Multiple sequence alignment - TraesCS1B01G083000

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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 TraesCS1B01G083000 chr1B 100.000 2872 0 0 1 2872 66949401 66952272 0.000000e+00 5304.0
1 TraesCS1B01G083000 chr7B 97.476 2417 49 4 458 2872 244284014 244281608 0.000000e+00 4115.0
2 TraesCS1B01G083000 chr2B 97.901 953 16 3 1924 2872 44915082 44916034 0.000000e+00 1646.0
3 TraesCS1B01G083000 chr2B 96.742 890 15 1 1038 1927 44910155 44911030 0.000000e+00 1471.0
4 TraesCS1B01G083000 chr2B 96.672 601 7 3 458 1053 44909180 44909772 0.000000e+00 987.0
5 TraesCS1B01G083000 chr2B 92.643 666 49 0 869 1534 379103810 379103145 0.000000e+00 959.0
6 TraesCS1B01G083000 chr2B 96.484 455 14 2 4 457 676743426 676742973 0.000000e+00 750.0
7 TraesCS1B01G083000 chr4A 91.309 886 41 19 2004 2872 37903178 37904044 0.000000e+00 1177.0
8 TraesCS1B01G083000 chr4A 95.494 466 20 1 1479 1944 37901923 37902387 0.000000e+00 743.0
9 TraesCS1B01G083000 chr4A 96.491 57 2 0 1953 2009 37903089 37903145 8.470000e-16 95.3
10 TraesCS1B01G083000 chr3B 90.374 883 50 10 2004 2872 244787242 244786381 0.000000e+00 1127.0
11 TraesCS1B01G083000 chr3B 94.011 551 31 2 1170 1719 244793047 244792498 0.000000e+00 833.0
12 TraesCS1B01G083000 chr3B 96.272 456 14 3 4 457 222146988 222147442 0.000000e+00 745.0
13 TraesCS1B01G083000 chr3B 93.443 305 19 1 1705 2009 244787578 244787275 4.360000e-123 451.0
14 TraesCS1B01G083000 chr2A 92.793 666 48 0 869 1534 227834779 227834114 0.000000e+00 965.0
15 TraesCS1B01G083000 chr2A 96.484 455 14 2 4 457 25350593 25351046 0.000000e+00 750.0
16 TraesCS1B01G083000 chr2D 92.354 667 49 2 869 1534 202086882 202086217 0.000000e+00 948.0
17 TraesCS1B01G083000 chr3A 96.725 458 13 2 4 460 580560619 580560163 0.000000e+00 761.0
18 TraesCS1B01G083000 chr3A 96.304 460 14 3 4 461 431863259 431863717 0.000000e+00 752.0
19 TraesCS1B01G083000 chr5B 96.514 459 13 3 2 458 72093622 72093165 0.000000e+00 756.0
20 TraesCS1B01G083000 chr5B 96.078 459 15 3 4 460 457449034 457448577 0.000000e+00 745.0
21 TraesCS1B01G083000 chr5B 96.256 454 14 3 5 457 700230262 700230713 0.000000e+00 741.0
22 TraesCS1B01G083000 chr6A 96.484 455 14 2 4 457 8202487 8202940 0.000000e+00 750.0
23 TraesCS1B01G083000 chr6A 92.526 388 28 1 1623 2009 540608215 540607828 3.230000e-154 555.0
24 TraesCS1B01G083000 chr6A 92.473 186 13 1 2310 2495 540607589 540607405 6.100000e-67 265.0
25 TraesCS1B01G083000 chr6A 93.706 143 9 0 2004 2146 540607795 540607653 6.230000e-52 215.0
26 TraesCS1B01G083000 chr6A 86.486 74 5 4 2174 2243 540607660 540607588 3.070000e-10 76.8
27 TraesCS1B01G083000 chr6D 93.299 388 25 1 1623 2009 394590576 394590189 3.210000e-159 571.0
28 TraesCS1B01G083000 chr6D 88.163 245 23 5 2004 2243 394590156 394589913 1.300000e-73 287.0
29 TraesCS1B01G083000 chr6D 90.526 190 18 0 2306 2495 394589918 394589729 4.750000e-63 252.0
30 TraesCS1B01G083000 chr6B 92.051 390 28 2 1623 2009 590565721 590565332 1.950000e-151 545.0
31 TraesCS1B01G083000 chr6B 92.105 190 15 0 2306 2495 590564945 590564756 4.720000e-68 268.0
32 TraesCS1B01G083000 chr1D 92.574 202 15 0 1782 1983 7200245 7200446 1.010000e-74 291.0
33 TraesCS1B01G083000 chr1D 96.319 163 6 0 1623 1785 7198183 7198345 4.720000e-68 268.0
34 TraesCS1B01G083000 chr1D 94.186 86 5 0 1526 1611 1851446 1851531 6.460000e-27 132.0
35 TraesCS1B01G083000 chr7A 82.836 134 9 12 515 640 51835290 51835163 1.090000e-19 108.0


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 TraesCS1B01G083000 chr1B 66949401 66952272 2871 False 5304.000000 5304 100.000000 1 2872 1 chr1B.!!$F1 2871
1 TraesCS1B01G083000 chr7B 244281608 244284014 2406 True 4115.000000 4115 97.476000 458 2872 1 chr7B.!!$R1 2414
2 TraesCS1B01G083000 chr2B 44915082 44916034 952 False 1646.000000 1646 97.901000 1924 2872 1 chr2B.!!$F1 948
3 TraesCS1B01G083000 chr2B 44909180 44911030 1850 False 1229.000000 1471 96.707000 458 1927 2 chr2B.!!$F2 1469
4 TraesCS1B01G083000 chr2B 379103145 379103810 665 True 959.000000 959 92.643000 869 1534 1 chr2B.!!$R1 665
