Multiple sequence alignment - TraesCS4A01G204400

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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 TraesCS4A01G204400 chr4A 100.000 4124 0 0 1 4124 495804606 495800483 0.000000e+00 7616.0
1 TraesCS4A01G204400 chr4A 100.000 33 0 0 232 264 65495684 65495652 1.240000e-05 62.1
2 TraesCS4A01G204400 chr4A 97.222 36 1 0 229 264 173794986 173795021 1.240000e-05 62.1
3 TraesCS4A01G204400 chr4A 100.000 33 0 0 232 264 373406766 373406734 1.240000e-05 62.1
4 TraesCS4A01G204400 chr4B 93.605 3190 140 24 499 3657 118298896 118295740 0.000000e+00 4702.0
5 TraesCS4A01G204400 chr4B 92.375 459 24 3 3676 4123 118294988 118294530 0.000000e+00 643.0
6 TraesCS4A01G204400 chr4D 93.985 2311 98 13 1383 3669 83284457 83282164 0.000000e+00 3459.0
7 TraesCS4A01G204400 chr4D 94.309 615 27 5 730 1343 83285065 83284458 0.000000e+00 935.0
8 TraesCS4A01G204400 chr4D 95.759 448 17 2 3676 4123 83281274 83280829 0.000000e+00 721.0
9 TraesCS4A01G204400 chr4D 87.938 257 21 3 466 720 83289646 83289398 1.120000e-75 294.0
10 TraesCS4A01G204400 chr4D 85.294 238 15 5 268 486 83443791 83443555 1.150000e-55 228.0
11 TraesCS4A01G204400 chr4D 96.296 135 4 1 266 400 83290006 83289873 1.930000e-53 220.0
12 TraesCS4A01G204400 chr6B 92.701 137 7 2 266 402 489721070 489720937 1.170000e-45 195.0
13 TraesCS4A01G204400 chr6A 97.297 37 1 0 229 265 460617631 460617667 3.440000e-06 63.9
14 TraesCS4A01G204400 chr3D 100.000 33 0 0 232 264 17896326 17896294 1.240000e-05 62.1
15 TraesCS4A01G204400 chr3A 97.222 36 1 0 229 264 155836657 155836692 1.240000e-05 62.1
16 TraesCS4A01G204400 chr1A 97.222 36 1 0 229 264 139643587 139643552 1.240000e-05 62.1
17 TraesCS4A01G204400 chr1A 100.000 33 0 0 232 264 277240646 277240614 1.240000e-05 62.1
18 TraesCS4A01G204400 chr1A 100.000 33 0 0 232 264 390500345 390500313 1.240000e-05 62.1


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 TraesCS4A01G204400 chr4A 495800483 495804606 4123 True 7616.0 7616 100.000000 1 4124 1 chr4A.!!$R3 4123
1 TraesCS4A01G204400 chr4B 118294530 118298896 4366 True 2672.5 4702 92.990000 499 4123 2 chr4B.!!$R1 3624
2 TraesCS4A01G204400 chr4D 83280829 83285065 4236 True 1705.0 3459 94.684333 730 4123 3 chr4D.!!$R2 3393
3 TraesCS4A01G204400 chr4D 83289398 83290006 608 True 257.0 294 92.117000 266 720 2 chr4D.!!$R3 454

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
151 152 0.035176 CGTCGAAAACCCCAACCCTA 59.965 55.0 0.00 0.00 0.00 3.53 F
153 154 0.037160 TCGAAAACCCCAACCCTAGC 59.963 55.0 0.00 0.00 0.00 3.42 F
215 216 0.038159 CGTCTTGAGACCTGGTGGAC 60.038 60.0 2.82 3.98 41.86 4.02 F
216 217 0.321996 GTCTTGAGACCTGGTGGACC 59.678 60.0 2.82 0.00 39.07 4.46 F
769 933 0.512952 CCGACCGTTCAAGCTTCAAG 59.487 55.0 0.00 0.00 0.00 3.02 F
2492 2674 0.400975 GCATCCCTCATCCTGCTGAT 59.599 55.0 0.00 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 1908 0.106149 ACTTCACACGTCCTGGAACC 59.894 55.000 0.00 0.00 0.00 3.62 R
1994 2170 4.092968 CGCCAAGATGTTTGGTAGTCTAAC 59.907 45.833 7.67 0.00 41.53 2.34 R
2024 2200 5.163814 GCTGAGCAAGTACCTGAGTTTTATG 60.164 44.000 0.00 0.00 0.00 1.90 R
2156 2333 7.156673 CCTTGACACATTGAATTGGAAAATCT 58.843 34.615 0.00 0.00 0.00 2.40 R
2655 2837 2.354259 ACCAACTACCTACTCGAGACG 58.646 52.381 21.68 9.07 0.00 4.18 R
3463 3652 0.748367 GGAATTCGGGAGGCTGGAAC 60.748 60.000 0.00 0.00 0.00 3.62 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 4.554036 GGCCGCACCCTCTCCATC 62.554 72.222 0.00 0.00 0.00 3.51
18 19 3.474570 GCCGCACCCTCTCCATCT 61.475 66.667 0.00 0.00 0.00 2.90
19 20 2.503061 CCGCACCCTCTCCATCTG 59.497 66.667 0.00 0.00 0.00 2.90
20 21 2.202987 CGCACCCTCTCCATCTGC 60.203 66.667 0.00 0.00 0.00 4.26
21 22 2.729479 CGCACCCTCTCCATCTGCT 61.729 63.158 0.00 0.00 0.00 4.24
22 23 1.606531 GCACCCTCTCCATCTGCTT 59.393 57.895 0.00 0.00 0.00 3.91
23 24 0.463474 GCACCCTCTCCATCTGCTTC 60.463 60.000 0.00 0.00 0.00 3.86
24 25 0.179936 CACCCTCTCCATCTGCTTCC 59.820 60.000 0.00 0.00 0.00 3.46
25 26 0.985490 ACCCTCTCCATCTGCTTCCC 60.985 60.000 0.00 0.00 0.00 3.97
26 27 1.704007 CCCTCTCCATCTGCTTCCCC 61.704 65.000 0.00 0.00 0.00 4.81
27 28 1.704007 CCTCTCCATCTGCTTCCCCC 61.704 65.000 0.00 0.00 0.00 5.40
48 49 3.736100 CATGAGCGCCGCACCAAA 61.736 61.111 13.36 0.00 0.00 3.28
49 50 3.434319 ATGAGCGCCGCACCAAAG 61.434 61.111 13.36 0.00 0.00 2.77
58 59 4.625800 GCACCAAAGCGAGGAGAT 57.374 55.556 0.00 0.00 0.00 2.75
59 60 2.093216 GCACCAAAGCGAGGAGATG 58.907 57.895 0.00 0.00 0.00 2.90
60 61 1.986575 GCACCAAAGCGAGGAGATGC 61.987 60.000 0.00 0.00 0.00 3.91
61 62 0.674581 CACCAAAGCGAGGAGATGCA 60.675 55.000 0.00 0.00 0.00 3.96
62 63 0.392193 ACCAAAGCGAGGAGATGCAG 60.392 55.000 0.00 0.00 0.00 4.41
63 64 1.712977 CCAAAGCGAGGAGATGCAGC 61.713 60.000 0.00 0.00 0.00 5.25
64 65 1.022982 CAAAGCGAGGAGATGCAGCA 61.023 55.000 4.07 0.00 0.00 4.41
65 66 1.023513 AAAGCGAGGAGATGCAGCAC 61.024 55.000 4.07 0.00 0.00 4.40
66 67 2.866085 AAGCGAGGAGATGCAGCACC 62.866 60.000 10.74 10.74 0.00 5.01
67 68 2.580815 CGAGGAGATGCAGCACCA 59.419 61.111 20.66 0.00 0.00 4.17
