Multiple sequence alignment - TraesCS6A01G184700

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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 TraesCS6A01G184700 chr6A 100.000 1573 0 0 1 1573 215595021 215596593 0.000000e+00 2905
1 TraesCS6A01G184700 chr6A 100.000 549 0 0 1811 2359 215596831 215597379 0.000000e+00 1014
2 TraesCS6A01G184700 chr5D 98.565 1115 15 1 460 1573 503225213 503224099 0.000000e+00 1969
3 TraesCS6A01G184700 chr5D 98.206 1115 19 1 460 1573 503271332 503272446 0.000000e+00 1947
4 TraesCS6A01G184700 chr5D 98.027 1115 20 2 460 1573 503235529 503234416 0.000000e+00 1936
5 TraesCS6A01G184700 chr5D 97.632 549 13 0 1811 2359 503224050 503223502 0.000000e+00 942
6 TraesCS6A01G184700 chr5D 97.863 468 9 1 1 468 6184796 6184330 0.000000e+00 808
7 TraesCS6A01G184700 chr5D 97.863 468 9 1 1 468 483807440 483806974 0.000000e+00 808
8 TraesCS6A01G184700 chr5D 98.060 464 9 0 1 464 503283444 503283907 0.000000e+00 808
9 TraesCS6A01G184700 chr3B 98.475 1115 16 1 460 1573 101918174 101917060 0.000000e+00 1964
10 TraesCS6A01G184700 chr3B 97.814 549 12 0 1811 2359 101917011 101916463 0.000000e+00 948
11 TraesCS6A01G184700 chr3D 98.386 1115 17 1 460 1573 24164120 24165234 0.000000e+00 1958
12 TraesCS6A01G184700 chr3D 98.291 468 7 1 1 468 598874948 598875414 0.000000e+00 819
13 TraesCS6A01G184700 chr3A 98.386 1115 17 1 460 1573 66010627 66011741 0.000000e+00 1958
14 TraesCS6A01G184700 chr3A 97.632 549 13 0 1811 2359 495095330 495094782 0.000000e+00 942
15 TraesCS6A01G184700 chr2B 98.386 1115 17 1 460 1573 449213281 449212167 0.000000e+00 1958
16 TraesCS6A01G184700 chr2B 98.117 1115 20 1 460 1573 474915437 474914323 0.000000e+00 1941
17 TraesCS6A01G184700 chr2B 97.632 549 13 0 1811 2359 449212118 449211570 0.000000e+00 942
18 TraesCS6A01G184700 chr1A 98.027 1115 21 1 460 1573 278527245 278528359 0.000000e+00 1936
19 TraesCS6A01G184700 chr1A 97.632 549 13 0 1811 2359 278531150 278531698 0.000000e+00 942
20 TraesCS6A01G184700 chr1D 97.996 549 11 0 1811 2359 254389257 254389805 0.000000e+00 953
21 TraesCS6A01G184700 chr1D 97.650 468 10 1 1 468 254402252 254402718 0.000000e+00 802
22 TraesCS6A01G184700 chr2D 97.802 546 12 0 1811 2356 628288321 628288866 0.000000e+00 942
23 TraesCS6A01G184700 chrUn 97.450 549 14 0 1811 2359 216512774 216513322 0.000000e+00 937
24 TraesCS6A01G184700 chrUn 97.450 549 14 0 1811 2359 286270609 286270061 0.000000e+00 937
25 TraesCS6A01G184700 chrUn 97.222 468 11 2 1 468 261572966 261572501 0.000000e+00 791
26 TraesCS6A01G184700 chr6D 98.077 468 8 1 1 468 45515425 45514959 0.000000e+00 813
27 TraesCS6A01G184700 chr5A 97.845 464 10 0 1 464 607203936 607203473 0.000000e+00 802
28 TraesCS6A01G184700 chr4A 97.028 471 13 1 1 471 309510977 309510508 0.000000e+00 791
29 TraesCS6A01G184700 chr4D 97.177 248 7 0 1326 1573 490365223 490364976 1.010000e-113 420
30 TraesCS6A01G184700 chr4D 96.581 117 4 0 1257 1373 163073919 163074035 6.650000e-46 195


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 TraesCS6A01G184700 chr6A 215595021 215597379 2358 False 1959.5 2905 100.0000 1 2359 2 chr6A.!!$F1 2358
1 TraesCS6A01G184700 chr5D 503271332 503272446 1114 False 1947.0 1947 98.2060 460 1573 1 chr5D.!!$F1 1113