5 TraesCS1B01G083000 chr4A 37901923 37904044 2121 False 671.766667 1177 94.431333 1479 2872 3 chr4A.!!$F1 1393
6 TraesCS1B01G083000 chr3B 244792498 244793047 549 True 833.000000 833 94.011000 1170 1719 1 chr3B.!!$R1 549
7 TraesCS1B01G083000 chr3B 244786381 244787578 1197 True 789.000000 1127 91.908500 1705 2872 2 chr3B.!!$R2 1167
8 TraesCS1B01G083000 chr2A 227834114 227834779 665 True 965.000000 965 92.793000 869 1534 1 chr2A.!!$R1 665
9 TraesCS1B01G083000 chr2D 202086217 202086882 665 True 948.000000 948 92.354000 869 1534 1 chr2D.!!$R1 665
10 TraesCS1B01G083000 chr6A 540607405 540608215 810 True 277.950000 555 91.297750 1623 2495 4 chr6A.!!$R1 872
11 TraesCS1B01G083000 chr6D 394589729 394590576 847 True 370.000000 571 90.662667 1623 2495 3 chr6D.!!$R1 872
12 TraesCS1B01G083000 chr6B 590564756 590565721 965 True 406.500000 545 92.078000 1623 2495 2 chr6B.!!$R1 872
13 TraesCS1B01G083000 chr1D 7198183 7200446 2263 False 279.500000 291 94.446500 1623 1983 2 chr1D.!!$F2 360

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
445 446 0.106217 CCAACTATCCCGGCCCATTT 60.106 55.0 0.0 0.0 0.00 2.32 F
447 448 0.106217 AACTATCCCGGCCCATTTGG 60.106 55.0 0.0 0.0 37.09 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 1987 0.035458 AGACAACTGCTACAGTGGGC 59.965 55.000 7.03 3.45 43.49 5.36 R
2150 5192 1.222936 CTCGGCCAGCAGAAGGAAT 59.777 57.895 2.24 0.00 0.00 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.608590 CATTATAGCTGGCCAAACGGG 59.391 52.381 7.01 0.00 40.85 5.28
55 56 2.515901 GGCACGGCCCATCCTAAT 59.484 61.111 0.00 0.00 44.06 1.73
56 57 1.600916 GGCACGGCCCATCCTAATC 60.601 63.158 0.00 0.00 44.06 1.75
57 58 1.961277 GCACGGCCCATCCTAATCG 60.961 63.158 0.00 0.00 0.00 3.34
58 59 1.445942 CACGGCCCATCCTAATCGT 59.554 57.895 0.00 0.00 0.00 3.73
59 60 0.880278 CACGGCCCATCCTAATCGTG 60.880 60.000 0.00 0.00 41.09 4.35
60 61 1.961277 CGGCCCATCCTAATCGTGC 60.961 63.158 0.00 0.00 0.00 5.34
61 62 1.600916 GGCCCATCCTAATCGTGCC 60.601 63.158 0.00 0.00 0.00 5.01
62 63 1.451936 GCCCATCCTAATCGTGCCT 59.548 57.895 0.00 0.00 0.00 4.75
63 64 0.886490 GCCCATCCTAATCGTGCCTG 60.886 60.000 0.00 0.00 0.00 4.85
64 65 0.250467 CCCATCCTAATCGTGCCTGG 60.250 60.000 0.00 0.00 0.00 4.45
65 66 0.886490 CCATCCTAATCGTGCCTGGC 60.886 60.000 12.87 12.87 0.00 4.85
66 67 0.179048 CATCCTAATCGTGCCTGGCA 60.179 55.000 19.30 19.30 35.60 4.92
94 95 2.930826 CCCACCTAGGCACGATTATT 57.069 50.000 9.30 0.00 35.39 1.40
96 97 4.553330 CCCACCTAGGCACGATTATTAT 57.447 45.455 9.30 0.00 35.39 1.28
97 98 5.670792 CCCACCTAGGCACGATTATTATA 57.329 43.478 9.30 0.00 35.39 0.98
98 99 5.416947 CCCACCTAGGCACGATTATTATAC 58.583 45.833 9.30 0.00 35.39 1.47
99 100 5.100259 CCACCTAGGCACGATTATTATACG 58.900 45.833 9.30 0.00 0.00 3.06
100 101 5.100259 CACCTAGGCACGATTATTATACGG 58.900 45.833 9.30 0.00 0.00 4.02
101 102 4.159135 ACCTAGGCACGATTATTATACGGG 59.841 45.833 9.30 0.00 0.00 5.28
105 106 2.950433 CACGATTATTATACGGGCCGT 58.050 47.619 35.91 35.91 44.35 5.68
106 107 2.664568 CACGATTATTATACGGGCCGTG 59.335 50.000 39.80 22.32 41.39 4.94
107 108 1.657094 CGATTATTATACGGGCCGTGC 59.343 52.381 39.80 16.99 41.39 5.34
158 159 2.202960 GGCACGGCCGTATGCTAA 60.203 61.111 33.70 0.00 39.62 3.09
159 160 1.597027 GGCACGGCCGTATGCTAAT 60.597 57.895 33.70 1.55 39.62 1.73
160 161 1.566018 GGCACGGCCGTATGCTAATC 61.566 60.000 33.70 14.31 39.62 1.75
161 162 1.886861 GCACGGCCGTATGCTAATCG 61.887 60.000 33.70 16.54 40.92 3.34
162 163 1.006571 ACGGCCGTATGCTAATCGG 60.007 57.895 33.34 0.00 45.94 4.18
163 164 1.736645 CGGCCGTATGCTAATCGGG 60.737 63.158 19.50 0.00 43.77 5.14
164 165 3.562635 GCCGTATGCTAATCGGGC 58.437 61.111 5.06 0.00 43.77 6.13
165 166 2.033194 GCCGTATGCTAATCGGGCC 61.033 63.158 0.00 0.00 43.77 5.80
166 167 1.736645 CCGTATGCTAATCGGGCCG 60.737 63.158 22.51 22.51 40.49 6.13
167 168 1.736645 CGTATGCTAATCGGGCCGG 60.737 63.158 27.98 11.17 0.00 6.13
168 169 2.033194 GTATGCTAATCGGGCCGGC 61.033 63.158 27.98 21.18 0.00 6.13
169 170 3.248446 TATGCTAATCGGGCCGGCC 62.248 63.158 38.57 38.57 0.00 6.13
