Multiple sequence alignment - TraesCS5D01G486200

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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 TraesCS5D01G486200 chr5D 100.000 2801 0 0 1 2801 521405791 521402991 0.000000e+00 5173.0
1 TraesCS5D01G486200 chr5D 90.113 708 48 11 1232 1920 35652495 35653199 0.000000e+00 900.0
2 TraesCS5D01G486200 chr5D 81.432 964 107 39 323 1252 35651550 35652475 0.000000e+00 723.0
3 TraesCS5D01G486200 chr5D 92.000 50 1 1 1953 2002 35653197 35653243 1.800000e-07 67.6
4 TraesCS5D01G486200 chr5B 94.801 1404 42 13 596 1989 657723198 657721816 0.000000e+00 2159.0
5 TraesCS5D01G486200 chr5B 80.789 786 69 41 2003 2723 657721644 657720876 8.830000e-150 540.0
6 TraesCS5D01G486200 chr5B 86.628 344 30 6 269 610 657723549 657723220 1.590000e-97 366.0
7 TraesCS5D01G486200 chr5B 77.224 281 44 11 2420 2685 175294262 175294537 2.250000e-31 147.0
8 TraesCS5D01G486200 chr5A 92.577 1401 59 18 627 1989 649785562 649784169 0.000000e+00 1969.0
9 TraesCS5D01G486200 chr5A 91.638 574 42 3 1232 1802 23907564 23906994 0.000000e+00 789.0
10 TraesCS5D01G486200 chr5A 89.860 572 53 4 1232 1802 24198340 24198907 0.000000e+00 730.0
11 TraesCS5D01G486200 chr5A 83.772 684 61 27 595 1252 24197661 24198320 1.110000e-168 603.0
12 TraesCS5D01G486200 chr5A 87.912 364 19 14 901 1252 23907934 23907584 3.360000e-109 405.0
13 TraesCS5D01G486200 chr5A 88.364 275 18 9 253 526 649786106 649785845 4.500000e-83 318.0
14 TraesCS5D01G486200 chr5A 78.780 410 55 20 429 820 23908366 23907971 2.150000e-61 246.0
15 TraesCS5D01G486200 chr5A 97.297 37 1 0 1953 1989 23906835 23906799 2.330000e-06 63.9
16 TraesCS5D01G486200 chrUn 82.450 1453 134 61 627 1990 271013833 271015253 0.000000e+00 1158.0
17 TraesCS5D01G486200 chrUn 82.450 1453 134 61 627 1990 280884520 280885940 0.000000e+00 1158.0
18 TraesCS5D01G486200 chrUn 85.122 820 61 22 1232 1990 318996604 318997423 0.000000e+00 782.0
19 TraesCS5D01G486200 chrUn 85.122 820 61 22 1232 1990 397775662 397776481 0.000000e+00 782.0
20 TraesCS5D01G486200 chrUn 84.579 629 60 15 627 1244 318995975 318996577 8.640000e-165 590.0
21 TraesCS5D01G486200 chrUn 85.330 409 37 6 836 1244 397775250 397775635 4.350000e-108 401.0
22 TraesCS5D01G486200 chr1D 94.416 197 11 0 1 197 491710205 491710401 1.260000e-78 303.0
23 TraesCS5D01G486200 chr1D 92.821 195 14 0 1 195 31414291 31414097 1.640000e-72 283.0
24 TraesCS5D01G486200 chr7D 94.416 197 10 1 1 197 379708477 379708672 4.530000e-78 302.0
25 TraesCS5D01G486200 chr6D 93.434 198 13 0 1 198 8996982 8997179 7.590000e-76 294.0
26 TraesCS5D01G486200 chr6D 92.821 195 14 0 1 195 461377781 461377587 1.640000e-72 283.0
27 TraesCS5D01G486200 chr3B 93.782 193 12 0 3 195 354018297 354018105 9.810000e-75 291.0
28 TraesCS5D01G486200 chr4D 93.367 196 10 3 1 195 25335465 25335272 1.270000e-73 287.0
29 TraesCS5D01G486200 chr4D 77.778 279 43 10 2420 2684 488243203 488242930 1.340000e-33 154.0
30 TraesCS5D01G486200 chr3D 94.624 186 9 1 10 195 329035037 329034853 1.270000e-73 287.0
31 TraesCS5D01G486200 chr2D 92.424 198 15 0 2 199 648266372 648266569 1.640000e-72 283.0
32 TraesCS5D01G486200 chr2D 76.703 279 47 9 2420 2684 41355908 41356182 3.760000e-29 139.0
33 TraesCS5D01G486200 chr2D 94.444 36 2 0 1938 1973 639674818 639674853 3.900000e-04 56.5
34 TraesCS5D01G486200 chr7A 77.455 275 50 8 2420 2684 462183109 462182837 1.340000e-33 154.0
35 TraesCS5D01G486200 chr7A 82.639 144 25 0 2420 2563 248899568 248899711 8.140000e-26 128.0
36 TraesCS5D01G486200 chr2A 77.536 276 49 8 2420 2684 560170693 560170420 1.340000e-33 154.0
37 TraesCS5D01G486200 chr2A 84.722 144 21 1 2420 2563 439453521 439453663 2.910000e-30 143.0
38 TraesCS5D01G486200 chr1B 76.703 279 47 9 2420 2684 598295934 598295660 3.760000e-29 139.0


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 TraesCS5D01G486200 chr5D 521402991 521405791 2800 True 5173.000000 5173 100.000000 1 2801 1 chr5D.!!$R1 2800
1 TraesCS5D01G486200 chr5D 35651550 35653243 1693 False 563.533333 900 87.848333 323 2002 3 chr5D.!!$F1 1679
2 TraesCS5D01G486200 chr5B 657720876 657723549 2673 True 1021.666667 2159 87.406000 269 2723 3 chr5B.!!$R1 2454
3 TraesCS5D01G486200 chr5A 649784169 649786106 1937 True 1143.500000 1969 90.470500 253 1989 2 chr5A.!!$R2 1736
4 TraesCS5D01G486200 chr5A 24197661 24198907 1246 False 666.500000 730 86.816000 595 1802 2 chr5A.!!$F1 1207
5 TraesCS5D01G486200 chr5A 23906799 23908366 1567 True 375.975000 789 88.906750 429 1989 4 chr5A.!!$R1 1560
6 TraesCS5D01G486200 chrUn 271013833 271015253 1420 False 1158.000000 1158 82.450000 627 1990 1 chrUn.!!$F1 1363
7 TraesCS5D01G486200 chrUn 280884520 280885940 1420 False 1158.000000 1158 82.450000 627 1990 1 chrUn.!!$F2 1363
8 TraesCS5D01G486200 chrUn 318995975 318997423 1448 False 686.000000 782 84.850500 627 1990 2 chrUn.!!$F3 1363
9 TraesCS5D01G486200 chrUn 397775250 397776481 1231 False 591.500000 782 85.226000 836 1990 2 chrUn.!!$F4 1154

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
105 106 0.035176 GAGGGATCTGCATCTGAGCC 59.965 60.0 0.23 0.23 37.2 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2747 1.069227 CCAGAAAGGCGGAAAGTTTCG 60.069 52.381 9.46 6.35 35.7 3.46 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 4.069232 CCGAGCAGAACCCGCAGA 62.069 66.667 0.00 0.00 0.00 4.26
