Multiple sequence alignment - TraesCS5A01G065400

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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 TraesCS5A01G065400 chr5A 100.000 2366 0 0 1 2366 70677518 70675153 0.000000e+00 4370.0
1 TraesCS5A01G065400 chr5B 93.851 1480 50 14 334 1791 83906561 83905101 0.000000e+00 2191.0
2 TraesCS5A01G065400 chr5B 87.106 349 43 2 1 348 83928596 83928249 6.130000e-106 394.0
3 TraesCS5A01G065400 chr5B 87.106 349 43 2 1 348 83934742 83934395 6.130000e-106 394.0
4 TraesCS5A01G065400 chr5D 96.184 1284 35 6 519 1791 75419789 75418509 0.000000e+00 2087.0
5 TraesCS5A01G065400 chr5D 93.913 575 31 3 1793 2366 449286979 449287550 0.000000e+00 865.0
6 TraesCS5A01G065400 chr5D 93.276 580 33 2 1793 2366 14738152 14737573 0.000000e+00 850.0
7 TraesCS5A01G065400 chr4D 95.122 574 27 1 1793 2366 494043173 494043745 0.000000e+00 904.0
8 TraesCS5A01G065400 chr4D 94.251 574 30 1 1793 2366 8142016 8141446 0.000000e+00 874.0
9 TraesCS5A01G065400 chr1D 94.774 574 29 1 1793 2366 267585 267013 0.000000e+00 893.0
10 TraesCS5A01G065400 chr7A 94.251 574 33 0 1793 2366 736318193 736317620 0.000000e+00 878.0
11 TraesCS5A01G065400 chr4B 93.554 574 35 2 1793 2366 69123902 69124473 0.000000e+00 854.0
12 TraesCS5A01G065400 chr7D 93.391 575 37 1 1793 2366 614243861 614244435 0.000000e+00 850.0
13 TraesCS5A01G065400 chr7D 77.019 161 24 9 179 329 90545203 90545046 1.950000e-11 80.5
14 TraesCS5A01G065400 chr7D 84.058 69 8 3 256 322 392645322 392645389 1.960000e-06 63.9
15 TraesCS5A01G065400 chr3B 93.380 574 38 0 1793 2366 26597170 26596597 0.000000e+00 850.0
16 TraesCS5A01G065400 chr6A 100.000 31 0 0 161 191 585466228 585466198 9.130000e-05 58.4


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 TraesCS5A01G065400 chr5A 70675153 70677518 2365 True 4370 4370 100.000 1 2366 1 chr5A.!!$R1 2365
1 TraesCS5A01G065400 chr5B 83905101 83906561 1460 True 2191 2191 93.851 334 1791 1 chr5B.!!$R1 1457
2 TraesCS5A01G065400 chr5D 75418509 75419789 1280 True 2087 2087 96.184 519 1791 1 chr5D.!!$R2 1272
3 TraesCS5A01G065400 chr5D 449286979 449287550 571 False 865 865 93.913 1793 2366 1 chr5D.!!$F1 573
4 TraesCS5A01G065400 chr5D 14737573 14738152 579 True 850 850 93.276 1793 2366 1 chr5D.!!$R1 573
5 TraesCS5A01G065400 chr4D 494043173 494043745 572 False 904 904 95.122 1793 2366 1 chr4D.!!$F1 573
6 TraesCS5A01G065400 chr4D 8141446 8142016 570 True 874 874 94.251 1793 2366 1 chr4D.!!$R1 573
7 TraesCS5A01G065400 chr1D 267013 267585 572 True 893 893 94.774 1793 2366 1 chr1D.!!$R1 573
8 TraesCS5A01G065400 chr7A 736317620 736318193 573 True 878 878 94.251 1793 2366 1 chr7A.!!$R1 573
9 TraesCS5A01G065400 chr4B 69123902 69124473 571 False 854 854 93.554 1793 2366 1 chr4B.!!$F1 573
10 TraesCS5A01G065400 chr7D 614243861 614244435 574 False 850 850 93.391 1793 2366 1 chr7D.!!$F2 573
11 TraesCS5A01G065400 chr3B 26596597 26597170 573 True 850 850 93.380 1793 2366 1 chr3B.!!$R1 573

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
331 332 0.098728 CCCAATGAACGAACATCGCC 59.901 55.0 0.0 0.0 45.12 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 2276 0.179045 ATCCACAACCATCTAGCCGC 60.179 55.0 0.0 0.0 0.0 6.53 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.270096 GATCCATCGTAAACTTAAACCGAG 57.730 41.667 0.00 0.00 0.00 4.63
24 25 3.928375 TCCATCGTAAACTTAAACCGAGC 59.072 43.478 0.00 0.00 0.00 5.03
25 26 3.241868 CCATCGTAAACTTAAACCGAGCG 60.242 47.826 0.00 0.00 0.00 5.03
26 27 2.327568 TCGTAAACTTAAACCGAGCGG 58.672 47.619 7.48 7.48 42.03 5.52
27 28 2.030363 TCGTAAACTTAAACCGAGCGGA 60.030 45.455 16.83 0.00 38.96 5.54
28 29 2.925563 CGTAAACTTAAACCGAGCGGAT 59.074 45.455 16.83 0.00 38.96 4.18
29 30 3.000376 CGTAAACTTAAACCGAGCGGATC 60.000 47.826 16.83 0.00 38.96 3.36
30 31 3.329929 AAACTTAAACCGAGCGGATCT 57.670 42.857 16.83 1.91 38.96 2.75
31 32 2.580966 ACTTAAACCGAGCGGATCTC 57.419 50.000 16.83 0.00 38.96 2.75
39 40 2.861375 GAGCGGATCTCGAAAGACG 58.139 57.895 7.64 0.00 42.43 4.18
40 41 0.099082 GAGCGGATCTCGAAAGACGT 59.901 55.000 7.64 0.00 42.43 4.34
41 42 0.179161 AGCGGATCTCGAAAGACGTG 60.179 55.000 0.00 0.00 42.43 4.49
42 43 0.456312 GCGGATCTCGAAAGACGTGT 60.456 55.000 0.00 0.00 42.43 4.49
43 44 1.536149 CGGATCTCGAAAGACGTGTC 58.464 55.000 0.00 0.00 42.43 3.67
44 45 1.536149 GGATCTCGAAAGACGTGTCG 58.464 55.000 0.00 0.00 43.13 4.35
45 46 1.536149 GATCTCGAAAGACGTGTCGG 58.464 55.000 11.60 4.75 43.13 4.79
46 47 1.129998 GATCTCGAAAGACGTGTCGGA 59.870 52.381 11.60 8.82 43.13 4.55
47 48 0.516001 TCTCGAAAGACGTGTCGGAG 59.484 55.000 11.60 7.04 43.13 4.63
48 49 0.516001 CTCGAAAGACGTGTCGGAGA 59.484 55.000 11.60 0.00 43.13 3.71
61 62 1.658994 TCGGAGACACAAAACCACAC 58.341 50.000 0.00 0.00 0.00 3.82
62 63 1.066071 TCGGAGACACAAAACCACACA 60.066 47.619 0.00 0.00 0.00 3.72
63 64 1.063469 CGGAGACACAAAACCACACAC 59.937 52.381 0.00 0.00 0.00 3.82
64 65 1.404035 GGAGACACAAAACCACACACC 59.596 52.381 0.00 0.00 0.00 4.16
65 66 1.404035 GAGACACAAAACCACACACCC 59.596 52.381 0.00 0.00 0.00 4.61
66 67 1.005450 AGACACAAAACCACACACCCT 59.995 47.619 0.00 0.00 0.00 4.34
