Multiple sequence alignment - TraesCS3A01G240400

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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 TraesCS3A01G240400 chr3A 100.000 2489 0 0 1 2489 451665948 451663460 0.000000e+00 4597.0
1 TraesCS3A01G240400 chr3A 98.479 1972 30 0 518 2489 451657594 451659565 0.000000e+00 3476.0
2 TraesCS3A01G240400 chr3A 95.886 1969 55 1 521 2489 259837722 259839664 0.000000e+00 3164.0
3 TraesCS3A01G240400 chr3A 98.514 471 7 0 51 521 451661277 451661747 0.000000e+00 832.0
4 TraesCS3A01G240400 chr3A 96.414 474 15 1 48 521 259841857 259841386 0.000000e+00 780.0
5 TraesCS3A01G240400 chr3A 82.594 293 44 5 2136 2426 631283728 631283441 4.110000e-63 252.0
6 TraesCS3A01G240400 chr3A 97.561 82 2 0 2044 2125 259839327 259839408 9.280000e-30 141.0
7 TraesCS3A01G240400 chr3B 98.276 1972 31 2 521 2489 703847543 703849514 0.000000e+00 3450.0
8 TraesCS3A01G240400 chr3B 98.945 474 3 2 49 521 703851705 703851233 0.000000e+00 846.0
9 TraesCS3A01G240400 chr3B 82.143 700 85 18 1457 2125 650604231 650603541 4.650000e-157 564.0
10 TraesCS3A01G240400 chr3B 82.650 317 43 11 2126 2440 650603620 650603314 1.130000e-68 270.0
11 TraesCS3A01G240400 chr3B 87.234 188 23 1 521 708 17323451 17323265 1.940000e-51 213.0
12 TraesCS3A01G240400 chr3B 97.561 82 2 0 2044 2125 703849150 703849231 9.280000e-30 141.0
13 TraesCS3A01G240400 chr3B 92.308 39 1 2 39 77 536429966 536430002 1.000000e-03 54.7
14 TraesCS3A01G240400 chr4A 90.843 1649 99 19 521 2125 703410863 703412503 0.000000e+00 2161.0
15 TraesCS3A01G240400 chr4A 93.169 366 20 3 2126 2489 703412425 703412787 1.310000e-147 532.0
16 TraesCS3A01G240400 chr5A 97.546 1141 27 1 520 1660 525733056 525734195 0.000000e+00 1951.0
17 TraesCS3A01G240400 chr5A 98.331 839 14 0 1651 2489 525734619 525735457 0.000000e+00 1472.0
18 TraesCS3A01G240400 chr5A 98.520 473 3 1 49 521 525737643 525737175 0.000000e+00 832.0
19 TraesCS3A01G240400 chr2A 84.940 498 45 8 942 1412 156666924 156667418 6.230000e-131 477.0
20 TraesCS3A01G240400 chr2D 85.115 477 44 10 945 1394 145363893 145363417 1.740000e-126 462.0
21 TraesCS3A01G240400 chr2B 84.277 477 48 10 945 1394 202921393 202920917 8.170000e-120 440.0
22 TraesCS3A01G240400 chr2B 95.000 40 0 2 10 49 316748239 316748202 7.430000e-06 62.1
23 TraesCS3A01G240400 chr2B 94.737 38 0 2 12 49 51987138 51987173 9.620000e-05 58.4
24 TraesCS3A01G240400 chr1B 86.921 367 36 11 2126 2489 463545464 463545107 3.860000e-108 401.0
25 TraesCS3A01G240400 chr1B 87.500 216 20 5 1914 2125 463545597 463545385 2.470000e-60 243.0
26 TraesCS3A01G240400 chr1B 93.182 44 1 2 41 82 499214168 499214125 2.070000e-06 63.9
27 TraesCS3A01G240400 chr1B 100.000 31 0 0 19 49 26717925 26717895 9.620000e-05 58.4
28 TraesCS3A01G240400 chr3D 80.782 307 48 7 2126 2426 487395370 487395069 1.930000e-56 230.0
29 TraesCS3A01G240400 chr4B 87.629 194 19 5 519 709 617432631 617432822 1.160000e-53 220.0
30 TraesCS3A01G240400 chr4B 100.000 31 0 0 19 49 489159058 489159088 9.620000e-05 58.4
31 TraesCS3A01G240400 chr6B 81.226 261 43 4 521 780 216416157 216416412 3.240000e-49 206.0
32 TraesCS3A01G240400 chr6B 100.000 31 0 0 19 49 481854120 481854150 9.620000e-05 58.4
33 TraesCS3A01G240400 chr1A 86.082 194 21 6 519 709 456936836 456936646 1.170000e-48 204.0
34 TraesCS3A01G240400 chr1A 97.059 34 1 0 16 49 60575833 60575800 9.620000e-05 58.4
35 TraesCS3A01G240400 chr1A 100.000 29 0 0 19 47 31945137 31945109 1.000000e-03 54.7
36 TraesCS3A01G240400 chr7B 81.452 124 20 3 663 786 63381522 63381642 5.670000e-17 99.0
37 TraesCS3A01G240400 chr6A 97.143 35 1 0 48 82 605673854 605673888 2.670000e-05 60.2
38 TraesCS3A01G240400 chr6A 97.143 35 1 0 48 82 605779873 605779907 2.670000e-05 60.2
39 TraesCS3A01G240400 chr6A 100.000 29 0 0 21 49 590675884 590675856 1.000000e-03 54.7
40 TraesCS3A01G240400 chrUn 94.737 38 0 2 12 49 221035906 221035941 9.620000e-05 58.4
41 TraesCS3A01G240400 chr5B 97.059 34 1 0 49 82 13825998 13825965 9.620000e-05 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 TraesCS3A01G240400 chr3A 451663460 451665948 2488 True 4597.0 4597 100.0000 1 2489 1 chr3A.!!$R2 2488
1 TraesCS3A01G240400 chr3A 451657594 451661747 4153 False 2154.0 3476 98.4965 51 2489 2 chr3A.!!$F2 2438
2 TraesCS3A01G240400 chr3A 259837722 259839664 1942 False 1652.5 3164 96.7235 521 2489 2 chr3A.!!$F1 1968
3 TraesCS3A01G240400 chr3B 703847543 703849514 1971 False 1795.5 3450 97.9185 521 2489 2 chr3B.!!$F2 1968
4 TraesCS3A01G240400 chr3B 650603314 650604231 917 True 417.0 564 82.3965 1457 2440 2 chr3B.!!$R3 983
5 TraesCS3A01G240400 chr4A 703410863 703412787 1924 False 1346.5 2161 92.0060 521 2489 2 chr4A.!!$F1 1968
6 TraesCS3A01G240400 chr5A 525733056 525735457 2401 False 1711.5 1951 97.9385 520 2489 2 chr5A.!!$F1 1969

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
511 512 0.108138 CACCGCCTTCTACCTCCTTG 60.108 60.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1578 1.278985 CCATCAGCACCAGGTACAAGA 59.721 52.381 0.0 0.0 0.0 3.02 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 9.813826 ACCTCTTTACCTACTAACTAGTAAACA 57.186 33.333 0.00 0.00 38.24 2.83
62 63 9.865321 CTTTACCTACTAACTAGTAAACATGCA 57.135 33.333 0.00 0.00 38.24 3.96
63 64 9.643693 TTTACCTACTAACTAGTAAACATGCAC 57.356 33.333 0.00 0.00 38.24 4.57
64 65 6.327934 ACCTACTAACTAGTAAACATGCACG 58.672 40.000 0.00 0.00 38.24 5.34
