Multiple sequence alignment - TraesCS5D01G193100

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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 TraesCS5D01G193100 chr5D 100.000 5503 0 0 817 6319 297307081 297312583 0.000000e+00 10163.0
1 TraesCS5D01G193100 chr5D 96.059 406 16 0 2806 3211 297308862 297309267 0.000000e+00 662.0
2 TraesCS5D01G193100 chr5D 96.059 406 16 0 2598 3003 297309070 297309475 0.000000e+00 662.0
3 TraesCS5D01G193100 chr5D 100.000 338 0 0 1 338 297306265 297306602 5.380000e-175 625.0
4 TraesCS5D01G193100 chr5D 94.498 309 14 2 1577 1885 297307537 297307842 2.060000e-129 473.0
5 TraesCS5D01G193100 chr5D 94.498 309 14 2 1273 1578 297307841 297308149 2.060000e-129 473.0
6 TraesCS5D01G193100 chr5D 97.475 198 5 0 3014 3211 297308862 297309059 7.850000e-89 339.0
7 TraesCS5D01G193100 chr5D 97.475 198 5 0 2598 2795 297309278 297309475 7.850000e-89 339.0
8 TraesCS5D01G193100 chr5D 83.333 114 19 0 91 204 108341849 108341962 8.660000e-19 106.0
9 TraesCS5D01G193100 chr5D 100.000 29 0 0 310 338 297306518 297306546 3.000000e-03 54.7
10 TraesCS5D01G193100 chr5D 100.000 29 0 0 254 282 297306574 297306602 3.000000e-03 54.7
11 TraesCS5D01G193100 chr5A 96.103 4722 117 17 817 5523 401763346 401758677 0.000000e+00 7638.0
12 TraesCS5D01G193100 chr5A 95.146 412 20 0 2598 3009 401761396 401760985 0.000000e+00 651.0
13 TraesCS5D01G193100 chr5A 95.567 406 18 0 2806 3211 401761604 401761199 0.000000e+00 651.0
14 TraesCS5D01G193100 chr5A 86.757 589 49 14 5729 6299 401758053 401757476 4.160000e-176 628.0
15 TraesCS5D01G193100 chr5A 92.429 317 19 3 1574 1885 401762916 401762600 1.250000e-121 448.0
16 TraesCS5D01G193100 chr5A 94.465 271 14 1 1309 1578 401762586 401762316 3.520000e-112 416.0
17 TraesCS5D01G193100 chr5A 97.980 198 4 0 3014 3211 401761604 401761407 1.690000e-90 344.0
18 TraesCS5D01G193100 chr5A 97.475 198 5 0 2598 2795 401761188 401760991 7.850000e-89 339.0
19 TraesCS5D01G193100 chr5A 91.518 224 6 3 5522 5734 401758644 401758423 4.790000e-76 296.0
20 TraesCS5D01G193100 chr5A 87.200 125 13 3 6023 6146 480631547 480631425 8.540000e-29 139.0
21 TraesCS5D01G193100 chr5A 81.818 165 29 1 48 211 607742009 607742173 3.070000e-28 137.0
22 TraesCS5D01G193100 chr5A 93.023 86 5 1 233 317 401763726 401763641 2.390000e-24 124.0
23 TraesCS5D01G193100 chr5B 95.612 2074 70 5 3454 5523 337465570 337467626 0.000000e+00 3306.0
24 TraesCS5D01G193100 chr5B 91.493 1246 61 20 1574 2795 337464285 337465509 0.000000e+00 1672.0
25 TraesCS5D01G193100 chr5B 97.120 764 19 3 817 1578 337463831 337464593 0.000000e+00 1286.0
26 TraesCS5D01G193100 chr5B 86.546 498 49 10 5809 6290 337468034 337468529 3.350000e-147 532.0
27 TraesCS5D01G193100 chr5B 95.486 288 12 1 5522 5809 337467659 337467945 5.770000e-125 459.0
28 TraesCS5D01G193100 chr5B 93.286 283 9 4 2999 3281 337465307 337465579 5.900000e-110 409.0
29 TraesCS5D01G193100 chr5B 90.141 213 11 4 2791 3003 337465307 337465509 1.040000e-67 268.0
30 TraesCS5D01G193100 chr5B 81.890 127 22 1 48 174 243408751 243408876 8.660000e-19 106.0
31 TraesCS5D01G193100 chr5B 86.667 90 2 7 233 314 337463651 337463738 2.430000e-14 91.6
32 TraesCS5D01G193100 chr3A 93.103 174 11 1 3283 3455 528529485 528529312 2.920000e-63 254.0
33 TraesCS5D01G193100 chr2B 92.179 179 13 1 3282 3459 54702719 54702541 1.050000e-62 252.0
34 TraesCS5D01G193100 chr7A 92.135 178 13 1 3282 3458 648121333 648121510 3.780000e-62 250.0
35 TraesCS5D01G193100 chr4D 91.620 179 13 2 3282 3459 218427665 218427842 4.890000e-61 246.0
36 TraesCS5D01G193100 chr4D 89.256 121 13 0 6029 6149 323605978 323606098 1.100000e-32 152.0
37 TraesCS5D01G193100 chr4A 91.620 179 14 1 3282 3459 167087994 167088172 4.890000e-61 246.0
38 TraesCS5D01G193100 chr2D 91.620 179 14 1 3282 3459 26740070 26740248 4.890000e-61 246.0
39 TraesCS5D01G193100 chr2D 91.620 179 14 1 3282 3459 502025808 502025630 4.890000e-61 246.0
40 TraesCS5D01G193100 chr4B 89.175 194 18 3 3273 3464 590434058 590433866 8.190000e-59 239.0
41 TraesCS5D01G193100 chr4B 87.603 121 15 0 6029 6149 404127564 404127684 2.380000e-29 141.0
42 TraesCS5D01G193100 chr4B 80.357 112 22 0 64 175 595465387 595465498 1.130000e-12 86.1
43 TraesCS5D01G193100 chr7D 84.579 214 28 3 1 210 538493749 538493537 2.310000e-49 207.0
44 TraesCS5D01G193100 chr7D 84.434 212 23 5 1 211 574070110 574069908 3.860000e-47 200.0
45 TraesCS5D01G193100 chr7D 79.245 212 35 5 1 211 494672210 494672413 8.540000e-29 139.0
46 TraesCS5D01G193100 chr3D 90.000 120 12 0 6029 6148 182423635 182423516 8.480000e-34 156.0
47 TraesCS5D01G193100 chr3D 87.838 74 9 0 130 203 98611077 98611150 3.140000e-13 87.9
48 TraesCS5D01G193100 chr6D 89.916 119 12 0 6029 6147 9359192 9359074 3.050000e-33 154.0
49 TraesCS5D01G193100 chr6D 79.894 189 20 7 1 174 462850533 462850348 8.600000e-24 122.0
50 TraesCS5D01G193100 chr2A 88.000 125 14 1 6026 6149 7679910 7680034 5.100000e-31 147.0
51 TraesCS5D01G193100 chr7B 80.095 211 27 5 2 211 680238543 680238347 6.600000e-30 143.0
52 TraesCS5D01G193100 chr6A 88.235 119 14 0 6029 6147 11163575 11163693 6.600000e-30 143.0
53 TraesCS5D01G193100 chr3B 79.141 163 30 4 52 211 167465119 167464958 6.700000e-20 110.0
54 TraesCS5D01G193100 chr1D 90.000 50 5 0 158 207 192364822 192364773 1.470000e-06 65.8


