Multiple sequence alignment - TraesCS6B01G216500

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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 TraesCS6B01G216500 chr6B 100.000 1501 0 0 1417 2917 297475326 297473826 0.000000e+00 2772
1 TraesCS6B01G216500 chr6B 100.000 1188 0 0 1 1188 297476742 297475555 0.000000e+00 2194
2 TraesCS6B01G216500 chr6B 97.382 382 8 1 50 429 388067868 388068249 0.000000e+00 649
3 TraesCS6B01G216500 chr6B 96.296 243 7 2 1 241 388024047 388024289 5.860000e-107 398
4 TraesCS6B01G216500 chr6B 95.567 203 6 2 47 246 592197115 592197317 3.630000e-84 322
5 TraesCS6B01G216500 chr5A 97.935 1501 31 0 1417 2917 19246588 19248088 0.000000e+00 2601
6 TraesCS6B01G216500 chr5A 98.296 939 10 2 256 1188 19245625 19246563 0.000000e+00 1640
7 TraesCS6B01G216500 chr7D 97.735 1501 34 0 1417 2917 381926256 381924756 0.000000e+00 2584
8 TraesCS6B01G216500 chr7D 97.668 1501 35 0 1417 2917 382052334 382050834 0.000000e+00 2579
9 TraesCS6B01G216500 chr7D 97.535 1501 34 1 1417 2917 381971515 381973012 0.000000e+00 2564
10 TraesCS6B01G216500 chr7D 97.468 1501 38 0 1417 2917 203502254 203500754 0.000000e+00 2562
11 TraesCS6B01G216500 chr7D 98.296 939 10 2 256 1188 382053297 382052359 0.000000e+00 1640
12 TraesCS6B01G216500 chr7B 97.668 1501 35 0 1417 2917 716876526 716878026 0.000000e+00 2579
13 TraesCS6B01G216500 chr7B 97.535 1501 37 0 1417 2917 716836315 716837815 0.000000e+00 2567
14 TraesCS6B01G216500 chr7B 98.394 934 14 1 256 1188 742992659 742991726 0.000000e+00 1640
15 TraesCS6B01G216500 chr7B 98.180 934 16 1 256 1188 716875568 716876501 0.000000e+00 1629
16 TraesCS6B01G216500 chr1A 97.602 1501 36 0 1417 2917 498688972 498690472 0.000000e+00 2573
17 TraesCS6B01G216500 chr1A 98.394 934 14 1 256 1188 498688014 498688947 0.000000e+00 1640
18 TraesCS6B01G216500 chrUn 97.465 1499 38 0 1417 2915 186206166 186207664 0.000000e+00 2558
19 TraesCS6B01G216500 chrUn 98.501 934 13 1 256 1188 186205208 186206141 0.000000e+00 1646
20 TraesCS6B01G216500 chr7A 98.608 934 12 1 256 1188 60282526 60281593 0.000000e+00 1652
21 TraesCS6B01G216500 chr2B 98.289 935 14 2 256 1188 112844416 112843482 0.000000e+00 1637
22 TraesCS6B01G216500 chr2B 98.287 934 15 1 256 1188 391164222 391163289 0.000000e+00 1635
23 TraesCS6B01G216500 chr1B 97.389 383 7 2 50 429 135015503 135015885 0.000000e+00 649
24 TraesCS6B01G216500 chr1B 96.414 251 7 2 1 249 135107302 135107052 2.090000e-111 412
25 TraesCS6B01G216500 chr1B 96.708 243 6 2 1 241 135102719 135102477 1.260000e-108 403
26 TraesCS6B01G216500 chr1B 96.708 243 6 2 1 241 471872765 471873007 1.260000e-108 403
27 TraesCS6B01G216500 chr1B 95.219 251 10 2 1 249 135061683 135061433 2.110000e-106 396
28 TraesCS6B01G216500 chr1B 100.000 94 0 0 1 94 534308038 534308131 1.070000e-39 174
29 TraesCS6B01G216500 chr3D 97.423 194 3 2 50 241 399710269 399710462 2.170000e-86 329
30 TraesCS6B01G216500 chr5D 98.462 65 1 0 1 65 324468206 324468270 6.610000e-22 115
31 TraesCS6B01G216500 chr5B 98.462 65 1 0 1 65 567251056 567250992 6.610000e-22 115
32 TraesCS6B01G216500 chr2D 98.462 65 1 0 1 65 322920820 322920884 6.610000e-22 115


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 TraesCS6B01G216500 chr6B 297473826 297476742 2916 True 2483.0 2772 100.0000 1 2917 2 chr6B.!!$R1 2916
1 TraesCS6B01G216500 chr5A 19245625 19248088 2463 False 2120.5 2601 98.1155 256 2917 2 chr5A.!!$F1 2661