32 33 2.048222 CGAGCAGAACCCGCAGAA 60.048 61.111 0.00 0.00 0.00 3.02
33 34 2.097038 CGAGCAGAACCCGCAGAAG 61.097 63.158 0.00 0.00 0.00 2.85
34 35 2.359230 AGCAGAACCCGCAGAAGC 60.359 61.111 0.00 0.00 37.42 3.86
35 36 3.435186 GCAGAACCCGCAGAAGCC 61.435 66.667 0.00 0.00 37.52 4.35
36 37 3.121030 CAGAACCCGCAGAAGCCG 61.121 66.667 0.00 0.00 37.52 5.52
37 38 3.311110 AGAACCCGCAGAAGCCGA 61.311 61.111 0.00 0.00 37.52 5.54
38 39 3.119096 GAACCCGCAGAAGCCGAC 61.119 66.667 0.00 0.00 37.52 4.79
39 40 4.699522 AACCCGCAGAAGCCGACC 62.700 66.667 0.00 0.00 37.52 4.79
43 44 4.124351 CGCAGAAGCCGACCCGTA 62.124 66.667 0.00 0.00 37.52 4.02
44 45 2.263540 GCAGAAGCCGACCCGTAA 59.736 61.111 0.00 0.00 33.58 3.18
45 46 1.375013 GCAGAAGCCGACCCGTAAA 60.375 57.895 0.00 0.00 33.58 2.01
46 47 0.952010 GCAGAAGCCGACCCGTAAAA 60.952 55.000 0.00 0.00 33.58 1.52
47 48 1.515081 CAGAAGCCGACCCGTAAAAA 58.485 50.000 0.00 0.00 0.00 1.94
67 68 5.840940 AAAAGCATAGTCCGCGAATATAC 57.159 39.130 8.23 0.00 0.00 1.47
68 69 4.785511 AAGCATAGTCCGCGAATATACT 57.214 40.909 8.23 5.47 0.00 2.12
69 70 4.785511 AGCATAGTCCGCGAATATACTT 57.214 40.909 8.23 0.00 0.00 2.24
70 71 5.135508 AGCATAGTCCGCGAATATACTTT 57.864 39.130 8.23 0.00 0.00 2.66
71 72 5.539048 AGCATAGTCCGCGAATATACTTTT 58.461 37.500 8.23 0.00 0.00 2.27
72 73 6.684686 AGCATAGTCCGCGAATATACTTTTA 58.315 36.000 8.23 0.00 0.00 1.52
73 74 7.321153 AGCATAGTCCGCGAATATACTTTTAT 58.679 34.615 8.23 0.00 0.00 1.40
74 75 7.275779 AGCATAGTCCGCGAATATACTTTTATG 59.724 37.037 8.23 5.28 0.00 1.90
75 76 5.840940 AGTCCGCGAATATACTTTTATGC 57.159 39.130 8.23 0.00 0.00 3.14
76 77 4.384846 AGTCCGCGAATATACTTTTATGCG 59.615 41.667 8.23 0.00 43.55 4.73
78 79 3.986128 CGCGAATATACTTTTATGCGGG 58.014 45.455 0.00 0.00 40.57 6.13
79 80 3.430895 CGCGAATATACTTTTATGCGGGT 59.569 43.478 0.00 0.00 38.24 5.28
80 81 4.433805 CGCGAATATACTTTTATGCGGGTC 60.434 45.833 0.00 0.00 38.24 4.46
81 82 4.142966 GCGAATATACTTTTATGCGGGTCC 60.143 45.833 0.00 0.00 32.27 4.46
82 83 4.090930 CGAATATACTTTTATGCGGGTCCG 59.909 45.833 4.85 4.85 43.09 4.79
83 84 2.994186 ATACTTTTATGCGGGTCCGT 57.006 45.000 11.25 0.00 42.09 4.69
84 85 2.766345 TACTTTTATGCGGGTCCGTT 57.234 45.000 11.25 2.15 42.09 4.44
85 86 1.900245 ACTTTTATGCGGGTCCGTTT 58.100 45.000 11.25 1.81 42.09 3.60
86 87 1.538075 ACTTTTATGCGGGTCCGTTTG 59.462 47.619 11.25 0.00 42.09 2.93
87 88 1.807742 CTTTTATGCGGGTCCGTTTGA 59.192 47.619 11.25 0.00 42.09 2.69
88 89 1.444836 TTTATGCGGGTCCGTTTGAG 58.555 50.000 11.25 0.00 42.09 3.02
89 90 0.391927 TTATGCGGGTCCGTTTGAGG 60.392 55.000 11.25 0.00 42.09 3.86
90 91 2.246761 TATGCGGGTCCGTTTGAGGG 62.247 60.000 11.25 0.00 42.09 4.30
91 92 4.011517 GCGGGTCCGTTTGAGGGA 62.012 66.667 11.25 0.00 42.09 4.20
92 93 2.987125 CGGGTCCGTTTGAGGGAT 59.013 61.111 0.55 0.00 34.33 3.85
93 94 1.153429 CGGGTCCGTTTGAGGGATC 60.153 63.158 0.55 0.00 34.33 3.36
94 95 1.614241 CGGGTCCGTTTGAGGGATCT 61.614 60.000 0.55 0.00 33.89 2.75
95 96 0.107654 GGGTCCGTTTGAGGGATCTG 60.108 60.000 0.00 0.00 33.89 2.90
96 97 0.744771 GGTCCGTTTGAGGGATCTGC 60.745 60.000 0.00 0.00 34.33 4.26
97 98 0.036388 GTCCGTTTGAGGGATCTGCA 60.036 55.000 0.00 0.00 34.33 4.41
98 99 0.911769 TCCGTTTGAGGGATCTGCAT 59.088 50.000 0.00 0.00 0.00 3.96
99 100 1.134401 TCCGTTTGAGGGATCTGCATC 60.134 52.381 0.00 0.00 0.00 3.91
100 101 1.134280 CCGTTTGAGGGATCTGCATCT 60.134 52.381 0.00 0.00 0.00 2.90
101 102 1.938577 CGTTTGAGGGATCTGCATCTG 59.061 52.381 0.00 0.00 0.00 2.90
102 103 2.419159 CGTTTGAGGGATCTGCATCTGA 60.419 50.000 0.00 0.00 0.00 3.27
103 104 3.204526 GTTTGAGGGATCTGCATCTGAG 58.795 50.000 0.00 0.00 0.00 3.35
104 105 0.757512 TGAGGGATCTGCATCTGAGC 59.242 55.000 0.00 0.00 0.00 4.26
105 106 0.035176 GAGGGATCTGCATCTGAGCC 59.965 60.000 0.23 0.23 37.20 4.70
106 107 4.796314 GGATCTGCATCTGAGCCC 57.204 61.111 0.00 0.00 32.92 5.19
107 108 2.144040 GGATCTGCATCTGAGCCCT 58.856 57.895 0.00 0.00 32.92 5.19
108 109 0.035176 GGATCTGCATCTGAGCCCTC 59.965 60.000 0.00 0.00 32.92 4.30
109 110 0.035176 GATCTGCATCTGAGCCCTCC 59.965 60.000 0.00 0.00 0.00 4.30
110 111 1.417288 ATCTGCATCTGAGCCCTCCC 61.417 60.000 0.00 0.00 0.00 4.30
111 112 3.457625 CTGCATCTGAGCCCTCCCG 62.458 68.421 0.00 0.00 0.00 5.14
112 113 4.925861 GCATCTGAGCCCTCCCGC 62.926 72.222 0.00 0.00 0.00 6.13
113 114 4.598894 CATCTGAGCCCTCCCGCG 62.599 72.222 0.00 0.00 0.00 6.46
139 140 2.539020 CAAAAGCGGTTTTGCGCG 59.461 55.556 32.29 14.91 44.56 6.86
140 141 1.941734 CAAAAGCGGTTTTGCGCGA 60.942 52.632 32.29 0.00 44.56 5.87
141 142 1.226717 AAAAGCGGTTTTGCGCGAA 60.227 47.368 23.38 5.81 40.67 4.70
142 143 1.476235 AAAAGCGGTTTTGCGCGAAC 61.476 50.000 23.38 13.55 40.67 3.95
143 144 2.331019 AAAGCGGTTTTGCGCGAACT 62.331 50.000 12.10 8.96 40.67 3.01
144 145 2.982038 AAGCGGTTTTGCGCGAACTG 62.982 55.000 23.39 23.39 40.67 3.16
145 146 3.091022 CGGTTTTGCGCGAACTGC 61.091 61.111 12.10 10.64 41.47 4.40
146 147 2.025441 GGTTTTGCGCGAACTGCA 59.975 55.556 12.10 0.00 46.97 4.41
154 155 2.351888 GCGAACTGCAAACGCGTT 60.352 55.556 20.79 20.79 45.45 4.84
155 156 1.937362 GCGAACTGCAAACGCGTTT 60.937 52.632 30.36 30.36 45.45 3.60
156 157 1.468340 GCGAACTGCAAACGCGTTTT 61.468 50.000 33.05 19.44 45.45 2.43
