Multiple sequence alignment - TraesCS3B01G228400

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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 TraesCS3B01G228400 chr3B 100.000 2354 0 0 1 2354 330586407 330588760 0.000000e+00 4348.0
1 TraesCS3B01G228400 chr1B 90.982 998 73 5 339 1332 415723232 415724216 0.000000e+00 1328.0
2 TraesCS3B01G228400 chr1B 86.077 1063 87 31 1328 2354 415736717 415737754 0.000000e+00 1086.0
3 TraesCS3B01G228400 chr1B 95.482 332 12 3 1 329 370698280 370697949 5.760000e-146 527.0
4 TraesCS3B01G228400 chr1B 91.781 146 9 1 634 779 670303410 670303268 1.430000e-47 200.0
5 TraesCS3B01G228400 chr1B 91.096 146 10 1 634 779 554649807 554649949 6.640000e-46 195.0
6 TraesCS3B01G228400 chr1B 85.430 151 12 9 294 441 313379292 313379435 5.240000e-32 148.0
7 TraesCS3B01G228400 chr6B 87.006 785 86 9 1580 2354 600613978 600614756 0.000000e+00 870.0
8 TraesCS3B01G228400 chr6B 96.084 332 11 2 1 330 37813878 37813547 7.400000e-150 540.0
9 TraesCS3B01G228400 chr6B 95.195 333 13 3 1 330 458093750 458094082 7.450000e-145 523.0
10 TraesCS3B01G228400 chr6B 91.373 255 22 0 2100 2354 709521050 709520796 1.340000e-92 350.0
11 TraesCS3B01G228400 chr6B 85.075 335 39 3 1580 1914 709521404 709521081 4.850000e-87 331.0
12 TraesCS3B01G228400 chr6B 89.961 259 22 2 1318 1575 709521700 709521445 4.850000e-87 331.0
13 TraesCS3B01G228400 chr6B 89.189 259 24 2 1318 1575 600613682 600613937 1.050000e-83 320.0
14 TraesCS3B01G228400 chr6B 91.781 146 9 1 634 779 17920378 17920236 1.430000e-47 200.0
15 TraesCS3B01G228400 chr6B 91.781 146 9 1 634 779 21185639 21185781 1.430000e-47 200.0
16 TraesCS3B01G228400 chr6B 91.781 146 9 1 634 779 21198938 21199080 1.430000e-47 200.0
17 TraesCS3B01G228400 chr6B 83.871 62 9 1 1984 2044 459382773 459382834 9.090000e-05 58.4
18 TraesCS3B01G228400 chr7A 86.752 785 88 9 1580 2354 95919612 95920390 0.000000e+00 859.0
19 TraesCS3B01G228400 chr7A 89.189 259 24 2 1318 1575 95919316 95919571 1.050000e-83 320.0
20 TraesCS3B01G228400 chr5B 96.386 332 10 2 1 330 71708420 71708751 1.590000e-151 545.0
21 TraesCS3B01G228400 chr5B 94.857 350 10 6 1 343 250844608 250844956 7.400000e-150 540.0
22 TraesCS3B01G228400 chr5B 92.308 39 2 1 2006 2044 616680805 616680842 1.000000e-03 54.7
23 TraesCS3B01G228400 chr7B 96.108 334 9 4 1 330 490114219 490114552 2.060000e-150 542.0
24 TraesCS3B01G228400 chr7B 95.195 333 13 3 1 330 154925560 154925228 7.450000e-145 523.0
25 TraesCS3B01G228400 chr7B 86.486 74 10 0 753 826 746429758 746429685 5.390000e-12 82.4
26 TraesCS3B01G228400 chr4B 95.783 332 11 3 1 330 223129859 223130189 1.240000e-147 532.0
27 TraesCS3B01G228400 chr4B 85.404 322 26 6 335 636 434365555 434365235 4.880000e-82 315.0
28 TraesCS3B01G228400 chr4B 89.831 177 15 3 334 509 157953243 157953417 8.470000e-55 224.0
29 TraesCS3B01G228400 chr1D 95.455 330 12 3 1 328 132247042 132247370 7.450000e-145 523.0
30 TraesCS3B01G228400 chr1D 86.697 218 19 6 320 528 236028767 236028983 1.410000e-57 233.0
31 TraesCS3B01G228400 chr1D 87.912 91 9 2 662 751 13187369 13187458 3.200000e-19 106.0
32 TraesCS3B01G228400 chr1D 92.683 41 3 0 2004 2044 409995975 409996015 2.530000e-05 60.2
33 TraesCS3B01G228400 chr4D 87.336 229 26 1 948 1176 55567178 55567403 2.320000e-65 259.0
34 TraesCS3B01G228400 chr4D 91.667 144 9 1 634 777 508474422 508474562 1.850000e-46 196.0
35 TraesCS3B01G228400 chr4A 87.336 229 26 1 948 1176 541358347 541358122 2.320000e-65 259.0
36 TraesCS3B01G228400 chr7D 89.855 207 12 6 330 528 366740498 366740703 8.350000e-65 257.0
37 TraesCS3B01G228400 chr7D 88.462 208 14 9 330 528 400233460 400233254 2.340000e-60 243.0
38 TraesCS3B01G228400 chr7D 83.607 61 8 2 1984 2043 622126342 622126401 3.270000e-04 56.5
39 TraesCS3B01G228400 chr1A 93.750 160 9 1 330 489 15518704 15518862 3.020000e-59 239.0
40 TraesCS3B01G228400 chr1A 92.949 156 10 1 319 474 190192482 190192328 2.350000e-55 226.0
41 TraesCS3B01G228400 chr6A 93.711 159 9 1 334 492 584487666 584487509 1.090000e-58 237.0
42 TraesCS3B01G228400 chr6A 91.781 146 9 1 634 779 68551801 68551943 1.430000e-47 200.0
43 TraesCS3B01G228400 chr2D 89.385 179 14 5 304 482 267299056 267299229 1.100000e-53 220.0
44 TraesCS3B01G228400 chr2D 91.241 137 9 1 643 779 331549211 331549078 1.440000e-42 183.0
45 TraesCS3B01G228400 chr3A 91.781 146 9 1 634 779 83206818 83206960 1.430000e-47 200.0
46 TraesCS3B01G228400 chr3A 100.000 28 0 0 2017 2044 727269988 727269961 4.000000e-03 52.8
