Multiple sequence alignment - TraesCS2D01G157200

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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 TraesCS2D01G157200 chr2D 100.000 4082 0 0 1 4082 100325562 100321481 0.000000e+00 7539.0
1 TraesCS2D01G157200 chr2D 88.092 697 67 9 1265 1957 104918498 104917814 0.000000e+00 813.0
2 TraesCS2D01G157200 chr2D 86.677 623 71 12 3464 4082 89212274 89212888 0.000000e+00 680.0
3 TraesCS2D01G157200 chr2D 86.720 625 68 14 3464 4082 104889084 104888469 0.000000e+00 680.0
4 TraesCS2D01G157200 chr2D 87.231 603 61 8 1265 1863 89198706 89199296 0.000000e+00 673.0
5 TraesCS2D01G157200 chr2D 87.267 322 30 4 954 1269 104922199 104921883 1.400000e-94 357.0
6 TraesCS2D01G157200 chr2D 93.305 239 15 1 1985 2223 104917326 104917089 6.490000e-93 351.0
7 TraesCS2D01G157200 chr2D 86.335 322 33 4 954 1269 89194981 89195297 1.410000e-89 340.0
8 TraesCS2D01G157200 chr2D 92.469 239 17 1 1985 2223 89199622 89199859 1.410000e-89 340.0
9 TraesCS2D01G157200 chr2D 91.367 139 10 2 3305 3441 89199864 89200002 5.390000e-44 189.0
10 TraesCS2D01G157200 chr2D 90.647 139 11 2 3305 3441 104917084 104916946 2.510000e-42 183.0
11 TraesCS2D01G157200 chr2D 94.186 86 5 0 1 86 100433426 100433511 9.210000e-27 132.0
12 TraesCS2D01G157200 chr2D 92.308 65 3 2 40 104 100433500 100433562 1.560000e-14 91.6
13 TraesCS2D01G157200 chr2B 94.625 3144 147 11 954 4082 152185396 152182260 0.000000e+00 4850.0
14 TraesCS2D01G157200 chr2B 87.500 824 85 14 3265 4081 152180917 152180105 0.000000e+00 935.0
15 TraesCS2D01G157200 chr2B 88.119 707 34 17 210 888 152186364 152185680 0.000000e+00 795.0
16 TraesCS2D01G157200 chr2B 91.964 560 41 1 1670 2225 143488823 143488264 0.000000e+00 782.0
17 TraesCS2D01G157200 chr2B 86.396 566 62 14 3521 4082 143487833 143487279 4.510000e-169 604.0
18 TraesCS2D01G157200 chr2B 93.077 130 9 0 237 366 152191154 152191025 1.500000e-44 191.0
19 TraesCS2D01G157200 chr2A 93.053 3138 195 18 954 4082 100141379 100138256 0.000000e+00 4566.0
20 TraesCS2D01G157200 chr2A 87.780 1072 81 19 1186 2225 90505283 90506336 0.000000e+00 1208.0
21 TraesCS2D01G157200 chr2A 86.146 794 75 22 3305 4082 90506336 90507110 0.000000e+00 824.0
22 TraesCS2D01G157200 chr2A 84.780 703 47 11 223 898 100190868 100190199 0.000000e+00 651.0
23 TraesCS2D01G157200 chr2A 93.651 189 12 0 9 197 100199591 100199403 2.400000e-72 283.0
24 TraesCS2D01G157200 chr2A 81.746 126 18 5 370 491 100200324 100200200 2.600000e-17 100.0
25 TraesCS2D01G157200 chr4B 93.023 43 3 0 4 46 386020991 386020949 3.410000e-06 63.9
26 TraesCS2D01G157200 chr3D 97.143 35 1 0 12 46 79506038 79506072 4.410000e-05 60.2


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 TraesCS2D01G157200 chr2D 100321481 100325562 4081 True 7539.000000 7539 100.000000 1 4082 1 chr2D.!!$R1 4081
1 TraesCS2D01G157200 chr2D 89212274 89212888 614 False 680.000000 680 86.677000 3464 4082 1 chr2D.!!$F1 618
2 TraesCS2D01G157200 chr2D 104888469 104889084 615 True 680.000000 680 86.720000 3464 4082 1 chr2D.!!$R2 618
3 TraesCS2D01G157200 chr2D 104916946 104922199 5253 True 426.000000 813 89.827750 954 3441 4 chr2D.!!$R3 2487
4 TraesCS2D01G157200 chr2D 89194981 89200002 5021 False 385.500000 673 89.350500 954 3441 4 chr2D.!!$F2 2487
5 TraesCS2D01G157200 chr2B 152180105 152186364 6259 True 2193.333333 4850 90.081333 210 4082 3 chr2B.!!$R3 3872
6 TraesCS2D01G157200 chr2B 143487279 143488823 1544 True 693.000000 782 89.180000 1670 4082 2 chr2B.!!$R2 2412
7 TraesCS2D01G157200 chr2A 100138256 100141379 3123 True 4566.000000 4566 93.053000 954 4082 1 chr2A.!!$R1 3128
8 TraesCS2D01G157200 chr2A 90505283 90507110 1827 False 1016.000000 1208 86.963000 1186 4082 2 chr2A.!!$F1 2896
9 TraesCS2D01G157200 chr2A 100190199 100190868 669 True 651.000000 651 84.780000 223 898 1 chr2A.!!$R2 675

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
165 166 0.036732 TGCACCCAGGACTCATGAAC 59.963 55.0 0.00 0.0 0.0 3.18 F
908 952 0.474184 CCGAGCCTTCCCCACAATAT 59.526 55.0 0.00 0.0 0.0 1.28 F
2592 6784 0.037046 CTTTGGGAAAGCATGGCCAC 60.037 55.0 8.16 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 5450 1.262417 CAATGATCACCGAATCAGCCG 59.738 52.381 0.0 0.0 38.96 5.52 R
2839 7031 0.837272 TCTATTTCTGCCCCTTCCCG 59.163 55.000 0.0 0.0 0.00 5.14 R
4002 10586 0.550914 AACTTGGACTGGGCTGTTGA 59.449 50.000 0.0 0.0 0.00 3.18 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
34 35 8.975410 ATTGCCTAGTTAATTAACGAAAAACC 57.025 30.769 19.92 8.75 40.96 3.27
35 36 6.601264 TGCCTAGTTAATTAACGAAAAACCG 58.399 36.000 19.92 4.87 40.96 4.44
36 37 6.023435 GCCTAGTTAATTAACGAAAAACCGG 58.977 40.000 19.92 13.03 40.96 5.28
37 38 6.545508 CCTAGTTAATTAACGAAAAACCGGG 58.454 40.000 19.92 8.84 40.96 5.73
38 39 4.797471 AGTTAATTAACGAAAAACCGGGC 58.203 39.130 19.92 0.00 40.96 6.13
39 40 2.728690 AATTAACGAAAAACCGGGCC 57.271 45.000 6.32 0.00 0.00 5.80
40 41 1.618487 ATTAACGAAAAACCGGGCCA 58.382 45.000 6.32 0.00 0.00 5.36
41 42 1.396653 TTAACGAAAAACCGGGCCAA 58.603 45.000 6.32 0.00 0.00 4.52
42 43 1.396653 TAACGAAAAACCGGGCCAAA 58.603 45.000 6.32 0.00 0.00 3.28
43 44 0.535797 AACGAAAAACCGGGCCAAAA 59.464 45.000 6.32 0.00 0.00 2.44
