Multiple sequence alignment - TraesCS7D01G212800

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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 TraesCS7D01G212800 chr7D 100.000 5455 0 0 1 5455 171302000 171307454 0.000000e+00 10074
1 TraesCS7D01G212800 chr7B 95.834 4873 99 29 653 5455 137784300 137789138 0.000000e+00 7779
2 TraesCS7D01G212800 chr7B 90.838 382 19 7 244 611 137783921 137784300 1.060000e-136 497
3 TraesCS7D01G212800 chr7B 77.320 194 39 5 62 252 726140518 726140327 5.780000e-20 110
4 TraesCS7D01G212800 chr7A 96.065 3939 115 16 1519 5455 174195954 174199854 0.000000e+00 6379
5 TraesCS7D01G212800 chr7A 90.916 1332 51 23 238 1523 174194623 174195930 0.000000e+00 1725
6 TraesCS7D01G212800 chr7A 90.763 249 23 0 3 251 263139900 263139652 3.150000e-87 333
7 TraesCS7D01G212800 chr2B 89.575 259 25 2 1 258 738498670 738498927 1.470000e-85 327
8 TraesCS7D01G212800 chr6A 84.663 326 48 2 4131 4455 521459143 521458819 1.900000e-84 324
9 TraesCS7D01G212800 chr6B 83.436 326 52 2 4131 4455 567408352 567408028 8.880000e-78 302
10 TraesCS7D01G212800 chr3A 88.934 244 27 0 7 250 648117809 648118052 8.880000e-78 302


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 TraesCS7D01G212800 chr7D 171302000 171307454 5454 False 10074 10074 100.0000 1 5455 1 chr7D.!!$F1 5454
1 TraesCS7D01G212800 chr7B 137783921 137789138 5217 False 4138 7779 93.3360 244 5455 2 chr7B.!!$F1 5211
2 TraesCS7D01G212800 chr7A 174194623 174199854 5231 False 4052 6379 93.4905 238 5455 2 chr7A.!!$F1 5217

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
25 26 0.108615 GGGGAGCGGATCATCGTATG 60.109 60.0 0.0 0.0 0.0 2.39 F
1163 1224 0.175073 CGTTCTAGGGGGTGTACTGC 59.825 60.0 0.0 0.0 0.0 4.40 F
1358 1436 0.694771 TCTGAAACATCTGCCTGCCT 59.305 50.0 0.0 0.0 0.0 4.75 F
1359 1437 0.809385 CTGAAACATCTGCCTGCCTG 59.191 55.0 0.0 0.0 0.0 4.85 F
1360 1438 1.246056 TGAAACATCTGCCTGCCTGC 61.246 55.0 0.0 0.0 0.0 4.85 F
3182 3300 0.111253 CCTTGCCTGAGTGGGAGTTT 59.889 55.0 0.0 0.0 37.5 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1222 1300 0.957395 AACAACATCAGAGGCAGGCG 60.957 55.000 0.0 0.0 0.00 5.52 R
1967 2081 1.553704 ACAGACCTCGGGTTAACATCC 59.446 52.381 8.1 0.0 35.25 3.51 R
2465 2580 2.068837 CACCAAATGCAACTGCGAAT 57.931 45.000 0.0 0.0 45.83 3.34 R
3182 3300 2.238898 GGAGGAGGCTAGCCAAAGTAAA 59.761 50.000 34.7 0.0 38.92 2.01 R
3402 3520 6.638468 ACTTTCAATTCTGCATCGTTCTTTTC 59.362 34.615 0.0 0.0 0.00 2.29 R
4758 4878 1.203065 GCAGCAAGAAAAGCACACAC 58.797 50.000 0.0 0.0 0.00 3.82 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 3.851955 TAACTCGGGGAGCGGATC 58.148 61.111 0.00 0.00 32.04 3.36
18 19 1.076559 TAACTCGGGGAGCGGATCA 60.077 57.895 0.00 0.00 32.04 2.92
19 20 0.469331 TAACTCGGGGAGCGGATCAT 60.469 55.000 0.00 0.00 32.04 2.45
20 21 1.749334 AACTCGGGGAGCGGATCATC 61.749 60.000 0.00 0.00 32.04 2.92
21 22 3.274455 CTCGGGGAGCGGATCATCG 62.274 68.421 0.00 0.00 0.00 3.84
22 23 3.606662 CGGGGAGCGGATCATCGT 61.607 66.667 0.00 0.00 0.00 3.73
23 24 2.265904 CGGGGAGCGGATCATCGTA 61.266 63.158 0.00 0.00 0.00 3.43
24 25 1.595993 CGGGGAGCGGATCATCGTAT 61.596 60.000 0.00 0.00 0.00 3.06
25 26 0.108615 GGGGAGCGGATCATCGTATG 60.109 60.000 0.00 0.00 0.00 2.39
26 27 0.108615 GGGAGCGGATCATCGTATGG 60.109 60.000 0.00 0.00 0.00 2.74
27 28 0.737715 GGAGCGGATCATCGTATGGC 60.738 60.000 0.00 0.00 0.00 4.40
28 29 1.073216 GAGCGGATCATCGTATGGCG 61.073 60.000 0.00 0.00 43.01 5.69
29 30 2.730672 GCGGATCATCGTATGGCGC 61.731 63.158 0.00 0.00 41.07 6.53
30 31 1.372872 CGGATCATCGTATGGCGCA 60.373 57.895 10.83 0.00 41.07 6.09
31 32 0.943835 CGGATCATCGTATGGCGCAA 60.944 55.000 10.83 0.00 41.07 4.85
32 33 1.442769 GGATCATCGTATGGCGCAAT 58.557 50.000 10.83 5.96 41.07 3.56
33 34 1.806542 GGATCATCGTATGGCGCAATT 59.193 47.619 10.83 0.00 41.07 2.32
34 35 3.000041 GGATCATCGTATGGCGCAATTA 59.000 45.455 10.83 0.00 41.07 1.40
35 36 3.623060 GGATCATCGTATGGCGCAATTAT 59.377 43.478 10.83 0.00 41.07 1.28
36 37 4.260375 GGATCATCGTATGGCGCAATTATC 60.260 45.833 10.83 0.99 41.07 1.75
