Multiple sequence alignment - TraesCS3D01G469600

Loading Multiple Alignment...

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 TraesCS3D01G469600 chr3D 100.000 2387 0 0 1 2387 571593723 571591337 0.000000e+00 4409
1 TraesCS3D01G469600 chr3D 98.799 1416 13 4 392 1805 589280874 589279461 0.000000e+00 2518
2 TraesCS3D01G469600 chr3D 90.925 573 47 3 1808 2378 595892727 595893296 0.000000e+00 765
3 TraesCS3D01G469600 chr5D 99.082 1416 10 3 392 1805 503216885 503218299 0.000000e+00 2540
4 TraesCS3D01G469600 chr5D 98.728 1415 17 1 392 1805 6187607 6189021 0.000000e+00 2512
5 TraesCS3D01G469600 chr5D 98.982 393 3 1 1 393 512408453 512408844 0.000000e+00 702
6 TraesCS3D01G469600 chr5D 98.728 393 4 1 1 393 512415389 512415780 0.000000e+00 697
7 TraesCS3D01G469600 chr5D 98.219 393 6 1 1 393 6179851 6180242 0.000000e+00 686
8 TraesCS3D01G469600 chr5D 97.716 394 6 3 1 393 503288396 503288005 0.000000e+00 675
9 TraesCS3D01G469600 chr6D 99.011 1416 11 3 392 1805 168253593 168255007 0.000000e+00 2534
10 TraesCS3D01G469600 chr6D 98.729 1416 13 4 392 1805 168250207 168251619 0.000000e+00 2510
11 TraesCS3D01G469600 chr6D 98.728 393 3 2 1 393 45510476 45510866 0.000000e+00 697
12 TraesCS3D01G469600 chrUn 98.941 1416 11 4 392 1805 93410963 93409550 0.000000e+00 2529
13 TraesCS3D01G469600 chrUn 98.941 1416 12 3 392 1805 216519935 216518521 0.000000e+00 2529
14 TraesCS3D01G469600 chr3B 98.799 1416 14 3 392 1805 201525691 201527105 0.000000e+00 2518
15 TraesCS3D01G469600 chr2D 98.729 1416 15 3 392 1805 272795226 272793812 0.000000e+00 2512
16 TraesCS3D01G469600 chr2D 90.085 585 49 5 1796 2378 63385707 63386284 0.000000e+00 750
17 TraesCS3D01G469600 chr2D 90.172 580 52 4 1801 2378 578494253 578493677 0.000000e+00 750
18 TraesCS3D01G469600 chr2D 90.653 567 45 5 1796 2360 1648415 1648975 0.000000e+00 747
19 TraesCS3D01G469600 chr2D 91.023 557 45 2 1806 2360 578550595 578550042 0.000000e+00 747
20 TraesCS3D01G469600 chr7B 91.111 585 43 5 1796 2378 106494410 106494987 0.000000e+00 784
21 TraesCS3D01G469600 chr4D 90.829 567 44 5 1796 2360 500231903 500232463 0.000000e+00 752
22 TraesCS3D01G469600 chr2B 90.261 575 50 5 1806 2378 556444490 556443920 0.000000e+00 747
23 TraesCS3D01G469600 chr7D 89.932 586 46 8 1796 2378 107828438 107829013 0.000000e+00 743
24 TraesCS3D01G469600 chr7D 98.982 393 3 1 1 393 77242338 77241947 0.000000e+00 702
25 TraesCS3D01G469600 chr7D 85.106 282 35 6 1790 2070 118569030 118568755 5.020000e-72 281
26 TraesCS3D01G469600 chr1D 98.728 393 4 1 1 393 254418149 254417758 0.000000e+00 697
27 TraesCS3D01G469600 chr1A 98.728 393 4 1 1 393 554459554 554459163 0.000000e+00 697
28 TraesCS3D01G469600 chr2A 97.964 393 7 1 1 393 334594971 334595362 0.000000e+00 680


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 TraesCS3D01G469600 chr3D 571591337 571593723 2386 True 4409 4409 100.000 1 2387 1 chr3D.!!$R1 2386
1 TraesCS3D01G469600 chr3D 589279461 589280874 1413 True 2518 2518 98.799 392 1805 1 chr3D.!!$R2 1413
2 TraesCS3D01G469600 chr3D 595892727 595893296 569 False 765 765 90.925 1808 2378 1 chr3D.!!$F1 570
3 TraesCS3D01G469600 chr5D 503216885 503218299 1414 False 2540 2540 99.082 392 1805 1 chr5D.!!$F3 1413
4 TraesCS3D01G469600 chr5D 6187607 6189021 1414 False 2512 2512 98.728 392 1805 1 chr5D.!!$F2 1413
5 TraesCS3D01G469600 chr6D 168250207 168255007 4800 False 2522 2534 98.870 392 1805 2 chr6D.!!$F2 1413
6 TraesCS3D01G469600 chrUn 93409550 93410963 1413 True 2529 2529 98.941 392 1805 1 chrUn.!!$R1 1413
7 TraesCS3D01G469600 chrUn 216518521 216519935 1414 True 2529 2529 98.941 392 1805 1 chrUn.!!$R2 1413
8 TraesCS3D01G469600 chr3B 201525691 201527105 1414 False 2518 2518 98.799 392 1805 1 chr3B.!!$F1 1413
9 TraesCS3D01G469600 chr2D 272793812 272795226 1414 True 2512 2512 98.729 392 1805 1 chr2D.!!$R1 1413
10 TraesCS3D01G469600 chr2D 63385707 63386284 577 False 750 750 90.085 1796 2378 1 chr2D.!!$F2 582
11 TraesCS3D01G469600 chr2D 578493677 578494253 576 True 750 750 90.172 1801 2378 1 chr2D.!!$R2 577
12 TraesCS3D01G469600 chr2D 1648415 1648975 560 False 747 747 90.653 1796 2360 1 chr2D.!!$F1 564
13 TraesCS3D01G469600 chr2D 578550042 578550595 553 True 747 747 91.023 1806 2360 1 chr2D.!!$R3 554
14 TraesCS3D01G469600 chr7B 106494410 106494987 577 False 784 784 91.111 1796 2378 1 chr7B.!!$F1 582
15 TraesCS3D01G469600 chr4D 500231903 500232463 560 False 752 752 90.829 1796 2360 1 chr4D.!!$F1 564
16 TraesCS3D01G469600 chr2B 556443920 556444490 570 True 747 747 90.261 1806 2378 1 chr2B.!!$R1 572
17 TraesCS3D01G469600 chr7D 107828438 107829013 575 False 743 743 89.932 1796 2378 1 chr7D.!!$F1 582

