Multiple sequence alignment - TraesCS4D01G137600

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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 TraesCS4D01G137600 chr4D 100.000 2718 0 0 1 2718 123338943 123336226 0.000000e+00 5020
1 TraesCS4D01G137600 chr4D 98.392 311 5 0 1 311 135040381 135040071 5.120000e-152 547
2 TraesCS4D01G137600 chr5A 99.091 2419 20 2 302 2718 19245671 19248089 0.000000e+00 4344
3 TraesCS4D01G137600 chr7D 99.008 2419 22 2 302 2718 381927173 381924755 0.000000e+00 4333
4 TraesCS4D01G137600 chr7D 99.008 2419 22 2 302 2718 382053251 382050833 0.000000e+00 4333
5 TraesCS4D01G137600 chr7D 98.884 2419 25 2 302 2718 203503171 203500753 0.000000e+00 4316
6 TraesCS4D01G137600 chr7D 98.639 2424 23 4 302 2718 381970593 381973013 0.000000e+00 4285
7 TraesCS4D01G137600 chr6D 98.719 2420 28 3 302 2718 124520695 124518276 0.000000e+00 4294
8 TraesCS4D01G137600 chr6D 98.392 311 5 0 1 311 430477325 430477635 5.120000e-152 547
9 TraesCS4D01G137600 chr7B 98.512 2419 29 3 302 2718 716875614 716878027 0.000000e+00 4261
10 TraesCS4D01G137600 chr7B 98.471 2420 29 4 302 2718 742992613 742990199 0.000000e+00 4257
11 TraesCS4D01G137600 chrUn 98.510 2416 29 3 302 2715 186205254 186207664 0.000000e+00 4255
12 TraesCS4D01G137600 chrUn 99.035 311 3 0 1 311 296252896 296253206 2.360000e-155 558
13 TraesCS4D01G137600 chrUn 98.392 311 5 0 1 311 246706118 246706428 5.120000e-152 547
14 TraesCS4D01G137600 chr3D 98.714 311 4 0 1 311 202633336 202633646 1.100000e-153 553
15 TraesCS4D01G137600 chr3D 98.392 311 5 0 1 311 498435951 498435641 5.120000e-152 547
16 TraesCS4D01G137600 chr1D 98.714 311 4 0 1 311 141349299 141348989 1.100000e-153 553
17 TraesCS4D01G137600 chr1D 98.392 311 5 0 1 311 350969820 350969510 5.120000e-152 547
18 TraesCS4D01G137600 chr2D 98.392 311 5 0 1 311 634990743 634991053 5.120000e-152 547


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 TraesCS4D01G137600 chr4D 123336226 123338943 2717 True 5020 5020 100.000 1 2718 1 chr4D.!!$R1 2717
1 TraesCS4D01G137600 chr5A 19245671 19248089 2418 False 4344 4344 99.091 302 2718 1 chr5A.!!$F1 2416
2 TraesCS4D01G137600 chr7D 381924755 381927173 2418 True 4333 4333 99.008 302 2718 1 chr7D.!!$R2 2416
3 TraesCS4D01G137600 chr7D 382050833 382053251 2418 True 4333 4333 99.008 302 2718 1 chr7D.!!$R3 2416
4 TraesCS4D01G137600 chr7D 203500753 203503171 2418 True 4316 4316 98.884 302 2718 1 chr7D.!!$R1 2416
5 TraesCS4D01G137600 chr7D 381970593 381973013 2420 False 4285 4285 98.639 302 2718 1 chr7D.!!$F1 2416
6 TraesCS4D01G137600 chr6D 124518276 124520695 2419 True 4294 4294 98.719 302 2718 1 chr6D.!!$R1 2416
7 TraesCS4D01G137600 chr7B 716875614 716878027 2413 False 4261 4261 98.512 302 2718 1 chr7B.!!$F1 2416
8 TraesCS4D01G137600 chr7B 742990199 742992613 2414 True 4257 4257 98.471 302 2718 1 chr7B.!!$R1 2416
9 TraesCS4D01G137600 chrUn 186205254 186207664 2410 False 4255 4255 98.510 302 2715 1 chrUn.!!$F1 2413


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
280 281 0.031857 TTGAAGGCCACACGCAATTG 59.968 50.0 5.01 0.0 40.31 2.32 F
287 288 0.238289 CCACACGCAATTGACTCACC 59.762 55.0 10.34 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1668 0.617820 ATACTGAGGTGCTCCCCGTT 60.618 55.000 0.0 0.0 0.00 4.44 R
1984 1993 2.909965 GCCGCTTTGGGTTGTGGA 60.910 61.111 0.0 0.0 38.63 4.02 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
19 20 2.969443 CCATTGTCGTCCACAGTTTC 57.031 50.000 0.00 0.00 35.97 2.78
20 21 1.535462 CCATTGTCGTCCACAGTTTCC 59.465 52.381 0.00 0.00 35.97 3.13
21 22 2.494059 CATTGTCGTCCACAGTTTCCT 58.506 47.619 0.00 0.00 35.97 3.36
22 23 2.702592 TTGTCGTCCACAGTTTCCTT 57.297 45.000 0.00 0.00 35.97 3.36
23 24 1.948104 TGTCGTCCACAGTTTCCTTG 58.052 50.000 0.00 0.00 0.00 3.61
24 25 1.208535 TGTCGTCCACAGTTTCCTTGT 59.791 47.619 0.00 0.00 0.00 3.16
25 26 1.865340 GTCGTCCACAGTTTCCTTGTC 59.135 52.381 0.00 0.00 0.00 3.18
26 27 0.859232 CGTCCACAGTTTCCTTGTCG 59.141 55.000 0.00 0.00 0.00 4.35
27 28 1.537348 CGTCCACAGTTTCCTTGTCGA 60.537 52.381 0.00 0.00 0.00 4.20
28 29 1.865340 GTCCACAGTTTCCTTGTCGAC 59.135 52.381 9.11 9.11 31.40 4.20
29 30 0.859232 CCACAGTTTCCTTGTCGACG 59.141 55.000 11.62 0.00 0.00 5.12
30 31 0.232303 CACAGTTTCCTTGTCGACGC 59.768 55.000 11.62 0.00 0.00 5.19
31 32 1.213094 ACAGTTTCCTTGTCGACGCG 61.213 55.000 11.62 3.53 0.00 6.01
32 33 0.937699 CAGTTTCCTTGTCGACGCGA 60.938 55.000 15.93 2.92 0.00 5.87
33 34 0.249155 AGTTTCCTTGTCGACGCGAA 60.249 50.000 15.93 9.19 37.72 4.70
34 35 0.161024 GTTTCCTTGTCGACGCGAAG 59.839 55.000 15.93 9.00 37.72 3.79
35 36 0.942410 TTTCCTTGTCGACGCGAAGG 60.942 55.000 21.47 21.47 37.72 3.46