157 158 0.223513 CGAACTGCAAACGCGTTTTG 59.776 50.000 33.05 26.38 46.57 2.44
184 185 3.161450 GGGATGCGGGGTCTGCTA 61.161 66.667 0.30 0.00 0.00 3.49
185 186 2.423446 GGATGCGGGGTCTGCTAG 59.577 66.667 0.30 0.00 0.00 3.42
186 187 2.134287 GGATGCGGGGTCTGCTAGA 61.134 63.158 0.00 0.00 0.00 2.43
187 188 1.365633 GATGCGGGGTCTGCTAGAG 59.634 63.158 0.00 0.00 0.00 2.43
188 189 1.381872 ATGCGGGGTCTGCTAGAGT 60.382 57.895 0.00 0.00 0.00 3.24
189 190 0.978146 ATGCGGGGTCTGCTAGAGTT 60.978 55.000 0.00 0.00 0.00 3.01
190 191 1.153549 GCGGGGTCTGCTAGAGTTG 60.154 63.158 0.00 0.00 0.00 3.16
191 192 1.153549 CGGGGTCTGCTAGAGTTGC 60.154 63.158 0.00 0.00 0.00 4.17
192 193 1.608717 CGGGGTCTGCTAGAGTTGCT 61.609 60.000 0.00 0.00 0.00 3.91
193 194 0.176910 GGGGTCTGCTAGAGTTGCTC 59.823 60.000 0.00 0.00 0.00 4.26
194 195 1.190643 GGGTCTGCTAGAGTTGCTCT 58.809 55.000 4.02 4.02 43.83 4.09
195 196 1.552792 GGGTCTGCTAGAGTTGCTCTT 59.447 52.381 3.87 0.00 41.50 2.85
196 197 2.761208 GGGTCTGCTAGAGTTGCTCTTA 59.239 50.000 3.87 0.00 41.50 2.10
197 198 3.181480 GGGTCTGCTAGAGTTGCTCTTAG 60.181 52.174 3.87 2.21 41.50 2.18
198 199 3.445805 GGTCTGCTAGAGTTGCTCTTAGT 59.554 47.826 3.87 0.00 41.50 2.24
199 200 4.641094 GGTCTGCTAGAGTTGCTCTTAGTA 59.359 45.833 3.87 0.34 41.50 1.82
200 201 5.449451 GGTCTGCTAGAGTTGCTCTTAGTAC 60.449 48.000 3.87 0.00 41.50 2.73
201 202 4.641094 TCTGCTAGAGTTGCTCTTAGTACC 59.359 45.833 3.87 0.00 41.50 3.34
202 203 3.377485 TGCTAGAGTTGCTCTTAGTACCG 59.623 47.826 3.87 0.00 41.50 4.02
203 204 3.626670 GCTAGAGTTGCTCTTAGTACCGA 59.373 47.826 3.87 0.00 41.50 4.69
204 205 4.260866 GCTAGAGTTGCTCTTAGTACCGAG 60.261 50.000 3.87 0.00 41.50 4.63
208 209 3.829754 GCTCTTAGTACCGAGCGAG 57.170 57.895 11.96 3.24 42.62 5.03
209 210 1.297664 GCTCTTAGTACCGAGCGAGA 58.702 55.000 11.96 0.00 42.62 4.04
210 211 1.262151 GCTCTTAGTACCGAGCGAGAG 59.738 57.143 11.96 6.91 42.62 3.20
224 225 2.969628 CGAGAGCCACTATCTTTGGT 57.030 50.000 0.00 0.00 36.40 3.67
226 227 4.592485 CGAGAGCCACTATCTTTGGTAT 57.408 45.455 0.00 0.00 36.40 2.73
227 228 4.551388 CGAGAGCCACTATCTTTGGTATC 58.449 47.826 0.00 0.00 36.40 2.24
228 229 4.279671 CGAGAGCCACTATCTTTGGTATCT 59.720 45.833 0.00 0.00 35.93 1.98
229 230 5.537188 GAGAGCCACTATCTTTGGTATCTG 58.463 45.833 3.80 0.00 34.38 2.90
230 231 4.061596 GAGCCACTATCTTTGGTATCTGC 58.938 47.826 0.00 0.00 36.40 4.26
231 232 3.713764 AGCCACTATCTTTGGTATCTGCT 59.286 43.478 0.00 0.00 36.40 4.24
232 233 4.901849 AGCCACTATCTTTGGTATCTGCTA 59.098 41.667 0.00 0.00 36.40 3.49
233 234 5.545723 AGCCACTATCTTTGGTATCTGCTAT 59.454 40.000 0.00 0.00 36.40 2.97
234 235 6.043706 AGCCACTATCTTTGGTATCTGCTATT 59.956 38.462 0.00 0.00 36.40 1.73
235 236 6.712547 GCCACTATCTTTGGTATCTGCTATTT 59.287 38.462 0.00 0.00 36.40 1.40
236 237 7.095017 GCCACTATCTTTGGTATCTGCTATTTC 60.095 40.741 0.00 0.00 36.40 2.17
237 238 8.153550 CCACTATCTTTGGTATCTGCTATTTCT 58.846 37.037 0.00 0.00 0.00 2.52
238 239 9.202273 CACTATCTTTGGTATCTGCTATTTCTC 57.798 37.037 0.00 0.00 0.00 2.87
239 240 8.928448 ACTATCTTTGGTATCTGCTATTTCTCA 58.072 33.333 0.00 0.00 0.00 3.27
240 241 9.421806 CTATCTTTGGTATCTGCTATTTCTCAG 57.578 37.037 0.00 0.00 0.00 3.35
241 242 7.423844 TCTTTGGTATCTGCTATTTCTCAGA 57.576 36.000 0.00 0.00 42.72 3.27
242 243 7.851228 TCTTTGGTATCTGCTATTTCTCAGAA 58.149 34.615 0.00 0.00 41.96 3.02
243 244 7.984050 TCTTTGGTATCTGCTATTTCTCAGAAG 59.016 37.037 0.00 0.00 41.96 2.85
244 245 7.423844 TTGGTATCTGCTATTTCTCAGAAGA 57.576 36.000 0.00 0.00 41.96 2.87
245 246 7.423844 TGGTATCTGCTATTTCTCAGAAGAA 57.576 36.000 0.00 0.00 41.96 2.52
275 276 5.909760 ACCTATGGTATCTGCTAGAAGGAT 58.090 41.667 0.00 0.00 32.11 3.24
317 319 0.114168 AACCTGGCATTACTTGGGCA 59.886 50.000 0.00 0.00 38.00 5.36
349 351 1.007849 CCAACCGCAAAAACCCGAG 60.008 57.895 0.00 0.00 0.00 4.63
370 372 3.694566 AGCCCGGTTCTAAGCAATTAAAG 59.305 43.478 0.00 0.00 0.00 1.85
377 379 5.629435 GGTTCTAAGCAATTAAAGTGTGCAC 59.371 40.000 10.75 10.75 40.83 4.57
378 380 5.029650 TCTAAGCAATTAAAGTGTGCACG 57.970 39.130 13.13 0.00 40.83 5.34
382 384 3.796178 AGCAATTAAAGTGTGCACGTTTG 59.204 39.130 21.34 13.45 40.83 2.93
547 552 1.115326 GCCCATGCCCAGGTTTATCC 61.115 60.000 0.00 0.00 0.00 2.59
548 553 0.823356 CCCATGCCCAGGTTTATCCG 60.823 60.000 0.00 0.00 41.99 4.18
559 564 4.526262 CCAGGTTTATCCGAGAGAGATCAT 59.474 45.833 0.00 0.00 41.99 2.45
560 565 5.712446 CCAGGTTTATCCGAGAGAGATCATA 59.288 44.000 0.00 0.00 41.99 2.15
561 566 6.379703 CCAGGTTTATCCGAGAGAGATCATAT 59.620 42.308 0.00 0.00 41.99 1.78
562 567 7.093552 CCAGGTTTATCCGAGAGAGATCATATT 60.094 40.741 0.00 0.00 41.99 1.28
567 572 8.870075 TTATCCGAGAGAGATCATATTCTCAA 57.130 34.615 11.15 2.95 43.82 3.02
568 573 7.773489 ATCCGAGAGAGATCATATTCTCAAA 57.227 36.000 11.15 2.68 43.82 2.69
614 678 3.568007 TCATGTGTCATCATGCATGGATG 59.432 43.478 25.97 23.96 43.18 3.51
872 1145 7.555639 TTAAGCGGTCAAAATAAACAAATCG 57.444 32.000 0.00 0.00 0.00 3.34
924 1200 3.994204 TGATGGATGTGCAATGCATAC 57.006 42.857 12.38 5.97 41.91 2.39
925 1201 3.558033 TGATGGATGTGCAATGCATACT 58.442 40.909 12.38 0.00 41.91 2.12
926 1202 3.566742 TGATGGATGTGCAATGCATACTC 59.433 43.478 12.38 8.54 41.91 2.59
927 1203 2.300433 TGGATGTGCAATGCATACTCC 58.700 47.619 12.38 17.30 41.91 3.85
978 1265 1.793480 CGCCGCACGTTTTCACAAAC 61.793 55.000 0.00 0.00 39.24 2.93
