Multiple sequence alignment - TraesCS4D01G313300

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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 TraesCS4D01G313300 chr4D 100.000 3177 0 0 1 3177 479413274 479410098 0.000000e+00 5867.0
1 TraesCS4D01G313300 chr4D 91.293 379 26 4 1 376 422930440 422930814 7.860000e-141 510.0
2 TraesCS4D01G313300 chr4D 80.124 161 32 0 1415 1575 479380701 479380541 1.550000e-23 121.0
3 TraesCS4D01G313300 chr4A 85.477 2410 137 80 578 2889 685787861 685785567 0.000000e+00 2314.0
4 TraesCS4D01G313300 chr4A 88.421 380 36 6 1 377 729055546 729055920 4.830000e-123 451.0
5 TraesCS4D01G313300 chr4A 87.895 380 39 5 1 377 731063895 731063520 1.050000e-119 440.0
6 TraesCS4D01G313300 chr4A 83.883 273 14 15 2933 3177 685785354 685785084 1.910000e-57 233.0
7 TraesCS4D01G313300 chr4A 80.255 157 29 2 1415 1569 685770347 685770191 2.000000e-22 117.0
8 TraesCS4D01G313300 chr4B 97.506 1163 24 3 1058 2217 606555183 606554023 0.000000e+00 1982.0
9 TraesCS4D01G313300 chr4B 93.904 935 35 10 2248 3177 606553850 606552933 0.000000e+00 1391.0
10 TraesCS4D01G313300 chr4B 91.983 711 23 16 374 1060 606555920 606555220 0.000000e+00 966.0
11 TraesCS4D01G313300 chr4B 78.882 161 34 0 1415 1575 606182091 606181931 3.350000e-20 110.0
12 TraesCS4D01G313300 chr6B 92.573 377 27 1 1 377 24856937 24857312 1.000000e-149 540.0
13 TraesCS4D01G313300 chr2D 91.316 380 29 2 1 377 5123528 5123906 1.690000e-142 516.0
14 TraesCS4D01G313300 chr5A 90.642 374 27 2 1 371 395693372 395693740 1.020000e-134 490.0
15 TraesCS4D01G313300 chr7D 90.212 378 32 3 1 375 593710023 593709648 3.680000e-134 488.0
16 TraesCS4D01G313300 chr7D 80.597 134 24 2 1413 1545 80979848 80979716 5.610000e-18 102.0
17 TraesCS4D01G313300 chr7B 89.572 374 34 3 7 376 55051993 55051621 1.330000e-128 470.0
18 TraesCS4D01G313300 chr7B 80.741 135 24 2 1413 1546 28506272 28506139 1.560000e-18 104.0
19 TraesCS4D01G313300 chr5D 88.503 374 38 5 7 376 387218599 387218227 6.250000e-122 448.0
20 TraesCS4D01G313300 chr7A 79.851 134 25 2 1413 1545 83635929 83635797 2.610000e-16 97.1
21 TraesCS4D01G313300 chr7A 78.417 139 30 0 1407 1545 109825513 109825651 1.210000e-14 91.6


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 TraesCS4D01G313300 chr4D 479410098 479413274 3176 True 5867.000000 5867 100.000000 1 3177 1 chr4D.!!$R2 3176
1 TraesCS4D01G313300 chr4A 685785084 685787861 2777 True 1273.500000 2314 84.680000 578 3177 2 chr4A.!!$R3 2599
2 TraesCS4D01G313300 chr4B 606552933 606555920 2987 True 1446.333333 1982 94.464333 374 3177 3 chr4B.!!$R2 2803

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
663 668 0.036765 AGTTCGGAATACAGGCGCAA 60.037 50.0 10.83 0.00 0.00 4.85 F
664 669 0.373716 GTTCGGAATACAGGCGCAAG 59.626 55.0 10.83 2.59 43.44 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2021 0.253044 CATGGACGGACTCATGGGTT 59.747 55.0 0.0 0.0 37.63 4.11 R
2645 2915 0.462759 CCCCCTCGATCTTGCTTGTC 60.463 60.0 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
17 18 2.598467 TCCGTGGGTTGCTTGGTT 59.402 55.556 0.00 0.00 0.00 3.67
18 19 1.826054 TCCGTGGGTTGCTTGGTTG 60.826 57.895 0.00 0.00 0.00 3.77
19 20 2.027460 CGTGGGTTGCTTGGTTGC 59.973 61.111 0.00 0.00 0.00 4.17
20 21 2.489275 CGTGGGTTGCTTGGTTGCT 61.489 57.895 0.00 0.00 0.00 3.91
21 22 1.822615 GTGGGTTGCTTGGTTGCTT 59.177 52.632 0.00 0.00 0.00 3.91
22 23 0.177836 GTGGGTTGCTTGGTTGCTTT 59.822 50.000 0.00 0.00 0.00 3.51
23 24 0.177604 TGGGTTGCTTGGTTGCTTTG 59.822 50.000 0.00 0.00 0.00 2.77
24 25 0.463620 GGGTTGCTTGGTTGCTTTGA 59.536 50.000 0.00 0.00 0.00 2.69
25 26 1.134551 GGGTTGCTTGGTTGCTTTGAA 60.135 47.619 0.00 0.00 0.00 2.69
26 27 2.204237 GGTTGCTTGGTTGCTTTGAAG 58.796 47.619 0.00 0.00 0.00 3.02
27 28 2.418609 GGTTGCTTGGTTGCTTTGAAGT 60.419 45.455 0.00 0.00 0.00 3.01
28 29 2.860136 GTTGCTTGGTTGCTTTGAAGTC 59.140 45.455 0.00 0.00 0.00 3.01
29 30 1.065401 TGCTTGGTTGCTTTGAAGTCG 59.935 47.619 0.00 0.00 0.00 4.18
30 31 1.600413 GCTTGGTTGCTTTGAAGTCGG 60.600 52.381 0.00 0.00 0.00 4.79
31 32 1.946768 CTTGGTTGCTTTGAAGTCGGA 59.053 47.619 0.00 0.00 0.00 4.55
32 33 1.593196 TGGTTGCTTTGAAGTCGGAG 58.407 50.000 0.00 0.00 0.00 4.63
33 34 0.238553 GGTTGCTTTGAAGTCGGAGC 59.761 55.000 0.00 0.00 35.74 4.70
34 35 1.230324 GTTGCTTTGAAGTCGGAGCT 58.770 50.000 0.00 0.00 36.16 4.09
35 36 1.069636 GTTGCTTTGAAGTCGGAGCTG 60.070 52.381 0.00 0.00 36.16 4.24
36 37 1.230635 TGCTTTGAAGTCGGAGCTGC 61.231 55.000 0.00 0.00 36.16 5.25
37 38 1.784062 CTTTGAAGTCGGAGCTGCG 59.216 57.895 22.84 22.84 0.00 5.18
38 39 1.630244 CTTTGAAGTCGGAGCTGCGG 61.630 60.000 27.80 9.24 0.00 5.69
39 40 2.377628 TTTGAAGTCGGAGCTGCGGT 62.378 55.000 27.80 12.67 0.00 5.68
40 41 2.811317 GAAGTCGGAGCTGCGGTG 60.811 66.667 27.80 0.00 0.00 4.94
41 42 4.379243 AAGTCGGAGCTGCGGTGG 62.379 66.667 27.80 0.00 0.00 4.61
43 44 4.803426 GTCGGAGCTGCGGTGGAG 62.803 72.222 27.80 0.00 0.00 3.86
62 63 3.838271 GAGTCCAGGCGGCGATGA 61.838 66.667 12.98 0.00 0.00 2.92
63 64 3.157217 GAGTCCAGGCGGCGATGAT 62.157 63.158 12.98 0.00 0.00 2.45
64 65 2.969238 GTCCAGGCGGCGATGATG 60.969 66.667 12.98 2.25 0.00 3.07
65 66 3.153781 TCCAGGCGGCGATGATGA 61.154 61.111 12.98 0.00 0.00 2.92
