Multiple sequence alignment - TraesCS5B01G295200

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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 TraesCS5B01G295200 chr5B 100.000 9099 0 0 1 9099 479192142 479201240 0.000000e+00 16803.0
1 TraesCS5B01G295200 chr5D 95.532 6669 192 43 2442 9029 398898247 398904890 0.000000e+00 10567.0
2 TraesCS5B01G295200 chr5D 96.945 2095 53 7 325 2415 398896167 398898254 0.000000e+00 3504.0
3 TraesCS5B01G295200 chr5D 95.580 181 8 0 22 202 398895984 398896164 3.210000e-74 291.0
4 TraesCS5B01G295200 chr5A 90.431 3271 198 62 259 3475 503940829 503944038 0.000000e+00 4200.0
5 TraesCS5B01G295200 chr5A 93.052 1612 83 9 4818 6415 503945305 503946901 0.000000e+00 2329.0
6 TraesCS5B01G295200 chr5A 81.802 1676 195 55 962 2593 109302745 109304354 0.000000e+00 1304.0
7 TraesCS5B01G295200 chr5A 84.675 1031 86 32 3879 4841 503944262 503945288 0.000000e+00 963.0
8 TraesCS5B01G295200 chr5A 93.120 625 36 7 6657 7276 503947077 503947699 0.000000e+00 909.0
9 TraesCS5B01G295200 chr5A 84.605 708 73 15 7560 8246 503948183 503948875 0.000000e+00 671.0
10 TraesCS5B01G295200 chr5A 89.868 227 18 5 7318 7544 503947705 503947926 4.160000e-73 287.0
11 TraesCS5B01G295200 chr6B 84.690 2162 183 86 5344 7390 718642968 718645096 0.000000e+00 2023.0
12 TraesCS5B01G295200 chr6B 89.673 1191 99 14 2536 3713 718640189 718641368 0.000000e+00 1496.0
13 TraesCS5B01G295200 chr6B 89.474 1102 95 10 1086 2178 718638655 718639744 0.000000e+00 1373.0
14 TraesCS5B01G295200 chr6B 82.613 1087 131 19 4266 5303 718641813 718642890 0.000000e+00 907.0
15 TraesCS5B01G295200 chr6B 81.132 689 75 26 6718 7393 669686405 669685759 1.360000e-137 501.0
16 TraesCS5B01G295200 chr6B 80.226 708 87 25 6718 7413 669739974 669739308 4.940000e-132 483.0
17 TraesCS5B01G295200 chr6B 86.779 416 33 12 3882 4277 718641365 718641778 2.330000e-120 444.0
18 TraesCS5B01G295200 chr6B 86.217 341 27 11 2223 2549 718639744 718640078 1.450000e-92 351.0
19 TraesCS5B01G295200 chr6B 84.817 191 25 2 874 1061 718638390 718638579 1.210000e-43 189.0
20 TraesCS5B01G295200 chr6A 90.119 1174 96 15 2550 3713 616759856 616758693 0.000000e+00 1507.0
21 TraesCS5B01G295200 chr6A 84.726 1532 159 30 706 2178 616761832 616760317 0.000000e+00 1463.0
22 TraesCS5B01G295200 chr6A 87.462 1300 109 28 5352 6618 616757082 616755804 0.000000e+00 1448.0
23 TraesCS5B01G295200 chr6A 83.090 1094 121 26 4266 5306 616758248 616757166 0.000000e+00 937.0
24 TraesCS5B01G295200 chr6A 82.464 844 100 27 6718 7525 616755687 616754856 0.000000e+00 695.0
25 TraesCS5B01G295200 chr6A 87.740 416 29 12 3882 4277 616758696 616758283 4.980000e-127 466.0
26 TraesCS5B01G295200 chr6A 84.348 345 29 11 2223 2549 616760317 616759980 1.910000e-81 315.0
27 TraesCS5B01G295200 chr6D 89.623 1195 104 17 2533 3713 473231937 473233125 0.000000e+00 1502.0
28 TraesCS5B01G295200 chr6D 88.629 1240 93 28 5344 6548 473234768 473235994 0.000000e+00 1465.0
29 TraesCS5B01G295200 chr6D 89.010 1101 98 10 1086 2178 473230483 473231568 0.000000e+00 1341.0
30 TraesCS5B01G295200 chr6D 83.302 1072 120 19 4276 5295 473233616 473234680 0.000000e+00 933.0
31 TraesCS5B01G295200 chr6D 84.286 840 84 31 6710 7516 473236190 473237014 0.000000e+00 776.0
32 TraesCS5B01G295200 chr6D 87.260 416 30 10 3882 4277 473233122 473233534 3.870000e-123 453.0
33 TraesCS5B01G295200 chr6D 83.582 335 30 10 2223 2540 473231568 473231894 3.210000e-74 291.0
34 TraesCS5B01G295200 chr6D 78.442 385 57 9 702 1061 473230028 473230411 2.560000e-55 228.0
35 TraesCS5B01G295200 chr1B 81.585 1678 196 57 962 2593 674639819 674638209 0.000000e+00 1282.0
36 TraesCS5B01G295200 chr1B 79.630 270 41 10 872 1134 545451871 545452133 2.020000e-41 182.0
37 TraesCS5B01G295200 chr2B 81.455 1677 199 56 962 2593 10670137 10671746 0.000000e+00 1271.0
38 TraesCS5B01G295200 chr2B 81.097 1677 198 60 962 2593 390973497 390971895 0.000000e+00 1230.0
39 TraesCS5B01G295200 chr2B 79.487 273 42 10 872 1136 736737482 736737216 2.020000e-41 182.0
40 TraesCS5B01G295200 chr2A 81.444 1676 202 53 962 2593 130176989 130175379 0.000000e+00 1271.0
41 TraesCS5B01G295200 chr2A 78.676 272 46 9 872 1134 537057165 537057433 4.370000e-38 171.0
42 TraesCS5B01G295200 chr4A 80.443 271 39 12 872 1134 696445616 696445880 2.590000e-45 195.0
43 TraesCS5B01G295200 chr7B 74.805 512 88 24 655 1134 697783979 697783477 9.320000e-45 193.0
44 TraesCS5B01G295200 chr7B 84.000 75 11 1 3728 3802 82692738 82692811 4.560000e-08 71.3
45 TraesCS5B01G295200 chr7D 95.238 42 1 1 3761 3802 80969773 80969813 2.120000e-06 65.8
46 TraesCS5B01G295200 chr7D 90.698 43 3 1 3761 3802 187108760 187108802 1.000000e-03 56.5
47 TraesCS5B01G295200 chr7A 95.238 42 1 1 3761 3802 83624327 83624367 2.120000e-06 65.8
48 TraesCS5B01G295200 chr7A 94.595 37 2 0 3763 3799 667224766 667224802 3.550000e-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 TraesCS5B01G295200 chr5B 479192142 479201240 9098 False 16803.000000 16803 100.000000 1 9099 1 chr5B.!!$F1 9098
1 TraesCS5B01G295200 chr5D 398895984 398904890 8906 False 4787.333333 10567 96.019000 22 9029 3 chr5D.!!$F1 9007
2 TraesCS5B01G295200 chr5A 503940829 503948875 8046 False 1559.833333 4200 89.291833 259 8246 6 chr5A.!!$F2 7987
