Multiple sequence alignment - TraesCS5B01G503500

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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 TraesCS5B01G503500 chr5B 100.000 2636 0 0 1 2636 670073566 670076201 0.000000e+00 4868.0
1 TraesCS5B01G503500 chr5B 91.613 155 7 4 120 272 50238000 50238150 2.660000e-50 209.0
2 TraesCS5B01G503500 chr5B 75.540 417 80 12 1908 2322 590358430 590358826 4.480000e-43 185.0
3 TraesCS5B01G503500 chr5B 75.399 313 59 17 1312 1615 570152346 570152043 4.580000e-28 135.0
4 TraesCS5B01G503500 chr5D 87.302 1961 177 36 727 2636 530834324 530836263 0.000000e+00 2176.0
5 TraesCS5B01G503500 chr5D 95.200 125 3 2 1 125 530832511 530832632 7.440000e-46 195.0
6 TraesCS5B01G503500 chr5D 73.430 414 96 12 1935 2344 565231281 565230878 2.730000e-30 143.0
7 TraesCS5B01G503500 chr5D 75.080 313 60 16 1312 1615 463375002 463374699 2.130000e-26 130.0
8 TraesCS5B01G503500 chr4A 89.274 1790 106 34 366 2102 641443625 641441869 0.000000e+00 2163.0
9 TraesCS5B01G503500 chr4A 91.011 534 36 4 2104 2636 641432459 641431937 0.000000e+00 710.0
10 TraesCS5B01G503500 chr4A 79.800 802 116 25 885 1657 516583095 516583879 2.310000e-150 542.0
11 TraesCS5B01G503500 chr4A 88.285 239 16 3 1199 1435 516608386 516608614 2.580000e-70 276.0
12 TraesCS5B01G503500 chr4A 90.833 120 9 1 1 120 641443821 641443704 2.720000e-35 159.0
13 TraesCS5B01G503500 chr4A 81.373 204 20 11 1695 1898 516609039 516609224 1.630000e-32 150.0
14 TraesCS5B01G503500 chr4D 79.028 782 128 24 901 1658 67326377 67325608 1.090000e-138 503.0
15 TraesCS5B01G503500 chr4B 81.978 455 47 18 1451 1898 99749688 99750114 1.160000e-93 353.0
16 TraesCS5B01G503500 chr4B 88.559 236 24 2 1214 1449 99749094 99749326 1.540000e-72 283.0
17 TraesCS5B01G503500 chr2B 78.834 463 83 11 1915 2371 587245561 587246014 5.520000e-77 298.0
18 TraesCS5B01G503500 chr2B 93.878 147 6 2 120 263 407233909 407234055 4.420000e-53 219.0
19 TraesCS5B01G503500 chr2B 91.250 160 11 3 119 278 349930714 349930558 5.710000e-52 215.0
20 TraesCS5B01G503500 chr5A 97.059 136 4 0 116 251 696840571 696840436 2.040000e-56 230.0
21 TraesCS5B01G503500 chr5A 97.059 136 4 0 116 251 696879660 696879525 2.040000e-56 230.0
22 TraesCS5B01G503500 chr1B 97.015 134 4 0 117 250 56893369 56893236 2.640000e-55 226.0
23 TraesCS5B01G503500 chr6B 96.324 136 5 0 117 252 641950832 641950697 9.490000e-55 224.0
24 TraesCS5B01G503500 chr7B 95.556 135 6 0 121 255 115521554 115521688 1.590000e-52 217.0
25 TraesCS5B01G503500 chr3D 93.243 148 9 1 118 264 11337919 11338066 1.590000e-52 217.0
26 TraesCS5B01G503500 chrUn 75.399 313 59 17 1312 1615 295600027 295599724 4.580000e-28 135.0
27 TraesCS5B01G503500 chrUn 75.399 313 59 17 1312 1615 310497483 310497786 4.580000e-28 135.0
28 TraesCS5B01G503500 chr2D 91.304 46 4 0 2198 2243 560398463 560398508 2.190000e-06 63.9


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 TraesCS5B01G503500 chr5B 670073566 670076201 2635 False 4868.0 4868 100.0000 1 2636 1 chr5B.!!$F3 2635
1 TraesCS5B01G503500 chr5D 530832511 530836263 3752 False 1185.5 2176 91.2510 1 2636 2 chr5D.!!$F1 2635
