Multiple sequence alignment - TraesCS7B01G146400

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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 TraesCS7B01G146400 chr7B 100.000 2555 0 0 1 2555 191137967 191140521 0.000000e+00 4719.0
1 TraesCS7B01G146400 chr7B 100.000 41 0 0 2773 2813 191140739 191140779 3.000000e-10 76.8
2 TraesCS7B01G146400 chr7D 88.850 2009 113 40 201 2139 210126116 210124149 0.000000e+00 2366.0
3 TraesCS7B01G146400 chr7D 92.718 412 18 4 2156 2555 210124162 210123751 4.040000e-163 584.0
4 TraesCS7B01G146400 chr7A 87.468 1540 90 39 1051 2555 222785795 222784324 0.000000e+00 1679.0
5 TraesCS7B01G146400 chr7A 87.648 591 17 10 426 985 222786658 222786093 1.100000e-178 636.0
6 TraesCS7B01G146400 chr5D 79.127 527 74 22 1115 1632 374661844 374662343 5.810000e-87 331.0
7 TraesCS7B01G146400 chr5B 96.825 189 6 0 1 189 536649923 536649735 1.630000e-82 316.0
8 TraesCS7B01G146400 chr5B 96.296 189 7 0 1 189 536601679 536601491 7.570000e-81 311.0
9 TraesCS7B01G146400 chr5B 78.077 520 81 25 1116 1632 447402739 447403228 5.890000e-77 298.0
10 TraesCS7B01G146400 chr3B 96.774 186 6 0 1 186 457941794 457941609 7.570000e-81 311.0
11 TraesCS7B01G146400 chr3B 96.257 187 7 0 1 187 186566034 186566220 9.790000e-80 307.0
12 TraesCS7B01G146400 chr3B 92.417 211 14 2 1 210 444704406 444704615 1.640000e-77 300.0
13 TraesCS7B01G146400 chr2B 96.774 186 6 0 1 186 538185414 538185599 7.570000e-81 311.0
14 TraesCS7B01G146400 chr6B 95.789 190 8 0 1 190 163184697 163184508 9.790000e-80 307.0
15 TraesCS7B01G146400 chr4B 96.257 187 7 0 1 187 527253517 527253703 9.790000e-80 307.0
16 TraesCS7B01G146400 chr1B 95.312 192 9 0 1 192 311471170 311471361 3.520000e-79 305.0
17 TraesCS7B01G146400 chr5A 88.325 197 23 0 1436 1632 476403109 476403305 1.300000e-58 237.0
18 TraesCS7B01G146400 chr5A 84.058 138 16 3 1116 1253 476402840 476402971 8.180000e-26 128.0


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 TraesCS7B01G146400 chr7B 191137967 191140779 2812 False 2397.9 4719 100.000 1 2813 2 chr7B.!!$F1 2812
1 TraesCS7B01G146400 chr7D 210123751 210126116 2365 True 1475.0 2366 90.784 201 2555 2 chr7D.!!$R1 2354
2 TraesCS7B01G146400 chr7A 222784324 222786658 2334 True 1157.5 1679 87.558 426 2555 2 chr7A.!!$R1 2129

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
333 334 0.103208 CTCAGTGGACCGATACAGGC 59.897 60.0 0.0 0.0 33.69 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 2598 0.17576 GCTGTCTATCCTTCGTGGCA 59.824 55.0 0.0 0.0 35.26 4.92 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
30 31 2.274920 GCTTTGAGCTTGAGCCAATC 57.725 50.000 0.00 0.00 43.38 2.67
31 32 1.135170 GCTTTGAGCTTGAGCCAATCC 60.135 52.381 0.00 0.00 43.38 3.01
32 33 2.444421 CTTTGAGCTTGAGCCAATCCT 58.556 47.619 0.00 0.00 43.38 3.24
33 34 2.592102 TTGAGCTTGAGCCAATCCTT 57.408 45.000 0.00 0.00 43.38 3.36
34 35 2.592102 TGAGCTTGAGCCAATCCTTT 57.408 45.000 0.00 0.00 43.38 3.11
35 36 2.880443 TGAGCTTGAGCCAATCCTTTT 58.120 42.857 0.00 0.00 43.38 2.27
36 37 2.559668 TGAGCTTGAGCCAATCCTTTTG 59.440 45.455 0.00 0.00 43.38 2.44
37 38 2.560105 GAGCTTGAGCCAATCCTTTTGT 59.440 45.455 0.00 0.00 43.38 2.83
38 39 2.560105 AGCTTGAGCCAATCCTTTTGTC 59.440 45.455 0.00 0.00 43.38 3.18
39 40 2.353109 GCTTGAGCCAATCCTTTTGTCC 60.353 50.000 0.00 0.00 34.31 4.02
40 41 2.978156 TGAGCCAATCCTTTTGTCCT 57.022 45.000 0.00 0.00 0.00 3.85
41 42 3.243359 TGAGCCAATCCTTTTGTCCTT 57.757 42.857 0.00 0.00 0.00 3.36
42 43 4.380843 TGAGCCAATCCTTTTGTCCTTA 57.619 40.909 0.00 0.00 0.00 2.69
43 44 4.335416 TGAGCCAATCCTTTTGTCCTTAG 58.665 43.478 0.00 0.00 0.00 2.18
44 45 3.092301 AGCCAATCCTTTTGTCCTTAGC 58.908 45.455 0.00 0.00 0.00 3.09
45 46 2.825532 GCCAATCCTTTTGTCCTTAGCA 59.174 45.455 0.00 0.00 0.00 3.49
46 47 3.448660 GCCAATCCTTTTGTCCTTAGCAT 59.551 43.478 0.00 0.00 0.00 3.79
47 48 4.081476 GCCAATCCTTTTGTCCTTAGCATT 60.081 41.667 0.00 0.00 0.00 3.56
48 49 5.569428 GCCAATCCTTTTGTCCTTAGCATTT 60.569 40.000 0.00 0.00 0.00 2.32
49 50 6.466812 CCAATCCTTTTGTCCTTAGCATTTT 58.533 36.000 0.00 0.00 0.00 1.82
50 51 6.369615 CCAATCCTTTTGTCCTTAGCATTTTG 59.630 38.462 0.00 0.00 0.00 2.44
51 52 6.916360 ATCCTTTTGTCCTTAGCATTTTGA 57.084 33.333 0.00 0.00 0.00 2.69
52 53 6.331369 TCCTTTTGTCCTTAGCATTTTGAG 57.669 37.500 0.00 0.00 0.00 3.02
53 54 5.243730 TCCTTTTGTCCTTAGCATTTTGAGG 59.756 40.000 0.00 0.00 0.00 3.86
54 55 5.467035 TTTTGTCCTTAGCATTTTGAGGG 57.533 39.130 0.00 0.00 0.00 4.30
55 56 4.380843 TTGTCCTTAGCATTTTGAGGGA 57.619 40.909 0.00 0.00 0.00 4.20
56 57 4.591321 TGTCCTTAGCATTTTGAGGGAT 57.409 40.909 0.00 0.00 0.00 3.85
