Multiple sequence alignment - TraesCS4B01G121800

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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 TraesCS4B01G121800 chr4B 100.000 3496 0 0 1 3496 144744338 144747833 0.000000e+00 6457
1 TraesCS4B01G121800 chr4D 94.990 3054 88 24 455 3496 101020990 101023990 0.000000e+00 4732
2 TraesCS4B01G121800 chr4D 97.468 158 2 1 40 195 101020660 101020817 5.750000e-68 268
3 TraesCS4B01G121800 chr4D 94.805 154 8 0 312 465 101020815 101020968 1.250000e-59 241
4 TraesCS4B01G121800 chr4A 94.320 2183 87 19 1335 3496 474744129 474741963 0.000000e+00 3310
5 TraesCS4B01G121800 chr4A 91.568 925 44 11 358 1273 474745029 474744130 0.000000e+00 1245
6 TraesCS4B01G121800 chr4A 94.545 110 4 2 1 109 474745224 474745116 6.000000e-38 169


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 TraesCS4B01G121800 chr4B 144744338 144747833 3495 False 6457.000000 6457 100.000000 1 3496 1 chr4B.!!$F1 3495
1 TraesCS4B01G121800 chr4D 101020660 101023990 3330 False 1747.000000 4732 95.754333 40 3496 3 chr4D.!!$F1 3456
2 TraesCS4B01G121800 chr4A 474741963 474745224 3261 True 1574.666667 3310 93.477667 1 3496 3 chr4A.!!$R1 3495

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
739 787 0.035317 TGTGCTGTGGACTGGACATC 59.965 55.000 6.87 0.0 40.12 3.06 F
740 788 0.322975 GTGCTGTGGACTGGACATCT 59.677 55.000 3.89 0.0 36.46 2.90 F
1092 1143 1.073897 GTGCTGGTTCAGGCTCCTT 59.926 57.895 0.00 0.0 31.21 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2140 0.036952 GAACTCTGGCTGCAGTGCTA 60.037 55.0 17.60 0.0 0.00 3.49 R
2329 2387 0.435388 CGTTGTTATGTACACGCGCA 59.565 50.0 5.73 0.0 36.21 6.09 R
3084 3146 0.107268 GTACAGTGTTGGGGTCGGTT 59.893 55.0 0.00 0.0 0.00 4.44 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
198 203 3.865700 GCACTGTGGCCAAAACTAC 57.134 52.632 7.24 0.00 0.00 2.73
199 204 1.318576 GCACTGTGGCCAAAACTACT 58.681 50.000 7.24 0.00 0.00 2.57
200 205 2.500229 GCACTGTGGCCAAAACTACTA 58.500 47.619 7.24 0.00 0.00 1.82
201 206 3.081804 GCACTGTGGCCAAAACTACTAT 58.918 45.455 7.24 0.00 0.00 2.12
202 207 3.119849 GCACTGTGGCCAAAACTACTATG 60.120 47.826 7.24 0.00 0.00 2.23
203 208 4.072131 CACTGTGGCCAAAACTACTATGT 58.928 43.478 7.24 0.00 0.00 2.29
204 209 4.518970 CACTGTGGCCAAAACTACTATGTT 59.481 41.667 7.24 0.00 0.00 2.71
205 210 5.009610 CACTGTGGCCAAAACTACTATGTTT 59.990 40.000 7.24 0.00 41.32 2.83
206 211 5.596772 ACTGTGGCCAAAACTACTATGTTTT 59.403 36.000 7.24 0.00 46.96 2.43
215 220 4.361451 ACTACTATGTTTTGCATGCTGC 57.639 40.909 20.33 6.82 45.29 5.25
216 221 4.012374 ACTACTATGTTTTGCATGCTGCT 58.988 39.130 20.33 0.34 45.31 4.24
217 222 3.498927 ACTATGTTTTGCATGCTGCTC 57.501 42.857 20.33 7.80 45.31 4.26
218 223 2.159476 ACTATGTTTTGCATGCTGCTCG 60.159 45.455 20.33 2.54 45.31 5.03
219 224 0.599558 ATGTTTTGCATGCTGCTCGT 59.400 45.000 20.33 5.89 45.31 4.18
220 225 0.385029 TGTTTTGCATGCTGCTCGTT 59.615 45.000 20.33 0.00 45.31 3.85
221 226 1.202394 TGTTTTGCATGCTGCTCGTTT 60.202 42.857 20.33 0.00 45.31 3.60
222 227 1.190763 GTTTTGCATGCTGCTCGTTTG 59.809 47.619 20.33 0.00 45.31 2.93
223 228 0.385029 TTTGCATGCTGCTCGTTTGT 59.615 45.000 20.33 0.00 45.31 2.83
224 229 0.385029 TTGCATGCTGCTCGTTTGTT 59.615 45.000 20.33 0.00 45.31 2.83
225 230 0.040157 TGCATGCTGCTCGTTTGTTC 60.040 50.000 20.33 0.00 45.31 3.18
