Multiple sequence alignment - TraesCS1A01G219000

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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 TraesCS1A01G219000 chr1A 100.000 3461 0 0 1 3461 387814379 387810919 0.000000e+00 6392
1 TraesCS1A01G219000 chr1D 92.646 3005 146 35 212 3184 308425920 308422959 0.000000e+00 4255
2 TraesCS1A01G219000 chr1D 93.421 152 10 0 3310 3461 308422898 308422747 3.480000e-55 226
3 TraesCS1A01G219000 chr1B 91.273 2876 137 39 602 3461 418052902 418050125 0.000000e+00 3816


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 TraesCS1A01G219000 chr1A 387810919 387814379 3460 True 6392.0 6392 100.0000 1 3461 1 chr1A.!!$R1 3460
1 TraesCS1A01G219000 chr1D 308422747 308425920 3173 True 2240.5 4255 93.0335 212 3461 2 chr1D.!!$R1 3249
2 TraesCS1A01G219000 chr1B 418050125 418052902 2777 True 3816.0 3816 91.2730 602 3461 1 chr1B.!!$R1 2859

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
110 111 0.101219 GCCGAACGAGTATACGGGTT 59.899 55.0 12.49 12.49 44.61 4.11 F
123 124 0.106918 ACGGGTTCTGTTCTGGCAAA 60.107 50.0 0.00 0.00 0.00 3.68 F
500 506 0.117742 TTCCGTTTCCTACCTCCCCT 59.882 55.0 0.00 0.00 0.00 4.79 F
559 565 0.389948 ATGACCTGCGTCCGTTTCTC 60.390 55.0 0.00 0.00 38.32 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1405 1420 0.339859 ACCACAGGCTCCTCAGGATA 59.660 55.000 0.00 0.00 0.00 2.59 R
1905 1920 1.421410 GCTGCGAGTAATGGTCGTGG 61.421 60.000 0.00 0.00 39.69 4.94 R
2283 2298 1.397692 GAGTTCGTCCTCGTGGAGTAG 59.602 57.143 6.43 2.01 44.16 2.57 R
2706 2726 2.002505 ACCTAGAGATGGTCCGATGG 57.997 55.000 0.00 0.00 31.03 3.51 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
19 20 4.824166 GCGCCGCGAACTCGTAGA 62.824 66.667 18.91 0.00 42.22 2.59
20 21 2.024305 CGCCGCGAACTCGTAGAT 59.976 61.111 8.23 0.00 42.22 1.98
21 22 1.277739 CGCCGCGAACTCGTAGATA 59.722 57.895 8.23 0.00 42.22 1.98
22 23 0.110328 CGCCGCGAACTCGTAGATAT 60.110 55.000 8.23 0.00 42.22 1.63
23 24 1.127397 CGCCGCGAACTCGTAGATATA 59.873 52.381 8.23 0.00 42.22 0.86
24 25 2.503871 GCCGCGAACTCGTAGATATAC 58.496 52.381 8.23 0.00 42.22 1.47
25 26 2.727298 GCCGCGAACTCGTAGATATACC 60.727 54.545 8.23 0.00 42.22 2.73
26 27 2.473540 CCGCGAACTCGTAGATATACCG 60.474 54.545 8.23 0.00 42.22 4.02
27 28 2.503871 GCGAACTCGTAGATATACCGC 58.496 52.381 0.51 3.08 42.22 5.68
28 29 2.096069 GCGAACTCGTAGATATACCGCA 60.096 50.000 11.49 0.00 42.22 5.69
29 30 3.477122 CGAACTCGTAGATATACCGCAC 58.523 50.000 0.00 0.00 33.89 5.34
30 31 3.477122 GAACTCGTAGATATACCGCACG 58.523 50.000 0.00 0.00 33.89 5.34
31 32 2.487934 ACTCGTAGATATACCGCACGT 58.512 47.619 0.00 0.00 33.89 4.49
32 33 2.222678 ACTCGTAGATATACCGCACGTG 59.777 50.000 12.28 12.28 33.89 4.49
33 34 2.212652 TCGTAGATATACCGCACGTGT 58.787 47.619 18.38 0.00 34.39 4.49
34 35 2.032636 TCGTAGATATACCGCACGTGTG 60.033 50.000 22.06 22.06 34.39 3.82
35 36 2.286595 CGTAGATATACCGCACGTGTGT 60.287 50.000 26.10 20.36 0.00 3.72
36 37 2.953466 AGATATACCGCACGTGTGTT 57.047 45.000 26.10 16.31 0.00 3.32
37 38 3.241067 AGATATACCGCACGTGTGTTT 57.759 42.857 26.10 15.65 0.00 2.83
38 39 3.592059 AGATATACCGCACGTGTGTTTT 58.408 40.909 26.10 11.31 0.00 2.43
39 40 3.369756 AGATATACCGCACGTGTGTTTTG 59.630 43.478 26.10 14.02 0.00 2.44
40 41 1.301423 ATACCGCACGTGTGTTTTGT 58.699 45.000 26.10 18.67 0.00 2.83
41 42 0.374063 TACCGCACGTGTGTTTTGTG 59.626 50.000 26.10 12.97 36.70 3.33
42 43 1.135731 CCGCACGTGTGTTTTGTGT 59.864 52.632 26.10 0.00 36.04 3.72
43 44 1.131037 CCGCACGTGTGTTTTGTGTG 61.131 55.000 26.10 5.89 42.25 3.82
44 45 0.453615 CGCACGTGTGTTTTGTGTGT 60.454 50.000 20.82 0.00 38.84 3.72
45 46 0.981240 GCACGTGTGTTTTGTGTGTG 59.019 50.000 18.38 0.00 36.04 3.82
46 47 1.664588 GCACGTGTGTTTTGTGTGTGT 60.665 47.619 18.38 0.00 36.04 3.72
47 48 1.975362 CACGTGTGTTTTGTGTGTGTG 59.025 47.619 7.58 0.00 0.00 3.82
48 49 1.604755 ACGTGTGTTTTGTGTGTGTGT 59.395 42.857 0.00 0.00 0.00 3.72
49 50 1.975362 CGTGTGTTTTGTGTGTGTGTG 59.025 47.619 0.00 0.00 0.00 3.82
50 51 2.603412 CGTGTGTTTTGTGTGTGTGTGT 60.603 45.455 0.00 0.00 0.00 3.72
51 52 2.723658 GTGTGTTTTGTGTGTGTGTGTG 59.276 45.455 0.00 0.00 0.00 3.82
52 53 2.287849 TGTGTTTTGTGTGTGTGTGTGG 60.288 45.455 0.00 0.00 0.00 4.17
53 54 1.270826 TGTTTTGTGTGTGTGTGTGGG 59.729 47.619 0.00 0.00 0.00 4.61
54 55 0.891373 TTTTGTGTGTGTGTGTGGGG 59.109 50.000 0.00 0.00 0.00 4.96
55 56 0.967887 TTTGTGTGTGTGTGTGGGGG 60.968 55.000 0.00 0.00 0.00 5.40
82 83 4.470170 GCCGGCCGCCGTAAAAAG 62.470 66.667 29.21 14.45 46.80 2.27
83 84 3.051479 CCGGCCGCCGTAAAAAGT 61.051 61.111 29.21 0.00 46.80 2.66
84 85 2.619165 CCGGCCGCCGTAAAAAGTT 61.619 57.895 29.21 0.00 46.80 2.66
85 86 1.283487 CGGCCGCCGTAAAAAGTTT 59.717 52.632 24.08 0.00 42.73 2.66
86 87 0.318022 CGGCCGCCGTAAAAAGTTTT 60.318 50.000 24.08 0.00 42.73 2.43
87 88 1.069364 CGGCCGCCGTAAAAAGTTTTA 60.069 47.619 24.08 0.00 42.73 1.52
88 89 2.318578 GGCCGCCGTAAAAAGTTTTAC 58.681 47.619 14.13 14.13 45.52 2.01
95 96 3.894782 GTAAAAAGTTTTACGGGCCGA 57.105 42.857 35.78 13.93 41.89 5.54
96 97 4.221926 GTAAAAAGTTTTACGGGCCGAA 57.778 40.909 35.78 19.41 41.89 4.30
97 98 2.780065 AAAAGTTTTACGGGCCGAAC 57.220 45.000 35.78 25.65 0.00 3.95
