Multiple sequence alignment - TraesCS7A01G117900

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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 TraesCS7A01G117900 chr7A 100.000 2430 0 0 1 2430 76193579 76191150 0.000000e+00 4488.0
1 TraesCS7A01G117900 chr7A 81.908 1415 197 36 455 1829 76489833 76488438 0.000000e+00 1140.0
2 TraesCS7A01G117900 chr7A 82.085 1362 163 55 455 1782 76501522 76500208 0.000000e+00 1088.0
3 TraesCS7A01G117900 chr7A 81.272 1415 202 41 455 1829 76412449 76411058 0.000000e+00 1086.0
4 TraesCS7A01G117900 chr7A 82.014 278 44 5 2145 2418 77024605 77024330 5.230000e-57 231.0
5 TraesCS7A01G117900 chr7B 95.718 1985 68 8 452 2430 12184638 12182665 0.000000e+00 3179.0
6 TraesCS7A01G117900 chr7B 82.961 1344 177 34 455 1763 12398567 12397241 0.000000e+00 1166.0
7 TraesCS7A01G117900 chr7B 81.523 1353 188 39 455 1782 12409606 12408291 0.000000e+00 1057.0
8 TraesCS7A01G117900 chr7B 77.518 1370 216 57 457 1768 13868367 13867032 0.000000e+00 739.0
9 TraesCS7A01G117900 chr7B 85.306 245 29 5 2145 2384 14065783 14065541 1.870000e-61 246.0
10 TraesCS7A01G117900 chr7B 82.787 244 39 2 2145 2385 13819323 13819080 5.260000e-52 215.0
11 TraesCS7A01G117900 chr7B 88.050 159 14 4 44 202 12193295 12193142 1.480000e-42 183.0
12 TraesCS7A01G117900 chr7B 86.777 121 13 2 59 178 13116816 13116698 5.450000e-27 132.0
13 TraesCS7A01G117900 chr7B 86.555 119 14 1 59 177 13808591 13808475 1.960000e-26 130.0
14 TraesCS7A01G117900 chr7B 85.950 121 14 2 59 178 14068243 14068125 2.540000e-25 126.0
15 TraesCS7A01G117900 chr7D 96.439 1685 45 6 749 2430 69661270 69659598 0.000000e+00 2765.0
16 TraesCS7A01G117900 chr7D 82.427 1343 185 33 455 1763 69819052 69817727 0.000000e+00 1125.0
17 TraesCS7A01G117900 chr7D 81.885 1358 172 49 455 1782 69872048 69870735 0.000000e+00 1077.0
18 TraesCS7A01G117900 chr7D 78.388 1365 211 50 452 1768 72169884 72171212 0.000000e+00 809.0
19 TraesCS7A01G117900 chr7D 79.027 658 116 16 1127 1768 71361876 71362527 4.800000e-117 431.0
20 TraesCS7A01G117900 chr7D 79.901 607 102 15 457 1053 71355957 71356553 6.210000e-116 427.0
21 TraesCS7A01G117900 chr7D 99.510 204 1 0 1 204 69661686 69661483 2.950000e-99 372.0
22 TraesCS7A01G117900 chr7D 85.470 351 47 2 1421 1768 71214603 71214254 1.780000e-96 363.0
23 TraesCS7A01G117900 chr7D 84.496 258 32 6 2133 2384 71546018 71545763 5.190000e-62 248.0
24 TraesCS7A01G117900 chr7D 88.333 120 12 1 59 178 71345272 71345389 2.520000e-30 143.0
25 TraesCS7A01G117900 chr7D 85.000 120 16 1 59 178 71355640 71355757 1.180000e-23 121.0
26 TraesCS7A01G117900 chr7D 100.000 54 0 0 312 365 69686570 69686623 1.540000e-17 100.0
27 TraesCS7A01G117900 chr7D 100.000 53 0 0 366 418 69661483 69661431 5.530000e-17 99.0
28 TraesCS7A01G117900 chrUn 77.712 1355 239 34 457 1768 82518161 82516827 0.000000e+00 771.0
29 TraesCS7A01G117900 chrUn 82.450 302 39 10 2089 2384 84246698 84246405 4.010000e-63 252.0
30 TraesCS7A01G117900 chrUn 84.082 245 32 5 2145 2384 82526201 82525959 1.880000e-56 230.0
31 TraesCS7A01G117900 chrUn 85.088 114 15 1 65 178 84248844 84248733 5.490000e-22 115.0
