Multiple sequence alignment - TraesCS5B01G249300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G249300 chr5B 100.000 3953 0 0 1 3953 431801046 431797094 0 7300
1 TraesCS5B01G249300 chr5B 95.759 448 16 3 1 446 649500538 649500092 0 719
2 TraesCS5B01G249300 chr5B 95.730 445 17 2 1 444 388974436 388973993 0 715
3 TraesCS5B01G249300 chr5D 94.497 3580 118 25 441 3953 365326599 365323032 0 5446
4 TraesCS5B01G249300 chr5A 93.400 3591 138 32 441 3953 466988051 466984482 0 5227
5 TraesCS5B01G249300 chr4A 97.506 441 10 1 1 440 736046195 736046635 0 752
6 TraesCS5B01G249300 chr2B 97.279 441 11 1 1 440 710985182 710985622 0 747
7 TraesCS5B01G249300 chr7B 96.599 441 12 3 1 440 651141482 651141920 0 728
8 TraesCS5B01G249300 chr7B 94.785 441 21 2 1 440 658404666 658405105 0 686
9 TraesCS5B01G249300 chrUn 96.163 443 15 2 1 442 87401766 87402207 0 723
10 TraesCS5B01G249300 chrUn 95.918 441 16 2 1 440 8819525 8819964 0 713
11 TraesCS5B01G249300 chr1A 97.122 417 11 1 24 440 465268835 465269250 0 702


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 TraesCS5B01G249300 chr5B 431797094 431801046 3952 True 7300 7300 100.000 1 3953 1 chr5B.!!$R2 3952
1 TraesCS5B01G249300 chr5D 365323032 365326599 3567 True 5446 5446 94.497 441 3953 1 chr5D.!!$R1 3512
2 TraesCS5B01G249300 chr5A 466984482 466988051 3569 True 5227 5227 93.400 441 3953 1 chr5A.!!$R1 3512

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
270 271 0.037303 CTGGAGCCGGGCAATATGAT 59.963 55.0 23.09 0.0 0.00 2.45 F
419 420 0.255033 GGTGGGCCTCTTTCGGTTAT 59.745 55.0 4.53 0.0 0.00 1.89 F
1176 1201 0.394899 GCATTGAACTGGAGAGGGGG 60.395 60.0 0.00 0.0 0.00 5.40 F
2628 2656 0.178944 TGGTCCCTCCTGTCTCGAAA 60.179 55.0 0.00 0.0 37.07 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1332 1357 0.321671 GACAGGGTGTTGAGCTGCTA 59.678 55.0 0.15 0.0 0.00 3.49 R
1372 1397 0.458543 CTACGGTCTCGCTGTTGCAT 60.459 55.0 0.00 0.0 40.63 3.96 R
2839 2867 0.748450 TGGAACTTGTCGAGGAACGT 59.252 50.0 0.00 0.0 43.13 3.99 R
3747 3835 0.960861 CTGACGGGAAAAGAAGGGCC 60.961 60.0 0.00 0.0 0.00 5.80 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
17 18 4.947147 GTGGTGGAGTTGGCGGCA 62.947 66.667 7.97 7.97 0.00 5.69
18 19 4.641645 TGGTGGAGTTGGCGGCAG 62.642 66.667 12.87 0.00 0.00 4.85
19 20 4.643387 GGTGGAGTTGGCGGCAGT 62.643 66.667 12.87 3.26 0.00 4.40
20 21 3.357079 GTGGAGTTGGCGGCAGTG 61.357 66.667 12.87 0.00 0.00 3.66
21 22 4.641645 TGGAGTTGGCGGCAGTGG 62.642 66.667 12.87 0.00 0.00 4.00
48 49 4.838152 CGGCGGTGGATGTGGAGG 62.838 72.222 0.00 0.00 0.00 4.30
49 50 3.717294 GGCGGTGGATGTGGAGGT 61.717 66.667 0.00 0.00 0.00 3.85
50 51 2.436646 GCGGTGGATGTGGAGGTG 60.437 66.667 0.00 0.00 0.00 4.00
51 52 2.268920 CGGTGGATGTGGAGGTGG 59.731 66.667 0.00 0.00 0.00 4.61
52 53 2.290287 CGGTGGATGTGGAGGTGGA 61.290 63.158 0.00 0.00 0.00 4.02
53 54 1.604378 GGTGGATGTGGAGGTGGAG 59.396 63.158 0.00 0.00 0.00 3.86
54 55 0.909610 GGTGGATGTGGAGGTGGAGA 60.910 60.000 0.00 0.00 0.00 3.71
55 56 0.250513 GTGGATGTGGAGGTGGAGAC 59.749 60.000 0.00 0.00 0.00 3.36
56 57 1.257750 TGGATGTGGAGGTGGAGACG 61.258 60.000 0.00 0.00 0.00 4.18
57 58 0.970937 GGATGTGGAGGTGGAGACGA 60.971 60.000 0.00 0.00 0.00 4.20
58 59 0.173708 GATGTGGAGGTGGAGACGAC 59.826 60.000 0.00 0.00 0.00 4.34
59 60 0.541998 ATGTGGAGGTGGAGACGACA 60.542 55.000 0.00 0.00 0.00 4.35
60 61 0.541998 TGTGGAGGTGGAGACGACAT 60.542 55.000 0.00 0.00 0.00 3.06
61 62 1.272258 TGTGGAGGTGGAGACGACATA 60.272 52.381 0.00 0.00 0.00 2.29
62 63 1.405821 GTGGAGGTGGAGACGACATAG 59.594 57.143 0.00 0.00 0.00 2.23
63 64 1.005569 TGGAGGTGGAGACGACATAGT 59.994 52.381 0.00 0.00 0.00 2.12
64 65 1.677052 GGAGGTGGAGACGACATAGTC 59.323 57.143 0.00 0.00 41.23 2.59
74 75 2.031360 GACATAGTCGAGACCCGGG 58.969 63.158 22.25 22.25 39.14 5.73
75 76 0.750911 GACATAGTCGAGACCCGGGT 60.751 60.000 30.81 30.81 39.14 5.28
76 77 0.548031 ACATAGTCGAGACCCGGGTA 59.452 55.000 30.38 9.85 39.14 3.69
77 78 0.950116 CATAGTCGAGACCCGGGTAC 59.050 60.000 30.38 21.77 39.14 3.34
103 104 2.364972 CCAAATTGGTAGGGCTAGGG 57.635 55.000 3.34 0.00 31.35 3.53
104 105 1.569072 CCAAATTGGTAGGGCTAGGGT 59.431 52.381 3.34 0.00 31.35 4.34
105 106 2.024369 CCAAATTGGTAGGGCTAGGGTT 60.024 50.000 3.34 0.00 31.35 4.11
106 107 3.288092 CAAATTGGTAGGGCTAGGGTTC 58.712 50.000 0.00 0.00 0.00 3.62
107 108 1.519498 ATTGGTAGGGCTAGGGTTCC 58.481 55.000 0.00 0.00 0.00 3.62
108 109 0.420272 TTGGTAGGGCTAGGGTTCCT 59.580 55.000 0.00 0.00 37.71 3.36
109 110 1.321978 TGGTAGGGCTAGGGTTCCTA 58.678 55.000 0.00 0.00 34.61 2.94
111 112 1.714541 GTAGGGCTAGGGTTCCTACC 58.285 60.000 7.35 0.00 44.29 3.18
112 113 0.186873 TAGGGCTAGGGTTCCTACCG 59.813 60.000 0.00 0.00 46.04 4.02
