Multiple sequence alignment - TraesCS2A01G540400

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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 TraesCS2A01G540400 chr2A 100.000 3455 0 0 1 3455 752338915 752335461 0.000000e+00 6381.0
1 TraesCS2A01G540400 chr2A 84.810 158 24 0 202 359 14824208 14824365 3.570000e-35 159.0
2 TraesCS2A01G540400 chr2A 86.458 96 13 0 196 291 729368493 729368398 4.720000e-19 106.0
3 TraesCS2A01G540400 chr2D 95.391 1497 45 9 622 2106 620686774 620685290 0.000000e+00 2361.0
4 TraesCS2A01G540400 chr2D 95.938 1354 50 3 2105 3455 620684977 620683626 0.000000e+00 2191.0
5 TraesCS2A01G540400 chr2D 92.975 242 17 0 372 613 620687135 620686894 1.530000e-93 353.0
6 TraesCS2A01G540400 chr2B 84.369 1094 112 35 695 1751 761329482 761328411 0.000000e+00 1018.0
7 TraesCS2A01G540400 chr2B 88.860 772 69 11 1848 2608 761328448 761327683 0.000000e+00 933.0
8 TraesCS2A01G540400 chr2B 80.556 432 70 7 1954 2372 761323226 761322796 1.550000e-83 320.0
9 TraesCS2A01G540400 chr2B 78.395 486 85 13 906 1386 761663233 761662763 7.250000e-77 298.0
10 TraesCS2A01G540400 chr2B 78.144 485 88 10 906 1386 761693122 761692652 3.370000e-75 292.0
11 TraesCS2A01G540400 chr2B 88.732 71 7 1 221 290 482701632 482701562 6.140000e-13 86.1
12 TraesCS2A01G540400 chr3D 82.033 423 66 8 1972 2386 82412948 82413368 5.490000e-93 351.0
13 TraesCS2A01G540400 chr3B 81.797 423 67 7 1972 2386 128949359 128949779 2.550000e-91 346.0
14 TraesCS2A01G540400 chr3B 84.375 96 15 0 196 291 821858612 821858707 1.020000e-15 95.3
15 TraesCS2A01G540400 chr3A 81.324 423 69 8 1972 2386 97974041 97974461 5.530000e-88 335.0
16 TraesCS2A01G540400 chr5B 78.261 207 25 9 196 382 140975000 140975206 7.840000e-22 115.0
17 TraesCS2A01G540400 chr1B 87.629 97 11 1 195 291 648707044 648707139 1.010000e-20 111.0
18 TraesCS2A01G540400 chr7D 85.714 98 12 2 195 291 180068150 180068246 6.100000e-18 102.0
19 TraesCS2A01G540400 chr5A 79.856 139 28 0 198 336 58032660 58032798 6.100000e-18 102.0
20 TraesCS2A01G540400 chr1D 77.114 201 26 5 202 382 483527556 483527356 7.890000e-17 99.0
21 TraesCS2A01G540400 chr7A 78.261 138 28 2 2841 2977 730564900 730564764 1.710000e-13 87.9


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 TraesCS2A01G540400 chr2A 752335461 752338915 3454 True 6381.0 6381 100.0000 1 3455 1 chr2A.!!$R2 3454
1 TraesCS2A01G540400 chr2D 620683626 620687135 3509 True 1635.0 2361 94.7680 372 3455 3 chr2D.!!$R1 3083
2 TraesCS2A01G540400 chr2B 761327683 761329482 1799 True 975.5 1018 86.6145 695 2608 2 chr2B.!!$R5 1913

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
308 309 0.038251 TCAGACTAGGCTTGCACGTG 60.038 55.0 12.28 12.28 0.0 4.49 F
1606 1750 0.035630 GAGTTCCACAGGCAGATGCT 60.036 55.0 4.59 0.00 41.7 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 2222 0.445436 GAAACGTGGCTCTGCATCAG 59.555 55.0 0.00 0.0 0.0 2.90 R
2716 3208 0.037790 TCCGACGAACATGACATGCA 60.038 50.0 15.49 0.0 0.0 3.96 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
22 23 3.884169 TGTCTTAACATGCTTCGTTTGC 58.116 40.909 0.00 0.00 0.00 3.68
23 24 3.563808 TGTCTTAACATGCTTCGTTTGCT 59.436 39.130 0.00 0.00 0.00 3.91
24 25 4.036262 TGTCTTAACATGCTTCGTTTGCTT 59.964 37.500 0.00 0.00 0.00 3.91
25 26 4.379793 GTCTTAACATGCTTCGTTTGCTTG 59.620 41.667 0.00 0.00 40.14 4.01
26 27 1.490621 AACATGCTTCGTTTGCTTGC 58.509 45.000 0.00 0.00 38.59 4.01
27 28 0.670162 ACATGCTTCGTTTGCTTGCT 59.330 45.000 0.00 0.85 38.59 3.91
28 29 1.879380 ACATGCTTCGTTTGCTTGCTA 59.121 42.857 0.00 0.00 38.59 3.49
29 30 2.095567 ACATGCTTCGTTTGCTTGCTAG 60.096 45.455 0.00 0.00 38.59 3.42
30 31 1.593196 TGCTTCGTTTGCTTGCTAGT 58.407 45.000 0.00 0.00 0.00 2.57
31 32 2.761559 TGCTTCGTTTGCTTGCTAGTA 58.238 42.857 0.00 0.00 0.00 1.82
32 33 3.334691 TGCTTCGTTTGCTTGCTAGTAT 58.665 40.909 0.00 0.00 0.00 2.12
33 34 3.751175 TGCTTCGTTTGCTTGCTAGTATT 59.249 39.130 0.00 0.00 0.00 1.89
34 35 4.215399 TGCTTCGTTTGCTTGCTAGTATTT 59.785 37.500 0.00 0.00 0.00 1.40
35 36 5.410132 TGCTTCGTTTGCTTGCTAGTATTTA 59.590 36.000 0.00 0.00 0.00 1.40
36 37 6.093495 TGCTTCGTTTGCTTGCTAGTATTTAT 59.907 34.615 0.00 0.00 0.00 1.40
37 38 6.967199 GCTTCGTTTGCTTGCTAGTATTTATT 59.033 34.615 0.00 0.00 0.00 1.40
38 39 7.484959 GCTTCGTTTGCTTGCTAGTATTTATTT 59.515 33.333 0.00 0.00 0.00 1.40
39 40 9.341899 CTTCGTTTGCTTGCTAGTATTTATTTT 57.658 29.630 0.00 0.00 0.00 1.82
66 67 8.661352 AAATTTCCCAACTAACTTGTCATTTG 57.339 30.769 0.00 0.00 0.00 2.32
67 68 4.846779 TCCCAACTAACTTGTCATTTGC 57.153 40.909 0.00 0.00 0.00 3.68
68 69 4.469657 TCCCAACTAACTTGTCATTTGCT 58.530 39.130 0.00 0.00 0.00 3.91
69 70 4.892934 TCCCAACTAACTTGTCATTTGCTT 59.107 37.500 0.00 0.00 0.00 3.91
70 71 4.984161 CCCAACTAACTTGTCATTTGCTTG 59.016 41.667 0.00 0.00 0.00 4.01
71 72 4.445385 CCAACTAACTTGTCATTTGCTTGC 59.555 41.667 0.00 0.00 0.00 4.01
72 73 5.284079 CAACTAACTTGTCATTTGCTTGCT 58.716 37.500 0.00 0.00 0.00 3.91
73 74 6.437928 CAACTAACTTGTCATTTGCTTGCTA 58.562 36.000 0.00 0.00 0.00 3.49
74 75 6.246420 ACTAACTTGTCATTTGCTTGCTAG 57.754 37.500 0.00 0.00 0.00 3.42
75 76 5.765182 ACTAACTTGTCATTTGCTTGCTAGT 59.235 36.000 0.00 0.00 0.00 2.57