32 TraesCS7A01G117900 chrUn 100.000 54 0 0 312 365 418329020 418328967 1.540000e-17 100.0
33 TraesCS7A01G117900 chr2B 79.242 660 111 18 1127 1768 723393955 723393304 1.030000e-118 436.0
34 TraesCS7A01G117900 chr2B 87.500 120 13 1 59 178 723403273 723403156 1.170000e-28 137.0
35 TraesCS7A01G117900 chr4D 100.000 54 0 0 312 365 35780483 35780536 1.540000e-17 100.0
36 TraesCS7A01G117900 chr4D 100.000 54 0 0 312 365 348384428 348384481 1.540000e-17 100.0
37 TraesCS7A01G117900 chr3D 100.000 54 0 0 312 365 158930434 158930487 1.540000e-17 100.0
38 TraesCS7A01G117900 chr3D 100.000 54 0 0 312 365 158936549 158936602 1.540000e-17 100.0
39 TraesCS7A01G117900 chr1D 100.000 54 0 0 312 365 177260807 177260860 1.540000e-17 100.0
40 TraesCS7A01G117900 chr1D 100.000 54 0 0 312 365 283876765 283876712 1.540000e-17 100.0
41 TraesCS7A01G117900 chr5D 100.000 53 0 0 313 365 432407485 432407433 5.530000e-17 99.0
42 TraesCS7A01G117900 chr6D 100.000 51 0 0 204 254 108471547 108471597 7.150000e-16 95.3


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 TraesCS7A01G117900 chr7A 76191150 76193579 2429 True 4488.000000 4488 100.000000 1 2430 1 chr7A.!!$R1 2429
1 TraesCS7A01G117900 chr7A 76488438 76489833 1395 True 1140.000000 1140 81.908000 455 1829 1 chr7A.!!$R3 1374
2 TraesCS7A01G117900 chr7A 76500208 76501522 1314 True 1088.000000 1088 82.085000 455 1782 1 chr7A.!!$R4 1327
3 TraesCS7A01G117900 chr7A 76411058 76412449 1391 True 1086.000000 1086 81.272000 455 1829 1 chr7A.!!$R2 1374
4 TraesCS7A01G117900 chr7B 12182665 12184638 1973 True 3179.000000 3179 95.718000 452 2430 1 chr7B.!!$R1 1978
5 TraesCS7A01G117900 chr7B 12397241 12398567 1326 True 1166.000000 1166 82.961000 455 1763 1 chr7B.!!$R3 1308
6 TraesCS7A01G117900 chr7B 12408291 12409606 1315 True 1057.000000 1057 81.523000 455 1782 1 chr7B.!!$R4 1327
7 TraesCS7A01G117900 chr7B 13867032 13868367 1335 True 739.000000 739 77.518000 457 1768 1 chr7B.!!$R8 1311
8 TraesCS7A01G117900 chr7D 69817727 69819052 1325 True 1125.000000 1125 82.427000 455 1763 1 chr7D.!!$R1 1308
9 TraesCS7A01G117900 chr7D 69659598 69661686 2088 True 1078.666667 2765 98.649667 1 2430 3 chr7D.!!$R5 2429
10 TraesCS7A01G117900 chr7D 69870735 69872048 1313 True 1077.000000 1077 81.885000 455 1782 1 chr7D.!!$R2 1327
11 TraesCS7A01G117900 chr7D 72169884 72171212 1328 False 809.000000 809 78.388000 452 1768 1 chr7D.!!$F4 1316
12 TraesCS7A01G117900 chr7D 71361876 71362527 651 False 431.000000 431 79.027000 1127 1768 1 chr7D.!!$F3 641
13 TraesCS7A01G117900 chr7D 71355640 71356553 913 False 274.000000 427 82.450500 59 1053 2 chr7D.!!$F5 994
14 TraesCS7A01G117900 chrUn 82516827 82518161 1334 True 771.000000 771 77.712000 457 1768 1 chrUn.!!$R1 1311
15 TraesCS7A01G117900 chr2B 723393304 723393955 651 True 436.000000 436 79.242000 1127 1768 1 chr2B.!!$R1 641

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
423 424 0.897621 CCAAGTGGATTTTCTGCCCC 59.102 55.000 0.00 0.0 37.39 5.80 F
1046 1143 1.227973 GCAGGATTCTTAGCCGGGG 60.228 63.158 2.18 0.0 34.10 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1350 0.318955 GCCATGTGACAACAGCCAAC 60.319 55.000 0.0 0.0 40.39 3.77 R
