Multiple sequence alignment - TraesCS4D01G281200

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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 TraesCS4D01G281200 chr4D 100.000 2634 0 0 658 3291 452383522 452386155 0.000000e+00 4865.0
1 TraesCS4D01G281200 chr4D 84.801 2316 264 43 986 3245 452312611 452314894 0.000000e+00 2246.0
2 TraesCS4D01G281200 chr4D 100.000 331 0 0 1 331 452382865 452383195 2.170000e-171 612.0
3 TraesCS4D01G281200 chr4D 78.711 512 86 8 1667 2165 452548853 452549354 1.470000e-83 320.0
4 TraesCS4D01G281200 chr4D 88.043 276 17 9 1 261 439296207 439295933 2.470000e-81 313.0
5 TraesCS4D01G281200 chr4B 92.215 2235 105 28 794 3000 565602372 565604565 0.000000e+00 3099.0
6 TraesCS4D01G281200 chr4B 85.153 2317 244 48 996 3245 565527038 565529321 0.000000e+00 2281.0
7 TraesCS4D01G281200 chr4A 93.666 1342 65 9 658 1989 14744947 14743616 0.000000e+00 1989.0
8 TraesCS4D01G281200 chr4A 90.580 1242 63 24 2070 3291 14738769 14737562 0.000000e+00 1596.0
9 TraesCS4D01G281200 chr4A 79.183 514 80 13 1667 2165 14358255 14357754 6.810000e-87 331.0
10 TraesCS4D01G281200 chr3A 80.448 982 161 22 828 1801 23671051 23670093 0.000000e+00 721.0
11 TraesCS4D01G281200 chr3A 77.812 987 195 18 816 1799 23725651 23724686 3.660000e-164 588.0
12 TraesCS4D01G281200 chr3A 77.947 984 185 22 828 1800 23691743 23690781 1.320000e-163 586.0
13 TraesCS4D01G281200 chr3A 78.579 901 169 18 907 1798 23700631 23699746 1.020000e-159 573.0
14 TraesCS4D01G281200 chr3D 80.224 981 171 16 816 1793 13334477 13335437 0.000000e+00 715.0
15 TraesCS4D01G281200 chr3D 79.859 993 151 26 816 1801 13335690 13336640 0.000000e+00 680.0
16 TraesCS4D01G281200 chr3B 80.179 782 152 3 1019 1800 19370592 19371370 1.700000e-162 582.0
17 TraesCS4D01G281200 chr6B 84.249 273 25 11 5 262 22660947 22661216 1.960000e-62 250.0
18 TraesCS4D01G281200 chr5B 95.745 47 2 0 217 263 571197939 571197893 3.520000e-10 76.8


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 TraesCS4D01G281200 chr4D 452382865 452386155 3290 False 2738.5 4865 100.0000 1 3291 2 chr4D.!!$F3 3290
1 TraesCS4D01G281200 chr4D 452312611 452314894 2283 False 2246.0 2246 84.8010 986 3245 1 chr4D.!!$F1 2259
2 TraesCS4D01G281200 chr4D 452548853 452549354 501 False 320.0 320 78.7110 1667 2165 1 chr4D.!!$F2 498
3 TraesCS4D01G281200 chr4B 565602372 565604565 2193 False 3099.0 3099 92.2150 794 3000 1 chr4B.!!$F2 2206
4 TraesCS4D01G281200 chr4B 565527038 565529321 2283 False 2281.0 2281 85.1530 996 3245 1 chr4B.!!$F1 2249
5 TraesCS4D01G281200 chr4A 14743616 14744947 1331 True 1989.0 1989 93.6660 658 1989 1 chr4A.!!$R3 1331
6 TraesCS4D01G281200 chr4A 14737562 14738769 1207 True 1596.0 1596 90.5800 2070 3291 1 chr4A.!!$R2 1221
7 TraesCS4D01G281200 chr4A 14357754 14358255 501 True 331.0 331 79.1830 1667 2165 1 chr4A.!!$R1 498
8 TraesCS4D01G281200 chr3A 23670093 23671051 958 True 721.0 721 80.4480 828 1801 1 chr3A.!!$R1 973
9 TraesCS4D01G281200 chr3A 23724686 23725651 965 True 588.0 588 77.8120 816 1799 1 chr3A.!!$R4 983
10 TraesCS4D01G281200 chr3A 23690781 23691743 962 True 586.0 586 77.9470 828 1800 1 chr3A.!!$R2 972
11 TraesCS4D01G281200 chr3A 23699746 23700631 885 True 573.0 573 78.5790 907 1798 1 chr3A.!!$R3 891