57 58 4.526970 TGTCCTTAGCATTTTGAGGGATC 58.473 43.478 0.00 0.00 0.00 3.36
58 59 3.885901 GTCCTTAGCATTTTGAGGGATCC 59.114 47.826 1.92 1.92 0.00 3.36
59 60 3.527253 TCCTTAGCATTTTGAGGGATCCA 59.473 43.478 15.23 0.00 0.00 3.41
60 61 3.633986 CCTTAGCATTTTGAGGGATCCAC 59.366 47.826 15.23 7.66 0.00 4.02
61 62 4.530875 CTTAGCATTTTGAGGGATCCACT 58.469 43.478 15.23 8.33 0.00 4.00
62 63 3.463048 AGCATTTTGAGGGATCCACTT 57.537 42.857 15.23 0.00 0.00 3.16
63 64 3.782992 AGCATTTTGAGGGATCCACTTT 58.217 40.909 15.23 0.00 0.00 2.66
64 65 4.162651 AGCATTTTGAGGGATCCACTTTT 58.837 39.130 15.23 0.00 0.00 2.27
65 66 4.221482 AGCATTTTGAGGGATCCACTTTTC 59.779 41.667 15.23 3.49 0.00 2.29
66 67 4.221482 GCATTTTGAGGGATCCACTTTTCT 59.779 41.667 15.23 0.00 0.00 2.52
67 68 5.623141 GCATTTTGAGGGATCCACTTTTCTC 60.623 44.000 15.23 10.12 0.00 2.87
68 69 5.324832 TTTTGAGGGATCCACTTTTCTCT 57.675 39.130 15.23 0.00 0.00 3.10
69 70 5.324832 TTTGAGGGATCCACTTTTCTCTT 57.675 39.130 15.23 0.00 0.00 2.85
70 71 4.559862 TGAGGGATCCACTTTTCTCTTC 57.440 45.455 15.23 0.00 0.00 2.87
71 72 3.264450 TGAGGGATCCACTTTTCTCTTCC 59.736 47.826 15.23 0.00 0.00 3.46
72 73 3.260205 AGGGATCCACTTTTCTCTTCCA 58.740 45.455 15.23 0.00 0.00 3.53
73 74 3.854994 AGGGATCCACTTTTCTCTTCCAT 59.145 43.478 15.23 0.00 0.00 3.41
74 75 3.950395 GGGATCCACTTTTCTCTTCCATG 59.050 47.826 15.23 0.00 0.00 3.66
75 76 3.379688 GGATCCACTTTTCTCTTCCATGC 59.620 47.826 6.95 0.00 0.00 4.06
76 77 2.795329 TCCACTTTTCTCTTCCATGCC 58.205 47.619 0.00 0.00 0.00 4.40
77 78 2.108075 TCCACTTTTCTCTTCCATGCCA 59.892 45.455 0.00 0.00 0.00 4.92
78 79 3.094572 CCACTTTTCTCTTCCATGCCAT 58.905 45.455 0.00 0.00 0.00 4.40
79 80 3.119245 CCACTTTTCTCTTCCATGCCATG 60.119 47.826 0.00 0.00 0.00 3.66
80 81 2.494870 ACTTTTCTCTTCCATGCCATGC 59.505 45.455 0.00 0.00 0.00 4.06
81 82 1.477553 TTTCTCTTCCATGCCATGCC 58.522 50.000 0.00 0.00 0.00 4.40
82 83 0.332293 TTCTCTTCCATGCCATGCCA 59.668 50.000 0.00 0.00 0.00 4.92
83 84 0.332293 TCTCTTCCATGCCATGCCAA 59.668 50.000 0.00 0.00 0.00 4.52
84 85 1.063492 TCTCTTCCATGCCATGCCAAT 60.063 47.619 0.00 0.00 0.00 3.16
85 86 1.340248 CTCTTCCATGCCATGCCAATC 59.660 52.381 0.00 0.00 0.00 2.67
86 87 1.116308 CTTCCATGCCATGCCAATCA 58.884 50.000 0.00 0.00 0.00 2.57
87 88 1.691976 CTTCCATGCCATGCCAATCAT 59.308 47.619 0.00 0.00 35.31 2.45
88 89 1.796017 TCCATGCCATGCCAATCATT 58.204 45.000 0.00 0.00 31.79 2.57
89 90 1.414550 TCCATGCCATGCCAATCATTG 59.585 47.619 0.00 0.00 31.79 2.82
90 91 1.414550 CCATGCCATGCCAATCATTGA 59.585 47.619 0.00 0.00 31.79 2.57
91 92 2.547855 CCATGCCATGCCAATCATTGAG 60.548 50.000 0.00 0.00 31.79 3.02
92 93 1.855295 TGCCATGCCAATCATTGAGT 58.145 45.000 0.00 0.00 31.79 3.41
93 94 2.181125 TGCCATGCCAATCATTGAGTT 58.819 42.857 0.00 0.00 31.79 3.01
94 95 2.568062 TGCCATGCCAATCATTGAGTTT 59.432 40.909 0.00 0.00 31.79 2.66
95 96 3.008157 TGCCATGCCAATCATTGAGTTTT 59.992 39.130 0.00 0.00 31.79 2.43
96 97 3.619929 GCCATGCCAATCATTGAGTTTTC 59.380 43.478 0.00 0.00 31.79 2.29
97 98 4.186159 CCATGCCAATCATTGAGTTTTCC 58.814 43.478 0.00 0.00 31.79 3.13
98 99 4.081309 CCATGCCAATCATTGAGTTTTCCT 60.081 41.667 0.00 0.00 31.79 3.36
99 100 5.127519 CCATGCCAATCATTGAGTTTTCCTA 59.872 40.000 0.00 0.00 31.79 2.94
100 101 6.351202 CCATGCCAATCATTGAGTTTTCCTAA 60.351 38.462 0.00 0.00 31.79 2.69
101 102 6.662865 TGCCAATCATTGAGTTTTCCTAAA 57.337 33.333 0.00 0.00 0.00 1.85
102 103 7.060383 TGCCAATCATTGAGTTTTCCTAAAA 57.940 32.000 0.00 0.00 0.00 1.52
103 104 7.678837 TGCCAATCATTGAGTTTTCCTAAAAT 58.321 30.769 0.00 0.00 32.22 1.82
104 105 8.811017 TGCCAATCATTGAGTTTTCCTAAAATA 58.189 29.630 0.00 0.00 32.22 1.40
105 106 9.822185 GCCAATCATTGAGTTTTCCTAAAATAT 57.178 29.630 0.00 0.00 32.22 1.28
145 146 8.944029 GCATTAGCTCAATGAGATATATGTTGT 58.056 33.333 15.38 0.00 45.99 3.32
165 166 9.705290 ATGTTGTTAGAAATTACCAAAATCACC 57.295 29.630 0.00 0.00 0.00 4.02
166 167 8.145122 TGTTGTTAGAAATTACCAAAATCACCC 58.855 33.333 0.00 0.00 0.00 4.61
167 168 7.841282 TGTTAGAAATTACCAAAATCACCCA 57.159 32.000 0.00 0.00 0.00 4.51
168 169 7.891561 TGTTAGAAATTACCAAAATCACCCAG 58.108 34.615 0.00 0.00 0.00 4.45
169 170 7.039363 TGTTAGAAATTACCAAAATCACCCAGG 60.039 37.037 0.00 0.00 0.00 4.45
170 171 4.777366 AGAAATTACCAAAATCACCCAGGG 59.223 41.667 2.85 2.85 0.00 4.45
171 172 4.412060 AATTACCAAAATCACCCAGGGA 57.588 40.909 14.54 0.00 0.00 4.20
172 173 4.625225 ATTACCAAAATCACCCAGGGAT 57.375 40.909 14.54 0.00 0.00 3.85
173 174 5.742562 ATTACCAAAATCACCCAGGGATA 57.257 39.130 14.54 0.00 0.00 2.59
174 175 3.669939 ACCAAAATCACCCAGGGATAG 57.330 47.619 14.54 1.22 0.00 2.08