65 66 6.071728 ACCTACTAACTAGTAAACATGCACGT 60.072 38.462 0.00 0.00 38.24 4.49
66 67 6.252869 CCTACTAACTAGTAAACATGCACGTG 59.747 42.308 12.28 12.28 38.24 4.49
67 68 3.806316 AACTAGTAAACATGCACGTGC 57.194 42.857 33.11 33.11 42.50 5.34
68 69 6.023182 ACTAACTAGTAAACATGCACGTGCA 61.023 40.000 41.97 41.97 44.72 4.57
69 70 7.451416 ACTAACTAGTAAACATGCACGTGCAA 61.451 38.462 43.14 26.22 44.19 4.08
70 71 9.355103 ACTAACTAGTAAACATGCACGTGCAAC 62.355 40.741 43.14 34.23 44.19 4.17
83 84 2.643044 TGCAACGCACGTTTCAAAC 58.357 47.368 5.55 0.00 36.00 2.93
84 85 0.169230 TGCAACGCACGTTTCAAACT 59.831 45.000 5.55 0.00 36.00 2.66
85 86 1.264672 GCAACGCACGTTTCAAACTT 58.735 45.000 5.55 0.00 36.00 2.66
86 87 2.159558 TGCAACGCACGTTTCAAACTTA 60.160 40.909 5.55 0.00 36.00 2.24
87 88 2.847133 GCAACGCACGTTTCAAACTTAA 59.153 40.909 5.55 0.00 36.00 1.85
88 89 3.301116 GCAACGCACGTTTCAAACTTAAA 59.699 39.130 5.55 0.00 36.00 1.52
89 90 4.773559 GCAACGCACGTTTCAAACTTAAAC 60.774 41.667 5.55 0.00 36.00 2.01
90 91 4.345271 ACGCACGTTTCAAACTTAAACT 57.655 36.364 0.00 0.00 35.20 2.66
91 92 5.467902 ACGCACGTTTCAAACTTAAACTA 57.532 34.783 0.00 0.00 35.20 2.24
92 93 5.867166 ACGCACGTTTCAAACTTAAACTAA 58.133 33.333 0.00 0.00 35.20 2.24
93 94 5.961263 ACGCACGTTTCAAACTTAAACTAAG 59.039 36.000 0.00 0.00 41.51 2.18
94 95 7.834934 AACGCACGTTTCAAACTTAAACTAAGT 60.835 33.333 1.93 0.00 42.05 2.24
163 164 6.641169 TGGTCAAATAAATACAGTGTTGCA 57.359 33.333 0.00 0.00 0.00 4.08
164 165 7.043961 TGGTCAAATAAATACAGTGTTGCAA 57.956 32.000 0.00 0.00 0.00 4.08
165 166 7.665690 TGGTCAAATAAATACAGTGTTGCAAT 58.334 30.769 0.59 0.00 0.00 3.56
166 167 7.812191 TGGTCAAATAAATACAGTGTTGCAATC 59.188 33.333 0.59 0.00 0.00 2.67
167 168 7.812191 GGTCAAATAAATACAGTGTTGCAATCA 59.188 33.333 0.59 0.00 0.00 2.57
168 169 9.357652 GTCAAATAAATACAGTGTTGCAATCAT 57.642 29.630 0.59 0.00 0.00 2.45
169 170 9.926158 TCAAATAAATACAGTGTTGCAATCATT 57.074 25.926 0.59 0.00 0.00 2.57
170 171 9.961266 CAAATAAATACAGTGTTGCAATCATTG 57.039 29.630 16.91 16.91 0.00 2.82
171 172 9.709495 AAATAAATACAGTGTTGCAATCATTGT 57.291 25.926 23.06 23.06 38.76 2.71
172 173 8.692110 ATAAATACAGTGTTGCAATCATTGTG 57.308 30.769 25.59 16.45 36.65 3.33
173 174 3.374220 ACAGTGTTGCAATCATTGTGG 57.626 42.857 20.73 4.27 35.17 4.17
174 175 2.957680 ACAGTGTTGCAATCATTGTGGA 59.042 40.909 20.73 0.00 35.17 4.02
175 176 3.575256 ACAGTGTTGCAATCATTGTGGAT 59.425 39.130 20.73 5.19 35.17 3.41
176 177 4.039488 ACAGTGTTGCAATCATTGTGGATT 59.961 37.500 20.73 4.93 37.99 3.01
177 178 4.992319 CAGTGTTGCAATCATTGTGGATTT 59.008 37.500 0.59 0.00 35.37 2.17
178 179 6.157904 CAGTGTTGCAATCATTGTGGATTTA 58.842 36.000 0.59 0.00 35.37 1.40
179 180 6.814644 CAGTGTTGCAATCATTGTGGATTTAT 59.185 34.615 0.59 0.00 35.37 1.40
180 181 6.814644 AGTGTTGCAATCATTGTGGATTTATG 59.185 34.615 0.59 0.00 35.37 1.90
181 182 6.036300 GTGTTGCAATCATTGTGGATTTATGG 59.964 38.462 0.59 0.00 35.37 2.74
182 183 5.936187 TGCAATCATTGTGGATTTATGGT 57.064 34.783 0.00 0.00 35.37 3.55
183 184 5.904941 TGCAATCATTGTGGATTTATGGTC 58.095 37.500 0.00 0.00 35.37 4.02
184 185 4.977963 GCAATCATTGTGGATTTATGGTCG 59.022 41.667 0.00 0.00 35.37 4.79
185 186 4.836125 ATCATTGTGGATTTATGGTCGC 57.164 40.909 0.00 0.00 0.00 5.19
186 187 2.611751 TCATTGTGGATTTATGGTCGCG 59.388 45.455 0.00 0.00 0.00 5.87
187 188 2.102070 TTGTGGATTTATGGTCGCGT 57.898 45.000 5.77 0.00 0.00 6.01
188 189 2.102070 TGTGGATTTATGGTCGCGTT 57.898 45.000 5.77 0.00 0.00 4.84
189 190 1.735018 TGTGGATTTATGGTCGCGTTG 59.265 47.619 5.77 0.00 0.00 4.10
190 191 0.730265 TGGATTTATGGTCGCGTTGC 59.270 50.000 5.77 0.00 0.00 4.17
191 192 1.014352 GGATTTATGGTCGCGTTGCT 58.986 50.000 5.77 0.00 0.00 3.91
192 193 1.268032 GGATTTATGGTCGCGTTGCTG 60.268 52.381 5.77 0.00 0.00 4.41
193 194 0.732571 ATTTATGGTCGCGTTGCTGG 59.267 50.000 5.77 0.00 0.00 4.85
194 195 0.320858 TTTATGGTCGCGTTGCTGGA 60.321 50.000 5.77 0.00 0.00 3.86
195 196 1.017177 TTATGGTCGCGTTGCTGGAC 61.017 55.000 5.77 0.00 0.00 4.02
196 197 2.161078 TATGGTCGCGTTGCTGGACA 62.161 55.000 5.77 0.00 32.39 4.02
197 198 2.970324 GGTCGCGTTGCTGGACAA 60.970 61.111 5.77 0.00 35.33 3.18
198 199 2.325082 GGTCGCGTTGCTGGACAAT 61.325 57.895 5.77 0.00 41.27 2.71
199 200 1.017177 GGTCGCGTTGCTGGACAATA 61.017 55.000 5.77 0.00 41.27 1.90
200 201 0.793861 GTCGCGTTGCTGGACAATAA 59.206 50.000 5.77 0.00 41.27 1.40
201 202 0.793861 TCGCGTTGCTGGACAATAAC 59.206 50.000 5.77 0.00 41.27 1.89
202 203 0.518355 CGCGTTGCTGGACAATAACG 60.518 55.000 0.00 13.14 46.07 3.18
203 204 0.793861 GCGTTGCTGGACAATAACGA 59.206 50.000 18.60 0.00 46.18 3.85
204 205 1.195900 GCGTTGCTGGACAATAACGAA 59.804 47.619 18.60 0.00 46.18 3.85
205 206 2.159572 GCGTTGCTGGACAATAACGAAT 60.160 45.455 18.60 0.00 46.18 3.34
206 207 3.416277 CGTTGCTGGACAATAACGAATG 58.584 45.455 12.49 0.00 46.18 2.67
207 208 3.120338 CGTTGCTGGACAATAACGAATGT 60.120 43.478 12.49 0.00 46.18 2.71
208 209 4.612712 CGTTGCTGGACAATAACGAATGTT 60.613 41.667 12.49 0.00 46.18 2.71
209 210 4.418013 TGCTGGACAATAACGAATGTTG 57.582 40.909 0.00 0.00 39.12 3.33
210 211 3.818210 TGCTGGACAATAACGAATGTTGT 59.182 39.130 7.54 7.54 44.90 3.32
211 212 4.277174 TGCTGGACAATAACGAATGTTGTT 59.723 37.500 8.78 0.00 42.63 2.83
212 213 5.219633 GCTGGACAATAACGAATGTTGTTT 58.780 37.500 8.78 0.00 42.63 2.83
213 214 5.342259 GCTGGACAATAACGAATGTTGTTTC 59.658 40.000 8.78 6.38 42.63 2.78
214 215 6.378710 TGGACAATAACGAATGTTGTTTCA 57.621 33.333 8.78 8.14 42.63 2.69
215 216 6.202937 TGGACAATAACGAATGTTGTTTCAC 58.797 36.000 8.78 3.38 42.63 3.18
