Multiple sequence alignment - TraesCS1D01G325700

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 TraesCS1D01G325700 chr1D 100.000 2510 0 0 1 2510 418260547 418263056 0.000000e+00 4636.0
1 TraesCS1D01G325700 chr1D 95.812 191 8 0 2256 2446 435794802 435794992 2.420000e-80 309.0
2 TraesCS1D01G325700 chr1D 100.000 133 0 0 139 271 194139899 194139767 1.930000e-61 246.0
3 TraesCS1D01G325700 chr1D 100.000 128 0 0 141 268 478911674 478911801 1.160000e-58 237.0
4 TraesCS1D01G325700 chr1A 91.829 1493 88 21 266 1735 515650292 515651773 0.000000e+00 2050.0
5 TraesCS1D01G325700 chr1A 97.101 138 4 0 138 275 539330575 539330712 1.500000e-57 233.0
6 TraesCS1D01G325700 chr1A 90.141 142 14 0 2 143 515650153 515650294 4.260000e-43 185.0
7 TraesCS1D01G325700 chr1B 92.838 1117 60 9 630 1735 565919370 565920477 0.000000e+00 1602.0
8 TraesCS1D01G325700 chr1B 77.013 596 89 32 660 1227 566016340 566016915 5.250000e-77 298.0
9 TraesCS1D01G325700 chr1B 97.143 140 3 1 141 279 623732111 623731972 4.170000e-58 235.0
10 TraesCS1D01G325700 chr1B 84.906 159 18 6 1579 1735 566019413 566019567 3.340000e-34 156.0
11 TraesCS1D01G325700 chr7D 95.248 505 20 3 1760 2260 566568944 566568440 0.000000e+00 797.0
12 TraesCS1D01G325700 chr7D 95.767 189 7 1 2256 2444 566568404 566568217 1.130000e-78 303.0
13 TraesCS1D01G325700 chr7D 89.286 56 5 1 267 321 23848409 23848464 4.480000e-08 69.4
14 TraesCS1D01G325700 chr7D 89.091 55 4 2 266 318 509733592 509733646 1.610000e-07 67.6
15 TraesCS1D01G325700 chr2A 95.238 504 20 3 1760 2260 207584714 207585216 0.000000e+00 795.0
16 TraesCS1D01G325700 chr2A 93.035 201 12 2 2256 2456 207585252 207585450 2.440000e-75 292.0
17 TraesCS1D01G325700 chr5A 95.050 505 20 4 1760 2260 41983180 41982677 0.000000e+00 789.0
18 TraesCS1D01G325700 chr6D 94.851 505 22 3 1760 2260 159017202 159017706 0.000000e+00 785.0
19 TraesCS1D01G325700 chr6D 95.812 191 7 1 2256 2445 159017742 159017932 8.720000e-80 307.0
20 TraesCS1D01G325700 chr6D 95.789 190 8 0 2256 2445 316959474 316959663 8.720000e-80 307.0
21 TraesCS1D01G325700 chr3D 94.653 505 23 3 1760 2260 290743159 290742655 0.000000e+00 780.0
22 TraesCS1D01G325700 chr3D 94.653 505 22 4 1760 2260 84992847 84993350 0.000000e+00 778.0
23 TraesCS1D01G325700 chr3D 82.892 415 68 3 1011 1423 508072533 508072946 1.100000e-98 370.0
24 TraesCS1D01G325700 chr3D 95.812 191 7 1 2256 2445 290742619 290742429 8.720000e-80 307.0
25 TraesCS1D01G325700 chr3D 95.288 191 9 0 2256 2446 84993386 84993576 1.130000e-78 303.0
26 TraesCS1D01G325700 chr3D 97.059 136 4 0 141 276 210622549 210622414 1.940000e-56 230.0
27 TraesCS1D01G325700 chr7B 94.257 505 25 3 1760 2260 710503982 710504486 0.000000e+00 769.0
28 TraesCS1D01G325700 chr7B 78.505 107 14 6 268 366 710991855 710991750 7.500000e-06 62.1
29 TraesCS1D01G325700 chr3B 94.059 505 26 3 1760 2260 30521516 30521012 0.000000e+00 763.0
30 TraesCS1D01G325700 chr3B 93.401 197 12 1 2256 2451 30520976 30520780 8.780000e-75 291.0
31 TraesCS1D01G325700 chr2D 94.059 505 23 5 1760 2260 128366536 128367037 0.000000e+00 760.0
32 TraesCS1D01G325700 chr3A 82.380 437 74 3 1011 1445 645634549 645634984 6.550000e-101 377.0
33 TraesCS1D01G325700 chr3A 87.273 55 5 2 266 318 741672678 741672624 7.500000e-06 62.1
34 TraesCS1D01G325700 chr5D 94.792 192 8 1 2256 2445 565966460 565966269 5.250000e-77 298.0
35 TraesCS1D01G325700 chr5D 98.473 131 2 0 139 269 261390289 261390159 5.400000e-57 231.0
36 TraesCS1D01G325700 chr5D 89.286 56 5 1 267 321 529085926 529085871 4.480000e-08 69.4
37 TraesCS1D01G325700 chr4B 97.080 137 4 0 139 275 180671291 180671155 5.400000e-57 231.0
38 TraesCS1D01G325700 chr4B 97.101 138 3 1 139 276 363315928 363315792 5.400000e-57 231.0
39 TraesCS1D01G325700 chr4B 93.023 43 3 0 272 314 283365276 283365318 2.080000e-06 63.9
40 TraesCS1D01G325700 chr6B 97.744 133 3 0 139 271 67527386 67527518 1.940000e-56 230.0
41 TraesCS1D01G325700 chr6B 89.583 48 4 1 268 314 26200324 26200371 2.700000e-05 60.2
42 TraesCS1D01G325700 chrUn 92.000 50 4 0 269 318 84439450 84439499 1.250000e-08 71.3
43 TraesCS1D01G325700 chr4D 88.462 52 4 2 269 318 1380294 1380345 7.500000e-06 62.1