175 176 2.926329 ACCAAAATCACCCAGGGATAGT 59.074 45.455 14.54 0.00 0.00 2.12
176 177 3.336694 ACCAAAATCACCCAGGGATAGTT 59.663 43.478 14.54 1.69 0.00 2.24
177 178 3.701040 CCAAAATCACCCAGGGATAGTTG 59.299 47.826 14.54 9.35 0.00 3.16
178 179 2.736670 AATCACCCAGGGATAGTTGC 57.263 50.000 14.54 0.00 0.00 4.17
179 180 1.595311 ATCACCCAGGGATAGTTGCA 58.405 50.000 14.54 0.00 0.00 4.08
180 181 0.618458 TCACCCAGGGATAGTTGCAC 59.382 55.000 14.54 0.00 0.00 4.57
181 182 0.620556 CACCCAGGGATAGTTGCACT 59.379 55.000 14.54 0.00 0.00 4.40
182 183 1.004745 CACCCAGGGATAGTTGCACTT 59.995 52.381 14.54 0.00 0.00 3.16
183 184 1.710809 ACCCAGGGATAGTTGCACTTT 59.289 47.619 14.54 0.00 0.00 2.66
184 185 2.290960 ACCCAGGGATAGTTGCACTTTC 60.291 50.000 14.54 0.00 0.00 2.62
185 186 2.290896 CCCAGGGATAGTTGCACTTTCA 60.291 50.000 0.00 0.00 29.36 2.69
186 187 3.012518 CCAGGGATAGTTGCACTTTCAG 58.987 50.000 0.00 0.00 29.36 3.02
187 188 3.307691 CCAGGGATAGTTGCACTTTCAGA 60.308 47.826 0.00 0.00 29.36 3.27
188 189 4.326826 CAGGGATAGTTGCACTTTCAGAA 58.673 43.478 0.00 0.00 29.36 3.02
189 190 4.394300 CAGGGATAGTTGCACTTTCAGAAG 59.606 45.833 0.00 0.00 38.87 2.85
190 191 3.127721 GGGATAGTTGCACTTTCAGAAGC 59.872 47.826 0.00 0.00 36.29 3.86
191 192 3.753272 GGATAGTTGCACTTTCAGAAGCA 59.247 43.478 0.00 0.00 36.29 3.91
192 193 4.378874 GGATAGTTGCACTTTCAGAAGCAC 60.379 45.833 0.00 0.00 36.62 4.40
193 194 2.368439 AGTTGCACTTTCAGAAGCACA 58.632 42.857 0.00 0.00 36.62 4.57
194 195 2.098117 AGTTGCACTTTCAGAAGCACAC 59.902 45.455 0.00 0.00 36.62 3.82
195 196 0.657312 TGCACTTTCAGAAGCACACG 59.343 50.000 0.00 0.00 36.29 4.49
196 197 0.937304 GCACTTTCAGAAGCACACGA 59.063 50.000 0.00 0.00 36.29 4.35
197 198 1.070309 GCACTTTCAGAAGCACACGAG 60.070 52.381 0.00 0.00 36.29 4.18
198 199 1.070309 CACTTTCAGAAGCACACGAGC 60.070 52.381 0.00 0.00 36.29 5.03
199 200 0.514691 CTTTCAGAAGCACACGAGCC 59.485 55.000 0.00 0.00 34.23 4.70
219 220 3.466881 GGGGGTGTTTTCTTGGGC 58.533 61.111 0.00 0.00 0.00 5.36
222 223 1.051556 GGGGTGTTTTCTTGGGCCAA 61.052 55.000 19.68 19.68 0.00 4.52
227 228 2.206536 TTTTCTTGGGCCAAGGCGG 61.207 57.895 38.45 19.95 41.33 6.13
247 248 2.344872 GTACGCGGGTTTGGGAGT 59.655 61.111 11.50 0.00 0.00 3.85
248 249 1.301953 GTACGCGGGTTTGGGAGTT 60.302 57.895 11.50 0.00 0.00 3.01
251 252 2.613506 CGCGGGTTTGGGAGTTGTC 61.614 63.158 0.00 0.00 0.00 3.18
261 262 3.998672 GAGTTGTCCGGACGCCCA 61.999 66.667 28.70 9.38 0.00 5.36
266 267 4.668118 GTCCGGACGCCCACGAAA 62.668 66.667 20.85 0.00 43.93 3.46
271 272 4.324991 GACGCCCACGAAACCCCT 62.325 66.667 0.00 0.00 43.93 4.79
272 273 4.324991 ACGCCCACGAAACCCCTC 62.325 66.667 0.00 0.00 43.93 4.30
273 274 4.323477 CGCCCACGAAACCCCTCA 62.323 66.667 0.00 0.00 43.93 3.86
274 275 2.671963 GCCCACGAAACCCCTCAC 60.672 66.667 0.00 0.00 0.00 3.51
275 276 2.358247 CCCACGAAACCCCTCACG 60.358 66.667 0.00 0.00 0.00 4.35
278 279 0.816421 CCACGAAACCCCTCACGTTT 60.816 55.000 0.00 0.00 36.86 3.60
279 280 0.306533 CACGAAACCCCTCACGTTTG 59.693 55.000 0.00 0.00 36.86 2.93
281 282 1.658114 GAAACCCCTCACGTTTGCC 59.342 57.895 0.00 0.00 33.65 4.52
282 283 0.822121 GAAACCCCTCACGTTTGCCT 60.822 55.000 0.00 0.00 33.65 4.75
283 284 0.822121 AAACCCCTCACGTTTGCCTC 60.822 55.000 0.00 0.00 32.30 4.70
285 286 2.742372 CCCTCACGTTTGCCTCCG 60.742 66.667 0.00 0.00 0.00 4.63
287 288 2.030562 CTCACGTTTGCCTCCGGT 59.969 61.111 0.00 0.00 0.00 5.28
291 292 0.236449 CACGTTTGCCTCCGGTTTAC 59.764 55.000 0.00 0.00 0.00 2.01
306 307 3.607542 CGGTTTACGGGTGAAAACATGTC 60.608 47.826 0.00 0.00 37.33 3.06
311 312 1.834188 GGGTGAAAACATGTCCGGAT 58.166 50.000 7.81 0.00 0.00 4.18
312 313 1.743394 GGGTGAAAACATGTCCGGATC 59.257 52.381 7.81 0.00 0.00 3.36
313 314 2.432444 GGTGAAAACATGTCCGGATCA 58.568 47.619 7.81 8.44 0.00 2.92
314 315 2.161609 GGTGAAAACATGTCCGGATCAC 59.838 50.000 19.33 19.33 36.01 3.06
319 320 1.561643 ACATGTCCGGATCACTCAGT 58.438 50.000 7.81 2.90 0.00 3.41
329 330 2.034812 GGATCACTCAGTGGACCGATAC 59.965 54.545 4.57 0.00 33.87 2.24
333 334 0.103208 CTCAGTGGACCGATACAGGC 59.897 60.000 0.00 0.00 33.69 4.85
338 339 3.845259 GACCGATACAGGCCCGCA 61.845 66.667 0.00 0.00 33.69 5.69
339 340 4.157120 ACCGATACAGGCCCGCAC 62.157 66.667 0.00 0.00 33.69 5.34
342 343 2.203070 GATACAGGCCCGCACTGG 60.203 66.667 0.00 0.00 40.23 4.00
352 353 1.577328 CCCGCACTGGATGACACAAC 61.577 60.000 0.00 0.00 42.00 3.32
354 355 0.235665 CGCACTGGATGACACAACAC 59.764 55.000 0.00 0.00 0.00 3.32
355 356 1.308047 GCACTGGATGACACAACACA 58.692 50.000 0.00 0.00 0.00 3.72
364 365 5.980698 GATGACACAACACATCCAGATAG 57.019 43.478 0.00 0.00 37.50 2.08
