Multiple sequence alignment - TraesCS2A01G449200

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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 TraesCS2A01G449200 chr2A 100.000 2546 0 0 1 2546 698829485 698826940 0.000000e+00 4702.0
1 TraesCS2A01G449200 chr2D 94.431 2065 78 20 510 2546 558242176 558240121 0.000000e+00 3142.0
2 TraesCS2A01G449200 chr2B 91.647 2131 112 23 444 2546 666655293 666653201 0.000000e+00 2889.0
3 TraesCS2A01G449200 chr2B 97.143 35 1 0 86 120 666655385 666655351 2.740000e-05 60.2
4 TraesCS2A01G449200 chr2B 100.000 29 0 0 172 200 399936256 399936228 1.000000e-03 54.7
5 TraesCS2A01G449200 chr1D 84.713 157 16 3 460 615 420083019 420083168 1.580000e-32 150.0
6 TraesCS2A01G449200 chr1D 100.000 28 0 0 172 199 237999974 237999947 5.000000e-03 52.8
7 TraesCS2A01G449200 chr3B 75.824 273 39 12 169 421 723270209 723270474 2.070000e-21 113.0
8 TraesCS2A01G449200 chr4D 98.077 52 1 0 1229 1280 478668240 478668189 9.700000e-15 91.6
9 TraesCS2A01G449200 chr4A 98.077 52 1 0 1229 1280 685301975 685301924 9.700000e-15 91.6
10 TraesCS2A01G449200 chr4B 78.676 136 25 4 255 389 440271078 440270946 1.250000e-13 87.9
11 TraesCS2A01G449200 chr7D 100.000 30 0 0 171 200 106632554 106632525 3.540000e-04 56.5
12 TraesCS2A01G449200 chr1A 92.308 39 3 0 164 202 14149363 14149401 3.540000e-04 56.5
13 TraesCS2A01G449200 chr1A 92.308 39 3 0 164 202 14157352 14157390 3.540000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G449200 chr2A 698826940 698829485 2545 True 4702.0 4702 100.000 1 2546 1 chr2A.!!$R1 2545
1 TraesCS2A01G449200 chr2D 558240121 558242176 2055 True 3142.0 3142 94.431 510 2546 1 chr2D.!!$R1 2036
2 TraesCS2A01G449200 chr2B 666653201 666655385 2184 True 1474.6 2889 94.395 86 2546 2 chr2B.!!$R2 2460

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
507 522 0.036306 ACTTTTACGCACTGGGAGGG 59.964 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 1916 0.037447 GGCTTCTAGATGGGCATCCC 59.963 60.0 12.65 0.0 45.71 3.85 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
26 27 9.803130 GAACAAGTTTTACGGATTAGAAGTTAC 57.197 33.333 0.00 0.00 0.00 2.50
27 28 8.891671 ACAAGTTTTACGGATTAGAAGTTACA 57.108 30.769 0.00 0.00 0.00 2.41
28 29 8.985805 ACAAGTTTTACGGATTAGAAGTTACAG 58.014 33.333 0.00 0.00 0.00 2.74
29 30 9.199982 CAAGTTTTACGGATTAGAAGTTACAGA 57.800 33.333 0.00 0.00 0.00 3.41
30 31 8.983307 AGTTTTACGGATTAGAAGTTACAGAG 57.017 34.615 0.00 0.00 0.00 3.35
31 32 8.583296 AGTTTTACGGATTAGAAGTTACAGAGT 58.417 33.333 0.00 0.00 0.00 3.24
32 33 8.645487 GTTTTACGGATTAGAAGTTACAGAGTG 58.355 37.037 0.00 0.00 0.00 3.51
33 34 7.692460 TTACGGATTAGAAGTTACAGAGTGA 57.308 36.000 0.00 0.00 0.00 3.41
34 35 6.585695 ACGGATTAGAAGTTACAGAGTGAA 57.414 37.500 0.00 0.00 0.00 3.18
35 36 6.989659 ACGGATTAGAAGTTACAGAGTGAAA 58.010 36.000 0.00 0.00 0.00 2.69
36 37 7.612677 ACGGATTAGAAGTTACAGAGTGAAAT 58.387 34.615 0.00 0.00 0.00 2.17
37 38 7.545965 ACGGATTAGAAGTTACAGAGTGAAATG 59.454 37.037 0.00 0.00 0.00 2.32
38 39 7.759886 CGGATTAGAAGTTACAGAGTGAAATGA 59.240 37.037 0.00 0.00 0.00 2.57
39 40 8.874816 GGATTAGAAGTTACAGAGTGAAATGAC 58.125 37.037 0.00 0.00 0.00 3.06
40 41 9.424319 GATTAGAAGTTACAGAGTGAAATGACA 57.576 33.333 0.00 0.00 0.00 3.58
41 42 9.950496 ATTAGAAGTTACAGAGTGAAATGACAT 57.050 29.630 0.00 0.00 0.00 3.06
42 43 7.664082 AGAAGTTACAGAGTGAAATGACATG 57.336 36.000 0.00 0.00 0.00 3.21
43 44 7.445121 AGAAGTTACAGAGTGAAATGACATGA 58.555 34.615 0.00 0.00 0.00 3.07
44 45 7.933577 AGAAGTTACAGAGTGAAATGACATGAA 59.066 33.333 0.00 0.00 0.00 2.57
45 46 7.426929 AGTTACAGAGTGAAATGACATGAAC 57.573 36.000 0.00 0.00 0.00 3.18
46 47 7.220030 AGTTACAGAGTGAAATGACATGAACT 58.780 34.615 0.00 0.00 0.00 3.01
47 48 5.936686 ACAGAGTGAAATGACATGAACTG 57.063 39.130 0.00 0.00 0.00 3.16
48 49 5.614308 ACAGAGTGAAATGACATGAACTGA 58.386 37.500 0.00 0.00 0.00 3.41
49 50 6.236409 ACAGAGTGAAATGACATGAACTGAT 58.764 36.000 0.00 0.00 0.00 2.90
50 51 7.389232 ACAGAGTGAAATGACATGAACTGATA 58.611 34.615 0.00 0.00 0.00 2.15
51 52 8.045507 ACAGAGTGAAATGACATGAACTGATAT 58.954 33.333 0.00 0.00 0.00 1.63
52 53 8.336080 CAGAGTGAAATGACATGAACTGATATG 58.664 37.037 0.00 0.00 0.00 1.78
53 54 7.498239 AGAGTGAAATGACATGAACTGATATGG 59.502 37.037 0.00 0.00 0.00 2.74
54 55 6.544931 AGTGAAATGACATGAACTGATATGGG 59.455 38.462 0.00 0.00 0.00 4.00
55 56 5.829391 TGAAATGACATGAACTGATATGGGG 59.171 40.000 0.00 0.00 0.00 4.96
56 57 3.862877 TGACATGAACTGATATGGGGG 57.137 47.619 0.00 0.00 0.00 5.40
57 58 3.122480 TGACATGAACTGATATGGGGGT 58.878 45.455 0.00 0.00 0.00 4.95
58 59 3.117926 TGACATGAACTGATATGGGGGTG 60.118 47.826 0.00 0.00 0.00 4.61
59 60 2.175499 ACATGAACTGATATGGGGGTGG 59.825 50.000 0.00 0.00 0.00 4.61
60 61 0.550914 TGAACTGATATGGGGGTGGC 59.449 55.000 0.00 0.00 0.00 5.01
61 62 0.178990 GAACTGATATGGGGGTGGCC 60.179 60.000 0.00 0.00 0.00 5.36
62 63 1.994885 AACTGATATGGGGGTGGCCG 61.995 60.000 0.00 0.00 0.00 6.13
63 64 3.174987 TGATATGGGGGTGGCCGG 61.175 66.667 0.00 0.00 0.00 6.13