216 217 6.183360 TGGACAATAACGAATGTTGTTTCACA 60.183 34.615 8.78 5.17 42.63 3.58
217 218 6.141685 GGACAATAACGAATGTTGTTTCACAC 59.858 38.462 8.78 0.00 42.63 3.82
218 219 6.556212 ACAATAACGAATGTTGTTTCACACA 58.444 32.000 0.00 0.00 40.03 3.72
219 220 7.199766 ACAATAACGAATGTTGTTTCACACAT 58.800 30.769 0.00 0.00 40.03 3.21
220 221 7.704472 ACAATAACGAATGTTGTTTCACACATT 59.296 29.630 0.00 0.00 40.03 2.71
221 222 7.851822 ATAACGAATGTTGTTTCACACATTC 57.148 32.000 12.90 12.90 39.87 2.67
224 225 4.606961 GAATGTTGTTTCACACATTCGGT 58.393 39.130 8.78 0.00 37.14 4.69
238 239 6.106877 CACATTCGGTGTTCTTATAGGTTG 57.893 41.667 0.00 0.00 42.75 3.77
239 240 5.642063 CACATTCGGTGTTCTTATAGGTTGT 59.358 40.000 0.00 0.00 42.75 3.32
240 241 6.814644 CACATTCGGTGTTCTTATAGGTTGTA 59.185 38.462 0.00 0.00 42.75 2.41
241 242 7.332430 CACATTCGGTGTTCTTATAGGTTGTAA 59.668 37.037 0.00 0.00 42.75 2.41
242 243 7.548075 ACATTCGGTGTTCTTATAGGTTGTAAG 59.452 37.037 0.00 0.00 38.01 2.34
243 244 6.839124 TCGGTGTTCTTATAGGTTGTAAGA 57.161 37.500 0.00 0.00 36.63 2.10
244 245 7.414222 TCGGTGTTCTTATAGGTTGTAAGAT 57.586 36.000 0.00 0.00 37.83 2.40
245 246 8.523915 TCGGTGTTCTTATAGGTTGTAAGATA 57.476 34.615 0.00 0.00 37.83 1.98
246 247 8.970020 TCGGTGTTCTTATAGGTTGTAAGATAA 58.030 33.333 0.00 0.00 37.83 1.75
247 248 9.760077 CGGTGTTCTTATAGGTTGTAAGATAAT 57.240 33.333 0.00 0.00 37.83 1.28
273 274 7.630242 TCAAATCTACCAATCCTTTCATCAC 57.370 36.000 0.00 0.00 0.00 3.06
274 275 7.174413 TCAAATCTACCAATCCTTTCATCACA 58.826 34.615 0.00 0.00 0.00 3.58
275 276 7.669304 TCAAATCTACCAATCCTTTCATCACAA 59.331 33.333 0.00 0.00 0.00 3.33
276 277 8.306038 CAAATCTACCAATCCTTTCATCACAAA 58.694 33.333 0.00 0.00 0.00 2.83
277 278 8.421249 AATCTACCAATCCTTTCATCACAAAA 57.579 30.769 0.00 0.00 0.00 2.44
278 279 8.599624 ATCTACCAATCCTTTCATCACAAAAT 57.400 30.769 0.00 0.00 0.00 1.82
279 280 8.055279 TCTACCAATCCTTTCATCACAAAATC 57.945 34.615 0.00 0.00 0.00 2.17
280 281 6.923199 ACCAATCCTTTCATCACAAAATCT 57.077 33.333 0.00 0.00 0.00 2.40
281 282 9.177608 CTACCAATCCTTTCATCACAAAATCTA 57.822 33.333 0.00 0.00 0.00 1.98
282 283 7.830739 ACCAATCCTTTCATCACAAAATCTAC 58.169 34.615 0.00 0.00 0.00 2.59
283 284 7.671398 ACCAATCCTTTCATCACAAAATCTACT 59.329 33.333 0.00 0.00 0.00 2.57
284 285 7.972277 CCAATCCTTTCATCACAAAATCTACTG 59.028 37.037 0.00 0.00 0.00 2.74
285 286 8.733458 CAATCCTTTCATCACAAAATCTACTGA 58.267 33.333 0.00 0.00 0.00 3.41
286 287 9.471702 AATCCTTTCATCACAAAATCTACTGAT 57.528 29.630 0.00 0.00 33.70 2.90
287 288 8.868522 TCCTTTCATCACAAAATCTACTGATT 57.131 30.769 0.00 0.00 44.08 2.57
297 298 4.606457 AATCTACTGATTTTGCAGACGC 57.394 40.909 0.00 0.00 39.68 5.19
298 299 4.002982 AATCTACTGATTTTGCAGACGCA 58.997 39.130 0.00 0.00 42.13 5.24
299 300 4.637534 AATCTACTGATTTTGCAGACGCAT 59.362 37.500 0.00 0.00 40.60 4.73
300 301 5.124457 AATCTACTGATTTTGCAGACGCATT 59.876 36.000 0.00 0.00 40.60 3.56
301 302 6.349611 AATCTACTGATTTTGCAGACGCATTT 60.350 34.615 0.00 0.00 40.60 2.32
302 303 7.788956 AATCTACTGATTTTGCAGACGCATTTT 60.789 33.333 0.00 0.00 40.60 1.82
309 310 3.011949 TGCAGACGCATTTTCCTTTTC 57.988 42.857 0.00 0.00 45.36 2.29
310 311 2.288152 TGCAGACGCATTTTCCTTTTCC 60.288 45.455 0.00 0.00 45.36 3.13
311 312 2.029918 GCAGACGCATTTTCCTTTTCCT 60.030 45.455 0.00 0.00 38.36 3.36
312 313 3.552890 GCAGACGCATTTTCCTTTTCCTT 60.553 43.478 0.00 0.00 38.36 3.36
313 314 4.229876 CAGACGCATTTTCCTTTTCCTTC 58.770 43.478 0.00 0.00 0.00 3.46
314 315 3.255888 AGACGCATTTTCCTTTTCCTTCC 59.744 43.478 0.00 0.00 0.00 3.46
315 316 2.962421 ACGCATTTTCCTTTTCCTTCCA 59.038 40.909 0.00 0.00 0.00 3.53
316 317 3.578282 ACGCATTTTCCTTTTCCTTCCAT 59.422 39.130 0.00 0.00 0.00 3.41
317 318 3.928375 CGCATTTTCCTTTTCCTTCCATG 59.072 43.478 0.00 0.00 0.00 3.66
318 319 4.256110 GCATTTTCCTTTTCCTTCCATGG 58.744 43.478 4.97 4.97 0.00 3.66
319 320 4.020307 GCATTTTCCTTTTCCTTCCATGGA 60.020 41.667 11.44 11.44 0.00 3.41
320 321 5.727434 CATTTTCCTTTTCCTTCCATGGAG 58.273 41.667 15.53 9.22 37.43 3.86
321 322 2.514458 TCCTTTTCCTTCCATGGAGC 57.486 50.000 15.53 0.00 37.43 4.70
322 323 1.005924 TCCTTTTCCTTCCATGGAGCC 59.994 52.381 15.53 0.00 37.43 4.70
323 324 1.478631 CTTTTCCTTCCATGGAGCCC 58.521 55.000 15.53 0.00 37.43 5.19
324 325 1.006400 CTTTTCCTTCCATGGAGCCCT 59.994 52.381 15.53 0.00 37.43 5.19
325 326 1.979809 TTTCCTTCCATGGAGCCCTA 58.020 50.000 15.53 0.00 37.43 3.53
326 327 1.511613 TTCCTTCCATGGAGCCCTAG 58.488 55.000 15.53 8.99 37.43 3.02
327 328 1.056700 TCCTTCCATGGAGCCCTAGC 61.057 60.000 15.53 0.00 40.32 3.42
328 329 1.348008 CCTTCCATGGAGCCCTAGCA 61.348 60.000 15.53 0.00 43.56 3.49
329 330 0.769873 CTTCCATGGAGCCCTAGCAT 59.230 55.000 15.53 0.00 43.56 3.79
330 331 1.144503 CTTCCATGGAGCCCTAGCATT 59.855 52.381 15.53 0.00 43.56 3.56
331 332 1.225373 TCCATGGAGCCCTAGCATTT 58.775 50.000 11.44 0.00 43.56 2.32
332 333 1.143684 TCCATGGAGCCCTAGCATTTC 59.856 52.381 11.44 0.00 43.56 2.17
333 334 1.133699 CCATGGAGCCCTAGCATTTCA 60.134 52.381 5.56 0.00 43.56 2.69
334 335 2.490351 CCATGGAGCCCTAGCATTTCAT 60.490 50.000 5.56 0.00 43.56 2.57
335 336 2.353357 TGGAGCCCTAGCATTTCATG 57.647 50.000 0.00 0.00 43.56 3.07
336 337 1.845791 TGGAGCCCTAGCATTTCATGA 59.154 47.619 0.00 0.00 43.56 3.07
337 338 2.444388 TGGAGCCCTAGCATTTCATGAT 59.556 45.455 0.00 0.00 43.56 2.45
338 339 3.117398 TGGAGCCCTAGCATTTCATGATT 60.117 43.478 0.00 0.00 43.56 2.57
339 340 3.255149 GGAGCCCTAGCATTTCATGATTG 59.745 47.826 0.00 0.00 43.56 2.67