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 TraesCS1D01G325700 chr1D 418260547 418263056 2509 False 4636.0 4636 100.0000 1 2510 1 chr1D.!!$F1 2509
1 TraesCS1D01G325700 chr1A 515650153 515651773 1620 False 1117.5 2050 90.9850 2 1735 2 chr1A.!!$F2 1733
2 TraesCS1D01G325700 chr1B 565919370 565920477 1107 False 1602.0 1602 92.8380 630 1735 1 chr1B.!!$F1 1105
3 TraesCS1D01G325700 chr1B 566016340 566019567 3227 False 227.0 298 80.9595 660 1735 2 chr1B.!!$F2 1075
4 TraesCS1D01G325700 chr7D 566568217 566568944 727 True 550.0 797 95.5075 1760 2444 2 chr7D.!!$R1 684
5 TraesCS1D01G325700 chr2A 207584714 207585450 736 False 543.5 795 94.1365 1760 2456 2 chr2A.!!$F1 696
6 TraesCS1D01G325700 chr5A 41982677 41983180 503 True 789.0 789 95.0500 1760 2260 1 chr5A.!!$R1 500
7 TraesCS1D01G325700 chr6D 159017202 159017932 730 False 546.0 785 95.3315 1760 2445 2 chr6D.!!$F2 685
8 TraesCS1D01G325700 chr3D 290742429 290743159 730 True 543.5 780 95.2325 1760 2445 2 chr3D.!!$R2 685
9 TraesCS1D01G325700 chr3D 84992847 84993576 729 False 540.5 778 94.9705 1760 2446 2 chr3D.!!$F2 686
10 TraesCS1D01G325700 chr7B 710503982 710504486 504 False 769.0 769 94.2570 1760 2260 1 chr7B.!!$F1 500
11 TraesCS1D01G325700 chr3B 30520780 30521516 736 True 527.0 763 93.7300 1760 2451 2 chr3B.!!$R1 691
12 TraesCS1D01G325700 chr2D 128366536 128367037 501 False 760.0 760 94.0590 1760 2260 1 chr2D.!!$F1 500

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
151 152 0.112801 GAGCCCTATACTCCCTCCGT 59.887 60.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1534 3921 0.034089 TCCATCTCGAGAGGCTCACA 60.034 55.0 21.29 3.83 0.0 3.58 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
58 59 6.627395 AACAAGATCACGTTACCATTTGAA 57.373 33.333 0.00 0.00 0.00 2.69
110 111 6.691255 TTACTAACCCACATTAACTGACCT 57.309 37.500 0.00 0.00 0.00 3.85
123 124 3.703001 ACTGACCTGTGTTATCCAAGG 57.297 47.619 0.00 0.00 0.00 3.61
125 126 3.650942 ACTGACCTGTGTTATCCAAGGAA 59.349 43.478 0.00 0.00 0.00 3.36
127 128 5.222130 ACTGACCTGTGTTATCCAAGGAAAT 60.222 40.000 0.00 0.00 0.00 2.17
136 137 7.719633 TGTGTTATCCAAGGAAATAATAGAGCC 59.280 37.037 0.00 0.00 0.00 4.70
140 141 7.837359 ATCCAAGGAAATAATAGAGCCCTAT 57.163 36.000 0.00 0.00 37.19 2.57
141 142 8.933522 ATCCAAGGAAATAATAGAGCCCTATA 57.066 34.615 0.00 0.00 34.63 1.31
142 143 8.147244 TCCAAGGAAATAATAGAGCCCTATAC 57.853 38.462 0.00 0.00 34.63 1.47
143 144 7.962003 TCCAAGGAAATAATAGAGCCCTATACT 59.038 37.037 0.00 0.00 34.63 2.12
144 145 8.261522 CCAAGGAAATAATAGAGCCCTATACTC 58.738 40.741 0.00 0.00 34.63 2.59
145 146 7.981475 AGGAAATAATAGAGCCCTATACTCC 57.019 40.000 0.00 0.00 34.63 3.85
146 147 6.904093 AGGAAATAATAGAGCCCTATACTCCC 59.096 42.308 0.00 0.00 34.63 4.30
147 148 6.904093 GGAAATAATAGAGCCCTATACTCCCT 59.096 42.308 0.00 0.00 34.63 4.20
148 149 7.070198 GGAAATAATAGAGCCCTATACTCCCTC 59.930 44.444 0.00 0.00 34.63 4.30
149 150 4.340328 AATAGAGCCCTATACTCCCTCC 57.660 50.000 0.00 0.00 34.63 4.30
150 151 0.406361 AGAGCCCTATACTCCCTCCG 59.594 60.000 0.00 0.00 34.56 4.63
151 152 0.112801 GAGCCCTATACTCCCTCCGT 59.887 60.000 0.00 0.00 0.00 4.69
152 153 0.112801 AGCCCTATACTCCCTCCGTC 59.887 60.000 0.00 0.00 0.00 4.79
153 154 0.899253 GCCCTATACTCCCTCCGTCC 60.899 65.000 0.00 0.00 0.00 4.79
154 155 0.251698 CCCTATACTCCCTCCGTCCC 60.252 65.000 0.00 0.00 0.00 4.46
155 156 0.481567 CCTATACTCCCTCCGTCCCA 59.518 60.000 0.00 0.00 0.00 4.37
156 157 1.133262 CCTATACTCCCTCCGTCCCAA 60.133 57.143 0.00 0.00 0.00 4.12
157 158 2.674420 CTATACTCCCTCCGTCCCAAA 58.326 52.381 0.00 0.00 0.00 3.28
158 159 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
159 160 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
160 161 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
161 162 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
162 163 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
163 164 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
164 165 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
165 166 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
166 167 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
167 168 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
168 169 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