47 TraesCS3B01G228400 chr3D 78.283 198 42 1 2158 2354 141348217 141348414 2.460000e-25 126.0
48 TraesCS3B01G228400 chr2B 86.301 73 10 0 753 825 122396315 122396243 1.940000e-11 80.5
49 TraesCS3B01G228400 chr5A 87.500 48 6 0 1997 2044 441180593 441180640 3.270000e-04 56.5


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 TraesCS3B01G228400 chr3B 330586407 330588760 2353 False 4348.000000 4348 100.0000 1 2354 1 chr3B.!!$F1 2353
1 TraesCS3B01G228400 chr1B 415723232 415724216 984 False 1328.000000 1328 90.9820 339 1332 1 chr1B.!!$F2 993
2 TraesCS3B01G228400 chr1B 415736717 415737754 1037 False 1086.000000 1086 86.0770 1328 2354 1 chr1B.!!$F3 1026
3 TraesCS3B01G228400 chr6B 600613682 600614756 1074 False 595.000000 870 88.0975 1318 2354 2 chr6B.!!$F5 1036
4 TraesCS3B01G228400 chr6B 709520796 709521700 904 True 337.333333 350 88.8030 1318 2354 3 chr6B.!!$R3 1036
5 TraesCS3B01G228400 chr7A 95919316 95920390 1074 False 589.500000 859 87.9705 1318 2354 2 chr7A.!!$F1 1036

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
576 581 0.249405 ATGGGCAACTGCAAACAACG 60.249 50.0 3.76 0.0 44.36 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 1658 1.18303 TCTCTTCCAAACGGCTCGGA 61.183 55.0 0.0 0.0 0.0 4.55 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
103 104 9.715121 TTTTAATTTGATGAGTTAGTAGGACGT 57.285 29.630 0.00 0.00 0.00 4.34
104 105 8.697846 TTAATTTGATGAGTTAGTAGGACGTG 57.302 34.615 0.00 0.00 0.00 4.49
105 106 4.713824 TTGATGAGTTAGTAGGACGTGG 57.286 45.455 0.00 0.00 0.00 4.94
106 107 3.021695 TGATGAGTTAGTAGGACGTGGG 58.978 50.000 0.00 0.00 0.00 4.61
107 108 1.843368 TGAGTTAGTAGGACGTGGGG 58.157 55.000 0.00 0.00 0.00 4.96
108 109 1.076024 TGAGTTAGTAGGACGTGGGGT 59.924 52.381 0.00 0.00 0.00 4.95
109 110 2.308570 TGAGTTAGTAGGACGTGGGGTA 59.691 50.000 0.00 0.00 0.00 3.69
110 111 3.053395 TGAGTTAGTAGGACGTGGGGTAT 60.053 47.826 0.00 0.00 0.00 2.73
111 112 3.956848 GAGTTAGTAGGACGTGGGGTATT 59.043 47.826 0.00 0.00 0.00 1.89
112 113 5.129368 AGTTAGTAGGACGTGGGGTATTA 57.871 43.478 0.00 0.00 0.00 0.98
113 114 5.709594 AGTTAGTAGGACGTGGGGTATTAT 58.290 41.667 0.00 0.00 0.00 1.28
114 115 6.138967 AGTTAGTAGGACGTGGGGTATTATT 58.861 40.000 0.00 0.00 0.00 1.40
115 116 7.297614 AGTTAGTAGGACGTGGGGTATTATTA 58.702 38.462 0.00 0.00 0.00 0.98
116 117 7.952368 AGTTAGTAGGACGTGGGGTATTATTAT 59.048 37.037 0.00 0.00 0.00 1.28
117 118 8.588472 GTTAGTAGGACGTGGGGTATTATTATT 58.412 37.037 0.00 0.00 0.00 1.40
118 119 7.622502 AGTAGGACGTGGGGTATTATTATTT 57.377 36.000 0.00 0.00 0.00 1.40
119 120 8.037723 AGTAGGACGTGGGGTATTATTATTTT 57.962 34.615 0.00 0.00 0.00 1.82
120 121 8.496916 AGTAGGACGTGGGGTATTATTATTTTT 58.503 33.333 0.00 0.00 0.00 1.94
138 139 4.859304 TTTTTAGGCTAGACGTGAGACA 57.141 40.909 0.00 0.00 0.00 3.41
139 140 4.436242 TTTTAGGCTAGACGTGAGACAG 57.564 45.455 0.00 0.00 0.00 3.51
140 141 2.783609 TAGGCTAGACGTGAGACAGT 57.216 50.000 0.00 0.00 0.00 3.55
141 142 1.912417 AGGCTAGACGTGAGACAGTT 58.088 50.000 0.00 0.00 0.00 3.16
142 143 1.542030 AGGCTAGACGTGAGACAGTTG 59.458 52.381 0.00 0.00 0.00 3.16
143 144 1.540267 GGCTAGACGTGAGACAGTTGA 59.460 52.381 0.00 0.00 0.00 3.18
144 145 2.414824 GGCTAGACGTGAGACAGTTGAG 60.415 54.545 0.00 0.00 0.00 3.02
145 146 2.226912 GCTAGACGTGAGACAGTTGAGT 59.773 50.000 0.00 0.00 0.00 3.41
146 147 3.304794 GCTAGACGTGAGACAGTTGAGTT 60.305 47.826 0.00 0.00 0.00 3.01
147 148 3.085443 AGACGTGAGACAGTTGAGTTG 57.915 47.619 0.00 0.00 0.00 3.16
148 149 2.128035 GACGTGAGACAGTTGAGTTGG 58.872 52.381 0.00 0.00 0.00 3.77
149 150 1.480954 ACGTGAGACAGTTGAGTTGGT 59.519 47.619 0.00 0.00 0.00 3.67
150 151 2.093658 ACGTGAGACAGTTGAGTTGGTT 60.094 45.455 0.00 0.00 0.00 3.67
151 152 2.540101 CGTGAGACAGTTGAGTTGGTTC 59.460 50.000 0.00 0.00 0.00 3.62
152 153 3.738281 CGTGAGACAGTTGAGTTGGTTCT 60.738 47.826 0.00 0.00 0.00 3.01
153 154 4.499188 CGTGAGACAGTTGAGTTGGTTCTA 60.499 45.833 0.00 0.00 0.00 2.10
154 155 4.985409 GTGAGACAGTTGAGTTGGTTCTAG 59.015 45.833 0.00 0.00 0.00 2.43
155 156 4.039245 TGAGACAGTTGAGTTGGTTCTAGG 59.961 45.833 0.00 0.00 0.00 3.02
156 157 3.325135 AGACAGTTGAGTTGGTTCTAGGG 59.675 47.826 0.00 0.00 0.00 3.53
157 158 3.314693 ACAGTTGAGTTGGTTCTAGGGA 58.685 45.455 0.00 0.00 0.00 4.20
158 159 3.714798 ACAGTTGAGTTGGTTCTAGGGAA 59.285 43.478 0.00 0.00 0.00 3.97
159 160 4.165372 ACAGTTGAGTTGGTTCTAGGGAAA 59.835 41.667 0.00 0.00 32.81 3.13