2 TraesCS6A01G184700 chr5D 503234416 503235529 1113 True 1936.0 1936 98.0270 460 1573 1 chr5D.!!$R3 1113
3 TraesCS6A01G184700 chr5D 503223502 503225213 1711 True 1455.5 1969 98.0985 460 2359 2 chr5D.!!$R4 1899
4 TraesCS6A01G184700 chr3B 101916463 101918174 1711 True 1456.0 1964 98.1445 460 2359 2 chr3B.!!$R1 1899
5 TraesCS6A01G184700 chr3D 24164120 24165234 1114 False 1958.0 1958 98.3860 460 1573 1 chr3D.!!$F1 1113
6 TraesCS6A01G184700 chr3A 66010627 66011741 1114 False 1958.0 1958 98.3860 460 1573 1 chr3A.!!$F1 1113
7 TraesCS6A01G184700 chr3A 495094782 495095330 548 True 942.0 942 97.6320 1811 2359 1 chr3A.!!$R1 548
8 TraesCS6A01G184700 chr2B 474914323 474915437 1114 True 1941.0 1941 98.1170 460 1573 1 chr2B.!!$R1 1113
9 TraesCS6A01G184700 chr2B 449211570 449213281 1711 True 1450.0 1958 98.0090 460 2359 2 chr2B.!!$R2 1899
10 TraesCS6A01G184700 chr1A 278527245 278531698 4453 False 1439.0 1936 97.8295 460 2359 2 chr1A.!!$F1 1899
11 TraesCS6A01G184700 chr1D 254389257 254389805 548 False 953.0 953 97.9960 1811 2359 1 chr1D.!!$F1 548
12 TraesCS6A01G184700 chr2D 628288321 628288866 545 False 942.0 942 97.8020 1811 2356 1 chr2D.!!$F1 545
13 TraesCS6A01G184700 chrUn 216512774 216513322 548 False 937.0 937 97.4500 1811 2359 1 chrUn.!!$F1 548
14 TraesCS6A01G184700 chrUn 286270061 286270609 548 True 937.0 937 97.4500 1811 2359 1 chrUn.!!$R2 548

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
185 186 0.393077 ATTCCCGTAGCGAGAATGGG 59.607 55.0 0.0 3.58 43.6 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 4791 2.808202 CGGAGTGGGGATAGCATTTCTG 60.808 54.545 0.0 0.0 0.0 3.02 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.349488 CGGTTTTGAAGGAGTTGAACC 57.651 47.619 0.00 0.00 34.61 3.62
21 22 2.685897 CGGTTTTGAAGGAGTTGAACCA 59.314 45.455 0.00 0.00 37.07 3.67
22 23 3.243068 CGGTTTTGAAGGAGTTGAACCAG 60.243 47.826 0.00 0.00 37.07 4.00
23 24 3.068165 GGTTTTGAAGGAGTTGAACCAGG 59.932 47.826 0.00 0.00 37.18 4.45
24 25 3.943671 TTTGAAGGAGTTGAACCAGGA 57.056 42.857 0.00 0.00 0.00 3.86
25 26 4.453480 TTTGAAGGAGTTGAACCAGGAT 57.547 40.909 0.00 0.00 0.00 3.24
26 27 4.453480 TTGAAGGAGTTGAACCAGGATT 57.547 40.909 0.00 0.00 0.00 3.01
27 28 4.453480 TGAAGGAGTTGAACCAGGATTT 57.547 40.909 0.00 0.00 0.00 2.17
28 29 4.398319 TGAAGGAGTTGAACCAGGATTTC 58.602 43.478 0.00 0.00 0.00 2.17
29 30 3.441500 AGGAGTTGAACCAGGATTTCC 57.558 47.619 0.00 0.00 0.00 3.13
30 31 2.716424 AGGAGTTGAACCAGGATTTCCA 59.284 45.455 0.00 0.00 38.89 3.53
31 32 3.140144 AGGAGTTGAACCAGGATTTCCAA 59.860 43.478 0.00 0.00 38.89 3.53
32 33 3.895041 GGAGTTGAACCAGGATTTCCAAA 59.105 43.478 0.00 0.00 38.89 3.28
33 34 4.528206 GGAGTTGAACCAGGATTTCCAAAT 59.472 41.667 0.00 0.00 38.89 2.32
34 35 5.473039 GAGTTGAACCAGGATTTCCAAATG 58.527 41.667 0.00 0.00 38.89 2.32
35 36 4.284234 AGTTGAACCAGGATTTCCAAATGG 59.716 41.667 0.00 0.83 38.89 3.16
36 37 4.125124 TGAACCAGGATTTCCAAATGGA 57.875 40.909 9.66 0.00 43.73 3.41
37 38 4.686891 TGAACCAGGATTTCCAAATGGAT 58.313 39.130 2.38 0.00 44.98 3.41
38 39 5.836705 TGAACCAGGATTTCCAAATGGATA 58.163 37.500 2.38 0.00 44.98 2.59
39 40 5.893255 TGAACCAGGATTTCCAAATGGATAG 59.107 40.000 2.38 0.00 44.98 2.08
40 41 4.808042 ACCAGGATTTCCAAATGGATAGG 58.192 43.478 2.38 0.00 44.98 2.57
