Multiple sequence alignment - TraesCS7D01G416200

Loading Multiple Alignment...

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 TraesCS7D01G416200 chr7D 100.000 5123 0 0 1 5123 535410029 535415151 0.000000e+00 9461.0
1 TraesCS7D01G416200 chr7B 96.910 3495 93 9 407 3886 575423987 575427481 0.000000e+00 5842.0
2 TraesCS7D01G416200 chr7B 95.933 3565 110 15 351 3886 577184694 577188252 0.000000e+00 5747.0
3 TraesCS7D01G416200 chr7B 86.938 467 33 13 4599 5054 575428305 575428754 2.750000e-137 499.0
4 TraesCS7D01G416200 chr7B 89.972 359 17 8 4230 4587 577188656 577188996 3.640000e-121 446.0
5 TraesCS7D01G416200 chr7B 92.208 308 16 5 4230 4536 575427883 575428183 3.670000e-116 429.0
6 TraesCS7D01G416200 chr7B 97.166 247 7 0 3956 4202 575427491 575427737 7.930000e-113 418.0
7 TraesCS7D01G416200 chr7B 95.984 249 8 1 3956 4202 577188262 577188510 2.220000e-108 403.0
8 TraesCS7D01G416200 chr7B 78.354 559 53 29 4599 5123 577189056 577189580 3.000000e-77 300.0
9 TraesCS7D01G416200 chr7B 87.678 211 9 4 3 197 577184396 577184605 3.990000e-56 230.0
10 TraesCS7D01G416200 chr7B 94.495 109 5 1 3 111 575423863 575423970 3.170000e-37 167.0
11 TraesCS7D01G416200 chr7B 90.625 64 5 1 4036 4099 577225453 577225515 3.290000e-12 84.2
12 TraesCS7D01G416200 chr7A 97.057 3432 95 4 407 3832 615380730 615384161 0.000000e+00 5773.0
13 TraesCS7D01G416200 chr7A 82.894 1403 176 26 836 2225 618192095 618190744 0.000000e+00 1203.0
14 TraesCS7D01G416200 chr7A 85.980 1077 139 6 2460 3525 618190683 618189608 0.000000e+00 1142.0
15 TraesCS7D01G416200 chr7A 96.715 548 16 2 3865 4410 615384500 615385047 0.000000e+00 911.0
16 TraesCS7D01G416200 chr7A 88.795 473 26 13 4599 5054 615385310 615385772 5.800000e-154 555.0
17 TraesCS7D01G416200 chr7A 83.838 297 38 6 3549 3837 618189610 618189316 1.820000e-69 274.0
18 TraesCS7D01G416200 chr7A 91.623 191 10 2 4397 4587 615385066 615385250 5.090000e-65 259.0
19 TraesCS7D01G416200 chr7A 96.330 109 3 1 3 111 615380610 615380717 1.470000e-40 178.0
20 TraesCS7D01G416200 chr7A 90.476 105 9 1 4290 4393 647857158 647857262 2.490000e-28 137.0


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 TraesCS7D01G416200 chr7D 535410029 535415151 5122 False 9461.0 9461 100.000000 1 5123 1 chr7D.!!$F1 5122
1 TraesCS7D01G416200 chr7B 575423863 575428754 4891 False 1471.0 5842 93.543400 3 5054 5 chr7B.!!$F2 5051
2 TraesCS7D01G416200 chr7B 577184396 577189580 5184 False 1425.2 5747 89.584200 3 5123 5 chr7B.!!$F3 5120
3 TraesCS7D01G416200 chr7A 615380610 615385772 5162 False 1535.2 5773 94.104000 3 5054 5 chr7A.!!$F2 5051
4 TraesCS7D01G416200 chr7A 618189316 618192095 2779 True 873.0 1203 84.237333 836 3837 3 chr7A.!!$R1 3001

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
242 259 0.322456 CCCATCACCACCACAATCGT 60.322 55.000 0.00 0.00 0.00 3.73 F
594 621 1.005037 AAACACTCGAGCATGCGGA 60.005 52.632 13.61 12.91 0.00 5.54 F
1980 2032 1.792006 CTTCCTTAGCAAACGACGGT 58.208 50.000 0.00 0.00 0.00 4.83 F
2616 2670 0.245539 TTAACTCTGAAGTCCGCCGG 59.754 55.000 0.00 0.00 33.48 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1199 1251 0.458669 CAGCCAGGCATCAAATGTCC 59.541 55.000 15.80 0.0 34.84 4.02 R
2075 2127 2.196319 GCCCAAGGCCTCAGATTTG 58.804 57.895 5.23 0.0 44.06 2.32 R