37 38 3.000041 TCATCGTATGGCGCAATTATCC 59.000 45.455 10.83 0.00 41.07 2.59
38 39 2.535012 TCGTATGGCGCAATTATCCA 57.465 45.000 10.83 0.00 41.07 3.41
39 40 2.839975 TCGTATGGCGCAATTATCCAA 58.160 42.857 10.83 0.00 41.07 3.53
40 41 2.805671 TCGTATGGCGCAATTATCCAAG 59.194 45.455 10.83 0.00 41.07 3.61
41 42 2.805671 CGTATGGCGCAATTATCCAAGA 59.194 45.455 10.83 0.00 33.04 3.02
42 43 3.249799 CGTATGGCGCAATTATCCAAGAA 59.750 43.478 10.83 0.00 33.04 2.52
43 44 4.260990 CGTATGGCGCAATTATCCAAGAAA 60.261 41.667 10.83 0.00 33.04 2.52
44 45 4.942761 ATGGCGCAATTATCCAAGAAAT 57.057 36.364 10.83 0.00 33.04 2.17
45 46 4.305989 TGGCGCAATTATCCAAGAAATC 57.694 40.909 10.83 0.00 0.00 2.17
46 47 3.698539 TGGCGCAATTATCCAAGAAATCA 59.301 39.130 10.83 0.00 0.00 2.57
47 48 4.159321 TGGCGCAATTATCCAAGAAATCAA 59.841 37.500 10.83 0.00 0.00 2.57
48 49 4.504097 GGCGCAATTATCCAAGAAATCAAC 59.496 41.667 10.83 0.00 0.00 3.18
49 50 4.504097 GCGCAATTATCCAAGAAATCAACC 59.496 41.667 0.30 0.00 0.00 3.77
50 51 5.649557 CGCAATTATCCAAGAAATCAACCA 58.350 37.500 0.00 0.00 0.00 3.67
51 52 6.098679 CGCAATTATCCAAGAAATCAACCAA 58.901 36.000 0.00 0.00 0.00 3.67
52 53 6.034898 CGCAATTATCCAAGAAATCAACCAAC 59.965 38.462 0.00 0.00 0.00 3.77
53 54 6.873076 GCAATTATCCAAGAAATCAACCAACA 59.127 34.615 0.00 0.00 0.00 3.33
54 55 7.387397 GCAATTATCCAAGAAATCAACCAACAA 59.613 33.333 0.00 0.00 0.00 2.83
55 56 9.270640 CAATTATCCAAGAAATCAACCAACAAA 57.729 29.630 0.00 0.00 0.00 2.83
56 57 8.831715 ATTATCCAAGAAATCAACCAACAAAC 57.168 30.769 0.00 0.00 0.00 2.93
57 58 5.930837 TCCAAGAAATCAACCAACAAACT 57.069 34.783 0.00 0.00 0.00 2.66
58 59 7.595819 ATCCAAGAAATCAACCAACAAACTA 57.404 32.000 0.00 0.00 0.00 2.24
59 60 6.801575 TCCAAGAAATCAACCAACAAACTAC 58.198 36.000 0.00 0.00 0.00 2.73
60 61 6.378564 TCCAAGAAATCAACCAACAAACTACA 59.621 34.615 0.00 0.00 0.00 2.74
61 62 6.697019 CCAAGAAATCAACCAACAAACTACAG 59.303 38.462 0.00 0.00 0.00 2.74
62 63 5.831997 AGAAATCAACCAACAAACTACAGC 58.168 37.500 0.00 0.00 0.00 4.40
63 64 5.594317 AGAAATCAACCAACAAACTACAGCT 59.406 36.000 0.00 0.00 0.00 4.24
64 65 5.852282 AATCAACCAACAAACTACAGCTT 57.148 34.783 0.00 0.00 0.00 3.74
65 66 5.852282 ATCAACCAACAAACTACAGCTTT 57.148 34.783 0.00 0.00 0.00 3.51
66 67 5.652994 TCAACCAACAAACTACAGCTTTT 57.347 34.783 0.00 0.00 0.00 2.27
67 68 6.761099 TCAACCAACAAACTACAGCTTTTA 57.239 33.333 0.00 0.00 0.00 1.52
68 69 7.341445 TCAACCAACAAACTACAGCTTTTAT 57.659 32.000 0.00 0.00 0.00 1.40
69 70 7.777095 TCAACCAACAAACTACAGCTTTTATT 58.223 30.769 0.00 0.00 0.00 1.40
70 71 8.254508 TCAACCAACAAACTACAGCTTTTATTT 58.745 29.630 0.00 0.00 0.00 1.40
71 72 8.539674 CAACCAACAAACTACAGCTTTTATTTC 58.460 33.333 0.00 0.00 0.00 2.17
72 73 7.777095 ACCAACAAACTACAGCTTTTATTTCA 58.223 30.769 0.00 0.00 0.00 2.69
73 74 8.421002 ACCAACAAACTACAGCTTTTATTTCAT 58.579 29.630 0.00 0.00 0.00 2.57
74 75 8.702438 CCAACAAACTACAGCTTTTATTTCATG 58.298 33.333 0.00 0.00 0.00 3.07
75 76 9.248291 CAACAAACTACAGCTTTTATTTCATGT 57.752 29.630 0.00 0.00 0.00 3.21
107 108 8.890472 AGTCTATGAGTCTAGGAGATCTAATGT 58.110 37.037 0.00 0.00 0.00 2.71
112 113 9.685276 ATGAGTCTAGGAGATCTAATGTAGATG 57.315 37.037 0.00 0.00 45.16 2.90
113 114 7.609918 TGAGTCTAGGAGATCTAATGTAGATGC 59.390 40.741 0.00 0.00 45.16 3.91
114 115 7.698912 AGTCTAGGAGATCTAATGTAGATGCT 58.301 38.462 0.00 1.03 45.16 3.79
115 116 7.829211 AGTCTAGGAGATCTAATGTAGATGCTC 59.171 40.741 0.00 8.57 45.16 4.26
116 117 7.609918 GTCTAGGAGATCTAATGTAGATGCTCA 59.390 40.741 17.20 6.19 45.16 4.26
117 118 6.588719 AGGAGATCTAATGTAGATGCTCAC 57.411 41.667 17.20 11.35 45.16 3.51
118 119 6.073981 AGGAGATCTAATGTAGATGCTCACA 58.926 40.000 17.20 0.00 45.16 3.58
119 120 6.552725 AGGAGATCTAATGTAGATGCTCACAA 59.447 38.462 17.20 0.00 45.16 3.33
120 121 6.644592 GGAGATCTAATGTAGATGCTCACAAC 59.355 42.308 17.20 5.75 45.16 3.32
121 122 7.358770 AGATCTAATGTAGATGCTCACAACT 57.641 36.000 2.53 0.00 45.16 3.16
122 123 7.790027 AGATCTAATGTAGATGCTCACAACTT 58.210 34.615 2.53 0.00 45.16 2.66
123 124 8.918116 AGATCTAATGTAGATGCTCACAACTTA 58.082 33.333 2.53 0.00 45.16 2.24
