Multiple sequence alignment - TraesCS1D01G321500

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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 TraesCS1D01G321500 chr1D 100.000 2668 0 0 1 2668 414942487 414939820 0.000000e+00 4927.0
1 TraesCS1D01G321500 chr1D 93.228 2348 97 27 337 2668 415054164 415051863 0.000000e+00 3398.0
2 TraesCS1D01G321500 chr1D 87.397 730 67 9 348 1075 415059249 415058543 0.000000e+00 815.0
3 TraesCS1D01G321500 chr1D 86.910 657 54 14 1165 1817 415145637 415145009 0.000000e+00 708.0
4 TraesCS1D01G321500 chr1D 85.981 535 49 9 1262 1796 416986038 416986546 1.400000e-152 549.0
5 TraesCS1D01G321500 chr1D 82.781 453 46 13 641 1061 416985510 416985962 2.510000e-100 375.0
6 TraesCS1D01G321500 chr1D 91.200 125 8 2 2059 2182 415144895 415144773 1.640000e-37 167.0
7 TraesCS1D01G321500 chr1D 93.056 72 5 0 409 480 415146663 415146592 3.630000e-19 106.0
8 TraesCS1D01G321500 chr1A 91.040 1663 74 38 485 2133 511636378 511634777 0.000000e+00 2176.0
9 TraesCS1D01G321500 chr1A 89.332 1706 110 21 337 2031 512040551 512038907 0.000000e+00 2076.0
10 TraesCS1D01G321500 chr1A 91.753 485 40 0 779 1263 512018426 512017942 0.000000e+00 675.0
11 TraesCS1D01G321500 chr1A 85.152 660 59 24 1166 1817 512461289 512460661 8.050000e-180 640.0
12 TraesCS1D01G321500 chr1A 88.825 519 30 13 337 853 511790866 511790374 1.760000e-171 612.0
13 TraesCS1D01G321500 chr1A 90.196 357 23 9 1702 2054 511784853 511784505 3.130000e-124 455.0
14 TraesCS1D01G321500 chr1A 82.540 441 48 11 641 1061 514256959 514257390 7.020000e-96 361.0
15 TraesCS1D01G321500 chr1A 91.393 244 18 1 954 1197 511789919 511789679 5.510000e-87 331.0
16 TraesCS1D01G321500 chr1A 89.604 202 20 1 1 201 511636672 511636471 3.410000e-64 255.0
17 TraesCS1D01G321500 chr1A 87.500 216 13 2 2123 2324 512011647 512011432 1.230000e-58 237.0
18 TraesCS1D01G321500 chr1A 93.578 109 7 0 635 743 512018530 512018422 2.130000e-36 163.0
19 TraesCS1D01G321500 chr1B 89.618 1676 113 26 348 2011 560789546 560787920 0.000000e+00 2074.0
20 TraesCS1D01G321500 chr1B 83.439 785 67 30 1168 1930 561157088 561156345 0.000000e+00 671.0
21 TraesCS1D01G321500 chr1B 85.981 535 56 10 1262 1796 563847816 563848331 3.000000e-154 555.0
22 TraesCS1D01G321500 chr1B 80.504 754 81 28 1173 1916 561256458 561255761 3.940000e-143 518.0
23 TraesCS1D01G321500 chr1B 84.412 340 43 7 2328 2666 595541322 595540992 2.560000e-85 326.0
24 TraesCS1D01G321500 chr1B 84.356 326 39 7 2343 2666 595604868 595604553 2.580000e-80 309.0
25 TraesCS1D01G321500 chr1B 79.505 444 44 18 641 1052 563847319 563847747 3.380000e-69 272.0
26 TraesCS1D01G321500 chr1B 77.947 526 49 29 482 962 561257453 561256950 1.570000e-67 267.0
27 TraesCS1D01G321500 chr1B 86.528 193 17 7 2029 2219 560786348 560786163 1.250000e-48 204.0
28 TraesCS1D01G321500 chr1B 80.162 247 24 11 2030 2272 560787699 560787474 7.640000e-36 161.0
29 TraesCS1D01G321500 chr1B 88.148 135 16 0 67 201 563786829 563786963 7.640000e-36 161.0
30 TraesCS1D01G321500 chr1B 75.714 210 31 9 1 206 561258094 561257901 1.320000e-13 87.9
31 TraesCS1D01G321500 chrUn 85.857 502 47 13 1299 1796 305658876 305659357 1.830000e-141 512.0
32 TraesCS1D01G321500 chrUn 86.957 138 17 1 200 336 335671970 335671833 1.280000e-33 154.0
33 TraesCS1D01G321500 chrUn 75.714 210 31 9 1 206 407336671 407336478 1.320000e-13 87.9
34 TraesCS1D01G321500 chr7D 88.724 337 36 2 2333 2668 41749128 41748793 6.870000e-111 411.0