41 42 4.482025 ACCAGGATTTCCAAATGGATAGGA 59.518 41.667 2.38 0.00 44.98 2.94
42 43 5.136737 ACCAGGATTTCCAAATGGATAGGAT 59.863 40.000 2.38 0.00 44.98 3.24
43 44 6.335311 ACCAGGATTTCCAAATGGATAGGATA 59.665 38.462 2.38 0.00 44.98 2.59
44 45 6.888632 CCAGGATTTCCAAATGGATAGGATAG 59.111 42.308 2.38 0.00 44.98 2.08
45 46 6.888632 CAGGATTTCCAAATGGATAGGATAGG 59.111 42.308 2.38 0.00 44.98 2.57
46 47 6.011274 AGGATTTCCAAATGGATAGGATAGGG 60.011 42.308 2.38 0.00 44.98 3.53
47 48 6.240586 GGATTTCCAAATGGATAGGATAGGGT 60.241 42.308 2.38 0.00 44.98 4.34
48 49 7.036863 GGATTTCCAAATGGATAGGATAGGGTA 60.037 40.741 2.38 0.00 44.98 3.69
49 50 7.905144 TTTCCAAATGGATAGGATAGGGTAT 57.095 36.000 2.38 0.00 44.98 2.73
50 51 7.905144 TTCCAAATGGATAGGATAGGGTATT 57.095 36.000 2.38 0.00 44.98 1.89
51 52 7.905144 TCCAAATGGATAGGATAGGGTATTT 57.095 36.000 0.00 0.00 39.78 1.40
52 53 7.928873 TCCAAATGGATAGGATAGGGTATTTC 58.071 38.462 0.00 0.00 39.78 2.17
53 54 7.744068 TCCAAATGGATAGGATAGGGTATTTCT 59.256 37.037 0.00 0.00 39.78 2.52
54 55 9.057911 CCAAATGGATAGGATAGGGTATTTCTA 57.942 37.037 0.00 0.00 37.39 2.10
89 90 9.729281 AGATAATCCAAATGCAAAAATTTGTCT 57.271 25.926 9.10 3.33 43.17 3.41
92 93 8.454570 AATCCAAATGCAAAAATTTGTCTTCT 57.545 26.923 9.10 0.00 43.17 2.85
93 94 9.558396 AATCCAAATGCAAAAATTTGTCTTCTA 57.442 25.926 9.10 0.00 43.17 2.10
94 95 8.954950 TCCAAATGCAAAAATTTGTCTTCTAA 57.045 26.923 9.10 0.00 43.17 2.10
95 96 9.388506 TCCAAATGCAAAAATTTGTCTTCTAAA 57.611 25.926 9.10 0.00 43.17 1.85
100 101 8.207521 TGCAAAAATTTGTCTTCTAAAAAGGG 57.792 30.769 7.64 0.00 40.24 3.95
101 102 8.043710 TGCAAAAATTTGTCTTCTAAAAAGGGA 58.956 29.630 7.64 0.00 40.24 4.20
102 103 8.888716 GCAAAAATTTGTCTTCTAAAAAGGGAA 58.111 29.630 7.64 0.00 40.24 3.97
121 122 7.678947 AGGGAAATATTGAATGAATAGAGCG 57.321 36.000 0.00 0.00 29.78 5.03
122 123 7.227156 AGGGAAATATTGAATGAATAGAGCGT 58.773 34.615 0.00 0.00 29.78 5.07
123 124 8.375506 AGGGAAATATTGAATGAATAGAGCGTA 58.624 33.333 0.00 0.00 29.78 4.42
124 125 8.999431 GGGAAATATTGAATGAATAGAGCGTAA 58.001 33.333 0.00 0.00 29.78 3.18
131 132 8.716646 TTGAATGAATAGAGCGTAAATTCTGA 57.283 30.769 0.00 0.00 32.12 3.27
132 133 8.716646 TGAATGAATAGAGCGTAAATTCTGAA 57.283 30.769 0.00 0.00 32.12 3.02
133 134 9.161629 TGAATGAATAGAGCGTAAATTCTGAAA 57.838 29.630 0.00 0.00 32.12 2.69
134 135 9.427127 GAATGAATAGAGCGTAAATTCTGAAAC 57.573 33.333 0.00 0.00 32.12 2.78
135 136 8.723942 ATGAATAGAGCGTAAATTCTGAAACT 57.276 30.769 0.00 0.00 32.12 2.66
136 137 8.547967 TGAATAGAGCGTAAATTCTGAAACTT 57.452 30.769 0.00 0.00 32.12 2.66
137 138 8.999431 TGAATAGAGCGTAAATTCTGAAACTTT 58.001 29.630 0.00 0.00 32.12 2.66
138 139 9.267096 GAATAGAGCGTAAATTCTGAAACTTTG 57.733 33.333 0.00 0.00 0.00 2.77
139 140 6.002062 AGAGCGTAAATTCTGAAACTTTGG 57.998 37.500 0.00 0.00 0.00 3.28
140 141 5.531287 AGAGCGTAAATTCTGAAACTTTGGT 59.469 36.000 0.00 0.00 0.00 3.67
141 142 6.708949 AGAGCGTAAATTCTGAAACTTTGGTA 59.291 34.615 0.00 0.00 0.00 3.25
142 143 7.390718 AGAGCGTAAATTCTGAAACTTTGGTAT 59.609 33.333 0.00 0.00 0.00 2.73
143 144 7.882179 AGCGTAAATTCTGAAACTTTGGTATT 58.118 30.769 0.00 0.00 0.00 1.89
144 145 8.357402 AGCGTAAATTCTGAAACTTTGGTATTT 58.643 29.630 0.00 0.00 0.00 1.40
145 146 8.635983 GCGTAAATTCTGAAACTTTGGTATTTC 58.364 33.333 0.00 0.00 35.73 2.17