57 58 4.238062 AGCAGCCCCCAAGCCAAA 62.238 61.111 0.00 0.00 0.00 3.28
58 59 3.698820 GCAGCCCCCAAGCCAAAG 61.699 66.667 0.00 0.00 0.00 2.77
59 60 2.203684 CAGCCCCCAAGCCAAAGT 60.204 61.111 0.00 0.00 0.00 2.66
60 61 2.118294 AGCCCCCAAGCCAAAGTC 59.882 61.111 0.00 0.00 0.00 3.01
61 62 2.118294 GCCCCCAAGCCAAAGTCT 59.882 61.111 0.00 0.00 0.00 3.24
62 63 2.278330 GCCCCCAAGCCAAAGTCTG 61.278 63.158 0.00 0.00 0.00 3.51
63 64 1.460255 CCCCCAAGCCAAAGTCTGA 59.540 57.895 0.00 0.00 0.00 3.27
64 65 0.610232 CCCCCAAGCCAAAGTCTGAG 60.610 60.000 0.00 0.00 0.00 3.35
65 66 0.401738 CCCCAAGCCAAAGTCTGAGA 59.598 55.000 0.00 0.00 0.00 3.27
66 67 1.005215 CCCCAAGCCAAAGTCTGAGAT 59.995 52.381 0.00 0.00 0.00 2.75
67 68 2.363683 CCCAAGCCAAAGTCTGAGATC 58.636 52.381 0.00 0.00 0.00 2.75
68 69 2.290514 CCCAAGCCAAAGTCTGAGATCA 60.291 50.000 0.00 0.00 0.00 2.92
69 70 3.008330 CCAAGCCAAAGTCTGAGATCAG 58.992 50.000 3.33 3.33 45.08 2.90
81 82 3.637432 CTGAGATCAGAACTCATACCGC 58.363 50.000 10.63 0.00 46.59 5.68
82 83 3.023832 TGAGATCAGAACTCATACCGCA 58.976 45.455 6.29 0.00 39.10 5.69
83 84 3.067320 TGAGATCAGAACTCATACCGCAG 59.933 47.826 6.29 0.00 39.10 5.18
84 85 3.027412 AGATCAGAACTCATACCGCAGT 58.973 45.455 0.00 0.00 0.00 4.40
85 86 3.449018 AGATCAGAACTCATACCGCAGTT 59.551 43.478 0.00 0.00 35.48 3.16
86 87 2.959516 TCAGAACTCATACCGCAGTTG 58.040 47.619 0.00 0.00 32.83 3.16
87 88 2.299013 TCAGAACTCATACCGCAGTTGT 59.701 45.455 0.00 0.00 32.83 3.32
88 89 2.413112 CAGAACTCATACCGCAGTTGTG 59.587 50.000 0.00 0.00 37.50 3.33
95 96 3.431055 CCGCAGTTGTGGCTTGAA 58.569 55.556 0.00 0.00 39.04 2.69
96 97 1.283793 CCGCAGTTGTGGCTTGAAG 59.716 57.895 0.00 0.00 39.04 3.02
97 98 1.283793 CGCAGTTGTGGCTTGAAGG 59.716 57.895 0.00 0.00 0.00 3.46
98 99 1.006922 GCAGTTGTGGCTTGAAGGC 60.007 57.895 12.27 12.27 41.77 4.35
105 106 4.503314 GGCTTGAAGGCCGCATGC 62.503 66.667 22.66 22.66 42.82 4.06
106 107 3.751246 GCTTGAAGGCCGCATGCA 61.751 61.111 24.52 7.94 43.89 3.96
107 108 2.964174 CTTGAAGGCCGCATGCAA 59.036 55.556 19.57 0.00 43.89 4.08
108 109 1.153901 CTTGAAGGCCGCATGCAAG 60.154 57.895 19.57 11.25 43.89 4.01
109 110 1.870055 CTTGAAGGCCGCATGCAAGT 61.870 55.000 19.57 0.00 43.89 3.16
110 111 1.462731 TTGAAGGCCGCATGCAAGTT 61.463 50.000 19.57 4.85 43.89 2.66
111 112 1.153958 GAAGGCCGCATGCAAGTTC 60.154 57.895 19.57 10.54 43.89 3.01
112 113 1.589716 GAAGGCCGCATGCAAGTTCT 61.590 55.000 19.57 7.56 43.89 3.01
113 114 1.181098 AAGGCCGCATGCAAGTTCTT 61.181 50.000 19.57 12.61 43.89 2.52
114 115 1.153958 GGCCGCATGCAAGTTCTTC 60.154 57.895 19.57 0.00 43.89 2.87
115 116 1.580942 GCCGCATGCAAGTTCTTCA 59.419 52.632 19.57 0.00 40.77 3.02
116 117 0.039256 GCCGCATGCAAGTTCTTCAA 60.039 50.000 19.57 0.00 40.77 2.69
117 118 1.403249 GCCGCATGCAAGTTCTTCAAT 60.403 47.619 19.57 0.00 40.77 2.57
118 119 2.159393 GCCGCATGCAAGTTCTTCAATA 60.159 45.455 19.57 0.00 40.77 1.90
119 120 3.489738 GCCGCATGCAAGTTCTTCAATAT 60.490 43.478 19.57 0.00 40.77 1.28
120 121 4.675510 CCGCATGCAAGTTCTTCAATATT 58.324 39.130 19.57 0.00 0.00 1.28
121 122 5.104374 CCGCATGCAAGTTCTTCAATATTT 58.896 37.500 19.57 0.00 0.00 1.40
122 123 6.264832 CCGCATGCAAGTTCTTCAATATTTA 58.735 36.000 19.57 0.00 0.00 1.40
123 124 6.415867 CCGCATGCAAGTTCTTCAATATTTAG 59.584 38.462 19.57 0.00 0.00 1.85
124 125 7.188834 CGCATGCAAGTTCTTCAATATTTAGA 58.811 34.615 19.57 0.00 0.00 2.10
125 126 7.375280 CGCATGCAAGTTCTTCAATATTTAGAG 59.625 37.037 19.57 0.00 0.00 2.43
126 127 8.400947 GCATGCAAGTTCTTCAATATTTAGAGA 58.599 33.333 14.21 0.00 0.00 3.10
127 128 9.932699 CATGCAAGTTCTTCAATATTTAGAGAG 57.067 33.333 0.00 0.00 0.00 3.20
128 129 9.678260 ATGCAAGTTCTTCAATATTTAGAGAGT 57.322 29.630 0.00 0.00 0.00 3.24
147 148 7.921787 AGAGAGTATGTGTTAGTACAAGATCG 58.078 38.462 0.00 0.00 35.69 3.69
148 149 6.496571 AGAGTATGTGTTAGTACAAGATCGC 58.503 40.000 0.00 0.00 35.69 4.58
149 150 5.271625 AGTATGTGTTAGTACAAGATCGCG 58.728 41.667 0.00 0.00 35.69 5.87
150 151 2.256174 TGTGTTAGTACAAGATCGCGC 58.744 47.619 0.00 0.00 35.69 6.86
151 152 2.094906 TGTGTTAGTACAAGATCGCGCT 60.095 45.455 5.56 0.00 35.69 5.92
152 153 3.127376 TGTGTTAGTACAAGATCGCGCTA 59.873 43.478 5.56 0.00 35.69 4.26
153 154 4.201980 TGTGTTAGTACAAGATCGCGCTAT 60.202 41.667 5.56 0.00 35.69 2.97
154 155 4.379204 GTGTTAGTACAAGATCGCGCTATC 59.621 45.833 13.69 13.69 35.69 2.08
155 156 4.035909 TGTTAGTACAAGATCGCGCTATCA 59.964 41.667 22.25 0.33 0.00 2.15
156 157 3.710326 AGTACAAGATCGCGCTATCAA 57.290 42.857 22.25 3.86 0.00 2.57
157 158 3.372954 AGTACAAGATCGCGCTATCAAC 58.627 45.455 22.25 14.18 0.00 3.18
158 159 2.586258 ACAAGATCGCGCTATCAACT 57.414 45.000 22.25 5.21 0.00 3.16
