Multiple sequence alignment - TraesCS1A01G157900

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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 TraesCS1A01G157900 chr1A 100.000 2546 0 0 1 2546 280605144 280602599 0.000000e+00 4702.0
1 TraesCS1A01G157900 chr1A 80.460 87 13 4 1454 1538 529126375 529126291 2.110000e-06 63.9
2 TraesCS1A01G157900 chr1B 91.298 1919 68 31 529 2428 312250181 312248343 0.000000e+00 2527.0
3 TraesCS1A01G157900 chr1B 86.777 242 31 1 1 241 605572070 605571829 4.180000e-68 268.0
4 TraesCS1A01G157900 chr1B 92.486 173 13 0 360 532 312250512 312250340 5.440000e-62 248.0
5 TraesCS1A01G157900 chr1B 95.238 105 5 0 2426 2530 312248149 312248045 1.570000e-37 167.0
6 TraesCS1A01G157900 chr1B 80.460 87 13 4 1454 1538 582021902 582021818 2.110000e-06 63.9
7 TraesCS1A01G157900 chr1D 92.947 1588 52 27 684 2253 218410692 218409147 0.000000e+00 2257.0
8 TraesCS1A01G157900 chr1D 92.881 295 11 2 410 695 218412869 218412576 1.090000e-113 420.0
9 TraesCS1A01G157900 chr1D 92.958 284 15 3 2248 2530 218408825 218408546 2.360000e-110 409.0
10 TraesCS1A01G157900 chr1D 84.375 64 8 2 1454 1516 430861108 430861046 7.610000e-06 62.1
11 TraesCS1A01G157900 chr3B 86.242 298 34 2 1 291 693570982 693571279 1.470000e-82 316.0
12 TraesCS1A01G157900 chr3B 85.855 304 28 4 1 291 228713253 228712952 2.460000e-80 309.0
13 TraesCS1A01G157900 chr5B 87.603 242 29 1 1 241 112572536 112572777 1.930000e-71 279.0
14 TraesCS1A01G157900 chr5B 85.294 204 22 5 1009 1212 60910160 60910355 1.190000e-48 204.0
15 TraesCS1A01G157900 chr5B 83.158 95 14 2 1453 1546 230782024 230781931 4.510000e-13 86.1
16 TraesCS1A01G157900 chr3A 85.145 276 29 3 28 291 556371792 556371517 3.230000e-69 272.0
17 TraesCS1A01G157900 chr3A 86.531 245 29 4 1003 1247 378305215 378305455 1.500000e-67 267.0
18 TraesCS1A01G157900 chr3D 83.142 261 28 12 1002 1247 288295770 288296029 9.170000e-55 224.0
19 TraesCS1A01G157900 chr3D 87.113 194 13 9 1004 1195 329686510 329686327 2.570000e-50 209.0
20 TraesCS1A01G157900 chr2A 79.630 324 53 11 1 318 379149765 379150081 1.190000e-53 220.0
21 TraesCS1A01G157900 chr5D 82.105 95 15 2 1453 1546 215256151 215256058 2.100000e-11 80.5
22 TraesCS1A01G157900 chr5D 95.833 48 2 0 1059 1106 564235257 564235210 7.550000e-11 78.7
23 TraesCS1A01G157900 chr5A 81.053 95 16 2 1453 1546 283111203 283111110 9.770000e-10 75.0
24 TraesCS1A01G157900 chr4B 97.500 40 1 0 1067 1106 140587431 140587470 4.550000e-08 69.4


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 TraesCS1A01G157900 chr1A 280602599 280605144 2545 True 4702.000000 4702 100.000000 1 2546 1 chr1A.!!$R1 2545
1 TraesCS1A01G157900 chr1B 312248045 312250512 2467 True 980.666667 2527 93.007333 360 2530 3 chr1B.!!$R3 2170
2 TraesCS1A01G157900 chr1D 218408546 218412869 4323 True 1028.666667 2257 92.928667 410 2530 3 chr1D.!!$R2 2120

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
226 227 0.10212 GTGGATCTGTCGGCTCTCAG 59.898 60.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 3792 0.744874 GTAGTACATCGAGCCAGCCA 59.255 55.0 0.0 0.0 0.0 4.75 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
20 21 4.452733 CGCCCTCCACTCCCGTTC 62.453 72.222 0.00 0.00 0.00 3.95
21 22 4.452733 GCCCTCCACTCCCGTTCG 62.453 72.222 0.00 0.00 0.00 3.95
22 23 2.995574 CCCTCCACTCCCGTTCGT 60.996 66.667 0.00 0.00 0.00 3.85
23 24 1.679977 CCCTCCACTCCCGTTCGTA 60.680 63.158 0.00 0.00 0.00 3.43
24 25 1.664321 CCCTCCACTCCCGTTCGTAG 61.664 65.000 0.00 0.00 0.00 3.51
25 26 0.679002 CCTCCACTCCCGTTCGTAGA 60.679 60.000 0.00 0.00 0.00 2.59
26 27 0.733729 CTCCACTCCCGTTCGTAGAG 59.266 60.000 7.58 7.58 38.43 2.43
27 28 0.679002 TCCACTCCCGTTCGTAGAGG 60.679 60.000 11.90 7.70 38.43 3.69
28 29 0.679002 CCACTCCCGTTCGTAGAGGA 60.679 60.000 11.90 2.43 38.43 3.71
33 34 3.123157 TCCCGTTCGTAGAGGAGATAG 57.877 52.381 0.00 0.00 38.43 2.08
34 35 2.152830 CCCGTTCGTAGAGGAGATAGG 58.847 57.143 0.00 0.00 38.43 2.57
35 36 2.224475 CCCGTTCGTAGAGGAGATAGGA 60.224 54.545 0.00 0.00 38.43 2.94
36 37 3.068560 CCGTTCGTAGAGGAGATAGGAG 58.931 54.545 0.00 0.00 38.43 3.69
37 38 3.068560 CGTTCGTAGAGGAGATAGGAGG 58.931 54.545 0.00 0.00 38.43 4.30
38 39 3.414269 GTTCGTAGAGGAGATAGGAGGG 58.586 54.545 0.00 0.00 38.43 4.30
39 40 1.351683 TCGTAGAGGAGATAGGAGGGC 59.648 57.143 0.00 0.00 0.00 5.19
40 41 1.074084 CGTAGAGGAGATAGGAGGGCA 59.926 57.143 0.00 0.00 0.00 5.36
41 42 2.521126 GTAGAGGAGATAGGAGGGCAC 58.479 57.143 0.00 0.00 0.00 5.01
42 43 0.178975 AGAGGAGATAGGAGGGCACG 60.179 60.000 0.00 0.00 0.00 5.34
43 44 0.468400 GAGGAGATAGGAGGGCACGT 60.468 60.000 0.00 0.00 0.00 4.49
44 45 0.468400 AGGAGATAGGAGGGCACGTC 60.468 60.000 0.00 0.00 43.26 4.34
45 46 1.655329 GAGATAGGAGGGCACGTCG 59.345 63.158 0.00 0.00 45.18 5.12
46 47 1.076923 AGATAGGAGGGCACGTCGT 60.077 57.895 0.00 0.00 45.18 4.34
47 48 1.102222 AGATAGGAGGGCACGTCGTC 61.102 60.000 0.00 0.00 45.18 4.20
48 49 2.389866 GATAGGAGGGCACGTCGTCG 62.390 65.000 0.00 0.00 45.18 5.12
65 66 4.451150 GTGGATCCGCGTGGCTCA 62.451 66.667 19.66 10.35 31.76 4.26
66 67 4.451150 TGGATCCGCGTGGCTCAC 62.451 66.667 19.66 10.09 31.76 3.51