76 77 6.934645 ACTAACTTGTCATTTGCTTGCTAGTA 59.065 34.615 0.00 0.00 0.00 1.82
77 78 6.824305 AACTTGTCATTTGCTTGCTAGTAT 57.176 33.333 0.00 0.00 0.00 2.12
78 79 6.824305 ACTTGTCATTTGCTTGCTAGTATT 57.176 33.333 0.00 0.00 0.00 1.89
79 80 7.219484 ACTTGTCATTTGCTTGCTAGTATTT 57.781 32.000 0.00 0.00 0.00 1.40
80 81 8.335532 ACTTGTCATTTGCTTGCTAGTATTTA 57.664 30.769 0.00 0.00 0.00 1.40
81 82 8.792633 ACTTGTCATTTGCTTGCTAGTATTTAA 58.207 29.630 0.00 0.00 0.00 1.52
82 83 9.282247 CTTGTCATTTGCTTGCTAGTATTTAAG 57.718 33.333 0.00 0.00 0.00 1.85
83 84 8.335532 TGTCATTTGCTTGCTAGTATTTAAGT 57.664 30.769 0.00 0.00 0.00 2.24
84 85 8.450964 TGTCATTTGCTTGCTAGTATTTAAGTC 58.549 33.333 0.00 0.00 0.00 3.01
85 86 8.450964 GTCATTTGCTTGCTAGTATTTAAGTCA 58.549 33.333 0.00 0.00 0.00 3.41
86 87 9.008965 TCATTTGCTTGCTAGTATTTAAGTCAA 57.991 29.630 0.00 0.00 0.00 3.18
87 88 9.065871 CATTTGCTTGCTAGTATTTAAGTCAAC 57.934 33.333 0.00 0.00 0.00 3.18
88 89 7.737972 TTGCTTGCTAGTATTTAAGTCAACA 57.262 32.000 0.00 0.00 0.00 3.33
89 90 7.129109 TGCTTGCTAGTATTTAAGTCAACAC 57.871 36.000 0.00 0.00 0.00 3.32
90 91 6.128661 TGCTTGCTAGTATTTAAGTCAACACG 60.129 38.462 0.00 0.00 0.00 4.49
91 92 6.128634 GCTTGCTAGTATTTAAGTCAACACGT 60.129 38.462 0.00 0.00 0.00 4.49
92 93 7.062605 GCTTGCTAGTATTTAAGTCAACACGTA 59.937 37.037 0.00 0.00 0.00 3.57
93 94 8.991243 TTGCTAGTATTTAAGTCAACACGTAT 57.009 30.769 0.00 0.00 0.00 3.06
94 95 8.402326 TGCTAGTATTTAAGTCAACACGTATG 57.598 34.615 0.00 0.00 0.00 2.39
95 96 8.030692 TGCTAGTATTTAAGTCAACACGTATGT 58.969 33.333 0.00 0.00 42.46 2.29
96 97 9.507280 GCTAGTATTTAAGTCAACACGTATGTA 57.493 33.333 0.00 0.00 38.45 2.29
99 100 9.695526 AGTATTTAAGTCAACACGTATGTACAA 57.304 29.630 0.00 0.00 38.45 2.41
100 101 9.731519 GTATTTAAGTCAACACGTATGTACAAC 57.268 33.333 0.00 0.00 38.45 3.32
101 102 7.767745 TTTAAGTCAACACGTATGTACAACA 57.232 32.000 0.00 0.00 38.45 3.33
102 103 7.767745 TTAAGTCAACACGTATGTACAACAA 57.232 32.000 0.00 0.00 38.45 2.83
103 104 6.854496 AAGTCAACACGTATGTACAACAAT 57.146 33.333 0.00 0.00 38.45 2.71
104 105 6.462073 AGTCAACACGTATGTACAACAATC 57.538 37.500 0.00 0.00 38.45 2.67
105 106 6.220930 AGTCAACACGTATGTACAACAATCT 58.779 36.000 0.00 0.00 38.45 2.40
106 107 6.704493 AGTCAACACGTATGTACAACAATCTT 59.296 34.615 0.00 0.00 38.45 2.40
107 108 7.007697 GTCAACACGTATGTACAACAATCTTC 58.992 38.462 0.00 0.00 38.45 2.87
108 109 6.702282 TCAACACGTATGTACAACAATCTTCA 59.298 34.615 0.00 0.00 38.45 3.02
109 110 6.706055 ACACGTATGTACAACAATCTTCAG 57.294 37.500 0.00 0.00 37.26 3.02
110 111 6.220930 ACACGTATGTACAACAATCTTCAGT 58.779 36.000 0.00 0.00 37.26 3.41
111 112 6.704493 ACACGTATGTACAACAATCTTCAGTT 59.296 34.615 0.00 0.00 37.26 3.16
112 113 7.225931 ACACGTATGTACAACAATCTTCAGTTT 59.774 33.333 0.00 0.00 37.26 2.66
113 114 8.067784 CACGTATGTACAACAATCTTCAGTTTT 58.932 33.333 0.00 0.00 0.00 2.43
114 115 8.617809 ACGTATGTACAACAATCTTCAGTTTTT 58.382 29.630 0.00 0.00 0.00 1.94
118 119 7.411274 TGTACAACAATCTTCAGTTTTTACCG 58.589 34.615 0.00 0.00 0.00 4.02
119 120 6.445357 ACAACAATCTTCAGTTTTTACCGT 57.555 33.333 0.00 0.00 0.00 4.83
120 121 6.492254 ACAACAATCTTCAGTTTTTACCGTC 58.508 36.000 0.00 0.00 0.00 4.79
121 122 6.094325 ACAACAATCTTCAGTTTTTACCGTCA 59.906 34.615 0.00 0.00 0.00 4.35
122 123 6.056428 ACAATCTTCAGTTTTTACCGTCAC 57.944 37.500 0.00 0.00 0.00 3.67
123 124 5.587043 ACAATCTTCAGTTTTTACCGTCACA 59.413 36.000 0.00 0.00 0.00 3.58
124 125 6.262273 ACAATCTTCAGTTTTTACCGTCACAT 59.738 34.615 0.00 0.00 0.00 3.21
125 126 6.877611 ATCTTCAGTTTTTACCGTCACATT 57.122 33.333 0.00 0.00 0.00 2.71
126 127 6.687081 TCTTCAGTTTTTACCGTCACATTT 57.313 33.333 0.00 0.00 0.00 2.32
127 128 7.090953 TCTTCAGTTTTTACCGTCACATTTT 57.909 32.000 0.00 0.00 0.00 1.82
128 129 8.211116 TCTTCAGTTTTTACCGTCACATTTTA 57.789 30.769 0.00 0.00 0.00 1.52
129 130 8.842280 TCTTCAGTTTTTACCGTCACATTTTAT 58.158 29.630 0.00 0.00 0.00 1.40
130 131 8.789881 TTCAGTTTTTACCGTCACATTTTATG 57.210 30.769 0.00 0.00 0.00 1.90
131 132 7.932335 TCAGTTTTTACCGTCACATTTTATGT 58.068 30.769 0.00 0.00 46.22 2.29
182 183 9.575868 TGTTATGTTATCTTTGAGTTAAACCCA 57.424 29.630 0.00 0.00 0.00 4.51
184 185 7.703058 ATGTTATCTTTGAGTTAAACCCAGG 57.297 36.000 0.00 0.00 0.00 4.45
185 186 5.475564 TGTTATCTTTGAGTTAAACCCAGGC 59.524 40.000 0.00 0.00 0.00 4.85
186 187 3.586470 TCTTTGAGTTAAACCCAGGCA 57.414 42.857 0.00 0.00 0.00 4.75
187 188 4.112634 TCTTTGAGTTAAACCCAGGCAT 57.887 40.909 0.00 0.00 0.00 4.40
188 189 3.826157 TCTTTGAGTTAAACCCAGGCATG 59.174 43.478 0.00 0.00 0.00 4.06
216 217 2.742372 CCCGGGCTTGACGTTCAG 60.742 66.667 8.08 0.00 0.00 3.02
217 218 2.742372 CCGGGCTTGACGTTCAGG 60.742 66.667 0.00 0.00 0.00 3.86
219 220 2.032681 GGGCTTGACGTTCAGGCT 59.967 61.111 17.49 0.00 46.99 4.58
220 221 2.328099 GGGCTTGACGTTCAGGCTG 61.328 63.158 8.58 8.58 46.99 4.85
221 222 2.328099 GGCTTGACGTTCAGGCTGG 61.328 63.158 15.73 0.62 46.99 4.85
222 223 2.328099 GCTTGACGTTCAGGCTGGG 61.328 63.158 15.73 7.11 44.80 4.45
223 224 2.281484 TTGACGTTCAGGCTGGGC 60.281 61.111 15.73 6.90 0.00 5.36
224 225 2.738213 CTTGACGTTCAGGCTGGGCT 62.738 60.000 15.73 0.00 0.00 5.19