159 160 2.893637 ACAAGATCGCGCTATCAACTT 58.106 42.857 22.25 6.85 0.00 2.66
160 161 4.041740 ACAAGATCGCGCTATCAACTTA 57.958 40.909 22.25 0.00 0.00 2.24
161 162 4.621991 ACAAGATCGCGCTATCAACTTAT 58.378 39.130 22.25 0.00 0.00 1.73
162 163 5.050490 ACAAGATCGCGCTATCAACTTATT 58.950 37.500 22.25 5.50 0.00 1.40
163 164 5.523916 ACAAGATCGCGCTATCAACTTATTT 59.476 36.000 22.25 4.83 0.00 1.40
164 165 5.830900 AGATCGCGCTATCAACTTATTTC 57.169 39.130 22.25 0.00 0.00 2.17
165 166 5.289595 AGATCGCGCTATCAACTTATTTCA 58.710 37.500 22.25 0.00 0.00 2.69
166 167 5.928839 AGATCGCGCTATCAACTTATTTCAT 59.071 36.000 22.25 0.00 0.00 2.57
167 168 5.576337 TCGCGCTATCAACTTATTTCATC 57.424 39.130 5.56 0.00 0.00 2.92
168 169 5.289595 TCGCGCTATCAACTTATTTCATCT 58.710 37.500 5.56 0.00 0.00 2.90
169 170 5.753438 TCGCGCTATCAACTTATTTCATCTT 59.247 36.000 5.56 0.00 0.00 2.40
170 171 6.257849 TCGCGCTATCAACTTATTTCATCTTT 59.742 34.615 5.56 0.00 0.00 2.52
171 172 6.571520 CGCGCTATCAACTTATTTCATCTTTC 59.428 38.462 5.56 0.00 0.00 2.62
172 173 7.517417 CGCGCTATCAACTTATTTCATCTTTCT 60.517 37.037 5.56 0.00 0.00 2.52
173 174 7.796197 GCGCTATCAACTTATTTCATCTTTCTC 59.204 37.037 0.00 0.00 0.00 2.87
174 175 8.000991 CGCTATCAACTTATTTCATCTTTCTCG 58.999 37.037 0.00 0.00 0.00 4.04
175 176 9.035607 GCTATCAACTTATTTCATCTTTCTCGA 57.964 33.333 0.00 0.00 0.00 4.04
178 179 9.605275 ATCAACTTATTTCATCTTTCTCGATGA 57.395 29.630 0.00 0.00 45.84 2.92
179 180 9.605275 TCAACTTATTTCATCTTTCTCGATGAT 57.395 29.630 4.53 0.00 46.49 2.45
185 186 8.600449 ATTTCATCTTTCTCGATGATTAGGAC 57.400 34.615 4.53 0.00 46.49 3.85
186 187 6.715347 TCATCTTTCTCGATGATTAGGACA 57.285 37.500 0.00 0.00 43.47 4.02
187 188 7.112452 TCATCTTTCTCGATGATTAGGACAA 57.888 36.000 0.00 0.00 43.47 3.18
188 189 7.555965 TCATCTTTCTCGATGATTAGGACAAA 58.444 34.615 0.00 0.00 43.47 2.83
189 190 8.040727 TCATCTTTCTCGATGATTAGGACAAAA 58.959 33.333 0.00 0.00 43.47 2.44
190 191 8.834465 CATCTTTCTCGATGATTAGGACAAAAT 58.166 33.333 0.00 0.00 42.63 1.82
191 192 8.792830 TCTTTCTCGATGATTAGGACAAAATT 57.207 30.769 0.00 0.00 0.00 1.82
192 193 8.668353 TCTTTCTCGATGATTAGGACAAAATTG 58.332 33.333 0.00 0.00 0.00 2.32
193 194 7.921786 TTCTCGATGATTAGGACAAAATTGT 57.078 32.000 0.00 0.00 45.65 2.71
194 195 9.443323 TTTCTCGATGATTAGGACAAAATTGTA 57.557 29.630 0.00 0.00 42.43 2.41
195 196 9.613428 TTCTCGATGATTAGGACAAAATTGTAT 57.387 29.630 0.00 0.00 42.43 2.29
196 197 9.261180 TCTCGATGATTAGGACAAAATTGTATC 57.739 33.333 0.00 0.00 42.43 2.24
197 198 8.378172 TCGATGATTAGGACAAAATTGTATCC 57.622 34.615 0.00 0.00 42.43 2.59
198 199 7.444183 TCGATGATTAGGACAAAATTGTATCCC 59.556 37.037 0.00 0.00 42.43 3.85
199 200 7.445402 CGATGATTAGGACAAAATTGTATCCCT 59.555 37.037 9.24 9.24 42.43 4.20
200 201 9.136323 GATGATTAGGACAAAATTGTATCCCTT 57.864 33.333 9.48 0.00 42.43 3.95
202 203 9.627123 TGATTAGGACAAAATTGTATCCCTTAG 57.373 33.333 9.48 0.00 42.43 2.18
203 204 8.996651 ATTAGGACAAAATTGTATCCCTTAGG 57.003 34.615 9.48 0.00 42.43 2.69
204 205 6.652205 AGGACAAAATTGTATCCCTTAGGA 57.348 37.500 0.00 0.00 44.15 2.94
205 206 7.039722 AGGACAAAATTGTATCCCTTAGGAA 57.960 36.000 0.00 0.00 43.57 3.36
206 207 6.890268 AGGACAAAATTGTATCCCTTAGGAAC 59.110 38.462 0.00 0.00 43.57 3.62
207 208 6.096423 GGACAAAATTGTATCCCTTAGGAACC 59.904 42.308 0.00 0.00 43.57 3.62
208 209 5.650703 ACAAAATTGTATCCCTTAGGAACCG 59.349 40.000 0.00 0.00 38.89 4.44
209 210 6.748908 ACAAAATTGTATCCCTTAGGAACCGT 60.749 38.462 0.00 0.00 38.89 4.83
210 211 7.529220 ACAAAATTGTATCCCTTAGGAACCGTA 60.529 37.037 0.00 0.00 38.89 4.02
215 216 1.483415 TCCCTTAGGAACCGTACATGC 59.517 52.381 0.00 0.00 40.08 4.06
216 217 1.208535 CCCTTAGGAACCGTACATGCA 59.791 52.381 0.00 0.00 33.47 3.96
217 218 2.277084 CCTTAGGAACCGTACATGCAC 58.723 52.381 0.00 0.00 0.00 4.57
218 219 2.277084 CTTAGGAACCGTACATGCACC 58.723 52.381 0.00 0.00 0.00 5.01
219 220 1.563924 TAGGAACCGTACATGCACCT 58.436 50.000 0.00 0.00 0.00 4.00
220 221 0.690762 AGGAACCGTACATGCACCTT 59.309 50.000 0.00 0.00 0.00 3.50
221 222 1.073284 AGGAACCGTACATGCACCTTT 59.927 47.619 0.00 0.00 0.00 3.11
222 223 1.199097 GGAACCGTACATGCACCTTTG 59.801 52.381 0.00 0.00 0.00 2.77
223 224 1.877443 GAACCGTACATGCACCTTTGT 59.123 47.619 0.00 0.00 0.00 2.83
224 225 1.975660 ACCGTACATGCACCTTTGTT 58.024 45.000 0.00 0.00 0.00 2.83
225 226 2.303175 ACCGTACATGCACCTTTGTTT 58.697 42.857 0.00 0.00 0.00 2.83
226 227 2.034053 ACCGTACATGCACCTTTGTTTG 59.966 45.455 0.00 0.00 0.00 2.93
227 228 2.606795 CCGTACATGCACCTTTGTTTGG 60.607 50.000 0.00 0.00 0.00 3.28
228 229 2.292016 CGTACATGCACCTTTGTTTGGA 59.708 45.455 0.00 0.00 0.00 3.53
229 230 3.057596 CGTACATGCACCTTTGTTTGGAT 60.058 43.478 0.00 0.00 0.00 3.41