68 69 1.812922 CGAGGAGATGCAGCACCAC 60.813 63.158 20.66 13.24 0.00 4.16
69 70 1.451028 GAGGAGATGCAGCACCACC 60.451 63.158 20.66 9.91 0.00 4.61
70 71 2.189191 GAGGAGATGCAGCACCACCA 62.189 60.000 20.66 0.00 0.00 4.17
71 72 1.748122 GGAGATGCAGCACCACCAG 60.748 63.158 13.89 0.00 0.00 4.00
72 73 2.360852 AGATGCAGCACCACCAGC 60.361 61.111 4.07 0.00 0.00 4.85
73 74 3.446570 GATGCAGCACCACCAGCC 61.447 66.667 0.00 0.00 0.00 4.85
74 75 3.933048 GATGCAGCACCACCAGCCT 62.933 63.158 0.00 0.00 0.00 4.58
75 76 3.518552 ATGCAGCACCACCAGCCTT 62.519 57.895 0.00 0.00 0.00 4.35
76 77 3.677648 GCAGCACCACCAGCCTTG 61.678 66.667 0.00 0.00 0.00 3.61
88 89 2.611225 CAGCCTTGGATCAGGTAGAC 57.389 55.000 0.00 0.00 36.15 2.59
89 90 1.115467 AGCCTTGGATCAGGTAGACG 58.885 55.000 0.00 0.00 36.15 4.18
90 91 0.530870 GCCTTGGATCAGGTAGACGC 60.531 60.000 0.00 0.00 36.15 5.19
91 92 0.105039 CCTTGGATCAGGTAGACGCC 59.895 60.000 0.00 0.00 0.00 5.68
92 93 0.249073 CTTGGATCAGGTAGACGCCG 60.249 60.000 0.00 0.00 0.00 6.46
93 94 0.968901 TTGGATCAGGTAGACGCCGT 60.969 55.000 0.00 0.00 0.00 5.68
94 95 1.359475 GGATCAGGTAGACGCCGTC 59.641 63.158 9.71 9.71 0.00 4.79
95 96 1.009900 GATCAGGTAGACGCCGTCG 60.010 63.158 12.13 0.00 37.67 5.12
96 97 2.985486 GATCAGGTAGACGCCGTCGC 62.985 65.000 12.13 8.85 37.67 5.19
97 98 4.849329 CAGGTAGACGCCGTCGCC 62.849 72.222 20.73 20.73 37.67 5.54
117 118 4.473520 CCCGAGCCACGCTGGATT 62.474 66.667 8.04 0.00 35.51 3.01
118 119 2.892425 CCGAGCCACGCTGGATTC 60.892 66.667 8.04 4.32 35.51 2.52
119 120 2.892425 CGAGCCACGCTGGATTCC 60.892 66.667 8.04 0.00 35.51 3.01
120 121 2.268920 GAGCCACGCTGGATTCCA 59.731 61.111 5.05 5.05 35.51 3.53
121 122 2.045926 AGCCACGCTGGATTCCAC 60.046 61.111 0.00 0.00 40.96 4.02
122 123 3.134127 GCCACGCTGGATTCCACC 61.134 66.667 0.00 0.00 40.96 4.61
123 124 2.350895 CCACGCTGGATTCCACCA 59.649 61.111 0.00 0.00 40.96 4.17
124 125 2.040544 CCACGCTGGATTCCACCAC 61.041 63.158 0.00 0.00 40.96 4.16
125 126 2.040544 CACGCTGGATTCCACCACC 61.041 63.158 0.00 0.00 35.91 4.61
126 127 2.224159 ACGCTGGATTCCACCACCT 61.224 57.895 0.00 0.00 35.91 4.00
127 128 0.907704 ACGCTGGATTCCACCACCTA 60.908 55.000 0.00 0.00 35.91 3.08
128 129 0.179073 CGCTGGATTCCACCACCTAG 60.179 60.000 0.00 0.00 35.91 3.02
129 130 1.204146 GCTGGATTCCACCACCTAGA 58.796 55.000 0.00 0.00 35.91 2.43
130 131 1.771255 GCTGGATTCCACCACCTAGAT 59.229 52.381 0.00 0.00 35.91 1.98
131 132 2.224402 GCTGGATTCCACCACCTAGATC 60.224 54.545 0.00 0.00 35.91 2.75
132 133 2.370189 CTGGATTCCACCACCTAGATCC 59.630 54.545 0.00 0.00 35.91 3.36
133 134 1.344763 GGATTCCACCACCTAGATCCG 59.655 57.143 0.00 0.00 0.00 4.18
134 135 2.040178 GATTCCACCACCTAGATCCGT 58.960 52.381 0.00 0.00 0.00 4.69
135 136 1.481871 TTCCACCACCTAGATCCGTC 58.518 55.000 0.00 0.00 0.00 4.79
136 137 0.750546 TCCACCACCTAGATCCGTCG 60.751 60.000 0.00 0.00 0.00 5.12
137 138 0.750546 CCACCACCTAGATCCGTCGA 60.751 60.000 0.00 0.00 0.00 4.20
138 139 1.100510 CACCACCTAGATCCGTCGAA 58.899 55.000 0.00 0.00 0.00 3.71
139 140 1.475280 CACCACCTAGATCCGTCGAAA 59.525 52.381 0.00 0.00 0.00 3.46
140 141 2.094390 CACCACCTAGATCCGTCGAAAA 60.094 50.000 0.00 0.00 0.00 2.29
141 142 2.094338 ACCACCTAGATCCGTCGAAAAC 60.094 50.000 0.00 0.00 0.00 2.43
142 143 2.537401 CACCTAGATCCGTCGAAAACC 58.463 52.381 0.00 0.00 0.00 3.27
143 144 1.479730 ACCTAGATCCGTCGAAAACCC 59.520 52.381 0.00 0.00 0.00 4.11
144 145 1.202498 CCTAGATCCGTCGAAAACCCC 60.202 57.143 0.00 0.00 0.00 4.95
145 146 1.479323 CTAGATCCGTCGAAAACCCCA 59.521 52.381 0.00 0.00 0.00 4.96
146 147 0.688487 AGATCCGTCGAAAACCCCAA 59.312 50.000 0.00 0.00 0.00 4.12
147 148 0.800631 GATCCGTCGAAAACCCCAAC 59.199 55.000 0.00 0.00 0.00 3.77
148 149 0.607217 ATCCGTCGAAAACCCCAACC 60.607 55.000 0.00 0.00 0.00 3.77
149 150 2.263021 CCGTCGAAAACCCCAACCC 61.263 63.158 0.00 0.00 0.00 4.11
150 151 1.228033 CGTCGAAAACCCCAACCCT 60.228 57.895 0.00 0.00 0.00 4.34
151 152 0.035176 CGTCGAAAACCCCAACCCTA 59.965 55.000 0.00 0.00 0.00 3.53
152 153 1.817357 GTCGAAAACCCCAACCCTAG 58.183 55.000 0.00 0.00 0.00 3.02
153 154 0.037160 TCGAAAACCCCAACCCTAGC 59.963 55.000 0.00 0.00 0.00 3.42
154 155 1.303091 CGAAAACCCCAACCCTAGCG 61.303 60.000 0.00 0.00 0.00 4.26
155 156 0.251033 GAAAACCCCAACCCTAGCGT 60.251 55.000 0.00 0.00 0.00 5.07
156 157 1.003464 GAAAACCCCAACCCTAGCGTA 59.997 52.381 0.00 0.00 0.00 4.42
157 158 0.616891 AAACCCCAACCCTAGCGTAG 59.383 55.000 0.00 0.00 0.00 3.51
158 159 1.269703 AACCCCAACCCTAGCGTAGG 61.270 60.000 4.60 4.60 45.81 3.18
168 169 0.938713 CTAGCGTAGGAGGACAGTCG 59.061 60.000 0.00 0.00 0.00 4.18
169 170 1.094073 TAGCGTAGGAGGACAGTCGC 61.094 60.000 0.00 0.00 43.16 5.19
170 171 2.799371 CGTAGGAGGACAGTCGCC 59.201 66.667 3.42 3.42 0.00 5.54
171 172 1.749638 CGTAGGAGGACAGTCGCCT 60.750 63.158 15.67 15.67 38.81 5.52
172 173 1.810532 GTAGGAGGACAGTCGCCTG 59.189 63.158 19.11 0.00 44.68 4.85
173 174 1.379977 TAGGAGGACAGTCGCCTGG 60.380 63.158 19.11 0.00 43.36 4.45
174 175 4.459089 GGAGGACAGTCGCCTGGC 62.459 72.222 9.11 9.11 46.86 4.85
191 192 4.436998 CGATCGCCCCCTATCGCC 62.437 72.222 0.26 0.00 38.61 5.54
