Multiple sequence alignment - TraesCS2A01G395500

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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 TraesCS2A01G395500 chr2A 100.000 2649 0 0 1 2649 648340470 648343118 0.000000e+00 4892.0
1 TraesCS2A01G395500 chr2B 87.092 1379 82 39 184 1490 590917864 590919218 0.000000e+00 1472.0
2 TraesCS2A01G395500 chr2B 92.495 533 19 5 1482 2014 590919554 590920065 0.000000e+00 743.0
3 TraesCS2A01G395500 chr2B 85.987 157 22 0 3 159 410436160 410436316 4.530000e-38 169.0
4 TraesCS2A01G395500 chr2D 91.260 984 39 20 533 1490 502929250 502930212 0.000000e+00 1297.0
5 TraesCS2A01G395500 chr2D 88.851 592 20 12 1482 2067 502930555 502931106 0.000000e+00 686.0
6 TraesCS2A01G395500 chr2D 83.913 460 66 6 2177 2630 502931413 502931870 1.460000e-117 433.0
7 TraesCS2A01G395500 chr6B 77.500 400 62 21 1115 1491 479299704 479300098 5.740000e-52 215.0
8 TraesCS2A01G395500 chr6D 77.330 397 60 24 1123 1493 341117433 341117041 9.610000e-50 207.0
9 TraesCS2A01G395500 chr4A 87.261 157 20 0 3 159 736531434 736531278 2.090000e-41 180.0
10 TraesCS2A01G395500 chr3A 87.261 157 20 0 3 159 129473928 129473772 2.090000e-41 180.0
11 TraesCS2A01G395500 chr3A 81.169 154 24 4 2065 2216 13542938 13542788 4.630000e-23 119.0
12 TraesCS2A01G395500 chr7B 86.709 158 19 2 3 159 645603002 645602846 9.750000e-40 174.0
13 TraesCS2A01G395500 chr7B 83.704 135 14 6 2061 2194 276734854 276734981 1.290000e-23 121.0
14 TraesCS2A01G395500 chr1B 86.624 157 21 0 3 159 621352267 621352423 9.750000e-40 174.0
15 TraesCS2A01G395500 chr3B 86.624 157 20 1 3 159 823595433 823595278 3.510000e-39 172.0
16 TraesCS2A01G395500 chr3B 77.586 174 31 6 2063 2231 145019804 145019634 6.030000e-17 99.0
17 TraesCS2A01G395500 chr4D 85.542 166 20 3 2065 2230 474951654 474951815 1.260000e-38 171.0
18 TraesCS2A01G395500 chr4D 87.719 57 6 1 2174 2230 488741004 488741059 6.120000e-07 65.8
19 TraesCS2A01G395500 chr5D 85.987 157 22 0 3 159 440804802 440804646 4.530000e-38 169.0
20 TraesCS2A01G395500 chr3D 85.987 157 22 0 3 159 55974359 55974515 4.530000e-38 169.0
21 TraesCS2A01G395500 chr1D 85.987 157 22 0 3 159 272313635 272313791 4.530000e-38 169.0
22 TraesCS2A01G395500 chr4B 82.895 152 22 3 2065 2215 27800099 27800247 1.650000e-27 134.0
23 TraesCS2A01G395500 chr6A 81.579 152 23 3 2065 2216 12080188 12080042 1.290000e-23 121.0
24 TraesCS2A01G395500 chrUn 87.302 63 5 3 2170 2231 334710683 334710623 4.730000e-08 69.4
25 TraesCS2A01G395500 chr5B 86.885 61 7 1 2170 2230 486364726 486364667 1.700000e-07 67.6


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 TraesCS2A01G395500 chr2A 648340470 648343118 2648 False 4892.000000 4892 100.0000 1 2649 1 chr2A.!!$F1 2648
1 TraesCS2A01G395500 chr2B 590917864 590920065 2201 False 1107.500000 1472 89.7935 184 2014 2 chr2B.!!$F2 1830
2 TraesCS2A01G395500 chr2D 502929250 502931870 2620 False 805.333333 1297 88.0080 533 2630 3 chr2D.!!$F1 2097

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
162 163 0.039035 AGCGTTAAATTCTGGGGCCA 59.961 50.0 4.39 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 2131 0.03496 GAGAAGGAGCAAAGGGACCC 60.035 60.0 0.59 0.59 0.0 4.46 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.403252 TTCTTCCAGAATCGAAGCCC 57.597 50.000 0.00 0.00 37.29 5.19
24 25 1.573108 TCTTCCAGAATCGAAGCCCT 58.427 50.000 0.00 0.00 37.29 5.19
25 26 1.482593 TCTTCCAGAATCGAAGCCCTC 59.517 52.381 0.00 0.00 37.29 4.30
26 27 0.541863 TTCCAGAATCGAAGCCCTCC 59.458 55.000 0.00 0.00 0.00 4.30
27 28 1.147153 CCAGAATCGAAGCCCTCCC 59.853 63.158 0.00 0.00 0.00 4.30
28 29 1.147153 CAGAATCGAAGCCCTCCCC 59.853 63.158 0.00 0.00 0.00 4.81
29 30 1.306997 AGAATCGAAGCCCTCCCCA 60.307 57.895 0.00 0.00 0.00 4.96
30 31 1.147153 GAATCGAAGCCCTCCCCAG 59.853 63.158 0.00 0.00 0.00 4.45
31 32 2.949705 GAATCGAAGCCCTCCCCAGC 62.950 65.000 0.00 0.00 0.00 4.85
32 33 4.722535 TCGAAGCCCTCCCCAGCT 62.723 66.667 0.00 0.00 42.40 4.24
35 36 2.204213 AAGCCCTCCCCAGCTTCT 60.204 61.111 0.00 0.00 46.11 2.85
36 37 1.854507 AAGCCCTCCCCAGCTTCTT 60.855 57.895 0.00 0.00 46.11 2.52
37 38 1.857638 AAGCCCTCCCCAGCTTCTTC 61.858 60.000 0.00 0.00 46.11 2.87
38 39 2.304831 GCCCTCCCCAGCTTCTTCT 61.305 63.158 0.00 0.00 0.00 2.85
39 40 0.983378 GCCCTCCCCAGCTTCTTCTA 60.983 60.000 0.00 0.00 0.00 2.10
40 41 1.127343 CCCTCCCCAGCTTCTTCTAG 58.873 60.000 0.00 0.00 0.00 2.43
41 42 1.343478 CCCTCCCCAGCTTCTTCTAGA 60.343 57.143 0.00 0.00 0.00 2.43
42 43 2.472029 CCTCCCCAGCTTCTTCTAGAA 58.528 52.381 4.81 4.81 32.50 2.10
43 44 3.044894 CCTCCCCAGCTTCTTCTAGAAT 58.955 50.000 5.44 0.00 33.13 2.40
44 45 3.070878 CCTCCCCAGCTTCTTCTAGAATC 59.929 52.174 5.44 0.00 33.13 2.52
45 46 3.966665 CTCCCCAGCTTCTTCTAGAATCT 59.033 47.826 5.44 0.00 33.13 2.40
46 47 4.366267 TCCCCAGCTTCTTCTAGAATCTT 58.634 43.478 5.44 0.00 33.13 2.40
47 48 4.407296 TCCCCAGCTTCTTCTAGAATCTTC 59.593 45.833 5.44 0.00 33.13 2.87
48 49 4.367450 CCCAGCTTCTTCTAGAATCTTCG 58.633 47.826 5.44 0.00 33.13 3.79
49 50 4.098654 CCCAGCTTCTTCTAGAATCTTCGA 59.901 45.833 5.44 0.00 33.13 3.71
50 51 5.280945 CCAGCTTCTTCTAGAATCTTCGAG 58.719 45.833 5.44 0.00 33.13 4.04
51 52 4.739716 CAGCTTCTTCTAGAATCTTCGAGC 59.260 45.833 5.44 9.12 33.13 5.03
