Multiple sequence alignment - TraesCS3D01G319000

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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 TraesCS3D01G319000 chr3D 100.000 4730 0 0 1 4730 432551319 432546590 0.000000e+00 8735.0
1 TraesCS3D01G319000 chr3D 87.542 297 20 8 5 297 432685755 432686038 1.270000e-85 327.0
2 TraesCS3D01G319000 chr3B 93.625 4361 157 56 291 4606 564780278 564775994 0.000000e+00 6401.0
3 TraesCS3D01G319000 chr3B 87.205 297 19 12 3 295 458329176 458328895 2.120000e-83 320.0
4 TraesCS3D01G319000 chr3A 94.266 3697 124 42 291 3953 570798839 570795197 0.000000e+00 5572.0
5 TraesCS3D01G319000 chr3A 86.164 318 18 12 4413 4730 570794501 570794210 2.120000e-83 320.0
6 TraesCS3D01G319000 chr3A 86.063 287 12 14 4167 4429 570794797 570794515 2.790000e-72 283.0
7 TraesCS3D01G319000 chr3A 80.000 235 11 15 3950 4162 570795125 570794905 1.770000e-29 141.0
8 TraesCS3D01G319000 chr6B 87.667 300 15 9 2 295 134275755 134275472 3.530000e-86 329.0
9 TraesCS3D01G319000 chr6B 96.552 58 0 1 3833 3890 713029388 713029443 1.400000e-15 95.3
10 TraesCS3D01G319000 chrUn 87.333 300 21 8 2 295 96121018 96121306 1.270000e-85 327.0
11 TraesCS3D01G319000 chrUn 96.552 58 0 1 3833 3890 93419387 93419442 1.400000e-15 95.3
12 TraesCS3D01G319000 chrUn 96.552 58 0 1 3833 3890 383640324 383640379 1.400000e-15 95.3
13 TraesCS3D01G319000 chr4B 86.913 298 17 7 3 295 43740917 43740637 9.880000e-82 315.0
14 TraesCS3D01G319000 chr7D 87.770 278 17 7 23 295 111081702 111081437 4.600000e-80 309.0
15 TraesCS3D01G319000 chr5D 87.726 277 18 6 23 295 411771490 411771226 4.600000e-80 309.0
16 TraesCS3D01G319000 chr5D 96.552 58 0 1 3833 3890 503210870 503210815 1.400000e-15 95.3
17 TraesCS3D01G319000 chr5D 96.552 58 0 1 3833 3890 560877430 560877375 1.400000e-15 95.3
18 TraesCS3D01G319000 chr7B 85.235 298 25 10 2 295 265393041 265392759 5.990000e-74 289.0
19 TraesCS3D01G319000 chr2A 85.612 278 24 7 23 295 778038608 778038342 1.300000e-70 278.0
20 TraesCS3D01G319000 chr1A 88.670 203 16 3 97 295 500975243 500975044 1.700000e-59 241.0
21 TraesCS3D01G319000 chr1A 96.552 58 0 1 3833 3890 352175233 352175178 1.400000e-15 95.3
22 TraesCS3D01G319000 chr6A 96.552 58 0 1 3833 3890 271182413 271182358 1.400000e-15 95.3
23 TraesCS3D01G319000 chr1D 96.552 58 0 1 3833 3890 144235666 144235611 1.400000e-15 95.3


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 TraesCS3D01G319000 chr3D 432546590 432551319 4729 True 8735 8735 100.00000 1 4730 1 chr3D.!!$R1 4729
1 TraesCS3D01G319000 chr3B 564775994 564780278 4284 True 6401 6401 93.62500 291 4606 1 chr3B.!!$R2 4315
2 TraesCS3D01G319000 chr3A 570794210 570798839 4629 True 1579 5572 86.62325 291 4730 4 chr3A.!!$R1 4439

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
463 476 0.033920 AACTGCACAGACATGCTCGA 59.966 50.0 4.31 0.0 46.28 4.04 F
751 769 1.316706 ACTCCTACTCTGAGCACCGC 61.317 60.0 4.19 0.0 32.98 5.68 F
815 833 1.376649 AGCTCCAACTGATTTCCCCT 58.623 50.0 0.00 0.0 0.00 4.79 F
2134 2166 0.964358 GCAGCTTCTTGGCATGGAGT 60.964 55.0 10.13 0.0 34.17 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1615 1647 1.242076 CTGAACTCCCTGCCAACTTG 58.758 55.000 0.00 0.00 0.00 3.16 R
1917 1949 1.537397 ACAGAAGAGCTCCCAGGCA 60.537 57.895 10.93 0.00 34.17 4.75 R
2814 2846 0.585357 CAAGCGGCATATGTGAGAGC 59.415 55.000 1.45 3.61 0.00 4.09 R
4020 4134 0.036765 TACCAACACCTGCCGATCAC 60.037 55.000 0.00 0.00 0.00 3.06 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
31 32 4.801330 TCACTCCATGATTGTAAGACGT 57.199 40.909 0.00 0.00 29.99 4.34
32 33 4.494484 TCACTCCATGATTGTAAGACGTG 58.506 43.478 0.00 0.00 29.99 4.49
33 34 3.062639 CACTCCATGATTGTAAGACGTGC 59.937 47.826 0.00 0.00 0.00 5.34
34 35 3.261580 CTCCATGATTGTAAGACGTGCA 58.738 45.455 0.00 0.00 0.00 4.57
35 36 3.872696 TCCATGATTGTAAGACGTGCAT 58.127 40.909 0.00 0.00 0.00 3.96
36 37 4.260985 TCCATGATTGTAAGACGTGCATT 58.739 39.130 0.00 0.00 0.00 3.56
37 38 4.094739 TCCATGATTGTAAGACGTGCATTG 59.905 41.667 0.00 0.00 0.00 2.82
38 39 3.469899 TGATTGTAAGACGTGCATTGC 57.530 42.857 0.46 0.46 0.00 3.56
39 40 2.810852 TGATTGTAAGACGTGCATTGCA 59.189 40.909 7.38 7.38 35.60 4.08
49 50 2.325218 TGCATTGCACGTGTAAGCA 58.675 47.368 26.47 26.47 39.32 3.91
50 51 0.880441 TGCATTGCACGTGTAAGCAT 59.120 45.000 26.47 11.02 40.94 3.79
51 52 1.261989 GCATTGCACGTGTAAGCATG 58.738 50.000 23.17 17.39 40.94 4.06
52 53 1.898938 CATTGCACGTGTAAGCATGG 58.101 50.000 23.17 7.60 40.94 3.66
53 54 1.199789 CATTGCACGTGTAAGCATGGT 59.800 47.619 23.17 3.74 40.94 3.55
54 55 0.590682 TTGCACGTGTAAGCATGGTG 59.409 50.000 15.43 0.00 40.94 4.17