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
53 54 0.036388 TTGGAACGTGGAGAGATGGC 60.036 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1859 5248 0.398318 GCCGGATCTAGCCCTTTGAT 59.602 55.0 5.05 0.0 0.0 2.57 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
23 24 6.850752 TCTTGCCTATATCATATCACGGAA 57.149 37.500 0.00 0.00 0.00 4.30
24 25 7.239763 TCTTGCCTATATCATATCACGGAAA 57.760 36.000 0.00 0.00 0.00 3.13
25 26 7.097192 TCTTGCCTATATCATATCACGGAAAC 58.903 38.462 0.00 0.00 0.00 2.78
26 27 5.730550 TGCCTATATCATATCACGGAAACC 58.269 41.667 0.00 0.00 0.00 3.27
27 28 5.483937 TGCCTATATCATATCACGGAAACCT 59.516 40.000 0.00 0.00 0.00 3.50
28 29 6.013725 TGCCTATATCATATCACGGAAACCTT 60.014 38.462 0.00 0.00 0.00 3.50
29 30 6.879458 GCCTATATCATATCACGGAAACCTTT 59.121 38.462 0.00 0.00 0.00 3.11
30 31 7.064728 GCCTATATCATATCACGGAAACCTTTC 59.935 40.741 0.00 0.00 36.46 2.62
31 32 7.275779 CCTATATCATATCACGGAAACCTTTCG 59.724 40.741 0.00 0.00 38.06 3.46
32 33 2.933906 TCATATCACGGAAACCTTTCGC 59.066 45.455 0.00 0.00 38.06 4.70
33 34 2.754946 TATCACGGAAACCTTTCGCT 57.245 45.000 0.00 0.00 38.06 4.93
34 35 1.892209 ATCACGGAAACCTTTCGCTT 58.108 45.000 0.00 0.00 38.06 4.68
35 36 1.670791 TCACGGAAACCTTTCGCTTT 58.329 45.000 0.00 0.00 38.06 3.51
36 37 1.332375 TCACGGAAACCTTTCGCTTTG 59.668 47.619 0.00 0.00 38.06 2.77
37 38 0.666374 ACGGAAACCTTTCGCTTTGG 59.334 50.000 0.00 0.00 38.06 3.28
38 39 0.948678 CGGAAACCTTTCGCTTTGGA 59.051 50.000 0.00 0.00 38.06 3.53
39 40 1.335496 CGGAAACCTTTCGCTTTGGAA 59.665 47.619 0.00 0.00 38.06 3.53
40 41 2.739292 GGAAACCTTTCGCTTTGGAAC 58.261 47.619 0.00 0.00 38.06 3.62
41 42 2.381589 GAAACCTTTCGCTTTGGAACG 58.618 47.619 0.00 0.00 0.00 3.95
42 43 1.385528 AACCTTTCGCTTTGGAACGT 58.614 45.000 0.00 0.00 0.00 3.99
43 44 0.661020 ACCTTTCGCTTTGGAACGTG 59.339 50.000 0.00 0.00 0.00 4.49
44 45 0.040425 CCTTTCGCTTTGGAACGTGG 60.040 55.000 0.00 0.00 0.00 4.94
45 46 0.941542 CTTTCGCTTTGGAACGTGGA 59.058 50.000 0.00 0.00 0.00 4.02
46 47 0.941542 TTTCGCTTTGGAACGTGGAG 59.058 50.000 0.00 0.00 0.00 3.86
47 48 0.105224 TTCGCTTTGGAACGTGGAGA 59.895 50.000 0.00 0.00 0.00 3.71
48 49 0.319555 TCGCTTTGGAACGTGGAGAG 60.320 55.000 0.00 0.00 0.00 3.20
49 50 0.319555 CGCTTTGGAACGTGGAGAGA 60.320 55.000 0.00 0.00 0.00 3.10
50 51 1.673033 CGCTTTGGAACGTGGAGAGAT 60.673 52.381 0.00 0.00 0.00 2.75
51 52 1.734465 GCTTTGGAACGTGGAGAGATG 59.266 52.381 0.00 0.00 0.00 2.90
52 53 2.350522 CTTTGGAACGTGGAGAGATGG 58.649 52.381 0.00 0.00 0.00 3.51
53 54 0.036388 TTGGAACGTGGAGAGATGGC 60.036 55.000 0.00 0.00 0.00 4.40
54 55 1.191489 TGGAACGTGGAGAGATGGCA 61.191 55.000 0.00 0.00 0.00 4.92
55 56 0.460987 GGAACGTGGAGAGATGGCAG 60.461 60.000 0.00 0.00 0.00 4.85
56 57 0.532573 GAACGTGGAGAGATGGCAGA 59.467 55.000 0.00 0.00 0.00 4.26
57 58 0.534412 AACGTGGAGAGATGGCAGAG 59.466 55.000 0.00 0.00 0.00 3.35
58 59 0.613292 ACGTGGAGAGATGGCAGAGT 60.613 55.000 0.00 0.00 0.00 3.24
59 60 0.179116 CGTGGAGAGATGGCAGAGTG 60.179 60.000 0.00 0.00 0.00 3.51
60 61 0.177604 GTGGAGAGATGGCAGAGTGG 59.822 60.000 0.00 0.00 0.00 4.00
61 62 0.041684 TGGAGAGATGGCAGAGTGGA 59.958 55.000 0.00 0.00 0.00 4.02
62 63 0.463620 GGAGAGATGGCAGAGTGGAC 59.536 60.000 0.00 0.00 0.00 4.02
63 64 1.484038 GAGAGATGGCAGAGTGGACT 58.516 55.000 0.00 0.00 0.00 3.85
64 65 2.660572 GAGAGATGGCAGAGTGGACTA 58.339 52.381 0.00 0.00 0.00 2.59
65 66 3.027412 GAGAGATGGCAGAGTGGACTAA 58.973 50.000 0.00 0.00 0.00 2.24
66 67 3.445008 AGAGATGGCAGAGTGGACTAAA 58.555 45.455 0.00 0.00 0.00 1.85
67 68 3.450457 AGAGATGGCAGAGTGGACTAAAG 59.550 47.826 0.00 0.00 0.00 1.85
68 69 2.093235 AGATGGCAGAGTGGACTAAAGC 60.093 50.000 0.00 0.00 0.00 3.51
69 70 0.037326 TGGCAGAGTGGACTAAAGCG 60.037 55.000 0.00 0.00 0.00 4.68
70 71 0.741221 GGCAGAGTGGACTAAAGCGG 60.741 60.000 0.00 0.00 0.00 5.52
71 72 1.362406 GCAGAGTGGACTAAAGCGGC 61.362 60.000 0.00 0.00 0.00 6.53
72 73 1.078759 CAGAGTGGACTAAAGCGGCG 61.079 60.000 0.51 0.51 0.00 6.46
73 74 1.810030 GAGTGGACTAAAGCGGCGG 60.810 63.158 9.78 0.00 0.00 6.13
74 75 2.221906 GAGTGGACTAAAGCGGCGGA 62.222 60.000 9.78 0.00 0.00 5.54
75 76 1.153429 GTGGACTAAAGCGGCGGAT 60.153 57.895 9.78 0.00 0.00 4.18
76 77 0.743345 GTGGACTAAAGCGGCGGATT 60.743 55.000 9.78 0.00 0.00 3.01
77 78 0.742990 TGGACTAAAGCGGCGGATTG 60.743 55.000 9.78 0.00 0.00 2.67
78 79 1.352056 GACTAAAGCGGCGGATTGC 59.648 57.895 9.78 0.00 45.38 3.56
79 80 1.078426 ACTAAAGCGGCGGATTGCT 60.078 52.632 9.78 0.00 45.43 3.91
80 81 0.177141 ACTAAAGCGGCGGATTGCTA 59.823 50.000 9.78 0.00 45.43 3.49
81 82 1.295792 CTAAAGCGGCGGATTGCTAA 58.704 50.000 9.78 0.00 45.43 3.09