230 231 3.389925 ACATGCACCTTTGTTTGGATG 57.610 42.857 0.00 1.99 44.63 3.51
231 232 2.070783 CATGCACCTTTGTTTGGATGC 58.929 47.619 0.00 0.00 35.19 3.91
232 233 0.392336 TGCACCTTTGTTTGGATGCC 59.608 50.000 0.00 0.00 33.70 4.40
233 234 0.667184 GCACCTTTGTTTGGATGCCG 60.667 55.000 0.00 0.00 0.00 5.69
234 235 0.958091 CACCTTTGTTTGGATGCCGA 59.042 50.000 0.00 0.00 0.00 5.54
235 236 1.545582 CACCTTTGTTTGGATGCCGAT 59.454 47.619 0.00 0.00 0.00 4.18
236 237 1.818674 ACCTTTGTTTGGATGCCGATC 59.181 47.619 0.00 0.00 0.00 3.69
237 238 2.094675 CCTTTGTTTGGATGCCGATCT 58.905 47.619 0.00 0.00 0.00 2.75
238 239 3.278574 CCTTTGTTTGGATGCCGATCTA 58.721 45.455 0.00 0.00 0.00 1.98
239 240 3.694072 CCTTTGTTTGGATGCCGATCTAA 59.306 43.478 0.00 0.00 0.00 2.10
240 241 4.339247 CCTTTGTTTGGATGCCGATCTAAT 59.661 41.667 0.00 0.00 29.90 1.73
241 242 5.530915 CCTTTGTTTGGATGCCGATCTAATA 59.469 40.000 0.00 0.00 29.90 0.98
242 243 6.207417 CCTTTGTTTGGATGCCGATCTAATAT 59.793 38.462 0.00 0.00 29.90 1.28
243 244 7.255590 CCTTTGTTTGGATGCCGATCTAATATT 60.256 37.037 0.00 0.00 29.90 1.28
244 245 6.558771 TGTTTGGATGCCGATCTAATATTG 57.441 37.500 0.00 0.00 29.90 1.90
245 246 6.061441 TGTTTGGATGCCGATCTAATATTGT 58.939 36.000 0.00 0.00 29.90 2.71
246 247 6.545666 TGTTTGGATGCCGATCTAATATTGTT 59.454 34.615 0.00 0.00 29.90 2.83
247 248 7.717436 TGTTTGGATGCCGATCTAATATTGTTA 59.283 33.333 0.00 0.00 29.90 2.41
248 249 7.667043 TTGGATGCCGATCTAATATTGTTAC 57.333 36.000 0.00 0.00 0.00 2.50
249 250 6.764379 TGGATGCCGATCTAATATTGTTACA 58.236 36.000 0.00 0.00 0.00 2.41
250 251 7.220740 TGGATGCCGATCTAATATTGTTACAA 58.779 34.615 0.00 0.00 0.00 2.41
251 252 7.882791 TGGATGCCGATCTAATATTGTTACAAT 59.117 33.333 15.22 15.22 0.00 2.71
252 253 9.378551 GGATGCCGATCTAATATTGTTACAATA 57.621 33.333 18.47 18.47 0.00 1.90
254 255 8.234887 TGCCGATCTAATATTGTTACAATACG 57.765 34.615 18.53 15.40 0.00 3.06
255 256 8.083462 TGCCGATCTAATATTGTTACAATACGA 58.917 33.333 18.53 15.03 0.00 3.43
256 257 8.918658 GCCGATCTAATATTGTTACAATACGAA 58.081 33.333 18.53 7.57 0.00 3.85
268 269 7.745015 TGTTACAATACGAAATACTTGAAGGC 58.255 34.615 0.00 0.00 0.00 4.35
269 270 5.813080 ACAATACGAAATACTTGAAGGCC 57.187 39.130 0.00 0.00 0.00 5.19
270 271 5.250200 ACAATACGAAATACTTGAAGGCCA 58.750 37.500 5.01 0.00 0.00 5.36
271 272 5.123344 ACAATACGAAATACTTGAAGGCCAC 59.877 40.000 5.01 0.00 0.00 5.01
272 273 3.134574 ACGAAATACTTGAAGGCCACA 57.865 42.857 5.01 1.11 0.00 4.17
273 274 2.812011 ACGAAATACTTGAAGGCCACAC 59.188 45.455 5.01 0.00 0.00 3.82
274 275 2.159707 CGAAATACTTGAAGGCCACACG 60.160 50.000 5.01 5.15 0.00 4.49
275 276 1.165270 AATACTTGAAGGCCACACGC 58.835 50.000 5.01 0.00 0.00 5.34
276 277 0.036164 ATACTTGAAGGCCACACGCA 59.964 50.000 5.01 0.00 40.31 5.24
277 278 0.179043 TACTTGAAGGCCACACGCAA 60.179 50.000 5.01 0.31 40.31 4.85
278 279 0.823356 ACTTGAAGGCCACACGCAAT 60.823 50.000 5.01 0.00 40.31 3.56
279 280 0.314935 CTTGAAGGCCACACGCAATT 59.685 50.000 5.01 0.00 40.31 2.32
280 281 0.031857 TTGAAGGCCACACGCAATTG 59.968 50.000 5.01 0.00 40.31 2.32
281 282 0.821301 TGAAGGCCACACGCAATTGA 60.821 50.000 10.34 0.00 40.31 2.57
282 283 0.387239 GAAGGCCACACGCAATTGAC 60.387 55.000 10.34 0.00 40.31 3.18
283 284 0.823356 AAGGCCACACGCAATTGACT 60.823 50.000 10.34 0.00 40.31 3.41
284 285 1.210155 GGCCACACGCAATTGACTC 59.790 57.895 10.34 0.00 40.31 3.36
285 286 1.514678 GGCCACACGCAATTGACTCA 61.515 55.000 10.34 0.00 40.31 3.41
286 287 0.385974 GCCACACGCAATTGACTCAC 60.386 55.000 10.34 0.00 37.47 3.51
287 288 0.238289 CCACACGCAATTGACTCACC 59.762 55.000 10.34 0.00 0.00 4.02
288 289 1.229428 CACACGCAATTGACTCACCT 58.771 50.000 10.34 0.00 0.00 4.00
289 290 2.412870 CACACGCAATTGACTCACCTA 58.587 47.619 10.34 0.00 0.00 3.08
290 291 2.157668 CACACGCAATTGACTCACCTAC 59.842 50.000 10.34 0.00 0.00 3.18
291 292 2.224185 ACACGCAATTGACTCACCTACA 60.224 45.455 10.34 0.00 0.00 2.74
292 293 3.002791 CACGCAATTGACTCACCTACAT 58.997 45.455 10.34 0.00 0.00 2.29
293 294 3.436704 CACGCAATTGACTCACCTACATT 59.563 43.478 10.34 0.00 0.00 2.71
294 295 4.072131 ACGCAATTGACTCACCTACATTT 58.928 39.130 10.34 0.00 0.00 2.32
295 296 4.518970 ACGCAATTGACTCACCTACATTTT 59.481 37.500 10.34 0.00 0.00 1.82
296 297 5.703592 ACGCAATTGACTCACCTACATTTTA 59.296 36.000 10.34 0.00 0.00 1.52
297 298 6.374333 ACGCAATTGACTCACCTACATTTTAT 59.626 34.615 10.34 0.00 0.00 1.40
298 299 6.688385 CGCAATTGACTCACCTACATTTTATG 59.312 38.462 10.34 0.00 0.00 1.90
299 300 6.473455 GCAATTGACTCACCTACATTTTATGC 59.527 38.462 10.34 0.00 0.00 3.14
300 301 7.629222 GCAATTGACTCACCTACATTTTATGCT 60.629 37.037 10.34 0.00 0.00 3.79
369 370 4.978083 ATGAACTGAGTGCCATTTGATC 57.022 40.909 0.00 0.00 0.00 2.92