67 68 1.822371 GACACAAAACCACACACCCTT 59.178 47.619 0.00 0.00 0.00 3.95
68 69 1.822371 ACACAAAACCACACACCCTTC 59.178 47.619 0.00 0.00 0.00 3.46
69 70 1.099689 ACAAAACCACACACCCTTCG 58.900 50.000 0.00 0.00 0.00 3.79
70 71 0.248866 CAAAACCACACACCCTTCGC 60.249 55.000 0.00 0.00 0.00 4.70
71 72 1.388837 AAAACCACACACCCTTCGCC 61.389 55.000 0.00 0.00 0.00 5.54
72 73 4.619227 ACCACACACCCTTCGCCG 62.619 66.667 0.00 0.00 0.00 6.46
74 75 4.619227 CACACACCCTTCGCCGGT 62.619 66.667 1.90 0.00 0.00 5.28
79 80 3.000819 ACCCTTCGCCGGTGATGA 61.001 61.111 27.41 10.58 30.39 2.92
80 81 2.202932 CCCTTCGCCGGTGATGAG 60.203 66.667 27.41 18.82 0.00 2.90
81 82 2.892425 CCTTCGCCGGTGATGAGC 60.892 66.667 27.41 0.00 0.00 4.26
82 83 2.125552 CTTCGCCGGTGATGAGCA 60.126 61.111 22.84 5.63 0.00 4.26
83 84 1.522355 CTTCGCCGGTGATGAGCAT 60.522 57.895 22.84 0.00 0.00 3.79
84 85 0.249447 CTTCGCCGGTGATGAGCATA 60.249 55.000 22.84 4.15 0.00 3.14
85 86 0.529773 TTCGCCGGTGATGAGCATAC 60.530 55.000 20.33 0.00 0.00 2.39
86 87 1.956170 CGCCGGTGATGAGCATACC 60.956 63.158 10.20 0.00 0.00 2.73
87 88 1.146041 GCCGGTGATGAGCATACCA 59.854 57.895 1.90 0.00 34.10 3.25
88 89 0.463654 GCCGGTGATGAGCATACCAA 60.464 55.000 1.90 0.00 34.10 3.67
89 90 1.299541 CCGGTGATGAGCATACCAAC 58.700 55.000 0.00 0.00 34.10 3.77
90 91 0.930310 CGGTGATGAGCATACCAACG 59.070 55.000 0.00 0.00 34.10 4.10
91 92 1.299541 GGTGATGAGCATACCAACGG 58.700 55.000 0.00 0.00 34.61 4.44
92 93 1.299541 GTGATGAGCATACCAACGGG 58.700 55.000 0.00 0.00 41.29 5.28
93 94 1.134521 GTGATGAGCATACCAACGGGA 60.135 52.381 0.00 0.00 38.05 5.14
94 95 1.134521 TGATGAGCATACCAACGGGAC 60.135 52.381 0.00 0.00 38.05 4.46
95 96 0.908910 ATGAGCATACCAACGGGACA 59.091 50.000 0.00 0.00 38.05 4.02
96 97 0.249120 TGAGCATACCAACGGGACAG 59.751 55.000 0.00 0.00 38.05 3.51
97 98 0.462047 GAGCATACCAACGGGACAGG 60.462 60.000 0.00 0.00 38.05 4.00
98 99 1.451387 GCATACCAACGGGACAGGG 60.451 63.158 0.00 0.00 38.05 4.45
99 100 1.906105 GCATACCAACGGGACAGGGA 61.906 60.000 0.00 0.00 38.05 4.20
100 101 0.837272 CATACCAACGGGACAGGGAT 59.163 55.000 0.00 0.00 38.05 3.85
101 102 2.043992 CATACCAACGGGACAGGGATA 58.956 52.381 0.00 0.00 38.05 2.59
102 103 1.784358 TACCAACGGGACAGGGATAG 58.216 55.000 0.00 0.00 38.05 2.08
103 104 0.981277 ACCAACGGGACAGGGATAGG 60.981 60.000 0.00 0.00 38.05 2.57
104 105 1.696097 CCAACGGGACAGGGATAGGG 61.696 65.000 0.00 0.00 35.59 3.53
105 106 2.070650 AACGGGACAGGGATAGGGC 61.071 63.158 0.00 0.00 0.00 5.19
106 107 2.445845 CGGGACAGGGATAGGGCA 60.446 66.667 0.00 0.00 0.00 5.36
107 108 2.511452 CGGGACAGGGATAGGGCAG 61.511 68.421 0.00 0.00 0.00 4.85
108 109 2.150051 GGGACAGGGATAGGGCAGG 61.150 68.421 0.00 0.00 0.00 4.85
109 110 2.150051 GGACAGGGATAGGGCAGGG 61.150 68.421 0.00 0.00 0.00 4.45
110 111 1.074471 GACAGGGATAGGGCAGGGA 60.074 63.158 0.00 0.00 0.00 4.20
111 112 0.694444 GACAGGGATAGGGCAGGGAA 60.694 60.000 0.00 0.00 0.00 3.97
112 113 0.695803 ACAGGGATAGGGCAGGGAAG 60.696 60.000 0.00 0.00 0.00 3.46
113 114 0.400525 CAGGGATAGGGCAGGGAAGA 60.401 60.000 0.00 0.00 0.00 2.87
114 115 0.400670 AGGGATAGGGCAGGGAAGAC 60.401 60.000 0.00 0.00 0.00 3.01
115 116 0.694444 GGGATAGGGCAGGGAAGACA 60.694 60.000 0.00 0.00 0.00 3.41
116 117 1.439543 GGATAGGGCAGGGAAGACAT 58.560 55.000 0.00 0.00 0.00 3.06
117 118 2.621070 GGATAGGGCAGGGAAGACATA 58.379 52.381 0.00 0.00 0.00 2.29
118 119 2.303311 GGATAGGGCAGGGAAGACATAC 59.697 54.545 0.00 0.00 0.00 2.39
119 120 2.868964 TAGGGCAGGGAAGACATACT 57.131 50.000 0.00 0.00 0.00 2.12
120 121 1.972588 AGGGCAGGGAAGACATACTT 58.027 50.000 0.00 0.00 42.03 2.24
121 122 2.279173 AGGGCAGGGAAGACATACTTT 58.721 47.619 0.00 0.00 39.13 2.66
122 123 2.239907 AGGGCAGGGAAGACATACTTTC 59.760 50.000 0.00 0.00 39.13 2.62
134 135 9.566432 GGAAGACATACTTTCCAATTGATATCT 57.434 33.333 7.12 0.00 39.13 1.98
177 178 9.489084 TTTTAATACAGTATAATCGCAGATGCT 57.511 29.630 2.95 0.00 45.12 3.79
178 179 8.689251 TTAATACAGTATAATCGCAGATGCTC 57.311 34.615 2.95 0.00 45.12 4.26
179 180 4.590850 ACAGTATAATCGCAGATGCTCA 57.409 40.909 2.95 0.00 45.12 4.26
180 181 4.302455 ACAGTATAATCGCAGATGCTCAC 58.698 43.478 2.95 0.00 45.12 3.51
181 182 4.202151 ACAGTATAATCGCAGATGCTCACA 60.202 41.667 2.95 0.00 45.12 3.58
182 183 4.928020 CAGTATAATCGCAGATGCTCACAT 59.072 41.667 2.95 0.00 45.12 3.21
183 184 6.095377 CAGTATAATCGCAGATGCTCACATA 58.905 40.000 2.95 0.00 45.12 2.29
184 185 6.034363 CAGTATAATCGCAGATGCTCACATAC 59.966 42.308 2.95 5.98 45.12 2.39
185 186 2.896745 ATCGCAGATGCTCACATACA 57.103 45.000 2.95 0.00 45.12 2.29
186 187 1.926561 TCGCAGATGCTCACATACAC 58.073 50.000 2.95 0.00 36.35 2.90
187 188 1.204467 TCGCAGATGCTCACATACACA 59.796 47.619 2.95 0.00 36.35 3.72
188 189 1.325640 CGCAGATGCTCACATACACAC 59.674 52.381 2.95 0.00 36.35 3.82
189 190 2.349590 GCAGATGCTCACATACACACA 58.650 47.619 0.00 0.00 36.35 3.72
190 191 2.094894 GCAGATGCTCACATACACACAC 59.905 50.000 0.00 0.00 36.35 3.82
191 192 2.674852 CAGATGCTCACATACACACACC 59.325 50.000 0.00 0.00 36.35 4.16
192 193 2.568956 AGATGCTCACATACACACACCT 59.431 45.455 0.00 0.00 36.35 4.00
193 194 2.455674 TGCTCACATACACACACCTC 57.544 50.000 0.00 0.00 0.00 3.85
194 195 1.970640 TGCTCACATACACACACCTCT 59.029 47.619 0.00 0.00 0.00 3.69