225 226 2.435059 GACGTTCAGGCTGGGCTC 60.435 66.667 15.73 0.80 0.00 4.70
226 227 3.240134 GACGTTCAGGCTGGGCTCA 62.240 63.158 15.73 0.00 0.00 4.26
227 228 2.435586 CGTTCAGGCTGGGCTCAG 60.436 66.667 15.73 10.01 43.64 3.35
228 229 2.045536 GTTCAGGCTGGGCTCAGG 60.046 66.667 17.16 0.00 41.19 3.86
240 241 2.732289 GCTCAGGCCTTGTTTTCCA 58.268 52.632 0.00 0.00 0.00 3.53
241 242 0.600057 GCTCAGGCCTTGTTTTCCAG 59.400 55.000 0.00 0.00 0.00 3.86
242 243 0.600057 CTCAGGCCTTGTTTTCCAGC 59.400 55.000 0.00 0.00 0.00 4.85
243 244 0.827507 TCAGGCCTTGTTTTCCAGCC 60.828 55.000 0.00 0.00 44.20 4.85
244 245 4.198087 GGCCTTGTTTTCCAGCCT 57.802 55.556 0.00 0.00 40.57 4.58
245 246 1.667722 GGCCTTGTTTTCCAGCCTG 59.332 57.895 0.00 0.00 40.57 4.85
246 247 1.667722 GCCTTGTTTTCCAGCCTGG 59.332 57.895 3.69 3.69 39.43 4.45
247 248 0.827507 GCCTTGTTTTCCAGCCTGGA 60.828 55.000 10.05 10.05 46.61 3.86
257 258 1.757118 TCCAGCCTGGAAGATAGTTCG 59.243 52.381 12.03 0.00 45.00 3.95
258 259 1.202580 CCAGCCTGGAAGATAGTTCGG 60.203 57.143 4.15 0.00 40.96 4.30
259 260 1.123928 AGCCTGGAAGATAGTTCGGG 58.876 55.000 0.00 0.00 34.07 5.14
260 261 0.533085 GCCTGGAAGATAGTTCGGGC 60.533 60.000 0.00 0.00 34.07 6.13
261 262 1.123928 CCTGGAAGATAGTTCGGGCT 58.876 55.000 0.00 0.00 34.07 5.19
262 263 1.202580 CCTGGAAGATAGTTCGGGCTG 60.203 57.143 0.00 0.00 34.07 4.85
263 264 0.830648 TGGAAGATAGTTCGGGCTGG 59.169 55.000 0.00 0.00 0.00 4.85
264 265 0.106894 GGAAGATAGTTCGGGCTGGG 59.893 60.000 0.00 0.00 0.00 4.45
265 266 0.533085 GAAGATAGTTCGGGCTGGGC 60.533 60.000 0.00 0.00 0.00 5.36
266 267 0.983378 AAGATAGTTCGGGCTGGGCT 60.983 55.000 0.00 0.00 0.00 5.19
267 268 1.069935 GATAGTTCGGGCTGGGCTC 59.930 63.158 0.00 0.00 0.00 4.70
276 277 4.722700 GCTGGGCTCGGGCTTCAA 62.723 66.667 7.48 0.00 38.73 2.69
277 278 2.437359 CTGGGCTCGGGCTTCAAG 60.437 66.667 7.48 0.00 38.73 3.02
278 279 3.249189 TGGGCTCGGGCTTCAAGT 61.249 61.111 7.48 0.00 38.73 3.16
279 280 2.034221 GGGCTCGGGCTTCAAGTT 59.966 61.111 7.48 0.00 38.73 2.66
280 281 1.603739 GGGCTCGGGCTTCAAGTTT 60.604 57.895 7.48 0.00 38.73 2.66
281 282 1.179174 GGGCTCGGGCTTCAAGTTTT 61.179 55.000 7.48 0.00 38.73 2.43
282 283 0.673985 GGCTCGGGCTTCAAGTTTTT 59.326 50.000 7.48 0.00 38.73 1.94
303 304 4.568152 TTGTTTTTCAGACTAGGCTTGC 57.432 40.909 0.00 0.00 0.00 4.01
304 305 3.550820 TGTTTTTCAGACTAGGCTTGCA 58.449 40.909 0.00 0.00 0.00 4.08
305 306 3.315191 TGTTTTTCAGACTAGGCTTGCAC 59.685 43.478 0.00 0.00 0.00 4.57
306 307 1.795768 TTTCAGACTAGGCTTGCACG 58.204 50.000 0.00 0.00 0.00 5.34
307 308 0.679505 TTCAGACTAGGCTTGCACGT 59.320 50.000 0.00 0.00 0.00 4.49
308 309 0.038251 TCAGACTAGGCTTGCACGTG 60.038 55.000 12.28 12.28 0.00 4.49
309 310 0.319900 CAGACTAGGCTTGCACGTGT 60.320 55.000 18.38 0.00 0.00 4.49
310 311 0.319900 AGACTAGGCTTGCACGTGTG 60.320 55.000 18.38 9.04 0.00 3.82
311 312 0.600255 GACTAGGCTTGCACGTGTGT 60.600 55.000 18.38 3.70 0.00 3.72
312 313 0.677288 ACTAGGCTTGCACGTGTGTA 59.323 50.000 18.38 1.01 0.00 2.90
313 314 1.068474 CTAGGCTTGCACGTGTGTAC 58.932 55.000 18.38 4.85 0.00 2.90
314 315 0.389757 TAGGCTTGCACGTGTGTACA 59.610 50.000 18.38 3.18 0.00 2.90
315 316 1.157870 AGGCTTGCACGTGTGTACAC 61.158 55.000 19.36 19.36 43.15 2.90
316 317 1.157870 GGCTTGCACGTGTGTACACT 61.158 55.000 25.60 3.90 44.34 3.55
317 318 1.493772 GCTTGCACGTGTGTACACTA 58.506 50.000 25.60 10.40 44.34 2.74
318 319 1.862201 GCTTGCACGTGTGTACACTAA 59.138 47.619 25.60 4.68 44.34 2.24
319 320 2.285756 GCTTGCACGTGTGTACACTAAA 59.714 45.455 25.60 3.90 44.34 1.85
320 321 3.242478 GCTTGCACGTGTGTACACTAAAA 60.242 43.478 25.60 11.01 44.34 1.52
321 322 4.728307 GCTTGCACGTGTGTACACTAAAAA 60.728 41.667 25.60 11.92 44.34 1.94
338 339 1.402787 AAAATAGCATTCTGGCCGGG 58.597 50.000 12.87 0.00 0.00 5.73
339 340 1.109323 AAATAGCATTCTGGCCGGGC 61.109 55.000 23.42 23.42 0.00 6.13
340 341 1.999634 AATAGCATTCTGGCCGGGCT 62.000 55.000 29.87 16.61 38.55 5.19
341 342 1.999634 ATAGCATTCTGGCCGGGCTT 62.000 55.000 29.87 8.53 36.10 4.35
342 343 2.210144 TAGCATTCTGGCCGGGCTTT 62.210 55.000 29.87 8.15 36.10 3.51
343 344 2.649129 GCATTCTGGCCGGGCTTTT 61.649 57.895 29.87 8.52 0.00 2.27
344 345 1.216178 CATTCTGGCCGGGCTTTTG 59.784 57.895 29.87 16.66 0.00 2.44
345 346 1.984026 ATTCTGGCCGGGCTTTTGG 60.984 57.895 29.87 13.41 0.00 3.28
346 347 4.676951 TCTGGCCGGGCTTTTGGG 62.677 66.667 29.87 11.70 0.00 4.12
350 351 3.625897 GCCGGGCTTTTGGGCTTT 61.626 61.111 12.87 0.00 43.52 3.51
351 352 2.279810 GCCGGGCTTTTGGGCTTTA 61.280 57.895 12.87 0.00 43.52 1.85
352 353 1.890174 CCGGGCTTTTGGGCTTTAG 59.110 57.895 0.00 0.00 40.65 1.85
353 354 1.604147 CCGGGCTTTTGGGCTTTAGG 61.604 60.000 0.00 0.00 40.65 2.69
354 355 1.596934 GGGCTTTTGGGCTTTAGGC 59.403 57.895 0.00 0.00 40.65 3.93
355 356 0.904865 GGGCTTTTGGGCTTTAGGCT 60.905 55.000 3.20 0.00 41.46 4.58
356 357 0.976641 GGCTTTTGGGCTTTAGGCTT 59.023 50.000 0.00 0.00 41.46 4.35
357 358 1.338105 GGCTTTTGGGCTTTAGGCTTG 60.338 52.381 0.00 0.00 41.46 4.01
358 359 1.618343 GCTTTTGGGCTTTAGGCTTGA 59.382 47.619 0.00 0.00 41.46 3.02
359 360 2.234661 GCTTTTGGGCTTTAGGCTTGAT 59.765 45.455 0.00 0.00 41.46 2.57
360 361 3.306989 GCTTTTGGGCTTTAGGCTTGATT 60.307 43.478 0.00 0.00 41.46 2.57