340 341 4.139786 GAGCCCTAGCATTTCATGATTGA 58.860 43.478 9.68 0.00 43.56 2.57
341 342 4.539726 AGCCCTAGCATTTCATGATTGAA 58.460 39.130 9.68 0.00 43.56 2.69
342 343 5.145564 AGCCCTAGCATTTCATGATTGAAT 58.854 37.500 9.68 0.00 40.71 2.57
343 344 5.601313 AGCCCTAGCATTTCATGATTGAATT 59.399 36.000 9.68 0.00 40.71 2.17
344 345 5.694910 GCCCTAGCATTTCATGATTGAATTG 59.305 40.000 9.68 6.34 42.26 2.32
345 346 6.684613 GCCCTAGCATTTCATGATTGAATTGT 60.685 38.462 9.68 0.00 41.77 2.71
346 347 6.921857 CCCTAGCATTTCATGATTGAATTGTC 59.078 38.462 9.68 5.40 41.77 3.18
347 348 7.417003 CCCTAGCATTTCATGATTGAATTGTCA 60.417 37.037 9.68 0.00 41.77 3.58
348 349 7.648112 CCTAGCATTTCATGATTGAATTGTCAG 59.352 37.037 9.68 8.35 41.77 3.51
349 350 5.810587 AGCATTTCATGATTGAATTGTCAGC 59.189 36.000 9.68 1.48 41.77 4.26
350 351 5.810587 GCATTTCATGATTGAATTGTCAGCT 59.189 36.000 9.68 0.00 41.77 4.24
351 352 6.976349 GCATTTCATGATTGAATTGTCAGCTA 59.024 34.615 9.68 0.00 41.77 3.32
352 353 7.652105 GCATTTCATGATTGAATTGTCAGCTAT 59.348 33.333 9.68 0.00 41.77 2.97
385 386 2.687700 AGACATGACAGTCCATCAGC 57.312 50.000 0.00 0.00 39.34 4.26
386 387 2.186243 AGACATGACAGTCCATCAGCT 58.814 47.619 0.00 0.00 39.34 4.24
387 388 3.369175 AGACATGACAGTCCATCAGCTA 58.631 45.455 0.00 0.00 39.34 3.32
388 389 3.966006 AGACATGACAGTCCATCAGCTAT 59.034 43.478 0.00 0.00 39.34 2.97
389 390 4.056740 GACATGACAGTCCATCAGCTATG 58.943 47.826 0.00 0.00 35.15 2.23
390 391 3.453717 ACATGACAGTCCATCAGCTATGT 59.546 43.478 0.00 0.00 33.34 2.29
391 392 4.651045 ACATGACAGTCCATCAGCTATGTA 59.349 41.667 0.00 0.00 33.34 2.29
392 393 4.926140 TGACAGTCCATCAGCTATGTAG 57.074 45.455 0.00 0.00 33.34 2.74
393 394 4.536765 TGACAGTCCATCAGCTATGTAGA 58.463 43.478 0.00 0.00 33.34 2.59
394 395 4.956075 TGACAGTCCATCAGCTATGTAGAA 59.044 41.667 0.00 0.00 33.34 2.10
395 396 5.600069 TGACAGTCCATCAGCTATGTAGAAT 59.400 40.000 0.00 0.00 33.34 2.40
396 397 5.851720 ACAGTCCATCAGCTATGTAGAATG 58.148 41.667 0.00 0.00 31.91 2.67
397 398 5.221601 ACAGTCCATCAGCTATGTAGAATGG 60.222 44.000 0.00 8.86 30.68 3.16
398 399 3.999663 GTCCATCAGCTATGTAGAATGGC 59.000 47.826 0.00 0.00 33.29 4.40
399 400 3.008375 TCCATCAGCTATGTAGAATGGCC 59.992 47.826 0.00 0.00 33.29 5.36
400 401 3.008813 CCATCAGCTATGTAGAATGGCCT 59.991 47.826 3.32 0.00 33.34 5.19
401 402 4.252073 CATCAGCTATGTAGAATGGCCTC 58.748 47.826 3.32 0.00 0.00 4.70
402 403 2.634940 TCAGCTATGTAGAATGGCCTCC 59.365 50.000 3.32 0.00 0.00 4.30
403 404 1.620819 AGCTATGTAGAATGGCCTCCG 59.379 52.381 3.32 0.00 0.00 4.63
404 405 1.344763 GCTATGTAGAATGGCCTCCGT 59.655 52.381 3.32 0.00 0.00 4.69
405 406 2.868044 GCTATGTAGAATGGCCTCCGTG 60.868 54.545 3.32 0.00 0.00 4.94
406 407 1.496060 ATGTAGAATGGCCTCCGTGA 58.504 50.000 3.32 0.00 0.00 4.35
407 408 0.824109 TGTAGAATGGCCTCCGTGAG 59.176 55.000 3.32 0.00 0.00 3.51
408 409 0.530870 GTAGAATGGCCTCCGTGAGC 60.531 60.000 3.32 0.00 0.00 4.26
409 410 0.975556 TAGAATGGCCTCCGTGAGCA 60.976 55.000 3.32 0.00 0.00 4.26
410 411 1.153086 GAATGGCCTCCGTGAGCAT 60.153 57.895 3.32 0.00 0.00 3.79
411 412 1.153086 AATGGCCTCCGTGAGCATC 60.153 57.895 3.32 0.00 0.00 3.91
427 428 5.179045 GAGCATCACTCATACCCAAATTG 57.821 43.478 0.00 0.00 45.49 2.32
428 429 3.956199 AGCATCACTCATACCCAAATTGG 59.044 43.478 4.74 4.74 37.25 3.16
429 430 3.491447 GCATCACTCATACCCAAATTGGC 60.491 47.826 6.48 0.00 35.79 4.52
430 431 3.737559 TCACTCATACCCAAATTGGCT 57.262 42.857 6.48 0.00 35.79 4.75
431 432 3.355378 TCACTCATACCCAAATTGGCTG 58.645 45.455 6.48 3.98 35.79 4.85
432 433 2.428171 CACTCATACCCAAATTGGCTGG 59.572 50.000 6.48 0.00 35.79 4.85
433 434 1.410153 CTCATACCCAAATTGGCTGGC 59.590 52.381 6.48 0.00 35.79 4.85
434 435 1.193323 CATACCCAAATTGGCTGGCA 58.807 50.000 6.48 0.00 35.79 4.92
435 436 1.134729 CATACCCAAATTGGCTGGCAC 60.135 52.381 6.48 0.00 35.79 5.01
436 437 0.178950 TACCCAAATTGGCTGGCACA 60.179 50.000 6.48 0.00 35.79 4.57
437 438 1.053264 ACCCAAATTGGCTGGCACAA 61.053 50.000 6.48 0.00 35.79 3.33
438 439 0.108207 CCCAAATTGGCTGGCACAAA 59.892 50.000 6.48 0.00 35.79 2.83
439 440 1.271488 CCCAAATTGGCTGGCACAAAT 60.271 47.619 6.48 0.00 35.79 2.32
440 441 2.078392 CCAAATTGGCTGGCACAAATC 58.922 47.619 2.29 0.00 38.70 2.17
441 442 2.289819 CCAAATTGGCTGGCACAAATCT 60.290 45.455 2.29 0.00 38.70 2.40
442 443 2.997986 CAAATTGGCTGGCACAAATCTC 59.002 45.455 2.29 0.00 38.70 2.75
443 444 1.927487 ATTGGCTGGCACAAATCTCA 58.073 45.000 2.29 0.00 38.70 3.27
444 445 1.702182 TTGGCTGGCACAAATCTCAA 58.298 45.000 2.29 0.00 38.70 3.02
445 446 1.702182 TGGCTGGCACAAATCTCAAA 58.298 45.000 0.00 0.00 38.70 2.69
446 447 1.614903 TGGCTGGCACAAATCTCAAAG 59.385 47.619 0.00 0.00 38.70 2.77
447 448 1.888512 GGCTGGCACAAATCTCAAAGA 59.111 47.619 0.00 0.00 38.70 2.52
448 449 2.297033 GGCTGGCACAAATCTCAAAGAA 59.703 45.455 0.00 0.00 38.70 2.52
449 450 3.243839 GGCTGGCACAAATCTCAAAGAAA 60.244 43.478 0.00 0.00 38.70 2.52
450 451 4.370917 GCTGGCACAAATCTCAAAGAAAA 58.629 39.130 0.00 0.00 38.70 2.29
451 452 4.810491 GCTGGCACAAATCTCAAAGAAAAA 59.190 37.500 0.00 0.00 38.70 1.94
471 472 3.665745 AAAATTGGCTAGCACAAGTGG 57.334 42.857 18.24 0.00 0.00 4.00
472 473 1.549203 AATTGGCTAGCACAAGTGGG 58.451 50.000 18.24 0.00 0.00 4.61
473 474 0.323725 ATTGGCTAGCACAAGTGGGG 60.324 55.000 18.24 0.00 0.00 4.96
474 475 1.715019 TTGGCTAGCACAAGTGGGGT 61.715 55.000 18.24 0.00 0.00 4.95
475 476 1.377333 GGCTAGCACAAGTGGGGTC 60.377 63.158 18.24 0.00 0.00 4.46
476 477 1.374947 GCTAGCACAAGTGGGGTCA 59.625 57.895 10.63 0.00 0.00 4.02
