Multiple sequence alignment - TraesCS3B01G314600

Loading Multiple Alignment...

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 TraesCS3B01G314600 chr3B 100.000 2024 0 0 1 2024 505837322 505835299 0.000000e+00 3738.0
1 TraesCS3B01G314600 chr3B 100.000 427 0 0 2380 2806 505834943 505834517 0.000000e+00 789.0
2 TraesCS3B01G314600 chr3B 91.003 289 24 1 1 287 785730961 785730673 3.390000e-104 388.0
3 TraesCS3B01G314600 chr3B 90.972 288 23 2 1 285 644931144 644931431 4.380000e-103 385.0
4 TraesCS3B01G314600 chr3B 90.592 287 25 1 1 285 558108794 558109080 2.040000e-101 379.0
5 TraesCS3B01G314600 chr3B 81.106 217 41 0 2432 2648 252673443 252673227 1.030000e-39 174.0
6 TraesCS3B01G314600 chr3B 80.423 189 33 4 1046 1232 799983086 799982900 1.050000e-29 141.0
7 TraesCS3B01G314600 chr3D 91.474 1642 47 26 442 2016 388535055 388533440 0.000000e+00 2170.0
8 TraesCS3B01G314600 chr3D 95.588 136 6 0 292 427 388535176 388535041 4.710000e-53 219.0
9 TraesCS3B01G314600 chr3D 79.021 143 27 3 2666 2805 108422499 108422357 8.270000e-16 95.3
10 TraesCS3B01G314600 chr3A 88.635 1531 80 39 525 2014 509799452 509797975 0.000000e+00 1777.0
11 TraesCS3B01G314600 chr3A 83.716 436 40 4 2380 2805 509797882 509797468 1.580000e-102 383.0
12 TraesCS3B01G314600 chr3A 84.314 102 16 0 1351 1452 428569856 428569755 1.780000e-17 100.0
13 TraesCS3B01G314600 chr3A 100.000 38 0 0 390 427 509799531 509799494 1.390000e-08 71.3
14 TraesCS3B01G314600 chr4B 91.034 290 24 1 1 288 39732800 39732511 9.420000e-105 390.0
15 TraesCS3B01G314600 chr4B 83.913 230 37 0 2395 2624 43168167 43167938 1.310000e-53 220.0
16 TraesCS3B01G314600 chr4B 80.769 208 28 10 1033 1232 662471010 662470807 4.840000e-33 152.0
17 TraesCS3B01G314600 chr4B 80.000 205 32 7 1034 1232 662458922 662458721 2.910000e-30 143.0
18 TraesCS3B01G314600 chr1B 90.444 293 25 2 3 293 51964940 51965231 1.580000e-102 383.0
19 TraesCS3B01G314600 chr6B 90.244 287 26 1 1 285 664020856 664021142 9.490000e-100 374.0
20 TraesCS3B01G314600 chr6B 83.740 246 39 1 2403 2648 258754661 258754905 6.040000e-57 231.0
21 TraesCS3B01G314600 chr6B 83.249 197 33 0 2452 2648 705475474 705475670 6.170000e-42 182.0
22 TraesCS3B01G314600 chr5B 89.420 293 28 2 1 291 478602677 478602968 1.590000e-97 366.0
23 TraesCS3B01G314600 chr5B 89.860 286 28 1 1 285 549630815 549630530 1.590000e-97 366.0
24 TraesCS3B01G314600 chr1D 89.691 291 25 4 1 287 470207107 470206818 1.590000e-97 366.0
25 TraesCS3B01G314600 chr2D 82.745 255 35 2 2403 2648 458507913 458507659 4.710000e-53 219.0
26 TraesCS3B01G314600 chr2D 82.014 139 22 3 2671 2806 470269745 470269883 6.350000e-22 115.0
27 TraesCS3B01G314600 chr5D 85.577 208 26 4 2397 2602 367647292 367647087 6.090000e-52 215.0
28 TraesCS3B01G314600 chr4D 82.353 255 36 5 2403 2648 57218940 57218686 2.190000e-51 213.0
29 TraesCS3B01G314600 chr4D 81.203 266 41 4 2393 2649 64370361 64370626 3.660000e-49 206.0
30 TraesCS3B01G314600 chr4D 81.675 191 27 8 1046 1232 506340130 506339944 4.840000e-33 152.0
31 TraesCS3B01G314600 chr4D 82.759 145 22 3 2664 2805 64371027 64371171 2.930000e-25 126.0
32 TraesCS3B01G314600 chr5A 80.628 191 29 8 1046 1232 702632566 702632380 1.050000e-29 141.0
33 TraesCS3B01G314600 chr5A 79.592 196 34 6 1039 1232 704342962 704343153 4.880000e-28 135.0
34 TraesCS3B01G314600 chrUn 78.571 196 39 3 1039 1232 109029192 109028998 2.930000e-25 126.0
35 TraesCS3B01G314600 chr7D 82.069 145 21 5 2664 2804 224467928 224468071 4.910000e-23 119.0
36 TraesCS3B01G314600 chr2B 90.909 55 4 1 1970 2024 677871776 677871829 3.880000e-09 73.1


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 TraesCS3B01G314600 chr3B 505834517 505837322 2805 True 2263.500000 3738 100.000000 1 2806 2 chr3B.!!$R4 2805
1 TraesCS3B01G314600 chr3D 388533440 388535176 1736 True 1194.500000 2170 93.531000 292 2016 2 chr3D.!!$R2 1724
2 TraesCS3B01G314600 chr3A 509797468 509799531 2063 True 743.766667 1777 90.783667 390 2805 3 chr3A.!!$R2 2415

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
313 314 0.036732 ATCCACAGCAAAGCGGAAGA 59.963 50.0 0.0 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 2025 0.529773 GCGCCAATCAGACGGTCATA 60.53 55.0 11.27 0.0 0.0 2.15 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