361 362 4.803924 GCTTTTGGGCTTTAGGCTTGATTT 60.804 41.667 0.00 0.00 41.46 2.17
362 363 4.535526 TTTGGGCTTTAGGCTTGATTTC 57.464 40.909 0.00 0.00 41.46 2.17
363 364 2.091541 TGGGCTTTAGGCTTGATTTCG 58.908 47.619 0.00 0.00 41.46 3.46
364 365 1.405463 GGGCTTTAGGCTTGATTTCGG 59.595 52.381 0.00 0.00 41.46 4.30
365 366 1.405463 GGCTTTAGGCTTGATTTCGGG 59.595 52.381 0.00 0.00 41.46 5.14
366 367 2.092323 GCTTTAGGCTTGATTTCGGGT 58.908 47.619 0.00 0.00 38.06 5.28
367 368 2.492088 GCTTTAGGCTTGATTTCGGGTT 59.508 45.455 0.00 0.00 38.06 4.11
368 369 3.673323 GCTTTAGGCTTGATTTCGGGTTG 60.673 47.826 0.00 0.00 38.06 3.77
369 370 2.122783 TAGGCTTGATTTCGGGTTGG 57.877 50.000 0.00 0.00 0.00 3.77
370 371 0.611896 AGGCTTGATTTCGGGTTGGG 60.612 55.000 0.00 0.00 0.00 4.12
374 375 0.958382 TTGATTTCGGGTTGGGCTCG 60.958 55.000 0.00 0.00 43.78 5.03
391 392 3.578456 GGGCATGACGACCAACAG 58.422 61.111 0.00 0.00 45.64 3.16
397 398 1.208052 CATGACGACCAACAGATCCCT 59.792 52.381 0.00 0.00 0.00 4.20
400 401 1.811266 CGACCAACAGATCCCTGCG 60.811 63.158 0.00 0.00 44.16 5.18
451 452 2.145958 TAGCTCGTCTCGTATAGCGT 57.854 50.000 0.00 0.00 39.94 5.07
461 462 5.336469 CGTCTCGTATAGCGTGTCTATTTTC 59.664 44.000 0.00 0.00 38.81 2.29
467 468 6.140895 CGTATAGCGTGTCTATTTTCAGTCTG 59.859 42.308 0.00 0.00 38.81 3.51
486 487 7.936847 TCAGTCTGTAAGTTAATGTGGAAATGT 59.063 33.333 0.00 0.00 33.76 2.71
816 931 3.107642 ACACCTCCTACGTGAAAACAG 57.892 47.619 0.00 0.00 35.17 3.16
841 956 7.234988 AGTCTTTACAGGTAGGTTTGTGTCTAT 59.765 37.037 0.00 0.00 0.00 1.98
842 957 7.544915 GTCTTTACAGGTAGGTTTGTGTCTATC 59.455 40.741 0.00 0.00 0.00 2.08
843 958 7.453752 TCTTTACAGGTAGGTTTGTGTCTATCT 59.546 37.037 0.00 0.00 0.00 1.98
844 959 5.662674 ACAGGTAGGTTTGTGTCTATCTC 57.337 43.478 0.00 0.00 0.00 2.75
845 960 5.334421 ACAGGTAGGTTTGTGTCTATCTCT 58.666 41.667 0.00 0.00 0.00 3.10
846 961 5.780793 ACAGGTAGGTTTGTGTCTATCTCTT 59.219 40.000 0.00 0.00 0.00 2.85
984 1119 4.442706 AGCTAGTGATTATTGTGGTTCCG 58.557 43.478 0.00 0.00 0.00 4.30
1039 1174 4.025401 GCAAGGACCCGCACAACG 62.025 66.667 0.00 0.00 43.15 4.10
1173 1308 2.034999 GTGGATTTGCGGGACCCA 59.965 61.111 12.15 0.00 0.00 4.51
1176 1311 1.379843 GGATTTGCGGGACCCACAT 60.380 57.895 12.15 0.00 0.00 3.21
1285 1420 2.203070 AGGCCCGAATTGCTAGCG 60.203 61.111 10.77 0.00 0.00 4.26
1317 1452 3.621394 GCGTCGGAGAAGATGCGC 61.621 66.667 0.00 0.00 43.36 6.09
1506 1641 1.588404 GTGTTCATACATCGGACGCTG 59.412 52.381 0.00 0.00 36.50 5.18
1525 1667 5.237996 ACGCTGGAGAAAACTTTTTACTACC 59.762 40.000 0.00 0.00 0.00 3.18
1606 1750 0.035630 GAGTTCCACAGGCAGATGCT 60.036 55.000 4.59 0.00 41.70 3.79
1615 1766 2.187946 GCAGATGCTAGCGGTGGT 59.812 61.111 10.77 0.00 38.21 4.16
1716 1882 1.005037 GAGACCGTGACCATGCACA 60.005 57.895 0.00 0.00 38.69 4.57
1748 1916 2.547218 CGTAGTACAACTGGCAACACCT 60.547 50.000 0.38 0.00 46.17 4.00
1749 1917 2.729028 AGTACAACTGGCAACACCTT 57.271 45.000 0.00 0.00 46.17 3.50
1750 1918 3.012934 AGTACAACTGGCAACACCTTT 57.987 42.857 0.00 0.00 46.17 3.11
1895 2063 0.250727 AACAGCCTTACATGCCGTGT 60.251 50.000 0.00 0.00 44.95 4.49
1898 2066 1.134818 CAGCCTTACATGCCGTGTAGA 60.135 52.381 0.00 0.00 43.79 2.59
2004 2179 2.342279 CCTGACCCGAAGCGAACA 59.658 61.111 0.00 0.00 0.00 3.18
2018 2193 3.628646 GAACACTGGGCCTGGCGAT 62.629 63.158 13.40 0.11 0.00 4.58
2019 2194 3.210012 AACACTGGGCCTGGCGATT 62.210 57.895 13.40 0.64 0.00 3.34
2047 2222 0.669625 CTCGGGGTTCTTCACGTTCC 60.670 60.000 0.00 0.00 0.00 3.62
2226 2715 2.671963 GAAAGCACCCGGGTGTCC 60.672 66.667 45.19 33.05 46.90 4.02
2356 2845 3.952508 TGCGCAAGGAGGCCTTCA 61.953 61.111 15.31 0.00 42.67 3.02
2484 2973 1.004745 AGCCATCACCAAAGACCGATT 59.995 47.619 0.00 0.00 0.00 3.34
2506 2995 6.729391 TTCGACCGATACAAAAATTCATGA 57.271 33.333 0.00 0.00 0.00 3.07
2570 3062 9.673283 TATATGATCATATATCCCATGTGGACA 57.327 33.333 25.21 6.23 39.25 4.02
2580 3072 3.648067 TCCCATGTGGACAAGATAGATCC 59.352 47.826 0.00 0.00 38.61 3.36
2608 3100 5.242393 AGACATCTGTGGAAGGTGAAAATTG 59.758 40.000 0.00 0.00 39.66 2.32
2620 3112 4.095610 GGTGAAAATTGCCGTTAAGATCG 58.904 43.478 0.00 0.00 0.00 3.69
2685 3177 5.262588 AGCTTCGTGTTGATTTCCTTTTT 57.737 34.783 0.00 0.00 0.00 1.94
2692 3184 7.093992 TCGTGTTGATTTCCTTTTTCAAAAGT 58.906 30.769 10.43 0.00 42.92 2.66
2699 3191 6.538945 TTTCCTTTTTCAAAAGTACTGGCT 57.461 33.333 10.43 0.00 42.92 4.75
2701 3193 4.953579 TCCTTTTTCAAAAGTACTGGCTGT 59.046 37.500 10.43 1.74 42.92 4.40
2716 3208 4.081087 ACTGGCTGTGATAAATTCCTACGT 60.081 41.667 0.00 0.00 0.00 3.57
2792 3284 0.752658 AGAATGGATGGATCGCGTCA 59.247 50.000 5.77 3.85 0.00 4.35
2814 3306 4.633565 CAGGTCAGGAGAAGAAAATACAGC 59.366 45.833 0.00 0.00 0.00 4.40
2822 3314 5.123979 GGAGAAGAAAATACAGCGGTTTCAT 59.876 40.000 0.00 0.00 34.40 2.57
2913 3405 8.141298 TGTTGATTTGGTCTAGTAGTATTGGA 57.859 34.615 0.00 0.00 0.00 3.53
2969 3461 6.495872 ACGGCTCCTATTATTTAGATGTACCA 59.504 38.462 0.00 0.00 0.00 3.25
3076 3568 6.877855 GCACACATATTATGATGACTCCTGAT 59.122 38.462 10.62 0.00 0.00 2.90
3092 3584 2.827322 CCTGATCATTTGTTGGAAGGCA 59.173 45.455 0.00 0.00 0.00 4.75
3119 3611 2.081462 GTTGGACCGAAACCATACAGG 58.919 52.381 0.00 0.00 45.67 4.00