52 53 4.048504 GCTTCTTCTAGAATCTTCGAGCC 58.951 47.826 5.44 0.00 33.13 4.70
53 54 4.202111 GCTTCTTCTAGAATCTTCGAGCCT 60.202 45.833 5.44 0.00 33.13 4.58
54 55 5.508200 TTCTTCTAGAATCTTCGAGCCTC 57.492 43.478 5.44 0.00 31.09 4.70
55 56 4.527944 TCTTCTAGAATCTTCGAGCCTCA 58.472 43.478 5.44 0.00 31.09 3.86
56 57 5.136828 TCTTCTAGAATCTTCGAGCCTCAT 58.863 41.667 5.44 0.00 31.09 2.90
57 58 5.596361 TCTTCTAGAATCTTCGAGCCTCATT 59.404 40.000 5.44 0.00 31.09 2.57
58 59 5.860941 TCTAGAATCTTCGAGCCTCATTT 57.139 39.130 0.00 0.00 31.09 2.32
59 60 5.595885 TCTAGAATCTTCGAGCCTCATTTG 58.404 41.667 0.00 0.00 31.09 2.32
60 61 4.213564 AGAATCTTCGAGCCTCATTTGT 57.786 40.909 0.00 0.00 0.00 2.83
61 62 4.583871 AGAATCTTCGAGCCTCATTTGTT 58.416 39.130 0.00 0.00 0.00 2.83
62 63 5.006386 AGAATCTTCGAGCCTCATTTGTTT 58.994 37.500 0.00 0.00 0.00 2.83
63 64 5.474876 AGAATCTTCGAGCCTCATTTGTTTT 59.525 36.000 0.00 0.00 0.00 2.43
64 65 6.655003 AGAATCTTCGAGCCTCATTTGTTTTA 59.345 34.615 0.00 0.00 0.00 1.52
65 66 5.607119 TCTTCGAGCCTCATTTGTTTTAC 57.393 39.130 0.00 0.00 0.00 2.01
66 67 5.060506 TCTTCGAGCCTCATTTGTTTTACA 58.939 37.500 0.00 0.00 0.00 2.41
67 68 5.529430 TCTTCGAGCCTCATTTGTTTTACAA 59.471 36.000 0.00 0.00 36.11 2.41
68 69 5.957842 TCGAGCCTCATTTGTTTTACAAT 57.042 34.783 0.00 0.00 38.00 2.71
69 70 5.938322 TCGAGCCTCATTTGTTTTACAATC 58.062 37.500 0.00 0.00 38.00 2.67
70 71 5.095490 CGAGCCTCATTTGTTTTACAATCC 58.905 41.667 0.00 0.00 38.00 3.01
71 72 5.106157 CGAGCCTCATTTGTTTTACAATCCT 60.106 40.000 0.00 0.00 38.00 3.24
72 73 6.093495 CGAGCCTCATTTGTTTTACAATCCTA 59.907 38.462 0.00 0.00 38.00 2.94
73 74 7.201732 CGAGCCTCATTTGTTTTACAATCCTAT 60.202 37.037 0.00 0.00 38.00 2.57
74 75 8.000780 AGCCTCATTTGTTTTACAATCCTATC 57.999 34.615 0.00 0.00 38.00 2.08
75 76 7.836183 AGCCTCATTTGTTTTACAATCCTATCT 59.164 33.333 0.00 0.00 38.00 1.98
76 77 9.120538 GCCTCATTTGTTTTACAATCCTATCTA 57.879 33.333 0.00 0.00 38.00 1.98
116 117 8.063200 AGTTAGTATTGTAAAAAGAATGGGGC 57.937 34.615 0.00 0.00 0.00 5.80
117 118 7.893833 AGTTAGTATTGTAAAAAGAATGGGGCT 59.106 33.333 0.00 0.00 0.00 5.19
118 119 6.775594 AGTATTGTAAAAAGAATGGGGCTC 57.224 37.500 0.00 0.00 0.00 4.70
119 120 6.252995 AGTATTGTAAAAAGAATGGGGCTCA 58.747 36.000 0.00 0.00 0.00 4.26
120 121 6.723977 AGTATTGTAAAAAGAATGGGGCTCAA 59.276 34.615 0.00 0.00 0.00 3.02
121 122 5.878406 TTGTAAAAAGAATGGGGCTCAAA 57.122 34.783 0.00 0.00 0.00 2.69
122 123 5.467035 TGTAAAAAGAATGGGGCTCAAAG 57.533 39.130 0.00 0.00 0.00 2.77
123 124 5.144100 TGTAAAAAGAATGGGGCTCAAAGA 58.856 37.500 0.00 0.00 0.00 2.52
124 125 5.779771 TGTAAAAAGAATGGGGCTCAAAGAT 59.220 36.000 0.00 0.00 0.00 2.40
125 126 5.830799 AAAAAGAATGGGGCTCAAAGATT 57.169 34.783 0.00 0.00 0.00 2.40
126 127 5.411831 AAAAGAATGGGGCTCAAAGATTC 57.588 39.130 0.00 0.00 0.00 2.52
127 128 4.328118 AAGAATGGGGCTCAAAGATTCT 57.672 40.909 0.00 0.00 35.38 2.40
128 129 3.629087 AGAATGGGGCTCAAAGATTCTG 58.371 45.455 0.26 0.00 33.19 3.02
129 130 2.449137 ATGGGGCTCAAAGATTCTGG 57.551 50.000 0.00 0.00 0.00 3.86
130 131 0.332632 TGGGGCTCAAAGATTCTGGG 59.667 55.000 0.00 0.00 0.00 4.45
131 132 0.625849 GGGGCTCAAAGATTCTGGGA 59.374 55.000 0.00 0.00 0.00 4.37
132 133 1.409381 GGGGCTCAAAGATTCTGGGAG 60.409 57.143 9.42 9.42 0.00 4.30
133 134 1.561542 GGGCTCAAAGATTCTGGGAGA 59.438 52.381 15.41 0.14 0.00 3.71
134 135 2.025887 GGGCTCAAAGATTCTGGGAGAA 60.026 50.000 15.41 0.00 38.78 2.87
135 136 3.277715 GGCTCAAAGATTCTGGGAGAAG 58.722 50.000 15.41 0.00 37.69 2.85
136 137 2.682352 GCTCAAAGATTCTGGGAGAAGC 59.318 50.000 15.41 0.00 40.68 3.86
142 143 3.902881 GATTCTGGGAGAAGCTGAGAA 57.097 47.619 0.00 0.00 37.62 2.87
143 144 4.213564 GATTCTGGGAGAAGCTGAGAAA 57.786 45.455 0.00 0.00 37.62 2.52
144 145 3.692257 TTCTGGGAGAAGCTGAGAAAG 57.308 47.619 0.00 0.00 29.50 2.62
157 158 4.406943 GCTGAGAAAGCGTTAAATTCTGG 58.593 43.478 0.00 0.00 43.45 3.86
158 159 4.672801 GCTGAGAAAGCGTTAAATTCTGGG 60.673 45.833 0.00 0.00 43.45 4.45
159 160 3.756434 TGAGAAAGCGTTAAATTCTGGGG 59.244 43.478 0.00 0.00 33.73 4.96
160 161 2.492088 AGAAAGCGTTAAATTCTGGGGC 59.508 45.455 0.00 0.00 32.42 5.80
161 162 1.182667 AAGCGTTAAATTCTGGGGCC 58.817 50.000 0.00 0.00 0.00 5.80
162 163 0.039035 AGCGTTAAATTCTGGGGCCA 59.961 50.000 4.39 0.00 0.00 5.36
163 164 1.111277 GCGTTAAATTCTGGGGCCAT 58.889 50.000 4.39 0.00 0.00 4.40
164 165 1.067060 GCGTTAAATTCTGGGGCCATC 59.933 52.381 4.39 0.00 0.00 3.51
165 166 2.654863 CGTTAAATTCTGGGGCCATCT 58.345 47.619 4.39 0.00 0.00 2.90
166 167 3.023832 CGTTAAATTCTGGGGCCATCTT 58.976 45.455 4.39 0.00 0.00 2.40
167 168 3.181487 CGTTAAATTCTGGGGCCATCTTG 60.181 47.826 4.39 0.00 0.00 3.02
168 169 1.197812 AAATTCTGGGGCCATCTTGC 58.802 50.000 4.39 0.00 0.00 4.01
175 176 2.283821 GGCCATCTTGCCCACCAA 60.284 61.111 0.00 0.00 46.11 3.67
176 177 1.912763 GGCCATCTTGCCCACCAAA 60.913 57.895 0.00 0.00 46.11 3.28
177 178 1.266867 GGCCATCTTGCCCACCAAAT 61.267 55.000 0.00 0.00 46.11 2.32
178 179 0.614812 GCCATCTTGCCCACCAAATT 59.385 50.000 0.00 0.00 31.94 1.82
179 180 1.830477 GCCATCTTGCCCACCAAATTA 59.170 47.619 0.00 0.00 31.94 1.40
180 181 2.159057 GCCATCTTGCCCACCAAATTAG 60.159 50.000 0.00 0.00 31.94 1.73
181 182 2.159057 CCATCTTGCCCACCAAATTAGC 60.159 50.000 0.00 0.00 31.94 3.09