3 TraesCS5B01G295200 chr5A 109302745 109304354 1609 False 1304.000000 1304 81.802000 962 2593 1 chr5A.!!$F1 1631
4 TraesCS5B01G295200 chr6B 718638390 718645096 6706 False 969.000000 2023 86.323286 874 7390 7 chr6B.!!$F1 6516
5 TraesCS5B01G295200 chr6B 669685759 669686405 646 True 501.000000 501 81.132000 6718 7393 1 chr6B.!!$R1 675
6 TraesCS5B01G295200 chr6B 669739308 669739974 666 True 483.000000 483 80.226000 6718 7413 1 chr6B.!!$R2 695
7 TraesCS5B01G295200 chr6A 616754856 616761832 6976 True 975.857143 1507 85.707000 706 7525 7 chr6A.!!$R1 6819
8 TraesCS5B01G295200 chr6D 473230028 473237014 6986 False 873.625000 1502 85.516750 702 7516 8 chr6D.!!$F1 6814
9 TraesCS5B01G295200 chr1B 674638209 674639819 1610 True 1282.000000 1282 81.585000 962 2593 1 chr1B.!!$R1 1631
10 TraesCS5B01G295200 chr2B 10670137 10671746 1609 False 1271.000000 1271 81.455000 962 2593 1 chr2B.!!$F1 1631
11 TraesCS5B01G295200 chr2B 390971895 390973497 1602 True 1230.000000 1230 81.097000 962 2593 1 chr2B.!!$R1 1631
12 TraesCS5B01G295200 chr2A 130175379 130176989 1610 True 1271.000000 1271 81.444000 962 2593 1 chr2A.!!$R1 1631

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
204 205 0.038599 TGGTAGTGTCGCCTGGAGTA 59.961 55.000 0.00 0.0 0.00 2.59 F
236 237 0.107456 ATATCCAGCGGCAGAACAGG 59.893 55.000 1.45 0.0 0.00 4.00 F
244 245 0.107508 CGGCAGAACAGGTGATGGAT 60.108 55.000 0.00 0.0 0.00 3.41 F
1354 1486 0.380378 TTTTCAGGTCTGCGCAACAC 59.620 50.000 13.05 11.3 0.00 3.32 F
1456 1589 2.557452 GGGTTCAACAACATGGAGGGAT 60.557 50.000 0.00 0.0 33.70 3.85 F
2213 2364 4.883585 CCATATCCTTTGCTTTGAGCTGTA 59.116 41.667 0.00 0.0 42.97 2.74 F
3575 3923 2.894307 AAAAGGTATTGCGCTCGTTC 57.106 45.000 9.73 0.0 0.00 3.95 F
3644 3996 0.098376 GAAGGCGAAGATGCAGCAAG 59.902 55.000 4.07 0.0 36.28 4.01 F
4951 5510 1.871039 CCCATTCCGCCAAGTTATACG 59.129 52.381 0.00 0.0 0.00 3.06 F
5593 6210 0.830648 CACCACCTGATCCATACGGT 59.169 55.000 0.00 0.0 0.00 4.83 F
7025 7773 0.772124 AAGGCCAAGTCTCCCTTCCA 60.772 55.000 5.01 0.0 33.88 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1763 3.848272 AACCACGGCAAGAATATGTTG 57.152 42.857 0.00 0.0 0.00 3.33 R
2213 2364 2.637165 AGAAAGTCAAGGGGTGAGGAT 58.363 47.619 0.00 0.0 36.74 3.24 R
2247 2404 4.580167 GCTGACCAGTTATTTCATATGCCA 59.420 41.667 0.00 0.0 0.00 4.92 R
2950 3294 0.323629 GTCGACCAGTCAATTGGGGA 59.676 55.000 3.51 0.0 42.76 4.81 R
3078 3422 1.272769 ACTCCTTGCTTCCGTAGTGAC 59.727 52.381 0.00 0.0 0.00 3.67 R
3644 3996 0.393537 CCACTGGCCCTCTCATGAAC 60.394 60.000 0.00 0.0 0.00 3.18 R
5036 5595 4.589216 ATTGTTGTGCTTGCATTACAGT 57.411 36.364 0.00 1.1 0.00 3.55 R
5593 6210 1.431243 ACCCCCAGCAATCCTAACAAA 59.569 47.619 0.00 0.0 0.00 2.83 R
6327 6970 1.774254 CAATGGGCCTGGTCCACTATA 59.226 52.381 24.79 0.0 41.42 1.31 R
7464 8235 1.119574 ACAGCAGTTACTCGGTGGGT 61.120 55.000 14.64 0.0 34.96 4.51 R
8884 9948 0.321653 AGATGACGTGGTTCCCTTGC 60.322 55.000 0.00 0.0 0.00 4.01 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
17 18 2.809706 CCGCGGATTAGACGGGAA 59.190 61.111 24.07 0.00 45.60 3.97
18 19 1.142314 CCGCGGATTAGACGGGAAA 59.858 57.895 24.07 0.00 45.60 3.13
19 20 1.149964 CCGCGGATTAGACGGGAAAC 61.150 60.000 24.07 0.00 45.60 2.78
31 32 1.934589 CGGGAAACGCACAGATCATA 58.065 50.000 0.00 0.00 34.82 2.15
90 91 1.602237 CGTTGGTGGGAGCATAGGT 59.398 57.895 0.00 0.00 0.00 3.08
136 137 1.337260 CGATCCTGTACATGGCTAGGC 60.337 57.143 9.85 9.85 0.00 3.93
156 157 2.412870 CCAAAATCGCCCTGTTTTTCC 58.587 47.619 0.00 0.00 29.19 3.13
167 168 5.755861 CGCCCTGTTTTTCCTTTTCATTTTA 59.244 36.000 0.00 0.00 0.00 1.52
179 180 7.479980 TCCTTTTCATTTTATTACTGCATCCG 58.520 34.615 0.00 0.00 0.00 4.18
190 191 1.410517 ACTGCATCCGTGATCTGGTAG 59.589 52.381 0.00 0.00 0.00 3.18
202 203 0.965866 TCTGGTAGTGTCGCCTGGAG 60.966 60.000 0.00 0.00 0.00 3.86
203 204 1.228769 TGGTAGTGTCGCCTGGAGT 60.229 57.895 0.00 0.00 0.00 3.85
204 205 0.038599 TGGTAGTGTCGCCTGGAGTA 59.961 55.000 0.00 0.00 0.00 2.59
205 206 0.455005 GGTAGTGTCGCCTGGAGTAC 59.545 60.000 0.00 0.00 0.00 2.73
206 207 1.171308 GTAGTGTCGCCTGGAGTACA 58.829 55.000 0.00 0.00 0.00 2.90
207 208 1.749634 GTAGTGTCGCCTGGAGTACAT 59.250 52.381 0.00 0.00 0.00 2.29
208 209 2.139323 AGTGTCGCCTGGAGTACATA 57.861 50.000 0.00 0.00 0.00 2.29
209 210 2.453521 AGTGTCGCCTGGAGTACATAA 58.546 47.619 0.00 0.00 0.00 1.90
210 211 2.427453 AGTGTCGCCTGGAGTACATAAG 59.573 50.000 0.00 0.00 0.00 1.73
211 212 2.426024 GTGTCGCCTGGAGTACATAAGA 59.574 50.000 0.00 0.00 0.00 2.10
212 213 3.068307 GTGTCGCCTGGAGTACATAAGAT 59.932 47.826 0.00 0.00 0.00 2.40
213 214 3.068165 TGTCGCCTGGAGTACATAAGATG 59.932 47.826 0.00 0.00 0.00 2.90
214 215 3.068307 GTCGCCTGGAGTACATAAGATGT 59.932 47.826 0.00 0.00 46.92 3.06
215 216 3.068165 TCGCCTGGAGTACATAAGATGTG 59.932 47.826 0.00 0.00 44.60 3.21
216 217 3.181475 CGCCTGGAGTACATAAGATGTGT 60.181 47.826 0.00 0.00 44.60 3.72
217 218 4.037565 CGCCTGGAGTACATAAGATGTGTA 59.962 45.833 0.00 0.00 44.60 2.90
218 219 5.279006 CGCCTGGAGTACATAAGATGTGTAT 60.279 44.000 0.00 0.00 44.60 2.29
219 220 6.072119 CGCCTGGAGTACATAAGATGTGTATA 60.072 42.308 0.00 0.00 44.60 1.47
220 221 7.363007 CGCCTGGAGTACATAAGATGTGTATAT 60.363 40.741 0.00 0.00 44.60 0.86
221 222 7.976734 GCCTGGAGTACATAAGATGTGTATATC 59.023 40.741 0.00 0.00 44.60 1.63