3280 3772 3.676093 CTGGAACTAGAAAGGTTGGACC 58.324 50.000 0.00 0.00 38.99 4.46
3283 3775 4.262617 GGAACTAGAAAGGTTGGACCATC 58.737 47.826 0.00 0.00 41.95 3.51
3284 3776 4.262617 GAACTAGAAAGGTTGGACCATCC 58.737 47.826 13.07 13.07 41.95 3.51
3285 3777 3.256704 ACTAGAAAGGTTGGACCATCCA 58.743 45.455 21.37 0.00 46.61 3.41
3300 3795 4.485875 ACCATCCAATACGTATAGGTCCA 58.514 43.478 8.83 0.00 0.00 4.02
3329 3824 6.764877 TGCAGAGTTAAAAGTTAACGAGAG 57.235 37.500 0.00 0.53 33.00 3.20
3346 3841 3.807622 CGAGAGGCTTGTTGAACTTTACA 59.192 43.478 0.00 0.00 0.00 2.41
3389 3884 2.999355 GGCAGCATTCGAGGATCTATTC 59.001 50.000 0.00 0.00 0.00 1.75
3437 3932 4.584874 TGATTTTTCCATCTCCGTGCTAA 58.415 39.130 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.563808 AGCAAACGAAGCATGTTAAGACA 59.436 39.130 0.00 0.00 40.71 3.41
2 3 4.147219 AGCAAACGAAGCATGTTAAGAC 57.853 40.909 0.00 0.00 0.00 3.01
3 4 4.536065 CAAGCAAACGAAGCATGTTAAGA 58.464 39.130 0.00 0.00 0.00 2.10
4 5 3.120121 GCAAGCAAACGAAGCATGTTAAG 59.880 43.478 0.00 0.00 33.58 1.85
5 6 3.049206 GCAAGCAAACGAAGCATGTTAA 58.951 40.909 0.00 0.00 33.58 2.01
7 8 1.067516 AGCAAGCAAACGAAGCATGTT 59.932 42.857 0.00 0.00 33.58 2.71
8 9 0.670162 AGCAAGCAAACGAAGCATGT 59.330 45.000 0.00 0.00 33.58 3.21
10 11 2.154462 ACTAGCAAGCAAACGAAGCAT 58.846 42.857 0.00 0.00 0.00 3.79
11 12 1.593196 ACTAGCAAGCAAACGAAGCA 58.407 45.000 0.00 0.00 0.00 3.91
13 14 8.895932 AAATAAATACTAGCAAGCAAACGAAG 57.104 30.769 0.00 0.00 0.00 3.79
40 41 9.108284 CAAATGACAAGTTAGTTGGGAAATTTT 57.892 29.630 4.72 0.00 40.90 1.82
41 42 7.226523 GCAAATGACAAGTTAGTTGGGAAATTT 59.773 33.333 4.72 0.00 40.90 1.82
42 43 6.705825 GCAAATGACAAGTTAGTTGGGAAATT 59.294 34.615 4.72 0.00 40.90 1.82
43 44 6.041979 AGCAAATGACAAGTTAGTTGGGAAAT 59.958 34.615 4.72 0.00 40.90 2.17
44 45 5.362430 AGCAAATGACAAGTTAGTTGGGAAA 59.638 36.000 4.72 0.00 40.90 3.13
45 46 4.892934 AGCAAATGACAAGTTAGTTGGGAA 59.107 37.500 4.72 0.00 40.90 3.97
46 47 4.469657 AGCAAATGACAAGTTAGTTGGGA 58.530 39.130 4.72 0.00 40.90 4.37
47 48 4.853924 AGCAAATGACAAGTTAGTTGGG 57.146 40.909 4.72 0.00 40.90 4.12
48 49 4.445385 GCAAGCAAATGACAAGTTAGTTGG 59.555 41.667 4.72 0.00 40.90 3.77
49 50 5.284079 AGCAAGCAAATGACAAGTTAGTTG 58.716 37.500 0.00 0.00 42.48 3.16
50 51 5.520376 AGCAAGCAAATGACAAGTTAGTT 57.480 34.783 0.00 0.00 0.00 2.24
51 52 5.765182 ACTAGCAAGCAAATGACAAGTTAGT 59.235 36.000 0.00 0.00 0.00 2.24
52 53 6.246420 ACTAGCAAGCAAATGACAAGTTAG 57.754 37.500 0.00 0.00 0.00 2.34
53 54 7.921786 ATACTAGCAAGCAAATGACAAGTTA 57.078 32.000 0.00 0.00 0.00 2.24
54 55 6.824305 ATACTAGCAAGCAAATGACAAGTT 57.176 33.333 0.00 0.00 0.00 2.66
55 56 6.824305 AATACTAGCAAGCAAATGACAAGT 57.176 33.333 0.00 0.00 0.00 3.16
56 57 9.282247 CTTAAATACTAGCAAGCAAATGACAAG 57.718 33.333 0.00 0.00 0.00 3.16
57 58 8.792633 ACTTAAATACTAGCAAGCAAATGACAA 58.207 29.630 0.00 0.00 0.00 3.18
58 59 8.335532 ACTTAAATACTAGCAAGCAAATGACA 57.664 30.769 0.00 0.00 0.00 3.58
59 60 8.450964 TGACTTAAATACTAGCAAGCAAATGAC 58.549 33.333 0.00 0.00 0.00 3.06
60 61 8.560355 TGACTTAAATACTAGCAAGCAAATGA 57.440 30.769 0.00 0.00 0.00 2.57
61 62 9.065871 GTTGACTTAAATACTAGCAAGCAAATG 57.934 33.333 0.00 0.00 0.00 2.32
62 63 8.792633 TGTTGACTTAAATACTAGCAAGCAAAT 58.207 29.630 0.00 0.00 0.00 2.32
63 64 8.073768 GTGTTGACTTAAATACTAGCAAGCAAA 58.926 33.333 0.00 0.00 0.00 3.68
64 65 7.570507 CGTGTTGACTTAAATACTAGCAAGCAA 60.571 37.037 0.00 0.00 0.00 3.91
65 66 6.128661 CGTGTTGACTTAAATACTAGCAAGCA 60.129 38.462 0.00 0.00 0.00 3.91
66 67 6.128634 ACGTGTTGACTTAAATACTAGCAAGC 60.129 38.462 0.00 0.00 0.00 4.01
67 68 7.347508 ACGTGTTGACTTAAATACTAGCAAG 57.652 36.000 0.00 0.00 0.00 4.01
68 69 8.865978 CATACGTGTTGACTTAAATACTAGCAA 58.134 33.333 0.00 0.00 0.00 3.91
69 70 8.030692 ACATACGTGTTGACTTAAATACTAGCA 58.969 33.333 0.00 0.00 34.01 3.49
70 71 8.403606 ACATACGTGTTGACTTAAATACTAGC 57.596 34.615 0.00 0.00 34.01 3.42
73 74 9.695526 TTGTACATACGTGTTGACTTAAATACT 57.304 29.630 0.00 0.00 39.77 2.12
74 75 9.731519 GTTGTACATACGTGTTGACTTAAATAC 57.268 33.333 0.00 0.00 39.77 1.89
75 76 9.473640 TGTTGTACATACGTGTTGACTTAAATA 57.526 29.630 0.00 0.00 39.77 1.40
76 77 8.367943 TGTTGTACATACGTGTTGACTTAAAT 57.632 30.769 0.00 0.00 39.77 1.40
77 78 7.767745 TGTTGTACATACGTGTTGACTTAAA 57.232 32.000 0.00 0.00 39.77 1.52
78 79 7.767745 TTGTTGTACATACGTGTTGACTTAA 57.232 32.000 0.00 0.00 39.77 1.85
79 80 7.868922 AGATTGTTGTACATACGTGTTGACTTA 59.131 33.333 0.00 0.00 39.77 2.24
80 81 6.704493 AGATTGTTGTACATACGTGTTGACTT 59.296 34.615 0.00 0.00 39.77 3.01
81 82 6.220930 AGATTGTTGTACATACGTGTTGACT 58.779 36.000 0.00 0.00 39.77 3.41
82 83 6.462073 AGATTGTTGTACATACGTGTTGAC 57.538 37.500 0.00 0.00 39.77 3.18
83 84 6.702282 TGAAGATTGTTGTACATACGTGTTGA 59.298 34.615 0.00 0.00 39.77 3.18
84 85 6.883129 TGAAGATTGTTGTACATACGTGTTG 58.117 36.000 0.00 0.00 39.77 3.33
85 86 6.704493 ACTGAAGATTGTTGTACATACGTGTT 59.296 34.615 0.00 0.00 39.77 3.32
86 87 6.220930 ACTGAAGATTGTTGTACATACGTGT 58.779 36.000 0.00 0.00 42.39 4.49
87 88 6.706055 ACTGAAGATTGTTGTACATACGTG 57.294 37.500 0.00 0.00 0.00 4.49