35 TraesCS1D01G321500 chr5D 86.280 328 40 4 2330 2655 27514153 27514477 4.230000e-93 351.0
36 TraesCS1D01G321500 chr5D 83.686 331 54 0 2336 2666 560011594 560011924 1.990000e-81 313.0
37 TraesCS1D01G321500 chr5D 89.855 138 13 1 200 336 148233695 148233558 2.730000e-40 176.0
38 TraesCS1D01G321500 chr4D 84.985 333 50 0 2334 2666 66549138 66548806 3.290000e-89 339.0
39 TraesCS1D01G321500 chr4A 83.082 331 55 1 2336 2666 604669734 604669405 1.550000e-77 300.0
40 TraesCS1D01G321500 chr2B 82.143 336 56 4 2333 2668 453963062 453962731 4.350000e-73 285.0
41 TraesCS1D01G321500 chr3D 98.333 120 2 0 218 337 7272735 7272854 7.480000e-51 211.0
42 TraesCS1D01G321500 chr2A 90.278 144 13 1 194 336 142699869 142700012 1.260000e-43 187.0
43 TraesCS1D01G321500 chr2A 87.500 144 17 1 198 340 582637479 582637622 5.910000e-37 165.0
44 TraesCS1D01G321500 chr5A 89.583 144 14 1 194 336 640919881 640920024 5.870000e-42 182.0
45 TraesCS1D01G321500 chr5A 89.130 138 14 1 200 336 37144802 37144665 1.270000e-38 171.0
46 TraesCS1D01G321500 chr2D 88.194 144 16 1 198 340 562855029 562854886 1.270000e-38 171.0
47 TraesCS1D01G321500 chr6A 86.806 144 18 1 194 336 603075305 603075448 2.750000e-35 159.0
48 TraesCS1D01G321500 chr3A 77.855 289 33 15 1879 2164 695949809 695949549 1.650000e-32 150.0


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 TraesCS1D01G321500 chr1D 414939820 414942487 2667 True 4927.000000 4927 100.000000 1 2668 1 chr1D.!!$R1 2667
1 TraesCS1D01G321500 chr1D 415051863 415054164 2301 True 3398.000000 3398 93.228000 337 2668 1 chr1D.!!$R2 2331
2 TraesCS1D01G321500 chr1D 415058543 415059249 706 True 815.000000 815 87.397000 348 1075 1 chr1D.!!$R3 727
3 TraesCS1D01G321500 chr1D 416985510 416986546 1036 False 462.000000 549 84.381000 641 1796 2 chr1D.!!$F1 1155
4 TraesCS1D01G321500 chr1D 415144773 415146663 1890 True 327.000000 708 90.388667 409 2182 3 chr1D.!!$R4 1773
5 TraesCS1D01G321500 chr1A 512038907 512040551 1644 True 2076.000000 2076 89.332000 337 2031 1 chr1A.!!$R3 1694
6 TraesCS1D01G321500 chr1A 511634777 511636672 1895 True 1215.500000 2176 90.322000 1 2133 2 chr1A.!!$R5 2132
7 TraesCS1D01G321500 chr1A 512460661 512461289 628 True 640.000000 640 85.152000 1166 1817 1 chr1A.!!$R4 651
8 TraesCS1D01G321500 chr1A 511789679 511790866 1187 True 471.500000 612 90.109000 337 1197 2 chr1A.!!$R6 860
9 TraesCS1D01G321500 chr1A 512017942 512018530 588 True 419.000000 675 92.665500 635 1263 2 chr1A.!!$R7 628
10 TraesCS1D01G321500 chr1B 560786163 560789546 3383 True 813.000000 2074 85.436000 348 2272 3 chr1B.!!$R4 1924
11 TraesCS1D01G321500 chr1B 561156345 561157088 743 True 671.000000 671 83.439000 1168 1930 1 chr1B.!!$R1 762
12 TraesCS1D01G321500 chr1B 563847319 563848331 1012 False 413.500000 555 82.743000 641 1796 2 chr1B.!!$F2 1155
13 TraesCS1D01G321500 chr1B 561255761 561258094 2333 True 290.966667 518 78.055000 1 1916 3 chr1B.!!$R5 1915

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
215 220 0.034863 TTTAGGCCCCGTCAATGTCC 60.035 55.0 0.0 0.0 0.0 4.02 F
231 236 0.107945 GTCCATCCACTCCACTGCTC 60.108 60.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1342 2496 1.153647 GCGACGGTCATGGTGATGA 60.154 57.895 9.1 0.0 36.16 2.92 R
2137 3591 2.358898 ACAAAAATGACGCTGCTGTTCT 59.641 40.909 0.0 0.0 0.00 3.01 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
22 23 4.351938 CCACCGCGAAGACGTCCA 62.352 66.667 13.01 0.00 41.98 4.02