113 114 2.138831 GGGCTAGGGTTCCTACCGG 61.139 68.421 0.00 0.00 46.04 5.28
114 115 2.804912 GGCTAGGGTTCCTACCGGC 61.805 68.421 0.00 0.00 46.04 6.13
115 116 1.761271 GCTAGGGTTCCTACCGGCT 60.761 63.158 0.00 0.00 46.04 5.52
116 117 1.746322 GCTAGGGTTCCTACCGGCTC 61.746 65.000 0.00 0.00 46.04 4.70
117 118 0.106116 CTAGGGTTCCTACCGGCTCT 60.106 60.000 0.00 0.00 46.04 4.09
118 119 1.144503 CTAGGGTTCCTACCGGCTCTA 59.855 57.143 0.00 0.00 46.04 2.43
119 120 0.396835 AGGGTTCCTACCGGCTCTAC 60.397 60.000 0.00 0.00 46.04 2.59
120 121 0.396835 GGGTTCCTACCGGCTCTACT 60.397 60.000 0.00 0.00 46.04 2.57
121 122 1.031235 GGTTCCTACCGGCTCTACTC 58.969 60.000 0.00 0.00 34.01 2.59
122 123 1.031235 GTTCCTACCGGCTCTACTCC 58.969 60.000 0.00 0.00 0.00 3.85
123 124 0.465097 TTCCTACCGGCTCTACTCCG 60.465 60.000 0.00 0.00 46.05 4.63
124 125 1.153005 CCTACCGGCTCTACTCCGT 60.153 63.158 0.00 0.00 45.09 4.69
125 126 0.107456 CCTACCGGCTCTACTCCGTA 59.893 60.000 0.00 0.00 45.09 4.02
126 127 1.510776 CTACCGGCTCTACTCCGTAG 58.489 60.000 0.00 0.00 45.09 3.51
142 143 3.655276 CGTAGGTTATACGGGCAGAAT 57.345 47.619 0.00 0.00 37.29 2.40
143 144 4.771590 CGTAGGTTATACGGGCAGAATA 57.228 45.455 0.00 0.00 37.29 1.75
144 145 4.730657 CGTAGGTTATACGGGCAGAATAG 58.269 47.826 0.00 0.00 37.29 1.73
145 146 3.679824 AGGTTATACGGGCAGAATAGC 57.320 47.619 0.00 0.00 0.00 2.97
146 147 2.029290 AGGTTATACGGGCAGAATAGCG 60.029 50.000 0.00 0.00 34.64 4.26
147 148 2.029649 GGTTATACGGGCAGAATAGCGA 60.030 50.000 0.00 0.00 34.64 4.93
148 149 3.243336 GTTATACGGGCAGAATAGCGAG 58.757 50.000 0.00 0.00 34.64 5.03
149 150 0.603569 ATACGGGCAGAATAGCGAGG 59.396 55.000 0.00 0.00 34.64 4.63
150 151 1.461091 TACGGGCAGAATAGCGAGGG 61.461 60.000 0.00 0.00 34.64 4.30
151 152 2.797278 CGGGCAGAATAGCGAGGGT 61.797 63.158 0.00 0.00 34.64 4.34
152 153 1.527370 GGGCAGAATAGCGAGGGTT 59.473 57.895 0.00 0.00 34.64 4.11
153 154 0.815615 GGGCAGAATAGCGAGGGTTG 60.816 60.000 0.00 0.00 34.64 3.77
154 155 0.815615 GGCAGAATAGCGAGGGTTGG 60.816 60.000 0.00 0.00 34.64 3.77
155 156 0.815615 GCAGAATAGCGAGGGTTGGG 60.816 60.000 0.00 0.00 0.00 4.12
156 157 0.179045 CAGAATAGCGAGGGTTGGGG 60.179 60.000 0.00 0.00 0.00 4.96
157 158 1.148498 GAATAGCGAGGGTTGGGGG 59.852 63.158 0.00 0.00 0.00 5.40
158 159 2.960359 GAATAGCGAGGGTTGGGGGC 62.960 65.000 0.00 0.00 0.00 5.80
202 203 4.856607 GCCGTCGCGAGGGAGAAG 62.857 72.222 42.80 21.81 38.58 2.85
203 204 3.132139 CCGTCGCGAGGGAGAAGA 61.132 66.667 37.75 0.00 38.58 2.87
204 205 2.697761 CCGTCGCGAGGGAGAAGAA 61.698 63.158 37.75 0.00 38.58 2.52
205 206 1.226435 CGTCGCGAGGGAGAAGAAG 60.226 63.158 20.58 0.00 0.00 2.85
206 207 1.139947 GTCGCGAGGGAGAAGAAGG 59.860 63.158 10.24 0.00 0.00 3.46
207 208 2.202810 CGCGAGGGAGAAGAAGGC 60.203 66.667 0.00 0.00 0.00 4.35
208 209 2.188207 GCGAGGGAGAAGAAGGCC 59.812 66.667 0.00 0.00 0.00 5.19
209 210 2.496817 CGAGGGAGAAGAAGGCCG 59.503 66.667 0.00 0.00 0.00 6.13
210 211 2.904131 GAGGGAGAAGAAGGCCGG 59.096 66.667 0.00 0.00 0.00 6.13
211 212 3.393149 GAGGGAGAAGAAGGCCGGC 62.393 68.421 21.18 21.18 0.00 6.13
212 213 4.840005 GGGAGAAGAAGGCCGGCG 62.840 72.222 22.54 0.00 0.00 6.46
213 214 4.840005 GGAGAAGAAGGCCGGCGG 62.840 72.222 24.35 24.35 0.00 6.13
228 229 4.404098 CGGCGGCTAGGGTTTGGT 62.404 66.667 7.61 0.00 0.00 3.67
229 230 2.750237 GGCGGCTAGGGTTTGGTG 60.750 66.667 0.00 0.00 0.00 4.17
230 231 3.440415 GCGGCTAGGGTTTGGTGC 61.440 66.667 0.00 0.00 0.00 5.01
231 232 3.124921 CGGCTAGGGTTTGGTGCG 61.125 66.667 0.00 0.00 0.00 5.34
232 233 2.750237 GGCTAGGGTTTGGTGCGG 60.750 66.667 0.00 0.00 0.00 5.69
233 234 3.440415 GCTAGGGTTTGGTGCGGC 61.440 66.667 0.00 0.00 0.00 6.53
234 235 2.351276 CTAGGGTTTGGTGCGGCT 59.649 61.111 0.00 0.00 0.00 5.52
235 236 2.033448 TAGGGTTTGGTGCGGCTG 59.967 61.111 0.00 0.00 0.00 4.85
236 237 3.561120 TAGGGTTTGGTGCGGCTGG 62.561 63.158 0.00 0.00 0.00 4.85
240 241 4.531426 TTTGGTGCGGCTGGGGTT 62.531 61.111 0.00 0.00 0.00 4.11
241 242 4.531426 TTGGTGCGGCTGGGGTTT 62.531 61.111 0.00 0.00 0.00 3.27
242 243 4.966787 TGGTGCGGCTGGGGTTTC 62.967 66.667 0.00 0.00 0.00 2.78
250 251 3.330720 CTGGGGTTTCCGGCTCCT 61.331 66.667 0.00 0.00 38.76 3.69
251 252 3.327404 TGGGGTTTCCGGCTCCTC 61.327 66.667 0.00 0.00 38.76 3.71
252 253 3.009714 GGGGTTTCCGGCTCCTCT 61.010 66.667 0.00 0.00 0.00 3.69
253 254 2.269241 GGGTTTCCGGCTCCTCTG 59.731 66.667 0.00 0.00 0.00 3.35
254 255 2.269241 GGTTTCCGGCTCCTCTGG 59.731 66.667 0.00 0.00 42.90 3.86
265 266 3.801997 CCTCTGGAGCCGGGCAAT 61.802 66.667 23.09 0.00 0.00 3.56
266 267 2.443394 CCTCTGGAGCCGGGCAATA 61.443 63.158 23.09 5.35 0.00 1.90
267 268 1.757306 CTCTGGAGCCGGGCAATAT 59.243 57.895 23.09 0.00 0.00 1.28