377 378 5.559770 TGAGTGCCATTTGATCAGTAAGAA 58.440 37.500 0.00 0.00 0.00 2.52
415 416 7.694093 AGGGATATGGAAAGGATGAAGTAATC 58.306 38.462 0.00 0.00 0.00 1.75
578 579 4.614967 AGGGGGTACTAACTAACAGCTA 57.385 45.455 0.00 0.00 0.00 3.32
1659 1668 2.526993 CGCGTCGTTCCAACAACCA 61.527 57.895 0.00 0.00 0.00 3.67
1895 1904 0.102300 GTGCACGGAAAACTGCCTTT 59.898 50.000 0.00 0.00 31.97 3.11
1918 1927 2.572104 GTCTCCCAACCTTACTCATGGT 59.428 50.000 0.00 0.00 38.35 3.55
1925 1934 5.321927 CCAACCTTACTCATGGTAACCTTT 58.678 41.667 0.00 0.00 35.69 3.11
1984 1993 1.273896 ACTGGGGCTAGGAAGTAAGCT 60.274 52.381 0.00 0.00 38.80 3.74
2073 2082 5.182487 TGCGTATGAGAACATTGTAATGGT 58.818 37.500 9.22 2.13 39.49 3.55
2111 2120 6.202954 CGAAATAGGATTCGTTTTGGCTAGAT 59.797 38.462 0.00 0.00 45.32 1.98
2113 2122 4.762289 AGGATTCGTTTTGGCTAGATCT 57.238 40.909 0.00 0.00 0.00 2.75
2238 2247 7.405292 AGTGATTGAATTCCTTCTATGGTTCA 58.595 34.615 2.27 0.00 32.29 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.535462 GGAAACTGTGGACGACAATGG 59.465 52.381 0.00 0.00 32.80 3.16
1 2 2.494059 AGGAAACTGTGGACGACAATG 58.506 47.619 0.00 0.00 41.13 2.82
2 3 2.878406 CAAGGAAACTGTGGACGACAAT 59.122 45.455 0.00 0.00 42.68 2.71
3 4 2.285083 CAAGGAAACTGTGGACGACAA 58.715 47.619 0.00 0.00 42.68 3.18
4 5 1.208535 ACAAGGAAACTGTGGACGACA 59.791 47.619 0.00 0.00 42.68 4.35
5 6 1.865340 GACAAGGAAACTGTGGACGAC 59.135 52.381 0.00 0.00 42.68 4.34
6 7 1.537348 CGACAAGGAAACTGTGGACGA 60.537 52.381 0.00 0.00 42.68 4.20
7 8 0.859232 CGACAAGGAAACTGTGGACG 59.141 55.000 0.00 0.00 42.68 4.79
8 9 1.865340 GTCGACAAGGAAACTGTGGAC 59.135 52.381 11.55 2.99 42.68 4.02
9 10 1.537348 CGTCGACAAGGAAACTGTGGA 60.537 52.381 17.16 0.00 42.68 4.02
10 11 0.859232 CGTCGACAAGGAAACTGTGG 59.141 55.000 17.16 0.00 42.68 4.17
11 12 0.232303 GCGTCGACAAGGAAACTGTG 59.768 55.000 17.16 0.00 42.68 3.66
12 13 1.213094 CGCGTCGACAAGGAAACTGT 61.213 55.000 17.16 0.00 42.68 3.55
13 14 0.937699 TCGCGTCGACAAGGAAACTG 60.938 55.000 17.16 0.00 42.68 3.16
14 15 0.249155 TTCGCGTCGACAAGGAAACT 60.249 50.000 17.16 0.00 37.87 2.66
15 16 0.161024 CTTCGCGTCGACAAGGAAAC 59.839 55.000 17.16 0.00 34.89 2.78
16 17 0.942410 CCTTCGCGTCGACAAGGAAA 60.942 55.000 22.52 6.52 36.36 3.13
17 18 1.372499 CCTTCGCGTCGACAAGGAA 60.372 57.895 22.52 16.63 36.36 3.36
18 19 2.257371 CCTTCGCGTCGACAAGGA 59.743 61.111 22.52 10.90 36.36 3.36
19 20 2.809601 CCCTTCGCGTCGACAAGG 60.810 66.667 20.84 20.84 34.89 3.61
20 21 2.809601 CCCCTTCGCGTCGACAAG 60.810 66.667 17.16 11.45 34.89 3.16
40 41 4.238062 TTTGGCTTGGGGGCTGCT 62.238 61.111 0.00 0.00 41.48 4.24
41 42 3.698820 CTTTGGCTTGGGGGCTGC 61.699 66.667 0.00 0.00 41.48 5.25
42 43 2.203684 ACTTTGGCTTGGGGGCTG 60.204 61.111 0.00 0.00 41.48 4.85
43 44 2.118294 GACTTTGGCTTGGGGGCT 59.882 61.111 0.00 0.00 41.48 5.19
44 45 2.118294 AGACTTTGGCTTGGGGGC 59.882 61.111 0.00 0.00 41.27 5.80
45 46 0.610232 CTCAGACTTTGGCTTGGGGG 60.610 60.000 0.00 0.00 0.00 5.40
46 47 0.401738 TCTCAGACTTTGGCTTGGGG 59.598 55.000 0.00 0.00 0.00 4.96
47 48 2.290514 TGATCTCAGACTTTGGCTTGGG 60.291 50.000 0.00 0.00 0.00 4.12
48 49 3.008330 CTGATCTCAGACTTTGGCTTGG 58.992 50.000 0.72 0.00 46.59 3.61
60 61 3.067320 TGCGGTATGAGTTCTGATCTCAG 59.933 47.826 19.74 10.11 43.66 3.35
61 62 3.023832 TGCGGTATGAGTTCTGATCTCA 58.976 45.455 17.97 17.97 44.37 3.27
62 63 3.067461 ACTGCGGTATGAGTTCTGATCTC 59.933 47.826 0.00 8.48 0.00 2.75
63 64 3.027412 ACTGCGGTATGAGTTCTGATCT 58.973 45.455 0.00 0.00 0.00 2.75
64 65 3.444703 ACTGCGGTATGAGTTCTGATC 57.555 47.619 0.00 0.00 0.00 2.92
65 66 3.055819 ACAACTGCGGTATGAGTTCTGAT 60.056 43.478 0.00 0.00 29.73 2.90
66 67 2.299013 ACAACTGCGGTATGAGTTCTGA 59.701 45.455 0.00 0.00 29.73 3.27
67 68 2.413112 CACAACTGCGGTATGAGTTCTG 59.587 50.000 0.00 0.00 29.73 3.02
68 69 2.612972 CCACAACTGCGGTATGAGTTCT 60.613 50.000 10.70 0.00 29.73 3.01
69 70 1.732259 CCACAACTGCGGTATGAGTTC 59.268 52.381 10.70 0.00 29.73 3.01
70 71 1.808411 CCACAACTGCGGTATGAGTT 58.192 50.000 10.70 0.00 32.48 3.01
71 72 0.673644 GCCACAACTGCGGTATGAGT 60.674 55.000 10.70 0.10 0.00 3.41
72 73 0.391661 AGCCACAACTGCGGTATGAG 60.392 55.000 10.70 5.25 0.00 2.90
73 74 0.036164 AAGCCACAACTGCGGTATGA 59.964 50.000 10.70 0.00 0.00 2.15
74 75 0.168788 CAAGCCACAACTGCGGTATG 59.831 55.000 0.00 0.05 0.00 2.39
75 76 0.036164 TCAAGCCACAACTGCGGTAT 59.964 50.000 0.00 0.00 0.00 2.73
76 77 0.179043 TTCAAGCCACAACTGCGGTA 60.179 50.000 0.00 0.00 0.00 4.02
77 78 1.447317 CTTCAAGCCACAACTGCGGT 61.447 55.000 0.00 0.00 0.00 5.68
78 79 1.283793 CTTCAAGCCACAACTGCGG 59.716 57.895 0.00 0.00 0.00 5.69
79 80 1.283793 CCTTCAAGCCACAACTGCG 59.716 57.895 0.00 0.00 0.00 5.18