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 TraesCS5D01G193100 chr5D 297306265 297312583 6318 False 2724.350000 10163 100.000000 1 6319 4 chr5D.!!$F2 6318
1 TraesCS5D01G193100 chr5D 297307537 297309475 1938 False 491.333333 662 96.010667 1273 3211 6 chr5D.!!$F3 1938
2 TraesCS5D01G193100 chr5A 401757476 401763726 6250 True 1153.500000 7638 94.046300 233 6299 10 chr5A.!!$R2 6066
3 TraesCS5D01G193100 chr5B 337463651 337468529 4878 False 1002.950000 3306 92.043875 233 6290 8 chr5B.!!$F2 6057

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
207 208 0.031585 CTGTCCGTTTGAGTCGTCCA 59.968 55.000 0.00 0.0 0.00 4.02 F
329 334 0.108756 GGGAGACTAACACCGTCAGC 60.109 60.000 0.00 0.0 33.89 4.26 F
337 342 0.109412 AACACCGTCAGCGTACTAGC 60.109 55.000 0.00 0.0 36.15 3.42 F
1196 1202 0.178861 TTCTTGGCTTCTCCCCTCCT 60.179 55.000 0.00 0.0 0.00 3.69 F
1197 1203 0.618968 TCTTGGCTTCTCCCCTCCTC 60.619 60.000 0.00 0.0 0.00 3.71 F
1728 2073 0.978146 AGTGGCGAATCCTAGGCTGT 60.978 55.000 2.96 0.0 35.26 4.40 F
3417 3781 2.158475 AGAAATCACAAGGAGGTGGCAA 60.158 45.455 0.00 0.0 39.27 4.52 F
3884 4248 0.036022 ACAGGAGGCTTCTTGCTGAC 59.964 55.000 7.92 0.0 42.39 3.51 F
3941 4305 0.178990 GGAACAAGCCACCAGAACCT 60.179 55.000 0.00 0.0 0.00 3.50 F
4892 5257 1.280710 TCTGGAACACACACACTGGTT 59.719 47.619 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1185 1191 0.116541 AAGAACCGAGGAGGGGAGAA 59.883 55.000 0.00 0.00 46.96 2.87 R
1194 1200 0.391793 GAAGGAGCCAAGAACCGAGG 60.392 60.000 0.00 0.00 0.00 4.63 R
1199 1205 0.519077 CAAGCGAAGGAGCCAAGAAC 59.481 55.000 0.00 0.00 38.01 3.01 R
3216 3580 3.420576 CACCAGTGCGAAAATAACAAACG 59.579 43.478 0.00 0.00 0.00 3.60 R
3388 3752 4.768968 CCTCCTTGTGATTTCTGACCAAAT 59.231 41.667 0.00 0.00 0.00 2.32 R
3884 4248 0.538057 TTCTGCTGCCCAGGAGTTTG 60.538 55.000 15.04 0.00 45.62 2.93 R
4829 5194 0.036010 CCACCACCAGAGGCAAGTAG 60.036 60.000 0.00 0.00 0.00 2.57 R
5081 5446 0.246635 GTGCCGCCAGAGAGAGTAAA 59.753 55.000 0.00 0.00 0.00 2.01 R
5095 5460 1.067142 ACTACCATATATGCGGTGCCG 60.067 52.381 7.24 6.22 43.09 5.69 R
6290 7185 1.071385 CCCCTCTCTCCATTCAATCCG 59.929 57.143 0.00 0.00 0.00 4.18 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
23 24 6.417191 TCGGTTCAAACTATGCTATTTGAC 57.583 37.500 0.00 0.00 42.87 3.18
24 25 6.170506 TCGGTTCAAACTATGCTATTTGACT 58.829 36.000 0.00 0.00 42.87 3.41
25 26 7.324935 TCGGTTCAAACTATGCTATTTGACTA 58.675 34.615 0.00 0.00 42.87 2.59
26 27 7.985184 TCGGTTCAAACTATGCTATTTGACTAT 59.015 33.333 0.00 0.00 42.87 2.12
27 28 9.256477 CGGTTCAAACTATGCTATTTGACTATA 57.744 33.333 0.00 0.00 42.87 1.31
64 65 8.647143 AAATTCGTATCAATGCAAAAATAGGG 57.353 30.769 0.00 0.00 0.00 3.53
65 66 5.181690 TCGTATCAATGCAAAAATAGGGC 57.818 39.130 0.00 0.00 0.00 5.19
66 67 3.974401 CGTATCAATGCAAAAATAGGGCG 59.026 43.478 0.00 0.00 0.00 6.13
67 68 2.957491 TCAATGCAAAAATAGGGCGG 57.043 45.000 0.00 0.00 0.00 6.13
68 69 2.175202 TCAATGCAAAAATAGGGCGGT 58.825 42.857 0.00 0.00 0.00 5.68
69 70 2.165437 TCAATGCAAAAATAGGGCGGTC 59.835 45.455 0.00 0.00 0.00 4.79
70 71 1.846007 ATGCAAAAATAGGGCGGTCA 58.154 45.000 0.00 0.00 0.00 4.02
71 72 1.173043 TGCAAAAATAGGGCGGTCAG 58.827 50.000 0.00 0.00 0.00 3.51
94 95 2.347630 CCATGCTGGCACATATGGG 58.652 57.895 7.80 3.61 44.22 4.00
95 96 0.468585 CCATGCTGGCACATATGGGT 60.469 55.000 6.86 0.00 44.22 4.51
96 97 0.956633 CATGCTGGCACATATGGGTC 59.043 55.000 1.51 1.51 38.20 4.46
97 98 0.535780 ATGCTGGCACATATGGGTCG 60.536 55.000 4.85 1.07 38.20 4.79
98 99 1.893808 GCTGGCACATATGGGTCGG 60.894 63.158 14.35 14.35 38.20 4.79
99 100 1.893808 CTGGCACATATGGGTCGGC 60.894 63.158 5.24 4.55 38.20 5.54
100 101 2.191908 GGCACATATGGGTCGGCA 59.808 61.111 6.86 0.00 0.00 5.69
101 102 2.186826 GGCACATATGGGTCGGCAC 61.187 63.158 6.86 0.00 0.00 5.01
127 128 2.776312 CGTGCTACGGACACATATCT 57.224 50.000 5.72 0.00 38.08 1.98
128 129 3.891056 CGTGCTACGGACACATATCTA 57.109 47.619 5.72 0.00 38.08 1.98
129 130 4.219143 CGTGCTACGGACACATATCTAA 57.781 45.455 5.72 0.00 38.08 2.10
130 131 4.603985 CGTGCTACGGACACATATCTAAA 58.396 43.478 5.72 0.00 38.08 1.85
131 132 5.038683 CGTGCTACGGACACATATCTAAAA 58.961 41.667 5.72 0.00 38.08 1.52
132 133 5.051907 CGTGCTACGGACACATATCTAAAAC 60.052 44.000 5.72 0.00 38.08 2.43
133 134 5.808540 GTGCTACGGACACATATCTAAAACA 59.191 40.000 0.51 0.00 37.96 2.83
134 135 6.019801 GTGCTACGGACACATATCTAAAACAG 60.020 42.308 0.51 0.00 37.96 3.16
135 136 5.462398 GCTACGGACACATATCTAAAACAGG 59.538 44.000 0.00 0.00 0.00 4.00
136 137 4.766375 ACGGACACATATCTAAAACAGGG 58.234 43.478 0.00 0.00 0.00 4.45
137 138 3.560068 CGGACACATATCTAAAACAGGGC 59.440 47.826 0.00 0.00 0.00 5.19
138 139 4.523083 GGACACATATCTAAAACAGGGCA 58.477 43.478 0.00 0.00 0.00 5.36
139 140 4.576463 GGACACATATCTAAAACAGGGCAG 59.424 45.833 0.00 0.00 0.00 4.85
140 141 5.428253 GACACATATCTAAAACAGGGCAGA 58.572 41.667 0.00 0.00 0.00 4.26
141 142 5.186198 ACACATATCTAAAACAGGGCAGAC 58.814 41.667 0.00 0.00 0.00 3.51
142 143 4.271049 CACATATCTAAAACAGGGCAGACG 59.729 45.833 0.00 0.00 0.00 4.18
143 144 1.739067 ATCTAAAACAGGGCAGACGC 58.261 50.000 0.00 0.00 37.44 5.19
165 166 2.516930 CAGGCGGCCGATCCAAAT 60.517 61.111 33.48 2.28 34.01 2.32
166 167 2.516930 AGGCGGCCGATCCAAATG 60.517 61.111 33.48 0.00 34.01 2.32