55 56 0.533978 TGCACGTGTAAGCATGGTGT 60.534 50.000 18.38 0.00 35.51 4.16
56 57 0.591170 GCACGTGTAAGCATGGTGTT 59.409 50.000 18.38 0.00 35.62 3.32
57 58 1.801771 GCACGTGTAAGCATGGTGTTA 59.198 47.619 18.38 0.00 35.62 2.41
58 59 2.418628 GCACGTGTAAGCATGGTGTTAT 59.581 45.455 18.38 0.00 35.62 1.89
59 60 3.727673 GCACGTGTAAGCATGGTGTTATG 60.728 47.826 18.38 0.00 35.62 1.90
60 61 3.006940 ACGTGTAAGCATGGTGTTATGG 58.993 45.455 0.00 0.00 35.99 2.74
61 62 3.266636 CGTGTAAGCATGGTGTTATGGA 58.733 45.455 0.00 0.00 0.00 3.41
62 63 3.063452 CGTGTAAGCATGGTGTTATGGAC 59.937 47.826 0.00 0.00 0.00 4.02
63 64 4.006989 GTGTAAGCATGGTGTTATGGACA 58.993 43.478 0.00 0.00 35.42 4.02
64 65 4.094887 GTGTAAGCATGGTGTTATGGACAG 59.905 45.833 0.00 0.00 39.39 3.51
65 66 2.425143 AGCATGGTGTTATGGACAGG 57.575 50.000 0.00 0.00 39.39 4.00
66 67 1.064463 AGCATGGTGTTATGGACAGGG 60.064 52.381 0.00 0.00 39.39 4.45
67 68 2.023788 GCATGGTGTTATGGACAGGGG 61.024 57.143 0.00 0.00 39.39 4.79
68 69 1.563879 CATGGTGTTATGGACAGGGGA 59.436 52.381 0.00 0.00 39.39 4.81
69 70 1.748732 TGGTGTTATGGACAGGGGAA 58.251 50.000 0.00 0.00 39.39 3.97
70 71 2.066592 TGGTGTTATGGACAGGGGAAA 58.933 47.619 0.00 0.00 39.39 3.13
71 72 2.447429 TGGTGTTATGGACAGGGGAAAA 59.553 45.455 0.00 0.00 39.39 2.29
72 73 3.117093 TGGTGTTATGGACAGGGGAAAAA 60.117 43.478 0.00 0.00 39.39 1.94
73 74 3.257375 GGTGTTATGGACAGGGGAAAAAC 59.743 47.826 0.00 0.00 39.39 2.43
74 75 3.892588 GTGTTATGGACAGGGGAAAAACA 59.107 43.478 0.00 0.00 39.39 2.83
75 76 4.342665 GTGTTATGGACAGGGGAAAAACAA 59.657 41.667 0.00 0.00 39.39 2.83
76 77 4.962995 TGTTATGGACAGGGGAAAAACAAA 59.037 37.500 0.00 0.00 33.40 2.83
77 78 5.425539 TGTTATGGACAGGGGAAAAACAAAA 59.574 36.000 0.00 0.00 33.40 2.44
78 79 6.100424 TGTTATGGACAGGGGAAAAACAAAAT 59.900 34.615 0.00 0.00 33.40 1.82
79 80 5.645056 ATGGACAGGGGAAAAACAAAATT 57.355 34.783 0.00 0.00 0.00 1.82
80 81 4.775236 TGGACAGGGGAAAAACAAAATTG 58.225 39.130 0.00 0.00 0.00 2.32
81 82 4.471386 TGGACAGGGGAAAAACAAAATTGA 59.529 37.500 0.00 0.00 0.00 2.57
82 83 5.131809 TGGACAGGGGAAAAACAAAATTGAT 59.868 36.000 0.00 0.00 0.00 2.57
83 84 6.327626 TGGACAGGGGAAAAACAAAATTGATA 59.672 34.615 0.00 0.00 0.00 2.15
84 85 6.649141 GGACAGGGGAAAAACAAAATTGATAC 59.351 38.462 0.00 0.00 0.00 2.24
85 86 6.220201 ACAGGGGAAAAACAAAATTGATACG 58.780 36.000 0.00 0.00 0.00 3.06
86 87 5.637387 CAGGGGAAAAACAAAATTGATACGG 59.363 40.000 0.00 0.00 0.00 4.02
87 88 5.305902 AGGGGAAAAACAAAATTGATACGGT 59.694 36.000 0.00 0.00 0.00 4.83
88 89 6.494146 AGGGGAAAAACAAAATTGATACGGTA 59.506 34.615 0.00 0.00 0.00 4.02
89 90 6.587226 GGGGAAAAACAAAATTGATACGGTAC 59.413 38.462 0.00 0.00 0.00 3.34
90 91 7.372714 GGGAAAAACAAAATTGATACGGTACT 58.627 34.615 0.00 0.00 0.00 2.73
91 92 8.513774 GGGAAAAACAAAATTGATACGGTACTA 58.486 33.333 0.00 0.00 0.00 1.82
92 93 9.550811 GGAAAAACAAAATTGATACGGTACTAG 57.449 33.333 0.00 0.00 0.00 2.57
93 94 9.550811 GAAAAACAAAATTGATACGGTACTAGG 57.449 33.333 0.00 0.00 0.00 3.02
94 95 8.851541 AAAACAAAATTGATACGGTACTAGGA 57.148 30.769 0.00 0.00 0.00 2.94
95 96 8.488651 AAACAAAATTGATACGGTACTAGGAG 57.511 34.615 0.00 0.00 0.00 3.69
96 97 7.179076 ACAAAATTGATACGGTACTAGGAGT 57.821 36.000 0.00 0.00 0.00 3.85
97 98 8.297470 ACAAAATTGATACGGTACTAGGAGTA 57.703 34.615 0.00 0.00 0.00 2.59
98 99 8.921205 ACAAAATTGATACGGTACTAGGAGTAT 58.079 33.333 0.00 0.00 32.65 2.12
107 108 9.972106 ATACGGTACTAGGAGTATATAAAAGCT 57.028 33.333 0.00 0.00 32.65 3.74
109 110 9.225436 ACGGTACTAGGAGTATATAAAAGCTAC 57.775 37.037 0.00 0.00 32.65 3.58
110 111 9.447157 CGGTACTAGGAGTATATAAAAGCTACT 57.553 37.037 0.00 0.00 32.65 2.57
157 158 5.930837 TTTTTATTGCCTTGGATACCAGG 57.069 39.130 0.00 0.00 33.81 4.45
158 159 4.871871 TTTATTGCCTTGGATACCAGGA 57.128 40.909 0.00 0.00 31.89 3.86
159 160 2.736670 ATTGCCTTGGATACCAGGAC 57.263 50.000 0.00 0.00 31.89 3.85
160 161 1.367346 TTGCCTTGGATACCAGGACA 58.633 50.000 0.00 0.00 31.89 4.02
161 162 0.911769 TGCCTTGGATACCAGGACAG 59.088 55.000 0.00 0.00 31.89 3.51
162 163 0.912486 GCCTTGGATACCAGGACAGT 59.088 55.000 0.00 0.00 31.89 3.55
163 164 1.134371 GCCTTGGATACCAGGACAGTC 60.134 57.143 0.00 0.00 31.89 3.51
164 165 2.187958 CCTTGGATACCAGGACAGTCA 58.812 52.381 2.17 0.00 31.89 3.41
165 166 2.774234 CCTTGGATACCAGGACAGTCAT 59.226 50.000 2.17 0.00 31.89 3.06
166 167 3.200825 CCTTGGATACCAGGACAGTCATT 59.799 47.826 2.17 0.00 31.89 2.57
167 168 4.446371 CTTGGATACCAGGACAGTCATTC 58.554 47.826 2.17 0.00 31.89 2.67
168 169 2.771943 TGGATACCAGGACAGTCATTCC 59.228 50.000 2.17 0.00 0.00 3.01
169 170 2.104963 GGATACCAGGACAGTCATTCCC 59.895 54.545 2.17 0.00 33.01 3.97