80 81 1.006922 GCCTTCAAGCCACAACTGC 60.007 57.895 0.00 0.00 0.00 4.40
89 90 3.285523 TTGCATGCGGCCTTCAAGC 62.286 57.895 14.09 13.08 43.89 4.01
90 91 1.153901 CTTGCATGCGGCCTTCAAG 60.154 57.895 14.09 5.24 43.89 3.02
91 92 1.462731 AACTTGCATGCGGCCTTCAA 61.463 50.000 14.09 0.00 43.89 2.69
92 93 1.865788 GAACTTGCATGCGGCCTTCA 61.866 55.000 14.09 0.00 43.89 3.02
93 94 1.153958 GAACTTGCATGCGGCCTTC 60.154 57.895 14.09 7.27 43.89 3.46
94 95 1.181098 AAGAACTTGCATGCGGCCTT 61.181 50.000 14.09 11.78 43.89 4.35
95 96 1.589716 GAAGAACTTGCATGCGGCCT 61.590 55.000 14.09 6.67 43.89 5.19
96 97 1.153958 GAAGAACTTGCATGCGGCC 60.154 57.895 14.09 0.00 43.89 6.13
97 98 0.039256 TTGAAGAACTTGCATGCGGC 60.039 50.000 14.09 0.00 45.13 6.53
98 99 2.642139 ATTGAAGAACTTGCATGCGG 57.358 45.000 14.09 10.98 0.00 5.69
99 100 7.188834 TCTAAATATTGAAGAACTTGCATGCG 58.811 34.615 14.09 1.59 0.00 4.73
100 101 8.400947 TCTCTAAATATTGAAGAACTTGCATGC 58.599 33.333 11.82 11.82 0.00 4.06
101 102 9.932699 CTCTCTAAATATTGAAGAACTTGCATG 57.067 33.333 0.00 0.00 0.00 4.06
102 103 9.678260 ACTCTCTAAATATTGAAGAACTTGCAT 57.322 29.630 0.00 0.00 0.00 3.96
121 122 9.043079 CGATCTTGTACTAACACATACTCTCTA 57.957 37.037 0.00 0.00 34.61 2.43
122 123 7.467539 GCGATCTTGTACTAACACATACTCTCT 60.468 40.741 0.00 0.00 34.61 3.10
123 124 6.633634 GCGATCTTGTACTAACACATACTCTC 59.366 42.308 0.00 0.00 34.61 3.20
124 125 6.496571 GCGATCTTGTACTAACACATACTCT 58.503 40.000 0.00 0.00 34.61 3.24
125 126 5.395778 CGCGATCTTGTACTAACACATACTC 59.604 44.000 0.00 0.00 34.61 2.59
126 127 5.271625 CGCGATCTTGTACTAACACATACT 58.728 41.667 0.00 0.00 34.61 2.12
127 128 4.085721 GCGCGATCTTGTACTAACACATAC 60.086 45.833 12.10 0.00 34.61 2.39
128 129 4.039703 GCGCGATCTTGTACTAACACATA 58.960 43.478 12.10 0.00 34.61 2.29
129 130 2.858344 GCGCGATCTTGTACTAACACAT 59.142 45.455 12.10 0.00 34.61 3.21
130 131 2.094906 AGCGCGATCTTGTACTAACACA 60.095 45.455 12.10 0.00 34.61 3.72
131 132 2.527100 AGCGCGATCTTGTACTAACAC 58.473 47.619 12.10 0.00 34.61 3.32
132 133 2.933495 AGCGCGATCTTGTACTAACA 57.067 45.000 12.10 0.00 0.00 2.41
133 134 4.534168 TGATAGCGCGATCTTGTACTAAC 58.466 43.478 27.21 0.00 0.00 2.34
134 135 4.823790 TGATAGCGCGATCTTGTACTAA 57.176 40.909 27.21 5.55 0.00 2.24
135 136 4.275196 AGTTGATAGCGCGATCTTGTACTA 59.725 41.667 27.21 6.24 0.00 1.82
136 137 3.066900 AGTTGATAGCGCGATCTTGTACT 59.933 43.478 27.21 20.78 0.00 2.73
137 138 3.372954 AGTTGATAGCGCGATCTTGTAC 58.627 45.455 27.21 19.30 0.00 2.90
138 139 3.710326 AGTTGATAGCGCGATCTTGTA 57.290 42.857 27.21 7.97 0.00 2.41
139 140 2.586258 AGTTGATAGCGCGATCTTGT 57.414 45.000 27.21 11.53 0.00 3.16
140 141 5.582439 AATAAGTTGATAGCGCGATCTTG 57.418 39.130 27.21 0.00 0.00 3.02
141 142 5.753438 TGAAATAAGTTGATAGCGCGATCTT 59.247 36.000 27.21 17.36 0.00 2.40
142 143 5.289595 TGAAATAAGTTGATAGCGCGATCT 58.710 37.500 27.21 12.53 0.00 2.75
143 144 5.576337 TGAAATAAGTTGATAGCGCGATC 57.424 39.130 21.90 21.90 0.00 3.69
144 145 5.928839 AGATGAAATAAGTTGATAGCGCGAT 59.071 36.000 12.10 5.99 0.00 4.58
145 146 5.289595 AGATGAAATAAGTTGATAGCGCGA 58.710 37.500 12.10 0.00 0.00 5.87
146 147 5.582439 AGATGAAATAAGTTGATAGCGCG 57.418 39.130 0.00 0.00 0.00 6.86
147 148 7.634522 AGAAAGATGAAATAAGTTGATAGCGC 58.365 34.615 0.00 0.00 0.00 5.92
148 149 8.000991 CGAGAAAGATGAAATAAGTTGATAGCG 58.999 37.037 0.00 0.00 0.00 4.26
149 150 9.035607 TCGAGAAAGATGAAATAAGTTGATAGC 57.964 33.333 0.00 0.00 0.00 2.97
164 165 7.776933 TTTGTCCTAATCATCGAGAAAGATG 57.223 36.000 0.00 0.89 46.90 2.90
165 166 8.970859 ATTTTGTCCTAATCATCGAGAAAGAT 57.029 30.769 0.00 0.00 0.00 2.40
166 167 8.668353 CAATTTTGTCCTAATCATCGAGAAAGA 58.332 33.333 0.00 0.00 0.00 2.52
167 168 8.454106 ACAATTTTGTCCTAATCATCGAGAAAG 58.546 33.333 0.00 0.00 36.50 2.62
168 169 8.335532 ACAATTTTGTCCTAATCATCGAGAAA 57.664 30.769 0.00 0.00 36.50 2.52
169 170 7.921786 ACAATTTTGTCCTAATCATCGAGAA 57.078 32.000 0.00 0.00 36.50 2.87
170 171 9.261180 GATACAATTTTGTCCTAATCATCGAGA 57.739 33.333 0.00 0.00 42.35 4.04
171 172 8.499162 GGATACAATTTTGTCCTAATCATCGAG 58.501 37.037 0.00 0.00 42.35 4.04
172 173 7.444183 GGGATACAATTTTGTCCTAATCATCGA 59.556 37.037 7.25 0.00 42.35 3.59
173 174 7.445402 AGGGATACAATTTTGTCCTAATCATCG 59.555 37.037 7.25 0.00 42.35 3.84
174 175 8.697507 AGGGATACAATTTTGTCCTAATCATC 57.302 34.615 7.25 0.00 42.35 2.92
176 177 9.627123 CTAAGGGATACAATTTTGTCCTAATCA 57.373 33.333 7.25 0.00 42.35 2.57
177 178 9.067986 CCTAAGGGATACAATTTTGTCCTAATC 57.932 37.037 7.25 0.00 37.42 1.75
178 179 8.787818 TCCTAAGGGATACAATTTTGTCCTAAT 58.212 33.333 7.25 0.00 38.43 1.73
179 180 8.165267 TCCTAAGGGATACAATTTTGTCCTAA 57.835 34.615 7.25 0.00 38.43 2.69
