Multiple sequence alignment - TraesCS3A01G270200

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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 TraesCS3A01G270200 chr3A 100.000 2561 0 0 1 2561 497297814 497300374 0.000000e+00 4730
1 TraesCS3A01G270200 chr3A 93.310 1136 41 12 239 1345 348998946 349000075 0.000000e+00 1644
2 TraesCS3A01G270200 chr4D 94.292 2365 94 17 235 2559 470199538 470197175 0.000000e+00 3581
3 TraesCS3A01G270200 chr2D 93.960 2351 98 19 234 2559 619850763 619853094 0.000000e+00 3515
4 TraesCS3A01G270200 chr2D 95.449 1736 74 5 826 2559 151998942 152000674 0.000000e+00 2763
5 TraesCS3A01G270200 chr2A 93.819 2346 112 23 235 2559 48627070 48624737 0.000000e+00 3498
6 TraesCS3A01G270200 chr7D 92.917 2372 98 25 234 2559 528558304 528560651 0.000000e+00 3386
7 TraesCS3A01G270200 chr7D 94.977 1752 79 8 812 2559 460797605 460799351 0.000000e+00 2739
8 TraesCS3A01G270200 chr3D 92.435 2353 146 13 234 2559 310403211 310405558 0.000000e+00 3330
9 TraesCS3A01G270200 chr3D 92.027 878 31 11 235 1077 446920236 446921109 0.000000e+00 1197
10 TraesCS3A01G270200 chr3D 83.544 237 17 9 1 231 374687097 374687317 4.320000e-48 202
11 TraesCS3A01G270200 chr6A 91.907 2360 153 28 234 2559 23001791 23004146 0.000000e+00 3265
12 TraesCS3A01G270200 chr6A 91.705 2387 138 36 227 2559 7013895 7016275 0.000000e+00 3256
13 TraesCS3A01G270200 chr2B 90.982 2362 164 34 235 2559 546616317 546618666 0.000000e+00 3136
14 TraesCS3A01G270200 chr5A 94.406 2038 75 11 280 2283 690036560 690038592 0.000000e+00 3096
15 TraesCS3A01G270200 chr5A 94.135 1722 68 10 235 1927 599226415 599228132 0.000000e+00 2590
16 TraesCS3A01G270200 chr6D 94.865 1889 68 16 695 2559 62138822 62140705 0.000000e+00 2924
17 TraesCS3A01G270200 chr5D 94.623 1432 53 16 235 1646 108135504 108136931 0.000000e+00 2196


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 TraesCS3A01G270200 chr3A 497297814 497300374 2560 False 4730 4730 100.000 1 2561 1 chr3A.!!$F2 2560
1 TraesCS3A01G270200 chr3A 348998946 349000075 1129 False 1644 1644 93.310 239 1345 1 chr3A.!!$F1 1106
2 TraesCS3A01G270200 chr4D 470197175 470199538 2363 True 3581 3581 94.292 235 2559 1 chr4D.!!$R1 2324
3 TraesCS3A01G270200 chr2D 619850763 619853094 2331 False 3515 3515 93.960 234 2559 1 chr2D.!!$F2 2325
4 TraesCS3A01G270200 chr2D 151998942 152000674 1732 False 2763 2763 95.449 826 2559 1 chr2D.!!$F1 1733
5 TraesCS3A01G270200 chr2A 48624737 48627070 2333 True 3498 3498 93.819 235 2559 1 chr2A.!!$R1 2324
6 TraesCS3A01G270200 chr7D 528558304 528560651 2347 False 3386 3386 92.917 234 2559 1 chr7D.!!$F2 2325
7 TraesCS3A01G270200 chr7D 460797605 460799351 1746 False 2739 2739 94.977 812 2559 1 chr7D.!!$F1 1747
8 TraesCS3A01G270200 chr3D 310403211 310405558 2347 False 3330 3330 92.435 234 2559 1 chr3D.!!$F1 2325
9 TraesCS3A01G270200 chr3D 446920236 446921109 873 False 1197 1197 92.027 235 1077 1 chr3D.!!$F3 842
10 TraesCS3A01G270200 chr6A 23001791 23004146 2355 False 3265 3265 91.907 234 2559 1 chr6A.!!$F2 2325
11 TraesCS3A01G270200 chr6A 7013895 7016275 2380 False 3256 3256 91.705 227 2559 1 chr6A.!!$F1 2332
12 TraesCS3A01G270200 chr2B 546616317 546618666 2349 False 3136 3136 90.982 235 2559 1 chr2B.!!$F1 2324
13 TraesCS3A01G270200 chr5A 690036560 690038592 2032 False 3096 3096 94.406 280 2283 1 chr5A.!!$F2 2003
14 TraesCS3A01G270200 chr5A 599226415 599228132 1717 False 2590 2590 94.135 235 1927 1 chr5A.!!$F1 1692