64 69 1.086067 CAGCACATGAAGATCGGCGT 61.086 55.000 6.85 0.00 0.00 5.68
72 77 1.202417 TGAAGATCGGCGTTGGAGATC 60.202 52.381 6.85 0.77 40.61 2.75
82 87 2.166664 GCGTTGGAGATCCTCTTACACT 59.833 50.000 0.00 0.00 36.82 3.55
90 95 5.777732 GGAGATCCTCTTACACTACATCCAT 59.222 44.000 0.00 0.00 0.00 3.41
104 109 7.176515 ACACTACATCCATAGTTGATTTTGCAA 59.823 33.333 0.00 0.00 32.92 4.08
105 110 8.192774 CACTACATCCATAGTTGATTTTGCAAT 58.807 33.333 0.00 0.00 32.92 3.56
109 114 8.199449 ACATCCATAGTTGATTTTGCAATTAGG 58.801 33.333 0.00 0.00 0.00 2.69
129 134 5.738619 AGGCATTGGACATATATACACGA 57.261 39.130 0.00 0.00 0.00 4.35
167 172 6.281405 ACACGATTCTTATTCTGGGTGATAC 58.719 40.000 0.00 0.00 0.00 2.24
196 201 5.693104 TCTCTTGTTTCGCGTATGTAAAGTT 59.307 36.000 5.77 0.00 0.00 2.66
197 202 6.201425 TCTCTTGTTTCGCGTATGTAAAGTTT 59.799 34.615 5.77 0.00 0.00 2.66
198 203 6.717413 TCTTGTTTCGCGTATGTAAAGTTTT 58.283 32.000 5.77 0.00 0.00 2.43
199 204 7.849496 TCTTGTTTCGCGTATGTAAAGTTTTA 58.151 30.769 5.77 0.00 0.00 1.52
200 205 8.005466 TCTTGTTTCGCGTATGTAAAGTTTTAG 58.995 33.333 5.77 0.00 0.00 1.85
201 206 6.592166 TGTTTCGCGTATGTAAAGTTTTAGG 58.408 36.000 5.77 0.00 0.00 2.69
202 207 4.845621 TCGCGTATGTAAAGTTTTAGGC 57.154 40.909 5.77 0.00 0.00 3.93
203 208 3.618150 TCGCGTATGTAAAGTTTTAGGCC 59.382 43.478 5.77 0.00 0.00 5.19
204 209 3.242511 CGCGTATGTAAAGTTTTAGGCCC 60.243 47.826 0.00 0.00 0.00 5.80
205 210 3.065786 GCGTATGTAAAGTTTTAGGCCCC 59.934 47.826 0.00 0.00 0.00 5.80
206 211 3.310501 CGTATGTAAAGTTTTAGGCCCCG 59.689 47.826 0.00 0.00 0.00 5.73
207 212 2.955342 TGTAAAGTTTTAGGCCCCGT 57.045 45.000 0.00 0.00 0.00 5.28
208 213 2.781923 TGTAAAGTTTTAGGCCCCGTC 58.218 47.619 0.00 0.00 0.00 4.79
209 214 2.106166 TGTAAAGTTTTAGGCCCCGTCA 59.894 45.455 0.00 0.00 0.00 4.35
210 215 2.368311 AAAGTTTTAGGCCCCGTCAA 57.632 45.000 0.00 0.00 0.00 3.18
211 216 2.597578 AAGTTTTAGGCCCCGTCAAT 57.402 45.000 0.00 0.00 0.00 2.57
212 217 1.834188 AGTTTTAGGCCCCGTCAATG 58.166 50.000 0.00 0.00 0.00 2.82
213 218 1.074889 AGTTTTAGGCCCCGTCAATGT 59.925 47.619 0.00 0.00 0.00 2.71
214 219 1.471287 GTTTTAGGCCCCGTCAATGTC 59.529 52.381 0.00 0.00 0.00 3.06
215 220 0.034863 TTTAGGCCCCGTCAATGTCC 60.035 55.000 0.00 0.00 0.00 4.02
216 221 1.202099 TTAGGCCCCGTCAATGTCCA 61.202 55.000 0.00 0.00 0.00 4.02
217 222 0.986019 TAGGCCCCGTCAATGTCCAT 60.986 55.000 0.00 0.00 0.00 3.41
218 223 1.823899 GGCCCCGTCAATGTCCATC 60.824 63.158 0.00 0.00 0.00 3.51
219 224 1.823899 GCCCCGTCAATGTCCATCC 60.824 63.158 0.00 0.00 0.00 3.51
220 225 1.607071 CCCCGTCAATGTCCATCCA 59.393 57.895 0.00 0.00 0.00 3.41
221 226 0.748005 CCCCGTCAATGTCCATCCAC 60.748 60.000 0.00 0.00 0.00 4.02
222 227 0.253044 CCCGTCAATGTCCATCCACT 59.747 55.000 0.00 0.00 0.00 4.00
223 228 1.656652 CCGTCAATGTCCATCCACTC 58.343 55.000 0.00 0.00 0.00 3.51
224 229 1.656652 CGTCAATGTCCATCCACTCC 58.343 55.000 0.00 0.00 0.00 3.85
225 230 1.066215 CGTCAATGTCCATCCACTCCA 60.066 52.381 0.00 0.00 0.00 3.86
226 231 2.359900 GTCAATGTCCATCCACTCCAC 58.640 52.381 0.00 0.00 0.00 4.02
227 232 2.026822 GTCAATGTCCATCCACTCCACT 60.027 50.000 0.00 0.00 0.00 4.00
228 233 2.026915 TCAATGTCCATCCACTCCACTG 60.027 50.000 0.00 0.00 0.00 3.66
229 234 0.254178 ATGTCCATCCACTCCACTGC 59.746 55.000 0.00 0.00 0.00 4.40
230 235 0.837691 TGTCCATCCACTCCACTGCT 60.838 55.000 0.00 0.00 0.00 4.24
231 236 0.107945 GTCCATCCACTCCACTGCTC 60.108 60.000 0.00 0.00 0.00 4.26
