Multiple sequence alignment - TraesCS3D01G288800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G288800 chr3D 100.000 4157 0 0 1 4157 397801579 397797423 0.000000e+00 7677.0
1 TraesCS3D01G288800 chr3D 94.693 848 40 1 3315 4157 551073569 551074416 0.000000e+00 1312.0
2 TraesCS3D01G288800 chr3D 93.585 873 45 6 3292 4157 339453180 339454048 0.000000e+00 1291.0
3 TraesCS3D01G288800 chr3A 93.220 2301 96 27 974 3231 517097216 517094933 0.000000e+00 3330.0
4 TraesCS3D01G288800 chr3A 88.498 426 28 12 237 655 517097661 517097250 2.890000e-136 496.0
5 TraesCS3D01G288800 chr3A 95.094 265 13 0 672 936 58274811 58275075 6.430000e-113 418.0
6 TraesCS3D01G288800 chr3A 93.818 275 17 0 673 947 739283831 739283557 8.310000e-112 414.0
7 TraesCS3D01G288800 chr3A 93.214 280 18 1 669 947 15125196 15124917 1.080000e-110 411.0
8 TraesCS3D01G288800 chr3A 93.214 280 18 1 669 947 15144934 15144655 1.080000e-110 411.0
9 TraesCS3D01G288800 chr3A 93.214 280 18 1 669 947 15148899 15148620 1.080000e-110 411.0
10 TraesCS3D01G288800 chr3A 88.824 170 16 2 37 204 517103840 517103672 5.450000e-49 206.0
11 TraesCS3D01G288800 chr3B 93.811 2246 68 28 1019 3223 523572053 523569838 0.000000e+00 3312.0
12 TraesCS3D01G288800 chr3B 90.503 179 4 9 492 658 523572291 523572114 1.500000e-54 224.0
13 TraesCS3D01G288800 chr3B 92.105 114 7 1 1 114 523572425 523572314 4.300000e-35 159.0
14 TraesCS3D01G288800 chr3B 100.000 30 0 0 52 81 523572317 523572288 5.810000e-04 56.5
15 TraesCS3D01G288800 chr2D 93.814 873 45 5 3292 4157 131276099 131275229 0.000000e+00 1304.0
16 TraesCS3D01G288800 chr2D 93.364 874 48 6 3292 4157 620188174 620189045 0.000000e+00 1284.0
17 TraesCS3D01G288800 chr2D 93.143 875 48 8 3292 4157 538957010 538956139 0.000000e+00 1273.0
18 TraesCS3D01G288800 chr1D 93.807 872 44 9 3292 4157 59531964 59532831 0.000000e+00 1303.0
19 TraesCS3D01G288800 chr6D 93.714 875 44 10 3292 4157 42089287 42088415 0.000000e+00 1301.0
20 TraesCS3D01G288800 chr5D 93.471 873 46 6 3292 4157 467427467 467426599 0.000000e+00 1286.0
21 TraesCS3D01G288800 chr7D 93.265 876 45 9 3292 4157 94405925 94405054 0.000000e+00 1279.0
22 TraesCS3D01G288800 chr1A 95.489 266 12 0 671 936 358543289 358543554 3.840000e-115 425.0
23 TraesCS3D01G288800 chr1A 94.737 266 14 0 671 936 164754287 164754552 8.310000e-112 414.0
24 TraesCS3D01G288800 chr1A 92.958 284 15 5 668 948 13709539 13709820 3.870000e-110 409.0
25 TraesCS3D01G288800 chr6A 95.113 266 13 0 671 936 390514096 390513831 1.790000e-113 420.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G288800 chr3D 397797423 397801579 4156 True 7677.000 7677 100.00000 1 4157 1 chr3D.!!$R1 4156
1 TraesCS3D01G288800 chr3D 551073569 551074416 847 False 1312.000 1312 94.69300 3315 4157 1 chr3D.!!$F2 842
2 TraesCS3D01G288800 chr3D 339453180 339454048 868 False 1291.000 1291 93.58500 3292 4157 1 chr3D.!!$F1 865
3 TraesCS3D01G288800 chr3A 517094933 517097661 2728 True 1913.000 3330 90.85900 237 3231 2 chr3A.!!$R5 2994
4 TraesCS3D01G288800 chr3A 15144655 15148899 4244 True 411.000 411 93.21400 669 947 2 chr3A.!!$R4 278
5 TraesCS3D01G288800 chr3B 523569838 523572425 2587 True 937.875 3312 94.10475 1 3223 4 chr3B.!!$R1 3222
6 TraesCS3D01G288800 chr2D 131275229 131276099 870 True 1304.000 1304 93.81400 3292 4157 1 chr2D.!!$R1 865
7 TraesCS3D01G288800 chr2D 620188174 620189045 871 False 1284.000 1284 93.36400 3292 4157 1 chr2D.!!$F1 865
8 TraesCS3D01G288800 chr2D 538956139 538957010 871 True 1273.000 1273 93.14300 3292 4157 1 chr2D.!!$R2 865
9 TraesCS3D01G288800 chr1D 59531964 59532831 867 False 1303.000 1303 93.80700 3292 4157 1 chr1D.!!$F1 865
10 TraesCS3D01G288800 chr6D 42088415 42089287 872 True 1301.000 1301 93.71400 3292 4157 1 chr6D.!!$R1 865
11 TraesCS3D01G288800 chr5D 467426599 467427467 868 True 1286.000 1286 93.47100 3292 4157 1 chr5D.!!$R1 865
12 TraesCS3D01G288800 chr7D 94405054 94405925 871 True 1279.000 1279 93.26500 3292 4157 1 chr7D.!!$R1 865

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
524 532 0.638746 CGTCGCTAAACTTAGGCGTG 59.361 55.0 6.46 0.0 34.38 5.34 F
2047 2131 0.108585 GGTGCCTGGTCTCTTTGTGA 59.891 55.0 0.00 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2352 2652 0.314302 AACCGGTCTTCTGACACGAG 59.686 55.0 8.04 0.00 44.61 4.18 R
3254 3584 0.166814 GAGTTGCTCCGATGCACAAC 59.833 55.0 7.36 7.36 43.20 3.32 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
27 28 0.963355 TACAAACAATCTGGCCCCGC 60.963 55.000 0.00 0.00 0.00 6.13
30 31 1.118356 AAACAATCTGGCCCCGCAAA 61.118 50.000 0.00 0.00 0.00 3.68
31 32 1.118356 AACAATCTGGCCCCGCAAAA 61.118 50.000 0.00 0.00 0.00 2.44
72 73 6.946340 TGGATAGCTTTAAACTGACTGATCA 58.054 36.000 0.00 0.00 0.00 2.92
94 95 2.632537 TGGACCCTTTCTTAAGAGCCT 58.367 47.619 5.12 0.00 32.92 4.58
95 96 2.986728 TGGACCCTTTCTTAAGAGCCTT 59.013 45.455 5.12 0.00 32.92 4.35