44 45 0.179105 ACGAAAAACCGGGCCAAAAC 60.179 50.000 6.32 0.00 0.00 2.43
45 46 0.876777 CGAAAAACCGGGCCAAAACC 60.877 55.000 6.32 0.00 0.00 3.27
52 53 3.351450 GGGCCAAAACCGAGTGTC 58.649 61.111 4.39 0.00 0.00 3.67
53 54 1.527380 GGGCCAAAACCGAGTGTCA 60.527 57.895 4.39 0.00 0.00 3.58
54 55 0.893727 GGGCCAAAACCGAGTGTCAT 60.894 55.000 4.39 0.00 0.00 3.06
55 56 0.521735 GGCCAAAACCGAGTGTCATC 59.478 55.000 0.00 0.00 0.00 2.92
56 57 0.165944 GCCAAAACCGAGTGTCATCG 59.834 55.000 0.00 0.00 42.36 3.84
57 58 1.790755 CCAAAACCGAGTGTCATCGA 58.209 50.000 0.00 0.00 45.56 3.59
58 59 2.139917 CCAAAACCGAGTGTCATCGAA 58.860 47.619 0.00 0.00 45.56 3.71
59 60 2.546368 CCAAAACCGAGTGTCATCGAAA 59.454 45.455 0.00 0.00 45.56 3.46
60 61 3.188460 CCAAAACCGAGTGTCATCGAAAT 59.812 43.478 0.00 0.00 45.56 2.17
61 62 4.390603 CCAAAACCGAGTGTCATCGAAATA 59.609 41.667 0.00 0.00 45.56 1.40
62 63 5.064707 CCAAAACCGAGTGTCATCGAAATAT 59.935 40.000 0.00 0.00 45.56 1.28
63 64 5.718649 AAACCGAGTGTCATCGAAATATG 57.281 39.130 0.00 0.00 45.56 1.78
64 65 4.386867 ACCGAGTGTCATCGAAATATGT 57.613 40.909 0.00 0.00 45.56 2.29
65 66 4.755411 ACCGAGTGTCATCGAAATATGTT 58.245 39.130 0.00 0.00 45.56 2.71
66 67 5.175859 ACCGAGTGTCATCGAAATATGTTT 58.824 37.500 0.00 0.00 45.56 2.83
67 68 6.334989 ACCGAGTGTCATCGAAATATGTTTA 58.665 36.000 0.00 0.00 45.56 2.01
68 69 6.814644 ACCGAGTGTCATCGAAATATGTTTAA 59.185 34.615 0.00 0.00 45.56 1.52
69 70 7.332430 ACCGAGTGTCATCGAAATATGTTTAAA 59.668 33.333 0.00 0.00 45.56 1.52
70 71 8.172484 CCGAGTGTCATCGAAATATGTTTAAAA 58.828 33.333 0.00 0.00 45.56 1.52
71 72 9.199184 CGAGTGTCATCGAAATATGTTTAAAAG 57.801 33.333 0.00 0.00 45.56 2.27
72 73 8.895932 AGTGTCATCGAAATATGTTTAAAAGC 57.104 30.769 0.00 0.00 0.00 3.51
73 74 8.730680 AGTGTCATCGAAATATGTTTAAAAGCT 58.269 29.630 0.00 0.00 0.00 3.74
74 75 9.000018 GTGTCATCGAAATATGTTTAAAAGCTC 58.000 33.333 0.00 0.00 0.00 4.09
75 76 8.726068 TGTCATCGAAATATGTTTAAAAGCTCA 58.274 29.630 0.00 0.00 0.00 4.26
76 77 9.554724 GTCATCGAAATATGTTTAAAAGCTCAA 57.445 29.630 0.00 0.00 0.00 3.02
80 81 9.405587 TCGAAATATGTTTAAAAGCTCAAAAGG 57.594 29.630 0.00 0.00 0.00 3.11
81 82 9.405587 CGAAATATGTTTAAAAGCTCAAAAGGA 57.594 29.630 0.00 0.00 0.00 3.36
86 87 8.593492 ATGTTTAAAAGCTCAAAAGGAATGTC 57.407 30.769 0.00 0.00 0.00 3.06
87 88 7.781056 TGTTTAAAAGCTCAAAAGGAATGTCT 58.219 30.769 0.00 0.00 0.00 3.41
88 89 8.257306 TGTTTAAAAGCTCAAAAGGAATGTCTT 58.743 29.630 0.00 0.00 0.00 3.01
89 90 9.744468 GTTTAAAAGCTCAAAAGGAATGTCTTA 57.256 29.630 0.00 0.00 0.00 2.10
93 94 9.836864 AAAAGCTCAAAAGGAATGTCTTAATTT 57.163 25.926 0.00 0.00 0.00 1.82
94 95 9.836864 AAAGCTCAAAAGGAATGTCTTAATTTT 57.163 25.926 0.00 0.00 0.00 1.82
95 96 9.481340 AAGCTCAAAAGGAATGTCTTAATTTTC 57.519 29.630 0.00 0.00 0.00 2.29
96 97 8.864087 AGCTCAAAAGGAATGTCTTAATTTTCT 58.136 29.630 0.00 0.00 0.00 2.52
97 98 8.919661 GCTCAAAAGGAATGTCTTAATTTTCTG 58.080 33.333 0.00 0.00 0.00 3.02
103 104 9.981460 AAGGAATGTCTTAATTTTCTGATAGGT 57.019 29.630 0.00 0.00 0.00 3.08
104 105 9.981460 AGGAATGTCTTAATTTTCTGATAGGTT 57.019 29.630 0.00 0.00 0.00 3.50
126 127 8.364142 AGGTTTTCAAGATAGATAGATTCTCGG 58.636 37.037 0.00 0.00 35.79 4.63
127 128 8.361139 GGTTTTCAAGATAGATAGATTCTCGGA 58.639 37.037 0.00 0.00 35.79 4.55
128 129 9.187455 GTTTTCAAGATAGATAGATTCTCGGAC 57.813 37.037 0.00 0.00 35.79 4.79
129 130 6.729391 TCAAGATAGATAGATTCTCGGACG 57.271 41.667 0.00 0.00 35.79 4.79
130 131 6.465084 TCAAGATAGATAGATTCTCGGACGA 58.535 40.000 0.00 0.00 35.79 4.20
131 132 6.935208 TCAAGATAGATAGATTCTCGGACGAA 59.065 38.462 0.00 0.00 35.79 3.85
132 133 7.444487 TCAAGATAGATAGATTCTCGGACGAAA 59.556 37.037 0.00 0.00 35.79 3.46
133 134 7.747155 AGATAGATAGATTCTCGGACGAAAA 57.253 36.000 0.00 0.00 35.79 2.29
134 135 7.586747 AGATAGATAGATTCTCGGACGAAAAC 58.413 38.462 0.00 0.00 35.79 2.43
135 136 5.578005 AGATAGATTCTCGGACGAAAACA 57.422 39.130 0.00 0.00 0.00 2.83
136 137 5.962433 AGATAGATTCTCGGACGAAAACAA 58.038 37.500 0.00 0.00 0.00 2.83
137 138 6.395629 AGATAGATTCTCGGACGAAAACAAA 58.604 36.000 0.00 0.00 0.00 2.83
138 139 6.872020 AGATAGATTCTCGGACGAAAACAAAA 59.128 34.615 0.00 0.00 0.00 2.44
139 140 5.344207 AGATTCTCGGACGAAAACAAAAG 57.656 39.130 0.00 0.00 0.00 2.27
140 141 3.955771 TTCTCGGACGAAAACAAAAGG 57.044 42.857 0.00 0.00 0.00 3.11
141 142 2.215196 TCTCGGACGAAAACAAAAGGG 58.785 47.619 0.00 0.00 0.00 3.95
142 143 2.158928 TCTCGGACGAAAACAAAAGGGA 60.159 45.455 0.00 0.00 0.00 4.20
143 144 2.614983 CTCGGACGAAAACAAAAGGGAA 59.385 45.455 0.00 0.00 0.00 3.97
144 145 3.015327 TCGGACGAAAACAAAAGGGAAA 58.985 40.909 0.00 0.00 0.00 3.13
145 146 3.633065 TCGGACGAAAACAAAAGGGAAAT 59.367 39.130 0.00 0.00 0.00 2.17
146 147 4.098196 TCGGACGAAAACAAAAGGGAAATT 59.902 37.500 0.00 0.00 0.00 1.82
147 148 4.208253 CGGACGAAAACAAAAGGGAAATTG 59.792 41.667 0.00 0.00 0.00 2.32
148 149 4.025229 GGACGAAAACAAAAGGGAAATTGC 60.025 41.667 0.00 0.00 0.00 3.56
149 150 4.508662 ACGAAAACAAAAGGGAAATTGCA 58.491 34.783 0.00 0.00 0.00 4.08
150 151 4.331443 ACGAAAACAAAAGGGAAATTGCAC 59.669 37.500 0.00 0.00 0.00 4.57
151 152 4.260579 CGAAAACAAAAGGGAAATTGCACC 60.261 41.667 0.00 0.00 0.00 5.01
152 153 2.928801 ACAAAAGGGAAATTGCACCC 57.071 45.000 1.76 1.76 45.88 4.61
