Multiple sequence alignment - TraesCS2B01G273300

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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 TraesCS2B01G273300 chr2B 100.000 4692 0 0 2075 6766 374678755 374683446 0.000000e+00 8665.0
1 TraesCS2B01G273300 chr2B 100.000 1859 0 0 1 1859 374676681 374678539 0.000000e+00 3434.0
2 TraesCS2B01G273300 chr2B 90.000 240 21 3 234 472 210653988 210654225 2.370000e-79 307.0
3 TraesCS2B01G273300 chr2B 80.982 163 28 3 2094 2254 525823939 525823778 7.120000e-25 126.0
4 TraesCS2B01G273300 chr2B 100.000 30 0 0 6270 6299 556190226 556190197 1.000000e-03 56.5
5 TraesCS2B01G273300 chr2D 95.521 3617 113 11 3165 6766 306484763 306488345 0.000000e+00 5736.0
6 TraesCS2B01G273300 chr2D 95.095 1366 43 14 464 1812 306482784 306484142 0.000000e+00 2130.0
7 TraesCS2B01G273300 chr2D 95.708 233 4 4 1 230 306482562 306482791 2.980000e-98 370.0
8 TraesCS2B01G273300 chr2D 90.254 236 21 2 234 468 200810110 200810344 2.370000e-79 307.0
9 TraesCS2B01G273300 chr2A 95.115 2989 98 17 3256 6229 385976473 385979428 0.000000e+00 4667.0
10 TraesCS2B01G273300 chr2A 93.806 1114 51 12 741 1847 385974675 385975777 0.000000e+00 1659.0
11 TraesCS2B01G273300 chr2A 94.966 437 19 3 6331 6766 385979474 385979908 0.000000e+00 682.0
12 TraesCS2B01G273300 chr2A 95.238 231 8 2 3 230 385970104 385970334 4.990000e-96 363.0
13 TraesCS2B01G273300 chr2A 90.217 276 23 3 464 735 385970327 385970602 2.320000e-94 357.0
14 TraesCS2B01G273300 chr2A 95.775 71 3 0 6263 6333 385979429 385979499 1.540000e-21 115.0
15 TraesCS2B01G273300 chr2A 87.778 90 9 1 6064 6151 524333404 524333493 3.340000e-18 104.0
16 TraesCS2B01G273300 chr2A 82.667 75 9 3 6344 6418 587277815 587277885 5.660000e-06 63.9
17 TraesCS2B01G273300 chr6D 80.995 1105 174 27 2094 3175 331537868 331538959 0.000000e+00 845.0
18 TraesCS2B01G273300 chr6D 81.153 1093 164 20 2101 3163 389704934 389706014 0.000000e+00 839.0
19 TraesCS2B01G273300 chr6D 87.500 88 9 1 6064 6149 90111817 90111904 4.320000e-17 100.0
20 TraesCS2B01G273300 chr6D 84.286 70 11 0 6270 6339 429020840 429020909 1.220000e-07 69.4
21 TraesCS2B01G273300 chr3B 80.905 1105 172 24 2099 3175 201992827 201993920 0.000000e+00 835.0
22 TraesCS2B01G273300 chr3A 80.888 1104 173 26 2098 3175 715578290 715579381 0.000000e+00 835.0
23 TraesCS2B01G273300 chr7B 80.622 1125 165 27 2096 3175 363222289 363223405 0.000000e+00 821.0
24 TraesCS2B01G273300 chr7B 80.492 1056 165 26 2157 3183 729235100 729234057 0.000000e+00 771.0
25 TraesCS2B01G273300 chr7B 84.043 94 13 1 6056 6149 450642204 450642113 9.350000e-14 89.8
26 TraesCS2B01G273300 chr7B 85.227 88 8 4 6064 6146 210863478 210863391 1.210000e-12 86.1
27 TraesCS2B01G273300 chr1A 80.651 1106 173 26 2099 3175 539708779 539709872 0.000000e+00 819.0
28 TraesCS2B01G273300 chr1A 78.345 1039 185 18 2159 3174 561648154 561647133 2.660000e-178 636.0
29 TraesCS2B01G273300 chr1A 86.667 75 9 1 6345 6419 545537459 545537532 1.560000e-11 82.4
30 TraesCS2B01G273300 chr3D 80.381 1101 177 24 2101 3175 518131199 518132286 0.000000e+00 800.0
31 TraesCS2B01G273300 chr3D 80.183 1090 181 18 2110 3173 584688141 584687061 0.000000e+00 784.0
32 TraesCS2B01G273300 chr3D 81.125 800 129 12 2394 3175 478422771 478423566 7.450000e-174 621.0
33 TraesCS2B01G273300 chr3D 90.909 231 20 1 237 466 282684139 282684369 6.590000e-80 309.0
34 TraesCS2B01G273300 chr3D 79.730 370 57 13 2099 2460 326117129 326116770 1.130000e-62 252.0
35 TraesCS2B01G273300 chr3D 79.670 182 32 5 2100 2279 268057340 268057518 7.120000e-25 126.0
36 TraesCS2B01G273300 chrUn 79.783 1108 185 24 2093 3173 349628243 349629338 0.000000e+00 769.0
37 TraesCS2B01G273300 chrUn 79.208 1111 183 25 2099 3173 290539033 290537935 0.000000e+00 730.0
38 TraesCS2B01G273300 chr7D 79.636 1100 187 19 2099 3173 16200290 16201377 0.000000e+00 756.0
39 TraesCS2B01G273300 chr7D 80.328 793 120 20 2099 2865 21712352 21711570 9.850000e-158 568.0
40 TraesCS2B01G273300 chr7D 82.077 597 81 16 2095 2676 60368227 60368812 2.840000e-133 486.0
41 TraesCS2B01G273300 chr7D 91.739 230 18 1 238 466 484967451 484967222 1.090000e-82 318.0
42 TraesCS2B01G273300 chr7D 90.909 231 19 2 236 465 432329214 432329443 6.590000e-80 309.0
43 TraesCS2B01G273300 chr7D 90.909 231 20 1 239 468 535881153 535881383 6.590000e-80 309.0
44 TraesCS2B01G273300 chr7D 96.875 32 1 0 6270 6301 59415082 59415113 3.000000e-03 54.7
45 TraesCS2B01G273300 chr6B 79.599 1098 188 18 2110 3184 132895936 132897020 0.000000e+00 754.0
46 TraesCS2B01G273300 chr6B 86.296 270 32 5 201 468 699977590 699977856 8.590000e-74 289.0
47 TraesCS2B01G273300 chr6B 100.000 35 0 0 6270 6304 646254526 646254560 1.580000e-06 65.8
48 TraesCS2B01G273300 chr5D 80.253 1028 168 19 2099 3100 310557474 310556456 0.000000e+00 741.0
49 TraesCS2B01G273300 chr5D 80.225 799 119 17 2099 2869 120783546 120782759 1.270000e-156 564.0
50 TraesCS2B01G273300 chr5D 89.855 69 5 1 6063 6129 442203726 442203794 3.360000e-13 87.9
51 TraesCS2B01G273300 chr7A 77.518 1112 212 17 2100 3184 42732038 42730938 9.570000e-178 634.0