222 223 8.470805 CCTGGAGTACATAAGATGTGTATATCC 58.529 40.741 2.33 11.29 44.60 2.59
223 224 8.950007 TGGAGTACATAAGATGTGTATATCCA 57.050 34.615 14.46 14.46 44.60 3.41
224 225 9.025041 TGGAGTACATAAGATGTGTATATCCAG 57.975 37.037 14.46 0.00 44.60 3.86
225 226 7.976734 GGAGTACATAAGATGTGTATATCCAGC 59.023 40.741 2.33 0.00 44.60 4.85
226 227 7.539436 AGTACATAAGATGTGTATATCCAGCG 58.461 38.462 2.33 0.00 44.60 5.18
227 228 5.724328 ACATAAGATGTGTATATCCAGCGG 58.276 41.667 0.00 0.00 43.01 5.52
228 229 2.751166 AGATGTGTATATCCAGCGGC 57.249 50.000 0.00 0.00 0.00 6.53
229 230 1.970640 AGATGTGTATATCCAGCGGCA 59.029 47.619 1.45 0.00 0.00 5.69
230 231 2.028658 AGATGTGTATATCCAGCGGCAG 60.029 50.000 1.45 0.00 0.00 4.85
231 232 1.408969 TGTGTATATCCAGCGGCAGA 58.591 50.000 1.45 0.00 0.00 4.26
232 233 1.760029 TGTGTATATCCAGCGGCAGAA 59.240 47.619 1.45 0.00 0.00 3.02
233 234 2.135933 GTGTATATCCAGCGGCAGAAC 58.864 52.381 1.45 0.00 0.00 3.01
234 235 1.760029 TGTATATCCAGCGGCAGAACA 59.240 47.619 1.45 0.00 0.00 3.18
235 236 2.224042 TGTATATCCAGCGGCAGAACAG 60.224 50.000 1.45 0.00 0.00 3.16
236 237 0.107456 ATATCCAGCGGCAGAACAGG 59.893 55.000 1.45 0.00 0.00 4.00
237 238 1.264749 TATCCAGCGGCAGAACAGGT 61.265 55.000 1.45 0.00 0.00 4.00
238 239 2.809861 ATCCAGCGGCAGAACAGGTG 62.810 60.000 1.45 0.00 41.02 4.00
239 240 2.031012 CAGCGGCAGAACAGGTGA 59.969 61.111 1.45 0.00 43.59 4.02
240 241 1.376424 CAGCGGCAGAACAGGTGAT 60.376 57.895 1.45 0.00 43.59 3.06
241 242 1.376424 AGCGGCAGAACAGGTGATG 60.376 57.895 1.45 0.00 0.00 3.07
242 243 2.401766 GCGGCAGAACAGGTGATGG 61.402 63.158 0.00 0.00 0.00 3.51
243 244 1.296392 CGGCAGAACAGGTGATGGA 59.704 57.895 0.00 0.00 0.00 3.41
244 245 0.107508 CGGCAGAACAGGTGATGGAT 60.108 55.000 0.00 0.00 0.00 3.41
245 246 1.386533 GGCAGAACAGGTGATGGATG 58.613 55.000 0.00 0.00 0.00 3.51
246 247 1.065199 GGCAGAACAGGTGATGGATGA 60.065 52.381 0.00 0.00 0.00 2.92
247 248 2.422519 GGCAGAACAGGTGATGGATGAT 60.423 50.000 0.00 0.00 0.00 2.45
248 249 2.617308 GCAGAACAGGTGATGGATGATG 59.383 50.000 0.00 0.00 0.00 3.07
249 250 3.683564 GCAGAACAGGTGATGGATGATGA 60.684 47.826 0.00 0.00 0.00 2.92
250 251 4.520179 CAGAACAGGTGATGGATGATGAA 58.480 43.478 0.00 0.00 0.00 2.57
251 252 5.131067 CAGAACAGGTGATGGATGATGAAT 58.869 41.667 0.00 0.00 0.00 2.57
252 253 5.008712 CAGAACAGGTGATGGATGATGAATG 59.991 44.000 0.00 0.00 0.00 2.67
253 254 4.515028 ACAGGTGATGGATGATGAATGT 57.485 40.909 0.00 0.00 0.00 2.71
254 255 4.204799 ACAGGTGATGGATGATGAATGTG 58.795 43.478 0.00 0.00 0.00 3.21
255 256 3.568430 CAGGTGATGGATGATGAATGTGG 59.432 47.826 0.00 0.00 0.00 4.17
256 257 3.460712 AGGTGATGGATGATGAATGTGGA 59.539 43.478 0.00 0.00 0.00 4.02
257 258 3.819337 GGTGATGGATGATGAATGTGGAG 59.181 47.826 0.00 0.00 0.00 3.86
274 275 1.272147 GGAGGGAGCCAACAGTTGAAT 60.272 52.381 15.36 2.33 0.00 2.57
278 279 3.074538 AGGGAGCCAACAGTTGAATTACT 59.925 43.478 15.36 4.62 0.00 2.24
315 316 2.972625 TCCAAAACTACTCTGCCATCG 58.027 47.619 0.00 0.00 0.00 3.84
606 630 9.073475 ACTTGGTATTTATTCAAGTGTTTGCTA 57.927 29.630 7.08 0.00 46.17 3.49
667 691 4.398319 ACAGTCAGGTGGTTGGAAATTAG 58.602 43.478 0.00 0.00 0.00 1.73
821 858 2.952310 GTTGGCCTATGTTGGAAGGATC 59.048 50.000 3.32 0.00 34.58 3.36
827 864 3.244353 CCTATGTTGGAAGGATCGCTCAT 60.244 47.826 0.00 0.00 34.58 2.90
838 875 4.626042 AGGATCGCTCATATGTCAACTTC 58.374 43.478 1.90 0.00 0.00 3.01
957 1010 2.971330 AGGCATTTTTGGTGGACAATCA 59.029 40.909 0.00 0.00 39.21 2.57
993 1046 1.867233 TGCTGACTCGCTTTTCTGTTC 59.133 47.619 0.00 0.00 0.00 3.18
1084 1201 6.966021 TGTTTACTGCCAATCTTAACAGTTC 58.034 36.000 0.00 0.00 42.97 3.01
1194 1322 0.998226 CAACTGCACGACCATTTGCG 60.998 55.000 0.00 0.00 41.96 4.85
1354 1486 0.380378 TTTTCAGGTCTGCGCAACAC 59.620 50.000 13.05 11.30 0.00 3.32
1456 1589 2.557452 GGGTTCAACAACATGGAGGGAT 60.557 50.000 0.00 0.00 33.70 3.85
1816 1961 7.898636 TCAAGGTTTATACTCAAATTTGGGGAT 59.101 33.333 19.70 19.70 35.94 3.85
2213 2364 4.883585 CCATATCCTTTGCTTTGAGCTGTA 59.116 41.667 0.00 0.00 42.97 2.74
2386 2557 8.152898 TGATGCTATAGTGTATTGCAGAATTCT 58.847 33.333 0.88 0.88 46.70 2.40
2950 3294 6.558009 CACTCCATTCGACATCAATGATTTT 58.442 36.000 0.00 0.00 33.69 1.82
3078 3422 3.317430 GCCAATCTCTCTAAATTGCAGGG 59.683 47.826 0.00 0.00 32.65 4.45
3331 3675 4.717877 TGCATGCCAGTTATTATACAGCT 58.282 39.130 16.68 0.00 0.00 4.24
3476 3823 4.382470 CGGTGATCTTCTCCTCAAGTCAAT 60.382 45.833 0.00 0.00 0.00 2.57
3499 3846 8.700644 CAATGAATGCTTACTACCGTTCTATAC 58.299 37.037 0.00 0.00 0.00 1.47
3543 3891 3.999663 CTCTACTTCTCTTGCCACCTTTG 59.000 47.826 0.00 0.00 0.00 2.77
3575 3923 2.894307 AAAAGGTATTGCGCTCGTTC 57.106 45.000 9.73 0.00 0.00 3.95
3644 3996 0.098376 GAAGGCGAAGATGCAGCAAG 59.902 55.000 4.07 0.00 36.28 4.01
3683 4038 2.490165 GCAAGACCATGCAGCTGAT 58.510 52.632 20.43 5.31 45.70 2.90
3708 4063 2.357952 GCCTCGCGGGAATTTAGAAAAT 59.642 45.455 8.08 0.00 37.23 1.82
3749 4104 4.730949 TGGTACTCCCTTCGTATCAAAG 57.269 45.455 0.00 0.00 0.00 2.77
3774 4129 8.929746 AGTATAAGACGTTTTAGCCTACAAAAC 58.070 33.333 4.75 0.00 40.74 2.43
3844 4199 4.594123 TGCCAAATCAAGGATGCATATG 57.406 40.909 0.00 0.00 0.00 1.78
4102 4496 3.319405 ACACAAGATGGGTATAGAGCTCG 59.681 47.826 8.37 0.00 28.13 5.03
4262 4657 9.930693 CATAGGTCCTACTCTTCATATAAAACC 57.069 37.037 0.00 0.00 0.00 3.27
