Multiple sequence alignment - TraesCS6B01G169100

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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 TraesCS6B01G169100 chr6B 100.000 3490 0 0 929 4418 179755132 179751643 0.000000e+00 6445
1 TraesCS6B01G169100 chr6B 100.000 462 0 0 1 462 179756060 179755599 0.000000e+00 854
2 TraesCS6B01G169100 chr6B 86.081 467 51 9 1 459 198963800 198964260 1.430000e-134 490
3 TraesCS6B01G169100 chr6D 97.649 3488 74 6 933 4418 96719780 96716299 0.000000e+00 5980
4 TraesCS6B01G169100 chr6A 96.249 3439 86 17 996 4418 115464872 115461461 0.000000e+00 5596
5 TraesCS6B01G169100 chr6A 84.402 468 54 11 1 462 564890982 564890528 4.060000e-120 442
6 TraesCS6B01G169100 chr4B 87.719 456 44 9 9 459 632120758 632121206 5.060000e-144 521
7 TraesCS6B01G169100 chr3B 87.281 456 47 6 1 452 720855744 720856192 1.100000e-140 510
8 TraesCS6B01G169100 chr3A 87.152 467 39 12 1 459 492327554 492328007 1.100000e-140 510
9 TraesCS6B01G169100 chr1D 87.364 459 40 10 1 455 204887830 204887386 1.100000e-140 510
10 TraesCS6B01G169100 chr7B 85.319 470 48 13 1 462 645196466 645196922 2.410000e-127 466
11 TraesCS6B01G169100 chr3D 85.746 456 47 10 9 459 608910802 608911244 2.410000e-127 466
12 TraesCS6B01G169100 chr7D 84.665 463 53 10 1 456 6571501 6571050 3.140000e-121 446


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 TraesCS6B01G169100 chr6B 179751643 179756060 4417 True 3649.5 6445 100.000 1 4418 2 chr6B.!!$R1 4417
1 TraesCS6B01G169100 chr6D 96716299 96719780 3481 True 5980.0 5980 97.649 933 4418 1 chr6D.!!$R1 3485
2 TraesCS6B01G169100 chr6A 115461461 115464872 3411 True 5596.0 5596 96.249 996 4418 1 chr6A.!!$R1 3422

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
457 458 0.036483 ATTGGGGCATTTTTCGGTGC 60.036 50.0 0.0 0.0 40.55 5.01 F
1722 1723 0.036306 GTGGGGTTCGTGTTGATCCT 59.964 55.0 0.0 0.0 36.78 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 1784 0.109597 CCAAGCTGGAATGCACGAAC 60.11 55.000 0.00 0.0 40.96 3.95 R
3480 3481 1.669779 GCAAATTGCACAAAAGTGGCA 59.33 42.857 13.73 0.0 44.26 4.92 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 3.893763 CGAGCGCCTCCTCATCGT 61.894 66.667 2.29 0.00 0.00 3.73
27 28 2.496817 GAGCGCCTCCTCATCGTT 59.503 61.111 2.29 0.00 0.00 3.85
28 29 1.590259 GAGCGCCTCCTCATCGTTC 60.590 63.158 2.29 0.00 0.00 3.95
29 30 2.956964 GCGCCTCCTCATCGTTCG 60.957 66.667 0.00 0.00 0.00 3.95
30 31 2.798689 CGCCTCCTCATCGTTCGA 59.201 61.111 0.00 0.00 0.00 3.71
31 32 1.298713 CGCCTCCTCATCGTTCGAG 60.299 63.158 0.80 0.00 0.00 4.04
32 33 1.810532 GCCTCCTCATCGTTCGAGT 59.189 57.895 0.80 0.00 0.00 4.18
33 34 0.248702 GCCTCCTCATCGTTCGAGTC 60.249 60.000 0.80 0.00 0.00 3.36
34 35 0.382515 CCTCCTCATCGTTCGAGTCC 59.617 60.000 0.80 0.00 0.00 3.85
35 36 1.095600 CTCCTCATCGTTCGAGTCCA 58.904 55.000 0.80 0.00 0.00 4.02
36 37 1.678627 CTCCTCATCGTTCGAGTCCAT 59.321 52.381 0.80 0.00 0.00 3.41
37 38 1.676529 TCCTCATCGTTCGAGTCCATC 59.323 52.381 0.80 0.00 0.00 3.51
45 46 4.933064 CGAGTCCATCGCCGAGCC 62.933 72.222 0.00 0.00 45.98 4.70
46 47 4.933064 GAGTCCATCGCCGAGCCG 62.933 72.222 0.00 0.00 0.00 5.52
56 57 4.697756 CCGAGCCGGGCAGACAAA 62.698 66.667 23.09 0.00 44.15 2.83
57 58 2.436646 CGAGCCGGGCAGACAAAT 60.437 61.111 23.09 0.00 0.00 2.32
58 59 2.464459 CGAGCCGGGCAGACAAATC 61.464 63.158 23.09 6.96 0.00 2.17
59 60 2.436646 AGCCGGGCAGACAAATCG 60.437 61.111 23.09 0.00 0.00 3.34
60 61 4.179579 GCCGGGCAGACAAATCGC 62.180 66.667 15.62 0.00 0.00 4.58
61 62 3.508840 CCGGGCAGACAAATCGCC 61.509 66.667 0.00 0.00 41.19 5.54
62 63 3.864686 CGGGCAGACAAATCGCCG 61.865 66.667 0.00 0.00 42.17 6.46
63 64 2.435938 GGGCAGACAAATCGCCGA 60.436 61.111 0.00 0.00 42.17 5.54
64 65 2.038269 GGGCAGACAAATCGCCGAA 61.038 57.895 0.00 0.00 42.17 4.30
65 66 1.134694 GGCAGACAAATCGCCGAAC 59.865 57.895 0.00 0.00 35.70 3.95
66 67 1.573829 GGCAGACAAATCGCCGAACA 61.574 55.000 0.00 0.00 35.70 3.18
67 68 0.447801 GCAGACAAATCGCCGAACAT 59.552 50.000 0.00 0.00 0.00 2.71
68 69 1.529826 GCAGACAAATCGCCGAACATC 60.530 52.381 0.00 0.00 0.00 3.06
69 70 2.002586 CAGACAAATCGCCGAACATCT 58.997 47.619 0.00 0.00 0.00 2.90
70 71 2.416547 CAGACAAATCGCCGAACATCTT 59.583 45.455 0.00 0.00 0.00 2.40
71 72 2.416547 AGACAAATCGCCGAACATCTTG 59.583 45.455 0.00 0.00 0.00 3.02
72 73 1.135689 ACAAATCGCCGAACATCTTGC 60.136 47.619 0.00 0.00 0.00 4.01
74 75 1.705337 AATCGCCGAACATCTTGCGG 61.705 55.000 0.00 0.00 46.51 5.69
75 76 3.864686 CGCCGAACATCTTGCGGG 61.865 66.667 0.00 0.00 44.92 6.13
76 77 2.746277 GCCGAACATCTTGCGGGT 60.746 61.111 0.00 0.00 44.92 5.28
77 78 3.039202 GCCGAACATCTTGCGGGTG 62.039 63.158 0.00 0.00 44.92 4.61
