Multiple sequence alignment - TraesCS4B01G150900

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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 TraesCS4B01G150900 chr4B 100.000 2801 0 0 1 2801 238168887 238171687 0.000000e+00 5173.0
1 TraesCS4B01G150900 chr4B 99.305 2301 14 1 409 2707 312784956 312782656 0.000000e+00 4159.0
2 TraesCS4B01G150900 chr4B 100.000 320 0 0 2852 3171 238171738 238172057 2.720000e-165 592.0
3 TraesCS4B01G150900 chr5B 99.248 2394 17 1 408 2801 311961640 311959248 0.000000e+00 4320.0
4 TraesCS4B01G150900 chr5B 100.000 320 0 0 2852 3171 185038505 185038186 2.720000e-165 592.0
5 TraesCS4B01G150900 chr5B 82.731 249 18 8 14 238 57871546 57871793 6.940000e-47 198.0
6 TraesCS4B01G150900 chr7A 98.998 2395 22 1 409 2801 473484341 473486735 0.000000e+00 4289.0
7 TraesCS4B01G150900 chr7A 99.000 2300 22 1 409 2707 533735222 533732923 0.000000e+00 4119.0
8 TraesCS4B01G150900 chr7A 100.000 320 0 0 2852 3171 65081971 65082290 2.720000e-165 592.0
9 TraesCS4B01G150900 chr7A 100.000 320 0 0 2852 3171 701578251 701577932 2.720000e-165 592.0
10 TraesCS4B01G150900 chr7A 84.783 184 12 7 222 403 283547434 283547603 1.510000e-38 171.0
11 TraesCS4B01G150900 chr7A 91.892 111 8 1 14 124 657582963 657583072 1.520000e-33 154.0
12 TraesCS4B01G150900 chr3A 98.956 2395 23 2 409 2801 444446559 444444165 0.000000e+00 4283.0
13 TraesCS4B01G150900 chr2A 98.873 2396 25 2 408 2801 630239154 630236759 0.000000e+00 4274.0
14 TraesCS4B01G150900 chr2A 96.386 83 3 0 2719 2801 630236940 630236858 1.530000e-28 137.0
15 TraesCS4B01G150900 chr3B 98.205 2396 40 2 408 2801 39640624 39638230 0.000000e+00 4183.0
16 TraesCS4B01G150900 chr3B 100.000 320 0 0 2852 3171 39637969 39637650 2.720000e-165 592.0
17 TraesCS4B01G150900 chr3B 83.212 137 14 7 231 365 536032277 536032406 2.000000e-22 117.0
18 TraesCS4B01G150900 chr3B 97.059 34 1 0 2768 2801 672733576 672733543 1.230000e-04 58.4
19 TraesCS4B01G150900 chr1A 98.162 2394 43 1 409 2801 237744560 237742167 0.000000e+00 4176.0
20 TraesCS4B01G150900 chr1A 99.130 2300 19 1 408 2707 27319262 27321560 0.000000e+00 4135.0
21 TraesCS4B01G150900 chr1A 100.000 320 0 0 2852 3171 237740973 237740654 2.720000e-165 592.0
22 TraesCS4B01G150900 chr1A 99.688 320 1 0 2852 3171 394244467 394244786 1.270000e-163 586.0
23 TraesCS4B01G150900 chrUn 100.000 320 0 0 2852 3171 448803005 448803324 2.720000e-165 592.0
24 TraesCS4B01G150900 chr7B 100.000 320 0 0 2852 3171 424539152 424538833 2.720000e-165 592.0
25 TraesCS4B01G150900 chr7B 86.667 180 10 6 231 408 74043303 74043136 1.500000e-43 187.0
26 TraesCS4B01G150900 chr4A 100.000 320 0 0 2852 3171 36320204 36319885 2.720000e-165 592.0
27 TraesCS4B01G150900 chr1B 93.750 240 12 2 9 246 659951569 659951331 1.080000e-94 357.0
28 TraesCS4B01G150900 chr1B 85.375 253 13 6 9 238 315569982 315569731 1.140000e-59 241.0
29 TraesCS4B01G150900 chr1B 86.486 185 10 7 223 405 655450771 655450942 4.180000e-44 189.0
30 TraesCS4B01G150900 chr1B 82.166 157 18 8 236 388 603382613 603382763 3.320000e-25 126.0
31 TraesCS4B01G150900 chr5A 87.168 226 25 4 14 238 43689452 43689674 1.460000e-63 254.0
32 TraesCS4B01G150900 chr5A 87.168 226 25 4 14 238 43775522 43775744 1.460000e-63 254.0
33 TraesCS4B01G150900 chr5A 86.726 226 26 4 14 238 43737376 43737598 6.790000e-62 248.0
34 TraesCS4B01G150900 chr5A 83.212 137 12 8 231 365 150807305 150807178 7.190000e-22 115.0
35 TraesCS4B01G150900 chr5A 79.755 163 17 10 231 388 514331140 514330989 1.560000e-18 104.0
36 TraesCS4B01G150900 chr7D 83.838 198 12 5 226 408 503944368 503944176 1.510000e-38 171.0
37 TraesCS4B01G150900 chr7D 91.892 111 9 0 14 124 310873770 310873880 4.230000e-34 156.0
38 TraesCS4B01G150900 chr7D 90.083 121 10 2 135 255 630185510 630185628 4.230000e-34 156.0
39 TraesCS4B01G150900 chr3D 92.793 111 8 0 14 124 87431450 87431560 9.100000e-36 161.0
40 TraesCS4B01G150900 chr1D 92.793 111 7 1 14 124 76950128 76950237 3.270000e-35 159.0
41 TraesCS4B01G150900 chr6B 92.308 104 7 1 135 238 133358531 133358429 2.550000e-31 147.0
42 TraesCS4B01G150900 chr2B 83.648 159 18 5 231 388 389023918 389024069 3.300000e-30 143.0
43 TraesCS4B01G150900 chr5D 82.963 135 14 6 232 365 483272597 483272471 2.590000e-21 113.0
44 TraesCS4B01G150900 chr5D 95.312 64 3 0 173 236 520420774 520420837 5.600000e-18 102.0