195 196 3.161866 TGCTCACATACACACACCTCTA 58.838 45.455 0.00 0.00 0.00 2.43
196 197 3.769300 TGCTCACATACACACACCTCTAT 59.231 43.478 0.00 0.00 0.00 1.98
197 198 4.115516 GCTCACATACACACACCTCTATG 58.884 47.826 0.00 0.00 0.00 2.23
198 199 4.142160 GCTCACATACACACACCTCTATGA 60.142 45.833 0.00 0.00 0.00 2.15
199 200 5.624509 GCTCACATACACACACCTCTATGAA 60.625 44.000 0.00 0.00 0.00 2.57
200 201 5.720202 TCACATACACACACCTCTATGAAC 58.280 41.667 0.00 0.00 0.00 3.18
201 202 4.870426 CACATACACACACCTCTATGAACC 59.130 45.833 0.00 0.00 0.00 3.62
202 203 4.081087 ACATACACACACCTCTATGAACCC 60.081 45.833 0.00 0.00 0.00 4.11
203 204 2.334977 ACACACACCTCTATGAACCCA 58.665 47.619 0.00 0.00 0.00 4.51
204 205 2.038557 ACACACACCTCTATGAACCCAC 59.961 50.000 0.00 0.00 0.00 4.61
205 206 2.038426 CACACACCTCTATGAACCCACA 59.962 50.000 0.00 0.00 0.00 4.17
206 207 2.038557 ACACACCTCTATGAACCCACAC 59.961 50.000 0.00 0.00 0.00 3.82
207 208 2.038426 CACACCTCTATGAACCCACACA 59.962 50.000 0.00 0.00 0.00 3.72
208 209 2.912956 ACACCTCTATGAACCCACACAT 59.087 45.455 0.00 0.00 0.00 3.21
209 210 3.273434 CACCTCTATGAACCCACACATG 58.727 50.000 0.00 0.00 0.00 3.21
210 211 2.292267 CCTCTATGAACCCACACATGC 58.708 52.381 0.00 0.00 0.00 4.06
211 212 2.356022 CCTCTATGAACCCACACATGCA 60.356 50.000 0.00 0.00 0.00 3.96
212 213 2.679837 CTCTATGAACCCACACATGCAC 59.320 50.000 0.00 0.00 0.00 4.57
213 214 1.745087 CTATGAACCCACACATGCACC 59.255 52.381 0.00 0.00 0.00 5.01
214 215 0.899717 ATGAACCCACACATGCACCC 60.900 55.000 0.00 0.00 0.00 4.61
215 216 2.203625 AACCCACACATGCACCCC 60.204 61.111 0.00 0.00 0.00 4.95
216 217 2.713531 GAACCCACACATGCACCCCT 62.714 60.000 0.00 0.00 0.00 4.79
217 218 1.431195 AACCCACACATGCACCCCTA 61.431 55.000 0.00 0.00 0.00 3.53
218 219 1.378514 CCCACACATGCACCCCTAC 60.379 63.158 0.00 0.00 0.00 3.18
219 220 1.685224 CCACACATGCACCCCTACT 59.315 57.895 0.00 0.00 0.00 2.57
220 221 0.392998 CCACACATGCACCCCTACTC 60.393 60.000 0.00 0.00 0.00 2.59
221 222 0.392998 CACACATGCACCCCTACTCC 60.393 60.000 0.00 0.00 0.00 3.85
222 223 0.547712 ACACATGCACCCCTACTCCT 60.548 55.000 0.00 0.00 0.00 3.69
223 224 1.273609 ACACATGCACCCCTACTCCTA 60.274 52.381 0.00 0.00 0.00 2.94
224 225 2.050144 CACATGCACCCCTACTCCTAT 58.950 52.381 0.00 0.00 0.00 2.57
225 226 2.050144 ACATGCACCCCTACTCCTATG 58.950 52.381 0.00 0.00 0.00 2.23
226 227 2.329267 CATGCACCCCTACTCCTATGA 58.671 52.381 0.00 0.00 0.00 2.15
227 228 2.088104 TGCACCCCTACTCCTATGAG 57.912 55.000 0.00 0.00 44.62 2.90
228 229 0.682292 GCACCCCTACTCCTATGAGC 59.318 60.000 0.00 0.00 42.74 4.26
229 230 0.962489 CACCCCTACTCCTATGAGCG 59.038 60.000 0.00 0.00 42.74 5.03
230 231 0.828343 ACCCCTACTCCTATGAGCGC 60.828 60.000 0.00 0.00 42.74 5.92
231 232 1.536943 CCCCTACTCCTATGAGCGCC 61.537 65.000 2.29 0.00 42.74 6.53
232 233 1.536943 CCCTACTCCTATGAGCGCCC 61.537 65.000 2.29 0.00 42.74 6.13
233 234 1.536943 CCTACTCCTATGAGCGCCCC 61.537 65.000 2.29 0.00 42.74 5.80
234 235 1.533273 TACTCCTATGAGCGCCCCC 60.533 63.158 2.29 0.00 42.74 5.40
235 236 3.996124 CTCCTATGAGCGCCCCCG 61.996 72.222 2.29 0.00 37.57 5.73
236 237 4.533124 TCCTATGAGCGCCCCCGA 62.533 66.667 2.29 0.00 36.29 5.14
237 238 3.996124 CCTATGAGCGCCCCCGAG 61.996 72.222 2.29 0.00 36.29 4.63
238 239 2.912542 CTATGAGCGCCCCCGAGA 60.913 66.667 2.29 0.00 36.29 4.04
239 240 2.203640 TATGAGCGCCCCCGAGAT 60.204 61.111 2.29 0.00 36.29 2.75
240 241 0.965866 CTATGAGCGCCCCCGAGATA 60.966 60.000 2.29 0.00 36.29 1.98
241 242 1.248785 TATGAGCGCCCCCGAGATAC 61.249 60.000 2.29 0.00 36.29 2.24
242 243 3.992317 GAGCGCCCCCGAGATACC 61.992 72.222 2.29 0.00 36.29 2.73
245 246 3.671411 CGCCCCCGAGATACCGAG 61.671 72.222 0.00 0.00 36.29 4.63
246 247 3.303928 GCCCCCGAGATACCGAGG 61.304 72.222 0.00 0.00 0.00 4.63
247 248 3.303928 CCCCCGAGATACCGAGGC 61.304 72.222 0.00 0.00 0.00 4.70
248 249 2.520982 CCCCGAGATACCGAGGCA 60.521 66.667 0.00 0.00 0.00 4.75
249 250 2.565645 CCCCGAGATACCGAGGCAG 61.566 68.421 0.00 0.00 0.00 4.85
250 251 2.336809 CCGAGATACCGAGGCAGC 59.663 66.667 0.00 0.00 0.00 5.25
251 252 2.490148 CCGAGATACCGAGGCAGCA 61.490 63.158 0.00 0.00 0.00 4.41
252 253 1.662608 CGAGATACCGAGGCAGCAT 59.337 57.895 0.00 0.00 0.00 3.79
253 254 0.881796 CGAGATACCGAGGCAGCATA 59.118 55.000 0.00 0.00 0.00 3.14
254 255 1.269723 CGAGATACCGAGGCAGCATAA 59.730 52.381 0.00 0.00 0.00 1.90
255 256 2.678324 GAGATACCGAGGCAGCATAAC 58.322 52.381 0.00 0.00 0.00 1.89
256 257 2.035961 GAGATACCGAGGCAGCATAACA 59.964 50.000 0.00 0.00 0.00 2.41
257 258 2.634940 AGATACCGAGGCAGCATAACAT 59.365 45.455 0.00 0.00 0.00 2.71
258 259 2.526304 TACCGAGGCAGCATAACATC 57.474 50.000 0.00 0.00 0.00 3.06
259 260 0.833287 ACCGAGGCAGCATAACATCT 59.167 50.000 0.00 0.00 0.00 2.90
260 261 1.210478 ACCGAGGCAGCATAACATCTT 59.790 47.619 0.00 0.00 0.00 2.40
261 262 1.600957 CCGAGGCAGCATAACATCTTG 59.399 52.381 0.00 0.00 0.00 3.02
262 263 2.554142 CGAGGCAGCATAACATCTTGA 58.446 47.619 0.00 0.00 0.00 3.02
263 264 2.543012 CGAGGCAGCATAACATCTTGAG 59.457 50.000 0.00 0.00 0.00 3.02
264 265 3.739209 CGAGGCAGCATAACATCTTGAGA 60.739 47.826 0.00 0.00 0.00 3.27
265 266 4.387598 GAGGCAGCATAACATCTTGAGAT 58.612 43.478 0.00 0.00 34.56 2.75
