Multiple sequence alignment - TraesCS7D01G462700

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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 TraesCS7D01G462700 chr7D 100.000 3497 0 0 1 3497 578063576 578067072 0.000000e+00 6458.0
1 TraesCS7D01G462700 chr7D 89.126 1453 121 16 927 2356 578049515 578050953 0.000000e+00 1773.0
2 TraesCS7D01G462700 chr7D 84.615 1339 143 24 1183 2503 578125261 578126554 0.000000e+00 1273.0
3 TraesCS7D01G462700 chr7D 85.990 207 15 10 742 942 578048500 578048698 3.540000e-50 209.0
4 TraesCS7D01G462700 chr7D 85.057 87 8 3 851 932 578048421 578048507 2.240000e-12 84.2
5 TraesCS7D01G462700 chr7D 95.652 46 2 0 627 672 578064157 578064202 1.350000e-09 75.0
6 TraesCS7D01G462700 chr7D 95.652 46 2 0 582 627 578064202 578064247 1.350000e-09 75.0
7 TraesCS7D01G462700 chr7B 96.686 1750 50 3 627 2371 641807794 641806048 0.000000e+00 2904.0
8 TraesCS7D01G462700 chr7B 84.484 1173 167 13 1189 2356 641783687 641782525 0.000000e+00 1144.0
9 TraesCS7D01G462700 chr7B 83.476 1168 175 12 1197 2356 641755489 641754332 0.000000e+00 1072.0
10 TraesCS7D01G462700 chr7B 85.843 996 110 17 1038 2010 641855691 641854704 0.000000e+00 1029.0
11 TraesCS7D01G462700 chr7B 93.558 326 14 3 2371 2689 641805987 641805662 2.440000e-131 479.0
12 TraesCS7D01G462700 chr7B 91.319 288 22 3 3207 3494 72078377 72078093 1.180000e-104 390.0
13 TraesCS7D01G462700 chr7B 91.003 289 22 1 3207 3495 532155423 532155707 1.520000e-103 387.0
14 TraesCS7D01G462700 chr7B 95.397 239 9 2 391 627 641807987 641807749 2.550000e-101 379.0
15 TraesCS7D01G462700 chr7B 89.474 285 17 5 2688 2962 532154627 532154908 7.180000e-92 348.0
16 TraesCS7D01G462700 chr7B 85.953 299 27 7 2676 2962 72079593 72079298 4.390000e-79 305.0
17 TraesCS7D01G462700 chr7B 88.189 254 21 6 2689 2934 644553971 644553719 9.490000e-76 294.0
18 TraesCS7D01G462700 chr7B 97.561 164 4 0 1 164 641808626 641808463 7.390000e-72 281.0
19 TraesCS7D01G462700 chr7B 89.573 211 8 7 778 984 641861082 641860882 4.480000e-64 255.0
20 TraesCS7D01G462700 chr7B 84.151 265 28 8 465 724 641870816 641870561 9.700000e-61 244.0
21 TraesCS7D01G462700 chr7B 87.054 224 15 11 2961 3179 2951214 2951428 1.250000e-59 241.0
22 TraesCS7D01G462700 chr7B 86.937 222 12 7 2961 3179 72079208 72079001 2.100000e-57 233.0
23 TraesCS7D01G462700 chr7B 82.759 261 21 13 870 1111 641764746 641764491 9.830000e-51 211.0
24 TraesCS7D01G462700 chr7B 82.949 217 16 10 2963 3179 644553586 644553391 3.590000e-40 176.0
25 TraesCS7D01G462700 chr7B 97.468 79 2 0 311 389 641808447 641808369 6.090000e-28 135.0
26 TraesCS7D01G462700 chr7B 79.856 139 19 8 982 1111 641787928 641787790 3.720000e-15 93.5
27 TraesCS7D01G462700 chr7B 100.000 34 0 0 801 834 641870320 641870287 2.910000e-06 63.9
28 TraesCS7D01G462700 chr7A 92.830 1311 58 9 1052 2356 670265795 670264515 0.000000e+00 1868.0
29 TraesCS7D01G462700 chr7A 85.284 1760 164 53 802 2508 670270361 670268644 0.000000e+00 1727.0
30 TraesCS7D01G462700 chr7A 93.175 337 13 6 677 1010 670266122 670265793 1.460000e-133 486.0
31 TraesCS7D01G462700 chr7A 91.349 289 21 1 3207 3495 1296744 1297028 3.270000e-105 392.0
32 TraesCS7D01G462700 chr7A 88.380 284 21 4 2689 2962 1295949 1296230 7.240000e-87 331.0
33 TraesCS7D01G462700 chr7A 84.404 218 25 5 2961 3177 108500805 108500596 4.580000e-49 206.0
34 TraesCS7D01G462700 chr7A 100.000 52 0 0 398 449 670266184 670266133 2.870000e-16 97.1
35 TraesCS7D01G462700 chr7A 85.714 84 8 4 851 930 670270944 670270861 6.220000e-13 86.1
36 TraesCS7D01G462700 chr3B 78.625 800 118 28 1477 2266 675559912 675560668 6.790000e-132 481.0
37 TraesCS7D01G462700 chr3B 88.153 287 18 6 2689 2962 733223620 733223337 9.360000e-86 327.0
38 TraesCS7D01G462700 chr3B 92.661 218 16 0 3207 3424 733220026 733219809 7.290000e-82 315.0
39 TraesCS7D01G462700 chr3B 82.857 140 20 4 23 160 302344341 302344478 4.740000e-24 122.0
40 TraesCS7D01G462700 chr3A 91.696 289 24 0 3207 3495 728045467 728045755 5.440000e-108 401.0
41 TraesCS7D01G462700 chr3A 86.842 228 18 5 2965 3192 728044414 728044629 9.700000e-61 244.0
42 TraesCS7D01G462700 chr2B 92.042 289 17 4 3207 3494 512194314 512194031 5.440000e-108 401.0
43 TraesCS7D01G462700 chr2B 89.545 220 15 2 2961 3179 512195133 512194921 4.450000e-69 272.0