167 168 3.595758 GGCGGCCGATCCAAATGG 61.596 66.667 33.48 0.00 34.01 3.16
180 181 3.712187 TCCAAATGGACAAAAAGCGAAC 58.288 40.909 0.00 0.00 39.78 3.95
181 182 3.131223 TCCAAATGGACAAAAAGCGAACA 59.869 39.130 0.00 0.00 39.78 3.18
182 183 3.868077 CCAAATGGACAAAAAGCGAACAA 59.132 39.130 0.00 0.00 37.39 2.83
183 184 4.331168 CCAAATGGACAAAAAGCGAACAAA 59.669 37.500 0.00 0.00 37.39 2.83
184 185 5.163814 CCAAATGGACAAAAAGCGAACAAAA 60.164 36.000 0.00 0.00 37.39 2.44
185 186 6.458070 CCAAATGGACAAAAAGCGAACAAAAT 60.458 34.615 0.00 0.00 37.39 1.82
186 187 5.905480 ATGGACAAAAAGCGAACAAAATC 57.095 34.783 0.00 0.00 0.00 2.17
187 188 3.794028 TGGACAAAAAGCGAACAAAATCG 59.206 39.130 0.00 0.00 45.41 3.34
194 195 3.274196 CGAACAAAATCGCTGTCCG 57.726 52.632 0.00 0.00 35.85 4.79
195 196 0.511221 CGAACAAAATCGCTGTCCGT 59.489 50.000 0.00 0.00 35.85 4.69
196 197 1.070175 CGAACAAAATCGCTGTCCGTT 60.070 47.619 0.00 0.00 35.85 4.44
197 198 2.601266 CGAACAAAATCGCTGTCCGTTT 60.601 45.455 0.00 0.00 35.85 3.60
198 199 2.399396 ACAAAATCGCTGTCCGTTTG 57.601 45.000 0.00 0.00 38.28 2.93
199 200 1.944024 ACAAAATCGCTGTCCGTTTGA 59.056 42.857 0.00 0.00 36.78 2.69
200 201 2.032030 ACAAAATCGCTGTCCGTTTGAG 60.032 45.455 0.00 0.00 36.78 3.02
201 202 1.878953 AAATCGCTGTCCGTTTGAGT 58.121 45.000 0.00 0.00 38.35 3.41
202 203 1.429463 AATCGCTGTCCGTTTGAGTC 58.571 50.000 0.00 0.00 38.35 3.36
203 204 0.732880 ATCGCTGTCCGTTTGAGTCG 60.733 55.000 0.00 0.00 38.35 4.18
204 205 1.660575 CGCTGTCCGTTTGAGTCGT 60.661 57.895 0.00 0.00 0.00 4.34
205 206 1.606350 CGCTGTCCGTTTGAGTCGTC 61.606 60.000 0.00 0.00 0.00 4.20
206 207 1.282930 GCTGTCCGTTTGAGTCGTCC 61.283 60.000 0.00 0.00 0.00 4.79
207 208 0.031585 CTGTCCGTTTGAGTCGTCCA 59.968 55.000 0.00 0.00 0.00 4.02
208 209 0.677288 TGTCCGTTTGAGTCGTCCAT 59.323 50.000 0.00 0.00 0.00 3.41
209 210 1.069513 TGTCCGTTTGAGTCGTCCATT 59.930 47.619 0.00 0.00 0.00 3.16
210 211 1.459592 GTCCGTTTGAGTCGTCCATTG 59.540 52.381 0.00 0.00 0.00 2.82
211 212 1.069513 TCCGTTTGAGTCGTCCATTGT 59.930 47.619 0.00 0.00 0.00 2.71
212 213 1.459592 CCGTTTGAGTCGTCCATTGTC 59.540 52.381 0.00 0.00 0.00 3.18
213 214 1.459592 CGTTTGAGTCGTCCATTGTCC 59.540 52.381 0.00 0.00 0.00 4.02
214 215 2.489971 GTTTGAGTCGTCCATTGTCCA 58.510 47.619 0.00 0.00 0.00 4.02
215 216 3.074412 GTTTGAGTCGTCCATTGTCCAT 58.926 45.455 0.00 0.00 0.00 3.41
216 217 3.417069 TTGAGTCGTCCATTGTCCATT 57.583 42.857 0.00 0.00 0.00 3.16
217 218 2.698803 TGAGTCGTCCATTGTCCATTG 58.301 47.619 0.00 0.00 0.00 2.82
218 219 2.301583 TGAGTCGTCCATTGTCCATTGA 59.698 45.455 0.00 0.00 0.00 2.57
219 220 3.244387 TGAGTCGTCCATTGTCCATTGAA 60.244 43.478 0.00 0.00 0.00 2.69
220 221 3.941483 GAGTCGTCCATTGTCCATTGAAT 59.059 43.478 0.00 0.00 0.00 2.57
221 222 5.097742 AGTCGTCCATTGTCCATTGAATA 57.902 39.130 0.00 0.00 0.00 1.75
222 223 5.684704 AGTCGTCCATTGTCCATTGAATAT 58.315 37.500 0.00 0.00 0.00 1.28
223 224 5.528690 AGTCGTCCATTGTCCATTGAATATG 59.471 40.000 0.00 0.00 0.00 1.78
224 225 4.275689 TCGTCCATTGTCCATTGAATATGC 59.724 41.667 0.00 0.00 0.00 3.14
225 226 4.276678 CGTCCATTGTCCATTGAATATGCT 59.723 41.667 0.00 0.00 0.00 3.79
226 227 5.561532 CGTCCATTGTCCATTGAATATGCTC 60.562 44.000 0.00 0.00 0.00 4.26
227 228 5.533903 GTCCATTGTCCATTGAATATGCTCT 59.466 40.000 0.00 0.00 0.00 4.09
228 229 6.712095 GTCCATTGTCCATTGAATATGCTCTA 59.288 38.462 0.00 0.00 0.00 2.43
229 230 7.229306 GTCCATTGTCCATTGAATATGCTCTAA 59.771 37.037 0.00 0.00 0.00 2.10
230 231 7.446319 TCCATTGTCCATTGAATATGCTCTAAG 59.554 37.037 0.00 0.00 0.00 2.18
231 232 7.309012 CCATTGTCCATTGAATATGCTCTAAGG 60.309 40.741 0.00 0.00 0.00 2.69
263 268 7.996758 AAGGAATTCAGAATAGGGAGACTAA 57.003 36.000 7.93 0.00 34.79 2.24
320 325 2.809952 CGGAGGGAGGGAGACTAAC 58.190 63.158 0.00 0.00 0.00 2.34
322 327 1.487300 GGAGGGAGGGAGACTAACAC 58.513 60.000 0.00 0.00 0.00 3.32
323 328 1.487300 GAGGGAGGGAGACTAACACC 58.513 60.000 0.00 0.00 0.00 4.16
324 329 0.324460 AGGGAGGGAGACTAACACCG 60.324 60.000 0.00 0.00 0.00 4.94
327 332 1.542492 GAGGGAGACTAACACCGTCA 58.458 55.000 0.00 0.00 41.41 4.35
328 333 1.473278 GAGGGAGACTAACACCGTCAG 59.527 57.143 0.00 0.00 41.41 3.51
329 334 0.108756 GGGAGACTAACACCGTCAGC 60.109 60.000 0.00 0.00 33.89 4.26
330 335 0.456312 GGAGACTAACACCGTCAGCG 60.456 60.000 0.00 0.00 33.89 5.18
331 336 0.240411 GAGACTAACACCGTCAGCGT 59.760 55.000 0.00 0.00 36.15 5.07
332 337 1.466167 GAGACTAACACCGTCAGCGTA 59.534 52.381 0.00 0.00 36.15 4.42
333 338 1.198637 AGACTAACACCGTCAGCGTAC 59.801 52.381 0.00 0.00 36.15 3.67
334 339 1.198637 GACTAACACCGTCAGCGTACT 59.801 52.381 0.00 0.00 36.15 2.73
336 341 2.417933 ACTAACACCGTCAGCGTACTAG 59.582 50.000 0.00 0.00 36.15 2.57
337 342 0.109412 AACACCGTCAGCGTACTAGC 60.109 55.000 0.00 0.00 36.15 3.42
915 920 2.809601 CACGCTCGAACCTTCCGG 60.810 66.667 0.00 0.00 0.00 5.14
1157 1163 3.007074 TCCACCAAATGCTACGTGAGTTA 59.993 43.478 0.00 0.00 46.40 2.24
1177 1183 2.671963 GCGCCGGAAACTCCCTTT 60.672 61.111 5.05 0.00 31.13 3.11
1178 1184 2.265904 GCGCCGGAAACTCCCTTTT 61.266 57.895 5.05 0.00 31.13 2.27
1179 1185 1.873863 CGCCGGAAACTCCCTTTTC 59.126 57.895 5.05 0.00 35.13 2.29
1180 1186 0.605589 CGCCGGAAACTCCCTTTTCT 60.606 55.000 5.05 0.00 36.02 2.52
1181 1187 1.617322 GCCGGAAACTCCCTTTTCTT 58.383 50.000 5.05 0.00 36.02 2.52