232 237 1.222936 CCATCCACTCCACTGCTCC 59.777 63.158 0.00 0.00 0.00 4.70
233 238 1.153489 CATCCACTCCACTGCTCCG 60.153 63.158 0.00 0.00 0.00 4.63
234 239 3.023949 ATCCACTCCACTGCTCCGC 62.024 63.158 0.00 0.00 0.00 5.54
235 240 3.699894 CCACTCCACTGCTCCGCT 61.700 66.667 0.00 0.00 0.00 5.52
236 241 2.125753 CACTCCACTGCTCCGCTC 60.126 66.667 0.00 0.00 0.00 5.03
237 242 3.386237 ACTCCACTGCTCCGCTCC 61.386 66.667 0.00 0.00 0.00 4.70
238 243 4.504916 CTCCACTGCTCCGCTCCG 62.505 72.222 0.00 0.00 0.00 4.63
250 255 3.760035 GCTCCGGAAGCGGACAGA 61.760 66.667 5.23 0.00 42.21 3.41
251 256 2.492090 CTCCGGAAGCGGACAGAG 59.508 66.667 5.23 0.00 33.99 3.35
252 257 3.708220 CTCCGGAAGCGGACAGAGC 62.708 68.421 5.23 0.00 33.99 4.09
254 259 2.507992 CGGAAGCGGACAGAGCTG 60.508 66.667 0.00 0.00 45.31 4.24
255 260 2.817396 GGAAGCGGACAGAGCTGC 60.817 66.667 0.00 0.00 45.31 5.25
256 261 2.047844 GAAGCGGACAGAGCTGCA 60.048 61.111 1.02 0.00 45.31 4.41
257 262 2.047465 AAGCGGACAGAGCTGCAG 60.047 61.111 10.11 10.11 45.31 4.41
258 263 2.778309 GAAGCGGACAGAGCTGCAGT 62.778 60.000 16.64 1.59 45.31 4.40
259 264 3.117171 GCGGACAGAGCTGCAGTG 61.117 66.667 16.64 8.48 39.93 3.66
260 265 2.653115 CGGACAGAGCTGCAGTGA 59.347 61.111 16.64 0.00 0.00 3.41
261 266 1.005748 CGGACAGAGCTGCAGTGAA 60.006 57.895 16.64 0.00 0.00 3.18
262 267 0.601046 CGGACAGAGCTGCAGTGAAA 60.601 55.000 16.64 0.00 0.00 2.69
263 268 1.597742 GGACAGAGCTGCAGTGAAAA 58.402 50.000 16.64 0.00 0.00 2.29
264 269 1.534595 GGACAGAGCTGCAGTGAAAAG 59.465 52.381 16.64 3.66 0.00 2.27
265 270 2.216898 GACAGAGCTGCAGTGAAAAGT 58.783 47.619 16.64 6.96 0.00 2.66
266 271 2.216898 ACAGAGCTGCAGTGAAAAGTC 58.783 47.619 16.64 0.00 0.00 3.01
267 272 2.158842 ACAGAGCTGCAGTGAAAAGTCT 60.159 45.455 16.64 0.14 0.00 3.24
268 273 2.877168 CAGAGCTGCAGTGAAAAGTCTT 59.123 45.455 16.64 0.00 0.00 3.01
269 274 2.877168 AGAGCTGCAGTGAAAAGTCTTG 59.123 45.455 16.64 0.00 0.00 3.02
270 275 1.952296 AGCTGCAGTGAAAAGTCTTGG 59.048 47.619 16.64 0.00 0.00 3.61
271 276 1.949525 GCTGCAGTGAAAAGTCTTGGA 59.050 47.619 16.64 0.00 0.00 3.53
272 277 2.031333 GCTGCAGTGAAAAGTCTTGGAG 60.031 50.000 16.64 0.00 33.67 3.86
273 278 1.949525 TGCAGTGAAAAGTCTTGGAGC 59.050 47.619 0.00 0.00 0.00 4.70
274 279 1.069636 GCAGTGAAAAGTCTTGGAGCG 60.070 52.381 0.00 0.00 0.00 5.03
275 280 1.532868 CAGTGAAAAGTCTTGGAGCGG 59.467 52.381 0.00 0.00 0.00 5.52
276 281 0.875059 GTGAAAAGTCTTGGAGCGGG 59.125 55.000 0.00 0.00 0.00 6.13
277 282 0.889186 TGAAAAGTCTTGGAGCGGGC 60.889 55.000 0.00 0.00 0.00 6.13
278 283 0.889186 GAAAAGTCTTGGAGCGGGCA 60.889 55.000 0.00 0.00 0.00 5.36
279 284 0.467290 AAAAGTCTTGGAGCGGGCAA 60.467 50.000 0.00 0.00 0.00 4.52
280 285 0.467290 AAAGTCTTGGAGCGGGCAAA 60.467 50.000 0.00 0.00 0.00 3.68
281 286 0.467290 AAGTCTTGGAGCGGGCAAAA 60.467 50.000 0.00 0.00 0.00 2.44
282 287 1.172812 AGTCTTGGAGCGGGCAAAAC 61.173 55.000 0.00 0.00 0.00 2.43
283 288 2.255252 CTTGGAGCGGGCAAAACG 59.745 61.111 0.00 0.00 0.00 3.60
284 289 2.203224 TTGGAGCGGGCAAAACGA 60.203 55.556 0.00 0.00 0.00 3.85
285 290 2.458006 CTTGGAGCGGGCAAAACGAC 62.458 60.000 0.00 0.00 0.00 4.34
286 291 4.084888 GGAGCGGGCAAAACGACG 62.085 66.667 0.00 0.00 0.00 5.12
290 295 4.084888 CGGGCAAAACGACGCTCC 62.085 66.667 0.00 0.00 0.00 4.70
291 296 4.084888 GGGCAAAACGACGCTCCG 62.085 66.667 0.00 0.00 0.00 4.63
292 297 4.736631 GGCAAAACGACGCTCCGC 62.737 66.667 0.00 0.00 0.00 5.54
293 298 4.007940 GCAAAACGACGCTCCGCA 62.008 61.111 0.00 0.00 0.00 5.69