126 127 4.387256 GGCACGTCTAGATATTCTTGATGC 59.613 45.833 0.00 6.92 38.32 3.91
128 129 4.618912 CACGTCTAGATATTCTTGATGCGG 59.381 45.833 0.00 0.00 38.32 5.69
130 131 5.221263 ACGTCTAGATATTCTTGATGCGGTT 60.221 40.000 0.00 0.00 38.32 4.44
131 132 5.692204 CGTCTAGATATTCTTGATGCGGTTT 59.308 40.000 0.00 0.00 31.48 3.27
132 133 6.346120 CGTCTAGATATTCTTGATGCGGTTTG 60.346 42.308 0.00 0.00 31.48 2.93
133 134 6.701841 GTCTAGATATTCTTGATGCGGTTTGA 59.298 38.462 0.00 0.00 31.48 2.69
134 135 7.224753 GTCTAGATATTCTTGATGCGGTTTGAA 59.775 37.037 0.00 0.00 31.48 2.69
135 136 6.757897 AGATATTCTTGATGCGGTTTGAAA 57.242 33.333 0.00 0.00 0.00 2.69
136 137 7.338800 AGATATTCTTGATGCGGTTTGAAAT 57.661 32.000 0.00 0.00 0.00 2.17
137 138 8.450578 AGATATTCTTGATGCGGTTTGAAATA 57.549 30.769 0.00 0.00 0.00 1.40
138 139 9.071276 AGATATTCTTGATGCGGTTTGAAATAT 57.929 29.630 0.00 0.00 0.00 1.28
139 140 9.121517 GATATTCTTGATGCGGTTTGAAATATG 57.878 33.333 0.00 0.00 0.00 1.78
140 141 6.507958 TTCTTGATGCGGTTTGAAATATGA 57.492 33.333 0.00 0.00 0.00 2.15
141 142 6.698008 TCTTGATGCGGTTTGAAATATGAT 57.302 33.333 0.00 0.00 0.00 2.45
142 143 7.099266 TCTTGATGCGGTTTGAAATATGATT 57.901 32.000 0.00 0.00 0.00 2.57
143 144 7.546358 TCTTGATGCGGTTTGAAATATGATTT 58.454 30.769 0.00 0.00 0.00 2.17
144 145 8.034215 TCTTGATGCGGTTTGAAATATGATTTT 58.966 29.630 0.00 0.00 0.00 1.82
145 146 8.545229 TTGATGCGGTTTGAAATATGATTTTT 57.455 26.923 0.00 0.00 0.00 1.94
146 147 9.645059 TTGATGCGGTTTGAAATATGATTTTTA 57.355 25.926 0.00 0.00 0.00 1.52
147 148 9.299963 TGATGCGGTTTGAAATATGATTTTTAG 57.700 29.630 0.00 0.00 0.00 1.85
148 149 8.647143 ATGCGGTTTGAAATATGATTTTTAGG 57.353 30.769 0.00 0.00 0.00 2.69
149 150 6.533367 TGCGGTTTGAAATATGATTTTTAGGC 59.467 34.615 0.00 0.00 0.00 3.93
150 151 6.019075 GCGGTTTGAAATATGATTTTTAGGCC 60.019 38.462 0.00 0.00 0.00 5.19
151 152 6.198216 CGGTTTGAAATATGATTTTTAGGCCG 59.802 38.462 0.00 0.00 0.00 6.13
152 153 6.478673 GGTTTGAAATATGATTTTTAGGCCGG 59.521 38.462 0.00 0.00 0.00 6.13
153 154 7.262048 GTTTGAAATATGATTTTTAGGCCGGA 58.738 34.615 5.05 0.00 0.00 5.14
154 155 7.595819 TTGAAATATGATTTTTAGGCCGGAT 57.404 32.000 5.05 0.00 0.00 4.18
155 156 7.595819 TGAAATATGATTTTTAGGCCGGATT 57.404 32.000 5.05 0.00 0.00 3.01
156 157 8.698973 TGAAATATGATTTTTAGGCCGGATTA 57.301 30.769 5.05 0.00 0.00 1.75
157 158 9.137459 TGAAATATGATTTTTAGGCCGGATTAA 57.863 29.630 5.05 0.00 0.00 1.40
158 159 9.974980 GAAATATGATTTTTAGGCCGGATTAAA 57.025 29.630 5.05 6.15 0.00 1.52
160 161 9.758651 AATATGATTTTTAGGCCGGATTAAAAC 57.241 29.630 17.84 11.22 30.77 2.43
161 162 6.591750 TGATTTTTAGGCCGGATTAAAACA 57.408 33.333 17.84 12.95 30.77 2.83
162 163 7.176589 TGATTTTTAGGCCGGATTAAAACAT 57.823 32.000 17.84 14.85 30.77 2.71
163 164 7.616313 TGATTTTTAGGCCGGATTAAAACATT 58.384 30.769 17.84 9.72 30.77 2.71
164 165 8.097662 TGATTTTTAGGCCGGATTAAAACATTT 58.902 29.630 17.84 7.99 30.77 2.32
165 166 8.856153 ATTTTTAGGCCGGATTAAAACATTTT 57.144 26.923 17.84 0.00 30.77 1.82
166 167 7.892778 TTTTAGGCCGGATTAAAACATTTTC 57.107 32.000 5.05 0.00 0.00 2.29
167 168 6.844097 TTAGGCCGGATTAAAACATTTTCT 57.156 33.333 5.05 0.00 0.00 2.52
168 169 5.738619 AGGCCGGATTAAAACATTTTCTT 57.261 34.783 5.05 0.00 0.00 2.52
169 170 5.478407 AGGCCGGATTAAAACATTTTCTTG 58.522 37.500 5.05 0.00 0.00 3.02
170 171 5.011635 AGGCCGGATTAAAACATTTTCTTGT 59.988 36.000 5.05 0.00 0.00 3.16
171 172 5.347635 GGCCGGATTAAAACATTTTCTTGTC 59.652 40.000 5.05 0.00 0.00 3.18
172 173 5.923684 GCCGGATTAAAACATTTTCTTGTCA 59.076 36.000 5.05 0.00 0.00 3.58
173 174 6.589907 GCCGGATTAAAACATTTTCTTGTCAT 59.410 34.615 5.05 0.00 0.00 3.06
174 175 7.117667 GCCGGATTAAAACATTTTCTTGTCATT 59.882 33.333 5.05 0.00 0.00 2.57
175 176 8.987890 CCGGATTAAAACATTTTCTTGTCATTT 58.012 29.630 0.00 0.00 0.00 2.32
185 186 9.260002 ACATTTTCTTGTCATTTATGTCAAACC 57.740 29.630 4.46 0.00 35.90 3.27
186 187 9.258826 CATTTTCTTGTCATTTATGTCAAACCA 57.741 29.630 4.46 0.00 35.90 3.67
187 188 9.829507 ATTTTCTTGTCATTTATGTCAAACCAA 57.170 25.926 4.46 0.00 35.90 3.67
188 189 9.658799 TTTTCTTGTCATTTATGTCAAACCAAA 57.341 25.926 4.46 2.49 35.90 3.28
189 190 8.641499 TTCTTGTCATTTATGTCAAACCAAAC 57.359 30.769 4.46 0.00 35.90 2.93
190 191 8.006298 TCTTGTCATTTATGTCAAACCAAACT 57.994 30.769 4.46 0.00 35.90 2.66
191 192 7.920151 TCTTGTCATTTATGTCAAACCAAACTG 59.080 33.333 4.46 0.00 35.90 3.16
192 193 7.106439 TGTCATTTATGTCAAACCAAACTGT 57.894 32.000 0.00 0.00 0.00 3.55
193 194 7.199766 TGTCATTTATGTCAAACCAAACTGTC 58.800 34.615 0.00 0.00 0.00 3.51
194 195 6.640907 GTCATTTATGTCAAACCAAACTGTCC 59.359 38.462 0.00 0.00 0.00 4.02
195 196 6.322456 TCATTTATGTCAAACCAAACTGTCCA 59.678 34.615 0.00 0.00 0.00 4.02
196 197 6.723298 TTTATGTCAAACCAAACTGTCCAT 57.277 33.333 0.00 0.00 0.00 3.41
197 198 7.825331 TTTATGTCAAACCAAACTGTCCATA 57.175 32.000 0.00 0.00 0.00 2.74