4470 4961 5.135383 AGCATTTAATAGAGATTGCTGCCA 58.865 37.500 0.00 0.00 38.87 4.92
4476 4967 4.978083 ATAGAGATTGCTGCCAAAGTTG 57.022 40.909 0.00 0.00 34.05 3.16
4788 5296 7.895429 TCTGATTTTTGGACCTATTCTTTCCAT 59.105 33.333 0.00 0.00 39.21 3.41
4795 5303 4.646492 GGACCTATTCTTTCCATGTGCAAT 59.354 41.667 0.00 0.00 0.00 3.56
4951 5510 1.871039 CCCATTCCGCCAAGTTATACG 59.129 52.381 0.00 0.00 0.00 3.06
5036 5595 5.607477 AGGAACAACTTCACGAGAATGTAA 58.393 37.500 2.87 0.00 32.31 2.41
5593 6210 0.830648 CACCACCTGATCCATACGGT 59.169 55.000 0.00 0.00 0.00 4.83
5801 6418 4.431131 CCGAGCAACCCCCAGCAT 62.431 66.667 0.00 0.00 0.00 3.79
5803 6420 1.978617 CGAGCAACCCCCAGCATTT 60.979 57.895 0.00 0.00 0.00 2.32
6158 6798 7.681939 TGGTTTCACTGGTTATCTCATTTAC 57.318 36.000 0.00 0.00 0.00 2.01
6280 6923 6.554982 TGATAAGGGAACATACTGCTATGTCT 59.445 38.462 0.00 0.00 41.92 3.41
6327 6970 9.614792 GAGAAATATTAACCTGTAACCTGTCAT 57.385 33.333 0.00 0.00 0.00 3.06
6458 7107 2.316108 TCATGACCCGCTTAGCATCTA 58.684 47.619 4.70 0.00 0.00 1.98
6465 7114 2.555199 CCGCTTAGCATCTAAAGCTGT 58.445 47.619 4.70 0.00 44.72 4.40
6469 7118 3.064545 GCTTAGCATCTAAAGCTGTGTGG 59.935 47.826 0.00 0.00 43.77 4.17
6647 7364 3.040147 TCTTGTCTTAACCCTTGCTCG 57.960 47.619 0.00 0.00 0.00 5.03
7025 7773 0.772124 AAGGCCAAGTCTCCCTTCCA 60.772 55.000 5.01 0.00 33.88 3.53
7058 7806 4.219115 TGGTAGGTGAAATTTTGCTTGGA 58.781 39.130 0.00 0.00 0.00 3.53
7059 7807 4.837860 TGGTAGGTGAAATTTTGCTTGGAT 59.162 37.500 0.00 0.00 0.00 3.41
7258 8015 3.093057 AGGTAGGTACTGTCTTCTGCAG 58.907 50.000 7.63 7.63 41.52 4.41
7355 8122 4.021544 GGAATAAATGTTCTGTGTGGCCAA 60.022 41.667 7.24 0.00 0.00 4.52
7464 8235 1.872952 GACACACACACATGCTGCTAA 59.127 47.619 0.00 0.00 0.00 3.09
7506 8277 4.454504 TGCTCGGTTCTCATTAGGAAAAAC 59.545 41.667 0.00 0.00 0.00 2.43
7622 8639 2.158827 TGACCCATGGACATTATCACCG 60.159 50.000 15.22 0.00 0.00 4.94
7738 8763 3.857157 AGCACTTCTGGTTCTTGGTTA 57.143 42.857 0.00 0.00 0.00 2.85
7946 8983 8.506437 TGTTTTGAGTGATGTTCTGCTAATAAG 58.494 33.333 0.00 0.00 0.00 1.73
7997 9039 3.880610 ACAAAATTGTAGCCGTTTCGAC 58.119 40.909 0.00 0.00 40.16 4.20
8089 9132 1.214062 CGATATGCGGAGAGGAGGC 59.786 63.158 0.00 0.00 36.03 4.70
8164 9212 2.784928 GGCACCGTCGTTAAACTTTTTG 59.215 45.455 0.00 0.00 0.00 2.44
8183 9231 4.301072 TTGCCTAGCTTCTTGGTACATT 57.699 40.909 0.00 0.00 39.30 2.71
8202 9250 1.688772 TATACGGGGAGTCTGTCTGC 58.311 55.000 0.00 0.00 36.22 4.26
8230 9278 4.134563 TCCTTGACAAACAGTTTAGGAGC 58.865 43.478 10.21 0.00 36.06 4.70
8233 9281 4.150897 TGACAAACAGTTTAGGAGCAGT 57.849 40.909 0.00 0.00 0.00 4.40
8241 9289 2.564947 AGTTTAGGAGCAGTCAGTCAGG 59.435 50.000 0.00 0.00 0.00 3.86
8256 9304 2.123769 AGGCTGCCTGTGTGCAAA 60.124 55.556 22.71 0.00 41.51 3.68
8330 9378 7.062956 GGGTTGCTTCCTTAAATTAATTCAACG 59.937 37.037 0.10 0.00 33.13 4.10
8348 9396 6.787085 TCAACGGAACAAAACAAACAAATT 57.213 29.167 0.00 0.00 0.00 1.82
8374 9422 2.873094 TCTTCTCCGACAGTGGTAGA 57.127 50.000 0.00 0.00 0.00 2.59
8376 9424 2.818432 TCTTCTCCGACAGTGGTAGAAC 59.182 50.000 0.00 0.00 0.00 3.01
8397 9445 2.074547 TGTTACTCGTTGGCTGTAGC 57.925 50.000 0.00 0.00 41.14 3.58
8465 9513 5.964958 ATTCTGCTCAAAGGATTTTTCGA 57.035 34.783 0.00 0.00 35.03 3.71
8467 9515 5.362556 TCTGCTCAAAGGATTTTTCGAAG 57.637 39.130 0.00 0.00 35.03 3.79
8471 9519 4.618912 GCTCAAAGGATTTTTCGAAGAAGC 59.381 41.667 8.07 8.07 37.96 3.86
8479 9527 8.341892 AGGATTTTTCGAAGAAGCTATTTTCT 57.658 30.769 15.16 1.71 45.90 2.52
8524 9572 2.043652 CAGCAGGGTTGATGGGGG 60.044 66.667 0.00 0.00 37.07 5.40
8530 9578 1.568597 CAGGGTTGATGGGGGTTGATA 59.431 52.381 0.00 0.00 0.00 2.15
8534 9582 3.397955 GGGTTGATGGGGGTTGATATAGT 59.602 47.826 0.00 0.00 0.00 2.12
8543 9591 3.005791 GGGGTTGATATAGTGCATTTGCC 59.994 47.826 0.00 0.00 41.18 4.52
8564 9612 3.869272 CCGCAGGCGCTTGTGATC 61.869 66.667 31.63 9.59 46.14 2.92
8569 9617 0.461548 CAGGCGCTTGTGATCTCCTA 59.538 55.000 11.99 0.00 0.00 2.94
8587 9635 5.926542 TCTCCTATTTCACAGAAAAGTCACG 59.073 40.000 0.00 0.00 0.00 4.35
8613 9677 3.256960 ATGGCGGAGGTGGTGGTT 61.257 61.111 0.00 0.00 0.00 3.67
8635 9699 3.134127 GAGGGTGATGCCGGTTGC 61.134 66.667 1.90 0.00 38.44 4.17
8680 9744 2.096013 GCTGGAGGTTGAAGATAAACGC 59.904 50.000 0.00 0.00 0.00 4.84
8683 9747 2.347755 GGAGGTTGAAGATAAACGCGAC 59.652 50.000 15.93 0.00 0.00 5.19
8713 9777 2.764128 GATCCGAGGGTGGCTGGA 60.764 66.667 0.00 0.00 34.45 3.86
8714 9778 2.285368 ATCCGAGGGTGGCTGGAA 60.285 61.111 0.00 0.00 33.48 3.53
8715 9779 2.317149 GATCCGAGGGTGGCTGGAAG 62.317 65.000 0.00 0.00 33.48 3.46
8734 9798 3.933861 AGCCTGGAACTTTACATAGGG 57.066 47.619 0.00 0.00 0.00 3.53
8761 9825 2.229062 TCCGTGATGTGTCTGTCTCTTC 59.771 50.000 0.00 0.00 0.00 2.87
8849 9913 2.597340 CCCGCAATCCACCCAGAT 59.403 61.111 0.00 0.00 0.00 2.90
8858 9922 4.899239 CACCCAGATCTCGCCGGC 62.899 72.222 19.07 19.07 0.00 6.13
8884 9948 2.819595 CCCGTTGCTCATCCACCG 60.820 66.667 0.00 0.00 0.00 4.94
8886 9950 2.741985 CGTTGCTCATCCACCGCA 60.742 61.111 0.00 0.00 0.00 5.69
8952 10026 2.851102 CCTCTCCCATCGCCCCAT 60.851 66.667 0.00 0.00 0.00 4.00
8953 10027 2.429058 CTCTCCCATCGCCCCATG 59.571 66.667 0.00 0.00 0.00 3.66
8981 10055 1.078567 GCCTGCCTCCTCAAGACAG 60.079 63.158 0.00 0.00 0.00 3.51
8985 10059 0.252239 TGCCTCCTCAAGACAGCCTA 60.252 55.000 0.00 0.00 0.00 3.93
