Multiple sequence alignment - TraesCS3D01G414200

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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 TraesCS3D01G414200 chr3D 100.000 2644 0 0 1 2644 526173594 526170951 0.000000e+00 4883.0
1 TraesCS3D01G414200 chr3D 86.325 117 11 1 2 113 481584255 481584139 3.570000e-24 122.0
2 TraesCS3D01G414200 chr3D 88.776 98 8 2 11 105 29340691 29340788 1.660000e-22 117.0
3 TraesCS3D01G414200 chr3D 85.345 116 10 3 1 111 361736046 361736159 2.150000e-21 113.0
4 TraesCS3D01G414200 chr3B 85.493 2068 139 70 304 2270 694785889 694783882 0.000000e+00 2008.0
5 TraesCS3D01G414200 chr3B 89.199 287 13 10 2375 2644 694783696 694783411 2.520000e-90 342.0
6 TraesCS3D01G414200 chr3B 93.651 63 2 2 2293 2354 694783820 694783759 2.800000e-15 93.5
7 TraesCS3D01G414200 chr3A 86.289 1838 121 68 636 2369 660269851 660268041 0.000000e+00 1877.0
8 TraesCS3D01G414200 chr3A 94.574 258 8 3 2362 2614 660268002 660267746 6.860000e-106 394.0
9 TraesCS3D01G414200 chr3A 82.721 272 23 8 304 552 660270161 660269891 1.230000e-53 220.0
10 TraesCS3D01G414200 chr7A 93.671 79 5 0 27 105 823653 823731 4.620000e-23 119.0
11 TraesCS3D01G414200 chr6D 88.660 97 10 1 12 108 346075874 346075779 1.660000e-22 117.0
12 TraesCS3D01G414200 chr5D 88.660 97 8 2 11 105 411841038 411841133 5.980000e-22 115.0
13 TraesCS3D01G414200 chr2D 87.755 98 11 1 5 102 364973575 364973671 2.150000e-21 113.0
14 TraesCS3D01G414200 chr2A 85.586 111 12 1 3 113 604132172 604132278 2.150000e-21 113.0
15 TraesCS3D01G414200 chr5A 86.538 104 9 4 4 105 308457095 308456995 2.780000e-20 110.0


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 TraesCS3D01G414200 chr3D 526170951 526173594 2643 True 4883.000000 4883 100.000000 1 2644 1 chr3D.!!$R2 2643
1 TraesCS3D01G414200 chr3B 694783411 694785889 2478 True 814.500000 2008 89.447667 304 2644 3 chr3B.!!$R1 2340
2 TraesCS3D01G414200 chr3A 660267746 660270161 2415 True 830.333333 1877 87.861333 304 2614 3 chr3A.!!$R1 2310

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
133 134 0.109342 ATTAGGCTGAGAATGGGCGG 59.891 55.0 0.00 0.0 0.0 6.13 F
232 233 0.179094 ACGCGCGAGGATAAAATGGA 60.179 50.0 39.36 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1552 0.381801 AAAATCATGGATGGCGCGAC 59.618 50.0 12.10 8.22 0.0 5.19 R
2022 2150 0.382515 CCTCTACAGACTACAGCGCC 59.617 60.0 2.29 0.00 0.0 6.53 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
17 18 2.483288 CCGAAAAATGGGCGACGG 59.517 61.111 0.00 0.00 34.77 4.79
18 19 2.202427 CGAAAAATGGGCGACGGC 60.202 61.111 13.84 13.84 38.90 5.68
19 20 2.202427 GAAAAATGGGCGACGGCG 60.202 61.111 6.12 6.12 41.24 6.46
20 21 3.677099 GAAAAATGGGCGACGGCGG 62.677 63.158 15.06 0.00 41.24 6.13
45 46 3.741476 GCAGGCGAGGGTTTGCTG 61.741 66.667 0.00 0.00 33.93 4.41
46 47 2.281761 CAGGCGAGGGTTTGCTGT 60.282 61.111 0.00 0.00 33.93 4.40
47 48 2.032681 AGGCGAGGGTTTGCTGTC 59.967 61.111 0.00 0.00 33.93 3.51
48 49 3.423154 GGCGAGGGTTTGCTGTCG 61.423 66.667 0.00 0.00 33.93 4.35
49 50 2.357034 GCGAGGGTTTGCTGTCGA 60.357 61.111 0.00 0.00 34.28 4.20
50 51 1.741770 GCGAGGGTTTGCTGTCGAT 60.742 57.895 0.00 0.00 34.28 3.59
51 52 0.459585 GCGAGGGTTTGCTGTCGATA 60.460 55.000 0.00 0.00 34.28 2.92
52 53 1.806623 GCGAGGGTTTGCTGTCGATAT 60.807 52.381 0.00 0.00 34.28 1.63
53 54 1.860950 CGAGGGTTTGCTGTCGATATG 59.139 52.381 0.00 0.00 34.28 1.78
54 55 2.213499 GAGGGTTTGCTGTCGATATGG 58.787 52.381 0.00 0.00 0.00 2.74
55 56 1.134098 AGGGTTTGCTGTCGATATGGG 60.134 52.381 0.00 0.00 0.00 4.00
56 57 1.408266 GGGTTTGCTGTCGATATGGGT 60.408 52.381 0.00 0.00 0.00 4.51
57 58 1.670811 GGTTTGCTGTCGATATGGGTG 59.329 52.381 0.00 0.00 0.00 4.61
58 59 1.670811 GTTTGCTGTCGATATGGGTGG 59.329 52.381 0.00 0.00 0.00 4.61
59 60 1.199615 TTGCTGTCGATATGGGTGGA 58.800 50.000 0.00 0.00 0.00 4.02
60 61 1.199615 TGCTGTCGATATGGGTGGAA 58.800 50.000 0.00 0.00 0.00 3.53
61 62 1.138859 TGCTGTCGATATGGGTGGAAG 59.861 52.381 0.00 0.00 0.00 3.46
62 63 1.412710 GCTGTCGATATGGGTGGAAGA 59.587 52.381 0.00 0.00 0.00 2.87
63 64 2.546795 GCTGTCGATATGGGTGGAAGAG 60.547 54.545 0.00 0.00 0.00 2.85
64 65 2.036475 CTGTCGATATGGGTGGAAGAGG 59.964 54.545 0.00 0.00 0.00 3.69
65 66 2.317040 GTCGATATGGGTGGAAGAGGA 58.683 52.381 0.00 0.00 0.00 3.71
66 67 2.900546 GTCGATATGGGTGGAAGAGGAT 59.099 50.000 0.00 0.00 0.00 3.24
67 68 2.899900 TCGATATGGGTGGAAGAGGATG 59.100 50.000 0.00 0.00 0.00 3.51
68 69 2.027745 CGATATGGGTGGAAGAGGATGG 60.028 54.545 0.00 0.00 0.00 3.51
69 70 1.140312 TATGGGTGGAAGAGGATGGC 58.860 55.000 0.00 0.00 0.00 4.40
70 71 1.649271 ATGGGTGGAAGAGGATGGCC 61.649 60.000 0.00 0.00 0.00 5.36
71 72 2.308722 GGGTGGAAGAGGATGGCCA 61.309 63.158 8.56 8.56 36.29 5.36
72 73 1.691219 GGTGGAAGAGGATGGCCAA 59.309 57.895 10.96 0.00 36.29 4.52
73 74 0.259938 GGTGGAAGAGGATGGCCAAT 59.740 55.000 10.96 0.00 36.29 3.16
