCTGAGGGTTTGACAAAAAT 57.039 36.364 1.27 0.00 0.00 1.82
5626 8328 5.122869 CAGTCCACTAATCCACAAGTCAATG 59.877 44.000 0.00 0.00 0.00 2.82
5629 8331 5.013079 TCCACTAATCCACAAGTCAATGACT 59.987 40.000 10.56 10.56 45.64 3.41
5632 8337 6.596888 CACTAATCCACAAGTCAATGACTCAT 59.403 38.462 17.02 4.96 42.59 2.90
5633 8338 7.765819 CACTAATCCACAAGTCAATGACTCATA 59.234 37.037 17.02 1.71 42.59 2.15
5634 8339 8.489489 ACTAATCCACAAGTCAATGACTCATAT 58.511 33.333 17.02 0.00 42.59 1.78
5635 8340 9.987272 CTAATCCACAAGTCAATGACTCATATA 57.013 33.333 17.02 3.47 42.59 0.86
5636 8341 8.668510 AATCCACAAGTCAATGACTCATATAC 57.331 34.615 17.02 0.00 42.59 1.47
5637 8342 7.181569 TCCACAAGTCAATGACTCATATACA 57.818 36.000 17.02 0.00 42.59 2.29
5638 8343 7.041721 TCCACAAGTCAATGACTCATATACAC 58.958 38.462 17.02 0.00 42.59 2.90
5639 8344 6.818142 CCACAAGTCAATGACTCATATACACA 59.182 38.462 17.02 0.00 42.59 3.72
5640 8345 7.334171 CCACAAGTCAATGACTCATATACACAA 59.666 37.037 17.02 0.00 42.59 3.33
5641 8346 8.171196 CACAAGTCAATGACTCATATACACAAC 58.829 37.037 17.02 0.00 42.59 3.32
5642 8347 8.097038 ACAAGTCAATGACTCATATACACAACT 58.903 33.333 17.02 0.00 42.59 3.16
5643 8348 8.939929 CAAGTCAATGACTCATATACACAACTT 58.060 33.333 17.02 0.00 42.59 2.66
5644 8349 8.484641 AGTCAATGACTCATATACACAACTTG 57.515 34.615 10.56 0.00 38.71 3.16
5645 8350 8.097038 AGTCAATGACTCATATACACAACTTGT 58.903 33.333 10.56 0.00 38.71 3.16
5646 8351 9.366216 GTCAATGACTCATATACACAACTTGTA 57.634 33.333 6.07 0.00 45.03 2.41
5647 8352 9.936759 TCAATGACTCATATACACAACTTGTAA 57.063 29.630 0.00 0.00 44.11 2.41
5687 8392 1.148310 CGGCGGCTATACAAATGGAG 58.852 55.000 7.61 0.00 0.00 3.86
5693 8398 4.389077 GCGGCTATACAAATGGAGATACAC 59.611 45.833 0.00 0.00 0.00 2.90
5747 8453 2.782925 TCCCAATATGCAGGGCTTCTTA 59.217 45.455 3.82 0.00 45.07 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.136260 AGCAAATCAAGCCCAAAAGGAAA 59.864 39.130 0.00 0.00 38.24 3.13
1 2 2.705127 AGCAAATCAAGCCCAAAAGGAA 59.295 40.909 0.00 0.00 38.24 3.36
2 3 2.037511 CAGCAAATCAAGCCCAAAAGGA 59.962 45.455 0.00 0.00 38.24 3.36
3 4 2.419667 CAGCAAATCAAGCCCAAAAGG 58.580 47.619 0.00 0.00 39.47 3.11
4 5 1.802365 GCAGCAAATCAAGCCCAAAAG 59.198 47.619 0.00 0.00 0.00 2.27
5 6 1.417145 AGCAGCAAATCAAGCCCAAAA 59.583 42.857 0.00 0.00 0.00 2.44
6 7 1.001181 GAGCAGCAAATCAAGCCCAAA 59.999 47.619 0.00 0.00 0.00 3.28