98 99 0.587768 AAAGTTTTACGGGCCGAACG 59.412 50.000 35.78 6.05 37.36 3.95
99 100 0.249826 AAGTTTTACGGGCCGAACGA 60.250 50.000 35.78 12.90 34.93 3.85
100 101 0.668401 AGTTTTACGGGCCGAACGAG 60.668 55.000 35.78 1.74 34.93 4.18
101 102 0.945743 GTTTTACGGGCCGAACGAGT 60.946 55.000 35.78 11.90 34.93 4.18
102 103 0.600557 TTTTACGGGCCGAACGAGTA 59.399 50.000 35.78 10.68 34.93 2.59
103 104 0.817013 TTTACGGGCCGAACGAGTAT 59.183 50.000 35.78 10.16 34.93 2.12
104 105 1.674359 TTACGGGCCGAACGAGTATA 58.326 50.000 35.78 8.96 34.93 1.47
105 106 0.944386 TACGGGCCGAACGAGTATAC 59.056 55.000 35.78 0.00 34.93 1.47
106 107 1.369689 CGGGCCGAACGAGTATACG 60.370 63.158 24.41 0.00 39.31 3.06
107 108 1.008079 GGGCCGAACGAGTATACGG 60.008 63.158 0.00 0.00 46.74 4.02
108 109 1.008079 GGCCGAACGAGTATACGGG 60.008 63.158 0.00 0.00 44.61 5.28
109 110 1.728490 GGCCGAACGAGTATACGGGT 61.728 60.000 0.00 0.00 44.61 5.28
110 111 0.101219 GCCGAACGAGTATACGGGTT 59.899 55.000 12.49 12.49 44.61 4.11
111 112 1.861605 GCCGAACGAGTATACGGGTTC 60.862 57.143 22.03 22.03 44.61 3.62
112 113 1.672881 CCGAACGAGTATACGGGTTCT 59.327 52.381 25.72 6.80 41.41 3.01
113 114 2.540361 CCGAACGAGTATACGGGTTCTG 60.540 54.545 25.72 20.19 41.41 3.02
114 115 2.096496 CGAACGAGTATACGGGTTCTGT 59.904 50.000 25.72 9.42 37.28 3.41
115 116 3.426695 CGAACGAGTATACGGGTTCTGTT 60.427 47.826 25.72 14.72 37.28 3.16
116 117 3.772060 ACGAGTATACGGGTTCTGTTC 57.228 47.619 0.00 0.00 37.61 3.18
117 118 3.350833 ACGAGTATACGGGTTCTGTTCT 58.649 45.455 0.00 0.00 37.61 3.01
118 119 3.128242 ACGAGTATACGGGTTCTGTTCTG 59.872 47.826 0.00 0.00 37.61 3.02
119 120 3.488721 CGAGTATACGGGTTCTGTTCTGG 60.489 52.174 0.00 0.00 0.00 3.86
120 121 2.167900 AGTATACGGGTTCTGTTCTGGC 59.832 50.000 0.00 0.00 0.00 4.85
121 122 0.981183 ATACGGGTTCTGTTCTGGCA 59.019 50.000 0.00 0.00 0.00 4.92
122 123 0.759959 TACGGGTTCTGTTCTGGCAA 59.240 50.000 0.00 0.00 0.00 4.52
123 124 0.106918 ACGGGTTCTGTTCTGGCAAA 60.107 50.000 0.00 0.00 0.00 3.68
124 125 1.028905 CGGGTTCTGTTCTGGCAAAA 58.971 50.000 0.00 0.00 0.00 2.44
125 126 1.407258 CGGGTTCTGTTCTGGCAAAAA 59.593 47.619 0.00 0.00 0.00 1.94
147 148 1.008079 GGCCGAACCCGTATACTCG 60.008 63.158 0.56 3.44 0.00 4.18
148 149 1.659644 GCCGAACCCGTATACTCGC 60.660 63.158 6.71 0.74 0.00 5.03
149 150 1.008079 CCGAACCCGTATACTCGCC 60.008 63.158 6.71 0.00 0.00 5.54
150 151 1.369689 CGAACCCGTATACTCGCCG 60.370 63.158 0.56 0.00 0.00 6.46
151 152 1.008079 GAACCCGTATACTCGCCGG 60.008 63.158 0.00 0.00 41.37 6.13
154 155 3.677527 CCGTATACTCGCCGGGAT 58.322 61.111 2.18 0.00 38.09 3.85
155 156 1.962144 CCGTATACTCGCCGGGATT 59.038 57.895 2.18 0.00 38.09 3.01
156 157 0.316204 CCGTATACTCGCCGGGATTT 59.684 55.000 2.18 0.00 38.09 2.17
157 158 1.269936 CCGTATACTCGCCGGGATTTT 60.270 52.381 2.18 0.00 38.09 1.82
158 159 2.030007 CCGTATACTCGCCGGGATTTTA 60.030 50.000 2.18 0.00 38.09 1.52
159 160 2.982470 CGTATACTCGCCGGGATTTTAC 59.018 50.000 2.18 2.74 0.00 2.01
160 161 2.144482 ATACTCGCCGGGATTTTACG 57.856 50.000 2.18 0.00 0.00 3.18
161 162 1.102154 TACTCGCCGGGATTTTACGA 58.898 50.000 2.18 0.00 0.00 3.43
162 163 2.589890 CTCGCCGGGATTTTACGAG 58.410 57.895 2.18 7.34 43.46 4.18
163 164 0.179119 CTCGCCGGGATTTTACGAGT 60.179 55.000 14.78 0.00 43.85 4.18
164 165 0.179129 TCGCCGGGATTTTACGAGTC 60.179 55.000 2.18 0.00 0.00 3.36
165 166 0.179119 CGCCGGGATTTTACGAGTCT 60.179 55.000 2.18 0.00 0.00 3.24
166 167 1.287425 GCCGGGATTTTACGAGTCTG 58.713 55.000 2.18 0.00 0.00 3.51
167 168 1.287425 CCGGGATTTTACGAGTCTGC 58.713 55.000 0.00 0.00 0.00 4.26
168 169 1.134788 CCGGGATTTTACGAGTCTGCT 60.135 52.381 0.00 0.00 0.00 4.24
169 170 2.100252 CCGGGATTTTACGAGTCTGCTA 59.900 50.000 0.00 0.00 0.00 3.49
170 171 3.372954 CGGGATTTTACGAGTCTGCTAG 58.627 50.000 0.00 0.00 0.00 3.42
171 172 3.066342 CGGGATTTTACGAGTCTGCTAGA 59.934 47.826 0.00 0.00 0.00 2.43
172 173 4.612943 GGGATTTTACGAGTCTGCTAGAG 58.387 47.826 0.00 0.00 0.00 2.43
173 174 4.098196 GGGATTTTACGAGTCTGCTAGAGT 59.902 45.833 0.00 0.00 0.00 3.24
174 175 5.394333 GGGATTTTACGAGTCTGCTAGAGTT 60.394 44.000 0.00 0.00 0.00 3.01
175 176 5.517054 GGATTTTACGAGTCTGCTAGAGTTG 59.483 44.000 0.00 6.67 35.59 3.16
176 177 4.436242 TTTACGAGTCTGCTAGAGTTGG 57.564 45.455 0.00 3.81 34.09 3.77
177 178 1.912417 ACGAGTCTGCTAGAGTTGGT 58.088 50.000 0.00 4.25 34.09 3.67
178 179 1.813786 ACGAGTCTGCTAGAGTTGGTC 59.186 52.381 0.00 0.00 34.09 4.02
179 180 2.088423 CGAGTCTGCTAGAGTTGGTCT 58.912 52.381 0.00 0.00 39.59 3.85
180 181 2.490115 CGAGTCTGCTAGAGTTGGTCTT 59.510 50.000 0.00 0.00 36.64 3.01
181 182 3.690139 CGAGTCTGCTAGAGTTGGTCTTA 59.310 47.826 0.00 0.00 36.64 2.10
182 183 4.156190 CGAGTCTGCTAGAGTTGGTCTTAA 59.844 45.833 0.00 0.00 36.64 1.85
183 184 5.646606 GAGTCTGCTAGAGTTGGTCTTAAG 58.353 45.833 0.00 0.00 36.64 1.85
184 185 5.326069 AGTCTGCTAGAGTTGGTCTTAAGA 58.674 41.667 0.00 0.00 36.64 2.10
185 186 5.184287 AGTCTGCTAGAGTTGGTCTTAAGAC 59.816 44.000 24.73 24.73 44.04 3.01
186 187 5.047943 GTCTGCTAGAGTTGGTCTTAAGACA 60.048 44.000 31.30 17.72 46.47 3.41
187 188 5.717178 TCTGCTAGAGTTGGTCTTAAGACAT 59.283 40.000 31.30 17.00 46.47 3.06
188 189 6.211584 TCTGCTAGAGTTGGTCTTAAGACATT 59.788 38.462 31.30 16.32 46.47 2.71