294 299 2.170985 CAAAACGACGCTCCGCAG 59.829 61.111 0.00 0.00 0.00 5.18
295 300 2.028484 AAAACGACGCTCCGCAGA 59.972 55.556 0.00 0.00 0.00 4.26
296 301 2.308039 AAAACGACGCTCCGCAGAC 61.308 57.895 0.00 0.00 0.00 3.51
297 302 4.719369 AACGACGCTCCGCAGACC 62.719 66.667 0.00 0.00 0.00 3.85
308 313 4.211986 GCAGACCCGCGGATTTTA 57.788 55.556 30.73 0.00 0.00 1.52
309 314 2.473457 GCAGACCCGCGGATTTTAA 58.527 52.632 30.73 0.00 0.00 1.52
310 315 0.377203 GCAGACCCGCGGATTTTAAG 59.623 55.000 30.73 10.69 0.00 1.85
311 316 1.014352 CAGACCCGCGGATTTTAAGG 58.986 55.000 30.73 9.82 0.00 2.69
312 317 0.906775 AGACCCGCGGATTTTAAGGA 59.093 50.000 30.73 0.00 0.00 3.36
313 318 1.134491 AGACCCGCGGATTTTAAGGAG 60.134 52.381 30.73 8.09 0.00 3.69
314 319 0.746923 ACCCGCGGATTTTAAGGAGC 60.747 55.000 30.73 0.00 0.00 4.70
315 320 1.444917 CCCGCGGATTTTAAGGAGCC 61.445 60.000 30.73 0.00 0.00 4.70
316 321 1.641677 CGCGGATTTTAAGGAGCCG 59.358 57.895 11.77 11.77 44.47 5.52
317 322 1.772063 CGCGGATTTTAAGGAGCCGG 61.772 60.000 16.13 0.00 42.09 6.13
318 323 2.022520 CGGATTTTAAGGAGCCGGC 58.977 57.895 21.89 21.89 38.40 6.13
319 324 1.772063 CGGATTTTAAGGAGCCGGCG 61.772 60.000 23.20 0.00 38.40 6.46
320 325 1.355563 GATTTTAAGGAGCCGGCGC 59.644 57.895 23.29 23.29 0.00 6.53
321 326 1.373590 GATTTTAAGGAGCCGGCGCA 61.374 55.000 31.51 10.50 37.52 6.09
322 327 0.751643 ATTTTAAGGAGCCGGCGCAT 60.752 50.000 31.51 23.40 37.52 4.73
323 328 0.963355 TTTTAAGGAGCCGGCGCATT 60.963 50.000 31.41 31.41 37.52 3.56
324 329 1.653094 TTTAAGGAGCCGGCGCATTG 61.653 55.000 35.00 0.00 37.52 2.82
381 681 9.554395 TGTTTCTTGCCTAAATATCATATCGAA 57.446 29.630 0.00 0.00 0.00 3.71
473 774 3.052082 CCACTTGGCAGCACGAGG 61.052 66.667 0.00 0.00 0.00 4.63
501 826 2.290260 TGGACCGAGGACTAGTCGTTTA 60.290 50.000 18.54 1.67 35.59 2.01
909 1331 4.329545 GTGCCGCCCAGGAAGACA 62.330 66.667 0.00 0.00 45.00 3.41
1315 2469 4.444024 CGCCACCAACGCGTCATG 62.444 66.667 14.44 8.34 44.55 3.07
1342 2496 1.204146 ATCCACTATGTTGCCTCCGT 58.796 50.000 0.00 0.00 0.00 4.69
1459 2634 1.599071 AGTGATGACTGTGTTGCAACG 59.401 47.619 23.79 12.70 0.00 4.10
2137 3591 1.516386 GCGACGAGAGCATCCGAAA 60.516 57.895 0.00 0.00 33.66 3.46
2148 3602 0.095935 CATCCGAAAGAACAGCAGCG 59.904 55.000 0.00 0.00 0.00 5.18
2191 3646 2.159667 TCAATGAATGAACTTCGCTGCG 60.160 45.455 17.25 17.25 36.60 5.18
2214 3669 5.059221 CGTGCAATTTCTAAAACGATTGACC 59.941 40.000 0.00 0.00 32.61 4.02
2230 3685 1.075374 TGACCAATAAAGTGCCAGCCT 59.925 47.619 0.00 0.00 0.00 4.58
2246 3707 1.220206 CCTACCACTGCTGCTCTGG 59.780 63.158 12.80 12.80 0.00 3.86
2283 3758 4.296690 ACAAGTGAACAAGTAGAGTACGC 58.703 43.478 0.00 0.00 0.00 4.42
2284 3759 4.202080 ACAAGTGAACAAGTAGAGTACGCA 60.202 41.667 0.00 0.00 0.00 5.24
2311 3786 5.771165 TGATAAGTGAGGGCGTATATACACA 59.229 40.000 13.22 2.54 0.00 3.72
2361 4005 2.047061 GAAAAGAAGGCAAAACCCCCT 58.953 47.619 0.00 0.00 40.58 4.79
2368 4012 0.408309 GGCAAAACCCCCTACCTCTT 59.592 55.000 0.00 0.00 0.00 2.85
2398 4042 3.978855 CGATGCATGCAACCATCTTATTG 59.021 43.478 26.68 4.65 36.55 1.90
2401 4045 5.001237 TGCATGCAACCATCTTATTGAAG 57.999 39.130 20.30 0.00 0.00 3.02
2455 4099 5.232463 GGCCCATAATCATAGTGCAAAATG 58.768 41.667 0.00 0.00 0.00 2.32
2514 4158 3.085533 AGAGCAGGCTACGATACCTATG 58.914 50.000 0.00 0.00 33.38 2.23
2519 4163 1.067071 GGCTACGATACCTATGCACCC 60.067 57.143 0.00 0.00 0.00 4.61
2531 4175 3.521126 CCTATGCACCCAGCCTATTATCT 59.479 47.826 0.00 0.00 44.83 1.98