1981 2142 4.019174 CACTAGGGTTTTGAGCCATTCAT 58.981 43.478 0.0 0.0 35.27 2.57 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
210 211 5.063180 ACAACATTATGTCATGCCTTGTG 57.937 39.130 0.00 0.00 27.71 3.33
211 212 4.766373 ACAACATTATGTCATGCCTTGTGA 59.234 37.500 0.00 0.00 27.71 3.58
212 213 5.419788 ACAACATTATGTCATGCCTTGTGAT 59.580 36.000 0.00 0.00 27.71 3.06
213 214 5.762825 ACATTATGTCATGCCTTGTGATC 57.237 39.130 0.00 0.00 0.00 2.92
214 215 5.443283 ACATTATGTCATGCCTTGTGATCT 58.557 37.500 0.00 0.00 0.00 2.75
215 216 5.530171 ACATTATGTCATGCCTTGTGATCTC 59.470 40.000 0.00 0.00 0.00 2.75
216 217 2.014335 TGTCATGCCTTGTGATCTCG 57.986 50.000 0.00 0.00 0.00 4.04
217 218 1.550072 TGTCATGCCTTGTGATCTCGA 59.450 47.619 0.00 0.00 0.00 4.04
218 219 2.028203 TGTCATGCCTTGTGATCTCGAA 60.028 45.455 0.00 0.00 0.00 3.71
219 220 2.349886 GTCATGCCTTGTGATCTCGAAC 59.650 50.000 0.00 0.00 0.00 3.95
220 221 2.028203 TCATGCCTTGTGATCTCGAACA 60.028 45.455 0.00 0.00 0.00 3.18
221 222 1.795768 TGCCTTGTGATCTCGAACAC 58.204 50.000 9.21 9.21 37.51 3.32
222 223 1.344438 TGCCTTGTGATCTCGAACACT 59.656 47.619 14.77 0.00 37.81 3.55
223 224 2.560981 TGCCTTGTGATCTCGAACACTA 59.439 45.455 14.77 8.82 37.81 2.74
224 225 2.924290 GCCTTGTGATCTCGAACACTAC 59.076 50.000 14.77 0.69 37.81 2.73
225 226 3.367498 GCCTTGTGATCTCGAACACTACT 60.367 47.826 14.77 0.00 37.81 2.57
226 227 4.810790 CCTTGTGATCTCGAACACTACTT 58.189 43.478 14.77 0.00 37.81 2.24
227 228 5.621555 GCCTTGTGATCTCGAACACTACTTA 60.622 44.000 14.77 0.00 37.81 2.24
228 229 6.565234 CCTTGTGATCTCGAACACTACTTAT 58.435 40.000 14.77 0.00 37.81 1.73
229 230 6.473778 CCTTGTGATCTCGAACACTACTTATG 59.526 42.308 14.77 0.00 37.81 1.90
230 231 6.753107 TGTGATCTCGAACACTACTTATGA 57.247 37.500 14.77 0.00 37.81 2.15
231 232 7.334844 TGTGATCTCGAACACTACTTATGAT 57.665 36.000 14.77 0.00 37.81 2.45
232 233 8.446599 TGTGATCTCGAACACTACTTATGATA 57.553 34.615 14.77 0.00 37.81 2.15
233 234 8.899771 TGTGATCTCGAACACTACTTATGATAA 58.100 33.333 14.77 0.00 37.81 1.75
234 235 9.900710 GTGATCTCGAACACTACTTATGATAAT 57.099 33.333 8.97 0.00 34.65 1.28
256 257 6.759497 ATAAGAAATCCAAAGTACAGTGGC 57.241 37.500 9.44 0.00 34.68 5.01
257 258 4.373156 AGAAATCCAAAGTACAGTGGCT 57.627 40.909 9.44 0.00 34.68 4.75
258 259 5.499004 AGAAATCCAAAGTACAGTGGCTA 57.501 39.130 9.44 0.00 34.68 3.93
259 260 6.067217 AGAAATCCAAAGTACAGTGGCTAT 57.933 37.500 9.44 0.00 34.68 2.97
260 261 7.195374 AGAAATCCAAAGTACAGTGGCTATA 57.805 36.000 9.44 0.00 34.68 1.31
261 262 7.275920 AGAAATCCAAAGTACAGTGGCTATAG 58.724 38.462 9.44 0.00 34.68 1.31
262 263 6.808321 AATCCAAAGTACAGTGGCTATAGA 57.192 37.500 3.21 0.00 34.68 1.98
263 264 6.808321 ATCCAAAGTACAGTGGCTATAGAA 57.192 37.500 3.21 0.00 34.68 2.10
264 265 6.614694 TCCAAAGTACAGTGGCTATAGAAA 57.385 37.500 3.21 0.00 34.68 2.52
265 266 6.640518 TCCAAAGTACAGTGGCTATAGAAAG 58.359 40.000 3.21 0.00 34.68 2.62
266 267 6.439375 TCCAAAGTACAGTGGCTATAGAAAGA 59.561 38.462 3.21 0.00 34.68 2.52
267 268 7.038587 TCCAAAGTACAGTGGCTATAGAAAGAA 60.039 37.037 3.21 0.00 34.68 2.52
268 269 7.606456 CCAAAGTACAGTGGCTATAGAAAGAAA 59.394 37.037 3.21 0.00 0.00 2.52
269 270 8.660373 CAAAGTACAGTGGCTATAGAAAGAAAG 58.340 37.037 3.21 0.00 0.00 2.62