45 TraesCS4B01G150900 chr6D 87.500 72 9 0 176 247 364852181 364852110 2.030000e-12 84.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G150900 chr4B 238168887 238172057 3170 False 2882.5 5173 100.0000 1 3171 2 chr4B.!!$F1 3170
1 TraesCS4B01G150900 chr4B 312782656 312784956 2300 True 4159.0 4159 99.3050 409 2707 1 chr4B.!!$R1 2298
2 TraesCS4B01G150900 chr5B 311959248 311961640 2392 True 4320.0 4320 99.2480 408 2801 1 chr5B.!!$R2 2393
3 TraesCS4B01G150900 chr7A 473484341 473486735 2394 False 4289.0 4289 98.9980 409 2801 1 chr7A.!!$F3 2392
4 TraesCS4B01G150900 chr7A 533732923 533735222 2299 True 4119.0 4119 99.0000 409 2707 1 chr7A.!!$R1 2298
5 TraesCS4B01G150900 chr3A 444444165 444446559 2394 True 4283.0 4283 98.9560 409 2801 1 chr3A.!!$R1 2392
6 TraesCS4B01G150900 chr2A 630236759 630239154 2395 True 2205.5 4274 97.6295 408 2801 2 chr2A.!!$R1 2393
7 TraesCS4B01G150900 chr3B 39637650 39640624 2974 True 2387.5 4183 99.1025 408 3171 2 chr3B.!!$R2 2763
8 TraesCS4B01G150900 chr1A 27319262 27321560 2298 False 4135.0 4135 99.1300 408 2707 1 chr1A.!!$F1 2299
9 TraesCS4B01G150900 chr1A 237740654 237744560 3906 True 2384.0 4176 99.0810 409 3171 2 chr1A.!!$R1 2762

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
214 215 0.035458 ACTTCTTCAAGAGCCCGTGG 59.965 55.0 0.0 0.00 33.34 4.94 F
340 341 0.036164 CCAATCGTGGTCCCACTCAA 59.964 55.0 14.2 0.87 44.16 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2141 0.029163 TGGCCTGGATCCCCTTGATA 60.029 55.0 9.90 0.0 32.41 2.15 R
2628 2632 1.422388 GGTCGACGGAACCAACTTAC 58.578 55.0 9.92 0.0 0.00 2.34 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
50 51 8.415192 TGATGTCGACAAAGTATATTTGTACC 57.585 34.615 24.13 0.00 42.11 3.34
51 52 7.493320 TGATGTCGACAAAGTATATTTGTACCC 59.507 37.037 24.13 0.00 42.11 3.69
52 53 6.108015 TGTCGACAAAGTATATTTGTACCCC 58.892 40.000 17.62 0.00 42.11 4.95
53 54 6.070653 TGTCGACAAAGTATATTTGTACCCCT 60.071 38.462 17.62 0.00 42.11 4.79
54 55 7.123997 TGTCGACAAAGTATATTTGTACCCCTA 59.876 37.037 17.62 0.00 42.11 3.53
55 56 7.650903 GTCGACAAAGTATATTTGTACCCCTAG 59.349 40.741 11.55 0.00 42.11 3.02
56 57 7.560991 TCGACAAAGTATATTTGTACCCCTAGA 59.439 37.037 6.00 0.00 42.11 2.43
57 58 7.866393 CGACAAAGTATATTTGTACCCCTAGAG 59.134 40.741 6.00 0.00 42.11 2.43
58 59 8.849543 ACAAAGTATATTTGTACCCCTAGAGA 57.150 34.615 4.26 0.00 40.47 3.10
59 60 9.448587 ACAAAGTATATTTGTACCCCTAGAGAT 57.551 33.333 4.26 0.00 40.47 2.75
67 68 7.989947 TTTGTACCCCTAGAGATATTTCAGT 57.010 36.000 0.00 0.00 0.00 3.41
68 69 7.598759 TTGTACCCCTAGAGATATTTCAGTC 57.401 40.000 0.00 0.00 0.00 3.51
69 70 6.679542 TGTACCCCTAGAGATATTTCAGTCA 58.320 40.000 0.00 0.00 0.00 3.41
70 71 7.306013 TGTACCCCTAGAGATATTTCAGTCAT 58.694 38.462 0.00 0.00 0.00 3.06
71 72 6.926630 ACCCCTAGAGATATTTCAGTCATC 57.073 41.667 0.00 0.00 0.00 2.92
72 73 6.385443 ACCCCTAGAGATATTTCAGTCATCA 58.615 40.000 0.00 0.00 0.00 3.07
73 74 6.846505 ACCCCTAGAGATATTTCAGTCATCAA 59.153 38.462 0.00 0.00 0.00 2.57
74 75 7.348274 ACCCCTAGAGATATTTCAGTCATCAAA 59.652 37.037 0.00 0.00 0.00 2.69
75 76 8.381636 CCCCTAGAGATATTTCAGTCATCAAAT 58.618 37.037 0.00 0.00 0.00 2.32
76 77 9.434420 CCCTAGAGATATTTCAGTCATCAAATC 57.566 37.037 0.00 0.00 0.00 2.17
77 78 9.993454 CCTAGAGATATTTCAGTCATCAAATCA 57.007 33.333 0.00 0.00 0.00 2.57
86 87 9.938280 ATTTCAGTCATCAAATCAATCATGTTT 57.062 25.926 0.00 0.00 0.00 2.83
87 88 8.751302 TTCAGTCATCAAATCAATCATGTTTG 57.249 30.769 9.80 9.80 33.06 2.93
88 89 6.809689 TCAGTCATCAAATCAATCATGTTTGC 59.190 34.615 11.02 0.00 32.44 3.68
89 90 6.035650 CAGTCATCAAATCAATCATGTTTGCC 59.964 38.462 11.02 0.00 32.44 4.52
90 91 5.292589 GTCATCAAATCAATCATGTTTGCCC 59.707 40.000 11.02 0.00 32.44 5.36
91 92 4.205065 TCAAATCAATCATGTTTGCCCC 57.795 40.909 11.02 0.00 32.44 5.80
92 93 3.055240 TCAAATCAATCATGTTTGCCCCC 60.055 43.478 11.02 0.00 32.44 5.40
93 94 2.250921 ATCAATCATGTTTGCCCCCA 57.749 45.000 11.02 0.00 0.00 4.96
94 95 2.021262 TCAATCATGTTTGCCCCCAA 57.979 45.000 11.02 0.00 0.00 4.12
95 96 1.901159 TCAATCATGTTTGCCCCCAAG 59.099 47.619 11.02 0.00 31.52 3.61
96 97 1.901159 CAATCATGTTTGCCCCCAAGA 59.099 47.619 3.65 0.00 31.52 3.02
97 98 2.302445 CAATCATGTTTGCCCCCAAGAA 59.698 45.455 3.65 0.00 31.52 2.52
98 99 2.094100 TCATGTTTGCCCCCAAGAAA 57.906 45.000 0.00 0.00 31.52 2.52
99 100 2.402564 TCATGTTTGCCCCCAAGAAAA 58.597 42.857 0.00 0.00 31.52 2.29