7 8 0.604578 GAGCAGCAAATCAAGCCCAA 59.395 50.000 0.00 0.00 0.00 4.12
8 9 1.588824 CGAGCAGCAAATCAAGCCCA 61.589 55.000 0.00 0.00 0.00 5.36
10 11 4.779819 CGAGCAGCAAATCAAGCC 57.220 55.556 0.00 0.00 0.00 4.35
23 24 3.818787 CACAATGCTGGGGCGAGC 61.819 66.667 0.39 0.39 42.25 5.03
24 25 1.973281 AACACAATGCTGGGGCGAG 60.973 57.895 0.00 0.00 42.25 5.03
25 26 2.115052 AACACAATGCTGGGGCGA 59.885 55.556 0.00 0.00 42.25 5.54
26 27 2.259204 CAACACAATGCTGGGGCG 59.741 61.111 0.00 0.00 42.25 6.13
29 30 1.952990 TGTACACAACACAATGCTGGG 59.047 47.619 0.00 0.00 31.43 4.45
30 31 3.706802 TTGTACACAACACAATGCTGG 57.293 42.857 0.00 0.00 38.00 4.85
35 36 6.403866 AACCATCATTGTACACAACACAAT 57.596 33.333 0.00 0.00 45.23 2.71
36 37 5.843673 AACCATCATTGTACACAACACAA 57.156 34.783 0.00 0.00 38.00 3.33
37 38 5.586339 CAAACCATCATTGTACACAACACA 58.414 37.500 0.00 0.00 38.00 3.72
38 39 4.444056 GCAAACCATCATTGTACACAACAC 59.556 41.667 0.00 0.00 38.00 3.32
39 40 4.340666 AGCAAACCATCATTGTACACAACA 59.659 37.500 0.00 0.00 38.86 3.33
40 41 4.870363 AGCAAACCATCATTGTACACAAC 58.130 39.130 0.00 0.00 38.86 3.32
41 42 5.528043 AAGCAAACCATCATTGTACACAA 57.472 34.783 0.00 0.00 40.51 3.33
42 43 5.527951 GAAAGCAAACCATCATTGTACACA 58.472 37.500 0.00 0.00 0.00 3.72
43 44 4.616802 CGAAAGCAAACCATCATTGTACAC 59.383 41.667 0.00 0.00 0.00 2.90
44 45 4.517075 TCGAAAGCAAACCATCATTGTACA 59.483 37.500 0.00 0.00 0.00 2.90
45 46 5.041951 TCGAAAGCAAACCATCATTGTAC 57.958 39.130 0.00 0.00 0.00 2.90
46 47 5.697473 TTCGAAAGCAAACCATCATTGTA 57.303 34.783 0.00 0.00 0.00 2.41
47 48 4.582701 TTCGAAAGCAAACCATCATTGT 57.417 36.364 0.00 0.00 0.00 2.71
48 49 6.092092 TGTATTCGAAAGCAAACCATCATTG 58.908 36.000 0.00 0.00 0.00 2.82
49 50 6.266168 TGTATTCGAAAGCAAACCATCATT 57.734 33.333 0.00 0.00 0.00 2.57
50 51 5.895636 TGTATTCGAAAGCAAACCATCAT 57.104 34.783 0.00 0.00 0.00 2.45
51 52 5.697473 TTGTATTCGAAAGCAAACCATCA 57.303 34.783 0.00 0.00 0.00 3.07
52 53 6.088085 CACTTTGTATTCGAAAGCAAACCATC 59.912 38.462 19.66 0.00 34.33 3.51
53 54 5.920273 CACTTTGTATTCGAAAGCAAACCAT 59.080 36.000 19.66 10.31 34.33 3.55
54 55 5.277825 CACTTTGTATTCGAAAGCAAACCA 58.722 37.500 19.66 6.93 34.33 3.67
56 57 4.679654 CCCACTTTGTATTCGAAAGCAAAC 59.320 41.667 19.66 8.11 34.33 2.93
57 58 4.261825 CCCCACTTTGTATTCGAAAGCAAA 60.262 41.667 21.19 21.19 34.33 3.68
59 60 2.817258 CCCCACTTTGTATTCGAAAGCA 59.183 45.455 0.00 0.94 34.33 3.91
