Multiple sequence alignment - TraesCS7D01G008100

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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 TraesCS7D01G008100 chr7D 100.000 2584 0 0 1 2584 3953956 3956539 0.000000e+00 4772
1 TraesCS7D01G008100 chr7D 95.113 2087 65 13 531 2584 3938232 3940314 0.000000e+00 3254
2 TraesCS7D01G008100 chr7D 99.142 466 4 0 1 466 562053986 562053521 0.000000e+00 839
3 TraesCS7D01G008100 chr4A 95.636 1925 68 5 467 2380 741332212 741330293 0.000000e+00 3075
4 TraesCS7D01G008100 chr4A 95.273 1925 79 4 467 2380 741381460 741379537 0.000000e+00 3040
5 TraesCS7D01G008100 chr4A 95.169 1925 81 4 467 2380 741345310 741343387 0.000000e+00 3029
6 TraesCS7D01G008100 chr4A 95.171 1926 80 5 467 2380 741389646 741387722 0.000000e+00 3029
7 TraesCS7D01G008100 chr4A 94.751 1924 87 4 467 2380 741314185 741312266 0.000000e+00 2981
8 TraesCS7D01G008100 chr4A 95.833 216 7 2 2370 2584 741330276 741330062 5.290000e-92 348
9 TraesCS7D01G008100 chr4A 94.419 215 12 0 2370 2584 741343368 741343154 5.330000e-87 331
10 TraesCS7D01G008100 chr4A 94.419 215 12 0 2370 2584 741379518 741379304 5.330000e-87 331
11 TraesCS7D01G008100 chr4A 94.091 220 7 3 2370 2584 741387705 741387487 1.920000e-86 329
12 TraesCS7D01G008100 chrUn 94.956 1923 71 10 469 2380 51344749 51346656 0.000000e+00 2990
13 TraesCS7D01G008100 chrUn 94.805 1925 88 4 467 2380 290419657 290421580 0.000000e+00 2990
14 TraesCS7D01G008100 chrUn 94.805 1925 88 4 467 2380 324111676 324113599 0.000000e+00 2990
15 TraesCS7D01G008100 chrUn 94.967 1828 76 5 564 2380 51354847 51356669 0.000000e+00 2852
16 TraesCS7D01G008100 chrUn 94.340 583 24 1 467 1040 392799912 392799330 0.000000e+00 885
17 TraesCS7D01G008100 chrUn 99.143 467 1 1 1 467 152288294 152288757 0.000000e+00 837
18 TraesCS7D01G008100 chrUn 96.296 216 6 2 2370 2584 290421597 290421811 1.140000e-93 353
19 TraesCS7D01G008100 chrUn 96.296 216 6 2 2370 2584 324113616 324113830 1.140000e-93 353
20 TraesCS7D01G008100 chrUn 94.419 215 12 0 2370 2584 51346675 51346889 5.330000e-87 331
21 TraesCS7D01G008100 chrUn 94.419 215 12 0 2370 2584 410325066 410325280 5.330000e-87 331
22 TraesCS7D01G008100 chr6D 99.356 466 3 0 1 466 47286615 47287080 0.000000e+00 845
23 TraesCS7D01G008100 chr5D 99.356 466 2 1 1 466 13824188 13823724 0.000000e+00 843
24 TraesCS7D01G008100 chr5D 99.143 467 2 2 1 467 68436391 68435927 0.000000e+00 839
25 TraesCS7D01G008100 chr4D 99.142 466 4 0 1 466 481513027 481513492 0.000000e+00 839
26 TraesCS7D01G008100 chr4D 98.936 470 1 3 1 469 478961880 478961414 0.000000e+00 837
27 TraesCS7D01G008100 chr1D 98.734 474 2 2 1 474 11855156 11854687 0.000000e+00 839
28 TraesCS7D01G008100 chr2D 96.933 489 13 2 1 489 625983770 625983284 0.000000e+00 819


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 TraesCS7D01G008100 chr7D 3953956 3956539 2583 False 4772.0 4772 100.0000 1 2584 1 chr7D.!!$F2 2583
1 TraesCS7D01G008100 chr7D 3938232 3940314 2082 False 3254.0 3254 95.1130 531 2584 1 chr7D.!!$F1 2053
2 TraesCS7D01G008100 chr4A 741312266 741314185 1919 True 2981.0 2981 94.7510 467 2380 1 chr4A.!!$R1 1913
3 TraesCS7D01G008100 chr4A 741330062 741332212 2150 True 1711.5 3075 95.7345 467 2584 2 chr4A.!!$R2 2117
4 TraesCS7D01G008100 chr4A 741379304 741381460 2156 True 1685.5 3040 94.8460 467 2584 2 chr4A.!!$R4 2117
5 TraesCS7D01G008100 chr4A 741343154 741345310 2156 True 1680.0 3029 94.7940 467 2584 2 chr4A.!!$R3 2117
6 TraesCS7D01G008100 chr4A 741387487 741389646 2159 True 1679.0 3029 94.6310 467 2584 2 chr4A.!!$R5 2117
7 TraesCS7D01G008100 chrUn 51354847 51356669 1822 False 2852.0 2852 94.9670 564 2380 1 chrUn.!!$F1 1816
8 TraesCS7D01G008100 chrUn 290419657 290421811 2154 False 1671.5 2990 95.5505 467 2584 2 chrUn.!!$F5 2117
9 TraesCS7D01G008100 chrUn 324111676 324113830 2154 False 1671.5 2990 95.5505 467 2584 2 chrUn.!!$F6 2117
10 TraesCS7D01G008100 chrUn 51344749 51346889 2140 False 1660.5 2990 94.6875 469 2584 2 chrUn.!!$F4 2115
11 TraesCS7D01G008100 chrUn 392799330 392799912 582 True 885.0 885 94.3400 467 1040 1 chrUn.!!$R1 573

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
330 331 0.035739 GCCACAAGAACCGGGACTAA 59.964 55.0 6.32 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1600 0.179234 TGAAATCCCGGCGCATAGAA 59.821 50.0 10.83 0.0 0.0 2.1 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
21 22 4.982241 ATATGGTCACCCGAGATTGAAT 57.018 40.909 0.00 0.00 0.00 2.57