100 101 2.103941 TCATGTTTGCCCCCAAGAAAAC 59.896 45.455 0.00 0.00 33.98 2.43
101 102 0.833949 TGTTTGCCCCCAAGAAAACC 59.166 50.000 0.00 0.00 32.72 3.27
102 103 1.128200 GTTTGCCCCCAAGAAAACCT 58.872 50.000 0.00 0.00 31.52 3.50
103 104 1.488812 GTTTGCCCCCAAGAAAACCTT 59.511 47.619 0.00 0.00 34.91 3.50
115 116 6.983474 CAAGAAAACCTTGTTTGTGGAAAT 57.017 33.333 0.00 0.00 45.52 2.17
116 117 7.376435 CAAGAAAACCTTGTTTGTGGAAATT 57.624 32.000 0.00 0.00 45.52 1.82
117 118 6.983474 AGAAAACCTTGTTTGTGGAAATTG 57.017 33.333 0.00 0.00 0.00 2.32
118 119 5.879777 AGAAAACCTTGTTTGTGGAAATTGG 59.120 36.000 0.00 0.00 0.00 3.16
119 120 5.428184 AAACCTTGTTTGTGGAAATTGGA 57.572 34.783 0.00 0.00 0.00 3.53
120 121 4.670896 ACCTTGTTTGTGGAAATTGGAG 57.329 40.909 0.00 0.00 0.00 3.86
121 122 4.285863 ACCTTGTTTGTGGAAATTGGAGA 58.714 39.130 0.00 0.00 0.00 3.71
122 123 4.901250 ACCTTGTTTGTGGAAATTGGAGAT 59.099 37.500 0.00 0.00 0.00 2.75
123 124 5.221501 ACCTTGTTTGTGGAAATTGGAGATG 60.222 40.000 0.00 0.00 0.00 2.90
124 125 5.010922 CCTTGTTTGTGGAAATTGGAGATGA 59.989 40.000 0.00 0.00 0.00 2.92
125 126 6.295462 CCTTGTTTGTGGAAATTGGAGATGAT 60.295 38.462 0.00 0.00 0.00 2.45
126 127 7.093814 CCTTGTTTGTGGAAATTGGAGATGATA 60.094 37.037 0.00 0.00 0.00 2.15
127 128 7.959658 TGTTTGTGGAAATTGGAGATGATAT 57.040 32.000 0.00 0.00 0.00 1.63
128 129 7.774134 TGTTTGTGGAAATTGGAGATGATATG 58.226 34.615 0.00 0.00 0.00 1.78
129 130 7.396907 TGTTTGTGGAAATTGGAGATGATATGT 59.603 33.333 0.00 0.00 0.00 2.29
130 131 7.959658 TTGTGGAAATTGGAGATGATATGTT 57.040 32.000 0.00 0.00 0.00 2.71
131 132 7.959658 TGTGGAAATTGGAGATGATATGTTT 57.040 32.000 0.00 0.00 0.00 2.83
132 133 8.365060 TGTGGAAATTGGAGATGATATGTTTT 57.635 30.769 0.00 0.00 0.00 2.43
133 134 8.814931 TGTGGAAATTGGAGATGATATGTTTTT 58.185 29.630 0.00 0.00 0.00 1.94
163 164 9.466497 AAGATGATATGTTTTTACACAGATGGT 57.534 29.630 0.00 0.00 28.56 3.55
208 209 9.600646 GTATTTCTTGTAAACTTCTTCAAGAGC 57.399 33.333 0.00 0.00 44.13 4.09
209 210 6.619801 TTCTTGTAAACTTCTTCAAGAGCC 57.380 37.500 0.00 0.00 44.13 4.70
210 211 5.063880 TCTTGTAAACTTCTTCAAGAGCCC 58.936 41.667 0.00 0.00 40.46 5.19
211 212 3.399330 TGTAAACTTCTTCAAGAGCCCG 58.601 45.455 0.00 0.00 33.34 6.13
212 213 2.640316 AAACTTCTTCAAGAGCCCGT 57.360 45.000 0.00 0.00 33.34 5.28
213 214 1.884235 AACTTCTTCAAGAGCCCGTG 58.116 50.000 0.00 0.00 33.34 4.94
214 215 0.035458 ACTTCTTCAAGAGCCCGTGG 59.965 55.000 0.00 0.00 33.34 4.94
215 216 3.916605 ACTTCTTCAAGAGCCCGTGGC 62.917 57.143 6.80 6.80 40.05 5.01
229 230 4.908687 TGGCAACGCACGAGCACT 62.909 61.111 5.50 0.00 42.27 4.40
230 231 4.077188 GGCAACGCACGAGCACTC 62.077 66.667 5.50 0.00 42.27 3.51
231 232 3.038417 GCAACGCACGAGCACTCT 61.038 61.111 5.50 0.00 42.27 3.24
232 233 1.733041 GCAACGCACGAGCACTCTA 60.733 57.895 5.50 0.00 42.27 2.43
233 234 1.945776 GCAACGCACGAGCACTCTAC 61.946 60.000 5.50 0.00 42.27 2.59
234 235 0.387367 CAACGCACGAGCACTCTACT 60.387 55.000 5.50 0.00 42.27 2.57
235 236 1.135774 CAACGCACGAGCACTCTACTA 60.136 52.381 5.50 0.00 42.27 1.82
236 237 0.727970 ACGCACGAGCACTCTACTAG 59.272 55.000 5.50 0.00 42.27 2.57
237 238 0.727970 CGCACGAGCACTCTACTAGT 59.272 55.000 5.50 0.00 42.27 2.57
238 239 1.931841 CGCACGAGCACTCTACTAGTA 59.068 52.381 5.50 1.89 42.27 1.82
239 240 2.350804 CGCACGAGCACTCTACTAGTAA 59.649 50.000 5.50 0.00 42.27 2.24
240 241 3.544440 CGCACGAGCACTCTACTAGTAAG 60.544 52.174 5.50 7.19 42.27 2.34
241 242 3.374678 GCACGAGCACTCTACTAGTAAGT 59.625 47.826 3.76 7.78 41.58 2.24
242 243 4.569966 GCACGAGCACTCTACTAGTAAGTA 59.430 45.833 3.76 0.00 41.58 2.24
243 244 5.276963 GCACGAGCACTCTACTAGTAAGTAG 60.277 48.000 3.76 6.28 46.72 2.57
244 245 7.613267 GCACGAGCACTCTACTAGTAAGTAGT 61.613 46.154 3.76 5.38 46.15 2.73
245 246 8.369192 GCACGAGCACTCTACTAGTAAGTAGTA 61.369 44.444 3.76 5.98 46.15 1.82
255 256 5.055812 ACTAGTAAGTAGTAGTAGCGCAGG 58.944 45.833 11.47 0.00 40.47 4.85
256 257 3.883669 AGTAAGTAGTAGTAGCGCAGGT 58.116 45.455 11.47 0.00 44.89 4.00
257 258 5.028549 AGTAAGTAGTAGTAGCGCAGGTA 57.971 43.478 11.47 0.00 40.68 3.08
258 259 5.431765 AGTAAGTAGTAGTAGCGCAGGTAA 58.568 41.667 11.47 0.00 44.25 2.85
259 260 4.897025 AAGTAGTAGTAGCGCAGGTAAG 57.103 45.455 11.47 0.00 44.25 2.34
260 261 4.148128 AGTAGTAGTAGCGCAGGTAAGA 57.852 45.455 11.47 0.00 44.25 2.10
261 262 3.876320 AGTAGTAGTAGCGCAGGTAAGAC 59.124 47.826 11.47 0.00 44.25 3.01
262 263 2.022934 AGTAGTAGCGCAGGTAAGACC 58.977 52.381 11.47 0.00 44.25 3.85