146 147 9.893305 CGTAAATTCTGAAACTTTGGTATTTCT 57.107 29.630 0.00 0.00 36.09 2.52
155 156 9.594478 TGAAACTTTGGTATTTCTTTTTCTTCC 57.406 29.630 0.00 0.00 36.09 3.46
156 157 8.642908 AAACTTTGGTATTTCTTTTTCTTCCG 57.357 30.769 0.00 0.00 0.00 4.30
157 158 6.745116 ACTTTGGTATTTCTTTTTCTTCCGG 58.255 36.000 0.00 0.00 0.00 5.14
158 159 6.548251 ACTTTGGTATTTCTTTTTCTTCCGGA 59.452 34.615 0.00 0.00 0.00 5.14
159 160 5.952526 TGGTATTTCTTTTTCTTCCGGAC 57.047 39.130 1.83 0.00 0.00 4.79
160 161 5.378332 TGGTATTTCTTTTTCTTCCGGACA 58.622 37.500 1.83 0.00 0.00 4.02
161 162 5.828859 TGGTATTTCTTTTTCTTCCGGACAA 59.171 36.000 1.83 0.00 0.00 3.18
162 163 6.321690 TGGTATTTCTTTTTCTTCCGGACAAA 59.678 34.615 1.83 3.21 0.00 2.83
163 164 7.147880 TGGTATTTCTTTTTCTTCCGGACAAAA 60.148 33.333 1.83 10.15 0.00 2.44
164 165 7.870954 GGTATTTCTTTTTCTTCCGGACAAAAT 59.129 33.333 17.37 10.95 0.00 1.82
165 166 9.902196 GTATTTCTTTTTCTTCCGGACAAAATA 57.098 29.630 17.37 9.81 0.00 1.40
167 168 9.996554 ATTTCTTTTTCTTCCGGACAAAATAAT 57.003 25.926 17.37 14.36 0.00 1.28
168 169 9.825109 TTTCTTTTTCTTCCGGACAAAATAATT 57.175 25.926 17.37 0.00 0.00 1.40
169 170 9.471084 TTCTTTTTCTTCCGGACAAAATAATTC 57.529 29.630 17.37 0.00 0.00 2.17
170 171 8.085909 TCTTTTTCTTCCGGACAAAATAATTCC 58.914 33.333 17.37 0.00 0.00 3.01
171 172 5.907866 TTCTTCCGGACAAAATAATTCCC 57.092 39.130 1.83 0.00 0.00 3.97
172 173 3.942748 TCTTCCGGACAAAATAATTCCCG 59.057 43.478 1.83 0.00 36.98 5.14
173 174 3.353370 TCCGGACAAAATAATTCCCGT 57.647 42.857 0.00 0.00 35.61 5.28
174 175 4.484537 TCCGGACAAAATAATTCCCGTA 57.515 40.909 0.00 0.00 35.61 4.02
175 176 4.444536 TCCGGACAAAATAATTCCCGTAG 58.555 43.478 0.00 0.00 35.61 3.51
176 177 3.002965 CCGGACAAAATAATTCCCGTAGC 59.997 47.826 0.00 0.00 35.61 3.58
177 178 3.302870 CGGACAAAATAATTCCCGTAGCG 60.303 47.826 0.00 0.00 33.02 4.26
178 179 3.872771 GGACAAAATAATTCCCGTAGCGA 59.127 43.478 0.00 0.00 0.00 4.93
179 180 4.025145 GGACAAAATAATTCCCGTAGCGAG 60.025 45.833 0.00 0.00 0.00 5.03
180 181 4.761975 ACAAAATAATTCCCGTAGCGAGA 58.238 39.130 0.00 0.00 0.00 4.04
181 182 5.180271 ACAAAATAATTCCCGTAGCGAGAA 58.820 37.500 0.00 0.00 0.00 2.87
182 183 5.820947 ACAAAATAATTCCCGTAGCGAGAAT 59.179 36.000 0.00 0.00 0.00 2.40
183 184 5.924475 AAATAATTCCCGTAGCGAGAATG 57.076 39.130 0.00 0.00 30.80 2.67
184 185 2.240493 AATTCCCGTAGCGAGAATGG 57.760 50.000 0.00 0.00 30.80 3.16
185 186 0.393077 ATTCCCGTAGCGAGAATGGG 59.607 55.000 0.00 3.58 43.60 4.00
186 187 3.533720 CCCGTAGCGAGAATGGGA 58.466 61.111 3.86 0.00 44.84 4.37
187 188 0.469331 TCCCGTAGCGAGAATGGGAT 60.469 55.000 7.72 0.00 45.49 3.85
188 189 0.393077 CCCGTAGCGAGAATGGGATT 59.607 55.000 3.86 0.00 44.84 3.01
189 190 1.202651 CCCGTAGCGAGAATGGGATTT 60.203 52.381 3.86 0.00 44.84 2.17
190 191 2.135933 CCGTAGCGAGAATGGGATTTC 58.864 52.381 0.00 0.00 0.00 2.17
191 192 2.135933 CGTAGCGAGAATGGGATTTCC 58.864 52.381 0.00 0.00 0.00 3.13
201 202 2.869101 TGGGATTTCCACAACGATCA 57.131 45.000 0.00 0.00 41.46 2.92
202 203 3.364460 TGGGATTTCCACAACGATCAT 57.636 42.857 0.00 0.00 41.46 2.45
203 204 4.495690 TGGGATTTCCACAACGATCATA 57.504 40.909 0.00 0.00 41.46 2.15
204 205 4.849518 TGGGATTTCCACAACGATCATAA 58.150 39.130 0.00 0.00 41.46 1.90
205 206 5.257262 TGGGATTTCCACAACGATCATAAA 58.743 37.500 0.00 0.00 41.46 1.40