189 190 6.769512 TGCTAGAGTTGGTCTTAAGACATTT 58.230 36.000 31.30 16.62 46.47 2.32
190 191 7.903145 TGCTAGAGTTGGTCTTAAGACATTTA 58.097 34.615 31.30 15.11 46.47 1.40
191 192 8.540388 TGCTAGAGTTGGTCTTAAGACATTTAT 58.460 33.333 31.30 16.07 46.47 1.40
192 193 9.384764 GCTAGAGTTGGTCTTAAGACATTTATT 57.615 33.333 31.30 17.21 46.47 1.40
200 201 9.681062 TGGTCTTAAGACATTTATTTTAGGAGG 57.319 33.333 31.30 0.00 46.47 4.30
201 202 9.121658 GGTCTTAAGACATTTATTTTAGGAGGG 57.878 37.037 31.30 0.00 46.47 4.30
202 203 9.901172 GTCTTAAGACATTTATTTTAGGAGGGA 57.099 33.333 27.12 0.00 44.18 4.20
204 205 9.343539 CTTAAGACATTTATTTTAGGAGGGAGG 57.656 37.037 0.00 0.00 0.00 4.30
205 206 6.267492 AGACATTTATTTTAGGAGGGAGGG 57.733 41.667 0.00 0.00 0.00 4.30
206 207 5.976870 AGACATTTATTTTAGGAGGGAGGGA 59.023 40.000 0.00 0.00 0.00 4.20
207 208 6.101881 AGACATTTATTTTAGGAGGGAGGGAG 59.898 42.308 0.00 0.00 0.00 4.30
208 209 5.736616 ACATTTATTTTAGGAGGGAGGGAGT 59.263 40.000 0.00 0.00 0.00 3.85
209 210 6.912561 ACATTTATTTTAGGAGGGAGGGAGTA 59.087 38.462 0.00 0.00 0.00 2.59
210 211 7.576649 ACATTTATTTTAGGAGGGAGGGAGTAT 59.423 37.037 0.00 0.00 0.00 2.12
211 212 9.112658 CATTTATTTTAGGAGGGAGGGAGTATA 57.887 37.037 0.00 0.00 0.00 1.47
212 213 9.875725 ATTTATTTTAGGAGGGAGGGAGTATAT 57.124 33.333 0.00 0.00 0.00 0.86
213 214 8.680820 TTATTTTAGGAGGGAGGGAGTATATG 57.319 38.462 0.00 0.00 0.00 1.78
214 215 5.698369 TTTAGGAGGGAGGGAGTATATGT 57.302 43.478 0.00 0.00 0.00 2.29
215 216 5.698369 TTAGGAGGGAGGGAGTATATGTT 57.302 43.478 0.00 0.00 0.00 2.71
216 217 4.578149 AGGAGGGAGGGAGTATATGTTT 57.422 45.455 0.00 0.00 0.00 2.83
254 257 2.343101 TGGAGATAGTTTTGGCGTTCG 58.657 47.619 0.00 0.00 0.00 3.95
259 262 5.050972 GGAGATAGTTTTGGCGTTCGAATAG 60.051 44.000 0.00 0.00 0.00 1.73
264 267 4.454504 AGTTTTGGCGTTCGAATAGAATGT 59.545 37.500 0.00 0.00 45.34 2.71
270 273 4.569564 GGCGTTCGAATAGAATGTAACCTT 59.430 41.667 0.00 0.00 45.34 3.50
284 287 3.949113 TGTAACCTTCAAAACCCTCACAC 59.051 43.478 0.00 0.00 0.00 3.82
288 291 3.835395 ACCTTCAAAACCCTCACACAAAA 59.165 39.130 0.00 0.00 0.00 2.44
289 292 4.284746 ACCTTCAAAACCCTCACACAAAAA 59.715 37.500 0.00 0.00 0.00 1.94
290 293 4.629634 CCTTCAAAACCCTCACACAAAAAC 59.370 41.667 0.00 0.00 0.00 2.43
324 328 6.202516 TGTGAGAACGGATTTTTGAAGTTT 57.797 33.333 0.00 0.00 0.00 2.66
350 354 1.219522 GGGGTTCGATTACGGATGCG 61.220 60.000 4.58 4.58 40.21 4.73
359 363 0.533491 TTACGGATGCGCTTACACCT 59.467 50.000 9.73 0.00 0.00 4.00
368 372 6.976349 CGGATGCGCTTACACCTATATTATAA 59.024 38.462 9.73 0.00 0.00 0.98
369 373 7.652105 CGGATGCGCTTACACCTATATTATAAT 59.348 37.037 9.73 2.97 0.00 1.28
372 378 8.845942 TGCGCTTACACCTATATTATAATACG 57.154 34.615 9.73 4.35 0.00 3.06
396 402 8.293867 ACGCTTTAATGCATGTTAAGTTCTTAA 58.706 29.630 13.17 1.47 0.00 1.85
417 423 5.481200 AAGATCATATCATGCATAAGCGC 57.519 39.130 0.00 0.00 46.23 5.92
420 426 2.743664 TCATATCATGCATAAGCGCACC 59.256 45.455 11.47 0.00 46.56 5.01
447 453 4.950205 TCTCAATATCAGCTGCATCAGA 57.050 40.909 9.47 7.15 32.44 3.27
448 454 4.884247 TCTCAATATCAGCTGCATCAGAG 58.116 43.478 9.47 13.07 32.44 3.35
483 489 9.928236 GAGTCTTCATAAACATGCTAAGATTTC 57.072 33.333 0.00 0.00 0.00 2.17
489 495 8.181573 TCATAAACATGCTAAGATTTCCGTTTC 58.818 33.333 0.00 0.00 0.00 2.78
495 501 4.224370 TGCTAAGATTTCCGTTTCCTACCT 59.776 41.667 0.00 0.00 0.00 3.08
496 502 4.809958 GCTAAGATTTCCGTTTCCTACCTC 59.190 45.833 0.00 0.00 0.00 3.85
498 504 2.504585 AGATTTCCGTTTCCTACCTCCC 59.495 50.000 0.00 0.00 0.00 4.30
499 505 0.986527 TTTCCGTTTCCTACCTCCCC 59.013 55.000 0.00 0.00 0.00 4.81
500 506 0.117742 TTCCGTTTCCTACCTCCCCT 59.882 55.000 0.00 0.00 0.00 4.79
501 507 0.117742 TCCGTTTCCTACCTCCCCTT 59.882 55.000 0.00 0.00 0.00 3.95
502 508 1.362237 TCCGTTTCCTACCTCCCCTTA 59.638 52.381 0.00 0.00 0.00 2.69
503 509 1.483827 CCGTTTCCTACCTCCCCTTAC 59.516 57.143 0.00 0.00 0.00 2.34
504 510 2.464782 CGTTTCCTACCTCCCCTTACT 58.535 52.381 0.00 0.00 0.00 2.24
505 511 2.429971 CGTTTCCTACCTCCCCTTACTC 59.570 54.545 0.00 0.00 0.00 2.59
507 513 1.702699 TCCTACCTCCCCTTACTCCA 58.297 55.000 0.00 0.00 0.00 3.86
508 514 2.233178 TCCTACCTCCCCTTACTCCAT 58.767 52.381 0.00 0.00 0.00 3.41
509 515 2.090719 TCCTACCTCCCCTTACTCCATG 60.091 54.545 0.00 0.00 0.00 3.66
510 516 2.090719 CCTACCTCCCCTTACTCCATGA 60.091 54.545 0.00 0.00 0.00 3.07
511 517 2.897823 ACCTCCCCTTACTCCATGAT 57.102 50.000 0.00 0.00 0.00 2.45
512 518 2.412591 ACCTCCCCTTACTCCATGATG 58.587 52.381 0.00 0.00 0.00 3.07
520 526 3.496130 CCTTACTCCATGATGTGCGAATC 59.504 47.826 0.00 0.00 0.00 2.52
524 530 4.313282 ACTCCATGATGTGCGAATCTATG 58.687 43.478 0.00 3.28 0.00 2.23
559 565 0.389948 ATGACCTGCGTCCGTTTCTC 60.390 55.000 0.00 0.00 38.32 2.87
739 745 3.576118 CCATCTCCATCTCGAACTACCAT 59.424 47.826 0.00 0.00 0.00 3.55
981 996 2.273449 CATTGCCTCGCCTCCCTT 59.727 61.111 0.00 0.00 0.00 3.95
996 1011 4.830046 GCCTCCCTTTTCTCTTTTCTTCTT 59.170 41.667 0.00 0.00 0.00 2.52
999 1014 4.584743 TCCCTTTTCTCTTTTCTTCTTGCC 59.415 41.667 0.00 0.00 0.00 4.52
1200 1215 2.125912 CACCTGCTCTTCGTCGGG 60.126 66.667 0.00 0.00 34.90 5.14
1212 1227 4.867599 GTCGGGATCGCCGTGTCC 62.868 72.222 18.33 3.28 36.13 4.02