1417 1758 0.320050 GAAGGCGGAGATGGAGGATC 59.680 60.000 0.00 0.00 0.00 3.36
1827 2219 0.179217 CACACATGCATGTTCCGTCG 60.179 55.000 29.48 18.82 39.39 5.12
1828 2220 0.320334 ACACATGCATGTTCCGTCGA 60.320 50.000 29.48 0.00 39.39 4.20
1829 2221 1.009078 CACATGCATGTTCCGTCGAT 58.991 50.000 29.48 1.90 39.39 3.59
1854 2271 4.264253 TCAGGTTTACAGATCTGCATTGG 58.736 43.478 22.83 6.82 0.00 3.16
1936 2426 6.727824 ATGTTGAGTTAACGATCCTGAAAG 57.272 37.500 0.00 0.00 42.34 2.62
1942 2432 7.861630 TGAGTTAACGATCCTGAAAGAAAAAG 58.138 34.615 0.00 0.00 34.07 2.27
1947 2437 7.996098 AACGATCCTGAAAGAAAAAGGATTA 57.004 32.000 4.99 0.00 43.91 1.75
1990 2481 8.106247 TGTTGGGTTAAGATGTTAACAAGATC 57.894 34.615 22.64 5.98 46.87 2.75
1991 2482 6.978343 TGGGTTAAGATGTTAACAAGATCG 57.022 37.500 22.64 0.00 46.87 3.69
2042 2692 8.554490 AGCTCTCCACTTAAGAGGATTATTTA 57.446 34.615 20.26 0.00 40.54 1.40
2076 2726 4.074970 CAAACTGATCAAGGGTAAGCTGT 58.925 43.478 0.00 0.00 0.00 4.40
2078 2728 2.026822 ACTGATCAAGGGTAAGCTGTGG 60.027 50.000 0.00 0.00 0.00 4.17
2081 2731 3.197766 TGATCAAGGGTAAGCTGTGGTAG 59.802 47.826 0.00 0.00 0.00 3.18
2092 2742 3.624777 AGCTGTGGTAGGGATGAAAATG 58.375 45.455 0.00 0.00 0.00 2.32
2097 2747 2.091885 TGGTAGGGATGAAAATGGAGCC 60.092 50.000 0.00 0.00 0.00 4.70
2115 2765 1.235724 CCGAAACTTTCCGCCTTTCT 58.764 50.000 0.00 0.00 0.00 2.52
2118 2768 1.954382 GAAACTTTCCGCCTTTCTGGT 59.046 47.619 0.00 0.00 38.35 4.00
2119 2769 1.318576 AACTTTCCGCCTTTCTGGTG 58.681 50.000 0.00 0.00 45.60 4.17
2120 2770 0.182775 ACTTTCCGCCTTTCTGGTGT 59.817 50.000 0.00 0.00 44.58 4.16
2121 2771 1.318576 CTTTCCGCCTTTCTGGTGTT 58.681 50.000 0.00 0.00 44.58 3.32
2122 2772 1.001378 CTTTCCGCCTTTCTGGTGTTG 60.001 52.381 0.00 0.00 44.58 3.33
2123 2773 1.452145 TTCCGCCTTTCTGGTGTTGC 61.452 55.000 0.00 0.00 44.58 4.17
2134 2801 1.923864 CTGGTGTTGCAAAACGGAAAC 59.076 47.619 13.58 0.04 0.00 2.78
2135 2802 1.272490 TGGTGTTGCAAAACGGAAACA 59.728 42.857 13.58 2.77 0.00 2.83
2136 2803 1.923864 GGTGTTGCAAAACGGAAACAG 59.076 47.619 13.58 0.00 33.45 3.16
2148 2822 9.353999 GCAAAACGGAAACAGAAATAGAATATT 57.646 29.630 0.00 0.00 0.00 1.28
2171 2855 1.434555 TATGCGGAAACACGGAACAG 58.565 50.000 0.00 0.00 37.83 3.16
2177 2861 1.462791 GAAACACGGAACAGCGTTTG 58.537 50.000 0.00 0.00 31.98 2.93
2178 2862 0.806241 AAACACGGAACAGCGTTTGT 59.194 45.000 0.00 0.00 43.45 2.83
2194 2878 4.201580 GCGTTTGTTTTTCAGTGAAACAGG 60.202 41.667 17.85 8.80 44.83 4.00
2228 2912 8.047310 ACCGAATCTTCTGTTTCCATTAATACT 58.953 33.333 0.00 0.00 0.00 2.12
2229 2913 8.893727 CCGAATCTTCTGTTTCCATTAATACTT 58.106 33.333 0.00 0.00 0.00 2.24
2277 2961 5.168526 TGAACATATGGCTATTTTGTCGC 57.831 39.130 7.80 0.00 0.00 5.19
2279 2963 3.820557 ACATATGGCTATTTTGTCGCCT 58.179 40.909 7.80 0.00 44.09 5.52
2282 2966 5.238650 ACATATGGCTATTTTGTCGCCTAAC 59.761 40.000 7.80 0.00 44.09 2.34
2319 3014 3.961480 TGAGCGGAATGGACTATATGG 57.039 47.619 0.00 0.00 0.00 2.74
2332 3027 3.541632 ACTATATGGCCCAACTTCAACG 58.458 45.455 0.00 0.00 0.00 4.10
2349 3044 7.108847 ACTTCAACGGTACTACTACTACATCT 58.891 38.462 0.00 0.00 0.00 2.90
2350 3045 8.260818 ACTTCAACGGTACTACTACTACATCTA 58.739 37.037 0.00 0.00 0.00 1.98
2351 3046 8.654230 TTCAACGGTACTACTACTACATCTAG 57.346 38.462 0.00 0.00 0.00 2.43
2352 3047 7.786030 TCAACGGTACTACTACTACATCTAGT 58.214 38.462 0.00 0.00 37.04 2.57
2353 3048 8.914011 TCAACGGTACTACTACTACATCTAGTA 58.086 37.037 0.00 0.00 34.79 1.82
2354 3049 9.703892 CAACGGTACTACTACTACATCTAGTAT 57.296 37.037 0.00 0.00 35.34 2.12
2363 3058 6.712998 ACTACTACATCTAGTATGACAGCCTG 59.287 42.308 8.56 0.00 35.34 4.85
2375 3070 3.928754 TGACAGCCTGATACCTAATCCT 58.071 45.455 0.00 0.00 33.22 3.24
2380 3075 6.773638 ACAGCCTGATACCTAATCCTTAATG 58.226 40.000 0.00 0.00 33.22 1.90
2381 3076 5.645497 CAGCCTGATACCTAATCCTTAATGC 59.355 44.000 0.00 0.00 33.22 3.56
2418 3114 5.796350 ACTTCAAAATATGTCGCTGGTAC 57.204 39.130 0.00 0.00 0.00 3.34
2445 3141 4.855388 CACTATTGTGATTTGAGCTGCAAC 59.145 41.667 1.02 0.00 46.55 4.17
2450 3146 3.313803 TGTGATTTGAGCTGCAACGTTTA 59.686 39.130 0.00 0.00 35.91 2.01
2453 3149 5.059710 GTGATTTGAGCTGCAACGTTTAATC 59.940 40.000 0.00 2.21 35.91 1.75
2464 3160 3.481112 ACGTTTAATCGTTTGATGCCC 57.519 42.857 5.76 0.00 41.37 5.36
2571 3290 6.822442 TGTAATCATCCTATCCGCTAAACAA 58.178 36.000 0.00 0.00 0.00 2.83
2610 3329 3.387699 CAGTTCATGGGGGTCTTTTGTTT 59.612 43.478 0.00 0.00 0.00 2.83
2617 3336 1.607148 GGGGTCTTTTGTTTCGGTGAG 59.393 52.381 0.00 0.00 0.00 3.51
2620 3339 2.540973 GGTCTTTTGTTTCGGTGAGCAC 60.541 50.000 0.00 0.00 0.00 4.40
2640 3359 1.938577 CTCGCTTCCATTCCATGTCTG 59.061 52.381 0.00 0.00 0.00 3.51
2649 3368 3.368427 CCATTCCATGTCTGTGTCGTACT 60.368 47.826 0.00 0.00 0.00 2.73
2650 3369 3.570926 TTCCATGTCTGTGTCGTACTC 57.429 47.619 0.00 0.00 0.00 2.59
2651 3370 1.467342 TCCATGTCTGTGTCGTACTCG 59.533 52.381 0.00 0.00 38.55 4.18
2652 3371 1.260206 CATGTCTGTGTCGTACTCGC 58.740 55.000 0.00 0.00 36.96 5.03
2666 3385 3.420162 CGTACTCGCTCTGTTTTCGTTTC 60.420 47.826 0.00 0.00 0.00 2.78
2669 3388 0.856641 CGCTCTGTTTTCGTTTCCGA 59.143 50.000 0.00 0.00 42.41 4.55
2690 3409 5.650703 CCGATAGTATTTGTTTCCAGGGTTT 59.349 40.000 0.00 0.00 0.00 3.27
2691 3410 6.183360 CCGATAGTATTTGTTTCCAGGGTTTC 60.183 42.308 0.00 0.00 0.00 2.78
2692 3411 6.373216 CGATAGTATTTGTTTCCAGGGTTTCA 59.627 38.462 0.00 0.00 0.00 2.69