67 68 4.148825 GGATCCGCGTGGCTCACT 62.149 66.667 19.66 0.00 31.76 3.41
68 69 2.583593 GATCCGCGTGGCTCACTC 60.584 66.667 13.80 0.48 30.49 3.51
69 70 4.148825 ATCCGCGTGGCTCACTCC 62.149 66.667 11.05 0.00 34.14 3.85
74 75 3.680786 CGTGGCTCACTCCGTCCA 61.681 66.667 4.21 0.00 31.34 4.02
75 76 2.048127 GTGGCTCACTCCGTCCAC 60.048 66.667 0.00 0.00 41.66 4.02
76 77 3.311110 TGGCTCACTCCGTCCACC 61.311 66.667 0.00 0.00 0.00 4.61
77 78 2.997897 GGCTCACTCCGTCCACCT 60.998 66.667 0.00 0.00 0.00 4.00
78 79 2.574399 GCTCACTCCGTCCACCTC 59.426 66.667 0.00 0.00 0.00 3.85
79 80 3.007973 GCTCACTCCGTCCACCTCC 62.008 68.421 0.00 0.00 0.00 4.30
80 81 2.675423 TCACTCCGTCCACCTCCG 60.675 66.667 0.00 0.00 0.00 4.63
81 82 4.436998 CACTCCGTCCACCTCCGC 62.437 72.222 0.00 0.00 0.00 5.54
82 83 4.988716 ACTCCGTCCACCTCCGCA 62.989 66.667 0.00 0.00 0.00 5.69
83 84 3.461773 CTCCGTCCACCTCCGCAT 61.462 66.667 0.00 0.00 0.00 4.73
84 85 3.432051 CTCCGTCCACCTCCGCATC 62.432 68.421 0.00 0.00 0.00 3.91
85 86 4.530857 CCGTCCACCTCCGCATCC 62.531 72.222 0.00 0.00 0.00 3.51
86 87 3.461773 CGTCCACCTCCGCATCCT 61.462 66.667 0.00 0.00 0.00 3.24
87 88 2.501610 GTCCACCTCCGCATCCTC 59.498 66.667 0.00 0.00 0.00 3.71
88 89 3.147595 TCCACCTCCGCATCCTCG 61.148 66.667 0.00 0.00 0.00 4.63
89 90 3.461773 CCACCTCCGCATCCTCGT 61.462 66.667 0.00 0.00 0.00 4.18
90 91 2.105128 CACCTCCGCATCCTCGTC 59.895 66.667 0.00 0.00 0.00 4.20
91 92 3.518998 ACCTCCGCATCCTCGTCG 61.519 66.667 0.00 0.00 0.00 5.12
92 93 4.933064 CCTCCGCATCCTCGTCGC 62.933 72.222 0.00 0.00 0.00 5.19
93 94 4.933064 CTCCGCATCCTCGTCGCC 62.933 72.222 0.00 0.00 0.00 5.54
132 133 4.971125 GACCCTATCGGCCGCAGC 62.971 72.222 23.51 3.67 38.76 5.25
134 135 4.320456 CCCTATCGGCCGCAGCAT 62.320 66.667 23.51 11.73 42.56 3.79
135 136 2.740055 CCTATCGGCCGCAGCATC 60.740 66.667 23.51 0.00 42.56 3.91
136 137 2.341543 CTATCGGCCGCAGCATCT 59.658 61.111 23.51 0.83 42.56 2.90
137 138 1.735920 CTATCGGCCGCAGCATCTC 60.736 63.158 23.51 0.00 42.56 2.75
138 139 3.226429 TATCGGCCGCAGCATCTCC 62.226 63.158 23.51 0.00 42.56 3.71
143 144 4.161295 CCGCAGCATCTCCGGGAA 62.161 66.667 0.00 0.00 38.42 3.97
144 145 2.587194 CGCAGCATCTCCGGGAAG 60.587 66.667 0.00 0.00 0.00 3.46
145 146 2.203126 GCAGCATCTCCGGGAAGG 60.203 66.667 0.00 0.00 42.97 3.46
146 147 2.203126 CAGCATCTCCGGGAAGGC 60.203 66.667 0.00 3.17 40.77 4.35
147 148 3.483869 AGCATCTCCGGGAAGGCC 61.484 66.667 0.00 0.00 40.77 5.19
156 157 3.324108 GGGAAGGCCCGGTACACA 61.324 66.667 0.00 0.00 46.48 3.72
157 158 2.751688 GGAAGGCCCGGTACACAA 59.248 61.111 0.00 0.00 0.00 3.33
158 159 1.073548 GGAAGGCCCGGTACACAAA 59.926 57.895 0.00 0.00 0.00 2.83
159 160 0.958876 GGAAGGCCCGGTACACAAAG 60.959 60.000 0.00 0.00 0.00 2.77
160 161 0.958876 GAAGGCCCGGTACACAAAGG 60.959 60.000 0.00 0.00 0.00 3.11
161 162 2.360726 GGCCCGGTACACAAAGGG 60.361 66.667 0.00 0.23 46.44 3.95
162 163 2.360726 GCCCGGTACACAAAGGGG 60.361 66.667 0.00 0.00 43.95 4.79
163 164 2.353573 CCCGGTACACAAAGGGGG 59.646 66.667 0.00 0.00 40.18 5.40
164 165 2.225596 CCCGGTACACAAAGGGGGA 61.226 63.158 0.00 0.00 40.18 4.81
165 166 1.298667 CCGGTACACAAAGGGGGAG 59.701 63.158 0.00 0.00 0.00 4.30
166 167 1.298667 CGGTACACAAAGGGGGAGG 59.701 63.158 0.00 0.00 0.00 4.30
167 168 1.001269 GGTACACAAAGGGGGAGGC 60.001 63.158 0.00 0.00 0.00 4.70
168 169 1.765074 GTACACAAAGGGGGAGGCA 59.235 57.895 0.00 0.00 0.00 4.75
169 170 0.331616 GTACACAAAGGGGGAGGCAT 59.668 55.000 0.00 0.00 0.00 4.40
170 171 0.331278 TACACAAAGGGGGAGGCATG 59.669 55.000 0.00 0.00 0.00 4.06
171 172 1.077265 CACAAAGGGGGAGGCATGT 59.923 57.895 0.00 0.00 0.00 3.21
172 173 0.331278 CACAAAGGGGGAGGCATGTA 59.669 55.000 0.00 0.00 0.00 2.29
173 174 1.063717 CACAAAGGGGGAGGCATGTAT 60.064 52.381 0.00 0.00 0.00 2.29
174 175 1.063717 ACAAAGGGGGAGGCATGTATG 60.064 52.381 0.00 0.00 0.00 2.39
175 176 0.557729 AAAGGGGGAGGCATGTATGG 59.442 55.000 0.00 0.00 0.00 2.74
176 177 1.363530 AAGGGGGAGGCATGTATGGG 61.364 60.000 0.00 0.00 0.00 4.00
177 178 1.774217 GGGGGAGGCATGTATGGGA 60.774 63.158 0.00 0.00 0.00 4.37
178 179 1.142688 GGGGGAGGCATGTATGGGAT 61.143 60.000 0.00 0.00 0.00 3.85
179 180 0.779997 GGGGAGGCATGTATGGGATT 59.220 55.000 0.00 0.00 0.00 3.01
180 181 1.548582 GGGGAGGCATGTATGGGATTG 60.549 57.143 0.00 0.00 0.00 2.67
181 182 1.145738 GGGAGGCATGTATGGGATTGT 59.854 52.381 0.00 0.00 0.00 2.71
182 183 2.508526 GGAGGCATGTATGGGATTGTC 58.491 52.381 0.00 0.00 0.00 3.18
183 184 2.146342 GAGGCATGTATGGGATTGTCG 58.854 52.381 0.00 0.00 0.00 4.35
184 185 1.768275 AGGCATGTATGGGATTGTCGA 59.232 47.619 0.00 0.00 0.00 4.20
185 186 2.146342 GGCATGTATGGGATTGTCGAG 58.854 52.381 0.00 0.00 0.00 4.04
186 187 1.532868 GCATGTATGGGATTGTCGAGC 59.467 52.381 0.00 0.00 0.00 5.03
187 188 2.146342 CATGTATGGGATTGTCGAGCC 58.854 52.381 0.00 0.00 0.00 4.70
191 192 4.547367 GGGATTGTCGAGCCCGGG 62.547 72.222 19.09 19.09 45.75 5.73
210 211 4.767255 GAGGTGGCGAGCAGGTGG 62.767 72.222 0.00 0.00 0.00 4.61
212 213 4.101448 GGTGGCGAGCAGGTGGAT 62.101 66.667 0.00 0.00 0.00 3.41
213 214 2.512515 GTGGCGAGCAGGTGGATC 60.513 66.667 0.00 0.00 0.00 3.36
214 215 2.685017 TGGCGAGCAGGTGGATCT 60.685 61.111 0.00 0.00 0.00 2.75
215 216 2.202987 GGCGAGCAGGTGGATCTG 60.203 66.667 0.00 0.00 37.79 2.90