74 75 1.396653 GTGGAAGAGGATGGCCAATG 58.603 55.000 10.96 0.00 36.29 2.82
75 76 1.002069 TGGAAGAGGATGGCCAATGT 58.998 50.000 10.96 0.00 36.29 2.71
76 77 1.341285 TGGAAGAGGATGGCCAATGTG 60.341 52.381 10.96 0.00 36.29 3.21
77 78 0.743097 GAAGAGGATGGCCAATGTGC 59.257 55.000 10.96 0.00 36.29 4.57
85 86 2.672996 GCCAATGTGCCACCGACT 60.673 61.111 0.00 0.00 0.00 4.18
86 87 1.376683 GCCAATGTGCCACCGACTA 60.377 57.895 0.00 0.00 0.00 2.59
87 88 1.369091 GCCAATGTGCCACCGACTAG 61.369 60.000 0.00 0.00 0.00 2.57
88 89 1.369091 CCAATGTGCCACCGACTAGC 61.369 60.000 0.00 0.00 0.00 3.42
89 90 0.673333 CAATGTGCCACCGACTAGCA 60.673 55.000 0.00 0.00 0.00 3.49
91 92 2.809601 GTGCCACCGACTAGCACG 60.810 66.667 0.00 3.42 46.43 5.34
92 93 4.735132 TGCCACCGACTAGCACGC 62.735 66.667 4.69 0.00 0.00 5.34
94 95 4.063967 CCACCGACTAGCACGCCA 62.064 66.667 4.69 0.00 0.00 5.69
95 96 2.507102 CACCGACTAGCACGCCAG 60.507 66.667 4.69 0.00 0.00 4.85
96 97 3.760035 ACCGACTAGCACGCCAGG 61.760 66.667 4.69 0.00 0.00 4.45
97 98 4.514577 CCGACTAGCACGCCAGGG 62.515 72.222 4.69 0.00 0.00 4.45
98 99 4.514577 CGACTAGCACGCCAGGGG 62.515 72.222 0.84 0.84 0.00 4.79
99 100 4.162690 GACTAGCACGCCAGGGGG 62.163 72.222 8.67 4.77 37.18 5.40
100 101 4.715130 ACTAGCACGCCAGGGGGA 62.715 66.667 8.67 0.00 35.59 4.81
101 102 3.854669 CTAGCACGCCAGGGGGAG 61.855 72.222 8.67 2.27 40.27 4.30
106 107 4.332543 ACGCCAGGGGGAGGAGAA 62.333 66.667 8.67 0.00 38.47 2.87
107 108 3.474570 CGCCAGGGGGAGGAGAAG 61.475 72.222 0.00 0.00 35.59 2.85
108 109 2.041265 GCCAGGGGGAGGAGAAGA 59.959 66.667 0.00 0.00 35.59 2.87
109 110 2.371259 GCCAGGGGGAGGAGAAGAC 61.371 68.421 0.00 0.00 35.59 3.01
110 111 1.081092 CCAGGGGGAGGAGAAGACA 59.919 63.158 0.00 0.00 35.59 3.41
111 112 1.268283 CCAGGGGGAGGAGAAGACAC 61.268 65.000 0.00 0.00 35.59 3.67
112 113 0.545309 CAGGGGGAGGAGAAGACACA 60.545 60.000 0.00 0.00 0.00 3.72
113 114 0.193574 AGGGGGAGGAGAAGACACAA 59.806 55.000 0.00 0.00 0.00 3.33
114 115 1.064825 GGGGGAGGAGAAGACACAAA 58.935 55.000 0.00 0.00 0.00 2.83
115 116 1.636003 GGGGGAGGAGAAGACACAAAT 59.364 52.381 0.00 0.00 0.00 2.32
116 117 2.041755 GGGGGAGGAGAAGACACAAATT 59.958 50.000 0.00 0.00 0.00 1.82
117 118 3.265995 GGGGGAGGAGAAGACACAAATTA 59.734 47.826 0.00 0.00 0.00 1.40
118 119 4.518249 GGGGAGGAGAAGACACAAATTAG 58.482 47.826 0.00 0.00 0.00 1.73
119 120 4.518249 GGGAGGAGAAGACACAAATTAGG 58.482 47.826 0.00 0.00 0.00 2.69
120 121 3.942115 GGAGGAGAAGACACAAATTAGGC 59.058 47.826 0.00 0.00 0.00 3.93
121 122 4.323868 GGAGGAGAAGACACAAATTAGGCT 60.324 45.833 0.00 0.00 0.00 4.58
122 123 4.583871 AGGAGAAGACACAAATTAGGCTG 58.416 43.478 0.00 0.00 0.00 4.85
123 124 4.287067 AGGAGAAGACACAAATTAGGCTGA 59.713 41.667 0.00 0.00 0.00 4.26
124 125 4.633565 GGAGAAGACACAAATTAGGCTGAG 59.366 45.833 0.00 0.00 0.00 3.35
125 126 5.482908 GAGAAGACACAAATTAGGCTGAGA 58.517 41.667 0.00 0.00 0.00 3.27
126 127 5.869579 AGAAGACACAAATTAGGCTGAGAA 58.130 37.500 0.00 0.00 0.00 2.87
127 128 6.479884 AGAAGACACAAATTAGGCTGAGAAT 58.520 36.000 0.00 0.00 0.00 2.40
128 129 6.373774 AGAAGACACAAATTAGGCTGAGAATG 59.626 38.462 0.00 0.00 0.00 2.67
129 130 4.946157 AGACACAAATTAGGCTGAGAATGG 59.054 41.667 0.00 0.00 0.00 3.16
130 131 4.019174 ACACAAATTAGGCTGAGAATGGG 58.981 43.478 0.00 0.00 0.00 4.00
131 132 3.026694 ACAAATTAGGCTGAGAATGGGC 58.973 45.455 0.00 0.00 0.00 5.36
132 133 1.972872 AATTAGGCTGAGAATGGGCG 58.027 50.000 0.00 0.00 0.00 6.13
133 134 0.109342 ATTAGGCTGAGAATGGGCGG 59.891 55.000 0.00 0.00 0.00 6.13
134 135 2.608970 TTAGGCTGAGAATGGGCGGC 62.609 60.000 0.00 0.00 35.68 6.53
135 136 4.802051 GGCTGAGAATGGGCGGCA 62.802 66.667 12.47 0.00 38.13 5.69
136 137 3.207669 GCTGAGAATGGGCGGCAG 61.208 66.667 12.47 0.00 36.43 4.85
137 138 2.515523 CTGAGAATGGGCGGCAGG 60.516 66.667 12.47 0.00 0.00 4.85
138 139 4.802051 TGAGAATGGGCGGCAGGC 62.802 66.667 12.47 0.57 42.96 4.85
146 147 4.770874 GGCGGCAGGCGGACTAAA 62.771 66.667 19.28 0.00 44.92 1.85
147 148 2.744709 GCGGCAGGCGGACTAAAA 60.745 61.111 19.28 0.00 0.00 1.52
148 149 2.750888 GCGGCAGGCGGACTAAAAG 61.751 63.158 19.28 0.00 0.00 2.27
149 150 2.750888 CGGCAGGCGGACTAAAAGC 61.751 63.158 8.89 0.00 0.00 3.51
150 151 2.750888 GGCAGGCGGACTAAAAGCG 61.751 63.158 0.00 0.00 0.00 4.68
151 152 2.750888 GCAGGCGGACTAAAAGCGG 61.751 63.158 0.00 0.00 0.00 5.52
152 153 1.079405 CAGGCGGACTAAAAGCGGA 60.079 57.895 0.00 0.00 0.00 5.54
153 154 0.462047 CAGGCGGACTAAAAGCGGAT 60.462 55.000 0.00 0.00 0.00 4.18
154 155 0.462047 AGGCGGACTAAAAGCGGATG 60.462 55.000 0.00 0.00 0.00 3.51
155 156 0.743345 GGCGGACTAAAAGCGGATGT 60.743 55.000 0.00 0.00 0.00 3.06
156 157 0.373716 GCGGACTAAAAGCGGATGTG 59.626 55.000 0.00 0.00 0.00 3.21
157 158 0.373716 CGGACTAAAAGCGGATGTGC 59.626 55.000 0.00 0.00 0.00 4.57
158 159 0.373716 GGACTAAAAGCGGATGTGCG 59.626 55.000 0.00 0.00 40.67 5.34
159 160 1.076332 GACTAAAAGCGGATGTGCGT 58.924 50.000 0.00 0.00 40.67 5.24