60 61 2.163613 CCCCCACTTTGTATTCGAAAGC 59.836 50.000 0.00 0.00 34.33 3.51
82 83 0.892755 CTTTACCGAAAAAGGCCCCC 59.107 55.000 0.00 0.00 33.64 5.40
83 84 1.913778 TCTTTACCGAAAAAGGCCCC 58.086 50.000 0.00 0.00 37.13 5.80
85 86 4.776795 TTCATCTTTACCGAAAAAGGCC 57.223 40.909 0.00 0.00 37.13 5.19
86 87 4.621460 GCTTTCATCTTTACCGAAAAAGGC 59.379 41.667 8.87 1.85 37.13 4.35
88 89 5.339611 CACGCTTTCATCTTTACCGAAAAAG 59.660 40.000 3.78 3.78 37.73 2.27
89 90 5.209240 CACGCTTTCATCTTTACCGAAAAA 58.791 37.500 0.00 0.00 0.00 1.94
91 92 3.187637 CCACGCTTTCATCTTTACCGAAA 59.812 43.478 0.00 0.00 0.00 3.46
92 93 2.739913 CCACGCTTTCATCTTTACCGAA 59.260 45.455 0.00 0.00 0.00 4.30
93 94 2.343101 CCACGCTTTCATCTTTACCGA 58.657 47.619 0.00 0.00 0.00 4.69
94 95 1.396996 CCCACGCTTTCATCTTTACCG 59.603 52.381 0.00 0.00 0.00 4.02
95 96 2.678336 CTCCCACGCTTTCATCTTTACC 59.322 50.000 0.00 0.00 0.00 2.85
96 97 2.678336 CCTCCCACGCTTTCATCTTTAC 59.322 50.000 0.00 0.00 0.00 2.01
97 98 2.355716 CCCTCCCACGCTTTCATCTTTA 60.356 50.000 0.00 0.00 0.00 1.85
98 99 1.614317 CCCTCCCACGCTTTCATCTTT 60.614 52.381 0.00 0.00 0.00 2.52
101 102 1.452108 CCCCTCCCACGCTTTCATC 60.452 63.158 0.00 0.00 0.00 2.92
102 103 2.677228 CCCCTCCCACGCTTTCAT 59.323 61.111 0.00 0.00 0.00 2.57
103 104 4.344865 GCCCCTCCCACGCTTTCA 62.345 66.667 0.00 0.00 0.00 2.69
104 105 2.193087 TAAGCCCCTCCCACGCTTTC 62.193 60.000 0.00 0.00 42.60 2.62
105 106 2.228480 TAAGCCCCTCCCACGCTTT 61.228 57.895 0.00 0.00 42.60 3.51
106 107 2.609610 TAAGCCCCTCCCACGCTT 60.610 61.111 0.00 0.00 44.67 4.68
107 108 3.400054 GTAAGCCCCTCCCACGCT 61.400 66.667 0.00 0.00 0.00 5.07
496 497 9.118367 TGGTAATCATCTCTATCTCTACTACCT 57.882 37.037 0.00 0.00 0.00 3.08
503 504 9.599056 TCATCTTTGGTAATCATCTCTATCTCT 57.401 33.333 0.00 0.00 0.00 3.10
507 508 9.282569 GCTTTCATCTTTGGTAATCATCTCTAT 57.717 33.333 0.00 0.00 0.00 1.98
537 3075 2.638325 TCATCTTTGGTAACCCCCTCA 58.362 47.619 0.00 0.00 0.00 3.86
597 3135 2.832201 GTCCTACGTCCCCCTCCG 60.832 72.222 0.00 0.00 0.00 4.63
599 3137 2.832201 CCGTCCTACGTCCCCCTC 60.832 72.222 0.00 0.00 40.58 4.30
660 3201 1.770294 ACCTGAATCCTCCGTCTCTC 58.230 55.000 0.00 0.00 0.00 3.20
665 3206 2.292323 ACCTCTAACCTGAATCCTCCGT 60.292 50.000 0.00 0.00 0.00 4.69
666 3207 2.362717 GACCTCTAACCTGAATCCTCCG 59.637 54.545 0.00 0.00 0.00 4.63
667 3208 3.639561 GAGACCTCTAACCTGAATCCTCC 59.360 52.174 0.00 0.00 0.00 4.30