198 199 5.705609 ATGTCAAACCAAACTGTCCATAC 57.294 39.130 0.00 0.00 0.00 2.39
199 200 3.886505 TGTCAAACCAAACTGTCCATACC 59.113 43.478 0.00 0.00 0.00 2.73
200 201 3.886505 GTCAAACCAAACTGTCCATACCA 59.113 43.478 0.00 0.00 0.00 3.25
201 202 4.023193 GTCAAACCAAACTGTCCATACCAG 60.023 45.833 0.00 0.00 36.01 4.00
202 203 3.876309 AACCAAACTGTCCATACCAGT 57.124 42.857 0.00 0.00 44.80 4.00
209 210 4.931661 ACTGTCCATACCAGTTATACCG 57.068 45.455 0.00 0.00 40.14 4.02
210 211 4.284178 ACTGTCCATACCAGTTATACCGT 58.716 43.478 0.00 0.00 40.14 4.83
211 212 4.713321 ACTGTCCATACCAGTTATACCGTT 59.287 41.667 0.00 0.00 40.14 4.44
212 213 5.013568 TGTCCATACCAGTTATACCGTTG 57.986 43.478 0.00 0.00 0.00 4.10
213 214 4.467082 TGTCCATACCAGTTATACCGTTGT 59.533 41.667 0.00 0.00 0.00 3.32
214 215 4.807304 GTCCATACCAGTTATACCGTTGTG 59.193 45.833 0.00 0.00 0.00 3.33
215 216 3.558418 CCATACCAGTTATACCGTTGTGC 59.442 47.826 0.00 0.00 0.00 4.57
216 217 2.843401 ACCAGTTATACCGTTGTGCA 57.157 45.000 0.00 0.00 0.00 4.57
217 218 3.343941 ACCAGTTATACCGTTGTGCAT 57.656 42.857 0.00 0.00 0.00 3.96
218 219 4.475051 ACCAGTTATACCGTTGTGCATA 57.525 40.909 0.00 0.00 0.00 3.14
219 220 5.031066 ACCAGTTATACCGTTGTGCATAT 57.969 39.130 0.00 0.00 0.00 1.78
220 221 4.814234 ACCAGTTATACCGTTGTGCATATG 59.186 41.667 0.00 0.00 0.00 1.78
221 222 4.814234 CCAGTTATACCGTTGTGCATATGT 59.186 41.667 4.29 0.00 0.00 2.29
222 223 5.986741 CCAGTTATACCGTTGTGCATATGTA 59.013 40.000 4.29 0.00 0.00 2.29
223 224 6.649141 CCAGTTATACCGTTGTGCATATGTAT 59.351 38.462 4.29 0.00 0.00 2.29
224 225 7.815549 CCAGTTATACCGTTGTGCATATGTATA 59.184 37.037 4.29 0.00 0.00 1.47
225 226 9.366216 CAGTTATACCGTTGTGCATATGTATAT 57.634 33.333 4.29 0.00 0.00 0.86
226 227 9.366216 AGTTATACCGTTGTGCATATGTATATG 57.634 33.333 4.29 7.37 42.30 1.78
227 228 9.361315 GTTATACCGTTGTGCATATGTATATGA 57.639 33.333 14.41 0.00 42.05 2.15
228 229 9.930693 TTATACCGTTGTGCATATGTATATGAA 57.069 29.630 14.41 2.58 42.05 2.57
229 230 8.840833 ATACCGTTGTGCATATGTATATGAAA 57.159 30.769 14.41 4.29 42.05 2.69
230 231 7.189693 ACCGTTGTGCATATGTATATGAAAG 57.810 36.000 14.41 4.27 42.05 2.62
231 232 6.204688 ACCGTTGTGCATATGTATATGAAAGG 59.795 38.462 14.41 12.72 42.05 3.11
232 233 6.426633 CCGTTGTGCATATGTATATGAAAGGA 59.573 38.462 14.41 0.00 42.05 3.36
233 234 7.290842 CGTTGTGCATATGTATATGAAAGGAC 58.709 38.462 14.41 4.54 42.05 3.85
234 235 7.571244 CGTTGTGCATATGTATATGAAAGGACC 60.571 40.741 14.41 0.00 42.05 4.46
235 236 6.836242 TGTGCATATGTATATGAAAGGACCA 58.164 36.000 14.41 0.58 42.05 4.02
242 243 9.998106 ATATGTATATGAAAGGACCACTACAAC 57.002 33.333 0.00 0.00 0.00 3.32
259 260 6.721321 ACTACAACAAGTGACATTTTTACGG 58.279 36.000 0.00 0.00 0.00 4.02
267 268 4.992951 AGTGACATTTTTACGGGAGTACAC 59.007 41.667 0.00 0.00 46.62 2.90
278 279 4.789807 ACGGGAGTACACATAGTGATACT 58.210 43.478 3.88 7.85 44.60 2.12
311 315 6.073765 GCGAATACAGTGATACACCCAATTAG 60.074 42.308 0.00 0.00 34.49 1.73
314 318 8.732746 AATACAGTGATACACCCAATTAGAAC 57.267 34.615 0.00 0.00 34.49 3.01
315 319 6.121776 ACAGTGATACACCCAATTAGAACA 57.878 37.500 0.00 0.00 34.49 3.18
323 330 8.738645 ATACACCCAATTAGAACAAAGAGATC 57.261 34.615 0.00 0.00 0.00 2.75
408 416 3.557595 CGAAGCACTGGATAAAGTCATCC 59.442 47.826 0.00 0.00 44.21 3.51
409 417 3.567478 AGCACTGGATAAAGTCATCCC 57.433 47.619 0.00 0.00 43.43 3.85
420 428 7.092444 TGGATAAAGTCATCCCAGAACATAACT 60.092 37.037 0.00 0.00 43.43 2.24
434 442 5.879223 AGAACATAACTGAAAGCATCTCCAG 59.121 40.000 0.00 0.00 37.60 3.86
437 445 3.777106 AACTGAAAGCATCTCCAGTGA 57.223 42.857 0.00 0.00 39.52 3.41
438 446 3.996921 ACTGAAAGCATCTCCAGTGAT 57.003 42.857 0.00 0.00 38.32 3.06
452 460 5.655090 TCTCCAGTGATATCGAAGTTAACCA 59.345 40.000 0.88 0.00 0.00 3.67
467 475 8.126700 CGAAGTTAACCAATGAAGTAAACTGTT 58.873 33.333 0.88 0.00 0.00 3.16
471 479 6.767524 AACCAATGAAGTAAACTGTTGACA 57.232 33.333 10.56 0.44 0.00 3.58
474 482 8.458573 ACCAATGAAGTAAACTGTTGACATAA 57.541 30.769 10.56 0.00 0.00 1.90
476 484 9.912634 CCAATGAAGTAAACTGTTGACATAAAT 57.087 29.630 10.56 0.00 0.00 1.40
524 532 0.638746 CGTCGCTAAACTTAGGCGTG 59.361 55.000 6.46 0.00 34.38 5.34
528 536 0.997196 GCTAAACTTAGGCGTGTCCG 59.003 55.000 0.00 0.00 40.77 4.79
610 618 7.445945 TCCAAGAAACACAAAAGAAAAAGGAA 58.554 30.769 0.00 0.00 0.00 3.36
612 620 7.602265 CCAAGAAACACAAAAGAAAAAGGAAGA 59.398 33.333 0.00 0.00 0.00 2.87
613 621 8.650714 CAAGAAACACAAAAGAAAAAGGAAGAG 58.349 33.333 0.00 0.00 0.00 2.85
614 622 8.122472 AGAAACACAAAAGAAAAAGGAAGAGA 57.878 30.769 0.00 0.00 0.00 3.10
615 623 8.246871 AGAAACACAAAAGAAAAAGGAAGAGAG 58.753 33.333 0.00 0.00 0.00 3.20
677 697 9.432982 AGTACTAGGTATCACTGTAGTAGTACT 57.567 37.037 8.14 8.14 41.31 2.73
678 698 9.691362 GTACTAGGTATCACTGTAGTAGTACTC 57.309 40.741 5.96 0.00 37.60 2.59
679 699 8.551682 ACTAGGTATCACTGTAGTAGTACTCT 57.448 38.462 5.96 0.00 37.60 3.24
680 700 8.641541 ACTAGGTATCACTGTAGTAGTACTCTC 58.358 40.741 5.96 2.46 37.60 3.20
