Multiple sequence alignment - TraesCS3B01G605900

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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 TraesCS3B01G605900 chr3B 100.000 2849 0 0 1 2849 824390739 824393587 0.000000e+00 5262.0
1 TraesCS3B01G605900 chr3B 94.505 2639 84 15 264 2849 764448953 764451583 0.000000e+00 4013.0
2 TraesCS3B01G605900 chr3B 98.947 190 2 0 3 192 809078462 809078651 9.780000e-90 340.0
3 TraesCS3B01G605900 chr3B 92.045 88 6 1 2487 2573 750678428 750678341 3.850000e-24 122.0
4 TraesCS3B01G605900 chrUn 94.505 2639 84 15 264 2849 232156160 232158790 0.000000e+00 4013.0
5 TraesCS3B01G605900 chrUn 94.505 2639 84 15 264 2849 237975199 237977829 0.000000e+00 4013.0
6 TraesCS3B01G605900 chr2D 76.408 1314 248 40 620 1897 84916881 84918168 0.000000e+00 652.0
7 TraesCS3B01G605900 chr2D 89.474 152 12 3 264 414 616608558 616608410 3.750000e-44 189.0
8 TraesCS3B01G605900 chr2D 97.143 35 1 0 218 252 523154914 523154948 3.070000e-05 60.2
9 TraesCS3B01G605900 chr2D 89.130 46 4 1 218 262 446304214 446304169 3.970000e-04 56.5
10 TraesCS3B01G605900 chr2B 76.619 1266 239 39 620 1851 137188961 137190203 0.000000e+00 645.0
11 TraesCS3B01G605900 chr2B 76.438 1269 246 38 620 1856 136951613 136952860 3.100000e-179 638.0
12 TraesCS3B01G605900 chr2B 76.438 1269 246 38 620 1856 137608693 137609940 3.100000e-179 638.0
13 TraesCS3B01G605900 chr2B 76.359 1269 247 37 620 1856 136806563 136807810 1.440000e-177 632.0
14 TraesCS3B01G605900 chr2A 76.053 1282 247 39 620 1863 84153881 84152622 1.880000e-171 612.0
15 TraesCS3B01G605900 chr2A 90.066 151 13 1 264 414 746803307 746803159 8.050000e-46 195.0
16 TraesCS3B01G605900 chr1B 88.199 161 16 3 264 422 683576051 683575892 3.750000e-44 189.0
17 TraesCS3B01G605900 chr1B 90.476 42 3 1 218 258 390879357 390879316 1.000000e-03 54.7
18 TraesCS3B01G605900 chr4D 88.961 154 13 3 264 416 401095712 401095862 1.350000e-43 187.0
19 TraesCS3B01G605900 chr4B 88.387 155 17 1 264 417 372048852 372049006 4.850000e-43 185.0
20 TraesCS3B01G605900 chr4B 92.941 85 6 0 2490 2574 614229157 614229241 1.070000e-24 124.0
21 TraesCS3B01G605900 chr4B 95.122 41 2 0 218 258 104742073 104742113 6.590000e-07 65.8
22 TraesCS3B01G605900 chr4B 92.857 42 3 0 218 259 372048845 372048886 8.520000e-06 62.1
23 TraesCS3B01G605900 chr1D 88.387 155 16 2 264 417 36843540 36843387 4.850000e-43 185.0
24 TraesCS3B01G605900 chr5B 71.159 690 169 25 756 1426 686211939 686211261 8.230000e-31 145.0
25 TraesCS3B01G605900 chr6A 88.785 107 11 1 2486 2592 453654442 453654547 2.300000e-26 130.0
26 TraesCS3B01G605900 chr7B 94.118 85 3 1 2490 2572 675025729 675025645 8.280000e-26 128.0
27 TraesCS3B01G605900 chr7B 87.379 103 10 3 2490 2589 312350062 312349960 6.450000e-22 115.0
28 TraesCS3B01G605900 chr7A 88.350 103 8 4 2490 2589 119515138 119515037 1.390000e-23 121.0
29 TraesCS3B01G605900 chr7A 94.872 39 2 0 218 256 138974599 138974561 8.520000e-06 62.1
30 TraesCS3B01G605900 chr5A 97.368 38 1 0 219 256 370240538 370240501 6.590000e-07 65.8
31 TraesCS3B01G605900 chr5D 90.909 44 3 1 219 262 379557106 379557148 1.100000e-04 58.4
32 TraesCS3B01G605900 chr6D 90.476 42 4 0 218 259 155836493 155836534 3.970000e-04 56.5


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 TraesCS3B01G605900 chr3B 824390739 824393587 2848 False 5262 5262 100.000 1 2849 1 chr3B.!!$F3 2848
1 TraesCS3B01G605900 chr3B 764448953 764451583 2630 False 4013 4013 94.505 264 2849 1 chr3B.!!$F1 2585
2 TraesCS3B01G605900 chrUn 232156160 232158790 2630 False 4013 4013 94.505 264 2849 1 chrUn.!!$F1 2585
3 TraesCS3B01G605900 chrUn 237975199 237977829 2630 False 4013 4013 94.505 264 2849 1 chrUn.!!$F2 2585
4 TraesCS3B01G605900 chr2D 84916881 84918168 1287 False 652 652 76.408 620 1897 1 chr2D.!!$F1 1277
5 TraesCS3B01G605900 chr2B 137188961 137190203 1242 False 645 645 76.619 620 1851 1 chr2B.!!$F3 1231
6 TraesCS3B01G605900 chr2B 136951613 136952860 1247 False 638 638 76.438 620 1856 1 chr2B.!!$F2 1236
7 TraesCS3B01G605900 chr2B 137608693 137609940 1247 False 638 638 76.438 620 1856 1 chr2B.!!$F4 1236
8 TraesCS3B01G605900 chr2B 136806563 136807810 1247 False 632 632 76.359 620 1856 1 chr2B.!!$F1 1236
9 TraesCS3B01G605900 chr2A 84152622 84153881 1259 True 612 612 76.053 620 1863 1 chr2A.!!$R1 1243

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
125 126 0.033503 TGAGAGGGTCGTGGATGCTA 60.034 55.0 0.00 0.0 0.00 3.49 F