226 231 0.239347 GCATGCTGCTCGTTTGTTCT 59.761 50.000 11.37 0.00 40.96 3.01
227 232 1.959747 CATGCTGCTCGTTTGTTCTG 58.040 50.000 0.00 0.00 0.00 3.02
228 233 1.532437 CATGCTGCTCGTTTGTTCTGA 59.468 47.619 0.00 0.00 0.00 3.27
229 234 1.662517 TGCTGCTCGTTTGTTCTGAA 58.337 45.000 0.00 0.00 0.00 3.02
230 235 1.330521 TGCTGCTCGTTTGTTCTGAAC 59.669 47.619 13.49 13.49 0.00 3.18
231 236 1.334149 GCTGCTCGTTTGTTCTGAACC 60.334 52.381 17.26 2.02 0.00 3.62
232 237 1.939934 CTGCTCGTTTGTTCTGAACCA 59.060 47.619 17.26 4.09 0.00 3.67
233 238 1.939934 TGCTCGTTTGTTCTGAACCAG 59.060 47.619 17.26 6.68 0.00 4.00
234 239 1.264288 GCTCGTTTGTTCTGAACCAGG 59.736 52.381 17.26 9.88 31.51 4.45
235 240 1.873591 CTCGTTTGTTCTGAACCAGGG 59.126 52.381 17.26 5.45 31.51 4.45
236 241 1.487142 TCGTTTGTTCTGAACCAGGGA 59.513 47.619 17.26 7.54 31.51 4.20
237 242 1.602377 CGTTTGTTCTGAACCAGGGAC 59.398 52.381 17.26 8.02 31.51 4.46
238 243 1.954382 GTTTGTTCTGAACCAGGGACC 59.046 52.381 17.26 0.00 31.51 4.46
239 244 0.476771 TTGTTCTGAACCAGGGACCC 59.523 55.000 17.26 0.59 31.51 4.46
240 245 1.003718 GTTCTGAACCAGGGACCCG 60.004 63.158 9.38 0.00 31.51 5.28
241 246 2.890766 TTCTGAACCAGGGACCCGC 61.891 63.158 4.40 0.00 31.51 6.13
242 247 3.636231 CTGAACCAGGGACCCGCA 61.636 66.667 4.40 0.00 0.00 5.69
243 248 2.933287 TGAACCAGGGACCCGCAT 60.933 61.111 4.40 0.00 0.00 4.73
244 249 2.438434 GAACCAGGGACCCGCATG 60.438 66.667 4.40 0.00 0.00 4.06
245 250 3.995506 GAACCAGGGACCCGCATGG 62.996 68.421 14.48 14.48 38.83 3.66
254 259 2.674754 CCCGCATGGTTACCTGGT 59.325 61.111 4.05 4.05 0.00 4.00
255 260 1.001393 CCCGCATGGTTACCTGGTT 60.001 57.895 3.84 0.00 0.00 3.67
256 261 0.610785 CCCGCATGGTTACCTGGTTT 60.611 55.000 3.84 0.00 0.00 3.27
257 262 1.253100 CCGCATGGTTACCTGGTTTT 58.747 50.000 3.84 0.00 0.00 2.43
258 263 1.067915 CCGCATGGTTACCTGGTTTTG 60.068 52.381 3.84 0.00 0.00 2.44
259 264 1.668628 CGCATGGTTACCTGGTTTTGC 60.669 52.381 3.84 6.84 0.00 3.68
260 265 1.618343 GCATGGTTACCTGGTTTTGCT 59.382 47.619 3.84 0.00 0.00 3.91
261 266 2.037121 GCATGGTTACCTGGTTTTGCTT 59.963 45.455 3.84 0.00 0.00 3.91
262 267 3.494223 GCATGGTTACCTGGTTTTGCTTT 60.494 43.478 3.84 0.00 0.00 3.51
263 268 4.306600 CATGGTTACCTGGTTTTGCTTTC 58.693 43.478 3.84 0.00 0.00 2.62
264 269 3.366396 TGGTTACCTGGTTTTGCTTTCA 58.634 40.909 3.84 0.00 0.00 2.69
265 270 3.383185 TGGTTACCTGGTTTTGCTTTCAG 59.617 43.478 3.84 0.00 0.00 3.02
266 271 3.383505 GGTTACCTGGTTTTGCTTTCAGT 59.616 43.478 3.84 0.00 0.00 3.41
267 272 4.142026 GGTTACCTGGTTTTGCTTTCAGTT 60.142 41.667 3.84 0.00 0.00 3.16
268 273 5.416083 GTTACCTGGTTTTGCTTTCAGTTT 58.584 37.500 3.84 0.00 0.00 2.66
269 274 4.123497 ACCTGGTTTTGCTTTCAGTTTC 57.877 40.909 0.00 0.00 0.00 2.78
270 275 3.769300 ACCTGGTTTTGCTTTCAGTTTCT 59.231 39.130 0.00 0.00 0.00 2.52
271 276 4.953579 ACCTGGTTTTGCTTTCAGTTTCTA 59.046 37.500 0.00 0.00 0.00 2.10
272 277 5.067805 ACCTGGTTTTGCTTTCAGTTTCTAG 59.932 40.000 0.00 0.00 0.00 2.43
273 278 5.067805 CCTGGTTTTGCTTTCAGTTTCTAGT 59.932 40.000 0.00 0.00 0.00 2.57
274 279 6.405842 CCTGGTTTTGCTTTCAGTTTCTAGTT 60.406 38.462 0.00 0.00 0.00 2.24
275 280 6.560711 TGGTTTTGCTTTCAGTTTCTAGTTC 58.439 36.000 0.00 0.00 0.00 3.01
276 281 5.977725 GGTTTTGCTTTCAGTTTCTAGTTCC 59.022 40.000 0.00 0.00 0.00 3.62
277 282 6.405397 GGTTTTGCTTTCAGTTTCTAGTTCCA 60.405 38.462 0.00 0.00 0.00 3.53
278 283 6.377327 TTTGCTTTCAGTTTCTAGTTCCAG 57.623 37.500 0.00 0.00 0.00 3.86