88 89 7.724305 AAACTGAAGATTGTTGTACATACGT 57.276 32.000 0.00 0.00 0.00 3.57
92 93 8.073768 CGGTAAAAACTGAAGATTGTTGTACAT 58.926 33.333 0.00 0.00 0.00 2.29
93 94 7.066043 ACGGTAAAAACTGAAGATTGTTGTACA 59.934 33.333 0.00 0.00 0.00 2.90
94 95 7.412063 ACGGTAAAAACTGAAGATTGTTGTAC 58.588 34.615 0.00 0.00 0.00 2.90
95 96 7.280428 TGACGGTAAAAACTGAAGATTGTTGTA 59.720 33.333 0.00 0.00 0.00 2.41
96 97 6.094325 TGACGGTAAAAACTGAAGATTGTTGT 59.906 34.615 0.00 0.00 0.00 3.32
97 98 6.413818 GTGACGGTAAAAACTGAAGATTGTTG 59.586 38.462 0.00 0.00 0.00 3.33
98 99 6.094325 TGTGACGGTAAAAACTGAAGATTGTT 59.906 34.615 0.00 0.00 0.00 2.83
99 100 5.587043 TGTGACGGTAAAAACTGAAGATTGT 59.413 36.000 0.00 0.00 0.00 2.71
100 101 6.055231 TGTGACGGTAAAAACTGAAGATTG 57.945 37.500 0.00 0.00 0.00 2.67
101 102 6.877611 ATGTGACGGTAAAAACTGAAGATT 57.122 33.333 0.00 0.00 0.00 2.40
102 103 6.877611 AATGTGACGGTAAAAACTGAAGAT 57.122 33.333 0.00 0.00 0.00 2.40
103 104 6.687081 AAATGTGACGGTAAAAACTGAAGA 57.313 33.333 0.00 0.00 0.00 2.87
104 105 8.901748 CATAAAATGTGACGGTAAAAACTGAAG 58.098 33.333 0.00 0.00 0.00 3.02
105 106 8.407064 ACATAAAATGTGACGGTAAAAACTGAA 58.593 29.630 0.00 0.00 43.01 3.02
106 107 7.932335 ACATAAAATGTGACGGTAAAAACTGA 58.068 30.769 0.00 0.00 43.01 3.41
156 157 9.575868 TGGGTTTAACTCAAAGATAACATAACA 57.424 29.630 0.00 0.00 0.00 2.41
158 159 9.238368 CCTGGGTTTAACTCAAAGATAACATAA 57.762 33.333 0.00 0.00 0.00 1.90
159 160 7.338449 GCCTGGGTTTAACTCAAAGATAACATA 59.662 37.037 0.00 0.00 0.00 2.29
160 161 6.152831 GCCTGGGTTTAACTCAAAGATAACAT 59.847 38.462 0.00 0.00 0.00 2.71
161 162 5.475564 GCCTGGGTTTAACTCAAAGATAACA 59.524 40.000 0.00 0.00 0.00 2.41
162 163 5.475564 TGCCTGGGTTTAACTCAAAGATAAC 59.524 40.000 0.00 0.00 0.00 1.89
163 164 5.636123 TGCCTGGGTTTAACTCAAAGATAA 58.364 37.500 0.00 0.00 0.00 1.75
164 165 5.249780 TGCCTGGGTTTAACTCAAAGATA 57.750 39.130 0.00 0.00 0.00 1.98
165 166 4.112634 TGCCTGGGTTTAACTCAAAGAT 57.887 40.909 0.00 0.00 0.00 2.40
166 167 3.586470 TGCCTGGGTTTAACTCAAAGA 57.414 42.857 0.00 0.00 0.00 2.52
167 168 3.056607 CCATGCCTGGGTTTAACTCAAAG 60.057 47.826 0.00 0.00 39.04 2.77
168 169 2.896685 CCATGCCTGGGTTTAACTCAAA 59.103 45.455 0.00 0.00 39.04 2.69
169 170 2.109128 TCCATGCCTGGGTTTAACTCAA 59.891 45.455 8.28 0.00 43.34 3.02
170 171 1.707989 TCCATGCCTGGGTTTAACTCA 59.292 47.619 8.28 0.00 43.34 3.41
171 172 2.092323 GTCCATGCCTGGGTTTAACTC 58.908 52.381 8.28 0.00 43.34 3.01
172 173 1.427368 TGTCCATGCCTGGGTTTAACT 59.573 47.619 8.28 0.00 43.34 2.24
173 174 1.818674 CTGTCCATGCCTGGGTTTAAC 59.181 52.381 8.28 0.00 43.34 2.01
174 175 1.890573 GCTGTCCATGCCTGGGTTTAA 60.891 52.381 8.28 0.00 43.34 1.52
175 176 0.323360 GCTGTCCATGCCTGGGTTTA 60.323 55.000 8.28 0.00 43.34 2.01
176 177 1.607467 GCTGTCCATGCCTGGGTTT 60.607 57.895 8.28 0.00 43.34 3.27
177 178 2.036256 GCTGTCCATGCCTGGGTT 59.964 61.111 8.28 0.00 43.34 4.11
178 179 4.052518 GGCTGTCCATGCCTGGGT 62.053 66.667 8.28 0.00 46.38 4.51
199 200 2.742372 CTGAACGTCAAGCCCGGG 60.742 66.667 19.09 19.09 0.00 5.73
200 201 2.742372 CCTGAACGTCAAGCCCGG 60.742 66.667 0.00 0.00 0.00 5.73
201 202 3.423154 GCCTGAACGTCAAGCCCG 61.423 66.667 0.00 0.00 27.82 6.13
202 203 2.032681 AGCCTGAACGTCAAGCCC 59.967 61.111 0.00 0.00 34.47 5.19
203 204 2.328099 CCAGCCTGAACGTCAAGCC 61.328 63.158 0.00 0.00 34.47 4.35
204 205 2.328099 CCCAGCCTGAACGTCAAGC 61.328 63.158 0.00 0.00 34.16 4.01
205 206 2.328099 GCCCAGCCTGAACGTCAAG 61.328 63.158 0.00 0.00 0.00 3.02
206 207 2.281484 GCCCAGCCTGAACGTCAA 60.281 61.111 0.00 0.00 0.00 3.18
207 208 3.240134 GAGCCCAGCCTGAACGTCA 62.240 63.158 0.00 0.00 0.00 4.35
208 209 2.435059 GAGCCCAGCCTGAACGTC 60.435 66.667 0.00 0.00 0.00 4.34
209 210 3.241530 TGAGCCCAGCCTGAACGT 61.242 61.111 0.00 0.00 0.00 3.99
210 211 2.435586 CTGAGCCCAGCCTGAACG 60.436 66.667 0.00 0.00 33.07 3.95
211 212 2.045536 CCTGAGCCCAGCCTGAAC 60.046 66.667 0.00 0.00 39.07 3.18
212 213 4.039092 GCCTGAGCCCAGCCTGAA 62.039 66.667 0.00 0.00 39.07 3.02
222 223 0.600057 CTGGAAAACAAGGCCTGAGC 59.400 55.000 5.69 0.00 38.76 4.26
223 224 0.600057 GCTGGAAAACAAGGCCTGAG 59.400 55.000 5.69 4.64 0.00 3.35
224 225 0.827507 GGCTGGAAAACAAGGCCTGA 60.828 55.000 5.69 0.00 37.42 3.86
225 226 0.829182 AGGCTGGAAAACAAGGCCTG 60.829 55.000 5.69 2.82 45.91 4.85
226 227 1.543690 AGGCTGGAAAACAAGGCCT 59.456 52.632 0.00 0.00 43.70 5.19
227 228 1.667722 CAGGCTGGAAAACAAGGCC 59.332 57.895 6.61 0.00 39.93 5.19
228 229 0.827507 TCCAGGCTGGAAAACAAGGC 60.828 55.000 33.38 0.00 45.00 4.35
229 230 3.437642 TCCAGGCTGGAAAACAAGG 57.562 52.632 33.38 4.40 45.00 3.61
237 238 1.757118 CGAACTATCTTCCAGGCTGGA 59.243 52.381 32.01 32.01 46.61 3.86
238 239 1.202580 CCGAACTATCTTCCAGGCTGG 60.203 57.143 28.01 28.01 39.43 4.85
239 240 1.202580 CCCGAACTATCTTCCAGGCTG 60.203 57.143 7.75 7.75 0.00 4.85
240 241 1.123928 CCCGAACTATCTTCCAGGCT 58.876 55.000 0.00 0.00 0.00 4.58
241 242 0.533085 GCCCGAACTATCTTCCAGGC 60.533 60.000 0.00 0.00 0.00 4.85
242 243 1.123928 AGCCCGAACTATCTTCCAGG 58.876 55.000 0.00 0.00 0.00 4.45
243 244 1.202580 CCAGCCCGAACTATCTTCCAG 60.203 57.143 0.00 0.00 0.00 3.86
244 245 0.830648 CCAGCCCGAACTATCTTCCA 59.169 55.000 0.00 0.00 0.00 3.53