2693 3412 7.414098 CGATAGTATTTGTTTCCAGGGTTTCAG 60.414 40.741 0.00 0.00 0.00 3.02
2706 3425 3.751698 AGGGTTTCAGTATTCGTTTCTGC 59.248 43.478 0.00 0.00 0.00 4.26
2710 3429 5.851703 GGTTTCAGTATTCGTTTCTGCTTTC 59.148 40.000 0.00 0.00 0.00 2.62
2711 3430 6.427150 GTTTCAGTATTCGTTTCTGCTTTCA 58.573 36.000 0.00 0.00 0.00 2.69
2746 3465 9.965824 ATATATATTTGTTTCCGCTTCCAAAAG 57.034 29.630 0.00 0.00 35.47 2.27
2747 3466 4.664150 ATTTGTTTCCGCTTCCAAAAGA 57.336 36.364 0.00 0.00 34.14 2.52
2748 3467 4.664150 TTTGTTTCCGCTTCCAAAAGAT 57.336 36.364 0.00 0.00 34.14 2.40
2749 3468 5.776173 TTTGTTTCCGCTTCCAAAAGATA 57.224 34.783 0.00 0.00 34.14 1.98
2750 3469 5.776173 TTGTTTCCGCTTCCAAAAGATAA 57.224 34.783 0.00 0.00 34.14 1.75
2751 3470 5.975693 TGTTTCCGCTTCCAAAAGATAAT 57.024 34.783 0.00 0.00 34.14 1.28
2752 3471 7.455641 TTGTTTCCGCTTCCAAAAGATAATA 57.544 32.000 0.00 0.00 34.14 0.98
2753 3472 7.639113 TGTTTCCGCTTCCAAAAGATAATAT 57.361 32.000 0.00 0.00 34.14 1.28
2754 3473 8.740123 TGTTTCCGCTTCCAAAAGATAATATA 57.260 30.769 0.00 0.00 34.14 0.86
2755 3474 9.179909 TGTTTCCGCTTCCAAAAGATAATATAA 57.820 29.630 0.00 0.00 34.14 0.98
2775 3494 9.830975 AATATAAAAATAAATGTTGGAGCACCC 57.169 29.630 0.00 0.00 34.81 4.61
2776 3495 5.559148 AAAAATAAATGTTGGAGCACCCA 57.441 34.783 0.00 0.00 44.93 4.51
2785 3504 2.873797 GGAGCACCCAGTTCCATTC 58.126 57.895 0.00 0.00 46.12 2.67
2786 3505 0.038166 GGAGCACCCAGTTCCATTCA 59.962 55.000 0.00 0.00 46.12 2.57
2787 3506 1.341383 GGAGCACCCAGTTCCATTCAT 60.341 52.381 0.00 0.00 46.12 2.57
2788 3507 2.450476 GAGCACCCAGTTCCATTCATT 58.550 47.619 0.00 0.00 0.00 2.57
2789 3508 2.827921 GAGCACCCAGTTCCATTCATTT 59.172 45.455 0.00 0.00 0.00 2.32
2790 3509 3.242011 AGCACCCAGTTCCATTCATTTT 58.758 40.909 0.00 0.00 0.00 1.82
2791 3510 3.259123 AGCACCCAGTTCCATTCATTTTC 59.741 43.478 0.00 0.00 0.00 2.29
2792 3511 3.836949 CACCCAGTTCCATTCATTTTCG 58.163 45.455 0.00 0.00 0.00 3.46
2793 3512 2.231235 ACCCAGTTCCATTCATTTTCGC 59.769 45.455 0.00 0.00 0.00 4.70
2794 3513 2.493278 CCCAGTTCCATTCATTTTCGCT 59.507 45.455 0.00 0.00 0.00 4.93
2795 3514 3.428045 CCCAGTTCCATTCATTTTCGCTC 60.428 47.826 0.00 0.00 0.00 5.03
2796 3515 3.428045 CCAGTTCCATTCATTTTCGCTCC 60.428 47.826 0.00 0.00 0.00 4.70
2797 3516 2.420022 AGTTCCATTCATTTTCGCTCCG 59.580 45.455 0.00 0.00 0.00 4.63
2798 3517 0.732571 TCCATTCATTTTCGCTCCGC 59.267 50.000 0.00 0.00 0.00 5.54
2799 3518 0.734889 CCATTCATTTTCGCTCCGCT 59.265 50.000 0.00 0.00 0.00 5.52
2800 3519 1.133025 CCATTCATTTTCGCTCCGCTT 59.867 47.619 0.00 0.00 0.00 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.589654 TTCTGCGGGTTCTGCTCGG 62.590 63.158 0.00 0.00 42.38 4.63
15 16 2.048222 TTCTGCGGGTTCTGCTCG 60.048 61.111 0.00 0.00 45.55 5.03
16 17 2.394563 GCTTCTGCGGGTTCTGCTC 61.395 63.158 0.00 0.00 0.00 4.26
17 18 2.359230 GCTTCTGCGGGTTCTGCT 60.359 61.111 0.00 0.00 0.00 4.24
18 19 3.435186 GGCTTCTGCGGGTTCTGC 61.435 66.667 0.00 0.00 40.82 4.26
19 20 3.121030 CGGCTTCTGCGGGTTCTG 61.121 66.667 0.00 0.00 40.82 3.02
20 21 3.311110 TCGGCTTCTGCGGGTTCT 61.311 61.111 0.00 0.00 40.82 3.01
21 22 3.119096 GTCGGCTTCTGCGGGTTC 61.119 66.667 0.00 0.00 40.82 3.62
22 23 4.699522 GGTCGGCTTCTGCGGGTT 62.700 66.667 0.00 0.00 40.82 4.11
26 27 3.636313 TTACGGGTCGGCTTCTGCG 62.636 63.158 0.00 0.00 40.82 5.18
27 28 0.952010 TTTTACGGGTCGGCTTCTGC 60.952 55.000 0.00 0.00 38.76 4.26
28 29 1.515081 TTTTTACGGGTCGGCTTCTG 58.485 50.000 0.00 0.00 0.00 3.02
44 45 5.989777 AGTATATTCGCGGACTATGCTTTTT 59.010 36.000 6.13 0.00 0.00 1.94
45 46 5.539048 AGTATATTCGCGGACTATGCTTTT 58.461 37.500 6.13 0.00 0.00 2.27
46 47 5.135508 AGTATATTCGCGGACTATGCTTT 57.864 39.130 6.13 0.00 0.00 3.51
47 48 4.785511 AGTATATTCGCGGACTATGCTT 57.214 40.909 6.13 0.00 0.00 3.91
48 49 4.785511 AAGTATATTCGCGGACTATGCT 57.214 40.909 6.13 7.23 0.00 3.79
49 50 5.840940 AAAAGTATATTCGCGGACTATGC 57.159 39.130 6.13 4.96 0.00 3.14
50 51 7.391786 GCATAAAAGTATATTCGCGGACTATG 58.608 38.462 6.13 4.93 0.00 2.23
51 52 6.252869 CGCATAAAAGTATATTCGCGGACTAT 59.747 38.462 6.13 3.77 37.94 2.12
52 53 5.570206 CGCATAAAAGTATATTCGCGGACTA 59.430 40.000 6.13 0.00 37.94 2.59
53 54 4.384846 CGCATAAAAGTATATTCGCGGACT 59.615 41.667 6.13 0.00 37.94 3.85
54 55 4.625135 CGCATAAAAGTATATTCGCGGAC 58.375 43.478 6.13 0.00 37.94 4.79
55 56 4.896562 CGCATAAAAGTATATTCGCGGA 57.103 40.909 6.13 0.00 37.94 5.54
57 58 3.430895 ACCCGCATAAAAGTATATTCGCG 59.569 43.478 0.00 0.00 41.05 5.87
58 59 4.142966 GGACCCGCATAAAAGTATATTCGC 60.143 45.833 0.00 0.00 0.00 4.70
59 60 4.090930 CGGACCCGCATAAAAGTATATTCG 59.909 45.833 0.00 0.00 0.00 3.34
60 61 4.992951 ACGGACCCGCATAAAAGTATATTC 59.007 41.667 8.55 0.00 44.19 1.75
61 62 4.964593 ACGGACCCGCATAAAAGTATATT 58.035 39.130 8.55 0.00 44.19 1.28
62 63 4.612264 ACGGACCCGCATAAAAGTATAT 57.388 40.909 8.55 0.00 44.19 0.86
63 64 4.405116 AACGGACCCGCATAAAAGTATA 57.595 40.909 8.55 0.00 44.19 1.47
64 65 2.994186 ACGGACCCGCATAAAAGTAT 57.006 45.000 8.55 0.00 44.19 2.12
65 66 2.743126 CAAACGGACCCGCATAAAAGTA 59.257 45.455 8.55 0.00 44.19 2.24
66 67 1.538075 CAAACGGACCCGCATAAAAGT 59.462 47.619 8.55 0.00 44.19 2.66
67 68 1.807742 TCAAACGGACCCGCATAAAAG 59.192 47.619 8.55 0.00 44.19 2.27
68 69 1.807742 CTCAAACGGACCCGCATAAAA 59.192 47.619 8.55 0.00 44.19 1.52
