Multiple sequence alignment - TraesCS2B01G312200

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 TraesCS2B01G312200 chr2B 100.000 2711 0 0 1 2711 447492032 447489322 0.000000e+00 5007.0
1 TraesCS2B01G312200 chr2B 94.805 77 4 0 291 367 185812922 185812846 1.320000e-23 121.0
2 TraesCS2B01G312200 chr2B 82.222 90 10 2 105 193 699222809 699222893 3.740000e-09 73.1
3 TraesCS2B01G312200 chr2D 93.496 2168 74 29 464 2602 376131617 376133746 0.000000e+00 3160.0
4 TraesCS2B01G312200 chr2D 93.506 77 5 0 291 367 489409510 489409434 6.130000e-22 115.0
5 TraesCS2B01G312200 chr2A 92.348 1712 76 24 553 2238 508514225 508515907 0.000000e+00 2385.0
6 TraesCS2B01G312200 chr2A 95.402 261 11 1 2449 2709 508516324 508516583 5.400000e-112 414.0
7 TraesCS2B01G312200 chr2A 93.333 165 9 2 2284 2447 508515916 508516079 2.700000e-60 243.0
8 TraesCS2B01G312200 chr3A 92.157 102 8 0 193 294 332556295 332556194 7.820000e-31 145.0
9 TraesCS2B01G312200 chr3A 77.108 249 49 5 471 712 70845648 70845401 1.310000e-28 137.0
10 TraesCS2B01G312200 chr3A 76.305 249 51 5 471 712 70844703 70844456 2.830000e-25 126.0
11 TraesCS2B01G312200 chr3A 92.857 42 2 1 105 145 720844109 720844150 2.920000e-05 60.2
12 TraesCS2B01G312200 chr3A 92.857 42 2 1 105 145 720849908 720849949 2.920000e-05 60.2
13 TraesCS2B01G312200 chr7A 90.476 105 10 0 190 294 627236809 627236913 3.640000e-29 139.0
14 TraesCS2B01G312200 chr7A 91.089 101 9 0 194 294 498590257 498590357 1.310000e-28 137.0
15 TraesCS2B01G312200 chr7A 93.506 77 5 0 291 367 573430869 573430945 6.130000e-22 115.0
16 TraesCS2B01G312200 chr4A 91.919 99 8 0 196 294 477033331 477033233 3.640000e-29 139.0
17 TraesCS2B01G312200 chr4A 93.506 77 5 0 291 367 477033295 477033219 6.130000e-22 115.0
18 TraesCS2B01G312200 chr3D 91.176 102 9 0 193 294 251316009 251316110 3.640000e-29 139.0
19 TraesCS2B01G312200 chr3D 87.611 113 12 2 184 294 172356565 172356677 2.190000e-26 130.0
20 TraesCS2B01G312200 chr3D 92.208 77 6 0 291 367 172356615 172356691 2.850000e-20 110.0
21 TraesCS2B01G312200 chr3D 92.208 77 6 0 291 367 383544122 383544046 2.850000e-20 110.0
22 TraesCS2B01G312200 chr6B 91.000 100 9 0 195 294 85784646 85784547 4.710000e-28 135.0
23 TraesCS2B01G312200 chr3B 91.000 100 9 0 195 294 421238969 421238870 4.710000e-28 135.0
24 TraesCS2B01G312200 chr3B 86.555 119 16 0 196 314 153587171 153587053 6.090000e-27 132.0
25 TraesCS2B01G312200 chr7B 94.805 77 4 0 291 367 533773394 533773470 1.320000e-23 121.0
26 TraesCS2B01G312200 chr7B 90.909 77 7 0 291 367 493525890 493525966 1.330000e-18 104.0
27 TraesCS2B01G312200 chr6A 85.567 97 14 0 291 387 153673684 153673588 4.780000e-18 102.0
28 TraesCS2B01G312200 chr1D 94.737 38 2 0 108 145 38911757 38911720 2.920000e-05 60.2
29 TraesCS2B01G312200 chr6D 96.774 31 1 0 105 135 470928164 470928134 5.000000e-03 52.8


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 TraesCS2B01G312200 chr2B 447489322 447492032 2710 True 5007 5007 100.000000 1 2711 1 chr2B.!!$R2 2710
1 TraesCS2B01G312200 chr2D 376131617 376133746 2129 False 3160 3160 93.496000 464 2602 1 chr2D.!!$F1 2138
2 TraesCS2B01G312200 chr2A 508514225 508516583 2358 False 1014 2385 93.694333 553 2709 3 chr2A.!!$F1 2156

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
163 164 0.258774 AACAAAGGTGTGTCTGCCCT 59.741 50.0 0.0 0.0 38.27 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 2171 1.094785 GCACATACGGCAAGGAACAT 58.905 50.0 0.0 0.0 0.0 2.71 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
36 37 7.602517 AATAATTTTGACCTGTTCTCTCTCG 57.397 36.000 0.00 0.00 0.00 4.04
37 38 4.873746 ATTTTGACCTGTTCTCTCTCGA 57.126 40.909 0.00 0.00 0.00 4.04
38 39 3.924918 TTTGACCTGTTCTCTCTCGAG 57.075 47.619 5.93 5.93 38.67 4.04
39 40 2.570415 TGACCTGTTCTCTCTCGAGT 57.430 50.000 13.13 0.00 38.45 4.18
40 41 2.155279 TGACCTGTTCTCTCTCGAGTG 58.845 52.381 13.13 10.53 38.45 3.51
41 42 2.224548 TGACCTGTTCTCTCTCGAGTGA 60.225 50.000 15.83 15.83 38.45 3.41
42 43 2.814919 GACCTGTTCTCTCTCGAGTGAA 59.185 50.000 17.19 14.20 38.24 3.18
43 44 2.817258 ACCTGTTCTCTCTCGAGTGAAG 59.183 50.000 17.19 11.59 40.32 3.02
44 45 3.078097 CCTGTTCTCTCTCGAGTGAAGA 58.922 50.000 17.19 12.83 40.32 2.87
45 46 3.119990 CCTGTTCTCTCTCGAGTGAAGAC 60.120 52.174 17.19 16.94 40.32 3.01
46 47 3.745799 TGTTCTCTCTCGAGTGAAGACT 58.254 45.455 17.19 0.00 40.32 3.24
47 48 4.895961 TGTTCTCTCTCGAGTGAAGACTA 58.104 43.478 17.19 7.78 40.32 2.59
48 49 5.306394 TGTTCTCTCTCGAGTGAAGACTAA 58.694 41.667 17.19 4.22 40.32 2.24
49 50 5.941058 TGTTCTCTCTCGAGTGAAGACTAAT 59.059 40.000 17.19 0.00 40.32 1.73
50 51 7.104290 TGTTCTCTCTCGAGTGAAGACTAATA 58.896 38.462 17.19 3.05 40.32 0.98
51 52 7.771361 TGTTCTCTCTCGAGTGAAGACTAATAT 59.229 37.037 17.19 0.00 40.32 1.28
52 53 8.617809 GTTCTCTCTCGAGTGAAGACTAATATT 58.382 37.037 17.19 0.00 40.32 1.28
53 54 8.373048 TCTCTCTCGAGTGAAGACTAATATTC 57.627 38.462 17.19 0.00 38.45 1.75
54 55 7.988028 TCTCTCTCGAGTGAAGACTAATATTCA 59.012 37.037 17.19 0.00 38.45 2.57
64 65 8.774546 TGAAGACTAATATTCACTCCATCTCT 57.225 34.615 0.00 0.00 31.09 3.10
65 66 9.868160 TGAAGACTAATATTCACTCCATCTCTA 57.132 33.333 0.00 0.00 31.09 2.43
70 71 9.717942 ACTAATATTCACTCCATCTCTAATTGC 57.282 33.333 0.00 0.00 0.00 3.56
71 72 9.941325 CTAATATTCACTCCATCTCTAATTGCT 57.059 33.333 0.00 0.00 0.00 3.91