268 269 0.604780 CTCTGGAGCCGGGCAATATG 60.605 60.000 23.09 7.22 0.00 1.78
269 270 1.053835 TCTGGAGCCGGGCAATATGA 61.054 55.000 23.09 9.53 0.00 2.15
270 271 0.037303 CTGGAGCCGGGCAATATGAT 59.963 55.000 23.09 0.00 0.00 2.45
271 272 1.278985 CTGGAGCCGGGCAATATGATA 59.721 52.381 23.09 0.00 0.00 2.15
272 273 1.278985 TGGAGCCGGGCAATATGATAG 59.721 52.381 23.09 0.00 0.00 2.08
273 274 1.555075 GGAGCCGGGCAATATGATAGA 59.445 52.381 23.09 0.00 0.00 1.98
274 275 2.027192 GGAGCCGGGCAATATGATAGAA 60.027 50.000 23.09 0.00 0.00 2.10
275 276 3.003480 GAGCCGGGCAATATGATAGAAC 58.997 50.000 23.09 0.00 0.00 3.01
276 277 2.639839 AGCCGGGCAATATGATAGAACT 59.360 45.455 23.09 0.00 0.00 3.01
277 278 3.838317 AGCCGGGCAATATGATAGAACTA 59.162 43.478 23.09 0.00 0.00 2.24
278 279 4.471386 AGCCGGGCAATATGATAGAACTAT 59.529 41.667 23.09 0.00 0.00 2.12
279 280 4.811557 GCCGGGCAATATGATAGAACTATC 59.188 45.833 15.62 13.08 41.67 2.08
280 281 5.395768 GCCGGGCAATATGATAGAACTATCT 60.396 44.000 15.62 9.71 41.80 1.98
281 282 6.644347 CCGGGCAATATGATAGAACTATCTT 58.356 40.000 18.55 15.42 41.80 2.40
282 283 7.106239 CCGGGCAATATGATAGAACTATCTTT 58.894 38.462 18.55 11.06 41.80 2.52
283 284 8.258007 CCGGGCAATATGATAGAACTATCTTTA 58.742 37.037 18.55 12.40 41.80 1.85
284 285 9.823647 CGGGCAATATGATAGAACTATCTTTAT 57.176 33.333 18.55 13.61 41.80 1.40
303 304 9.941664 ATCTTTATTGCTTAATCTCAAACGATG 57.058 29.630 0.00 0.00 0.00 3.84
304 305 8.946085 TCTTTATTGCTTAATCTCAAACGATGT 58.054 29.630 0.00 0.00 0.00 3.06
305 306 9.214953 CTTTATTGCTTAATCTCAAACGATGTC 57.785 33.333 0.00 0.00 0.00 3.06
306 307 6.992063 ATTGCTTAATCTCAAACGATGTCT 57.008 33.333 0.00 0.00 0.00 3.41
307 308 6.801539 TTGCTTAATCTCAAACGATGTCTT 57.198 33.333 0.00 0.00 0.00 3.01
308 309 7.899178 TTGCTTAATCTCAAACGATGTCTTA 57.101 32.000 0.00 0.00 0.00 2.10
309 310 7.290857 TGCTTAATCTCAAACGATGTCTTAC 57.709 36.000 0.00 0.00 0.00 2.34
310 311 6.871492 TGCTTAATCTCAAACGATGTCTTACA 59.129 34.615 0.00 0.00 0.00 2.41
311 312 7.386573 TGCTTAATCTCAAACGATGTCTTACAA 59.613 33.333 0.00 0.00 0.00 2.41
312 313 7.688578 GCTTAATCTCAAACGATGTCTTACAAC 59.311 37.037 0.00 0.00 0.00 3.32
313 314 8.827177 TTAATCTCAAACGATGTCTTACAACT 57.173 30.769 0.00 0.00 0.00 3.16
314 315 9.917129 TTAATCTCAAACGATGTCTTACAACTA 57.083 29.630 0.00 0.00 0.00 2.24
315 316 8.467402 AATCTCAAACGATGTCTTACAACTAG 57.533 34.615 0.00 0.00 0.00 2.57
316 317 6.978338 TCTCAAACGATGTCTTACAACTAGT 58.022 36.000 0.00 0.00 0.00 2.57
317 318 8.102800 TCTCAAACGATGTCTTACAACTAGTA 57.897 34.615 0.00 0.00 0.00 1.82
318 319 8.737175 TCTCAAACGATGTCTTACAACTAGTAT 58.263 33.333 0.00 0.00 31.53 2.12
319 320 9.355215 CTCAAACGATGTCTTACAACTAGTATT 57.645 33.333 0.00 0.00 31.53 1.89
320 321 9.701098 TCAAACGATGTCTTACAACTAGTATTT 57.299 29.630 0.00 0.00 31.53 1.40
376 377 6.530019 AATTTGCCTAAGATAACTTGTGGG 57.470 37.500 0.00 0.00 37.53 4.61
377 378 4.650972 TTGCCTAAGATAACTTGTGGGT 57.349 40.909 0.00 0.00 37.53 4.51
378 379 4.216411 TGCCTAAGATAACTTGTGGGTC 57.784 45.455 0.00 0.00 37.53 4.46
379 380 3.585289 TGCCTAAGATAACTTGTGGGTCA 59.415 43.478 0.00 0.00 37.53 4.02
380 381 4.042311 TGCCTAAGATAACTTGTGGGTCAA 59.958 41.667 0.00 0.00 37.53 3.18
396 397 4.353383 GGTCAAGCCCCTAATACTAAGG 57.647 50.000 0.00 0.00 0.00 2.69
397 398 3.496337 GGTCAAGCCCCTAATACTAAGGC 60.496 52.174 0.00 0.00 44.20 4.35
398 399 2.709397 TCAAGCCCCTAATACTAAGGCC 59.291 50.000 0.00 0.00 45.00 5.19
399 400 1.743589 AGCCCCTAATACTAAGGCCC 58.256 55.000 0.00 0.00 45.00 5.80
400 401 0.323957 GCCCCTAATACTAAGGCCCG 59.676 60.000 0.00 0.00 37.66 6.13
401 402 0.981943 CCCCTAATACTAAGGCCCGG 59.018 60.000 0.00 0.00 32.34 5.73
402 403 1.725803 CCCTAATACTAAGGCCCGGT 58.274 55.000 0.00 0.00 32.34 5.28
403 404 1.346722 CCCTAATACTAAGGCCCGGTG 59.653 57.143 0.00 0.00 32.34 4.94
404 405 1.346722 CCTAATACTAAGGCCCGGTGG 59.653 57.143 0.00 0.00 0.00 4.61
414 415 4.778143 CCCGGTGGGCCTCTTTCG 62.778 72.222 4.53 0.00 35.35 3.46
415 416 4.778143 CCGGTGGGCCTCTTTCGG 62.778 72.222 4.53 6.22 0.00 4.30
416 417 4.016706 CGGTGGGCCTCTTTCGGT 62.017 66.667 4.53 0.00 0.00 4.69
417 418 2.434774 GGTGGGCCTCTTTCGGTT 59.565 61.111 4.53 0.00 0.00 4.44
418 419 1.681076 GGTGGGCCTCTTTCGGTTA 59.319 57.895 4.53 0.00 0.00 2.85
419 420 0.255033 GGTGGGCCTCTTTCGGTTAT 59.745 55.000 4.53 0.00 0.00 1.89
420 421 1.487558 GGTGGGCCTCTTTCGGTTATA 59.512 52.381 4.53 0.00 0.00 0.98
421 422 2.484947 GGTGGGCCTCTTTCGGTTATAG 60.485 54.545 4.53 0.00 0.00 1.31
422 423 2.433239 GTGGGCCTCTTTCGGTTATAGA 59.567 50.000 4.53 0.00 0.00 1.98
423 424 2.433239 TGGGCCTCTTTCGGTTATAGAC 59.567 50.000 4.53 0.00 0.00 2.59
424 425 2.224233 GGGCCTCTTTCGGTTATAGACC 60.224 54.545 0.84 0.00 45.55 3.85