1266 1281 3.082579 GCGGGTCGAGAAGGATGCT 62.083 63.158 0.00 0.00 0.00 3.79
1299 1314 4.125695 AAGGCGGACGCGAGGTAC 62.126 66.667 15.93 0.00 43.06 3.34
1833 1848 4.029809 AGTTACCACCCTGCGGCC 62.030 66.667 0.00 0.00 0.00 6.13
1905 1920 0.390998 GCACAAGAGGCAGAGGAGAC 60.391 60.000 0.00 0.00 0.00 3.36
1950 1965 1.202521 TCGCAGAGCTTCAACAGTTCA 60.203 47.619 0.00 0.00 35.18 3.18
1998 2013 1.338200 ACGCCAAGAAGCTCTTTCGAT 60.338 47.619 16.53 0.00 40.86 3.59
2012 2027 1.384989 TTCGATGGCTCCTCCTCGTC 61.385 60.000 0.00 0.00 37.05 4.20
2013 2028 2.725008 GATGGCTCCTCCTCGTCG 59.275 66.667 0.00 0.00 35.26 5.12
2014 2029 3.492311 GATGGCTCCTCCTCGTCGC 62.492 68.421 0.00 0.00 35.26 5.19
2067 2082 1.005215 ACAATCAGGCCAAGAGAAGGG 59.995 52.381 5.01 0.00 0.00 3.95
2092 2107 3.640967 CCAACCCAAAATCCAAGAAGTGA 59.359 43.478 0.00 0.00 0.00 3.41
2094 2109 3.230976 ACCCAAAATCCAAGAAGTGACC 58.769 45.455 0.00 0.00 0.00 4.02
2427 2442 0.888619 TCGCGTCCATCAAGAAGTCT 59.111 50.000 5.77 0.00 0.00 3.24
2430 2445 1.363744 CGTCCATCAAGAAGTCTGCC 58.636 55.000 0.00 0.00 0.00 4.85
2468 2483 2.951745 CGGCAAGTAGCTCGCTCG 60.952 66.667 0.00 0.00 44.79 5.03
2708 2728 3.299503 TCATCAAGAGGTCGATGATCCA 58.700 45.455 0.00 0.00 42.31 3.41
2709 2729 3.899980 TCATCAAGAGGTCGATGATCCAT 59.100 43.478 0.00 0.00 42.31 3.41
2710 2730 4.021632 TCATCAAGAGGTCGATGATCCATC 60.022 45.833 0.00 0.00 42.31 3.51
2727 2747 2.700897 CCATCGGACCATCTCTAGGTTT 59.299 50.000 0.00 0.00 40.09 3.27
2770 2799 2.417515 GCCTAAGTGACTGCTGGAGTAC 60.418 54.545 0.48 1.71 33.83 2.73
2813 2842 4.024670 ACTGACCACCTGTAGTATTCTCC 58.975 47.826 0.00 0.00 0.00 3.71
2821 2850 5.586243 CACCTGTAGTATTCTCCATTTGGTG 59.414 44.000 0.00 0.00 36.34 4.17
2833 2862 5.778241 TCTCCATTTGGTGAGTAGTTCAGTA 59.222 40.000 0.00 0.00 36.21 2.74
2969 2998 5.712917 GGTGGTCCAAAATTATCCAGTTGTA 59.287 40.000 0.00 0.00 0.00 2.41
2983 3020 2.282555 CAGTTGTATTCACTGCGATCGG 59.717 50.000 18.30 3.26 0.00 4.18
2996 3033 4.242475 CTGCGATCGGCCTGTAATTAATA 58.758 43.478 18.30 0.00 42.61 0.98
3000 3037 6.205853 TGCGATCGGCCTGTAATTAATATTTT 59.794 34.615 18.30 0.00 42.61 1.82
3001 3038 6.523201 GCGATCGGCCTGTAATTAATATTTTG 59.477 38.462 18.30 0.00 34.80 2.44
3002 3039 7.581476 CGATCGGCCTGTAATTAATATTTTGT 58.419 34.615 7.38 0.00 0.00 2.83
3003 3040 8.073768 CGATCGGCCTGTAATTAATATTTTGTT 58.926 33.333 7.38 0.00 0.00 2.83
3004 3041 9.180678 GATCGGCCTGTAATTAATATTTTGTTG 57.819 33.333 0.00 0.00 0.00 3.33
3005 3042 8.057536 TCGGCCTGTAATTAATATTTTGTTGT 57.942 30.769 0.00 0.00 0.00 3.32
3006 3043 8.524487 TCGGCCTGTAATTAATATTTTGTTGTT 58.476 29.630 0.00 0.00 0.00 2.83
3007 3044 8.591312 CGGCCTGTAATTAATATTTTGTTGTTG 58.409 33.333 0.00 0.00 0.00 3.33
3008 3045 9.430623 GGCCTGTAATTAATATTTTGTTGTTGT 57.569 29.630 0.00 0.00 0.00 3.32
3084 3127 0.298707 CGATTCACTGATTCGCCACG 59.701 55.000 9.69 0.00 30.83 4.94
3085 3128 0.652592 GATTCACTGATTCGCCACGG 59.347 55.000 0.00 0.00 0.00 4.94
3086 3129 0.249120 ATTCACTGATTCGCCACGGA 59.751 50.000 0.00 0.00 0.00 4.69
3087 3130 0.669318 TTCACTGATTCGCCACGGAC 60.669 55.000 0.00 0.00 0.00 4.79
3105 3150 1.230635 ACACTGCGCACCAGATTCAC 61.231 55.000 5.66 0.00 44.64 3.18
3116 3161 4.680708 GCACCAGATTCACCGAGATAGAAA 60.681 45.833 0.00 0.00 0.00 2.52
3139 3184 4.640789 ATGACTCATGTTCTACGTCTCC 57.359 45.455 0.00 0.00 0.00 3.71
3156 3201 1.740025 CTCCTCTTGCGAAAACATCCC 59.260 52.381 0.00 0.00 0.00 3.85
3234 3279 9.044646 TGAGATCATTTGGATTTCCCATTTTTA 57.955 29.630 0.00 0.00 46.10 1.52
3235 3280 9.317936 GAGATCATTTGGATTTCCCATTTTTAC 57.682 33.333 0.00 0.00 46.10 2.01
3236 3281 9.050154 AGATCATTTGGATTTCCCATTTTTACT 57.950 29.630 0.00 0.00 46.10 2.24
3238 3283 8.845413 TCATTTGGATTTCCCATTTTTACTTG 57.155 30.769 0.00 0.00 46.10 3.16
3239 3284 7.390162 TCATTTGGATTTCCCATTTTTACTTGC 59.610 33.333 0.00 0.00 46.10 4.01
3283 3328 7.689446 CTGTTAGTATGGCAGCTATAGTAGA 57.311 40.000 11.89 4.61 0.00 2.59
3284 3329 8.112016 CTGTTAGTATGGCAGCTATAGTAGAA 57.888 38.462 11.89 5.67 0.00 2.10
3285 3330 8.112016 TGTTAGTATGGCAGCTATAGTAGAAG 57.888 38.462 11.89 0.00 0.00 2.85
3286 3331 7.724506 TGTTAGTATGGCAGCTATAGTAGAAGT 59.275 37.037 11.89 0.00 0.00 3.01
3287 3332 8.578151 GTTAGTATGGCAGCTATAGTAGAAGTT 58.422 37.037 11.89 0.00 0.00 2.66
3288 3333 7.604657 AGTATGGCAGCTATAGTAGAAGTTT 57.395 36.000 4.32 0.00 0.00 2.66
3289 3334 8.024145 AGTATGGCAGCTATAGTAGAAGTTTT 57.976 34.615 4.32 0.00 0.00 2.43
3290 3335 8.487028 AGTATGGCAGCTATAGTAGAAGTTTTT 58.513 33.333 4.32 0.00 0.00 1.94
3330 3381 7.558444 AGCTATAGTAGAAGTTGAGTAGCTTGT 59.442 37.037 0.84 0.00 40.29 3.16
3338 3389 6.651225 AGAAGTTGAGTAGCTTGTATTTGGTC 59.349 38.462 0.00 0.00 0.00 4.02
3358 3409 0.818040 GTTGGGACTTGGAAGCACGT 60.818 55.000 0.00 0.00 0.00 4.49
3453 3504 2.089201 CATCATGCTGAAACTGCTCCA 58.911 47.619 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.503871 GTATATCTACGAGTTCGCGGC 58.496 52.381 6.13 0.00 44.43 6.53
5 6 2.473540 CGGTATATCTACGAGTTCGCGG 60.474 54.545 6.13 0.00 44.43 6.46
6 7 2.755616 CGGTATATCTACGAGTTCGCG 58.244 52.381 0.00 0.00 44.43 5.87
7 8 2.096069 TGCGGTATATCTACGAGTTCGC 60.096 50.000 0.73 0.00 44.43 4.70
8 9 3.477122 GTGCGGTATATCTACGAGTTCG 58.523 50.000 0.00 0.00 46.33 3.95