82 83 1.873591 CTAAAGCGGCGGATTGCTAAT 59.126 47.619 9.78 0.00 45.43 1.73
83 84 0.663153 AAAGCGGCGGATTGCTAATC 59.337 50.000 9.78 0.00 45.43 1.75
98 99 8.460831 GATTGCTAATCCGTTGTACAATTTTT 57.539 30.769 12.26 6.45 31.60 1.94
115 116 1.881591 TTTTTGGTACCGAGGGTTCG 58.118 50.000 7.57 0.00 46.29 3.95
129 130 2.907634 GGGTTCGAATCCCTCTCTTTC 58.092 52.381 17.16 0.00 41.58 2.62
130 131 2.420269 GGGTTCGAATCCCTCTCTTTCC 60.420 54.545 17.16 0.09 41.58 3.13
131 132 2.541556 GTTCGAATCCCTCTCTTTCCG 58.458 52.381 0.00 0.00 0.00 4.30
132 133 0.460311 TCGAATCCCTCTCTTTCCGC 59.540 55.000 0.00 0.00 0.00 5.54
133 134 0.461961 CGAATCCCTCTCTTTCCGCT 59.538 55.000 0.00 0.00 0.00 5.52
134 135 1.537135 CGAATCCCTCTCTTTCCGCTC 60.537 57.143 0.00 0.00 0.00 5.03
135 136 0.833949 AATCCCTCTCTTTCCGCTCC 59.166 55.000 0.00 0.00 0.00 4.70
136 137 1.051556 ATCCCTCTCTTTCCGCTCCC 61.052 60.000 0.00 0.00 0.00 4.30
137 138 1.687493 CCCTCTCTTTCCGCTCCCT 60.687 63.158 0.00 0.00 0.00 4.20
138 139 1.268283 CCCTCTCTTTCCGCTCCCTT 61.268 60.000 0.00 0.00 0.00 3.95
139 140 0.107945 CCTCTCTTTCCGCTCCCTTG 60.108 60.000 0.00 0.00 0.00 3.61
140 141 0.107945 CTCTCTTTCCGCTCCCTTGG 60.108 60.000 0.00 0.00 0.00 3.61
141 142 0.544357 TCTCTTTCCGCTCCCTTGGA 60.544 55.000 0.00 0.00 0.00 3.53
142 143 0.543749 CTCTTTCCGCTCCCTTGGAT 59.456 55.000 0.00 0.00 33.42 3.41
143 144 0.541863 TCTTTCCGCTCCCTTGGATC 59.458 55.000 0.00 0.00 33.42 3.36
144 145 0.253044 CTTTCCGCTCCCTTGGATCA 59.747 55.000 0.00 0.00 33.42 2.92
145 146 0.918983 TTTCCGCTCCCTTGGATCAT 59.081 50.000 0.00 0.00 33.42 2.45
146 147 0.918983 TTCCGCTCCCTTGGATCATT 59.081 50.000 0.00 0.00 33.42 2.57
147 148 0.918983 TCCGCTCCCTTGGATCATTT 59.081 50.000 0.00 0.00 0.00 2.32
148 149 1.027357 CCGCTCCCTTGGATCATTTG 58.973 55.000 0.00 0.00 0.00 2.32
149 150 1.027357 CGCTCCCTTGGATCATTTGG 58.973 55.000 0.00 0.00 0.00 3.28
150 151 1.406903 GCTCCCTTGGATCATTTGGG 58.593 55.000 0.00 0.38 39.22 4.12
151 152 1.063717 GCTCCCTTGGATCATTTGGGA 60.064 52.381 12.41 12.41 43.93 4.37
152 153 2.659428 CTCCCTTGGATCATTTGGGAC 58.341 52.381 9.90 0.00 41.57 4.46
153 154 2.243221 CTCCCTTGGATCATTTGGGACT 59.757 50.000 9.90 0.00 41.57 3.85
154 155 2.654385 TCCCTTGGATCATTTGGGACTT 59.346 45.455 9.90 0.00 41.57 3.01
155 156 3.077391 TCCCTTGGATCATTTGGGACTTT 59.923 43.478 9.90 0.00 41.57 2.66
156 157 3.448660 CCCTTGGATCATTTGGGACTTTC 59.551 47.826 6.49 0.00 40.23 2.62
157 158 3.129287 CCTTGGATCATTTGGGACTTTCG 59.871 47.826 0.00 0.00 0.00 3.46
158 159 3.712016 TGGATCATTTGGGACTTTCGA 57.288 42.857 0.00 0.00 0.00 3.71
159 160 4.027674 TGGATCATTTGGGACTTTCGAA 57.972 40.909 0.00 0.00 0.00 3.71
160 161 4.599041 TGGATCATTTGGGACTTTCGAAT 58.401 39.130 0.00 0.00 0.00 3.34
161 162 5.016173 TGGATCATTTGGGACTTTCGAATT 58.984 37.500 0.00 0.00 0.00 2.17
162 163 5.105797 TGGATCATTTGGGACTTTCGAATTG 60.106 40.000 0.00 0.00 0.00 2.32
163 164 4.782019 TCATTTGGGACTTTCGAATTGG 57.218 40.909 0.00 0.00 0.00 3.16
164 165 4.402829 TCATTTGGGACTTTCGAATTGGA 58.597 39.130 0.00 0.00 0.00 3.53
165 166 4.830046 TCATTTGGGACTTTCGAATTGGAA 59.170 37.500 0.00 0.00 0.00 3.53
166 167 5.303078 TCATTTGGGACTTTCGAATTGGAAA 59.697 36.000 13.99 13.99 34.87 3.13
177 178 5.880054 TCGAATTGGAAAGAATTCTGACC 57.120 39.130 9.17 15.19 39.32 4.02
178 179 4.700213 TCGAATTGGAAAGAATTCTGACCC 59.300 41.667 21.01 16.63 39.32 4.46
179 180 4.142381 CGAATTGGAAAGAATTCTGACCCC 60.142 45.833 21.01 14.76 39.32 4.95
180 181 2.899303 TGGAAAGAATTCTGACCCCC 57.101 50.000 21.01 13.44 35.79 5.40
181 182 1.004277 TGGAAAGAATTCTGACCCCCG 59.996 52.381 21.01 0.00 35.79 5.73
182 183 1.682087 GGAAAGAATTCTGACCCCCGG 60.682 57.143 9.17 0.00 35.79 5.73
183 184 1.280998 GAAAGAATTCTGACCCCCGGA 59.719 52.381 9.17 0.00 32.57 5.14
184 185 1.596496 AAGAATTCTGACCCCCGGAT 58.404 50.000 9.17 0.00 0.00 4.18
185 186 1.596496 AGAATTCTGACCCCCGGATT 58.404 50.000 7.30 0.00 0.00 3.01
186 187 1.923148 AGAATTCTGACCCCCGGATTT 59.077 47.619 7.30 0.00 0.00 2.17
187 188 2.311841 AGAATTCTGACCCCCGGATTTT 59.688 45.455 7.30 0.00 0.00 1.82
188 189 2.437085 ATTCTGACCCCCGGATTTTC 57.563 50.000 0.73 0.00 0.00 2.29
189 190 1.368374 TTCTGACCCCCGGATTTTCT 58.632 50.000 0.73 0.00 0.00 2.52
190 191 0.909623 TCTGACCCCCGGATTTTCTC 59.090 55.000 0.73 0.00 0.00 2.87
191 192 0.618458 CTGACCCCCGGATTTTCTCA 59.382 55.000 0.73 0.00 0.00 3.27
192 193 1.212935 CTGACCCCCGGATTTTCTCAT 59.787 52.381 0.73 0.00 0.00 2.90
193 194 2.438021 CTGACCCCCGGATTTTCTCATA 59.562 50.000 0.73 0.00 0.00 2.15
194 195 2.438021 TGACCCCCGGATTTTCTCATAG 59.562 50.000 0.73 0.00 0.00 2.23
195 196 2.704065 GACCCCCGGATTTTCTCATAGA 59.296 50.000 0.73 0.00 0.00 1.98
196 197 3.327439 ACCCCCGGATTTTCTCATAGAT 58.673 45.455 0.73 0.00 0.00 1.98