15 TraesCS3A01G270200 chr6D 62138822 62140705 1883 False 2924 2924 94.865 695 2559 1 chr6D.!!$F1 1864
16 TraesCS3A01G270200 chr5D 108135504 108136931 1427 False 2196 2196 94.623 235 1646 1 chr5D.!!$F1 1411

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
214 215 0.101759 TGAACGTATACGAGCCAGGC 59.898 55.0 30.77 1.84 43.02 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2113 2294 0.463654 ACGTGTGAGTGCCAACATGT 60.464 50.0 0.0 0.0 0.0 3.21 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 2.723124 AAATTTGGCACGGACATCAC 57.277 45.000 0.00 0.00 0.00 3.06
20 21 0.521291 AATTTGGCACGGACATCACG 59.479 50.000 0.00 0.00 37.36 4.35
21 22 1.922135 ATTTGGCACGGACATCACGC 61.922 55.000 0.00 0.00 34.00 5.34
22 23 3.816367 TTGGCACGGACATCACGCA 62.816 57.895 0.00 0.00 34.00 5.24
23 24 3.788766 GGCACGGACATCACGCAC 61.789 66.667 0.00 0.00 34.00 5.34
24 25 2.738521 GCACGGACATCACGCACT 60.739 61.111 0.00 0.00 34.00 4.40
25 26 2.730672 GCACGGACATCACGCACTC 61.731 63.158 0.00 0.00 34.00 3.51
26 27 2.126463 ACGGACATCACGCACTCG 60.126 61.111 0.00 0.00 42.43 4.18
27 28 2.880879 CGGACATCACGCACTCGG 60.881 66.667 0.00 0.00 40.69 4.63
28 29 3.188786 GGACATCACGCACTCGGC 61.189 66.667 0.00 0.00 40.69 5.54
29 30 3.188786 GACATCACGCACTCGGCC 61.189 66.667 0.00 0.00 40.31 6.13
30 31 3.932580 GACATCACGCACTCGGCCA 62.933 63.158 2.24 0.00 40.31 5.36
31 32 2.512286 CATCACGCACTCGGCCAT 60.512 61.111 2.24 0.00 40.31 4.40
32 33 2.202932 ATCACGCACTCGGCCATC 60.203 61.111 2.24 0.00 40.31 3.51
33 34 2.725312 ATCACGCACTCGGCCATCT 61.725 57.895 2.24 0.00 40.31 2.90
34 35 2.244117 ATCACGCACTCGGCCATCTT 62.244 55.000 2.24 0.00 40.31 2.40
35 36 2.034879 CACGCACTCGGCCATCTTT 61.035 57.895 2.24 0.00 40.31 2.52
36 37 1.741770 ACGCACTCGGCCATCTTTC 60.742 57.895 2.24 0.00 40.31 2.62
37 38 1.448540 CGCACTCGGCCATCTTTCT 60.449 57.895 2.24 0.00 40.31 2.52
38 39 1.424493 CGCACTCGGCCATCTTTCTC 61.424 60.000 2.24 0.00 40.31 2.87
39 40 1.424493 GCACTCGGCCATCTTTCTCG 61.424 60.000 2.24 0.00 36.11 4.04
40 41 0.173481 CACTCGGCCATCTTTCTCGA 59.827 55.000 2.24 0.00 0.00 4.04
41 42 0.895530 ACTCGGCCATCTTTCTCGAA 59.104 50.000 2.24 0.00 0.00 3.71
42 43 1.275291 ACTCGGCCATCTTTCTCGAAA 59.725 47.619 2.24 0.00 0.00 3.46
43 44 2.289444 ACTCGGCCATCTTTCTCGAAAA 60.289 45.455 2.24 0.00 0.00 2.29
44 45 2.742053 CTCGGCCATCTTTCTCGAAAAA 59.258 45.455 2.24 0.00 0.00 1.94
105 106 2.009681 AAAAATTTCACTCCCGGGCT 57.990 45.000 18.49 0.00 0.00 5.19
106 107 1.545841 AAAATTTCACTCCCGGGCTC 58.454 50.000 18.49 0.00 0.00 4.70
107 108 0.404040 AAATTTCACTCCCGGGCTCA 59.596 50.000 18.49 0.00 0.00 4.26
108 109 0.625849 AATTTCACTCCCGGGCTCAT 59.374 50.000 18.49 0.00 0.00 2.90
109 110 0.181350 ATTTCACTCCCGGGCTCATC 59.819 55.000 18.49 0.00 0.00 2.92
110 111 0.909610 TTTCACTCCCGGGCTCATCT 60.910 55.000 18.49 0.00 0.00 2.90
111 112 1.617018 TTCACTCCCGGGCTCATCTG 61.617 60.000 18.49 4.06 0.00 2.90
112 113 2.060383 CACTCCCGGGCTCATCTGA 61.060 63.158 18.49 0.00 0.00 3.27
113 114 1.760086 ACTCCCGGGCTCATCTGAG 60.760 63.158 18.49 7.96 44.75 3.35
114 115 1.456518 CTCCCGGGCTCATCTGAGA 60.457 63.158 18.49 0.00 44.74 3.27
120 121 2.907703 GGCTCATCTGAGACTGGGA 58.092 57.895 11.34 0.00 46.61 4.37
121 122 0.752054 GGCTCATCTGAGACTGGGAG 59.248 60.000 11.34 0.00 46.61 4.30
122 123 0.104671 GCTCATCTGAGACTGGGAGC 59.895 60.000 11.34 10.18 44.74 4.70
123 124 0.752054 CTCATCTGAGACTGGGAGCC 59.248 60.000 0.72 0.00 44.74 4.70
124 125 1.039785 TCATCTGAGACTGGGAGCCG 61.040 60.000 0.00 0.00 0.00 5.52
