Multiple sequence alignment - TraesCS3D01G486300

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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 TraesCS3D01G486300 chr3D 100.000 2810 0 0 1 2810 582213935 582216744 0.000000e+00 5190.0
1 TraesCS3D01G486300 chr3D 84.314 204 23 5 1370 1570 582192344 582192541 1.030000e-44 191.0
2 TraesCS3D01G486300 chr3D 74.444 180 34 10 2614 2785 581985056 581984881 1.810000e-07 67.6
3 TraesCS3D01G486300 chr3B 95.203 1084 34 10 821 1891 779283401 779282323 0.000000e+00 1698.0
4 TraesCS3D01G486300 chr3B 94.754 915 25 14 1910 2808 779282270 779281363 0.000000e+00 1402.0
5 TraesCS3D01G486300 chr3B 93.750 480 19 4 318 795 779283860 779283390 0.000000e+00 710.0
6 TraesCS3D01G486300 chr3B 74.860 179 31 10 2613 2782 779577874 779578047 5.020000e-08 69.4
7 TraesCS3D01G486300 chr5A 96.541 318 10 1 1 317 450158413 450158096 2.480000e-145 525.0
8 TraesCS3D01G486300 chr5A 95.342 322 15 0 1 322 505505856 505505535 1.930000e-141 512.0
9 TraesCS3D01G486300 chr7A 96.203 316 12 0 2 317 636887691 636888006 4.150000e-143 518.0
10 TraesCS3D01G486300 chr7A 95.268 317 14 1 1 317 257789865 257789550 4.180000e-138 501.0
11 TraesCS3D01G486300 chr7A 94.969 318 14 2 1 317 34967758 34967442 5.410000e-137 497.0
12 TraesCS3D01G486300 chr1A 95.899 317 13 0 1 317 51979967 51979651 5.370000e-142 514.0
13 TraesCS3D01G486300 chr2B 95.584 317 14 0 1 317 798804754 798805070 2.500000e-140 508.0
14 TraesCS3D01G486300 chr2A 95.584 317 14 0 1 317 413333266 413332950 2.500000e-140 508.0
15 TraesCS3D01G486300 chrUn 94.704 321 14 3 1 319 33372171 33372490 1.940000e-136 496.0


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 TraesCS3D01G486300 chr3D 582213935 582216744 2809 False 5190 5190 100.000 1 2810 1 chr3D.!!$F2 2809
1 TraesCS3D01G486300 chr3B 779281363 779283860 2497 True 1270 1698 94.569 318 2808 3 chr3B.!!$R1 2490

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
315 316 0.036294 GAGCTCCAAAACGCCCTACT 60.036 55.0 0.87 0.0 0.00 2.57 F
1115 1122 0.599466 CGCATCGTCTCCATCTGCAT 60.599 55.0 0.00 0.0 33.13 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1228 1235 0.46546 GCCTGTGTTTGTGGAGTGGA 60.465 55.0 0.00 0.00 0.0 4.02 R
2677 2744 0.45541 GCTGAATTTGTGGCCGCATA 59.545 50.0 21.95 16.66 0.0 3.14 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
46 47 8.761575 AAAGCATATGTGTGTAAATTTTCAGG 57.238 30.769 4.29 0.00 0.00 3.86
47 48 7.701539 AGCATATGTGTGTAAATTTTCAGGA 57.298 32.000 4.29 0.00 0.00 3.86
48 49 8.297470 AGCATATGTGTGTAAATTTTCAGGAT 57.703 30.769 4.29 0.00 0.00 3.24
49 50 8.192774 AGCATATGTGTGTAAATTTTCAGGATG 58.807 33.333 4.29 0.00 37.54 3.51
68 69 9.177608 TCAGGATGAAATACCTTAAAATGAGTG 57.822 33.333 0.00 0.00 45.97 3.51
69 70 7.917505 CAGGATGAAATACCTTAAAATGAGTGC 59.082 37.037 0.00 0.00 39.69 4.40
70 71 7.836183 AGGATGAAATACCTTAAAATGAGTGCT 59.164 33.333 0.00 0.00 31.95 4.40
71 72 9.120538 GGATGAAATACCTTAAAATGAGTGCTA 57.879 33.333 0.00 0.00 0.00 3.49
72 73 9.937175 GATGAAATACCTTAAAATGAGTGCTAC 57.063 33.333 0.00 0.00 0.00 3.58
73 74 8.856153 TGAAATACCTTAAAATGAGTGCTACA 57.144 30.769 0.00 0.00 0.00 2.74
74 75 8.726988 TGAAATACCTTAAAATGAGTGCTACAC 58.273 33.333 0.00 0.00 34.10 2.90
75 76 8.630054 AAATACCTTAAAATGAGTGCTACACA 57.370 30.769 0.00 0.00 36.74 3.72
76 77 8.630054 AATACCTTAAAATGAGTGCTACACAA 57.370 30.769 0.00 0.00 36.74 3.33
77 78 6.952773 ACCTTAAAATGAGTGCTACACAAA 57.047 33.333 0.00 0.00 36.74 2.83
78 79 7.341445 ACCTTAAAATGAGTGCTACACAAAA 57.659 32.000 0.00 0.00 36.74 2.44
79 80 7.777095 ACCTTAAAATGAGTGCTACACAAAAA 58.223 30.769 0.00 0.00 36.74 1.94
80 81 7.920682 ACCTTAAAATGAGTGCTACACAAAAAG 59.079 33.333 0.00 0.00 36.74 2.27
81 82 8.134895 CCTTAAAATGAGTGCTACACAAAAAGA 58.865 33.333 0.00 0.00 36.74 2.52
82 83 9.515020 CTTAAAATGAGTGCTACACAAAAAGAA 57.485 29.630 0.00 0.00 36.74 2.52
83 84 7.755582 AAAATGAGTGCTACACAAAAAGAAC 57.244 32.000 0.00 0.00 36.74 3.01
84 85 6.449635 AATGAGTGCTACACAAAAAGAACA 57.550 33.333 0.00 0.00 36.74 3.18
85 86 5.888691 TGAGTGCTACACAAAAAGAACAA 57.111 34.783 0.00 0.00 36.74 2.83
86 87 6.260870 TGAGTGCTACACAAAAAGAACAAA 57.739 33.333 0.00 0.00 36.74 2.83
87 88 6.862209 TGAGTGCTACACAAAAAGAACAAAT 58.138 32.000 0.00 0.00 36.74 2.32
88 89 6.972328 TGAGTGCTACACAAAAAGAACAAATC 59.028 34.615 0.00 0.00 36.74 2.17
89 90 7.100458 AGTGCTACACAAAAAGAACAAATCT 57.900 32.000 0.00 0.00 37.04 2.40
90 91 6.974622 AGTGCTACACAAAAAGAACAAATCTG 59.025 34.615 0.00 0.00 36.13 2.90