197 198 4.499472 ACCCCCGGATTTTCTCATAGATA 58.501 43.478 0.73 0.00 0.00 1.98
198 199 4.911522 ACCCCCGGATTTTCTCATAGATAA 59.088 41.667 0.73 0.00 0.00 1.75
199 200 5.371472 ACCCCCGGATTTTCTCATAGATAAA 59.629 40.000 0.73 0.00 0.00 1.40
200 201 6.045577 ACCCCCGGATTTTCTCATAGATAAAT 59.954 38.462 0.73 0.00 0.00 1.40
201 202 6.375455 CCCCCGGATTTTCTCATAGATAAATG 59.625 42.308 0.73 0.00 0.00 2.32
202 203 6.942576 CCCCGGATTTTCTCATAGATAAATGT 59.057 38.462 0.73 0.00 0.00 2.71
203 204 8.100791 CCCCGGATTTTCTCATAGATAAATGTA 58.899 37.037 0.73 0.00 0.00 2.29
204 205 8.936864 CCCGGATTTTCTCATAGATAAATGTAC 58.063 37.037 0.73 0.00 0.00 2.90
205 206 8.648097 CCGGATTTTCTCATAGATAAATGTACG 58.352 37.037 0.00 0.00 0.00 3.67
206 207 9.406828 CGGATTTTCTCATAGATAAATGTACGA 57.593 33.333 0.00 0.00 0.00 3.43
250 251 4.663636 AACTGAATTTTTACTCCTCGCG 57.336 40.909 0.00 0.00 0.00 5.87
251 252 3.660865 ACTGAATTTTTACTCCTCGCGT 58.339 40.909 5.77 0.00 0.00 6.01
252 253 3.678548 ACTGAATTTTTACTCCTCGCGTC 59.321 43.478 5.77 0.00 0.00 5.19
253 254 2.997986 TGAATTTTTACTCCTCGCGTCC 59.002 45.455 5.77 0.00 0.00 4.79
254 255 2.754946 ATTTTTACTCCTCGCGTCCA 57.245 45.000 5.77 0.00 0.00 4.02
255 256 2.074547 TTTTTACTCCTCGCGTCCAG 57.925 50.000 5.77 2.47 0.00 3.86
256 257 0.245539 TTTTACTCCTCGCGTCCAGG 59.754 55.000 5.77 5.90 0.00 4.45
257 258 0.609957 TTTACTCCTCGCGTCCAGGA 60.610 55.000 13.75 13.75 37.75 3.86
258 259 0.395311 TTACTCCTCGCGTCCAGGAT 60.395 55.000 14.70 8.45 39.44 3.24
259 260 0.395311 TACTCCTCGCGTCCAGGATT 60.395 55.000 14.70 11.97 39.44 3.01
260 261 1.066587 CTCCTCGCGTCCAGGATTC 59.933 63.158 14.70 0.00 39.44 2.52
261 262 2.107141 CCTCGCGTCCAGGATTCC 59.893 66.667 5.77 0.00 31.91 3.01
262 263 2.278857 CTCGCGTCCAGGATTCCG 60.279 66.667 5.77 0.00 0.00 4.30
263 264 3.064987 CTCGCGTCCAGGATTCCGT 62.065 63.158 5.77 0.00 0.00 4.69
264 265 2.582498 CGCGTCCAGGATTCCGTC 60.582 66.667 0.00 0.00 0.00 4.79
272 273 3.721868 GGATTCCGTCCTGGGTCA 58.278 61.111 0.00 0.00 44.16 4.02
273 274 2.221918 GGATTCCGTCCTGGGTCAT 58.778 57.895 0.00 0.00 44.16 3.06
274 275 0.546598 GGATTCCGTCCTGGGTCATT 59.453 55.000 0.00 0.00 44.16 2.57
275 276 1.766496 GGATTCCGTCCTGGGTCATTA 59.234 52.381 0.00 0.00 44.16 1.90
276 277 2.224305 GGATTCCGTCCTGGGTCATTAG 60.224 54.545 0.00 0.00 44.16 1.73
277 278 2.241281 TTCCGTCCTGGGTCATTAGA 57.759 50.000 0.00 0.00 38.76 2.10
278 279 2.471815 TCCGTCCTGGGTCATTAGAT 57.528 50.000 0.00 0.00 38.76 1.98
279 280 3.605726 TCCGTCCTGGGTCATTAGATA 57.394 47.619 0.00 0.00 38.76 1.98
280 281 3.918566 TCCGTCCTGGGTCATTAGATAA 58.081 45.455 0.00 0.00 38.76 1.75
281 282 3.895656 TCCGTCCTGGGTCATTAGATAAG 59.104 47.826 0.00 0.00 38.76 1.73
282 283 3.895656 CCGTCCTGGGTCATTAGATAAGA 59.104 47.826 0.00 0.00 0.00 2.10
283 284 4.344102 CCGTCCTGGGTCATTAGATAAGAA 59.656 45.833 0.00 0.00 0.00 2.52
284 285 5.012148 CCGTCCTGGGTCATTAGATAAGAAT 59.988 44.000 0.00 0.00 0.00 2.40
285 286 6.159988 CGTCCTGGGTCATTAGATAAGAATC 58.840 44.000 0.00 0.00 0.00 2.52
286 287 6.468543 GTCCTGGGTCATTAGATAAGAATCC 58.531 44.000 0.00 0.00 31.98 3.01
287 288 6.043243 GTCCTGGGTCATTAGATAAGAATCCA 59.957 42.308 0.00 0.00 31.98 3.41
288 289 6.619437 TCCTGGGTCATTAGATAAGAATCCAA 59.381 38.462 0.00 0.00 31.98 3.53
289 290 7.128728 TCCTGGGTCATTAGATAAGAATCCAAA 59.871 37.037 0.00 0.00 31.98 3.28
290 291 7.446625 CCTGGGTCATTAGATAAGAATCCAAAG 59.553 40.741 0.00 0.00 31.98 2.77
291 292 8.101309 TGGGTCATTAGATAAGAATCCAAAGA 57.899 34.615 0.00 0.00 31.98 2.52
292 293 8.727149 TGGGTCATTAGATAAGAATCCAAAGAT 58.273 33.333 0.00 0.00 31.98 2.40
305 306 8.924511 AGAATCCAAAGATAAAGAGTGAAACA 57.075 30.769 0.00 0.00 32.62 2.83
306 307 9.354673 AGAATCCAAAGATAAAGAGTGAAACAA 57.645 29.630 0.00 0.00 32.62 2.83
307 308 9.965824 GAATCCAAAGATAAAGAGTGAAACAAA 57.034 29.630 0.00 0.00 32.62 2.83
308 309 9.971922 AATCCAAAGATAAAGAGTGAAACAAAG 57.028 29.630 0.00 0.00 32.62 2.77
309 310 8.746052 TCCAAAGATAAAGAGTGAAACAAAGA 57.254 30.769 0.00 0.00 41.43 2.52
310 311 9.184523 TCCAAAGATAAAGAGTGAAACAAAGAA 57.815 29.630 0.00 0.00 41.43 2.52
311 312 9.971922 CCAAAGATAAAGAGTGAAACAAAGAAT 57.028 29.630 0.00 0.00 41.43 2.40
350 351 7.573968 AACAGAAAGTTTGAGAGTAAGCATT 57.426 32.000 0.00 0.00 37.03 3.56
351 352 8.677148 AACAGAAAGTTTGAGAGTAAGCATTA 57.323 30.769 0.00 0.00 37.03 1.90
352 353 8.560374 AACAGAAAGTTTGAGAGTAAGCATTAC 58.440 33.333 0.00 0.00 44.43 1.89
415 416 2.099405 CCCAATTTGCGACCTACCATT 58.901 47.619 0.00 0.00 0.00 3.16
1071 4460 3.450904 ACCTAGCCAACACTTAGATCCA 58.549 45.455 0.00 0.00 0.00 3.41
1278 4667 5.829391 TGTGATTTCTATGTTATGCATGGCT 59.171 36.000 10.16 0.00 38.47 4.75