125 126 1.760086 ATCTGAGACTGGGAGCCGG 60.760 63.158 0.00 0.00 35.68 6.13
126 127 3.465403 CTGAGACTGGGAGCCGGG 61.465 72.222 2.18 0.00 33.40 5.73
135 136 3.706373 GGAGCCGGGCTGAGTCAA 61.706 66.667 29.31 0.00 39.88 3.18
136 137 2.347490 GAGCCGGGCTGAGTCAAA 59.653 61.111 29.31 0.00 39.88 2.69
137 138 1.302511 GAGCCGGGCTGAGTCAAAA 60.303 57.895 29.31 0.00 39.88 2.44
138 139 0.678048 GAGCCGGGCTGAGTCAAAAT 60.678 55.000 29.31 0.00 39.88 1.82
139 140 0.962356 AGCCGGGCTGAGTCAAAATG 60.962 55.000 23.19 0.00 37.57 2.32
140 141 1.508088 CCGGGCTGAGTCAAAATGC 59.492 57.895 0.00 0.00 0.00 3.56
141 142 1.508088 CGGGCTGAGTCAAAATGCC 59.492 57.895 11.73 11.73 42.56 4.40
142 143 0.962356 CGGGCTGAGTCAAAATGCCT 60.962 55.000 17.80 0.00 42.84 4.75
143 144 0.813821 GGGCTGAGTCAAAATGCCTC 59.186 55.000 17.80 7.26 42.84 4.70
144 145 1.538047 GGCTGAGTCAAAATGCCTCA 58.462 50.000 12.66 0.00 40.36 3.86
145 146 2.097825 GGCTGAGTCAAAATGCCTCAT 58.902 47.619 12.66 0.00 40.36 2.90
146 147 2.098770 GGCTGAGTCAAAATGCCTCATC 59.901 50.000 12.66 0.00 40.36 2.92
147 148 2.098770 GCTGAGTCAAAATGCCTCATCC 59.901 50.000 0.00 0.00 34.90 3.51
148 149 2.686915 CTGAGTCAAAATGCCTCATCCC 59.313 50.000 0.00 0.00 34.90 3.85
149 150 2.027385 GAGTCAAAATGCCTCATCCCC 58.973 52.381 0.00 0.00 0.00 4.81
150 151 1.642762 AGTCAAAATGCCTCATCCCCT 59.357 47.619 0.00 0.00 0.00 4.79
151 152 2.027385 GTCAAAATGCCTCATCCCCTC 58.973 52.381 0.00 0.00 0.00 4.30
152 153 1.925255 TCAAAATGCCTCATCCCCTCT 59.075 47.619 0.00 0.00 0.00 3.69
153 154 2.092212 TCAAAATGCCTCATCCCCTCTC 60.092 50.000 0.00 0.00 0.00 3.20
154 155 0.849417 AAATGCCTCATCCCCTCTCC 59.151 55.000 0.00 0.00 0.00 3.71
155 156 1.414061 AATGCCTCATCCCCTCTCCG 61.414 60.000 0.00 0.00 0.00 4.63
156 157 2.444895 GCCTCATCCCCTCTCCGT 60.445 66.667 0.00 0.00 0.00 4.69
157 158 1.152525 GCCTCATCCCCTCTCCGTA 60.153 63.158 0.00 0.00 0.00 4.02
158 159 0.759436 GCCTCATCCCCTCTCCGTAA 60.759 60.000 0.00 0.00 0.00 3.18
159 160 1.041437 CCTCATCCCCTCTCCGTAAC 58.959 60.000 0.00 0.00 0.00 2.50
160 161 1.041437 CTCATCCCCTCTCCGTAACC 58.959 60.000 0.00 0.00 0.00 2.85
161 162 0.635009 TCATCCCCTCTCCGTAACCT 59.365 55.000 0.00 0.00 0.00 3.50
162 163 1.854939 TCATCCCCTCTCCGTAACCTA 59.145 52.381 0.00 0.00 0.00 3.08
163 164 2.449730 TCATCCCCTCTCCGTAACCTAT 59.550 50.000 0.00 0.00 0.00 2.57
164 165 3.116862 TCATCCCCTCTCCGTAACCTATT 60.117 47.826 0.00 0.00 0.00 1.73
165 166 2.674420 TCCCCTCTCCGTAACCTATTG 58.326 52.381 0.00 0.00 0.00 1.90
166 167 1.692519 CCCCTCTCCGTAACCTATTGG 59.307 57.143 0.00 0.00 39.83 3.16
167 168 2.674420 CCCTCTCCGTAACCTATTGGA 58.326 52.381 0.00 0.00 37.04 3.53
168 169 3.240302 CCCTCTCCGTAACCTATTGGAT 58.760 50.000 0.00 0.00 37.04 3.41
169 170 3.006967 CCCTCTCCGTAACCTATTGGATG 59.993 52.174 0.00 0.00 37.04 3.51
170 171 3.641906 CCTCTCCGTAACCTATTGGATGT 59.358 47.826 0.00 0.00 37.04 3.06
171 172 4.101119 CCTCTCCGTAACCTATTGGATGTT 59.899 45.833 0.00 0.00 37.04 2.71
172 173 5.018539 TCTCCGTAACCTATTGGATGTTG 57.981 43.478 0.00 0.00 37.04 3.33
173 174 4.712829 TCTCCGTAACCTATTGGATGTTGA 59.287 41.667 0.00 0.00 37.04 3.18
174 175 4.761975 TCCGTAACCTATTGGATGTTGAC 58.238 43.478 0.00 0.00 37.04 3.18
175 176 3.875134 CCGTAACCTATTGGATGTTGACC 59.125 47.826 0.00 0.00 37.04 4.02
176 177 3.875134 CGTAACCTATTGGATGTTGACCC 59.125 47.826 0.00 0.00 37.04 4.46
177 178 3.382083 AACCTATTGGATGTTGACCCC 57.618 47.619 0.00 0.00 37.04 4.95
178 179 2.573463 ACCTATTGGATGTTGACCCCT 58.427 47.619 0.00 0.00 37.04 4.79