182 183 1.555967 TCTTGCCCACCAAATTAGCC 58.444 50.000 0.00 0.00 31.94 3.93
186 187 2.264455 TGCCCACCAAATTAGCCAATT 58.736 42.857 0.00 0.00 35.84 2.32
195 196 6.980397 CACCAAATTAGCCAATTAGGTCAATC 59.020 38.462 0.00 0.00 40.61 2.67
199 200 7.732222 AATTAGCCAATTAGGTCAATCCAAA 57.268 32.000 0.00 0.00 40.61 3.28
202 203 5.522641 AGCCAATTAGGTCAATCCAAAGAT 58.477 37.500 0.00 0.00 40.61 2.40
205 206 6.127366 GCCAATTAGGTCAATCCAAAGATTCA 60.127 38.462 0.00 0.00 39.19 2.57
206 207 7.418254 GCCAATTAGGTCAATCCAAAGATTCAT 60.418 37.037 0.00 0.00 39.19 2.57
211 212 5.776716 AGGTCAATCCAAAGATTCATGTTGT 59.223 36.000 0.00 0.00 40.89 3.32
217 218 4.278170 TCCAAAGATTCATGTTGTCCACAC 59.722 41.667 0.00 0.00 38.61 3.82
219 220 2.426522 AGATTCATGTTGTCCACACGG 58.573 47.619 0.00 0.00 38.61 4.94
223 224 0.867746 CATGTTGTCCACACGGTGAG 59.132 55.000 16.29 6.89 38.61 3.51
228 229 3.923864 TCCACACGGTGAGCGCTT 61.924 61.111 13.26 0.00 35.23 4.68
230 231 2.094659 CCACACGGTGAGCGCTTAG 61.095 63.158 13.26 6.07 35.23 2.18
234 235 1.200483 CACGGTGAGCGCTTAGTATG 58.800 55.000 13.26 4.28 0.00 2.39
238 240 3.119388 ACGGTGAGCGCTTAGTATGTTTA 60.119 43.478 13.26 0.00 0.00 2.01
245 247 3.787826 CGCTTAGTATGTTTAGCATGCG 58.212 45.455 13.01 0.00 43.61 4.73
248 250 4.035208 GCTTAGTATGTTTAGCATGCGGTT 59.965 41.667 13.01 0.00 43.61 4.44
252 254 8.890124 TTAGTATGTTTAGCATGCGGTTAATA 57.110 30.769 13.01 6.69 43.61 0.98
254 256 8.391075 AGTATGTTTAGCATGCGGTTAATATT 57.609 30.769 13.01 3.80 43.61 1.28
310 312 4.426736 TGAGAATCTATCAATGCCAGCA 57.573 40.909 0.00 0.00 34.92 4.41
315 317 5.996513 AGAATCTATCAATGCCAGCACTAAG 59.003 40.000 0.00 0.00 0.00 2.18
320 322 7.606349 TCTATCAATGCCAGCACTAAGTATAG 58.394 38.462 0.00 0.00 35.14 1.31
322 324 6.425210 TCAATGCCAGCACTAAGTATAGAT 57.575 37.500 0.00 0.00 33.15 1.98
324 326 7.282585 TCAATGCCAGCACTAAGTATAGATTT 58.717 34.615 0.00 0.00 33.15 2.17
325 327 8.428852 TCAATGCCAGCACTAAGTATAGATTTA 58.571 33.333 0.00 0.00 33.15 1.40
356 358 9.686683 GCATAAATAACATCCCACCTAATATCT 57.313 33.333 0.00 0.00 0.00 1.98
370 372 7.931407 CCACCTAATATCTGTGTGCAACTAATA 59.069 37.037 0.00 0.00 38.04 0.98
454 466 8.937884 TCAAAATATCAATGCCTGTGATTTTTG 58.062 29.630 19.37 19.37 40.04 2.44
455 467 8.937884 CAAAATATCAATGCCTGTGATTTTTGA 58.062 29.630 19.94 0.00 40.42 2.69
456 468 8.712285 AAATATCAATGCCTGTGATTTTTGAG 57.288 30.769 8.15 0.00 36.16 3.02
457 469 5.988310 ATCAATGCCTGTGATTTTTGAGA 57.012 34.783 0.00 0.00 31.54 3.27
459 471 6.349243 TCAATGCCTGTGATTTTTGAGAAT 57.651 33.333 0.00 0.00 0.00 2.40
460 472 6.392354 TCAATGCCTGTGATTTTTGAGAATC 58.608 36.000 0.00 0.00 36.73 2.52
485 515 5.375417 TCCAAAATATCTGTGTGCAACTG 57.625 39.130 0.00 0.00 38.04 3.16
486 516 4.218200 TCCAAAATATCTGTGTGCAACTGG 59.782 41.667 0.00 0.00 38.04 4.00
492 522 4.551702 ATCTGTGTGCAACTGGTATACA 57.448 40.909 5.01 0.00 38.04 2.29
493 523 4.551702 TCTGTGTGCAACTGGTATACAT 57.448 40.909 5.01 0.00 38.04 2.29
494 524 4.905429 TCTGTGTGCAACTGGTATACATT 58.095 39.130 5.01 0.00 38.04 2.71
495 525 4.694982 TCTGTGTGCAACTGGTATACATTG 59.305 41.667 5.01 7.21 38.04 2.82
496 526 3.190327 TGTGTGCAACTGGTATACATTGC 59.810 43.478 22.32 22.32 40.66 3.56
497 527 2.752354 TGTGCAACTGGTATACATTGCC 59.248 45.455 24.42 18.81 40.10 4.52
498 528 3.016736 GTGCAACTGGTATACATTGCCT 58.983 45.455 24.42 0.00 40.10 4.75
499 529 4.196193 GTGCAACTGGTATACATTGCCTA 58.804 43.478 24.42 12.29 40.10 3.93
500 530 4.638421 GTGCAACTGGTATACATTGCCTAA 59.362 41.667 24.42 11.80 40.10 2.69
501 531 5.299279 GTGCAACTGGTATACATTGCCTAAT 59.701 40.000 24.42 0.00 40.10 1.73
502 532 5.890985 TGCAACTGGTATACATTGCCTAATT 59.109 36.000 24.42 0.00 40.10 1.40
503 533 6.379703 TGCAACTGGTATACATTGCCTAATTT 59.620 34.615 24.42 0.00 40.10 1.82
504 534 7.093552 TGCAACTGGTATACATTGCCTAATTTT 60.094 33.333 24.42 0.00 40.10 1.82
505 535 7.763985 GCAACTGGTATACATTGCCTAATTTTT 59.236 33.333 20.08 0.00 37.49 1.94
594 659 3.170791 AGGATCAACGTGTGCATCTAG 57.829 47.619 0.00 0.00 0.00 2.43
623 694 4.360405 ATGCACCGGGGTTGGGAC 62.360 66.667 5.12 0.00 0.00 4.46
849 932 2.783288 GGAGTCGGTCATCGGGTCC 61.783 68.421 0.00 0.00 39.77 4.46
911 994 3.179265 CAACCGGACGCACGCTAG 61.179 66.667 9.46 0.00 0.00 3.42
1031 1123 4.562425 ACCACCACCAGCACACCG 62.562 66.667 0.00 0.00 0.00 4.94
1066 1158 1.456518 CTCTCATCCTCCCTGCCGA 60.457 63.158 0.00 0.00 0.00 5.54
1109 1206 3.706373 GGACGCTTCTCCTGGGCA 61.706 66.667 0.00 0.00 0.00 5.36
1110 1207 2.347490 GACGCTTCTCCTGGGCAA 59.653 61.111 0.00 0.00 0.00 4.52
1111 1208 1.743252 GACGCTTCTCCTGGGCAAG 60.743 63.158 0.00 0.00 0.00 4.01
1201 1303 2.043450 CTCCTCCTCCTGCTCGGT 60.043 66.667 0.00 0.00 0.00 4.69
1617 2075 4.844420 CGGAGCTGTGGATCTTCC 57.156 61.111 0.00 0.00 36.96 3.46
1618 2076 2.206635 CGGAGCTGTGGATCTTCCT 58.793 57.895 0.00 0.00 37.46 3.36
1619 2077 0.539051 CGGAGCTGTGGATCTTCCTT 59.461 55.000 0.00 0.00 37.46 3.36
1672 2131 1.135867 CGTTCCGGGTGCAAAATTTG 58.864 50.000 0.00 0.57 0.00 2.32
1700 2160 1.450491 GCTCCTTCTCTTTCCCCGC 60.450 63.158 0.00 0.00 0.00 6.13
1717 2177 3.411351 CGTTGGTCAGGCCGTTCG 61.411 66.667 0.00 0.00 41.21 3.95
1736 2196 2.173382 CCGCTCGGCTTTTCGTTG 59.827 61.111 0.00 0.00 0.00 4.10
1751 2211 7.306632 GGCTTTTCGTTGCATATACTAGTAGTG 60.307 40.741 13.29 10.56 0.00 2.74