216 217 2.581354 GCGAGCAGGTGGATCTGT 59.419 61.111 0.00 0.00 37.12 3.41
217 218 1.520342 GCGAGCAGGTGGATCTGTC 60.520 63.158 0.00 0.00 37.12 3.51
218 219 1.226802 CGAGCAGGTGGATCTGTCG 60.227 63.158 0.00 0.00 37.12 4.35
219 220 1.142748 GAGCAGGTGGATCTGTCGG 59.857 63.158 0.00 0.00 37.12 4.79
220 221 2.512515 GCAGGTGGATCTGTCGGC 60.513 66.667 0.00 0.00 37.12 5.54
221 222 3.023949 GCAGGTGGATCTGTCGGCT 62.024 63.158 0.00 0.00 37.12 5.52
222 223 1.142748 CAGGTGGATCTGTCGGCTC 59.857 63.158 0.00 0.00 0.00 4.70
223 224 1.000993 AGGTGGATCTGTCGGCTCT 59.999 57.895 0.00 0.00 0.00 4.09
224 225 1.040339 AGGTGGATCTGTCGGCTCTC 61.040 60.000 0.00 0.00 0.00 3.20
225 226 1.323271 GGTGGATCTGTCGGCTCTCA 61.323 60.000 0.00 0.00 0.00 3.27
226 227 0.102120 GTGGATCTGTCGGCTCTCAG 59.898 60.000 0.00 0.00 0.00 3.35
227 228 1.067250 GGATCTGTCGGCTCTCAGC 59.933 63.158 0.00 0.00 41.46 4.26
228 229 1.670949 GGATCTGTCGGCTCTCAGCA 61.671 60.000 0.00 0.00 44.75 4.41
229 230 0.388659 GATCTGTCGGCTCTCAGCAT 59.611 55.000 0.00 0.00 44.75 3.79
230 231 0.104487 ATCTGTCGGCTCTCAGCATG 59.896 55.000 0.00 0.00 44.75 4.06
231 232 1.217511 CTGTCGGCTCTCAGCATGT 59.782 57.895 0.00 0.00 44.75 3.21
232 233 1.079612 TGTCGGCTCTCAGCATGTG 60.080 57.895 0.00 0.00 44.75 3.21
233 234 1.812922 GTCGGCTCTCAGCATGTGG 60.813 63.158 0.00 0.00 44.75 4.17
234 235 2.513204 CGGCTCTCAGCATGTGGG 60.513 66.667 0.00 0.00 44.75 4.61
235 236 2.124403 GGCTCTCAGCATGTGGGG 60.124 66.667 0.00 0.00 44.75 4.96
236 237 2.827642 GCTCTCAGCATGTGGGGC 60.828 66.667 0.00 0.00 41.89 5.80
237 238 2.513204 CTCTCAGCATGTGGGGCG 60.513 66.667 0.00 0.00 37.40 6.13
238 239 4.100084 TCTCAGCATGTGGGGCGG 62.100 66.667 0.00 0.00 37.40 6.13
275 276 4.933064 GAGATCGGCGGCGAGGTG 62.933 72.222 36.74 7.40 0.00 4.00
277 278 4.933064 GATCGGCGGCGAGGTGAG 62.933 72.222 36.74 5.78 0.00 3.51
284 285 4.394712 GGCGAGGTGAGGTGGGTG 62.395 72.222 0.00 0.00 0.00 4.61
285 286 4.394712 GCGAGGTGAGGTGGGTGG 62.395 72.222 0.00 0.00 0.00 4.61
286 287 3.706373 CGAGGTGAGGTGGGTGGG 61.706 72.222 0.00 0.00 0.00 4.61
287 288 2.203938 GAGGTGAGGTGGGTGGGA 60.204 66.667 0.00 0.00 0.00 4.37
288 289 1.616628 GAGGTGAGGTGGGTGGGAT 60.617 63.158 0.00 0.00 0.00 3.85
289 290 1.915078 GAGGTGAGGTGGGTGGGATG 61.915 65.000 0.00 0.00 0.00 3.51
290 291 2.677228 GTGAGGTGGGTGGGATGG 59.323 66.667 0.00 0.00 0.00 3.51
291 292 2.613696 TGAGGTGGGTGGGATGGG 60.614 66.667 0.00 0.00 0.00 4.00
292 293 2.614013 GAGGTGGGTGGGATGGGT 60.614 66.667 0.00 0.00 0.00 4.51
293 294 2.941025 AGGTGGGTGGGATGGGTG 60.941 66.667 0.00 0.00 0.00 4.61
294 295 4.060667 GGTGGGTGGGATGGGTGG 62.061 72.222 0.00 0.00 0.00 4.61
295 296 4.060667 GTGGGTGGGATGGGTGGG 62.061 72.222 0.00 0.00 0.00 4.61
298 299 4.060667 GGTGGGATGGGTGGGGTG 62.061 72.222 0.00 0.00 0.00 4.61
299 300 4.060667 GTGGGATGGGTGGGGTGG 62.061 72.222 0.00 0.00 0.00 4.61
300 301 4.293696 TGGGATGGGTGGGGTGGA 62.294 66.667 0.00 0.00 0.00 4.02
301 302 3.420482 GGGATGGGTGGGGTGGAG 61.420 72.222 0.00 0.00 0.00 3.86
302 303 2.614013 GGATGGGTGGGGTGGAGT 60.614 66.667 0.00 0.00 0.00 3.85
303 304 2.677228 GATGGGTGGGGTGGAGTG 59.323 66.667 0.00 0.00 0.00 3.51
304 305 2.941025 ATGGGTGGGGTGGAGTGG 60.941 66.667 0.00 0.00 0.00 4.00
305 306 3.515383 ATGGGTGGGGTGGAGTGGA 62.515 63.158 0.00 0.00 0.00 4.02
306 307 3.330720 GGGTGGGGTGGAGTGGAG 61.331 72.222 0.00 0.00 0.00 3.86
307 308 2.529389 GGTGGGGTGGAGTGGAGT 60.529 66.667 0.00 0.00 0.00 3.85
308 309 2.593956 GGTGGGGTGGAGTGGAGTC 61.594 68.421 0.00 0.00 0.00 3.36
309 310 2.603473 TGGGGTGGAGTGGAGTCG 60.603 66.667 0.00 0.00 0.00 4.18
310 311 4.083862 GGGGTGGAGTGGAGTCGC 62.084 72.222 0.00 0.00 0.00 5.19
311 312 4.436998 GGGTGGAGTGGAGTCGCG 62.437 72.222 0.00 0.00 0.00 5.87
312 313 4.436998 GGTGGAGTGGAGTCGCGG 62.437 72.222 6.13 0.00 0.00 6.46
313 314 3.681835 GTGGAGTGGAGTCGCGGT 61.682 66.667 6.13 0.00 0.00 5.68
314 315 3.371063 TGGAGTGGAGTCGCGGTC 61.371 66.667 6.13 3.15 0.00 4.79
315 316 4.477975 GGAGTGGAGTCGCGGTCG 62.478 72.222 6.13 0.00 0.00 4.79
319 320 4.717629 TGGAGTCGCGGTCGCAAG 62.718 66.667 15.68 0.17 42.06 4.01
320 321 4.719369 GGAGTCGCGGTCGCAAGT 62.719 66.667 15.68 0.00 42.06 3.16
321 322 3.470567 GAGTCGCGGTCGCAAGTG 61.471 66.667 15.68 0.00 42.06 3.16
322 323 3.891586 GAGTCGCGGTCGCAAGTGA 62.892 63.158 15.68 1.60 42.06 3.41
323 324 3.470567 GTCGCGGTCGCAAGTGAG 61.471 66.667 15.68 0.00 42.06 3.51
324 325 3.666253 TCGCGGTCGCAAGTGAGA 61.666 61.111 15.68 0.53 42.06 3.27
325 326 3.175240 CGCGGTCGCAAGTGAGAG 61.175 66.667 15.68 0.00 42.06 3.20
326 327 3.482783 GCGGTCGCAAGTGAGAGC 61.483 66.667 10.67 4.40 41.49 4.09
327 328 2.049156 CGGTCGCAAGTGAGAGCA 60.049 61.111 13.39 0.00 41.36 4.26
328 329 1.446792 CGGTCGCAAGTGAGAGCAT 60.447 57.895 13.39 0.00 41.36 3.79
329 330 1.690283 CGGTCGCAAGTGAGAGCATG 61.690 60.000 13.39 0.00 41.36 4.06
330 331 0.390340 GGTCGCAAGTGAGAGCATGA 60.390 55.000 9.02 0.00 41.04 3.07
331 332 0.997932 GTCGCAAGTGAGAGCATGAG 59.002 55.000 0.00 0.00 39.48 2.90
332 333 0.605083 TCGCAAGTGAGAGCATGAGT 59.395 50.000 0.00 0.00 39.48 3.41
333 334 0.997932 CGCAAGTGAGAGCATGAGTC 59.002 55.000 0.00 0.00 0.00 3.36