91 92 6.972328 GTGCTACACAAAAAGAACAAATCTGA 59.028 34.615 0.00 0.00 34.71 3.27
92 93 7.166473 GTGCTACACAAAAAGAACAAATCTGAG 59.834 37.037 0.00 0.00 34.71 3.35
93 94 6.638468 GCTACACAAAAAGAACAAATCTGAGG 59.362 38.462 0.00 0.00 38.79 3.86
94 95 5.351458 ACACAAAAAGAACAAATCTGAGGC 58.649 37.500 0.00 0.00 38.79 4.70
95 96 5.127682 ACACAAAAAGAACAAATCTGAGGCT 59.872 36.000 0.00 0.00 38.79 4.58
96 97 6.044682 CACAAAAAGAACAAATCTGAGGCTT 58.955 36.000 0.00 0.00 38.79 4.35
97 98 6.536224 CACAAAAAGAACAAATCTGAGGCTTT 59.464 34.615 0.00 0.00 38.79 3.51
98 99 7.064966 CACAAAAAGAACAAATCTGAGGCTTTT 59.935 33.333 0.00 0.00 38.79 2.27
99 100 7.607607 ACAAAAAGAACAAATCTGAGGCTTTTT 59.392 29.630 0.00 0.00 38.97 1.94
100 101 9.097257 CAAAAAGAACAAATCTGAGGCTTTTTA 57.903 29.630 0.00 0.00 37.87 1.52
101 102 8.877808 AAAAGAACAAATCTGAGGCTTTTTAG 57.122 30.769 0.00 0.00 38.79 1.85
102 103 7.588497 AAGAACAAATCTGAGGCTTTTTAGT 57.412 32.000 0.00 0.00 38.79 2.24
103 104 8.691661 AAGAACAAATCTGAGGCTTTTTAGTA 57.308 30.769 0.00 0.00 38.79 1.82
104 105 8.329203 AGAACAAATCTGAGGCTTTTTAGTAG 57.671 34.615 0.00 0.00 36.88 2.57
105 106 8.157476 AGAACAAATCTGAGGCTTTTTAGTAGA 58.843 33.333 0.00 0.00 36.88 2.59
106 107 8.870075 AACAAATCTGAGGCTTTTTAGTAGAT 57.130 30.769 0.00 0.00 0.00 1.98
107 108 8.273780 ACAAATCTGAGGCTTTTTAGTAGATG 57.726 34.615 0.00 0.00 0.00 2.90
108 109 6.934048 AATCTGAGGCTTTTTAGTAGATGC 57.066 37.500 0.00 0.00 0.00 3.91
109 110 4.433615 TCTGAGGCTTTTTAGTAGATGCG 58.566 43.478 0.00 0.00 0.00 4.73
110 111 2.936498 TGAGGCTTTTTAGTAGATGCGC 59.064 45.455 0.00 0.00 0.00 6.09
111 112 3.198872 GAGGCTTTTTAGTAGATGCGCT 58.801 45.455 9.73 0.00 0.00 5.92
112 113 4.142026 TGAGGCTTTTTAGTAGATGCGCTA 60.142 41.667 9.73 0.00 0.00 4.26
113 114 4.962155 AGGCTTTTTAGTAGATGCGCTAT 58.038 39.130 9.73 0.00 0.00 2.97
114 115 5.368989 AGGCTTTTTAGTAGATGCGCTATT 58.631 37.500 9.73 0.00 0.00 1.73
115 116 5.467063 AGGCTTTTTAGTAGATGCGCTATTC 59.533 40.000 9.73 2.95 0.00 1.75
116 117 5.236478 GGCTTTTTAGTAGATGCGCTATTCA 59.764 40.000 9.73 0.00 0.00 2.57
117 118 6.073003 GGCTTTTTAGTAGATGCGCTATTCAT 60.073 38.462 9.73 0.00 0.00 2.57
118 119 7.012358 GCTTTTTAGTAGATGCGCTATTCATC 58.988 38.462 9.73 2.22 40.34 2.92
119 120 7.421530 TTTTTAGTAGATGCGCTATTCATCC 57.578 36.000 9.73 0.00 40.79 3.51
120 121 5.984695 TTAGTAGATGCGCTATTCATCCT 57.015 39.130 9.73 0.00 40.79 3.24
121 122 4.448537 AGTAGATGCGCTATTCATCCTC 57.551 45.455 9.73 0.00 40.79 3.71
122 123 3.829026 AGTAGATGCGCTATTCATCCTCA 59.171 43.478 9.73 0.00 40.79 3.86
123 124 3.758755 AGATGCGCTATTCATCCTCAA 57.241 42.857 9.73 0.00 40.79 3.02
124 125 4.077300 AGATGCGCTATTCATCCTCAAA 57.923 40.909 9.73 0.00 40.79 2.69
125 126 4.063689 AGATGCGCTATTCATCCTCAAAG 58.936 43.478 9.73 0.00 40.79 2.77
126 127 3.266510 TGCGCTATTCATCCTCAAAGT 57.733 42.857 9.73 0.00 0.00 2.66
127 128 3.198068 TGCGCTATTCATCCTCAAAGTC 58.802 45.455 9.73 0.00 0.00 3.01
128 129 2.545946 GCGCTATTCATCCTCAAAGTCC 59.454 50.000 0.00 0.00 0.00 3.85
129 130 3.797039 CGCTATTCATCCTCAAAGTCCA 58.203 45.455 0.00 0.00 0.00 4.02
130 131 4.384056 CGCTATTCATCCTCAAAGTCCAT 58.616 43.478 0.00 0.00 0.00 3.41
131 132 4.212847 CGCTATTCATCCTCAAAGTCCATG 59.787 45.833 0.00 0.00 0.00 3.66
132 133 5.371526 GCTATTCATCCTCAAAGTCCATGA 58.628 41.667 0.00 0.00 0.00 3.07
133 134 5.824624 GCTATTCATCCTCAAAGTCCATGAA 59.175 40.000 0.00 0.00 37.75 2.57
134 135 6.489361 GCTATTCATCCTCAAAGTCCATGAAT 59.511 38.462 9.68 9.68 43.42 2.57
135 136 7.014038 GCTATTCATCCTCAAAGTCCATGAATT 59.986 37.037 9.96 0.00 39.92 2.17
136 137 7.729124 ATTCATCCTCAAAGTCCATGAATTT 57.271 32.000 0.00 0.00 39.92 1.82
137 138 6.519679 TCATCCTCAAAGTCCATGAATTTG 57.480 37.500 9.93 9.93 45.19 2.32
138 139 6.012113 TCATCCTCAAAGTCCATGAATTTGT 58.988 36.000 14.32 0.00 44.49 2.83
139 140 5.964958 TCCTCAAAGTCCATGAATTTGTC 57.035 39.130 14.32 0.00 44.49 3.18
140 141 5.634118 TCCTCAAAGTCCATGAATTTGTCT 58.366 37.500 14.32 0.00 44.49 3.41
141 142 6.070656 TCCTCAAAGTCCATGAATTTGTCTT 58.929 36.000 14.32 0.00 44.49 3.01
142 143 6.550854 TCCTCAAAGTCCATGAATTTGTCTTT 59.449 34.615 14.32 3.09 44.49 2.52
143 144 7.069826 TCCTCAAAGTCCATGAATTTGTCTTTT 59.930 33.333 14.32 0.00 44.49 2.27
144 145 7.712205 CCTCAAAGTCCATGAATTTGTCTTTTT 59.288 33.333 14.32 0.00 44.49 1.94
164 165 3.763097 TTGCACAGATCGCATTTTAGG 57.237 42.857 0.00 0.00 39.58 2.69
165 166 2.016318 TGCACAGATCGCATTTTAGGG 58.984 47.619 0.00 0.00 33.55 3.53
166 167 2.017049 GCACAGATCGCATTTTAGGGT 58.983 47.619 0.00 0.00 0.00 4.34
167 168 3.202906 GCACAGATCGCATTTTAGGGTA 58.797 45.455 0.00 0.00 0.00 3.69