2 TraesCS5B01G503500 chr4A 641441869 641443821 1952 True 1161.0 2163 90.0535 1 2102 2 chr4A.!!$R2 2101
3 TraesCS5B01G503500 chr4A 641431937 641432459 522 True 710.0 710 91.0110 2104 2636 1 chr4A.!!$R1 532
4 TraesCS5B01G503500 chr4A 516583095 516583879 784 False 542.0 542 79.8000 885 1657 1 chr4A.!!$F1 772
5 TraesCS5B01G503500 chr4A 516608386 516609224 838 False 213.0 276 84.8290 1199 1898 2 chr4A.!!$F2 699
6 TraesCS5B01G503500 chr4D 67325608 67326377 769 True 503.0 503 79.0280 901 1658 1 chr4D.!!$R1 757
7 TraesCS5B01G503500 chr4B 99749094 99750114 1020 False 318.0 353 85.2685 1214 1898 2 chr4B.!!$F1 684

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
142 144 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.0 44.66 2.17 F
145 147 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1078 2366 0.250467 AGCACAAGAAGCATCACCGT 60.250 50.000 0.0 0.0 0.0 4.83 R
1762 3671 1.066143 CGCTGTTTCACATAGGTCCCT 60.066 52.381 0.0 0.0 0.0 4.20 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
33 34 2.091830 AGGATGTCAGGATCGGTCTACA 60.092 50.000 0.00 0.00 0.00 2.74
34 35 2.034812 GGATGTCAGGATCGGTCTACAC 59.965 54.545 0.00 0.00 0.00 2.90
50 51 4.021719 GTCTACACTACCACAAAGGCTGTA 60.022 45.833 0.00 0.00 43.14 2.74
98 99 7.601508 TCCTTGTCTACGAAATACTTTCCTTTC 59.398 37.037 0.00 0.00 36.30 2.62
102 103 8.365647 TGTCTACGAAATACTTTCCTTTCTTCT 58.634 33.333 0.00 0.00 36.30 2.85
129 131 9.800433 GTAAAGAGTCTACAAAATACTACTCCC 57.200 37.037 0.00 0.00 35.13 4.30
130 132 8.667592 AAAGAGTCTACAAAATACTACTCCCT 57.332 34.615 0.00 0.00 35.13 4.20
131 133 7.885009 AGAGTCTACAAAATACTACTCCCTC 57.115 40.000 0.00 0.00 35.13 4.30
132 134 6.834969 AGAGTCTACAAAATACTACTCCCTCC 59.165 42.308 0.00 0.00 35.13 4.30
133 135 5.593502 AGTCTACAAAATACTACTCCCTCCG 59.406 44.000 0.00 0.00 0.00 4.63
134 136 5.359292 GTCTACAAAATACTACTCCCTCCGT 59.641 44.000 0.00 0.00 0.00 4.69
135 137 4.732672 ACAAAATACTACTCCCTCCGTC 57.267 45.455 0.00 0.00 0.00 4.79
136 138 3.450096 ACAAAATACTACTCCCTCCGTCC 59.550 47.826 0.00 0.00 0.00 4.79
137 139 1.978454 AATACTACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
138 140 0.110104 ATACTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
139 141 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
140 142 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
141 143 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
142 144 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
143 145 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
144 146 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
145 147 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
146 148 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
147 149 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
148 150 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
149 151 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
150 152 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
151 153 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
152 154 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
153 155 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