169 170 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
170 171 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
171 172 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
172 173 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
173 174 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
174 175 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
175 176 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
176 177 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
177 178 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
178 179 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
186 187 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
187 188 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
189 190 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
190 191 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
197 198 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
198 199 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
199 200 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
200 201 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
201 202 7.919091 GTCTAAATACGGATGTATCAAGTCACA 59.081 37.037 0.00 0.00 40.42 3.58
202 203 8.638873 TCTAAATACGGATGTATCAAGTCACAT 58.361 33.333 0.00 0.00 40.42 3.21
203 204 9.261180 CTAAATACGGATGTATCAAGTCACATT 57.739 33.333 0.00 0.00 40.42 2.71
204 205 8.506168 AAATACGGATGTATCAAGTCACATTT 57.494 30.769 0.00 0.00 40.42 2.32
205 206 8.506168 AATACGGATGTATCAAGTCACATTTT 57.494 30.769 0.00 0.00 40.42 1.82
206 207 9.607988 AATACGGATGTATCAAGTCACATTTTA 57.392 29.630 0.00 0.00 40.42 1.52
207 208 7.539712 ACGGATGTATCAAGTCACATTTTAG 57.460 36.000 0.00 0.00 35.55 1.85
208 209 7.103641 ACGGATGTATCAAGTCACATTTTAGT 58.896 34.615 0.00 0.00 35.55 2.24
209 210 8.255206 ACGGATGTATCAAGTCACATTTTAGTA 58.745 33.333 0.00 0.00 35.55 1.82
210 211 9.261180 CGGATGTATCAAGTCACATTTTAGTAT 57.739 33.333 0.00 0.00 35.55 2.12
241 242 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
242 243 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
243 244 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
244 245 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
245 246 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
246 247 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
254 255 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
255 256 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
256 257 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
257 258 8.359642 CAAATCTAAGACAAGAATTTTGGGACA 58.640 33.333 5.68 0.00 28.49 4.02
258 259 7.693969 ATCTAAGACAAGAATTTTGGGACAG 57.306 36.000 5.68 0.00 42.39 3.51
259 260 6.837312 TCTAAGACAAGAATTTTGGGACAGA 58.163 36.000 5.68 0.00 42.39 3.41
260 261 6.936900 TCTAAGACAAGAATTTTGGGACAGAG 59.063 38.462 5.68 0.00 42.39 3.35
261 262 4.401925 AGACAAGAATTTTGGGACAGAGG 58.598 43.478 5.68 0.00 42.39 3.69
262 263 3.500343 ACAAGAATTTTGGGACAGAGGG 58.500 45.455 5.68 0.00 42.39 4.30
263 264 3.140144 ACAAGAATTTTGGGACAGAGGGA 59.860 43.478 5.68 0.00 42.39 4.20
264 265 3.728385 AGAATTTTGGGACAGAGGGAG 57.272 47.619 0.00 0.00 42.39 4.30
282 283 1.591619 GAGTACAAAATAGCGTCGCCC 59.408 52.381 14.86 0.00 0.00 6.13
283 284 0.654160 GTACAAAATAGCGTCGCCCC 59.346 55.000 14.86 0.00 0.00 5.80
285 286 0.322187 ACAAAATAGCGTCGCCCCTT 60.322 50.000 14.86 1.94 0.00 3.95
289 290 2.632987 AATAGCGTCGCCCCTTAAAT 57.367 45.000 14.86 0.00 0.00 1.40
293 326 0.237498 GCGTCGCCCCTTAAATATGC 59.763 55.000 5.75 0.00 0.00 3.14
299 332 5.291128 CGTCGCCCCTTAAATATGCTATTAG 59.709 44.000 0.00 0.00 0.00 1.73
316 349 3.835378 TTAGCGAGACATTGTACACGA 57.165 42.857 0.00 0.00 0.00 4.35
323 356 5.449304 CGAGACATTGTACACGATATAGCA 58.551 41.667 0.00 0.00 0.00 3.49
329 362 7.323420 ACATTGTACACGATATAGCATGCTAT 58.677 34.615 35.68 35.68 41.58 2.97
330 363 7.819415 ACATTGTACACGATATAGCATGCTATT 59.181 33.333 37.80 26.53 39.65 1.73
331 364 9.301153 CATTGTACACGATATAGCATGCTATTA 57.699 33.333 37.80 25.23 39.65 0.98
332 365 8.911247 TTGTACACGATATAGCATGCTATTAG 57.089 34.615 37.80 29.52 39.65 1.73
333 366 6.972901 TGTACACGATATAGCATGCTATTAGC 59.027 38.462 37.80 26.28 42.82 3.09
345 378 2.815478 GCTATTAGCAGCCCTATAGCG 58.185 52.381 10.83 0.00 41.89 4.26