160 161 1.060698 GACTAAAAGCGGATGTGCGTC 59.939 52.381 0.00 0.00 40.67 5.19
161 162 0.373716 CTAAAAGCGGATGTGCGTCC 59.626 55.000 0.43 0.43 40.67 4.79
167 168 2.776072 GGATGTGCGTCCGTTTCG 59.224 61.111 0.00 0.00 0.00 3.46
190 191 3.656045 CGCGTTGGCCCGACTTTT 61.656 61.111 0.00 0.00 35.02 2.27
191 192 2.254350 GCGTTGGCCCGACTTTTC 59.746 61.111 0.00 0.00 0.00 2.29
192 193 2.951458 CGTTGGCCCGACTTTTCC 59.049 61.111 0.00 0.00 0.00 3.13
193 194 2.951458 GTTGGCCCGACTTTTCCG 59.049 61.111 0.00 0.00 0.00 4.30
194 195 1.895231 GTTGGCCCGACTTTTCCGT 60.895 57.895 0.00 0.00 0.00 4.69
195 196 1.598685 TTGGCCCGACTTTTCCGTC 60.599 57.895 0.00 0.00 0.00 4.79
196 197 2.745100 GGCCCGACTTTTCCGTCC 60.745 66.667 0.00 0.00 0.00 4.79
197 198 3.116531 GCCCGACTTTTCCGTCCG 61.117 66.667 0.00 0.00 0.00 4.79
198 199 3.116531 CCCGACTTTTCCGTCCGC 61.117 66.667 0.00 0.00 0.00 5.54
199 200 3.475774 CCGACTTTTCCGTCCGCG 61.476 66.667 0.00 0.00 37.95 6.46
200 201 4.130281 CGACTTTTCCGTCCGCGC 62.130 66.667 0.00 0.00 36.67 6.86
201 202 3.785499 GACTTTTCCGTCCGCGCC 61.785 66.667 0.00 0.00 36.67 6.53
210 211 3.774702 GTCCGCGCCGACTCAAAC 61.775 66.667 19.66 0.00 0.00 2.93
218 219 4.117372 CGACTCAAACGGACGCGC 62.117 66.667 5.73 0.00 0.00 6.86
219 220 4.117372 GACTCAAACGGACGCGCG 62.117 66.667 30.96 30.96 0.00 6.86
220 221 4.634133 ACTCAAACGGACGCGCGA 62.634 61.111 39.36 10.55 0.00 5.87
221 222 3.827784 CTCAAACGGACGCGCGAG 61.828 66.667 39.36 27.35 0.00 5.03
224 225 4.430765 AAACGGACGCGCGAGGAT 62.431 61.111 39.36 15.03 0.00 3.24
225 226 3.055080 AAACGGACGCGCGAGGATA 62.055 57.895 39.36 0.00 0.00 2.59
226 227 2.546645 AAACGGACGCGCGAGGATAA 62.547 55.000 39.36 0.00 0.00 1.75
227 228 2.278336 CGGACGCGCGAGGATAAA 60.278 61.111 39.36 0.00 0.00 1.40
228 229 1.874915 CGGACGCGCGAGGATAAAA 60.875 57.895 39.36 0.00 0.00 1.52
229 230 1.213094 CGGACGCGCGAGGATAAAAT 61.213 55.000 39.36 10.81 0.00 1.82
230 231 0.232303 GGACGCGCGAGGATAAAATG 59.768 55.000 39.36 2.23 0.00 2.32
231 232 0.232303 GACGCGCGAGGATAAAATGG 59.768 55.000 39.36 1.99 0.00 3.16
232 233 0.179094 ACGCGCGAGGATAAAATGGA 60.179 50.000 39.36 0.00 0.00 3.41
233 234 1.148310 CGCGCGAGGATAAAATGGAT 58.852 50.000 28.94 0.00 0.00 3.41
234 235 1.126846 CGCGCGAGGATAAAATGGATC 59.873 52.381 28.94 0.00 0.00 3.36
235 236 1.126846 GCGCGAGGATAAAATGGATCG 59.873 52.381 12.10 0.00 0.00 3.69
236 237 1.726791 CGCGAGGATAAAATGGATCGG 59.273 52.381 0.00 0.00 0.00 4.18
237 238 2.767505 GCGAGGATAAAATGGATCGGT 58.232 47.619 0.00 0.00 0.00 4.69
238 239 2.480419 GCGAGGATAAAATGGATCGGTG 59.520 50.000 0.00 0.00 0.00 4.94
239 240 2.480419 CGAGGATAAAATGGATCGGTGC 59.520 50.000 0.00 0.00 0.00 5.01
240 241 2.480419 GAGGATAAAATGGATCGGTGCG 59.520 50.000 0.00 0.00 0.00 5.34
241 242 2.158813 AGGATAAAATGGATCGGTGCGT 60.159 45.455 0.00 0.00 0.00 5.24
242 243 2.616842 GGATAAAATGGATCGGTGCGTT 59.383 45.455 0.00 0.00 0.00 4.84
243 244 3.548014 GGATAAAATGGATCGGTGCGTTG 60.548 47.826 0.00 0.00 0.00 4.10
244 245 0.525761 AAAATGGATCGGTGCGTTGG 59.474 50.000 0.00 0.00 0.00 3.77
245 246 0.322098 AAATGGATCGGTGCGTTGGA 60.322 50.000 0.00 0.00 0.00 3.53
246 247 0.744414 AATGGATCGGTGCGTTGGAG 60.744 55.000 0.00 0.00 0.00 3.86
247 248 1.899437 ATGGATCGGTGCGTTGGAGT 61.899 55.000 0.00 0.00 0.00 3.85
248 249 1.375523 GGATCGGTGCGTTGGAGTT 60.376 57.895 0.00 0.00 0.00 3.01
249 250 1.635663 GGATCGGTGCGTTGGAGTTG 61.636 60.000 0.00 0.00 0.00 3.16
250 251 2.240612 GATCGGTGCGTTGGAGTTGC 62.241 60.000 0.00 0.00 0.00 4.17
251 252 2.731691 ATCGGTGCGTTGGAGTTGCT 62.732 55.000 0.00 0.00 0.00 3.91
252 253 2.946762 GGTGCGTTGGAGTTGCTC 59.053 61.111 0.00 0.00 0.00 4.26
253 254 1.598130 GGTGCGTTGGAGTTGCTCT 60.598 57.895 0.00 0.00 0.00 4.09
254 255 0.320421 GGTGCGTTGGAGTTGCTCTA 60.320 55.000 0.00 0.00 0.00 2.43
255 256 1.508632 GTGCGTTGGAGTTGCTCTAA 58.491 50.000 0.00 0.00 0.00 2.10
256 257 1.194772 GTGCGTTGGAGTTGCTCTAAC 59.805 52.381 13.14 13.14 44.66 2.34
261 262 4.224715 GTTGGAGTTGCTCTAACAAACC 57.775 45.455 16.75 0.69 46.43 3.27
262 263 3.857157 TGGAGTTGCTCTAACAAACCT 57.143 42.857 0.00 0.00 41.88 3.50
263 264 4.164843 TGGAGTTGCTCTAACAAACCTT 57.835 40.909 0.00 0.00 41.88 3.50
264 265 4.532834 TGGAGTTGCTCTAACAAACCTTT 58.467 39.130 0.00 0.00 41.88 3.11
265 266 4.953579 TGGAGTTGCTCTAACAAACCTTTT 59.046 37.500 0.00 0.00 41.88 2.27
266 267 5.420739 TGGAGTTGCTCTAACAAACCTTTTT 59.579 36.000 0.00 0.00 41.88 1.94
294 295 8.929746 TCTAGAGAGCATGCAAAATTTATATCG 58.070 33.333 21.98 0.00 0.00 2.92
295 296 7.502120 AGAGAGCATGCAAAATTTATATCGT 57.498 32.000 21.98 0.00 0.00 3.73
296 297 8.607441 AGAGAGCATGCAAAATTTATATCGTA 57.393 30.769 21.98 0.00 0.00 3.43
297 298 9.056005 AGAGAGCATGCAAAATTTATATCGTAA 57.944 29.630 21.98 0.00 0.00 3.18
298 299 9.107367 GAGAGCATGCAAAATTTATATCGTAAC 57.893 33.333 21.98 0.00 0.00 2.50
299 300 8.840321 AGAGCATGCAAAATTTATATCGTAACT 58.160 29.630 21.98 0.00 0.00 2.24