154 156 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
155 157 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
156 158 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
157 159 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
158 160 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
159 161 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
160 162 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
161 163 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
169 171 9.918630 ACTTGTCATCAAAATGAATAAAAGAGG 57.081 29.630 0.00 0.00 43.42 3.69
214 216 8.349568 AGTTTTAGATACATCCCTTTTTGTCC 57.650 34.615 0.00 0.00 0.00 4.02
215 217 7.947890 AGTTTTAGATACATCCCTTTTTGTCCA 59.052 33.333 0.00 0.00 0.00 4.02
216 218 8.749354 GTTTTAGATACATCCCTTTTTGTCCAT 58.251 33.333 0.00 0.00 0.00 3.41
217 219 8.893563 TTTAGATACATCCCTTTTTGTCCATT 57.106 30.769 0.00 0.00 0.00 3.16
218 220 8.893563 TTAGATACATCCCTTTTTGTCCATTT 57.106 30.769 0.00 0.00 0.00 2.32
219 221 7.797121 AGATACATCCCTTTTTGTCCATTTT 57.203 32.000 0.00 0.00 0.00 1.82
220 222 7.614494 AGATACATCCCTTTTTGTCCATTTTG 58.386 34.615 0.00 0.00 0.00 2.44
221 223 5.885449 ACATCCCTTTTTGTCCATTTTGA 57.115 34.783 0.00 0.00 0.00 2.69
222 224 6.438186 ACATCCCTTTTTGTCCATTTTGAT 57.562 33.333 0.00 0.00 0.00 2.57
223 225 6.232692 ACATCCCTTTTTGTCCATTTTGATG 58.767 36.000 0.00 0.00 33.80 3.07
224 226 6.043012 ACATCCCTTTTTGTCCATTTTGATGA 59.957 34.615 0.00 0.00 32.39 2.92
225 227 5.852827 TCCCTTTTTGTCCATTTTGATGAC 58.147 37.500 0.00 0.00 0.00 3.06
226 228 5.365025 TCCCTTTTTGTCCATTTTGATGACA 59.635 36.000 0.00 0.00 0.00 3.58
227 229 6.054295 CCCTTTTTGTCCATTTTGATGACAA 58.946 36.000 0.00 0.00 34.47 3.18
228 230 6.203338 CCCTTTTTGTCCATTTTGATGACAAG 59.797 38.462 0.00 0.00 37.13 3.16
229 231 6.762661 CCTTTTTGTCCATTTTGATGACAAGT 59.237 34.615 0.00 0.00 37.13 3.16
230 232 7.925483 CCTTTTTGTCCATTTTGATGACAAGTA 59.075 33.333 0.00 0.00 37.13 2.24
231 233 9.480053 CTTTTTGTCCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.13 2.12
232 234 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
233 235 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
234 236 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
235 237 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
236 238 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
237 239 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
238 240 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
239 241 7.485913 CCATTTTGATGACAAGTATTTTCGGAG 59.514 37.037 0.00 0.00 37.32 4.63
240 242 6.494893 TTTGATGACAAGTATTTTCGGAGG 57.505 37.500 0.00 0.00 37.32 4.30
241 243 4.513442 TGATGACAAGTATTTTCGGAGGG 58.487 43.478 0.00 0.00 0.00 4.30
242 244 4.224147 TGATGACAAGTATTTTCGGAGGGA 59.776 41.667 0.00 0.00 0.00 4.20
243 245 4.202245 TGACAAGTATTTTCGGAGGGAG 57.798 45.455 0.00 0.00 0.00 4.30
244 246 3.055385 TGACAAGTATTTTCGGAGGGAGG 60.055 47.826 0.00 0.00 0.00 4.30
245 247 2.238898 ACAAGTATTTTCGGAGGGAGGG 59.761 50.000 0.00 0.00 0.00 4.30
246 248 2.504175 CAAGTATTTTCGGAGGGAGGGA 59.496 50.000 0.00 0.00 0.00 4.20