168 169 3.815401 GCACAGATCGCATTTTAGGGTAT 59.185 43.478 0.00 0.00 0.00 2.73
169 170 4.275936 GCACAGATCGCATTTTAGGGTATT 59.724 41.667 0.00 0.00 0.00 1.89
170 171 5.221048 GCACAGATCGCATTTTAGGGTATTT 60.221 40.000 0.00 0.00 0.00 1.40
171 172 6.680378 GCACAGATCGCATTTTAGGGTATTTT 60.680 38.462 0.00 0.00 0.00 1.82
172 173 7.468084 GCACAGATCGCATTTTAGGGTATTTTA 60.468 37.037 0.00 0.00 0.00 1.52
173 174 8.567948 CACAGATCGCATTTTAGGGTATTTTAT 58.432 33.333 0.00 0.00 0.00 1.40
174 175 8.784043 ACAGATCGCATTTTAGGGTATTTTATC 58.216 33.333 0.00 0.00 0.00 1.75
175 176 8.237267 CAGATCGCATTTTAGGGTATTTTATCC 58.763 37.037 0.00 0.00 0.00 2.59
176 177 8.164070 AGATCGCATTTTAGGGTATTTTATCCT 58.836 33.333 0.00 0.00 43.23 3.24
177 178 7.739498 TCGCATTTTAGGGTATTTTATCCTC 57.261 36.000 0.00 0.00 38.98 3.71
178 179 7.284074 TCGCATTTTAGGGTATTTTATCCTCA 58.716 34.615 0.00 0.00 38.98 3.86
179 180 7.776030 TCGCATTTTAGGGTATTTTATCCTCAA 59.224 33.333 0.00 0.00 38.98 3.02
180 181 8.410141 CGCATTTTAGGGTATTTTATCCTCAAA 58.590 33.333 0.00 0.00 38.98 2.69
258 259 6.959671 TTTTTGAAACTGAAAAGTGCGAAT 57.040 29.167 0.00 0.00 0.00 3.34
259 260 6.959671 TTTTGAAACTGAAAAGTGCGAATT 57.040 29.167 0.00 0.00 0.00 2.17
260 261 6.959671 TTTGAAACTGAAAAGTGCGAATTT 57.040 29.167 0.00 0.00 0.00 1.82
261 262 6.959671 TTGAAACTGAAAAGTGCGAATTTT 57.040 29.167 0.00 0.00 32.68 1.82
262 263 6.329838 TGAAACTGAAAAGTGCGAATTTTG 57.670 33.333 0.00 0.00 30.22 2.44
263 264 6.096036 TGAAACTGAAAAGTGCGAATTTTGA 58.904 32.000 0.00 0.00 30.22 2.69
264 265 6.587990 TGAAACTGAAAAGTGCGAATTTTGAA 59.412 30.769 0.00 0.00 30.22 2.69
265 266 7.277539 TGAAACTGAAAAGTGCGAATTTTGAAT 59.722 29.630 0.00 0.00 30.22 2.57
266 267 7.538303 AACTGAAAAGTGCGAATTTTGAATT 57.462 28.000 0.00 0.00 30.22 2.17
267 268 7.538303 ACTGAAAAGTGCGAATTTTGAATTT 57.462 28.000 0.00 0.00 30.22 1.82
268 269 7.973601 ACTGAAAAGTGCGAATTTTGAATTTT 58.026 26.923 0.00 0.00 30.22 1.82
269 270 8.450180 ACTGAAAAGTGCGAATTTTGAATTTTT 58.550 25.926 0.00 0.00 30.22 1.94
270 271 8.819152 TGAAAAGTGCGAATTTTGAATTTTTC 57.181 26.923 14.33 14.33 34.38 2.29
271 272 8.446273 TGAAAAGTGCGAATTTTGAATTTTTCA 58.554 25.926 17.79 17.79 38.76 2.69
290 291 2.900547 AAAAATCCGGCCTCCATGG 58.099 52.632 4.97 4.97 39.35 3.66
291 292 0.334676 AAAAATCCGGCCTCCATGGA 59.665 50.000 15.27 15.27 38.35 3.41
292 293 0.106519 AAAATCCGGCCTCCATGGAG 60.107 55.000 31.69 31.69 41.63 3.86
300 301 3.160047 CTCCATGGAGGCCGAGCT 61.160 66.667 31.14 0.00 38.51 4.09
301 302 3.157252 TCCATGGAGGCCGAGCTC 61.157 66.667 11.44 2.73 37.29 4.09
302 303 4.247380 CCATGGAGGCCGAGCTCC 62.247 72.222 5.56 0.00 40.05 4.70
305 306 2.927856 TGGAGGCCGAGCTCCAAA 60.928 61.111 8.96 0.00 45.68 3.28
306 307 2.351276 GGAGGCCGAGCTCCAAAA 59.649 61.111 8.47 0.00 39.45 2.44
307 308 2.041115 GGAGGCCGAGCTCCAAAAC 61.041 63.158 8.47 0.00 39.45 2.43
308 309 2.358737 AGGCCGAGCTCCAAAACG 60.359 61.111 8.47 0.00 0.00 3.60
309 310 4.103103 GGCCGAGCTCCAAAACGC 62.103 66.667 8.47 0.23 0.00 4.84
310 311 4.103103 GCCGAGCTCCAAAACGCC 62.103 66.667 8.47 0.00 0.00 5.68
311 312 3.431725 CCGAGCTCCAAAACGCCC 61.432 66.667 8.47 0.00 0.00 6.13
312 313 2.358737 CGAGCTCCAAAACGCCCT 60.359 61.111 8.47 0.00 0.00 5.19
313 314 1.079405 CGAGCTCCAAAACGCCCTA 60.079 57.895 8.47 0.00 0.00 3.53
314 315 1.359459 CGAGCTCCAAAACGCCCTAC 61.359 60.000 8.47 0.00 0.00 3.18
315 316 0.036294 GAGCTCCAAAACGCCCTACT 60.036 55.000 0.87 0.00 0.00 2.57
316 317 0.036294 AGCTCCAAAACGCCCTACTC 60.036 55.000 0.00 0.00 0.00 2.59
368 369 5.223382 ACGTTATTGTGTCTGTTCTCTCTG 58.777 41.667 0.00 0.00 0.00 3.35
437 438 5.874810 TGTCTATGACATGGTGAAAACTAGC 59.125 40.000 0.00 0.00 37.67 3.42
439 440 3.500448 TGACATGGTGAAAACTAGCCA 57.500 42.857 0.00 0.00 35.28 4.75
440 441 3.411446 TGACATGGTGAAAACTAGCCAG 58.589 45.455 0.00 0.00 34.18 4.85
441 442 2.162408 GACATGGTGAAAACTAGCCAGC 59.838 50.000 0.00 0.00 34.18 4.85
442 443 2.161855 CATGGTGAAAACTAGCCAGCA 58.838 47.619 8.59 8.59 41.60 4.41
443 444 2.584835 TGGTGAAAACTAGCCAGCAT 57.415 45.000 0.00 0.00 33.98 3.79
444 445 2.875296 TGGTGAAAACTAGCCAGCATT 58.125 42.857 0.00 0.00 33.98 3.56
445 446 3.230134 TGGTGAAAACTAGCCAGCATTT 58.770 40.909 0.00 0.00 33.98 2.32
446 447 3.640967 TGGTGAAAACTAGCCAGCATTTT 59.359 39.130 0.00 0.00 33.98 1.82
500 501 4.855531 ACAACGTAACCTTTTCATCTTGC 58.144 39.130 0.00 0.00 0.00 4.01
512 513 1.212688 TCATCTTGCCATACACCAGGG 59.787 52.381 0.00 0.00 0.00 4.45
592 593 4.160439 AGAATAGGATTTCAGCTGTCGTCA 59.840 41.667 14.67 0.00 0.00 4.35