2576 4220 2.027751 GCCCGTGCTATCGTCTCC 59.972 66.667 0.00 0.00 33.53 3.71
2589 4594 0.670546 CGTCTCCGAATGGTTGCACT 60.671 55.000 0.00 0.00 35.63 4.40
2593 4598 2.086869 CTCCGAATGGTTGCACTCAAT 58.913 47.619 0.00 0.00 34.29 2.57
2602 4607 3.386078 TGGTTGCACTCAATAGCCAAAAA 59.614 39.130 0.00 0.00 34.29 1.94
2605 4610 4.503741 TGCACTCAATAGCCAAAAACTC 57.496 40.909 0.00 0.00 0.00 3.01
2642 4647 5.356426 TGAGTGATTAATGACCACATACGG 58.644 41.667 1.04 0.00 35.50 4.02
2655 4660 3.113322 CACATACGGATCCACGTTGTAG 58.887 50.000 13.41 0.00 46.25 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 45 1.202110 CGATCTTCATGTGCTGGTTGC 60.202 52.381 0.00 0.00 43.25 4.17
42 47 1.742761 CCGATCTTCATGTGCTGGTT 58.257 50.000 0.00 0.00 0.00 3.67
49 54 0.249120 TCCAACGCCGATCTTCATGT 59.751 50.000 0.00 0.00 0.00 3.21
52 57 0.824109 ATCTCCAACGCCGATCTTCA 59.176 50.000 0.00 0.00 0.00 3.02
53 58 1.492720 GATCTCCAACGCCGATCTTC 58.507 55.000 0.00 0.00 32.75 2.87
72 77 7.348080 TCAACTATGGATGTAGTGTAAGAGG 57.652 40.000 0.00 0.00 35.20 3.69
90 95 6.817641 CCAATGCCTAATTGCAAAATCAACTA 59.182 34.615 1.71 0.00 45.84 2.24
104 109 7.847096 TCGTGTATATATGTCCAATGCCTAAT 58.153 34.615 0.00 0.00 0.00 1.73
105 110 7.234661 TCGTGTATATATGTCCAATGCCTAA 57.765 36.000 0.00 0.00 0.00 2.69
109 114 4.929211 TGCTCGTGTATATATGTCCAATGC 59.071 41.667 0.00 0.00 0.00 3.56
146 151 7.969536 AATGTATCACCCAGAATAAGAATCG 57.030 36.000 0.00 0.00 0.00 3.34
167 172 5.382303 ACATACGCGAAACAAGAGAAAATG 58.618 37.500 15.93 0.05 0.00 2.32
196 201 0.034863 GGACATTGACGGGGCCTAAA 60.035 55.000 0.84 0.00 0.00 1.85
197 202 1.202099 TGGACATTGACGGGGCCTAA 61.202 55.000 0.84 0.00 0.00 2.69
198 203 0.986019 ATGGACATTGACGGGGCCTA 60.986 55.000 0.84 0.00 0.00 3.93
199 204 2.270874 GATGGACATTGACGGGGCCT 62.271 60.000 0.84 0.00 0.00 5.19
200 205 1.823899 GATGGACATTGACGGGGCC 60.824 63.158 0.00 0.00 0.00 5.80
201 206 1.823899 GGATGGACATTGACGGGGC 60.824 63.158 0.00 0.00 0.00 5.80
202 207 0.748005 GTGGATGGACATTGACGGGG 60.748 60.000 0.00 0.00 0.00 5.73
203 208 0.253044 AGTGGATGGACATTGACGGG 59.747 55.000 0.00 0.00 0.00 5.28
204 209 1.656652 GAGTGGATGGACATTGACGG 58.343 55.000 0.00 0.00 0.00 4.79
205 210 1.066215 TGGAGTGGATGGACATTGACG 60.066 52.381 0.00 0.00 0.00 4.35
206 211 2.026822 AGTGGAGTGGATGGACATTGAC 60.027 50.000 0.00 0.00 0.00 3.18
207 212 2.026915 CAGTGGAGTGGATGGACATTGA 60.027 50.000 0.00 0.00 0.00 2.57
208 213 2.362736 CAGTGGAGTGGATGGACATTG 58.637 52.381 0.00 0.00 0.00 2.82
209 214 1.340405 GCAGTGGAGTGGATGGACATT 60.340 52.381 0.00 0.00 0.00 2.71
210 215 0.254178 GCAGTGGAGTGGATGGACAT 59.746 55.000 0.00 0.00 0.00 3.06
211 216 0.837691 AGCAGTGGAGTGGATGGACA 60.838 55.000 0.00 0.00 0.00 4.02
212 217 0.107945 GAGCAGTGGAGTGGATGGAC 60.108 60.000 0.00 0.00 0.00 4.02
213 218 1.267574 GGAGCAGTGGAGTGGATGGA 61.268 60.000 0.00 0.00 0.00 3.41
214 219 1.222936 GGAGCAGTGGAGTGGATGG 59.777 63.158 0.00 0.00 0.00 3.51
215 220 1.153489 CGGAGCAGTGGAGTGGATG 60.153 63.158 0.00 0.00 0.00 3.51
216 221 3.303189 CGGAGCAGTGGAGTGGAT 58.697 61.111 0.00 0.00 0.00 3.41
237 242 2.507992 CAGCTCTGTCCGCTTCCG 60.508 66.667 0.00 0.00 35.07 4.30
238 243 2.817396 GCAGCTCTGTCCGCTTCC 60.817 66.667 0.00 0.00 35.07 3.46
239 244 2.047844 TGCAGCTCTGTCCGCTTC 60.048 61.111 0.00 0.00 35.07 3.86
240 245 2.047465 CTGCAGCTCTGTCCGCTT 60.047 61.111 0.00 0.00 35.07 4.68
241 246 3.309506 ACTGCAGCTCTGTCCGCT 61.310 61.111 15.27 0.00 38.49 5.52
242 247 3.117171 CACTGCAGCTCTGTCCGC 61.117 66.667 15.27 0.00 0.00 5.54