365 366 4.890158 TGACACAACACATCCAGATAGT 57.110 40.909 0.00 0.00 0.00 2.12
366 367 5.993748 TGACACAACACATCCAGATAGTA 57.006 39.130 0.00 0.00 0.00 1.82
367 368 6.544928 TGACACAACACATCCAGATAGTAT 57.455 37.500 0.00 0.00 0.00 2.12
368 369 6.573434 TGACACAACACATCCAGATAGTATC 58.427 40.000 1.55 1.55 0.00 2.24
394 395 1.060308 CGTATGCGGGCGTTTTGAG 59.940 57.895 0.00 0.00 0.00 3.02
400 401 3.733960 GGGCGTTTTGAGGGTCGC 61.734 66.667 0.00 0.00 46.42 5.19
406 407 1.146485 TTTTGAGGGTCGCCGTTGA 59.854 52.632 0.00 0.00 0.00 3.18
413 414 2.032634 GGTCGCCGTTGAAGATGCA 61.033 57.895 0.00 0.00 0.00 3.96
414 415 1.132640 GTCGCCGTTGAAGATGCAC 59.867 57.895 0.00 0.00 0.00 4.57
415 416 2.032634 TCGCCGTTGAAGATGCACC 61.033 57.895 0.00 0.00 0.00 5.01
429 430 3.429043 GCACCAAGCATCAACCATG 57.571 52.632 0.00 0.00 44.79 3.66
474 484 0.176680 GAAAGATGAGCCTCGCCTCA 59.823 55.000 3.37 3.37 45.16 3.86
664 691 4.778427 TCCCTCCTAAGAAAGAAAGAGACC 59.222 45.833 0.00 0.00 0.00 3.85
665 692 4.382147 CCCTCCTAAGAAAGAAAGAGACCG 60.382 50.000 0.00 0.00 0.00 4.79
669 696 0.325272 AGAAAGAAAGAGACCGCCCC 59.675 55.000 0.00 0.00 0.00 5.80
670 697 1.003718 AAAGAAAGAGACCGCCCCG 60.004 57.895 0.00 0.00 0.00 5.73
817 861 1.549037 GCACTGGAAATAACCACCCCA 60.549 52.381 0.00 0.00 35.91 4.96
818 862 2.883026 CACTGGAAATAACCACCCCAA 58.117 47.619 0.00 0.00 35.91 4.12
819 863 2.560981 CACTGGAAATAACCACCCCAAC 59.439 50.000 0.00 0.00 35.91 3.77
820 864 2.176045 CTGGAAATAACCACCCCAACC 58.824 52.381 0.00 0.00 35.91 3.77
821 865 1.203199 TGGAAATAACCACCCCAACCC 60.203 52.381 0.00 0.00 34.77 4.11
951 1001 3.347590 TCGCCTCCTCCTCCTCCA 61.348 66.667 0.00 0.00 0.00 3.86
978 1040 2.646175 CCCCAAAGCCTCGACTCGA 61.646 63.158 0.29 0.29 0.00 4.04
993 1055 0.604243 CTCGATCGATCCCGTCTCCT 60.604 60.000 19.78 0.00 37.05 3.69
996 1058 2.148558 GATCGATCCCGTCTCCTGCC 62.149 65.000 14.76 0.00 37.05 4.85
1089 1383 0.874607 GCGGGATTGTGTAGCTACCG 60.875 60.000 21.01 15.70 42.47 4.02
1091 1385 1.535437 CGGGATTGTGTAGCTACCGTC 60.535 57.143 21.01 12.55 35.47 4.79
1095 1389 3.243134 GGATTGTGTAGCTACCGTCTCTC 60.243 52.174 21.01 9.86 0.00 3.20
1096 1390 2.783609 TGTGTAGCTACCGTCTCTCT 57.216 50.000 21.01 0.00 0.00 3.10
1104 1398 4.244802 CCGTCTCTCTCGGCTCGC 62.245 72.222 0.00 0.00 41.48 5.03
1108 1402 4.567385 CTCTCTCGGCTCGCAGGC 62.567 72.222 0.55 0.55 37.44 4.85
1481 1784 4.927782 AAGCGCGTTGGCCTGACA 62.928 61.111 8.43 0.00 35.02 3.58
1484 1787 4.680237 CGCGTTGGCCTGACAGGA 62.680 66.667 26.25 1.63 37.67 3.86
1592 1895 4.467084 GACGCCATCGCCAGGGAA 62.467 66.667 0.00 0.00 39.84 3.97
1638 1941 2.672714 TCGTTCGGTTCTGATCAACAG 58.327 47.619 0.00 0.00 46.97 3.16
1648 1951 0.756294 TGATCAACAGGACACCACGT 59.244 50.000 0.00 0.00 0.00 4.49
1649 1952 1.270094 TGATCAACAGGACACCACGTC 60.270 52.381 0.00 0.00 44.57 4.34
1650 1953 1.000955 GATCAACAGGACACCACGTCT 59.999 52.381 0.00 0.00 44.70 4.18
1651 1954 1.694844 TCAACAGGACACCACGTCTA 58.305 50.000 0.00 0.00 44.70 2.59
1653 1956 0.313043 AACAGGACACCACGTCTACG 59.687 55.000 0.04 0.04 44.70 3.51
1654 1957 1.443872 CAGGACACCACGTCTACGC 60.444 63.158 1.74 0.00 44.70 4.42
1655 1958 2.503375 GGACACCACGTCTACGCG 60.503 66.667 3.53 3.53 44.70 6.01
1656 1959 2.253452 GACACCACGTCTACGCGT 59.747 61.111 19.17 19.17 46.88 6.01
1657 1960 1.497278 GACACCACGTCTACGCGTA 59.503 57.895 19.40 19.40 43.83 4.42
1682 1988 1.466167 GCGAAATCTGAAGCAGCAGAA 59.534 47.619 11.78 0.00 46.94 3.02
1772 2084 5.590976 AAAGGAGAGGAAGGTGAAAGATT 57.409 39.130 0.00 0.00 0.00 2.40
1964 2291 9.541143 TCATTTCTATGATGCACTATTCGTTAA 57.459 29.630 0.00 0.00 35.87 2.01
1998 2336 0.250727 CTTTTTCTCCCACTGGCCGA 60.251 55.000 0.00 0.00 0.00 5.54
2000 2338 1.415672 TTTTCTCCCACTGGCCGAGT 61.416 55.000 0.00 0.00 34.02 4.18
2049 2387 2.749621 GTTTGGATCGCTCTGTTGGATT 59.250 45.455 0.00 0.00 0.00 3.01
2060 2398 1.673009 GTTGGATTGGTTCGGCGGA 60.673 57.895 7.21 0.00 0.00 5.54
2065 2403 1.379527 GATTGGTTCGGCGGAGAATT 58.620 50.000 7.21 0.00 32.25 2.17
2073 2414 2.040939 TCGGCGGAGAATTATTGGGTA 58.959 47.619 7.21 0.00 0.00 3.69
2080 2421 4.729868 GGAGAATTATTGGGTAGGTGCAT 58.270 43.478 0.00 0.00 0.00 3.96
2085 2426 5.904984 ATTATTGGGTAGGTGCATCTGTA 57.095 39.130 10.55 0.00 0.00 2.74
2087 2428 2.247699 TGGGTAGGTGCATCTGTACT 57.752 50.000 10.55 0.00 0.00 2.73
2091 2432 3.262420 GGTAGGTGCATCTGTACTTGTG 58.738 50.000 10.55 0.00 0.00 3.33
2100 2441 4.779082 GCATCTGTACTTGTGCGTTTATCG 60.779 45.833 0.00 0.00 43.12 2.92
2116 2460 5.730802 CGTTTATCGCGTACAAATTCATGTT 59.269 36.000 5.77 0.00 34.75 2.71
2118 2462 7.201199 CGTTTATCGCGTACAAATTCATGTTTT 60.201 33.333 5.77 0.00 34.75 2.43