1742 5131 4.980805 TCCGGTTCTGTGCGTGCC 62.981 66.667 0.00 0.00 0.00 5.01
1851 5240 1.908793 CACCGGTCAGACCCAGTCT 60.909 63.158 14.46 0.00 44.44 3.24
1859 5248 3.143010 AGACCCAGTCTGTCGGAAA 57.857 52.632 0.00 0.00 41.76 3.13
1866 5255 2.744202 CCAGTCTGTCGGAAATCAAAGG 59.256 50.000 0.00 0.00 0.00 3.11
1907 5296 0.178955 TGTCAGGGTTAGACGGGACA 60.179 55.000 0.00 0.00 38.83 4.02
1985 5377 3.357079 GTGGAAGCGTGGTGGCAG 61.357 66.667 0.00 0.00 34.64 4.85
2085 5477 1.515521 GCCACCACAGCTTACACACC 61.516 60.000 0.00 0.00 0.00 4.16
2087 5479 1.545428 CCACCACAGCTTACACACCAT 60.545 52.381 0.00 0.00 0.00 3.55
2158 5550 3.056393 TCATGGAAAACGGACTATCACGT 60.056 43.478 0.00 0.00 46.48 4.49
2215 5607 4.761975 TGAAAGTTTCACCGTAACTGTCT 58.238 39.130 14.35 0.00 39.53 3.41
2234 5626 7.535997 ACTGTCTGTTTTCTTAACAAAAGTCC 58.464 34.615 0.00 0.00 0.00 3.85
2266 5658 2.481449 GGAGCTCACGTCGTATGGATTT 60.481 50.000 17.19 0.00 0.00 2.17
2383 5778 7.851822 ATATATTAAAAATGCAAAGCCGTCG 57.148 32.000 0.00 0.00 0.00 5.12
2384 5779 2.339728 TAAAAATGCAAAGCCGTCGG 57.660 45.000 6.99 6.99 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.850752 TTCCGTGATATGATATAGGCAAGA 57.149 37.500 0.00 0.00 0.00 3.02
1 2 6.313905 GGTTTCCGTGATATGATATAGGCAAG 59.686 42.308 0.00 0.00 0.00 4.01
2 3 6.013725 AGGTTTCCGTGATATGATATAGGCAA 60.014 38.462 0.00 0.00 0.00 4.52
5 6 7.275779 CGAAAGGTTTCCGTGATATGATATAGG 59.724 40.741 0.00 0.00 33.68 2.57
6 7 7.201444 GCGAAAGGTTTCCGTGATATGATATAG 60.201 40.741 0.00 0.00 33.68 1.31
7 8 6.588756 GCGAAAGGTTTCCGTGATATGATATA 59.411 38.462 0.00 0.00 33.68 0.86
8 9 5.408604 GCGAAAGGTTTCCGTGATATGATAT 59.591 40.000 0.00 0.00 33.68 1.63
9 10 4.748102 GCGAAAGGTTTCCGTGATATGATA 59.252 41.667 0.00 0.00 33.68 2.15
10 11 3.560068 GCGAAAGGTTTCCGTGATATGAT 59.440 43.478 0.00 0.00 33.68 2.45
11 12 2.933906 GCGAAAGGTTTCCGTGATATGA 59.066 45.455 0.00 0.00 33.68 2.15
12 13 2.936498 AGCGAAAGGTTTCCGTGATATG 59.064 45.455 0.00 0.00 40.01 1.78
13 14 3.261981 AGCGAAAGGTTTCCGTGATAT 57.738 42.857 0.00 0.00 40.01 1.63
14 15 2.754946 AGCGAAAGGTTTCCGTGATA 57.245 45.000 0.00 0.00 40.01 2.15
15 16 3.625745 AGCGAAAGGTTTCCGTGAT 57.374 47.368 0.00 0.00 40.01 3.06
25 26 0.040425 CCACGTTCCAAAGCGAAAGG 60.040 55.000 0.00 0.00 0.00 3.11
26 27 0.941542 TCCACGTTCCAAAGCGAAAG 59.058 50.000 0.00 0.00 0.00 2.62
27 28 0.941542 CTCCACGTTCCAAAGCGAAA 59.058 50.000 0.00 0.00 0.00 3.46
28 29 0.105224 TCTCCACGTTCCAAAGCGAA 59.895 50.000 0.00 0.00 0.00 4.70
29 30 0.319555 CTCTCCACGTTCCAAAGCGA 60.320 55.000 0.00 0.00 0.00 4.93
30 31 0.319555 TCTCTCCACGTTCCAAAGCG 60.320 55.000 0.00 0.00 0.00 4.68
31 32 1.734465 CATCTCTCCACGTTCCAAAGC 59.266 52.381 0.00 0.00 0.00 3.51
32 33 2.350522 CCATCTCTCCACGTTCCAAAG 58.649 52.381 0.00 0.00 0.00 2.77
33 34 1.610624 GCCATCTCTCCACGTTCCAAA 60.611 52.381 0.00 0.00 0.00 3.28
34 35 0.036388 GCCATCTCTCCACGTTCCAA 60.036 55.000 0.00 0.00 0.00 3.53
35 36 1.191489 TGCCATCTCTCCACGTTCCA 61.191 55.000 0.00 0.00 0.00 3.53
36 37 0.460987 CTGCCATCTCTCCACGTTCC 60.461 60.000 0.00 0.00 0.00 3.62
37 38 0.532573 TCTGCCATCTCTCCACGTTC 59.467 55.000 0.00 0.00 0.00 3.95
38 39 0.534412 CTCTGCCATCTCTCCACGTT 59.466 55.000 0.00 0.00 0.00 3.99
39 40 0.613292 ACTCTGCCATCTCTCCACGT 60.613 55.000 0.00 0.00 0.00 4.49
40 41 0.179116 CACTCTGCCATCTCTCCACG 60.179 60.000 0.00 0.00 0.00 4.94
41 42 0.177604 CCACTCTGCCATCTCTCCAC 59.822 60.000 0.00 0.00 0.00 4.02
42 43 0.041684 TCCACTCTGCCATCTCTCCA 59.958 55.000 0.00 0.00 0.00 3.86
43 44 0.463620 GTCCACTCTGCCATCTCTCC 59.536 60.000 0.00 0.00 0.00 3.71
44 45 1.484038 AGTCCACTCTGCCATCTCTC 58.516 55.000 0.00 0.00 0.00 3.20
45 46 2.836636 TAGTCCACTCTGCCATCTCT 57.163 50.000 0.00 0.00 0.00 3.10
46 47 3.791245 CTTTAGTCCACTCTGCCATCTC 58.209 50.000 0.00 0.00 0.00 2.75
47 48 2.093235 GCTTTAGTCCACTCTGCCATCT 60.093 50.000 0.00 0.00 0.00 2.90
48 49 2.284190 GCTTTAGTCCACTCTGCCATC 58.716 52.381 0.00 0.00 0.00 3.51
49 50 1.406069 CGCTTTAGTCCACTCTGCCAT 60.406 52.381 0.00 0.00 0.00 4.40
50 51 0.037326 CGCTTTAGTCCACTCTGCCA 60.037 55.000 0.00 0.00 0.00 4.92
51 52 0.741221 CCGCTTTAGTCCACTCTGCC 60.741 60.000 0.00 0.00 0.00 4.85
52 53 1.362406 GCCGCTTTAGTCCACTCTGC 61.362 60.000 0.00 0.00 0.00 4.26
53 54 1.078759 CGCCGCTTTAGTCCACTCTG 61.079 60.000 0.00 0.00 0.00 3.35
54 55 1.215647 CGCCGCTTTAGTCCACTCT 59.784 57.895 0.00 0.00 0.00 3.24
55 56 1.810030 CCGCCGCTTTAGTCCACTC 60.810 63.158 0.00 0.00 0.00 3.51
56 57 1.614241 ATCCGCCGCTTTAGTCCACT 61.614 55.000 0.00 0.00 0.00 4.00
57 58 0.743345 AATCCGCCGCTTTAGTCCAC 60.743 55.000 0.00 0.00 0.00 4.02
58 59 0.742990 CAATCCGCCGCTTTAGTCCA 60.743 55.000 0.00 0.00 0.00 4.02
59 60 2.014594 CAATCCGCCGCTTTAGTCC 58.985 57.895 0.00 0.00 0.00 3.85