69 70 1.444836 CTCAAACGGACCCGCATAAA 58.555 50.000 8.55 0.00 44.19 1.40
70 71 0.391927 CCTCAAACGGACCCGCATAA 60.392 55.000 8.55 0.00 44.19 1.90
71 72 1.219664 CCTCAAACGGACCCGCATA 59.780 57.895 8.55 0.00 44.19 3.14
72 73 2.046314 CCTCAAACGGACCCGCAT 60.046 61.111 8.55 0.00 44.19 4.73
73 74 4.323477 CCCTCAAACGGACCCGCA 62.323 66.667 8.55 0.00 44.19 5.69
74 75 3.325201 ATCCCTCAAACGGACCCGC 62.325 63.158 8.55 0.00 44.19 6.13
75 76 1.153429 GATCCCTCAAACGGACCCG 60.153 63.158 6.94 6.94 46.03 5.28
76 77 0.107654 CAGATCCCTCAAACGGACCC 60.108 60.000 0.00 0.00 30.39 4.46
77 78 0.744771 GCAGATCCCTCAAACGGACC 60.745 60.000 0.00 0.00 30.39 4.46
78 79 0.036388 TGCAGATCCCTCAAACGGAC 60.036 55.000 0.00 0.00 30.39 4.79
79 80 0.911769 ATGCAGATCCCTCAAACGGA 59.088 50.000 0.00 0.00 0.00 4.69
80 81 1.134280 AGATGCAGATCCCTCAAACGG 60.134 52.381 0.00 0.00 0.00 4.44
81 82 1.938577 CAGATGCAGATCCCTCAAACG 59.061 52.381 0.00 0.00 0.00 3.60
82 83 3.204526 CTCAGATGCAGATCCCTCAAAC 58.795 50.000 0.00 0.00 0.00 2.93
83 84 2.421107 GCTCAGATGCAGATCCCTCAAA 60.421 50.000 0.00 0.00 0.00 2.69
84 85 1.140452 GCTCAGATGCAGATCCCTCAA 59.860 52.381 0.00 0.00 0.00 3.02
85 86 0.757512 GCTCAGATGCAGATCCCTCA 59.242 55.000 0.00 0.00 0.00 3.86
86 87 0.035176 GGCTCAGATGCAGATCCCTC 59.965 60.000 0.00 0.00 34.04 4.30
87 88 1.417288 GGGCTCAGATGCAGATCCCT 61.417 60.000 6.19 0.00 38.21 4.20
88 89 1.072852 GGGCTCAGATGCAGATCCC 59.927 63.158 0.00 0.00 34.59 3.85
89 90 0.035176 GAGGGCTCAGATGCAGATCC 59.965 60.000 0.00 0.00 34.04 3.36
90 91 0.035176 GGAGGGCTCAGATGCAGATC 59.965 60.000 0.00 0.00 34.04 2.75
91 92 1.417288 GGGAGGGCTCAGATGCAGAT 61.417 60.000 0.00 0.00 34.04 2.90
92 93 2.068821 GGGAGGGCTCAGATGCAGA 61.069 63.158 0.00 0.00 34.04 4.26
93 94 2.509916 GGGAGGGCTCAGATGCAG 59.490 66.667 0.00 0.00 34.04 4.41
94 95 3.473647 CGGGAGGGCTCAGATGCA 61.474 66.667 0.00 0.00 34.04 3.96
95 96 4.925861 GCGGGAGGGCTCAGATGC 62.926 72.222 0.00 0.00 0.00 3.91
96 97 4.598894 CGCGGGAGGGCTCAGATG 62.599 72.222 0.00 0.00 35.48 2.90
128 129 3.091022 GCAGTTCGCGCAAAACCG 61.091 61.111 16.51 9.59 0.00 4.44
129 130 1.587613 TTGCAGTTCGCGCAAAACC 60.588 52.632 16.51 5.74 45.91 3.27
130 131 3.990141 TTGCAGTTCGCGCAAAAC 58.010 50.000 8.75 11.52 45.91 2.43
134 135 4.954680 GCGTTTGCAGTTCGCGCA 62.955 61.111 8.75 0.00 46.97 6.09
137 138 1.468340 AAAACGCGTTTGCAGTTCGC 61.468 50.000 35.31 17.67 45.28 4.70
138 139 0.223513 CAAAACGCGTTTGCAGTTCG 59.776 50.000 35.31 15.11 40.25 3.95
167 168 3.161450 TAGCAGACCCCGCATCCC 61.161 66.667 0.00 0.00 0.00 3.85
168 169 2.093537 CTCTAGCAGACCCCGCATCC 62.094 65.000 0.00 0.00 0.00 3.51
169 170 1.365633 CTCTAGCAGACCCCGCATC 59.634 63.158 0.00 0.00 0.00 3.91
170 171 0.978146 AACTCTAGCAGACCCCGCAT 60.978 55.000 0.00 0.00 0.00 4.73
171 172 1.609501 AACTCTAGCAGACCCCGCA 60.610 57.895 0.00 0.00 0.00 5.69
172 173 1.153549 CAACTCTAGCAGACCCCGC 60.154 63.158 0.00 0.00 0.00 6.13
173 174 1.153549 GCAACTCTAGCAGACCCCG 60.154 63.158 0.00 0.00 0.00 5.73
174 175 0.176910 GAGCAACTCTAGCAGACCCC 59.823 60.000 0.00 0.00 0.00 4.95
175 176 1.190643 AGAGCAACTCTAGCAGACCC 58.809 55.000 0.00 0.00 39.28 4.46
176 177 3.445805 ACTAAGAGCAACTCTAGCAGACC 59.554 47.826 0.00 0.00 40.28 3.85
177 178 4.712122 ACTAAGAGCAACTCTAGCAGAC 57.288 45.455 0.00 0.00 40.28 3.51
178 179 4.641094 GGTACTAAGAGCAACTCTAGCAGA 59.359 45.833 0.00 0.00 40.28 4.26
179 180 4.496673 CGGTACTAAGAGCAACTCTAGCAG 60.497 50.000 0.00 0.00 40.28 4.24
180 181 3.377485 CGGTACTAAGAGCAACTCTAGCA 59.623 47.826 0.00 0.00 40.28 3.49
181 182 3.626670 TCGGTACTAAGAGCAACTCTAGC 59.373 47.826 0.00 0.00 40.28 3.42
182 183 5.412526 CTCGGTACTAAGAGCAACTCTAG 57.587 47.826 0.00 0.00 40.28 2.43
191 192 1.262151 GCTCTCGCTCGGTACTAAGAG 59.738 57.143 8.49 8.49 37.54 2.85
192 193 1.297664 GCTCTCGCTCGGTACTAAGA 58.702 55.000 0.00 0.00 0.00 2.10
193 194 0.308376 GGCTCTCGCTCGGTACTAAG 59.692 60.000 0.00 0.00 36.09 2.18
194 195 0.393402 TGGCTCTCGCTCGGTACTAA 60.393 55.000 0.00 0.00 36.09 2.24
195 196 1.094073 GTGGCTCTCGCTCGGTACTA 61.094 60.000 0.00 0.00 36.09 1.82
196 197 2.045242 TGGCTCTCGCTCGGTACT 60.045 61.111 0.00 0.00 36.09 2.73
197 198 1.094073 TAGTGGCTCTCGCTCGGTAC 61.094 60.000 0.00 0.00 37.42 3.34
198 199 0.179026 ATAGTGGCTCTCGCTCGGTA 60.179 55.000 0.00 0.00 37.42 4.02
199 200 1.448922 GATAGTGGCTCTCGCTCGGT 61.449 60.000 0.00 0.00 37.42 4.69
200 201 1.169661 AGATAGTGGCTCTCGCTCGG 61.170 60.000 0.00 0.00 37.42 4.63
201 202 0.665835 AAGATAGTGGCTCTCGCTCG 59.334 55.000 0.00 0.00 37.42 5.03
202 203 2.468831 CAAAGATAGTGGCTCTCGCTC 58.531 52.381 0.00 0.00 37.42 5.03
203 204 1.137872 CCAAAGATAGTGGCTCTCGCT 59.862 52.381 0.00 0.00 39.84 4.93
204 205 1.134670 ACCAAAGATAGTGGCTCTCGC 60.135 52.381 0.00 0.00 40.02 5.03
205 206 2.969628 ACCAAAGATAGTGGCTCTCG 57.030 50.000 0.00 0.00 40.02 4.04
206 207 5.537188 CAGATACCAAAGATAGTGGCTCTC 58.463 45.833 0.00 0.00 40.02 3.20
207 208 4.202305 GCAGATACCAAAGATAGTGGCTCT 60.202 45.833 0.00 0.00 40.02 4.09
208 209 4.061596 GCAGATACCAAAGATAGTGGCTC 58.938 47.826 0.00 0.00 40.02 4.70
209 210 3.713764 AGCAGATACCAAAGATAGTGGCT 59.286 43.478 0.00 0.00 40.02 4.75
210 211 4.078639 AGCAGATACCAAAGATAGTGGC 57.921 45.455 0.00 0.00 40.02 5.01
211 212 8.153550 AGAAATAGCAGATACCAAAGATAGTGG 58.846 37.037 0.00 0.00 42.28 4.00
212 213 9.202273 GAGAAATAGCAGATACCAAAGATAGTG 57.798 37.037 0.00 0.00 0.00 2.74