266 267 4.789807 AGGCAGCATAACATCTTGAGATT 58.210 39.130 0.00 0.00 31.21 2.40
267 268 4.579340 AGGCAGCATAACATCTTGAGATTG 59.421 41.667 0.00 0.00 31.21 2.67
268 269 4.577693 GGCAGCATAACATCTTGAGATTGA 59.422 41.667 0.00 0.00 31.21 2.57
269 270 5.505324 GGCAGCATAACATCTTGAGATTGAC 60.505 44.000 0.00 0.00 31.21 3.18
270 271 5.735324 CAGCATAACATCTTGAGATTGACG 58.265 41.667 0.00 0.00 31.21 4.35
271 272 5.521372 CAGCATAACATCTTGAGATTGACGA 59.479 40.000 0.00 0.00 31.21 4.20
272 273 6.036408 CAGCATAACATCTTGAGATTGACGAA 59.964 38.462 0.00 0.00 31.21 3.85
273 274 6.595326 AGCATAACATCTTGAGATTGACGAAA 59.405 34.615 0.00 0.00 31.21 3.46
274 275 7.281774 AGCATAACATCTTGAGATTGACGAAAT 59.718 33.333 0.00 0.00 31.21 2.17
275 276 7.585573 GCATAACATCTTGAGATTGACGAAATC 59.414 37.037 7.29 7.29 44.44 2.17
276 277 8.606602 CATAACATCTTGAGATTGACGAAATCA 58.393 33.333 14.85 0.00 46.21 2.57
277 278 7.621428 AACATCTTGAGATTGACGAAATCAT 57.379 32.000 14.85 3.97 46.21 2.45
278 279 7.244166 ACATCTTGAGATTGACGAAATCATC 57.756 36.000 14.85 10.71 46.21 2.92
279 280 6.820152 ACATCTTGAGATTGACGAAATCATCA 59.180 34.615 14.85 12.38 46.21 3.07
280 281 6.653273 TCTTGAGATTGACGAAATCATCAC 57.347 37.500 14.85 6.70 46.21 3.06
281 282 6.165577 TCTTGAGATTGACGAAATCATCACA 58.834 36.000 14.85 8.44 46.21 3.58
282 283 6.650390 TCTTGAGATTGACGAAATCATCACAA 59.350 34.615 14.85 13.05 46.21 3.33
283 284 6.413018 TGAGATTGACGAAATCATCACAAG 57.587 37.500 14.85 0.00 46.21 3.16
284 285 5.163824 TGAGATTGACGAAATCATCACAAGC 60.164 40.000 14.85 0.00 46.21 4.01
285 286 3.454042 TTGACGAAATCATCACAAGCG 57.546 42.857 0.00 0.00 37.11 4.68
286 287 1.128507 TGACGAAATCATCACAAGCGC 59.871 47.619 0.00 0.00 29.99 5.92
287 288 0.447801 ACGAAATCATCACAAGCGCC 59.552 50.000 2.29 0.00 0.00 6.53
288 289 0.729116 CGAAATCATCACAAGCGCCT 59.271 50.000 2.29 0.00 0.00 5.52
289 290 1.267732 CGAAATCATCACAAGCGCCTC 60.268 52.381 2.29 0.00 0.00 4.70
290 291 0.729116 AAATCATCACAAGCGCCTCG 59.271 50.000 2.29 0.00 0.00 4.63
305 306 4.221873 TCGCAGTCAACGAGAACG 57.778 55.556 0.00 0.00 45.75 3.95
318 319 3.455619 CGAGAACGTCTTTTCCCAATG 57.544 47.619 0.00 0.00 34.56 2.82
319 320 3.064207 CGAGAACGTCTTTTCCCAATGA 58.936 45.455 0.00 0.00 34.56 2.57
320 321 3.496884 CGAGAACGTCTTTTCCCAATGAA 59.503 43.478 0.00 0.00 34.56 2.57
321 322 4.610680 CGAGAACGTCTTTTCCCAATGAAC 60.611 45.833 0.00 0.00 31.50 3.18
322 323 3.250040 AGAACGTCTTTTCCCAATGAACG 59.750 43.478 0.00 0.00 31.05 3.95
323 324 2.841215 ACGTCTTTTCCCAATGAACGA 58.159 42.857 0.00 0.00 31.05 3.85
324 325 3.207778 ACGTCTTTTCCCAATGAACGAA 58.792 40.909 0.00 0.00 31.05 3.85
325 326 3.002965 ACGTCTTTTCCCAATGAACGAAC 59.997 43.478 0.00 0.00 31.05 3.95
326 327 3.002862 CGTCTTTTCCCAATGAACGAACA 59.997 43.478 0.00 0.00 31.05 3.18
327 328 4.320202 CGTCTTTTCCCAATGAACGAACAT 60.320 41.667 0.00 0.00 31.05 2.71
328 329 5.154222 GTCTTTTCCCAATGAACGAACATC 58.846 41.667 0.00 0.00 31.05 3.06
329 330 3.822594 TTTCCCAATGAACGAACATCG 57.177 42.857 0.00 0.00 46.93 3.84
330 331 1.083489 TCCCAATGAACGAACATCGC 58.917 50.000 0.00 0.00 45.12 4.58
331 332 0.098728 CCCAATGAACGAACATCGCC 59.901 55.000 0.00 0.00 45.12 5.54
332 333 0.247655 CCAATGAACGAACATCGCCG 60.248 55.000 0.00 0.00 45.12 6.46
344 345 3.988379 ACATCGCCGAAAAATGCATAT 57.012 38.095 0.00 0.00 0.00 1.78
367 368 5.074804 TGCTAGTGTCAAGTGTAGGACTTA 58.925 41.667 0.00 0.00 43.52 2.24
388 389 2.765969 CTGGTGGGCTGGTTCCAT 59.234 61.111 0.00 0.00 36.58 3.41
394 395 0.251297 TGGGCTGGTTCCATCACAAG 60.251 55.000 0.00 0.00 0.00 3.16
395 396 0.967380 GGGCTGGTTCCATCACAAGG 60.967 60.000 0.00 0.00 0.00 3.61
402 403 2.584835 TTCCATCACAAGGAACCTGG 57.415 50.000 0.00 0.00 40.11 4.45
462 463 6.030849 TGTCGTTTAATCAATAAAATGCCGG 58.969 36.000 0.00 0.00 35.33 6.13
469 470 6.403866 AATCAATAAAATGCCGGCATTCTA 57.596 33.333 45.33 38.53 44.86 2.10
526 531 7.013942 ACACTAAGGAGAATACATATACGTGCA 59.986 37.037 0.00 0.00 0.00 4.57
572 578 7.538575 ACTAATTAGTCAAAATCACACATGCC 58.461 34.615 12.50 0.00 0.00 4.40
701 707 5.917541 TTAACAACTTGCAGTAGTAGTGC 57.082 39.130 21.00 21.00 44.57 4.40
755 761 1.068753 CAGTGCTAGCGATGAGGGG 59.931 63.158 10.77 0.00 0.00 4.79
945 951 3.586470 ACTAGCTAGCTTCAGCCTCTA 57.414 47.619 24.88 0.00 42.84 2.43
989 999 3.513662 GATCTCGGATCGATCGACTAGA 58.486 50.000 22.06 19.18 34.61 2.43
990 1000 3.596310 TCTCGGATCGATCGACTAGAT 57.404 47.619 22.06 3.42 43.51 1.98
1068 1081 1.585006 CGAGAGCACCAAGTACCGT 59.415 57.895 0.00 0.00 0.00 4.83
1345 1358 2.284625 ACATGCTCAGGGACGGGA 60.285 61.111 0.00 0.00 0.00 5.14
1388 1401 5.710984 ACACTACCGAATTTGAGTACTGAG 58.289 41.667 0.00 0.00 0.00 3.35
1507 1520 2.855963 GTGCTTTGCATGCATGTATGTC 59.144 45.455 26.79 15.72 41.91 3.06
1611 1626 5.159209 CCCTGTATTAATCGTACGTGATCC 58.841 45.833 16.05 0.00 0.00 3.36
1678 1699 5.726308 TGGATTAATCACCTTCTTCTCCTCA 59.274 40.000 17.07 0.00 0.00 3.86
1679 1700 6.388100 TGGATTAATCACCTTCTTCTCCTCAT 59.612 38.462 17.07 0.00 0.00 2.90
1695 1716 1.226262 CATTTAGTCCCCACCCCCG 59.774 63.158 0.00 0.00 0.00 5.73
1778 1803 9.683069 CAAGCCTATATGATTAATGTTTTCCAC 57.317 33.333 0.00 0.00 0.00 4.02
1779 1804 8.409358 AGCCTATATGATTAATGTTTTCCACC 57.591 34.615 0.00 0.00 0.00 4.61