9 10 3.059325 ACGTGCGGTATATCTACGAGTTC 60.059 47.826 14.17 0.00 38.08 3.01
10 11 2.874701 ACGTGCGGTATATCTACGAGTT 59.125 45.455 14.17 0.00 38.08 3.01
11 12 2.222678 CACGTGCGGTATATCTACGAGT 59.777 50.000 0.82 0.00 38.08 4.18
12 13 2.222678 ACACGTGCGGTATATCTACGAG 59.777 50.000 17.22 9.88 38.08 4.18
13 14 2.032636 CACACGTGCGGTATATCTACGA 60.033 50.000 17.22 0.00 38.08 3.43
14 15 2.286595 ACACACGTGCGGTATATCTACG 60.287 50.000 17.22 7.77 40.30 3.51
15 16 3.344904 ACACACGTGCGGTATATCTAC 57.655 47.619 17.22 0.00 0.00 2.59
16 17 4.374843 AAACACACGTGCGGTATATCTA 57.625 40.909 17.22 0.00 0.00 1.98
17 18 2.953466 AACACACGTGCGGTATATCT 57.047 45.000 17.22 0.00 0.00 1.98
18 19 3.123959 ACAAAACACACGTGCGGTATATC 59.876 43.478 17.22 0.00 0.00 1.63
19 20 3.068560 ACAAAACACACGTGCGGTATAT 58.931 40.909 17.22 2.06 0.00 0.86
20 21 2.221286 CACAAAACACACGTGCGGTATA 59.779 45.455 17.22 0.00 0.00 1.47
21 22 1.003331 CACAAAACACACGTGCGGTAT 60.003 47.619 17.22 4.54 0.00 2.73
22 23 0.374063 CACAAAACACACGTGCGGTA 59.626 50.000 17.22 0.00 0.00 4.02
23 24 1.135731 CACAAAACACACGTGCGGT 59.864 52.632 17.22 11.80 0.00 5.68
24 25 1.131037 CACACAAAACACACGTGCGG 61.131 55.000 17.22 11.07 33.89 5.69
25 26 0.453615 ACACACAAAACACACGTGCG 60.454 50.000 17.22 9.16 33.89 5.34
26 27 0.981240 CACACACAAAACACACGTGC 59.019 50.000 17.22 0.00 33.89 5.34
27 28 1.975362 CACACACACAAAACACACGTG 59.025 47.619 15.48 15.48 36.70 4.49
28 29 1.604755 ACACACACACAAAACACACGT 59.395 42.857 0.00 0.00 0.00 4.49
29 30 1.975362 CACACACACACAAAACACACG 59.025 47.619 0.00 0.00 0.00 4.49
30 31 2.723658 CACACACACACACAAAACACAC 59.276 45.455 0.00 0.00 0.00 3.82
31 32 2.287849 CCACACACACACACAAAACACA 60.288 45.455 0.00 0.00 0.00 3.72
32 33 2.323959 CCACACACACACACAAAACAC 58.676 47.619 0.00 0.00 0.00 3.32
33 34 1.270826 CCCACACACACACACAAAACA 59.729 47.619 0.00 0.00 0.00 2.83
34 35 1.403514 CCCCACACACACACACAAAAC 60.404 52.381 0.00 0.00 0.00 2.43
35 36 0.891373 CCCCACACACACACACAAAA 59.109 50.000 0.00 0.00 0.00 2.44
36 37 0.967887 CCCCCACACACACACACAAA 60.968 55.000 0.00 0.00 0.00 2.83
37 38 1.379176 CCCCCACACACACACACAA 60.379 57.895 0.00 0.00 0.00 3.33
38 39 2.273776 CCCCCACACACACACACA 59.726 61.111 0.00 0.00 0.00 3.72
68 69 2.318578 GTAAAACTTTTTACGGCGGCC 58.681 47.619 13.24 9.54 41.89 6.13
75 76 3.894782 TCGGCCCGTAAAACTTTTTAC 57.105 42.857 1.63 12.67 45.52 2.01
76 77 3.303659 CGTTCGGCCCGTAAAACTTTTTA 60.304 43.478 1.63 0.00 0.00 1.52
77 78 2.541383 CGTTCGGCCCGTAAAACTTTTT 60.541 45.455 1.63 0.00 0.00 1.94
78 79 1.002576 CGTTCGGCCCGTAAAACTTTT 60.003 47.619 1.63 0.00 0.00 2.27
79 80 0.587768 CGTTCGGCCCGTAAAACTTT 59.412 50.000 1.63 0.00 0.00 2.66
80 81 0.249826 TCGTTCGGCCCGTAAAACTT 60.250 50.000 1.63 0.00 0.00 2.66
81 82 0.668401 CTCGTTCGGCCCGTAAAACT 60.668 55.000 1.63 0.00 0.00 2.66
82 83 0.945743 ACTCGTTCGGCCCGTAAAAC 60.946 55.000 1.63 0.00 0.00 2.43
83 84 0.600557 TACTCGTTCGGCCCGTAAAA 59.399 50.000 1.63 0.00 0.00 1.52
84 85 0.817013 ATACTCGTTCGGCCCGTAAA 59.183 50.000 1.63 0.00 0.00 2.01
85 86 1.333619 GTATACTCGTTCGGCCCGTAA 59.666 52.381 1.63 0.00 0.00 3.18
86 87 0.944386 GTATACTCGTTCGGCCCGTA 59.056 55.000 1.63 0.00 0.00 4.02
87 88 1.729881 GTATACTCGTTCGGCCCGT 59.270 57.895 1.63 0.00 0.00 5.28
88 89 1.369689 CGTATACTCGTTCGGCCCG 60.370 63.158 0.00 0.00 0.00 6.13
89 90 1.008079 CCGTATACTCGTTCGGCCC 60.008 63.158 0.00 0.00 36.68 5.80
90 91 1.008079 CCCGTATACTCGTTCGGCC 60.008 63.158 0.56 0.00 41.38 6.13
91 92 0.101219 AACCCGTATACTCGTTCGGC 59.899 55.000 0.56 0.00 41.38 5.54
92 93 1.672881 AGAACCCGTATACTCGTTCGG 59.327 52.381 18.60 7.85 39.63 4.30
93 94 2.096496 ACAGAACCCGTATACTCGTTCG 59.904 50.000 18.60 16.42 39.63 3.95
94 95 3.772060 ACAGAACCCGTATACTCGTTC 57.228 47.619 17.70 17.70 35.84 3.95
95 96 3.760684 AGAACAGAACCCGTATACTCGTT 59.239 43.478 0.56 2.92 0.00 3.85
96 97 3.128242 CAGAACAGAACCCGTATACTCGT 59.872 47.826 0.56 0.00 0.00 4.18
97 98 3.488721 CCAGAACAGAACCCGTATACTCG 60.489 52.174 0.56 0.00 0.00 4.18
98 99 3.737355 GCCAGAACAGAACCCGTATACTC 60.737 52.174 0.56 0.00 0.00 2.59
99 100 2.167900 GCCAGAACAGAACCCGTATACT 59.832 50.000 0.56 0.00 0.00 2.12
100 101 2.093869 TGCCAGAACAGAACCCGTATAC 60.094 50.000 0.00 0.00 0.00 1.47
101 102 2.181125 TGCCAGAACAGAACCCGTATA 58.819 47.619 0.00 0.00 0.00 1.47
102 103 0.981183 TGCCAGAACAGAACCCGTAT 59.019 50.000 0.00 0.00 0.00 3.06
103 104 0.759959 TTGCCAGAACAGAACCCGTA 59.240 50.000 0.00 0.00 0.00 4.02
104 105 0.106918 TTTGCCAGAACAGAACCCGT 60.107 50.000 0.00 0.00 0.00 5.28
105 106 1.028905 TTTTGCCAGAACAGAACCCG 58.971 50.000 0.00 0.00 0.00 5.28
129 130 1.008079 CGAGTATACGGGTTCGGCC 60.008 63.158 0.00 0.00 41.39 6.13
130 131 1.659644 GCGAGTATACGGGTTCGGC 60.660 63.158 12.47 3.74 41.39 5.54
131 132 1.008079 GGCGAGTATACGGGTTCGG 60.008 63.158 12.47 0.00 41.39 4.30
132 133 1.369689 CGGCGAGTATACGGGTTCG 60.370 63.158 0.00 7.64 43.02 3.95
133 134 1.008079 CCGGCGAGTATACGGGTTC 60.008 63.158 9.30 0.00 43.69 3.62
134 135 3.122850 CCGGCGAGTATACGGGTT 58.877 61.111 9.30 0.00 43.69 4.11
137 138 0.316204 AAATCCCGGCGAGTATACGG 59.684 55.000 9.30 0.00 46.79 4.02
138 139 2.144482 AAAATCCCGGCGAGTATACG 57.856 50.000 9.30 0.00 0.00 3.06