12 TraesCS4D01G281200 chr3D 13334477 13336640 2163 False 697.5 715 80.0415 816 1801 2 chr3D.!!$F1 985
13 TraesCS4D01G281200 chr3B 19370592 19371370 778 False 582.0 582 80.1790 1019 1800 1 chr3B.!!$F1 781

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
170 171 0.250234 TTCAGATCCTGTGCGAAGGG 59.750 55.0 4.76 0.00 37.96 3.95 F
219 220 0.457853 TCAGATGGTAGCGCAACGAC 60.458 55.0 11.47 1.14 0.00 4.34 F
232 233 0.665972 CAACGACCGGCCCAAATTTG 60.666 55.0 11.40 11.40 0.00 2.32 F
277 278 0.751643 GCCCAGTTCCCGCACATAAT 60.752 55.0 0.00 0.00 0.00 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2453 1.082366 CCTTTCGCGAAACCAACCG 60.082 57.895 29.22 18.06 0.00 4.44 R
2133 2580 5.004448 CGAGTGTAGAAGCTCATATAGGGA 58.996 45.833 0.00 0.00 0.00 4.20 R
2182 2629 7.041372 AGCAAACATATGAAAGTTTACACGTCT 60.041 33.333 10.38 0.00 36.28 4.18 R
2368 2844 7.654116 GTCAGAGATTAACCAAATAGAGCCTAC 59.346 40.741 0.00 0.00 0.00 3.18 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
24 25 7.878547 ATGATGTTTTGTTTTTGTTGGGATT 57.121 28.000 0.00 0.00 0.00 3.01
25 26 7.693969 TGATGTTTTGTTTTTGTTGGGATTT 57.306 28.000 0.00 0.00 0.00 2.17
26 27 8.115490 TGATGTTTTGTTTTTGTTGGGATTTT 57.885 26.923 0.00 0.00 0.00 1.82
27 28 8.579863 TGATGTTTTGTTTTTGTTGGGATTTTT 58.420 25.926 0.00 0.00 0.00 1.94
28 29 8.978564 ATGTTTTGTTTTTGTTGGGATTTTTC 57.021 26.923 0.00 0.00 0.00 2.29
29 30 8.171164 TGTTTTGTTTTTGTTGGGATTTTTCT 57.829 26.923 0.00 0.00 0.00 2.52
30 31 8.633561 TGTTTTGTTTTTGTTGGGATTTTTCTT 58.366 25.926 0.00 0.00 0.00 2.52
31 32 8.910666 GTTTTGTTTTTGTTGGGATTTTTCTTG 58.089 29.630 0.00 0.00 0.00 3.02
32 33 6.188400 TGTTTTTGTTGGGATTTTTCTTGC 57.812 33.333 0.00 0.00 0.00 4.01
35 36 7.279758 TGTTTTTGTTGGGATTTTTCTTGCTAG 59.720 33.333 0.00 0.00 0.00 3.42
36 37 5.467035 TTGTTGGGATTTTTCTTGCTAGG 57.533 39.130 0.00 0.00 0.00 3.02
37 38 4.735369 TGTTGGGATTTTTCTTGCTAGGA 58.265 39.130 0.00 0.00 0.00 2.94
38 39 5.144100 TGTTGGGATTTTTCTTGCTAGGAA 58.856 37.500 0.00 0.00 0.00 3.36
39 40 5.600484 TGTTGGGATTTTTCTTGCTAGGAAA 59.400 36.000 0.00 0.00 0.00 3.13
40 41 5.722021 TGGGATTTTTCTTGCTAGGAAAC 57.278 39.130 0.68 0.00 33.22 2.78
41 42 5.144100 TGGGATTTTTCTTGCTAGGAAACA 58.856 37.500 0.68 0.00 33.22 2.83
43 44 5.010617 GGGATTTTTCTTGCTAGGAAACACA 59.989 40.000 0.68 0.00 33.22 3.72
45 46 6.239036 GGATTTTTCTTGCTAGGAAACACAGT 60.239 38.462 0.68 0.00 33.22 3.55
47 48 3.126001 TCTTGCTAGGAAACACAGTGG 57.874 47.619 5.31 0.00 0.00 4.00
48 49 1.537202 CTTGCTAGGAAACACAGTGGC 59.463 52.381 5.31 0.00 0.00 5.01
50 51 1.298859 GCTAGGAAACACAGTGGCCG 61.299 60.000 5.31 0.00 0.00 6.13
51 52 0.320374 CTAGGAAACACAGTGGCCGA 59.680 55.000 5.31 0.00 0.00 5.54
53 54 0.606401 AGGAAACACAGTGGCCGATG 60.606 55.000 5.31 1.00 0.00 3.84
54 55 0.605319 GGAAACACAGTGGCCGATGA 60.605 55.000 13.56 0.00 0.00 2.92
55 56 0.517316 GAAACACAGTGGCCGATGAC 59.483 55.000 13.56 0.00 0.00 3.06
57 58 2.094757 AACACAGTGGCCGATGACGA 62.095 55.000 13.56 0.00 42.66 4.20
58 59 2.094659 CACAGTGGCCGATGACGAC 61.095 63.158 13.56 0.00 42.66 4.34
59 60 2.261361 CAGTGGCCGATGACGACA 59.739 61.111 0.00 0.00 42.66 4.35
61 62 1.374252 AGTGGCCGATGACGACAAC 60.374 57.895 0.00 0.00 42.66 3.32
62 63 2.431771 TGGCCGATGACGACAACG 60.432 61.111 10.27 10.27 42.66 4.10
