Multiple sequence alignment - TraesCS2A01G461400

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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 TraesCS2A01G461400 chr2A 100.000 2597 0 0 1 2597 707242622 707240026 0.000000e+00 4796
1 TraesCS2A01G461400 chr2A 91.294 402 30 5 6 405 707226444 707226046 6.320000e-151 544
2 TraesCS2A01G461400 chr2D 95.496 2198 63 5 403 2597 441866708 441864544 0.000000e+00 3478
3 TraesCS2A01G461400 chr2D 92.195 410 25 6 1 405 567679886 567679479 8.060000e-160 573
4 TraesCS2A01G461400 chr2D 90.196 408 33 6 1 405 567932904 567932501 2.290000e-145 525
5 TraesCS2A01G461400 chr5B 94.909 2200 93 9 402 2597 455767612 455769796 0.000000e+00 3424
6 TraesCS2A01G461400 chr5B 93.075 491 25 6 404 894 680542622 680542141 0.000000e+00 710
7 TraesCS2A01G461400 chr4A 94.811 2197 79 12 406 2597 577896267 577898433 0.000000e+00 3393
8 TraesCS2A01G461400 chr4A 93.851 1057 52 8 428 1480 721923186 721924233 0.000000e+00 1580
9 TraesCS2A01G461400 chr4A 96.491 855 22 3 1746 2597 721924243 721925092 0.000000e+00 1406
10 TraesCS2A01G461400 chr2B 95.137 1645 73 3 957 2594 764417904 764416260 0.000000e+00 2588
11 TraesCS2A01G461400 chr2B 94.292 1349 61 10 741 2082 112483787 112482448 0.000000e+00 2050
12 TraesCS2A01G461400 chr2B 91.440 514 34 4 406 918 112484291 112483787 0.000000e+00 697
13 TraesCS2A01G461400 chr2B 89.873 237 20 2 173 405 680447276 680447040 4.200000e-78 302
14 TraesCS2A01G461400 chr1B 93.577 1697 64 14 408 2094 655064662 655063001 0.000000e+00 2488
15 TraesCS2A01G461400 chr5D 93.935 1319 67 6 402 1719 384262497 384263803 0.000000e+00 1980
16 TraesCS2A01G461400 chr5D 95.358 1034 44 3 1187 2217 448748302 448749334 0.000000e+00 1640
17 TraesCS2A01G461400 chr5D 92.268 957 49 4 1644 2597 384263770 384264704 0.000000e+00 1334
18 TraesCS2A01G461400 chr5D 92.139 776 47 6 408 1183 448747442 448748203 0.000000e+00 1083
19 TraesCS2A01G461400 chr7D 91.987 1273 65 7 589 1855 41119045 41117804 0.000000e+00 1751
20 TraesCS2A01G461400 chr7D 94.821 753 33 3 1851 2597 41112981 41112229 0.000000e+00 1170
21 TraesCS2A01G461400 chr7B 90.366 1038 85 10 1441 2470 680271357 680272387 0.000000e+00 1349
22 TraesCS2A01G461400 chr3B 92.745 827 55 4 1775 2597 485684835 485685660 0.000000e+00 1190


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 TraesCS2A01G461400 chr2A 707240026 707242622 2596 True 4796.0 4796 100.0000 1 2597 1 chr2A.!!$R2 2596
1 TraesCS2A01G461400 chr2D 441864544 441866708 2164 True 3478.0 3478 95.4960 403 2597 1 chr2D.!!$R1 2194
2 TraesCS2A01G461400 chr5B 455767612 455769796 2184 False 3424.0 3424 94.9090 402 2597 1 chr5B.!!$F1 2195
3 TraesCS2A01G461400 chr4A 577896267 577898433 2166 False 3393.0 3393 94.8110 406 2597 1 chr4A.!!$F1 2191
4 TraesCS2A01G461400 chr4A 721923186 721925092 1906 False 1493.0 1580 95.1710 428 2597 2 chr4A.!!$F2 2169
5 TraesCS2A01G461400 chr2B 764416260 764417904 1644 True 2588.0 2588 95.1370 957 2594 1 chr2B.!!$R2 1637
6 TraesCS2A01G461400 chr2B 112482448 112484291 1843 True 1373.5 2050 92.8660 406 2082 2 chr2B.!!$R3 1676
7 TraesCS2A01G461400 chr1B 655063001 655064662 1661 True 2488.0 2488 93.5770 408 2094 1 chr1B.!!$R1 1686
8 TraesCS2A01G461400 chr5D 384262497 384264704 2207 False 1657.0 1980 93.1015 402 2597 2 chr5D.!!$F1 2195
9 TraesCS2A01G461400 chr5D 448747442 448749334 1892 False 1361.5 1640 93.7485 408 2217 2 chr5D.!!$F2 1809
10 TraesCS2A01G461400 chr7D 41117804 41119045 1241 True 1751.0 1751 91.9870 589 1855 1 chr7D.!!$R2 1266
11 TraesCS2A01G461400 chr7D 41112229 41112981 752 True 1170.0 1170 94.8210 1851 2597 1 chr7D.!!$R1 746
12 TraesCS2A01G461400 chr7B 680271357 680272387 1030 False 1349.0 1349 90.3660 1441 2470 1 chr7B.!!$F1 1029
13 TraesCS2A01G461400 chr3B 485684835 485685660 825 False 1190.0 1190 92.7450 1775 2597 1 chr3B.!!$F1 822

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
225 226 0.035152 TCAAGCGGACATGGATTGCT 60.035 50.0 0.0 0.0 37.53 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 2300 3.27096 TCCTTCTCCTCTCCTTCTAGCTT 59.729 47.826 0.0 0.0 0.0 3.74 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
29 30 9.084533 AGTTAAAGGGCAAGTATTTTATTCACA 57.915 29.630 0.00 0.00 0.00 3.58
30 31 9.869757 GTTAAAGGGCAAGTATTTTATTCACAT 57.130 29.630 0.00 0.00 0.00 3.21
33 34 9.869757 AAAGGGCAAGTATTTTATTCACATAAC 57.130 29.630 0.00 0.00 0.00 1.89
34 35 8.588290 AGGGCAAGTATTTTATTCACATAACA 57.412 30.769 0.00 0.00 0.00 2.41
35 36 9.030452 AGGGCAAGTATTTTATTCACATAACAA 57.970 29.630 0.00 0.00 0.00 2.83
36 37 9.646427 GGGCAAGTATTTTATTCACATAACAAA 57.354 29.630 0.00 0.00 0.00 2.83
54 55 9.916397 CATAACAAAAATAGTTCGATACTCACC 57.084 33.333 3.94 0.00 38.33 4.02
55 56 7.972832 AACAAAAATAGTTCGATACTCACCA 57.027 32.000 3.94 0.00 38.33 4.17
56 57 7.972832 ACAAAAATAGTTCGATACTCACCAA 57.027 32.000 3.94 0.00 38.33 3.67
57 58 8.385898 ACAAAAATAGTTCGATACTCACCAAA 57.614 30.769 3.94 0.00 38.33 3.28
58 59 9.010029 ACAAAAATAGTTCGATACTCACCAAAT 57.990 29.630 3.94 0.00 38.33 2.32
63 64 9.915629 AATAGTTCGATACTCACCAAATATCTC 57.084 33.333 3.94 0.00 38.33 2.75
64 65 7.589958 AGTTCGATACTCACCAAATATCTCT 57.410 36.000 0.00 0.00 28.23 3.10