346 379 2.815478 CTATTAGCAGCCCTATAGCGC 58.185 52.381 0.00 0.00 38.01 5.92
347 380 1.270907 ATTAGCAGCCCTATAGCGCT 58.729 50.000 17.26 17.26 42.40 5.92
348 381 0.603569 TTAGCAGCCCTATAGCGCTC 59.396 55.000 16.34 0.00 40.94 5.03
349 382 0.251386 TAGCAGCCCTATAGCGCTCT 60.251 55.000 16.34 6.94 40.94 4.09
350 383 0.251386 AGCAGCCCTATAGCGCTCTA 60.251 55.000 16.34 8.00 37.86 2.43
351 384 0.820871 GCAGCCCTATAGCGCTCTAT 59.179 55.000 16.34 5.31 38.89 1.98
378 411 4.335082 TTCAATGGTTTTATCTCGTGCG 57.665 40.909 0.00 0.00 0.00 5.34
379 412 2.095213 TCAATGGTTTTATCTCGTGCGC 59.905 45.455 0.00 0.00 0.00 6.09
380 413 1.014352 ATGGTTTTATCTCGTGCGCC 58.986 50.000 4.18 0.00 0.00 6.53
384 417 0.391130 TTTTATCTCGTGCGCCTGCT 60.391 50.000 4.18 0.00 43.34 4.24
401 434 1.686587 TGCTCTCTCGGACAGTTGAAA 59.313 47.619 0.00 0.00 0.00 2.69
455 488 5.350365 CGGGATTGTAATGAACCCATATACG 59.650 44.000 0.00 0.00 40.45 3.06
457 490 6.370718 GGGATTGTAATGAACCCATATACGAC 59.629 42.308 0.00 0.00 40.20 4.34
469 508 4.480541 CCATATACGACTGCTCTGATCAC 58.519 47.826 0.00 0.00 0.00 3.06
470 509 4.217334 CCATATACGACTGCTCTGATCACT 59.783 45.833 0.00 0.00 0.00 3.41
473 512 2.437413 ACGACTGCTCTGATCACTGTA 58.563 47.619 0.00 0.00 0.00 2.74
492 531 5.940470 ACTGTAGATTTGGAGTGATTGGTTC 59.060 40.000 0.00 0.00 0.00 3.62
524 563 1.349688 ACTGCAACCGTAGAAATGGGA 59.650 47.619 0.00 0.00 35.92 4.37
539 578 3.652581 GGGAGAACACCCCTTTGAG 57.347 57.895 0.00 0.00 43.81 3.02
555 595 1.600916 GAGTGTGGTTGCTGGTCCC 60.601 63.158 0.00 0.00 0.00 4.46
572 612 0.824109 CCCATAGAGCCGTTGACTGA 59.176 55.000 0.00 0.00 0.00 3.41
580 620 1.680735 AGCCGTTGACTGAAATGCAAA 59.319 42.857 0.00 0.00 0.00 3.68
581 621 2.297033 AGCCGTTGACTGAAATGCAAAT 59.703 40.909 0.00 0.00 0.00 2.32
646 686 4.333633 CGAAGGAGAACATCAAGCTTTC 57.666 45.455 0.00 0.00 0.00 2.62
647 687 3.999663 CGAAGGAGAACATCAAGCTTTCT 59.000 43.478 0.00 0.00 32.14 2.52
835 894 4.082245 ACGGTAGCAAATGAAATTCCCTTG 60.082 41.667 0.00 0.00 33.67 3.61
875 934 2.857380 ATCACGCTCGCTCACTCACG 62.857 60.000 0.00 0.00 0.00 4.35
877 936 4.767841 CGCTCGCTCACTCACGCT 62.768 66.667 0.00 0.00 0.00 5.07
878 937 2.878520 GCTCGCTCACTCACGCTC 60.879 66.667 0.00 0.00 0.00 5.03
887 946 1.001293 TCACTCACGCTCTGCTTCATT 59.999 47.619 0.00 0.00 0.00 2.57
948 1010 2.225255 GTCTCCTTGCTTCAGTTTGCTC 59.775 50.000 0.00 0.00 0.00 4.26
1203 1268 2.606519 TTCACTACCCCCGCAGCT 60.607 61.111 0.00 0.00 0.00 4.24
1365 2871 1.901085 GGTCATCCTCAGGCTCGTT 59.099 57.895 0.00 0.00 0.00 3.85
1378 2884 4.243008 TCGTTGGCGGTCTTGGCA 62.243 61.111 0.00 0.00 43.36 4.92
1487 3874 0.737715 GGCGAGTACACCAAGAGCTG 60.738 60.000 0.00 0.00 0.00 4.24
1510 3897 1.107114 CTCTGGCTACCACGTCTGAT 58.893 55.000 0.00 0.00 0.00 2.90
1530 3917 1.303888 CTGGTTCAGCTGTGGCCAT 60.304 57.895 9.72 0.00 39.73 4.40
1534 3921 1.153524 TTCAGCTGTGGCCATTGGT 59.846 52.632 9.72 7.88 39.73 3.67
1535 3922 1.180456 TTCAGCTGTGGCCATTGGTG 61.180 55.000 24.82 24.82 39.73 4.17
1536 3923 1.904865 CAGCTGTGGCCATTGGTGT 60.905 57.895 23.39 1.62 39.73 4.16
1543 3930 2.048603 GGCCATTGGTGTGAGCCTC 61.049 63.158 4.26 0.00 40.57 4.70
1564 3953 2.556189 CTCGAGATGGATGAACGGAGAT 59.444 50.000 6.58 0.00 0.00 2.75
1573 3962 3.489738 GGATGAACGGAGATGCAAAATGG 60.490 47.826 0.00 0.00 0.00 3.16
1702 4100 3.605726 TCTGGTATAATCGTGGAGGGA 57.394 47.619 0.00 0.00 0.00 4.20
1718 4116 4.584325 TGGAGGGAATTTCTTTGTTCACTG 59.416 41.667 0.00 0.00 38.17 3.66
1735 4133 9.436957 TTGTTCACTGTATTAAGAAAGATCCTC 57.563 33.333 0.00 0.00 0.00 3.71
1736 4134 7.759886 TGTTCACTGTATTAAGAAAGATCCTCG 59.240 37.037 0.00 0.00 0.00 4.63
1737 4135 6.273825 TCACTGTATTAAGAAAGATCCTCGC 58.726 40.000 0.00 0.00 0.00 5.03
1738 4136 6.042777 CACTGTATTAAGAAAGATCCTCGCA 58.957 40.000 0.00 0.00 0.00 5.10
1739 4137 6.199908 CACTGTATTAAGAAAGATCCTCGCAG 59.800 42.308 0.00 0.00 0.00 5.18
1740 4138 5.601662 TGTATTAAGAAAGATCCTCGCAGG 58.398 41.667 0.00 0.00 36.46 4.85
1741 4139 3.543680 TTAAGAAAGATCCTCGCAGGG 57.456 47.619 2.86 0.00 35.59 4.45
1742 4140 0.107459 AAGAAAGATCCTCGCAGGGC 60.107 55.000 2.86 0.00 35.59 5.19
1794 4192 7.040478 CCACTAAAGGTCAAAATCTTCATGTGA 60.040 37.037 0.00 0.00 0.00 3.58
1808 4207 6.068670 TCTTCATGTGATATCTTCGTAGGGA 58.931 40.000 3.98 0.00 0.00 4.20