2881 2944 2.920524 TCGCAGGTCCAAAACTTGTAA 58.079 42.857 0.00 0.0 37.30 2.41 R
4540 5072 0.179468 AGTGGTTGCCGTTACACAGT 59.821 50.000 0.00 0.0 36.35 3.55 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
52 53 3.296854 AGATCTAACGTGCTGGGACATA 58.703 45.455 0.00 0.00 38.20 2.29
60 61 3.196901 ACGTGCTGGGACATATGAAACTA 59.803 43.478 10.38 0.00 38.20 2.24
121 122 7.970102 ACTATTTCAGTGTACCTGGTCTAAAA 58.030 34.615 0.63 0.00 41.83 1.52
138 139 9.672086 TGGTCTAAAATTTTGACTTTTCGTATG 57.328 29.630 21.83 0.00 0.00 2.39
139 140 9.673454 GGTCTAAAATTTTGACTTTTCGTATGT 57.327 29.630 21.83 0.00 0.00 2.29
142 143 9.672086 CTAAAATTTTGACTTTTCGTATGTGGA 57.328 29.630 13.76 0.00 0.00 4.02
174 191 0.532640 TTCACGGGGATGATGCATCG 60.533 55.000 21.34 11.58 41.35 3.84
189 206 1.740025 GCATCGGCTACTTGCTTTCTT 59.260 47.619 0.00 0.00 42.39 2.52
190 207 2.223135 GCATCGGCTACTTGCTTTCTTC 60.223 50.000 0.00 0.00 42.39 2.87
191 208 3.265791 CATCGGCTACTTGCTTTCTTCT 58.734 45.455 0.00 0.00 42.39 2.85
192 209 3.402628 TCGGCTACTTGCTTTCTTCTT 57.597 42.857 0.00 0.00 42.39 2.52
193 210 4.530710 TCGGCTACTTGCTTTCTTCTTA 57.469 40.909 0.00 0.00 42.39 2.10
194 211 4.495422 TCGGCTACTTGCTTTCTTCTTAG 58.505 43.478 0.00 0.00 42.39 2.18
195 212 4.219944 TCGGCTACTTGCTTTCTTCTTAGA 59.780 41.667 0.00 0.00 42.39 2.10
196 213 5.105310 TCGGCTACTTGCTTTCTTCTTAGAT 60.105 40.000 0.00 0.00 42.39 1.98
197 214 5.582665 CGGCTACTTGCTTTCTTCTTAGATT 59.417 40.000 0.00 0.00 42.39 2.40
198 215 6.237969 CGGCTACTTGCTTTCTTCTTAGATTC 60.238 42.308 0.00 0.00 42.39 2.52
199 216 6.037720 GGCTACTTGCTTTCTTCTTAGATTCC 59.962 42.308 0.00 0.00 42.39 3.01
200 217 6.037720 GCTACTTGCTTTCTTCTTAGATTCCC 59.962 42.308 0.00 0.00 38.95 3.97
201 218 5.880901 ACTTGCTTTCTTCTTAGATTCCCA 58.119 37.500 0.00 0.00 0.00 4.37
202 219 5.942826 ACTTGCTTTCTTCTTAGATTCCCAG 59.057 40.000 0.00 0.00 0.00 4.45
203 220 4.265073 TGCTTTCTTCTTAGATTCCCAGC 58.735 43.478 0.00 0.00 0.00 4.85
204 221 3.629855 GCTTTCTTCTTAGATTCCCAGCC 59.370 47.826 0.00 0.00 0.00 4.85
205 222 3.543680 TTCTTCTTAGATTCCCAGCCG 57.456 47.619 0.00 0.00 0.00 5.52
206 223 2.747177 TCTTCTTAGATTCCCAGCCGA 58.253 47.619 0.00 0.00 0.00 5.54
207 224 2.695666 TCTTCTTAGATTCCCAGCCGAG 59.304 50.000 0.00 0.00 0.00 4.63
208 225 1.414158 TCTTAGATTCCCAGCCGAGG 58.586 55.000 0.00 0.00 0.00 4.63
216 233 3.535962 CCAGCCGAGGGAGCTCTC 61.536 72.222 14.64 10.30 38.95 3.20
217 234 2.441901 CAGCCGAGGGAGCTCTCT 60.442 66.667 18.34 18.34 38.95 3.10
218 235 2.441901 AGCCGAGGGAGCTCTCTG 60.442 66.667 24.07 13.26 34.91 3.35
219 236 4.219999 GCCGAGGGAGCTCTCTGC 62.220 72.222 24.07 16.05 43.29 4.26
240 257 1.281867 TCTCCCATCACCACCACAATC 59.718 52.381 0.00 0.00 0.00 2.67
242 259 0.322456 CCCATCACCACCACAATCGT 60.322 55.000 0.00 0.00 0.00 3.73
243 260 1.065782 CCCATCACCACCACAATCGTA 60.066 52.381 0.00 0.00 0.00 3.43
245 262 2.354704 CCATCACCACCACAATCGTAGT 60.355 50.000 0.00 0.00 0.00 2.73
246 263 3.118920 CCATCACCACCACAATCGTAGTA 60.119 47.826 0.00 0.00 0.00 1.82
247 264 3.861276 TCACCACCACAATCGTAGTAG 57.139 47.619 0.00 0.00 0.00 2.57
254 271 4.451629 CCACAATCGTAGTAGTGGTCTT 57.548 45.455 0.00 0.00 44.95 3.01
255 272 4.421948 CCACAATCGTAGTAGTGGTCTTC 58.578 47.826 0.00 0.00 44.95 2.87
283 307 7.730672 TTTAGGAGAGAGCATCATATAGCAT 57.269 36.000 0.00 0.00 37.82 3.79
284 308 5.857471 AGGAGAGAGCATCATATAGCATC 57.143 43.478 0.00 0.00 37.82 3.91