535 557 6.761312 TGAAATGAGCAAACAAGATCCAAAT 58.239 32.000 0.00 0.00 0.00 2.32
571 593 2.232208 GGCAGCAACTTGAGGCTATTTT 59.768 45.455 0.00 0.00 38.56 1.82
572 594 3.248266 GCAGCAACTTGAGGCTATTTTG 58.752 45.455 0.00 0.00 38.56 2.44
587 609 5.175859 GCTATTTTGTGGTGTGCTAGACTA 58.824 41.667 0.00 0.00 0.00 2.59
600 622 7.009357 GGTGTGCTAGACTATTTAACTCGAAAG 59.991 40.741 0.00 0.00 0.00 2.62
693 718 7.183475 AGGATATATGTCTGCCATACTTCCAAT 59.817 37.037 9.87 0.00 40.10 3.16
694 719 7.831193 GGATATATGTCTGCCATACTTCCAATT 59.169 37.037 0.00 0.00 38.83 2.32
695 720 9.236006 GATATATGTCTGCCATACTTCCAATTT 57.764 33.333 0.00 0.00 38.83 1.82
808 833 1.133976 GCAGGGCATCTACCACTGAAT 60.134 52.381 0.00 0.00 32.68 2.57
810 835 3.624777 CAGGGCATCTACCACTGAATTT 58.375 45.455 0.00 0.00 32.68 1.82
828 853 8.084684 ACTGAATTTTGAGATAAAGTGCTTTCC 58.915 33.333 0.00 0.00 34.23 3.13
929 954 5.008331 TCTTTCTTCCTCTTGCTACGAGTA 58.992 41.667 0.00 0.00 0.00 2.59
1104 1129 1.630878 AGTAGCAAAACTGAGGGGAGG 59.369 52.381 0.00 0.00 0.00 4.30
1176 1201 0.394899 GCATTGAACTGGAGAGGGGG 60.395 60.000 0.00 0.00 0.00 5.40
1332 1357 1.003580 ACAAGGAATCAGATGCACCGT 59.996 47.619 0.00 0.00 0.00 4.83
1347 1372 1.741770 CCGTAGCAGCTCAACACCC 60.742 63.158 0.00 0.00 0.00 4.61
1372 1397 0.895530 CTCTCCTACTGGAAACGGCA 59.104 55.000 0.00 0.00 42.66 5.69
1620 1645 3.876309 AAAGGCTTTGTAGGGAAGACA 57.124 42.857 12.53 0.00 34.49 3.41
1701 1726 1.946283 GCTGCTTACCTCCTTGACCAC 60.946 57.143 0.00 0.00 0.00 4.16
1705 1730 1.833787 TTACCTCCTTGACCACGGCC 61.834 60.000 0.00 0.00 0.00 6.13
2013 2038 2.092968 TGACAACTTTGGAGTGCAGACT 60.093 45.455 0.00 0.00 35.91 3.24
2118 2143 3.205519 TCCATCCCTTTCTCTGAGGAA 57.794 47.619 4.59 0.89 36.33 3.36
2259 2284 1.123246 AAGGTGCAGCATTTGGCCTT 61.123 50.000 19.63 8.17 46.50 4.35
2262 2287 0.249996 GTGCAGCATTTGGCCTTTGT 60.250 50.000 3.32 0.00 46.50 2.83
2325 2353 4.137543 GGAAAGAAGAAGAGCCAAGTGAA 58.862 43.478 0.00 0.00 0.00 3.18
2403 2431 1.065854 CCAGAAGCCGGAGTTGAAGAT 60.066 52.381 5.05 0.00 0.00 2.40
2502 2530 0.482446 TTGGTCCCATGAAGGCAAGT 59.518 50.000 0.00 0.00 35.39 3.16
2550 2578 2.031120 GAGTGTGATGAGGAGGAGGAG 58.969 57.143 0.00 0.00 0.00 3.69
2566 2594 3.303938 GAGGAGGATGACAAGGAGATGA 58.696 50.000 0.00 0.00 0.00 2.92
2625 2653 2.716017 GCTGGTCCCTCCTGTCTCG 61.716 68.421 0.00 0.00 37.45 4.04
2628 2656 0.178944 TGGTCCCTCCTGTCTCGAAA 60.179 55.000 0.00 0.00 37.07 3.46
2678 2706 2.381961 TCCATGGGAAAGCTAAACCCTT 59.618 45.455 13.02 12.54 43.59 3.95
2837 2865 2.683933 GGGCTCCGAGGAGTGGAA 60.684 66.667 19.22 0.00 43.70 3.53
2839 2867 2.283529 GGCTCCGAGGAGTGGAACA 61.284 63.158 19.22 0.00 43.70 3.18
2859 2887 1.137479 ACGTTCCTCGACAAGTTCCAA 59.863 47.619 0.00 0.00 42.86 3.53
2898 2926 3.044305 GAAGCACGGAAGCACGCT 61.044 61.111 0.00 0.00 37.37 5.07
2963 2991 3.181449 TGCCAGTTTTGAAGGTAGCAGTA 60.181 43.478 0.00 0.00 0.00 2.74
3070 3108 1.887854 TGTGTTTGGACTACGGATCGA 59.112 47.619 0.00 0.00 0.00 3.59
3155 3198 1.062002 CGCAAAGTGTGTCTTCGTGTT 59.938 47.619 0.00 0.00 35.02 3.32
3165 3208 3.247648 GTGTCTTCGTGTTTGTGCATAGT 59.752 43.478 0.00 0.00 0.00 2.12
3183 3226 9.226345 GTGCATAGTTTTAGCTTTTGACATATC 57.774 33.333 0.00 0.00 0.00 1.63
3184 3227 8.955388 TGCATAGTTTTAGCTTTTGACATATCA 58.045 29.630 0.00 0.00 0.00 2.15
3257 3303 4.473520 AACGCCGGGCTCCATCAG 62.474 66.667 18.34 1.54 0.00 2.90
3361 3407 9.577110 CCGAGACGCTTACCATAATAATAATAA 57.423 33.333 0.00 0.00 0.00 1.40
3389 3435 7.078249 AGTATGAATATGCACCTGGATTACA 57.922 36.000 0.00 0.00 0.00 2.41
3390 3436 7.693132 AGTATGAATATGCACCTGGATTACAT 58.307 34.615 0.00 0.82 0.00 2.29
3391 3437 8.825774 AGTATGAATATGCACCTGGATTACATA 58.174 33.333 0.00 3.14 0.00 2.29
3392 3438 9.618890 GTATGAATATGCACCTGGATTACATAT 57.381 33.333 0.00 5.34 35.89 1.78
3395 3441 9.617523 TGAATATGCACCTGGATTACATATATG 57.382 33.333 11.29 11.29 33.85 1.78
3396 3442 9.618890 GAATATGCACCTGGATTACATATATGT 57.381 33.333 21.57 21.57 44.48 2.29
3400 3446 8.144862 TGCACCTGGATTACATATATGTATCA 57.855 34.615 23.01 19.07 42.32 2.15
3401 3447 8.771286 TGCACCTGGATTACATATATGTATCAT 58.229 33.333 23.01 15.72 42.32 2.45
3402 3448 9.265901 GCACCTGGATTACATATATGTATCATC 57.734 37.037 23.01 21.41 42.32 2.92
3423 3504 4.973168 TCTGTTTACATCTCTGCTTTGGT 58.027 39.130 0.00 0.00 0.00 3.67
3437 3518 2.606795 GCTTTGGTGCTTTTGATGCGTA 60.607 45.455 0.00 0.00 0.00 4.42
3474 3555 3.454375 GTGGGATAGTACGTTGATGTGG 58.546 50.000 0.00 0.00 0.00 4.17
3484 3565 1.797713 CGTTGATGTGGTACGAGCGAT 60.798 52.381 0.00 0.00 37.47 4.58
3496 3577 1.478510 ACGAGCGATTGATCTGGAACT 59.521 47.619 0.00 0.00 0.00 3.01
3522 3603 1.296056 CGGGTAGTGTCAAAAGGGCG 61.296 60.000 0.00 0.00 0.00 6.13