44 TraesCS7D01G462700 chr5A 91.034 290 20 3 3207 3495 369852999 369852715 1.520000e-103 387.0
45 TraesCS7D01G462700 chr5A 87.458 295 24 5 2678 2962 369853804 369853513 9.360000e-86 327.0
46 TraesCS7D01G462700 chr5A 86.207 290 28 8 2684 2963 566782642 566782929 1.580000e-78 303.0
47 TraesCS7D01G462700 chr6A 87.589 282 23 5 2689 2959 595665811 595666091 2.030000e-82 316.0
48 TraesCS7D01G462700 chr6A 87.671 219 11 4 2961 3179 595666175 595666377 1.250000e-59 241.0
49 TraesCS7D01G462700 chr6B 92.166 217 17 0 3207 3423 653868856 653868640 1.220000e-79 307.0
50 TraesCS7D01G462700 chr6B 87.215 219 12 4 2961 3179 653869683 653869481 5.840000e-58 235.0
51 TraesCS7D01G462700 chr6B 83.945 218 26 5 2961 3177 136911500 136911709 2.130000e-47 200.0
52 TraesCS7D01G462700 chr1D 88.163 245 24 4 2689 2930 437009697 437009455 1.590000e-73 287.0
53 TraesCS7D01G462700 chr1D 83.959 293 39 5 3207 3495 437987644 437987356 1.240000e-69 274.0
54 TraesCS7D01G462700 chr1D 90.351 114 9 2 3075 3188 2591799 2591910 7.820000e-32 148.0
55 TraesCS7D01G462700 chr6D 87.500 128 10 5 2963 3090 266774986 266774865 3.640000e-30 143.0
56 TraesCS7D01G462700 chr6D 87.129 101 7 4 2961 3061 49841614 49841520 3.690000e-20 110.0
57 TraesCS7D01G462700 chr6D 87.129 101 7 4 2961 3061 394873418 394873512 3.690000e-20 110.0


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 TraesCS7D01G462700 chr7D 578063576 578067072 3496 False 2202.666667 6458 97.101333 1 3497 3 chr7D.!!$F3 3496
1 TraesCS7D01G462700 chr7D 578125261 578126554 1293 False 1273.000000 1273 84.615000 1183 2503 1 chr7D.!!$F1 1320
2 TraesCS7D01G462700 chr7D 578048421 578050953 2532 False 688.733333 1773 86.724333 742 2356 3 chr7D.!!$F2 1614
3 TraesCS7D01G462700 chr7B 641782525 641783687 1162 True 1144.000000 1144 84.484000 1189 2356 1 chr7B.!!$R3 1167
4 TraesCS7D01G462700 chr7B 641754332 641755489 1157 True 1072.000000 1072 83.476000 1197 2356 1 chr7B.!!$R1 1159
5 TraesCS7D01G462700 chr7B 641854704 641855691 987 True 1029.000000 1029 85.843000 1038 2010 1 chr7B.!!$R5 972
6 TraesCS7D01G462700 chr7B 641805662 641808626 2964 True 835.600000 2904 96.134000 1 2689 5 chr7B.!!$R8 2688
7 TraesCS7D01G462700 chr7B 532154627 532155707 1080 False 367.500000 387 90.238500 2688 3495 2 chr7B.!!$F2 807
8 TraesCS7D01G462700 chr7B 72078093 72079593 1500 True 309.333333 390 88.069667 2676 3494 3 chr7B.!!$R7 818
9 TraesCS7D01G462700 chr7B 644553391 644553971 580 True 235.000000 294 85.569000 2689 3179 2 chr7B.!!$R10 490
10 TraesCS7D01G462700 chr7A 670264515 670270944 6429 True 852.840000 1868 91.400600 398 2508 5 chr7A.!!$R2 2110
11 TraesCS7D01G462700 chr7A 1295949 1297028 1079 False 361.500000 392 89.864500 2689 3495 2 chr7A.!!$F1 806
12 TraesCS7D01G462700 chr3B 675559912 675560668 756 False 481.000000 481 78.625000 1477 2266 1 chr3B.!!$F2 789
13 TraesCS7D01G462700 chr3B 733219809 733223620 3811 True 321.000000 327 90.407000 2689 3424 2 chr3B.!!$R1 735
14 TraesCS7D01G462700 chr3A 728044414 728045755 1341 False 322.500000 401 89.269000 2965 3495 2 chr3A.!!$F1 530
15 TraesCS7D01G462700 chr2B 512194031 512195133 1102 True 336.500000 401 90.793500 2961 3494 2 chr2B.!!$R1 533
16 TraesCS7D01G462700 chr5A 369852715 369853804 1089 True 357.000000 387 89.246000 2678 3495 2 chr5A.!!$R1 817
17 TraesCS7D01G462700 chr6A 595665811 595666377 566 False 278.500000 316 87.630000 2689 3179 2 chr6A.!!$F1 490
18 TraesCS7D01G462700 chr6B 653868640 653869683 1043 True 271.000000 307 89.690500 2961 3423 2 chr6B.!!$R1 462

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
264 265 0.033228 CCTCCTGGCTAGCGATGAAG 59.967 60.0 9.00 2.69 0.00 3.02 F
265 266 0.033228 CTCCTGGCTAGCGATGAAGG 59.967 60.0 9.00 10.21 0.00 3.46 F
270 271 0.034616 GGCTAGCGATGAAGGCAGAT 59.965 55.0 9.00 0.00 38.14 2.90 F
283 284 0.038166 GGCAGATGGTGGGAGAACAA 59.962 55.0 0.00 0.00 0.00 2.83 F
2192 8220 0.105593 AGCATACTGCCATCGACCAG 59.894 55.0 7.73 7.73 46.52 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 3363 2.202797 GAGATCTGCCGCTGCGAA 60.203 61.111 25.45 10.45 41.78 4.70 R
1754 3485 2.671619 GCGTGTGGCTGCCCTTAA 60.672 61.111 17.53 0.00 39.11 1.85 R
2466 8565 8.906867 AGCATTGCAATTTAATAGTGTGATAGT 58.093 29.630 9.83 0.00 0.00 2.12 R
2474 8573 7.431249 CAGATGGAGCATTGCAATTTAATAGT 58.569 34.615 9.83 0.00 0.00 2.12 R