206 207 5.124776 TGGGATTTCCACAACGATCATAAAC 59.875 40.000 0.00 0.00 41.46 2.01
207 208 5.449999 GGGATTTCCACAACGATCATAAACC 60.450 44.000 0.00 0.00 37.91 3.27
208 209 5.449999 GGATTTCCACAACGATCATAAACCC 60.450 44.000 0.00 0.00 35.64 4.11
209 210 3.992943 TCCACAACGATCATAAACCCT 57.007 42.857 0.00 0.00 0.00 4.34
210 211 4.295141 TCCACAACGATCATAAACCCTT 57.705 40.909 0.00 0.00 0.00 3.95
211 212 4.258543 TCCACAACGATCATAAACCCTTC 58.741 43.478 0.00 0.00 0.00 3.46
212 213 4.006989 CCACAACGATCATAAACCCTTCA 58.993 43.478 0.00 0.00 0.00 3.02
213 214 4.640201 CCACAACGATCATAAACCCTTCAT 59.360 41.667 0.00 0.00 0.00 2.57
214 215 5.820423 CCACAACGATCATAAACCCTTCATA 59.180 40.000 0.00 0.00 0.00 2.15
215 216 6.486657 CCACAACGATCATAAACCCTTCATAT 59.513 38.462 0.00 0.00 0.00 1.78
216 217 7.659799 CCACAACGATCATAAACCCTTCATATA 59.340 37.037 0.00 0.00 0.00 0.86
217 218 8.712363 CACAACGATCATAAACCCTTCATATAG 58.288 37.037 0.00 0.00 0.00 1.31
218 219 8.647796 ACAACGATCATAAACCCTTCATATAGA 58.352 33.333 0.00 0.00 0.00 1.98
219 220 9.489084 CAACGATCATAAACCCTTCATATAGAA 57.511 33.333 0.00 0.00 34.41 2.10
221 222 9.877178 ACGATCATAAACCCTTCATATAGAATC 57.123 33.333 0.00 0.00 35.25 2.52
276 277 8.746052 TTTGTAATCCAATAATCGATCTTGGT 57.254 30.769 26.59 17.25 40.28 3.67
277 278 8.746052 TTGTAATCCAATAATCGATCTTGGTT 57.254 30.769 26.59 22.56 40.28 3.67
278 279 9.839817 TTGTAATCCAATAATCGATCTTGGTTA 57.160 29.630 26.59 21.92 40.28 2.85
279 280 9.489084 TGTAATCCAATAATCGATCTTGGTTAG 57.511 33.333 26.59 11.33 40.28 2.34
280 281 7.986085 AATCCAATAATCGATCTTGGTTAGG 57.014 36.000 26.59 11.66 40.28 2.69
281 282 6.740944 TCCAATAATCGATCTTGGTTAGGA 57.259 37.500 26.59 13.21 40.28 2.94
282 283 7.316393 TCCAATAATCGATCTTGGTTAGGAT 57.684 36.000 26.59 2.28 40.28 3.24
283 284 7.161404 TCCAATAATCGATCTTGGTTAGGATG 58.839 38.462 26.59 9.59 40.28 3.51
284 285 7.016170 TCCAATAATCGATCTTGGTTAGGATGA 59.984 37.037 26.59 11.70 40.28 2.92
285 286 7.826252 CCAATAATCGATCTTGGTTAGGATGAT 59.174 37.037 22.61 0.00 35.70 2.45
286 287 9.224267 CAATAATCGATCTTGGTTAGGATGATT 57.776 33.333 0.00 0.00 0.00 2.57
289 290 8.608844 AATCGATCTTGGTTAGGATGATTAAC 57.391 34.615 0.00 0.00 0.00 2.01
290 291 6.522054 TCGATCTTGGTTAGGATGATTAACC 58.478 40.000 7.13 7.13 46.63 2.85
298 299 7.886405 GGTTAGGATGATTAACCGAGTTATC 57.114 40.000 0.00 0.00 40.30 1.75
299 300 6.872547 GGTTAGGATGATTAACCGAGTTATCC 59.127 42.308 0.00 0.00 40.30 2.59
300 301 7.439381 GTTAGGATGATTAACCGAGTTATCCA 58.561 38.462 13.87 8.68 32.44 3.41
301 302 6.494666 AGGATGATTAACCGAGTTATCCAA 57.505 37.500 13.87 0.00 32.44 3.53
302 303 6.895782 AGGATGATTAACCGAGTTATCCAAA 58.104 36.000 13.87 0.00 32.44 3.28
303 304 7.343357 AGGATGATTAACCGAGTTATCCAAAA 58.657 34.615 13.87 0.00 32.44 2.44
304 305 7.832187 AGGATGATTAACCGAGTTATCCAAAAA 59.168 33.333 13.87 0.00 32.44 1.94
334 335 9.306280 CTGCTGATACATTCGAATAATTAAACG 57.694 33.333 10.97 0.00 0.00 3.60
335 336 8.822855 TGCTGATACATTCGAATAATTAAACGT 58.177 29.630 10.97 4.60 0.00 3.99
336 337 9.646336 GCTGATACATTCGAATAATTAAACGTT 57.354 29.630 10.97 0.00 0.00 3.99
342 343 9.666626 ACATTCGAATAATTAAACGTTTCACAA 57.333 25.926 18.42 7.01 0.00 3.33
344 345 9.887406 ATTCGAATAATTAAACGTTTCACAAGT 57.113 25.926 18.42 8.45 0.00 3.16
347 348 9.801714 CGAATAATTAAACGTTTCACAAGTAGT 57.198 29.630 18.42 9.29 0.00 2.73