247 249 2.399580 AGTATTTTCGGAGGGAGGGAG 58.600 52.381 0.00 0.00 0.00 4.30
248 250 2.117051 GTATTTTCGGAGGGAGGGAGT 58.883 52.381 0.00 0.00 0.00 3.85
249 251 2.563039 ATTTTCGGAGGGAGGGAGTA 57.437 50.000 0.00 0.00 0.00 2.59
252 254 3.693526 TTTCGGAGGGAGGGAGTATAA 57.306 47.619 0.00 0.00 0.00 0.98
258 260 5.430745 TCGGAGGGAGGGAGTATAAAATTTT 59.569 40.000 8.75 8.75 0.00 1.82
284 286 5.708948 TCCAATAAAAAGCTTGTCGATTGG 58.291 37.500 24.86 24.86 42.03 3.16
285 287 4.327087 CCAATAAAAAGCTTGTCGATTGGC 59.673 41.667 21.72 0.00 36.48 4.52
295 297 0.808847 GTCGATTGGCGGTAAGGACC 60.809 60.000 0.00 0.00 43.03 4.46
317 319 6.121590 ACCATTGTTACATCTCATGCATGTA 58.878 36.000 25.43 15.60 35.95 2.29
349 351 7.232127 CCTGGATTTTCTATGCTGTGGAATATT 59.768 37.037 0.00 0.00 0.00 1.28
350 352 9.288576 CTGGATTTTCTATGCTGTGGAATATTA 57.711 33.333 0.00 0.00 0.00 0.98
351 353 9.639563 TGGATTTTCTATGCTGTGGAATATTAA 57.360 29.630 0.00 0.00 0.00 1.40
364 366 7.168219 TGTGGAATATTAATATCTGAGGCACC 58.832 38.462 8.42 4.13 0.00 5.01
391 393 3.243267 ACCAACCGTGCAGTTTGATTAAC 60.243 43.478 0.00 0.00 36.99 2.01
426 428 0.813184 TCGGACCATCTGTTACGTCC 59.187 55.000 0.00 0.00 41.20 4.79
469 471 1.378531 TTCCAACATGCACTATCGCC 58.621 50.000 0.00 0.00 0.00 5.54
534 542 5.619981 GCCATGACTCTTATTTTGGTCACAC 60.620 44.000 0.00 0.00 40.71 3.82
620 633 3.714798 ACCCCACTACGGATGAATAACAT 59.285 43.478 0.00 0.00 42.47 2.71
696 715 9.620660 GGAAAAACGTGAAGATGTACAATTATT 57.379 29.630 0.00 0.00 0.00 1.40
751 1997 2.489971 TCACCACCGACAACAGAAATC 58.510 47.619 0.00 0.00 0.00 2.17
764 2010 3.920231 CAGAAATCTGGTGATCCTCCA 57.080 47.619 2.38 6.57 40.20 3.86
799 2057 8.713708 TTCCTCCAAAACCACAATCTAAAATA 57.286 30.769 0.00 0.00 0.00 1.40
833 2091 1.520342 GACCGCTGATCCTCTGCAC 60.520 63.158 6.78 0.00 40.74 4.57
849 2107 2.039624 ACTGTGCTCCCCGGATCT 59.960 61.111 0.73 0.00 0.00 2.75
881 2139 2.905736 ACCATTGGCCAAGCAAAGTATT 59.094 40.909 24.94 0.00 0.00 1.89
882 2140 3.055891 ACCATTGGCCAAGCAAAGTATTC 60.056 43.478 24.94 0.00 0.00 1.75
934 2192 3.870419 CCACTTCATAGAGCAGCTTTCTC 59.130 47.826 0.00 3.01 0.00 2.87
1052 2340 5.522460 GCACAAAGTCACAGACACTTACTTA 59.478 40.000 0.00 0.00 32.71 2.24
1053 2341 6.202954 GCACAAAGTCACAGACACTTACTTAT 59.797 38.462 0.00 0.00 32.71 1.73
1078 2366 2.528564 CTCAAGAAATGGCCAAGGGAA 58.471 47.619 10.96 0.00 0.00 3.97
1099 2390 0.807496 GGTGATGCTTCTTGTGCTCC 59.193 55.000 0.88 0.00 0.00 4.70
1673 3388 3.446161 AGGGCTTTTATTTACTTTCGGCC 59.554 43.478 0.00 0.00 36.70 6.13
1691 3411 1.551883 GCCATGCTTTGAGATTTGGGT 59.448 47.619 0.00 0.00 0.00 4.51
1695 3603 4.240096 CATGCTTTGAGATTTGGGTGTTC 58.760 43.478 0.00 0.00 0.00 3.18
1697 3605 3.960102 TGCTTTGAGATTTGGGTGTTCTT 59.040 39.130 0.00 0.00 0.00 2.52
1700 3608 5.463392 GCTTTGAGATTTGGGTGTTCTTTTC 59.537 40.000 0.00 0.00 0.00 2.29
1701 3609 6.683861 GCTTTGAGATTTGGGTGTTCTTTTCT 60.684 38.462 0.00 0.00 0.00 2.52
1702 3610 6.790232 TTGAGATTTGGGTGTTCTTTTCTT 57.210 33.333 0.00 0.00 0.00 2.52
1703 3611 6.147864 TGAGATTTGGGTGTTCTTTTCTTG 57.852 37.500 0.00 0.00 0.00 3.02
1726 3634 5.104859 TGTGTCCTAAATATCGGTGCCTTTA 60.105 40.000 0.00 0.00 0.00 1.85