78 79 1.671054 CCGAACATCTTGCGGGTGT 60.671 57.895 0.00 0.00 41.29 4.16
79 80 1.497278 CGAACATCTTGCGGGTGTG 59.503 57.895 0.00 0.00 0.00 3.82
80 81 1.875963 GAACATCTTGCGGGTGTGG 59.124 57.895 0.00 0.00 0.00 4.17
81 82 0.889186 GAACATCTTGCGGGTGTGGT 60.889 55.000 0.00 0.00 0.00 4.16
82 83 1.172180 AACATCTTGCGGGTGTGGTG 61.172 55.000 0.00 0.00 0.00 4.17
83 84 2.034066 ATCTTGCGGGTGTGGTGG 59.966 61.111 0.00 0.00 0.00 4.61
84 85 3.567579 ATCTTGCGGGTGTGGTGGG 62.568 63.158 0.00 0.00 0.00 4.61
100 101 4.367023 GGCGCACACCCGTCAGTA 62.367 66.667 10.83 0.00 32.16 2.74
101 102 3.110178 GCGCACACCCGTCAGTAC 61.110 66.667 0.30 0.00 0.00 2.73
102 103 2.337170 CGCACACCCGTCAGTACA 59.663 61.111 0.00 0.00 0.00 2.90
103 104 2.019951 CGCACACCCGTCAGTACAC 61.020 63.158 0.00 0.00 0.00 2.90
104 105 1.366366 GCACACCCGTCAGTACACT 59.634 57.895 0.00 0.00 0.00 3.55
105 106 0.944311 GCACACCCGTCAGTACACTG 60.944 60.000 2.84 2.84 45.08 3.66
106 107 0.944311 CACACCCGTCAGTACACTGC 60.944 60.000 4.43 0.00 43.46 4.40
107 108 1.374252 CACCCGTCAGTACACTGCC 60.374 63.158 4.43 0.00 43.46 4.85
108 109 1.533273 ACCCGTCAGTACACTGCCT 60.533 57.895 4.43 0.00 43.46 4.75
109 110 1.215647 CCCGTCAGTACACTGCCTC 59.784 63.158 4.43 0.00 43.46 4.70
110 111 1.251527 CCCGTCAGTACACTGCCTCT 61.252 60.000 4.43 0.00 43.46 3.69
111 112 0.109086 CCGTCAGTACACTGCCTCTG 60.109 60.000 4.43 0.00 43.46 3.35
112 113 0.734253 CGTCAGTACACTGCCTCTGC 60.734 60.000 4.43 0.00 43.46 4.26
113 114 0.734253 GTCAGTACACTGCCTCTGCG 60.734 60.000 4.43 0.00 43.46 5.18
114 115 1.179174 TCAGTACACTGCCTCTGCGT 61.179 55.000 4.43 0.00 43.46 5.24
115 116 1.010935 CAGTACACTGCCTCTGCGTG 61.011 60.000 0.00 7.58 43.14 5.34
116 117 2.048222 TACACTGCCTCTGCGTGC 60.048 61.111 8.61 0.00 42.07 5.34
117 118 3.589654 TACACTGCCTCTGCGTGCC 62.590 63.158 8.61 0.00 42.07 5.01
118 119 4.994471 CACTGCCTCTGCGTGCCA 62.994 66.667 0.00 0.00 41.78 4.92
119 120 4.694233 ACTGCCTCTGCGTGCCAG 62.694 66.667 0.00 0.00 43.17 4.85
129 130 2.281208 CGTGCCAGAACCCGGAAA 60.281 61.111 0.73 0.00 0.00 3.13
130 131 1.894756 CGTGCCAGAACCCGGAAAA 60.895 57.895 0.73 0.00 0.00 2.29
131 132 1.448922 CGTGCCAGAACCCGGAAAAA 61.449 55.000 0.73 0.00 0.00 1.94
132 133 0.966179 GTGCCAGAACCCGGAAAAAT 59.034 50.000 0.73 0.00 0.00 1.82
133 134 1.067846 GTGCCAGAACCCGGAAAAATC 60.068 52.381 0.73 0.00 0.00 2.17
134 135 1.253100 GCCAGAACCCGGAAAAATCA 58.747 50.000 0.73 0.00 0.00 2.57
135 136 1.067846 GCCAGAACCCGGAAAAATCAC 60.068 52.381 0.73 0.00 0.00 3.06
136 137 1.544246 CCAGAACCCGGAAAAATCACC 59.456 52.381 0.73 0.00 0.00 4.02
137 138 1.544246 CAGAACCCGGAAAAATCACCC 59.456 52.381 0.73 0.00 0.00 4.61
138 139 0.524414 GAACCCGGAAAAATCACCCG 59.476 55.000 0.73 0.00 42.64 5.28
142 143 1.791662 CGGAAAAATCACCCGGACG 59.208 57.895 0.73 0.00 39.59 4.79
143 144 1.641123 CGGAAAAATCACCCGGACGG 61.641 60.000 0.73 3.25 39.59 4.79
153 154 3.760035 CCGGACGGTGGTGGAGAG 61.760 72.222 0.00 0.00 0.00 3.20
154 155 3.760035 CGGACGGTGGTGGAGAGG 61.760 72.222 0.00 0.00 0.00 3.69
155 156 4.083862 GGACGGTGGTGGAGAGGC 62.084 72.222 0.00 0.00 0.00 4.70
156 157 2.997897 GACGGTGGTGGAGAGGCT 60.998 66.667 0.00 0.00 0.00 4.58
157 158 3.302347 GACGGTGGTGGAGAGGCTG 62.302 68.421 0.00 0.00 0.00 4.85
158 159 4.767255 CGGTGGTGGAGAGGCTGC 62.767 72.222 0.00 0.00 0.00 5.25
159 160 4.416738 GGTGGTGGAGAGGCTGCC 62.417 72.222 11.65 11.65 0.00 4.85
160 161 4.767255 GTGGTGGAGAGGCTGCCG 62.767 72.222 13.96 0.00 0.00 5.69
175 176 3.488090 CCGCGGCGAAACCTCTTC 61.488 66.667 25.92 0.00 35.61 2.87
176 177 2.432628 CGCGGCGAAACCTCTTCT 60.433 61.111 19.16 0.00 35.61 2.85
177 178 2.445438 CGCGGCGAAACCTCTTCTC 61.445 63.158 19.16 0.00 35.61 2.87
178 179 1.079750 GCGGCGAAACCTCTTCTCT 60.080 57.895 12.98 0.00 35.61 3.10
179 180 0.670854 GCGGCGAAACCTCTTCTCTT 60.671 55.000 12.98 0.00 35.61 2.85
180 181 1.797025 CGGCGAAACCTCTTCTCTTT 58.203 50.000 0.00 0.00 35.61 2.52
181 182 2.143925 CGGCGAAACCTCTTCTCTTTT 58.856 47.619 0.00 0.00 35.61 2.27
182 183 2.157863 CGGCGAAACCTCTTCTCTTTTC 59.842 50.000 0.00 0.00 35.61 2.29
183 184 2.484651 GGCGAAACCTCTTCTCTTTTCC 59.515 50.000 0.00 0.00 34.51 3.13
184 185 2.157863 GCGAAACCTCTTCTCTTTTCCG 59.842 50.000 0.00 0.00 0.00 4.30
185 186 2.737252 CGAAACCTCTTCTCTTTTCCGG 59.263 50.000 0.00 0.00 0.00 5.14
186 187 2.186532 AACCTCTTCTCTTTTCCGGC 57.813 50.000 0.00 0.00 0.00 6.13
187 188 0.037232 ACCTCTTCTCTTTTCCGGCG 60.037 55.000 0.00 0.00 0.00 6.46
188 189 0.246635 CCTCTTCTCTTTTCCGGCGA 59.753 55.000 9.30 0.00 0.00 5.54
189 190 1.634702 CTCTTCTCTTTTCCGGCGAG 58.365 55.000 9.30 0.00 0.00 5.03
190 191 0.246635 TCTTCTCTTTTCCGGCGAGG 59.753 55.000 9.30 0.00 42.97 4.63