215 216 0.039437 GCGGCGAGATCGATTTAGGA 60.039 55.0 12.98 0.0 43.02 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1432 1443 0.170561 CCTACAACCACGTCCTCTCG 59.829 60.000 0.00 0.0 0.0 4.04 R
2159 2227 2.044946 GGCGGCCTTTGGATGTCT 60.045 61.111 12.87 0.0 0.0 3.41 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 2.789249 GCACCGTCGCCATAAACC 59.211 61.111 0.00 0.00 0.00 3.27
24 25 2.757056 GCACCGTCGCCATAAACCC 61.757 63.158 0.00 0.00 0.00 4.11
25 26 2.110352 CACCGTCGCCATAAACCCC 61.110 63.158 0.00 0.00 0.00 4.95
26 27 2.269562 CCGTCGCCATAAACCCCA 59.730 61.111 0.00 0.00 0.00 4.96
27 28 2.110352 CCGTCGCCATAAACCCCAC 61.110 63.158 0.00 0.00 0.00 4.61
28 29 2.110352 CGTCGCCATAAACCCCACC 61.110 63.158 0.00 0.00 0.00 4.61
29 30 2.110352 GTCGCCATAAACCCCACCG 61.110 63.158 0.00 0.00 0.00 4.94
30 31 2.045731 CGCCATAAACCCCACCGT 60.046 61.111 0.00 0.00 0.00 4.83
31 32 2.403378 CGCCATAAACCCCACCGTG 61.403 63.158 0.00 0.00 0.00 4.94
32 33 2.049767 GCCATAAACCCCACCGTGG 61.050 63.158 10.95 10.95 37.25 4.94
33 34 1.686416 CCATAAACCCCACCGTGGA 59.314 57.895 19.81 0.00 40.96 4.02
34 35 0.393808 CCATAAACCCCACCGTGGAG 60.394 60.000 19.81 8.53 40.96 3.86
35 36 0.393808 CATAAACCCCACCGTGGAGG 60.394 60.000 19.81 19.08 40.96 4.30
36 37 2.206182 ATAAACCCCACCGTGGAGGC 62.206 60.000 19.81 0.00 46.52 4.70
40 41 3.322466 CCCACCGTGGAGGCTCTT 61.322 66.667 19.81 0.00 46.52 2.85
41 42 2.046892 CCACCGTGGAGGCTCTTG 60.047 66.667 12.68 4.41 46.52 3.02
42 43 2.743718 CACCGTGGAGGCTCTTGT 59.256 61.111 15.23 3.85 46.52 3.16
43 44 1.374758 CACCGTGGAGGCTCTTGTC 60.375 63.158 15.23 0.00 46.52 3.18
44 45 2.266055 CCGTGGAGGCTCTTGTCC 59.734 66.667 15.23 0.00 0.00 4.02
45 46 2.286523 CCGTGGAGGCTCTTGTCCT 61.287 63.158 15.23 0.00 36.46 3.85
49 50 4.136978 GAGGCTCTTGTCCTCCCA 57.863 61.111 7.40 0.00 43.32 4.37
50 51 1.599576 GAGGCTCTTGTCCTCCCAC 59.400 63.158 7.40 0.00 43.32 4.61
51 52 0.907230 GAGGCTCTTGTCCTCCCACT 60.907 60.000 7.40 0.00 43.32 4.00
52 53 1.197430 AGGCTCTTGTCCTCCCACTG 61.197 60.000 0.00 0.00 0.00 3.66
53 54 1.298014 GCTCTTGTCCTCCCACTGG 59.702 63.158 0.00 0.00 0.00 4.00
54 55 1.986413 CTCTTGTCCTCCCACTGGG 59.014 63.158 7.97 7.97 46.11 4.45
55 56 2.190488 CTCTTGTCCTCCCACTGGGC 62.190 65.000 9.60 0.00 43.94 5.36
56 57 2.121963 TTGTCCTCCCACTGGGCT 60.122 61.111 9.60 0.00 43.94 5.19
57 58 1.774217 TTGTCCTCCCACTGGGCTT 60.774 57.895 9.60 0.00 43.94 4.35
58 59 1.779061 TTGTCCTCCCACTGGGCTTC 61.779 60.000 9.60 0.90 43.94 3.86
59 60 2.206900 TCCTCCCACTGGGCTTCA 59.793 61.111 9.60 0.00 43.94 3.02
60 61 1.463214 TCCTCCCACTGGGCTTCAA 60.463 57.895 9.60 0.00 43.94 2.69
61 62 1.303643 CCTCCCACTGGGCTTCAAC 60.304 63.158 9.60 0.00 43.94 3.18
62 63 1.455849 CTCCCACTGGGCTTCAACA 59.544 57.895 9.60 0.00 43.94 3.33
63 64 0.038744 CTCCCACTGGGCTTCAACAT 59.961 55.000 9.60 0.00 43.94 2.71
64 65 1.281867 CTCCCACTGGGCTTCAACATA 59.718 52.381 9.60 0.00 43.94 2.29
65 66 1.281867 TCCCACTGGGCTTCAACATAG 59.718 52.381 9.60 0.00 43.94 2.23
66 67 1.281867 CCCACTGGGCTTCAACATAGA 59.718 52.381 0.00 0.00 35.35 1.98
67 68 2.290896 CCCACTGGGCTTCAACATAGAA 60.291 50.000 0.00 0.00 35.35 2.10
68 69 2.749621 CCACTGGGCTTCAACATAGAAC 59.250 50.000 0.00 0.00 0.00 3.01
69 70 2.416547 CACTGGGCTTCAACATAGAACG 59.583 50.000 0.00 0.00 0.00 3.95
70 71 1.398390 CTGGGCTTCAACATAGAACGC 59.602 52.381 0.00 0.00 0.00 4.84
71 72 1.271108 TGGGCTTCAACATAGAACGCA 60.271 47.619 0.00 0.00 0.00 5.24
72 73 1.810151 GGGCTTCAACATAGAACGCAA 59.190 47.619 0.00 0.00 0.00 4.85
74 75 2.509870 GCTTCAACATAGAACGCAAGC 58.490 47.619 0.00 0.00 45.62 4.01
75 76 2.762472 CTTCAACATAGAACGCAAGCG 58.238 47.619 13.50 13.50 46.03 4.68
76 77 1.075542 TCAACATAGAACGCAAGCGG 58.924 50.000 19.30 2.05 44.69 5.52
77 78 0.521242 CAACATAGAACGCAAGCGGC 60.521 55.000 19.30 10.17 44.69 6.53
78 79 0.953471 AACATAGAACGCAAGCGGCA 60.953 50.000 19.30 0.91 45.17 5.69
79 80 0.953471 ACATAGAACGCAAGCGGCAA 60.953 50.000 19.30 1.64 45.17 4.52
80 81 0.247814 CATAGAACGCAAGCGGCAAG 60.248 55.000 19.30 0.00 45.17 4.01
81 82 0.391130 ATAGAACGCAAGCGGCAAGA 60.391 50.000 19.30 0.31 45.17 3.02
82 83 1.014044 TAGAACGCAAGCGGCAAGAG 61.014 55.000 19.30 0.00 45.17 2.85
83 84 2.280797 AACGCAAGCGGCAAGAGA 60.281 55.556 19.30 0.00 45.17 3.10
84 85 2.233007 GAACGCAAGCGGCAAGAGAG 62.233 60.000 19.30 0.00 45.17 3.20
85 86 3.494336 CGCAAGCGGCAAGAGAGG 61.494 66.667 6.55 0.00 45.17 3.69
86 87 3.808656 GCAAGCGGCAAGAGAGGC 61.809 66.667 1.45 0.00 43.97 4.70
87 88 2.359107 CAAGCGGCAAGAGAGGCA 60.359 61.111 1.45 0.00 0.00 4.75
88 89 2.046507 AAGCGGCAAGAGAGGCAG 60.047 61.111 1.45 0.00 0.00 4.85
89 90 2.587247 AAGCGGCAAGAGAGGCAGA 61.587 57.895 1.45 0.00 0.00 4.26