2 TraesCS6B01G216500 chr7D 381924756 381926256 1500 True 2584.0 2584 97.7350 1417 2917 1 chr7D.!!$R2 1500
3 TraesCS6B01G216500 chr7D 381971515 381973012 1497 False 2564.0 2564 97.5350 1417 2917 1 chr7D.!!$F1 1500
4 TraesCS6B01G216500 chr7D 203500754 203502254 1500 True 2562.0 2562 97.4680 1417 2917 1 chr7D.!!$R1 1500
5 TraesCS6B01G216500 chr7D 382050834 382053297 2463 True 2109.5 2579 97.9820 256 2917 2 chr7D.!!$R3 2661
6 TraesCS6B01G216500 chr7B 716836315 716837815 1500 False 2567.0 2567 97.5350 1417 2917 1 chr7B.!!$F1 1500
7 TraesCS6B01G216500 chr7B 716875568 716878026 2458 False 2104.0 2579 97.9240 256 2917 2 chr7B.!!$F2 2661
8 TraesCS6B01G216500 chr7B 742991726 742992659 933 True 1640.0 1640 98.3940 256 1188 1 chr7B.!!$R1 932
9 TraesCS6B01G216500 chr1A 498688014 498690472 2458 False 2106.5 2573 97.9980 256 2917 2 chr1A.!!$F1 2661
10 TraesCS6B01G216500 chrUn 186205208 186207664 2456 False 2102.0 2558 97.9830 256 2915 2 chrUn.!!$F1 2659
11 TraesCS6B01G216500 chr7A 60281593 60282526 933 True 1652.0 1652 98.6080 256 1188 1 chr7A.!!$R1 932
12 TraesCS6B01G216500 chr2B 112843482 112844416 934 True 1637.0 1637 98.2890 256 1188 1 chr2B.!!$R1 932
13 TraesCS6B01G216500 chr2B 391163289 391164222 933 True 1635.0 1635 98.2870 256 1188 1 chr2B.!!$R2 932

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
235 236 0.111446 TTCAAATCGGGTTCCTGGCA 59.889 50.0 0.0 0.0 0.0 4.92 F
236 237 0.331278 TCAAATCGGGTTCCTGGCAT 59.669 50.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1120 1127 0.033503 TGGAGTGATCCAGTAGCCGA 60.034 55.0 0.0 0.0 34.33 5.54 R
2130 2137 1.188863 AGCGTTATAGGTCGTTGGGT 58.811 50.0 0.0 0.0 0.00 4.51 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
21 22 4.853924 CATTTATAGGCGGGCTTGATTT 57.146 40.909 10.13 0.00 0.00 2.17
22 23 5.200368 CATTTATAGGCGGGCTTGATTTT 57.800 39.130 10.13 0.00 0.00 1.82
23 24 5.600696 CATTTATAGGCGGGCTTGATTTTT 58.399 37.500 10.13 0.00 0.00 1.94
24 25 4.911514 TTATAGGCGGGCTTGATTTTTC 57.088 40.909 10.13 0.00 0.00 2.29
25 26 1.091537 TAGGCGGGCTTGATTTTTCG 58.908 50.000 10.13 0.00 0.00 3.46
26 27 0.608035 AGGCGGGCTTGATTTTTCGA 60.608 50.000 0.00 0.00 0.00 3.71
27 28 0.455815 GGCGGGCTTGATTTTTCGAT 59.544 50.000 0.00 0.00 0.00 3.59
28 29 1.135112 GGCGGGCTTGATTTTTCGATT 60.135 47.619 0.00 0.00 0.00 3.34
29 30 2.606108 GCGGGCTTGATTTTTCGATTT 58.394 42.857 0.00 0.00 0.00 2.17
30 31 2.345341 GCGGGCTTGATTTTTCGATTTG 59.655 45.455 0.00 0.00 0.00 2.32
31 32 2.345341 CGGGCTTGATTTTTCGATTTGC 59.655 45.455 0.00 0.00 0.00 3.68
32 33 3.324993 GGGCTTGATTTTTCGATTTGCA 58.675 40.909 0.00 0.00 0.00 4.08
33 34 3.934579 GGGCTTGATTTTTCGATTTGCAT 59.065 39.130 0.00 0.00 0.00 3.96
34 35 4.392754 GGGCTTGATTTTTCGATTTGCATT 59.607 37.500 0.00 0.00 0.00 3.56
35 36 5.580297 GGGCTTGATTTTTCGATTTGCATTA 59.420 36.000 0.00 0.00 0.00 1.90
36 37 6.258507 GGGCTTGATTTTTCGATTTGCATTAT 59.741 34.615 0.00 0.00 0.00 1.28
37 38 7.339953 GGCTTGATTTTTCGATTTGCATTATC 58.660 34.615 0.00 0.00 0.00 1.75
38 39 7.339953 GCTTGATTTTTCGATTTGCATTATCC 58.660 34.615 0.00 0.00 0.00 2.59
39 40 7.448588 TTGATTTTTCGATTTGCATTATCCG 57.551 32.000 0.00 0.00 0.00 4.18
40 41 6.559810 TGATTTTTCGATTTGCATTATCCGT 58.440 32.000 0.00 0.00 0.00 4.69
41 42 7.032580 TGATTTTTCGATTTGCATTATCCGTT 58.967 30.769 0.00 0.00 0.00 4.44
42 43 6.624710 TTTTTCGATTTGCATTATCCGTTG 57.375 33.333 0.00 0.00 0.00 4.10
43 44 3.961477 TCGATTTGCATTATCCGTTGG 57.039 42.857 0.00 0.00 0.00 3.77
44 45 3.536570 TCGATTTGCATTATCCGTTGGA 58.463 40.909 0.00 0.00 35.55 3.53