192 193 2.997897 GATCGCCCCCTATCGCCT 60.998 66.667 0.00 0.00 0.00 5.52
193 194 2.526873 ATCGCCCCCTATCGCCTT 60.527 61.111 0.00 0.00 0.00 4.35
194 195 1.229082 ATCGCCCCCTATCGCCTTA 60.229 57.895 0.00 0.00 0.00 2.69
195 196 1.258445 ATCGCCCCCTATCGCCTTAG 61.258 60.000 0.00 0.00 0.00 2.18
196 197 2.347866 GCCCCCTATCGCCTTAGC 59.652 66.667 0.00 0.00 0.00 3.09
207 208 3.052181 GCCTTAGCGTCTTGAGACC 57.948 57.895 5.61 0.00 41.86 3.85
208 209 0.533032 GCCTTAGCGTCTTGAGACCT 59.467 55.000 5.61 6.50 41.86 3.85
209 210 1.737363 GCCTTAGCGTCTTGAGACCTG 60.737 57.143 5.61 0.00 41.86 4.00
210 211 1.134965 CCTTAGCGTCTTGAGACCTGG 60.135 57.143 5.61 0.00 41.86 4.45
211 212 1.546476 CTTAGCGTCTTGAGACCTGGT 59.454 52.381 0.00 0.00 41.86 4.00
212 213 0.888619 TAGCGTCTTGAGACCTGGTG 59.111 55.000 2.82 0.00 41.86 4.17
213 214 1.374758 GCGTCTTGAGACCTGGTGG 60.375 63.158 2.82 0.00 41.86 4.61
214 215 1.816863 GCGTCTTGAGACCTGGTGGA 61.817 60.000 2.82 0.00 41.86 4.02
215 216 0.038159 CGTCTTGAGACCTGGTGGAC 60.038 60.000 2.82 3.98 41.86 4.02
216 217 0.321996 GTCTTGAGACCTGGTGGACC 59.678 60.000 2.82 0.00 39.07 4.46
217 218 0.836400 TCTTGAGACCTGGTGGACCC 60.836 60.000 2.82 0.00 37.04 4.46
218 219 1.842381 CTTGAGACCTGGTGGACCCC 61.842 65.000 2.82 0.00 37.04 4.95
219 220 2.122954 GAGACCTGGTGGACCCCT 59.877 66.667 2.82 0.00 37.04 4.79
220 221 1.990614 GAGACCTGGTGGACCCCTC 60.991 68.421 2.82 0.00 37.04 4.30
221 222 3.391382 GACCTGGTGGACCCCTCG 61.391 72.222 2.82 0.00 37.04 4.63
228 229 4.332543 TGGACCCCTCGCCTCCTT 62.333 66.667 0.00 0.00 0.00 3.36
229 230 2.042230 GGACCCCTCGCCTCCTTA 60.042 66.667 0.00 0.00 0.00 2.69
230 231 1.459730 GGACCCCTCGCCTCCTTAT 60.460 63.158 0.00 0.00 0.00 1.73
231 232 1.749033 GACCCCTCGCCTCCTTATG 59.251 63.158 0.00 0.00 0.00 1.90
232 233 2.384653 GACCCCTCGCCTCCTTATGC 62.385 65.000 0.00 0.00 0.00 3.14
233 234 2.143419 CCCCTCGCCTCCTTATGCT 61.143 63.158 0.00 0.00 0.00 3.79
234 235 1.700042 CCCCTCGCCTCCTTATGCTT 61.700 60.000 0.00 0.00 0.00 3.91
235 236 1.048601 CCCTCGCCTCCTTATGCTTA 58.951 55.000 0.00 0.00 0.00 3.09
236 237 1.416401 CCCTCGCCTCCTTATGCTTAA 59.584 52.381 0.00 0.00 0.00 1.85
237 238 2.484889 CCTCGCCTCCTTATGCTTAAC 58.515 52.381 0.00 0.00 0.00 2.01
238 239 2.484889 CTCGCCTCCTTATGCTTAACC 58.515 52.381 0.00 0.00 0.00 2.85
239 240 2.103263 CTCGCCTCCTTATGCTTAACCT 59.897 50.000 0.00 0.00 0.00 3.50
240 241 3.302161 TCGCCTCCTTATGCTTAACCTA 58.698 45.455 0.00 0.00 0.00 3.08
241 242 3.321111 TCGCCTCCTTATGCTTAACCTAG 59.679 47.826 0.00 0.00 0.00 3.02
242 243 3.403968 GCCTCCTTATGCTTAACCTAGC 58.596 50.000 0.00 0.00 41.59 3.42
243 244 3.071747 GCCTCCTTATGCTTAACCTAGCT 59.928 47.826 0.00 0.00 41.76 3.32
244 245 4.445019 GCCTCCTTATGCTTAACCTAGCTT 60.445 45.833 0.00 0.00 41.76 3.74
245 246 5.685728 CCTCCTTATGCTTAACCTAGCTTT 58.314 41.667 0.00 0.00 41.76 3.51
246 247 5.760743 CCTCCTTATGCTTAACCTAGCTTTC 59.239 44.000 0.00 0.00 41.76 2.62
247 248 5.357257 TCCTTATGCTTAACCTAGCTTTCG 58.643 41.667 0.00 0.00 41.76 3.46
248 249 5.128171 TCCTTATGCTTAACCTAGCTTTCGA 59.872 40.000 0.00 0.00 41.76 3.71
249 250 5.992217 CCTTATGCTTAACCTAGCTTTCGAT 59.008 40.000 0.00 0.00 41.76 3.59
250 251 6.146347 CCTTATGCTTAACCTAGCTTTCGATC 59.854 42.308 0.00 0.00 41.76 3.69
251 252 4.737855 TGCTTAACCTAGCTTTCGATCT 57.262 40.909 0.00 0.00 41.76 2.75
252 253 4.683832 TGCTTAACCTAGCTTTCGATCTC 58.316 43.478 0.00 0.00 41.76 2.75
253 254 4.402793 TGCTTAACCTAGCTTTCGATCTCT 59.597 41.667 0.00 0.00 41.76 3.10
254 255 4.979815 GCTTAACCTAGCTTTCGATCTCTC 59.020 45.833 0.00 0.00 38.15 3.20
255 256 5.221165 GCTTAACCTAGCTTTCGATCTCTCT 60.221 44.000 0.00 0.00 38.15 3.10
256 257 6.681865 GCTTAACCTAGCTTTCGATCTCTCTT 60.682 42.308 0.00 0.00 38.15 2.85
257 258 4.647424 ACCTAGCTTTCGATCTCTCTTG 57.353 45.455 0.00 0.00 0.00 3.02
258 259 4.020543 ACCTAGCTTTCGATCTCTCTTGT 58.979 43.478 0.00 0.00 0.00 3.16
259 260 4.464597 ACCTAGCTTTCGATCTCTCTTGTT 59.535 41.667 0.00 0.00 0.00 2.83
260 261 5.046950 ACCTAGCTTTCGATCTCTCTTGTTT 60.047 40.000 0.00 0.00 0.00 2.83
261 262 5.518487 CCTAGCTTTCGATCTCTCTTGTTTC 59.482 44.000 0.00 0.00 0.00 2.78
262 263 5.146010 AGCTTTCGATCTCTCTTGTTTCT 57.854 39.130 0.00 0.00 0.00 2.52
263 264 5.546526 AGCTTTCGATCTCTCTTGTTTCTT 58.453 37.500 0.00 0.00 0.00 2.52
264 265 5.994668 AGCTTTCGATCTCTCTTGTTTCTTT 59.005 36.000 0.00 0.00 0.00 2.52
298 299 8.136165 AGGTGTACTTATTATAAGCGAACTCAG 58.864 37.037 11.50 0.00 0.00 3.35
385 386 0.907486 CATGGGCTGGAGAAGACTGA 59.093 55.000 0.00 0.00 32.61 3.41
435 450 7.145932 AGCACAAATAGATGGTGAAGTTAAC 57.854 36.000 0.00 0.00 34.52 2.01
439 454 8.023128 CACAAATAGATGGTGAAGTTAACTTGG 58.977 37.037 25.17 0.00 36.11 3.61
441 456 7.923414 AATAGATGGTGAAGTTAACTTGGAC 57.077 36.000 25.17 19.01 36.11 4.02
442 457 5.304686 AGATGGTGAAGTTAACTTGGACA 57.695 39.130 25.17 18.68 36.11 4.02
444 459 7.016153 AGATGGTGAAGTTAACTTGGACATA 57.984 36.000 25.17 13.37 36.11 2.29
456 477 9.769093 GTTAACTTGGACATAACATGTTACATC 57.231 33.333 20.26 18.42 45.03 3.06
459 621 9.733556 AACTTGGACATAACATGTTACATCTAA 57.266 29.630 20.26 19.99 45.03 2.10