2119 2463 5.990745 ATCGCGTACAAATTCATGTTTTG 57.009 34.783 5.77 16.88 39.43 2.44
2120 2464 5.096954 TCGCGTACAAATTCATGTTTTGA 57.903 34.783 22.13 9.61 37.48 2.69
2121 2465 5.143660 TCGCGTACAAATTCATGTTTTGAG 58.856 37.500 22.13 15.74 37.48 3.02
2122 2466 4.201391 CGCGTACAAATTCATGTTTTGAGC 60.201 41.667 22.13 20.47 37.48 4.26
2124 2468 5.174761 GCGTACAAATTCATGTTTTGAGCAA 59.825 36.000 22.13 8.61 37.48 3.91
2125 2469 6.292061 GCGTACAAATTCATGTTTTGAGCAAA 60.292 34.615 22.13 0.00 37.48 3.68
2126 2470 7.616673 CGTACAAATTCATGTTTTGAGCAAAA 58.383 30.769 22.13 4.39 37.48 2.44
2127 2471 8.274939 CGTACAAATTCATGTTTTGAGCAAAAT 58.725 29.630 22.13 7.83 41.64 1.82
2128 2472 9.934190 GTACAAATTCATGTTTTGAGCAAAATT 57.066 25.926 22.13 4.12 41.64 1.82
2130 2474 9.291664 ACAAATTCATGTTTTGAGCAAAATTTG 57.708 25.926 22.13 18.51 41.64 2.32
2131 2475 8.747666 CAAATTCATGTTTTGAGCAAAATTTGG 58.252 29.630 11.11 0.00 41.64 3.28
2132 2476 5.421212 TCATGTTTTGAGCAAAATTTGGC 57.579 34.783 9.71 9.71 41.64 4.52
2133 2477 4.880120 TCATGTTTTGAGCAAAATTTGGCA 59.120 33.333 19.63 0.00 41.64 4.92
2134 2478 4.879104 TGTTTTGAGCAAAATTTGGCAG 57.121 36.364 19.63 0.00 41.64 4.85
2135 2479 3.626670 TGTTTTGAGCAAAATTTGGCAGG 59.373 39.130 19.63 0.00 41.64 4.85
2136 2480 1.881591 TTGAGCAAAATTTGGCAGGC 58.118 45.000 19.63 8.88 0.00 4.85
2137 2481 0.319727 TGAGCAAAATTTGGCAGGCG 60.320 50.000 19.63 0.00 0.00 5.52
2138 2482 0.319813 GAGCAAAATTTGGCAGGCGT 60.320 50.000 19.63 0.00 0.00 5.68
2139 2483 0.319813 AGCAAAATTTGGCAGGCGTC 60.320 50.000 19.63 0.00 0.00 5.19
2140 2484 0.599728 GCAAAATTTGGCAGGCGTCA 60.600 50.000 12.87 0.00 0.00 4.35
2141 2485 1.139163 CAAAATTTGGCAGGCGTCAC 58.861 50.000 0.00 0.00 0.00 3.67
2142 2486 0.033366 AAAATTTGGCAGGCGTCACC 59.967 50.000 0.00 0.00 39.61 4.02
2143 2487 1.815817 AAATTTGGCAGGCGTCACCC 61.816 55.000 0.00 0.00 40.58 4.61
2159 2503 6.490877 CGTCACCCGCAAAAATAATAATTC 57.509 37.500 0.00 0.00 0.00 2.17
2162 2506 4.208253 CACCCGCAAAAATAATAATTCGCC 59.792 41.667 0.00 0.00 0.00 5.54
2192 2536 2.159572 GGTGAAATCGACATGTTTCGGG 60.160 50.000 0.00 0.00 39.58 5.14
2202 2546 0.768622 ATGTTTCGGGTGGGAACTCA 59.231 50.000 0.00 0.00 0.00 3.41
2248 2592 0.036164 TTCTGTGGATTGTGGGTCGG 59.964 55.000 0.00 0.00 0.00 4.79
2254 2598 2.856988 ATTGTGGGTCGGGGTGGT 60.857 61.111 0.00 0.00 0.00 4.16
2279 2623 0.382515 GAAGGATAGACAGCGACGCT 59.617 55.000 18.46 18.46 40.77 5.07
2549 2912 7.592903 GCGATTTTTCTTTAATCCATCTCATCC 59.407 37.037 0.00 0.00 0.00 3.51
2805 3168 3.050275 GCAGGCGTCGGCTTTCTT 61.050 61.111 19.96 0.00 35.88 2.52
2806 3169 1.740296 GCAGGCGTCGGCTTTCTTA 60.740 57.895 19.96 0.00 35.88 2.10
2807 3170 1.967597 GCAGGCGTCGGCTTTCTTAC 61.968 60.000 19.96 1.00 35.88 2.34
2808 3171 1.079336 AGGCGTCGGCTTTCTTACC 60.079 57.895 16.63 0.00 39.81 2.85
2809 3172 1.079336 GGCGTCGGCTTTCTTACCT 60.079 57.895 12.17 0.00 39.81 3.08
2810 3173 1.082679 GGCGTCGGCTTTCTTACCTC 61.083 60.000 12.17 0.00 39.81 3.85
2811 3174 0.108756 GCGTCGGCTTTCTTACCTCT 60.109 55.000 0.00 0.00 35.83 3.69
2812 3175 1.672145 GCGTCGGCTTTCTTACCTCTT 60.672 52.381 0.00 0.00 35.83 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.135170 GGATTGGCTCAAGCTCAAAGC 60.135 52.381 1.46 6.43 42.84 3.51
12 13 2.444421 AGGATTGGCTCAAGCTCAAAG 58.556 47.619 1.46 0.00 41.70 2.77
13 14 2.592102 AGGATTGGCTCAAGCTCAAA 57.408 45.000 1.46 0.00 41.70 2.69
14 15 2.592102 AAGGATTGGCTCAAGCTCAA 57.408 45.000 1.46 5.34 41.70 3.02
15 16 2.559668 CAAAAGGATTGGCTCAAGCTCA 59.440 45.455 1.46 0.00 41.70 4.26
16 17 2.560105 ACAAAAGGATTGGCTCAAGCTC 59.440 45.455 1.46 0.00 41.70 4.09
17 18 2.560105 GACAAAAGGATTGGCTCAAGCT 59.440 45.455 1.46 0.00 41.70 3.74
18 19 2.353109 GGACAAAAGGATTGGCTCAAGC 60.353 50.000 0.00 0.00 41.14 4.01
19 20 3.160269 AGGACAAAAGGATTGGCTCAAG 58.840 45.455 0.00 0.00 0.00 3.02
20 21 3.243359 AGGACAAAAGGATTGGCTCAA 57.757 42.857 0.00 0.00 0.00 3.02
21 22 2.978156 AGGACAAAAGGATTGGCTCA 57.022 45.000 0.00 0.00 0.00 4.26
22 23 3.129462 GCTAAGGACAAAAGGATTGGCTC 59.871 47.826 0.00 0.00 0.00 4.70
23 24 3.092301 GCTAAGGACAAAAGGATTGGCT 58.908 45.455 0.00 0.00 0.00 4.75
24 25 2.825532 TGCTAAGGACAAAAGGATTGGC 59.174 45.455 0.00 0.00 0.00 4.52
25 26 5.665916 AATGCTAAGGACAAAAGGATTGG 57.334 39.130 0.00 0.00 31.14 3.16
26 27 7.153985 TCAAAATGCTAAGGACAAAAGGATTG 58.846 34.615 0.00 0.00 32.47 2.67
27 28 7.301868 TCAAAATGCTAAGGACAAAAGGATT 57.698 32.000 0.00 0.00 33.35 3.01
28 29 6.071165 CCTCAAAATGCTAAGGACAAAAGGAT 60.071 38.462 0.00 0.00 0.00 3.24
29 30 5.243730 CCTCAAAATGCTAAGGACAAAAGGA 59.756 40.000 0.00 0.00 0.00 3.36