300 301 9.450807 GAGCATGCAAAATTTATATCGTAACTT 57.549 29.630 21.98 0.00 0.00 2.66
301 302 9.801873 AGCATGCAAAATTTATATCGTAACTTT 57.198 25.926 21.98 0.00 0.00 2.66
335 336 7.667219 AGGAAAGTCAATTATCTTCTTGAAGCA 59.333 33.333 5.56 0.00 33.45 3.91
337 338 6.434018 AGTCAATTATCTTCTTGAAGCAGC 57.566 37.500 5.56 0.00 33.45 5.25
355 357 0.503961 GCGTTGCTCAACAATGTTGC 59.496 50.000 20.34 10.98 45.50 4.17
356 358 0.771756 CGTTGCTCAACAATGTTGCG 59.228 50.000 20.34 15.81 41.27 4.85
361 363 1.268999 GCTCAACAATGTTGCGGACAA 60.269 47.619 20.34 2.24 42.62 3.18
376 378 6.438259 TGCGGACAATTTATTTCGGATTTA 57.562 33.333 0.00 0.00 0.00 1.40
439 442 2.477863 CCGAAACAAAAGATGCCGATCC 60.478 50.000 0.00 0.00 0.00 3.36
480 483 1.875963 CAAGCATTCCACGTGACCC 59.124 57.895 19.30 0.21 0.00 4.46
483 486 1.745489 GCATTCCACGTGACCCTCC 60.745 63.158 19.30 0.00 0.00 4.30
507 530 1.534729 GAATTTGTGGAACGCTCCCT 58.465 50.000 1.61 0.00 42.39 4.20
552 575 4.408182 AGATCCCTGCAACATACTGTAC 57.592 45.455 0.00 0.00 0.00 2.90
553 576 3.774766 AGATCCCTGCAACATACTGTACA 59.225 43.478 0.00 0.00 0.00 2.90
584 610 3.121019 CGTGACCGGATCCTCCTC 58.879 66.667 9.46 1.77 33.30 3.71
585 611 2.491022 CGTGACCGGATCCTCCTCC 61.491 68.421 9.46 0.00 33.30 4.30
601 627 1.563435 CTCCGCATGGCATCGATCAC 61.563 60.000 17.04 0.00 34.14 3.06
627 653 2.726760 GCTCAAACACGATAGATAGCGG 59.273 50.000 2.36 0.00 39.75 5.52
628 654 3.309388 CTCAAACACGATAGATAGCGGG 58.691 50.000 0.00 0.00 45.17 6.13
639 665 5.871524 CGATAGATAGCGGGTAACAGTAGTA 59.128 44.000 0.00 0.00 39.76 1.82
655 681 0.388649 AGTAGCGCCGAGAACAACTG 60.389 55.000 2.29 0.00 0.00 3.16
696 723 3.202906 CGAGATGGCGGAAGGAATTAAA 58.797 45.455 0.00 0.00 0.00 1.52
697 724 3.625764 CGAGATGGCGGAAGGAATTAAAA 59.374 43.478 0.00 0.00 0.00 1.52
698 725 4.495844 CGAGATGGCGGAAGGAATTAAAAC 60.496 45.833 0.00 0.00 0.00 2.43
700 727 1.813786 TGGCGGAAGGAATTAAAACCG 59.186 47.619 0.00 0.00 42.63 4.44
778 808 2.896243 TCGCGCGGCTTAATTAAAAA 57.104 40.000 31.69 1.65 0.00 1.94
801 831 2.694616 AGGAGGGGCGGCCAATTA 60.695 61.111 30.95 0.00 0.00 1.40
887 936 1.580059 TTATTTCACTCGGCCTCCCT 58.420 50.000 0.00 0.00 0.00 4.20
888 937 1.120530 TATTTCACTCGGCCTCCCTC 58.879 55.000 0.00 0.00 0.00 4.30
929 978 2.610374 TCGGTTACCTCAATTATTGCGC 59.390 45.455 0.00 0.00 0.00 6.09
930 979 2.286772 CGGTTACCTCAATTATTGCGCC 60.287 50.000 4.18 0.00 0.00 6.53
931 980 2.949644 GGTTACCTCAATTATTGCGCCT 59.050 45.455 4.18 0.00 0.00 5.52
932 981 3.380320 GGTTACCTCAATTATTGCGCCTT 59.620 43.478 4.18 0.00 0.00 4.35
1122 1186 2.658268 CACGACGTGCTGCAGACA 60.658 61.111 20.43 12.49 0.00 3.41
1128 1192 3.349006 GTGCTGCAGACACACGGG 61.349 66.667 26.21 0.00 37.96 5.28
1221 1285 3.721706 CTGGAGTCCCCCTGCACC 61.722 72.222 6.74 0.00 36.48 5.01
1254 1318 2.262292 GGCCTGCGGTACAACGTA 59.738 61.111 0.00 0.00 35.98 3.57
1359 1423 4.415332 AGCATCCGCGTCGACGTT 62.415 61.111 35.48 17.54 45.49 3.99
1470 1534 4.519437 TCGCGCATCCTCCTGCAG 62.519 66.667 8.75 6.78 42.40 4.41
1488 1552 3.261951 CCGCATCAGGTAACGCCG 61.262 66.667 0.00 0.00 43.70 6.46
1507 1571 0.381801 GTCGCGCCATCCATGATTTT 59.618 50.000 0.00 0.00 0.00 1.82
1521 1585 1.211949 TGATTTTCCCTCCCCATCGAC 59.788 52.381 0.00 0.00 0.00 4.20
1561 1628 3.214328 ACAGTTGCAACCTCCTAACAAG 58.786 45.455 25.62 5.93 0.00 3.16
1603 1670 2.280186 GCCGCAGATTAGGGACGG 60.280 66.667 0.00 0.00 46.50 4.79
1743 1820 3.119673 CGGCTAGTGTGCAGATAGATAGG 60.120 52.174 0.00 0.00 34.04 2.57
1762 1839 2.616842 AGGTGTGGTCATTCGTTTTGTC 59.383 45.455 0.00 0.00 0.00 3.18
1812 1906 3.047280 CCGCTGCGTGCCAAAGTA 61.047 61.111 21.59 0.00 38.78 2.24
1856 1950 2.564975 CGTGTACTTCTCCGGCGT 59.435 61.111 6.01 0.00 0.00 5.68
1857 1951 1.796151 CGTGTACTTCTCCGGCGTA 59.204 57.895 6.01 0.00 0.00 4.42
1879 1976 1.523758 GCCGATCGCCATATTTTCCT 58.476 50.000 10.32 0.00 0.00 3.36
1880 1977 1.197721 GCCGATCGCCATATTTTCCTG 59.802 52.381 10.32 0.00 0.00 3.86
1896 1993 2.134354 TCCTGGGTAATGGATGATGCA 58.866 47.619 0.00 0.00 0.00 3.96
1898 1995 2.823747 CCTGGGTAATGGATGATGCATG 59.176 50.000 2.46 0.00 0.00 4.06
1899 1996 3.493334 CTGGGTAATGGATGATGCATGT 58.507 45.455 2.46 0.00 0.00 3.21
1904 2011 5.536161 GGGTAATGGATGATGCATGTAAAGT 59.464 40.000 2.46 0.00 0.00 2.66
1916 2023 7.710044 TGATGCATGTAAAGTTTTTGTGTGATT 59.290 29.630 2.46 0.00 0.00 2.57
1918 2025 8.572828 TGCATGTAAAGTTTTTGTGTGATTAG 57.427 30.769 0.00 0.00 0.00 1.73
1948 2061 5.680619 TCGTTGGGTTCTGCATATTATTCT 58.319 37.500 0.00 0.00 0.00 2.40
1950 2063 6.038161 TCGTTGGGTTCTGCATATTATTCTTG 59.962 38.462 0.00 0.00 0.00 3.02
1982 2110 0.820871 CCTTTCTCCTCACTCCCTCG 59.179 60.000 0.00 0.00 0.00 4.63
2008 2136 3.314080 TGTCAAATCCAACCGAACTGAAC 59.686 43.478 0.00 0.00 0.00 3.18
2009 2137 3.564225 GTCAAATCCAACCGAACTGAACT 59.436 43.478 0.00 0.00 0.00 3.01
2011 2139 3.485463 AATCCAACCGAACTGAACTGA 57.515 42.857 0.00 0.00 0.00 3.41
2012 2140 2.992124 TCCAACCGAACTGAACTGAA 57.008 45.000 0.00 0.00 0.00 3.02