65 66 8.012957 AGTTCGATACTCACCAAATATCTCTT 57.987 34.615 0.00 0.00 28.23 2.85
66 67 9.132923 AGTTCGATACTCACCAAATATCTCTTA 57.867 33.333 0.00 0.00 28.23 2.10
67 68 9.745880 GTTCGATACTCACCAAATATCTCTTAA 57.254 33.333 0.00 0.00 0.00 1.85
103 104 9.813446 ATACATACTCCTACCTTTTAAAGTTCG 57.187 33.333 3.91 0.00 0.00 3.95
104 105 7.899973 ACATACTCCTACCTTTTAAAGTTCGA 58.100 34.615 3.91 0.00 0.00 3.71
105 106 8.370182 ACATACTCCTACCTTTTAAAGTTCGAA 58.630 33.333 3.91 0.00 0.00 3.71
106 107 9.379791 CATACTCCTACCTTTTAAAGTTCGAAT 57.620 33.333 0.00 0.00 0.00 3.34
108 109 8.768957 ACTCCTACCTTTTAAAGTTCGAATAC 57.231 34.615 0.00 0.00 0.00 1.89
109 110 8.591940 ACTCCTACCTTTTAAAGTTCGAATACT 58.408 33.333 0.00 0.00 0.00 2.12
127 128 9.537192 TCGAATACTATTCATTTTACCAATCGT 57.463 29.630 9.08 0.00 0.00 3.73
128 129 9.793245 CGAATACTATTCATTTTACCAATCGTC 57.207 33.333 9.08 0.00 0.00 4.20
132 133 8.658499 ACTATTCATTTTACCAATCGTCTACC 57.342 34.615 0.00 0.00 0.00 3.18
133 134 8.483758 ACTATTCATTTTACCAATCGTCTACCT 58.516 33.333 0.00 0.00 0.00 3.08
134 135 9.326413 CTATTCATTTTACCAATCGTCTACCTT 57.674 33.333 0.00 0.00 0.00 3.50
135 136 6.978343 TCATTTTACCAATCGTCTACCTTG 57.022 37.500 0.00 0.00 0.00 3.61
136 137 5.878116 TCATTTTACCAATCGTCTACCTTGG 59.122 40.000 7.29 7.29 44.06 3.61
137 138 3.899052 TTACCAATCGTCTACCTTGGG 57.101 47.619 11.63 0.00 43.02 4.12
138 139 1.946984 ACCAATCGTCTACCTTGGGA 58.053 50.000 11.63 0.00 43.02 4.37
139 140 2.478292 ACCAATCGTCTACCTTGGGAT 58.522 47.619 11.63 0.00 43.02 3.85
140 141 2.434702 ACCAATCGTCTACCTTGGGATC 59.565 50.000 11.63 0.00 43.02 3.36
141 142 2.434336 CCAATCGTCTACCTTGGGATCA 59.566 50.000 0.00 0.00 36.58 2.92
142 143 3.118408 CCAATCGTCTACCTTGGGATCAA 60.118 47.826 0.00 0.00 36.58 2.57
143 144 4.513442 CAATCGTCTACCTTGGGATCAAA 58.487 43.478 0.00 0.00 31.77 2.69
144 145 3.604875 TCGTCTACCTTGGGATCAAAC 57.395 47.619 0.00 0.00 31.77 2.93
145 146 3.170717 TCGTCTACCTTGGGATCAAACT 58.829 45.455 0.00 0.00 31.77 2.66
146 147 3.581332 TCGTCTACCTTGGGATCAAACTT 59.419 43.478 0.00 0.00 31.77 2.66
147 148 4.041198 TCGTCTACCTTGGGATCAAACTTT 59.959 41.667 0.00 0.00 31.77 2.66
148 149 4.154195 CGTCTACCTTGGGATCAAACTTTG 59.846 45.833 0.00 0.00 31.77 2.77
149 150 5.070685 GTCTACCTTGGGATCAAACTTTGT 58.929 41.667 1.44 0.00 31.77 2.83
150 151 5.181433 GTCTACCTTGGGATCAAACTTTGTC 59.819 44.000 1.44 0.00 31.77 3.18
151 152 3.909732 ACCTTGGGATCAAACTTTGTCA 58.090 40.909 1.44 0.00 31.77 3.58
152 153 3.636764 ACCTTGGGATCAAACTTTGTCAC 59.363 43.478 1.44 1.48 31.77 3.67
153 154 3.304659 CCTTGGGATCAAACTTTGTCACG 60.305 47.826 1.44 0.00 31.77 4.35
154 155 1.606668 TGGGATCAAACTTTGTCACGC 59.393 47.619 1.44 4.24 0.00 5.34
155 156 1.606668 GGGATCAAACTTTGTCACGCA 59.393 47.619 1.44 0.00 0.00 5.24
156 157 2.034053 GGGATCAAACTTTGTCACGCAA 59.966 45.455 1.44 0.00 34.87 4.85
157 158 3.305335 GGGATCAAACTTTGTCACGCAAT 60.305 43.478 1.44 0.00 36.89 3.56
158 159 4.298332 GGATCAAACTTTGTCACGCAATT 58.702 39.130 1.44 0.00 36.89 2.32
159 160 4.382754 GGATCAAACTTTGTCACGCAATTC 59.617 41.667 1.44 0.00 36.89 2.17
160 161 3.358775 TCAAACTTTGTCACGCAATTCG 58.641 40.909 1.44 0.00 45.38 3.34
161 162 1.753956 AACTTTGTCACGCAATTCGC 58.246 45.000 0.00 0.00 43.23 4.70
162 163 0.040425 ACTTTGTCACGCAATTCGCC 60.040 50.000 0.00 0.00 43.23 5.54
163 164 0.729140 CTTTGTCACGCAATTCGCCC 60.729 55.000 0.00 0.00 43.23 6.13
164 165 2.136196 TTTGTCACGCAATTCGCCCC 62.136 55.000 0.00 0.00 43.23 5.80
165 166 4.160635 GTCACGCAATTCGCCCCG 62.161 66.667 0.00 0.00 43.23 5.73
183 184 2.125106 GGCACCGCCTCGAATTCT 60.125 61.111 3.52 0.00 46.69 2.40
184 185 1.143183 GGCACCGCCTCGAATTCTA 59.857 57.895 3.52 0.00 46.69 2.10
185 186 0.249911 GGCACCGCCTCGAATTCTAT 60.250 55.000 3.52 0.00 46.69 1.98
186 187 1.583054 GCACCGCCTCGAATTCTATT 58.417 50.000 3.52 0.00 0.00 1.73
187 188 1.527311 GCACCGCCTCGAATTCTATTC 59.473 52.381 3.52 0.00 0.00 1.75
188 189 2.803492 GCACCGCCTCGAATTCTATTCT 60.803 50.000 3.52 0.00 0.00 2.40
189 190 2.797156 CACCGCCTCGAATTCTATTCTG 59.203 50.000 3.52 0.00 0.00 3.02
190 191 2.693591 ACCGCCTCGAATTCTATTCTGA 59.306 45.455 3.52 0.00 0.00 3.27
191 192 3.322254 ACCGCCTCGAATTCTATTCTGAT 59.678 43.478 3.52 0.00 0.00 2.90
192 193 3.923461 CCGCCTCGAATTCTATTCTGATC 59.077 47.826 3.52 0.00 0.00 2.92
193 194 4.550422 CGCCTCGAATTCTATTCTGATCA 58.450 43.478 3.52 0.00 0.00 2.92
194 195 4.984785 CGCCTCGAATTCTATTCTGATCAA 59.015 41.667 3.52 0.00 0.00 2.57
195 196 5.636965 CGCCTCGAATTCTATTCTGATCAAT 59.363 40.000 3.52 0.00 0.00 2.57
196 197 6.400834 CGCCTCGAATTCTATTCTGATCAATG 60.401 42.308 3.52 0.00 0.00 2.82
197 198 6.128336 GCCTCGAATTCTATTCTGATCAATGG 60.128 42.308 3.52 0.00 0.00 3.16
198 199 7.157347 CCTCGAATTCTATTCTGATCAATGGA 58.843 38.462 3.52 0.00 0.00 3.41
199 200 7.823310 CCTCGAATTCTATTCTGATCAATGGAT 59.177 37.037 3.52 0.00 36.13 3.41
200 201 8.543862 TCGAATTCTATTCTGATCAATGGATG 57.456 34.615 3.52 0.00 32.67 3.51
201 202 7.118825 TCGAATTCTATTCTGATCAATGGATGC 59.881 37.037 3.52 0.00 32.67 3.91
202 203 7.119407 CGAATTCTATTCTGATCAATGGATGCT 59.881 37.037 3.52 0.00 32.67 3.79
203 204 8.707796 AATTCTATTCTGATCAATGGATGCTT 57.292 30.769 0.00 0.00 32.67 3.91
204 205 7.506328 TTCTATTCTGATCAATGGATGCTTG 57.494 36.000 0.00 0.00 32.67 4.01