52 TraesCS2B01G273300 chr4B 80.000 795 119 16 2407 3177 476888135 476888913 9.920000e-153 551.0
53 TraesCS2B01G273300 chr1D 90.598 234 19 3 234 466 439829779 439830010 2.370000e-79 307.0
54 TraesCS2B01G273300 chr1D 91.549 71 3 3 6061 6129 476230763 476230694 2.010000e-15 95.3
55 TraesCS2B01G273300 chr1D 84.884 86 11 1 6064 6147 279101376 279101461 1.210000e-12 86.1
56 TraesCS2B01G273300 chr1D 76.471 170 29 7 1 167 404290008 404290169 1.560000e-11 82.4
57 TraesCS2B01G273300 chr5A 86.940 268 27 7 206 468 85822280 85822016 1.850000e-75 294.0
58 TraesCS2B01G273300 chr6A 100.000 33 0 0 6272 6304 574243948 574243980 2.040000e-05 62.1
59 TraesCS2B01G273300 chr4A 85.000 60 9 0 6270 6329 3450396 3450337 2.040000e-05 62.1
60 TraesCS2B01G273300 chr5B 94.737 38 1 1 6270 6306 652625338 652625301 2.640000e-04 58.4


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 TraesCS2B01G273300 chr2B 374676681 374683446 6765 False 6049.500000 8665 100.000000 1 6766 2 chr2B.!!$F2 6765
1 TraesCS2B01G273300 chr2D 306482562 306488345 5783 False 2745.333333 5736 95.441333 1 6766 3 chr2D.!!$F2 6765
2 TraesCS2B01G273300 chr2A 385974675 385979908 5233 False 1780.750000 4667 94.915500 741 6766 4 chr2A.!!$F4 6025
3 TraesCS2B01G273300 chr6D 331537868 331538959 1091 False 845.000000 845 80.995000 2094 3175 1 chr6D.!!$F2 1081
4 TraesCS2B01G273300 chr6D 389704934 389706014 1080 False 839.000000 839 81.153000 2101 3163 1 chr6D.!!$F3 1062
5 TraesCS2B01G273300 chr3B 201992827 201993920 1093 False 835.000000 835 80.905000 2099 3175 1 chr3B.!!$F1 1076
6 TraesCS2B01G273300 chr3A 715578290 715579381 1091 False 835.000000 835 80.888000 2098 3175 1 chr3A.!!$F1 1077
7 TraesCS2B01G273300 chr7B 363222289 363223405 1116 False 821.000000 821 80.622000 2096 3175 1 chr7B.!!$F1 1079
8 TraesCS2B01G273300 chr7B 729234057 729235100 1043 True 771.000000 771 80.492000 2157 3183 1 chr7B.!!$R3 1026
9 TraesCS2B01G273300 chr1A 539708779 539709872 1093 False 819.000000 819 80.651000 2099 3175 1 chr1A.!!$F1 1076
10 TraesCS2B01G273300 chr1A 561647133 561648154 1021 True 636.000000 636 78.345000 2159 3174 1 chr1A.!!$R1 1015
11 TraesCS2B01G273300 chr3D 518131199 518132286 1087 False 800.000000 800 80.381000 2101 3175 1 chr3D.!!$F4 1074
12 TraesCS2B01G273300 chr3D 584687061 584688141 1080 True 784.000000 784 80.183000 2110 3173 1 chr3D.!!$R2 1063
13 TraesCS2B01G273300 chr3D 478422771 478423566 795 False 621.000000 621 81.125000 2394 3175 1 chr3D.!!$F3 781
14 TraesCS2B01G273300 chrUn 349628243 349629338 1095 False 769.000000 769 79.783000 2093 3173 1 chrUn.!!$F1 1080
15 TraesCS2B01G273300 chrUn 290537935 290539033 1098 True 730.000000 730 79.208000 2099 3173 1 chrUn.!!$R1 1074
16 TraesCS2B01G273300 chr7D 16200290 16201377 1087 False 756.000000 756 79.636000 2099 3173 1 chr7D.!!$F1 1074
17 TraesCS2B01G273300 chr7D 21711570 21712352 782 True 568.000000 568 80.328000 2099 2865 1 chr7D.!!$R1 766
18 TraesCS2B01G273300 chr7D 60368227 60368812 585 False 486.000000 486 82.077000 2095 2676 1 chr7D.!!$F3 581
19 TraesCS2B01G273300 chr6B 132895936 132897020 1084 False 754.000000 754 79.599000 2110 3184 1 chr6B.!!$F1 1074
20 TraesCS2B01G273300 chr5D 310556456 310557474 1018 True 741.000000 741 80.253000 2099 3100 1 chr5D.!!$R2 1001
21 TraesCS2B01G273300 chr5D 120782759 120783546 787 True 564.000000 564 80.225000 2099 2869 1 chr5D.!!$R1 770
22 TraesCS2B01G273300 chr7A 42730938 42732038 1100 True 634.000000 634 77.518000 2100 3184 1 chr7A.!!$R1 1084
23 TraesCS2B01G273300 chr4B 476888135 476888913 778 False 551.000000 551 80.000000 2407 3177 1 chr4B.!!$F1 770

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
244 248 0.113776 TACCTTCGTCCTGTCCTGGT 59.886 55.0 0.00 0.00 0.00 4.00 F
246 250 0.396811 CCTTCGTCCTGTCCTGGTTT 59.603 55.0 0.00 0.00 0.00 3.27 F
1084 1104 0.671251 CCTATCGGCGCTTCTCTCTT 59.329 55.0 7.64 0.00 0.00 2.85 F
2530 3047 0.250467 ACCATATAAGGCAGGCGCTG 60.250 55.0 7.64 4.78 38.60 5.18 F
3168 3713 0.244450 TACCGCGAACGATCCAAAGT 59.756 50.0 8.23 0.00 43.93 2.66 F
3678 4228 0.680618 TTGAACCAGCAATGCAAGGG 59.319 50.0 18.45 13.73 31.81 3.95 F
4642 5193 0.388659 GGTTGGCATTGTCAGCAACA 59.611 50.0 7.42 0.00 37.44 3.33 F
4884 5435 0.546122 TTGCAGCCCGTGGATTAGAT 59.454 50.0 0.00 0.00 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 1334 0.322816 GGAAGAGCCTGTTGATGCCA 60.323 55.000 0.00 0.00 0.00 4.92 R
2156 2626 0.963355 GGCCGGGTGTTGCTCATTTA 60.963 55.000 2.18 0.00 0.00 1.40 R
2589 3106 0.032403 CACCCACATGTGTTGGCAAG 59.968 55.000 23.79 7.03 34.44 4.01 R
4336 4887 0.730265 GGGATTCGCGCACAATGTAA 59.270 50.000 8.75 0.00 0.00 2.41 R
4343 4894 1.160329 ATAGCAAGGGATTCGCGCAC 61.160 55.000 8.75 0.00 0.00 5.34 R
5549 6100 0.035439 GCCGAGAATCTCCAAACCCA 60.035 55.000 4.47 0.00 0.00 4.51 R
5624 6175 2.731451 GCCTTCTTCAAATTCGCCAAAC 59.269 45.455 0.00 0.00 0.00 2.93 R
6602 7167 2.814336 TGTTGTGTTGTAACAGTGCACA 59.186 40.909 21.04 0.00 40.05 4.57 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
235 239 4.304537 GGAGTTCATACTACCTTCGTCC 57.695 50.000 0.00 0.00 33.84 4.79
236 240 3.952967 GGAGTTCATACTACCTTCGTCCT 59.047 47.826 0.00 0.00 33.84 3.85