3179 11816 1.067821 GCTGTATCTTGAGACGGAGGG 59.932 57.143 8.23 0.00 0.00 4.30 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
59 60 7.029390 AGTAGGGTATTATATCAACCATGGGT 58.971 38.462 18.09 6.57 37.65 4.51
137 138 1.829222 TCTCCACCCTACCGAAATCAC 59.171 52.381 0.00 0.00 0.00 3.06
148 149 1.993370 CCGAAATCACTGACGGTCTTC 59.007 52.381 9.88 2.91 40.42 2.87
164 165 1.412710 TCTTCGGTACCATCATGCCTC 59.587 52.381 13.54 0.00 0.00 4.70
165 166 0.468226 TTCGGTACCATCATGCCTCC 59.532 55.000 13.54 0.00 0.00 4.30
166 167 0.398522 TCGGTACCATCATGCCTCCT 60.399 55.000 13.54 0.00 0.00 3.69
167 168 0.034059 CGGTACCATCATGCCTCCTC 59.966 60.000 13.54 0.00 0.00 3.71
168 169 0.398318 GGTACCATCATGCCTCCTCC 59.602 60.000 7.15 0.00 0.00 4.30
169 170 1.428869 GTACCATCATGCCTCCTCCT 58.571 55.000 0.00 0.00 0.00 3.69
170 171 1.346068 GTACCATCATGCCTCCTCCTC 59.654 57.143 0.00 0.00 0.00 3.71
171 172 1.370437 CCATCATGCCTCCTCCTCG 59.630 63.158 0.00 0.00 0.00 4.63
172 173 1.301558 CATCATGCCTCCTCCTCGC 60.302 63.158 0.00 0.00 0.00 5.03
173 174 1.459158 ATCATGCCTCCTCCTCGCT 60.459 57.895 0.00 0.00 0.00 4.93
174 175 0.178950 ATCATGCCTCCTCCTCGCTA 60.179 55.000 0.00 0.00 0.00 4.26
175 176 0.825425 TCATGCCTCCTCCTCGCTAG 60.825 60.000 0.00 0.00 0.00 3.42
176 177 2.206536 ATGCCTCCTCCTCGCTAGC 61.207 63.158 4.06 4.06 0.00 3.42
177 178 3.972276 GCCTCCTCCTCGCTAGCG 61.972 72.222 30.91 30.91 41.35 4.26
178 179 3.291383 CCTCCTCCTCGCTAGCGG 61.291 72.222 34.76 24.53 40.25 5.52
179 180 3.972276 CTCCTCCTCGCTAGCGGC 61.972 72.222 34.76 0.00 40.25 6.53
197 198 2.349755 GGCTACAGGCGGTTTGGA 59.650 61.111 0.00 0.00 42.94 3.53
198 199 1.077716 GGCTACAGGCGGTTTGGAT 60.078 57.895 0.00 0.00 42.94 3.41
199 200 1.095807 GGCTACAGGCGGTTTGGATC 61.096 60.000 0.00 0.00 42.94 3.36
200 201 1.429148 GCTACAGGCGGTTTGGATCG 61.429 60.000 0.00 0.00 0.00 3.69
205 206 2.791927 GCGGTTTGGATCGCCTTC 59.208 61.111 0.00 0.00 45.42 3.46
206 207 1.745489 GCGGTTTGGATCGCCTTCT 60.745 57.895 0.00 0.00 45.42 2.85
207 208 1.305930 GCGGTTTGGATCGCCTTCTT 61.306 55.000 0.00 0.00 45.42 2.52
208 209 2.010043 GCGGTTTGGATCGCCTTCTTA 61.010 52.381 0.00 0.00 45.42 2.10
209 210 1.933853 CGGTTTGGATCGCCTTCTTAG 59.066 52.381 0.00 0.00 34.31 2.18
210 211 2.418197 CGGTTTGGATCGCCTTCTTAGA 60.418 50.000 0.00 0.00 34.31 2.10
211 212 3.741388 CGGTTTGGATCGCCTTCTTAGAT 60.741 47.826 0.00 0.00 34.31 1.98
212 213 3.561725 GGTTTGGATCGCCTTCTTAGATG 59.438 47.826 0.00 0.00 34.31 2.90
229 230 1.008327 GATGGTTTTGGGGAAGGGGAT 59.992 52.381 0.00 0.00 0.00 3.85
230 231 0.116143 TGGTTTTGGGGAAGGGGATG 59.884 55.000 0.00 0.00 0.00 3.51
231 232 0.617535 GGTTTTGGGGAAGGGGATGG 60.618 60.000 0.00 0.00 0.00 3.51
232 233 0.617535 GTTTTGGGGAAGGGGATGGG 60.618 60.000 0.00 0.00 0.00 4.00
233 234 0.782115 TTTTGGGGAAGGGGATGGGA 60.782 55.000 0.00 0.00 0.00 4.37
234 235 1.221213 TTTGGGGAAGGGGATGGGAG 61.221 60.000 0.00 0.00 0.00 4.30
235 236 2.778717 GGGGAAGGGGATGGGAGG 60.779 72.222 0.00 0.00 0.00 4.30
236 237 2.044620 GGGAAGGGGATGGGAGGT 59.955 66.667 0.00 0.00 0.00 3.85
237 238 2.386935 GGGAAGGGGATGGGAGGTG 61.387 68.421 0.00 0.00 0.00 4.00
238 239 2.386935 GGAAGGGGATGGGAGGTGG 61.387 68.421 0.00 0.00 0.00 4.61
239 240 1.307866 GAAGGGGATGGGAGGTGGA 60.308 63.158 0.00 0.00 0.00 4.02
240 241 0.699231 GAAGGGGATGGGAGGTGGAT 60.699 60.000 0.00 0.00 0.00 3.41
241 242 0.995675 AAGGGGATGGGAGGTGGATG 60.996 60.000 0.00 0.00 0.00 3.51
242 243 2.517919 GGGATGGGAGGTGGATGC 59.482 66.667 0.00 0.00 0.00 3.91
243 244 2.386100 GGGATGGGAGGTGGATGCA 61.386 63.158 0.00 0.00 0.00 3.96
244 245 1.150081 GGATGGGAGGTGGATGCAG 59.850 63.158 0.00 0.00 0.00 4.41
245 246 1.527844 GATGGGAGGTGGATGCAGC 60.528 63.158 8.54 8.54 0.00 5.25
246 247 2.972892 GATGGGAGGTGGATGCAGCC 62.973 65.000 15.83 15.83 0.00 4.85
247 248 3.415087 GGGAGGTGGATGCAGCCT 61.415 66.667 23.69 11.94 34.93 4.58
248 249 2.191641 GGAGGTGGATGCAGCCTC 59.808 66.667 23.69 18.99 45.92 4.70
249 250 2.191641 GAGGTGGATGCAGCCTCC 59.808 66.667 30.23 30.23 42.09 4.30
250 251 2.285969 AGGTGGATGCAGCCTCCT 60.286 61.111 33.44 33.44 44.85 3.69
251 252 2.124403 GGTGGATGCAGCCTCCTG 60.124 66.667 30.11 0.00 42.13 3.86
252 253 2.124403 GTGGATGCAGCCTCCTGG 60.124 66.667 23.69 0.00 39.54 4.45
262 263 3.862142 CCTCCTGGCTAGCGATGA 58.138 61.111 9.00 6.59 0.00 2.92
263 264 2.127839 CCTCCTGGCTAGCGATGAA 58.872 57.895 9.00 0.00 0.00 2.57
264 265 0.033228 CCTCCTGGCTAGCGATGAAG 59.967 60.000 9.00 2.69 0.00 3.02