124 125 9.190858 GATCTAATGTAGATGCTCACAACTTAG 57.809 37.037 2.53 0.00 45.16 2.18
125 126 6.980978 TCTAATGTAGATGCTCACAACTTAGC 59.019 38.462 0.00 0.00 39.25 3.09
126 127 3.511699 TGTAGATGCTCACAACTTAGCG 58.488 45.455 0.00 0.00 41.77 4.26
127 128 3.192633 TGTAGATGCTCACAACTTAGCGA 59.807 43.478 0.00 0.00 41.77 4.93
128 129 2.886081 AGATGCTCACAACTTAGCGAG 58.114 47.619 0.00 0.00 41.77 5.03
129 130 2.493675 AGATGCTCACAACTTAGCGAGA 59.506 45.455 0.00 0.00 41.77 4.04
130 131 2.065993 TGCTCACAACTTAGCGAGAC 57.934 50.000 0.00 0.00 41.77 3.36
131 132 0.985549 GCTCACAACTTAGCGAGACG 59.014 55.000 0.00 0.00 0.00 4.18
142 143 3.538841 CGAGACGCGCACTTTCTT 58.461 55.556 5.73 0.00 0.00 2.52
143 144 1.853319 CGAGACGCGCACTTTCTTT 59.147 52.632 5.73 0.00 0.00 2.52
144 145 0.449507 CGAGACGCGCACTTTCTTTG 60.450 55.000 5.73 0.00 0.00 2.77
145 146 0.722799 GAGACGCGCACTTTCTTTGC 60.723 55.000 5.73 0.00 36.57 3.68
146 147 1.725973 GACGCGCACTTTCTTTGCC 60.726 57.895 5.73 0.00 36.57 4.52
147 148 2.117941 GACGCGCACTTTCTTTGCCT 62.118 55.000 5.73 0.00 36.57 4.75
148 149 1.727022 CGCGCACTTTCTTTGCCTG 60.727 57.895 8.75 0.00 36.57 4.85
149 150 2.018324 GCGCACTTTCTTTGCCTGC 61.018 57.895 0.30 0.00 36.57 4.85
150 151 1.656441 CGCACTTTCTTTGCCTGCT 59.344 52.632 0.00 0.00 36.57 4.24
151 152 0.662374 CGCACTTTCTTTGCCTGCTG 60.662 55.000 0.00 0.00 36.57 4.41
152 153 0.319297 GCACTTTCTTTGCCTGCTGG 60.319 55.000 5.03 5.03 33.58 4.85
153 154 0.316204 CACTTTCTTTGCCTGCTGGG 59.684 55.000 12.06 1.66 38.36 4.45
163 164 3.376078 CTGCTGGGCGCCATGTTT 61.376 61.111 30.85 0.00 38.05 2.83
164 165 3.636313 CTGCTGGGCGCCATGTTTG 62.636 63.158 30.85 11.71 38.05 2.93
165 166 4.440127 GCTGGGCGCCATGTTTGG 62.440 66.667 30.85 10.20 46.66 3.28
166 167 2.990967 CTGGGCGCCATGTTTGGT 60.991 61.111 30.85 0.00 45.57 3.67
167 168 2.522923 TGGGCGCCATGTTTGGTT 60.523 55.556 30.85 0.00 45.57 3.67
168 169 1.228583 TGGGCGCCATGTTTGGTTA 60.229 52.632 30.85 0.00 45.57 2.85
169 170 1.247419 TGGGCGCCATGTTTGGTTAG 61.247 55.000 30.85 0.00 45.57 2.34
170 171 1.510844 GGCGCCATGTTTGGTTAGG 59.489 57.895 24.80 0.00 45.57 2.69
171 172 1.153842 GCGCCATGTTTGGTTAGGC 60.154 57.895 0.00 0.00 45.57 3.93
172 173 1.510844 CGCCATGTTTGGTTAGGCC 59.489 57.895 0.00 0.00 45.57 5.19
173 174 1.247419 CGCCATGTTTGGTTAGGCCA 61.247 55.000 5.01 0.00 45.57 5.36
182 183 4.235731 GTTAGGCCAACCGGATGG 57.764 61.111 25.72 25.72 42.76 3.51
183 184 1.453197 GTTAGGCCAACCGGATGGG 60.453 63.158 29.87 18.02 42.76 4.00
184 185 1.616930 TTAGGCCAACCGGATGGGA 60.617 57.895 29.87 0.19 42.76 4.37
185 186 0.991355 TTAGGCCAACCGGATGGGAT 60.991 55.000 29.87 12.10 42.76 3.85
186 187 0.991355 TAGGCCAACCGGATGGGATT 60.991 55.000 29.87 11.46 42.76 3.01
187 188 1.828224 GGCCAACCGGATGGGATTC 60.828 63.158 29.87 14.32 41.01 2.52
188 189 1.828224 GCCAACCGGATGGGATTCC 60.828 63.158 29.87 10.92 41.01 3.01
189 190 1.922821 CCAACCGGATGGGATTCCT 59.077 57.895 22.68 0.00 40.75 3.36
190 191 0.258774 CCAACCGGATGGGATTCCTT 59.741 55.000 22.68 0.00 40.75 3.36
191 192 1.341976 CCAACCGGATGGGATTCCTTT 60.342 52.381 22.68 0.00 40.75 3.11
192 193 2.024414 CAACCGGATGGGATTCCTTTC 58.976 52.381 9.46 0.10 40.75 2.62
193 194 0.180406 ACCGGATGGGATTCCTTTCG 59.820 55.000 9.46 0.00 40.75 3.46
194 195 0.180406 CCGGATGGGATTCCTTTCGT 59.820 55.000 5.90 0.00 37.46 3.85
195 196 1.583054 CGGATGGGATTCCTTTCGTC 58.417 55.000 2.01 0.00 35.25 4.20
196 197 1.810412 CGGATGGGATTCCTTTCGTCC 60.810 57.143 2.01 5.74 35.25 4.79
197 198 1.211949 GGATGGGATTCCTTTCGTCCA 59.788 52.381 11.71 0.00 33.62 4.02
198 199 2.158608 GGATGGGATTCCTTTCGTCCAT 60.159 50.000 11.71 0.00 37.66 3.41
199 200 2.418368 TGGGATTCCTTTCGTCCATG 57.582 50.000 2.01 0.00 33.62 3.66
200 201 1.633432 TGGGATTCCTTTCGTCCATGT 59.367 47.619 2.01 0.00 33.62 3.21
201 202 2.841266 TGGGATTCCTTTCGTCCATGTA 59.159 45.455 2.01 0.00 33.62 2.29
202 203 3.264706 TGGGATTCCTTTCGTCCATGTAA 59.735 43.478 2.01 0.00 33.62 2.41
203 204 4.263550 TGGGATTCCTTTCGTCCATGTAAA 60.264 41.667 2.01 0.00 33.62 2.01