334 335 0.997932 GCAAGTGAGAGCATGAGTCG 59.002 55.000 0.00 0.00 0.00 4.18
335 336 0.997932 CAAGTGAGAGCATGAGTCGC 59.002 55.000 0.00 0.00 0.00 5.19
336 337 0.108424 AAGTGAGAGCATGAGTCGCC 60.108 55.000 0.00 0.00 0.00 5.54
337 338 0.969917 AGTGAGAGCATGAGTCGCCT 60.970 55.000 0.00 0.00 0.00 5.52
338 339 0.108424 GTGAGAGCATGAGTCGCCTT 60.108 55.000 0.00 0.00 0.00 4.35
339 340 1.135139 GTGAGAGCATGAGTCGCCTTA 59.865 52.381 0.00 0.00 0.00 2.69
340 341 2.034878 TGAGAGCATGAGTCGCCTTAT 58.965 47.619 0.00 0.00 0.00 1.73
341 342 2.432146 TGAGAGCATGAGTCGCCTTATT 59.568 45.455 0.00 0.00 0.00 1.40
342 343 3.118629 TGAGAGCATGAGTCGCCTTATTT 60.119 43.478 0.00 0.00 0.00 1.40
343 344 3.462021 AGAGCATGAGTCGCCTTATTTC 58.538 45.455 0.00 0.00 0.00 2.17
344 345 3.133721 AGAGCATGAGTCGCCTTATTTCT 59.866 43.478 0.00 0.00 0.00 2.52
345 346 3.462021 AGCATGAGTCGCCTTATTTCTC 58.538 45.455 0.00 0.00 0.00 2.87
346 347 2.219674 GCATGAGTCGCCTTATTTCTCG 59.780 50.000 0.00 0.00 0.00 4.04
347 348 3.448686 CATGAGTCGCCTTATTTCTCGT 58.551 45.455 0.00 0.00 0.00 4.18
348 349 3.146618 TGAGTCGCCTTATTTCTCGTC 57.853 47.619 0.00 0.00 0.00 4.20
349 350 2.490509 TGAGTCGCCTTATTTCTCGTCA 59.509 45.455 0.00 0.00 0.00 4.35
350 351 2.853003 GAGTCGCCTTATTTCTCGTCAC 59.147 50.000 0.00 0.00 0.00 3.67
351 352 1.582502 GTCGCCTTATTTCTCGTCACG 59.417 52.381 0.00 0.00 0.00 4.35
352 353 1.200716 TCGCCTTATTTCTCGTCACGT 59.799 47.619 0.00 0.00 0.00 4.49
353 354 2.419673 TCGCCTTATTTCTCGTCACGTA 59.580 45.455 0.00 0.00 0.00 3.57
354 355 2.782192 CGCCTTATTTCTCGTCACGTAG 59.218 50.000 0.00 0.00 0.00 3.51
355 356 3.486375 CGCCTTATTTCTCGTCACGTAGA 60.486 47.826 0.00 0.00 0.00 2.59
356 357 4.608951 GCCTTATTTCTCGTCACGTAGAT 58.391 43.478 0.00 0.00 0.00 1.98
357 358 4.676018 GCCTTATTTCTCGTCACGTAGATC 59.324 45.833 0.00 0.00 0.00 2.75
358 359 5.213675 CCTTATTTCTCGTCACGTAGATCC 58.786 45.833 0.00 0.00 0.00 3.36
363 364 3.865446 TCTCGTCACGTAGATCCTACAA 58.135 45.455 0.00 0.00 0.00 2.41
416 417 1.759445 GATCTGCTGGCCTCTTCACTA 59.241 52.381 3.32 0.00 0.00 2.74
429 430 3.202906 TCTTCACTATTTACGCATGGCC 58.797 45.455 0.00 0.00 0.00 5.36
430 431 3.118408 TCTTCACTATTTACGCATGGCCT 60.118 43.478 3.32 0.00 0.00 5.19
472 473 2.027100 AAGAGGACACGATCCCCTTTTC 60.027 50.000 6.83 0.00 42.78 2.29
496 497 2.125350 GCGGGCAGAAGAGGACAG 60.125 66.667 0.00 0.00 0.00 3.51
542 705 4.218635 GCCAGCAGCTACTATGTATACTCA 59.781 45.833 4.17 0.00 38.99 3.41
552 715 8.826710 GCTACTATGTATACTCATGTGCAAAAA 58.173 33.333 4.17 0.00 0.00 1.94
774 2843 1.379527 CCCCATTAAAGTCACTCCGC 58.620 55.000 0.00 0.00 0.00 5.54
799 2868 3.751518 ACAAACCTTATCCACACCACTC 58.248 45.455 0.00 0.00 0.00 3.51
800 2869 3.081804 CAAACCTTATCCACACCACTCC 58.918 50.000 0.00 0.00 0.00 3.85
1312 3381 1.619363 TGGTCCAAGATCCTGGGGG 60.619 63.158 10.55 0.00 37.06 5.40
1560 3630 2.040988 TGATCCTGATCCGGCCCA 60.041 61.111 0.00 0.00 37.02 5.36
1658 3728 4.586001 TGATCGGTGATGAGAATGAGATGA 59.414 41.667 0.00 0.00 0.00 2.92
1659 3729 4.581077 TCGGTGATGAGAATGAGATGAG 57.419 45.455 0.00 0.00 0.00 2.90
1660 3730 4.210331 TCGGTGATGAGAATGAGATGAGA 58.790 43.478 0.00 0.00 0.00 3.27
1661 3731 4.831710 TCGGTGATGAGAATGAGATGAGAT 59.168 41.667 0.00 0.00 0.00 2.75
1663 3733 4.691685 GGTGATGAGAATGAGATGAGATGC 59.308 45.833 0.00 0.00 0.00 3.91
1665 3735 5.407084 GTGATGAGAATGAGATGAGATGCAG 59.593 44.000 0.00 0.00 0.00 4.41
1667 3737 3.071167 TGAGAATGAGATGAGATGCAGGG 59.929 47.826 0.00 0.00 0.00 4.45
1668 3738 3.315596 AGAATGAGATGAGATGCAGGGA 58.684 45.455 0.00 0.00 0.00 4.20
1669 3739 3.325425 AGAATGAGATGAGATGCAGGGAG 59.675 47.826 0.00 0.00 0.00 4.30
1670 3740 2.466547 TGAGATGAGATGCAGGGAGA 57.533 50.000 0.00 0.00 0.00 3.71
1722 3792 1.539124 AGTTTTCCCCGGAGAGGCT 60.539 57.895 0.73 0.00 39.21 4.58
1743 3813 0.317938 GCTGGCTCGATGTACTACCG 60.318 60.000 0.00 0.00 0.00 4.02
1746 3816 0.384669 GGCTCGATGTACTACCGCTT 59.615 55.000 0.00 0.00 0.00 4.68
1870 3955 1.207089 TGCCATCACCAGCAGTAGTAC 59.793 52.381 0.00 0.00 33.08 2.73
2005 4090 2.291475 TGTTGGGATTATTGGCAGAGCA 60.291 45.455 0.00 0.00 0.00 4.26
2008 4093 2.444388 TGGGATTATTGGCAGAGCAGAT 59.556 45.455 0.00 0.00 0.00 2.90
2009 4094 3.117398 TGGGATTATTGGCAGAGCAGATT 60.117 43.478 0.00 0.00 0.00 2.40
2010 4095 3.893813 GGGATTATTGGCAGAGCAGATTT 59.106 43.478 0.00 0.00 0.00 2.17
2128 4213 5.280215 GGATAGGGAAGAGAGAGAGAGAGAG 60.280 52.000 0.00 0.00 0.00 3.20
2132 4217 4.202305 GGGAAGAGAGAGAGAGAGAGAGAG 60.202 54.167 0.00 0.00 0.00 3.20
2133 4218 4.651503 GGAAGAGAGAGAGAGAGAGAGAGA 59.348 50.000 0.00 0.00 0.00 3.10
2134 4219 5.221422 GGAAGAGAGAGAGAGAGAGAGAGAG 60.221 52.000 0.00 0.00 0.00 3.20
2135 4220 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2136 4221 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2137 4222 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2138 4223 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2139 4224 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2140 4225 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2141 4226 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2142 4227 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2143 4228 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2144 4229 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2145 4230 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2146 4231 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
