Multiple sequence alignment - TraesCS2A01G578100

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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 TraesCS2A01G578100 chr2A 100.000 2435 0 0 1 2435 771618301 771620735 0.000000e+00 4497
1 TraesCS2A01G578100 chr2D 95.150 2227 93 7 217 2435 645894872 645897091 0.000000e+00 3500
2 TraesCS2A01G578100 chr3D 99.550 222 1 0 1 222 3363074 3362853 2.920000e-109 405
3 TraesCS2A01G578100 chr7B 100.000 218 0 0 1 218 748183538 748183321 1.050000e-108 403
4 TraesCS2A01G578100 chr7B 100.000 217 0 0 1 217 99220913 99221129 3.770000e-108 401
5 TraesCS2A01G578100 chrUn 100.000 217 0 0 1 217 2002337 2002121 3.770000e-108 401
6 TraesCS2A01G578100 chr6D 100.000 217 0 0 1 217 432917487 432917703 3.770000e-108 401
7 TraesCS2A01G578100 chr6D 91.915 235 17 2 1878 2110 440639732 440639498 6.490000e-86 327
8 TraesCS2A01G578100 chr6D 89.540 239 23 2 1873 2110 433481398 433481161 3.930000e-78 302
9 TraesCS2A01G578100 chr6B 100.000 217 0 0 1 217 2609742 2609958 3.770000e-108 401
10 TraesCS2A01G578100 chr5B 99.548 221 0 1 1 220 63282093 63282313 3.770000e-108 401
11 TraesCS2A01G578100 chr4D 100.000 217 0 0 1 217 419308235 419308019 3.770000e-108 401
12 TraesCS2A01G578100 chr4D 88.281 256 26 4 1858 2110 315080520 315080266 1.090000e-78 303
13 TraesCS2A01G578100 chr1D 100.000 217 0 0 1 217 59878306 59878522 3.770000e-108 401
14 TraesCS2A01G578100 chr6A 91.667 240 18 2 1873 2110 588601127 588600888 5.020000e-87 331
15 TraesCS2A01G578100 chr6A 87.854 247 26 3 1872 2115 601961371 601961126 1.100000e-73 287
16 TraesCS2A01G578100 chr7D 86.842 266 27 8 1861 2121 22601258 22600996 8.520000e-75 291
17 TraesCS2A01G578100 chr4A 87.698 252 27 4 1861 2110 160254575 160254824 8.520000e-75 291
18 TraesCS2A01G578100 chr5D 87.854 247 28 2 1869 2114 273526070 273526315 3.060000e-74 289


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 TraesCS2A01G578100 chr2A 771618301 771620735 2434 False 4497 4497 100.00 1 2435 1 chr2A.!!$F1 2434
1 TraesCS2A01G578100 chr2D 645894872 645897091 2219 False 3500 3500 95.15 217 2435 1 chr2D.!!$F1 2218

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
155 156 0.032017 AGAGGCCGGGTGATACTCTT 60.032 55.000 2.18 0.0 35.1 2.85 F
156 157 1.217183 AGAGGCCGGGTGATACTCTTA 59.783 52.381 2.18 0.0 35.1 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1176 1181 0.106268 TTCCTGCAGCCCAAAGACAA 60.106 50.0 8.66 0.0 0.0 3.18 R
1829 1837 0.237498 GTGGGCGGAAGAGAAAAACG 59.763 55.0 0.00 0.0 0.0 3.60 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
20 21 4.530857 CCGGCTCGGTCCACCATC 62.531 72.222 5.56 0.00 42.73 3.51
21 22 3.461773 CGGCTCGGTCCACCATCT 61.462 66.667 0.00 0.00 35.14 2.90
22 23 2.501610 GGCTCGGTCCACCATCTC 59.498 66.667 0.00 0.00 35.14 2.75
23 24 2.060980 GGCTCGGTCCACCATCTCT 61.061 63.158 0.00 0.00 35.14 3.10
24 25 1.617947 GGCTCGGTCCACCATCTCTT 61.618 60.000 0.00 0.00 35.14 2.85
25 26 0.250513 GCTCGGTCCACCATCTCTTT 59.749 55.000 0.00 0.00 35.14 2.52
26 27 1.740718 GCTCGGTCCACCATCTCTTTC 60.741 57.143 0.00 0.00 35.14 2.62
27 28 0.530744 TCGGTCCACCATCTCTTTCG 59.469 55.000 0.00 0.00 35.14 3.46
28 29 0.530744 CGGTCCACCATCTCTTTCGA 59.469 55.000 0.00 0.00 35.14 3.71
29 30 1.736032 CGGTCCACCATCTCTTTCGAC 60.736 57.143 0.00 0.00 35.14 4.20
30 31 1.275291 GGTCCACCATCTCTTTCGACA 59.725 52.381 0.00 0.00 35.64 4.35
31 32 2.093447 GGTCCACCATCTCTTTCGACAT 60.093 50.000 0.00 0.00 35.64 3.06
32 33 3.132289 GGTCCACCATCTCTTTCGACATA 59.868 47.826 0.00 0.00 35.64 2.29
33 34 4.363999 GTCCACCATCTCTTTCGACATAG 58.636 47.826 0.00 0.00 0.00 2.23
34 35 3.384789 TCCACCATCTCTTTCGACATAGG 59.615 47.826 0.00 0.00 0.00 2.57
35 36 3.126831 CACCATCTCTTTCGACATAGGC 58.873 50.000 0.00 0.00 0.00 3.93
36 37 2.766263 ACCATCTCTTTCGACATAGGCA 59.234 45.455 0.00 0.00 0.00 4.75
37 38 3.389329 ACCATCTCTTTCGACATAGGCAT 59.611 43.478 0.00 0.00 0.00 4.40
38 39 4.588951 ACCATCTCTTTCGACATAGGCATA 59.411 41.667 0.00 0.00 0.00 3.14
39 40 5.167121 CCATCTCTTTCGACATAGGCATAG 58.833 45.833 0.00 0.00 0.00 2.23
40 41 5.279206 CCATCTCTTTCGACATAGGCATAGT 60.279 44.000 0.00 0.00 0.00 2.12
41 42 5.188327 TCTCTTTCGACATAGGCATAGTG 57.812 43.478 0.00 0.00 0.00 2.74
42 43 4.645136 TCTCTTTCGACATAGGCATAGTGT 59.355 41.667 0.00 0.00 0.00 3.55
43 44 4.933330 TCTTTCGACATAGGCATAGTGTC 58.067 43.478 9.48 9.48 39.02 3.67
47 48 3.014604 GACATAGGCATAGTGTCGGTC 57.985 52.381 5.60 0.00 33.73 4.79
48 49 2.623889 GACATAGGCATAGTGTCGGTCT 59.376 50.000 5.60 0.00 33.73 3.85