477 478 0.250727 GCTAGCACAAGTGGGGTCAA 60.251 55.000 10.63 0.00 0.00 3.18
478 479 1.817740 GCTAGCACAAGTGGGGTCAAA 60.818 52.381 10.63 0.00 0.00 2.69
479 480 2.582052 CTAGCACAAGTGGGGTCAAAA 58.418 47.619 2.00 0.00 0.00 2.44
480 481 1.111277 AGCACAAGTGGGGTCAAAAC 58.889 50.000 2.00 0.00 0.00 2.43
481 482 1.111277 GCACAAGTGGGGTCAAAACT 58.889 50.000 2.00 0.00 0.00 2.66
482 483 1.202405 GCACAAGTGGGGTCAAAACTG 60.202 52.381 2.00 0.00 0.00 3.16
483 484 1.111277 ACAAGTGGGGTCAAAACTGC 58.889 50.000 0.00 0.00 0.00 4.40
484 485 1.110442 CAAGTGGGGTCAAAACTGCA 58.890 50.000 0.00 0.00 0.00 4.41
485 486 1.067516 CAAGTGGGGTCAAAACTGCAG 59.932 52.381 13.48 13.48 0.00 4.41
486 487 1.109323 AGTGGGGTCAAAACTGCAGC 61.109 55.000 15.27 0.00 0.00 5.25
487 488 1.109323 GTGGGGTCAAAACTGCAGCT 61.109 55.000 15.27 0.00 0.00 4.24
488 489 0.396974 TGGGGTCAAAACTGCAGCTT 60.397 50.000 15.27 4.71 0.00 3.74
489 490 0.315251 GGGGTCAAAACTGCAGCTTC 59.685 55.000 15.27 0.00 0.00 3.86
490 491 1.322442 GGGTCAAAACTGCAGCTTCT 58.678 50.000 15.27 0.00 0.00 2.85
491 492 1.000938 GGGTCAAAACTGCAGCTTCTG 60.001 52.381 15.27 9.31 34.12 3.02
500 501 2.670934 CAGCTTCTGCACCGCCTT 60.671 61.111 0.00 0.00 42.74 4.35
501 502 2.359230 AGCTTCTGCACCGCCTTC 60.359 61.111 0.00 0.00 42.74 3.46
502 503 2.359230 GCTTCTGCACCGCCTTCT 60.359 61.111 0.00 0.00 39.41 2.85
503 504 1.079127 GCTTCTGCACCGCCTTCTA 60.079 57.895 0.00 0.00 39.41 2.10
504 505 1.362406 GCTTCTGCACCGCCTTCTAC 61.362 60.000 0.00 0.00 39.41 2.59
505 506 0.741221 CTTCTGCACCGCCTTCTACC 60.741 60.000 0.00 0.00 0.00 3.18
506 507 1.192146 TTCTGCACCGCCTTCTACCT 61.192 55.000 0.00 0.00 0.00 3.08
507 508 1.153549 CTGCACCGCCTTCTACCTC 60.154 63.158 0.00 0.00 0.00 3.85
508 509 2.187163 GCACCGCCTTCTACCTCC 59.813 66.667 0.00 0.00 0.00 4.30
509 510 2.359967 GCACCGCCTTCTACCTCCT 61.360 63.158 0.00 0.00 0.00 3.69
510 511 1.900545 GCACCGCCTTCTACCTCCTT 61.901 60.000 0.00 0.00 0.00 3.36
511 512 0.108138 CACCGCCTTCTACCTCCTTG 60.108 60.000 0.00 0.00 0.00 3.61
512 513 0.252103 ACCGCCTTCTACCTCCTTGA 60.252 55.000 0.00 0.00 0.00 3.02
513 514 0.902531 CCGCCTTCTACCTCCTTGAA 59.097 55.000 0.00 0.00 0.00 2.69
514 515 1.278127 CCGCCTTCTACCTCCTTGAAA 59.722 52.381 0.00 0.00 0.00 2.69
515 516 2.347731 CGCCTTCTACCTCCTTGAAAC 58.652 52.381 0.00 0.00 0.00 2.78
516 517 2.347731 GCCTTCTACCTCCTTGAAACG 58.652 52.381 0.00 0.00 0.00 3.60
517 518 2.028385 GCCTTCTACCTCCTTGAAACGA 60.028 50.000 0.00 0.00 0.00 3.85
518 519 3.556423 GCCTTCTACCTCCTTGAAACGAA 60.556 47.826 0.00 0.00 0.00 3.85
594 595 2.882927 AGCTACACAGAACAACACGA 57.117 45.000 0.00 0.00 0.00 4.35
655 656 7.658167 TGATCTAACGGTCAAGATTACACAAAA 59.342 33.333 7.22 0.00 32.60 2.44
1314 1336 1.360393 TTGAGGGCCTTGACCACCTT 61.360 55.000 7.89 0.00 29.21 3.50
1375 1397 0.657312 CAGCAACGTCTTCAGCAACA 59.343 50.000 0.00 0.00 0.00 3.33
1545 1578 5.353394 TCGTACTGGATTAGGAATGCTTT 57.647 39.130 0.00 0.00 0.00 3.51
1837 2339 3.881688 GCTATACCGACAACCTAGAGTGA 59.118 47.826 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 9.813826 TGTTTACTAGTTAGTAGGTAAAGAGGT 57.186 33.333 0.00 0.00 39.69 3.85
36 37 9.865321 TGCATGTTTACTAGTTAGTAGGTAAAG 57.135 33.333 0.00 0.00 39.69 1.85
37 38 9.643693 GTGCATGTTTACTAGTTAGTAGGTAAA 57.356 33.333 0.00 0.00 39.69 2.01
38 39 7.970061 CGTGCATGTTTACTAGTTAGTAGGTAA 59.030 37.037 0.00 0.00 39.69 2.85
39 40 7.121168 ACGTGCATGTTTACTAGTTAGTAGGTA 59.879 37.037 5.51 0.00 39.69 3.08
40 41 6.071728 ACGTGCATGTTTACTAGTTAGTAGGT 60.072 38.462 5.51 0.00 39.69 3.08
41 42 6.252869 CACGTGCATGTTTACTAGTTAGTAGG 59.747 42.308 9.37 0.00 39.69 3.18
42 43 6.237490 GCACGTGCATGTTTACTAGTTAGTAG 60.237 42.308 34.52 0.00 39.22 2.57
43 44 5.574055 GCACGTGCATGTTTACTAGTTAGTA 59.426 40.000 34.52 0.00 41.59 1.82
44 45 4.387862 GCACGTGCATGTTTACTAGTTAGT 59.612 41.667 34.52 0.00 41.59 2.24
45 46 4.882447 GCACGTGCATGTTTACTAGTTAG 58.118 43.478 34.52 0.00 41.59 2.34
46 47 4.914312 GCACGTGCATGTTTACTAGTTA 57.086 40.909 34.52 0.00 41.59 2.24
47 48 3.806316 GCACGTGCATGTTTACTAGTT 57.194 42.857 34.52 0.00 41.59 2.24
65 66 0.169230 AGTTTGAAACGTGCGTTGCA 59.831 45.000 13.48 13.48 41.51 4.08
66 67 1.264672 AAGTTTGAAACGTGCGTTGC 58.735 45.000 10.81 9.55 38.47 4.17
67 68 4.555747 AGTTTAAGTTTGAAACGTGCGTTG 59.444 37.500 10.81 0.00 40.88 4.10
68 69 4.725359 AGTTTAAGTTTGAAACGTGCGTT 58.275 34.783 6.75 3.97 40.88 4.84
69 70 4.345271 AGTTTAAGTTTGAAACGTGCGT 57.655 36.364 6.75 0.00 40.88 5.24
70 71 5.961263 ACTTAGTTTAAGTTTGAAACGTGCG 59.039 36.000 6.75 0.00 46.27 5.34
71 72 8.998558 ATACTTAGTTTAAGTTTGAAACGTGC 57.001 30.769 6.75 0.00 46.27 5.34
137 138 8.965819 TGCAACACTGTATTTATTTGACCATAT 58.034 29.630 0.00 0.00 0.00 1.78
138 139 8.341892 TGCAACACTGTATTTATTTGACCATA 57.658 30.769 0.00 0.00 0.00 2.74
139 140 7.225784 TGCAACACTGTATTTATTTGACCAT 57.774 32.000 0.00 0.00 0.00 3.55
140 141 6.641169 TGCAACACTGTATTTATTTGACCA 57.359 33.333 0.00 0.00 0.00 4.02
141 142 7.812191 TGATTGCAACACTGTATTTATTTGACC 59.188 33.333 0.00 0.00 0.00 4.02
142 143 8.741101 TGATTGCAACACTGTATTTATTTGAC 57.259 30.769 0.00 0.00 0.00 3.18
143 144 9.926158 AATGATTGCAACACTGTATTTATTTGA 57.074 25.926 0.00 0.00 0.00 2.69
144 145 9.961266 CAATGATTGCAACACTGTATTTATTTG 57.039 29.630 0.00 0.00 0.00 2.32
145 146 9.709495 ACAATGATTGCAACACTGTATTTATTT 57.291 25.926 12.27 0.00 0.00 1.40
146 147 9.142515 CACAATGATTGCAACACTGTATTTATT 57.857 29.630 13.14 0.00 0.00 1.40
147 148 7.760794 CCACAATGATTGCAACACTGTATTTAT 59.239 33.333 13.14 0.00 0.00 1.40