279 284 5.036117 TGCTTTCAGTTTCTAGTTCCAGT 57.964 39.130 0.00 0.00 0.00 4.00
280 285 5.437060 TGCTTTCAGTTTCTAGTTCCAGTT 58.563 37.500 0.00 0.00 0.00 3.16
281 286 5.885912 TGCTTTCAGTTTCTAGTTCCAGTTT 59.114 36.000 0.00 0.00 0.00 2.66
282 287 6.183360 TGCTTTCAGTTTCTAGTTCCAGTTTG 60.183 38.462 0.00 0.00 0.00 2.93
283 288 6.038271 GCTTTCAGTTTCTAGTTCCAGTTTGA 59.962 38.462 0.00 0.00 0.00 2.69
284 289 7.255277 GCTTTCAGTTTCTAGTTCCAGTTTGAT 60.255 37.037 0.00 0.00 0.00 2.57
285 290 7.496529 TTCAGTTTCTAGTTCCAGTTTGATG 57.503 36.000 0.00 0.00 0.00 3.07
286 291 6.591935 TCAGTTTCTAGTTCCAGTTTGATGT 58.408 36.000 0.00 0.00 0.00 3.06
287 292 7.054124 TCAGTTTCTAGTTCCAGTTTGATGTT 58.946 34.615 0.00 0.00 0.00 2.71
288 293 7.556275 TCAGTTTCTAGTTCCAGTTTGATGTTT 59.444 33.333 0.00 0.00 0.00 2.83
289 294 7.645340 CAGTTTCTAGTTCCAGTTTGATGTTTG 59.355 37.037 0.00 0.00 0.00 2.93
290 295 5.689383 TCTAGTTCCAGTTTGATGTTTGC 57.311 39.130 0.00 0.00 0.00 3.68
291 296 5.376625 TCTAGTTCCAGTTTGATGTTTGCT 58.623 37.500 0.00 0.00 0.00 3.91
292 297 4.574599 AGTTCCAGTTTGATGTTTGCTC 57.425 40.909 0.00 0.00 0.00 4.26
293 298 3.953612 AGTTCCAGTTTGATGTTTGCTCA 59.046 39.130 0.00 0.00 0.00 4.26
294 299 3.988379 TCCAGTTTGATGTTTGCTCAC 57.012 42.857 0.00 0.00 0.00 3.51
295 300 3.554934 TCCAGTTTGATGTTTGCTCACT 58.445 40.909 0.00 0.00 0.00 3.41
296 301 4.713553 TCCAGTTTGATGTTTGCTCACTA 58.286 39.130 0.00 0.00 0.00 2.74
297 302 5.316167 TCCAGTTTGATGTTTGCTCACTAT 58.684 37.500 0.00 0.00 0.00 2.12
298 303 5.181811 TCCAGTTTGATGTTTGCTCACTATG 59.818 40.000 0.00 0.00 0.00 2.23
299 304 5.396484 CAGTTTGATGTTTGCTCACTATGG 58.604 41.667 0.00 0.00 0.00 2.74
300 305 5.048504 CAGTTTGATGTTTGCTCACTATGGT 60.049 40.000 0.00 0.00 0.00 3.55
301 306 5.536161 AGTTTGATGTTTGCTCACTATGGTT 59.464 36.000 0.00 0.00 0.00 3.67
302 307 6.040842 AGTTTGATGTTTGCTCACTATGGTTT 59.959 34.615 0.00 0.00 0.00 3.27
303 308 5.627499 TGATGTTTGCTCACTATGGTTTC 57.373 39.130 0.00 0.00 0.00 2.78
304 309 5.316167 TGATGTTTGCTCACTATGGTTTCT 58.684 37.500 0.00 0.00 0.00 2.52
305 310 5.412594 TGATGTTTGCTCACTATGGTTTCTC 59.587 40.000 0.00 0.00 0.00 2.87
306 311 4.973168 TGTTTGCTCACTATGGTTTCTCT 58.027 39.130 0.00 0.00 0.00 3.10
307 312 6.109156 TGTTTGCTCACTATGGTTTCTCTA 57.891 37.500 0.00 0.00 0.00 2.43
308 313 6.530120 TGTTTGCTCACTATGGTTTCTCTAA 58.470 36.000 0.00 0.00 0.00 2.10
309 314 7.168219 TGTTTGCTCACTATGGTTTCTCTAAT 58.832 34.615 0.00 0.00 0.00 1.73
310 315 7.119699 TGTTTGCTCACTATGGTTTCTCTAATG 59.880 37.037 0.00 0.00 0.00 1.90
337 342 3.007506 TCGATGAGGAGGCTTGTTGTTTA 59.992 43.478 0.00 0.00 0.00 2.01
378 383 5.461526 GTTGGACAAGCCTTTGATTCTTAC 58.538 41.667 0.00 0.00 37.73 2.34
452 457 2.094597 TGGCATGCATGTGTTTTCTAGC 60.095 45.455 26.79 9.02 0.00 3.42
453 458 2.094597 GGCATGCATGTGTTTTCTAGCA 60.095 45.455 26.79 0.00 36.34 3.49
529 572 5.843969 ACCCAGGAAATAAAGGACAAAACAT 59.156 36.000 0.00 0.00 0.00 2.71
541 584 5.227908 AGGACAAAACATCGTGTAGTACAG 58.772 41.667 2.39 0.00 0.00 2.74
579 622 1.878070 TGCGAAGGCAGCAATTCTG 59.122 52.632 0.00 1.80 46.21 3.02
616 664 1.286354 CCGTACGTGACAAATGGCGT 61.286 55.000 15.21 0.00 40.76 5.68
617 665 1.338765 CGTACGTGACAAATGGCGTA 58.661 50.000 7.22 0.00 38.56 4.42
618 666 1.921887 CGTACGTGACAAATGGCGTAT 59.078 47.619 7.22 0.00 40.98 3.06
638 686 6.557291 GTATTACATACGTAGCCTCTGTCT 57.443 41.667 0.08 0.00 0.00 3.41
