Multiple sequence alignment - TraesCS5B01G311900

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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 TraesCS5B01G311900 chr5B 100.000 2936 0 0 1 2936 493482322 493479387 0.000000e+00 5422.0
1 TraesCS5B01G311900 chr5B 90.826 763 66 3 1117 1876 493516810 493516049 0.000000e+00 1018.0
2 TraesCS5B01G311900 chr5B 84.428 533 52 17 450 966 493517392 493516875 2.030000e-136 496.0
3 TraesCS5B01G311900 chr5B 83.965 343 49 5 1233 1575 493695441 493695105 1.010000e-84 324.0
4 TraesCS5B01G311900 chr5B 100.000 41 0 0 2123 2163 493514059 493514019 3.140000e-10 76.8
5 TraesCS5B01G311900 chr5D 94.029 1658 50 16 451 2085 410953721 410952090 0.000000e+00 2468.0
6 TraesCS5B01G311900 chr5D 91.495 823 60 4 1123 1945 411149415 411148603 0.000000e+00 1123.0
7 TraesCS5B01G311900 chr5D 83.811 593 67 18 451 1033 411150018 411149445 1.200000e-148 536.0
8 TraesCS5B01G311900 chr5D 86.118 389 29 15 2082 2467 410952004 410951638 2.120000e-106 396.0
9 TraesCS5B01G311900 chr5D 85.131 343 45 5 1233 1575 411225760 411225424 2.170000e-91 346.0
10 TraesCS5B01G311900 chr5D 83.901 323 41 7 1242 1563 411790599 411790287 6.150000e-77 298.0
11 TraesCS5B01G311900 chr5D 95.238 126 6 0 329 454 410953900 410953775 1.780000e-47 200.0
12 TraesCS5B01G311900 chr5D 80.992 121 12 5 2123 2243 411142028 411141919 5.210000e-13 86.1
13 TraesCS5B01G311900 chr5D 100.000 37 0 0 1935 1971 411142678 411142642 5.250000e-08 69.4
14 TraesCS5B01G311900 chr5A 92.683 1394 70 8 1088 2464 522883507 522882129 0.000000e+00 1980.0
15 TraesCS5B01G311900 chr5A 91.591 880 64 3 1117 1994 522956871 522956000 0.000000e+00 1206.0
16 TraesCS5B01G311900 chr5A 84.257 343 48 5 1233 1575 523148706 523148370 2.180000e-86 329.0
17 TraesCS5B01G311900 chr5A 94.410 161 7 1 465 623 522884187 522884027 2.260000e-61 246.0
18 TraesCS5B01G311900 chr5A 84.120 233 6 11 820 1051 522884028 522883826 2.310000e-46 196.0
19 TraesCS5B01G311900 chr5A 89.630 135 13 1 1995 2128 522949411 522949277 1.400000e-38 171.0
20 TraesCS5B01G311900 chr6A 85.000 500 50 8 2460 2936 373082607 373082110 4.400000e-133 484.0
21 TraesCS5B01G311900 chrUn 87.075 294 32 3 2464 2756 351362967 351362679 7.850000e-86 327.0
22 TraesCS5B01G311900 chrUn 87.075 294 32 3 2464 2756 357664896 357664608 7.850000e-86 327.0
23 TraesCS5B01G311900 chrUn 85.240 271 12 14 2693 2936 351362645 351362376 1.350000e-63 254.0
24 TraesCS5B01G311900 chrUn 84.502 271 14 10 2693 2936 357664574 357664305 2.920000e-60 243.0
25 TraesCS5B01G311900 chr1A 88.028 284 23 9 1 275 292338271 292337990 2.820000e-85 326.0
26 TraesCS5B01G311900 chr2D 90.650 246 17 3 1 244 542742643 542742884 3.650000e-84 322.0
27 TraesCS5B01G311900 chr2D 87.956 274 20 8 3 269 564704475 564704742 7.900000e-81 311.0
28 TraesCS5B01G311900 chr2D 95.652 46 2 0 2484 2529 157009228 157009183 1.130000e-09 75.0
29 TraesCS5B01G311900 chr7A 87.778 270 21 9 2 263 46281078 46281343 3.680000e-79 305.0
30 TraesCS5B01G311900 chr1B 88.015 267 20 8 1 260 161207652 161207913 3.680000e-79 305.0
31 TraesCS5B01G311900 chr1B 79.661 118 20 4 2468 2583 57809021 57809136 6.740000e-12 82.4
32 TraesCS5B01G311900 chr7D 86.716 271 24 10 3 268 626924066 626924329 1.030000e-74 291.0
33 TraesCS5B01G311900 chr3B 86.131 274 28 7 1 269 48982057 48981789 1.330000e-73 287.0
34 TraesCS5B01G311900 chr3B 85.507 276 27 10 1 269 328461987 328462256 2.880000e-70 276.0
35 TraesCS5B01G311900 chr3B 100.000 33 0 0 2483 2515 813256700 813256668 8.790000e-06 62.1
36 TraesCS5B01G311900 chr3A 85.017 287 37 3 2471 2756 45124348 45124067 1.330000e-73 287.0
37 TraesCS5B01G311900 chr3A 92.157 153 7 3 2691 2838 45124036 45123884 8.240000e-51 211.0
38 TraesCS5B01G311900 chr3A 92.308 78 6 0 2859 2936 45123814 45123737 8.600000e-21 111.0
39 TraesCS5B01G311900 chr3A 96.970 33 1 0 2483 2515 17375117 17375085 4.090000e-04 56.5
40 TraesCS5B01G311900 chr4A 85.199 277 26 13 1 269 730883226 730882957 1.340000e-68 270.0
41 TraesCS5B01G311900 chr4D 90.000 80 7 1 2858 2936 487059385 487059464 5.180000e-18 102.0
42 TraesCS5B01G311900 chr3D 86.275 102 4 8 2691 2790 126982942 126982849 5.180000e-18 102.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G311900 chr5B 493479387 493482322 2935 True 5422.000000 5422 100.000000 1 2936 1 chr5B.!!$R1 2935