148 149 7.040132 TCCACAATGATTGCAACACTGTATTTA 60.040 33.333 13.14 1.57 0.00 1.40
149 150 5.927689 CCACAATGATTGCAACACTGTATTT 59.072 36.000 13.14 0.00 0.00 1.40
150 151 5.243507 TCCACAATGATTGCAACACTGTATT 59.756 36.000 13.14 2.29 0.00 1.89
151 152 4.766373 TCCACAATGATTGCAACACTGTAT 59.234 37.500 13.14 0.00 0.00 2.29
152 153 4.140536 TCCACAATGATTGCAACACTGTA 58.859 39.130 13.14 0.95 0.00 2.74
153 154 2.957680 TCCACAATGATTGCAACACTGT 59.042 40.909 0.00 5.79 0.00 3.55
154 155 3.646611 TCCACAATGATTGCAACACTG 57.353 42.857 0.00 5.12 0.00 3.66
155 156 4.877378 AATCCACAATGATTGCAACACT 57.123 36.364 0.00 0.00 33.77 3.55
156 157 6.036300 CCATAAATCCACAATGATTGCAACAC 59.964 38.462 0.00 0.00 35.21 3.32
157 158 6.107343 CCATAAATCCACAATGATTGCAACA 58.893 36.000 0.00 2.38 35.21 3.33
158 159 6.108015 ACCATAAATCCACAATGATTGCAAC 58.892 36.000 0.00 0.00 35.21 4.17
159 160 6.297080 ACCATAAATCCACAATGATTGCAA 57.703 33.333 0.00 0.00 35.21 4.08
160 161 5.450274 CGACCATAAATCCACAATGATTGCA 60.450 40.000 4.84 0.00 35.21 4.08
161 162 4.977963 CGACCATAAATCCACAATGATTGC 59.022 41.667 4.84 0.00 35.21 3.56
162 163 4.977963 GCGACCATAAATCCACAATGATTG 59.022 41.667 3.16 3.16 35.21 2.67
163 164 4.261155 CGCGACCATAAATCCACAATGATT 60.261 41.667 0.00 0.00 36.53 2.57
164 165 3.250762 CGCGACCATAAATCCACAATGAT 59.749 43.478 0.00 0.00 0.00 2.45
165 166 2.611751 CGCGACCATAAATCCACAATGA 59.388 45.455 0.00 0.00 0.00 2.57
166 167 2.354510 ACGCGACCATAAATCCACAATG 59.645 45.455 15.93 0.00 0.00 2.82
167 168 2.639065 ACGCGACCATAAATCCACAAT 58.361 42.857 15.93 0.00 0.00 2.71
168 169 2.102070 ACGCGACCATAAATCCACAA 57.898 45.000 15.93 0.00 0.00 3.33
169 170 1.735018 CAACGCGACCATAAATCCACA 59.265 47.619 15.93 0.00 0.00 4.17
170 171 1.531058 GCAACGCGACCATAAATCCAC 60.531 52.381 15.93 0.00 0.00 4.02
171 172 0.730265 GCAACGCGACCATAAATCCA 59.270 50.000 15.93 0.00 0.00 3.41
172 173 1.014352 AGCAACGCGACCATAAATCC 58.986 50.000 15.93 0.00 0.00 3.01
173 174 1.268032 CCAGCAACGCGACCATAAATC 60.268 52.381 15.93 0.00 0.00 2.17
174 175 0.732571 CCAGCAACGCGACCATAAAT 59.267 50.000 15.93 0.00 0.00 1.40
175 176 0.320858 TCCAGCAACGCGACCATAAA 60.321 50.000 15.93 0.00 0.00 1.40
176 177 1.017177 GTCCAGCAACGCGACCATAA 61.017 55.000 15.93 0.00 0.00 1.90
177 178 1.447140 GTCCAGCAACGCGACCATA 60.447 57.895 15.93 0.00 0.00 2.74
178 179 2.742372 GTCCAGCAACGCGACCAT 60.742 61.111 15.93 0.00 0.00 3.55
179 180 3.632736 TATTGTCCAGCAACGCGACCA 62.633 52.381 15.93 0.00 40.28 4.02
180 181 1.017177 TATTGTCCAGCAACGCGACC 61.017 55.000 15.93 0.00 40.28 4.79
181 182 0.793861 TTATTGTCCAGCAACGCGAC 59.206 50.000 15.93 0.83 40.28 5.19
182 183 0.793861 GTTATTGTCCAGCAACGCGA 59.206 50.000 15.93 0.00 40.28 5.87
183 184 0.518355 CGTTATTGTCCAGCAACGCG 60.518 55.000 3.53 3.53 40.28 6.01
184 185 0.793861 TCGTTATTGTCCAGCAACGC 59.206 50.000 9.35 0.00 42.51 4.84
185 186 3.120338 ACATTCGTTATTGTCCAGCAACG 60.120 43.478 8.37 8.37 43.76 4.10
186 187 4.419522 ACATTCGTTATTGTCCAGCAAC 57.580 40.909 0.00 0.00 40.28 4.17
187 188 4.277174 ACAACATTCGTTATTGTCCAGCAA 59.723 37.500 0.00 0.00 35.74 3.91
188 189 3.818210 ACAACATTCGTTATTGTCCAGCA 59.182 39.130 0.00 0.00 30.82 4.41
189 190 4.419522 ACAACATTCGTTATTGTCCAGC 57.580 40.909 0.00 0.00 30.82 4.85
190 191 6.359617 GTGAAACAACATTCGTTATTGTCCAG 59.640 38.462 0.00 0.00 35.54 3.86
191 192 6.202937 GTGAAACAACATTCGTTATTGTCCA 58.797 36.000 0.00 0.00 35.54 4.02
192 193 6.669485 GTGAAACAACATTCGTTATTGTCC 57.331 37.500 0.00 0.00 35.54 4.02
216 217 5.801380 ACAACCTATAAGAACACCGAATGT 58.199 37.500 0.00 0.00 46.42 2.71
217 218 7.762615 TCTTACAACCTATAAGAACACCGAATG 59.237 37.037 0.00 0.00 36.06 2.67
218 219 7.844009 TCTTACAACCTATAAGAACACCGAAT 58.156 34.615 0.00 0.00 36.06 3.34
219 220 7.230849 TCTTACAACCTATAAGAACACCGAA 57.769 36.000 0.00 0.00 36.06 4.30
220 221 6.839124 TCTTACAACCTATAAGAACACCGA 57.161 37.500 0.00 0.00 36.06 4.69
221 222 9.760077 ATTATCTTACAACCTATAAGAACACCG 57.240 33.333 0.00 0.00 40.97 4.94
247 248 9.342308 GTGATGAAAGGATTGGTAGATTTGATA 57.658 33.333 0.00 0.00 0.00 2.15
248 249 7.835682 TGTGATGAAAGGATTGGTAGATTTGAT 59.164 33.333 0.00 0.00 0.00 2.57
249 250 7.174413 TGTGATGAAAGGATTGGTAGATTTGA 58.826 34.615 0.00 0.00 0.00 2.69
250 251 7.395190 TGTGATGAAAGGATTGGTAGATTTG 57.605 36.000 0.00 0.00 0.00 2.32
251 252 8.421249 TTTGTGATGAAAGGATTGGTAGATTT 57.579 30.769 0.00 0.00 0.00 2.17
252 253 8.421249 TTTTGTGATGAAAGGATTGGTAGATT 57.579 30.769 0.00 0.00 0.00 2.40
253 254 8.599624 ATTTTGTGATGAAAGGATTGGTAGAT 57.400 30.769 0.00 0.00 0.00 1.98
254 255 7.890127 AGATTTTGTGATGAAAGGATTGGTAGA 59.110 33.333 0.00 0.00 0.00 2.59
255 256 8.059798 AGATTTTGTGATGAAAGGATTGGTAG 57.940 34.615 0.00 0.00 0.00 3.18
256 257 8.956426 GTAGATTTTGTGATGAAAGGATTGGTA 58.044 33.333 0.00 0.00 0.00 3.25
257 258 6.923199 AGATTTTGTGATGAAAGGATTGGT 57.077 33.333 0.00 0.00 0.00 3.67
258 259 7.972277 CAGTAGATTTTGTGATGAAAGGATTGG 59.028 37.037 0.00 0.00 0.00 3.16
259 260 8.733458 TCAGTAGATTTTGTGATGAAAGGATTG 58.267 33.333 0.00 0.00 0.00 2.67
260 261 8.868522 TCAGTAGATTTTGTGATGAAAGGATT 57.131 30.769 0.00 0.00 0.00 3.01
261 262 9.471702 AATCAGTAGATTTTGTGATGAAAGGAT 57.528 29.630 0.00 0.00 41.64 3.24
262 263 8.868522 AATCAGTAGATTTTGTGATGAAAGGA 57.131 30.769 0.00 0.00 41.64 3.36
276 277 4.606457 GCGTCTGCAAAATCAGTAGATT 57.394 40.909 0.00 0.00 42.92 2.40
290 291 2.029918 AGGAAAAGGAAAATGCGTCTGC 60.030 45.455 0.00 0.00 43.20 4.26
291 292 3.923017 AGGAAAAGGAAAATGCGTCTG 57.077 42.857 0.00 0.00 0.00 3.51