64 65 4.660938 GATATGGGGGTGGCCGGC 62.661 72.222 21.18 21.18 0.00 6.13
71 72 4.256180 GGGTGGCCGGCTCCATAG 62.256 72.222 30.78 0.00 38.57 2.23
72 73 3.480133 GGTGGCCGGCTCCATAGT 61.480 66.667 28.56 0.00 38.57 2.12
73 74 2.203070 GTGGCCGGCTCCATAGTG 60.203 66.667 28.56 0.00 38.57 2.74
74 75 3.479203 TGGCCGGCTCCATAGTGG 61.479 66.667 28.56 0.00 39.43 4.00
75 76 3.161450 GGCCGGCTCCATAGTGGA 61.161 66.667 28.56 0.00 45.98 4.02
84 85 2.734755 TCCATAGTGGAATGCAAGGG 57.265 50.000 0.00 0.00 45.00 3.95
88 89 0.331278 TAGTGGAATGCAAGGGGTGG 59.669 55.000 0.00 0.00 0.00 4.61
120 121 4.517815 GGCCGCATCCGTCCGTAA 62.518 66.667 0.00 0.00 0.00 3.18
121 122 2.509786 GCCGCATCCGTCCGTAAA 60.510 61.111 0.00 0.00 0.00 2.01
123 124 1.637478 GCCGCATCCGTCCGTAAAAA 61.637 55.000 0.00 0.00 0.00 1.94
125 126 1.399089 CCGCATCCGTCCGTAAAAATT 59.601 47.619 0.00 0.00 0.00 1.82
126 127 2.436670 CGCATCCGTCCGTAAAAATTG 58.563 47.619 0.00 0.00 0.00 2.32
127 128 2.182014 GCATCCGTCCGTAAAAATTGC 58.818 47.619 0.00 0.00 0.00 3.56
128 129 2.792749 CATCCGTCCGTAAAAATTGCC 58.207 47.619 0.00 0.00 0.00 4.52
130 131 0.179184 CCGTCCGTAAAAATTGCCCG 60.179 55.000 0.00 0.00 0.00 6.13
147 162 1.801771 CCCGTACGTTGAGCATTTTCA 59.198 47.619 15.21 0.00 0.00 2.69
150 165 2.720590 CGTACGTTGAGCATTTTCACCG 60.721 50.000 7.22 0.00 38.70 4.94
158 173 2.035321 GAGCATTTTCACCGAAACCCAA 59.965 45.455 0.00 0.00 30.83 4.12
171 186 5.829391 ACCGAAACCCAAACTTATAACAGTT 59.171 36.000 0.00 0.00 38.74 3.16
172 187 6.997476 ACCGAAACCCAAACTTATAACAGTTA 59.003 34.615 0.00 0.00 35.87 2.24
173 188 7.666804 ACCGAAACCCAAACTTATAACAGTTAT 59.333 33.333 10.71 10.71 35.87 1.89
174 189 9.165035 CCGAAACCCAAACTTATAACAGTTATA 57.835 33.333 8.72 8.72 35.87 0.98
175 190 9.977762 CGAAACCCAAACTTATAACAGTTATAC 57.022 33.333 11.93 0.00 35.87 1.47
178 193 9.457436 AACCCAAACTTATAACAGTTATACCTG 57.543 33.333 11.93 8.44 35.87 4.00
179 194 8.050930 ACCCAAACTTATAACAGTTATACCTGG 58.949 37.037 11.93 13.93 35.87 4.45
180 195 7.012989 CCCAAACTTATAACAGTTATACCTGGC 59.987 40.741 11.93 0.00 35.87 4.85
181 196 7.012989 CCAAACTTATAACAGTTATACCTGGCC 59.987 40.741 11.93 0.00 35.87 5.36
182 197 6.818281 ACTTATAACAGTTATACCTGGCCA 57.182 37.500 11.93 4.71 36.75 5.36
183 198 7.388638 ACTTATAACAGTTATACCTGGCCAT 57.611 36.000 5.51 0.00 36.75 4.40
184 199 7.224297 ACTTATAACAGTTATACCTGGCCATG 58.776 38.462 5.51 6.06 36.75 3.66
185 200 3.297134 AACAGTTATACCTGGCCATGG 57.703 47.619 5.51 13.05 36.75 3.66
186 201 1.494721 ACAGTTATACCTGGCCATGGG 59.505 52.381 20.97 16.10 36.75 4.00
187 202 1.774254 CAGTTATACCTGGCCATGGGA 59.226 52.381 17.65 12.89 0.00 4.37
188 203 2.376518 CAGTTATACCTGGCCATGGGAT 59.623 50.000 17.65 18.59 32.00 3.85
189 204 3.587061 CAGTTATACCTGGCCATGGGATA 59.413 47.826 17.65 17.64 29.52 2.59
190 205 3.587506 AGTTATACCTGGCCATGGGATAC 59.412 47.826 20.06 15.91 30.58 2.24
204 219 3.815407 GATACCCGACCCGGCCCTA 62.815 68.421 0.00 0.00 46.86 3.53
205 220 3.170146 ATACCCGACCCGGCCCTAT 62.170 63.158 0.00 0.00 46.86 2.57
206 221 3.815407 TACCCGACCCGGCCCTATC 62.815 68.421 0.00 0.00 46.86 2.08
207 222 4.936081 CCCGACCCGGCCCTATCT 62.936 72.222 0.00 0.00 46.86 1.98
208 223 2.842936 CCGACCCGGCCCTATCTT 60.843 66.667 0.00 0.00 41.17 2.40
209 224 2.421739 CGACCCGGCCCTATCTTG 59.578 66.667 0.00 0.00 0.00 3.02
210 225 2.111251 GACCCGGCCCTATCTTGC 59.889 66.667 0.00 0.00 0.00 4.01
211 226 2.366972 ACCCGGCCCTATCTTGCT 60.367 61.111 0.00 0.00 0.00 3.91
212 227 2.384653 GACCCGGCCCTATCTTGCTC 62.385 65.000 0.00 0.00 0.00 4.26
213 228 2.443394 CCCGGCCCTATCTTGCTCA 61.443 63.158 0.00 0.00 0.00 4.26
214 229 1.227674 CCGGCCCTATCTTGCTCAC 60.228 63.158 0.00 0.00 0.00 3.51
215 230 1.592669 CGGCCCTATCTTGCTCACG 60.593 63.158 0.00 0.00 0.00 4.35
216 231 1.227674 GGCCCTATCTTGCTCACGG 60.228 63.158 0.00 0.00 0.00 4.94
217 232 1.227674 GCCCTATCTTGCTCACGGG 60.228 63.158 0.00 0.00 34.79 5.28
218 233 1.227674 CCCTATCTTGCTCACGGGC 60.228 63.158 0.00 0.00 0.00 6.13
219 234 1.227674 CCTATCTTGCTCACGGGCC 60.228 63.158 0.00 0.00 0.00 5.80
220 235 1.522092 CTATCTTGCTCACGGGCCA 59.478 57.895 4.39 0.00 0.00 5.36
221 236 0.531532 CTATCTTGCTCACGGGCCAG 60.532 60.000 4.39 1.85 0.00 4.85
222 237 2.593468 TATCTTGCTCACGGGCCAGC 62.593 60.000 4.39 5.26 36.08 4.85
238 253 3.248764 GCCATGGGCCTGAGATCT 58.751 61.111 15.13 0.00 44.06 2.75
239 254 2.456627 GCCATGGGCCTGAGATCTA 58.543 57.895 15.13 0.00 44.06 1.98
240 255 0.324285 GCCATGGGCCTGAGATCTAG 59.676 60.000 15.13 0.00 44.06 2.43
241 256 2.021262 CCATGGGCCTGAGATCTAGA 57.979 55.000 2.85 0.00 0.00 2.43
242 257 1.622811 CCATGGGCCTGAGATCTAGAC 59.377 57.143 2.85 0.00 0.00 2.59
243 258 1.622811 CATGGGCCTGAGATCTAGACC 59.377 57.143 4.53 0.00 0.00 3.85
244 259 0.105453 TGGGCCTGAGATCTAGACCC 60.105 60.000 4.53 13.30 36.36 4.46
245 260 1.182385 GGGCCTGAGATCTAGACCCG 61.182 65.000 0.84 0.00 0.00 5.28
246 261 0.178987 GGCCTGAGATCTAGACCCGA 60.179 60.000 0.00 0.00 0.00 5.14
247 262 1.549037 GGCCTGAGATCTAGACCCGAT 60.549 57.143 0.00 0.00 0.00 4.18
248 263 1.543802 GCCTGAGATCTAGACCCGATG 59.456 57.143 0.00 0.00 0.00 3.84