90 91 1.908340 AAGCGGCAAGAGAGGCAGAT 61.908 55.000 1.45 0.00 0.00 2.90
91 92 2.178890 GCGGCAAGAGAGGCAGATG 61.179 63.158 0.00 0.00 0.00 2.90
92 93 1.523258 CGGCAAGAGAGGCAGATGG 60.523 63.158 0.00 0.00 0.00 3.51
93 94 1.153005 GGCAAGAGAGGCAGATGGG 60.153 63.158 0.00 0.00 0.00 4.00
94 95 1.606531 GCAAGAGAGGCAGATGGGT 59.393 57.895 0.00 0.00 0.00 4.51
95 96 0.747283 GCAAGAGAGGCAGATGGGTG 60.747 60.000 0.00 0.00 0.00 4.61
96 97 0.907486 CAAGAGAGGCAGATGGGTGA 59.093 55.000 0.00 0.00 0.00 4.02
97 98 0.908198 AAGAGAGGCAGATGGGTGAC 59.092 55.000 0.00 0.00 0.00 3.67
98 99 0.252421 AGAGAGGCAGATGGGTGACA 60.252 55.000 0.00 0.00 0.00 3.58
99 100 0.177604 GAGAGGCAGATGGGTGACAG 59.822 60.000 0.00 0.00 0.00 3.51
100 101 0.546267 AGAGGCAGATGGGTGACAGT 60.546 55.000 0.00 0.00 0.00 3.55
101 102 0.326264 GAGGCAGATGGGTGACAGTT 59.674 55.000 0.00 0.00 0.00 3.16
102 103 0.326264 AGGCAGATGGGTGACAGTTC 59.674 55.000 0.00 0.00 0.00 3.01
103 104 0.678048 GGCAGATGGGTGACAGTTCC 60.678 60.000 0.00 0.00 0.00 3.62
104 105 1.021390 GCAGATGGGTGACAGTTCCG 61.021 60.000 0.00 0.00 0.00 4.30
105 106 0.391661 CAGATGGGTGACAGTTCCGG 60.392 60.000 0.00 0.00 0.00 5.14
106 107 0.836400 AGATGGGTGACAGTTCCGGT 60.836 55.000 0.00 0.00 0.00 5.28
107 108 0.673644 GATGGGTGACAGTTCCGGTG 60.674 60.000 0.00 0.00 0.00 4.94
108 109 1.125093 ATGGGTGACAGTTCCGGTGA 61.125 55.000 0.00 0.00 0.00 4.02
109 110 1.004918 GGGTGACAGTTCCGGTGAG 60.005 63.158 0.00 0.00 0.00 3.51
110 111 1.469335 GGGTGACAGTTCCGGTGAGA 61.469 60.000 0.00 0.00 0.00 3.27
111 112 0.038159 GGTGACAGTTCCGGTGAGAG 60.038 60.000 0.00 0.00 0.00 3.20
112 113 0.038159 GTGACAGTTCCGGTGAGAGG 60.038 60.000 0.00 0.00 0.00 3.69
113 114 1.185618 TGACAGTTCCGGTGAGAGGG 61.186 60.000 0.00 0.00 0.00 4.30
114 115 1.152312 ACAGTTCCGGTGAGAGGGT 60.152 57.895 0.00 0.00 0.00 4.34
115 116 1.186267 ACAGTTCCGGTGAGAGGGTC 61.186 60.000 0.00 0.00 0.00 4.46
116 117 1.977544 AGTTCCGGTGAGAGGGTCG 60.978 63.158 0.00 0.00 0.00 4.79
117 118 2.116772 TTCCGGTGAGAGGGTCGT 59.883 61.111 0.00 0.00 0.00 4.34
118 119 2.273179 TTCCGGTGAGAGGGTCGTG 61.273 63.158 0.00 0.00 0.00 4.35
119 120 3.760035 CCGGTGAGAGGGTCGTGG 61.760 72.222 0.00 0.00 0.00 4.94
120 121 2.675423 CGGTGAGAGGGTCGTGGA 60.675 66.667 0.00 0.00 0.00 4.02
121 122 2.052690 CGGTGAGAGGGTCGTGGAT 61.053 63.158 0.00 0.00 0.00 3.41
122 123 1.517832 GGTGAGAGGGTCGTGGATG 59.482 63.158 0.00 0.00 0.00 3.51
123 124 1.153549 GTGAGAGGGTCGTGGATGC 60.154 63.158 0.00 0.00 0.00 3.91
124 125 1.305297 TGAGAGGGTCGTGGATGCT 60.305 57.895 0.00 0.00 0.00 3.79
125 126 0.033503 TGAGAGGGTCGTGGATGCTA 60.034 55.000 0.00 0.00 0.00 3.49
126 127 0.671251 GAGAGGGTCGTGGATGCTAG 59.329 60.000 0.00 0.00 0.00 3.42
127 128 0.757188 AGAGGGTCGTGGATGCTAGG 60.757 60.000 0.00 0.00 0.00 3.02
128 129 1.749334 GAGGGTCGTGGATGCTAGGG 61.749 65.000 0.00 0.00 0.00 3.53
129 130 2.109181 GGTCGTGGATGCTAGGGC 59.891 66.667 0.00 0.00 39.26 5.19
130 131 2.279517 GTCGTGGATGCTAGGGCG 60.280 66.667 0.00 0.00 42.25 6.13
131 132 3.536917 TCGTGGATGCTAGGGCGG 61.537 66.667 0.00 0.00 42.25 6.13
132 133 3.536917 CGTGGATGCTAGGGCGGA 61.537 66.667 0.00 0.00 42.25 5.54
133 134 2.423446 GTGGATGCTAGGGCGGAG 59.577 66.667 0.00 0.00 42.25 4.63
134 135 2.844362 TGGATGCTAGGGCGGAGG 60.844 66.667 0.00 0.00 42.25 4.30
135 136 2.844839 GGATGCTAGGGCGGAGGT 60.845 66.667 0.00 0.00 42.25 3.85
136 137 2.423446 GATGCTAGGGCGGAGGTG 59.577 66.667 0.00 0.00 42.25 4.00
137 138 2.365635 ATGCTAGGGCGGAGGTGT 60.366 61.111 0.00 0.00 42.25 4.16
138 139 2.370647 GATGCTAGGGCGGAGGTGTC 62.371 65.000 0.00 0.00 42.25 3.67
139 140 3.851128 GCTAGGGCGGAGGTGTCC 61.851 72.222 0.00 0.00 39.88 4.02
147 148 3.708210 GGAGGTGTCCGATGGTGA 58.292 61.111 0.00 0.00 31.37 4.02
148 149 1.517832 GGAGGTGTCCGATGGTGAG 59.482 63.158 0.00 0.00 31.37 3.51
149 150 1.517832 GAGGTGTCCGATGGTGAGG 59.482 63.158 0.00 0.00 0.00 3.86
150 151 1.229209 AGGTGTCCGATGGTGAGGT 60.229 57.895 0.00 0.00 0.00 3.85
151 152 0.040646 AGGTGTCCGATGGTGAGGTA 59.959 55.000 0.00 0.00 0.00 3.08
152 153 0.175073 GGTGTCCGATGGTGAGGTAC 59.825 60.000 0.00 0.00 0.00 3.34
181 182 3.472726 GGGGTCGGCGGTGGATAA 61.473 66.667 7.21 0.00 0.00 1.75
182 183 2.202974 GGGTCGGCGGTGGATAAC 60.203 66.667 7.21 0.00 0.00 1.89
183 184 2.202974 GGTCGGCGGTGGATAACC 60.203 66.667 7.21 0.60 46.60 2.85
196 197 2.981784 TGGATAACCAGATCCTCCATGG 59.018 50.000 4.97 4.97 45.07 3.66
197 198 2.290577 GGATAACCAGATCCTCCATGGC 60.291 54.545 6.96 0.00 42.03 4.40
198 199 0.758734 TAACCAGATCCTCCATGGCG 59.241 55.000 6.96 0.00 37.64 5.69