1791 1816 5.736951 TGTTTTCCACCTAATTGATTGGG 57.263 39.130 4.74 4.74 43.32 4.12
1800 1825 1.312884 AATTGATTGGGCCTCCTCCT 58.687 50.000 4.53 0.00 0.00 3.69
1955 1986 1.449601 GCAATCTTCCTCGGCCGAA 60.450 57.895 30.53 14.85 0.00 4.30
2228 2261 0.548926 TGGAGGTGGTGGCCATCTTA 60.549 55.000 18.94 0.00 46.20 2.10
2270 2303 1.398390 GATGGTTGTGGATTCTCGCAC 59.602 52.381 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.276726 GCTCGGTTTAAGTTTACGATGGATC 60.277 44.000 0.00 0.00 32.75 3.36
1 2 4.569564 GCTCGGTTTAAGTTTACGATGGAT 59.430 41.667 0.00 0.00 32.75 3.41
5 6 2.925563 CCGCTCGGTTTAAGTTTACGAT 59.074 45.455 0.00 0.00 32.75 3.73
6 7 2.030363 TCCGCTCGGTTTAAGTTTACGA 60.030 45.455 8.28 0.00 36.47 3.43
7 8 2.327568 TCCGCTCGGTTTAAGTTTACG 58.672 47.619 8.28 0.00 36.47 3.18
8 9 4.179298 AGATCCGCTCGGTTTAAGTTTAC 58.821 43.478 8.28 0.00 36.47 2.01
9 10 4.427312 GAGATCCGCTCGGTTTAAGTTTA 58.573 43.478 8.28 0.00 33.17 2.01
10 11 3.259902 GAGATCCGCTCGGTTTAAGTTT 58.740 45.455 8.28 0.00 33.17 2.66
11 12 2.889852 GAGATCCGCTCGGTTTAAGTT 58.110 47.619 8.28 0.00 33.17 2.66
12 13 2.580966 GAGATCCGCTCGGTTTAAGT 57.419 50.000 8.28 0.00 33.17 2.24
21 22 0.099082 ACGTCTTTCGAGATCCGCTC 59.901 55.000 0.00 0.00 42.86 5.03
22 23 0.179161 CACGTCTTTCGAGATCCGCT 60.179 55.000 0.00 0.00 42.86 5.52
23 24 0.456312 ACACGTCTTTCGAGATCCGC 60.456 55.000 0.00 0.00 42.86 5.54
24 25 1.536149 GACACGTCTTTCGAGATCCG 58.464 55.000 0.00 0.00 42.86 4.18
25 26 1.536149 CGACACGTCTTTCGAGATCC 58.464 55.000 5.05 0.00 42.86 3.36
26 27 1.129998 TCCGACACGTCTTTCGAGATC 59.870 52.381 11.34 0.00 42.86 2.75
27 28 1.130749 CTCCGACACGTCTTTCGAGAT 59.869 52.381 11.34 0.00 42.86 2.75
28 29 0.516001 CTCCGACACGTCTTTCGAGA 59.484 55.000 11.34 6.91 42.86 4.04
29 30 0.516001 TCTCCGACACGTCTTTCGAG 59.484 55.000 11.34 7.65 42.86 4.04
30 31 0.236711 GTCTCCGACACGTCTTTCGA 59.763 55.000 11.34 0.00 43.23 3.71
31 32 0.040692 TGTCTCCGACACGTCTTTCG 60.041 55.000 4.18 4.18 37.67 3.46
32 33 3.859650 TGTCTCCGACACGTCTTTC 57.140 52.632 0.00 0.00 37.67 2.62
40 41 1.066071 TGTGGTTTTGTGTCTCCGACA 60.066 47.619 0.00 0.00 40.50 4.35
41 42 1.329599 GTGTGGTTTTGTGTCTCCGAC 59.670 52.381 0.00 0.00 0.00 4.79
42 43 1.066071 TGTGTGGTTTTGTGTCTCCGA 60.066 47.619 0.00 0.00 0.00 4.55
43 44 1.063469 GTGTGTGGTTTTGTGTCTCCG 59.937 52.381 0.00 0.00 0.00 4.63
44 45 1.404035 GGTGTGTGGTTTTGTGTCTCC 59.596 52.381 0.00 0.00 0.00 3.71
45 46 1.404035 GGGTGTGTGGTTTTGTGTCTC 59.596 52.381 0.00 0.00 0.00 3.36
46 47 1.005450 AGGGTGTGTGGTTTTGTGTCT 59.995 47.619 0.00 0.00 0.00 3.41
47 48 1.470051 AGGGTGTGTGGTTTTGTGTC 58.530 50.000 0.00 0.00 0.00 3.67
48 49 1.822371 GAAGGGTGTGTGGTTTTGTGT 59.178 47.619 0.00 0.00 0.00 3.72
49 50 1.202245 CGAAGGGTGTGTGGTTTTGTG 60.202 52.381 0.00 0.00 0.00 3.33
50 51 1.099689 CGAAGGGTGTGTGGTTTTGT 58.900 50.000 0.00 0.00 0.00 2.83
51 52 0.248866 GCGAAGGGTGTGTGGTTTTG 60.249 55.000 0.00 0.00 0.00 2.44
52 53 1.388837 GGCGAAGGGTGTGTGGTTTT 61.389 55.000 0.00 0.00 0.00 2.43
53 54 1.826487 GGCGAAGGGTGTGTGGTTT 60.826 57.895 0.00 0.00 0.00 3.27
54 55 2.203294 GGCGAAGGGTGTGTGGTT 60.203 61.111 0.00 0.00 0.00 3.67
55 56 4.619227 CGGCGAAGGGTGTGTGGT 62.619 66.667 0.00 0.00 0.00 4.16
57 58 4.619227 ACCGGCGAAGGGTGTGTG 62.619 66.667 9.30 0.00 36.14 3.82
62 63 3.000819 TCATCACCGGCGAAGGGT 61.001 61.111 9.30 0.00 38.65 4.34
63 64 2.202932 CTCATCACCGGCGAAGGG 60.203 66.667 9.30 0.00 35.02 3.95
64 65 2.892425 GCTCATCACCGGCGAAGG 60.892 66.667 9.30 0.00 37.30 3.46
65 66 0.249447 TATGCTCATCACCGGCGAAG 60.249 55.000 9.30 0.00 0.00 3.79
66 67 0.529773 GTATGCTCATCACCGGCGAA 60.530 55.000 9.30 0.00 0.00 4.70
67 68 1.067416 GTATGCTCATCACCGGCGA 59.933 57.895 9.30 0.00 0.00 5.54
68 69 1.956170 GGTATGCTCATCACCGGCG 60.956 63.158 0.00 0.00 0.00 6.46
69 70 0.463654 TTGGTATGCTCATCACCGGC 60.464 55.000 0.00 0.00 34.94 6.13
70 71 1.299541 GTTGGTATGCTCATCACCGG 58.700 55.000 0.00 0.00 34.94 5.28
71 72 0.930310 CGTTGGTATGCTCATCACCG 59.070 55.000 0.00 0.00 34.94 4.94
72 73 1.299541 CCGTTGGTATGCTCATCACC 58.700 55.000 0.00 0.00 0.00 4.02
73 74 1.134521 TCCCGTTGGTATGCTCATCAC 60.135 52.381 0.00 0.00 0.00 3.06
74 75 1.134521 GTCCCGTTGGTATGCTCATCA 60.135 52.381 0.00 0.00 0.00 3.07
75 76 1.134521 TGTCCCGTTGGTATGCTCATC 60.135 52.381 0.00 0.00 0.00 2.92
76 77 0.908910 TGTCCCGTTGGTATGCTCAT 59.091 50.000 0.00 0.00 0.00 2.90
77 78 0.249120 CTGTCCCGTTGGTATGCTCA 59.751 55.000 0.00 0.00 0.00 4.26
78 79 0.462047 CCTGTCCCGTTGGTATGCTC 60.462 60.000 0.00 0.00 0.00 4.26
79 80 1.602237 CCTGTCCCGTTGGTATGCT 59.398 57.895 0.00 0.00 0.00 3.79
80 81 1.451387 CCCTGTCCCGTTGGTATGC 60.451 63.158 0.00 0.00 0.00 3.14
81 82 0.837272 ATCCCTGTCCCGTTGGTATG 59.163 55.000 0.00 0.00 0.00 2.39
82 83 2.326428 CTATCCCTGTCCCGTTGGTAT 58.674 52.381 0.00 0.00 0.00 2.73
83 84 1.690209 CCTATCCCTGTCCCGTTGGTA 60.690 57.143 0.00 0.00 0.00 3.25
84 85 0.981277 CCTATCCCTGTCCCGTTGGT 60.981 60.000 0.00 0.00 0.00 3.67
85 86 1.696097 CCCTATCCCTGTCCCGTTGG 61.696 65.000 0.00 0.00 0.00 3.77
86 87 1.830145 CCCTATCCCTGTCCCGTTG 59.170 63.158 0.00 0.00 0.00 4.10
87 88 2.070650 GCCCTATCCCTGTCCCGTT 61.071 63.158 0.00 0.00 0.00 4.44