1 TraesCS5B01G311900 chr5B 493514019 493517392 3373 True 530.266667 1018 91.751333 450 2163 3 chr5B.!!$R3 1713
2 TraesCS5B01G311900 chr5D 410951638 410953900 2262 True 1021.333333 2468 91.795000 329 2467 3 chr5D.!!$R3 2138
3 TraesCS5B01G311900 chr5D 411148603 411150018 1415 True 829.500000 1123 87.653000 451 1945 2 chr5D.!!$R5 1494
4 TraesCS5B01G311900 chr5A 522956000 522956871 871 True 1206.000000 1206 91.591000 1117 1994 1 chr5A.!!$R2 877
5 TraesCS5B01G311900 chr5A 522882129 522884187 2058 True 807.333333 1980 90.404333 465 2464 3 chr5A.!!$R4 1999
6 TraesCS5B01G311900 chrUn 351362376 351362967 591 True 290.500000 327 86.157500 2464 2936 2 chrUn.!!$R1 472
7 TraesCS5B01G311900 chrUn 357664305 357664896 591 True 285.000000 327 85.788500 2464 2936 2 chrUn.!!$R2 472
8 TraesCS5B01G311900 chr3A 45123737 45124348 611 True 203.000000 287 89.827333 2471 2936 3 chr3A.!!$R2 465

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
649 710 0.03889 GCCAAAGAGGGAAGAAGCCT 59.961 55.0 0.0 0.0 38.09 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2382 4644 0.464036 AGATCATTCGCGGGCTAACA 59.536 50.0 6.13 0.0 0.0 2.41 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
26 27 8.758715 GGATAATGCACTTTTGATTAAGATTGC 58.241 33.333 0.00 0.00 31.42 3.56
27 28 9.304731 GATAATGCACTTTTGATTAAGATTGCA 57.695 29.630 7.93 7.93 39.73 4.08
28 29 9.826574 ATAATGCACTTTTGATTAAGATTGCAT 57.173 25.926 11.15 11.15 43.71 3.96
29 30 7.766219 ATGCACTTTTGATTAAGATTGCATC 57.234 32.000 11.15 0.00 40.73 3.91
30 31 6.101332 TGCACTTTTGATTAAGATTGCATCC 58.899 36.000 2.42 0.00 34.29 3.51
31 32 6.071221 TGCACTTTTGATTAAGATTGCATCCT 60.071 34.615 2.42 0.00 34.29 3.24
32 33 7.122501 TGCACTTTTGATTAAGATTGCATCCTA 59.877 33.333 2.42 0.00 34.29 2.94
33 34 7.646922 GCACTTTTGATTAAGATTGCATCCTAG 59.353 37.037 0.00 0.00 31.24 3.02
34 35 8.896744 CACTTTTGATTAAGATTGCATCCTAGA 58.103 33.333 0.00 0.00 0.00 2.43
35 36 9.638176 ACTTTTGATTAAGATTGCATCCTAGAT 57.362 29.630 0.00 0.00 0.00 1.98
141 142 8.776376 AAAATGTGTTAAATTTGGAGCTATGG 57.224 30.769 0.00 0.00 0.00 2.74
142 143 7.480760 AATGTGTTAAATTTGGAGCTATGGT 57.519 32.000 0.00 0.00 0.00 3.55
143 144 6.909550 TGTGTTAAATTTGGAGCTATGGTT 57.090 33.333 0.00 0.00 0.00 3.67
144 145 7.296628 TGTGTTAAATTTGGAGCTATGGTTT 57.703 32.000 0.00 0.00 0.00 3.27
145 146 8.410673 TGTGTTAAATTTGGAGCTATGGTTTA 57.589 30.769 0.00 0.00 0.00 2.01
146 147 8.519526 TGTGTTAAATTTGGAGCTATGGTTTAG 58.480 33.333 0.00 0.00 0.00 1.85
147 148 8.736244 GTGTTAAATTTGGAGCTATGGTTTAGA 58.264 33.333 0.00 0.00 0.00 2.10
148 149 8.736244 TGTTAAATTTGGAGCTATGGTTTAGAC 58.264 33.333 0.00 0.00 0.00 2.59
149 150 8.736244 GTTAAATTTGGAGCTATGGTTTAGACA 58.264 33.333 0.00 0.00 0.00 3.41
150 151 7.775053 AAATTTGGAGCTATGGTTTAGACAA 57.225 32.000 0.00 0.00 0.00 3.18
151 152 7.961326 AATTTGGAGCTATGGTTTAGACAAT 57.039 32.000 0.00 0.00 0.00 2.71
152 153 9.474313 AAATTTGGAGCTATGGTTTAGACAATA 57.526 29.630 0.00 0.00 0.00 1.90
153 154 9.646522 AATTTGGAGCTATGGTTTAGACAATAT 57.353 29.630 0.00 0.00 0.00 1.28
154 155 8.450578 TTTGGAGCTATGGTTTAGACAATATG 57.549 34.615 0.00 0.00 0.00 1.78
155 156 7.373617 TGGAGCTATGGTTTAGACAATATGA 57.626 36.000 0.00 0.00 0.00 2.15
156 157 7.445121 TGGAGCTATGGTTTAGACAATATGAG 58.555 38.462 0.00 0.00 0.00 2.90
157 158 7.071196 TGGAGCTATGGTTTAGACAATATGAGT 59.929 37.037 0.00 0.00 0.00 3.41
158 159 8.585881 GGAGCTATGGTTTAGACAATATGAGTA 58.414 37.037 0.00 0.00 0.00 2.59
160 161 9.935241 AGCTATGGTTTAGACAATATGAGTATG 57.065 33.333 0.00 0.00 0.00 2.39
161 162 9.712305 GCTATGGTTTAGACAATATGAGTATGT 57.288 33.333 0.00 0.00 0.00 2.29
188 189 6.751514 AAAACATTTGATATGTACTGCGGA 57.248 33.333 0.00 0.00 0.00 5.54
189 190 6.942532 AAACATTTGATATGTACTGCGGAT 57.057 33.333 0.00 0.00 0.00 4.18
190 191 6.942532 AACATTTGATATGTACTGCGGATT 57.057 33.333 0.00 0.00 0.00 3.01
191 192 6.942532 ACATTTGATATGTACTGCGGATTT 57.057 33.333 0.00 0.00 0.00 2.17
192 193 8.445275 AACATTTGATATGTACTGCGGATTTA 57.555 30.769 0.00 0.00 0.00 1.40
193 194 8.445275 ACATTTGATATGTACTGCGGATTTAA 57.555 30.769 0.00 0.00 0.00 1.52
194 195 9.066892 ACATTTGATATGTACTGCGGATTTAAT 57.933 29.630 0.00 0.00 0.00 1.40
195 196 9.333497 CATTTGATATGTACTGCGGATTTAATG 57.667 33.333 0.00 0.00 0.00 1.90
196 197 8.445275 TTTGATATGTACTGCGGATTTAATGT 57.555 30.769 0.00 0.00 0.00 2.71