249 264 2.166829 CCTGAGATCTAGACCCGATGG 58.833 57.143 0.00 0.00 37.80 3.51
250 265 1.543802 CTGAGATCTAGACCCGATGGC 59.456 57.143 0.00 0.00 33.59 4.40
251 266 0.892063 GAGATCTAGACCCGATGGCC 59.108 60.000 0.00 0.00 33.59 5.36
252 267 0.896019 AGATCTAGACCCGATGGCCG 60.896 60.000 0.00 0.00 38.18 6.13
272 287 3.399181 CCGGGCCTAGGCTTGACA 61.399 66.667 32.18 0.00 41.60 3.58
273 288 2.746375 CCGGGCCTAGGCTTGACAT 61.746 63.158 32.18 0.00 41.60 3.06
274 289 1.407656 CCGGGCCTAGGCTTGACATA 61.408 60.000 32.18 0.00 41.60 2.29
275 290 0.687354 CGGGCCTAGGCTTGACATAT 59.313 55.000 32.18 0.00 41.60 1.78
276 291 1.072331 CGGGCCTAGGCTTGACATATT 59.928 52.381 32.18 0.00 41.60 1.28
277 292 2.487265 CGGGCCTAGGCTTGACATATTT 60.487 50.000 32.18 0.00 41.60 1.40
278 293 2.887152 GGGCCTAGGCTTGACATATTTG 59.113 50.000 32.18 0.00 41.60 2.32
279 294 3.555966 GGCCTAGGCTTGACATATTTGT 58.444 45.455 32.18 0.00 41.60 2.83
280 295 3.316308 GGCCTAGGCTTGACATATTTGTG 59.684 47.826 32.18 0.00 41.60 3.33
281 296 4.199310 GCCTAGGCTTGACATATTTGTGA 58.801 43.478 27.17 0.00 35.55 3.58
282 297 4.823989 GCCTAGGCTTGACATATTTGTGAT 59.176 41.667 27.17 0.00 35.55 3.06
283 298 5.300286 GCCTAGGCTTGACATATTTGTGATT 59.700 40.000 27.17 0.00 35.55 2.57
284 299 6.183360 GCCTAGGCTTGACATATTTGTGATTT 60.183 38.462 27.17 0.00 35.55 2.17
285 300 7.013274 GCCTAGGCTTGACATATTTGTGATTTA 59.987 37.037 27.17 0.00 35.55 1.40
286 301 8.562892 CCTAGGCTTGACATATTTGTGATTTAG 58.437 37.037 0.00 0.00 35.79 1.85
287 302 9.330063 CTAGGCTTGACATATTTGTGATTTAGA 57.670 33.333 0.00 0.00 35.79 2.10
288 303 8.218338 AGGCTTGACATATTTGTGATTTAGAG 57.782 34.615 0.00 0.00 35.79 2.43
289 304 8.049117 AGGCTTGACATATTTGTGATTTAGAGA 58.951 33.333 0.00 0.00 35.79 3.10
290 305 8.677300 GGCTTGACATATTTGTGATTTAGAGAA 58.323 33.333 0.00 0.00 35.79 2.87
291 306 9.713740 GCTTGACATATTTGTGATTTAGAGAAG 57.286 33.333 0.00 0.00 35.79 2.85
293 308 8.737168 TGACATATTTGTGATTTAGAGAAGGG 57.263 34.615 0.00 0.00 35.79 3.95
294 309 7.283127 TGACATATTTGTGATTTAGAGAAGGGC 59.717 37.037 0.00 0.00 35.79 5.19
295 310 6.547510 ACATATTTGTGATTTAGAGAAGGGCC 59.452 38.462 0.00 0.00 33.85 5.80
296 311 3.366052 TTGTGATTTAGAGAAGGGCCC 57.634 47.619 16.46 16.46 0.00 5.80
297 312 1.209504 TGTGATTTAGAGAAGGGCCCG 59.790 52.381 18.44 0.00 0.00 6.13
298 313 1.485066 GTGATTTAGAGAAGGGCCCGA 59.515 52.381 18.44 0.00 0.00 5.14
299 314 1.485066 TGATTTAGAGAAGGGCCCGAC 59.515 52.381 18.44 14.86 0.00 4.79
300 315 0.837940 ATTTAGAGAAGGGCCCGACC 59.162 55.000 18.44 9.73 37.93 4.79
312 327 4.418328 CCGACCCGATGCCCCAAA 62.418 66.667 0.00 0.00 0.00 3.28
313 328 2.824041 CGACCCGATGCCCCAAAG 60.824 66.667 0.00 0.00 0.00 2.77
314 329 3.140814 GACCCGATGCCCCAAAGC 61.141 66.667 0.00 0.00 0.00 3.51
315 330 4.759205 ACCCGATGCCCCAAAGCC 62.759 66.667 0.00 0.00 0.00 4.35
316 331 4.447342 CCCGATGCCCCAAAGCCT 62.447 66.667 0.00 0.00 0.00 4.58
317 332 3.142838 CCGATGCCCCAAAGCCTG 61.143 66.667 0.00 0.00 0.00 4.85
318 333 3.142838 CGATGCCCCAAAGCCTGG 61.143 66.667 0.00 0.00 45.97 4.45
319 334 3.464494 GATGCCCCAAAGCCTGGC 61.464 66.667 11.65 11.65 44.90 4.85
336 351 2.793946 CGGGCTTTTCCGCTGATG 59.206 61.111 0.00 0.00 43.71 3.07
337 352 2.764314 CGGGCTTTTCCGCTGATGG 61.764 63.158 0.00 0.00 43.71 3.51
338 353 1.378514 GGGCTTTTCCGCTGATGGA 60.379 57.895 0.00 0.00 35.83 3.41
339 354 1.657751 GGGCTTTTCCGCTGATGGAC 61.658 60.000 0.00 0.00 37.89 4.02
340 355 0.678048 GGCTTTTCCGCTGATGGACT 60.678 55.000 0.00 0.00 37.89 3.85
341 356 1.168714 GCTTTTCCGCTGATGGACTT 58.831 50.000 0.00 0.00 37.89 3.01
342 357 1.135575 GCTTTTCCGCTGATGGACTTG 60.136 52.381 0.00 0.00 37.89 3.16
343 358 1.470098 CTTTTCCGCTGATGGACTTGG 59.530 52.381 0.00 0.00 37.89 3.61
344 359 0.960364 TTTCCGCTGATGGACTTGGC 60.960 55.000 0.00 0.00 37.89 4.52
345 360 2.819984 TTCCGCTGATGGACTTGGCC 62.820 60.000 0.00 0.00 37.89 5.36
346 361 2.270205 CGCTGATGGACTTGGCCT 59.730 61.111 3.32 0.00 0.00 5.19
347 362 2.110967 CGCTGATGGACTTGGCCTG 61.111 63.158 3.32 0.00 0.00 4.85
348 363 1.751927 GCTGATGGACTTGGCCTGG 60.752 63.158 3.32 0.00 0.00 4.45
349 364 1.077212 CTGATGGACTTGGCCTGGG 60.077 63.158 3.32 0.00 0.00 4.45
350 365 2.440980 GATGGACTTGGCCTGGGC 60.441 66.667 14.23 14.23 41.06 5.36
362 377 0.908198 GCCTGGGCCTGATATCTAGG 59.092 60.000 12.58 13.78 38.39 3.02
370 385 1.821753 CCTGATATCTAGGCCAGACGG 59.178 57.143 5.01 0.00 35.62 4.79
393 408 4.798682 CCAGGTCCGGGCCTAGGT 62.799 72.222 31.20 1.77 37.04 3.08
394 409 2.687566 CAGGTCCGGGCCTAGGTT 60.688 66.667 31.20 1.25 37.04 3.50
395 410 2.124312 AGGTCCGGGCCTAGGTTT 59.876 61.111 30.70 0.00 37.04 3.27
396 411 1.540617 AGGTCCGGGCCTAGGTTTT 60.541 57.895 30.70 0.00 37.04 2.43
397 412 1.138228 AGGTCCGGGCCTAGGTTTTT 61.138 55.000 30.70 0.00 37.04 1.94
418 433 7.500720 TTTTTGTAGTAGGCTTTGTTAGACC 57.499 36.000 0.00 0.00 29.01 3.85
419 434 4.813750 TGTAGTAGGCTTTGTTAGACCC 57.186 45.455 0.00 0.00 29.01 4.46
420 435 3.194116 TGTAGTAGGCTTTGTTAGACCCG 59.806 47.826 0.00 0.00 29.01 5.28
421 436 2.532843 AGTAGGCTTTGTTAGACCCGA 58.467 47.619 0.00 0.00 29.01 5.14