1766 3675 4.519540 GCAAGTTGCAAGAATAAAGGGA 57.480 40.909 22.90 0.00 44.26 4.20
1801 3710 4.595198 GCGAAAGGCGTATACTTTTTCT 57.405 40.909 15.46 0.85 43.41 2.52
1802 3711 4.966249 GCGAAAGGCGTATACTTTTTCTT 58.034 39.130 15.46 5.33 43.41 2.52
1803 3712 6.098367 GCGAAAGGCGTATACTTTTTCTTA 57.902 37.500 15.46 0.00 43.41 2.10
1876 3803 7.725251 AGCCTTGTATTTTGAACTTTTGATGA 58.275 30.769 0.00 0.00 0.00 2.92
1917 3844 3.369400 CAAATTCGCGGGGGCACA 61.369 61.111 6.13 0.00 0.00 4.57
1927 3854 3.297620 GGGGCACACACCTGCAAG 61.298 66.667 0.00 0.00 39.08 4.01
1981 3909 2.034305 CCGAAGTAGTTGGATCCCGTAG 59.966 54.545 9.90 0.00 0.00 3.51
1998 3926 3.714391 CGTAGGTGGGCATACTAAGTTC 58.286 50.000 0.00 0.00 30.44 3.01
2035 3963 7.955324 TCGTTGAAATGTACGATTTTTCATCTC 59.045 33.333 11.44 7.01 41.38 2.75
2065 3993 1.584175 TTTTCTCGCACGCCTTTACA 58.416 45.000 0.00 0.00 0.00 2.41
2156 4084 3.490526 GGTCGCACGTACTAAGTTTCAAA 59.509 43.478 0.00 0.00 0.00 2.69
2255 4190 6.786103 GTCAAGAGAAACACGAATACGAAAAG 59.214 38.462 0.00 0.00 42.66 2.27
2343 4278 2.827642 GCCTGAGGGACTGCATGC 60.828 66.667 11.82 11.82 41.55 4.06
2357 4292 1.079612 CATGCTGTGAGACCTGCGA 60.080 57.895 0.00 0.00 32.52 5.10
2421 4356 2.223377 GGTTACAACACGGCTTCTCTTG 59.777 50.000 0.00 0.00 0.00 3.02
2435 4370 0.888619 CTCTTGCCGGTAGACACTGA 59.111 55.000 1.90 0.00 32.22 3.41
2451 4386 2.679837 CACTGACATCGCCTAAAGCAAT 59.320 45.455 0.00 0.00 44.04 3.56
2608 4544 7.332430 TGAAGTAAAATACACGTATGGTCCTTG 59.668 37.037 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.366266 TCGTTACAGCCTTTGTGGTAGT 59.634 45.455 0.00 0.00 41.10 2.73
34 35 2.735134 GTCGTTACAGCCTTTGTGGTAG 59.265 50.000 0.00 0.00 41.10 3.18
50 51 1.094785 GGTGCATAATGCTGGTCGTT 58.905 50.000 0.00 0.00 45.31 3.85
125 127 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
126 128 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
127 129 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
128 130 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
129 131 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
130 132 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
131 133 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
132 134 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
133 135 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
134 136 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
135 137 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
136 138 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
143 145 9.918630 CCTCTTTTATTCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
188 190 9.457436 GGACAAAAAGGGATGTATCTAAAACTA 57.543 33.333 0.00 0.00 0.00 2.24
189 191 7.947890 TGGACAAAAAGGGATGTATCTAAAACT 59.052 33.333 0.00 0.00 0.00 2.66
190 192 8.117813 TGGACAAAAAGGGATGTATCTAAAAC 57.882 34.615 0.00 0.00 0.00 2.43
191 193 8.893563 ATGGACAAAAAGGGATGTATCTAAAA 57.106 30.769 0.00 0.00 0.00 1.52
192 194 8.893563 AATGGACAAAAAGGGATGTATCTAAA 57.106 30.769 0.00 0.00 0.00 1.85
193 195 8.893563 AAATGGACAAAAAGGGATGTATCTAA 57.106 30.769 0.00 0.00 0.00 2.10
194 196 8.748412 CAAAATGGACAAAAAGGGATGTATCTA 58.252 33.333 0.00 0.00 0.00 1.98