664 665 2.810870 ACCACCCATTTGCCGTATTA 57.189 45.000 0.00 0.00 0.00 0.98
665 666 3.306472 ACCACCCATTTGCCGTATTAT 57.694 42.857 0.00 0.00 0.00 1.28
666 667 4.440826 ACCACCCATTTGCCGTATTATA 57.559 40.909 0.00 0.00 0.00 0.98
667 668 4.993028 ACCACCCATTTGCCGTATTATAT 58.007 39.130 0.00 0.00 0.00 0.86
668 669 5.390387 ACCACCCATTTGCCGTATTATATT 58.610 37.500 0.00 0.00 0.00 1.28
680 681 7.041721 TGCCGTATTATATTCCATCTCATGAC 58.958 38.462 0.00 0.00 0.00 3.06
689 691 2.436911 TCCATCTCATGACCATCACCAG 59.563 50.000 0.00 0.00 0.00 4.00
690 692 2.486727 CCATCTCATGACCATCACCAGG 60.487 54.545 0.00 0.00 0.00 4.45
745 747 8.461249 AAGAAAGCATGCAGTTTATAGATCAT 57.539 30.769 21.98 0.00 0.00 2.45
860 862 5.012893 CCAAGATAAGGGAATATTCTGCCC 58.987 45.833 14.95 8.82 42.37 5.36
872 875 8.924303 GGGAATATTCTGCCCTATTTTACTTTT 58.076 33.333 14.95 0.00 38.85 2.27
949 952 8.192110 TGTGTTTGTTCTCCCAAAAGTAAATAC 58.808 33.333 0.00 0.00 36.17 1.89
950 953 7.377662 GTGTTTGTTCTCCCAAAAGTAAATACG 59.622 37.037 0.00 0.00 36.17 3.06
984 987 2.719426 ACGAGACGGTGGAAAACTAG 57.281 50.000 0.00 0.00 0.00 2.57
1010 1013 6.437928 TCGCATTATTGAATATGCAAACTCC 58.562 36.000 0.00 0.00 39.80 3.85
1115 1122 0.599466 CGCATCGTCTCCATCTGCAT 60.599 55.000 0.00 0.00 33.13 3.96
1153 1160 1.078848 GCATCGTCTCTGCCTGGTT 60.079 57.895 0.00 0.00 33.44 3.67
1156 1163 2.842394 ATCGTCTCTGCCTGGTTGCG 62.842 60.000 0.00 0.00 0.00 4.85
1166 1173 4.953868 TGGTTGCGTCCACGTCCG 62.954 66.667 0.36 0.00 42.22 4.79
1215 1222 2.352225 CCGATCGAGGTCCATCTCATTC 60.352 54.545 18.66 0.00 33.59 2.67
1225 1232 3.069443 GTCCATCTCATTCTCCTCTCCAC 59.931 52.174 0.00 0.00 0.00 4.02
1228 1235 3.464720 TCTCATTCTCCTCTCCACAGT 57.535 47.619 0.00 0.00 0.00 3.55
1229 1236 3.360867 TCTCATTCTCCTCTCCACAGTC 58.639 50.000 0.00 0.00 0.00 3.51
1230 1237 2.430332 CTCATTCTCCTCTCCACAGTCC 59.570 54.545 0.00 0.00 0.00 3.85
1231 1238 2.182827 CATTCTCCTCTCCACAGTCCA 58.817 52.381 0.00 0.00 0.00 4.02
1232 1239 1.633774 TTCTCCTCTCCACAGTCCAC 58.366 55.000 0.00 0.00 0.00 4.02
1239 1246 0.758734 CTCCACAGTCCACTCCACAA 59.241 55.000 0.00 0.00 0.00 3.33
1252 1259 0.323816 TCCACAAACACAGGCCACAA 60.324 50.000 5.01 0.00 0.00 3.33
1260 1267 2.198287 ACAGGCCACAAAGCAGCTG 61.198 57.895 10.11 10.11 0.00 4.24
1261 1268 1.900016 CAGGCCACAAAGCAGCTGA 60.900 57.895 20.43 0.00 0.00 4.26
1262 1269 1.076192 AGGCCACAAAGCAGCTGAT 59.924 52.632 20.43 8.90 0.00 2.90
1264 1271 0.319405 GGCCACAAAGCAGCTGATTT 59.681 50.000 23.65 23.65 33.44 2.17
1266 1273 1.670967 GCCACAAAGCAGCTGATTTCC 60.671 52.381 26.22 11.65 30.39 3.13
1269 1276 3.572584 CACAAAGCAGCTGATTTCCTTC 58.427 45.455 26.22 1.01 30.39 3.46
1783 1798 1.424493 CTGCGTCTTCTTCGGCATCC 61.424 60.000 0.00 0.00 0.00 3.51
1891 1906 5.594725 CAGGTACTCTAGTCTTGCCATCTAA 59.405 44.000 0.00 0.00 34.60 2.10
1892 1907 6.096987 CAGGTACTCTAGTCTTGCCATCTAAA 59.903 42.308 0.00 0.00 34.60 1.85
1893 1908 6.841755 AGGTACTCTAGTCTTGCCATCTAAAT 59.158 38.462 0.00 0.00 0.00 1.40
1894 1909 8.005388 AGGTACTCTAGTCTTGCCATCTAAATA 58.995 37.037 0.00 0.00 0.00 1.40
1895 1910 8.808092 GGTACTCTAGTCTTGCCATCTAAATAT 58.192 37.037 0.00 0.00 0.00 1.28
1896 1911 9.849166 GTACTCTAGTCTTGCCATCTAAATATC 57.151 37.037 0.00 0.00 0.00 1.63
1897 1912 8.719645 ACTCTAGTCTTGCCATCTAAATATCT 57.280 34.615 0.00 0.00 0.00 1.98
1898 1913 9.815306 ACTCTAGTCTTGCCATCTAAATATCTA 57.185 33.333 0.00 0.00 0.00 1.98
1904 1919 7.609532 GTCTTGCCATCTAAATATCTATTGGCT 59.390 37.037 11.81 0.00 40.26 4.75
1906 1921 9.107177 CTTGCCATCTAAATATCTATTGGCTAG 57.893 37.037 11.81 9.73 40.26 3.42
1907 1922 8.150827 TGCCATCTAAATATCTATTGGCTAGT 57.849 34.615 11.81 0.00 40.26 2.57
1908 1923 8.043113 TGCCATCTAAATATCTATTGGCTAGTG 58.957 37.037 11.81 0.00 40.26 2.74
2058 2111 2.959707 CACCCTTCTAGCTACCTAGTGG 59.040 54.545 0.00 0.00 41.49 4.00
2080 2133 3.942115 GCTGAATTACTGGAAAGACCCTC 59.058 47.826 0.00 0.00 38.00 4.30
2117 2170 2.286294 GTGTTTCTGTGAGCTGTGACAG 59.714 50.000 8.52 8.52 40.89 3.51
2118 2171 2.168313 TGTTTCTGTGAGCTGTGACAGA 59.832 45.455 18.18 13.39 45.39 3.41
2238 2291 8.915871 TGCTGCTGAAATGTTCTAATTTATTC 57.084 30.769 0.00 0.00 29.89 1.75
2278 2331 5.114780 TGCTCAAGATAAATCTCTCACTGC 58.885 41.667 0.00 0.00 35.76 4.40
2300 2353 3.431486 CCAGAGAATGTAGAGGGAAGCAC 60.431 52.174 0.00 0.00 0.00 4.40
2312 2365 1.115467 GGAAGCACTAGCCTAGCTCA 58.885 55.000 0.00 0.00 43.56 4.26
2325 2378 4.657969 AGCCTAGCTCAATCCAAAGAGTAT 59.342 41.667 0.00 0.00 30.62 2.12
2330 2383 7.605691 CCTAGCTCAATCCAAAGAGTATTATGG 59.394 40.741 0.00 0.00 34.39 2.74