205 206 6.834107 TCTATTCTGATCAATGGATGCTTGA 58.166 36.000 0.00 2.61 37.06 3.02
206 207 7.459234 TCTATTCTGATCAATGGATGCTTGAT 58.541 34.615 10.21 10.21 44.04 2.57
220 221 2.028420 CTTGATCAAGCGGACATGGA 57.972 50.000 21.96 0.00 0.00 3.41
221 222 2.569059 CTTGATCAAGCGGACATGGAT 58.431 47.619 21.96 0.00 0.00 3.41
222 223 2.715749 TGATCAAGCGGACATGGATT 57.284 45.000 0.00 0.00 0.00 3.01
223 224 2.291365 TGATCAAGCGGACATGGATTG 58.709 47.619 0.00 0.00 32.34 2.67
224 225 1.002033 GATCAAGCGGACATGGATTGC 60.002 52.381 0.00 0.00 31.22 3.56
225 226 0.035152 TCAAGCGGACATGGATTGCT 60.035 50.000 0.00 0.00 37.53 3.91
226 227 1.209261 TCAAGCGGACATGGATTGCTA 59.791 47.619 0.00 0.00 34.19 3.49
227 228 1.331756 CAAGCGGACATGGATTGCTAC 59.668 52.381 0.00 0.00 34.19 3.58
228 229 0.541392 AGCGGACATGGATTGCTACA 59.459 50.000 0.00 0.00 33.37 2.74
229 230 0.657840 GCGGACATGGATTGCTACAC 59.342 55.000 0.00 0.00 0.00 2.90
230 231 1.743772 GCGGACATGGATTGCTACACT 60.744 52.381 0.00 0.00 0.00 3.55
231 232 1.935873 CGGACATGGATTGCTACACTG 59.064 52.381 0.00 0.00 0.00 3.66
232 233 1.672881 GGACATGGATTGCTACACTGC 59.327 52.381 0.00 0.00 0.00 4.40
233 234 2.636830 GACATGGATTGCTACACTGCT 58.363 47.619 0.00 0.00 0.00 4.24
234 235 2.611292 GACATGGATTGCTACACTGCTC 59.389 50.000 0.00 0.00 0.00 4.26
235 236 1.596260 CATGGATTGCTACACTGCTCG 59.404 52.381 0.00 0.00 0.00 5.03
236 237 0.108186 TGGATTGCTACACTGCTCGG 60.108 55.000 0.00 0.00 0.00 4.63
237 238 0.108138 GGATTGCTACACTGCTCGGT 60.108 55.000 0.00 0.00 0.00 4.69
238 239 1.676014 GGATTGCTACACTGCTCGGTT 60.676 52.381 0.00 0.00 0.00 4.44
239 240 2.076863 GATTGCTACACTGCTCGGTTT 58.923 47.619 0.00 0.00 0.00 3.27
240 241 2.823924 TTGCTACACTGCTCGGTTTA 57.176 45.000 0.00 0.00 0.00 2.01
241 242 2.363788 TGCTACACTGCTCGGTTTAG 57.636 50.000 0.00 0.00 0.00 1.85
242 243 1.616865 TGCTACACTGCTCGGTTTAGT 59.383 47.619 4.53 0.00 0.00 2.24
243 244 1.993370 GCTACACTGCTCGGTTTAGTG 59.007 52.381 0.00 0.00 45.48 2.74
244 245 2.352421 GCTACACTGCTCGGTTTAGTGA 60.352 50.000 10.24 0.00 43.35 3.41
245 246 2.150397 ACACTGCTCGGTTTAGTGAC 57.850 50.000 10.24 0.00 43.35 3.67
246 247 1.687123 ACACTGCTCGGTTTAGTGACT 59.313 47.619 10.24 0.00 43.35 3.41
247 248 2.288273 ACACTGCTCGGTTTAGTGACTC 60.288 50.000 10.24 0.00 43.35 3.36
248 249 1.961394 ACTGCTCGGTTTAGTGACTCA 59.039 47.619 0.00 0.00 0.00 3.41
249 250 2.364324 ACTGCTCGGTTTAGTGACTCAA 59.636 45.455 0.00 0.00 0.00 3.02
250 251 3.181469 ACTGCTCGGTTTAGTGACTCAAA 60.181 43.478 0.00 0.00 0.00 2.69
251 252 3.799366 TGCTCGGTTTAGTGACTCAAAA 58.201 40.909 0.00 0.00 0.00 2.44
252 253 4.385825 TGCTCGGTTTAGTGACTCAAAAT 58.614 39.130 0.00 0.00 0.00 1.82
253 254 5.543714 TGCTCGGTTTAGTGACTCAAAATA 58.456 37.500 0.00 0.00 0.00 1.40
254 255 5.407387 TGCTCGGTTTAGTGACTCAAAATAC 59.593 40.000 0.00 0.00 0.00 1.89
255 256 5.407387 GCTCGGTTTAGTGACTCAAAATACA 59.593 40.000 0.00 0.00 0.00 2.29
256 257 6.092259 GCTCGGTTTAGTGACTCAAAATACAT 59.908 38.462 0.00 0.00 0.00 2.29
257 258 7.591006 TCGGTTTAGTGACTCAAAATACATC 57.409 36.000 0.00 0.00 0.00 3.06
258 259 7.156000 TCGGTTTAGTGACTCAAAATACATCA 58.844 34.615 0.00 0.00 0.00 3.07
259 260 7.822334 TCGGTTTAGTGACTCAAAATACATCAT 59.178 33.333 0.00 0.00 0.00 2.45
260 261 9.093970 CGGTTTAGTGACTCAAAATACATCATA 57.906 33.333 0.00 0.00 0.00 2.15
268 269 9.942850 TGACTCAAAATACATCATAGAAGAACA 57.057 29.630 0.00 0.00 0.00 3.18
276 277 9.911788 AATACATCATAGAAGAACATGAAAGGT 57.088 29.630 0.00 0.00 34.96 3.50
278 279 8.048534 ACATCATAGAAGAACATGAAAGGTTG 57.951 34.615 0.00 0.00 43.10 3.77
279 280 7.667219 ACATCATAGAAGAACATGAAAGGTTGT 59.333 33.333 0.00 0.00 43.10 3.32
280 281 8.517878 CATCATAGAAGAACATGAAAGGTTGTT 58.482 33.333 0.00 0.00 46.93 2.83
281 282 9.739276 ATCATAGAAGAACATGAAAGGTTGTTA 57.261 29.630 0.00 0.00 44.26 2.41
282 283 9.567776 TCATAGAAGAACATGAAAGGTTGTTAA 57.432 29.630 0.00 0.00 44.26 2.01
285 286 8.926715 AGAAGAACATGAAAGGTTGTTAAAAC 57.073 30.769 0.00 0.00 44.26 2.43
286 287 8.527810 AGAAGAACATGAAAGGTTGTTAAAACA 58.472 29.630 0.00 0.00 44.26 2.83
287 288 9.313118 GAAGAACATGAAAGGTTGTTAAAACAT 57.687 29.630 0.00 0.00 44.26 2.71
288 289 8.647143 AGAACATGAAAGGTTGTTAAAACATG 57.353 30.769 0.00 0.00 43.10 3.21
289 290 8.257306 AGAACATGAAAGGTTGTTAAAACATGT 58.743 29.630 0.00 0.00 43.10 3.21
290 291 9.522804 GAACATGAAAGGTTGTTAAAACATGTA 57.477 29.630 0.00 0.00 43.10 2.29
319 320 8.915057 AATTTCATAGAACCTGTATCATGGAG 57.085 34.615 0.00 0.00 0.00 3.86
320 321 7.437713 TTTCATAGAACCTGTATCATGGAGT 57.562 36.000 0.00 0.00 0.00 3.85
321 322 7.437713 TTCATAGAACCTGTATCATGGAGTT 57.562 36.000 0.00 0.00 0.00 3.01
322 323 7.437713 TCATAGAACCTGTATCATGGAGTTT 57.562 36.000 0.00 0.00 0.00 2.66
323 324 7.500992 TCATAGAACCTGTATCATGGAGTTTC 58.499 38.462 0.00 0.00 0.00 2.78
324 325 5.104259 AGAACCTGTATCATGGAGTTTCC 57.896 43.478 0.00 0.00 36.96 3.13
325 326 3.933861 ACCTGTATCATGGAGTTTCCC 57.066 47.619 0.00 0.00 35.03 3.97
326 327 3.464828 ACCTGTATCATGGAGTTTCCCT 58.535 45.455 0.00 0.00 35.03 4.20
327 328 3.852578 ACCTGTATCATGGAGTTTCCCTT 59.147 43.478 0.00 0.00 35.03 3.95
328 329 5.036916 ACCTGTATCATGGAGTTTCCCTTA 58.963 41.667 0.00 0.00 35.03 2.69