245 246 0.106894 CCCAGCCCGAACTATCTTCC 59.893 60.000 0.00 0.00 0.00 3.46
246 247 0.533085 GCCCAGCCCGAACTATCTTC 60.533 60.000 0.00 0.00 0.00 2.87
247 248 0.983378 AGCCCAGCCCGAACTATCTT 60.983 55.000 0.00 0.00 0.00 2.40
248 249 1.383248 AGCCCAGCCCGAACTATCT 60.383 57.895 0.00 0.00 0.00 1.98
249 250 1.069935 GAGCCCAGCCCGAACTATC 59.930 63.158 0.00 0.00 0.00 2.08
250 251 2.797278 CGAGCCCAGCCCGAACTAT 61.797 63.158 0.00 0.00 0.00 2.12
251 252 3.458163 CGAGCCCAGCCCGAACTA 61.458 66.667 0.00 0.00 0.00 2.24
259 260 4.722700 TTGAAGCCCGAGCCCAGC 62.723 66.667 0.00 0.00 41.25 4.85
260 261 2.437359 CTTGAAGCCCGAGCCCAG 60.437 66.667 0.00 0.00 41.25 4.45
261 262 2.351924 AAACTTGAAGCCCGAGCCCA 62.352 55.000 0.00 0.00 41.25 5.36
262 263 1.179174 AAAACTTGAAGCCCGAGCCC 61.179 55.000 0.00 0.00 41.25 5.19
263 264 0.673985 AAAAACTTGAAGCCCGAGCC 59.326 50.000 0.00 0.00 41.25 4.70
279 280 5.810074 GCAAGCCTAGTCTGAAAAACAAAAA 59.190 36.000 0.00 0.00 0.00 1.94
280 281 5.105554 TGCAAGCCTAGTCTGAAAAACAAAA 60.106 36.000 0.00 0.00 0.00 2.44
281 282 4.400884 TGCAAGCCTAGTCTGAAAAACAAA 59.599 37.500 0.00 0.00 0.00 2.83
282 283 3.951037 TGCAAGCCTAGTCTGAAAAACAA 59.049 39.130 0.00 0.00 0.00 2.83
283 284 3.315191 GTGCAAGCCTAGTCTGAAAAACA 59.685 43.478 0.00 0.00 0.00 2.83
284 285 3.607078 CGTGCAAGCCTAGTCTGAAAAAC 60.607 47.826 0.00 0.00 0.00 2.43
285 286 2.548057 CGTGCAAGCCTAGTCTGAAAAA 59.452 45.455 0.00 0.00 0.00 1.94
286 287 2.143122 CGTGCAAGCCTAGTCTGAAAA 58.857 47.619 0.00 0.00 0.00 2.29
287 288 1.070134 ACGTGCAAGCCTAGTCTGAAA 59.930 47.619 0.00 0.00 0.00 2.69
288 289 0.679505 ACGTGCAAGCCTAGTCTGAA 59.320 50.000 0.00 0.00 0.00 3.02
289 290 0.038251 CACGTGCAAGCCTAGTCTGA 60.038 55.000 0.82 0.00 0.00 3.27
290 291 0.319900 ACACGTGCAAGCCTAGTCTG 60.320 55.000 17.22 0.00 0.00 3.51
291 292 0.319900 CACACGTGCAAGCCTAGTCT 60.320 55.000 17.22 0.00 0.00 3.24
292 293 0.600255 ACACACGTGCAAGCCTAGTC 60.600 55.000 17.22 0.00 0.00 2.59
293 294 0.677288 TACACACGTGCAAGCCTAGT 59.323 50.000 17.22 4.30 0.00 2.57
294 295 1.068474 GTACACACGTGCAAGCCTAG 58.932 55.000 17.22 0.00 0.00 3.02
295 296 0.389757 TGTACACACGTGCAAGCCTA 59.610 50.000 17.22 0.00 34.53 3.93
296 297 1.145156 TGTACACACGTGCAAGCCT 59.855 52.632 17.22 0.00 34.53 4.58
297 298 1.278637 GTGTACACACGTGCAAGCC 59.721 57.895 21.14 0.41 39.61 4.35
298 299 4.893241 GTGTACACACGTGCAAGC 57.107 55.556 21.14 4.62 39.61 4.01
318 319 1.756538 CCCGGCCAGAATGCTATTTTT 59.243 47.619 2.24 0.00 31.97 1.94
319 320 1.402787 CCCGGCCAGAATGCTATTTT 58.597 50.000 2.24 0.00 31.97 1.82
320 321 1.109323 GCCCGGCCAGAATGCTATTT 61.109 55.000 2.24 0.00 31.97 1.40
321 322 1.529244 GCCCGGCCAGAATGCTATT 60.529 57.895 2.24 0.00 31.97 1.73
322 323 1.999634 AAGCCCGGCCAGAATGCTAT 62.000 55.000 5.55 0.00 31.97 2.97
323 324 2.210144 AAAGCCCGGCCAGAATGCTA 62.210 55.000 5.55 0.00 31.97 3.49
324 325 3.590466 AAAGCCCGGCCAGAATGCT 62.590 57.895 5.55 0.00 31.97 3.79
325 326 2.649129 AAAAGCCCGGCCAGAATGC 61.649 57.895 5.55 0.00 31.97 3.56
326 327 1.216178 CAAAAGCCCGGCCAGAATG 59.784 57.895 5.55 0.00 0.00 2.67
327 328 1.984026 CCAAAAGCCCGGCCAGAAT 60.984 57.895 5.55 0.00 0.00 2.40
328 329 2.600173 CCAAAAGCCCGGCCAGAA 60.600 61.111 5.55 0.00 0.00 3.02
329 330 4.676951 CCCAAAAGCCCGGCCAGA 62.677 66.667 5.55 0.00 0.00 3.86
333 334 2.225791 CTAAAGCCCAAAAGCCCGGC 62.226 60.000 0.00 0.00 43.35 6.13
334 335 1.604147 CCTAAAGCCCAAAAGCCCGG 61.604 60.000 0.00 0.00 0.00 5.73
335 336 1.890174 CCTAAAGCCCAAAAGCCCG 59.110 57.895 0.00 0.00 0.00 6.13
336 337 0.904865 AGCCTAAAGCCCAAAAGCCC 60.905 55.000 0.00 0.00 45.47 5.19
337 338 0.976641 AAGCCTAAAGCCCAAAAGCC 59.023 50.000 0.00 0.00 45.47 4.35
338 339 1.618343 TCAAGCCTAAAGCCCAAAAGC 59.382 47.619 0.00 0.00 45.47 3.51
339 340 4.541973 AATCAAGCCTAAAGCCCAAAAG 57.458 40.909 0.00 0.00 45.47 2.27
340 341 4.560513 CGAAATCAAGCCTAAAGCCCAAAA 60.561 41.667 0.00 0.00 45.47 2.44
341 342 3.056891 CGAAATCAAGCCTAAAGCCCAAA 60.057 43.478 0.00 0.00 45.47 3.28
342 343 2.491693 CGAAATCAAGCCTAAAGCCCAA 59.508 45.455 0.00 0.00 45.47 4.12
343 344 2.091541 CGAAATCAAGCCTAAAGCCCA 58.908 47.619 0.00 0.00 45.47 5.36
344 345 1.405463 CCGAAATCAAGCCTAAAGCCC 59.595 52.381 0.00 0.00 45.47 5.19
345 346 1.405463 CCCGAAATCAAGCCTAAAGCC 59.595 52.381 0.00 0.00 45.47 4.35
346 347 2.092323 ACCCGAAATCAAGCCTAAAGC 58.908 47.619 0.00 0.00 44.25 3.51
347 348 3.119495 CCAACCCGAAATCAAGCCTAAAG 60.119 47.826 0.00 0.00 0.00 1.85
348 349 2.823154 CCAACCCGAAATCAAGCCTAAA 59.177 45.455 0.00 0.00 0.00 1.85
349 350 2.442413 CCAACCCGAAATCAAGCCTAA 58.558 47.619 0.00 0.00 0.00 2.69
350 351 1.340600 CCCAACCCGAAATCAAGCCTA 60.341 52.381 0.00 0.00 0.00 3.93
351 352 0.611896 CCCAACCCGAAATCAAGCCT 60.612 55.000 0.00 0.00 0.00 4.58
352 353 1.890174 CCCAACCCGAAATCAAGCC 59.110 57.895 0.00 0.00 0.00 4.35
353 354 1.215382 GCCCAACCCGAAATCAAGC 59.785 57.895 0.00 0.00 0.00 4.01
354 355 0.811281 GAGCCCAACCCGAAATCAAG 59.189 55.000 0.00 0.00 0.00 3.02
355 356 0.958382 CGAGCCCAACCCGAAATCAA 60.958 55.000 0.00 0.00 0.00 2.57
356 357 1.376683 CGAGCCCAACCCGAAATCA 60.377 57.895 0.00 0.00 0.00 2.57
357 358 2.112815 CCGAGCCCAACCCGAAATC 61.113 63.158 0.00 0.00 0.00 2.17