209 210 3.051081 GGAATGGCCTATCTAGCTGTG 57.949 52.381 3.32 0.00 0.00 3.66
210 211 2.289945 GGAATGGCCTATCTAGCTGTGG 60.290 54.545 3.32 0.00 0.00 4.17
211 212 2.109229 ATGGCCTATCTAGCTGTGGT 57.891 50.000 3.32 0.00 0.00 4.16
212 213 1.123077 TGGCCTATCTAGCTGTGGTG 58.877 55.000 3.32 0.00 0.00 4.17
213 214 0.394565 GGCCTATCTAGCTGTGGTGG 59.605 60.000 0.00 0.00 0.00 4.61
214 215 0.394565 GCCTATCTAGCTGTGGTGGG 59.605 60.000 0.00 0.00 0.00 4.61
215 216 1.794714 CCTATCTAGCTGTGGTGGGT 58.205 55.000 0.00 0.00 0.00 4.51
216 217 1.414181 CCTATCTAGCTGTGGTGGGTG 59.586 57.143 0.00 0.00 0.00 4.61
217 218 1.414181 CTATCTAGCTGTGGTGGGTGG 59.586 57.143 0.00 0.00 0.00 4.61
218 219 0.547712 ATCTAGCTGTGGTGGGTGGT 60.548 55.000 0.00 0.00 0.00 4.16
219 220 1.003355 CTAGCTGTGGTGGGTGGTG 60.003 63.158 0.00 0.00 0.00 4.17
220 221 2.469465 CTAGCTGTGGTGGGTGGTGG 62.469 65.000 0.00 0.00 0.00 4.61
221 222 4.974721 GCTGTGGTGGGTGGTGGG 62.975 72.222 0.00 0.00 0.00 4.61
222 223 4.974721 CTGTGGTGGGTGGTGGGC 62.975 72.222 0.00 0.00 0.00 5.36
275 276 2.617215 GGGGGTGGGGGTGAATCT 60.617 66.667 0.00 0.00 0.00 2.40
276 277 2.683475 GGGGTGGGGGTGAATCTG 59.317 66.667 0.00 0.00 0.00 2.90
277 278 2.683475 GGGTGGGGGTGAATCTGG 59.317 66.667 0.00 0.00 0.00 3.86
278 279 1.928567 GGGTGGGGGTGAATCTGGA 60.929 63.158 0.00 0.00 0.00 3.86
279 280 1.303282 GGTGGGGGTGAATCTGGAC 59.697 63.158 0.00 0.00 0.00 4.02
280 281 1.078426 GTGGGGGTGAATCTGGACG 60.078 63.158 0.00 0.00 0.00 4.79
281 282 2.297895 TGGGGGTGAATCTGGACGG 61.298 63.158 0.00 0.00 0.00 4.79
282 283 2.298661 GGGGGTGAATCTGGACGGT 61.299 63.158 0.00 0.00 0.00 4.83
283 284 1.683441 GGGGTGAATCTGGACGGTT 59.317 57.895 0.00 0.00 0.00 4.44
284 285 0.676782 GGGGTGAATCTGGACGGTTG 60.677 60.000 0.00 0.00 0.00 3.77
285 286 0.676782 GGGTGAATCTGGACGGTTGG 60.677 60.000 0.00 0.00 0.00 3.77
286 287 1.305930 GGTGAATCTGGACGGTTGGC 61.306 60.000 0.00 0.00 0.00 4.52
287 288 0.321653 GTGAATCTGGACGGTTGGCT 60.322 55.000 0.00 0.00 0.00 4.75
288 289 0.400213 TGAATCTGGACGGTTGGCTT 59.600 50.000 0.00 0.00 0.00 4.35
289 290 0.804989 GAATCTGGACGGTTGGCTTG 59.195 55.000 0.00 0.00 0.00 4.01
290 291 0.400213 AATCTGGACGGTTGGCTTGA 59.600 50.000 0.00 0.00 0.00 3.02
291 292 0.321653 ATCTGGACGGTTGGCTTGAC 60.322 55.000 0.00 0.00 0.00 3.18
292 293 1.071471 CTGGACGGTTGGCTTGACT 59.929 57.895 0.00 0.00 0.00 3.41
293 294 0.535102 CTGGACGGTTGGCTTGACTT 60.535 55.000 0.00 0.00 0.00 3.01
294 295 0.106918 TGGACGGTTGGCTTGACTTT 60.107 50.000 0.00 0.00 0.00 2.66
295 296 1.029681 GGACGGTTGGCTTGACTTTT 58.970 50.000 0.00 0.00 0.00 2.27
296 297 1.001706 GGACGGTTGGCTTGACTTTTC 60.002 52.381 0.00 0.00 0.00 2.29
297 298 0.661020 ACGGTTGGCTTGACTTTTCG 59.339 50.000 0.00 0.00 0.00 3.46
298 299 0.660300 CGGTTGGCTTGACTTTTCGC 60.660 55.000 0.00 0.00 0.00 4.70
299 300 0.318699 GGTTGGCTTGACTTTTCGCC 60.319 55.000 0.00 0.00 42.78 5.54
300 301 0.668535 GTTGGCTTGACTTTTCGCCT 59.331 50.000 0.00 0.00 42.90 5.52
301 302 0.667993 TTGGCTTGACTTTTCGCCTG 59.332 50.000 0.00 0.00 42.90 4.85
302 303 0.179032 TGGCTTGACTTTTCGCCTGA 60.179 50.000 0.00 0.00 42.90 3.86
303 304 0.238553 GGCTTGACTTTTCGCCTGAC 59.761 55.000 0.00 0.00 39.42 3.51
304 305 0.944386 GCTTGACTTTTCGCCTGACA 59.056 50.000 0.00 0.00 0.00 3.58
305 306 1.069636 GCTTGACTTTTCGCCTGACAG 60.070 52.381 0.00 0.00 0.00 3.51
306 307 2.213499 CTTGACTTTTCGCCTGACAGT 58.787 47.619 0.93 0.00 0.00 3.55
307 308 1.581934 TGACTTTTCGCCTGACAGTG 58.418 50.000 0.93 0.00 0.00 3.66
308 309 1.134521 TGACTTTTCGCCTGACAGTGT 60.135 47.619 0.00 0.00 0.00 3.55
309 310 1.261619 GACTTTTCGCCTGACAGTGTG 59.738 52.381 0.00 0.23 0.00 3.82
310 311 0.588252 CTTTTCGCCTGACAGTGTGG 59.412 55.000 0.00 0.00 0.00 4.17
311 312 1.444119 TTTTCGCCTGACAGTGTGGC 61.444 55.000 13.41 13.41 42.94 5.01
312 313 3.825160 TTCGCCTGACAGTGTGGCC 62.825 63.158 16.71 0.00 43.42 5.36
314 315 3.958860 GCCTGACAGTGTGGCCCT 61.959 66.667 12.58 0.00 40.71 5.19
315 316 2.592993 GCCTGACAGTGTGGCCCTA 61.593 63.158 12.58 0.00 40.71 3.53
316 317 1.599047 CCTGACAGTGTGGCCCTAG 59.401 63.158 0.00 0.00 0.00 3.02
317 318 1.599047 CTGACAGTGTGGCCCTAGG 59.401 63.158 0.00 0.06 0.00 3.02
318 319 1.152118 TGACAGTGTGGCCCTAGGT 60.152 57.895 8.29 0.00 0.00 3.08
319 320 1.296715 GACAGTGTGGCCCTAGGTG 59.703 63.158 8.29 0.00 0.00 4.00
320 321 1.461461 ACAGTGTGGCCCTAGGTGT 60.461 57.895 8.29 0.11 0.00 4.16
321 322 1.003355 CAGTGTGGCCCTAGGTGTG 60.003 63.158 8.29 0.00 0.00 3.82
322 323 2.359975 GTGTGGCCCTAGGTGTGC 60.360 66.667 8.29 3.81 0.00 4.57
323 324 2.529136 TGTGGCCCTAGGTGTGCT 60.529 61.111 8.29 0.00 0.00 4.40
324 325 2.153401 TGTGGCCCTAGGTGTGCTT 61.153 57.895 8.29 0.00 0.00 3.91