270 271 6.879400 AGTACAGTGGCTATAGAAAGAAAGG 58.121 40.000 3.21 0.00 0.00 3.11
271 272 6.668283 AGTACAGTGGCTATAGAAAGAAAGGA 59.332 38.462 3.21 0.00 0.00 3.36
272 273 6.374417 ACAGTGGCTATAGAAAGAAAGGAA 57.626 37.500 3.21 0.00 0.00 3.36
273 274 6.410540 ACAGTGGCTATAGAAAGAAAGGAAG 58.589 40.000 3.21 0.00 0.00 3.46
274 275 6.213600 ACAGTGGCTATAGAAAGAAAGGAAGA 59.786 38.462 3.21 0.00 0.00 2.87
275 276 6.760770 CAGTGGCTATAGAAAGAAAGGAAGAG 59.239 42.308 3.21 0.00 0.00 2.85
276 277 6.442244 AGTGGCTATAGAAAGAAAGGAAGAGT 59.558 38.462 3.21 0.00 0.00 3.24
277 278 7.037945 AGTGGCTATAGAAAGAAAGGAAGAGTT 60.038 37.037 3.21 0.00 0.00 3.01
278 279 7.279090 GTGGCTATAGAAAGAAAGGAAGAGTTC 59.721 40.741 3.21 0.00 0.00 3.01
279 280 6.477360 GGCTATAGAAAGAAAGGAAGAGTTCG 59.523 42.308 3.21 0.00 0.00 3.95
280 281 7.259161 GCTATAGAAAGAAAGGAAGAGTTCGA 58.741 38.462 3.21 0.00 0.00 3.71
281 282 7.923878 GCTATAGAAAGAAAGGAAGAGTTCGAT 59.076 37.037 3.21 0.00 0.00 3.59
282 283 9.810545 CTATAGAAAGAAAGGAAGAGTTCGATT 57.189 33.333 0.00 0.00 0.00 3.34
283 284 6.793492 AGAAAGAAAGGAAGAGTTCGATTG 57.207 37.500 0.00 0.00 0.00 2.67
284 285 5.180304 AGAAAGAAAGGAAGAGTTCGATTGC 59.820 40.000 0.00 0.00 0.00 3.56
285 286 4.278975 AGAAAGGAAGAGTTCGATTGCT 57.721 40.909 0.00 0.00 0.00 3.91
286 287 4.646572 AGAAAGGAAGAGTTCGATTGCTT 58.353 39.130 0.00 0.00 38.53 3.91
287 288 4.453819 AGAAAGGAAGAGTTCGATTGCTTG 59.546 41.667 4.32 0.00 37.19 4.01
288 289 2.704572 AGGAAGAGTTCGATTGCTTGG 58.295 47.619 0.00 0.00 0.00 3.61
289 290 2.303022 AGGAAGAGTTCGATTGCTTGGA 59.697 45.455 0.00 0.00 0.00 3.53
290 291 2.675348 GGAAGAGTTCGATTGCTTGGAG 59.325 50.000 0.00 0.00 0.00 3.86
291 292 3.589988 GAAGAGTTCGATTGCTTGGAGA 58.410 45.455 0.00 0.00 0.00 3.71
292 293 3.685139 AGAGTTCGATTGCTTGGAGAA 57.315 42.857 0.00 0.00 0.00 2.87
293 294 3.594134 AGAGTTCGATTGCTTGGAGAAG 58.406 45.455 0.00 0.00 0.00 2.85
294 295 2.675348 GAGTTCGATTGCTTGGAGAAGG 59.325 50.000 0.00 0.00 0.00 3.46
295 296 2.039084 AGTTCGATTGCTTGGAGAAGGT 59.961 45.455 0.00 0.00 0.00 3.50
296 297 3.260884 AGTTCGATTGCTTGGAGAAGGTA 59.739 43.478 0.00 0.00 0.00 3.08
297 298 4.080863 AGTTCGATTGCTTGGAGAAGGTAT 60.081 41.667 0.00 0.00 0.00 2.73
298 299 4.487714 TCGATTGCTTGGAGAAGGTATT 57.512 40.909 0.00 0.00 0.00 1.89
299 300 4.442706 TCGATTGCTTGGAGAAGGTATTC 58.557 43.478 0.00 0.00 35.52 1.75
301 302 4.878397 CGATTGCTTGGAGAAGGTATTCTT 59.122 41.667 0.00 0.00 45.98 2.52
302 303 5.007136 CGATTGCTTGGAGAAGGTATTCTTC 59.993 44.000 0.00 0.00 45.98 2.87
312 313 5.074584 GAAGGTATTCTTCTTGGTCGACT 57.925 43.478 16.46 0.00 46.30 4.18
313 314 5.480205 GAAGGTATTCTTCTTGGTCGACTT 58.520 41.667 16.46 0.00 46.30 3.01
314 315 5.485209 AGGTATTCTTCTTGGTCGACTTT 57.515 39.130 16.46 0.00 0.00 2.66
315 316 5.866207 AGGTATTCTTCTTGGTCGACTTTT 58.134 37.500 16.46 0.00 0.00 2.27
316 317 6.296803 AGGTATTCTTCTTGGTCGACTTTTT 58.703 36.000 16.46 0.00 0.00 1.94
317 318 6.204882 AGGTATTCTTCTTGGTCGACTTTTTG 59.795 38.462 16.46 2.37 0.00 2.44
318 319 3.963383 TCTTCTTGGTCGACTTTTTGC 57.037 42.857 16.46 0.00 0.00 3.68
319 320 3.275143 TCTTCTTGGTCGACTTTTTGCA 58.725 40.909 16.46 0.12 0.00 4.08