422 437 2.233186 AGTAGGCTTTGTTAGACCCGAC 59.767 50.000 0.00 0.00 29.01 4.79
423 438 0.323957 AGGCTTTGTTAGACCCGACC 59.676 55.000 0.00 0.00 29.01 4.79
424 439 0.675837 GGCTTTGTTAGACCCGACCC 60.676 60.000 0.00 0.00 0.00 4.46
425 440 1.017701 GCTTTGTTAGACCCGACCCG 61.018 60.000 0.00 0.00 0.00 5.28
426 441 0.604578 CTTTGTTAGACCCGACCCGA 59.395 55.000 0.00 0.00 0.00 5.14
427 442 0.318120 TTTGTTAGACCCGACCCGAC 59.682 55.000 0.00 0.00 0.00 4.79
428 443 0.827089 TTGTTAGACCCGACCCGACA 60.827 55.000 0.00 0.00 0.00 4.35
429 444 0.612732 TGTTAGACCCGACCCGACAT 60.613 55.000 0.00 0.00 0.00 3.06
430 445 1.340893 TGTTAGACCCGACCCGACATA 60.341 52.381 0.00 0.00 0.00 2.29
431 446 1.959282 GTTAGACCCGACCCGACATAT 59.041 52.381 0.00 0.00 0.00 1.78
432 447 1.612676 TAGACCCGACCCGACATATG 58.387 55.000 0.00 0.00 0.00 1.78
433 448 1.113517 AGACCCGACCCGACATATGG 61.114 60.000 7.80 0.00 0.00 2.74
434 449 2.030562 CCCGACCCGACATATGGC 59.969 66.667 7.80 2.25 0.00 4.40
458 473 9.649167 GGCGAGGTATAATAATAGTACACAAAT 57.351 33.333 0.00 0.00 0.00 2.32
500 515 9.791820 ATACTTTTACAAAAACTTTTACGCACT 57.208 25.926 0.00 0.00 0.00 4.40
501 516 7.944997 ACTTTTACAAAAACTTTTACGCACTG 58.055 30.769 0.00 0.00 0.00 3.66
502 517 6.872670 TTTACAAAAACTTTTACGCACTGG 57.127 33.333 0.00 0.00 0.00 4.00
503 518 3.776340 ACAAAAACTTTTACGCACTGGG 58.224 40.909 0.00 0.00 0.00 4.45
504 519 3.444388 ACAAAAACTTTTACGCACTGGGA 59.556 39.130 0.00 0.00 0.00 4.37
505 520 3.982576 AAAACTTTTACGCACTGGGAG 57.017 42.857 0.00 0.00 0.00 4.30
506 521 1.892209 AACTTTTACGCACTGGGAGG 58.108 50.000 0.00 0.00 0.00 4.30
507 522 0.036306 ACTTTTACGCACTGGGAGGG 59.964 55.000 0.00 0.00 0.00 4.30
508 523 1.302993 TTTTACGCACTGGGAGGGC 60.303 57.895 0.00 0.00 42.41 5.19
679 694 2.575694 ACGTACACAACACAACCGTA 57.424 45.000 0.00 0.00 0.00 4.02
764 779 2.373169 CAGGTGATACTACCCATGCCAT 59.627 50.000 0.00 0.00 41.83 4.40
777 792 1.135315 CATGCCATAGTTTGCGCAAGT 60.135 47.619 23.68 16.81 35.87 3.16
783 798 3.304659 CCATAGTTTGCGCAAGTTTCTGT 60.305 43.478 23.68 14.67 41.68 3.41
792 807 1.202132 GCAAGTTTCTGTGTGTCGCAA 60.202 47.619 0.00 0.00 0.00 4.85
883 900 2.900269 AAAACCCCACAACCCCCACC 62.900 60.000 0.00 0.00 0.00 4.61
988 1005 2.107953 CGGGAGCTGAGCTAAGCC 59.892 66.667 20.16 10.96 44.68 4.35
1433 1457 2.264480 CGTGTTCATCCCCAGCGA 59.736 61.111 0.00 0.00 0.00 4.93
1558 1582 2.952245 CGTGAACCGGAGAGACGT 59.048 61.111 9.46 0.00 0.00 4.34
1573 1597 3.053291 CGTGCCCGCCTTTTGCTA 61.053 61.111 0.00 0.00 38.05 3.49
1574 1598 2.877691 GTGCCCGCCTTTTGCTAG 59.122 61.111 0.00 0.00 38.05 3.42
1575 1599 3.061848 TGCCCGCCTTTTGCTAGC 61.062 61.111 8.10 8.10 38.05 3.42
1577 1601 2.765356 GCCCGCCTTTTGCTAGCTC 61.765 63.158 17.23 0.00 38.05 4.09
1584 1609 2.427506 CCTTTTGCTAGCTCCTTCGTT 58.572 47.619 17.23 0.00 0.00 3.85
1621 1646 0.108615 CGTCTTCCAGTTCGAGCCAT 60.109 55.000 0.00 0.00 0.00 4.40
1673 1699 1.519751 CCCGACAAAACCGCCATTGA 61.520 55.000 0.00 0.00 0.00 2.57
1786 1819 1.665916 CGGCGCCTCGATTGATCAT 60.666 57.895 26.68 0.00 0.00 2.45
1794 1827 4.092529 CGCCTCGATTGATCATAGATTTGG 59.907 45.833 0.00 0.00 0.00 3.28
1812 1845 4.927978 TTGGTTTCCATCATCGTTTTGT 57.072 36.364 0.00 0.00 31.53 2.83
1839 1872 1.745489 GGCAGGGTTTAGGCGACAG 60.745 63.158 0.00 0.00 0.00 3.51
1840 1873 1.745489 GCAGGGTTTAGGCGACAGG 60.745 63.158 0.00 0.00 0.00 4.00
1877 1916 0.169230 CACCGAGGAGTTCTGTCTCG 59.831 60.000 0.00 0.00 46.73 4.04
1954 1993 9.396022 GGTTCCTTTAATCTATGATGAAGTGAA 57.604 33.333 0.00 0.00 0.00 3.18
1992 2031 6.291322 CGACATACTTGCAGAGATTTACTTCG 60.291 42.308 3.37 0.00 0.00 3.79
2036 2075 7.012327 ACCGAATTTCAGATACAACATGTATGG 59.988 37.037 7.68 0.00 43.08 2.74
2109 2152 8.189119 AGAATCTAACTCATCTAAGGTCCATC 57.811 38.462 0.00 0.00 0.00 3.51
2132 2175 2.226437 CACCGGAGTTTCATCAAACCTG 59.774 50.000 9.46 0.00 42.72 4.00
2139 2182 5.885912 GGAGTTTCATCAAACCTGCCTAATA 59.114 40.000 0.00 0.00 42.72 0.98
2146 2189 2.362077 CAAACCTGCCTAATACATGCCC 59.638 50.000 0.00 0.00 0.00 5.36
2207 2250 6.263842 TGAATTTTCAGCAGTGTTCTCATTCT 59.736 34.615 0.00 0.00 32.50 2.40
2274 2319 3.198409 TCCTATGCCACACAGCTATTG 57.802 47.619 0.00 0.00 0.00 1.90
2390 2436 5.178797 CGAGAAAGATGTCCAAGGTAATGT 58.821 41.667 0.00 0.00 0.00 2.71
2440 2486 5.882557 GCCATCAGTTGATTTCTTCTAGGAA 59.117 40.000 0.00 0.00 31.21 3.36
2458 2504 9.589111 TTCTAGGAAAATTTAAACCAAACACAC 57.411 29.630 10.24 0.00 0.00 3.82
2459 2505 8.198778 TCTAGGAAAATTTAAACCAAACACACC 58.801 33.333 10.24 0.00 0.00 4.16
2460 2506 6.712276 AGGAAAATTTAAACCAAACACACCA 58.288 32.000 10.24 0.00 0.00 4.17
2461 2507 7.342581 AGGAAAATTTAAACCAAACACACCAT 58.657 30.769 10.24 0.00 0.00 3.55
2462 2508 7.831690 AGGAAAATTTAAACCAAACACACCATT 59.168 29.630 10.24 0.00 0.00 3.16
2463 2509 7.912773 GGAAAATTTAAACCAAACACACCATTG 59.087 33.333 0.00 0.00 0.00 2.82
2464 2510 7.929941 AAATTTAAACCAAACACACCATTGT 57.070 28.000 0.00 0.00 35.84 2.71
2465 2511 7.546778 AATTTAAACCAAACACACCATTGTC 57.453 32.000 0.00 0.00 31.66 3.18
2466 2512 5.923733 TTAAACCAAACACACCATTGTCT 57.076 34.783 0.00 0.00 31.66 3.41