681 701 7.679732 AGGTATCACTGTAGTAGTACTCTCT 57.320 40.000 5.96 2.00 37.60 3.10
682 702 8.093118 AGGTATCACTGTAGTAGTACTCTCTT 57.907 38.462 5.96 0.00 37.60 2.85
688 708 4.764172 TGTAGTAGTACTCTCTTCGGTCC 58.236 47.826 5.96 0.00 0.00 4.46
789 809 6.428465 ACATTCACGTAACAACACCAATATCA 59.572 34.615 0.00 0.00 0.00 2.15
801 821 9.071276 ACAACACCAATATCATTAGATTCATCC 57.929 33.333 0.00 0.00 35.67 3.51
939 959 5.678955 AAAAGAGCGAAGGGATTACTACT 57.321 39.130 0.00 0.00 0.00 2.57
941 961 5.771153 AAGAGCGAAGGGATTACTACTAC 57.229 43.478 0.00 0.00 0.00 2.73
947 967 5.297776 GCGAAGGGATTACTACTACACTACA 59.702 44.000 0.00 0.00 0.00 2.74
949 969 7.469732 GCGAAGGGATTACTACTACACTACATT 60.470 40.741 0.00 0.00 0.00 2.71
950 970 9.060347 CGAAGGGATTACTACTACACTACATTA 57.940 37.037 0.00 0.00 0.00 1.90
953 973 8.730948 AGGGATTACTACTACACTACATTAGGA 58.269 37.037 0.00 0.00 0.00 2.94
969 989 6.674573 ACATTAGGAGAGAGGTACACTACAT 58.325 40.000 0.00 0.00 0.00 2.29
1118 1165 3.864983 AAAGCACGGAGGGGGAGGA 62.865 63.158 0.00 0.00 0.00 3.71
1125 1172 3.478274 GAGGGGGAGGAGCAGCAG 61.478 72.222 0.00 0.00 0.00 4.24
1197 1250 4.268757 CCCCCTTTCTTCTCCCCA 57.731 61.111 0.00 0.00 0.00 4.96
1295 1368 1.219664 GGTACGCATGCACCCACTA 59.780 57.895 19.57 0.00 0.00 2.74
1329 1402 0.678048 GAGTGGAAAAGATGCCGCCT 60.678 55.000 0.00 0.00 35.28 5.52
1331 1404 1.378514 TGGAAAAGATGCCGCCTCC 60.379 57.895 0.00 0.00 0.00 4.30
1647 1720 1.269051 CCGTTTGGCTTGGTGTTCTTC 60.269 52.381 0.00 0.00 0.00 2.87
1648 1721 1.269051 CGTTTGGCTTGGTGTTCTTCC 60.269 52.381 0.00 0.00 0.00 3.46
1655 1728 3.004839 GGCTTGGTGTTCTTCCTTTTCTC 59.995 47.826 0.00 0.00 0.00 2.87
1744 1822 3.058160 CTTGGAACCGGCAGGCAG 61.058 66.667 0.00 0.00 42.76 4.85
1808 1892 7.121974 TCAATCATCGTTCTTTTGTTCTCTC 57.878 36.000 0.00 0.00 0.00 3.20
1827 1911 6.354938 TCTCTCTGATTGATTGATCCTTTGG 58.645 40.000 0.00 0.00 0.00 3.28
2004 2088 3.706373 GCCGACCAGAGCCTTGGA 61.706 66.667 10.83 0.00 40.87 3.53
2047 2131 0.108585 GGTGCCTGGTCTCTTTGTGA 59.891 55.000 0.00 0.00 0.00 3.58
2052 2136 1.902508 CCTGGTCTCTTTGTGAGGCTA 59.097 52.381 0.00 0.00 46.12 3.93
2256 2553 4.241555 GATGCCCTCACCGCCGAT 62.242 66.667 0.00 0.00 0.00 4.18
2424 2724 3.181487 ACACAGGCTTTGTTCATTGTGAC 60.181 43.478 0.00 0.00 38.16 3.67
2804 3112 0.038343 GCTGCATCGAGGAGGAGATC 60.038 60.000 0.00 0.00 35.99 2.75
2815 3123 1.698506 GAGGAGATCGATGAGGTGGT 58.301 55.000 0.54 0.00 0.00 4.16
2890 3200 4.393062 GTGAAGATTGCTTGCTTGCTAGTA 59.607 41.667 6.02 0.00 33.61 1.82
2947 3257 9.581099 GTCTGTTCTTTCTTTATTTTGGTTTGA 57.419 29.630 0.00 0.00 0.00 2.69
3017 3329 9.350357 CTTCTCATTCTGGTTTTTGTATGAATG 57.650 33.333 0.00 0.00 40.90 2.67
3018 3330 7.829725 TCTCATTCTGGTTTTTGTATGAATGG 58.170 34.615 11.80 5.27 40.33 3.16
3019 3331 7.669304 TCTCATTCTGGTTTTTGTATGAATGGA 59.331 33.333 11.80 6.96 40.33 3.41
3033 3349 4.292186 TGAATGGAGGAGAGGTTTTGAG 57.708 45.455 0.00 0.00 0.00 3.02
3143 3460 6.101650 ACTCAGATATCGATGTGCCATAAA 57.898 37.500 8.54 0.00 0.00 1.40
3231 3561 2.957491 TTTGTTCCTGCAAGTTGTGG 57.043 45.000 4.48 7.63 0.00 4.17
3232 3562 0.459489 TTGTTCCTGCAAGTTGTGGC 59.541 50.000 4.48 0.00 0.00 5.01
3233 3563 1.363807 GTTCCTGCAAGTTGTGGCC 59.636 57.895 4.48 0.00 0.00 5.36
3234 3564 1.076412 TTCCTGCAAGTTGTGGCCA 60.076 52.632 0.00 0.00 0.00 5.36
3235 3565 0.469705 TTCCTGCAAGTTGTGGCCAT 60.470 50.000 9.72 0.00 0.00 4.40
3236 3566 0.895100 TCCTGCAAGTTGTGGCCATC 60.895 55.000 9.72 3.12 0.00 3.51
3237 3567 1.588082 CTGCAAGTTGTGGCCATCC 59.412 57.895 9.72 0.00 0.00 3.51
3238 3568 2.203972 CTGCAAGTTGTGGCCATCCG 62.204 60.000 9.72 0.00 34.14 4.18
3239 3569 1.971167 GCAAGTTGTGGCCATCCGA 60.971 57.895 9.72 0.00 34.14 4.55
3240 3570 1.523154 GCAAGTTGTGGCCATCCGAA 61.523 55.000 9.72 0.00 34.14 4.30
3241 3571 1.176527 CAAGTTGTGGCCATCCGAAT 58.823 50.000 9.72 0.00 34.14 3.34
3242 3572 1.545582 CAAGTTGTGGCCATCCGAATT 59.454 47.619 9.72 0.00 34.14 2.17
3243 3573 1.923356 AGTTGTGGCCATCCGAATTT 58.077 45.000 9.72 0.00 34.14 1.82
3244 3574 1.545582 AGTTGTGGCCATCCGAATTTG 59.454 47.619 9.72 0.00 34.14 2.32
3245 3575 1.272212 GTTGTGGCCATCCGAATTTGT 59.728 47.619 9.72 0.00 34.14 2.83
3246 3576 1.626686 TGTGGCCATCCGAATTTGTT 58.373 45.000 9.72 0.00 34.14 2.83
3247 3577 1.543802 TGTGGCCATCCGAATTTGTTC 59.456 47.619 9.72 0.00 34.14 3.18
3248 3578 1.135112 GTGGCCATCCGAATTTGTTCC 60.135 52.381 9.72 0.00 34.14 3.62
3249 3579 1.272425 TGGCCATCCGAATTTGTTCCT 60.272 47.619 0.00 0.00 34.14 3.36
3250 3580 1.134946 GGCCATCCGAATTTGTTCCTG 59.865 52.381 0.00 0.00 0.00 3.86
3251 3581 1.469767 GCCATCCGAATTTGTTCCTGC 60.470 52.381 0.00 0.00 0.00 4.85
3252 3582 1.818060 CCATCCGAATTTGTTCCTGCA 59.182 47.619 0.00 0.00 0.00 4.41
3253 3583 2.230992 CCATCCGAATTTGTTCCTGCAA 59.769 45.455 0.00 0.00 0.00 4.08
3254 3584 3.504863 CATCCGAATTTGTTCCTGCAAG 58.495 45.455 0.00 0.00 0.00 4.01