160 161 5.130350 CAGTTGAGTTGGTTCTAGGGAAAA 58.870 41.667 0.00 0.00 32.81 2.29
161 162 5.239525 CAGTTGAGTTGGTTCTAGGGAAAAG 59.760 44.000 0.00 0.00 32.81 2.27
162 163 5.104067 AGTTGAGTTGGTTCTAGGGAAAAGT 60.104 40.000 0.00 0.00 32.81 2.66
163 164 6.100714 AGTTGAGTTGGTTCTAGGGAAAAGTA 59.899 38.462 0.00 0.00 32.81 2.24
164 165 5.861727 TGAGTTGGTTCTAGGGAAAAGTAC 58.138 41.667 0.00 0.00 32.81 2.73
165 166 5.605488 TGAGTTGGTTCTAGGGAAAAGTACT 59.395 40.000 0.00 0.00 32.81 2.73
166 167 5.866207 AGTTGGTTCTAGGGAAAAGTACTG 58.134 41.667 0.00 0.00 32.81 2.74
167 168 5.605488 AGTTGGTTCTAGGGAAAAGTACTGA 59.395 40.000 0.00 0.00 32.81 3.41
168 169 5.740290 TGGTTCTAGGGAAAAGTACTGAG 57.260 43.478 0.00 0.00 32.81 3.35
169 170 5.399991 TGGTTCTAGGGAAAAGTACTGAGA 58.600 41.667 0.00 0.00 32.81 3.27
170 171 5.480772 TGGTTCTAGGGAAAAGTACTGAGAG 59.519 44.000 0.00 0.00 32.81 3.20
171 172 5.715753 GGTTCTAGGGAAAAGTACTGAGAGA 59.284 44.000 0.00 0.00 32.81 3.10
172 173 6.210984 GGTTCTAGGGAAAAGTACTGAGAGAA 59.789 42.308 0.00 0.00 32.81 2.87
173 174 7.256225 GGTTCTAGGGAAAAGTACTGAGAGAAA 60.256 40.741 0.00 0.00 32.81 2.52
174 175 7.850935 TCTAGGGAAAAGTACTGAGAGAAAA 57.149 36.000 0.00 0.00 0.00 2.29
175 176 7.668492 TCTAGGGAAAAGTACTGAGAGAAAAC 58.332 38.462 0.00 0.00 0.00 2.43
176 177 6.502074 AGGGAAAAGTACTGAGAGAAAACT 57.498 37.500 0.00 0.00 0.00 2.66
177 178 6.526526 AGGGAAAAGTACTGAGAGAAAACTC 58.473 40.000 0.00 0.00 37.42 3.01
178 179 6.099845 AGGGAAAAGTACTGAGAGAAAACTCA 59.900 38.462 0.00 0.00 43.39 3.41
190 191 8.731275 TGAGAGAAAACTCAGTTTACATTGAA 57.269 30.769 2.38 0.00 41.21 2.69
191 192 9.173021 TGAGAGAAAACTCAGTTTACATTGAAA 57.827 29.630 2.38 0.00 41.21 2.69
200 201 8.624776 ACTCAGTTTACATTGAAAAAGAAGAGG 58.375 33.333 0.00 0.00 0.00 3.69
201 202 8.746052 TCAGTTTACATTGAAAAAGAAGAGGA 57.254 30.769 0.00 0.00 0.00 3.71
202 203 9.184523 TCAGTTTACATTGAAAAAGAAGAGGAA 57.815 29.630 0.00 0.00 0.00 3.36
203 204 9.455847 CAGTTTACATTGAAAAAGAAGAGGAAG 57.544 33.333 0.00 0.00 0.00 3.46
204 205 9.408648 AGTTTACATTGAAAAAGAAGAGGAAGA 57.591 29.630 0.00 0.00 0.00 2.87
212 213 9.807649 TTGAAAAAGAAGAGGAAGAAAATTCAG 57.192 29.630 0.00 0.00 0.00 3.02
213 214 9.189156 TGAAAAAGAAGAGGAAGAAAATTCAGA 57.811 29.630 0.00 0.00 0.00 3.27
265 266 9.907229 AAAGGAAGTAGGAAGGTCTATAAAATG 57.093 33.333 0.00 0.00 0.00 2.32
266 267 8.035448 AGGAAGTAGGAAGGTCTATAAAATGG 57.965 38.462 0.00 0.00 0.00 3.16
267 268 7.628101 AGGAAGTAGGAAGGTCTATAAAATGGT 59.372 37.037 0.00 0.00 0.00 3.55
268 269 8.272889 GGAAGTAGGAAGGTCTATAAAATGGTT 58.727 37.037 0.00 0.00 0.00 3.67
269 270 9.110502 GAAGTAGGAAGGTCTATAAAATGGTTG 57.889 37.037 0.00 0.00 0.00 3.77
270 271 7.574607 AGTAGGAAGGTCTATAAAATGGTTGG 58.425 38.462 0.00 0.00 0.00 3.77
271 272 6.652205 AGGAAGGTCTATAAAATGGTTGGA 57.348 37.500 0.00 0.00 0.00 3.53
272 273 6.424032 AGGAAGGTCTATAAAATGGTTGGAC 58.576 40.000 0.00 0.00 0.00 4.02
273 274 5.296035 GGAAGGTCTATAAAATGGTTGGACG 59.704 44.000 0.00 0.00 0.00 4.79
274 275 5.687166 AGGTCTATAAAATGGTTGGACGA 57.313 39.130 0.00 0.00 0.00 4.20
275 276 6.057321 AGGTCTATAAAATGGTTGGACGAA 57.943 37.500 0.00 0.00 0.00 3.85
276 277 5.878669 AGGTCTATAAAATGGTTGGACGAAC 59.121 40.000 0.00 0.00 0.00 3.95
277 278 5.220529 GGTCTATAAAATGGTTGGACGAACG 60.221 44.000 0.00 0.00 35.12 3.95
278 279 5.577945 GTCTATAAAATGGTTGGACGAACGA 59.422 40.000 0.14 0.00 35.12 3.85
279 280 4.673534 ATAAAATGGTTGGACGAACGAC 57.326 40.909 0.14 0.00 35.12 4.34
280 281 1.956297 AAATGGTTGGACGAACGACA 58.044 45.000 0.14 0.00 35.12 4.35
281 282 1.508632 AATGGTTGGACGAACGACAG 58.491 50.000 0.14 0.00 35.12 3.51
282 283 0.320421 ATGGTTGGACGAACGACAGG 60.320 55.000 0.14 0.00 35.12 4.00
283 284 1.068585 GGTTGGACGAACGACAGGT 59.931 57.895 0.14 0.00 35.12 4.00
284 285 0.531311 GGTTGGACGAACGACAGGTT 60.531 55.000 0.14 0.00 42.96 3.50
285 286 1.292992 GTTGGACGAACGACAGGTTT 58.707 50.000 0.14 0.00 39.50 3.27
286 287 2.472816 GTTGGACGAACGACAGGTTTA 58.527 47.619 0.14 0.00 39.50 2.01
287 288 2.865551 GTTGGACGAACGACAGGTTTAA 59.134 45.455 0.14 0.00 39.50 1.52
288 289 2.472816 TGGACGAACGACAGGTTTAAC 58.527 47.619 0.14 0.00 39.50 2.01
289 290 1.453148 GGACGAACGACAGGTTTAACG 59.547 52.381 0.14 0.00 39.50 3.18
290 291 1.453148 GACGAACGACAGGTTTAACGG 59.547 52.381 0.14 0.00 39.50 4.44
291 292 1.066908 ACGAACGACAGGTTTAACGGA 59.933 47.619 0.14 0.00 39.50 4.69
292 293 2.126467 CGAACGACAGGTTTAACGGAA 58.874 47.619 0.00 0.00 39.50 4.30
293 294 2.097250 CGAACGACAGGTTTAACGGAAC 60.097 50.000 0.00 0.00 39.50 3.62