1775 2236 7.171337 GTGCAAATTTAGAAAGGCTTCATCAAA 59.829 33.333 0.00 0.00 33.64 2.69
1777 2238 8.385858 GCAAATTTAGAAAGGCTTCATCAAATC 58.614 33.333 0.00 0.00 33.64 2.17
1810 2271 6.315393 TGAGCGTACAAATTTAGGAAGGATTC 59.685 38.462 0.00 0.00 46.67 2.52
1820 2281 6.814954 TTTAGGAAGGATTCTACATCAGCT 57.185 37.500 0.00 0.00 46.56 4.24
1826 2287 4.491675 AGGATTCTACATCAGCTGAGGAT 58.508 43.478 33.21 16.90 0.00 3.24
1827 2288 4.906664 AGGATTCTACATCAGCTGAGGATT 59.093 41.667 33.21 15.51 0.00 3.01
1828 2289 5.369110 AGGATTCTACATCAGCTGAGGATTT 59.631 40.000 33.21 14.77 0.00 2.17
1829 2290 6.060788 GGATTCTACATCAGCTGAGGATTTT 58.939 40.000 33.21 14.41 0.00 1.82
1830 2291 6.545298 GGATTCTACATCAGCTGAGGATTTTT 59.455 38.462 33.21 14.03 0.00 1.94
1831 2292 6.992063 TTCTACATCAGCTGAGGATTTTTC 57.008 37.500 33.21 0.00 0.00 2.29
1832 2293 5.431765 TCTACATCAGCTGAGGATTTTTCC 58.568 41.667 33.21 0.00 0.00 3.13
1878 2339 1.852633 AGTGGCAGGAAATTTAGGCC 58.147 50.000 16.36 16.36 44.82 5.19
1938 2401 7.697691 TCTACTAGTAGTACCGTTGTTATTGC 58.302 38.462 25.58 0.00 34.84 3.56
1939 2402 6.521151 ACTAGTAGTACCGTTGTTATTGCT 57.479 37.500 0.00 0.00 0.00 3.91
1940 2403 7.630242 ACTAGTAGTACCGTTGTTATTGCTA 57.370 36.000 0.00 0.00 0.00 3.49
1941 2404 7.475840 ACTAGTAGTACCGTTGTTATTGCTAC 58.524 38.462 0.00 0.00 0.00 3.58
1942 2405 6.521151 AGTAGTACCGTTGTTATTGCTACT 57.479 37.500 0.00 0.00 34.78 2.57
1943 2406 6.558909 AGTAGTACCGTTGTTATTGCTACTC 58.441 40.000 0.00 0.00 34.61 2.59
2016 2479 9.049050 TGTTCTGGAATGGTAGTAAATTAGGTA 57.951 33.333 0.00 0.00 0.00 3.08
2042 2507 5.859205 ATGAACATATTTGGCCCTTCTTC 57.141 39.130 0.00 0.00 0.00 2.87
2052 2517 2.105134 TGGCCCTTCTTCGAAACTTACA 59.895 45.455 0.00 0.00 0.00 2.41
2074 2539 9.537192 TTACAATACAAAATACTACTCCATCCG 57.463 33.333 0.00 0.00 0.00 4.18
2075 2540 7.788026 ACAATACAAAATACTACTCCATCCGA 58.212 34.615 0.00 0.00 0.00 4.55
2076 2541 8.429641 ACAATACAAAATACTACTCCATCCGAT 58.570 33.333 0.00 0.00 0.00 4.18
2079 2544 7.787725 ACAAAATACTACTCCATCCGATTTC 57.212 36.000 0.00 0.00 0.00 2.17
2080 2545 7.565680 ACAAAATACTACTCCATCCGATTTCT 58.434 34.615 0.00 0.00 0.00 2.52
2081 2546 8.701895 ACAAAATACTACTCCATCCGATTTCTA 58.298 33.333 0.00 0.00 0.00 2.10
2082 2547 9.542462 CAAAATACTACTCCATCCGATTTCTAA 57.458 33.333 0.00 0.00 0.00 2.10
2092 2557 9.929180 CTCCATCCGATTTCTAAATATAAGACA 57.071 33.333 0.00 0.00 0.00 3.41
2159 2698 7.441017 AGACATGCTTTAGAGGATAGATTCAC 58.559 38.462 0.00 0.00 32.09 3.18
2160 2699 6.529220 ACATGCTTTAGAGGATAGATTCACC 58.471 40.000 0.00 0.00 32.09 4.02
2163 2702 5.163301 TGCTTTAGAGGATAGATTCACCCAC 60.163 44.000 0.00 0.00 0.00 4.61
2190 2854 6.869695 TGCTCCGTATGTAGTTTCTTATTGA 58.130 36.000 0.00 0.00 0.00 2.57
2239 2903 8.517323 AGATATGAAGGGAGTATTTTGGATCT 57.483 34.615 0.00 0.00 0.00 2.75
2241 2905 6.581388 ATGAAGGGAGTATTTTGGATCTGA 57.419 37.500 0.00 0.00 0.00 3.27
2268 2932 0.666274 CGACAGACGTAGCCTTTGCA 60.666 55.000 0.00 0.00 37.29 4.08
2272 2936 0.666577 AGACGTAGCCTTTGCACGAC 60.667 55.000 13.48 9.04 41.40 4.34
2280 2944 2.954753 CTTTGCACGACGCCCTGAC 61.955 63.158 0.00 0.00 41.33 3.51
2331 2995 2.887360 GGCTAGGCCGTCGTGTTA 59.113 61.111 4.61 0.00 39.62 2.41
2339 3003 2.818432 AGGCCGTCGTGTTATATCTAGG 59.182 50.000 0.00 0.00 0.00 3.02
2343 3007 3.742882 CCGTCGTGTTATATCTAGGTCGA 59.257 47.826 0.00 0.00 0.00 4.20
2344 3008 4.143158 CCGTCGTGTTATATCTAGGTCGAG 60.143 50.000 0.00 0.00 0.00 4.04
2345 3009 4.666149 CGTCGTGTTATATCTAGGTCGAGC 60.666 50.000 6.48 6.48 0.00 5.03
2348 3012 4.142859 CGTGTTATATCTAGGTCGAGCCTC 60.143 50.000 11.73 0.00 46.96 4.70
2349 3013 4.760715 GTGTTATATCTAGGTCGAGCCTCA 59.239 45.833 11.73 0.00 46.96 3.86
2351 3015 3.799432 ATATCTAGGTCGAGCCTCAGT 57.201 47.619 11.73 0.00 46.96 3.41
2352 3016 1.975660 ATCTAGGTCGAGCCTCAGTC 58.024 55.000 11.73 0.00 46.96 3.51
2360 3024 1.979693 GAGCCTCAGTCCCAGACGT 60.980 63.158 0.00 0.00 37.67 4.34
2361 3025 1.939769 GAGCCTCAGTCCCAGACGTC 61.940 65.000 7.70 7.70 37.67 4.34
2449 3113 6.542821 AGGATAAAATCTGTCCACTTTCACA 58.457 36.000 0.00 0.00 34.42 3.58
2450 3114 6.431234 AGGATAAAATCTGTCCACTTTCACAC 59.569 38.462 0.00 0.00 34.42 3.82
2451 3115 6.206634 GGATAAAATCTGTCCACTTTCACACA 59.793 38.462 0.00 0.00 32.23 3.72
2463 3127 5.509501 CCACTTTCACACAAATTGGTAGCAT 60.510 40.000 0.00 0.00 0.00 3.79
2464 3128 5.984926 CACTTTCACACAAATTGGTAGCATT 59.015 36.000 0.00 0.00 0.00 3.56
2466 3130 3.911868 TCACACAAATTGGTAGCATTGC 58.088 40.909 0.00 0.00 0.00 3.56
2467 3131 3.573538 TCACACAAATTGGTAGCATTGCT 59.426 39.130 16.63 16.63 43.41 3.91
2489 3153 8.867112 TGCTAGTATAATTTCTCGTAAACAGG 57.133 34.615 0.00 0.00 0.00 4.00
2539 3206 7.933396 AGAGGCAAAAATTCCAGAAAAATTTG 58.067 30.769 0.00 9.64 36.65 2.32
2551 3218 5.879777 CCAGAAAAATTTGGTGTTTTGACCT 59.120 36.000 0.00 0.00 36.88 3.85
2565 3232 8.387354 GGTGTTTTGACCTTTTTATGAAAGTTG 58.613 33.333 0.00 0.00 32.69 3.16
2569 3236 5.757886 TGACCTTTTTATGAAAGTTGAGCG 58.242 37.500 0.00 0.00 0.00 5.03
2571 3238 6.002062 ACCTTTTTATGAAAGTTGAGCGAG 57.998 37.500 0.00 0.00 0.00 5.03
2574 3241 6.744537 CCTTTTTATGAAAGTTGAGCGAGATG 59.255 38.462 0.00 0.00 0.00 2.90
2580 3247 1.261480 AGTTGAGCGAGATGTGACCT 58.739 50.000 0.00 0.00 0.00 3.85
2621 3289 8.712228 AAAGATCTGACCTTTTTCCTATTGTT 57.288 30.769 0.00 0.00 30.32 2.83