179 180 2.926329 ACCTATTGGATGTTGACCCCTT 59.074 45.455 0.00 0.00 37.04 3.95
180 181 3.290710 CCTATTGGATGTTGACCCCTTG 58.709 50.000 0.00 0.00 34.57 3.61
181 182 2.236489 ATTGGATGTTGACCCCTTGG 57.764 50.000 0.00 0.00 37.80 3.61
193 194 3.222855 CCTTGGGCACGGCAACAA 61.223 61.111 0.00 0.00 0.00 2.83
194 195 2.027460 CTTGGGCACGGCAACAAC 59.973 61.111 0.00 0.00 0.00 3.32
195 196 2.441164 TTGGGCACGGCAACAACT 60.441 55.556 0.00 0.00 0.00 3.16
196 197 2.682256 CTTGGGCACGGCAACAACTG 62.682 60.000 0.00 0.00 0.00 3.16
197 198 2.904866 GGGCACGGCAACAACTGA 60.905 61.111 0.00 0.00 0.00 3.41
198 199 2.485795 GGGCACGGCAACAACTGAA 61.486 57.895 0.00 0.00 0.00 3.02
199 200 1.299089 GGCACGGCAACAACTGAAC 60.299 57.895 0.00 0.00 0.00 3.18
200 201 1.654137 GCACGGCAACAACTGAACG 60.654 57.895 0.00 0.00 34.35 3.95
201 202 1.719117 CACGGCAACAACTGAACGT 59.281 52.632 0.00 0.00 39.70 3.99
202 203 0.931702 CACGGCAACAACTGAACGTA 59.068 50.000 0.00 0.00 37.86 3.57
203 204 1.529438 CACGGCAACAACTGAACGTAT 59.471 47.619 0.00 0.00 37.86 3.06
204 205 2.732500 CACGGCAACAACTGAACGTATA 59.267 45.455 0.00 0.00 37.86 1.47
205 206 2.733026 ACGGCAACAACTGAACGTATAC 59.267 45.455 0.00 0.00 38.07 1.47
206 207 2.222420 CGGCAACAACTGAACGTATACG 60.222 50.000 23.24 23.24 46.33 3.06
207 208 2.988493 GGCAACAACTGAACGTATACGA 59.012 45.455 30.77 8.60 43.02 3.43
208 209 3.060363 GGCAACAACTGAACGTATACGAG 59.940 47.826 30.77 19.60 43.02 4.18
209 210 3.481467 GCAACAACTGAACGTATACGAGC 60.481 47.826 30.77 20.57 43.02 5.03
210 211 2.872370 ACAACTGAACGTATACGAGCC 58.128 47.619 30.77 18.01 43.02 4.70
211 212 2.229543 ACAACTGAACGTATACGAGCCA 59.770 45.455 30.77 21.03 43.02 4.75
212 213 2.846039 ACTGAACGTATACGAGCCAG 57.154 50.000 30.77 28.59 43.02 4.85
213 214 1.404391 ACTGAACGTATACGAGCCAGG 59.596 52.381 30.77 16.33 43.02 4.45
214 215 0.101759 TGAACGTATACGAGCCAGGC 59.898 55.000 30.77 1.84 43.02 4.85
215 216 0.384669 GAACGTATACGAGCCAGGCT 59.615 55.000 30.77 16.12 43.88 4.58
216 217 0.102481 AACGTATACGAGCCAGGCTG 59.898 55.000 30.77 13.98 39.88 4.85
217 218 1.007271 CGTATACGAGCCAGGCTGG 60.007 63.158 29.44 29.44 39.88 4.85
218 219 1.367840 GTATACGAGCCAGGCTGGG 59.632 63.158 33.43 19.95 39.88 4.45
225 226 4.066139 GCCAGGCTGGGTTCCCAT 62.066 66.667 33.43 0.00 38.19 4.00
231 232 1.152673 GCTGGGTTCCCATCCATCC 60.153 63.158 11.26 0.00 35.33 3.51
268 270 3.433615 TGTTTTGACCCTTTTTGCAAACG 59.566 39.130 12.39 6.03 30.77 3.60
374 379 4.908487 CTACCGCCGCCCCCTCTA 62.908 72.222 0.00 0.00 0.00 2.43
422 435 2.972505 CGTTGGCAGGCGTTGACT 60.973 61.111 5.56 0.00 35.09 3.41
632 662 4.650085 CCCCCTAGATCCACTCCC 57.350 66.667 0.00 0.00 0.00 4.30
657 687 2.352960 GCTTGAGATTTCATCGGTGGAC 59.647 50.000 0.00 0.00 32.27 4.02
784 815 2.558265 TGATGTTGTTGTGTGTGCAC 57.442 45.000 10.75 10.75 45.44 4.57
1205 1374 4.070009 GACGTTGGATTGGGAGTAAAGTT 58.930 43.478 0.00 0.00 0.00 2.66
1283 1452 3.223423 AGTAGACGCATCACAAGACAG 57.777 47.619 0.00 0.00 0.00 3.51
1412 1583 1.472480 CCCCAATTGTTCTAGCCAACG 59.528 52.381 4.43 0.00 0.00 4.10
1499 1670 6.765036 GCTATTCCTCATGTTGAAGAAGATGA 59.235 38.462 0.00 0.00 39.04 2.92
1529 1700 5.798132 TCATGTTGAAGAAGATGCTAGTGT 58.202 37.500 0.00 0.00 33.73 3.55
1589 1766 3.860536 GCTTACTCGGACAATGAAGAGAC 59.139 47.826 10.11 0.00 34.98 3.36
1646 1823 0.888736 CGGCAACAAGACATGGACCA 60.889 55.000 0.00 0.00 0.00 4.02
1664 1841 4.237018 GACCATACCCTCCCTTATAACCA 58.763 47.826 0.00 0.00 0.00 3.67
1729 1906 3.129262 TGGATGAGGATGGGTTGACTA 57.871 47.619 0.00 0.00 0.00 2.59