391 392 6.877611 ACAACTAACAACTATTTCCACAGG 57.122 37.500 0.00 0.00 0.00 4.00
392 393 6.362248 ACAACTAACAACTATTTCCACAGGT 58.638 36.000 0.00 0.00 0.00 4.00
393 394 6.831868 ACAACTAACAACTATTTCCACAGGTT 59.168 34.615 0.00 0.00 0.00 3.50
394 395 7.012989 ACAACTAACAACTATTTCCACAGGTTC 59.987 37.037 0.00 0.00 0.00 3.62
395 396 6.597562 ACTAACAACTATTTCCACAGGTTCA 58.402 36.000 0.00 0.00 0.00 3.18
396 397 6.710744 ACTAACAACTATTTCCACAGGTTCAG 59.289 38.462 0.00 0.00 0.00 3.02
397 398 5.304686 ACAACTATTTCCACAGGTTCAGA 57.695 39.130 0.00 0.00 0.00 3.27
398 399 5.690865 ACAACTATTTCCACAGGTTCAGAA 58.309 37.500 0.00 0.00 0.00 3.02
399 400 5.531287 ACAACTATTTCCACAGGTTCAGAAC 59.469 40.000 4.52 4.52 0.00 3.01
421 422 5.151297 CCATTTAATCCATAATGGTGGGC 57.849 43.478 0.00 0.00 43.69 5.36
422 423 4.592351 CCATTTAATCCATAATGGTGGGCA 59.408 41.667 0.00 0.00 43.69 5.36
423 424 5.071519 CCATTTAATCCATAATGGTGGGCAA 59.928 40.000 0.00 0.00 43.69 4.52
424 425 6.409005 CCATTTAATCCATAATGGTGGGCAAA 60.409 38.462 0.00 0.00 43.69 3.68
425 426 6.821616 TTTAATCCATAATGGTGGGCAAAT 57.178 33.333 0.00 0.00 39.03 2.32
426 427 4.693042 AATCCATAATGGTGGGCAAATG 57.307 40.909 0.00 0.00 39.03 2.32
427 428 1.761784 TCCATAATGGTGGGCAAATGC 59.238 47.619 0.00 0.00 39.03 3.56
428 429 1.485480 CCATAATGGTGGGCAAATGCA 59.515 47.619 7.80 0.00 36.22 3.96
429 430 2.105134 CCATAATGGTGGGCAAATGCAT 59.895 45.455 7.80 0.00 36.22 3.96
430 431 3.324268 CCATAATGGTGGGCAAATGCATA 59.676 43.478 0.00 0.00 36.22 3.14
431 432 4.202336 CCATAATGGTGGGCAAATGCATAA 60.202 41.667 0.00 0.00 36.22 1.90
432 433 3.996921 AATGGTGGGCAAATGCATAAA 57.003 38.095 0.00 0.00 44.36 1.40
433 434 4.506937 AATGGTGGGCAAATGCATAAAT 57.493 36.364 0.00 0.00 44.36 1.40
434 435 5.627182 AATGGTGGGCAAATGCATAAATA 57.373 34.783 0.00 0.00 44.36 1.40
435 436 5.829062 ATGGTGGGCAAATGCATAAATAT 57.171 34.783 0.00 0.00 44.36 1.28
436 437 6.931790 ATGGTGGGCAAATGCATAAATATA 57.068 33.333 0.00 0.00 44.36 0.86
437 438 6.931790 TGGTGGGCAAATGCATAAATATAT 57.068 33.333 0.00 0.00 44.36 0.86
438 439 7.313740 TGGTGGGCAAATGCATAAATATATT 57.686 32.000 0.00 0.00 44.36 1.28
439 440 7.385267 TGGTGGGCAAATGCATAAATATATTC 58.615 34.615 0.00 0.00 44.36 1.75
440 441 6.818142 GGTGGGCAAATGCATAAATATATTCC 59.182 38.462 0.00 0.00 44.36 3.01
441 442 7.310609 GGTGGGCAAATGCATAAATATATTCCT 60.311 37.037 0.00 0.00 44.36 3.36
442 443 7.546667 GTGGGCAAATGCATAAATATATTCCTG 59.453 37.037 0.00 1.14 44.36 3.86
443 444 7.454066 TGGGCAAATGCATAAATATATTCCTGA 59.546 33.333 0.00 0.00 44.36 3.86
444 445 8.313292 GGGCAAATGCATAAATATATTCCTGAA 58.687 33.333 0.00 0.00 44.36 3.02
445 446 9.709495 GGCAAATGCATAAATATATTCCTGAAA 57.291 29.630 0.00 0.00 44.36 2.69
455 456 8.986929 AAATATATTCCTGAAAGAGAAGTGGG 57.013 34.615 0.00 0.00 34.07 4.61
456 457 7.698163 ATATATTCCTGAAAGAGAAGTGGGT 57.302 36.000 0.00 0.00 34.07 4.51
457 458 8.798975 ATATATTCCTGAAAGAGAAGTGGGTA 57.201 34.615 0.00 0.00 34.07 3.69
458 459 4.891992 TTCCTGAAAGAGAAGTGGGTAG 57.108 45.455 0.00 0.00 34.07 3.18
459 460 4.127918 TCCTGAAAGAGAAGTGGGTAGA 57.872 45.455 0.00 0.00 34.07 2.59
460 461 3.833070 TCCTGAAAGAGAAGTGGGTAGAC 59.167 47.826 0.00 0.00 34.07 2.59
461 462 3.578716 CCTGAAAGAGAAGTGGGTAGACA 59.421 47.826 0.00 0.00 34.07 3.41
