Multiple sequence alignment - TraesCS1D01G000700

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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 TraesCS1D01G000700 chr1D 100.000 2741 0 0 1 2741 211267 208527 0.000000e+00 5062.0
1 TraesCS1D01G000700 chr1D 93.373 166 11 0 2576 2741 122222 122057 2.110000e-61 246.0
2 TraesCS1D01G000700 chr1D 86.905 84 7 2 2527 2607 122313 122231 1.050000e-14 91.6
3 TraesCS1D01G000700 chr1A 93.314 1705 89 11 381 2075 4052548 4054237 0.000000e+00 2494.0
4 TraesCS1D01G000700 chr1A 86.636 651 43 17 2134 2741 4054234 4054883 0.000000e+00 680.0
5 TraesCS1D01G000700 chr1A 73.184 537 106 20 1211 1738 4049931 4050438 2.830000e-35 159.0
6 TraesCS1D01G000700 chr1B 92.221 1337 73 18 587 1909 5175116 5176435 0.000000e+00 1864.0
7 TraesCS1D01G000700 chr1B 85.082 858 52 20 1907 2741 5176692 5177496 0.000000e+00 806.0
8 TraesCS1D01G000700 chr1B 84.884 258 37 1 342 599 5174843 5175098 2.710000e-65 259.0
9 TraesCS1D01G000700 chr1B 97.222 36 1 0 2068 2103 112354572 112354607 8.200000e-06 62.1
10 TraesCS1D01G000700 chr7B 91.979 187 13 2 17 202 643480952 643481137 7.530000e-66 261.0
11 TraesCS1D01G000700 chr7B 97.222 36 1 0 2068 2103 485475450 485475415 8.200000e-06 62.1
12 TraesCS1D01G000700 chr7D 90.050 201 18 2 3 202 15771447 15771646 2.710000e-65 259.0
13 TraesCS1D01G000700 chr7D 89.340 197 16 4 4 199 400193098 400192906 2.730000e-60 243.0
14 TraesCS1D01G000700 chr4B 89.055 201 20 2 3 202 446767883 446767684 5.860000e-62 248.0
15 TraesCS1D01G000700 chr2B 87.273 220 21 6 1 218 702720795 702721009 7.580000e-61 244.0
16 TraesCS1D01G000700 chr2B 88.060 201 20 4 3 202 199405412 199405215 4.560000e-58 235.0
17 TraesCS1D01G000700 chr2A 88.557 201 20 3 3 202 762186985 762186787 9.810000e-60 241.0
18 TraesCS1D01G000700 chr6D 88.060 201 21 3 3 202 343124504 343124702 4.560000e-58 235.0
19 TraesCS1D01G000700 chr4D 88.060 201 21 3 3 202 447335185 447334987 4.560000e-58 235.0
20 TraesCS1D01G000700 chr6B 82.051 78 8 3 2067 2138 114836286 114836363 8.200000e-06 62.1
21 TraesCS1D01G000700 chr6B 97.222 36 1 0 2068 2103 267798658 267798623 8.200000e-06 62.1
22 TraesCS1D01G000700 chr2D 97.222 36 1 0 2068 2103 549418167 549418202 8.200000e-06 62.1
23 TraesCS1D01G000700 chrUn 92.857 42 2 1 2060 2101 110290435 110290475 2.950000e-05 60.2
24 TraesCS1D01G000700 chrUn 92.857 42 2 1 2060 2101 187683144 187683184 2.950000e-05 60.2
25 TraesCS1D01G000700 chrUn 92.857 42 2 1 2060 2101 307658760 307658720 2.950000e-05 60.2


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 TraesCS1D01G000700 chr1D 208527 211267 2740 True 5062.000000 5062 100.000000 1 2741 1 chr1D.!!$R1 2740
1 TraesCS1D01G000700 chr1A 4049931 4054883 4952 False 1111.000000 2494 84.378000 381 2741 3 chr1A.!!$F1 2360
2 TraesCS1D01G000700 chr1B 5174843 5177496 2653 False 976.333333 1864 87.395667 342 2741 3 chr1B.!!$F2 2399

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
322 323 0.322366 TGATGAAACGCCTGGATGCA 60.322 50.0 0.00 0.00 0.0 3.96 F
1329 3607 0.322456 TGGTAATGTGGGAGCAGTGC 60.322 55.0 7.13 7.13 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1480 3758 0.909610 TGGCTAGAACCCAGACCCTG 60.910 60.000 0.00 0.00 0.00 4.45 R
2304 4882 1.068055 GCAACCAATCAGAGTGGCTTG 60.068 52.381 17.11 18.64 40.02 4.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.553079 TTGAAGCGCGAACAACTTTT 57.447 40.000 12.10 0.00 0.00 2.27
20 21 2.553079 TGAAGCGCGAACAACTTTTT 57.447 40.000 12.10 0.00 0.00 1.94
21 22 3.677190 TGAAGCGCGAACAACTTTTTA 57.323 38.095 12.10 0.00 0.00 1.52
22 23 4.017380 TGAAGCGCGAACAACTTTTTAA 57.983 36.364 12.10 0.00 0.00 1.52
24 25 4.497608 TGAAGCGCGAACAACTTTTTAAAG 59.502 37.500 12.10 0.80 41.73 1.85
25 26 2.787129 AGCGCGAACAACTTTTTAAAGC 59.213 40.909 12.10 0.00 39.63 3.51
26 27 2.532317 GCGCGAACAACTTTTTAAAGCA 59.468 40.909 12.10 0.00 39.63 3.91
27 28 3.598447 GCGCGAACAACTTTTTAAAGCAC 60.598 43.478 12.10 0.00 39.63 4.40
28 29 3.061469 CGCGAACAACTTTTTAAAGCACC 60.061 43.478 0.00 0.00 39.63 5.01
29 30 3.061469 GCGAACAACTTTTTAAAGCACCG 60.061 43.478 2.23 1.82 39.63 4.94
30 31 4.344448 CGAACAACTTTTTAAAGCACCGA 58.656 39.130 2.23 0.00 39.63 4.69
32 33 4.705337 ACAACTTTTTAAAGCACCGACA 57.295 36.364 2.23 0.00 39.63 4.35
33 34 5.257082 ACAACTTTTTAAAGCACCGACAT 57.743 34.783 2.23 0.00 39.63 3.06
34 35 5.656480 ACAACTTTTTAAAGCACCGACATT 58.344 33.333 2.23 0.00 39.63 2.71
35 36 6.103330 ACAACTTTTTAAAGCACCGACATTT 58.897 32.000 2.23 0.00 39.63 2.32
36 37 6.592220 ACAACTTTTTAAAGCACCGACATTTT 59.408 30.769 2.23 0.00 39.63 1.82
37 38 7.118535 ACAACTTTTTAAAGCACCGACATTTTT 59.881 29.630 2.23 0.00 39.63 1.94
65 66 9.425577 AGTTTTGAGAACAAATTTTTAAACGGA 57.574 25.926 0.00 0.00 43.99 4.69
66 67 9.683651 GTTTTGAGAACAAATTTTTAAACGGAG 57.316 29.630 0.00 0.00 43.99 4.63
67 68 9.640963 TTTTGAGAACAAATTTTTAAACGGAGA 57.359 25.926 0.00 0.00 43.99 3.71