263 264 1.066757 GTAGTAGCGCAGGTAAGACCC 59.933 57.143 11.47 0.00 44.25 4.46
264 265 0.324460 AGTAGCGCAGGTAAGACCCT 60.324 55.000 11.47 0.00 44.25 4.34
265 266 0.102663 GTAGCGCAGGTAAGACCCTC 59.897 60.000 11.47 0.00 44.25 4.30
266 267 0.323999 TAGCGCAGGTAAGACCCTCA 60.324 55.000 11.47 0.00 39.75 3.86
267 268 1.448013 GCGCAGGTAAGACCCTCAC 60.448 63.158 0.30 0.00 39.75 3.51
268 269 1.153823 CGCAGGTAAGACCCTCACG 60.154 63.158 0.00 0.00 39.75 4.35
269 270 1.874345 CGCAGGTAAGACCCTCACGT 61.874 60.000 0.00 0.00 39.75 4.49
270 271 0.320697 GCAGGTAAGACCCTCACGTT 59.679 55.000 0.00 0.00 39.75 3.99
271 272 1.547372 GCAGGTAAGACCCTCACGTTA 59.453 52.381 0.00 0.00 39.75 3.18
272 273 2.673326 GCAGGTAAGACCCTCACGTTAC 60.673 54.545 0.00 0.00 39.75 2.50
273 274 2.824341 CAGGTAAGACCCTCACGTTACT 59.176 50.000 0.00 0.00 39.75 2.24
274 275 4.012374 CAGGTAAGACCCTCACGTTACTA 58.988 47.826 0.00 0.00 39.75 1.82
275 276 4.013050 AGGTAAGACCCTCACGTTACTAC 58.987 47.826 0.00 0.00 39.75 2.73
276 277 4.013050 GGTAAGACCCTCACGTTACTACT 58.987 47.826 0.00 0.00 30.04 2.57
277 278 5.045578 AGGTAAGACCCTCACGTTACTACTA 60.046 44.000 0.00 0.00 39.75 1.82
278 279 5.648092 GGTAAGACCCTCACGTTACTACTAA 59.352 44.000 0.00 0.00 30.04 2.24
279 280 5.893897 AAGACCCTCACGTTACTACTAAG 57.106 43.478 0.00 0.00 0.00 2.18
280 281 3.693578 AGACCCTCACGTTACTACTAAGC 59.306 47.826 0.00 0.00 0.00 3.09
281 282 2.421424 ACCCTCACGTTACTACTAAGCG 59.579 50.000 0.00 0.00 0.00 4.68
282 283 2.421424 CCCTCACGTTACTACTAAGCGT 59.579 50.000 0.00 0.00 36.13 5.07
286 287 3.166657 CACGTTACTACTAAGCGTGTCC 58.833 50.000 7.15 0.00 45.07 4.02
287 288 2.813754 ACGTTACTACTAAGCGTGTCCA 59.186 45.455 0.00 0.00 34.36 4.02
288 289 3.166657 CGTTACTACTAAGCGTGTCCAC 58.833 50.000 0.00 0.00 0.00 4.02
289 290 3.505836 GTTACTACTAAGCGTGTCCACC 58.494 50.000 0.00 0.00 0.00 4.61
290 291 0.893447 ACTACTAAGCGTGTCCACCC 59.107 55.000 0.00 0.00 0.00 4.61
291 292 0.175073 CTACTAAGCGTGTCCACCCC 59.825 60.000 0.00 0.00 0.00 4.95
292 293 0.542467 TACTAAGCGTGTCCACCCCA 60.542 55.000 0.00 0.00 0.00 4.96
293 294 1.079127 CTAAGCGTGTCCACCCCAG 60.079 63.158 0.00 0.00 0.00 4.45
294 295 3.248446 TAAGCGTGTCCACCCCAGC 62.248 63.158 0.00 0.00 0.00 4.85
300 301 4.176752 GTCCACCCCAGCCCGATC 62.177 72.222 0.00 0.00 0.00 3.69
308 309 4.008933 CAGCCCGATCCCCCGATC 62.009 72.222 0.00 0.00 41.43 3.69
311 312 3.626924 CCCGATCCCCCGATCCAC 61.627 72.222 0.00 0.00 41.77 4.02
312 313 3.626924 CCGATCCCCCGATCCACC 61.627 72.222 0.00 0.00 41.77 4.61
313 314 3.626924 CGATCCCCCGATCCACCC 61.627 72.222 0.00 0.00 41.77 4.61
314 315 3.249961 GATCCCCCGATCCACCCC 61.250 72.222 0.00 0.00 39.29 4.95
338 339 4.617875 CCAATCGTGGTCCCACTC 57.382 61.111 14.20 0.00 44.16 3.51
339 340 1.676968 CCAATCGTGGTCCCACTCA 59.323 57.895 14.20 1.57 44.16 3.41
340 341 0.036164 CCAATCGTGGTCCCACTCAA 59.964 55.000 14.20 0.87 44.16 3.02
341 342 1.156736 CAATCGTGGTCCCACTCAAC 58.843 55.000 14.20 0.00 44.16 3.18
342 343 0.036306 AATCGTGGTCCCACTCAACC 59.964 55.000 14.20 0.00 44.16 3.77
343 344 1.838073 ATCGTGGTCCCACTCAACCC 61.838 60.000 14.20 0.00 44.16 4.11
344 345 2.813726 CGTGGTCCCACTCAACCCA 61.814 63.158 14.20 0.00 44.16 4.51
345 346 1.228154 GTGGTCCCACTCAACCCAC 60.228 63.158 9.24 0.00 43.12 4.61
346 347 2.434774 GGTCCCACTCAACCCACC 59.565 66.667 0.00 0.00 0.00 4.61
347 348 2.434774 GTCCCACTCAACCCACCC 59.565 66.667 0.00 0.00 0.00 4.61
348 349 2.856988 TCCCACTCAACCCACCCC 60.857 66.667 0.00 0.00 0.00 4.95
349 350 3.979497 CCCACTCAACCCACCCCC 61.979 72.222 0.00 0.00 0.00 5.40
350 351 4.344865 CCACTCAACCCACCCCCG 62.345 72.222 0.00 0.00 0.00 5.73
351 352 4.344865 CACTCAACCCACCCCCGG 62.345 72.222 0.00 0.00 0.00 5.73
362 363 3.719497 CCCCCGGCCCGTCTAAAA 61.719 66.667 0.85 0.00 0.00 1.52
363 364 2.352039 CCCCGGCCCGTCTAAAAA 59.648 61.111 0.85 0.00 0.00 1.94
380 381 3.502123 AAAAAGTTCACCTCCGATCCA 57.498 42.857 0.00 0.00 0.00 3.41
381 382 2.770164 AAAGTTCACCTCCGATCCAG 57.230 50.000 0.00 0.00 0.00 3.86
382 383 1.938585 AAGTTCACCTCCGATCCAGA 58.061 50.000 0.00 0.00 0.00 3.86
383 384 2.166907 AGTTCACCTCCGATCCAGAT 57.833 50.000 0.00 0.00 0.00 2.90
384 385 2.035632 AGTTCACCTCCGATCCAGATC 58.964 52.381 0.00 0.00 34.56 2.75
385 386 1.069358 GTTCACCTCCGATCCAGATCC 59.931 57.143 2.11 0.00 34.40 3.36
386 387 0.470080 TCACCTCCGATCCAGATCCC 60.470 60.000 2.11 0.00 34.40 3.85