1182 1188 1.269723 GCCGGAAACTCCCTTTTCTTG 59.730 52.381 5.05 0.00 36.02 3.02
1183 1189 1.886542 CCGGAAACTCCCTTTTCTTGG 59.113 52.381 0.00 0.00 36.02 3.61
1184 1190 1.269723 CGGAAACTCCCTTTTCTTGGC 59.730 52.381 0.00 0.00 36.02 4.52
1185 1191 2.598565 GGAAACTCCCTTTTCTTGGCT 58.401 47.619 0.00 0.00 36.02 4.75
1186 1192 2.965831 GGAAACTCCCTTTTCTTGGCTT 59.034 45.455 0.00 0.00 36.02 4.35
1187 1193 3.005897 GGAAACTCCCTTTTCTTGGCTTC 59.994 47.826 0.00 0.00 36.02 3.86
1188 1194 3.602205 AACTCCCTTTTCTTGGCTTCT 57.398 42.857 0.00 0.00 0.00 2.85
1189 1195 3.147553 ACTCCCTTTTCTTGGCTTCTC 57.852 47.619 0.00 0.00 0.00 2.87
1190 1196 2.224892 ACTCCCTTTTCTTGGCTTCTCC 60.225 50.000 0.00 0.00 0.00 3.71
1191 1197 1.075536 TCCCTTTTCTTGGCTTCTCCC 59.924 52.381 0.00 0.00 0.00 4.30
1192 1198 1.550327 CCTTTTCTTGGCTTCTCCCC 58.450 55.000 0.00 0.00 0.00 4.81
1193 1199 1.076187 CCTTTTCTTGGCTTCTCCCCT 59.924 52.381 0.00 0.00 0.00 4.79
1194 1200 2.441410 CTTTTCTTGGCTTCTCCCCTC 58.559 52.381 0.00 0.00 0.00 4.30
1195 1201 0.698818 TTTCTTGGCTTCTCCCCTCC 59.301 55.000 0.00 0.00 0.00 4.30
1196 1202 0.178861 TTCTTGGCTTCTCCCCTCCT 60.179 55.000 0.00 0.00 0.00 3.69
1197 1203 0.618968 TCTTGGCTTCTCCCCTCCTC 60.619 60.000 0.00 0.00 0.00 3.71
1198 1204 1.965754 CTTGGCTTCTCCCCTCCTCG 61.966 65.000 0.00 0.00 0.00 4.63
1199 1205 3.157949 GGCTTCTCCCCTCCTCGG 61.158 72.222 0.00 0.00 0.00 4.63
1219 1248 1.237285 TTCTTGGCTCCTTCGCTTGC 61.237 55.000 0.00 0.00 0.00 4.01
1269 1298 2.290323 GCTAGTTCTTGAAAGGAGCCCA 60.290 50.000 0.00 0.00 0.00 5.36
1592 1937 4.410743 GCTTGCGTCCTGCCTTGC 62.411 66.667 0.00 0.00 45.60 4.01
1593 1938 3.741476 CTTGCGTCCTGCCTTGCC 61.741 66.667 0.00 0.00 45.60 4.52
1594 1939 4.577677 TTGCGTCCTGCCTTGCCA 62.578 61.111 0.00 0.00 45.60 4.92
1599 1944 4.269523 TCCTGCCTTGCCACGCTT 62.270 61.111 0.00 0.00 0.00 4.68
1600 1945 2.359850 CCTGCCTTGCCACGCTTA 60.360 61.111 0.00 0.00 0.00 3.09
1601 1946 2.401766 CCTGCCTTGCCACGCTTAG 61.402 63.158 0.00 0.00 0.00 2.18
1602 1947 2.359850 TGCCTTGCCACGCTTAGG 60.360 61.111 0.00 0.00 35.36 2.69
1728 2073 0.978146 AGTGGCGAATCCTAGGCTGT 60.978 55.000 2.96 0.00 35.26 4.40
1819 2164 9.458374 TTCTGAATTCAAGGAACGAATTTTTAC 57.542 29.630 9.88 0.00 41.87 2.01
1831 2176 6.728089 ACGAATTTTTACCCCCTTTTGTTA 57.272 33.333 0.00 0.00 0.00 2.41
3216 3580 6.818142 CCCTTCATTTTAAACATGGATTGGTC 59.182 38.462 0.00 0.00 0.00 4.02
3403 3767 3.427909 GCATGCGATTTGGTCAGAAATCA 60.428 43.478 0.00 0.00 40.83 2.57
3417 3781 2.158475 AGAAATCACAAGGAGGTGGCAA 60.158 45.455 0.00 0.00 39.27 4.52
3594 3958 9.659135 TCCTTGGATCATAAATTAAACCATGAT 57.341 29.630 0.00 8.12 40.06 2.45
3824 4188 4.137635 TCCTTACGGAACCTAAGAAGGGG 61.138 52.174 0.00 0.00 40.00 4.79
3884 4248 0.036022 ACAGGAGGCTTCTTGCTGAC 59.964 55.000 7.92 0.00 42.39 3.51
3941 4305 0.178990 GGAACAAGCCACCAGAACCT 60.179 55.000 0.00 0.00 0.00 3.50
4044 4408 1.901159 AGGTATGCCAATTGCTTTGCA 59.099 42.857 9.14 9.14 42.00 4.08
4114 4478 5.413499 GTTACATCATGCTTGGATTGCTTT 58.587 37.500 0.00 0.00 0.00 3.51
4391 4755 1.540267 TGGGATACGAGCTCTAATCGC 59.460 52.381 23.81 23.81 43.91 4.58
4410 4774 2.345641 CGCATGGTTAGTTCTCTTGACG 59.654 50.000 0.00 0.00 0.00 4.35
4413 4778 4.143094 GCATGGTTAGTTCTCTTGACGTTC 60.143 45.833 0.00 0.00 0.00 3.95
4438 4803 8.810427 TCTTTTTCTTGTACTGTAGTGTAAACG 58.190 33.333 0.00 0.00 0.00 3.60
4439 4804 8.477984 TTTTTCTTGTACTGTAGTGTAAACGT 57.522 30.769 0.00 0.00 0.00 3.99
4441 4806 9.579768 TTTTCTTGTACTGTAGTGTAAACGTAA 57.420 29.630 0.00 0.00 0.00 3.18
4450 4815 5.579119 TGTAGTGTAAACGTAATGGCTCATG 59.421 40.000 0.00 0.00 0.00 3.07
4654 5019 1.407437 GCAGAGGTATGTGGGTTGAGG 60.407 57.143 0.00 0.00 0.00 3.86
4745 5110 3.459232 TGGCGTCTTCTAATCCATCTG 57.541 47.619 0.00 0.00 0.00 2.90
4829 5194 2.019984 GGTGTCCATTCCAGAGCAATC 58.980 52.381 0.00 0.00 0.00 2.67
4892 5257 1.280710 TCTGGAACACACACACTGGTT 59.719 47.619 0.00 0.00 0.00 3.67
4963 5328 7.861629 TCTGGAATAAGAATGAAAAGGAGCTA 58.138 34.615 0.00 0.00 0.00 3.32
5081 5446 2.821969 CTCTGCTTGGCACAGGTATTTT 59.178 45.455 5.40 0.00 42.39 1.82
5143 5508 7.252708 TGATTGCTTGTTTATGCTGTTGATAG 58.747 34.615 0.00 0.00 0.00 2.08
5154 5520 6.630444 ATGCTGTTGATAGACATGATTTCC 57.370 37.500 0.00 0.00 0.00 3.13
5157 5523 5.819379 GCTGTTGATAGACATGATTTCCTGA 59.181 40.000 0.00 0.00 0.00 3.86
5282 5648 3.052082 CCTGCAGCCAAGACCGTG 61.052 66.667 8.66 0.00 0.00 4.94
5371 5737 6.355397 TCGCCGTATATACTAGTATGAAGC 57.645 41.667 23.09 16.54 0.00 3.86
5372 5738 6.111382 TCGCCGTATATACTAGTATGAAGCT 58.889 40.000 23.09 1.39 0.00 3.74
5373 5739 6.596888 TCGCCGTATATACTAGTATGAAGCTT 59.403 38.462 23.09 0.00 0.00 3.74
5374 5740 7.765819 TCGCCGTATATACTAGTATGAAGCTTA 59.234 37.037 23.09 3.91 0.00 3.09
5375 5741 7.850003 CGCCGTATATACTAGTATGAAGCTTAC 59.150 40.741 23.09 13.45 0.00 2.34
5408 5777 6.320494 ACATATTCTCTCGTACCTGATCAC 57.680 41.667 0.00 0.00 0.00 3.06
5422 5791 5.769835 ACCTGATCACCATCCATATTTTGT 58.230 37.500 0.00 0.00 0.00 2.83
5423 5792 6.197168 ACCTGATCACCATCCATATTTTGTT 58.803 36.000 0.00 0.00 0.00 2.83
5432 5801 6.153340 ACCATCCATATTTTGTTGGAGTTGAG 59.847 38.462 0.00 0.00 44.87 3.02
5451 5820 2.218603 AGCAACTTGGAACTGTAACCG 58.781 47.619 0.00 0.00 0.00 4.44
5467 5836 6.038825 ACTGTAACCGTCTTCTGATCTGATAG 59.961 42.308 2.84 4.70 0.00 2.08