170 171 1.580059 TACCAGGACAGTCATTCCCC 58.420 55.000 2.17 0.00 33.01 4.81
171 172 1.208165 ACCAGGACAGTCATTCCCCC 61.208 60.000 2.17 0.00 33.01 5.40
172 173 1.221840 CAGGACAGTCATTCCCCCG 59.778 63.158 2.17 0.00 33.01 5.73
173 174 1.229529 AGGACAGTCATTCCCCCGT 60.230 57.895 2.17 0.00 33.01 5.28
174 175 0.042131 AGGACAGTCATTCCCCCGTA 59.958 55.000 2.17 0.00 33.01 4.02
175 176 0.906775 GGACAGTCATTCCCCCGTAA 59.093 55.000 2.17 0.00 0.00 3.18
176 177 1.279846 GGACAGTCATTCCCCCGTAAA 59.720 52.381 2.17 0.00 0.00 2.01
177 178 2.353323 GACAGTCATTCCCCCGTAAAC 58.647 52.381 0.00 0.00 0.00 2.01
178 179 1.982958 ACAGTCATTCCCCCGTAAACT 59.017 47.619 0.00 0.00 0.00 2.66
179 180 2.374170 ACAGTCATTCCCCCGTAAACTT 59.626 45.455 0.00 0.00 0.00 2.66
180 181 3.583966 ACAGTCATTCCCCCGTAAACTTA 59.416 43.478 0.00 0.00 0.00 2.24
181 182 3.937079 CAGTCATTCCCCCGTAAACTTAC 59.063 47.826 0.00 0.00 0.00 2.34
182 183 3.583966 AGTCATTCCCCCGTAAACTTACA 59.416 43.478 0.87 0.00 33.28 2.41
183 184 3.686241 GTCATTCCCCCGTAAACTTACAC 59.314 47.826 0.87 0.00 33.28 2.90
184 185 2.453983 TTCCCCCGTAAACTTACACG 57.546 50.000 0.87 0.00 37.89 4.49
194 195 5.966335 CGTAAACTTACACGGGTATTATGC 58.034 41.667 0.00 0.00 34.57 3.14
195 196 5.750067 CGTAAACTTACACGGGTATTATGCT 59.250 40.000 0.00 0.00 34.57 3.79
196 197 6.917477 CGTAAACTTACACGGGTATTATGCTA 59.083 38.462 0.00 0.00 34.57 3.49
197 198 7.113965 CGTAAACTTACACGGGTATTATGCTAG 59.886 40.741 0.00 0.00 34.57 3.42
198 199 5.464030 ACTTACACGGGTATTATGCTAGG 57.536 43.478 0.00 0.00 0.00 3.02
199 200 4.897670 ACTTACACGGGTATTATGCTAGGT 59.102 41.667 0.00 0.00 0.00 3.08
200 201 5.010415 ACTTACACGGGTATTATGCTAGGTC 59.990 44.000 0.00 0.00 0.00 3.85
201 202 3.302161 ACACGGGTATTATGCTAGGTCA 58.698 45.455 0.00 0.00 0.00 4.02
202 203 3.901844 ACACGGGTATTATGCTAGGTCAT 59.098 43.478 0.00 0.00 0.00 3.06
203 204 4.245660 CACGGGTATTATGCTAGGTCATG 58.754 47.826 0.00 0.00 0.00 3.07
204 205 3.901844 ACGGGTATTATGCTAGGTCATGT 59.098 43.478 0.00 0.00 0.00 3.21
205 206 4.347000 ACGGGTATTATGCTAGGTCATGTT 59.653 41.667 0.00 0.00 0.00 2.71
206 207 5.163237 ACGGGTATTATGCTAGGTCATGTTT 60.163 40.000 0.00 0.00 0.00 2.83
207 208 5.179368 CGGGTATTATGCTAGGTCATGTTTG 59.821 44.000 0.00 0.00 0.00 2.93
208 209 6.062095 GGGTATTATGCTAGGTCATGTTTGT 58.938 40.000 0.00 0.00 0.00 2.83
209 210 6.546034 GGGTATTATGCTAGGTCATGTTTGTT 59.454 38.462 0.00 0.00 0.00 2.83
210 211 7.717875 GGGTATTATGCTAGGTCATGTTTGTTA 59.282 37.037 0.00 0.00 0.00 2.41
211 212 9.116067 GGTATTATGCTAGGTCATGTTTGTTAA 57.884 33.333 0.00 0.00 0.00 2.01
217 218 8.630054 TGCTAGGTCATGTTTGTTAAATAAGT 57.370 30.769 0.00 0.00 0.00 2.24
218 219 9.073475 TGCTAGGTCATGTTTGTTAAATAAGTT 57.927 29.630 0.00 0.00 0.00 2.66
219 220 9.908152 GCTAGGTCATGTTTGTTAAATAAGTTT 57.092 29.630 0.00 0.00 0.00 2.66
222 223 9.965824 AGGTCATGTTTGTTAAATAAGTTTCAG 57.034 29.630 0.00 0.00 0.00 3.02
223 224 9.959749 GGTCATGTTTGTTAAATAAGTTTCAGA 57.040 29.630 0.00 0.00 0.00 3.27
272 273 7.810766 TTAATTGATTTTTCAACTCGGATGC 57.189 32.000 0.00 0.00 31.89 3.91
273 274 4.844998 TTGATTTTTCAACTCGGATGCA 57.155 36.364 0.00 0.00 0.00 3.96
274 275 5.389859 TTGATTTTTCAACTCGGATGCAT 57.610 34.783 0.00 0.00 0.00 3.96
275 276 5.389859 TGATTTTTCAACTCGGATGCATT 57.610 34.783 0.00 0.00 0.00 3.56
276 277 5.162794 TGATTTTTCAACTCGGATGCATTG 58.837 37.500 0.00 0.00 0.00 2.82
277 278 3.574284 TTTTCAACTCGGATGCATTGG 57.426 42.857 0.00 0.00 0.00 3.16
278 279 0.810648 TTCAACTCGGATGCATTGGC 59.189 50.000 0.00 0.00 41.68 4.52
279 280 1.031571 TCAACTCGGATGCATTGGCC 61.032 55.000 0.00 0.00 40.13 5.36
280 281 2.114670 AACTCGGATGCATTGGCCG 61.115 57.895 16.96 16.96 46.08 6.13
281 282 3.282157 CTCGGATGCATTGGCCGG 61.282 66.667 21.23 10.96 44.87 6.13
287 288 2.996153 TGCATTGGCCGGCATGTT 60.996 55.556 30.85 6.69 40.13 2.71
288 289 2.202783 GCATTGGCCGGCATGTTC 60.203 61.111 30.85 11.16 0.00 3.18
289 290 2.495866 CATTGGCCGGCATGTTCC 59.504 61.111 30.85 10.31 0.00 3.62
293 294 1.814772 TTGGCCGGCATGTTCCAAAG 61.815 55.000 30.85 0.00 35.83 2.77
367 370 1.986378 CTGTCATTGACCGTCTCGAAC 59.014 52.381 14.05 0.00 0.00 3.95
391 394 4.084013 ACATCGGAGATCAACGTTGAAAAC 60.084 41.667 32.69 24.58 45.12 2.43
416 429 1.325640 CACTGTCACTATGCACGCATC 59.674 52.381 7.99 0.00 37.82 3.91
418 431 2.274437 CTGTCACTATGCACGCATCTT 58.726 47.619 7.99 0.00 37.82 2.40
419 432 2.001872 TGTCACTATGCACGCATCTTG 58.998 47.619 7.99 7.07 37.82 3.02
420 433 2.270923 GTCACTATGCACGCATCTTGA 58.729 47.619 7.99 9.28 37.82 3.02
421 434 2.029728 GTCACTATGCACGCATCTTGAC 59.970 50.000 21.08 21.08 39.22 3.18
422 435 2.001872 CACTATGCACGCATCTTGACA 58.998 47.619 7.99 0.00 37.82 3.58