2467 2513 7.406031 TTTAAACCAAACACACCATTGTCTA 57.594 32.000 0.00 0.00 31.66 2.59
2468 2514 7.589958 TTAAACCAAACACACCATTGTCTAT 57.410 32.000 0.00 0.00 31.66 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.803130 GTAACTTCTAATCCGTAAAACTTGTTC 57.197 33.333 0.00 0.00 0.00 3.18
1 2 9.328845 TGTAACTTCTAATCCGTAAAACTTGTT 57.671 29.630 0.00 0.00 0.00 2.83
2 3 8.891671 TGTAACTTCTAATCCGTAAAACTTGT 57.108 30.769 0.00 0.00 0.00 3.16
3 4 9.199982 TCTGTAACTTCTAATCCGTAAAACTTG 57.800 33.333 0.00 0.00 0.00 3.16
4 5 9.420551 CTCTGTAACTTCTAATCCGTAAAACTT 57.579 33.333 0.00 0.00 0.00 2.66
5 6 8.583296 ACTCTGTAACTTCTAATCCGTAAAACT 58.417 33.333 0.00 0.00 0.00 2.66
6 7 8.645487 CACTCTGTAACTTCTAATCCGTAAAAC 58.355 37.037 0.00 0.00 0.00 2.43
7 8 8.579006 TCACTCTGTAACTTCTAATCCGTAAAA 58.421 33.333 0.00 0.00 0.00 1.52
8 9 8.114331 TCACTCTGTAACTTCTAATCCGTAAA 57.886 34.615 0.00 0.00 0.00 2.01
9 10 7.692460 TCACTCTGTAACTTCTAATCCGTAA 57.308 36.000 0.00 0.00 0.00 3.18
10 11 7.692460 TTCACTCTGTAACTTCTAATCCGTA 57.308 36.000 0.00 0.00 0.00 4.02
11 12 6.585695 TTCACTCTGTAACTTCTAATCCGT 57.414 37.500 0.00 0.00 0.00 4.69
12 13 7.759886 TCATTTCACTCTGTAACTTCTAATCCG 59.240 37.037 0.00 0.00 0.00 4.18
13 14 8.874816 GTCATTTCACTCTGTAACTTCTAATCC 58.125 37.037 0.00 0.00 0.00 3.01
14 15 9.424319 TGTCATTTCACTCTGTAACTTCTAATC 57.576 33.333 0.00 0.00 0.00 1.75
15 16 9.950496 ATGTCATTTCACTCTGTAACTTCTAAT 57.050 29.630 0.00 0.00 0.00 1.73
16 17 9.208022 CATGTCATTTCACTCTGTAACTTCTAA 57.792 33.333 0.00 0.00 0.00 2.10
17 18 8.585018 TCATGTCATTTCACTCTGTAACTTCTA 58.415 33.333 0.00 0.00 0.00 2.10
18 19 7.445121 TCATGTCATTTCACTCTGTAACTTCT 58.555 34.615 0.00 0.00 0.00 2.85
19 20 7.658179 TCATGTCATTTCACTCTGTAACTTC 57.342 36.000 0.00 0.00 0.00 3.01
20 21 7.716998 AGTTCATGTCATTTCACTCTGTAACTT 59.283 33.333 0.00 0.00 0.00 2.66
21 22 7.172190 CAGTTCATGTCATTTCACTCTGTAACT 59.828 37.037 0.00 0.00 0.00 2.24
22 23 7.171508 TCAGTTCATGTCATTTCACTCTGTAAC 59.828 37.037 0.00 0.00 0.00 2.50
23 24 7.216494 TCAGTTCATGTCATTTCACTCTGTAA 58.784 34.615 0.00 0.00 0.00 2.41
24 25 6.758254 TCAGTTCATGTCATTTCACTCTGTA 58.242 36.000 0.00 0.00 0.00 2.74
25 26 5.614308 TCAGTTCATGTCATTTCACTCTGT 58.386 37.500 0.00 0.00 0.00 3.41
26 27 6.738832 ATCAGTTCATGTCATTTCACTCTG 57.261 37.500 0.00 0.00 0.00 3.35
27 28 7.498239 CCATATCAGTTCATGTCATTTCACTCT 59.502 37.037 0.00 0.00 0.00 3.24
28 29 7.255035 CCCATATCAGTTCATGTCATTTCACTC 60.255 40.741 0.00 0.00 0.00 3.51
29 30 6.544931 CCCATATCAGTTCATGTCATTTCACT 59.455 38.462 0.00 0.00 0.00 3.41
30 31 6.238842 CCCCATATCAGTTCATGTCATTTCAC 60.239 42.308 0.00 0.00 0.00 3.18
31 32 5.829391 CCCCATATCAGTTCATGTCATTTCA 59.171 40.000 0.00 0.00 0.00 2.69
32 33 5.242393 CCCCCATATCAGTTCATGTCATTTC 59.758 44.000 0.00 0.00 0.00 2.17
33 34 5.142639 CCCCCATATCAGTTCATGTCATTT 58.857 41.667 0.00 0.00 0.00 2.32
34 35 4.168675 ACCCCCATATCAGTTCATGTCATT 59.831 41.667 0.00 0.00 0.00 2.57
35 36 3.723681 ACCCCCATATCAGTTCATGTCAT 59.276 43.478 0.00 0.00 0.00 3.06
36 37 3.117926 CACCCCCATATCAGTTCATGTCA 60.118 47.826 0.00 0.00 0.00 3.58
37 38 3.480470 CACCCCCATATCAGTTCATGTC 58.520 50.000 0.00 0.00 0.00 3.06
38 39 2.175499 CCACCCCCATATCAGTTCATGT 59.825 50.000 0.00 0.00 0.00 3.21
39 40 2.867624 CCACCCCCATATCAGTTCATG 58.132 52.381 0.00 0.00 0.00 3.07
40 41 1.145738 GCCACCCCCATATCAGTTCAT 59.854 52.381 0.00 0.00 0.00 2.57
41 42 0.550914 GCCACCCCCATATCAGTTCA 59.449 55.000 0.00 0.00 0.00 3.18
42 43 0.178990 GGCCACCCCCATATCAGTTC 60.179 60.000 0.00 0.00 0.00 3.01
43 44 1.930520 GGCCACCCCCATATCAGTT 59.069 57.895 0.00 0.00 0.00 3.16
44 45 2.452064 CGGCCACCCCCATATCAGT 61.452 63.158 2.24 0.00 0.00 3.41
45 46 2.431683 CGGCCACCCCCATATCAG 59.568 66.667 2.24 0.00 0.00 2.90
46 47 3.174987 CCGGCCACCCCCATATCA 61.175 66.667 2.24 0.00 0.00 2.15
47 48 4.660938 GCCGGCCACCCCCATATC 62.661 72.222 18.11 0.00 0.00 1.63
54 55 4.256180 CTATGGAGCCGGCCACCC 62.256 72.222 29.24 24.70 41.56 4.61
55 56 3.480133 ACTATGGAGCCGGCCACC 61.480 66.667 26.15 26.61 41.56 4.61
56 57 2.203070 CACTATGGAGCCGGCCAC 60.203 66.667 26.15 17.58 41.56 5.01
57 58 3.479203 CCACTATGGAGCCGGCCA 61.479 66.667 26.15 16.30 40.96 5.36
58 59 3.161450 TCCACTATGGAGCCGGCC 61.161 66.667 26.15 15.07 42.67 6.13
65 66 1.215173 CCCCTTGCATTCCACTATGGA 59.785 52.381 0.00 0.00 46.61 3.41
66 67 1.063717 ACCCCTTGCATTCCACTATGG 60.064 52.381 0.00 0.00 39.43 2.74
67 68 2.026641 CACCCCTTGCATTCCACTATG 58.973 52.381 0.00 0.00 0.00 2.23
68 69 1.063717 CCACCCCTTGCATTCCACTAT 60.064 52.381 0.00 0.00 0.00 2.12
69 70 0.331278 CCACCCCTTGCATTCCACTA 59.669 55.000 0.00 0.00 0.00 2.74
70 71 1.077265 CCACCCCTTGCATTCCACT 59.923 57.895 0.00 0.00 0.00 4.00
71 72 1.984026 CCCACCCCTTGCATTCCAC 60.984 63.158 0.00 0.00 0.00 4.02
72 73 2.444696 CCCACCCCTTGCATTCCA 59.555 61.111 0.00 0.00 0.00 3.53
73 74 2.364186 CCCCACCCCTTGCATTCC 60.364 66.667 0.00 0.00 0.00 3.01
74 75 3.076916 GCCCCACCCCTTGCATTC 61.077 66.667 0.00 0.00 0.00 2.67
78 79 2.847366 TAATTCGCCCCACCCCTTGC 62.847 60.000 0.00 0.00 0.00 4.01