191 192 3.702048 GGCACGCCAGGACCACTA 61.702 66.667 2.36 0.00 35.81 2.74
192 193 2.345991 GCACGCCAGGACCACTAA 59.654 61.111 0.00 0.00 0.00 2.24
193 194 1.078426 GCACGCCAGGACCACTAAT 60.078 57.895 0.00 0.00 0.00 1.73
194 195 1.090052 GCACGCCAGGACCACTAATC 61.090 60.000 0.00 0.00 0.00 1.75
195 196 0.537188 CACGCCAGGACCACTAATCT 59.463 55.000 0.00 0.00 0.00 2.40
196 197 1.754803 CACGCCAGGACCACTAATCTA 59.245 52.381 0.00 0.00 0.00 1.98
197 198 1.755380 ACGCCAGGACCACTAATCTAC 59.245 52.381 0.00 0.00 0.00 2.59
198 199 1.068741 CGCCAGGACCACTAATCTACC 59.931 57.143 0.00 0.00 0.00 3.18
199 200 2.399580 GCCAGGACCACTAATCTACCT 58.600 52.381 0.00 0.00 0.00 3.08
200 201 2.365941 GCCAGGACCACTAATCTACCTC 59.634 54.545 0.00 0.00 0.00 3.85
201 202 2.966516 CCAGGACCACTAATCTACCTCC 59.033 54.545 0.00 0.00 0.00 4.30
202 203 3.374318 CCAGGACCACTAATCTACCTCCT 60.374 52.174 0.00 0.00 0.00 3.69
203 204 4.140994 CCAGGACCACTAATCTACCTCCTA 60.141 50.000 0.00 0.00 0.00 2.94
204 205 5.459831 CCAGGACCACTAATCTACCTCCTAT 60.460 48.000 0.00 0.00 0.00 2.57
205 206 6.078664 CAGGACCACTAATCTACCTCCTATT 58.921 44.000 0.00 0.00 0.00 1.73
206 207 6.555360 CAGGACCACTAATCTACCTCCTATTT 59.445 42.308 0.00 0.00 0.00 1.40
207 208 7.071321 CAGGACCACTAATCTACCTCCTATTTT 59.929 40.741 0.00 0.00 0.00 1.82
208 209 7.071321 AGGACCACTAATCTACCTCCTATTTTG 59.929 40.741 0.00 0.00 0.00 2.44
209 210 6.592870 ACCACTAATCTACCTCCTATTTTGC 58.407 40.000 0.00 0.00 0.00 3.68
210 211 6.157994 ACCACTAATCTACCTCCTATTTTGCA 59.842 38.462 0.00 0.00 0.00 4.08
211 212 6.483640 CCACTAATCTACCTCCTATTTTGCAC 59.516 42.308 0.00 0.00 0.00 4.57
212 213 7.047891 CACTAATCTACCTCCTATTTTGCACA 58.952 38.462 0.00 0.00 0.00 4.57
213 214 7.011482 CACTAATCTACCTCCTATTTTGCACAC 59.989 40.741 0.00 0.00 0.00 3.82
214 215 5.700402 ATCTACCTCCTATTTTGCACACT 57.300 39.130 0.00 0.00 0.00 3.55
215 216 4.832248 TCTACCTCCTATTTTGCACACTG 58.168 43.478 0.00 0.00 0.00 3.66
216 217 3.788227 ACCTCCTATTTTGCACACTGA 57.212 42.857 0.00 0.00 0.00 3.41
217 218 3.679389 ACCTCCTATTTTGCACACTGAG 58.321 45.455 0.00 0.00 0.00 3.35
218 219 2.421424 CCTCCTATTTTGCACACTGAGC 59.579 50.000 0.00 0.00 0.00 4.26
219 220 2.076100 TCCTATTTTGCACACTGAGCG 58.924 47.619 0.00 0.00 33.85 5.03
220 221 1.806542 CCTATTTTGCACACTGAGCGT 59.193 47.619 0.00 0.00 33.85 5.07
221 222 2.226437 CCTATTTTGCACACTGAGCGTT 59.774 45.455 0.00 0.00 33.85 4.84
222 223 2.869233 ATTTTGCACACTGAGCGTTT 57.131 40.000 0.00 0.00 33.85 3.60
223 224 2.645730 TTTTGCACACTGAGCGTTTT 57.354 40.000 0.00 0.00 33.85 2.43
224 225 2.645730 TTTGCACACTGAGCGTTTTT 57.354 40.000 0.00 0.00 33.85 1.94
225 226 3.766676 TTTGCACACTGAGCGTTTTTA 57.233 38.095 0.00 0.00 33.85 1.52
226 227 3.332761 TTGCACACTGAGCGTTTTTAG 57.667 42.857 0.00 0.00 33.85 1.85
227 228 1.002900 TGCACACTGAGCGTTTTTAGC 60.003 47.619 0.00 0.00 33.85 3.09
228 229 1.663161 GCACACTGAGCGTTTTTAGCC 60.663 52.381 0.00 0.00 34.64 3.93
229 230 1.873591 CACACTGAGCGTTTTTAGCCT 59.126 47.619 0.00 0.00 34.64 4.58
230 231 3.064207 CACACTGAGCGTTTTTAGCCTA 58.936 45.455 0.00 0.00 34.64 3.93
231 232 3.684788 CACACTGAGCGTTTTTAGCCTAT 59.315 43.478 0.00 0.00 34.64 2.57
232 233 4.154195 CACACTGAGCGTTTTTAGCCTATT 59.846 41.667 0.00 0.00 34.64 1.73
233 234 4.760204 ACACTGAGCGTTTTTAGCCTATTT 59.240 37.500 0.00 0.00 34.64 1.40
234 235 5.240844 ACACTGAGCGTTTTTAGCCTATTTT 59.759 36.000 0.00 0.00 34.64 1.82
235 236 6.149633 CACTGAGCGTTTTTAGCCTATTTTT 58.850 36.000 0.00 0.00 34.64 1.94
236 237 7.040961 ACACTGAGCGTTTTTAGCCTATTTTTA 60.041 33.333 0.00 0.00 34.64 1.52
237 238 7.270579 CACTGAGCGTTTTTAGCCTATTTTTAC 59.729 37.037 0.00 0.00 34.64 2.01
238 239 6.614160 TGAGCGTTTTTAGCCTATTTTTACC 58.386 36.000 0.00 0.00 34.64 2.85
239 240 6.431852 TGAGCGTTTTTAGCCTATTTTTACCT 59.568 34.615 0.00 0.00 34.64 3.08
240 241 6.617879 AGCGTTTTTAGCCTATTTTTACCTG 58.382 36.000 0.00 0.00 34.64 4.00
241 242 6.208007 AGCGTTTTTAGCCTATTTTTACCTGT 59.792 34.615 0.00 0.00 34.64 4.00
242 243 6.864685 GCGTTTTTAGCCTATTTTTACCTGTT 59.135 34.615 0.00 0.00 0.00 3.16