303 304 5.694231 GGTTTAACGGAACCTTATGTTGT 57.306 39.130 9.53 0.00 44.55 3.32
304 305 6.075762 GGTTTAACGGAACCTTATGTTGTT 57.924 37.500 9.53 0.00 44.55 2.83
305 306 6.506147 GGTTTAACGGAACCTTATGTTGTTT 58.494 36.000 9.53 0.00 44.55 2.83
306 307 6.638063 GGTTTAACGGAACCTTATGTTGTTTC 59.362 38.462 9.53 0.00 44.55 2.78
307 308 7.420002 GTTTAACGGAACCTTATGTTGTTTCT 58.580 34.615 0.00 0.00 37.29 2.52
308 309 8.558700 GTTTAACGGAACCTTATGTTGTTTCTA 58.441 33.333 0.00 0.00 37.29 2.10
309 310 8.851541 TTAACGGAACCTTATGTTGTTTCTAT 57.148 30.769 0.00 0.00 37.29 1.98
310 311 9.941325 TTAACGGAACCTTATGTTGTTTCTATA 57.059 29.630 0.00 0.00 37.29 1.31
356 357 7.095187 CCCTAATAATAAAGCACGGAATGACTC 60.095 40.741 0.00 0.00 0.00 3.36
357 358 6.619801 AATAATAAAGCACGGAATGACTCC 57.380 37.500 0.00 0.00 41.40 3.85
380 381 1.606224 GGGTTCACCGTCACAATACGT 60.606 52.381 0.00 0.00 41.27 3.57
383 384 3.002553 GGTTCACCGTCACAATACGTTTT 59.997 43.478 0.00 0.00 41.27 2.43
517 518 3.944250 ATCCAGTTGGGCCTTGGCG 62.944 63.158 4.53 0.00 36.21 5.69
532 537 3.130516 CCTTGGCGTCTCTCTATTGTACA 59.869 47.826 0.00 0.00 0.00 2.90
576 581 0.249405 ATGGGCAACTGCAAACAACG 60.249 50.000 3.76 0.00 44.36 4.10
577 582 2.237066 GGGCAACTGCAAACAACGC 61.237 57.895 3.76 0.00 44.36 4.84
578 583 2.237066 GGCAACTGCAAACAACGCC 61.237 57.895 3.76 0.00 44.36 5.68
586 591 1.544777 GCAAACAACGCCGCGATTTT 61.545 50.000 21.79 11.91 0.00 1.82
602 607 7.515643 CCGCGATTTTCTAAATAAATATCCGT 58.484 34.615 8.23 0.00 0.00 4.69
635 640 4.894784 ACATAAAGAAGGAAGAGAACGCA 58.105 39.130 0.00 0.00 0.00 5.24
683 688 4.415332 GTCGTGCCTCGCTCGGAA 62.415 66.667 8.06 0.00 44.06 4.30
686 691 3.760035 GTGCCTCGCTCGGAAGGA 61.760 66.667 0.00 0.00 0.00 3.36
687 692 2.759973 TGCCTCGCTCGGAAGGAT 60.760 61.111 0.00 0.00 0.00 3.24
688 693 2.279784 GCCTCGCTCGGAAGGATG 60.280 66.667 0.00 0.00 0.00 3.51
689 694 2.419198 CCTCGCTCGGAAGGATGG 59.581 66.667 0.00 0.00 0.00 3.51
690 695 2.127869 CCTCGCTCGGAAGGATGGA 61.128 63.158 0.00 0.00 0.00 3.41
691 696 1.467678 CCTCGCTCGGAAGGATGGAT 61.468 60.000 0.00 0.00 0.00 3.41
692 697 0.319383 CTCGCTCGGAAGGATGGATG 60.319 60.000 0.00 0.00 0.00 3.51
693 698 0.755327 TCGCTCGGAAGGATGGATGA 60.755 55.000 0.00 0.00 0.00 2.92
694 699 0.598680 CGCTCGGAAGGATGGATGAC 60.599 60.000 0.00 0.00 0.00 3.06
695 700 0.598680 GCTCGGAAGGATGGATGACG 60.599 60.000 0.00 0.00 0.00 4.35
696 701 0.598680 CTCGGAAGGATGGATGACGC 60.599 60.000 0.00 0.00 0.00 5.19
697 702 1.043116 TCGGAAGGATGGATGACGCT 61.043 55.000 0.00 0.00 0.00 5.07
698 703 0.598680 CGGAAGGATGGATGACGCTC 60.599 60.000 0.00 0.00 0.00 5.03
699 704 0.598680 GGAAGGATGGATGACGCTCG 60.599 60.000 0.00 0.00 0.00 5.03
700 705 1.218230 GAAGGATGGATGACGCTCGC 61.218 60.000 0.00 0.00 0.00 5.03
701 706 2.650813 AAGGATGGATGACGCTCGCC 62.651 60.000 0.00 0.00 0.00 5.54
702 707 3.032609 GATGGATGACGCTCGCCG 61.033 66.667 0.00 0.00 44.21 6.46
703 708 4.592192 ATGGATGACGCTCGCCGG 62.592 66.667 0.00 0.00 42.52 6.13
744 749 3.250323 CTGATGCGCGTCGAGGTG 61.250 66.667 23.73 14.06 0.00 4.00
761 766 2.183046 GGAGCAGCAGAGGACGAC 59.817 66.667 0.00 0.00 0.00 4.34
800 805 1.594331 GGTGTCGGATATTCAAGGGC 58.406 55.000 0.00 0.00 0.00 5.19
803 808 0.602905 GTCGGATATTCAAGGGCCGG 60.603 60.000 0.00 0.00 42.10 6.13
850 855 1.224592 GACCATGGATGCGGAGGTT 59.775 57.895 21.47 0.00 31.57 3.50
917 922 3.114616 CAGTCGCGCTTCTGGTGG 61.115 66.667 17.06 0.00 0.00 4.61
972 977 4.415332 CGGCAAAGCAGCAGCAGG 62.415 66.667 3.17 0.00 45.49 4.85
983 988 4.106925 CAGCAGGGCCCTCCTCAC 62.107 72.222 25.77 9.39 46.12 3.51
1047 1052 2.124403 CTGAGCCTGGCCATCCAC 60.124 66.667 16.57 0.00 37.47 4.02
1061 1066 1.837051 TCCACGAGGACAAGCTGGT 60.837 57.895 0.00 0.00 39.61 4.00
1079 1084 2.281484 GCCACCAGCGTTCCTCAA 60.281 61.111 0.00 0.00 0.00 3.02
1080 1085 1.896660 GCCACCAGCGTTCCTCAAA 60.897 57.895 0.00 0.00 0.00 2.69
1099 1104 3.933048 GAGCTGCCCATGCTGGTGT 62.933 63.158 0.00 0.00 45.53 4.16
1103 1108 4.722700 GCCCATGCTGGTGTCCGT 62.723 66.667 0.00 0.00 35.17 4.69
1113 1118 3.349006 GTGTCCGTGCTGCACAGG 61.349 66.667 29.86 28.04 33.40 4.00
1144 1149 3.512516 GGACCATGAAGCTGGCGC 61.513 66.667 0.00 0.00 40.15 6.53
1145 1150 3.512516 GACCATGAAGCTGGCGCC 61.513 66.667 22.73 22.73 40.15 6.53
1190 1195 0.602905 CGGCGACCAAGAAAAGAGGT 60.603 55.000 0.00 0.00 38.63 3.85
1224 1229 5.519722 GTGAAGGTCACGAACAAATCAAAT 58.480 37.500 0.00 0.00 37.67 2.32
1225 1230 5.399301 GTGAAGGTCACGAACAAATCAAATG 59.601 40.000 0.00 0.00 37.67 2.32