387 388 1.152226 ACCTCCGATCCAGATCCCC 60.152 63.158 2.11 0.00 34.40 4.81
388 389 1.157276 CCTCCGATCCAGATCCCCT 59.843 63.158 2.11 0.00 34.40 4.79
389 390 0.902516 CCTCCGATCCAGATCCCCTC 60.903 65.000 2.11 0.00 34.40 4.30
390 391 0.902516 CTCCGATCCAGATCCCCTCC 60.903 65.000 2.11 0.00 34.40 4.30
391 392 1.152247 CCGATCCAGATCCCCTCCA 60.152 63.158 2.11 0.00 34.40 3.86
392 393 1.476007 CCGATCCAGATCCCCTCCAC 61.476 65.000 2.11 0.00 34.40 4.02
393 394 1.476007 CGATCCAGATCCCCTCCACC 61.476 65.000 2.11 0.00 34.40 4.61
394 395 0.104725 GATCCAGATCCCCTCCACCT 60.105 60.000 0.00 0.00 31.76 4.00
395 396 0.104725 ATCCAGATCCCCTCCACCTC 60.105 60.000 0.00 0.00 0.00 3.85
396 397 1.768077 CCAGATCCCCTCCACCTCC 60.768 68.421 0.00 0.00 0.00 4.30
397 398 1.003442 CAGATCCCCTCCACCTCCA 59.997 63.158 0.00 0.00 0.00 3.86
398 399 1.003573 AGATCCCCTCCACCTCCAC 59.996 63.158 0.00 0.00 0.00 4.02
399 400 2.042930 ATCCCCTCCACCTCCACC 59.957 66.667 0.00 0.00 0.00 4.61
400 401 2.553438 GATCCCCTCCACCTCCACCT 62.553 65.000 0.00 0.00 0.00 4.00
401 402 2.553438 ATCCCCTCCACCTCCACCTC 62.553 65.000 0.00 0.00 0.00 3.85
402 403 2.689034 CCCTCCACCTCCACCTCC 60.689 72.222 0.00 0.00 0.00 4.30
403 404 3.077556 CCTCCACCTCCACCTCCG 61.078 72.222 0.00 0.00 0.00 4.63
404 405 2.037367 CTCCACCTCCACCTCCGA 59.963 66.667 0.00 0.00 0.00 4.55
405 406 2.037367 TCCACCTCCACCTCCGAG 59.963 66.667 0.00 0.00 0.00 4.63
406 407 3.775654 CCACCTCCACCTCCGAGC 61.776 72.222 0.00 0.00 0.00 5.03
906 907 5.465056 GGCTTTTTGATTTGGTTGATTTCGA 59.535 36.000 0.00 0.00 0.00 3.71
971 972 2.303022 TCCCTTTCAGCGTTGAAGATCT 59.697 45.455 14.48 0.00 43.76 2.75
1526 1527 7.094634 CCTGTGCTTCTGAAGTAACATGTTTAT 60.095 37.037 17.78 2.71 30.48 1.40
1629 1633 3.191735 GCAAAATGCATTGTTGAAGCC 57.808 42.857 25.38 12.37 44.26 4.35
1873 1877 2.860009 CTGGCTGATATGAAGGCACAT 58.140 47.619 7.06 3.08 44.44 3.21
2137 2141 3.451902 CAGAGGAGAAGCTGAAGGAGAAT 59.548 47.826 0.00 0.00 34.06 2.40
2628 2632 1.474330 GAAGCCCATGTTGGTTAGGG 58.526 55.000 0.00 0.00 44.37 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.042008 GGTACAAATATACTTTGTCGACATCAT 57.958 33.333 20.80 12.18 42.10 2.45
25 26 7.493320 GGGTACAAATATACTTTGTCGACATCA 59.507 37.037 20.80 8.45 42.10 3.07
26 27 7.042254 GGGGTACAAATATACTTTGTCGACATC 60.042 40.741 20.80 0.00 42.10 3.06
27 28 6.764560 GGGGTACAAATATACTTTGTCGACAT 59.235 38.462 20.80 7.28 42.10 3.06
28 29 6.070653 AGGGGTACAAATATACTTTGTCGACA 60.071 38.462 15.76 15.76 42.10 4.35
29 30 6.343703 AGGGGTACAAATATACTTTGTCGAC 58.656 40.000 9.11 9.11 42.10 4.20
30 31 6.549433 AGGGGTACAAATATACTTTGTCGA 57.451 37.500 13.21 0.00 42.10 4.20
31 32 7.719483 TCTAGGGGTACAAATATACTTTGTCG 58.281 38.462 13.21 0.00 42.10 4.35
32 33 8.921205 TCTCTAGGGGTACAAATATACTTTGTC 58.079 37.037 13.21 8.07 42.10 3.18
33 34 8.849543 TCTCTAGGGGTACAAATATACTTTGT 57.150 34.615 13.90 13.90 44.03 2.83
41 42 9.670442 ACTGAAATATCTCTAGGGGTACAAATA 57.330 33.333 0.00 0.00 0.00 1.40
42 43 8.568617 ACTGAAATATCTCTAGGGGTACAAAT 57.431 34.615 0.00 0.00 0.00 2.32
43 44 7.622081 TGACTGAAATATCTCTAGGGGTACAAA 59.378 37.037 0.00 0.00 0.00 2.83
44 45 7.130099 TGACTGAAATATCTCTAGGGGTACAA 58.870 38.462 0.00 0.00 0.00 2.41
45 46 6.679542 TGACTGAAATATCTCTAGGGGTACA 58.320 40.000 0.00 0.00 0.00 2.90
46 47 7.451877 TGATGACTGAAATATCTCTAGGGGTAC 59.548 40.741 0.00 0.00 0.00 3.34
47 48 7.535738 TGATGACTGAAATATCTCTAGGGGTA 58.464 38.462 0.00 0.00 0.00 3.69
48 49 6.385443 TGATGACTGAAATATCTCTAGGGGT 58.615 40.000 0.00 0.00 0.00 4.95
49 50 6.924913 TGATGACTGAAATATCTCTAGGGG 57.075 41.667 0.00 0.00 0.00 4.79
50 51 9.434420 GATTTGATGACTGAAATATCTCTAGGG 57.566 37.037 0.00 0.00 0.00 3.53
51 52 9.993454 TGATTTGATGACTGAAATATCTCTAGG 57.007 33.333 0.00 0.00 0.00 3.02
60 61 9.938280 AAACATGATTGATTTGATGACTGAAAT 57.062 25.926 0.00 0.00 0.00 2.17
61 62 9.198837 CAAACATGATTGATTTGATGACTGAAA 57.801 29.630 9.99 0.00 35.73 2.69
62 63 7.329962 GCAAACATGATTGATTTGATGACTGAA 59.670 33.333 18.88 0.00 35.73 3.02
63 64 6.809689 GCAAACATGATTGATTTGATGACTGA 59.190 34.615 18.88 0.00 35.73 3.41
64 65 6.035650 GGCAAACATGATTGATTTGATGACTG 59.964 38.462 18.88 0.00 35.73 3.51
65 66 6.103997 GGCAAACATGATTGATTTGATGACT 58.896 36.000 18.88 0.00 35.73 3.41
66 67 5.292589 GGGCAAACATGATTGATTTGATGAC 59.707 40.000 18.88 0.00 35.73 3.06
67 68 5.421277 GGGCAAACATGATTGATTTGATGA 58.579 37.500 18.88 0.00 35.73 2.92
68 69 4.573201 GGGGCAAACATGATTGATTTGATG 59.427 41.667 18.88 0.00 35.73 3.07