23 24 4.982241 ATGGTCACCCGAGATTGAATAT 57.018 40.909 0.00 0.00 0.00 1.28
24 25 7.733773 ATATGGTCACCCGAGATTGAATATA 57.266 36.000 0.00 0.00 0.00 0.86
25 26 6.627087 ATGGTCACCCGAGATTGAATATAT 57.373 37.500 0.00 0.00 0.00 0.86
26 27 7.733773 ATGGTCACCCGAGATTGAATATATA 57.266 36.000 0.00 0.00 0.00 0.86
27 28 7.733773 TGGTCACCCGAGATTGAATATATAT 57.266 36.000 0.00 0.00 0.00 0.86
28 29 8.146053 TGGTCACCCGAGATTGAATATATATT 57.854 34.615 7.72 7.72 0.00 1.28
29 30 9.262240 TGGTCACCCGAGATTGAATATATATTA 57.738 33.333 7.97 0.00 0.00 0.98
58 59 7.880160 TTCCTCTTGAATTCTTCTTGTTTGA 57.120 32.000 7.05 0.00 0.00 2.69
59 60 7.880160 TCCTCTTGAATTCTTCTTGTTTGAA 57.120 32.000 7.05 0.00 0.00 2.69
60 61 8.292444 TCCTCTTGAATTCTTCTTGTTTGAAA 57.708 30.769 7.05 0.00 0.00 2.69
61 62 8.917088 TCCTCTTGAATTCTTCTTGTTTGAAAT 58.083 29.630 7.05 0.00 0.00 2.17
62 63 9.538508 CCTCTTGAATTCTTCTTGTTTGAAATT 57.461 29.630 7.05 0.00 0.00 1.82
71 72 9.761504 TTCTTCTTGTTTGAAATTTCATATGCA 57.238 25.926 21.10 13.98 37.00 3.96
72 73 9.932207 TCTTCTTGTTTGAAATTTCATATGCAT 57.068 25.926 21.10 3.79 37.00 3.96
73 74 9.967245 CTTCTTGTTTGAAATTTCATATGCATG 57.033 29.630 21.10 16.75 37.00 4.06
74 75 9.491675 TTCTTGTTTGAAATTTCATATGCATGT 57.508 25.926 21.10 0.00 37.00 3.21
104 105 8.991243 AGTAGCGTAAAATATGTGTACTGAAA 57.009 30.769 0.00 0.00 0.00 2.69
105 106 8.866956 AGTAGCGTAAAATATGTGTACTGAAAC 58.133 33.333 0.00 0.00 0.00 2.78
106 107 7.900782 AGCGTAAAATATGTGTACTGAAACT 57.099 32.000 0.00 0.00 0.00 2.66
107 108 8.319143 AGCGTAAAATATGTGTACTGAAACTT 57.681 30.769 0.00 0.00 0.00 2.66
108 109 8.780249 AGCGTAAAATATGTGTACTGAAACTTT 58.220 29.630 0.00 0.00 0.00 2.66
176 177 8.542497 AAAACACTCCAAACTAAAAAGAAACC 57.458 30.769 0.00 0.00 0.00 3.27
177 178 6.844097 ACACTCCAAACTAAAAAGAAACCA 57.156 33.333 0.00 0.00 0.00 3.67
178 179 6.863275 ACACTCCAAACTAAAAAGAAACCAG 58.137 36.000 0.00 0.00 0.00 4.00
179 180 6.127451 ACACTCCAAACTAAAAAGAAACCAGG 60.127 38.462 0.00 0.00 0.00 4.45
180 181 5.955959 ACTCCAAACTAAAAAGAAACCAGGT 59.044 36.000 0.00 0.00 0.00 4.00
181 182 6.439375 ACTCCAAACTAAAAAGAAACCAGGTT 59.561 34.615 0.00 0.00 0.00 3.50
182 183 7.038587 ACTCCAAACTAAAAAGAAACCAGGTTT 60.039 33.333 18.10 18.10 38.54 3.27
183 184 8.363761 TCCAAACTAAAAAGAAACCAGGTTTA 57.636 30.769 18.08 0.05 35.77 2.01
184 185 8.471609 TCCAAACTAAAAAGAAACCAGGTTTAG 58.528 33.333 18.08 12.44 35.77 1.85
185 186 7.709182 CCAAACTAAAAAGAAACCAGGTTTAGG 59.291 37.037 18.08 5.85 35.77 2.69
186 187 6.971726 ACTAAAAAGAAACCAGGTTTAGGG 57.028 37.500 18.08 6.79 35.77 3.53
187 188 5.836898 ACTAAAAAGAAACCAGGTTTAGGGG 59.163 40.000 18.08 7.27 35.77 4.79
188 189 2.992847 AAGAAACCAGGTTTAGGGGG 57.007 50.000 18.08 0.00 35.77 5.40
208 209 1.471287 GGCTAAAACCCTAAACCTGCG 59.529 52.381 0.00 0.00 0.00 5.18
209 210 1.471287 GCTAAAACCCTAAACCTGCGG 59.529 52.381 0.00 0.00 0.00 5.69
210 211 2.876892 GCTAAAACCCTAAACCTGCGGA 60.877 50.000 0.00 0.00 0.00 5.54
211 212 1.905637 AAAACCCTAAACCTGCGGAG 58.094 50.000 0.00 0.00 0.00 4.63
212 213 0.037734 AAACCCTAAACCTGCGGAGG 59.962 55.000 22.94 22.94 46.21 4.30
213 214 0.838987 AACCCTAAACCTGCGGAGGA 60.839 55.000 31.46 6.29 42.93 3.71
221 222 3.309582 CTGCGGAGGAGCCCTTTA 58.690 61.111 0.00 0.00 40.50 1.85
222 223 1.144936 CTGCGGAGGAGCCCTTTAG 59.855 63.158 0.00 0.00 40.50 1.85
223 224 1.612442 TGCGGAGGAGCCCTTTAGT 60.612 57.895 0.00 0.00 31.76 2.24
224 225 1.144276 GCGGAGGAGCCCTTTAGTC 59.856 63.158 0.00 0.00 31.76 2.59
225 226 1.823976 CGGAGGAGCCCTTTAGTCC 59.176 63.158 0.00 0.00 31.76 3.85
226 227 1.687297 CGGAGGAGCCCTTTAGTCCC 61.687 65.000 0.00 0.00 31.76 4.46
227 228 1.687297 GGAGGAGCCCTTTAGTCCCG 61.687 65.000 0.00 0.00 31.76 5.14
228 229 1.687297 GAGGAGCCCTTTAGTCCCGG 61.687 65.000 0.00 0.00 31.76 5.73
229 230 1.993948 GGAGCCCTTTAGTCCCGGT 60.994 63.158 0.00 0.00 0.00 5.28
230 231 1.559965 GGAGCCCTTTAGTCCCGGTT 61.560 60.000 0.00 0.00 0.00 4.44
231 232 0.392595 GAGCCCTTTAGTCCCGGTTG 60.393 60.000 0.00 0.00 0.00 3.77
232 233 1.378119 GCCCTTTAGTCCCGGTTGG 60.378 63.158 0.00 0.00 0.00 3.77
233 234 1.378119 CCCTTTAGTCCCGGTTGGC 60.378 63.158 0.00 0.00 0.00 4.52
234 235 1.378119 CCTTTAGTCCCGGTTGGCC 60.378 63.158 0.00 0.00 0.00 5.36
235 236 1.377229 CTTTAGTCCCGGTTGGCCA 59.623 57.895 0.00 0.00 34.09 5.36
236 237 0.958876 CTTTAGTCCCGGTTGGCCAC 60.959 60.000 3.88 0.00 34.09 5.01
237 238 2.734948 TTTAGTCCCGGTTGGCCACG 62.735 60.000 3.88 6.91 34.09 4.94
241 242 4.323477 CCCGGTTGGCCACGAGAA 62.323 66.667 16.74 0.00 34.09 2.87
242 243 3.047877 CCGGTTGGCCACGAGAAC 61.048 66.667 16.74 6.64 34.09 3.01