73 74 9.638176 AATATTCACTCCATCTCTAATTGCTTT 57.362 29.630 0.00 0.00 0.00 3.51
74 75 7.951347 ATTCACTCCATCTCTAATTGCTTTT 57.049 32.000 0.00 0.00 0.00 2.27
75 76 6.992063 TCACTCCATCTCTAATTGCTTTTC 57.008 37.500 0.00 0.00 0.00 2.29
76 77 6.715280 TCACTCCATCTCTAATTGCTTTTCT 58.285 36.000 0.00 0.00 0.00 2.52
77 78 7.170965 TCACTCCATCTCTAATTGCTTTTCTT 58.829 34.615 0.00 0.00 0.00 2.52
78 79 8.321353 TCACTCCATCTCTAATTGCTTTTCTTA 58.679 33.333 0.00 0.00 0.00 2.10
79 80 8.610896 CACTCCATCTCTAATTGCTTTTCTTAG 58.389 37.037 0.00 0.00 0.00 2.18
80 81 8.543774 ACTCCATCTCTAATTGCTTTTCTTAGA 58.456 33.333 0.00 0.00 32.22 2.10
81 82 9.558396 CTCCATCTCTAATTGCTTTTCTTAGAT 57.442 33.333 0.00 0.00 32.61 1.98
82 83 9.911788 TCCATCTCTAATTGCTTTTCTTAGATT 57.088 29.630 0.00 0.00 32.61 2.40
92 93 9.950496 ATTGCTTTTCTTAGATTTCTCTAGACA 57.050 29.630 0.00 0.00 35.43 3.41
93 94 8.994429 TGCTTTTCTTAGATTTCTCTAGACAG 57.006 34.615 0.00 0.00 35.43 3.51
94 95 8.037758 TGCTTTTCTTAGATTTCTCTAGACAGG 58.962 37.037 0.00 0.00 35.43 4.00
95 96 8.254508 GCTTTTCTTAGATTTCTCTAGACAGGA 58.745 37.037 0.00 0.00 35.43 3.86
102 103 9.702253 TTAGATTTCTCTAGACAGGAATAGTGT 57.298 33.333 0.00 0.00 35.43 3.55
103 104 8.232913 AGATTTCTCTAGACAGGAATAGTGTC 57.767 38.462 0.00 0.00 44.02 3.67
111 112 5.584253 GACAGGAATAGTGTCTAGCAAGA 57.416 43.478 0.00 0.00 41.05 3.02
112 113 5.587289 GACAGGAATAGTGTCTAGCAAGAG 58.413 45.833 0.00 0.00 41.05 2.85
113 114 5.265191 ACAGGAATAGTGTCTAGCAAGAGA 58.735 41.667 0.00 0.00 30.45 3.10
114 115 5.896678 ACAGGAATAGTGTCTAGCAAGAGAT 59.103 40.000 0.00 0.00 30.45 2.75
115 116 6.040391 ACAGGAATAGTGTCTAGCAAGAGATC 59.960 42.308 0.00 0.00 30.45 2.75
116 117 6.040278 CAGGAATAGTGTCTAGCAAGAGATCA 59.960 42.308 0.00 0.00 30.45 2.92
117 118 6.782000 AGGAATAGTGTCTAGCAAGAGATCAT 59.218 38.462 0.00 0.00 30.45 2.45
118 119 6.867816 GGAATAGTGTCTAGCAAGAGATCATG 59.132 42.308 0.00 0.00 30.45 3.07
119 120 4.669206 AGTGTCTAGCAAGAGATCATGG 57.331 45.455 0.00 0.00 30.45 3.66
120 121 4.285020 AGTGTCTAGCAAGAGATCATGGA 58.715 43.478 0.00 0.00 30.45 3.41
121 122 4.900652 AGTGTCTAGCAAGAGATCATGGAT 59.099 41.667 0.00 0.00 30.45 3.41
122 123 4.989797 GTGTCTAGCAAGAGATCATGGATG 59.010 45.833 0.00 0.00 30.45 3.51
123 124 4.897670 TGTCTAGCAAGAGATCATGGATGA 59.102 41.667 0.00 0.00 35.08 2.92
124 125 5.364735 TGTCTAGCAAGAGATCATGGATGAA 59.635 40.000 0.00 0.00 34.57 2.57
125 126 5.695816 GTCTAGCAAGAGATCATGGATGAAC 59.304 44.000 0.00 0.00 34.57 3.18
126 127 4.774660 AGCAAGAGATCATGGATGAACT 57.225 40.909 0.00 0.00 41.78 3.01
127 128 5.883685 AGCAAGAGATCATGGATGAACTA 57.116 39.130 0.00 0.00 39.60 2.24
128 129 5.856156 AGCAAGAGATCATGGATGAACTAG 58.144 41.667 0.00 0.00 39.60 2.57
129 130 4.451774 GCAAGAGATCATGGATGAACTAGC 59.548 45.833 0.00 2.34 39.60 3.42
130 131 5.608449 CAAGAGATCATGGATGAACTAGCA 58.392 41.667 0.00 0.00 39.60 3.49
131 132 5.883685 AGAGATCATGGATGAACTAGCAA 57.116 39.130 0.00 0.00 39.60 3.91
132 133 5.856156 AGAGATCATGGATGAACTAGCAAG 58.144 41.667 0.00 0.00 39.60 4.01
133 134 5.601729 AGAGATCATGGATGAACTAGCAAGA 59.398 40.000 0.00 0.00 39.60 3.02
134 135 5.856156 AGATCATGGATGAACTAGCAAGAG 58.144 41.667 0.00 0.00 38.03 2.85
135 136 5.601729 AGATCATGGATGAACTAGCAAGAGA 59.398 40.000 0.00 0.00 38.03 3.10
136 137 5.682234 TCATGGATGAACTAGCAAGAGAA 57.318 39.130 0.00 0.00 33.08 2.87
137 138 6.053632 TCATGGATGAACTAGCAAGAGAAA 57.946 37.500 0.00 0.00 33.08 2.52
138 139 6.475504 TCATGGATGAACTAGCAAGAGAAAA 58.524 36.000 0.00 0.00 33.08 2.29
139 140 6.942005 TCATGGATGAACTAGCAAGAGAAAAA 59.058 34.615 0.00 0.00 33.08 1.94
161 162 2.492019 GAAACAAAGGTGTGTCTGCC 57.508 50.000 0.00 0.00 38.75 4.85
162 163 1.067060 GAAACAAAGGTGTGTCTGCCC 59.933 52.381 0.00 0.00 38.75 5.36
163 164 0.258774 AACAAAGGTGTGTCTGCCCT 59.741 50.000 0.00 0.00 38.27 5.19
164 165 0.258774 ACAAAGGTGTGTCTGCCCTT 59.741 50.000 0.00 0.00 40.27 3.95
165 166 1.493022 ACAAAGGTGTGTCTGCCCTTA 59.507 47.619 0.00 0.00 37.60 2.69
166 167 2.092103 ACAAAGGTGTGTCTGCCCTTAA 60.092 45.455 0.00 0.00 37.60 1.85
167 168 2.955660 CAAAGGTGTGTCTGCCCTTAAA 59.044 45.455 0.00 0.00 37.60 1.52
168 169 2.271944 AGGTGTGTCTGCCCTTAAAC 57.728 50.000 0.00 0.00 0.00 2.01
169 170 1.774856 AGGTGTGTCTGCCCTTAAACT 59.225 47.619 0.00 0.00 0.00 2.66
170 171 2.174854 AGGTGTGTCTGCCCTTAAACTT 59.825 45.455 0.00 0.00 0.00 2.66
171 172 2.956333 GGTGTGTCTGCCCTTAAACTTT 59.044 45.455 0.00 0.00 0.00 2.66
172 173 3.243401 GGTGTGTCTGCCCTTAAACTTTG 60.243 47.826 0.00 0.00 0.00 2.77
173 174 2.955660 TGTGTCTGCCCTTAAACTTTGG 59.044 45.455 0.00 0.00 0.00 3.28
174 175 2.956333 GTGTCTGCCCTTAAACTTTGGT 59.044 45.455 0.00 0.00 0.00 3.67
175 176 2.955660 TGTCTGCCCTTAAACTTTGGTG 59.044 45.455 0.00 0.00 0.00 4.17
176 177 3.219281 GTCTGCCCTTAAACTTTGGTGA 58.781 45.455 0.00 0.00 0.00 4.02
177 178 3.253432 GTCTGCCCTTAAACTTTGGTGAG 59.747 47.826 0.00 0.00 0.00 3.51
178 179 3.137544 TCTGCCCTTAAACTTTGGTGAGA 59.862 43.478 0.00 0.00 0.00 3.27
179 180 3.888930 CTGCCCTTAAACTTTGGTGAGAA 59.111 43.478 0.00 0.00 0.00 2.87
180 181 4.479158 TGCCCTTAAACTTTGGTGAGAAT 58.521 39.130 0.00 0.00 0.00 2.40
181 182 5.636123 TGCCCTTAAACTTTGGTGAGAATA 58.364 37.500 0.00 0.00 0.00 1.75
182 183 6.071984 TGCCCTTAAACTTTGGTGAGAATAA 58.928 36.000 0.00 0.00 0.00 1.40