69 70 4.384427 GGGGGCAAACATGATTGATTTGAT 60.384 41.667 18.88 0.00 35.73 2.57
70 71 3.055240 GGGGGCAAACATGATTGATTTGA 60.055 43.478 18.88 0.00 35.73 2.69
71 72 3.272581 GGGGGCAAACATGATTGATTTG 58.727 45.455 18.88 10.12 36.58 2.32
72 73 2.911636 TGGGGGCAAACATGATTGATTT 59.088 40.909 18.88 0.00 31.84 2.17
73 74 2.549082 TGGGGGCAAACATGATTGATT 58.451 42.857 18.88 0.00 31.84 2.57
74 75 2.250921 TGGGGGCAAACATGATTGAT 57.749 45.000 18.88 0.00 31.84 2.57
75 76 1.901159 CTTGGGGGCAAACATGATTGA 59.099 47.619 18.88 0.00 31.84 2.57
76 77 1.901159 TCTTGGGGGCAAACATGATTG 59.099 47.619 11.12 11.12 0.00 2.67
77 78 2.323999 TCTTGGGGGCAAACATGATT 57.676 45.000 0.00 0.00 0.00 2.57
78 79 2.323999 TTCTTGGGGGCAAACATGAT 57.676 45.000 0.00 0.00 0.00 2.45
79 80 2.094100 TTTCTTGGGGGCAAACATGA 57.906 45.000 0.00 0.00 0.00 3.07
80 81 2.493035 GTTTTCTTGGGGGCAAACATG 58.507 47.619 0.00 0.00 0.00 3.21
81 82 1.419762 GGTTTTCTTGGGGGCAAACAT 59.580 47.619 0.00 0.00 31.85 2.71
82 83 0.833949 GGTTTTCTTGGGGGCAAACA 59.166 50.000 0.00 0.00 31.85 2.83
83 84 1.128200 AGGTTTTCTTGGGGGCAAAC 58.872 50.000 0.00 0.00 0.00 2.93
84 85 1.488393 CAAGGTTTTCTTGGGGGCAAA 59.512 47.619 0.00 0.00 46.81 3.68
85 86 1.127343 CAAGGTTTTCTTGGGGGCAA 58.873 50.000 0.00 0.00 46.81 4.52
86 87 2.833244 CAAGGTTTTCTTGGGGGCA 58.167 52.632 0.00 0.00 46.81 5.36
93 94 6.374053 CCAATTTCCACAAACAAGGTTTTCTT 59.626 34.615 0.00 0.00 35.79 2.52
94 95 5.879777 CCAATTTCCACAAACAAGGTTTTCT 59.120 36.000 0.00 0.00 0.00 2.52
95 96 5.877564 TCCAATTTCCACAAACAAGGTTTTC 59.122 36.000 0.00 0.00 0.00 2.29
96 97 5.810095 TCCAATTTCCACAAACAAGGTTTT 58.190 33.333 0.00 0.00 0.00 2.43
97 98 5.188751 TCTCCAATTTCCACAAACAAGGTTT 59.811 36.000 0.00 0.00 0.00 3.27
98 99 4.714308 TCTCCAATTTCCACAAACAAGGTT 59.286 37.500 0.00 0.00 0.00 3.50
99 100 4.285863 TCTCCAATTTCCACAAACAAGGT 58.714 39.130 0.00 0.00 0.00 3.50
100 101 4.935352 TCTCCAATTTCCACAAACAAGG 57.065 40.909 0.00 0.00 0.00 3.61
101 102 6.088016 TCATCTCCAATTTCCACAAACAAG 57.912 37.500 0.00 0.00 0.00 3.16
102 103 6.669125 ATCATCTCCAATTTCCACAAACAA 57.331 33.333 0.00 0.00 0.00 2.83
103 104 7.396907 ACATATCATCTCCAATTTCCACAAACA 59.603 33.333 0.00 0.00 0.00 2.83
104 105 7.775120 ACATATCATCTCCAATTTCCACAAAC 58.225 34.615 0.00 0.00 0.00 2.93
105 106 7.959658 ACATATCATCTCCAATTTCCACAAA 57.040 32.000 0.00 0.00 0.00 2.83
106 107 7.959658 AACATATCATCTCCAATTTCCACAA 57.040 32.000 0.00 0.00 0.00 3.33
107 108 7.959658 AAACATATCATCTCCAATTTCCACA 57.040 32.000 0.00 0.00 0.00 4.17
137 138 9.466497 ACCATCTGTGTAAAAACATATCATCTT 57.534 29.630 0.00 0.00 0.00 2.40
138 139 8.896744 CACCATCTGTGTAAAAACATATCATCT 58.103 33.333 0.00 0.00 40.26 2.90
182 183 9.600646 GCTCTTGAAGAAGTTTACAAGAAATAC 57.399 33.333 15.64 7.30 44.76 1.89
183 184 8.784043 GGCTCTTGAAGAAGTTTACAAGAAATA 58.216 33.333 15.64 1.96 44.76 1.40
184 185 7.255625 GGGCTCTTGAAGAAGTTTACAAGAAAT 60.256 37.037 15.64 0.00 44.76 2.17
185 186 6.039382 GGGCTCTTGAAGAAGTTTACAAGAAA 59.961 38.462 15.64 2.66 44.76 2.52
186 187 5.531287 GGGCTCTTGAAGAAGTTTACAAGAA 59.469 40.000 15.64 6.08 44.76 2.52
187 188 5.063880 GGGCTCTTGAAGAAGTTTACAAGA 58.936 41.667 14.71 14.71 43.79 3.02
188 189 4.083802 CGGGCTCTTGAAGAAGTTTACAAG 60.084 45.833 0.00 0.00 40.37 3.16
189 190 3.813166 CGGGCTCTTGAAGAAGTTTACAA 59.187 43.478 0.00 0.00 0.00 2.41
190 191 3.181458 ACGGGCTCTTGAAGAAGTTTACA 60.181 43.478 0.00 0.00 0.00 2.41
191 192 3.186613 CACGGGCTCTTGAAGAAGTTTAC 59.813 47.826 0.00 0.00 0.00 2.01
192 193 3.399330 CACGGGCTCTTGAAGAAGTTTA 58.601 45.455 0.00 0.00 0.00 2.01
193 194 2.222027 CACGGGCTCTTGAAGAAGTTT 58.778 47.619 0.00 0.00 0.00 2.66
194 195 1.543429 CCACGGGCTCTTGAAGAAGTT 60.543 52.381 0.00 0.00 0.00 2.66
195 196 0.035458 CCACGGGCTCTTGAAGAAGT 59.965 55.000 0.00 0.00 0.00 3.01
196 197 1.301677 GCCACGGGCTCTTGAAGAAG 61.302 60.000 7.58 0.00 46.69 2.85
197 198 1.302511 GCCACGGGCTCTTGAAGAA 60.303 57.895 7.58 0.00 46.69 2.52
198 199 2.347490 GCCACGGGCTCTTGAAGA 59.653 61.111 7.58 0.00 46.69 2.87
211 212 4.666532 GTGCTCGTGCGTTGCCAC 62.667 66.667 4.84 0.00 43.34 5.01
212 213 4.908687 AGTGCTCGTGCGTTGCCA 62.909 61.111 4.84 0.00 43.34 4.92
213 214 4.077188 GAGTGCTCGTGCGTTGCC 62.077 66.667 4.84 0.00 43.34 4.52
214 215 1.733041 TAGAGTGCTCGTGCGTTGC 60.733 57.895 4.84 5.71 43.34 4.17
215 216 0.387367 AGTAGAGTGCTCGTGCGTTG 60.387 55.000 4.84 0.00 43.34 4.10