2622 3290 9.807921 AAAGATCTGACCTTTTTCCTATTGTTA 57.192 29.630 0.00 0.00 30.32 2.41
2630 3298 6.120220 CCTTTTTCCTATTGTTAGGGTCGAT 58.880 40.000 0.00 0.00 44.60 3.59
2631 3299 6.038271 CCTTTTTCCTATTGTTAGGGTCGATG 59.962 42.308 0.00 0.00 44.60 3.84
2632 3300 5.943349 TTTCCTATTGTTAGGGTCGATGA 57.057 39.130 0.00 0.00 44.60 2.92
2633 3301 4.931661 TCCTATTGTTAGGGTCGATGAC 57.068 45.455 0.00 0.00 44.60 3.06
2634 3302 3.317149 TCCTATTGTTAGGGTCGATGACG 59.683 47.826 0.00 0.00 44.60 4.35
2635 3303 2.596904 ATTGTTAGGGTCGATGACGG 57.403 50.000 0.00 0.00 40.21 4.79
2636 3304 1.259609 TTGTTAGGGTCGATGACGGT 58.740 50.000 0.00 0.00 40.21 4.83
2637 3305 2.127271 TGTTAGGGTCGATGACGGTA 57.873 50.000 0.00 0.00 40.21 4.02
2638 3306 2.658285 TGTTAGGGTCGATGACGGTAT 58.342 47.619 0.00 0.00 40.21 2.73
2639 3307 2.359848 TGTTAGGGTCGATGACGGTATG 59.640 50.000 0.00 0.00 40.21 2.39
2640 3308 1.612676 TAGGGTCGATGACGGTATGG 58.387 55.000 0.00 0.00 40.21 2.74
2641 3309 0.396695 AGGGTCGATGACGGTATGGT 60.397 55.000 0.00 0.00 40.21 3.55
2642 3310 1.133699 AGGGTCGATGACGGTATGGTA 60.134 52.381 0.00 0.00 40.21 3.25
2643 3311 1.891150 GGGTCGATGACGGTATGGTAT 59.109 52.381 0.00 0.00 40.21 2.73
2644 3312 3.084039 GGGTCGATGACGGTATGGTATA 58.916 50.000 0.00 0.00 40.21 1.47
2645 3313 3.507233 GGGTCGATGACGGTATGGTATAA 59.493 47.826 0.00 0.00 40.21 0.98
2646 3314 4.479619 GGTCGATGACGGTATGGTATAAC 58.520 47.826 0.00 0.00 40.21 1.89
2647 3315 4.217118 GGTCGATGACGGTATGGTATAACT 59.783 45.833 0.00 0.00 40.21 2.24
2648 3316 5.152097 GTCGATGACGGTATGGTATAACTG 58.848 45.833 0.00 0.00 40.21 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.482593 GAGGGCTTCGATTCTGGAAGA 59.517 52.381 5.77 0.00 44.68 2.87
6 7 1.474143 GGAGGGCTTCGATTCTGGAAG 60.474 57.143 0.00 0.00 42.93 3.46
7 8 0.541863 GGAGGGCTTCGATTCTGGAA 59.458 55.000 0.00 0.00 0.00 3.53
8 9 1.338136 GGGAGGGCTTCGATTCTGGA 61.338 60.000 0.00 0.00 0.00 3.86
9 10 1.147153 GGGAGGGCTTCGATTCTGG 59.853 63.158 0.00 0.00 0.00 3.86
10 11 1.147153 GGGGAGGGCTTCGATTCTG 59.853 63.158 0.00 0.00 0.00 3.02
11 12 1.306997 TGGGGAGGGCTTCGATTCT 60.307 57.895 0.00 0.00 0.00 2.40
12 13 1.147153 CTGGGGAGGGCTTCGATTC 59.853 63.158 0.00 0.00 0.00 2.52
13 14 3.049080 GCTGGGGAGGGCTTCGATT 62.049 63.158 0.00 0.00 0.00 3.34
14 15 3.483869 GCTGGGGAGGGCTTCGAT 61.484 66.667 0.00 0.00 0.00 3.59
15 16 4.722535 AGCTGGGGAGGGCTTCGA 62.723 66.667 0.00 0.00 0.00 3.71
16 17 3.689002 GAAGCTGGGGAGGGCTTCG 62.689 68.421 11.05 0.00 31.20 3.79
17 18 1.857638 AAGAAGCTGGGGAGGGCTTC 61.858 60.000 16.71 16.71 38.95 3.86
18 19 1.854507 AAGAAGCTGGGGAGGGCTT 60.855 57.895 0.00 0.00 0.00 4.35
19 20 2.204213 AAGAAGCTGGGGAGGGCT 60.204 61.111 0.00 0.00 0.00 5.19
20 21 0.983378 TAGAAGAAGCTGGGGAGGGC 60.983 60.000 0.00 0.00 0.00 5.19
21 22 1.127343 CTAGAAGAAGCTGGGGAGGG 58.873 60.000 0.00 0.00 0.00 4.30
22 23 2.166907 TCTAGAAGAAGCTGGGGAGG 57.833 55.000 0.00 0.00 0.00 4.30
23 24 4.335400 GATTCTAGAAGAAGCTGGGGAG 57.665 50.000 11.53 0.00 37.62 4.30
30 31 4.048504 GGCTCGAAGATTCTAGAAGAAGC 58.951 47.826 11.53 11.71 40.68 3.86
31 32 5.067153 TGAGGCTCGAAGATTCTAGAAGAAG 59.933 44.000 11.53 3.37 37.69 2.85
32 33 4.950475 TGAGGCTCGAAGATTCTAGAAGAA 59.050 41.667 11.53 0.00 38.78 2.52
33 34 4.527944 TGAGGCTCGAAGATTCTAGAAGA 58.472 43.478 11.53 1.47 33.89 2.87
34 35 4.909696 TGAGGCTCGAAGATTCTAGAAG 57.090 45.455 11.53 0.00 33.89 2.85
35 36 5.860941 AATGAGGCTCGAAGATTCTAGAA 57.139 39.130 7.82 7.82 33.89 2.10
36 37 5.127845 ACAAATGAGGCTCGAAGATTCTAGA 59.872 40.000 10.42 0.00 33.89 2.43
37 38 5.355596 ACAAATGAGGCTCGAAGATTCTAG 58.644 41.667 10.42 1.47 33.89 2.43
38 39 5.344743 ACAAATGAGGCTCGAAGATTCTA 57.655 39.130 10.42 0.00 33.89 2.10
39 40 4.213564 ACAAATGAGGCTCGAAGATTCT 57.786 40.909 10.42 0.00 33.89 2.40
40 41 4.954092 AACAAATGAGGCTCGAAGATTC 57.046 40.909 10.42 0.00 33.89 2.52
41 42 5.712152 AAAACAAATGAGGCTCGAAGATT 57.288 34.783 10.42 0.81 33.89 2.40
42 43 5.705441 TGTAAAACAAATGAGGCTCGAAGAT 59.295 36.000 10.42 0.00 33.89 2.40
43 44 5.060506 TGTAAAACAAATGAGGCTCGAAGA 58.939 37.500 10.42 0.00 0.00 2.87
44 45 5.356882 TGTAAAACAAATGAGGCTCGAAG 57.643 39.130 10.42 2.35 0.00 3.79
45 46 5.759506 TTGTAAAACAAATGAGGCTCGAA 57.240 34.783 10.42 0.00 34.76 3.71
46 47 5.106317 GGATTGTAAAACAAATGAGGCTCGA 60.106 40.000 10.42 0.00 41.96 4.04
47 48 5.095490 GGATTGTAAAACAAATGAGGCTCG 58.905 41.667 10.42 0.00 41.96 5.03
48 49 6.272822 AGGATTGTAAAACAAATGAGGCTC 57.727 37.500 7.79 7.79 41.96 4.70
49 50 7.836183 AGATAGGATTGTAAAACAAATGAGGCT 59.164 33.333 0.00 0.00 41.96 4.58
50 51 8.000780 AGATAGGATTGTAAAACAAATGAGGC 57.999 34.615 0.00 0.00 41.96 4.70
90 91 9.181061 GCCCCATTCTTTTTACAATACTAACTA 57.819 33.333 0.00 0.00 0.00 2.24
91 92 7.893833 AGCCCCATTCTTTTTACAATACTAACT 59.106 33.333 0.00 0.00 0.00 2.24
92 93 8.063200 AGCCCCATTCTTTTTACAATACTAAC 57.937 34.615 0.00 0.00 0.00 2.34
93 94 7.891183 TGAGCCCCATTCTTTTTACAATACTAA 59.109 33.333 0.00 0.00 0.00 2.24
94 95 7.406916 TGAGCCCCATTCTTTTTACAATACTA 58.593 34.615 0.00 0.00 0.00 1.82
95 96 6.252995 TGAGCCCCATTCTTTTTACAATACT 58.747 36.000 0.00 0.00 0.00 2.12
96 97 6.524101 TGAGCCCCATTCTTTTTACAATAC 57.476 37.500 0.00 0.00 0.00 1.89
97 98 7.453126 TCTTTGAGCCCCATTCTTTTTACAATA 59.547 33.333 0.00 0.00 0.00 1.90