462 463 4.040461 CCTGAAAGAGAAGTGGGTAGACAA 59.960 45.833 0.00 0.00 34.07 3.18
463 464 5.454755 CCTGAAAGAGAAGTGGGTAGACAAA 60.455 44.000 0.00 0.00 34.07 2.83
567 568 1.168714 GAAGCATCCCAAAAGCGTCT 58.831 50.000 0.00 0.00 34.62 4.18
752 753 3.141767 TGGATCCGTACATCTCGATCT 57.858 47.619 7.39 0.00 0.00 2.75
778 779 9.964354 TGAAAAGAATCAATAGAAGGAGAATCA 57.036 29.630 0.00 0.00 36.25 2.57
1113 3856 7.675619 AGTTTCATTTTCCCAGAATGTATCCTT 59.324 33.333 0.00 0.00 36.23 3.36
1295 4038 5.286558 TCCAAACGAACAATTTCAACGAAAC 59.713 36.000 0.00 0.00 34.23 2.78
1440 4183 6.351796 GGGGAATGTTTTTATGTGGTGCTAAT 60.352 38.462 0.00 0.00 0.00 1.73
1476 4219 7.885399 ACTATCTTTGTAGCTCCAGAATGTTTT 59.115 33.333 0.00 0.00 0.00 2.43
1871 4614 5.514500 ACACAAATGTATAACTCCCCAGT 57.486 39.130 0.00 0.00 37.26 4.00
1927 4670 2.777459 TGGGTTTAAGCTTTCCCCAA 57.223 45.000 21.64 10.21 42.30 4.12
1953 4696 5.198965 CCTTTTCATCAATGGACTCCTGAT 58.801 41.667 0.00 0.00 32.27 2.90
1968 4711 5.867903 CTCCTGATGTCTATGAAGGAGTT 57.132 43.478 8.56 0.00 45.98 3.01
2048 4791 5.634896 CAAAACTCCATAGACATGCAGAAC 58.365 41.667 0.00 0.00 0.00 3.01
2082 4825 2.500098 CCCACTCCGACCAAGATAGAAA 59.500 50.000 0.00 0.00 0.00 2.52
2290 5033 3.261897 GTGGGTTCTCATCCTTCAGAGAA 59.738 47.826 0.00 0.00 45.71 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.685897 TGGTTCAACTCCTTCAAAACCG 59.314 45.455 0.00 0.00 39.17 4.44
1 2 3.068165 CCTGGTTCAACTCCTTCAAAACC 59.932 47.826 0.00 0.00 37.31 3.27
2 3 3.951680 TCCTGGTTCAACTCCTTCAAAAC 59.048 43.478 0.00 0.00 0.00 2.43
3 4 4.243793 TCCTGGTTCAACTCCTTCAAAA 57.756 40.909 0.00 0.00 0.00 2.44
4 5 3.943671 TCCTGGTTCAACTCCTTCAAA 57.056 42.857 0.00 0.00 0.00 2.69
5 6 4.453480 AATCCTGGTTCAACTCCTTCAA 57.547 40.909 0.00 0.00 0.00 2.69
6 7 4.398319 GAAATCCTGGTTCAACTCCTTCA 58.602 43.478 0.00 0.00 0.00 3.02
7 8 3.759086 GGAAATCCTGGTTCAACTCCTTC 59.241 47.826 0.00 0.00 0.00 3.46
8 9 3.140144 TGGAAATCCTGGTTCAACTCCTT 59.860 43.478 0.44 0.00 36.82 3.36
9 10 2.716424 TGGAAATCCTGGTTCAACTCCT 59.284 45.455 0.44 0.00 36.82 3.69
10 11 3.154827 TGGAAATCCTGGTTCAACTCC 57.845 47.619 0.44 0.00 36.82 3.85
11 12 5.473039 CATTTGGAAATCCTGGTTCAACTC 58.527 41.667 0.44 0.00 36.82 3.01
12 13 4.284234 CCATTTGGAAATCCTGGTTCAACT 59.716 41.667 0.44 0.00 37.39 3.16
13 14 4.283212 TCCATTTGGAAATCCTGGTTCAAC 59.717 41.667 0.00 0.00 42.18 3.18
14 15 4.487804 TCCATTTGGAAATCCTGGTTCAA 58.512 39.130 0.00 0.00 42.18 2.69
15 16 4.125124 TCCATTTGGAAATCCTGGTTCA 57.875 40.909 0.00 0.00 42.18 3.18
28 29 7.933223 AGAAATACCCTATCCTATCCATTTGG 58.067 38.462 0.00 0.00 0.00 3.28
63 64 9.729281 AGACAAATTTTTGCATTTGGATTATCT 57.271 25.926 13.50 5.49 45.04 1.98
66 67 9.558396 AGAAGACAAATTTTTGCATTTGGATTA 57.442 25.926 13.50 0.00 45.04 1.75
67 68 8.454570 AGAAGACAAATTTTTGCATTTGGATT 57.545 26.923 13.50 8.22 45.04 3.01
68 69 9.558396 TTAGAAGACAAATTTTTGCATTTGGAT 57.442 25.926 13.50 1.10 45.04 3.41
69 70 8.954950 TTAGAAGACAAATTTTTGCATTTGGA 57.045 26.923 13.50 0.00 45.04 3.53
74 75 8.839343 CCCTTTTTAGAAGACAAATTTTTGCAT 58.161 29.630 3.00 0.00 41.79 3.96
75 76 8.043710 TCCCTTTTTAGAAGACAAATTTTTGCA 58.956 29.630 3.00 0.00 41.79 4.08
76 77 8.432110 TCCCTTTTTAGAAGACAAATTTTTGC 57.568 30.769 3.00 0.00 41.79 3.68
95 96 8.571336 CGCTCTATTCATTCAATATTTCCCTTT 58.429 33.333 0.00 0.00 0.00 3.11