325 326 1.074951 GTGGCCCTAGGTGTGCTTT 59.925 57.895 8.29 0.00 0.00 3.51
326 327 0.539669 GTGGCCCTAGGTGTGCTTTT 60.540 55.000 8.29 0.00 0.00 2.27
327 328 0.251165 TGGCCCTAGGTGTGCTTTTC 60.251 55.000 8.29 0.00 0.00 2.29
328 329 0.965866 GGCCCTAGGTGTGCTTTTCC 60.966 60.000 8.29 0.00 0.00 3.13
329 330 0.965866 GCCCTAGGTGTGCTTTTCCC 60.966 60.000 8.29 0.00 0.00 3.97
330 331 0.698818 CCCTAGGTGTGCTTTTCCCT 59.301 55.000 8.29 0.00 0.00 4.20
331 332 1.075536 CCCTAGGTGTGCTTTTCCCTT 59.924 52.381 8.29 0.00 0.00 3.95
332 333 2.162681 CCTAGGTGTGCTTTTCCCTTG 58.837 52.381 0.00 0.00 0.00 3.61
333 334 1.541588 CTAGGTGTGCTTTTCCCTTGC 59.458 52.381 0.00 0.00 0.00 4.01
334 335 1.007387 GGTGTGCTTTTCCCTTGCG 60.007 57.895 0.00 0.00 0.00 4.85
335 336 1.661509 GTGTGCTTTTCCCTTGCGC 60.662 57.895 0.00 0.00 37.67 6.09
336 337 2.049156 GTGCTTTTCCCTTGCGCC 60.049 61.111 4.18 0.00 0.00 6.53
337 338 3.669344 TGCTTTTCCCTTGCGCCG 61.669 61.111 4.18 0.00 0.00 6.46
338 339 4.419939 GCTTTTCCCTTGCGCCGG 62.420 66.667 4.18 5.21 0.00 6.13
339 340 2.671619 CTTTTCCCTTGCGCCGGA 60.672 61.111 5.05 8.98 0.00 5.14
340 341 2.671619 TTTTCCCTTGCGCCGGAG 60.672 61.111 5.05 1.55 0.00 4.63
374 375 3.953775 CCCCCAGTGTGTCGGCTT 61.954 66.667 0.00 0.00 0.00 4.35
375 376 2.358737 CCCCAGTGTGTCGGCTTC 60.359 66.667 0.00 0.00 0.00 3.86
376 377 2.738521 CCCAGTGTGTCGGCTTCG 60.739 66.667 0.00 0.00 0.00 3.79
377 378 2.738521 CCAGTGTGTCGGCTTCGG 60.739 66.667 0.00 0.00 34.13 4.30
378 379 3.414700 CAGTGTGTCGGCTTCGGC 61.415 66.667 0.00 0.00 39.24 5.54
388 389 3.567797 GCTTCGGCCTGCGATCAC 61.568 66.667 0.00 0.00 34.32 3.06
389 390 2.892425 CTTCGGCCTGCGATCACC 60.892 66.667 0.00 0.00 0.00 4.02
390 391 4.812476 TTCGGCCTGCGATCACCG 62.812 66.667 0.00 0.00 46.97 4.94
399 400 2.360600 CGATCACCGGGCCCAAAA 60.361 61.111 24.92 3.75 33.91 2.44
400 401 1.974343 CGATCACCGGGCCCAAAAA 60.974 57.895 24.92 4.19 33.91 1.94
401 402 1.890174 GATCACCGGGCCCAAAAAG 59.110 57.895 24.92 4.27 0.00 2.27
402 403 1.604147 GATCACCGGGCCCAAAAAGG 61.604 60.000 24.92 17.28 37.03 3.11
422 423 3.264897 CGAGCCAGCGGAATTCGG 61.265 66.667 8.57 8.57 39.69 4.30
423 424 3.577313 GAGCCAGCGGAATTCGGC 61.577 66.667 25.75 25.75 45.23 5.54
426 427 3.564027 CCAGCGGAATTCGGCGTC 61.564 66.667 26.34 10.17 45.36 5.19
427 428 2.509336 CAGCGGAATTCGGCGTCT 60.509 61.111 26.34 11.40 45.36 4.18
428 429 2.100631 CAGCGGAATTCGGCGTCTT 61.101 57.895 26.34 11.08 45.36 3.01
429 430 2.100631 AGCGGAATTCGGCGTCTTG 61.101 57.895 26.34 0.00 45.36 3.02
430 431 3.089784 CGGAATTCGGCGTCTTGG 58.910 61.111 6.85 0.00 34.75 3.61
431 432 2.461110 CGGAATTCGGCGTCTTGGG 61.461 63.158 6.85 0.00 34.75 4.12
432 433 2.112815 GGAATTCGGCGTCTTGGGG 61.113 63.158 6.85 0.00 0.00 4.96
433 434 2.045340 AATTCGGCGTCTTGGGGG 60.045 61.111 6.85 0.00 0.00 5.40
434 435 4.796495 ATTCGGCGTCTTGGGGGC 62.796 66.667 6.85 0.00 0.00 5.80
441 442 3.508840 GTCTTGGGGGCGCGATTG 61.509 66.667 12.10 0.00 0.00 2.67
442 443 4.794648 TCTTGGGGGCGCGATTGG 62.795 66.667 12.10 0.00 0.00 3.16
451 452 4.908790 CGCGATTGGGGCATTTTT 57.091 50.000 0.00 0.00 0.00 1.94
452 453 2.664567 CGCGATTGGGGCATTTTTC 58.335 52.632 0.00 0.00 0.00 2.29
453 454 1.139226 CGCGATTGGGGCATTTTTCG 61.139 55.000 0.00 0.00 0.00 3.46
454 455 0.805711 GCGATTGGGGCATTTTTCGG 60.806 55.000 0.00 0.00 0.00 4.30
455 456 0.530288 CGATTGGGGCATTTTTCGGT 59.470 50.000 0.00 0.00 0.00 4.69
456 457 1.735369 CGATTGGGGCATTTTTCGGTG 60.735 52.381 0.00 0.00 0.00 4.94
457 458 0.036483 ATTGGGGCATTTTTCGGTGC 60.036 50.000 0.00 0.00 40.55 5.01
461 462 3.860717 GCATTTTTCGGTGCCAGC 58.139 55.556 0.00 0.00 35.35 4.85
992 993 3.432326 CCCTTCTACTTGCCGCTAAATCT 60.432 47.826 0.00 0.00 0.00 2.40
1040 1041 3.114616 CGCTGTCGTGCTCCAAGG 61.115 66.667 0.00 0.00 0.00 3.61
1710 1711 1.380302 GATGTGCAGGAGTGGGGTT 59.620 57.895 0.00 0.00 0.00 4.11
1722 1723 0.036306 GTGGGGTTCGTGTTGATCCT 59.964 55.000 0.00 0.00 36.78 3.24
1728 1729 0.107643 TTCGTGTTGATCCTGTGGCA 59.892 50.000 0.00 0.00 0.00 4.92
1743 1744 2.169561 TGTGGCAGTGTCAAGTGTTCTA 59.830 45.455 0.00 0.00 0.00 2.10
1746 1747 2.224305 GGCAGTGTCAAGTGTTCTAGGT 60.224 50.000 0.00 0.00 0.00 3.08
1780 1781 4.090057 GCGCCAGCGAGTTCAACC 62.090 66.667 17.53 0.00 42.83 3.77
1783 1784 1.576421 GCCAGCGAGTTCAACCTTG 59.424 57.895 0.00 0.00 0.00 3.61
1788 1789 0.935196 GCGAGTTCAACCTTGTTCGT 59.065 50.000 0.00 0.00 33.62 3.85
1791 1792 1.668751 GAGTTCAACCTTGTTCGTGCA 59.331 47.619 0.00 0.00 0.00 4.57
2023 2024 5.106712 GCTTTGGAAGTATTGAACGTGATGA 60.107 40.000 0.00 0.00 0.00 2.92
2202 2203 5.776744 GAGGAACTGCATCAAGAAACAATT 58.223 37.500 0.00 0.00 41.55 2.32
3060 3061 4.476297 TGCCATGCAAAGATGATCCTATT 58.524 39.130 0.00 0.00 34.76 1.73