98 99 6.269769 TCTTTGAGCCCCATTCTTTTTACAAT 59.730 34.615 0.00 0.00 0.00 2.71
99 100 5.600484 TCTTTGAGCCCCATTCTTTTTACAA 59.400 36.000 0.00 0.00 0.00 2.41
100 101 5.144100 TCTTTGAGCCCCATTCTTTTTACA 58.856 37.500 0.00 0.00 0.00 2.41
101 102 5.722021 TCTTTGAGCCCCATTCTTTTTAC 57.278 39.130 0.00 0.00 0.00 2.01
102 103 6.725834 AGAATCTTTGAGCCCCATTCTTTTTA 59.274 34.615 0.00 0.00 31.11 1.52
103 104 5.545335 AGAATCTTTGAGCCCCATTCTTTTT 59.455 36.000 0.00 0.00 31.11 1.94
104 105 5.046807 CAGAATCTTTGAGCCCCATTCTTTT 60.047 40.000 0.00 0.00 32.59 2.27
105 106 4.465305 CAGAATCTTTGAGCCCCATTCTTT 59.535 41.667 0.00 0.00 32.59 2.52
106 107 4.021916 CAGAATCTTTGAGCCCCATTCTT 58.978 43.478 0.00 0.00 32.59 2.52
107 108 3.626729 CCAGAATCTTTGAGCCCCATTCT 60.627 47.826 0.00 0.00 34.75 2.40
108 109 2.692041 CCAGAATCTTTGAGCCCCATTC 59.308 50.000 0.00 0.00 0.00 2.67
109 110 2.625087 CCCAGAATCTTTGAGCCCCATT 60.625 50.000 0.00 0.00 0.00 3.16
110 111 1.063417 CCCAGAATCTTTGAGCCCCAT 60.063 52.381 0.00 0.00 0.00 4.00
111 112 0.332632 CCCAGAATCTTTGAGCCCCA 59.667 55.000 0.00 0.00 0.00 4.96
112 113 0.625849 TCCCAGAATCTTTGAGCCCC 59.374 55.000 0.00 0.00 0.00 5.80
113 114 1.561542 TCTCCCAGAATCTTTGAGCCC 59.438 52.381 1.93 0.00 0.00 5.19
114 115 3.277715 CTTCTCCCAGAATCTTTGAGCC 58.722 50.000 1.93 0.00 33.13 4.70
115 116 2.682352 GCTTCTCCCAGAATCTTTGAGC 59.318 50.000 1.93 0.00 33.13 4.26
116 117 3.940221 CAGCTTCTCCCAGAATCTTTGAG 59.060 47.826 0.00 0.62 33.13 3.02
117 118 3.584406 TCAGCTTCTCCCAGAATCTTTGA 59.416 43.478 0.00 0.00 33.13 2.69
118 119 3.940221 CTCAGCTTCTCCCAGAATCTTTG 59.060 47.826 0.00 0.00 33.13 2.77
119 120 3.843027 TCTCAGCTTCTCCCAGAATCTTT 59.157 43.478 0.00 0.00 33.13 2.52
120 121 3.448934 TCTCAGCTTCTCCCAGAATCTT 58.551 45.455 0.00 0.00 33.13 2.40
121 122 3.113191 TCTCAGCTTCTCCCAGAATCT 57.887 47.619 0.00 0.00 33.13 2.40
122 123 3.902881 TTCTCAGCTTCTCCCAGAATC 57.097 47.619 0.00 0.00 33.13 2.52
123 124 3.621958 GCTTTCTCAGCTTCTCCCAGAAT 60.622 47.826 0.00 0.00 46.27 2.40
124 125 2.289945 GCTTTCTCAGCTTCTCCCAGAA 60.290 50.000 0.00 0.00 46.27 3.02
125 126 1.277557 GCTTTCTCAGCTTCTCCCAGA 59.722 52.381 0.00 0.00 46.27 3.86
126 127 1.736612 GCTTTCTCAGCTTCTCCCAG 58.263 55.000 0.00 0.00 46.27 4.45
127 128 3.944476 GCTTTCTCAGCTTCTCCCA 57.056 52.632 0.00 0.00 46.27 4.37
135 136 4.406943 CCAGAATTTAACGCTTTCTCAGC 58.593 43.478 0.00 0.00 46.31 4.26
136 137 4.142600 CCCCAGAATTTAACGCTTTCTCAG 60.143 45.833 0.00 0.00 0.00 3.35
137 138 3.756434 CCCCAGAATTTAACGCTTTCTCA 59.244 43.478 0.00 0.00 0.00 3.27
138 139 3.427638 GCCCCAGAATTTAACGCTTTCTC 60.428 47.826 0.00 0.00 0.00 2.87
139 140 2.492088 GCCCCAGAATTTAACGCTTTCT 59.508 45.455 0.00 0.00 0.00 2.52
140 141 2.416836 GGCCCCAGAATTTAACGCTTTC 60.417 50.000 0.00 0.00 0.00 2.62
141 142 1.548719 GGCCCCAGAATTTAACGCTTT 59.451 47.619 0.00 0.00 0.00 3.51
142 143 1.182667 GGCCCCAGAATTTAACGCTT 58.817 50.000 0.00 0.00 0.00 4.68
143 144 0.039035 TGGCCCCAGAATTTAACGCT 59.961 50.000 0.00 0.00 0.00 5.07
144 145 1.067060 GATGGCCCCAGAATTTAACGC 59.933 52.381 0.00 0.00 0.00 4.84
145 146 2.654863 AGATGGCCCCAGAATTTAACG 58.345 47.619 0.00 0.00 0.00 3.18
146 147 3.430790 GCAAGATGGCCCCAGAATTTAAC 60.431 47.826 0.00 0.00 0.00 2.01
147 148 2.765699 GCAAGATGGCCCCAGAATTTAA 59.234 45.455 0.00 0.00 0.00 1.52
148 149 2.387757 GCAAGATGGCCCCAGAATTTA 58.612 47.619 0.00 0.00 0.00 1.40
149 150 1.197812 GCAAGATGGCCCCAGAATTT 58.802 50.000 0.00 0.00 0.00 1.82
150 151 2.906268 GCAAGATGGCCCCAGAATT 58.094 52.632 0.00 0.00 0.00 2.17
151 152 4.692930 GCAAGATGGCCCCAGAAT 57.307 55.556 0.00 0.00 0.00 2.40
159 160 0.614812 AATTTGGTGGGCAAGATGGC 59.385 50.000 0.00 0.00 42.88 4.40
160 161 2.159057 GCTAATTTGGTGGGCAAGATGG 60.159 50.000 0.00 0.00 0.00 3.51
161 162 2.159057 GGCTAATTTGGTGGGCAAGATG 60.159 50.000 0.00 0.00 0.00 2.90
162 163 2.110578 GGCTAATTTGGTGGGCAAGAT 58.889 47.619 0.00 0.00 0.00 2.40
163 164 1.203112 TGGCTAATTTGGTGGGCAAGA 60.203 47.619 0.00 0.00 0.00 3.02
164 165 1.265236 TGGCTAATTTGGTGGGCAAG 58.735 50.000 0.00 0.00 0.00 4.01
165 166 1.722034 TTGGCTAATTTGGTGGGCAA 58.278 45.000 0.00 0.00 40.84 4.52
166 167 1.949799 ATTGGCTAATTTGGTGGGCA 58.050 45.000 0.00 0.00 0.00 5.36
167 168 3.181466 CCTAATTGGCTAATTTGGTGGGC 60.181 47.826 22.06 0.00 41.38 5.36
168 169 4.670896 CCTAATTGGCTAATTTGGTGGG 57.329 45.455 22.06 10.58 41.38 4.61
173 174 7.111247 TGGATTGACCTAATTGGCTAATTTG 57.889 36.000 13.63 11.31 40.22 2.32
174 175 7.732222 TTGGATTGACCTAATTGGCTAATTT 57.268 32.000 13.63 0.00 40.22 1.82
175 176 7.619302 TCTTTGGATTGACCTAATTGGCTAATT 59.381 33.333 12.96 12.96 40.22 1.40
176 177 7.125391 TCTTTGGATTGACCTAATTGGCTAAT 58.875 34.615 0.00 0.00 40.22 1.73
177 178 6.489603 TCTTTGGATTGACCTAATTGGCTAA 58.510 36.000 0.00 0.00 40.22 3.09
178 179 6.073447 TCTTTGGATTGACCTAATTGGCTA 57.927 37.500 0.00 0.00 40.22 3.93
179 180 4.934356 TCTTTGGATTGACCTAATTGGCT 58.066 39.130 0.00 0.00 40.22 4.75
180 181 5.859205 ATCTTTGGATTGACCTAATTGGC 57.141 39.130 0.00 0.00 40.22 4.52
181 182 7.408756 TGAATCTTTGGATTGACCTAATTGG 57.591 36.000 0.00 0.00 41.68 3.16
182 183 8.472413 ACATGAATCTTTGGATTGACCTAATTG 58.528 33.333 0.00 0.00 41.68 2.32
186 187 6.947733 ACAACATGAATCTTTGGATTGACCTA 59.052 34.615 0.00 0.00 41.68 3.08