3524 3605 1.583495 GGTAGTGTCAAAAGGGCGCC 61.583 60.000 21.18 21.18 0.00 6.53
3610 3698 3.033909 CCAGTGTCCAGATGACCAGATA 58.966 50.000 0.00 0.00 43.78 1.98
3712 3800 2.657237 CCTGGGGAGTGTCGTCAC 59.343 66.667 4.52 4.52 44.15 3.67
3804 3892 0.032130 GTCACACGCCAGAGTGAGAA 59.968 55.000 8.57 0.00 45.89 2.87
3809 3897 0.969149 ACGCCAGAGTGAGAACATCA 59.031 50.000 0.00 0.00 34.79 3.07
3812 3900 2.417787 CGCCAGAGTGAGAACATCATCA 60.418 50.000 0.00 0.00 40.92 3.07
3816 3904 5.425630 CCAGAGTGAGAACATCATCATCAA 58.574 41.667 0.00 0.00 40.92 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.947147 TGCCGCCAACTCCACCAC 62.947 66.667 0.00 0.00 0.00 4.16
1 2 4.641645 CTGCCGCCAACTCCACCA 62.642 66.667 0.00 0.00 0.00 4.17
2 3 4.643387 ACTGCCGCCAACTCCACC 62.643 66.667 0.00 0.00 0.00 4.61
3 4 3.357079 CACTGCCGCCAACTCCAC 61.357 66.667 0.00 0.00 0.00 4.02
4 5 4.641645 CCACTGCCGCCAACTCCA 62.642 66.667 0.00 0.00 0.00 3.86
31 32 4.838152 CCTCCACATCCACCGCCG 62.838 72.222 0.00 0.00 0.00 6.46
32 33 3.717294 ACCTCCACATCCACCGCC 61.717 66.667 0.00 0.00 0.00 6.13
33 34 2.436646 CACCTCCACATCCACCGC 60.437 66.667 0.00 0.00 0.00 5.68
34 35 2.244117 CTCCACCTCCACATCCACCG 62.244 65.000 0.00 0.00 0.00 4.94
35 36 0.909610 TCTCCACCTCCACATCCACC 60.910 60.000 0.00 0.00 0.00 4.61
36 37 0.250513 GTCTCCACCTCCACATCCAC 59.749 60.000 0.00 0.00 0.00 4.02
37 38 1.257750 CGTCTCCACCTCCACATCCA 61.258 60.000 0.00 0.00 0.00 3.41
38 39 0.970937 TCGTCTCCACCTCCACATCC 60.971 60.000 0.00 0.00 0.00 3.51
39 40 0.173708 GTCGTCTCCACCTCCACATC 59.826 60.000 0.00 0.00 0.00 3.06
40 41 0.541998 TGTCGTCTCCACCTCCACAT 60.542 55.000 0.00 0.00 0.00 3.21
41 42 0.541998 ATGTCGTCTCCACCTCCACA 60.542 55.000 0.00 0.00 0.00 4.17
42 43 1.405821 CTATGTCGTCTCCACCTCCAC 59.594 57.143 0.00 0.00 0.00 4.02
43 44 1.005569 ACTATGTCGTCTCCACCTCCA 59.994 52.381 0.00 0.00 0.00 3.86
44 45 1.677052 GACTATGTCGTCTCCACCTCC 59.323 57.143 0.00 0.00 0.00 4.30
56 57 0.750911 ACCCGGGTCTCGACTATGTC 60.751 60.000 24.16 0.00 42.43 3.06
57 58 0.548031 TACCCGGGTCTCGACTATGT 59.452 55.000 34.27 2.51 42.43 2.29
58 59 0.950116 GTACCCGGGTCTCGACTATG 59.050 60.000 34.27 0.00 42.43 2.23
59 60 0.179006 GGTACCCGGGTCTCGACTAT 60.179 60.000 34.27 4.09 42.43 2.12
60 61 1.224592 GGTACCCGGGTCTCGACTA 59.775 63.158 34.27 7.92 42.43 2.59
61 62 2.044551 GGTACCCGGGTCTCGACT 60.045 66.667 34.27 5.96 42.43 4.18
62 63 2.044551 AGGTACCCGGGTCTCGAC 60.045 66.667 34.27 23.16 42.43 4.20
63 64 1.929860 ATCAGGTACCCGGGTCTCGA 61.930 60.000 34.27 22.56 42.43 4.04
64 65 0.179009 TATCAGGTACCCGGGTCTCG 60.179 60.000 34.27 17.67 38.88 4.04
65 66 1.326328 GTATCAGGTACCCGGGTCTC 58.674 60.000 34.27 24.01 0.00 3.36
66 67 0.105811 GGTATCAGGTACCCGGGTCT 60.106 60.000 34.27 20.50 46.08 3.85
67 68 2.434317 GGTATCAGGTACCCGGGTC 58.566 63.158 34.27 21.53 46.08 4.46
68 69 4.713911 GGTATCAGGTACCCGGGT 57.286 61.111 32.66 32.66 46.08 5.28
84 85 1.569072 ACCCTAGCCCTACCAATTTGG 59.431 52.381 14.02 14.02 45.02 3.28
85 86 3.288092 GAACCCTAGCCCTACCAATTTG 58.712 50.000 0.00 0.00 0.00 2.32
86 87 2.243994 GGAACCCTAGCCCTACCAATTT 59.756 50.000 0.00 0.00 0.00 1.82
87 88 1.850998 GGAACCCTAGCCCTACCAATT 59.149 52.381 0.00 0.00 0.00 2.32
88 89 1.010917 AGGAACCCTAGCCCTACCAAT 59.989 52.381 0.00 0.00 28.47 3.16
89 90 0.420272 AGGAACCCTAGCCCTACCAA 59.580 55.000 0.00 0.00 28.47 3.67
90 91 1.062658 GTAGGAACCCTAGCCCTACCA 60.063 57.143 13.47 0.00 44.02 3.25
91 92 1.714541 GTAGGAACCCTAGCCCTACC 58.285 60.000 13.47 0.00 44.02 3.18
92 93 1.714541 GGTAGGAACCCTAGCCCTAC 58.285 60.000 10.28 15.01 45.66 3.18
98 99 0.106116 AGAGCCGGTAGGAACCCTAG 60.106 60.000 1.90 0.00 43.54 3.02
99 100 1.133668 GTAGAGCCGGTAGGAACCCTA 60.134 57.143 1.90 0.00 43.54 3.53
100 101 0.396835 GTAGAGCCGGTAGGAACCCT 60.397 60.000 1.90 0.00 43.54 4.34
101 102 0.396835 AGTAGAGCCGGTAGGAACCC 60.397 60.000 1.90 0.00 43.54 4.11
102 103 1.031235 GAGTAGAGCCGGTAGGAACC 58.969 60.000 1.90 0.00 42.95 3.62
103 104 1.031235 GGAGTAGAGCCGGTAGGAAC 58.969 60.000 1.90 0.00 41.02 3.62
104 105 0.465097 CGGAGTAGAGCCGGTAGGAA 60.465 60.000 1.90 0.00 44.87 3.36
105 106 1.147824 CGGAGTAGAGCCGGTAGGA 59.852 63.158 1.90 0.00 44.87 2.94
106 107 3.747266 CGGAGTAGAGCCGGTAGG 58.253 66.667 1.90 0.00 44.87 3.18
122 123 3.655276 ATTCTGCCCGTATAACCTACG 57.345 47.619 0.00 0.00 40.30 3.51
123 124 4.492611 GCTATTCTGCCCGTATAACCTAC 58.507 47.826 0.00 0.00 0.00 3.18
124 125 3.192001 CGCTATTCTGCCCGTATAACCTA 59.808 47.826 0.00 0.00 0.00 3.08
125 126 2.029290 CGCTATTCTGCCCGTATAACCT 60.029 50.000 0.00 0.00 0.00 3.50
126 127 2.029649 TCGCTATTCTGCCCGTATAACC 60.030 50.000 0.00 0.00 0.00 2.85
127 128 3.243336 CTCGCTATTCTGCCCGTATAAC 58.757 50.000 0.00 0.00 0.00 1.89
