Multiple sequence alignment - TraesCS4B01G240200

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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 TraesCS4B01G240200 chr4B 100.000 6390 0 0 1 6390 498378771 498372382 0.000000e+00 11801.0
1 TraesCS4B01G240200 chr4B 99.048 105 1 0 162 266 32922891 32922787 8.460000e-44 189.0
2 TraesCS4B01G240200 chr4B 96.250 80 1 1 4238 4315 12501386 12501307 5.200000e-26 130.0
3 TraesCS4B01G240200 chr4B 98.630 73 1 0 15 87 498378684 498378612 5.200000e-26 130.0
4 TraesCS4B01G240200 chr4B 98.630 73 1 0 88 160 498378757 498378685 5.200000e-26 130.0
5 TraesCS4B01G240200 chr4D 95.397 2868 79 27 625 3454 402531701 402528849 0.000000e+00 4516.0
6 TraesCS4B01G240200 chr4D 94.799 2884 78 34 3534 6390 402528711 402525873 0.000000e+00 4429.0
7 TraesCS4B01G240200 chr4D 98.305 59 0 1 3452 3510 402528768 402528711 1.130000e-17 102.0
8 TraesCS4B01G240200 chr4D 93.333 45 3 0 120 164 402532236 402532192 4.130000e-07 67.6
9 TraesCS4B01G240200 chr4D 92.683 41 3 0 47 87 402532236 402532196 6.920000e-05 60.2
10 TraesCS4B01G240200 chr4A 92.014 3043 137 37 258 3240 60021595 60018599 0.000000e+00 4176.0
11 TraesCS4B01G240200 chr4A 92.157 969 54 15 4313 5264 60017245 60016282 0.000000e+00 1349.0
12 TraesCS4B01G240200 chr4A 95.540 583 19 4 3663 4239 60017824 60017243 0.000000e+00 926.0
13 TraesCS4B01G240200 chr4A 89.934 457 26 7 5705 6155 60015613 60015171 7.190000e-159 571.0
14 TraesCS4B01G240200 chr4A 93.574 249 9 4 3418 3666 60018110 60017869 1.310000e-96 364.0
15 TraesCS4B01G240200 chr4A 90.783 217 10 5 6147 6360 60015020 60014811 1.360000e-71 281.0
16 TraesCS4B01G240200 chr4A 85.124 242 29 3 5264 5505 60016197 60015963 2.300000e-59 241.0
17 TraesCS4B01G240200 chr4A 95.139 144 7 0 3277 3420 60018306 60018163 1.790000e-55 228.0
18 TraesCS4B01G240200 chr4A 96.296 81 2 1 4238 4318 724795866 724795787 1.450000e-26 132.0
19 TraesCS4B01G240200 chr4A 90.000 50 5 0 1 50 60021710 60021661 1.490000e-06 65.8
20 TraesCS4B01G240200 chr5D 99.048 105 1 0 155 259 500862443 500862547 8.460000e-44 189.0
21 TraesCS4B01G240200 chr2B 99.048 105 1 0 160 264 764831276 764831172 8.460000e-44 189.0
22 TraesCS4B01G240200 chr2B 93.023 86 3 1 4238 4323 779647359 779647277 8.700000e-24 122.0
23 TraesCS4B01G240200 chr1B 100.000 101 0 0 160 260 328139683 328139783 3.040000e-43 187.0
24 TraesCS4B01G240200 chr1B 95.536 112 3 2 150 260 263273954 263274064 1.830000e-40 178.0
25 TraesCS4B01G240200 chr6D 100.000 100 0 0 160 259 466538129 466538228 1.090000e-42 185.0
26 TraesCS4B01G240200 chr6B 100.000 100 0 0 161 260 651412631 651412730 1.090000e-42 185.0
27 TraesCS4B01G240200 chr6B 91.209 91 6 1 4236 4324 135505595 135505685 8.700000e-24 122.0
28 TraesCS4B01G240200 chr6B 98.305 59 1 0 3236 3294 76149799 76149741 3.150000e-18 104.0
29 TraesCS4B01G240200 chr6B 96.491 57 2 0 3237 3293 512256584 512256528 1.900000e-15 95.3
30 TraesCS4B01G240200 chr5B 96.396 111 4 0 154 264 91884425 91884535 3.930000e-42 183.0
31 TraesCS4B01G240200 chr7B 98.077 104 2 0 161 264 591048766 591048663 1.420000e-41 182.0
32 TraesCS4B01G240200 chr5A 97.468 79 1 1 4240 4318 655994172 655994095 4.020000e-27 134.0
33 TraesCS4B01G240200 chr7D 92.473 93 2 4 4228 4315 29876364 29876456 1.870000e-25 128.0
34 TraesCS4B01G240200 chr7D 94.048 84 4 1 4238 4320 234073752 234073669 6.730000e-25 126.0
35 TraesCS4B01G240200 chr2D 93.103 87 4 1 4231 4315 188810511 188810597 6.730000e-25 126.0
36 TraesCS4B01G240200 chr7A 100.000 54 0 0 3237 3290 83529725 83529672 4.080000e-17 100.0
37 TraesCS4B01G240200 chr3B 98.182 55 1 0 3237 3291 450376593 450376647 5.270000e-16 97.1
38 TraesCS4B01G240200 chr2A 98.214 56 0 1 3237 3291 654910273 654910328 5.270000e-16 97.1
39 TraesCS4B01G240200 chr3A 96.491 57 2 0 3237 3293 420334702 420334758 1.900000e-15 95.3
40 TraesCS4B01G240200 chr1D 96.552 58 1 1 3237 3293 47948792 47948849 1.900000e-15 95.3
41 TraesCS4B01G240200 chr3D 92.188 64 4 1 3229 3291 424659638 424659575 8.820000e-14 89.8


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 TraesCS4B01G240200 chr4B 498372382 498378771 6389 True 4020.333333 11801 99.086667 1 6390 3 chr4B.!!$R3 6389
1 TraesCS4B01G240200 chr4D 402525873 402532236 6363 True 1834.960000 4516 94.903400 47 6390 5 chr4D.!!$R1 6343
2 TraesCS4B01G240200 chr4A 60014811 60021710 6899 True 911.311111 4176 91.585000 1 6360 9 chr4A.!!$R2 6359

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
388 389 0.109153 TGATCCCATGCCATCGAAGG 59.891 55.0 1.31 1.31 0.00 3.46 F
2141 2316 0.036388 TCGAAGCCTGTCACATTCCC 60.036 55.0 0.00 0.00 0.00 3.97 F
3835 4486 0.105862 ATTGGCCATCCCCATGTCAG 60.106 55.0 6.09 0.00 34.21 3.51 F
4617 5285 0.526662 AAAACGTCACCAAACCGCAA 59.473 45.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 2528 0.251297 TCATGTCCTTGCCAACAGGG 60.251 55.000 0.0 0.0 44.36 4.45 R
3896 4549 2.226330 TCATCAAAACGAAGTGGTGGG 58.774 47.619 0.0 0.0 45.00 4.61 R
5385 6140 0.166814 GCACACGCTTCAAGATCACC 59.833 55.000 0.0 0.0 34.30 4.02 R