265 266 0.033228 CTCCTGGCTAGCGATGAAGG 59.967 60.000 9.00 10.21 0.00 3.46
266 267 1.596477 CCTGGCTAGCGATGAAGGC 60.596 63.158 9.00 0.00 38.68 4.35
267 268 1.144716 CTGGCTAGCGATGAAGGCA 59.855 57.895 9.00 0.00 45.01 4.75
268 269 1.144716 TGGCTAGCGATGAAGGCAG 59.855 57.895 9.00 0.00 42.67 4.85
269 270 1.329913 TGGCTAGCGATGAAGGCAGA 61.330 55.000 9.00 0.00 42.67 4.26
270 271 0.034616 GGCTAGCGATGAAGGCAGAT 59.965 55.000 9.00 0.00 38.14 2.90
271 272 1.146637 GCTAGCGATGAAGGCAGATG 58.853 55.000 0.00 0.00 0.00 2.90
272 273 1.793258 CTAGCGATGAAGGCAGATGG 58.207 55.000 0.00 0.00 0.00 3.51
273 274 1.069823 CTAGCGATGAAGGCAGATGGT 59.930 52.381 0.00 0.00 0.00 3.55
274 275 0.463295 AGCGATGAAGGCAGATGGTG 60.463 55.000 0.00 0.00 0.00 4.17
275 276 1.442526 GCGATGAAGGCAGATGGTGG 61.443 60.000 0.00 0.00 0.00 4.61
276 277 0.816825 CGATGAAGGCAGATGGTGGG 60.817 60.000 0.00 0.00 0.00 4.61
277 278 0.548031 GATGAAGGCAGATGGTGGGA 59.452 55.000 0.00 0.00 0.00 4.37
278 279 0.549950 ATGAAGGCAGATGGTGGGAG 59.450 55.000 0.00 0.00 0.00 4.30
279 280 0.547471 TGAAGGCAGATGGTGGGAGA 60.547 55.000 0.00 0.00 0.00 3.71
280 281 0.620556 GAAGGCAGATGGTGGGAGAA 59.379 55.000 0.00 0.00 0.00 2.87
281 282 0.329596 AAGGCAGATGGTGGGAGAAC 59.670 55.000 0.00 0.00 0.00 3.01
282 283 0.842030 AGGCAGATGGTGGGAGAACA 60.842 55.000 0.00 0.00 0.00 3.18
283 284 0.038166 GGCAGATGGTGGGAGAACAA 59.962 55.000 0.00 0.00 0.00 2.83
284 285 1.457346 GCAGATGGTGGGAGAACAAG 58.543 55.000 0.00 0.00 0.00 3.16
285 286 1.003580 GCAGATGGTGGGAGAACAAGA 59.996 52.381 0.00 0.00 0.00 3.02
286 287 2.356535 GCAGATGGTGGGAGAACAAGAT 60.357 50.000 0.00 0.00 0.00 2.40
287 288 3.276857 CAGATGGTGGGAGAACAAGATG 58.723 50.000 0.00 0.00 0.00 2.90
288 289 2.240667 AGATGGTGGGAGAACAAGATGG 59.759 50.000 0.00 0.00 0.00 3.51
289 290 0.698238 TGGTGGGAGAACAAGATGGG 59.302 55.000 0.00 0.00 0.00 4.00
290 291 0.991920 GGTGGGAGAACAAGATGGGA 59.008 55.000 0.00 0.00 0.00 4.37
291 292 1.354368 GGTGGGAGAACAAGATGGGAA 59.646 52.381 0.00 0.00 0.00 3.97
292 293 2.225017 GGTGGGAGAACAAGATGGGAAA 60.225 50.000 0.00 0.00 0.00 3.13
293 294 3.084786 GTGGGAGAACAAGATGGGAAAG 58.915 50.000 0.00 0.00 0.00 2.62
294 295 2.041620 TGGGAGAACAAGATGGGAAAGG 59.958 50.000 0.00 0.00 0.00 3.11
295 296 2.308866 GGGAGAACAAGATGGGAAAGGA 59.691 50.000 0.00 0.00 0.00 3.36
296 297 3.615155 GGAGAACAAGATGGGAAAGGAG 58.385 50.000 0.00 0.00 0.00 3.69
297 298 3.264450 GGAGAACAAGATGGGAAAGGAGA 59.736 47.826 0.00 0.00 0.00 3.71
298 299 4.512484 GAGAACAAGATGGGAAAGGAGAG 58.488 47.826 0.00 0.00 0.00 3.20
299 300 4.171234 AGAACAAGATGGGAAAGGAGAGA 58.829 43.478 0.00 0.00 0.00 3.10
300 301 3.990959 ACAAGATGGGAAAGGAGAGAC 57.009 47.619 0.00 0.00 0.00 3.36
301 302 2.234908 ACAAGATGGGAAAGGAGAGACG 59.765 50.000 0.00 0.00 0.00 4.18
302 303 0.827368 AGATGGGAAAGGAGAGACGC 59.173 55.000 0.00 0.00 0.00 5.19
303 304 0.537188 GATGGGAAAGGAGAGACGCA 59.463 55.000 0.00 0.00 0.00 5.24
304 305 0.539051 ATGGGAAAGGAGAGACGCAG 59.461 55.000 0.00 0.00 0.00 5.18
318 319 2.438800 ACGCAGTGATAGAGTAGGGT 57.561 50.000 0.00 0.00 42.51 4.34
336 337 1.271597 GGTTTCAGTGGAGGCAGATGT 60.272 52.381 0.00 0.00 0.00 3.06
390 391 3.792401 TGTGGGAGCAGTAAATATGACG 58.208 45.455 0.00 0.00 0.00 4.35
391 392 3.449377 TGTGGGAGCAGTAAATATGACGA 59.551 43.478 0.00 0.00 0.00 4.20
392 393 4.051922 GTGGGAGCAGTAAATATGACGAG 58.948 47.826 0.00 0.00 0.00 4.18
395 777 4.299978 GGAGCAGTAAATATGACGAGGAC 58.700 47.826 0.00 0.00 0.00 3.85
480 863 2.435059 GCTGTGGCGTCCTCTTCC 60.435 66.667 0.00 0.00 0.00 3.46
536 919 1.064166 CCAAAGCCATGGATCCTGTCT 60.064 52.381 18.40 1.05 43.54 3.41
547 930 5.452341 TGGATCCTGTCTGACTAGAGTAA 57.548 43.478 14.23 0.00 32.48 2.24
548 931 6.019656 TGGATCCTGTCTGACTAGAGTAAT 57.980 41.667 14.23 0.00 32.48 1.89
604 987 2.506472 GTGGATCCTTCCTCGCCC 59.494 66.667 14.23 0.00 43.07 6.13
605 988 2.768344 TGGATCCTTCCTCGCCCC 60.768 66.667 14.23 0.00 43.07 5.80
606 989 3.561241 GGATCCTTCCTCGCCCCC 61.561 72.222 3.84 0.00 39.14 5.40
607 990 3.930012 GATCCTTCCTCGCCCCCG 61.930 72.222 0.00 0.00 0.00 5.73
620 1003 4.096003 CCCCGCGTCTCCATGGTT 62.096 66.667 12.58 0.00 0.00 3.67
621 1004 2.819595 CCCGCGTCTCCATGGTTG 60.820 66.667 12.58 6.40 0.00 3.77
622 1005 2.264480 CCGCGTCTCCATGGTTGA 59.736 61.111 12.58 8.83 0.00 3.18
623 1006 1.153369 CCGCGTCTCCATGGTTGAT 60.153 57.895 12.58 0.00 0.00 2.57
