Multiple sequence alignment - TraesCS3B01G236000

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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 TraesCS3B01G236000 chr3B 100.000 2234 0 0 1 2234 368845565 368847798 0.000000e+00 4126
1 TraesCS3B01G236000 chrUn 96.201 1895 58 5 354 2234 171007966 171006072 0.000000e+00 3088
2 TraesCS3B01G236000 chr6B 96.097 1896 58 7 354 2234 596602178 596604072 0.000000e+00 3077
3 TraesCS3B01G236000 chr7A 95.937 1895 63 5 354 2234 638507985 638509879 0.000000e+00 3061
4 TraesCS3B01G236000 chr7A 96.371 1846 61 5 395 2234 708245256 708243411 0.000000e+00 3033
5 TraesCS3B01G236000 chr1B 95.831 1895 64 6 354 2234 672540903 672539010 0.000000e+00 3048
6 TraesCS3B01G236000 chr1B 94.663 356 17 2 1 354 609080004 609079649 3.240000e-153 551
7 TraesCS3B01G236000 chr2B 95.781 1896 65 6 354 2234 391225563 391227458 0.000000e+00 3044
8 TraesCS3B01G236000 chr7B 95.675 1896 64 7 354 2234 54050186 54052078 0.000000e+00 3031
9 TraesCS3B01G236000 chr5B 95.570 1896 69 6 354 2234 567279675 567277780 0.000000e+00 3022
10 TraesCS3B01G236000 chr1D 96.152 1845 61 5 395 2234 212445943 212447782 0.000000e+00 3005
11 TraesCS3B01G236000 chr1D 95.170 352 17 0 1 352 213466321 213465970 6.970000e-155 556
12 TraesCS3B01G236000 chr2D 94.915 354 17 1 1 353 581606350 581605997 9.020000e-154 553
13 TraesCS3B01G236000 chr2D 94.167 360 20 1 1 359 599319618 599319259 4.190000e-152 547
14 TraesCS3B01G236000 chr3D 94.199 362 19 2 1 360 424804852 424804491 3.240000e-153 551
15 TraesCS3B01G236000 chr5A 93.750 368 18 5 1 364 318094081 318094447 4.190000e-152 547
16 TraesCS3B01G236000 chr7D 93.243 370 23 2 1 368 530774814 530774445 5.430000e-151 544
17 TraesCS3B01G236000 chr7D 93.261 371 20 5 1 368 146771520 146771152 1.950000e-150 542
18 TraesCS3B01G236000 chr4D 94.350 354 18 2 1 353 493684655 493685007 1.950000e-150 542


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 TraesCS3B01G236000 chr3B 368845565 368847798 2233 False 4126 4126 100.000 1 2234 1 chr3B.!!$F1 2233
1 TraesCS3B01G236000 chrUn 171006072 171007966 1894 True 3088 3088 96.201 354 2234 1 chrUn.!!$R1 1880
2 TraesCS3B01G236000 chr6B 596602178 596604072 1894 False 3077 3077 96.097 354 2234 1 chr6B.!!$F1 1880
3 TraesCS3B01G236000 chr7A 638507985 638509879 1894 False 3061 3061 95.937 354 2234 1 chr7A.!!$F1 1880
4 TraesCS3B01G236000 chr7A 708243411 708245256 1845 True 3033 3033 96.371 395 2234 1 chr7A.!!$R1 1839
5 TraesCS3B01G236000 chr1B 672539010 672540903 1893 True 3048 3048 95.831 354 2234 1 chr1B.!!$R2 1880
6 TraesCS3B01G236000 chr2B 391225563 391227458 1895 False 3044 3044 95.781 354 2234 1 chr2B.!!$F1 1880
7 TraesCS3B01G236000 chr7B 54050186 54052078 1892 False 3031 3031 95.675 354 2234 1 chr7B.!!$F1 1880
8 TraesCS3B01G236000 chr5B 567277780 567279675 1895 True 3022 3022 95.570 354 2234 1 chr5B.!!$R1 1880
9 TraesCS3B01G236000 chr1D 212445943 212447782 1839 False 3005 3005 96.152 395 2234 1 chr1D.!!$F1 1839

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
41 42 0.023229 CATGCGCGTACGTGTACAAG 59.977 55.0 27.72 14.43 42.83 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 1806 0.54341 TGGGGCACTTCGAAGGTCTA 60.543 55.0 27.86 10.05 0.0 2.59 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
17 18 3.782042 GTTAGAGCCAACGCCTCG 58.218 61.111 0.00 0.00 34.57 4.63
18 19 2.125673 TTAGAGCCAACGCCTCGC 60.126 61.111 0.00 0.00 34.57 5.03
19 20 2.938086 TTAGAGCCAACGCCTCGCA 61.938 57.895 0.00 0.00 34.57 5.10
20 21 3.642778 TAGAGCCAACGCCTCGCAC 62.643 63.158 0.00 0.00 34.57 5.34
24 25 3.049674 CCAACGCCTCGCACACAT 61.050 61.111 0.00 0.00 0.00 3.21
25 26 2.174107 CAACGCCTCGCACACATG 59.826 61.111 0.00 0.00 0.00 3.21
34 35 3.773630 GCACACATGCGCGTACGT 61.774 61.111 17.90 0.00 43.33 3.57
35 36 2.093799 CACACATGCGCGTACGTG 59.906 61.111 21.37 21.37 42.83 4.49
36 37 2.355363 ACACATGCGCGTACGTGT 60.355 55.556 22.82 22.82 42.83 4.49
37 38 1.081309 ACACATGCGCGTACGTGTA 60.081 52.632 26.63 24.73 40.66 2.90
38 39 1.339134 CACATGCGCGTACGTGTAC 59.661 57.895 27.72 14.14 42.83 2.90
39 40 1.081309 ACATGCGCGTACGTGTACA 60.081 52.632 27.72 19.03 42.83 2.90
40 41 0.663867 ACATGCGCGTACGTGTACAA 60.664 50.000 27.72 13.14 42.83 2.41
41 42 0.023229 CATGCGCGTACGTGTACAAG 59.977 55.000 27.72 14.43 42.83 3.16
42 43 0.109643 ATGCGCGTACGTGTACAAGA 60.110 50.000 27.72 7.75 42.83 3.02
43 44 0.726787 TGCGCGTACGTGTACAAGAG 60.727 55.000 27.72 7.42 42.83 2.85