197 198 7.652300 TGATATGTACTGCGGATTTAATGTC 57.348 36.000 0.00 0.00 0.00 3.06
198 199 7.213678 TGATATGTACTGCGGATTTAATGTCA 58.786 34.615 0.00 0.00 0.00 3.58
199 200 5.991328 ATGTACTGCGGATTTAATGTCAG 57.009 39.130 0.00 0.00 0.00 3.51
200 201 5.079689 TGTACTGCGGATTTAATGTCAGA 57.920 39.130 0.00 0.00 0.00 3.27
201 202 5.483811 TGTACTGCGGATTTAATGTCAGAA 58.516 37.500 0.00 0.00 0.00 3.02
202 203 5.935206 TGTACTGCGGATTTAATGTCAGAAA 59.065 36.000 0.00 0.00 0.00 2.52
203 204 6.597672 TGTACTGCGGATTTAATGTCAGAAAT 59.402 34.615 0.00 0.00 0.00 2.17
204 205 7.766738 TGTACTGCGGATTTAATGTCAGAAATA 59.233 33.333 0.00 0.00 0.00 1.40
205 206 7.807977 ACTGCGGATTTAATGTCAGAAATAT 57.192 32.000 0.00 0.00 0.00 1.28
206 207 7.865707 ACTGCGGATTTAATGTCAGAAATATC 58.134 34.615 0.00 0.00 0.00 1.63
207 208 7.498900 ACTGCGGATTTAATGTCAGAAATATCA 59.501 33.333 0.00 0.00 0.00 2.15
208 209 7.864686 TGCGGATTTAATGTCAGAAATATCAG 58.135 34.615 0.00 0.00 0.00 2.90
209 210 7.041167 TGCGGATTTAATGTCAGAAATATCAGG 60.041 37.037 0.00 0.00 0.00 3.86
210 211 7.573843 GCGGATTTAATGTCAGAAATATCAGGG 60.574 40.741 0.00 0.00 0.00 4.45
211 212 7.094634 CGGATTTAATGTCAGAAATATCAGGGG 60.095 40.741 0.00 0.00 0.00 4.79
212 213 7.177392 GGATTTAATGTCAGAAATATCAGGGGG 59.823 40.741 0.00 0.00 0.00 5.40
213 214 6.590656 TTAATGTCAGAAATATCAGGGGGT 57.409 37.500 0.00 0.00 0.00 4.95
214 215 5.472301 AATGTCAGAAATATCAGGGGGTT 57.528 39.130 0.00 0.00 0.00 4.11
215 216 4.946160 TGTCAGAAATATCAGGGGGTTT 57.054 40.909 0.00 0.00 0.00 3.27
216 217 5.269554 TGTCAGAAATATCAGGGGGTTTT 57.730 39.130 0.00 0.00 0.00 2.43
217 218 5.261216 TGTCAGAAATATCAGGGGGTTTTC 58.739 41.667 0.00 0.00 0.00 2.29
218 219 5.015178 TGTCAGAAATATCAGGGGGTTTTCT 59.985 40.000 0.00 0.00 37.17 2.52
219 220 6.216662 TGTCAGAAATATCAGGGGGTTTTCTA 59.783 38.462 0.00 0.00 35.48 2.10
220 221 7.091993 TGTCAGAAATATCAGGGGGTTTTCTAT 60.092 37.037 0.00 0.00 35.48 1.98
221 222 8.437575 GTCAGAAATATCAGGGGGTTTTCTATA 58.562 37.037 0.00 0.00 35.48 1.31
222 223 9.009675 TCAGAAATATCAGGGGGTTTTCTATAA 57.990 33.333 0.00 0.00 35.48 0.98
223 224 9.640952 CAGAAATATCAGGGGGTTTTCTATAAA 57.359 33.333 0.00 0.00 35.48 1.40
229 230 7.891498 TCAGGGGGTTTTCTATAAAAATAGC 57.109 36.000 0.00 0.00 36.37 2.97
230 231 7.415086 TCAGGGGGTTTTCTATAAAAATAGCA 58.585 34.615 0.00 0.00 36.37 3.49
231 232 8.065007 TCAGGGGGTTTTCTATAAAAATAGCAT 58.935 33.333 0.00 0.00 36.37 3.79
232 233 8.143835 CAGGGGGTTTTCTATAAAAATAGCATG 58.856 37.037 0.00 0.00 36.37 4.06
233 234 8.065007 AGGGGGTTTTCTATAAAAATAGCATGA 58.935 33.333 0.00 0.00 36.37 3.07
234 235 8.141909 GGGGGTTTTCTATAAAAATAGCATGAC 58.858 37.037 0.00 0.00 36.37 3.06
235 236 7.860872 GGGGTTTTCTATAAAAATAGCATGACG 59.139 37.037 0.00 0.00 36.37 4.35
236 237 7.860872 GGGTTTTCTATAAAAATAGCATGACGG 59.139 37.037 0.00 0.00 36.37 4.79
237 238 8.617809 GGTTTTCTATAAAAATAGCATGACGGA 58.382 33.333 0.00 0.00 36.37 4.69
275 276 9.768662 TTTTATTAGTAGGTAATAGAAAGCGGG 57.231 33.333 0.00 0.00 35.44 6.13
276 277 6.990908 ATTAGTAGGTAATAGAAAGCGGGT 57.009 37.500 0.00 0.00 28.76 5.28
277 278 4.667519 AGTAGGTAATAGAAAGCGGGTG 57.332 45.455 0.00 0.00 0.00 4.61
278 279 4.284178 AGTAGGTAATAGAAAGCGGGTGA 58.716 43.478 0.00 0.00 0.00 4.02
279 280 4.713321 AGTAGGTAATAGAAAGCGGGTGAA 59.287 41.667 0.00 0.00 0.00 3.18
280 281 4.563140 AGGTAATAGAAAGCGGGTGAAA 57.437 40.909 0.00 0.00 0.00 2.69
281 282 4.913784 AGGTAATAGAAAGCGGGTGAAAA 58.086 39.130 0.00 0.00 0.00 2.29
282 283 4.698780 AGGTAATAGAAAGCGGGTGAAAAC 59.301 41.667 0.00 0.00 0.00 2.43
283 284 4.142534 GGTAATAGAAAGCGGGTGAAAACC 60.143 45.833 0.00 0.00 0.00 3.27
284 285 1.900245 TAGAAAGCGGGTGAAAACCC 58.100 50.000 3.69 3.69 46.43 4.11
294 295 3.414269 GGGTGAAAACCCTTTATCGTCA 58.586 45.455 6.68 0.00 46.39 4.35
295 296 4.014406 GGGTGAAAACCCTTTATCGTCAT 58.986 43.478 6.68 0.00 46.39 3.06
296 297 4.461431 GGGTGAAAACCCTTTATCGTCATT 59.539 41.667 6.68 0.00 46.39 2.57
297 298 5.047590 GGGTGAAAACCCTTTATCGTCATTT 60.048 40.000 6.68 0.00 46.39 2.32
298 299 6.452242 GGTGAAAACCCTTTATCGTCATTTT 58.548 36.000 0.00 0.00 0.00 1.82
299 300 7.309316 GGGTGAAAACCCTTTATCGTCATTTTA 60.309 37.037 6.68 0.00 46.39 1.52
300 301 7.539710 GGTGAAAACCCTTTATCGTCATTTTAC 59.460 37.037 0.00 0.00 0.00 2.01
301 302 8.294577 GTGAAAACCCTTTATCGTCATTTTACT 58.705 33.333 0.00 0.00 0.00 2.24
302 303 8.508875 TGAAAACCCTTTATCGTCATTTTACTC 58.491 33.333 0.00 0.00 0.00 2.59