204 205 4.095932 GGGATTCCTTTCGTCCATGTAAAC 59.904 45.833 2.01 0.00 33.62 2.01
205 206 4.201783 GGATTCCTTTCGTCCATGTAAACG 60.202 45.833 6.27 6.27 40.17 3.60
206 207 2.690786 TCCTTTCGTCCATGTAAACGG 58.309 47.619 11.18 0.00 39.31 4.44
207 208 2.037511 TCCTTTCGTCCATGTAAACGGT 59.962 45.455 11.18 0.00 39.31 4.83
208 209 2.158841 CCTTTCGTCCATGTAAACGGTG 59.841 50.000 11.18 4.20 39.31 4.94
209 210 1.149987 TTCGTCCATGTAAACGGTGC 58.850 50.000 11.18 0.00 39.31 5.01
210 211 1.009903 TCGTCCATGTAAACGGTGCG 61.010 55.000 11.18 0.00 39.31 5.34
211 212 1.009903 CGTCCATGTAAACGGTGCGA 61.010 55.000 5.01 0.00 35.32 5.10
212 213 0.441145 GTCCATGTAAACGGTGCGAC 59.559 55.000 0.00 0.00 0.00 5.19
213 214 1.009903 TCCATGTAAACGGTGCGACG 61.010 55.000 0.00 0.00 40.31 5.12
214 215 1.418367 CATGTAAACGGTGCGACGG 59.582 57.895 0.00 0.00 38.39 4.79
215 216 1.005867 ATGTAAACGGTGCGACGGT 60.006 52.632 0.00 0.00 38.39 4.83
216 217 0.600782 ATGTAAACGGTGCGACGGTT 60.601 50.000 8.21 8.21 46.73 4.44
218 219 1.135867 GTAAACGGTGCGACGGTTTA 58.864 50.000 18.80 18.80 45.61 2.01
219 220 1.858091 TAAACGGTGCGACGGTTTAA 58.142 45.000 19.65 10.46 45.61 1.52
220 221 1.228533 AAACGGTGCGACGGTTTAAT 58.771 45.000 17.08 2.03 45.61 1.40
221 222 2.077413 AACGGTGCGACGGTTTAATA 57.923 45.000 0.00 0.00 38.27 0.98
222 223 2.077413 ACGGTGCGACGGTTTAATAA 57.923 45.000 0.00 0.00 38.39 1.40
223 224 2.411904 ACGGTGCGACGGTTTAATAAA 58.588 42.857 0.00 0.00 38.39 1.40
224 225 2.805099 ACGGTGCGACGGTTTAATAAAA 59.195 40.909 0.00 0.00 38.39 1.52
225 226 3.249559 ACGGTGCGACGGTTTAATAAAAA 59.750 39.130 0.00 0.00 38.39 1.94
241 242 1.652563 AAAAACTCGCGAGGTTGCC 59.347 52.632 37.70 0.00 38.57 4.52
242 243 0.818040 AAAAACTCGCGAGGTTGCCT 60.818 50.000 37.70 21.35 38.57 4.75
291 293 4.782691 TGTCTGGAACTAATCTGGATCCAA 59.217 41.667 17.00 7.48 39.54 3.53
305 307 2.570135 GATCCAAGCTCCCAGTCATTC 58.430 52.381 0.00 0.00 0.00 2.67
343 345 1.201181 AGTCTGAGAGCACGCTTGTAG 59.799 52.381 0.00 0.00 0.00 2.74
500 515 1.071814 ACGCGAGCTTTTTACCCCA 59.928 52.632 15.93 0.00 0.00 4.96
588 605 1.044231 TTCCGGTTCCCTATAGCGCA 61.044 55.000 11.47 0.00 35.35 6.09
592 609 0.750850 GGTTCCCTATAGCGCACAGA 59.249 55.000 11.47 0.00 0.00 3.41
593 610 1.269831 GGTTCCCTATAGCGCACAGAG 60.270 57.143 11.47 3.06 0.00 3.35
594 611 1.040646 TTCCCTATAGCGCACAGAGG 58.959 55.000 11.47 13.06 0.00 3.69
595 612 1.005630 CCCTATAGCGCACAGAGGC 60.006 63.158 11.47 0.00 0.00 4.70
596 613 1.742146 CCTATAGCGCACAGAGGCA 59.258 57.895 11.47 0.00 0.00 4.75
857 895 2.671177 CGCCTGCTCCGTGTTTGAG 61.671 63.158 0.00 0.00 0.00 3.02
883 933 3.589654 TACACTCCACGCAGCCAGC 62.590 63.158 0.00 0.00 40.87 4.85
978 1028 4.691359 CAAGCTTGCCCTGCCCCT 62.691 66.667 14.65 0.00 0.00 4.79
979 1029 4.691359 AAGCTTGCCCTGCCCCTG 62.691 66.667 0.00 0.00 0.00 4.45
1138 1199 1.633774 GTGTCTCCCTCTTCTGTCCA 58.366 55.000 0.00 0.00 0.00 4.02
1163 1224 0.175073 CGTTCTAGGGGGTGTACTGC 59.825 60.000 0.00 0.00 0.00 4.40
1222 1300 1.526917 CCACCGAATCCATGGCTCC 60.527 63.158 6.96 0.00 0.00 4.70
1251 1329 4.151335 CCTCTGATGTTGTTTCTTCAGTCG 59.849 45.833 0.00 0.00 39.24 4.18
1351 1429 3.982701 TGCGCAAATTTCTGAAACATCTG 59.017 39.130 8.16 2.23 0.00 2.90
1352 1430 3.181537 GCGCAAATTTCTGAAACATCTGC 60.182 43.478 0.30 10.34 0.00 4.26
1353 1431 3.365820 CGCAAATTTCTGAAACATCTGCC 59.634 43.478 4.73 0.00 0.00 4.85
1354 1432 4.563061 GCAAATTTCTGAAACATCTGCCT 58.437 39.130 4.73 0.00 0.00 4.75
1355 1433 4.387862 GCAAATTTCTGAAACATCTGCCTG 59.612 41.667 4.73 0.00 0.00 4.85
1356 1434 3.863142 ATTTCTGAAACATCTGCCTGC 57.137 42.857 4.73 0.00 0.00 4.85
1357 1435 1.538047 TTCTGAAACATCTGCCTGCC 58.462 50.000 0.00 0.00 0.00 4.85
1358 1436 0.694771 TCTGAAACATCTGCCTGCCT 59.305 50.000 0.00 0.00 0.00 4.75
1359 1437 0.809385 CTGAAACATCTGCCTGCCTG 59.191 55.000 0.00 0.00 0.00 4.85
1360 1438 1.246056 TGAAACATCTGCCTGCCTGC 61.246 55.000 0.00 0.00 0.00 4.85
1361 1439 1.941999 GAAACATCTGCCTGCCTGCC 61.942 60.000 0.00 0.00 0.00 4.85
1362 1440 2.436596 AAACATCTGCCTGCCTGCCT 62.437 55.000 0.00 0.00 0.00 4.75