2147 4232 5.539574 AGAGAGAGAGAGAGAGAGAGAGATG 59.460 48.000 0.00 0.00 0.00 2.90
2192 4277 1.344953 CCTGATTGGACGATGGGGGA 61.345 60.000 0.00 0.00 38.35 4.81
2276 4688 3.244181 GCATTGCCTCCAAAAAGAAGGAA 60.244 43.478 0.00 0.00 34.05 3.36
2298 4710 2.220479 AAAATAGCGACCCGAGTAGC 57.780 50.000 0.00 0.00 44.22 3.58
2300 4712 0.669077 AATAGCGACCCGAGTAGCAG 59.331 55.000 4.81 0.00 46.08 4.24
2333 4745 4.255301 TGAACAAACACCTCACGTTTAGT 58.745 39.130 0.00 0.00 34.87 2.24
2368 4780 4.970662 CCAATGGTTTGGTAGATCACAG 57.029 45.455 0.00 0.00 46.27 3.66
2380 4792 3.162202 AGATCACAGCTGATGAAGACG 57.838 47.619 23.35 0.00 37.24 4.18
2381 4793 2.495270 AGATCACAGCTGATGAAGACGT 59.505 45.455 23.35 5.00 37.24 4.34
2482 5091 3.630769 CCTCATGCAGCATGTATCACTTT 59.369 43.478 30.38 0.00 40.31 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.452733 GAACGGGAGTGGAGGGCG 62.453 72.222 0.00 0.00 46.69 6.13
4 5 4.452733 CGAACGGGAGTGGAGGGC 62.453 72.222 0.00 0.00 46.69 5.19
5 6 1.664321 CTACGAACGGGAGTGGAGGG 61.664 65.000 0.00 0.00 46.69 4.30
6 7 0.679002 TCTACGAACGGGAGTGGAGG 60.679 60.000 0.00 0.00 46.69 4.30
7 8 0.733729 CTCTACGAACGGGAGTGGAG 59.266 60.000 0.00 5.68 46.69 3.86
8 9 0.679002 CCTCTACGAACGGGAGTGGA 60.679 60.000 11.32 0.00 46.69 4.02
9 10 0.679002 TCCTCTACGAACGGGAGTGG 60.679 60.000 14.14 12.51 46.69 4.00
10 11 0.733729 CTCCTCTACGAACGGGAGTG 59.266 60.000 14.14 6.27 46.69 3.51
12 13 1.970092 ATCTCCTCTACGAACGGGAG 58.030 55.000 9.69 9.69 44.69 4.30
13 14 2.224475 CCTATCTCCTCTACGAACGGGA 60.224 54.545 0.00 0.00 0.00 5.14
14 15 2.152830 CCTATCTCCTCTACGAACGGG 58.847 57.143 0.00 0.00 0.00 5.28
15 16 3.068560 CTCCTATCTCCTCTACGAACGG 58.931 54.545 0.00 0.00 0.00 4.44
16 17 3.068560 CCTCCTATCTCCTCTACGAACG 58.931 54.545 0.00 0.00 0.00 3.95
17 18 3.414269 CCCTCCTATCTCCTCTACGAAC 58.586 54.545 0.00 0.00 0.00 3.95
18 19 2.224818 GCCCTCCTATCTCCTCTACGAA 60.225 54.545 0.00 0.00 0.00 3.85
19 20 1.351683 GCCCTCCTATCTCCTCTACGA 59.648 57.143 0.00 0.00 0.00 3.43
20 21 1.074084 TGCCCTCCTATCTCCTCTACG 59.926 57.143 0.00 0.00 0.00 3.51
21 22 2.521126 GTGCCCTCCTATCTCCTCTAC 58.479 57.143 0.00 0.00 0.00 2.59
22 23 1.074084 CGTGCCCTCCTATCTCCTCTA 59.926 57.143 0.00 0.00 0.00 2.43
23 24 0.178975 CGTGCCCTCCTATCTCCTCT 60.179 60.000 0.00 0.00 0.00 3.69
24 25 0.468400 ACGTGCCCTCCTATCTCCTC 60.468 60.000 0.00 0.00 0.00 3.71
25 26 0.468400 GACGTGCCCTCCTATCTCCT 60.468 60.000 0.00 0.00 0.00 3.69
26 27 1.797211 CGACGTGCCCTCCTATCTCC 61.797 65.000 0.00 0.00 0.00 3.71
27 28 1.102222 ACGACGTGCCCTCCTATCTC 61.102 60.000 0.00 0.00 0.00 2.75
28 29 1.076923 ACGACGTGCCCTCCTATCT 60.077 57.895 0.00 0.00 0.00 1.98
29 30 1.359475 GACGACGTGCCCTCCTATC 59.641 63.158 4.58 0.00 0.00 2.08
30 31 2.478890 CGACGACGTGCCCTCCTAT 61.479 63.158 4.58 0.00 34.56 2.57
31 32 3.129502 CGACGACGTGCCCTCCTA 61.130 66.667 4.58 0.00 34.56 2.94
42 43 4.471726 ACGCGGATCCACGACGAC 62.472 66.667 27.99 1.60 37.04 4.34
43 44 4.470170 CACGCGGATCCACGACGA 62.470 66.667 27.99 0.00 37.04 4.20
52 53 4.148825 GGAGTGAGCCACGCGGAT 62.149 66.667 12.47 0.00 39.64 4.18
66 67 3.432051 GATGCGGAGGTGGACGGAG 62.432 68.421 0.00 0.00 33.04 4.63
67 68 3.458163 GATGCGGAGGTGGACGGA 61.458 66.667 0.00 0.00 34.31 4.69
68 69 4.530857 GGATGCGGAGGTGGACGG 62.531 72.222 0.00 0.00 0.00 4.79
69 70 3.432051 GAGGATGCGGAGGTGGACG 62.432 68.421 0.00 0.00 0.00 4.79
70 71 2.501610 GAGGATGCGGAGGTGGAC 59.498 66.667 0.00 0.00 0.00 4.02
71 72 3.147595 CGAGGATGCGGAGGTGGA 61.148 66.667 0.00 0.00 0.00 4.02
72 73 3.432051 GACGAGGATGCGGAGGTGG 62.432 68.421 0.00 0.00 35.12 4.61
73 74 2.105128 GACGAGGATGCGGAGGTG 59.895 66.667 0.00 0.00 35.12 4.00
74 75 3.518998 CGACGAGGATGCGGAGGT 61.519 66.667 0.00 0.00 35.12 3.85
75 76 4.933064 GCGACGAGGATGCGGAGG 62.933 72.222 0.00 0.00 35.12 4.30
76 77 4.933064 GGCGACGAGGATGCGGAG 62.933 72.222 0.00 0.00 35.12 4.63
106 107 1.505353 CGATAGGGTCGGTATCGCC 59.495 63.158 0.00 0.00 46.47 5.54
119 120 1.735920 GAGATGCTGCGGCCGATAG 60.736 63.158 33.48 26.17 37.74 2.08
120 121 2.340078 GAGATGCTGCGGCCGATA 59.660 61.111 33.48 16.46 37.74 2.92
121 122 4.615815 GGAGATGCTGCGGCCGAT 62.616 66.667 33.48 14.15 37.74 4.18
127 128 2.587194 CTTCCCGGAGATGCTGCG 60.587 66.667 0.73 1.20 44.57 5.18
128 129 2.203126 CCTTCCCGGAGATGCTGC 60.203 66.667 0.73 0.00 33.16 5.25
129 130 2.203126 GCCTTCCCGGAGATGCTG 60.203 66.667 0.73 0.00 33.16 4.41
130 131 3.483869 GGCCTTCCCGGAGATGCT 61.484 66.667 0.73 0.00 33.16 3.79
131 132 4.570874 GGGCCTTCCCGGAGATGC 62.571 72.222 0.73 4.80 43.94 3.91
140 141 0.958876 CTTTGTGTACCGGGCCTTCC 60.959 60.000 6.32 0.00 0.00 3.46
141 142 0.958876 CCTTTGTGTACCGGGCCTTC 60.959 60.000 6.32 0.00 0.00 3.46
142 143 1.074248 CCTTTGTGTACCGGGCCTT 59.926 57.895 6.32 0.00 0.00 4.35
143 144 2.754375 CCTTTGTGTACCGGGCCT 59.246 61.111 6.32 0.00 0.00 5.19
144 145 2.360726 CCCTTTGTGTACCGGGCC 60.361 66.667 6.32 0.00 0.00 5.80
145 146 2.360726 CCCCTTTGTGTACCGGGC 60.361 66.667 6.32 0.00 35.29 6.13