303 304 6.997239 AACCCTTTATCGTCATTTTACTCC 57.003 37.500 0.00 0.00 0.00 3.85
304 305 6.309389 ACCCTTTATCGTCATTTTACTCCT 57.691 37.500 0.00 0.00 0.00 3.69
305 306 6.718294 ACCCTTTATCGTCATTTTACTCCTT 58.282 36.000 0.00 0.00 0.00 3.36
306 307 6.822170 ACCCTTTATCGTCATTTTACTCCTTC 59.178 38.462 0.00 0.00 0.00 3.46
307 308 6.018994 CCCTTTATCGTCATTTTACTCCTTCG 60.019 42.308 0.00 0.00 0.00 3.79
308 309 6.018994 CCTTTATCGTCATTTTACTCCTTCGG 60.019 42.308 0.00 0.00 0.00 4.30
309 310 4.730949 ATCGTCATTTTACTCCTTCGGA 57.269 40.909 0.00 0.00 0.00 4.55
310 311 3.841643 TCGTCATTTTACTCCTTCGGAC 58.158 45.455 0.00 0.00 0.00 4.79
311 312 3.256383 TCGTCATTTTACTCCTTCGGACA 59.744 43.478 0.00 0.00 0.00 4.02
312 313 3.367025 CGTCATTTTACTCCTTCGGACAC 59.633 47.826 0.00 0.00 0.00 3.67
313 314 3.683340 GTCATTTTACTCCTTCGGACACC 59.317 47.826 0.00 0.00 0.00 4.16
314 315 2.845363 TTTTACTCCTTCGGACACCC 57.155 50.000 0.00 0.00 0.00 4.61
315 316 0.978907 TTTACTCCTTCGGACACCCC 59.021 55.000 0.00 0.00 0.00 4.95
316 317 0.115745 TTACTCCTTCGGACACCCCT 59.884 55.000 0.00 0.00 0.00 4.79
317 318 0.324091 TACTCCTTCGGACACCCCTC 60.324 60.000 0.00 0.00 0.00 4.30
318 319 2.678934 TCCTTCGGACACCCCTCG 60.679 66.667 0.00 0.00 0.00 4.63
319 320 2.995574 CCTTCGGACACCCCTCGT 60.996 66.667 0.00 0.00 0.00 4.18
320 321 2.580601 CCTTCGGACACCCCTCGTT 61.581 63.158 0.00 0.00 0.00 3.85
321 322 1.370064 CTTCGGACACCCCTCGTTT 59.630 57.895 0.00 0.00 0.00 3.60
322 323 0.669625 CTTCGGACACCCCTCGTTTC 60.670 60.000 0.00 0.00 0.00 2.78
323 324 2.047560 CGGACACCCCTCGTTTCC 60.048 66.667 0.00 0.00 37.89 3.13
324 325 2.874664 CGGACACCCCTCGTTTCCA 61.875 63.158 0.00 0.00 40.83 3.53
325 326 1.003718 GGACACCCCTCGTTTCCAG 60.004 63.158 0.00 0.00 40.55 3.86
326 327 1.003718 GACACCCCTCGTTTCCAGG 60.004 63.158 0.00 0.00 0.00 4.45
327 328 2.359975 CACCCCTCGTTTCCAGGC 60.360 66.667 0.00 0.00 0.00 4.85
346 347 2.806244 GGCGCCAATTCGATATACAACT 59.194 45.455 24.80 0.00 0.00 3.16
370 371 6.837992 TCAAAACAAGTCTACAACACACTTC 58.162 36.000 0.00 0.00 0.00 3.01
407 408 0.092351 CGCTACAAAAGGTACGCGTG 59.908 55.000 24.59 5.41 40.97 5.34
414 415 1.435577 AAAGGTACGCGTGTCATTCC 58.564 50.000 24.59 13.70 0.00 3.01
424 425 3.841624 CGTGTCATTCCATCACGTATG 57.158 47.619 8.44 0.00 46.11 2.39
478 536 0.039256 CAAAACCTGGTCACATGCCG 60.039 55.000 0.00 0.00 0.00 5.69
492 550 2.423538 ACATGCCGATCTTGTAAAAGCC 59.576 45.455 0.00 0.00 32.07 4.35
536 597 8.960591 TCTTCATATTTCCTGTCAAAAATCCTC 58.039 33.333 0.00 0.00 0.00 3.71
635 696 1.557371 TCCATAGATCGTGTGGCCAAA 59.443 47.619 7.24 0.00 37.35 3.28
648 709 0.967887 GGCCAAAGAGGGAAGAAGCC 60.968 60.000 0.00 0.00 38.09 4.35
649 710 0.038890 GCCAAAGAGGGAAGAAGCCT 59.961 55.000 0.00 0.00 38.09 4.58
664 725 1.694639 AGCCTATATAAACGCGACGC 58.305 50.000 15.93 10.49 0.00 5.19
863 935 4.994471 CGACCAGCAGCACCAGCA 62.994 66.667 0.00 0.00 45.49 4.41
892 964 1.660560 GGCGCATTCTGCTTCCATGT 61.661 55.000 10.83 0.00 42.25 3.21
1062 1157 1.552337 CTACCTCAAGCTCAAGCCAGA 59.448 52.381 0.00 0.00 43.38 3.86
1107 1483 3.360886 GCTCAAGCTCAGCTAGACC 57.639 57.895 0.00 0.00 38.25 3.85
1639 2015 4.415332 CGTGTACCTGCCGTCGCT 62.415 66.667 0.00 0.00 35.36 4.93
1858 2234 2.382882 CCTCTGGAGCTACTGATGTCA 58.617 52.381 5.92 0.00 0.00 3.58
1984 2390 7.009999 CCGTTTGTCAATTCTTTGTTTGAATCA 59.990 33.333 0.00 0.00 33.90 2.57
2055 2462 1.639298 GCCTGAATGTCACTGTCGGC 61.639 60.000 0.00 0.00 0.00 5.54
2092 4208 0.033366 AAACGGGTTTGCAGAATGGC 59.967 50.000 0.00 0.00 35.86 4.40
2168 4421 7.863375 CCAGAACCAGAAATATCTTACGAGTAG 59.137 40.741 0.00 0.00 32.03 2.57
2172 4425 5.625721 CCAGAAATATCTTACGAGTAGTGCG 59.374 44.000 0.00 0.00 32.03 5.34
2180 4433 2.050350 CGAGTAGTGCGGAAGGGGA 61.050 63.158 0.00 0.00 0.00 4.81
2193 4446 2.529389 GGGGAGTGTGTCTGGGGT 60.529 66.667 0.00 0.00 0.00 4.95
2195 4448 1.073199 GGGAGTGTGTCTGGGGTTG 59.927 63.158 0.00 0.00 0.00 3.77
2199 4452 2.304761 GGAGTGTGTCTGGGGTTGATTA 59.695 50.000 0.00 0.00 0.00 1.75
2202 4455 4.998051 AGTGTGTCTGGGGTTGATTATTT 58.002 39.130 0.00 0.00 0.00 1.40
2203 4456 5.010282 AGTGTGTCTGGGGTTGATTATTTC 58.990 41.667 0.00 0.00 0.00 2.17
2229 4482 4.819761 GGCCATCAGCGCTGTCGA 62.820 66.667 34.70 18.40 45.17 4.20
2251 4504 6.028368 CGATTCACTCGTTAGTCATTAGTGT 58.972 40.000 0.00 0.00 42.56 3.55