285 309 5.270794 AGGAGAGAGCATCATATAGCATCA 58.729 41.667 0.00 0.00 37.82 3.07
286 310 5.720520 AGGAGAGAGCATCATATAGCATCAA 59.279 40.000 0.00 0.00 37.82 2.57
287 311 6.044046 GGAGAGAGCATCATATAGCATCAAG 58.956 44.000 0.00 0.00 37.82 3.02
288 312 5.979993 AGAGAGCATCATATAGCATCAAGG 58.020 41.667 0.00 0.00 37.82 3.61
289 313 5.100344 AGAGCATCATATAGCATCAAGGG 57.900 43.478 0.00 0.00 37.82 3.95
290 314 4.781621 AGAGCATCATATAGCATCAAGGGA 59.218 41.667 0.00 0.00 37.82 4.20
291 315 5.429109 AGAGCATCATATAGCATCAAGGGAT 59.571 40.000 0.00 0.00 37.82 3.85
292 316 6.614496 AGAGCATCATATAGCATCAAGGGATA 59.386 38.462 0.00 0.00 37.82 2.59
293 317 6.590068 AGCATCATATAGCATCAAGGGATAC 58.410 40.000 0.00 0.00 30.87 2.24
294 318 6.157471 AGCATCATATAGCATCAAGGGATACA 59.843 38.462 0.00 0.00 39.74 2.29
295 319 6.825213 GCATCATATAGCATCAAGGGATACAA 59.175 38.462 0.00 0.00 39.74 2.41
296 320 7.501559 GCATCATATAGCATCAAGGGATACAAT 59.498 37.037 0.00 0.00 39.74 2.71
297 321 9.404848 CATCATATAGCATCAAGGGATACAATT 57.595 33.333 0.00 0.00 39.74 2.32
302 326 8.970859 ATAGCATCAAGGGATACAATTATAGC 57.029 34.615 0.00 0.00 39.74 2.97
303 327 5.877012 AGCATCAAGGGATACAATTATAGCG 59.123 40.000 0.00 0.00 39.74 4.26
304 328 5.874810 GCATCAAGGGATACAATTATAGCGA 59.125 40.000 0.00 0.00 39.74 4.93
305 329 6.036517 GCATCAAGGGATACAATTATAGCGAG 59.963 42.308 0.00 0.00 39.74 5.03
306 330 6.665992 TCAAGGGATACAATTATAGCGAGT 57.334 37.500 0.00 0.00 39.74 4.18
307 331 7.770366 TCAAGGGATACAATTATAGCGAGTA 57.230 36.000 0.00 0.00 39.74 2.59
308 332 7.600065 TCAAGGGATACAATTATAGCGAGTAC 58.400 38.462 0.00 0.00 39.74 2.73
309 333 7.231925 TCAAGGGATACAATTATAGCGAGTACA 59.768 37.037 0.00 0.00 39.74 2.90
310 334 6.921914 AGGGATACAATTATAGCGAGTACAC 58.078 40.000 0.00 0.00 39.74 2.90
311 335 6.720288 AGGGATACAATTATAGCGAGTACACT 59.280 38.462 0.00 0.00 39.74 3.55
312 336 7.028361 GGGATACAATTATAGCGAGTACACTC 58.972 42.308 0.00 0.00 37.81 3.51
325 349 7.197017 AGCGAGTACACTCAACTGAATAATAG 58.803 38.462 9.88 0.00 43.00 1.73
326 350 6.973474 GCGAGTACACTCAACTGAATAATAGT 59.027 38.462 9.88 0.00 43.00 2.12
348 372 7.415592 AGTTAGTTACCACTACTCATTACCC 57.584 40.000 0.00 0.00 35.05 3.69
349 373 6.955851 AGTTAGTTACCACTACTCATTACCCA 59.044 38.462 0.00 0.00 35.05 4.51
355 379 4.595781 ACCACTACTCATTACCCAACAGAA 59.404 41.667 0.00 0.00 0.00 3.02
376 400 7.411313 CAGAATTCTGCCCAACATAGCTATGT 61.411 42.308 29.70 29.70 41.65 2.29
400 424 9.890629 TGTTTAGATAGTTAGATGTGATGCTTT 57.109 29.630 0.00 0.00 0.00 3.51
403 427 9.755804 TTAGATAGTTAGATGTGATGCTTTCAG 57.244 33.333 0.00 0.00 34.17 3.02
404 428 6.705381 AGATAGTTAGATGTGATGCTTTCAGC 59.295 38.462 0.00 0.00 42.82 4.26
405 429 4.841422 AGTTAGATGTGATGCTTTCAGCT 58.159 39.130 0.00 0.00 42.97 4.24
441 465 1.905894 AGGAAGAGCTGGAACTCCTTC 59.094 52.381 0.00 0.00 37.39 3.46
594 621 1.005037 AAACACTCGAGCATGCGGA 60.005 52.632 13.61 12.91 0.00 5.54
692 729 7.585867 TGTCTTGATATCTTAGTAGCTTAGCG 58.414 38.462 3.98 0.00 0.00 4.26
693 730 6.525280 GTCTTGATATCTTAGTAGCTTAGCGC 59.475 42.308 0.00 0.00 39.57 5.92
717 755 3.005897 ACTGTTAGTGTCAGACGCAATCT 59.994 43.478 16.50 0.00 38.66 2.40
758 796 8.338072 TGTTGTTACTCTTGAAAAACAGGTTA 57.662 30.769 0.00 0.00 33.70 2.85
887 930 2.289010 CCTGCAGCCATACGATGTCATA 60.289 50.000 8.66 0.00 0.00 2.15