44 45 0.453282 GCGCGTACGTGTACAAGAGA 60.453 55.000 27.72 0.10 42.83 3.10
45 46 1.954437 CGCGTACGTGTACAAGAGAA 58.046 50.000 20.36 0.00 35.87 2.87
46 47 2.309693 CGCGTACGTGTACAAGAGAAA 58.690 47.619 20.36 0.00 35.87 2.52
47 48 2.088056 CGCGTACGTGTACAAGAGAAAC 59.912 50.000 20.36 6.96 35.87 2.78
48 49 3.044986 GCGTACGTGTACAAGAGAAACA 58.955 45.455 17.90 0.00 35.87 2.83
49 50 3.671928 GCGTACGTGTACAAGAGAAACAT 59.328 43.478 17.90 0.00 35.87 2.71
50 51 4.432503 GCGTACGTGTACAAGAGAAACATG 60.433 45.833 17.90 0.00 35.87 3.21
51 52 4.432503 CGTACGTGTACAAGAGAAACATGC 60.433 45.833 16.00 0.00 35.87 4.06
52 53 3.462982 ACGTGTACAAGAGAAACATGCA 58.537 40.909 16.00 0.00 34.23 3.96
53 54 3.247648 ACGTGTACAAGAGAAACATGCAC 59.752 43.478 16.00 0.00 34.23 4.57
54 55 3.363970 CGTGTACAAGAGAAACATGCACC 60.364 47.826 2.23 0.00 0.00 5.01
55 56 2.805671 TGTACAAGAGAAACATGCACCG 59.194 45.455 0.00 0.00 0.00 4.94
56 57 0.593128 ACAAGAGAAACATGCACCGC 59.407 50.000 0.00 0.00 0.00 5.68
57 58 0.877071 CAAGAGAAACATGCACCGCT 59.123 50.000 0.00 0.00 0.00 5.52
58 59 1.135859 CAAGAGAAACATGCACCGCTC 60.136 52.381 0.00 0.00 0.00 5.03
59 60 1.016130 AGAGAAACATGCACCGCTCG 61.016 55.000 0.00 0.00 0.00 5.03
60 61 1.970917 GAGAAACATGCACCGCTCGG 61.971 60.000 6.79 6.79 42.03 4.63
61 62 3.667429 GAAACATGCACCGCTCGGC 62.667 63.158 8.41 0.00 39.32 5.54
79 80 2.608368 CCCCAACCTCCCACCGTA 60.608 66.667 0.00 0.00 0.00 4.02
80 81 2.225596 CCCCAACCTCCCACCGTAA 61.226 63.158 0.00 0.00 0.00 3.18
81 82 1.002990 CCCAACCTCCCACCGTAAC 60.003 63.158 0.00 0.00 0.00 2.50
82 83 1.002990 CCAACCTCCCACCGTAACC 60.003 63.158 0.00 0.00 0.00 2.85
83 84 1.375013 CAACCTCCCACCGTAACCG 60.375 63.158 0.00 0.00 0.00 4.44
104 105 2.803956 GGAACTCCCCGAAATTTTCCT 58.196 47.619 3.61 0.00 31.54 3.36
105 106 3.162666 GGAACTCCCCGAAATTTTCCTT 58.837 45.455 3.61 0.00 31.54 3.36
106 107 3.056821 GGAACTCCCCGAAATTTTCCTTG 60.057 47.826 3.61 0.00 31.54 3.61
107 108 1.893137 ACTCCCCGAAATTTTCCTTGC 59.107 47.619 3.61 0.00 0.00 4.01
108 109 1.204704 CTCCCCGAAATTTTCCTTGCC 59.795 52.381 3.61 0.00 0.00 4.52
109 110 0.249120 CCCCGAAATTTTCCTTGCCC 59.751 55.000 3.61 0.00 0.00 5.36
110 111 1.266178 CCCGAAATTTTCCTTGCCCT 58.734 50.000 3.61 0.00 0.00 5.19
111 112 1.623311 CCCGAAATTTTCCTTGCCCTT 59.377 47.619 3.61 0.00 0.00 3.95
112 113 2.612721 CCCGAAATTTTCCTTGCCCTTG 60.613 50.000 3.61 0.00 0.00 3.61
113 114 2.068519 CGAAATTTTCCTTGCCCTTGC 58.931 47.619 3.61 0.00 38.26 4.01
114 115 2.289010 CGAAATTTTCCTTGCCCTTGCT 60.289 45.455 3.61 0.00 38.71 3.91
115 116 3.743521 GAAATTTTCCTTGCCCTTGCTT 58.256 40.909 0.00 0.00 38.71 3.91
116 117 3.407424 AATTTTCCTTGCCCTTGCTTC 57.593 42.857 0.00 0.00 38.71 3.86
117 118 2.086610 TTTTCCTTGCCCTTGCTTCT 57.913 45.000 0.00 0.00 38.71 2.85
118 119 2.969821 TTTCCTTGCCCTTGCTTCTA 57.030 45.000 0.00 0.00 38.71 2.10
119 120 2.200373 TTCCTTGCCCTTGCTTCTAC 57.800 50.000 0.00 0.00 38.71 2.59
120 121 0.328258 TCCTTGCCCTTGCTTCTACC 59.672 55.000 0.00 0.00 38.71 3.18
121 122 0.038166 CCTTGCCCTTGCTTCTACCA 59.962 55.000 0.00 0.00 38.71 3.25
122 123 1.168714 CTTGCCCTTGCTTCTACCAC 58.831 55.000 0.00 0.00 38.71 4.16
123 124 0.605319 TTGCCCTTGCTTCTACCACG 60.605 55.000 0.00 0.00 38.71 4.94
124 125 1.745489 GCCCTTGCTTCTACCACGG 60.745 63.158 0.00 0.00 33.53 4.94
125 126 1.677552 CCCTTGCTTCTACCACGGT 59.322 57.895 0.00 0.00 0.00 4.83
126 127 0.036306 CCCTTGCTTCTACCACGGTT 59.964 55.000 0.00 0.00 0.00 4.44
127 128 1.544759 CCCTTGCTTCTACCACGGTTT 60.545 52.381 0.00 0.00 0.00 3.27
128 129 2.227194 CCTTGCTTCTACCACGGTTTT 58.773 47.619 0.00 0.00 0.00 2.43
129 130 2.621526 CCTTGCTTCTACCACGGTTTTT 59.378 45.455 0.00 0.00 0.00 1.94
145 146 1.243902 TTTTTCTGTCATGGACGGCC 58.756 50.000 0.00 0.00 38.67 6.13
146 147 0.608035 TTTTCTGTCATGGACGGCCC 60.608 55.000 3.83 0.00 38.67 5.80
154 155 4.413928 TGGACGGCCCAAAGAATG 57.586 55.556 3.83 0.00 43.29 2.67
155 156 1.458486 TGGACGGCCCAAAGAATGT 59.542 52.632 3.83 0.00 43.29 2.71
156 157 0.608035 TGGACGGCCCAAAGAATGTC 60.608 55.000 3.83 0.00 43.29 3.06
157 158 0.608035 GGACGGCCCAAAGAATGTCA 60.608 55.000 0.00 0.00 34.14 3.58
158 159 1.463674 GACGGCCCAAAGAATGTCAT 58.536 50.000 0.00 0.00 0.00 3.06
159 160 1.133025 GACGGCCCAAAGAATGTCATG 59.867 52.381 0.00 0.00 0.00 3.07
160 161 0.179129 CGGCCCAAAGAATGTCATGC 60.179 55.000 0.00 0.00 0.00 4.06
161 162 0.896923 GGCCCAAAGAATGTCATGCA 59.103 50.000 0.00 0.00 0.00 3.96
162 163 1.134907 GGCCCAAAGAATGTCATGCAG 60.135 52.381 0.00 0.00 0.00 4.41