329 330 5.672194 ACCTGTATCATGGAGTTTCCCTTAT 59.328 40.000 0.00 0.00 35.03 1.73
330 331 6.160459 ACCTGTATCATGGAGTTTCCCTTATT 59.840 38.462 0.00 0.00 35.03 1.40
331 332 7.062957 CCTGTATCATGGAGTTTCCCTTATTT 58.937 38.462 0.00 0.00 35.03 1.40
332 333 7.561356 CCTGTATCATGGAGTTTCCCTTATTTT 59.439 37.037 0.00 0.00 35.03 1.82
333 334 8.519799 TGTATCATGGAGTTTCCCTTATTTTC 57.480 34.615 0.00 0.00 35.03 2.29
334 335 6.699575 ATCATGGAGTTTCCCTTATTTTCG 57.300 37.500 0.00 0.00 35.03 3.46
335 336 5.566469 TCATGGAGTTTCCCTTATTTTCGT 58.434 37.500 0.00 0.00 35.03 3.85
336 337 5.414454 TCATGGAGTTTCCCTTATTTTCGTG 59.586 40.000 0.00 0.00 35.03 4.35
337 338 4.076394 TGGAGTTTCCCTTATTTTCGTGG 58.924 43.478 0.00 0.00 35.03 4.94
338 339 4.077108 GGAGTTTCCCTTATTTTCGTGGT 58.923 43.478 0.00 0.00 0.00 4.16
339 340 4.521639 GGAGTTTCCCTTATTTTCGTGGTT 59.478 41.667 0.00 0.00 0.00 3.67
340 341 5.010314 GGAGTTTCCCTTATTTTCGTGGTTT 59.990 40.000 0.00 0.00 0.00 3.27
341 342 6.461927 GGAGTTTCCCTTATTTTCGTGGTTTT 60.462 38.462 0.00 0.00 0.00 2.43
342 343 6.277605 AGTTTCCCTTATTTTCGTGGTTTTG 58.722 36.000 0.00 0.00 0.00 2.44
343 344 4.857509 TCCCTTATTTTCGTGGTTTTGG 57.142 40.909 0.00 0.00 0.00 3.28
344 345 4.471548 TCCCTTATTTTCGTGGTTTTGGA 58.528 39.130 0.00 0.00 0.00 3.53
345 346 5.081032 TCCCTTATTTTCGTGGTTTTGGAT 58.919 37.500 0.00 0.00 0.00 3.41
346 347 6.246919 TCCCTTATTTTCGTGGTTTTGGATA 58.753 36.000 0.00 0.00 0.00 2.59
347 348 6.893005 TCCCTTATTTTCGTGGTTTTGGATAT 59.107 34.615 0.00 0.00 0.00 1.63
348 349 6.978080 CCCTTATTTTCGTGGTTTTGGATATG 59.022 38.462 0.00 0.00 0.00 1.78
349 350 7.363443 CCCTTATTTTCGTGGTTTTGGATATGT 60.363 37.037 0.00 0.00 0.00 2.29
350 351 7.487829 CCTTATTTTCGTGGTTTTGGATATGTG 59.512 37.037 0.00 0.00 0.00 3.21
351 352 3.840890 TTCGTGGTTTTGGATATGTGC 57.159 42.857 0.00 0.00 0.00 4.57
352 353 2.784347 TCGTGGTTTTGGATATGTGCA 58.216 42.857 0.00 0.00 0.00 4.57
353 354 2.486203 TCGTGGTTTTGGATATGTGCAC 59.514 45.455 10.75 10.75 0.00 4.57
354 355 2.227626 CGTGGTTTTGGATATGTGCACA 59.772 45.455 24.08 24.08 0.00 4.57
355 356 3.119531 CGTGGTTTTGGATATGTGCACAT 60.120 43.478 33.20 33.20 40.22 3.21
356 357 4.095632 CGTGGTTTTGGATATGTGCACATA 59.904 41.667 35.03 35.03 42.38 2.29
357 358 5.392487 CGTGGTTTTGGATATGTGCACATAA 60.392 40.000 36.12 22.76 41.60 1.90
358 359 6.035843 GTGGTTTTGGATATGTGCACATAAG 58.964 40.000 36.12 0.00 41.60 1.73
359 360 5.043248 GGTTTTGGATATGTGCACATAAGC 58.957 41.667 36.12 29.41 41.60 3.09
360 361 4.916983 TTTGGATATGTGCACATAAGCC 57.083 40.909 36.12 34.70 41.60 4.35
361 362 2.862541 TGGATATGTGCACATAAGCCC 58.137 47.619 35.21 32.57 41.60 5.19
362 363 2.442878 TGGATATGTGCACATAAGCCCT 59.557 45.455 35.21 25.12 41.60 5.19
363 364 3.650461 TGGATATGTGCACATAAGCCCTA 59.350 43.478 35.21 25.04 41.60 3.53
364 365 4.003648 GGATATGTGCACATAAGCCCTAC 58.996 47.826 36.12 20.63 41.60 3.18
365 366 4.504864 GGATATGTGCACATAAGCCCTACA 60.505 45.833 36.12 17.85 41.60 2.74
366 367 3.582998 ATGTGCACATAAGCCCTACAT 57.417 42.857 30.50 2.60 34.26 2.29
367 368 2.917933 TGTGCACATAAGCCCTACATC 58.082 47.619 17.42 0.00 0.00 3.06
368 369 2.505407 TGTGCACATAAGCCCTACATCT 59.495 45.455 17.42 0.00 0.00 2.90
369 370 3.134458 GTGCACATAAGCCCTACATCTC 58.866 50.000 13.17 0.00 0.00 2.75
370 371 3.041211 TGCACATAAGCCCTACATCTCT 58.959 45.455 0.00 0.00 0.00 3.10
371 372 4.039245 GTGCACATAAGCCCTACATCTCTA 59.961 45.833 13.17 0.00 0.00 2.43
372 373 4.039245 TGCACATAAGCCCTACATCTCTAC 59.961 45.833 0.00 0.00 0.00 2.59
373 374 4.282195 GCACATAAGCCCTACATCTCTACT 59.718 45.833 0.00 0.00 0.00 2.57
374 375 5.777802 CACATAAGCCCTACATCTCTACTG 58.222 45.833 0.00 0.00 0.00 2.74
375 376 4.282195 ACATAAGCCCTACATCTCTACTGC 59.718 45.833 0.00 0.00 0.00 4.40
376 377 2.765689 AGCCCTACATCTCTACTGCT 57.234 50.000 0.00 0.00 0.00 4.24
377 378 2.593026 AGCCCTACATCTCTACTGCTC 58.407 52.381 0.00 0.00 0.00 4.26
378 379 1.268352 GCCCTACATCTCTACTGCTCG 59.732 57.143 0.00 0.00 0.00 5.03
379 380 2.577700 CCCTACATCTCTACTGCTCGT 58.422 52.381 0.00 0.00 0.00 4.18
380 381 2.952978 CCCTACATCTCTACTGCTCGTT 59.047 50.000 0.00 0.00 0.00 3.85
381 382 3.381908 CCCTACATCTCTACTGCTCGTTT 59.618 47.826 0.00 0.00 0.00 3.60
382 383 4.355437 CCTACATCTCTACTGCTCGTTTG 58.645 47.826 0.00 0.00 0.00 2.93
383 384 4.096532 CCTACATCTCTACTGCTCGTTTGA 59.903 45.833 0.00 0.00 0.00 2.69
384 385 4.727507 ACATCTCTACTGCTCGTTTGAT 57.272 40.909 0.00 0.00 0.00 2.57
385 386 4.428209 ACATCTCTACTGCTCGTTTGATG 58.572 43.478 0.00 0.00 34.52 3.07
386 387 2.881074 TCTCTACTGCTCGTTTGATGC 58.119 47.619 0.00 0.00 0.00 3.91
387 388 2.493675 TCTCTACTGCTCGTTTGATGCT 59.506 45.455 0.00 0.00 0.00 3.79
388 389 2.602211 CTCTACTGCTCGTTTGATGCTG 59.398 50.000 0.00 0.00 0.00 4.41
389 390 2.029020 TCTACTGCTCGTTTGATGCTGT 60.029 45.455 0.00 0.00 40.78 4.40
390 391 1.597742 ACTGCTCGTTTGATGCTGTT 58.402 45.000 0.00 0.00 35.85 3.16
391 392 1.265095 ACTGCTCGTTTGATGCTGTTG 59.735 47.619 0.00 0.00 35.85 3.33
392 393 0.592637 TGCTCGTTTGATGCTGTTGG 59.407 50.000 0.00 0.00 0.00 3.77
393 394 0.109597 GCTCGTTTGATGCTGTTGGG 60.110 55.000 0.00 0.00 0.00 4.12
394 395 1.522668 CTCGTTTGATGCTGTTGGGA 58.477 50.000 0.00 0.00 0.00 4.37
395 396 2.086869 CTCGTTTGATGCTGTTGGGAT 58.913 47.619 0.00 0.00 0.00 3.85