88 89 2.446036 GCCCTATCCCTGTCCCGT 60.446 66.667 0.00 0.00 0.00 5.28
89 90 2.445845 TGCCCTATCCCTGTCCCG 60.446 66.667 0.00 0.00 0.00 5.14
90 91 2.150051 CCTGCCCTATCCCTGTCCC 61.150 68.421 0.00 0.00 0.00 4.46
91 92 2.150051 CCCTGCCCTATCCCTGTCC 61.150 68.421 0.00 0.00 0.00 4.02
92 93 0.694444 TTCCCTGCCCTATCCCTGTC 60.694 60.000 0.00 0.00 0.00 3.51
93 94 0.695803 CTTCCCTGCCCTATCCCTGT 60.696 60.000 0.00 0.00 0.00 4.00
94 95 0.400525 TCTTCCCTGCCCTATCCCTG 60.401 60.000 0.00 0.00 0.00 4.45
95 96 0.400670 GTCTTCCCTGCCCTATCCCT 60.401 60.000 0.00 0.00 0.00 4.20
96 97 0.694444 TGTCTTCCCTGCCCTATCCC 60.694 60.000 0.00 0.00 0.00 3.85
97 98 1.439543 ATGTCTTCCCTGCCCTATCC 58.560 55.000 0.00 0.00 0.00 2.59
98 99 3.243724 AGTATGTCTTCCCTGCCCTATC 58.756 50.000 0.00 0.00 0.00 2.08
99 100 3.352611 AGTATGTCTTCCCTGCCCTAT 57.647 47.619 0.00 0.00 0.00 2.57
100 101 2.868964 AGTATGTCTTCCCTGCCCTA 57.131 50.000 0.00 0.00 0.00 3.53
101 102 1.972588 AAGTATGTCTTCCCTGCCCT 58.027 50.000 0.00 0.00 0.00 5.19
102 103 2.644676 GAAAGTATGTCTTCCCTGCCC 58.355 52.381 0.00 0.00 35.02 5.36
103 104 2.026262 TGGAAAGTATGTCTTCCCTGCC 60.026 50.000 0.00 0.00 31.46 4.85
104 105 3.350219 TGGAAAGTATGTCTTCCCTGC 57.650 47.619 0.00 0.00 31.46 4.85
105 106 5.945784 TCAATTGGAAAGTATGTCTTCCCTG 59.054 40.000 5.42 0.00 31.46 4.45
106 107 6.139679 TCAATTGGAAAGTATGTCTTCCCT 57.860 37.500 5.42 0.00 31.46 4.20
107 108 8.697507 ATATCAATTGGAAAGTATGTCTTCCC 57.302 34.615 5.42 0.00 35.02 3.97
108 109 9.566432 AGATATCAATTGGAAAGTATGTCTTCC 57.434 33.333 5.42 0.00 35.02 3.46
169 170 2.094894 GTGTGTGTATGTGAGCATCTGC 59.905 50.000 0.00 0.00 42.49 4.26
170 171 2.674852 GGTGTGTGTATGTGAGCATCTG 59.325 50.000 0.00 0.00 36.58 2.90
171 172 2.568956 AGGTGTGTGTATGTGAGCATCT 59.431 45.455 0.00 0.00 36.58 2.90
172 173 2.932614 GAGGTGTGTGTATGTGAGCATC 59.067 50.000 0.00 0.00 36.58 3.91
173 174 2.568956 AGAGGTGTGTGTATGTGAGCAT 59.431 45.455 0.00 0.00 39.03 3.79
174 175 1.970640 AGAGGTGTGTGTATGTGAGCA 59.029 47.619 0.00 0.00 0.00 4.26
175 176 2.751166 AGAGGTGTGTGTATGTGAGC 57.249 50.000 0.00 0.00 0.00 4.26
176 177 5.582689 TCATAGAGGTGTGTGTATGTGAG 57.417 43.478 0.00 0.00 0.00 3.51
177 178 5.337250 GGTTCATAGAGGTGTGTGTATGTGA 60.337 44.000 0.00 0.00 0.00 3.58
178 179 4.870426 GGTTCATAGAGGTGTGTGTATGTG 59.130 45.833 0.00 0.00 0.00 3.21
179 180 4.081087 GGGTTCATAGAGGTGTGTGTATGT 60.081 45.833 0.00 0.00 0.00 2.29
180 181 4.081142 TGGGTTCATAGAGGTGTGTGTATG 60.081 45.833 0.00 0.00 0.00 2.39
181 182 4.081087 GTGGGTTCATAGAGGTGTGTGTAT 60.081 45.833 0.00 0.00 0.00 2.29
182 183 3.259876 GTGGGTTCATAGAGGTGTGTGTA 59.740 47.826 0.00 0.00 0.00 2.90
183 184 2.038557 GTGGGTTCATAGAGGTGTGTGT 59.961 50.000 0.00 0.00 0.00 3.72
184 185 2.038426 TGTGGGTTCATAGAGGTGTGTG 59.962 50.000 0.00 0.00 0.00 3.82
185 186 2.038557 GTGTGGGTTCATAGAGGTGTGT 59.961 50.000 0.00 0.00 0.00 3.72
186 187 2.038426 TGTGTGGGTTCATAGAGGTGTG 59.962 50.000 0.00 0.00 0.00 3.82
187 188 2.334977 TGTGTGGGTTCATAGAGGTGT 58.665 47.619 0.00 0.00 0.00 4.16
188 189 3.273434 CATGTGTGGGTTCATAGAGGTG 58.727 50.000 0.00 0.00 0.00 4.00
189 190 2.356125 GCATGTGTGGGTTCATAGAGGT 60.356 50.000 0.00 0.00 0.00 3.85
190 191 2.292267 GCATGTGTGGGTTCATAGAGG 58.708 52.381 0.00 0.00 0.00 3.69
191 192 2.679837 GTGCATGTGTGGGTTCATAGAG 59.320 50.000 0.00 0.00 0.00 2.43
192 193 2.617788 GGTGCATGTGTGGGTTCATAGA 60.618 50.000 0.00 0.00 0.00 1.98
193 194 1.745087 GGTGCATGTGTGGGTTCATAG 59.255 52.381 0.00 0.00 0.00 2.23
194 195 1.615651 GGGTGCATGTGTGGGTTCATA 60.616 52.381 0.00 0.00 0.00 2.15
195 196 0.899717 GGGTGCATGTGTGGGTTCAT 60.900 55.000 0.00 0.00 0.00 2.57
196 197 1.530419 GGGTGCATGTGTGGGTTCA 60.530 57.895 0.00 0.00 0.00 3.18
197 198 2.275380 GGGGTGCATGTGTGGGTTC 61.275 63.158 0.00 0.00 0.00 3.62
198 199 1.431195 TAGGGGTGCATGTGTGGGTT 61.431 55.000 0.00 0.00 0.00 4.11
199 200 1.850289 TAGGGGTGCATGTGTGGGT 60.850 57.895 0.00 0.00 0.00 4.51
200 201 1.378514 GTAGGGGTGCATGTGTGGG 60.379 63.158 0.00 0.00 0.00 4.61
201 202 0.392998 GAGTAGGGGTGCATGTGTGG 60.393 60.000 0.00 0.00 0.00 4.17
202 203 0.392998 GGAGTAGGGGTGCATGTGTG 60.393 60.000 0.00 0.00 0.00 3.82
203 204 0.547712 AGGAGTAGGGGTGCATGTGT 60.548 55.000 0.00 0.00 0.00 3.72
204 205 1.496060 TAGGAGTAGGGGTGCATGTG 58.504 55.000 0.00 0.00 0.00 3.21
205 206 2.050144 CATAGGAGTAGGGGTGCATGT 58.950 52.381 0.00 0.00 0.00 3.21
206 207 2.301296 CTCATAGGAGTAGGGGTGCATG 59.699 54.545 0.00 0.00 36.36 4.06
207 208 2.614259 CTCATAGGAGTAGGGGTGCAT 58.386 52.381 0.00 0.00 36.36 3.96
208 209 2.034799 GCTCATAGGAGTAGGGGTGCA 61.035 57.143 6.23 0.00 43.37 4.57
209 210 0.682292 GCTCATAGGAGTAGGGGTGC 59.318 60.000 6.23 0.00 43.37 5.01
210 211 0.962489 CGCTCATAGGAGTAGGGGTG 59.038 60.000 6.23 0.00 43.37 4.61
211 212 0.828343 GCGCTCATAGGAGTAGGGGT 60.828 60.000 6.23 0.00 43.37 4.95
212 213 1.536943 GGCGCTCATAGGAGTAGGGG 61.537 65.000 7.64 0.00 43.37 4.79
213 214 1.536943 GGGCGCTCATAGGAGTAGGG 61.537 65.000 7.64 0.00 43.37 3.53
214 215 1.536943 GGGGCGCTCATAGGAGTAGG 61.537 65.000 10.74 0.00 43.37 3.18
215 216 1.536943 GGGGGCGCTCATAGGAGTAG 61.537 65.000 10.74 2.18 43.37 2.57
216 217 1.533273 GGGGGCGCTCATAGGAGTA 60.533 63.158 10.74 0.00 43.37 2.59