183 184 6.015772 TGCCCTTAAACTTTGGTGAGAATAAC 60.016 38.462 0.00 0.00 0.00 1.89
184 185 6.571731 GCCCTTAAACTTTGGTGAGAATAACC 60.572 42.308 0.00 0.00 41.50 2.85
185 186 6.349033 CCCTTAAACTTTGGTGAGAATAACCG 60.349 42.308 0.00 0.00 45.55 4.44
186 187 6.349033 CCTTAAACTTTGGTGAGAATAACCGG 60.349 42.308 0.00 0.00 45.55 5.28
187 188 4.360951 AACTTTGGTGAGAATAACCGGA 57.639 40.909 9.46 0.00 45.55 5.14
188 189 4.569719 ACTTTGGTGAGAATAACCGGAT 57.430 40.909 9.46 0.00 45.55 4.18
189 190 5.687166 ACTTTGGTGAGAATAACCGGATA 57.313 39.130 9.46 0.00 45.55 2.59
190 191 6.248569 ACTTTGGTGAGAATAACCGGATAT 57.751 37.500 9.46 2.37 45.55 1.63
191 192 6.659824 ACTTTGGTGAGAATAACCGGATATT 58.340 36.000 16.13 16.13 45.55 1.28
192 193 7.116736 ACTTTGGTGAGAATAACCGGATATTT 58.883 34.615 17.09 8.24 45.55 1.40
193 194 8.269317 ACTTTGGTGAGAATAACCGGATATTTA 58.731 33.333 17.09 1.61 45.55 1.40
194 195 9.116067 CTTTGGTGAGAATAACCGGATATTTAA 57.884 33.333 17.09 4.87 45.55 1.52
195 196 9.635404 TTTGGTGAGAATAACCGGATATTTAAT 57.365 29.630 17.09 7.71 45.55 1.40
197 198 9.715121 TGGTGAGAATAACCGGATATTTAATAC 57.285 33.333 17.09 13.24 45.55 1.89
198 199 9.939802 GGTGAGAATAACCGGATATTTAATACT 57.060 33.333 17.09 9.74 22.58 2.12
201 202 9.597170 GAGAATAACCGGATATTTAATACTCCC 57.403 37.037 17.09 2.86 0.00 4.30
202 203 9.335211 AGAATAACCGGATATTTAATACTCCCT 57.665 33.333 17.09 4.91 0.00 4.20
203 204 9.597170 GAATAACCGGATATTTAATACTCCCTC 57.403 37.037 17.09 0.00 0.00 4.30
204 205 6.370186 AACCGGATATTTAATACTCCCTCC 57.630 41.667 9.46 1.60 0.00 4.30
205 206 4.465305 ACCGGATATTTAATACTCCCTCCG 59.535 45.833 9.46 13.80 42.97 4.63
206 207 4.465305 CCGGATATTTAATACTCCCTCCGT 59.535 45.833 17.30 0.00 42.06 4.69
207 208 5.046807 CCGGATATTTAATACTCCCTCCGTT 60.047 44.000 17.30 0.00 42.06 4.44
208 209 6.098017 CGGATATTTAATACTCCCTCCGTTC 58.902 44.000 12.96 0.00 39.53 3.95
209 210 6.404708 GGATATTTAATACTCCCTCCGTTCC 58.595 44.000 0.00 0.00 0.00 3.62
210 211 6.013984 GGATATTTAATACTCCCTCCGTTCCA 60.014 42.308 0.00 0.00 0.00 3.53
211 212 5.703730 ATTTAATACTCCCTCCGTTCCAA 57.296 39.130 0.00 0.00 0.00 3.53
212 213 5.502089 TTTAATACTCCCTCCGTTCCAAA 57.498 39.130 0.00 0.00 0.00 3.28
213 214 5.703730 TTAATACTCCCTCCGTTCCAAAT 57.296 39.130 0.00 0.00 0.00 2.32
214 215 3.560636 ATACTCCCTCCGTTCCAAATG 57.439 47.619 0.00 0.00 0.00 2.32
215 216 1.358152 ACTCCCTCCGTTCCAAATGA 58.642 50.000 0.00 0.00 0.00 2.57
216 217 1.279271 ACTCCCTCCGTTCCAAATGAG 59.721 52.381 0.00 0.00 0.00 2.90
217 218 1.279271 CTCCCTCCGTTCCAAATGAGT 59.721 52.381 0.00 0.00 0.00 3.41
218 219 1.702957 TCCCTCCGTTCCAAATGAGTT 59.297 47.619 0.00 0.00 0.00 3.01
219 220 1.812571 CCCTCCGTTCCAAATGAGTTG 59.187 52.381 0.00 0.00 36.94 3.16
220 221 2.552155 CCCTCCGTTCCAAATGAGTTGA 60.552 50.000 0.00 0.00 39.87 3.18
221 222 3.146066 CCTCCGTTCCAAATGAGTTGAA 58.854 45.455 0.00 0.00 39.87 2.69
222 223 3.758554 CCTCCGTTCCAAATGAGTTGAAT 59.241 43.478 0.00 0.00 39.87 2.57
223 224 4.218417 CCTCCGTTCCAAATGAGTTGAATT 59.782 41.667 0.00 0.00 39.87 2.17
224 225 5.414454 CCTCCGTTCCAAATGAGTTGAATTA 59.586 40.000 0.00 0.00 39.87 1.40
225 226 6.403636 CCTCCGTTCCAAATGAGTTGAATTAG 60.404 42.308 0.00 0.00 39.87 1.73
226 227 6.234920 TCCGTTCCAAATGAGTTGAATTAGA 58.765 36.000 0.00 0.00 39.87 2.10
227 228 6.884295 TCCGTTCCAAATGAGTTGAATTAGAT 59.116 34.615 0.00 0.00 39.87 1.98
228 229 7.393234 TCCGTTCCAAATGAGTTGAATTAGATT 59.607 33.333 0.00 0.00 39.87 2.40
229 230 8.028938 CCGTTCCAAATGAGTTGAATTAGATTT 58.971 33.333 0.00 0.00 39.87 2.17
230 231 8.853345 CGTTCCAAATGAGTTGAATTAGATTTG 58.147 33.333 0.00 0.00 39.87 2.32
231 232 9.696917 GTTCCAAATGAGTTGAATTAGATTTGT 57.303 29.630 0.00 0.00 39.87 2.83
232 233 9.912634 TTCCAAATGAGTTGAATTAGATTTGTC 57.087 29.630 0.00 0.00 39.87 3.18
233 234 9.300681 TCCAAATGAGTTGAATTAGATTTGTCT 57.699 29.630 0.00 0.00 39.87 3.41
264 265 9.383519 ACCAATGTATCTAGACACATTTTAGTG 57.616 33.333 23.60 14.31 42.09 2.74
278 279 8.420374 CACATTTTAGTGTTAGATACATCCGT 57.580 34.615 0.00 0.00 39.39 4.69
279 280 9.524106 CACATTTTAGTGTTAGATACATCCGTA 57.476 33.333 0.00 0.00 39.39 4.02
322 323 8.053026 ACTGATGTATCTAGACACGTTTTAGT 57.947 34.615 0.00 1.03 30.52 2.24
323 324 7.968956 ACTGATGTATCTAGACACGTTTTAGTG 59.031 37.037 0.00 0.00 46.83 2.74
335 336 6.310020 CACGTTTTAGTGTTAGATACGTCC 57.690 41.667 0.00 0.00 38.52 4.79
336 337 5.858049 CACGTTTTAGTGTTAGATACGTCCA 59.142 40.000 0.00 0.00 38.52 4.02
337 338 6.529125 CACGTTTTAGTGTTAGATACGTCCAT 59.471 38.462 0.00 0.00 38.52 3.41
338 339 7.697710 CACGTTTTAGTGTTAGATACGTCCATA 59.302 37.037 0.00 0.00 38.52 2.74
339 340 8.408601 ACGTTTTAGTGTTAGATACGTCCATAT 58.591 33.333 0.00 0.00 36.14 1.78
340 341 8.899776 CGTTTTAGTGTTAGATACGTCCATATC 58.100 37.037 0.00 0.00 32.55 1.63
341 342 9.962783 GTTTTAGTGTTAGATACGTCCATATCT 57.037 33.333 0.00 0.00 43.08 1.98
345 346 8.550710 AGTGTTAGATACGTCCATATCTAGAC 57.449 38.462 0.00 0.75 42.43 2.59
346 347 8.155510 AGTGTTAGATACGTCCATATCTAGACA 58.844 37.037 0.00 4.50 42.43 3.41
347 348 8.781196 GTGTTAGATACGTCCATATCTAGACAA 58.219 37.037 15.13 0.00 42.43 3.18
348 349 9.346005 TGTTAGATACGTCCATATCTAGACAAA 57.654 33.333 0.00 0.00 42.43 2.83
351 352 8.871629 AGATACGTCCATATCTAGACAAATCT 57.128 34.615 0.00 0.00 39.63 2.40
352 353 9.961264 AGATACGTCCATATCTAGACAAATCTA 57.039 33.333 0.00 0.00 39.63 1.98