79 80 0.323908 TTAATTCGCCCCACCCCTTG 60.324 55.000 0.00 0.00 0.00 3.61
80 81 0.033503 CTTAATTCGCCCCACCCCTT 60.034 55.000 0.00 0.00 0.00 3.95
81 82 1.613061 CTTAATTCGCCCCACCCCT 59.387 57.895 0.00 0.00 0.00 4.79
82 83 1.455032 CCTTAATTCGCCCCACCCC 60.455 63.158 0.00 0.00 0.00 4.95
83 84 0.465642 CTCCTTAATTCGCCCCACCC 60.466 60.000 0.00 0.00 0.00 4.61
84 85 0.465642 CCTCCTTAATTCGCCCCACC 60.466 60.000 0.00 0.00 0.00 4.61
88 89 1.528542 GGCCCTCCTTAATTCGCCC 60.529 63.158 0.00 0.00 0.00 6.13
120 121 1.068816 GCTCAACGTACGGGCAATTTT 60.069 47.619 21.06 0.00 0.00 1.82
121 122 0.519961 GCTCAACGTACGGGCAATTT 59.480 50.000 21.06 0.00 0.00 1.82
123 124 0.392461 ATGCTCAACGTACGGGCAAT 60.392 50.000 21.06 10.68 36.49 3.56
125 126 0.604243 AAATGCTCAACGTACGGGCA 60.604 50.000 21.06 21.66 37.32 5.36
126 127 0.519961 AAAATGCTCAACGTACGGGC 59.480 50.000 21.06 17.10 0.00 6.13
127 128 1.801771 TGAAAATGCTCAACGTACGGG 59.198 47.619 21.06 11.50 0.00 5.28
128 129 2.412325 GGTGAAAATGCTCAACGTACGG 60.412 50.000 21.06 2.32 0.00 4.02
147 162 5.379187 ACTGTTATAAGTTTGGGTTTCGGT 58.621 37.500 0.00 0.00 0.00 4.69
158 173 7.202972 TGGCCAGGTATAACTGTTATAAGTT 57.797 36.000 18.96 7.56 42.89 2.66
171 186 2.557869 GGTATCCCATGGCCAGGTATA 58.442 52.381 17.55 10.82 0.00 1.47
172 187 1.372501 GGTATCCCATGGCCAGGTAT 58.627 55.000 17.55 11.85 0.00 2.73
173 188 0.770557 GGGTATCCCATGGCCAGGTA 60.771 60.000 17.55 4.21 44.65 3.08
174 189 2.084930 GGGTATCCCATGGCCAGGT 61.085 63.158 17.55 0.00 44.65 4.00
175 190 2.846532 GGGTATCCCATGGCCAGG 59.153 66.667 13.05 12.17 44.65 4.45
176 191 2.146724 TCGGGTATCCCATGGCCAG 61.147 63.158 13.05 2.86 45.83 4.85
177 192 2.040359 TCGGGTATCCCATGGCCA 60.040 61.111 8.56 8.56 45.83 5.36
178 193 2.430367 GTCGGGTATCCCATGGCC 59.570 66.667 6.09 1.21 45.83 5.36
179 194 2.430367 GGTCGGGTATCCCATGGC 59.570 66.667 6.09 0.00 45.83 4.40
180 195 2.879233 CGGGTCGGGTATCCCATGG 61.879 68.421 4.14 4.14 45.83 3.66
181 196 2.741092 CGGGTCGGGTATCCCATG 59.259 66.667 5.64 0.00 45.83 3.66
182 197 2.525877 CCGGGTCGGGTATCCCAT 60.526 66.667 5.64 0.00 45.83 4.00
192 207 2.421739 CAAGATAGGGCCGGGTCG 59.578 66.667 2.18 0.00 0.00 4.79
193 208 2.111251 GCAAGATAGGGCCGGGTC 59.889 66.667 2.18 0.00 0.00 4.46
194 209 2.366972 AGCAAGATAGGGCCGGGT 60.367 61.111 2.18 0.00 0.00 5.28
195 210 2.427753 GAGCAAGATAGGGCCGGG 59.572 66.667 2.18 0.00 0.00 5.73
196 211 1.227674 GTGAGCAAGATAGGGCCGG 60.228 63.158 0.00 0.00 0.00 6.13
197 212 1.592669 CGTGAGCAAGATAGGGCCG 60.593 63.158 0.00 0.00 0.00 6.13
198 213 1.227674 CCGTGAGCAAGATAGGGCC 60.228 63.158 0.00 0.00 0.00 5.80
199 214 1.227674 CCCGTGAGCAAGATAGGGC 60.228 63.158 0.00 0.00 31.58 5.19
200 215 1.227674 GCCCGTGAGCAAGATAGGG 60.228 63.158 0.00 0.00 41.65 3.53
201 216 1.227674 GGCCCGTGAGCAAGATAGG 60.228 63.158 0.00 0.00 0.00 2.57
202 217 0.531532 CTGGCCCGTGAGCAAGATAG 60.532 60.000 0.00 0.00 35.67 2.08
203 218 1.522092 CTGGCCCGTGAGCAAGATA 59.478 57.895 0.00 0.00 35.67 1.98
204 219 2.270205 CTGGCCCGTGAGCAAGAT 59.730 61.111 0.00 0.00 35.67 2.40
205 220 4.704833 GCTGGCCCGTGAGCAAGA 62.705 66.667 7.89 0.00 35.67 3.02
222 237 1.622811 GTCTAGATCTCAGGCCCATGG 59.377 57.143 4.14 4.14 0.00 3.66
223 238 1.622811 GGTCTAGATCTCAGGCCCATG 59.377 57.143 0.00 0.00 31.16 3.66
224 239 2.022718 GGTCTAGATCTCAGGCCCAT 57.977 55.000 0.00 0.00 31.16 4.00
225 240 3.541224 GGTCTAGATCTCAGGCCCA 57.459 57.895 0.00 0.00 31.16 5.36
227 242 0.178987 TCGGGTCTAGATCTCAGGCC 60.179 60.000 0.00 6.40 37.04 5.19
228 243 1.543802 CATCGGGTCTAGATCTCAGGC 59.456 57.143 0.00 0.00 0.00 4.85
229 244 2.166829 CCATCGGGTCTAGATCTCAGG 58.833 57.143 0.00 0.00 0.00 3.86
230 245 1.543802 GCCATCGGGTCTAGATCTCAG 59.456 57.143 0.00 0.00 36.17 3.35
231 246 1.621992 GCCATCGGGTCTAGATCTCA 58.378 55.000 0.00 0.00 36.17 3.27
232 247 0.892063 GGCCATCGGGTCTAGATCTC 59.108 60.000 0.00 0.00 35.27 2.75
233 248 0.896019 CGGCCATCGGGTCTAGATCT 60.896 60.000 2.24 0.00 36.31 2.75
234 249 1.587054 CGGCCATCGGGTCTAGATC 59.413 63.158 2.24 0.00 36.31 2.75
235 250 3.778955 CGGCCATCGGGTCTAGAT 58.221 61.111 2.24 0.00 36.31 1.98
255 270 1.407656 TATGTCAAGCCTAGGCCCGG 61.408 60.000 30.42 19.24 43.17 5.73
256 271 0.687354 ATATGTCAAGCCTAGGCCCG 59.313 55.000 30.42 21.01 43.17 6.13
257 272 2.887152 CAAATATGTCAAGCCTAGGCCC 59.113 50.000 30.42 15.83 43.17 5.80
258 273 3.316308 CACAAATATGTCAAGCCTAGGCC 59.684 47.826 30.42 15.30 38.86 5.19
259 274 4.199310 TCACAAATATGTCAAGCCTAGGC 58.801 43.478 27.19 27.19 37.82 3.93
260 275 6.949352 AATCACAAATATGTCAAGCCTAGG 57.051 37.500 3.67 3.67 37.82 3.02
261 276 9.330063 TCTAAATCACAAATATGTCAAGCCTAG 57.670 33.333 0.00 0.00 37.82 3.02
262 277 9.330063 CTCTAAATCACAAATATGTCAAGCCTA 57.670 33.333 0.00 0.00 37.82 3.93
263 278 8.049117 TCTCTAAATCACAAATATGTCAAGCCT 58.951 33.333 0.00 0.00 37.82 4.58
264 279 8.213518 TCTCTAAATCACAAATATGTCAAGCC 57.786 34.615 0.00 0.00 37.82 4.35
265 280 9.713740 CTTCTCTAAATCACAAATATGTCAAGC 57.286 33.333 0.00 0.00 37.82 4.01
267 282 9.177608 CCCTTCTCTAAATCACAAATATGTCAA 57.822 33.333 0.00 0.00 37.82 3.18