63 64 2.126228 GGCCGATGACGACAACGA 60.126 61.111 17.82 0.00 43.20 3.85
66 67 2.497092 CCGATGACGACAACGAGCG 61.497 63.158 17.82 5.13 43.20 5.03
68 69 1.154093 GATGACGACAACGAGCGGA 60.154 57.895 0.00 0.00 42.66 5.54
69 70 1.134530 GATGACGACAACGAGCGGAG 61.135 60.000 0.00 0.00 42.66 4.63
70 71 2.504244 GACGACAACGAGCGGAGG 60.504 66.667 0.00 0.00 42.66 4.30
91 92 4.477975 CGACGGGCGACTCAGGTC 62.478 72.222 0.00 0.00 44.57 3.85
119 120 2.760385 GTGGGAGACGAGGGGAGG 60.760 72.222 0.00 0.00 0.00 4.30
121 122 2.363361 GGGAGACGAGGGGAGGAA 59.637 66.667 0.00 0.00 0.00 3.36
125 126 4.493747 GACGAGGGGAGGAACGCG 62.494 72.222 3.53 3.53 36.00 6.01
143 144 2.593436 CCGGCCGGTTGTTGACTT 60.593 61.111 36.64 0.00 0.00 3.01
144 145 2.613506 CCGGCCGGTTGTTGACTTC 61.614 63.158 36.64 0.00 0.00 3.01
145 146 1.597027 CGGCCGGTTGTTGACTTCT 60.597 57.895 20.10 0.00 0.00 2.85
146 147 1.164041 CGGCCGGTTGTTGACTTCTT 61.164 55.000 20.10 0.00 0.00 2.52
147 148 1.029681 GGCCGGTTGTTGACTTCTTT 58.970 50.000 1.90 0.00 0.00 2.52
148 149 1.407618 GGCCGGTTGTTGACTTCTTTT 59.592 47.619 1.90 0.00 0.00 2.27
149 150 2.159156 GGCCGGTTGTTGACTTCTTTTT 60.159 45.455 1.90 0.00 0.00 1.94
169 170 2.099141 TTTCAGATCCTGTGCGAAGG 57.901 50.000 0.00 0.00 38.84 3.46
170 171 0.250234 TTCAGATCCTGTGCGAAGGG 59.750 55.000 4.76 0.00 37.96 3.95
171 172 0.614697 TCAGATCCTGTGCGAAGGGA 60.615 55.000 4.76 0.00 37.96 4.20
175 176 0.984230 ATCCTGTGCGAAGGGAAGAA 59.016 50.000 4.76 0.00 37.96 2.52
177 178 1.291877 CCTGTGCGAAGGGAAGAACG 61.292 60.000 0.00 0.00 33.28 3.95
179 180 2.033194 GTGCGAAGGGAAGAACGGG 61.033 63.158 0.00 0.00 0.00 5.28
180 181 2.211410 TGCGAAGGGAAGAACGGGA 61.211 57.895 0.00 0.00 0.00 5.14
181 182 1.448013 GCGAAGGGAAGAACGGGAG 60.448 63.158 0.00 0.00 0.00 4.30
182 183 1.218316 CGAAGGGAAGAACGGGAGG 59.782 63.158 0.00 0.00 0.00 4.30
183 184 1.255667 CGAAGGGAAGAACGGGAGGA 61.256 60.000 0.00 0.00 0.00 3.71
184 185 0.537653 GAAGGGAAGAACGGGAGGAG 59.462 60.000 0.00 0.00 0.00 3.69
185 186 0.910088 AAGGGAAGAACGGGAGGAGG 60.910 60.000 0.00 0.00 0.00 4.30
187 188 1.199425 GGGAAGAACGGGAGGAGGTT 61.199 60.000 0.00 0.00 0.00 3.50
188 189 0.691332 GGAAGAACGGGAGGAGGTTT 59.309 55.000 0.00 0.00 0.00 3.27
190 191 2.093606 GGAAGAACGGGAGGAGGTTTAG 60.094 54.545 0.00 0.00 0.00 1.85
191 192 2.322339 AGAACGGGAGGAGGTTTAGT 57.678 50.000 0.00 0.00 0.00 2.24
192 193 3.463048 AGAACGGGAGGAGGTTTAGTA 57.537 47.619 0.00 0.00 0.00 1.82
193 194 3.363627 AGAACGGGAGGAGGTTTAGTAG 58.636 50.000 0.00 0.00 0.00 2.57
195 196 1.360507 ACGGGAGGAGGTTTAGTAGGT 59.639 52.381 0.00 0.00 0.00 3.08
197 198 2.622452 CGGGAGGAGGTTTAGTAGGTCA 60.622 54.545 0.00 0.00 0.00 4.02
198 199 3.447950 GGGAGGAGGTTTAGTAGGTCAA 58.552 50.000 0.00 0.00 0.00 3.18
199 200 3.842436 GGGAGGAGGTTTAGTAGGTCAAA 59.158 47.826 0.00 0.00 0.00 2.69
200 201 4.473922 GGGAGGAGGTTTAGTAGGTCAAAT 59.526 45.833 0.00 0.00 0.00 2.32
201 202 5.396548 GGGAGGAGGTTTAGTAGGTCAAATC 60.397 48.000 0.00 0.00 0.00 2.17
202 203 5.189145 GGAGGAGGTTTAGTAGGTCAAATCA 59.811 44.000 0.00 0.00 0.00 2.57
203 204 6.301169 AGGAGGTTTAGTAGGTCAAATCAG 57.699 41.667 0.00 0.00 0.00 2.90
204 205 6.023603 AGGAGGTTTAGTAGGTCAAATCAGA 58.976 40.000 0.00 0.00 0.00 3.27
205 206 6.674419 AGGAGGTTTAGTAGGTCAAATCAGAT 59.326 38.462 0.00 0.00 0.00 2.90