45 46 4.133820 TCGATTTGCATTATCCGTTGGAT 58.866 39.130 3.49 3.49 45.40 3.41
46 47 4.213270 TCGATTTGCATTATCCGTTGGATC 59.787 41.667 0.71 0.00 42.11 3.36
47 48 4.613622 CGATTTGCATTATCCGTTGGATCC 60.614 45.833 4.20 4.20 42.11 3.36
48 49 3.289407 TTGCATTATCCGTTGGATCCA 57.711 42.857 11.44 11.44 42.11 3.41
49 50 3.289407 TGCATTATCCGTTGGATCCAA 57.711 42.857 23.63 23.63 42.11 3.53
50 51 3.625853 TGCATTATCCGTTGGATCCAAA 58.374 40.909 28.64 14.24 42.11 3.28
51 52 4.214310 TGCATTATCCGTTGGATCCAAAT 58.786 39.130 28.64 20.08 42.11 2.32
52 53 4.278170 TGCATTATCCGTTGGATCCAAATC 59.722 41.667 28.64 16.13 42.11 2.17
69 70 9.863650 GATCCAAATCCATATCATTATCCTGAT 57.136 33.333 0.00 0.00 39.22 2.90
145 146 9.999660 TGACATAGATACAAGTACTCTACTAGG 57.000 37.037 0.00 1.43 38.26 3.02
151 152 9.733556 AGATACAAGTACTCTACTAGGATGATG 57.266 37.037 0.00 0.00 38.26 3.07
152 153 6.642707 ACAAGTACTCTACTAGGATGATGC 57.357 41.667 0.00 0.00 38.26 3.91
153 154 6.129874 ACAAGTACTCTACTAGGATGATGCA 58.870 40.000 0.00 0.00 38.26 3.96
154 155 6.039941 ACAAGTACTCTACTAGGATGATGCAC 59.960 42.308 0.00 0.00 38.26 4.57
155 156 5.696030 AGTACTCTACTAGGATGATGCACA 58.304 41.667 0.00 0.00 37.23 4.57
156 157 6.129874 AGTACTCTACTAGGATGATGCACAA 58.870 40.000 0.00 0.00 37.23 3.33
157 158 6.780031 AGTACTCTACTAGGATGATGCACAAT 59.220 38.462 0.00 0.00 37.23 2.71
158 159 7.945109 AGTACTCTACTAGGATGATGCACAATA 59.055 37.037 0.00 0.00 37.23 1.90
159 160 7.603180 ACTCTACTAGGATGATGCACAATAA 57.397 36.000 0.00 0.00 0.00 1.40
160 161 8.023021 ACTCTACTAGGATGATGCACAATAAA 57.977 34.615 0.00 0.00 0.00 1.40
161 162 8.654997 ACTCTACTAGGATGATGCACAATAAAT 58.345 33.333 0.00 0.00 0.00 1.40
164 165 9.935241 CTACTAGGATGATGCACAATAAATAGT 57.065 33.333 0.00 0.00 0.00 2.12
165 166 8.839310 ACTAGGATGATGCACAATAAATAGTC 57.161 34.615 0.00 0.00 0.00 2.59
166 167 8.432013 ACTAGGATGATGCACAATAAATAGTCA 58.568 33.333 0.00 0.00 0.00 3.41
167 168 7.741027 AGGATGATGCACAATAAATAGTCAG 57.259 36.000 0.00 0.00 0.00 3.51
168 169 6.713903 AGGATGATGCACAATAAATAGTCAGG 59.286 38.462 0.00 0.00 0.00 3.86
169 170 6.712095 GGATGATGCACAATAAATAGTCAGGA 59.288 38.462 0.00 0.00 0.00 3.86
170 171 7.392673 GGATGATGCACAATAAATAGTCAGGAT 59.607 37.037 0.00 0.00 0.00 3.24
171 172 9.440773 GATGATGCACAATAAATAGTCAGGATA 57.559 33.333 0.00 0.00 0.00 2.59
172 173 8.837788 TGATGCACAATAAATAGTCAGGATAG 57.162 34.615 0.00 0.00 0.00 2.08
173 174 7.388776 TGATGCACAATAAATAGTCAGGATAGC 59.611 37.037 0.00 0.00 0.00 2.97
174 175 6.830912 TGCACAATAAATAGTCAGGATAGCT 58.169 36.000 0.00 0.00 0.00 3.32
175 176 6.931281 TGCACAATAAATAGTCAGGATAGCTC 59.069 38.462 0.00 0.00 0.00 4.09
176 177 6.931281 GCACAATAAATAGTCAGGATAGCTCA 59.069 38.462 0.00 0.00 0.00 4.26
177 178 7.117523 GCACAATAAATAGTCAGGATAGCTCAG 59.882 40.741 0.00 0.00 0.00 3.35
178 179 8.147058 CACAATAAATAGTCAGGATAGCTCAGT 58.853 37.037 0.00 0.00 0.00 3.41
179 180 8.709308 ACAATAAATAGTCAGGATAGCTCAGTT 58.291 33.333 0.00 0.00 0.00 3.16
180 181 8.986847 CAATAAATAGTCAGGATAGCTCAGTTG 58.013 37.037 0.00 0.00 0.00 3.16
181 182 5.543507 AATAGTCAGGATAGCTCAGTTGG 57.456 43.478 0.00 0.00 0.00 3.77
182 183 2.826488 AGTCAGGATAGCTCAGTTGGT 58.174 47.619 0.00 0.00 0.00 3.67
183 184 3.982516 AGTCAGGATAGCTCAGTTGGTA 58.017 45.455 0.00 0.00 0.00 3.25
184 185 3.957497 AGTCAGGATAGCTCAGTTGGTAG 59.043 47.826 0.00 0.00 0.00 3.18
185 186 3.954904 GTCAGGATAGCTCAGTTGGTAGA 59.045 47.826 0.00 0.00 0.00 2.59
186 187 4.037446 GTCAGGATAGCTCAGTTGGTAGAG 59.963 50.000 0.00 0.00 35.01 2.43