29 30 3.186106 CATGCGTCCATGGCGAAA 58.814 55.556 26.00 16.05 44.07 3.46
30 31 1.729276 CATGCGTCCATGGCGAAAT 59.271 52.632 26.00 17.23 44.07 2.17
31 32 0.101040 CATGCGTCCATGGCGAAATT 59.899 50.000 26.00 5.10 44.07 1.82
32 33 0.381801 ATGCGTCCATGGCGAAATTC 59.618 50.000 26.00 12.31 0.00 2.17
33 34 1.297598 GCGTCCATGGCGAAATTCG 60.298 57.895 26.00 11.47 43.89 3.34
68 69 3.217743 GGGTCGTAGGAGGCGGAG 61.218 72.222 0.00 0.00 0.00 4.63
69 70 2.124403 GGTCGTAGGAGGCGGAGA 60.124 66.667 0.00 0.00 0.00 3.71
70 71 2.188161 GGTCGTAGGAGGCGGAGAG 61.188 68.421 0.00 0.00 0.00 3.20
71 72 2.188161 GTCGTAGGAGGCGGAGAGG 61.188 68.421 0.00 0.00 0.00 3.69
72 73 2.907917 CGTAGGAGGCGGAGAGGG 60.908 72.222 0.00 0.00 0.00 4.30
73 74 2.601868 GTAGGAGGCGGAGAGGGA 59.398 66.667 0.00 0.00 0.00 4.20
74 75 1.076192 GTAGGAGGCGGAGAGGGAA 60.076 63.158 0.00 0.00 0.00 3.97
75 76 1.110518 GTAGGAGGCGGAGAGGGAAG 61.111 65.000 0.00 0.00 0.00 3.46
76 77 1.287038 TAGGAGGCGGAGAGGGAAGA 61.287 60.000 0.00 0.00 0.00 2.87
77 78 2.131067 GGAGGCGGAGAGGGAAGAG 61.131 68.421 0.00 0.00 0.00 2.85
78 79 1.380650 GAGGCGGAGAGGGAAGAGT 60.381 63.158 0.00 0.00 0.00 3.24
79 80 1.671901 GAGGCGGAGAGGGAAGAGTG 61.672 65.000 0.00 0.00 0.00 3.51
80 81 2.185608 GCGGAGAGGGAAGAGTGC 59.814 66.667 0.00 0.00 0.00 4.40
81 82 2.492090 CGGAGAGGGAAGAGTGCG 59.508 66.667 0.00 0.00 0.00 5.34
82 83 2.046864 CGGAGAGGGAAGAGTGCGA 61.047 63.158 0.00 0.00 0.00 5.10
83 84 1.513622 GGAGAGGGAAGAGTGCGAC 59.486 63.158 0.00 0.00 0.00 5.19
84 85 1.137825 GAGAGGGAAGAGTGCGACG 59.862 63.158 0.00 0.00 0.00 5.12
85 86 2.507324 GAGGGAAGAGTGCGACGC 60.507 66.667 14.19 14.19 0.00 5.19
86 87 4.421479 AGGGAAGAGTGCGACGCG 62.421 66.667 16.14 3.53 0.00 6.01
87 88 4.415332 GGGAAGAGTGCGACGCGA 62.415 66.667 15.93 1.28 0.00 5.87
88 89 2.876645 GGAAGAGTGCGACGCGAG 60.877 66.667 15.93 7.68 0.00 5.03
89 90 3.537297 GAAGAGTGCGACGCGAGC 61.537 66.667 15.93 18.93 0.00 5.03
126 127 3.972276 GAAAGCGGGCGCACCAAA 61.972 61.111 10.83 0.00 44.88 3.28
127 128 3.281359 GAAAGCGGGCGCACCAAAT 62.281 57.895 10.83 0.00 44.88 2.32
128 129 1.928706 GAAAGCGGGCGCACCAAATA 61.929 55.000 10.83 0.00 44.88 1.40
129 130 2.207788 AAAGCGGGCGCACCAAATAC 62.208 55.000 10.83 0.00 44.88 1.89
130 131 3.436055 GCGGGCGCACCAAATACA 61.436 61.111 10.83 0.00 40.22 2.29
131 132 2.483288 CGGGCGCACCAAATACAC 59.517 61.111 10.83 0.00 40.22 2.90
132 133 2.882132 GGGCGCACCAAATACACC 59.118 61.111 10.83 0.00 39.85 4.16
133 134 2.483288 GGCGCACCAAATACACCG 59.517 61.111 10.83 0.00 35.26 4.94
134 135 2.202427 GCGCACCAAATACACCGC 60.202 61.111 0.30 0.00 34.50 5.68
135 136 2.097538 CGCACCAAATACACCGCG 59.902 61.111 0.00 0.00 36.47 6.46
136 137 2.202427 GCACCAAATACACCGCGC 60.202 61.111 0.00 0.00 0.00 6.86
137 138 2.097538 CACCAAATACACCGCGCG 59.902 61.111 25.67 25.67 0.00 6.86
138 139 3.122323 ACCAAATACACCGCGCGG 61.122 61.111 44.88 44.88 42.03 6.46
167 168 4.204891 CGACCGCGCGTCCAATTC 62.205 66.667 29.95 13.06 38.36 2.17
168 169 4.204891 GACCGCGCGTCCAATTCG 62.205 66.667 29.95 13.09 35.23 3.34
170 171 3.784412 CCGCGCGTCCAATTCGTT 61.784 61.111 29.95 0.00 0.00 3.85
171 172 2.446253 CCGCGCGTCCAATTCGTTA 61.446 57.895 29.95 0.00 0.00 3.18
172 173 1.634225 CGCGCGTCCAATTCGTTAT 59.366 52.632 24.19 0.00 0.00 1.89
173 174 0.847670 CGCGCGTCCAATTCGTTATA 59.152 50.000 24.19 0.00 0.00 0.98
174 175 1.136992 CGCGCGTCCAATTCGTTATAG 60.137 52.381 24.19 0.00 0.00 1.31
175 176 1.396815 GCGCGTCCAATTCGTTATAGC 60.397 52.381 8.43 0.00 0.00 2.97
176 177 1.136992 CGCGTCCAATTCGTTATAGCG 60.137 52.381 2.12 2.12 39.14 4.26
177 178 1.396815 GCGTCCAATTCGTTATAGCGC 60.397 52.381 0.00 0.00 35.77 5.92
178 179 1.136992 CGTCCAATTCGTTATAGCGCG 60.137 52.381 0.00 0.00 0.00 6.86
179 180 0.856641 TCCAATTCGTTATAGCGCGC 59.143 50.000 26.66 26.66 0.00 6.86
180 181 0.579630 CCAATTCGTTATAGCGCGCA 59.420 50.000 35.10 19.76 0.00 6.09
181 182 1.194547 CCAATTCGTTATAGCGCGCAT 59.805 47.619 35.10 24.95 0.00 4.73
182 183 2.225086 CAATTCGTTATAGCGCGCATG 58.775 47.619 35.10 18.00 0.00 4.06
183 184 1.778334 ATTCGTTATAGCGCGCATGA 58.222 45.000 35.10 20.19 0.00 3.07
184 185 1.778334 TTCGTTATAGCGCGCATGAT 58.222 45.000 35.10 24.12 0.00 2.45
185 186 1.778334 TCGTTATAGCGCGCATGATT 58.222 45.000 35.10 15.14 0.00 2.57
186 187 2.131972 TCGTTATAGCGCGCATGATTT 58.868 42.857 35.10 14.29 0.00 2.17