180 181 7.758820 TCCTAAGGGATACAATTTTGTCCTA 57.241 36.000 7.25 0.00 38.43 2.94
181 182 6.652205 TCCTAAGGGATACAATTTTGTCCT 57.348 37.500 7.25 0.00 38.43 3.85
182 183 6.096423 GGTTCCTAAGGGATACAATTTTGTCC 59.904 42.308 0.00 0.00 41.87 4.02
183 184 6.183360 CGGTTCCTAAGGGATACAATTTTGTC 60.183 42.308 0.00 0.00 41.87 3.18
184 185 5.650703 CGGTTCCTAAGGGATACAATTTTGT 59.349 40.000 1.08 1.08 41.87 2.83
185 186 5.650703 ACGGTTCCTAAGGGATACAATTTTG 59.349 40.000 0.00 0.00 41.87 2.44
186 187 5.823312 ACGGTTCCTAAGGGATACAATTTT 58.177 37.500 0.00 0.00 41.87 1.82
187 188 5.446260 ACGGTTCCTAAGGGATACAATTT 57.554 39.130 0.00 0.00 41.87 1.82
188 189 5.426185 TGTACGGTTCCTAAGGGATACAATT 59.574 40.000 0.00 0.00 41.87 2.32
189 190 4.964262 TGTACGGTTCCTAAGGGATACAAT 59.036 41.667 0.00 0.00 41.87 2.71
190 191 4.352009 TGTACGGTTCCTAAGGGATACAA 58.648 43.478 0.00 0.00 41.87 2.41
191 192 3.979911 TGTACGGTTCCTAAGGGATACA 58.020 45.455 0.00 0.00 41.87 2.29
192 193 4.798593 GCATGTACGGTTCCTAAGGGATAC 60.799 50.000 0.00 0.00 41.87 2.24
193 194 3.322828 GCATGTACGGTTCCTAAGGGATA 59.677 47.826 0.00 0.00 41.87 2.59
194 195 2.104281 GCATGTACGGTTCCTAAGGGAT 59.896 50.000 0.00 0.00 41.87 3.85
195 196 1.483415 GCATGTACGGTTCCTAAGGGA 59.517 52.381 0.00 0.00 40.36 4.20
196 197 1.208535 TGCATGTACGGTTCCTAAGGG 59.791 52.381 0.00 0.00 0.00 3.95
197 198 2.277084 GTGCATGTACGGTTCCTAAGG 58.723 52.381 0.00 0.00 0.00 2.69
198 199 2.093658 AGGTGCATGTACGGTTCCTAAG 60.094 50.000 7.89 0.00 0.00 2.18
199 200 1.903860 AGGTGCATGTACGGTTCCTAA 59.096 47.619 7.89 0.00 0.00 2.69
200 201 1.563924 AGGTGCATGTACGGTTCCTA 58.436 50.000 7.89 0.00 0.00 2.94
201 202 0.690762 AAGGTGCATGTACGGTTCCT 59.309 50.000 7.89 0.00 0.00 3.36
202 203 1.199097 CAAAGGTGCATGTACGGTTCC 59.801 52.381 7.89 0.00 0.00 3.62
203 204 1.877443 ACAAAGGTGCATGTACGGTTC 59.123 47.619 7.89 0.00 0.00 3.62
204 205 1.975660 ACAAAGGTGCATGTACGGTT 58.024 45.000 7.89 1.32 0.00 4.44
205 206 1.975660 AACAAAGGTGCATGTACGGT 58.024 45.000 7.89 1.11 0.00 4.83
206 207 2.606795 CCAAACAAAGGTGCATGTACGG 60.607 50.000 7.89 0.00 0.00 4.02
207 208 2.292016 TCCAAACAAAGGTGCATGTACG 59.708 45.455 7.89 0.00 0.00 3.67
208 209 4.236935 CATCCAAACAAAGGTGCATGTAC 58.763 43.478 5.22 5.22 0.00 2.90
209 210 3.305950 GCATCCAAACAAAGGTGCATGTA 60.306 43.478 0.00 0.00 35.03 2.29
210 211 2.548493 GCATCCAAACAAAGGTGCATGT 60.548 45.455 0.00 0.00 35.03 3.21
211 212 2.070783 GCATCCAAACAAAGGTGCATG 58.929 47.619 0.00 0.00 35.03 4.06
212 213 1.002315 GGCATCCAAACAAAGGTGCAT 59.998 47.619 0.00 0.00 35.94 3.96
213 214 0.392336 GGCATCCAAACAAAGGTGCA 59.608 50.000 0.00 0.00 35.94 4.57
214 215 0.667184 CGGCATCCAAACAAAGGTGC 60.667 55.000 0.00 0.00 34.54 5.01
215 216 0.958091 TCGGCATCCAAACAAAGGTG 59.042 50.000 0.00 0.00 0.00 4.00
216 217 1.818674 GATCGGCATCCAAACAAAGGT 59.181 47.619 0.00 0.00 0.00 3.50
217 218 2.094675 AGATCGGCATCCAAACAAAGG 58.905 47.619 0.00 0.00 0.00 3.11
218 219 4.963276 TTAGATCGGCATCCAAACAAAG 57.037 40.909 0.00 0.00 0.00 2.77
219 220 7.068103 ACAATATTAGATCGGCATCCAAACAAA 59.932 33.333 0.00 0.00 0.00 2.83
220 221 6.545666 ACAATATTAGATCGGCATCCAAACAA 59.454 34.615 0.00 0.00 0.00 2.83
221 222 6.061441 ACAATATTAGATCGGCATCCAAACA 58.939 36.000 0.00 0.00 0.00 2.83
222 223 6.560253 ACAATATTAGATCGGCATCCAAAC 57.440 37.500 0.00 0.00 0.00 2.93
223 224 7.717436 TGTAACAATATTAGATCGGCATCCAAA 59.283 33.333 0.00 0.00 0.00 3.28
224 225 7.220740 TGTAACAATATTAGATCGGCATCCAA 58.779 34.615 0.00 0.00 0.00 3.53
225 226 6.764379 TGTAACAATATTAGATCGGCATCCA 58.236 36.000 0.00 0.00 0.00 3.41
226 227 7.667043 TTGTAACAATATTAGATCGGCATCC 57.333 36.000 0.00 0.00 0.00 3.51
228 229 8.869897 CGTATTGTAACAATATTAGATCGGCAT 58.130 33.333 0.00 0.00 0.00 4.40
229 230 8.083462 TCGTATTGTAACAATATTAGATCGGCA 58.917 33.333 0.00 0.00 0.00 5.69
230 231 8.456904 TCGTATTGTAACAATATTAGATCGGC 57.543 34.615 0.00 0.00 0.00 5.54
242 243 8.231837 GCCTTCAAGTATTTCGTATTGTAACAA 58.768 33.333 0.00 0.00 0.00 2.83
243 244 7.148373 GGCCTTCAAGTATTTCGTATTGTAACA 60.148 37.037 0.00 0.00 0.00 2.41
244 245 7.148373 TGGCCTTCAAGTATTTCGTATTGTAAC 60.148 37.037 3.32 0.00 0.00 2.50
245 246 6.879993 TGGCCTTCAAGTATTTCGTATTGTAA 59.120 34.615 3.32 0.00 0.00 2.41
246 247 6.314400 GTGGCCTTCAAGTATTTCGTATTGTA 59.686 38.462 3.32 0.00 0.00 2.41
247 248 5.123344 GTGGCCTTCAAGTATTTCGTATTGT 59.877 40.000 3.32 0.00 0.00 2.71
248 249 5.123186 TGTGGCCTTCAAGTATTTCGTATTG 59.877 40.000 3.32 0.00 0.00 1.90
249 250 5.123344 GTGTGGCCTTCAAGTATTTCGTATT 59.877 40.000 3.32 0.00 0.00 1.89
250 251 4.634443 GTGTGGCCTTCAAGTATTTCGTAT 59.366 41.667 3.32 0.00 0.00 3.06
251 252 3.998341 GTGTGGCCTTCAAGTATTTCGTA 59.002 43.478 3.32 0.00 0.00 3.43