2422 4686 0.601558 CGAGGACTCCTTGTTCCGAA 59.398 55.000 0.00 0.00 31.76 4.30
2450 4714 6.708054 AGATTTGCTATTCTAAGTTGATCCGG 59.292 38.462 0.00 0.00 0.00 5.14
2469 4733 7.777910 TGATCCGGAAATAGATTTTGTAATGGT 59.222 33.333 9.01 0.00 0.00 3.55
2558 4822 0.842030 TCATGTGGCCAGAAGGGAGT 60.842 55.000 5.11 0.00 40.01 3.85
2574 4838 0.252197 GAGTGCGACCCCACCTTATT 59.748 55.000 0.00 0.00 36.38 1.40
2606 4870 2.512485 TTTCTACGTTGACTTCGGCA 57.488 45.000 0.00 0.00 0.00 5.69
2609 4873 0.788391 CTACGTTGACTTCGGCAACC 59.212 55.000 6.97 0.00 41.88 3.77
2610 4874 0.600782 TACGTTGACTTCGGCAACCC 60.601 55.000 6.97 0.00 41.88 4.11
2656 4920 2.651361 CACGCTTCCCTGTCGACT 59.349 61.111 17.92 0.00 0.00 4.18
2659 4923 1.006102 CGCTTCCCTGTCGACTGTT 60.006 57.895 17.92 0.00 0.00 3.16
2661 4925 1.569479 GCTTCCCTGTCGACTGTTGC 61.569 60.000 17.92 12.46 0.00 4.17
2671 4936 3.246112 ACTGTTGCTACCCCGCCA 61.246 61.111 0.00 0.00 0.00 5.69
2687 4952 1.225704 CCATTCCCCTGCCTGACTC 59.774 63.158 0.00 0.00 0.00 3.36
2689 4954 2.370445 ATTCCCCTGCCTGACTCGG 61.370 63.158 0.00 0.00 0.00 4.63
2723 4988 2.986290 CCACACATGGCCGGAGTA 59.014 61.111 5.05 0.00 39.82 2.59
2724 4989 1.526887 CCACACATGGCCGGAGTAT 59.473 57.895 5.05 0.00 39.82 2.12
2824 5191 4.481368 AATACTGGTGGCTTCGTATGAA 57.519 40.909 0.00 0.00 0.00 2.57
2838 5232 2.356135 GTATGAAGACGCCACACCAAT 58.644 47.619 0.00 0.00 0.00 3.16
2846 5240 1.478510 ACGCCACACCAATGTTTCAAA 59.521 42.857 0.00 0.00 36.72 2.69
2851 5245 1.127701 CACCAATGTTTCAAACGGCG 58.872 50.000 4.80 4.80 0.00 6.46
2853 5247 1.135333 ACCAATGTTTCAAACGGCGTT 59.865 42.857 21.19 21.19 0.00 4.84
2855 5249 2.189342 CAATGTTTCAAACGGCGTTGT 58.811 42.857 27.50 13.45 0.00 3.32
2856 5250 1.833860 ATGTTTCAAACGGCGTTGTG 58.166 45.000 27.50 23.43 0.00 3.33
2862 5256 1.402259 TCAAACGGCGTTGTGATTTGT 59.598 42.857 27.50 4.58 33.10 2.83
2864 5258 1.833860 AACGGCGTTGTGATTTGTTG 58.166 45.000 26.22 0.00 0.00 3.33
2871 5265 3.798548 GCGTTGTGATTTGTTGGAACCAT 60.799 43.478 0.00 0.00 0.00 3.55
2930 5346 4.666512 ACCAGATCAAGTTTTGCTACCAT 58.333 39.130 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.758715 GCAATCTTAATCAAAAGTGCATTATCC 58.241 33.333 0.00 0.00 31.93 2.59
1 2 9.304731 TGCAATCTTAATCAAAAGTGCATTATC 57.695 29.630 0.00 0.00 35.05 1.75
3 4 9.304731 GATGCAATCTTAATCAAAAGTGCATTA 57.695 29.630 9.99 0.00 43.56 1.90
4 5 7.279313 GGATGCAATCTTAATCAAAAGTGCATT 59.721 33.333 9.99 0.00 43.56 3.56
5 6 6.759827 GGATGCAATCTTAATCAAAAGTGCAT 59.240 34.615 8.62 8.62 44.93 3.96
6 7 6.071221 AGGATGCAATCTTAATCAAAAGTGCA 60.071 34.615 0.00 0.00 44.71 4.57
7 8 6.335777 AGGATGCAATCTTAATCAAAAGTGC 58.664 36.000 0.00 0.00 44.71 4.40
8 9 8.896744 TCTAGGATGCAATCTTAATCAAAAGTG 58.103 33.333 0.00 0.00 44.71 3.16
9 10 9.638176 ATCTAGGATGCAATCTTAATCAAAAGT 57.362 29.630 0.00 0.00 44.71 2.66
115 116 9.868277 CCATAGCTCCAAATTTAACACATTTTA 57.132 29.630 0.00 0.00 0.00 1.52
116 117 8.374743 ACCATAGCTCCAAATTTAACACATTTT 58.625 29.630 0.00 0.00 0.00 1.82
117 118 7.906327 ACCATAGCTCCAAATTTAACACATTT 58.094 30.769 0.00 0.00 0.00 2.32
118 119 7.480760 ACCATAGCTCCAAATTTAACACATT 57.519 32.000 0.00 0.00 0.00 2.71
119 120 7.480760 AACCATAGCTCCAAATTTAACACAT 57.519 32.000 0.00 0.00 0.00 3.21
120 121 6.909550 AACCATAGCTCCAAATTTAACACA 57.090 33.333 0.00 0.00 0.00 3.72
121 122 8.736244 TCTAAACCATAGCTCCAAATTTAACAC 58.264 33.333 0.00 0.00 0.00 3.32
122 123 8.736244 GTCTAAACCATAGCTCCAAATTTAACA 58.264 33.333 0.00 0.00 0.00 2.41
123 124 8.736244 TGTCTAAACCATAGCTCCAAATTTAAC 58.264 33.333 0.00 0.00 0.00 2.01
124 125 8.871629 TGTCTAAACCATAGCTCCAAATTTAA 57.128 30.769 0.00 0.00 0.00 1.52
125 126 8.871629 TTGTCTAAACCATAGCTCCAAATTTA 57.128 30.769 0.00 0.00 0.00 1.40
126 127 7.775053 TTGTCTAAACCATAGCTCCAAATTT 57.225 32.000 0.00 0.00 0.00 1.82
127 128 7.961326 ATTGTCTAAACCATAGCTCCAAATT 57.039 32.000 0.00 0.00 0.00 1.82
128 129 9.071276 CATATTGTCTAAACCATAGCTCCAAAT 57.929 33.333 0.00 0.00 0.00 2.32
129 130 8.271458 TCATATTGTCTAAACCATAGCTCCAAA 58.729 33.333 0.00 0.00 0.00 3.28
130 131 7.801104 TCATATTGTCTAAACCATAGCTCCAA 58.199 34.615 0.00 0.00 0.00 3.53
131 132 7.071196 ACTCATATTGTCTAAACCATAGCTCCA 59.929 37.037 0.00 0.00 0.00 3.86
132 133 7.445945 ACTCATATTGTCTAAACCATAGCTCC 58.554 38.462 0.00 0.00 0.00 4.70
134 135 9.935241 CATACTCATATTGTCTAAACCATAGCT 57.065 33.333 0.00 0.00 0.00 3.32