187 188 2.542178 TCGTTATAGCGCGCATGATTTT 59.458 40.909 35.10 13.45 0.00 1.82
188 189 3.001838 TCGTTATAGCGCGCATGATTTTT 59.998 39.130 35.10 12.60 0.00 1.94
189 190 3.116217 CGTTATAGCGCGCATGATTTTTG 59.884 43.478 35.10 10.25 0.00 2.44
190 191 1.480205 ATAGCGCGCATGATTTTTGC 58.520 45.000 35.10 0.00 36.74 3.68
191 192 0.169894 TAGCGCGCATGATTTTTGCA 59.830 45.000 35.10 0.00 40.14 4.08
192 193 1.057668 GCGCGCATGATTTTTGCAC 59.942 52.632 29.10 0.00 40.14 4.57
193 194 1.337810 CGCGCATGATTTTTGCACG 59.662 52.632 8.75 0.00 40.14 5.34
194 195 1.057668 GCGCATGATTTTTGCACGC 59.942 52.632 0.30 0.00 40.14 5.34
195 196 1.703439 CGCATGATTTTTGCACGCC 59.297 52.632 0.00 0.00 40.14 5.68
196 197 1.685640 CGCATGATTTTTGCACGCCC 61.686 55.000 0.00 0.00 40.14 6.13
197 198 1.685640 GCATGATTTTTGCACGCCCG 61.686 55.000 0.00 0.00 39.90 6.13
198 199 1.445926 ATGATTTTTGCACGCCCGC 60.446 52.632 0.00 0.00 0.00 6.13
199 200 1.876497 ATGATTTTTGCACGCCCGCT 61.876 50.000 0.00 0.00 0.00 5.52
200 201 2.049248 ATTTTTGCACGCCCGCTG 60.049 55.556 0.00 0.00 0.00 5.18
201 202 3.572196 ATTTTTGCACGCCCGCTGG 62.572 57.895 0.00 0.00 0.00 4.85
247 248 2.918600 GTTAAAACGGCCTAATTTGCGG 59.081 45.455 0.00 5.90 35.42 5.69
248 249 0.389296 AAAACGGCCTAATTTGCGGC 60.389 50.000 0.00 0.00 45.55 6.53
252 253 4.905193 GCCTAATTTGCGGCGCGG 62.905 66.667 28.09 21.22 36.45 6.46
253 254 4.905193 CCTAATTTGCGGCGCGGC 62.905 66.667 30.55 30.55 0.00 6.53
271 272 3.006706 GCTAGTTTAGCGCGGCTG 58.993 61.111 8.83 0.00 42.62 4.85
272 273 1.810030 GCTAGTTTAGCGCGGCTGT 60.810 57.895 8.83 0.00 42.62 4.40
273 274 1.359459 GCTAGTTTAGCGCGGCTGTT 61.359 55.000 8.83 0.00 42.62 3.16
274 275 0.370273 CTAGTTTAGCGCGGCTGTTG 59.630 55.000 8.83 0.00 40.10 3.33
275 276 1.017177 TAGTTTAGCGCGGCTGTTGG 61.017 55.000 8.83 0.00 40.10 3.77
276 277 2.031314 TTTAGCGCGGCTGTTGGA 59.969 55.556 8.83 0.00 40.10 3.53
277 278 2.032634 TTTAGCGCGGCTGTTGGAG 61.033 57.895 8.83 0.00 40.10 3.86
278 279 2.443260 TTTAGCGCGGCTGTTGGAGA 62.443 55.000 8.83 0.00 40.10 3.71
279 280 2.238847 TTAGCGCGGCTGTTGGAGAT 62.239 55.000 8.83 0.00 40.10 2.75
280 281 2.906182 TAGCGCGGCTGTTGGAGATG 62.906 60.000 8.83 0.00 40.10 2.90
281 282 3.869272 CGCGGCTGTTGGAGATGC 61.869 66.667 0.00 0.00 0.00 3.91
282 283 2.437359 GCGGCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 0.00 3.79
283 284 2.467826 GCGGCTGTTGGAGATGCTC 61.468 63.158 0.00 0.00 0.00 4.26
284 285 1.220206 CGGCTGTTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
285 286 0.461548 CGGCTGTTGGAGATGCTCTA 59.538 55.000 0.00 0.00 0.00 2.43
286 287 1.134699 CGGCTGTTGGAGATGCTCTAA 60.135 52.381 0.00 0.00 0.00 2.10
287 288 2.677902 CGGCTGTTGGAGATGCTCTAAA 60.678 50.000 0.00 0.00 33.06 1.85
288 289 2.941720 GGCTGTTGGAGATGCTCTAAAG 59.058 50.000 0.00 0.00 33.06 1.85
289 290 2.941720 GCTGTTGGAGATGCTCTAAAGG 59.058 50.000 0.00 0.00 33.06 3.11
290 291 2.941720 CTGTTGGAGATGCTCTAAAGGC 59.058 50.000 0.00 0.00 33.06 4.35
313 314 0.036732 ATCCACAGCAAAGCGGAAGA 59.963 50.000 0.00 0.00 0.00 2.87
333 334 0.232303 CCAAACGTTGAGAGCGTGTC 59.768 55.000 0.00 0.00 42.10 3.67
359 360 2.985847 GCCTGTTCCACCCTGCAC 60.986 66.667 0.00 0.00 0.00 4.57
363 364 1.507141 CTGTTCCACCCTGCACGTTC 61.507 60.000 0.00 0.00 0.00 3.95
388 389 2.750637 CTGCCAAGCTGCTCCCAG 60.751 66.667 1.00 6.21 42.13 4.45
423 424 5.140747 CTGAAAGCTCAGTACAGTTACCT 57.859 43.478 0.00 0.00 43.64 3.08
424 425 4.883083 TGAAAGCTCAGTACAGTTACCTG 58.117 43.478 0.00 0.00 44.68 4.00
425 426 5.509840 CTGAAAGCTCAGTACAGTTACCTGT 60.510 44.000 0.00 0.00 45.73 4.00
426 427 6.960620 CTGAAAGCTCAGTACAGTTACCTGTT 60.961 42.308 0.00 0.00 45.16 3.16
427 428 8.378324 CTGAAAGCTCAGTACAGTTACCTGTTT 61.378 40.741 0.00 0.00 45.16 2.83
484 485 1.582968 CCAACGCATTTGAGCAGCT 59.417 52.632 0.00 0.00 37.39 4.24
489 490 1.515736 GCATTTGAGCAGCTTCCGC 60.516 57.895 0.00 0.00 0.00 5.54
496 497 2.817396 GCAGCTTCCGCTCTGGTC 60.817 66.667 0.00 0.00 45.15 4.02
602 608 0.749091 TTTGAGCGGAGATGCCATGG 60.749 55.000 7.63 7.63 35.94 3.66
775 782 1.211567 CCCCAACACCCCATCACCTA 61.212 60.000 0.00 0.00 0.00 3.08
842 851 1.964223 CGGAGCGGGGCAGATATATAT 59.036 52.381 0.00 0.00 0.00 0.86
944 980 1.334869 CAGAGAACAACAAGCCCACAC 59.665 52.381 0.00 0.00 0.00 3.82
945 981 0.668535 GAGAACAACAAGCCCACACC 59.331 55.000 0.00 0.00 0.00 4.16