358 359 2.045340 CCGAGCCCAACCCGAAAT 60.045 61.111 0.00 0.00 0.00 2.17
359 360 4.338710 CCCGAGCCCAACCCGAAA 62.339 66.667 0.00 0.00 0.00 3.46
364 365 4.424711 TCATGCCCGAGCCCAACC 62.425 66.667 0.00 0.00 38.69 3.77
365 366 3.134127 GTCATGCCCGAGCCCAAC 61.134 66.667 0.00 0.00 38.69 3.77
366 367 4.776322 CGTCATGCCCGAGCCCAA 62.776 66.667 0.00 0.00 38.69 4.12
374 375 0.392998 ATCTGTTGGTCGTCATGCCC 60.393 55.000 0.00 0.00 0.00 5.36
400 401 1.687123 TCCTCCTATTTAGCGACCTGC 59.313 52.381 0.00 0.00 46.98 4.85
448 449 5.634020 ACTTACAGACTGAAAATAGACACGC 59.366 40.000 10.08 0.00 0.00 5.34
461 462 8.099364 ACATTTCCACATTAACTTACAGACTG 57.901 34.615 0.00 0.00 0.00 3.51
693 805 4.647853 AGTAATGCGTATAAGGACACTCCA 59.352 41.667 0.00 0.00 39.61 3.86
694 806 5.197682 AGTAATGCGTATAAGGACACTCC 57.802 43.478 0.00 0.00 36.58 3.85
699 811 3.497262 GCCCAAGTAATGCGTATAAGGAC 59.503 47.826 0.00 0.00 0.00 3.85
798 911 2.963782 AGACTGTTTTCACGTAGGAGGT 59.036 45.455 0.00 0.00 0.00 3.85
816 931 5.608449 AGACACAAACCTACCTGTAAAGAC 58.392 41.667 0.00 0.00 0.00 3.01
841 956 4.256920 GCAGAGCCATACAAAGAAAGAGA 58.743 43.478 0.00 0.00 0.00 3.10
842 957 4.612932 GCAGAGCCATACAAAGAAAGAG 57.387 45.455 0.00 0.00 0.00 2.85
1039 1174 2.678336 CTGCCCCAAAGTCGAAGTAATC 59.322 50.000 0.00 0.00 0.00 1.75
1273 1408 3.474823 CGAACACGCTAGCAATTCG 57.525 52.632 22.66 22.66 36.56 3.34
1463 1598 1.218316 CAGAAGTGGCGGTAGTCCC 59.782 63.158 0.00 0.00 0.00 4.46
1506 1641 7.563888 ACAGTGGTAGTAAAAAGTTTTCTCC 57.436 36.000 0.32 1.70 0.00 3.71
1538 1680 7.074507 ACGATTAACACAAGTTACACAACAA 57.925 32.000 0.00 0.00 39.80 2.83
1606 1750 0.602638 CAGCTTGTCAACCACCGCTA 60.603 55.000 0.00 0.00 31.49 4.26
1615 1766 1.013596 CAACACCGTCAGCTTGTCAA 58.986 50.000 0.00 0.00 0.00 3.18
1672 1838 2.167861 GTCTCCACGATCTTGCGCC 61.168 63.158 4.18 0.00 33.86 6.53
1716 1882 5.336213 CCAGTTGTACTACGTACCAGTTGAT 60.336 44.000 1.74 0.00 38.14 2.57
1772 1940 1.663695 CTACATAAGGGTGTTGCCGG 58.336 55.000 0.00 0.00 38.44 6.13
1773 1941 1.014352 GCTACATAAGGGTGTTGCCG 58.986 55.000 2.77 0.00 42.41 5.69
1895 2063 1.804151 GATTGCACGTTGTGGCTTCTA 59.196 47.619 0.00 0.00 33.64 2.10
1898 2066 1.032014 AAGATTGCACGTTGTGGCTT 58.968 45.000 0.00 0.00 33.64 4.35
2004 2179 3.329889 TGAATCGCCAGGCCCAGT 61.330 61.111 5.63 0.00 0.00 4.00
2018 2193 2.091102 GAACCCCGAGTCCGTGTGAA 62.091 60.000 0.00 0.00 0.00 3.18
2019 2194 2.522436 AACCCCGAGTCCGTGTGA 60.522 61.111 0.00 0.00 0.00 3.58
2047 2222 0.445436 GAAACGTGGCTCTGCATCAG 59.555 55.000 0.00 0.00 0.00 2.90
2071 2246 3.730761 GTGCCGGAACAGCTGCAG 61.731 66.667 15.27 10.11 33.80 4.41
2087 2262 3.314331 CCCACCTGTCTGGCTCGT 61.314 66.667 0.00 0.00 40.22 4.18
2090 2265 2.833913 CCAACCCACCTGTCTGGCT 61.834 63.158 0.00 0.00 40.22 4.75
2258 2747 3.391665 CTGAGGGGCGCTACCTTGG 62.392 68.421 21.88 14.74 38.79 3.61
2271 2760 4.101448 CCCACGGCTTCCCTGAGG 62.101 72.222 0.00 0.00 0.00 3.86
2475 2964 2.019249 TGTATCGGTCGAATCGGTCTT 58.981 47.619 1.76 0.00 0.00 3.01
2484 2973 6.729391 TTCATGAATTTTTGTATCGGTCGA 57.271 33.333 3.38 0.00 0.00 4.20
2570 3062 7.786943 TCCACAGATGTCTAAAGGATCTATCTT 59.213 37.037 0.00 0.00 0.00 2.40
2580 3072 5.152623 TCACCTTCCACAGATGTCTAAAG 57.847 43.478 0.00 0.00 0.00 1.85
2608 3100 3.245519 GTCCAGATTTCGATCTTAACGGC 59.754 47.826 0.00 0.00 0.00 5.68
2666 3158 7.891183 TTTTGAAAAAGGAAATCAACACGAA 57.109 28.000 0.00 0.00 33.13 3.85
2685 3177 7.094377 GGAATTTATCACAGCCAGTACTTTTGA 60.094 37.037 0.00 0.00 0.00 2.69
2692 3184 5.128171 ACGTAGGAATTTATCACAGCCAGTA 59.872 40.000 0.00 0.00 0.00 2.74
2699 3191 5.182487 ACATGCACGTAGGAATTTATCACA 58.818 37.500 0.00 0.00 0.00 3.58
2701 3193 5.423886 TGACATGCACGTAGGAATTTATCA 58.576 37.500 0.00 0.00 0.00 2.15
2716 3208 0.037790 TCCGACGAACATGACATGCA 60.038 50.000 15.49 0.00 0.00 3.96
2759 3251 3.084039 TCCATTCTGAGATTGTTGGTGC 58.916 45.455 3.95 0.00 0.00 5.01
2792 3284 4.621747 CGCTGTATTTTCTTCTCCTGACCT 60.622 45.833 0.00 0.00 0.00 3.85
2814 3306 2.507339 ACTTGCAAACCATGAAACCG 57.493 45.000 0.00 0.00 0.00 4.44
2822 3314 4.980573 ACCAAGAGTATACTTGCAAACCA 58.019 39.130 6.88 0.00 43.83 3.67
2913 3405 7.931015 TCAGTTATTCAATGGACTATACCCT 57.069 36.000 0.00 0.00 0.00 4.34
3076 3568 5.716228 ACTATCATTGCCTTCCAACAAATGA 59.284 36.000 0.00 0.00 35.99 2.57
3092 3584 4.295141 TGGTTTCGGTCCAACTATCATT 57.705 40.909 0.00 0.00 31.50 2.57
3137 3629 3.074412 AGTTTTGATACTGCTTGGGTCG 58.926 45.455 0.00 0.00 0.00 4.79
3280 3772 6.097915 AGTTGGACCTATACGTATTGGATG 57.902 41.667 33.41 14.31 33.61 3.51
3283 3775 5.524971 TGAGTTGGACCTATACGTATTGG 57.475 43.478 27.63 27.63 35.19 3.16
3284 3776 5.405571 GCATGAGTTGGACCTATACGTATTG 59.594 44.000 14.33 11.73 0.00 1.90
3285 3777 5.069914 TGCATGAGTTGGACCTATACGTATT 59.930 40.000 14.33 0.00 0.00 1.89
3286 3778 4.587262 TGCATGAGTTGGACCTATACGTAT 59.413 41.667 13.54 13.54 0.00 3.06
3287 3779 3.955551 TGCATGAGTTGGACCTATACGTA 59.044 43.478 0.00 0.00 0.00 3.57
3329 3824 4.226761 CCGATTGTAAAGTTCAACAAGCC 58.773 43.478 11.51 5.52 38.45 4.35
3346 3841 2.238646 TCCACATAAGCACTTCCCGATT 59.761 45.455 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.