135 136 9.712305 ACATACTCATATTGTCTAAACCATAGC 57.288 33.333 0.00 0.00 0.00 2.97
164 165 7.151999 TCCGCAGTACATATCAAATGTTTTT 57.848 32.000 0.00 0.00 33.76 1.94
165 166 6.751514 TCCGCAGTACATATCAAATGTTTT 57.248 33.333 0.00 0.00 33.76 2.43
166 167 6.942532 ATCCGCAGTACATATCAAATGTTT 57.057 33.333 0.00 0.00 33.76 2.83
167 168 6.942532 AATCCGCAGTACATATCAAATGTT 57.057 33.333 0.00 0.00 33.76 2.71
168 169 6.942532 AAATCCGCAGTACATATCAAATGT 57.057 33.333 0.00 0.00 36.13 2.71
169 170 9.333497 CATTAAATCCGCAGTACATATCAAATG 57.667 33.333 0.00 0.00 0.00 2.32
170 171 9.066892 ACATTAAATCCGCAGTACATATCAAAT 57.933 29.630 0.00 0.00 0.00 2.32
171 172 8.445275 ACATTAAATCCGCAGTACATATCAAA 57.555 30.769 0.00 0.00 0.00 2.69
172 173 7.713073 TGACATTAAATCCGCAGTACATATCAA 59.287 33.333 0.00 0.00 0.00 2.57
173 174 7.213678 TGACATTAAATCCGCAGTACATATCA 58.786 34.615 0.00 0.00 0.00 2.15
174 175 7.598869 TCTGACATTAAATCCGCAGTACATATC 59.401 37.037 0.00 0.00 0.00 1.63
175 176 7.441836 TCTGACATTAAATCCGCAGTACATAT 58.558 34.615 0.00 0.00 0.00 1.78
176 177 6.811954 TCTGACATTAAATCCGCAGTACATA 58.188 36.000 0.00 0.00 0.00 2.29
177 178 5.670485 TCTGACATTAAATCCGCAGTACAT 58.330 37.500 0.00 0.00 0.00 2.29
178 179 5.079689 TCTGACATTAAATCCGCAGTACA 57.920 39.130 0.00 0.00 0.00 2.90
179 180 6.417191 TTTCTGACATTAAATCCGCAGTAC 57.583 37.500 0.00 0.00 0.00 2.73
180 181 8.902540 ATATTTCTGACATTAAATCCGCAGTA 57.097 30.769 0.00 0.00 0.00 2.74
181 182 7.498900 TGATATTTCTGACATTAAATCCGCAGT 59.501 33.333 0.00 0.00 0.00 4.40
182 183 7.864686 TGATATTTCTGACATTAAATCCGCAG 58.135 34.615 0.00 0.00 0.00 5.18
183 184 7.041167 CCTGATATTTCTGACATTAAATCCGCA 60.041 37.037 0.52 0.00 0.00 5.69
184 185 7.301054 CCTGATATTTCTGACATTAAATCCGC 58.699 38.462 0.52 0.00 0.00 5.54
185 186 7.094634 CCCCTGATATTTCTGACATTAAATCCG 60.095 40.741 0.52 0.00 0.00 4.18
186 187 7.177392 CCCCCTGATATTTCTGACATTAAATCC 59.823 40.741 0.52 0.00 0.00 3.01
187 188 7.725844 ACCCCCTGATATTTCTGACATTAAATC 59.274 37.037 0.52 0.00 0.00 2.17
188 189 7.595488 ACCCCCTGATATTTCTGACATTAAAT 58.405 34.615 2.55 2.55 0.00 1.40
189 190 6.980577 ACCCCCTGATATTTCTGACATTAAA 58.019 36.000 0.00 0.00 0.00 1.52
190 191 6.590656 ACCCCCTGATATTTCTGACATTAA 57.409 37.500 0.00 0.00 0.00 1.40
191 192 6.590656 AACCCCCTGATATTTCTGACATTA 57.409 37.500 0.00 0.00 0.00 1.90
192 193 5.472301 AACCCCCTGATATTTCTGACATT 57.528 39.130 0.00 0.00 0.00 2.71
193 194 5.472301 AAACCCCCTGATATTTCTGACAT 57.528 39.130 0.00 0.00 0.00 3.06
194 195 4.946160 AAACCCCCTGATATTTCTGACA 57.054 40.909 0.00 0.00 0.00 3.58
195 196 5.510430 AGAAAACCCCCTGATATTTCTGAC 58.490 41.667 0.00 0.00 38.52 3.51
196 197 5.796502 AGAAAACCCCCTGATATTTCTGA 57.203 39.130 0.00 0.00 38.52 3.27
197 198 9.640952 TTTATAGAAAACCCCCTGATATTTCTG 57.359 33.333 8.81 0.00 39.80 3.02
203 204 9.582648 GCTATTTTTATAGAAAACCCCCTGATA 57.417 33.333 0.00 0.00 34.24 2.15
204 205 8.065007 TGCTATTTTTATAGAAAACCCCCTGAT 58.935 33.333 0.00 0.00 34.24 2.90
205 206 7.415086 TGCTATTTTTATAGAAAACCCCCTGA 58.585 34.615 0.00 0.00 34.24 3.86
206 207 7.654022 TGCTATTTTTATAGAAAACCCCCTG 57.346 36.000 0.00 0.00 34.24 4.45
207 208 8.065007 TCATGCTATTTTTATAGAAAACCCCCT 58.935 33.333 0.00 0.00 34.24 4.79
208 209 8.141909 GTCATGCTATTTTTATAGAAAACCCCC 58.858 37.037 0.00 0.00 34.24 5.40
209 210 7.860872 CGTCATGCTATTTTTATAGAAAACCCC 59.139 37.037 0.00 0.00 34.24 4.95
210 211 7.860872 CCGTCATGCTATTTTTATAGAAAACCC 59.139 37.037 0.00 0.00 34.24 4.11
211 212 8.617809 TCCGTCATGCTATTTTTATAGAAAACC 58.382 33.333 0.00 0.00 34.24 3.27
249 250 9.768662 CCCGCTTTCTATTACCTACTAATAAAA 57.231 33.333 0.00 0.00 28.61 1.52
250 251 8.927411 ACCCGCTTTCTATTACCTACTAATAAA 58.073 33.333 0.00 0.00 28.61 1.40
251 252 8.362639 CACCCGCTTTCTATTACCTACTAATAA 58.637 37.037 0.00 0.00 28.61 1.40
252 253 7.725397 TCACCCGCTTTCTATTACCTACTAATA 59.275 37.037 0.00 0.00 0.00 0.98
253 254 6.552350 TCACCCGCTTTCTATTACCTACTAAT 59.448 38.462 0.00 0.00 0.00 1.73
254 255 5.893255 TCACCCGCTTTCTATTACCTACTAA 59.107 40.000 0.00 0.00 0.00 2.24
255 256 5.448654 TCACCCGCTTTCTATTACCTACTA 58.551 41.667 0.00 0.00 0.00 1.82
256 257 4.284178 TCACCCGCTTTCTATTACCTACT 58.716 43.478 0.00 0.00 0.00 2.57
257 258 4.660789 TCACCCGCTTTCTATTACCTAC 57.339 45.455 0.00 0.00 0.00 3.18
258 259 5.680594 TTTCACCCGCTTTCTATTACCTA 57.319 39.130 0.00 0.00 0.00 3.08
259 260 4.563140 TTTCACCCGCTTTCTATTACCT 57.437 40.909 0.00 0.00 0.00 3.08