217 218 2.844839 GGGGGCGCTCATAGGAGT 60.845 66.667 10.74 0.00 43.37 3.85
218 219 3.996124 CGGGGGCGCTCATAGGAG 61.996 72.222 10.74 0.00 44.33 3.69
219 220 4.533124 TCGGGGGCGCTCATAGGA 62.533 66.667 10.74 0.00 0.00 2.94
220 221 3.996124 CTCGGGGGCGCTCATAGG 61.996 72.222 10.74 0.00 0.00 2.57
221 222 0.965866 TATCTCGGGGGCGCTCATAG 60.966 60.000 10.74 2.51 0.00 2.23
222 223 1.076014 TATCTCGGGGGCGCTCATA 59.924 57.895 10.74 0.00 0.00 2.15
223 224 2.203640 TATCTCGGGGGCGCTCAT 60.204 61.111 10.74 0.00 0.00 2.90
224 225 3.224324 GTATCTCGGGGGCGCTCA 61.224 66.667 10.74 0.00 0.00 4.26
225 226 3.992317 GGTATCTCGGGGGCGCTC 61.992 72.222 7.64 1.18 0.00 5.03
228 229 3.671411 CTCGGTATCTCGGGGGCG 61.671 72.222 0.00 0.00 0.00 6.13
229 230 3.303928 CCTCGGTATCTCGGGGGC 61.304 72.222 0.00 0.00 46.39 5.80
232 233 3.043419 CTGCCTCGGTATCTCGGG 58.957 66.667 0.00 0.00 0.00 5.14
233 234 1.810606 ATGCTGCCTCGGTATCTCGG 61.811 60.000 0.00 0.00 0.00 4.63
234 235 0.881796 TATGCTGCCTCGGTATCTCG 59.118 55.000 0.00 0.00 0.00 4.04
235 236 2.035961 TGTTATGCTGCCTCGGTATCTC 59.964 50.000 0.00 0.00 0.00 2.75
236 237 2.039418 TGTTATGCTGCCTCGGTATCT 58.961 47.619 0.00 0.00 0.00 1.98
237 238 2.526304 TGTTATGCTGCCTCGGTATC 57.474 50.000 0.00 0.00 0.00 2.24
238 239 2.634940 AGATGTTATGCTGCCTCGGTAT 59.365 45.455 0.00 0.00 0.00 2.73
239 240 2.039418 AGATGTTATGCTGCCTCGGTA 58.961 47.619 0.00 0.00 0.00 4.02
240 241 0.833287 AGATGTTATGCTGCCTCGGT 59.167 50.000 0.00 0.00 0.00 4.69
241 242 1.600957 CAAGATGTTATGCTGCCTCGG 59.399 52.381 0.00 0.00 0.00 4.63
242 243 2.543012 CTCAAGATGTTATGCTGCCTCG 59.457 50.000 0.00 0.00 0.00 4.63
243 244 3.801698 TCTCAAGATGTTATGCTGCCTC 58.198 45.455 0.00 0.00 0.00 4.70
244 245 3.920231 TCTCAAGATGTTATGCTGCCT 57.080 42.857 0.00 0.00 0.00 4.75
245 246 4.577693 TCAATCTCAAGATGTTATGCTGCC 59.422 41.667 0.00 0.00 34.49 4.85
246 247 5.508872 GTCAATCTCAAGATGTTATGCTGC 58.491 41.667 0.00 0.00 34.49 5.25
247 248 5.521372 TCGTCAATCTCAAGATGTTATGCTG 59.479 40.000 0.00 0.00 34.49 4.41
248 249 5.664457 TCGTCAATCTCAAGATGTTATGCT 58.336 37.500 0.00 0.00 34.49 3.79
249 250 5.973651 TCGTCAATCTCAAGATGTTATGC 57.026 39.130 0.00 0.00 34.49 3.14
250 251 8.606602 TGATTTCGTCAATCTCAAGATGTTATG 58.393 33.333 10.22 0.00 41.91 1.90
251 252 8.722480 TGATTTCGTCAATCTCAAGATGTTAT 57.278 30.769 10.22 0.00 41.91 1.89
252 253 8.722480 ATGATTTCGTCAATCTCAAGATGTTA 57.278 30.769 10.22 0.00 41.91 2.41
253 254 7.335171 TGATGATTTCGTCAATCTCAAGATGTT 59.665 33.333 0.00 0.00 41.91 2.71
254 255 6.820152 TGATGATTTCGTCAATCTCAAGATGT 59.180 34.615 0.00 0.00 41.91 3.06
255 256 7.124471 GTGATGATTTCGTCAATCTCAAGATG 58.876 38.462 4.11 0.00 42.83 2.90
256 257 6.820152 TGTGATGATTTCGTCAATCTCAAGAT 59.180 34.615 4.11 0.00 42.83 2.40
257 258 6.165577 TGTGATGATTTCGTCAATCTCAAGA 58.834 36.000 4.11 0.00 42.83 3.02
258 259 6.413018 TGTGATGATTTCGTCAATCTCAAG 57.587 37.500 4.11 0.00 42.83 3.02
259 260 6.621380 GCTTGTGATGATTTCGTCAATCTCAA 60.621 38.462 4.11 4.33 42.83 3.02
260 261 5.163824 GCTTGTGATGATTTCGTCAATCTCA 60.164 40.000 4.11 8.68 42.83 3.27
261 262 5.261661 GCTTGTGATGATTTCGTCAATCTC 58.738 41.667 4.11 6.94 42.83 2.75
262 263 4.201753 CGCTTGTGATGATTTCGTCAATCT 60.202 41.667 4.11 0.00 42.83 2.40
263 264 4.024438 CGCTTGTGATGATTTCGTCAATC 58.976 43.478 4.11 3.88 42.83 2.67
264 265 3.728864 GCGCTTGTGATGATTTCGTCAAT 60.729 43.478 0.00 0.00 42.83 2.57
265 266 2.412716 GCGCTTGTGATGATTTCGTCAA 60.413 45.455 0.00 0.00 42.83 3.18
266 267 1.128507 GCGCTTGTGATGATTTCGTCA 59.871 47.619 0.00 0.00 42.06 4.35
267 268 1.529826 GGCGCTTGTGATGATTTCGTC 60.530 52.381 7.64 0.00 0.00 4.20
268 269 0.447801 GGCGCTTGTGATGATTTCGT 59.552 50.000 7.64 0.00 0.00 3.85
269 270 0.729116 AGGCGCTTGTGATGATTTCG 59.271 50.000 7.64 0.00 0.00 3.46
270 271 1.267732 CGAGGCGCTTGTGATGATTTC 60.268 52.381 7.64 0.00 0.00 2.17
271 272 0.729116 CGAGGCGCTTGTGATGATTT 59.271 50.000 7.64 0.00 0.00 2.17
272 273 2.387309 CGAGGCGCTTGTGATGATT 58.613 52.632 7.64 0.00 0.00 2.57
273 274 4.115279 CGAGGCGCTTGTGATGAT 57.885 55.556 7.64 0.00 0.00 2.45
288 289 4.221873 CGTTCTCGTTGACTGCGA 57.778 55.556 0.00 0.00 36.85 5.10
295 296 8.369869 TTCATTGGGAAAAGACGTTCTCGTTG 62.370 42.308 0.00 0.00 40.64 4.10
296 297 6.428992 TTCATTGGGAAAAGACGTTCTCGTT 61.429 40.000 0.00 0.00 40.64 3.85
297 298 4.980554 TTCATTGGGAAAAGACGTTCTCGT 60.981 41.667 0.00 0.00 42.15 4.18
298 299 3.064207 TCATTGGGAAAAGACGTTCTCG 58.936 45.455 0.00 0.00 43.34 4.04
299 300 4.610680 CGTTCATTGGGAAAAGACGTTCTC 60.611 45.833 0.00 0.00 37.23 2.87
300 301 3.250040 CGTTCATTGGGAAAAGACGTTCT 59.750 43.478 0.00 0.00 37.23 3.01
301 302 3.249080 TCGTTCATTGGGAAAAGACGTTC 59.751 43.478 0.00 0.00 37.23 3.95
302 303 3.207778 TCGTTCATTGGGAAAAGACGTT 58.792 40.909 0.00 0.00 37.23 3.99
303 304 2.841215 TCGTTCATTGGGAAAAGACGT 58.159 42.857 0.00 0.00 37.23 4.34
304 305 3.002862 TGTTCGTTCATTGGGAAAAGACG 59.997 43.478 0.00 0.00 37.23 4.18
305 306 4.561735 TGTTCGTTCATTGGGAAAAGAC 57.438 40.909 0.00 0.00 37.23 3.01
306 307 4.083537 CGATGTTCGTTCATTGGGAAAAGA 60.084 41.667 0.00 0.00 37.23 2.52
307 308 4.158384 CGATGTTCGTTCATTGGGAAAAG 58.842 43.478 0.00 0.00 37.23 2.27
308 309 3.610585 GCGATGTTCGTTCATTGGGAAAA 60.611 43.478 10.18 0.00 42.81 2.29