8986 10060 0.176910 GCCTCCTCAAGACAGCCTAC 59.823 60.000 0.00 0.00 0.00 3.18
8987 10061 1.561643 CCTCCTCAAGACAGCCTACA 58.438 55.000 0.00 0.00 0.00 2.74
8988 10062 2.114616 CCTCCTCAAGACAGCCTACAT 58.885 52.381 0.00 0.00 0.00 2.29
8989 10063 2.102252 CCTCCTCAAGACAGCCTACATC 59.898 54.545 0.00 0.00 0.00 3.06
8990 10064 2.102252 CTCCTCAAGACAGCCTACATCC 59.898 54.545 0.00 0.00 0.00 3.51
8991 10065 1.833630 CCTCAAGACAGCCTACATCCA 59.166 52.381 0.00 0.00 0.00 3.41
8992 10066 2.419297 CCTCAAGACAGCCTACATCCAC 60.419 54.545 0.00 0.00 0.00 4.02
8993 10067 1.555075 TCAAGACAGCCTACATCCACC 59.445 52.381 0.00 0.00 0.00 4.61
8994 10068 0.912486 AAGACAGCCTACATCCACCC 59.088 55.000 0.00 0.00 0.00 4.61
8999 10073 2.919043 CCTACATCCACCCTGCCC 59.081 66.667 0.00 0.00 0.00 5.36
9029 10103 4.641645 CGTGCCCAACTCCCTGCA 62.642 66.667 0.00 0.00 0.00 4.41
9030 10104 2.036256 GTGCCCAACTCCCTGCAT 59.964 61.111 0.00 0.00 35.96 3.96
9031 10105 2.048603 GTGCCCAACTCCCTGCATC 61.049 63.158 0.00 0.00 35.96 3.91
9032 10106 2.825836 GCCCAACTCCCTGCATCG 60.826 66.667 0.00 0.00 0.00 3.84
9033 10107 2.124570 CCCAACTCCCTGCATCGG 60.125 66.667 0.00 0.00 0.00 4.18
9034 10108 2.124570 CCAACTCCCTGCATCGGG 60.125 66.667 4.59 4.59 46.13 5.14
9040 10114 4.489771 CCCTGCATCGGGGGACAC 62.490 72.222 2.49 0.00 45.99 3.67
9041 10115 4.489771 CCTGCATCGGGGGACACC 62.490 72.222 0.00 0.00 39.11 4.16
9042 10116 3.402681 CTGCATCGGGGGACACCT 61.403 66.667 0.00 0.00 40.03 4.00
9045 10119 4.838152 CATCGGGGGACACCTGCG 62.838 72.222 0.00 0.00 45.92 5.18
9068 10142 2.049802 GTCGGGCTGTTCGACGAA 60.050 61.111 6.10 6.10 45.53 3.85
9069 10143 1.662446 GTCGGGCTGTTCGACGAAA 60.662 57.895 12.67 2.31 45.53 3.46
9070 10144 1.012486 GTCGGGCTGTTCGACGAAAT 61.012 55.000 12.67 0.00 45.53 2.17
9071 10145 1.011968 TCGGGCTGTTCGACGAAATG 61.012 55.000 12.67 9.10 31.79 2.32
9072 10146 1.134694 GGGCTGTTCGACGAAATGC 59.865 57.895 20.78 20.78 0.00 3.56
9073 10147 1.134694 GGCTGTTCGACGAAATGCC 59.865 57.895 27.63 27.63 35.98 4.40
9074 10148 1.298859 GGCTGTTCGACGAAATGCCT 61.299 55.000 31.09 0.00 38.34 4.75
9075 10149 0.095417 GCTGTTCGACGAAATGCCTC 59.905 55.000 12.67 0.00 0.00 4.70
9076 10150 1.714794 CTGTTCGACGAAATGCCTCT 58.285 50.000 12.67 0.00 0.00 3.69
9077 10151 1.656095 CTGTTCGACGAAATGCCTCTC 59.344 52.381 12.67 0.00 0.00 3.20
9078 10152 1.272490 TGTTCGACGAAATGCCTCTCT 59.728 47.619 12.67 0.00 0.00 3.10
9079 10153 1.656095 GTTCGACGAAATGCCTCTCTG 59.344 52.381 12.67 0.00 0.00 3.35
9080 10154 1.173913 TCGACGAAATGCCTCTCTGA 58.826 50.000 0.00 0.00 0.00 3.27
9081 10155 1.133216 TCGACGAAATGCCTCTCTGAG 59.867 52.381 0.00 0.00 0.00 3.35
9082 10156 1.133216 CGACGAAATGCCTCTCTGAGA 59.867 52.381 7.24 7.24 0.00 3.27
9083 10157 2.535331 GACGAAATGCCTCTCTGAGAC 58.465 52.381 2.58 0.00 0.00 3.36
9084 10158 1.135257 ACGAAATGCCTCTCTGAGACG 60.135 52.381 2.58 6.66 0.00 4.18
9085 10159 1.135257 CGAAATGCCTCTCTGAGACGT 60.135 52.381 2.58 0.00 0.00 4.34
9086 10160 2.672478 CGAAATGCCTCTCTGAGACGTT 60.672 50.000 2.58 0.25 0.00 3.99
9087 10161 2.376808 AATGCCTCTCTGAGACGTTG 57.623 50.000 2.58 0.00 0.00 4.10
9088 10162 0.108424 ATGCCTCTCTGAGACGTTGC 60.108 55.000 2.58 5.21 0.00 4.17
9089 10163 1.803519 GCCTCTCTGAGACGTTGCG 60.804 63.158 2.58 0.00 0.00 4.85
9090 10164 1.581954 CCTCTCTGAGACGTTGCGT 59.418 57.895 2.58 0.00 45.10 5.24
9091 10165 0.039074 CCTCTCTGAGACGTTGCGTT 60.039 55.000 2.58 0.00 41.37 4.84
9092 10166 1.332178 CTCTCTGAGACGTTGCGTTC 58.668 55.000 2.58 0.00 41.37 3.95
9093 10167 0.039437 TCTCTGAGACGTTGCGTTCC 60.039 55.000 2.58 0.00 41.37 3.62
9094 10168 1.337817 CTCTGAGACGTTGCGTTCCG 61.338 60.000 0.00 0.00 41.37 4.30
9095 10169 2.355363 TGAGACGTTGCGTTCCGG 60.355 61.111 0.00 0.00 41.37 5.14
9096 10170 3.110178 GAGACGTTGCGTTCCGGG 61.110 66.667 0.00 0.00 41.37 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.142314 TTTCCCGTCTAATCCGCGG 59.858 57.895 22.12 22.12 44.55 6.46
1 2 1.477030 CGTTTCCCGTCTAATCCGCG 61.477 60.000 0.00 0.00 0.00 6.46
2 3 1.759293 GCGTTTCCCGTCTAATCCGC 61.759 60.000 0.00 0.00 39.32 5.54
3 4 0.458889 TGCGTTTCCCGTCTAATCCG 60.459 55.000 0.00 0.00 39.32 4.18
4 5 1.004595 GTGCGTTTCCCGTCTAATCC 58.995 55.000 0.00 0.00 39.32 3.01
5 6 1.659098 CTGTGCGTTTCCCGTCTAATC 59.341 52.381 0.00 0.00 39.32 1.75
6 7 1.274167 TCTGTGCGTTTCCCGTCTAAT 59.726 47.619 0.00 0.00 39.32 1.73
7 8 0.675083 TCTGTGCGTTTCCCGTCTAA 59.325 50.000 0.00 0.00 39.32 2.10
8 9 0.892755 ATCTGTGCGTTTCCCGTCTA 59.107 50.000 0.00 0.00 39.32 2.59
9 10 0.389948 GATCTGTGCGTTTCCCGTCT 60.390 55.000 0.00 0.00 39.32 4.18
10 11 0.669318 TGATCTGTGCGTTTCCCGTC 60.669 55.000 0.00 0.00 39.32 4.79
11 12 0.036388 ATGATCTGTGCGTTTCCCGT 60.036 50.000 0.00 0.00 39.32 5.28
12 13 1.593006 GTATGATCTGTGCGTTTCCCG 59.407 52.381 0.00 0.00 40.40 5.14
13 14 1.940613 GGTATGATCTGTGCGTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
14 15 2.609459 CAGGTATGATCTGTGCGTTTCC 59.391 50.000 0.00 0.00 0.00 3.13
15 16 2.030946 GCAGGTATGATCTGTGCGTTTC 59.969 50.000 0.00 0.00 34.89 2.78
16 17 2.009774 GCAGGTATGATCTGTGCGTTT 58.990 47.619 0.00 0.00 34.89 3.60
17 18 1.066215 TGCAGGTATGATCTGTGCGTT 60.066 47.619 0.00 0.00 36.92 4.84
18 19 0.536724 TGCAGGTATGATCTGTGCGT 59.463 50.000 0.00 0.00 36.92 5.24
19 20 1.875009 ATGCAGGTATGATCTGTGCG 58.125 50.000 0.00 0.00 36.92 5.34