139 140 2.982470 CGTAAAATCCCGGCGAGTATAC 59.018 50.000 9.30 3.07 0.00 1.47
140 141 2.884012 TCGTAAAATCCCGGCGAGTATA 59.116 45.455 9.30 0.00 0.00 1.47
141 142 1.682854 TCGTAAAATCCCGGCGAGTAT 59.317 47.619 9.30 0.00 0.00 2.12
142 143 1.066002 CTCGTAAAATCCCGGCGAGTA 59.934 52.381 9.30 0.00 42.54 2.59
143 144 0.179119 CTCGTAAAATCCCGGCGAGT 60.179 55.000 9.30 2.62 42.54 4.18
144 145 2.589890 CTCGTAAAATCCCGGCGAG 58.410 57.895 9.30 10.30 42.01 5.03
145 146 0.179129 GACTCGTAAAATCCCGGCGA 60.179 55.000 9.30 0.00 0.00 5.54
146 147 0.179119 AGACTCGTAAAATCCCGGCG 60.179 55.000 0.00 0.00 0.00 6.46
147 148 1.287425 CAGACTCGTAAAATCCCGGC 58.713 55.000 0.00 0.00 0.00 6.13
148 149 1.134788 AGCAGACTCGTAAAATCCCGG 60.135 52.381 0.00 0.00 0.00 5.73
149 150 2.295253 AGCAGACTCGTAAAATCCCG 57.705 50.000 0.00 0.00 0.00 5.14
150 151 4.098196 ACTCTAGCAGACTCGTAAAATCCC 59.902 45.833 0.00 0.00 0.00 3.85
151 152 5.251601 ACTCTAGCAGACTCGTAAAATCC 57.748 43.478 0.00 0.00 0.00 3.01
152 153 5.517054 CCAACTCTAGCAGACTCGTAAAATC 59.483 44.000 0.00 0.00 0.00 2.17
153 154 5.047235 ACCAACTCTAGCAGACTCGTAAAAT 60.047 40.000 0.00 0.00 0.00 1.82
154 155 4.280174 ACCAACTCTAGCAGACTCGTAAAA 59.720 41.667 0.00 0.00 0.00 1.52
155 156 3.825014 ACCAACTCTAGCAGACTCGTAAA 59.175 43.478 0.00 0.00 0.00 2.01
156 157 3.418995 ACCAACTCTAGCAGACTCGTAA 58.581 45.455 0.00 0.00 0.00 3.18
157 158 3.008330 GACCAACTCTAGCAGACTCGTA 58.992 50.000 0.00 0.00 0.00 3.43
158 159 1.813786 GACCAACTCTAGCAGACTCGT 59.186 52.381 0.00 0.00 0.00 4.18
159 160 2.088423 AGACCAACTCTAGCAGACTCG 58.912 52.381 0.00 0.00 0.00 4.18
160 161 5.416326 TCTTAAGACCAACTCTAGCAGACTC 59.584 44.000 0.00 0.00 0.00 3.36
161 162 5.184287 GTCTTAAGACCAACTCTAGCAGACT 59.816 44.000 22.74 0.00 39.07 3.24
162 163 5.047943 TGTCTTAAGACCAACTCTAGCAGAC 60.048 44.000 28.43 3.45 44.15 3.51
163 164 5.077564 TGTCTTAAGACCAACTCTAGCAGA 58.922 41.667 28.43 6.29 44.15 4.26
164 165 5.392767 TGTCTTAAGACCAACTCTAGCAG 57.607 43.478 28.43 0.00 44.15 4.24
165 166 6.360370 AATGTCTTAAGACCAACTCTAGCA 57.640 37.500 28.43 9.83 44.15 3.49
166 167 8.950208 ATAAATGTCTTAAGACCAACTCTAGC 57.050 34.615 28.43 4.55 44.15 3.42
174 175 9.681062 CCTCCTAAAATAAATGTCTTAAGACCA 57.319 33.333 28.43 18.36 44.15 4.02
175 176 9.121658 CCCTCCTAAAATAAATGTCTTAAGACC 57.878 37.037 28.43 13.89 44.15 3.85
176 177 9.901172 TCCCTCCTAAAATAAATGTCTTAAGAC 57.099 33.333 25.73 25.73 44.97 3.01
178 179 9.343539 CCTCCCTCCTAAAATAAATGTCTTAAG 57.656 37.037 0.00 0.00 0.00 1.85
179 180 8.279361 CCCTCCCTCCTAAAATAAATGTCTTAA 58.721 37.037 0.00 0.00 0.00 1.85
180 181 7.630127 TCCCTCCCTCCTAAAATAAATGTCTTA 59.370 37.037 0.00 0.00 0.00 2.10
181 182 6.450352 TCCCTCCCTCCTAAAATAAATGTCTT 59.550 38.462 0.00 0.00 0.00 3.01
182 183 5.976870 TCCCTCCCTCCTAAAATAAATGTCT 59.023 40.000 0.00 0.00 0.00 3.41
183 184 6.126449 ACTCCCTCCCTCCTAAAATAAATGTC 60.126 42.308 0.00 0.00 0.00 3.06
184 185 5.736616 ACTCCCTCCCTCCTAAAATAAATGT 59.263 40.000 0.00 0.00 0.00 2.71
185 186 6.267492 ACTCCCTCCCTCCTAAAATAAATG 57.733 41.667 0.00 0.00 0.00 2.32
186 187 9.875725 ATATACTCCCTCCCTCCTAAAATAAAT 57.124 33.333 0.00 0.00 0.00 1.40
187 188 9.112658 CATATACTCCCTCCCTCCTAAAATAAA 57.887 37.037 0.00 0.00 0.00 1.40
188 189 8.246615 ACATATACTCCCTCCCTCCTAAAATAA 58.753 37.037 0.00 0.00 0.00 1.40
189 190 7.786968 ACATATACTCCCTCCCTCCTAAAATA 58.213 38.462 0.00 0.00 0.00 1.40
190 191 6.644882 ACATATACTCCCTCCCTCCTAAAAT 58.355 40.000 0.00 0.00 0.00 1.82
191 192 6.051946 ACATATACTCCCTCCCTCCTAAAA 57.948 41.667 0.00 0.00 0.00 1.52
192 193 5.698369 ACATATACTCCCTCCCTCCTAAA 57.302 43.478 0.00 0.00 0.00 1.85
193 194 5.698369 AACATATACTCCCTCCCTCCTAA 57.302 43.478 0.00 0.00 0.00 2.69
194 195 5.698369 AAACATATACTCCCTCCCTCCTA 57.302 43.478 0.00 0.00 0.00 2.94
195 196 4.578149 AAACATATACTCCCTCCCTCCT 57.422 45.455 0.00 0.00 0.00 3.69
196 197 5.338463 GCATAAACATATACTCCCTCCCTCC 60.338 48.000 0.00 0.00 0.00 4.30
197 198 5.624738 CGCATAAACATATACTCCCTCCCTC 60.625 48.000 0.00 0.00 0.00 4.30
198 199 4.223032 CGCATAAACATATACTCCCTCCCT 59.777 45.833 0.00 0.00 0.00 4.20
199 200 4.222145 TCGCATAAACATATACTCCCTCCC 59.778 45.833 0.00 0.00 0.00 4.30
200 201 5.401531 TCGCATAAACATATACTCCCTCC 57.598 43.478 0.00 0.00 0.00 4.30
201 202 6.688578 TCTTCGCATAAACATATACTCCCTC 58.311 40.000 0.00 0.00 0.00 4.30
202 203 6.493802 TCTCTTCGCATAAACATATACTCCCT 59.506 38.462 0.00 0.00 0.00 4.20
203 204 6.688578 TCTCTTCGCATAAACATATACTCCC 58.311 40.000 0.00 0.00 0.00 4.30
210 211 8.773645 CCAACAATATCTCTTCGCATAAACATA 58.226 33.333 0.00 0.00 0.00 2.29
211 212 7.498900 TCCAACAATATCTCTTCGCATAAACAT 59.501 33.333 0.00 0.00 0.00 2.71
212 213 6.821160 TCCAACAATATCTCTTCGCATAAACA 59.179 34.615 0.00 0.00 0.00 2.83
213 214 7.224753 TCTCCAACAATATCTCTTCGCATAAAC 59.775 37.037 0.00 0.00 0.00 2.01
214 215 7.272244 TCTCCAACAATATCTCTTCGCATAAA 58.728 34.615 0.00 0.00 0.00 1.40
215 216 6.816136 TCTCCAACAATATCTCTTCGCATAA 58.184 36.000 0.00 0.00 0.00 1.90
216 217 6.405278 TCTCCAACAATATCTCTTCGCATA 57.595 37.500 0.00 0.00 0.00 3.14
232 233 3.424433 CGAACGCCAAAACTATCTCCAAC 60.424 47.826 0.00 0.00 0.00 3.77
254 257 8.349568 AGGGTTTTGAAGGTTACATTCTATTC 57.650 34.615 11.03 0.81 0.00 1.75