163 164 1.820519 GCCCAAAGAATGTCATGCAGA 59.179 47.619 0.00 0.00 0.00 4.26
164 165 2.429610 GCCCAAAGAATGTCATGCAGAT 59.570 45.455 0.00 0.00 0.00 2.90
165 166 3.737047 GCCCAAAGAATGTCATGCAGATG 60.737 47.826 0.00 0.00 0.00 2.90
166 167 3.444916 CCAAAGAATGTCATGCAGATGC 58.555 45.455 0.00 0.00 42.50 3.91
167 168 3.105937 CAAAGAATGTCATGCAGATGCG 58.894 45.455 0.00 0.00 45.83 4.73
168 169 2.034104 AGAATGTCATGCAGATGCGT 57.966 45.000 0.00 0.00 45.83 5.24
169 170 1.938577 AGAATGTCATGCAGATGCGTC 59.061 47.619 0.00 0.00 45.83 5.19
170 171 1.938577 GAATGTCATGCAGATGCGTCT 59.061 47.619 1.48 1.48 45.83 4.18
171 172 1.579698 ATGTCATGCAGATGCGTCTC 58.420 50.000 5.16 2.05 45.83 3.36
172 173 0.460811 TGTCATGCAGATGCGTCTCC 60.461 55.000 5.16 0.00 45.83 3.71
173 174 1.227060 TCATGCAGATGCGTCTCCG 60.227 57.895 5.16 0.00 45.83 4.63
174 175 2.107750 ATGCAGATGCGTCTCCGG 59.892 61.111 5.16 0.00 45.83 5.14
175 176 4.819761 TGCAGATGCGTCTCCGGC 62.820 66.667 5.16 7.63 45.83 6.13
177 178 4.899239 CAGATGCGTCTCCGGCCC 62.899 72.222 5.16 0.00 30.42 5.80
192 193 2.746277 CCCGCCCAGGACGAAAAG 60.746 66.667 0.00 0.00 45.00 2.27
193 194 3.431725 CCGCCCAGGACGAAAAGC 61.432 66.667 0.00 0.00 45.00 3.51
194 195 3.431725 CGCCCAGGACGAAAAGCC 61.432 66.667 0.00 0.00 0.00 4.35
195 196 3.062466 GCCCAGGACGAAAAGCCC 61.062 66.667 0.00 0.00 0.00 5.19
196 197 2.434331 CCCAGGACGAAAAGCCCA 59.566 61.111 0.00 0.00 0.00 5.36
197 198 1.000896 CCCAGGACGAAAAGCCCAT 60.001 57.895 0.00 0.00 0.00 4.00
198 199 0.611896 CCCAGGACGAAAAGCCCATT 60.612 55.000 0.00 0.00 0.00 3.16
199 200 1.256812 CCAGGACGAAAAGCCCATTT 58.743 50.000 0.00 0.00 0.00 2.32
200 201 1.618343 CCAGGACGAAAAGCCCATTTT 59.382 47.619 0.00 0.00 43.88 1.82
210 211 5.750352 AAAAGCCCATTTTCTGTCATGAT 57.250 34.783 0.00 0.00 36.31 2.45
211 212 4.996788 AAGCCCATTTTCTGTCATGATC 57.003 40.909 0.00 0.00 0.00 2.92
212 213 4.246712 AGCCCATTTTCTGTCATGATCT 57.753 40.909 0.00 0.00 0.00 2.75
213 214 4.607239 AGCCCATTTTCTGTCATGATCTT 58.393 39.130 0.00 0.00 0.00 2.40
214 215 5.021458 AGCCCATTTTCTGTCATGATCTTT 58.979 37.500 0.00 0.00 0.00 2.52
215 216 5.482878 AGCCCATTTTCTGTCATGATCTTTT 59.517 36.000 0.00 0.00 0.00 2.27
216 217 5.579511 GCCCATTTTCTGTCATGATCTTTTG 59.420 40.000 0.00 0.00 0.00 2.44
217 218 6.694447 CCCATTTTCTGTCATGATCTTTTGT 58.306 36.000 0.00 0.00 0.00 2.83
218 219 6.810182 CCCATTTTCTGTCATGATCTTTTGTC 59.190 38.462 0.00 0.00 0.00 3.18
219 220 7.372714 CCATTTTCTGTCATGATCTTTTGTCA 58.627 34.615 0.00 0.00 0.00 3.58
220 221 7.327761 CCATTTTCTGTCATGATCTTTTGTCAC 59.672 37.037 0.00 0.00 0.00 3.67
221 222 6.940831 TTTCTGTCATGATCTTTTGTCACA 57.059 33.333 0.00 0.00 0.00 3.58
222 223 6.549912 TTCTGTCATGATCTTTTGTCACAG 57.450 37.500 0.00 0.00 0.00 3.66
223 224 5.857268 TCTGTCATGATCTTTTGTCACAGA 58.143 37.500 0.00 0.32 29.27 3.41
224 225 6.290605 TCTGTCATGATCTTTTGTCACAGAA 58.709 36.000 0.00 0.00 29.02 3.02
225 226 6.426025 TCTGTCATGATCTTTTGTCACAGAAG 59.574 38.462 1.47 1.47 29.02 2.85
226 227 6.057533 TGTCATGATCTTTTGTCACAGAAGT 58.942 36.000 7.89 0.00 29.38 3.01
227 228 7.216494 TGTCATGATCTTTTGTCACAGAAGTA 58.784 34.615 7.89 0.00 29.38 2.24
228 229 7.386025 TGTCATGATCTTTTGTCACAGAAGTAG 59.614 37.037 7.89 0.00 29.38 2.57
229 230 6.875726 TCATGATCTTTTGTCACAGAAGTAGG 59.124 38.462 7.89 0.00 29.38 3.18
230 231 6.419484 TGATCTTTTGTCACAGAAGTAGGA 57.581 37.500 7.89 0.00 29.38 2.94
231 232 6.459066 TGATCTTTTGTCACAGAAGTAGGAG 58.541 40.000 7.89 0.00 29.38 3.69
232 233 4.632153 TCTTTTGTCACAGAAGTAGGAGC 58.368 43.478 7.89 0.00 29.38 4.70
233 234 3.402628 TTTGTCACAGAAGTAGGAGCC 57.597 47.619 0.00 0.00 0.00 4.70
234 235 1.267121 TGTCACAGAAGTAGGAGCCC 58.733 55.000 0.00 0.00 0.00 5.19
235 236 1.267121 GTCACAGAAGTAGGAGCCCA 58.733 55.000 0.00 0.00 0.00 5.36
236 237 1.066787 GTCACAGAAGTAGGAGCCCAC 60.067 57.143 0.00 0.00 0.00 4.61
237 238 0.250513 CACAGAAGTAGGAGCCCACC 59.749 60.000 0.00 0.00 0.00 4.61
238 239 0.178903 ACAGAAGTAGGAGCCCACCA 60.179 55.000 0.00 0.00 0.00 4.17
239 240 0.250513 CAGAAGTAGGAGCCCACCAC 59.749 60.000 0.00 0.00 0.00 4.16
240 241 0.178903 AGAAGTAGGAGCCCACCACA 60.179 55.000 0.00 0.00 0.00 4.17
241 242 0.912486 GAAGTAGGAGCCCACCACAT 59.088 55.000 0.00 0.00 0.00 3.21
242 243 0.912486 AAGTAGGAGCCCACCACATC 59.088 55.000 0.00 0.00 0.00 3.06
243 244 0.043334 AGTAGGAGCCCACCACATCT 59.957 55.000 0.00 0.00 0.00 2.90
244 245 1.291033 AGTAGGAGCCCACCACATCTA 59.709 52.381 0.00 0.00 0.00 1.98
245 246 2.090494 AGTAGGAGCCCACCACATCTAT 60.090 50.000 0.00 0.00 0.00 1.98