3255 3585 2.582052 TCCGAATTTGTTCCTGCAAGT 58.418 42.857 0.00 0.00 0.00 3.16
3256 3586 2.955660 TCCGAATTTGTTCCTGCAAGTT 59.044 40.909 0.00 0.00 32.28 2.66
3257 3587 3.052036 CCGAATTTGTTCCTGCAAGTTG 58.948 45.455 0.00 0.00 30.26 3.16
3258 3588 3.490761 CCGAATTTGTTCCTGCAAGTTGT 60.491 43.478 4.48 0.00 30.26 3.32
3259 3589 3.486841 CGAATTTGTTCCTGCAAGTTGTG 59.513 43.478 4.48 0.00 30.26 3.33
3269 3599 2.246841 CAAGTTGTGCATCGGAGCA 58.753 52.632 0.00 0.00 43.35 4.26
3273 3603 2.209466 AGTTGTGCATCGGAGCAACTC 61.209 52.381 11.22 0.00 45.55 3.01
3282 3612 3.608432 GAGCAACTCCAATGGGGC 58.392 61.111 0.00 0.00 36.21 5.80
3283 3613 2.361610 AGCAACTCCAATGGGGCG 60.362 61.111 0.00 0.00 36.21 6.13
3284 3614 2.361104 GCAACTCCAATGGGGCGA 60.361 61.111 0.00 0.00 36.21 5.54
3285 3615 2.700773 GCAACTCCAATGGGGCGAC 61.701 63.158 0.00 0.00 36.21 5.19
3326 3656 1.802715 CGTATCCAAACGGACGCGT 60.803 57.895 13.85 13.85 39.19 6.01
3740 4786 1.213013 GCTGTCACACTCGTCGGAT 59.787 57.895 0.00 0.00 0.00 4.18
3969 5584 2.281761 CCTCAACAACCAGCGGCT 60.282 61.111 0.00 0.00 0.00 5.52
4101 6862 1.677300 ATCACAAATTCCGCCGCCA 60.677 52.632 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.372675 GGGGCCAGATTGTTTGTACCTAT 60.373 47.826 4.39 0.00 0.00 2.57
10 11 1.814772 TTGCGGGGCCAGATTGTTTG 61.815 55.000 8.22 0.00 0.00 2.93
72 73 3.593780 AGGCTCTTAAGAAAGGGTCCATT 59.406 43.478 6.63 0.00 38.70 3.16
94 95 0.319211 CTAGACGTGCCGGACAACAA 60.319 55.000 5.05 0.00 0.00 2.83
95 96 1.174078 TCTAGACGTGCCGGACAACA 61.174 55.000 5.05 0.00 0.00 3.33
110 111 7.482654 TTCAAACCGCATCAAGAATATCTAG 57.517 36.000 0.00 0.00 0.00 2.43
114 115 8.849168 TCATATTTCAAACCGCATCAAGAATAT 58.151 29.630 0.00 0.00 0.00 1.28
116 117 7.099266 TCATATTTCAAACCGCATCAAGAAT 57.901 32.000 0.00 0.00 0.00 2.40
118 119 6.698008 ATCATATTTCAAACCGCATCAAGA 57.302 33.333 0.00 0.00 0.00 3.02
119 120 7.760131 AAATCATATTTCAAACCGCATCAAG 57.240 32.000 0.00 0.00 0.00 3.02
120 121 8.545229 AAAAATCATATTTCAAACCGCATCAA 57.455 26.923 0.00 0.00 0.00 2.57
121 122 9.299963 CTAAAAATCATATTTCAAACCGCATCA 57.700 29.630 0.00 0.00 0.00 3.07
122 123 8.755018 CCTAAAAATCATATTTCAAACCGCATC 58.245 33.333 0.00 0.00 0.00 3.91
123 124 7.224557 GCCTAAAAATCATATTTCAAACCGCAT 59.775 33.333 0.00 0.00 0.00 4.73
124 125 6.533367 GCCTAAAAATCATATTTCAAACCGCA 59.467 34.615 0.00 0.00 0.00 5.69
125 126 6.019075 GGCCTAAAAATCATATTTCAAACCGC 60.019 38.462 0.00 0.00 0.00 5.68
126 127 6.198216 CGGCCTAAAAATCATATTTCAAACCG 59.802 38.462 0.00 0.00 0.00 4.44
128 129 7.262048 TCCGGCCTAAAAATCATATTTCAAAC 58.738 34.615 0.00 0.00 0.00 2.93
130 131 7.595819 ATCCGGCCTAAAAATCATATTTCAA 57.404 32.000 0.00 0.00 0.00 2.69
131 132 7.595819 AATCCGGCCTAAAAATCATATTTCA 57.404 32.000 0.00 0.00 0.00 2.69
132 133 9.974980 TTTAATCCGGCCTAAAAATCATATTTC 57.025 29.630 0.00 0.00 0.00 2.17
134 135 9.758651 GTTTTAATCCGGCCTAAAAATCATATT 57.241 29.630 17.17 2.71 30.85 1.28
135 136 8.919145 TGTTTTAATCCGGCCTAAAAATCATAT 58.081 29.630 17.17 0.00 30.85 1.78
136 137 8.294954 TGTTTTAATCCGGCCTAAAAATCATA 57.705 30.769 17.17 4.97 30.85 2.15
137 138 7.176589 TGTTTTAATCCGGCCTAAAAATCAT 57.823 32.000 17.17 0.00 30.85 2.45
138 139 6.591750 TGTTTTAATCCGGCCTAAAAATCA 57.408 33.333 17.17 11.71 30.85 2.57
139 140 8.487313 AAATGTTTTAATCCGGCCTAAAAATC 57.513 30.769 17.17 9.96 30.85 2.17
140 141 8.856153 AAAATGTTTTAATCCGGCCTAAAAAT 57.144 26.923 17.17 12.11 30.85 1.82
141 142 8.151596 AGAAAATGTTTTAATCCGGCCTAAAAA 58.848 29.630 17.17 9.72 30.85 1.94
142 143 7.672240 AGAAAATGTTTTAATCCGGCCTAAAA 58.328 30.769 13.48 13.48 0.00 1.52
143 144 7.234661 AGAAAATGTTTTAATCCGGCCTAAA 57.765 32.000 0.00 0.00 0.00 1.85
144 145 6.844097 AGAAAATGTTTTAATCCGGCCTAA 57.156 33.333 0.00 0.00 0.00 2.69
145 146 6.209788 ACAAGAAAATGTTTTAATCCGGCCTA 59.790 34.615 0.00 0.00 0.00 3.93
146 147 5.011635 ACAAGAAAATGTTTTAATCCGGCCT 59.988 36.000 0.00 0.00 0.00 5.19
147 148 5.234752 ACAAGAAAATGTTTTAATCCGGCC 58.765 37.500 0.00 0.00 0.00 6.13
148 149 5.923684 TGACAAGAAAATGTTTTAATCCGGC 59.076 36.000 0.00 0.00 32.57 6.13
149 150 8.532977 AATGACAAGAAAATGTTTTAATCCGG 57.467 30.769 0.00 0.00 32.57 5.14
159 160 9.260002 GGTTTGACATAAATGACAAGAAAATGT 57.740 29.630 7.66 0.00 41.76 2.71
160 161 9.258826 TGGTTTGACATAAATGACAAGAAAATG 57.741 29.630 7.66 0.00 41.76 2.32
161 162 9.829507 TTGGTTTGACATAAATGACAAGAAAAT 57.170 25.926 7.66 0.00 41.76 1.82
162 163 9.658799 TTTGGTTTGACATAAATGACAAGAAAA 57.341 25.926 7.66 7.46 41.76 2.29
163 164 9.092876 GTTTGGTTTGACATAAATGACAAGAAA 57.907 29.630 7.66 6.52 41.76 2.52
164 165 8.474025 AGTTTGGTTTGACATAAATGACAAGAA 58.526 29.630 7.66 2.05 41.76 2.52
165 166 7.920151 CAGTTTGGTTTGACATAAATGACAAGA 59.080 33.333 7.66 0.00 41.76 3.02
166 167 7.706179 ACAGTTTGGTTTGACATAAATGACAAG 59.294 33.333 7.66 0.00 41.76 3.16
167 168 7.551585 ACAGTTTGGTTTGACATAAATGACAA 58.448 30.769 4.16 4.16 39.82 3.18