30 31 5.473039 CCTCAAAATGCTAAGGACAAAAGG 58.527 41.667 0.00 0.00 0.00 3.11
31 32 5.243730 TCCCTCAAAATGCTAAGGACAAAAG 59.756 40.000 0.00 0.00 0.00 2.27
32 33 5.144100 TCCCTCAAAATGCTAAGGACAAAA 58.856 37.500 0.00 0.00 0.00 2.44
33 34 4.735369 TCCCTCAAAATGCTAAGGACAAA 58.265 39.130 0.00 0.00 0.00 2.83
34 35 4.380843 TCCCTCAAAATGCTAAGGACAA 57.619 40.909 0.00 0.00 0.00 3.18
35 36 4.526970 GATCCCTCAAAATGCTAAGGACA 58.473 43.478 0.00 0.00 0.00 4.02
36 37 3.885901 GGATCCCTCAAAATGCTAAGGAC 59.114 47.826 0.00 0.00 0.00 3.85
37 38 3.527253 TGGATCCCTCAAAATGCTAAGGA 59.473 43.478 9.90 0.00 0.00 3.36
38 39 3.633986 GTGGATCCCTCAAAATGCTAAGG 59.366 47.826 9.90 0.00 0.00 2.69
39 40 4.530875 AGTGGATCCCTCAAAATGCTAAG 58.469 43.478 9.90 0.00 0.00 2.18
40 41 4.591321 AGTGGATCCCTCAAAATGCTAA 57.409 40.909 9.90 0.00 0.00 3.09
41 42 4.591321 AAGTGGATCCCTCAAAATGCTA 57.409 40.909 9.90 0.00 0.00 3.49
42 43 3.463048 AAGTGGATCCCTCAAAATGCT 57.537 42.857 9.90 0.00 0.00 3.79
43 44 4.221482 AGAAAAGTGGATCCCTCAAAATGC 59.779 41.667 9.90 0.00 0.00 3.56
44 45 5.713861 AGAGAAAAGTGGATCCCTCAAAATG 59.286 40.000 9.90 0.00 0.00 2.32
45 46 5.896963 AGAGAAAAGTGGATCCCTCAAAAT 58.103 37.500 9.90 0.00 0.00 1.82
46 47 5.324832 AGAGAAAAGTGGATCCCTCAAAA 57.675 39.130 9.90 0.00 0.00 2.44
47 48 5.316987 GAAGAGAAAAGTGGATCCCTCAAA 58.683 41.667 9.90 0.00 0.00 2.69
48 49 4.263506 GGAAGAGAAAAGTGGATCCCTCAA 60.264 45.833 9.90 0.00 0.00 3.02
49 50 3.264450 GGAAGAGAAAAGTGGATCCCTCA 59.736 47.826 9.90 0.00 0.00 3.86
50 51 3.264450 TGGAAGAGAAAAGTGGATCCCTC 59.736 47.826 9.90 7.31 0.00 4.30
51 52 3.260205 TGGAAGAGAAAAGTGGATCCCT 58.740 45.455 9.90 2.84 0.00 4.20
52 53 3.721087 TGGAAGAGAAAAGTGGATCCC 57.279 47.619 9.90 0.11 0.00 3.85
53 54 3.379688 GCATGGAAGAGAAAAGTGGATCC 59.620 47.826 4.20 4.20 0.00 3.36
54 55 3.379688 GGCATGGAAGAGAAAAGTGGATC 59.620 47.826 0.00 0.00 0.00 3.36
55 56 3.245371 TGGCATGGAAGAGAAAAGTGGAT 60.245 43.478 0.00 0.00 0.00 3.41
56 57 2.108075 TGGCATGGAAGAGAAAAGTGGA 59.892 45.455 0.00 0.00 0.00 4.02
57 58 2.517959 TGGCATGGAAGAGAAAAGTGG 58.482 47.619 0.00 0.00 0.00 4.00
58 59 3.675228 GCATGGCATGGAAGAGAAAAGTG 60.675 47.826 27.48 0.00 0.00 3.16
59 60 2.494870 GCATGGCATGGAAGAGAAAAGT 59.505 45.455 27.48 0.00 0.00 2.66
60 61 2.159142 GGCATGGCATGGAAGAGAAAAG 60.159 50.000 27.48 0.00 0.00 2.27
61 62 1.826720 GGCATGGCATGGAAGAGAAAA 59.173 47.619 27.48 0.00 0.00 2.29
62 63 1.272592 TGGCATGGCATGGAAGAGAAA 60.273 47.619 27.48 0.00 0.00 2.52
63 64 0.332293 TGGCATGGCATGGAAGAGAA 59.668 50.000 27.48 0.00 0.00 2.87
64 65 0.332293 TTGGCATGGCATGGAAGAGA 59.668 50.000 27.48 1.89 0.00 3.10
65 66 1.340248 GATTGGCATGGCATGGAAGAG 59.660 52.381 27.48 2.65 0.00 2.85
66 67 1.342175 TGATTGGCATGGCATGGAAGA 60.342 47.619 27.48 7.20 0.00 2.87
67 68 1.116308 TGATTGGCATGGCATGGAAG 58.884 50.000 27.48 3.82 0.00 3.46
68 69 1.796017 ATGATTGGCATGGCATGGAA 58.204 45.000 27.48 8.45 35.42 3.53
69 70 1.414550 CAATGATTGGCATGGCATGGA 59.585 47.619 27.48 8.86 37.28 3.41
70 71 1.414550 TCAATGATTGGCATGGCATGG 59.585 47.619 27.48 5.66 37.28 3.66
71 72 2.102420 ACTCAATGATTGGCATGGCATG 59.898 45.455 23.96 22.99 37.28 4.06
72 73 2.394632 ACTCAATGATTGGCATGGCAT 58.605 42.857 23.96 12.99 37.28 4.40
73 74 1.855295 ACTCAATGATTGGCATGGCA 58.145 45.000 19.43 19.43 37.28 4.92
74 75 2.973694 AACTCAATGATTGGCATGGC 57.026 45.000 13.29 13.29 37.28 4.40
75 76 4.081309 AGGAAAACTCAATGATTGGCATGG 60.081 41.667 5.20 0.00 37.28 3.66
76 77 5.080969 AGGAAAACTCAATGATTGGCATG 57.919 39.130 5.20 0.00 37.28 4.06
77 78 6.855763 TTAGGAAAACTCAATGATTGGCAT 57.144 33.333 5.20 0.00 39.43 4.40
78 79 6.662865 TTTAGGAAAACTCAATGATTGGCA 57.337 33.333 5.20 0.00 0.00 4.92
79 80 9.822185 ATATTTTAGGAAAACTCAATGATTGGC 57.178 29.630 5.20 0.00 32.37 4.52
119 120 8.944029 ACAACATATATCTCATTGAGCTAATGC 58.056 33.333 8.89 0.00 44.69 3.56
139 140 9.705290 GGTGATTTTGGTAATTTCTAACAACAT 57.295 29.630 0.00 0.00 0.00 2.71
140 141 8.145122 GGGTGATTTTGGTAATTTCTAACAACA 58.855 33.333 0.00 0.00 0.00 3.33
141 142 8.145122 TGGGTGATTTTGGTAATTTCTAACAAC 58.855 33.333 0.00 0.00 0.00 3.32
142 143 8.251383 TGGGTGATTTTGGTAATTTCTAACAA 57.749 30.769 0.00 0.00 0.00 2.83
143 144 7.039363 CCTGGGTGATTTTGGTAATTTCTAACA 60.039 37.037 0.00 0.00 0.00 2.41
144 145 7.320399 CCTGGGTGATTTTGGTAATTTCTAAC 58.680 38.462 0.00 0.00 0.00 2.34
145 146 6.439058 CCCTGGGTGATTTTGGTAATTTCTAA 59.561 38.462 3.97 0.00 0.00 2.10
146 147 5.955355 CCCTGGGTGATTTTGGTAATTTCTA 59.045 40.000 3.97 0.00 0.00 2.10
147 148 4.777366 CCCTGGGTGATTTTGGTAATTTCT 59.223 41.667 3.97 0.00 0.00 2.52