423 436 2.002586 ACTATGCACGCATCTTGACAC 58.997 47.619 7.99 0.00 37.82 3.67
424 437 1.328680 CTATGCACGCATCTTGACACC 59.671 52.381 7.99 0.00 37.82 4.16
447 460 4.717233 TGTCTTGTTTGCACATTCAACT 57.283 36.364 0.00 0.00 31.06 3.16
449 462 3.243643 GTCTTGTTTGCACATTCAACTGC 59.756 43.478 0.00 0.00 31.06 4.40
452 465 2.094338 TGTTTGCACATTCAACTGCACA 60.094 40.909 0.00 0.00 43.07 4.57
463 476 0.033920 AACTGCACAGACATGCTCGA 59.966 50.000 4.31 0.00 46.28 4.04
473 486 3.134792 ATGCTCGAGCTCGACCGT 61.135 61.111 33.84 25.56 44.22 4.83
574 588 2.310233 CGCAGTCAAGTCACCACCG 61.310 63.158 0.00 0.00 0.00 4.94
577 591 3.041940 GTCAAGTCACCACCGCCG 61.042 66.667 0.00 0.00 0.00 6.46
615 629 4.373116 GTCGCCACCTTCCTCGCA 62.373 66.667 0.00 0.00 0.00 5.10
685 703 1.689233 CCCCGTCCATCTTCCTCCA 60.689 63.158 0.00 0.00 0.00 3.86
687 705 1.522569 CCGTCCATCTTCCTCCACC 59.477 63.158 0.00 0.00 0.00 4.61
750 768 2.039818 TACTCCTACTCTGAGCACCG 57.960 55.000 4.19 0.00 32.98 4.94
751 769 1.316706 ACTCCTACTCTGAGCACCGC 61.317 60.000 4.19 0.00 32.98 5.68
752 770 2.010582 CTCCTACTCTGAGCACCGCC 62.011 65.000 4.19 0.00 0.00 6.13
786 804 2.323999 TTTGTCCATTTCCCATGGCT 57.676 45.000 6.09 0.00 39.01 4.75
815 833 1.376649 AGCTCCAACTGATTTCCCCT 58.623 50.000 0.00 0.00 0.00 4.79
864 893 3.376935 CTTCCGCCTCCGTGCATCT 62.377 63.158 0.00 0.00 0.00 2.90
1615 1647 5.292765 ACATCAATGTCGTCATCTACATCC 58.707 41.667 0.00 0.00 35.87 3.51
2061 2093 3.693471 CGGGCCATGGCAAGCAAA 61.693 61.111 36.56 0.00 44.11 3.68
2069 2101 1.113788 ATGGCAAGCAAACACACTGT 58.886 45.000 0.00 0.00 0.00 3.55
2134 2166 0.964358 GCAGCTTCTTGGCATGGAGT 60.964 55.000 10.13 0.00 34.17 3.85
2516 2548 1.425066 ACCAGGTGCAGAGAAATGGAA 59.575 47.619 0.00 0.00 0.00 3.53
2758 2790 6.094048 GCAGTACCTTGATTTGTATCACACAT 59.906 38.462 0.00 0.00 40.42 3.21
2798 2830 1.686052 GGAGCTAGGATCACTGGTCAG 59.314 57.143 0.00 0.00 31.06 3.51
2814 2846 2.031516 CAGTCTGCGGTTCCTGCTG 61.032 63.158 0.00 0.00 0.00 4.41
2916 2948 3.640029 TCAGTTACGGAGACTGGAAAGTT 59.360 43.478 12.95 0.00 43.61 2.66
3076 3108 3.313249 TCTGATGATAAAAGCATGCGGTG 59.687 43.478 13.01 0.00 0.00 4.94
3189 3221 0.615331 AGGTGATCATTGACGGCAGT 59.385 50.000 0.00 0.00 0.00 4.40
3351 3383 0.109272 GGTGCGTCGAGAATCTGTCA 60.109 55.000 0.00 0.00 0.00 3.58
3516 3548 3.785887 TGTATCTCCAAGGCCTACCAAAT 59.214 43.478 5.16 0.00 39.06 2.32
3617 3649 4.821805 CCTCAAGAGGCTTAAACTTGTTGA 59.178 41.667 11.91 1.52 42.44 3.18
3778 3811 6.758416 GGCCCAAAATTTCAGAGATACATTTC 59.242 38.462 0.00 0.00 0.00 2.17
3781 3814 7.267857 CCAAAATTTCAGAGATACATTTCCCC 58.732 38.462 0.00 0.00 0.00 4.81
3797 3830 4.241555 CCTCGCTTATGCCGGGCT 62.242 66.667 21.46 8.36 35.36 5.19
3827 3860 1.305930 GCATTCGACGGGCCTTTCTT 61.306 55.000 0.84 0.00 0.00 2.52
3828 3861 0.447801 CATTCGACGGGCCTTTCTTG 59.552 55.000 0.84 0.00 0.00 3.02
3905 3948 5.534207 AAAAGATGCTTGGTGTTGATCAA 57.466 34.783 3.38 3.38 0.00 2.57
3991 4105 3.080300 TGTTTTTGTGTGGACTGGACT 57.920 42.857 0.00 0.00 0.00 3.85
4012 4126 5.877491 ACTATGCACATCTGATGAATGGAT 58.123 37.500 23.59 19.03 31.73 3.41
4017 4131 4.388165 GCACATCTGATGAATGGATCGTAG 59.612 45.833 23.59 0.00 0.00 3.51
4018 4132 4.388165 CACATCTGATGAATGGATCGTAGC 59.612 45.833 23.59 0.00 0.00 3.58
4020 4134 4.248691 TCTGATGAATGGATCGTAGCAG 57.751 45.455 0.00 0.00 0.00 4.24
4026 4140 2.713895 ATGGATCGTAGCAGTGATCG 57.286 50.000 0.00 0.00 41.50 3.69
4047 4161 4.345547 TCGGCAGGTGTTGGTATGAATATA 59.654 41.667 0.00 0.00 0.00 0.86
4080 4202 2.996631 ACCAGTGCTGATCCAAATCTC 58.003 47.619 0.02 0.00 32.75 2.75
4122 4248 4.001652 CTGATGCAGCTAACATATCCCTG 58.998 47.826 2.53 0.00 0.00 4.45
4124 4250 1.151668 GCAGCTAACATATCCCTGCG 58.848 55.000 0.00 0.00 39.39 5.18
4126 4252 2.138320 CAGCTAACATATCCCTGCGTG 58.862 52.381 0.00 0.00 0.00 5.34
4187 4433 9.520515 AAAACTAACTGTGATTGATGTATCCTT 57.479 29.630 0.00 0.00 0.00 3.36
4232 4478 9.227777 GGCTAAAGATGAAAAGAAAACCTAGTA 57.772 33.333 0.00 0.00 0.00 1.82
4240 4486 8.232913 TGAAAAGAAAACCTAGTAGTTGCAAT 57.767 30.769 0.59 0.00 0.00 3.56
4275 4529 0.041488 CCGATGTACGTACCTCGAGC 60.041 60.000 38.05 18.51 43.76 5.03
4317 4575 1.550524 TCCTGATTCTAGCGTTGCTGT 59.449 47.619 0.70 0.00 40.10 4.40
4318 4576 2.758423 TCCTGATTCTAGCGTTGCTGTA 59.242 45.455 0.70 0.00 40.10 2.74
4416 4690 4.265507 AACGGGGAGGACTGGGGT 62.266 66.667 0.00 0.00 0.00 4.95
4499 4803 1.672854 CTGACGCGGGGATCCAACTA 61.673 60.000 15.23 0.00 0.00 2.24
4612 4922 4.873746 GATCTAATTGATCGACCCCTCA 57.126 45.455 0.00 0.00 41.68 3.86
4613 4923 5.215252 GATCTAATTGATCGACCCCTCAA 57.785 43.478 1.91 1.91 41.68 3.02