355 356 7.887381 ACGTCCATATCTAGACAAATCTAAGG 58.113 38.462 0.00 0.00 36.98 2.69
356 357 6.809196 CGTCCATATCTAGACAAATCTAAGGC 59.191 42.308 0.00 0.00 36.98 4.35
357 358 7.523873 CGTCCATATCTAGACAAATCTAAGGCA 60.524 40.741 0.00 0.00 36.98 4.75
358 359 8.150945 GTCCATATCTAGACAAATCTAAGGCAA 58.849 37.037 0.00 0.00 36.98 4.52
359 360 8.150945 TCCATATCTAGACAAATCTAAGGCAAC 58.849 37.037 0.00 0.00 36.98 4.17
360 361 8.153550 CCATATCTAGACAAATCTAAGGCAACT 58.846 37.037 0.00 0.00 43.01 3.16
365 366 9.959721 TCTAGACAAATCTAAGGCAACTAATTT 57.040 29.630 0.00 0.00 41.07 1.82
366 367 9.994432 CTAGACAAATCTAAGGCAACTAATTTG 57.006 33.333 9.96 9.96 46.28 2.32
367 368 9.733556 TAGACAAATCTAAGGCAACTAATTTGA 57.266 29.630 15.57 0.00 45.10 2.69
379 380 8.856490 GGCAACTAATTTGACATCGAAATAAT 57.144 30.769 0.00 0.00 43.70 1.28
380 381 9.944663 GGCAACTAATTTGACATCGAAATAATA 57.055 29.630 0.00 0.00 43.70 0.98
391 392 9.378551 TGACATCGAAATAATATATGCCTAACC 57.621 33.333 0.00 0.00 0.00 2.85
392 393 9.378551 GACATCGAAATAATATATGCCTAACCA 57.621 33.333 0.00 0.00 0.00 3.67
393 394 9.162764 ACATCGAAATAATATATGCCTAACCAC 57.837 33.333 0.00 0.00 0.00 4.16
394 395 9.161629 CATCGAAATAATATATGCCTAACCACA 57.838 33.333 0.00 0.00 0.00 4.17
395 396 9.905713 ATCGAAATAATATATGCCTAACCACAT 57.094 29.630 0.00 0.00 0.00 3.21
405 406 6.686484 ATGCCTAACCACATATCATACTGA 57.314 37.500 0.00 0.00 0.00 3.41
406 407 6.493189 TGCCTAACCACATATCATACTGAA 57.507 37.500 0.00 0.00 0.00 3.02
407 408 6.524734 TGCCTAACCACATATCATACTGAAG 58.475 40.000 0.00 0.00 0.00 3.02
408 409 5.934625 GCCTAACCACATATCATACTGAAGG 59.065 44.000 0.00 0.00 0.00 3.46
409 410 6.464465 GCCTAACCACATATCATACTGAAGGT 60.464 42.308 0.00 0.00 0.00 3.50
410 411 7.256190 GCCTAACCACATATCATACTGAAGGTA 60.256 40.741 0.00 0.00 34.62 3.08
411 412 8.647796 CCTAACCACATATCATACTGAAGGTAA 58.352 37.037 0.00 0.00 33.74 2.85
414 415 9.920946 AACCACATATCATACTGAAGGTAAATT 57.079 29.630 0.00 0.00 33.74 1.82
415 416 9.920946 ACCACATATCATACTGAAGGTAAATTT 57.079 29.630 0.00 0.00 33.74 1.82
422 423 8.268850 TCATACTGAAGGTAAATTTTCTCTGC 57.731 34.615 0.00 0.00 33.74 4.26
423 424 5.613358 ACTGAAGGTAAATTTTCTCTGCG 57.387 39.130 0.00 0.00 0.00 5.18
424 425 4.083271 ACTGAAGGTAAATTTTCTCTGCGC 60.083 41.667 0.00 0.00 0.00 6.09
425 426 4.072131 TGAAGGTAAATTTTCTCTGCGCT 58.928 39.130 9.73 0.00 0.00 5.92
426 427 4.518970 TGAAGGTAAATTTTCTCTGCGCTT 59.481 37.500 9.73 0.00 0.00 4.68
427 428 5.703592 TGAAGGTAAATTTTCTCTGCGCTTA 59.296 36.000 9.73 0.00 0.00 3.09
428 429 6.374333 TGAAGGTAAATTTTCTCTGCGCTTAT 59.626 34.615 9.73 0.00 0.00 1.73
429 430 6.759497 AGGTAAATTTTCTCTGCGCTTATT 57.241 33.333 9.73 0.00 0.00 1.40
430 431 7.158099 AGGTAAATTTTCTCTGCGCTTATTT 57.842 32.000 9.73 6.55 0.00 1.40
431 432 8.276252 AGGTAAATTTTCTCTGCGCTTATTTA 57.724 30.769 9.73 5.65 0.00 1.40
432 433 8.736244 AGGTAAATTTTCTCTGCGCTTATTTAA 58.264 29.630 9.73 0.00 0.00 1.52
433 434 9.349145 GGTAAATTTTCTCTGCGCTTATTTAAA 57.651 29.630 9.73 2.83 0.00 1.52
436 437 9.476202 AAATTTTCTCTGCGCTTATTTAAACTT 57.524 25.926 9.73 0.23 0.00 2.66
437 438 8.675040 ATTTTCTCTGCGCTTATTTAAACTTC 57.325 30.769 9.73 0.00 0.00 3.01
438 439 6.795098 TTCTCTGCGCTTATTTAAACTTCA 57.205 33.333 9.73 0.00 0.00 3.02
439 440 6.985188 TCTCTGCGCTTATTTAAACTTCAT 57.015 33.333 9.73 0.00 0.00 2.57
440 441 6.775088 TCTCTGCGCTTATTTAAACTTCATG 58.225 36.000 9.73 0.00 0.00 3.07
441 442 6.371548 TCTCTGCGCTTATTTAAACTTCATGT 59.628 34.615 9.73 0.00 0.00 3.21
442 443 6.908825 TCTGCGCTTATTTAAACTTCATGTT 58.091 32.000 9.73 0.00 41.29 2.71
496 497 6.222389 TCATGTTTGAAAGCTGGTAAAATGG 58.778 36.000 0.00 0.00 0.00 3.16
504 505 7.734942 TGAAAGCTGGTAAAATGGAGAAAAAT 58.265 30.769 0.00 0.00 0.00 1.82
505 506 7.872483 TGAAAGCTGGTAAAATGGAGAAAAATC 59.128 33.333 0.00 0.00 0.00 2.17
511 512 9.573133 CTGGTAAAATGGAGAAAAATCATACAC 57.427 33.333 0.00 0.00 0.00 2.90
603 605 8.378172 TGATATCAACCCATCGAACTAAAATC 57.622 34.615 1.98 0.00 0.00 2.17
615 617 2.622436 ACTAAAATCGAGTGAGCCAGC 58.378 47.619 0.00 0.00 0.00 4.85
634 636 1.468520 GCGTTGGCTCAAAATCAGCTA 59.531 47.619 0.00 0.00 37.05 3.32
635 637 2.095263 GCGTTGGCTCAAAATCAGCTAA 60.095 45.455 0.00 0.00 35.21 3.09
646 648 7.165483 GCTCAAAATCAGCTAATTTCTCAATCG 59.835 37.037 0.00 0.00 33.75 3.34
651 653 5.111989 TCAGCTAATTTCTCAATCGACCTG 58.888 41.667 0.00 0.00 0.00 4.00
669 671 8.786826 TCGACCTGAATAAAATGTTCATACTT 57.213 30.769 0.00 0.00 35.26 2.24
719 730 4.446385 TCGAACCAAAATACAACGTCTGAG 59.554 41.667 0.00 0.00 0.00 3.35
723 734 3.120199 CCAAAATACAACGTCTGAGCCTG 60.120 47.826 0.00 0.00 0.00 4.85
726 737 0.888619 TACAACGTCTGAGCCTGGAG 59.111 55.000 0.00 0.00 0.00 3.86
754 777 2.603473 AGCCTATCGCGCCCCATA 60.603 61.111 0.00 0.00 44.76 2.74
755 778 2.434359 GCCTATCGCGCCCCATAC 60.434 66.667 0.00 0.00 0.00 2.39
777 800 1.098712 AACCGAGCCGAGCAACAAAA 61.099 50.000 0.00 0.00 0.00 2.44
825 848 1.516169 CAGCCGCGCCCATAAAAAC 60.516 57.895 0.00 0.00 0.00 2.43
838 861 4.101741 CCCATAAAAACTGAAACCCACCAA 59.898 41.667 0.00 0.00 0.00 3.67
847 877 1.686587 GAAACCCACCAAACCTCCTTG 59.313 52.381 0.00 0.00 0.00 3.61
1536 1580 2.810012 CGACGATGACGAGCTCCGA 61.810 63.158 14.91 0.00 42.66 4.55
1674 1718 0.307146 GAGATCTTCGACGGGTACGG 59.693 60.000 0.00 0.00 46.48 4.02
1740 1784 1.446907 GTGATGTGGCTCTGGACTTG 58.553 55.000 0.00 0.00 0.00 3.16