1839 2020 0.400213 TTGACGGTGGGCTGAGATTT 59.600 50.000 0.00 0.00 0.00 2.17
1878 2059 0.240945 CGTGCCCCAAATTCAGTGAC 59.759 55.000 0.00 0.00 0.00 3.67
1888 2069 0.608640 ATTCAGTGACCCTCGACCAC 59.391 55.000 0.00 0.00 0.00 4.16
1889 2070 0.757561 TTCAGTGACCCTCGACCACA 60.758 55.000 0.00 0.00 33.53 4.17
2025 2206 7.821359 TGTTGGTCATTCAAATCAAAAACTTCA 59.179 29.630 0.00 0.00 0.00 3.02
2028 2209 8.040132 TGGTCATTCAAATCAAAAACTTCAGTT 58.960 29.630 0.00 0.00 40.50 3.16
2070 2251 3.737559 AGGTTGCAAATGGATGGTCTA 57.262 42.857 0.00 0.00 0.00 2.59
2113 2294 1.547675 GGGCAATGGGTGTTGAAGAGA 60.548 52.381 0.00 0.00 0.00 3.10
2184 2365 0.311790 GGACACCGTCAACTCACGTA 59.688 55.000 0.00 0.00 38.14 3.57
2225 2406 9.872721 ACAAATTGTTGCATCAAATATCACATA 57.127 25.926 13.88 0.00 38.39 2.29
2233 2414 8.467963 TGCATCAAATATCACATAATCCAACT 57.532 30.769 0.00 0.00 0.00 3.16
2244 2425 5.649395 CACATAATCCAACTGTGAAGGTCAT 59.351 40.000 0.00 0.00 42.20 3.06
2353 2534 2.954318 GTTGCATGGTGATTATGAGGCT 59.046 45.455 0.00 0.00 0.00 4.58
2459 2642 1.464997 GTTTCGTCATGCCTTCTGGAC 59.535 52.381 0.00 0.00 34.57 4.02
2478 2661 3.006752 GGACCTTTGGACAATGCATTGAA 59.993 43.478 38.99 23.42 40.14 2.69
2520 2703 4.083431 CCGGTCTTGTCTATAGATGGTACG 60.083 50.000 5.57 7.13 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.068610 CGTGATGTCCGTGCCAAATTT 60.069 47.619 0.00 0.00 0.00 1.82
1 2 0.521291 CGTGATGTCCGTGCCAAATT 59.479 50.000 0.00 0.00 0.00 1.82
2 3 1.922135 GCGTGATGTCCGTGCCAAAT 61.922 55.000 0.00 0.00 0.00 2.32
6 7 3.788766 GTGCGTGATGTCCGTGCC 61.789 66.667 0.00 0.00 0.00 5.01
8 9 2.436539 CGAGTGCGTGATGTCCGTG 61.437 63.158 0.00 0.00 0.00 4.94
9 10 2.126463 CGAGTGCGTGATGTCCGT 60.126 61.111 0.00 0.00 0.00 4.69
10 11 2.880879 CCGAGTGCGTGATGTCCG 60.881 66.667 0.00 0.00 35.23 4.79
12 13 3.188786 GGCCGAGTGCGTGATGTC 61.189 66.667 0.00 0.00 42.61 3.06
13 14 3.315142 ATGGCCGAGTGCGTGATGT 62.315 57.895 0.00 0.00 42.61 3.06
14 15 2.512286 ATGGCCGAGTGCGTGATG 60.512 61.111 0.00 0.00 42.61 3.07
15 16 2.202932 GATGGCCGAGTGCGTGAT 60.203 61.111 0.00 0.00 42.61 3.06
16 17 2.449031 AAAGATGGCCGAGTGCGTGA 62.449 55.000 0.00 0.00 42.61 4.35
17 18 1.970917 GAAAGATGGCCGAGTGCGTG 61.971 60.000 0.00 0.00 42.61 5.34
18 19 1.741770 GAAAGATGGCCGAGTGCGT 60.742 57.895 0.00 0.00 42.61 5.24
19 20 1.424493 GAGAAAGATGGCCGAGTGCG 61.424 60.000 0.00 0.00 42.61 5.34
20 21 1.424493 CGAGAAAGATGGCCGAGTGC 61.424 60.000 0.00 0.00 40.16 4.40
21 22 0.173481 TCGAGAAAGATGGCCGAGTG 59.827 55.000 0.00 0.00 0.00 3.51
22 23 0.895530 TTCGAGAAAGATGGCCGAGT 59.104 50.000 0.00 0.00 0.00 4.18
23 24 2.010145 TTTCGAGAAAGATGGCCGAG 57.990 50.000 0.00 0.00 0.00 4.63
24 25 2.465860 TTTTCGAGAAAGATGGCCGA 57.534 45.000 0.00 0.00 0.00 5.54
86 87 1.893137 GAGCCCGGGAGTGAAATTTTT 59.107 47.619 29.31 0.00 0.00 1.94
87 88 1.203001 TGAGCCCGGGAGTGAAATTTT 60.203 47.619 29.31 0.00 0.00 1.82
88 89 0.404040 TGAGCCCGGGAGTGAAATTT 59.596 50.000 29.31 0.00 0.00 1.82
89 90 0.625849 ATGAGCCCGGGAGTGAAATT 59.374 50.000 29.31 0.00 0.00 1.82
90 91 0.181350 GATGAGCCCGGGAGTGAAAT 59.819 55.000 29.31 8.04 0.00 2.17
91 92 0.909610 AGATGAGCCCGGGAGTGAAA 60.910 55.000 29.31 2.41 0.00 2.69
92 93 1.306141 AGATGAGCCCGGGAGTGAA 60.306 57.895 29.31 4.14 0.00 3.18
93 94 2.060383 CAGATGAGCCCGGGAGTGA 61.060 63.158 29.31 4.34 0.00 3.41
94 95 2.025767 CTCAGATGAGCCCGGGAGTG 62.026 65.000 29.31 11.23 35.13 3.51
95 96 1.760086 CTCAGATGAGCCCGGGAGT 60.760 63.158 29.31 10.93 35.13 3.85
96 97 1.456518 TCTCAGATGAGCCCGGGAG 60.457 63.158 29.31 10.39 41.80 4.30