953 999 5.946298 TGCATTTACATGAAGCTTCTTCAG 58.054 37.500 26.09 15.20 31.07 3.02
954 1000 4.797349 GCATTTACATGAAGCTTCTTCAGC 59.203 41.667 26.09 14.88 39.88 4.26
1325 1377 4.034510 CGGATTCTTCAAGAGGAAATTCCG 59.965 45.833 16.99 16.99 42.75 4.30
1408 1460 3.123804 CGAATTCAGCGGCTAACTACAT 58.876 45.455 0.26 0.00 0.00 2.29
1625 1677 3.373110 GGCATGGGAGGTCTAGGAAAAAT 60.373 47.826 0.00 0.00 0.00 1.82
1827 1879 5.830991 ACTAATCGAGGAACTTCAGAGCTAT 59.169 40.000 0.00 0.00 41.55 2.97
1980 2032 1.792006 CTTCCTTAGCAAACGACGGT 58.208 50.000 0.00 0.00 0.00 4.83
2280 2334 6.651086 TCTGAATCTCAGCTTGAATGATCTT 58.349 36.000 0.00 0.00 43.95 2.40
2616 2670 0.245539 TTAACTCTGAAGTCCGCCGG 59.754 55.000 0.00 0.00 33.48 6.13
2877 2940 2.094390 AGCATCGCTCGGTAAACTTACA 60.094 45.455 2.25 0.00 30.62 2.41
2881 2944 3.981211 TCGCTCGGTAAACTTACAAACT 58.019 40.909 2.25 0.00 35.37 2.66
2901 2964 2.623878 TACAAGTTTTGGACCTGCGA 57.376 45.000 0.00 0.00 34.12 5.10
3095 3158 9.383519 TGTTTCAGCCAATAAAGATCTACTTAG 57.616 33.333 0.00 0.00 37.93 2.18
3105 3168 0.676736 ATCTACTTAGGCAGCTCGGC 59.323 55.000 0.00 2.19 41.61 5.54
3546 3610 1.863454 CGATTGAGATTGAGGAAGGCG 59.137 52.381 0.00 0.00 0.00 5.52
3657 3721 8.083828 ACAGAAGATGGTTCTAACAGATATGT 57.916 34.615 0.00 0.00 0.00 2.29
3954 4333 3.573538 TCAATAAGCAAACACCATGCAGT 59.426 39.130 0.00 0.00 46.22 4.40
4268 4767 4.082081 CCCAACATTTTCATAAGCTGCAGA 60.082 41.667 20.43 0.00 0.00 4.26
4341 4841 2.737376 GGTCGTTGACCCAGACGC 60.737 66.667 4.60 0.00 46.19 5.19
4425 4957 2.682856 TCTTGTGCAGGGCGATTATTTC 59.317 45.455 0.00 0.00 0.00 2.17
4530 5062 4.306600 GGGGAGTGTTGTAGCAAAATTTG 58.693 43.478 0.57 0.57 0.00 2.32
4536 5068 7.115378 GGAGTGTTGTAGCAAAATTTGAATCTG 59.885 37.037 10.26 0.00 0.00 2.90
4538 5070 7.649306 AGTGTTGTAGCAAAATTTGAATCTGTC 59.351 33.333 10.26 0.00 0.00 3.51
4540 5072 8.845227 TGTTGTAGCAAAATTTGAATCTGTCTA 58.155 29.630 10.26 0.00 0.00 2.59
4541 5073 9.118236 GTTGTAGCAAAATTTGAATCTGTCTAC 57.882 33.333 10.26 9.54 0.00 2.59
4543 5075 8.506437 TGTAGCAAAATTTGAATCTGTCTACTG 58.494 33.333 10.26 0.85 0.00 2.74
4545 5077 7.365741 AGCAAAATTTGAATCTGTCTACTGTG 58.634 34.615 10.26 0.00 0.00 3.66
4546 5078 7.013655 AGCAAAATTTGAATCTGTCTACTGTGT 59.986 33.333 10.26 0.00 0.00 3.72
4547 5079 8.289618 GCAAAATTTGAATCTGTCTACTGTGTA 58.710 33.333 10.26 0.00 0.00 2.90
4587 5152 1.336125 GCTGATGCAAATGGCTCTACC 59.664 52.381 0.00 0.00 45.15 3.18
4588 5153 1.600957 CTGATGCAAATGGCTCTACCG 59.399 52.381 0.00 0.00 45.15 4.02
4590 5155 2.169561 TGATGCAAATGGCTCTACCGTA 59.830 45.455 0.00 0.00 45.15 4.02
4591 5156 3.181455 TGATGCAAATGGCTCTACCGTAT 60.181 43.478 0.00 0.00 45.15 3.06
4592 5157 2.833794 TGCAAATGGCTCTACCGTATC 58.166 47.619 0.00 0.00 45.15 2.24
4593 5158 1.792949 GCAAATGGCTCTACCGTATCG 59.207 52.381 0.00 0.00 43.94 2.92
4594 5159 2.545113 GCAAATGGCTCTACCGTATCGA 60.545 50.000 0.00 0.00 43.94 3.59
4595 5160 3.309388 CAAATGGCTCTACCGTATCGAG 58.691 50.000 0.00 0.00 43.94 4.04
4596 5161 1.535833 ATGGCTCTACCGTATCGAGG 58.464 55.000 0.00 0.00 43.94 4.63
4597 5162 1.170919 TGGCTCTACCGTATCGAGGC 61.171 60.000 12.12 12.12 46.76 4.70
4651 5281 5.050091 ACACTGCTGTTTTTCTAAGTCATCG 60.050 40.000 0.00 0.00 0.00 3.84
4659 5289 9.118236 CTGTTTTTCTAAGTCATCGGAAAATTC 57.882 33.333 0.00 0.00 37.46 2.17
4803 5461 6.416455 TGCACATTTCTAAAACTAAAGTTGCG 59.584 34.615 0.00 0.00 38.44 4.85