259 262 5.300792 TGTGAGGGTTTTGAAGGTTACATTC 59.699 40.000 2.55 2.55 0.00 2.67
264 267 4.237976 TGTGTGAGGGTTTTGAAGGTTA 57.762 40.909 0.00 0.00 0.00 2.85
270 273 4.322349 CCAGTTTTTGTGTGAGGGTTTTGA 60.322 41.667 0.00 0.00 0.00 2.69
284 287 5.240891 TCTCACATCTAGCTCCAGTTTTTG 58.759 41.667 0.00 0.00 0.00 2.44
288 291 3.119316 CGTTCTCACATCTAGCTCCAGTT 60.119 47.826 0.00 0.00 0.00 3.16
289 292 2.425312 CGTTCTCACATCTAGCTCCAGT 59.575 50.000 0.00 0.00 0.00 4.00
290 293 2.223688 CCGTTCTCACATCTAGCTCCAG 60.224 54.545 0.00 0.00 0.00 3.86
330 334 1.219522 GCATCCGTAATCGAACCCCG 61.220 60.000 0.00 0.00 39.71 5.73
344 348 8.888579 ATTATAATATAGGTGTAAGCGCATCC 57.111 34.615 11.47 4.11 40.95 3.51
368 372 7.985476 AGAACTTAACATGCATTAAAGCGTAT 58.015 30.769 0.00 0.00 37.31 3.06
369 373 7.372451 AGAACTTAACATGCATTAAAGCGTA 57.628 32.000 0.00 0.00 37.31 4.42
372 378 9.840427 TCTTAAGAACTTAACATGCATTAAAGC 57.160 29.630 1.68 0.00 32.26 3.51
396 402 4.510571 TGCGCTTATGCATGATATGATCT 58.489 39.130 10.16 0.00 40.62 2.75
417 423 5.735354 GCAGCTGATATTGAGAAAATGGGTG 60.735 44.000 20.43 0.00 0.00 4.61
420 426 5.509716 TGCAGCTGATATTGAGAAAATGG 57.490 39.130 20.43 0.00 0.00 3.16
447 453 6.705302 TGTTTATGAAGACTCTGCTCATTCT 58.295 36.000 0.00 0.00 0.00 2.40
448 454 6.974932 TGTTTATGAAGACTCTGCTCATTC 57.025 37.500 0.00 0.00 0.00 2.67
483 489 1.483827 GTAAGGGGAGGTAGGAAACGG 59.516 57.143 0.00 0.00 0.00 4.44
489 495 2.090719 TCATGGAGTAAGGGGAGGTAGG 60.091 54.545 0.00 0.00 0.00 3.18
495 501 1.490490 GCACATCATGGAGTAAGGGGA 59.510 52.381 0.00 0.00 0.00 4.81
496 502 1.811558 CGCACATCATGGAGTAAGGGG 60.812 57.143 0.00 0.00 0.00 4.79
498 504 2.602257 TCGCACATCATGGAGTAAGG 57.398 50.000 0.00 0.00 0.00 2.69
499 505 4.375272 AGATTCGCACATCATGGAGTAAG 58.625 43.478 0.00 0.00 0.00 2.34
500 506 4.406648 AGATTCGCACATCATGGAGTAA 57.593 40.909 0.00 0.00 0.00 2.24
501 507 5.473039 CATAGATTCGCACATCATGGAGTA 58.527 41.667 0.00 0.00 0.00 2.59
502 508 2.996249 AGATTCGCACATCATGGAGT 57.004 45.000 0.00 0.00 0.00 3.85
503 509 3.683340 CCATAGATTCGCACATCATGGAG 59.317 47.826 13.11 0.00 35.72 3.86
504 510 3.667360 CCATAGATTCGCACATCATGGA 58.333 45.455 13.11 0.00 35.72 3.41
505 511 2.161012 GCCATAGATTCGCACATCATGG 59.839 50.000 13.62 13.62 36.22 3.66
507 513 3.130280 TGCCATAGATTCGCACATCAT 57.870 42.857 0.00 0.00 0.00 2.45
508 514 2.613595 GTTGCCATAGATTCGCACATCA 59.386 45.455 0.00 0.00 30.84 3.07
509 515 2.613595 TGTTGCCATAGATTCGCACATC 59.386 45.455 0.00 0.00 30.84 3.06
510 516 2.642427 TGTTGCCATAGATTCGCACAT 58.358 42.857 0.00 0.00 30.84 3.21
511 517 2.106477 TGTTGCCATAGATTCGCACA 57.894 45.000 0.00 0.00 30.84 4.57
512 518 2.855953 GCATGTTGCCATAGATTCGCAC 60.856 50.000 0.00 0.00 37.42 5.34
535 541 0.036388 ACGGACGCAGGTCATGATTT 60.036 50.000 0.00 0.00 45.28 2.17
559 565 1.734465 GTCTCTCAGGTTGAATTGCGG 59.266 52.381 0.00 0.00 0.00 5.69
684 690 3.448686 TCGCGATGAAGAGAGGAATTTC 58.551 45.455 3.71 0.00 0.00 2.17
782 789 5.066634 TGACTTGGTAGAGTTGAGATCGATC 59.933 44.000 17.91 17.91 0.00 3.69
783 790 4.950475 TGACTTGGTAGAGTTGAGATCGAT 59.050 41.667 0.00 0.00 0.00 3.59
784 791 4.332828 TGACTTGGTAGAGTTGAGATCGA 58.667 43.478 0.00 0.00 0.00 3.59
785 792 4.703645 TGACTTGGTAGAGTTGAGATCG 57.296 45.455 0.00 0.00 0.00 3.69
855 862 3.691498 CACGGATTAAATTCCTTTCGCC 58.309 45.455 0.00 0.00 33.30 5.54
938 948 1.059942 CGCGCCCTTTAAAGCTTTTG 58.940 50.000 18.47 8.15 0.00 2.44
974 984 5.278709 GCAAGAAGAAAAGAGAAAAGGGAGG 60.279 44.000 0.00 0.00 0.00 4.30
981 996 4.262164 GCCATGGCAAGAAGAAAAGAGAAA 60.262 41.667 32.08 0.00 41.49 2.52
1299 1314 1.874019 CTGGAACATCCGCGAGACG 60.874 63.158 8.23 0.00 40.17 4.18
1405 1420 0.339859 ACCACAGGCTCCTCAGGATA 59.660 55.000 0.00 0.00 0.00 2.59
1407 1422 1.610673 GACCACAGGCTCCTCAGGA 60.611 63.158 9.44 0.00 0.00 3.86
1410 1425 1.556373 CCATGACCACAGGCTCCTCA 61.556 60.000 0.00 0.00 0.00 3.86
1569 1584 2.741092 GAAGGGAGCACGGTGTCA 59.259 61.111 10.24 0.00 0.00 3.58
1626 1641 4.803426 CTGCTCGGAGTCGGTGGC 62.803 72.222 6.90 9.87 36.95 5.01
1797 1812 4.323477 TGGACAAGGAACGGCGGG 62.323 66.667 13.24 0.00 0.00 6.13
1905 1920 1.421410 GCTGCGAGTAATGGTCGTGG 61.421 60.000 0.00 0.00 39.69 4.94
1950 1965 3.130693 GCGAGGAGTTGGTGTAAGTAGAT 59.869 47.826 0.00 0.00 0.00 1.98
2014 2029 2.579787 GACTGACGGCGATGACGG 60.580 66.667 16.62 9.50 39.02 4.79
2067 2082 4.528206 ACTTCTTGGATTTTGGGTTGGATC 59.472 41.667 0.00 0.00 0.00 3.36
2092 2107 2.257676 GGCTTCGTCTTCGTCGGT 59.742 61.111 0.00 0.00 38.33 4.69
2094 2109 2.874780 CCGGCTTCGTCTTCGTCG 60.875 66.667 0.00 0.00 38.33 5.12
2279 2294 2.045131 GTCCTCGTGGAGTAGGCGT 61.045 63.158 6.43 0.00 44.16 5.68
2283 2298 1.397692 GAGTTCGTCCTCGTGGAGTAG 59.602 57.143 6.43 2.01 44.16 2.57
2706 2726 2.002505 ACCTAGAGATGGTCCGATGG 57.997 55.000 0.00 0.00 31.03 3.51
2707 2727 5.730296 ATAAACCTAGAGATGGTCCGATG 57.270 43.478 0.00 0.00 36.69 3.84
2708 2728 8.437274 AATTATAAACCTAGAGATGGTCCGAT 57.563 34.615 0.00 0.00 36.69 4.18
2709 2729 7.850935 AATTATAAACCTAGAGATGGTCCGA 57.149 36.000 0.00 0.00 36.69 4.55
2710 2730 8.251721 CCTAATTATAAACCTAGAGATGGTCCG 58.748 40.741 0.00 0.00 36.69 4.79
2711 2731 8.041919 GCCTAATTATAAACCTAGAGATGGTCC 58.958 40.741 0.00 0.00 36.69 4.46