268 283 7.283127 GCCCTTCTCTAAATCACAAATATGTCA 59.717 37.037 0.00 0.00 37.82 3.58
269 284 7.255277 GGCCCTTCTCTAAATCACAAATATGTC 60.255 40.741 0.00 0.00 37.82 3.06
270 285 6.547510 GGCCCTTCTCTAAATCACAAATATGT 59.452 38.462 0.00 0.00 41.61 2.29
271 286 6.015940 GGGCCCTTCTCTAAATCACAAATATG 60.016 42.308 17.04 0.00 0.00 1.78
272 287 6.071320 GGGCCCTTCTCTAAATCACAAATAT 58.929 40.000 17.04 0.00 0.00 1.28
273 288 5.445964 GGGCCCTTCTCTAAATCACAAATA 58.554 41.667 17.04 0.00 0.00 1.40
274 289 4.281657 GGGCCCTTCTCTAAATCACAAAT 58.718 43.478 17.04 0.00 0.00 2.32
275 290 3.697166 GGGCCCTTCTCTAAATCACAAA 58.303 45.455 17.04 0.00 0.00 2.83
276 291 2.355716 CGGGCCCTTCTCTAAATCACAA 60.356 50.000 22.43 0.00 0.00 3.33
277 292 1.209504 CGGGCCCTTCTCTAAATCACA 59.790 52.381 22.43 0.00 0.00 3.58
278 293 1.485066 TCGGGCCCTTCTCTAAATCAC 59.515 52.381 22.43 0.00 0.00 3.06
279 294 1.485066 GTCGGGCCCTTCTCTAAATCA 59.515 52.381 22.43 0.00 0.00 2.57
280 295 1.202663 GGTCGGGCCCTTCTCTAAATC 60.203 57.143 22.43 0.00 0.00 2.17
281 296 0.837940 GGTCGGGCCCTTCTCTAAAT 59.162 55.000 22.43 0.00 0.00 1.40
282 297 2.293877 GGTCGGGCCCTTCTCTAAA 58.706 57.895 22.43 0.00 0.00 1.85
283 298 4.045469 GGTCGGGCCCTTCTCTAA 57.955 61.111 22.43 0.00 0.00 2.10
295 310 4.418328 TTTGGGGCATCGGGTCGG 62.418 66.667 0.00 0.00 0.00 4.79
296 311 2.824041 CTTTGGGGCATCGGGTCG 60.824 66.667 0.00 0.00 0.00 4.79
297 312 3.140814 GCTTTGGGGCATCGGGTC 61.141 66.667 0.00 0.00 0.00 4.46
298 313 4.759205 GGCTTTGGGGCATCGGGT 62.759 66.667 0.00 0.00 40.53 5.28
299 314 4.447342 AGGCTTTGGGGCATCGGG 62.447 66.667 0.00 0.00 43.56 5.14
300 315 3.142838 CAGGCTTTGGGGCATCGG 61.143 66.667 0.00 0.00 43.56 4.18
301 316 3.142838 CCAGGCTTTGGGGCATCG 61.143 66.667 0.00 0.00 43.75 3.84
320 335 1.378514 TCCATCAGCGGAAAAGCCC 60.379 57.895 0.00 0.00 38.01 5.19
321 336 0.678048 AGTCCATCAGCGGAAAAGCC 60.678 55.000 0.00 0.00 36.62 4.35
322 337 1.135575 CAAGTCCATCAGCGGAAAAGC 60.136 52.381 0.00 0.00 36.62 3.51
323 338 1.470098 CCAAGTCCATCAGCGGAAAAG 59.530 52.381 0.00 0.00 36.62 2.27
324 339 1.533625 CCAAGTCCATCAGCGGAAAA 58.466 50.000 0.00 0.00 36.62 2.29
325 340 0.960364 GCCAAGTCCATCAGCGGAAA 60.960 55.000 0.00 0.00 36.62 3.13
326 341 1.377202 GCCAAGTCCATCAGCGGAA 60.377 57.895 0.00 0.00 36.62 4.30
327 342 2.268920 GCCAAGTCCATCAGCGGA 59.731 61.111 0.00 0.00 0.00 5.54
328 343 2.825836 GGCCAAGTCCATCAGCGG 60.826 66.667 0.00 0.00 0.00 5.52
329 344 2.110967 CAGGCCAAGTCCATCAGCG 61.111 63.158 5.01 0.00 0.00 5.18
330 345 1.751927 CCAGGCCAAGTCCATCAGC 60.752 63.158 5.01 0.00 0.00 4.26
331 346 1.077212 CCCAGGCCAAGTCCATCAG 60.077 63.158 5.01 0.00 0.00 2.90
332 347 3.089838 CCCAGGCCAAGTCCATCA 58.910 61.111 5.01 0.00 0.00 3.07
333 348 2.440980 GCCCAGGCCAAGTCCATC 60.441 66.667 5.01 0.00 34.56 3.51
343 358 0.908198 CCTAGATATCAGGCCCAGGC 59.092 60.000 5.32 0.00 41.06 4.85
350 365 1.821753 CCGTCTGGCCTAGATATCAGG 59.178 57.143 3.32 10.58 37.83 3.86
376 391 4.798682 ACCTAGGCCCGGACCTGG 62.799 72.222 21.23 17.31 41.34 4.45
377 392 1.848886 AAAACCTAGGCCCGGACCTG 61.849 60.000 21.23 6.03 41.34 4.00
378 393 1.138228 AAAAACCTAGGCCCGGACCT 61.138 55.000 15.88 15.88 44.31 3.85
379 394 1.381463 AAAAACCTAGGCCCGGACC 59.619 57.895 15.24 0.00 0.00 4.46
394 409 6.487668 GGGTCTAACAAAGCCTACTACAAAAA 59.512 38.462 0.00 0.00 0.00 1.94
395 410 5.999600 GGGTCTAACAAAGCCTACTACAAAA 59.000 40.000 0.00 0.00 0.00 2.44
396 411 5.554070 GGGTCTAACAAAGCCTACTACAAA 58.446 41.667 0.00 0.00 0.00 2.83
397 412 4.322198 CGGGTCTAACAAAGCCTACTACAA 60.322 45.833 0.00 0.00 31.98 2.41
398 413 3.194116 CGGGTCTAACAAAGCCTACTACA 59.806 47.826 0.00 0.00 31.98 2.74
399 414 3.445096 TCGGGTCTAACAAAGCCTACTAC 59.555 47.826 0.00 0.00 31.98 2.73
400 415 3.445096 GTCGGGTCTAACAAAGCCTACTA 59.555 47.826 0.00 0.00 31.98 1.82
401 416 2.233186 GTCGGGTCTAACAAAGCCTACT 59.767 50.000 0.00 0.00 31.98 2.57
402 417 2.614779 GTCGGGTCTAACAAAGCCTAC 58.385 52.381 0.00 0.00 31.98 3.18
403 418 1.551883 GGTCGGGTCTAACAAAGCCTA 59.448 52.381 0.00 0.00 31.98 3.93
404 419 0.323957 GGTCGGGTCTAACAAAGCCT 59.676 55.000 0.00 0.00 31.98 4.58
405 420 0.675837 GGGTCGGGTCTAACAAAGCC 60.676 60.000 0.00 0.00 0.00 4.35
406 421 1.017701 CGGGTCGGGTCTAACAAAGC 61.018 60.000 0.00 0.00 0.00 3.51
407 422 0.604578 TCGGGTCGGGTCTAACAAAG 59.395 55.000 0.00 0.00 0.00 2.77
408 423 0.318120 GTCGGGTCGGGTCTAACAAA 59.682 55.000 0.00 0.00 0.00 2.83
409 424 0.827089 TGTCGGGTCGGGTCTAACAA 60.827 55.000 0.00 0.00 0.00 2.83
410 425 0.612732 ATGTCGGGTCGGGTCTAACA 60.613 55.000 0.00 0.00 0.00 2.41
411 426 1.392589 TATGTCGGGTCGGGTCTAAC 58.607 55.000 0.00 0.00 0.00 2.34
412 427 1.958579 CATATGTCGGGTCGGGTCTAA 59.041 52.381 0.00 0.00 0.00 2.10
413 428 1.612676 CATATGTCGGGTCGGGTCTA 58.387 55.000 0.00 0.00 0.00 2.59
414 429 1.113517 CCATATGTCGGGTCGGGTCT 61.114 60.000 1.24 0.00 0.00 3.85
415 430 1.366366 CCATATGTCGGGTCGGGTC 59.634 63.158 1.24 0.00 0.00 4.46
416 431 2.803817 GCCATATGTCGGGTCGGGT 61.804 63.158 1.24 0.00 0.00 5.28
417 432 2.030562 GCCATATGTCGGGTCGGG 59.969 66.667 1.24 0.00 0.00 5.14