206 207 6.763610 GGAGGTTTAGTAGGTCAAATCAGATG 59.236 42.308 0.00 0.00 0.00 2.90
207 208 6.653989 AGGTTTAGTAGGTCAAATCAGATGG 58.346 40.000 0.00 0.00 0.00 3.51
208 209 6.215636 AGGTTTAGTAGGTCAAATCAGATGGT 59.784 38.462 0.00 0.00 0.00 3.55
210 211 7.711339 GGTTTAGTAGGTCAAATCAGATGGTAG 59.289 40.741 0.00 0.00 0.00 3.18
211 212 5.283457 AGTAGGTCAAATCAGATGGTAGC 57.717 43.478 0.00 0.00 0.00 3.58
213 214 1.599542 GGTCAAATCAGATGGTAGCGC 59.400 52.381 0.00 0.00 0.00 5.92
214 215 2.279741 GTCAAATCAGATGGTAGCGCA 58.720 47.619 11.47 0.00 0.00 6.09
215 216 2.677836 GTCAAATCAGATGGTAGCGCAA 59.322 45.455 11.47 0.00 0.00 4.85
216 217 2.677836 TCAAATCAGATGGTAGCGCAAC 59.322 45.455 11.47 0.00 0.00 4.17
217 218 1.290203 AATCAGATGGTAGCGCAACG 58.710 50.000 11.47 0.00 0.00 4.10
218 219 0.459899 ATCAGATGGTAGCGCAACGA 59.540 50.000 11.47 0.00 0.00 3.85
219 220 0.457853 TCAGATGGTAGCGCAACGAC 60.458 55.000 11.47 1.14 0.00 4.34
220 221 1.153628 AGATGGTAGCGCAACGACC 60.154 57.895 11.47 12.02 43.94 4.79
221 222 2.508439 ATGGTAGCGCAACGACCG 60.508 61.111 11.47 0.00 46.47 4.79
222 223 4.728102 TGGTAGCGCAACGACCGG 62.728 66.667 11.47 0.00 46.47 5.28
229 230 3.370231 GCAACGACCGGCCCAAAT 61.370 61.111 0.00 0.00 0.00 2.32
230 231 2.926420 GCAACGACCGGCCCAAATT 61.926 57.895 0.00 0.00 0.00 1.82
232 233 0.665972 CAACGACCGGCCCAAATTTG 60.666 55.000 11.40 11.40 0.00 2.32
233 234 0.824182 AACGACCGGCCCAAATTTGA 60.824 50.000 19.86 0.00 0.00 2.69
234 235 1.241315 ACGACCGGCCCAAATTTGAG 61.241 55.000 19.86 7.62 0.00 3.02
235 236 1.215382 GACCGGCCCAAATTTGAGC 59.785 57.895 19.86 17.73 0.00 4.26
238 239 2.578664 GGCCCAAATTTGAGCCGG 59.421 61.111 25.52 15.72 42.28 6.13
242 243 2.875711 CAAATTTGAGCCGGCGCG 60.876 61.111 25.44 0.00 41.18 6.86
243 244 4.776647 AAATTTGAGCCGGCGCGC 62.777 61.111 25.94 25.94 41.18 6.86
267 268 3.842869 CAGAGTACTGCCCAGTTCC 57.157 57.895 0.00 0.00 42.54 3.62
270 271 2.436115 GTACTGCCCAGTTCCCGC 60.436 66.667 6.21 0.00 42.54 6.13
271 272 2.925706 TACTGCCCAGTTCCCGCA 60.926 61.111 6.21 0.00 42.54 5.69
274 275 3.925630 CTGCCCAGTTCCCGCACAT 62.926 63.158 0.00 0.00 0.00 3.21
275 276 2.270850 GCCCAGTTCCCGCACATA 59.729 61.111 0.00 0.00 0.00 2.29
276 277 1.377987 GCCCAGTTCCCGCACATAA 60.378 57.895 0.00 0.00 0.00 1.90
277 278 0.751643 GCCCAGTTCCCGCACATAAT 60.752 55.000 0.00 0.00 0.00 1.28
279 280 1.676006 CCCAGTTCCCGCACATAATTC 59.324 52.381 0.00 0.00 0.00 2.17
281 282 2.643551 CAGTTCCCGCACATAATTCCT 58.356 47.619 0.00 0.00 0.00 3.36
282 283 3.433031 CCAGTTCCCGCACATAATTCCTA 60.433 47.826 0.00 0.00 0.00 2.94
283 284 4.389374 CAGTTCCCGCACATAATTCCTAT 58.611 43.478 0.00 0.00 0.00 2.57
284 285 5.512404 CCAGTTCCCGCACATAATTCCTATA 60.512 44.000 0.00 0.00 0.00 1.31
286 287 7.327975 CAGTTCCCGCACATAATTCCTATATA 58.672 38.462 0.00 0.00 0.00 0.86
288 289 8.548877 AGTTCCCGCACATAATTCCTATATATT 58.451 33.333 0.00 0.00 0.00 1.28
289 290 9.826574 GTTCCCGCACATAATTCCTATATATTA 57.173 33.333 0.00 0.00 0.00 0.98
323 324 8.538409 AATACCAAGCAAATGATTCAAACTTC 57.462 30.769 0.00 0.00 0.00 3.01
325 326 4.692155 CCAAGCAAATGATTCAAACTTCCC 59.308 41.667 0.00 0.00 0.00 3.97
327 328 6.295236 CCAAGCAAATGATTCAAACTTCCCTA 60.295 38.462 0.00 0.00 0.00 3.53
328 329 6.916360 AGCAAATGATTCAAACTTCCCTAA 57.084 33.333 0.00 0.00 0.00 2.69