292 293 3.255888 GGAAGGAAAAGGAAAATGCGTCT 59.744 43.478 0.00 0.00 0.00 4.18
293 294 3.005367 TGGAAGGAAAAGGAAAATGCGTC 59.995 43.478 0.00 0.00 0.00 5.19
294 295 2.962421 TGGAAGGAAAAGGAAAATGCGT 59.038 40.909 0.00 0.00 0.00 5.24
295 296 3.658757 TGGAAGGAAAAGGAAAATGCG 57.341 42.857 0.00 0.00 0.00 4.73
296 297 4.020307 TCCATGGAAGGAAAAGGAAAATGC 60.020 41.667 13.46 0.00 33.93 3.56
297 298 5.727434 CTCCATGGAAGGAAAAGGAAAATG 58.273 41.667 17.00 0.00 37.20 2.32
298 299 4.223700 GCTCCATGGAAGGAAAAGGAAAAT 59.776 41.667 17.00 0.00 37.20 1.82
299 300 3.578282 GCTCCATGGAAGGAAAAGGAAAA 59.422 43.478 17.00 0.00 37.20 2.29
300 301 3.165071 GCTCCATGGAAGGAAAAGGAAA 58.835 45.455 17.00 0.00 37.20 3.13
301 302 2.557452 GGCTCCATGGAAGGAAAAGGAA 60.557 50.000 17.00 0.00 37.20 3.36
302 303 1.005924 GGCTCCATGGAAGGAAAAGGA 59.994 52.381 17.00 0.00 37.20 3.36
303 304 1.478631 GGCTCCATGGAAGGAAAAGG 58.521 55.000 17.00 2.23 37.20 3.11
304 305 1.006400 AGGGCTCCATGGAAGGAAAAG 59.994 52.381 17.00 3.03 37.20 2.27
305 306 1.084018 AGGGCTCCATGGAAGGAAAA 58.916 50.000 17.00 0.00 37.20 2.29
306 307 1.846439 CTAGGGCTCCATGGAAGGAAA 59.154 52.381 17.00 0.76 37.20 3.13
307 308 1.511613 CTAGGGCTCCATGGAAGGAA 58.488 55.000 17.00 0.00 37.20 3.36
308 309 1.056700 GCTAGGGCTCCATGGAAGGA 61.057 60.000 17.00 0.00 36.00 3.36
309 310 1.348008 TGCTAGGGCTCCATGGAAGG 61.348 60.000 17.00 6.24 39.59 3.46
310 311 0.769873 ATGCTAGGGCTCCATGGAAG 59.230 55.000 17.00 10.94 39.59 3.46
311 312 1.225373 AATGCTAGGGCTCCATGGAA 58.775 50.000 17.00 0.00 39.59 3.53
312 313 1.143684 GAAATGCTAGGGCTCCATGGA 59.856 52.381 15.27 15.27 39.59 3.41
313 314 1.133699 TGAAATGCTAGGGCTCCATGG 60.134 52.381 4.97 4.97 39.59 3.66
314 315 2.353357 TGAAATGCTAGGGCTCCATG 57.647 50.000 0.00 0.00 39.59 3.66
315 316 2.444388 TCATGAAATGCTAGGGCTCCAT 59.556 45.455 0.00 0.00 46.21 3.41
316 317 1.845791 TCATGAAATGCTAGGGCTCCA 59.154 47.619 0.00 0.00 46.21 3.86
317 318 2.645838 TCATGAAATGCTAGGGCTCC 57.354 50.000 0.00 0.00 46.21 4.70
318 319 4.139786 TCAATCATGAAATGCTAGGGCTC 58.860 43.478 0.00 0.00 46.21 4.70
319 320 4.174704 TCAATCATGAAATGCTAGGGCT 57.825 40.909 0.00 0.00 46.21 5.19
320 321 4.924305 TTCAATCATGAAATGCTAGGGC 57.076 40.909 0.00 0.00 46.21 5.19
321 322 6.812998 ACAATTCAATCATGAAATGCTAGGG 58.187 36.000 0.00 0.00 46.07 3.53
322 323 7.485810 TGACAATTCAATCATGAAATGCTAGG 58.514 34.615 0.00 0.00 46.07 3.02
323 324 7.167635 GCTGACAATTCAATCATGAAATGCTAG 59.832 37.037 0.00 6.49 46.07 3.42
324 325 6.976349 GCTGACAATTCAATCATGAAATGCTA 59.024 34.615 0.00 0.00 46.07 3.49
325 326 5.810587 GCTGACAATTCAATCATGAAATGCT 59.189 36.000 0.00 0.00 46.07 3.79
326 327 5.810587 AGCTGACAATTCAATCATGAAATGC 59.189 36.000 0.00 0.00 46.07 3.56
359 360 8.256605 GCTGATGGACTGTCATGTCTATATAAT 58.743 37.037 10.38 0.00 38.08 1.28
360 361 7.452813 AGCTGATGGACTGTCATGTCTATATAA 59.547 37.037 10.38 0.00 38.08 0.98
361 362 6.950619 AGCTGATGGACTGTCATGTCTATATA 59.049 38.462 10.38 0.00 38.08 0.86
362 363 5.779260 AGCTGATGGACTGTCATGTCTATAT 59.221 40.000 10.38 0.00 38.08 0.86
363 364 5.143369 AGCTGATGGACTGTCATGTCTATA 58.857 41.667 10.38 0.00 38.08 1.31
364 365 3.966006 AGCTGATGGACTGTCATGTCTAT 59.034 43.478 10.38 0.00 40.13 1.98
365 366 3.369175 AGCTGATGGACTGTCATGTCTA 58.631 45.455 10.38 0.00 37.16 2.59
366 367 2.186243 AGCTGATGGACTGTCATGTCT 58.814 47.619 10.38 0.00 37.16 3.41
367 368 2.687700 AGCTGATGGACTGTCATGTC 57.312 50.000 10.38 4.94 36.31 3.06
368 369 3.453717 ACATAGCTGATGGACTGTCATGT 59.546 43.478 10.38 5.35 40.18 3.21
369 370 4.069300 ACATAGCTGATGGACTGTCATG 57.931 45.455 10.38 4.74 40.18 3.07
370 371 5.143369 TCTACATAGCTGATGGACTGTCAT 58.857 41.667 10.38 1.49 40.18 3.06
371 372 4.536765 TCTACATAGCTGATGGACTGTCA 58.463 43.478 10.38 0.00 40.18 3.58
372 373 5.521906 TTCTACATAGCTGATGGACTGTC 57.478 43.478 0.00 0.00 40.18 3.51
373 374 5.221601 CCATTCTACATAGCTGATGGACTGT 60.222 44.000 0.00 0.00 40.18 3.55
374 375 5.236282 CCATTCTACATAGCTGATGGACTG 58.764 45.833 0.00 0.00 40.18 3.51
375 376 4.262808 GCCATTCTACATAGCTGATGGACT 60.263 45.833 14.70 0.00 40.18 3.85
376 377 3.999663 GCCATTCTACATAGCTGATGGAC 59.000 47.826 14.70 6.96 40.18 4.02
377 378 3.008375 GGCCATTCTACATAGCTGATGGA 59.992 47.826 0.00 0.00 40.18 3.41
378 379 3.008813 AGGCCATTCTACATAGCTGATGG 59.991 47.826 5.01 0.02 40.18 3.51
379 380 4.252073 GAGGCCATTCTACATAGCTGATG 58.748 47.826 5.01 0.00 41.79 3.07
380 381 3.262915 GGAGGCCATTCTACATAGCTGAT 59.737 47.826 5.01 0.00 0.00 2.90
381 382 2.634940 GGAGGCCATTCTACATAGCTGA 59.365 50.000 5.01 0.00 0.00 4.26
382 383 2.611473 CGGAGGCCATTCTACATAGCTG 60.611 54.545 5.01 0.00 0.00 4.24
383 384 1.620819 CGGAGGCCATTCTACATAGCT 59.379 52.381 5.01 0.00 0.00 3.32
384 385 1.344763 ACGGAGGCCATTCTACATAGC 59.655 52.381 5.01 0.00 0.00 2.97
385 386 2.628178 TCACGGAGGCCATTCTACATAG 59.372 50.000 5.01 0.00 0.00 2.23
386 387 2.628178 CTCACGGAGGCCATTCTACATA 59.372 50.000 5.01 0.00 0.00 2.29
387 388 1.414181 CTCACGGAGGCCATTCTACAT 59.586 52.381 5.01 0.00 0.00 2.29
388 389 0.824109 CTCACGGAGGCCATTCTACA 59.176 55.000 5.01 0.00 0.00 2.74
389 390 0.530870 GCTCACGGAGGCCATTCTAC 60.531 60.000 5.01 0.00 0.00 2.59
390 391 0.975556 TGCTCACGGAGGCCATTCTA 60.976 55.000 5.01 0.00 0.00 2.10
391 392 1.630126 ATGCTCACGGAGGCCATTCT 61.630 55.000 5.01 0.00 0.00 2.40
392 393 1.153086 ATGCTCACGGAGGCCATTC 60.153 57.895 5.01 0.00 0.00 2.67
393 394 1.153086 GATGCTCACGGAGGCCATT 60.153 57.895 5.01 0.00 0.00 3.16
394 395 2.369633 TGATGCTCACGGAGGCCAT 61.370 57.895 5.01 0.00 0.00 4.40