246 247 1.135094 AGGAGCCCACCACATCTATG 58.865 55.000 0.00 0.00 0.00 2.23
247 248 1.131638 GGAGCCCACCACATCTATGA 58.868 55.000 0.00 0.00 0.00 2.15
248 249 1.701847 GGAGCCCACCACATCTATGAT 59.298 52.381 0.00 0.00 0.00 2.45
249 250 2.551721 GGAGCCCACCACATCTATGATG 60.552 54.545 6.06 6.06 0.00 3.07
250 251 2.369860 GAGCCCACCACATCTATGATGA 59.630 50.000 13.63 0.00 0.00 2.92
251 252 2.984604 AGCCCACCACATCTATGATGAT 59.015 45.455 13.63 0.00 0.00 2.45
252 253 4.170449 AGCCCACCACATCTATGATGATA 58.830 43.478 13.63 0.00 0.00 2.15
253 254 4.019860 AGCCCACCACATCTATGATGATAC 60.020 45.833 13.63 0.00 0.00 2.24
254 255 4.836825 CCCACCACATCTATGATGATACC 58.163 47.826 13.63 0.00 0.00 2.73
255 256 4.498241 CCACCACATCTATGATGATACCG 58.502 47.826 13.63 0.06 0.00 4.02
256 257 4.498241 CACCACATCTATGATGATACCGG 58.502 47.826 13.63 0.00 0.00 5.28
257 258 3.515502 ACCACATCTATGATGATACCGGG 59.484 47.826 6.32 0.00 0.00 5.73
258 259 3.515502 CCACATCTATGATGATACCGGGT 59.484 47.826 6.32 4.46 0.00 5.28
259 260 4.020218 CCACATCTATGATGATACCGGGTT 60.020 45.833 4.31 0.00 0.00 4.11
260 261 5.513094 CCACATCTATGATGATACCGGGTTT 60.513 44.000 4.31 0.00 0.00 3.27
261 262 5.997746 CACATCTATGATGATACCGGGTTTT 59.002 40.000 4.31 0.00 0.00 2.43
262 263 5.997746 ACATCTATGATGATACCGGGTTTTG 59.002 40.000 4.31 0.00 0.00 2.44
263 264 5.623956 TCTATGATGATACCGGGTTTTGT 57.376 39.130 4.31 0.00 0.00 2.83
264 265 5.607477 TCTATGATGATACCGGGTTTTGTC 58.393 41.667 4.31 0.82 0.00 3.18
265 266 3.704800 TGATGATACCGGGTTTTGTCA 57.295 42.857 4.31 5.88 0.00 3.58
266 267 3.340034 TGATGATACCGGGTTTTGTCAC 58.660 45.455 4.31 2.17 0.00 3.67
267 268 2.932855 TGATACCGGGTTTTGTCACA 57.067 45.000 4.31 0.00 0.00 3.58
268 269 3.210232 TGATACCGGGTTTTGTCACAA 57.790 42.857 4.31 0.00 0.00 3.33
269 270 3.757270 TGATACCGGGTTTTGTCACAAT 58.243 40.909 4.31 0.00 0.00 2.71
270 271 4.145807 TGATACCGGGTTTTGTCACAATT 58.854 39.130 4.31 0.00 0.00 2.32
271 272 5.314529 TGATACCGGGTTTTGTCACAATTA 58.685 37.500 4.31 0.00 0.00 1.40
272 273 5.946972 TGATACCGGGTTTTGTCACAATTAT 59.053 36.000 4.31 0.00 0.00 1.28
273 274 4.776795 ACCGGGTTTTGTCACAATTATC 57.223 40.909 6.32 0.00 0.00 1.75
274 275 4.145807 ACCGGGTTTTGTCACAATTATCA 58.854 39.130 6.32 0.00 0.00 2.15
275 276 4.770010 ACCGGGTTTTGTCACAATTATCAT 59.230 37.500 6.32 0.00 0.00 2.45
276 277 5.105917 ACCGGGTTTTGTCACAATTATCATC 60.106 40.000 6.32 0.00 0.00 2.92
277 278 5.105957 CCGGGTTTTGTCACAATTATCATCA 60.106 40.000 0.00 0.00 0.00 3.07
278 279 6.405731 CCGGGTTTTGTCACAATTATCATCAT 60.406 38.462 0.00 0.00 0.00 2.45
279 280 7.201776 CCGGGTTTTGTCACAATTATCATCATA 60.202 37.037 0.00 0.00 0.00 2.15
280 281 8.352201 CGGGTTTTGTCACAATTATCATCATAT 58.648 33.333 0.00 0.00 0.00 1.78
325 326 4.827304 AAAAATTGTTCGGCCCAAAATG 57.173 36.364 0.00 0.00 0.00 2.32
326 327 3.483808 AAATTGTTCGGCCCAAAATGT 57.516 38.095 0.00 0.00 0.00 2.71
327 328 2.741759 ATTGTTCGGCCCAAAATGTC 57.258 45.000 0.00 0.00 0.00 3.06
328 329 1.403814 TTGTTCGGCCCAAAATGTCA 58.596 45.000 0.00 0.00 0.00 3.58
329 330 0.671251 TGTTCGGCCCAAAATGTCAC 59.329 50.000 0.00 0.00 0.00 3.67
330 331 0.386731 GTTCGGCCCAAAATGTCACG 60.387 55.000 0.00 0.00 0.00 4.35
331 332 1.519751 TTCGGCCCAAAATGTCACGG 61.520 55.000 0.00 0.00 0.00 4.94
332 333 1.969064 CGGCCCAAAATGTCACGGA 60.969 57.895 0.00 0.00 0.00 4.69
333 334 1.312371 CGGCCCAAAATGTCACGGAT 61.312 55.000 0.00 0.00 0.00 4.18
334 335 0.173255 GGCCCAAAATGTCACGGATG 59.827 55.000 0.00 0.00 0.00 3.51
335 336 0.887933 GCCCAAAATGTCACGGATGT 59.112 50.000 0.00 0.00 0.00 3.06
337 338 1.885887 CCCAAAATGTCACGGATGTGT 59.114 47.619 0.00 0.00 46.49 3.72
338 339 2.095263 CCCAAAATGTCACGGATGTGTC 60.095 50.000 0.00 0.00 46.49 3.67
339 340 2.813754 CCAAAATGTCACGGATGTGTCT 59.186 45.455 0.00 0.00 46.49 3.41
340 341 3.253188 CCAAAATGTCACGGATGTGTCTT 59.747 43.478 0.00 0.00 46.49 3.01
341 342 4.261572 CCAAAATGTCACGGATGTGTCTTT 60.262 41.667 0.00 0.00 46.49 2.52
342 343 5.280945 CAAAATGTCACGGATGTGTCTTTT 58.719 37.500 0.00 0.00 46.49 2.27
343 344 5.514274 AAATGTCACGGATGTGTCTTTTT 57.486 34.783 0.00 0.00 46.49 1.94
452 463 6.833041 TGGATATTAAGGAAGCCGTATTTCA 58.167 36.000 0.00 0.00 0.00 2.69
488 499 4.096003 GCTGGGCTTAGGGTGCGA 62.096 66.667 0.00 0.00 0.00 5.10
625 636 3.346315 TGAATGTCGTCGGGTACTCTTA 58.654 45.455 0.00 0.00 0.00 2.10
633 644 3.095332 GTCGGGTACTCTTAACTTCCCT 58.905 50.000 0.00 0.00 33.41 4.20
663 674 2.898612 TGTAACCGTCACCTGTAATCCA 59.101 45.455 0.00 0.00 0.00 3.41
697 708 0.613853 CACCCCCTAGAGTGGACGAA 60.614 60.000 0.00 0.00 0.00 3.85