146 147 2.193087 CTCCCCCTTTGTGTACCGGG 62.193 65.000 6.32 0.00 36.42 5.73
147 148 1.298667 CTCCCCCTTTGTGTACCGG 59.701 63.158 0.00 0.00 0.00 5.28
148 149 1.298667 CCTCCCCCTTTGTGTACCG 59.701 63.158 0.00 0.00 0.00 4.02
149 150 1.001269 GCCTCCCCCTTTGTGTACC 60.001 63.158 0.00 0.00 0.00 3.34
150 151 0.331616 ATGCCTCCCCCTTTGTGTAC 59.668 55.000 0.00 0.00 0.00 2.90
151 152 0.331278 CATGCCTCCCCCTTTGTGTA 59.669 55.000 0.00 0.00 0.00 2.90
152 153 1.077265 CATGCCTCCCCCTTTGTGT 59.923 57.895 0.00 0.00 0.00 3.72
153 154 0.331278 TACATGCCTCCCCCTTTGTG 59.669 55.000 0.00 0.00 0.00 3.33
154 155 1.063717 CATACATGCCTCCCCCTTTGT 60.064 52.381 0.00 0.00 0.00 2.83
155 156 1.696063 CATACATGCCTCCCCCTTTG 58.304 55.000 0.00 0.00 0.00 2.77
156 157 0.557729 CCATACATGCCTCCCCCTTT 59.442 55.000 0.00 0.00 0.00 3.11
157 158 1.363530 CCCATACATGCCTCCCCCTT 61.364 60.000 0.00 0.00 0.00 3.95
158 159 1.775877 CCCATACATGCCTCCCCCT 60.776 63.158 0.00 0.00 0.00 4.79
159 160 1.142688 ATCCCATACATGCCTCCCCC 61.143 60.000 0.00 0.00 0.00 5.40
160 161 0.779997 AATCCCATACATGCCTCCCC 59.220 55.000 0.00 0.00 0.00 4.81
161 162 1.145738 ACAATCCCATACATGCCTCCC 59.854 52.381 0.00 0.00 0.00 4.30
162 163 2.508526 GACAATCCCATACATGCCTCC 58.491 52.381 0.00 0.00 0.00 4.30
163 164 2.146342 CGACAATCCCATACATGCCTC 58.854 52.381 0.00 0.00 0.00 4.70
164 165 1.768275 TCGACAATCCCATACATGCCT 59.232 47.619 0.00 0.00 0.00 4.75
165 166 2.146342 CTCGACAATCCCATACATGCC 58.854 52.381 0.00 0.00 0.00 4.40
166 167 1.532868 GCTCGACAATCCCATACATGC 59.467 52.381 0.00 0.00 0.00 4.06
167 168 2.146342 GGCTCGACAATCCCATACATG 58.854 52.381 0.00 0.00 0.00 3.21
168 169 1.072331 GGGCTCGACAATCCCATACAT 59.928 52.381 3.22 0.00 39.82 2.29
169 170 0.468226 GGGCTCGACAATCCCATACA 59.532 55.000 3.22 0.00 39.82 2.29
170 171 0.600255 CGGGCTCGACAATCCCATAC 60.600 60.000 0.00 0.00 40.05 2.39
171 172 1.745890 CGGGCTCGACAATCCCATA 59.254 57.895 0.00 0.00 40.05 2.74
172 173 2.505982 CGGGCTCGACAATCCCAT 59.494 61.111 0.00 0.00 40.05 4.00
173 174 3.781307 CCGGGCTCGACAATCCCA 61.781 66.667 8.08 0.00 40.05 4.37
174 175 4.547367 CCCGGGCTCGACAATCCC 62.547 72.222 8.08 0.00 39.00 3.85
193 194 4.767255 CCACCTGCTCGCCACCTC 62.767 72.222 0.00 0.00 0.00 3.85
195 196 4.101448 ATCCACCTGCTCGCCACC 62.101 66.667 0.00 0.00 0.00 4.61
196 197 2.512515 GATCCACCTGCTCGCCAC 60.513 66.667 0.00 0.00 0.00 5.01
197 198 2.685017 AGATCCACCTGCTCGCCA 60.685 61.111 0.00 0.00 0.00 5.69
198 199 2.202987 CAGATCCACCTGCTCGCC 60.203 66.667 0.00 0.00 0.00 5.54
199 200 1.520342 GACAGATCCACCTGCTCGC 60.520 63.158 0.00 0.00 37.68 5.03
200 201 1.226802 CGACAGATCCACCTGCTCG 60.227 63.158 0.00 0.00 37.68 5.03
201 202 1.142748 CCGACAGATCCACCTGCTC 59.857 63.158 0.00 0.00 37.68 4.26
202 203 3.023949 GCCGACAGATCCACCTGCT 62.024 63.158 0.00 0.00 37.68 4.24
203 204 2.512515 GCCGACAGATCCACCTGC 60.513 66.667 0.00 0.00 37.68 4.85
204 205 1.142748 GAGCCGACAGATCCACCTG 59.857 63.158 0.00 0.00 39.93 4.00
205 206 1.000993 AGAGCCGACAGATCCACCT 59.999 57.895 0.00 0.00 0.00 4.00
206 207 1.323271 TGAGAGCCGACAGATCCACC 61.323 60.000 0.00 0.00 0.00 4.61
207 208 0.102120 CTGAGAGCCGACAGATCCAC 59.898 60.000 0.00 0.00 36.38 4.02
208 209 1.670949 GCTGAGAGCCGACAGATCCA 61.671 60.000 0.00 0.00 34.48 3.41
209 210 1.067250 GCTGAGAGCCGACAGATCC 59.933 63.158 0.00 0.00 34.48 3.36
210 211 0.388659 ATGCTGAGAGCCGACAGATC 59.611 55.000 0.00 0.00 41.51 2.75
211 212 0.104487 CATGCTGAGAGCCGACAGAT 59.896 55.000 0.00 0.00 41.51 2.90
212 213 1.253593 ACATGCTGAGAGCCGACAGA 61.254 55.000 0.00 0.00 41.51 3.41
213 214 1.082679 CACATGCTGAGAGCCGACAG 61.083 60.000 0.00 0.00 41.51 3.51
214 215 1.079612 CACATGCTGAGAGCCGACA 60.080 57.895 0.00 0.00 41.51 4.35
215 216 1.812922 CCACATGCTGAGAGCCGAC 60.813 63.158 0.00 0.00 41.51 4.79
216 217 2.580815 CCACATGCTGAGAGCCGA 59.419 61.111 0.00 0.00 41.51 5.54
217 218 2.513204 CCCACATGCTGAGAGCCG 60.513 66.667 0.00 0.00 41.51 5.52
218 219 2.124403 CCCCACATGCTGAGAGCC 60.124 66.667 0.00 0.00 41.51 4.70
219 220 2.827642 GCCCCACATGCTGAGAGC 60.828 66.667 0.00 0.00 42.82 4.09
220 221 2.513204 CGCCCCACATGCTGAGAG 60.513 66.667 0.00 0.00 0.00 3.20
221 222 4.100084 CCGCCCCACATGCTGAGA 62.100 66.667 0.00 0.00 0.00 3.27
258 259 4.933064 CACCTCGCCGCCGATCTC 62.933 72.222 0.00 0.00 43.47 2.75
260 261 4.933064 CTCACCTCGCCGCCGATC 62.933 72.222 0.00 0.00 43.47 3.69
267 268 4.394712 CACCCACCTCACCTCGCC 62.395 72.222 0.00 0.00 0.00 5.54
268 269 4.394712 CCACCCACCTCACCTCGC 62.395 72.222 0.00 0.00 0.00 5.03
269 270 3.706373 CCCACCCACCTCACCTCG 61.706 72.222 0.00 0.00 0.00 4.63
270 271 1.616628 ATCCCACCCACCTCACCTC 60.617 63.158 0.00 0.00 0.00 3.85
271 272 1.925455 CATCCCACCCACCTCACCT 60.925 63.158 0.00 0.00 0.00 4.00
272 273 2.677228 CATCCCACCCACCTCACC 59.323 66.667 0.00 0.00 0.00 4.02
273 274 2.677228 CCATCCCACCCACCTCAC 59.323 66.667 0.00 0.00 0.00 3.51
274 275 2.613696 CCCATCCCACCCACCTCA 60.614 66.667 0.00 0.00 0.00 3.86
275 276 2.614013 ACCCATCCCACCCACCTC 60.614 66.667 0.00 0.00 0.00 3.85
276 277 2.941025 CACCCATCCCACCCACCT 60.941 66.667 0.00 0.00 0.00 4.00
277 278 4.060667 CCACCCATCCCACCCACC 62.061 72.222 0.00 0.00 0.00 4.61