1815 4214 4.954202 TGATATCTTCGTAGGGAGTTGTGT 59.046 41.667 3.98 0.00 0.00 3.72
1839 4238 1.148310 CAAAGACAACCTCGCACGAT 58.852 50.000 0.00 0.00 0.00 3.73
1965 4364 8.465999 TCATCCAAATAGCGTCAAATTTGTATT 58.534 29.630 17.47 11.03 40.08 1.89
1993 4392 5.526846 CCACAAGTGTTGCCAATATTTTTGT 59.473 36.000 0.00 0.00 0.00 2.83
2008 4407 2.500509 TTTGTTCATTGGTTGGACGC 57.499 45.000 0.00 0.00 36.52 5.19
2013 4412 3.190327 TGTTCATTGGTTGGACGCTATTG 59.810 43.478 0.00 0.00 36.52 1.90
2040 4439 8.455682 CAAATAGGTTCAAAACGCTAATAAGGA 58.544 33.333 0.00 0.00 0.00 3.36
2077 4476 5.337250 CCTTAATGTGGTCGCTATGGCTATA 60.337 44.000 0.00 0.00 36.09 1.31
2356 4798 4.081406 AGAATTGGCTGTGTGCATCTTAA 58.919 39.130 0.00 0.00 45.15 1.85
2384 4826 1.153429 GGCCGGGTGTCACTCATAC 60.153 63.158 2.18 0.00 0.00 2.39
2395 4837 6.338146 GGTGTCACTCATACTGCTTTGTATA 58.662 40.000 2.35 0.00 32.48 1.47
2396 4838 6.986817 GGTGTCACTCATACTGCTTTGTATAT 59.013 38.462 2.35 0.00 32.48 0.86
2465 4907 7.745620 AAAATTAAGAAAGATCCTGTGTCGT 57.254 32.000 0.00 0.00 0.00 4.34
2466 4908 6.727824 AATTAAGAAAGATCCTGTGTCGTG 57.272 37.500 0.00 0.00 0.00 4.35
2467 4909 5.462530 TTAAGAAAGATCCTGTGTCGTGA 57.537 39.130 0.00 0.00 0.00 4.35
2468 4910 4.543590 AAGAAAGATCCTGTGTCGTGAT 57.456 40.909 0.00 0.00 0.00 3.06
2469 4911 4.116747 AGAAAGATCCTGTGTCGTGATC 57.883 45.455 0.00 0.00 36.08 2.92
2470 4912 3.511540 AGAAAGATCCTGTGTCGTGATCA 59.488 43.478 0.00 0.00 37.86 2.92
2471 4913 3.961480 AAGATCCTGTGTCGTGATCAA 57.039 42.857 0.00 0.00 37.86 2.57
2472 4914 4.478206 AAGATCCTGTGTCGTGATCAAT 57.522 40.909 0.00 0.00 37.86 2.57
2473 4915 4.478206 AGATCCTGTGTCGTGATCAATT 57.522 40.909 0.00 0.00 37.86 2.32
2474 4916 5.598416 AGATCCTGTGTCGTGATCAATTA 57.402 39.130 0.00 0.00 37.86 1.40
2475 4917 6.166984 AGATCCTGTGTCGTGATCAATTAT 57.833 37.500 0.00 0.00 37.86 1.28
2476 4918 6.586344 AGATCCTGTGTCGTGATCAATTATT 58.414 36.000 0.00 0.00 37.86 1.40
2477 4919 6.703607 AGATCCTGTGTCGTGATCAATTATTC 59.296 38.462 0.00 0.00 37.86 1.75
2478 4920 5.977635 TCCTGTGTCGTGATCAATTATTCT 58.022 37.500 0.00 0.00 0.00 2.40
2479 4921 7.107639 TCCTGTGTCGTGATCAATTATTCTA 57.892 36.000 0.00 0.00 0.00 2.10
2480 4922 6.978659 TCCTGTGTCGTGATCAATTATTCTAC 59.021 38.462 0.00 0.00 0.00 2.59
2481 4923 6.980978 CCTGTGTCGTGATCAATTATTCTACT 59.019 38.462 0.00 0.00 0.00 2.57
2482 4924 8.135529 CCTGTGTCGTGATCAATTATTCTACTA 58.864 37.037 0.00 0.00 0.00 1.82
2483 4925 9.175060 CTGTGTCGTGATCAATTATTCTACTAG 57.825 37.037 0.00 0.00 0.00 2.57
2484 4926 8.683615 TGTGTCGTGATCAATTATTCTACTAGT 58.316 33.333 0.00 0.00 0.00 2.57
2485 4927 8.959058 GTGTCGTGATCAATTATTCTACTAGTG 58.041 37.037 5.39 0.00 0.00 2.74
2486 4928 8.899771 TGTCGTGATCAATTATTCTACTAGTGA 58.100 33.333 5.39 0.00 0.00 3.41
2487 4929 9.900710 GTCGTGATCAATTATTCTACTAGTGAT 57.099 33.333 5.39 0.00 0.00 3.06
2500 4942 8.830915 TTCTACTAGTGATTCCTCTCAAATCT 57.169 34.615 5.39 0.00 34.80 2.40
2501 4943 8.830915 TCTACTAGTGATTCCTCTCAAATCTT 57.169 34.615 5.39 0.00 34.80 2.40
2502 4944 9.922477 TCTACTAGTGATTCCTCTCAAATCTTA 57.078 33.333 5.39 0.00 34.80 2.10
2505 4947 9.041354 ACTAGTGATTCCTCTCAAATCTTAACT 57.959 33.333 0.00 0.00 34.80 2.24
2506 4948 9.311916 CTAGTGATTCCTCTCAAATCTTAACTG 57.688 37.037 0.00 0.00 34.80 3.16
2507 4949 7.684529 AGTGATTCCTCTCAAATCTTAACTGT 58.315 34.615 0.00 0.00 34.80 3.55
2508 4950 8.160106 AGTGATTCCTCTCAAATCTTAACTGTT 58.840 33.333 0.00 0.00 34.80 3.16
2509 4951 9.436957 GTGATTCCTCTCAAATCTTAACTGTTA 57.563 33.333 0.00 0.00 34.80 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.039270 TGTTAGAATAATTAGAACAGAGCGCA 58.961 34.615 11.47 0.00 0.00 6.09
40 41 6.721571 TTCTCTTCAAATGGTAACGTGATC 57.278 37.500 0.00 0.00 42.51 2.92
58 59 8.854614 ATGCTCACTTGTTATAAGTTTTCTCT 57.145 30.769 0.00 0.00 0.00 3.10
94 95 3.140325 ACACAGGTCAGTTAATGTGGG 57.860 47.619 8.81 0.00 45.71 4.61
95 96 5.354234 GGATAACACAGGTCAGTTAATGTGG 59.646 44.000 8.81 0.00 45.71 4.17
110 111 7.719633 GGCTCTATTATTTCCTTGGATAACACA 59.280 37.037 0.00 0.00 0.00 3.72
123 124 7.070198 GGAGGGAGTATAGGGCTCTATTATTTC 59.930 44.444 12.34 4.82 37.39 2.17
125 126 6.445577 GGAGGGAGTATAGGGCTCTATTATT 58.554 44.000 12.34 0.00 37.39 1.40
127 128 4.079901 CGGAGGGAGTATAGGGCTCTATTA 60.080 50.000 12.34 0.00 37.39 0.98