260 261 4.142534 GGTTTTCACCCGCTTTCTATTACC 60.143 45.833 0.00 0.00 37.03 2.85
261 262 4.978186 GGTTTTCACCCGCTTTCTATTAC 58.022 43.478 0.00 0.00 37.03 1.89
274 275 5.638596 AATGACGATAAAGGGTTTTCACC 57.361 39.130 0.00 0.00 43.37 4.02
275 276 8.294577 AGTAAAATGACGATAAAGGGTTTTCAC 58.705 33.333 0.00 0.00 0.00 3.18
276 277 8.398878 AGTAAAATGACGATAAAGGGTTTTCA 57.601 30.769 0.00 0.00 0.00 2.69
277 278 7.966753 GGAGTAAAATGACGATAAAGGGTTTTC 59.033 37.037 0.00 0.00 0.00 2.29
278 279 7.668469 AGGAGTAAAATGACGATAAAGGGTTTT 59.332 33.333 0.00 0.00 0.00 2.43
279 280 7.173032 AGGAGTAAAATGACGATAAAGGGTTT 58.827 34.615 0.00 0.00 0.00 3.27
280 281 6.718294 AGGAGTAAAATGACGATAAAGGGTT 58.282 36.000 0.00 0.00 0.00 4.11
281 282 6.309389 AGGAGTAAAATGACGATAAAGGGT 57.691 37.500 0.00 0.00 0.00 4.34
282 283 6.018994 CGAAGGAGTAAAATGACGATAAAGGG 60.019 42.308 0.00 0.00 0.00 3.95
283 284 6.934210 CGAAGGAGTAAAATGACGATAAAGG 58.066 40.000 0.00 0.00 0.00 3.11
303 304 0.669625 GAAACGAGGGGTGTCCGAAG 60.670 60.000 0.00 0.00 41.52 3.79
304 305 1.368579 GAAACGAGGGGTGTCCGAA 59.631 57.895 0.00 0.00 41.52 4.30
305 306 2.576832 GGAAACGAGGGGTGTCCGA 61.577 63.158 0.00 0.00 43.14 4.55
306 307 2.047560 GGAAACGAGGGGTGTCCG 60.048 66.667 0.00 0.00 43.14 4.79
308 309 1.003718 CCTGGAAACGAGGGGTGTC 60.004 63.158 0.00 0.00 31.56 3.67
309 310 3.157680 CCTGGAAACGAGGGGTGT 58.842 61.111 0.00 0.00 0.00 4.16
310 311 2.359975 GCCTGGAAACGAGGGGTG 60.360 66.667 0.00 0.00 31.62 4.61
311 312 4.016706 CGCCTGGAAACGAGGGGT 62.017 66.667 0.00 0.00 37.05 4.95
314 315 4.697756 TGGCGCCTGGAAACGAGG 62.698 66.667 29.70 0.00 33.40 4.63
315 316 1.586154 AATTGGCGCCTGGAAACGAG 61.586 55.000 29.70 0.00 0.00 4.18
316 317 1.582610 GAATTGGCGCCTGGAAACGA 61.583 55.000 29.70 0.07 0.00 3.85
317 318 1.154035 GAATTGGCGCCTGGAAACG 60.154 57.895 29.70 0.00 0.00 3.60
318 319 1.154035 CGAATTGGCGCCTGGAAAC 60.154 57.895 29.70 12.81 0.00 2.78
319 320 0.679640 ATCGAATTGGCGCCTGGAAA 60.680 50.000 29.70 14.30 0.00 3.13
320 321 0.179234 TATCGAATTGGCGCCTGGAA 59.821 50.000 29.70 14.72 0.00 3.53
321 322 0.396435 ATATCGAATTGGCGCCTGGA 59.604 50.000 29.70 14.90 0.00 3.86
322 323 1.732259 GTATATCGAATTGGCGCCTGG 59.268 52.381 29.70 9.12 0.00 4.45
323 324 2.412870 TGTATATCGAATTGGCGCCTG 58.587 47.619 29.70 12.21 0.00 4.85
324 325 2.806244 GTTGTATATCGAATTGGCGCCT 59.194 45.455 29.70 7.33 0.00 5.52
325 326 2.806244 AGTTGTATATCGAATTGGCGCC 59.194 45.455 22.73 22.73 0.00 6.53
326 327 3.493129 TGAGTTGTATATCGAATTGGCGC 59.507 43.478 0.00 0.00 0.00 6.53
327 328 5.651172 TTGAGTTGTATATCGAATTGGCG 57.349 39.130 0.00 0.00 0.00 5.69
346 347 6.653320 AGAAGTGTGTTGTAGACTTGTTTTGA 59.347 34.615 0.00 0.00 42.40 2.69
370 371 1.512734 GATTGCTTTGTGCGGCGAG 60.513 57.895 12.98 0.00 46.63 5.03
391 392 2.505628 TGACACGCGTACCTTTTGTA 57.494 45.000 13.44 0.00 0.00 2.41
407 408 2.218759 GCGTCATACGTGATGGAATGAC 59.781 50.000 14.21 14.21 44.73 3.06
414 415 0.573987 CTGCTGCGTCATACGTGATG 59.426 55.000 0.00 0.00 44.73 3.07
424 425 1.741770 ATCCCGTTTCTGCTGCGTC 60.742 57.895 0.00 0.00 0.00 5.19
478 536 1.401905 CCCGCTGGCTTTTACAAGATC 59.598 52.381 0.00 0.00 30.57 2.75
492 550 0.234884 GAAGTTTCAACGTCCCGCTG 59.765 55.000 0.00 0.00 32.33 5.18
635 696 5.279556 GCGTTTATATAGGCTTCTTCCCTCT 60.280 44.000 0.00 0.00 33.88 3.69
664 725 6.780706 AATATCTAACCATTTAAGGCGACG 57.219 37.500 0.00 0.00 0.00 5.12
956 1030 9.489084 TGCGCTCATTTATAGTTATTCATAGTT 57.511 29.630 9.73 0.00 0.00 2.24
957 1031 8.926710 GTGCGCTCATTTATAGTTATTCATAGT 58.073 33.333 9.73 0.00 0.00 2.12
958 1032 9.144747 AGTGCGCTCATTTATAGTTATTCATAG 57.855 33.333 9.73 0.00 0.00 2.23
959 1033 9.140286 GAGTGCGCTCATTTATAGTTATTCATA 57.860 33.333 22.25 0.00 41.29 2.15
960 1034 7.875041 AGAGTGCGCTCATTTATAGTTATTCAT 59.125 33.333 28.02 0.00 44.00 2.57
961 1035 7.169813 CAGAGTGCGCTCATTTATAGTTATTCA 59.830 37.037 28.02 0.00 44.00 2.57
962 1036 7.505646 CAGAGTGCGCTCATTTATAGTTATTC 58.494 38.462 28.02 0.00 44.00 1.75
963 1037 6.073548 GCAGAGTGCGCTCATTTATAGTTATT 60.074 38.462 28.02 0.45 44.00 1.40
964 1038 5.406780 GCAGAGTGCGCTCATTTATAGTTAT 59.593 40.000 28.02 0.66 44.00 1.89
965 1039 4.745125 GCAGAGTGCGCTCATTTATAGTTA 59.255 41.667 28.02 0.00 44.00 2.24
1106 1482 1.586154 GCTTGGTGGAATGTGGTCGG 61.586 60.000 0.00 0.00 0.00 4.79
1107 1483 1.875963 GCTTGGTGGAATGTGGTCG 59.124 57.895 0.00 0.00 0.00 4.79