2013 2141 3.485463 TCCAACCGAACTGAACTGAAT 57.515 42.857 0.00 0.00 0.00 2.57
2015 2143 2.157668 CCAACCGAACTGAACTGAATCG 59.842 50.000 0.00 0.00 0.00 3.34
2017 2145 2.673833 ACCGAACTGAACTGAATCGTC 58.326 47.619 0.00 0.00 0.00 4.20
2018 2146 1.993370 CCGAACTGAACTGAATCGTCC 59.007 52.381 0.00 0.00 0.00 4.79
2020 2148 2.352814 CGAACTGAACTGAATCGTCCCT 60.353 50.000 0.00 0.00 0.00 4.20
2021 2149 3.665190 GAACTGAACTGAATCGTCCCTT 58.335 45.455 0.00 0.00 0.00 3.95
2022 2150 3.045601 ACTGAACTGAATCGTCCCTTG 57.954 47.619 0.00 0.00 0.00 3.61
2071 2199 1.200716 CGTTGTTCCCTGTACTAGCGA 59.799 52.381 0.00 0.00 0.00 4.93
2076 2204 2.039818 TCCCTGTACTAGCGACTCTG 57.960 55.000 0.00 0.00 0.00 3.35
2231 2379 0.520404 GGTGCTGTTGACTGATGCAG 59.480 55.000 0.00 0.00 37.52 4.41
2319 2505 2.004733 CAATCAATCAGCACAGCTCGA 58.995 47.619 0.00 0.00 36.40 4.04
2351 2537 3.064987 CTCGGAGATCGCGGTGGTT 62.065 63.158 6.13 0.00 39.05 3.67
2359 2545 0.034337 ATCGCGGTGGTTGTTGTACT 59.966 50.000 6.13 0.00 0.00 2.73
2427 2671 2.113139 CCACTCAACAAGCCGGGT 59.887 61.111 0.00 0.00 0.00 5.28
2524 2773 1.902508 GGGAAGCGAGATGATGGGATA 59.097 52.381 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.483288 CCGTCGCCCATTTTTCGG 59.517 61.111 0.00 0.00 0.00 4.30
1 2 2.202427 GCCGTCGCCCATTTTTCG 60.202 61.111 0.00 0.00 0.00 3.46
2 3 2.202427 CGCCGTCGCCCATTTTTC 60.202 61.111 0.00 0.00 0.00 2.29
28 29 3.741476 CAGCAAACCCTCGCCTGC 61.741 66.667 0.00 0.00 34.96 4.85
29 30 2.281761 ACAGCAAACCCTCGCCTG 60.282 61.111 0.00 0.00 0.00 4.85
30 31 2.032681 GACAGCAAACCCTCGCCT 59.967 61.111 0.00 0.00 0.00 5.52
31 32 3.423154 CGACAGCAAACCCTCGCC 61.423 66.667 0.00 0.00 0.00 5.54
32 33 0.459585 TATCGACAGCAAACCCTCGC 60.460 55.000 0.00 0.00 0.00 5.03
33 34 1.860950 CATATCGACAGCAAACCCTCG 59.139 52.381 0.00 0.00 0.00 4.63
34 35 2.213499 CCATATCGACAGCAAACCCTC 58.787 52.381 0.00 0.00 0.00 4.30
35 36 1.134098 CCCATATCGACAGCAAACCCT 60.134 52.381 0.00 0.00 0.00 4.34
36 37 1.308998 CCCATATCGACAGCAAACCC 58.691 55.000 0.00 0.00 0.00 4.11
37 38 1.670811 CACCCATATCGACAGCAAACC 59.329 52.381 0.00 0.00 0.00 3.27
38 39 1.670811 CCACCCATATCGACAGCAAAC 59.329 52.381 0.00 0.00 0.00 2.93
39 40 1.557371 TCCACCCATATCGACAGCAAA 59.443 47.619 0.00 0.00 0.00 3.68
40 41 1.199615 TCCACCCATATCGACAGCAA 58.800 50.000 0.00 0.00 0.00 3.91
41 42 1.138859 CTTCCACCCATATCGACAGCA 59.861 52.381 0.00 0.00 0.00 4.41
42 43 1.412710 TCTTCCACCCATATCGACAGC 59.587 52.381 0.00 0.00 0.00 4.40
43 44 2.036475 CCTCTTCCACCCATATCGACAG 59.964 54.545 0.00 0.00 0.00 3.51
44 45 2.039418 CCTCTTCCACCCATATCGACA 58.961 52.381 0.00 0.00 0.00 4.35
45 46 2.317040 TCCTCTTCCACCCATATCGAC 58.683 52.381 0.00 0.00 0.00 4.20
46 47 2.767644 TCCTCTTCCACCCATATCGA 57.232 50.000 0.00 0.00 0.00 3.59
47 48 2.027745 CCATCCTCTTCCACCCATATCG 60.028 54.545 0.00 0.00 0.00 2.92
48 49 2.290577 GCCATCCTCTTCCACCCATATC 60.291 54.545 0.00 0.00 0.00 1.63
49 50 1.707427 GCCATCCTCTTCCACCCATAT 59.293 52.381 0.00 0.00 0.00 1.78
50 51 1.140312 GCCATCCTCTTCCACCCATA 58.860 55.000 0.00 0.00 0.00 2.74
51 52 1.649271 GGCCATCCTCTTCCACCCAT 61.649 60.000 0.00 0.00 0.00 4.00
52 53 2.308722 GGCCATCCTCTTCCACCCA 61.309 63.158 0.00 0.00 0.00 4.51
53 54 1.863155 TTGGCCATCCTCTTCCACCC 61.863 60.000 6.09 0.00 0.00 4.61
54 55 0.259938 ATTGGCCATCCTCTTCCACC 59.740 55.000 6.09 0.00 0.00 4.61
55 56 1.341383 ACATTGGCCATCCTCTTCCAC 60.341 52.381 6.09 0.00 0.00 4.02
56 57 1.002069 ACATTGGCCATCCTCTTCCA 58.998 50.000 6.09 0.00 0.00 3.53
57 58 1.396653 CACATTGGCCATCCTCTTCC 58.603 55.000 6.09 0.00 0.00 3.46
58 59 0.743097 GCACATTGGCCATCCTCTTC 59.257 55.000 6.09 0.00 0.00 2.87
59 60 2.892025 GCACATTGGCCATCCTCTT 58.108 52.632 6.09 0.00 0.00 2.85
60 61 4.672251 GCACATTGGCCATCCTCT 57.328 55.556 6.09 0.00 0.00 3.69
68 69 1.369091 CTAGTCGGTGGCACATTGGC 61.369 60.000 20.82 10.05 44.52 4.52
69 70 1.369091 GCTAGTCGGTGGCACATTGG 61.369 60.000 20.82 5.45 44.52 3.16
70 71 0.673333 TGCTAGTCGGTGGCACATTG 60.673 55.000 20.82 8.68 44.52 2.82
71 72 1.676968 TGCTAGTCGGTGGCACATT 59.323 52.632 20.82 3.88 44.52 2.71
72 73 3.387716 TGCTAGTCGGTGGCACAT 58.612 55.556 20.82 4.57 44.52 3.21
75 76 4.735132 GCGTGCTAGTCGGTGGCA 62.735 66.667 10.39 0.00 41.05 4.92
77 78 3.989698 CTGGCGTGCTAGTCGGTGG 62.990 68.421 10.39 0.00 0.00 4.61
78 79 2.507102 CTGGCGTGCTAGTCGGTG 60.507 66.667 10.39 0.00 0.00 4.94
79 80 3.760035 CCTGGCGTGCTAGTCGGT 61.760 66.667 4.49 0.00 0.00 4.69
80 81 4.514577 CCCTGGCGTGCTAGTCGG 62.515 72.222 4.49 0.00 0.00 4.79
81 82 4.514577 CCCCTGGCGTGCTAGTCG 62.515 72.222 4.49 5.38 0.00 4.18
82 83 4.162690 CCCCCTGGCGTGCTAGTC 62.163 72.222 4.49 0.00 0.00 2.59
83 84 4.715130 TCCCCCTGGCGTGCTAGT 62.715 66.667 4.49 0.00 0.00 2.57
84 85 3.854669 CTCCCCCTGGCGTGCTAG 61.855 72.222 0.00 0.00 0.00 3.42
89 90 4.332543 TTCTCCTCCCCCTGGCGT 62.333 66.667 0.00 0.00 0.00 5.68
90 91 3.474570 CTTCTCCTCCCCCTGGCG 61.475 72.222 0.00 0.00 0.00 5.69