278 279 4.060667 CCCACCCATCCCACCCAC 62.061 72.222 0.00 0.00 0.00 4.61
281 282 4.060667 CACCCCACCCATCCCACC 62.061 72.222 0.00 0.00 0.00 4.61
282 283 4.060667 CCACCCCACCCATCCCAC 62.061 72.222 0.00 0.00 0.00 4.61
283 284 4.293696 TCCACCCCACCCATCCCA 62.294 66.667 0.00 0.00 0.00 4.37
284 285 3.420482 CTCCACCCCACCCATCCC 61.420 72.222 0.00 0.00 0.00 3.85
285 286 2.614013 ACTCCACCCCACCCATCC 60.614 66.667 0.00 0.00 0.00 3.51
286 287 2.677228 CACTCCACCCCACCCATC 59.323 66.667 0.00 0.00 0.00 3.51
287 288 2.941025 CCACTCCACCCCACCCAT 60.941 66.667 0.00 0.00 0.00 4.00
288 289 4.194497 TCCACTCCACCCCACCCA 62.194 66.667 0.00 0.00 0.00 4.51
289 290 3.330720 CTCCACTCCACCCCACCC 61.331 72.222 0.00 0.00 0.00 4.61
290 291 2.529389 ACTCCACTCCACCCCACC 60.529 66.667 0.00 0.00 0.00 4.61
291 292 2.943978 CGACTCCACTCCACCCCAC 61.944 68.421 0.00 0.00 0.00 4.61
292 293 2.603473 CGACTCCACTCCACCCCA 60.603 66.667 0.00 0.00 0.00 4.96
293 294 4.083862 GCGACTCCACTCCACCCC 62.084 72.222 0.00 0.00 0.00 4.95
294 295 4.436998 CGCGACTCCACTCCACCC 62.437 72.222 0.00 0.00 0.00 4.61
295 296 4.436998 CCGCGACTCCACTCCACC 62.437 72.222 8.23 0.00 0.00 4.61
296 297 3.628280 GACCGCGACTCCACTCCAC 62.628 68.421 8.23 0.00 0.00 4.02
297 298 3.371063 GACCGCGACTCCACTCCA 61.371 66.667 8.23 0.00 0.00 3.86
298 299 4.477975 CGACCGCGACTCCACTCC 62.478 72.222 8.23 0.00 40.82 3.85
302 303 4.717629 CTTGCGACCGCGACTCCA 62.718 66.667 8.23 0.00 45.51 3.86
303 304 4.719369 ACTTGCGACCGCGACTCC 62.719 66.667 8.23 0.00 45.51 3.85
304 305 3.470567 CACTTGCGACCGCGACTC 61.471 66.667 8.23 0.00 45.51 3.36
305 306 3.898627 CTCACTTGCGACCGCGACT 62.899 63.158 8.23 0.00 45.51 4.18
306 307 3.470567 CTCACTTGCGACCGCGAC 61.471 66.667 8.23 0.00 45.51 5.19
307 308 3.610791 CTCTCACTTGCGACCGCGA 62.611 63.158 8.23 7.04 45.51 5.87
308 309 3.175240 CTCTCACTTGCGACCGCG 61.175 66.667 9.91 0.00 45.51 6.46
309 310 3.482783 GCTCTCACTTGCGACCGC 61.483 66.667 7.53 7.53 42.35 5.68
310 311 1.446792 ATGCTCTCACTTGCGACCG 60.447 57.895 0.00 0.00 0.00 4.79
311 312 0.390340 TCATGCTCTCACTTGCGACC 60.390 55.000 0.00 0.00 0.00 4.79
312 313 0.997932 CTCATGCTCTCACTTGCGAC 59.002 55.000 0.00 0.00 0.00 5.19
313 314 0.605083 ACTCATGCTCTCACTTGCGA 59.395 50.000 0.00 0.00 0.00 5.10
314 315 0.997932 GACTCATGCTCTCACTTGCG 59.002 55.000 0.00 0.00 0.00 4.85
315 316 0.997932 CGACTCATGCTCTCACTTGC 59.002 55.000 0.00 0.00 0.00 4.01
316 317 0.997932 GCGACTCATGCTCTCACTTG 59.002 55.000 0.00 0.00 0.00 3.16
317 318 0.108424 GGCGACTCATGCTCTCACTT 60.108 55.000 0.00 0.00 0.00 3.16
318 319 0.969917 AGGCGACTCATGCTCTCACT 60.970 55.000 0.00 0.00 32.90 3.41
319 320 0.108424 AAGGCGACTCATGCTCTCAC 60.108 55.000 0.00 0.00 42.68 3.51
320 321 1.474330 TAAGGCGACTCATGCTCTCA 58.526 50.000 0.00 0.00 42.68 3.27
321 322 2.810439 ATAAGGCGACTCATGCTCTC 57.190 50.000 0.00 0.00 42.68 3.20
322 323 3.133721 AGAAATAAGGCGACTCATGCTCT 59.866 43.478 0.00 0.00 42.68 4.09
323 324 3.462021 AGAAATAAGGCGACTCATGCTC 58.538 45.455 0.00 0.00 42.68 4.26
324 325 3.462021 GAGAAATAAGGCGACTCATGCT 58.538 45.455 0.00 0.00 42.68 3.79
325 326 2.219674 CGAGAAATAAGGCGACTCATGC 59.780 50.000 0.00 0.00 42.68 4.06
326 327 3.448686 ACGAGAAATAAGGCGACTCATG 58.551 45.455 0.00 0.00 42.68 3.07
327 328 3.130516 TGACGAGAAATAAGGCGACTCAT 59.869 43.478 0.00 0.00 42.68 2.90
328 329 2.490509 TGACGAGAAATAAGGCGACTCA 59.509 45.455 0.00 0.00 42.68 3.41
329 330 2.853003 GTGACGAGAAATAAGGCGACTC 59.147 50.000 0.00 0.00 42.68 3.36
331 332 1.582502 CGTGACGAGAAATAAGGCGAC 59.417 52.381 0.00 0.00 0.00 5.19
332 333 1.200716 ACGTGACGAGAAATAAGGCGA 59.799 47.619 13.70 0.00 0.00 5.54
333 334 1.625616 ACGTGACGAGAAATAAGGCG 58.374 50.000 13.70 0.00 0.00 5.52
334 335 4.025015 TCTACGTGACGAGAAATAAGGC 57.975 45.455 13.70 0.00 0.00 4.35
335 336 5.008811 AGGATCTACGTGACGAGAAATAAGG 59.991 44.000 13.70 0.00 0.00 2.69
336 337 6.062434 AGGATCTACGTGACGAGAAATAAG 57.938 41.667 13.70 0.00 0.00 1.73
337 338 6.539826 TGTAGGATCTACGTGACGAGAAATAA 59.460 38.462 13.70 0.00 0.00 1.40
338 339 6.051074 TGTAGGATCTACGTGACGAGAAATA 58.949 40.000 13.70 2.97 0.00 1.40
339 340 4.880120 TGTAGGATCTACGTGACGAGAAAT 59.120 41.667 13.70 0.00 0.00 2.17
340 341 4.256110 TGTAGGATCTACGTGACGAGAAA 58.744 43.478 13.70 0.00 0.00 2.52
341 342 3.865446 TGTAGGATCTACGTGACGAGAA 58.135 45.455 13.70 0.00 0.00 2.87
342 343 3.531934 TGTAGGATCTACGTGACGAGA 57.468 47.619 13.70 10.74 0.00 4.04
343 344 4.815040 ATTGTAGGATCTACGTGACGAG 57.185 45.455 13.70 4.98 0.00 4.18
344 345 5.571784 AAATTGTAGGATCTACGTGACGA 57.428 39.130 13.70 0.00 0.00 4.20
345 346 6.642683 AAAAATTGTAGGATCTACGTGACG 57.357 37.500 2.24 2.24 0.00 4.35
371 372 4.912317 TTATTGTGGTAACCAGGCAGTA 57.088 40.909 0.00 0.00 32.34 2.74
378 379 5.359576 GCAGATCCATTTATTGTGGTAACCA 59.640 40.000 0.00 0.00 37.96 3.67
379 380 5.594317 AGCAGATCCATTTATTGTGGTAACC 59.406 40.000 0.00 0.00 37.96 2.85
386 387 2.961062 GGCCAGCAGATCCATTTATTGT 59.039 45.455 0.00 0.00 0.00 2.71
416 417 3.784338 CAAATCAAGGCCATGCGTAAAT 58.216 40.909 5.01 0.00 0.00 1.40
429 430 2.230992 TGAAATCCGTGGGCAAATCAAG 59.769 45.455 0.00 0.00 0.00 3.02
430 431 2.242926 TGAAATCCGTGGGCAAATCAA 58.757 42.857 0.00 0.00 0.00 2.57