97 98 1.758514 GTCTCAGATGAGCCCGGGA 60.759 63.158 29.31 2.74 41.80 5.14
98 99 1.760086 AGTCTCAGATGAGCCCGGG 60.760 63.158 19.09 19.09 41.80 5.73
99 100 1.440893 CAGTCTCAGATGAGCCCGG 59.559 63.158 4.92 0.00 41.80 5.73
100 101 1.440893 CCAGTCTCAGATGAGCCCG 59.559 63.158 4.92 0.00 41.80 6.13
101 102 0.689080 TCCCAGTCTCAGATGAGCCC 60.689 60.000 4.92 0.00 41.80 5.19
102 103 0.752054 CTCCCAGTCTCAGATGAGCC 59.248 60.000 4.92 0.00 41.80 4.70
103 104 0.104671 GCTCCCAGTCTCAGATGAGC 59.895 60.000 4.92 0.00 41.80 4.26
104 105 0.752054 GGCTCCCAGTCTCAGATGAG 59.248 60.000 3.33 3.33 43.36 2.90
105 106 1.039785 CGGCTCCCAGTCTCAGATGA 61.040 60.000 0.00 0.00 0.00 2.92
106 107 1.440893 CGGCTCCCAGTCTCAGATG 59.559 63.158 0.00 0.00 0.00 2.90
107 108 1.760086 CCGGCTCCCAGTCTCAGAT 60.760 63.158 0.00 0.00 0.00 2.90
108 109 2.363018 CCGGCTCCCAGTCTCAGA 60.363 66.667 0.00 0.00 0.00 3.27
109 110 3.465403 CCCGGCTCCCAGTCTCAG 61.465 72.222 0.00 0.00 0.00 3.35
118 119 2.748058 TTTTGACTCAGCCCGGCTCC 62.748 60.000 9.68 0.00 36.40 4.70
119 120 0.678048 ATTTTGACTCAGCCCGGCTC 60.678 55.000 9.68 0.00 36.40 4.70
120 121 0.962356 CATTTTGACTCAGCCCGGCT 60.962 55.000 5.94 5.94 40.77 5.52
121 122 1.508088 CATTTTGACTCAGCCCGGC 59.492 57.895 0.00 0.00 0.00 6.13
122 123 1.508088 GCATTTTGACTCAGCCCGG 59.492 57.895 0.00 0.00 0.00 5.73
123 124 0.962356 AGGCATTTTGACTCAGCCCG 60.962 55.000 0.00 0.00 46.35 6.13
124 125 2.967270 AGGCATTTTGACTCAGCCC 58.033 52.632 0.00 0.00 46.35 5.19
130 131 1.642762 AGGGGATGAGGCATTTTGACT 59.357 47.619 0.00 0.00 39.41 3.41
131 132 2.027385 GAGGGGATGAGGCATTTTGAC 58.973 52.381 0.00 0.00 0.00 3.18
132 133 1.925255 AGAGGGGATGAGGCATTTTGA 59.075 47.619 0.00 0.00 0.00 2.69
133 134 2.305009 GAGAGGGGATGAGGCATTTTG 58.695 52.381 0.00 0.00 0.00 2.44
134 135 1.216427 GGAGAGGGGATGAGGCATTTT 59.784 52.381 0.00 0.00 0.00 1.82
135 136 0.849417 GGAGAGGGGATGAGGCATTT 59.151 55.000 0.00 0.00 0.00 2.32
136 137 1.414061 CGGAGAGGGGATGAGGCATT 61.414 60.000 0.00 0.00 0.00 3.56
137 138 1.840650 CGGAGAGGGGATGAGGCAT 60.841 63.158 0.00 0.00 0.00 4.40
138 139 1.944896 TACGGAGAGGGGATGAGGCA 61.945 60.000 0.00 0.00 0.00 4.75
139 140 0.759436 TTACGGAGAGGGGATGAGGC 60.759 60.000 0.00 0.00 0.00 4.70
140 141 1.041437 GTTACGGAGAGGGGATGAGG 58.959 60.000 0.00 0.00 0.00 3.86
141 142 1.041437 GGTTACGGAGAGGGGATGAG 58.959 60.000 0.00 0.00 0.00 2.90
142 143 0.635009 AGGTTACGGAGAGGGGATGA 59.365 55.000 0.00 0.00 0.00 2.92
143 144 2.376695 TAGGTTACGGAGAGGGGATG 57.623 55.000 0.00 0.00 0.00 3.51
144 145 3.240302 CAATAGGTTACGGAGAGGGGAT 58.760 50.000 0.00 0.00 0.00 3.85
145 146 2.674420 CAATAGGTTACGGAGAGGGGA 58.326 52.381 0.00 0.00 0.00 4.81
146 147 1.692519 CCAATAGGTTACGGAGAGGGG 59.307 57.143 0.00 0.00 0.00 4.79
147 148 2.674420 TCCAATAGGTTACGGAGAGGG 58.326 52.381 0.00 0.00 35.89 4.30
148 149 3.641906 ACATCCAATAGGTTACGGAGAGG 59.358 47.826 0.00 0.00 35.89 3.69
149 150 4.939052 ACATCCAATAGGTTACGGAGAG 57.061 45.455 0.00 0.00 35.89 3.20
150 151 4.712829 TCAACATCCAATAGGTTACGGAGA 59.287 41.667 0.00 0.00 35.89 3.71
151 152 4.809426 GTCAACATCCAATAGGTTACGGAG 59.191 45.833 0.00 0.00 35.89 4.63
152 153 4.383335 GGTCAACATCCAATAGGTTACGGA 60.383 45.833 0.00 0.00 35.89 4.69
153 154 3.875134 GGTCAACATCCAATAGGTTACGG 59.125 47.826 0.00 0.00 35.89 4.02
154 155 3.875134 GGGTCAACATCCAATAGGTTACG 59.125 47.826 0.00 0.00 35.89 3.18
155 156 4.079958 AGGGGTCAACATCCAATAGGTTAC 60.080 45.833 0.00 0.00 35.89 2.50