195 197 7.454380 TCAAAATGGACAAAAAGGGATGTATCT 59.546 33.333 0.00 0.00 0.00 1.98
196 198 7.610865 TCAAAATGGACAAAAAGGGATGTATC 58.389 34.615 0.00 0.00 0.00 2.24
197 199 7.552050 TCAAAATGGACAAAAAGGGATGTAT 57.448 32.000 0.00 0.00 0.00 2.29
198 200 6.985653 TCAAAATGGACAAAAAGGGATGTA 57.014 33.333 0.00 0.00 0.00 2.29
199 201 5.885449 TCAAAATGGACAAAAAGGGATGT 57.115 34.783 0.00 0.00 0.00 3.06
200 202 6.369615 GTCATCAAAATGGACAAAAAGGGATG 59.630 38.462 0.00 0.00 33.42 3.51
201 203 6.043012 TGTCATCAAAATGGACAAAAAGGGAT 59.957 34.615 0.00 0.00 33.42 3.85
202 204 5.365025 TGTCATCAAAATGGACAAAAAGGGA 59.635 36.000 0.00 0.00 33.42 4.20
203 205 5.609423 TGTCATCAAAATGGACAAAAAGGG 58.391 37.500 0.00 0.00 33.42 3.95
204 206 6.762661 ACTTGTCATCAAAATGGACAAAAAGG 59.237 34.615 7.70 0.11 34.98 3.11
205 207 7.775397 ACTTGTCATCAAAATGGACAAAAAG 57.225 32.000 7.70 0.11 34.98 2.27
206 208 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
207 209 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
208 210 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
209 211 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
210 212 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
211 213 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
212 214 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
213 215 7.312154 TCCGAAAATACTTGTCATCAAAATGG 58.688 34.615 0.00 0.00 33.42 3.16
214 216 7.485913 CCTCCGAAAATACTTGTCATCAAAATG 59.514 37.037 0.00 0.00 32.87 2.32
215 217 7.362920 CCCTCCGAAAATACTTGTCATCAAAAT 60.363 37.037 0.00 0.00 32.87 1.82
216 218 6.072175 CCCTCCGAAAATACTTGTCATCAAAA 60.072 38.462 0.00 0.00 32.87 2.44
217 219 5.414454 CCCTCCGAAAATACTTGTCATCAAA 59.586 40.000 0.00 0.00 32.87 2.69
218 220 4.941263 CCCTCCGAAAATACTTGTCATCAA 59.059 41.667 0.00 0.00 0.00 2.57
219 221 4.224147 TCCCTCCGAAAATACTTGTCATCA 59.776 41.667 0.00 0.00 0.00 3.07
220 222 4.766375 TCCCTCCGAAAATACTTGTCATC 58.234 43.478 0.00 0.00 0.00 2.92
221 223 4.384208 CCTCCCTCCGAAAATACTTGTCAT 60.384 45.833 0.00 0.00 0.00 3.06
222 224 3.055385 CCTCCCTCCGAAAATACTTGTCA 60.055 47.826 0.00 0.00 0.00 3.58
223 225 3.532542 CCTCCCTCCGAAAATACTTGTC 58.467 50.000 0.00 0.00 0.00 3.18
224 226 2.238898 CCCTCCCTCCGAAAATACTTGT 59.761 50.000 0.00 0.00 0.00 3.16
225 227 2.504175 TCCCTCCCTCCGAAAATACTTG 59.496 50.000 0.00 0.00 0.00 3.16
226 228 2.772515 CTCCCTCCCTCCGAAAATACTT 59.227 50.000 0.00 0.00 0.00 2.24
227 229 2.292984 ACTCCCTCCCTCCGAAAATACT 60.293 50.000 0.00 0.00 0.00 2.12
228 230 2.117051 ACTCCCTCCCTCCGAAAATAC 58.883 52.381 0.00 0.00 0.00 1.89
229 231 2.563039 ACTCCCTCCCTCCGAAAATA 57.437 50.000 0.00 0.00 0.00 1.40
230 232 2.563039 TACTCCCTCCCTCCGAAAAT 57.437 50.000 0.00 0.00 0.00 1.82
231 233 2.563039 ATACTCCCTCCCTCCGAAAA 57.437 50.000 0.00 0.00 0.00 2.29
232 234 3.693526 TTATACTCCCTCCCTCCGAAA 57.306 47.619 0.00 0.00 0.00 3.46
233 235 3.693526 TTTATACTCCCTCCCTCCGAA 57.306 47.619 0.00 0.00 0.00 4.30
234 236 3.693526 TTTTATACTCCCTCCCTCCGA 57.306 47.619 0.00 0.00 0.00 4.55
235 237 4.976540 AATTTTATACTCCCTCCCTCCG 57.023 45.455 0.00 0.00 0.00 4.63
236 238 6.669631 TGAAAATTTTATACTCCCTCCCTCC 58.330 40.000 2.75 0.00 0.00 4.30