1804 1848 0.604073 TTGTGGCGTTGTAGATCGGA 59.396 50.000 0.00 0.00 0.00 4.55
2044 2088 5.793457 GGTTTATTTTTGTCCACTCGAATCG 59.207 40.000 0.00 0.00 0.00 3.34
2074 2118 8.630917 TGGTATTTCGGTTTTGTTTCTTTATCA 58.369 29.630 0.00 0.00 0.00 2.15
2101 2145 7.461807 CGTGATATCACACAATTGCATTTTGTC 60.462 37.037 30.15 2.55 46.75 3.18
2106 2150 3.122297 CACAATTGCATTTTGTCGTGGT 58.878 40.909 5.05 0.00 35.18 4.16
2107 2151 4.202060 ACACAATTGCATTTTGTCGTGGTA 60.202 37.500 5.05 0.00 35.18 3.25
2177 2221 9.710900 TCTAATCGTAATTGATATGCTGTTCAT 57.289 29.630 0.00 0.00 39.17 2.57
2221 2265 7.814264 AGAGAATTTCAGAGTTCATTGTGTT 57.186 32.000 0.00 0.00 0.00 3.32
2247 2291 2.251409 ATGATCCCACGCAGAATCTG 57.749 50.000 5.78 5.78 34.12 2.90
2280 2325 8.546597 TTTCGAATTCAGAGTTCATTATGTCA 57.453 30.769 6.22 0.00 0.00 3.58
2281 2326 8.722480 TTCGAATTCAGAGTTCATTATGTCAT 57.278 30.769 6.22 0.00 0.00 3.06
2282 2327 9.816354 TTCGAATTCAGAGTTCATTATGTCATA 57.184 29.630 6.22 0.00 0.00 2.15
2349 2398 0.316196 GCATTGCCGCTTATGTCGTC 60.316 55.000 0.00 0.00 0.00 4.20
2434 2484 9.483489 TTCTAGTGTATGGTCTTATTAGGTGAA 57.517 33.333 0.00 0.00 0.00 3.18
2445 2741 9.722184 GGTCTTATTAGGTGAACTTTTCTTAGT 57.278 33.333 0.00 0.00 0.00 2.24
2618 2918 9.937175 GTCTTATCCAGCAAAATAGATAAACAC 57.063 33.333 0.00 0.00 32.40 3.32
2641 2941 4.099266 CCACCAACTTCTTTGAACCATTCA 59.901 41.667 0.00 0.00 37.39 2.57
2672 2972 9.268268 TGTTTTTCTCTTTATGTGTCGATACTT 57.732 29.630 13.73 9.69 0.00 2.24
2710 3010 6.545504 CATACACTGCTGAAAACTGTAGTT 57.454 37.500 0.00 0.00 40.50 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.507249 CGAGAGAGAACAGGTCAAAATTATTTT 58.493 33.333 0.00 0.00 0.00 1.82
11 12 7.878127 TCGAGAGAGAACAGGTCAAAATTATTT 59.122 33.333 0.00 0.00 34.84 1.40
12 13 7.386851 TCGAGAGAGAACAGGTCAAAATTATT 58.613 34.615 0.00 0.00 34.84 1.40
13 14 6.936279 TCGAGAGAGAACAGGTCAAAATTAT 58.064 36.000 0.00 0.00 34.84 1.28
14 15 6.340962 TCGAGAGAGAACAGGTCAAAATTA 57.659 37.500 0.00 0.00 34.84 1.40
15 16 5.215252 TCGAGAGAGAACAGGTCAAAATT 57.785 39.130 0.00 0.00 34.84 1.82
16 17 4.873746 TCGAGAGAGAACAGGTCAAAAT 57.126 40.909 0.00 0.00 34.84 1.82
30 31 7.921787 GTGAATATTAGTCTTCACTCGAGAGA 58.078 38.462 21.68 14.84 44.94 3.10
39 40 8.774546 AGAGATGGAGTGAATATTAGTCTTCA 57.225 34.615 0.00 0.00 0.00 3.02
44 45 9.717942 GCAATTAGAGATGGAGTGAATATTAGT 57.282 33.333 0.00 0.00 0.00 2.24
45 46 9.941325 AGCAATTAGAGATGGAGTGAATATTAG 57.059 33.333 0.00 0.00 0.00 1.73
47 48 9.638176 AAAGCAATTAGAGATGGAGTGAATATT 57.362 29.630 0.00 0.00 0.00 1.28
48 49 9.638176 AAAAGCAATTAGAGATGGAGTGAATAT 57.362 29.630 0.00 0.00 0.00 1.28
49 50 9.113838 GAAAAGCAATTAGAGATGGAGTGAATA 57.886 33.333 0.00 0.00 0.00 1.75
50 51 7.833183 AGAAAAGCAATTAGAGATGGAGTGAAT 59.167 33.333 0.00 0.00 0.00 2.57
51 52 7.170965 AGAAAAGCAATTAGAGATGGAGTGAA 58.829 34.615 0.00 0.00 0.00 3.18
52 53 6.715280 AGAAAAGCAATTAGAGATGGAGTGA 58.285 36.000 0.00 0.00 0.00 3.41
53 54 6.998968 AGAAAAGCAATTAGAGATGGAGTG 57.001 37.500 0.00 0.00 0.00 3.51
54 55 8.543774 TCTAAGAAAAGCAATTAGAGATGGAGT 58.456 33.333 0.00 0.00 32.11 3.85
55 56 8.954950 TCTAAGAAAAGCAATTAGAGATGGAG 57.045 34.615 0.00 0.00 32.11 3.86
56 57 9.911788 AATCTAAGAAAAGCAATTAGAGATGGA 57.088 29.630 0.00 0.00 38.54 3.41
66 67 9.950496 TGTCTAGAGAAATCTAAGAAAAGCAAT 57.050 29.630 0.00 0.00 0.00 3.56
67 68 9.429359 CTGTCTAGAGAAATCTAAGAAAAGCAA 57.571 33.333 0.00 0.00 0.00 3.91
68 69 8.037758 CCTGTCTAGAGAAATCTAAGAAAAGCA 58.962 37.037 0.00 0.00 0.00 3.91
69 70 8.254508 TCCTGTCTAGAGAAATCTAAGAAAAGC 58.745 37.037 0.00 0.00 0.00 3.51
76 77 9.702253 ACACTATTCCTGTCTAGAGAAATCTAA 57.298 33.333 0.00 0.00 0.00 2.10
77 78 9.344772 GACACTATTCCTGTCTAGAGAAATCTA 57.655 37.037 0.00 0.00 35.99 1.98
78 79 8.058847 AGACACTATTCCTGTCTAGAGAAATCT 58.941 37.037 0.00 0.00 45.35 2.40
79 80 8.232913 AGACACTATTCCTGTCTAGAGAAATC 57.767 38.462 0.00 0.00 45.35 2.17
87 88 6.424032 TCTTGCTAGACACTATTCCTGTCTA 58.576 40.000 7.79 7.79 45.35 2.59
89 90 5.358442 TCTCTTGCTAGACACTATTCCTGTC 59.642 44.000 0.00 0.00 38.70 3.51
90 91 5.265191 TCTCTTGCTAGACACTATTCCTGT 58.735 41.667 0.00 0.00 0.00 4.00
91 92 5.843673 TCTCTTGCTAGACACTATTCCTG 57.156 43.478 0.00 0.00 0.00 3.86
92 93 6.132658 TGATCTCTTGCTAGACACTATTCCT 58.867 40.000 0.00 0.00 0.00 3.36
93 94 6.398234 TGATCTCTTGCTAGACACTATTCC 57.602 41.667 0.00 0.00 0.00 3.01
94 95 6.867816 CCATGATCTCTTGCTAGACACTATTC 59.132 42.308 0.00 0.00 0.00 1.75
95 96 6.552725 TCCATGATCTCTTGCTAGACACTATT 59.447 38.462 0.00 0.00 0.00 1.73
96 97 6.073981 TCCATGATCTCTTGCTAGACACTAT 58.926 40.000 0.00 0.00 0.00 2.12
97 98 5.449553 TCCATGATCTCTTGCTAGACACTA 58.550 41.667 0.00 0.00 0.00 2.74
98 99 4.285020 TCCATGATCTCTTGCTAGACACT 58.715 43.478 0.00 0.00 0.00 3.55
99 100 4.662468 TCCATGATCTCTTGCTAGACAC 57.338 45.455 0.00 0.00 0.00 3.67
100 101 4.897670 TCATCCATGATCTCTTGCTAGACA 59.102 41.667 0.00 0.00 0.00 3.41
101 102 5.465532 TCATCCATGATCTCTTGCTAGAC 57.534 43.478 0.00 0.00 0.00 2.59
102 103 5.601729 AGTTCATCCATGATCTCTTGCTAGA 59.398 40.000 0.00 0.00 36.56 2.43
103 104 5.856156 AGTTCATCCATGATCTCTTGCTAG 58.144 41.667 0.00 0.00 36.56 3.42
104 105 5.883685 AGTTCATCCATGATCTCTTGCTA 57.116 39.130 0.00 0.00 36.56 3.49
105 106 4.774660 AGTTCATCCATGATCTCTTGCT 57.225 40.909 0.00 0.00 36.56 3.91
106 107 4.451774 GCTAGTTCATCCATGATCTCTTGC 59.548 45.833 0.00 5.84 37.80 4.01