770 783 3.950397 TCACTTTCCCGTATGAGCATTT 58.050 40.909 0.00 0.00 0.00 2.32
862 875 4.052229 CGTCTGAGGGTTCGCCGT 62.052 66.667 0.00 0.00 38.45 5.68
902 915 1.646977 ACACTAGGCTACCCTTCTCCT 59.353 52.381 0.00 0.00 42.87 3.69
1031 1044 0.258774 AAGCCCCGCACCTCATTAAT 59.741 50.000 0.00 0.00 0.00 1.40
1100 1116 2.028476 CGGGAGTGATGTACAACAAGGA 60.028 50.000 7.47 0.00 0.00 3.36
1128 1144 2.583441 CCACCTTCTCACGGAGCCA 61.583 63.158 0.00 0.00 0.00 4.75
1171 1187 2.044252 CTCCCAGCCAGCAAGCAT 60.044 61.111 0.55 0.00 34.23 3.79
1211 1227 6.065976 AGTCATGGAAGTGTGGATAAATCA 57.934 37.500 0.00 0.00 0.00 2.57
1215 1231 6.891361 TCATGGAAGTGTGGATAAATCAACAT 59.109 34.615 3.55 0.00 42.32 2.71
1294 1310 2.173996 TCTCAAGTTTTTCGGGGTCCTT 59.826 45.455 0.00 0.00 0.00 3.36
1301 1317 1.651737 TTTCGGGGTCCTTGAGATCA 58.348 50.000 0.00 0.00 0.00 2.92
1371 1387 4.139786 GCATTTCAAGATGGCCTCTATCA 58.860 43.478 3.32 0.00 32.41 2.15
1374 1390 4.630644 TTCAAGATGGCCTCTATCATCC 57.369 45.455 3.32 0.00 40.27 3.51
1388 1404 4.964897 TCTATCATCCTTTTGAGAGCCTCA 59.035 41.667 0.00 1.25 38.87 3.86
1394 1410 2.618709 CCTTTTGAGAGCCTCACGTTTT 59.381 45.455 4.59 0.00 40.46 2.43
1440 1456 2.092429 AGAGACAAAAGCAGTCCCACAA 60.092 45.455 0.00 0.00 36.68 3.33
1445 1461 3.706086 ACAAAAGCAGTCCCACAAGAAAT 59.294 39.130 0.00 0.00 0.00 2.17
1596 1613 8.535690 ACTTTAAACTTAGAGTCCGATTCTTG 57.464 34.615 0.00 0.00 0.00 3.02
1767 1785 1.301953 GTGGCGTTTCCGGTAAGGT 60.302 57.895 13.92 0.00 41.99 3.50
1788 1806 2.045047 TGGAATCTCAAGGAGGGTCTCT 59.955 50.000 0.00 0.00 0.00 3.10
1902 1920 3.561960 CCCTTTGTTCCTCATCACCATCA 60.562 47.826 0.00 0.00 0.00 3.07
1921 1939 7.336679 CACCATCACAATAACAATAAGGAGACA 59.663 37.037 0.00 0.00 0.00 3.41
1922 1940 8.055181 ACCATCACAATAACAATAAGGAGACAT 58.945 33.333 0.00 0.00 0.00 3.06
2002 2022 2.035632 TGTTGGGCTTGGATTCGTTTT 58.964 42.857 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.049674 ATGTGTGCGAGGCGTTGG 61.050 61.111 0.00 0.00 0.00 3.77
8 9 2.174107 CATGTGTGCGAGGCGTTG 59.826 61.111 0.00 0.00 0.00 4.10
9 10 3.726517 GCATGTGTGCGAGGCGTT 61.727 61.111 0.00 0.00 42.28 4.84
18 19 1.338526 TACACGTACGCGCATGTGTG 61.339 55.000 35.98 24.98 45.81 3.82
19 20 2.355363 ACACGTACGCGCATGTGT 60.355 55.556 27.44 27.44 42.47 3.72
20 21 1.338526 TGTACACGTACGCGCATGTG 61.339 55.000 26.16 26.16 42.83 3.21
21 22 0.663867 TTGTACACGTACGCGCATGT 60.664 50.000 16.72 14.48 42.83 3.21
22 23 0.023229 CTTGTACACGTACGCGCATG 59.977 55.000 16.72 8.69 42.83 4.06
23 24 0.109643 TCTTGTACACGTACGCGCAT 60.110 50.000 16.72 0.00 42.83 4.73
24 25 0.726787 CTCTTGTACACGTACGCGCA 60.727 55.000 16.72 6.37 42.83 6.09
25 26 0.453282 TCTCTTGTACACGTACGCGC 60.453 55.000 16.72 0.00 42.83 6.86
26 27 1.954437 TTCTCTTGTACACGTACGCG 58.046 50.000 16.72 8.78 44.93 6.01
27 28 3.044986 TGTTTCTCTTGTACACGTACGC 58.955 45.455 16.72 0.00 38.85 4.42
28 29 4.432503 GCATGTTTCTCTTGTACACGTACG 60.433 45.833 15.01 15.01 38.85 3.67
29 30 4.446385 TGCATGTTTCTCTTGTACACGTAC 59.554 41.667 0.00 0.22 36.63 3.67
30 31 4.446385 GTGCATGTTTCTCTTGTACACGTA 59.554 41.667 0.00 0.00 37.01 3.57
31 32 3.247648 GTGCATGTTTCTCTTGTACACGT 59.752 43.478 0.00 0.00 37.01 4.49
32 33 3.363970 GGTGCATGTTTCTCTTGTACACG 60.364 47.826 0.00 0.00 38.09 4.49
33 34 3.363970 CGGTGCATGTTTCTCTTGTACAC 60.364 47.826 0.00 0.00 38.09 2.90
34 35 2.805671 CGGTGCATGTTTCTCTTGTACA 59.194 45.455 0.00 0.00 38.09 2.90
35 36 2.412847 GCGGTGCATGTTTCTCTTGTAC 60.413 50.000 0.00 0.00 36.58 2.90
36 37 1.804151 GCGGTGCATGTTTCTCTTGTA 59.196 47.619 0.00 0.00 0.00 2.41
37 38 0.593128 GCGGTGCATGTTTCTCTTGT 59.407 50.000 0.00 0.00 0.00 3.16
38 39 0.877071 AGCGGTGCATGTTTCTCTTG 59.123 50.000 0.00 0.00 0.00 3.02
39 40 1.160137 GAGCGGTGCATGTTTCTCTT 58.840 50.000 0.00 0.00 0.00 2.85
40 41 1.016130 CGAGCGGTGCATGTTTCTCT 61.016 55.000 0.00 0.00 0.00 3.10
41 42 1.421485 CGAGCGGTGCATGTTTCTC 59.579 57.895 0.00 0.00 0.00 2.87
42 43 2.034879 CCGAGCGGTGCATGTTTCT 61.035 57.895 0.00 0.00 0.00 2.52
43 44 2.480555 CCGAGCGGTGCATGTTTC 59.519 61.111 0.00 0.00 0.00 2.78
44 45 3.737172 GCCGAGCGGTGCATGTTT 61.737 61.111 10.94 0.00 37.65 2.83
62 63 2.225596 TTACGGTGGGAGGTTGGGG 61.226 63.158 0.00 0.00 0.00 4.96
63 64 1.002990 GTTACGGTGGGAGGTTGGG 60.003 63.158 0.00 0.00 0.00 4.12
64 65 1.002990 GGTTACGGTGGGAGGTTGG 60.003 63.158 0.00 0.00 0.00 3.77
65 66 1.375013 CGGTTACGGTGGGAGGTTG 60.375 63.158 0.00 0.00 36.18 3.77
66 67 3.062639 CGGTTACGGTGGGAGGTT 58.937 61.111 0.00 0.00 36.18 3.50