5516 5885 7.593273 CAGAGAGAAGTTTATCGCGATTTAGAT 59.407 37.037 28.81 11.41 0.00 1.98
5543 5946 4.217118 GCCTGCAAATATGAGGTCCTAATG 59.783 45.833 0.00 0.00 0.00 1.90
5683 6097 1.339929 AGCATTCCGTTGTTTTCCACC 59.660 47.619 0.00 0.00 0.00 4.61
5696 6110 4.097286 TGTTTTCCACCTTGCTTACTGTTC 59.903 41.667 0.00 0.00 0.00 3.18
5718 6132 3.548770 TCTGCTCCTAATGCATTCAAGG 58.451 45.455 16.86 17.93 39.86 3.61
5744 6532 7.639945 AGTGTGTTATAACTCTTTGTTTCTGC 58.360 34.615 16.33 0.00 39.89 4.26
5824 6701 6.488683 AGATCGTACTAGAAGATAAGCAAGCT 59.511 38.462 0.00 0.00 0.00 3.74
5854 6731 4.511826 GGCGGTAAGTCCTATTTGAAGATG 59.488 45.833 0.00 0.00 0.00 2.90
5978 6856 7.538575 ACAAAATAGTGACATCTAAACCATGC 58.461 34.615 0.00 0.00 0.00 4.06
6006 6885 9.844257 CTTTATCTTCTTCCAGGATGATTAGTT 57.156 33.333 5.88 0.68 39.69 2.24
6010 6889 8.324191 TCTTCTTCCAGGATGATTAGTTGTAT 57.676 34.615 5.88 0.00 39.69 2.29
6011 6890 9.434275 TCTTCTTCCAGGATGATTAGTTGTATA 57.566 33.333 5.88 0.00 39.69 1.47
6041 6935 6.015688 TCACCACAATATATACTTCCTCCGTC 60.016 42.308 0.00 0.00 0.00 4.79
6042 6936 6.015350 CACCACAATATATACTTCCTCCGTCT 60.015 42.308 0.00 0.00 0.00 4.18
6058 6952 2.592897 CCGTCTCGAATTACTTGTCGTG 59.407 50.000 0.00 0.00 38.41 4.35
6078 6972 8.310382 TGTCGTGGAAATGGATAAAAATGAATT 58.690 29.630 0.00 0.00 0.00 2.17
6121 7015 9.095065 ACGTCTAGATACATCCATTTTTAACAC 57.905 33.333 0.00 0.00 0.00 3.32
6146 7041 7.181125 ACAAGTAATTTCAGACAGAGGGAGTAT 59.819 37.037 0.00 0.00 0.00 2.12
6159 7054 3.762823 GAGGGAGTATATTCCTACACCGG 59.237 52.174 13.49 0.00 37.40 5.28
6202 7097 2.385803 GAGAGGGGTTCGATTCTACCA 58.614 52.381 6.36 0.00 36.10 3.25
6238 7133 8.867935 GTGGATATTAGATCGATTGATGAGTTG 58.132 37.037 0.00 0.00 34.09 3.16
6247 7142 6.892310 TCGATTGATGAGTTGTGTAATCTG 57.108 37.500 0.00 0.00 0.00 2.90
6269 7164 5.284864 TGATCGTAGATGAGATCAAGCAAC 58.715 41.667 5.76 0.00 46.93 4.17
6290 7185 0.386838 GGCAATGGCAGGAGCATTAC 59.613 55.000 0.58 0.00 44.61 1.89
6299 7194 2.880890 GCAGGAGCATTACGGATTGAAT 59.119 45.455 0.00 0.00 41.58 2.57
6300 7195 3.304257 GCAGGAGCATTACGGATTGAATG 60.304 47.826 0.00 0.00 41.58 2.67
6301 7196 3.251729 CAGGAGCATTACGGATTGAATGG 59.748 47.826 0.00 0.00 34.29 3.16
6302 7197 3.136443 AGGAGCATTACGGATTGAATGGA 59.864 43.478 0.00 0.00 34.29 3.41
6303 7198 3.499918 GGAGCATTACGGATTGAATGGAG 59.500 47.826 0.00 0.00 34.29 3.86
6304 7199 4.380531 GAGCATTACGGATTGAATGGAGA 58.619 43.478 0.00 0.00 34.29 3.71
6305 7200 4.384056 AGCATTACGGATTGAATGGAGAG 58.616 43.478 0.00 0.00 34.29 3.20
6306 7201 4.101585 AGCATTACGGATTGAATGGAGAGA 59.898 41.667 0.00 0.00 34.29 3.10
6307 7202 4.450419 GCATTACGGATTGAATGGAGAGAG 59.550 45.833 0.00 0.00 34.29 3.20
6308 7203 4.672587 TTACGGATTGAATGGAGAGAGG 57.327 45.455 0.00 0.00 0.00 3.69
6309 7204 1.765314 ACGGATTGAATGGAGAGAGGG 59.235 52.381 0.00 0.00 0.00 4.30
6310 7205 1.071385 CGGATTGAATGGAGAGAGGGG 59.929 57.143 0.00 0.00 0.00 4.79
6311 7206 1.423161 GGATTGAATGGAGAGAGGGGG 59.577 57.143 0.00 0.00 0.00 5.40
6312 7207 0.849417 ATTGAATGGAGAGAGGGGGC 59.151 55.000 0.00 0.00 0.00 5.80
6313 7208 1.626356 TTGAATGGAGAGAGGGGGCG 61.626 60.000 0.00 0.00 0.00 6.13
6314 7209 2.770048 AATGGAGAGAGGGGGCGG 60.770 66.667 0.00 0.00 0.00 6.13
6315 7210 3.332393 AATGGAGAGAGGGGGCGGA 62.332 63.158 0.00 0.00 0.00 5.54
6316 7211 2.840203 AATGGAGAGAGGGGGCGGAA 62.840 60.000 0.00 0.00 0.00 4.30
6317 7212 2.446802 GGAGAGAGGGGGCGGAAT 60.447 66.667 0.00 0.00 0.00 3.01
6318 7213 1.152312 GGAGAGAGGGGGCGGAATA 60.152 63.158 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.170506 AGTCAAATAGCATAGTTTGAACCGA 58.829 36.000 2.50 0.00 43.56 4.69
38 39 9.743057 CCCTATTTTTGCATTGATACGAATTTA 57.257 29.630 0.00 0.00 0.00 1.40
39 40 7.224557 GCCCTATTTTTGCATTGATACGAATTT 59.775 33.333 0.00 0.00 0.00 1.82
40 41 6.701400 GCCCTATTTTTGCATTGATACGAATT 59.299 34.615 0.00 0.00 0.00 2.17
41 42 6.215845 GCCCTATTTTTGCATTGATACGAAT 58.784 36.000 0.00 0.00 0.00 3.34
42 43 5.587289 GCCCTATTTTTGCATTGATACGAA 58.413 37.500 0.00 0.00 0.00 3.85
43 44 4.260990 CGCCCTATTTTTGCATTGATACGA 60.261 41.667 0.00 0.00 0.00 3.43
44 45 3.974401 CGCCCTATTTTTGCATTGATACG 59.026 43.478 0.00 0.00 0.00 3.06
45 46 4.202111 ACCGCCCTATTTTTGCATTGATAC 60.202 41.667 0.00 0.00 0.00 2.24
46 47 3.957497 ACCGCCCTATTTTTGCATTGATA 59.043 39.130 0.00 0.00 0.00 2.15
47 48 2.765699 ACCGCCCTATTTTTGCATTGAT 59.234 40.909 0.00 0.00 0.00 2.57
48 49 2.165437 GACCGCCCTATTTTTGCATTGA 59.835 45.455 0.00 0.00 0.00 2.57
49 50 2.094286 TGACCGCCCTATTTTTGCATTG 60.094 45.455 0.00 0.00 0.00 2.82
50 51 2.166254 CTGACCGCCCTATTTTTGCATT 59.834 45.455 0.00 0.00 0.00 3.56
51 52 1.750778 CTGACCGCCCTATTTTTGCAT 59.249 47.619 0.00 0.00 0.00 3.96
52 53 1.173043 CTGACCGCCCTATTTTTGCA 58.827 50.000 0.00 0.00 0.00 4.08
53 54 0.179137 GCTGACCGCCCTATTTTTGC 60.179 55.000 0.00 0.00 0.00 3.68
77 78 0.956633 GACCCATATGTGCCAGCATG 59.043 55.000 1.24 0.00 0.00 4.06
78 79 0.535780 CGACCCATATGTGCCAGCAT 60.536 55.000 1.24 0.00 0.00 3.79
79 80 1.153188 CGACCCATATGTGCCAGCA 60.153 57.895 1.24 0.00 0.00 4.41
80 81 1.893808 CCGACCCATATGTGCCAGC 60.894 63.158 1.24 0.00 0.00 4.85
81 82 1.893808 GCCGACCCATATGTGCCAG 60.894 63.158 1.24 0.00 0.00 4.85
82 83 2.191908 GCCGACCCATATGTGCCA 59.808 61.111 1.24 0.00 0.00 4.92
83 84 2.186826 GTGCCGACCCATATGTGCC 61.187 63.158 1.24 0.00 0.00 5.01