49 50 3.819337 GACATAGGCATAGTGTCGGTCTA 59.181 47.826 5.60 0.00 33.73 2.59
50 51 4.408276 ACATAGGCATAGTGTCGGTCTAT 58.592 43.478 0.00 0.00 0.00 1.98
51 52 5.567430 ACATAGGCATAGTGTCGGTCTATA 58.433 41.667 0.00 0.00 0.00 1.31
52 53 5.648526 ACATAGGCATAGTGTCGGTCTATAG 59.351 44.000 0.00 0.00 0.00 1.31
53 54 4.368565 AGGCATAGTGTCGGTCTATAGA 57.631 45.455 0.00 0.00 0.00 1.98
54 55 4.073549 AGGCATAGTGTCGGTCTATAGAC 58.926 47.826 22.47 22.47 44.04 2.59
55 56 4.073549 GGCATAGTGTCGGTCTATAGACT 58.926 47.826 27.68 12.77 44.20 3.24
56 57 4.154556 GGCATAGTGTCGGTCTATAGACTC 59.845 50.000 27.68 18.26 44.20 3.36
57 58 4.998672 GCATAGTGTCGGTCTATAGACTCT 59.001 45.833 27.68 19.65 44.20 3.24
58 59 6.164876 GCATAGTGTCGGTCTATAGACTCTA 58.835 44.000 27.68 20.73 43.21 2.43
59 60 6.091169 GCATAGTGTCGGTCTATAGACTCTAC 59.909 46.154 27.68 22.20 42.44 2.59
60 61 5.874897 AGTGTCGGTCTATAGACTCTACT 57.125 43.478 27.68 22.20 44.20 2.57
61 62 5.603596 AGTGTCGGTCTATAGACTCTACTG 58.396 45.833 27.68 11.08 44.20 2.74
62 63 5.129155 AGTGTCGGTCTATAGACTCTACTGT 59.871 44.000 27.68 13.69 44.20 3.55
63 64 5.816777 GTGTCGGTCTATAGACTCTACTGTT 59.183 44.000 27.68 0.00 44.20 3.16
64 65 5.816258 TGTCGGTCTATAGACTCTACTGTTG 59.184 44.000 27.68 10.15 44.20 3.33
65 66 4.815308 TCGGTCTATAGACTCTACTGTTGC 59.185 45.833 27.68 9.82 44.20 4.17
66 67 4.023878 CGGTCTATAGACTCTACTGTTGCC 60.024 50.000 27.68 9.57 44.20 4.52
67 68 4.023878 GGTCTATAGACTCTACTGTTGCCG 60.024 50.000 27.68 0.00 44.20 5.69
68 69 4.815308 GTCTATAGACTCTACTGTTGCCGA 59.185 45.833 23.12 0.00 41.65 5.54
69 70 5.296283 GTCTATAGACTCTACTGTTGCCGAA 59.704 44.000 23.12 0.00 41.65 4.30
70 71 6.016943 GTCTATAGACTCTACTGTTGCCGAAT 60.017 42.308 23.12 0.00 41.65 3.34
71 72 3.963428 AGACTCTACTGTTGCCGAATT 57.037 42.857 0.00 0.00 0.00 2.17
72 73 3.589988 AGACTCTACTGTTGCCGAATTG 58.410 45.455 0.00 0.00 0.00 2.32
73 74 3.006967 AGACTCTACTGTTGCCGAATTGT 59.993 43.478 0.00 0.00 0.00 2.71
74 75 3.326747 ACTCTACTGTTGCCGAATTGTC 58.673 45.455 0.00 0.00 0.00 3.18
90 91 7.061752 CGAATTGTCGGTCTTTTATCTTTCT 57.938 36.000 0.00 0.00 43.81 2.52
91 92 8.181487 CGAATTGTCGGTCTTTTATCTTTCTA 57.819 34.615 0.00 0.00 43.81 2.10
92 93 8.108782 CGAATTGTCGGTCTTTTATCTTTCTAC 58.891 37.037 0.00 0.00 43.81 2.59
93 94 9.152595 GAATTGTCGGTCTTTTATCTTTCTACT 57.847 33.333 0.00 0.00 0.00 2.57
94 95 9.503399 AATTGTCGGTCTTTTATCTTTCTACTT 57.497 29.630 0.00 0.00 0.00 2.24
97 98 9.798994 TGTCGGTCTTTTATCTTTCTACTTATC 57.201 33.333 0.00 0.00 0.00 1.75
98 99 9.798994 GTCGGTCTTTTATCTTTCTACTTATCA 57.201 33.333 0.00 0.00 0.00 2.15
109 110 8.282455 TCTTTCTACTTATCAGACTACTGGTG 57.718 38.462 0.00 0.00 43.60 4.17
110 111 7.889073 TCTTTCTACTTATCAGACTACTGGTGT 59.111 37.037 0.00 0.00 43.60 4.16
111 112 8.418597 TTTCTACTTATCAGACTACTGGTGTT 57.581 34.615 0.00 0.00 43.60 3.32
112 113 8.418597 TTCTACTTATCAGACTACTGGTGTTT 57.581 34.615 0.00 0.00 43.60 2.83
113 114 7.827701 TCTACTTATCAGACTACTGGTGTTTG 58.172 38.462 0.00 0.00 43.60 2.93
114 115 5.794894 ACTTATCAGACTACTGGTGTTTGG 58.205 41.667 0.00 0.00 43.60 3.28
115 116 2.543777 TCAGACTACTGGTGTTTGGC 57.456 50.000 0.00 0.00 43.60 4.52
116 117 2.047061 TCAGACTACTGGTGTTTGGCT 58.953 47.619 0.00 0.00 43.60 4.75
117 118 2.146342 CAGACTACTGGTGTTTGGCTG 58.854 52.381 0.00 0.00 40.14 4.85
118 119 1.768870 AGACTACTGGTGTTTGGCTGT 59.231 47.619 0.00 0.00 0.00 4.40
119 120 1.873591 GACTACTGGTGTTTGGCTGTG 59.126 52.381 0.00 0.00 0.00 3.66
120 121 1.211949 ACTACTGGTGTTTGGCTGTGT 59.788 47.619 0.00 0.00 0.00 3.72
121 122 1.603802 CTACTGGTGTTTGGCTGTGTG 59.396 52.381 0.00 0.00 0.00 3.82
122 123 1.066257 CTGGTGTTTGGCTGTGTGC 59.934 57.895 0.00 0.00 41.94 4.57
123 124 1.665264 CTGGTGTTTGGCTGTGTGCA 61.665 55.000 0.00 0.00 45.15 4.57
124 125 1.042003 TGGTGTTTGGCTGTGTGCAT 61.042 50.000 0.00 0.00 45.15 3.96
125 126 0.318955 GGTGTTTGGCTGTGTGCATC 60.319 55.000 0.00 0.00 45.15 3.91
126 127 0.318955 GTGTTTGGCTGTGTGCATCC 60.319 55.000 0.00 0.00 45.15 3.51
127 128 0.467844 TGTTTGGCTGTGTGCATCCT 60.468 50.000 0.00 0.00 45.15 3.24
128 129 1.202867 TGTTTGGCTGTGTGCATCCTA 60.203 47.619 0.00 0.00 45.15 2.94
129 130 1.470098 GTTTGGCTGTGTGCATCCTAG 59.530 52.381 0.00 0.00 45.15 3.02
130 131 0.692476 TTGGCTGTGTGCATCCTAGT 59.308 50.000 0.00 0.00 45.15 2.57
131 132 0.692476 TGGCTGTGTGCATCCTAGTT 59.308 50.000 0.00 0.00 45.15 2.24
132 133 1.905894 TGGCTGTGTGCATCCTAGTTA 59.094 47.619 0.00 0.00 45.15 2.24
133 134 2.505407 TGGCTGTGTGCATCCTAGTTAT 59.495 45.455 0.00 0.00 45.15 1.89