66 67 2.969238 CCAGGCGGCGATGATGAC 60.969 66.667 12.98 0.00 0.00 3.06
67 68 2.202919 CAGGCGGCGATGATGACA 60.203 61.111 12.98 0.00 0.00 3.58
68 69 2.107750 AGGCGGCGATGATGACAG 59.892 61.111 12.98 0.00 0.00 3.51
69 70 2.969238 GGCGGCGATGATGACAGG 60.969 66.667 12.98 0.00 0.00 4.00
70 71 3.643978 GCGGCGATGATGACAGGC 61.644 66.667 12.98 0.00 0.00 4.85
71 72 2.202919 CGGCGATGATGACAGGCA 60.203 61.111 0.00 0.00 33.18 4.75
72 73 2.528743 CGGCGATGATGACAGGCAC 61.529 63.158 0.00 0.00 33.18 5.01
73 74 1.153289 GGCGATGATGACAGGCACT 60.153 57.895 0.00 0.00 43.88 4.40
74 75 1.156645 GGCGATGATGACAGGCACTC 61.157 60.000 0.00 0.00 34.60 3.51
75 76 1.485838 GCGATGATGACAGGCACTCG 61.486 60.000 1.19 1.19 34.60 4.18
76 77 0.873312 CGATGATGACAGGCACTCGG 60.873 60.000 0.00 0.00 34.60 4.63
77 78 0.176680 GATGATGACAGGCACTCGGT 59.823 55.000 0.00 0.00 34.60 4.69
78 79 0.107993 ATGATGACAGGCACTCGGTG 60.108 55.000 0.25 0.25 34.60 4.94
79 80 1.448540 GATGACAGGCACTCGGTGG 60.449 63.158 6.23 0.00 34.60 4.61
80 81 2.172483 GATGACAGGCACTCGGTGGT 62.172 60.000 6.23 0.00 34.60 4.16
81 82 2.048127 GACAGGCACTCGGTGGTC 60.048 66.667 6.23 2.48 34.60 4.02
82 83 3.916392 GACAGGCACTCGGTGGTCG 62.916 68.421 6.23 0.00 34.60 4.79
83 84 3.991051 CAGGCACTCGGTGGTCGT 61.991 66.667 6.23 0.00 34.60 4.34
84 85 3.231736 AGGCACTCGGTGGTCGTT 61.232 61.111 6.23 0.00 40.32 3.85
85 86 2.280592 GGCACTCGGTGGTCGTTT 60.281 61.111 6.23 0.00 40.32 3.60
86 87 2.604174 GGCACTCGGTGGTCGTTTG 61.604 63.158 6.23 0.00 40.32 2.93
87 88 2.935955 CACTCGGTGGTCGTTTGC 59.064 61.111 0.00 0.00 40.32 3.68
88 89 2.660552 ACTCGGTGGTCGTTTGCG 60.661 61.111 0.00 0.00 40.32 4.85
89 90 3.411351 CTCGGTGGTCGTTTGCGG 61.411 66.667 0.00 0.00 40.32 5.69
90 91 4.224274 TCGGTGGTCGTTTGCGGT 62.224 61.111 0.00 0.00 40.32 5.68
91 92 4.007940 CGGTGGTCGTTTGCGGTG 62.008 66.667 0.00 0.00 38.89 4.94
92 93 2.589442 GGTGGTCGTTTGCGGTGA 60.589 61.111 0.00 0.00 38.89 4.02
93 94 2.604174 GGTGGTCGTTTGCGGTGAG 61.604 63.158 0.00 0.00 38.89 3.51
126 127 2.874701 CAAGTCCTGCATATTTCCCTCG 59.125 50.000 0.00 0.00 0.00 4.63
127 128 2.119495 AGTCCTGCATATTTCCCTCGT 58.881 47.619 0.00 0.00 0.00 4.18
128 129 2.158900 AGTCCTGCATATTTCCCTCGTG 60.159 50.000 0.00 0.00 0.00 4.35
129 130 2.115427 TCCTGCATATTTCCCTCGTGA 58.885 47.619 0.00 0.00 0.00 4.35
130 131 2.705658 TCCTGCATATTTCCCTCGTGAT 59.294 45.455 0.00 0.00 0.00 3.06
131 132 3.901222 TCCTGCATATTTCCCTCGTGATA 59.099 43.478 0.00 0.00 0.00 2.15
132 133 3.997021 CCTGCATATTTCCCTCGTGATAC 59.003 47.826 0.00 0.00 0.00 2.24
133 134 4.262635 CCTGCATATTTCCCTCGTGATACT 60.263 45.833 0.00 0.00 0.00 2.12
134 135 4.883083 TGCATATTTCCCTCGTGATACTC 58.117 43.478 0.00 0.00 0.00 2.59
135 136 3.921021 GCATATTTCCCTCGTGATACTCG 59.079 47.826 0.00 0.00 0.00 4.18
136 137 4.558898 GCATATTTCCCTCGTGATACTCGT 60.559 45.833 0.00 0.00 0.00 4.18
137 138 3.712091 ATTTCCCTCGTGATACTCGTC 57.288 47.619 0.00 0.00 0.00 4.20
138 139 1.012086 TTCCCTCGTGATACTCGTCG 58.988 55.000 0.00 0.00 0.00 5.12
139 140 0.107993 TCCCTCGTGATACTCGTCGT 60.108 55.000 0.00 0.00 0.00 4.34
140 141 0.304098 CCCTCGTGATACTCGTCGTC 59.696 60.000 0.00 0.00 0.00 4.20
141 142 1.004595 CCTCGTGATACTCGTCGTCA 58.995 55.000 0.00 0.00 0.00 4.35
142 143 1.395954 CCTCGTGATACTCGTCGTCAA 59.604 52.381 0.00 0.00 0.00 3.18
143 144 2.159612 CCTCGTGATACTCGTCGTCAAA 60.160 50.000 0.00 0.00 0.00 2.69
144 145 3.092135 CTCGTGATACTCGTCGTCAAAG 58.908 50.000 0.00 0.00 0.00 2.77
145 146 2.481568 TCGTGATACTCGTCGTCAAAGT 59.518 45.455 0.00 0.00 0.00 2.66
146 147 2.839026 CGTGATACTCGTCGTCAAAGTC 59.161 50.000 0.00 0.00 0.00 3.01
147 148 2.839026 GTGATACTCGTCGTCAAAGTCG 59.161 50.000 0.00 0.00 0.00 4.18
148 149 2.159612 TGATACTCGTCGTCAAAGTCGG 60.160 50.000 0.00 0.00 0.00 4.79
149 150 1.511850 TACTCGTCGTCAAAGTCGGA 58.488 50.000 0.00 0.00 0.00 4.55
150 151 0.237761 ACTCGTCGTCAAAGTCGGAG 59.762 55.000 0.00 0.00 0.00 4.63
151 152 1.066114 CTCGTCGTCAAAGTCGGAGC 61.066 60.000 0.00 0.00 0.00 4.70
152 153 2.087009 CGTCGTCAAAGTCGGAGCC 61.087 63.158 0.00 0.00 0.00 4.70
153 154 2.087009 GTCGTCAAAGTCGGAGCCG 61.087 63.158 1.74 1.74 41.35 5.52
154 155 2.049433 CGTCAAAGTCGGAGCCGT 60.049 61.111 8.96 0.00 40.74 5.68
155 156 2.087009 CGTCAAAGTCGGAGCCGTC 61.087 63.158 8.96 3.27 40.74 4.79
156 157 2.087009 GTCAAAGTCGGAGCCGTCG 61.087 63.158 8.96 0.00 40.74 5.12
157 158 2.809601 CAAAGTCGGAGCCGTCGG 60.810 66.667 6.99 6.99 40.74 4.79
158 159 3.300765 AAAGTCGGAGCCGTCGGT 61.301 61.111 13.94 0.00 40.74 4.69
159 160 2.864471 AAAGTCGGAGCCGTCGGTT 61.864 57.895 13.94 6.77 40.74 4.44
160 161 3.569049 AAGTCGGAGCCGTCGGTTG 62.569 63.158 13.94 0.50 40.74 3.77
161 162 4.353437 GTCGGAGCCGTCGGTTGT 62.353 66.667 13.94 0.00 40.74 3.32
162 163 3.608662 TCGGAGCCGTCGGTTGTT 61.609 61.111 13.94 0.00 40.74 2.83
163 164 2.663852 CGGAGCCGTCGGTTGTTT 60.664 61.111 13.94 0.00 34.35 2.83
164 165 2.943653 GGAGCCGTCGGTTGTTTG 59.056 61.111 13.94 0.00 0.00 2.93
165 166 2.251371 GAGCCGTCGGTTGTTTGC 59.749 61.111 13.94 0.00 0.00 3.68
166 167 3.573489 GAGCCGTCGGTTGTTTGCG 62.573 63.158 13.94 0.00 0.00 4.85
169 170 4.287967 CGTCGGTTGTTTGCGCGT 62.288 61.111 8.43 0.00 0.00 6.01
170 171 2.720750 GTCGGTTGTTTGCGCGTG 60.721 61.111 8.43 0.00 0.00 5.34