84 85 2.803956 AGGAAAATTTCGGGGAGTTCC 58.196 47.619 0.00 0.00 35.74 3.62
85 86 3.614150 GCAAGGAAAATTTCGGGGAGTTC 60.614 47.826 0.00 0.00 0.00 3.01
86 87 2.299013 GCAAGGAAAATTTCGGGGAGTT 59.701 45.455 0.00 0.00 0.00 3.01
87 88 1.893137 GCAAGGAAAATTTCGGGGAGT 59.107 47.619 0.00 0.00 0.00 3.85
88 89 1.204704 GGCAAGGAAAATTTCGGGGAG 59.795 52.381 0.00 0.00 0.00 4.30
89 90 1.262417 GGCAAGGAAAATTTCGGGGA 58.738 50.000 0.00 0.00 0.00 4.81
90 91 0.249120 GGGCAAGGAAAATTTCGGGG 59.751 55.000 0.00 0.00 0.00 5.73
91 92 1.266178 AGGGCAAGGAAAATTTCGGG 58.734 50.000 0.00 0.00 0.00 5.14
92 93 2.687370 CAAGGGCAAGGAAAATTTCGG 58.313 47.619 0.00 0.00 0.00 4.30
93 94 2.068519 GCAAGGGCAAGGAAAATTTCG 58.931 47.619 0.00 0.00 40.72 3.46
94 95 3.407424 AGCAAGGGCAAGGAAAATTTC 57.593 42.857 0.00 0.00 44.61 2.17
95 96 3.392285 AGAAGCAAGGGCAAGGAAAATTT 59.608 39.130 0.00 0.00 44.61 1.82
96 97 2.974794 AGAAGCAAGGGCAAGGAAAATT 59.025 40.909 0.00 0.00 44.61 1.82
97 98 2.613129 AGAAGCAAGGGCAAGGAAAAT 58.387 42.857 0.00 0.00 44.61 1.82
98 99 2.086610 AGAAGCAAGGGCAAGGAAAA 57.913 45.000 0.00 0.00 44.61 2.29
99 100 2.514803 GTAGAAGCAAGGGCAAGGAAA 58.485 47.619 0.00 0.00 44.61 3.13
100 101 1.271926 GGTAGAAGCAAGGGCAAGGAA 60.272 52.381 0.00 0.00 44.61 3.36
101 102 0.328258 GGTAGAAGCAAGGGCAAGGA 59.672 55.000 0.00 0.00 44.61 3.36
102 103 0.038166 TGGTAGAAGCAAGGGCAAGG 59.962 55.000 0.00 0.00 44.61 3.61
103 104 1.168714 GTGGTAGAAGCAAGGGCAAG 58.831 55.000 0.00 0.00 44.61 4.01
104 105 0.605319 CGTGGTAGAAGCAAGGGCAA 60.605 55.000 0.00 0.00 44.61 4.52
105 106 1.003839 CGTGGTAGAAGCAAGGGCA 60.004 57.895 0.00 0.00 44.61 5.36
106 107 1.745489 CCGTGGTAGAAGCAAGGGC 60.745 63.158 3.54 0.00 40.69 5.19
107 108 0.036306 AACCGTGGTAGAAGCAAGGG 59.964 55.000 14.07 6.10 46.95 3.95
109 110 3.982576 AAAAACCGTGGTAGAAGCAAG 57.017 42.857 0.00 0.00 0.00 4.01
126 127 1.243902 GGCCGTCCATGACAGAAAAA 58.756 50.000 0.00 0.00 32.09 1.94
127 128 0.608035 GGGCCGTCCATGACAGAAAA 60.608 55.000 0.00 0.00 35.00 2.29
128 129 1.002624 GGGCCGTCCATGACAGAAA 60.003 57.895 0.00 0.00 35.00 2.52
129 130 1.773856 TTGGGCCGTCCATGACAGAA 61.774 55.000 0.00 0.00 46.52 3.02
130 131 1.773856 TTTGGGCCGTCCATGACAGA 61.774 55.000 0.00 0.00 46.52 3.41
131 132 1.303236 TTTGGGCCGTCCATGACAG 60.303 57.895 0.00 0.00 46.52 3.51
132 133 1.303236 CTTTGGGCCGTCCATGACA 60.303 57.895 0.00 0.00 46.52 3.58
133 134 0.608035 TTCTTTGGGCCGTCCATGAC 60.608 55.000 0.00 0.00 46.52 3.06
134 135 0.331278 ATTCTTTGGGCCGTCCATGA 59.669 50.000 0.00 0.00 46.52 3.07
135 136 0.457035 CATTCTTTGGGCCGTCCATG 59.543 55.000 0.00 0.00 46.52 3.66
136 137 0.039618 ACATTCTTTGGGCCGTCCAT 59.960 50.000 0.00 0.00 46.52 3.41
137 138 0.608035 GACATTCTTTGGGCCGTCCA 60.608 55.000 0.00 0.00 45.43 4.02
138 139 0.608035 TGACATTCTTTGGGCCGTCC 60.608 55.000 0.00 0.00 0.00 4.79
139 140 1.133025 CATGACATTCTTTGGGCCGTC 59.867 52.381 0.00 0.00 0.00 4.79
140 141 1.176527 CATGACATTCTTTGGGCCGT 58.823 50.000 0.00 0.00 0.00 5.68
141 142 0.179129 GCATGACATTCTTTGGGCCG 60.179 55.000 0.00 0.00 0.00 6.13
142 143 0.896923 TGCATGACATTCTTTGGGCC 59.103 50.000 0.00 0.00 0.00 5.80
143 144 1.820519 TCTGCATGACATTCTTTGGGC 59.179 47.619 0.00 0.00 0.00 5.36
144 145 3.737047 GCATCTGCATGACATTCTTTGGG 60.737 47.826 0.00 0.00 41.59 4.12
145 146 3.444916 GCATCTGCATGACATTCTTTGG 58.555 45.455 0.00 0.00 41.59 3.28
146 147 3.105937 CGCATCTGCATGACATTCTTTG 58.894 45.455 0.00 0.00 42.21 2.77
147 148 2.751259 ACGCATCTGCATGACATTCTTT 59.249 40.909 0.00 0.00 42.21 2.52
148 149 2.353889 GACGCATCTGCATGACATTCTT 59.646 45.455 0.00 0.00 42.21 2.52
149 150 1.938577 GACGCATCTGCATGACATTCT 59.061 47.619 0.00 0.00 42.21 2.40
150 151 1.938577 AGACGCATCTGCATGACATTC 59.061 47.619 0.00 0.00 42.21 2.67
151 152 1.938577 GAGACGCATCTGCATGACATT 59.061 47.619 0.00 0.00 42.21 2.71
152 153 1.579698 GAGACGCATCTGCATGACAT 58.420 50.000 0.00 0.00 42.21 3.06
153 154 0.460811 GGAGACGCATCTGCATGACA 60.461 55.000 0.00 0.00 42.66 3.58
154 155 2.305405 GGAGACGCATCTGCATGAC 58.695 57.895 0.00 0.00 42.66 3.06
155 156 4.842292 GGAGACGCATCTGCATGA 57.158 55.556 0.00 0.00 42.66 3.07
175 176 2.746277 CTTTTCGTCCTGGGCGGG 60.746 66.667 21.87 5.25 0.00 6.13
176 177 3.431725 GCTTTTCGTCCTGGGCGG 61.432 66.667 21.87 5.53 0.00 6.13
177 178 3.431725 GGCTTTTCGTCCTGGGCG 61.432 66.667 15.85 15.85 0.00 6.13
178 179 3.062466 GGGCTTTTCGTCCTGGGC 61.062 66.667 0.00 0.00 33.40 5.36
179 180 0.611896 AATGGGCTTTTCGTCCTGGG 60.612 55.000 0.00 0.00 38.58 4.45