243 244 7.148869 GCGTTTTTAGCCTATTTTTACCTGTTG 60.149 37.037 0.00 0.00 0.00 3.33
244 245 7.327518 CGTTTTTAGCCTATTTTTACCTGTTGG 59.672 37.037 0.00 0.00 39.83 3.77
245 246 5.907866 TTAGCCTATTTTTACCTGTTGGC 57.092 39.130 0.00 0.00 39.40 4.52
246 247 3.096852 AGCCTATTTTTACCTGTTGGCC 58.903 45.455 0.00 0.00 39.90 5.36
247 248 2.167693 GCCTATTTTTACCTGTTGGCCC 59.832 50.000 0.00 0.00 36.63 5.80
248 249 3.436243 CCTATTTTTACCTGTTGGCCCA 58.564 45.455 0.00 0.00 36.63 5.36
249 250 4.030216 CCTATTTTTACCTGTTGGCCCAT 58.970 43.478 0.00 0.00 36.63 4.00
250 251 5.205056 CCTATTTTTACCTGTTGGCCCATA 58.795 41.667 0.00 0.00 36.63 2.74
251 252 5.838521 CCTATTTTTACCTGTTGGCCCATAT 59.161 40.000 0.00 0.00 36.63 1.78
252 253 6.326323 CCTATTTTTACCTGTTGGCCCATATT 59.674 38.462 0.00 0.00 36.63 1.28
253 254 7.507616 CCTATTTTTACCTGTTGGCCCATATTA 59.492 37.037 0.00 0.00 36.63 0.98
254 255 6.783708 TTTTTACCTGTTGGCCCATATTAG 57.216 37.500 0.00 0.00 36.63 1.73
255 256 4.447138 TTACCTGTTGGCCCATATTAGG 57.553 45.455 0.00 1.97 36.63 2.69
256 257 2.498441 ACCTGTTGGCCCATATTAGGA 58.502 47.619 0.00 0.00 36.63 2.94
257 258 3.063650 ACCTGTTGGCCCATATTAGGAT 58.936 45.455 0.00 0.00 36.63 3.24
258 259 4.247814 ACCTGTTGGCCCATATTAGGATA 58.752 43.478 0.00 0.00 36.63 2.59
259 260 4.042934 ACCTGTTGGCCCATATTAGGATAC 59.957 45.833 0.00 0.00 36.63 2.24
260 261 4.042809 CCTGTTGGCCCATATTAGGATACA 59.957 45.833 0.00 0.00 41.41 2.29
261 262 5.281193 CCTGTTGGCCCATATTAGGATACAT 60.281 44.000 0.00 0.00 41.41 2.29
262 263 6.069673 CCTGTTGGCCCATATTAGGATACATA 60.070 42.308 0.00 0.00 41.41 2.29
263 264 7.336475 TGTTGGCCCATATTAGGATACATAA 57.664 36.000 0.00 0.00 41.41 1.90
264 265 7.760607 TGTTGGCCCATATTAGGATACATAAA 58.239 34.615 0.00 0.00 41.41 1.40
265 266 8.228206 TGTTGGCCCATATTAGGATACATAAAA 58.772 33.333 0.00 0.00 41.41 1.52
266 267 9.084533 GTTGGCCCATATTAGGATACATAAAAA 57.915 33.333 0.00 0.00 41.41 1.94
296 297 4.749245 AAAAGTTAATCAGGTCGTGCTG 57.251 40.909 0.00 0.00 0.00 4.41
297 298 3.402628 AAGTTAATCAGGTCGTGCTGT 57.597 42.857 0.00 0.00 0.00 4.40
298 299 2.688507 AGTTAATCAGGTCGTGCTGTG 58.311 47.619 0.00 0.00 0.00 3.66
299 300 1.128692 GTTAATCAGGTCGTGCTGTGC 59.871 52.381 0.00 0.00 0.00 4.57
300 301 0.391130 TAATCAGGTCGTGCTGTGCC 60.391 55.000 0.00 0.00 0.00 5.01
301 302 3.939837 ATCAGGTCGTGCTGTGCCG 62.940 63.158 0.00 0.00 0.00 5.69
332 333 4.748144 CCCTTCAGGCCCAGGCAC 62.748 72.222 11.50 0.00 44.11 5.01
373 374 4.733542 GGCCCGGCCTGTTTAGCA 62.734 66.667 22.31 0.00 46.69 3.49
374 375 3.440415 GCCCGGCCTGTTTAGCAC 61.440 66.667 0.00 0.00 0.00 4.40
375 376 3.124921 CCCGGCCTGTTTAGCACG 61.125 66.667 0.00 0.00 0.00 5.34
376 377 2.358247 CCGGCCTGTTTAGCACGT 60.358 61.111 0.00 0.00 0.00 4.49
377 378 2.677003 CCGGCCTGTTTAGCACGTG 61.677 63.158 12.28 12.28 0.00 4.49
378 379 1.959226 CGGCCTGTTTAGCACGTGT 60.959 57.895 18.38 6.65 0.00 4.49
379 380 1.866925 GGCCTGTTTAGCACGTGTC 59.133 57.895 18.38 9.62 0.00 3.67
380 381 1.491563 GCCTGTTTAGCACGTGTCG 59.508 57.895 18.38 0.00 0.00 4.35
381 382 1.219522 GCCTGTTTAGCACGTGTCGT 61.220 55.000 18.38 4.92 42.36 4.34
436 437 4.581093 GGCCGGCCCAACTATCCC 62.581 72.222 36.64 5.01 0.00 3.85
437 438 4.929707 GCCGGCCCAACTATCCCG 62.930 72.222 18.11 0.00 40.39 5.14
439 440 4.929707 CGGCCCAACTATCCCGGC 62.930 72.222 0.00 0.00 40.85 6.13
441 442 4.581093 GCCCAACTATCCCGGCCC 62.581 72.222 0.00 0.00 35.23 5.80
442 443 3.093835 CCCAACTATCCCGGCCCA 61.094 66.667 0.00 0.00 0.00 5.36
443 444 2.460853 CCCAACTATCCCGGCCCAT 61.461 63.158 0.00 0.00 0.00 4.00
444 445 1.536676 CCAACTATCCCGGCCCATT 59.463 57.895 0.00 0.00 0.00 3.16
445 446 0.106217 CCAACTATCCCGGCCCATTT 60.106 55.000 0.00 0.00 0.00 2.32
446 447 1.032014 CAACTATCCCGGCCCATTTG 58.968 55.000 0.00 0.00 0.00 2.32
447 448 0.106217 AACTATCCCGGCCCATTTGG 60.106 55.000 0.00 0.00 37.09 3.28
528 529 1.069568 CACGTTTGTGTGTGTGTGTGT 60.070 47.619 0.00 0.00 41.34 3.72
529 530 1.069568 ACGTTTGTGTGTGTGTGTGTG 60.070 47.619 0.00 0.00 0.00 3.82
530 531 1.069568 CGTTTGTGTGTGTGTGTGTGT 60.070 47.619 0.00 0.00 0.00 3.72
531 532 2.315011 GTTTGTGTGTGTGTGTGTGTG 58.685 47.619 0.00 0.00 0.00 3.82