1226 1231 4.503741 AGGTCACGAACAAATCAAATGG 57.496 40.909 0.00 0.00 0.00 3.16
1255 1260 2.982470 CGCAAGAAATCCAAAAGAGCAC 59.018 45.455 0.00 0.00 43.02 4.40
1264 1269 1.202806 CCAAAAGAGCACACCCAGAGA 60.203 52.381 0.00 0.00 0.00 3.10
1277 1282 1.484240 CCCAGAGAAGAAAGAGCCGAT 59.516 52.381 0.00 0.00 0.00 4.18
1297 1302 1.531739 GGCCGGTGCAAGAAATCCAA 61.532 55.000 1.90 0.00 40.13 3.53
1299 1304 0.527565 CCGGTGCAAGAAATCCAAGG 59.472 55.000 0.00 0.00 0.00 3.61
1316 1321 0.961358 AGGAAGAGTCGACAGGGACG 60.961 60.000 19.50 0.00 41.81 4.79
1338 1343 0.682209 GCTGGGACATGAGCATGGTT 60.682 55.000 14.35 0.00 42.91 3.67
1351 1356 1.750193 CATGGTTGCCCAACGAGTAT 58.250 50.000 5.19 0.00 46.04 2.12
1359 1364 0.815734 CCCAACGAGTATGAGACGGT 59.184 55.000 0.00 0.00 0.00 4.83
1360 1365 1.203994 CCCAACGAGTATGAGACGGTT 59.796 52.381 0.00 0.00 32.06 4.44
1433 1438 2.267961 GGCCGTCGTGGGATTTCT 59.732 61.111 0.00 0.00 38.63 2.52
1577 1583 1.229951 TGGAGCTTGGGGGTGATCT 60.230 57.895 0.00 0.00 0.00 2.75
1601 1643 0.836400 AGGTGTCGTGGATCTGGGTT 60.836 55.000 0.00 0.00 0.00 4.11
1616 1658 1.224592 GGTTGGGATGTGGCGAGAT 59.775 57.895 0.00 0.00 0.00 2.75
1732 1776 0.976073 TTCTTCTAGACCAGCCGGGG 60.976 60.000 2.18 0.00 42.91 5.73
1737 1781 3.326385 TAGACCAGCCGGGGGTGAT 62.326 63.158 18.00 0.00 45.42 3.06
1744 1788 3.479203 CCGGGGGTGATGCTAGCA 61.479 66.667 21.85 21.85 0.00 3.49
1746 1790 1.149174 CGGGGGTGATGCTAGCATT 59.851 57.895 30.08 14.80 36.70 3.56
1751 1795 1.656652 GGTGATGCTAGCATTCACGT 58.343 50.000 31.40 16.50 36.70 4.49
1797 1841 2.038387 AGCGTCCACTGTTTGTTCTT 57.962 45.000 0.00 0.00 0.00 2.52
1881 1925 8.015087 CACGTGTACACTCATTTTTATGAACAT 58.985 33.333 23.01 0.00 0.00 2.71
1883 1927 9.689075 CGTGTACACTCATTTTTATGAACATAG 57.311 33.333 23.01 0.00 0.00 2.23
1916 1960 2.679837 CCTACGAGCACATGCAAAAGAT 59.320 45.455 6.64 0.00 45.16 2.40
1925 1969 4.744570 CACATGCAAAAGATTGAGCTGAT 58.255 39.130 0.00 0.00 38.94 2.90
1929 1973 7.590322 CACATGCAAAAGATTGAGCTGATATAC 59.410 37.037 0.00 0.00 38.94 1.47
1930 1974 7.501559 ACATGCAAAAGATTGAGCTGATATACT 59.498 33.333 0.00 0.00 38.94 2.12
1931 1975 8.996271 CATGCAAAAGATTGAGCTGATATACTA 58.004 33.333 0.00 0.00 38.94 1.82
1954 2000 6.777213 ACCTAGATGATTTACGAAGTCACT 57.223 37.500 0.00 0.00 43.93 3.41
1955 2001 7.876936 ACCTAGATGATTTACGAAGTCACTA 57.123 36.000 0.00 0.00 43.93 2.74
1997 2046 4.202556 TGGAAACATCTCCCAGTCAATTCA 60.203 41.667 0.00 0.00 34.22 2.57
2023 2072 9.500785 ACATCACCGAAAATCCAAAAATAAATT 57.499 25.926 0.00 0.00 0.00 1.82
2065 2114 1.992557 ACTTGAACCTTATGGGCTGGA 59.007 47.619 0.00 0.00 39.10 3.86
2082 2135 4.262463 GGCTGGATATAACACGATCCTTCA 60.262 45.833 0.00 0.00 41.99 3.02
2085 2138 6.428159 GCTGGATATAACACGATCCTTCAAAT 59.572 38.462 0.00 0.00 41.99 2.32
2098 2151 4.081406 TCCTTCAAATCATCCAACCACAG 58.919 43.478 0.00 0.00 0.00 3.66
2226 2279 6.347160 GGTTATTAGGTCGTGAACACTGAAAC 60.347 42.308 3.51 3.60 0.00 2.78
2237 2290 4.613448 TGAACACTGAAACGAAAACAAACG 59.387 37.500 0.00 0.00 0.00 3.60
2345 2398 7.430441 ACTTGCACGTCCAATAAACTAAATTT 58.570 30.769 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 9.715121 ACGTCCTACTAACTCATCAAATTAAAA 57.285 29.630 0.00 0.00 0.00 1.52
78 79 9.146984 CACGTCCTACTAACTCATCAAATTAAA 57.853 33.333 0.00 0.00 0.00 1.52
79 80 7.762615 CCACGTCCTACTAACTCATCAAATTAA 59.237 37.037 0.00 0.00 0.00 1.40
80 81 7.262772 CCACGTCCTACTAACTCATCAAATTA 58.737 38.462 0.00 0.00 0.00 1.40
81 82 6.106673 CCACGTCCTACTAACTCATCAAATT 58.893 40.000 0.00 0.00 0.00 1.82
82 83 5.395324 CCCACGTCCTACTAACTCATCAAAT 60.395 44.000 0.00 0.00 0.00 2.32
83 84 4.081862 CCCACGTCCTACTAACTCATCAAA 60.082 45.833 0.00 0.00 0.00 2.69
84 85 3.446161 CCCACGTCCTACTAACTCATCAA 59.554 47.826 0.00 0.00 0.00 2.57
85 86 3.021695 CCCACGTCCTACTAACTCATCA 58.978 50.000 0.00 0.00 0.00 3.07
86 87 2.361438 CCCCACGTCCTACTAACTCATC 59.639 54.545 0.00 0.00 0.00 2.92
87 88 2.292061 ACCCCACGTCCTACTAACTCAT 60.292 50.000 0.00 0.00 0.00 2.90
88 89 1.076024 ACCCCACGTCCTACTAACTCA 59.924 52.381 0.00 0.00 0.00 3.41
89 90 1.844687 ACCCCACGTCCTACTAACTC 58.155 55.000 0.00 0.00 0.00 3.01
90 91 3.677156 ATACCCCACGTCCTACTAACT 57.323 47.619 0.00 0.00 0.00 2.24
91 92 6.410942 AATAATACCCCACGTCCTACTAAC 57.589 41.667 0.00 0.00 0.00 2.34
92 93 8.725606 AATAATAATACCCCACGTCCTACTAA 57.274 34.615 0.00 0.00 0.00 2.24
93 94 8.725606 AAATAATAATACCCCACGTCCTACTA 57.274 34.615 0.00 0.00 0.00 1.82
94 95 7.622502 AAATAATAATACCCCACGTCCTACT 57.377 36.000 0.00 0.00 0.00 2.57