180 181 1.256812 AAATGGGCTTTTCGTCCTGG 58.743 50.000 0.00 0.00 38.58 4.45
181 182 2.946564 GAAAATGGGCTTTTCGTCCTG 58.053 47.619 0.00 0.00 42.34 3.86
188 189 5.482878 AGATCATGACAGAAAATGGGCTTTT 59.517 36.000 0.00 0.00 39.78 2.27
189 190 5.021458 AGATCATGACAGAAAATGGGCTTT 58.979 37.500 0.00 0.00 0.00 3.51
190 191 4.607239 AGATCATGACAGAAAATGGGCTT 58.393 39.130 0.00 0.00 0.00 4.35
191 192 4.246712 AGATCATGACAGAAAATGGGCT 57.753 40.909 0.00 0.00 0.00 5.19
192 193 4.996788 AAGATCATGACAGAAAATGGGC 57.003 40.909 0.00 0.00 0.00 5.36
193 194 6.694447 ACAAAAGATCATGACAGAAAATGGG 58.306 36.000 0.00 0.00 0.00 4.00
194 195 7.327761 GTGACAAAAGATCATGACAGAAAATGG 59.672 37.037 0.00 0.00 0.00 3.16
195 196 7.863877 TGTGACAAAAGATCATGACAGAAAATG 59.136 33.333 0.00 0.00 0.00 2.32
196 197 7.944061 TGTGACAAAAGATCATGACAGAAAAT 58.056 30.769 0.00 0.00 0.00 1.82
197 198 7.282901 TCTGTGACAAAAGATCATGACAGAAAA 59.717 33.333 0.00 0.00 28.96 2.29
198 199 6.767423 TCTGTGACAAAAGATCATGACAGAAA 59.233 34.615 0.00 0.00 28.96 2.52
199 200 6.290605 TCTGTGACAAAAGATCATGACAGAA 58.709 36.000 0.00 0.00 28.96 3.02
200 201 5.857268 TCTGTGACAAAAGATCATGACAGA 58.143 37.500 0.00 0.00 29.22 3.41
201 202 6.204301 ACTTCTGTGACAAAAGATCATGACAG 59.796 38.462 5.54 0.00 0.00 3.51
202 203 6.057533 ACTTCTGTGACAAAAGATCATGACA 58.942 36.000 5.54 0.00 0.00 3.58
203 204 6.551385 ACTTCTGTGACAAAAGATCATGAC 57.449 37.500 5.54 0.00 0.00 3.06
204 205 6.875726 CCTACTTCTGTGACAAAAGATCATGA 59.124 38.462 5.54 0.00 0.00 3.07
205 206 6.875726 TCCTACTTCTGTGACAAAAGATCATG 59.124 38.462 5.54 0.00 0.00 3.07
206 207 7.009179 TCCTACTTCTGTGACAAAAGATCAT 57.991 36.000 5.54 0.00 0.00 2.45
207 208 6.419484 TCCTACTTCTGTGACAAAAGATCA 57.581 37.500 5.54 0.00 0.00 2.92
208 209 5.350091 GCTCCTACTTCTGTGACAAAAGATC 59.650 44.000 5.54 0.00 0.00 2.75
209 210 5.241662 GCTCCTACTTCTGTGACAAAAGAT 58.758 41.667 5.54 0.00 0.00 2.40
210 211 4.503296 GGCTCCTACTTCTGTGACAAAAGA 60.503 45.833 5.54 0.00 0.00 2.52
211 212 3.748568 GGCTCCTACTTCTGTGACAAAAG 59.251 47.826 0.00 0.00 0.00 2.27
212 213 3.496160 GGGCTCCTACTTCTGTGACAAAA 60.496 47.826 0.00 0.00 0.00 2.44
213 214 2.038557 GGGCTCCTACTTCTGTGACAAA 59.961 50.000 0.00 0.00 0.00 2.83
214 215 1.623811 GGGCTCCTACTTCTGTGACAA 59.376 52.381 0.00 0.00 0.00 3.18
215 216 1.267121 GGGCTCCTACTTCTGTGACA 58.733 55.000 0.00 0.00 0.00 3.58
216 217 1.066787 GTGGGCTCCTACTTCTGTGAC 60.067 57.143 0.00 0.00 0.00 3.67
217 218 1.267121 GTGGGCTCCTACTTCTGTGA 58.733 55.000 0.00 0.00 0.00 3.58
218 219 0.250513 GGTGGGCTCCTACTTCTGTG 59.749 60.000 2.46 0.00 0.00 3.66
219 220 0.178903 TGGTGGGCTCCTACTTCTGT 60.179 55.000 2.46 0.00 0.00 3.41
220 221 0.250513 GTGGTGGGCTCCTACTTCTG 59.749 60.000 2.46 0.00 0.00 3.02
221 222 0.178903 TGTGGTGGGCTCCTACTTCT 60.179 55.000 2.46 0.00 0.00 2.85
222 223 0.912486 ATGTGGTGGGCTCCTACTTC 59.088 55.000 2.46 0.00 0.00 3.01
223 224 0.912486 GATGTGGTGGGCTCCTACTT 59.088 55.000 2.46 0.00 0.00 2.24
224 225 0.043334 AGATGTGGTGGGCTCCTACT 59.957 55.000 2.46 0.00 0.00 2.57
225 226 1.789523 TAGATGTGGTGGGCTCCTAC 58.210 55.000 0.00 0.00 0.00 3.18
226 227 2.090775 TCATAGATGTGGTGGGCTCCTA 60.091 50.000 0.00 0.00 0.00 2.94
227 228 1.135094 CATAGATGTGGTGGGCTCCT 58.865 55.000 0.00 0.00 0.00 3.69
228 229 1.131638 TCATAGATGTGGTGGGCTCC 58.868 55.000 0.00 0.00 0.00 4.70
229 230 2.369860 TCATCATAGATGTGGTGGGCTC 59.630 50.000 6.86 0.00 0.00 4.70
230 231 2.411583 TCATCATAGATGTGGTGGGCT 58.588 47.619 6.86 0.00 0.00 5.19
231 232 2.936919 TCATCATAGATGTGGTGGGC 57.063 50.000 6.86 0.00 0.00 5.36
232 233 4.621510 CGGTATCATCATAGATGTGGTGGG 60.622 50.000 6.86 0.00 0.00 4.61
233 234 4.498241 CGGTATCATCATAGATGTGGTGG 58.502 47.826 6.86 0.00 0.00 4.61
234 235 4.498241 CCGGTATCATCATAGATGTGGTG 58.502 47.826 6.86 0.00 0.00 4.17
235 236 3.515502 CCCGGTATCATCATAGATGTGGT 59.484 47.826 0.00 0.00 0.00 4.16
236 237 3.515502 ACCCGGTATCATCATAGATGTGG 59.484 47.826 0.00 3.53 0.00 4.17
237 238 4.808414 ACCCGGTATCATCATAGATGTG 57.192 45.455 0.00 0.00 0.00 3.21
238 239 5.825593 AAACCCGGTATCATCATAGATGT 57.174 39.130 0.00 0.00 0.00 3.06
239 240 5.997746 ACAAAACCCGGTATCATCATAGATG 59.002 40.000 0.00 0.62 0.00 2.90
240 241 6.183361 TGACAAAACCCGGTATCATCATAGAT 60.183 38.462 0.00 0.00 0.00 1.98
241 242 5.129650 TGACAAAACCCGGTATCATCATAGA 59.870 40.000 0.00 0.00 0.00 1.98
242 243 5.236478 GTGACAAAACCCGGTATCATCATAG 59.764 44.000 0.00 0.00 0.00 2.23
243 244 5.120399 GTGACAAAACCCGGTATCATCATA 58.880 41.667 0.00 0.00 0.00 2.15