199 200 1.987807 AACCAGATCCTCCATGGCGG 61.988 60.000 15.13 15.13 37.64 6.13
200 201 2.281345 CAGATCCTCCATGGCGGC 60.281 66.667 16.49 0.00 35.26 6.53
201 202 3.933722 AGATCCTCCATGGCGGCG 61.934 66.667 16.49 0.51 35.26 6.46
202 203 3.928779 GATCCTCCATGGCGGCGA 61.929 66.667 16.49 0.00 35.26 5.54
203 204 3.873026 GATCCTCCATGGCGGCGAG 62.873 68.421 16.49 2.98 35.26 5.03
205 206 3.933722 CCTCCATGGCGGCGAGAT 61.934 66.667 12.98 0.00 33.14 2.75
206 207 2.356793 CTCCATGGCGGCGAGATC 60.357 66.667 12.98 0.00 33.14 2.75
207 208 4.284860 TCCATGGCGGCGAGATCG 62.285 66.667 12.98 0.00 43.27 3.69
208 209 4.284860 CCATGGCGGCGAGATCGA 62.285 66.667 12.98 0.00 43.02 3.59
209 210 2.048784 CATGGCGGCGAGATCGAT 60.049 61.111 12.98 0.00 43.02 3.59
210 211 1.665916 CATGGCGGCGAGATCGATT 60.666 57.895 12.98 0.00 43.02 3.34
211 212 1.069765 ATGGCGGCGAGATCGATTT 59.930 52.632 12.98 0.00 43.02 2.17
212 213 0.317160 ATGGCGGCGAGATCGATTTA 59.683 50.000 12.98 0.00 43.02 1.40
213 214 0.318699 TGGCGGCGAGATCGATTTAG 60.319 55.000 12.98 0.00 43.02 1.85
214 215 1.009389 GGCGGCGAGATCGATTTAGG 61.009 60.000 12.98 0.00 43.02 2.69
215 216 0.039437 GCGGCGAGATCGATTTAGGA 60.039 55.000 12.98 0.00 43.02 2.94
216 217 1.602165 GCGGCGAGATCGATTTAGGAA 60.602 52.381 12.98 0.00 43.02 3.36
217 218 2.052157 CGGCGAGATCGATTTAGGAAC 58.948 52.381 0.00 0.00 43.02 3.62
218 219 2.405172 GGCGAGATCGATTTAGGAACC 58.595 52.381 6.39 0.00 43.02 3.62
219 220 2.405172 GCGAGATCGATTTAGGAACCC 58.595 52.381 6.39 0.00 43.02 4.11
220 221 2.036089 GCGAGATCGATTTAGGAACCCT 59.964 50.000 6.39 0.00 43.02 4.34
221 222 3.857756 GCGAGATCGATTTAGGAACCCTC 60.858 52.174 6.39 0.00 43.02 4.30
222 223 3.305471 CGAGATCGATTTAGGAACCCTCC 60.305 52.174 0.00 0.00 43.02 4.30
223 224 6.618266 CGAGATCGATTTAGGAACCCTCCG 62.618 54.167 0.00 0.00 43.96 4.63
234 235 3.908643 GAACCCTCCGTTCCTAAATCT 57.091 47.619 0.00 0.00 44.46 2.40
236 237 5.349061 GAACCCTCCGTTCCTAAATCTAA 57.651 43.478 0.00 0.00 44.46 2.10
237 238 5.354842 AACCCTCCGTTCCTAAATCTAAG 57.645 43.478 0.00 0.00 0.00 2.18
238 239 4.359996 ACCCTCCGTTCCTAAATCTAAGT 58.640 43.478 0.00 0.00 0.00 2.24
239 240 4.405036 ACCCTCCGTTCCTAAATCTAAGTC 59.595 45.833 0.00 0.00 0.00 3.01
240 241 4.650131 CCCTCCGTTCCTAAATCTAAGTCT 59.350 45.833 0.00 0.00 0.00 3.24
241 242 5.128991 CCCTCCGTTCCTAAATCTAAGTCTT 59.871 44.000 0.00 0.00 0.00 3.01
242 243 6.351966 CCCTCCGTTCCTAAATCTAAGTCTTT 60.352 42.308 0.00 0.00 0.00 2.52
243 244 7.104290 CCTCCGTTCCTAAATCTAAGTCTTTT 58.896 38.462 0.00 0.00 0.00 2.27
244 245 7.606839 CCTCCGTTCCTAAATCTAAGTCTTTTT 59.393 37.037 0.00 0.00 0.00 1.94
245 246 9.649167 CTCCGTTCCTAAATCTAAGTCTTTTTA 57.351 33.333 0.00 0.00 0.00 1.52
412 414 5.014228 ACTTGTATTTAGGAAAGCAGGGAGT 59.986 40.000 0.00 0.00 0.00 3.85
426 428 4.591072 AGCAGGGAGTAGATATCAAGTTCC 59.409 45.833 5.32 6.30 0.00 3.62
455 457 6.485648 TCTCAGGGTAAAAACTAAGAAGTTGC 59.514 38.462 0.00 0.00 45.37 4.17
471 473 1.997606 GTTGCGTGTTTCGGTATAGCT 59.002 47.619 0.00 0.00 40.26 3.32
501 503 3.111853 TCAGATGTTCCATGCCGATAC 57.888 47.619 0.00 0.00 0.00 2.24
517 519 5.350365 TGCCGATACATGTCTTGTTCTAAAC 59.650 40.000 0.00 0.00 39.87 2.01
538 540 7.749539 AAACGAACTTAATGTTTGGTGAAAG 57.250 32.000 0.00 0.00 38.96 2.62
541 543 6.540914 ACGAACTTAATGTTTGGTGAAAGAGA 59.459 34.615 0.00 0.00 42.83 3.10
724 732 4.329462 TGTAGAAAATTTTGCCACACCC 57.671 40.909 8.47 0.00 0.00 4.61
955 966 2.930023 GCTCATCAGCATATCACCGGAG 60.930 54.545 9.46 0.00 46.06 4.63
1070 1081 3.570550 AGTTACATGCGCTTTTTGGGTTA 59.429 39.130 9.73 0.00 0.00 2.85
1136 1147 4.391830 CCTAGTTGATGTTTACACGTGCAT 59.608 41.667 17.22 10.89 0.00 3.96
1211 1222 2.026262 GGTTCCTTATGGCTCCACTCAA 60.026 50.000 0.00 0.00 0.00 3.02
1317 1328 5.230182 CCCTTTGTTGGTGAAGCTAAATTC 58.770 41.667 0.00 0.00 0.00 2.17
1432 1443 3.795488 GCAGGAAGTAACAGTTTTGTGGC 60.795 47.826 0.00 0.00 37.67 5.01
1778 1807 2.476619 CTCACCGCGATTCATACATTCC 59.523 50.000 8.23 0.00 0.00 3.01
1843 1872 2.535485 CTTGGTCTATGGTGCCGGCA 62.535 60.000 29.03 29.03 0.00 5.69
1852 1881 2.639286 GTGCCGGCAAGTGAACAG 59.361 61.111 34.66 0.00 0.00 3.16
1856 1885 1.845809 GCCGGCAAGTGAACAGTCAG 61.846 60.000 24.80 0.00 33.27 3.51
1915 1945 1.535462 CCTGACAACGGCAGGTTTTAG 59.465 52.381 7.78 0.00 46.19 1.85
1917 1947 1.141254 TGACAACGGCAGGTTTTAGGA 59.859 47.619 0.00 0.00 36.49 2.94
1918 1948 1.534163 GACAACGGCAGGTTTTAGGAC 59.466 52.381 0.00 0.00 36.49 3.85
1919 1949 1.142262 ACAACGGCAGGTTTTAGGACT 59.858 47.619 0.00 0.00 36.49 3.85
1921 1951 1.892209 ACGGCAGGTTTTAGGACTTG 58.108 50.000 0.00 0.00 0.00 3.16