520 682 4.809426 GTGACATAGACGGACCCTTAAATG 59.191 45.833 0.00 0.00 0.00 2.32
525 687 7.396418 ACATAGACGGACCCTTAAATGTTTTA 58.604 34.615 0.00 0.00 0.00 1.52
536 698 9.100197 ACCCTTAAATGTTTTATCAGGATTTGT 57.900 29.630 0.00 0.00 0.00 2.83
739 903 4.981806 TTGTATGCTAGTTTTGGATGGC 57.018 40.909 0.00 0.00 0.00 4.40
747 911 2.331893 TTTTGGATGGCTGGCGTCG 61.332 57.895 16.06 0.00 0.00 5.12
769 933 0.512952 CCGACCGTTCAAGCTTCAAG 59.487 55.000 0.00 0.00 0.00 3.02
889 1062 1.757423 AAATTGCCACCCAGCCACAC 61.757 55.000 0.00 0.00 0.00 3.82
890 1063 2.943369 AATTGCCACCCAGCCACACA 62.943 55.000 0.00 0.00 0.00 3.72
891 1064 4.584518 TGCCACCCAGCCACACAG 62.585 66.667 0.00 0.00 0.00 3.66
892 1065 4.269523 GCCACCCAGCCACACAGA 62.270 66.667 0.00 0.00 0.00 3.41
893 1066 2.281761 CCACCCAGCCACACAGAC 60.282 66.667 0.00 0.00 0.00 3.51
894 1067 2.281761 CACCCAGCCACACAGACC 60.282 66.667 0.00 0.00 0.00 3.85
970 1143 1.616994 CCCCGAGCCAGAAATTCCTTT 60.617 52.381 0.00 0.00 0.00 3.11
976 1149 2.558359 AGCCAGAAATTCCTTTTCCGTG 59.442 45.455 0.00 0.00 44.06 4.94
1026 1200 2.822701 GGTTCGGTGGCGGATTCC 60.823 66.667 0.00 0.00 0.00 3.01
1089 1263 2.695359 GCCAACTCCGTCAGATTTGTA 58.305 47.619 0.00 0.00 34.23 2.41
1191 1365 1.479323 TGCTAATTCTACGGCGGAACT 59.521 47.619 13.24 0.00 0.00 3.01
1244 1418 1.961394 TCTCGTGTTAGTGCTGGACTT 59.039 47.619 7.25 0.00 35.96 3.01
1279 1453 3.062639 AGCTTCTTGCAATGTTCGATACG 59.937 43.478 0.00 0.00 45.94 3.06
1368 1542 1.534595 GAGCAATTGAGCATCCGGATC 59.465 52.381 15.88 9.84 36.85 3.36
1381 1555 4.713946 GGATCAACAGGAACCGCA 57.286 55.556 0.00 0.00 0.00 5.69
1389 1563 6.016276 GGATCAACAGGAACCGCAAATAATAT 60.016 38.462 0.00 0.00 0.00 1.28
1561 1735 3.589735 ACCTAACATACATGTCCCAACCA 59.410 43.478 0.00 0.00 40.80 3.67
1617 1791 3.067106 GACACATGTCATCGGTCAAAGT 58.933 45.455 7.15 0.00 44.18 2.66
1626 1800 2.908073 CGGTCAAAGTGCTGGTGCC 61.908 63.158 0.00 0.00 38.71 5.01
1665 1839 2.224793 GGGCTGAGGTTAGGACAAAAGT 60.225 50.000 0.00 0.00 0.00 2.66
1715 1889 9.645128 ATCTGGATGTTATGTTTCATAATTCCA 57.355 29.630 21.56 21.56 32.58 3.53
1734 1908 4.156477 TCCAGGGTTTAACCTTTGGATTG 58.844 43.478 25.52 10.00 42.64 2.67
1757 1931 1.068588 TCCAGGACGTGTGAAGTTCTG 59.931 52.381 4.17 0.00 43.18 3.02
1829 2005 6.187727 TCTCCTACTTTGTTTTCATCACCT 57.812 37.500 0.00 0.00 0.00 4.00
1844 2020 6.314899 TCATCACCTGAGACTAAGAGAGTA 57.685 41.667 0.00 0.00 39.06 2.59
1867 2043 8.425703 AGTAAAACAAAAAGCTTTAGGCCATAA 58.574 29.630 13.10 0.00 43.05 1.90
1910 2086 7.081976 GGTCTGTTTGGTATAATTGTCAACAC 58.918 38.462 0.00 0.00 0.00 3.32
1911 2087 7.255312 GGTCTGTTTGGTATAATTGTCAACACA 60.255 37.037 0.00 0.00 0.00 3.72
1993 2169 8.311836 GTGCATAGTAAGTCTATATGGCCTAAA 58.688 37.037 3.32 0.00 37.26 1.85
1994 2170 8.531982 TGCATAGTAAGTCTATATGGCCTAAAG 58.468 37.037 3.32 0.00 37.26 1.85
2024 2200 1.987770 CAAACATCTTGGCGCATGTTC 59.012 47.619 20.11 0.00 41.42 3.18
2420 2602 6.013898 TGTCTGTTCAAGATCCTCATTCTCTT 60.014 38.462 0.00 0.00 37.23 2.85
2492 2674 0.400975 GCATCCCTCATCCTGCTGAT 59.599 55.000 0.00 0.00 0.00 2.90
2527 2709 8.470805 CAACATAAGAGTTCAGACTACAGGTAT 58.529 37.037 0.00 0.00 35.88 2.73
2533 2715 8.228035 AGAGTTCAGACTACAGGTATTGTATC 57.772 38.462 0.00 0.00 41.30 2.24
2655 2837 3.594603 TCTGCTACTTCCTACAGTTGC 57.405 47.619 1.01 1.01 43.41 4.17
2684 2866 7.318141 TCGAGTAGGTAGTTGGTTTTCTAATG 58.682 38.462 0.00 0.00 0.00 1.90
2749 2931 3.129109 GTTGGGTAGCTTATTAGGTCGC 58.871 50.000 0.00 0.00 33.36 5.19
2765 2947 4.149598 AGGTCGCCTTTCCTTTACAAATT 58.850 39.130 0.00 0.00 0.00 1.82
2862 3044 9.593134 TTTGGATTAAATTCAATTCCAATACCG 57.407 29.630 13.61 0.00 35.95 4.02
2876 3058 3.502211 CCAATACCGGAACTATCAATGCC 59.498 47.826 9.46 0.00 0.00 4.40
2914 3096 4.287766 ACCACTTCCCAGTTTCACTATC 57.712 45.455 0.00 0.00 0.00 2.08
2981 3163 1.693606 TGTTGTGCTGTCAGGAGATCA 59.306 47.619 1.14 0.00 0.00 2.92
3204 3390 1.467342 GCGGGTTAGTTGCGATTTCTT 59.533 47.619 0.00 0.00 0.00 2.52
3237 3423 3.843619 TGTCTATGGGTCAATGTCTGGAA 59.156 43.478 0.00 0.00 0.00 3.53
3304 3490 2.362077 ACACTGGAATGTTGGAGTTTGC 59.638 45.455 0.00 0.00 0.00 3.68
3372 3561 2.558359 GTCCAAACACTCTGGAATTGGG 59.442 50.000 3.28 0.00 44.55 4.12
3384 3573 3.430453 TGGAATTGGGTTCAGAATCACC 58.570 45.455 0.00 0.00 38.64 4.02
3444 3633 4.082571 ACTCTTTGGATTGCAGGAATTTCG 60.083 41.667 0.00 0.00 0.00 3.46
3474 3663 1.276622 TCTGTAAGGTTCCAGCCTCC 58.723 55.000 0.00 0.00 38.03 4.30
3475 3664 0.253327 CTGTAAGGTTCCAGCCTCCC 59.747 60.000 0.00 0.00 38.03 4.30
3481 3670 0.748367 GGTTCCAGCCTCCCGAATTC 60.748 60.000 0.00 0.00 0.00 2.17
3545 3745 2.421248 CCTCTGGAATTTCAGGCTCTCC 60.421 54.545 13.96 0.00 35.58 3.71
3657 3858 3.558505 GTTTCACTGTGATGTCATGTGC 58.441 45.455 11.86 0.00 35.07 4.57
3669 3870 1.067295 TCATGTGCCCCACTCTTTCT 58.933 50.000 0.00 0.00 35.11 2.52
3670 3871 1.171308 CATGTGCCCCACTCTTTCTG 58.829 55.000 0.00 0.00 35.11 3.02
3671 3872 0.773644 ATGTGCCCCACTCTTTCTGT 59.226 50.000 0.00 0.00 35.11 3.41
3672 3873 1.429930 TGTGCCCCACTCTTTCTGTA 58.570 50.000 0.00 0.00 35.11 2.74