68 69 9.640963 TTTGAGAACAAATTTTTAAACGGAGAA 57.359 25.926 0.00 0.00 40.47 2.87
70 71 8.244802 TGAGAACAAATTTTTAAACGGAGAACA 58.755 29.630 0.00 0.00 0.00 3.18
72 73 9.594478 AGAACAAATTTTTAAACGGAGAACAAT 57.406 25.926 0.00 0.00 0.00 2.71
84 85 7.477144 AACGGAGAACAATTTTGAAAAATCC 57.523 32.000 0.00 0.00 37.62 3.01
86 87 5.118510 CGGAGAACAATTTTGAAAAATCCCG 59.881 40.000 0.00 0.00 37.62 5.14
88 89 6.704050 GGAGAACAATTTTGAAAAATCCCGAA 59.296 34.615 0.00 0.00 37.62 4.30
112 113 4.385358 AATTTGGAAGCGTGAACTTTGT 57.615 36.364 0.00 0.00 0.00 2.83
113 114 3.859411 TTTGGAAGCGTGAACTTTGTT 57.141 38.095 0.00 0.00 0.00 2.83
114 115 3.859411 TTGGAAGCGTGAACTTTGTTT 57.141 38.095 0.00 0.00 0.00 2.83
115 116 3.859411 TGGAAGCGTGAACTTTGTTTT 57.141 38.095 0.00 0.00 0.00 2.43
116 117 3.506810 TGGAAGCGTGAACTTTGTTTTG 58.493 40.909 0.00 0.00 0.00 2.44
118 119 4.170256 GGAAGCGTGAACTTTGTTTTGAA 58.830 39.130 0.00 0.00 0.00 2.69
119 120 4.803613 GGAAGCGTGAACTTTGTTTTGAAT 59.196 37.500 0.00 0.00 0.00 2.57
120 121 5.974751 GGAAGCGTGAACTTTGTTTTGAATA 59.025 36.000 0.00 0.00 0.00 1.75
121 122 6.075046 GGAAGCGTGAACTTTGTTTTGAATAC 60.075 38.462 0.00 0.00 0.00 1.89
124 125 5.330498 GCGTGAACTTTGTTTTGAATACGTG 60.330 40.000 0.00 0.00 0.00 4.49
126 127 6.466413 CGTGAACTTTGTTTTGAATACGTGAA 59.534 34.615 0.00 0.00 0.00 3.18
130 131 8.522178 AACTTTGTTTTGAATACGTGAACAAA 57.478 26.923 0.00 10.56 43.71 2.83
131 132 8.522178 ACTTTGTTTTGAATACGTGAACAAAA 57.478 26.923 17.67 17.67 44.59 2.44
132 133 9.145865 ACTTTGTTTTGAATACGTGAACAAAAT 57.854 25.926 21.50 12.39 44.59 1.82
136 137 9.746711 TGTTTTGAATACGTGAACAAAATTTTG 57.253 25.926 25.73 25.73 41.74 2.44
137 138 9.959775 GTTTTGAATACGTGAACAAAATTTTGA 57.040 25.926 32.20 11.69 41.74 2.69
143 144 6.267500 ACGTGAACAAAATTTTGAAATCCG 57.733 33.333 32.20 26.63 40.55 4.18
144 145 5.233263 ACGTGAACAAAATTTTGAAATCCGG 59.767 36.000 32.20 21.03 40.55 5.14
145 146 5.233263 CGTGAACAAAATTTTGAAATCCGGT 59.767 36.000 32.20 8.94 40.55 5.28
147 148 7.560700 GTGAACAAAATTTTGAAATCCGGTAC 58.439 34.615 32.20 17.44 40.55 3.34
148 149 7.222999 GTGAACAAAATTTTGAAATCCGGTACA 59.777 33.333 32.20 14.88 40.55 2.90
149 150 7.928706 TGAACAAAATTTTGAAATCCGGTACAT 59.071 29.630 32.20 6.92 40.55 2.29
150 151 8.669946 AACAAAATTTTGAAATCCGGTACATT 57.330 26.923 32.20 12.04 40.55 2.71
152 153 9.114952 ACAAAATTTTGAAATCCGGTACATTTT 57.885 25.926 32.20 5.56 40.55 1.82
153 154 9.592720 CAAAATTTTGAAATCCGGTACATTTTC 57.407 29.630 23.72 5.61 40.55 2.29
154 155 9.554395 AAAATTTTGAAATCCGGTACATTTTCT 57.446 25.926 1.75 0.00 0.00 2.52
155 156 8.532977 AATTTTGAAATCCGGTACATTTTCTG 57.467 30.769 0.00 0.00 0.00 3.02
156 157 6.885952 TTTGAAATCCGGTACATTTTCTGA 57.114 33.333 0.00 0.00 0.00 3.27
157 158 6.885952 TTGAAATCCGGTACATTTTCTGAA 57.114 33.333 0.00 0.00 0.00 3.02
158 159 7.461182 TTGAAATCCGGTACATTTTCTGAAT 57.539 32.000 0.00 0.00 0.00 2.57
159 160 7.461182 TGAAATCCGGTACATTTTCTGAATT 57.539 32.000 0.00 0.00 0.00 2.17
160 161 7.891561 TGAAATCCGGTACATTTTCTGAATTT 58.108 30.769 0.00 0.00 0.00 1.82
162 163 9.503427 GAAATCCGGTACATTTTCTGAATTTAG 57.497 33.333 0.00 0.00 0.00 1.85
163 164 8.801882 AATCCGGTACATTTTCTGAATTTAGA 57.198 30.769 0.00 0.00 0.00 2.10
164 165 8.801882 ATCCGGTACATTTTCTGAATTTAGAA 57.198 30.769 8.50 8.50 35.02 2.10
165 166 8.624367 TCCGGTACATTTTCTGAATTTAGAAA 57.376 30.769 18.54 18.54 43.02 2.52
166 167 8.726988 TCCGGTACATTTTCTGAATTTAGAAAG 58.273 33.333 20.64 14.69 44.73 2.62
168 169 9.893305 CGGTACATTTTCTGAATTTAGAAAGTT 57.107 29.630 20.64 12.56 44.73 2.66
220 221 5.845985 TTTGCAAACATGAACGTTTTGAA 57.154 30.435 8.05 3.14 36.98 2.69
221 222 5.845985 TTGCAAACATGAACGTTTTGAAA 57.154 30.435 16.28 8.63 36.98 2.69
223 224 6.030379 TGCAAACATGAACGTTTTGAAATC 57.970 33.333 16.28 0.00 36.98 2.17
225 226 5.655576 CAAACATGAACGTTTTGAAATCCG 58.344 37.500 16.28 0.00 36.98 4.18
226 227 3.896122 ACATGAACGTTTTGAAATCCGG 58.104 40.909 16.28 0.00 0.00 5.14
228 229 4.515944 ACATGAACGTTTTGAAATCCGGTA 59.484 37.500 16.28 0.00 0.00 4.02
229 230 4.471157 TGAACGTTTTGAAATCCGGTAC 57.529 40.909 0.46 0.00 0.00 3.34
230 231 3.875727 TGAACGTTTTGAAATCCGGTACA 59.124 39.130 0.46 0.00 0.00 2.90
231 232 4.515944 TGAACGTTTTGAAATCCGGTACAT 59.484 37.500 0.46 0.00 0.00 2.29
232 233 5.008811 TGAACGTTTTGAAATCCGGTACATT 59.991 36.000 0.46 0.00 0.00 2.71
233 234 5.441709 ACGTTTTGAAATCCGGTACATTT 57.558 34.783 0.00 0.00 0.00 2.32
234 235 5.834169 ACGTTTTGAAATCCGGTACATTTT 58.166 33.333 0.00 0.00 0.00 1.82
236 237 6.146898 CGTTTTGAAATCCGGTACATTTTCT 58.853 36.000 0.00 0.00 0.00 2.52
237 238 6.087555 CGTTTTGAAATCCGGTACATTTTCTG 59.912 38.462 0.00 0.00 0.00 3.02
238 239 5.637006 TTGAAATCCGGTACATTTTCTGG 57.363 39.130 0.00 0.00 0.00 3.86
240 241 4.698304 TGAAATCCGGTACATTTTCTGGAC 59.302 41.667 0.00 0.00 41.19 4.02
241 242 2.373540 TCCGGTACATTTTCTGGACG 57.626 50.000 0.00 0.00 39.90 4.79