95 96 8.681486 AAAAATAATAATACCCCACGTCCTAC 57.319 34.615 0.00 0.00 0.00 3.18
117 118 4.280174 ACTGTCTCACGTCTAGCCTAAAAA 59.720 41.667 0.00 0.00 0.00 1.94
118 119 3.825014 ACTGTCTCACGTCTAGCCTAAAA 59.175 43.478 0.00 0.00 0.00 1.52
119 120 3.418995 ACTGTCTCACGTCTAGCCTAAA 58.581 45.455 0.00 0.00 0.00 1.85
120 121 3.069079 ACTGTCTCACGTCTAGCCTAA 57.931 47.619 0.00 0.00 0.00 2.69
121 122 2.747989 CAACTGTCTCACGTCTAGCCTA 59.252 50.000 0.00 0.00 0.00 3.93
122 123 1.542030 CAACTGTCTCACGTCTAGCCT 59.458 52.381 0.00 0.00 0.00 4.58
123 124 1.540267 TCAACTGTCTCACGTCTAGCC 59.460 52.381 0.00 0.00 0.00 3.93
124 125 2.226912 ACTCAACTGTCTCACGTCTAGC 59.773 50.000 0.00 0.00 0.00 3.42
125 126 4.222886 CAACTCAACTGTCTCACGTCTAG 58.777 47.826 0.00 0.00 0.00 2.43
126 127 3.004419 CCAACTCAACTGTCTCACGTCTA 59.996 47.826 0.00 0.00 0.00 2.59
127 128 2.223829 CCAACTCAACTGTCTCACGTCT 60.224 50.000 0.00 0.00 0.00 4.18
128 129 2.128035 CCAACTCAACTGTCTCACGTC 58.872 52.381 0.00 0.00 0.00 4.34
129 130 1.480954 ACCAACTCAACTGTCTCACGT 59.519 47.619 0.00 0.00 0.00 4.49
130 131 2.225068 ACCAACTCAACTGTCTCACG 57.775 50.000 0.00 0.00 0.00 4.35
131 132 3.798202 AGAACCAACTCAACTGTCTCAC 58.202 45.455 0.00 0.00 0.00 3.51
132 133 4.039245 CCTAGAACCAACTCAACTGTCTCA 59.961 45.833 0.00 0.00 0.00 3.27
133 134 4.561105 CCTAGAACCAACTCAACTGTCTC 58.439 47.826 0.00 0.00 0.00 3.36
134 135 3.325135 CCCTAGAACCAACTCAACTGTCT 59.675 47.826 0.00 0.00 0.00 3.41
135 136 3.323979 TCCCTAGAACCAACTCAACTGTC 59.676 47.826 0.00 0.00 0.00 3.51
136 137 3.314693 TCCCTAGAACCAACTCAACTGT 58.685 45.455 0.00 0.00 0.00 3.55
137 138 4.351874 TTCCCTAGAACCAACTCAACTG 57.648 45.455 0.00 0.00 0.00 3.16
138 139 5.104067 ACTTTTCCCTAGAACCAACTCAACT 60.104 40.000 0.00 0.00 0.00 3.16
139 140 5.131067 ACTTTTCCCTAGAACCAACTCAAC 58.869 41.667 0.00 0.00 0.00 3.18
140 141 5.382664 ACTTTTCCCTAGAACCAACTCAA 57.617 39.130 0.00 0.00 0.00 3.02
141 142 5.605488 AGTACTTTTCCCTAGAACCAACTCA 59.395 40.000 0.00 0.00 0.00 3.41
142 143 5.932883 CAGTACTTTTCCCTAGAACCAACTC 59.067 44.000 0.00 0.00 0.00 3.01
143 144 5.605488 TCAGTACTTTTCCCTAGAACCAACT 59.395 40.000 0.00 0.00 0.00 3.16
144 145 5.861727 TCAGTACTTTTCCCTAGAACCAAC 58.138 41.667 0.00 0.00 0.00 3.77
145 146 5.842328 TCTCAGTACTTTTCCCTAGAACCAA 59.158 40.000 0.00 0.00 0.00 3.67
146 147 5.399991 TCTCAGTACTTTTCCCTAGAACCA 58.600 41.667 0.00 0.00 0.00 3.67
147 148 5.715753 TCTCTCAGTACTTTTCCCTAGAACC 59.284 44.000 0.00 0.00 0.00 3.62
148 149 6.837471 TCTCTCAGTACTTTTCCCTAGAAC 57.163 41.667 0.00 0.00 0.00 3.01
149 150 7.850935 TTTCTCTCAGTACTTTTCCCTAGAA 57.149 36.000 0.00 0.00 0.00 2.10
150 151 7.509659 AGTTTTCTCTCAGTACTTTTCCCTAGA 59.490 37.037 0.00 0.00 0.00 2.43
151 152 7.672240 AGTTTTCTCTCAGTACTTTTCCCTAG 58.328 38.462 0.00 0.00 0.00 3.02
152 153 7.289317 TGAGTTTTCTCTCAGTACTTTTCCCTA 59.711 37.037 0.00 0.00 46.30 3.53
153 154 6.099845 TGAGTTTTCTCTCAGTACTTTTCCCT 59.900 38.462 0.00 0.00 46.30 4.20
154 155 6.289064 TGAGTTTTCTCTCAGTACTTTTCCC 58.711 40.000 0.00 0.00 46.30 3.97
165 166 8.731275 TTCAATGTAAACTGAGTTTTCTCTCA 57.269 30.769 16.49 8.52 46.30 3.27
174 175 8.624776 CCTCTTCTTTTTCAATGTAAACTGAGT 58.375 33.333 0.00 0.00 0.00 3.41
175 176 8.840321 TCCTCTTCTTTTTCAATGTAAACTGAG 58.160 33.333 0.00 0.00 0.00 3.35
176 177 8.746052 TCCTCTTCTTTTTCAATGTAAACTGA 57.254 30.769 0.00 0.00 0.00 3.41
177 178 9.455847 CTTCCTCTTCTTTTTCAATGTAAACTG 57.544 33.333 0.00 0.00 0.00 3.16
178 179 9.408648 TCTTCCTCTTCTTTTTCAATGTAAACT 57.591 29.630 0.00 0.00 0.00 2.66
186 187 9.807649 CTGAATTTTCTTCCTCTTCTTTTTCAA 57.192 29.630 0.00 0.00 0.00 2.69
187 188 9.189156 TCTGAATTTTCTTCCTCTTCTTTTTCA 57.811 29.630 0.00 0.00 0.00 2.69
239 240 9.907229 CATTTTATAGACCTTCCTACTTCCTTT 57.093 33.333 0.00 0.00 0.00 3.11
240 241 8.495260 CCATTTTATAGACCTTCCTACTTCCTT 58.505 37.037 0.00 0.00 0.00 3.36
241 242 7.628101 ACCATTTTATAGACCTTCCTACTTCCT 59.372 37.037 0.00 0.00 0.00 3.36
242 243 7.803131 ACCATTTTATAGACCTTCCTACTTCC 58.197 38.462 0.00 0.00 0.00 3.46
243 244 9.110502 CAACCATTTTATAGACCTTCCTACTTC 57.889 37.037 0.00 0.00 0.00 3.01
244 245 8.053355 CCAACCATTTTATAGACCTTCCTACTT 58.947 37.037 0.00 0.00 0.00 2.24
245 246 7.404980 TCCAACCATTTTATAGACCTTCCTACT 59.595 37.037 0.00 0.00 0.00 2.57
246 247 7.498239 GTCCAACCATTTTATAGACCTTCCTAC 59.502 40.741 0.00 0.00 0.00 3.18
247 248 7.571025 GTCCAACCATTTTATAGACCTTCCTA 58.429 38.462 0.00 0.00 0.00 2.94
248 249 6.424032 GTCCAACCATTTTATAGACCTTCCT 58.576 40.000 0.00 0.00 0.00 3.36