134 135 2.874701 GGCTGTGTGCATCCTAGTTATG 59.125 50.000 0.00 0.00 45.15 1.90
142 143 3.051081 CATCCTAGTTATGCAGAGGCC 57.949 52.381 0.00 0.00 40.13 5.19
143 144 1.040646 TCCTAGTTATGCAGAGGCCG 58.959 55.000 0.00 0.00 40.13 6.13
144 145 0.034059 CCTAGTTATGCAGAGGCCGG 59.966 60.000 0.00 0.00 40.13 6.13
145 146 0.034059 CTAGTTATGCAGAGGCCGGG 59.966 60.000 2.18 0.00 40.13 5.73
146 147 0.689745 TAGTTATGCAGAGGCCGGGT 60.690 55.000 2.18 0.00 40.13 5.28
147 148 1.819632 GTTATGCAGAGGCCGGGTG 60.820 63.158 2.18 0.00 40.13 4.61
148 149 1.992834 TTATGCAGAGGCCGGGTGA 60.993 57.895 2.18 0.00 40.13 4.02
149 150 1.344953 TTATGCAGAGGCCGGGTGAT 61.345 55.000 2.18 0.00 40.13 3.06
150 151 0.471022 TATGCAGAGGCCGGGTGATA 60.471 55.000 2.18 0.00 40.13 2.15
151 152 2.044806 ATGCAGAGGCCGGGTGATAC 62.045 60.000 2.18 0.00 40.13 2.24
152 153 2.435693 GCAGAGGCCGGGTGATACT 61.436 63.158 2.18 0.00 0.00 2.12
153 154 1.742768 CAGAGGCCGGGTGATACTC 59.257 63.158 2.18 0.00 0.00 2.59
154 155 0.757188 CAGAGGCCGGGTGATACTCT 60.757 60.000 2.18 0.00 38.96 3.24
155 156 0.032017 AGAGGCCGGGTGATACTCTT 60.032 55.000 2.18 0.00 35.10 2.85
156 157 1.217183 AGAGGCCGGGTGATACTCTTA 59.783 52.381 2.18 0.00 35.10 2.10
157 158 2.037144 GAGGCCGGGTGATACTCTTAA 58.963 52.381 2.18 0.00 0.00 1.85
158 159 2.633481 GAGGCCGGGTGATACTCTTAAT 59.367 50.000 2.18 0.00 0.00 1.40
159 160 2.368875 AGGCCGGGTGATACTCTTAATG 59.631 50.000 2.18 0.00 0.00 1.90
160 161 2.143925 GCCGGGTGATACTCTTAATGC 58.856 52.381 2.18 0.00 0.00 3.56
161 162 2.224305 GCCGGGTGATACTCTTAATGCT 60.224 50.000 2.18 0.00 0.00 3.79
162 163 3.744530 GCCGGGTGATACTCTTAATGCTT 60.745 47.826 2.18 0.00 0.00 3.91
163 164 4.451900 CCGGGTGATACTCTTAATGCTTT 58.548 43.478 0.00 0.00 0.00 3.51
164 165 4.273480 CCGGGTGATACTCTTAATGCTTTG 59.727 45.833 0.00 0.00 0.00 2.77
165 166 4.876107 CGGGTGATACTCTTAATGCTTTGT 59.124 41.667 0.00 0.00 0.00 2.83
166 167 6.046593 CGGGTGATACTCTTAATGCTTTGTA 58.953 40.000 0.00 0.00 0.00 2.41
167 168 6.706270 CGGGTGATACTCTTAATGCTTTGTAT 59.294 38.462 0.00 0.00 0.00 2.29
168 169 7.095607 CGGGTGATACTCTTAATGCTTTGTATC 60.096 40.741 10.94 10.94 37.69 2.24
169 170 7.715249 GGGTGATACTCTTAATGCTTTGTATCA 59.285 37.037 14.27 14.27 41.84 2.15
172 173 9.890629 TGATACTCTTAATGCTTTGTATCACTT 57.109 29.630 14.27 0.00 40.32 3.16
175 176 8.621532 ACTCTTAATGCTTTGTATCACTTTGA 57.378 30.769 0.00 0.00 0.00 2.69
176 177 9.236006 ACTCTTAATGCTTTGTATCACTTTGAT 57.764 29.630 0.00 0.00 40.72 2.57
177 178 9.499585 CTCTTAATGCTTTGTATCACTTTGATG 57.500 33.333 0.00 0.00 37.70 3.07
178 179 7.970061 TCTTAATGCTTTGTATCACTTTGATGC 59.030 33.333 0.00 0.00 37.70 3.91
179 180 5.909621 ATGCTTTGTATCACTTTGATGCT 57.090 34.783 5.94 0.00 39.71 3.79
180 181 7.395190 AATGCTTTGTATCACTTTGATGCTA 57.605 32.000 5.94 0.00 39.71 3.49
181 182 6.182039 TGCTTTGTATCACTTTGATGCTAC 57.818 37.500 5.94 0.00 39.71 3.58
182 183 5.704978 TGCTTTGTATCACTTTGATGCTACA 59.295 36.000 5.94 0.00 39.71 2.74
183 184 6.375174 TGCTTTGTATCACTTTGATGCTACAT 59.625 34.615 5.94 0.00 39.71 2.29
184 185 7.094248 TGCTTTGTATCACTTTGATGCTACATT 60.094 33.333 5.94 0.00 39.71 2.71
185 186 7.756722 GCTTTGTATCACTTTGATGCTACATTT 59.243 33.333 5.94 0.00 39.71 2.32
186 187 9.630098 CTTTGTATCACTTTGATGCTACATTTT 57.370 29.630 5.94 0.00 39.71 1.82
187 188 8.969121 TTGTATCACTTTGATGCTACATTTTG 57.031 30.769 5.94 0.00 39.71 2.44
188 189 8.334263 TGTATCACTTTGATGCTACATTTTGA 57.666 30.769 5.94 0.00 39.71 2.69
189 190 8.453320 TGTATCACTTTGATGCTACATTTTGAG 58.547 33.333 5.94 0.00 39.71 3.02
190 191 7.692460 ATCACTTTGATGCTACATTTTGAGA 57.308 32.000 0.00 0.00 35.43 3.27
191 192 7.692460 TCACTTTGATGCTACATTTTGAGAT 57.308 32.000 0.00 0.00 0.00 2.75
192 193 8.791327 TCACTTTGATGCTACATTTTGAGATA 57.209 30.769 0.00 0.00 0.00 1.98
193 194 9.230122 TCACTTTGATGCTACATTTTGAGATAA 57.770 29.630 0.00 0.00 0.00 1.75
201 202 9.669353 ATGCTACATTTTGAGATAATAAAAGCG 57.331 29.630 0.00 0.00 0.00 4.68
202 203 7.643764 TGCTACATTTTGAGATAATAAAAGCGC 59.356 33.333 0.00 0.00 0.00 5.92
203 204 7.113544 GCTACATTTTGAGATAATAAAAGCGCC 59.886 37.037 2.29 0.00 0.00 6.53
204 205 6.273071 ACATTTTGAGATAATAAAAGCGCCC 58.727 36.000 2.29 0.00 0.00 6.13
205 206 6.096846 ACATTTTGAGATAATAAAAGCGCCCT 59.903 34.615 2.29 0.00 0.00 5.19
206 207 6.524101 TTTTGAGATAATAAAAGCGCCCTT 57.476 33.333 2.29 0.00 0.00 3.95
207 208 6.524101 TTTGAGATAATAAAAGCGCCCTTT 57.476 33.333 2.29 7.08 42.93 3.11
208 209 7.633193 TTTGAGATAATAAAAGCGCCCTTTA 57.367 32.000 2.29 9.36 40.30 1.85
209 210 7.817418 TTGAGATAATAAAAGCGCCCTTTAT 57.183 32.000 15.73 15.73 40.30 1.40