107 108 5.608449 TGCTAGTTCATCCATGATCTCTTG 58.392 41.667 0.00 0.90 37.80 3.02
108 109 5.883685 TGCTAGTTCATCCATGATCTCTT 57.116 39.130 0.00 0.00 37.80 2.85
109 110 5.601729 TCTTGCTAGTTCATCCATGATCTCT 59.398 40.000 0.00 0.80 37.80 3.10
110 111 5.851720 TCTTGCTAGTTCATCCATGATCTC 58.148 41.667 0.00 0.00 37.80 2.75
111 112 5.601729 TCTCTTGCTAGTTCATCCATGATCT 59.398 40.000 0.00 5.64 39.46 2.75
112 113 5.851720 TCTCTTGCTAGTTCATCCATGATC 58.148 41.667 0.00 0.00 36.56 2.92
113 114 5.883685 TCTCTTGCTAGTTCATCCATGAT 57.116 39.130 0.00 0.00 36.56 2.45
114 115 5.682234 TTCTCTTGCTAGTTCATCCATGA 57.318 39.130 0.00 0.00 34.44 3.07
115 116 6.748333 TTTTCTCTTGCTAGTTCATCCATG 57.252 37.500 0.00 0.00 0.00 3.66
137 138 4.929211 GCAGACACACCTTTGTTTCTTTTT 59.071 37.500 0.00 0.00 39.32 1.94
138 139 4.494484 GCAGACACACCTTTGTTTCTTTT 58.506 39.130 0.00 0.00 39.32 2.27
139 140 3.119137 GGCAGACACACCTTTGTTTCTTT 60.119 43.478 0.00 0.00 39.32 2.52
140 141 2.427095 GGCAGACACACCTTTGTTTCTT 59.573 45.455 0.00 0.00 39.32 2.52
141 142 2.024414 GGCAGACACACCTTTGTTTCT 58.976 47.619 0.00 0.00 42.44 2.52
142 143 1.067060 GGGCAGACACACCTTTGTTTC 59.933 52.381 0.00 0.00 31.66 2.78
143 144 1.111277 GGGCAGACACACCTTTGTTT 58.889 50.000 0.00 0.00 31.66 2.83
144 145 0.258774 AGGGCAGACACACCTTTGTT 59.741 50.000 0.00 0.00 31.66 2.83
145 146 0.258774 AAGGGCAGACACACCTTTGT 59.741 50.000 0.00 0.00 41.65 2.83
146 147 2.270352 TAAGGGCAGACACACCTTTG 57.730 50.000 0.00 0.00 41.65 2.77
147 148 2.956333 GTTTAAGGGCAGACACACCTTT 59.044 45.455 0.00 0.00 41.65 3.11
148 149 2.174854 AGTTTAAGGGCAGACACACCTT 59.825 45.455 0.00 0.00 45.90 3.50
149 150 1.774856 AGTTTAAGGGCAGACACACCT 59.225 47.619 0.00 0.00 35.78 4.00
150 151 2.271944 AGTTTAAGGGCAGACACACC 57.728 50.000 0.00 0.00 0.00 4.16
151 152 3.243401 CCAAAGTTTAAGGGCAGACACAC 60.243 47.826 0.00 0.00 0.00 3.82
152 153 2.955660 CCAAAGTTTAAGGGCAGACACA 59.044 45.455 0.00 0.00 0.00 3.72
153 154 2.956333 ACCAAAGTTTAAGGGCAGACAC 59.044 45.455 0.00 0.00 0.00 3.67
154 155 2.955660 CACCAAAGTTTAAGGGCAGACA 59.044 45.455 0.00 0.00 0.00 3.41
155 156 3.219281 TCACCAAAGTTTAAGGGCAGAC 58.781 45.455 0.00 0.00 0.00 3.51
156 157 3.137544 TCTCACCAAAGTTTAAGGGCAGA 59.862 43.478 0.00 0.00 0.00 4.26
157 158 3.486383 TCTCACCAAAGTTTAAGGGCAG 58.514 45.455 0.00 0.00 0.00 4.85
158 159 3.586470 TCTCACCAAAGTTTAAGGGCA 57.414 42.857 0.00 0.00 0.00 5.36
159 160 6.387465 GTTATTCTCACCAAAGTTTAAGGGC 58.613 40.000 0.00 0.00 0.00 5.19
160 161 6.349033 CGGTTATTCTCACCAAAGTTTAAGGG 60.349 42.308 0.00 0.00 33.36 3.95
161 162 6.349033 CCGGTTATTCTCACCAAAGTTTAAGG 60.349 42.308 0.00 0.00 33.36 2.69
162 163 6.428771 TCCGGTTATTCTCACCAAAGTTTAAG 59.571 38.462 0.00 0.00 33.36 1.85
163 164 6.297582 TCCGGTTATTCTCACCAAAGTTTAA 58.702 36.000 0.00 0.00 33.36 1.52
164 165 5.867330 TCCGGTTATTCTCACCAAAGTTTA 58.133 37.500 0.00 0.00 33.36 2.01
165 166 4.721132 TCCGGTTATTCTCACCAAAGTTT 58.279 39.130 0.00 0.00 33.36 2.66
166 167 4.360951 TCCGGTTATTCTCACCAAAGTT 57.639 40.909 0.00 0.00 33.36 2.66
167 168 4.569719 ATCCGGTTATTCTCACCAAAGT 57.430 40.909 0.00 0.00 33.36 2.66
168 169 7.568199 AAATATCCGGTTATTCTCACCAAAG 57.432 36.000 16.32 0.00 33.36 2.77
169 170 9.635404 ATTAAATATCCGGTTATTCTCACCAAA 57.365 29.630 16.32 5.50 33.36 3.28
171 172 9.715121 GTATTAAATATCCGGTTATTCTCACCA 57.285 33.333 16.32 0.90 33.36 4.17
172 173 9.939802 AGTATTAAATATCCGGTTATTCTCACC 57.060 33.333 16.32 7.01 0.00 4.02
175 176 9.597170 GGGAGTATTAAATATCCGGTTATTCTC 57.403 37.037 16.32 16.05 32.30 2.87
176 177 9.335211 AGGGAGTATTAAATATCCGGTTATTCT 57.665 33.333 16.32 9.78 32.30 2.40
177 178 9.597170 GAGGGAGTATTAAATATCCGGTTATTC 57.403 37.037 16.32 5.74 32.30 1.75
178 179 8.546322 GGAGGGAGTATTAAATATCCGGTTATT 58.454 37.037 11.30 11.30 32.30 1.40
179 180 7.147776 CGGAGGGAGTATTAAATATCCGGTTAT 60.148 40.741 0.00 0.00 43.53 1.89
180 181 6.153340 CGGAGGGAGTATTAAATATCCGGTTA 59.847 42.308 0.00 0.00 43.53 2.85
181 182 5.046807 CGGAGGGAGTATTAAATATCCGGTT 60.047 44.000 0.00 0.00 43.53 4.44
182 183 4.465305 CGGAGGGAGTATTAAATATCCGGT 59.535 45.833 0.00 0.00 43.53 5.28
183 184 5.007385 CGGAGGGAGTATTAAATATCCGG 57.993 47.826 0.00 0.00 43.53 5.14
185 186 6.013984 TGGAACGGAGGGAGTATTAAATATCC 60.014 42.308 0.00 0.00 0.00 2.59
186 187 7.001099 TGGAACGGAGGGAGTATTAAATATC 57.999 40.000 0.00 0.00 0.00 1.63
187 188 7.383156 TTGGAACGGAGGGAGTATTAAATAT 57.617 36.000 0.00 0.00 0.00 1.28
188 189 6.811634 TTGGAACGGAGGGAGTATTAAATA 57.188 37.500 0.00 0.00 0.00 1.40
189 190 5.703730 TTGGAACGGAGGGAGTATTAAAT 57.296 39.130 0.00 0.00 0.00 1.40
190 191 5.502089 TTTGGAACGGAGGGAGTATTAAA 57.498 39.130 0.00 0.00 0.00 1.52
191 192 5.190132 TCATTTGGAACGGAGGGAGTATTAA 59.810 40.000 0.00 0.00 0.00 1.40
192 193 4.717778 TCATTTGGAACGGAGGGAGTATTA 59.282 41.667 0.00 0.00 0.00 0.98
193 194 3.521937 TCATTTGGAACGGAGGGAGTATT 59.478 43.478 0.00 0.00 0.00 1.89
194 195 3.112263 TCATTTGGAACGGAGGGAGTAT 58.888 45.455 0.00 0.00 0.00 2.12
195 196 2.500098 CTCATTTGGAACGGAGGGAGTA 59.500 50.000 0.00 0.00 0.00 2.59
196 197 1.279271 CTCATTTGGAACGGAGGGAGT 59.721 52.381 0.00 0.00 0.00 3.85
197 198 1.279271 ACTCATTTGGAACGGAGGGAG 59.721 52.381 0.00 0.00 0.00 4.30
198 199 1.358152 ACTCATTTGGAACGGAGGGA 58.642 50.000 0.00 0.00 0.00 4.20
199 200 1.812571 CAACTCATTTGGAACGGAGGG 59.187 52.381 0.00 0.00 0.00 4.30