237 241 4.202030 GGAGTTCATACTACCTTCGTCCTG 60.202 50.000 0.00 0.00 33.84 3.86
238 242 4.342359 AGTTCATACTACCTTCGTCCTGT 58.658 43.478 0.00 0.00 31.21 4.00
239 243 4.398673 AGTTCATACTACCTTCGTCCTGTC 59.601 45.833 0.00 0.00 31.21 3.51
240 244 3.285484 TCATACTACCTTCGTCCTGTCC 58.715 50.000 0.00 0.00 0.00 4.02
241 245 3.053842 TCATACTACCTTCGTCCTGTCCT 60.054 47.826 0.00 0.00 0.00 3.85
242 246 1.546961 ACTACCTTCGTCCTGTCCTG 58.453 55.000 0.00 0.00 0.00 3.86
243 247 0.818296 CTACCTTCGTCCTGTCCTGG 59.182 60.000 0.00 0.00 0.00 4.45
244 248 0.113776 TACCTTCGTCCTGTCCTGGT 59.886 55.000 0.00 0.00 0.00 4.00
245 249 0.763223 ACCTTCGTCCTGTCCTGGTT 60.763 55.000 0.00 0.00 0.00 3.67
246 250 0.396811 CCTTCGTCCTGTCCTGGTTT 59.603 55.000 0.00 0.00 0.00 3.27
247 251 1.621814 CCTTCGTCCTGTCCTGGTTTA 59.378 52.381 0.00 0.00 0.00 2.01
248 252 2.236395 CCTTCGTCCTGTCCTGGTTTAT 59.764 50.000 0.00 0.00 0.00 1.40
249 253 3.307480 CCTTCGTCCTGTCCTGGTTTATT 60.307 47.826 0.00 0.00 0.00 1.40
250 254 3.328382 TCGTCCTGTCCTGGTTTATTG 57.672 47.619 0.00 0.00 0.00 1.90
251 255 2.027561 TCGTCCTGTCCTGGTTTATTGG 60.028 50.000 0.00 0.00 0.00 3.16
252 256 2.290071 CGTCCTGTCCTGGTTTATTGGT 60.290 50.000 0.00 0.00 0.00 3.67
253 257 3.344515 GTCCTGTCCTGGTTTATTGGTC 58.655 50.000 0.00 0.00 0.00 4.02
254 258 2.307686 TCCTGTCCTGGTTTATTGGTCC 59.692 50.000 0.00 0.00 0.00 4.46
255 259 2.620627 CCTGTCCTGGTTTATTGGTCCC 60.621 54.545 0.00 0.00 0.00 4.46
256 260 1.356398 TGTCCTGGTTTATTGGTCCCC 59.644 52.381 0.00 0.00 0.00 4.81
257 261 1.639108 GTCCTGGTTTATTGGTCCCCT 59.361 52.381 0.00 0.00 0.00 4.79
258 262 2.042569 GTCCTGGTTTATTGGTCCCCTT 59.957 50.000 0.00 0.00 0.00 3.95
259 263 2.725227 TCCTGGTTTATTGGTCCCCTTT 59.275 45.455 0.00 0.00 0.00 3.11
260 264 2.831526 CCTGGTTTATTGGTCCCCTTTG 59.168 50.000 0.00 0.00 0.00 2.77
261 265 3.501385 CCTGGTTTATTGGTCCCCTTTGA 60.501 47.826 0.00 0.00 0.00 2.69
262 266 4.156477 CTGGTTTATTGGTCCCCTTTGAA 58.844 43.478 0.00 0.00 0.00 2.69
263 267 4.557705 TGGTTTATTGGTCCCCTTTGAAA 58.442 39.130 0.00 0.00 0.00 2.69
264 268 5.158889 TGGTTTATTGGTCCCCTTTGAAAT 58.841 37.500 0.00 0.00 0.00 2.17
265 269 5.608860 TGGTTTATTGGTCCCCTTTGAAATT 59.391 36.000 0.00 0.00 0.00 1.82
266 270 6.101881 TGGTTTATTGGTCCCCTTTGAAATTT 59.898 34.615 0.00 0.00 0.00 1.82
267 271 6.429692 GGTTTATTGGTCCCCTTTGAAATTTG 59.570 38.462 0.00 0.00 0.00 2.32
268 272 6.755542 TTATTGGTCCCCTTTGAAATTTGT 57.244 33.333 0.00 0.00 0.00 2.83
269 273 4.414337 TTGGTCCCCTTTGAAATTTGTG 57.586 40.909 0.00 0.00 0.00 3.33
270 274 3.379452 TGGTCCCCTTTGAAATTTGTGT 58.621 40.909 0.00 0.00 0.00 3.72
271 275 3.386402 TGGTCCCCTTTGAAATTTGTGTC 59.614 43.478 0.00 0.00 0.00 3.67
272 276 3.386402 GGTCCCCTTTGAAATTTGTGTCA 59.614 43.478 0.00 0.00 0.00 3.58
273 277 4.141824 GGTCCCCTTTGAAATTTGTGTCAA 60.142 41.667 0.00 0.00 31.99 3.18
274 278 5.423886 GTCCCCTTTGAAATTTGTGTCAAA 58.576 37.500 0.00 0.00 40.52 2.69
275 279 6.054941 GTCCCCTTTGAAATTTGTGTCAAAT 58.945 36.000 0.00 2.42 41.57 2.32
276 280 6.542005 GTCCCCTTTGAAATTTGTGTCAAATT 59.458 34.615 12.69 12.69 41.57 1.82
277 281 7.066887 GTCCCCTTTGAAATTTGTGTCAAATTT 59.933 33.333 23.83 23.83 41.57 1.82
278 282 7.613411 TCCCCTTTGAAATTTGTGTCAAATTTT 59.387 29.630 24.17 13.96 41.57 1.82
279 283 8.897752 CCCCTTTGAAATTTGTGTCAAATTTTA 58.102 29.630 24.17 19.99 41.57 1.52
353 357 8.330466 TCGTTGGATTTGTATTTCAACATAGT 57.670 30.769 0.00 0.00 37.98 2.12
354 358 8.788806 TCGTTGGATTTGTATTTCAACATAGTT 58.211 29.630 0.00 0.00 37.98 2.24
355 359 9.405587 CGTTGGATTTGTATTTCAACATAGTTT 57.594 29.630 0.00 0.00 37.98 2.66
395 399 8.604640 TTTTATGACATGCATGAACATTTTGT 57.395 26.923 32.75 16.89 37.87 2.83
396 400 8.604640 TTTATGACATGCATGAACATTTTGTT 57.395 26.923 32.75 16.30 39.76 2.83
397 401 5.908916 TGACATGCATGAACATTTTGTTG 57.091 34.783 32.75 3.42 41.28 3.33
398 402 4.750598 TGACATGCATGAACATTTTGTTGG 59.249 37.500 32.75 1.29 41.28 3.77
399 403 4.706035 ACATGCATGAACATTTTGTTGGT 58.294 34.783 32.75 2.07 41.28 3.67
400 404 5.124645 ACATGCATGAACATTTTGTTGGTT 58.875 33.333 32.75 1.36 41.28 3.67
401 405 6.286758 ACATGCATGAACATTTTGTTGGTTA 58.713 32.000 32.75 0.00 41.28 2.85
402 406 6.765036 ACATGCATGAACATTTTGTTGGTTAA 59.235 30.769 32.75 0.00 41.28 2.01
403 407 7.281774 ACATGCATGAACATTTTGTTGGTTAAA 59.718 29.630 32.75 0.00 41.28 1.52
404 408 7.798596 TGCATGAACATTTTGTTGGTTAAAT 57.201 28.000 0.00 0.00 41.28 1.40
405 409 8.218338 TGCATGAACATTTTGTTGGTTAAATT 57.782 26.923 0.00 0.00 41.28 1.82
406 410 8.680903 TGCATGAACATTTTGTTGGTTAAATTT 58.319 25.926 0.00 0.00 41.28 1.82
413 417 9.838339 ACATTTTGTTGGTTAAATTTATGGTCA 57.162 25.926 0.00 0.00 0.00 4.02
438 442 9.866936 CAAAATTTGACACAAAATACAATGAGG 57.133 29.630 0.00 0.00 0.00 3.86
439 443 9.829507 AAAATTTGACACAAAATACAATGAGGA 57.170 25.926 0.00 0.00 0.00 3.71
440 444 8.816640 AATTTGACACAAAATACAATGAGGAC 57.183 30.769 0.00 0.00 0.00 3.85
441 445 5.957842 TGACACAAAATACAATGAGGACC 57.042 39.130 0.00 0.00 0.00 4.46
442 446 5.380900 TGACACAAAATACAATGAGGACCA 58.619 37.500 0.00 0.00 0.00 4.02
443 447 5.830457 TGACACAAAATACAATGAGGACCAA 59.170 36.000 0.00 0.00 0.00 3.67
444 448 6.493115 TGACACAAAATACAATGAGGACCAAT 59.507 34.615 0.00 0.00 0.00 3.16