193 194 3.685139 CTCAGTTGGTAGAGCAAAGGA 57.315 47.619 0.00 0.00 0.00 3.36
194 195 4.213564 CTCAGTTGGTAGAGCAAAGGAT 57.786 45.455 0.00 0.00 0.00 3.24
195 196 4.583871 CTCAGTTGGTAGAGCAAAGGATT 58.416 43.478 0.00 0.00 0.00 3.01
196 197 4.326826 TCAGTTGGTAGAGCAAAGGATTG 58.673 43.478 0.00 0.00 39.65 2.67
197 198 4.041567 TCAGTTGGTAGAGCAAAGGATTGA 59.958 41.667 0.00 0.00 38.94 2.57
198 199 4.761739 CAGTTGGTAGAGCAAAGGATTGAA 59.238 41.667 0.00 0.00 38.94 2.69
199 200 5.241506 CAGTTGGTAGAGCAAAGGATTGAAA 59.758 40.000 0.00 0.00 38.94 2.69
200 201 5.833131 AGTTGGTAGAGCAAAGGATTGAAAA 59.167 36.000 0.00 0.00 38.94 2.29
201 202 6.494835 AGTTGGTAGAGCAAAGGATTGAAAAT 59.505 34.615 0.00 0.00 38.94 1.82
202 203 6.515272 TGGTAGAGCAAAGGATTGAAAATC 57.485 37.500 0.00 0.00 38.94 2.17
203 204 5.418840 TGGTAGAGCAAAGGATTGAAAATCC 59.581 40.000 10.46 10.46 38.94 3.01
211 212 4.286297 AGGATTGAAAATCCTCGTGTCA 57.714 40.909 14.49 0.00 44.86 3.58
212 213 4.003648 AGGATTGAAAATCCTCGTGTCAC 58.996 43.478 14.49 0.00 44.86 3.67
213 214 3.127030 GGATTGAAAATCCTCGTGTCACC 59.873 47.826 11.06 0.00 35.36 4.02
214 215 2.920724 TGAAAATCCTCGTGTCACCA 57.079 45.000 0.00 0.00 0.00 4.17
215 216 2.766313 TGAAAATCCTCGTGTCACCAG 58.234 47.619 0.00 0.00 0.00 4.00
216 217 2.104111 TGAAAATCCTCGTGTCACCAGT 59.896 45.455 0.00 0.00 0.00 4.00
217 218 2.930826 AAATCCTCGTGTCACCAGTT 57.069 45.000 0.00 0.00 0.00 3.16
218 219 2.457366 AATCCTCGTGTCACCAGTTC 57.543 50.000 0.00 0.00 0.00 3.01
219 220 1.338107 ATCCTCGTGTCACCAGTTCA 58.662 50.000 0.00 0.00 0.00 3.18
220 221 1.116308 TCCTCGTGTCACCAGTTCAA 58.884 50.000 0.00 0.00 0.00 2.69
221 222 1.483004 TCCTCGTGTCACCAGTTCAAA 59.517 47.619 0.00 0.00 0.00 2.69
222 223 2.104111 TCCTCGTGTCACCAGTTCAAAT 59.896 45.455 0.00 0.00 0.00 2.32
223 224 2.480419 CCTCGTGTCACCAGTTCAAATC 59.520 50.000 0.00 0.00 0.00 2.17
224 225 2.131972 TCGTGTCACCAGTTCAAATCG 58.868 47.619 0.00 0.00 0.00 3.34
225 226 1.194547 CGTGTCACCAGTTCAAATCGG 59.805 52.381 0.00 0.00 0.00 4.18
226 227 1.535462 GTGTCACCAGTTCAAATCGGG 59.465 52.381 0.00 0.00 0.00 5.14
227 228 1.142060 TGTCACCAGTTCAAATCGGGT 59.858 47.619 0.00 0.00 34.00 5.28
228 229 2.227194 GTCACCAGTTCAAATCGGGTT 58.773 47.619 0.00 0.00 31.58 4.11
229 230 2.225727 GTCACCAGTTCAAATCGGGTTC 59.774 50.000 0.00 0.00 31.58 3.62
230 231 1.539827 CACCAGTTCAAATCGGGTTCC 59.460 52.381 0.00 0.00 31.58 3.62
231 232 1.423921 ACCAGTTCAAATCGGGTTCCT 59.576 47.619 0.00 0.00 29.81 3.36
232 233 1.812571 CCAGTTCAAATCGGGTTCCTG 59.187 52.381 0.00 0.00 0.00 3.86
233 234 1.812571 CAGTTCAAATCGGGTTCCTGG 59.187 52.381 0.00 0.00 0.00 4.45
234 235 0.526211 GTTCAAATCGGGTTCCTGGC 59.474 55.000 0.00 0.00 0.00 4.85
235 236 0.111446 TTCAAATCGGGTTCCTGGCA 59.889 50.000 0.00 0.00 0.00 4.92
236 237 0.331278 TCAAATCGGGTTCCTGGCAT 59.669 50.000 0.00 0.00 0.00 4.40
237 238 1.562008 TCAAATCGGGTTCCTGGCATA 59.438 47.619 0.00 0.00 0.00 3.14
238 239 1.949525 CAAATCGGGTTCCTGGCATAG 59.050 52.381 0.00 0.00 0.00 2.23
239 240 1.507140 AATCGGGTTCCTGGCATAGA 58.493 50.000 0.00 0.00 0.00 1.98
240 241 1.507140 ATCGGGTTCCTGGCATAGAA 58.493 50.000 0.00 0.00 0.00 2.10
241 242 1.281419 TCGGGTTCCTGGCATAGAAA 58.719 50.000 2.06 0.00 0.00 2.52
242 243 1.631388 TCGGGTTCCTGGCATAGAAAA 59.369 47.619 2.06 0.00 0.00 2.29
243 244 2.040545 TCGGGTTCCTGGCATAGAAAAA 59.959 45.455 2.06 0.00 0.00 1.94
559 561 2.079911 TCCACCCCGAAACCAAGGT 61.080 57.895 0.00 0.00 0.00 3.50