243 244 3.047877 CGGTTGGCCACGAGAACC 61.048 66.667 3.88 9.64 36.55 3.62
244 245 3.047877 GGTTGGCCACGAGAACCG 61.048 66.667 3.88 0.00 45.44 4.44
245 246 3.047877 GTTGGCCACGAGAACCGG 61.048 66.667 3.88 0.00 43.93 5.28
246 247 4.323477 TTGGCCACGAGAACCGGG 62.323 66.667 3.88 0.00 43.93 5.73
248 249 4.754667 GGCCACGAGAACCGGGAC 62.755 72.222 6.32 0.00 46.66 4.46
249 250 3.692406 GCCACGAGAACCGGGACT 61.692 66.667 6.32 4.01 46.66 3.85
250 251 2.345760 GCCACGAGAACCGGGACTA 61.346 63.158 6.32 0.00 46.66 2.59
251 252 1.880819 GCCACGAGAACCGGGACTAA 61.881 60.000 6.32 0.00 46.66 2.24
252 253 0.604578 CCACGAGAACCGGGACTAAA 59.395 55.000 6.32 0.00 46.66 1.85
253 254 1.403780 CCACGAGAACCGGGACTAAAG 60.404 57.143 6.32 2.68 46.66 1.85
254 255 0.893447 ACGAGAACCGGGACTAAAGG 59.107 55.000 6.32 0.00 43.93 3.11
255 256 0.893447 CGAGAACCGGGACTAAAGGT 59.107 55.000 6.32 0.00 40.50 3.50
256 257 1.135170 CGAGAACCGGGACTAAAGGTC 60.135 57.143 6.32 0.00 43.79 3.85
264 265 1.521141 GACTAAAGGTCCTCCGCCC 59.479 63.158 0.00 0.00 38.93 6.13
265 266 1.969200 GACTAAAGGTCCTCCGCCCC 61.969 65.000 0.00 0.00 38.93 5.80
266 267 3.078836 TAAAGGTCCTCCGCCCCG 61.079 66.667 0.00 0.00 39.05 5.73
267 268 3.605412 TAAAGGTCCTCCGCCCCGA 62.605 63.158 0.00 0.00 39.05 5.14
299 300 4.636435 CCACGTGGACGGGCCTTT 62.636 66.667 31.31 0.00 42.34 3.11
300 301 2.344500 CACGTGGACGGGCCTTTA 59.656 61.111 7.95 0.00 44.95 1.85
301 302 1.740296 CACGTGGACGGGCCTTTAG 60.740 63.158 7.95 0.00 44.95 1.85
302 303 2.212110 ACGTGGACGGGCCTTTAGT 61.212 57.895 0.84 0.00 44.95 2.24
303 304 1.447314 CGTGGACGGGCCTTTAGTC 60.447 63.158 0.84 7.66 37.63 2.59
305 306 2.588439 GGACGGGCCTTTAGTCCC 59.412 66.667 21.39 9.76 46.40 4.46
309 310 2.588439 GGGCCTTTAGTCCCGGTC 59.412 66.667 0.84 0.00 32.00 4.79
310 311 2.295602 GGGCCTTTAGTCCCGGTCA 61.296 63.158 0.84 0.00 32.00 4.02
311 312 1.221021 GGCCTTTAGTCCCGGTCAG 59.779 63.158 0.00 0.00 0.00 3.51
312 313 1.449778 GCCTTTAGTCCCGGTCAGC 60.450 63.158 0.00 0.00 0.00 4.26
313 314 1.221021 CCTTTAGTCCCGGTCAGCC 59.779 63.158 0.00 0.00 0.00 4.85
314 315 1.550130 CCTTTAGTCCCGGTCAGCCA 61.550 60.000 0.00 0.00 34.09 4.75
315 316 0.391263 CTTTAGTCCCGGTCAGCCAC 60.391 60.000 0.00 0.00 34.09 5.01
316 317 1.122632 TTTAGTCCCGGTCAGCCACA 61.123 55.000 0.00 0.00 34.09 4.17
317 318 1.122632 TTAGTCCCGGTCAGCCACAA 61.123 55.000 0.00 0.00 34.09 3.33
318 319 1.541310 TAGTCCCGGTCAGCCACAAG 61.541 60.000 0.00 0.00 34.09 3.16
319 320 2.525629 TCCCGGTCAGCCACAAGA 60.526 61.111 0.00 0.00 34.09 3.02
320 321 2.144078 TCCCGGTCAGCCACAAGAA 61.144 57.895 0.00 0.00 34.09 2.52
321 322 1.966451 CCCGGTCAGCCACAAGAAC 60.966 63.158 0.00 0.00 34.09 3.01
322 323 1.966451 CCGGTCAGCCACAAGAACC 60.966 63.158 0.00 0.00 34.09 3.62
323 324 2.317609 CGGTCAGCCACAAGAACCG 61.318 63.158 0.00 0.00 34.09 4.44
324 325 1.966451 GGTCAGCCACAAGAACCGG 60.966 63.158 0.00 0.00 34.09 5.28
325 326 1.966451 GTCAGCCACAAGAACCGGG 60.966 63.158 6.32 0.00 0.00 5.73
326 327 2.144078 TCAGCCACAAGAACCGGGA 61.144 57.895 6.32 0.00 0.00 5.14
327 328 1.966451 CAGCCACAAGAACCGGGAC 60.966 63.158 6.32 0.00 0.00 4.46
328 329 2.147387 AGCCACAAGAACCGGGACT 61.147 57.895 6.32 0.73 0.00 3.85
329 330 0.834687 AGCCACAAGAACCGGGACTA 60.835 55.000 6.32 0.00 0.00 2.59
330 331 0.035739 GCCACAAGAACCGGGACTAA 59.964 55.000 6.32 0.00 0.00 2.24
331 332 1.543871 GCCACAAGAACCGGGACTAAA 60.544 52.381 6.32 0.00 0.00 1.85
332 333 2.423577 CCACAAGAACCGGGACTAAAG 58.576 52.381 6.32 1.44 0.00 1.85
333 334 1.804748 CACAAGAACCGGGACTAAAGC 59.195 52.381 6.32 0.00 0.00 3.51
334 335 1.271217 ACAAGAACCGGGACTAAAGCC 60.271 52.381 6.32 0.00 0.00 4.35
335 336 1.003233 CAAGAACCGGGACTAAAGCCT 59.997 52.381 6.32 0.00 0.00 4.58
336 337 1.359168 AGAACCGGGACTAAAGCCTT 58.641 50.000 6.32 0.00 0.00 4.35
337 338 1.703513 AGAACCGGGACTAAAGCCTTT 59.296 47.619 6.32 0.00 0.00 3.11
338 339 2.908351 AGAACCGGGACTAAAGCCTTTA 59.092 45.455 6.32 0.00 0.00 1.85
339 340 3.055312 AGAACCGGGACTAAAGCCTTTAG 60.055 47.826 20.10 20.10 46.26 1.85
346 347 2.005971 CTAAAGCCTTTAGTCGCGGT 57.994 50.000 14.78 0.00 38.21 5.68
347 348 1.925185 CTAAAGCCTTTAGTCGCGGTC 59.075 52.381 14.78 0.00 38.21 4.79
348 349 0.672711 AAAGCCTTTAGTCGCGGTCC 60.673 55.000 6.13 0.00 0.00 4.46
349 350 2.830704 AAGCCTTTAGTCGCGGTCCG 62.831 60.000 6.99 6.99 38.61 4.79
350 351 2.570181 CCTTTAGTCGCGGTCCGT 59.430 61.111 13.94 0.00 38.35 4.69
351 352 1.802636 CCTTTAGTCGCGGTCCGTA 59.197 57.895 13.94 0.00 38.35 4.02
352 353 0.171007 CCTTTAGTCGCGGTCCGTAA 59.829 55.000 13.94 0.27 38.35 3.18