396 397 3.270027 CTCGTTTGATGCTGTTGGGATA 58.730 45.455 0.00 0.00 0.00 2.59
397 398 3.879295 CTCGTTTGATGCTGTTGGGATAT 59.121 43.478 0.00 0.00 0.00 1.63
398 399 4.269183 TCGTTTGATGCTGTTGGGATATT 58.731 39.130 0.00 0.00 0.00 1.28
399 400 5.432645 TCGTTTGATGCTGTTGGGATATTA 58.567 37.500 0.00 0.00 0.00 0.98
400 401 6.061441 TCGTTTGATGCTGTTGGGATATTAT 58.939 36.000 0.00 0.00 0.00 1.28
401 402 6.545666 TCGTTTGATGCTGTTGGGATATTATT 59.454 34.615 0.00 0.00 0.00 1.40
537 538 1.202651 CCTGAGACCGTTCCAAACAGT 60.203 52.381 0.00 0.00 0.00 3.55
553 554 0.107017 CAGTCTGGCCGGGATTTCAT 60.107 55.000 12.87 0.00 0.00 2.57
635 639 0.924090 CGCCAGATCGAGCACTTTAC 59.076 55.000 2.38 0.00 0.00 2.01
754 759 1.361993 GATCTGCTCCAGCGACGAT 59.638 57.895 0.00 0.00 45.83 3.73
760 765 0.593618 GCTCCAGCGACGATGATCTA 59.406 55.000 15.87 0.00 0.00 1.98
827 1003 4.320456 CCTCCTATGGCGCCGCAT 62.320 66.667 23.90 13.63 0.00 4.73
828 1004 2.281070 CTCCTATGGCGCCGCATT 60.281 61.111 23.90 9.15 0.00 3.56
829 1005 1.893808 CTCCTATGGCGCCGCATTT 60.894 57.895 23.90 6.41 0.00 2.32
830 1006 2.121564 CTCCTATGGCGCCGCATTTG 62.122 60.000 23.90 8.08 0.00 2.32
831 1007 2.332514 CTATGGCGCCGCATTTGG 59.667 61.111 23.90 3.42 0.00 3.28
914 1090 5.382664 AAGTGGGAAAAAGTAGGTTCTGA 57.617 39.130 0.00 0.00 0.00 3.27
1096 1275 2.212761 TTGGGGGTGATGAGGGGT 59.787 61.111 0.00 0.00 0.00 4.95
1144 1323 0.827507 TTTGCAGGAGGTCAAAGGGC 60.828 55.000 0.00 0.00 0.00 5.19
1450 1725 3.002656 AGTGCAAGTTGTTGAGAATGTCG 59.997 43.478 4.48 0.00 35.46 4.35
1594 1873 5.531122 TGTAGTTGACAGTGAGCTAGTTT 57.469 39.130 0.00 0.00 32.86 2.66
1820 2168 4.081420 TGAAGATTCAGAAGTGGTAGAGCC 60.081 45.833 0.00 0.00 33.39 4.70
1877 2247 4.473444 AGAGAAACAAAAGGCTGGATTGA 58.527 39.130 13.01 0.00 0.00 2.57
2068 2444 6.966534 ATGACAGTGAAATTCCAAACTTCT 57.033 33.333 0.00 0.00 0.00 2.85
2251 2627 1.612462 CCAGCAGGACAAGCAGATTCA 60.612 52.381 0.00 0.00 36.89 2.57
2361 2739 3.056322 AGCACTTCATTCTTGCAAATCCC 60.056 43.478 0.00 0.00 38.81 3.85
2574 2952 5.363580 AGTTTGTTTGGATCCAACTGACAAT 59.636 36.000 30.25 20.13 35.48 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.084533 TGTGAATAAAATACTTGCCCTTTAACT 57.915 29.630 0.00 0.00 0.00 2.24
4 5 9.869757 ATGTGAATAAAATACTTGCCCTTTAAC 57.130 29.630 0.00 0.00 0.00 2.01
7 8 9.869757 GTTATGTGAATAAAATACTTGCCCTTT 57.130 29.630 0.00 0.00 0.00 3.11
8 9 9.030452 TGTTATGTGAATAAAATACTTGCCCTT 57.970 29.630 0.00 0.00 0.00 3.95
9 10 8.588290 TGTTATGTGAATAAAATACTTGCCCT 57.412 30.769 0.00 0.00 0.00 5.19
10 11 9.646427 TTTGTTATGTGAATAAAATACTTGCCC 57.354 29.630 0.00 0.00 0.00 5.36
28 29 9.916397 GGTGAGTATCGAACTATTTTTGTTATG 57.084 33.333 0.00 0.00 39.07 1.90
29 30 9.661563 TGGTGAGTATCGAACTATTTTTGTTAT 57.338 29.630 0.00 0.00 39.07 1.89
30 31 9.491675 TTGGTGAGTATCGAACTATTTTTGTTA 57.508 29.630 0.00 0.00 39.07 2.41
31 32 7.972832 TGGTGAGTATCGAACTATTTTTGTT 57.027 32.000 0.00 0.00 39.07 2.83
32 33 7.972832 TTGGTGAGTATCGAACTATTTTTGT 57.027 32.000 0.00 0.00 39.07 2.83
37 38 9.915629 GAGATATTTGGTGAGTATCGAACTATT 57.084 33.333 0.00 0.00 39.07 1.73
38 39 9.303116 AGAGATATTTGGTGAGTATCGAACTAT 57.697 33.333 0.00 0.00 39.07 2.12
39 40 8.693120 AGAGATATTTGGTGAGTATCGAACTA 57.307 34.615 0.00 0.00 39.07 2.24
40 41 7.589958 AGAGATATTTGGTGAGTATCGAACT 57.410 36.000 0.00 0.00 42.80 3.01
41 42 9.745880 TTAAGAGATATTTGGTGAGTATCGAAC 57.254 33.333 0.00 0.00 38.61 3.95
77 78 9.813446 CGAACTTTAAAAGGTAGGAGTATGTAT 57.187 33.333 0.00 0.00 0.00 2.29
78 79 9.023962 TCGAACTTTAAAAGGTAGGAGTATGTA 57.976 33.333 0.00 0.00 0.00 2.29
79 80 7.899973 TCGAACTTTAAAAGGTAGGAGTATGT 58.100 34.615 0.00 0.00 0.00 2.29
80 81 8.767478 TTCGAACTTTAAAAGGTAGGAGTATG 57.233 34.615 0.00 0.00 0.00 2.39
82 83 9.860898 GTATTCGAACTTTAAAAGGTAGGAGTA 57.139 33.333 0.00 0.00 0.00 2.59
83 84 8.591940 AGTATTCGAACTTTAAAAGGTAGGAGT 58.408 33.333 0.00 0.00 0.00 3.85
84 85 8.999220 AGTATTCGAACTTTAAAAGGTAGGAG 57.001 34.615 0.00 0.00 0.00 3.69
101 102 9.537192 ACGATTGGTAAAATGAATAGTATTCGA 57.463 29.630 16.29 7.65 0.00 3.71
102 103 9.793245 GACGATTGGTAAAATGAATAGTATTCG 57.207 33.333 16.29 4.82 0.00 3.34
106 107 9.754382 GGTAGACGATTGGTAAAATGAATAGTA 57.246 33.333 0.00 0.00 0.00 1.82
107 108 8.483758 AGGTAGACGATTGGTAAAATGAATAGT 58.516 33.333 0.00 0.00 0.00 2.12
108 109 8.888579 AGGTAGACGATTGGTAAAATGAATAG 57.111 34.615 0.00 0.00 0.00 1.73
109 110 9.104965 CAAGGTAGACGATTGGTAAAATGAATA 57.895 33.333 0.00 0.00 0.00 1.75
110 111 7.067008 CCAAGGTAGACGATTGGTAAAATGAAT 59.933 37.037 0.00 0.00 38.92 2.57
111 112 6.373216 CCAAGGTAGACGATTGGTAAAATGAA 59.627 38.462 0.00 0.00 38.92 2.57
112 113 5.878116 CCAAGGTAGACGATTGGTAAAATGA 59.122 40.000 0.00 0.00 38.92 2.57
113 114 5.065988 CCCAAGGTAGACGATTGGTAAAATG 59.934 44.000 11.96 0.00 41.60 2.32
114 115 5.045432 TCCCAAGGTAGACGATTGGTAAAAT 60.045 40.000 11.96 0.00 41.60 1.82
115 116 4.286549 TCCCAAGGTAGACGATTGGTAAAA 59.713 41.667 11.96 0.00 41.60 1.52
116 117 3.839490 TCCCAAGGTAGACGATTGGTAAA 59.161 43.478 11.96 0.00 41.60 2.01
117 118 3.443052 TCCCAAGGTAGACGATTGGTAA 58.557 45.455 11.96 1.39 41.60 2.85
118 119 3.104519 TCCCAAGGTAGACGATTGGTA 57.895 47.619 11.96 0.00 41.60 3.25
119 120 1.946984 TCCCAAGGTAGACGATTGGT 58.053 50.000 11.96 0.00 41.60 3.67