5913 6836 0.179073 CCATCACTCCATCACCCGAC 60.179 60.000 0.0 0.0 0.00 4.79 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
35 36 4.201861 GGCTGCACTAGAAACAATAGAAGC 60.202 45.833 0.50 0.00 0.00 3.86
39 40 5.178797 GCACTAGAAACAATAGAAGCAGGA 58.821 41.667 0.00 0.00 0.00 3.86
40 41 5.064071 GCACTAGAAACAATAGAAGCAGGAC 59.936 44.000 0.00 0.00 0.00 3.85
44 45 7.885399 ACTAGAAACAATAGAAGCAGGACAAAT 59.115 33.333 0.00 0.00 0.00 2.32
55 56 8.814038 AGAAGCAGGACAAATTATAACTCAAT 57.186 30.769 0.00 0.00 0.00 2.57
56 57 8.897752 AGAAGCAGGACAAATTATAACTCAATC 58.102 33.333 0.00 0.00 0.00 2.67
58 59 7.118723 AGCAGGACAAATTATAACTCAATCCA 58.881 34.615 7.14 0.00 0.00 3.41
59 60 7.284034 AGCAGGACAAATTATAACTCAATCCAG 59.716 37.037 7.14 2.02 0.00 3.86
62 63 9.178758 AGGACAAATTATAACTCAATCCAGAAC 57.821 33.333 7.14 0.00 0.00 3.01
63 64 8.956426 GGACAAATTATAACTCAATCCAGAACA 58.044 33.333 0.00 0.00 0.00 3.18
64 65 9.994432 GACAAATTATAACTCAATCCAGAACAG 57.006 33.333 0.00 0.00 0.00 3.16
65 66 9.520515 ACAAATTATAACTCAATCCAGAACAGT 57.479 29.630 0.00 0.00 0.00 3.55
68 69 9.739276 AATTATAACTCAATCCAGAACAGTTCA 57.261 29.630 15.85 0.00 0.00 3.18
69 70 8.547967 TTATAACTCAATCCAGAACAGTTCAC 57.452 34.615 15.85 0.00 0.00 3.18
70 71 4.696479 ACTCAATCCAGAACAGTTCACT 57.304 40.909 15.85 0.00 0.00 3.41
73 74 5.992217 ACTCAATCCAGAACAGTTCACTAAC 59.008 40.000 15.85 0.00 35.72 2.34
77 78 6.867662 ATCCAGAACAGTTCACTAACAAAG 57.132 37.500 15.85 0.00 38.12 2.77
78 79 5.123227 TCCAGAACAGTTCACTAACAAAGG 58.877 41.667 15.85 3.49 38.12 3.11
79 80 4.275936 CCAGAACAGTTCACTAACAAAGGG 59.724 45.833 15.85 0.00 38.12 3.95
80 81 3.883489 AGAACAGTTCACTAACAAAGGGC 59.117 43.478 15.85 0.00 38.12 5.19
81 82 3.290948 ACAGTTCACTAACAAAGGGCA 57.709 42.857 0.00 0.00 38.12 5.36
82 83 3.832527 ACAGTTCACTAACAAAGGGCAT 58.167 40.909 0.00 0.00 38.12 4.40
83 84 4.980573 ACAGTTCACTAACAAAGGGCATA 58.019 39.130 0.00 0.00 38.12 3.14
84 85 5.003804 ACAGTTCACTAACAAAGGGCATAG 58.996 41.667 0.00 0.00 38.12 2.23
85 86 4.010349 AGTTCACTAACAAAGGGCATAGC 58.990 43.478 0.00 0.00 38.12 2.97
86 87 4.010349 GTTCACTAACAAAGGGCATAGCT 58.990 43.478 0.00 0.00 35.56 3.32
87 88 3.873910 TCACTAACAAAGGGCATAGCTC 58.126 45.455 0.00 0.00 0.00 4.09
88 89 3.519510 TCACTAACAAAGGGCATAGCTCT 59.480 43.478 0.00 0.00 43.58 4.09
89 90 3.624861 CACTAACAAAGGGCATAGCTCTG 59.375 47.826 0.00 0.00 39.10 3.35
90 91 1.467920 AACAAAGGGCATAGCTCTGC 58.532 50.000 15.34 15.34 39.10 4.26
91 92 0.329261 ACAAAGGGCATAGCTCTGCA 59.671 50.000 23.66 0.00 39.10 4.41
92 93 1.064166 ACAAAGGGCATAGCTCTGCAT 60.064 47.619 23.66 10.32 39.10 3.96
93 94 2.029623 CAAAGGGCATAGCTCTGCATT 58.970 47.619 23.66 15.21 39.10 3.56
94 95 3.216800 CAAAGGGCATAGCTCTGCATTA 58.783 45.455 23.66 0.00 39.10 1.90
95 96 2.855209 AGGGCATAGCTCTGCATTAG 57.145 50.000 23.66 0.00 38.31 1.73
96 97 2.333069 AGGGCATAGCTCTGCATTAGA 58.667 47.619 23.66 0.00 38.31 2.10
97 98 2.707791 AGGGCATAGCTCTGCATTAGAA 59.292 45.455 23.66 0.00 38.31 2.10
98 99 3.137176 AGGGCATAGCTCTGCATTAGAAA 59.863 43.478 23.66 0.00 38.31 2.52
99 100 3.251972 GGGCATAGCTCTGCATTAGAAAC 59.748 47.826 23.66 5.46 44.12 2.78
100 101 3.879295 GGCATAGCTCTGCATTAGAAACA 59.121 43.478 23.66 0.00 44.12 2.83
101 102 4.336433 GGCATAGCTCTGCATTAGAAACAA 59.664 41.667 23.66 0.00 44.12 2.83
102 103 5.009410 GGCATAGCTCTGCATTAGAAACAAT 59.991 40.000 23.66 0.00 44.12 2.71
103 104 6.205464 GGCATAGCTCTGCATTAGAAACAATA 59.795 38.462 23.66 0.00 44.12 1.90
104 105 7.296660 GCATAGCTCTGCATTAGAAACAATAG 58.703 38.462 18.39 0.00 41.87 1.73
105 106 7.172190 GCATAGCTCTGCATTAGAAACAATAGA 59.828 37.037 18.39 0.00 41.87 1.98
106 107 9.049523 CATAGCTCTGCATTAGAAACAATAGAA 57.950 33.333 0.00 0.00 34.32 2.10
107 108 7.551035 AGCTCTGCATTAGAAACAATAGAAG 57.449 36.000 0.54 0.00 34.32 2.85
108 109 6.038050 AGCTCTGCATTAGAAACAATAGAAGC 59.962 38.462 0.54 0.00 34.32 3.86
109 110 6.183360 GCTCTGCATTAGAAACAATAGAAGCA 60.183 38.462 0.54 0.00 34.32 3.91
110 111 7.312657 TCTGCATTAGAAACAATAGAAGCAG 57.687 36.000 0.00 0.00 45.04 4.24
111 112 6.317140 TCTGCATTAGAAACAATAGAAGCAGG 59.683 38.462 0.00 0.00 44.14 4.85
112 113 6.179756 TGCATTAGAAACAATAGAAGCAGGA 58.820 36.000 0.00 0.00 0.00 3.86
113 114 6.094048 TGCATTAGAAACAATAGAAGCAGGAC 59.906 38.462 0.00 0.00 0.00 3.85
114 115 6.094048 GCATTAGAAACAATAGAAGCAGGACA 59.906 38.462 0.00 0.00 0.00 4.02
115 116 7.362056 GCATTAGAAACAATAGAAGCAGGACAA 60.362 37.037 0.00 0.00 0.00 3.18
116 117 8.514594 CATTAGAAACAATAGAAGCAGGACAAA 58.485 33.333 0.00 0.00 0.00 2.83
117 118 8.635765 TTAGAAACAATAGAAGCAGGACAAAT 57.364 30.769 0.00 0.00 0.00 2.32
118 119 7.530426 AGAAACAATAGAAGCAGGACAAATT 57.470 32.000 0.00 0.00 0.00 1.82
119 120 8.635765 AGAAACAATAGAAGCAGGACAAATTA 57.364 30.769 0.00 0.00 0.00 1.40
120 121 9.247861 AGAAACAATAGAAGCAGGACAAATTAT 57.752 29.630 0.00 0.00 0.00 1.28
152 153 4.275936 CCAGAACAGTTCACTAACAAAGGG 59.724 45.833 15.85 0.00 38.12 3.95
155 156 3.832527 ACAGTTCACTAACAAAGGGCAT 58.167 40.909 0.00 0.00 38.12 4.40
164 165 5.753921 CACTAACAAAGGGCATAGCTACTAC 59.246 44.000 0.00 0.00 0.00 2.73
165 166 5.661759 ACTAACAAAGGGCATAGCTACTACT 59.338 40.000 0.00 0.00 0.00 2.57