171 172 3.196394 TCGGTTGTTTGCGCGTGT 61.196 55.556 8.43 0.00 0.00 4.49
172 173 3.016203 CGGTTGTTTGCGCGTGTG 61.016 61.111 8.43 0.00 0.00 3.82
173 174 2.653766 GGTTGTTTGCGCGTGTGG 60.654 61.111 8.43 0.00 0.00 4.17
174 175 3.319316 GTTGTTTGCGCGTGTGGC 61.319 61.111 8.43 0.00 38.69 5.01
175 176 4.560856 TTGTTTGCGCGTGTGGCC 62.561 61.111 8.43 0.00 38.94 5.36
177 178 4.341502 GTTTGCGCGTGTGGCCAT 62.342 61.111 9.72 0.00 38.94 4.40
178 179 4.036804 TTTGCGCGTGTGGCCATC 62.037 61.111 9.72 4.56 38.94 3.51
182 183 3.049674 CGCGTGTGGCCATCTGTT 61.050 61.111 9.72 0.00 38.94 3.16
183 184 2.562912 GCGTGTGGCCATCTGTTG 59.437 61.111 9.72 0.00 34.80 3.33
216 217 3.583383 GCTTGCCCAGCTGTACTG 58.417 61.111 13.81 0.00 46.27 2.74
217 218 2.694760 GCTTGCCCAGCTGTACTGC 61.695 63.158 16.28 16.28 46.27 4.40
218 219 1.302752 CTTGCCCAGCTGTACTGCA 60.303 57.895 24.38 12.64 45.78 4.41
219 220 1.302752 TTGCCCAGCTGTACTGCAG 60.303 57.895 24.38 13.48 45.78 4.41
227 228 3.902515 CTGTACTGCAGCTCTGTGT 57.097 52.632 15.27 0.00 38.52 3.72
228 229 2.160822 CTGTACTGCAGCTCTGTGTT 57.839 50.000 15.27 0.00 38.52 3.32
229 230 2.487934 CTGTACTGCAGCTCTGTGTTT 58.512 47.619 15.27 0.00 38.52 2.83
230 231 2.478134 CTGTACTGCAGCTCTGTGTTTC 59.522 50.000 15.27 0.00 38.52 2.78
231 232 2.158971 TGTACTGCAGCTCTGTGTTTCA 60.159 45.455 15.27 0.00 0.00 2.69
232 233 2.267174 ACTGCAGCTCTGTGTTTCAT 57.733 45.000 15.27 0.00 0.00 2.57
233 234 1.878088 ACTGCAGCTCTGTGTTTCATG 59.122 47.619 15.27 0.00 0.00 3.07
234 235 1.878088 CTGCAGCTCTGTGTTTCATGT 59.122 47.619 0.00 0.00 0.00 3.21
235 236 1.875514 TGCAGCTCTGTGTTTCATGTC 59.124 47.619 0.00 0.00 0.00 3.06
236 237 1.136141 GCAGCTCTGTGTTTCATGTCG 60.136 52.381 0.00 0.00 0.00 4.35
237 238 1.462283 CAGCTCTGTGTTTCATGTCGG 59.538 52.381 0.00 0.00 0.00 4.79
238 239 1.070758 AGCTCTGTGTTTCATGTCGGT 59.929 47.619 0.00 0.00 0.00 4.69
239 240 1.195448 GCTCTGTGTTTCATGTCGGTG 59.805 52.381 0.00 0.00 0.00 4.94
240 241 1.800586 CTCTGTGTTTCATGTCGGTGG 59.199 52.381 0.00 0.00 0.00 4.61
241 242 0.238289 CTGTGTTTCATGTCGGTGGC 59.762 55.000 0.00 0.00 0.00 5.01
242 243 1.169661 TGTGTTTCATGTCGGTGGCC 61.170 55.000 0.00 0.00 0.00 5.36
243 244 1.149401 TGTTTCATGTCGGTGGCCA 59.851 52.632 0.00 0.00 0.00 5.36
244 245 0.888736 TGTTTCATGTCGGTGGCCAG 60.889 55.000 5.11 0.00 0.00 4.85
245 246 0.605319 GTTTCATGTCGGTGGCCAGA 60.605 55.000 5.11 0.00 0.00 3.86
246 247 0.327924 TTTCATGTCGGTGGCCAGAT 59.672 50.000 5.11 0.00 0.00 2.90
247 248 0.327924 TTCATGTCGGTGGCCAGATT 59.672 50.000 5.11 0.00 0.00 2.40
248 249 0.392863 TCATGTCGGTGGCCAGATTG 60.393 55.000 5.11 3.65 0.00 2.67
249 250 1.077501 ATGTCGGTGGCCAGATTGG 60.078 57.895 5.11 0.00 41.55 3.16
258 259 2.751436 CCAGATTGGCCGGTGGTG 60.751 66.667 1.90 0.00 0.00 4.17
259 260 3.443045 CAGATTGGCCGGTGGTGC 61.443 66.667 1.90 0.00 0.00 5.01
266 267 3.310307 GCCGGTGGTGCCCATTTT 61.310 61.111 1.90 0.00 35.28 1.82
267 268 2.656055 CCGGTGGTGCCCATTTTG 59.344 61.111 0.00 0.00 35.28 2.44
268 269 2.206536 CCGGTGGTGCCCATTTTGT 61.207 57.895 0.00 0.00 35.28 2.83
269 270 1.006337 CGGTGGTGCCCATTTTGTG 60.006 57.895 0.00 0.00 35.28 3.33
279 280 2.389962 CCATTTTGTGGGCTGGATTG 57.610 50.000 0.00 0.00 44.79 2.67
280 281 1.624813 CCATTTTGTGGGCTGGATTGT 59.375 47.619 0.00 0.00 44.79 2.71
281 282 2.613474 CCATTTTGTGGGCTGGATTGTG 60.613 50.000 0.00 0.00 44.79 3.33
282 283 1.786937 TTTTGTGGGCTGGATTGTGT 58.213 45.000 0.00 0.00 0.00 3.72
283 284 1.327303 TTTGTGGGCTGGATTGTGTC 58.673 50.000 0.00 0.00 0.00 3.67
284 285 0.888736 TTGTGGGCTGGATTGTGTCG 60.889 55.000 0.00 0.00 0.00 4.35
285 286 2.040544 GTGGGCTGGATTGTGTCGG 61.041 63.158 0.00 0.00 0.00 4.79
286 287 2.351276 GGGCTGGATTGTGTCGGT 59.649 61.111 0.00 0.00 0.00 4.69
287 288 1.303317 GGGCTGGATTGTGTCGGTT 60.303 57.895 0.00 0.00 0.00 4.44
288 289 1.305930 GGGCTGGATTGTGTCGGTTC 61.306 60.000 0.00 0.00 0.00 3.62
289 290 1.305930 GGCTGGATTGTGTCGGTTCC 61.306 60.000 0.00 0.00 0.00 3.62
290 291 0.605319 GCTGGATTGTGTCGGTTCCA 60.605 55.000 0.00 0.00 36.81 3.53
291 292 1.442769 CTGGATTGTGTCGGTTCCAG 58.557 55.000 3.62 3.62 46.66 3.86
292 293 0.605319 TGGATTGTGTCGGTTCCAGC 60.605 55.000 0.00 0.00 33.40 4.85
293 294 1.305930 GGATTGTGTCGGTTCCAGCC 61.306 60.000 0.00 0.00 0.00 4.85
294 295 1.303317 ATTGTGTCGGTTCCAGCCC 60.303 57.895 0.00 0.00 0.00 5.19
295 296 3.818121 TTGTGTCGGTTCCAGCCCG 62.818 63.158 0.00 0.00 46.83 6.13
303 304 1.253100 GGTTCCAGCCCGATTTTTCA 58.747 50.000 0.00 0.00 0.00 2.69
304 305 1.824852 GGTTCCAGCCCGATTTTTCAT 59.175 47.619 0.00 0.00 0.00 2.57
305 306 2.159240 GGTTCCAGCCCGATTTTTCATC 60.159 50.000 0.00 0.00 0.00 2.92
306 307 2.491693 GTTCCAGCCCGATTTTTCATCA 59.508 45.455 0.00 0.00 0.00 3.07
307 308 2.801483 TCCAGCCCGATTTTTCATCAA 58.199 42.857 0.00 0.00 0.00 2.57
308 309 3.364549 TCCAGCCCGATTTTTCATCAAT 58.635 40.909 0.00 0.00 0.00 2.57
309 310 3.768757 TCCAGCCCGATTTTTCATCAATT 59.231 39.130 0.00 0.00 0.00 2.32
310 311 4.952957 TCCAGCCCGATTTTTCATCAATTA 59.047 37.500 0.00 0.00 0.00 1.40
311 312 5.420421 TCCAGCCCGATTTTTCATCAATTAA 59.580 36.000 0.00 0.00 0.00 1.40
312 313 5.519927 CCAGCCCGATTTTTCATCAATTAAC 59.480 40.000 0.00 0.00 0.00 2.01
313 314 5.519927 CAGCCCGATTTTTCATCAATTAACC 59.480 40.000 0.00 0.00 0.00 2.85