3673 3874 1.771854 TGTGCCCCACTCTTTCTGTAA 59.228 47.619 0.00 0.00 35.11 2.41
3674 3875 2.224523 TGTGCCCCACTCTTTCTGTAAG 60.225 50.000 0.00 0.00 35.11 2.34
3713 4804 6.689669 GCTGTACTTTTAAAACACATCACGTT 59.310 34.615 9.81 0.00 0.00 3.99
3753 4844 0.512518 GCGAATTTGTTGCCCAAAGC 59.487 50.000 5.12 0.57 45.79 3.51
3979 5072 8.637196 AAGGTTTCTTCGATTTTTCTTCCTAT 57.363 30.769 0.00 0.00 0.00 2.57
4043 5136 1.608717 ATTCGCCCTCGTGAAGCTCT 61.609 55.000 0.00 0.00 41.62 4.09
4080 5182 6.884096 TGTACTCACATTTTGCAAAGTTTG 57.116 33.333 12.41 12.77 0.00 2.93
4085 5187 6.817641 ACTCACATTTTGCAAAGTTTGAATCA 59.182 30.769 19.85 5.10 0.00 2.57
4086 5188 7.010738 ACTCACATTTTGCAAAGTTTGAATCAG 59.989 33.333 19.85 12.84 0.00 2.90
4118 5220 4.274705 CCATACTGGCGTGCAAAATATACA 59.725 41.667 0.00 0.00 0.00 2.29
4123 5225 5.588648 ACTGGCGTGCAAAATATACAAGTAT 59.411 36.000 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.554036 GATGGAGAGGGTGCGGCC 62.554 72.222 0.00 0.00 0.00 6.13
1 2 3.474570 AGATGGAGAGGGTGCGGC 61.475 66.667 0.00 0.00 0.00 6.53
2 3 2.503061 CAGATGGAGAGGGTGCGG 59.497 66.667 0.00 0.00 0.00 5.69
3 4 2.202987 GCAGATGGAGAGGGTGCG 60.203 66.667 0.00 0.00 0.00 5.34
5 6 0.179936 GGAAGCAGATGGAGAGGGTG 59.820 60.000 0.00 0.00 0.00 4.61
7 8 1.704007 GGGGAAGCAGATGGAGAGGG 61.704 65.000 0.00 0.00 0.00 4.30
8 9 1.704007 GGGGGAAGCAGATGGAGAGG 61.704 65.000 0.00 0.00 0.00 3.69
31 32 3.672255 CTTTGGTGCGGCGCTCATG 62.672 63.158 33.26 19.89 0.00 3.07
32 33 3.434319 CTTTGGTGCGGCGCTCAT 61.434 61.111 33.26 0.00 0.00 2.90
41 42 1.986575 GCATCTCCTCGCTTTGGTGC 61.987 60.000 0.00 0.00 0.00 5.01
42 43 0.674581 TGCATCTCCTCGCTTTGGTG 60.675 55.000 0.00 0.00 0.00 4.17
43 44 0.392193 CTGCATCTCCTCGCTTTGGT 60.392 55.000 0.00 0.00 0.00 3.67
44 45 1.712977 GCTGCATCTCCTCGCTTTGG 61.713 60.000 0.00 0.00 0.00 3.28
45 46 1.022982 TGCTGCATCTCCTCGCTTTG 61.023 55.000 0.00 0.00 0.00 2.77
46 47 1.023513 GTGCTGCATCTCCTCGCTTT 61.024 55.000 5.27 0.00 0.00 3.51
47 48 1.449246 GTGCTGCATCTCCTCGCTT 60.449 57.895 5.27 0.00 0.00 4.68
48 49 2.186384 GTGCTGCATCTCCTCGCT 59.814 61.111 5.27 0.00 0.00 4.93
49 50 2.894387 GGTGCTGCATCTCCTCGC 60.894 66.667 5.27 0.00 0.00 5.03
50 51 1.812922 GTGGTGCTGCATCTCCTCG 60.813 63.158 14.82 0.00 0.00 4.63
51 52 1.451028 GGTGGTGCTGCATCTCCTC 60.451 63.158 23.06 12.64 0.00 3.71
52 53 2.194388 CTGGTGGTGCTGCATCTCCT 62.194 60.000 28.19 0.00 30.38 3.69
53 54 1.748122 CTGGTGGTGCTGCATCTCC 60.748 63.158 23.45 23.45 0.00 3.71
54 55 2.404995 GCTGGTGGTGCTGCATCTC 61.405 63.158 14.82 10.49 0.00 2.75
55 56 2.360852 GCTGGTGGTGCTGCATCT 60.361 61.111 14.82 0.00 0.00 2.90
56 57 3.446570 GGCTGGTGGTGCTGCATC 61.447 66.667 5.27 5.56 0.00 3.91
57 58 3.518552 AAGGCTGGTGGTGCTGCAT 62.519 57.895 5.27 0.00 0.00 3.96
58 59 4.208403 AAGGCTGGTGGTGCTGCA 62.208 61.111 0.00 0.00 0.00 4.41
59 60 3.677648 CAAGGCTGGTGGTGCTGC 61.678 66.667 0.00 0.00 0.00 5.25
60 61 2.776370 ATCCAAGGCTGGTGGTGCTG 62.776 60.000 5.18 0.00 43.97 4.41
61 62 2.490270 GATCCAAGGCTGGTGGTGCT 62.490 60.000 5.18 0.00 43.97 4.40
62 63 2.036256 ATCCAAGGCTGGTGGTGC 59.964 61.111 5.18 0.00 43.97 5.01
63 64 0.679002 CTGATCCAAGGCTGGTGGTG 60.679 60.000 5.18 0.00 43.97 4.17
64 65 1.687612 CTGATCCAAGGCTGGTGGT 59.312 57.895 5.18 0.00 43.97 4.16
65 66 1.077212 CCTGATCCAAGGCTGGTGG 60.077 63.158 0.00 0.00 43.97 4.61
66 67 0.911769 TACCTGATCCAAGGCTGGTG 59.088 55.000 0.00 0.00 43.97 4.17
67 68 1.207791 CTACCTGATCCAAGGCTGGT 58.792 55.000 0.00 0.00 43.97 4.00
68 69 1.139853 GTCTACCTGATCCAAGGCTGG 59.860 57.143 0.00 0.00 45.08 4.85
69 70 1.202463 CGTCTACCTGATCCAAGGCTG 60.202 57.143 0.00 0.00 41.46 4.85
70 71 1.115467 CGTCTACCTGATCCAAGGCT 58.885 55.000 0.00 0.00 41.46 4.58
71 72 0.530870 GCGTCTACCTGATCCAAGGC 60.531 60.000 0.00 0.00 41.46 4.35
72 73 0.105039 GGCGTCTACCTGATCCAAGG 59.895 60.000 0.00 0.00 43.57 3.61
73 74 0.249073 CGGCGTCTACCTGATCCAAG 60.249 60.000 0.00 0.00 0.00 3.61
74 75 0.968901 ACGGCGTCTACCTGATCCAA 60.969 55.000 6.77 0.00 0.00 3.53
75 76 1.379443 ACGGCGTCTACCTGATCCA 60.379 57.895 6.77 0.00 0.00 3.41
76 77 1.359475 GACGGCGTCTACCTGATCC 59.641 63.158 31.15 2.27 0.00 3.36
77 78 1.009900 CGACGGCGTCTACCTGATC 60.010 63.158 33.90 8.91 0.00 2.92
78 79 3.108343 CGACGGCGTCTACCTGAT 58.892 61.111 33.90 0.00 0.00 2.90
79 80 3.807538 GCGACGGCGTCTACCTGA 61.808 66.667 33.90 0.00 40.36 3.86
80 81 4.849329 GGCGACGGCGTCTACCTG 62.849 72.222 33.90 20.72 39.48 4.00
100 101 4.473520 AATCCAGCGTGGCTCGGG 62.474 66.667 11.21 4.59 36.40 5.14
101 102 2.892425 GAATCCAGCGTGGCTCGG 60.892 66.667 11.21 0.00 36.40 4.63
102 103 2.892425 GGAATCCAGCGTGGCTCG 60.892 66.667 4.32 4.32 36.40 5.03
103 104 2.109126 GTGGAATCCAGCGTGGCTC 61.109 63.158 0.27 0.00 36.40 4.70
104 105 2.045926 GTGGAATCCAGCGTGGCT 60.046 61.111 0.27 0.00 40.77 4.75
105 106 3.134127 GGTGGAATCCAGCGTGGC 61.134 66.667 16.19 0.00 42.21 5.01
111 112 2.370189 GGATCTAGGTGGTGGAATCCAG 59.630 54.545 0.27 0.00 38.23 3.86
112 113 2.408565 GGATCTAGGTGGTGGAATCCA 58.591 52.381 0.00 0.00 34.85 3.41
113 114 1.344763 CGGATCTAGGTGGTGGAATCC 59.655 57.143 0.00 0.00 0.00 3.01