946 982 1.101049 AGAACAACAAGCCCACACCG 61.101 55.000 0.00 0.00 0.00 4.94
947 983 1.077357 AACAACAAGCCCACACCGA 60.077 52.632 0.00 0.00 0.00 4.69
948 984 1.101049 AACAACAAGCCCACACCGAG 61.101 55.000 0.00 0.00 0.00 4.63
949 985 2.594592 AACAAGCCCACACCGAGC 60.595 61.111 0.00 0.00 0.00 5.03
950 986 3.414136 AACAAGCCCACACCGAGCA 62.414 57.895 0.00 0.00 0.00 4.26
951 987 3.052082 CAAGCCCACACCGAGCAG 61.052 66.667 0.00 0.00 0.00 4.24
952 988 3.241530 AAGCCCACACCGAGCAGA 61.242 61.111 0.00 0.00 0.00 4.26
953 989 3.245668 AAGCCCACACCGAGCAGAG 62.246 63.158 0.00 0.00 0.00 3.35
955 991 4.007644 CCCACACCGAGCAGAGCA 62.008 66.667 0.00 0.00 0.00 4.26
956 992 2.433838 CCACACCGAGCAGAGCAG 60.434 66.667 0.00 0.00 0.00 4.24
957 993 2.433838 CACACCGAGCAGAGCAGG 60.434 66.667 0.00 0.00 35.40 4.85
958 994 2.601666 ACACCGAGCAGAGCAGGA 60.602 61.111 9.83 0.00 33.94 3.86
959 995 2.210013 ACACCGAGCAGAGCAGGAA 61.210 57.895 9.83 0.00 33.94 3.36
960 996 1.739562 CACCGAGCAGAGCAGGAAC 60.740 63.158 9.83 0.00 33.94 3.62
961 997 2.210013 ACCGAGCAGAGCAGGAACA 61.210 57.895 9.83 0.00 33.94 3.18
989 1026 2.433239 GGCTTCCTTATCCGGTTGTAGA 59.567 50.000 0.00 0.00 0.00 2.59
1071 1111 1.814211 CGTTCGTGGCGAAGACGTTT 61.814 55.000 4.11 0.00 46.54 3.60
1080 1120 1.136336 GCGAAGACGTTTCACATGGTC 60.136 52.381 0.00 0.00 41.98 4.02
1215 1255 4.735132 TTCGCCAGCTTCGTCCGG 62.735 66.667 0.00 0.00 0.00 5.14
1291 1341 7.617329 TCATTATATGTATGCCTACTCTGCTCT 59.383 37.037 0.74 0.00 0.00 4.09
1293 1343 1.410517 TGTATGCCTACTCTGCTCTGC 59.589 52.381 0.74 0.00 0.00 4.26
1298 1348 0.746063 CCTACTCTGCTCTGCTCAGG 59.254 60.000 0.00 0.00 32.63 3.86
1300 1350 1.824230 CTACTCTGCTCTGCTCAGGTT 59.176 52.381 0.00 0.00 32.63 3.50
1301 1351 0.321021 ACTCTGCTCTGCTCAGGTTG 59.679 55.000 0.00 0.00 32.63 3.77
1308 1369 0.819259 TCTGCTCAGGTTGTTGTGGC 60.819 55.000 0.00 0.00 0.00 5.01
1326 1387 0.177604 GCTGTGCTCATACCTGCTCT 59.822 55.000 0.00 0.00 0.00 4.09
1327 1388 1.937278 CTGTGCTCATACCTGCTCTG 58.063 55.000 0.00 0.00 0.00 3.35
1328 1389 0.107993 TGTGCTCATACCTGCTCTGC 60.108 55.000 0.00 0.00 0.00 4.26
1329 1390 0.177604 GTGCTCATACCTGCTCTGCT 59.822 55.000 0.00 0.00 0.00 4.24
1330 1391 0.463204 TGCTCATACCTGCTCTGCTC 59.537 55.000 0.00 0.00 0.00 4.26
1334 1395 1.760086 ATACCTGCTCTGCTCGCCT 60.760 57.895 0.00 0.00 0.00 5.52
1493 1554 3.941657 GAGGGAGCTGTGCGTGGAC 62.942 68.421 0.00 0.00 0.00 4.02
1730 1791 0.899717 GTGGCAAGGATTCAAGCCCA 60.900 55.000 4.44 0.00 46.45 5.36
1802 1883 2.742372 CGTGCCGTTCCCCTTCTG 60.742 66.667 0.00 0.00 0.00 3.02
1941 2041 4.631131 TGCTAATATGACCGTCTGATTGG 58.369 43.478 0.00 3.17 0.00 3.16
2011 2111 8.573035 TGTGTTTTTCTAAAGTGGGTTCATATC 58.427 33.333 0.00 0.00 0.00 1.63
2401 2501 0.881796 CTATACATCTGCTCGCCGGA 59.118 55.000 5.05 0.00 0.00 5.14
2415 2515 0.180406 GCCGGACCCTCATATGTTGT 59.820 55.000 5.05 0.00 0.00 3.32
2431 2531 2.276201 GTTGTGCCGCACATCTACATA 58.724 47.619 26.22 7.36 44.16 2.29
2441 2541 5.050091 CCGCACATCTACATACCTCAAATTC 60.050 44.000 0.00 0.00 0.00 2.17
2461 2570 2.026641 CCGTTCCTCAAATCCATGCAT 58.973 47.619 0.00 0.00 0.00 3.96
2472 2581 5.941647 TCAAATCCATGCATGTCGATCATAT 59.058 36.000 24.58 4.34 34.67 1.78
2533 2642 6.421801 AGCAAAGCAAATCATAGTTGAACAAC 59.578 34.615 9.33 9.33 41.45 3.32
2535 2644 6.655078 AAGCAAATCATAGTTGAACAACCT 57.345 33.333 13.07 4.94 42.06 3.50
2543 2652 7.004555 TCATAGTTGAACAACCTAGACATGT 57.995 36.000 13.07 0.00 42.06 3.21
2561 2670 8.752766 AGACATGTCAAAATGAAATCAATGTC 57.247 30.769 27.02 11.46 0.00 3.06
2571 2680 2.315925 AATCAATGTCCGAGCGTGAT 57.684 45.000 0.00 0.00 0.00 3.06
2583 2692 1.228063 GCGTGATGGATGGCCTCAT 60.228 57.895 3.32 5.34 36.09 2.90
2594 2703 0.752658 TGGCCTCATATCACTGACCG 59.247 55.000 3.32 0.00 0.00 4.79
2612 2721 2.496817 GGCACCTACTCCGAGCAG 59.503 66.667 0.00 0.00 0.00 4.24
2613 2722 2.052690 GGCACCTACTCCGAGCAGA 61.053 63.158 0.00 0.00 0.00 4.26
2614 2723 1.605058 GGCACCTACTCCGAGCAGAA 61.605 60.000 0.00 0.00 0.00 3.02
2615 2724 0.461961 GCACCTACTCCGAGCAGAAT 59.538 55.000 0.00 0.00 0.00 2.40
2616 2725 1.681793 GCACCTACTCCGAGCAGAATA 59.318 52.381 0.00 0.00 0.00 1.75
2617 2726 2.544069 GCACCTACTCCGAGCAGAATAC 60.544 54.545 0.00 0.00 0.00 1.89
2618 2727 1.948145 ACCTACTCCGAGCAGAATACG 59.052 52.381 0.00 0.00 0.00 3.06
2619 2728 1.948145 CCTACTCCGAGCAGAATACGT 59.052 52.381 0.00 0.00 0.00 3.57