156 157 4.863415 GGGAAATTGCACCCAGGA 57.137 55.556 5.25 0.00 44.96 3.86
157 158 2.276869 GGGAAATTGCACCCAGGAC 58.723 57.895 5.25 0.00 44.96 3.85
158 159 0.251787 GGGAAATTGCACCCAGGACT 60.252 55.000 5.25 0.00 44.96 3.85
159 160 1.177401 GGAAATTGCACCCAGGACTC 58.823 55.000 0.00 0.00 0.00 3.36
160 161 1.547675 GGAAATTGCACCCAGGACTCA 60.548 52.381 0.00 0.00 0.00 3.41
161 162 2.450476 GAAATTGCACCCAGGACTCAT 58.550 47.619 0.00 0.00 0.00 2.90
162 163 1.843368 AATTGCACCCAGGACTCATG 58.157 50.000 0.00 0.00 0.00 3.07
163 164 0.994247 ATTGCACCCAGGACTCATGA 59.006 50.000 0.00 0.00 0.00 3.07
164 165 0.770499 TTGCACCCAGGACTCATGAA 59.230 50.000 0.00 0.00 0.00 2.57
165 166 0.036732 TGCACCCAGGACTCATGAAC 59.963 55.000 0.00 0.00 0.00 3.18
166 167 0.036732 GCACCCAGGACTCATGAACA 59.963 55.000 0.00 0.00 0.00 3.18
167 168 1.813513 CACCCAGGACTCATGAACAC 58.186 55.000 0.00 0.00 0.00 3.32
168 169 1.349026 CACCCAGGACTCATGAACACT 59.651 52.381 0.00 0.00 0.00 3.55
169 170 1.349026 ACCCAGGACTCATGAACACTG 59.651 52.381 11.32 11.32 0.00 3.66
170 171 1.446907 CCAGGACTCATGAACACTGC 58.553 55.000 12.35 0.00 0.00 4.40
171 172 1.002888 CCAGGACTCATGAACACTGCT 59.997 52.381 12.35 0.00 0.00 4.24
172 173 2.551721 CCAGGACTCATGAACACTGCTT 60.552 50.000 12.35 0.00 0.00 3.91
173 174 2.483106 CAGGACTCATGAACACTGCTTG 59.517 50.000 0.00 0.00 0.00 4.01
174 175 1.808945 GGACTCATGAACACTGCTTGG 59.191 52.381 0.00 0.00 0.00 3.61
175 176 2.550855 GGACTCATGAACACTGCTTGGA 60.551 50.000 0.00 0.00 0.00 3.53
176 177 3.341823 GACTCATGAACACTGCTTGGAT 58.658 45.455 0.00 0.00 0.00 3.41
177 178 3.341823 ACTCATGAACACTGCTTGGATC 58.658 45.455 0.00 0.00 0.00 3.36
178 179 2.349590 TCATGAACACTGCTTGGATCG 58.650 47.619 0.00 0.00 0.00 3.69
179 180 1.089920 ATGAACACTGCTTGGATCGC 58.910 50.000 0.00 0.00 0.00 4.58
180 181 0.955428 TGAACACTGCTTGGATCGCC 60.955 55.000 0.00 0.00 0.00 5.54
181 182 0.955428 GAACACTGCTTGGATCGCCA 60.955 55.000 0.00 0.00 44.17 5.69
191 192 1.737838 TGGATCGCCAAAACTAGCTG 58.262 50.000 0.00 0.00 42.49 4.24
192 193 1.003118 TGGATCGCCAAAACTAGCTGT 59.997 47.619 0.00 0.00 42.49 4.40
193 194 2.235155 TGGATCGCCAAAACTAGCTGTA 59.765 45.455 0.00 0.00 42.49 2.74
194 195 2.608090 GGATCGCCAAAACTAGCTGTAC 59.392 50.000 0.00 0.00 0.00 2.90
195 196 2.823924 TCGCCAAAACTAGCTGTACA 57.176 45.000 0.00 0.00 0.00 2.90
196 197 3.328382 TCGCCAAAACTAGCTGTACAT 57.672 42.857 0.00 0.00 0.00 2.29
197 198 4.459390 TCGCCAAAACTAGCTGTACATA 57.541 40.909 0.00 0.00 0.00 2.29
198 199 4.178540 TCGCCAAAACTAGCTGTACATAC 58.821 43.478 0.00 0.00 0.00 2.39
199 200 3.000078 CGCCAAAACTAGCTGTACATACG 60.000 47.826 0.00 0.00 0.00 3.06
200 201 3.930848 GCCAAAACTAGCTGTACATACGT 59.069 43.478 0.00 0.00 0.00 3.57
201 202 4.390909 GCCAAAACTAGCTGTACATACGTT 59.609 41.667 0.00 0.00 0.00 3.99
202 203 5.106830 GCCAAAACTAGCTGTACATACGTTT 60.107 40.000 0.00 1.77 0.00 3.60
203 204 6.531439 CCAAAACTAGCTGTACATACGTTTC 58.469 40.000 0.00 0.00 0.00 2.78
204 205 6.146510 CCAAAACTAGCTGTACATACGTTTCA 59.853 38.462 0.00 0.00 0.00 2.69
205 206 7.307514 CCAAAACTAGCTGTACATACGTTTCAA 60.308 37.037 0.00 0.00 0.00 2.69
206 207 7.718272 AAACTAGCTGTACATACGTTTCAAA 57.282 32.000 0.00 0.00 0.00 2.69
207 208 7.718272 AACTAGCTGTACATACGTTTCAAAA 57.282 32.000 0.00 0.00 0.00 2.44
208 209 7.718272 ACTAGCTGTACATACGTTTCAAAAA 57.282 32.000 0.00 0.00 0.00 1.94
396 397 4.974438 TCCGGGGTGCCCTTGAGT 62.974 66.667 0.00 0.00 42.67 3.41
438 439 1.892819 CGCCAGCCTCCAGAAAGAGA 61.893 60.000 0.00 0.00 35.82 3.10
442 443 2.224257 CCAGCCTCCAGAAAGAGATAGC 60.224 54.545 0.00 0.00 35.82 2.97
568 599 2.830370 CCCTTCATGGAAGCCGCC 60.830 66.667 0.46 0.00 38.24 6.13
576 607 4.168291 GGAAGCCGCCTCCTCCTG 62.168 72.222 0.26 0.00 0.00 3.86
583 614 2.364842 GCCTCCTCCTGCTCCTCA 60.365 66.667 0.00 0.00 0.00 3.86
659 693 2.360350 CAATGGCGGAGTGCTGGT 60.360 61.111 0.00 0.00 45.43 4.00
662 696 0.827507 AATGGCGGAGTGCTGGTTTT 60.828 50.000 0.00 0.00 45.43 2.43
882 926 4.927425 GTGTAGTAGTCCGCATTTCTGAAA 59.073 41.667 5.15 5.15 0.00 2.69
888 932 4.359706 AGTCCGCATTTCTGAAAACAAAC 58.640 39.130 6.95 3.06 0.00 2.93
900 944 0.826256 AAACAAACCCGAGCCTTCCC 60.826 55.000 0.00 0.00 0.00 3.97
902 946 2.856988 AAACCCGAGCCTTCCCCA 60.857 61.111 0.00 0.00 0.00 4.96
903 947 3.205851 AAACCCGAGCCTTCCCCAC 62.206 63.158 0.00 0.00 0.00 4.61
904 948 4.974438 ACCCGAGCCTTCCCCACA 62.974 66.667 0.00 0.00 0.00 4.17
905 949 3.646715 CCCGAGCCTTCCCCACAA 61.647 66.667 0.00 0.00 0.00 3.33
907 951 1.632018 CCCGAGCCTTCCCCACAATA 61.632 60.000 0.00 0.00 0.00 1.90
908 952 0.474184 CCGAGCCTTCCCCACAATAT 59.526 55.000 0.00 0.00 0.00 1.28
910 954 1.134098 CGAGCCTTCCCCACAATATGT 60.134 52.381 0.00 0.00 0.00 2.29
924 968 3.773119 ACAATATGTGAACCTCCTACGGT 59.227 43.478 0.00 0.00 39.48 4.83
925 969 4.957954 ACAATATGTGAACCTCCTACGGTA 59.042 41.667 0.00 0.00 35.89 4.02
926 970 5.601313 ACAATATGTGAACCTCCTACGGTAT 59.399 40.000 0.00 0.00 35.89 2.73
927 971 5.979288 ATATGTGAACCTCCTACGGTATC 57.021 43.478 0.00 0.00 35.89 2.24
928 972 2.381911 TGTGAACCTCCTACGGTATCC 58.618 52.381 0.00 0.00 35.89 2.59
943 987 4.338379 GGTATCCGATGGAGTAAAAGCT 57.662 45.455 0.00 0.00 34.05 3.74
945 989 5.850614 GGTATCCGATGGAGTAAAAGCTTA 58.149 41.667 0.00 0.00 34.05 3.09