166 167 4.674281 ACAAAGGGCATAGCTACTACTC 57.326 45.455 0.00 0.00 0.00 2.59
167 168 3.388350 ACAAAGGGCATAGCTACTACTCC 59.612 47.826 0.00 0.00 0.00 3.85
168 169 2.312424 AGGGCATAGCTACTACTCCC 57.688 55.000 0.00 2.57 33.65 4.30
169 170 1.790157 AGGGCATAGCTACTACTCCCT 59.210 52.381 11.99 11.99 36.78 4.20
170 171 2.172679 GGGCATAGCTACTACTCCCTC 58.827 57.143 0.00 0.00 31.95 4.30
171 172 2.172679 GGCATAGCTACTACTCCCTCC 58.827 57.143 0.00 0.00 0.00 4.30
172 173 1.813786 GCATAGCTACTACTCCCTCCG 59.186 57.143 0.00 0.00 0.00 4.63
173 174 2.814842 GCATAGCTACTACTCCCTCCGT 60.815 54.545 0.00 0.00 0.00 4.69
174 175 2.926778 TAGCTACTACTCCCTCCGTC 57.073 55.000 0.00 0.00 0.00 4.79
175 176 0.183252 AGCTACTACTCCCTCCGTCC 59.817 60.000 0.00 0.00 0.00 4.79
176 177 0.822944 GCTACTACTCCCTCCGTCCC 60.823 65.000 0.00 0.00 0.00 4.46
177 178 0.549950 CTACTACTCCCTCCGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
178 179 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
179 180 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
180 181 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
181 182 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
182 183 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
183 184 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
184 185 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
185 186 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
186 187 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
187 188 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
188 189 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
189 190 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
190 191 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
191 192 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
192 193 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
193 194 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
194 195 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
195 196 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
196 197 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
197 198 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
198 199 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
199 200 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
200 201 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
201 202 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
204 205 8.535690 AATAAGTGTCTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
205 206 5.793030 AGTGTCTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
206 207 5.774630 AGTGTCTCAACTTTGTACTAGCTC 58.225 41.667 0.00 0.00 0.00 4.09
207 208 5.536916 AGTGTCTCAACTTTGTACTAGCTCT 59.463 40.000 0.00 0.00 0.00 4.09
208 209 6.715718 AGTGTCTCAACTTTGTACTAGCTCTA 59.284 38.462 0.00 0.00 0.00 2.43
209 210 7.024768 GTGTCTCAACTTTGTACTAGCTCTAG 58.975 42.308 0.00 2.55 39.04 2.43
211 212 7.881751 TGTCTCAACTTTGTACTAGCTCTAGTA 59.118 37.037 11.59 11.59 43.98 1.82
235 236 7.801716 ACAAATTTGTACTAAGCTCAAGACA 57.198 32.000 22.10 0.00 40.16 3.41
236 237 7.639945 ACAAATTTGTACTAAGCTCAAGACAC 58.360 34.615 22.10 2.09 40.16 3.67
237 238 7.499232 ACAAATTTGTACTAAGCTCAAGACACT 59.501 33.333 22.10 0.00 40.16 3.55
238 239 8.345565 CAAATTTGTACTAAGCTCAAGACACTT 58.654 33.333 10.15 0.00 0.00 3.16
239 240 9.555727 AAATTTGTACTAAGCTCAAGACACTTA 57.444 29.630 3.19 0.00 0.00 2.24
240 241 9.726438 AATTTGTACTAAGCTCAAGACACTTAT 57.274 29.630 3.19 0.00 0.00 1.73
241 242 9.726438 ATTTGTACTAAGCTCAAGACACTTATT 57.274 29.630 3.19 0.00 0.00 1.40
242 243 9.555727 TTTGTACTAAGCTCAAGACACTTATTT 57.444 29.630 3.19 0.00 0.00 1.40
243 244 9.555727 TTGTACTAAGCTCAAGACACTTATTTT 57.444 29.630 3.19 0.00 0.00 1.82
244 245 8.988934 TGTACTAAGCTCAAGACACTTATTTTG 58.011 33.333 3.19 0.00 0.00 2.44
245 246 7.440523 ACTAAGCTCAAGACACTTATTTTGG 57.559 36.000 3.19 0.00 0.00 3.28
246 247 5.712152 AAGCTCAAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
247 248 4.985538 AGCTCAAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
248 249 4.762251 AGCTCAAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
249 250 4.378459 GCTCAAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
250 251 4.069304 TCAAGACACTTATTTTGGGACGG 58.931 43.478 0.00 0.00 0.00 4.79
251 252 4.069304 CAAGACACTTATTTTGGGACGGA 58.931 43.478 0.00 0.00 0.00 4.69
252 253 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
253 254 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
254 255 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
255 256 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
256 257 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
257 258 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
258 259 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
292 293 7.175816 TCAACCAAGCTTTAGTGTTGCATATTA 59.824 33.333 17.01 3.46 36.97 0.98
293 294 7.645058 ACCAAGCTTTAGTGTTGCATATTAT 57.355 32.000 0.00 0.00 0.00 1.28
294 295 8.066612 ACCAAGCTTTAGTGTTGCATATTATT 57.933 30.769 0.00 0.00 0.00 1.40
295 296 8.190784 ACCAAGCTTTAGTGTTGCATATTATTC 58.809 33.333 0.00 0.00 0.00 1.75