353 354 1.542544 CTTTAGTCGCGGTCCGTAAG 58.457 55.000 13.94 5.19 38.35 2.34
354 355 1.131126 CTTTAGTCGCGGTCCGTAAGA 59.869 52.381 13.94 7.60 43.02 2.10
355 356 0.729116 TTAGTCGCGGTCCGTAAGAG 59.271 55.000 13.94 0.05 43.02 2.85
356 357 1.091771 TAGTCGCGGTCCGTAAGAGG 61.092 60.000 13.94 0.00 43.02 3.69
357 358 3.818787 TCGCGGTCCGTAAGAGGC 61.819 66.667 13.94 0.00 43.02 4.70
361 362 3.818787 GGTCCGTAAGAGGCGCGA 61.819 66.667 12.10 0.00 43.02 5.87
362 363 2.578981 GTCCGTAAGAGGCGCGAC 60.579 66.667 12.10 7.34 43.02 5.19
363 364 2.749044 TCCGTAAGAGGCGCGACT 60.749 61.111 18.34 18.34 43.02 4.18
364 365 1.450134 TCCGTAAGAGGCGCGACTA 60.450 57.895 18.29 0.00 43.02 2.59
365 366 1.026182 TCCGTAAGAGGCGCGACTAA 61.026 55.000 18.29 0.00 43.02 2.24
366 367 0.179156 CCGTAAGAGGCGCGACTAAA 60.179 55.000 18.29 0.00 43.02 1.85
367 368 1.189403 CGTAAGAGGCGCGACTAAAG 58.811 55.000 18.29 1.48 43.02 1.85
368 369 1.557651 GTAAGAGGCGCGACTAAAGG 58.442 55.000 18.29 0.00 0.00 3.11
369 370 0.458669 TAAGAGGCGCGACTAAAGGG 59.541 55.000 18.29 0.00 0.00 3.95
370 371 2.202892 GAGGCGCGACTAAAGGGG 60.203 66.667 18.29 0.00 0.00 4.79
371 372 3.735037 GAGGCGCGACTAAAGGGGG 62.735 68.421 18.29 0.00 0.00 5.40
388 389 2.850439 GGGGGTTGTCTTTAGTCGC 58.150 57.895 0.00 0.00 0.00 5.19
389 390 1.017701 GGGGGTTGTCTTTAGTCGCG 61.018 60.000 0.00 0.00 0.00 5.87
390 391 1.632948 GGGGTTGTCTTTAGTCGCGC 61.633 60.000 0.00 0.00 0.00 6.86
391 392 0.947180 GGGTTGTCTTTAGTCGCGCA 60.947 55.000 8.75 0.00 0.00 6.09
392 393 1.076332 GGTTGTCTTTAGTCGCGCAT 58.924 50.000 8.75 0.00 0.00 4.73
393 394 2.264813 GGTTGTCTTTAGTCGCGCATA 58.735 47.619 8.75 0.00 0.00 3.14
394 395 2.864343 GGTTGTCTTTAGTCGCGCATAT 59.136 45.455 8.75 0.00 0.00 1.78
395 396 3.308866 GGTTGTCTTTAGTCGCGCATATT 59.691 43.478 8.75 0.00 0.00 1.28
396 397 4.201783 GGTTGTCTTTAGTCGCGCATATTT 60.202 41.667 8.75 0.00 0.00 1.40
397 398 5.005971 GGTTGTCTTTAGTCGCGCATATTTA 59.994 40.000 8.75 0.00 0.00 1.40
398 399 5.883328 TGTCTTTAGTCGCGCATATTTAG 57.117 39.130 8.75 0.00 0.00 1.85
399 400 5.345702 TGTCTTTAGTCGCGCATATTTAGT 58.654 37.500 8.75 0.00 0.00 2.24
400 401 5.457799 TGTCTTTAGTCGCGCATATTTAGTC 59.542 40.000 8.75 0.00 0.00 2.59
401 402 4.980434 TCTTTAGTCGCGCATATTTAGTCC 59.020 41.667 8.75 0.00 0.00 3.85
402 403 2.150397 AGTCGCGCATATTTAGTCCC 57.850 50.000 8.75 0.00 0.00 4.46
403 404 0.782384 GTCGCGCATATTTAGTCCCG 59.218 55.000 8.75 0.00 0.00 5.14
404 405 0.319211 TCGCGCATATTTAGTCCCGG 60.319 55.000 8.75 0.00 0.00 5.73
405 406 0.599204 CGCGCATATTTAGTCCCGGT 60.599 55.000 8.75 0.00 0.00 5.28
406 407 1.589803 GCGCATATTTAGTCCCGGTT 58.410 50.000 0.30 0.00 0.00 4.44
407 408 1.263217 GCGCATATTTAGTCCCGGTTG 59.737 52.381 0.30 0.00 0.00 3.77
408 409 1.263217 CGCATATTTAGTCCCGGTTGC 59.737 52.381 0.00 0.00 0.00 4.17
409 410 2.294074 GCATATTTAGTCCCGGTTGCA 58.706 47.619 0.00 0.00 0.00 4.08
410 411 2.032924 GCATATTTAGTCCCGGTTGCAC 59.967 50.000 0.00 0.00 0.00 4.57
411 412 3.275143 CATATTTAGTCCCGGTTGCACA 58.725 45.455 0.00 0.00 0.00 4.57
412 413 1.821216 ATTTAGTCCCGGTTGCACAG 58.179 50.000 0.00 0.00 0.00 3.66
413 414 0.887387 TTTAGTCCCGGTTGCACAGC 60.887 55.000 0.00 0.00 0.00 4.40
414 415 2.741486 TTAGTCCCGGTTGCACAGCC 62.741 60.000 0.00 0.00 0.00 4.85
420 421 4.643387 GGTTGCACAGCCGGGACT 62.643 66.667 2.18 0.00 0.00 3.85
421 422 2.345991 GTTGCACAGCCGGGACTA 59.654 61.111 2.18 0.00 0.00 2.59
422 423 1.302192 GTTGCACAGCCGGGACTAA 60.302 57.895 2.18 0.00 0.00 2.24
423 424 0.887387 GTTGCACAGCCGGGACTAAA 60.887 55.000 2.18 0.00 0.00 1.85
424 425 0.605319 TTGCACAGCCGGGACTAAAG 60.605 55.000 2.18 0.00 0.00 1.85
425 426 1.745489 GCACAGCCGGGACTAAAGG 60.745 63.158 2.18 0.00 0.00 3.11
429 430 2.669240 GCCGGGACTAAAGGCTGT 59.331 61.111 2.18 0.00 46.83 4.40
430 431 1.002502 GCCGGGACTAAAGGCTGTT 60.003 57.895 2.18 0.00 46.83 3.16
431 432 1.305930 GCCGGGACTAAAGGCTGTTG 61.306 60.000 2.18 0.00 46.83 3.33
432 433 1.305930 CCGGGACTAAAGGCTGTTGC 61.306 60.000 0.00 0.00 38.76 4.17
433 434 1.635663 CGGGACTAAAGGCTGTTGCG 61.636 60.000 0.00 0.00 40.82 4.85
434 435 0.321298 GGGACTAAAGGCTGTTGCGA 60.321 55.000 0.00 0.00 40.82 5.10
435 436 1.519408 GGACTAAAGGCTGTTGCGAA 58.481 50.000 0.00 0.00 40.82 4.70
436 437 1.197036 GGACTAAAGGCTGTTGCGAAC 59.803 52.381 0.00 0.00 40.82 3.95
437 438 1.197036 GACTAAAGGCTGTTGCGAACC 59.803 52.381 0.00 0.00 40.82 3.62
438 439 0.165944 CTAAAGGCTGTTGCGAACCG 59.834 55.000 0.00 0.00 40.82 4.44
439 440 1.231958 TAAAGGCTGTTGCGAACCGG 61.232 55.000 0.00 0.00 40.82 5.28
442 443 3.723348 GCTGTTGCGAACCGGGAC 61.723 66.667 6.32 0.00 0.00 4.46