314 315 5.186797 AGCCCGATTTTTCATCAATTAACCA 59.813 36.000 0.00 0.00 0.00 3.67
315 316 5.519927 GCCCGATTTTTCATCAATTAACCAG 59.480 40.000 0.00 0.00 0.00 4.00
316 317 6.042143 CCCGATTTTTCATCAATTAACCAGG 58.958 40.000 0.00 0.00 0.00 4.45
317 318 5.519927 CCGATTTTTCATCAATTAACCAGGC 59.480 40.000 0.00 0.00 0.00 4.85
318 319 6.098679 CGATTTTTCATCAATTAACCAGGCA 58.901 36.000 0.00 0.00 0.00 4.75
319 320 6.589523 CGATTTTTCATCAATTAACCAGGCAA 59.410 34.615 0.00 0.00 0.00 4.52
320 321 7.278424 CGATTTTTCATCAATTAACCAGGCAAT 59.722 33.333 0.00 0.00 0.00 3.56
321 322 8.866970 ATTTTTCATCAATTAACCAGGCAATT 57.133 26.923 0.00 0.00 0.00 2.32
322 323 7.903995 TTTTCATCAATTAACCAGGCAATTC 57.096 32.000 0.00 0.00 0.00 2.17
323 324 6.855763 TTCATCAATTAACCAGGCAATTCT 57.144 33.333 0.00 0.00 0.00 2.40
324 325 6.455360 TCATCAATTAACCAGGCAATTCTC 57.545 37.500 0.00 0.00 0.00 2.87
325 326 5.360714 TCATCAATTAACCAGGCAATTCTCC 59.639 40.000 0.00 0.00 0.00 3.71
326 327 4.934356 TCAATTAACCAGGCAATTCTCCT 58.066 39.130 0.00 0.00 0.00 3.69
327 328 5.332743 TCAATTAACCAGGCAATTCTCCTT 58.667 37.500 0.00 0.00 0.00 3.36
328 329 5.418840 TCAATTAACCAGGCAATTCTCCTTC 59.581 40.000 0.00 0.00 0.00 3.46
329 330 4.657814 TTAACCAGGCAATTCTCCTTCT 57.342 40.909 0.00 0.00 0.00 2.85
330 331 3.532641 AACCAGGCAATTCTCCTTCTT 57.467 42.857 0.00 0.00 0.00 2.52
331 332 4.657814 AACCAGGCAATTCTCCTTCTTA 57.342 40.909 0.00 0.00 0.00 2.10
332 333 4.657814 ACCAGGCAATTCTCCTTCTTAA 57.342 40.909 0.00 0.00 0.00 1.85
333 334 5.198602 ACCAGGCAATTCTCCTTCTTAAT 57.801 39.130 0.00 0.00 0.00 1.40
334 335 5.583932 ACCAGGCAATTCTCCTTCTTAATT 58.416 37.500 0.00 0.00 0.00 1.40
335 336 6.731467 ACCAGGCAATTCTCCTTCTTAATTA 58.269 36.000 0.00 0.00 0.00 1.40
336 337 7.182060 ACCAGGCAATTCTCCTTCTTAATTAA 58.818 34.615 0.00 0.00 0.00 1.40
337 338 7.841222 ACCAGGCAATTCTCCTTCTTAATTAAT 59.159 33.333 0.00 0.00 0.00 1.40
338 339 8.139989 CCAGGCAATTCTCCTTCTTAATTAATG 58.860 37.037 0.00 0.00 0.00 1.90
339 340 8.906867 CAGGCAATTCTCCTTCTTAATTAATGA 58.093 33.333 0.00 0.00 0.00 2.57
340 341 9.479549 AGGCAATTCTCCTTCTTAATTAATGAA 57.520 29.630 0.00 4.56 0.00 2.57
359 360 6.849588 ATGAAAATGACAAAGTCTTTTGCC 57.150 33.333 10.50 7.52 46.05 4.52
360 361 5.976458 TGAAAATGACAAAGTCTTTTGCCT 58.024 33.333 10.50 0.00 46.05 4.75
361 362 6.405538 TGAAAATGACAAAGTCTTTTGCCTT 58.594 32.000 10.50 0.00 46.05 4.35
362 363 6.313411 TGAAAATGACAAAGTCTTTTGCCTTG 59.687 34.615 10.50 0.00 46.05 3.61
363 364 5.343307 AATGACAAAGTCTTTTGCCTTGT 57.657 34.783 0.00 0.00 46.05 3.16
364 365 4.799564 TGACAAAGTCTTTTGCCTTGTT 57.200 36.364 0.00 0.00 46.05 2.83
365 366 5.146010 TGACAAAGTCTTTTGCCTTGTTT 57.854 34.783 0.00 0.00 46.05 2.83
366 367 5.167845 TGACAAAGTCTTTTGCCTTGTTTC 58.832 37.500 0.00 0.00 46.05 2.78
367 368 5.146010 ACAAAGTCTTTTGCCTTGTTTCA 57.854 34.783 0.00 0.00 46.05 2.69
368 369 5.546526 ACAAAGTCTTTTGCCTTGTTTCAA 58.453 33.333 0.00 0.00 46.05 2.69
369 370 5.994668 ACAAAGTCTTTTGCCTTGTTTCAAA 59.005 32.000 0.00 0.00 46.05 2.69
370 371 6.484977 ACAAAGTCTTTTGCCTTGTTTCAAAA 59.515 30.769 0.00 0.00 46.05 2.44
371 372 7.012799 ACAAAGTCTTTTGCCTTGTTTCAAAAA 59.987 29.630 0.00 0.00 46.05 1.94
392 393 2.295253 AAAATGAGGACCTCGTAGCG 57.705 50.000 16.80 0.00 32.35 4.26
401 402 1.255667 ACCTCGTAGCGAACCACCAT 61.256 55.000 0.00 0.00 34.74 3.55
482 485 6.106673 CGGATACATAAACAACAAGAGGAGT 58.893 40.000 0.00 0.00 0.00 3.85
518 521 4.389687 ACGATTGGTAACGTCCACATAAAC 59.610 41.667 0.00 0.00 38.34 2.01
536 539 9.028185 CACATAAACTACTCCGATTAGGTAAAC 57.972 37.037 0.00 0.00 41.99 2.01
538 541 9.245962 CATAAACTACTCCGATTAGGTAAACTG 57.754 37.037 0.00 0.00 41.99 3.16
539 542 7.472334 AAACTACTCCGATTAGGTAAACTGA 57.528 36.000 0.00 0.00 41.99 3.41
556 559 4.644103 ACTGAGATGCATACAATTTGCC 57.356 40.909 0.00 0.00 39.39 4.52
557 560 3.382546 ACTGAGATGCATACAATTTGCCC 59.617 43.478 0.00 0.00 39.39 5.36
558 561 2.694628 TGAGATGCATACAATTTGCCCC 59.305 45.455 0.00 0.00 39.39 5.80
559 562 2.036346 GAGATGCATACAATTTGCCCCC 59.964 50.000 0.00 0.00 39.39 5.40
599 604 2.167662 TCTATCTGCCTTGACGACACA 58.832 47.619 0.00 0.00 0.00 3.72
663 668 0.036765 AGTTCGGAATACAGGCGCAA 60.037 50.000 10.83 0.00 0.00 4.85
664 669 0.373716 GTTCGGAATACAGGCGCAAG 59.626 55.000 10.83 2.59 43.44 4.01
730 735 2.103538 CCGGTACAGTACGCGCAT 59.896 61.111 5.73 0.00 0.00 4.73
792 797 1.079336 GAACCGGCACTGGACTACC 60.079 63.158 0.00 0.00 0.00 3.18
793 798 2.830704 GAACCGGCACTGGACTACCG 62.831 65.000 0.00 0.00 45.21 4.02
794 799 4.814294 CCGGCACTGGACTACCGC 62.814 72.222 0.00 0.00 44.29 5.68
916 922 4.077184 CCACGCTCCGCCCAGTTA 62.077 66.667 0.00 0.00 0.00 2.24
923 929 4.770874 CCGCCCAGTTACCCACCG 62.771 72.222 0.00 0.00 0.00 4.94
947 961 3.909086 AAACCTGCAGCTCGCCTCC 62.909 63.158 8.66 0.00 41.33 4.30
1004 1033 3.473647 CGCCTCCTGCCATCCTCA 61.474 66.667 0.00 0.00 36.24 3.86
1042 1074 5.126779 CCTCCTCCTATTTCTTAACTTGCC 58.873 45.833 0.00 0.00 0.00 4.52
1048 1080 1.627864 TTTCTTAACTTGCCCCAGCC 58.372 50.000 0.00 0.00 38.69 4.85
1071 1150 2.528818 GGGGCGATCCATCCATCCA 61.529 63.158 0.00 0.00 37.22 3.41
1651 1742 1.679898 CCCTCGAGGAATATGGCCC 59.320 63.158 33.39 0.00 38.24 5.80
1734 1831 3.339141 GTCCTTGTCCATGGACTTCTTC 58.661 50.000 37.92 23.77 46.37 2.87