301 302 5.991328 AGTGTTGCATATTATTCCGTGAG 57.009 39.130 0.00 0.00 0.00 3.51
311 312 2.839486 ATTCCGTGAGAGCTGAACAA 57.161 45.000 0.00 0.00 0.00 2.83
317 318 1.346068 GTGAGAGCTGAACAACTCCCT 59.654 52.381 0.00 0.00 33.18 4.20
318 319 1.345741 TGAGAGCTGAACAACTCCCTG 59.654 52.381 0.00 0.00 33.18 4.45
331 332 3.197927 ACTCCCTGGAGACTCAGATTT 57.802 47.619 19.85 0.00 44.53 2.17
334 335 4.026744 CTCCCTGGAGACTCAGATTTACA 58.973 47.826 7.45 0.00 44.53 2.41
337 338 4.020218 CCCTGGAGACTCAGATTTACACAA 60.020 45.833 4.53 0.00 36.93 3.33
379 380 2.621998 CAATTCCAGTCTGATCCCATGC 59.378 50.000 0.00 0.00 0.00 4.06
384 385 0.395686 AGTCTGATCCCATGCCATCG 59.604 55.000 0.00 0.00 0.00 3.84
385 386 0.394192 GTCTGATCCCATGCCATCGA 59.606 55.000 0.00 0.00 0.00 3.59
386 387 1.130777 TCTGATCCCATGCCATCGAA 58.869 50.000 0.00 0.00 0.00 3.71
387 388 1.071228 TCTGATCCCATGCCATCGAAG 59.929 52.381 0.00 0.00 0.00 3.79
388 389 0.109153 TGATCCCATGCCATCGAAGG 59.891 55.000 1.31 1.31 0.00 3.46
389 390 0.607489 GATCCCATGCCATCGAAGGG 60.607 60.000 9.05 5.43 40.98 3.95
416 417 0.466922 GCCTTGGGGGACATCATCAG 60.467 60.000 0.00 0.00 37.23 2.90
487 497 0.168788 CAATCGGAAGCACGCAACAT 59.831 50.000 0.00 0.00 0.00 2.71
566 576 0.953471 CGATCCAACCGCTCAAACCA 60.953 55.000 0.00 0.00 0.00 3.67
698 828 1.305633 CTCACCTGAGGAGGAGGCA 60.306 63.158 4.99 0.00 42.93 4.75
949 1091 3.272334 GCGCGGGCCATACTTCTG 61.272 66.667 14.45 0.00 0.00 3.02
1089 1244 3.695606 GTGAGTGGGAGCCAGCGA 61.696 66.667 0.00 0.00 32.34 4.93
1143 1298 2.160205 GGCTGTTTGACTAACCCCTTC 58.840 52.381 0.00 0.00 35.81 3.46
1495 1661 2.464865 CGGATGCTGCTAACAGTAGTC 58.535 52.381 0.00 0.00 46.30 2.59
1497 1663 2.099263 GGATGCTGCTAACAGTAGTCGA 59.901 50.000 0.00 0.00 46.30 4.20
1505 1671 7.676605 CTGCTAACAGTAGTCGAGTAGACGC 62.677 52.000 0.00 0.00 45.52 5.19
1527 1693 5.182950 CGCTCATGTCTGATTCCTAGTATCT 59.817 44.000 0.00 0.00 0.00 1.98
1541 1707 8.929260 TTCCTAGTATCTACGATGTATTTCCA 57.071 34.615 0.00 0.00 0.00 3.53
1618 1784 1.142688 AAGAGTGGGTGGAGGCCATT 61.143 55.000 5.01 0.00 35.28 3.16
1684 1850 0.178992 TGGAGAAACTGGCACCCAAG 60.179 55.000 0.00 0.00 30.80 3.61
1708 1874 1.374252 CGAGCCTGTTTACCTGCGT 60.374 57.895 0.00 0.00 0.00 5.24
1847 2014 5.430007 TGTGATTATTGTAGGGGGTTAACG 58.570 41.667 0.00 0.00 0.00 3.18
1850 2017 6.426025 GTGATTATTGTAGGGGGTTAACGATC 59.574 42.308 0.00 0.00 0.00 3.69
1976 2144 6.817270 ATTTTGTTGCTATGAAATCGATGC 57.183 33.333 0.00 0.00 0.00 3.91
1983 2151 3.061831 GCTATGAAATCGATGCCAGATCG 59.938 47.826 0.00 0.00 42.38 3.69
2138 2313 0.322975 AGCTCGAAGCCTGTCACATT 59.677 50.000 3.66 0.00 43.77 2.71
2140 2315 1.363744 CTCGAAGCCTGTCACATTCC 58.636 55.000 0.00 0.00 0.00 3.01
2141 2316 0.036388 TCGAAGCCTGTCACATTCCC 60.036 55.000 0.00 0.00 0.00 3.97
2142 2317 0.321564 CGAAGCCTGTCACATTCCCA 60.322 55.000 0.00 0.00 0.00 4.37
2238 2414 5.221303 TGCATAAGGCTGAAATTATCCTTGC 60.221 40.000 2.89 0.63 45.15 4.01
2346 2528 2.200923 AAATGCTTGCCCCAATGCCC 62.201 55.000 0.00 0.00 0.00 5.36
2597 2784 3.163594 GCGCACACATTAACTGATGTTC 58.836 45.455 0.30 0.00 38.15 3.18
2750 2937 0.675522 CGGGTTTGTAAGGTCGGCAT 60.676 55.000 0.00 0.00 0.00 4.40
3173 3378 3.998341 CTGTTGGGGATTTTGCAGAATTG 59.002 43.478 3.69 0.00 0.00 2.32
3314 3775 1.681264 TGCAGACACTCACTTCTTCGA 59.319 47.619 0.00 0.00 0.00 3.71
3540 4139 4.906065 TCATCCATAACTCAATTGCAGC 57.094 40.909 0.00 0.00 0.00 5.25
3549 4148 5.458041 AACTCAATTGCAGCACTAACAAT 57.542 34.783 0.00 0.00 35.59 2.71
3657 4256 5.215160 GCTCAATGGTTTTGTAGAAGTGTG 58.785 41.667 0.00 0.00 0.00 3.82
3835 4486 0.105862 ATTGGCCATCCCCATGTCAG 60.106 55.000 6.09 0.00 34.21 3.51
3896 4549 1.975660 TGTCTGGTGGTTGGCTTAAC 58.024 50.000 0.00 0.00 38.60 2.01
4161 4815 4.906065 TGATCATTTGGAGTATGCTTGC 57.094 40.909 0.00 0.00 0.00 4.01
4165 4819 5.818136 TCATTTGGAGTATGCTTGCTTAC 57.182 39.130 9.68 9.68 0.00 2.34
4212 4866 4.521146 CATCTGTGGGCTTGATTTACTCT 58.479 43.478 0.00 0.00 0.00 3.24
4350 5004 7.890127 ACCTTGAACATTTATCAAATCTCCTGA 59.110 33.333 0.00 0.00 36.43 3.86
4520 5188 4.441079 GGAGGGCTTGATTTTGTGATCATG 60.441 45.833 0.00 0.00 36.05 3.07
4612 5280 1.914389 GCGCAAAACGTCACCAAAC 59.086 52.632 0.30 0.00 46.11 2.93
4617 5285 0.526662 AAAACGTCACCAAACCGCAA 59.473 45.000 0.00 0.00 0.00 4.85
4764 5432 6.430000 GCTTTGTGTGAAGTTCTCCCTTTATA 59.570 38.462 4.17 0.00 0.00 0.98
4904 5572 7.502561 AGTTAGGCAAAAAGTTACAGTTGATCT 59.497 33.333 0.00 0.00 0.00 2.75
4908 5576 6.417930 GGCAAAAAGTTACAGTTGATCTGAAC 59.582 38.462 0.00 0.00 46.27 3.18
5022 5690 6.464222 TGTCCTGATTGTGACCTTAAACTAG 58.536 40.000 0.00 0.00 0.00 2.57
5031 5699 3.514309 TGACCTTAAACTAGAGACCAGCC 59.486 47.826 0.00 0.00 0.00 4.85
5049 5717 2.435437 AGCCTTTTGTGTTTCTTGGCAT 59.565 40.909 0.00 0.00 41.12 4.40
5118 5786 6.371278 TGAGACGATAGGGTTTATCTTAGGT 58.629 40.000 0.00 0.00 43.77 3.08
5121 5789 6.264970 AGACGATAGGGTTTATCTTAGGTCAC 59.735 42.308 0.00 0.00 43.77 3.67
5144 5814 5.239525 ACAGCATATTCCCGCTAGATTTTTC 59.760 40.000 0.00 0.00 36.50 2.29
5207 5877 4.634184 TGTAGAGTATTGTCCTCGCTTC 57.366 45.455 0.00 0.00 34.08 3.86