395 396 3.002583 TGATGCTCACGGAGGCCA 61.003 61.111 5.01 0.00 0.00 5.36
396 397 2.512515 GTGATGCTCACGGAGGCC 60.513 66.667 0.00 0.00 37.67 5.19
403 404 8.337104 CCAATTTGGGTATGAGTGATGCTCAC 62.337 46.154 7.60 7.88 44.55 3.51
404 405 6.383695 CCAATTTGGGTATGAGTGATGCTCA 61.384 44.000 7.60 0.00 45.23 4.26
405 406 4.037208 CCAATTTGGGTATGAGTGATGCTC 59.963 45.833 7.60 0.00 38.09 4.26
406 407 3.956199 CCAATTTGGGTATGAGTGATGCT 59.044 43.478 7.60 0.00 32.67 3.79
407 408 3.491447 GCCAATTTGGGTATGAGTGATGC 60.491 47.826 17.03 0.00 38.19 3.91
408 409 4.311816 GCCAATTTGGGTATGAGTGATG 57.688 45.455 17.03 0.00 38.19 3.07
419 420 0.108207 TTTGTGCCAGCCAATTTGGG 59.892 50.000 17.03 1.92 38.19 4.12
420 421 2.078392 GATTTGTGCCAGCCAATTTGG 58.922 47.619 11.27 11.27 41.55 3.28
421 422 2.997986 GAGATTTGTGCCAGCCAATTTG 59.002 45.455 0.00 0.00 0.00 2.32
422 423 2.633967 TGAGATTTGTGCCAGCCAATTT 59.366 40.909 0.00 0.00 0.00 1.82
423 424 2.250031 TGAGATTTGTGCCAGCCAATT 58.750 42.857 0.00 0.00 0.00 2.32
424 425 1.927487 TGAGATTTGTGCCAGCCAAT 58.073 45.000 0.00 0.00 0.00 3.16
425 426 1.702182 TTGAGATTTGTGCCAGCCAA 58.298 45.000 0.00 0.00 0.00 4.52
426 427 1.614903 CTTTGAGATTTGTGCCAGCCA 59.385 47.619 0.00 0.00 0.00 4.75
427 428 1.888512 TCTTTGAGATTTGTGCCAGCC 59.111 47.619 0.00 0.00 0.00 4.85
428 429 3.648339 TTCTTTGAGATTTGTGCCAGC 57.352 42.857 0.00 0.00 0.00 4.85
450 451 3.244181 CCCACTTGTGCTAGCCAATTTTT 60.244 43.478 13.29 0.00 0.00 1.94
451 452 2.299867 CCCACTTGTGCTAGCCAATTTT 59.700 45.455 13.29 1.46 0.00 1.82
452 453 1.895131 CCCACTTGTGCTAGCCAATTT 59.105 47.619 13.29 3.75 0.00 1.82
453 454 1.549203 CCCACTTGTGCTAGCCAATT 58.451 50.000 13.29 7.53 0.00 2.32
454 455 0.323725 CCCCACTTGTGCTAGCCAAT 60.324 55.000 13.29 4.17 0.00 3.16
455 456 1.074775 CCCCACTTGTGCTAGCCAA 59.925 57.895 13.29 14.43 0.00 4.52
456 457 2.124507 GACCCCACTTGTGCTAGCCA 62.125 60.000 13.29 7.05 0.00 4.75
457 458 1.377333 GACCCCACTTGTGCTAGCC 60.377 63.158 13.29 4.15 0.00 3.93
458 459 0.250727 TTGACCCCACTTGTGCTAGC 60.251 55.000 8.10 8.10 0.00 3.42
459 460 2.270352 TTTGACCCCACTTGTGCTAG 57.730 50.000 0.00 0.00 0.00 3.42
460 461 2.092103 AGTTTTGACCCCACTTGTGCTA 60.092 45.455 0.00 0.00 0.00 3.49
461 462 1.111277 GTTTTGACCCCACTTGTGCT 58.889 50.000 0.00 0.00 0.00 4.40
462 463 1.111277 AGTTTTGACCCCACTTGTGC 58.889 50.000 0.00 0.00 0.00 4.57
463 464 1.202405 GCAGTTTTGACCCCACTTGTG 60.202 52.381 0.00 0.00 0.00 3.33
464 465 1.111277 GCAGTTTTGACCCCACTTGT 58.889 50.000 0.00 0.00 0.00 3.16
465 466 1.067516 CTGCAGTTTTGACCCCACTTG 59.932 52.381 5.25 0.00 0.00 3.16
466 467 1.402787 CTGCAGTTTTGACCCCACTT 58.597 50.000 5.25 0.00 0.00 3.16
467 468 1.109323 GCTGCAGTTTTGACCCCACT 61.109 55.000 16.64 0.00 0.00 4.00
468 469 1.109323 AGCTGCAGTTTTGACCCCAC 61.109 55.000 16.64 0.00 0.00 4.61
469 470 0.396974 AAGCTGCAGTTTTGACCCCA 60.397 50.000 16.64 0.00 0.00 4.96
470 471 0.315251 GAAGCTGCAGTTTTGACCCC 59.685 55.000 17.41 0.00 0.00 4.95
471 472 1.000938 CAGAAGCTGCAGTTTTGACCC 60.001 52.381 17.41 4.13 0.00 4.46
472 473 2.412421 CAGAAGCTGCAGTTTTGACC 57.588 50.000 17.41 4.50 0.00 4.02
483 484 2.670934 AAGGCGGTGCAGAAGCTG 60.671 61.111 7.73 0.00 42.74 4.24
484 485 1.544825 TAGAAGGCGGTGCAGAAGCT 61.545 55.000 7.73 0.00 42.74 3.74
485 486 1.079127 TAGAAGGCGGTGCAGAAGC 60.079 57.895 0.00 0.00 42.57 3.86
486 487 0.741221 GGTAGAAGGCGGTGCAGAAG 60.741 60.000 0.00 0.00 0.00 2.85
487 488 1.192146 AGGTAGAAGGCGGTGCAGAA 61.192 55.000 0.00 0.00 0.00 3.02
488 489 1.605058 GAGGTAGAAGGCGGTGCAGA 61.605 60.000 0.00 0.00 0.00 4.26
489 490 1.153549 GAGGTAGAAGGCGGTGCAG 60.154 63.158 0.00 0.00 0.00 4.41
490 491 2.656069 GGAGGTAGAAGGCGGTGCA 61.656 63.158 0.00 0.00 0.00 4.57
491 492 1.900545 AAGGAGGTAGAAGGCGGTGC 61.901 60.000 0.00 0.00 0.00 5.01
492 493 0.108138 CAAGGAGGTAGAAGGCGGTG 60.108 60.000 0.00 0.00 0.00 4.94
493 494 0.252103 TCAAGGAGGTAGAAGGCGGT 60.252 55.000 0.00 0.00 0.00 5.68
494 495 0.902531 TTCAAGGAGGTAGAAGGCGG 59.097 55.000 0.00 0.00 0.00 6.13
495 496 2.347731 GTTTCAAGGAGGTAGAAGGCG 58.652 52.381 0.00 0.00 0.00 5.52
496 497 2.028385 TCGTTTCAAGGAGGTAGAAGGC 60.028 50.000 0.00 0.00 0.00 4.35
497 498 3.955650 TCGTTTCAAGGAGGTAGAAGG 57.044 47.619 0.00 0.00 0.00 3.46
498 499 7.493367 AGATATTCGTTTCAAGGAGGTAGAAG 58.507 38.462 0.00 0.00 0.00 2.85
499 500 7.342284 AGAGATATTCGTTTCAAGGAGGTAGAA 59.658 37.037 0.00 0.00 0.00 2.10
500 501 6.834451 AGAGATATTCGTTTCAAGGAGGTAGA 59.166 38.462 0.00 0.00 0.00 2.59
501 502 7.045126 AGAGATATTCGTTTCAAGGAGGTAG 57.955 40.000 0.00 0.00 0.00 3.18
502 503 7.778853 AGTAGAGATATTCGTTTCAAGGAGGTA 59.221 37.037 0.00 0.00 0.00 3.08
503 504 5.941555 AGAGATATTCGTTTCAAGGAGGT 57.058 39.130 0.00 0.00 0.00 3.85
504 505 7.045126 AGTAGAGATATTCGTTTCAAGGAGG 57.955 40.000 0.00 0.00 0.00 4.30
505 506 8.842280 AGTAGTAGAGATATTCGTTTCAAGGAG 58.158 37.037 0.00 0.00 0.00 3.69
506 507 8.749026 AGTAGTAGAGATATTCGTTTCAAGGA 57.251 34.615 0.00 0.00 0.00 3.36
594 595 3.199946 TGATCGGGAGGCTGTAATTTCTT 59.800 43.478 0.00 0.00 0.00 2.52
655 656 5.373222 TGCTAAGTGTACTTTTGATGTGGT 58.627 37.500 2.20 0.00 37.40 4.16
1375 1397 2.489938 ATTACATGGTCGGTGTTGCT 57.510 45.000 0.00 0.00 0.00 3.91
1545 1578 1.278985 CCATCAGCACCAGGTACAAGA 59.721 52.381 0.00 0.00 0.00 3.02
1837 2339 5.506708 AGAGTGAAGTGTTAAACCAACCTT 58.493 37.500 0.00 0.00 36.20 3.50
1909 2411 7.155328 ACAGAAAATAGCTACCGATTATGAGG 58.845 38.462 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.