4614 4924 5.611374 GATCTAATTGATCGACCCCTCAAA 58.389 41.667 3.47 0.00 41.68 2.69
4615 4925 5.429681 TCTAATTGATCGACCCCTCAAAA 57.570 39.130 3.47 0.00 35.20 2.44
4616 4926 5.811190 TCTAATTGATCGACCCCTCAAAAA 58.189 37.500 3.47 0.00 35.20 1.94
4655 4965 5.451937 CGAATTGATTAGCCTCAGTCACCTA 60.452 44.000 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.494484 CACGTCTTACAATCATGGAGTGA 58.506 43.478 0.27 0.00 42.06 3.41
11 12 3.062639 GCACGTCTTACAATCATGGAGTG 59.937 47.826 0.00 0.00 33.62 3.51
12 13 3.262420 GCACGTCTTACAATCATGGAGT 58.738 45.455 0.00 0.00 0.00 3.85
13 14 3.261580 TGCACGTCTTACAATCATGGAG 58.738 45.455 0.00 0.00 0.00 3.86
14 15 3.326836 TGCACGTCTTACAATCATGGA 57.673 42.857 0.00 0.00 0.00 3.41
15 16 4.345288 CAATGCACGTCTTACAATCATGG 58.655 43.478 0.00 0.00 0.00 3.66
16 17 3.787634 GCAATGCACGTCTTACAATCATG 59.212 43.478 0.00 0.00 0.00 3.07
17 18 3.439825 TGCAATGCACGTCTTACAATCAT 59.560 39.130 2.72 0.00 31.71 2.45
18 19 2.810852 TGCAATGCACGTCTTACAATCA 59.189 40.909 2.72 0.00 31.71 2.57
19 20 3.469899 TGCAATGCACGTCTTACAATC 57.530 42.857 2.72 0.00 31.71 2.67
31 32 0.880441 ATGCTTACACGTGCAATGCA 59.120 45.000 24.61 24.61 42.74 3.96
32 33 1.261989 CATGCTTACACGTGCAATGC 58.738 50.000 17.22 17.34 42.74 3.56
33 34 1.199789 ACCATGCTTACACGTGCAATG 59.800 47.619 17.22 11.80 42.74 2.82
34 35 1.199789 CACCATGCTTACACGTGCAAT 59.800 47.619 17.22 0.00 42.74 3.56
35 36 0.590682 CACCATGCTTACACGTGCAA 59.409 50.000 17.22 8.50 42.74 4.08
36 37 0.533978 ACACCATGCTTACACGTGCA 60.534 50.000 17.22 8.30 43.67 4.57
37 38 0.591170 AACACCATGCTTACACGTGC 59.409 50.000 17.22 1.22 34.29 5.34
38 39 3.181511 CCATAACACCATGCTTACACGTG 60.182 47.826 15.48 15.48 36.13 4.49
39 40 3.006940 CCATAACACCATGCTTACACGT 58.993 45.455 0.00 0.00 0.00 4.49
40 41 3.063452 GTCCATAACACCATGCTTACACG 59.937 47.826 0.00 0.00 0.00 4.49
41 42 4.006989 TGTCCATAACACCATGCTTACAC 58.993 43.478 0.00 0.00 31.20 2.90
42 43 4.260985 CTGTCCATAACACCATGCTTACA 58.739 43.478 0.00 0.00 33.24 2.41
43 44 3.627577 CCTGTCCATAACACCATGCTTAC 59.372 47.826 0.00 0.00 33.24 2.34
44 45 3.371487 CCCTGTCCATAACACCATGCTTA 60.371 47.826 0.00 0.00 33.24 3.09
45 46 2.621407 CCCTGTCCATAACACCATGCTT 60.621 50.000 0.00 0.00 33.24 3.91
46 47 1.064463 CCCTGTCCATAACACCATGCT 60.064 52.381 0.00 0.00 33.24 3.79
47 48 1.392589 CCCTGTCCATAACACCATGC 58.607 55.000 0.00 0.00 33.24 4.06
48 49 1.563879 TCCCCTGTCCATAACACCATG 59.436 52.381 0.00 0.00 33.24 3.66
49 50 1.979809 TCCCCTGTCCATAACACCAT 58.020 50.000 0.00 0.00 33.24 3.55
50 51 1.748732 TTCCCCTGTCCATAACACCA 58.251 50.000 0.00 0.00 33.24 4.17
51 52 2.891191 TTTCCCCTGTCCATAACACC 57.109 50.000 0.00 0.00 33.24 4.16
52 53 3.892588 TGTTTTTCCCCTGTCCATAACAC 59.107 43.478 0.00 0.00 33.24 3.32
53 54 4.186077 TGTTTTTCCCCTGTCCATAACA 57.814 40.909 0.00 0.00 36.18 2.41
54 55 5.538849 TTTGTTTTTCCCCTGTCCATAAC 57.461 39.130 0.00 0.00 0.00 1.89
55 56 6.755542 ATTTTGTTTTTCCCCTGTCCATAA 57.244 33.333 0.00 0.00 0.00 1.90
56 57 6.327626 TCAATTTTGTTTTTCCCCTGTCCATA 59.672 34.615 0.00 0.00 0.00 2.74
57 58 5.131809 TCAATTTTGTTTTTCCCCTGTCCAT 59.868 36.000 0.00 0.00 0.00 3.41
58 59 4.471386 TCAATTTTGTTTTTCCCCTGTCCA 59.529 37.500 0.00 0.00 0.00 4.02
59 60 5.029807 TCAATTTTGTTTTTCCCCTGTCC 57.970 39.130 0.00 0.00 0.00 4.02
60 61 6.364976 CGTATCAATTTTGTTTTTCCCCTGTC 59.635 38.462 0.00 0.00 0.00 3.51
61 62 6.220201 CGTATCAATTTTGTTTTTCCCCTGT 58.780 36.000 0.00 0.00 0.00 4.00
62 63 5.637387 CCGTATCAATTTTGTTTTTCCCCTG 59.363 40.000 0.00 0.00 0.00 4.45
63 64 5.305902 ACCGTATCAATTTTGTTTTTCCCCT 59.694 36.000 0.00 0.00 0.00 4.79
64 65 5.543714 ACCGTATCAATTTTGTTTTTCCCC 58.456 37.500 0.00 0.00 0.00 4.81
65 66 7.372714 AGTACCGTATCAATTTTGTTTTTCCC 58.627 34.615 0.00 0.00 0.00 3.97
66 67 9.550811 CTAGTACCGTATCAATTTTGTTTTTCC 57.449 33.333 0.00 0.00 0.00 3.13
67 68 9.550811 CCTAGTACCGTATCAATTTTGTTTTTC 57.449 33.333 0.00 0.00 0.00 2.29
68 69 9.287373 TCCTAGTACCGTATCAATTTTGTTTTT 57.713 29.630 0.00 0.00 0.00 1.94
69 70 8.851541 TCCTAGTACCGTATCAATTTTGTTTT 57.148 30.769 0.00 0.00 0.00 2.43
70 71 8.098912 ACTCCTAGTACCGTATCAATTTTGTTT 58.901 33.333 0.00 0.00 0.00 2.83
71 72 7.618137 ACTCCTAGTACCGTATCAATTTTGTT 58.382 34.615 0.00 0.00 0.00 2.83
72 73 7.179076 ACTCCTAGTACCGTATCAATTTTGT 57.821 36.000 0.00 0.00 0.00 2.83
81 82 9.972106 AGCTTTTATATACTCCTAGTACCGTAT 57.028 33.333 0.00 0.00 32.84 3.06
83 84 9.225436 GTAGCTTTTATATACTCCTAGTACCGT 57.775 37.037 0.00 0.00 32.84 4.83
84 85 9.447157 AGTAGCTTTTATATACTCCTAGTACCG 57.553 37.037 0.00 0.00 32.84 4.02
135 136 5.420739 GTCCTGGTATCCAAGGCAATAAAAA 59.579 40.000 0.00 0.00 30.80 1.94