237 239 7.448777 GGATGAAAATTTTATACTCCCTCCCTC 59.551 40.741 2.75 0.00 0.00 4.30
238 240 7.091537 TGGATGAAAATTTTATACTCCCTCCCT 60.092 37.037 2.75 0.00 0.00 4.20
239 241 7.066781 TGGATGAAAATTTTATACTCCCTCCC 58.933 38.462 2.75 0.00 0.00 4.30
240 242 8.533569 TTGGATGAAAATTTTATACTCCCTCC 57.466 34.615 2.75 3.40 0.00 4.30
258 260 6.757897 ATCGACAAGCTTTTTATTGGATGA 57.242 33.333 0.00 0.00 0.00 2.92
278 280 4.120085 GGTCCTTACCGCCAATCG 57.880 61.111 0.00 0.00 35.62 3.34
295 297 8.565416 AGAATACATGCATGAGATGTAACAATG 58.435 33.333 32.75 2.93 39.23 2.82
317 319 4.583489 CAGCATAGAAAATCCAGGCAGAAT 59.417 41.667 0.00 0.00 0.00 2.40
349 351 0.317160 CGCCGGTGCCTCAGATATTA 59.683 55.000 0.00 0.00 0.00 0.98
350 352 1.069765 CGCCGGTGCCTCAGATATT 59.930 57.895 0.00 0.00 0.00 1.28
351 353 1.832608 TCGCCGGTGCCTCAGATAT 60.833 57.895 11.05 0.00 0.00 1.63
352 354 2.441348 TCGCCGGTGCCTCAGATA 60.441 61.111 11.05 0.00 0.00 1.98
353 355 4.148825 GTCGCCGGTGCCTCAGAT 62.149 66.667 11.05 0.00 0.00 2.90
397 399 1.625818 AGATGGTCCGAGAGCTTTGTT 59.374 47.619 0.00 0.00 0.00 2.83
398 400 1.066573 CAGATGGTCCGAGAGCTTTGT 60.067 52.381 0.00 0.00 0.00 2.83
399 401 1.066573 ACAGATGGTCCGAGAGCTTTG 60.067 52.381 0.00 3.84 0.00 2.77
400 402 1.270907 ACAGATGGTCCGAGAGCTTT 58.729 50.000 0.00 0.00 0.00 3.51
401 403 1.270907 AACAGATGGTCCGAGAGCTT 58.729 50.000 0.00 0.00 0.00 3.74
402 404 1.751924 GTAACAGATGGTCCGAGAGCT 59.248 52.381 0.00 0.00 0.00 4.09
407 409 0.813184 GGACGTAACAGATGGTCCGA 59.187 55.000 0.00 0.00 39.53 4.55
439 441 2.991190 GCATGTTGGAATTTGCTGACAG 59.009 45.455 0.00 0.00 32.41 3.51
443 445 3.034721 AGTGCATGTTGGAATTTGCTG 57.965 42.857 0.00 0.00 36.10 4.41
444 446 4.439153 CGATAGTGCATGTTGGAATTTGCT 60.439 41.667 0.00 0.00 36.10 3.91
447 449 3.181487 GGCGATAGTGCATGTTGGAATTT 60.181 43.478 0.00 0.00 36.28 1.82
469 471 7.530010 CATTTCTACCATTGTACTTGGAGTTG 58.470 38.462 18.63 8.13 37.69 3.16
534 542 5.811100 CCACTGATTAGATCGATGATCATGG 59.189 44.000 14.30 12.58 41.12 3.66
622 635 1.501741 CACTTTTGGCACCGGATCG 59.498 57.895 9.46 0.00 0.00 3.69
623 636 1.212751 GCACTTTTGGCACCGGATC 59.787 57.895 9.46 0.00 0.00 3.36
624 637 3.365535 GCACTTTTGGCACCGGAT 58.634 55.556 9.46 0.00 0.00 4.18
684 703 8.703743 ACAACATATGGGCAAATAATTGTACAT 58.296 29.630 7.80 7.09 38.85 2.29
696 715 5.722263 CAGAAATCAACAACATATGGGCAA 58.278 37.500 7.80 0.00 0.00 4.52
761 2007 0.539986 GGAGGAATGTTAGCGGTGGA 59.460 55.000 0.00 0.00 0.00 4.02
762 2008 0.251916 TGGAGGAATGTTAGCGGTGG 59.748 55.000 0.00 0.00 0.00 4.61
764 2010 2.817844 GTTTTGGAGGAATGTTAGCGGT 59.182 45.455 0.00 0.00 0.00 5.68
767 2013 3.572255 TGTGGTTTTGGAGGAATGTTAGC 59.428 43.478 0.00 0.00 0.00 3.09
799 2057 2.682856 GCGGTCATGATGTTGGTTGTAT 59.317 45.455 0.00 0.00 0.00 2.29
805 2063 1.600957 GATCAGCGGTCATGATGTTGG 59.399 52.381 0.00 0.00 37.52 3.77
833 2091 2.503061 CAGATCCGGGGAGCACAG 59.497 66.667 0.00 0.00 32.23 3.66
881 2139 1.004277 GGTAGGGCAACATGGACAAGA 59.996 52.381 0.00 0.00 39.74 3.02
882 2140 1.271871 TGGTAGGGCAACATGGACAAG 60.272 52.381 0.00 0.00 39.74 3.16
934 2192 0.249868 TGGGCTCTAATTGGCGATCG 60.250 55.000 11.69 11.69 0.00 3.69