4855 5514 7.120579 TCGGTTTATGTTGCATAAAGAATCAGT 59.879 33.333 12.79 0.00 0.00 3.41
4865 5524 8.893219 TGCATAAAGAATCAGTGGTCTTATAG 57.107 34.615 9.54 5.21 32.90 1.31
4951 5611 2.499289 ACCATCTGATGAGAGTGGACAC 59.501 50.000 18.92 0.00 33.96 3.67
4952 5612 2.765135 CCATCTGATGAGAGTGGACACT 59.235 50.000 18.92 4.35 45.84 3.55
4953 5613 3.197333 CCATCTGATGAGAGTGGACACTT 59.803 47.826 18.92 0.00 42.66 3.16
4954 5614 4.403752 CCATCTGATGAGAGTGGACACTTA 59.596 45.833 18.92 0.00 42.66 2.24
4955 5615 5.347342 CATCTGATGAGAGTGGACACTTAC 58.653 45.833 12.27 4.92 42.66 2.34
4956 5616 4.407365 TCTGATGAGAGTGGACACTTACA 58.593 43.478 6.40 10.00 42.66 2.41
4957 5617 4.460731 TCTGATGAGAGTGGACACTTACAG 59.539 45.833 6.40 11.06 42.66 2.74
4958 5618 4.152647 TGATGAGAGTGGACACTTACAGT 58.847 43.478 6.40 1.95 42.66 3.55
5054 5723 0.454196 GTGGTGCGTTGGTTTTCACT 59.546 50.000 0.00 0.00 0.00 3.41
5055 5724 1.135228 GTGGTGCGTTGGTTTTCACTT 60.135 47.619 0.00 0.00 0.00 3.16
5056 5725 1.546476 TGGTGCGTTGGTTTTCACTTT 59.454 42.857 0.00 0.00 0.00 2.66
5057 5726 2.028930 TGGTGCGTTGGTTTTCACTTTT 60.029 40.909 0.00 0.00 0.00 2.27
5058 5727 2.601314 GGTGCGTTGGTTTTCACTTTTC 59.399 45.455 0.00 0.00 0.00 2.29
5059 5728 3.246619 GTGCGTTGGTTTTCACTTTTCA 58.753 40.909 0.00 0.00 0.00 2.69
5060 5729 3.060230 GTGCGTTGGTTTTCACTTTTCAC 59.940 43.478 0.00 0.00 0.00 3.18
5073 5742 4.104738 TCACTTTTCACCTCCATTTCCTCT 59.895 41.667 0.00 0.00 0.00 3.69
5074 5743 4.829492 CACTTTTCACCTCCATTTCCTCTT 59.171 41.667 0.00 0.00 0.00 2.85
5090 5759 2.094854 CCTCTTTGCTTGGTTGCATCTC 60.095 50.000 0.00 0.00 42.96 2.75
5103 5772 4.148825 ATCTCGTCTGGTGCGGCC 62.149 66.667 0.00 0.00 37.90 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.898472 AGATGATCCAGGATGCTACCG 59.102 52.381 6.70 0.00 34.73 4.02
1 2 3.072184 ACAAGATGATCCAGGATGCTACC 59.928 47.826 6.70 0.00 31.97 3.18
52 53 5.488341 ACCATGCGTAGACTTTAGTTTCAT 58.512 37.500 0.00 0.00 0.00 2.57
60 61 2.299013 TGACTGACCATGCGTAGACTTT 59.701 45.455 0.00 0.00 0.00 2.66
121 122 8.561738 ACTATCCACATACGAAAAGTCAAAAT 57.438 30.769 0.00 0.00 0.00 1.82
139 140 2.094906 CGTGAAGTGGACGAACTATCCA 60.095 50.000 0.00 0.00 44.20 3.41
140 141 2.527100 CGTGAAGTGGACGAACTATCC 58.473 52.381 0.00 0.00 39.21 2.59
142 143 1.203994 CCCGTGAAGTGGACGAACTAT 59.796 52.381 0.00 0.00 39.21 2.12
143 144 0.599558 CCCGTGAAGTGGACGAACTA 59.400 55.000 0.00 0.00 39.21 2.24
174 191 6.037720 GGAATCTAAGAAGAAAGCAAGTAGCC 59.962 42.308 0.00 0.00 38.70 3.93
189 206 1.414158 CCTCGGCTGGGAATCTAAGA 58.586 55.000 0.00 0.00 0.00 2.10
190 207 3.997672 CCTCGGCTGGGAATCTAAG 57.002 57.895 0.00 0.00 0.00 2.18
199 216 3.535962 GAGAGCTCCCTCGGCTGG 61.536 72.222 10.93 0.00 43.05 4.85
200 217 2.441901 AGAGAGCTCCCTCGGCTG 60.442 66.667 10.93 0.00 43.05 4.85
201 218 2.441901 CAGAGAGCTCCCTCGGCT 60.442 66.667 10.93 0.00 43.05 5.52
202 219 4.219999 GCAGAGAGCTCCCTCGGC 62.220 72.222 10.93 11.14 44.42 5.54
211 228 0.104671 GTGATGGGAGAGCAGAGAGC 59.895 60.000 0.00 0.00 46.19 4.09
212 229 0.752054 GGTGATGGGAGAGCAGAGAG 59.248 60.000 0.00 0.00 0.00 3.20
213 230 0.041684 TGGTGATGGGAGAGCAGAGA 59.958 55.000 0.00 0.00 0.00 3.10
214 231 0.177604 GTGGTGATGGGAGAGCAGAG 59.822 60.000 0.00 0.00 0.00 3.35
215 232 1.267574 GGTGGTGATGGGAGAGCAGA 61.268 60.000 0.00 0.00 0.00 4.26