329 330 7.301868 AGCAAATGATTCAAACTTCCCTAAA 57.698 32.000 0.00 0.00 0.00 1.85
330 331 7.734942 AGCAAATGATTCAAACTTCCCTAAAA 58.265 30.769 0.00 0.00 0.00 1.52
748 749 2.299013 ACGGCATCTCTAACTGTTGTCA 59.701 45.455 2.69 0.00 0.00 3.58
764 765 3.781307 CAGAACGGGCCCCATCGA 61.781 66.667 18.66 0.00 0.00 3.59
848 1248 2.215478 CTGTTCGTTCGAGGCAAGCG 62.215 60.000 0.00 0.00 0.00 4.68
872 1272 3.984749 GCGGCGCCCCTTTTTCAA 61.985 61.111 23.58 0.00 0.00 2.69
1163 1573 4.840005 CCCCGCCTTCCTTCGCTC 62.840 72.222 0.00 0.00 0.00 5.03
1563 1975 2.094182 GGTAGAGAAGACCATGTTCGCA 60.094 50.000 0.00 0.00 36.91 5.10
1986 2427 1.414181 CTCTCGTGGATGGTAGGCAAT 59.586 52.381 0.00 0.00 0.00 3.56
2012 2453 0.966875 TTGGATGGCAGATGCACACC 60.967 55.000 7.19 6.77 44.36 4.16
2133 2580 1.270907 AGACCTTCGAGCCAGTCATT 58.729 50.000 8.34 0.00 0.00 2.57
2153 2600 7.039363 AGTCATTCCCTATATGAGCTTCTACAC 60.039 40.741 0.00 0.00 32.96 2.90
2177 2624 9.217278 CACTCGAGGTACTATATAGCTTCTTTA 57.783 37.037 18.41 0.00 41.55 1.85
2336 2806 8.221251 TGTCTTATTTTACCATACCATATGGCA 58.779 33.333 22.18 9.77 42.82 4.92
2368 2844 4.186077 TCCACTAGGGTCTCTAATCCAG 57.814 50.000 0.00 0.00 38.11 3.86
2417 2908 4.853468 TGGGTTAGATAACATGGCAGAA 57.147 40.909 0.00 0.00 37.92 3.02
2500 3006 5.230726 CAGTCTGATCACAAAACTTGTTTGC 59.769 40.000 0.00 0.00 43.23 3.68
2593 3101 1.153229 GTACCGATGGTCAAGCCCC 60.153 63.158 0.00 0.00 37.09 5.80
2627 3135 8.576936 AGAGTTTTCTTTAACTAAGACTGACG 57.423 34.615 0.00 0.00 42.50 4.35
2726 3234 3.255642 TGACCAGCAAGGATTTTGTAAGC 59.744 43.478 1.83 0.00 41.22 3.09
2768 3279 4.142816 GCTCATTAGCGGCGATAATCAAAT 60.143 41.667 25.63 5.84 39.39 2.32
2921 3440 6.865726 TGTGCAAGTAACAAATTTATTGCGAT 59.134 30.769 14.24 0.00 44.49 4.58
3164 3685 8.403236 ACAATTTTCTTGGTACTGACTACAAAC 58.597 33.333 0.00 0.00 0.00 2.93
3248 3771 4.816392 ACGGATATCCAAAACCAAAAAGC 58.184 39.130 21.70 0.00 35.14 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.878547 AATCCCAACAAAAACAAAACATCAT 57.121 28.000 0.00 0.00 0.00 2.45
2 3 8.978564 AAAAATCCCAACAAAAACAAAACATC 57.021 26.923 0.00 0.00 0.00 3.06
4 5 8.171164 AGAAAAATCCCAACAAAAACAAAACA 57.829 26.923 0.00 0.00 0.00 2.83
5 6 8.910666 CAAGAAAAATCCCAACAAAAACAAAAC 58.089 29.630 0.00 0.00 0.00 2.43
6 7 7.596621 GCAAGAAAAATCCCAACAAAAACAAAA 59.403 29.630 0.00 0.00 0.00 2.44
8 9 6.432472 AGCAAGAAAAATCCCAACAAAAACAA 59.568 30.769 0.00 0.00 0.00 2.83
9 10 5.942826 AGCAAGAAAAATCCCAACAAAAACA 59.057 32.000 0.00 0.00 0.00 2.83
10 11 6.435430 AGCAAGAAAAATCCCAACAAAAAC 57.565 33.333 0.00 0.00 0.00 2.43
11 12 6.765512 CCTAGCAAGAAAAATCCCAACAAAAA 59.234 34.615 0.00 0.00 0.00 1.94
13 14 5.600484 TCCTAGCAAGAAAAATCCCAACAAA 59.400 36.000 0.00 0.00 0.00 2.83
14 15 5.144100 TCCTAGCAAGAAAAATCCCAACAA 58.856 37.500 0.00 0.00 0.00 2.83
19 20 5.010617 TGTGTTTCCTAGCAAGAAAAATCCC 59.989 40.000 0.00 0.00 35.13 3.85
21 22 6.638468 CACTGTGTTTCCTAGCAAGAAAAATC 59.362 38.462 0.00 0.00 35.13 2.17
22 23 6.461509 CCACTGTGTTTCCTAGCAAGAAAAAT 60.462 38.462 7.08 0.00 35.13 1.82
24 25 4.338118 CCACTGTGTTTCCTAGCAAGAAAA 59.662 41.667 7.08 0.00 35.13 2.29
25 26 3.882888 CCACTGTGTTTCCTAGCAAGAAA 59.117 43.478 7.08 0.00 0.00 2.52
26 27 3.476552 CCACTGTGTTTCCTAGCAAGAA 58.523 45.455 7.08 0.00 0.00 2.52
27 28 2.810400 GCCACTGTGTTTCCTAGCAAGA 60.810 50.000 7.08 0.00 0.00 3.02