1052 2340 4.161001 CCTTGGCCATTTCTTGAGCTAAAT 59.839 41.667 6.09 0.00 0.00 1.40
1053 2341 3.511146 CCTTGGCCATTTCTTGAGCTAAA 59.489 43.478 6.09 0.00 0.00 1.85
1078 2366 0.250467 AGCACAAGAAGCATCACCGT 60.250 50.000 0.00 0.00 0.00 4.83
1116 2407 3.602513 CTGCTGGGCTTCGCTCACT 62.603 63.158 0.00 0.00 32.27 3.41
1569 3222 1.374758 GAAGTCGAGCCAGTGGGTG 60.375 63.158 20.91 11.32 36.17 4.61
1640 3293 7.819415 AGTAAATAAAAGCCCTCAAAGCATTTC 59.181 33.333 0.00 0.00 35.03 2.17
1673 3388 3.947910 ACACCCAAATCTCAAAGCATG 57.052 42.857 0.00 0.00 0.00 4.06
1691 3411 8.717821 CGATATTTAGGACACAAGAAAAGAACA 58.282 33.333 0.00 0.00 0.00 3.18
1695 3603 7.464358 CACCGATATTTAGGACACAAGAAAAG 58.536 38.462 0.00 0.00 0.00 2.27
1697 3605 5.353123 GCACCGATATTTAGGACACAAGAAA 59.647 40.000 0.00 0.00 0.00 2.52
1700 3608 3.560068 GGCACCGATATTTAGGACACAAG 59.440 47.826 0.00 0.00 0.00 3.16
1701 3609 3.199071 AGGCACCGATATTTAGGACACAA 59.801 43.478 0.00 0.00 0.00 3.33
1702 3610 2.769663 AGGCACCGATATTTAGGACACA 59.230 45.455 0.00 0.00 0.00 3.72
1703 3611 3.470645 AGGCACCGATATTTAGGACAC 57.529 47.619 0.00 0.00 0.00 3.67
1726 3634 3.571590 TGCCAGACAATTAACCCAAGTT 58.428 40.909 0.00 0.00 40.15 2.66
1762 3671 1.066143 CGCTGTTTCACATAGGTCCCT 60.066 52.381 0.00 0.00 0.00 4.20
1763 3672 1.066430 TCGCTGTTTCACATAGGTCCC 60.066 52.381 0.00 0.00 0.00 4.46
1766 3675 3.074412 CCTTTCGCTGTTTCACATAGGT 58.926 45.455 0.00 0.00 0.00 3.08
1823 3732 5.391310 GCATCTCTCGAGCAAAAAGATGAAA 60.391 40.000 30.53 3.90 43.82 2.69
1825 3734 3.620374 GCATCTCTCGAGCAAAAAGATGA 59.380 43.478 30.53 11.15 43.82 2.92
1826 3735 3.373130 TGCATCTCTCGAGCAAAAAGATG 59.627 43.478 25.62 25.62 43.90 2.90
1827 3736 3.603532 TGCATCTCTCGAGCAAAAAGAT 58.396 40.909 7.81 7.66 34.97 2.40
1876 3803 6.149308 TGCGTCTTTGATCTTACACATCAATT 59.851 34.615 0.00 0.00 39.46 2.32
1909 3836 4.912395 TTGCAGGTGTGTGCCCCC 62.912 66.667 0.00 0.00 43.28 5.40
1981 3909 5.354842 ACTTAGAACTTAGTATGCCCACC 57.645 43.478 0.00 0.00 0.00 4.61
1983 3911 6.877322 GTGAAACTTAGAACTTAGTATGCCCA 59.123 38.462 0.00 0.00 0.00 5.36
2102 4030 5.872070 TCACGATATTTGTGCATGTAACTGA 59.128 36.000 0.00 0.00 37.26 3.41
2108 4036 6.193514 TGAAATCACGATATTTGTGCATGT 57.806 33.333 0.00 0.00 37.26 3.21
2111 4039 5.500825 CGATGAAATCACGATATTTGTGCA 58.499 37.500 4.81 0.00 45.97 4.57
2207 4135 6.653989 ACGAGGACTTTCAAATAAGATCCAT 58.346 36.000 0.00 0.00 32.46 3.41
2297 4232 9.745323 GCTTTTATTTTTGGATTCTGATTTTCG 57.255 29.630 0.00 0.00 0.00 3.46
2305 4240 6.596497 CAGGCATGCTTTTATTTTTGGATTCT 59.404 34.615 18.92 0.00 0.00 2.40
2309 4244 5.480642 TCAGGCATGCTTTTATTTTTGGA 57.519 34.783 18.92 0.00 0.00 3.53
2325 4260 2.672908 CATGCAGTCCCTCAGGCA 59.327 61.111 0.00 0.00 41.00 4.75
2343 4278 2.125753 GGCTCGCAGGTCTCACAG 60.126 66.667 0.00 0.00 0.00 3.66
2357 4292 1.892819 CTGGACGAGGATGTGTGGCT 61.893 60.000 0.00 0.00 0.00 4.75
2421 4356 0.525668 CGATGTCAGTGTCTACCGGC 60.526 60.000 0.00 0.00 0.00 6.13
2451 4386 1.888436 AATCGAGAGGCCTTGCGACA 61.888 55.000 26.55 11.33 35.44 4.35
2593 4529 3.399330 CAAGTTCAAGGACCATACGTGT 58.601 45.455 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.