213 214 8.928448 TGAGAAATAGCAGATACCAAAGATAGT 58.072 33.333 0.00 0.00 0.00 2.12
214 215 9.421806 CTGAGAAATAGCAGATACCAAAGATAG 57.578 37.037 0.00 0.00 34.06 2.08
215 216 9.147732 TCTGAGAAATAGCAGATACCAAAGATA 57.852 33.333 0.00 0.00 36.31 1.98
216 217 8.027524 TCTGAGAAATAGCAGATACCAAAGAT 57.972 34.615 0.00 0.00 36.31 2.40
217 218 7.423844 TCTGAGAAATAGCAGATACCAAAGA 57.576 36.000 0.00 0.00 36.31 2.52
218 219 7.984050 TCTTCTGAGAAATAGCAGATACCAAAG 59.016 37.037 0.00 0.00 40.51 2.77
219 220 7.851228 TCTTCTGAGAAATAGCAGATACCAAA 58.149 34.615 0.00 0.00 40.51 3.28
220 221 7.423844 TCTTCTGAGAAATAGCAGATACCAA 57.576 36.000 0.00 0.00 40.51 3.67
221 222 7.423844 TTCTTCTGAGAAATAGCAGATACCA 57.576 36.000 0.00 0.00 40.51 3.25
248 249 7.127339 TCCTTCTAGCAGATACCATAGGTTTTT 59.873 37.037 0.00 0.00 37.09 1.94
249 250 6.615726 TCCTTCTAGCAGATACCATAGGTTTT 59.384 38.462 0.00 0.00 37.09 2.43
250 251 6.143915 TCCTTCTAGCAGATACCATAGGTTT 58.856 40.000 0.00 0.00 37.09 3.27
251 252 5.716979 TCCTTCTAGCAGATACCATAGGTT 58.283 41.667 0.00 0.00 37.09 3.50
261 262 4.240881 TGCCAAAATCCTTCTAGCAGAT 57.759 40.909 0.00 0.00 0.00 2.90
275 276 6.707440 TTAGTTGAAGAGTTGATGCCAAAA 57.293 33.333 0.00 0.00 33.49 2.44
317 319 3.117813 TGCGGTTGGGCTTTATATAACCT 60.118 43.478 0.00 0.00 38.84 3.50
333 335 2.725641 GCTCGGGTTTTTGCGGTT 59.274 55.556 0.00 0.00 0.00 4.44
349 351 3.442625 ACTTTAATTGCTTAGAACCGGGC 59.557 43.478 6.32 0.00 0.00 6.13
361 363 4.101112 CAAACGTGCACACTTTAATTGC 57.899 40.909 18.64 0.00 36.76 3.56
411 415 5.531122 TGAACTACATCTATACTGCCCAC 57.469 43.478 0.00 0.00 0.00 4.61
481 486 2.422939 TGGGCTCCAGATATAGGCTT 57.577 50.000 0.00 0.00 0.00 4.35
614 678 6.549912 TCTGAGATATGTTAATGTGCATGC 57.450 37.500 11.82 11.82 0.00 4.06
690 929 3.570926 TCCATCCATCGTAATACTCGC 57.429 47.619 0.00 0.00 0.00 5.03
1169 1468 2.189521 CCACGATGGGGTAGTGCC 59.810 66.667 0.00 0.00 32.67 5.01
1379 1720 1.284982 CTCCAAGAACACGCTCACCG 61.285 60.000 0.00 0.00 44.21 4.94
1417 1758 3.429141 CTGCGCCAGCTCCTTGTG 61.429 66.667 4.18 0.00 45.42 3.33
1505 1858 2.962786 CGTTCCCGTCGTTGCACA 60.963 61.111 0.00 0.00 0.00 4.57
1827 2219 5.363101 TGCAGATCTGTAAACCTGATGATC 58.637 41.667 23.38 2.74 32.43 2.92
1828 2220 5.363562 TGCAGATCTGTAAACCTGATGAT 57.636 39.130 23.38 0.00 32.43 2.45
1829 2221 4.824479 TGCAGATCTGTAAACCTGATGA 57.176 40.909 23.38 0.00 32.43 2.92
1854 2271 2.161410 TGCAACATAACGACTCAATGGC 59.839 45.455 0.00 0.00 0.00 4.40
1936 2426 6.887002 AGGATCTTCAGGTGTAATCCTTTTTC 59.113 38.462 0.00 0.00 42.80 2.29
1942 2432 7.283329 ACAAATAGGATCTTCAGGTGTAATCC 58.717 38.462 0.00 0.00 36.87 3.01
1947 2437 5.256474 CCAACAAATAGGATCTTCAGGTGT 58.744 41.667 0.00 0.00 0.00 4.16
2042 2692 6.293626 CCTTGATCAGTTTGACGTTTGAGATT 60.294 38.462 0.00 0.00 0.00 2.40
2050 2700 2.930826 ACCCTTGATCAGTTTGACGT 57.069 45.000 0.00 0.00 0.00 4.34
2061 2711 2.505819 CCTACCACAGCTTACCCTTGAT 59.494 50.000 0.00 0.00 0.00 2.57
2076 2726 2.091885 GGCTCCATTTTCATCCCTACCA 60.092 50.000 0.00 0.00 0.00 3.25
2078 2728 2.158813 TCGGCTCCATTTTCATCCCTAC 60.159 50.000 0.00 0.00 0.00 3.18
2081 2731 1.762708 TTCGGCTCCATTTTCATCCC 58.237 50.000 0.00 0.00 0.00 3.85
2097 2747 1.069227 CCAGAAAGGCGGAAAGTTTCG 60.069 52.381 9.46 6.35 35.70 3.46
2115 2765 1.272490 TGTTTCCGTTTTGCAACACCA 59.728 42.857 10.04 0.00 32.54 4.17
2118 2768 3.577649 TTCTGTTTCCGTTTTGCAACA 57.422 38.095 0.00 0.00 32.54 3.33
2119 2769 5.974751 TCTATTTCTGTTTCCGTTTTGCAAC 59.025 36.000 0.00 0.00 0.00 4.17
2120 2770 6.137794 TCTATTTCTGTTTCCGTTTTGCAA 57.862 33.333 0.00 0.00 0.00 4.08
2121 2771 5.759506 TCTATTTCTGTTTCCGTTTTGCA 57.240 34.783 0.00 0.00 0.00 4.08
2122 2772 8.911247 ATATTCTATTTCTGTTTCCGTTTTGC 57.089 30.769 0.00 0.00 0.00 3.68
2148 2822 3.066342 TGTTCCGTGTTTCCGCATAAAAA 59.934 39.130 0.00 0.00 0.00 1.94
2153 2827 1.852067 GCTGTTCCGTGTTTCCGCAT 61.852 55.000 0.00 0.00 0.00 4.73
2171 2855 4.201580 CCTGTTTCACTGAAAAACAAACGC 60.202 41.667 5.76 0.00 43.78 4.84
2177 2861 2.851824 CGCACCTGTTTCACTGAAAAAC 59.148 45.455 5.76 0.00 37.18 2.43
2178 2862 2.159310 CCGCACCTGTTTCACTGAAAAA 60.159 45.455 5.76 0.00 33.14 1.94
2180 2864 1.021202 CCGCACCTGTTTCACTGAAA 58.979 50.000 0.00 0.00 0.00 2.69
2181 2865 0.179234 TCCGCACCTGTTTCACTGAA 59.821 50.000 0.00 0.00 0.00 3.02
2182 2866 0.179234 TTCCGCACCTGTTTCACTGA 59.821 50.000 0.00 0.00 0.00 3.41
2183 2867 1.021202 TTTCCGCACCTGTTTCACTG 58.979 50.000 0.00 0.00 0.00 3.66
2184 2868 1.021968 GTTTCCGCACCTGTTTCACT 58.978 50.000 0.00 0.00 0.00 3.41
2253 2937 6.898041 GCGACAAAATAGCCATATGTTCATA 58.102 36.000 1.24 0.00 0.00 2.15
2282 2966 9.897744 ATTCCGCTCATTATAATTATGTGTTTG 57.102 29.630 8.28 0.00 0.00 2.93
2304 2999 3.074538 AGTTGGGCCATATAGTCCATTCC 59.925 47.826 7.26 0.00 0.00 3.01
2319 3014 2.071540 GTAGTACCGTTGAAGTTGGGC 58.928 52.381 0.00 0.00 0.00 5.36
2349 3044 6.663953 GGATTAGGTATCAGGCTGTCATACTA 59.336 42.308 19.73 12.64 34.77 1.82
2350 3045 5.482175 GGATTAGGTATCAGGCTGTCATACT 59.518 44.000 19.73 13.40 34.77 2.12
2351 3046 5.482175 AGGATTAGGTATCAGGCTGTCATAC 59.518 44.000 15.27 14.96 34.77 2.39
2352 3047 5.655394 AGGATTAGGTATCAGGCTGTCATA 58.345 41.667 15.27 2.97 34.77 2.15
2353 3048 4.497516 AGGATTAGGTATCAGGCTGTCAT 58.502 43.478 15.27 4.05 34.77 3.06