128 129 2.230508 CCTCGCTATTCTGCCCGTATAA 59.769 50.000 0.00 0.00 0.00 0.98
129 130 1.816835 CCTCGCTATTCTGCCCGTATA 59.183 52.381 0.00 0.00 0.00 1.47
130 131 0.603569 CCTCGCTATTCTGCCCGTAT 59.396 55.000 0.00 0.00 0.00 3.06
131 132 1.461091 CCCTCGCTATTCTGCCCGTA 61.461 60.000 0.00 0.00 0.00 4.02
132 133 2.797278 CCCTCGCTATTCTGCCCGT 61.797 63.158 0.00 0.00 0.00 5.28
133 134 2.029666 CCCTCGCTATTCTGCCCG 59.970 66.667 0.00 0.00 0.00 6.13
134 135 0.815615 CAACCCTCGCTATTCTGCCC 60.816 60.000 0.00 0.00 0.00 5.36
135 136 0.815615 CCAACCCTCGCTATTCTGCC 60.816 60.000 0.00 0.00 0.00 4.85
136 137 0.815615 CCCAACCCTCGCTATTCTGC 60.816 60.000 0.00 0.00 0.00 4.26
137 138 0.179045 CCCCAACCCTCGCTATTCTG 60.179 60.000 0.00 0.00 0.00 3.02
138 139 1.345715 CCCCCAACCCTCGCTATTCT 61.346 60.000 0.00 0.00 0.00 2.40
139 140 1.148498 CCCCCAACCCTCGCTATTC 59.852 63.158 0.00 0.00 0.00 1.75
140 141 3.056754 GCCCCCAACCCTCGCTATT 62.057 63.158 0.00 0.00 0.00 1.73
141 142 3.489513 GCCCCCAACCCTCGCTAT 61.490 66.667 0.00 0.00 0.00 2.97
185 186 4.856607 CTTCTCCCTCGCGACGGC 62.857 72.222 18.06 0.00 0.00 5.68
186 187 2.600122 CTTCTTCTCCCTCGCGACGG 62.600 65.000 16.94 16.94 0.00 4.79
187 188 1.226435 CTTCTTCTCCCTCGCGACG 60.226 63.158 3.71 0.04 0.00 5.12
188 189 1.139947 CCTTCTTCTCCCTCGCGAC 59.860 63.158 3.71 0.00 0.00 5.19
189 190 2.711922 GCCTTCTTCTCCCTCGCGA 61.712 63.158 9.26 9.26 0.00 5.87
190 191 2.202810 GCCTTCTTCTCCCTCGCG 60.203 66.667 0.00 0.00 0.00 5.87
191 192 2.188207 GGCCTTCTTCTCCCTCGC 59.812 66.667 0.00 0.00 0.00 5.03
192 193 2.496817 CGGCCTTCTTCTCCCTCG 59.503 66.667 0.00 0.00 0.00 4.63
193 194 2.904131 CCGGCCTTCTTCTCCCTC 59.096 66.667 0.00 0.00 0.00 4.30
194 195 3.403558 GCCGGCCTTCTTCTCCCT 61.404 66.667 18.11 0.00 0.00 4.20
195 196 4.840005 CGCCGGCCTTCTTCTCCC 62.840 72.222 23.46 0.00 0.00 4.30
196 197 4.840005 CCGCCGGCCTTCTTCTCC 62.840 72.222 23.46 0.00 0.00 3.71
211 212 4.404098 ACCAAACCCTAGCCGCCG 62.404 66.667 0.00 0.00 0.00 6.46
212 213 2.750237 CACCAAACCCTAGCCGCC 60.750 66.667 0.00 0.00 0.00 6.13
213 214 3.440415 GCACCAAACCCTAGCCGC 61.440 66.667 0.00 0.00 0.00 6.53
214 215 3.124921 CGCACCAAACCCTAGCCG 61.125 66.667 0.00 0.00 0.00 5.52
215 216 2.750237 CCGCACCAAACCCTAGCC 60.750 66.667 0.00 0.00 0.00 3.93
216 217 3.440415 GCCGCACCAAACCCTAGC 61.440 66.667 0.00 0.00 0.00 3.42
217 218 2.040544 CAGCCGCACCAAACCCTAG 61.041 63.158 0.00 0.00 0.00 3.02
218 219 2.033448 CAGCCGCACCAAACCCTA 59.967 61.111 0.00 0.00 0.00 3.53
219 220 4.974721 CCAGCCGCACCAAACCCT 62.975 66.667 0.00 0.00 0.00 4.34
223 224 4.531426 AACCCCAGCCGCACCAAA 62.531 61.111 0.00 0.00 0.00 3.28
224 225 4.531426 AAACCCCAGCCGCACCAA 62.531 61.111 0.00 0.00 0.00 3.67
225 226 4.966787 GAAACCCCAGCCGCACCA 62.967 66.667 0.00 0.00 0.00 4.17
233 234 3.330720 AGGAGCCGGAAACCCCAG 61.331 66.667 5.05 0.00 34.14 4.45
234 235 3.327404 GAGGAGCCGGAAACCCCA 61.327 66.667 5.05 0.00 34.14 4.96
235 236 3.009714 AGAGGAGCCGGAAACCCC 61.010 66.667 5.05 0.00 0.00 4.95
236 237 2.269241 CAGAGGAGCCGGAAACCC 59.731 66.667 5.05 0.00 0.00 4.11
237 238 2.245438 CTCCAGAGGAGCCGGAAACC 62.245 65.000 5.05 4.51 43.29 3.27
238 239 1.219393 CTCCAGAGGAGCCGGAAAC 59.781 63.158 5.05 0.00 43.29 2.78
239 240 3.713650 CTCCAGAGGAGCCGGAAA 58.286 61.111 5.05 0.00 43.29 3.13
247 248 2.889521 TATTGCCCGGCTCCAGAGGA 62.890 60.000 11.61 0.00 0.00 3.71
248 249 1.772819 ATATTGCCCGGCTCCAGAGG 61.773 60.000 11.61 0.00 0.00 3.69
249 250 0.604780 CATATTGCCCGGCTCCAGAG 60.605 60.000 11.61 0.00 0.00 3.35
250 251 1.053835 TCATATTGCCCGGCTCCAGA 61.054 55.000 11.61 0.00 0.00 3.86
251 252 0.037303 ATCATATTGCCCGGCTCCAG 59.963 55.000 11.61 0.00 0.00 3.86
252 253 1.278985 CTATCATATTGCCCGGCTCCA 59.721 52.381 11.61 0.00 0.00 3.86
253 254 1.555075 TCTATCATATTGCCCGGCTCC 59.445 52.381 11.61 0.00 0.00 4.70
254 255 3.003480 GTTCTATCATATTGCCCGGCTC 58.997 50.000 11.61 0.00 0.00 4.70
255 256 2.639839 AGTTCTATCATATTGCCCGGCT 59.360 45.455 11.61 0.00 0.00 5.52
256 257 3.059352 AGTTCTATCATATTGCCCGGC 57.941 47.619 1.04 1.04 0.00 6.13
257 258 6.227298 AGATAGTTCTATCATATTGCCCGG 57.773 41.667 18.24 0.00 0.00 5.73
258 259 9.823647 ATAAAGATAGTTCTATCATATTGCCCG 57.176 33.333 18.24 0.00 0.00 6.13
277 278 9.941664 CATCGTTTGAGATTAAGCAATAAAGAT 57.058 29.630 0.00 0.00 0.00 2.40
278 279 8.946085 ACATCGTTTGAGATTAAGCAATAAAGA 58.054 29.630 0.00 0.00 0.00 2.52
279 280 9.214953 GACATCGTTTGAGATTAAGCAATAAAG 57.785 33.333 0.00 0.00 0.00 1.85
280 281 8.946085 AGACATCGTTTGAGATTAAGCAATAAA 58.054 29.630 0.00 0.00 0.00 1.40
281 282 8.492673 AGACATCGTTTGAGATTAAGCAATAA 57.507 30.769 0.00 0.00 0.00 1.40
282 283 8.492673 AAGACATCGTTTGAGATTAAGCAATA 57.507 30.769 0.00 0.00 0.00 1.90