624 1007 1.154205 CCGCGTCTCCATGGTTGATC 61.154 60.000 12.58 7.04 0.00 2.92
625 1008 1.154205 CGCGTCTCCATGGTTGATCC 61.154 60.000 12.58 6.09 0.00 3.36
635 1018 0.808125 TGGTTGATCCAATTTCGCGG 59.192 50.000 6.13 0.00 44.12 6.46
636 1019 1.091537 GGTTGATCCAATTTCGCGGA 58.908 50.000 6.13 0.00 35.97 5.54
637 1020 1.676006 GGTTGATCCAATTTCGCGGAT 59.324 47.619 6.13 0.00 44.89 4.18
641 1024 2.348411 ATCCAATTTCGCGGATCCTT 57.652 45.000 10.75 0.00 37.46 3.36
642 1025 1.663695 TCCAATTTCGCGGATCCTTC 58.336 50.000 10.75 0.18 0.00 3.46
643 1026 0.663153 CCAATTTCGCGGATCCTTCC 59.337 55.000 10.75 0.00 38.81 3.46
644 1027 1.668419 CAATTTCGCGGATCCTTCCT 58.332 50.000 10.75 0.00 40.17 3.36
645 1028 1.599542 CAATTTCGCGGATCCTTCCTC 59.400 52.381 10.75 0.00 40.17 3.71
726 1109 6.217294 GCTCTCACCCAGTAGATGTATTTAC 58.783 44.000 0.00 0.00 0.00 2.01
777 1162 7.598118 CCTAGAAAGATGAGTGCACTGTATATG 59.402 40.741 27.27 3.73 0.00 1.78
1161 2868 4.621087 GCTTGGGCCAACAGGGGT 62.621 66.667 16.66 0.00 37.04 4.95
1180 2887 2.203788 ACTTGACGGAGGGCCTCA 60.204 61.111 33.27 12.63 31.08 3.86
1272 2979 1.260538 TGGACATCTCCAGCGAGCTT 61.261 55.000 0.00 0.00 42.15 3.74
1584 3305 4.373116 AACGTCACGCTGCGGGAT 62.373 61.111 30.86 12.93 42.67 3.85
1686 3408 0.179134 CCTACTTCTTCGTGCTCCCG 60.179 60.000 0.00 0.00 0.00 5.14
1735 3466 3.123620 GCTTGAGCTGGGCAGACG 61.124 66.667 0.00 0.00 38.21 4.18
1736 3467 2.435586 CTTGAGCTGGGCAGACGG 60.436 66.667 0.00 0.00 0.00 4.79
2001 8022 2.919856 AGGATCCGATCGCAGGGG 60.920 66.667 10.32 0.00 0.00 4.79
2024 8045 2.985282 TCCGGTGAACGCTACGGT 60.985 61.111 0.00 0.00 46.06 4.83
2192 8220 0.105593 AGCATACTGCCATCGACCAG 59.894 55.000 7.73 7.73 46.52 4.00
2403 8499 2.099141 TGCTTAGCGTCAGATTGCTT 57.901 45.000 5.53 0.00 42.48 3.91
2441 8540 8.665685 AGTATTGTTGGATTGTATTTCGAGTTC 58.334 33.333 0.00 0.00 0.00 3.01
2459 8558 1.444933 TCCCATTTCAGTCACCCTGT 58.555 50.000 0.00 0.00 42.19 4.00
2466 8565 1.419381 TCAGTCACCCTGTTGTGCTA 58.581 50.000 0.00 0.00 42.19 3.49
2474 8573 2.903784 ACCCTGTTGTGCTACTATCACA 59.096 45.455 0.00 0.00 42.10 3.58
2546 8648 1.193203 CACATTTGCGCGGCTAGATAG 59.807 52.381 8.83 0.00 0.00 2.08
2549 8651 3.056821 ACATTTGCGCGGCTAGATAGATA 60.057 43.478 8.83 0.00 0.00 1.98
2732 8835 2.132762 AGAACTTGGCGTAAACAGTCG 58.867 47.619 0.00 0.00 0.00 4.18
2781 8884 4.859798 CGTTAAAGTGGTGCAAAAACTTGA 59.140 37.500 9.86 1.54 34.46 3.02
2799 8902 2.488952 TGACTTGAGCGTGCAAATACA 58.511 42.857 0.00 0.00 0.00 2.29
2800 8903 2.875317 TGACTTGAGCGTGCAAATACAA 59.125 40.909 0.00 0.00 0.00 2.41
2899 9002 0.605319 GGTGAAGATTGGGCGTGTGA 60.605 55.000 0.00 0.00 0.00 3.58
2900 9003 0.517316 GTGAAGATTGGGCGTGTGAC 59.483 55.000 0.00 0.00 0.00 3.67
2901 9004 0.396435 TGAAGATTGGGCGTGTGACT 59.604 50.000 0.00 0.00 0.00 3.41
2902 9005 1.079503 GAAGATTGGGCGTGTGACTC 58.920 55.000 0.00 0.00 0.00 3.36
2913 9022 3.251004 GGCGTGTGACTCTTTGAAGAAAT 59.749 43.478 0.00 0.00 34.03 2.17
3037 9259 4.811024 CGCACCAGATAATAGTTGTGTCAT 59.189 41.667 0.00 0.00 0.00 3.06
3038 9260 5.983118 CGCACCAGATAATAGTTGTGTCATA 59.017 40.000 0.00 0.00 0.00 2.15
3039 9261 6.074302 CGCACCAGATAATAGTTGTGTCATAC 60.074 42.308 0.00 0.00 0.00 2.39
3040 9262 6.761242 GCACCAGATAATAGTTGTGTCATACA 59.239 38.462 0.00 0.00 37.56 2.29
3041 9263 7.042456 GCACCAGATAATAGTTGTGTCATACAG 60.042 40.741 0.00 0.00 41.10 2.74
3042 9264 8.197439 CACCAGATAATAGTTGTGTCATACAGA 58.803 37.037 0.00 0.00 41.10 3.41
3043 9265 8.417106 ACCAGATAATAGTTGTGTCATACAGAG 58.583 37.037 0.00 0.00 41.10 3.35
3179 11816 3.887916 AGGAGGACCTACCAGATACTC 57.112 52.381 0.00 0.00 45.83 2.59
3188 11825 0.927767 ACCAGATACTCCCTCCGTCT 59.072 55.000 0.00 0.00 0.00 4.18
3189 11826 1.133730 ACCAGATACTCCCTCCGTCTC 60.134 57.143 0.00 0.00 0.00 3.36
3192 11829 2.621055 CAGATACTCCCTCCGTCTCAAG 59.379 54.545 0.00 0.00 0.00 3.02
3197 11834 2.025226 ACTCCCTCCGTCTCAAGATACA 60.025 50.000 0.00 0.00 0.00 2.29
3198 11835 2.621055 CTCCCTCCGTCTCAAGATACAG 59.379 54.545 0.00 0.00 0.00 2.74
3199 11836 1.067821 CCCTCCGTCTCAAGATACAGC 59.932 57.143 0.00 0.00 0.00 4.40
3200 11837 1.067821 CCTCCGTCTCAAGATACAGCC 59.932 57.143 0.00 0.00 0.00 4.85
3201 11838 0.738975 TCCGTCTCAAGATACAGCCG 59.261 55.000 0.00 0.00 0.00 5.52
3202 11839 0.456221 CCGTCTCAAGATACAGCCGT 59.544 55.000 0.00 0.00 0.00 5.68
3203 11840 1.550065 CGTCTCAAGATACAGCCGTG 58.450 55.000 0.00 0.00 0.00 4.94