216 217 1.130749 CTAGTAGAGTGCTCGTGCGTT 59.869 52.381 4.84 0.00 43.34 4.84
217 218 0.727970 CTAGTAGAGTGCTCGTGCGT 59.272 55.000 4.84 0.00 43.34 5.24
218 219 0.727970 ACTAGTAGAGTGCTCGTGCG 59.272 55.000 3.59 0.00 43.34 5.34
219 220 3.374678 ACTTACTAGTAGAGTGCTCGTGC 59.625 47.826 3.59 1.71 39.39 5.34
231 232 6.183360 ACCTGCGCTACTACTACTTACTAGTA 60.183 42.308 9.73 0.00 36.95 1.82
232 233 5.055812 CCTGCGCTACTACTACTTACTAGT 58.944 45.833 9.73 0.00 39.24 2.57
233 234 5.055812 ACCTGCGCTACTACTACTTACTAG 58.944 45.833 9.73 0.00 0.00 2.57
234 235 5.028549 ACCTGCGCTACTACTACTTACTA 57.971 43.478 9.73 0.00 0.00 1.82
235 236 3.883669 ACCTGCGCTACTACTACTTACT 58.116 45.455 9.73 0.00 0.00 2.24
236 237 5.525378 TCTTACCTGCGCTACTACTACTTAC 59.475 44.000 9.73 0.00 0.00 2.34
237 238 5.525378 GTCTTACCTGCGCTACTACTACTTA 59.475 44.000 9.73 0.00 0.00 2.24
238 239 4.335037 GTCTTACCTGCGCTACTACTACTT 59.665 45.833 9.73 0.00 0.00 2.24
239 240 3.876320 GTCTTACCTGCGCTACTACTACT 59.124 47.826 9.73 0.00 0.00 2.57
240 241 3.003171 GGTCTTACCTGCGCTACTACTAC 59.997 52.174 9.73 0.00 34.73 2.73
241 242 3.209410 GGTCTTACCTGCGCTACTACTA 58.791 50.000 9.73 0.00 34.73 1.82
242 243 2.022934 GGTCTTACCTGCGCTACTACT 58.977 52.381 9.73 0.00 34.73 2.57
243 244 1.066757 GGGTCTTACCTGCGCTACTAC 59.933 57.143 9.73 0.00 38.64 2.73
244 245 1.064166 AGGGTCTTACCTGCGCTACTA 60.064 52.381 9.73 0.00 40.04 1.82
245 246 0.324460 AGGGTCTTACCTGCGCTACT 60.324 55.000 9.73 0.00 40.04 2.57
246 247 0.102663 GAGGGTCTTACCTGCGCTAC 59.897 60.000 9.73 0.00 42.10 3.58
247 248 0.323999 TGAGGGTCTTACCTGCGCTA 60.324 55.000 9.73 0.00 42.10 4.26
248 249 1.609501 TGAGGGTCTTACCTGCGCT 60.610 57.895 9.73 0.00 42.10 5.92
249 250 1.448013 GTGAGGGTCTTACCTGCGC 60.448 63.158 0.00 0.00 42.10 6.09
250 251 1.153823 CGTGAGGGTCTTACCTGCG 60.154 63.158 0.00 0.00 42.10 5.18
251 252 0.320697 AACGTGAGGGTCTTACCTGC 59.679 55.000 0.00 0.00 42.10 4.85
252 253 2.824341 AGTAACGTGAGGGTCTTACCTG 59.176 50.000 0.00 0.00 42.10 4.00
253 254 3.166560 AGTAACGTGAGGGTCTTACCT 57.833 47.619 0.00 0.00 45.57 3.08
254 255 4.013050 AGTAGTAACGTGAGGGTCTTACC 58.987 47.826 0.00 0.00 37.60 2.85
255 256 6.676700 GCTTAGTAGTAACGTGAGGGTCTTAC 60.677 46.154 0.00 0.00 0.00 2.34
256 257 5.355350 GCTTAGTAGTAACGTGAGGGTCTTA 59.645 44.000 0.00 0.00 0.00 2.10
257 258 4.157472 GCTTAGTAGTAACGTGAGGGTCTT 59.843 45.833 0.00 0.00 0.00 3.01
258 259 3.693578 GCTTAGTAGTAACGTGAGGGTCT 59.306 47.826 0.00 0.00 0.00 3.85
259 260 3.486542 CGCTTAGTAGTAACGTGAGGGTC 60.487 52.174 0.00 0.00 0.00 4.46
260 261 2.421424 CGCTTAGTAGTAACGTGAGGGT 59.579 50.000 0.00 0.00 0.00 4.34
261 262 2.421424 ACGCTTAGTAGTAACGTGAGGG 59.579 50.000 13.52 3.92 35.33 4.30
262 263 3.754188 ACGCTTAGTAGTAACGTGAGG 57.246 47.619 13.52 0.00 35.33 3.86
266 267 2.813754 TGGACACGCTTAGTAGTAACGT 59.186 45.455 10.30 10.30 37.47 3.99
267 268 3.166657 GTGGACACGCTTAGTAGTAACG 58.833 50.000 9.37 9.37 0.00 3.18
268 269 3.505836 GGTGGACACGCTTAGTAGTAAC 58.494 50.000 0.00 0.00 0.00 2.50
269 270 2.493278 GGGTGGACACGCTTAGTAGTAA 59.507 50.000 11.67 0.00 40.60 2.24
270 271 2.094675 GGGTGGACACGCTTAGTAGTA 58.905 52.381 11.67 0.00 40.60 1.82
271 272 0.893447 GGGTGGACACGCTTAGTAGT 59.107 55.000 11.67 0.00 40.60 2.73
272 273 0.175073 GGGGTGGACACGCTTAGTAG 59.825 60.000 17.25 0.00 42.97 2.57
273 274 0.542467 TGGGGTGGACACGCTTAGTA 60.542 55.000 17.25 0.00 42.97 1.82
274 275 1.827399 CTGGGGTGGACACGCTTAGT 61.827 60.000 17.25 0.00 42.97 2.24
275 276 1.079127 CTGGGGTGGACACGCTTAG 60.079 63.158 17.25 12.54 42.97 2.18
276 277 3.065306 CTGGGGTGGACACGCTTA 58.935 61.111 17.25 7.80 42.97 3.09
277 278 4.643387 GCTGGGGTGGACACGCTT 62.643 66.667 17.25 0.00 42.97 4.68
283 284 4.176752 GATCGGGCTGGGGTGGAC 62.177 72.222 0.00 0.00 0.00 4.02
291 292 4.008933 GATCGGGGGATCGGGCTG 62.009 72.222 0.00 0.00 0.00 4.85
294 295 3.626924 GTGGATCGGGGGATCGGG 61.627 72.222 0.00 0.00 32.60 5.14
295 296 3.626924 GGTGGATCGGGGGATCGG 61.627 72.222 0.00 0.00 32.60 4.18
296 297 3.626924 GGGTGGATCGGGGGATCG 61.627 72.222 0.00 0.00 32.60 3.69
297 298 3.249961 GGGGTGGATCGGGGGATC 61.250 72.222 0.00 0.00 0.00 3.36
327 328 1.228154 GTGGGTTGAGTGGGACCAC 60.228 63.158 13.53 13.53 46.50 4.16
328 329 2.457323 GGTGGGTTGAGTGGGACCA 61.457 63.158 0.00 0.00 37.68 4.02
329 330 2.434774 GGTGGGTTGAGTGGGACC 59.565 66.667 0.00 0.00 35.14 4.46
330 331 2.434774 GGGTGGGTTGAGTGGGAC 59.565 66.667 0.00 0.00 0.00 4.46