445 449 7.667635 TGACACAAAATACAATGAGGACCAATA 59.332 33.333 0.00 0.00 0.00 1.90
446 450 8.415950 ACACAAAATACAATGAGGACCAATAA 57.584 30.769 0.00 0.00 0.00 1.40
447 451 8.865090 ACACAAAATACAATGAGGACCAATAAA 58.135 29.630 0.00 0.00 0.00 1.40
448 452 9.139174 CACAAAATACAATGAGGACCAATAAAC 57.861 33.333 0.00 0.00 0.00 2.01
449 453 8.311109 ACAAAATACAATGAGGACCAATAAACC 58.689 33.333 0.00 0.00 0.00 3.27
450 454 8.310382 CAAAATACAATGAGGACCAATAAACCA 58.690 33.333 0.00 0.00 0.00 3.67
451 455 7.645058 AATACAATGAGGACCAATAAACCAG 57.355 36.000 0.00 0.00 0.00 4.00
452 456 4.344104 ACAATGAGGACCAATAAACCAGG 58.656 43.478 0.00 0.00 0.00 4.45
453 457 4.044065 ACAATGAGGACCAATAAACCAGGA 59.956 41.667 0.00 0.00 0.00 3.86
454 458 3.713826 TGAGGACCAATAAACCAGGAC 57.286 47.619 0.00 0.00 0.00 3.85
455 459 2.027561 TGAGGACCAATAAACCAGGACG 60.028 50.000 0.00 0.00 0.00 4.79
456 460 1.280998 AGGACCAATAAACCAGGACGG 59.719 52.381 0.00 0.00 42.50 4.79
457 461 1.279846 GGACCAATAAACCAGGACGGA 59.720 52.381 0.00 0.00 38.63 4.69
458 462 2.629051 GACCAATAAACCAGGACGGAG 58.371 52.381 0.00 0.00 38.63 4.63
459 463 1.280998 ACCAATAAACCAGGACGGAGG 59.719 52.381 0.00 0.00 38.63 4.30
460 464 1.280998 CCAATAAACCAGGACGGAGGT 59.719 52.381 0.00 0.00 40.61 3.85
461 465 2.502538 CCAATAAACCAGGACGGAGGTA 59.497 50.000 0.00 0.00 37.07 3.08
462 466 3.431766 CCAATAAACCAGGACGGAGGTAG 60.432 52.174 0.00 0.00 37.07 3.18
463 467 2.610438 TAAACCAGGACGGAGGTAGT 57.390 50.000 0.00 0.00 37.07 2.73
464 468 2.610438 AAACCAGGACGGAGGTAGTA 57.390 50.000 0.00 0.00 37.07 1.82
465 469 1.844687 AACCAGGACGGAGGTAGTAC 58.155 55.000 0.00 0.00 37.07 2.73
466 470 0.998145 ACCAGGACGGAGGTAGTACT 59.002 55.000 0.00 0.00 36.07 2.73
467 471 2.200081 ACCAGGACGGAGGTAGTACTA 58.800 52.381 0.00 0.00 36.07 1.82
468 472 2.092699 ACCAGGACGGAGGTAGTACTAC 60.093 54.545 22.53 22.53 36.07 2.73
469 473 5.274279 ACCAGGACGGAGGTAGTACTACC 62.274 56.522 35.57 35.57 46.22 3.18
556 560 4.388165 CAGTTTGACAACATGCAACACAAA 59.612 37.500 0.00 0.00 35.05 2.83
559 563 4.917887 TGACAACATGCAACACAAAAAC 57.082 36.364 0.00 0.00 0.00 2.43
580 585 8.532977 AAAACCTCATGAATGTAAATTTTCCG 57.467 30.769 0.00 0.00 0.00 4.30
627 632 2.043801 AGGGAGCCTCAAGTTCTACTCT 59.956 50.000 0.00 0.00 0.00 3.24
643 648 7.833183 AGTTCTACTCTCTCCGTTCCTAAATAA 59.167 37.037 0.00 0.00 0.00 1.40
726 739 3.726557 AGATCCACTCATTTTGCTCCA 57.273 42.857 0.00 0.00 0.00 3.86
931 951 3.379445 TCCTCCGTCCCTCGCAAC 61.379 66.667 0.00 0.00 38.35 4.17
1084 1104 0.671251 CCTATCGGCGCTTCTCTCTT 59.329 55.000 7.64 0.00 0.00 2.85
1174 1194 3.744719 CGTTCCACGCCTCTCCGA 61.745 66.667 0.00 0.00 33.65 4.55
1622 1645 3.234630 TTGCTTCGGACTGACGGGG 62.235 63.158 0.00 0.00 0.00 5.73
1631 1654 3.260380 TCGGACTGACGGGGTAAAATTTA 59.740 43.478 0.00 0.00 0.00 1.40
1663 1686 6.430925 AGTGCTGTTGTGATAATTTAGCAAGA 59.569 34.615 0.00 0.00 40.81 3.02
1685 1708 5.192522 AGAGGTCTATTGATTCCAACCATGT 59.807 40.000 0.00 0.00 34.72 3.21
1726 1749 9.577110 CATGTAGCTTCACAATATTGACAAATT 57.423 29.630 22.16 6.06 30.84 1.82
1765 1788 6.403866 AATCACTGAATTTTGCAAGTACCA 57.596 33.333 0.00 0.00 0.00 3.25
1773 1796 4.846779 TTTTGCAAGTACCAGTGGAATC 57.153 40.909 18.40 5.54 0.00 2.52
1784 1807 2.616510 CCAGTGGAATCTGGTCAGAACC 60.617 54.545 1.68 15.43 46.92 3.62
1836 1859 5.864418 TTTATACGGCTACCTGATGACTT 57.136 39.130 0.00 0.00 0.00 3.01
1838 1861 7.534723 TTTATACGGCTACCTGATGACTTAT 57.465 36.000 0.00 0.00 0.00 1.73
1847 1870 8.585881 GGCTACCTGATGACTTATTGAATACTA 58.414 37.037 0.00 0.00 0.00 1.82
1858 1881 9.482627 GACTTATTGAATACTATGTTCCTCCAG 57.517 37.037 0.00 0.00 0.00 3.86
2184 2655 1.635817 AACACCCGGCCTCTGCATAT 61.636 55.000 0.00 0.00 40.13 1.78
2203 2674 2.099141 TCTAAGATGCACACAGCCAC 57.901 50.000 0.00 0.00 44.83 5.01
2224 2715 5.006746 CCACACTCAAACAGTCTGACTAAAC 59.993 44.000 10.47 0.00 30.26 2.01
2248 2739 3.596214 ACGACATAAGGGCAACAGTAAG 58.404 45.455 0.00 0.00 39.74 2.34
2258 2749 3.352648 GGCAACAGTAAGGCCATAGAAA 58.647 45.455 5.01 0.00 46.92 2.52
2279 2770 2.384828 ACCGACACTATGCCTATGTCA 58.615 47.619 4.65 0.00 42.37 3.58
2280 2771 2.965831 ACCGACACTATGCCTATGTCAT 59.034 45.455 4.65 0.00 42.37 3.06
2282 2773 4.218635 ACCGACACTATGCCTATGTCATAG 59.781 45.833 12.29 12.29 45.39 2.23
2287 2778 4.440839 CTATGCCTATGTCATAGTCGCA 57.559 45.455 19.71 19.71 38.86 5.10
2293 2784 2.044806 ATGTCATAGTCGCAGGGGGC 62.045 60.000 0.00 0.00 39.90 5.80
2325 2833 1.691976 CCGGAGATTATGCTACCACCA 59.308 52.381 0.00 0.00 0.00 4.17
2355 2864 1.442886 AAAATCTCCCTGGCCACCCA 61.443 55.000 0.00 0.00 39.32 4.51
2386 2895 3.476552 CATACACACCACCTTGAACAGT 58.523 45.455 0.00 0.00 0.00 3.55
2428 2937 5.744171 TGCAACATAGACCACATATGAAGT 58.256 37.500 10.38 5.89 35.15 3.01
2458 2967 2.749621 AGAGCGGAAAATAACCTGCAAG 59.250 45.455 0.00 0.00 32.57 4.01
2530 3047 0.250467 ACCATATAAGGCAGGCGCTG 60.250 55.000 7.64 4.78 38.60 5.18
2563 3080 6.730960 TTAGCGTTGTAAACCTATTTGGAG 57.269 37.500 0.00 0.00 46.28 3.86
2589 3106 3.281727 TCCAGCCAGTGACCATAAATC 57.718 47.619 0.00 0.00 0.00 2.17
2593 3110 3.019564 AGCCAGTGACCATAAATCTTGC 58.980 45.455 0.00 0.00 0.00 4.01