1533 1647 4.074970 AGCGAATCACCCAATCATATTCC 58.925 43.478 0.00 0.00 0.00 3.01
1554 1668 6.137794 TCCTTGCATGTTTTTACTTTTCGA 57.862 33.333 0.00 0.00 0.00 3.71
1650 1764 1.742308 TAGGAAACCTGACCAGCCTT 58.258 50.000 0.00 0.00 34.61 4.35
1680 1794 2.310538 TGAGTGTGCTCTTCTCACTGA 58.689 47.619 4.62 0.00 46.16 3.41
1688 1802 4.862018 GTGCTCTTCTCACTGACACTTATC 59.138 45.833 0.00 0.00 0.00 1.75
1877 1991 3.172106 TCCGTGGGCCACCTTGAA 61.172 61.111 30.03 8.90 37.76 2.69
1916 2030 4.833380 TGAGCTCTACTGTACAAACCTCTT 59.167 41.667 16.19 0.00 0.00 2.85
1942 2056 3.495193 CACTTCTTGTGCATATGTGTGC 58.505 45.455 4.29 0.00 45.25 4.57
1967 2081 4.385447 CGTTGCATAATTGTTGTTCCTTGG 59.615 41.667 0.00 0.00 0.00 3.61
2197 2312 1.366366 CCTAAGTGGCCCGATACCG 59.634 63.158 0.00 0.00 0.00 4.02
2232 2347 4.651778 AGAACATACAAGTAAGGCTGCAA 58.348 39.130 0.50 0.00 0.00 4.08
2465 2580 4.545610 CGATGAAAGCTAAAAGCCACAAA 58.454 39.130 0.00 0.00 43.77 2.83
2468 2583 6.183360 CGATGAAAGCTAAAAGCCACAAATTC 60.183 38.462 0.00 0.00 43.77 2.17
2657 2772 6.293298 CCTGATAATTGATGAAGCACTGCTAC 60.293 42.308 3.33 0.00 38.25 3.58
2796 2911 2.030958 CGGACACGTTTACAGGGGC 61.031 63.158 0.00 0.00 34.81 5.80
3182 3300 0.111253 CCTTGCCTGAGTGGGAGTTT 59.889 55.000 0.00 0.00 37.50 2.66
3402 3520 5.578005 AGAATTTTCAGATGTCATGCCTG 57.422 39.130 0.00 0.00 0.00 4.85
3466 3584 6.015504 CCGAACGTGAAAAAGACATAGAATG 58.984 40.000 0.00 0.00 0.00 2.67
4085 4205 1.164411 CATAACTGCAAACGCCCTGA 58.836 50.000 0.00 0.00 0.00 3.86
4119 4239 4.033817 GCTTAAGTTAGCTCATGACAGCAG 59.966 45.833 9.38 0.00 42.40 4.24
4753 4873 7.346751 TGTATTTTCTCTTTGGCAGTCTTTT 57.653 32.000 0.00 0.00 0.00 2.27
4837 4957 7.012610 CAGAATCCATTGCTGATGTGTACATAA 59.987 37.037 0.00 0.00 36.57 1.90
4838 4958 7.722728 AGAATCCATTGCTGATGTGTACATAAT 59.277 33.333 0.00 0.00 36.57 1.28
4839 4959 8.922931 AATCCATTGCTGATGTGTACATAATA 57.077 30.769 0.00 0.00 36.57 0.98
4915 5035 7.716799 ACTCCATACAGCCAAAATATTTCAA 57.283 32.000 0.10 0.00 0.00 2.69
4922 5042 6.340522 ACAGCCAAAATATTTCAATGTAGCC 58.659 36.000 0.10 0.00 0.00 3.93
5332 5452 1.009552 TCCAAGGGGCAGATCTCCTTA 59.990 52.381 12.57 0.00 38.70 2.69
5450 5570 2.283298 CAATCGTGTGGGATCCTTCAG 58.717 52.381 12.58 0.13 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.749334 GATGATCCGCTCCCCGAGTT 61.749 60.000 0.00 0.00 40.02 3.01
2 3 2.123251 ATGATCCGCTCCCCGAGT 60.123 61.111 0.00 0.00 40.02 4.18
3 4 2.653702 GATGATCCGCTCCCCGAG 59.346 66.667 0.00 0.00 40.02 4.63
4 5 2.685804 TACGATGATCCGCTCCCCGA 62.686 60.000 0.00 0.00 40.02 5.14
5 6 1.595993 ATACGATGATCCGCTCCCCG 61.596 60.000 0.00 0.00 0.00 5.73
6 7 0.108615 CATACGATGATCCGCTCCCC 60.109 60.000 0.00 0.00 0.00 4.81
7 8 0.108615 CCATACGATGATCCGCTCCC 60.109 60.000 0.00 0.00 0.00 4.30
8 9 0.737715 GCCATACGATGATCCGCTCC 60.738 60.000 0.00 0.00 0.00 4.70
9 10 2.743195 GCCATACGATGATCCGCTC 58.257 57.895 0.00 0.00 0.00 5.03
10 11 4.996976 GCCATACGATGATCCGCT 57.003 55.556 0.00 0.00 0.00 5.52
21 22 4.829064 TTCTTGGATAATTGCGCCATAC 57.171 40.909 4.18 0.00 0.00 2.39
22 23 5.534278 TGATTTCTTGGATAATTGCGCCATA 59.466 36.000 4.18 0.00 0.00 2.74
23 24 4.341806 TGATTTCTTGGATAATTGCGCCAT 59.658 37.500 4.18 0.00 0.00 4.40
24 25 3.698539 TGATTTCTTGGATAATTGCGCCA 59.301 39.130 4.18 0.00 0.00 5.69
25 26 4.305989 TGATTTCTTGGATAATTGCGCC 57.694 40.909 4.18 0.00 0.00 6.53
26 27 4.504097 GGTTGATTTCTTGGATAATTGCGC 59.496 41.667 0.00 0.00 0.00 6.09
27 28 5.649557 TGGTTGATTTCTTGGATAATTGCG 58.350 37.500 0.00 0.00 0.00 4.85
28 29 6.873076 TGTTGGTTGATTTCTTGGATAATTGC 59.127 34.615 0.00 0.00 0.00 3.56
29 30 8.830201 TTGTTGGTTGATTTCTTGGATAATTG 57.170 30.769 0.00 0.00 0.00 2.32
30 31 9.271828 GTTTGTTGGTTGATTTCTTGGATAATT 57.728 29.630 0.00 0.00 0.00 1.40
31 32 8.650490 AGTTTGTTGGTTGATTTCTTGGATAAT 58.350 29.630 0.00 0.00 0.00 1.28
32 33 8.017418 AGTTTGTTGGTTGATTTCTTGGATAA 57.983 30.769 0.00 0.00 0.00 1.75
33 34 7.595819 AGTTTGTTGGTTGATTTCTTGGATA 57.404 32.000 0.00 0.00 0.00 2.59
34 35 6.484364 AGTTTGTTGGTTGATTTCTTGGAT 57.516 33.333 0.00 0.00 0.00 3.41