684 686 7.414222 AAGGTTCGGATCACTTACTATACAA 57.586 36.000 0.00 0.00 0.00 2.41
1067 1069 1.361543 ACTGGACAGGGGTAAGCTCTA 59.638 52.381 4.14 0.00 0.00 2.43
1120 1127 1.275421 GGCACTTCTAGGCCCCTTCT 61.275 60.000 0.00 0.00 44.53 2.85
1588 1595 3.965888 AAGCGAAGGGAATGAGCTT 57.034 47.368 0.00 0.00 42.51 3.74
1600 1607 0.619505 ATGAGCTTGGCTGCTTCTCT 59.380 50.000 0.00 0.00 44.17 3.10
1667 1674 1.153901 CCATTGGCGCTTTGCTCTG 60.154 57.895 7.64 0.00 45.43 3.35
1668 1675 1.582968 CATTGGCGCTTTGCTCTGT 59.417 52.632 7.64 0.00 45.43 3.41
1830 1837 2.879103 TTTGAAAGGAATCGAGGCCT 57.121 45.000 3.86 3.86 35.61 5.19
1856 1863 1.897398 GCTCGCGTCGTTCCAACAAT 61.897 55.000 5.77 0.00 0.00 2.71
1897 1904 3.229652 CGATCGCGTGCAGTAACTA 57.770 52.632 5.77 0.00 0.00 2.24
1971 1978 2.888414 TCGTGTAGTGATTGTGGACTCA 59.112 45.455 0.00 0.00 0.00 3.41
2124 2131 3.525800 ACCTTACTCATGGCAACCTTT 57.474 42.857 0.00 0.00 0.00 3.11
2200 2207 2.520741 CCCACAACCCAAAGCGGT 60.521 61.111 0.00 0.00 37.93 5.68
2248 2255 2.130512 CGGCTAACGGGGGTATTCT 58.869 57.895 0.00 0.00 39.42 2.40
2251 2258 1.211212 GGCTAACGGGGGTATTCTTGT 59.789 52.381 0.00 0.00 0.00 3.16
2572 2579 6.818416 CAATGCTGCAGAAAAAGAAGATTTC 58.182 36.000 20.43 0.00 37.11 2.17
2659 2666 3.004752 AGGCGCAATAGAAAGGAATGT 57.995 42.857 10.83 0.00 0.00 2.71
2733 2740 5.788450 GAGTCAAAAGAGAGATTGAGTCCA 58.212 41.667 10.71 0.00 44.57 4.02
2761 2768 1.155155 GGGGTTTTCTTGGGGCTCA 59.845 57.895 0.00 0.00 0.00 4.26
2801 2808 2.295070 GCCCCACAAGTTGTTAATTCGT 59.705 45.455 5.57 0.00 0.00 3.85
2843 2850 5.843019 AAGGGAAGGACTTATTCTCAACA 57.157 39.130 0.00 0.00 28.99 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.853924 AAATCAAGCCCGCCTATAAATG 57.146 40.909 0.00 0.00 0.00 2.32
3 4 3.314080 CGAAAAATCAAGCCCGCCTATAA 59.686 43.478 0.00 0.00 0.00 0.98
5 6 1.676006 CGAAAAATCAAGCCCGCCTAT 59.324 47.619 0.00 0.00 0.00 2.57
6 7 1.091537 CGAAAAATCAAGCCCGCCTA 58.908 50.000 0.00 0.00 0.00 3.93
7 8 0.608035 TCGAAAAATCAAGCCCGCCT 60.608 50.000 0.00 0.00 0.00 5.52
8 9 0.455815 ATCGAAAAATCAAGCCCGCC 59.544 50.000 0.00 0.00 0.00 6.13
9 10 2.278026 AATCGAAAAATCAAGCCCGC 57.722 45.000 0.00 0.00 0.00 6.13
10 11 2.345341 GCAAATCGAAAAATCAAGCCCG 59.655 45.455 0.00 0.00 0.00 6.13
11 12 3.324993 TGCAAATCGAAAAATCAAGCCC 58.675 40.909 0.00 0.00 0.00 5.19
12 13 5.535043 AATGCAAATCGAAAAATCAAGCC 57.465 34.783 0.00 0.00 0.00 4.35
13 14 7.339953 GGATAATGCAAATCGAAAAATCAAGC 58.660 34.615 0.00 0.00 0.00 4.01
14 15 7.220683 ACGGATAATGCAAATCGAAAAATCAAG 59.779 33.333 0.00 0.00 0.00 3.02
15 16 7.032580 ACGGATAATGCAAATCGAAAAATCAA 58.967 30.769 0.00 0.00 0.00 2.57
16 17 6.559810 ACGGATAATGCAAATCGAAAAATCA 58.440 32.000 0.00 0.00 0.00 2.57
17 18 7.329582 CAACGGATAATGCAAATCGAAAAATC 58.670 34.615 0.00 0.00 0.00 2.17
18 19 6.255453 CCAACGGATAATGCAAATCGAAAAAT 59.745 34.615 0.00 0.00 0.00 1.82
19 20 5.574830 CCAACGGATAATGCAAATCGAAAAA 59.425 36.000 0.00 0.00 0.00 1.94
20 21 5.098893 CCAACGGATAATGCAAATCGAAAA 58.901 37.500 0.00 0.00 0.00 2.29
21 22 4.396478 TCCAACGGATAATGCAAATCGAAA 59.604 37.500 0.00 0.00 0.00 3.46
22 23 3.942115 TCCAACGGATAATGCAAATCGAA 59.058 39.130 0.00 0.00 0.00 3.71
23 24 3.536570 TCCAACGGATAATGCAAATCGA 58.463 40.909 0.00 0.00 0.00 3.59
24 25 3.961477 TCCAACGGATAATGCAAATCG 57.039 42.857 0.00 0.00 0.00 3.34
25 26 4.278170 TGGATCCAACGGATAATGCAAATC 59.722 41.667 13.46 0.00 43.27 2.17
26 27 4.214310 TGGATCCAACGGATAATGCAAAT 58.786 39.130 13.46 0.00 43.27 2.32
27 28 3.625853 TGGATCCAACGGATAATGCAAA 58.374 40.909 13.46 0.00 43.27 3.68