242 243 0.725117 CCGGTACATTTTCTGGACGC 59.275 55.000 0.00 0.00 39.90 5.19
244 245 2.006888 CGGTACATTTTCTGGACGCAT 58.993 47.619 0.00 0.00 39.90 4.73
246 247 3.807622 CGGTACATTTTCTGGACGCATAT 59.192 43.478 0.00 0.00 39.90 1.78
247 248 4.272504 CGGTACATTTTCTGGACGCATATT 59.727 41.667 0.00 0.00 39.90 1.28
249 250 5.971202 GGTACATTTTCTGGACGCATATTTG 59.029 40.000 0.00 0.00 39.90 2.32
250 251 5.643379 ACATTTTCTGGACGCATATTTGT 57.357 34.783 0.00 0.00 0.00 2.83
252 253 6.454795 ACATTTTCTGGACGCATATTTGTTT 58.545 32.000 0.00 0.00 0.00 2.83
253 254 6.928492 ACATTTTCTGGACGCATATTTGTTTT 59.072 30.769 0.00 0.00 0.00 2.43
256 257 6.561737 TTCTGGACGCATATTTGTTTTGTA 57.438 33.333 0.00 0.00 0.00 2.41
258 259 5.123186 TCTGGACGCATATTTGTTTTGTAGG 59.877 40.000 0.00 0.00 0.00 3.18
259 260 4.762765 TGGACGCATATTTGTTTTGTAGGT 59.237 37.500 0.00 0.00 0.00 3.08
260 261 5.241949 TGGACGCATATTTGTTTTGTAGGTT 59.758 36.000 0.00 0.00 0.00 3.50
262 263 6.088883 GGACGCATATTTGTTTTGTAGGTTTG 59.911 38.462 0.00 0.00 0.00 2.93
263 264 6.508777 ACGCATATTTGTTTTGTAGGTTTGT 58.491 32.000 0.00 0.00 0.00 2.83
264 265 7.649973 ACGCATATTTGTTTTGTAGGTTTGTA 58.350 30.769 0.00 0.00 0.00 2.41
265 266 7.806014 ACGCATATTTGTTTTGTAGGTTTGTAG 59.194 33.333 0.00 0.00 0.00 2.74
266 267 7.201316 CGCATATTTGTTTTGTAGGTTTGTAGC 60.201 37.037 0.00 0.00 0.00 3.58
267 268 7.812669 GCATATTTGTTTTGTAGGTTTGTAGCT 59.187 33.333 0.00 0.00 35.90 3.32
268 269 9.691362 CATATTTGTTTTGTAGGTTTGTAGCTT 57.309 29.630 0.00 0.00 33.36 3.74
279 280 9.953565 TGTAGGTTTGTAGCTTAATTAACAGAT 57.046 29.630 0.00 0.00 33.36 2.90
281 282 8.281212 AGGTTTGTAGCTTAATTAACAGATGG 57.719 34.615 0.00 0.00 0.00 3.51
282 283 6.972901 GGTTTGTAGCTTAATTAACAGATGGC 59.027 38.462 0.00 0.00 0.00 4.40
283 284 7.148069 GGTTTGTAGCTTAATTAACAGATGGCT 60.148 37.037 10.93 10.93 0.00 4.75
284 285 7.938140 TTGTAGCTTAATTAACAGATGGCTT 57.062 32.000 11.29 0.02 0.00 4.35
287 288 6.199937 AGCTTAATTAACAGATGGCTTGTG 57.800 37.500 0.00 0.00 0.00 3.33
288 289 5.945784 AGCTTAATTAACAGATGGCTTGTGA 59.054 36.000 4.48 0.00 0.00 3.58
289 290 6.604795 AGCTTAATTAACAGATGGCTTGTGAT 59.395 34.615 4.48 0.00 0.00 3.06
290 291 7.123247 AGCTTAATTAACAGATGGCTTGTGATT 59.877 33.333 4.48 5.07 0.00 2.57
293 294 7.472334 AATTAACAGATGGCTTGTGATTTCT 57.528 32.000 4.48 0.00 0.00 2.52
294 295 6.500684 TTAACAGATGGCTTGTGATTTCTC 57.499 37.500 4.48 0.00 0.00 2.87
295 296 4.298103 ACAGATGGCTTGTGATTTCTCT 57.702 40.909 4.48 0.00 0.00 3.10
296 297 4.660168 ACAGATGGCTTGTGATTTCTCTT 58.340 39.130 4.48 0.00 0.00 2.85
297 298 4.458295 ACAGATGGCTTGTGATTTCTCTTG 59.542 41.667 4.48 0.00 0.00 3.02
298 299 3.442977 AGATGGCTTGTGATTTCTCTTGC 59.557 43.478 0.00 0.00 0.00 4.01
299 300 2.585330 TGGCTTGTGATTTCTCTTGCA 58.415 42.857 0.00 0.00 0.00 4.08
303 304 4.082354 GGCTTGTGATTTCTCTTGCAGATT 60.082 41.667 0.00 0.00 0.00 2.40
306 307 6.625300 GCTTGTGATTTCTCTTGCAGATTGAT 60.625 38.462 0.00 0.00 0.00 2.57
307 308 6.190954 TGTGATTTCTCTTGCAGATTGATG 57.809 37.500 0.00 0.00 0.00 3.07
308 309 5.941647 TGTGATTTCTCTTGCAGATTGATGA 59.058 36.000 0.00 0.00 0.00 2.92
311 312 7.272948 GTGATTTCTCTTGCAGATTGATGAAAC 59.727 37.037 0.00 0.00 0.00 2.78
312 313 4.934075 TCTCTTGCAGATTGATGAAACG 57.066 40.909 0.00 0.00 0.00 3.60
313 314 3.125829 TCTCTTGCAGATTGATGAAACGC 59.874 43.478 0.00 0.00 0.00 4.84
314 315 2.162208 TCTTGCAGATTGATGAAACGCC 59.838 45.455 0.00 0.00 0.00 5.68
315 316 1.825090 TGCAGATTGATGAAACGCCT 58.175 45.000 0.00 0.00 0.00 5.52
316 317 1.469703 TGCAGATTGATGAAACGCCTG 59.530 47.619 0.00 0.00 0.00 4.85
317 318 1.202222 GCAGATTGATGAAACGCCTGG 60.202 52.381 0.00 0.00 0.00 4.45
321 322 0.810648 TTGATGAAACGCCTGGATGC 59.189 50.000 0.00 0.00 0.00 3.91
322 323 0.322366 TGATGAAACGCCTGGATGCA 60.322 50.000 0.00 0.00 0.00 3.96
324 325 2.221169 GATGAAACGCCTGGATGCATA 58.779 47.619 0.00 0.00 0.00 3.14
325 326 2.346766 TGAAACGCCTGGATGCATAT 57.653 45.000 0.00 0.00 0.00 1.78
326 327 2.221169 TGAAACGCCTGGATGCATATC 58.779 47.619 0.00 0.00 0.00 1.63
328 329 3.070878 TGAAACGCCTGGATGCATATCTA 59.929 43.478 0.00 0.00 33.68 1.98
329 330 3.988976 AACGCCTGGATGCATATCTAT 57.011 42.857 0.00 0.00 33.68 1.98
330 331 3.988976 ACGCCTGGATGCATATCTATT 57.011 42.857 0.00 0.00 33.68 1.73
331 332 3.866651 ACGCCTGGATGCATATCTATTC 58.133 45.455 0.00 0.00 33.68 1.75
332 333 3.261643 ACGCCTGGATGCATATCTATTCA 59.738 43.478 0.00 0.00 33.68 2.57
333 334 4.080695 ACGCCTGGATGCATATCTATTCAT 60.081 41.667 0.00 0.00 33.68 2.57
334 335 5.129320 ACGCCTGGATGCATATCTATTCATA 59.871 40.000 0.00 0.00 33.68 2.15
335 336 5.464722 CGCCTGGATGCATATCTATTCATAC 59.535 44.000 0.00 0.00 33.68 2.39
336 337 6.590068 GCCTGGATGCATATCTATTCATACT 58.410 40.000 0.00 0.00 33.68 2.12
337 338 7.052873 GCCTGGATGCATATCTATTCATACTT 58.947 38.462 0.00 0.00 33.68 2.24
338 339 8.206867 GCCTGGATGCATATCTATTCATACTTA 58.793 37.037 0.00 0.00 33.68 2.24