148 149 4.775253 TCCCTGGGTGATTTTGGTAATTTC 59.225 41.667 13.56 0.00 0.00 2.17
149 150 4.757692 TCCCTGGGTGATTTTGGTAATTT 58.242 39.130 13.56 0.00 0.00 1.82
150 151 4.412060 TCCCTGGGTGATTTTGGTAATT 57.588 40.909 13.56 0.00 0.00 1.40
151 152 4.625225 ATCCCTGGGTGATTTTGGTAAT 57.375 40.909 13.56 0.00 0.00 1.89
152 153 4.542525 ACTATCCCTGGGTGATTTTGGTAA 59.457 41.667 13.56 0.00 0.00 2.85
153 154 4.116113 ACTATCCCTGGGTGATTTTGGTA 58.884 43.478 13.56 0.00 0.00 3.25
154 155 2.926329 ACTATCCCTGGGTGATTTTGGT 59.074 45.455 13.56 0.00 0.00 3.67
155 156 3.669939 ACTATCCCTGGGTGATTTTGG 57.330 47.619 13.56 0.00 0.00 3.28
156 157 3.131046 GCAACTATCCCTGGGTGATTTTG 59.869 47.826 13.56 11.60 0.00 2.44
157 158 3.245586 TGCAACTATCCCTGGGTGATTTT 60.246 43.478 13.56 0.00 0.00 1.82
158 159 2.311542 TGCAACTATCCCTGGGTGATTT 59.688 45.455 13.56 0.00 0.00 2.17
159 160 1.922447 TGCAACTATCCCTGGGTGATT 59.078 47.619 13.56 0.59 0.00 2.57
160 161 1.212935 GTGCAACTATCCCTGGGTGAT 59.787 52.381 13.56 2.03 0.00 3.06
161 162 0.618458 GTGCAACTATCCCTGGGTGA 59.382 55.000 13.56 0.60 0.00 4.02
162 163 3.175133 GTGCAACTATCCCTGGGTG 57.825 57.895 13.56 4.13 0.00 4.61
174 175 2.454055 GTGTGCTTCTGAAAGTGCAAC 58.546 47.619 4.62 3.29 43.19 4.17
175 176 1.063912 CGTGTGCTTCTGAAAGTGCAA 59.936 47.619 4.62 0.00 43.19 4.08
176 177 0.657312 CGTGTGCTTCTGAAAGTGCA 59.343 50.000 0.00 0.00 40.65 4.57
177 178 0.937304 TCGTGTGCTTCTGAAAGTGC 59.063 50.000 0.00 0.00 34.79 4.40
178 179 1.070309 GCTCGTGTGCTTCTGAAAGTG 60.070 52.381 0.00 0.00 34.79 3.16
179 180 1.221414 GCTCGTGTGCTTCTGAAAGT 58.779 50.000 0.00 0.00 34.79 2.66
180 181 0.514691 GGCTCGTGTGCTTCTGAAAG 59.485 55.000 0.00 0.00 35.47 2.62
181 182 1.221466 CGGCTCGTGTGCTTCTGAAA 61.221 55.000 0.00 0.00 0.00 2.69
182 183 1.664649 CGGCTCGTGTGCTTCTGAA 60.665 57.895 0.00 0.00 0.00 3.02
183 184 2.049156 CGGCTCGTGTGCTTCTGA 60.049 61.111 0.00 0.00 0.00 3.27
184 185 3.114616 CCGGCTCGTGTGCTTCTG 61.115 66.667 0.00 0.00 0.00 3.02
185 186 4.379243 CCCGGCTCGTGTGCTTCT 62.379 66.667 0.00 0.00 0.00 2.85
203 204 1.051556 TTGGCCCAAGAAAACACCCC 61.052 55.000 0.00 0.00 0.00 4.95
227 228 3.113979 CCCAAACCCGCGTACGAC 61.114 66.667 21.65 9.57 43.93 4.34
230 231 1.301953 AACTCCCAAACCCGCGTAC 60.302 57.895 4.92 0.00 0.00 3.67
231 232 1.301874 CAACTCCCAAACCCGCGTA 60.302 57.895 4.92 0.00 0.00 4.42
235 236 1.964373 CGGACAACTCCCAAACCCG 60.964 63.158 0.00 0.00 31.93 5.28
261 262 1.441732 GCAAACGTGAGGGGTTTCGT 61.442 55.000 0.00 0.00 35.53 3.85
263 264 0.822121 AGGCAAACGTGAGGGGTTTC 60.822 55.000 0.00 0.00 35.53 2.78
266 267 2.430367 GAGGCAAACGTGAGGGGT 59.570 61.111 0.00 0.00 0.00 4.95
285 286 3.304861 GGACATGTTTTCACCCGTAAACC 60.305 47.826 0.00 0.00 32.95 3.27
287 288 2.548904 CGGACATGTTTTCACCCGTAAA 59.451 45.455 12.03 0.00 36.55 2.01
291 292 0.604243 TCCGGACATGTTTTCACCCG 60.604 55.000 13.02 13.02 38.99 5.28
295 296 3.244387 TGAGTGATCCGGACATGTTTTCA 60.244 43.478 6.12 0.85 0.00 2.69
301 302 1.472201 CCACTGAGTGATCCGGACATG 60.472 57.143 15.33 2.14 35.23 3.21
303 304 0.251608 TCCACTGAGTGATCCGGACA 60.252 55.000 15.33 4.15 35.23 4.02
306 307 1.517832 GGTCCACTGAGTGATCCGG 59.482 63.158 15.33 0.00 35.23 5.14
311 312 2.092323 CTGTATCGGTCCACTGAGTGA 58.908 52.381 15.33 0.00 35.23 3.41
312 313 1.135139 CCTGTATCGGTCCACTGAGTG 59.865 57.143 5.42 5.42 34.27 3.51
313 314 1.475403 CCTGTATCGGTCCACTGAGT 58.525 55.000 0.00 0.00 34.27 3.41
314 315 0.103208 GCCTGTATCGGTCCACTGAG 59.897 60.000 0.00 0.00 34.27 3.35
329 330 4.100084 TCATCCAGTGCGGGCCTG 62.100 66.667 7.41 7.41 34.36 4.85
333 334 1.302431 TTGTGTCATCCAGTGCGGG 60.302 57.895 0.00 0.00 34.36 6.13
342 343 5.423015 ACTATCTGGATGTGTTGTGTCATC 58.577 41.667 0.00 0.00 39.49 2.92
352 353 3.751698 TCGGACGATACTATCTGGATGTG 59.248 47.826 0.00 0.00 0.00 3.21
354 355 4.724303 GTTCGGACGATACTATCTGGATG 58.276 47.826 0.00 0.00 0.00 3.51
377 378 1.427819 CCTCAAAACGCCCGCATAC 59.572 57.895 0.00 0.00 0.00 2.39
394 395 2.750888 GCATCTTCAACGGCGACCC 61.751 63.158 16.62 0.00 0.00 4.46
400 401 0.109597 GCTTGGTGCATCTTCAACGG 60.110 55.000 0.00 0.00 42.31 4.44
401 402 3.389741 GCTTGGTGCATCTTCAACG 57.610 52.632 0.00 0.00 42.31 4.10
447 457 4.261994 GCGAGGCTCATCTTTCTTCTATCT 60.262 45.833 15.95 0.00 0.00 1.98
452 462 1.134551 AGGCGAGGCTCATCTTTCTTC 60.135 52.381 15.95 0.00 0.00 2.87
474 484 1.107538 TCTGCTTCGTAGGCGGCTAT 61.108 55.000 22.63 0.00 38.89 2.97
671 698 4.039357 CTGTGCTGTGCTGCCTGC 62.039 66.667 0.00 5.20 43.25 4.85
951 1001 1.229496 GGCTTTGGGGAAATGGGGT 60.229 57.895 0.00 0.00 0.00 4.95
978 1040 2.203771 GGCAGGAGACGGGATCGAT 61.204 63.158 0.00 0.00 40.11 3.59