1922 1952 1.142262 ACGGCAGGTTTTAGGACTTGT 59.858 47.619 0.00 0.00 0.00 3.16
1944 1988 6.768078 TGTAGTTTTCGTTCTTGTTGACTTC 58.232 36.000 0.00 0.00 0.00 3.01
1977 2021 6.977502 CCTATCTATGTTGAACTCAGTCAGTG 59.022 42.308 0.00 0.00 34.56 3.66
1980 2024 4.955811 ATGTTGAACTCAGTCAGTGGTA 57.044 40.909 0.00 0.00 34.56 3.25
1988 2032 7.097192 TGAACTCAGTCAGTGGTATATTCAAC 58.903 38.462 0.00 0.00 34.56 3.18
2016 2062 3.326588 AGGCACACATACTCAGGTTAACA 59.673 43.478 8.10 0.00 0.00 2.41
2037 2086 4.933400 ACAGCATTTTTGATGGATCTTTGC 59.067 37.500 0.00 0.00 0.00 3.68
2074 2123 4.164413 TGCAAGTCTAGTAGGAGAGCTCTA 59.836 45.833 18.25 0.00 0.00 2.43
2082 2131 7.817962 GTCTAGTAGGAGAGCTCTATTAGACTG 59.182 44.444 25.69 15.99 44.57 3.51
2087 2136 6.848069 AGGAGAGCTCTATTAGACTGTACAT 58.152 40.000 18.25 0.00 0.00 2.29
2159 2227 4.202377 TGTTCTTAGAATGGGAACGGAACA 60.202 41.667 0.00 0.00 41.27 3.18
2198 2267 1.694150 TCAGTTACCAGCTGCAAGTCT 59.306 47.619 8.66 0.00 35.30 3.24
2264 2333 7.069455 TGGTCAGCTATTACTATAACTTGAGCA 59.931 37.037 0.00 0.00 0.00 4.26
2297 2366 3.003275 ACTGACATGTTAAAAGTGCCACG 59.997 43.478 0.00 0.00 0.00 4.94
2302 2371 4.022762 ACATGTTAAAAGTGCCACGCATAA 60.023 37.500 0.00 0.00 41.91 1.90
2305 2374 4.276183 TGTTAAAAGTGCCACGCATAAAGA 59.724 37.500 0.00 0.00 41.91 2.52
2309 2378 1.665679 AGTGCCACGCATAAAGAATCG 59.334 47.619 0.00 0.00 41.91 3.34
2311 2380 1.663643 TGCCACGCATAAAGAATCGAC 59.336 47.619 0.00 0.00 31.71 4.20
2313 2382 2.351726 GCCACGCATAAAGAATCGACTT 59.648 45.455 0.00 0.00 0.00 3.01
2340 2409 4.382901 GGCCATCTGGACAATATTTTTGCA 60.383 41.667 0.00 0.00 44.76 4.08
2349 2418 8.948631 TGGACAATATTTTTGCAAAAAGTGTA 57.051 26.923 33.47 24.21 40.78 2.90
2350 2419 9.553064 TGGACAATATTTTTGCAAAAAGTGTAT 57.447 25.926 33.47 25.07 40.78 2.29
2371 2440 9.685828 GTGTATCTGTAAAATTAAACTGCCAAA 57.314 29.630 0.00 0.00 0.00 3.28
2388 2457 3.243401 GCCAAAGTTGAACGACAGGAAAT 60.243 43.478 0.00 0.00 0.00 2.17
2414 2483 2.236146 TCTCCACAACTTATGCGATGGT 59.764 45.455 0.00 0.00 0.00 3.55
2462 2533 6.587990 GTGTGATAGTATCAGTCATATGGTGC 59.412 42.308 13.24 0.00 40.53 5.01
2475 2546 4.096231 TCATATGGTGCGAAAATTCTGGTG 59.904 41.667 2.13 0.00 0.00 4.17
2483 2554 0.318120 AAAATTCTGGTGGGCAAGCG 59.682 50.000 0.00 0.00 0.00 4.68
2624 2700 2.511145 GCAGAGCTCGCTTGAGGG 60.511 66.667 19.01 1.64 40.26 4.30
2634 2710 1.223487 GCTTGAGGGGATGGCGTTA 59.777 57.895 0.00 0.00 0.00 3.18
2684 2760 3.876198 GCGGTGGTATGGCGCTTG 61.876 66.667 7.64 0.00 0.00 4.01
2737 2813 2.813474 CAGCGACGGGAATTGCGA 60.813 61.111 0.00 0.00 33.84 5.10
2745 2821 3.929948 GGAATTGCGAGGCGAGCG 61.930 66.667 0.00 0.00 37.44 5.03
2803 2879 1.068748 GTAGCACTTGAGGTCGTCGAA 60.069 52.381 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.757056 GGGTTTATGGCGACGGTGC 61.757 63.158 0.00 0.00 0.00 5.01
7 8 2.110352 GGGGTTTATGGCGACGGTG 61.110 63.158 0.00 0.00 0.00 4.94
8 9 2.269883 GGGGTTTATGGCGACGGT 59.730 61.111 0.00 0.00 0.00 4.83
9 10 2.110352 GTGGGGTTTATGGCGACGG 61.110 63.158 0.00 0.00 0.00 4.79
10 11 2.110352 GGTGGGGTTTATGGCGACG 61.110 63.158 0.00 0.00 0.00 5.12
11 12 2.110352 CGGTGGGGTTTATGGCGAC 61.110 63.158 0.00 0.00 0.00 5.19
12 13 2.269562 CGGTGGGGTTTATGGCGA 59.730 61.111 0.00 0.00 0.00 5.54
13 14 2.045731 ACGGTGGGGTTTATGGCG 60.046 61.111 0.00 0.00 0.00 5.69
14 15 2.049767 CCACGGTGGGGTTTATGGC 61.050 63.158 19.63 0.00 32.67 4.40
15 16 0.393808 CTCCACGGTGGGGTTTATGG 60.394 60.000 26.07 0.00 38.32 2.74
16 17 0.393808 CCTCCACGGTGGGGTTTATG 60.394 60.000 24.83 6.08 35.80 1.90
17 18 1.996086 CCTCCACGGTGGGGTTTAT 59.004 57.895 24.83 0.00 35.80 1.40
18 19 2.897762 GCCTCCACGGTGGGGTTTA 61.898 63.158 24.83 5.83 35.80 2.01
19 20 4.280019 GCCTCCACGGTGGGGTTT 62.280 66.667 24.83 0.00 35.80 3.27
23 24 3.322466 AAGAGCCTCCACGGTGGG 61.322 66.667 26.07 16.38 38.32 4.61
24 25 2.046892 CAAGAGCCTCCACGGTGG 60.047 66.667 21.27 21.27 39.43 4.61
25 26 1.374758 GACAAGAGCCTCCACGGTG 60.375 63.158 0.00 0.00 34.25 4.94
26 27 2.584391 GGACAAGAGCCTCCACGGT 61.584 63.158 0.00 0.00 34.25 4.83
27 28 2.232298 GAGGACAAGAGCCTCCACGG 62.232 65.000 0.00 0.00 44.96 4.94
28 29 1.216710 GAGGACAAGAGCCTCCACG 59.783 63.158 0.00 0.00 44.96 4.94
33 34 1.159664 AGTGGGAGGACAAGAGCCT 59.840 57.895 0.00 0.00 38.81 4.58
34 35 1.298014 CAGTGGGAGGACAAGAGCC 59.702 63.158 0.00 0.00 0.00 4.70
35 36 1.298014 CCAGTGGGAGGACAAGAGC 59.702 63.158 0.00 0.00 35.59 4.09
47 48 2.749621 GTTCTATGTTGAAGCCCAGTGG 59.250 50.000 0.63 0.63 0.00 4.00
48 49 2.416547 CGTTCTATGTTGAAGCCCAGTG 59.583 50.000 0.00 0.00 0.00 3.66
49 50 2.699954 CGTTCTATGTTGAAGCCCAGT 58.300 47.619 0.00 0.00 0.00 4.00