243 248 0.601046 TTTCACTGCAGCTCTGTCCG 60.601 55.000 15.27 0.00 0.00 4.79
244 249 1.534595 CTTTTCACTGCAGCTCTGTCC 59.465 52.381 15.27 0.00 0.00 4.02
245 250 2.216898 ACTTTTCACTGCAGCTCTGTC 58.783 47.619 15.27 0.00 0.00 3.51
246 251 2.158842 AGACTTTTCACTGCAGCTCTGT 60.159 45.455 15.27 5.50 0.00 3.41
247 252 2.492012 AGACTTTTCACTGCAGCTCTG 58.508 47.619 15.27 4.87 0.00 3.35
248 253 2.877168 CAAGACTTTTCACTGCAGCTCT 59.123 45.455 15.27 0.00 0.00 4.09
249 254 2.031333 CCAAGACTTTTCACTGCAGCTC 60.031 50.000 15.27 0.00 0.00 4.09
250 255 1.952296 CCAAGACTTTTCACTGCAGCT 59.048 47.619 15.27 0.00 0.00 4.24
251 256 1.949525 TCCAAGACTTTTCACTGCAGC 59.050 47.619 15.27 0.00 0.00 5.25
252 257 2.031333 GCTCCAAGACTTTTCACTGCAG 60.031 50.000 13.48 13.48 0.00 4.41
253 258 1.949525 GCTCCAAGACTTTTCACTGCA 59.050 47.619 0.00 0.00 0.00 4.41
254 259 1.069636 CGCTCCAAGACTTTTCACTGC 60.070 52.381 0.00 0.00 0.00 4.40
255 260 1.532868 CCGCTCCAAGACTTTTCACTG 59.467 52.381 0.00 0.00 0.00 3.66
256 261 1.543429 CCCGCTCCAAGACTTTTCACT 60.543 52.381 0.00 0.00 0.00 3.41
257 262 0.875059 CCCGCTCCAAGACTTTTCAC 59.125 55.000 0.00 0.00 0.00 3.18
258 263 0.889186 GCCCGCTCCAAGACTTTTCA 60.889 55.000 0.00 0.00 0.00 2.69
259 264 0.889186 TGCCCGCTCCAAGACTTTTC 60.889 55.000 0.00 0.00 0.00 2.29
260 265 0.467290 TTGCCCGCTCCAAGACTTTT 60.467 50.000 0.00 0.00 0.00 2.27
261 266 0.467290 TTTGCCCGCTCCAAGACTTT 60.467 50.000 0.00 0.00 0.00 2.66
262 267 0.467290 TTTTGCCCGCTCCAAGACTT 60.467 50.000 0.00 0.00 0.00 3.01
263 268 1.150536 TTTTGCCCGCTCCAAGACT 59.849 52.632 0.00 0.00 0.00 3.24
264 269 1.285950 GTTTTGCCCGCTCCAAGAC 59.714 57.895 0.00 0.00 0.00 3.01
265 270 2.258013 CGTTTTGCCCGCTCCAAGA 61.258 57.895 0.00 0.00 0.00 3.02
266 271 2.255252 CGTTTTGCCCGCTCCAAG 59.745 61.111 0.00 0.00 0.00 3.61
267 272 2.203224 TCGTTTTGCCCGCTCCAA 60.203 55.556 0.00 0.00 0.00 3.53
268 273 2.975799 GTCGTTTTGCCCGCTCCA 60.976 61.111 0.00 0.00 0.00 3.86
269 274 4.084888 CGTCGTTTTGCCCGCTCC 62.085 66.667 0.00 0.00 0.00 4.70
270 275 4.736631 GCGTCGTTTTGCCCGCTC 62.737 66.667 0.00 0.00 42.66 5.03
272 277 4.736631 GAGCGTCGTTTTGCCCGC 62.737 66.667 0.00 0.00 46.07 6.13
273 278 4.084888 GGAGCGTCGTTTTGCCCG 62.085 66.667 0.00 0.00 0.00 6.13
274 279 4.084888 CGGAGCGTCGTTTTGCCC 62.085 66.667 0.00 0.00 0.00 5.36
291 296 0.377203 CTTAAAATCCGCGGGTCTGC 59.623 55.000 27.83 0.00 0.00 4.26
292 297 1.014352 CCTTAAAATCCGCGGGTCTG 58.986 55.000 27.83 7.19 0.00 3.51
293 298 0.906775 TCCTTAAAATCCGCGGGTCT 59.093 50.000 27.83 12.11 0.00 3.85
294 299 1.296727 CTCCTTAAAATCCGCGGGTC 58.703 55.000 27.83 0.00 0.00 4.46
295 300 0.746923 GCTCCTTAAAATCCGCGGGT 60.747 55.000 27.83 18.03 0.00 5.28
296 301 1.444917 GGCTCCTTAAAATCCGCGGG 61.445 60.000 27.83 6.84 0.00 6.13
297 302 1.772063 CGGCTCCTTAAAATCCGCGG 61.772 60.000 22.12 22.12 33.36 6.46
298 303 1.641677 CGGCTCCTTAAAATCCGCG 59.358 57.895 0.00 0.00 33.36 6.46
299 304 2.022520 CCGGCTCCTTAAAATCCGC 58.977 57.895 0.00 0.00 38.85 5.54
300 305 1.772063 CGCCGGCTCCTTAAAATCCG 61.772 60.000 26.68 0.00 39.79 4.18
301 306 2.022520 CGCCGGCTCCTTAAAATCC 58.977 57.895 26.68 0.00 0.00 3.01
302 307 1.355563 GCGCCGGCTCCTTAAAATC 59.644 57.895 26.68 0.00 35.83 2.17
303 308 0.751643 ATGCGCCGGCTCCTTAAAAT 60.752 50.000 26.68 1.23 40.82 1.82
304 309 0.963355 AATGCGCCGGCTCCTTAAAA 60.963 50.000 26.68 0.00 40.82 1.52
305 310 1.377987 AATGCGCCGGCTCCTTAAA 60.378 52.632 26.68 0.00 40.82 1.52