443 444 2.030562 CTGTTGCGAACCGGGACT 59.969 61.111 6.32 0.00 0.00 3.85
444 445 1.290955 CTGTTGCGAACCGGGACTA 59.709 57.895 6.32 0.00 0.00 2.59
445 446 0.320073 CTGTTGCGAACCGGGACTAA 60.320 55.000 6.32 0.00 0.00 2.24
446 447 0.106335 TGTTGCGAACCGGGACTAAA 59.894 50.000 6.32 0.00 0.00 1.85
447 448 0.794473 GTTGCGAACCGGGACTAAAG 59.206 55.000 6.32 0.00 0.00 1.85
448 449 0.320946 TTGCGAACCGGGACTAAAGG 60.321 55.000 6.32 0.00 0.00 3.11
449 450 1.449070 GCGAACCGGGACTAAAGGG 60.449 63.158 6.32 0.00 0.00 3.95
450 451 1.449070 CGAACCGGGACTAAAGGGC 60.449 63.158 6.32 0.00 0.00 5.19
451 452 1.896122 CGAACCGGGACTAAAGGGCT 61.896 60.000 6.32 0.00 0.00 5.19
452 453 0.327259 GAACCGGGACTAAAGGGCTT 59.673 55.000 6.32 0.00 0.00 4.35
453 454 0.775542 AACCGGGACTAAAGGGCTTT 59.224 50.000 6.32 0.00 36.63 3.51
454 455 0.775542 ACCGGGACTAAAGGGCTTTT 59.224 50.000 6.32 0.00 34.23 2.27
455 456 1.146359 ACCGGGACTAAAGGGCTTTTT 59.854 47.619 6.32 0.00 34.23 1.94
559 560 8.795786 TTTGCTCGCATTATATTTCCAATAAC 57.204 30.769 0.00 0.00 0.00 1.89
978 988 8.097038 AGTCTTAGATCATCAGCAAGTTTTGTA 58.903 33.333 0.00 0.00 0.00 2.41
993 1003 9.124807 GCAAGTTTTGTAAGATAAACATACACC 57.875 33.333 0.00 0.00 36.85 4.16
1196 1207 3.864583 TGCAAAATTCTTGACAAGTGTGC 59.135 39.130 14.75 12.59 0.00 4.57
1357 1369 4.218417 GTCATTGAGTATTGCAAGTTGGGT 59.782 41.667 4.94 0.00 0.00 4.51
1388 1400 0.248458 CGTCTGCAACACCACAAACC 60.248 55.000 0.00 0.00 0.00 3.27
1473 1485 7.088589 TGATTGTTTCTAAAGCAAGCTATCC 57.911 36.000 0.00 0.00 30.85 2.59
1578 1590 3.253230 GTTGAATTTGCCGCAGCTATTT 58.747 40.909 0.00 0.00 40.80 1.40
1588 1600 4.580167 TGCCGCAGCTATTTCATAAGAAAT 59.420 37.500 10.51 10.51 45.28 2.17
1612 1624 2.828095 CGCCGGGATTTCATGCCA 60.828 61.111 2.18 0.00 41.46 4.92
1641 1653 4.437820 GTCGAAATGTTCTTGTTGTCTTGC 59.562 41.667 0.00 0.00 0.00 4.01
1708 1720 8.506140 TTTTTGTTTCTTTGCATCTATCGAAG 57.494 30.769 0.00 0.00 0.00 3.79
1784 1797 3.529948 TGGTGTGCCATTTCCTTGT 57.470 47.368 0.00 0.00 40.46 3.16
1799 1812 3.734463 TCCTTGTGAAAATGTGCTCGTA 58.266 40.909 0.00 0.00 0.00 3.43
1844 1858 8.567948 ACAGTATCCAATAAAAGTGTCAACTTG 58.432 33.333 0.00 0.00 46.15 3.16
1976 1990 1.370587 CGTCGGACCACTCTCCTCTC 61.371 65.000 1.91 0.00 0.00 3.20
1980 1994 0.750182 GGACCACTCTCCTCTCCTCG 60.750 65.000 0.00 0.00 0.00 4.63
1992 2006 2.619332 CCTCTCCTCGAACTCTTCCTGA 60.619 54.545 0.00 0.00 0.00 3.86
2250 2264 1.676678 GCCGCCACTCCTGTCATCTA 61.677 60.000 0.00 0.00 0.00 1.98
2252 2266 0.387202 CGCCACTCCTGTCATCTAGG 59.613 60.000 0.00 0.00 36.63 3.02
2329 2343 1.626321 TCGGGTGGACTTTGCTATGAA 59.374 47.619 0.00 0.00 0.00 2.57
2336 2350 5.335191 GGTGGACTTTGCTATGAAAGAACAG 60.335 44.000 0.00 0.00 36.58 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 9.761504 TGCATATGAAATTTCAAACAAGAAGAA 57.238 25.926 23.91 1.93 41.13 2.52
46 47 9.932207 ATGCATATGAAATTTCAAACAAGAAGA 57.068 25.926 23.91 4.00 41.13 2.87
47 48 9.967245 CATGCATATGAAATTTCAAACAAGAAG 57.033 29.630 23.91 9.77 41.13 2.85
48 49 9.491675 ACATGCATATGAAATTTCAAACAAGAA 57.508 25.926 23.91 8.45 41.13 2.52
79 80 8.866956 GTTTCAGTACACATATTTTACGCTACT 58.133 33.333 0.00 0.00 0.00 2.57
80 81 8.866956 AGTTTCAGTACACATATTTTACGCTAC 58.133 33.333 0.00 0.00 0.00 3.58
81 82 8.991243 AGTTTCAGTACACATATTTTACGCTA 57.009 30.769 0.00 0.00 0.00 4.26
82 83 7.900782 AGTTTCAGTACACATATTTTACGCT 57.099 32.000 0.00 0.00 0.00 5.07
83 84 8.944212 AAAGTTTCAGTACACATATTTTACGC 57.056 30.769 0.00 0.00 0.00 4.42
150 151 9.642327 GGTTTCTTTTTAGTTTGGAGTGTTTTA 57.358 29.630 0.00 0.00 0.00 1.52
151 152 8.151596 TGGTTTCTTTTTAGTTTGGAGTGTTTT 58.848 29.630 0.00 0.00 0.00 2.43
152 153 7.672240 TGGTTTCTTTTTAGTTTGGAGTGTTT 58.328 30.769 0.00 0.00 0.00 2.83
153 154 7.234661 TGGTTTCTTTTTAGTTTGGAGTGTT 57.765 32.000 0.00 0.00 0.00 3.32
154 155 6.127451 CCTGGTTTCTTTTTAGTTTGGAGTGT 60.127 38.462 0.00 0.00 0.00 3.55
155 156 6.127451 ACCTGGTTTCTTTTTAGTTTGGAGTG 60.127 38.462 0.00 0.00 0.00 3.51
156 157 5.955959 ACCTGGTTTCTTTTTAGTTTGGAGT 59.044 36.000 0.00 0.00 0.00 3.85
157 158 6.465439 ACCTGGTTTCTTTTTAGTTTGGAG 57.535 37.500 0.00 0.00 0.00 3.86
158 159 6.860790 AACCTGGTTTCTTTTTAGTTTGGA 57.139 33.333 6.18 0.00 0.00 3.53
159 160 7.709182 CCTAAACCTGGTTTCTTTTTAGTTTGG 59.291 37.037 26.95 7.28 37.01 3.28
160 161 7.709182 CCCTAAACCTGGTTTCTTTTTAGTTTG 59.291 37.037 26.95 6.67 37.01 2.93
161 162 7.147620 CCCCTAAACCTGGTTTCTTTTTAGTTT 60.148 37.037 26.95 2.76 37.01 2.66
162 163 6.325545 CCCCTAAACCTGGTTTCTTTTTAGTT 59.674 38.462 26.95 3.28 37.01 2.24