156 157 4.116113 AGGGGTCAACATCCAATAGGTTA 58.884 43.478 0.00 0.00 35.89 2.85
157 158 2.926329 AGGGGTCAACATCCAATAGGTT 59.074 45.455 0.00 0.00 35.89 3.50
158 159 2.573463 AGGGGTCAACATCCAATAGGT 58.427 47.619 0.00 0.00 35.89 3.08
159 160 3.290710 CAAGGGGTCAACATCCAATAGG 58.709 50.000 0.00 0.00 0.00 2.57
160 161 3.290710 CCAAGGGGTCAACATCCAATAG 58.709 50.000 0.00 0.00 0.00 1.73
161 162 2.024464 CCCAAGGGGTCAACATCCAATA 60.024 50.000 0.00 0.00 38.25 1.90
162 163 1.273211 CCCAAGGGGTCAACATCCAAT 60.273 52.381 0.00 0.00 38.25 3.16
163 164 0.114168 CCCAAGGGGTCAACATCCAA 59.886 55.000 0.00 0.00 38.25 3.53
164 165 1.773635 CCCAAGGGGTCAACATCCA 59.226 57.895 0.00 0.00 38.25 3.41
165 166 1.682344 GCCCAAGGGGTCAACATCC 60.682 63.158 7.36 0.00 46.51 3.51
166 167 1.076549 TGCCCAAGGGGTCAACATC 59.923 57.895 7.36 0.00 46.51 3.06
167 168 1.228862 GTGCCCAAGGGGTCAACAT 60.229 57.895 7.36 0.00 46.51 2.71
168 169 2.197324 GTGCCCAAGGGGTCAACA 59.803 61.111 7.36 0.00 46.51 3.33
169 170 2.983592 CGTGCCCAAGGGGTCAAC 60.984 66.667 7.36 0.00 46.51 3.18
170 171 4.278513 CCGTGCCCAAGGGGTCAA 62.279 66.667 7.36 0.00 46.51 3.18
176 177 3.222855 TTGTTGCCGTGCCCAAGG 61.223 61.111 0.00 0.00 0.00 3.61
177 178 2.027460 GTTGTTGCCGTGCCCAAG 59.973 61.111 0.00 0.00 0.00 3.61
178 179 2.441164 AGTTGTTGCCGTGCCCAA 60.441 55.556 0.00 0.00 0.00 4.12
179 180 3.215568 CAGTTGTTGCCGTGCCCA 61.216 61.111 0.00 0.00 0.00 5.36
180 181 2.485795 TTCAGTTGTTGCCGTGCCC 61.486 57.895 0.00 0.00 0.00 5.36
181 182 1.299089 GTTCAGTTGTTGCCGTGCC 60.299 57.895 0.00 0.00 0.00 5.01
182 183 1.654137 CGTTCAGTTGTTGCCGTGC 60.654 57.895 0.00 0.00 0.00 5.34
183 184 0.931702 TACGTTCAGTTGTTGCCGTG 59.068 50.000 0.00 0.00 36.18 4.94
184 185 1.873698 ATACGTTCAGTTGTTGCCGT 58.126 45.000 0.00 0.00 37.66 5.68
185 186 2.222420 CGTATACGTTCAGTTGTTGCCG 60.222 50.000 17.16 0.00 34.11 5.69
186 187 2.988493 TCGTATACGTTCAGTTGTTGCC 59.012 45.455 23.67 0.00 40.80 4.52
187 188 3.481467 GCTCGTATACGTTCAGTTGTTGC 60.481 47.826 23.67 10.19 40.80 4.17
188 189 3.060363 GGCTCGTATACGTTCAGTTGTTG 59.940 47.826 23.67 5.15 40.80 3.33
189 190 3.248266 GGCTCGTATACGTTCAGTTGTT 58.752 45.455 23.67 0.00 40.80 2.83
190 191 2.229543 TGGCTCGTATACGTTCAGTTGT 59.770 45.455 23.67 0.00 40.80 3.32
191 192 2.852413 CTGGCTCGTATACGTTCAGTTG 59.148 50.000 23.67 7.02 40.80 3.16
192 193 2.159282 CCTGGCTCGTATACGTTCAGTT 60.159 50.000 23.67 0.00 40.80 3.16
193 194 1.404391 CCTGGCTCGTATACGTTCAGT 59.596 52.381 23.67 0.00 40.80 3.41
194 195 1.864435 GCCTGGCTCGTATACGTTCAG 60.864 57.143 23.67 23.95 40.80 3.02
195 196 0.101759 GCCTGGCTCGTATACGTTCA 59.898 55.000 23.67 17.79 40.80 3.18
196 197 0.384669 AGCCTGGCTCGTATACGTTC 59.615 55.000 23.67 15.92 40.80 3.95
197 198 0.102481 CAGCCTGGCTCGTATACGTT 59.898 55.000 20.49 0.00 36.40 3.99
198 199 1.734137 CAGCCTGGCTCGTATACGT 59.266 57.895 20.49 0.00 36.40 3.57
199 200 1.007271 CCAGCCTGGCTCGTATACG 60.007 63.158 20.49 19.23 36.40 3.06
200 201 1.367840 CCCAGCCTGGCTCGTATAC 59.632 63.158 20.49 0.00 36.40 1.47
201 202 0.689745 AACCCAGCCTGGCTCGTATA 60.690 55.000 20.49 0.00 36.40 1.47
202 203 1.972660 GAACCCAGCCTGGCTCGTAT 61.973 60.000 20.49 5.70 36.40 3.06
203 204 2.606519 AACCCAGCCTGGCTCGTA 60.607 61.111 20.49 0.00 36.40 3.43
204 205 4.021925 GAACCCAGCCTGGCTCGT 62.022 66.667 20.49 15.11 36.40 4.18
205 206 4.785453 GGAACCCAGCCTGGCTCG 62.785 72.222 20.49 13.06 36.40 5.03
218 219 0.259938 AGCCTTGGATGGATGGGAAC 59.740 55.000 0.00 0.00 0.00 3.62
219 220 1.905839 TAGCCTTGGATGGATGGGAA 58.094 50.000 0.00 0.00 0.00 3.97