216 233 1.222936 GGTGGTGATGGGAGAGCAG 59.777 63.158 0.00 0.00 0.00 4.24
217 234 1.538629 TGGTGGTGATGGGAGAGCA 60.539 57.895 0.00 0.00 0.00 4.26
218 235 1.078143 GTGGTGGTGATGGGAGAGC 60.078 63.158 0.00 0.00 0.00 4.09
219 236 0.692476 TTGTGGTGGTGATGGGAGAG 59.308 55.000 0.00 0.00 0.00 3.20
223 240 0.322456 ACGATTGTGGTGGTGATGGG 60.322 55.000 0.00 0.00 0.00 4.00
225 242 2.972625 ACTACGATTGTGGTGGTGATG 58.027 47.619 0.48 0.00 38.51 3.07
261 285 6.430007 TGATGCTATATGATGCTCTCTCCTA 58.570 40.000 0.00 0.00 0.00 2.94
263 287 5.595257 TGATGCTATATGATGCTCTCTCC 57.405 43.478 0.00 0.00 0.00 3.71
280 304 5.874810 TCGCTATAATTGTATCCCTTGATGC 59.125 40.000 0.00 0.00 34.50 3.91
281 305 7.099764 ACTCGCTATAATTGTATCCCTTGATG 58.900 38.462 0.00 0.00 32.18 3.07
283 307 6.665992 ACTCGCTATAATTGTATCCCTTGA 57.334 37.500 0.00 0.00 0.00 3.02
284 308 7.328737 GTGTACTCGCTATAATTGTATCCCTTG 59.671 40.741 0.00 0.00 0.00 3.61
285 309 7.232941 AGTGTACTCGCTATAATTGTATCCCTT 59.767 37.037 0.00 0.00 32.17 3.95
286 310 6.720288 AGTGTACTCGCTATAATTGTATCCCT 59.280 38.462 0.00 0.00 32.17 4.20
287 311 6.921914 AGTGTACTCGCTATAATTGTATCCC 58.078 40.000 0.00 0.00 32.17 3.85
288 312 7.591165 TGAGTGTACTCGCTATAATTGTATCC 58.409 38.462 7.46 0.00 45.72 2.59
289 313 8.903723 GTTGAGTGTACTCGCTATAATTGTATC 58.096 37.037 7.46 0.00 45.72 2.24
290 314 8.630917 AGTTGAGTGTACTCGCTATAATTGTAT 58.369 33.333 7.46 0.00 45.72 2.29
291 315 7.913821 CAGTTGAGTGTACTCGCTATAATTGTA 59.086 37.037 7.46 0.00 45.72 2.41
292 316 6.752351 CAGTTGAGTGTACTCGCTATAATTGT 59.248 38.462 7.46 0.00 45.72 2.71
293 317 6.972901 TCAGTTGAGTGTACTCGCTATAATTG 59.027 38.462 7.46 3.71 45.72 2.32
294 318 7.096884 TCAGTTGAGTGTACTCGCTATAATT 57.903 36.000 7.46 0.00 45.72 1.40
295 319 6.694877 TCAGTTGAGTGTACTCGCTATAAT 57.305 37.500 7.46 0.00 45.72 1.28
296 320 6.505044 TTCAGTTGAGTGTACTCGCTATAA 57.495 37.500 7.46 4.35 45.72 0.98
297 321 6.694877 ATTCAGTTGAGTGTACTCGCTATA 57.305 37.500 7.46 1.62 45.72 1.31
298 322 5.584253 ATTCAGTTGAGTGTACTCGCTAT 57.416 39.130 7.46 0.00 45.72 2.97
299 323 6.505044 TTATTCAGTTGAGTGTACTCGCTA 57.495 37.500 7.46 0.00 45.72 4.26
300 324 3.944055 ATTCAGTTGAGTGTACTCGCT 57.056 42.857 7.46 5.55 45.72 4.93
301 325 6.973474 ACTATTATTCAGTTGAGTGTACTCGC 59.027 38.462 7.46 3.52 45.72 5.03
302 326 8.912787 AACTATTATTCAGTTGAGTGTACTCG 57.087 34.615 7.46 0.00 45.72 4.18
325 349 7.174107 TGGGTAATGAGTAGTGGTAACTAAC 57.826 40.000 0.00 0.00 40.59 2.34
326 350 7.235193 TGTTGGGTAATGAGTAGTGGTAACTAA 59.765 37.037 0.00 0.00 40.59 2.24
333 357 4.819105 TCTGTTGGGTAATGAGTAGTGG 57.181 45.455 0.00 0.00 0.00 4.00
334 358 7.065085 CAGAATTCTGTTGGGTAATGAGTAGTG 59.935 40.741 24.65 0.00 39.09 2.74
335 359 7.106239 CAGAATTCTGTTGGGTAATGAGTAGT 58.894 38.462 24.65 0.00 39.09 2.73
336 360 6.037610 GCAGAATTCTGTTGGGTAATGAGTAG 59.962 42.308 30.88 5.40 45.45 2.57
337 361 5.880332 GCAGAATTCTGTTGGGTAATGAGTA 59.120 40.000 30.88 0.00 45.45 2.59
338 362 4.702131 GCAGAATTCTGTTGGGTAATGAGT 59.298 41.667 30.88 0.00 45.45 3.41
339 363 4.096984 GGCAGAATTCTGTTGGGTAATGAG 59.903 45.833 30.88 6.75 45.45 2.90
340 364 4.016444 GGCAGAATTCTGTTGGGTAATGA 58.984 43.478 30.88 0.00 45.45 2.57
341 365 3.131046 GGGCAGAATTCTGTTGGGTAATG 59.869 47.826 30.88 8.24 45.45 1.90
342 366 3.245586 TGGGCAGAATTCTGTTGGGTAAT 60.246 43.478 30.88 0.00 45.45 1.89