2620 2729 2.031857 CCTACTCCGAGCAGAATACGTC 60.032 54.545 0.00 0.00 0.00 4.34
2621 2730 0.377554 ACTCCGAGCAGAATACGTCG 59.622 55.000 0.00 0.00 0.00 5.12
2622 2731 0.377554 CTCCGAGCAGAATACGTCGT 59.622 55.000 2.21 2.21 0.00 4.34
2623 2732 0.098200 TCCGAGCAGAATACGTCGTG 59.902 55.000 8.47 0.00 0.00 4.35
2624 2733 0.179171 CCGAGCAGAATACGTCGTGT 60.179 55.000 8.47 0.00 0.00 4.49
2625 2734 1.614385 CGAGCAGAATACGTCGTGTT 58.386 50.000 8.47 7.75 0.00 3.32
2626 2735 1.983605 CGAGCAGAATACGTCGTGTTT 59.016 47.619 8.47 1.36 0.00 2.83
2627 2736 2.026507 CGAGCAGAATACGTCGTGTTTC 59.973 50.000 8.47 10.97 0.00 2.78
2628 2737 2.984471 GAGCAGAATACGTCGTGTTTCA 59.016 45.455 18.98 0.00 0.00 2.69
2629 2738 2.987149 AGCAGAATACGTCGTGTTTCAG 59.013 45.455 18.98 14.27 0.00 3.02
2630 2739 2.092211 GCAGAATACGTCGTGTTTCAGG 59.908 50.000 18.98 13.58 0.00 3.86
2631 2740 2.092211 CAGAATACGTCGTGTTTCAGGC 59.908 50.000 18.98 4.64 0.00 4.85
2632 2741 1.058695 GAATACGTCGTGTTTCAGGCG 59.941 52.381 8.47 0.00 0.00 5.52
2651 2760 0.454600 GGAATACGTCGTGCTCCAGA 59.545 55.000 17.96 0.00 0.00 3.86
2676 2785 2.191513 GCGTCATGCCCATGCTCAT 61.192 57.895 3.41 0.00 38.65 2.90
2692 2801 2.813908 ATTCACGCCCGAACGAGC 60.814 61.111 4.02 0.00 36.70 5.03
2694 2803 1.940883 ATTCACGCCCGAACGAGCTA 61.941 55.000 4.02 0.00 36.70 3.32
2696 2805 4.125695 ACGCCCGAACGAGCTACC 62.126 66.667 4.02 0.00 36.70 3.18
2712 2821 2.031420 GCTACCGCGAGTCACATACATA 60.031 50.000 8.23 0.00 0.00 2.29
2713 2822 3.549423 GCTACCGCGAGTCACATACATAA 60.549 47.826 8.23 0.00 0.00 1.90
2715 2824 3.184541 ACCGCGAGTCACATACATAAAC 58.815 45.455 8.23 0.00 0.00 2.01
2717 2826 3.183754 CGCGAGTCACATACATAAACCA 58.816 45.455 0.00 0.00 0.00 3.67
2718 2827 3.000078 CGCGAGTCACATACATAAACCAC 60.000 47.826 0.00 0.00 0.00 4.16
2720 2829 5.345702 GCGAGTCACATACATAAACCACTA 58.654 41.667 0.00 0.00 0.00 2.74
2726 2835 6.202954 GTCACATACATAAACCACTAGCATCC 59.797 42.308 0.00 0.00 0.00 3.51
2734 2843 4.530857 ACTAGCATCCGCGTGGGC 62.531 66.667 16.49 11.85 45.49 5.36
2778 2888 1.902508 TCGCCTTGAATTCTCCTCTGT 59.097 47.619 7.05 0.00 0.00 3.41
2786 2896 3.054139 TGAATTCTCCTCTGTCCCAATGG 60.054 47.826 7.05 0.00 0.00 3.16
2798 2908 3.277133 CAATGGGGTTGGACAGCG 58.723 61.111 0.00 0.00 34.06 5.18
2805 2915 0.035820 GGGTTGGACAGCGTAATCCA 60.036 55.000 0.20 0.20 43.42 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.340453 ATTTCGCCATGGACGCATGC 62.340 55.000 18.40 7.91 0.00 4.06
12 13 0.101040 AATTTCGCCATGGACGCATG 59.899 50.000 18.40 0.00 0.00 4.06
13 14 0.381801 GAATTTCGCCATGGACGCAT 59.618 50.000 18.40 10.88 0.00 4.73
14 15 1.800032 GAATTTCGCCATGGACGCA 59.200 52.632 18.40 6.36 0.00 5.24
15 16 1.297598 CGAATTTCGCCATGGACGC 60.298 57.895 18.40 0.00 31.14 5.19
16 17 4.974468 CGAATTTCGCCATGGACG 57.026 55.556 18.40 18.60 31.14 4.79
51 52 3.217743 CTCCGCCTCCTACGACCC 61.218 72.222 0.00 0.00 0.00 4.46
52 53 2.124403 TCTCCGCCTCCTACGACC 60.124 66.667 0.00 0.00 0.00 4.79
53 54 2.188161 CCTCTCCGCCTCCTACGAC 61.188 68.421 0.00 0.00 0.00 4.34
54 55 2.192443 CCTCTCCGCCTCCTACGA 59.808 66.667 0.00 0.00 0.00 3.43
55 56 2.905935 TTCCCTCTCCGCCTCCTACG 62.906 65.000 0.00 0.00 0.00 3.51
56 57 1.076192 TTCCCTCTCCGCCTCCTAC 60.076 63.158 0.00 0.00 0.00 3.18
57 58 1.230497 CTTCCCTCTCCGCCTCCTA 59.770 63.158 0.00 0.00 0.00 2.94
58 59 2.042435 CTTCCCTCTCCGCCTCCT 60.042 66.667 0.00 0.00 0.00 3.69
59 60 2.042843 TCTTCCCTCTCCGCCTCC 60.043 66.667 0.00 0.00 0.00 4.30
60 61 1.380650 ACTCTTCCCTCTCCGCCTC 60.381 63.158 0.00 0.00 0.00 4.70
61 62 1.684049 CACTCTTCCCTCTCCGCCT 60.684 63.158 0.00 0.00 0.00 5.52
62 63 2.896443 CACTCTTCCCTCTCCGCC 59.104 66.667 0.00 0.00 0.00 6.13
63 64 2.185608 GCACTCTTCCCTCTCCGC 59.814 66.667 0.00 0.00 0.00 5.54
64 65 2.046864 TCGCACTCTTCCCTCTCCG 61.047 63.158 0.00 0.00 0.00 4.63
65 66 1.513622 GTCGCACTCTTCCCTCTCC 59.486 63.158 0.00 0.00 0.00 3.71
66 67 1.137825 CGTCGCACTCTTCCCTCTC 59.862 63.158 0.00 0.00 0.00 3.20
67 68 2.995872 GCGTCGCACTCTTCCCTCT 61.996 63.158 13.44 0.00 0.00 3.69
68 69 2.507324 GCGTCGCACTCTTCCCTC 60.507 66.667 13.44 0.00 0.00 4.30
69 70 4.421479 CGCGTCGCACTCTTCCCT 62.421 66.667 18.75 0.00 0.00 4.20
70 71 4.415332 TCGCGTCGCACTCTTCCC 62.415 66.667 18.75 0.00 0.00 3.97
71 72 2.876645 CTCGCGTCGCACTCTTCC 60.877 66.667 18.75 0.00 0.00 3.46