418 433 2.355837 CGCCATATGTCGGGTCGG 60.356 66.667 0.00 0.00 0.00 4.79
419 434 1.371758 CTCGCCATATGTCGGGTCG 60.372 63.158 6.28 0.00 0.00 4.79
420 435 1.006102 CCTCGCCATATGTCGGGTC 60.006 63.158 5.18 0.00 0.00 4.46
421 436 0.468585 TACCTCGCCATATGTCGGGT 60.469 55.000 18.62 18.62 34.97 5.28
422 437 0.895530 ATACCTCGCCATATGTCGGG 59.104 55.000 6.28 2.08 0.00 5.14
423 438 3.861276 TTATACCTCGCCATATGTCGG 57.139 47.619 6.28 1.27 0.00 4.79
424 439 8.350722 ACTATTATTATACCTCGCCATATGTCG 58.649 37.037 0.00 0.00 0.00 4.35
429 444 9.465199 TGTGTACTATTATTATACCTCGCCATA 57.535 33.333 0.00 0.00 0.00 2.74
430 445 8.357290 TGTGTACTATTATTATACCTCGCCAT 57.643 34.615 0.00 0.00 0.00 4.40
431 446 7.764141 TGTGTACTATTATTATACCTCGCCA 57.236 36.000 0.00 0.00 0.00 5.69
432 447 9.649167 ATTTGTGTACTATTATTATACCTCGCC 57.351 33.333 0.00 0.00 0.00 5.54
447 462 9.177608 ACGTAAGACTACCATATTTGTGTACTA 57.822 33.333 0.00 0.00 43.62 1.82
448 463 8.059798 ACGTAAGACTACCATATTTGTGTACT 57.940 34.615 0.00 0.00 43.62 2.73
449 464 9.956720 ATACGTAAGACTACCATATTTGTGTAC 57.043 33.333 0.00 0.00 43.62 2.90
497 512 3.465403 CTCTCCGCCCTCCCAGTG 61.465 72.222 0.00 0.00 0.00 3.66
498 513 4.787280 CCTCTCCGCCCTCCCAGT 62.787 72.222 0.00 0.00 0.00 4.00
501 516 3.161853 TATCCCTCTCCGCCCTCCC 62.162 68.421 0.00 0.00 0.00 4.30
502 517 1.608046 CTATCCCTCTCCGCCCTCC 60.608 68.421 0.00 0.00 0.00 4.30
503 518 0.404812 TACTATCCCTCTCCGCCCTC 59.595 60.000 0.00 0.00 0.00 4.30
504 519 0.858369 TTACTATCCCTCTCCGCCCT 59.142 55.000 0.00 0.00 0.00 5.19
505 520 0.967662 GTTACTATCCCTCTCCGCCC 59.032 60.000 0.00 0.00 0.00 6.13
506 521 0.967662 GGTTACTATCCCTCTCCGCC 59.032 60.000 0.00 0.00 0.00 6.13
507 522 1.340568 GTGGTTACTATCCCTCTCCGC 59.659 57.143 0.00 0.00 0.00 5.54
508 523 1.962100 GGTGGTTACTATCCCTCTCCG 59.038 57.143 0.00 0.00 0.00 4.63
764 779 2.680841 ACACAGAAACTTGCGCAAACTA 59.319 40.909 25.01 0.94 0.00 2.24
777 792 1.295792 GAGGTTGCGACACACAGAAA 58.704 50.000 6.39 0.00 0.00 2.52
783 798 2.661537 CTGCGAGGTTGCGACACA 60.662 61.111 6.39 0.00 37.81 3.72
792 807 2.254546 TTTGTTCATGTCTGCGAGGT 57.745 45.000 0.00 0.00 0.00 3.85
883 900 1.103987 TAGAGGCTGCTAGTGAGGCG 61.104 60.000 0.00 0.00 40.84 5.52
1433 1457 3.295273 TGGAGAGCAGCACGTCGT 61.295 61.111 0.00 0.00 0.00 4.34
1573 1597 0.956633 TCACACGTAACGAAGGAGCT 59.043 50.000 0.00 0.00 0.00 4.09
1574 1598 1.992170 ATCACACGTAACGAAGGAGC 58.008 50.000 0.00 0.00 0.00 4.70
1575 1599 3.834610 AGAATCACACGTAACGAAGGAG 58.165 45.455 0.00 0.00 0.00 3.69
1577 1601 4.985044 AAAGAATCACACGTAACGAAGG 57.015 40.909 0.00 0.00 0.00 3.46
1584 1609 6.529125 GGAAGACGAATAAAGAATCACACGTA 59.471 38.462 0.00 0.00 33.10 3.57
1621 1646 6.104665 TGCCATTATTCATTCGATGCAAAAA 58.895 32.000 0.00 0.00 0.00 1.94
1673 1699 0.560688 TCCCCTTTGGAGGCTTTGTT 59.439 50.000 0.00 0.00 42.09 2.83
1745 1778 5.163591 CGAGGCCCACATATATTATACGACA 60.164 44.000 0.00 0.00 0.00 4.35
1786 1819 7.040062 ACAAAACGATGATGGAAACCAAATCTA 60.040 33.333 0.00 0.00 36.95 1.98
1794 1827 7.116819 GTGAAAAACAAAACGATGATGGAAAC 58.883 34.615 0.00 0.00 0.00 2.78
1834 1867 1.854743 CATCATAACTGTCGCCTGTCG 59.145 52.381 0.00 0.00 40.15 4.35
1835 1868 2.604914 CACATCATAACTGTCGCCTGTC 59.395 50.000 0.00 0.00 0.00 3.51
1837 1870 2.604914 GTCACATCATAACTGTCGCCTG 59.395 50.000 0.00 0.00 0.00 4.85
1839 1872 2.348666 GTGTCACATCATAACTGTCGCC 59.651 50.000 0.00 0.00 0.00 5.54
1840 1873 2.348666 GGTGTCACATCATAACTGTCGC 59.651 50.000 5.12 0.00 0.00 5.19
1877 1916 0.037447 GGCTTCTAGATGGGCATCCC 59.963 60.000 12.65 0.00 45.71 3.85
1954 1993 7.589395 TGCAAGTATGTCGTTGAAATGTAATT 58.411 30.769 0.00 0.00 38.98 1.40
1972 2011 5.401531 ACCGAAGTAAATCTCTGCAAGTA 57.598 39.130 0.00 0.00 33.76 2.24
1992 2031 9.524496 AAATTCGGTATCCCCTATAATAAAACC 57.476 33.333 0.00 0.00 0.00 3.27
2014 2053 7.557358 TGCTCCATACATGTTGTATCTGAAATT 59.443 33.333 2.30 0.00 41.28 1.82
2036 2075 3.852536 CGTAGTTGTAGCTAGTGTTGCTC 59.147 47.826 0.00 0.00 41.46 4.26
2090 2129 5.598830 GGTGAGATGGACCTTAGATGAGTTA 59.401 44.000 0.00 0.00 0.00 2.24
2109 2152 2.484264 GGTTTGATGAAACTCCGGTGAG 59.516 50.000 11.17 0.00 41.21 3.51
2132 2175 2.228822 CCGATTTGGGCATGTATTAGGC 59.771 50.000 0.00 0.00 34.76 3.93
2139 2182 2.306847 GGATTACCGATTTGGGCATGT 58.693 47.619 0.00 0.00 44.64 3.21
2195 2238 5.382618 AATTGCCTGAAGAATGAGAACAC 57.617 39.130 0.00 0.00 0.00 3.32
2207 2250 3.252554 ACCTGGGTAAAATTGCCTGAA 57.747 42.857 0.00 0.00 33.03 3.02
2251 2296 2.048444 AGCTGTGTGGCATAGGATTG 57.952 50.000 0.00 0.00 34.17 2.67
2274 2319 5.295787 TCAACATATTAGAATTGGTGACCGC 59.704 40.000 0.00 0.00 32.38 5.68
2390 2436 5.533528 TCGGAATGGTATCGACTAGAAATCA 59.466 40.000 0.00 0.00 0.00 2.57
2440 2486 7.826744 AGACAATGGTGTGTTTGGTTTAAATTT 59.173 29.630 0.00 0.00 38.41 1.82
2452 2498 8.107095 ACCACTAATAATAGACAATGGTGTGTT 58.893 33.333 0.00 0.00 38.41 3.32
2468 2514 9.519191 TCTGTTGTGTACTAGTACCACTAATAA 57.481 33.333 26.41 11.70 35.26 1.40


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

AutoCloner maintained by Alex Coulton.