244 245 3.945285 GTGACAAAACCCGGTATCATCAT 59.055 43.478 0.00 0.00 0.00 2.45
245 246 3.244596 TGTGACAAAACCCGGTATCATCA 60.245 43.478 0.00 0.00 0.00 3.07
246 247 3.340034 TGTGACAAAACCCGGTATCATC 58.660 45.455 0.00 0.00 0.00 2.92
247 248 3.426787 TGTGACAAAACCCGGTATCAT 57.573 42.857 0.00 0.00 0.00 2.45
248 249 2.932855 TGTGACAAAACCCGGTATCA 57.067 45.000 0.00 0.00 0.00 2.15
249 250 4.776795 AATTGTGACAAAACCCGGTATC 57.223 40.909 0.62 0.00 0.00 2.24
250 251 5.946972 TGATAATTGTGACAAAACCCGGTAT 59.053 36.000 0.62 0.00 0.00 2.73
251 252 5.314529 TGATAATTGTGACAAAACCCGGTA 58.685 37.500 0.62 0.00 0.00 4.02
252 253 4.145807 TGATAATTGTGACAAAACCCGGT 58.854 39.130 0.62 0.00 0.00 5.28
253 254 4.775058 TGATAATTGTGACAAAACCCGG 57.225 40.909 0.62 0.00 0.00 5.73
254 255 5.948588 TGATGATAATTGTGACAAAACCCG 58.051 37.500 0.62 0.00 0.00 5.28
304 305 4.203226 ACATTTTGGGCCGAACAATTTTT 58.797 34.783 5.46 0.00 0.00 1.94
305 306 3.812609 GACATTTTGGGCCGAACAATTTT 59.187 39.130 5.46 0.00 0.00 1.82
306 307 3.181461 TGACATTTTGGGCCGAACAATTT 60.181 39.130 5.46 0.00 0.00 1.82
307 308 2.366916 TGACATTTTGGGCCGAACAATT 59.633 40.909 5.46 0.00 0.00 2.32
308 309 1.967066 TGACATTTTGGGCCGAACAAT 59.033 42.857 5.46 1.12 0.00 2.71
309 310 1.067821 GTGACATTTTGGGCCGAACAA 59.932 47.619 5.46 0.00 0.00 2.83
310 311 0.671251 GTGACATTTTGGGCCGAACA 59.329 50.000 5.46 0.00 0.00 3.18
311 312 0.386731 CGTGACATTTTGGGCCGAAC 60.387 55.000 5.46 0.00 0.00 3.95
312 313 1.519751 CCGTGACATTTTGGGCCGAA 61.520 55.000 0.79 0.79 0.00 4.30
313 314 1.969064 CCGTGACATTTTGGGCCGA 60.969 57.895 0.00 0.00 0.00 5.54
314 315 1.312371 ATCCGTGACATTTTGGGCCG 61.312 55.000 0.00 0.00 0.00 6.13
315 316 0.173255 CATCCGTGACATTTTGGGCC 59.827 55.000 0.00 0.00 0.00 5.80
316 317 0.887933 ACATCCGTGACATTTTGGGC 59.112 50.000 0.00 0.00 0.00 5.36
317 318 1.885887 ACACATCCGTGACATTTTGGG 59.114 47.619 0.00 0.00 46.80 4.12
318 319 2.813754 AGACACATCCGTGACATTTTGG 59.186 45.455 0.00 0.00 46.80 3.28
319 320 4.488126 AAGACACATCCGTGACATTTTG 57.512 40.909 0.00 0.00 46.80 2.44
320 321 5.514274 AAAAGACACATCCGTGACATTTT 57.486 34.783 0.00 1.58 46.80 1.82
321 322 5.514274 AAAAAGACACATCCGTGACATTT 57.486 34.783 0.00 0.00 46.80 2.32
371 372 2.904434 CCGGGCCTAGGTTATATGTTCT 59.096 50.000 11.31 0.00 0.00 3.01
382 383 2.590092 CCTTCAACCGGGCCTAGG 59.410 66.667 6.32 14.87 0.00 3.02
401 412 2.860971 AAGGGGGCTGGACTGCTT 60.861 61.111 1.31 0.00 0.00 3.91
407 418 0.486879 ATTTCAACAAGGGGGCTGGA 59.513 50.000 0.00 0.00 0.00 3.86
452 463 1.472376 GCTTCTCGGAGCTGCTATTGT 60.472 52.381 0.15 0.00 39.57 2.71
625 636 2.683211 ACAAGAATGGCAGGGAAGTT 57.317 45.000 0.00 0.00 0.00 2.66
633 644 2.147958 GTGACGGTTACAAGAATGGCA 58.852 47.619 0.00 0.00 0.00 4.92
770 783 9.078990 CTCTTCCACTGACTTATATATGTACCA 57.921 37.037 1.48 0.00 0.00 3.25
862 875 2.293122 GTGTAAGCACAGCAATGAACCA 59.707 45.455 0.00 0.00 44.64 3.67
1088 1104 3.810941 GACGGAAATGTCCTTGTTGTACA 59.189 43.478 0.00 0.00 42.44 2.90
1100 1116 1.697432 TGAGAAGGTGGACGGAAATGT 59.303 47.619 0.00 0.00 0.00 2.71
1171 1187 6.440647 TCCATGACTTCTAGAGGAAAGCTAAA 59.559 38.462 9.14 0.00 33.07 1.85
1277 1293 2.173996 TCTCAAGGACCCCGAAAAACTT 59.826 45.455 0.00 0.00 0.00 2.66
1294 1310 5.661056 ACTCGACCTAAAATGTGATCTCA 57.339 39.130 0.00 0.00 0.00 3.27
1301 1317 4.438472 GCGTCTCTACTCGACCTAAAATGT 60.438 45.833 0.00 0.00 0.00 2.71
1371 1387 1.625818 ACGTGAGGCTCTCAAAAGGAT 59.374 47.619 16.72 0.00 42.46 3.24
1374 1390 3.304057 GGAAAACGTGAGGCTCTCAAAAG 60.304 47.826 16.72 0.00 42.46 2.27
1596 1613 6.970484 TCTACTTTGTCTTTGGAAGAATTGC 58.030 36.000 0.00 0.00 39.67 3.56
1767 1785 2.045047 AGAGACCCTCCTTGAGATTCCA 59.955 50.000 0.00 0.00 0.00 3.53
1788 1806 0.543410 TGGGGCACTTCGAAGGTCTA 60.543 55.000 27.86 10.05 0.00 2.59
1858 1876 3.619979 GCCGGGGAGATCATCGAAATTAT 60.620 47.826 2.18 0.00 0.00 1.28
1902 1920 7.336931 GTCACCATGTCTCCTTATTGTTATTGT 59.663 37.037 0.00 0.00 0.00 2.71
1921 1939 3.348647 TTTGGATGACGATGTCACCAT 57.651 42.857 16.42 0.00 45.65 3.55
1922 1940 2.849294 TTTGGATGACGATGTCACCA 57.151 45.000 13.54 13.54 45.65 4.17
1940 1958 5.110814 CCTTTGGGGTTTTCTTTTCCTTT 57.889 39.130 0.00 0.00 0.00 3.11
1965 1985 4.941263 CCCAACAAGTAGAATTCCATTCGA 59.059 41.667 0.65 0.00 43.92 3.71
1985 2005 1.698506 ACAAAACGAATCCAAGCCCA 58.301 45.000 0.00 0.00 0.00 5.36
2060 2080 6.183360 GCGATTGGCTTCACTTTAGATTTTTG 60.183 38.462 0.00 0.00 39.11 2.44


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

AutoCloner maintained by Alex Coulton.