3345 3346 1.546029 CAGACGGTCAGTGGAGAATCA 59.454 52.381 11.27 0.00 36.25 2.57
3480 3481 6.782082 TCAGTGATAGCTGAATTCAGTAGT 57.218 37.500 30.88 20.18 45.45 2.73
3731 3734 1.860326 GAGCGCAAAAGCAATTGTTGT 59.140 42.857 11.47 0.00 40.15 3.32
3805 3808 8.383175 TCCATTTACTTTTTCAGTCAGTATCCT 58.617 33.333 0.00 0.00 36.88 3.24
3813 3816 7.962964 TTTTCAGTCAGTATCCTTAAGTGTG 57.037 36.000 0.97 0.00 0.00 3.82
3885 3888 0.614979 GTCTGGAGGGCAGAGTGGTA 60.615 60.000 0.00 0.00 0.00 3.25
3970 3974 4.816786 TTACGTTTAACTTCCTTGTGCC 57.183 40.909 0.00 0.00 0.00 5.01
4015 4019 6.395426 TGAAATTTTGATCAGTTGCTCTGT 57.605 33.333 0.00 0.00 43.97 3.41
4066 4070 0.538287 GTTGCAGACAAGGGAGGCTT 60.538 55.000 0.00 0.00 36.16 4.35
4394 4412 6.493116 CATTCATAGCTTCAGAATGGTTGAC 58.507 40.000 19.59 0.00 42.90 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.417275 AACGATGAGGAGGCGCTCG 62.417 63.158 7.64 9.60 35.56 5.03
10 11 1.590259 GAACGATGAGGAGGCGCTC 60.590 63.158 7.64 2.45 0.00 5.03
11 12 2.496817 GAACGATGAGGAGGCGCT 59.503 61.111 7.64 0.00 0.00 5.92
12 13 2.956964 CGAACGATGAGGAGGCGC 60.957 66.667 0.00 0.00 0.00 6.53
13 14 1.298713 CTCGAACGATGAGGAGGCG 60.299 63.158 0.00 0.00 0.00 5.52
14 15 0.248702 GACTCGAACGATGAGGAGGC 60.249 60.000 0.00 0.00 37.79 4.70
15 16 0.382515 GGACTCGAACGATGAGGAGG 59.617 60.000 0.00 0.00 37.79 4.30
16 17 1.095600 TGGACTCGAACGATGAGGAG 58.904 55.000 0.00 0.00 37.79 3.69
17 18 1.676529 GATGGACTCGAACGATGAGGA 59.323 52.381 0.00 0.00 37.79 3.71
18 19 2.126914 GATGGACTCGAACGATGAGG 57.873 55.000 0.00 0.00 37.79 3.86
29 30 4.933064 CGGCTCGGCGATGGACTC 62.933 72.222 11.27 0.00 0.00 3.36
40 41 2.436646 ATTTGTCTGCCCGGCTCG 60.437 61.111 11.61 1.78 0.00 5.03
41 42 2.464459 CGATTTGTCTGCCCGGCTC 61.464 63.158 11.61 2.06 0.00 4.70
42 43 2.436646 CGATTTGTCTGCCCGGCT 60.437 61.111 11.61 0.00 0.00 5.52
43 44 4.179579 GCGATTTGTCTGCCCGGC 62.180 66.667 1.04 1.04 0.00 6.13
44 45 3.508840 GGCGATTTGTCTGCCCGG 61.509 66.667 0.00 0.00 43.06 5.73
45 46 3.864686 CGGCGATTTGTCTGCCCG 61.865 66.667 0.00 0.00 46.12 6.13
46 47 2.038269 TTCGGCGATTTGTCTGCCC 61.038 57.895 11.76 0.00 46.12 5.36
47 48 1.134694 GTTCGGCGATTTGTCTGCC 59.865 57.895 11.76 0.00 45.39 4.85
48 49 0.447801 ATGTTCGGCGATTTGTCTGC 59.552 50.000 11.76 0.00 0.00 4.26
49 50 2.002586 AGATGTTCGGCGATTTGTCTG 58.997 47.619 11.76 0.00 0.00 3.51
50 51 2.386661 AGATGTTCGGCGATTTGTCT 57.613 45.000 11.76 9.49 0.00 3.41
51 52 2.774007 CAAGATGTTCGGCGATTTGTC 58.226 47.619 11.76 7.19 0.00 3.18
52 53 1.135689 GCAAGATGTTCGGCGATTTGT 60.136 47.619 11.76 0.00 0.00 2.83
53 54 1.538276 GCAAGATGTTCGGCGATTTG 58.462 50.000 11.76 11.62 0.00 2.32
54 55 0.096976 CGCAAGATGTTCGGCGATTT 59.903 50.000 11.76 0.00 43.89 2.17
55 56 1.705337 CCGCAAGATGTTCGGCGATT 61.705 55.000 11.76 0.00 43.89 3.34
56 57 2.173669 CCGCAAGATGTTCGGCGAT 61.174 57.895 11.76 0.00 43.89 4.58
57 58 2.813474 CCGCAAGATGTTCGGCGA 60.813 61.111 4.99 4.99 43.89 5.54
58 59 3.864686 CCCGCAAGATGTTCGGCG 61.865 66.667 0.00 0.00 41.98 6.46
59 60 2.746277 ACCCGCAAGATGTTCGGC 60.746 61.111 7.62 0.00 41.68 5.54
60 61 1.671054 ACACCCGCAAGATGTTCGG 60.671 57.895 6.53 6.53 42.58 4.30
61 62 1.497278 CACACCCGCAAGATGTTCG 59.503 57.895 0.00 0.00 43.02 3.95
62 63 0.889186 ACCACACCCGCAAGATGTTC 60.889 55.000 0.00 0.00 43.02 3.18
63 64 1.150536 ACCACACCCGCAAGATGTT 59.849 52.632 0.00 0.00 43.02 2.71
64 65 1.600636 CACCACACCCGCAAGATGT 60.601 57.895 0.00 0.00 43.02 3.06
65 66 2.334946 CCACCACACCCGCAAGATG 61.335 63.158 0.00 0.00 43.02 2.90
66 67 2.034066 CCACCACACCCGCAAGAT 59.966 61.111 0.00 0.00 43.02 2.40
67 68 4.263572 CCCACCACACCCGCAAGA 62.264 66.667 0.00 0.00 43.02 3.02
83 84 4.367023 TACTGACGGGTGTGCGCC 62.367 66.667 4.18 0.00 0.00 6.53
84 85 3.110178 GTACTGACGGGTGTGCGC 61.110 66.667 0.00 0.00 0.00 6.09
85 86 2.019951 GTGTACTGACGGGTGTGCG 61.020 63.158 0.00 0.00 0.00 5.34
86 87 0.944311 CAGTGTACTGACGGGTGTGC 60.944 60.000 6.15 0.00 46.59 4.57
87 88 0.944311 GCAGTGTACTGACGGGTGTG 60.944 60.000 15.78 0.00 46.59 3.82
88 89 1.366366 GCAGTGTACTGACGGGTGT 59.634 57.895 15.78 0.00 46.59 4.16
89 90 1.374252 GGCAGTGTACTGACGGGTG 60.374 63.158 15.78 0.00 46.59 4.61
90 91 3.057337 GGCAGTGTACTGACGGGT 58.943 61.111 15.78 0.00 46.59 5.28
95 96 1.179174 ACGCAGAGGCAGTGTACTGA 61.179 55.000 15.78 0.00 46.59 3.41
96 97 1.010935 CACGCAGAGGCAGTGTACTG 61.011 60.000 7.64 7.64 46.40 2.74
97 98 1.290324 CACGCAGAGGCAGTGTACT 59.710 57.895 0.00 0.00 41.24 2.73
98 99 2.383527 GCACGCAGAGGCAGTGTAC 61.384 63.158 11.20 0.00 42.46 2.90
99 100 2.048222 GCACGCAGAGGCAGTGTA 60.048 61.111 11.20 0.00 42.46 2.90