168 169 7.106439 ACAGTTTGGTTTGACATAAATGACA 57.894 32.000 0.00 0.00 0.00 3.58
169 170 6.640907 GGACAGTTTGGTTTGACATAAATGAC 59.359 38.462 0.00 0.00 0.00 3.06
170 171 6.322456 TGGACAGTTTGGTTTGACATAAATGA 59.678 34.615 0.00 0.00 0.00 2.57
171 172 6.511416 TGGACAGTTTGGTTTGACATAAATG 58.489 36.000 0.00 0.00 0.00 2.32
172 173 6.723298 TGGACAGTTTGGTTTGACATAAAT 57.277 33.333 0.00 0.00 0.00 1.40
173 174 6.723298 ATGGACAGTTTGGTTTGACATAAA 57.277 33.333 0.00 0.00 0.00 1.40
174 175 6.207810 GGTATGGACAGTTTGGTTTGACATAA 59.792 38.462 0.00 0.00 0.00 1.90
175 176 5.708230 GGTATGGACAGTTTGGTTTGACATA 59.292 40.000 0.00 0.00 0.00 2.29
176 177 4.522789 GGTATGGACAGTTTGGTTTGACAT 59.477 41.667 0.00 0.00 0.00 3.06
177 178 3.886505 GGTATGGACAGTTTGGTTTGACA 59.113 43.478 0.00 0.00 0.00 3.58
178 179 3.886505 TGGTATGGACAGTTTGGTTTGAC 59.113 43.478 0.00 0.00 0.00 3.18
179 180 4.141287 CTGGTATGGACAGTTTGGTTTGA 58.859 43.478 0.00 0.00 0.00 2.69
180 181 3.888930 ACTGGTATGGACAGTTTGGTTTG 59.111 43.478 0.00 0.00 46.38 2.93
181 182 4.178956 ACTGGTATGGACAGTTTGGTTT 57.821 40.909 0.00 0.00 46.38 3.27
182 183 3.876309 ACTGGTATGGACAGTTTGGTT 57.124 42.857 0.00 0.00 46.38 3.67
189 190 4.931661 ACGGTATAACTGGTATGGACAG 57.068 45.455 0.00 0.00 41.64 3.51
190 191 4.467082 ACAACGGTATAACTGGTATGGACA 59.533 41.667 0.00 0.00 0.00 4.02
191 192 4.807304 CACAACGGTATAACTGGTATGGAC 59.193 45.833 0.00 0.00 0.00 4.02
192 193 4.681244 GCACAACGGTATAACTGGTATGGA 60.681 45.833 0.00 0.00 0.00 3.41
193 194 3.558418 GCACAACGGTATAACTGGTATGG 59.442 47.826 0.00 0.00 0.00 2.74
194 195 4.185394 TGCACAACGGTATAACTGGTATG 58.815 43.478 0.00 0.00 0.00 2.39
195 196 4.475051 TGCACAACGGTATAACTGGTAT 57.525 40.909 0.00 0.00 0.00 2.73
196 197 3.957591 TGCACAACGGTATAACTGGTA 57.042 42.857 0.00 0.00 0.00 3.25
197 198 2.843401 TGCACAACGGTATAACTGGT 57.157 45.000 0.00 0.00 0.00 4.00
198 199 4.814234 ACATATGCACAACGGTATAACTGG 59.186 41.667 1.58 0.00 0.00 4.00
199 200 5.984233 ACATATGCACAACGGTATAACTG 57.016 39.130 1.58 0.00 0.00 3.16
200 201 9.366216 CATATACATATGCACAACGGTATAACT 57.634 33.333 1.58 0.00 34.37 2.24
201 202 9.361315 TCATATACATATGCACAACGGTATAAC 57.639 33.333 1.58 0.00 39.90 1.89
202 203 9.930693 TTCATATACATATGCACAACGGTATAA 57.069 29.630 1.58 0.00 39.90 0.98
203 204 9.930693 TTTCATATACATATGCACAACGGTATA 57.069 29.630 1.58 0.00 39.90 1.47
204 205 8.840833 TTTCATATACATATGCACAACGGTAT 57.159 30.769 1.58 0.00 39.90 2.73
205 206 7.386573 CCTTTCATATACATATGCACAACGGTA 59.613 37.037 1.58 0.00 39.90 4.02
206 207 6.204688 CCTTTCATATACATATGCACAACGGT 59.795 38.462 1.58 0.00 39.90 4.83
207 208 6.426633 TCCTTTCATATACATATGCACAACGG 59.573 38.462 1.58 2.71 39.90 4.44
208 209 7.290842 GTCCTTTCATATACATATGCACAACG 58.709 38.462 1.58 0.00 39.90 4.10
209 210 7.228507 TGGTCCTTTCATATACATATGCACAAC 59.771 37.037 1.58 0.88 39.90 3.32
210 211 7.228507 GTGGTCCTTTCATATACATATGCACAA 59.771 37.037 1.58 0.00 39.90 3.33
211 212 6.710295 GTGGTCCTTTCATATACATATGCACA 59.290 38.462 1.58 0.00 39.90 4.57
212 213 6.936900 AGTGGTCCTTTCATATACATATGCAC 59.063 38.462 1.58 5.48 39.90 4.57
213 214 7.078249 AGTGGTCCTTTCATATACATATGCA 57.922 36.000 1.58 0.00 39.90 3.96
214 215 8.094548 TGTAGTGGTCCTTTCATATACATATGC 58.905 37.037 1.58 0.00 39.90 3.14
215 216 9.996554 TTGTAGTGGTCCTTTCATATACATATG 57.003 33.333 0.00 0.00 41.10 1.78
216 217 9.998106 GTTGTAGTGGTCCTTTCATATACATAT 57.002 33.333 0.00 0.00 0.00 1.78
217 218 8.983789 TGTTGTAGTGGTCCTTTCATATACATA 58.016 33.333 0.00 0.00 0.00 2.29
218 219 7.857456 TGTTGTAGTGGTCCTTTCATATACAT 58.143 34.615 0.00 0.00 0.00 2.29
219 220 7.247456 TGTTGTAGTGGTCCTTTCATATACA 57.753 36.000 0.00 0.00 0.00 2.29
220 221 7.822822 ACTTGTTGTAGTGGTCCTTTCATATAC 59.177 37.037 0.00 0.00 0.00 1.47
221 222 7.822334 CACTTGTTGTAGTGGTCCTTTCATATA 59.178 37.037 0.00 0.00 41.43 0.86
222 223 6.655003 CACTTGTTGTAGTGGTCCTTTCATAT 59.345 38.462 0.00 0.00 41.43 1.78
223 224 5.995282 CACTTGTTGTAGTGGTCCTTTCATA 59.005 40.000 0.00 0.00 41.43 2.15
224 225 4.821805 CACTTGTTGTAGTGGTCCTTTCAT 59.178 41.667 0.00 0.00 41.43 2.57
225 226 4.080807 TCACTTGTTGTAGTGGTCCTTTCA 60.081 41.667 0.00 0.00 44.47 2.69
226 227 4.272748 GTCACTTGTTGTAGTGGTCCTTTC 59.727 45.833 0.00 0.00 44.47 2.62
227 228 4.196971 GTCACTTGTTGTAGTGGTCCTTT 58.803 43.478 0.00 0.00 44.47 3.11
228 229 3.199071 TGTCACTTGTTGTAGTGGTCCTT 59.801 43.478 0.00 0.00 44.47 3.36
229 230 2.769663 TGTCACTTGTTGTAGTGGTCCT 59.230 45.455 0.00 0.00 44.47 3.85
230 231 3.188159 TGTCACTTGTTGTAGTGGTCC 57.812 47.619 0.00 0.00 44.47 4.46
231 232 5.751243 AAATGTCACTTGTTGTAGTGGTC 57.249 39.130 0.00 0.00 44.47 4.02
232 233 6.524101 AAAAATGTCACTTGTTGTAGTGGT 57.476 33.333 0.00 0.00 44.47 4.16
233 234 6.631238 CGTAAAAATGTCACTTGTTGTAGTGG 59.369 38.462 0.00 0.00 44.47 4.00
234 235 6.631238 CCGTAAAAATGTCACTTGTTGTAGTG 59.369 38.462 0.00 0.00 45.46 2.74
235 236 6.238538 CCCGTAAAAATGTCACTTGTTGTAGT 60.239 38.462 0.00 0.00 0.00 2.73