210 211 7.435068 TGAGATAATAAAAGCGCCCTTTATC 57.565 36.000 19.70 16.57 40.30 1.75
211 212 6.147164 TGAGATAATAAAAGCGCCCTTTATCG 59.853 38.462 19.70 0.00 40.30 2.92
212 213 6.228258 AGATAATAAAAGCGCCCTTTATCGA 58.772 36.000 19.70 13.69 40.30 3.59
213 214 6.708949 AGATAATAAAAGCGCCCTTTATCGAA 59.291 34.615 19.70 12.05 40.30 3.71
214 215 5.570234 AATAAAAGCGCCCTTTATCGAAA 57.430 34.783 19.70 0.75 40.30 3.46
215 216 3.926821 AAAAGCGCCCTTTATCGAAAA 57.073 38.095 2.29 0.00 40.30 2.29
238 239 1.952296 CAAGCATCCCCATCTACTTGC 59.048 52.381 0.00 0.00 0.00 4.01
278 279 4.170468 CCAAGTGGGCTATTGACCTTAT 57.830 45.455 0.00 0.00 43.49 1.73
310 311 6.939730 TCAAATGACTAACTGCTTGTGGAATA 59.060 34.615 0.00 0.00 0.00 1.75
318 319 3.181434 ACTGCTTGTGGAATAACTTGGGA 60.181 43.478 0.00 0.00 0.00 4.37
322 323 2.773487 TGTGGAATAACTTGGGACACG 58.227 47.619 0.00 0.00 39.29 4.49
473 474 6.040955 GGATAAGGGAAAACATGGAGGAATTC 59.959 42.308 0.00 0.00 0.00 2.17
586 591 4.631131 GCTAAAGCTGTCAAATTTGGGTT 58.369 39.130 17.90 10.74 38.21 4.11
616 621 5.891551 GGATGGTAGGACATGGTAAAAACAT 59.108 40.000 0.00 0.00 0.00 2.71
680 685 5.045578 AGCTATGCAATACCGGGATCTTTAT 60.046 40.000 6.32 0.00 0.00 1.40
863 868 3.417101 TGTGGCAATATGAAAACTCCGT 58.583 40.909 0.00 0.00 0.00 4.69
917 922 1.446016 AGTTTTAGAGGGGTGGTGCT 58.554 50.000 0.00 0.00 0.00 4.40
969 974 2.512692 TCCCACCCAGAATTCATGTG 57.487 50.000 8.44 10.95 0.00 3.21
1002 1007 3.713858 TTGTTCCACAACAAGCTCATG 57.286 42.857 0.00 0.00 45.73 3.07
1004 1009 2.880268 TGTTCCACAACAAGCTCATGAG 59.120 45.455 18.84 18.84 39.69 2.90
1078 1083 7.439157 TTCTGTTCTTGTAATGAGTCCATTG 57.561 36.000 0.00 0.00 42.55 2.82
1117 1122 3.411446 TGCATAGTAGCAAAGCAAGTGT 58.589 40.909 0.00 0.00 42.46 3.55
1170 1175 5.014228 ACCTTTAGGGAGCAATGTTACTTCT 59.986 40.000 0.10 0.00 40.27 2.85
1174 1179 8.506168 TTTAGGGAGCAATGTTACTTCTATTG 57.494 34.615 0.00 0.00 35.47 1.90
1187 1192 3.507622 ACTTCTATTGCTTGTCTTTGGGC 59.492 43.478 0.00 0.00 0.00 5.36
1228 1233 8.470040 AGATGCTTTAAATACAATTTGTGCTG 57.530 30.769 12.30 0.00 0.00 4.41
1298 1306 6.352222 GGAGTTTCTTGGATATCTCTCAACCA 60.352 42.308 2.05 0.00 0.00 3.67
1333 1341 4.901868 AGTCATACCGCTGGTTAGAAAAA 58.098 39.130 5.57 0.00 37.09 1.94
1406 1414 5.920840 GCTAATATGTTCAGCAGACGATACA 59.079 40.000 0.00 0.00 35.35 2.29
1412 1420 1.926510 TCAGCAGACGATACATTTGCG 59.073 47.619 0.00 0.00 39.63 4.85
1414 1422 1.660607 AGCAGACGATACATTTGCGTG 59.339 47.619 0.00 0.00 38.51 5.34
1433 1441 0.616679 GTGTAGCTGGAGTGGGGGTA 60.617 60.000 0.00 0.00 0.00 3.69
1477 1485 1.443828 GAGGTCATCTCCCGGAAGC 59.556 63.158 0.73 0.00 36.52 3.86
1483 1491 1.002274 ATCTCCCGGAAGCTGACCT 59.998 57.895 0.73 0.00 0.00 3.85
1497 1505 1.374758 GACCTTGGAGCTGGTGACG 60.375 63.158 0.00 0.00 36.59 4.35
1501 1509 0.247460 CTTGGAGCTGGTGACGATGA 59.753 55.000 0.00 0.00 0.00 2.92
1594 1602 2.091152 GCGTCGCCATTCATAGTTTG 57.909 50.000 5.75 0.00 0.00 2.93
1627 1635 9.618890 CTTGTAATATTGGAAGAAATCTCCAGA 57.381 33.333 0.00 0.00 34.72 3.86
1641 1649 6.884280 AATCTCCAGAAGAATGTTTTTCGT 57.116 33.333 0.00 0.00 37.61 3.85
1656 1664 4.961435 TTTTCGTTTTCGTAGTTTGGGT 57.039 36.364 0.00 0.00 44.46 4.51
1676 1684 9.646427 TTTGGGTCCATTATTTTTAATCTTTCG 57.354 29.630 0.00 0.00 0.00 3.46
1692 1700 4.475944 TCTTTCGCTGCTTTTATGCTTTC 58.524 39.130 0.00 0.00 0.00 2.62
1723 1731 1.924731 TGAGACCTGTACTGGACCTG 58.075 55.000 24.19 0.00 0.00 4.00
1742 1750 2.695147 CTGGGTTTGGTCAAGCTTCTTT 59.305 45.455 0.00 0.00 33.01 2.52
1747 1755 5.335976 GGGTTTGGTCAAGCTTCTTTCTATG 60.336 44.000 0.00 0.00 33.01 2.23
1780 1788 0.405973 GGAGCTCCCCCTGTTTTTCT 59.594 55.000 23.19 0.00 0.00 2.52
1845 1853 2.804527 AGTTACGTTTTTCTCTTCCGCC 59.195 45.455 0.00 0.00 0.00 6.13
1975 1983 7.120726 GTGAGTTATAGGCCACAAAAAGTATGT 59.879 37.037 5.01 0.00 0.00 2.29
2046 2055 8.530311 TGACATGTTGCCAATATTTTATTGACT 58.470 29.630 0.00 0.00 0.00 3.41
2110 2119 4.689612 TGTATACAGAAATGGAGGGAGC 57.310 45.455 0.08 0.00 0.00 4.70
2125 2134 4.563786 GGAGGGAGCATAATTGTAGTAGGC 60.564 50.000 0.00 0.00 0.00 3.93
2148 2157 4.563184 CGTATTTTCTTGCTTCGACTAGCT 59.437 41.667 10.30 0.00 41.76 3.32
2182 2191 7.603784 GGCTTGACCATATTTTTCACTTTCAAT 59.396 33.333 0.00 0.00 38.86 2.57
2184 2193 7.887996 TGACCATATTTTTCACTTTCAATGC 57.112 32.000 0.00 0.00 0.00 3.56
2209 2218 3.972368 CATCTCCATGCATAGGGGG 57.028 57.895 13.15 5.98 0.00 5.40
2232 2241 1.351350 GGGGGTGCCTATTCACTATCC 59.649 57.143 0.00 0.00 37.16 2.59
2246 2255 7.787725 ATTCACTATCCGGTGACTTTTATTC 57.212 36.000 0.00 0.00 44.55 1.75