1924 2021 2.934932 TGCTGCCCATCCACCTCA 60.935 61.111 0.00 0.00 0.00 3.86
1956 2053 1.577468 GTCCATGACACACACACGAA 58.423 50.000 0.00 0.00 32.09 3.85
2211 2315 1.003355 ACTGGCTTGATCCACGGTG 60.003 57.895 0.00 0.00 31.74 4.94
2238 2346 1.884926 GCGGCTGCTAGCTAGTTGG 60.885 63.158 21.62 12.67 41.99 3.77
2421 2669 2.167861 GGATCAGACGTCAAGCGCC 61.168 63.158 19.50 8.44 46.11 6.53
2538 2807 4.623932 ATTGCTCGCTCCATTATCCTTA 57.376 40.909 0.00 0.00 0.00 2.69
2541 2810 3.388024 TGCTCGCTCCATTATCCTTACTT 59.612 43.478 0.00 0.00 0.00 2.24
2567 2836 5.409826 GTCTCCTTCACGAACTGATTTGATT 59.590 40.000 0.00 0.00 0.00 2.57
2568 2837 5.997746 TCTCCTTCACGAACTGATTTGATTT 59.002 36.000 0.00 0.00 0.00 2.17
2569 2838 6.000891 TCCTTCACGAACTGATTTGATTTG 57.999 37.500 0.00 0.00 0.00 2.32
2570 2839 5.762711 TCCTTCACGAACTGATTTGATTTGA 59.237 36.000 0.00 0.00 0.00 2.69
2571 2840 6.430925 TCCTTCACGAACTGATTTGATTTGAT 59.569 34.615 0.00 0.00 0.00 2.57
2640 2910 3.080765 TGGACGGTGGCGATGGAT 61.081 61.111 0.00 0.00 0.00 3.41
2853 3140 1.534163 CATAAGCCACGCATCCATCAG 59.466 52.381 0.00 0.00 0.00 2.90
2873 3163 3.456277 CAGCACTAATCCTACTCCCCTTT 59.544 47.826 0.00 0.00 0.00 3.11
2893 3200 6.154363 CCCTTTCTCTCTTCTGAGATACTTGT 59.846 42.308 0.00 0.00 46.93 3.16
2909 3216 8.353423 AGATACTTGTTTTGATGGTTAAGCAT 57.647 30.769 19.65 19.65 0.00 3.79
2914 3221 5.923204 TGTTTTGATGGTTAAGCATTTGGT 58.077 33.333 20.42 0.00 0.00 3.67
2915 3222 5.988561 TGTTTTGATGGTTAAGCATTTGGTC 59.011 36.000 20.42 9.55 0.00 4.02
2916 3223 4.433186 TTGATGGTTAAGCATTTGGTCG 57.567 40.909 20.42 0.00 0.00 4.79
2917 3224 3.680490 TGATGGTTAAGCATTTGGTCGA 58.320 40.909 20.42 0.00 0.00 4.20
2918 3225 3.438781 TGATGGTTAAGCATTTGGTCGAC 59.561 43.478 20.42 7.13 0.00 4.20
2983 3450 0.465705 CGCCAGAGGGACACATGTAT 59.534 55.000 0.00 0.00 35.59 2.29
2984 3451 1.686587 CGCCAGAGGGACACATGTATA 59.313 52.381 0.00 0.00 35.59 1.47
2988 3455 4.697514 CCAGAGGGACACATGTATACAAG 58.302 47.826 10.14 8.20 35.59 3.16
3134 3629 3.361158 TGTGCAACGGCCAATCGG 61.361 61.111 2.24 0.00 42.39 4.18
3173 3668 5.234329 CGCAAACTAACAAAGAGAGAGACAA 59.766 40.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.826054 CAACCAAGCAACCCACGGA 60.826 57.895 0.00 0.00 0.00 4.69
1 2 2.727544 CAACCAAGCAACCCACGG 59.272 61.111 0.00 0.00 0.00 4.94
2 3 2.015227 AAGCAACCAAGCAACCCACG 62.015 55.000 0.00 0.00 36.85 4.94
3 4 0.177836 AAAGCAACCAAGCAACCCAC 59.822 50.000 0.00 0.00 36.85 4.61
4 5 0.177604 CAAAGCAACCAAGCAACCCA 59.822 50.000 0.00 0.00 36.85 4.51
5 6 0.463620 TCAAAGCAACCAAGCAACCC 59.536 50.000 0.00 0.00 36.85 4.11
6 7 2.204237 CTTCAAAGCAACCAAGCAACC 58.796 47.619 0.00 0.00 36.85 3.77
7 8 2.860136 GACTTCAAAGCAACCAAGCAAC 59.140 45.455 0.00 0.00 36.85 4.17
8 9 2.479389 CGACTTCAAAGCAACCAAGCAA 60.479 45.455 0.00 0.00 36.85 3.91
9 10 1.065401 CGACTTCAAAGCAACCAAGCA 59.935 47.619 0.00 0.00 36.85 3.91
10 11 1.600413 CCGACTTCAAAGCAACCAAGC 60.600 52.381 0.00 0.00 0.00 4.01
11 12 1.946768 TCCGACTTCAAAGCAACCAAG 59.053 47.619 0.00 0.00 0.00 3.61
12 13 1.946768 CTCCGACTTCAAAGCAACCAA 59.053 47.619 0.00 0.00 0.00 3.67
13 14 1.593196 CTCCGACTTCAAAGCAACCA 58.407 50.000 0.00 0.00 0.00 3.67
14 15 0.238553 GCTCCGACTTCAAAGCAACC 59.761 55.000 0.00 0.00 34.86 3.77
15 16 1.069636 CAGCTCCGACTTCAAAGCAAC 60.070 52.381 0.00 0.00 37.22 4.17
16 17 1.229428 CAGCTCCGACTTCAAAGCAA 58.771 50.000 0.00 0.00 37.22 3.91
17 18 1.230635 GCAGCTCCGACTTCAAAGCA 61.231 55.000 0.00 0.00 37.22 3.91
18 19 1.499502 GCAGCTCCGACTTCAAAGC 59.500 57.895 0.00 0.00 34.95 3.51
19 20 1.630244 CCGCAGCTCCGACTTCAAAG 61.630 60.000 0.00 0.00 0.00 2.77
20 21 1.667830 CCGCAGCTCCGACTTCAAA 60.668 57.895 0.00 0.00 0.00 2.69
21 22 2.048222 CCGCAGCTCCGACTTCAA 60.048 61.111 0.00 0.00 0.00 2.69
22 23 3.303135 ACCGCAGCTCCGACTTCA 61.303 61.111 0.00 0.00 0.00 3.02
23 24 2.811317 CACCGCAGCTCCGACTTC 60.811 66.667 0.00 0.00 0.00 3.01
24 25 4.379243 CCACCGCAGCTCCGACTT 62.379 66.667 0.00 0.00 0.00 3.01
26 27 4.803426 CTCCACCGCAGCTCCGAC 62.803 72.222 0.00 0.00 0.00 4.79
33 34 4.803426 GGACTCGCTCCACCGCAG 62.803 72.222 0.00 0.00 39.21 5.18
35 36 4.803426 CTGGACTCGCTCCACCGC 62.803 72.222 0.00 0.00 44.99 5.68
36 37 4.135153 CCTGGACTCGCTCCACCG 62.135 72.222 0.00 0.00 44.99 4.94
37 38 4.459089 GCCTGGACTCGCTCCACC 62.459 72.222 0.00 0.00 44.99 4.61
38 39 4.803426 CGCCTGGACTCGCTCCAC 62.803 72.222 0.00 0.00 44.99 4.02
45 46 3.157217 ATCATCGCCGCCTGGACTC 62.157 63.158 0.00 0.00 37.49 3.36
46 47 3.157252 ATCATCGCCGCCTGGACT 61.157 61.111 0.00 0.00 37.49 3.85
47 48 2.969238 CATCATCGCCGCCTGGAC 60.969 66.667 0.00 0.00 37.49 4.02
48 49 3.153781 TCATCATCGCCGCCTGGA 61.154 61.111 0.00 0.00 37.49 3.86
49 50 2.969238 GTCATCATCGCCGCCTGG 60.969 66.667 0.00 0.00 38.77 4.45
50 51 2.202919 TGTCATCATCGCCGCCTG 60.203 61.111 0.00 0.00 0.00 4.85
51 52 2.107750 CTGTCATCATCGCCGCCT 59.892 61.111 0.00 0.00 0.00 5.52
52 53 2.969238 CCTGTCATCATCGCCGCC 60.969 66.667 0.00 0.00 0.00 6.13
53 54 3.643978 GCCTGTCATCATCGCCGC 61.644 66.667 0.00 0.00 0.00 6.53
54 55 2.202919 TGCCTGTCATCATCGCCG 60.203 61.111 0.00 0.00 0.00 6.46
55 56 1.153289 AGTGCCTGTCATCATCGCC 60.153 57.895 0.00 0.00 0.00 5.54
56 57 1.485838 CGAGTGCCTGTCATCATCGC 61.486 60.000 0.00 0.00 0.00 4.58