28 29 1.537202 GCCACTGTGTTTCCTAGCAAG 59.463 52.381 7.08 0.00 0.00 4.01
29 30 1.604604 GCCACTGTGTTTCCTAGCAA 58.395 50.000 7.08 0.00 0.00 3.91
30 31 0.250727 GGCCACTGTGTTTCCTAGCA 60.251 55.000 7.08 0.00 0.00 3.49
31 32 1.298859 CGGCCACTGTGTTTCCTAGC 61.299 60.000 2.24 0.85 0.00 3.42
32 33 0.320374 TCGGCCACTGTGTTTCCTAG 59.680 55.000 2.24 0.00 0.00 3.02
35 36 0.605319 TCATCGGCCACTGTGTTTCC 60.605 55.000 2.24 4.23 0.00 3.13
36 37 0.517316 GTCATCGGCCACTGTGTTTC 59.483 55.000 2.24 0.00 0.00 2.78
37 38 1.227999 CGTCATCGGCCACTGTGTTT 61.228 55.000 2.24 0.00 0.00 2.83
38 39 1.667830 CGTCATCGGCCACTGTGTT 60.668 57.895 2.24 0.00 0.00 3.32
39 40 2.048222 CGTCATCGGCCACTGTGT 60.048 61.111 2.24 0.00 0.00 3.72
40 41 2.094659 GTCGTCATCGGCCACTGTG 61.095 63.158 2.24 0.00 35.48 3.66
41 42 2.094757 TTGTCGTCATCGGCCACTGT 62.095 55.000 2.24 0.00 41.33 3.55
43 44 1.374252 GTTGTCGTCATCGGCCACT 60.374 57.895 2.24 0.00 41.33 4.00
45 46 2.431771 CGTTGTCGTCATCGGCCA 60.432 61.111 2.24 0.00 41.33 5.36
47 48 2.789203 GCTCGTTGTCGTCATCGGC 61.789 63.158 12.02 10.54 42.45 5.54
48 49 2.497092 CGCTCGTTGTCGTCATCGG 61.497 63.158 12.02 5.60 37.37 4.18
50 51 1.134530 CTCCGCTCGTTGTCGTCATC 61.135 60.000 0.00 0.00 38.33 2.92
51 52 1.154016 CTCCGCTCGTTGTCGTCAT 60.154 57.895 0.00 0.00 38.33 3.06
53 54 2.504244 CCTCCGCTCGTTGTCGTC 60.504 66.667 0.00 0.00 38.33 4.20
54 55 4.719369 GCCTCCGCTCGTTGTCGT 62.719 66.667 0.00 0.00 38.33 4.34
74 75 4.477975 GACCTGAGTCGCCCGTCG 62.478 72.222 0.00 0.00 40.15 5.12
102 103 2.760385 CCTCCCCTCGTCTCCCAC 60.760 72.222 0.00 0.00 0.00 4.61
104 105 2.059190 GTTCCTCCCCTCGTCTCCC 61.059 68.421 0.00 0.00 0.00 4.30
105 106 2.416432 CGTTCCTCCCCTCGTCTCC 61.416 68.421 0.00 0.00 0.00 3.71
106 107 3.066233 GCGTTCCTCCCCTCGTCTC 62.066 68.421 0.00 0.00 0.00 3.36
107 108 3.069318 GCGTTCCTCCCCTCGTCT 61.069 66.667 0.00 0.00 0.00 4.18
108 109 4.493747 CGCGTTCCTCCCCTCGTC 62.494 72.222 0.00 0.00 0.00 4.20
126 127 2.593436 AAGTCAACAACCGGCCGG 60.593 61.111 42.17 42.17 42.03 6.13
127 128 1.164041 AAGAAGTCAACAACCGGCCG 61.164 55.000 21.04 21.04 0.00 6.13
128 129 1.029681 AAAGAAGTCAACAACCGGCC 58.970 50.000 0.00 0.00 0.00 6.13
148 149 2.813754 CCTTCGCACAGGATCTGAAAAA 59.186 45.455 1.59 0.00 35.71 1.94
149 150 2.426522 CCTTCGCACAGGATCTGAAAA 58.573 47.619 1.59 0.00 35.71 2.29
150 151 1.339055 CCCTTCGCACAGGATCTGAAA 60.339 52.381 1.59 0.00 35.71 2.69
152 153 0.614697 TCCCTTCGCACAGGATCTGA 60.615 55.000 1.59 0.00 35.71 3.27
153 154 0.250234 TTCCCTTCGCACAGGATCTG 59.750 55.000 0.00 0.00 35.71 2.90
154 155 0.539051 CTTCCCTTCGCACAGGATCT 59.461 55.000 0.00 0.00 35.71 2.75
155 156 0.537188 TCTTCCCTTCGCACAGGATC 59.463 55.000 0.00 0.00 35.71 3.36
156 157 0.984230 TTCTTCCCTTCGCACAGGAT 59.016 50.000 0.00 0.00 35.71 3.24
157 158 0.034896 GTTCTTCCCTTCGCACAGGA 59.965 55.000 0.00 0.00 35.71 3.86
159 160 1.291877 CCGTTCTTCCCTTCGCACAG 61.292 60.000 0.00 0.00 0.00 3.66
160 161 1.301401 CCGTTCTTCCCTTCGCACA 60.301 57.895 0.00 0.00 0.00 4.57
161 162 2.033194 CCCGTTCTTCCCTTCGCAC 61.033 63.158 0.00 0.00 0.00 5.34
162 163 2.167398 CTCCCGTTCTTCCCTTCGCA 62.167 60.000 0.00 0.00 0.00 5.10
163 164 1.448013 CTCCCGTTCTTCCCTTCGC 60.448 63.158 0.00 0.00 0.00 4.70
165 166 0.537653 CTCCTCCCGTTCTTCCCTTC 59.462 60.000 0.00 0.00 0.00 3.46