136 137 4.953579 GTCCTGGTATCCAAGGCAATAAAA 59.046 41.667 0.00 0.00 30.80 1.52
137 138 4.017958 TGTCCTGGTATCCAAGGCAATAAA 60.018 41.667 0.00 0.00 30.80 1.40
138 139 3.525609 TGTCCTGGTATCCAAGGCAATAA 59.474 43.478 0.00 0.00 30.80 1.40
139 140 3.119319 TGTCCTGGTATCCAAGGCAATA 58.881 45.455 0.00 0.00 30.80 1.90
140 141 1.922447 TGTCCTGGTATCCAAGGCAAT 59.078 47.619 0.00 0.00 30.80 3.56
141 142 1.281867 CTGTCCTGGTATCCAAGGCAA 59.718 52.381 0.00 0.00 30.80 4.52
142 143 0.911769 CTGTCCTGGTATCCAAGGCA 59.088 55.000 0.00 0.00 30.80 4.75
143 144 0.912486 ACTGTCCTGGTATCCAAGGC 59.088 55.000 0.00 0.00 30.80 4.35
144 145 2.187958 TGACTGTCCTGGTATCCAAGG 58.812 52.381 5.17 0.00 30.80 3.61
145 146 4.446371 GAATGACTGTCCTGGTATCCAAG 58.554 47.826 5.17 0.00 30.80 3.61
146 147 3.199946 GGAATGACTGTCCTGGTATCCAA 59.800 47.826 5.17 0.00 30.80 3.53
147 148 2.771943 GGAATGACTGTCCTGGTATCCA 59.228 50.000 5.17 0.00 31.94 3.41
148 149 2.104963 GGGAATGACTGTCCTGGTATCC 59.895 54.545 5.17 4.14 35.33 2.59
149 150 2.104963 GGGGAATGACTGTCCTGGTATC 59.895 54.545 5.17 0.00 35.33 2.24
150 151 2.127708 GGGGAATGACTGTCCTGGTAT 58.872 52.381 5.17 0.00 35.33 2.73
151 152 1.580059 GGGGAATGACTGTCCTGGTA 58.420 55.000 5.17 0.00 35.33 3.25
152 153 1.208165 GGGGGAATGACTGTCCTGGT 61.208 60.000 5.17 0.00 35.33 4.00
153 154 1.609783 GGGGGAATGACTGTCCTGG 59.390 63.158 5.17 0.00 35.33 4.45
154 155 1.221840 CGGGGGAATGACTGTCCTG 59.778 63.158 5.17 0.00 35.33 3.86
155 156 0.042131 TACGGGGGAATGACTGTCCT 59.958 55.000 5.17 0.00 35.33 3.85
156 157 0.906775 TTACGGGGGAATGACTGTCC 59.093 55.000 5.17 0.00 0.00 4.02
157 158 2.027469 AGTTTACGGGGGAATGACTGTC 60.027 50.000 0.00 0.00 0.00 3.51
158 159 1.982958 AGTTTACGGGGGAATGACTGT 59.017 47.619 0.00 0.00 0.00 3.55
159 160 2.781681 AGTTTACGGGGGAATGACTG 57.218 50.000 0.00 0.00 0.00 3.51
160 161 3.583966 TGTAAGTTTACGGGGGAATGACT 59.416 43.478 0.00 0.00 36.45 3.41
161 162 3.686241 GTGTAAGTTTACGGGGGAATGAC 59.314 47.826 0.00 0.00 36.45 3.06
162 163 3.617045 CGTGTAAGTTTACGGGGGAATGA 60.617 47.826 4.88 0.00 36.45 2.57
163 164 2.674357 CGTGTAAGTTTACGGGGGAATG 59.326 50.000 4.88 0.00 36.45 2.67
164 165 2.976589 CGTGTAAGTTTACGGGGGAAT 58.023 47.619 4.88 0.00 36.45 3.01
165 166 2.453983 CGTGTAAGTTTACGGGGGAA 57.546 50.000 4.88 0.00 36.45 3.97
171 172 5.750067 AGCATAATACCCGTGTAAGTTTACG 59.250 40.000 5.63 5.63 39.83 3.18
172 173 7.383300 CCTAGCATAATACCCGTGTAAGTTTAC 59.617 40.741 0.00 0.00 0.00 2.01
173 174 7.069826 ACCTAGCATAATACCCGTGTAAGTTTA 59.930 37.037 0.00 0.00 0.00 2.01
174 175 6.126968 ACCTAGCATAATACCCGTGTAAGTTT 60.127 38.462 0.00 0.00 0.00 2.66
175 176 5.364735 ACCTAGCATAATACCCGTGTAAGTT 59.635 40.000 0.00 0.00 0.00 2.66
176 177 4.897670 ACCTAGCATAATACCCGTGTAAGT 59.102 41.667 0.00 0.00 0.00 2.24
177 178 5.010314 TGACCTAGCATAATACCCGTGTAAG 59.990 44.000 0.00 0.00 0.00 2.34
178 179 4.894705 TGACCTAGCATAATACCCGTGTAA 59.105 41.667 0.00 0.00 0.00 2.41
179 180 4.472496 TGACCTAGCATAATACCCGTGTA 58.528 43.478 0.00 0.00 0.00 2.90
180 181 3.302161 TGACCTAGCATAATACCCGTGT 58.698 45.455 0.00 0.00 0.00 4.49
181 182 4.245660 CATGACCTAGCATAATACCCGTG 58.754 47.826 0.00 0.00 0.00 4.94
182 183 3.901844 ACATGACCTAGCATAATACCCGT 59.098 43.478 0.00 0.00 0.00 5.28
183 184 4.537135 ACATGACCTAGCATAATACCCG 57.463 45.455 0.00 0.00 0.00 5.28
184 185 6.062095 ACAAACATGACCTAGCATAATACCC 58.938 40.000 0.00 0.00 0.00 3.69
185 186 7.568199 AACAAACATGACCTAGCATAATACC 57.432 36.000 0.00 0.00 0.00 2.73
191 192 9.243105 ACTTATTTAACAAACATGACCTAGCAT 57.757 29.630 0.00 0.00 0.00 3.79
192 193 8.630054 ACTTATTTAACAAACATGACCTAGCA 57.370 30.769 0.00 0.00 0.00 3.49
193 194 9.908152 AAACTTATTTAACAAACATGACCTAGC 57.092 29.630 0.00 0.00 0.00 3.42
196 197 9.965824 CTGAAACTTATTTAACAAACATGACCT 57.034 29.630 0.00 0.00 0.00 3.85
197 198 9.959749 TCTGAAACTTATTTAACAAACATGACC 57.040 29.630 0.00 0.00 0.00 4.02
246 247 8.707839 GCATCCGAGTTGAAAAATCAATTAAAA 58.292 29.630 0.00 0.00 41.81 1.52
247 248 7.869937 TGCATCCGAGTTGAAAAATCAATTAAA 59.130 29.630 0.00 0.00 41.81 1.52
248 249 7.374272 TGCATCCGAGTTGAAAAATCAATTAA 58.626 30.769 0.00 0.00 41.81 1.40
249 250 6.918626 TGCATCCGAGTTGAAAAATCAATTA 58.081 32.000 0.00 0.00 41.81 1.40
250 251 5.782047 TGCATCCGAGTTGAAAAATCAATT 58.218 33.333 0.00 0.00 41.81 2.32
251 252 5.389859 TGCATCCGAGTTGAAAAATCAAT 57.610 34.783 0.00 0.00 41.81 2.57
252 253 4.844998 TGCATCCGAGTTGAAAAATCAA 57.155 36.364 0.00 0.00 41.81 2.57
253 254 5.162794 CAATGCATCCGAGTTGAAAAATCA 58.837 37.500 0.00 0.00 41.81 2.57
254 255 4.563976 CCAATGCATCCGAGTTGAAAAATC 59.436 41.667 0.00 0.00 37.61 2.17
255 256 4.497300 CCAATGCATCCGAGTTGAAAAAT 58.503 39.130 0.00 0.00 0.00 1.82