72 73 3.537297 GCTCGCGTCGCACTCTTC 61.537 66.667 18.75 0.00 0.00 2.87
109 110 1.928706 TATTTGGTGCGCCCGCTTTC 61.929 55.000 15.15 4.68 42.51 2.62
110 111 1.974343 TATTTGGTGCGCCCGCTTT 60.974 52.632 15.15 0.00 42.51 3.51
111 112 2.360600 TATTTGGTGCGCCCGCTT 60.361 55.556 15.15 0.00 42.51 4.68
112 113 3.131478 GTATTTGGTGCGCCCGCT 61.131 61.111 15.15 0.00 42.51 5.52
113 114 3.436055 TGTATTTGGTGCGCCCGC 61.436 61.111 15.15 5.60 42.35 6.13
114 115 2.483288 GTGTATTTGGTGCGCCCG 59.517 61.111 15.15 0.00 35.15 6.13
115 116 2.882132 GGTGTATTTGGTGCGCCC 59.118 61.111 15.15 6.44 37.14 6.13
116 117 2.483288 CGGTGTATTTGGTGCGCC 59.517 61.111 10.11 10.11 39.45 6.53
117 118 2.202427 GCGGTGTATTTGGTGCGC 60.202 61.111 0.00 0.00 0.00 6.09
118 119 2.097538 CGCGGTGTATTTGGTGCG 59.902 61.111 0.00 0.00 39.57 5.34
119 120 2.202427 GCGCGGTGTATTTGGTGC 60.202 61.111 8.83 0.00 0.00 5.01
120 121 2.097538 CGCGCGGTGTATTTGGTG 59.902 61.111 24.84 0.00 0.00 4.17
121 122 3.122323 CCGCGCGGTGTATTTGGT 61.122 61.111 39.71 0.00 0.00 3.67
122 123 3.871574 CCCGCGCGGTGTATTTGG 61.872 66.667 43.12 24.12 0.00 3.28
123 124 0.876777 TATCCCGCGCGGTGTATTTG 60.877 55.000 43.12 27.71 0.00 2.32
124 125 0.599204 CTATCCCGCGCGGTGTATTT 60.599 55.000 43.12 23.92 0.00 1.40
125 126 1.006571 CTATCCCGCGCGGTGTATT 60.007 57.895 43.12 25.58 0.00 1.89
126 127 2.649034 CTATCCCGCGCGGTGTAT 59.351 61.111 43.12 33.19 0.00 2.29
127 128 4.274700 GCTATCCCGCGCGGTGTA 62.275 66.667 43.12 32.23 0.00 2.90
151 152 4.204891 CGAATTGGACGCGCGGTC 62.205 66.667 35.22 26.18 45.31 4.79
152 153 4.960497 TATAACGAATTGGACGCGCGGT 62.960 50.000 35.22 19.76 0.00 5.68
153 154 1.758319 ATAACGAATTGGACGCGCGG 61.758 55.000 35.22 15.89 0.00 6.46
154 155 0.847670 TATAACGAATTGGACGCGCG 59.152 50.000 30.96 30.96 0.00 6.86
155 156 1.396815 GCTATAACGAATTGGACGCGC 60.397 52.381 5.73 0.00 0.00 6.86
156 157 1.136992 CGCTATAACGAATTGGACGCG 60.137 52.381 3.53 3.53 34.06 6.01
157 158 1.396815 GCGCTATAACGAATTGGACGC 60.397 52.381 0.00 0.00 36.82 5.19
158 159 1.136992 CGCGCTATAACGAATTGGACG 60.137 52.381 5.56 0.00 34.06 4.79
159 160 1.396815 GCGCGCTATAACGAATTGGAC 60.397 52.381 26.67 0.00 34.06 4.02
160 161 0.856641 GCGCGCTATAACGAATTGGA 59.143 50.000 26.67 0.00 34.06 3.53
161 162 0.579630 TGCGCGCTATAACGAATTGG 59.420 50.000 33.29 0.00 34.06 3.16
162 163 2.096958 TCATGCGCGCTATAACGAATTG 60.097 45.455 33.29 12.93 34.06 2.32
163 164 2.131972 TCATGCGCGCTATAACGAATT 58.868 42.857 33.29 0.93 34.06 2.17
164 165 1.778334 TCATGCGCGCTATAACGAAT 58.222 45.000 33.29 11.87 34.06 3.34
165 166 1.778334 ATCATGCGCGCTATAACGAA 58.222 45.000 33.29 9.65 34.06 3.85
166 167 1.778334 AATCATGCGCGCTATAACGA 58.222 45.000 33.29 18.31 34.06 3.85
167 168 2.577300 AAATCATGCGCGCTATAACG 57.423 45.000 33.29 13.58 0.00 3.18
168 169 3.121696 GCAAAAATCATGCGCGCTATAAC 60.122 43.478 33.29 1.73 33.57 1.89
169 170 3.042189 GCAAAAATCATGCGCGCTATAA 58.958 40.909 33.29 12.75 33.57 0.98
170 171 2.032675 TGCAAAAATCATGCGCGCTATA 59.967 40.909 33.29 17.28 46.76 1.31
171 172 1.202279 TGCAAAAATCATGCGCGCTAT 60.202 42.857 33.29 20.49 46.76 2.97
172 173 0.169894 TGCAAAAATCATGCGCGCTA 59.830 45.000 33.29 19.04 46.76 4.26
173 174 1.080637 TGCAAAAATCATGCGCGCT 60.081 47.368 33.29 15.19 46.76 5.92
174 175 1.057668 GTGCAAAAATCATGCGCGC 59.942 52.632 27.26 27.26 46.76 6.86
176 177 1.057668 GCGTGCAAAAATCATGCGC 59.942 52.632 0.00 0.00 46.76 6.09
177 178 1.685640 GGGCGTGCAAAAATCATGCG 61.686 55.000 0.00 0.00 46.76 4.73
178 179 1.685640 CGGGCGTGCAAAAATCATGC 61.686 55.000 0.00 0.00 43.66 4.06
179 180 1.685640 GCGGGCGTGCAAAAATCATG 61.686 55.000 0.00 0.00 34.15 3.07
180 181 1.445926 GCGGGCGTGCAAAAATCAT 60.446 52.632 0.00 0.00 34.15 2.45
181 182 2.049618 GCGGGCGTGCAAAAATCA 60.050 55.556 0.00 0.00 34.15 2.57
182 183 2.088178 CAGCGGGCGTGCAAAAATC 61.088 57.895 3.15 0.00 37.31 2.17
183 184 2.049248 CAGCGGGCGTGCAAAAAT 60.049 55.556 3.15 0.00 37.31 1.82
184 185 4.277593 CCAGCGGGCGTGCAAAAA 62.278 61.111 3.15 0.00 37.31 1.94
226 227 2.918600 CCGCAAATTAGGCCGTTTTAAC 59.081 45.455 0.00 0.00 0.00 2.01
227 228 3.219052 CCGCAAATTAGGCCGTTTTAA 57.781 42.857 0.00 0.00 0.00 1.52
228 229 2.923605 CCGCAAATTAGGCCGTTTTA 57.076 45.000 0.00 0.00 0.00 1.52
229 230 3.804601 CCGCAAATTAGGCCGTTTT 57.195 47.368 0.00 0.00 0.00 2.43