28 29 3.289407 TGGATCCAACGGATAATGCAA 57.711 42.857 13.46 0.00 43.27 4.08
29 30 3.289407 TTGGATCCAACGGATAATGCA 57.711 42.857 23.63 0.00 43.27 3.96
30 31 4.798574 GATTTGGATCCAACGGATAATGC 58.201 43.478 27.04 7.31 43.27 3.56
43 44 9.863650 ATCAGGATAATGATATGGATTTGGATC 57.136 33.333 0.00 0.00 38.15 3.36
119 120 9.999660 CCTAGTAGAGTACTTGTATCTATGTCA 57.000 37.037 0.00 0.00 40.14 3.58
125 126 9.733556 CATCATCCTAGTAGAGTACTTGTATCT 57.266 37.037 0.00 0.00 40.14 1.98
126 127 8.455682 GCATCATCCTAGTAGAGTACTTGTATC 58.544 40.741 0.00 0.00 40.14 2.24
127 128 7.945109 TGCATCATCCTAGTAGAGTACTTGTAT 59.055 37.037 0.00 0.00 40.14 2.29
128 129 7.228906 GTGCATCATCCTAGTAGAGTACTTGTA 59.771 40.741 0.00 0.00 40.14 2.41
129 130 6.039941 GTGCATCATCCTAGTAGAGTACTTGT 59.960 42.308 0.00 0.00 40.14 3.16
130 131 6.039829 TGTGCATCATCCTAGTAGAGTACTTG 59.960 42.308 0.00 0.00 40.14 3.16
131 132 6.129874 TGTGCATCATCCTAGTAGAGTACTT 58.870 40.000 0.00 0.00 40.14 2.24
132 133 5.696030 TGTGCATCATCCTAGTAGAGTACT 58.304 41.667 0.00 0.00 42.68 2.73
133 134 6.392625 TTGTGCATCATCCTAGTAGAGTAC 57.607 41.667 0.00 0.00 0.00 2.73
134 135 8.706322 TTATTGTGCATCATCCTAGTAGAGTA 57.294 34.615 0.00 0.00 0.00 2.59
135 136 7.603180 TTATTGTGCATCATCCTAGTAGAGT 57.397 36.000 0.00 0.00 0.00 3.24
138 139 9.935241 ACTATTTATTGTGCATCATCCTAGTAG 57.065 33.333 0.00 0.00 0.00 2.57
139 140 9.929180 GACTATTTATTGTGCATCATCCTAGTA 57.071 33.333 0.00 0.00 0.00 1.82
140 141 8.432013 TGACTATTTATTGTGCATCATCCTAGT 58.568 33.333 0.00 0.00 0.00 2.57
141 142 8.837788 TGACTATTTATTGTGCATCATCCTAG 57.162 34.615 0.00 0.00 0.00 3.02
142 143 7.879677 CCTGACTATTTATTGTGCATCATCCTA 59.120 37.037 0.00 0.00 0.00 2.94
143 144 6.713903 CCTGACTATTTATTGTGCATCATCCT 59.286 38.462 0.00 0.00 0.00 3.24
144 145 6.712095 TCCTGACTATTTATTGTGCATCATCC 59.288 38.462 0.00 0.00 0.00 3.51
145 146 7.734924 TCCTGACTATTTATTGTGCATCATC 57.265 36.000 0.00 0.00 0.00 2.92
146 147 9.445878 CTATCCTGACTATTTATTGTGCATCAT 57.554 33.333 0.00 0.00 0.00 2.45
147 148 7.388776 GCTATCCTGACTATTTATTGTGCATCA 59.611 37.037 0.00 0.00 0.00 3.07
148 149 7.605691 AGCTATCCTGACTATTTATTGTGCATC 59.394 37.037 0.00 0.00 0.00 3.91
149 150 7.456725 AGCTATCCTGACTATTTATTGTGCAT 58.543 34.615 0.00 0.00 0.00 3.96
150 151 6.830912 AGCTATCCTGACTATTTATTGTGCA 58.169 36.000 0.00 0.00 0.00 4.57
151 152 6.931281 TGAGCTATCCTGACTATTTATTGTGC 59.069 38.462 0.00 0.00 0.00 4.57
152 153 8.147058 ACTGAGCTATCCTGACTATTTATTGTG 58.853 37.037 0.00 0.00 0.00 3.33
153 154 8.256356 ACTGAGCTATCCTGACTATTTATTGT 57.744 34.615 0.00 0.00 0.00 2.71
154 155 8.986847 CAACTGAGCTATCCTGACTATTTATTG 58.013 37.037 0.00 0.00 0.00 1.90
155 156 8.153550 CCAACTGAGCTATCCTGACTATTTATT 58.846 37.037 0.00 0.00 0.00 1.40
156 157 7.291182 ACCAACTGAGCTATCCTGACTATTTAT 59.709 37.037 0.00 0.00 0.00 1.40
157 158 6.611642 ACCAACTGAGCTATCCTGACTATTTA 59.388 38.462 0.00 0.00 0.00 1.40
158 159 5.426833 ACCAACTGAGCTATCCTGACTATTT 59.573 40.000 0.00 0.00 0.00 1.40
159 160 4.965532 ACCAACTGAGCTATCCTGACTATT 59.034 41.667 0.00 0.00 0.00 1.73
160 161 4.551671 ACCAACTGAGCTATCCTGACTAT 58.448 43.478 0.00 0.00 0.00 2.12
161 162 3.982516 ACCAACTGAGCTATCCTGACTA 58.017 45.455 0.00 0.00 0.00 2.59
162 163 2.826488 ACCAACTGAGCTATCCTGACT 58.174 47.619 0.00 0.00 0.00 3.41
163 164 3.954904 TCTACCAACTGAGCTATCCTGAC 59.045 47.826 0.00 0.00 0.00 3.51
164 165 4.211125 CTCTACCAACTGAGCTATCCTGA 58.789 47.826 0.00 0.00 0.00 3.86