2267 2276 5.188327 TCTAACAACTAGATGATGCTCCG 57.812 43.478 7.05 0.00 31.28 4.63
2269 2278 1.482182 ACAACTAGATGATGCTCCGCA 59.518 47.619 7.05 0.00 44.86 5.69
2270 2279 1.863454 CAACTAGATGATGCTCCGCAC 59.137 52.381 0.00 0.00 43.04 5.34
2287 2296 1.377202 ACGTTGATGCGGGAATGCT 60.377 52.632 0.00 0.00 35.98 3.79
2292 2301 2.880890 GTTGATGCGGGAATGCTTAGAT 59.119 45.455 0.00 0.00 35.36 1.98
2404 2413 2.863704 GCCATAGGCGCAAAATGAATCC 60.864 50.000 10.83 0.00 39.62 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.432051 GAGATGGTGGACCGAGCCG 62.432 68.421 0.00 0.00 39.43 5.52
5 6 1.617947 AAGAGATGGTGGACCGAGCC 61.618 60.000 0.00 0.00 39.43 4.70
6 7 0.250513 AAAGAGATGGTGGACCGAGC 59.749 55.000 0.00 0.00 39.43 5.03
7 8 1.469940 CGAAAGAGATGGTGGACCGAG 60.470 57.143 0.00 0.00 39.43 4.63
8 9 0.530744 CGAAAGAGATGGTGGACCGA 59.469 55.000 0.00 0.00 39.43 4.69
9 10 0.530744 TCGAAAGAGATGGTGGACCG 59.469 55.000 0.00 0.00 35.34 4.79
10 11 1.275291 TGTCGAAAGAGATGGTGGACC 59.725 52.381 0.00 0.00 43.49 4.46
11 12 2.743636 TGTCGAAAGAGATGGTGGAC 57.256 50.000 0.00 0.00 43.49 4.02
12 13 3.384789 CCTATGTCGAAAGAGATGGTGGA 59.615 47.826 0.00 0.00 44.62 4.02
13 14 3.722147 CCTATGTCGAAAGAGATGGTGG 58.278 50.000 0.00 0.00 44.62 4.61
14 15 3.126831 GCCTATGTCGAAAGAGATGGTG 58.873 50.000 0.00 0.00 44.62 4.17
15 16 2.766263 TGCCTATGTCGAAAGAGATGGT 59.234 45.455 0.00 0.00 44.62 3.55
16 17 3.459232 TGCCTATGTCGAAAGAGATGG 57.541 47.619 0.00 0.00 44.62 3.51
17 18 5.632764 CACTATGCCTATGTCGAAAGAGATG 59.367 44.000 0.00 0.00 44.62 2.90
18 19 5.303078 ACACTATGCCTATGTCGAAAGAGAT 59.697 40.000 0.00 0.00 46.77 2.75
19 20 4.645136 ACACTATGCCTATGTCGAAAGAGA 59.355 41.667 0.00 0.00 43.49 3.10
20 21 4.938080 ACACTATGCCTATGTCGAAAGAG 58.062 43.478 0.00 0.00 43.49 2.85
21 22 4.933330 GACACTATGCCTATGTCGAAAGA 58.067 43.478 0.00 0.00 33.94 2.52
27 28 2.623889 AGACCGACACTATGCCTATGTC 59.376 50.000 0.00 0.00 39.50 3.06
28 29 2.667470 AGACCGACACTATGCCTATGT 58.333 47.619 0.00 0.00 0.00 2.29
29 30 5.880887 TCTATAGACCGACACTATGCCTATG 59.119 44.000 0.00 0.00 33.43 2.23
30 31 5.881443 GTCTATAGACCGACACTATGCCTAT 59.119 44.000 20.40 0.00 39.07 2.57
31 32 5.012871 AGTCTATAGACCGACACTATGCCTA 59.987 44.000 25.93 0.00 45.85 3.93
32 33 4.073549 GTCTATAGACCGACACTATGCCT 58.926 47.826 20.40 0.00 39.07 4.75
33 34 4.073549 AGTCTATAGACCGACACTATGCC 58.926 47.826 25.93 0.16 45.85 4.40
34 35 4.998672 AGAGTCTATAGACCGACACTATGC 59.001 45.833 25.93 0.36 45.85 3.14
35 36 7.329962 CAGTAGAGTCTATAGACCGACACTATG 59.670 44.444 25.93 14.30 45.85 2.23
36 37 7.015487 ACAGTAGAGTCTATAGACCGACACTAT 59.985 40.741 25.93 12.65 45.85 2.12
37 38 6.323482 ACAGTAGAGTCTATAGACCGACACTA 59.677 42.308 25.93 18.06 45.85 2.74
38 39 5.129155 ACAGTAGAGTCTATAGACCGACACT 59.871 44.000 25.93 20.11 45.85 3.55
39 40 5.358922 ACAGTAGAGTCTATAGACCGACAC 58.641 45.833 25.93 18.55 45.85 3.67
40 41 5.611128 ACAGTAGAGTCTATAGACCGACA 57.389 43.478 25.93 9.14 45.85 4.35
41 42 5.277442 GCAACAGTAGAGTCTATAGACCGAC 60.277 48.000 25.93 21.42 45.85 4.79
42 43 4.815308 GCAACAGTAGAGTCTATAGACCGA 59.185 45.833 25.93 12.97 45.85 4.69
43 44 4.023878 GGCAACAGTAGAGTCTATAGACCG 60.024 50.000 25.93 12.16 45.85 4.79
44 45 4.023878 CGGCAACAGTAGAGTCTATAGACC 60.024 50.000 25.93 18.03 45.85 3.85
45 46 4.815308 TCGGCAACAGTAGAGTCTATAGAC 59.185 45.833 22.97 22.97 45.08 2.59
46 47 5.032327 TCGGCAACAGTAGAGTCTATAGA 57.968 43.478 2.51 0.00 0.00 1.98
47 48 5.752892 TTCGGCAACAGTAGAGTCTATAG 57.247 43.478 2.51 1.91 0.00 1.31
48 49 6.096423 ACAATTCGGCAACAGTAGAGTCTATA 59.904 38.462 2.51 0.00 0.00 1.31
49 50 5.105310 ACAATTCGGCAACAGTAGAGTCTAT 60.105 40.000 2.51 0.00 0.00 1.98
50 51 4.219944 ACAATTCGGCAACAGTAGAGTCTA 59.780 41.667 0.00 0.00 0.00 2.59
51 52 3.006967 ACAATTCGGCAACAGTAGAGTCT 59.993 43.478 0.00 0.00 0.00 3.24
52 53 3.326747 ACAATTCGGCAACAGTAGAGTC 58.673 45.455 0.00 0.00 0.00 3.36
53 54 3.326747 GACAATTCGGCAACAGTAGAGT 58.673 45.455 0.00 0.00 0.00 3.24
54 55 2.345641 CGACAATTCGGCAACAGTAGAG 59.654 50.000 0.00 0.00 41.89 2.43
55 56 2.333926 CGACAATTCGGCAACAGTAGA 58.666 47.619 0.00 0.00 41.89 2.59
56 57 2.787723 CGACAATTCGGCAACAGTAG 57.212 50.000 0.00 0.00 41.89 2.57
66 67 7.061752 AGAAAGATAAAAGACCGACAATTCG 57.938 36.000 0.00 0.00 45.44 3.34
67 68 9.152595 AGTAGAAAGATAAAAGACCGACAATTC 57.847 33.333 0.00 0.00 0.00 2.17
68 69 9.503399 AAGTAGAAAGATAAAAGACCGACAATT 57.497 29.630 0.00 0.00 0.00 2.32
71 72 9.798994 GATAAGTAGAAAGATAAAAGACCGACA 57.201 33.333 0.00 0.00 0.00 4.35