20 21 4.153655 CACATATGCAGGTATGATCTGTGC 59.846 45.833 13.09 0.00 35.96 4.57
31 32 1.521457 CGCGGACACATATGCAGGT 60.521 57.895 1.58 0.00 0.00 4.00
136 137 2.037121 AGGAAAAACAGGGCGATTTTGG 59.963 45.455 0.00 0.00 30.45 3.28
143 144 2.880963 TGAAAAGGAAAAACAGGGCG 57.119 45.000 0.00 0.00 0.00 6.13
156 157 7.967854 TCACGGATGCAGTAATAAAATGAAAAG 59.032 33.333 0.00 0.00 0.00 2.27
167 168 2.435805 ACCAGATCACGGATGCAGTAAT 59.564 45.455 8.11 0.00 0.00 1.89
179 180 0.818296 AGGCGACACTACCAGATCAC 59.182 55.000 0.00 0.00 0.00 3.06
190 191 2.426024 TCTTATGTACTCCAGGCGACAC 59.574 50.000 0.00 0.00 0.00 3.67
202 203 6.752351 CCGCTGGATATACACATCTTATGTAC 59.248 42.308 0.00 0.00 42.70 2.90
203 204 6.627287 GCCGCTGGATATACACATCTTATGTA 60.627 42.308 0.00 0.00 42.70 2.29
204 205 5.724328 CCGCTGGATATACACATCTTATGT 58.276 41.667 0.00 0.00 46.22 2.29
205 206 4.568359 GCCGCTGGATATACACATCTTATG 59.432 45.833 0.00 0.00 0.00 1.90
206 207 4.222810 TGCCGCTGGATATACACATCTTAT 59.777 41.667 0.00 0.00 0.00 1.73
207 208 3.576550 TGCCGCTGGATATACACATCTTA 59.423 43.478 0.00 0.00 0.00 2.10
208 209 2.368548 TGCCGCTGGATATACACATCTT 59.631 45.455 0.00 0.00 0.00 2.40
209 210 1.970640 TGCCGCTGGATATACACATCT 59.029 47.619 0.00 0.00 0.00 2.90
210 211 2.029020 TCTGCCGCTGGATATACACATC 60.029 50.000 0.00 0.00 0.00 3.06
211 212 1.970640 TCTGCCGCTGGATATACACAT 59.029 47.619 0.00 0.00 0.00 3.21
212 213 1.408969 TCTGCCGCTGGATATACACA 58.591 50.000 0.00 0.00 0.00 3.72
213 214 2.135933 GTTCTGCCGCTGGATATACAC 58.864 52.381 0.00 0.00 0.00 2.90
214 215 1.760029 TGTTCTGCCGCTGGATATACA 59.240 47.619 0.00 0.00 0.00 2.29
215 216 2.408050 CTGTTCTGCCGCTGGATATAC 58.592 52.381 0.00 0.00 0.00 1.47
216 217 1.344438 CCTGTTCTGCCGCTGGATATA 59.656 52.381 0.00 0.00 0.00 0.86
217 218 0.107456 CCTGTTCTGCCGCTGGATAT 59.893 55.000 0.00 0.00 0.00 1.63
218 219 1.264749 ACCTGTTCTGCCGCTGGATA 61.265 55.000 0.00 0.00 0.00 2.59
219 220 2.270205 CCTGTTCTGCCGCTGGAT 59.730 61.111 0.00 0.00 0.00 3.41
220 221 3.241530 ACCTGTTCTGCCGCTGGA 61.242 61.111 0.00 0.00 0.00 3.86
221 222 2.809861 ATCACCTGTTCTGCCGCTGG 62.810 60.000 0.00 0.00 0.00 4.85
222 223 1.376424 ATCACCTGTTCTGCCGCTG 60.376 57.895 0.00 0.00 0.00 5.18
223 224 1.376424 CATCACCTGTTCTGCCGCT 60.376 57.895 0.00 0.00 0.00 5.52
224 225 2.401766 CCATCACCTGTTCTGCCGC 61.402 63.158 0.00 0.00 0.00 6.53
225 226 0.107508 ATCCATCACCTGTTCTGCCG 60.108 55.000 0.00 0.00 0.00 5.69
226 227 1.065199 TCATCCATCACCTGTTCTGCC 60.065 52.381 0.00 0.00 0.00 4.85
227 228 2.408271 TCATCCATCACCTGTTCTGC 57.592 50.000 0.00 0.00 0.00 4.26
228 229 4.146745 TCATCATCCATCACCTGTTCTG 57.853 45.455 0.00 0.00 0.00 3.02
229 230 4.849813 TTCATCATCCATCACCTGTTCT 57.150 40.909 0.00 0.00 0.00 3.01
230 231 4.885907 ACATTCATCATCCATCACCTGTTC 59.114 41.667 0.00 0.00 0.00 3.18
231 232 4.643334 CACATTCATCATCCATCACCTGTT 59.357 41.667 0.00 0.00 0.00 3.16
232 233 4.204799 CACATTCATCATCCATCACCTGT 58.795 43.478 0.00 0.00 0.00 4.00
233 234 3.568430 CCACATTCATCATCCATCACCTG 59.432 47.826 0.00 0.00 0.00 4.00
234 235 3.460712 TCCACATTCATCATCCATCACCT 59.539 43.478 0.00 0.00 0.00 4.00
235 236 3.819337 CTCCACATTCATCATCCATCACC 59.181 47.826 0.00 0.00 0.00 4.02
236 237 3.819337 CCTCCACATTCATCATCCATCAC 59.181 47.826 0.00 0.00 0.00 3.06
237 238 3.181437 CCCTCCACATTCATCATCCATCA 60.181 47.826 0.00 0.00 0.00 3.07
238 239 3.073503 TCCCTCCACATTCATCATCCATC 59.926 47.826 0.00 0.00 0.00 3.51
239 240 3.058341 TCCCTCCACATTCATCATCCAT 58.942 45.455 0.00 0.00 0.00 3.41
240 241 2.440627 CTCCCTCCACATTCATCATCCA 59.559 50.000 0.00 0.00 0.00 3.41
241 242 2.813354 GCTCCCTCCACATTCATCATCC 60.813 54.545 0.00 0.00 0.00 3.51
242 243 2.502295 GCTCCCTCCACATTCATCATC 58.498 52.381 0.00 0.00 0.00 2.92
243 244 1.144503 GGCTCCCTCCACATTCATCAT 59.855 52.381 0.00 0.00 0.00 2.45
244 245 0.548031 GGCTCCCTCCACATTCATCA 59.452 55.000 0.00 0.00 0.00 3.07
245 246 0.548031 TGGCTCCCTCCACATTCATC 59.452 55.000 0.00 0.00 0.00 2.92
246 247 1.002069 TTGGCTCCCTCCACATTCAT 58.998 50.000 0.00 0.00 35.50 2.57
247 248 0.038166 GTTGGCTCCCTCCACATTCA 59.962 55.000 0.00 0.00 35.50 2.57
248 249 0.038166 TGTTGGCTCCCTCCACATTC 59.962 55.000 0.00 0.00 35.50 2.67
249 250 0.038744 CTGTTGGCTCCCTCCACATT 59.961 55.000 0.00 0.00 35.50 2.71
250 251 1.136329 ACTGTTGGCTCCCTCCACAT 61.136 55.000 0.00 0.00 35.50 3.21
251 252 1.352622 AACTGTTGGCTCCCTCCACA 61.353 55.000 0.00 0.00 35.50 4.17
252 253 0.890996 CAACTGTTGGCTCCCTCCAC 60.891 60.000 12.66 0.00 35.50 4.02
253 254 1.059584 TCAACTGTTGGCTCCCTCCA 61.060 55.000 19.55 0.00 0.00 3.86
254 255 0.110486 TTCAACTGTTGGCTCCCTCC 59.890 55.000 19.55 0.00 0.00 4.30
255 256 2.206576 ATTCAACTGTTGGCTCCCTC 57.793 50.000 19.55 0.00 0.00 4.30
256 257 2.683211 AATTCAACTGTTGGCTCCCT 57.317 45.000 19.55 0.00 0.00 4.20
257 258 3.191371 CAGTAATTCAACTGTTGGCTCCC 59.809 47.826 19.55 6.52 41.63 4.30
506 529 6.822676 ACAGAATGATGCAGAAAAACCAAAAA 59.177 30.769 0.00 0.00 39.69 1.94
507 530 6.347696 ACAGAATGATGCAGAAAAACCAAAA 58.652 32.000 0.00 0.00 39.69 2.44
511 534 6.849588 AAAACAGAATGATGCAGAAAAACC 57.150 33.333 0.00 0.00 39.69 3.27
606 630 2.024918 CTGTTGAGCAGCAAACGGT 58.975 52.632 10.36 0.00 38.44 4.83
653 677 3.431415 AGAAGGCCTAATTTCCAACCAC 58.569 45.455 5.16 0.00 0.00 4.16
667 691 4.319549 CGAGTGTGAAACTAAAAGAAGGCC 60.320 45.833 0.00 0.00 40.07 5.19