2354 3049 3.928754 AGGATTAGGTATCAGGCTGTCA 58.071 45.455 15.27 0.13 34.77 3.58
2363 3058 3.939592 GGGCGCATTAAGGATTAGGTATC 59.060 47.826 10.83 0.00 0.00 2.24
2418 3114 3.620374 AGCTCAAATCACAATAGTGCTCG 59.380 43.478 0.00 0.00 45.49 5.03
2445 3141 3.757745 AGGGCATCAAACGATTAAACG 57.242 42.857 3.32 3.32 39.31 3.60
2464 3160 7.193377 ACTTTGGCAGCATAAAAATTTGAAG 57.807 32.000 0.00 0.00 0.00 3.02
2582 3301 2.127708 GACCCCCATGAACTGTAGGAT 58.872 52.381 0.00 0.00 0.00 3.24
2584 3303 1.584724 AGACCCCCATGAACTGTAGG 58.415 55.000 0.00 0.00 0.00 3.18
2585 3304 3.721087 AAAGACCCCCATGAACTGTAG 57.279 47.619 0.00 0.00 0.00 2.74
2586 3305 3.139397 ACAAAAGACCCCCATGAACTGTA 59.861 43.478 0.00 0.00 0.00 2.74
2587 3306 2.091333 ACAAAAGACCCCCATGAACTGT 60.091 45.455 0.00 0.00 0.00 3.55
2588 3307 2.597455 ACAAAAGACCCCCATGAACTG 58.403 47.619 0.00 0.00 0.00 3.16
2589 3308 3.328535 AACAAAAGACCCCCATGAACT 57.671 42.857 0.00 0.00 0.00 3.01
2590 3309 3.552068 CGAAACAAAAGACCCCCATGAAC 60.552 47.826 0.00 0.00 0.00 3.18
2591 3310 2.625790 CGAAACAAAAGACCCCCATGAA 59.374 45.455 0.00 0.00 0.00 2.57
2592 3311 2.235016 CGAAACAAAAGACCCCCATGA 58.765 47.619 0.00 0.00 0.00 3.07
2593 3312 1.272212 CCGAAACAAAAGACCCCCATG 59.728 52.381 0.00 0.00 0.00 3.66
2594 3313 1.133294 ACCGAAACAAAAGACCCCCAT 60.133 47.619 0.00 0.00 0.00 4.00
2596 3315 0.671796 CACCGAAACAAAAGACCCCC 59.328 55.000 0.00 0.00 0.00 5.40
2597 3316 1.607148 CTCACCGAAACAAAAGACCCC 59.393 52.381 0.00 0.00 0.00 4.95
2598 3317 1.001706 GCTCACCGAAACAAAAGACCC 60.002 52.381 0.00 0.00 0.00 4.46
2599 3318 1.673920 TGCTCACCGAAACAAAAGACC 59.326 47.619 0.00 0.00 0.00 3.85
2617 3336 0.379669 CATGGAATGGAAGCGAGTGC 59.620 55.000 0.00 0.00 41.79 4.40
2629 3348 3.427638 CGAGTACGACACAGACATGGAAT 60.428 47.826 0.00 0.00 42.66 3.01
2640 3359 2.047679 AAACAGAGCGAGTACGACAC 57.952 50.000 0.00 0.00 42.66 3.67
2666 3385 4.777463 ACCCTGGAAACAAATACTATCGG 58.223 43.478 0.00 0.00 42.06 4.18
2669 3388 7.238710 ACTGAAACCCTGGAAACAAATACTAT 58.761 34.615 0.00 0.00 42.06 2.12
2690 3409 6.612247 TTTGAAAGCAGAAACGAATACTGA 57.388 33.333 0.00 0.00 34.07 3.41
2691 3410 7.678194 TTTTTGAAAGCAGAAACGAATACTG 57.322 32.000 0.00 0.00 35.14 2.74
2720 3439 9.965824 CTTTTGGAAGCGGAAACAAATATATAT 57.034 29.630 0.00 0.00 33.40 0.86
2721 3440 9.179909 TCTTTTGGAAGCGGAAACAAATATATA 57.820 29.630 0.00 0.00 33.40 0.86
2722 3441 8.062065 TCTTTTGGAAGCGGAAACAAATATAT 57.938 30.769 0.00 0.00 33.40 0.86
2723 3442 7.455641 TCTTTTGGAAGCGGAAACAAATATA 57.544 32.000 0.00 0.00 33.40 0.86
2724 3443 6.339587 TCTTTTGGAAGCGGAAACAAATAT 57.660 33.333 0.00 0.00 33.40 1.28
2725 3444 5.776173 TCTTTTGGAAGCGGAAACAAATA 57.224 34.783 0.00 0.00 33.40 1.40
2726 3445 4.664150 TCTTTTGGAAGCGGAAACAAAT 57.336 36.364 0.00 0.00 33.40 2.32
2727 3446 4.664150 ATCTTTTGGAAGCGGAAACAAA 57.336 36.364 0.00 0.00 32.75 2.83
2728 3447 5.776173 TTATCTTTTGGAAGCGGAAACAA 57.224 34.783 0.00 0.00 32.75 2.83
2729 3448 5.975693 ATTATCTTTTGGAAGCGGAAACA 57.024 34.783 0.00 0.00 32.75 2.83
2749 3468 9.830975 GGGTGCTCCAACATTTATTTTTATATT 57.169 29.630 7.20 0.00 35.00 1.28
2750 3469 8.986991 TGGGTGCTCCAACATTTATTTTTATAT 58.013 29.630 7.20 0.00 43.84 0.86
2751 3470 8.367660 TGGGTGCTCCAACATTTATTTTTATA 57.632 30.769 7.20 0.00 43.84 0.98
2752 3471 7.038373 ACTGGGTGCTCCAACATTTATTTTTAT 60.038 33.333 7.20 0.00 46.51 1.40
2753 3472 6.268847 ACTGGGTGCTCCAACATTTATTTTTA 59.731 34.615 7.20 0.00 46.51 1.52
2754 3473 5.071653 ACTGGGTGCTCCAACATTTATTTTT 59.928 36.000 7.20 0.00 46.51 1.94
2755 3474 4.592778 ACTGGGTGCTCCAACATTTATTTT 59.407 37.500 7.20 0.00 46.51 1.82
2756 3475 4.159557 ACTGGGTGCTCCAACATTTATTT 58.840 39.130 7.20 0.00 46.51 1.40
2757 3476 3.778265 ACTGGGTGCTCCAACATTTATT 58.222 40.909 7.20 0.00 46.51 1.40
2758 3477 3.456380 ACTGGGTGCTCCAACATTTAT 57.544 42.857 7.20 0.00 46.51 1.40
2759 3478 2.969821 ACTGGGTGCTCCAACATTTA 57.030 45.000 7.20 0.00 46.51 1.40
2760 3479 1.963515 GAACTGGGTGCTCCAACATTT 59.036 47.619 7.20 0.00 46.51 2.32
2761 3480 1.620822 GAACTGGGTGCTCCAACATT 58.379 50.000 7.20 0.00 46.51 2.71
2762 3481 0.251341 GGAACTGGGTGCTCCAACAT 60.251 55.000 7.20 0.00 46.51 2.71
2763 3482 1.150536 GGAACTGGGTGCTCCAACA 59.849 57.895 7.20 0.00 46.51 3.33
2764 3483 0.251341 ATGGAACTGGGTGCTCCAAC 60.251 55.000 7.20 0.00 46.51 3.77
2765 3484 0.482446 AATGGAACTGGGTGCTCCAA 59.518 50.000 7.20 0.00 46.51 3.53
2766 3485 0.038166 GAATGGAACTGGGTGCTCCA 59.962 55.000 7.20 3.14 44.14 3.86
2767 3486 0.038166 TGAATGGAACTGGGTGCTCC 59.962 55.000 0.00 0.00 0.00 4.70
2768 3487 2.134789 ATGAATGGAACTGGGTGCTC 57.865 50.000 0.00 0.00 0.00 4.26
2769 3488 2.610438 AATGAATGGAACTGGGTGCT 57.390 45.000 0.00 0.00 0.00 4.40
2770 3489 3.588955 GAAAATGAATGGAACTGGGTGC 58.411 45.455 0.00 0.00 0.00 5.01
2771 3490 3.836949 CGAAAATGAATGGAACTGGGTG 58.163 45.455 0.00 0.00 0.00 4.61
2772 3491 2.231235 GCGAAAATGAATGGAACTGGGT 59.769 45.455 0.00 0.00 0.00 4.51
2773 3492 2.493278 AGCGAAAATGAATGGAACTGGG 59.507 45.455 0.00 0.00 0.00 4.45
2774 3493 3.428045 GGAGCGAAAATGAATGGAACTGG 60.428 47.826 0.00 0.00 0.00 4.00
2775 3494 3.728864 CGGAGCGAAAATGAATGGAACTG 60.729 47.826 0.00 0.00 0.00 3.16
2776 3495 2.420022 CGGAGCGAAAATGAATGGAACT 59.580 45.455 0.00 0.00 0.00 3.01
2777 3496 2.785679 CGGAGCGAAAATGAATGGAAC 58.214 47.619 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.