236 237 4.905193 GCCGCGCCGCAAATTAGG 62.905 66.667 15.97 1.30 0.00 2.69
255 256 0.370273 CAACAGCCGCGCTAAACTAG 59.630 55.000 5.56 0.00 36.40 2.57
256 257 1.017177 CCAACAGCCGCGCTAAACTA 61.017 55.000 5.56 0.00 36.40 2.24
257 258 2.325082 CCAACAGCCGCGCTAAACT 61.325 57.895 5.56 0.00 36.40 2.66
258 259 2.175811 CCAACAGCCGCGCTAAAC 59.824 61.111 5.56 0.00 36.40 2.01
259 260 2.031314 TCCAACAGCCGCGCTAAA 59.969 55.556 5.56 0.00 36.40 1.85
260 261 2.238847 ATCTCCAACAGCCGCGCTAA 62.239 55.000 5.56 0.00 36.40 3.09
261 262 2.721167 ATCTCCAACAGCCGCGCTA 61.721 57.895 5.56 0.00 36.40 4.26
262 263 4.087892 ATCTCCAACAGCCGCGCT 62.088 61.111 5.56 0.00 40.77 5.92
263 264 3.869272 CATCTCCAACAGCCGCGC 61.869 66.667 0.00 0.00 0.00 6.86
264 265 3.869272 GCATCTCCAACAGCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
265 266 2.437359 AGCATCTCCAACAGCCGC 60.437 61.111 0.00 0.00 0.00 6.53
266 267 3.805267 GAGCATCTCCAACAGCCG 58.195 61.111 0.00 0.00 0.00 5.52
277 278 4.158394 TGTGGATTTTGCCTTTAGAGCATC 59.842 41.667 0.00 0.00 40.59 3.91
278 279 4.088634 TGTGGATTTTGCCTTTAGAGCAT 58.911 39.130 0.00 0.00 40.59 3.79
279 280 3.495331 TGTGGATTTTGCCTTTAGAGCA 58.505 40.909 0.00 0.00 38.81 4.26
280 281 3.674410 GCTGTGGATTTTGCCTTTAGAGC 60.674 47.826 0.00 0.00 0.00 4.09
281 282 3.507233 TGCTGTGGATTTTGCCTTTAGAG 59.493 43.478 0.00 0.00 0.00 2.43
282 283 3.495331 TGCTGTGGATTTTGCCTTTAGA 58.505 40.909 0.00 0.00 0.00 2.10
283 284 3.940209 TGCTGTGGATTTTGCCTTTAG 57.060 42.857 0.00 0.00 0.00 1.85
284 285 4.630111 CTTTGCTGTGGATTTTGCCTTTA 58.370 39.130 0.00 0.00 0.00 1.85
285 286 3.469739 CTTTGCTGTGGATTTTGCCTTT 58.530 40.909 0.00 0.00 0.00 3.11
286 287 2.807837 GCTTTGCTGTGGATTTTGCCTT 60.808 45.455 0.00 0.00 0.00 4.35
287 288 1.270465 GCTTTGCTGTGGATTTTGCCT 60.270 47.619 0.00 0.00 0.00 4.75
288 289 1.150827 GCTTTGCTGTGGATTTTGCC 58.849 50.000 0.00 0.00 0.00 4.52
289 290 0.785979 CGCTTTGCTGTGGATTTTGC 59.214 50.000 0.00 0.00 0.00 3.68
290 291 1.000385 TCCGCTTTGCTGTGGATTTTG 60.000 47.619 3.73 0.00 41.18 2.44
313 314 0.461339 ACACGCTCTCAACGTTTGGT 60.461 50.000 0.00 0.00 42.96 3.67
333 334 1.824852 GGTGGAACAGGCCTAAAATGG 59.175 52.381 3.98 0.00 41.80 3.16
359 360 0.387622 CTTGGCAGCATGTTGGAACG 60.388 55.000 11.80 0.00 39.31 3.95
484 485 1.066858 GTTGAGATGACCAGAGCGGAA 60.067 52.381 0.00 0.00 38.63 4.30
496 497 3.429822 GGAAATGGTGCATGGTTGAGATG 60.430 47.826 0.00 0.00 0.00 2.90
602 608 2.159819 TTGTGCTGTCTCCTCCTCGC 62.160 60.000 0.00 0.00 0.00 5.03
751 758 0.611896 GATGGGGTGTTGGGGTTCAG 60.612 60.000 0.00 0.00 0.00 3.02
827 836 5.817816 GGTGAGAAAATATATATCTGCCCCG 59.182 44.000 5.85 0.00 0.00 5.73
842 851 4.933400 GGTGACGCTTTATAGGTGAGAAAA 59.067 41.667 0.00 0.00 0.00 2.29
874 886 2.168621 CGCGCGCAGATATTTCGG 59.831 61.111 32.61 6.38 0.00 4.30
944 980 1.447489 CTGTTCCTGCTCTGCTCGG 60.447 63.158 0.00 0.00 0.00 4.63
945 981 2.099431 GCTGTTCCTGCTCTGCTCG 61.099 63.158 0.00 0.00 0.00 5.03
946 982 2.099431 CGCTGTTCCTGCTCTGCTC 61.099 63.158 0.00 0.00 0.00 4.26
947 983 2.047465 CGCTGTTCCTGCTCTGCT 60.047 61.111 0.00 0.00 0.00 4.24
948 984 2.047844 TCGCTGTTCCTGCTCTGC 60.048 61.111 0.00 0.00 0.00 4.26
949 985 2.099431 GCTCGCTGTTCCTGCTCTG 61.099 63.158 0.00 0.00 0.00 3.35
950 986 2.264166 GCTCGCTGTTCCTGCTCT 59.736 61.111 0.00 0.00 0.00 4.09
951 987 3.184683 CGCTCGCTGTTCCTGCTC 61.185 66.667 0.00 0.00 0.00 4.26
952 988 4.749310 CCGCTCGCTGTTCCTGCT 62.749 66.667 0.00 0.00 0.00 4.24
989 1026 0.250513 GCTTCCCATGGACGAAGAGT 59.749 55.000 26.19 0.00 38.18 3.24
1062 1102 2.096218 GCTGACCATGTGAAACGTCTTC 60.096 50.000 0.00 0.00 42.39 2.87
1215 1255 1.347320 GTACGTAGGTGTTGAGCTGC 58.653 55.000 0.00 0.00 0.00 5.25
1291 1341 1.102809 CAGCCACAACAACCTGAGCA 61.103 55.000 0.00 0.00 0.00 4.26
1293 1343 0.664761 CACAGCCACAACAACCTGAG 59.335 55.000 0.00 0.00 0.00 3.35
1298 1348 0.670162 ATGAGCACAGCCACAACAAC 59.330 50.000 0.00 0.00 0.00 3.32
1300 1350 1.522668 GTATGAGCACAGCCACAACA 58.477 50.000 0.00 0.00 0.00 3.33
1301 1351 0.804989 GGTATGAGCACAGCCACAAC 59.195 55.000 3.33 0.00 0.00 3.32
1308 1369 1.937278 CAGAGCAGGTATGAGCACAG 58.063 55.000 0.00 0.00 0.00 3.66
1334 1395 2.165167 CCCTGAGATCAAAGCAGCAAA 58.835 47.619 0.00 0.00 0.00 3.68
1489 1550 2.636412 CGCACCTCCTCTTCGTCCA 61.636 63.158 0.00 0.00 0.00 4.02
1493 1554 4.148825 CCCCGCACCTCCTCTTCG 62.149 72.222 0.00 0.00 0.00 3.79