343 367 2.109128 TGGGCAGAATTCTGTTGGGTAA 59.891 45.455 30.88 11.65 45.45 2.85
344 368 1.707989 TGGGCAGAATTCTGTTGGGTA 59.292 47.619 30.88 13.06 45.45 3.69
345 369 0.482446 TGGGCAGAATTCTGTTGGGT 59.518 50.000 30.88 0.00 45.45 4.51
346 370 1.273327 GTTGGGCAGAATTCTGTTGGG 59.727 52.381 30.88 10.80 45.45 4.12
347 371 1.962807 TGTTGGGCAGAATTCTGTTGG 59.037 47.619 30.88 11.16 45.45 3.77
348 372 3.947910 ATGTTGGGCAGAATTCTGTTG 57.052 42.857 30.88 12.30 45.45 3.33
349 373 3.445096 GCTATGTTGGGCAGAATTCTGTT 59.555 43.478 30.88 13.31 45.45 3.16
355 379 4.443978 ACATAGCTATGTTGGGCAGAAT 57.556 40.909 29.70 6.91 43.99 2.40
397 421 4.389374 TGGACTGTAGGAAAAGCTGAAAG 58.611 43.478 0.00 0.00 0.00 2.62
399 423 3.646162 TCTGGACTGTAGGAAAAGCTGAA 59.354 43.478 0.00 0.00 0.00 3.02
400 424 3.239449 TCTGGACTGTAGGAAAAGCTGA 58.761 45.455 0.00 0.00 0.00 4.26
401 425 3.594134 CTCTGGACTGTAGGAAAAGCTG 58.406 50.000 0.00 0.00 0.00 4.24
402 426 2.569404 CCTCTGGACTGTAGGAAAAGCT 59.431 50.000 0.00 0.00 31.64 3.74
403 427 2.567615 TCCTCTGGACTGTAGGAAAAGC 59.432 50.000 0.00 0.00 36.47 3.51
404 428 4.528596 TCTTCCTCTGGACTGTAGGAAAAG 59.471 45.833 10.19 1.84 46.13 2.27
405 429 4.489737 TCTTCCTCTGGACTGTAGGAAAA 58.510 43.478 10.19 0.00 46.13 2.29
441 465 3.253432 GCTACAAGGAAAACAGGAACAGG 59.747 47.826 0.00 0.00 0.00 4.00
475 499 7.663493 GGATCCCTCCAATTTCTATTGTAAGAG 59.337 40.741 0.00 0.00 41.64 2.85
530 557 5.661056 TGAAGTTTCTCCATGTATCTCGT 57.339 39.130 0.00 0.00 0.00 4.18
531 558 6.276091 TGATGAAGTTTCTCCATGTATCTCG 58.724 40.000 0.00 0.00 0.00 4.04
543 570 5.827797 TGTGGCTTTTACTGATGAAGTTTCT 59.172 36.000 0.00 0.00 40.56 2.52
692 729 2.251893 GCGTCTGACACTAACAGTAGC 58.748 52.381 8.73 0.00 36.81 3.58
693 730 3.554259 TGCGTCTGACACTAACAGTAG 57.446 47.619 8.73 0.00 36.81 2.57
694 731 3.994204 TTGCGTCTGACACTAACAGTA 57.006 42.857 8.73 0.00 36.81 2.74
717 755 4.717233 ACAACAGATGAGCACAAAACAA 57.283 36.364 0.00 0.00 0.00 2.83
776 814 7.094634 CCATGTGTAGGATGGATAAATTGCTAC 60.095 40.741 0.00 0.00 42.81 3.58
953 999 1.066303 AGCAGACTAGCACTACATCGC 59.934 52.381 0.00 0.00 36.85 4.58
954 1000 2.098280 ACAGCAGACTAGCACTACATCG 59.902 50.000 0.00 0.00 36.85 3.84
1197 1249 1.565759 AGCCAGGCATCAAATGTCCTA 59.434 47.619 15.80 0.00 35.83 2.94
1199 1251 0.458669 CAGCCAGGCATCAAATGTCC 59.541 55.000 15.80 0.00 34.84 4.02
1271 1323 2.162408 GCAGCTTGCGAAGTTAGGAAAT 59.838 45.455 0.00 0.00 31.71 2.17
1325 1377 1.736681 CTGCAAAGCTCTTAGCCTGAC 59.263 52.381 0.00 0.00 43.77 3.51
1408 1460 8.335532 ACAGAAATTCCATAACGATCTTTCAA 57.664 30.769 0.00 0.00 0.00 2.69
1625 1677 6.724893 TGTAGATACTGCTTGCTATGGTTA 57.275 37.500 0.00 0.00 0.00 2.85
1827 1879 8.762645 ACAATCAGATATTTCTTGTCCTGTAGA 58.237 33.333 0.00 0.00 0.00 2.59
1980 2032 6.524101 AGAACTTTAAGCTCCACAACAAAA 57.476 33.333 0.00 0.00 0.00 2.44
2075 2127 2.196319 GCCCAAGGCCTCAGATTTG 58.804 57.895 5.23 0.00 44.06 2.32
2280 2334 7.233348 AGGAAGCAATTCTTTAAATGACTTGGA 59.767 33.333 13.95 0.00 34.56 3.53
2616 2670 3.709987 AGCATGCTTCTGAACAAACAAC 58.290 40.909 16.30 0.00 0.00 3.32
2881 2944 2.920524 TCGCAGGTCCAAAACTTGTAA 58.079 42.857 0.00 0.00 37.30 2.41
3095 3158 4.742201 TCAACTCGCCGAGCTGCC 62.742 66.667 15.20 0.00 32.04 4.85
3105 3168 3.906998 ACTTCTCATCAGTGTCAACTCG 58.093 45.455 0.00 0.00 32.98 4.18
3438 3502 6.463995 TGTTAATTGTTCCCCATCATAAGC 57.536 37.500 0.00 0.00 0.00 3.09