50 51 1.398390 GCGTTCTATGTTGAAGCCCAG 59.602 52.381 0.00 0.00 0.00 4.45
51 52 1.271108 TGCGTTCTATGTTGAAGCCCA 60.271 47.619 0.00 0.00 0.00 5.36
52 53 1.448985 TGCGTTCTATGTTGAAGCCC 58.551 50.000 0.00 0.00 0.00 5.19
53 54 2.729156 GCTTGCGTTCTATGTTGAAGCC 60.729 50.000 0.00 0.00 0.00 4.35
54 55 2.509870 GCTTGCGTTCTATGTTGAAGC 58.490 47.619 0.00 0.00 0.00 3.86
55 56 2.474526 CCGCTTGCGTTCTATGTTGAAG 60.475 50.000 13.97 0.00 0.00 3.02
56 57 1.463056 CCGCTTGCGTTCTATGTTGAA 59.537 47.619 13.97 0.00 0.00 2.69
57 58 1.075542 CCGCTTGCGTTCTATGTTGA 58.924 50.000 13.97 0.00 0.00 3.18
58 59 0.521242 GCCGCTTGCGTTCTATGTTG 60.521 55.000 13.97 0.00 0.00 3.33
59 60 0.953471 TGCCGCTTGCGTTCTATGTT 60.953 50.000 13.97 0.00 45.60 2.71
60 61 0.953471 TTGCCGCTTGCGTTCTATGT 60.953 50.000 13.97 0.00 45.60 2.29
61 62 0.247814 CTTGCCGCTTGCGTTCTATG 60.248 55.000 13.97 0.00 45.60 2.23
62 63 0.391130 TCTTGCCGCTTGCGTTCTAT 60.391 50.000 13.97 0.00 45.60 1.98
63 64 1.005512 TCTTGCCGCTTGCGTTCTA 60.006 52.632 13.97 2.14 45.60 2.10
64 65 2.280797 TCTTGCCGCTTGCGTTCT 60.281 55.556 13.97 0.00 45.60 3.01
65 66 2.174349 CTCTTGCCGCTTGCGTTC 59.826 61.111 13.97 5.99 45.60 3.95
66 67 2.280797 TCTCTTGCCGCTTGCGTT 60.281 55.556 13.97 0.00 45.60 4.84
67 68 2.740055 CTCTCTTGCCGCTTGCGT 60.740 61.111 13.97 0.00 45.60 5.24
68 69 3.494336 CCTCTCTTGCCGCTTGCG 61.494 66.667 8.14 8.14 45.60 4.85
69 70 3.808656 GCCTCTCTTGCCGCTTGC 61.809 66.667 0.00 0.00 41.77 4.01
70 71 2.359107 TGCCTCTCTTGCCGCTTG 60.359 61.111 0.00 0.00 0.00 4.01
71 72 1.908340 ATCTGCCTCTCTTGCCGCTT 61.908 55.000 0.00 0.00 0.00 4.68
72 73 2.365586 ATCTGCCTCTCTTGCCGCT 61.366 57.895 0.00 0.00 0.00 5.52
73 74 2.178890 CATCTGCCTCTCTTGCCGC 61.179 63.158 0.00 0.00 0.00 6.53
74 75 1.523258 CCATCTGCCTCTCTTGCCG 60.523 63.158 0.00 0.00 0.00 5.69
75 76 1.153005 CCCATCTGCCTCTCTTGCC 60.153 63.158 0.00 0.00 0.00 4.52
76 77 0.747283 CACCCATCTGCCTCTCTTGC 60.747 60.000 0.00 0.00 0.00 4.01
77 78 0.907486 TCACCCATCTGCCTCTCTTG 59.093 55.000 0.00 0.00 0.00 3.02
78 79 0.908198 GTCACCCATCTGCCTCTCTT 59.092 55.000 0.00 0.00 0.00 2.85
79 80 0.252421 TGTCACCCATCTGCCTCTCT 60.252 55.000 0.00 0.00 0.00 3.10
80 81 0.177604 CTGTCACCCATCTGCCTCTC 59.822 60.000 0.00 0.00 0.00 3.20
81 82 0.546267 ACTGTCACCCATCTGCCTCT 60.546 55.000 0.00 0.00 0.00 3.69
82 83 0.326264 AACTGTCACCCATCTGCCTC 59.674 55.000 0.00 0.00 0.00 4.70
83 84 0.326264 GAACTGTCACCCATCTGCCT 59.674 55.000 0.00 0.00 0.00 4.75
84 85 0.678048 GGAACTGTCACCCATCTGCC 60.678 60.000 0.00 0.00 0.00 4.85
85 86 1.021390 CGGAACTGTCACCCATCTGC 61.021 60.000 0.00 0.00 0.00 4.26
86 87 0.391661 CCGGAACTGTCACCCATCTG 60.392 60.000 0.00 0.00 0.00 2.90
87 88 0.836400 ACCGGAACTGTCACCCATCT 60.836 55.000 9.46 0.00 0.00 2.90
88 89 0.673644 CACCGGAACTGTCACCCATC 60.674 60.000 9.46 0.00 0.00 3.51
89 90 1.125093 TCACCGGAACTGTCACCCAT 61.125 55.000 9.46 0.00 0.00 4.00
90 91 1.754380 CTCACCGGAACTGTCACCCA 61.754 60.000 9.46 0.00 0.00 4.51
91 92 1.004918 CTCACCGGAACTGTCACCC 60.005 63.158 9.46 0.00 0.00 4.61
92 93 0.038159 CTCTCACCGGAACTGTCACC 60.038 60.000 9.46 0.00 0.00 4.02
93 94 0.038159 CCTCTCACCGGAACTGTCAC 60.038 60.000 9.46 0.00 0.00 3.67
94 95 1.185618 CCCTCTCACCGGAACTGTCA 61.186 60.000 9.46 0.00 0.00 3.58
95 96 1.186267 ACCCTCTCACCGGAACTGTC 61.186 60.000 9.46 0.00 0.00 3.51
96 97 1.152312 ACCCTCTCACCGGAACTGT 60.152 57.895 9.46 0.00 0.00 3.55
97 98 1.592223 GACCCTCTCACCGGAACTG 59.408 63.158 9.46 0.00 0.00 3.16
98 99 1.977544 CGACCCTCTCACCGGAACT 60.978 63.158 9.46 0.00 0.00 3.01
99 100 2.273912 ACGACCCTCTCACCGGAAC 61.274 63.158 9.46 0.00 0.00 3.62
100 101 2.116772 ACGACCCTCTCACCGGAA 59.883 61.111 9.46 0.00 0.00 4.30
101 102 2.675423 CACGACCCTCTCACCGGA 60.675 66.667 9.46 0.00 0.00 5.14
102 103 3.760035 CCACGACCCTCTCACCGG 61.760 72.222 0.00 0.00 0.00 5.28
103 104 2.052690 ATCCACGACCCTCTCACCG 61.053 63.158 0.00 0.00 0.00 4.94
104 105 1.517832 CATCCACGACCCTCTCACC 59.482 63.158 0.00 0.00 0.00 4.02
105 106 1.153549 GCATCCACGACCCTCTCAC 60.154 63.158 0.00 0.00 0.00 3.51
106 107 0.033503 TAGCATCCACGACCCTCTCA 60.034 55.000 0.00 0.00 0.00 3.27
107 108 0.671251 CTAGCATCCACGACCCTCTC 59.329 60.000 0.00 0.00 0.00 3.20
108 109 0.757188 CCTAGCATCCACGACCCTCT 60.757 60.000 0.00 0.00 0.00 3.69
109 110 1.742768 CCTAGCATCCACGACCCTC 59.257 63.158 0.00 0.00 0.00 4.30
110 111 1.762460 CCCTAGCATCCACGACCCT 60.762 63.158 0.00 0.00 0.00 4.34
111 112 2.822399 CCCTAGCATCCACGACCC 59.178 66.667 0.00 0.00 0.00 4.46
112 113 2.109181 GCCCTAGCATCCACGACC 59.891 66.667 0.00 0.00 39.53 4.79