668 3209 3.316868 CGAGACCTCTAACCTGAATCCTC 59.683 52.174 0.00 0.00 0.00 3.71
669 3210 3.053544 TCGAGACCTCTAACCTGAATCCT 60.054 47.826 0.00 0.00 0.00 3.24
670 3211 3.288964 TCGAGACCTCTAACCTGAATCC 58.711 50.000 0.00 0.00 0.00 3.01
746 3319 2.092429 TCTATTGGGCTTTACAGGCTGG 60.092 50.000 20.34 1.38 45.26 4.85
778 3351 0.953960 GTTCGTGCCTTCCAATCCGT 60.954 55.000 0.00 0.00 0.00 4.69
781 3354 0.442699 GTCGTTCGTGCCTTCCAATC 59.557 55.000 0.00 0.00 0.00 2.67
824 3397 3.322254 GGCAGCTACTCCTGTGTGTATAT 59.678 47.826 0.00 0.00 35.28 0.86
825 3398 2.693591 GGCAGCTACTCCTGTGTGTATA 59.306 50.000 0.00 0.00 35.28 1.47
826 3399 1.482593 GGCAGCTACTCCTGTGTGTAT 59.517 52.381 0.00 0.00 35.28 2.29
829 3402 0.671781 GTGGCAGCTACTCCTGTGTG 60.672 60.000 0.70 0.00 35.28 3.82
907 3484 0.908180 GGAGGAGGACGAAGGGGAAA 60.908 60.000 0.00 0.00 0.00 3.13
1414 3998 3.610911 AGAGCTCCGGAAAATAAACAGG 58.389 45.455 10.93 0.00 0.00 4.00
1426 4010 1.652012 GTCAGATCGAGAGCTCCGG 59.348 63.158 19.88 9.51 0.00 5.14
1580 4164 5.233689 GCACCTAACCATAAGACGAACATAC 59.766 44.000 0.00 0.00 0.00 2.39
1771 4358 5.159209 GTTTCCACTTTCTTGCATCAGATG 58.841 41.667 5.98 5.98 0.00 2.90
1810 4410 9.256228 ACCAGATATATTGATACAGTTACGGAT 57.744 33.333 0.00 0.00 0.00 4.18
1886 4486 1.133199 TGGAAGCATTGGGTCCTGTTT 60.133 47.619 0.00 0.00 0.00 2.83
2016 4616 3.410631 TGAGACGCTTATTTTGGGACA 57.589 42.857 0.00 0.00 0.00 4.02
2516 5126 7.147620 CCACTAGTAATTAACCATGGTCCTACA 60.148 40.741 20.07 0.68 0.00 2.74
2656 5266 0.250727 TCCAAAACAGGGAGGCGAAG 60.251 55.000 0.00 0.00 0.00 3.79
2729 5339 9.346725 CACTCTCTAAAATATTCTTTGCCAAAC 57.653 33.333 0.00 0.00 0.00 2.93
2932 5544 4.216902 TGAGTTGAAACATCAATGCCTGAG 59.783 41.667 0.00 0.00 37.52 3.35
3760 6383 1.140052 TCCCTCTGTCTTGCGAAAACA 59.860 47.619 0.00 0.00 0.00 2.83
3868 6491 5.945155 TGTAACATATCCAAACGAAAAGCC 58.055 37.500 0.00 0.00 0.00 4.35
4239 6871 4.095185 GCAGGTGTGTAAATAATTACGGCA 59.905 41.667 0.00 0.00 43.59 5.69
4333 6965 7.920682 GGATGTGCCAACTAATTAATAAAGTGG 59.079 37.037 4.59 8.55 36.34 4.00
4647 7303 7.337689 TGATGACCTTCAAGGATCAAATTGTAG 59.662 37.037 11.59 0.19 37.67 2.74
4792 7448 4.022068 TCCAGCATCAAAATGTGAAGGAAC 60.022 41.667 0.00 0.00 40.50 3.62
4793 7449 4.151121 TCCAGCATCAAAATGTGAAGGAA 58.849 39.130 0.00 0.00 40.50 3.36
4794 7450 3.765381 TCCAGCATCAAAATGTGAAGGA 58.235 40.909 0.00 0.00 40.50 3.36