84 85 2.534019 CGTGCCGACCCATATGTGC 61.534 63.158 1.24 0.00 0.00 4.57
85 86 0.742990 AACGTGCCGACCCATATGTG 60.743 55.000 1.24 0.00 0.00 3.21
86 87 0.825410 TAACGTGCCGACCCATATGT 59.175 50.000 1.24 0.00 0.00 2.29
87 88 1.942677 TTAACGTGCCGACCCATATG 58.057 50.000 0.00 0.00 0.00 1.78
88 89 2.282407 GTTTAACGTGCCGACCCATAT 58.718 47.619 0.00 0.00 0.00 1.78
89 90 1.724429 GTTTAACGTGCCGACCCATA 58.276 50.000 0.00 0.00 0.00 2.74
90 91 1.293267 CGTTTAACGTGCCGACCCAT 61.293 55.000 9.54 0.00 36.74 4.00
91 92 1.955157 CGTTTAACGTGCCGACCCA 60.955 57.895 9.54 0.00 36.74 4.51
92 93 2.855325 CGTTTAACGTGCCGACCC 59.145 61.111 9.54 0.00 36.74 4.46
102 103 2.126467 TGTGTCCGTAGCACGTTTAAC 58.874 47.619 7.68 0.00 40.58 2.01
103 104 2.505628 TGTGTCCGTAGCACGTTTAA 57.494 45.000 7.68 0.00 40.58 1.52
104 105 2.728690 ATGTGTCCGTAGCACGTTTA 57.271 45.000 7.68 0.00 40.58 2.01
105 106 2.728690 TATGTGTCCGTAGCACGTTT 57.271 45.000 7.68 0.00 40.58 3.60
106 107 2.426024 AGATATGTGTCCGTAGCACGTT 59.574 45.455 7.68 0.00 40.58 3.99
107 108 2.022195 AGATATGTGTCCGTAGCACGT 58.978 47.619 7.68 0.00 40.58 4.49
108 109 2.776312 AGATATGTGTCCGTAGCACG 57.224 50.000 2.27 2.27 42.11 5.34
109 110 5.808540 TGTTTTAGATATGTGTCCGTAGCAC 59.191 40.000 0.00 0.00 0.00 4.40
110 111 5.968254 TGTTTTAGATATGTGTCCGTAGCA 58.032 37.500 0.00 0.00 0.00 3.49
111 112 5.462398 CCTGTTTTAGATATGTGTCCGTAGC 59.538 44.000 0.00 0.00 0.00 3.58
112 113 5.983720 CCCTGTTTTAGATATGTGTCCGTAG 59.016 44.000 0.00 0.00 0.00 3.51
113 114 5.682990 GCCCTGTTTTAGATATGTGTCCGTA 60.683 44.000 0.00 0.00 0.00 4.02
114 115 4.766375 CCCTGTTTTAGATATGTGTCCGT 58.234 43.478 0.00 0.00 0.00 4.69
115 116 3.560068 GCCCTGTTTTAGATATGTGTCCG 59.440 47.826 0.00 0.00 0.00 4.79
116 117 4.523083 TGCCCTGTTTTAGATATGTGTCC 58.477 43.478 0.00 0.00 0.00 4.02
117 118 5.294552 GTCTGCCCTGTTTTAGATATGTGTC 59.705 44.000 0.00 0.00 0.00 3.67
118 119 5.186198 GTCTGCCCTGTTTTAGATATGTGT 58.814 41.667 0.00 0.00 0.00 3.72
119 120 4.271049 CGTCTGCCCTGTTTTAGATATGTG 59.729 45.833 0.00 0.00 0.00 3.21
120 121 4.442706 CGTCTGCCCTGTTTTAGATATGT 58.557 43.478 0.00 0.00 0.00 2.29
121 122 3.248602 GCGTCTGCCCTGTTTTAGATATG 59.751 47.826 0.00 0.00 33.98 1.78
122 123 3.467803 GCGTCTGCCCTGTTTTAGATAT 58.532 45.455 0.00 0.00 33.98 1.63
123 124 2.901249 GCGTCTGCCCTGTTTTAGATA 58.099 47.619 0.00 0.00 33.98 1.98
124 125 1.739067 GCGTCTGCCCTGTTTTAGAT 58.261 50.000 0.00 0.00 33.98 1.98
125 126 3.226884 GCGTCTGCCCTGTTTTAGA 57.773 52.632 0.00 0.00 33.98 2.10
148 149 2.516930 ATTTGGATCGGCCGCCTG 60.517 61.111 23.51 1.17 40.66 4.85
149 150 2.516930 CATTTGGATCGGCCGCCT 60.517 61.111 23.51 10.55 40.66 5.52
150 151 3.595758 CCATTTGGATCGGCCGCC 61.596 66.667 23.51 18.27 40.66 6.13
151 152 2.515991 TCCATTTGGATCGGCCGC 60.516 61.111 23.51 7.37 39.78 6.53
159 160 3.131223 TGTTCGCTTTTTGTCCATTTGGA 59.869 39.130 0.00 0.00 43.08 3.53
160 161 3.452474 TGTTCGCTTTTTGTCCATTTGG 58.548 40.909 0.00 0.00 0.00 3.28
161 162 5.462034 TTTGTTCGCTTTTTGTCCATTTG 57.538 34.783 0.00 0.00 0.00 2.32
162 163 6.509358 CGATTTTGTTCGCTTTTTGTCCATTT 60.509 34.615 0.00 0.00 31.60 2.32
163 164 5.051106 CGATTTTGTTCGCTTTTTGTCCATT 60.051 36.000 0.00 0.00 31.60 3.16
164 165 4.444056 CGATTTTGTTCGCTTTTTGTCCAT 59.556 37.500 0.00 0.00 31.60 3.41
165 166 3.794028 CGATTTTGTTCGCTTTTTGTCCA 59.206 39.130 0.00 0.00 31.60 4.02
166 167 4.354725 CGATTTTGTTCGCTTTTTGTCC 57.645 40.909 0.00 0.00 31.60 4.02
176 177 3.274196 CGGACAGCGATTTTGTTCG 57.726 52.632 0.00 0.00 40.73 3.95
177 178 2.681152 AACGGACAGCGATTTTGTTC 57.319 45.000 0.00 0.00 0.00 3.18
178 179 2.356382 TCAAACGGACAGCGATTTTGTT 59.644 40.909 0.00 0.00 0.00 2.83
179 180 1.944024 TCAAACGGACAGCGATTTTGT 59.056 42.857 0.00 0.00 0.00 2.83
180 181 2.032030 ACTCAAACGGACAGCGATTTTG 60.032 45.455 0.00 0.00 0.00 2.44
181 182 2.218603 ACTCAAACGGACAGCGATTTT 58.781 42.857 0.00 0.00 0.00 1.82
182 183 1.798813 GACTCAAACGGACAGCGATTT 59.201 47.619 0.00 0.00 0.00 2.17
183 184 1.429463 GACTCAAACGGACAGCGATT 58.571 50.000 0.00 0.00 0.00 3.34
184 185 0.732880 CGACTCAAACGGACAGCGAT 60.733 55.000 0.00 0.00 0.00 4.58
185 186 1.371267 CGACTCAAACGGACAGCGA 60.371 57.895 0.00 0.00 0.00 4.93
186 187 1.606350 GACGACTCAAACGGACAGCG 61.606 60.000 0.00 0.00 34.93 5.18
187 188 1.282930 GGACGACTCAAACGGACAGC 61.283 60.000 0.00 0.00 34.93 4.40
188 189 0.031585 TGGACGACTCAAACGGACAG 59.968 55.000 0.00 0.00 34.93 3.51
189 190 0.677288 ATGGACGACTCAAACGGACA 59.323 50.000 0.00 0.00 34.93 4.02
190 191 1.459592 CAATGGACGACTCAAACGGAC 59.540 52.381 0.00 0.00 34.93 4.79
191 192 1.069513 ACAATGGACGACTCAAACGGA 59.930 47.619 0.00 0.00 34.93 4.69
192 193 1.459592 GACAATGGACGACTCAAACGG 59.540 52.381 0.00 0.00 34.93 4.44
193 194 1.459592 GGACAATGGACGACTCAAACG 59.540 52.381 0.00 0.00 0.00 3.60
194 195 2.489971 TGGACAATGGACGACTCAAAC 58.510 47.619 0.00 0.00 0.00 2.93
195 196 2.920724 TGGACAATGGACGACTCAAA 57.079 45.000 0.00 0.00 0.00 2.69
196 197 3.073678 CAATGGACAATGGACGACTCAA 58.926 45.455 0.00 0.00 0.00 3.02
197 198 2.301583 TCAATGGACAATGGACGACTCA 59.698 45.455 0.00 0.00 0.00 3.41
198 199 2.972625 TCAATGGACAATGGACGACTC 58.027 47.619 0.00 0.00 0.00 3.36
199 200 3.417069 TTCAATGGACAATGGACGACT 57.583 42.857 0.00 0.00 0.00 4.18
200 201 5.751680 CATATTCAATGGACAATGGACGAC 58.248 41.667 0.00 0.00 0.00 4.34