113 114 2.279517 CGCCCTAGCATCCACGAC 60.280 66.667 0.00 0.00 39.83 4.34
114 115 3.536917 CCGCCCTAGCATCCACGA 61.537 66.667 0.00 0.00 39.83 4.35
115 116 3.506059 CTCCGCCCTAGCATCCACG 62.506 68.421 0.00 0.00 39.83 4.94
116 117 2.423446 CTCCGCCCTAGCATCCAC 59.577 66.667 0.00 0.00 39.83 4.02
117 118 2.844362 CCTCCGCCCTAGCATCCA 60.844 66.667 0.00 0.00 39.83 3.41
118 119 2.844839 ACCTCCGCCCTAGCATCC 60.845 66.667 0.00 0.00 39.83 3.51
119 120 2.370647 GACACCTCCGCCCTAGCATC 62.371 65.000 0.00 0.00 39.83 3.91
120 121 2.365635 ACACCTCCGCCCTAGCAT 60.366 61.111 0.00 0.00 39.83 3.79
121 122 3.075005 GACACCTCCGCCCTAGCA 61.075 66.667 0.00 0.00 39.83 3.49
122 123 3.851128 GGACACCTCCGCCCTAGC 61.851 72.222 0.00 0.00 0.00 3.42
130 131 1.517832 CTCACCATCGGACACCTCC 59.482 63.158 0.00 0.00 0.00 4.30
131 132 1.258445 ACCTCACCATCGGACACCTC 61.258 60.000 0.00 0.00 0.00 3.85
132 133 0.040646 TACCTCACCATCGGACACCT 59.959 55.000 0.00 0.00 0.00 4.00
133 134 0.175073 GTACCTCACCATCGGACACC 59.825 60.000 0.00 0.00 0.00 4.16
134 135 3.735181 GTACCTCACCATCGGACAC 57.265 57.895 0.00 0.00 0.00 3.67
143 144 1.520666 CACCATCCGGTACCTCACC 59.479 63.158 10.90 0.00 46.94 4.02
144 145 1.153429 GCACCATCCGGTACCTCAC 60.153 63.158 10.90 0.00 46.94 3.51
145 146 2.717044 CGCACCATCCGGTACCTCA 61.717 63.158 10.90 0.00 46.94 3.86
146 147 2.106332 CGCACCATCCGGTACCTC 59.894 66.667 10.90 0.00 46.94 3.85
147 148 3.467226 CCGCACCATCCGGTACCT 61.467 66.667 10.90 0.00 46.94 3.08
148 149 4.540735 CCCGCACCATCCGGTACC 62.541 72.222 0.16 0.16 46.94 3.34
149 150 4.540735 CCCCGCACCATCCGGTAC 62.541 72.222 0.00 0.00 46.94 3.34
164 165 3.472726 TTATCCACCGCCGACCCC 61.473 66.667 0.00 0.00 0.00 4.95
165 166 2.202974 GTTATCCACCGCCGACCC 60.203 66.667 0.00 0.00 0.00 4.46
166 167 2.202974 GGTTATCCACCGCCGACC 60.203 66.667 0.00 0.00 35.12 4.79
174 175 3.244700 CCATGGAGGATCTGGTTATCCAC 60.245 52.174 5.56 0.00 46.81 4.02
175 176 2.981784 CCATGGAGGATCTGGTTATCCA 59.018 50.000 5.56 0.00 46.81 3.41
176 177 2.290577 GCCATGGAGGATCTGGTTATCC 60.291 54.545 18.40 0.00 45.06 2.59
177 178 2.613977 CGCCATGGAGGATCTGGTTATC 60.614 54.545 18.40 0.00 41.22 1.75
178 179 1.349026 CGCCATGGAGGATCTGGTTAT 59.651 52.381 18.40 0.00 41.22 1.89
179 180 0.758734 CGCCATGGAGGATCTGGTTA 59.241 55.000 18.40 0.00 41.22 2.85
180 181 1.528824 CGCCATGGAGGATCTGGTT 59.471 57.895 18.40 0.00 41.22 3.67
181 182 2.446848 CCGCCATGGAGGATCTGGT 61.447 63.158 29.31 0.00 42.00 4.00
182 183 2.429058 CCGCCATGGAGGATCTGG 59.571 66.667 29.31 6.99 42.00 3.86
183 184 2.281345 GCCGCCATGGAGGATCTG 60.281 66.667 36.03 11.34 42.00 2.90
184 185 3.933722 CGCCGCCATGGAGGATCT 61.934 66.667 36.03 0.00 42.00 2.75
185 186 3.873026 CTCGCCGCCATGGAGGATC 62.873 68.421 36.03 19.05 42.00 3.36
186 187 3.933722 CTCGCCGCCATGGAGGAT 61.934 66.667 36.03 0.00 42.00 3.24
188 189 3.873026 GATCTCGCCGCCATGGAGG 62.873 68.421 28.87 28.87 42.00 4.30
189 190 2.356793 GATCTCGCCGCCATGGAG 60.357 66.667 18.40 13.36 42.00 3.86
190 191 4.284860 CGATCTCGCCGCCATGGA 62.285 66.667 18.40 0.00 42.00 3.41
191 192 3.580100 ATCGATCTCGCCGCCATGG 62.580 63.158 7.63 7.63 39.60 3.66
192 193 1.224069 AAATCGATCTCGCCGCCATG 61.224 55.000 0.00 0.00 39.60 3.66
193 194 0.317160 TAAATCGATCTCGCCGCCAT 59.683 50.000 0.00 0.00 39.60 4.40
194 195 0.318699 CTAAATCGATCTCGCCGCCA 60.319 55.000 0.00 0.00 39.60 5.69
195 196 1.009389 CCTAAATCGATCTCGCCGCC 61.009 60.000 0.00 0.00 39.60 6.13
196 197 0.039437 TCCTAAATCGATCTCGCCGC 60.039 55.000 0.00 0.00 39.60 6.53
197 198 2.052157 GTTCCTAAATCGATCTCGCCG 58.948 52.381 0.00 0.00 39.60 6.46
198 199 2.405172 GGTTCCTAAATCGATCTCGCC 58.595 52.381 0.00 0.00 39.60 5.54
199 200 2.036089 AGGGTTCCTAAATCGATCTCGC 59.964 50.000 0.00 0.00 33.30 5.03
200 201 3.305471 GGAGGGTTCCTAAATCGATCTCG 60.305 52.174 0.00 0.00 40.58 4.04
201 202 3.305471 CGGAGGGTTCCTAAATCGATCTC 60.305 52.174 0.00 0.00 41.67 2.75
202 203 2.628657 CGGAGGGTTCCTAAATCGATCT 59.371 50.000 0.00 0.00 41.67 2.75
203 204 2.364647 ACGGAGGGTTCCTAAATCGATC 59.635 50.000 0.00 0.00 41.67 3.69
204 205 2.395619 ACGGAGGGTTCCTAAATCGAT 58.604 47.619 0.00 0.00 41.67 3.59
205 206 1.856629 ACGGAGGGTTCCTAAATCGA 58.143 50.000 0.00 0.00 41.67 3.59
206 207 2.685850 AACGGAGGGTTCCTAAATCG 57.314 50.000 0.00 0.00 41.67 3.34
215 216 4.781621 ACTTAGATTTAGGAACGGAGGGTT 59.218 41.667 0.00 0.00 42.96 4.11
216 217 4.359996 ACTTAGATTTAGGAACGGAGGGT 58.640 43.478 0.00 0.00 0.00 4.34
217 218 4.650131 AGACTTAGATTTAGGAACGGAGGG 59.350 45.833 0.00 0.00 0.00 4.30
218 219 5.855740 AGACTTAGATTTAGGAACGGAGG 57.144 43.478 0.00 0.00 0.00 4.30