114 115 2.036089 GACGGATCTAGGTGGTGGAATC 59.964 54.545 0.00 0.00 0.00 2.52
115 116 2.040178 GACGGATCTAGGTGGTGGAAT 58.960 52.381 0.00 0.00 0.00 3.01
116 117 1.481871 GACGGATCTAGGTGGTGGAA 58.518 55.000 0.00 0.00 0.00 3.53
117 118 0.750546 CGACGGATCTAGGTGGTGGA 60.751 60.000 0.00 0.00 0.00 4.02
118 119 0.750546 TCGACGGATCTAGGTGGTGG 60.751 60.000 0.00 0.00 0.00 4.61
119 120 1.100510 TTCGACGGATCTAGGTGGTG 58.899 55.000 0.00 0.00 0.00 4.17
120 121 1.843368 TTTCGACGGATCTAGGTGGT 58.157 50.000 0.00 0.00 0.00 4.16
121 122 2.537401 GTTTTCGACGGATCTAGGTGG 58.463 52.381 0.00 0.00 0.00 4.61
122 123 2.537401 GGTTTTCGACGGATCTAGGTG 58.463 52.381 0.00 0.00 0.00 4.00
123 124 1.479730 GGGTTTTCGACGGATCTAGGT 59.520 52.381 0.00 0.00 0.00 3.08
124 125 1.202498 GGGGTTTTCGACGGATCTAGG 60.202 57.143 0.00 0.00 0.00 3.02
125 126 1.479323 TGGGGTTTTCGACGGATCTAG 59.521 52.381 0.00 0.00 0.00 2.43
126 127 1.559368 TGGGGTTTTCGACGGATCTA 58.441 50.000 0.00 0.00 0.00 1.98
127 128 0.688487 TTGGGGTTTTCGACGGATCT 59.312 50.000 0.00 0.00 0.00 2.75
128 129 0.800631 GTTGGGGTTTTCGACGGATC 59.199 55.000 0.00 0.00 0.00 3.36
129 130 0.607217 GGTTGGGGTTTTCGACGGAT 60.607 55.000 0.00 0.00 0.00 4.18
130 131 1.227913 GGTTGGGGTTTTCGACGGA 60.228 57.895 0.00 0.00 0.00 4.69
131 132 2.263021 GGGTTGGGGTTTTCGACGG 61.263 63.158 0.00 0.00 0.00 4.79
132 133 0.035176 TAGGGTTGGGGTTTTCGACG 59.965 55.000 0.00 0.00 0.00 5.12
133 134 1.817357 CTAGGGTTGGGGTTTTCGAC 58.183 55.000 0.00 0.00 0.00 4.20
134 135 0.037160 GCTAGGGTTGGGGTTTTCGA 59.963 55.000 0.00 0.00 0.00 3.71
135 136 1.303091 CGCTAGGGTTGGGGTTTTCG 61.303 60.000 0.00 0.00 0.00 3.46
136 137 0.251033 ACGCTAGGGTTGGGGTTTTC 60.251 55.000 6.62 0.00 0.00 2.29
137 138 1.003928 CTACGCTAGGGTTGGGGTTTT 59.996 52.381 18.45 0.00 33.13 2.43
138 139 0.616891 CTACGCTAGGGTTGGGGTTT 59.383 55.000 18.45 0.00 33.13 3.27
139 140 1.269703 CCTACGCTAGGGTTGGGGTT 61.270 60.000 25.95 1.37 42.42 4.11
140 141 1.688187 CCTACGCTAGGGTTGGGGT 60.688 63.158 25.95 2.86 42.42 4.95
141 142 1.382146 TCCTACGCTAGGGTTGGGG 60.382 63.158 30.32 22.53 46.24 4.96
142 143 1.400530 CCTCCTACGCTAGGGTTGGG 61.401 65.000 30.32 24.44 46.24 4.12
143 144 0.396695 TCCTCCTACGCTAGGGTTGG 60.397 60.000 27.15 27.15 46.24 3.77
144 145 0.745468 GTCCTCCTACGCTAGGGTTG 59.255 60.000 18.45 15.55 46.24 3.77
145 146 0.333993 TGTCCTCCTACGCTAGGGTT 59.666 55.000 18.45 2.60 46.24 4.11
146 147 0.106619 CTGTCCTCCTACGCTAGGGT 60.107 60.000 17.36 17.36 46.24 4.34
147 148 0.106619 ACTGTCCTCCTACGCTAGGG 60.107 60.000 5.05 5.05 46.24 3.53
149 150 0.938713 CGACTGTCCTCCTACGCTAG 59.061 60.000 1.55 0.00 0.00 3.42
150 151 1.094073 GCGACTGTCCTCCTACGCTA 61.094 60.000 1.55 0.00 42.19 4.26
151 152 2.408241 GCGACTGTCCTCCTACGCT 61.408 63.158 1.55 0.00 42.19 5.07
152 153 2.102553 GCGACTGTCCTCCTACGC 59.897 66.667 1.55 0.00 39.33 4.42
153 154 1.749638 AGGCGACTGTCCTCCTACG 60.750 63.158 12.81 0.00 41.13 3.51
154 155 4.340620 AGGCGACTGTCCTCCTAC 57.659 61.111 12.81 0.00 41.13 3.18
174 175 4.436998 GGCGATAGGGGGCGATCG 62.437 72.222 11.69 11.69 46.07 3.69
175 176 1.255667 TAAGGCGATAGGGGGCGATC 61.256 60.000 0.00 0.00 34.74 3.69
176 177 1.229082 TAAGGCGATAGGGGGCGAT 60.229 57.895 0.00 0.00 34.74 4.58
177 178 1.906824 CTAAGGCGATAGGGGGCGA 60.907 63.158 0.00 0.00 34.74 5.54
178 179 2.657237 CTAAGGCGATAGGGGGCG 59.343 66.667 0.00 0.00 34.74 6.13
179 180 2.347866 GCTAAGGCGATAGGGGGC 59.652 66.667 0.00 0.00 0.00 5.80
189 190 0.533032 AGGTCTCAAGACGCTAAGGC 59.467 55.000 4.17 0.00 45.65 4.35
190 191 1.134965 CCAGGTCTCAAGACGCTAAGG 60.135 57.143 4.17 0.00 45.65 2.69
191 192 1.546476 ACCAGGTCTCAAGACGCTAAG 59.454 52.381 4.17 1.89 45.65 2.18
192 193 1.272490 CACCAGGTCTCAAGACGCTAA 59.728 52.381 4.17 0.00 45.65 3.09
193 194 0.888619 CACCAGGTCTCAAGACGCTA 59.111 55.000 4.17 0.00 45.65 4.26
194 195 1.668294 CACCAGGTCTCAAGACGCT 59.332 57.895 4.17 0.63 45.65 5.07
195 196 1.374758 CCACCAGGTCTCAAGACGC 60.375 63.158 4.17 0.00 45.65 5.19
196 197 0.038159 GTCCACCAGGTCTCAAGACG 60.038 60.000 4.17 0.00 45.65 4.18
197 198 0.321996 GGTCCACCAGGTCTCAAGAC 59.678 60.000 1.37 1.37 38.98 3.01
198 199 0.836400 GGGTCCACCAGGTCTCAAGA 60.836 60.000 0.00 0.00 39.85 3.02
199 200 1.679898 GGGTCCACCAGGTCTCAAG 59.320 63.158 0.00 0.00 39.85 3.02
200 201 1.846124 GGGGTCCACCAGGTCTCAA 60.846 63.158 0.00 0.00 42.91 3.02
201 202 2.203938 GGGGTCCACCAGGTCTCA 60.204 66.667 0.00 0.00 42.91 3.27
202 203 1.990614 GAGGGGTCCACCAGGTCTC 60.991 68.421 0.00 0.00 42.91 3.36
203 204 2.122954 GAGGGGTCCACCAGGTCT 59.877 66.667 0.00 0.00 42.91 3.85
204 205 3.391382 CGAGGGGTCCACCAGGTC 61.391 72.222 0.00 0.00 42.91 3.85
211 212 2.252012 ATAAGGAGGCGAGGGGTCCA 62.252 60.000 0.00 0.00 32.23 4.02
212 213 1.459730 ATAAGGAGGCGAGGGGTCC 60.460 63.158 0.00 0.00 0.00 4.46
213 214 1.749033 CATAAGGAGGCGAGGGGTC 59.251 63.158 0.00 0.00 0.00 4.46
214 215 2.444256 GCATAAGGAGGCGAGGGGT 61.444 63.158 0.00 0.00 0.00 4.95
215 216 1.700042 AAGCATAAGGAGGCGAGGGG 61.700 60.000 0.00 0.00 37.47 4.79
216 217 1.048601 TAAGCATAAGGAGGCGAGGG 58.951 55.000 0.00 0.00 37.47 4.30