60 61 1.090052 AGCAATCCGCCGCTTTAGTC 61.090 55.000 0.00 0.00 44.04 2.59
61 62 0.177141 TAGCAATCCGCCGCTTTAGT 59.823 50.000 0.00 0.00 44.04 2.24
62 63 1.295792 TTAGCAATCCGCCGCTTTAG 58.704 50.000 0.00 0.00 44.04 1.85
63 64 1.871039 GATTAGCAATCCGCCGCTTTA 59.129 47.619 0.00 0.00 44.04 1.85
64 65 0.663153 GATTAGCAATCCGCCGCTTT 59.337 50.000 0.00 0.00 44.04 3.51
65 66 2.321213 GATTAGCAATCCGCCGCTT 58.679 52.632 0.00 0.00 44.04 4.68
66 67 4.049393 GATTAGCAATCCGCCGCT 57.951 55.556 0.00 0.00 44.04 5.52
73 74 8.460831 AAAAATTGTACAACGGATTAGCAATC 57.539 30.769 11.22 0.00 37.17 2.67
96 97 1.415659 TCGAACCCTCGGTACCAAAAA 59.584 47.619 13.54 0.00 45.49 1.94
97 98 1.047002 TCGAACCCTCGGTACCAAAA 58.953 50.000 13.54 0.00 45.49 2.44
98 99 1.047002 TTCGAACCCTCGGTACCAAA 58.953 50.000 13.54 0.00 45.49 3.28
99 100 1.205417 GATTCGAACCCTCGGTACCAA 59.795 52.381 13.54 0.00 45.49 3.67
100 101 0.819582 GATTCGAACCCTCGGTACCA 59.180 55.000 13.54 0.00 45.49 3.25
101 102 0.103755 GGATTCGAACCCTCGGTACC 59.896 60.000 0.00 0.16 45.49 3.34
102 103 0.103755 GGGATTCGAACCCTCGGTAC 59.896 60.000 21.61 0.00 45.49 3.34
103 104 2.508361 GGGATTCGAACCCTCGGTA 58.492 57.895 21.61 0.00 45.49 4.02
104 105 3.306379 GGGATTCGAACCCTCGGT 58.694 61.111 21.61 0.00 45.49 4.69
110 111 2.738964 CGGAAAGAGAGGGATTCGAACC 60.739 54.545 0.00 4.00 0.00 3.62
111 112 2.541556 CGGAAAGAGAGGGATTCGAAC 58.458 52.381 0.00 0.00 0.00 3.95
112 113 1.134788 GCGGAAAGAGAGGGATTCGAA 60.135 52.381 0.00 0.00 0.00 3.71
113 114 0.460311 GCGGAAAGAGAGGGATTCGA 59.540 55.000 0.00 0.00 0.00 3.71
114 115 0.461961 AGCGGAAAGAGAGGGATTCG 59.538 55.000 0.00 0.00 0.00 3.34
115 116 1.202592 GGAGCGGAAAGAGAGGGATTC 60.203 57.143 0.00 0.00 0.00 2.52
116 117 0.833949 GGAGCGGAAAGAGAGGGATT 59.166 55.000 0.00 0.00 0.00 3.01
117 118 1.051556 GGGAGCGGAAAGAGAGGGAT 61.052 60.000 0.00 0.00 0.00 3.85
118 119 1.686110 GGGAGCGGAAAGAGAGGGA 60.686 63.158 0.00 0.00 0.00 4.20
119 120 1.268283 AAGGGAGCGGAAAGAGAGGG 61.268 60.000 0.00 0.00 0.00 4.30
120 121 0.107945 CAAGGGAGCGGAAAGAGAGG 60.108 60.000 0.00 0.00 0.00 3.69
121 122 0.107945 CCAAGGGAGCGGAAAGAGAG 60.108 60.000 0.00 0.00 0.00 3.20
122 123 0.544357 TCCAAGGGAGCGGAAAGAGA 60.544 55.000 0.00 0.00 0.00 3.10
123 124 0.543749 ATCCAAGGGAGCGGAAAGAG 59.456 55.000 0.00 0.00 34.05 2.85
124 125 0.541863 GATCCAAGGGAGCGGAAAGA 59.458 55.000 0.00 0.00 34.05 2.52
125 126 0.253044 TGATCCAAGGGAGCGGAAAG 59.747 55.000 0.00 0.00 41.58 2.62
126 127 0.918983 ATGATCCAAGGGAGCGGAAA 59.081 50.000 0.00 0.00 41.58 3.13
127 128 0.918983 AATGATCCAAGGGAGCGGAA 59.081 50.000 0.00 0.00 41.58 4.30
128 129 0.918983 AAATGATCCAAGGGAGCGGA 59.081 50.000 0.00 0.00 41.58 5.54
129 130 1.027357 CAAATGATCCAAGGGAGCGG 58.973 55.000 0.00 0.00 41.58 5.52
130 131 1.027357 CCAAATGATCCAAGGGAGCG 58.973 55.000 0.00 0.00 41.58 5.03
131 132 1.063717 TCCCAAATGATCCAAGGGAGC 60.064 52.381 7.91 0.00 43.39 4.70
133 134 2.287584 AGTCCCAAATGATCCAAGGGA 58.712 47.619 7.91 7.91 45.94 4.20
134 135 2.834638 AGTCCCAAATGATCCAAGGG 57.165 50.000 0.00 0.00 40.98 3.95
135 136 3.129287 CGAAAGTCCCAAATGATCCAAGG 59.871 47.826 0.00 0.00 0.00 3.61
136 137 4.009675 TCGAAAGTCCCAAATGATCCAAG 58.990 43.478 0.00 0.00 0.00 3.61
137 138 4.027674 TCGAAAGTCCCAAATGATCCAA 57.972 40.909 0.00 0.00 0.00 3.53
138 139 3.712016 TCGAAAGTCCCAAATGATCCA 57.288 42.857 0.00 0.00 0.00 3.41
139 140 5.343249 CAATTCGAAAGTCCCAAATGATCC 58.657 41.667 0.00 0.00 0.00 3.36
140 141 5.125417 TCCAATTCGAAAGTCCCAAATGATC 59.875 40.000 0.00 0.00 0.00 2.92
141 142 5.016173 TCCAATTCGAAAGTCCCAAATGAT 58.984 37.500 0.00 0.00 0.00 2.45
142 143 4.402829 TCCAATTCGAAAGTCCCAAATGA 58.597 39.130 0.00 0.00 0.00 2.57
143 144 4.782019 TCCAATTCGAAAGTCCCAAATG 57.218 40.909 0.00 0.00 0.00 2.32
144 145 5.538433 TCTTTCCAATTCGAAAGTCCCAAAT 59.462 36.000 20.49 0.00 45.89 2.32
145 146 4.890581 TCTTTCCAATTCGAAAGTCCCAAA 59.109 37.500 20.49 2.80 45.89 3.28
146 147 4.465886 TCTTTCCAATTCGAAAGTCCCAA 58.534 39.130 20.49 3.40 45.89 4.12
147 148 4.093472 TCTTTCCAATTCGAAAGTCCCA 57.907 40.909 20.49 3.71 45.89 4.37
148 149 5.644977 ATTCTTTCCAATTCGAAAGTCCC 57.355 39.130 20.49 0.00 45.89 4.46
149 150 6.803807 CAGAATTCTTTCCAATTCGAAAGTCC 59.196 38.462 20.49 11.01 45.89 3.85
150 151 7.535599 GTCAGAATTCTTTCCAATTCGAAAGTC 59.464 37.037 20.49 13.26 45.89 3.01
151 152 7.363431 GTCAGAATTCTTTCCAATTCGAAAGT 58.637 34.615 20.49 6.24 45.89 2.66
152 153 6.803807 GGTCAGAATTCTTTCCAATTCGAAAG 59.196 38.462 16.73 16.73 46.72 2.62
153 154 6.294508 GGGTCAGAATTCTTTCCAATTCGAAA 60.295 38.462 20.53 0.00 44.40 3.46
154 155 5.183140 GGGTCAGAATTCTTTCCAATTCGAA 59.817 40.000 20.53 0.00 44.40 3.71