320 321 3.882888 TCTTCTTGGTCGACTTTTTGCAT 59.117 39.130 16.46 0.00 0.00 3.96
321 322 5.060506 TCTTCTTGGTCGACTTTTTGCATA 58.939 37.500 16.46 0.00 0.00 3.14
322 323 5.529430 TCTTCTTGGTCGACTTTTTGCATAA 59.471 36.000 16.46 1.34 0.00 1.90
323 324 5.759506 TCTTGGTCGACTTTTTGCATAAA 57.240 34.783 16.46 2.28 0.00 1.40
324 325 6.137794 TCTTGGTCGACTTTTTGCATAAAA 57.862 33.333 16.46 5.46 34.13 1.52
325 326 6.565234 TCTTGGTCGACTTTTTGCATAAAAA 58.435 32.000 16.46 0.34 41.96 1.94
326 327 7.206687 TCTTGGTCGACTTTTTGCATAAAAAT 58.793 30.769 16.46 0.00 42.89 1.82
327 328 8.353684 TCTTGGTCGACTTTTTGCATAAAAATA 58.646 29.630 16.46 0.00 42.89 1.40
328 329 9.139174 CTTGGTCGACTTTTTGCATAAAAATAT 57.861 29.630 16.46 0.00 42.89 1.28
329 330 9.482627 TTGGTCGACTTTTTGCATAAAAATATT 57.517 25.926 16.46 0.00 42.89 1.28
330 331 9.482627 TGGTCGACTTTTTGCATAAAAATATTT 57.517 25.926 16.46 0.00 42.89 1.40
423 424 0.897621 CCAAGTGGATTTTCTGCCCC 59.102 55.000 0.00 0.00 37.39 5.80
424 425 1.550869 CCAAGTGGATTTTCTGCCCCT 60.551 52.381 0.00 0.00 37.39 4.79
434 435 5.891551 GGATTTTCTGCCCCTTATTTGACTA 59.108 40.000 0.00 0.00 0.00 2.59
435 436 6.039829 GGATTTTCTGCCCCTTATTTGACTAG 59.960 42.308 0.00 0.00 0.00 2.57
436 437 5.514500 TTTCTGCCCCTTATTTGACTAGT 57.486 39.130 0.00 0.00 0.00 2.57
437 438 4.487714 TCTGCCCCTTATTTGACTAGTG 57.512 45.455 0.00 0.00 0.00 2.74
438 439 4.101114 TCTGCCCCTTATTTGACTAGTGA 58.899 43.478 0.00 0.00 0.00 3.41
439 440 4.534500 TCTGCCCCTTATTTGACTAGTGAA 59.466 41.667 0.00 0.00 0.00 3.18
440 441 5.013704 TCTGCCCCTTATTTGACTAGTGAAA 59.986 40.000 10.01 10.01 0.00 2.69
441 442 5.636123 TGCCCCTTATTTGACTAGTGAAAA 58.364 37.500 11.61 7.14 0.00 2.29
442 443 6.071984 TGCCCCTTATTTGACTAGTGAAAAA 58.928 36.000 11.61 4.73 0.00 1.94
444 445 7.234577 TGCCCCTTATTTGACTAGTGAAAAATT 59.765 33.333 11.61 0.00 0.00 1.82
445 446 8.094548 GCCCCTTATTTGACTAGTGAAAAATTT 58.905 33.333 11.61 0.00 0.00 1.82
447 448 9.341899 CCCTTATTTGACTAGTGAAAAATTTCG 57.658 33.333 11.61 0.00 40.01 3.46
448 449 9.341899 CCTTATTTGACTAGTGAAAAATTTCGG 57.658 33.333 11.61 3.74 40.01 4.30
449 450 8.736751 TTATTTGACTAGTGAAAAATTTCGGC 57.263 30.769 11.61 0.00 40.01 5.54
450 451 5.759506 TTGACTAGTGAAAAATTTCGGCA 57.240 34.783 0.00 0.00 40.01 5.69
471 562 4.141482 GCAGTTAGATGGGGAGGTTATTCA 60.141 45.833 0.00 0.00 0.00 2.57
666 761 3.118629 TGAAGCCATCACCAGTAGATCAC 60.119 47.826 0.00 0.00 31.50 3.06
668 763 2.697751 AGCCATCACCAGTAGATCACTC 59.302 50.000 0.00 0.00 34.26 3.51
814 911 7.544566 GCTGATCAAATTTCACAGAATTCATGT 59.455 33.333 8.44 6.48 0.00 3.21
1046 1143 1.227973 GCAGGATTCTTAGCCGGGG 60.228 63.158 2.18 0.00 34.10 5.73
1063 1160 2.228103 CGGGGTAAGAAAAGCCTGAAAC 59.772 50.000 0.00 0.00 44.67 2.78
1071 1169 4.948847 AGAAAAGCCTGAAACAAATGACC 58.051 39.130 0.00 0.00 0.00 4.02
1207 1330 4.903045 ACCTTTAGTGCCAGCTTAACTA 57.097 40.909 0.00 0.00 0.00 2.24
1239 1362 1.873591 CTGGTAGTGTTGGCTGTTGTC 59.126 52.381 0.00 0.00 0.00 3.18
1265 1388 3.496884 TGGCAAGTTCTGTTTGTATCGTC 59.503 43.478 0.00 0.00 0.00 4.20
1332 1462 6.840780 ACTTTATTTCTGCATGGCTAAACT 57.159 33.333 0.00 0.00 0.00 2.66
1377 1517 2.625314 CCCGAATGATCTACTCTGCTGA 59.375 50.000 0.00 0.00 0.00 4.26