2393 2447 3.184683 CGCGTGCTTCTCTGCTCC 61.185 66.667 0.00 0.00 0.00 4.70
2395 2449 2.507992 CGTGCTTCTCTGCTCCGG 60.508 66.667 0.00 0.00 0.00 5.14
2404 2458 0.107214 CTCTGCTCCGGTCTCTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
2405 2459 0.107410 TCTGCTCCGGTCTCTCTCTC 60.107 60.000 0.00 0.00 0.00 3.20
2406 2460 0.107214 CTGCTCCGGTCTCTCTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
2407 2461 0.107410 TGCTCCGGTCTCTCTCTCTC 60.107 60.000 0.00 0.00 0.00 3.20
2408 2462 0.180406 GCTCCGGTCTCTCTCTCTCT 59.820 60.000 0.00 0.00 0.00 3.10
2409 2463 1.810412 GCTCCGGTCTCTCTCTCTCTC 60.810 61.905 0.00 0.00 0.00 3.20
2410 2464 1.762957 CTCCGGTCTCTCTCTCTCTCT 59.237 57.143 0.00 0.00 0.00 3.10
2677 2744 3.201266 TGGTTGTACCAGTCCTCACTTTT 59.799 43.478 0.00 0.00 44.79 2.27
2735 2802 5.970317 TGTCACAGTTACTTCGAGGATTA 57.030 39.130 0.00 0.00 0.00 1.75
2773 2840 9.625747 TGAATTCTATCATGTTTGCACCTAATA 57.374 29.630 7.05 0.00 0.00 0.98
2785 2852 8.052748 TGTTTGCACCTAATAATCTGGTTCTAT 58.947 33.333 0.00 0.00 30.72 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.853555 CCTGAAAATTTACACACATATGCTTTA 57.146 29.630 1.58 0.00 0.00 1.85
21 22 8.584157 TCCTGAAAATTTACACACATATGCTTT 58.416 29.630 1.58 0.00 0.00 3.51
22 23 8.121305 TCCTGAAAATTTACACACATATGCTT 57.879 30.769 1.58 0.00 0.00 3.91
23 24 7.701539 TCCTGAAAATTTACACACATATGCT 57.298 32.000 1.58 0.00 0.00 3.79
24 25 8.190122 TCATCCTGAAAATTTACACACATATGC 58.810 33.333 1.58 0.00 0.00 3.14
41 42 9.753674 ACTCATTTTAAGGTATTTCATCCTGAA 57.246 29.630 0.00 0.00 34.03 3.02
42 43 9.177608 CACTCATTTTAAGGTATTTCATCCTGA 57.822 33.333 0.00 0.00 33.97 3.86
43 44 7.917505 GCACTCATTTTAAGGTATTTCATCCTG 59.082 37.037 0.00 0.00 33.97 3.86
44 45 7.836183 AGCACTCATTTTAAGGTATTTCATCCT 59.164 33.333 0.00 0.00 35.34 3.24
45 46 8.000780 AGCACTCATTTTAAGGTATTTCATCC 57.999 34.615 0.00 0.00 0.00 3.51
46 47 9.937175 GTAGCACTCATTTTAAGGTATTTCATC 57.063 33.333 0.00 0.00 0.00 2.92
47 48 9.461312 TGTAGCACTCATTTTAAGGTATTTCAT 57.539 29.630 0.00 0.00 0.00 2.57
48 49 8.726988 GTGTAGCACTCATTTTAAGGTATTTCA 58.273 33.333 0.00 0.00 0.00 2.69
49 50 8.726988 TGTGTAGCACTCATTTTAAGGTATTTC 58.273 33.333 0.90 0.00 35.11 2.17
50 51 8.630054 TGTGTAGCACTCATTTTAAGGTATTT 57.370 30.769 0.90 0.00 35.11 1.40
51 52 8.630054 TTGTGTAGCACTCATTTTAAGGTATT 57.370 30.769 0.90 0.00 35.11 1.89
52 53 8.630054 TTTGTGTAGCACTCATTTTAAGGTAT 57.370 30.769 0.90 0.00 35.11 2.73
53 54 8.453238 TTTTGTGTAGCACTCATTTTAAGGTA 57.547 30.769 0.90 0.00 35.11 3.08
54 55 6.952773 TTTGTGTAGCACTCATTTTAAGGT 57.047 33.333 0.90 0.00 35.11 3.50
55 56 8.134895 TCTTTTTGTGTAGCACTCATTTTAAGG 58.865 33.333 0.90 0.00 35.11 2.69
56 57 9.515020 TTCTTTTTGTGTAGCACTCATTTTAAG 57.485 29.630 0.90 0.00 35.11 1.85
57 58 9.296400 GTTCTTTTTGTGTAGCACTCATTTTAA 57.704 29.630 0.90 0.00 35.11 1.52
58 59 8.462811 TGTTCTTTTTGTGTAGCACTCATTTTA 58.537 29.630 0.90 0.00 35.11 1.52
59 60 7.319646 TGTTCTTTTTGTGTAGCACTCATTTT 58.680 30.769 0.90 0.00 35.11 1.82
60 61 6.862209 TGTTCTTTTTGTGTAGCACTCATTT 58.138 32.000 0.90 0.00 35.11 2.32
61 62 6.449635 TGTTCTTTTTGTGTAGCACTCATT 57.550 33.333 0.90 0.00 35.11 2.57
62 63 6.449635 TTGTTCTTTTTGTGTAGCACTCAT 57.550 33.333 0.90 0.00 35.11 2.90
63 64 5.888691 TTGTTCTTTTTGTGTAGCACTCA 57.111 34.783 0.90 0.00 35.11 3.41
64 65 7.166473 CAGATTTGTTCTTTTTGTGTAGCACTC 59.834 37.037 0.90 0.00 31.39 3.51
65 66 6.974622 CAGATTTGTTCTTTTTGTGTAGCACT 59.025 34.615 0.90 0.00 31.39 4.40
66 67 6.972328 TCAGATTTGTTCTTTTTGTGTAGCAC 59.028 34.615 0.00 0.00 29.93 4.40
67 68 7.094508 TCAGATTTGTTCTTTTTGTGTAGCA 57.905 32.000 0.00 0.00 29.93 3.49
68 69 6.638468 CCTCAGATTTGTTCTTTTTGTGTAGC 59.362 38.462 0.00 0.00 29.93 3.58
69 70 6.638468 GCCTCAGATTTGTTCTTTTTGTGTAG 59.362 38.462 0.00 0.00 29.93 2.74
70 71 6.321181 AGCCTCAGATTTGTTCTTTTTGTGTA 59.679 34.615 0.00 0.00 29.93 2.90
71 72 5.127682 AGCCTCAGATTTGTTCTTTTTGTGT 59.872 36.000 0.00 0.00 29.93 3.72
72 73 5.594926 AGCCTCAGATTTGTTCTTTTTGTG 58.405 37.500 0.00 0.00 29.93 3.33
73 74 5.859205 AGCCTCAGATTTGTTCTTTTTGT 57.141 34.783 0.00 0.00 29.93 2.83
74 75 7.543947 AAAAGCCTCAGATTTGTTCTTTTTG 57.456 32.000 0.00 0.00 30.45 2.44
75 76 9.317936 CTAAAAAGCCTCAGATTTGTTCTTTTT 57.682 29.630 18.76 18.76 39.05 1.94
76 77 8.478066 ACTAAAAAGCCTCAGATTTGTTCTTTT 58.522 29.630 0.00 0.00 30.45 2.27
77 78 8.011844 ACTAAAAAGCCTCAGATTTGTTCTTT 57.988 30.769 0.00 0.00 30.45 2.52
78 79 7.588497 ACTAAAAAGCCTCAGATTTGTTCTT 57.412 32.000 0.00 0.00 30.45 2.52