120 121 2.434336 TGATCCCAAGGTAGACGATTGG 59.566 50.000 7.84 7.84 42.59 3.16
121 122 3.819564 TGATCCCAAGGTAGACGATTG 57.180 47.619 0.00 0.00 0.00 2.67
122 123 4.225267 AGTTTGATCCCAAGGTAGACGATT 59.775 41.667 0.00 0.00 33.23 3.34
123 124 3.775316 AGTTTGATCCCAAGGTAGACGAT 59.225 43.478 0.00 0.00 33.23 3.73
124 125 3.170717 AGTTTGATCCCAAGGTAGACGA 58.829 45.455 0.00 0.00 33.23 4.20
125 126 3.611766 AGTTTGATCCCAAGGTAGACG 57.388 47.619 0.00 0.00 33.23 4.18
126 127 5.070685 ACAAAGTTTGATCCCAAGGTAGAC 58.929 41.667 22.23 0.00 33.23 2.59
127 128 5.163141 TGACAAAGTTTGATCCCAAGGTAGA 60.163 40.000 22.23 0.00 33.23 2.59
128 129 5.048713 GTGACAAAGTTTGATCCCAAGGTAG 60.049 44.000 22.23 0.00 33.23 3.18
129 130 4.825085 GTGACAAAGTTTGATCCCAAGGTA 59.175 41.667 22.23 0.00 33.23 3.08
130 131 3.636764 GTGACAAAGTTTGATCCCAAGGT 59.363 43.478 22.23 0.00 33.23 3.50
131 132 3.304659 CGTGACAAAGTTTGATCCCAAGG 60.305 47.826 22.23 6.38 33.23 3.61
132 133 3.853307 GCGTGACAAAGTTTGATCCCAAG 60.853 47.826 22.23 14.91 33.23 3.61
133 134 2.034053 GCGTGACAAAGTTTGATCCCAA 59.966 45.455 22.23 0.00 0.00 4.12
134 135 1.606668 GCGTGACAAAGTTTGATCCCA 59.393 47.619 22.23 10.70 0.00 4.37
135 136 1.606668 TGCGTGACAAAGTTTGATCCC 59.393 47.619 22.23 6.60 0.00 3.85
136 137 3.347958 TTGCGTGACAAAGTTTGATCC 57.652 42.857 22.23 10.69 34.56 3.36
137 138 4.087085 CGAATTGCGTGACAAAGTTTGATC 59.913 41.667 22.23 14.91 42.86 2.92
138 139 3.974401 CGAATTGCGTGACAAAGTTTGAT 59.026 39.130 22.23 6.51 42.86 2.57
139 140 3.358775 CGAATTGCGTGACAAAGTTTGA 58.641 40.909 22.23 0.00 42.86 2.69
140 141 2.097925 GCGAATTGCGTGACAAAGTTTG 60.098 45.455 14.13 14.13 42.86 2.93
141 142 2.116366 GCGAATTGCGTGACAAAGTTT 58.884 42.857 0.00 0.00 42.86 2.66
142 143 1.753956 GCGAATTGCGTGACAAAGTT 58.246 45.000 0.00 0.00 42.86 2.66
143 144 3.454941 GCGAATTGCGTGACAAAGT 57.545 47.368 0.00 0.00 42.86 2.66
167 168 1.527311 GAATAGAATTCGAGGCGGTGC 59.473 52.381 0.00 0.00 0.00 5.01
168 169 2.797156 CAGAATAGAATTCGAGGCGGTG 59.203 50.000 0.00 0.00 0.00 4.94
169 170 2.693591 TCAGAATAGAATTCGAGGCGGT 59.306 45.455 0.00 0.00 0.00 5.68
170 171 3.371102 TCAGAATAGAATTCGAGGCGG 57.629 47.619 0.00 0.00 0.00 6.13
171 172 4.550422 TGATCAGAATAGAATTCGAGGCG 58.450 43.478 0.00 0.00 0.00 5.52
172 173 6.128336 CCATTGATCAGAATAGAATTCGAGGC 60.128 42.308 0.00 0.00 0.00 4.70
173 174 7.157347 TCCATTGATCAGAATAGAATTCGAGG 58.843 38.462 0.00 0.00 0.00 4.63
174 175 8.657729 CATCCATTGATCAGAATAGAATTCGAG 58.342 37.037 0.00 0.00 0.00 4.04
175 176 7.118825 GCATCCATTGATCAGAATAGAATTCGA 59.881 37.037 0.00 0.00 0.00 3.71
176 177 7.119407 AGCATCCATTGATCAGAATAGAATTCG 59.881 37.037 0.00 0.00 0.00 3.34
177 178 8.338072 AGCATCCATTGATCAGAATAGAATTC 57.662 34.615 0.00 0.00 0.00 2.17
178 179 8.577296 CAAGCATCCATTGATCAGAATAGAATT 58.423 33.333 0.00 0.00 0.00 2.17
179 180 7.942894 TCAAGCATCCATTGATCAGAATAGAAT 59.057 33.333 0.00 0.00 31.86 2.40
180 181 7.284820 TCAAGCATCCATTGATCAGAATAGAA 58.715 34.615 0.00 0.00 31.86 2.10
181 182 6.834107 TCAAGCATCCATTGATCAGAATAGA 58.166 36.000 0.00 0.00 31.86 1.98
182 183 7.689446 ATCAAGCATCCATTGATCAGAATAG 57.311 36.000 0.00 0.00 42.33 1.73
201 202 2.028420 TCCATGTCCGCTTGATCAAG 57.972 50.000 27.82 27.82 41.24 3.02
202 203 2.684374 CAATCCATGTCCGCTTGATCAA 59.316 45.455 8.12 8.12 0.00 2.57
203 204 2.291365 CAATCCATGTCCGCTTGATCA 58.709 47.619 0.00 0.00 0.00 2.92
204 205 1.002033 GCAATCCATGTCCGCTTGATC 60.002 52.381 0.00 0.00 0.00 2.92
205 206 1.027357 GCAATCCATGTCCGCTTGAT 58.973 50.000 0.00 0.00 0.00 2.57
206 207 0.035152 AGCAATCCATGTCCGCTTGA 60.035 50.000 0.00 0.00 0.00 3.02
207 208 1.331756 GTAGCAATCCATGTCCGCTTG 59.668 52.381 2.10 0.00 34.18 4.01
208 209 1.065491 TGTAGCAATCCATGTCCGCTT 60.065 47.619 2.10 0.00 34.18 4.68
209 210 0.541392 TGTAGCAATCCATGTCCGCT 59.459 50.000 0.00 0.00 36.72 5.52
210 211 0.657840 GTGTAGCAATCCATGTCCGC 59.342 55.000 0.00 0.00 0.00 5.54
211 212 1.935873 CAGTGTAGCAATCCATGTCCG 59.064 52.381 0.00 0.00 0.00 4.79
212 213 1.672881 GCAGTGTAGCAATCCATGTCC 59.327 52.381 0.00 0.00 0.00 4.02
213 214 2.611292 GAGCAGTGTAGCAATCCATGTC 59.389 50.000 0.00 0.00 36.85 3.06
214 215 2.636830 GAGCAGTGTAGCAATCCATGT 58.363 47.619 0.00 0.00 36.85 3.21
215 216 1.596260 CGAGCAGTGTAGCAATCCATG 59.404 52.381 0.00 0.00 36.85 3.66
216 217 1.473965 CCGAGCAGTGTAGCAATCCAT 60.474 52.381 0.00 0.00 36.85 3.41
217 218 0.108186 CCGAGCAGTGTAGCAATCCA 60.108 55.000 0.00 0.00 36.85 3.41
218 219 0.108138 ACCGAGCAGTGTAGCAATCC 60.108 55.000 0.00 0.00 36.85 3.01
219 220 1.726853 AACCGAGCAGTGTAGCAATC 58.273 50.000 0.00 0.00 36.85 2.67
220 221 2.185004 AAACCGAGCAGTGTAGCAAT 57.815 45.000 0.00 0.00 36.85 3.56
221 222 2.036733 ACTAAACCGAGCAGTGTAGCAA 59.963 45.455 0.00 0.00 31.66 3.91
222 223 1.616865 ACTAAACCGAGCAGTGTAGCA 59.383 47.619 0.00 0.00 31.66 3.49
223 224 1.993370 CACTAAACCGAGCAGTGTAGC 59.007 52.381 0.00 0.00 35.91 3.58
224 225 3.057456 AGTCACTAAACCGAGCAGTGTAG 60.057 47.826 0.00 0.00 40.44 2.74
225 226 2.889045 AGTCACTAAACCGAGCAGTGTA 59.111 45.455 0.00 0.00 40.44 2.90
226 227 1.687123 AGTCACTAAACCGAGCAGTGT 59.313 47.619 0.00 0.00 40.44 3.55
227 228 2.288213 TGAGTCACTAAACCGAGCAGTG 60.288 50.000 0.00 0.00 40.83 3.66