2600 3117 4.022416 GTGACCATAAATCTTGCCAACACA 60.022 41.667 0.00 0.00 0.00 3.72
2649 3166 4.743057 TTGGATGACTGACCATGTAGAG 57.257 45.455 0.00 0.00 36.02 2.43
2756 3290 4.163458 TGTCTTTGGTCAGTACAACTCCTT 59.837 41.667 0.00 0.00 0.00 3.36
2778 3312 4.075682 TGCCGAAGATACCACATGAAAAA 58.924 39.130 0.00 0.00 0.00 1.94
2821 3356 2.828520 TGGCCTTCCAAATTTGCGAATA 59.171 40.909 12.92 3.34 39.99 1.75
2849 3384 2.807967 CACTGGAATTTCTGAGTGCGAA 59.192 45.455 12.91 0.00 30.14 4.70
2918 3453 1.079127 CCAGCGAAAGACATCCCGT 60.079 57.895 0.00 0.00 0.00 5.28
2942 3477 5.046591 TCCTTGTGTCAGGTTAATCGAATCT 60.047 40.000 0.00 0.00 35.15 2.40
2949 3484 6.602009 TGTCAGGTTAATCGAATCTAGTCTGA 59.398 38.462 0.00 0.00 0.00 3.27
2975 3510 3.863142 AGATTCTGCCATGACAAAAGC 57.137 42.857 0.00 0.00 0.00 3.51
3025 3560 4.042684 AGAAATATTCAGAGGGGATGAGCC 59.957 45.833 0.00 0.00 0.00 4.70
3136 3681 6.264744 CACTTATCCTCCCAGAAACGTATCTA 59.735 42.308 0.00 0.00 0.00 1.98
3151 3696 1.316651 ATCTACGAGCCGTCCCTTAC 58.683 55.000 3.45 0.00 41.54 2.34
3158 3703 2.507769 CCGTCCCTTACCGCGAAC 60.508 66.667 8.23 0.00 0.00 3.95
3168 3713 0.244450 TACCGCGAACGATCCAAAGT 59.756 50.000 8.23 0.00 43.93 2.66
3196 3741 7.601073 AAAAGTTGCTTCAAAGAAGGAAAAG 57.399 32.000 13.93 0.00 29.52 2.27
3197 3742 5.921962 AGTTGCTTCAAAGAAGGAAAAGT 57.078 34.783 13.93 1.82 29.52 2.66
3198 3743 5.654497 AGTTGCTTCAAAGAAGGAAAAGTG 58.346 37.500 13.93 0.00 29.52 3.16
3209 3754 6.187727 AGAAGGAAAAGTGAACTCCATACA 57.812 37.500 0.00 0.00 0.00 2.29
3210 3755 6.601332 AGAAGGAAAAGTGAACTCCATACAA 58.399 36.000 0.00 0.00 0.00 2.41
3262 3807 2.926165 CAAGCTTGCTAGTTTGCTGTC 58.074 47.619 14.65 0.00 36.10 3.51
3265 3810 1.466558 GCTTGCTAGTTTGCTGTCCTC 59.533 52.381 0.00 0.00 0.00 3.71
3273 3822 5.877564 GCTAGTTTGCTGTCCTCTATTTCTT 59.122 40.000 0.00 0.00 0.00 2.52
3308 3857 1.406539 GTGGCCTTGTATTGCATCTGG 59.593 52.381 3.32 0.00 0.00 3.86
3329 3878 1.202758 TGGTTGACCAGTTACTGCAGG 60.203 52.381 19.93 1.64 42.01 4.85
3346 3895 2.420129 GCAGGAAACGGTACAGGATCAT 60.420 50.000 0.00 0.00 0.00 2.45
3374 3923 9.403110 CTTGTTATTTCTCAGAAGAACAAATGG 57.597 33.333 21.32 12.13 44.90 3.16
3384 3933 3.967332 AGAACAAATGGGCCATCTTTG 57.033 42.857 24.27 24.27 36.26 2.77
3401 3950 7.624764 GCCATCTTTGCAAGGAAAATTAATGTG 60.625 37.037 15.81 5.77 0.00 3.21
3420 3969 5.850557 TGTGATTTCCTGTGAACAAATGT 57.149 34.783 0.00 0.00 0.00 2.71
3429 3978 9.522804 TTTCCTGTGAACAAATGTACAATAAAC 57.477 29.630 0.00 0.00 0.00 2.01
3459 4008 9.848710 AAAGATCTCTCATGACATATTGACATT 57.151 29.630 0.00 0.00 30.83 2.71
3494 4043 8.284945 TGTTCAAGATTAGGATTTTGATGAGG 57.715 34.615 0.00 0.00 36.58 3.86
3556 4105 6.127394 TGGCAAGATGCTATTTTCTGCAAATA 60.127 34.615 2.00 0.00 44.28 1.40
3619 4169 5.316987 AGCCTAGTTTTTCTGTTGCTACAT 58.683 37.500 0.34 0.00 32.86 2.29
3628 4178 5.627499 TTCTGTTGCTACATTGATGGTTC 57.373 39.130 0.34 0.00 32.86 3.62
3633 4183 5.186198 GTTGCTACATTGATGGTTCTACCT 58.814 41.667 0.00 0.00 39.58 3.08
3678 4228 0.680618 TTGAACCAGCAATGCAAGGG 59.319 50.000 18.45 13.73 31.81 3.95
3779 4329 3.753272 CGTCACAATGAGAAGAATGGGTT 59.247 43.478 0.00 0.00 0.00 4.11
3780 4330 4.378770 CGTCACAATGAGAAGAATGGGTTG 60.379 45.833 0.00 0.00 0.00 3.77
3942 4492 6.401581 GCTCGACAAGTTGAGAAGGAATTTAG 60.402 42.308 19.20 0.00 42.44 1.85
4012 4562 4.564041 TCAGTCAGCAAATGAGAACTCTC 58.436 43.478 0.00 0.00 39.07 3.20
4028 4578 6.533730 AGAACTCTCAATTATGGTGTTGACA 58.466 36.000 0.00 0.00 31.55 3.58
4078 4628 8.447053 GTTATTGATCTTTTGAGAAGAGGTGTC 58.553 37.037 0.00 0.00 0.00 3.67
4093 4643 6.783708 AGAGGTGTCCTAAACTTATCAGAG 57.216 41.667 0.00 0.00 31.76 3.35
4175 4725 3.584406 TGTTGAGGTGATCATGGAGAAGT 59.416 43.478 0.00 0.00 37.89 3.01
4189 4739 0.744281 AGAAGTTGCCACAAAACCGG 59.256 50.000 0.00 0.00 0.00 5.28
4303 4854 5.842907 AGTGACTTTTTGTCTTATTTGCCC 58.157 37.500 0.00 0.00 45.54 5.36
4322 4873 4.705023 TGCCCTAAGACCTTTAATCTTTGC 59.295 41.667 0.00 0.00 37.57 3.68
4332 4883 4.354587 CTTTAATCTTTGCGCTGGGAATC 58.645 43.478 9.73 0.00 0.00 2.52
4336 4887 1.065199 TCTTTGCGCTGGGAATCATCT 60.065 47.619 9.73 0.00 0.00 2.90
4343 4894 3.304257 GCGCTGGGAATCATCTTACATTG 60.304 47.826 0.00 0.00 0.00 2.82
4347 4898 3.627123 TGGGAATCATCTTACATTGTGCG 59.373 43.478 0.00 0.00 0.00 5.34
4348 4899 3.548818 GGGAATCATCTTACATTGTGCGC 60.549 47.826 0.00 0.00 0.00 6.09
4362 4913 1.146041 TGCGCGAATCCCTTGCTAT 59.854 52.632 12.10 0.00 0.00 2.97
4436 4987 9.406828 ACTTTGTTTACTTTTCTTTGTCAGTTC 57.593 29.630 0.00 0.00 0.00 3.01
4465 5016 7.774694 TCTGGGTTAGAATTTTAGGGGAATA 57.225 36.000 0.00 0.00 30.84 1.75
4478 5029 9.845740 ATTTTAGGGGAATAATTTGGCAATTAC 57.154 29.630 0.00 0.00 37.62 1.89
4642 5193 0.388659 GGTTGGCATTGTCAGCAACA 59.611 50.000 7.42 0.00 37.44 3.33
4695 5246 1.225426 GGAGCATGCTGATGGTGGA 59.775 57.895 28.27 0.00 40.47 4.02
4705 5256 2.673043 GCTGATGGTGGAAAGTGCATTG 60.673 50.000 0.00 0.00 0.00 2.82
4833 5384 3.428316 GGACACTCTCAGGATTTCGAGAC 60.428 52.174 0.00 0.00 34.60 3.36
4834 5385 3.157881 ACACTCTCAGGATTTCGAGACA 58.842 45.455 0.00 0.00 34.60 3.41
4884 5435 0.546122 TTGCAGCCCGTGGATTAGAT 59.454 50.000 0.00 0.00 0.00 1.98
4981 5532 5.025453 ACCCAAAAATATGATTGCTCTGGT 58.975 37.500 0.00 0.00 0.00 4.00