166 167 0.910088 CCTCCTCCCGTTCTTCCCTT 60.910 60.000 0.00 0.00 0.00 3.95
168 169 1.199425 AACCTCCTCCCGTTCTTCCC 61.199 60.000 0.00 0.00 0.00 3.97
169 170 0.691332 AAACCTCCTCCCGTTCTTCC 59.309 55.000 0.00 0.00 0.00 3.46
170 171 2.566279 ACTAAACCTCCTCCCGTTCTTC 59.434 50.000 0.00 0.00 0.00 2.87
171 172 2.617658 ACTAAACCTCCTCCCGTTCTT 58.382 47.619 0.00 0.00 0.00 2.52
175 176 1.360507 ACCTACTAAACCTCCTCCCGT 59.639 52.381 0.00 0.00 0.00 5.28
177 178 3.111741 TGACCTACTAAACCTCCTCCC 57.888 52.381 0.00 0.00 0.00 4.30
179 180 6.154706 TCTGATTTGACCTACTAAACCTCCTC 59.845 42.308 0.00 0.00 0.00 3.71
180 181 6.023603 TCTGATTTGACCTACTAAACCTCCT 58.976 40.000 0.00 0.00 0.00 3.69
181 182 6.295719 TCTGATTTGACCTACTAAACCTCC 57.704 41.667 0.00 0.00 0.00 4.30
182 183 6.763610 CCATCTGATTTGACCTACTAAACCTC 59.236 42.308 0.00 0.00 0.00 3.85
183 184 6.215636 ACCATCTGATTTGACCTACTAAACCT 59.784 38.462 0.00 0.00 0.00 3.50
184 185 6.415573 ACCATCTGATTTGACCTACTAAACC 58.584 40.000 0.00 0.00 0.00 3.27
185 186 7.224949 GCTACCATCTGATTTGACCTACTAAAC 59.775 40.741 0.00 0.00 0.00 2.01
187 188 6.461092 CGCTACCATCTGATTTGACCTACTAA 60.461 42.308 0.00 0.00 0.00 2.24
188 189 5.009710 CGCTACCATCTGATTTGACCTACTA 59.990 44.000 0.00 0.00 0.00 1.82
190 191 4.051922 CGCTACCATCTGATTTGACCTAC 58.948 47.826 0.00 0.00 0.00 3.18
191 192 3.492656 GCGCTACCATCTGATTTGACCTA 60.493 47.826 0.00 0.00 0.00 3.08
192 193 2.743183 GCGCTACCATCTGATTTGACCT 60.743 50.000 0.00 0.00 0.00 3.85
193 194 1.599542 GCGCTACCATCTGATTTGACC 59.400 52.381 0.00 0.00 0.00 4.02
195 196 2.677836 GTTGCGCTACCATCTGATTTGA 59.322 45.455 11.09 0.00 0.00 2.69
197 198 1.665679 CGTTGCGCTACCATCTGATTT 59.334 47.619 16.22 0.00 0.00 2.17
198 199 1.134818 TCGTTGCGCTACCATCTGATT 60.135 47.619 16.22 0.00 0.00 2.57
199 200 0.459899 TCGTTGCGCTACCATCTGAT 59.540 50.000 16.22 0.00 0.00 2.90
200 201 0.457853 GTCGTTGCGCTACCATCTGA 60.458 55.000 16.22 4.52 0.00 3.27
201 202 1.421410 GGTCGTTGCGCTACCATCTG 61.421 60.000 16.22 2.09 33.28 2.90
202 203 1.153628 GGTCGTTGCGCTACCATCT 60.154 57.895 16.22 0.00 33.28 2.90
203 204 2.514013 CGGTCGTTGCGCTACCATC 61.514 63.158 16.22 2.89 32.55 3.51
204 205 2.508439 CGGTCGTTGCGCTACCAT 60.508 61.111 16.22 0.00 32.55 3.55
205 206 4.728102 CCGGTCGTTGCGCTACCA 62.728 66.667 16.22 0.00 32.55 3.25
213 214 0.665972 CAAATTTGGGCCGGTCGTTG 60.666 55.000 10.49 0.00 0.00 4.10
214 215 0.824182 TCAAATTTGGGCCGGTCGTT 60.824 50.000 17.90 0.00 0.00 3.85
215 216 1.228306 TCAAATTTGGGCCGGTCGT 60.228 52.632 17.90 0.00 0.00 4.34
216 217 1.506262 CTCAAATTTGGGCCGGTCG 59.494 57.895 17.90 0.00 0.00 4.79
225 226 2.875711 CGCGCCGGCTCAAATTTG 60.876 61.111 26.68 12.15 36.88 2.32
226 227 4.776647 GCGCGCCGGCTCAAATTT 62.777 61.111 26.68 0.00 36.88 1.82
250 251 1.258445 CGGGAACTGGGCAGTACTCT 61.258 60.000 0.00 0.00 41.58 3.24
253 254 2.436115 GCGGGAACTGGGCAGTAC 60.436 66.667 0.00 0.00 41.58 2.73
254 255 2.925706 TGCGGGAACTGGGCAGTA 60.926 61.111 0.00 0.00 41.58 2.74
257 258 2.130821 TTATGTGCGGGAACTGGGCA 62.131 55.000 0.00 0.00 33.56 5.36
258 259 0.751643 ATTATGTGCGGGAACTGGGC 60.752 55.000 0.00 0.00 33.56 5.36
259 260 1.676006 GAATTATGTGCGGGAACTGGG 59.324 52.381 0.00 0.00 33.56 4.45
260 261 1.676006 GGAATTATGTGCGGGAACTGG 59.324 52.381 0.00 0.00 33.56 4.00