165 166 4.582701 CTCTACCAACTGAGCTATCCTG 57.417 50.000 0.00 0.00 0.00 3.86
173 174 3.685139 TCCTTTGCTCTACCAACTGAG 57.315 47.619 0.00 0.00 0.00 3.35
174 175 4.041567 TCAATCCTTTGCTCTACCAACTGA 59.958 41.667 0.00 0.00 32.61 3.41
175 176 4.326826 TCAATCCTTTGCTCTACCAACTG 58.673 43.478 0.00 0.00 32.61 3.16
176 177 4.640771 TCAATCCTTTGCTCTACCAACT 57.359 40.909 0.00 0.00 32.61 3.16
177 178 5.705609 TTTCAATCCTTTGCTCTACCAAC 57.294 39.130 0.00 0.00 32.61 3.77
178 179 6.071391 GGATTTTCAATCCTTTGCTCTACCAA 60.071 38.462 8.09 0.00 35.36 3.67
179 180 5.418840 GGATTTTCAATCCTTTGCTCTACCA 59.581 40.000 8.09 0.00 35.36 3.25
180 181 5.654209 AGGATTTTCAATCCTTTGCTCTACC 59.346 40.000 11.63 0.00 45.78 3.18
181 182 6.765915 AGGATTTTCAATCCTTTGCTCTAC 57.234 37.500 11.63 0.00 45.78 2.59
189 190 8.875604 TGGTGACACGAGGATTTTCAATCCTT 62.876 42.308 17.35 3.75 41.65 3.36
190 191 7.496639 TGGTGACACGAGGATTTTCAATCCT 62.497 44.000 16.46 16.46 43.31 3.24
191 192 3.127030 GGTGACACGAGGATTTTCAATCC 59.873 47.826 7.35 7.35 38.47 3.01
192 193 3.751175 TGGTGACACGAGGATTTTCAATC 59.249 43.478 0.00 0.00 33.40 2.67
193 194 3.750371 TGGTGACACGAGGATTTTCAAT 58.250 40.909 0.00 0.00 33.40 2.57
194 195 3.138304 CTGGTGACACGAGGATTTTCAA 58.862 45.455 9.59 0.00 35.60 2.69
195 196 2.104111 ACTGGTGACACGAGGATTTTCA 59.896 45.455 20.07 0.00 35.60 2.69
196 197 2.767505 ACTGGTGACACGAGGATTTTC 58.232 47.619 20.07 0.00 35.60 2.29
197 198 2.930826 ACTGGTGACACGAGGATTTT 57.069 45.000 20.07 0.00 35.60 1.82
198 199 2.104111 TGAACTGGTGACACGAGGATTT 59.896 45.455 20.07 7.04 35.60 2.17
199 200 1.691976 TGAACTGGTGACACGAGGATT 59.308 47.619 20.07 7.70 35.60 3.01
200 201 1.338107 TGAACTGGTGACACGAGGAT 58.662 50.000 20.07 9.68 35.60 3.24
201 202 1.116308 TTGAACTGGTGACACGAGGA 58.884 50.000 20.07 2.92 35.60 3.71
202 203 1.948104 TTTGAACTGGTGACACGAGG 58.052 50.000 20.07 6.13 35.60 4.63
203 204 2.155732 CGATTTGAACTGGTGACACGAG 59.844 50.000 15.28 15.28 35.60 4.18
204 205 2.131972 CGATTTGAACTGGTGACACGA 58.868 47.619 0.00 0.00 35.60 4.35
205 206 1.194547 CCGATTTGAACTGGTGACACG 59.805 52.381 0.00 0.00 35.60 4.49
206 207 1.535462 CCCGATTTGAACTGGTGACAC 59.465 52.381 0.00 0.00 35.60 3.67
207 208 1.142060 ACCCGATTTGAACTGGTGACA 59.858 47.619 0.00 0.00 39.59 3.58
208 209 1.892209 ACCCGATTTGAACTGGTGAC 58.108 50.000 0.00 0.00 0.00 3.67
209 210 2.500229 GAACCCGATTTGAACTGGTGA 58.500 47.619 0.00 0.00 0.00 4.02
210 211 1.539827 GGAACCCGATTTGAACTGGTG 59.460 52.381 0.00 0.00 0.00 4.17
211 212 1.423921 AGGAACCCGATTTGAACTGGT 59.576 47.619 0.00 0.00 0.00 4.00
212 213 1.812571 CAGGAACCCGATTTGAACTGG 59.187 52.381 0.00 0.00 0.00 4.00
213 214 1.812571 CCAGGAACCCGATTTGAACTG 59.187 52.381 0.00 0.00 0.00 3.16
214 215 1.886655 GCCAGGAACCCGATTTGAACT 60.887 52.381 0.00 0.00 0.00 3.01
215 216 0.526211 GCCAGGAACCCGATTTGAAC 59.474 55.000 0.00 0.00 0.00 3.18
216 217 0.111446 TGCCAGGAACCCGATTTGAA 59.889 50.000 0.00 0.00 0.00 2.69
217 218 0.331278 ATGCCAGGAACCCGATTTGA 59.669 50.000 0.00 0.00 0.00 2.69
218 219 1.949525 CTATGCCAGGAACCCGATTTG 59.050 52.381 0.00 0.00 0.00 2.32
219 220 1.843851 TCTATGCCAGGAACCCGATTT 59.156 47.619 0.00 0.00 0.00 2.17
220 221 1.507140 TCTATGCCAGGAACCCGATT 58.493 50.000 0.00 0.00 0.00 3.34
221 222 1.507140 TTCTATGCCAGGAACCCGAT 58.493 50.000 0.00 0.00 0.00 4.18
222 223 1.281419 TTTCTATGCCAGGAACCCGA 58.719 50.000 0.00 0.00 0.00 5.14
223 224 2.122783 TTTTCTATGCCAGGAACCCG 57.877 50.000 0.00 0.00 0.00 5.28
240 241 2.817258 TGGAATTCGGCAGATCGTTTTT 59.183 40.909 0.00 0.00 0.00 1.94