256 257 3.860378 GCCAATGCATCCGAGTTGAAAAA 60.860 43.478 0.00 0.00 37.47 1.94
257 258 2.352617 GCCAATGCATCCGAGTTGAAAA 60.353 45.455 0.00 0.00 37.47 2.29
258 259 1.202114 GCCAATGCATCCGAGTTGAAA 59.798 47.619 0.00 0.00 37.47 2.69
259 260 0.810648 GCCAATGCATCCGAGTTGAA 59.189 50.000 0.00 0.00 37.47 2.69
260 261 1.031571 GGCCAATGCATCCGAGTTGA 61.032 55.000 0.00 0.00 40.13 3.18
261 262 1.434696 GGCCAATGCATCCGAGTTG 59.565 57.895 0.00 0.00 40.13 3.16
262 263 2.114670 CGGCCAATGCATCCGAGTT 61.115 57.895 17.93 0.00 45.53 3.01
263 264 2.514592 CGGCCAATGCATCCGAGT 60.515 61.111 17.93 0.00 45.53 4.18
264 265 3.282157 CCGGCCAATGCATCCGAG 61.282 66.667 22.93 11.58 45.53 4.63
267 268 3.228759 ATGCCGGCCAATGCATCC 61.229 61.111 26.77 0.00 44.58 3.51
268 269 2.028484 CATGCCGGCCAATGCATC 59.972 61.111 26.77 0.00 45.98 3.91
270 271 2.996153 AACATGCCGGCCAATGCA 60.996 55.556 26.77 13.30 42.52 3.96
271 272 2.202783 GAACATGCCGGCCAATGC 60.203 61.111 26.77 6.99 0.00 3.56
272 273 1.886253 TTGGAACATGCCGGCCAATG 61.886 55.000 26.77 23.81 39.30 2.82
273 274 1.190833 TTTGGAACATGCCGGCCAAT 61.191 50.000 26.77 9.10 39.87 3.16
274 275 1.814772 CTTTGGAACATGCCGGCCAA 61.815 55.000 26.77 16.83 39.30 4.52
275 276 2.203552 TTTGGAACATGCCGGCCA 60.204 55.556 26.77 12.96 39.30 5.36
276 277 1.976474 TCTTTGGAACATGCCGGCC 60.976 57.895 26.77 7.68 39.30 6.13
277 278 1.212751 GTCTTTGGAACATGCCGGC 59.787 57.895 22.73 22.73 39.30 6.13
278 279 0.893270 TGGTCTTTGGAACATGCCGG 60.893 55.000 0.00 0.00 39.30 6.13
279 280 0.240945 GTGGTCTTTGGAACATGCCG 59.759 55.000 0.00 0.00 41.59 5.69
280 281 1.270550 CTGTGGTCTTTGGAACATGCC 59.729 52.381 0.00 0.00 41.59 4.40
281 282 1.956477 ACTGTGGTCTTTGGAACATGC 59.044 47.619 0.00 0.00 41.59 4.06
282 283 2.951642 ACACTGTGGTCTTTGGAACATG 59.048 45.455 13.09 0.00 41.59 3.21
283 284 2.951642 CACACTGTGGTCTTTGGAACAT 59.048 45.455 13.09 0.00 41.59 2.71
284 285 2.364632 CACACTGTGGTCTTTGGAACA 58.635 47.619 13.09 0.00 36.74 3.18
285 286 1.065551 GCACACTGTGGTCTTTGGAAC 59.934 52.381 13.09 0.00 33.64 3.62
286 287 1.064758 AGCACACTGTGGTCTTTGGAA 60.065 47.619 13.09 0.00 40.38 3.53
287 288 0.546122 AGCACACTGTGGTCTTTGGA 59.454 50.000 13.09 0.00 40.38 3.53
288 289 1.873591 GTAGCACACTGTGGTCTTTGG 59.126 52.381 17.00 0.00 43.42 3.28
289 290 1.873591 GGTAGCACACTGTGGTCTTTG 59.126 52.381 17.00 1.88 43.42 2.77
293 294 2.027625 GCGGTAGCACACTGTGGTC 61.028 63.158 17.00 9.15 43.42 4.02
367 370 2.606108 TCAACGTTGATCTCCGATGTG 58.394 47.619 26.53 0.00 31.01 3.21
391 394 2.375173 TGCATAGTGACAGTGCAGAG 57.625 50.000 10.20 0.00 43.30 3.35
420 433 2.166829 TGTGCAAACAAGACAAGGTGT 58.833 42.857 0.00 0.00 0.00 4.16
421 434 2.937469 TGTGCAAACAAGACAAGGTG 57.063 45.000 0.00 0.00 0.00 4.00
422 435 3.446873 TGAATGTGCAAACAAGACAAGGT 59.553 39.130 0.00 0.00 0.00 3.50
423 436 4.044336 TGAATGTGCAAACAAGACAAGG 57.956 40.909 0.00 0.00 0.00 3.61
424 437 5.005012 CAGTTGAATGTGCAAACAAGACAAG 59.995 40.000 0.00 0.00 0.00 3.16
449 462 1.138636 CGAGCTCGAGCATGTCTGTG 61.139 60.000 36.87 14.18 45.16 3.66
452 465 3.911137 TCGAGCTCGAGCATGTCT 58.089 55.556 36.87 18.07 44.22 3.41
496 509 4.680237 TTCGTCAGGCGGGCTGTG 62.680 66.667 27.88 21.50 41.72 3.66
532 546 4.745751 CGTCGGGCGGGCTGTTTA 62.746 66.667 10.43 0.00 36.85 2.01
552 566 2.607892 GGTGACTTGACTGCGCCAC 61.608 63.158 4.18 2.34 32.58 5.01
582 596 4.969196 ACTGGCGTGGCGAGTGTG 62.969 66.667 4.45 0.00 45.23 3.82
583 597 4.664677 GACTGGCGTGGCGAGTGT 62.665 66.667 9.99 0.00 46.79 3.55
615 629 4.363990 CACCGGCTCACTGCGACT 62.364 66.667 0.00 0.00 44.05 4.18
687 705 1.970917 GAGAAATGCACACCCGCGAG 61.971 60.000 8.23 0.00 33.35 5.03
697 715 1.202758 AGGAACACACGGAGAAATGCA 60.203 47.619 0.00 0.00 0.00 3.96
786 804 0.550914 AGTTGGAGCTTGTGGGTGAA 59.449 50.000 0.00 0.00 0.00 3.18
864 893 2.729028 GGGGGCTAATTACTGAAGCA 57.271 50.000 0.00 0.00 38.01 3.91
946 978 2.187946 CGAGCGAGGCCTGGATTT 59.812 61.111 20.35 2.53 0.00 2.17
967 999 0.747255 GAGCCGAATGCCTCACTCTA 59.253 55.000 0.00 0.00 42.71 2.43
971 1003 3.567797 GCGAGCCGAATGCCTCAC 61.568 66.667 0.00 0.00 42.71 3.51
1113 1145 1.216710 CTTGAGCTCGTCCACCTCC 59.783 63.158 9.64 0.00 0.00 4.30
1615 1647 1.242076 CTGAACTCCCTGCCAACTTG 58.758 55.000 0.00 0.00 0.00 3.16
1917 1949 1.537397 ACAGAAGAGCTCCCAGGCA 60.537 57.895 10.93 0.00 34.17 4.75
2061 2093 4.887071 TGCTTCCATTCTTTTACAGTGTGT 59.113 37.500 5.88 0.00 0.00 3.72
2069 2101 2.509569 TGGCGTGCTTCCATTCTTTTA 58.490 42.857 0.00 0.00 0.00 1.52
2134 2166 3.181329 TGAGAGGCATAAGAAGGTCCAA 58.819 45.455 0.00 0.00 0.00 3.53
2516 2548 3.771160 AAATCCGCTCGGCCTCGT 61.771 61.111 0.00 0.00 37.69 4.18