72 73 9.798994 TGATAAGTAGAAAGATAAAAGACCGAC 57.201 33.333 0.00 0.00 0.00 4.79
83 84 8.908903 CACCAGTAGTCTGATAAGTAGAAAGAT 58.091 37.037 0.00 0.00 43.76 2.40
84 85 7.889073 ACACCAGTAGTCTGATAAGTAGAAAGA 59.111 37.037 0.00 0.00 43.76 2.52
85 86 8.057536 ACACCAGTAGTCTGATAAGTAGAAAG 57.942 38.462 0.00 0.00 43.76 2.62
86 87 8.418597 AACACCAGTAGTCTGATAAGTAGAAA 57.581 34.615 0.00 0.00 43.76 2.52
87 88 8.304596 CAAACACCAGTAGTCTGATAAGTAGAA 58.695 37.037 0.00 0.00 43.76 2.10
88 89 7.093902 CCAAACACCAGTAGTCTGATAAGTAGA 60.094 40.741 0.00 0.00 43.76 2.59
89 90 7.036220 CCAAACACCAGTAGTCTGATAAGTAG 58.964 42.308 0.00 0.00 43.76 2.57
90 91 6.573680 GCCAAACACCAGTAGTCTGATAAGTA 60.574 42.308 0.00 0.00 43.76 2.24
91 92 5.794894 CCAAACACCAGTAGTCTGATAAGT 58.205 41.667 0.00 0.00 43.76 2.24
92 93 4.631813 GCCAAACACCAGTAGTCTGATAAG 59.368 45.833 0.00 0.00 43.76 1.73
93 94 4.286032 AGCCAAACACCAGTAGTCTGATAA 59.714 41.667 0.00 0.00 43.76 1.75
94 95 3.838317 AGCCAAACACCAGTAGTCTGATA 59.162 43.478 0.00 0.00 43.76 2.15
95 96 2.639839 AGCCAAACACCAGTAGTCTGAT 59.360 45.455 0.00 0.00 43.76 2.90
96 97 2.047061 AGCCAAACACCAGTAGTCTGA 58.953 47.619 0.00 0.00 43.76 3.27
97 98 2.146342 CAGCCAAACACCAGTAGTCTG 58.854 52.381 0.00 0.00 41.01 3.51
98 99 1.768870 ACAGCCAAACACCAGTAGTCT 59.231 47.619 0.00 0.00 0.00 3.24
99 100 1.873591 CACAGCCAAACACCAGTAGTC 59.126 52.381 0.00 0.00 0.00 2.59
100 101 1.211949 ACACAGCCAAACACCAGTAGT 59.788 47.619 0.00 0.00 0.00 2.73
101 102 1.603802 CACACAGCCAAACACCAGTAG 59.396 52.381 0.00 0.00 0.00 2.57
102 103 1.674359 CACACAGCCAAACACCAGTA 58.326 50.000 0.00 0.00 0.00 2.74
103 104 1.666209 GCACACAGCCAAACACCAGT 61.666 55.000 0.00 0.00 37.23 4.00
104 105 1.066257 GCACACAGCCAAACACCAG 59.934 57.895 0.00 0.00 37.23 4.00
105 106 1.042003 ATGCACACAGCCAAACACCA 61.042 50.000 0.00 0.00 44.83 4.17
106 107 0.318955 GATGCACACAGCCAAACACC 60.319 55.000 0.00 0.00 44.83 4.16
107 108 3.184094 GATGCACACAGCCAAACAC 57.816 52.632 0.00 0.00 44.83 3.32
122 123 2.611473 CGGCCTCTGCATAACTAGGATG 60.611 54.545 0.00 0.00 40.13 3.51
123 124 1.620819 CGGCCTCTGCATAACTAGGAT 59.379 52.381 0.00 0.00 40.13 3.24
124 125 1.040646 CGGCCTCTGCATAACTAGGA 58.959 55.000 0.00 0.00 40.13 2.94
125 126 0.034059 CCGGCCTCTGCATAACTAGG 59.966 60.000 0.00 0.00 40.13 3.02
126 127 0.034059 CCCGGCCTCTGCATAACTAG 59.966 60.000 0.00 0.00 40.13 2.57
127 128 0.689745 ACCCGGCCTCTGCATAACTA 60.690 55.000 0.00 0.00 40.13 2.24
128 129 1.995626 ACCCGGCCTCTGCATAACT 60.996 57.895 0.00 0.00 40.13 2.24
129 130 1.819632 CACCCGGCCTCTGCATAAC 60.820 63.158 0.00 0.00 40.13 1.89
130 131 1.344953 ATCACCCGGCCTCTGCATAA 61.345 55.000 0.00 0.00 40.13 1.90
131 132 0.471022 TATCACCCGGCCTCTGCATA 60.471 55.000 0.00 0.00 40.13 3.14
132 133 1.766059 TATCACCCGGCCTCTGCAT 60.766 57.895 0.00 0.00 40.13 3.96
133 134 2.364973 TATCACCCGGCCTCTGCA 60.365 61.111 0.00 0.00 40.13 4.41
134 135 2.109181 GTATCACCCGGCCTCTGC 59.891 66.667 0.00 0.00 0.00 4.26
135 136 0.757188 AGAGTATCACCCGGCCTCTG 60.757 60.000 0.00 0.00 37.82 3.35
136 137 0.032017 AAGAGTATCACCCGGCCTCT 60.032 55.000 0.00 0.00 37.82 3.69
137 138 1.700955 TAAGAGTATCACCCGGCCTC 58.299 55.000 0.00 0.00 37.82 4.70
138 139 2.170012 TTAAGAGTATCACCCGGCCT 57.830 50.000 0.00 0.00 37.82 5.19
139 140 2.767505 CATTAAGAGTATCACCCGGCC 58.232 52.381 0.00 0.00 37.82 6.13
140 141 2.143925 GCATTAAGAGTATCACCCGGC 58.856 52.381 0.00 0.00 37.82 6.13
141 142 3.753294 AGCATTAAGAGTATCACCCGG 57.247 47.619 0.00 0.00 37.82 5.73
142 143 4.876107 ACAAAGCATTAAGAGTATCACCCG 59.124 41.667 0.00 0.00 37.82 5.28
143 144 7.715249 TGATACAAAGCATTAAGAGTATCACCC 59.285 37.037 8.51 0.00 41.41 4.61
144 145 8.662781 TGATACAAAGCATTAAGAGTATCACC 57.337 34.615 8.51 0.00 41.41 4.02
146 147 9.890629 AAGTGATACAAAGCATTAAGAGTATCA 57.109 29.630 8.51 8.51 43.00 2.15
149 150 9.719355 TCAAAGTGATACAAAGCATTAAGAGTA 57.281 29.630 0.00 0.00 0.00 2.59
150 151 8.621532 TCAAAGTGATACAAAGCATTAAGAGT 57.378 30.769 0.00 0.00 0.00 3.24
151 152 9.499585 CATCAAAGTGATACAAAGCATTAAGAG 57.500 33.333 0.00 0.00 34.28 2.85
152 153 7.970061 GCATCAAAGTGATACAAAGCATTAAGA 59.030 33.333 0.00 0.00 34.28 2.10
153 154 7.972277 AGCATCAAAGTGATACAAAGCATTAAG 59.028 33.333 0.00 0.00 34.28 1.85
154 155 7.829725 AGCATCAAAGTGATACAAAGCATTAA 58.170 30.769 0.00 0.00 34.28 1.40
155 156 7.395190 AGCATCAAAGTGATACAAAGCATTA 57.605 32.000 0.00 0.00 34.28 1.90
156 157 6.276832 AGCATCAAAGTGATACAAAGCATT 57.723 33.333 0.00 0.00 34.28 3.56
157 158 5.909621 AGCATCAAAGTGATACAAAGCAT 57.090 34.783 0.00 0.00 34.28 3.79