228 229 1.961394 TGAGTCACTAAACCGAGCAGT 59.039 47.619 0.00 0.00 0.00 4.40
229 230 2.724977 TGAGTCACTAAACCGAGCAG 57.275 50.000 0.00 0.00 0.00 4.24
230 231 3.462483 TTTGAGTCACTAAACCGAGCA 57.538 42.857 0.00 0.00 0.00 4.26
231 232 5.407387 TGTATTTTGAGTCACTAAACCGAGC 59.593 40.000 0.00 0.00 0.00 5.03
232 233 7.330946 TGATGTATTTTGAGTCACTAAACCGAG 59.669 37.037 0.00 0.00 0.00 4.63
233 234 7.156000 TGATGTATTTTGAGTCACTAAACCGA 58.844 34.615 0.00 0.00 0.00 4.69
234 235 7.359262 TGATGTATTTTGAGTCACTAAACCG 57.641 36.000 0.00 0.00 0.00 4.44
242 243 9.942850 TGTTCTTCTATGATGTATTTTGAGTCA 57.057 29.630 0.00 0.00 0.00 3.41
250 251 9.911788 ACCTTTCATGTTCTTCTATGATGTATT 57.088 29.630 0.00 0.00 33.68 1.89
251 252 9.911788 AACCTTTCATGTTCTTCTATGATGTAT 57.088 29.630 0.00 0.00 33.68 2.29
252 253 9.166173 CAACCTTTCATGTTCTTCTATGATGTA 57.834 33.333 0.00 0.00 33.68 2.29
253 254 7.667219 ACAACCTTTCATGTTCTTCTATGATGT 59.333 33.333 0.00 0.00 33.68 3.06
254 255 8.048534 ACAACCTTTCATGTTCTTCTATGATG 57.951 34.615 0.00 0.00 33.68 3.07
255 256 8.641498 AACAACCTTTCATGTTCTTCTATGAT 57.359 30.769 0.00 0.00 34.84 2.45
256 257 9.567776 TTAACAACCTTTCATGTTCTTCTATGA 57.432 29.630 0.00 0.00 40.14 2.15
260 261 8.527810 TGTTTTAACAACCTTTCATGTTCTTCT 58.472 29.630 0.00 0.00 40.14 2.85
261 262 8.696410 TGTTTTAACAACCTTTCATGTTCTTC 57.304 30.769 0.00 0.00 40.14 2.87
262 263 9.097257 CATGTTTTAACAACCTTTCATGTTCTT 57.903 29.630 0.00 0.00 43.03 2.52
263 264 8.257306 ACATGTTTTAACAACCTTTCATGTTCT 58.743 29.630 0.00 0.00 43.03 3.01
264 265 8.419076 ACATGTTTTAACAACCTTTCATGTTC 57.581 30.769 0.00 0.00 43.03 3.18
294 295 8.497745 ACTCCATGATACAGGTTCTATGAAATT 58.502 33.333 0.00 0.00 0.00 1.82
295 296 8.038862 ACTCCATGATACAGGTTCTATGAAAT 57.961 34.615 0.00 0.00 0.00 2.17
296 297 7.437713 ACTCCATGATACAGGTTCTATGAAA 57.562 36.000 0.00 0.00 0.00 2.69
297 298 7.437713 AACTCCATGATACAGGTTCTATGAA 57.562 36.000 0.00 0.00 0.00 2.57
298 299 7.419057 GGAAACTCCATGATACAGGTTCTATGA 60.419 40.741 0.00 0.00 34.73 2.15
299 300 6.708054 GGAAACTCCATGATACAGGTTCTATG 59.292 42.308 0.00 0.00 34.73 2.23
300 301 6.183361 GGGAAACTCCATGATACAGGTTCTAT 60.183 42.308 0.00 0.00 38.64 1.98
301 302 5.130477 GGGAAACTCCATGATACAGGTTCTA 59.870 44.000 0.00 0.00 38.64 2.10
302 303 4.080299 GGGAAACTCCATGATACAGGTTCT 60.080 45.833 0.00 0.00 38.64 3.01
303 304 4.080299 AGGGAAACTCCATGATACAGGTTC 60.080 45.833 0.00 0.00 38.64 3.62
304 305 3.852578 AGGGAAACTCCATGATACAGGTT 59.147 43.478 0.00 0.00 38.64 3.50
305 306 3.464828 AGGGAAACTCCATGATACAGGT 58.535 45.455 0.00 0.00 38.64 4.00
306 307 4.510167 AAGGGAAACTCCATGATACAGG 57.490 45.455 0.00 0.00 38.64 4.00
307 308 8.525290 AAAATAAGGGAAACTCCATGATACAG 57.475 34.615 0.00 0.00 38.64 2.74
308 309 7.282224 CGAAAATAAGGGAAACTCCATGATACA 59.718 37.037 0.00 0.00 38.64 2.29
309 310 7.282450 ACGAAAATAAGGGAAACTCCATGATAC 59.718 37.037 0.00 0.00 38.64 2.24
310 311 7.282224 CACGAAAATAAGGGAAACTCCATGATA 59.718 37.037 0.00 0.00 38.64 2.15
311 312 6.095440 CACGAAAATAAGGGAAACTCCATGAT 59.905 38.462 0.00 0.00 38.64 2.45
312 313 5.414454 CACGAAAATAAGGGAAACTCCATGA 59.586 40.000 0.00 0.00 38.64 3.07
313 314 5.393027 CCACGAAAATAAGGGAAACTCCATG 60.393 44.000 0.00 0.00 38.64 3.66
314 315 4.705023 CCACGAAAATAAGGGAAACTCCAT 59.295 41.667 0.00 0.00 38.64 3.41
315 316 4.076394 CCACGAAAATAAGGGAAACTCCA 58.924 43.478 0.00 0.00 38.64 3.86
316 317 4.077108 ACCACGAAAATAAGGGAAACTCC 58.923 43.478 0.00 0.00 35.23 3.85
317 318 5.700722 AACCACGAAAATAAGGGAAACTC 57.299 39.130 0.00 0.00 0.00 3.01
318 319 6.277605 CAAAACCACGAAAATAAGGGAAACT 58.722 36.000 0.00 0.00 0.00 2.66
319 320 5.464057 CCAAAACCACGAAAATAAGGGAAAC 59.536 40.000 0.00 0.00 0.00 2.78
320 321 5.363005 TCCAAAACCACGAAAATAAGGGAAA 59.637 36.000 0.00 0.00 0.00 3.13
321 322 4.894114 TCCAAAACCACGAAAATAAGGGAA 59.106 37.500 0.00 0.00 0.00 3.97
322 323 4.471548 TCCAAAACCACGAAAATAAGGGA 58.528 39.130 0.00 0.00 0.00 4.20
323 324 4.857509 TCCAAAACCACGAAAATAAGGG 57.142 40.909 0.00 0.00 0.00 3.95
324 325 7.487829 CACATATCCAAAACCACGAAAATAAGG 59.512 37.037 0.00 0.00 0.00 2.69
325 326 7.009174 GCACATATCCAAAACCACGAAAATAAG 59.991 37.037 0.00 0.00 0.00 1.73
326 327 6.809196 GCACATATCCAAAACCACGAAAATAA 59.191 34.615 0.00 0.00 0.00 1.40
327 328 6.071896 TGCACATATCCAAAACCACGAAAATA 60.072 34.615 0.00 0.00 0.00 1.40
328 329 5.167845 GCACATATCCAAAACCACGAAAAT 58.832 37.500 0.00 0.00 0.00 1.82
329 330 4.038042 TGCACATATCCAAAACCACGAAAA 59.962 37.500 0.00 0.00 0.00 2.29
330 331 3.570125 TGCACATATCCAAAACCACGAAA 59.430 39.130 0.00 0.00 0.00 3.46
331 332 3.057876 GTGCACATATCCAAAACCACGAA 60.058 43.478 13.17 0.00 0.00 3.85
332 333 2.486203 GTGCACATATCCAAAACCACGA 59.514 45.455 13.17 0.00 0.00 4.35
333 334 2.227626 TGTGCACATATCCAAAACCACG 59.772 45.455 17.42 0.00 0.00 4.94
334 335 3.932545 TGTGCACATATCCAAAACCAC 57.067 42.857 17.42 0.00 0.00 4.16
335 336 5.394005 GCTTATGTGCACATATCCAAAACCA 60.394 40.000 33.93 18.11 38.49 3.67
336 337 5.043248 GCTTATGTGCACATATCCAAAACC 58.957 41.667 33.93 12.55 38.49 3.27
337 338 5.043248 GGCTTATGTGCACATATCCAAAAC 58.957 41.667 33.93 18.86 38.49 2.43
338 339 4.099266 GGGCTTATGTGCACATATCCAAAA 59.901 41.667 34.98 24.75 38.49 2.44
339 340 3.636300 GGGCTTATGTGCACATATCCAAA 59.364 43.478 34.98 25.26 38.49 3.28