100 101 4.996434 GGCACGCAGAGGCAGTGT 62.996 66.667 11.20 0.00 44.07 3.55
105 106 3.426568 GTTCTGGCACGCAGAGGC 61.427 66.667 0.00 0.00 45.02 4.70
106 107 2.743928 GGTTCTGGCACGCAGAGG 60.744 66.667 0.00 0.00 0.00 3.69
107 108 2.743928 GGGTTCTGGCACGCAGAG 60.744 66.667 0.00 0.00 0.00 3.35
108 109 4.680237 CGGGTTCTGGCACGCAGA 62.680 66.667 0.00 0.00 0.00 4.26
112 113 1.448922 TTTTTCCGGGTTCTGGCACG 61.449 55.000 0.00 0.00 34.63 5.34
113 114 0.966179 ATTTTTCCGGGTTCTGGCAC 59.034 50.000 0.00 0.00 0.00 5.01
114 115 1.253100 GATTTTTCCGGGTTCTGGCA 58.747 50.000 0.00 0.00 0.00 4.92
115 116 1.067846 GTGATTTTTCCGGGTTCTGGC 60.068 52.381 0.00 0.00 0.00 4.85
116 117 1.544246 GGTGATTTTTCCGGGTTCTGG 59.456 52.381 0.00 0.00 0.00 3.86
117 118 1.544246 GGGTGATTTTTCCGGGTTCTG 59.456 52.381 0.00 0.00 0.00 3.02
118 119 1.884928 CGGGTGATTTTTCCGGGTTCT 60.885 52.381 0.00 0.00 40.07 3.01
119 120 0.524414 CGGGTGATTTTTCCGGGTTC 59.476 55.000 0.00 0.00 40.07 3.62
120 121 2.648593 CGGGTGATTTTTCCGGGTT 58.351 52.632 0.00 0.00 40.07 4.11
121 122 4.408378 CGGGTGATTTTTCCGGGT 57.592 55.556 0.00 0.00 40.07 5.28
124 125 1.641123 CCGTCCGGGTGATTTTTCCG 61.641 60.000 0.00 0.00 43.05 4.30
125 126 2.177044 CCGTCCGGGTGATTTTTCC 58.823 57.895 0.00 0.00 0.00 3.13
136 137 3.760035 CTCTCCACCACCGTCCGG 61.760 72.222 3.76 3.76 42.03 5.14
137 138 3.760035 CCTCTCCACCACCGTCCG 61.760 72.222 0.00 0.00 0.00 4.79
138 139 4.083862 GCCTCTCCACCACCGTCC 62.084 72.222 0.00 0.00 0.00 4.79
139 140 2.997897 AGCCTCTCCACCACCGTC 60.998 66.667 0.00 0.00 0.00 4.79
140 141 3.314331 CAGCCTCTCCACCACCGT 61.314 66.667 0.00 0.00 0.00 4.83
141 142 4.767255 GCAGCCTCTCCACCACCG 62.767 72.222 0.00 0.00 0.00 4.94
142 143 4.416738 GGCAGCCTCTCCACCACC 62.417 72.222 3.29 0.00 0.00 4.61
143 144 4.767255 CGGCAGCCTCTCCACCAC 62.767 72.222 10.54 0.00 0.00 4.16
158 159 3.488090 GAAGAGGTTTCGCCGCGG 61.488 66.667 24.05 24.05 42.28 6.46
159 160 2.432628 AGAAGAGGTTTCGCCGCG 60.433 61.111 6.39 6.39 42.28 6.46
160 161 0.670854 AAGAGAAGAGGTTTCGCCGC 60.671 55.000 0.00 0.00 43.70 6.53
161 162 1.797025 AAAGAGAAGAGGTTTCGCCG 58.203 50.000 0.00 0.00 43.70 6.46
162 163 2.484651 GGAAAAGAGAAGAGGTTTCGCC 59.515 50.000 0.00 0.00 32.01 5.54
163 164 2.157863 CGGAAAAGAGAAGAGGTTTCGC 59.842 50.000 0.00 0.00 32.01 4.70
164 165 2.737252 CCGGAAAAGAGAAGAGGTTTCG 59.263 50.000 0.00 0.00 32.01 3.46
165 166 2.484651 GCCGGAAAAGAGAAGAGGTTTC 59.515 50.000 5.05 0.00 0.00 2.78
166 167 2.505405 GCCGGAAAAGAGAAGAGGTTT 58.495 47.619 5.05 0.00 0.00 3.27
167 168 1.608283 CGCCGGAAAAGAGAAGAGGTT 60.608 52.381 5.05 0.00 0.00 3.50
168 169 0.037232 CGCCGGAAAAGAGAAGAGGT 60.037 55.000 5.05 0.00 0.00 3.85
169 170 0.246635 TCGCCGGAAAAGAGAAGAGG 59.753 55.000 5.05 0.00 0.00 3.69
170 171 1.634702 CTCGCCGGAAAAGAGAAGAG 58.365 55.000 5.05 0.00 34.13 2.85
171 172 0.246635 CCTCGCCGGAAAAGAGAAGA 59.753 55.000 5.05 0.00 34.13 2.87
172 173 0.246635 TCCTCGCCGGAAAAGAGAAG 59.753 55.000 5.05 0.00 39.40 2.85
173 174 2.358039 TCCTCGCCGGAAAAGAGAA 58.642 52.632 5.05 0.00 39.40 2.87
174 175 4.107029 TCCTCGCCGGAAAAGAGA 57.893 55.556 5.05 0.00 39.40 3.10
184 185 1.205893 CTAGATAGGCCATTCCTCGCC 59.794 57.143 5.01 0.00 43.20 5.54
185 186 1.404851 GCTAGATAGGCCATTCCTCGC 60.405 57.143 5.01 0.15 43.20 5.03
186 187 2.094286 CAGCTAGATAGGCCATTCCTCG 60.094 54.545 5.01 0.00 43.20 4.63
187 188 2.903135 ACAGCTAGATAGGCCATTCCTC 59.097 50.000 5.01 0.00 43.20 3.71
189 190 2.289945 CCACAGCTAGATAGGCCATTCC 60.290 54.545 5.01 0.00 0.00 3.01
190 191 2.370189 ACCACAGCTAGATAGGCCATTC 59.630 50.000 5.01 0.10 0.00 2.67
191 192 2.105477 CACCACAGCTAGATAGGCCATT 59.895 50.000 5.01 0.00 0.00 3.16
192 193 1.696336 CACCACAGCTAGATAGGCCAT 59.304 52.381 5.01 0.00 0.00 4.40
193 194 1.123077 CACCACAGCTAGATAGGCCA 58.877 55.000 5.01 0.00 0.00 5.36
194 195 0.394565 CCACCACAGCTAGATAGGCC 59.605 60.000 0.00 0.00 0.00 5.19
195 196 0.394565 CCCACCACAGCTAGATAGGC 59.605 60.000 0.00 0.00 0.00 3.93
196 197 1.414181 CACCCACCACAGCTAGATAGG 59.586 57.143 0.00 0.00 0.00 2.57
197 198 1.414181 CCACCCACCACAGCTAGATAG 59.586 57.143 0.00 0.00 0.00 2.08
198 199 1.273609 ACCACCCACCACAGCTAGATA 60.274 52.381 0.00 0.00 0.00 1.98
199 200 0.547712 ACCACCCACCACAGCTAGAT 60.548 55.000 0.00 0.00 0.00 1.98
200 201 1.152118 ACCACCCACCACAGCTAGA 60.152 57.895 0.00 0.00 0.00 2.43
201 202 1.003355 CACCACCCACCACAGCTAG 60.003 63.158 0.00 0.00 0.00 3.42
202 203 2.525124 CCACCACCCACCACAGCTA 61.525 63.158 0.00 0.00 0.00 3.32
203 204 3.889692 CCACCACCCACCACAGCT 61.890 66.667 0.00 0.00 0.00 4.24
204 205 4.974721 CCCACCACCCACCACAGC 62.975 72.222 0.00 0.00 0.00 4.40
205 206 4.974721 GCCCACCACCCACCACAG 62.975 72.222 0.00 0.00 0.00 3.66