158 159 5.704978 TGTAGCATCAAAGTGATACAAAGCA 59.295 36.000 2.88 0.00 44.98 3.91
159 160 6.182039 TGTAGCATCAAAGTGATACAAAGC 57.818 37.500 2.88 0.00 44.98 3.51
164 165 8.668353 TCTCAAAATGTAGCATCAAAGTGATAC 58.332 33.333 0.00 0.00 40.43 2.24
165 166 8.791327 TCTCAAAATGTAGCATCAAAGTGATA 57.209 30.769 0.00 0.00 34.28 2.15
166 167 7.692460 TCTCAAAATGTAGCATCAAAGTGAT 57.308 32.000 0.00 0.00 37.65 3.06
167 168 7.692460 ATCTCAAAATGTAGCATCAAAGTGA 57.308 32.000 0.00 0.00 0.00 3.41
175 176 9.669353 CGCTTTTATTATCTCAAAATGTAGCAT 57.331 29.630 0.00 0.00 0.00 3.79
176 177 7.643764 GCGCTTTTATTATCTCAAAATGTAGCA 59.356 33.333 0.00 0.00 0.00 3.49
177 178 7.113544 GGCGCTTTTATTATCTCAAAATGTAGC 59.886 37.037 7.64 0.00 0.00 3.58
178 179 7.591426 GGGCGCTTTTATTATCTCAAAATGTAG 59.409 37.037 7.64 0.00 0.00 2.74
179 180 7.284489 AGGGCGCTTTTATTATCTCAAAATGTA 59.716 33.333 7.64 0.00 0.00 2.29
180 181 6.096846 AGGGCGCTTTTATTATCTCAAAATGT 59.903 34.615 7.64 0.00 0.00 2.71
181 182 6.507023 AGGGCGCTTTTATTATCTCAAAATG 58.493 36.000 7.64 0.00 0.00 2.32
182 183 6.715347 AGGGCGCTTTTATTATCTCAAAAT 57.285 33.333 7.64 0.00 0.00 1.82
183 184 6.524101 AAGGGCGCTTTTATTATCTCAAAA 57.476 33.333 10.73 0.00 0.00 2.44
184 185 6.524101 AAAGGGCGCTTTTATTATCTCAAA 57.476 33.333 21.93 0.00 0.00 2.69
185 186 7.307751 CGATAAAGGGCGCTTTTATTATCTCAA 60.308 37.037 30.56 11.58 32.42 3.02
186 187 6.147164 CGATAAAGGGCGCTTTTATTATCTCA 59.853 38.462 30.56 12.27 32.42 3.27
187 188 6.367969 TCGATAAAGGGCGCTTTTATTATCTC 59.632 38.462 30.56 15.50 32.42 2.75
188 189 6.228258 TCGATAAAGGGCGCTTTTATTATCT 58.772 36.000 30.56 9.43 32.42 1.98
189 190 6.476243 TCGATAAAGGGCGCTTTTATTATC 57.524 37.500 30.56 24.08 32.42 1.75
190 191 6.870971 TTCGATAAAGGGCGCTTTTATTAT 57.129 33.333 30.56 19.13 32.42 1.28
191 192 6.680874 TTTCGATAAAGGGCGCTTTTATTA 57.319 33.333 30.56 15.38 32.42 0.98
192 193 5.570234 TTTCGATAAAGGGCGCTTTTATT 57.430 34.783 30.56 17.35 32.42 1.40
193 194 5.570234 TTTTCGATAAAGGGCGCTTTTAT 57.430 34.783 30.56 20.97 34.36 1.40
194 195 5.373981 TTTTTCGATAAAGGGCGCTTTTA 57.626 34.783 30.56 17.78 0.00 1.52
195 196 3.926821 TTTTCGATAAAGGGCGCTTTT 57.073 38.095 30.56 19.07 0.00 2.27
196 197 3.833442 CTTTTTCGATAAAGGGCGCTTT 58.167 40.909 28.79 28.79 32.67 3.51
197 198 2.415491 GCTTTTTCGATAAAGGGCGCTT 60.415 45.455 23.86 10.73 36.00 4.68
198 199 1.132453 GCTTTTTCGATAAAGGGCGCT 59.868 47.619 23.86 0.00 36.00 5.92
199 200 1.135517 TGCTTTTTCGATAAAGGGCGC 60.136 47.619 23.86 14.15 36.00 6.53
200 201 2.911819 TGCTTTTTCGATAAAGGGCG 57.088 45.000 23.86 5.90 36.00 6.13
201 202 2.923655 GCTTGCTTTTTCGATAAAGGGC 59.076 45.455 23.86 15.01 36.00 5.19
202 203 4.173036 TGCTTGCTTTTTCGATAAAGGG 57.827 40.909 23.86 6.80 36.00 3.95
203 204 4.800471 GGATGCTTGCTTTTTCGATAAAGG 59.200 41.667 23.86 12.40 36.00 3.11
204 205 4.800471 GGGATGCTTGCTTTTTCGATAAAG 59.200 41.667 20.09 20.09 38.00 1.85
205 206 4.381505 GGGGATGCTTGCTTTTTCGATAAA 60.382 41.667 1.08 1.08 0.00 1.40
206 207 3.130340 GGGGATGCTTGCTTTTTCGATAA 59.870 43.478 0.00 0.00 0.00 1.75
207 208 2.687935 GGGGATGCTTGCTTTTTCGATA 59.312 45.455 0.00 0.00 0.00 2.92
208 209 1.478105 GGGGATGCTTGCTTTTTCGAT 59.522 47.619 0.00 0.00 0.00 3.59
209 210 0.887933 GGGGATGCTTGCTTTTTCGA 59.112 50.000 0.00 0.00 0.00 3.71
210 211 0.602562 TGGGGATGCTTGCTTTTTCG 59.397 50.000 0.00 0.00 0.00 3.46
211 212 2.498885 AGATGGGGATGCTTGCTTTTTC 59.501 45.455 0.00 0.00 0.00 2.29
212 213 2.543635 AGATGGGGATGCTTGCTTTTT 58.456 42.857 0.00 0.00 0.00 1.94
213 214 2.242882 AGATGGGGATGCTTGCTTTT 57.757 45.000 0.00 0.00 0.00 2.27
214 215 2.243221 AGTAGATGGGGATGCTTGCTTT 59.757 45.455 0.00 0.00 0.00 3.51
215 216 1.849039 AGTAGATGGGGATGCTTGCTT 59.151 47.619 0.00 0.00 0.00 3.91
238 239 3.832527 TGGGGAACTTGAAAAAGGAGAG 58.167 45.455 0.00 0.00 0.00 3.20
278 279 9.066892 ACAAGCAGTTAGTCATTTGAGAATTAA 57.933 29.630 0.00 0.00 0.00 1.40
310 311 2.375014 ATTTTCCCGTGTCCCAAGTT 57.625 45.000 0.00 0.00 0.00 2.66
318 319 4.222124 AGCTAGATGAATTTTCCCGTGT 57.778 40.909 0.00 0.00 0.00 4.49
322 323 5.009110 GCCAGTTAGCTAGATGAATTTTCCC 59.991 44.000 8.44 0.00 0.00 3.97
473 474 9.935241 AGTAAGACATATATTTGGCATCTACAG 57.065 33.333 1.62 0.00 0.00 2.74
496 497 6.001460 CACTACAGAAAATGTTTGGGGAGTA 58.999 40.000 0.00 0.00 39.96 2.59
586 591 4.566837 ACCATGTCCTACCATCCATCTAA 58.433 43.478 0.00 0.00 0.00 2.10
616 621 4.077982 ACCATAGATCCTCCCAGAACCTAA 60.078 45.833 0.00 0.00 0.00 2.69
680 685 2.354103 GCACTGGTCTCTACAGATGCAA 60.354 50.000 0.00 0.00 39.97 4.08