155 156 4.700213 GGGTCAGAATTCTTTCCAATTCGA 59.300 41.667 20.53 5.46 44.40 3.71
156 157 4.142381 GGGGTCAGAATTCTTTCCAATTCG 60.142 45.833 20.53 3.48 44.40 3.34
157 158 4.160439 GGGGGTCAGAATTCTTTCCAATTC 59.840 45.833 20.53 8.56 41.37 2.17
158 159 4.096681 GGGGGTCAGAATTCTTTCCAATT 58.903 43.478 20.53 0.00 31.84 2.32
159 160 3.713003 GGGGGTCAGAATTCTTTCCAAT 58.287 45.455 20.53 0.00 31.84 3.16
160 161 2.554344 CGGGGGTCAGAATTCTTTCCAA 60.554 50.000 20.53 0.00 31.84 3.53
161 162 1.004277 CGGGGGTCAGAATTCTTTCCA 59.996 52.381 20.53 0.10 31.84 3.53
162 163 1.682087 CCGGGGGTCAGAATTCTTTCC 60.682 57.143 4.86 10.79 31.84 3.13
163 164 1.280998 TCCGGGGGTCAGAATTCTTTC 59.719 52.381 4.86 1.70 0.00 2.62
164 165 1.368374 TCCGGGGGTCAGAATTCTTT 58.632 50.000 4.86 0.00 0.00 2.52
165 166 1.596496 ATCCGGGGGTCAGAATTCTT 58.404 50.000 4.86 0.00 0.00 2.52
166 167 1.596496 AATCCGGGGGTCAGAATTCT 58.404 50.000 0.88 0.88 0.00 2.40
167 168 2.437085 AAATCCGGGGGTCAGAATTC 57.563 50.000 0.00 0.00 0.00 2.17
168 169 2.311841 AGAAAATCCGGGGGTCAGAATT 59.688 45.455 0.00 0.00 0.00 2.17
169 170 1.923148 AGAAAATCCGGGGGTCAGAAT 59.077 47.619 0.00 0.00 0.00 2.40
170 171 1.280998 GAGAAAATCCGGGGGTCAGAA 59.719 52.381 0.00 0.00 0.00 3.02
171 172 0.909623 GAGAAAATCCGGGGGTCAGA 59.090 55.000 0.00 0.00 0.00 3.27
172 173 0.618458 TGAGAAAATCCGGGGGTCAG 59.382 55.000 0.00 0.00 0.00 3.51
173 174 1.295020 ATGAGAAAATCCGGGGGTCA 58.705 50.000 0.00 0.00 0.00 4.02
174 175 2.704065 TCTATGAGAAAATCCGGGGGTC 59.296 50.000 0.00 0.00 0.00 4.46
175 176 2.771688 TCTATGAGAAAATCCGGGGGT 58.228 47.619 0.00 0.00 0.00 4.95
176 177 5.499004 TTATCTATGAGAAAATCCGGGGG 57.501 43.478 0.00 0.00 0.00 5.40
177 178 6.942576 ACATTTATCTATGAGAAAATCCGGGG 59.057 38.462 0.00 0.00 0.00 5.73
178 179 7.986085 ACATTTATCTATGAGAAAATCCGGG 57.014 36.000 0.00 0.00 0.00 5.73
179 180 8.648097 CGTACATTTATCTATGAGAAAATCCGG 58.352 37.037 0.00 0.00 0.00 5.14
180 181 9.406828 TCGTACATTTATCTATGAGAAAATCCG 57.593 33.333 0.00 0.00 0.00 4.18
227 228 5.008316 ACGCGAGGAGTAAAAATTCAGTTTT 59.992 36.000 15.93 0.00 41.69 2.43
228 229 4.514066 ACGCGAGGAGTAAAAATTCAGTTT 59.486 37.500 15.93 0.00 0.00 2.66
229 230 4.062991 ACGCGAGGAGTAAAAATTCAGTT 58.937 39.130 15.93 0.00 0.00 3.16
230 231 3.660865 ACGCGAGGAGTAAAAATTCAGT 58.339 40.909 15.93 0.00 0.00 3.41
231 232 3.062234 GGACGCGAGGAGTAAAAATTCAG 59.938 47.826 15.93 0.00 0.00 3.02
232 233 2.997986 GGACGCGAGGAGTAAAAATTCA 59.002 45.455 15.93 0.00 0.00 2.57
233 234 2.997986 TGGACGCGAGGAGTAAAAATTC 59.002 45.455 15.93 0.00 0.00 2.17
234 235 3.000727 CTGGACGCGAGGAGTAAAAATT 58.999 45.455 15.93 0.00 0.00 1.82
235 236 2.618053 CTGGACGCGAGGAGTAAAAAT 58.382 47.619 15.93 0.00 0.00 1.82
236 237 1.337447 CCTGGACGCGAGGAGTAAAAA 60.337 52.381 15.93 0.00 30.68 1.94
237 238 0.245539 CCTGGACGCGAGGAGTAAAA 59.754 55.000 15.93 0.00 30.68 1.52
238 239 0.609957 TCCTGGACGCGAGGAGTAAA 60.610 55.000 15.93 0.00 33.54 2.01
239 240 0.395311 ATCCTGGACGCGAGGAGTAA 60.395 55.000 15.93 0.00 41.41 2.24
240 241 0.395311 AATCCTGGACGCGAGGAGTA 60.395 55.000 15.93 0.00 41.41 2.59
241 242 1.668101 GAATCCTGGACGCGAGGAGT 61.668 60.000 15.93 14.88 41.41 3.85
242 243 1.066587 GAATCCTGGACGCGAGGAG 59.933 63.158 15.93 4.41 41.41 3.69
243 244 2.423898 GGAATCCTGGACGCGAGGA 61.424 63.158 15.93 16.23 42.25 3.71
244 245 2.107141 GGAATCCTGGACGCGAGG 59.893 66.667 15.93 10.08 0.00 4.63
245 246 2.278857 CGGAATCCTGGACGCGAG 60.279 66.667 15.93 0.00 0.00 5.03
246 247 3.060020 GACGGAATCCTGGACGCGA 62.060 63.158 15.93 0.00 0.00 5.87
247 248 2.582498 GACGGAATCCTGGACGCG 60.582 66.667 3.53 3.53 0.00 6.01
248 249 2.202892 GGACGGAATCCTGGACGC 60.203 66.667 0.00 0.00 45.22 5.19
256 257 2.698797 TCTAATGACCCAGGACGGAATC 59.301 50.000 0.00 0.00 36.56 2.52
257 258 2.759355 TCTAATGACCCAGGACGGAAT 58.241 47.619 0.00 0.00 36.56 3.01
258 259 2.241281 TCTAATGACCCAGGACGGAA 57.759 50.000 0.00 0.00 36.56 4.30
259 260 2.471815 ATCTAATGACCCAGGACGGA 57.528 50.000 0.00 0.00 36.56 4.69
260 261 3.895656 TCTTATCTAATGACCCAGGACGG 59.104 47.826 0.00 0.00 0.00 4.79
261 262 5.531122 TTCTTATCTAATGACCCAGGACG 57.469 43.478 0.00 0.00 0.00 4.79
262 263 6.043243 TGGATTCTTATCTAATGACCCAGGAC 59.957 42.308 0.00 0.00 0.00 3.85
263 264 6.150332 TGGATTCTTATCTAATGACCCAGGA 58.850 40.000 0.00 0.00 0.00 3.86
264 265 6.439636 TGGATTCTTATCTAATGACCCAGG 57.560 41.667 0.00 0.00 0.00 4.45
265 266 8.213679 TCTTTGGATTCTTATCTAATGACCCAG 58.786 37.037 0.00 0.00 33.45 4.45
266 267 8.101309 TCTTTGGATTCTTATCTAATGACCCA 57.899 34.615 0.00 0.00 33.45 4.51
279 280 9.354673 TGTTTCACTCTTTATCTTTGGATTCTT 57.645 29.630 0.00 0.00 33.71 2.52
280 281 8.924511 TGTTTCACTCTTTATCTTTGGATTCT 57.075 30.769 0.00 0.00 33.71 2.40