91 92 2.041265 TCTTCTCCTCCCCCTGGC 59.959 66.667 0.00 0.00 0.00 4.85
92 93 1.081092 TGTCTTCTCCTCCCCCTGG 59.919 63.158 0.00 0.00 0.00 4.45
93 94 0.545309 TGTGTCTTCTCCTCCCCCTG 60.545 60.000 0.00 0.00 0.00 4.45
94 95 0.193574 TTGTGTCTTCTCCTCCCCCT 59.806 55.000 0.00 0.00 0.00 4.79
95 96 1.064825 TTTGTGTCTTCTCCTCCCCC 58.935 55.000 0.00 0.00 0.00 5.40
96 97 3.441500 AATTTGTGTCTTCTCCTCCCC 57.558 47.619 0.00 0.00 0.00 4.81
97 98 4.518249 CCTAATTTGTGTCTTCTCCTCCC 58.482 47.826 0.00 0.00 0.00 4.30
98 99 3.942115 GCCTAATTTGTGTCTTCTCCTCC 59.058 47.826 0.00 0.00 0.00 4.30
99 100 4.633565 CAGCCTAATTTGTGTCTTCTCCTC 59.366 45.833 0.00 0.00 0.00 3.71
100 101 4.287067 TCAGCCTAATTTGTGTCTTCTCCT 59.713 41.667 0.00 0.00 0.00 3.69
101 102 4.579869 TCAGCCTAATTTGTGTCTTCTCC 58.420 43.478 0.00 0.00 0.00 3.71
102 103 5.482908 TCTCAGCCTAATTTGTGTCTTCTC 58.517 41.667 0.00 0.00 0.00 2.87
103 104 5.489792 TCTCAGCCTAATTTGTGTCTTCT 57.510 39.130 0.00 0.00 0.00 2.85
104 105 6.404074 CCATTCTCAGCCTAATTTGTGTCTTC 60.404 42.308 0.00 0.00 0.00 2.87
105 106 5.416952 CCATTCTCAGCCTAATTTGTGTCTT 59.583 40.000 0.00 0.00 0.00 3.01
106 107 4.946157 CCATTCTCAGCCTAATTTGTGTCT 59.054 41.667 0.00 0.00 0.00 3.41
107 108 4.096984 CCCATTCTCAGCCTAATTTGTGTC 59.903 45.833 0.00 0.00 0.00 3.67
108 109 4.019174 CCCATTCTCAGCCTAATTTGTGT 58.981 43.478 0.00 0.00 0.00 3.72
109 110 3.181483 GCCCATTCTCAGCCTAATTTGTG 60.181 47.826 0.00 0.00 0.00 3.33
110 111 3.026694 GCCCATTCTCAGCCTAATTTGT 58.973 45.455 0.00 0.00 0.00 2.83
111 112 2.033801 CGCCCATTCTCAGCCTAATTTG 59.966 50.000 0.00 0.00 0.00 2.32
112 113 2.301346 CGCCCATTCTCAGCCTAATTT 58.699 47.619 0.00 0.00 0.00 1.82
113 114 1.477558 CCGCCCATTCTCAGCCTAATT 60.478 52.381 0.00 0.00 0.00 1.40
114 115 0.109342 CCGCCCATTCTCAGCCTAAT 59.891 55.000 0.00 0.00 0.00 1.73
115 116 1.526887 CCGCCCATTCTCAGCCTAA 59.473 57.895 0.00 0.00 0.00 2.69
116 117 3.106986 GCCGCCCATTCTCAGCCTA 62.107 63.158 0.00 0.00 0.00 3.93
117 118 4.496336 GCCGCCCATTCTCAGCCT 62.496 66.667 0.00 0.00 0.00 4.58
118 119 4.802051 TGCCGCCCATTCTCAGCC 62.802 66.667 0.00 0.00 0.00 4.85
119 120 3.207669 CTGCCGCCCATTCTCAGC 61.208 66.667 0.00 0.00 0.00 4.26
120 121 2.515523 CCTGCCGCCCATTCTCAG 60.516 66.667 0.00 0.00 0.00 3.35
121 122 4.802051 GCCTGCCGCCCATTCTCA 62.802 66.667 0.00 0.00 0.00 3.27
129 130 4.770874 TTTAGTCCGCCTGCCGCC 62.771 66.667 0.00 0.00 35.03 6.13
130 131 2.744709 TTTTAGTCCGCCTGCCGC 60.745 61.111 0.00 0.00 35.03 6.53
131 132 2.750888 GCTTTTAGTCCGCCTGCCG 61.751 63.158 0.00 0.00 0.00 5.69
132 133 2.750888 CGCTTTTAGTCCGCCTGCC 61.751 63.158 0.00 0.00 0.00 4.85
133 134 2.750888 CCGCTTTTAGTCCGCCTGC 61.751 63.158 0.00 0.00 0.00 4.85
134 135 0.462047 ATCCGCTTTTAGTCCGCCTG 60.462 55.000 0.00 0.00 0.00 4.85
135 136 0.462047 CATCCGCTTTTAGTCCGCCT 60.462 55.000 0.00 0.00 0.00 5.52
136 137 0.743345 ACATCCGCTTTTAGTCCGCC 60.743 55.000 0.00 0.00 0.00 6.13
137 138 0.373716 CACATCCGCTTTTAGTCCGC 59.626 55.000 0.00 0.00 0.00 5.54
138 139 0.373716 GCACATCCGCTTTTAGTCCG 59.626 55.000 0.00 0.00 0.00 4.79
139 140 0.373716 CGCACATCCGCTTTTAGTCC 59.626 55.000 0.00 0.00 0.00 3.85
140 141 1.060698 GACGCACATCCGCTTTTAGTC 59.939 52.381 0.00 0.00 0.00 2.59
141 142 1.076332 GACGCACATCCGCTTTTAGT 58.924 50.000 0.00 0.00 0.00 2.24
142 143 0.373716 GGACGCACATCCGCTTTTAG 59.626 55.000 0.00 0.00 0.00 1.85
143 144 2.462503 GGACGCACATCCGCTTTTA 58.537 52.632 0.00 0.00 0.00 1.52
144 145 3.263941 GGACGCACATCCGCTTTT 58.736 55.556 0.00 0.00 0.00 2.27
150 151 2.776072 CGAAACGGACGCACATCC 59.224 61.111 0.00 0.00 35.16 3.51
174 175 2.254350 GAAAAGTCGGGCCAACGC 59.746 61.111 4.39 0.00 0.00 4.84
175 176 2.951458 GGAAAAGTCGGGCCAACG 59.049 61.111 4.39 0.00 0.00 4.10
176 177 1.848932 GACGGAAAAGTCGGGCCAAC 61.849 60.000 4.39 1.37 0.00 3.77
177 178 1.598685 GACGGAAAAGTCGGGCCAA 60.599 57.895 4.39 0.00 0.00 4.52
178 179 2.031465 GACGGAAAAGTCGGGCCA 59.969 61.111 4.39 0.00 0.00 5.36
179 180 2.745100 GGACGGAAAAGTCGGGCC 60.745 66.667 0.00 0.00 44.39 5.80
180 181 3.116531 CGGACGGAAAAGTCGGGC 61.117 66.667 0.00 0.00 41.81 6.13
181 182 3.116531 GCGGACGGAAAAGTCGGG 61.117 66.667 6.77 0.00 41.81 5.14
182 183 3.475774 CGCGGACGGAAAAGTCGG 61.476 66.667 0.00 1.16 41.81 4.79
183 184 4.130281 GCGCGGACGGAAAAGTCG 62.130 66.667 8.83 0.00 41.81 4.18
184 185 3.785499 GGCGCGGACGGAAAAGTC 61.785 66.667 8.83 0.00 40.57 3.01
193 194 3.774702 GTTTGAGTCGGCGCGGAC 61.775 66.667 33.39 33.39 37.19 4.79
197 198 3.774702 GTCCGTTTGAGTCGGCGC 61.775 66.667 0.00 0.00 46.49 6.53
198 199 3.467119 CGTCCGTTTGAGTCGGCG 61.467 66.667 0.00 0.00 46.49 6.46
199 200 3.774702 GCGTCCGTTTGAGTCGGC 61.775 66.667 0.00 0.00 46.49 5.54
201 202 4.117372 GCGCGTCCGTTTGAGTCG 62.117 66.667 8.43 0.00 36.67 4.18
202 203 4.117372 CGCGCGTCCGTTTGAGTC 62.117 66.667 24.19 0.00 36.67 3.36
203 204 4.634133 TCGCGCGTCCGTTTGAGT 62.634 61.111 30.98 0.00 36.67 3.41