4833 7489 2.642139 AAGTGATGAAATGGCTTGCG 57.358 45.000 0.00 0.00 0.00 4.85
4836 7492 5.047802 ACGATTCAAAGTGATGAAATGGCTT 60.048 36.000 0.00 0.00 42.22 4.35
4841 7497 4.380867 GGCCACGATTCAAAGTGATGAAAT 60.381 41.667 0.00 0.00 42.22 2.17
4904 7560 7.418408 CCAATTCTGATTTGACAGATGATGAG 58.582 38.462 12.51 0.00 44.67 2.90
5070 7729 5.471456 CCTTGAACATAGATAGATTGTGCCC 59.529 44.000 0.00 0.00 0.00 5.36
5082 7741 8.134202 TGTTTGATAGAGACCTTGAACATAGA 57.866 34.615 0.00 0.00 0.00 1.98
5123 7783 7.929785 CCGCTTATAAGTCTTAAACTATGGGAA 59.070 37.037 13.91 0.00 37.17 3.97
5150 7810 5.390567 GCCGGGAATTTAAGAAGCGTATATG 60.391 44.000 2.18 0.00 0.00 1.78
5155 7815 1.092348 GCCGGGAATTTAAGAAGCGT 58.908 50.000 2.18 0.00 0.00 5.07
5265 7926 0.812811 AATGTCGCAGCAGCATCGAT 60.813 50.000 11.39 0.00 42.27 3.59
5266 7927 1.423721 GAATGTCGCAGCAGCATCGA 61.424 55.000 0.82 5.08 42.27 3.59
5267 7928 1.011463 GAATGTCGCAGCAGCATCG 60.011 57.895 0.82 0.00 42.27 3.84
5270 7931 2.028420 AATAGAATGTCGCAGCAGCA 57.972 45.000 0.82 0.00 42.27 4.41
5272 7933 4.556135 CACAAAAATAGAATGTCGCAGCAG 59.444 41.667 0.00 0.00 0.00 4.24
5273 7934 4.023279 ACACAAAAATAGAATGTCGCAGCA 60.023 37.500 0.00 0.00 0.00 4.41
5274 7935 4.475944 ACACAAAAATAGAATGTCGCAGC 58.524 39.130 0.00 0.00 0.00 5.25
5308 7974 3.567530 ACATGAAACGATGACGACGTAA 58.432 40.909 0.00 0.00 43.16 3.18
5315 7981 5.868257 TGCATCTAAACATGAAACGATGAC 58.132 37.500 17.45 11.78 32.21 3.06
5316 7982 6.493449 TTGCATCTAAACATGAAACGATGA 57.507 33.333 17.45 6.20 32.21 2.92
5331 7997 8.748412 GGTGGGCATTTAATATAATTGCATCTA 58.252 33.333 14.99 0.00 0.00 1.98
5332 7998 7.235193 TGGTGGGCATTTAATATAATTGCATCT 59.765 33.333 14.99 0.00 0.00 2.90
5333 7999 7.385267 TGGTGGGCATTTAATATAATTGCATC 58.615 34.615 14.99 9.31 0.00 3.91
5334 8000 7.016465 ACTGGTGGGCATTTAATATAATTGCAT 59.984 33.333 14.99 0.00 0.00 3.96
5335 8001 6.326064 ACTGGTGGGCATTTAATATAATTGCA 59.674 34.615 14.99 0.00 0.00 4.08
5336 8002 6.758254 ACTGGTGGGCATTTAATATAATTGC 58.242 36.000 7.94 7.94 0.00 3.56
5337 8003 7.950512 TGACTGGTGGGCATTTAATATAATTG 58.049 34.615 0.00 0.00 0.00 2.32
5338 8004 8.546083 TTGACTGGTGGGCATTTAATATAATT 57.454 30.769 0.00 0.00 30.17 1.40
5339 8005 8.725606 ATTGACTGGTGGGCATTTAATATAAT 57.274 30.769 0.00 0.00 30.17 1.28
5340 8006 9.821240 ATATTGACTGGTGGGCATTTAATATAA 57.179 29.630 0.00 0.00 30.17 0.98
5341 8007 9.461312 GATATTGACTGGTGGGCATTTAATATA 57.539 33.333 0.00 0.00 30.17 0.86