57 58 0.873312 CCGAGTGCCTGTCATCATCG 60.873 60.000 0.00 0.00 0.00 3.84
58 59 0.176680 ACCGAGTGCCTGTCATCATC 59.823 55.000 0.00 0.00 0.00 2.92
59 60 0.107993 CACCGAGTGCCTGTCATCAT 60.108 55.000 0.00 0.00 0.00 2.45
60 61 1.293179 CACCGAGTGCCTGTCATCA 59.707 57.895 0.00 0.00 0.00 3.07
61 62 1.448540 CCACCGAGTGCCTGTCATC 60.449 63.158 0.00 0.00 31.34 2.92
62 63 2.172483 GACCACCGAGTGCCTGTCAT 62.172 60.000 0.00 0.00 31.34 3.06
63 64 2.842462 ACCACCGAGTGCCTGTCA 60.842 61.111 0.00 0.00 31.34 3.58
64 65 2.048127 GACCACCGAGTGCCTGTC 60.048 66.667 0.00 0.00 31.34 3.51
65 66 3.991051 CGACCACCGAGTGCCTGT 61.991 66.667 0.00 0.00 41.76 4.00
66 67 2.989055 AAACGACCACCGAGTGCCTG 62.989 60.000 0.00 0.00 41.76 4.85
67 68 2.803817 AAACGACCACCGAGTGCCT 61.804 57.895 0.00 0.00 41.76 4.75
68 69 2.280592 AAACGACCACCGAGTGCC 60.281 61.111 0.00 0.00 41.76 5.01
69 70 2.935955 CAAACGACCACCGAGTGC 59.064 61.111 0.00 0.00 41.76 4.40
70 71 2.935955 GCAAACGACCACCGAGTG 59.064 61.111 0.00 0.00 41.76 3.51
71 72 2.660552 CGCAAACGACCACCGAGT 60.661 61.111 0.00 0.00 43.93 4.18
72 73 3.411351 CCGCAAACGACCACCGAG 61.411 66.667 0.00 0.00 43.93 4.63
73 74 4.224274 ACCGCAAACGACCACCGA 62.224 61.111 0.00 0.00 43.93 4.69
74 75 4.007940 CACCGCAAACGACCACCG 62.008 66.667 0.00 0.00 43.93 4.94
75 76 2.589442 TCACCGCAAACGACCACC 60.589 61.111 0.00 0.00 43.93 4.61
76 77 2.935955 CTCACCGCAAACGACCAC 59.064 61.111 0.00 0.00 43.93 4.16
77 78 2.970324 GCTCACCGCAAACGACCA 60.970 61.111 0.00 0.00 43.93 4.02
105 106 2.874701 CGAGGGAAATATGCAGGACTTG 59.125 50.000 0.00 0.00 0.00 3.16
106 107 2.505819 ACGAGGGAAATATGCAGGACTT 59.494 45.455 0.00 0.00 0.00 3.01
107 108 2.119495 ACGAGGGAAATATGCAGGACT 58.881 47.619 0.00 0.00 0.00 3.85
108 109 2.158957 TCACGAGGGAAATATGCAGGAC 60.159 50.000 0.00 0.00 0.00 3.85
109 110 2.115427 TCACGAGGGAAATATGCAGGA 58.885 47.619 0.00 0.00 0.00 3.86
110 111 2.620251 TCACGAGGGAAATATGCAGG 57.380 50.000 0.00 0.00 0.00 4.85
111 112 4.887748 AGTATCACGAGGGAAATATGCAG 58.112 43.478 0.00 0.00 0.00 4.41
112 113 4.558697 CGAGTATCACGAGGGAAATATGCA 60.559 45.833 0.00 0.00 33.17 3.96
113 114 3.921021 CGAGTATCACGAGGGAAATATGC 59.079 47.826 0.00 0.00 33.17 3.14
114 115 5.122512 ACGAGTATCACGAGGGAAATATG 57.877 43.478 0.00 0.00 33.17 1.78
115 116 4.083431 CGACGAGTATCACGAGGGAAATAT 60.083 45.833 0.00 0.00 36.85 1.28
116 117 3.249320 CGACGAGTATCACGAGGGAAATA 59.751 47.826 0.00 0.00 36.85 1.40
117 118 2.033049 CGACGAGTATCACGAGGGAAAT 59.967 50.000 0.00 0.00 36.85 2.17
118 119 1.399440 CGACGAGTATCACGAGGGAAA 59.601 52.381 0.00 0.00 36.85 3.13
119 120 1.012086 CGACGAGTATCACGAGGGAA 58.988 55.000 0.00 0.00 36.85 3.97
120 121 0.107993 ACGACGAGTATCACGAGGGA 60.108 55.000 0.00 0.00 37.81 4.20
121 122 0.304098 GACGACGAGTATCACGAGGG 59.696 60.000 0.00 0.00 37.81 4.30
122 123 1.004595 TGACGACGAGTATCACGAGG 58.995 55.000 0.00 0.00 37.81 4.63
123 124 2.800694 TTGACGACGAGTATCACGAG 57.199 50.000 0.00 0.00 37.81 4.18
124 125 2.481568 ACTTTGACGACGAGTATCACGA 59.518 45.455 0.00 0.00 37.81 4.35
125 126 2.839026 GACTTTGACGACGAGTATCACG 59.161 50.000 0.00 0.00 39.66 4.35
126 127 2.839026 CGACTTTGACGACGAGTATCAC 59.161 50.000 0.00 0.00 33.17 3.06
127 128 2.159612 CCGACTTTGACGACGAGTATCA 60.160 50.000 0.00 0.00 33.17 2.15
128 129 2.094894 TCCGACTTTGACGACGAGTATC 59.905 50.000 0.00 0.00 0.00 2.24
129 130 2.079158 TCCGACTTTGACGACGAGTAT 58.921 47.619 0.00 0.00 0.00 2.12
130 131 1.462283 CTCCGACTTTGACGACGAGTA 59.538 52.381 0.00 0.00 0.00 2.59
131 132 0.237761 CTCCGACTTTGACGACGAGT 59.762 55.000 0.00 0.00 0.00 4.18
132 133 1.066114 GCTCCGACTTTGACGACGAG 61.066 60.000 0.00 0.00 0.00 4.18
133 134 1.081641 GCTCCGACTTTGACGACGA 60.082 57.895 0.00 0.00 0.00 4.20
134 135 2.087009 GGCTCCGACTTTGACGACG 61.087 63.158 0.00 0.00 0.00 5.12
135 136 2.087009 CGGCTCCGACTTTGACGAC 61.087 63.158 1.35 0.00 42.83 4.34
136 137 2.257371 CGGCTCCGACTTTGACGA 59.743 61.111 1.35 0.00 42.83 4.20
137 138 2.049433 ACGGCTCCGACTTTGACG 60.049 61.111 15.95 0.00 42.83 4.35
138 139 2.087009 CGACGGCTCCGACTTTGAC 61.087 63.158 15.95 0.00 42.83 3.18
139 140 2.257371 CGACGGCTCCGACTTTGA 59.743 61.111 15.95 0.00 42.83 2.69
140 141 2.809601 CCGACGGCTCCGACTTTG 60.810 66.667 15.95 0.00 42.83 2.77
141 142 2.864471 AACCGACGGCTCCGACTTT 61.864 57.895 15.39 0.00 42.83 2.66
142 143 3.300765 AACCGACGGCTCCGACTT 61.301 61.111 15.39 0.00 42.83 3.01
143 144 4.052229 CAACCGACGGCTCCGACT 62.052 66.667 15.39 0.00 42.83 4.18
144 145 3.853597 AACAACCGACGGCTCCGAC 62.854 63.158 15.39 8.05 42.83 4.79
145 146 3.154584 AAACAACCGACGGCTCCGA 62.155 57.895 15.39 0.00 42.83 4.55
146 147 2.663852 AAACAACCGACGGCTCCG 60.664 61.111 15.39 6.79 46.03 4.63
147 148 2.943653 CAAACAACCGACGGCTCC 59.056 61.111 15.39 0.00 0.00 4.70
148 149 2.251371 GCAAACAACCGACGGCTC 59.749 61.111 15.39 0.00 0.00 4.70
149 150 3.645975 CGCAAACAACCGACGGCT 61.646 61.111 15.39 0.00 0.00 5.52
152 153 4.287967 ACGCGCAAACAACCGACG 62.288 61.111 5.73 0.00 0.00 5.12
153 154 2.720750 CACGCGCAAACAACCGAC 60.721 61.111 5.73 0.00 0.00 4.79
154 155 3.196394 ACACGCGCAAACAACCGA 61.196 55.556 5.73 0.00 0.00 4.69
155 156 3.016203 CACACGCGCAAACAACCG 61.016 61.111 5.73 0.00 0.00 4.44