367 368 6.737720 ACATGCTCTGTATCATTCTTAGGA 57.262 37.500 0.00 0.00 35.91 2.94
369 370 7.743749 ACATGCTCTGTATCATTCTTAGGAAT 58.256 34.615 0.00 0.00 38.29 3.01
370 371 7.877097 ACATGCTCTGTATCATTCTTAGGAATC 59.123 37.037 0.00 0.00 36.85 2.52
371 372 6.763355 TGCTCTGTATCATTCTTAGGAATCC 58.237 40.000 0.00 0.00 39.87 3.01
373 374 6.688073 TCTGTATCATTCTTAGGAATCCCC 57.312 41.667 0.00 0.00 39.87 4.81
374 375 5.246203 TCTGTATCATTCTTAGGAATCCCCG 59.754 44.000 0.00 0.00 39.87 5.73
375 376 4.286032 TGTATCATTCTTAGGAATCCCCGG 59.714 45.833 0.00 0.00 39.87 5.73
376 377 2.771688 TCATTCTTAGGAATCCCCGGT 58.228 47.619 0.00 0.00 39.87 5.28
377 378 2.438021 TCATTCTTAGGAATCCCCGGTG 59.562 50.000 0.00 0.00 39.87 4.94
379 380 0.326238 TCTTAGGAATCCCCGGTGCT 60.326 55.000 0.00 0.00 40.87 4.40
380 381 1.062734 TCTTAGGAATCCCCGGTGCTA 60.063 52.381 0.00 0.00 40.87 3.49
381 382 1.766496 CTTAGGAATCCCCGGTGCTAA 59.234 52.381 0.00 1.95 40.87 3.09
382 383 1.125633 TAGGAATCCCCGGTGCTAAC 58.874 55.000 0.00 0.00 40.87 2.34
383 384 0.912487 AGGAATCCCCGGTGCTAACA 60.912 55.000 0.00 0.00 40.87 2.41
384 385 0.746923 GGAATCCCCGGTGCTAACAC 60.747 60.000 0.00 0.00 46.66 3.32
386 387 1.483415 GAATCCCCGGTGCTAACACTA 59.517 52.381 0.00 0.00 46.57 2.74
400 2648 5.874810 TGCTAACACTAGTCATGAACAATCC 59.125 40.000 0.00 0.00 0.00 3.01
401 2649 5.294552 GCTAACACTAGTCATGAACAATCCC 59.705 44.000 0.00 0.00 0.00 3.85
406 2654 3.703001 AGTCATGAACAATCCCGAACT 57.297 42.857 0.00 0.00 0.00 3.01
407 2655 4.021102 AGTCATGAACAATCCCGAACTT 57.979 40.909 0.00 0.00 0.00 2.66
451 2699 7.962373 TGATTATCTTAACGATTTGCACAACAG 59.038 33.333 0.00 0.00 33.48 3.16
457 2705 2.548057 ACGATTTGCACAACAGTACAGG 59.452 45.455 0.00 0.00 0.00 4.00
462 2710 5.899120 TTTGCACAACAGTACAGGTTTAA 57.101 34.783 0.00 0.00 0.00 1.52
472 2720 7.739498 ACAGTACAGGTTTAATTCGACAAAT 57.261 32.000 0.00 0.00 0.00 2.32
473 2721 8.836268 ACAGTACAGGTTTAATTCGACAAATA 57.164 30.769 0.00 0.00 0.00 1.40
476 2724 9.886132 AGTACAGGTTTAATTCGACAAATAGAT 57.114 29.630 0.00 0.00 0.00 1.98
498 2746 5.046910 TGGAATCTTGAACAAATCTTCGC 57.953 39.130 0.00 0.00 0.00 4.70
499 2747 4.082787 TGGAATCTTGAACAAATCTTCGCC 60.083 41.667 0.00 0.00 0.00 5.54
507 2755 4.213270 TGAACAAATCTTCGCCTGTACTTG 59.787 41.667 0.00 0.00 0.00 3.16
508 2756 4.002906 ACAAATCTTCGCCTGTACTTGA 57.997 40.909 0.00 0.00 0.00 3.02
552 2800 4.570772 CCTGTACGACATTACAATCCTTGG 59.429 45.833 0.00 0.00 31.52 3.61
565 2813 2.507407 TCCTTGGCATGTAAAGGGAC 57.493 50.000 21.41 0.00 42.77 4.46
585 2863 4.631377 GGACTTTGACGAATCATGTCATCA 59.369 41.667 0.00 0.00 45.10 3.07
639 2917 4.720046 TGTATCTTTACAGGCCACACAAA 58.280 39.130 5.01 0.00 33.37 2.83
651 2929 5.584251 CAGGCCACACAAAATTACAAACTTT 59.416 36.000 5.01 0.00 0.00 2.66
659 2937 7.221259 ACACAAAATTACAAACTTTAGTTCGGC 59.779 33.333 0.00 0.00 37.25 5.54
660 2938 7.221067 CACAAAATTACAAACTTTAGTTCGGCA 59.779 33.333 0.00 0.00 37.25 5.69
763 3041 8.116753 GGATCGATGTTTGACATGTAAAGTAAG 58.883 37.037 0.54 0.00 39.27 2.34
832 3110 7.264221 TGATACATGCAACAACAAAGAACTTT 58.736 30.769 0.00 0.00 0.00 2.66
846 3124 5.624344 AAGAACTTTGATGATCAGTGCAG 57.376 39.130 0.09 0.00 0.00 4.41
879 3157 2.080286 AGTAGTTGCACCTAACGCAG 57.920 50.000 0.00 0.00 41.18 5.18
891 3169 2.942376 CCTAACGCAGCATACCAAATGA 59.058 45.455 0.00 0.00 0.00 2.57
1133 3411 3.261981 ACCCTTTACTGCATTCCGTAG 57.738 47.619 0.00 0.00 0.00 3.51
1164 3442 0.863799 CGCAACATCCATCATCTCCG 59.136 55.000 0.00 0.00 0.00 4.63
1170 3448 1.278413 CATCCATCATCTCCGGAGCAT 59.722 52.381 27.39 17.35 30.84 3.79
1272 3550 1.561076 AGCCCAGTTGCTGATATGTCA 59.439 47.619 0.00 0.00 40.90 3.58
1329 3607 0.322456 TGGTAATGTGGGAGCAGTGC 60.322 55.000 7.13 7.13 0.00 4.40
1368 3646 0.322816 TCCCCAAGCAGTCAAGATGC 60.323 55.000 0.00 0.00 44.18 3.91
1410 3688 2.478134 GCACGCCATTATTTTGCAACAA 59.522 40.909 0.00 0.00 33.24 2.83
1480 3758 4.303282 ACAACAAGGTCAACAACAACAAC 58.697 39.130 0.00 0.00 0.00 3.32
1481 3759 4.202161 ACAACAAGGTCAACAACAACAACA 60.202 37.500 0.00 0.00 0.00 3.33
1482 3760 4.173036 ACAAGGTCAACAACAACAACAG 57.827 40.909 0.00 0.00 0.00 3.16
1487 3765 2.752903 GTCAACAACAACAACAGGGTCT 59.247 45.455 0.00 0.00 0.00 3.85
1569 3856 3.209410 GACATGGGTGATTCAGACCATC 58.791 50.000 16.18 7.25 41.56 3.51
1665 3952 1.142097 GGGCGGCTACTGAGAAGAC 59.858 63.158 9.56 0.00 0.00 3.01
1926 4475 9.238368 AGCTTTGTATGTAGCAAAATAACCTTA 57.762 29.630 0.00 0.00 39.85 2.69
1992 4541 7.001653 TCCCTATTAAGGTAAGGAGTAAGGT 57.998 40.000 0.00 0.00 41.89 3.50
1999 4556 4.276642 AGGTAAGGAGTAAGGTCTAACCG 58.723 47.826 0.00 0.00 44.90 4.44
2006 4563 2.636403 AGTAAGGTCTAACCGCAAACCT 59.364 45.455 0.00 0.00 44.90 3.50
2009 4566 1.972795 AGGTCTAACCGCAAACCTACA 59.027 47.619 0.00 0.00 44.90 2.74
2024 4581 4.910458 ACCTACACTTTAATGGTGAGCT 57.090 40.909 13.63 0.00 38.01 4.09
2082 4639 9.411189 CAACTAGTTCTAAATAGTACTCCCTCT 57.589 37.037 4.77 0.00 38.70 3.69