35 36 5.930837 AGTTTGTTGGTTGATTTCTTGGA 57.069 34.783 0.00 0.00 0.00 3.53
36 37 6.568869 TGTAGTTTGTTGGTTGATTTCTTGG 58.431 36.000 0.00 0.00 0.00 3.61
37 38 6.198966 GCTGTAGTTTGTTGGTTGATTTCTTG 59.801 38.462 0.00 0.00 0.00 3.02
38 39 6.096846 AGCTGTAGTTTGTTGGTTGATTTCTT 59.903 34.615 0.00 0.00 0.00 2.52
39 40 5.594317 AGCTGTAGTTTGTTGGTTGATTTCT 59.406 36.000 0.00 0.00 0.00 2.52
40 41 5.831997 AGCTGTAGTTTGTTGGTTGATTTC 58.168 37.500 0.00 0.00 0.00 2.17
41 42 5.852282 AGCTGTAGTTTGTTGGTTGATTT 57.148 34.783 0.00 0.00 0.00 2.17
42 43 5.852282 AAGCTGTAGTTTGTTGGTTGATT 57.148 34.783 0.00 0.00 0.00 2.57
43 44 5.852282 AAAGCTGTAGTTTGTTGGTTGAT 57.148 34.783 0.00 0.00 0.00 2.57
44 45 5.652994 AAAAGCTGTAGTTTGTTGGTTGA 57.347 34.783 0.00 0.00 0.00 3.18
45 46 8.419076 AAATAAAAGCTGTAGTTTGTTGGTTG 57.581 30.769 0.00 0.00 0.00 3.77
46 47 8.254508 TGAAATAAAAGCTGTAGTTTGTTGGTT 58.745 29.630 0.00 0.00 0.00 3.67
47 48 7.777095 TGAAATAAAAGCTGTAGTTTGTTGGT 58.223 30.769 0.00 0.00 0.00 3.67
48 49 8.702438 CATGAAATAAAAGCTGTAGTTTGTTGG 58.298 33.333 0.00 0.00 0.00 3.77
49 50 9.248291 ACATGAAATAAAAGCTGTAGTTTGTTG 57.752 29.630 0.00 0.00 0.00 3.33
81 82 8.890472 ACATTAGATCTCCTAGACTCATAGACT 58.110 37.037 0.00 0.00 0.00 3.24
86 87 9.685276 CATCTACATTAGATCTCCTAGACTCAT 57.315 37.037 0.00 0.00 43.41 2.90
87 88 7.609918 GCATCTACATTAGATCTCCTAGACTCA 59.390 40.741 0.00 0.00 43.41 3.41
88 89 7.829211 AGCATCTACATTAGATCTCCTAGACTC 59.171 40.741 0.00 0.00 43.41 3.36
89 90 7.698912 AGCATCTACATTAGATCTCCTAGACT 58.301 38.462 0.00 0.00 43.41 3.24
90 91 7.609918 TGAGCATCTACATTAGATCTCCTAGAC 59.390 40.741 0.00 0.00 43.41 2.59
91 92 7.609918 GTGAGCATCTACATTAGATCTCCTAGA 59.390 40.741 0.00 0.00 43.41 2.43
92 93 7.392953 TGTGAGCATCTACATTAGATCTCCTAG 59.607 40.741 0.00 0.00 43.41 3.02
93 94 7.234355 TGTGAGCATCTACATTAGATCTCCTA 58.766 38.462 0.00 0.00 43.41 2.94
94 95 6.073981 TGTGAGCATCTACATTAGATCTCCT 58.926 40.000 0.00 0.00 43.41 3.69
95 96 6.338214 TGTGAGCATCTACATTAGATCTCC 57.662 41.667 0.00 9.45 43.41 3.71
96 97 7.432869 AGTTGTGAGCATCTACATTAGATCTC 58.567 38.462 0.00 11.68 43.41 2.75
97 98 7.358770 AGTTGTGAGCATCTACATTAGATCT 57.641 36.000 0.00 0.00 43.41 2.75
98 99 9.190858 CTAAGTTGTGAGCATCTACATTAGATC 57.809 37.037 0.00 0.00 43.41 2.75
99 100 7.655328 GCTAAGTTGTGAGCATCTACATTAGAT 59.345 37.037 0.00 0.00 46.06 1.98
100 101 6.980978 GCTAAGTTGTGAGCATCTACATTAGA 59.019 38.462 0.00 0.00 38.62 2.10
101 102 6.074623 CGCTAAGTTGTGAGCATCTACATTAG 60.075 42.308 0.00 0.00 38.69 1.73
102 103 5.748630 CGCTAAGTTGTGAGCATCTACATTA 59.251 40.000 0.00 0.00 38.69 1.90
103 104 4.568359 CGCTAAGTTGTGAGCATCTACATT 59.432 41.667 0.00 0.00 38.69 2.71
104 105 4.115516 CGCTAAGTTGTGAGCATCTACAT 58.884 43.478 0.00 0.00 38.69 2.29
105 106 3.192633 TCGCTAAGTTGTGAGCATCTACA 59.807 43.478 0.00 0.00 38.69 2.74
106 107 3.770666 TCGCTAAGTTGTGAGCATCTAC 58.229 45.455 0.00 0.00 38.69 2.59
107 108 3.694566 TCTCGCTAAGTTGTGAGCATCTA 59.305 43.478 9.61 0.00 42.44 1.98
108 109 2.493675 TCTCGCTAAGTTGTGAGCATCT 59.506 45.455 9.61 0.00 42.44 2.90
109 110 2.600867 GTCTCGCTAAGTTGTGAGCATC 59.399 50.000 9.61 0.00 42.44 3.91
110 111 2.611518 GTCTCGCTAAGTTGTGAGCAT 58.388 47.619 9.61 0.00 42.44 3.79
111 112 1.666023 CGTCTCGCTAAGTTGTGAGCA 60.666 52.381 9.61 0.00 42.44 4.26
112 113 0.985549 CGTCTCGCTAAGTTGTGAGC 59.014 55.000 9.61 0.00 42.44 4.26
125 126 0.449507 CAAAGAAAGTGCGCGTCTCG 60.450 55.000 8.43 0.00 42.12 4.04
126 127 0.722799 GCAAAGAAAGTGCGCGTCTC 60.723 55.000 8.43 0.91 31.20 3.36
127 128 1.279840 GCAAAGAAAGTGCGCGTCT 59.720 52.632 8.43 3.79 31.20 4.18
128 129 1.725973 GGCAAAGAAAGTGCGCGTC 60.726 57.895 8.43 0.00 43.18 5.19
129 130 2.186826 AGGCAAAGAAAGTGCGCGT 61.187 52.632 8.43 0.00 43.18 6.01
130 131 1.727022 CAGGCAAAGAAAGTGCGCG 60.727 57.895 0.00 0.00 43.18 6.86
131 132 2.018324 GCAGGCAAAGAAAGTGCGC 61.018 57.895 0.00 0.00 43.18 6.09
132 133 0.662374 CAGCAGGCAAAGAAAGTGCG 60.662 55.000 0.00 0.00 43.18 5.34
133 134 0.319297 CCAGCAGGCAAAGAAAGTGC 60.319 55.000 0.00 0.00 41.45 4.40
134 135 0.316204 CCCAGCAGGCAAAGAAAGTG 59.684 55.000 0.00 0.00 0.00 3.16