309 310 2.095466 GCGATGTTCGTTCATTGGGAAA 60.095 45.455 10.18 0.00 42.81 3.13
310 311 1.466950 GCGATGTTCGTTCATTGGGAA 59.533 47.619 10.18 0.00 42.81 3.97
311 312 1.083489 GCGATGTTCGTTCATTGGGA 58.917 50.000 10.18 0.00 42.81 4.37
312 313 0.098728 GGCGATGTTCGTTCATTGGG 59.901 55.000 10.18 1.21 42.81 4.12
313 314 0.247655 CGGCGATGTTCGTTCATTGG 60.248 55.000 0.00 2.95 42.81 3.16
314 315 0.718904 TCGGCGATGTTCGTTCATTG 59.281 50.000 4.99 5.79 42.81 2.82
315 316 1.434555 TTCGGCGATGTTCGTTCATT 58.565 45.000 11.76 0.00 42.81 2.57
316 317 1.434555 TTTCGGCGATGTTCGTTCAT 58.565 45.000 11.76 0.00 42.81 2.57
317 318 1.218763 TTTTCGGCGATGTTCGTTCA 58.781 45.000 11.76 0.00 42.81 3.18
318 319 2.303707 TTTTTCGGCGATGTTCGTTC 57.696 45.000 11.76 0.00 42.81 3.95
319 320 2.580589 CATTTTTCGGCGATGTTCGTT 58.419 42.857 11.76 0.00 42.81 3.85
320 321 1.727857 GCATTTTTCGGCGATGTTCGT 60.728 47.619 11.76 0.00 42.81 3.85
321 322 0.907171 GCATTTTTCGGCGATGTTCG 59.093 50.000 11.76 0.65 43.89 3.95
322 323 1.975837 TGCATTTTTCGGCGATGTTC 58.024 45.000 11.76 0.00 0.00 3.18
323 324 2.652941 ATGCATTTTTCGGCGATGTT 57.347 40.000 11.76 0.00 0.00 2.71
324 325 3.631144 CATATGCATTTTTCGGCGATGT 58.369 40.909 11.76 0.00 0.00 3.06
325 326 2.406024 GCATATGCATTTTTCGGCGATG 59.594 45.455 22.84 7.21 41.59 3.84
326 327 2.294233 AGCATATGCATTTTTCGGCGAT 59.706 40.909 28.62 0.81 45.16 4.58
327 328 1.675483 AGCATATGCATTTTTCGGCGA 59.325 42.857 28.62 4.99 45.16 5.54
328 329 2.124011 AGCATATGCATTTTTCGGCG 57.876 45.000 28.62 0.00 45.16 6.46
329 330 3.976942 CACTAGCATATGCATTTTTCGGC 59.023 43.478 28.62 0.00 45.16 5.54
330 331 5.173774 ACACTAGCATATGCATTTTTCGG 57.826 39.130 28.62 11.90 45.16 4.30
331 332 5.809464 TGACACTAGCATATGCATTTTTCG 58.191 37.500 28.62 12.51 45.16 3.46
332 333 7.219535 CACTTGACACTAGCATATGCATTTTTC 59.780 37.037 28.62 18.19 45.16 2.29
344 345 3.497332 AGTCCTACACTTGACACTAGCA 58.503 45.455 0.00 0.00 33.89 3.49
388 389 0.038166 GATGGCCAGGTTCCTTGTGA 59.962 55.000 13.05 0.00 0.00 3.58
394 395 1.452833 GCTCAGATGGCCAGGTTCC 60.453 63.158 13.05 0.00 0.00 3.62
395 396 0.833287 TAGCTCAGATGGCCAGGTTC 59.167 55.000 13.05 3.69 0.00 3.62
401 402 3.760580 AAGTATGTAGCTCAGATGGCC 57.239 47.619 0.00 0.00 0.00 5.36
402 403 4.954875 AGAAAGTATGTAGCTCAGATGGC 58.045 43.478 0.00 0.00 0.00 4.40
441 442 4.800993 TGCCGGCATTTTATTGATTAAACG 59.199 37.500 29.03 0.00 29.47 3.60
483 488 8.407832 TCCTTAGTGTCGAATGAAATAATCGTA 58.592 33.333 0.00 0.00 37.79 3.43
486 491 8.873215 TCTCCTTAGTGTCGAATGAAATAATC 57.127 34.615 0.00 0.00 0.00 1.75
487 492 9.838339 ATTCTCCTTAGTGTCGAATGAAATAAT 57.162 29.630 0.00 0.00 0.00 1.28
606 612 0.907704 AATGCCCTGTACCTGGACGA 60.908 55.000 0.00 0.00 0.00 4.20
701 707 8.782533 AAAGCTCAACGTTACAATTTAAGAAG 57.217 30.769 0.00 0.00 0.00 2.85
740 746 3.550431 GGCCCCTCATCGCTAGCA 61.550 66.667 16.45 2.17 0.00 3.49
755 761 1.810030 GAGATTGTGGACGACGGGC 60.810 63.158 0.00 0.00 0.00 6.13
786 792 4.620332 GCCCTAATGGATCGATTCTCTCTG 60.620 50.000 6.19 0.00 35.39 3.35
899 905 0.322008 TTGTGTGTGTGCTGTGTGGA 60.322 50.000 0.00 0.00 0.00 4.02
945 951 6.183347 TCGTTCTTAGCTAACCCTAGTAAGT 58.817 40.000 0.86 0.00 0.00 2.24
989 999 3.136626 GCCACCCTCCATTACTTAGTGAT 59.863 47.826 0.00 0.00 0.00 3.06
990 1000 2.504175 GCCACCCTCCATTACTTAGTGA 59.496 50.000 0.00 0.00 0.00 3.41
991 1001 2.741878 CGCCACCCTCCATTACTTAGTG 60.742 54.545 0.00 0.00 0.00 2.74
994 1007 0.834612 CCGCCACCCTCCATTACTTA 59.165 55.000 0.00 0.00 0.00 2.24
1017 1030 2.593978 CCAGCCTGATCACCCCAG 59.406 66.667 0.00 0.00 0.00 4.45
1032 1045 3.089874 CCTCCGCCATCCTTCCCA 61.090 66.667 0.00 0.00 0.00 4.37
1345 1358 6.790319 AGTGTTAATTATTCCTTCCACCACT 58.210 36.000 0.00 0.00 0.00 4.00
1507 1520 8.408601 CCTAAGAATACTGGAAATCCAACATTG 58.591 37.037 3.35 0.00 46.97 2.82
1633 1654 5.184864 TCCAACAAGCAACCCAATTACATAG 59.815 40.000 0.00 0.00 0.00 2.23
1634 1655 5.080337 TCCAACAAGCAACCCAATTACATA 58.920 37.500 0.00 0.00 0.00 2.29
1635 1656 3.900601 TCCAACAAGCAACCCAATTACAT 59.099 39.130 0.00 0.00 0.00 2.29
1678 1699 0.550638 TTCGGGGGTGGGGACTAAAT 60.551 55.000 0.00 0.00 0.00 1.40
1679 1700 0.550638 ATTCGGGGGTGGGGACTAAA 60.551 55.000 0.00 0.00 0.00 1.85
1727 1748 6.073873 GCAATTCAGATCCTCTACAGATTTCG 60.074 42.308 0.00 0.00 0.00 3.46
1778 1803 2.489802 GGAGGAGGCCCAATCAATTAGG 60.490 54.545 0.00 0.00 33.88 2.69
1779 1804 2.444766 AGGAGGAGGCCCAATCAATTAG 59.555 50.000 0.00 0.00 33.88 1.73
1933 1964 2.125147 CCGAGGAAGATTGCCGCA 60.125 61.111 0.00 0.00 0.00 5.69
1955 1986 2.502492 CGCCACCCAGATCCGATCT 61.502 63.158 4.96 4.96 41.15 2.75
2047 2078 1.799181 CGCCGACGTGATCTCTTCATT 60.799 52.381 0.00 0.00 36.54 2.57
2101 2132 1.141881 CTCGAGGAACCACCATCCG 59.858 63.158 3.91 0.00 42.03 4.18
2130 2161 1.425428 CGCGCCAGAACAAAGGATC 59.575 57.895 0.00 0.00 0.00 3.36
2243 2276 0.179045 ATCCACAACCATCTAGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
2270 2303 3.528370 CTCTACGCCGGGACTGGG 61.528 72.222 2.18 0.00 0.00 4.45
2310 2343 1.135527 CCCGAGTCATAGCACGGTTTA 59.864 52.381 0.00 0.00 43.22 2.01


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

AutoCloner maintained by Alex Coulton.