156 157 2.653766 CCACACGCGCAAACAACC 60.654 61.111 5.73 0.00 0.00 3.77
157 158 3.319316 GCCACACGCGCAAACAAC 61.319 61.111 5.73 0.00 0.00 3.32
158 159 4.560856 GGCCACACGCGCAAACAA 62.561 61.111 5.73 0.00 38.94 2.83
160 161 4.341502 ATGGCCACACGCGCAAAC 62.342 61.111 8.16 0.00 38.94 2.93
161 162 4.036804 GATGGCCACACGCGCAAA 62.037 61.111 8.16 0.00 38.94 3.68
165 166 3.049674 AACAGATGGCCACACGCG 61.050 61.111 8.16 3.53 38.94 6.01
166 167 2.562912 CAACAGATGGCCACACGC 59.437 61.111 8.16 0.00 0.00 5.34
167 168 3.266964 CCAACAGATGGCCACACG 58.733 61.111 8.16 0.47 43.80 4.49
200 201 1.302752 TGCAGTACAGCTGGGCAAG 60.303 57.895 19.93 4.89 45.14 4.01
201 202 1.302752 CTGCAGTACAGCTGGGCAA 60.303 57.895 19.93 6.34 45.14 4.52
202 203 2.348620 CTGCAGTACAGCTGGGCA 59.651 61.111 19.93 19.33 45.14 5.36
210 211 2.158971 TGAAACACAGAGCTGCAGTACA 60.159 45.455 16.64 0.00 0.00 2.90
211 212 2.483876 TGAAACACAGAGCTGCAGTAC 58.516 47.619 16.64 9.76 0.00 2.73
212 213 2.908688 TGAAACACAGAGCTGCAGTA 57.091 45.000 16.64 0.00 0.00 2.74
213 214 1.878088 CATGAAACACAGAGCTGCAGT 59.122 47.619 16.64 1.59 0.00 4.40
214 215 1.878088 ACATGAAACACAGAGCTGCAG 59.122 47.619 10.11 10.11 0.00 4.41
215 216 1.875514 GACATGAAACACAGAGCTGCA 59.124 47.619 0.00 0.00 0.00 4.41
216 217 1.136141 CGACATGAAACACAGAGCTGC 60.136 52.381 0.00 0.00 0.00 5.25
217 218 1.462283 CCGACATGAAACACAGAGCTG 59.538 52.381 0.00 0.00 0.00 4.24
218 219 1.070758 ACCGACATGAAACACAGAGCT 59.929 47.619 0.00 0.00 0.00 4.09
219 220 1.195448 CACCGACATGAAACACAGAGC 59.805 52.381 0.00 0.00 0.00 4.09
220 221 1.800586 CCACCGACATGAAACACAGAG 59.199 52.381 0.00 0.00 0.00 3.35
221 222 1.877637 CCACCGACATGAAACACAGA 58.122 50.000 0.00 0.00 0.00 3.41
222 223 0.238289 GCCACCGACATGAAACACAG 59.762 55.000 0.00 0.00 0.00 3.66
223 224 1.169661 GGCCACCGACATGAAACACA 61.170 55.000 0.00 0.00 0.00 3.72
224 225 1.169661 TGGCCACCGACATGAAACAC 61.170 55.000 0.00 0.00 0.00 3.32
225 226 0.888736 CTGGCCACCGACATGAAACA 60.889 55.000 0.00 0.00 0.00 2.83
226 227 0.605319 TCTGGCCACCGACATGAAAC 60.605 55.000 0.00 0.00 0.00 2.78
227 228 0.327924 ATCTGGCCACCGACATGAAA 59.672 50.000 0.00 0.00 0.00 2.69
228 229 0.327924 AATCTGGCCACCGACATGAA 59.672 50.000 0.00 0.00 0.00 2.57
229 230 0.392863 CAATCTGGCCACCGACATGA 60.393 55.000 0.00 0.00 0.00 3.07
230 231 1.378882 CCAATCTGGCCACCGACATG 61.379 60.000 0.00 1.94 0.00 3.21
231 232 1.077501 CCAATCTGGCCACCGACAT 60.078 57.895 0.00 0.00 0.00 3.06
232 233 2.350895 CCAATCTGGCCACCGACA 59.649 61.111 0.00 0.00 0.00 4.35
242 243 3.443045 GCACCACCGGCCAATCTG 61.443 66.667 0.00 0.00 0.00 2.90
261 262 2.037511 ACACAATCCAGCCCACAAAATG 59.962 45.455 0.00 0.00 0.00 2.32
262 263 2.299867 GACACAATCCAGCCCACAAAAT 59.700 45.455 0.00 0.00 0.00 1.82
263 264 1.686052 GACACAATCCAGCCCACAAAA 59.314 47.619 0.00 0.00 0.00 2.44
264 265 1.327303 GACACAATCCAGCCCACAAA 58.673 50.000 0.00 0.00 0.00 2.83
265 266 0.888736 CGACACAATCCAGCCCACAA 60.889 55.000 0.00 0.00 0.00 3.33
266 267 1.302431 CGACACAATCCAGCCCACA 60.302 57.895 0.00 0.00 0.00 4.17
267 268 2.040544 CCGACACAATCCAGCCCAC 61.041 63.158 0.00 0.00 0.00 4.61
268 269 2.063015 AACCGACACAATCCAGCCCA 62.063 55.000 0.00 0.00 0.00 5.36
269 270 1.303317 AACCGACACAATCCAGCCC 60.303 57.895 0.00 0.00 0.00 5.19
270 271 1.305930 GGAACCGACACAATCCAGCC 61.306 60.000 0.00 0.00 32.08 4.85
271 272 0.605319 TGGAACCGACACAATCCAGC 60.605 55.000 0.00 0.00 37.05 4.85
272 273 3.623848 TGGAACCGACACAATCCAG 57.376 52.632 0.00 0.00 37.05 3.86
273 274 0.605319 GCTGGAACCGACACAATCCA 60.605 55.000 0.00 0.00 39.57 3.41
274 275 1.305930 GGCTGGAACCGACACAATCC 61.306 60.000 0.00 0.00 0.00 3.01
275 276 1.305930 GGGCTGGAACCGACACAATC 61.306 60.000 0.00 0.00 0.00 2.67
276 277 1.303317 GGGCTGGAACCGACACAAT 60.303 57.895 0.00 0.00 0.00 2.71
277 278 2.112297 GGGCTGGAACCGACACAA 59.888 61.111 0.00 0.00 0.00 3.33
284 285 1.253100 TGAAAAATCGGGCTGGAACC 58.747 50.000 0.00 0.00 0.00 3.62
285 286 2.491693 TGATGAAAAATCGGGCTGGAAC 59.508 45.455 0.00 0.00 0.00 3.62
286 287 2.801483 TGATGAAAAATCGGGCTGGAA 58.199 42.857 0.00 0.00 0.00 3.53
287 288 2.505650 TGATGAAAAATCGGGCTGGA 57.494 45.000 0.00 0.00 0.00 3.86
288 289 3.806625 ATTGATGAAAAATCGGGCTGG 57.193 42.857 0.00 0.00 0.00 4.85
289 290 5.519927 GGTTAATTGATGAAAAATCGGGCTG 59.480 40.000 0.00 0.00 0.00 4.85
290 291 5.186797 TGGTTAATTGATGAAAAATCGGGCT 59.813 36.000 0.00 0.00 0.00 5.19
291 292 5.415221 TGGTTAATTGATGAAAAATCGGGC 58.585 37.500 0.00 0.00 0.00 6.13
292 293 6.042143 CCTGGTTAATTGATGAAAAATCGGG 58.958 40.000 0.00 0.00 0.00 5.14
293 294 5.519927 GCCTGGTTAATTGATGAAAAATCGG 59.480 40.000 0.00 0.00 0.00 4.18
294 295 6.098679 TGCCTGGTTAATTGATGAAAAATCG 58.901 36.000 0.00 0.00 0.00 3.34
295 296 7.903995 TTGCCTGGTTAATTGATGAAAAATC 57.096 32.000 0.00 0.00 0.00 2.17
296 297 8.866970 AATTGCCTGGTTAATTGATGAAAAAT 57.133 26.923 9.31 0.00 0.00 1.82
297 298 8.156165 AGAATTGCCTGGTTAATTGATGAAAAA 58.844 29.630 13.33 0.00 0.00 1.94
298 299 7.678837 AGAATTGCCTGGTTAATTGATGAAAA 58.321 30.769 13.33 0.00 0.00 2.29
299 300 7.243604 AGAATTGCCTGGTTAATTGATGAAA 57.756 32.000 13.33 0.00 0.00 2.69
300 301 6.127366 GGAGAATTGCCTGGTTAATTGATGAA 60.127 38.462 13.33 0.00 0.00 2.57
301 302 5.360714 GGAGAATTGCCTGGTTAATTGATGA 59.639 40.000 13.33 0.00 0.00 2.92