136 137 0.481567 TGGGACGGAGGGAGTATAGG 59.518 60.000 0.00 0.00 0.00 2.57
140 141 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
141 142 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
142 143 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
143 144 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
144 145 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
145 146 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
146 147 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
147 148 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
148 149 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
149 150 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
150 151 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
151 152 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
152 153 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
160 161 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
161 162 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
163 164 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
164 165 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
171 172 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
172 173 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
173 174 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
174 175 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
175 176 7.919091 TGTGACTTGATACATCCGTATTTAGAC 59.081 37.037 0.00 0.00 38.48 2.59
176 177 8.002984 TGTGACTTGATACATCCGTATTTAGA 57.997 34.615 0.00 0.00 38.48 2.10
177 178 8.818141 ATGTGACTTGATACATCCGTATTTAG 57.182 34.615 0.00 0.00 38.48 1.85
178 179 9.607988 AAATGTGACTTGATACATCCGTATTTA 57.392 29.630 0.00 0.00 38.48 1.40
179 180 8.506168 AAATGTGACTTGATACATCCGTATTT 57.494 30.769 0.00 0.00 38.48 1.40
180 181 8.506168 AAAATGTGACTTGATACATCCGTATT 57.494 30.769 0.00 0.00 38.48 1.89
181 182 9.261180 CTAAAATGTGACTTGATACATCCGTAT 57.739 33.333 0.00 0.00 41.16 3.06
182 183 8.255206 ACTAAAATGTGACTTGATACATCCGTA 58.745 33.333 0.00 0.00 36.56 4.02
183 184 7.103641 ACTAAAATGTGACTTGATACATCCGT 58.896 34.615 0.00 0.00 36.56 4.69
184 185 7.539712 ACTAAAATGTGACTTGATACATCCG 57.460 36.000 0.00 0.00 36.56 4.18
215 216 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
216 217 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
217 218 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
218 219 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
219 220 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
220 221 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
228 229 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
229 230 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
230 231 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
231 232 8.359642 TGTCCCAAAATTCTTGTCTTAGATTTG 58.640 33.333 0.00 0.00 29.84 2.32
232 233 8.477419 TGTCCCAAAATTCTTGTCTTAGATTT 57.523 30.769 0.00 0.00 0.00 2.17
233 234 7.944554 TCTGTCCCAAAATTCTTGTCTTAGATT 59.055 33.333 0.00 0.00 0.00 2.40
234 235 7.461749 TCTGTCCCAAAATTCTTGTCTTAGAT 58.538 34.615 0.00 0.00 0.00 1.98
235 236 6.837312 TCTGTCCCAAAATTCTTGTCTTAGA 58.163 36.000 0.00 0.00 0.00 2.10
236 237 6.150140 CCTCTGTCCCAAAATTCTTGTCTTAG 59.850 42.308 0.00 0.00 0.00 2.18
237 238 6.003950 CCTCTGTCCCAAAATTCTTGTCTTA 58.996 40.000 0.00 0.00 0.00 2.10
238 239 4.829492 CCTCTGTCCCAAAATTCTTGTCTT 59.171 41.667 0.00 0.00 0.00 3.01
239 240 4.401925 CCTCTGTCCCAAAATTCTTGTCT 58.598 43.478 0.00 0.00 0.00 3.41
240 241 3.507622 CCCTCTGTCCCAAAATTCTTGTC 59.492 47.826 0.00 0.00 0.00 3.18
241 242 3.140144 TCCCTCTGTCCCAAAATTCTTGT 59.860 43.478 0.00 0.00 0.00 3.16
242 243 3.760684 CTCCCTCTGTCCCAAAATTCTTG 59.239 47.826 0.00 0.00 0.00 3.02
243 244 3.399305 ACTCCCTCTGTCCCAAAATTCTT 59.601 43.478 0.00 0.00 0.00 2.52
244 245 2.989571 ACTCCCTCTGTCCCAAAATTCT 59.010 45.455 0.00 0.00 0.00 2.40
245 246 3.441500 ACTCCCTCTGTCCCAAAATTC 57.558 47.619 0.00 0.00 0.00 2.17
246 247 3.655777 TGTACTCCCTCTGTCCCAAAATT 59.344 43.478 0.00 0.00 0.00 1.82
247 248 3.256704 TGTACTCCCTCTGTCCCAAAAT 58.743 45.455 0.00 0.00 0.00 1.82
248 249 2.696775 TGTACTCCCTCTGTCCCAAAA 58.303 47.619 0.00 0.00 0.00 2.44