79 80 8.157476 TCTACTAAAAAGCCTCAGATTTGTTCT 58.843 33.333 0.00 0.00 30.45 3.01
80 81 8.324163 TCTACTAAAAAGCCTCAGATTTGTTC 57.676 34.615 0.00 0.00 30.45 3.18
81 82 8.734386 CATCTACTAAAAAGCCTCAGATTTGTT 58.266 33.333 0.00 0.00 30.45 2.83
82 83 7.148171 GCATCTACTAAAAAGCCTCAGATTTGT 60.148 37.037 0.00 0.00 30.45 2.83
83 84 7.192232 GCATCTACTAAAAAGCCTCAGATTTG 58.808 38.462 0.00 0.00 30.45 2.32
84 85 6.037610 CGCATCTACTAAAAAGCCTCAGATTT 59.962 38.462 0.00 0.00 31.52 2.17
85 86 5.525378 CGCATCTACTAAAAAGCCTCAGATT 59.475 40.000 0.00 0.00 0.00 2.40
86 87 5.053145 CGCATCTACTAAAAAGCCTCAGAT 58.947 41.667 0.00 0.00 0.00 2.90
87 88 4.433615 CGCATCTACTAAAAAGCCTCAGA 58.566 43.478 0.00 0.00 0.00 3.27
88 89 3.001736 GCGCATCTACTAAAAAGCCTCAG 59.998 47.826 0.30 0.00 0.00 3.35
89 90 2.936498 GCGCATCTACTAAAAAGCCTCA 59.064 45.455 0.30 0.00 0.00 3.86
90 91 3.198872 AGCGCATCTACTAAAAAGCCTC 58.801 45.455 11.47 0.00 0.00 4.70
91 92 3.268023 AGCGCATCTACTAAAAAGCCT 57.732 42.857 11.47 0.00 0.00 4.58
92 93 5.236478 TGAATAGCGCATCTACTAAAAAGCC 59.764 40.000 11.47 0.00 0.00 4.35
93 94 6.287107 TGAATAGCGCATCTACTAAAAAGC 57.713 37.500 11.47 0.00 0.00 3.51
94 95 7.386299 AGGATGAATAGCGCATCTACTAAAAAG 59.614 37.037 11.47 0.00 41.39 2.27
95 96 7.217200 AGGATGAATAGCGCATCTACTAAAAA 58.783 34.615 11.47 0.00 41.39 1.94
96 97 6.759272 AGGATGAATAGCGCATCTACTAAAA 58.241 36.000 11.47 0.00 41.39 1.52
97 98 6.015434 TGAGGATGAATAGCGCATCTACTAAA 60.015 38.462 11.47 0.00 41.39 1.85
98 99 5.476945 TGAGGATGAATAGCGCATCTACTAA 59.523 40.000 11.47 0.00 41.39 2.24
99 100 5.010282 TGAGGATGAATAGCGCATCTACTA 58.990 41.667 11.47 0.00 41.39 1.82
100 101 3.829026 TGAGGATGAATAGCGCATCTACT 59.171 43.478 11.47 4.89 41.39 2.57
101 102 4.179926 TGAGGATGAATAGCGCATCTAC 57.820 45.455 11.47 2.84 41.39 2.59
102 103 4.871933 TTGAGGATGAATAGCGCATCTA 57.128 40.909 11.47 0.00 41.39 1.98
103 104 3.758755 TTGAGGATGAATAGCGCATCT 57.241 42.857 11.47 0.00 41.39 2.90
104 105 3.812053 ACTTTGAGGATGAATAGCGCATC 59.188 43.478 11.47 5.45 41.03 3.91
105 106 3.812053 GACTTTGAGGATGAATAGCGCAT 59.188 43.478 11.47 0.00 0.00 4.73
106 107 3.198068 GACTTTGAGGATGAATAGCGCA 58.802 45.455 11.47 0.00 0.00 6.09
107 108 2.545946 GGACTTTGAGGATGAATAGCGC 59.454 50.000 0.00 0.00 0.00 5.92
108 109 3.797039 TGGACTTTGAGGATGAATAGCG 58.203 45.455 0.00 0.00 0.00 4.26
109 110 5.371526 TCATGGACTTTGAGGATGAATAGC 58.628 41.667 0.00 0.00 0.00 2.97
110 111 8.461249 AATTCATGGACTTTGAGGATGAATAG 57.539 34.615 0.00 0.00 0.00 1.73
111 112 8.689061 CAAATTCATGGACTTTGAGGATGAATA 58.311 33.333 0.00 0.00 35.26 1.75
112 113 7.179694 ACAAATTCATGGACTTTGAGGATGAAT 59.820 33.333 16.97 0.00 36.28 2.57
113 114 6.494491 ACAAATTCATGGACTTTGAGGATGAA 59.506 34.615 16.97 0.00 36.28 2.57
114 115 6.012113 ACAAATTCATGGACTTTGAGGATGA 58.988 36.000 16.97 0.00 36.28 2.92
115 116 6.152323 AGACAAATTCATGGACTTTGAGGATG 59.848 38.462 16.97 0.00 36.28 3.51
116 117 6.251471 AGACAAATTCATGGACTTTGAGGAT 58.749 36.000 16.97 1.57 36.28 3.24
117 118 5.634118 AGACAAATTCATGGACTTTGAGGA 58.366 37.500 16.97 0.00 36.28 3.71
118 119 5.972107 AGACAAATTCATGGACTTTGAGG 57.028 39.130 16.97 0.00 36.28 3.86
119 120 8.652810 AAAAAGACAAATTCATGGACTTTGAG 57.347 30.769 16.97 0.00 36.28 3.02
141 142 4.922692 CCTAAAATGCGATCTGTGCAAAAA 59.077 37.500 0.00 0.00 46.87 1.94
142 143 4.484236 CCTAAAATGCGATCTGTGCAAAA 58.516 39.130 0.00 0.00 46.87 2.44
143 144 3.119531 CCCTAAAATGCGATCTGTGCAAA 60.120 43.478 0.00 0.00 46.87 3.68
144 145 2.423185 CCCTAAAATGCGATCTGTGCAA 59.577 45.455 0.00 0.00 46.87 4.08
146 147 2.017049 ACCCTAAAATGCGATCTGTGC 58.983 47.619 0.00 0.00 0.00 4.57
147 148 6.377327 AAATACCCTAAAATGCGATCTGTG 57.623 37.500 0.00 0.00 0.00 3.66
148 149 8.691661 ATAAAATACCCTAAAATGCGATCTGT 57.308 30.769 0.00 0.00 0.00 3.41
149 150 8.237267 GGATAAAATACCCTAAAATGCGATCTG 58.763 37.037 0.00 0.00 0.00 2.90
150 151 8.164070 AGGATAAAATACCCTAAAATGCGATCT 58.836 33.333 0.00 0.00 0.00 2.75
151 152 8.336801 AGGATAAAATACCCTAAAATGCGATC 57.663 34.615 0.00 0.00 0.00 3.69
152 153 7.942341 TGAGGATAAAATACCCTAAAATGCGAT 59.058 33.333 0.00 0.00 0.00 4.58
153 154 7.284074 TGAGGATAAAATACCCTAAAATGCGA 58.716 34.615 0.00 0.00 0.00 5.10
154 155 7.504924 TGAGGATAAAATACCCTAAAATGCG 57.495 36.000 0.00 0.00 0.00 4.73
235 236 6.959671 ATTCGCACTTTTCAGTTTCAAAAA 57.040 29.167 0.00 0.00 0.00 1.94
236 237 6.959671 AATTCGCACTTTTCAGTTTCAAAA 57.040 29.167 0.00 0.00 0.00 2.44
237 238 6.959671 AAATTCGCACTTTTCAGTTTCAAA 57.040 29.167 0.00 0.00 0.00 2.69
238 239 6.587990 TCAAAATTCGCACTTTTCAGTTTCAA 59.412 30.769 0.00 0.00 0.00 2.69