219 220 8.549338 AAAAAGACTTAGATTTAGGAACGGAG 57.451 34.615 0.00 0.00 0.00 4.63
308 309 9.698309 ACTCTAAAATATGTCTACATTCATCCG 57.302 33.333 0.12 0.00 37.76 4.18
387 388 5.253330 TCCCTGCTTTCCTAAATACAAGTG 58.747 41.667 0.00 0.00 0.00 3.16
392 394 6.481434 TCTACTCCCTGCTTTCCTAAATAC 57.519 41.667 0.00 0.00 0.00 1.89
426 428 7.715686 ACTTCTTAGTTTTTACCCTGAGAACAG 59.284 37.037 0.00 0.00 43.12 3.16
455 457 4.843984 CACAAAAAGCTATACCGAAACACG 59.156 41.667 0.00 0.00 42.18 4.49
517 519 6.851330 GTCTCTTTCACCAAACATTAAGTTCG 59.149 38.462 0.00 0.00 40.26 3.95
538 540 7.148407 ACACGTCAATGGAGAAAAATATGTCTC 60.148 37.037 0.00 3.71 39.70 3.36
541 543 6.817765 ACACGTCAATGGAGAAAAATATGT 57.182 33.333 0.00 0.00 0.00 2.29
724 732 3.526931 TGAAGCTGAGGTAAATCTCGG 57.473 47.619 0.00 0.00 41.74 4.63
1070 1081 9.796242 AGGAGAAGATAAGATACCCATATGAAT 57.204 33.333 3.65 0.00 0.00 2.57
1116 1127 4.829064 AATGCACGTGTAAACATCAACT 57.171 36.364 18.38 0.00 0.00 3.16
1317 1328 9.512435 CCTTTAAAGAGCACAATCTGATAAATG 57.488 33.333 16.98 0.00 0.00 2.32
1432 1443 0.170561 CCTACAACCACGTCCTCTCG 59.829 60.000 0.00 0.00 0.00 4.04
1778 1807 3.437795 CCTGCCTTGCGCCTTCTG 61.438 66.667 4.18 0.00 36.24 3.02
1843 1872 2.098117 GTGCAAAGCTGACTGTTCACTT 59.902 45.455 0.00 0.00 0.00 3.16
1852 1881 3.499918 ACTATGTGAAGTGCAAAGCTGAC 59.500 43.478 0.00 0.00 0.00 3.51
1856 1885 4.084900 GCAAAACTATGTGAAGTGCAAAGC 60.085 41.667 0.00 0.00 0.00 3.51
1911 1941 7.550196 ACAAGAACGAAAACTACAAGTCCTAAA 59.450 33.333 0.00 0.00 0.00 1.85
1915 1945 5.729974 ACAAGAACGAAAACTACAAGTCC 57.270 39.130 0.00 0.00 0.00 3.85
1917 1947 6.370718 AGTCAACAAGAACGAAAACTACAAGT 59.629 34.615 0.00 0.00 0.00 3.16
1918 1948 6.772078 AGTCAACAAGAACGAAAACTACAAG 58.228 36.000 0.00 0.00 0.00 3.16
1919 1949 6.730960 AGTCAACAAGAACGAAAACTACAA 57.269 33.333 0.00 0.00 0.00 2.41
1921 1951 5.894807 CGAAGTCAACAAGAACGAAAACTAC 59.105 40.000 0.00 0.00 0.00 2.73
1922 1952 5.577945 ACGAAGTCAACAAGAACGAAAACTA 59.422 36.000 0.00 0.00 29.74 2.24
1944 1988 6.982852 AGTTCAACATAGATAGGGTGATACG 58.017 40.000 0.00 0.00 33.36 3.06
1977 2021 6.127758 TGTGTGCCTTTCATGTTGAATATACC 60.128 38.462 0.00 0.00 36.11 2.73
1980 2024 5.981088 TGTGTGCCTTTCATGTTGAATAT 57.019 34.783 0.00 0.00 36.11 1.28
1988 2032 3.376234 CCTGAGTATGTGTGCCTTTCATG 59.624 47.826 0.00 0.00 0.00 3.07
2016 2062 5.416271 AGCAAAGATCCATCAAAAATGCT 57.584 34.783 0.00 0.00 36.83 3.79
2066 2115 9.635404 AAAGTATGTACAGTCTAATAGAGCTCT 57.365 33.333 22.17 22.17 0.00 4.09
2067 2116 9.887406 GAAAGTATGTACAGTCTAATAGAGCTC 57.113 37.037 5.27 5.27 0.00 4.09
2087 2136 8.415950 AACCACACATTATTGGAATGAAAGTA 57.584 30.769 4.36 0.00 36.28 2.24
2159 2227 2.044946 GGCGGCCTTTGGATGTCT 60.045 61.111 12.87 0.00 0.00 3.41
2268 2337 8.699749 GGCACTTTTAACATGTCAGTTAATTTC 58.300 33.333 0.00 0.00 41.89 2.17
2288 2357 2.095853 CGATTCTTTATGCGTGGCACTT 59.904 45.455 16.72 2.98 43.04 3.16
2297 2366 4.024809 GGCCTGTAAGTCGATTCTTTATGC 60.025 45.833 0.00 0.00 0.00 3.14
2302 2371 3.452627 AGATGGCCTGTAAGTCGATTCTT 59.547 43.478 3.32 0.00 0.00 2.52
2305 2374 2.158900 CCAGATGGCCTGTAAGTCGATT 60.159 50.000 3.32 0.00 41.33 3.34
2309 2378 1.555075 TGTCCAGATGGCCTGTAAGTC 59.445 52.381 3.32 0.00 41.33 3.01
2311 2380 2.787473 TTGTCCAGATGGCCTGTAAG 57.213 50.000 3.32 0.00 41.33 2.34
2313 2382 5.387113 AAATATTGTCCAGATGGCCTGTA 57.613 39.130 3.32 0.00 41.33 2.74
2349 2418 9.260002 CAACTTTGGCAGTTTAATTTTACAGAT 57.740 29.630 0.00 0.00 43.89 2.90
2350 2419 8.470805 TCAACTTTGGCAGTTTAATTTTACAGA 58.529 29.630 0.00 0.00 43.89 3.41
2351 2420 8.641499 TCAACTTTGGCAGTTTAATTTTACAG 57.359 30.769 0.00 0.00 43.89 2.74
2371 2440 4.389374 ACATGATTTCCTGTCGTTCAACT 58.611 39.130 0.00 0.00 0.00 3.16
2381 2450 4.330250 AGTTGTGGAGACATGATTTCCTG 58.670 43.478 0.00 0.00 46.14 3.86
2388 2457 3.056179 TCGCATAAGTTGTGGAGACATGA 60.056 43.478 0.00 0.00 46.14 3.07
2396 2465 2.352651 CAGACCATCGCATAAGTTGTGG 59.647 50.000 1.52 0.00 36.45 4.17
2414 2483 7.156876 ACAGTTTTTGTGAGATCAAAACAGA 57.843 32.000 16.28 2.56 43.76 3.41
2462 2533 1.669795 GCTTGCCCACCAGAATTTTCG 60.670 52.381 0.00 0.00 0.00 3.46
2475 2546 2.747855 CCTGTTCCTCGCTTGCCC 60.748 66.667 0.00 0.00 0.00 5.36
2624 2700 0.931005 CTTCGAGCTTAACGCCATCC 59.069 55.000 0.00 0.00 40.39 3.51
2647 2723 2.587194 CCTTGCTCCTCGCCATCG 60.587 66.667 0.00 0.00 38.05 3.84
2782 2858 0.522180 CGACGACCTCAAGTGCTACT 59.478 55.000 0.00 0.00 0.00 2.57
2813 2889 1.226717 GGAGCTCGTCGTCCACATC 60.227 63.158 7.83 0.00 32.55 3.06


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

AutoCloner maintained by Alex Coulton.