5472 6227 1.442769 GAAGACGGCAGATTTCAGCA 58.557 50.000 0.00 0.00 0.00 4.41
5473 6228 2.012673 GAAGACGGCAGATTTCAGCAT 58.987 47.619 0.00 0.00 0.00 3.79
5486 6241 7.545965 GCAGATTTCAGCATATACCGTACTAAT 59.454 37.037 0.00 0.00 0.00 1.73
5545 6337 3.428589 GGACCGGTTGTACTGTACATCTC 60.429 52.174 20.31 12.80 38.68 2.75
5577 6369 6.707440 TTGGCAAGTGATTTCTTTAGTTCA 57.293 33.333 0.00 0.00 0.00 3.18
5594 6386 7.520451 TTAGTTCACGAGCCATATACAGTAT 57.480 36.000 0.00 0.00 0.00 2.12
5595 6387 6.015027 AGTTCACGAGCCATATACAGTATC 57.985 41.667 0.00 0.00 0.00 2.24
5691 6586 3.739300 ACGTTTCAGTGAATCTTGTACGG 59.261 43.478 22.50 10.15 0.00 4.02
5824 6744 2.202932 GCGCGAGGATGTGTGGAT 60.203 61.111 12.10 0.00 0.00 3.41
6036 6964 3.303135 TGCAAGAGCCCGAGTCGT 61.303 61.111 12.31 0.00 41.13 4.34
6037 6965 2.048127 GCAAGAGCCCGAGTCGTT 60.048 61.111 12.31 0.00 33.58 3.85
6049 6977 2.288273 CCGAGTCGTTCTTGTCTTCCTT 60.288 50.000 12.31 0.00 0.00 3.36
6115 7043 1.728971 GAAACGTGTGGAGCTGATGAG 59.271 52.381 0.00 0.00 0.00 2.90
6130 7058 4.482386 CTGATGAGATGTTGCTTTTGTGG 58.518 43.478 0.00 0.00 0.00 4.17
6134 7062 3.890756 TGAGATGTTGCTTTTGTGGTGAT 59.109 39.130 0.00 0.00 0.00 3.06
6135 7063 4.232221 GAGATGTTGCTTTTGTGGTGATG 58.768 43.478 0.00 0.00 0.00 3.07
6136 7064 3.890756 AGATGTTGCTTTTGTGGTGATGA 59.109 39.130 0.00 0.00 0.00 2.92
6144 7072 4.681483 GCTTTTGTGGTGATGAAAGTTAGC 59.319 41.667 0.00 0.00 32.97 3.09
6145 7232 4.846779 TTTGTGGTGATGAAAGTTAGCC 57.153 40.909 0.00 0.00 0.00 3.93
6207 7297 2.530460 TGCTAGAAATGGCCAATGGT 57.470 45.000 10.96 0.00 0.00 3.55
6220 7310 3.202906 GCCAATGGTTGCGTCTCTATTA 58.797 45.455 0.00 0.00 0.00 0.98
6242 7332 2.154462 CGATCCCATGCAGAAATACCC 58.846 52.381 0.00 0.00 0.00 3.69
6244 7334 0.555769 TCCCATGCAGAAATACCCCC 59.444 55.000 0.00 0.00 0.00 5.40
6258 7348 0.539669 ACCCCCAGCTTTTTCTTCCG 60.540 55.000 0.00 0.00 0.00 4.30
6259 7349 1.250840 CCCCCAGCTTTTTCTTCCGG 61.251 60.000 0.00 0.00 0.00 5.14
6260 7350 0.539669 CCCCAGCTTTTTCTTCCGGT 60.540 55.000 0.00 0.00 0.00 5.28
6307 7398 9.988350 ATAAAACTCAAGAGCATGTTTTATACG 57.012 29.630 16.18 0.00 45.58 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.632589 TCTAGTGCAGCCAAGAGTGA 58.367 50.000 0.00 0.00 0.00 3.41
35 36 8.737168 TCTGGATTGAGTTATAATTTGTCCTG 57.263 34.615 0.00 0.00 0.00 3.86
39 40 9.520515 ACTGTTCTGGATTGAGTTATAATTTGT 57.479 29.630 0.00 0.00 0.00 2.83
44 45 8.375506 AGTGAACTGTTCTGGATTGAGTTATAA 58.624 33.333 20.18 0.00 0.00 0.98
50 51 5.991606 TGTTAGTGAACTGTTCTGGATTGAG 59.008 40.000 20.18 0.00 36.45 3.02
52 53 6.618287 TTGTTAGTGAACTGTTCTGGATTG 57.382 37.500 20.18 0.00 36.45 2.67
55 56 5.123227 CCTTTGTTAGTGAACTGTTCTGGA 58.877 41.667 20.18 3.82 36.45 3.86
56 57 4.275936 CCCTTTGTTAGTGAACTGTTCTGG 59.724 45.833 20.18 8.75 36.45 3.86
58 59 3.883489 GCCCTTTGTTAGTGAACTGTTCT 59.117 43.478 20.18 4.96 36.45 3.01
59 60 3.630312 TGCCCTTTGTTAGTGAACTGTTC 59.370 43.478 13.49 13.49 36.45 3.18
62 63 4.142600 GCTATGCCCTTTGTTAGTGAACTG 60.143 45.833 0.00 0.00 36.45 3.16
63 64 4.010349 GCTATGCCCTTTGTTAGTGAACT 58.990 43.478 0.00 0.00 36.45 3.01
64 65 4.010349 AGCTATGCCCTTTGTTAGTGAAC 58.990 43.478 0.00 0.00 36.00 3.18
65 66 4.019321 AGAGCTATGCCCTTTGTTAGTGAA 60.019 41.667 0.00 0.00 0.00 3.18
66 67 3.519510 AGAGCTATGCCCTTTGTTAGTGA 59.480 43.478 0.00 0.00 0.00 3.41
67 68 3.624861 CAGAGCTATGCCCTTTGTTAGTG 59.375 47.826 0.00 0.00 0.00 2.74
68 69 3.878778 CAGAGCTATGCCCTTTGTTAGT 58.121 45.455 0.00 0.00 0.00 2.24
69 70 2.615912 GCAGAGCTATGCCCTTTGTTAG 59.384 50.000 22.72 0.00 40.43 2.34
70 71 2.026356 TGCAGAGCTATGCCCTTTGTTA 60.026 45.455 29.15 6.24 45.91 2.41
73 74 1.688772 ATGCAGAGCTATGCCCTTTG 58.311 50.000 29.15 0.00 45.91 2.77
77 78 2.847327 TCTAATGCAGAGCTATGCCC 57.153 50.000 29.15 4.91 45.91 5.36
78 79 3.879295 TGTTTCTAATGCAGAGCTATGCC 59.121 43.478 29.15 12.36 45.91 4.40
79 80 5.490139 TTGTTTCTAATGCAGAGCTATGC 57.510 39.130 26.11 26.11 46.68 3.14
80 81 8.599055 TCTATTGTTTCTAATGCAGAGCTATG 57.401 34.615 3.34 3.34 33.83 2.23
81 82 9.270640 CTTCTATTGTTTCTAATGCAGAGCTAT 57.729 33.333 0.00 0.00 33.83 2.97
82 83 7.225538 GCTTCTATTGTTTCTAATGCAGAGCTA 59.774 37.037 0.00 0.00 33.83 3.32
83 84 6.038050 GCTTCTATTGTTTCTAATGCAGAGCT 59.962 38.462 0.00 0.00 33.83 4.09
84 85 6.183360 TGCTTCTATTGTTTCTAATGCAGAGC 60.183 38.462 0.00 0.00 33.83 4.09
85 86 7.312657 TGCTTCTATTGTTTCTAATGCAGAG 57.687 36.000 0.00 0.00 33.83 3.35
86 87 6.317140 CCTGCTTCTATTGTTTCTAATGCAGA 59.683 38.462 0.00 0.00 44.51 4.26
87 88 6.317140 TCCTGCTTCTATTGTTTCTAATGCAG 59.683 38.462 0.00 0.00 42.34 4.41
88 89 6.094048 GTCCTGCTTCTATTGTTTCTAATGCA 59.906 38.462 0.00 0.00 0.00 3.96
89 90 6.094048 TGTCCTGCTTCTATTGTTTCTAATGC 59.906 38.462 0.00 0.00 0.00 3.56
90 91 7.615582 TGTCCTGCTTCTATTGTTTCTAATG 57.384 36.000 0.00 0.00 0.00 1.90
91 92 8.635765 TTTGTCCTGCTTCTATTGTTTCTAAT 57.364 30.769 0.00 0.00 0.00 1.73
92 93 8.635765 ATTTGTCCTGCTTCTATTGTTTCTAA 57.364 30.769 0.00 0.00 0.00 2.10
93 94 8.635765 AATTTGTCCTGCTTCTATTGTTTCTA 57.364 30.769 0.00 0.00 0.00 2.10
94 95 7.530426 AATTTGTCCTGCTTCTATTGTTTCT 57.470 32.000 0.00 0.00 0.00 2.52