2712 2732 8.817876 AGCCTAATTATAAACCTAGAGATGGTC 58.182 37.037 0.00 0.00 36.69 4.02
2713 2733 8.598041 CAGCCTAATTATAAACCTAGAGATGGT 58.402 37.037 0.00 0.00 39.91 3.55
2727 2747 7.049799 GGCAAACCAATTCAGCCTAATTATA 57.950 36.000 0.00 0.00 42.01 0.98
2752 2779 2.561419 GTGGTACTCCAGCAGTCACTTA 59.439 50.000 0.00 0.00 45.24 2.24
2753 2780 1.344763 GTGGTACTCCAGCAGTCACTT 59.655 52.381 0.00 0.00 45.24 3.16
2770 2799 5.641209 CAGTTGGAGAAGAAAGATACAGTGG 59.359 44.000 0.00 0.00 0.00 4.00
2813 2842 7.441157 TGAACTTACTGAACTACTCACCAAATG 59.559 37.037 0.00 0.00 0.00 2.32
2821 2850 5.859648 GTGAGCTGAACTTACTGAACTACTC 59.140 44.000 0.00 0.00 32.24 2.59
2833 2862 3.142174 GCTGTAAAGGTGAGCTGAACTT 58.858 45.455 0.00 0.00 0.00 2.66
2969 2998 1.522355 CAGGCCGATCGCAGTGAAT 60.522 57.895 10.32 0.00 40.31 2.57
2996 3033 7.020914 ACAACAACAACAACAACAACAAAAT 57.979 28.000 0.00 0.00 0.00 1.82
3000 3037 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
3001 3038 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
3002 3039 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
3003 3040 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
3004 3041 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
3005 3042 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
3006 3043 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
3007 3044 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
3008 3045 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
3009 3046 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
3010 3047 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
3011 3048 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
3012 3049 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
3013 3050 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
3014 3051 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
3015 3052 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
3016 3053 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
3017 3054 7.358435 CGATTACAACAACAACAACAACAACAA 60.358 33.333 0.00 0.00 0.00 2.83
3018 3055 6.088217 CGATTACAACAACAACAACAACAACA 59.912 34.615 0.00 0.00 0.00 3.33
3084 3127 1.639298 GAATCTGGTGCGCAGTGTCC 61.639 60.000 12.22 9.52 0.00 4.02
3085 3128 0.950555 TGAATCTGGTGCGCAGTGTC 60.951 55.000 12.22 0.00 0.00 3.67
3086 3129 1.071299 TGAATCTGGTGCGCAGTGT 59.929 52.632 12.22 0.00 0.00 3.55
3087 3130 1.499056 GTGAATCTGGTGCGCAGTG 59.501 57.895 12.22 3.75 0.00 3.66
3105 3150 7.493971 AGAACATGAGTCATTTTTCTATCTCGG 59.506 37.037 19.04 2.03 27.95 4.63
3116 3161 5.186021 AGGAGACGTAGAACATGAGTCATTT 59.814 40.000 1.86 1.73 34.56 2.32
3192 3237 9.729281 AAATGATCTCACTTAAAATTGCCAAAT 57.271 25.926 0.00 0.00 0.00 2.32
3193 3238 8.991026 CAAATGATCTCACTTAAAATTGCCAAA 58.009 29.630 0.00 0.00 0.00 3.28
3197 3242 8.937634 ATCCAAATGATCTCACTTAAAATTGC 57.062 30.769 0.00 0.00 0.00 3.56
3201 3246 8.531146 GGGAAATCCAAATGATCTCACTTAAAA 58.469 33.333 1.22 0.00 37.91 1.52
3225 3270 5.533154 TCCATATACCGCAAGTAAAAATGGG 59.467 40.000 15.73 0.00 38.79 4.00
3234 3279 6.538742 GCACATATAATCCATATACCGCAAGT 59.461 38.462 0.00 0.00 29.33 3.16
3235 3280 6.763135 AGCACATATAATCCATATACCGCAAG 59.237 38.462 0.00 0.00 29.33 4.01
3236 3281 6.538381 CAGCACATATAATCCATATACCGCAA 59.462 38.462 0.00 0.00 29.33 4.85
3238 3283 6.049149 ACAGCACATATAATCCATATACCGC 58.951 40.000 0.00 0.00 29.33 5.68
3239 3284 9.249457 CTAACAGCACATATAATCCATATACCG 57.751 37.037 0.00 0.00 29.33 4.02
3291 3336 9.472361 CTTCTACTATAGCTATTACCGCAAAAA 57.528 33.333 12.39 0.00 0.00 1.94
3292 3337 8.636213 ACTTCTACTATAGCTATTACCGCAAAA 58.364 33.333 12.39 0.00 0.00 2.44
3293 3338 8.174733 ACTTCTACTATAGCTATTACCGCAAA 57.825 34.615 12.39 0.00 0.00 3.68
3294 3339 7.756395 ACTTCTACTATAGCTATTACCGCAA 57.244 36.000 12.39 0.00 0.00 4.85
3295 3340 7.446319 TCAACTTCTACTATAGCTATTACCGCA 59.554 37.037 12.39 0.00 0.00 5.69
3296 3341 7.814642 TCAACTTCTACTATAGCTATTACCGC 58.185 38.462 12.39 0.00 0.00 5.68
3297 3342 9.001542 ACTCAACTTCTACTATAGCTATTACCG 57.998 37.037 12.39 1.37 0.00 4.02
3301 3346 9.802039 AGCTACTCAACTTCTACTATAGCTATT 57.198 33.333 12.39 0.00 41.67 1.73
3302 3347 9.802039 AAGCTACTCAACTTCTACTATAGCTAT 57.198 33.333 11.77 11.77 42.42 2.97
3303 3348 9.058174 CAAGCTACTCAACTTCTACTATAGCTA 57.942 37.037 0.00 0.00 42.42 3.32
3304 3349 7.558444 ACAAGCTACTCAACTTCTACTATAGCT 59.442 37.037 0.00 0.00 44.51 3.32
3305 3350 7.708998 ACAAGCTACTCAACTTCTACTATAGC 58.291 38.462 0.00 0.00 35.18 2.97
3330 3381 2.372504 TCCAAGTCCCAACGACCAAATA 59.627 45.455 0.00 0.00 43.08 1.40
3338 3389 1.841663 CGTGCTTCCAAGTCCCAACG 61.842 60.000 0.00 0.00 0.00 4.10
3358 3409 3.676172 CGTCAACATCGCACTAACCTTAA 59.324 43.478 0.00 0.00 0.00 1.85
3396 3447 2.821546 TGCAGGCGAATACAGATACAC 58.178 47.619 0.00 0.00 0.00 2.90
3399 3450 2.037641 AGCATGCAGGCGAATACAGATA 59.962 45.455 21.98 0.00 39.27 1.98
3406 3457 0.171903 GACAAAGCATGCAGGCGAAT 59.828 50.000 21.98 5.56 39.27 3.34
3409 3460 0.524816 GATGACAAAGCATGCAGGCG 60.525 55.000 21.98 6.43 39.27 5.52


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

AutoCloner maintained by Alex Coulton.