258 259 2.617215 AGATTCACCCCCACCCCC 60.617 66.667 0.00 0.00 0.00 5.40
259 260 2.683475 CAGATTCACCCCCACCCC 59.317 66.667 0.00 0.00 0.00 4.95
260 261 1.928567 TCCAGATTCACCCCCACCC 60.929 63.158 0.00 0.00 0.00 4.61
261 262 1.303282 GTCCAGATTCACCCCCACC 59.697 63.158 0.00 0.00 0.00 4.61
262 263 1.078426 CGTCCAGATTCACCCCCAC 60.078 63.158 0.00 0.00 0.00 4.61
263 264 2.297895 CCGTCCAGATTCACCCCCA 61.298 63.158 0.00 0.00 0.00 4.96
264 265 1.848886 AACCGTCCAGATTCACCCCC 61.849 60.000 0.00 0.00 0.00 5.40
265 266 0.676782 CAACCGTCCAGATTCACCCC 60.677 60.000 0.00 0.00 0.00 4.95
266 267 0.676782 CCAACCGTCCAGATTCACCC 60.677 60.000 0.00 0.00 0.00 4.61
267 268 1.305930 GCCAACCGTCCAGATTCACC 61.306 60.000 0.00 0.00 0.00 4.02
268 269 0.321653 AGCCAACCGTCCAGATTCAC 60.322 55.000 0.00 0.00 0.00 3.18
269 270 0.400213 AAGCCAACCGTCCAGATTCA 59.600 50.000 0.00 0.00 0.00 2.57
270 271 0.804989 CAAGCCAACCGTCCAGATTC 59.195 55.000 0.00 0.00 0.00 2.52
271 272 0.400213 TCAAGCCAACCGTCCAGATT 59.600 50.000 0.00 0.00 0.00 2.40
272 273 0.321653 GTCAAGCCAACCGTCCAGAT 60.322 55.000 0.00 0.00 0.00 2.90
273 274 1.070786 GTCAAGCCAACCGTCCAGA 59.929 57.895 0.00 0.00 0.00 3.86
274 275 0.535102 AAGTCAAGCCAACCGTCCAG 60.535 55.000 0.00 0.00 0.00 3.86
275 276 0.106918 AAAGTCAAGCCAACCGTCCA 60.107 50.000 0.00 0.00 0.00 4.02
276 277 1.001706 GAAAAGTCAAGCCAACCGTCC 60.002 52.381 0.00 0.00 0.00 4.79
277 278 1.333791 CGAAAAGTCAAGCCAACCGTC 60.334 52.381 0.00 0.00 0.00 4.79
278 279 0.661020 CGAAAAGTCAAGCCAACCGT 59.339 50.000 0.00 0.00 0.00 4.83
279 280 0.660300 GCGAAAAGTCAAGCCAACCG 60.660 55.000 0.00 0.00 0.00 4.44
280 281 3.179433 GCGAAAAGTCAAGCCAACC 57.821 52.632 0.00 0.00 0.00 3.77
285 286 0.944386 TGTCAGGCGAAAAGTCAAGC 59.056 50.000 0.00 0.00 0.00 4.01
286 287 2.032549 CACTGTCAGGCGAAAAGTCAAG 60.033 50.000 4.53 0.00 0.00 3.02
287 288 1.939934 CACTGTCAGGCGAAAAGTCAA 59.060 47.619 4.53 0.00 0.00 3.18
288 289 1.134521 ACACTGTCAGGCGAAAAGTCA 60.135 47.619 4.53 0.00 0.00 3.41
289 290 1.261619 CACACTGTCAGGCGAAAAGTC 59.738 52.381 4.53 0.00 0.00 3.01
290 291 1.299541 CACACTGTCAGGCGAAAAGT 58.700 50.000 4.53 0.00 0.00 2.66
291 292 0.588252 CCACACTGTCAGGCGAAAAG 59.412 55.000 4.53 0.00 0.00 2.27
292 293 1.444119 GCCACACTGTCAGGCGAAAA 61.444 55.000 4.53 0.00 38.86 2.29
293 294 1.891919 GCCACACTGTCAGGCGAAA 60.892 57.895 4.53 0.00 38.86 3.46
294 295 2.280797 GCCACACTGTCAGGCGAA 60.281 61.111 4.53 0.00 38.86 4.70
298 299 1.599047 CTAGGGCCACACTGTCAGG 59.401 63.158 6.18 0.00 0.00 3.86
299 300 1.194781 ACCTAGGGCCACACTGTCAG 61.195 60.000 14.81 0.00 0.00 3.51
300 301 1.152118 ACCTAGGGCCACACTGTCA 60.152 57.895 14.81 0.00 0.00 3.58
301 302 1.296715 CACCTAGGGCCACACTGTC 59.703 63.158 14.81 0.00 0.00 3.51
302 303 1.461461 ACACCTAGGGCCACACTGT 60.461 57.895 14.81 3.22 0.00 3.55
303 304 1.003355 CACACCTAGGGCCACACTG 60.003 63.158 14.81 2.51 0.00 3.66
304 305 2.895424 GCACACCTAGGGCCACACT 61.895 63.158 14.81 0.00 42.32 3.55
305 306 2.359975 GCACACCTAGGGCCACAC 60.360 66.667 14.81 0.00 42.32 3.82
311 312 0.698818 AGGGAAAAGCACACCTAGGG 59.301 55.000 14.81 4.64 0.00 3.53
312 313 2.162681 CAAGGGAAAAGCACACCTAGG 58.837 52.381 7.41 7.41 31.88 3.02
313 314 1.541588 GCAAGGGAAAAGCACACCTAG 59.458 52.381 0.00 0.00 31.88 3.02
314 315 1.616159 GCAAGGGAAAAGCACACCTA 58.384 50.000 0.00 0.00 31.88 3.08
315 316 1.455383 CGCAAGGGAAAAGCACACCT 61.455 55.000 0.00 0.00 34.04 4.00
316 317 1.007387 CGCAAGGGAAAAGCACACC 60.007 57.895 0.00 0.00 0.00 4.16
317 318 1.661509 GCGCAAGGGAAAAGCACAC 60.662 57.895 0.30 0.00 38.28 3.82
318 319 2.727544 GCGCAAGGGAAAAGCACA 59.272 55.556 0.30 0.00 38.28 4.57
319 320 2.049156 GGCGCAAGGGAAAAGCAC 60.049 61.111 10.83 0.00 38.28 4.40
320 321 3.669344 CGGCGCAAGGGAAAAGCA 61.669 61.111 10.83 0.00 38.28 3.91
321 322 4.419939 CCGGCGCAAGGGAAAAGC 62.420 66.667 10.83 0.00 38.28 3.51
322 323 2.671619 TCCGGCGCAAGGGAAAAG 60.672 61.111 19.03 0.00 38.28 2.27
323 324 2.671619 CTCCGGCGCAAGGGAAAA 60.672 61.111 19.03 1.39 38.28 2.29
357 358 3.901797 GAAGCCGACACACTGGGGG 62.902 68.421 0.00 0.00 0.00 5.40
358 359 2.358737 GAAGCCGACACACTGGGG 60.359 66.667 0.00 0.00 0.00 4.96
359 360 2.738521 CGAAGCCGACACACTGGG 60.739 66.667 0.00 0.00 38.22 4.45
360 361 2.738521 CCGAAGCCGACACACTGG 60.739 66.667 0.00 0.00 38.22 4.00
361 362 3.414700 GCCGAAGCCGACACACTG 61.415 66.667 0.00 0.00 38.22 3.66
382 383 1.933115 CTTTTTGGGCCCGGTGATCG 61.933 60.000 19.37 0.00 38.88 3.69
383 384 1.604147 CCTTTTTGGGCCCGGTGATC 61.604 60.000 19.37 0.00 0.00 2.92
384 385 1.609210 CCTTTTTGGGCCCGGTGAT 60.609 57.895 19.37 0.00 0.00 3.06
385 386 2.203567 CCTTTTTGGGCCCGGTGA 60.204 61.111 19.37 2.00 0.00 4.02