863 868 4.141413 ACAGGGCAATAGATGAATACTGCA 60.141 41.667 0.00 0.00 0.00 4.41
969 974 2.297701 TGGAACAAGAGCCACAAGAAC 58.702 47.619 0.00 0.00 31.92 3.01
1002 1007 4.716794 TCTTCTCGAGGTTATCCCTACTC 58.283 47.826 13.56 0.00 46.51 2.59
1004 1009 4.716794 TCTCTTCTCGAGGTTATCCCTAC 58.283 47.826 13.56 0.00 46.51 3.18
1018 1023 9.454859 TTTAGGATTCCTGAATTTTCTCTTCTC 57.545 33.333 15.80 0.00 34.61 2.87
1117 1122 5.899631 AAGAACTCACTAACTTTACCCCA 57.100 39.130 0.00 0.00 0.00 4.96
1170 1175 1.545582 GCAGCCCAAAGACAAGCAATA 59.454 47.619 0.00 0.00 0.00 1.90
1174 1179 1.288127 CTGCAGCCCAAAGACAAGC 59.712 57.895 0.00 0.00 0.00 4.01
1176 1181 0.106268 TTCCTGCAGCCCAAAGACAA 60.106 50.000 8.66 0.00 0.00 3.18
1178 1183 1.039856 TTTTCCTGCAGCCCAAAGAC 58.960 50.000 8.66 0.00 0.00 3.01
1187 1192 4.260170 AGCATCTAGACTTTTTCCTGCAG 58.740 43.478 6.78 6.78 0.00 4.41
1217 1222 2.313234 CGAGAACAGCAGCACAAATTG 58.687 47.619 0.00 0.00 0.00 2.32
1221 1226 2.253758 GCCGAGAACAGCAGCACAA 61.254 57.895 0.00 0.00 0.00 3.33
1228 1233 2.328099 CCACAAGGCCGAGAACAGC 61.328 63.158 0.00 0.00 0.00 4.40
1298 1306 4.138290 CGGTATGACTAGACACCAGATCT 58.862 47.826 0.00 0.00 0.00 2.75
1333 1341 2.270434 TCTTTGTAGATCAGGCCCCT 57.730 50.000 0.00 0.00 0.00 4.79
1384 1392 8.764287 CAAATGTATCGTCTGCTGAACATATTA 58.236 33.333 8.51 0.00 0.00 0.98
1387 1395 5.006649 GCAAATGTATCGTCTGCTGAACATA 59.993 40.000 8.51 0.41 0.00 2.29
1396 1404 2.411748 ACACACGCAAATGTATCGTCTG 59.588 45.455 0.00 0.00 33.84 3.51
1406 1414 1.270839 ACTCCAGCTACACACGCAAAT 60.271 47.619 0.00 0.00 0.00 2.32
1412 1420 1.296715 CCCCACTCCAGCTACACAC 59.703 63.158 0.00 0.00 0.00 3.82
1414 1422 0.616679 TACCCCCACTCCAGCTACAC 60.617 60.000 0.00 0.00 0.00 2.90
1433 1441 2.917713 TAATGCCAGGGTTCATGGTT 57.082 45.000 0.00 0.00 40.17 3.67
1446 1454 5.577351 GAGATGACCTCCAGCATTAATGCC 61.577 50.000 31.77 17.61 44.09 4.40
1477 1485 0.321122 GTCACCAGCTCCAAGGTCAG 60.321 60.000 0.00 0.00 35.52 3.51
1483 1491 0.904649 ATCATCGTCACCAGCTCCAA 59.095 50.000 0.00 0.00 0.00 3.53
1627 1635 8.580431 CAAACTACGAAAACGAAAAACATTCTT 58.420 29.630 0.00 0.00 0.00 2.52
1641 1649 7.527568 AAATAATGGACCCAAACTACGAAAA 57.472 32.000 0.00 0.00 0.00 2.29
1656 1664 7.771183 AGCAGCGAAAGATTAAAAATAATGGA 58.229 30.769 0.00 0.00 0.00 3.41
1692 1700 3.131396 ACAGGTCTCAAGTGTTTTAGCG 58.869 45.455 0.00 0.00 0.00 4.26
1723 1731 2.959030 AGAAAGAAGCTTGACCAAACCC 59.041 45.455 2.10 0.00 0.00 4.11
1742 1750 1.839994 CCCTGGCTCCACTTTCATAGA 59.160 52.381 0.00 0.00 0.00 1.98
1747 1755 1.377856 GCTCCCTGGCTCCACTTTC 60.378 63.158 0.00 0.00 0.00 2.62
1812 1820 9.103048 GAGAAAAACGTAACTAAATGTGTGATG 57.897 33.333 0.00 0.00 0.00 3.07
1816 1824 8.340443 GGAAGAGAAAAACGTAACTAAATGTGT 58.660 33.333 0.00 0.00 0.00 3.72
1819 1827 6.518736 GCGGAAGAGAAAAACGTAACTAAATG 59.481 38.462 0.00 0.00 0.00 2.32
1829 1837 0.237498 GTGGGCGGAAGAGAAAAACG 59.763 55.000 0.00 0.00 0.00 3.60
1830 1838 1.314730 TGTGGGCGGAAGAGAAAAAC 58.685 50.000 0.00 0.00 0.00 2.43
1876 1884 4.141482 GGCCTTGTATACTGAAATGGAGGA 60.141 45.833 4.17 0.00 0.00 3.71
1891 1899 8.588290 ACATAAAAATATGAAGTGGCCTTGTA 57.412 30.769 3.32 0.00 0.00 2.41
1959 1967 4.021544 TCCAATGACATACTTTTTGTGGCC 60.022 41.667 0.00 0.00 0.00 5.36
1975 1983 5.725325 TCTTTCAAATGTGCATCCAATGA 57.275 34.783 0.00 0.00 0.00 2.57
2057 2066 9.603921 ACTTCATTTTTCATGTCAAACTTTGAT 57.396 25.926 7.47 0.00 42.47 2.57
2064 2073 5.055812 GGCCACTTCATTTTTCATGTCAAA 58.944 37.500 0.00 0.00 0.00 2.69
2072 2081 6.919721 TGTATACAAGGCCACTTCATTTTTC 58.080 36.000 5.01 0.00 33.81 2.29
2110 2119 9.864034 CAAGAAAATACGCCTACTACAATTATG 57.136 33.333 0.00 0.00 0.00 1.90
2125 2134 4.563184 AGCTAGTCGAAGCAAGAAAATACG 59.437 41.667 11.49 0.00 45.30 3.06
2148 2157 8.865090 TGAAAAATATGGTCAAGCCTTTTAGAA 58.135 29.630 0.00 0.00 38.35 2.10
2215 2224 1.692519 ACCGGATAGTGAATAGGCACC 59.307 52.381 9.46 0.00 39.59 5.01
2227 2236 8.601476 GTTGTTAGAATAAAAGTCACCGGATAG 58.399 37.037 9.46 0.00 0.00 2.08
2232 2241 8.752766 TCTAGTTGTTAGAATAAAAGTCACCG 57.247 34.615 0.00 0.00 35.46 4.94
2267 2276 1.226379 CATTCCCGCATCAACGTGC 60.226 57.895 0.00 0.00 41.65 5.34
2269 2278 0.960364 AAGCATTCCCGCATCAACGT 60.960 50.000 0.00 0.00 0.00 3.99
2270 2279 1.003545 CTAAGCATTCCCGCATCAACG 60.004 52.381 0.00 0.00 0.00 4.10
2391 2400 2.296831 TGCATGGGATTCATTTTGCG 57.703 45.000 0.00 0.00 33.01 4.85
2404 2413 4.213694 GCATCTGAGACTTCTTATGCATGG 59.786 45.833 10.16 2.09 39.68 3.66


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

AutoCloner maintained by Alex Coulton.