306 311 2.112198 CAATGCGCCGGCTCCTTAA 61.112 57.895 26.68 0.00 40.82 1.85
307 312 2.513666 CAATGCGCCGGCTCCTTA 60.514 61.111 26.68 0.00 40.82 2.69
325 330 0.800631 GAAACTAAAGCCCCGTTCGG 59.199 55.000 4.08 4.08 0.00 4.30
326 331 0.441145 CGAAACTAAAGCCCCGTTCG 59.559 55.000 0.00 0.00 0.00 3.95
327 332 0.167470 GCGAAACTAAAGCCCCGTTC 59.833 55.000 0.00 0.00 0.00 3.95
328 333 0.535553 TGCGAAACTAAAGCCCCGTT 60.536 50.000 0.00 0.00 0.00 4.44
329 334 0.322187 ATGCGAAACTAAAGCCCCGT 60.322 50.000 0.00 0.00 0.00 5.28
330 335 1.658994 TATGCGAAACTAAAGCCCCG 58.341 50.000 0.00 0.00 0.00 5.73
331 336 3.211045 TCATATGCGAAACTAAAGCCCC 58.789 45.455 0.00 0.00 0.00 5.80
332 337 4.757149 AGATCATATGCGAAACTAAAGCCC 59.243 41.667 0.00 0.00 0.00 5.19
333 338 5.237344 ACAGATCATATGCGAAACTAAAGCC 59.763 40.000 0.00 0.00 0.00 4.35
334 339 6.292389 ACAGATCATATGCGAAACTAAAGC 57.708 37.500 0.00 0.00 0.00 3.51
335 340 8.607459 AGAAACAGATCATATGCGAAACTAAAG 58.393 33.333 0.00 0.00 0.00 1.85
381 681 6.556974 TCCATCTTCTCATGATCTTTCACT 57.443 37.500 0.00 0.00 33.85 3.41
473 774 1.153549 GTCCTCGGTCCAGATGCAC 60.154 63.158 0.00 0.00 0.00 4.57
477 778 1.475392 CGACTAGTCCTCGGTCCAGAT 60.475 57.143 17.23 0.00 0.00 2.90
501 826 4.123545 GGTGGGGCCTGGCGTAAT 62.124 66.667 13.40 0.00 0.00 1.89
519 844 0.600557 AGCCAACAGAGAGACAGACG 59.399 55.000 0.00 0.00 0.00 4.18
553 894 1.789464 GAGATGCTGATTTACTCGCGG 59.211 52.381 6.13 0.00 0.00 6.46
766 1149 3.319198 ATGGGCCGACGTGTCCTT 61.319 61.111 0.00 0.23 0.00 3.36
1315 2469 3.561725 GGCAACATAGTGGATTGAGTAGC 59.438 47.826 0.00 0.00 0.00 3.58
1342 2496 1.153647 GCGACGGTCATGGTGATGA 60.154 57.895 9.10 0.00 36.16 2.92
1459 2634 3.181505 CGTCTCCTGCATATAGATCCGTC 60.182 52.174 0.00 0.00 0.00 4.79
2137 3591 2.358898 ACAAAAATGACGCTGCTGTTCT 59.641 40.909 0.00 0.00 0.00 3.01
2191 3646 5.918011 TGGTCAATCGTTTTAGAAATTGCAC 59.082 36.000 0.00 0.00 0.00 4.57
2214 3669 2.423538 GTGGTAGGCTGGCACTTTATTG 59.576 50.000 3.38 0.00 0.00 1.90
2230 3685 2.665000 GCCAGAGCAGCAGTGGTA 59.335 61.111 13.29 0.00 39.53 3.25
2246 3707 0.804989 CTTGTTTGGATCGGAGTGGC 59.195 55.000 0.00 0.00 0.00 5.01
2283 3758 0.108804 ACGCCCTCACTTATCACGTG 60.109 55.000 9.94 9.94 0.00 4.49
2284 3759 1.466856 TACGCCCTCACTTATCACGT 58.533 50.000 0.00 0.00 36.17 4.49
2341 3985 2.047061 AGGGGGTTTTGCCTTCTTTTC 58.953 47.619 0.00 0.00 37.43 2.29
2356 4000 2.037772 CGATTGATGAAGAGGTAGGGGG 59.962 54.545 0.00 0.00 0.00 5.40
2514 4158 1.202806 TGCAGATAATAGGCTGGGTGC 60.203 52.381 0.00 0.00 41.94 5.01
2519 4163 1.151668 GGCGTGCAGATAATAGGCTG 58.848 55.000 0.00 0.00 35.28 4.85
2531 4175 1.505807 CCGATTTGAATGGCGTGCA 59.494 52.632 0.00 0.00 0.00 4.57
2571 4215 1.079503 GAGTGCAACCATTCGGAGAC 58.920 55.000 0.00 0.00 37.80 3.36
2576 4220 2.223340 GGCTATTGAGTGCAACCATTCG 60.223 50.000 0.00 0.00 37.80 3.34
2589 4594 3.075283 TCCAGGGAGTTTTTGGCTATTGA 59.925 43.478 0.00 0.00 31.94 2.57
2593 4598 2.879103 CTCCAGGGAGTTTTTGGCTA 57.121 50.000 7.19 0.00 37.47 3.93
2605 4610 0.251354 CACTCATGTGGACTCCAGGG 59.749 60.000 0.00 0.00 40.33 4.45
2617 4622 6.073602 CCGTATGTGGTCATTAATCACTCATG 60.074 42.308 9.46 0.00 35.70 3.07
2626 4631 4.699637 GTGGATCCGTATGTGGTCATTAA 58.300 43.478 7.39 0.00 35.70 1.40
2632 4637 0.899720 AACGTGGATCCGTATGTGGT 59.100 50.000 7.39 0.00 40.85 4.16
2642 4647 2.656560 ACAGAGCTACAACGTGGATC 57.343 50.000 0.00 0.00 29.78 3.36


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

AutoCloner maintained by Alex Coulton.