3546 3610 6.374333 TCCAAAGTATGTAGAACCTTCATTGC 59.626 38.462 0.00 0.00 0.00 3.56
3837 3909 5.846164 AGATTTTTGGGGGACTTGAGATTTT 59.154 36.000 0.00 0.00 0.00 1.82
3848 3920 3.238597 CTGGTTTGAGATTTTTGGGGGA 58.761 45.455 0.00 0.00 0.00 4.81
4205 4681 2.613133 TGCACGGTTAAGGTTGTTACAC 59.387 45.455 0.00 0.00 0.00 2.90
4268 4767 3.176924 ACAGCCCGATATATCTCCTGT 57.823 47.619 17.15 17.15 0.00 4.00
4341 4841 1.019673 CTCCATCCAAATGAGCACCG 58.980 55.000 0.00 0.00 34.61 4.94
4497 5029 2.351706 ACACTCCCCGCAAAAACTAA 57.648 45.000 0.00 0.00 0.00 2.24
4498 5030 1.950909 CAACACTCCCCGCAAAAACTA 59.049 47.619 0.00 0.00 0.00 2.24
4499 5031 0.744281 CAACACTCCCCGCAAAAACT 59.256 50.000 0.00 0.00 0.00 2.66
4500 5032 0.458260 ACAACACTCCCCGCAAAAAC 59.542 50.000 0.00 0.00 0.00 2.43
4507 5039 1.600023 TTTTGCTACAACACTCCCCG 58.400 50.000 0.00 0.00 0.00 5.73
4530 5062 3.858238 GCCGTTACACAGTAGACAGATTC 59.142 47.826 0.00 0.00 0.00 2.52
4536 5068 2.064014 GGTTGCCGTTACACAGTAGAC 58.936 52.381 0.00 0.00 0.00 2.59
4538 5070 1.796459 GTGGTTGCCGTTACACAGTAG 59.204 52.381 0.00 0.00 34.16 2.57
4540 5072 0.179468 AGTGGTTGCCGTTACACAGT 59.821 50.000 0.00 0.00 36.35 3.55
4541 5073 0.586319 CAGTGGTTGCCGTTACACAG 59.414 55.000 0.00 0.00 36.35 3.66
4543 5075 1.796459 CTACAGTGGTTGCCGTTACAC 59.204 52.381 0.00 0.00 0.00 2.90
4545 5077 2.443887 TCTACAGTGGTTGCCGTTAC 57.556 50.000 0.00 0.00 0.00 2.50
4546 5078 3.331150 CAATCTACAGTGGTTGCCGTTA 58.669 45.455 0.00 0.00 0.00 3.18
4547 5079 2.151202 CAATCTACAGTGGTTGCCGTT 58.849 47.619 0.00 0.00 0.00 4.44
4548 5080 1.808411 CAATCTACAGTGGTTGCCGT 58.192 50.000 0.00 0.00 0.00 5.68
4549 5081 0.447801 GCAATCTACAGTGGTTGCCG 59.552 55.000 10.92 0.00 40.66 5.69
4551 5083 2.426522 TCAGCAATCTACAGTGGTTGC 58.573 47.619 12.97 12.97 45.37 4.17
4592 5157 1.364626 AAAGCTTGCTCGATGCCTCG 61.365 55.000 0.00 4.89 46.41 4.63
4593 5158 1.656652 TAAAGCTTGCTCGATGCCTC 58.343 50.000 0.00 0.00 42.00 4.70
4594 5159 2.338577 ATAAAGCTTGCTCGATGCCT 57.661 45.000 0.00 0.00 42.00 4.75
4595 5160 2.098117 ACAATAAAGCTTGCTCGATGCC 59.902 45.455 0.00 0.00 42.00 4.40
4596 5161 3.411415 ACAATAAAGCTTGCTCGATGC 57.589 42.857 0.00 0.00 43.25 3.91
4597 5162 5.858049 TCAAAACAATAAAGCTTGCTCGATG 59.142 36.000 0.00 0.00 0.00 3.84
4601 5225 7.698836 TTCTTCAAAACAATAAAGCTTGCTC 57.301 32.000 0.00 0.00 0.00 4.26
4635 5265 9.118236 CTGAATTTTCCGATGACTTAGAAAAAC 57.882 33.333 0.00 0.00 40.47 2.43
4736 5367 2.476854 CGCAAAGCCTAAACTGATGCTC 60.477 50.000 0.00 0.00 33.43 4.26
4855 5514 5.630415 ATGGCTTAACAGCTATAAGACCA 57.370 39.130 22.25 22.25 45.03 4.02
4865 5524 0.457443 GGCTCCAATGGCTTAACAGC 59.543 55.000 0.00 0.00 46.52 4.40
4929 5589 3.701542 GTGTCCACTCTCATCAGATGGTA 59.298 47.826 10.67 0.00 32.87 3.25
5054 5723 4.039124 GCAAAGAGGAAATGGAGGTGAAAA 59.961 41.667 0.00 0.00 0.00 2.29
5055 5724 3.573967 GCAAAGAGGAAATGGAGGTGAAA 59.426 43.478 0.00 0.00 0.00 2.69
5056 5725 3.157087 GCAAAGAGGAAATGGAGGTGAA 58.843 45.455 0.00 0.00 0.00 3.18
5057 5726 2.376518 AGCAAAGAGGAAATGGAGGTGA 59.623 45.455 0.00 0.00 0.00 4.02
5058 5727 2.800250 AGCAAAGAGGAAATGGAGGTG 58.200 47.619 0.00 0.00 0.00 4.00
5059 5728 3.160269 CAAGCAAAGAGGAAATGGAGGT 58.840 45.455 0.00 0.00 0.00 3.85
5060 5729 2.494870 CCAAGCAAAGAGGAAATGGAGG 59.505 50.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.