532 533 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
533 534 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
534 535 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
535 536 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
685 686 7.816995 GCCATGAAAATAAAATGTTGTGGTCTA 59.183 33.333 0.00 0.00 0.00 2.59
719 720 3.077359 AGCTGCTCAAGTGTAACAATCC 58.923 45.455 0.00 0.00 41.43 3.01
904 906 9.190317 GAAAGGTCTATTCCCAAATTTCTGTAT 57.810 33.333 0.00 0.00 0.00 2.29
907 909 8.336235 AGGTCTATTCCCAAATTTCTGTATCAA 58.664 33.333 0.00 0.00 0.00 2.57
1199 1603 3.119388 ACAAATGAAATCGACATGGCAGG 60.119 43.478 0.00 0.00 0.00 4.85
1489 1893 6.014755 TCTCTCTCCTAAGATTGTGCATATGG 60.015 42.308 4.56 0.00 0.00 2.74
1583 1987 2.038164 TGCCTCATATGCAAGCTCCTAG 59.962 50.000 0.00 0.00 35.40 3.02
1594 1998 1.045911 AGCTCCTAGCCCACTGTAGC 61.046 60.000 0.00 0.00 43.77 3.58
1675 2079 5.552870 ATGTACTCCATCTGGTTGGATAC 57.447 43.478 0.00 6.93 44.66 2.24
1858 4165 6.988522 ACGGGCAATTTTACTTTTATCAGTT 58.011 32.000 0.00 0.00 0.00 3.16
2047 5088 1.408340 TCAACCGTTTCACCTCACGTA 59.592 47.619 0.00 0.00 34.47 3.57
2408 5571 5.393866 ACCTAAACTGTTCCATCACCAAAT 58.606 37.500 0.00 0.00 0.00 2.32
2448 5611 0.319405 CCCCGACAAACCTTCGTACT 59.681 55.000 0.00 0.00 34.56 2.73
2669 5837 1.379977 AGGGAAGCGTCATCGAGGA 60.380 57.895 0.00 0.00 39.71 3.71
2684 5852 1.667724 CGAGGAATGGCTGATGTCAAC 59.332 52.381 0.00 0.00 0.00 3.18
2733 5901 4.932200 CCTTTAACTCCTGATCTGTGTCAC 59.068 45.833 0.00 0.00 0.00 3.67
2734 5902 5.279708 CCTTTAACTCCTGATCTGTGTCACT 60.280 44.000 4.27 0.00 0.00 3.41
2735 5903 3.951775 AACTCCTGATCTGTGTCACTC 57.048 47.619 4.27 0.00 0.00 3.51
2736 5904 2.175202 ACTCCTGATCTGTGTCACTCC 58.825 52.381 4.27 0.00 0.00 3.85
2737 5905 1.480137 CTCCTGATCTGTGTCACTCCC 59.520 57.143 4.27 0.00 0.00 4.30
2738 5906 1.077828 TCCTGATCTGTGTCACTCCCT 59.922 52.381 4.27 0.00 0.00 4.20
2739 5907 1.480137 CCTGATCTGTGTCACTCCCTC 59.520 57.143 4.27 0.00 0.00 4.30
2740 5908 2.455557 CTGATCTGTGTCACTCCCTCT 58.544 52.381 4.27 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.487576 CCCGTTTGGCCAGCTATAA 57.512 52.632 5.11 0.00 0.00 0.98
39 40 1.961277 CGATTAGGATGGGCCGTGC 60.961 63.158 9.57 9.57 43.43 5.34
40 41 0.880278 CACGATTAGGATGGGCCGTG 60.880 60.000 1.02 0.00 43.43 4.94
41 42 1.445942 CACGATTAGGATGGGCCGT 59.554 57.895 0.00 0.00 43.43 5.68
42 43 1.961277 GCACGATTAGGATGGGCCG 60.961 63.158 0.00 0.00 43.43 6.13
43 44 1.600916 GGCACGATTAGGATGGGCC 60.601 63.158 0.00 0.00 0.00 5.80
44 45 0.886490 CAGGCACGATTAGGATGGGC 60.886 60.000 0.00 0.00 0.00 5.36
45 46 0.250467 CCAGGCACGATTAGGATGGG 60.250 60.000 0.00 0.00 0.00 4.00
46 47 0.886490 GCCAGGCACGATTAGGATGG 60.886 60.000 6.55 0.00 0.00 3.51
47 48 0.179048 TGCCAGGCACGATTAGGATG 60.179 55.000 11.22 0.00 31.71 3.51
48 49 2.220953 TGCCAGGCACGATTAGGAT 58.779 52.632 11.22 0.00 31.71 3.24
49 50 3.720494 TGCCAGGCACGATTAGGA 58.280 55.556 11.22 0.00 31.71 2.94
75 76 2.930826 AATAATCGTGCCTAGGTGGG 57.069 50.000 11.31 0.00 36.00 4.61
76 77 5.100259 CGTATAATAATCGTGCCTAGGTGG 58.900 45.833 11.31 0.00 39.35 4.61
77 78 5.100259 CCGTATAATAATCGTGCCTAGGTG 58.900 45.833 11.31 0.80 0.00 4.00
78 79 4.159135 CCCGTATAATAATCGTGCCTAGGT 59.841 45.833 11.31 0.00 0.00 3.08
79 80 4.679662 CCCGTATAATAATCGTGCCTAGG 58.320 47.826 3.67 3.67 0.00 3.02
80 81 4.110482 GCCCGTATAATAATCGTGCCTAG 58.890 47.826 0.00 0.00 0.00 3.02
81 82 3.119029 GGCCCGTATAATAATCGTGCCTA 60.119 47.826 0.00 0.00 42.74 3.93
82 83 2.354403 GGCCCGTATAATAATCGTGCCT 60.354 50.000 0.00 0.00 42.74 4.75
83 84 2.004733 GGCCCGTATAATAATCGTGCC 58.995 52.381 0.00 0.00 40.23 5.01
84 85 1.657094 CGGCCCGTATAATAATCGTGC 59.343 52.381 0.00 0.00 0.00 5.34
85 86 2.664568 CACGGCCCGTATAATAATCGTG 59.335 50.000 9.25 0.00 38.32 4.35
86 87 2.927871 GCACGGCCCGTATAATAATCGT 60.928 50.000 9.25 0.00 38.32 3.73
87 88 1.657094 GCACGGCCCGTATAATAATCG 59.343 52.381 9.25 0.00 38.32 3.34
88 89 2.004733 GGCACGGCCCGTATAATAATC 58.995 52.381 9.25 0.00 44.06 1.75
89 90 2.103537 GGCACGGCCCGTATAATAAT 57.896 50.000 9.25 0.00 44.06 1.28