283 284 6.992063 AGACATCGTTTGAGATTAAGCAAT 57.008 33.333 0.00 0.00 0.00 3.56
284 285 6.801539 AAGACATCGTTTGAGATTAAGCAA 57.198 33.333 0.00 0.00 0.00 3.91
285 286 6.871492 TGTAAGACATCGTTTGAGATTAAGCA 59.129 34.615 0.00 0.00 0.00 3.91
286 287 7.290857 TGTAAGACATCGTTTGAGATTAAGC 57.709 36.000 0.00 0.00 0.00 3.09
287 288 8.926710 AGTTGTAAGACATCGTTTGAGATTAAG 58.073 33.333 0.00 0.00 0.00 1.85
288 289 8.827177 AGTTGTAAGACATCGTTTGAGATTAA 57.173 30.769 0.00 0.00 0.00 1.40
289 290 9.569167 CTAGTTGTAAGACATCGTTTGAGATTA 57.431 33.333 0.00 0.00 0.00 1.75
290 291 8.088981 ACTAGTTGTAAGACATCGTTTGAGATT 58.911 33.333 0.00 0.00 0.00 2.40
291 292 7.603651 ACTAGTTGTAAGACATCGTTTGAGAT 58.396 34.615 0.00 0.00 0.00 2.75
292 293 6.978338 ACTAGTTGTAAGACATCGTTTGAGA 58.022 36.000 0.00 0.00 0.00 3.27
293 294 8.912787 ATACTAGTTGTAAGACATCGTTTGAG 57.087 34.615 0.00 0.00 34.45 3.02
294 295 9.701098 AAATACTAGTTGTAAGACATCGTTTGA 57.299 29.630 0.00 0.00 34.45 2.69
350 351 8.695456 CCCACAAGTTATCTTAGGCAAATTATT 58.305 33.333 0.00 0.00 32.07 1.40
351 352 7.839200 ACCCACAAGTTATCTTAGGCAAATTAT 59.161 33.333 0.00 0.00 32.07 1.28
352 353 7.179269 ACCCACAAGTTATCTTAGGCAAATTA 58.821 34.615 0.00 0.00 32.07 1.40
353 354 6.016555 ACCCACAAGTTATCTTAGGCAAATT 58.983 36.000 0.00 0.00 32.07 1.82
354 355 5.580022 ACCCACAAGTTATCTTAGGCAAAT 58.420 37.500 0.00 0.00 32.07 2.32
355 356 4.993028 ACCCACAAGTTATCTTAGGCAAA 58.007 39.130 0.00 0.00 32.07 3.68
356 357 4.042311 TGACCCACAAGTTATCTTAGGCAA 59.958 41.667 0.00 0.00 32.07 4.52
357 358 3.585289 TGACCCACAAGTTATCTTAGGCA 59.415 43.478 0.00 0.00 32.07 4.75
358 359 4.216411 TGACCCACAAGTTATCTTAGGC 57.784 45.455 0.69 0.00 32.07 3.93
375 376 3.496337 GCCTTAGTATTAGGGGCTTGACC 60.496 52.174 0.00 0.00 39.68 4.02
376 377 3.496337 GGCCTTAGTATTAGGGGCTTGAC 60.496 52.174 11.85 0.00 45.03 3.18
377 378 2.709397 GGCCTTAGTATTAGGGGCTTGA 59.291 50.000 11.85 0.00 45.03 3.02
378 379 2.224793 GGGCCTTAGTATTAGGGGCTTG 60.225 54.545 17.20 0.00 46.87 4.01
379 380 2.063425 GGGCCTTAGTATTAGGGGCTT 58.937 52.381 17.20 0.00 46.87 4.35
380 381 1.743589 GGGCCTTAGTATTAGGGGCT 58.256 55.000 17.20 0.00 46.87 5.19
381 382 0.323957 CGGGCCTTAGTATTAGGGGC 59.676 60.000 10.87 10.87 46.95 5.80
382 383 0.981943 CCGGGCCTTAGTATTAGGGG 59.018 60.000 0.84 0.00 33.19 4.79
383 384 1.346722 CACCGGGCCTTAGTATTAGGG 59.653 57.143 6.32 0.00 33.19 3.53
384 385 1.346722 CCACCGGGCCTTAGTATTAGG 59.653 57.143 6.32 0.00 35.80 2.69
385 386 1.346722 CCCACCGGGCCTTAGTATTAG 59.653 57.143 6.32 0.00 35.35 1.73
386 387 1.426751 CCCACCGGGCCTTAGTATTA 58.573 55.000 6.32 0.00 35.35 0.98
387 388 2.227737 CCCACCGGGCCTTAGTATT 58.772 57.895 6.32 0.00 35.35 1.89
388 389 3.981313 CCCACCGGGCCTTAGTAT 58.019 61.111 6.32 0.00 35.35 2.12
398 399 4.778143 CCGAAAGAGGCCCACCGG 62.778 72.222 0.00 0.00 42.76 5.28
399 400 2.175035 TAACCGAAAGAGGCCCACCG 62.175 60.000 0.00 0.00 42.76 4.94
400 401 0.255033 ATAACCGAAAGAGGCCCACC 59.745 55.000 0.00 0.00 33.69 4.61
401 402 2.433239 TCTATAACCGAAAGAGGCCCAC 59.567 50.000 0.00 0.00 33.69 4.61
402 403 2.433239 GTCTATAACCGAAAGAGGCCCA 59.567 50.000 0.00 0.00 33.69 5.36
403 404 2.224233 GGTCTATAACCGAAAGAGGCCC 60.224 54.545 0.00 0.00 38.58 5.80
404 405 3.109044 GGTCTATAACCGAAAGAGGCC 57.891 52.381 0.00 0.00 38.58 5.19
422 423 5.712917 ACATAATTGTTATGACCGGTTTGGT 59.287 36.000 9.42 0.00 44.35 3.67
423 424 6.202516 ACATAATTGTTATGACCGGTTTGG 57.797 37.500 9.42 0.00 44.52 3.28
424 425 8.455682 ACTAACATAATTGTTATGACCGGTTTG 58.544 33.333 9.42 0.00 44.99 2.93
425 426 8.570068 ACTAACATAATTGTTATGACCGGTTT 57.430 30.769 9.42 1.66 44.99 3.27
426 427 9.101655 GTACTAACATAATTGTTATGACCGGTT 57.898 33.333 9.42 0.00 44.99 4.44
427 428 8.480501 AGTACTAACATAATTGTTATGACCGGT 58.519 33.333 6.92 6.92 44.99 5.28
428 429 8.882415 AGTACTAACATAATTGTTATGACCGG 57.118 34.615 14.66 0.00 44.99 5.28
535 557 1.068434 GCTGCCACAAAACAAAGCCTA 59.932 47.619 0.00 0.00 0.00 3.93
571 593 6.354794 AGTTAAATAGTCTAGCACACCACA 57.645 37.500 0.00 0.00 0.00 4.17
572 594 5.515626 CGAGTTAAATAGTCTAGCACACCAC 59.484 44.000 0.00 0.00 0.00 4.16
600 622 6.322491 GGTAATGGCATGAGTTTCTACAAAC 58.678 40.000 0.00 0.00 42.14 2.93
786 811 0.035152 CAGTGGTAGATGCCCTGCAA 60.035 55.000 0.00 0.00 43.62 4.08
808 833 6.038825 TCAACGGAAAGCACTTTATCTCAAAA 59.961 34.615 0.00 0.00 32.11 2.44
810 835 5.060506 TCAACGGAAAGCACTTTATCTCAA 58.939 37.500 0.00 0.00 32.11 3.02
828 853 0.518636 CACACCCTCTTGCATCAACG 59.481 55.000 0.00 0.00 0.00 4.10
852 877 9.720874 ATCAATAGTAGGCCATAGATGAAGATA 57.279 33.333 5.01 0.00 0.00 1.98
929 954 1.615384 GCCCACCAGAGAAGCAAGAAT 60.615 52.381 0.00 0.00 0.00 2.40