405 406 3.264897 CCGAATTCCGCTGGCTCG 61.265 66.667 0.00 0.00 36.84 5.03
406 407 3.577313 GCCGAATTCCGCTGGCTC 61.577 66.667 13.14 0.00 44.16 4.70
409 410 3.564027 GACGCCGAATTCCGCTGG 61.564 66.667 15.29 5.17 36.84 4.85
410 411 2.100631 AAGACGCCGAATTCCGCTG 61.101 57.895 15.29 11.44 36.84 5.18
411 412 2.100631 CAAGACGCCGAATTCCGCT 61.101 57.895 15.29 6.32 36.84 5.52
412 413 2.399611 CAAGACGCCGAATTCCGC 59.600 61.111 8.53 8.53 36.84 5.54
413 414 2.461110 CCCAAGACGCCGAATTCCG 61.461 63.158 0.00 1.04 38.18 4.30
414 415 2.112815 CCCCAAGACGCCGAATTCC 61.113 63.158 0.00 0.00 0.00 3.01
415 416 2.112815 CCCCCAAGACGCCGAATTC 61.113 63.158 0.00 0.00 0.00 2.17
416 417 2.045340 CCCCCAAGACGCCGAATT 60.045 61.111 0.00 0.00 0.00 2.17
417 418 4.796495 GCCCCCAAGACGCCGAAT 62.796 66.667 0.00 0.00 0.00 3.34
424 425 3.508840 CAATCGCGCCCCCAAGAC 61.509 66.667 0.00 0.00 0.00 3.01
425 426 4.794648 CCAATCGCGCCCCCAAGA 62.795 66.667 0.00 0.00 0.00 3.02
432 433 2.850806 AAAAATGCCCCAATCGCGCC 62.851 55.000 0.00 0.00 0.00 6.53
433 434 1.420641 GAAAAATGCCCCAATCGCGC 61.421 55.000 0.00 0.00 0.00 6.86
434 435 1.139226 CGAAAAATGCCCCAATCGCG 61.139 55.000 0.00 0.00 0.00 5.87
435 436 0.805711 CCGAAAAATGCCCCAATCGC 60.806 55.000 0.00 0.00 0.00 4.58
436 437 0.530288 ACCGAAAAATGCCCCAATCG 59.470 50.000 0.00 0.00 0.00 3.34
437 438 2.006552 GCACCGAAAAATGCCCCAATC 61.007 52.381 0.00 0.00 35.73 2.67
438 439 0.036483 GCACCGAAAAATGCCCCAAT 60.036 50.000 0.00 0.00 35.73 3.16
439 440 1.369321 GCACCGAAAAATGCCCCAA 59.631 52.632 0.00 0.00 35.73 4.12
440 441 3.055580 GCACCGAAAAATGCCCCA 58.944 55.556 0.00 0.00 35.73 4.96
444 445 3.860717 GCTGGCACCGAAAAATGC 58.139 55.556 0.00 0.00 41.29 3.56
928 929 4.623863 AGTATGGGAATGGCTGGATTTTT 58.376 39.130 0.00 0.00 0.00 1.94
929 930 4.270317 AGTATGGGAATGGCTGGATTTT 57.730 40.909 0.00 0.00 0.00 1.82
930 931 3.979501 AGTATGGGAATGGCTGGATTT 57.020 42.857 0.00 0.00 0.00 2.17
931 932 3.979501 AAGTATGGGAATGGCTGGATT 57.020 42.857 0.00 0.00 0.00 3.01
935 936 4.019174 AGACAAAAGTATGGGAATGGCTG 58.981 43.478 0.00 0.00 0.00 4.85
966 967 2.100631 CGGCAAGTAGAAGGGCACG 61.101 63.158 0.00 0.00 0.00 5.34
1028 1029 3.258228 ATGCAGCCTTGGAGCACGA 62.258 57.895 8.88 0.00 41.60 4.35
1040 1041 2.486966 GGTTCCGCTTGATGCAGC 59.513 61.111 0.00 0.00 43.06 5.25
1494 1495 2.448582 AAGCCCGACCTTGACCACA 61.449 57.895 0.00 0.00 0.00 4.17
1689 1690 1.222936 CCCACTCCTGCACATCCTC 59.777 63.158 0.00 0.00 0.00 3.71
1710 1711 0.320683 CTGCCACAGGATCAACACGA 60.321 55.000 0.00 0.00 0.00 4.35
1722 1723 1.065491 AGAACACTTGACACTGCCACA 60.065 47.619 0.00 0.00 0.00 4.17
1728 1729 3.383825 ACGAACCTAGAACACTTGACACT 59.616 43.478 0.00 0.00 0.00 3.55
1743 1744 3.649986 GCTTGTGCGCACGAACCT 61.650 61.111 33.22 0.00 0.00 3.50
1746 1747 3.648982 CCAGCTTGTGCGCACGAA 61.649 61.111 33.22 25.38 45.42 3.85
1780 1781 0.877071 AGCTGGAATGCACGAACAAG 59.123 50.000 0.00 0.00 34.99 3.16
1783 1784 0.109597 CCAAGCTGGAATGCACGAAC 60.110 55.000 0.00 0.00 40.96 3.95
1788 1789 1.980232 CTGCCCAAGCTGGAATGCA 60.980 57.895 4.00 0.00 40.96 3.96
1791 1792 1.980772 GCACTGCCCAAGCTGGAAT 60.981 57.895 4.00 0.00 40.96 3.01
1818 1819 4.261572 CCAAAGCCTTTTCTGACGATCAAA 60.262 41.667 0.00 0.00 0.00 2.69
2202 2203 3.057315 GCTGCATTTTCCTAAACAGCTCA 60.057 43.478 5.59 0.00 38.94 4.26
3060 3061 2.438021 AGCAAGTAGAACTTCCCACACA 59.562 45.455 0.00 0.00 36.03 3.72
3345 3346 6.921857 CACTCTCTTGATTGCTGAACATTTTT 59.078 34.615 0.00 0.00 0.00 1.94
3479 3480 2.539344 GCAAATTGCACAAAAGTGGCAC 60.539 45.455 13.73 10.29 44.26 5.01
3480 3481 1.669779 GCAAATTGCACAAAAGTGGCA 59.330 42.857 13.73 0.00 44.26 4.92
3731 3734 3.297134 ACTTACCCTCGTATAACCGGA 57.703 47.619 9.46 0.00 0.00 5.14
3832 3835 5.473162 TGTGGAGTGGTAATCAAAGTCAATG 59.527 40.000 0.00 0.00 0.00 2.82
3833 3836 5.630121 TGTGGAGTGGTAATCAAAGTCAAT 58.370 37.500 0.00 0.00 0.00 2.57
3834 3837 5.042463 TGTGGAGTGGTAATCAAAGTCAA 57.958 39.130 0.00 0.00 0.00 3.18
3885 3888 2.512476 ACAACCAGGTACAGAAAAGGGT 59.488 45.455 0.00 0.00 0.00 4.34
4015 4019 2.323968 TGAGTTGTGTGCAGCAAGTA 57.676 45.000 0.00 0.00 30.49 2.24
4066 4070 1.614413 TGCTGATTGTGATGCTTGCAA 59.386 42.857 0.00 0.00 0.00 4.08
4084 4088 4.355543 TTTGTTTCAGAGTTGTGACTGC 57.644 40.909 0.00 0.00 35.88 4.40
4204 4222 4.083271 GCCGATAATGAAGAAACCCTATGC 60.083 45.833 0.00 0.00 0.00 3.14
4263 4281 8.732746 AAGTCAATACAAAGGCTATACGAAAT 57.267 30.769 0.00 0.00 0.00 2.17
4272 4290 4.010349 GCACCTAAGTCAATACAAAGGCT 58.990 43.478 0.00 0.00 34.63 4.58
4273 4291 3.756434 TGCACCTAAGTCAATACAAAGGC 59.244 43.478 0.00 0.00 34.63 4.35


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

AutoCloner maintained by Alex Coulton.