2153 4731 5.190528 AGGGAGTATATGGCATTGGTATCAG 59.809 44.000 4.78 0.00 0.00 2.90
2155 4733 6.156256 GGGAGTATATGGCATTGGTATCAGTA 59.844 42.308 4.78 0.00 0.00 2.74
2304 4882 4.639135 AACTCAAACAGACAAAGGAAGC 57.361 40.909 0.00 0.00 0.00 3.86
2340 4946 1.779061 TTGCTTCCGCCCTCCTCTTT 61.779 55.000 0.00 0.00 34.43 2.52
2367 4973 7.329717 CACAGAATAAAGAAGCTAGTCTCGTTT 59.670 37.037 0.00 0.00 0.00 3.60
2373 4979 3.929610 AGAAGCTAGTCTCGTTTTGCATC 59.070 43.478 0.00 0.00 0.00 3.91
2429 5036 5.799213 ACTTTCTAGAGACCACTCCATTTG 58.201 41.667 0.00 0.00 43.53 2.32
2521 5128 9.785982 ATAAAGAAAAGGCCATCTTCTATCTAC 57.214 33.333 16.03 0.00 34.90 2.59
2555 5162 2.071607 GCTGTAGCTGGCTTGAGTAGC 61.072 57.143 0.00 0.00 42.86 3.58
2580 5187 6.071896 CCATCATCATCATCATCCCAAAGAAG 60.072 42.308 0.00 0.00 0.00 2.85
2582 5189 6.665695 TCATCATCATCATCCCAAAGAAGAA 58.334 36.000 0.00 0.00 0.00 2.52
2585 5206 6.354938 TCATCATCATCCCAAAGAAGAAGAG 58.645 40.000 0.00 0.00 0.00 2.85
2604 5225 3.843027 AGAGGAGGAAGAAGAAGATGCAA 59.157 43.478 0.00 0.00 0.00 4.08
2649 5270 4.964897 TCCTTCATGCTCTTCATCCTTCTA 59.035 41.667 0.00 0.00 31.79 2.10
2655 5276 2.028567 GCTCTTCATCCTTCTATCCCCG 60.029 54.545 0.00 0.00 0.00 5.73
2661 5282 2.217745 CCTTCTATCCCCGGGGCTC 61.218 68.421 36.68 0.00 34.68 4.70
2662 5283 2.122547 TTCTATCCCCGGGGCTCC 60.123 66.667 36.68 0.00 34.68 4.70
2676 5297 1.414866 GGCTCCTCTTCCAGATCCCC 61.415 65.000 0.00 0.00 0.00 4.81
2685 5306 1.227102 CCAGATCCCCGGCAAATCA 59.773 57.895 0.00 0.00 0.00 2.57
2721 5342 0.793861 GCAAATTCCACACGAGCGTA 59.206 50.000 0.00 0.00 0.00 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.553079 AAAAAGTTGTTCGCGCTTCA 57.447 40.000 5.56 0.00 0.00 3.02
2 3 4.603173 GCTTTAAAAAGTTGTTCGCGCTTC 60.603 41.667 5.56 0.00 38.28 3.86
5 6 2.532317 TGCTTTAAAAAGTTGTTCGCGC 59.468 40.909 0.00 0.00 38.28 6.86
6 7 3.061469 GGTGCTTTAAAAAGTTGTTCGCG 60.061 43.478 0.00 0.00 38.28 5.87
7 8 3.061469 CGGTGCTTTAAAAAGTTGTTCGC 60.061 43.478 4.50 0.00 38.28 4.70
8 9 4.203563 GTCGGTGCTTTAAAAAGTTGTTCG 59.796 41.667 4.50 3.11 38.28 3.95
9 10 5.096849 TGTCGGTGCTTTAAAAAGTTGTTC 58.903 37.500 4.50 0.00 38.28 3.18
11 12 4.705337 TGTCGGTGCTTTAAAAAGTTGT 57.295 36.364 4.50 0.00 38.28 3.32
13 14 7.603963 AAAAATGTCGGTGCTTTAAAAAGTT 57.396 28.000 4.50 0.00 38.28 2.66
39 40 9.425577 TCCGTTTAAAAATTTGTTCTCAAAACT 57.574 25.926 0.00 0.00 44.97 2.66
40 41 9.683651 CTCCGTTTAAAAATTTGTTCTCAAAAC 57.316 29.630 0.00 0.00 44.97 2.43
41 42 9.640963 TCTCCGTTTAAAAATTTGTTCTCAAAA 57.359 25.926 0.00 0.00 44.97 2.44
43 44 9.078753 GTTCTCCGTTTAAAAATTTGTTCTCAA 57.921 29.630 0.00 0.00 0.00 3.02
44 45 8.244802 TGTTCTCCGTTTAAAAATTTGTTCTCA 58.755 29.630 0.00 0.00 0.00 3.27
45 46 8.623310 TGTTCTCCGTTTAAAAATTTGTTCTC 57.377 30.769 0.00 0.00 0.00 2.87
46 47 8.989653 TTGTTCTCCGTTTAAAAATTTGTTCT 57.010 26.923 0.00 0.00 0.00 3.01
59 60 7.011950 GGGATTTTTCAAAATTGTTCTCCGTTT 59.988 33.333 0.00 0.00 38.64 3.60
61 62 5.989168 GGGATTTTTCAAAATTGTTCTCCGT 59.011 36.000 0.00 0.00 38.64 4.69
63 64 6.220201 TCGGGATTTTTCAAAATTGTTCTCC 58.780 36.000 0.00 0.00 38.64 3.71
64 65 7.707774 TTCGGGATTTTTCAAAATTGTTCTC 57.292 32.000 0.00 0.00 38.64 2.87
65 66 8.499403 TTTTCGGGATTTTTCAAAATTGTTCT 57.501 26.923 0.00 0.00 38.64 3.01
88 89 5.641636 ACAAAGTTCACGCTTCCAAATTTTT 59.358 32.000 0.00 0.00 0.00 1.94
92 93 4.385358 AACAAAGTTCACGCTTCCAAAT 57.615 36.364 0.00 0.00 0.00 2.32
93 94 3.859411 AACAAAGTTCACGCTTCCAAA 57.141 38.095 0.00 0.00 0.00 3.28
94 95 3.859411 AAACAAAGTTCACGCTTCCAA 57.141 38.095 0.00 0.00 0.00 3.53
95 96 3.191581 TCAAAACAAAGTTCACGCTTCCA 59.808 39.130 0.00 0.00 0.00 3.53
96 97 3.765026 TCAAAACAAAGTTCACGCTTCC 58.235 40.909 0.00 0.00 0.00 3.46
97 98 5.949233 ATTCAAAACAAAGTTCACGCTTC 57.051 34.783 0.00 0.00 0.00 3.86
98 99 5.454232 CGTATTCAAAACAAAGTTCACGCTT 59.546 36.000 0.00 0.00 0.00 4.68
99 100 4.967575 CGTATTCAAAACAAAGTTCACGCT 59.032 37.500 0.00 0.00 0.00 5.07
100 101 4.731480 ACGTATTCAAAACAAAGTTCACGC 59.269 37.500 0.00 0.00 0.00 5.34
101 102 5.960683 TCACGTATTCAAAACAAAGTTCACG 59.039 36.000 0.00 0.00 0.00 4.35
103 104 7.306213 TGTTCACGTATTCAAAACAAAGTTCA 58.694 30.769 0.00 0.00 0.00 3.18
104 105 7.728580 TGTTCACGTATTCAAAACAAAGTTC 57.271 32.000 0.00 0.00 0.00 3.01
105 106 8.522178 TTTGTTCACGTATTCAAAACAAAGTT 57.478 26.923 7.42 0.00 41.99 2.66
106 107 8.522178 TTTTGTTCACGTATTCAAAACAAAGT 57.478 26.923 15.05 0.00 45.28 2.66
107 108 9.965748 AATTTTGTTCACGTATTCAAAACAAAG 57.034 25.926 18.79 0.00 45.28 2.77
110 111 9.746711 CAAAATTTTGTTCACGTATTCAAAACA 57.253 25.926 20.57 8.19 40.72 2.83
116 117 9.791838 GGATTTCAAAATTTTGTTCACGTATTC 57.208 29.630 25.98 12.89 39.18 1.75
118 119 7.115663 CCGGATTTCAAAATTTTGTTCACGTAT 59.884 33.333 25.98 12.34 39.18 3.06
119 120 6.418226 CCGGATTTCAAAATTTTGTTCACGTA 59.582 34.615 25.98 6.48 39.18 3.57
120 121 5.233263 CCGGATTTCAAAATTTTGTTCACGT 59.767 36.000 25.98 10.83 39.18 4.49