987 1049 4.803426 CGAGCGTGGGCAGGAGAC 62.803 72.222 0.00 0.00 43.41 3.36
1077 1371 2.630158 GAGAGAGACGGTAGCTACACA 58.370 52.381 24.75 0.00 0.00 3.72
1080 1374 1.219646 CCGAGAGAGACGGTAGCTAC 58.780 60.000 15.88 15.88 44.57 3.58
1089 1383 2.407210 CTGCGAGCCGAGAGAGAC 59.593 66.667 0.00 0.00 0.00 3.36
1091 1385 4.567385 GCCTGCGAGCCGAGAGAG 62.567 72.222 0.00 0.00 0.00 3.20
1104 1398 3.254654 CGCCATGACGTACGCCTG 61.255 66.667 16.72 10.10 0.00 4.85
1108 1402 3.913573 GCTGCGCCATGACGTACG 61.914 66.667 15.01 15.01 34.88 3.67
1109 1403 3.913573 CGCTGCGCCATGACGTAC 61.914 66.667 9.88 0.00 34.88 3.67
1295 1592 3.771160 GCGGGCGAAGAGGAAGGA 61.771 66.667 0.00 0.00 0.00 3.36
1472 1775 2.989639 CGGAATCCTGTCAGGCCA 59.010 61.111 14.64 0.00 34.61 5.36
1481 1784 4.473520 CACCGGCAGCGGAATCCT 62.474 66.667 8.49 0.00 0.00 3.24
1649 1952 2.941964 ATTTCGCCGGGTACGCGTAG 62.942 60.000 27.61 20.82 39.43 3.51
1650 1953 2.935122 GATTTCGCCGGGTACGCGTA 62.935 60.000 27.61 16.41 39.43 4.42
1651 1954 4.440127 ATTTCGCCGGGTACGCGT 62.440 61.111 27.61 19.17 39.43 6.01
1653 1956 2.202837 AGATTTCGCCGGGTACGC 60.203 61.111 2.18 0.00 39.22 4.42
1654 1957 0.458889 TTCAGATTTCGCCGGGTACG 60.459 55.000 2.18 0.00 40.55 3.67
1655 1958 1.287425 CTTCAGATTTCGCCGGGTAC 58.713 55.000 2.18 0.00 0.00 3.34
1656 1959 0.461339 GCTTCAGATTTCGCCGGGTA 60.461 55.000 2.18 0.00 0.00 3.69
1657 1960 1.745489 GCTTCAGATTTCGCCGGGT 60.745 57.895 2.18 0.00 0.00 5.28
1682 1988 5.130705 AGGAAAGAAAGGAAAAGAGTGGT 57.869 39.130 0.00 0.00 0.00 4.16
1954 2281 7.331193 AGGTTGACAGCTAAAGTTAACGAATAG 59.669 37.037 0.00 5.63 36.63 1.73
1964 2291 5.299531 GGAGAAAAAGGTTGACAGCTAAAGT 59.700 40.000 0.00 0.00 0.00 2.66
1998 2336 4.256920 GTTGAGCTGTCATGGACAATACT 58.743 43.478 0.00 0.00 42.26 2.12
2000 2338 3.008923 TGGTTGAGCTGTCATGGACAATA 59.991 43.478 0.00 0.00 42.26 1.90
2049 2387 2.285083 CAATAATTCTCCGCCGAACCA 58.715 47.619 0.00 0.00 0.00 3.67
2060 2398 5.103940 ACAGATGCACCTACCCAATAATTCT 60.104 40.000 0.00 0.00 0.00 2.40
2065 2403 4.295201 AGTACAGATGCACCTACCCAATA 58.705 43.478 0.00 0.00 0.00 1.90
2073 2414 1.813513 GCACAAGTACAGATGCACCT 58.186 50.000 9.58 0.00 38.00 4.00
2100 2441 4.679197 TGCTCAAAACATGAATTTGTACGC 59.321 37.500 20.27 19.68 37.67 4.42
2116 2460 2.220313 GCCTGCCAAATTTTGCTCAAA 58.780 42.857 14.62 0.00 0.00 2.69
2118 2462 0.319727 CGCCTGCCAAATTTTGCTCA 60.320 50.000 14.62 3.47 0.00 4.26
2119 2463 0.319813 ACGCCTGCCAAATTTTGCTC 60.320 50.000 14.62 4.34 0.00 4.26
2120 2464 0.319813 GACGCCTGCCAAATTTTGCT 60.320 50.000 14.62 0.00 0.00 3.91
2121 2465 0.599728 TGACGCCTGCCAAATTTTGC 60.600 50.000 7.29 7.29 0.00 3.68
2122 2466 1.139163 GTGACGCCTGCCAAATTTTG 58.861 50.000 1.99 1.99 0.00 2.44
2124 2468 1.665442 GGTGACGCCTGCCAAATTT 59.335 52.632 0.00 0.00 0.00 1.82
2125 2469 2.275380 GGGTGACGCCTGCCAAATT 61.275 57.895 4.75 0.00 37.43 1.82
2126 2470 2.676471 GGGTGACGCCTGCCAAAT 60.676 61.111 4.75 0.00 37.43 2.32
2137 2481 5.051973 GCGAATTATTATTTTTGCGGGTGAC 60.052 40.000 0.00 0.00 0.00 3.67
2138 2482 5.038033 GCGAATTATTATTTTTGCGGGTGA 58.962 37.500 0.00 0.00 0.00 4.02
2139 2483 4.208253 GGCGAATTATTATTTTTGCGGGTG 59.792 41.667 0.00 0.00 0.00 4.61
2140 2484 4.142138 TGGCGAATTATTATTTTTGCGGGT 60.142 37.500 0.00 0.00 0.00 5.28
2141 2485 4.363999 TGGCGAATTATTATTTTTGCGGG 58.636 39.130 0.00 0.00 0.00 6.13
2142 2486 4.444056 CCTGGCGAATTATTATTTTTGCGG 59.556 41.667 0.00 0.00 0.00 5.69
2143 2487 4.085107 GCCTGGCGAATTATTATTTTTGCG 60.085 41.667 1.35 0.00 0.00 4.85
2144 2488 5.328886 GCCTGGCGAATTATTATTTTTGC 57.671 39.130 1.35 0.00 0.00 3.68
2162 2506 1.593006 GTCGATTTCACCATACGCCTG 59.407 52.381 0.00 0.00 0.00 4.85
2192 2536 1.014564 GTGCTACGCTGAGTTCCCAC 61.015 60.000 0.00 0.00 0.00 4.61
2202 2546 2.742372 CGCCTTTGGTGCTACGCT 60.742 61.111 0.00 0.00 0.00 5.07
2248 2592 1.906105 TATCCTTCGTGGCACCACCC 61.906 60.000 12.86 0.00 43.49 4.61
2254 2598 0.175760 GCTGTCTATCCTTCGTGGCA 59.824 55.000 0.00 0.00 35.26 4.92
2267 2611 2.694829 AAAACGGAGCGTCGCTGTCT 62.695 55.000 27.16 0.16 39.99 3.41
2279 2623 0.878523 CGGTCTGTGCAGAAAACGGA 60.879 55.000 3.19 0.00 39.48 4.69
2788 3151 1.740296 TAAGAAAGCCGACGCCTGC 60.740 57.895 0.00 0.00 34.57 4.85
2789 3152 1.359459 GGTAAGAAAGCCGACGCCTG 61.359 60.000 0.00 0.00 34.57 4.85
2790 3153 1.079336 GGTAAGAAAGCCGACGCCT 60.079 57.895 0.00 0.00 34.57 5.52
2791 3154 1.079336 AGGTAAGAAAGCCGACGCC 60.079 57.895 0.00 0.00 34.57 5.68
2792 3155 0.108756 AGAGGTAAGAAAGCCGACGC 60.109 55.000 0.00 0.00 0.00 5.19
2793 3156 2.365408 AAGAGGTAAGAAAGCCGACG 57.635 50.000 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.