1430 1575 8.512956 AGATGTTTTCTCACAATTCTGATTGAG 58.487 33.333 6.17 0.00 44.37 3.02
1728 1884 3.960102 TGCCTTTGTCATGGTTCTTCTTT 59.040 39.130 0.00 0.00 0.00 2.52
1729 1885 4.405358 TGCCTTTGTCATGGTTCTTCTTTT 59.595 37.500 0.00 0.00 0.00 2.27
1894 2054 5.459434 TGCAATGAATTTTATATGCACTGCG 59.541 36.000 0.00 0.00 38.73 5.18
1900 2060 7.706159 TGAATTTTATATGCACTGCGAAGAAT 58.294 30.769 0.00 0.00 0.00 2.40
1903 2063 7.739022 TTTTATATGCACTGCGAAGAATTTG 57.261 32.000 0.00 0.00 0.00 2.32
1907 2067 3.779759 TGCACTGCGAAGAATTTGTTTT 58.220 36.364 0.00 0.00 0.00 2.43
1913 2074 5.108385 TGCGAAGAATTTGTTTTCCTCTC 57.892 39.130 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 6.779860 TGAAAGGCTCATCCCTAATAATACC 58.220 40.000 0.00 0.00 33.97 2.73
203 204 2.086054 AGTGTTCGAGATCACAAGGC 57.914 50.000 14.41 0.00 37.07 4.35
204 205 4.442375 AGTAGTGTTCGAGATCACAAGG 57.558 45.455 14.41 0.00 37.07 3.61
205 206 7.251281 TCATAAGTAGTGTTCGAGATCACAAG 58.749 38.462 14.41 0.47 37.07 3.16
206 207 7.153217 TCATAAGTAGTGTTCGAGATCACAA 57.847 36.000 14.41 0.00 37.07 3.33
207 208 6.753107 TCATAAGTAGTGTTCGAGATCACA 57.247 37.500 14.41 2.48 37.07 3.58
208 209 9.900710 ATTATCATAAGTAGTGTTCGAGATCAC 57.099 33.333 6.26 6.26 35.13 3.06
230 231 8.903820 GCCACTGTACTTTGGATTTCTTATTAT 58.096 33.333 15.32 0.00 34.46 1.28
231 232 8.107095 AGCCACTGTACTTTGGATTTCTTATTA 58.893 33.333 15.32 0.00 34.46 0.98
232 233 6.948309 AGCCACTGTACTTTGGATTTCTTATT 59.052 34.615 15.32 0.00 34.46 1.40
233 234 6.485171 AGCCACTGTACTTTGGATTTCTTAT 58.515 36.000 15.32 0.00 34.46 1.73
234 235 5.876357 AGCCACTGTACTTTGGATTTCTTA 58.124 37.500 15.32 0.00 34.46 2.10
235 236 4.729868 AGCCACTGTACTTTGGATTTCTT 58.270 39.130 15.32 0.00 34.46 2.52
236 237 4.373156 AGCCACTGTACTTTGGATTTCT 57.627 40.909 15.32 2.58 34.46 2.52
237 238 7.272978 TCTATAGCCACTGTACTTTGGATTTC 58.727 38.462 15.32 0.62 34.46 2.17
238 239 7.195374 TCTATAGCCACTGTACTTTGGATTT 57.805 36.000 15.32 8.17 34.46 2.17
239 240 6.808321 TCTATAGCCACTGTACTTTGGATT 57.192 37.500 15.32 6.72 34.46 3.01
240 241 6.808321 TTCTATAGCCACTGTACTTTGGAT 57.192 37.500 15.32 12.06 34.46 3.41
241 242 6.439375 TCTTTCTATAGCCACTGTACTTTGGA 59.561 38.462 15.32 0.00 34.46 3.53
242 243 6.640518 TCTTTCTATAGCCACTGTACTTTGG 58.359 40.000 8.54 8.54 35.81 3.28
243 244 8.547967 TTTCTTTCTATAGCCACTGTACTTTG 57.452 34.615 0.00 0.00 0.00 2.77
244 245 7.824779 CCTTTCTTTCTATAGCCACTGTACTTT 59.175 37.037 0.00 0.00 0.00 2.66
245 246 7.180408 TCCTTTCTTTCTATAGCCACTGTACTT 59.820 37.037 0.00 0.00 0.00 2.24
246 247 6.668283 TCCTTTCTTTCTATAGCCACTGTACT 59.332 38.462 0.00 0.00 0.00 2.73
247 248 6.875076 TCCTTTCTTTCTATAGCCACTGTAC 58.125 40.000 0.00 0.00 0.00 2.90
248 249 7.399191 TCTTCCTTTCTTTCTATAGCCACTGTA 59.601 37.037 0.00 0.00 0.00 2.74
249 250 6.213600 TCTTCCTTTCTTTCTATAGCCACTGT 59.786 38.462 0.00 0.00 0.00 3.55
250 251 6.644347 TCTTCCTTTCTTTCTATAGCCACTG 58.356 40.000 0.00 0.00 0.00 3.66
251 252 6.442244 ACTCTTCCTTTCTTTCTATAGCCACT 59.558 38.462 0.00 0.00 0.00 4.00
252 253 6.645306 ACTCTTCCTTTCTTTCTATAGCCAC 58.355 40.000 0.00 0.00 0.00 5.01
253 254 6.875972 ACTCTTCCTTTCTTTCTATAGCCA 57.124 37.500 0.00 0.00 0.00 4.75
254 255 6.477360 CGAACTCTTCCTTTCTTTCTATAGCC 59.523 42.308 0.00 0.00 0.00 3.93