98 99 9.686683 AGTTATAATTTGTCCTGCTTCTATTGT 57.313 29.630 0.00 0.00 0.00 2.71
100 101 9.905713 TGAGTTATAATTTGTCCTGCTTCTATT 57.094 29.630 0.00 0.00 0.00 1.73
101 102 9.905713 TTGAGTTATAATTTGTCCTGCTTCTAT 57.094 29.630 0.00 0.00 0.00 1.98
102 103 9.905713 ATTGAGTTATAATTTGTCCTGCTTCTA 57.094 29.630 0.00 0.00 0.00 2.10
103 104 8.814038 ATTGAGTTATAATTTGTCCTGCTTCT 57.186 30.769 0.00 0.00 0.00 2.85
104 105 8.131731 GGATTGAGTTATAATTTGTCCTGCTTC 58.868 37.037 0.00 0.00 0.00 3.86
105 106 7.615365 TGGATTGAGTTATAATTTGTCCTGCTT 59.385 33.333 0.00 0.00 0.00 3.91
106 107 7.118723 TGGATTGAGTTATAATTTGTCCTGCT 58.881 34.615 0.00 0.00 0.00 4.24
107 108 7.283127 TCTGGATTGAGTTATAATTTGTCCTGC 59.717 37.037 0.00 0.00 0.00 4.85
108 109 8.737168 TCTGGATTGAGTTATAATTTGTCCTG 57.263 34.615 0.00 0.00 0.00 3.86
109 110 9.178758 GTTCTGGATTGAGTTATAATTTGTCCT 57.821 33.333 0.00 0.00 0.00 3.85
110 111 8.956426 TGTTCTGGATTGAGTTATAATTTGTCC 58.044 33.333 0.00 0.00 0.00 4.02
111 112 9.994432 CTGTTCTGGATTGAGTTATAATTTGTC 57.006 33.333 0.00 0.00 0.00 3.18
112 113 9.520515 ACTGTTCTGGATTGAGTTATAATTTGT 57.479 29.630 0.00 0.00 0.00 2.83
115 116 9.739276 TGAACTGTTCTGGATTGAGTTATAATT 57.261 29.630 20.18 0.00 0.00 1.40
116 117 9.167311 GTGAACTGTTCTGGATTGAGTTATAAT 57.833 33.333 20.18 0.00 0.00 1.28
117 118 8.375506 AGTGAACTGTTCTGGATTGAGTTATAA 58.624 33.333 20.18 0.00 0.00 0.98
118 119 7.907389 AGTGAACTGTTCTGGATTGAGTTATA 58.093 34.615 20.18 0.00 0.00 0.98
119 120 6.773638 AGTGAACTGTTCTGGATTGAGTTAT 58.226 36.000 20.18 0.00 0.00 1.89
120 121 6.174720 AGTGAACTGTTCTGGATTGAGTTA 57.825 37.500 20.18 0.00 0.00 2.24
121 122 5.041191 AGTGAACTGTTCTGGATTGAGTT 57.959 39.130 20.18 0.00 0.00 3.01
122 123 4.696479 AGTGAACTGTTCTGGATTGAGT 57.304 40.909 20.18 0.00 0.00 3.41
123 124 5.991606 TGTTAGTGAACTGTTCTGGATTGAG 59.008 40.000 20.18 0.00 36.45 3.02
152 153 1.813786 CGGAGGGAGTAGTAGCTATGC 59.186 57.143 0.00 0.00 0.00 3.14
155 156 1.419387 GGACGGAGGGAGTAGTAGCTA 59.581 57.143 0.00 0.00 0.00 3.32
164 165 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
165 166 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
166 167 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
167 168 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
168 169 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
169 170 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
170 171 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
171 172 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
172 173 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
173 174 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
174 175 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
175 176 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
178 179 8.989980 GCTAGTACAAAGTTGAGACACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
179 180 8.368668 AGCTAGTACAAAGTTGAGACACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
180 181 7.897864 AGCTAGTACAAAGTTGAGACACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
181 182 7.230913 AGAGCTAGTACAAAGTTGAGACACTTA 59.769 37.037 0.00 0.00 35.87 2.24
182 183 6.041069 AGAGCTAGTACAAAGTTGAGACACTT 59.959 38.462 0.00 0.00 38.74 3.16
183 184 5.536916 AGAGCTAGTACAAAGTTGAGACACT 59.463 40.000 0.00 0.00 0.00 3.55
184 185 5.774630 AGAGCTAGTACAAAGTTGAGACAC 58.225 41.667 0.00 0.00 0.00 3.67
185 186 6.715718 ACTAGAGCTAGTACAAAGTTGAGACA 59.284 38.462 8.35 0.00 43.98 3.41
186 187 7.148355 ACTAGAGCTAGTACAAAGTTGAGAC 57.852 40.000 8.35 0.00 43.98 3.36
210 211 8.770828 GTGTCTTGAGCTTAGTACAAATTTGTA 58.229 33.333 23.91 23.91 42.35 2.41
211 212 7.499232 AGTGTCTTGAGCTTAGTACAAATTTGT 59.501 33.333 25.99 25.99 44.86 2.83
212 213 7.865707 AGTGTCTTGAGCTTAGTACAAATTTG 58.134 34.615 16.67 16.67 0.00 2.32
213 214 8.451908 AAGTGTCTTGAGCTTAGTACAAATTT 57.548 30.769 0.00 0.00 0.00 1.82
214 215 9.726438 ATAAGTGTCTTGAGCTTAGTACAAATT 57.274 29.630 0.00 0.00 0.00 1.82
215 216 9.726438 AATAAGTGTCTTGAGCTTAGTACAAAT 57.274 29.630 0.00 0.00 0.00 2.32
216 217 9.555727 AAATAAGTGTCTTGAGCTTAGTACAAA 57.444 29.630 0.00 0.00 0.00 2.83
217 218 9.555727 AAAATAAGTGTCTTGAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
218 219 8.988934 CAAAATAAGTGTCTTGAGCTTAGTACA 58.011 33.333 0.00 0.00 0.00 2.90
219 220 8.443937 CCAAAATAAGTGTCTTGAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
220 221 7.606456 CCCAAAATAAGTGTCTTGAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
221 222 6.431234 CCCAAAATAAGTGTCTTGAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
222 223 6.655003 TCCCAAAATAAGTGTCTTGAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
223 224 6.430000 GTCCCAAAATAAGTGTCTTGAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
224 225 5.241728 GTCCCAAAATAAGTGTCTTGAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
225 226 4.762251 GTCCCAAAATAAGTGTCTTGAGCT 59.238 41.667 0.00 0.00 0.00 4.09
226 227 4.378459 CGTCCCAAAATAAGTGTCTTGAGC 60.378 45.833 0.00 0.00 0.00 4.26
227 228 4.154195 CCGTCCCAAAATAAGTGTCTTGAG 59.846 45.833 0.00 0.00 0.00 3.02
228 229 4.069304 CCGTCCCAAAATAAGTGTCTTGA 58.931 43.478 0.00 0.00 0.00 3.02