719 767 7.052873 TCCTTAGGATAGTATATAGGACGTGC 58.947 42.308 0.00 0.00 0.00 5.34
732 780 2.280389 CGTGCTGTGCTGTGGACT 60.280 61.111 0.00 0.00 0.00 3.85
733 781 2.601398 CGTGCTGTGCTGTGGACTG 61.601 63.158 0.00 0.00 0.00 3.51
734 782 2.111669 TGCTGTGCTGTGGACTGG 59.888 61.111 0.00 0.00 0.00 4.00
735 783 2.427320 GCTGTGCTGTGGACTGGA 59.573 61.111 0.00 0.00 0.00 3.86
736 784 1.963338 GCTGTGCTGTGGACTGGAC 60.963 63.158 2.02 2.02 36.85 4.02
737 785 1.447217 CTGTGCTGTGGACTGGACA 59.553 57.895 9.92 9.92 42.00 4.02
738 786 0.035881 CTGTGCTGTGGACTGGACAT 59.964 55.000 10.59 0.00 42.88 3.06
739 787 0.035317 TGTGCTGTGGACTGGACATC 59.965 55.000 6.87 0.00 40.12 3.06
740 788 0.322975 GTGCTGTGGACTGGACATCT 59.677 55.000 3.89 0.00 36.46 2.90
741 789 1.550524 GTGCTGTGGACTGGACATCTA 59.449 52.381 3.89 0.00 36.46 1.98
742 790 2.169352 GTGCTGTGGACTGGACATCTAT 59.831 50.000 3.89 0.00 36.46 1.98
743 791 2.840038 TGCTGTGGACTGGACATCTATT 59.160 45.455 0.00 0.00 0.00 1.73
744 792 3.264193 TGCTGTGGACTGGACATCTATTT 59.736 43.478 0.00 0.00 0.00 1.40
745 793 4.263462 TGCTGTGGACTGGACATCTATTTT 60.263 41.667 0.00 0.00 0.00 1.82
746 794 4.702131 GCTGTGGACTGGACATCTATTTTT 59.298 41.667 0.00 0.00 0.00 1.94
747 795 5.163713 GCTGTGGACTGGACATCTATTTTTC 60.164 44.000 0.00 0.00 0.00 2.29
748 796 5.253330 TGTGGACTGGACATCTATTTTTCC 58.747 41.667 0.00 0.00 0.00 3.13
749 797 5.014123 TGTGGACTGGACATCTATTTTTCCT 59.986 40.000 0.00 0.00 0.00 3.36
754 802 7.875554 GGACTGGACATCTATTTTTCCTATCTC 59.124 40.741 0.00 0.00 0.00 2.75
934 982 9.804758 GCCTATATAAATAGCTCGTCACTAAAT 57.195 33.333 0.00 0.00 34.78 1.40
948 996 2.193865 CTAAATGGCACGCAACCGCA 62.194 55.000 0.00 0.00 38.40 5.69
1092 1143 1.073897 GTGCTGGTTCAGGCTCCTT 59.926 57.895 0.00 0.00 31.21 3.36
1099 1150 1.151810 TTCAGGCTCCTTCCCCTGT 60.152 57.895 6.57 0.00 46.83 4.00
1322 1373 7.548780 TGCATGCACTAGTTTTTCTTTTTCTTT 59.451 29.630 18.46 0.00 0.00 2.52
1323 1374 8.390354 GCATGCACTAGTTTTTCTTTTTCTTTT 58.610 29.630 14.21 0.00 0.00 2.27
1376 1427 6.261158 GTCTCAGGGGAACAAAATATAGCTTC 59.739 42.308 0.00 0.00 0.00 3.86
1403 1456 8.431910 AACTACATTCTTCTAAGAACTACCCA 57.568 34.615 7.29 0.00 46.80 4.51
1423 1476 7.253905 ACCCACTCTGTAAGCTTTTATAAGA 57.746 36.000 3.20 0.34 32.92 2.10
1449 1502 8.788806 ACGTTTTATGATCACACTTATTTTCCA 58.211 29.630 0.00 0.00 0.00 3.53
1637 1695 2.734606 GTGGTTTTTGCGGGATAAAAGC 59.265 45.455 0.00 0.00 40.36 3.51
1697 1755 7.442969 ACAATAACAAGGAAATCTCGTGTTACA 59.557 33.333 0.00 0.00 36.41 2.41
1714 1772 6.197282 CGTGTTACAGATTGATACTAGCACAG 59.803 42.308 0.00 0.00 0.00 3.66
1899 1957 4.283363 AGACATCAAAGATGTGACTGCT 57.717 40.909 16.55 5.17 31.52 4.24
1964 2022 3.718815 GGTTACAGTAGCAGCTACCATC 58.281 50.000 26.20 13.52 37.65 3.51
2078 2136 2.033448 TGGATCACCCACCAACGC 59.967 61.111 0.00 0.00 40.82 4.84
2082 2140 3.469863 ATCACCCACCAACGCGTGT 62.470 57.895 14.98 3.90 31.47 4.49
2160 2218 3.694535 TGGTTAACGAAATTGCAACGT 57.305 38.095 0.00 4.20 41.97 3.99
2170 2228 4.030529 CGAAATTGCAACGTTGAATCATCC 59.969 41.667 31.62 12.27 0.00 3.51
2185 2243 3.021269 TCATCCGCCGATGTGTTATAC 57.979 47.619 13.63 0.00 45.32 1.47
2246 2304 1.748122 CTCTGCGCTTGCCTCCATT 60.748 57.895 9.73 0.00 38.03 3.16
2328 2386 0.603707 CAGCACAATCGACCAGGTGT 60.604 55.000 0.00 0.00 33.88 4.16
2329 2387 0.108585 AGCACAATCGACCAGGTGTT 59.891 50.000 0.00 0.00 33.88 3.32