742 772 0.809385 CAGTGAGGAAATGCAGCCAG 59.191 55.000 5.91 0.00 0.00 4.85
821 858 5.049828 TGGTATGAAGTTGACATATGAGCG 58.950 41.667 10.38 0.00 33.70 5.03
838 875 9.624697 ATTGCGCATAATATTTAACTTGGTATG 57.375 29.630 12.75 0.00 0.00 2.39
857 897 6.216569 TGTAAATTAAAGGACAAATTGCGCA 58.783 32.000 5.66 5.66 0.00 6.09
957 1010 4.080469 AGTCAGCACTCAGGATCAAATGAT 60.080 41.667 0.00 0.00 37.51 2.45
993 1046 2.097629 CAGCAAGCCAGACATTGATGAG 59.902 50.000 0.00 0.00 43.65 2.90
1194 1322 4.397417 CCAGATTGACCAGAAAAGGATGTC 59.603 45.833 0.00 0.00 0.00 3.06
1354 1486 6.579666 TTGGAAGACTGAAATTTCCATGAG 57.420 37.500 15.48 8.49 46.96 2.90
1456 1589 4.665451 TGAAGCAAATCTCCCAGAAATGA 58.335 39.130 0.00 0.00 0.00 2.57
1622 1763 3.848272 AACCACGGCAAGAATATGTTG 57.152 42.857 0.00 0.00 0.00 3.33
1816 1961 4.286297 ACAGAATTTCGATTCCCACTGA 57.714 40.909 0.00 0.00 0.00 3.41
2098 2243 9.285770 GCTAAAACATAAAGCTTAGCGTAAATT 57.714 29.630 0.00 0.00 37.56 1.82
2213 2364 2.637165 AGAAAGTCAAGGGGTGAGGAT 58.363 47.619 0.00 0.00 36.74 3.24
2245 2402 6.449635 TGACCAGTTATTTCATATGCCAAC 57.550 37.500 0.00 0.00 0.00 3.77
2247 2404 4.580167 GCTGACCAGTTATTTCATATGCCA 59.420 41.667 0.00 0.00 0.00 4.92
2262 2419 7.389232 TGAAACCTATATCATATGCTGACCAG 58.611 38.462 0.00 0.00 36.48 4.00
2400 2572 6.678568 ATGCCTATTGCTCTAGATAGTGTT 57.321 37.500 0.00 0.00 42.00 3.32
2410 2582 5.264395 AGGTAACAAAATGCCTATTGCTCT 58.736 37.500 0.00 0.00 39.58 4.09
2412 2584 5.126061 CAGAGGTAACAAAATGCCTATTGCT 59.874 40.000 0.00 0.00 35.34 3.91
2484 2677 2.223711 ACAGGAATTCCAACAACGTTGC 60.224 45.455 27.61 8.84 38.89 4.17
2670 3004 9.899226 TCATGAGACTATCACGATTGTATAAAG 57.101 33.333 0.00 0.00 41.91 1.85
2852 3196 3.706086 GGTTGCATTTGGTTCTGGGATAT 59.294 43.478 0.00 0.00 0.00 1.63
2950 3294 0.323629 GTCGACCAGTCAATTGGGGA 59.676 55.000 3.51 0.00 42.76 4.81
3032 3376 5.957774 CCAAGAATCCTCCAAAAATAGGGAA 59.042 40.000 0.00 0.00 33.40 3.97
3078 3422 1.272769 ACTCCTTGCTTCCGTAGTGAC 59.727 52.381 0.00 0.00 0.00 3.67
3331 3675 3.617284 TCAATCAGTACAGAGTAGCGGA 58.383 45.455 0.00 0.00 0.00 5.54
3452 3799 2.494073 GACTTGAGGAGAAGATCACCGT 59.506 50.000 0.00 0.00 32.07 4.83
3476 3823 7.337480 TGTATAGAACGGTAGTAAGCATTCA 57.663 36.000 0.00 0.00 0.00 2.57
3499 3846 7.651808 AGAGAACACAAAAATACCTGTCAATG 58.348 34.615 0.00 0.00 0.00 2.82
3543 3891 6.035758 CGCAATACCTTTTAGTTAGGTCAGTC 59.964 42.308 0.00 0.00 44.74 3.51
3575 3923 4.980590 TGGTGTGCTATAAATTTCGCTTG 58.019 39.130 0.00 0.00 0.00 4.01
3644 3996 0.393537 CCACTGGCCCTCTCATGAAC 60.394 60.000 0.00 0.00 0.00 3.18
3774 4129 4.876107 ACCTCTGCACCAAAATATAAGACG 59.124 41.667 0.00 0.00 0.00 4.18
3953 4310 6.349777 CCCTTTTATCTAAATGTCGTTTGGCA 60.350 38.462 0.00 0.00 0.00 4.92
4692 5199 6.183360 GCACAAAAGTTGACCAAACAAATGAT 60.183 34.615 0.00 0.00 41.61 2.45
4788 5296 7.684913 AGCATTAAAGCATAAGCATATTGCACA 60.685 33.333 17.19 0.00 45.49 4.57
4795 5303 8.634335 TTATGGAGCATTAAAGCATAAGCATA 57.366 30.769 5.36 0.00 45.49 3.14
5036 5595 4.589216 ATTGTTGTGCTTGCATTACAGT 57.411 36.364 0.00 1.10 0.00 3.55
5394 6008 9.668497 AGTTTAGTGGTCTTAGTCCAATATTTC 57.332 33.333 6.52 2.06 35.85 2.17
5593 6210 1.431243 ACCCCCAGCAATCCTAACAAA 59.569 47.619 0.00 0.00 0.00 2.83
5801 6418 4.080356 ACAGATATTGGCAGCTACCTGAAA 60.080 41.667 4.19 0.00 41.77 2.69
5803 6420 3.041211 ACAGATATTGGCAGCTACCTGA 58.959 45.455 4.19 0.00 41.77 3.86
6280 6923 6.394809 TCTCTAGTGTTATGCGTTTGATCAA 58.605 36.000 3.38 3.38 0.00 2.57
6327 6970 1.774254 CAATGGGCCTGGTCCACTATA 59.226 52.381 24.79 0.00 41.42 1.31
6374 7020 9.533831 AAGATGAATAAATCCACAAGGTTACTT 57.466 29.630 0.00 0.00 37.43 2.24
6458 7107 2.665165 TGGAAACATCCACACAGCTTT 58.335 42.857 0.00 0.00 34.33 3.51
6549 7234 5.976534 TGCTAAACATAACTTGTGCAACTTG 59.023 36.000 0.00 0.00 38.99 3.16
7025 7773 1.700739 TCACCTACCAATTTGGGACGT 59.299 47.619 19.39 8.32 43.37 4.34
7258 8015 6.072893 ACCAACGACAATATAAGTGTTTCACC 60.073 38.462 0.00 0.00 34.49 4.02
7309 8066 6.053005 CCTTCCGAATAGTTGCCAATAAGTA 58.947 40.000 0.00 0.00 0.00 2.24
7310 8067 4.881850 CCTTCCGAATAGTTGCCAATAAGT 59.118 41.667 0.00 0.00 0.00 2.24
7311 8068 5.123227 TCCTTCCGAATAGTTGCCAATAAG 58.877 41.667 0.00 0.00 0.00 1.73
7312 8069 5.105567 TCCTTCCGAATAGTTGCCAATAA 57.894 39.130 0.00 0.00 0.00 1.40
7313 8070 4.764050 TCCTTCCGAATAGTTGCCAATA 57.236 40.909 0.00 0.00 0.00 1.90
7314 8071 3.644966 TCCTTCCGAATAGTTGCCAAT 57.355 42.857 0.00 0.00 0.00 3.16
7316 8073 3.644966 ATTCCTTCCGAATAGTTGCCA 57.355 42.857 0.00 0.00 39.53 4.92
7327 8094 5.391950 CCACACAGAACATTTATTCCTTCCG 60.392 44.000 0.00 0.00 0.00 4.30
7464 8235 1.119574 ACAGCAGTTACTCGGTGGGT 61.120 55.000 14.64 0.00 34.96 4.51
7665 8690 1.918293 ACCTGCATTCGAGACCCCA 60.918 57.895 0.00 0.00 0.00 4.96
7781 8809 1.880027 CGAGGTTTCCCACTTTTCAGG 59.120 52.381 0.00 0.00 0.00 3.86
7946 8983 6.566197 ACAAGAAGTCAACTCATTCAATCC 57.434 37.500 0.00 0.00 0.00 3.01
7965 9002 6.742718 CGGCTACAATTTTGTCTCAATACAAG 59.257 38.462 0.00 0.00 42.35 3.16
7997 9039 1.402968 CAGTCGAATTGCATCCCAAGG 59.597 52.381 0.00 0.00 36.76 3.61
8089 9132 1.892819 TTCTCCTCCTTCAGCAGCCG 61.893 60.000 0.00 0.00 0.00 5.52
8164 9212 5.634020 CGTATAATGTACCAAGAAGCTAGGC 59.366 44.000 0.00 0.00 0.00 3.93
8183 9231 1.064240 TGCAGACAGACTCCCCGTATA 60.064 52.381 0.00 0.00 0.00 1.47