249 250 5.296035 CGTCCAACCATTTTATAGACCTTCC 59.704 44.000 0.00 0.00 0.00 3.46
250 251 6.110707 TCGTCCAACCATTTTATAGACCTTC 58.889 40.000 0.00 0.00 0.00 3.46
251 252 6.057321 TCGTCCAACCATTTTATAGACCTT 57.943 37.500 0.00 0.00 0.00 3.50
252 253 5.687166 TCGTCCAACCATTTTATAGACCT 57.313 39.130 0.00 0.00 0.00 3.85
253 254 5.220529 CGTTCGTCCAACCATTTTATAGACC 60.221 44.000 0.00 0.00 0.00 3.85
254 255 5.577945 TCGTTCGTCCAACCATTTTATAGAC 59.422 40.000 0.00 0.00 0.00 2.59
255 256 5.577945 GTCGTTCGTCCAACCATTTTATAGA 59.422 40.000 0.00 0.00 0.00 1.98
256 257 5.349270 TGTCGTTCGTCCAACCATTTTATAG 59.651 40.000 0.00 0.00 0.00 1.31
257 258 5.236282 TGTCGTTCGTCCAACCATTTTATA 58.764 37.500 0.00 0.00 0.00 0.98
258 259 4.066490 TGTCGTTCGTCCAACCATTTTAT 58.934 39.130 0.00 0.00 0.00 1.40
259 260 3.464907 TGTCGTTCGTCCAACCATTTTA 58.535 40.909 0.00 0.00 0.00 1.52
260 261 2.289547 CTGTCGTTCGTCCAACCATTTT 59.710 45.455 0.00 0.00 0.00 1.82
261 262 1.871039 CTGTCGTTCGTCCAACCATTT 59.129 47.619 0.00 0.00 0.00 2.32
262 263 1.508632 CTGTCGTTCGTCCAACCATT 58.491 50.000 0.00 0.00 0.00 3.16
263 264 0.320421 CCTGTCGTTCGTCCAACCAT 60.320 55.000 0.00 0.00 0.00 3.55
264 265 1.068417 CCTGTCGTTCGTCCAACCA 59.932 57.895 0.00 0.00 0.00 3.67
265 266 0.531311 AACCTGTCGTTCGTCCAACC 60.531 55.000 0.00 0.00 0.00 3.77
266 267 1.292992 AAACCTGTCGTTCGTCCAAC 58.707 50.000 0.00 0.00 31.78 3.77
267 268 2.865551 GTTAAACCTGTCGTTCGTCCAA 59.134 45.455 0.00 0.00 31.78 3.53
268 269 2.472816 GTTAAACCTGTCGTTCGTCCA 58.527 47.619 0.00 0.00 31.78 4.02
269 270 1.453148 CGTTAAACCTGTCGTTCGTCC 59.547 52.381 0.00 0.00 31.78 4.79
270 271 1.453148 CCGTTAAACCTGTCGTTCGTC 59.547 52.381 0.00 0.00 31.78 4.20
271 272 1.066908 TCCGTTAAACCTGTCGTTCGT 59.933 47.619 0.00 0.00 31.78 3.85
272 273 1.769733 TCCGTTAAACCTGTCGTTCG 58.230 50.000 0.00 0.00 31.78 3.95
273 274 2.221749 GGTTCCGTTAAACCTGTCGTTC 59.778 50.000 4.78 0.00 44.45 3.95
274 275 2.212652 GGTTCCGTTAAACCTGTCGTT 58.787 47.619 4.78 0.00 44.45 3.85
275 276 1.869774 GGTTCCGTTAAACCTGTCGT 58.130 50.000 4.78 0.00 44.45 4.34
282 283 7.420002 AGAAACAACATAAGGTTCCGTTAAAC 58.580 34.615 0.00 0.00 37.72 2.01
283 284 7.571080 AGAAACAACATAAGGTTCCGTTAAA 57.429 32.000 0.00 0.00 37.72 1.52
284 285 8.851541 ATAGAAACAACATAAGGTTCCGTTAA 57.148 30.769 0.00 0.00 37.72 2.01
326 327 9.396022 CATTCCGTGCTTTATTATTAGGGATAT 57.604 33.333 0.00 0.00 0.00 1.63
327 328 8.598916 TCATTCCGTGCTTTATTATTAGGGATA 58.401 33.333 0.00 0.00 0.00 2.59
328 329 7.390718 GTCATTCCGTGCTTTATTATTAGGGAT 59.609 37.037 0.00 0.00 0.00 3.85
329 330 6.708949 GTCATTCCGTGCTTTATTATTAGGGA 59.291 38.462 0.00 0.00 0.00 4.20
330 331 6.710744 AGTCATTCCGTGCTTTATTATTAGGG 59.289 38.462 0.00 0.00 0.00 3.53
331 332 7.095187 GGAGTCATTCCGTGCTTTATTATTAGG 60.095 40.741 0.00 0.00 35.91 2.69
332 333 7.797819 GGAGTCATTCCGTGCTTTATTATTAG 58.202 38.462 0.00 0.00 35.91 1.73
333 334 7.724305 GGAGTCATTCCGTGCTTTATTATTA 57.276 36.000 0.00 0.00 35.91 0.98
334 335 6.619801 GGAGTCATTCCGTGCTTTATTATT 57.380 37.500 0.00 0.00 35.91 1.40
350 351 1.677552 GGTGAACCCACGGAGTCAT 59.322 57.895 0.00 0.00 41.61 3.06
356 357 2.663852 GTGACGGTGAACCCACGG 60.664 66.667 0.00 0.00 44.09 4.94
357 358 0.882927 ATTGTGACGGTGAACCCACG 60.883 55.000 0.00 0.00 44.09 4.94
360 361 1.073177 CGTATTGTGACGGTGAACCC 58.927 55.000 0.00 0.00 39.19 4.11
383 384 3.564644 TGAAAGCGTAAAATCACGGGAAA 59.435 39.130 0.00 0.00 42.18 3.13
397 398 7.820044 TGTTTTAAATTCAAACTGAAAGCGT 57.180 28.000 12.20 0.00 40.12 5.07
429 430 8.856153 TTGCAGAGATAAAATTTAGTACCACA 57.144 30.769 0.00 0.00 0.00 4.17
445 446 6.914259 TCGAGTCGATAAATATTGCAGAGAT 58.086 36.000 12.09 0.00 0.00 2.75
462 463 0.924363 CGTAGCGGTCAATCGAGTCG 60.924 60.000 6.09 6.09 0.00 4.18
532 537 5.126707 CCGGTCACTGTTTACCTCTATTAGT 59.873 44.000 0.00 0.00 33.34 2.24
549 554 2.040544 CAGTTGCCCATCCGGTCAC 61.041 63.158 0.00 0.00 0.00 3.67
576 581 6.464834 CGGATATTTATTTAGAAAATCGCGGC 59.535 38.462 6.13 0.00 0.00 6.53
577 582 7.515643 ACGGATATTTATTTAGAAAATCGCGG 58.484 34.615 6.13 0.00 0.00 6.46
578 583 9.456797 GTACGGATATTTATTTAGAAAATCGCG 57.543 33.333 0.00 0.00 0.00 5.87
602 607 8.892723 TCTTCCTTCTTTATGTATACGTTCGTA 58.107 33.333 2.23 7.50 0.00 3.43
678 683 1.043116 AGCGTCATCCATCCTTCCGA 61.043 55.000 0.00 0.00 0.00 4.55
682 687 1.227380 GCGAGCGTCATCCATCCTT 60.227 57.895 0.00 0.00 0.00 3.36
683 688 2.419198 GCGAGCGTCATCCATCCT 59.581 61.111 0.00 0.00 0.00 3.24