201 202 4.275689 GCATATTCAATGGACAATGGACGA 59.724 41.667 0.00 0.00 0.00 4.20
202 203 4.276678 AGCATATTCAATGGACAATGGACG 59.723 41.667 0.00 0.00 0.00 4.79
203 204 5.533903 AGAGCATATTCAATGGACAATGGAC 59.466 40.000 0.00 0.00 0.00 4.02
204 205 5.698104 AGAGCATATTCAATGGACAATGGA 58.302 37.500 0.00 0.00 0.00 3.41
205 206 7.309012 CCTTAGAGCATATTCAATGGACAATGG 60.309 40.741 0.00 0.00 0.00 3.16
206 207 7.591165 CCTTAGAGCATATTCAATGGACAATG 58.409 38.462 0.00 0.00 0.00 2.82
207 208 6.208204 GCCTTAGAGCATATTCAATGGACAAT 59.792 38.462 0.00 0.00 0.00 2.71
208 209 5.532406 GCCTTAGAGCATATTCAATGGACAA 59.468 40.000 0.00 0.00 0.00 3.18
209 210 5.065914 GCCTTAGAGCATATTCAATGGACA 58.934 41.667 0.00 0.00 0.00 4.02
210 211 4.457257 GGCCTTAGAGCATATTCAATGGAC 59.543 45.833 0.00 0.00 0.00 4.02
211 212 4.352001 AGGCCTTAGAGCATATTCAATGGA 59.648 41.667 0.00 0.00 0.00 3.41
212 213 4.660168 AGGCCTTAGAGCATATTCAATGG 58.340 43.478 0.00 0.00 0.00 3.16
213 214 7.750229 TTTAGGCCTTAGAGCATATTCAATG 57.250 36.000 12.58 0.00 0.00 2.82
214 215 8.766994 TTTTTAGGCCTTAGAGCATATTCAAT 57.233 30.769 12.58 0.00 0.00 2.57
263 268 1.505353 GCTAGTACGCTGACGGTGT 59.495 57.895 5.66 5.66 46.04 4.16
294 299 2.669240 CCTCCCTCCGGGTTGAAC 59.331 66.667 0.00 0.00 44.74 3.18
314 319 1.198637 AGTACGCTGACGGTGTTAGTC 59.801 52.381 5.66 0.00 46.04 2.59
317 322 1.131126 GCTAGTACGCTGACGGTGTTA 59.869 52.381 5.66 0.00 46.04 2.41
318 323 0.109412 GCTAGTACGCTGACGGTGTT 60.109 55.000 5.66 0.00 46.04 3.32
320 325 4.379221 GCTAGTACGCTGACGGTG 57.621 61.111 0.00 0.00 46.04 4.94
915 920 2.000447 CAAGAATCGACCGAGGGAAAC 59.000 52.381 0.00 0.00 0.00 2.78
978 983 2.032620 GAAGAGGGACAGCGAGGAATA 58.967 52.381 0.00 0.00 0.00 1.75
1171 1177 1.075536 GGGAGAAGCCAAGAAAAGGGA 59.924 52.381 0.00 0.00 38.95 4.20
1177 1183 0.178861 AGGAGGGGAGAAGCCAAGAA 60.179 55.000 0.00 0.00 38.95 2.52
1178 1184 0.618968 GAGGAGGGGAGAAGCCAAGA 60.619 60.000 0.00 0.00 38.95 3.02
1179 1185 1.911471 GAGGAGGGGAGAAGCCAAG 59.089 63.158 0.00 0.00 38.95 3.61
1180 1186 1.990060 CGAGGAGGGGAGAAGCCAA 60.990 63.158 0.00 0.00 38.95 4.52
1181 1187 2.364317 CGAGGAGGGGAGAAGCCA 60.364 66.667 0.00 0.00 38.95 4.75
1182 1188 3.157949 CCGAGGAGGGGAGAAGCC 61.158 72.222 0.00 0.00 35.97 4.35
1183 1189 1.962321 GAACCGAGGAGGGGAGAAGC 61.962 65.000 0.00 0.00 46.96 3.86
1184 1190 0.324830 AGAACCGAGGAGGGGAGAAG 60.325 60.000 0.00 0.00 46.96 2.85
1185 1191 0.116541 AAGAACCGAGGAGGGGAGAA 59.883 55.000 0.00 0.00 46.96 2.87
1186 1192 0.614979 CAAGAACCGAGGAGGGGAGA 60.615 60.000 0.00 0.00 46.96 3.71
1187 1193 1.617947 CCAAGAACCGAGGAGGGGAG 61.618 65.000 0.00 0.00 46.96 4.30
1188 1194 1.612442 CCAAGAACCGAGGAGGGGA 60.612 63.158 0.00 0.00 46.96 4.81
1189 1195 2.990479 CCAAGAACCGAGGAGGGG 59.010 66.667 0.00 0.00 46.96 4.79
1190 1196 2.245438 GAGCCAAGAACCGAGGAGGG 62.245 65.000 0.00 0.00 46.96 4.30
1192 1198 1.219393 GGAGCCAAGAACCGAGGAG 59.781 63.158 0.00 0.00 0.00 3.69
1193 1199 0.836400 AAGGAGCCAAGAACCGAGGA 60.836 55.000 0.00 0.00 0.00 3.71
1194 1200 0.391793 GAAGGAGCCAAGAACCGAGG 60.392 60.000 0.00 0.00 0.00 4.63
1195 1201 0.737715 CGAAGGAGCCAAGAACCGAG 60.738 60.000 0.00 0.00 0.00 4.63
1196 1202 1.292223 CGAAGGAGCCAAGAACCGA 59.708 57.895 0.00 0.00 0.00 4.69
1197 1203 2.391389 GCGAAGGAGCCAAGAACCG 61.391 63.158 0.00 0.00 0.00 4.44
1198 1204 0.606673 AAGCGAAGGAGCCAAGAACC 60.607 55.000 0.00 0.00 38.01 3.62
1199 1205 0.519077 CAAGCGAAGGAGCCAAGAAC 59.481 55.000 0.00 0.00 38.01 3.01
1219 1248 1.753073 GGCAACCATCAAGGGATTCAG 59.247 52.381 0.00 0.00 43.89 3.02
1596 1941 1.869132 CCCGTTAATAACCGCCTAAGC 59.131 52.381 0.00 0.00 0.00 3.09
1597 1942 3.457610 TCCCGTTAATAACCGCCTAAG 57.542 47.619 0.00 0.00 0.00 2.18
1598 1943 3.134442 ACATCCCGTTAATAACCGCCTAA 59.866 43.478 0.00 0.00 0.00 2.69
1599 1944 2.699846 ACATCCCGTTAATAACCGCCTA 59.300 45.455 0.00 0.00 0.00 3.93
1600 1945 1.487558 ACATCCCGTTAATAACCGCCT 59.512 47.619 0.00 0.00 0.00 5.52
1601 1946 1.957668 ACATCCCGTTAATAACCGCC 58.042 50.000 0.00 0.00 0.00 6.13
1602 1947 3.487879 CCAAACATCCCGTTAATAACCGC 60.488 47.826 0.00 0.00 36.59 5.68
1603 1948 3.690628 ACCAAACATCCCGTTAATAACCG 59.309 43.478 0.00 0.00 36.59 4.44
1604 1949 4.701171 TGACCAAACATCCCGTTAATAACC 59.299 41.667 0.00 0.00 36.59 2.85
1605 1950 5.883503 TGACCAAACATCCCGTTAATAAC 57.116 39.130 0.00 0.00 36.59 1.89
1606 1951 7.394923 AGAAATGACCAAACATCCCGTTAATAA 59.605 33.333 0.00 0.00 36.59 1.40
1607 1952 6.887545 AGAAATGACCAAACATCCCGTTAATA 59.112 34.615 0.00 0.00 36.59 0.98
1608 1953 5.714806 AGAAATGACCAAACATCCCGTTAAT 59.285 36.000 0.00 0.00 36.59 1.40
1609 1954 5.048364 CAGAAATGACCAAACATCCCGTTAA 60.048 40.000 0.00 0.00 36.59 2.01
1610 1955 4.457603 CAGAAATGACCAAACATCCCGTTA 59.542 41.667 0.00 0.00 36.59 3.18
1611 1956 3.255642 CAGAAATGACCAAACATCCCGTT 59.744 43.478 0.00 0.00 40.50 4.44
1612 1957 2.819608 CAGAAATGACCAAACATCCCGT 59.180 45.455 0.00 0.00 0.00 5.28
1613 1958 3.081061 TCAGAAATGACCAAACATCCCG 58.919 45.455 0.00 0.00 0.00 5.14
1614 1959 5.243730 TCTTTCAGAAATGACCAAACATCCC 59.756 40.000 0.00 0.00 0.00 3.85
1640 1985 0.763035 ACTGGAATACGGGGCCATAC 59.237 55.000 4.39 0.00 0.00 2.39
1831 2176 0.974010 CCAATCAACAGCAGCCCCAT 60.974 55.000 0.00 0.00 0.00 4.00
3216 3580 3.420576 CACCAGTGCGAAAATAACAAACG 59.579 43.478 0.00 0.00 0.00 3.60