217 218 2.484889 GTTAAGCATAAGGAGGCGAGG 58.515 52.381 0.00 0.00 37.47 4.63
218 219 2.103263 AGGTTAAGCATAAGGAGGCGAG 59.897 50.000 7.52 0.00 37.47 5.03
219 220 2.116238 AGGTTAAGCATAAGGAGGCGA 58.884 47.619 7.52 0.00 37.47 5.54
220 221 2.622064 AGGTTAAGCATAAGGAGGCG 57.378 50.000 7.52 0.00 37.47 5.52
221 222 3.071747 AGCTAGGTTAAGCATAAGGAGGC 59.928 47.826 7.52 0.00 45.30 4.70
222 223 4.965200 AGCTAGGTTAAGCATAAGGAGG 57.035 45.455 7.52 0.00 45.30 4.30
223 224 5.463724 CGAAAGCTAGGTTAAGCATAAGGAG 59.536 44.000 7.76 0.00 45.30 3.69
224 225 5.128171 TCGAAAGCTAGGTTAAGCATAAGGA 59.872 40.000 7.76 0.00 45.30 3.36
225 226 5.357257 TCGAAAGCTAGGTTAAGCATAAGG 58.643 41.667 7.76 0.00 45.30 2.69
226 227 6.926272 AGATCGAAAGCTAGGTTAAGCATAAG 59.074 38.462 7.76 2.69 45.30 1.73
227 228 6.817184 AGATCGAAAGCTAGGTTAAGCATAA 58.183 36.000 7.76 0.00 45.30 1.90
228 229 6.265649 AGAGATCGAAAGCTAGGTTAAGCATA 59.734 38.462 7.76 0.00 45.30 3.14
229 230 5.069781 AGAGATCGAAAGCTAGGTTAAGCAT 59.930 40.000 7.76 0.00 45.30 3.79
230 231 4.402793 AGAGATCGAAAGCTAGGTTAAGCA 59.597 41.667 7.76 0.00 45.30 3.91
231 232 4.939271 AGAGATCGAAAGCTAGGTTAAGC 58.061 43.478 7.76 0.00 43.11 3.09
232 233 6.385649 AGAGAGATCGAAAGCTAGGTTAAG 57.614 41.667 7.76 5.36 0.00 1.85
233 234 6.153000 ACAAGAGAGATCGAAAGCTAGGTTAA 59.847 38.462 7.76 0.00 0.00 2.01
234 235 5.652891 ACAAGAGAGATCGAAAGCTAGGTTA 59.347 40.000 7.76 0.00 0.00 2.85
235 236 4.464597 ACAAGAGAGATCGAAAGCTAGGTT 59.535 41.667 0.12 0.12 0.00 3.50
236 237 4.020543 ACAAGAGAGATCGAAAGCTAGGT 58.979 43.478 0.00 0.00 0.00 3.08
237 238 4.647424 ACAAGAGAGATCGAAAGCTAGG 57.353 45.455 0.00 0.00 0.00 3.02
238 239 6.329496 AGAAACAAGAGAGATCGAAAGCTAG 58.671 40.000 0.00 0.00 0.00 3.42
239 240 6.274157 AGAAACAAGAGAGATCGAAAGCTA 57.726 37.500 0.00 0.00 0.00 3.32
240 241 5.146010 AGAAACAAGAGAGATCGAAAGCT 57.854 39.130 0.00 0.00 0.00 3.74
241 242 5.854431 AAGAAACAAGAGAGATCGAAAGC 57.146 39.130 0.00 0.00 0.00 3.51
242 243 6.073331 AGCAAAGAAACAAGAGAGATCGAAAG 60.073 38.462 0.00 0.00 0.00 2.62
243 244 5.760253 AGCAAAGAAACAAGAGAGATCGAAA 59.240 36.000 0.00 0.00 0.00 3.46
244 245 5.178252 CAGCAAAGAAACAAGAGAGATCGAA 59.822 40.000 0.00 0.00 0.00 3.71
245 246 4.687948 CAGCAAAGAAACAAGAGAGATCGA 59.312 41.667 0.00 0.00 0.00 3.59
246 247 4.450419 ACAGCAAAGAAACAAGAGAGATCG 59.550 41.667 0.00 0.00 0.00 3.69
247 248 5.238214 ACACAGCAAAGAAACAAGAGAGATC 59.762 40.000 0.00 0.00 0.00 2.75
248 249 5.128919 ACACAGCAAAGAAACAAGAGAGAT 58.871 37.500 0.00 0.00 0.00 2.75
249 250 4.517285 ACACAGCAAAGAAACAAGAGAGA 58.483 39.130 0.00 0.00 0.00 3.10
250 251 4.889832 ACACAGCAAAGAAACAAGAGAG 57.110 40.909 0.00 0.00 0.00 3.20
251 252 4.816385 CCTACACAGCAAAGAAACAAGAGA 59.184 41.667 0.00 0.00 0.00 3.10
252 253 4.576463 ACCTACACAGCAAAGAAACAAGAG 59.424 41.667 0.00 0.00 0.00 2.85
253 254 4.335315 CACCTACACAGCAAAGAAACAAGA 59.665 41.667 0.00 0.00 0.00 3.02
254 255 4.096382 ACACCTACACAGCAAAGAAACAAG 59.904 41.667 0.00 0.00 0.00 3.16
255 256 4.013728 ACACCTACACAGCAAAGAAACAA 58.986 39.130 0.00 0.00 0.00 2.83
256 257 3.616219 ACACCTACACAGCAAAGAAACA 58.384 40.909 0.00 0.00 0.00 2.83
257 258 4.814771 AGTACACCTACACAGCAAAGAAAC 59.185 41.667 0.00 0.00 0.00 2.78
258 259 5.031066 AGTACACCTACACAGCAAAGAAA 57.969 39.130 0.00 0.00 0.00 2.52
259 260 4.682778 AGTACACCTACACAGCAAAGAA 57.317 40.909 0.00 0.00 0.00 2.52
260 261 4.682778 AAGTACACCTACACAGCAAAGA 57.317 40.909 0.00 0.00 0.00 2.52
261 262 8.718102 ATAATAAGTACACCTACACAGCAAAG 57.282 34.615 0.00 0.00 0.00 2.77
263 264 9.811995 CTTATAATAAGTACACCTACACAGCAA 57.188 33.333 0.00 0.00 0.00 3.91
264 265 7.924412 GCTTATAATAAGTACACCTACACAGCA 59.076 37.037 0.00 0.00 0.00 4.41
298 299 4.146443 GCTCGTTGTGCAATGAAAAGTTAC 59.854 41.667 8.02 0.00 36.06 2.50
340 341 1.286880 CAAGGCAGGCTGGAAAACG 59.713 57.895 17.64 0.00 0.00 3.60
342 343 2.563798 CGCAAGGCAGGCTGGAAAA 61.564 57.895 17.64 0.00 0.00 2.29
407 422 6.006449 ACTTCACCATCTATTTGTGCTTCTT 58.994 36.000 0.00 0.00 0.00 2.52
474 636 7.679453 TCACCACTACCTTATTTCTTTAGGGTA 59.321 37.037 0.00 0.00 33.88 3.69
483 645 6.696148 CGTCTATGTCACCACTACCTTATTTC 59.304 42.308 0.00 0.00 0.00 2.17
497 659 4.460948 TTTAAGGGTCCGTCTATGTCAC 57.539 45.455 0.00 0.00 0.00 3.67
520 682 7.865385 TGCAACTACAACAAATCCTGATAAAAC 59.135 33.333 0.00 0.00 0.00 2.43
525 687 6.040842 AGTTTGCAACTACAACAAATCCTGAT 59.959 34.615 0.00 0.00 40.69 2.90
536 698 7.147143 TGACAACTTTAGTTTGCAACTACAA 57.853 32.000 0.00 2.23 43.30 2.41
540 702 8.442384 CAAAAATGACAACTTTAGTTTGCAACT 58.558 29.630 0.00 2.51 45.40 3.16
592 754 6.474102 GGCAACTTTAGTTTTCAAATCGAACA 59.526 34.615 0.00 0.00 35.83 3.18
687 851 7.222611 CCCTTATTTCCTTATTTCAAACATGCG 59.777 37.037 0.00 0.00 0.00 4.73
747 911 1.289800 GAAGCTTGAACGGTCGGTCC 61.290 60.000 2.10 0.00 0.00 4.46
751 915 0.110644 GCTTGAAGCTTGAACGGTCG 60.111 55.000 10.44 0.00 38.45 4.79
769 933 2.281484 TCAAACTGACGCCCCTGC 60.281 61.111 0.00 0.00 0.00 4.85
909 1082 4.125695 GGTTAGAGGCGTCGGCGT 62.126 66.667 12.58 7.52 41.24 5.68
970 1143 2.125832 GAATCGACGGGCACGGAA 60.126 61.111 15.46 0.00 46.48 4.30