255 256 7.259161 TCGAACTCTTCCTTTCTTTCTATAGC 58.741 38.462 0.00 0.00 0.00 2.97
256 257 9.810545 AATCGAACTCTTCCTTTCTTTCTATAG 57.189 33.333 0.00 0.00 0.00 1.31
257 258 9.587772 CAATCGAACTCTTCCTTTCTTTCTATA 57.412 33.333 0.00 0.00 0.00 1.31
258 259 7.065204 GCAATCGAACTCTTCCTTTCTTTCTAT 59.935 37.037 0.00 0.00 0.00 1.98
259 260 6.369065 GCAATCGAACTCTTCCTTTCTTTCTA 59.631 38.462 0.00 0.00 0.00 2.10
260 261 5.180304 GCAATCGAACTCTTCCTTTCTTTCT 59.820 40.000 0.00 0.00 0.00 2.52
261 262 5.180304 AGCAATCGAACTCTTCCTTTCTTTC 59.820 40.000 0.00 0.00 0.00 2.62
262 263 5.066593 AGCAATCGAACTCTTCCTTTCTTT 58.933 37.500 0.00 0.00 0.00 2.52
263 264 4.646572 AGCAATCGAACTCTTCCTTTCTT 58.353 39.130 0.00 0.00 0.00 2.52
264 265 4.278975 AGCAATCGAACTCTTCCTTTCT 57.721 40.909 0.00 0.00 0.00 2.52
265 266 4.378874 CCAAGCAATCGAACTCTTCCTTTC 60.379 45.833 0.00 0.00 0.00 2.62
266 267 3.503748 CCAAGCAATCGAACTCTTCCTTT 59.496 43.478 0.00 0.00 0.00 3.11
267 268 3.077359 CCAAGCAATCGAACTCTTCCTT 58.923 45.455 0.00 0.00 0.00 3.36
268 269 2.303022 TCCAAGCAATCGAACTCTTCCT 59.697 45.455 0.00 0.00 0.00 3.36
269 270 2.675348 CTCCAAGCAATCGAACTCTTCC 59.325 50.000 0.00 0.00 0.00 3.46
270 271 3.589988 TCTCCAAGCAATCGAACTCTTC 58.410 45.455 0.00 0.00 0.00 2.87
271 272 3.685139 TCTCCAAGCAATCGAACTCTT 57.315 42.857 0.00 0.00 0.00 2.85
272 273 3.594134 CTTCTCCAAGCAATCGAACTCT 58.406 45.455 0.00 0.00 0.00 3.24
273 274 2.675348 CCTTCTCCAAGCAATCGAACTC 59.325 50.000 0.00 0.00 0.00 3.01
274 275 2.039084 ACCTTCTCCAAGCAATCGAACT 59.961 45.455 0.00 0.00 0.00 3.01
275 276 2.427506 ACCTTCTCCAAGCAATCGAAC 58.572 47.619 0.00 0.00 0.00 3.95
276 277 2.859165 ACCTTCTCCAAGCAATCGAA 57.141 45.000 0.00 0.00 0.00 3.71
277 278 4.162320 AGAATACCTTCTCCAAGCAATCGA 59.838 41.667 0.00 0.00 37.09 3.59
278 279 4.446371 AGAATACCTTCTCCAAGCAATCG 58.554 43.478 0.00 0.00 37.09 3.34
279 280 6.370433 GAAGAATACCTTCTCCAAGCAATC 57.630 41.667 0.00 0.00 46.03 2.67
291 292 5.485209 AAGTCGACCAAGAAGAATACCTT 57.515 39.130 13.01 0.00 37.93 3.50
292 293 5.485209 AAAGTCGACCAAGAAGAATACCT 57.515 39.130 13.01 0.00 0.00 3.08
293 294 6.371389 CAAAAAGTCGACCAAGAAGAATACC 58.629 40.000 13.01 0.00 0.00 2.73
294 295 5.851703 GCAAAAAGTCGACCAAGAAGAATAC 59.148 40.000 13.01 0.00 0.00 1.89
295 296 5.529430 TGCAAAAAGTCGACCAAGAAGAATA 59.471 36.000 13.01 0.00 0.00 1.75
296 297 4.338118 TGCAAAAAGTCGACCAAGAAGAAT 59.662 37.500 13.01 0.00 0.00 2.40
297 298 3.692101 TGCAAAAAGTCGACCAAGAAGAA 59.308 39.130 13.01 0.00 0.00 2.52
298 299 3.275143 TGCAAAAAGTCGACCAAGAAGA 58.725 40.909 13.01 0.00 0.00 2.87
299 300 3.691049 TGCAAAAAGTCGACCAAGAAG 57.309 42.857 13.01 0.00 0.00 2.85
300 301 5.759506 TTATGCAAAAAGTCGACCAAGAA 57.240 34.783 13.01 0.00 0.00 2.52
301 302 5.759506 TTTATGCAAAAAGTCGACCAAGA 57.240 34.783 13.01 0.00 0.00 3.02
302 303 6.820470 TTTTTATGCAAAAAGTCGACCAAG 57.180 33.333 13.01 0.00 38.42 3.61
303 304 9.482627 AATATTTTTATGCAAAAAGTCGACCAA 57.517 25.926 13.01 0.00 44.57 3.67
304 305 9.482627 AAATATTTTTATGCAAAAAGTCGACCA 57.517 25.926 13.01 1.73 44.57 4.02
362 363 9.975218 ACAGTTTTATCTGATAAAATACCCTGT 57.025 29.630 28.75 28.75 43.98 4.00