468 469 1.115467 TCTGCCCGCAAAAAGGAAAA 58.885 45.000 0.00 0.00 0.00 2.29
472 473 0.242017 CTCTTCTGCCCGCAAAAAGG 59.758 55.000 10.10 0.00 0.00 3.11
496 497 0.676782 CCAACGAACCCATGAGACCC 60.677 60.000 0.00 0.00 0.00 4.46
542 705 0.248825 TCGCTTGCGTTTTTGCACAT 60.249 45.000 14.70 0.00 46.25 3.21
552 715 1.128692 GAGTATTTGCTTCGCTTGCGT 59.871 47.619 14.70 0.00 0.00 5.24
774 2843 3.566322 TGGTGTGGATAAGGTTTGTTTCG 59.434 43.478 0.00 0.00 0.00 3.46
809 2878 0.105408 GGTTTTATAGCGGCGGGAGA 59.895 55.000 9.78 0.00 0.00 3.71
928 2997 2.970974 GAGGAGGCGCACAAGCAAC 61.971 63.158 10.83 0.00 42.27 4.17
1278 3347 1.447838 CCAGTCGGGGATGTTGACG 60.448 63.158 0.00 0.00 37.69 4.35
1560 3630 4.266070 CGATCGATCGCCGTGGGT 62.266 66.667 32.34 0.00 43.84 4.51
1573 3643 1.097547 TCGTAAGGGGACGGACGATC 61.098 60.000 0.00 0.00 43.95 3.69
1613 3683 7.925703 TCACAAACTACTCGTAGAAGAAAAG 57.074 36.000 10.83 0.00 36.97 2.27
1614 3684 7.325338 CGATCACAAACTACTCGTAGAAGAAAA 59.675 37.037 10.83 0.00 36.97 2.29
1658 3728 3.719479 TCTCTACTACTCTCCCTGCATCT 59.281 47.826 0.00 0.00 0.00 2.90
1659 3729 4.093472 TCTCTACTACTCTCCCTGCATC 57.907 50.000 0.00 0.00 0.00 3.91
1660 3730 4.740154 ATCTCTACTACTCTCCCTGCAT 57.260 45.455 0.00 0.00 0.00 3.96
1661 3731 4.211125 CAATCTCTACTACTCTCCCTGCA 58.789 47.826 0.00 0.00 0.00 4.41
1663 3733 4.798882 ACCAATCTCTACTACTCTCCCTG 58.201 47.826 0.00 0.00 0.00 4.45
1665 3735 6.239092 GCTTAACCAATCTCTACTACTCTCCC 60.239 46.154 0.00 0.00 0.00 4.30
1667 3737 6.548251 AGGCTTAACCAATCTCTACTACTCTC 59.452 42.308 0.00 0.00 43.14 3.20
1668 3738 6.436890 AGGCTTAACCAATCTCTACTACTCT 58.563 40.000 0.00 0.00 43.14 3.24
1669 3739 6.548251 AGAGGCTTAACCAATCTCTACTACTC 59.452 42.308 0.00 0.00 43.14 2.59
1670 3740 6.322712 CAGAGGCTTAACCAATCTCTACTACT 59.677 42.308 0.00 0.00 43.14 2.57
1722 3792 0.744874 GTAGTACATCGAGCCAGCCA 59.255 55.000 0.00 0.00 0.00 4.75
1743 3813 5.734855 TGTTAAGGAGCAATCGATTAAGC 57.265 39.130 10.97 11.25 0.00 3.09
1746 3816 7.768582 TCATCTTTGTTAAGGAGCAATCGATTA 59.231 33.333 10.97 0.00 32.02 1.75
1794 3876 2.034532 TGGGCAGCACATGGACAG 59.965 61.111 0.00 0.00 0.00 3.51
1806 3888 1.250328 CAGCAAGAAATCAGTGGGCA 58.750 50.000 0.00 0.00 0.00 5.36
1808 3890 1.915141 ACCAGCAAGAAATCAGTGGG 58.085 50.000 0.00 0.00 0.00 4.61
1867 3952 9.896263 GGCAGATCATTTTAGTAGTACTAGTAC 57.104 37.037 23.03 23.03 31.47 2.73
1870 3955 7.868415 GGTGGCAGATCATTTTAGTAGTACTAG 59.132 40.741 9.90 0.00 31.47 2.57
2005 4090 6.437477 AGGCTCCCTTTTTAAATCGAAAATCT 59.563 34.615 0.00 0.00 0.00 2.40
2008 4093 6.717997 ACTAGGCTCCCTTTTTAAATCGAAAA 59.282 34.615 0.00 0.00 34.61 2.29
2009 4094 6.243148 ACTAGGCTCCCTTTTTAAATCGAAA 58.757 36.000 0.00 0.00 34.61 3.46
2010 4095 5.812286 ACTAGGCTCCCTTTTTAAATCGAA 58.188 37.500 0.00 0.00 34.61 3.71
2128 4213 4.590647 TCTCCATCTCTCTCTCTCTCTCTC 59.409 50.000 0.00 0.00 0.00 3.20
2132 4217 4.963318 TCTCTCCATCTCTCTCTCTCTC 57.037 50.000 0.00 0.00 0.00 3.20
2133 4218 4.042560 CCATCTCTCCATCTCTCTCTCTCT 59.957 50.000 0.00 0.00 0.00 3.10
2134 4219 4.042062 TCCATCTCTCCATCTCTCTCTCTC 59.958 50.000 0.00 0.00 0.00 3.20
2135 4220 3.982730 TCCATCTCTCCATCTCTCTCTCT 59.017 47.826 0.00 0.00 0.00 3.10
2136 4221 4.042062 TCTCCATCTCTCCATCTCTCTCTC 59.958 50.000 0.00 0.00 0.00 3.20
2137 4222 3.982730 TCTCCATCTCTCCATCTCTCTCT 59.017 47.826 0.00 0.00 0.00 3.10
2138 4223 4.371624 TCTCCATCTCTCCATCTCTCTC 57.628 50.000 0.00 0.00 0.00 3.20
2139 4224 4.812403 TTCTCCATCTCTCCATCTCTCT 57.188 45.455 0.00 0.00 0.00 3.10
2140 4225 4.895297 ACTTTCTCCATCTCTCCATCTCTC 59.105 45.833 0.00 0.00 0.00 3.20
2141 4226 4.650588 CACTTTCTCCATCTCTCCATCTCT 59.349 45.833 0.00 0.00 0.00 3.10
2142 4227 4.202243 CCACTTTCTCCATCTCTCCATCTC 60.202 50.000 0.00 0.00 0.00 2.75
2143 4228 3.710677 CCACTTTCTCCATCTCTCCATCT 59.289 47.826 0.00 0.00 0.00 2.90
2144 4229 3.181456 CCCACTTTCTCCATCTCTCCATC 60.181 52.174 0.00 0.00 0.00 3.51
2145 4230 2.776536 CCCACTTTCTCCATCTCTCCAT 59.223 50.000 0.00 0.00 0.00 3.41
2146 4231 2.191400 CCCACTTTCTCCATCTCTCCA 58.809 52.381 0.00 0.00 0.00 3.86
2147 4232 2.433970 CTCCCACTTTCTCCATCTCTCC 59.566 54.545 0.00 0.00 0.00 3.71
2276 4688 4.202182 TGCTACTCGGGTCGCTATTTTTAT 60.202 41.667 13.61 0.00 35.53 1.40
2298 4710 5.392380 GGTGTTTGTTCATATTCCTGCTCTG 60.392 44.000 0.00 0.00 0.00 3.35
2300 4712 4.702131 AGGTGTTTGTTCATATTCCTGCTC 59.298 41.667 0.00 0.00 0.00 4.26
2349 4761 4.012374 CAGCTGTGATCTACCAAACCATT 58.988 43.478 5.25 0.00 0.00 3.16
2357 4769 4.367450 GTCTTCATCAGCTGTGATCTACC 58.633 47.826 14.67 1.26 41.85 3.18
2358 4770 4.041049 CGTCTTCATCAGCTGTGATCTAC 58.959 47.826 14.67 12.59 41.85 2.59
2359 4771 3.696548 ACGTCTTCATCAGCTGTGATCTA 59.303 43.478 14.67 1.90 41.85 1.98
2367 4779 2.441410 TCTCTGACGTCTTCATCAGCT 58.559 47.619 17.92 0.00 41.82 4.24
2368 4780 2.929531 TCTCTGACGTCTTCATCAGC 57.070 50.000 17.92 0.00 41.82 4.26
2380 4792 1.544691 TGACCGGTAGCTTTCTCTGAC 59.455 52.381 7.34 0.00 0.00 3.51
2381 4793 1.919240 TGACCGGTAGCTTTCTCTGA 58.081 50.000 7.34 0.00 0.00 3.27
2482 5091 1.202794 TGTGAGCCAGCATGAGTTTCA 60.203 47.619 0.00 0.00 39.69 2.69


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

AutoCloner maintained by Alex Coulton.