252 253 2.812011 GTGTGGCCTTCAAGTATTTCGT 59.188 45.455 3.32 0.00 0.00 3.85
253 254 2.159707 CGTGTGGCCTTCAAGTATTTCG 60.160 50.000 3.32 0.00 0.00 3.46
254 255 2.414161 GCGTGTGGCCTTCAAGTATTTC 60.414 50.000 3.32 0.00 34.80 2.17
255 256 1.539827 GCGTGTGGCCTTCAAGTATTT 59.460 47.619 3.32 0.00 34.80 1.40
256 257 1.165270 GCGTGTGGCCTTCAAGTATT 58.835 50.000 3.32 0.00 34.80 1.89
257 258 0.036164 TGCGTGTGGCCTTCAAGTAT 59.964 50.000 3.32 0.00 42.61 2.12
258 259 0.179043 TTGCGTGTGGCCTTCAAGTA 60.179 50.000 3.32 2.68 42.61 2.24
259 260 0.823356 ATTGCGTGTGGCCTTCAAGT 60.823 50.000 3.32 0.00 42.61 3.16
260 261 0.314935 AATTGCGTGTGGCCTTCAAG 59.685 50.000 3.32 7.18 42.61 3.02
261 262 0.031857 CAATTGCGTGTGGCCTTCAA 59.968 50.000 3.32 1.15 42.61 2.69
262 263 0.821301 TCAATTGCGTGTGGCCTTCA 60.821 50.000 3.32 0.00 42.61 3.02
263 264 0.387239 GTCAATTGCGTGTGGCCTTC 60.387 55.000 3.32 0.00 42.61 3.46
264 265 0.823356 AGTCAATTGCGTGTGGCCTT 60.823 50.000 3.32 0.00 42.61 4.35
265 266 1.228245 AGTCAATTGCGTGTGGCCT 60.228 52.632 3.32 0.00 42.61 5.19
266 267 1.210155 GAGTCAATTGCGTGTGGCC 59.790 57.895 0.00 0.00 42.61 5.36
267 268 0.385974 GTGAGTCAATTGCGTGTGGC 60.386 55.000 0.00 0.00 43.96 5.01
268 269 0.238289 GGTGAGTCAATTGCGTGTGG 59.762 55.000 0.00 0.00 0.00 4.17
269 270 1.229428 AGGTGAGTCAATTGCGTGTG 58.771 50.000 0.00 0.00 0.00 3.82
270 271 2.224185 TGTAGGTGAGTCAATTGCGTGT 60.224 45.455 0.00 0.00 0.00 4.49
271 272 2.412870 TGTAGGTGAGTCAATTGCGTG 58.587 47.619 0.00 0.00 0.00 5.34
272 273 2.831685 TGTAGGTGAGTCAATTGCGT 57.168 45.000 0.00 0.00 0.00 5.24
273 274 4.685169 AAATGTAGGTGAGTCAATTGCG 57.315 40.909 0.00 0.00 0.00 4.85
274 275 6.473455 GCATAAAATGTAGGTGAGTCAATTGC 59.527 38.462 0.00 0.00 0.00 3.56
275 276 7.765307 AGCATAAAATGTAGGTGAGTCAATTG 58.235 34.615 0.00 0.00 0.00 2.32
276 277 7.067494 GGAGCATAAAATGTAGGTGAGTCAATT 59.933 37.037 0.00 0.00 0.00 2.32
277 278 6.543831 GGAGCATAAAATGTAGGTGAGTCAAT 59.456 38.462 0.00 0.00 0.00 2.57
278 279 5.880332 GGAGCATAAAATGTAGGTGAGTCAA 59.120 40.000 0.00 0.00 0.00 3.18
279 280 5.428253 GGAGCATAAAATGTAGGTGAGTCA 58.572 41.667 0.00 0.00 0.00 3.41
280 281 4.816925 GGGAGCATAAAATGTAGGTGAGTC 59.183 45.833 0.00 0.00 0.00 3.36
281 282 4.227300 TGGGAGCATAAAATGTAGGTGAGT 59.773 41.667 0.00 0.00 0.00 3.41
282 283 4.576463 GTGGGAGCATAAAATGTAGGTGAG 59.424 45.833 0.00 0.00 0.00 3.51
283 284 4.523083 GTGGGAGCATAAAATGTAGGTGA 58.477 43.478 0.00 0.00 0.00 4.02
284 285 3.632145 GGTGGGAGCATAAAATGTAGGTG 59.368 47.826 0.00 0.00 0.00 4.00
285 286 3.372675 GGGTGGGAGCATAAAATGTAGGT 60.373 47.826 0.00 0.00 0.00 3.08
286 287 3.117512 AGGGTGGGAGCATAAAATGTAGG 60.118 47.826 0.00 0.00 0.00 3.18
287 288 4.170468 AGGGTGGGAGCATAAAATGTAG 57.830 45.455 0.00 0.00 0.00 2.74
288 289 4.601406 AAGGGTGGGAGCATAAAATGTA 57.399 40.909 0.00 0.00 0.00 2.29
289 290 3.473113 AAGGGTGGGAGCATAAAATGT 57.527 42.857 0.00 0.00 0.00 2.71
290 291 4.026052 AGAAAGGGTGGGAGCATAAAATG 58.974 43.478 0.00 0.00 0.00 2.32
291 292 4.337264 AGAAAGGGTGGGAGCATAAAAT 57.663 40.909 0.00 0.00 0.00 1.82
292 293 3.825908 AGAAAGGGTGGGAGCATAAAA 57.174 42.857 0.00 0.00 0.00 1.52
293 294 3.825908 AAGAAAGGGTGGGAGCATAAA 57.174 42.857 0.00 0.00 0.00 1.40
294 295 3.075283 TCAAAGAAAGGGTGGGAGCATAA 59.925 43.478 0.00 0.00 0.00 1.90
295 296 2.647299 TCAAAGAAAGGGTGGGAGCATA 59.353 45.455 0.00 0.00 0.00 3.14
296 297 1.428912 TCAAAGAAAGGGTGGGAGCAT 59.571 47.619 0.00 0.00 0.00 3.79
297 298 0.850100 TCAAAGAAAGGGTGGGAGCA 59.150 50.000 0.00 0.00 0.00 4.26
298 299 1.613925 GTTCAAAGAAAGGGTGGGAGC 59.386 52.381 0.00 0.00 0.00 4.70
299 300 2.158460 AGGTTCAAAGAAAGGGTGGGAG 60.158 50.000 0.00 0.00 0.00 4.30
300 301 1.856920 AGGTTCAAAGAAAGGGTGGGA 59.143 47.619 0.00 0.00 0.00 4.37
369 370 4.238514 CTCTCCCTTGTTCGTTCTTACTG 58.761 47.826 0.00 0.00 0.00 2.74
377 378 2.544844 TATCCCTCTCCCTTGTTCGT 57.455 50.000 0.00 0.00 0.00 3.85
415 416 6.402222 ACTACTAGCAATGACTTCCTCTTTG 58.598 40.000 0.00 0.00 37.19 2.77
578 579 1.906824 TGCGGTTCGGAGAGGACTT 60.907 57.895 0.00 0.00 38.43 3.01
703 705 3.372206 AGAATCATCTTGAAAACGCTCCG 59.628 43.478 0.00 0.00 29.15 4.63
1659 1668 0.617820 ATACTGAGGTGCTCCCCGTT 60.618 55.000 0.00 0.00 0.00 4.44
1984 1993 2.909965 GCCGCTTTGGGTTGTGGA 60.910 61.111 0.00 0.00 38.63 4.02
2073 2082 3.964688 TCCTATTTCGGCTATGACCTTCA 59.035 43.478 0.00 0.00 0.00 3.02
2111 2120 7.103641 GTCAAATATATAGCGGATTTGGGAGA 58.896 38.462 7.65 0.00 39.79 3.71
2113 2122 6.653320 GTGTCAAATATATAGCGGATTTGGGA 59.347 38.462 7.65 0.00 39.79 4.37
2238 2247 9.095065 GTTATATTCGTACTGGTTTCTCATGTT 57.905 33.333 0.00 0.00 0.00 2.71



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

AutoCloner maintained by Alex Coulton.