204 205 3.827784 CTCGCGCGTCCGTTTGAG 61.828 66.667 30.98 13.33 36.67 3.02
207 208 2.546645 TTATCCTCGCGCGTCCGTTT 62.547 55.000 30.98 13.19 36.67 3.60
208 209 2.546645 TTTATCCTCGCGCGTCCGTT 62.547 55.000 30.98 14.27 36.67 4.44
209 210 2.546645 TTTTATCCTCGCGCGTCCGT 62.547 55.000 30.98 16.72 36.67 4.69
210 211 1.213094 ATTTTATCCTCGCGCGTCCG 61.213 55.000 30.98 18.49 37.57 4.79
211 212 0.232303 CATTTTATCCTCGCGCGTCC 59.768 55.000 30.98 0.00 0.00 4.79
212 213 0.232303 CCATTTTATCCTCGCGCGTC 59.768 55.000 30.98 0.00 0.00 5.19
213 214 0.179094 TCCATTTTATCCTCGCGCGT 60.179 50.000 30.98 13.33 0.00 6.01
214 215 1.126846 GATCCATTTTATCCTCGCGCG 59.873 52.381 26.76 26.76 0.00 6.86
215 216 1.126846 CGATCCATTTTATCCTCGCGC 59.873 52.381 0.00 0.00 0.00 6.86
216 217 1.726791 CCGATCCATTTTATCCTCGCG 59.273 52.381 0.00 0.00 0.00 5.87
217 218 2.480419 CACCGATCCATTTTATCCTCGC 59.520 50.000 0.00 0.00 0.00 5.03
218 219 2.480419 GCACCGATCCATTTTATCCTCG 59.520 50.000 0.00 0.00 0.00 4.63
219 220 2.480419 CGCACCGATCCATTTTATCCTC 59.520 50.000 0.00 0.00 0.00 3.71
220 221 2.158813 ACGCACCGATCCATTTTATCCT 60.159 45.455 0.00 0.00 0.00 3.24
221 222 2.218603 ACGCACCGATCCATTTTATCC 58.781 47.619 0.00 0.00 0.00 2.59
222 223 3.548014 CCAACGCACCGATCCATTTTATC 60.548 47.826 0.00 0.00 0.00 1.75
223 224 2.357637 CCAACGCACCGATCCATTTTAT 59.642 45.455 0.00 0.00 0.00 1.40
224 225 1.740585 CCAACGCACCGATCCATTTTA 59.259 47.619 0.00 0.00 0.00 1.52
225 226 0.525761 CCAACGCACCGATCCATTTT 59.474 50.000 0.00 0.00 0.00 1.82
226 227 0.322098 TCCAACGCACCGATCCATTT 60.322 50.000 0.00 0.00 0.00 2.32
227 228 0.744414 CTCCAACGCACCGATCCATT 60.744 55.000 0.00 0.00 0.00 3.16
228 229 1.153369 CTCCAACGCACCGATCCAT 60.153 57.895 0.00 0.00 0.00 3.41
229 230 2.107041 AACTCCAACGCACCGATCCA 62.107 55.000 0.00 0.00 0.00 3.41
230 231 1.375523 AACTCCAACGCACCGATCC 60.376 57.895 0.00 0.00 0.00 3.36
231 232 1.787847 CAACTCCAACGCACCGATC 59.212 57.895 0.00 0.00 0.00 3.69
232 233 2.325082 GCAACTCCAACGCACCGAT 61.325 57.895 0.00 0.00 0.00 4.18
233 234 2.970324 GCAACTCCAACGCACCGA 60.970 61.111 0.00 0.00 0.00 4.69
234 235 2.954753 GAGCAACTCCAACGCACCG 61.955 63.158 0.00 0.00 0.00 4.94
235 236 0.320421 TAGAGCAACTCCAACGCACC 60.320 55.000 0.00 0.00 0.00 5.01
236 237 1.194772 GTTAGAGCAACTCCAACGCAC 59.805 52.381 0.00 0.00 34.06 5.34
237 238 1.202592 TGTTAGAGCAACTCCAACGCA 60.203 47.619 2.34 0.00 35.48 5.24
238 239 1.508632 TGTTAGAGCAACTCCAACGC 58.491 50.000 2.34 0.00 35.48 4.84
239 240 3.303791 GGTTTGTTAGAGCAACTCCAACG 60.304 47.826 2.34 0.00 35.48 4.10
240 241 3.883489 AGGTTTGTTAGAGCAACTCCAAC 59.117 43.478 0.00 0.00 38.05 3.77
241 242 4.164843 AGGTTTGTTAGAGCAACTCCAA 57.835 40.909 0.00 0.00 38.05 3.53
242 243 3.857157 AGGTTTGTTAGAGCAACTCCA 57.143 42.857 0.00 0.00 38.05 3.86
243 244 5.515797 AAAAGGTTTGTTAGAGCAACTCC 57.484 39.130 0.00 0.00 38.05 3.85
268 269 8.929746 CGATATAAATTTTGCATGCTCTCTAGA 58.070 33.333 20.33 0.00 0.00 2.43
269 270 8.715998 ACGATATAAATTTTGCATGCTCTCTAG 58.284 33.333 20.33 0.72 0.00 2.43
270 271 8.607441 ACGATATAAATTTTGCATGCTCTCTA 57.393 30.769 20.33 3.45 0.00 2.43
271 272 7.502120 ACGATATAAATTTTGCATGCTCTCT 57.498 32.000 20.33 1.15 0.00 3.10
272 273 9.107367 GTTACGATATAAATTTTGCATGCTCTC 57.893 33.333 20.33 0.00 0.00 3.20
273 274 8.840321 AGTTACGATATAAATTTTGCATGCTCT 58.160 29.630 20.33 0.00 0.00 4.09
274 275 9.450807 AAGTTACGATATAAATTTTGCATGCTC 57.549 29.630 20.33 2.63 0.00 4.26
275 276 9.801873 AAAGTTACGATATAAATTTTGCATGCT 57.198 25.926 20.33 0.00 0.00 3.79
307 308 9.837525 CTTCAAGAAGATAATTGACTTTCCTTG 57.162 33.333 3.76 14.41 40.79 3.61
335 336 1.865248 GCAACATTGTTGAGCAACGCT 60.865 47.619 29.04 0.00 43.94 5.07
337 338 0.771756 CGCAACATTGTTGAGCAACG 59.228 50.000 29.04 19.16 43.94 4.10
404 407 4.285807 TGTTTCGGCCAATGATTAATCG 57.714 40.909 10.80 0.00 0.00 3.34
480 483 0.958382 TTCCACAAATTCCGCGGGAG 60.958 55.000 27.83 7.60 31.21 4.30
483 486 1.154301 CGTTCCACAAATTCCGCGG 60.154 57.895 22.12 22.12 0.00 6.46
507 530 1.593209 GAACTCCGTCGTGGCACAA 60.593 57.895 19.09 0.00 44.16 3.33
552 575 0.888736 TCACGGTTTGCCCATGAGTG 60.889 55.000 0.00 0.00 0.00 3.51
553 576 0.889186 GTCACGGTTTGCCCATGAGT 60.889 55.000 0.00 0.00 29.88 3.41
583 609 1.595109 GTGATCGATGCCATGCGGA 60.595 57.895 0.54 0.00 0.00 5.54
584 610 1.888638 TGTGATCGATGCCATGCGG 60.889 57.895 0.54 0.00 0.00 5.69
585 611 1.277739 GTGTGATCGATGCCATGCG 59.722 57.895 0.54 0.00 0.00 4.73
589 615 1.450134 GCTGGTGTGATCGATGCCA 60.450 57.895 0.54 5.07 0.00 4.92
601 627 2.959516 TCTATCGTGTTTGAGCTGGTG 58.040 47.619 0.00 0.00 0.00 4.17
627 653 0.734889 TCGGCGCTACTACTGTTACC 59.265 55.000 7.64 0.00 0.00 2.85
628 654 1.667724 TCTCGGCGCTACTACTGTTAC 59.332 52.381 7.64 0.00 0.00 2.50
629 655 2.028420 TCTCGGCGCTACTACTGTTA 57.972 50.000 7.64 0.00 0.00 2.41
630 656 1.135460 GTTCTCGGCGCTACTACTGTT 60.135 52.381 7.64 0.00 0.00 3.16