229 230 4.069304 TCCGTCCCAAAATAAGTGTCTTG 58.931 43.478 0.00 0.00 0.00 3.02
230 231 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
231 232 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
232 233 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
233 234 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
234 235 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
235 236 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
236 237 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
237 238 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
238 239 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
239 240 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
240 241 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
241 242 1.273381 TGATACTCCCTCCGTCCCAAA 60.273 52.381 0.00 0.00 0.00 3.28
242 243 0.337082 TGATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
243 244 0.561184 ATGATACTCCCTCCGTCCCA 59.439 55.000 0.00 0.00 0.00 4.37
244 245 0.969894 CATGATACTCCCTCCGTCCC 59.030 60.000 0.00 0.00 0.00 4.46
245 246 0.969894 CCATGATACTCCCTCCGTCC 59.030 60.000 0.00 0.00 0.00 4.79
246 247 1.996798 TCCATGATACTCCCTCCGTC 58.003 55.000 0.00 0.00 0.00 4.79
247 248 2.158310 TGATCCATGATACTCCCTCCGT 60.158 50.000 0.00 0.00 0.00 4.69
248 249 2.529632 TGATCCATGATACTCCCTCCG 58.470 52.381 0.00 0.00 0.00 4.63
249 250 3.008485 GGTTGATCCATGATACTCCCTCC 59.992 52.174 0.00 0.00 35.97 4.30
250 251 3.648067 TGGTTGATCCATGATACTCCCTC 59.352 47.826 0.00 0.00 41.93 4.30
251 252 3.668821 TGGTTGATCCATGATACTCCCT 58.331 45.455 0.00 0.00 41.93 4.20
252 253 4.392940 CTTGGTTGATCCATGATACTCCC 58.607 47.826 0.00 0.00 46.60 4.30
253 254 3.817647 GCTTGGTTGATCCATGATACTCC 59.182 47.826 0.00 0.00 46.60 3.85
254 255 4.712476 AGCTTGGTTGATCCATGATACTC 58.288 43.478 0.00 0.00 46.60 2.59
255 256 4.785346 AGCTTGGTTGATCCATGATACT 57.215 40.909 0.00 0.00 46.60 2.12
256 257 5.841957 AAAGCTTGGTTGATCCATGATAC 57.158 39.130 0.00 0.00 46.60 2.24
257 258 6.543465 CACTAAAGCTTGGTTGATCCATGATA 59.457 38.462 0.00 0.00 46.60 2.15
258 259 5.359009 CACTAAAGCTTGGTTGATCCATGAT 59.641 40.000 0.00 0.00 46.60 2.45
281 282 4.511454 GCTCTCACGGAATAATATGCAACA 59.489 41.667 0.00 0.00 0.00 3.33
292 293 2.037772 AGTTGTTCAGCTCTCACGGAAT 59.962 45.455 0.00 0.00 0.00 3.01
293 294 1.412710 AGTTGTTCAGCTCTCACGGAA 59.587 47.619 0.00 0.00 0.00 4.30
294 295 1.000163 GAGTTGTTCAGCTCTCACGGA 60.000 52.381 8.92 0.00 0.00 4.69
295 296 1.423395 GAGTTGTTCAGCTCTCACGG 58.577 55.000 8.92 0.00 0.00 4.94
301 302 0.687354 TCCAGGGAGTTGTTCAGCTC 59.313 55.000 7.89 7.89 0.00 4.09
311 312 2.938428 AATCTGAGTCTCCAGGGAGT 57.062 50.000 14.70 0.00 42.49 3.85
317 318 5.071788 ACCTTTGTGTAAATCTGAGTCTCCA 59.928 40.000 0.00 0.00 0.00 3.86
318 319 5.552178 ACCTTTGTGTAAATCTGAGTCTCC 58.448 41.667 0.00 0.00 0.00 3.71
331 332 3.314080 GTGCAAGCTACAACCTTTGTGTA 59.686 43.478 1.73 0.00 45.03 2.90
337 338 2.558359 GGAATGTGCAAGCTACAACCTT 59.442 45.455 0.00 0.00 0.00 3.50
379 380 2.203394 CCCCATGCCCTTCGATGG 60.203 66.667 10.36 10.36 39.18 3.51
394 395 4.143301 GATGTCCCCCAAGGCCCC 62.143 72.222 0.00 0.00 34.51 5.80
395 396 2.647003 GATGATGTCCCCCAAGGCCC 62.647 65.000 0.00 0.00 34.51 5.80
416 417 6.205270 CGGACTAAGAGTAGATTAGGGAGAAC 59.795 46.154 0.00 0.00 35.06 3.01
474 484 0.099436 GGGATGATGTTGCGTGCTTC 59.901 55.000 0.00 0.00 0.00 3.86
476 486 1.750399 GGGGATGATGTTGCGTGCT 60.750 57.895 0.00 0.00 0.00 4.40
487 497 3.037549 GTGGCAAAATATTGGGGGATGA 58.962 45.455 0.00 0.00 37.02 2.92
566 576 2.675317 GCGGAGTAGTGTGATTTCAGCT 60.675 50.000 0.00 0.00 0.00 4.24
675 805 2.493973 CTCCTCAGGTGAGCGCTC 59.506 66.667 30.42 30.42 40.75 5.03
723 853 4.803908 GCCTTCAAGGGGCCTCCG 62.804 72.222 5.33 0.00 43.49 4.63
949 1091 2.237392 AGGGATCACAGTTTGACTAGCC 59.763 50.000 0.00 0.00 36.92 3.93
960 1102 1.739049 GAGGAGCGAGGGATCACAG 59.261 63.158 0.00 0.00 0.00 3.66
1089 1244 3.835395 CAGGGTTTAGAGACAGACTCCTT 59.165 47.826 0.00 0.00 45.96 3.36
1143 1298 3.077556 CGTCTGGTGGGAGGGGAG 61.078 72.222 0.00 0.00 0.00 4.30
1495 1661 1.666189 TCAGACATGAGCGTCTACTCG 59.334 52.381 0.00 0.00 44.49 4.18
1497 1663 3.067461 GGAATCAGACATGAGCGTCTACT 59.933 47.826 0.00 0.00 44.49 2.57
1505 1671 7.604545 TCGTAGATACTAGGAATCAGACATGAG 59.395 40.741 0.00 0.00 39.29 2.90
1527 1693 8.499403 TTCACATGAATTGGAAATACATCGTA 57.501 30.769 0.00 0.00 0.00 3.43
1556 1722 3.804873 GGGATCTGTCATCGCTTAAGAAC 59.195 47.826 6.67 0.00 0.00 3.01
1559 1725 3.742433 AGGGATCTGTCATCGCTTAAG 57.258 47.619 0.00 0.00 37.98 1.85
1618 1784 3.625897 CACAGACCTGCACCCCGA 61.626 66.667 0.00 0.00 0.00 5.14
1660 1826 1.609072 GGTGCCAGTTTCTCCAACTTC 59.391 52.381 0.00 0.00 43.89 3.01
1684 1850 1.134560 AGGTAAACAGGCTCGTCGATC 59.865 52.381 0.00 0.00 0.00 3.69
1816 1983 6.459573 CCCCCTACAATAATCACATTTCGTTG 60.460 42.308 0.00 0.00 0.00 4.10
1817 1984 5.592688 CCCCCTACAATAATCACATTTCGTT 59.407 40.000 0.00 0.00 0.00 3.85
1847 2014 6.152932 ACCAAATTGCATATCAACCAGATC 57.847 37.500 0.00 0.00 37.53 2.75
1850 2017 5.933463 ACAAACCAAATTGCATATCAACCAG 59.067 36.000 0.00 0.00 37.53 4.00