121 122 5.233263 ACCGGATTTCAAAATTTTGTTCACG 59.767 36.000 25.98 22.42 39.18 4.35
124 125 7.701809 TGTACCGGATTTCAAAATTTTGTTC 57.298 32.000 25.98 20.34 39.18 3.18
126 127 8.669946 AAATGTACCGGATTTCAAAATTTTGT 57.330 26.923 25.98 10.91 39.18 2.83
130 131 8.364142 TCAGAAAATGTACCGGATTTCAAAATT 58.636 29.630 9.46 0.00 34.91 1.82
131 132 7.891561 TCAGAAAATGTACCGGATTTCAAAAT 58.108 30.769 9.46 0.00 34.91 1.82
132 133 7.278461 TCAGAAAATGTACCGGATTTCAAAA 57.722 32.000 9.46 0.00 34.91 2.44
134 135 6.885952 TTCAGAAAATGTACCGGATTTCAA 57.114 33.333 9.46 0.17 34.91 2.69
135 136 7.461182 AATTCAGAAAATGTACCGGATTTCA 57.539 32.000 9.46 1.34 34.91 2.69
136 137 9.503427 CTAAATTCAGAAAATGTACCGGATTTC 57.497 33.333 9.46 10.50 33.13 2.17
137 138 9.238368 TCTAAATTCAGAAAATGTACCGGATTT 57.762 29.630 9.46 0.00 0.00 2.17
138 139 8.801882 TCTAAATTCAGAAAATGTACCGGATT 57.198 30.769 9.46 0.00 0.00 3.01
141 142 8.512138 ACTTTCTAAATTCAGAAAATGTACCGG 58.488 33.333 5.30 0.00 42.43 5.28
196 197 6.228273 TCAAAACGTTCATGTTTGCAAAAA 57.772 29.167 14.67 9.42 41.01 1.94
197 198 5.845985 TCAAAACGTTCATGTTTGCAAAA 57.154 30.435 14.67 5.00 41.01 2.44
198 199 5.845985 TTCAAAACGTTCATGTTTGCAAA 57.154 30.435 8.05 8.05 41.01 3.68
199 200 5.845985 TTTCAAAACGTTCATGTTTGCAA 57.154 30.435 0.00 0.00 41.01 4.08
200 201 5.006165 GGATTTCAAAACGTTCATGTTTGCA 59.994 36.000 0.00 0.00 41.01 4.08
201 202 5.431309 GGATTTCAAAACGTTCATGTTTGC 58.569 37.500 0.00 0.00 41.01 3.68
205 206 3.316868 ACCGGATTTCAAAACGTTCATGT 59.683 39.130 9.46 0.00 0.00 3.21
206 207 3.896122 ACCGGATTTCAAAACGTTCATG 58.104 40.909 9.46 4.35 0.00 3.07
208 209 3.875727 TGTACCGGATTTCAAAACGTTCA 59.124 39.130 9.46 0.00 0.00 3.18
209 210 4.471157 TGTACCGGATTTCAAAACGTTC 57.529 40.909 9.46 0.00 0.00 3.95
211 212 5.441709 AAATGTACCGGATTTCAAAACGT 57.558 34.783 9.46 0.00 0.00 3.99
212 213 6.087555 CAGAAAATGTACCGGATTTCAAAACG 59.912 38.462 9.46 0.00 34.91 3.60
214 215 6.265649 TCCAGAAAATGTACCGGATTTCAAAA 59.734 34.615 9.46 0.00 34.91 2.44
215 216 5.770663 TCCAGAAAATGTACCGGATTTCAAA 59.229 36.000 9.46 0.00 34.91 2.69
216 217 5.182380 GTCCAGAAAATGTACCGGATTTCAA 59.818 40.000 9.46 0.00 34.91 2.69
217 218 4.698304 GTCCAGAAAATGTACCGGATTTCA 59.302 41.667 9.46 1.34 34.91 2.69
218 219 4.201783 CGTCCAGAAAATGTACCGGATTTC 60.202 45.833 9.46 10.50 33.13 2.17
220 221 3.267483 CGTCCAGAAAATGTACCGGATT 58.733 45.455 9.46 0.00 0.00 3.01
221 222 2.901249 CGTCCAGAAAATGTACCGGAT 58.099 47.619 9.46 0.00 0.00 4.18
223 224 0.725117 GCGTCCAGAAAATGTACCGG 59.275 55.000 0.00 0.00 0.00 5.28
225 226 5.751243 AATATGCGTCCAGAAAATGTACC 57.249 39.130 0.00 0.00 0.00 3.34
226 227 6.551736 ACAAATATGCGTCCAGAAAATGTAC 58.448 36.000 0.00 0.00 0.00 2.90
228 229 5.643379 ACAAATATGCGTCCAGAAAATGT 57.357 34.783 0.00 0.00 0.00 2.71
229 230 6.949578 AAACAAATATGCGTCCAGAAAATG 57.050 33.333 0.00 0.00 0.00 2.32
230 231 6.928492 ACAAAACAAATATGCGTCCAGAAAAT 59.072 30.769 0.00 0.00 0.00 1.82
231 232 6.276847 ACAAAACAAATATGCGTCCAGAAAA 58.723 32.000 0.00 0.00 0.00 2.29
232 233 5.837437 ACAAAACAAATATGCGTCCAGAAA 58.163 33.333 0.00 0.00 0.00 2.52
233 234 5.446143 ACAAAACAAATATGCGTCCAGAA 57.554 34.783 0.00 0.00 0.00 3.02
234 235 5.123186 CCTACAAAACAAATATGCGTCCAGA 59.877 40.000 0.00 0.00 0.00 3.86
236 237 4.762765 ACCTACAAAACAAATATGCGTCCA 59.237 37.500 0.00 0.00 0.00 4.02
237 238 5.305139 ACCTACAAAACAAATATGCGTCC 57.695 39.130 0.00 0.00 0.00 4.79
238 239 6.639279 ACAAACCTACAAAACAAATATGCGTC 59.361 34.615 0.00 0.00 0.00 5.19
240 241 7.201316 GCTACAAACCTACAAAACAAATATGCG 60.201 37.037 0.00 0.00 0.00 4.73
241 242 7.812669 AGCTACAAACCTACAAAACAAATATGC 59.187 33.333 0.00 0.00 0.00 3.14
242 243 9.691362 AAGCTACAAACCTACAAAACAAATATG 57.309 29.630 0.00 0.00 0.00 1.78
252 253 9.781633 TCTGTTAATTAAGCTACAAACCTACAA 57.218 29.630 0.00 0.00 0.00 2.41
253 254 9.953565 ATCTGTTAATTAAGCTACAAACCTACA 57.046 29.630 0.00 0.00 0.00 2.74
256 257 7.148069 GCCATCTGTTAATTAAGCTACAAACCT 60.148 37.037 0.00 0.00 0.00 3.50
258 259 7.762382 AGCCATCTGTTAATTAAGCTACAAAC 58.238 34.615 0.00 0.00 0.00 2.93
259 260 7.938140 AGCCATCTGTTAATTAAGCTACAAA 57.062 32.000 0.00 0.00 0.00 2.83
260 261 7.393234 ACAAGCCATCTGTTAATTAAGCTACAA 59.607 33.333 7.55 0.00 0.00 2.41
262 263 7.065803 TCACAAGCCATCTGTTAATTAAGCTAC 59.934 37.037 7.55 0.00 0.00 3.58
263 264 7.109501 TCACAAGCCATCTGTTAATTAAGCTA 58.890 34.615 7.55 0.00 0.00 3.32
264 265 5.945784 TCACAAGCCATCTGTTAATTAAGCT 59.054 36.000 0.00 0.00 0.00 3.74
265 266 6.194796 TCACAAGCCATCTGTTAATTAAGC 57.805 37.500 0.00 0.00 0.00 3.09
266 267 9.294030 GAAATCACAAGCCATCTGTTAATTAAG 57.706 33.333 0.00 0.00 0.00 1.85
267 268 9.023962 AGAAATCACAAGCCATCTGTTAATTAA 57.976 29.630 0.00 0.00 0.00 1.40
268 269 8.579850 AGAAATCACAAGCCATCTGTTAATTA 57.420 30.769 0.00 0.00 0.00 1.40
271 272 6.240894 AGAGAAATCACAAGCCATCTGTTAA 58.759 36.000 0.00 0.00 0.00 2.01