195 196 4.549458 GTGTGGACAACATGAATCTTTGG 58.451 43.478 0.00 0.00 41.97 3.28
205 206 0.884704 GCTCACCGTGTGGACAACAT 60.885 55.000 0.00 0.00 41.97 2.71
206 207 1.522806 GCTCACCGTGTGGACAACA 60.523 57.895 0.00 0.00 39.21 3.33
211 212 2.486636 CTAAGCGCTCACCGTGTGGA 62.487 60.000 12.06 0.00 39.71 4.02
217 218 1.922570 AACATACTAAGCGCTCACCG 58.077 50.000 12.06 1.56 40.75 4.94
219 220 3.863424 TGCTAAACATACTAAGCGCTCAC 59.137 43.478 12.06 0.00 37.80 3.51
223 224 3.545633 GCATGCTAAACATACTAAGCGC 58.454 45.455 11.37 0.00 36.64 5.92
228 229 9.496873 AATATTAACCGCATGCTAAACATACTA 57.503 29.630 17.13 0.00 36.64 1.82
307 309 7.827701 TGCGCTATAAATCTATACTTAGTGCT 58.172 34.615 9.73 0.00 41.41 4.40
320 322 8.673711 TGGGATGTTATTTATGCGCTATAAATC 58.326 33.333 26.54 19.02 44.71 2.17
322 324 7.094549 GGTGGGATGTTATTTATGCGCTATAAA 60.095 37.037 19.88 19.88 43.40 1.40
324 326 5.878116 GGTGGGATGTTATTTATGCGCTATA 59.122 40.000 9.73 1.91 0.00 1.31
325 327 4.700213 GGTGGGATGTTATTTATGCGCTAT 59.300 41.667 9.73 3.00 0.00 2.97
340 342 4.067896 GCACACAGATATTAGGTGGGATG 58.932 47.826 8.31 0.31 38.18 3.51
342 344 3.111484 TGCACACAGATATTAGGTGGGA 58.889 45.455 8.31 0.00 38.18 4.37
356 358 5.097742 AGGCAGTATATTAGTTGCACACA 57.902 39.130 0.00 0.00 38.27 3.72
406 410 8.750515 TTGAATGATATTAACTGGCATTCTCA 57.249 30.769 0.46 0.00 43.07 3.27
425 437 8.657074 AATCACAGGCATTGATATTTTGAATG 57.343 30.769 1.72 0.00 32.29 2.67
442 454 7.870509 TGGATAGATTCTCAAAAATCACAGG 57.129 36.000 0.00 0.00 37.98 4.00
454 466 8.502387 GCACACAGATATTTTGGATAGATTCTC 58.498 37.037 0.00 0.00 0.00 2.87
455 467 7.994911 TGCACACAGATATTTTGGATAGATTCT 59.005 33.333 0.00 0.00 0.00 2.40
456 468 8.158169 TGCACACAGATATTTTGGATAGATTC 57.842 34.615 0.00 0.00 0.00 2.52
457 469 8.408601 GTTGCACACAGATATTTTGGATAGATT 58.591 33.333 0.00 0.00 0.00 2.40
459 471 7.066163 CAGTTGCACACAGATATTTTGGATAGA 59.934 37.037 0.00 0.00 0.00 1.98
460 472 7.191551 CAGTTGCACACAGATATTTTGGATAG 58.808 38.462 0.00 0.00 0.00 2.08
474 504 3.190327 GCAATGTATACCAGTTGCACACA 59.810 43.478 22.42 0.00 44.63 3.72
505 535 9.348476 TGCATGATGTTAATATTAGGCAGTTAA 57.652 29.630 11.30 0.00 30.13 2.01
506 536 8.916628 TGCATGATGTTAATATTAGGCAGTTA 57.083 30.769 11.30 0.00 30.13 2.24
507 537 7.822161 TGCATGATGTTAATATTAGGCAGTT 57.178 32.000 11.30 0.00 30.13 3.16
545 610 3.230976 TCTTTCCGCCTAGATGCATAGA 58.769 45.455 0.00 0.00 0.00 1.98
558 623 2.094762 TCCTTAAGTGCTCTTTCCGC 57.905 50.000 6.31 0.00 35.36 5.54
594 659 1.153309 GGTGCATGTACCCGTACCC 60.153 63.158 21.39 0.00 35.26 3.69
823 906 3.450115 GACCGACTCCCAGTCCCG 61.450 72.222 0.00 0.00 42.12 5.14
1024 1110 2.733593 GTGAGGACGACGGTGTGC 60.734 66.667 0.00 0.00 0.00 4.57
1031 1123 0.667792 GAGGCAAGTGTGAGGACGAC 60.668 60.000 0.00 0.00 0.00 4.34
1105 1202 3.376918 GCTTGCCTGTCCTTGCCC 61.377 66.667 0.00 0.00 0.00 5.36
1109 1206 1.302033 CTGTCGCTTGCCTGTCCTT 60.302 57.895 0.00 0.00 0.00 3.36
1110 1207 2.345244 CTGTCGCTTGCCTGTCCT 59.655 61.111 0.00 0.00 0.00 3.85
1111 1208 2.743928 CCTGTCGCTTGCCTGTCC 60.744 66.667 0.00 0.00 0.00 4.02
1112 1209 3.426568 GCCTGTCGCTTGCCTGTC 61.427 66.667 0.00 0.00 0.00 3.51
1113 1210 3.557903 ATGCCTGTCGCTTGCCTGT 62.558 57.895 0.00 0.00 38.78 4.00
1114 1211 2.749044 ATGCCTGTCGCTTGCCTG 60.749 61.111 0.00 0.00 38.78 4.85
1115 1212 2.749044 CATGCCTGTCGCTTGCCT 60.749 61.111 0.00 0.00 36.01 4.75
1116 1213 3.818787 CCATGCCTGTCGCTTGCC 61.819 66.667 0.00 0.00 40.46 4.52
1117 1214 3.818787 CCCATGCCTGTCGCTTGC 61.819 66.667 0.00 0.00 40.46 4.01
1118 1215 3.818787 GCCCATGCCTGTCGCTTG 61.819 66.667 0.00 0.00 41.25 4.01
1201 1303 2.682494 AGGAAGCGGCGGAGGTAA 60.682 61.111 9.78 0.00 0.00 2.85
1360 1468 1.884464 CTCGATGACCATGGCCGTG 60.884 63.158 18.73 18.73 0.00 4.94
1616 2074 7.967890 ACAAATTTAATTGGCAGAAGAAAGG 57.032 32.000 0.00 0.00 34.56 3.11
1617 2075 9.044150 TCAACAAATTTAATTGGCAGAAGAAAG 57.956 29.630 12.19 0.00 34.56 2.62
1618 2076 8.954950 TCAACAAATTTAATTGGCAGAAGAAA 57.045 26.923 12.19 0.00 34.56 2.52
1619 2077 8.991026 CATCAACAAATTTAATTGGCAGAAGAA 58.009 29.630 12.19 0.00 34.56 2.52
1672 2131 0.034960 GAGAAGGAGCAAAGGGACCC 60.035 60.000 0.59 0.59 0.00 4.46
1700 2160 3.411351 CGAACGGCCTGACCAACG 61.411 66.667 0.00 0.00 39.03 4.10
1724 2184 3.944422 AGTATATGCAACGAAAAGCCG 57.056 42.857 0.00 0.00 0.00 5.52
1751 2211 7.656707 TTTGATGAAGCCTTTCTAAATTTGC 57.343 32.000 0.00 0.00 34.31 3.68
1810 2271 5.435291 AGGAAAAATCCTCAGCTGATGTAG 58.565 41.667 18.63 5.19 34.41 2.74
1820 2281 5.896678 TGGTTTCAGAAAGGAAAAATCCTCA 59.103 36.000 0.00 0.00 39.65 3.86
1826 2287 7.060383 TGCATATGGTTTCAGAAAGGAAAAA 57.940 32.000 4.56 0.00 38.41 1.94
1827 2288 6.662865 TGCATATGGTTTCAGAAAGGAAAA 57.337 33.333 4.56 0.00 38.41 2.29
1828 2289 6.127366 GGATGCATATGGTTTCAGAAAGGAAA 60.127 38.462 0.00 0.00 34.56 3.13
1829 2290 5.360714 GGATGCATATGGTTTCAGAAAGGAA 59.639 40.000 0.00 0.00 0.00 3.36
1830 2291 4.889409 GGATGCATATGGTTTCAGAAAGGA 59.111 41.667 0.00 0.00 0.00 3.36
1831 2292 4.891756 AGGATGCATATGGTTTCAGAAAGG 59.108 41.667 0.00 0.00 0.00 3.11
1832 2293 5.221185 CCAGGATGCATATGGTTTCAGAAAG 60.221 44.000 18.34 0.00 31.97 2.62
1878 2339 3.989698 CTGCGGCTGTACTGTCGGG 62.990 68.421 25.01 2.27 35.39 5.14