3268 12739 6.554334 AAAACGTGTGTATGCTTCTATGTT 57.446 33.333 0.00 0.00 0.00 2.71
3306 12777 2.290514 ACTGATGGTTAGCTGCACATGT 60.291 45.455 1.02 0.00 0.00 3.21
3354 12825 5.898972 AGAATCCCTTGGCTGCATATTTTTA 59.101 36.000 0.50 0.00 0.00 1.52
3407 12879 2.063979 TAGGACCCACCGGATGCAG 61.064 63.158 9.46 0.00 44.74 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 2.802719 GGTTTTACCCAGATTCAGCCA 58.197 47.619 0.00 0.00 30.04 4.75
137 138 0.815734 ATGGTACCGAAGACCGTCAG 59.184 55.000 7.57 0.00 40.09 3.51
148 149 0.034059 GAGGAGGCATGATGGTACCG 59.966 60.000 7.57 0.00 0.00 4.02
178 179 3.799755 CAAACCGCCTGTAGCCGC 61.800 66.667 0.00 0.00 38.78 6.53
179 180 2.869503 ATCCAAACCGCCTGTAGCCG 62.870 60.000 0.00 0.00 38.78 5.52
180 181 1.077716 ATCCAAACCGCCTGTAGCC 60.078 57.895 0.00 0.00 38.78 3.93
181 182 1.429148 CGATCCAAACCGCCTGTAGC 61.429 60.000 0.00 0.00 38.52 3.58
182 183 1.429148 GCGATCCAAACCGCCTGTAG 61.429 60.000 0.00 0.00 45.06 2.74
183 184 1.448893 GCGATCCAAACCGCCTGTA 60.449 57.895 0.00 0.00 45.06 2.74
184 185 2.746277 GCGATCCAAACCGCCTGT 60.746 61.111 0.00 0.00 45.06 4.00
189 190 1.933853 CTAAGAAGGCGATCCAAACCG 59.066 52.381 0.00 0.00 33.74 4.44
190 191 3.261981 TCTAAGAAGGCGATCCAAACC 57.738 47.619 0.00 0.00 33.74 3.27
191 192 3.561725 CCATCTAAGAAGGCGATCCAAAC 59.438 47.826 0.00 0.00 33.74 2.93
192 193 3.199946 ACCATCTAAGAAGGCGATCCAAA 59.800 43.478 0.00 0.00 33.74 3.28
193 194 2.771943 ACCATCTAAGAAGGCGATCCAA 59.228 45.455 0.00 0.00 33.74 3.53
194 195 2.398588 ACCATCTAAGAAGGCGATCCA 58.601 47.619 0.00 0.00 33.74 3.41
195 196 3.477210 AACCATCTAAGAAGGCGATCC 57.523 47.619 0.00 0.00 0.00 3.36
196 197 4.035675 CCAAAACCATCTAAGAAGGCGATC 59.964 45.833 0.00 0.00 0.00 3.69
197 198 3.947834 CCAAAACCATCTAAGAAGGCGAT 59.052 43.478 0.00 0.00 0.00 4.58
198 199 3.343617 CCAAAACCATCTAAGAAGGCGA 58.656 45.455 0.00 0.00 0.00 5.54
199 200 2.423538 CCCAAAACCATCTAAGAAGGCG 59.576 50.000 0.00 0.00 0.00 5.52
200 201 2.760650 CCCCAAAACCATCTAAGAAGGC 59.239 50.000 0.00 0.00 0.00 4.35
201 202 4.316025 TCCCCAAAACCATCTAAGAAGG 57.684 45.455 0.00 0.00 0.00 3.46
202 203 4.706962 CCTTCCCCAAAACCATCTAAGAAG 59.293 45.833 0.00 0.00 0.00 2.85
203 204 4.510205 CCCTTCCCCAAAACCATCTAAGAA 60.510 45.833 0.00 0.00 0.00 2.52
204 205 3.011257 CCCTTCCCCAAAACCATCTAAGA 59.989 47.826 0.00 0.00 0.00 2.10
205 206 3.365472 CCCTTCCCCAAAACCATCTAAG 58.635 50.000 0.00 0.00 0.00 2.18
206 207 2.043801 CCCCTTCCCCAAAACCATCTAA 59.956 50.000 0.00 0.00 0.00 2.10
207 208 1.643811 CCCCTTCCCCAAAACCATCTA 59.356 52.381 0.00 0.00 0.00 1.98
208 209 0.413434 CCCCTTCCCCAAAACCATCT 59.587 55.000 0.00 0.00 0.00 2.90
209 210 0.411848 TCCCCTTCCCCAAAACCATC 59.588 55.000 0.00 0.00 0.00 3.51
210 211 1.101195 ATCCCCTTCCCCAAAACCAT 58.899 50.000 0.00 0.00 0.00 3.55
211 212 0.116143 CATCCCCTTCCCCAAAACCA 59.884 55.000 0.00 0.00 0.00 3.67
212 213 0.617535 CCATCCCCTTCCCCAAAACC 60.618 60.000 0.00 0.00 0.00 3.27
229 230 3.731728 GGCTGCATCCACCTCCCA 61.732 66.667 0.55 0.00 0.00 4.37
230 231 3.412624 GAGGCTGCATCCACCTCCC 62.413 68.421 9.69 0.00 43.54 4.30
231 232 2.191641 GAGGCTGCATCCACCTCC 59.808 66.667 9.69 0.00 43.54 4.30
232 233 2.373707 AGGAGGCTGCATCCACCTC 61.374 63.158 31.96 16.00 42.50 3.85
233 234 2.285969 AGGAGGCTGCATCCACCT 60.286 61.111 31.96 18.64 41.53 4.00
234 235 2.124403 CAGGAGGCTGCATCCACC 60.124 66.667 31.96 14.54 39.47 4.61
235 236 2.124403 CCAGGAGGCTGCATCCAC 60.124 66.667 31.96 9.16 39.47 4.02
245 246 0.033228 CTTCATCGCTAGCCAGGAGG 59.967 60.000 9.66 0.00 38.23 4.30
246 247 0.033228 CCTTCATCGCTAGCCAGGAG 59.967 60.000 9.66 3.10 0.00 3.69
247 248 2.032860 GCCTTCATCGCTAGCCAGGA 62.033 60.000 9.66 0.00 0.00 3.86
248 249 1.596477 GCCTTCATCGCTAGCCAGG 60.596 63.158 9.66 8.04 0.00 4.45
249 250 0.879400 CTGCCTTCATCGCTAGCCAG 60.879 60.000 9.66 4.04 0.00 4.85
250 251 1.144716 CTGCCTTCATCGCTAGCCA 59.855 57.895 9.66 0.00 0.00 4.75
251 252 0.034616 ATCTGCCTTCATCGCTAGCC 59.965 55.000 9.66 0.00 0.00 3.93
252 253 1.146637 CATCTGCCTTCATCGCTAGC 58.853 55.000 4.06 4.06 0.00 3.42
253 254 1.069823 ACCATCTGCCTTCATCGCTAG 59.930 52.381 0.00 0.00 0.00 3.42
254 255 1.123077 ACCATCTGCCTTCATCGCTA 58.877 50.000 0.00 0.00 0.00 4.26
255 256 0.463295 CACCATCTGCCTTCATCGCT 60.463 55.000 0.00 0.00 0.00 4.93
256 257 1.442526 CCACCATCTGCCTTCATCGC 61.443 60.000 0.00 0.00 0.00 4.58