135 136 2.737503 CCCAGCAGGCAAAGAAAGT 58.262 52.632 0.00 0.00 0.00 2.66
149 150 1.247419 TAACCAAACATGGCGCCCAG 61.247 55.000 26.77 19.13 36.75 4.45
150 151 1.228583 TAACCAAACATGGCGCCCA 60.229 52.632 26.77 12.96 38.19 5.36
151 152 1.510844 CTAACCAAACATGGCGCCC 59.489 57.895 26.77 6.44 0.00 6.13
152 153 1.510844 CCTAACCAAACATGGCGCC 59.489 57.895 22.73 22.73 0.00 6.53
153 154 1.153842 GCCTAACCAAACATGGCGC 60.154 57.895 0.00 0.00 33.96 6.53
154 155 1.510844 GGCCTAACCAAACATGGCG 59.489 57.895 0.00 0.00 44.07 5.69
165 166 1.453197 CCCATCCGGTTGGCCTAAC 60.453 63.158 23.99 6.92 38.60 2.34
166 167 0.991355 ATCCCATCCGGTTGGCCTAA 60.991 55.000 23.99 10.51 35.29 2.69
167 168 0.991355 AATCCCATCCGGTTGGCCTA 60.991 55.000 23.99 12.76 35.29 3.93
168 169 2.284515 GAATCCCATCCGGTTGGCCT 62.285 60.000 23.99 11.40 35.29 5.19
169 170 1.828224 GAATCCCATCCGGTTGGCC 60.828 63.158 23.99 10.06 35.29 5.36
170 171 1.828224 GGAATCCCATCCGGTTGGC 60.828 63.158 23.99 11.44 35.29 4.52
171 172 0.258774 AAGGAATCCCATCCGGTTGG 59.741 55.000 22.69 22.69 44.60 3.77
172 173 2.024414 GAAAGGAATCCCATCCGGTTG 58.976 52.381 0.00 2.69 44.60 3.77
173 174 1.408266 CGAAAGGAATCCCATCCGGTT 60.408 52.381 0.00 0.00 44.60 4.44
174 175 0.180406 CGAAAGGAATCCCATCCGGT 59.820 55.000 0.00 0.00 44.60 5.28
175 176 0.180406 ACGAAAGGAATCCCATCCGG 59.820 55.000 0.00 0.00 44.60 5.14
176 177 1.583054 GACGAAAGGAATCCCATCCG 58.417 55.000 0.00 0.00 44.60 4.18
177 178 1.211949 TGGACGAAAGGAATCCCATCC 59.788 52.381 0.00 0.00 39.96 3.51
178 179 2.710096 TGGACGAAAGGAATCCCATC 57.290 50.000 0.00 0.00 33.88 3.51
179 180 2.242196 ACATGGACGAAAGGAATCCCAT 59.758 45.455 0.00 0.00 35.00 4.00
180 181 1.633432 ACATGGACGAAAGGAATCCCA 59.367 47.619 0.00 0.00 33.88 4.37
181 182 2.420058 ACATGGACGAAAGGAATCCC 57.580 50.000 0.00 0.00 0.00 3.85
182 183 4.201783 CGTTTACATGGACGAAAGGAATCC 60.202 45.833 11.56 0.00 41.53 3.01
183 184 4.201783 CCGTTTACATGGACGAAAGGAATC 60.202 45.833 16.71 0.00 41.53 2.52
184 185 3.687698 CCGTTTACATGGACGAAAGGAAT 59.312 43.478 16.71 0.00 41.53 3.01
185 186 3.068560 CCGTTTACATGGACGAAAGGAA 58.931 45.455 16.71 0.00 41.53 3.36
186 187 2.037511 ACCGTTTACATGGACGAAAGGA 59.962 45.455 16.71 0.00 41.53 3.36
187 188 2.158841 CACCGTTTACATGGACGAAAGG 59.841 50.000 16.71 6.47 41.53 3.11
188 189 2.412325 GCACCGTTTACATGGACGAAAG 60.412 50.000 16.71 9.08 41.53 2.62
189 190 1.532007 GCACCGTTTACATGGACGAAA 59.468 47.619 16.71 1.26 41.53 3.46
190 191 1.149987 GCACCGTTTACATGGACGAA 58.850 50.000 16.71 0.00 41.53 3.85
191 192 1.009903 CGCACCGTTTACATGGACGA 61.010 55.000 16.71 0.00 41.53 4.20
192 193 1.009903 TCGCACCGTTTACATGGACG 61.010 55.000 10.41 10.41 38.90 4.79
193 194 0.441145 GTCGCACCGTTTACATGGAC 59.559 55.000 0.00 0.00 32.58 4.02
194 195 1.009903 CGTCGCACCGTTTACATGGA 61.010 55.000 0.00 0.00 32.58 3.41
195 196 1.418367 CGTCGCACCGTTTACATGG 59.582 57.895 0.00 0.00 34.78 3.66
196 197 1.286354 ACCGTCGCACCGTTTACATG 61.286 55.000 0.00 0.00 0.00 3.21
197 198 0.600782 AACCGTCGCACCGTTTACAT 60.601 50.000 0.00 0.00 0.00 2.29
198 199 0.809241 AAACCGTCGCACCGTTTACA 60.809 50.000 4.78 0.00 0.00 2.41
199 200 1.135867 TAAACCGTCGCACCGTTTAC 58.864 50.000 8.00 0.00 0.00 2.01
200 201 1.858091 TTAAACCGTCGCACCGTTTA 58.142 45.000 8.00 8.00 0.00 2.01
201 202 1.228533 ATTAAACCGTCGCACCGTTT 58.771 45.000 9.33 9.33 0.00 3.60
202 203 2.077413 TATTAAACCGTCGCACCGTT 57.923 45.000 0.00 0.00 0.00 4.44
203 204 2.077413 TTATTAAACCGTCGCACCGT 57.923 45.000 0.00 0.00 0.00 4.83
204 205 3.452466 TTTTATTAAACCGTCGCACCG 57.548 42.857 0.00 0.00 0.00 4.94
223 224 0.818040 AGGCAACCTCGCGAGTTTTT 60.818 50.000 32.41 19.90 37.17 1.94
224 225 0.034337 TAGGCAACCTCGCGAGTTTT 59.966 50.000 32.41 22.31 34.61 2.43
225 226 0.034337 TTAGGCAACCTCGCGAGTTT 59.966 50.000 32.41 23.91 34.61 2.66
226 227 0.034337 TTTAGGCAACCTCGCGAGTT 59.966 50.000 32.41 23.04 34.61 3.01
227 228 0.034337 TTTTAGGCAACCTCGCGAGT 59.966 50.000 32.41 18.81 34.61 4.18
228 229 1.153353 TTTTTAGGCAACCTCGCGAG 58.847 50.000 29.06 29.06 34.61 5.03