2396 2454 3.133014 CAGGAGGCGATGATCCGT 58.867 61.111 0.00 0.00 40.73 4.69
2518 2576 2.164827 CACTTGTACACCATGCATGCAT 59.835 45.455 27.46 27.46 37.08 3.96
2620 2678 6.661377 TGCCAATTAAGTTATCAACAAGGCTA 59.339 34.615 0.00 0.00 38.07 3.93
2621 2679 7.341769 TGCCAATTAAGTTATCAACAAGGCTAT 59.658 33.333 0.00 0.00 38.07 2.97
2622 2680 7.649306 GCCAATTAAGTTATCAACAAGGCTATG 59.351 37.037 0.00 0.00 34.59 2.23
2623 2681 8.686334 CCAATTAAGTTATCAACAAGGCTATGT 58.314 33.333 0.00 0.00 34.24 2.29
3156 3218 2.586245 CTCATCTCCGCCTTGCCA 59.414 61.111 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.251251 ATGGTCCAACAGAAAGCAGC 58.749 50.000 0.00 0.00 0.00 5.25
30 31 3.553508 CCAAATGGTCCAACAGAAAGCAG 60.554 47.826 0.00 0.00 0.00 4.24
31 32 2.364970 CCAAATGGTCCAACAGAAAGCA 59.635 45.455 0.00 0.00 0.00 3.91
32 33 2.627699 TCCAAATGGTCCAACAGAAAGC 59.372 45.455 0.00 0.00 36.34 3.51
33 34 4.584325 TCTTCCAAATGGTCCAACAGAAAG 59.416 41.667 0.00 0.00 36.34 2.62
36 37 3.486383 GTCTTCCAAATGGTCCAACAGA 58.514 45.455 0.00 0.00 36.34 3.41
37 38 2.558359 GGTCTTCCAAATGGTCCAACAG 59.442 50.000 0.00 0.00 36.34 3.16
208 213 1.532437 TCAGAACAAACGAGCAGCATG 59.468 47.619 0.00 0.00 40.87 4.06
209 214 1.882912 TCAGAACAAACGAGCAGCAT 58.117 45.000 0.00 0.00 0.00 3.79
210 215 1.330521 GTTCAGAACAAACGAGCAGCA 59.669 47.619 8.54 0.00 0.00 4.41
211 216 1.334149 GGTTCAGAACAAACGAGCAGC 60.334 52.381 15.36 0.00 0.00 5.25
212 217 1.939934 TGGTTCAGAACAAACGAGCAG 59.060 47.619 15.36 0.00 0.00 4.24
213 218 1.939934 CTGGTTCAGAACAAACGAGCA 59.060 47.619 15.36 1.30 32.44 4.26
214 219 1.264288 CCTGGTTCAGAACAAACGAGC 59.736 52.381 15.36 0.00 32.87 5.03
215 220 1.873591 CCCTGGTTCAGAACAAACGAG 59.126 52.381 15.36 2.81 32.44 4.18
216 221 1.487142 TCCCTGGTTCAGAACAAACGA 59.513 47.619 15.36 2.43 32.44 3.85
217 222 1.602377 GTCCCTGGTTCAGAACAAACG 59.398 52.381 15.36 0.08 32.44 3.60
218 223 1.954382 GGTCCCTGGTTCAGAACAAAC 59.046 52.381 15.36 0.00 32.44 2.93
219 224 1.133606 GGGTCCCTGGTTCAGAACAAA 60.134 52.381 15.36 1.95 32.44 2.83
220 225 0.476771 GGGTCCCTGGTTCAGAACAA 59.523 55.000 15.36 2.60 32.44 2.83
221 226 1.764571 CGGGTCCCTGGTTCAGAACA 61.765 60.000 15.36 0.97 32.44 3.18
222 227 1.003718 CGGGTCCCTGGTTCAGAAC 60.004 63.158 6.29 4.52 32.44 3.01
223 228 2.890766 GCGGGTCCCTGGTTCAGAA 61.891 63.158 6.29 0.00 32.44 3.02
224 229 3.319198 GCGGGTCCCTGGTTCAGA 61.319 66.667 6.29 0.00 32.44 3.27
225 230 2.971598 ATGCGGGTCCCTGGTTCAG 61.972 63.158 6.29 0.00 0.00 3.02
226 231 2.933287 ATGCGGGTCCCTGGTTCA 60.933 61.111 6.29 0.00 0.00 3.18
227 232 2.438434 CATGCGGGTCCCTGGTTC 60.438 66.667 6.29 0.00 0.00 3.62
228 233 4.047125 CCATGCGGGTCCCTGGTT 62.047 66.667 6.29 0.00 0.00 3.67
237 242 0.610785 AAACCAGGTAACCATGCGGG 60.611 55.000 0.00 0.00 44.81 6.13
238 243 1.067915 CAAAACCAGGTAACCATGCGG 60.068 52.381 0.00 0.00 38.77 5.69
239 244 1.668628 GCAAAACCAGGTAACCATGCG 60.669 52.381 0.00 0.00 37.17 4.73
240 245 1.618343 AGCAAAACCAGGTAACCATGC 59.382 47.619 0.00 0.00 37.17 4.06
241 246 4.202202 TGAAAGCAAAACCAGGTAACCATG 60.202 41.667 0.00 0.00 37.17 3.66
242 247 3.964031 TGAAAGCAAAACCAGGTAACCAT 59.036 39.130 0.00 0.00 37.17 3.55
243 248 3.366396 TGAAAGCAAAACCAGGTAACCA 58.634 40.909 0.00 0.00 37.17 3.67
244 249 3.383505 ACTGAAAGCAAAACCAGGTAACC 59.616 43.478 0.00 0.00 37.60 2.85
245 250 4.649088 ACTGAAAGCAAAACCAGGTAAC 57.351 40.909 0.00 0.00 37.60 2.50