946 990 6.285990 GGTATCCGATGGAGTAAAAGCTTAA 58.714 40.000 0.00 0.00 34.05 1.85
948 992 4.178540 TCCGATGGAGTAAAAGCTTAACG 58.821 43.478 0.00 0.00 0.00 3.18
949 993 3.308866 CCGATGGAGTAAAAGCTTAACGG 59.691 47.826 0.00 0.00 0.00 4.44
951 995 4.267928 CGATGGAGTAAAAGCTTAACGGAG 59.732 45.833 0.00 0.00 0.00 4.63
952 996 3.934068 TGGAGTAAAAGCTTAACGGAGG 58.066 45.455 0.00 0.00 0.00 4.30
964 1226 4.168291 CGGAGGGCTTCTGGGCTC 62.168 72.222 0.00 0.00 40.65 4.70
1018 1292 3.417275 ATGCTCTTCTCCGCCGTCG 62.417 63.158 0.00 0.00 0.00 5.12
1157 1437 3.541713 GCTCCTCCGGCTCCGATT 61.542 66.667 10.28 0.00 42.83 3.34
1310 5004 2.203070 GCTCGACGGAATGCCCAT 60.203 61.111 0.00 0.00 34.14 4.00
1390 5084 2.361357 AGGCGCTGGAGACGTACT 60.361 61.111 7.64 0.00 0.00 2.73
1504 5204 2.497675 GGCCGGATGATAAGAGAGCATA 59.502 50.000 5.05 0.00 33.16 3.14
1659 5376 3.799753 GCGTGGACTGCGATGATT 58.200 55.556 0.00 0.00 0.00 2.57
1690 5407 0.750546 GCATGCAGGAGATTGGCTCA 60.751 55.000 14.21 0.00 45.81 4.26
1733 5450 3.966665 AGGATGAGATCAGAAGGGTTCTC 59.033 47.826 0.00 0.00 38.11 2.87
1764 5481 2.756760 GGTGATCATTGCCACTGTCATT 59.243 45.455 0.00 0.00 33.99 2.57
1850 5575 4.507710 TGTGGAGTTGCTGATGATAACTC 58.492 43.478 0.00 0.00 45.87 3.01
1990 6179 1.934589 TTCGCAGAACGGGATGTATG 58.065 50.000 0.00 0.00 45.90 2.39
2142 6331 6.433847 TTCTCCTTAAGACATGGACTTGAA 57.566 37.500 3.36 8.29 32.27 2.69
2550 6742 1.756430 TGACAGAGCGAGATACTGCT 58.244 50.000 0.00 0.00 45.90 4.24
2592 6784 0.037046 CTTTGGGAAAGCATGGCCAC 60.037 55.000 8.16 0.00 0.00 5.01
2611 6803 3.251729 CCACGAAGATCAAGCCATAATGG 59.748 47.826 0.00 0.00 41.55 3.16
2704 6896 1.208052 GTCATGCAGGCCTTACTGAGA 59.792 52.381 0.00 0.00 40.97 3.27
2722 6914 2.884639 GAGAAGGGCTTGCACTTTTACA 59.115 45.455 11.64 0.00 0.00 2.41
2839 7031 6.277918 CTTGGAAGTTCATTTCAAGTTTGC 57.722 37.500 5.01 0.00 45.90 3.68
2848 7040 0.825840 TTCAAGTTTGCGGGAAGGGG 60.826 55.000 0.00 0.00 0.00 4.79
2879 7071 1.272092 TGTTCTTGGATGCCTCTTGGG 60.272 52.381 0.00 0.00 38.36 4.12
2907 7099 3.064545 GCAGAGTGCATAACAGAATGGAC 59.935 47.826 0.00 0.79 45.53 4.02
2985 7177 7.972277 GGCTATCATATTTTGCTGTCCAATATG 59.028 37.037 5.20 5.20 40.22 1.78
3076 7268 9.349713 TGAAGAATATAACAGGAAACAGTTTGT 57.650 29.630 2.34 0.00 40.81 2.83
3101 7293 3.611766 AGTTGATCGGACCCTAAGTTG 57.388 47.619 0.00 0.00 0.00 3.16
3124 7316 8.383619 GTTGTGGATCGCATATATTAATCAGTC 58.616 37.037 0.00 0.00 0.00 3.51
3144 7336 8.888579 TCAGTCTTTTACTAAACCAAGAGAAG 57.111 34.615 0.00 0.00 35.76 2.85
3151 7343 7.958053 TTACTAAACCAAGAGAAGCACTAAC 57.042 36.000 0.00 0.00 0.00 2.34
3263 7455 7.181569 ACCTTATGGTTAAATTTGTCCCATG 57.818 36.000 19.99 11.17 46.05 3.66
3319 9677 1.594862 GTGCACAGATAATGTCGAGCC 59.405 52.381 13.17 0.00 41.41 4.70
3322 9680 2.739932 GCACAGATAATGTCGAGCCTGT 60.740 50.000 0.00 0.00 41.41 4.00
3327 9685 1.271856 TAATGTCGAGCCTGTGGGAA 58.728 50.000 0.00 0.00 33.58 3.97
3328 9686 0.321653 AATGTCGAGCCTGTGGGAAC 60.322 55.000 0.00 0.00 33.58 3.62
3345 9708 3.927142 GGGAACGTATGTCAGAGAAACAG 59.073 47.826 0.00 0.00 0.00 3.16
3433 9797 3.127030 GGCGAATAAAAGGTGAACTGGAG 59.873 47.826 0.00 0.00 0.00 3.86
3438 9802 7.012421 GCGAATAAAAGGTGAACTGGAGAATAT 59.988 37.037 0.00 0.00 0.00 1.28
3461 9908 7.759489 ATTTAGTGCATTGTACTTCTTTGGA 57.241 32.000 12.74 0.00 0.00 3.53
3462 9909 6.554334 TTAGTGCATTGTACTTCTTTGGAC 57.446 37.500 12.74 0.00 0.00 4.02
3596 10176 8.908786 ACTTCACATTTCATTCTCTTTGACTA 57.091 30.769 0.00 0.00 0.00 2.59
3597 10177 8.997323 ACTTCACATTTCATTCTCTTTGACTAG 58.003 33.333 0.00 0.00 0.00 2.57
3605 10185 7.724490 TCATTCTCTTTGACTAGAATCAGGA 57.276 36.000 0.00 0.00 39.79 3.86
3608 10188 9.044150 CATTCTCTTTGACTAGAATCAGGATTC 57.956 37.037 12.93 12.93 45.66 2.52
3638 10218 7.944061 AGAACATGTTGAATGTCTTCATTTCA 58.056 30.769 17.58 0.00 43.33 2.69
3642 10222 6.075762 TGTTGAATGTCTTCATTTCACAGG 57.924 37.500 0.00 0.00 43.33 4.00
3657 10237 1.067635 CACAGGCCTGTTTTGGTATGC 60.068 52.381 36.06 0.00 42.83 3.14
3658 10238 1.255882 CAGGCCTGTTTTGGTATGCA 58.744 50.000 25.53 0.00 0.00 3.96
3660 10240 2.036992 CAGGCCTGTTTTGGTATGCAAA 59.963 45.455 25.53 0.00 0.00 3.68
3701 10282 6.157994 TGCTTAGTACCCTGAATCCTTATTGT 59.842 38.462 0.00 0.00 0.00 2.71
3704 10285 6.893020 AGTACCCTGAATCCTTATTGTTCT 57.107 37.500 0.00 0.00 0.00 3.01
3708 10289 5.711976 ACCCTGAATCCTTATTGTTCTGTTG 59.288 40.000 0.00 0.00 0.00 3.33
3716 10297 4.549458 CTTATTGTTCTGTTGGCAACCTG 58.451 43.478 26.31 18.69 0.00 4.00
3726 10307 2.887152 GTTGGCAACCTGATCTGTTCTT 59.113 45.455 19.57 0.00 0.00 2.52
3732 10313 4.437930 GCAACCTGATCTGTTCTTATGCAC 60.438 45.833 0.00 0.00 0.00 4.57
3784 10365 5.139435 TCATGACTTCACCAAGTACTCTG 57.861 43.478 0.00 0.00 43.37 3.35
3790 10371 6.774170 TGACTTCACCAAGTACTCTGTTACTA 59.226 38.462 0.00 0.00 43.37 1.82
3822 10403 8.640063 ACAGCTAATGGCATGATAAATCATTA 57.360 30.769 0.00 0.00 45.23 1.90
3823 10404 9.251440 ACAGCTAATGGCATGATAAATCATTAT 57.749 29.630 0.00 0.00 45.23 1.28
3829 10410 9.772605 AATGGCATGATAAATCATTATAAGGGA 57.227 29.630 0.00 0.00 44.70 4.20
3830 10411 9.772605 ATGGCATGATAAATCATTATAAGGGAA 57.227 29.630 0.00 0.00 44.70 3.97