1026 1200 2.876645 GAGAAGGTCGACGCGCTG 60.877 66.667 5.73 0.00 0.00 5.18
1045 1219 1.139853 GGTGTGATCCTCCTCCATGAC 59.860 57.143 0.00 0.00 0.00 3.06
1089 1263 1.689273 GTCACTCACTCCTGGTTGAGT 59.311 52.381 20.84 20.84 46.35 3.41
1191 1365 3.447229 TCTTCTCTAATCATGCGTCCACA 59.553 43.478 0.00 0.00 0.00 4.17
1244 1418 4.400884 TGCAAGAAGCTAGAAACAACCAAA 59.599 37.500 0.00 0.00 45.94 3.28
1279 1453 2.961741 TCCATGTCTATCTCTGCACTCC 59.038 50.000 0.00 0.00 0.00 3.85
1368 1542 6.915843 GGTAATATTATTTGCGGTTCCTGTTG 59.084 38.462 0.00 0.00 0.00 3.33
1493 1667 0.813184 AAGAATCATTGGCGCAGTGG 59.187 50.000 10.83 0.00 0.00 4.00
1561 1735 5.013704 TGGTGTGAACATTCCTACCAGTATT 59.986 40.000 11.10 0.00 37.30 1.89
1580 1754 4.634012 TGTGTCTAGGCTATTTTGGTGT 57.366 40.909 0.00 0.00 0.00 4.16
1626 1800 3.371021 AGACCCTCTGACTGTGCG 58.629 61.111 0.00 0.00 0.00 5.34
1665 1839 5.246656 TCCCGGAAGTAAATTAAGTGACTCA 59.753 40.000 0.73 0.00 0.00 3.41
1715 1889 4.207698 ACCAATCCAAAGGTTAAACCCT 57.792 40.909 0.00 0.00 39.75 4.34
1734 1908 0.106149 ACTTCACACGTCCTGGAACC 59.894 55.000 0.00 0.00 0.00 3.62
1745 1919 6.903883 TGAAAAGAGTACAGAACTTCACAC 57.096 37.500 0.00 0.00 39.07 3.82
1780 1956 7.989947 ACTAGAGTATTTATCTTCCAACCCA 57.010 36.000 0.00 0.00 0.00 4.51
1829 2005 8.827677 GCTTTTTGTTTTACTCTCTTAGTCTCA 58.172 33.333 0.00 0.00 39.80 3.27
1844 2020 7.505258 TCTTATGGCCTAAAGCTTTTTGTTTT 58.495 30.769 18.47 2.07 43.05 2.43
1939 2115 6.094048 ACATTTTGCAGCAACTAAGACGATAT 59.906 34.615 7.54 0.00 0.00 1.63
1993 2169 5.246307 GCCAAGATGTTTGGTAGTCTAACT 58.754 41.667 7.67 0.00 41.53 2.24
1994 2170 4.092968 CGCCAAGATGTTTGGTAGTCTAAC 59.907 45.833 7.67 0.00 41.53 2.34
2024 2200 5.163814 GCTGAGCAAGTACCTGAGTTTTATG 60.164 44.000 0.00 0.00 0.00 1.90
2156 2333 7.156673 CCTTGACACATTGAATTGGAAAATCT 58.843 34.615 0.00 0.00 0.00 2.40
2268 2446 4.126437 GCCACCAAACAGTTAAGCAAAAT 58.874 39.130 0.00 0.00 0.00 1.82
2420 2602 7.279615 TGTGAGTAGAAGATGAAACCAGAAAA 58.720 34.615 0.00 0.00 0.00 2.29
2492 2674 9.042008 GTCTGAACTCTTATGTTGACTTTGTTA 57.958 33.333 0.00 0.00 0.00 2.41
2527 2709 6.648879 TCAGGATCATATGACACGATACAA 57.351 37.500 7.78 0.00 0.00 2.41
2655 2837 2.354259 ACCAACTACCTACTCGAGACG 58.646 52.381 21.68 9.07 0.00 4.18
2786 2968 1.408702 ACACCATGGAAGCAACAACAC 59.591 47.619 21.47 0.00 0.00 3.32
2788 2970 2.472816 CAACACCATGGAAGCAACAAC 58.527 47.619 21.47 0.00 0.00 3.32
2862 3044 3.179443 TGAGACGGCATTGATAGTTCC 57.821 47.619 0.00 0.00 0.00 3.62
2876 3058 1.338674 TGGTTAGTGGGCAATGAGACG 60.339 52.381 0.00 0.00 0.00 4.18
2914 3096 3.798202 CTTTCTTCAGGGGATTAGACGG 58.202 50.000 0.00 0.00 0.00 4.79
2981 3163 6.154021 AGCATCTTTCATTACATCCTTTGCTT 59.846 34.615 0.00 0.00 32.03 3.91
3175 3361 0.322322 AACTAACCCGCATTCCGACA 59.678 50.000 0.00 0.00 40.02 4.35
3204 3390 3.189606 ACCCATAGACACCTCAAATGGA 58.810 45.455 1.26 0.00 39.60 3.41
3316 3505 8.712228 AAACCTTCTTGGAGATTGAGTTAATT 57.288 30.769 0.00 0.00 39.71 1.40
3318 3507 8.533569 AAAAACCTTCTTGGAGATTGAGTTAA 57.466 30.769 0.00 0.00 39.71 2.01
3320 3509 8.533569 TTAAAAACCTTCTTGGAGATTGAGTT 57.466 30.769 0.00 0.00 39.71 3.01
3321 3510 8.533569 TTTAAAAACCTTCTTGGAGATTGAGT 57.466 30.769 0.00 0.00 39.71 3.41
3322 3511 8.084684 CCTTTAAAAACCTTCTTGGAGATTGAG 58.915 37.037 0.00 0.00 39.71 3.02
3372 3561 2.557924 TGTGCCATTGGTGATTCTGAAC 59.442 45.455 4.26 0.00 0.00 3.18
3384 3573 2.991190 GTTGATTGCTCTTGTGCCATTG 59.009 45.455 0.00 0.00 0.00 2.82
3463 3652 0.748367 GGAATTCGGGAGGCTGGAAC 60.748 60.000 0.00 0.00 0.00 3.62
3474 3663 1.098050 CCAAAGAGCCTGGAATTCGG 58.902 55.000 0.00 0.00 35.85 4.30
3475 3664 2.113860 TCCAAAGAGCCTGGAATTCG 57.886 50.000 0.00 0.00 40.08 3.34
3481 3670 5.982890 TTTTTAAGATCCAAAGAGCCTGG 57.017 39.130 0.00 0.00 35.05 4.45
3545 3745 9.801873 AATTGGTACCATCATTTTTAAGATTCG 57.198 29.630 17.17 0.00 0.00 3.34
3623 3824 5.888724 TCACAGTGAAACCAAAATTCCTACA 59.111 36.000 0.00 0.00 37.80 2.74
3635 3836 3.610114 GCACATGACATCACAGTGAAACC 60.610 47.826 7.50 0.07 37.80 3.27
3657 3858 3.072476 TCAACCTTACAGAAAGAGTGGGG 59.928 47.826 0.00 0.00 37.38 4.96
3669 3870 2.438021 AGCACCTGAGTTCAACCTTACA 59.562 45.455 0.00 0.00 0.00 2.41
3670 3871 2.808543 CAGCACCTGAGTTCAACCTTAC 59.191 50.000 0.00 0.00 32.44 2.34
3671 3872 2.438021 ACAGCACCTGAGTTCAACCTTA 59.562 45.455 0.00 0.00 35.18 2.69
3672 3873 1.212935 ACAGCACCTGAGTTCAACCTT 59.787 47.619 0.00 0.00 35.18 3.50
3673 3874 0.839946 ACAGCACCTGAGTTCAACCT 59.160 50.000 0.00 0.00 35.18 3.50
3674 3875 2.143925 GTACAGCACCTGAGTTCAACC 58.856 52.381 0.00 0.00 35.18 3.77
3713 4804 3.740321 GCTGAAAATTGCGAAAATGGTGA 59.260 39.130 0.00 0.00 0.00 4.02
3753 4844 5.152097 GTGAACTCATGCAATCAACTTCTG 58.848 41.667 0.00 0.00 0.00 3.02
3897 4988 5.681982 CGTTGTTGCCACGATTTAAACTTTA 59.318 36.000 0.00 0.00 0.00 1.85
3898 4989 4.501198 CGTTGTTGCCACGATTTAAACTTT 59.499 37.500 0.00 0.00 0.00 2.66
4080 5182 3.311871 CAGTATGGCTGTGCTTCTGATTC 59.688 47.826 0.00 0.00 40.27 2.52


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

AutoCloner maintained by Alex Coulton.