163 164 5.836898 CCCCTAAACCTGGTTTCTTTTTAGT 59.163 40.000 26.95 4.03 37.01 2.24
164 165 5.245301 CCCCCTAAACCTGGTTTCTTTTTAG 59.755 44.000 26.95 17.19 37.01 1.85
165 166 5.149239 CCCCCTAAACCTGGTTTCTTTTTA 58.851 41.667 26.95 8.87 37.01 1.52
166 167 3.971305 CCCCCTAAACCTGGTTTCTTTTT 59.029 43.478 26.95 6.26 37.01 1.94
167 168 3.583228 CCCCCTAAACCTGGTTTCTTTT 58.417 45.455 26.95 7.01 37.01 2.27
168 169 3.254093 CCCCCTAAACCTGGTTTCTTT 57.746 47.619 26.95 7.40 37.01 2.52
169 170 2.992847 CCCCCTAAACCTGGTTTCTT 57.007 50.000 26.95 7.77 37.01 2.52
188 189 1.471287 CGCAGGTTTAGGGTTTTAGCC 59.529 52.381 0.00 0.00 35.59 3.93
189 190 2.913777 CGCAGGTTTAGGGTTTTAGC 57.086 50.000 0.00 0.00 0.00 3.09
204 205 1.144936 CTAAAGGGCTCCTCCGCAG 59.855 63.158 0.00 0.00 34.94 5.18
205 206 1.612442 ACTAAAGGGCTCCTCCGCA 60.612 57.895 0.00 0.00 34.94 5.69
206 207 1.144276 GACTAAAGGGCTCCTCCGC 59.856 63.158 0.00 0.00 34.94 5.54
207 208 1.687297 GGGACTAAAGGGCTCCTCCG 61.687 65.000 0.00 0.00 34.94 4.63
208 209 1.687297 CGGGACTAAAGGGCTCCTCC 61.687 65.000 0.00 0.00 30.89 4.30
209 210 1.687297 CCGGGACTAAAGGGCTCCTC 61.687 65.000 0.00 0.00 30.89 3.71
210 211 1.689582 CCGGGACTAAAGGGCTCCT 60.690 63.158 0.00 0.00 33.87 3.69
211 212 1.559965 AACCGGGACTAAAGGGCTCC 61.560 60.000 6.32 0.00 0.00 4.70
212 213 0.392595 CAACCGGGACTAAAGGGCTC 60.393 60.000 6.32 0.00 0.00 4.70
213 214 1.683441 CAACCGGGACTAAAGGGCT 59.317 57.895 6.32 0.00 0.00 5.19
214 215 1.378119 CCAACCGGGACTAAAGGGC 60.378 63.158 6.32 0.00 40.01 5.19
215 216 1.378119 GCCAACCGGGACTAAAGGG 60.378 63.158 6.32 0.00 40.01 3.95
216 217 1.378119 GGCCAACCGGGACTAAAGG 60.378 63.158 6.32 0.00 43.78 3.11
217 218 4.313819 GGCCAACCGGGACTAAAG 57.686 61.111 6.32 0.00 43.78 1.85
224 225 4.323477 TTCTCGTGGCCAACCGGG 62.323 66.667 7.24 8.50 39.70 5.73
225 226 3.047877 GTTCTCGTGGCCAACCGG 61.048 66.667 7.24 0.00 39.70 5.28
226 227 3.047877 GGTTCTCGTGGCCAACCG 61.048 66.667 7.24 8.56 39.70 4.44
227 228 3.047877 CGGTTCTCGTGGCCAACC 61.048 66.667 7.24 10.79 36.91 3.77
228 229 3.047877 CCGGTTCTCGTGGCCAAC 61.048 66.667 7.24 0.03 37.11 3.77
229 230 4.323477 CCCGGTTCTCGTGGCCAA 62.323 66.667 7.24 0.00 37.11 4.52
231 232 4.754667 GTCCCGGTTCTCGTGGCC 62.755 72.222 0.00 0.00 37.11 5.36
232 233 1.880819 TTAGTCCCGGTTCTCGTGGC 61.881 60.000 0.00 0.00 37.11 5.01
233 234 0.604578 TTTAGTCCCGGTTCTCGTGG 59.395 55.000 0.00 0.00 37.11 4.94
234 235 1.403780 CCTTTAGTCCCGGTTCTCGTG 60.404 57.143 0.00 0.00 37.11 4.35
235 236 0.893447 CCTTTAGTCCCGGTTCTCGT 59.107 55.000 0.00 0.00 37.11 4.18
236 237 0.893447 ACCTTTAGTCCCGGTTCTCG 59.107 55.000 0.00 0.00 38.88 4.04
237 238 2.669300 GACCTTTAGTCCCGGTTCTC 57.331 55.000 0.00 0.00 39.84 2.87
246 247 1.521141 GGGCGGAGGACCTTTAGTC 59.479 63.158 0.00 0.00 45.51 2.59
247 248 1.993948 GGGGCGGAGGACCTTTAGT 60.994 63.158 0.00 0.00 43.03 2.24
248 249 2.908796 GGGGCGGAGGACCTTTAG 59.091 66.667 0.00 0.00 43.03 1.85
249 250 3.078836 CGGGGCGGAGGACCTTTA 61.079 66.667 0.00 0.00 43.03 1.85
282 283 3.242897 TAAAGGCCCGTCCACGTGG 62.243 63.158 29.26 29.26 37.29 4.94
283 284 1.740296 CTAAAGGCCCGTCCACGTG 60.740 63.158 9.08 9.08 37.29 4.49
284 285 2.163601 GACTAAAGGCCCGTCCACGT 62.164 60.000 0.00 0.00 37.29 4.49
285 286 1.447314 GACTAAAGGCCCGTCCACG 60.447 63.158 0.00 0.00 37.29 4.94
286 287 1.078637 GGACTAAAGGCCCGTCCAC 60.079 63.158 20.23 2.00 45.08 4.02
287 288 3.395630 GGACTAAAGGCCCGTCCA 58.604 61.111 20.23 0.00 45.08 4.02
288 289 2.588439 GGGACTAAAGGCCCGTCC 59.412 66.667 18.06 18.06 45.02 4.79
292 293 2.253403 CTGACCGGGACTAAAGGCCC 62.253 65.000 11.29 11.29 41.11 5.80
293 294 1.221021 CTGACCGGGACTAAAGGCC 59.779 63.158 6.32 0.00 0.00 5.19
294 295 1.449778 GCTGACCGGGACTAAAGGC 60.450 63.158 6.32 0.00 0.00 4.35
295 296 1.221021 GGCTGACCGGGACTAAAGG 59.779 63.158 6.32 0.00 0.00 3.11
296 297 0.391263 GTGGCTGACCGGGACTAAAG 60.391 60.000 6.32 0.00 39.70 1.85
297 298 1.122632 TGTGGCTGACCGGGACTAAA 61.123 55.000 6.32 0.00 39.70 1.85
298 299 1.122632 TTGTGGCTGACCGGGACTAA 61.123 55.000 6.32 0.00 39.70 2.24
299 300 1.534476 TTGTGGCTGACCGGGACTA 60.534 57.895 6.32 0.00 39.70 2.59
300 301 2.847234 TTGTGGCTGACCGGGACT 60.847 61.111 6.32 0.00 39.70 3.85
301 302 2.358737 CTTGTGGCTGACCGGGAC 60.359 66.667 6.32 0.00 39.70 4.46
302 303 2.144078 TTCTTGTGGCTGACCGGGA 61.144 57.895 6.32 0.00 39.70 5.14
303 304 1.966451 GTTCTTGTGGCTGACCGGG 60.966 63.158 6.32 0.00 39.70 5.73
304 305 1.966451 GGTTCTTGTGGCTGACCGG 60.966 63.158 0.00 0.00 39.70 5.28
305 306 2.317609 CGGTTCTTGTGGCTGACCG 61.318 63.158 0.00 0.00 39.70 4.79