200 201 2.778299 TCAACTCATTTGGAACGGAGG 58.222 47.619 0.00 0.00 35.69 4.30
201 202 5.376854 AATTCAACTCATTTGGAACGGAG 57.623 39.130 0.00 0.00 35.69 4.63
202 203 6.234920 TCTAATTCAACTCATTTGGAACGGA 58.765 36.000 0.00 0.00 35.69 4.69
203 204 6.494893 TCTAATTCAACTCATTTGGAACGG 57.505 37.500 0.00 0.00 35.69 4.44
204 205 8.853345 CAAATCTAATTCAACTCATTTGGAACG 58.147 33.333 0.00 0.00 35.69 3.95
205 206 9.696917 ACAAATCTAATTCAACTCATTTGGAAC 57.303 29.630 0.00 0.00 36.14 3.62
206 207 9.912634 GACAAATCTAATTCAACTCATTTGGAA 57.087 29.630 0.00 0.00 36.14 3.53
207 208 9.300681 AGACAAATCTAATTCAACTCATTTGGA 57.699 29.630 0.00 0.00 36.14 3.53
253 254 8.420374 ACGGATGTATCTAACACTAAAATGTG 57.580 34.615 0.00 0.00 42.09 3.21
269 270 9.961264 TCTAGATTTGTCTAGATACGGATGTAT 57.039 33.333 10.30 0.00 42.49 2.29
296 297 9.170734 ACTAAAACGTGTCTAGATACATCAGTA 57.829 33.333 18.39 4.32 34.10 2.74
297 298 7.968956 CACTAAAACGTGTCTAGATACATCAGT 59.031 37.037 18.39 10.62 0.00 3.41
298 299 7.968956 ACACTAAAACGTGTCTAGATACATCAG 59.031 37.037 18.39 10.10 44.32 2.90
299 300 7.823665 ACACTAAAACGTGTCTAGATACATCA 58.176 34.615 18.39 0.00 44.32 3.07
300 301 8.684973 AACACTAAAACGTGTCTAGATACATC 57.315 34.615 18.39 0.00 46.71 3.06
301 302 9.784680 CTAACACTAAAACGTGTCTAGATACAT 57.215 33.333 18.39 1.14 46.71 2.29
302 303 9.002600 TCTAACACTAAAACGTGTCTAGATACA 57.997 33.333 18.39 0.27 46.71 2.29
306 307 8.171196 CGTATCTAACACTAAAACGTGTCTAGA 58.829 37.037 0.00 13.18 46.71 2.43
307 308 7.959651 ACGTATCTAACACTAAAACGTGTCTAG 59.040 37.037 0.00 0.00 46.71 2.43
308 309 7.806690 ACGTATCTAACACTAAAACGTGTCTA 58.193 34.615 0.00 0.00 46.71 2.59
309 310 6.672147 ACGTATCTAACACTAAAACGTGTCT 58.328 36.000 0.00 0.00 46.71 3.41
310 311 6.032880 GGACGTATCTAACACTAAAACGTGTC 59.967 42.308 2.03 0.00 46.71 3.67
312 313 5.858049 TGGACGTATCTAACACTAAAACGTG 59.142 40.000 2.03 0.00 41.61 4.49
313 314 6.012658 TGGACGTATCTAACACTAAAACGT 57.987 37.500 0.00 0.00 43.92 3.99
314 315 8.792831 ATATGGACGTATCTAACACTAAAACG 57.207 34.615 0.00 0.00 35.17 3.60
315 316 9.962783 AGATATGGACGTATCTAACACTAAAAC 57.037 33.333 11.36 0.00 39.13 2.43
319 320 9.650539 GTCTAGATATGGACGTATCTAACACTA 57.349 37.037 17.43 2.56 41.00 2.74
320 321 8.155510 TGTCTAGATATGGACGTATCTAACACT 58.844 37.037 17.43 0.49 41.00 3.55
321 322 8.320396 TGTCTAGATATGGACGTATCTAACAC 57.680 38.462 17.43 16.35 41.00 3.32
322 323 8.913487 TTGTCTAGATATGGACGTATCTAACA 57.087 34.615 17.43 18.42 41.00 2.41
325 326 9.961264 AGATTTGTCTAGATATGGACGTATCTA 57.039 33.333 16.39 16.39 40.79 1.98
326 327 8.871629 AGATTTGTCTAGATATGGACGTATCT 57.128 34.615 15.98 15.98 42.50 1.98
329 330 9.011095 CCTTAGATTTGTCTAGATATGGACGTA 57.989 37.037 0.00 0.00 35.45 3.57
330 331 7.524038 GCCTTAGATTTGTCTAGATATGGACGT 60.524 40.741 0.00 0.00 35.45 4.34
331 332 6.809196 GCCTTAGATTTGTCTAGATATGGACG 59.191 42.308 0.00 0.00 35.45 4.79
332 333 7.671302 TGCCTTAGATTTGTCTAGATATGGAC 58.329 38.462 0.00 0.00 0.00 4.02
333 334 7.855784 TGCCTTAGATTTGTCTAGATATGGA 57.144 36.000 0.00 0.00 0.00 3.41
334 335 8.153550 AGTTGCCTTAGATTTGTCTAGATATGG 58.846 37.037 0.00 0.00 0.00 2.74
339 340 9.959721 AAATTAGTTGCCTTAGATTTGTCTAGA 57.040 29.630 0.00 0.00 0.00 2.43
340 341 9.994432 CAAATTAGTTGCCTTAGATTTGTCTAG 57.006 33.333 0.00 0.00 32.62 2.43
341 342 9.733556 TCAAATTAGTTGCCTTAGATTTGTCTA 57.266 29.630 0.00 0.00 37.13 2.59
342 343 8.515414 GTCAAATTAGTTGCCTTAGATTTGTCT 58.485 33.333 0.00 0.00 37.13 3.41
343 344 8.296713 TGTCAAATTAGTTGCCTTAGATTTGTC 58.703 33.333 0.00 0.00 37.13 3.18
344 345 8.177119 TGTCAAATTAGTTGCCTTAGATTTGT 57.823 30.769 0.00 0.00 37.13 2.83
345 346 9.294030 GATGTCAAATTAGTTGCCTTAGATTTG 57.706 33.333 0.00 0.00 37.13 2.32
346 347 8.184192 CGATGTCAAATTAGTTGCCTTAGATTT 58.816 33.333 0.00 0.00 37.13 2.17
347 348 7.552687 TCGATGTCAAATTAGTTGCCTTAGATT 59.447 33.333 0.00 0.00 37.13 2.40
348 349 7.047891 TCGATGTCAAATTAGTTGCCTTAGAT 58.952 34.615 0.00 0.00 37.13 1.98
349 350 6.403049 TCGATGTCAAATTAGTTGCCTTAGA 58.597 36.000 0.00 0.00 37.13 2.10
350 351 6.662414 TCGATGTCAAATTAGTTGCCTTAG 57.338 37.500 0.00 0.00 37.13 2.18
351 352 7.441890 TTTCGATGTCAAATTAGTTGCCTTA 57.558 32.000 0.00 0.00 37.13 2.69
352 353 5.957842 TTCGATGTCAAATTAGTTGCCTT 57.042 34.783 0.00 0.00 37.13 4.35
353 354 5.957842 TTTCGATGTCAAATTAGTTGCCT 57.042 34.783 0.00 0.00 37.13 4.75
354 355 8.856490 ATTATTTCGATGTCAAATTAGTTGCC 57.144 30.769 0.00 0.00 37.13 4.52
365 366 9.378551 GGTTAGGCATATATTATTTCGATGTCA 57.621 33.333 0.00 0.00 0.00 3.58
366 367 9.378551 TGGTTAGGCATATATTATTTCGATGTC 57.621 33.333 0.00 0.00 0.00 3.06
367 368 9.162764 GTGGTTAGGCATATATTATTTCGATGT 57.837 33.333 0.00 0.00 0.00 3.06
368 369 9.161629 TGTGGTTAGGCATATATTATTTCGATG 57.838 33.333 0.00 0.00 0.00 3.84
369 370 9.905713 ATGTGGTTAGGCATATATTATTTCGAT 57.094 29.630 0.00 0.00 0.00 3.59
379 380 9.487442 TCAGTATGATATGTGGTTAGGCATATA 57.513 33.333 0.00 0.00 42.56 0.86
380 381 8.379428 TCAGTATGATATGTGGTTAGGCATAT 57.621 34.615 0.00 0.00 42.56 1.78
381 382 7.790782 TCAGTATGATATGTGGTTAGGCATA 57.209 36.000 0.00 0.00 42.56 3.14
382 383 6.686484 TCAGTATGATATGTGGTTAGGCAT 57.314 37.500 0.00 0.00 42.56 4.40
398 399 7.182761 CGCAGAGAAAATTTACCTTCAGTATG 58.817 38.462 0.00 0.00 37.54 2.39
399 400 6.183360 GCGCAGAGAAAATTTACCTTCAGTAT 60.183 38.462 0.30 0.00 0.00 2.12