3831 10412 9.023962 TGGCATGATAAATCATTATAAGGGAAC 57.976 33.333 0.00 0.00 44.70 3.62
3832 10413 9.023962 GGCATGATAAATCATTATAAGGGAACA 57.976 33.333 0.00 0.00 44.70 3.18
3849 10430 8.887036 AAGGGAACAAAACAAAATGATACTTC 57.113 30.769 0.00 0.00 0.00 3.01
3871 10452 2.235650 TGAGCTCAGGTGATTTCCAGAG 59.764 50.000 13.74 0.00 41.85 3.35
3874 10455 2.746362 GCTCAGGTGATTTCCAGAGTTG 59.254 50.000 6.92 0.00 41.28 3.16
3924 10505 3.120385 TGTCGCAGGCAATCGCAG 61.120 61.111 0.00 0.00 42.02 5.18
3939 10520 2.646930 TCGCAGTTCCCGATCTACTAA 58.353 47.619 0.00 0.00 0.00 2.24
3950 10531 6.366340 TCCCGATCTACTAATCTGAAGTTCT 58.634 40.000 4.17 0.00 0.00 3.01
3973 10557 7.560368 TCTTTTTATGTGACACCCAATGTTTT 58.440 30.769 2.45 0.00 43.56 2.43
4044 10628 1.546476 ACGTCCAGAACTCCAGATGTC 59.454 52.381 0.00 0.00 0.00 3.06
4052 10636 4.328440 CAGAACTCCAGATGTCGATGTTTC 59.672 45.833 0.00 0.00 0.00 2.78
4053 10637 3.961480 ACTCCAGATGTCGATGTTTCA 57.039 42.857 0.00 0.00 0.00 2.69
4054 10638 4.478206 ACTCCAGATGTCGATGTTTCAT 57.522 40.909 0.00 0.00 0.00 2.57
4067 10651 8.620416 TGTCGATGTTTCATAAGAAAATATGGG 58.380 33.333 0.00 0.00 44.75 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.414295 GGTTTTTCGTTAATTAACTAGGCAATT 57.586 29.630 22.57 8.37 34.12 2.32
9 10 7.751793 CGGTTTTTCGTTAATTAACTAGGCAAT 59.248 33.333 22.57 0.00 34.12 3.56
10 11 7.076983 CGGTTTTTCGTTAATTAACTAGGCAA 58.923 34.615 22.57 8.96 34.12 4.52
11 12 6.348376 CCGGTTTTTCGTTAATTAACTAGGCA 60.348 38.462 22.57 4.94 34.12 4.75
12 13 6.023435 CCGGTTTTTCGTTAATTAACTAGGC 58.977 40.000 22.57 10.04 34.12 3.93
13 14 6.545508 CCCGGTTTTTCGTTAATTAACTAGG 58.454 40.000 22.57 10.21 34.12 3.02
14 15 6.023435 GCCCGGTTTTTCGTTAATTAACTAG 58.977 40.000 22.57 10.84 34.12 2.57
15 16 5.106357 GGCCCGGTTTTTCGTTAATTAACTA 60.106 40.000 22.57 11.86 34.12 2.24
16 17 4.321156 GGCCCGGTTTTTCGTTAATTAACT 60.321 41.667 22.57 0.00 34.12 2.24
17 18 3.919804 GGCCCGGTTTTTCGTTAATTAAC 59.080 43.478 16.87 16.87 0.00 2.01
18 19 3.571401 TGGCCCGGTTTTTCGTTAATTAA 59.429 39.130 0.00 0.00 0.00 1.40
19 20 3.152341 TGGCCCGGTTTTTCGTTAATTA 58.848 40.909 0.00 0.00 0.00 1.40
20 21 1.962100 TGGCCCGGTTTTTCGTTAATT 59.038 42.857 0.00 0.00 0.00 1.40
21 22 1.618487 TGGCCCGGTTTTTCGTTAAT 58.382 45.000 0.00 0.00 0.00 1.40
22 23 1.396653 TTGGCCCGGTTTTTCGTTAA 58.603 45.000 0.00 0.00 0.00 2.01
23 24 1.396653 TTTGGCCCGGTTTTTCGTTA 58.603 45.000 0.00 0.00 0.00 3.18
24 25 0.535797 TTTTGGCCCGGTTTTTCGTT 59.464 45.000 0.00 0.00 0.00 3.85
25 26 0.179105 GTTTTGGCCCGGTTTTTCGT 60.179 50.000 0.00 0.00 0.00 3.85
26 27 0.876777 GGTTTTGGCCCGGTTTTTCG 60.877 55.000 0.00 0.00 0.00 3.46
27 28 0.876777 CGGTTTTGGCCCGGTTTTTC 60.877 55.000 0.00 0.00 41.78 2.29
28 29 1.144276 CGGTTTTGGCCCGGTTTTT 59.856 52.632 0.00 0.00 41.78 1.94
29 30 1.740332 CTCGGTTTTGGCCCGGTTTT 61.740 55.000 0.00 0.00 45.51 2.43
30 31 2.123812 TCGGTTTTGGCCCGGTTT 60.124 55.556 0.00 0.00 45.51 3.27
31 32 2.596338 CTCGGTTTTGGCCCGGTT 60.596 61.111 0.00 0.00 45.51 4.44
32 33 3.881104 ACTCGGTTTTGGCCCGGT 61.881 61.111 0.00 0.00 45.51 5.28
33 34 3.361977 CACTCGGTTTTGGCCCGG 61.362 66.667 0.00 0.00 45.51 5.73
34 35 2.593436 ACACTCGGTTTTGGCCCG 60.593 61.111 0.00 0.00 46.83 6.13
35 36 0.893727 ATGACACTCGGTTTTGGCCC 60.894 55.000 0.00 0.00 0.00 5.80
36 37 0.521735 GATGACACTCGGTTTTGGCC 59.478 55.000 0.00 0.00 0.00 5.36
37 38 0.165944 CGATGACACTCGGTTTTGGC 59.834 55.000 0.00 0.00 35.03 4.52
38 39 1.790755 TCGATGACACTCGGTTTTGG 58.209 50.000 7.22 0.00 39.13 3.28
39 40 3.870723 TTTCGATGACACTCGGTTTTG 57.129 42.857 0.00 0.00 39.13 2.44
40 41 5.642063 ACATATTTCGATGACACTCGGTTTT 59.358 36.000 0.00 0.00 39.13 2.43
41 42 5.175859 ACATATTTCGATGACACTCGGTTT 58.824 37.500 0.00 0.00 39.13 3.27
42 43 4.755411 ACATATTTCGATGACACTCGGTT 58.245 39.130 0.00 0.00 39.13 4.44
43 44 4.386867 ACATATTTCGATGACACTCGGT 57.613 40.909 0.00 0.00 39.13 4.69
44 45 5.718649 AAACATATTTCGATGACACTCGG 57.281 39.130 0.00 0.00 39.13 4.63
45 46 9.199184 CTTTTAAACATATTTCGATGACACTCG 57.801 33.333 0.00 2.15 39.99 4.18
46 47 9.000018 GCTTTTAAACATATTTCGATGACACTC 58.000 33.333 0.00 0.00 0.00 3.51
47 48 8.730680 AGCTTTTAAACATATTTCGATGACACT 58.269 29.630 0.00 0.00 0.00 3.55
48 49 8.895932 AGCTTTTAAACATATTTCGATGACAC 57.104 30.769 0.00 0.00 0.00 3.67
49 50 8.726068 TGAGCTTTTAAACATATTTCGATGACA 58.274 29.630 0.00 0.00 0.00 3.58
50 51 9.554724 TTGAGCTTTTAAACATATTTCGATGAC 57.445 29.630 0.00 0.00 0.00 3.06
54 55 9.405587 CCTTTTGAGCTTTTAAACATATTTCGA 57.594 29.630 0.00 0.00 0.00 3.71
55 56 9.405587 TCCTTTTGAGCTTTTAAACATATTTCG 57.594 29.630 0.00 0.00 0.00 3.46
60 61 9.691362 GACATTCCTTTTGAGCTTTTAAACATA 57.309 29.630 0.00 0.00 0.00 2.29
61 62 8.424133 AGACATTCCTTTTGAGCTTTTAAACAT 58.576 29.630 0.00 0.00 0.00 2.71
62 63 7.781056 AGACATTCCTTTTGAGCTTTTAAACA 58.219 30.769 0.00 0.00 0.00 2.83
63 64 8.648557 AAGACATTCCTTTTGAGCTTTTAAAC 57.351 30.769 0.00 0.00 0.00 2.01
67 68 9.836864 AAATTAAGACATTCCTTTTGAGCTTTT 57.163 25.926 0.00 0.00 0.00 2.27
68 69 9.836864 AAAATTAAGACATTCCTTTTGAGCTTT 57.163 25.926 0.00 0.00 0.00 3.51
69 70 9.481340 GAAAATTAAGACATTCCTTTTGAGCTT 57.519 29.630 0.00 0.00 0.00 3.74
70 71 8.864087 AGAAAATTAAGACATTCCTTTTGAGCT 58.136 29.630 0.00 0.00 0.00 4.09