306 307 1.966451 CCGGTTCTTGTGGCTGACC 60.966 63.158 0.00 0.00 0.00 4.02
307 308 1.966451 CCCGGTTCTTGTGGCTGAC 60.966 63.158 0.00 0.00 0.00 3.51
308 309 2.144078 TCCCGGTTCTTGTGGCTGA 61.144 57.895 0.00 0.00 0.00 4.26
309 310 1.966451 GTCCCGGTTCTTGTGGCTG 60.966 63.158 0.00 0.00 0.00 4.85
310 311 0.834687 TAGTCCCGGTTCTTGTGGCT 60.835 55.000 0.00 0.00 0.00 4.75
311 312 0.035739 TTAGTCCCGGTTCTTGTGGC 59.964 55.000 0.00 0.00 0.00 5.01
312 313 2.423577 CTTTAGTCCCGGTTCTTGTGG 58.576 52.381 0.00 0.00 0.00 4.17
313 314 1.804748 GCTTTAGTCCCGGTTCTTGTG 59.195 52.381 0.00 0.00 0.00 3.33
314 315 1.271217 GGCTTTAGTCCCGGTTCTTGT 60.271 52.381 0.00 0.00 0.00 3.16
315 316 1.003233 AGGCTTTAGTCCCGGTTCTTG 59.997 52.381 0.00 0.00 0.00 3.02
316 317 1.359168 AGGCTTTAGTCCCGGTTCTT 58.641 50.000 0.00 0.00 0.00 2.52
317 318 1.359168 AAGGCTTTAGTCCCGGTTCT 58.641 50.000 0.00 0.15 0.00 3.01
318 319 2.195741 AAAGGCTTTAGTCCCGGTTC 57.804 50.000 11.52 0.00 0.00 3.62
319 320 3.345508 CTAAAGGCTTTAGTCCCGGTT 57.654 47.619 30.21 2.75 38.21 4.44
327 328 1.925185 GACCGCGACTAAAGGCTTTAG 59.075 52.381 34.37 34.37 46.26 1.85
328 329 1.404583 GGACCGCGACTAAAGGCTTTA 60.405 52.381 18.11 18.11 0.00 1.85
329 330 0.672711 GGACCGCGACTAAAGGCTTT 60.673 55.000 17.76 17.76 0.00 3.51
330 331 1.079336 GGACCGCGACTAAAGGCTT 60.079 57.895 8.23 0.00 0.00 4.35
331 332 2.577593 GGACCGCGACTAAAGGCT 59.422 61.111 8.23 0.00 0.00 4.58
332 333 2.270297 TACGGACCGCGACTAAAGGC 62.270 60.000 15.39 0.00 0.00 4.35
333 334 0.171007 TTACGGACCGCGACTAAAGG 59.829 55.000 15.39 0.00 0.00 3.11
334 335 1.131126 TCTTACGGACCGCGACTAAAG 59.869 52.381 15.39 8.36 0.00 1.85
335 336 1.131126 CTCTTACGGACCGCGACTAAA 59.869 52.381 15.39 0.00 0.00 1.85
336 337 0.729116 CTCTTACGGACCGCGACTAA 59.271 55.000 15.39 4.10 0.00 2.24
337 338 1.091771 CCTCTTACGGACCGCGACTA 61.092 60.000 15.39 0.00 0.00 2.59
338 339 2.404995 CCTCTTACGGACCGCGACT 61.405 63.158 15.39 0.00 0.00 4.18
339 340 2.101770 CCTCTTACGGACCGCGAC 59.898 66.667 15.39 0.17 0.00 5.19
340 341 3.818787 GCCTCTTACGGACCGCGA 61.819 66.667 15.39 7.37 0.00 5.87
344 345 3.818787 TCGCGCCTCTTACGGACC 61.819 66.667 0.00 0.00 0.00 4.46
345 346 1.709147 TAGTCGCGCCTCTTACGGAC 61.709 60.000 0.00 0.00 33.64 4.79
346 347 1.026182 TTAGTCGCGCCTCTTACGGA 61.026 55.000 0.00 0.00 0.00 4.69
347 348 0.179156 TTTAGTCGCGCCTCTTACGG 60.179 55.000 0.00 0.00 0.00 4.02
348 349 1.189403 CTTTAGTCGCGCCTCTTACG 58.811 55.000 0.00 0.00 0.00 3.18
349 350 1.557651 CCTTTAGTCGCGCCTCTTAC 58.442 55.000 0.00 0.00 0.00 2.34
350 351 0.458669 CCCTTTAGTCGCGCCTCTTA 59.541 55.000 0.00 0.00 0.00 2.10
351 352 1.218316 CCCTTTAGTCGCGCCTCTT 59.782 57.895 0.00 0.00 0.00 2.85
352 353 2.722201 CCCCTTTAGTCGCGCCTCT 61.722 63.158 0.00 2.63 0.00 3.69
353 354 2.202892 CCCCTTTAGTCGCGCCTC 60.203 66.667 0.00 0.00 0.00 4.70
354 355 3.782443 CCCCCTTTAGTCGCGCCT 61.782 66.667 0.00 0.00 0.00 5.52
370 371 1.017701 CGCGACTAAAGACAACCCCC 61.018 60.000 0.00 0.00 0.00 5.40
371 372 1.632948 GCGCGACTAAAGACAACCCC 61.633 60.000 12.10 0.00 0.00 4.95
372 373 0.947180 TGCGCGACTAAAGACAACCC 60.947 55.000 12.10 0.00 0.00 4.11
373 374 1.076332 ATGCGCGACTAAAGACAACC 58.924 50.000 12.10 0.00 0.00 3.77
374 375 4.516092 AATATGCGCGACTAAAGACAAC 57.484 40.909 12.10 0.00 0.00 3.32
375 376 5.808540 ACTAAATATGCGCGACTAAAGACAA 59.191 36.000 12.10 0.00 0.00 3.18
376 377 5.345702 ACTAAATATGCGCGACTAAAGACA 58.654 37.500 12.10 0.00 0.00 3.41
377 378 5.107951 GGACTAAATATGCGCGACTAAAGAC 60.108 44.000 12.10 0.00 0.00 3.01
378 379 4.980434 GGACTAAATATGCGCGACTAAAGA 59.020 41.667 12.10 0.00 0.00 2.52
379 380 4.150098 GGGACTAAATATGCGCGACTAAAG 59.850 45.833 12.10 0.00 0.00 1.85
380 381 4.053295 GGGACTAAATATGCGCGACTAAA 58.947 43.478 12.10 0.00 0.00 1.85
381 382 3.645884 GGGACTAAATATGCGCGACTAA 58.354 45.455 12.10 0.00 0.00 2.24
382 383 2.351060 CGGGACTAAATATGCGCGACTA 60.351 50.000 12.10 0.00 38.72 2.59
383 384 1.602165 CGGGACTAAATATGCGCGACT 60.602 52.381 12.10 0.00 38.72 4.18
384 385 0.782384 CGGGACTAAATATGCGCGAC 59.218 55.000 12.10 0.88 38.72 5.19
385 386 0.319211 CCGGGACTAAATATGCGCGA 60.319 55.000 12.10 0.00 38.72 5.87
386 387 0.599204 ACCGGGACTAAATATGCGCG 60.599 55.000 6.32 0.00 36.61 6.86
387 388 1.263217 CAACCGGGACTAAATATGCGC 59.737 52.381 6.32 0.00 0.00 6.09
388 389 1.263217 GCAACCGGGACTAAATATGCG 59.737 52.381 6.32 0.00 0.00 4.73
389 390 2.032924 GTGCAACCGGGACTAAATATGC 59.967 50.000 6.32 2.60 34.56 3.14
390 391 3.275143 TGTGCAACCGGGACTAAATATG 58.725 45.455 6.32 0.00 38.87 1.78