331 332 2.856988 GGGGTGGGTTGAGTGGGA 60.857 66.667 0.00 0.00 0.00 4.37
332 333 3.979497 GGGGGTGGGTTGAGTGGG 61.979 72.222 0.00 0.00 0.00 4.61
333 334 4.344865 CGGGGGTGGGTTGAGTGG 62.345 72.222 0.00 0.00 0.00 4.00
334 335 4.344865 CCGGGGGTGGGTTGAGTG 62.345 72.222 0.00 0.00 0.00 3.51
345 346 3.270941 TTTTTAGACGGGCCGGGGG 62.271 63.158 31.78 2.04 0.00 5.40
346 347 2.352039 TTTTTAGACGGGCCGGGG 59.648 61.111 31.78 2.48 0.00 5.73
360 361 3.072476 TCTGGATCGGAGGTGAACTTTTT 59.928 43.478 0.00 0.00 0.00 1.94
361 362 2.637872 TCTGGATCGGAGGTGAACTTTT 59.362 45.455 0.00 0.00 0.00 2.27
362 363 2.257207 TCTGGATCGGAGGTGAACTTT 58.743 47.619 0.00 0.00 0.00 2.66
363 364 1.938585 TCTGGATCGGAGGTGAACTT 58.061 50.000 0.00 0.00 0.00 2.66
364 365 2.035632 GATCTGGATCGGAGGTGAACT 58.964 52.381 0.00 0.00 0.00 3.01
365 366 1.069358 GGATCTGGATCGGAGGTGAAC 59.931 57.143 4.75 0.00 38.69 3.18
366 367 1.414158 GGATCTGGATCGGAGGTGAA 58.586 55.000 4.75 0.00 38.69 3.18
367 368 0.470080 GGGATCTGGATCGGAGGTGA 60.470 60.000 4.75 0.00 38.69 4.02
368 369 1.476007 GGGGATCTGGATCGGAGGTG 61.476 65.000 4.75 0.00 38.69 4.00
369 370 1.152226 GGGGATCTGGATCGGAGGT 60.152 63.158 4.75 0.00 38.69 3.85
370 371 0.902516 GAGGGGATCTGGATCGGAGG 60.903 65.000 4.75 0.00 38.69 4.30
371 372 0.902516 GGAGGGGATCTGGATCGGAG 60.903 65.000 4.75 0.00 38.69 4.63
372 373 1.156330 GGAGGGGATCTGGATCGGA 59.844 63.158 4.75 0.00 38.69 4.55
373 374 1.152247 TGGAGGGGATCTGGATCGG 60.152 63.158 4.75 0.00 38.69 4.18
374 375 1.476007 GGTGGAGGGGATCTGGATCG 61.476 65.000 4.75 0.00 38.69 3.69
375 376 0.104725 AGGTGGAGGGGATCTGGATC 60.105 60.000 2.24 2.24 37.11 3.36
376 377 0.104725 GAGGTGGAGGGGATCTGGAT 60.105 60.000 0.00 0.00 0.00 3.41
377 378 1.314867 GAGGTGGAGGGGATCTGGA 59.685 63.158 0.00 0.00 0.00 3.86
378 379 1.768077 GGAGGTGGAGGGGATCTGG 60.768 68.421 0.00 0.00 0.00 3.86
379 380 1.003442 TGGAGGTGGAGGGGATCTG 59.997 63.158 0.00 0.00 0.00 2.90
380 381 1.003573 GTGGAGGTGGAGGGGATCT 59.996 63.158 0.00 0.00 0.00 2.75
381 382 2.073101 GGTGGAGGTGGAGGGGATC 61.073 68.421 0.00 0.00 0.00 3.36
382 383 2.042930 GGTGGAGGTGGAGGGGAT 59.957 66.667 0.00 0.00 0.00 3.85
383 384 3.208592 AGGTGGAGGTGGAGGGGA 61.209 66.667 0.00 0.00 0.00 4.81
384 385 2.689034 GAGGTGGAGGTGGAGGGG 60.689 72.222 0.00 0.00 0.00 4.79
385 386 2.689034 GGAGGTGGAGGTGGAGGG 60.689 72.222 0.00 0.00 0.00 4.30
386 387 3.077556 CGGAGGTGGAGGTGGAGG 61.078 72.222 0.00 0.00 0.00 4.30
387 388 2.037367 TCGGAGGTGGAGGTGGAG 59.963 66.667 0.00 0.00 0.00 3.86
388 389 2.037367 CTCGGAGGTGGAGGTGGA 59.963 66.667 0.00 0.00 0.00 4.02
389 390 3.775654 GCTCGGAGGTGGAGGTGG 61.776 72.222 7.20 0.00 32.10 4.61
390 391 3.775654 GGCTCGGAGGTGGAGGTG 61.776 72.222 7.20 0.00 32.10 4.00
393 394 3.522731 CTCGGCTCGGAGGTGGAG 61.523 72.222 7.20 0.00 34.62 3.86
394 395 2.488771 TAACTCGGCTCGGAGGTGGA 62.489 60.000 7.20 0.00 38.39 4.02
395 396 1.601419 TTAACTCGGCTCGGAGGTGG 61.601 60.000 7.20 0.00 38.39 4.61
396 397 0.460311 ATTAACTCGGCTCGGAGGTG 59.540 55.000 7.20 0.00 38.39 4.00
397 398 1.192428 AATTAACTCGGCTCGGAGGT 58.808 50.000 7.20 5.07 38.39 3.85
398 399 2.100252 TGTAATTAACTCGGCTCGGAGG 59.900 50.000 7.20 0.00 38.39 4.30
399 400 3.114065 GTGTAATTAACTCGGCTCGGAG 58.886 50.000 0.00 0.00 39.97 4.63
400 401 2.478370 CGTGTAATTAACTCGGCTCGGA 60.478 50.000 0.00 0.00 40.50 4.55
401 402 1.850441 CGTGTAATTAACTCGGCTCGG 59.150 52.381 0.00 0.00 40.50 4.63
402 403 2.789208 TCGTGTAATTAACTCGGCTCG 58.211 47.619 0.00 0.00 43.50 5.03
403 404 5.517904 ACTATCGTGTAATTAACTCGGCTC 58.482 41.667 0.00 0.00 43.50 4.70
404 405 5.511234 ACTATCGTGTAATTAACTCGGCT 57.489 39.130 0.00 0.00 43.50 5.52
405 406 5.626955 GGTACTATCGTGTAATTAACTCGGC 59.373 44.000 0.00 0.00 43.50 5.54
406 407 6.634436 GTGGTACTATCGTGTAATTAACTCGG 59.366 42.308 0.00 0.00 43.50 4.63
602 603 2.106938 CTATTGAGCGAGCGGGCA 59.893 61.111 4.87 0.00 34.64 5.36
906 907 4.385478 AAATGCCCAAATCAAAACCCAT 57.615 36.364 0.00 0.00 0.00 4.00
971 972 1.768870 GCTCAAGCCCCTGGTAATCTA 59.231 52.381 0.00 0.00 34.31 1.98
1629 1633 0.680921 ATCTTCAACCATGGCCCACG 60.681 55.000 13.04 0.00 0.00 4.94
1873 1877 4.592942 ACTCTGCATCTTTCTTTGCCATA 58.407 39.130 0.00 0.00 38.08 2.74
2137 2141 0.029163 TGGCCTGGATCCCCTTGATA 60.029 55.000 9.90 0.00 32.41 2.15
2628 2632 1.422388 GGTCGACGGAACCAACTTAC 58.578 55.000 9.92 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.