4995 5546 1.195448 CTCTGGTCGTTTGATGTGCAC 59.805 52.381 10.75 10.75 0.00 4.57
5294 5845 1.160137 CCAAGGTTGCAGCTACAGAC 58.840 55.000 9.30 0.00 0.00 3.51
5306 5857 1.906757 CTACAGACGAAGCTGCAGAG 58.093 55.000 20.43 7.64 39.51 3.35
5329 5880 7.763528 AGAGCTGTTTAATGTTATGAGAGACAG 59.236 37.037 0.00 0.00 36.11 3.51
5386 5937 1.176619 TCCTCTTTCAGCCACGACGA 61.177 55.000 0.00 0.00 0.00 4.20
5430 5981 2.034558 CGTGGCTTTGGTGATTTTGACT 59.965 45.455 0.00 0.00 0.00 3.41
5466 6017 2.233605 TAATCGTGCTGGGTGGTCCG 62.234 60.000 0.00 0.00 38.76 4.79
6008 6559 1.704628 TCTTGTGCCCCTCATGAAAGA 59.295 47.619 0.00 0.00 0.00 2.52
6010 6561 2.425143 TGTGCCCCTCATGAAAGATC 57.575 50.000 0.00 0.00 0.00 2.75
6011 6562 1.634973 TGTGCCCCTCATGAAAGATCA 59.365 47.619 0.00 0.00 40.57 2.92
6012 6563 2.041485 TGTGCCCCTCATGAAAGATCAA 59.959 45.455 0.00 0.00 39.49 2.57
6013 6564 2.424956 GTGCCCCTCATGAAAGATCAAC 59.575 50.000 0.00 0.00 39.49 3.18
6014 6565 2.041485 TGCCCCTCATGAAAGATCAACA 59.959 45.455 0.00 0.00 39.49 3.33
6519 7084 7.414436 TCAAAAAGAGTTTGATCCAGTTTACG 58.586 34.615 0.00 0.00 33.90 3.18
6534 7099 4.994852 CAGTTTACGAGGAAAACCTGATCA 59.005 41.667 0.00 0.00 37.51 2.92
6602 7167 7.227156 AGAAGATAGAAAACACAGAACACCAT 58.773 34.615 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.769677 ATATATACTACCACTGTACCACATCAT 57.230 33.333 0.00 0.00 0.00 2.45
197 201 5.045869 TGAACTCCCTTCGATCCAAATAAGT 60.046 40.000 0.00 0.00 0.00 2.24
230 234 2.027561 CCAATAAACCAGGACAGGACGA 60.028 50.000 0.00 0.00 0.00 4.20
231 235 2.290071 ACCAATAAACCAGGACAGGACG 60.290 50.000 0.00 0.00 0.00 4.79
232 236 3.344515 GACCAATAAACCAGGACAGGAC 58.655 50.000 0.00 0.00 0.00 3.85
233 237 2.307686 GGACCAATAAACCAGGACAGGA 59.692 50.000 0.00 0.00 0.00 3.86
234 238 2.620627 GGGACCAATAAACCAGGACAGG 60.621 54.545 0.00 0.00 0.00 4.00
235 239 2.723273 GGGACCAATAAACCAGGACAG 58.277 52.381 0.00 0.00 0.00 3.51
236 240 2.891191 GGGACCAATAAACCAGGACA 57.109 50.000 0.00 0.00 0.00 4.02
251 255 4.664150 TGACACAAATTTCAAAGGGGAC 57.336 40.909 0.00 0.00 0.00 4.46
252 256 5.683876 TTTGACACAAATTTCAAAGGGGA 57.316 34.783 0.00 0.00 36.92 4.81
253 257 6.940831 AATTTGACACAAATTTCAAAGGGG 57.059 33.333 14.14 0.00 43.21 4.79
327 331 8.956426 ACTATGTTGAAATACAAATCCAACGAT 58.044 29.630 0.00 0.00 40.36 3.73
328 332 8.330466 ACTATGTTGAAATACAAATCCAACGA 57.670 30.769 0.00 0.00 40.36 3.85
329 333 8.964420 AACTATGTTGAAATACAAATCCAACG 57.036 30.769 0.00 0.00 40.36 4.10
369 373 9.053840 ACAAAATGTTCATGCATGTCATAAAAA 57.946 25.926 26.70 13.06 33.19 1.94
370 374 8.604640 ACAAAATGTTCATGCATGTCATAAAA 57.395 26.923 26.70 13.36 33.19 1.52
371 375 8.496751 CAACAAAATGTTCATGCATGTCATAAA 58.503 29.630 26.70 14.33 38.77 1.40
372 376 7.117956 CCAACAAAATGTTCATGCATGTCATAA 59.882 33.333 26.70 14.62 38.77 1.90
373 377 6.590677 CCAACAAAATGTTCATGCATGTCATA 59.409 34.615 26.70 16.11 38.77 2.15
374 378 5.410132 CCAACAAAATGTTCATGCATGTCAT 59.590 36.000 25.43 24.28 38.77 3.06
375 379 4.750598 CCAACAAAATGTTCATGCATGTCA 59.249 37.500 25.43 23.31 38.77 3.58
376 380 4.751098 ACCAACAAAATGTTCATGCATGTC 59.249 37.500 25.43 19.05 38.77 3.06
377 381 4.706035 ACCAACAAAATGTTCATGCATGT 58.294 34.783 25.43 4.01 38.77 3.21
378 382 5.676532 AACCAACAAAATGTTCATGCATG 57.323 34.783 21.07 21.07 38.77 4.06
379 383 7.798596 TTTAACCAACAAAATGTTCATGCAT 57.201 28.000 0.00 0.00 38.77 3.96
380 384 7.798596 ATTTAACCAACAAAATGTTCATGCA 57.201 28.000 0.00 0.00 38.77 3.96
387 391 9.838339 TGACCATAAATTTAACCAACAAAATGT 57.162 25.926 1.21 0.00 0.00 2.71
412 416 9.866936 CCTCATTGTATTTTGTGTCAAATTTTG 57.133 29.630 2.59 2.59 0.00 2.44
413 417 9.829507 TCCTCATTGTATTTTGTGTCAAATTTT 57.170 25.926 0.00 0.00 0.00 1.82
414 418 9.260002 GTCCTCATTGTATTTTGTGTCAAATTT 57.740 29.630 0.00 0.00 0.00 1.82
415 419 7.872483 GGTCCTCATTGTATTTTGTGTCAAATT 59.128 33.333 0.00 0.00 0.00 1.82
416 420 7.015098 TGGTCCTCATTGTATTTTGTGTCAAAT 59.985 33.333 0.00 0.00 0.00 2.32
417 421 6.322456 TGGTCCTCATTGTATTTTGTGTCAAA 59.678 34.615 0.00 0.00 0.00 2.69
418 422 5.830457 TGGTCCTCATTGTATTTTGTGTCAA 59.170 36.000 0.00 0.00 0.00 3.18
419 423 5.380900 TGGTCCTCATTGTATTTTGTGTCA 58.619 37.500 0.00 0.00 0.00 3.58
420 424 5.957842 TGGTCCTCATTGTATTTTGTGTC 57.042 39.130 0.00 0.00 0.00 3.67
421 425 6.916360 ATTGGTCCTCATTGTATTTTGTGT 57.084 33.333 0.00 0.00 0.00 3.72
422 426 9.139174 GTTTATTGGTCCTCATTGTATTTTGTG 57.861 33.333 0.00 0.00 0.00 3.33
423 427 8.311109 GGTTTATTGGTCCTCATTGTATTTTGT 58.689 33.333 0.00 0.00 0.00 2.83
424 428 8.310382 TGGTTTATTGGTCCTCATTGTATTTTG 58.690 33.333 0.00 0.00 0.00 2.44
425 429 8.429237 TGGTTTATTGGTCCTCATTGTATTTT 57.571 30.769 0.00 0.00 0.00 1.82
426 430 7.124147 CCTGGTTTATTGGTCCTCATTGTATTT 59.876 37.037 0.00 0.00 0.00 1.40
427 431 6.607198 CCTGGTTTATTGGTCCTCATTGTATT 59.393 38.462 0.00 0.00 0.00 1.89
428 432 6.069088 TCCTGGTTTATTGGTCCTCATTGTAT 60.069 38.462 0.00 0.00 0.00 2.29
429 433 5.251932 TCCTGGTTTATTGGTCCTCATTGTA 59.748 40.000 0.00 0.00 0.00 2.41
430 434 4.044065 TCCTGGTTTATTGGTCCTCATTGT 59.956 41.667 0.00 0.00 0.00 2.71
431 435 4.399303 GTCCTGGTTTATTGGTCCTCATTG 59.601 45.833 0.00 0.00 0.00 2.82