71 72 8.919661 CAGAAAATTAAGACATTCCTTTTGAGC 58.080 33.333 0.00 0.00 0.00 4.26
77 78 9.981460 ACCTATCAGAAAATTAAGACATTCCTT 57.019 29.630 0.00 0.00 0.00 3.36
78 79 9.981460 AACCTATCAGAAAATTAAGACATTCCT 57.019 29.630 0.00 0.00 0.00 3.36
100 101 8.364142 CCGAGAATCTATCTATCTTGAAAACCT 58.636 37.037 0.00 0.00 38.96 3.50
101 102 8.361139 TCCGAGAATCTATCTATCTTGAAAACC 58.639 37.037 0.00 0.00 38.96 3.27
102 103 9.187455 GTCCGAGAATCTATCTATCTTGAAAAC 57.813 37.037 0.00 0.00 38.96 2.43
103 104 8.076781 CGTCCGAGAATCTATCTATCTTGAAAA 58.923 37.037 0.00 0.00 38.96 2.29
104 105 7.444487 TCGTCCGAGAATCTATCTATCTTGAAA 59.556 37.037 0.00 0.00 38.96 2.69
105 106 6.935208 TCGTCCGAGAATCTATCTATCTTGAA 59.065 38.462 0.00 0.00 38.96 2.69
106 107 6.465084 TCGTCCGAGAATCTATCTATCTTGA 58.535 40.000 0.00 0.00 38.96 3.02
107 108 6.729391 TCGTCCGAGAATCTATCTATCTTG 57.271 41.667 0.00 0.00 38.96 3.02
108 109 7.747155 TTTCGTCCGAGAATCTATCTATCTT 57.253 36.000 0.00 0.00 38.96 2.40
109 110 7.228906 TGTTTTCGTCCGAGAATCTATCTATCT 59.771 37.037 0.00 0.00 38.96 1.98
110 111 7.361127 TGTTTTCGTCCGAGAATCTATCTATC 58.639 38.462 0.00 0.00 38.96 2.08
111 112 7.273320 TGTTTTCGTCCGAGAATCTATCTAT 57.727 36.000 0.00 0.00 38.96 1.98
112 113 6.688637 TGTTTTCGTCCGAGAATCTATCTA 57.311 37.500 0.00 0.00 38.96 1.98
113 114 5.578005 TGTTTTCGTCCGAGAATCTATCT 57.422 39.130 0.00 0.00 42.61 1.98
114 115 6.642683 TTTGTTTTCGTCCGAGAATCTATC 57.357 37.500 0.00 0.00 0.00 2.08
115 116 6.092259 CCTTTTGTTTTCGTCCGAGAATCTAT 59.908 38.462 0.00 0.00 0.00 1.98
116 117 5.407387 CCTTTTGTTTTCGTCCGAGAATCTA 59.593 40.000 0.00 0.00 0.00 1.98
117 118 4.213482 CCTTTTGTTTTCGTCCGAGAATCT 59.787 41.667 0.00 0.00 0.00 2.40
118 119 4.464112 CCTTTTGTTTTCGTCCGAGAATC 58.536 43.478 0.00 0.00 0.00 2.52
119 120 3.252458 CCCTTTTGTTTTCGTCCGAGAAT 59.748 43.478 0.00 0.00 0.00 2.40
120 121 2.614983 CCCTTTTGTTTTCGTCCGAGAA 59.385 45.455 0.00 0.00 0.00 2.87
121 122 2.158928 TCCCTTTTGTTTTCGTCCGAGA 60.159 45.455 0.00 0.00 0.00 4.04
122 123 2.215196 TCCCTTTTGTTTTCGTCCGAG 58.785 47.619 0.00 0.00 0.00 4.63
123 124 2.328819 TCCCTTTTGTTTTCGTCCGA 57.671 45.000 0.00 0.00 0.00 4.55
124 125 3.423996 TTTCCCTTTTGTTTTCGTCCG 57.576 42.857 0.00 0.00 0.00 4.79
125 126 4.025229 GCAATTTCCCTTTTGTTTTCGTCC 60.025 41.667 0.00 0.00 0.00 4.79
126 127 4.568760 TGCAATTTCCCTTTTGTTTTCGTC 59.431 37.500 0.00 0.00 0.00 4.20
127 128 4.331443 GTGCAATTTCCCTTTTGTTTTCGT 59.669 37.500 0.00 0.00 0.00 3.85
128 129 4.260579 GGTGCAATTTCCCTTTTGTTTTCG 60.261 41.667 0.00 0.00 0.00 3.46
129 130 4.036262 GGGTGCAATTTCCCTTTTGTTTTC 59.964 41.667 2.83 0.00 40.48 2.29
130 131 3.951037 GGGTGCAATTTCCCTTTTGTTTT 59.049 39.130 2.83 0.00 40.48 2.43
131 132 3.054065 TGGGTGCAATTTCCCTTTTGTTT 60.054 39.130 11.17 0.00 43.74 2.83
132 133 2.507471 TGGGTGCAATTTCCCTTTTGTT 59.493 40.909 11.17 0.00 43.74 2.83
133 134 2.104622 CTGGGTGCAATTTCCCTTTTGT 59.895 45.455 11.17 0.00 43.74 2.83
134 135 2.550639 CCTGGGTGCAATTTCCCTTTTG 60.551 50.000 11.17 0.41 43.74 2.44
135 136 1.699083 CCTGGGTGCAATTTCCCTTTT 59.301 47.619 11.17 0.00 43.74 2.27
136 137 1.132881 TCCTGGGTGCAATTTCCCTTT 60.133 47.619 11.17 0.00 43.74 3.11
137 138 0.486879 TCCTGGGTGCAATTTCCCTT 59.513 50.000 11.17 0.00 43.74 3.95
138 139 0.251787 GTCCTGGGTGCAATTTCCCT 60.252 55.000 11.17 0.00 43.74 4.20
139 140 0.251787 AGTCCTGGGTGCAATTTCCC 60.252 55.000 3.10 3.10 43.67 3.97
140 141 1.177401 GAGTCCTGGGTGCAATTTCC 58.823 55.000 0.00 0.00 0.00 3.13
141 142 1.909700 TGAGTCCTGGGTGCAATTTC 58.090 50.000 0.00 0.00 0.00 2.17
142 143 2.173519 CATGAGTCCTGGGTGCAATTT 58.826 47.619 0.00 0.00 0.00 1.82
143 144 1.355381 TCATGAGTCCTGGGTGCAATT 59.645 47.619 0.00 0.00 0.00 2.32
144 145 0.994247 TCATGAGTCCTGGGTGCAAT 59.006 50.000 0.00 0.00 0.00 3.56
145 146 0.770499 TTCATGAGTCCTGGGTGCAA 59.230 50.000 0.00 0.00 0.00 4.08
146 147 0.036732 GTTCATGAGTCCTGGGTGCA 59.963 55.000 0.00 0.00 0.00 4.57
147 148 0.036732 TGTTCATGAGTCCTGGGTGC 59.963 55.000 0.00 0.00 0.00 5.01
148 149 1.349026 AGTGTTCATGAGTCCTGGGTG 59.651 52.381 0.00 0.00 0.00 4.61
149 150 1.349026 CAGTGTTCATGAGTCCTGGGT 59.651 52.381 0.00 0.00 0.00 4.51
150 151 1.947678 GCAGTGTTCATGAGTCCTGGG 60.948 57.143 15.24 0.00 0.00 4.45
151 152 1.002888 AGCAGTGTTCATGAGTCCTGG 59.997 52.381 15.24 0.00 0.00 4.45
152 153 2.469274 AGCAGTGTTCATGAGTCCTG 57.531 50.000 11.25 11.25 0.00 3.86
153 154 2.551721 CCAAGCAGTGTTCATGAGTCCT 60.552 50.000 0.00 0.00 0.00 3.85
154 155 1.808945 CCAAGCAGTGTTCATGAGTCC 59.191 52.381 0.00 0.00 0.00 3.85
155 156 2.771089 TCCAAGCAGTGTTCATGAGTC 58.229 47.619 0.00 0.00 0.00 3.36
156 157 2.936919 TCCAAGCAGTGTTCATGAGT 57.063 45.000 0.00 0.00 0.00 3.41
157 158 2.350804 CGATCCAAGCAGTGTTCATGAG 59.649 50.000 0.00 0.00 0.00 2.90
158 159 2.349590 CGATCCAAGCAGTGTTCATGA 58.650 47.619 0.00 0.00 0.00 3.07
159 160 1.202110 GCGATCCAAGCAGTGTTCATG 60.202 52.381 0.00 0.00 34.19 3.07
160 161 1.089920 GCGATCCAAGCAGTGTTCAT 58.910 50.000 0.00 0.00 34.19 2.57
161 162 0.955428 GGCGATCCAAGCAGTGTTCA 60.955 55.000 0.00 0.00 36.08 3.18
162 163 0.955428 TGGCGATCCAAGCAGTGTTC 60.955 55.000 0.00 0.00 39.99 3.18
163 164 0.537143 TTGGCGATCCAAGCAGTGTT 60.537 50.000 0.00 0.00 46.89 3.32
164 165 1.073025 TTGGCGATCCAAGCAGTGT 59.927 52.632 0.00 0.00 46.89 3.55