220 221 1.905839 TTAGCCTTGGATGGATGGGA 58.094 50.000 0.00 0.00 0.00 4.37
221 222 2.754012 TTTAGCCTTGGATGGATGGG 57.246 50.000 0.00 0.00 0.00 4.00
222 223 4.261741 CGAAATTTAGCCTTGGATGGATGG 60.262 45.833 0.00 0.00 0.00 3.51
223 224 4.339247 ACGAAATTTAGCCTTGGATGGATG 59.661 41.667 0.00 0.00 0.00 3.51
224 225 4.339247 CACGAAATTTAGCCTTGGATGGAT 59.661 41.667 0.00 0.00 0.00 3.41
225 226 3.694072 CACGAAATTTAGCCTTGGATGGA 59.306 43.478 0.00 0.00 0.00 3.41
231 232 5.174943 GGTCAAAACACGAAATTTAGCCTTG 59.825 40.000 0.00 0.00 0.00 3.61
268 270 2.024414 CGGGGGTCAAATCCTGATTTC 58.976 52.381 2.19 0.00 38.84 2.17
374 379 0.606401 CCGTCAAATGACCTGCCACT 60.606 55.000 7.91 0.00 41.86 4.00
376 381 1.971167 GCCGTCAAATGACCTGCCA 60.971 57.895 7.91 0.00 41.86 4.92
379 384 0.670546 AGTCGCCGTCAAATGACCTG 60.671 55.000 7.91 1.35 41.86 4.00
415 425 0.313987 GGCCCTTTTCCAAGTCAACG 59.686 55.000 0.00 0.00 0.00 4.10
416 426 1.704641 AGGCCCTTTTCCAAGTCAAC 58.295 50.000 0.00 0.00 0.00 3.18
417 427 2.490168 GGTAGGCCCTTTTCCAAGTCAA 60.490 50.000 0.00 0.00 0.00 3.18
422 435 1.303806 GCGGTAGGCCCTTTTCCAA 60.304 57.895 0.00 0.00 34.80 3.53
549 574 4.171234 AGAAGATGAGTGGGGAAGAAGAA 58.829 43.478 0.00 0.00 0.00 2.52
632 662 3.012518 ACCGATGAAATCTCAAGCAAGG 58.987 45.455 0.00 0.00 42.58 3.61
657 687 0.740737 GGTGATGAAAATGCTCCGGG 59.259 55.000 0.00 0.00 0.00 5.73
784 815 7.765695 ACCCTAACCATAAATGCATCATAAG 57.234 36.000 0.00 0.00 0.00 1.73
995 1164 7.786178 ACATTTACGAGCTTATGCATCTAAA 57.214 32.000 0.19 0.00 42.74 1.85
1205 1374 4.346709 TGATGGGCATACTCTTTAATCGGA 59.653 41.667 0.00 0.00 0.00 4.55
1283 1452 3.006247 GTGGCAAAGATCTCAAGAGACC 58.994 50.000 1.20 0.00 40.75 3.85
1412 1583 1.818674 CATTGGGTTGGCTACTTGGTC 59.181 52.381 0.00 0.00 0.00 4.02
1499 1670 7.288560 AGCATCTTCTTCAACATGAGGAATAT 58.711 34.615 0.00 2.33 40.83 1.28
1529 1700 7.576861 ACAATAGCATCATCATCAACATGAA 57.423 32.000 0.00 0.00 42.53 2.57
1589 1766 6.790232 AGTTACCAATTGGATTGTAATGGG 57.210 37.500 31.22 0.00 38.59 4.00
1646 1823 7.029390 ACACATATGGTTATAAGGGAGGGTAT 58.971 38.462 7.80 0.00 0.00 2.73
1664 1841 5.778241 TCATCCGAGTTATACCCACACATAT 59.222 40.000 0.00 0.00 0.00 1.78
1729 1906 7.202016 TCTTGTAGATTTCATTTTCTTGCGT 57.798 32.000 0.00 0.00 0.00 5.24
1878 2059 1.812571 CCTCATTTTTGTGGTCGAGGG 59.187 52.381 0.00 0.00 37.07 4.30
1888 2069 6.203808 TGAGCATTCTCATCCTCATTTTTG 57.796 37.500 0.00 0.00 43.95 2.44
2070 2251 5.278120 CCGGTTTCTTTGATTTTTCTACCGT 60.278 40.000 0.00 0.00 43.14 4.83
2113 2294 0.463654 ACGTGTGAGTGCCAACATGT 60.464 50.000 0.00 0.00 0.00 3.21
2184 2365 9.277783 GCAACAATTTGTATCCTAGATACTCAT 57.722 33.333 14.13 5.32 34.90 2.90
2225 2406 4.104383 ACATGACCTTCACAGTTGGATT 57.896 40.909 0.00 0.00 0.00 3.01
2244 2425 6.298361 TCCTCAATTGAAGACATGAGAAACA 58.702 36.000 9.88 0.00 41.38 2.83
2260 2441 4.948004 GGGTATCCGAAAAGTTCCTCAATT 59.052 41.667 0.00 0.00 0.00 2.32
2353 2534 7.062322 ACATCTTGGGAAGAATGTTATATGCA 58.938 34.615 0.00 0.00 41.63 3.96
2447 2630 1.075601 TCCAAAGGTCCAGAAGGCAT 58.924 50.000 0.00 0.00 33.74 4.40
2459 2642 2.997986 GCTTCAATGCATTGTCCAAAGG 59.002 45.455 32.67 18.05 38.84 3.11
2478 2661 1.949525 GGGCGACAATACATGAATGCT 59.050 47.619 0.00 0.00 0.00 3.79
2486 2669 0.390603 CAAGACCGGGCGACAATACA 60.391 55.000 6.32 0.00 0.00 2.29
2520 2703 5.170748 CCCTTGTATTTGCCAATCAAGAAC 58.829 41.667 16.93 0.85 38.06 3.01


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

AutoCloner maintained by Alex Coulton.