257 258 0.816825 CCCACCATCTGCCTTCATCG 60.817 60.000 0.00 0.00 0.00 3.84
258 259 0.548031 TCCCACCATCTGCCTTCATC 59.452 55.000 0.00 0.00 0.00 2.92
259 260 0.549950 CTCCCACCATCTGCCTTCAT 59.450 55.000 0.00 0.00 0.00 2.57
260 261 0.547471 TCTCCCACCATCTGCCTTCA 60.547 55.000 0.00 0.00 0.00 3.02
261 262 0.620556 TTCTCCCACCATCTGCCTTC 59.379 55.000 0.00 0.00 0.00 3.46
262 263 0.329596 GTTCTCCCACCATCTGCCTT 59.670 55.000 0.00 0.00 0.00 4.35
263 264 0.842030 TGTTCTCCCACCATCTGCCT 60.842 55.000 0.00 0.00 0.00 4.75
264 265 0.038166 TTGTTCTCCCACCATCTGCC 59.962 55.000 0.00 0.00 0.00 4.85
265 266 1.003580 TCTTGTTCTCCCACCATCTGC 59.996 52.381 0.00 0.00 0.00 4.26
266 267 3.276857 CATCTTGTTCTCCCACCATCTG 58.723 50.000 0.00 0.00 0.00 2.90
267 268 2.240667 CCATCTTGTTCTCCCACCATCT 59.759 50.000 0.00 0.00 0.00 2.90
268 269 2.648059 CCATCTTGTTCTCCCACCATC 58.352 52.381 0.00 0.00 0.00 3.51
269 270 1.285962 CCCATCTTGTTCTCCCACCAT 59.714 52.381 0.00 0.00 0.00 3.55
270 271 0.698238 CCCATCTTGTTCTCCCACCA 59.302 55.000 0.00 0.00 0.00 4.17
271 272 0.991920 TCCCATCTTGTTCTCCCACC 59.008 55.000 0.00 0.00 0.00 4.61
272 273 2.879103 TTCCCATCTTGTTCTCCCAC 57.121 50.000 0.00 0.00 0.00 4.61
273 274 2.041620 CCTTTCCCATCTTGTTCTCCCA 59.958 50.000 0.00 0.00 0.00 4.37
274 275 2.308866 TCCTTTCCCATCTTGTTCTCCC 59.691 50.000 0.00 0.00 0.00 4.30
275 276 3.264450 TCTCCTTTCCCATCTTGTTCTCC 59.736 47.826 0.00 0.00 0.00 3.71
276 277 4.223923 TCTCTCCTTTCCCATCTTGTTCTC 59.776 45.833 0.00 0.00 0.00 2.87
277 278 4.019771 GTCTCTCCTTTCCCATCTTGTTCT 60.020 45.833 0.00 0.00 0.00 3.01
278 279 4.257731 GTCTCTCCTTTCCCATCTTGTTC 58.742 47.826 0.00 0.00 0.00 3.18
279 280 3.307059 CGTCTCTCCTTTCCCATCTTGTT 60.307 47.826 0.00 0.00 0.00 2.83
280 281 2.234908 CGTCTCTCCTTTCCCATCTTGT 59.765 50.000 0.00 0.00 0.00 3.16
281 282 2.898705 CGTCTCTCCTTTCCCATCTTG 58.101 52.381 0.00 0.00 0.00 3.02
282 283 1.208293 GCGTCTCTCCTTTCCCATCTT 59.792 52.381 0.00 0.00 0.00 2.40
283 284 0.827368 GCGTCTCTCCTTTCCCATCT 59.173 55.000 0.00 0.00 0.00 2.90
284 285 0.537188 TGCGTCTCTCCTTTCCCATC 59.463 55.000 0.00 0.00 0.00 3.51
285 286 0.539051 CTGCGTCTCTCCTTTCCCAT 59.461 55.000 0.00 0.00 0.00 4.00
286 287 0.832135 ACTGCGTCTCTCCTTTCCCA 60.832 55.000 0.00 0.00 0.00 4.37
287 288 0.390472 CACTGCGTCTCTCCTTTCCC 60.390 60.000 0.00 0.00 0.00 3.97
288 289 0.603569 TCACTGCGTCTCTCCTTTCC 59.396 55.000 0.00 0.00 0.00 3.13
289 290 2.663826 ATCACTGCGTCTCTCCTTTC 57.336 50.000 0.00 0.00 0.00 2.62
290 291 3.357203 TCTATCACTGCGTCTCTCCTTT 58.643 45.455 0.00 0.00 0.00 3.11
291 292 2.948979 CTCTATCACTGCGTCTCTCCTT 59.051 50.000 0.00 0.00 0.00 3.36
292 293 2.092646 ACTCTATCACTGCGTCTCTCCT 60.093 50.000 0.00 0.00 0.00 3.69
293 294 2.294074 ACTCTATCACTGCGTCTCTCC 58.706 52.381 0.00 0.00 0.00 3.71
294 295 3.496884 CCTACTCTATCACTGCGTCTCTC 59.503 52.174 0.00 0.00 0.00 3.20
295 296 3.472652 CCTACTCTATCACTGCGTCTCT 58.527 50.000 0.00 0.00 0.00 3.10
296 297 2.550606 CCCTACTCTATCACTGCGTCTC 59.449 54.545 0.00 0.00 0.00 3.36
297 298 2.092321 ACCCTACTCTATCACTGCGTCT 60.092 50.000 0.00 0.00 0.00 4.18
298 299 2.299521 ACCCTACTCTATCACTGCGTC 58.700 52.381 0.00 0.00 0.00 5.19
299 300 2.438800 ACCCTACTCTATCACTGCGT 57.561 50.000 0.00 0.00 0.00 5.24
300 301 3.130516 TGAAACCCTACTCTATCACTGCG 59.869 47.826 0.00 0.00 0.00 5.18
301 302 4.160626 ACTGAAACCCTACTCTATCACTGC 59.839 45.833 0.00 0.00 0.00 4.40
302 303 5.394663 CCACTGAAACCCTACTCTATCACTG 60.395 48.000 0.00 0.00 0.00 3.66
303 304 4.712337 CCACTGAAACCCTACTCTATCACT 59.288 45.833 0.00 0.00 0.00 3.41
304 305 4.710375 TCCACTGAAACCCTACTCTATCAC 59.290 45.833 0.00 0.00 0.00 3.06
305 306 4.942944 TCCACTGAAACCCTACTCTATCA 58.057 43.478 0.00 0.00 0.00 2.15
306 307 4.342665 CCTCCACTGAAACCCTACTCTATC 59.657 50.000 0.00 0.00 0.00 2.08
307 308 4.290942 CCTCCACTGAAACCCTACTCTAT 58.709 47.826 0.00 0.00 0.00 1.98
308 309 3.709587 CCTCCACTGAAACCCTACTCTA 58.290 50.000 0.00 0.00 0.00 2.43
309 310 2.541466 CCTCCACTGAAACCCTACTCT 58.459 52.381 0.00 0.00 0.00 3.24
310 311 1.066071 GCCTCCACTGAAACCCTACTC 60.066 57.143 0.00 0.00 0.00 2.59
311 312 0.984995 GCCTCCACTGAAACCCTACT 59.015 55.000 0.00 0.00 0.00 2.57
318 319 2.637382 TGTACATCTGCCTCCACTGAAA 59.363 45.455 0.00 0.00 0.00 2.69
336 337 1.487300 TAACCCAGCGCATAGGTGTA 58.513 50.000 11.47 5.86 46.29 2.90
389 390 2.397413 AAAGGCACCACAGGTCCTCG 62.397 60.000 7.37 0.00 34.05 4.63