165 166 3.985877 TTGGCGATCCAAGCAGTG 58.014 55.556 0.00 0.00 46.89 3.66
172 173 1.003118 ACAGCTAGTTTTGGCGATCCA 59.997 47.619 0.00 0.00 41.55 3.41
173 174 1.739067 ACAGCTAGTTTTGGCGATCC 58.261 50.000 0.00 0.00 35.69 3.36
174 175 3.259064 TGTACAGCTAGTTTTGGCGATC 58.741 45.455 0.00 0.00 35.69 3.69
175 176 3.328382 TGTACAGCTAGTTTTGGCGAT 57.672 42.857 0.00 0.00 35.69 4.58
176 177 2.823924 TGTACAGCTAGTTTTGGCGA 57.176 45.000 0.00 0.00 35.69 5.54
177 178 3.000078 CGTATGTACAGCTAGTTTTGGCG 60.000 47.826 0.33 0.00 35.69 5.69
178 179 3.930848 ACGTATGTACAGCTAGTTTTGGC 59.069 43.478 0.33 0.00 0.00 4.52
179 180 6.146510 TGAAACGTATGTACAGCTAGTTTTGG 59.853 38.462 16.89 0.00 31.57 3.28
180 181 7.112528 TGAAACGTATGTACAGCTAGTTTTG 57.887 36.000 16.89 0.00 31.57 2.44
181 182 7.718272 TTGAAACGTATGTACAGCTAGTTTT 57.282 32.000 16.89 6.40 31.57 2.43
182 183 7.718272 TTTGAAACGTATGTACAGCTAGTTT 57.282 32.000 16.21 16.21 33.71 2.66
183 184 7.718272 TTTTGAAACGTATGTACAGCTAGTT 57.282 32.000 0.33 2.53 0.00 2.24
184 185 7.718272 TTTTTGAAACGTATGTACAGCTAGT 57.282 32.000 0.33 0.00 0.00 2.57
208 209 5.302360 TGCTCCGATGTACAACTAGTTTTT 58.698 37.500 5.07 0.00 0.00 1.94
219 220 4.217754 TGTTTTGTTTGCTCCGATGTAC 57.782 40.909 0.00 0.00 0.00 2.90
225 226 2.979813 GCATACTGTTTTGTTTGCTCCG 59.020 45.455 0.00 0.00 40.19 4.63
438 439 3.584848 AGGCGATATCCTTCTTTGGCTAT 59.415 43.478 0.00 0.00 30.82 2.97
442 443 1.876156 GCAGGCGATATCCTTCTTTGG 59.124 52.381 0.00 0.00 33.25 3.28
568 599 3.219224 GCTGAGGAGCAGGAGGAG 58.781 66.667 0.00 0.00 45.46 3.69
576 607 1.227118 GCTAGAACGGCTGAGGAGC 60.227 63.158 0.00 0.00 45.40 4.70
632 666 4.596180 CGCCATTGACATCGCCGC 62.596 66.667 0.00 0.00 0.00 6.53
643 677 0.827507 AAAACCAGCACTCCGCCATT 60.828 50.000 0.00 0.00 44.04 3.16
659 693 3.059386 GGCCGGCGACATGGAAAA 61.059 61.111 22.54 0.00 0.00 2.29
740 777 5.012148 AGGACGCAGGTTTAGAGCAATATAT 59.988 40.000 0.00 0.00 0.00 0.86
741 778 4.344102 AGGACGCAGGTTTAGAGCAATATA 59.656 41.667 0.00 0.00 0.00 0.86
742 779 3.134804 AGGACGCAGGTTTAGAGCAATAT 59.865 43.478 0.00 0.00 0.00 1.28
821 865 8.245195 TGGAAGGCTAAAATTTTGTTAAGACT 57.755 30.769 13.76 7.29 0.00 3.24
825 869 8.030106 CGGTATGGAAGGCTAAAATTTTGTTAA 58.970 33.333 13.76 0.00 0.00 2.01
837 881 2.057137 ACGTACGGTATGGAAGGCTA 57.943 50.000 21.06 0.00 0.00 3.93
859 903 4.106029 TCAGAAATGCGGACTACTACAC 57.894 45.455 0.00 0.00 0.00 2.90
882 926 1.228459 GGGAAGGCTCGGGTTTGTT 60.228 57.895 0.00 0.00 0.00 2.83
888 932 1.632018 TATTGTGGGGAAGGCTCGGG 61.632 60.000 0.00 0.00 0.00 5.14
922 966 4.338379 AGCTTTTACTCCATCGGATACC 57.662 45.455 0.00 0.00 0.00 2.73
924 968 5.981315 CGTTAAGCTTTTACTCCATCGGATA 59.019 40.000 3.20 0.00 0.00 2.59
925 969 4.809426 CGTTAAGCTTTTACTCCATCGGAT 59.191 41.667 3.20 0.00 0.00 4.18
926 970 4.178540 CGTTAAGCTTTTACTCCATCGGA 58.821 43.478 3.20 0.00 0.00 4.55
927 971 3.308866 CCGTTAAGCTTTTACTCCATCGG 59.691 47.826 3.20 1.02 0.00 4.18
928 972 4.178540 TCCGTTAAGCTTTTACTCCATCG 58.821 43.478 3.20 0.00 0.00 3.84
929 973 4.571176 CCTCCGTTAAGCTTTTACTCCATC 59.429 45.833 3.20 0.00 0.00 3.51
930 974 4.514401 CCTCCGTTAAGCTTTTACTCCAT 58.486 43.478 3.20 0.00 0.00 3.41
931 975 3.307199 CCCTCCGTTAAGCTTTTACTCCA 60.307 47.826 3.20 0.00 0.00 3.86
932 976 3.268330 CCCTCCGTTAAGCTTTTACTCC 58.732 50.000 3.20 0.00 0.00 3.85
933 977 2.676839 GCCCTCCGTTAAGCTTTTACTC 59.323 50.000 3.20 0.00 0.00 2.59
934 978 2.305052 AGCCCTCCGTTAAGCTTTTACT 59.695 45.455 3.20 0.00 29.27 2.24
935 979 2.708051 AGCCCTCCGTTAAGCTTTTAC 58.292 47.619 3.20 2.59 29.27 2.01
936 980 3.008704 AGAAGCCCTCCGTTAAGCTTTTA 59.991 43.478 3.20 0.00 45.20 1.52
937 981 2.160205 GAAGCCCTCCGTTAAGCTTTT 58.840 47.619 3.20 0.00 45.20 2.27
940 984 0.250513 CAGAAGCCCTCCGTTAAGCT 59.749 55.000 0.00 0.00 37.10 3.74
941 985 0.744771 CCAGAAGCCCTCCGTTAAGC 60.745 60.000 0.00 0.00 0.00 3.09
942 986 0.107654 CCCAGAAGCCCTCCGTTAAG 60.108 60.000 0.00 0.00 0.00 1.85
943 987 1.988015 CCCAGAAGCCCTCCGTTAA 59.012 57.895 0.00 0.00 0.00 2.01
945 989 4.035102 GCCCAGAAGCCCTCCGTT 62.035 66.667 0.00 0.00 0.00 4.44
948 992 3.011517 TGAGCCCAGAAGCCCTCC 61.012 66.667 0.00 0.00 0.00 4.30
949 993 1.992277 TCTGAGCCCAGAAGCCCTC 60.992 63.158 0.00 0.00 45.74 4.30
1039 1319 2.492090 CGAGGCAGGAGAACGGAG 59.508 66.667 0.00 0.00 0.00 4.63
1390 5084 3.144871 ATCGTCGACCATCGCCCA 61.145 61.111 10.58 0.00 40.21 5.36
1427 5121 2.812178 CGGGCGGGTACGTGAAAG 60.812 66.667 0.00 0.00 43.45 2.62
1526 5243 3.118454 CATTGGGCTTCGCGTCGT 61.118 61.111 5.77 0.00 0.00 4.34
1659 5376 2.045634 GCATGCACAGCTCCTCCA 60.046 61.111 14.21 0.00 0.00 3.86
1690 5407 5.647658 TCCTATTGAACAAACTCATCGCATT 59.352 36.000 0.00 0.00 0.00 3.56
1733 5450 1.262417 CAATGATCACCGAATCAGCCG 59.738 52.381 0.00 0.00 38.96 5.52
1850 5575 4.572985 TCAACCAGAGCATTTGAAACAG 57.427 40.909 0.00 0.00 0.00 3.16
1990 6179 3.609103 AAACAAACTGACACTCGCATC 57.391 42.857 0.00 0.00 0.00 3.91
2142 6331 2.027653 GCTCCCTAGAAACTTGCTCTGT 60.028 50.000 0.00 0.00 0.00 3.41
2514 6706 6.513066 GCTCTGTCATCAGCTGAAAAATATCC 60.513 42.308 22.50 3.30 41.10 2.59
2592 6784 6.808008 AATACCATTATGGCTTGATCTTCG 57.192 37.500 11.72 0.00 42.67 3.79