1938 2401 3.508012 AGTGTCAGCAGTTGTAGGAGTAG 59.492 47.826 0.00 0.00 0.00 2.57
1939 2402 3.255888 CAGTGTCAGCAGTTGTAGGAGTA 59.744 47.826 0.00 0.00 0.00 2.59
1940 2403 2.036475 CAGTGTCAGCAGTTGTAGGAGT 59.964 50.000 0.00 0.00 0.00 3.85
1941 2404 2.297315 TCAGTGTCAGCAGTTGTAGGAG 59.703 50.000 0.00 0.00 0.00 3.69
1942 2405 2.316108 TCAGTGTCAGCAGTTGTAGGA 58.684 47.619 0.00 0.00 0.00 2.94
1943 2406 2.820059 TCAGTGTCAGCAGTTGTAGG 57.180 50.000 0.00 0.00 0.00 3.18
2016 2479 7.019656 AGAAGGGCCAAATATGTTCATTTTT 57.980 32.000 6.18 0.00 0.00 1.94
2027 2490 4.028993 AGTTTCGAAGAAGGGCCAAATA 57.971 40.909 6.18 0.00 45.90 1.40
2033 2496 5.410439 TGTATTGTAAGTTTCGAAGAAGGGC 59.590 40.000 0.00 0.00 45.90 5.19
2034 2497 7.429636 TTGTATTGTAAGTTTCGAAGAAGGG 57.570 36.000 0.00 0.00 45.90 3.95
2052 2517 9.847224 AAATCGGATGGAGTAGTATTTTGTATT 57.153 29.630 0.00 0.00 0.00 1.89
2133 2672 8.580720 GTGAATCTATCCTCTAAAGCATGTCTA 58.419 37.037 0.00 0.00 0.00 2.59
2134 2673 7.441017 GTGAATCTATCCTCTAAAGCATGTCT 58.559 38.462 0.00 0.00 0.00 3.41
2135 2674 6.648725 GGTGAATCTATCCTCTAAAGCATGTC 59.351 42.308 0.00 0.00 0.00 3.06
2140 2679 5.071115 AGTGGGTGAATCTATCCTCTAAAGC 59.929 44.000 0.00 0.00 0.00 3.51
2153 2692 0.804989 CGGAGCAAAGTGGGTGAATC 59.195 55.000 0.00 0.00 0.00 2.52
2159 2698 2.093658 ACTACATACGGAGCAAAGTGGG 60.094 50.000 0.00 0.00 0.00 4.61
2160 2699 3.247006 ACTACATACGGAGCAAAGTGG 57.753 47.619 0.00 0.00 0.00 4.00
2163 2702 7.772332 ATAAGAAACTACATACGGAGCAAAG 57.228 36.000 0.00 0.00 0.00 2.77
2216 2880 8.280258 TCAGATCCAAAATACTCCCTTCATAT 57.720 34.615 0.00 0.00 0.00 1.78
2217 2881 7.690454 TCAGATCCAAAATACTCCCTTCATA 57.310 36.000 0.00 0.00 0.00 2.15
2219 2883 6.581388 ATCAGATCCAAAATACTCCCTTCA 57.419 37.500 0.00 0.00 0.00 3.02
2248 2912 0.388134 GCAAAGGCTACGTCTGTCGA 60.388 55.000 0.00 0.00 38.95 4.20
2250 2914 0.790814 GTGCAAAGGCTACGTCTGTC 59.209 55.000 0.00 0.00 41.91 3.51
2251 2915 0.944311 CGTGCAAAGGCTACGTCTGT 60.944 55.000 0.00 0.00 41.91 3.41
2252 2916 0.666274 TCGTGCAAAGGCTACGTCTG 60.666 55.000 7.35 0.00 41.75 3.51
2253 2917 0.666577 GTCGTGCAAAGGCTACGTCT 60.667 55.000 7.35 0.00 41.75 4.18
2254 2918 1.779683 GTCGTGCAAAGGCTACGTC 59.220 57.895 7.35 0.00 41.75 4.34
2255 2919 2.019951 CGTCGTGCAAAGGCTACGT 61.020 57.895 7.35 0.00 41.75 3.57
2256 2920 2.769617 CGTCGTGCAAAGGCTACG 59.230 61.111 1.19 1.19 42.12 3.51
2257 2921 2.474712 GCGTCGTGCAAAGGCTAC 59.525 61.111 7.56 0.00 45.45 3.58
2280 2944 1.476007 AATCTAGCAGGGCGCCCTAG 61.476 60.000 46.42 37.58 46.28 3.02
2317 2981 4.005650 CCTAGATATAACACGACGGCCTA 58.994 47.826 0.00 0.00 0.00 3.93
2323 2987 4.378253 GGCTCGACCTAGATATAACACGAC 60.378 50.000 0.00 0.00 34.51 4.34
2339 3003 1.679305 TCTGGGACTGAGGCTCGAC 60.679 63.158 10.42 5.28 0.00 4.20
2343 3007 1.979693 GACGTCTGGGACTGAGGCT 60.980 63.158 8.70 0.00 44.10 4.58
2344 3008 1.608717 ATGACGTCTGGGACTGAGGC 61.609 60.000 17.92 0.00 44.10 4.70
2345 3009 0.174389 CATGACGTCTGGGACTGAGG 59.826 60.000 17.92 0.00 45.38 3.86
2347 3011 1.627864 TTCATGACGTCTGGGACTGA 58.372 50.000 17.92 7.18 0.00 3.41
2348 3012 2.455674 TTTCATGACGTCTGGGACTG 57.544 50.000 17.92 5.01 0.00 3.51
2349 3013 3.485463 TTTTTCATGACGTCTGGGACT 57.515 42.857 17.92 0.00 0.00 3.85
2351 3015 4.014569 TCATTTTTCATGACGTCTGGGA 57.985 40.909 17.92 8.60 0.00 4.37
2352 3016 4.970662 ATCATTTTTCATGACGTCTGGG 57.029 40.909 17.92 6.24 0.00 4.45
2421 3085 8.923270 TGAAAGTGGACAGATTTTATCCTTTTT 58.077 29.630 0.00 0.00 33.34 1.94
2428 3092 7.581213 TTGTGTGAAAGTGGACAGATTTTAT 57.419 32.000 0.00 0.00 0.00 1.40
2430 3094 5.913137 TTGTGTGAAAGTGGACAGATTTT 57.087 34.783 0.00 0.00 0.00 1.82
2440 3104 4.930963 TGCTACCAATTTGTGTGAAAGTG 58.069 39.130 0.00 0.00 0.00 3.16
2446 3110 3.916761 AGCAATGCTACCAATTTGTGTG 58.083 40.909 5.69 0.00 36.99 3.82
2449 3113 8.746052 TTATACTAGCAATGCTACCAATTTGT 57.254 30.769 11.40 8.41 40.44 2.83
2463 3127 9.309516 CCTGTTTACGAGAAATTATACTAGCAA 57.690 33.333 0.00 0.00 0.00 3.91
2464 3128 8.472413 ACCTGTTTACGAGAAATTATACTAGCA 58.528 33.333 0.00 0.00 0.00 3.49
2527 3194 5.879777 AGGTCAAAACACCAAATTTTTCTGG 59.120 36.000 0.00 0.00 39.16 3.86
2529 3196 7.994425 AAAGGTCAAAACACCAAATTTTTCT 57.006 28.000 0.00 0.00 39.16 2.52
2539 3206 8.387354 CAACTTTCATAAAAAGGTCAAAACACC 58.613 33.333 2.91 0.00 36.58 4.16
2551 3218 7.041440 TCACATCTCGCTCAACTTTCATAAAAA 60.041 33.333 0.00 0.00 0.00 1.94
2556 3223 3.681897 GTCACATCTCGCTCAACTTTCAT 59.318 43.478 0.00 0.00 0.00 2.57
2565 3232 0.247736 ACCAAGGTCACATCTCGCTC 59.752 55.000 0.00 0.00 0.00 5.03
2569 3236 5.712152 AAATTGAACCAAGGTCACATCTC 57.288 39.130 0.00 0.00 0.00 2.75
2596 3264 8.712228 AACAATAGGAAAAAGGTCAGATCTTT 57.288 30.769 2.48 2.48 36.15 2.52
2597 3265 9.454859 CTAACAATAGGAAAAAGGTCAGATCTT 57.545 33.333 0.00 0.00 0.00 2.40
2608 3276 8.532277 CGTCATCGACCCTAACAATAGGAAAAA 61.532 40.741 3.46 0.00 44.43 1.94
2615 3283 3.025978 ACCGTCATCGACCCTAACAATA 58.974 45.455 0.00 0.00 39.71 1.90
2618 3286 2.127271 TACCGTCATCGACCCTAACA 57.873 50.000 0.00 0.00 39.71 2.41
2621 3289 1.133699 ACCATACCGTCATCGACCCTA 60.134 52.381 0.00 0.00 39.71 3.53
2622 3290 0.396695 ACCATACCGTCATCGACCCT 60.397 55.000 0.00 0.00 39.71 4.34


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

AutoCloner maintained by Alex Coulton.