390 391 0.890996 CAAAGGCACCACAGGTCCTC 60.891 60.000 7.37 0.00 34.05 3.71
391 392 1.151450 CAAAGGCACCACAGGTCCT 59.849 57.895 0.00 0.00 35.71 3.85
392 393 2.564721 GCAAAGGCACCACAGGTCC 61.565 63.158 0.00 0.00 40.72 4.46
434 817 5.123186 CGTATTTTCCTCAACCATGTAAGCA 59.877 40.000 0.00 0.00 0.00 3.91
480 863 1.535462 CGGAAACCACCTAACTTGCAG 59.465 52.381 0.00 0.00 0.00 4.41
527 910 7.575414 TGAATTACTCTAGTCAGACAGGATC 57.425 40.000 2.66 0.00 0.00 3.36
536 919 4.345257 GGAGGCCATGAATTACTCTAGTCA 59.655 45.833 5.01 0.00 0.00 3.41
603 986 4.096003 AACCATGGAGACGCGGGG 62.096 66.667 21.47 2.37 0.00 5.73
604 987 2.593468 ATCAACCATGGAGACGCGGG 62.593 60.000 21.47 1.69 0.00 6.13
605 988 1.153369 ATCAACCATGGAGACGCGG 60.153 57.895 21.47 0.00 0.00 6.46
606 989 1.154205 GGATCAACCATGGAGACGCG 61.154 60.000 21.47 3.53 38.79 6.01
607 990 0.107703 TGGATCAACCATGGAGACGC 60.108 55.000 21.47 11.13 44.64 5.19
617 1000 1.091537 TCCGCGAAATTGGATCAACC 58.908 50.000 8.23 0.00 39.54 3.77
623 1006 1.663695 GAAGGATCCGCGAAATTGGA 58.336 50.000 8.23 0.00 38.95 3.53
624 1007 0.663153 GGAAGGATCCGCGAAATTGG 59.337 55.000 8.23 0.00 35.59 3.16
634 1017 3.561241 GGGGGCGAGGAAGGATCC 61.561 72.222 2.48 2.48 46.98 3.36
635 1018 3.930012 CGGGGGCGAGGAAGGATC 61.930 72.222 0.00 0.00 0.00 3.36
663 1046 7.095229 GGGCTTAAATCAAATTTCTGGTTCAAC 60.095 37.037 0.00 0.00 33.82 3.18
726 1109 1.576356 GCTGTAATCTTCCTCCTGCG 58.424 55.000 0.00 0.00 0.00 5.18
777 1162 6.437793 AGGCCCTGTGATCACTATATAAGTAC 59.562 42.308 25.55 8.11 35.76 2.73
1020 2689 3.088789 ACGGTCTCTGGATGTAGTTCT 57.911 47.619 0.00 0.00 0.00 3.01
1161 2868 2.203788 AGGCCCTCCGTCAAGTGA 60.204 61.111 0.00 0.00 37.47 3.41
1180 2887 4.592192 CGTCTGCGCCGGGATGAT 62.592 66.667 4.18 0.00 0.00 2.45
1272 2979 4.624364 CCGCACTGCACCCAGACA 62.624 66.667 1.11 0.00 41.77 3.41
1353 3068 4.195334 ACGGATGATGGGCAGGGC 62.195 66.667 0.00 0.00 0.00 5.19
1641 3363 2.202797 GAGATCTGCCGCTGCGAA 60.203 61.111 25.45 10.45 41.78 4.70
1754 3485 2.671619 GCGTGTGGCTGCCCTTAA 60.672 61.111 17.53 0.00 39.11 1.85
2466 8565 8.906867 AGCATTGCAATTTAATAGTGTGATAGT 58.093 29.630 9.83 0.00 0.00 2.12
2474 8573 7.431249 CAGATGGAGCATTGCAATTTAATAGT 58.569 34.615 9.83 0.00 0.00 2.12
2525 8627 1.439353 ATCTAGCCGCGCAAATGTGG 61.439 55.000 8.75 0.00 42.55 4.17
2546 8648 5.835113 AACCTAACAACACATGGCATATC 57.165 39.130 0.00 0.00 0.00 1.63
2549 8651 6.603940 AATAAACCTAACAACACATGGCAT 57.396 33.333 0.00 0.00 0.00 4.40
2582 8684 8.206325 ACATTTCATCTTCTAGCTAACACATG 57.794 34.615 0.00 0.00 0.00 3.21
2627 8730 6.968263 TTTGTCCACACATCTTTCCATAAA 57.032 33.333 0.00 0.00 30.55 1.40
2642 8745 2.496111 TCCGTGGTGTATTTTGTCCAC 58.504 47.619 0.00 0.00 44.54 4.02
2699 8802 0.320697 AAGTTCTAGCACCACCGGTC 59.679 55.000 2.59 0.00 31.02 4.79
2732 8835 1.661112 CGCAAGTTCTAGCACTAAGGC 59.339 52.381 0.00 0.03 0.00 4.35
2734 8837 1.661112 GCCGCAAGTTCTAGCACTAAG 59.339 52.381 0.00 0.00 0.00 2.18
2781 8884 3.253188 ACATTGTATTTGCACGCTCAAGT 59.747 39.130 0.00 0.00 0.00 3.16
2799 8902 7.043854 CCGACGTATACAAACGAGATTTACATT 60.044 37.037 3.32 0.00 45.68 2.71
2800 8903 6.415867 CCGACGTATACAAACGAGATTTACAT 59.584 38.462 3.32 0.00 45.68 2.29
3108 11744 2.742348 TCCCACGGCTGTATCTTCTTA 58.258 47.619 0.00 0.00 0.00 2.10
3170 11807 1.133761 TGAGACGGAGGGAGTATCTGG 60.134 57.143 0.00 0.00 31.72 3.86
3179 11816 1.067821 GCTGTATCTTGAGACGGAGGG 59.932 57.143 8.23 0.00 0.00 4.30
3188 11825 2.401583 ATTGCACGGCTGTATCTTGA 57.598 45.000 0.00 0.00 0.00 3.02
3189 11826 4.332543 TCTTAATTGCACGGCTGTATCTTG 59.667 41.667 0.00 0.00 0.00 3.02
3192 11829 5.237344 AGAATCTTAATTGCACGGCTGTATC 59.763 40.000 0.00 0.00 0.00 2.24
3197 11834 5.648092 ACTAAAGAATCTTAATTGCACGGCT 59.352 36.000 0.00 0.00 0.00 5.52
3198 11835 5.880341 ACTAAAGAATCTTAATTGCACGGC 58.120 37.500 0.00 0.00 0.00 5.68
3268 12739 2.629617 TCAGTCAAGAGCTCACATCACA 59.370 45.455 17.77 0.00 0.00 3.58
3306 12777 2.029110 CCGGTAACCTCGGTCTAAACAA 60.029 50.000 0.00 0.00 42.33 2.83
3330 12801 3.607490 AATATGCAGCCAAGGGATTCT 57.393 42.857 0.00 0.00 0.00 2.40
3390 12862 2.815684 TACTGCATCCGGTGGGTCCT 62.816 60.000 0.00 0.00 33.83 3.85
3407 12879 1.489560 AAGGCCCCTGTCAGGTGTAC 61.490 60.000 17.85 4.31 31.93 2.90
3459 12932 4.023193 CCGCTGTTAGTGACTTCCAAAAAT 60.023 41.667 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.