1730 1791 1.867919 CGATCCGCCGCCTCTTATCT 61.868 60.000 0.00 0.00 0.00 1.98
1802 1883 3.983044 AGAACACCTGTCCCAGATTAC 57.017 47.619 0.00 0.00 32.44 1.89
1924 2024 1.873903 GCGCCAATCAGACGGTCATAT 60.874 52.381 11.27 0.13 0.00 1.78
1925 2025 0.529773 GCGCCAATCAGACGGTCATA 60.530 55.000 11.27 0.00 0.00 2.15
1926 2026 1.815421 GCGCCAATCAGACGGTCAT 60.815 57.895 11.27 0.00 0.00 3.06
1941 2041 0.744874 TGGAGTGACTACTATGGCGC 59.255 55.000 0.00 0.00 37.25 6.53
1994 2094 5.510861 CGGGGTAGATATGAACCCACTTTAG 60.511 48.000 19.30 4.50 44.01 1.85
2394 2494 1.046472 AACATATGAGGGTCCGGCGA 61.046 55.000 9.30 0.00 0.00 5.54
2395 2495 0.880278 CAACATATGAGGGTCCGGCG 60.880 60.000 10.38 0.00 0.00 6.46
2401 2501 0.748005 GCGGCACAACATATGAGGGT 60.748 55.000 10.38 1.29 0.00 4.34
2415 2515 1.068588 GAGGTATGTAGATGTGCGGCA 59.931 52.381 0.00 0.00 0.00 5.69
2431 2531 3.502123 TTGAGGAACGGAATTTGAGGT 57.498 42.857 0.00 0.00 0.00 3.85
2441 2541 1.462616 TGCATGGATTTGAGGAACGG 58.537 50.000 0.00 0.00 0.00 4.44
2533 2642 9.297586 CATTGATTTCATTTTGACATGTCTAGG 57.702 33.333 25.55 13.08 0.00 3.02
2535 2644 9.844790 GACATTGATTTCATTTTGACATGTCTA 57.155 29.630 25.55 16.43 33.07 2.59
2543 2652 5.401550 GCTCGGACATTGATTTCATTTTGA 58.598 37.500 0.00 0.00 0.00 2.69
2561 2670 2.969238 GCCATCCATCACGCTCGG 60.969 66.667 0.00 0.00 0.00 4.63
2571 2680 2.369860 GTCAGTGATATGAGGCCATCCA 59.630 50.000 5.01 0.00 34.31 3.41
2583 2692 0.032912 TAGGTGCCCGGTCAGTGATA 60.033 55.000 0.00 0.00 0.00 2.15
2594 2703 3.075005 TGCTCGGAGTAGGTGCCC 61.075 66.667 6.90 0.00 0.00 5.36
2602 2711 0.377554 CGACGTATTCTGCTCGGAGT 59.622 55.000 6.90 0.00 0.00 3.85
2611 2720 2.334838 GCCTGAAACACGACGTATTCT 58.665 47.619 19.98 1.59 0.00 2.40
2612 2721 1.058695 CGCCTGAAACACGACGTATTC 59.941 52.381 15.18 15.18 0.00 1.75
2613 2722 1.065358 CGCCTGAAACACGACGTATT 58.935 50.000 0.00 0.00 0.00 1.89
2614 2723 0.734942 CCGCCTGAAACACGACGTAT 60.735 55.000 0.00 0.00 0.00 3.06
2615 2724 1.372004 CCGCCTGAAACACGACGTA 60.372 57.895 0.00 0.00 0.00 3.57
2616 2725 2.632136 TTCCGCCTGAAACACGACGT 62.632 55.000 0.00 0.00 0.00 4.34
2617 2726 1.289109 ATTCCGCCTGAAACACGACG 61.289 55.000 0.00 0.00 36.33 5.12
2618 2727 1.392510 GTATTCCGCCTGAAACACGAC 59.607 52.381 0.00 0.00 36.33 4.34
2619 2728 1.717194 GTATTCCGCCTGAAACACGA 58.283 50.000 0.00 0.00 36.33 4.35
2620 2729 0.368907 CGTATTCCGCCTGAAACACG 59.631 55.000 6.70 6.70 38.37 4.49
2621 2730 1.392510 GACGTATTCCGCCTGAAACAC 59.607 52.381 0.00 0.00 41.42 3.32
2622 2731 1.717194 GACGTATTCCGCCTGAAACA 58.283 50.000 0.00 0.00 41.42 2.83
2623 2732 0.643820 CGACGTATTCCGCCTGAAAC 59.356 55.000 0.00 0.00 41.42 2.78
2624 2733 0.244450 ACGACGTATTCCGCCTGAAA 59.756 50.000 0.00 0.00 41.42 2.69
2625 2734 0.457166 CACGACGTATTCCGCCTGAA 60.457 55.000 0.00 0.00 41.42 3.02
2626 2735 1.138036 CACGACGTATTCCGCCTGA 59.862 57.895 0.00 0.00 41.42 3.86
2627 2736 2.514013 GCACGACGTATTCCGCCTG 61.514 63.158 0.00 0.00 41.42 4.85
2628 2737 2.202703 GCACGACGTATTCCGCCT 60.203 61.111 0.00 0.00 41.42 5.52
2629 2738 2.202703 AGCACGACGTATTCCGCC 60.203 61.111 0.00 0.00 41.42 6.13
2630 2739 2.228914 GGAGCACGACGTATTCCGC 61.229 63.158 12.49 6.66 41.42 5.54
2631 2740 0.866061 CTGGAGCACGACGTATTCCG 60.866 60.000 19.21 12.88 44.03 4.30
2632 2741 0.454600 TCTGGAGCACGACGTATTCC 59.545 55.000 18.25 18.25 0.00 3.01
2676 2785 2.628696 TAGCTCGTTCGGGCGTGAA 61.629 57.895 11.35 0.00 0.00 3.18
2692 2801 2.776312 ATGTATGTGACTCGCGGTAG 57.224 50.000 6.13 0.00 0.00 3.18
2694 2803 3.184541 GTTTATGTATGTGACTCGCGGT 58.815 45.455 6.13 2.39 0.00 5.68
2696 2805 3.000078 GTGGTTTATGTATGTGACTCGCG 60.000 47.826 0.00 0.00 0.00 5.87
2712 2821 1.019278 CACGCGGATGCTAGTGGTTT 61.019 55.000 12.47 0.00 39.65 3.27
2713 2822 1.447838 CACGCGGATGCTAGTGGTT 60.448 57.895 12.47 0.00 39.65 3.67
2715 2824 2.586079 CCACGCGGATGCTAGTGG 60.586 66.667 12.47 12.10 43.22 4.00
2717 2826 4.530857 GCCCACGCGGATGCTAGT 62.531 66.667 12.47 0.00 39.65 2.57
2736 2845 0.735471 GGCCATTTCGGAGAGCTTTC 59.265 55.000 0.00 0.00 38.43 2.62
2764 2874 3.054139 CCATTGGGACAGAGGAGAATTCA 60.054 47.826 8.44 0.00 42.39 2.57
2786 2896 0.035820 TGGATTACGCTGTCCAACCC 60.036 55.000 1.21 0.00 41.36 4.11


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

AutoCloner maintained by Alex Coulton.