263 264 8.732746 AATATATAGGAATTATGTGCGGGAAC 57.267 34.615 0.00 0.00 0.00 3.62
298 299 7.603784 GGAAGTTTGAATCATTTGCTTGGTATT 59.396 33.333 0.00 0.00 0.00 1.89
299 300 7.099120 GGAAGTTTGAATCATTTGCTTGGTAT 58.901 34.615 0.00 0.00 0.00 2.73
301 302 5.299949 GGAAGTTTGAATCATTTGCTTGGT 58.700 37.500 0.00 0.00 0.00 3.67
302 303 4.692155 GGGAAGTTTGAATCATTTGCTTGG 59.308 41.667 0.00 0.00 0.00 3.61
303 304 5.544650 AGGGAAGTTTGAATCATTTGCTTG 58.455 37.500 0.00 0.00 0.00 4.01
304 305 5.813513 AGGGAAGTTTGAATCATTTGCTT 57.186 34.783 0.00 0.00 0.00 3.91
306 307 7.961325 TTTTAGGGAAGTTTGAATCATTTGC 57.039 32.000 0.00 0.00 0.00 3.68
672 673 8.041919 AGTAGTTTACTAAAGAGGAATTGGAGC 58.958 37.037 0.00 0.00 37.23 4.70
732 733 4.322049 CCCGTTCTGACAACAGTTAGAGAT 60.322 45.833 0.00 0.00 43.81 2.75
738 739 0.818040 GGCCCGTTCTGACAACAGTT 60.818 55.000 0.00 0.00 43.81 3.16
748 749 3.470888 CTCGATGGGGCCCGTTCT 61.471 66.667 20.68 2.03 0.00 3.01
764 765 0.035056 AACTGGGCTGCGCTATTTCT 60.035 50.000 17.81 0.00 0.00 2.52
869 1269 2.664851 CGCCCGCTGTTGAGTTGA 60.665 61.111 0.00 0.00 0.00 3.18
870 1270 4.389576 GCGCCCGCTGTTGAGTTG 62.390 66.667 5.27 0.00 38.26 3.16
897 1297 2.354305 GCGGCAGCAATAGCATGC 60.354 61.111 10.51 10.51 46.78 4.06
899 1299 3.282157 CCGCGGCAGCAATAGCAT 61.282 61.111 14.67 0.00 45.49 3.79
1162 1572 2.652095 CGTGAAAGGCCCGGTAGGA 61.652 63.158 0.00 0.00 41.02 2.94
1163 1573 2.125269 CGTGAAAGGCCCGGTAGG 60.125 66.667 0.00 0.00 39.47 3.18
1563 1975 4.985538 AGTCTCGGATGAGTAAACGAAT 57.014 40.909 0.00 0.00 43.09 3.34
1931 2360 4.034975 GGAGAATCTTTTCAAGCTCGATGG 59.965 45.833 0.00 0.00 34.08 3.51
1986 2427 1.213678 CATCTGCCATCCAAGAAGGGA 59.786 52.381 0.00 0.00 42.21 4.20
2012 2453 1.082366 CCTTTCGCGAAACCAACCG 60.082 57.895 29.22 18.06 0.00 4.44
2133 2580 5.004448 CGAGTGTAGAAGCTCATATAGGGA 58.996 45.833 0.00 0.00 0.00 4.20
2182 2629 7.041372 AGCAAACATATGAAAGTTTACACGTCT 60.041 33.333 10.38 0.00 36.28 4.18
2368 2844 7.654116 GTCAGAGATTAACCAAATAGAGCCTAC 59.346 40.741 0.00 0.00 0.00 3.18
2417 2908 5.066505 GGCTGCTAGCAGTTGTTAATATGTT 59.933 40.000 37.91 0.00 44.75 2.71
2470 2975 6.949352 AGTTTTGTGATCAGACTGAAATGT 57.051 33.333 9.70 0.00 0.00 2.71
2500 3006 7.607991 ACTTCTGTACCCAAGAATGATGTTTAG 59.392 37.037 7.68 0.00 0.00 1.85
2548 3056 4.339814 TCAGGTTTTACCGCACTTGATTTT 59.660 37.500 0.00 0.00 44.90 1.82
2549 3057 3.886505 TCAGGTTTTACCGCACTTGATTT 59.113 39.130 0.00 0.00 44.90 2.17
2550 3058 3.482436 TCAGGTTTTACCGCACTTGATT 58.518 40.909 0.00 0.00 44.90 2.57
2551 3059 3.134574 TCAGGTTTTACCGCACTTGAT 57.865 42.857 0.00 0.00 44.90 2.57
2553 3061 3.701532 TTTCAGGTTTTACCGCACTTG 57.298 42.857 0.00 0.00 44.90 3.16
2593 3101 9.777575 TTAGTTAAAGAAAACTCTTTTTGTCCG 57.222 29.630 5.51 0.00 40.20 4.79
2627 3135 7.668525 ACTACTTGCTAGTTTAATTGACCAC 57.331 36.000 6.03 0.00 30.80 4.16
2712 3220 5.106555 CGACATCACTGCTTACAAAATCCTT 60.107 40.000 0.00 0.00 0.00 3.36
2794 3307 6.998673 GCTGGTCCCAATACTATTCTAACAAT 59.001 38.462 0.00 0.00 0.00 2.71
3200 3722 6.183360 ACCTATTTCCATCATAAGTTGCAAGC 60.183 38.462 0.00 0.00 0.00 4.01
3203 3725 6.481976 CGTACCTATTTCCATCATAAGTTGCA 59.518 38.462 0.00 0.00 0.00 4.08
3204 3726 6.073222 CCGTACCTATTTCCATCATAAGTTGC 60.073 42.308 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.