2758 2790 3.010027 TCCCTTGGCAGTGATTTGATGTA 59.990 43.478 0.00 0.00 0.00 2.29
2798 2830 3.426568 GCAGCAGGAACCGCAGAC 61.427 66.667 9.40 0.00 0.00 3.51
2814 2846 0.585357 CAAGCGGCATATGTGAGAGC 59.415 55.000 1.45 3.61 0.00 4.09
2916 2948 1.774254 ACACCATTTCCACTCTCACCA 59.226 47.619 0.00 0.00 0.00 4.17
3076 3108 2.484594 GGAGCTCTATCTTTGTCAGGCC 60.485 54.545 14.64 0.00 0.00 5.19
3189 3221 2.673775 TGGGGCAATCAGTTTCTTCA 57.326 45.000 0.00 0.00 0.00 3.02
3351 3383 4.080129 AGGCAGTACCAGATGAACAATGAT 60.080 41.667 0.00 0.00 43.14 2.45
3516 3548 1.826340 TACTGCTCAGCGCCCTCAAA 61.826 55.000 2.29 0.00 38.05 2.69
3612 3644 1.202557 ACCTTTAGTTCCGCGTCAACA 60.203 47.619 17.54 4.32 0.00 3.33
3617 3649 2.231964 TGTATCACCTTTAGTTCCGCGT 59.768 45.455 4.92 0.00 0.00 6.01
3781 3814 1.376609 AAAAGCCCGGCATAAGCGAG 61.377 55.000 13.15 0.00 43.41 5.03
3823 3856 8.879342 TTTTATTTTCTTCGAAATGCCAAGAA 57.121 26.923 0.00 0.00 34.94 2.52
3827 3860 7.170658 CCTGTTTTTATTTTCTTCGAAATGCCA 59.829 33.333 0.00 0.00 31.96 4.92
3828 3861 7.170828 ACCTGTTTTTATTTTCTTCGAAATGCC 59.829 33.333 0.00 0.00 31.96 4.40
3905 3948 6.433404 GCATATCAATCCCTGAATTCAGTGAT 59.567 38.462 28.25 28.25 41.70 3.06
3966 4079 4.282195 TCCAGTCCACACAAAAACAAAAGT 59.718 37.500 0.00 0.00 0.00 2.66
3991 4105 4.933400 CGATCCATTCATCAGATGTGCATA 59.067 41.667 10.34 0.00 0.00 3.14
4012 4126 1.433471 CTGCCGATCACTGCTACGA 59.567 57.895 0.00 0.00 0.00 3.43
4017 4131 1.672356 AACACCTGCCGATCACTGC 60.672 57.895 0.00 0.00 0.00 4.40
4018 4132 1.300971 CCAACACCTGCCGATCACTG 61.301 60.000 0.00 0.00 0.00 3.66
4020 4134 0.036765 TACCAACACCTGCCGATCAC 60.037 55.000 0.00 0.00 0.00 3.06
4026 4140 6.570378 GCAATATATTCATACCAACACCTGCC 60.570 42.308 0.00 0.00 0.00 4.85
4067 4182 5.632764 CGTACTGCATAGAGATTTGGATCAG 59.367 44.000 0.00 0.00 34.60 2.90
4080 4202 1.788258 CCATCAGCCGTACTGCATAG 58.212 55.000 12.05 1.47 46.76 2.23
4114 4240 1.070445 GCAGAGCACGCAGGGATAT 59.930 57.895 0.00 0.00 0.00 1.63
4122 4248 1.080974 AATTTGCAGCAGAGCACGC 60.081 52.632 0.00 0.00 45.61 5.34
4124 4250 2.442084 GCAATTTGCAGCAGAGCAC 58.558 52.632 16.35 0.00 45.61 4.40
4164 4307 9.988815 GATAAGGATACATCAATCACAGTTAGT 57.011 33.333 0.00 0.00 41.41 2.24
4187 4433 9.383519 CTTTAGCCAAGTCTAAAATCTGTGATA 57.616 33.333 0.00 0.00 37.88 2.15
4220 4466 6.428159 CACAGATTGCAACTACTAGGTTTTCT 59.572 38.462 0.00 0.00 0.00 2.52
4232 4478 2.079158 CCGTCATCACAGATTGCAACT 58.921 47.619 0.00 0.00 0.00 3.16
4233 4479 1.131126 CCCGTCATCACAGATTGCAAC 59.869 52.381 0.00 0.00 0.00 4.17
4234 4480 1.452110 CCCGTCATCACAGATTGCAA 58.548 50.000 0.00 0.00 0.00 4.08
4240 4486 4.451150 GGCGCCCGTCATCACAGA 62.451 66.667 18.11 0.00 0.00 3.41
4275 4529 5.179742 GGAATTCTAGATGAGATTGCAGCAG 59.820 44.000 5.23 0.00 32.88 4.24
4317 4575 3.994392 GTGAAGTCCAGATTCGCTGTTTA 59.006 43.478 0.00 0.00 43.33 2.01
4318 4576 2.808543 GTGAAGTCCAGATTCGCTGTTT 59.191 45.455 0.00 0.00 43.33 2.83
4392 4666 0.905337 AGTCCTCCCCGTTCCTGAAG 60.905 60.000 0.00 0.00 0.00 3.02
4416 4690 0.899720 CAGTTGGAGGTAGGCGGTAA 59.100 55.000 0.00 0.00 0.00 2.85
4512 4816 0.729116 CTATGCGCACAACCTTGGAG 59.271 55.000 14.90 0.00 0.00 3.86
4540 4844 9.813826 CCATAGTATAATTCCAATCCCTCTTTT 57.186 33.333 0.00 0.00 0.00 2.27
4619 4929 9.512588 AGGCTAATCAATTCGATCAATTAGAAT 57.487 29.630 15.74 0.00 32.48 2.40
4620 4930 8.908786 AGGCTAATCAATTCGATCAATTAGAA 57.091 30.769 15.74 0.00 32.48 2.10
4621 4931 8.150296 TGAGGCTAATCAATTCGATCAATTAGA 58.850 33.333 15.74 0.91 32.48 2.10
4622 4932 8.315391 TGAGGCTAATCAATTCGATCAATTAG 57.685 34.615 10.59 10.59 32.48 1.73
4623 4933 7.933577 ACTGAGGCTAATCAATTCGATCAATTA 59.066 33.333 0.00 0.00 32.48 1.40
4624 4934 6.769822 ACTGAGGCTAATCAATTCGATCAATT 59.230 34.615 0.00 0.00 34.79 2.32
4625 4935 6.294473 ACTGAGGCTAATCAATTCGATCAAT 58.706 36.000 0.00 0.00 31.11 2.57
4626 4936 5.674525 ACTGAGGCTAATCAATTCGATCAA 58.325 37.500 0.00 0.00 31.11 2.57
4627 4937 5.163416 TGACTGAGGCTAATCAATTCGATCA 60.163 40.000 0.00 0.00 31.11 2.92
4628 4938 5.176590 GTGACTGAGGCTAATCAATTCGATC 59.823 44.000 0.00 0.00 31.11 3.69
4629 4939 5.053145 GTGACTGAGGCTAATCAATTCGAT 58.947 41.667 0.00 0.00 35.12 3.59
4630 4940 4.433615 GTGACTGAGGCTAATCAATTCGA 58.566 43.478 0.00 0.00 0.00 3.71
4631 4941 3.557595 GGTGACTGAGGCTAATCAATTCG 59.442 47.826 0.00 0.00 0.00 3.34
4632 4942 4.775236 AGGTGACTGAGGCTAATCAATTC 58.225 43.478 0.00 0.00 41.13 2.17
4633 4943 4.851639 AGGTGACTGAGGCTAATCAATT 57.148 40.909 0.00 0.00 41.13 2.32
4689 5002 9.638239 TCTGGTTTGCTTAATTTACATCAATTC 57.362 29.630 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.