272 273 5.809001 AGAGAAATCACAAGCCATCTGTTA 58.191 37.500 0.00 0.00 0.00 2.41
273 274 4.660168 AGAGAAATCACAAGCCATCTGTT 58.340 39.130 0.00 0.00 0.00 3.16
274 275 4.298103 AGAGAAATCACAAGCCATCTGT 57.702 40.909 0.00 0.00 0.00 3.41
275 276 4.674623 GCAAGAGAAATCACAAGCCATCTG 60.675 45.833 0.00 0.00 0.00 2.90
277 278 3.192001 TGCAAGAGAAATCACAAGCCATC 59.808 43.478 0.00 0.00 0.00 3.51
279 280 2.555325 CTGCAAGAGAAATCACAAGCCA 59.445 45.455 0.00 0.00 34.07 4.75
280 281 2.816087 TCTGCAAGAGAAATCACAAGCC 59.184 45.455 0.00 0.00 38.67 4.35
294 295 2.163010 AGGCGTTTCATCAATCTGCAAG 59.837 45.455 0.00 0.00 0.00 4.01
295 296 2.095110 CAGGCGTTTCATCAATCTGCAA 60.095 45.455 0.00 0.00 0.00 4.08
296 297 1.469703 CAGGCGTTTCATCAATCTGCA 59.530 47.619 0.00 0.00 0.00 4.41
297 298 1.202222 CCAGGCGTTTCATCAATCTGC 60.202 52.381 0.00 0.00 0.00 4.26
298 299 2.358957 TCCAGGCGTTTCATCAATCTG 58.641 47.619 0.00 0.00 0.00 2.90
299 300 2.787473 TCCAGGCGTTTCATCAATCT 57.213 45.000 0.00 0.00 0.00 2.40
303 304 0.322366 TGCATCCAGGCGTTTCATCA 60.322 50.000 0.00 0.00 36.28 3.07
306 307 2.158769 AGATATGCATCCAGGCGTTTCA 60.159 45.455 0.19 0.00 34.47 2.69
307 308 2.498167 AGATATGCATCCAGGCGTTTC 58.502 47.619 0.19 0.00 36.28 2.78
308 309 2.645838 AGATATGCATCCAGGCGTTT 57.354 45.000 0.19 0.00 36.28 3.60
311 312 3.865446 TGAATAGATATGCATCCAGGCG 58.135 45.455 0.19 0.00 36.28 5.52
312 313 6.590068 AGTATGAATAGATATGCATCCAGGC 58.410 40.000 0.19 0.00 33.94 4.85
341 342 7.287696 TCCTAAGAATGATACAGAGCATGTACA 59.712 37.037 0.00 0.00 47.00 2.90
342 343 7.661968 TCCTAAGAATGATACAGAGCATGTAC 58.338 38.462 4.14 0.00 47.00 2.90
343 344 8.874156 ATTCCTAAGAATGATACAGAGCATGTA 58.126 33.333 4.49 4.49 43.53 2.29
344 345 6.737720 TCCTAAGAATGATACAGAGCATGT 57.262 37.500 0.00 0.02 46.45 3.21
345 346 7.333921 GGATTCCTAAGAATGATACAGAGCATG 59.666 40.741 0.00 0.00 42.93 4.06
346 347 7.393216 GGATTCCTAAGAATGATACAGAGCAT 58.607 38.462 0.00 0.00 42.93 3.79
347 348 6.239714 GGGATTCCTAAGAATGATACAGAGCA 60.240 42.308 2.01 0.00 42.93 4.26
348 349 6.169800 GGGATTCCTAAGAATGATACAGAGC 58.830 44.000 2.01 0.00 42.93 4.09
349 350 6.573289 CGGGGATTCCTAAGAATGATACAGAG 60.573 46.154 2.01 0.00 42.93 3.35
350 351 5.246203 CGGGGATTCCTAAGAATGATACAGA 59.754 44.000 2.01 0.00 42.93 3.41
352 353 4.286032 CCGGGGATTCCTAAGAATGATACA 59.714 45.833 2.01 0.00 42.93 2.29
353 354 4.286291 ACCGGGGATTCCTAAGAATGATAC 59.714 45.833 6.32 0.00 42.93 2.24
354 355 4.286032 CACCGGGGATTCCTAAGAATGATA 59.714 45.833 6.32 0.00 42.93 2.15
355 356 3.073062 CACCGGGGATTCCTAAGAATGAT 59.927 47.826 6.32 0.00 42.93 2.45
356 357 2.438021 CACCGGGGATTCCTAAGAATGA 59.562 50.000 6.32 0.00 42.93 2.57
358 359 1.143073 GCACCGGGGATTCCTAAGAAT 59.857 52.381 8.67 0.00 45.63 2.40
360 361 0.326238 AGCACCGGGGATTCCTAAGA 60.326 55.000 8.67 0.00 0.00 2.10
361 362 1.420430 TAGCACCGGGGATTCCTAAG 58.580 55.000 8.67 0.00 0.00 2.18
362 363 1.487558 GTTAGCACCGGGGATTCCTAA 59.512 52.381 8.67 1.91 0.00 2.69
363 364 1.125633 GTTAGCACCGGGGATTCCTA 58.874 55.000 8.67 0.00 0.00 2.94
364 365 0.912487 TGTTAGCACCGGGGATTCCT 60.912 55.000 8.67 0.00 0.00 3.36
365 366 0.746923 GTGTTAGCACCGGGGATTCC 60.747 60.000 8.67 0.00 39.61 3.01
367 368 1.485066 CTAGTGTTAGCACCGGGGATT 59.515 52.381 8.67 0.00 46.35 3.01
369 370 0.251922 ACTAGTGTTAGCACCGGGGA 60.252 55.000 8.67 0.00 46.35 4.81
370 371 0.175073 GACTAGTGTTAGCACCGGGG 59.825 60.000 6.32 0.84 46.35 5.73
371 372 0.892755 TGACTAGTGTTAGCACCGGG 59.107 55.000 6.32 0.00 46.35 5.73
373 374 3.503827 TCATGACTAGTGTTAGCACCG 57.496 47.619 0.00 0.77 46.35 4.94
374 375 4.566004 TGTTCATGACTAGTGTTAGCACC 58.434 43.478 0.00 0.00 46.35 5.01
375 376 6.183360 GGATTGTTCATGACTAGTGTTAGCAC 60.183 42.308 0.00 0.72 45.57 4.40
376 377 5.874810 GGATTGTTCATGACTAGTGTTAGCA 59.125 40.000 0.00 0.00 0.00 3.49
377 378 5.294552 GGGATTGTTCATGACTAGTGTTAGC 59.705 44.000 0.00 0.00 0.00 3.09
379 380 5.186215 TCGGGATTGTTCATGACTAGTGTTA 59.814 40.000 0.00 0.00 0.00 2.41
380 381 4.020573 TCGGGATTGTTCATGACTAGTGTT 60.021 41.667 0.00 0.00 0.00 3.32
381 382 3.513912 TCGGGATTGTTCATGACTAGTGT 59.486 43.478 0.00 0.00 0.00 3.55
382 383 4.123497 TCGGGATTGTTCATGACTAGTG 57.877 45.455 0.00 0.00 0.00 2.74
383 384 4.223032 AGTTCGGGATTGTTCATGACTAGT 59.777 41.667 0.00 0.00 0.00 2.57
384 385 4.759782 AGTTCGGGATTGTTCATGACTAG 58.240 43.478 0.00 0.00 0.00 2.57
386 387 3.703001 AGTTCGGGATTGTTCATGACT 57.297 42.857 0.00 0.00 0.00 3.41
400 2648 6.842163 AGTATTGTTTGCTGAATAAGTTCGG 58.158 36.000 0.00 0.00 42.50 4.30
401 2649 8.150300 CAAGTATTGTTTGCTGAATAAGTTCG 57.850 34.615 0.00 0.00 42.34 3.95
441 2689 6.458232 AATTAAACCTGTACTGTTGTGCAA 57.542 33.333 0.00 0.00 38.28 4.08
451 2699 9.916397 CATCTATTTGTCGAATTAAACCTGTAC 57.084 33.333 0.00 0.00 0.00 2.90
462 2710 8.616076 GTTCAAGATTCCATCTATTTGTCGAAT 58.384 33.333 0.00 0.00 39.08 3.34
472 2720 7.201644 GCGAAGATTTGTTCAAGATTCCATCTA 60.202 37.037 0.00 0.00 39.08 1.98