685 690 3.032609 CGGCGAGCGTCATCCATC 61.033 66.667 0.00 0.00 0.00 3.51
686 691 4.592192 CCGGCGAGCGTCATCCAT 62.592 66.667 9.30 0.00 0.00 3.41
744 749 2.183046 GTCGTCCTCTGCTGCTCC 59.817 66.667 0.00 0.00 0.00 4.70
751 756 2.885861 CCTTCCCGTCGTCCTCTG 59.114 66.667 0.00 0.00 0.00 3.35
761 766 4.033776 TGCCTCCTTGCCTTCCCG 62.034 66.667 0.00 0.00 0.00 5.14
803 808 2.519780 ATCGTCCTCTCCTCCGGC 60.520 66.667 0.00 0.00 0.00 6.13
820 825 1.257750 CCATGGTCGACTGTCTCCCA 61.258 60.000 16.46 14.92 0.00 4.37
850 855 2.076100 CTGCTCGTACCTGATGCAAAA 58.924 47.619 0.00 0.00 33.07 2.44
881 886 1.377994 CTGAAGCCCAAGCCACTCT 59.622 57.895 0.00 0.00 41.25 3.24
917 922 4.247380 CCGGGCATGCTCTCCCTC 62.247 72.222 17.16 0.00 40.41 4.30
1000 1005 2.125512 GTGCCCGAAGAGCGTCAT 60.126 61.111 0.00 0.00 38.67 3.06
1047 1052 2.743928 GGCACCAGCTTGTCCTCG 60.744 66.667 0.00 0.00 41.70 4.63
1061 1066 2.616797 TTTGAGGAACGCTGGTGGCA 62.617 55.000 0.00 0.00 41.91 4.92
1099 1104 4.007644 CTCCCTGTGCAGCACGGA 62.008 66.667 32.47 24.78 42.79 4.69
1103 1108 2.672908 CCATCTCCCTGTGCAGCA 59.327 61.111 0.00 0.00 0.00 4.41
1113 1118 4.176752 GTCCCCGTGGCCATCTCC 62.177 72.222 9.72 0.00 0.00 3.71
1114 1119 4.176752 GGTCCCCGTGGCCATCTC 62.177 72.222 9.72 0.00 0.00 2.75
1145 1150 4.680237 TGCGGGTGTTGCTCTCCG 62.680 66.667 0.00 0.00 44.70 4.63
1147 1152 3.426568 GCTGCGGGTGTTGCTCTC 61.427 66.667 0.00 0.00 0.00 3.20
1168 1173 3.308878 CTTTTCTTGGTCGCCGCCG 62.309 63.158 0.00 0.00 0.00 6.46
1190 1195 3.118775 CGTGACCTTCACCCATATCTCAA 60.119 47.826 0.76 0.00 44.20 3.02
1224 1229 0.615331 ATTTCTTGCGCCTCTCTCCA 59.385 50.000 4.18 0.00 0.00 3.86
1225 1230 1.294857 GATTTCTTGCGCCTCTCTCC 58.705 55.000 4.18 0.00 0.00 3.71
1226 1231 1.294857 GGATTTCTTGCGCCTCTCTC 58.705 55.000 4.18 0.00 0.00 3.20
1255 1260 1.674221 CGGCTCTTTCTTCTCTGGGTG 60.674 57.143 0.00 0.00 0.00 4.61
1277 1282 1.976474 GGATTTCTTGCACCGGCCA 60.976 57.895 0.00 0.00 40.13 5.36
1283 1288 3.823304 ACTCTTCCTTGGATTTCTTGCAC 59.177 43.478 0.00 0.00 0.00 4.57
1297 1302 0.961358 CGTCCCTGTCGACTCTTCCT 60.961 60.000 17.92 0.00 0.00 3.36
1299 1304 1.242665 ACCGTCCCTGTCGACTCTTC 61.243 60.000 17.92 3.02 0.00 2.87
1316 1321 2.352422 TGCTCATGTCCCAGCACC 59.648 61.111 2.85 0.00 40.80 5.01
1338 1343 0.172578 CGTCTCATACTCGTTGGGCA 59.827 55.000 0.00 0.00 0.00 5.36
1345 1350 1.531264 CCGACAACCGTCTCATACTCG 60.531 57.143 0.00 0.00 40.23 4.18
1351 1356 1.174078 TAGCACCGACAACCGTCTCA 61.174 55.000 0.00 0.00 40.23 3.27
1359 1364 0.109272 CTTCGCTCTAGCACCGACAA 60.109 55.000 2.44 0.00 42.21 3.18
1360 1365 1.506718 CTTCGCTCTAGCACCGACA 59.493 57.895 2.44 0.00 42.21 4.35
1433 1438 4.818863 TATCCCGTCCGCCACCGA 62.819 66.667 0.00 0.00 36.29 4.69
1478 1483 2.049433 GGCACGAGCTACACACGT 60.049 61.111 4.48 0.00 46.98 4.49
1479 1484 1.446099 ATGGCACGAGCTACACACG 60.446 57.895 4.48 0.00 41.70 4.49
1577 1583 1.987855 GATCCACGACACCTGGGGA 60.988 63.158 1.10 0.00 0.00 4.81
1601 1643 2.796193 CGGATCTCGCCACATCCCA 61.796 63.158 0.00 0.00 35.97 4.37
1616 1658 1.183030 TCTCTTCCAAACGGCTCGGA 61.183 55.000 0.00 0.00 0.00 4.55
1732 1776 1.656652 ACGTGAATGCTAGCATCACC 58.343 50.000 31.89 24.25 35.31 4.02
1760 1804 1.730612 GCTAACAGGTCCGTGTAAAGC 59.269 52.381 9.94 9.94 34.36 3.51
1843 1887 8.156994 TGAGTGTACACGTGTATATATTAGCA 57.843 34.615 29.58 17.55 36.20 3.49
1916 1960 9.760926 AATCATCTAGGTAGTATATCAGCTCAA 57.239 33.333 0.00 0.00 0.00 3.02
1929 1973 7.932335 AGTGACTTCGTAAATCATCTAGGTAG 58.068 38.462 0.00 0.00 0.00 3.18
1930 1974 7.876936 AGTGACTTCGTAAATCATCTAGGTA 57.123 36.000 0.00 0.00 0.00 3.08
1931 1975 6.777213 AGTGACTTCGTAAATCATCTAGGT 57.223 37.500 0.00 0.00 0.00 3.08
1954 2000 3.195610 CCATTGACTATGAGCCGCCTATA 59.804 47.826 0.00 0.00 36.26 1.31
1955 2001 2.027745 CCATTGACTATGAGCCGCCTAT 60.028 50.000 0.00 0.00 36.26 2.57
1989 2038 5.095490 GGATTTTCGGTGATGTGAATTGAC 58.905 41.667 0.00 0.00 0.00 3.18
1997 2046 9.500785 AATTTATTTTTGGATTTTCGGTGATGT 57.499 25.926 0.00 0.00 0.00 3.06
2023 2072 5.298276 AGTTTTGGTGCTCGTATTTTTCTGA 59.702 36.000 0.00 0.00 0.00 3.27
2065 2114 8.156820 TGGATGATTTGAAGGATCGTGTTATAT 58.843 33.333 0.00 0.00 0.00 0.86
2162 2215 5.163447 TGTGAGGGATATAAACGGAGTCAAG 60.163 44.000 0.00 0.00 45.00 3.02
2226 2279 7.799447 TCCTTTTATGTATGACGTTTGTTTTCG 59.201 33.333 0.00 0.00 0.00 3.46
2320 2373 6.569179 ATTTAGTTTATTGGACGTGCAAGT 57.431 33.333 26.48 16.77 0.00 3.16


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

AutoCloner maintained by Alex Coulton.