90 91 3.610637 GGCACGGCCCGTATAATAA 57.389 52.632 9.25 0.00 44.06 1.40
141 142 1.566018 GATTAGCATACGGCCGTGCC 61.566 60.000 40.02 25.85 46.50 5.01
142 143 1.860078 GATTAGCATACGGCCGTGC 59.140 57.895 40.02 33.52 46.50 5.34
143 144 1.282248 CCGATTAGCATACGGCCGTG 61.282 60.000 40.02 25.57 46.50 4.94
144 145 1.006571 CCGATTAGCATACGGCCGT 60.007 57.895 36.01 36.01 46.50 5.68
145 146 1.736645 CCCGATTAGCATACGGCCG 60.737 63.158 26.86 26.86 46.50 6.13
146 147 2.033194 GCCCGATTAGCATACGGCC 61.033 63.158 0.00 0.00 46.50 6.13
147 148 2.033194 GGCCCGATTAGCATACGGC 61.033 63.158 0.00 0.00 44.45 5.68
148 149 1.736645 CGGCCCGATTAGCATACGG 60.737 63.158 0.00 0.00 45.24 4.02
149 150 1.736645 CCGGCCCGATTAGCATACG 60.737 63.158 3.71 0.00 0.00 3.06
150 151 2.033194 GCCGGCCCGATTAGCATAC 61.033 63.158 18.11 0.00 0.00 2.39
151 152 2.345991 GCCGGCCCGATTAGCATA 59.654 61.111 18.11 0.00 0.00 3.14
152 153 4.643387 GGCCGGCCCGATTAGCAT 62.643 66.667 36.64 0.00 0.00 3.79
174 175 2.536997 ATTAGTGGTCCTGGCGTGCC 62.537 60.000 3.30 3.30 0.00 5.01
175 176 1.078426 ATTAGTGGTCCTGGCGTGC 60.078 57.895 0.00 0.00 0.00 5.34
176 177 0.537188 AGATTAGTGGTCCTGGCGTG 59.463 55.000 0.00 0.00 0.00 5.34
177 178 1.755380 GTAGATTAGTGGTCCTGGCGT 59.245 52.381 0.00 0.00 0.00 5.68
178 179 1.068741 GGTAGATTAGTGGTCCTGGCG 59.931 57.143 0.00 0.00 0.00 5.69
179 180 2.365941 GAGGTAGATTAGTGGTCCTGGC 59.634 54.545 0.00 0.00 0.00 4.85
180 181 2.966516 GGAGGTAGATTAGTGGTCCTGG 59.033 54.545 0.00 0.00 0.00 4.45
181 182 3.917300 AGGAGGTAGATTAGTGGTCCTG 58.083 50.000 0.00 0.00 31.59 3.86
182 183 5.952161 ATAGGAGGTAGATTAGTGGTCCT 57.048 43.478 0.00 0.00 36.84 3.85
183 184 6.997942 AAATAGGAGGTAGATTAGTGGTCC 57.002 41.667 0.00 0.00 0.00 4.46
184 185 6.706716 GCAAAATAGGAGGTAGATTAGTGGTC 59.293 42.308 0.00 0.00 0.00 4.02
185 186 6.157994 TGCAAAATAGGAGGTAGATTAGTGGT 59.842 38.462 0.00 0.00 0.00 4.16
186 187 6.483640 GTGCAAAATAGGAGGTAGATTAGTGG 59.516 42.308 0.00 0.00 0.00 4.00
187 188 7.011482 GTGTGCAAAATAGGAGGTAGATTAGTG 59.989 40.741 0.00 0.00 0.00 2.74
188 189 7.048512 GTGTGCAAAATAGGAGGTAGATTAGT 58.951 38.462 0.00 0.00 0.00 2.24
189 190 7.225538 CAGTGTGCAAAATAGGAGGTAGATTAG 59.774 40.741 0.00 0.00 0.00 1.73
190 191 7.047891 CAGTGTGCAAAATAGGAGGTAGATTA 58.952 38.462 0.00 0.00 0.00 1.75
191 192 5.882557 CAGTGTGCAAAATAGGAGGTAGATT 59.117 40.000 0.00 0.00 0.00 2.40
192 193 5.189736 TCAGTGTGCAAAATAGGAGGTAGAT 59.810 40.000 0.00 0.00 0.00 1.98
193 194 4.530553 TCAGTGTGCAAAATAGGAGGTAGA 59.469 41.667 0.00 0.00 0.00 2.59
194 195 4.832248 TCAGTGTGCAAAATAGGAGGTAG 58.168 43.478 0.00 0.00 0.00 3.18
195 196 4.832248 CTCAGTGTGCAAAATAGGAGGTA 58.168 43.478 0.00 0.00 0.00 3.08
196 197 3.679389 CTCAGTGTGCAAAATAGGAGGT 58.321 45.455 0.00 0.00 0.00 3.85
197 198 2.421424 GCTCAGTGTGCAAAATAGGAGG 59.579 50.000 12.18 0.00 0.00 4.30
198 199 2.094894 CGCTCAGTGTGCAAAATAGGAG 59.905 50.000 16.75 0.00 0.00 3.69
199 200 2.076100 CGCTCAGTGTGCAAAATAGGA 58.924 47.619 16.75 0.00 0.00 2.94
200 201 1.806542 ACGCTCAGTGTGCAAAATAGG 59.193 47.619 16.75 1.82 0.00 2.57
201 202 3.542712 AACGCTCAGTGTGCAAAATAG 57.457 42.857 16.75 2.49 0.00 1.73
202 203 3.980646 AAACGCTCAGTGTGCAAAATA 57.019 38.095 16.75 0.00 0.00 1.40
203 204 2.869233 AAACGCTCAGTGTGCAAAAT 57.131 40.000 16.75 0.00 0.00 1.82
204 205 2.645730 AAAACGCTCAGTGTGCAAAA 57.354 40.000 16.75 0.00 0.00 2.44
205 206 2.645730 AAAAACGCTCAGTGTGCAAA 57.354 40.000 16.75 0.00 0.00 3.68
206 207 2.540769 GCTAAAAACGCTCAGTGTGCAA 60.541 45.455 16.75 0.00 0.00 4.08
207 208 1.002900 GCTAAAAACGCTCAGTGTGCA 60.003 47.619 16.75 0.00 0.00 4.57
208 209 1.663161 GGCTAAAAACGCTCAGTGTGC 60.663 52.381 7.12 7.12 0.00 4.57
209 210 1.873591 AGGCTAAAAACGCTCAGTGTG 59.126 47.619 0.00 0.00 0.00 3.82
210 211 2.256117 AGGCTAAAAACGCTCAGTGT 57.744 45.000 0.00 0.00 0.00 3.55
211 212 4.946784 AATAGGCTAAAAACGCTCAGTG 57.053 40.909 0.00 0.00 0.00 3.66
212 213 5.959618 AAAATAGGCTAAAAACGCTCAGT 57.040 34.783 0.00 0.00 0.00 3.41
213 214 6.745907 GGTAAAAATAGGCTAAAAACGCTCAG 59.254 38.462 0.00 0.00 0.00 3.35