239 240 6.096036 TCAAAATTCGCACTTTTCAGTTTCA 58.904 32.000 0.00 0.00 0.00 2.69
240 241 6.567769 TCAAAATTCGCACTTTTCAGTTTC 57.432 33.333 0.00 0.00 0.00 2.78
241 242 6.959671 TTCAAAATTCGCACTTTTCAGTTT 57.040 29.167 0.00 0.00 0.00 2.66
242 243 7.538303 AATTCAAAATTCGCACTTTTCAGTT 57.462 28.000 0.00 0.00 0.00 3.16
243 244 7.538303 AAATTCAAAATTCGCACTTTTCAGT 57.462 28.000 0.00 0.00 0.00 3.41
244 245 8.825064 AAAAATTCAAAATTCGCACTTTTCAG 57.175 26.923 0.00 0.00 0.00 3.02
245 246 8.446273 TGAAAAATTCAAAATTCGCACTTTTCA 58.554 25.926 0.00 0.00 37.71 2.69
246 247 8.819152 TGAAAAATTCAAAATTCGCACTTTTC 57.181 26.923 0.00 0.00 36.59 2.29
272 273 0.334676 TCCATGGAGGCCGGATTTTT 59.665 50.000 11.44 0.00 37.29 1.94
273 274 0.106519 CTCCATGGAGGCCGGATTTT 60.107 55.000 31.14 0.00 38.51 1.82
274 275 1.533711 CTCCATGGAGGCCGGATTT 59.466 57.895 31.14 0.00 38.51 2.17
275 276 3.244616 CTCCATGGAGGCCGGATT 58.755 61.111 31.14 0.00 38.51 3.01
283 284 3.160047 AGCTCGGCCTCCATGGAG 61.160 66.667 31.69 31.69 41.63 3.86
284 285 3.157252 GAGCTCGGCCTCCATGGA 61.157 66.667 15.27 15.27 38.35 3.41
290 291 2.391389 CGTTTTGGAGCTCGGCCTC 61.391 63.158 7.83 0.00 0.00 4.70
291 292 2.358737 CGTTTTGGAGCTCGGCCT 60.359 61.111 7.83 0.00 0.00 5.19
292 293 4.103103 GCGTTTTGGAGCTCGGCC 62.103 66.667 7.83 0.00 0.00 6.13
293 294 4.103103 GGCGTTTTGGAGCTCGGC 62.103 66.667 7.83 4.17 41.00 5.54
294 295 2.515996 TAGGGCGTTTTGGAGCTCGG 62.516 60.000 7.83 0.00 39.21 4.63
295 296 1.079405 TAGGGCGTTTTGGAGCTCG 60.079 57.895 7.83 0.00 39.21 5.03
296 297 0.036294 AGTAGGGCGTTTTGGAGCTC 60.036 55.000 4.71 4.71 0.00 4.09
297 298 0.036294 GAGTAGGGCGTTTTGGAGCT 60.036 55.000 0.00 0.00 0.00 4.09
298 299 1.025113 GGAGTAGGGCGTTTTGGAGC 61.025 60.000 0.00 0.00 0.00 4.70
299 300 0.323629 TGGAGTAGGGCGTTTTGGAG 59.676 55.000 0.00 0.00 0.00 3.86
300 301 0.766131 TTGGAGTAGGGCGTTTTGGA 59.234 50.000 0.00 0.00 0.00 3.53
301 302 1.743394 GATTGGAGTAGGGCGTTTTGG 59.257 52.381 0.00 0.00 0.00 3.28
302 303 2.711542 AGATTGGAGTAGGGCGTTTTG 58.288 47.619 0.00 0.00 0.00 2.44
303 304 3.518303 AGTAGATTGGAGTAGGGCGTTTT 59.482 43.478 0.00 0.00 0.00 2.43
304 305 3.105283 AGTAGATTGGAGTAGGGCGTTT 58.895 45.455 0.00 0.00 0.00 3.60
305 306 2.748388 AGTAGATTGGAGTAGGGCGTT 58.252 47.619 0.00 0.00 0.00 4.84
306 307 2.456073 AGTAGATTGGAGTAGGGCGT 57.544 50.000 0.00 0.00 0.00 5.68
307 308 3.458189 CAAAGTAGATTGGAGTAGGGCG 58.542 50.000 0.00 0.00 0.00 6.13
308 309 3.118223 AGCAAAGTAGATTGGAGTAGGGC 60.118 47.826 0.00 0.00 0.00 5.19
309 310 4.762289 AGCAAAGTAGATTGGAGTAGGG 57.238 45.455 0.00 0.00 0.00 3.53
310 311 7.454260 AAAAAGCAAAGTAGATTGGAGTAGG 57.546 36.000 0.00 0.00 0.00 3.18
339 340 8.521176 AGAGAACAGACACAATAACGTAGTAAT 58.479 33.333 0.00 0.00 45.00 1.89
344 345 6.206048 TCAGAGAGAACAGACACAATAACGTA 59.794 38.462 0.00 0.00 0.00 3.57
474 475 6.056428 AGATGAAAAGGTTACGTTGTCAAC 57.944 37.500 13.59 11.31 0.00 3.18
481 482 3.482436 TGGCAAGATGAAAAGGTTACGT 58.518 40.909 0.00 0.00 0.00 3.57
500 501 0.701731 TGGTTTCCCCTGGTGTATGG 59.298 55.000 0.00 0.00 0.00 2.74
528 529 8.174422 GCAAAAGCTTCAAGTTTTGTTTGATAA 58.826 29.630 18.42 0.00 42.92 1.75
539 540 4.819769 TGTCTTTGCAAAAGCTTCAAGTT 58.180 34.783 13.84 0.00 0.00 2.66
567 568 4.872691 ACGACAGCTGAAATCCTATTCTTG 59.127 41.667 23.35 0.00 0.00 3.02
626 627 2.378038 GTACATCCCACTACCCACGTA 58.622 52.381 0.00 0.00 0.00 3.57
664 665 5.311385 TGGTGATGGTCATGAGATGGAATAT 59.689 40.000 0.00 0.00 0.00 1.28
665 666 4.659835 TGGTGATGGTCATGAGATGGAATA 59.340 41.667 0.00 0.00 0.00 1.75
666 667 3.460712 TGGTGATGGTCATGAGATGGAAT 59.539 43.478 0.00 0.00 0.00 3.01
667 668 2.845586 TGGTGATGGTCATGAGATGGAA 59.154 45.455 0.00 0.00 0.00 3.53
668 669 2.436911 CTGGTGATGGTCATGAGATGGA 59.563 50.000 0.00 0.00 0.00 3.41
680 681 2.629617 AGAACAAAAAGCCTGGTGATGG 59.370 45.455 0.00 0.00 0.00 3.51
689 691 2.613595 CCTTTGCCAAGAACAAAAAGCC 59.386 45.455 0.00 0.00 36.63 4.35
690 692 2.613595 CCCTTTGCCAAGAACAAAAAGC 59.386 45.455 0.00 0.00 36.63 3.51
745 747 4.545208 TTGTTTCCATCGTCTGGTCATA 57.455 40.909 6.66 0.00 46.08 2.15
855 857 7.462571 ACTTGGTAAAAGTAAAATAGGGCAG 57.537 36.000 0.00 0.00 0.00 4.85
856 858 7.842887 AACTTGGTAAAAGTAAAATAGGGCA 57.157 32.000 0.00 0.00 0.00 5.36
887 890 5.659048 AATGAACGAGAGAAAACAGACAC 57.341 39.130 0.00 0.00 0.00 3.67
935 938 8.314143 TCTGTAACTTCGTATTTACTTTTGGG 57.686 34.615 4.42 0.00 0.00 4.12
949 952 5.422040 CGTCTCGTATACTCTGTAACTTCG 58.578 45.833 0.56 0.00 0.00 3.79