242 243 5.467399 TGTACTCCCGTAAAAATGTCACTTG 59.533 40.000 0.00 0.00 0.00 3.16
288 292 8.827677 GTTCTAATTGGGTGTATCACTGTATTC 58.172 37.037 0.06 0.00 34.40 1.75
314 318 9.472361 AGTGTTTTCATTTGAATGATCTCTTTG 57.528 29.630 7.20 0.00 44.27 2.77
386 394 3.557595 GGATGACTTTATCCAGTGCTTCG 59.442 47.826 0.00 0.00 44.90 3.79
408 416 5.065731 GGAGATGCTTTCAGTTATGTTCTGG 59.934 44.000 0.00 0.00 34.15 3.86
409 417 5.645067 TGGAGATGCTTTCAGTTATGTTCTG 59.355 40.000 0.00 0.00 0.00 3.02
420 428 4.342092 TCGATATCACTGGAGATGCTTTCA 59.658 41.667 3.12 0.00 0.00 2.69
434 442 8.197988 ACTTCATTGGTTAACTTCGATATCAC 57.802 34.615 5.42 0.00 0.00 3.06
438 446 9.715121 AGTTTACTTCATTGGTTAACTTCGATA 57.285 29.630 5.42 0.00 34.35 2.92
474 482 9.496873 GGTGCTGGGTTTTAGTTTATTTTAATT 57.503 29.630 0.00 0.00 0.00 1.40
476 484 8.019656 TGGTGCTGGGTTTTAGTTTATTTTAA 57.980 30.769 0.00 0.00 0.00 1.52
483 491 4.022676 CGTAATGGTGCTGGGTTTTAGTTT 60.023 41.667 0.00 0.00 0.00 2.66
484 492 3.504520 CGTAATGGTGCTGGGTTTTAGTT 59.495 43.478 0.00 0.00 0.00 2.24
485 493 3.078837 CGTAATGGTGCTGGGTTTTAGT 58.921 45.455 0.00 0.00 0.00 2.24
486 494 3.078837 ACGTAATGGTGCTGGGTTTTAG 58.921 45.455 0.00 0.00 0.00 1.85
487 495 3.075884 GACGTAATGGTGCTGGGTTTTA 58.924 45.455 0.00 0.00 0.00 1.52
488 496 1.883926 GACGTAATGGTGCTGGGTTTT 59.116 47.619 0.00 0.00 0.00 2.43
658 678 7.169645 CGAAGAGAGTACTACTACAGTGATACC 59.830 44.444 0.00 0.00 38.24 2.73
659 679 7.169645 CCGAAGAGAGTACTACTACAGTGATAC 59.830 44.444 0.00 0.00 38.24 2.24
660 680 7.147759 ACCGAAGAGAGTACTACTACAGTGATA 60.148 40.741 0.00 0.00 38.24 2.15
663 683 5.177326 ACCGAAGAGAGTACTACTACAGTG 58.823 45.833 0.00 0.00 38.24 3.66
664 684 5.418676 GACCGAAGAGAGTACTACTACAGT 58.581 45.833 0.00 0.00 41.62 3.55
665 685 4.810491 GGACCGAAGAGAGTACTACTACAG 59.190 50.000 0.00 0.00 0.00 2.74
666 686 4.469227 AGGACCGAAGAGAGTACTACTACA 59.531 45.833 0.00 0.00 0.00 2.74
667 687 5.022282 AGGACCGAAGAGAGTACTACTAC 57.978 47.826 0.00 0.00 0.00 2.73
668 688 5.690464 AAGGACCGAAGAGAGTACTACTA 57.310 43.478 0.00 0.00 0.00 1.82
669 689 4.573021 AAGGACCGAAGAGAGTACTACT 57.427 45.455 0.00 0.00 0.00 2.57
670 690 5.641783 AAAAGGACCGAAGAGAGTACTAC 57.358 43.478 0.00 0.00 0.00 2.73
671 691 6.944862 AGTAAAAAGGACCGAAGAGAGTACTA 59.055 38.462 0.00 0.00 0.00 1.82
673 693 6.023357 AGTAAAAAGGACCGAAGAGAGTAC 57.977 41.667 0.00 0.00 0.00 2.73
674 694 6.008960 AGAGTAAAAAGGACCGAAGAGAGTA 58.991 40.000 0.00 0.00 0.00 2.59
675 695 4.833938 AGAGTAAAAAGGACCGAAGAGAGT 59.166 41.667 0.00 0.00 0.00 3.24
676 696 5.164954 CAGAGTAAAAAGGACCGAAGAGAG 58.835 45.833 0.00 0.00 0.00 3.20
677 697 4.560919 GCAGAGTAAAAAGGACCGAAGAGA 60.561 45.833 0.00 0.00 0.00 3.10
678 698 3.680458 GCAGAGTAAAAAGGACCGAAGAG 59.320 47.826 0.00 0.00 0.00 2.85
679 699 3.070446 TGCAGAGTAAAAAGGACCGAAGA 59.930 43.478 0.00 0.00 0.00 2.87
680 700 3.399330 TGCAGAGTAAAAAGGACCGAAG 58.601 45.455 0.00 0.00 0.00 3.79
681 701 3.478857 TGCAGAGTAAAAAGGACCGAA 57.521 42.857 0.00 0.00 0.00 4.30
682 702 3.695830 ATGCAGAGTAAAAAGGACCGA 57.304 42.857 0.00 0.00 0.00 4.69
688 708 9.774742 GACAAACCTAATATGCAGAGTAAAAAG 57.225 33.333 0.00 0.00 0.00 2.27
892 912 2.679837 CTCTGCACATTAGATTTGCCGT 59.320 45.455 0.00 0.00 35.26 5.68
920 940 4.579753 GTGTAGTAGTAATCCCTTCGCTCT 59.420 45.833 0.00 0.00 0.00 4.09
923 943 4.915158 AGTGTAGTAGTAATCCCTTCGC 57.085 45.455 0.00 0.00 0.00 4.70
926 946 9.364653 CCTAATGTAGTGTAGTAGTAATCCCTT 57.635 37.037 0.00 0.00 0.00 3.95
935 955 7.511268 ACCTCTCTCCTAATGTAGTGTAGTAG 58.489 42.308 0.00 0.00 0.00 2.57
938 958 7.227116 GTGTACCTCTCTCCTAATGTAGTGTAG 59.773 44.444 0.00 0.00 0.00 2.74
939 959 7.052873 GTGTACCTCTCTCCTAATGTAGTGTA 58.947 42.308 0.00 0.00 0.00 2.90
941 961 6.123651 AGTGTACCTCTCTCCTAATGTAGTG 58.876 44.000 0.00 0.00 0.00 2.74
947 967 7.945664 CCTAATGTAGTGTACCTCTCTCCTAAT 59.054 40.741 0.00 0.00 0.00 1.73
949 969 6.618610 TCCTAATGTAGTGTACCTCTCTCCTA 59.381 42.308 0.00 0.00 0.00 2.94
950 970 5.432390 TCCTAATGTAGTGTACCTCTCTCCT 59.568 44.000 0.00 0.00 0.00 3.69
953 973 6.387513 TCTCTCCTAATGTAGTGTACCTCTCT 59.612 42.308 0.00 0.00 0.00 3.10
957 977 5.399267 CCCTCTCTCCTAATGTAGTGTACCT 60.399 48.000 0.00 0.00 0.00 3.08
958 978 4.828387 CCCTCTCTCCTAATGTAGTGTACC 59.172 50.000 0.00 0.00 0.00 3.34
969 989 1.497286 GCCTCTCTCCCTCTCTCCTAA 59.503 57.143 0.00 0.00 0.00 2.69
1118 1165 2.282147 CTAGACTCGCTGCTGCTGCT 62.282 60.000 25.43 10.26 40.48 4.24
1124 1171 1.436195 CTCGCTCTAGACTCGCTGCT 61.436 60.000 0.00 0.00 0.00 4.24
1125 1172 1.010125 CTCGCTCTAGACTCGCTGC 60.010 63.158 5.10 0.00 0.00 5.25
1126 1173 1.003972 CTTCTCGCTCTAGACTCGCTG 60.004 57.143 5.10 2.17 0.00 5.18
1197 1250 1.602327 GCGACGGGACTAAGAAGGGT 61.602 60.000 0.00 0.00 0.00 4.34
1285 1350 3.618351 GAGAGTAGTAGTAGTGGGTGCA 58.382 50.000 0.00 0.00 0.00 4.57
1286 1351 2.950975 GGAGAGTAGTAGTAGTGGGTGC 59.049 54.545 0.00 0.00 0.00 5.01