246 251 5.420739 AGAAACTGAAAGCAAAACCAGGTAA 59.579 36.000 0.00 0.00 37.60 2.85
247 252 4.953579 AGAAACTGAAAGCAAAACCAGGTA 59.046 37.500 0.00 0.00 37.60 3.08
248 253 3.769300 AGAAACTGAAAGCAAAACCAGGT 59.231 39.130 0.00 0.00 37.60 4.00
249 254 4.391405 AGAAACTGAAAGCAAAACCAGG 57.609 40.909 0.00 0.00 37.60 4.45
250 255 6.136541 ACTAGAAACTGAAAGCAAAACCAG 57.863 37.500 0.00 0.00 37.60 4.00
251 256 6.405397 GGAACTAGAAACTGAAAGCAAAACCA 60.405 38.462 0.00 0.00 37.60 3.67
252 257 5.977725 GGAACTAGAAACTGAAAGCAAAACC 59.022 40.000 0.00 0.00 37.60 3.27
253 258 6.560711 TGGAACTAGAAACTGAAAGCAAAAC 58.439 36.000 0.00 0.00 37.60 2.43
254 259 6.377146 ACTGGAACTAGAAACTGAAAGCAAAA 59.623 34.615 0.00 0.00 37.60 2.44
255 260 5.885912 ACTGGAACTAGAAACTGAAAGCAAA 59.114 36.000 0.00 0.00 37.60 3.68
256 261 5.437060 ACTGGAACTAGAAACTGAAAGCAA 58.563 37.500 0.00 0.00 37.60 3.91
257 262 5.036117 ACTGGAACTAGAAACTGAAAGCA 57.964 39.130 0.00 0.00 37.60 3.91
258 263 6.038271 TCAAACTGGAACTAGAAACTGAAAGC 59.962 38.462 0.00 0.00 37.60 3.51
259 264 7.553881 TCAAACTGGAACTAGAAACTGAAAG 57.446 36.000 0.00 0.00 42.29 2.62
260 265 7.556275 ACATCAAACTGGAACTAGAAACTGAAA 59.444 33.333 0.00 0.00 0.00 2.69
261 266 7.054124 ACATCAAACTGGAACTAGAAACTGAA 58.946 34.615 0.00 0.00 0.00 3.02
262 267 6.591935 ACATCAAACTGGAACTAGAAACTGA 58.408 36.000 0.00 0.00 0.00 3.41
263 268 6.867662 ACATCAAACTGGAACTAGAAACTG 57.132 37.500 0.00 0.00 0.00 3.16
264 269 7.682021 GCAAACATCAAACTGGAACTAGAAACT 60.682 37.037 0.00 0.00 0.00 2.66
265 270 6.417930 GCAAACATCAAACTGGAACTAGAAAC 59.582 38.462 0.00 0.00 0.00 2.78
266 271 6.321181 AGCAAACATCAAACTGGAACTAGAAA 59.679 34.615 0.00 0.00 0.00 2.52
267 272 5.827797 AGCAAACATCAAACTGGAACTAGAA 59.172 36.000 0.00 0.00 0.00 2.10
268 273 5.376625 AGCAAACATCAAACTGGAACTAGA 58.623 37.500 0.00 0.00 0.00 2.43
269 274 5.239306 TGAGCAAACATCAAACTGGAACTAG 59.761 40.000 0.00 0.00 0.00 2.57
270 275 5.008613 GTGAGCAAACATCAAACTGGAACTA 59.991 40.000 0.00 0.00 0.00 2.24
271 276 3.953612 TGAGCAAACATCAAACTGGAACT 59.046 39.130 0.00 0.00 0.00 3.01
272 277 4.044426 GTGAGCAAACATCAAACTGGAAC 58.956 43.478 0.00 0.00 0.00 3.62
273 278 3.953612 AGTGAGCAAACATCAAACTGGAA 59.046 39.130 0.00 0.00 0.00 3.53
274 279 3.554934 AGTGAGCAAACATCAAACTGGA 58.445 40.909 0.00 0.00 0.00 3.86
275 280 3.996150 AGTGAGCAAACATCAAACTGG 57.004 42.857 0.00 0.00 0.00 4.00
276 281 5.048504 ACCATAGTGAGCAAACATCAAACTG 60.049 40.000 0.00 0.00 0.00 3.16
277 282 5.072741 ACCATAGTGAGCAAACATCAAACT 58.927 37.500 0.00 0.00 0.00 2.66
278 283 5.376854 ACCATAGTGAGCAAACATCAAAC 57.623 39.130 0.00 0.00 0.00 2.93
279 284 6.265196 AGAAACCATAGTGAGCAAACATCAAA 59.735 34.615 0.00 0.00 0.00 2.69
280 285 5.769662 AGAAACCATAGTGAGCAAACATCAA 59.230 36.000 0.00 0.00 0.00 2.57
281 286 5.316167 AGAAACCATAGTGAGCAAACATCA 58.684 37.500 0.00 0.00 0.00 3.07
282 287 5.645497 AGAGAAACCATAGTGAGCAAACATC 59.355 40.000 0.00 0.00 0.00 3.06
283 288 5.564550 AGAGAAACCATAGTGAGCAAACAT 58.435 37.500 0.00 0.00 0.00 2.71
284 289 4.973168 AGAGAAACCATAGTGAGCAAACA 58.027 39.130 0.00 0.00 0.00 2.83
285 290 7.334421 TCATTAGAGAAACCATAGTGAGCAAAC 59.666 37.037 0.00 0.00 0.00 2.93
286 291 7.394016 TCATTAGAGAAACCATAGTGAGCAAA 58.606 34.615 0.00 0.00 0.00 3.68
287 292 6.946340 TCATTAGAGAAACCATAGTGAGCAA 58.054 36.000 0.00 0.00 0.00 3.91
288 293 6.544928 TCATTAGAGAAACCATAGTGAGCA 57.455 37.500 0.00 0.00 0.00 4.26