8202 9250 3.996150 ACTGTTTGTCAAGGAGCATTG 57.004 42.857 0.00 0.00 0.00 2.82
8241 9289 0.388134 CAGATTTGCACACAGGCAGC 60.388 55.000 0.00 0.00 45.88 5.25
8256 9304 6.515200 GCAAGAGAGAAAATATGCATGCAGAT 60.515 38.462 26.69 24.21 34.10 2.90
8269 9317 6.126863 TCTATCCAAAGGCAAGAGAGAAAA 57.873 37.500 0.00 0.00 0.00 2.29
8270 9318 5.762179 TCTATCCAAAGGCAAGAGAGAAA 57.238 39.130 0.00 0.00 0.00 2.52
8330 9378 9.497030 GATAAACCAATTTGTTTGTTTTGTTCC 57.503 29.630 15.85 0.00 38.79 3.62
8348 9396 3.056107 CCACTGTCGGAGAAGATAAACCA 60.056 47.826 0.00 0.00 39.69 3.67
8374 9422 2.914059 ACAGCCAACGAGTAACAAGTT 58.086 42.857 0.00 0.00 0.00 2.66
8376 9424 2.412089 GCTACAGCCAACGAGTAACAAG 59.588 50.000 0.00 0.00 34.31 3.16
8397 9445 5.396362 CGCCGATAAAATGTAAGCAGAATTG 59.604 40.000 0.00 0.00 0.00 2.32
8465 9513 4.385754 CCCCTGGCTAGAAAATAGCTTCTT 60.386 45.833 0.00 0.00 40.25 2.52
8467 9515 3.481453 CCCCTGGCTAGAAAATAGCTTC 58.519 50.000 0.00 0.00 40.25 3.86
8497 9545 2.629137 TCAACCCTGCTGACTAAACGTA 59.371 45.455 0.00 0.00 0.00 3.57
8524 9572 4.552166 ACGGCAAATGCACTATATCAAC 57.448 40.909 7.80 0.00 44.36 3.18
8564 9612 5.120830 CCGTGACTTTTCTGTGAAATAGGAG 59.879 44.000 0.00 0.00 0.00 3.69
8569 9617 3.815809 TCCCGTGACTTTTCTGTGAAAT 58.184 40.909 0.00 0.00 0.00 2.17
8577 9625 0.326927 TCCCCATCCCGTGACTTTTC 59.673 55.000 0.00 0.00 0.00 2.29
8587 9635 3.958860 CTCCGCCATCCCCATCCC 61.959 72.222 0.00 0.00 0.00 3.85
8603 9667 3.953775 CTCGGCCAACCACCACCT 61.954 66.667 2.24 0.00 34.57 4.00
8617 9681 2.819595 CAACCGGCATCACCCTCG 60.820 66.667 0.00 0.00 33.26 4.63
8635 9699 4.115199 CCCTTCTTCCCAGCCCCG 62.115 72.222 0.00 0.00 0.00 5.73
8680 9744 1.143305 GATCTCAATCCCATGCGTCG 58.857 55.000 0.00 0.00 0.00 5.12
8713 9777 3.850173 TCCCTATGTAAAGTTCCAGGCTT 59.150 43.478 0.00 0.00 0.00 4.35
8714 9778 3.460825 TCCCTATGTAAAGTTCCAGGCT 58.539 45.455 0.00 0.00 0.00 4.58
8715 9779 3.926058 TCCCTATGTAAAGTTCCAGGC 57.074 47.619 0.00 0.00 0.00 4.85
8716 9780 4.941873 GTGTTCCCTATGTAAAGTTCCAGG 59.058 45.833 0.00 0.00 0.00 4.45
8717 9781 5.805728 AGTGTTCCCTATGTAAAGTTCCAG 58.194 41.667 0.00 0.00 0.00 3.86
8718 9782 5.280317 GGAGTGTTCCCTATGTAAAGTTCCA 60.280 44.000 0.00 0.00 37.53 3.53
8719 9783 5.183969 GGAGTGTTCCCTATGTAAAGTTCC 58.816 45.833 0.00 0.00 37.53 3.62
8720 9784 4.868734 CGGAGTGTTCCCTATGTAAAGTTC 59.131 45.833 0.00 0.00 40.67 3.01
8761 9825 1.399855 CGGACAGAGTATATGCGTCGG 60.400 57.143 0.00 0.00 0.00 4.79
8823 9887 3.140814 GATTGCGGGGAGGTTGCC 61.141 66.667 0.00 0.00 0.00 4.52
8824 9888 3.140814 GGATTGCGGGGAGGTTGC 61.141 66.667 0.00 0.00 0.00 4.17
8837 9901 1.832912 GGCGAGATCTGGGTGGATT 59.167 57.895 0.00 0.00 0.00 3.01
8838 9902 2.502492 CGGCGAGATCTGGGTGGAT 61.502 63.158 0.00 0.00 0.00 3.41
8867 9931 2.819595 CGGTGGATGAGCAACGGG 60.820 66.667 0.00 0.00 0.00 5.28
8884 9948 0.321653 AGATGACGTGGTTCCCTTGC 60.322 55.000 0.00 0.00 0.00 4.01
8886 9950 0.321653 GCAGATGACGTGGTTCCCTT 60.322 55.000 0.00 0.00 0.00 3.95
8981 10055 2.193248 GGCAGGGTGGATGTAGGC 59.807 66.667 0.00 0.00 0.00 3.93
8985 10059 3.341629 CCAGGGCAGGGTGGATGT 61.342 66.667 0.00 0.00 35.67 3.06
8986 10060 4.133373 CCCAGGGCAGGGTGGATG 62.133 72.222 6.12 0.00 44.24 3.51
9015 10089 2.825836 CGATGCAGGGAGTTGGGC 60.826 66.667 0.00 0.00 0.00 5.36
9052 10126 1.011968 CATTTCGTCGAACAGCCCGA 61.012 55.000 7.29 0.00 0.00 5.14
9053 10127 1.419922 CATTTCGTCGAACAGCCCG 59.580 57.895 7.29 0.00 0.00 6.13
9054 10128 1.134694 GCATTTCGTCGAACAGCCC 59.865 57.895 7.29 0.00 0.00 5.19
9055 10129 1.134694 GGCATTTCGTCGAACAGCC 59.865 57.895 25.31 25.31 35.59 4.85
9056 10130 0.095417 GAGGCATTTCGTCGAACAGC 59.905 55.000 17.89 17.89 0.00 4.40
9057 10131 1.656095 GAGAGGCATTTCGTCGAACAG 59.344 52.381 7.29 4.36 34.90 3.16
9058 10132 1.272490 AGAGAGGCATTTCGTCGAACA 59.728 47.619 7.29 0.00 34.90 3.18
9059 10133 1.656095 CAGAGAGGCATTTCGTCGAAC 59.344 52.381 7.29 0.00 34.90 3.95
9060 10134 1.544246 TCAGAGAGGCATTTCGTCGAA 59.456 47.619 2.90 2.90 34.90 3.71
9061 10135 1.133216 CTCAGAGAGGCATTTCGTCGA 59.867 52.381 0.00 0.00 34.90 4.20
9062 10136 1.133216 TCTCAGAGAGGCATTTCGTCG 59.867 52.381 0.00 0.00 34.90 5.12
9063 10137 2.535331 GTCTCAGAGAGGCATTTCGTC 58.465 52.381 0.00 0.00 34.02 4.20
9064 10138 1.135257 CGTCTCAGAGAGGCATTTCGT 60.135 52.381 7.19 0.00 33.34 3.85
9065 10139 1.135257 ACGTCTCAGAGAGGCATTTCG 60.135 52.381 18.31 10.68 33.34 3.46
9066 10140 2.663826 ACGTCTCAGAGAGGCATTTC 57.336 50.000 18.31 0.00 33.34 2.17
9067 10141 2.693069 CAACGTCTCAGAGAGGCATTT 58.307 47.619 18.31 4.65 33.34 2.32
9068 10142 1.674221 GCAACGTCTCAGAGAGGCATT 60.674 52.381 18.31 5.31 33.34 3.56
9069 10143 0.108424 GCAACGTCTCAGAGAGGCAT 60.108 55.000 18.31 6.62 33.34 4.40
9070 10144 1.290324 GCAACGTCTCAGAGAGGCA 59.710 57.895 18.31 0.00 33.34 4.75
9071 10145 1.803519 CGCAACGTCTCAGAGAGGC 60.804 63.158 18.31 10.66 33.69 4.70
9072 10146 0.039074 AACGCAACGTCTCAGAGAGG 60.039 55.000 17.04 17.04 39.99 3.69
9073 10147 1.332178 GAACGCAACGTCTCAGAGAG 58.668 55.000 0.00 0.00 39.99 3.20
9074 10148 0.039437 GGAACGCAACGTCTCAGAGA 60.039 55.000 0.00 0.00 39.99 3.10
9075 10149 2.435741 GGAACGCAACGTCTCAGAG 58.564 57.895 0.00 0.00 39.99 3.35
9076 10150 4.647654 GGAACGCAACGTCTCAGA 57.352 55.556 0.00 0.00 39.99 3.27


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

AutoCloner maintained by Alex Coulton.