1888 2055 8.546597 TTTTCAATTCGAGAAGTGATACATCA 57.453 30.769 15.24 0.00 43.60 3.07
1992 2160 3.330267 AGAAAGTCAAAGGCTAGCTTCG 58.670 45.455 15.72 2.10 0.00 3.79
2138 2313 5.185454 CAACTACTGTTCTATGCATTGGGA 58.815 41.667 3.54 0.00 33.52 4.37
2140 2315 6.500684 AACAACTACTGTTCTATGCATTGG 57.499 37.500 3.54 0.00 45.50 3.16
2346 2528 0.251297 TCATGTCCTTGCCAACAGGG 60.251 55.000 0.00 0.00 44.36 4.45
2398 2580 8.398665 ACACTGTCAAAGCTTTTACTTAAAGAG 58.601 33.333 20.94 12.75 45.00 2.85
2399 2581 8.181573 CACACTGTCAAAGCTTTTACTTAAAGA 58.818 33.333 20.94 6.33 45.00 2.52
2400 2582 7.044052 GCACACTGTCAAAGCTTTTACTTAAAG 60.044 37.037 20.94 13.62 44.99 1.85
2707 2894 7.147479 CCGGATGGAGGGAGTATCATATATTTT 60.147 40.741 0.00 0.00 37.49 1.82
2750 2937 4.039852 GGTCAAATTGGAACCTAAAAGCCA 59.960 41.667 0.00 0.00 0.00 4.75
2876 3065 7.786030 TGGGTTTTTATGTCTTCAATTTGACA 58.214 30.769 0.00 7.77 45.56 3.58
3121 3316 8.133627 GGATAAAACGCAGATTGTAGTACTAGA 58.866 37.037 1.87 0.00 0.00 2.43
3122 3317 8.136165 AGGATAAAACGCAGATTGTAGTACTAG 58.864 37.037 1.87 0.00 0.00 2.57
3173 3378 3.142174 GGGAATGTAAGACATAGCCAGC 58.858 50.000 11.34 0.00 37.97 4.85
3353 3814 2.489073 CCTCCTTTTATAAGCCCGGCAT 60.489 50.000 13.15 1.26 0.00 4.40
3522 4121 3.689347 AGTGCTGCAATTGAGTTATGGA 58.311 40.909 10.34 0.00 0.00 3.41
3896 4549 2.226330 TCATCAAAACGAAGTGGTGGG 58.774 47.619 0.00 0.00 45.00 4.61
4068 4721 3.182572 CGAACTTATAAGATGCAGTCGCC 59.817 47.826 19.38 0.00 37.32 5.54
4161 4815 5.823045 GGATGGAAATCTAACCAGTGGTAAG 59.177 44.000 17.09 0.00 39.62 2.34
4165 4819 4.202441 CTGGATGGAAATCTAACCAGTGG 58.798 47.826 7.91 7.91 39.68 4.00
4405 5059 4.512571 CCTCCAAAAACAAGCCATGAAAAG 59.487 41.667 0.00 0.00 0.00 2.27
4494 5161 3.303938 TCACAAAATCAAGCCCTCCAAA 58.696 40.909 0.00 0.00 0.00 3.28
4520 5188 5.358298 AGAAAAATAGGCAAGTGAACGTC 57.642 39.130 0.00 0.00 0.00 4.34
4605 5273 1.663135 CTTTTTGGTTGCGGTTTGGTG 59.337 47.619 0.00 0.00 0.00 4.17
4612 5280 2.275318 TGCTTTTCTTTTTGGTTGCGG 58.725 42.857 0.00 0.00 0.00 5.69
4617 5285 7.920160 TCATTTTCTTGCTTTTCTTTTTGGT 57.080 28.000 0.00 0.00 0.00 3.67
4844 5512 0.691078 GATCTACCACTGGCCAGGGA 60.691 60.000 37.27 23.26 32.29 4.20
4904 5572 2.695359 GGTAACTGATGCTTCCGTTCA 58.305 47.619 11.76 0.00 32.41 3.18
4908 5576 1.135083 ACTCGGTAACTGATGCTTCCG 60.135 52.381 0.00 0.00 39.40 4.30
5022 5690 2.952310 AGAAACACAAAAGGCTGGTCTC 59.048 45.455 0.00 0.00 0.00 3.36
5031 5699 6.215121 TGTGATATGCCAAGAAACACAAAAG 58.785 36.000 0.00 0.00 34.63 2.27
5049 5717 3.745975 CGTGAAAGCAAGAGGTTGTGATA 59.254 43.478 0.00 0.00 35.92 2.15
5118 5786 2.316108 TCTAGCGGGAATATGCTGTGA 58.684 47.619 0.00 0.00 42.46 3.58
5121 5789 5.471456 AGAAAAATCTAGCGGGAATATGCTG 59.529 40.000 0.00 0.00 42.46 4.41
5207 5877 8.433421 AATAAACTGGATAACATAGGAACACG 57.567 34.615 0.00 0.00 0.00 4.49
5385 6140 0.166814 GCACACGCTTCAAGATCACC 59.833 55.000 0.00 0.00 34.30 4.02
5386 6141 0.867746 TGCACACGCTTCAAGATCAC 59.132 50.000 0.00 0.00 39.64 3.06
5473 6228 8.963725 CCATCAGATGGTTATTAGTACGGTATA 58.036 37.037 20.30 0.00 45.54 1.47
5513 6268 1.529948 AACCGGTCCGACTGTCAGA 60.530 57.895 14.39 0.00 0.00 3.27
5577 6369 8.191446 GTGATAATGATACTGTATATGGCTCGT 58.809 37.037 0.00 0.00 0.00 4.18
5594 6386 4.079844 TCTCCCCAAAGCATGTGATAATGA 60.080 41.667 0.00 0.00 0.00 2.57
5595 6387 4.209538 TCTCCCCAAAGCATGTGATAATG 58.790 43.478 0.00 0.00 0.00 1.90
5691 6586 4.254492 GTCCAGAATTCCAAGACTGGTAC 58.746 47.826 0.00 0.00 46.68 3.34
5911 6834 0.826715 ATCACTCCATCACCCGACTG 59.173 55.000 0.00 0.00 0.00 3.51
5912 6835 0.826715 CATCACTCCATCACCCGACT 59.173 55.000 0.00 0.00 0.00 4.18
5913 6836 0.179073 CCATCACTCCATCACCCGAC 60.179 60.000 0.00 0.00 0.00 4.79
6003 6926 2.807045 CACAGGCTGACGAGACGC 60.807 66.667 23.66 0.00 29.20 5.19
6095 7023 1.728971 CTCATCAGCTCCACACGTTTC 59.271 52.381 0.00 0.00 0.00 2.78
6115 7043 4.241590 TCATCACCACAAAAGCAACATC 57.758 40.909 0.00 0.00 0.00 3.06
6130 7058 5.693814 CAACAGAAGGCTAACTTTCATCAC 58.306 41.667 0.00 0.00 40.21 3.06
6134 7062 2.884639 GGCAACAGAAGGCTAACTTTCA 59.115 45.455 0.00 0.00 40.21 2.69
6135 7063 2.884639 TGGCAACAGAAGGCTAACTTTC 59.115 45.455 0.00 0.00 46.17 2.62
6136 7064 2.944129 TGGCAACAGAAGGCTAACTTT 58.056 42.857 0.00 0.00 46.17 2.66
6207 7297 2.030185 GGGATCGCTAATAGAGACGCAA 60.030 50.000 1.84 0.00 0.00 4.85
6220 7310 2.498167 GTATTTCTGCATGGGATCGCT 58.502 47.619 11.46 0.00 0.00 4.93
6242 7332 0.598065 CACCGGAAGAAAAAGCTGGG 59.402 55.000 9.46 0.00 32.25 4.45
6244 7334 1.318576 ACCACCGGAAGAAAAAGCTG 58.681 50.000 9.46 0.00 0.00 4.24
6258 7348 9.754382 TTATATAGAACTTGTTCGAATACCACC 57.246 33.333 0.00 0.00 0.00 4.61
6288 7378 6.754675 TCGATTCGTATAAAACATGCTCTTGA 59.245 34.615 5.89 0.00 0.00 3.02
6292 7383 8.044983 CGATATCGATTCGTATAAAACATGCTC 58.955 37.037 20.50 0.00 43.02 4.26
6293 7384 7.753580 TCGATATCGATTCGTATAAAACATGCT 59.246 33.333 23.48 0.00 44.22 3.79
6294 7385 7.881634 TCGATATCGATTCGTATAAAACATGC 58.118 34.615 23.48 0.00 44.22 4.06
6369 7461 1.077787 CGGTGCCAGGCCTATGAAA 60.078 57.895 3.98 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.