214 215 6.431852 AGGTAAAAATAGGCTAAAAACGCTCA 59.568 34.615 0.00 0.00 0.00 4.26
215 216 6.745907 CAGGTAAAAATAGGCTAAAAACGCTC 59.254 38.462 0.00 0.00 0.00 5.03
216 217 6.208007 ACAGGTAAAAATAGGCTAAAAACGCT 59.792 34.615 0.00 0.00 0.00 5.07
217 218 6.384224 ACAGGTAAAAATAGGCTAAAAACGC 58.616 36.000 0.00 0.00 0.00 4.84
218 219 7.327518 CCAACAGGTAAAAATAGGCTAAAAACG 59.672 37.037 0.00 0.00 0.00 3.60
219 220 7.117236 GCCAACAGGTAAAAATAGGCTAAAAAC 59.883 37.037 0.00 0.00 37.89 2.43
220 221 7.156000 GCCAACAGGTAAAAATAGGCTAAAAA 58.844 34.615 0.00 0.00 37.89 1.94
221 222 6.295405 GGCCAACAGGTAAAAATAGGCTAAAA 60.295 38.462 0.00 0.00 40.61 1.52
222 223 5.186215 GGCCAACAGGTAAAAATAGGCTAAA 59.814 40.000 0.00 0.00 40.61 1.85
223 224 4.707934 GGCCAACAGGTAAAAATAGGCTAA 59.292 41.667 0.00 0.00 40.61 3.09
224 225 4.274978 GGCCAACAGGTAAAAATAGGCTA 58.725 43.478 0.00 0.00 40.61 3.93
225 226 3.096852 GGCCAACAGGTAAAAATAGGCT 58.903 45.455 0.00 0.00 40.61 4.58
226 227 2.167693 GGGCCAACAGGTAAAAATAGGC 59.832 50.000 4.39 0.00 40.08 3.93
227 228 3.436243 TGGGCCAACAGGTAAAAATAGG 58.564 45.455 2.13 0.00 0.00 2.57
228 229 6.976934 ATATGGGCCAACAGGTAAAAATAG 57.023 37.500 11.89 0.00 0.00 1.73
229 230 7.507616 CCTAATATGGGCCAACAGGTAAAAATA 59.492 37.037 11.89 0.00 0.00 1.40
230 231 6.326323 CCTAATATGGGCCAACAGGTAAAAAT 59.674 38.462 11.89 0.00 0.00 1.82
231 232 5.659079 CCTAATATGGGCCAACAGGTAAAAA 59.341 40.000 11.89 0.00 0.00 1.94
232 233 5.044030 TCCTAATATGGGCCAACAGGTAAAA 60.044 40.000 11.89 0.00 0.00 1.52
233 234 4.479056 TCCTAATATGGGCCAACAGGTAAA 59.521 41.667 11.89 0.00 0.00 2.01
234 235 4.048600 TCCTAATATGGGCCAACAGGTAA 58.951 43.478 11.89 0.00 0.00 2.85
235 236 3.671079 TCCTAATATGGGCCAACAGGTA 58.329 45.455 11.89 0.00 0.00 3.08
236 237 2.498441 TCCTAATATGGGCCAACAGGT 58.502 47.619 11.89 0.00 0.00 4.00
237 238 3.814504 ATCCTAATATGGGCCAACAGG 57.185 47.619 11.89 14.64 0.00 4.00
238 239 5.241403 TGTATCCTAATATGGGCCAACAG 57.759 43.478 11.89 5.14 0.00 3.16
239 240 5.858876 ATGTATCCTAATATGGGCCAACA 57.141 39.130 11.89 7.42 0.00 3.33
240 241 8.644374 TTTTATGTATCCTAATATGGGCCAAC 57.356 34.615 11.89 0.35 0.00 3.77
274 275 4.578928 ACAGCACGACCTGATTAACTTTTT 59.421 37.500 12.64 0.00 36.67 1.94
275 276 4.024048 CACAGCACGACCTGATTAACTTTT 60.024 41.667 12.64 0.00 36.67 2.27
276 277 3.498397 CACAGCACGACCTGATTAACTTT 59.502 43.478 12.64 0.00 36.67 2.66
277 278 3.067106 CACAGCACGACCTGATTAACTT 58.933 45.455 12.64 0.00 36.67 2.66
278 279 2.688507 CACAGCACGACCTGATTAACT 58.311 47.619 12.64 0.00 36.67 2.24
279 280 1.128692 GCACAGCACGACCTGATTAAC 59.871 52.381 12.64 0.00 36.67 2.01
280 281 1.438651 GCACAGCACGACCTGATTAA 58.561 50.000 12.64 0.00 36.67 1.40
281 282 0.391130 GGCACAGCACGACCTGATTA 60.391 55.000 12.64 0.00 36.67 1.75
282 283 1.672356 GGCACAGCACGACCTGATT 60.672 57.895 12.64 0.00 36.67 2.57
283 284 2.046892 GGCACAGCACGACCTGAT 60.047 61.111 12.64 0.00 36.67 2.90
284 285 4.662961 CGGCACAGCACGACCTGA 62.663 66.667 12.64 0.00 36.67 3.86
315 316 4.748144 GTGCCTGGGCCTGAAGGG 62.748 72.222 12.58 4.03 41.09 3.95
357 358 3.440415 GTGCTAAACAGGCCGGGC 61.440 66.667 22.67 22.67 0.00 6.13
358 359 3.124921 CGTGCTAAACAGGCCGGG 61.125 66.667 8.08 1.20 0.00 5.73
359 360 2.358247 ACGTGCTAAACAGGCCGG 60.358 61.111 0.00 0.00 37.69 6.13
360 361 1.897398 GACACGTGCTAAACAGGCCG 61.897 60.000 17.22 0.00 37.69 6.13
361 362 1.866925 GACACGTGCTAAACAGGCC 59.133 57.895 17.22 0.00 37.69 5.19
362 363 1.219522 ACGACACGTGCTAAACAGGC 61.220 55.000 17.22 0.00 39.18 4.85
363 364 2.895039 ACGACACGTGCTAAACAGG 58.105 52.632 17.22 0.00 39.18 4.00
419 420 4.581093 GGGATAGTTGGGCCGGCC 62.581 72.222 38.57 38.57 0.00 6.13
420 421 4.929707 CGGGATAGTTGGGCCGGC 62.930 72.222 21.18 21.18 0.00 6.13
421 422 4.250305 CCGGGATAGTTGGGCCGG 62.250 72.222 0.00 0.00 34.60 6.13
422 423 4.929707 GCCGGGATAGTTGGGCCG 62.930 72.222 2.18 0.00 39.67 6.13
424 425 4.581093 GGGCCGGGATAGTTGGGC 62.581 72.222 2.18 0.00 46.84 5.36
425 426 2.006805 AATGGGCCGGGATAGTTGGG 62.007 60.000 2.18 0.00 0.00 4.12
426 427 0.106217 AAATGGGCCGGGATAGTTGG 60.106 55.000 2.18 0.00 0.00 3.77