432 436 4.600062 GTCCTGGTTTATTGGTCCTCATT 58.400 43.478 0.00 0.00 0.00 2.57
433 437 3.370527 CGTCCTGGTTTATTGGTCCTCAT 60.371 47.826 0.00 0.00 0.00 2.90
434 438 2.027561 CGTCCTGGTTTATTGGTCCTCA 60.028 50.000 0.00 0.00 0.00 3.86
435 439 2.629051 CGTCCTGGTTTATTGGTCCTC 58.371 52.381 0.00 0.00 0.00 3.71
436 440 1.280998 CCGTCCTGGTTTATTGGTCCT 59.719 52.381 0.00 0.00 0.00 3.85
437 441 1.279846 TCCGTCCTGGTTTATTGGTCC 59.720 52.381 0.00 0.00 39.52 4.46
438 442 2.629051 CTCCGTCCTGGTTTATTGGTC 58.371 52.381 0.00 0.00 39.52 4.02
439 443 1.280998 CCTCCGTCCTGGTTTATTGGT 59.719 52.381 0.00 0.00 39.52 3.67
440 444 1.280998 ACCTCCGTCCTGGTTTATTGG 59.719 52.381 0.00 0.00 39.52 3.16
441 445 2.781681 ACCTCCGTCCTGGTTTATTG 57.218 50.000 0.00 0.00 39.52 1.90
442 446 3.447950 ACTACCTCCGTCCTGGTTTATT 58.552 45.455 0.00 0.00 39.52 1.40
443 447 3.111741 ACTACCTCCGTCCTGGTTTAT 57.888 47.619 0.00 0.00 39.52 1.40
444 448 2.610438 ACTACCTCCGTCCTGGTTTA 57.390 50.000 0.00 0.00 39.52 2.01
445 449 2.174360 GTACTACCTCCGTCCTGGTTT 58.826 52.381 0.00 0.00 39.52 3.27
446 450 1.357079 AGTACTACCTCCGTCCTGGTT 59.643 52.381 0.00 0.00 39.52 3.67
447 451 0.998145 AGTACTACCTCCGTCCTGGT 59.002 55.000 0.00 0.00 39.52 4.00
448 452 2.570135 GTAGTACTACCTCCGTCCTGG 58.430 57.143 20.47 0.00 40.09 4.45
519 523 7.771361 TGTTGTCAAACTGGAAAGTATCTACAA 59.229 33.333 0.00 0.00 37.19 2.41
520 524 7.276658 TGTTGTCAAACTGGAAAGTATCTACA 58.723 34.615 0.00 0.00 37.19 2.74
534 538 3.865011 TGTGTTGCATGTTGTCAAACT 57.135 38.095 0.00 0.00 37.19 2.66
556 560 7.666623 ACGGAAAATTTACATTCATGAGGTTT 58.333 30.769 7.32 0.00 0.00 3.27
559 563 9.801873 ATTAACGGAAAATTTACATTCATGAGG 57.198 29.630 0.00 0.00 0.00 3.86
612 617 3.349022 ACGGAGAGAGTAGAACTTGAGG 58.651 50.000 0.00 0.00 0.00 3.86
627 632 8.913487 AAAAGACTTTTATTTAGGAACGGAGA 57.087 30.769 11.51 0.00 0.00 3.71
704 717 5.378230 TGGAGCAAAATGAGTGGATCTAT 57.622 39.130 0.00 0.00 0.00 1.98
710 723 6.698008 TTACATATGGAGCAAAATGAGTGG 57.302 37.500 7.80 0.00 0.00 4.00
1068 1088 0.383949 GAGAAGAGAGAAGCGCCGAT 59.616 55.000 2.29 0.00 0.00 4.18
1314 1334 0.322816 GGAAGAGCCTGTTGATGCCA 60.323 55.000 0.00 0.00 0.00 4.92
1322 1342 1.229951 TGGATGGGGAAGAGCCTGT 60.230 57.895 0.00 0.00 36.66 4.00
1645 1668 9.905713 AATAGACCTCTTGCTAAATTATCACAA 57.094 29.630 0.00 0.00 0.00 3.33
1663 1686 5.456921 ACATGGTTGGAATCAATAGACCT 57.543 39.130 0.00 0.00 35.10 3.85
1726 1749 8.690203 TTCAGTGATTTGTGATTTCCTTTCTA 57.310 30.769 0.00 0.00 0.00 2.10
1820 1843 4.322080 TCAATAAGTCATCAGGTAGCCG 57.678 45.455 0.00 0.00 0.00 5.52
2078 2101 7.905604 AAAAACAACTTTTTCCTCTTTCAGG 57.094 32.000 0.00 0.00 35.04 3.86
2105 2575 3.632145 AGTTAATAAAAGCGGCCCTCATG 59.368 43.478 0.00 0.00 0.00 3.07
2108 2578 3.275999 TGAGTTAATAAAAGCGGCCCTC 58.724 45.455 0.00 0.00 0.00 4.30
2110 2580 4.443913 TTTGAGTTAATAAAAGCGGCCC 57.556 40.909 0.00 0.00 0.00 5.80
2113 2583 7.753132 TGCTACATTTTGAGTTAATAAAAGCGG 59.247 33.333 0.00 0.00 0.00 5.52
2152 2622 2.161609 CCGGGTGTTGCTCATTTACTTC 59.838 50.000 0.00 0.00 0.00 3.01
2156 2626 0.963355 GGCCGGGTGTTGCTCATTTA 60.963 55.000 2.18 0.00 0.00 1.40
2184 2655 1.347378 TGTGGCTGTGTGCATCTTAGA 59.653 47.619 0.00 0.00 45.15 2.10
2203 2674 6.662414 TTGTTTAGTCAGACTGTTTGAGTG 57.338 37.500 13.84 0.00 33.83 3.51
2224 2715 2.552315 ACTGTTGCCCTTATGTCGTTTG 59.448 45.455 0.00 0.00 0.00 2.93
2248 2739 2.109425 AGTGTCGGTTTTCTATGGCC 57.891 50.000 0.00 0.00 0.00 5.36
2258 2749 2.764010 TGACATAGGCATAGTGTCGGTT 59.236 45.455 12.80 0.00 43.88 4.44
2325 2833 4.777366 CCAGGGAGATTTTTACCCAACATT 59.223 41.667 0.00 0.00 45.43 2.71
2340 2848 4.270153 AGTGGGTGGCCAGGGAGA 62.270 66.667 5.11 0.00 0.00 3.71
2355 2864 0.321298 GGTGTGTATGCGGTTGGAGT 60.321 55.000 0.00 0.00 0.00 3.85
2386 2895 2.223641 GCAACGTATGGAGTATCGACCA 60.224 50.000 0.00 0.00 40.57 4.02
2390 2899 3.183754 TGTTGCAACGTATGGAGTATCG 58.816 45.455 23.79 0.00 34.37 2.92
2428 2937 2.760634 TTTTCCGCTCTATGCACTGA 57.239 45.000 0.00 0.00 43.06 3.41
2563 3080 0.678048 GGTCACTGGCTGGATGGAAC 60.678 60.000 0.00 0.00 0.00 3.62
2589 3106 0.032403 CACCCACATGTGTTGGCAAG 59.968 55.000 23.79 7.03 34.44 4.01
2593 3110 2.091541 GTATCCACCCACATGTGTTGG 58.908 52.381 27.07 27.07 36.93 3.77
2600 3117 4.157656 CGTTCAATTTGTATCCACCCACAT 59.842 41.667 0.00 0.00 0.00 3.21
2668 3188 4.836125 TTGCAATCAAACACCTCTTCTC 57.164 40.909 0.00 0.00 0.00 2.87
2756 3290 3.342377 TTTCATGTGGTATCTTCGGCA 57.658 42.857 0.00 0.00 0.00 5.69
2783 3317 4.082125 AGGCCAAGATTCCACTAAAAGTG 58.918 43.478 5.01 0.00 45.53 3.16
2821 3356 7.542025 GCACTCAGAAATTCCAGTGAATAATT 58.458 34.615 20.63 0.00 40.34 1.40
2849 3384 1.299165 CTCTATGTACCGCGCGCTT 60.299 57.895 30.48 18.37 0.00 4.68
2918 3453 4.610605 TTCGATTAACCTGACACAAGGA 57.389 40.909 0.00 0.00 40.02 3.36
2942 3477 7.288621 TCATGGCAGAATCTTCTATTCAGACTA 59.711 37.037 0.00 0.00 35.34 2.59
2949 3484 7.630082 GCTTTTGTCATGGCAGAATCTTCTATT 60.630 37.037 3.47 0.00 35.34 1.73
2982 3517 5.432885 TCTTTCAGACGGGATTTGTTTTC 57.567 39.130 0.00 0.00 0.00 2.29
2983 3518 5.845391 TTCTTTCAGACGGGATTTGTTTT 57.155 34.783 0.00 0.00 0.00 2.43
3110 3654 3.170717 ACGTTTCTGGGAGGATAAGTGA 58.829 45.455 0.00 0.00 0.00 3.41