473 2721 6.404074 GCGAAGATTTGTTCAAGATTCCATCT 60.404 38.462 0.00 0.00 42.61 2.90
476 2724 4.082787 GGCGAAGATTTGTTCAAGATTCCA 60.083 41.667 0.00 0.00 0.00 3.53
492 2740 1.961394 ACACTCAAGTACAGGCGAAGA 59.039 47.619 0.00 0.00 0.00 2.87
497 2745 4.833390 AGGATTTACACTCAAGTACAGGC 58.167 43.478 0.00 0.00 0.00 4.85
498 2746 9.530633 GTATAAGGATTTACACTCAAGTACAGG 57.469 37.037 0.00 0.00 0.00 4.00
552 2800 3.071479 TCGTCAAAGTCCCTTTACATGC 58.929 45.455 0.00 0.00 31.96 4.06
565 2813 6.600246 AGATGATGACATGATTCGTCAAAG 57.400 37.500 11.12 0.00 45.91 2.77
616 2894 4.359434 TGTGTGGCCTGTAAAGATACAA 57.641 40.909 3.32 0.00 41.36 2.41
639 2917 6.380095 TGTGCCGAACTAAAGTTTGTAATT 57.620 33.333 8.85 0.00 38.56 1.40
651 2929 1.234615 GCTTGCCTTGTGCCGAACTA 61.235 55.000 0.00 0.00 40.16 2.24
659 2937 5.886960 AAACTAGATTAGCTTGCCTTGTG 57.113 39.130 0.00 0.00 0.00 3.33
660 2938 6.038714 GCATAAACTAGATTAGCTTGCCTTGT 59.961 38.462 0.00 0.00 0.00 3.16
832 3110 4.070009 GCATATTCCTGCACTGATCATCA 58.930 43.478 0.00 0.00 41.87 3.07
846 3124 6.458342 GGTGCAACTACTTACAAGCATATTCC 60.458 42.308 0.00 0.00 36.74 3.01
879 3157 4.883083 TCGGACTCTATCATTTGGTATGC 58.117 43.478 0.00 0.00 0.00 3.14
891 3169 2.950781 TGGATGCTTCTCGGACTCTAT 58.049 47.619 0.00 0.00 0.00 1.98
951 3229 5.063438 CCTATTTATAACCGACATGGCATCG 59.937 44.000 0.00 0.00 43.94 3.84
1164 3442 1.648467 GCGGAGTTGGTTGATGCTCC 61.648 60.000 0.00 0.00 42.90 4.70
1170 3448 2.281484 GGCTGCGGAGTTGGTTGA 60.281 61.111 5.62 0.00 0.00 3.18
1329 3607 3.181516 GGATCGCTTTTAGTTGCTGACAG 60.182 47.826 0.00 0.00 0.00 3.51
1368 3646 2.047274 ACGTTGTGGATGGCCTCG 60.047 61.111 3.32 0.00 34.31 4.63
1410 3688 5.592688 AGTAGCTTGTACCAATTGTTGTTGT 59.407 36.000 4.43 0.00 0.00 3.32
1430 3708 1.339151 GCTGAGGTTGGGTGGAAGTAG 60.339 57.143 0.00 0.00 0.00 2.57
1480 3758 0.909610 TGGCTAGAACCCAGACCCTG 60.910 60.000 0.00 0.00 0.00 4.45
1481 3759 1.474307 TGGCTAGAACCCAGACCCT 59.526 57.895 0.00 0.00 0.00 4.34
1482 3760 4.147135 TGGCTAGAACCCAGACCC 57.853 61.111 0.00 0.00 0.00 4.46
1487 3765 1.422977 TTGTGGCTGGCTAGAACCCA 61.423 55.000 0.00 0.00 0.00 4.51
1643 3930 1.264749 TTCTCAGTAGCCGCCCATGT 61.265 55.000 0.00 0.00 0.00 3.21
1665 3952 6.418226 CCATTTTTCGGATACTAGAACTCTCG 59.582 42.308 0.00 0.00 0.00 4.04
1671 3958 6.110707 GTGGTCCATTTTTCGGATACTAGAA 58.889 40.000 0.00 0.00 34.32 2.10
1949 4498 3.317993 GGGATCTAGCTCAGTCTGACTTC 59.682 52.174 7.77 0.47 0.00 3.01
1992 4541 3.756933 AAGTGTAGGTTTGCGGTTAGA 57.243 42.857 0.00 0.00 0.00 2.10
1999 4556 5.699097 TCACCATTAAAGTGTAGGTTTGC 57.301 39.130 8.39 0.00 36.58 3.68
2006 4563 6.530120 TCAGAAAGCTCACCATTAAAGTGTA 58.470 36.000 8.39 0.00 36.58 2.90
2009 4566 7.530426 AATTCAGAAAGCTCACCATTAAAGT 57.470 32.000 0.00 0.00 0.00 2.66
2024 4581 7.880160 TCTCAAGAAGGTCAAAATTCAGAAA 57.120 32.000 0.00 0.00 0.00 2.52
2106 4663 8.689972 CCCTCCGTAAAGAAAGTACTATTTAGA 58.310 37.037 0.00 0.00 0.00 2.10
2107 4664 8.689972 TCCCTCCGTAAAGAAAGTACTATTTAG 58.310 37.037 0.00 0.00 0.00 1.85
2109 4666 7.179872 ACTCCCTCCGTAAAGAAAGTACTATTT 59.820 37.037 0.00 0.89 0.00 1.40
2111 4668 6.193504 ACTCCCTCCGTAAAGAAAGTACTAT 58.806 40.000 0.00 0.00 0.00 2.12
2114 4671 4.797800 ACTCCCTCCGTAAAGAAAGTAC 57.202 45.455 0.00 0.00 0.00 2.73
2116 4673 6.041751 CCATATACTCCCTCCGTAAAGAAAGT 59.958 42.308 0.00 0.00 0.00 2.66
2117 4674 6.456501 CCATATACTCCCTCCGTAAAGAAAG 58.543 44.000 0.00 0.00 0.00 2.62
2130 4708 5.045578 ACTGATACCAATGCCATATACTCCC 60.046 44.000 0.00 0.00 0.00 4.30
2153 4731 8.732746 ACAGTAAAATCTTACATGGACCATAC 57.267 34.615 6.67 0.00 40.03 2.39
2155 4733 7.122650 CCAACAGTAAAATCTTACATGGACCAT 59.877 37.037 0.00 0.00 40.03 3.55
2304 4882 1.068055 GCAACCAATCAGAGTGGCTTG 60.068 52.381 17.11 18.64 40.02 4.01
2340 4946 6.151312 ACGAGACTAGCTTCTTTATTCTGTGA 59.849 38.462 0.00 0.00 0.00 3.58
2373 4979 7.013274 TCTGAAAGAACTTGTGGTTTCCATAAG 59.987 37.037 18.80 18.80 46.58 1.73
2466 5073 2.364970 TGGCTTTCCATTCTTTGTGTGG 59.635 45.455 0.00 0.00 37.47 4.17
2520 5127 3.572255 GCTACAGCTATGCTTCTAGAGGT 59.428 47.826 3.55 0.00 36.40 3.85
2521 5128 4.173036 GCTACAGCTATGCTTCTAGAGG 57.827 50.000 0.00 0.00 36.40 3.69
2555 5162 5.321927 TCTTTGGGATGATGATGATGATGG 58.678 41.667 0.00 0.00 0.00 3.51
2580 5187 4.081198 TGCATCTTCTTCTTCCTCCTCTTC 60.081 45.833 0.00 0.00 0.00 2.87
2582 5189 3.448934 TGCATCTTCTTCTTCCTCCTCT 58.551 45.455 0.00 0.00 0.00 3.69
2585 5206 3.938334 GTCTTGCATCTTCTTCTTCCTCC 59.062 47.826 0.00 0.00 0.00 4.30
2604 5225 4.640690 AGCACCGGACCCCAGTCT 62.641 66.667 9.46 0.00 43.05 3.24
2649 5270 4.109656 AAGAGGAGCCCCGGGGAT 62.110 66.667 44.86 40.65 37.50 3.85
2676 5297 1.636340 GATCGTCCGTGATTTGCCG 59.364 57.895 0.00 0.00 0.00 5.69
2685 5306 4.175489 CCGCACTCGATCGTCCGT 62.175 66.667 15.94 8.22 38.10 4.69
2721 5342 2.557555 TGTGGATGAGGATGGAGACT 57.442 50.000 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.