950 953 5.293079 ACCGTCTCGTATACTCTGTAACTTC 59.707 44.000 0.56 0.00 0.00 3.01
963 966 3.428589 GCTAGTTTTCCACCGTCTCGTAT 60.429 47.826 0.00 0.00 0.00 3.06
984 987 5.916883 AGTTTGCATATTCAATAATGCGAGC 59.083 36.000 3.17 3.56 42.48 5.03
1010 1013 1.453745 CGGTGGGATGGGTTGGATG 60.454 63.158 0.00 0.00 0.00 3.51
1082 1089 3.604129 ATGCGCGGTGGATGTGACA 62.604 57.895 8.83 0.00 0.00 3.58
1115 1122 0.946528 GCGGCAGATATGCATGTGAA 59.053 50.000 15.27 0.00 36.33 3.18
1153 1160 3.547249 GAAGACGGACGTGGACGCA 62.547 63.158 0.53 0.00 44.43 5.24
1156 1163 2.865343 ATATGAAGACGGACGTGGAC 57.135 50.000 0.53 0.00 0.00 4.02
1166 1173 4.988540 TGGCACACGCTATTATATGAAGAC 59.011 41.667 0.00 0.00 38.60 3.01
1215 1222 1.181786 GAGTGGACTGTGGAGAGGAG 58.818 60.000 0.00 0.00 0.00 3.69
1225 1232 1.942657 CTGTGTTTGTGGAGTGGACTG 59.057 52.381 0.00 0.00 0.00 3.51
1228 1235 0.465460 GCCTGTGTTTGTGGAGTGGA 60.465 55.000 0.00 0.00 0.00 4.02
1229 1236 1.455383 GGCCTGTGTTTGTGGAGTGG 61.455 60.000 0.00 0.00 0.00 4.00
1230 1237 0.751277 TGGCCTGTGTTTGTGGAGTG 60.751 55.000 3.32 0.00 0.00 3.51
1231 1238 0.751643 GTGGCCTGTGTTTGTGGAGT 60.752 55.000 3.32 0.00 0.00 3.85
1232 1239 0.751277 TGTGGCCTGTGTTTGTGGAG 60.751 55.000 3.32 0.00 0.00 3.86
1239 1246 2.019897 GCTGCTTTGTGGCCTGTGTT 62.020 55.000 3.32 0.00 0.00 3.32
1252 1259 2.289945 ACGAGAAGGAAATCAGCTGCTT 60.290 45.455 9.47 1.96 0.00 3.91
1260 1267 1.345176 CGCGCACGAGAAGGAAATC 59.655 57.895 8.75 0.00 43.93 2.17
1261 1268 2.100631 CCGCGCACGAGAAGGAAAT 61.101 57.895 8.75 0.00 43.93 2.17
1262 1269 2.736995 CCGCGCACGAGAAGGAAA 60.737 61.111 8.75 0.00 43.93 3.13
1324 1339 2.717011 CGGCAACAACAATAACAACGAC 59.283 45.455 0.00 0.00 0.00 4.34
1480 1495 2.361357 CTCCTCGTCCTCGGTGGT 60.361 66.667 0.00 0.00 37.69 4.16
1797 1812 1.212616 GATGGAATCAAGGCTCGACG 58.787 55.000 0.00 0.00 44.70 5.12
1891 1906 9.950496 CTAATCAACCACTAGCCAATAGATATT 57.050 33.333 0.00 0.00 35.30 1.28
1892 1907 9.105844 ACTAATCAACCACTAGCCAATAGATAT 57.894 33.333 0.00 0.00 35.30 1.63
1893 1908 8.367911 CACTAATCAACCACTAGCCAATAGATA 58.632 37.037 0.00 0.00 35.30 1.98
1894 1909 7.147479 ACACTAATCAACCACTAGCCAATAGAT 60.147 37.037 0.00 0.00 35.30 1.98
1895 1910 6.156256 ACACTAATCAACCACTAGCCAATAGA 59.844 38.462 0.00 0.00 35.30 1.98
1896 1911 6.258727 CACACTAATCAACCACTAGCCAATAG 59.741 42.308 0.00 0.00 37.53 1.73
1897 1912 6.112734 CACACTAATCAACCACTAGCCAATA 58.887 40.000 0.00 0.00 0.00 1.90
1898 1913 4.943705 CACACTAATCAACCACTAGCCAAT 59.056 41.667 0.00 0.00 0.00 3.16
1899 1914 4.323417 CACACTAATCAACCACTAGCCAA 58.677 43.478 0.00 0.00 0.00 4.52
1901 1916 3.270877 CCACACTAATCAACCACTAGCC 58.729 50.000 0.00 0.00 0.00 3.93
1902 1917 2.678336 GCCACACTAATCAACCACTAGC 59.322 50.000 0.00 0.00 0.00 3.42
1904 1919 3.326588 AGTGCCACACTAATCAACCACTA 59.673 43.478 0.00 0.00 43.46 2.74
1906 1921 2.504367 AGTGCCACACTAATCAACCAC 58.496 47.619 0.00 0.00 43.46 4.16
1907 1922 2.949177 AGTGCCACACTAATCAACCA 57.051 45.000 0.00 0.00 43.46 3.67
1940 1989 1.968017 CCATCACAGCGGCACACTT 60.968 57.895 1.45 0.00 0.00 3.16
1941 1990 2.359107 CCATCACAGCGGCACACT 60.359 61.111 1.45 0.00 0.00 3.55
2058 2111 3.942115 GAGGGTCTTTCCAGTAATTCAGC 59.058 47.826 0.00 0.00 38.11 4.26
2062 2115 8.582891 AATATAGGAGGGTCTTTCCAGTAATT 57.417 34.615 0.00 0.00 37.18 1.40
2238 2291 7.140705 TCTTGAGCAATTAGAACAAACACATG 58.859 34.615 0.00 0.00 0.00 3.21
2278 2331 2.768527 TGCTTCCCTCTACATTCTCTGG 59.231 50.000 0.00 0.00 0.00 3.86
2300 2353 4.100808 ACTCTTTGGATTGAGCTAGGCTAG 59.899 45.833 17.33 17.33 39.88 3.42
2393 2447 2.695666 AGAGAGAGAGAGAGAGAGACCG 59.304 54.545 0.00 0.00 0.00 4.79
2395 2449 4.892934 AGAGAGAGAGAGAGAGAGAGAGAC 59.107 50.000 0.00 0.00 0.00 3.36
2404 2458 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2405 2459 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2406 2460 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2407 2461 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2408 2462 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2409 2463 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2410 2464 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2511 2577 6.459670 ACATTGTGTTGTATGCATGATGAT 57.540 33.333 10.16 0.00 0.00 2.45
2579 2645 1.381165 GGACACCAAACACGGCTGTT 61.381 55.000 0.00 0.00 42.81 3.16
2590 2656 1.521450 GAGACTCGACGGGACACCAA 61.521 60.000 0.00 0.00 36.13 3.67
2677 2744 0.455410 GCTGAATTTGTGGCCGCATA 59.545 50.000 21.95 16.66 0.00 3.14


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

AutoCloner maintained by Alex Coulton.