1104 1129 1.065564 ACTCTCTTCCAGCTCAATGGC 60.066 52.381 0.00 0.00 40.41 4.40
1176 1201 0.874390 TCACAGAGTGCGCATTTTCC 59.126 50.000 15.91 0.00 32.98 3.13
1332 1357 0.321671 GACAGGGTGTTGAGCTGCTA 59.678 55.000 0.15 0.00 0.00 3.49
1347 1372 3.127895 CGTTTCCAGTAGGAGAGAGACAG 59.872 52.174 0.00 0.00 46.74 3.51
1372 1397 0.458543 CTACGGTCTCGCTGTTGCAT 60.459 55.000 0.00 0.00 40.63 3.96
1620 1645 2.856000 AGGCCTGGCTGTCCAAGT 60.856 61.111 19.68 0.00 42.91 3.16
1701 1726 1.139163 GAACATTTGCAAAGTGGCCG 58.861 50.000 18.19 4.30 37.94 6.13
1705 1730 3.731652 TGGAGGAACATTTGCAAAGTG 57.268 42.857 18.19 16.61 39.72 3.16
2013 2038 5.044919 ACCATGGTCAATAGGAATGAGTTCA 60.045 40.000 13.00 0.00 36.01 3.18
2118 2143 8.149647 TCCAAATTTGCAATGTATTCAAGTTCT 58.850 29.630 12.92 0.00 0.00 3.01
2207 2232 1.526917 GTTGACAGCACCAGCACCT 60.527 57.895 0.00 0.00 45.49 4.00
2259 2284 5.477607 TCTCTCCTATTTCGGACAAACAA 57.522 39.130 0.00 0.00 0.00 2.83
2262 2287 5.932619 TCATCTCTCCTATTTCGGACAAA 57.067 39.130 0.00 0.00 0.00 2.83
2325 2353 2.818432 CTCCATGCAAAGAAGCTCAAGT 59.182 45.455 0.00 0.00 34.99 3.16
2403 2431 1.899142 TGGGTGAAGTCATCATCGTCA 59.101 47.619 0.00 0.00 40.31 4.35
2502 2530 3.743521 CTTTGACAGTGGATTCCTGTGA 58.256 45.455 3.95 0.00 43.00 3.58
2550 2578 4.102210 TCCTTGATCATCTCCTTGTCATCC 59.898 45.833 0.00 0.00 0.00 3.51
2566 2594 2.122768 GGGGTCAGAGTCATCCTTGAT 58.877 52.381 0.00 0.00 33.56 2.57
2604 2632 0.907230 AGACAGGAGGGACCAGCTTC 60.907 60.000 0.00 0.00 42.04 3.86
2625 2653 2.733593 AGCGACGCGGACAGTTTC 60.734 61.111 15.18 0.00 0.00 2.78
2628 2656 3.898627 CTTCAGCGACGCGGACAGT 62.899 63.158 22.20 0.00 31.79 3.55
2837 2865 1.537562 GGAACTTGTCGAGGAACGTGT 60.538 52.381 0.00 0.00 43.13 4.49
2839 2867 0.748450 TGGAACTTGTCGAGGAACGT 59.252 50.000 0.00 0.00 43.13 3.99
2881 2909 3.044305 AGCGTGCTTCCGTGCTTC 61.044 61.111 0.00 0.00 32.89 3.86
2963 2991 5.667466 CATCTACATTACCTTTGGGTACGT 58.333 41.667 0.00 0.00 46.62 3.57
3070 3108 3.140144 CCACCTCTATCTTCTCCTCTCCT 59.860 52.174 0.00 0.00 0.00 3.69
3155 3198 6.800543 TGTCAAAAGCTAAAACTATGCACAA 58.199 32.000 0.00 0.00 0.00 3.33
3183 3226 6.751888 AGACGAAAGAAAGAACAAACCATTTG 59.248 34.615 0.00 0.00 45.95 2.32
3184 3227 6.751888 CAGACGAAAGAAAGAACAAACCATTT 59.248 34.615 0.00 0.00 0.00 2.32
3363 3409 8.825774 TGTAATCCAGGTGCATATTCATACTAT 58.174 33.333 0.00 0.00 0.00 2.12
3366 3412 7.928307 ATGTAATCCAGGTGCATATTCATAC 57.072 36.000 0.00 0.00 0.00 2.39
3391 3437 9.650539 GCAGAGATGTAAACAGATGATACATAT 57.349 33.333 12.59 10.80 39.64 1.78
3392 3438 8.864087 AGCAGAGATGTAAACAGATGATACATA 58.136 33.333 12.59 0.00 39.64 2.29
3393 3439 7.733969 AGCAGAGATGTAAACAGATGATACAT 58.266 34.615 12.51 12.51 41.60 2.29
3394 3440 7.117285 AGCAGAGATGTAAACAGATGATACA 57.883 36.000 5.97 5.97 34.35 2.29
3395 3441 8.333908 CAAAGCAGAGATGTAAACAGATGATAC 58.666 37.037 0.00 0.00 0.00 2.24
3396 3442 7.496920 CCAAAGCAGAGATGTAAACAGATGATA 59.503 37.037 0.00 0.00 0.00 2.15
3397 3443 6.318144 CCAAAGCAGAGATGTAAACAGATGAT 59.682 38.462 0.00 0.00 0.00 2.45
3398 3444 5.645067 CCAAAGCAGAGATGTAAACAGATGA 59.355 40.000 0.00 0.00 0.00 2.92
3399 3445 5.413833 ACCAAAGCAGAGATGTAAACAGATG 59.586 40.000 0.00 0.00 0.00 2.90
3400 3446 5.413833 CACCAAAGCAGAGATGTAAACAGAT 59.586 40.000 0.00 0.00 0.00 2.90
3401 3447 4.756642 CACCAAAGCAGAGATGTAAACAGA 59.243 41.667 0.00 0.00 0.00 3.41
3402 3448 4.614535 GCACCAAAGCAGAGATGTAAACAG 60.615 45.833 0.00 0.00 0.00 3.16
3406 3487 3.423539 AGCACCAAAGCAGAGATGTAA 57.576 42.857 0.00 0.00 36.85 2.41
3410 3491 3.225104 TCAAAAGCACCAAAGCAGAGAT 58.775 40.909 0.00 0.00 36.85 2.75
3423 3504 3.980646 ACAACTTACGCATCAAAAGCA 57.019 38.095 0.00 0.00 0.00 3.91
3437 3518 2.169769 TCCCACGTTCTCTCAACAACTT 59.830 45.455 0.00 0.00 0.00 2.66
3474 3555 2.776312 TCCAGATCAATCGCTCGTAC 57.224 50.000 0.00 0.00 0.00 3.67
3496 3577 3.278668 TTTGACACTACCCGAACCAAA 57.721 42.857 0.00 0.00 0.00 3.28
3522 3603 1.377987 TTTCTACGGCACATGGGGC 60.378 57.895 12.39 12.39 0.00 5.80
3524 3605 1.468520 CAAGTTTCTACGGCACATGGG 59.531 52.381 0.00 0.00 0.00 4.00
3610 3698 2.097036 TCCGTTACCAGACATGTCGAT 58.903 47.619 19.85 11.77 34.09 3.59
3746 3834 1.379146 GACGGGAAAAGAAGGGCCT 59.621 57.895 0.00 0.00 0.00 5.19
3747 3835 0.960861 CTGACGGGAAAAGAAGGGCC 60.961 60.000 0.00 0.00 0.00 5.80
3804 3892 3.736720 CGACCTCCATTGATGATGATGT 58.263 45.455 0.00 0.00 38.03 3.06
3809 3897 3.209410 GAAAGCGACCTCCATTGATGAT 58.791 45.455 0.00 0.00 0.00 2.45
3812 3900 1.561542 AGGAAAGCGACCTCCATTGAT 59.438 47.619 0.00 0.00 33.83 2.57
3816 3904 1.078143 GCAGGAAAGCGACCTCCAT 60.078 57.895 0.00 0.00 35.35 3.41


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

AutoCloner maintained by Alex Coulton.