427 428 1.032014 CAAATGGGCCGGGATAGTTG 58.968 55.000 2.18 0.00 0.00 3.16
428 429 0.106217 CCAAATGGGCCGGGATAGTT 60.106 55.000 2.18 0.00 0.00 2.24
429 430 1.536676 CCAAATGGGCCGGGATAGT 59.463 57.895 2.18 0.00 0.00 2.12
430 431 4.500265 CCAAATGGGCCGGGATAG 57.500 61.111 2.18 0.00 0.00 2.08
439 440 2.664402 AGTATAGCTGGCCAAATGGG 57.336 50.000 7.01 0.00 40.85 4.00
440 441 2.887152 GGAAGTATAGCTGGCCAAATGG 59.113 50.000 7.01 0.00 38.53 3.16
441 442 2.887152 GGGAAGTATAGCTGGCCAAATG 59.113 50.000 7.01 0.00 0.00 2.32
442 443 2.513738 TGGGAAGTATAGCTGGCCAAAT 59.486 45.455 7.01 3.30 0.00 2.32
443 444 1.919654 TGGGAAGTATAGCTGGCCAAA 59.080 47.619 7.01 0.00 0.00 3.28
444 445 1.590591 TGGGAAGTATAGCTGGCCAA 58.409 50.000 7.01 0.00 0.00 4.52
445 446 1.699634 GATGGGAAGTATAGCTGGCCA 59.300 52.381 4.71 4.71 0.00 5.36
446 447 1.338200 CGATGGGAAGTATAGCTGGCC 60.338 57.143 0.00 0.00 0.00 5.36
447 448 1.618837 TCGATGGGAAGTATAGCTGGC 59.381 52.381 0.00 0.00 0.00 4.85
448 449 2.628178 TGTCGATGGGAAGTATAGCTGG 59.372 50.000 0.00 0.00 0.00 4.85
449 450 3.553096 GGTGTCGATGGGAAGTATAGCTG 60.553 52.174 0.00 0.00 0.00 4.24
450 451 2.628657 GGTGTCGATGGGAAGTATAGCT 59.371 50.000 0.00 0.00 0.00 3.32
451 452 2.628657 AGGTGTCGATGGGAAGTATAGC 59.371 50.000 0.00 0.00 0.00 2.97
452 453 3.553096 GCAGGTGTCGATGGGAAGTATAG 60.553 52.174 0.00 0.00 0.00 1.31
453 454 2.364324 GCAGGTGTCGATGGGAAGTATA 59.636 50.000 0.00 0.00 0.00 1.47
454 455 1.139058 GCAGGTGTCGATGGGAAGTAT 59.861 52.381 0.00 0.00 0.00 2.12
455 456 0.535335 GCAGGTGTCGATGGGAAGTA 59.465 55.000 0.00 0.00 0.00 2.24
456 457 1.296715 GCAGGTGTCGATGGGAAGT 59.703 57.895 0.00 0.00 0.00 3.01
528 529 2.208132 ACCAAAAGGTCACACACACA 57.792 45.000 0.00 0.00 0.00 3.72
529 530 2.490115 TGAACCAAAAGGTCACACACAC 59.510 45.455 0.00 0.00 0.00 3.82
530 531 2.752354 CTGAACCAAAAGGTCACACACA 59.248 45.455 0.00 0.00 0.00 3.72
531 532 2.752903 ACTGAACCAAAAGGTCACACAC 59.247 45.455 0.00 0.00 0.00 3.82
532 533 3.080300 ACTGAACCAAAAGGTCACACA 57.920 42.857 0.00 0.00 0.00 3.72
533 534 4.450082 AAACTGAACCAAAAGGTCACAC 57.550 40.909 0.00 0.00 0.00 3.82
534 535 5.476091 AAAAACTGAACCAAAAGGTCACA 57.524 34.783 0.00 0.00 0.00 3.58
685 686 5.767168 ACTTGAGCAGCTAAGAAATGAAACT 59.233 36.000 14.83 0.00 0.00 2.66
719 720 5.056480 TGGTAGATTGAAAGACAGTGTGTG 58.944 41.667 0.00 0.00 0.00 3.82
904 906 5.869579 AGAAGGTCTTAGAATGTGCTTTGA 58.130 37.500 0.00 0.00 0.00 2.69
907 909 7.335422 CACATAAGAAGGTCTTAGAATGTGCTT 59.665 37.037 14.66 0.00 40.77 3.91
1199 1603 3.620374 CGCCTCAACTATCATATGATGCC 59.380 47.826 25.44 0.00 36.05 4.40
1489 1893 6.598064 ACTCTATGCCAAACATACCAACTAAC 59.402 38.462 0.00 0.00 40.38 2.34
1583 1987 0.035458 AGACAACTGCTACAGTGGGC 59.965 55.000 7.03 3.45 43.49 5.36
1858 4165 3.586470 TTAAACTTCACAGGCCCTCAA 57.414 42.857 0.00 0.00 0.00 3.02
1944 4254 8.606602 CACTTGATCAATTCATTTACTCATCGA 58.393 33.333 8.96 0.00 33.34 3.59
1994 4997 3.321682 CCAAAGGCATGAAAGAACCTTCA 59.678 43.478 0.00 0.00 41.65 3.02
2047 5088 9.769093 GCAAGTGTATGTAAAACTCGATTTATT 57.231 29.630 0.00 0.00 0.00 1.40
2150 5192 1.222936 CTCGGCCAGCAGAAGGAAT 59.777 57.895 2.24 0.00 0.00 3.01
2408 5571 5.280830 GGGGGTGGATCTGTAGTTTCTTTAA 60.281 44.000 0.00 0.00 0.00 1.52
2448 5611 7.274603 TGGCATCGATGAATGATTTTTATCA 57.725 32.000 29.20 4.61 34.73 2.15
2669 5837 2.079158 CTCACGTTGACATCAGCCATT 58.921 47.619 0.00 0.00 0.00 3.16
2684 5852 2.376808 AGGATTGACAGAAGCTCACG 57.623 50.000 0.00 0.00 0.00 4.35
2733 5901 3.312890 AGAGAGAGAGAGAGAGAGGGAG 58.687 54.545 0.00 0.00 0.00 4.30
2734 5902 3.051803 AGAGAGAGAGAGAGAGAGAGGGA 60.052 52.174 0.00 0.00 0.00 4.20
2735 5903 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
2736 5904 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
2737 5905 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
2738 5906 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
2739 5907 4.501229 GCAGAGAGAGAGAGAGAGAGAGAG 60.501 54.167 0.00 0.00 0.00 3.20
2740 5908 3.386078 GCAGAGAGAGAGAGAGAGAGAGA 59.614 52.174 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.