631 657 0.450983 GTTCTCGGCGCTACTACTGT 59.549 55.000 7.64 0.00 0.00 3.55
639 665 0.531974 TTTCAGTTGTTCTCGGCGCT 60.532 50.000 7.64 0.00 0.00 5.92
655 681 0.386478 CTGCTCGGCAACTGCTTTTC 60.386 55.000 1.06 0.00 38.41 2.29
669 695 3.723235 TTCCGCCATCTCGCTGCTC 62.723 63.158 0.00 0.00 0.00 4.26
670 696 3.729965 CTTCCGCCATCTCGCTGCT 62.730 63.158 0.00 0.00 0.00 4.24
801 831 7.268186 GCGTTTTATTTAATTTGTTACGCCT 57.732 32.000 0.00 0.00 44.09 5.52
809 839 5.637387 ACCTGCCAGCGTTTTATTTAATTTG 59.363 36.000 0.00 0.00 0.00 2.32
810 840 5.637387 CACCTGCCAGCGTTTTATTTAATTT 59.363 36.000 0.00 0.00 0.00 1.82
811 841 5.167845 CACCTGCCAGCGTTTTATTTAATT 58.832 37.500 0.00 0.00 0.00 1.40
858 907 3.554337 CCGAGTGAAATAATCTACGGGGG 60.554 52.174 0.00 0.00 36.16 5.40
902 951 6.458342 GCAATAATTGAGGTAACCGAAGAAGG 60.458 42.308 0.00 0.00 37.30 3.46
903 952 6.487103 GCAATAATTGAGGTAACCGAAGAAG 58.513 40.000 0.00 0.00 37.17 2.85
904 953 5.064198 CGCAATAATTGAGGTAACCGAAGAA 59.936 40.000 0.00 0.00 37.17 2.52
905 954 4.569162 CGCAATAATTGAGGTAACCGAAGA 59.431 41.667 0.00 0.00 37.17 2.87
929 978 3.878667 GAGGGGCGGATGGGAAGG 61.879 72.222 0.00 0.00 0.00 3.46
930 979 2.403132 GATGAGGGGCGGATGGGAAG 62.403 65.000 0.00 0.00 0.00 3.46
931 980 2.368192 ATGAGGGGCGGATGGGAA 60.368 61.111 0.00 0.00 0.00 3.97
932 981 2.849162 GATGAGGGGCGGATGGGA 60.849 66.667 0.00 0.00 0.00 4.37
1365 1429 0.591741 CGAAGTAGATGACGCCGGAC 60.592 60.000 5.05 0.00 0.00 4.79
1470 1534 3.573491 GGCGTTACCTGATGCGGC 61.573 66.667 0.00 0.00 42.13 6.53
1473 1537 2.514013 CGACGGCGTTACCTGATGC 61.514 63.158 16.19 0.00 35.61 3.91
1488 1552 0.381801 AAAATCATGGATGGCGCGAC 59.618 50.000 12.10 8.22 0.00 5.19
1493 1557 1.966354 GGAGGGAAAATCATGGATGGC 59.034 52.381 0.00 0.00 0.00 4.40
1494 1558 2.601905 GGGAGGGAAAATCATGGATGG 58.398 52.381 0.00 0.00 0.00 3.51
1507 1571 1.381327 GAGTGTCGATGGGGAGGGA 60.381 63.158 0.00 0.00 0.00 4.20
1521 1585 4.217118 ACTGTACTACTACAAACGGGAGTG 59.783 45.833 0.00 0.00 46.69 3.51
1561 1628 4.759183 ACAGAGAAGACCAATTCAAGAAGC 59.241 41.667 0.00 0.00 0.00 3.86
1631 1698 5.423704 AATCATCCCATCATTGTTGCAAA 57.576 34.783 0.00 0.00 0.00 3.68
1743 1820 3.617669 CAGACAAAACGAATGACCACAC 58.382 45.455 0.00 0.00 0.00 3.82
1866 1963 3.255642 CCATTACCCAGGAAAATATGGCG 59.744 47.826 0.00 0.00 35.10 5.69
1868 1965 6.314120 TCATCCATTACCCAGGAAAATATGG 58.686 40.000 0.00 0.00 37.48 2.74
1879 1976 3.598693 ACATGCATCATCCATTACCCA 57.401 42.857 0.00 0.00 0.00 4.51
1880 1977 5.536161 ACTTTACATGCATCATCCATTACCC 59.464 40.000 0.00 0.00 0.00 3.69
1904 2011 7.490962 ACGAAGATCACTAATCACACAAAAA 57.509 32.000 0.00 0.00 36.79 1.94
1916 2023 3.616560 GCAGAACCCAACGAAGATCACTA 60.617 47.826 0.00 0.00 0.00 2.74
1918 2025 1.464997 GCAGAACCCAACGAAGATCAC 59.535 52.381 0.00 0.00 0.00 3.06
1948 2061 0.465460 AAAGGCACTGACGCTTCCAA 60.465 50.000 0.00 0.00 40.86 3.53
1950 2063 0.603975 AGAAAGGCACTGACGCTTCC 60.604 55.000 0.00 0.00 40.86 3.46
1982 2110 1.808411 TCGGTTGGATTTGACAGAGC 58.192 50.000 0.00 0.00 0.00 4.09
2008 2136 2.464459 GCGCCAAGGGACGATTCAG 61.464 63.158 0.00 0.00 0.00 3.02
2009 2137 2.435938 GCGCCAAGGGACGATTCA 60.436 61.111 0.00 0.00 0.00 2.57
2011 2139 1.895020 TACAGCGCCAAGGGACGATT 61.895 55.000 2.29 0.00 0.00 3.34
2012 2140 2.298158 CTACAGCGCCAAGGGACGAT 62.298 60.000 2.29 0.00 0.00 3.73
2013 2141 2.992689 TACAGCGCCAAGGGACGA 60.993 61.111 2.29 0.00 0.00 4.20
2015 2143 1.448013 GACTACAGCGCCAAGGGAC 60.448 63.158 2.29 0.00 0.00 4.46
2017 2145 1.448540 CAGACTACAGCGCCAAGGG 60.449 63.158 2.29 0.00 0.00 3.95
2018 2146 0.530744 TACAGACTACAGCGCCAAGG 59.469 55.000 2.29 0.00 0.00 3.61
2020 2148 1.472878 CTCTACAGACTACAGCGCCAA 59.527 52.381 2.29 0.00 0.00 4.52
2021 2149 1.095600 CTCTACAGACTACAGCGCCA 58.904 55.000 2.29 0.00 0.00 5.69
2022 2150 0.382515 CCTCTACAGACTACAGCGCC 59.617 60.000 2.29 0.00 0.00 6.53
2071 2199 1.601197 AGTGGTCGAGCGACAGAGT 60.601 57.895 22.49 9.86 46.20 3.24
2076 2204 3.649277 ATGCCAGTGGTCGAGCGAC 62.649 63.158 11.74 14.17 43.87 5.19
2082 2210 0.677731 ACATTGGATGCCAGTGGTCG 60.678 55.000 11.74 0.00 44.06 4.79
2127 2255 3.067742 CCTTTCAGATCATGGTGAATGGC 59.932 47.826 17.45 0.00 39.66 4.40
2231 2379 5.175859 TCAGTTTAATCGGGATGTCAGAAC 58.824 41.667 0.00 0.00 0.00 3.01
2274 2423 1.113517 TCCCGGGGATCGATTGAGAC 61.114 60.000 23.50 0.00 42.43 3.36
2276 2425 0.468226 TTTCCCGGGGATCGATTGAG 59.532 55.000 23.50 0.00 42.43 3.02
2319 2505 2.362632 CGAGGGAGGAGGAACGGT 60.363 66.667 0.00 0.00 0.00 4.83
2351 2537 4.617253 ACTGCATGGACTTAGTACAACA 57.383 40.909 0.00 2.39 26.61 3.33
2359 2545 3.428452 GCGTACTGTACTGCATGGACTTA 60.428 47.826 21.28 0.00 0.00 2.24
2427 2671 4.357947 GCGCTCACTGACACGGGA 62.358 66.667 0.00 0.00 0.00 5.14
2473 2717 2.675423 GTTCCGGCTTCCAACCCC 60.675 66.667 0.00 0.00 0.00 4.95
2524 2773 0.546598 CCCCTCCGTATTCCAGCTTT 59.453 55.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.