3136 3681 3.446570 CGGTAAGGGACGGCTCGT 61.447 66.667 0.00 0.00 45.10 4.18
3151 3696 1.419922 CACTTTGGATCGTTCGCGG 59.580 57.895 6.13 0.00 41.70 6.46
3168 3713 5.186797 TCCTTCTTTGAAGCAACTTTTTCCA 59.813 36.000 2.08 0.00 0.00 3.53
3175 3720 5.418840 TCACTTTTCCTTCTTTGAAGCAACT 59.581 36.000 2.08 0.00 0.00 3.16
3176 3721 5.650543 TCACTTTTCCTTCTTTGAAGCAAC 58.349 37.500 2.08 0.00 0.00 4.17
3177 3722 5.913137 TCACTTTTCCTTCTTTGAAGCAA 57.087 34.783 2.08 0.00 0.00 3.91
3178 3723 5.418840 AGTTCACTTTTCCTTCTTTGAAGCA 59.581 36.000 2.08 0.00 0.00 3.91
3179 3724 5.895928 AGTTCACTTTTCCTTCTTTGAAGC 58.104 37.500 2.08 0.00 0.00 3.86
3220 3765 6.976934 TGCTCTACATGGTCATATTAGTCA 57.023 37.500 0.00 0.00 0.00 3.41
3259 3804 5.221521 CCGATGGATCAAGAAATAGAGGACA 60.222 44.000 0.00 0.00 0.00 4.02
3260 3805 5.233988 CCGATGGATCAAGAAATAGAGGAC 58.766 45.833 0.00 0.00 0.00 3.85
3262 3807 3.999663 GCCGATGGATCAAGAAATAGAGG 59.000 47.826 0.00 0.00 0.00 3.69
3265 3810 5.240183 ACATTGCCGATGGATCAAGAAATAG 59.760 40.000 0.00 0.00 40.21 1.73
3273 3822 1.102809 GCCACATTGCCGATGGATCA 61.103 55.000 0.00 0.00 40.21 2.92
3308 3857 1.873591 CTGCAGTAACTGGTCAACCAC 59.126 52.381 5.25 0.00 42.01 4.16
3327 3876 2.434702 GGATGATCCTGTACCGTTTCCT 59.565 50.000 3.71 0.00 32.53 3.36
3346 3895 8.746052 TTTGTTCTTCTGAGAAATAACAAGGA 57.254 30.769 23.21 14.23 43.21 3.36
3401 3950 9.906660 TTATTGTACATTTGTTCACAGGAAATC 57.093 29.630 0.00 0.00 34.13 2.17
3429 3978 9.543783 TCAATATGTCATGAGAGATCTTTCAAG 57.456 33.333 18.89 14.89 0.00 3.02
3472 4021 8.108999 TGAACCTCATCAAAATCCTAATCTTGA 58.891 33.333 0.00 0.00 32.67 3.02
3487 4036 7.855784 ATAGGTATACACATGAACCTCATCA 57.144 36.000 5.01 0.00 41.44 3.07
3520 4069 3.704566 AGCATCTTGCCAATTGACATGAT 59.295 39.130 14.72 14.72 46.52 2.45
3605 4155 5.769662 AGAACCATCAATGTAGCAACAGAAA 59.230 36.000 0.00 0.00 39.49 2.52
3619 4169 3.788227 AGCACAAGGTAGAACCATCAA 57.212 42.857 0.00 0.00 41.95 2.57
3628 4178 1.802960 CTGCACAGAAGCACAAGGTAG 59.197 52.381 0.00 0.00 40.11 3.18
3633 4183 1.875009 CTCTCTGCACAGAAGCACAA 58.125 50.000 1.42 0.00 40.11 3.33
3678 4228 1.468054 GCACGGCCAATCATGTCTTTC 60.468 52.381 2.24 0.00 0.00 2.62
3779 4329 7.070821 ACAGTTCTAAAGTAGAAAGAGAACCCA 59.929 37.037 8.95 0.00 45.56 4.51
3780 4330 7.443477 ACAGTTCTAAAGTAGAAAGAGAACCC 58.557 38.462 8.95 0.00 45.56 4.11
3843 4393 5.929697 GCATGCAGCAGACTATACAATTA 57.070 39.130 14.21 0.00 44.79 1.40
3942 4492 5.068987 AGAGTGTCTAATGGAGCAGATTCTC 59.931 44.000 0.00 0.00 0.00 2.87
4012 4562 5.782047 ACCACAATGTCAACACCATAATTG 58.218 37.500 0.00 0.00 0.00 2.32
4028 4578 1.203050 CCCTGGAGTTCCAACCACAAT 60.203 52.381 1.99 0.00 46.97 2.71
4078 4628 9.401058 ACAAATTGGATCTCTGATAAGTTTAGG 57.599 33.333 0.00 0.00 0.00 2.69
4303 4854 5.447818 CCAGCGCAAAGATTAAAGGTCTTAG 60.448 44.000 11.47 0.00 34.97 2.18
4322 4873 3.879295 ACAATGTAAGATGATTCCCAGCG 59.121 43.478 0.00 0.00 36.05 5.18
4332 4883 2.804421 TTCGCGCACAATGTAAGATG 57.196 45.000 8.75 0.00 0.00 2.90
4336 4887 0.730265 GGGATTCGCGCACAATGTAA 59.270 50.000 8.75 0.00 0.00 2.41
4343 4894 1.160329 ATAGCAAGGGATTCGCGCAC 61.160 55.000 8.75 0.00 0.00 5.34
4410 4961 9.406828 GAACTGACAAAGAAAAGTAAACAAAGT 57.593 29.630 0.00 0.00 0.00 2.66
4414 4965 7.027161 GCTGAACTGACAAAGAAAAGTAAACA 58.973 34.615 0.00 0.00 0.00 2.83
4415 4966 7.027161 TGCTGAACTGACAAAGAAAAGTAAAC 58.973 34.615 0.00 0.00 0.00 2.01
4419 4970 5.591877 AGATGCTGAACTGACAAAGAAAAGT 59.408 36.000 0.00 0.00 0.00 2.66
4436 4987 5.300286 CCCTAAAATTCTAACCCAGATGCTG 59.700 44.000 0.00 0.00 31.77 4.41
4705 5256 8.706035 TGCTTCTCGTTTAGTTTGAGTAAATAC 58.294 33.333 0.00 0.00 0.00 1.89
4833 5384 1.812571 ACAAGGATGTTAAAGCGGCTG 59.187 47.619 1.81 0.00 35.91 4.85
4834 5385 2.200373 ACAAGGATGTTAAAGCGGCT 57.800 45.000 0.00 0.00 35.91 5.52
4884 5435 8.647796 CCACTTACTAGATCAACATTGGGTATA 58.352 37.037 0.00 0.00 0.00 1.47
4981 5532 1.193650 GCTAACGTGCACATCAAACGA 59.806 47.619 18.64 0.00 39.64 3.85
4995 5546 8.087982 ACATGATATTCCAAGTTATGCTAACG 57.912 34.615 0.00 0.00 0.00 3.18
5306 5857 7.463383 CGACTGTCTCTCATAACATTAAACAGC 60.463 40.741 6.21 0.00 36.04 4.40
5329 5880 3.440228 GTTCCAACTGATCTAGAGCGAC 58.560 50.000 3.11 0.00 0.00 5.19
5466 6017 0.472471 TATCTTGAACCCGCATCCCC 59.528 55.000 0.00 0.00 0.00 4.81
5549 6100 0.035439 GCCGAGAATCTCCAAACCCA 60.035 55.000 4.47 0.00 0.00 4.51
5624 6175 2.731451 GCCTTCTTCAAATTCGCCAAAC 59.269 45.455 0.00 0.00 0.00 2.93
5928 6479 4.046462 GCATGCATCGCAATTATTCTGTT 58.954 39.130 14.21 0.00 43.62 3.16
6008 6559 5.539574 TGACCAAACATTTCAGGATGTTGAT 59.460 36.000 4.23 0.00 46.53 2.57
6010 6561 5.199024 TGACCAAACATTTCAGGATGTTG 57.801 39.130 4.23 0.00 46.53 3.33
6349 6914 9.221933 TGAACAAACACGGTAAAACATATCTAT 57.778 29.630 0.00 0.00 0.00 1.98
6350 6915 8.497554 GTGAACAAACACGGTAAAACATATCTA 58.502 33.333 0.00 0.00 0.00 1.98
6402 6967 7.338710 TCCCTCAGAGTTTTGGATATGTTAAG 58.661 38.462 0.00 0.00 0.00 1.85
6534 7099 5.310451 TGTACCTCGGCACTTAAGATTTTT 58.690 37.500 10.09 0.00 0.00 1.94
6602 7167 2.814336 TGTTGTGTTGTAACAGTGCACA 59.186 40.909 21.04 0.00 40.05 4.57
6735 7301 4.651045 TCCAGAGAGATGCTACATTTGCTA 59.349 41.667 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.