2611 6803 9.334947 TCCATCTCTCTTCATTTGATCAAATAC 57.665 33.333 28.61 0.00 38.84 1.89
2704 6896 4.503123 GGAATTGTAAAAGTGCAAGCCCTT 60.503 41.667 0.00 0.00 32.50 3.95
2722 6914 8.635765 ATGTTGTAGTCTTGTAACATGGAATT 57.364 30.769 0.00 0.00 40.93 2.17
2806 6998 3.411446 TGAACTTCCAAGCATCGTCAAT 58.589 40.909 0.00 0.00 0.00 2.57
2839 7031 0.837272 TCTATTTCTGCCCCTTCCCG 59.163 55.000 0.00 0.00 0.00 5.14
2848 7040 5.506982 GGCATCCAAGAACATCTATTTCTGC 60.507 44.000 0.00 0.00 33.46 4.26
2907 7099 3.240069 GTTTGCAACTAGCTCAGCAATG 58.760 45.455 13.45 0.00 45.23 2.82
2928 7120 6.094603 CACTGGGGTTCTTCTCAAATATTCTG 59.905 42.308 0.00 0.00 0.00 3.02
2940 7132 2.409948 CAGGATCACTGGGGTTCTTC 57.590 55.000 0.00 0.00 43.70 2.87
2985 7177 2.292569 CCACATTCCAGCATCAGCATAC 59.707 50.000 0.00 0.00 45.49 2.39
3076 7268 6.117975 ACTTAGGGTCCGATCAACTTAAAA 57.882 37.500 0.00 0.00 0.00 1.52
3089 7281 1.742750 GCGATCCACAACTTAGGGTCC 60.743 57.143 0.00 0.00 31.08 4.46
3101 7293 8.709386 AAGACTGATTAATATATGCGATCCAC 57.291 34.615 0.00 0.00 0.00 4.02
3124 7316 7.497925 AGTGCTTCTCTTGGTTTAGTAAAAG 57.502 36.000 0.00 0.00 0.00 2.27
3144 7336 2.769893 TCCTAACCAAACCGTTAGTGC 58.230 47.619 7.50 0.00 42.40 4.40
3151 7343 4.763279 AGGTGTATTTTCCTAACCAAACCG 59.237 41.667 0.00 0.00 33.13 4.44
3319 9677 2.492088 TCTCTGACATACGTTCCCACAG 59.508 50.000 0.00 0.00 0.00 3.66
3322 9680 3.322541 TGTTTCTCTGACATACGTTCCCA 59.677 43.478 0.00 0.00 0.00 4.37
3327 9685 3.944055 AGCTGTTTCTCTGACATACGT 57.056 42.857 0.00 0.00 0.00 3.57
3328 9686 4.795795 CAGTAGCTGTTTCTCTGACATACG 59.204 45.833 0.00 0.00 0.00 3.06
3345 9708 1.999024 GAGCTTGCTGAAGACAGTAGC 59.001 52.381 0.00 13.91 45.21 3.58
3438 9802 6.770785 AGTCCAAAGAAGTACAATGCACTAAA 59.229 34.615 0.00 0.00 0.00 1.85
3461 9908 2.439409 TGCAGCAATGCACTAATGAGT 58.561 42.857 8.35 0.00 40.23 3.41
3483 9931 2.293677 TGCATAAGACTGCAGGTACG 57.706 50.000 19.93 0.80 46.76 3.67
3545 10125 7.590279 TCTAACCTTAAACAAATTAGCACAGC 58.410 34.615 0.00 0.00 0.00 4.40
3637 10217 1.067635 GCATACCAAAACAGGCCTGTG 60.068 52.381 38.35 26.86 44.13 3.66
3638 10218 6.538281 GTTTGCATACCAAAACAGGCCTGT 62.538 45.833 33.20 33.20 44.48 4.00
3642 10222 3.385193 AGTTTGCATACCAAAACAGGC 57.615 42.857 3.47 0.00 44.48 4.85
3701 10282 2.158623 ACAGATCAGGTTGCCAACAGAA 60.159 45.455 10.18 0.00 0.00 3.02
3704 10285 2.158623 AGAACAGATCAGGTTGCCAACA 60.159 45.455 10.18 0.00 0.00 3.33
3708 10289 3.065925 GCATAAGAACAGATCAGGTTGCC 59.934 47.826 7.42 0.00 0.00 4.52
3716 10297 8.857216 CAAAGAAAATGTGCATAAGAACAGATC 58.143 33.333 0.00 0.00 36.53 2.75
3726 10307 8.526978 TGCTAATTACCAAAGAAAATGTGCATA 58.473 29.630 0.00 0.00 0.00 3.14
3732 10313 9.090692 CAATCCTGCTAATTACCAAAGAAAATG 57.909 33.333 0.00 0.00 0.00 2.32
3750 10331 4.919754 GTGAAGTCATGAAAACAATCCTGC 59.080 41.667 0.00 0.00 0.00 4.85
3784 10365 8.827177 TGCCATTAGCTGTACATTATAGTAAC 57.173 34.615 0.00 0.00 44.23 2.50
3790 10371 9.519191 TTTATCATGCCATTAGCTGTACATTAT 57.481 29.630 0.00 0.00 44.23 1.28
3803 10384 9.772605 TCCCTTATAATGATTTATCATGCCATT 57.227 29.630 6.01 0.00 46.22 3.16
3804 10385 9.772605 TTCCCTTATAATGATTTATCATGCCAT 57.227 29.630 6.01 3.82 46.22 4.40
3823 10404 9.974980 GAAGTATCATTTTGTTTTGTTCCCTTA 57.025 29.630 0.00 0.00 0.00 2.69
3824 10405 8.704668 AGAAGTATCATTTTGTTTTGTTCCCTT 58.295 29.630 0.00 0.00 0.00 3.95
3825 10406 8.143835 CAGAAGTATCATTTTGTTTTGTTCCCT 58.856 33.333 0.00 0.00 0.00 4.20
3826 10407 8.141268 TCAGAAGTATCATTTTGTTTTGTTCCC 58.859 33.333 0.00 0.00 0.00 3.97
3827 10408 9.185192 CTCAGAAGTATCATTTTGTTTTGTTCC 57.815 33.333 0.00 0.00 0.00 3.62
3829 10410 8.416329 AGCTCAGAAGTATCATTTTGTTTTGTT 58.584 29.630 0.00 0.00 0.00 2.83
3830 10411 7.945134 AGCTCAGAAGTATCATTTTGTTTTGT 58.055 30.769 0.00 0.00 0.00 2.83
3831 10412 8.077991 TGAGCTCAGAAGTATCATTTTGTTTTG 58.922 33.333 13.74 0.00 0.00 2.44
3832 10413 8.169977 TGAGCTCAGAAGTATCATTTTGTTTT 57.830 30.769 13.74 0.00 0.00 2.43
3849 10430 2.235650 TCTGGAAATCACCTGAGCTCAG 59.764 50.000 32.84 32.84 43.40 3.35
3871 10452 1.502163 AAGTCTGACTGCGCTGCAAC 61.502 55.000 11.71 12.62 38.41 4.17
3874 10455 0.948141 AAGAAGTCTGACTGCGCTGC 60.948 55.000 11.71 7.89 0.00 5.25
3924 10505 6.394025 ACTTCAGATTAGTAGATCGGGAAC 57.606 41.667 0.00 0.00 0.00 3.62
3939 10520 7.040409 GGGTGTCACATAAAAAGAACTTCAGAT 60.040 37.037 5.12 0.00 0.00 2.90
3981 10565 5.547465 TGATGTTTCTTCCGAACACTACAT 58.453 37.500 0.00 0.00 32.43 2.29
3983 10567 5.235616 TGTTGATGTTTCTTCCGAACACTAC 59.764 40.000 0.00 0.00 0.00 2.73
3988 10572 3.555518 GCTGTTGATGTTTCTTCCGAAC 58.444 45.455 0.00 0.00 0.00 3.95
4002 10586 0.550914 AACTTGGACTGGGCTGTTGA 59.449 50.000 0.00 0.00 0.00 3.18
4008 10592 0.818040 ACGTCAAACTTGGACTGGGC 60.818 55.000 0.00 0.00 33.11 5.36
4009 10593 1.226746 GACGTCAAACTTGGACTGGG 58.773 55.000 11.55 0.00 33.11 4.45
4044 10628 6.863126 GCCCCATATTTTCTTATGAAACATCG 59.137 38.462 3.41 0.00 41.34 3.84
4052 10636 6.839124 TGCATAGCCCCATATTTTCTTATG 57.161 37.500 0.00 0.00 0.00 1.90
4053 10637 9.719433 AATATGCATAGCCCCATATTTTCTTAT 57.281 29.630 12.79 0.00 40.07 1.73
4054 10638 8.970020 CAATATGCATAGCCCCATATTTTCTTA 58.030 33.333 12.79 0.00 40.68 2.10


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

AutoCloner maintained by Alex Coulton.