5342 8008 8.172741 AGATATTGACTGGTGGGCATTTAATAT 58.827 33.333 0.00 0.00 30.17 1.28
5343 8009 7.526041 AGATATTGACTGGTGGGCATTTAATA 58.474 34.615 0.00 0.00 30.17 0.98
5344 8010 6.376248 AGATATTGACTGGTGGGCATTTAAT 58.624 36.000 0.00 0.00 30.17 1.40
5345 8011 5.765510 AGATATTGACTGGTGGGCATTTAA 58.234 37.500 0.00 0.00 30.17 1.52
5346 8012 5.387113 AGATATTGACTGGTGGGCATTTA 57.613 39.130 0.00 0.00 30.17 1.40
5347 8013 4.255510 AGATATTGACTGGTGGGCATTT 57.744 40.909 0.00 0.00 30.17 2.32
5348 8014 3.959495 AGATATTGACTGGTGGGCATT 57.041 42.857 0.00 0.00 30.17 3.56
5349 8015 3.959495 AAGATATTGACTGGTGGGCAT 57.041 42.857 0.00 0.00 30.17 4.40
5350 8016 3.780294 ACTAAGATATTGACTGGTGGGCA 59.220 43.478 0.00 0.00 0.00 5.36
5351 8017 4.130118 CACTAAGATATTGACTGGTGGGC 58.870 47.826 0.00 0.00 0.00 5.36
5352 8018 5.359194 ACACTAAGATATTGACTGGTGGG 57.641 43.478 0.00 0.00 0.00 4.61
5353 8019 7.687941 AAAACACTAAGATATTGACTGGTGG 57.312 36.000 0.00 0.00 0.00 4.61
5375 8041 4.920640 TTTACCTCACCAATCGCAAAAA 57.079 36.364 0.00 0.00 0.00 1.94
5495 8179 1.779569 AGGCACGAGAACAGTAAACG 58.220 50.000 0.00 0.00 0.00 3.60
5502 8188 3.325870 CATTAGTCAAGGCACGAGAACA 58.674 45.455 0.00 0.00 0.00 3.18
5560 8246 4.811024 CAGCATAAGGAAGAATTAGACGCA 59.189 41.667 0.00 0.00 0.00 5.24
5599 8299 3.650942 ACTTGTGGATTAGTGGACTGGAA 59.349 43.478 0.00 0.00 0.00 3.53
5640 8345 7.477945 AGCCTATGTACTACAACTTACAAGT 57.522 36.000 0.00 0.00 42.04 3.16
5641 8346 8.136165 CCTAGCCTATGTACTACAACTTACAAG 58.864 40.741 0.00 0.00 32.07 3.16
5642 8347 7.417116 GCCTAGCCTATGTACTACAACTTACAA 60.417 40.741 0.00 0.00 32.07 2.41
5643 8348 6.040166 GCCTAGCCTATGTACTACAACTTACA 59.960 42.308 0.00 0.00 32.83 2.41
5644 8349 6.445475 GCCTAGCCTATGTACTACAACTTAC 58.555 44.000 0.00 0.00 0.00 2.34
5645 8350 5.240183 CGCCTAGCCTATGTACTACAACTTA 59.760 44.000 0.00 0.00 0.00 2.24
5646 8351 4.037684 CGCCTAGCCTATGTACTACAACTT 59.962 45.833 0.00 0.00 0.00 2.66
5647 8352 3.568853 CGCCTAGCCTATGTACTACAACT 59.431 47.826 0.00 0.00 0.00 3.16
5648 8353 3.305199 CCGCCTAGCCTATGTACTACAAC 60.305 52.174 0.00 0.00 0.00 3.32
5687 8392 1.662309 CGAGTATGTCCGCCGTGTATC 60.662 57.143 0.00 0.00 0.00 2.24
5693 8398 0.457166 TTGAACGAGTATGTCCGCCG 60.457 55.000 0.00 0.00 0.00 6.46
5747 8453 6.681729 TGGTCAAGGTATTTTCAGACTAGT 57.318 37.500 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.