229 230 3.309052 TTTTTAGGCAACCTCGCGA 57.691 47.368 9.26 9.26 34.61 5.87
305 307 2.673368 GACTTGAACGAACTAGGCATGG 59.327 50.000 0.00 0.00 0.00 3.66
343 345 1.954382 GACCCCACACAAGGAAGAAAC 59.046 52.381 0.00 0.00 0.00 2.78
445 447 2.599659 GATTTTTGCGAGCTCCCTTTG 58.400 47.619 8.47 0.00 0.00 2.77
500 515 4.637977 TGGTTCGTTTTTACTTTTACGGGT 59.362 37.500 0.00 0.00 34.93 5.28
595 612 3.406200 CTGACCTGAGGCCCCCTG 61.406 72.222 0.00 0.00 31.76 4.45
596 613 4.748798 CCTGACCTGAGGCCCCCT 62.749 72.222 0.00 0.00 36.03 4.79
809 847 3.314388 GAAAAGCACGGAGGCTGCG 62.314 63.158 27.12 27.12 45.07 5.18
857 895 0.643820 GCGTGGAGTGTAACGTATGC 59.356 55.000 0.00 0.00 45.86 3.14
974 1024 4.767892 AAGGGAGGGAGGCAGGGG 62.768 72.222 0.00 0.00 0.00 4.79
975 1025 3.093172 GAAGGGAGGGAGGCAGGG 61.093 72.222 0.00 0.00 0.00 4.45
976 1026 3.093172 GGAAGGGAGGGAGGCAGG 61.093 72.222 0.00 0.00 0.00 4.85
977 1027 2.041928 AGGAAGGGAGGGAGGCAG 59.958 66.667 0.00 0.00 0.00 4.85
978 1028 2.041265 GAGGAAGGGAGGGAGGCA 59.959 66.667 0.00 0.00 0.00 4.75
979 1029 3.157949 CGAGGAAGGGAGGGAGGC 61.158 72.222 0.00 0.00 0.00 4.70
983 1033 2.378634 ATTGCCGAGGAAGGGAGGG 61.379 63.158 0.00 0.00 31.78 4.30
1138 1199 1.273666 ACACCCCCTAGAACGATTCCT 60.274 52.381 0.00 0.00 0.00 3.36
1163 1224 1.811679 GCGGGCGGAGAAGAAGAAG 60.812 63.158 0.00 0.00 0.00 2.85
1222 1300 0.957395 AACAACATCAGAGGCAGGCG 60.957 55.000 0.00 0.00 0.00 5.52
1533 1647 7.167302 TGTCATCGAAAAGTAAAAACATGCAAG 59.833 33.333 0.00 0.00 0.00 4.01
1554 1668 2.224523 TGAAAGAAGAAGGGCGTGTCAT 60.225 45.455 0.00 0.00 0.00 3.06
1650 1764 3.425659 AGAGCACACTCACATAGTCTCA 58.574 45.455 0.00 0.00 46.09 3.27
1680 1794 5.808366 TGGAACTCTGAACAGATAAGTGT 57.192 39.130 4.96 0.00 36.76 3.55
1688 1802 5.972107 ATGGAAAATGGAACTCTGAACAG 57.028 39.130 0.00 0.00 0.00 3.16
1859 1973 2.969300 TTTCAAGGTGGCCCACGGAC 62.969 60.000 7.99 0.00 34.83 4.79
1942 2056 2.341168 GGAACAACAATTATGCAACGCG 59.659 45.455 3.53 3.53 0.00 6.01
1967 2081 1.553704 ACAGACCTCGGGTTAACATCC 59.446 52.381 8.10 0.00 35.25 3.51
2197 2312 4.016444 TGTATGTTCTTGCCAAAGATCCC 58.984 43.478 0.00 0.00 42.04 3.85
2232 2347 4.978099 ACAAGGATGAACACAATCTGAGT 58.022 39.130 0.00 0.00 0.00 3.41
2283 2398 9.113838 CAGCTTAAACTTGATACAGGTTCATAT 57.886 33.333 0.00 0.00 32.63 1.78
2446 2561 4.981674 CGAATTTGTGGCTTTTAGCTTTCA 59.018 37.500 0.00 0.00 41.99 2.69
2465 2580 2.068837 CACCAAATGCAACTGCGAAT 57.931 45.000 0.00 0.00 45.83 3.34
2657 2772 3.275999 TCCATGTGTTGATCTGCATCAG 58.724 45.455 0.00 0.00 40.28 2.90
3182 3300 2.238898 GGAGGAGGCTAGCCAAAGTAAA 59.761 50.000 34.70 0.00 38.92 2.01
3402 3520 6.638468 ACTTTCAATTCTGCATCGTTCTTTTC 59.362 34.615 0.00 0.00 0.00 2.29
4027 4147 5.733676 AGTGCTTTTCATTTCAGGTTGTTT 58.266 33.333 0.00 0.00 0.00 2.83
4085 4205 5.605534 AGCTAACTTAAGCATCATCGATGT 58.394 37.500 24.09 9.70 45.30 3.06
4119 4239 3.603532 TCTTCACCTGATCATCAAGCAC 58.396 45.455 0.00 0.00 0.00 4.40
4753 4873 4.152045 CAGCAAGAAAAGCACACACAAAAA 59.848 37.500 0.00 0.00 0.00 1.94
4758 4878 1.203065 GCAGCAAGAAAAGCACACAC 58.797 50.000 0.00 0.00 0.00 3.82
4760 4880 2.144482 ATGCAGCAAGAAAAGCACAC 57.856 45.000 0.00 0.00 40.14 3.82
4761 4881 2.894763 AATGCAGCAAGAAAAGCACA 57.105 40.000 0.00 0.00 40.14 4.57
4762 4882 3.556775 TGAAAATGCAGCAAGAAAAGCAC 59.443 39.130 0.00 0.00 40.14 4.40
4837 4957 4.202111 GGGTTTTGCGCAACCTGATATTAT 60.202 41.667 26.09 0.00 45.12 1.28
4838 4958 3.129638 GGGTTTTGCGCAACCTGATATTA 59.870 43.478 26.09 6.26 45.12 0.98
4839 4959 2.094234 GGGTTTTGCGCAACCTGATATT 60.094 45.455 26.09 0.00 45.12 1.28
4851 4971 4.804108 TCATGTATTTTGAGGGTTTTGCG 58.196 39.130 0.00 0.00 0.00 4.85
4915 5035 1.311859 TTATCGTCGTCGGGCTACAT 58.688 50.000 1.55 0.00 37.69 2.29
4922 5042 4.631377 TGGTATAGGTATTATCGTCGTCGG 59.369 45.833 1.55 0.00 37.69 4.79
5332 5452 0.247736 CGACCTACCTCAGCAAGCTT 59.752 55.000 0.00 0.00 0.00 3.74
5422 5542 1.348250 CCACACGATTGGATTCGCG 59.652 57.895 0.00 0.00 42.82 5.87


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

AutoCloner maintained by Alex Coulton.