1218 1594 4.602259 CGACCACACAGGCACGGT 62.602 66.667 0.00 0.00 43.14 4.83
1427 1803 3.916544 CCGAGCAGGGCGAGCATA 61.917 66.667 2.67 0.00 35.97 3.14
1639 2015 2.423290 TTCGTCGGCATTGTCCACGA 62.423 55.000 7.02 7.02 37.64 4.35
1786 2162 1.604308 TTCTCCCAGTACGACGGCA 60.604 57.895 0.00 0.00 0.00 5.69
1984 2390 5.674569 GCATGCTGTAAAACACTTGATCGAT 60.675 40.000 11.37 0.00 0.00 3.59
2015 2422 6.370718 CAGGCGGTGTTTTCTTATACTAGTTT 59.629 38.462 0.00 0.00 0.00 2.66
2016 2423 5.873164 CAGGCGGTGTTTTCTTATACTAGTT 59.127 40.000 0.00 0.00 0.00 2.24
2017 2424 5.186409 TCAGGCGGTGTTTTCTTATACTAGT 59.814 40.000 0.00 0.00 0.00 2.57
2018 2425 5.657474 TCAGGCGGTGTTTTCTTATACTAG 58.343 41.667 0.00 0.00 0.00 2.57
2019 2426 5.664294 TCAGGCGGTGTTTTCTTATACTA 57.336 39.130 0.00 0.00 0.00 1.82
2020 2427 4.546829 TCAGGCGGTGTTTTCTTATACT 57.453 40.909 0.00 0.00 0.00 2.12
2021 2428 5.123344 ACATTCAGGCGGTGTTTTCTTATAC 59.877 40.000 0.00 0.00 0.00 1.47
2092 4208 1.804748 GAACGGCACCTTACTTTGGAG 59.195 52.381 0.00 0.00 0.00 3.86
2168 4421 2.358737 CACACTCCCCTTCCGCAC 60.359 66.667 0.00 0.00 0.00 5.34
2172 4425 1.679898 CCAGACACACTCCCCTTCC 59.320 63.158 0.00 0.00 0.00 3.46
2180 4433 4.657814 AATAATCAACCCCAGACACACT 57.342 40.909 0.00 0.00 0.00 3.55
2229 4482 6.100004 CCACACTAATGACTAACGAGTGAAT 58.900 40.000 7.30 0.00 39.94 2.57
2237 4490 6.854496 TCAACAACCACACTAATGACTAAC 57.146 37.500 0.00 0.00 0.00 2.34
2251 4504 4.136796 CTCACCTCATTCTTCAACAACCA 58.863 43.478 0.00 0.00 0.00 3.67
2291 4545 4.474651 TCTTTGGCATCTTCCCTCTAATGA 59.525 41.667 0.00 0.00 0.00 2.57
2292 4546 4.785301 TCTTTGGCATCTTCCCTCTAATG 58.215 43.478 0.00 0.00 0.00 1.90
2302 4556 4.603131 ACATACCACATCTTTGGCATCTT 58.397 39.130 0.00 0.00 40.77 2.40
2330 4584 2.235402 ACTGTAGTATCCAACCCAACCG 59.765 50.000 0.00 0.00 0.00 4.44
2382 4644 0.464036 AGATCATTCGCGGGCTAACA 59.536 50.000 6.13 0.00 0.00 2.41
2422 4686 9.336171 GGATCAACTTAGAATAGCAAATCTCTT 57.664 33.333 0.00 0.00 0.00 2.85
2469 4733 2.983930 GCGCCGGGTGCAAACATTA 61.984 57.895 26.78 0.00 41.33 1.90
2558 4822 0.912487 AGGAATAAGGTGGGGTCGCA 60.912 55.000 0.00 0.00 0.00 5.10
2587 4851 2.512485 TGCCGAAGTCAACGTAGAAA 57.488 45.000 0.00 0.00 0.00 2.52
2588 4852 2.129607 GTTGCCGAAGTCAACGTAGAA 58.870 47.619 0.00 0.00 36.43 2.10
2589 4853 1.774639 GTTGCCGAAGTCAACGTAGA 58.225 50.000 0.00 0.00 36.43 2.59
2602 4866 1.520787 GAGTATGTCGGGGTTGCCG 60.521 63.158 0.00 0.00 0.00 5.69
2606 4870 1.129058 GATGGGAGTATGTCGGGGTT 58.871 55.000 0.00 0.00 0.00 4.11
2609 4873 0.969894 GAGGATGGGAGTATGTCGGG 59.030 60.000 0.00 0.00 0.00 5.14
2610 4874 2.002505 AGAGGATGGGAGTATGTCGG 57.997 55.000 0.00 0.00 0.00 4.79
2615 4879 2.334023 GGAGCAAGAGGATGGGAGTAT 58.666 52.381 0.00 0.00 0.00 2.12
2640 4904 1.745320 AACAGTCGACAGGGAAGCGT 61.745 55.000 19.50 0.00 0.00 5.07
2641 4905 1.006102 AACAGTCGACAGGGAAGCG 60.006 57.895 19.50 0.00 0.00 4.68
2649 4913 1.669440 GGGGTAGCAACAGTCGACA 59.331 57.895 19.50 0.00 0.00 4.35
2653 4917 2.436115 GGCGGGGTAGCAACAGTC 60.436 66.667 0.00 0.00 39.27 3.51
2656 4920 1.377987 GAATGGCGGGGTAGCAACA 60.378 57.895 0.00 0.00 39.27 3.33
2659 4923 3.804329 GGGAATGGCGGGGTAGCA 61.804 66.667 0.00 0.00 39.27 3.49
2661 4925 2.772622 AGGGGAATGGCGGGGTAG 60.773 66.667 0.00 0.00 0.00 3.18
2671 4936 2.370445 CCGAGTCAGGCAGGGGAAT 61.370 63.158 0.00 0.00 0.00 3.01
2718 4983 2.480416 CGAGCACTCCAGTTCATACTCC 60.480 54.545 0.00 0.00 30.26 3.85
2723 4988 1.078848 GGCGAGCACTCCAGTTCAT 60.079 57.895 0.00 0.00 0.00 2.57
2724 4989 2.343758 GGCGAGCACTCCAGTTCA 59.656 61.111 0.00 0.00 0.00 3.18
2788 5155 3.947834 CCAGTATTACCTTCCAGCTTTGG 59.052 47.826 0.00 0.00 0.00 3.28
2805 5172 3.520290 CTTCATACGAAGCCACCAGTA 57.480 47.619 0.00 0.00 42.17 2.74
2824 5191 0.951558 GAAACATTGGTGTGGCGTCT 59.048 50.000 0.00 0.00 38.92 4.18
2838 5232 0.803117 TCACAACGCCGTTTGAAACA 59.197 45.000 8.93 0.00 0.00 2.83
2846 5240 0.030101 CCAACAAATCACAACGCCGT 59.970 50.000 0.00 0.00 0.00 5.68
2851 5245 5.689961 GTGTATGGTTCCAACAAATCACAAC 59.310 40.000 0.00 0.00 0.00 3.32
2853 5247 4.889995 TGTGTATGGTTCCAACAAATCACA 59.110 37.500 0.00 0.00 0.00 3.58
2855 5249 6.662865 AATGTGTATGGTTCCAACAAATCA 57.337 33.333 0.00 0.00 0.00 2.57
2856 5250 7.961325 AAAATGTGTATGGTTCCAACAAATC 57.039 32.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.