419 420 6.584185 TTTTTCACTAGTCAAATAAGGGGC 57.416 37.500 0.00 0.00 0.00 5.80
423 424 8.850452 GCCGAAATTTTTCACTAGTCAAATAAG 58.150 33.333 0.00 0.00 37.01 1.73
424 425 8.353684 TGCCGAAATTTTTCACTAGTCAAATAA 58.646 29.630 0.00 0.00 37.01 1.40
434 435 6.381801 CATCTAACTGCCGAAATTTTTCACT 58.618 36.000 4.12 0.00 37.01 3.41
435 436 5.572896 CCATCTAACTGCCGAAATTTTTCAC 59.427 40.000 4.12 0.00 37.01 3.18
436 437 5.336372 CCCATCTAACTGCCGAAATTTTTCA 60.336 40.000 4.12 0.00 37.01 2.69
437 438 5.102313 CCCATCTAACTGCCGAAATTTTTC 58.898 41.667 0.00 0.00 0.00 2.29
438 439 4.081697 CCCCATCTAACTGCCGAAATTTTT 60.082 41.667 0.00 0.00 0.00 1.94
439 440 3.447229 CCCCATCTAACTGCCGAAATTTT 59.553 43.478 0.00 0.00 0.00 1.82
440 441 3.023832 CCCCATCTAACTGCCGAAATTT 58.976 45.455 0.00 0.00 0.00 1.82
441 442 2.241176 TCCCCATCTAACTGCCGAAATT 59.759 45.455 0.00 0.00 0.00 1.82
442 443 1.843851 TCCCCATCTAACTGCCGAAAT 59.156 47.619 0.00 0.00 0.00 2.17
444 445 0.830648 CTCCCCATCTAACTGCCGAA 59.169 55.000 0.00 0.00 0.00 4.30
445 446 1.048724 CCTCCCCATCTAACTGCCGA 61.049 60.000 0.00 0.00 0.00 5.54
447 448 0.919710 AACCTCCCCATCTAACTGCC 59.080 55.000 0.00 0.00 0.00 4.85
448 449 4.141482 TGAATAACCTCCCCATCTAACTGC 60.141 45.833 0.00 0.00 0.00 4.40
449 450 5.630415 TGAATAACCTCCCCATCTAACTG 57.370 43.478 0.00 0.00 0.00 3.16
450 451 6.043706 CAGATGAATAACCTCCCCATCTAACT 59.956 42.308 0.00 0.00 41.17 2.24
471 562 7.255730 GCCAATAGAATTTGATAAGGTGCAGAT 60.256 37.037 0.00 0.00 0.00 2.90
666 761 5.574891 TTCTCTTTCCTCTCTTGATCGAG 57.425 43.478 3.24 3.24 0.00 4.04
668 763 5.900425 TGATTCTCTTTCCTCTCTTGATCG 58.100 41.667 0.00 0.00 0.00 3.69
814 911 4.202141 GCATTTTGGACATTAGCAGCCATA 60.202 41.667 0.00 0.00 0.00 2.74
1024 1121 1.625818 CCGGCTAAGAATCCTGCCTAT 59.374 52.381 0.00 0.00 42.90 2.57
1046 1143 6.420903 GGTCATTTGTTTCAGGCTTTTCTTAC 59.579 38.462 0.00 0.00 0.00 2.34
1071 1169 9.093970 TGAAACAGAACTGTAATTACCATATCG 57.906 33.333 13.01 1.12 44.13 2.92
1106 1211 5.312974 TGCAGGGGATAATCCATCATTAGAA 59.687 40.000 0.00 0.00 38.64 2.10
1207 1330 6.291377 CCAACACTACCAGATTGCTATATGT 58.709 40.000 2.24 0.00 0.00 2.29
1227 1350 0.318955 GCCATGTGACAACAGCCAAC 60.319 55.000 0.00 0.00 40.39 3.77
1239 1362 3.441496 ACAAACAGAACTTGCCATGTG 57.559 42.857 0.00 0.00 0.00 3.21
1265 1388 1.013596 TGCCAAAACTATCATCGGCG 58.986 50.000 0.00 0.00 42.57 6.46
1332 1462 8.977412 GGGAAATGAAATAACAATAGAAAGGGA 58.023 33.333 0.00 0.00 0.00 4.20
1728 1884 2.816337 CGGGGCTAAAAGTTCCTGGAAA 60.816 50.000 11.40 0.00 0.00 3.13
1729 1885 1.271707 CGGGGCTAAAAGTTCCTGGAA 60.272 52.381 4.68 4.68 0.00 3.53
1894 2054 9.755804 ATCAAAAGAGAGGAAAACAAATTCTTC 57.244 29.630 0.00 0.00 36.10 2.87
1900 2060 8.533569 AACCTATCAAAAGAGAGGAAAACAAA 57.466 30.769 12.65 0.00 37.05 2.83
1903 2063 6.943146 AGGAACCTATCAAAAGAGAGGAAAAC 59.057 38.462 12.65 1.31 37.05 2.43
1907 2067 4.471386 CCAGGAACCTATCAAAAGAGAGGA 59.529 45.833 12.65 0.00 37.05 3.71
1913 2074 7.112779 ACTCAATACCAGGAACCTATCAAAAG 58.887 38.462 0.00 0.00 0.00 2.27
1981 2142 4.019174 CACTAGGGTTTTGAGCCATTCAT 58.981 43.478 0.00 0.00 35.27 2.57
2347 2508 4.890158 TCAAATCTCTAAGCTCCACACA 57.110 40.909 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.