400 401 5.121768 GCGCAGAGAAAATTTACCTTCAGTA 59.878 40.000 0.30 0.00 0.00 2.74
401 402 4.083271 GCGCAGAGAAAATTTACCTTCAGT 60.083 41.667 0.30 0.00 0.00 3.41
402 403 4.154918 AGCGCAGAGAAAATTTACCTTCAG 59.845 41.667 11.47 0.00 0.00 3.02
403 404 4.072131 AGCGCAGAGAAAATTTACCTTCA 58.928 39.130 11.47 0.00 0.00 3.02
404 405 4.686839 AGCGCAGAGAAAATTTACCTTC 57.313 40.909 11.47 0.00 0.00 3.46
405 406 6.759497 ATAAGCGCAGAGAAAATTTACCTT 57.241 33.333 11.47 0.00 0.00 3.50
406 407 6.759497 AATAAGCGCAGAGAAAATTTACCT 57.241 33.333 11.47 0.00 0.00 3.08
407 408 8.905103 TTAAATAAGCGCAGAGAAAATTTACC 57.095 30.769 11.47 0.00 0.00 2.85
410 411 9.476202 AAGTTTAAATAAGCGCAGAGAAAATTT 57.524 25.926 11.47 6.95 0.00 1.82
411 412 9.129209 GAAGTTTAAATAAGCGCAGAGAAAATT 57.871 29.630 11.47 7.50 0.00 1.82
412 413 8.296713 TGAAGTTTAAATAAGCGCAGAGAAAAT 58.703 29.630 11.47 0.00 0.00 1.82
413 414 7.644490 TGAAGTTTAAATAAGCGCAGAGAAAA 58.356 30.769 11.47 0.00 0.00 2.29
414 415 7.197071 TGAAGTTTAAATAAGCGCAGAGAAA 57.803 32.000 11.47 0.00 0.00 2.52
415 416 6.795098 TGAAGTTTAAATAAGCGCAGAGAA 57.205 33.333 11.47 0.00 0.00 2.87
416 417 6.371548 ACATGAAGTTTAAATAAGCGCAGAGA 59.628 34.615 11.47 0.00 0.00 3.10
417 418 6.546395 ACATGAAGTTTAAATAAGCGCAGAG 58.454 36.000 11.47 0.00 0.00 3.35
418 419 6.494893 ACATGAAGTTTAAATAAGCGCAGA 57.505 33.333 11.47 0.00 0.00 4.26
485 486 9.573133 GTGTATGATTTTTCTCCATTTTACCAG 57.427 33.333 0.00 0.00 0.00 4.00
486 487 8.240682 CGTGTATGATTTTTCTCCATTTTACCA 58.759 33.333 0.00 0.00 0.00 3.25
488 489 9.274065 GTCGTGTATGATTTTTCTCCATTTTAC 57.726 33.333 0.00 0.00 0.00 2.01
589 590 4.026475 GGCTCACTCGATTTTAGTTCGATG 60.026 45.833 0.00 0.00 43.93 3.84
592 593 3.250744 TGGCTCACTCGATTTTAGTTCG 58.749 45.455 0.00 0.00 37.94 3.95
593 594 3.062774 GCTGGCTCACTCGATTTTAGTTC 59.937 47.826 0.00 0.00 0.00 3.01
594 595 3.003480 GCTGGCTCACTCGATTTTAGTT 58.997 45.455 0.00 0.00 0.00 2.24
596 597 1.590238 CGCTGGCTCACTCGATTTTAG 59.410 52.381 0.00 0.00 0.00 1.85
597 598 1.067142 ACGCTGGCTCACTCGATTTTA 60.067 47.619 0.00 0.00 0.00 1.52
598 599 0.320771 ACGCTGGCTCACTCGATTTT 60.321 50.000 0.00 0.00 0.00 1.82
603 605 3.114616 CCAACGCTGGCTCACTCG 61.115 66.667 0.00 0.00 35.39 4.18
615 617 3.829886 TTAGCTGATTTTGAGCCAACG 57.170 42.857 0.00 0.00 37.12 4.10
623 625 7.430502 GGTCGATTGAGAAATTAGCTGATTTTG 59.569 37.037 16.68 0.00 29.75 2.44
634 636 9.793252 CATTTTATTCAGGTCGATTGAGAAATT 57.207 29.630 0.00 0.00 0.00 1.82
635 637 8.960591 ACATTTTATTCAGGTCGATTGAGAAAT 58.039 29.630 0.00 2.62 0.00 2.17
692 695 6.086241 CAGACGTTGTATTTTGGTTCGATTTG 59.914 38.462 0.00 0.00 0.00 2.32
695 699 4.992319 TCAGACGTTGTATTTTGGTTCGAT 59.008 37.500 0.00 0.00 0.00 3.59
719 730 2.192608 CTGCAACGAAAGCTCCAGGC 62.193 60.000 0.00 0.00 42.19 4.85
723 734 0.673644 TAGGCTGCAACGAAAGCTCC 60.674 55.000 0.50 0.00 39.46 4.70
726 737 0.026803 CGATAGGCTGCAACGAAAGC 59.973 55.000 0.50 0.00 38.76 3.51
731 743 4.285149 GCGCGATAGGCTGCAACG 62.285 66.667 12.10 2.42 39.72 4.10
754 777 0.739813 GTTGCTCGGCTCGGTTATGT 60.740 55.000 0.00 0.00 0.00 2.29
755 778 0.739462 TGTTGCTCGGCTCGGTTATG 60.739 55.000 0.00 0.00 0.00 1.90
825 848 1.133482 AGGAGGTTTGGTGGGTTTCAG 60.133 52.381 0.00 0.00 0.00 3.02
838 861 1.501654 GGGGAGAAGGCAAGGAGGTT 61.502 60.000 0.00 0.00 0.00 3.50
921 953 4.589675 GTGCGGGTGGGGGTTGAA 62.590 66.667 0.00 0.00 0.00 2.69
1494 1538 1.156736 GTTCGTCCCACTTGTCCATG 58.843 55.000 0.00 0.00 0.00 3.66
1740 1784 8.364142 ACCAATCTATGACTCTAAGCTGAATAC 58.636 37.037 0.00 0.00 0.00 1.89
1804 1848 7.017254 TGTTACCTTACTTTCTCATCTTCCCTT 59.983 37.037 0.00 0.00 0.00 3.95
1853 1897 4.384846 CACTGAGATCAAAATTGCAAGCAC 59.615 41.667 4.94 0.00 0.00 4.40
2044 2088 7.940178 AGAAACAAAACCGAAATACCATTTC 57.060 32.000 2.22 2.22 0.00 2.17
2074 2118 5.565592 AATGCAATTGTGTGATATCACGT 57.434 34.783 26.56 12.65 42.05 4.49
2127 2171 1.094785 GCACATACGGCAAGGAACAT 58.905 50.000 0.00 0.00 0.00 2.71
2132 2176 1.331756 GAGAATGCACATACGGCAAGG 59.668 52.381 0.00 0.00 45.60 3.61
2177 2221 2.254152 AGGAAGTAGGCAGACATGGA 57.746 50.000 0.00 0.00 0.00 3.41
2221 2265 3.028130 TCTGCGTGGGATCATACTGTTA 58.972 45.455 0.00 0.00 0.00 2.41
2247 2291 5.476752 ACTCTGAATTCGAAAGCATAAGC 57.523 39.130 0.00 0.00 42.56 3.09
2280 2325 7.337480 TGAGTTTGATACATTGCTTGCATAT 57.663 32.000 0.00 0.00 0.00 1.78
2281 2326 6.756299 TGAGTTTGATACATTGCTTGCATA 57.244 33.333 0.00 0.00 0.00 3.14
2282 2327 5.648178 TGAGTTTGATACATTGCTTGCAT 57.352 34.783 0.00 0.00 0.00 3.96
2317 2366 2.545532 CGGCAATGCTTTCCAACAAAGA 60.546 45.455 4.82 0.00 0.00 2.52
2349 2398 1.269051 GCACCAACCAAAGTTCTTCCG 60.269 52.381 0.00 0.00 32.45 4.30
2392 2441 9.830186 ATACACTAGAATACCTTATGACTGGAT 57.170 33.333 0.00 0.00 0.00 3.41
2483 2783 5.448632 GCCACCAATCCAAACTAGTAAATCG 60.449 44.000 0.00 0.00 0.00 3.34
2618 2918 4.099266 TGAATGGTTCAAAGAAGTTGGTGG 59.901 41.667 0.00 0.00 37.85 4.61
2641 2941 8.783093 TCGACACATAAAGAGAAAAACATCATT 58.217 29.630 0.00 0.00 0.00 2.57
2659 2959 5.755375 CAGCCAAGAATAAGTATCGACACAT 59.245 40.000 0.00 0.00 0.00 3.21
2672 2972 3.278574 GTGTATGCCACAGCCAAGAATA 58.721 45.455 0.00 0.00 43.92 1.75
2675 2975 3.248043 GTGTATGCCACAGCCAAGA 57.752 52.632 0.00 0.00 43.92 3.02


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

AutoCloner maintained by Alex Coulton.