3387 3751 5.105997 CCTCCTTGTGATTTCTGACCAAATC 60.106 44.000 0.00 0.00 41.41 2.17
3388 3752 4.768968 CCTCCTTGTGATTTCTGACCAAAT 59.231 41.667 0.00 0.00 0.00 2.32
3403 3767 1.734388 GCGTTTTGCCACCTCCTTGT 61.734 55.000 0.00 0.00 37.76 3.16
3417 3781 2.413634 GCTAGGCGTTAATTGTGCGTTT 60.414 45.455 0.00 0.00 0.00 3.60
3594 3958 4.217550 GCTGGAAGTTGGTACATAAAAGCA 59.782 41.667 0.00 0.00 39.30 3.91
3726 4090 3.244700 CCCTGCCATTATAGAAGACCCAG 60.245 52.174 0.00 0.00 0.00 4.45
3824 4188 1.886542 ACCACGGCTTCATTTTCCTTC 59.113 47.619 0.00 0.00 0.00 3.46
3884 4248 0.538057 TTCTGCTGCCCAGGAGTTTG 60.538 55.000 15.04 0.00 45.62 2.93
3941 4305 1.001764 CTGTGGCAGCATCCCTTCA 60.002 57.895 0.00 0.00 0.00 3.02
4044 4408 4.713792 AGAACCAGAAGATCCACAAACT 57.286 40.909 0.00 0.00 0.00 2.66
4131 4495 0.105039 GGGGCATCTAACGTCCTCTG 59.895 60.000 0.00 0.00 0.00 3.35
4382 4746 5.837437 AGAGAACTAACCATGCGATTAGAG 58.163 41.667 13.52 0.00 33.44 2.43
4391 4755 5.230942 AGAACGTCAAGAGAACTAACCATG 58.769 41.667 0.00 0.00 0.00 3.66
4413 4778 8.598075 ACGTTTACACTACAGTACAAGAAAAAG 58.402 33.333 0.00 0.52 0.00 2.27
4645 5010 0.475632 ATCCTGACCACCTCAACCCA 60.476 55.000 0.00 0.00 0.00 4.51
4654 5019 0.807496 GCTGCAAAGATCCTGACCAC 59.193 55.000 0.00 0.00 0.00 4.16
4745 5110 3.118038 TGGAGCCATCTATTGTAACCCAC 60.118 47.826 0.00 0.00 0.00 4.61
4751 5116 6.763715 AAACCTATGGAGCCATCTATTGTA 57.236 37.500 5.06 0.00 37.82 2.41
4829 5194 0.036010 CCACCACCAGAGGCAAGTAG 60.036 60.000 0.00 0.00 0.00 2.57
4892 5257 7.770433 CCCAGTATCAACAGAATTCAGACATAA 59.230 37.037 8.44 0.00 0.00 1.90
5081 5446 0.246635 GTGCCGCCAGAGAGAGTAAA 59.753 55.000 0.00 0.00 0.00 2.01
5084 5449 3.386237 GGTGCCGCCAGAGAGAGT 61.386 66.667 0.00 0.00 37.17 3.24
5095 5460 1.067142 ACTACCATATATGCGGTGCCG 60.067 52.381 7.24 6.22 43.09 5.69
5103 5468 8.557592 ACAAGCAATCATCACTACCATATATG 57.442 34.615 5.68 5.68 0.00 1.78
5154 5520 7.272084 GCTCTGCAACAAACATAAAAGTATCAG 59.728 37.037 0.00 0.00 0.00 2.90
5157 5523 6.389906 GGCTCTGCAACAAACATAAAAGTAT 58.610 36.000 0.00 0.00 0.00 2.12
5282 5648 5.181690 TGAAACTAAACATTCCAGTGTGC 57.818 39.130 0.00 0.00 31.49 4.57
5375 5741 9.828852 GGTACGAGAGAATATGTACATCTTTAG 57.171 37.037 12.68 3.09 39.08 1.85
5396 5765 4.808414 ATATGGATGGTGATCAGGTACG 57.192 45.455 0.00 0.00 0.00 3.67
5408 5777 6.528537 TCAACTCCAACAAAATATGGATGG 57.471 37.500 0.00 0.00 44.41 3.51
5432 5801 1.944709 ACGGTTACAGTTCCAAGTTGC 59.055 47.619 0.00 0.00 0.00 4.17
5451 5820 5.275067 AGTTGCCTATCAGATCAGAAGAC 57.725 43.478 0.00 0.00 0.00 3.01
5467 5836 5.988561 TGAACAAAATGATGGTTAAGTTGCC 59.011 36.000 0.00 0.00 0.00 4.52
5516 5885 4.079787 AGGACCTCATATTTGCAGGCTTTA 60.080 41.667 0.00 0.00 0.00 1.85
5683 6097 2.999355 GGAGCAGAGAACAGTAAGCAAG 59.001 50.000 0.00 0.00 0.00 4.01
5696 6110 3.564644 CCTTGAATGCATTAGGAGCAGAG 59.435 47.826 19.64 9.88 46.36 3.35
5718 6132 7.798982 GCAGAAACAAAGAGTTATAACACACTC 59.201 37.037 17.65 6.31 40.26 3.51
5744 6532 7.813148 TGACTAGAACTTCTATCGGAAAAAGTG 59.187 37.037 0.00 0.00 32.53 3.16
5824 6701 2.658422 GACTTACCGCCCGAACCA 59.342 61.111 0.00 0.00 0.00 3.67
5834 6711 8.261522 ACTTCTCATCTTCAAATAGGACTTACC 58.738 37.037 0.00 0.00 39.35 2.85
5854 6731 6.756542 ACCTGCAAAAATTAACACAACTTCTC 59.243 34.615 0.00 0.00 0.00 2.87
5954 6831 7.765307 AGCATGGTTTAGATGTCACTATTTTG 58.235 34.615 0.00 0.00 0.00 2.44
5978 6856 9.709495 CTAATCATCCTGGAAGAAGATAAAGAG 57.291 37.037 5.64 0.00 34.07 2.85
6012 6891 8.867097 GGAGGAAGTATATATTGTGGTGAAGTA 58.133 37.037 0.00 0.00 0.00 2.24
6013 6892 7.471539 CGGAGGAAGTATATATTGTGGTGAAGT 60.472 40.741 0.00 0.00 0.00 3.01
6015 6894 6.325545 ACGGAGGAAGTATATATTGTGGTGAA 59.674 38.462 0.00 0.00 0.00 3.18
6017 6896 6.015350 AGACGGAGGAAGTATATATTGTGGTG 60.015 42.308 0.00 0.00 0.00 4.17
6018 6897 6.075984 AGACGGAGGAAGTATATATTGTGGT 58.924 40.000 0.00 0.00 0.00 4.16
6031 6925 4.106197 CAAGTAATTCGAGACGGAGGAAG 58.894 47.826 0.00 0.00 0.00 3.46
6041 6935 5.445939 CCATTTCCACGACAAGTAATTCGAG 60.446 44.000 0.00 0.00 38.63 4.04
6042 6936 4.390603 CCATTTCCACGACAAGTAATTCGA 59.609 41.667 0.00 0.00 38.63 3.71
6116 7010 6.934645 CCCTCTGTCTGAAATTACTTGTGTTA 59.065 38.462 0.00 0.00 0.00 2.41
6117 7011 5.765182 CCCTCTGTCTGAAATTACTTGTGTT 59.235 40.000 0.00 0.00 0.00 3.32
6119 7013 5.551233 TCCCTCTGTCTGAAATTACTTGTG 58.449 41.667 0.00 0.00 0.00 3.33
6121 7015 5.799213 ACTCCCTCTGTCTGAAATTACTTG 58.201 41.667 0.00 0.00 0.00 3.16
6130 7025 5.671463 AGGAATATACTCCCTCTGTCTGA 57.329 43.478 0.00 0.00 35.95 3.27
6146 7041 1.111116 CCTCGGCCGGTGTAGGAATA 61.111 60.000 27.83 0.00 0.00 1.75
6159 7054 1.079405 TCACCATTTCGTCCTCGGC 60.079 57.895 0.00 0.00 37.69 5.54
6202 7097 7.670364 TCGATCTAATATCCACACAACATGAT 58.330 34.615 0.00 0.00 0.00 2.45
6238 7133 7.811653 TGATCTCATCTACGATCAGATTACAC 58.188 38.462 0.00 0.00 40.62 2.90
6243 7138 5.476254 TGCTTGATCTCATCTACGATCAGAT 59.524 40.000 0.00 0.00 44.66 2.90
6247 7142 4.381270 CGTTGCTTGATCTCATCTACGATC 59.619 45.833 0.00 0.00 37.22 3.69
6290 7185 1.071385 CCCCTCTCTCCATTCAATCCG 59.929 57.143 0.00 0.00 0.00 4.18
6299 7194 1.956639 TATTCCGCCCCCTCTCTCCA 61.957 60.000 0.00 0.00 0.00 3.86
6300 7195 1.152312 TATTCCGCCCCCTCTCTCC 60.152 63.158 0.00 0.00 0.00 3.71
6301 7196 4.621269 TATTCCGCCCCCTCTCTC 57.379 61.111 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.