289 294 7.849804 TTTCATTAGAGAAACCATAGTGAGC 57.150 36.000 0.00 0.00 32.88 4.26
291 296 9.098355 CGATTTTCATTAGAGAAACCATAGTGA 57.902 33.333 0.00 0.00 37.24 3.41
292 297 9.098355 TCGATTTTCATTAGAGAAACCATAGTG 57.902 33.333 0.00 0.00 37.24 2.74
293 298 9.838339 ATCGATTTTCATTAGAGAAACCATAGT 57.162 29.630 0.00 0.00 37.24 2.12
295 300 9.830975 TCATCGATTTTCATTAGAGAAACCATA 57.169 29.630 0.00 0.00 37.24 2.74
296 301 8.737168 TCATCGATTTTCATTAGAGAAACCAT 57.263 30.769 0.00 0.00 37.24 3.55
297 302 7.280876 CCTCATCGATTTTCATTAGAGAAACCA 59.719 37.037 0.00 0.00 37.24 3.67
298 303 7.495934 TCCTCATCGATTTTCATTAGAGAAACC 59.504 37.037 0.00 0.00 37.24 3.27
299 304 8.425577 TCCTCATCGATTTTCATTAGAGAAAC 57.574 34.615 0.00 0.00 37.24 2.78
300 305 7.712639 CCTCCTCATCGATTTTCATTAGAGAAA 59.287 37.037 0.00 0.00 35.82 2.52
301 306 7.212976 CCTCCTCATCGATTTTCATTAGAGAA 58.787 38.462 0.00 0.00 0.00 2.87
302 307 6.739843 GCCTCCTCATCGATTTTCATTAGAGA 60.740 42.308 0.00 0.00 0.00 3.10
303 308 5.407995 GCCTCCTCATCGATTTTCATTAGAG 59.592 44.000 0.00 0.00 0.00 2.43
304 309 5.070981 AGCCTCCTCATCGATTTTCATTAGA 59.929 40.000 0.00 0.00 0.00 2.10
305 310 5.303971 AGCCTCCTCATCGATTTTCATTAG 58.696 41.667 0.00 0.00 0.00 1.73
306 311 5.296151 AGCCTCCTCATCGATTTTCATTA 57.704 39.130 0.00 0.00 0.00 1.90
307 312 4.162040 AGCCTCCTCATCGATTTTCATT 57.838 40.909 0.00 0.00 0.00 2.57
308 313 3.853355 AGCCTCCTCATCGATTTTCAT 57.147 42.857 0.00 0.00 0.00 2.57
309 314 3.273434 CAAGCCTCCTCATCGATTTTCA 58.727 45.455 0.00 0.00 0.00 2.69
310 315 3.274288 ACAAGCCTCCTCATCGATTTTC 58.726 45.455 0.00 0.00 0.00 2.29
378 383 3.760035 CGAGTGGACACCTCGGGG 61.760 72.222 0.00 0.00 37.02 5.73
391 396 4.100498 TGGTTTGACTCTTTCTTACCGAGT 59.900 41.667 0.00 0.00 40.46 4.18
392 397 4.448060 GTGGTTTGACTCTTTCTTACCGAG 59.552 45.833 0.00 0.00 33.44 4.63
397 402 5.623956 TCAGGTGGTTTGACTCTTTCTTA 57.376 39.130 0.00 0.00 0.00 2.10
452 457 0.736636 ACATGCATGCCGACTTCATG 59.263 50.000 26.53 12.50 43.02 3.07
453 458 1.942657 GTACATGCATGCCGACTTCAT 59.057 47.619 26.53 6.25 0.00 2.57
529 572 1.271762 ACTCAGGGCTGTACTACACGA 60.272 52.381 0.00 0.00 0.00 4.35
541 584 2.113860 TAACTTGCATCACTCAGGGC 57.886 50.000 0.00 0.00 0.00 5.19
565 608 1.870055 CGCACCAGAATTGCTGCCTT 61.870 55.000 0.00 0.00 43.50 4.35
579 622 1.217882 GGTATGTCTATGCACGCACC 58.782 55.000 0.00 0.00 0.00 5.01
616 664 6.060136 ACAGACAGAGGCTACGTATGTAATA 58.940 40.000 12.74 0.00 33.60 0.98
617 665 4.888239 ACAGACAGAGGCTACGTATGTAAT 59.112 41.667 12.74 0.00 33.60 1.89
618 666 4.267536 ACAGACAGAGGCTACGTATGTAA 58.732 43.478 12.74 0.00 33.60 2.41
638 686 1.729586 AGGCCAGACTAAGTCCAACA 58.270 50.000 5.01 0.00 32.18 3.33
719 767 0.035881 ATGTCCAGTCCACAGCACAG 59.964 55.000 0.00 0.00 0.00 3.66
747 795 9.732130 CCCATAAATCTTAGGAAAAGAGATAGG 57.268 37.037 0.00 0.00 30.33 2.57
748 796 9.225436 GCCCATAAATCTTAGGAAAAGAGATAG 57.775 37.037 0.00 0.00 30.33 2.08
749 797 8.723365 TGCCCATAAATCTTAGGAAAAGAGATA 58.277 33.333 0.00 0.00 30.33 1.98
754 802 5.893824 ACCTGCCCATAAATCTTAGGAAAAG 59.106 40.000 0.00 0.00 0.00 2.27
784 832 3.077556 ACCTGCTACTGCCTCCCG 61.078 66.667 0.00 0.00 38.71 5.14
790 838 2.421424 CAGGAAAATCACCTGCTACTGC 59.579 50.000 0.00 0.00 46.30 4.40
875 923 8.715191 AGCAATTTGTCTTGTTGTTTATTTCA 57.285 26.923 0.00 0.00 0.00 2.69
948 996 0.605589 GTGCGCCTGCCTATCTATCT 59.394 55.000 4.18 0.00 41.78 1.98