241 242 2.420022 CTGGAATTCGGCAGATCGTTTT 59.580 45.455 5.97 0.00 0.00 2.43
242 243 2.009774 CTGGAATTCGGCAGATCGTTT 58.990 47.619 5.97 0.00 0.00 3.60
243 244 1.066143 ACTGGAATTCGGCAGATCGTT 60.066 47.619 15.93 0.00 0.00 3.85
244 245 0.537188 ACTGGAATTCGGCAGATCGT 59.463 50.000 15.93 0.00 0.00 3.73
245 246 2.509052 TACTGGAATTCGGCAGATCG 57.491 50.000 15.93 0.00 0.00 3.69
246 247 3.002759 GCTTTACTGGAATTCGGCAGATC 59.997 47.826 15.93 0.00 0.00 2.75
247 248 2.945668 GCTTTACTGGAATTCGGCAGAT 59.054 45.455 15.93 5.74 0.00 2.90
248 249 2.356135 GCTTTACTGGAATTCGGCAGA 58.644 47.619 15.93 0.00 0.00 4.26
249 250 1.401905 GGCTTTACTGGAATTCGGCAG 59.598 52.381 9.42 9.42 0.00 4.85
250 251 1.004277 AGGCTTTACTGGAATTCGGCA 59.996 47.619 0.00 0.00 0.00 5.69
251 252 1.751437 AGGCTTTACTGGAATTCGGC 58.249 50.000 0.00 0.00 0.00 5.54
252 253 4.962155 AGATAGGCTTTACTGGAATTCGG 58.038 43.478 0.00 0.00 0.00 4.30
253 254 4.681942 CGAGATAGGCTTTACTGGAATTCG 59.318 45.833 0.00 0.00 0.00 3.34
254 255 4.449405 GCGAGATAGGCTTTACTGGAATTC 59.551 45.833 0.00 0.00 0.00 2.17
255 256 4.101741 AGCGAGATAGGCTTTACTGGAATT 59.898 41.667 0.00 0.00 37.50 2.17
256 257 3.643792 AGCGAGATAGGCTTTACTGGAAT 59.356 43.478 0.00 0.00 37.50 3.01
257 258 3.031736 AGCGAGATAGGCTTTACTGGAA 58.968 45.455 0.00 0.00 37.50 3.53
258 259 2.667470 AGCGAGATAGGCTTTACTGGA 58.333 47.619 0.00 0.00 37.50 3.86
559 561 6.073314 AGGACTCAGTTGTTAGTTAGTACCA 58.927 40.000 0.00 0.00 0.00 3.25
574 576 0.961358 CGGTTCGGAGAGGACTCAGT 60.961 60.000 1.75 0.00 44.22 3.41
660 662 7.414222 TTGTATAGTAAGTGATCCGAACCTT 57.586 36.000 0.00 0.00 0.00 3.50
946 948 1.413808 GGGGAGAGAGTGGAGCCTATT 60.414 57.143 0.00 0.00 0.00 1.73
992 994 0.319900 CGTTATCCCCATCTCAGCCG 60.320 60.000 0.00 0.00 0.00 5.52
1067 1069 4.943705 CCACACTTGGCTCTACACATTTAT 59.056 41.667 0.00 0.00 35.56 1.40
1120 1127 0.033503 TGGAGTGATCCAGTAGCCGA 60.034 55.000 0.00 0.00 34.33 5.54
1495 1502 9.617975 GGCTGATTGCAAAAGATATCTTAATAC 57.382 33.333 18.23 9.08 45.15 1.89
1500 1507 4.343239 GGGGCTGATTGCAAAAGATATCTT 59.657 41.667 12.37 12.37 45.15 2.40
1588 1595 1.842920 TGTGGGAGAGAAGCAGCCA 60.843 57.895 0.00 0.00 0.00 4.75
1600 1607 4.041198 ACGGAGAAATAAAGAAGTGTGGGA 59.959 41.667 0.00 0.00 0.00 4.37
1667 1674 7.468141 AACCCTCCAATGAAGAAATAAGAAC 57.532 36.000 0.00 0.00 0.00 3.01
1668 1675 6.374333 CGAACCCTCCAATGAAGAAATAAGAA 59.626 38.462 0.00 0.00 0.00 2.52
1856 1863 4.671590 TGAGGTGCTCCCCGTCGA 62.672 66.667 0.00 0.00 0.00 4.20
1897 1904 4.224762 GCCTTAGGTGTAATAGGACTCCT 58.775 47.826 2.31 2.31 43.86 3.69
1971 1978 3.506455 CCGTCGACTCCATATCCTTGTAT 59.494 47.826 14.70 0.00 0.00 2.29
2130 2137 1.188863 AGCGTTATAGGTCGTTGGGT 58.811 50.000 0.00 0.00 0.00 4.51
2248 2255 8.100164 TCTCCATTACAATGTTCTCATACACAA 58.900 33.333 0.00 0.00 34.60 3.33
2251 2258 7.770433 CCTTCTCCATTACAATGTTCTCATACA 59.230 37.037 0.00 0.00 34.60 2.29
2428 2435 5.191727 TGGTTTCTCATGTGGAACCATAT 57.808 39.130 28.95 0.00 34.36 1.78
2572 2579 5.992217 GCTTCCTATGAGGGTACATTACAAG 59.008 44.000 0.00 0.00 35.59 3.16
2586 2593 6.092122 CGTGTTTCTATTGTTGCTTCCTATGA 59.908 38.462 0.00 0.00 0.00 2.15
2761 2768 4.538089 GGGGCCCTATCTATTCAATCTCTT 59.462 45.833 24.38 0.00 0.00 2.85
2801 2808 0.109532 TTGTGTGAATTCCCCAGCGA 59.890 50.000 2.27 0.00 0.00 4.93
2864 2871 5.715070 TGATGGAAAACAACTTTCACGTTT 58.285 33.333 0.00 0.00 44.61 3.60


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

AutoCloner maintained by Alex Coulton.