249 250 2.409064 TGTACTCCCTCTGTCCCAAA 57.591 50.000 0.00 0.00 0.00 3.28
250 251 2.409064 TTGTACTCCCTCTGTCCCAA 57.591 50.000 0.00 0.00 0.00 4.12
251 252 2.409064 TTTGTACTCCCTCTGTCCCA 57.591 50.000 0.00 0.00 0.00 4.37
252 253 4.683671 GCTATTTTGTACTCCCTCTGTCCC 60.684 50.000 0.00 0.00 0.00 4.46
253 254 4.443621 GCTATTTTGTACTCCCTCTGTCC 58.556 47.826 0.00 0.00 0.00 4.02
254 255 4.113354 CGCTATTTTGTACTCCCTCTGTC 58.887 47.826 0.00 0.00 0.00 3.51
255 256 3.514309 ACGCTATTTTGTACTCCCTCTGT 59.486 43.478 0.00 0.00 0.00 3.41
256 257 4.113354 GACGCTATTTTGTACTCCCTCTG 58.887 47.826 0.00 0.00 0.00 3.35
257 258 3.181489 CGACGCTATTTTGTACTCCCTCT 60.181 47.826 0.00 0.00 0.00 3.69
258 259 3.114065 CGACGCTATTTTGTACTCCCTC 58.886 50.000 0.00 0.00 0.00 4.30
259 260 2.737679 GCGACGCTATTTTGTACTCCCT 60.738 50.000 13.73 0.00 0.00 4.20
260 261 1.591619 GCGACGCTATTTTGTACTCCC 59.408 52.381 13.73 0.00 0.00 4.30
261 262 1.591619 GGCGACGCTATTTTGTACTCC 59.408 52.381 20.77 0.00 0.00 3.85
262 263 1.591619 GGGCGACGCTATTTTGTACTC 59.408 52.381 20.77 0.00 0.00 2.59
263 264 1.648504 GGGCGACGCTATTTTGTACT 58.351 50.000 20.77 0.00 0.00 2.73
264 265 0.654160 GGGGCGACGCTATTTTGTAC 59.346 55.000 20.77 0.00 40.76 2.90
282 283 8.709386 ATGTCTCGCTAATAGCATATTTAAGG 57.291 34.615 13.15 0.00 42.58 2.69
283 284 9.964253 CAATGTCTCGCTAATAGCATATTTAAG 57.036 33.333 13.15 0.00 42.58 1.85
289 290 6.861572 GTGTACAATGTCTCGCTAATAGCATA 59.138 38.462 13.15 0.00 42.58 3.14
293 326 5.507974 TCGTGTACAATGTCTCGCTAATAG 58.492 41.667 0.00 0.00 0.00 1.73
299 332 4.321217 GCTATATCGTGTACAATGTCTCGC 59.679 45.833 0.00 0.00 0.00 5.03
358 391 2.095213 GCGCACGAGATAAAACCATTGA 59.905 45.455 0.30 0.00 0.00 2.57
359 392 2.440501 GCGCACGAGATAAAACCATTG 58.559 47.619 0.30 0.00 0.00 2.82
361 394 1.014352 GGCGCACGAGATAAAACCAT 58.986 50.000 10.83 0.00 0.00 3.55
372 405 4.121669 GAGAGAGCAGGCGCACGA 62.122 66.667 10.83 0.00 42.27 4.35
378 411 1.882989 AACTGTCCGAGAGAGCAGGC 61.883 60.000 0.00 0.00 37.11 4.85
379 412 0.108898 CAACTGTCCGAGAGAGCAGG 60.109 60.000 0.00 0.00 37.11 4.85
380 413 0.884514 TCAACTGTCCGAGAGAGCAG 59.115 55.000 0.00 0.00 38.17 4.24
384 417 4.336889 ACATTTTCAACTGTCCGAGAGA 57.663 40.909 0.00 0.00 0.00 3.10
401 434 2.965572 ATTGGCTGCGCAATTACATT 57.034 40.000 13.05 1.88 0.00 2.71
455 488 4.916983 ATCTACAGTGATCAGAGCAGTC 57.083 45.455 0.00 0.00 0.00 3.51
457 490 4.809958 CCAAATCTACAGTGATCAGAGCAG 59.190 45.833 0.00 0.00 0.00 4.24
469 508 5.063944 CGAACCAATCACTCCAAATCTACAG 59.936 44.000 0.00 0.00 0.00 2.74
470 509 4.935205 CGAACCAATCACTCCAAATCTACA 59.065 41.667 0.00 0.00 0.00 2.74
473 512 4.021102 ACGAACCAATCACTCCAAATCT 57.979 40.909 0.00 0.00 0.00 2.40
492 531 1.719780 GGTTGCAGTTTCTCTCGTACG 59.280 52.381 9.53 9.53 0.00 3.67
524 563 1.133792 CCACACTCAAAGGGGTGTTCT 60.134 52.381 0.00 0.00 43.65 3.01
539 578 0.037590 TATGGGACCAGCAACCACAC 59.962 55.000 0.00 0.00 37.05 3.82
555 595 3.242543 GCATTTCAGTCAACGGCTCTATG 60.243 47.826 0.00 0.00 0.00 2.23
580 620 7.068226 AGGCTTTCGGTGCTTACATTTTATTAT 59.932 33.333 0.00 0.00 0.00 1.28
581 621 6.376018 AGGCTTTCGGTGCTTACATTTTATTA 59.624 34.615 0.00 0.00 0.00 0.98
589 629 2.843401 TTAGGCTTTCGGTGCTTACA 57.157 45.000 0.00 0.00 0.00 2.41
616 656 1.968493 TGTTCTCCTTCGGTGCTTACT 59.032 47.619 0.00 0.00 0.00 2.24
646 686 1.882623 GGACTGCCCTTCTGACAAAAG 59.117 52.381 0.00 0.00 0.00 2.27
647 687 1.214175 TGGACTGCCCTTCTGACAAAA 59.786 47.619 0.00 0.00 35.38 2.44
835 894 5.411361 TGATTAATATAGTCAATGGCGTGCC 59.589 40.000 3.30 3.30 0.00 5.01
875 934 3.072944 AGAGTGTTGAATGAAGCAGAGC 58.927 45.455 0.00 0.00 0.00 4.09
876 935 4.313282 TGAGAGTGTTGAATGAAGCAGAG 58.687 43.478 0.00 0.00 0.00 3.35
877 936 4.341366 TGAGAGTGTTGAATGAAGCAGA 57.659 40.909 0.00 0.00 0.00 4.26
878 937 4.514441 ACTTGAGAGTGTTGAATGAAGCAG 59.486 41.667 0.00 0.00 33.99 4.24
887 946 2.158957 GGTGGTGACTTGAGAGTGTTGA 60.159 50.000 0.00 0.00 35.88 3.18
948 1010 5.049818 GCTGATTTATTCTTGATCACTCCCG 60.050 44.000 0.00 0.00 0.00 5.14
1378 2884 2.125512 GAGCACGAAGATGGCGGT 60.126 61.111 0.00 0.00 0.00 5.68
1491 3878 1.107114 ATCAGACGTGGTAGCCAGAG 58.893 55.000 0.00 0.00 32.34 3.35
1510 3897 1.228245 GGCCACAGCTGAACCAGAA 60.228 57.895 23.35 0.00 39.73 3.02