302 303 5.361857 AGGAGAATTGCCTGGTTAATTGATG 59.638 40.000 13.33 0.00 33.59 3.07
303 304 5.522641 AGGAGAATTGCCTGGTTAATTGAT 58.477 37.500 13.33 4.92 33.59 2.57
304 305 4.934356 AGGAGAATTGCCTGGTTAATTGA 58.066 39.130 13.33 0.00 33.59 2.57
305 306 5.420104 AGAAGGAGAATTGCCTGGTTAATTG 59.580 40.000 13.33 0.00 35.50 2.32
306 307 5.583932 AGAAGGAGAATTGCCTGGTTAATT 58.416 37.500 9.72 9.72 35.50 1.40
307 308 5.198602 AGAAGGAGAATTGCCTGGTTAAT 57.801 39.130 0.00 0.00 35.50 1.40
308 309 4.657814 AGAAGGAGAATTGCCTGGTTAA 57.342 40.909 0.00 0.00 35.50 2.01
309 310 4.657814 AAGAAGGAGAATTGCCTGGTTA 57.342 40.909 0.00 0.00 35.50 2.85
310 311 3.532641 AAGAAGGAGAATTGCCTGGTT 57.467 42.857 0.00 0.00 35.50 3.67
311 312 4.657814 TTAAGAAGGAGAATTGCCTGGT 57.342 40.909 0.00 0.00 35.50 4.00
312 313 7.645058 TTAATTAAGAAGGAGAATTGCCTGG 57.355 36.000 0.00 0.00 35.50 4.45
313 314 8.906867 TCATTAATTAAGAAGGAGAATTGCCTG 58.093 33.333 3.94 0.00 35.50 4.85
314 315 9.479549 TTCATTAATTAAGAAGGAGAATTGCCT 57.520 29.630 3.94 0.00 37.35 4.75
333 334 8.825745 GGCAAAAGACTTTGTCATTTTCATTAA 58.174 29.630 0.06 0.00 44.90 1.40
334 335 8.364129 GGCAAAAGACTTTGTCATTTTCATTA 57.636 30.769 0.06 0.00 44.90 1.90
335 336 7.250445 GGCAAAAGACTTTGTCATTTTCATT 57.750 32.000 0.06 0.00 44.90 2.57
336 337 6.849588 GGCAAAAGACTTTGTCATTTTCAT 57.150 33.333 0.06 0.00 44.90 2.57
344 345 5.167845 TGAAACAAGGCAAAAGACTTTGTC 58.832 37.500 0.06 0.00 45.72 3.18
345 346 5.146010 TGAAACAAGGCAAAAGACTTTGT 57.854 34.783 0.06 0.00 43.34 2.83
346 347 6.479095 TTTGAAACAAGGCAAAAGACTTTG 57.521 33.333 0.06 0.00 44.11 2.77
347 348 7.503521 TTTTTGAAACAAGGCAAAAGACTTT 57.496 28.000 0.00 0.00 42.71 2.66
372 373 2.232941 TCGCTACGAGGTCCTCATTTTT 59.767 45.455 19.15 0.03 0.00 1.94
410 411 6.098716 TGGGGAAAACCTGATTATAATGGT 57.901 37.500 1.78 2.11 40.03 3.55
429 430 1.548269 ACCAACGCATTGTAAATGGGG 59.452 47.619 17.84 6.24 36.44 4.96
482 485 6.305399 CGTTACCAATCGTTAGTTCGAAACTA 59.695 38.462 0.00 1.29 42.81 2.24
518 521 6.939132 TCTCAGTTTACCTAATCGGAGTAG 57.061 41.667 5.53 5.53 32.63 2.57
536 539 3.243636 GGGGCAAATTGTATGCATCTCAG 60.244 47.826 0.19 0.00 45.60 3.35
538 541 2.036346 GGGGGCAAATTGTATGCATCTC 59.964 50.000 0.19 0.00 45.60 2.75
539 542 2.041701 GGGGGCAAATTGTATGCATCT 58.958 47.619 0.19 0.00 45.60 2.90
599 604 4.189188 AATCGCGCCGCTCGTACT 62.189 61.111 7.78 0.00 41.07 2.73
620 625 1.011968 TTGTCCGGCTCGACGAATTG 61.012 55.000 0.00 0.00 35.40 2.32
688 693 2.202479 GCGGCTGCATCGTTTTCC 60.202 61.111 14.08 0.00 42.15 3.13
916 922 2.281002 GGTTTGTACGCGGTGGGT 60.281 61.111 12.47 0.00 0.00 4.51
923 929 1.497722 GAGCTGCAGGTTTGTACGC 59.502 57.895 21.18 0.86 0.00 4.42
947 961 0.462759 GGCGAGTGATCCAAGGAAGG 60.463 60.000 0.00 0.00 0.00 3.46
1004 1033 0.395724 GGAGGCGTTGAAATGGGGAT 60.396 55.000 0.00 0.00 0.00 3.85
1048 1080 4.664677 GATGGATCGCCCCGACCG 62.665 72.222 0.00 0.00 39.18 4.79
1055 1095 0.742281 CGATGGATGGATGGATCGCC 60.742 60.000 0.00 0.00 32.13 5.54
1924 2021 0.253044 CATGGACGGACTCATGGGTT 59.747 55.000 0.00 0.00 37.63 4.11
1956 2053 4.189188 CGAACCGGCCGATCGAGT 62.189 66.667 34.96 20.30 38.82 4.18
2421 2669 1.972640 CTGCGCGATCGATGTTACTAG 59.027 52.381 21.57 0.99 38.10 2.57
2541 2810 1.601166 TCAGTTCGTGAAGGAGACGA 58.399 50.000 0.00 0.00 43.83 4.20
2556 2825 6.377996 TCCGATCCAAATCAAATCAAATCAGT 59.622 34.615 0.00 0.00 31.76 3.41
2567 2836 4.253685 GTCTCAAGTCCGATCCAAATCAA 58.746 43.478 0.00 0.00 31.76 2.57
2568 2837 3.260632 TGTCTCAAGTCCGATCCAAATCA 59.739 43.478 0.00 0.00 31.76 2.57
2569 2838 3.861840 TGTCTCAAGTCCGATCCAAATC 58.138 45.455 0.00 0.00 0.00 2.17
2570 2839 3.981071 TGTCTCAAGTCCGATCCAAAT 57.019 42.857 0.00 0.00 0.00 2.32
2571 2840 3.323691 TCTTGTCTCAAGTCCGATCCAAA 59.676 43.478 8.93 0.00 0.00 3.28
2637 2907 1.855360 GATCTTGCTTGTCGTCGATCC 59.145 52.381 0.00 0.00 0.00 3.36
2640 2910 0.519961 TCGATCTTGCTTGTCGTCGA 59.480 50.000 0.00 0.00 36.77 4.20
2645 2915 0.462759 CCCCCTCGATCTTGCTTGTC 60.463 60.000 0.00 0.00 0.00 3.18
2819 3106 5.466728 CGTGGCTTATGTAAGTATGCTGATT 59.533 40.000 2.11 0.00 35.75 2.57
2824 3111 2.869801 TGCGTGGCTTATGTAAGTATGC 59.130 45.455 12.37 12.37 36.25 3.14
2853 3140 3.712218 AGAAAGGGGAGTAGGATTAGTGC 59.288 47.826 0.00 0.00 0.00 4.40
2893 3200 5.010112 TCGACCAAATGCTTAACCATCAAAA 59.990 36.000 0.00 0.00 0.00 2.44
2909 3216 1.006571 GCCACTCGAGTCGACCAAA 60.007 57.895 16.96 0.00 0.00 3.28
2914 3221 1.285950 CACTTGCCACTCGAGTCGA 59.714 57.895 16.96 15.64 37.32 4.20
2915 3222 1.734477 CCACTTGCCACTCGAGTCG 60.734 63.158 16.96 11.05 37.32 4.18
2916 3223 0.946221 CACCACTTGCCACTCGAGTC 60.946 60.000 16.96 6.17 37.32 3.36
2917 3224 1.069765 CACCACTTGCCACTCGAGT 59.930 57.895 13.58 13.58 40.05 4.18
2918 3225 1.669115 CCACCACTTGCCACTCGAG 60.669 63.158 11.84 11.84 0.00 4.04
2983 3450 2.768527 CCATGGAGAGAAGAGGCTTGTA 59.231 50.000 5.56 0.00 0.00 2.41
2984 3451 1.558756 CCATGGAGAGAAGAGGCTTGT 59.441 52.381 5.56 0.00 0.00 3.16
2988 3455 1.148048 GGCCATGGAGAGAAGAGGC 59.852 63.158 18.40 0.00 41.29 4.70
3080 3563 0.036388 AAACCTCACATGCGGACGAT 60.036 50.000 0.00 0.00 0.00 3.73
3150 3645 6.423042 GTTGTCTCTCTCTTTGTTAGTTTGC 58.577 40.000 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.