1329 1402 6.313519 AGCATACACAAATCTAGAAAGGGA 57.686 37.500 0.00 0.00 0.00 4.20
1331 1404 6.678900 GCCAAGCATACACAAATCTAGAAAGG 60.679 42.308 0.00 0.00 0.00 3.11
1647 1720 3.490348 ACATGGTCAAGGTGAGAAAAGG 58.510 45.455 0.00 0.00 0.00 3.11
1648 1721 4.580167 TGAACATGGTCAAGGTGAGAAAAG 59.420 41.667 12.03 0.00 0.00 2.27
1808 1892 3.069158 GGGCCAAAGGATCAATCAATCAG 59.931 47.826 4.39 0.00 0.00 2.90
1827 1911 4.805719 GCTTTTGCTTTTACTCATATGGGC 59.194 41.667 1.33 0.00 43.35 5.36
2003 2087 3.557228 AGAATCCAATGCTCCTCTGTC 57.443 47.619 0.00 0.00 0.00 3.51
2004 2088 3.265221 TGAAGAATCCAATGCTCCTCTGT 59.735 43.478 0.00 0.00 0.00 3.41
2047 2131 1.680314 GGCCTTTGCTGCTTAGCCT 60.680 57.895 0.29 0.00 37.42 4.58
2052 2136 0.606604 CATTCAGGCCTTTGCTGCTT 59.393 50.000 0.00 0.00 37.74 3.91
2256 2553 1.148273 AAAGTGCAACGAGCCCTCA 59.852 52.632 0.00 0.00 45.86 3.86
2352 2652 0.314302 AACCGGTCTTCTGACACGAG 59.686 55.000 8.04 0.00 44.61 4.18
2418 2718 5.282055 ACTCTTCATCTTCACAGTCACAA 57.718 39.130 0.00 0.00 0.00 3.33
2424 2724 5.167121 CAGGTGTACTCTTCATCTTCACAG 58.833 45.833 0.00 0.00 0.00 3.66
2595 2895 3.777925 CACGAACCAGAAGCGGCG 61.778 66.667 0.51 0.51 0.00 6.46
2804 3112 1.219124 CTCCACCACCACCTCATCG 59.781 63.158 0.00 0.00 0.00 3.84
2815 3123 0.107361 CAGCATCATGAGCTCCACCA 60.107 55.000 12.15 0.00 41.14 4.17
2857 3165 2.490903 AGCAATCTTCACCAATGCAGAC 59.509 45.455 0.00 0.00 39.42 3.51
2947 3257 2.551071 GCTGCTGAGTCCTACCAAGTTT 60.551 50.000 0.00 0.00 0.00 2.66
3017 3329 4.225267 TGGATAACTCAAAACCTCTCCTCC 59.775 45.833 0.00 0.00 0.00 4.30
3018 3330 5.046231 ACTGGATAACTCAAAACCTCTCCTC 60.046 44.000 0.00 0.00 0.00 3.71
3019 3331 4.846940 ACTGGATAACTCAAAACCTCTCCT 59.153 41.667 0.00 0.00 0.00 3.69
3033 3349 3.134458 GCTATGGCAGACACTGGATAAC 58.866 50.000 0.00 0.00 38.54 1.89
3181 3500 3.989817 GCCACAACTTGCAGGATTAAAAG 59.010 43.478 1.40 0.00 0.00 2.27
3231 3561 1.469767 GCAGGAACAAATTCGGATGGC 60.470 52.381 0.00 0.00 35.48 4.40
3232 3562 1.818060 TGCAGGAACAAATTCGGATGG 59.182 47.619 0.00 0.00 35.48 3.51
3233 3563 3.057315 ACTTGCAGGAACAAATTCGGATG 60.057 43.478 1.40 0.00 35.48 3.51
3234 3564 3.157087 ACTTGCAGGAACAAATTCGGAT 58.843 40.909 1.40 0.00 35.48 4.18
3235 3565 2.582052 ACTTGCAGGAACAAATTCGGA 58.418 42.857 1.40 0.00 35.48 4.55
3236 3566 3.052036 CAACTTGCAGGAACAAATTCGG 58.948 45.455 1.40 0.00 35.48 4.30
3237 3567 3.486841 CACAACTTGCAGGAACAAATTCG 59.513 43.478 1.40 0.00 35.48 3.34
3251 3581 0.592637 TTGCTCCGATGCACAACTTG 59.407 50.000 0.00 0.00 43.20 3.16
3252 3582 0.593128 GTTGCTCCGATGCACAACTT 59.407 50.000 8.03 0.00 43.20 2.66
3253 3583 0.250467 AGTTGCTCCGATGCACAACT 60.250 50.000 11.22 11.22 45.86 3.16
3254 3584 0.166814 GAGTTGCTCCGATGCACAAC 59.833 55.000 7.36 7.36 43.20 3.32
3255 3585 0.955428 GGAGTTGCTCCGATGCACAA 60.955 55.000 0.00 0.00 41.08 3.33
3256 3586 1.375908 GGAGTTGCTCCGATGCACA 60.376 57.895 0.00 0.00 41.08 4.57
3257 3587 3.490890 GGAGTTGCTCCGATGCAC 58.509 61.111 0.00 0.00 41.08 4.57
3265 3595 2.409870 CGCCCCATTGGAGTTGCTC 61.410 63.158 3.62 0.00 35.39 4.26
3266 3596 2.361610 CGCCCCATTGGAGTTGCT 60.362 61.111 3.62 0.00 35.39 3.91
3267 3597 2.361104 TCGCCCCATTGGAGTTGC 60.361 61.111 3.62 0.53 35.07 4.17
3268 3598 2.046285 GGTCGCCCCATTGGAGTTG 61.046 63.158 3.62 0.00 35.07 3.16
3269 3599 2.355115 GGTCGCCCCATTGGAGTT 59.645 61.111 3.62 0.00 35.07 3.01
3279 3609 1.455032 CCCCTTTAATGGGTCGCCC 60.455 63.158 21.73 7.87 45.70 6.13
3280 3610 0.750546 GTCCCCTTTAATGGGTCGCC 60.751 60.000 21.73 6.06 45.70 5.54
3281 3611 0.750546 GGTCCCCTTTAATGGGTCGC 60.751 60.000 21.73 12.50 45.70 5.19
3282 3612 0.621609 TGGTCCCCTTTAATGGGTCG 59.378 55.000 21.73 10.16 45.70 4.79
3283 3613 2.453521 GTTGGTCCCCTTTAATGGGTC 58.546 52.381 21.73 14.91 45.70 4.46
3284 3614 1.272258 CGTTGGTCCCCTTTAATGGGT 60.272 52.381 21.73 0.00 45.70 4.51
3285 3615 1.272258 ACGTTGGTCCCCTTTAATGGG 60.272 52.381 17.77 17.77 46.68 4.00
3286 3616 2.209690 ACGTTGGTCCCCTTTAATGG 57.790 50.000 0.26 0.26 0.00 3.16
3287 3617 2.352323 GCAACGTTGGTCCCCTTTAATG 60.352 50.000 28.33 0.00 0.00 1.90
3288 3618 1.890489 GCAACGTTGGTCCCCTTTAAT 59.110 47.619 28.33 0.00 0.00 1.40
3289 3619 1.320507 GCAACGTTGGTCCCCTTTAA 58.679 50.000 28.33 0.00 0.00 1.52
3290 3620 0.885596 CGCAACGTTGGTCCCCTTTA 60.886 55.000 28.33 0.00 0.00 1.85
3298 3628 1.264826 GTTTGGATACGCAACGTTGGT 59.735 47.619 28.33 24.07 41.54 3.67
3532 4502 2.359230 GCGGCAGCTGGAAGAGTT 60.359 61.111 17.12 0.00 41.01 3.01
3641 4685 2.035626 CTGTGCGGTGGGGGAAAT 59.964 61.111 0.00 0.00 0.00 2.17
3642 4686 4.966787 GCTGTGCGGTGGGGGAAA 62.967 66.667 0.00 0.00 0.00 3.13
3908 5523 2.030717 CCAATATCTCCTCCTCGTCGTG 60.031 54.545 0.00 0.00 0.00 4.35
3969 5584 0.179004 AATGGAGCCACGGAACAACA 60.179 50.000 0.00 0.00 0.00 3.33
4101 6862 3.031736 ACATGCCTACTCATACGGAACT 58.968 45.455 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.