1530 3917 0.539669 TCTCGAGAGGCTCACACCAA 60.540 55.000 18.26 0.00 0.00 3.67
1534 3921 0.034089 TCCATCTCGAGAGGCTCACA 60.034 55.000 21.29 3.83 0.00 3.58
1535 3922 1.000385 CATCCATCTCGAGAGGCTCAC 60.000 57.143 21.29 9.85 0.00 3.51
1536 3923 1.133668 TCATCCATCTCGAGAGGCTCA 60.134 52.381 21.29 7.73 0.00 4.26
1543 3930 1.950216 TCTCCGTTCATCCATCTCGAG 59.050 52.381 5.93 5.93 0.00 4.04
1692 4090 3.502123 ACAAAGAAATTCCCTCCACGA 57.498 42.857 0.00 0.00 0.00 4.35
1718 4116 4.991687 CCCTGCGAGGATCTTTCTTAATAC 59.008 45.833 4.00 0.00 37.67 1.89
1743 4141 2.399611 GATACAGTTGCGCCGTGC 59.600 61.111 4.18 0.00 46.70 5.34
1744 4142 1.348538 TTCGATACAGTTGCGCCGTG 61.349 55.000 4.18 1.41 0.00 4.94
1745 4143 1.076533 CTTCGATACAGTTGCGCCGT 61.077 55.000 4.18 0.00 0.00 5.68
1746 4144 0.800683 TCTTCGATACAGTTGCGCCG 60.801 55.000 4.18 0.00 0.00 6.46
1747 4145 1.571919 ATCTTCGATACAGTTGCGCC 58.428 50.000 4.18 0.00 0.00 6.53
1748 4146 2.033662 GGAATCTTCGATACAGTTGCGC 60.034 50.000 0.00 0.00 0.00 6.09
1749 4147 3.000322 GTGGAATCTTCGATACAGTTGCG 60.000 47.826 0.00 0.00 0.00 4.85
1750 4148 4.184629 AGTGGAATCTTCGATACAGTTGC 58.815 43.478 0.00 0.00 0.00 4.17
1751 4149 7.010552 CCTTTAGTGGAATCTTCGATACAGTTG 59.989 40.741 0.00 0.00 0.00 3.16
1752 4150 7.042335 CCTTTAGTGGAATCTTCGATACAGTT 58.958 38.462 0.00 0.00 0.00 3.16
1753 4151 6.154706 ACCTTTAGTGGAATCTTCGATACAGT 59.845 38.462 0.00 0.00 0.00 3.55
1754 4152 6.574350 ACCTTTAGTGGAATCTTCGATACAG 58.426 40.000 0.00 0.00 0.00 2.74
1755 4153 6.153851 TGACCTTTAGTGGAATCTTCGATACA 59.846 38.462 0.00 0.00 0.00 2.29
1756 4154 6.570692 TGACCTTTAGTGGAATCTTCGATAC 58.429 40.000 0.00 0.00 0.00 2.24
1757 4155 6.785337 TGACCTTTAGTGGAATCTTCGATA 57.215 37.500 0.00 0.00 0.00 2.92
1758 4156 5.677319 TGACCTTTAGTGGAATCTTCGAT 57.323 39.130 0.00 0.00 0.00 3.59
1794 4192 5.934402 AACACAACTCCCTACGAAGATAT 57.066 39.130 0.00 0.00 0.00 1.63
1808 4207 5.014202 AGGTTGTCTTTGGTTAACACAACT 58.986 37.500 25.58 15.59 44.12 3.16
1815 4214 2.614983 GTGCGAGGTTGTCTTTGGTTAA 59.385 45.455 0.00 0.00 0.00 2.01
1965 4364 2.904866 GGCAACACTTGTGGGCGA 60.905 61.111 5.72 0.00 34.73 5.54
1993 4392 2.163412 GCAATAGCGTCCAACCAATGAA 59.837 45.455 0.00 0.00 0.00 2.57
2008 4407 6.092748 AGCGTTTTGAACCTATTTGCAATAG 58.907 36.000 0.00 4.56 0.00 1.73
2013 4412 7.220108 CCTTATTAGCGTTTTGAACCTATTTGC 59.780 37.037 0.00 0.00 0.00 3.68
2040 4439 2.106511 ACATTAAGGCATACGCTCCCAT 59.893 45.455 0.00 0.00 38.60 4.00
2110 4511 4.443034 CCGGAAAATAACCTGTAGAGGAGG 60.443 50.000 13.94 0.00 42.93 4.30
2356 4798 1.149174 CACCCGGCCTCTGCATAAT 59.851 57.895 0.00 0.00 40.13 1.28
2446 4888 5.185056 TGATCACGACACAGGATCTTTCTTA 59.815 40.000 0.00 0.00 38.55 2.10
2449 4891 3.849911 TGATCACGACACAGGATCTTTC 58.150 45.455 0.00 0.00 38.55 2.62
2453 4895 6.703607 AGAATAATTGATCACGACACAGGATC 59.296 38.462 0.00 0.00 38.29 3.36
2454 4896 6.586344 AGAATAATTGATCACGACACAGGAT 58.414 36.000 0.00 0.00 0.00 3.24
2455 4897 5.977635 AGAATAATTGATCACGACACAGGA 58.022 37.500 0.00 0.00 0.00 3.86
2456 4898 6.980978 AGTAGAATAATTGATCACGACACAGG 59.019 38.462 0.00 0.00 0.00 4.00
2457 4899 7.993821 AGTAGAATAATTGATCACGACACAG 57.006 36.000 0.00 0.00 0.00 3.66
2458 4900 8.683615 ACTAGTAGAATAATTGATCACGACACA 58.316 33.333 3.59 0.00 0.00 3.72
2459 4901 8.959058 CACTAGTAGAATAATTGATCACGACAC 58.041 37.037 3.59 0.00 0.00 3.67
2460 4902 8.899771 TCACTAGTAGAATAATTGATCACGACA 58.100 33.333 3.59 0.00 0.00 4.35
2461 4903 9.900710 ATCACTAGTAGAATAATTGATCACGAC 57.099 33.333 3.59 0.00 0.00 4.34
2474 4916 9.432982 AGATTTGAGAGGAATCACTAGTAGAAT 57.567 33.333 3.59 0.00 36.26 2.40
2475 4917 8.830915 AGATTTGAGAGGAATCACTAGTAGAA 57.169 34.615 3.59 0.00 36.26 2.10
2476 4918 8.830915 AAGATTTGAGAGGAATCACTAGTAGA 57.169 34.615 3.59 0.00 36.26 2.59
2479 4921 9.041354 AGTTAAGATTTGAGAGGAATCACTAGT 57.959 33.333 0.00 0.00 36.26 2.57
2480 4922 9.311916 CAGTTAAGATTTGAGAGGAATCACTAG 57.688 37.037 0.00 0.00 36.26 2.57
2481 4923 8.816894 ACAGTTAAGATTTGAGAGGAATCACTA 58.183 33.333 0.00 0.00 36.26 2.74
2482 4924 7.684529 ACAGTTAAGATTTGAGAGGAATCACT 58.315 34.615 0.00 0.00 36.26 3.41
2483 4925 7.913674 ACAGTTAAGATTTGAGAGGAATCAC 57.086 36.000 0.00 0.00 36.26 3.06


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

AutoCloner maintained by Alex Coulton.