281 282 9.965824 TTTGTTTCACTCTTTATCTTTGGATTC 57.034 29.630 0.00 0.00 33.71 2.52
282 283 9.971922 CTTTGTTTCACTCTTTATCTTTGGATT 57.028 29.630 0.00 0.00 33.71 3.01
283 284 9.354673 TCTTTGTTTCACTCTTTATCTTTGGAT 57.645 29.630 0.00 0.00 36.07 3.41
284 285 8.746052 TCTTTGTTTCACTCTTTATCTTTGGA 57.254 30.769 0.00 0.00 0.00 3.53
285 286 9.971922 ATTCTTTGTTTCACTCTTTATCTTTGG 57.028 29.630 0.00 0.00 0.00 3.28
295 296 9.429359 CAGTAGTGATATTCTTTGTTTCACTCT 57.571 33.333 7.11 3.31 44.27 3.24
296 297 9.209175 ACAGTAGTGATATTCTTTGTTTCACTC 57.791 33.333 4.09 1.37 44.27 3.51
322 323 9.772973 TGCTTACTCTCAAACTTTCTGTTTATA 57.227 29.630 0.00 0.00 46.11 0.98
323 324 8.677148 TGCTTACTCTCAAACTTTCTGTTTAT 57.323 30.769 0.00 0.00 46.11 1.40
324 325 8.677148 ATGCTTACTCTCAAACTTTCTGTTTA 57.323 30.769 0.00 0.00 46.11 2.01
326 327 7.573968 AATGCTTACTCTCAAACTTTCTGTT 57.426 32.000 0.00 0.00 41.29 3.16
327 328 7.715249 TGTAATGCTTACTCTCAAACTTTCTGT 59.285 33.333 7.33 0.00 37.06 3.41
328 329 8.087982 TGTAATGCTTACTCTCAAACTTTCTG 57.912 34.615 7.33 0.00 37.06 3.02
329 330 8.854614 ATGTAATGCTTACTCTCAAACTTTCT 57.145 30.769 7.33 0.00 37.06 2.52
335 336 9.547753 GGAGATTATGTAATGCTTACTCTCAAA 57.452 33.333 16.05 4.92 36.31 2.69
336 337 8.704668 TGGAGATTATGTAATGCTTACTCTCAA 58.295 33.333 16.05 8.85 36.31 3.02
337 338 8.250143 TGGAGATTATGTAATGCTTACTCTCA 57.750 34.615 16.05 0.00 36.31 3.27
338 339 9.202273 CTTGGAGATTATGTAATGCTTACTCTC 57.798 37.037 0.00 10.88 37.06 3.20
339 340 8.928448 TCTTGGAGATTATGTAATGCTTACTCT 58.072 33.333 0.00 3.06 37.06 3.24
340 341 9.717942 ATCTTGGAGATTATGTAATGCTTACTC 57.282 33.333 7.33 0.00 32.41 2.59
368 369 9.020731 GGAACTGGTAATCTATTCCTTCAAAAA 57.979 33.333 0.00 0.00 36.65 1.94
369 370 7.614192 GGGAACTGGTAATCTATTCCTTCAAAA 59.386 37.037 0.00 0.00 39.09 2.44
370 371 7.116736 GGGAACTGGTAATCTATTCCTTCAAA 58.883 38.462 0.00 0.00 39.09 2.69
371 372 6.353602 GGGGAACTGGTAATCTATTCCTTCAA 60.354 42.308 0.00 0.00 39.09 2.69
372 373 5.132144 GGGGAACTGGTAATCTATTCCTTCA 59.868 44.000 0.00 0.00 39.09 3.02
373 374 5.456330 GGGGGAACTGGTAATCTATTCCTTC 60.456 48.000 0.00 0.00 39.09 3.46
374 375 4.415846 GGGGGAACTGGTAATCTATTCCTT 59.584 45.833 0.00 0.00 39.09 3.36
375 376 3.981375 GGGGGAACTGGTAATCTATTCCT 59.019 47.826 0.00 0.00 39.09 3.36
376 377 3.720002 TGGGGGAACTGGTAATCTATTCC 59.280 47.826 0.00 0.00 38.50 3.01
377 378 5.382664 TTGGGGGAACTGGTAATCTATTC 57.617 43.478 0.00 0.00 0.00 1.75
378 379 6.355588 AATTGGGGGAACTGGTAATCTATT 57.644 37.500 0.00 0.00 0.00 1.73
379 380 6.136155 CAAATTGGGGGAACTGGTAATCTAT 58.864 40.000 0.00 0.00 0.00 1.98
380 381 5.515106 CAAATTGGGGGAACTGGTAATCTA 58.485 41.667 0.00 0.00 0.00 1.98
381 382 4.352893 CAAATTGGGGGAACTGGTAATCT 58.647 43.478 0.00 0.00 0.00 2.40
382 383 3.118775 GCAAATTGGGGGAACTGGTAATC 60.119 47.826 0.00 0.00 0.00 1.75
383 384 2.837591 GCAAATTGGGGGAACTGGTAAT 59.162 45.455 0.00 0.00 0.00 1.89
384 385 2.252714 GCAAATTGGGGGAACTGGTAA 58.747 47.619 0.00 0.00 0.00 2.85
385 386 1.888826 CGCAAATTGGGGGAACTGGTA 60.889 52.381 1.77 0.00 0.00 3.25
386 387 1.184970 CGCAAATTGGGGGAACTGGT 61.185 55.000 1.77 0.00 0.00 4.00
387 388 0.897863 TCGCAAATTGGGGGAACTGG 60.898 55.000 10.15 0.00 0.00 4.00
388 389 0.243636 GTCGCAAATTGGGGGAACTG 59.756 55.000 10.15 0.00 0.00 3.16
389 390 0.898326 GGTCGCAAATTGGGGGAACT 60.898 55.000 10.15 0.00 32.67 3.01
390 391 0.898326 AGGTCGCAAATTGGGGGAAC 60.898 55.000 10.15 1.04 35.35 3.62
460 461 0.322906 TGGTTGGCCATACAATCGCA 60.323 50.000 6.09 0.00 40.46 5.10
979 4367 3.062466 GGCGGTGAAGGGAAAGCC 61.062 66.667 0.00 0.00 37.61 4.35
1742 5131 9.918630 AATATGGAGAAGACAAAATTGTTTGAG 57.081 29.630 6.21 0.00 45.99 3.02
1851 5240 2.569853 TCTAGCCCTTTGATTTCCGACA 59.430 45.455 0.00 0.00 0.00 4.35
1853 5242 3.181454 GGATCTAGCCCTTTGATTTCCGA 60.181 47.826 0.00 0.00 0.00 4.55
1859 5248 0.398318 GCCGGATCTAGCCCTTTGAT 59.602 55.000 5.05 0.00 0.00 2.57
1866 5255 4.344474 CGACCGCCGGATCTAGCC 62.344 72.222 11.71 0.00 33.91 3.93
1936 5328 4.954970 CCACCGCAACACCTGGCT 62.955 66.667 0.00 0.00 0.00 4.75
2158 5550 0.109723 CCCGGGTCTGAAGGTTTCAA 59.890 55.000 14.18 0.00 39.58 2.69
2210 5602 7.535139 TGGACTTTTGTTAAGAAAACAGACAG 58.465 34.615 6.43 0.00 0.00 3.51
2215 5607 9.883142 ATTCATTGGACTTTTGTTAAGAAAACA 57.117 25.926 6.43 1.73 0.00 2.83
2234 5626 1.860950 CGTGAGCTCCGGTATTCATTG 59.139 52.381 12.15 0.00 0.00 2.82
2266 5658 5.772672 ACATGACCTGTTTAAATAGTTGGCA 59.227 36.000 10.61 5.43 32.90 4.92
2365 5760 1.667467 GCCGACGGCTTTGCATTTTTA 60.667 47.619 31.30 0.00 46.69 1.52


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

AutoCloner maintained by Alex Coulton.