1168 1219 2.649034 GAACGACCGGACAGAGCA 59.351 61.111 9.46 0.00 0.00 4.26
1376 1427 9.152595 GGGTAGTTCTTAGAAGAATGTAGTTTG 57.847 37.037 7.91 0.00 45.83 2.93
1390 1443 5.419471 AGCTTACAGAGTGGGTAGTTCTTAG 59.581 44.000 0.00 0.00 0.00 2.18
1403 1456 8.828688 AAACGTCTTATAAAAGCTTACAGAGT 57.171 30.769 0.00 0.00 32.36 3.24
1423 1476 8.788806 TGGAAAATAAGTGTGATCATAAAACGT 58.211 29.630 0.00 0.00 0.00 3.99
1468 1521 6.042093 AGTCTGTTGGAAGTCATAGAAAGTGA 59.958 38.462 0.00 0.00 0.00 3.41
1551 1608 7.624360 TCTTATTTCGACATAATTGGCAAGT 57.376 32.000 5.96 5.58 0.00 3.16
1613 1671 4.608948 TTTATCCCGCAAAAACCACATT 57.391 36.364 0.00 0.00 0.00 2.71
1614 1672 4.565022 CTTTTATCCCGCAAAAACCACAT 58.435 39.130 0.00 0.00 0.00 3.21
1617 1675 2.608261 CGCTTTTATCCCGCAAAAACCA 60.608 45.455 0.00 0.00 0.00 3.67
1618 1676 1.989864 CGCTTTTATCCCGCAAAAACC 59.010 47.619 0.00 0.00 0.00 3.27
1619 1677 2.668250 ACGCTTTTATCCCGCAAAAAC 58.332 42.857 0.00 0.00 0.00 2.43
1620 1678 4.705337 ATACGCTTTTATCCCGCAAAAA 57.295 36.364 0.00 0.00 0.00 1.94
1621 1679 4.877251 ACTATACGCTTTTATCCCGCAAAA 59.123 37.500 0.00 0.00 0.00 2.44
1626 1684 7.755591 TCAGTATACTATACGCTTTTATCCCG 58.244 38.462 4.74 0.00 0.00 5.14
1697 1755 8.936864 GTTTTGTTACTGTGCTAGTATCAATCT 58.063 33.333 17.78 0.00 44.70 2.40
1899 1957 9.896645 AAATGAGCTTATGATAAGAGAGTTCAA 57.103 29.630 15.98 0.00 32.65 2.69
1964 2022 6.640092 GCTGAAATTCTTGAAAGGAAGAACTG 59.360 38.462 0.00 0.00 43.14 3.16
2071 2129 1.954146 CAGTGCTACACGCGTTGGT 60.954 57.895 10.22 8.51 43.27 3.67
2078 2136 2.357396 TGGCTGCAGTGCTACACG 60.357 61.111 17.60 0.89 39.64 4.49
2082 2140 0.036952 GAACTCTGGCTGCAGTGCTA 60.037 55.000 17.60 0.00 0.00 3.49
2091 2149 2.964310 ATGCGCTGGAACTCTGGCT 61.964 57.895 9.73 0.00 0.00 4.75
2133 2191 4.023536 TGCAATTTCGTTAACCAACCTCTC 60.024 41.667 0.00 0.00 0.00 3.20
2147 2205 4.030529 GGATGATTCAACGTTGCAATTTCG 59.969 41.667 23.47 4.14 0.00 3.46
2149 2207 3.919804 CGGATGATTCAACGTTGCAATTT 59.080 39.130 23.47 13.80 0.00 1.82
2170 2228 1.850640 GGCGTATAACACATCGGCG 59.149 57.895 0.00 0.00 38.83 6.46
2226 2284 2.359230 GGAGGCAAGCGCAGAGTT 60.359 61.111 11.47 0.00 41.24 3.01
2313 2371 1.227999 CGCAACACCTGGTCGATTGT 61.228 55.000 13.59 0.05 0.00 2.71
2328 2386 1.136584 CGTTGTTATGTACACGCGCAA 60.137 47.619 5.73 0.00 36.21 4.85
2329 2387 0.435388 CGTTGTTATGTACACGCGCA 59.565 50.000 5.73 0.00 36.21 6.09
2372 2430 2.763292 ATCGCCTCCTGCTGCTCT 60.763 61.111 0.00 0.00 38.05 4.09
2518 2576 1.982395 CTAGGCGTCACCCAGACCA 60.982 63.158 0.00 0.00 44.66 4.02
2620 2678 5.642063 CGTGGTACATCTGGAACTTTAACAT 59.358 40.000 0.00 0.00 44.52 2.71
2621 2679 4.992319 CGTGGTACATCTGGAACTTTAACA 59.008 41.667 0.00 0.00 44.52 2.41
2622 2680 4.142966 GCGTGGTACATCTGGAACTTTAAC 60.143 45.833 0.00 0.00 44.52 2.01
2623 2681 3.998341 GCGTGGTACATCTGGAACTTTAA 59.002 43.478 0.00 0.00 44.52 1.52
2672 2730 4.555262 AGGATGTTTTGCGGTGTTAATTG 58.445 39.130 0.00 0.00 0.00 2.32
2768 2826 3.751175 TGTAAAATGGCAGGATATAGCGC 59.249 43.478 0.00 0.00 0.00 5.92
3084 3146 0.107268 GTACAGTGTTGGGGTCGGTT 59.893 55.000 0.00 0.00 0.00 4.44
3156 3218 2.090999 GGATCCTACCTTCTCACCCTCT 60.091 54.545 3.84 0.00 0.00 3.69
3162 3224 2.292521 ACTGCAGGATCCTACCTTCTCA 60.293 50.000 19.93 3.35 38.32 3.27


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

AutoCloner maintained by Alex Coulton.