391 392 3.541632 CTGTGCAACCGGGACTAAATAT 58.458 45.455 6.32 0.00 38.87 1.28
392 393 2.937873 GCTGTGCAACCGGGACTAAATA 60.938 50.000 6.32 0.00 38.87 1.40
393 394 1.821216 CTGTGCAACCGGGACTAAAT 58.179 50.000 6.32 0.00 38.87 1.40
394 395 0.887387 GCTGTGCAACCGGGACTAAA 60.887 55.000 6.32 0.00 38.87 1.85
395 396 1.302192 GCTGTGCAACCGGGACTAA 60.302 57.895 6.32 0.00 38.87 2.24
396 397 2.345991 GCTGTGCAACCGGGACTA 59.654 61.111 6.32 0.00 38.87 2.59
397 398 4.643387 GGCTGTGCAACCGGGACT 62.643 66.667 6.32 0.00 38.87 3.85
403 404 2.741486 TTAGTCCCGGCTGTGCAACC 62.741 60.000 0.00 0.00 34.36 3.77
404 405 0.887387 TTTAGTCCCGGCTGTGCAAC 60.887 55.000 0.00 0.00 37.35 4.17
405 406 0.605319 CTTTAGTCCCGGCTGTGCAA 60.605 55.000 0.00 0.00 0.00 4.08
406 407 1.003839 CTTTAGTCCCGGCTGTGCA 60.004 57.895 0.00 0.00 0.00 4.57
407 408 1.745489 CCTTTAGTCCCGGCTGTGC 60.745 63.158 0.00 0.00 0.00 4.57
408 409 1.745489 GCCTTTAGTCCCGGCTGTG 60.745 63.158 0.00 0.00 40.62 3.66
409 410 2.669240 GCCTTTAGTCCCGGCTGT 59.331 61.111 0.00 0.00 40.62 4.40
412 413 1.002502 AACAGCCTTTAGTCCCGGC 60.003 57.895 0.00 0.00 44.09 6.13
413 414 1.305930 GCAACAGCCTTTAGTCCCGG 61.306 60.000 0.00 0.00 0.00 5.73
414 415 1.635663 CGCAACAGCCTTTAGTCCCG 61.636 60.000 0.00 0.00 0.00 5.14
415 416 0.321298 TCGCAACAGCCTTTAGTCCC 60.321 55.000 0.00 0.00 0.00 4.46
416 417 1.197036 GTTCGCAACAGCCTTTAGTCC 59.803 52.381 0.00 0.00 0.00 3.85
417 418 1.197036 GGTTCGCAACAGCCTTTAGTC 59.803 52.381 2.28 0.00 0.00 2.59
418 419 1.235724 GGTTCGCAACAGCCTTTAGT 58.764 50.000 2.28 0.00 0.00 2.24
419 420 0.165944 CGGTTCGCAACAGCCTTTAG 59.834 55.000 2.28 0.00 0.00 1.85
420 421 1.231958 CCGGTTCGCAACAGCCTTTA 61.232 55.000 0.00 0.00 0.00 1.85
421 422 2.551912 CCGGTTCGCAACAGCCTTT 61.552 57.895 0.00 0.00 0.00 3.11
422 423 2.978010 CCGGTTCGCAACAGCCTT 60.978 61.111 0.00 0.00 0.00 4.35
425 426 2.775032 TAGTCCCGGTTCGCAACAGC 62.775 60.000 0.00 0.00 0.00 4.40
426 427 0.320073 TTAGTCCCGGTTCGCAACAG 60.320 55.000 0.00 0.00 0.00 3.16
427 428 0.106335 TTTAGTCCCGGTTCGCAACA 59.894 50.000 0.00 0.00 0.00 3.33
428 429 0.794473 CTTTAGTCCCGGTTCGCAAC 59.206 55.000 0.00 0.00 0.00 4.17
429 430 0.320946 CCTTTAGTCCCGGTTCGCAA 60.321 55.000 0.00 0.00 0.00 4.85
430 431 1.294138 CCTTTAGTCCCGGTTCGCA 59.706 57.895 0.00 0.00 0.00 5.10
431 432 1.449070 CCCTTTAGTCCCGGTTCGC 60.449 63.158 0.00 0.00 0.00 4.70
432 433 1.449070 GCCCTTTAGTCCCGGTTCG 60.449 63.158 0.00 0.00 0.00 3.95
433 434 0.327259 AAGCCCTTTAGTCCCGGTTC 59.673 55.000 0.00 0.00 0.00 3.62
434 435 0.775542 AAAGCCCTTTAGTCCCGGTT 59.224 50.000 0.00 0.00 0.00 4.44
435 436 0.775542 AAAAGCCCTTTAGTCCCGGT 59.224 50.000 0.00 0.00 31.63 5.28
436 437 1.919240 AAAAAGCCCTTTAGTCCCGG 58.081 50.000 0.00 0.00 31.63 5.73
559 560 8.420374 AACTACATGTGGAAAATATAGTCACG 57.580 34.615 16.98 0.00 16.74 4.35
978 988 7.387948 GCCATATTCTCGGTGTATGTTTATCTT 59.612 37.037 0.00 0.00 0.00 2.40
993 1003 4.150627 CGACTATTGGTTGCCATATTCTCG 59.849 45.833 0.00 0.00 31.53 4.04
1152 1163 1.601162 CCACACAAGCTTGCACATGTC 60.601 52.381 26.27 0.00 0.00 3.06
1305 1317 2.092861 TCGTCTGGGAAAACAAACCTCA 60.093 45.455 0.00 0.00 0.00 3.86
1357 1369 1.375908 GCAGACGGAGGACATGCAA 60.376 57.895 0.00 0.00 36.88 4.08
1412 1424 6.172136 AGCAGCAATAAGATAGTCAGATGT 57.828 37.500 0.00 0.00 0.00 3.06
1462 1474 0.841961 TGCATGGAGGATAGCTTGCT 59.158 50.000 0.00 0.00 0.00 3.91
1473 1485 0.873312 CCGACGATGACTGCATGGAG 60.873 60.000 13.34 13.34 34.11 3.86
1578 1590 3.745975 CCGGCGCATAGAATTTCTTATGA 59.254 43.478 10.83 0.00 0.00 2.15
1588 1600 0.179234 TGAAATCCCGGCGCATAGAA 59.821 50.000 10.83 0.00 0.00 2.10
1612 1624 7.657761 AGACAACAAGAACATTTCGACTATCTT 59.342 33.333 0.00 0.00 34.02 2.40
1708 1720 1.742768 CCCGGAGCTATCACACCTC 59.257 63.158 0.73 0.00 0.00 3.85
1886 1900 5.945784 TGCAGAAAAACCTGAAGCATAGTAT 59.054 36.000 0.00 0.00 36.29 2.12
1976 1990 1.896465 AGGTTCAGGAAGAGTTCGAGG 59.104 52.381 0.00 0.00 0.00 4.63
1980 1994 2.301583 AGAGCAGGTTCAGGAAGAGTTC 59.698 50.000 0.00 0.00 0.00 3.01
1992 2006 0.984995 GAACCAGGGTAGAGCAGGTT 59.015 55.000 7.33 7.33 44.69 3.50
2034 2048 1.077265 ATGGTGGTTCCCAGGCTTG 59.923 57.895 0.00 0.00 38.07 4.01
2250 2264 0.182775 ACAGAAAAAGTGGTCGCCCT 59.817 50.000 0.00 0.00 0.00 5.19
2252 2266 1.594331 AGACAGAAAAAGTGGTCGCC 58.406 50.000 0.00 0.00 35.49 5.54
2329 2343 2.554032 CAAAGACAATCCGGCTGTTCTT 59.446 45.455 10.00 11.01 0.00 2.52
2336 2350 1.064654 GAGCATCAAAGACAATCCGGC 59.935 52.381 0.00 0.00 33.17 6.13


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

AutoCloner maintained by Alex Coulton.