340 341 3.117550 AGGGCTTATGTGCACATATCCAA 60.118 43.478 34.98 25.52 39.15 3.53
341 342 2.442878 AGGGCTTATGTGCACATATCCA 59.557 45.455 34.98 24.63 39.15 3.41
342 343 3.146104 AGGGCTTATGTGCACATATCC 57.854 47.619 33.93 32.26 39.15 2.59
343 344 4.641396 TGTAGGGCTTATGTGCACATATC 58.359 43.478 33.93 27.12 39.15 1.63
344 345 4.705110 TGTAGGGCTTATGTGCACATAT 57.295 40.909 33.93 23.09 39.15 1.78
345 346 4.347876 AGATGTAGGGCTTATGTGCACATA 59.652 41.667 31.03 31.03 39.15 2.29
346 347 3.137176 AGATGTAGGGCTTATGTGCACAT 59.863 43.478 33.20 33.20 39.15 3.21
347 348 2.505407 AGATGTAGGGCTTATGTGCACA 59.495 45.455 24.08 24.08 39.15 4.57
348 349 3.134458 GAGATGTAGGGCTTATGTGCAC 58.866 50.000 10.75 10.75 36.44 4.57
349 350 3.041211 AGAGATGTAGGGCTTATGTGCA 58.959 45.455 0.00 0.00 34.04 4.57
350 351 3.760580 AGAGATGTAGGGCTTATGTGC 57.239 47.619 0.00 0.00 0.00 4.57
351 352 5.777802 CAGTAGAGATGTAGGGCTTATGTG 58.222 45.833 0.00 0.00 0.00 3.21
352 353 4.282195 GCAGTAGAGATGTAGGGCTTATGT 59.718 45.833 0.00 0.00 0.00 2.29
353 354 4.526262 AGCAGTAGAGATGTAGGGCTTATG 59.474 45.833 0.00 0.00 0.00 1.90
354 355 4.746466 AGCAGTAGAGATGTAGGGCTTAT 58.254 43.478 0.00 0.00 0.00 1.73
355 356 4.145807 GAGCAGTAGAGATGTAGGGCTTA 58.854 47.826 0.00 0.00 0.00 3.09
356 357 2.962421 GAGCAGTAGAGATGTAGGGCTT 59.038 50.000 0.00 0.00 0.00 4.35
357 358 2.593026 GAGCAGTAGAGATGTAGGGCT 58.407 52.381 0.00 0.00 0.00 5.19
358 359 1.268352 CGAGCAGTAGAGATGTAGGGC 59.732 57.143 0.00 0.00 0.00 5.19
359 360 2.577700 ACGAGCAGTAGAGATGTAGGG 58.422 52.381 0.00 0.00 0.00 3.53
360 361 4.096532 TCAAACGAGCAGTAGAGATGTAGG 59.903 45.833 0.00 0.00 0.00 3.18
361 362 5.236655 TCAAACGAGCAGTAGAGATGTAG 57.763 43.478 0.00 0.00 0.00 2.74
362 363 5.582550 CATCAAACGAGCAGTAGAGATGTA 58.417 41.667 0.00 0.00 34.06 2.29
363 364 4.428209 CATCAAACGAGCAGTAGAGATGT 58.572 43.478 0.00 0.00 34.06 3.06
364 365 3.244814 GCATCAAACGAGCAGTAGAGATG 59.755 47.826 0.00 0.00 37.96 2.90
365 366 3.131933 AGCATCAAACGAGCAGTAGAGAT 59.868 43.478 0.00 0.00 0.00 2.75
366 367 2.493675 AGCATCAAACGAGCAGTAGAGA 59.506 45.455 0.00 0.00 0.00 3.10
367 368 2.602211 CAGCATCAAACGAGCAGTAGAG 59.398 50.000 0.00 0.00 0.00 2.43
368 369 2.029020 ACAGCATCAAACGAGCAGTAGA 60.029 45.455 0.00 0.00 0.00 2.59
369 370 2.341257 ACAGCATCAAACGAGCAGTAG 58.659 47.619 0.00 0.00 0.00 2.57
370 371 2.455674 ACAGCATCAAACGAGCAGTA 57.544 45.000 0.00 0.00 0.00 2.74
371 372 1.265095 CAACAGCATCAAACGAGCAGT 59.735 47.619 0.00 0.00 0.00 4.40
372 373 1.400629 CCAACAGCATCAAACGAGCAG 60.401 52.381 0.00 0.00 0.00 4.24
373 374 0.592637 CCAACAGCATCAAACGAGCA 59.407 50.000 0.00 0.00 0.00 4.26
374 375 0.109597 CCCAACAGCATCAAACGAGC 60.110 55.000 0.00 0.00 0.00 5.03
375 376 1.522668 TCCCAACAGCATCAAACGAG 58.477 50.000 0.00 0.00 0.00 4.18
376 377 2.198827 ATCCCAACAGCATCAAACGA 57.801 45.000 0.00 0.00 0.00 3.85
377 378 4.637483 AATATCCCAACAGCATCAAACG 57.363 40.909 0.00 0.00 0.00 3.60
380 381 8.805175 CCAATAATAATATCCCAACAGCATCAA 58.195 33.333 0.00 0.00 0.00 2.57
381 382 8.169393 TCCAATAATAATATCCCAACAGCATCA 58.831 33.333 0.00 0.00 0.00 3.07
382 383 8.579850 TCCAATAATAATATCCCAACAGCATC 57.420 34.615 0.00 0.00 0.00 3.91
383 384 8.954834 TTCCAATAATAATATCCCAACAGCAT 57.045 30.769 0.00 0.00 0.00 3.79
384 385 8.774546 TTTCCAATAATAATATCCCAACAGCA 57.225 30.769 0.00 0.00 0.00 4.41
400 401 9.602568 GGGTTTGTTTTAGACTTTTTCCAATAA 57.397 29.630 0.00 0.00 0.00 1.40
401 402 8.983789 AGGGTTTGTTTTAGACTTTTTCCAATA 58.016 29.630 0.00 0.00 0.00 1.90
537 538 2.230130 AAAATGAAATCCCGGCCAGA 57.770 45.000 2.24 0.00 0.00 3.86
564 568 1.063806 CGCCAACTCTCTCTGTTTCG 58.936 55.000 0.00 0.00 0.00 3.46
635 639 2.099405 GACTCCTCCTCTCTCAACTGG 58.901 57.143 0.00 0.00 0.00 4.00
734 739 1.153765 CGTCGCTGGAGCAGATCAA 60.154 57.895 0.00 0.00 42.21 2.57
827 1003 3.831323 TCAGAGAGGTCAAAATGCCAAA 58.169 40.909 0.00 0.00 0.00 3.28
828 1004 3.507162 TCAGAGAGGTCAAAATGCCAA 57.493 42.857 0.00 0.00 0.00 4.52
829 1005 3.149196 GTTCAGAGAGGTCAAAATGCCA 58.851 45.455 0.00 0.00 0.00 4.92
830 1006 3.149196 TGTTCAGAGAGGTCAAAATGCC 58.851 45.455 0.00 0.00 0.00 4.40
831 1007 4.380233 CCATGTTCAGAGAGGTCAAAATGC 60.380 45.833 0.00 0.00 0.00 3.56
832 1008 5.005740 TCCATGTTCAGAGAGGTCAAAATG 58.994 41.667 0.00 0.00 0.00 2.32
833 1009 5.246981 TCCATGTTCAGAGAGGTCAAAAT 57.753 39.130 0.00 0.00 0.00 1.82
932 1108 6.932960 ACCTTGTGCTAGTACGAACTAAAATT 59.067 34.615 6.48 0.00 37.75 1.82
1096 1275 5.566429 GCTTGTCTCTCTCAATCTCTGACAA 60.566 44.000 0.00 0.00 39.57 3.18
1144 1323 9.784680 CTTCAGTTCCATATGATCTTTCAAAAG 57.215 33.333 3.65 0.00 34.96 2.27
1594 1873 6.631971 TTGTGACACTGCAAATTCATCTTA 57.368 33.333 7.20 0.00 0.00 2.10
1820 2168 5.957798 TGAATTTTCTTGCATGCCTTCTAG 58.042 37.500 16.68 4.97 0.00 2.43
1877 2247 6.529220 AGAACTGCTTCACTTGTATCTCTTT 58.471 36.000 0.00 0.00 0.00 2.52
1927 2300 3.270960 TCCTTCTCCTCTCCTTCTAGCTT 59.729 47.826 0.00 0.00 0.00 3.74
2068 2444 5.592282 TGCTTTTGAAGACCATTGACAACTA 59.408 36.000 0.00 0.00 0.00 2.24
2282 2658 4.530875 CCTATTCTCTCTGTTTTGGGCAT 58.469 43.478 0.00 0.00 0.00 4.40
2361 2739 7.384660 GCTTTCATACTCTCTATCTTCCACATG 59.615 40.741 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.