96 97 7.721399 ACGCTCTATTCATTCAATATTTCCCTT 59.279 33.333 0.00 0.00 0.00 3.95
97 98 7.227156 ACGCTCTATTCATTCAATATTTCCCT 58.773 34.615 0.00 0.00 0.00 4.20
98 99 7.440523 ACGCTCTATTCATTCAATATTTCCC 57.559 36.000 0.00 0.00 0.00 3.97
105 106 9.330063 TCAGAATTTACGCTCTATTCATTCAAT 57.670 29.630 0.00 0.00 32.11 2.57
106 107 8.716646 TCAGAATTTACGCTCTATTCATTCAA 57.283 30.769 0.00 0.00 32.11 2.69
107 108 8.716646 TTCAGAATTTACGCTCTATTCATTCA 57.283 30.769 0.00 0.00 32.11 2.57
108 109 9.427127 GTTTCAGAATTTACGCTCTATTCATTC 57.573 33.333 0.00 0.00 32.11 2.67
109 110 9.167311 AGTTTCAGAATTTACGCTCTATTCATT 57.833 29.630 0.00 0.00 32.11 2.57
110 111 8.723942 AGTTTCAGAATTTACGCTCTATTCAT 57.276 30.769 0.00 0.00 32.11 2.57
111 112 8.547967 AAGTTTCAGAATTTACGCTCTATTCA 57.452 30.769 0.00 0.00 32.11 2.57
112 113 9.267096 CAAAGTTTCAGAATTTACGCTCTATTC 57.733 33.333 0.00 0.00 0.00 1.75
113 114 8.237267 CCAAAGTTTCAGAATTTACGCTCTATT 58.763 33.333 0.00 0.00 0.00 1.73
114 115 7.390718 ACCAAAGTTTCAGAATTTACGCTCTAT 59.609 33.333 0.00 0.00 0.00 1.98
115 116 6.708949 ACCAAAGTTTCAGAATTTACGCTCTA 59.291 34.615 0.00 0.00 0.00 2.43
116 117 5.531287 ACCAAAGTTTCAGAATTTACGCTCT 59.469 36.000 0.00 0.00 0.00 4.09
117 118 5.758924 ACCAAAGTTTCAGAATTTACGCTC 58.241 37.500 0.00 0.00 0.00 5.03
118 119 5.767816 ACCAAAGTTTCAGAATTTACGCT 57.232 34.783 0.00 0.00 0.00 5.07
119 120 8.515473 AAATACCAAAGTTTCAGAATTTACGC 57.485 30.769 0.00 0.00 0.00 4.42
120 121 9.893305 AGAAATACCAAAGTTTCAGAATTTACG 57.107 29.630 0.00 0.00 36.92 3.18
129 130 9.594478 GGAAGAAAAAGAAATACCAAAGTTTCA 57.406 29.630 0.00 0.00 36.92 2.69
130 131 8.752254 CGGAAGAAAAAGAAATACCAAAGTTTC 58.248 33.333 0.00 0.00 35.18 2.78
131 132 7.709182 CCGGAAGAAAAAGAAATACCAAAGTTT 59.291 33.333 0.00 0.00 0.00 2.66
132 133 7.068962 TCCGGAAGAAAAAGAAATACCAAAGTT 59.931 33.333 0.00 0.00 0.00 2.66
133 134 6.548251 TCCGGAAGAAAAAGAAATACCAAAGT 59.452 34.615 0.00 0.00 0.00 2.66
134 135 6.861572 GTCCGGAAGAAAAAGAAATACCAAAG 59.138 38.462 5.23 0.00 0.00 2.77
135 136 6.321690 TGTCCGGAAGAAAAAGAAATACCAAA 59.678 34.615 5.23 0.00 0.00 3.28
136 137 5.828859 TGTCCGGAAGAAAAAGAAATACCAA 59.171 36.000 5.23 0.00 0.00 3.67
137 138 5.378332 TGTCCGGAAGAAAAAGAAATACCA 58.622 37.500 5.23 0.00 0.00 3.25
138 139 5.952526 TGTCCGGAAGAAAAAGAAATACC 57.047 39.130 5.23 0.00 0.00 2.73
139 140 8.812147 ATTTTGTCCGGAAGAAAAAGAAATAC 57.188 30.769 20.77 0.78 33.14 1.89
141 142 9.996554 ATTATTTTGTCCGGAAGAAAAAGAAAT 57.003 25.926 21.97 18.94 33.14 2.17
142 143 9.825109 AATTATTTTGTCCGGAAGAAAAAGAAA 57.175 25.926 21.97 18.06 33.14 2.52
143 144 9.471084 GAATTATTTTGTCCGGAAGAAAAAGAA 57.529 29.630 20.77 20.94 33.14 2.52
144 145 8.085909 GGAATTATTTTGTCCGGAAGAAAAAGA 58.914 33.333 20.77 15.43 33.14 2.52
145 146 7.330946 GGGAATTATTTTGTCCGGAAGAAAAAG 59.669 37.037 20.77 0.00 33.14 2.27
146 147 7.156000 GGGAATTATTTTGTCCGGAAGAAAAA 58.844 34.615 20.77 19.44 29.28 1.94
147 148 6.570764 CGGGAATTATTTTGTCCGGAAGAAAA 60.571 38.462 19.71 19.71 34.55 2.29
148 149 5.106078 CGGGAATTATTTTGTCCGGAAGAAA 60.106 40.000 5.23 11.01 34.55 2.52
149 150 4.396790 CGGGAATTATTTTGTCCGGAAGAA 59.603 41.667 5.23 0.10 34.55 2.52
150 151 3.942748 CGGGAATTATTTTGTCCGGAAGA 59.057 43.478 5.23 0.00 34.55 2.87
151 152 3.692593 ACGGGAATTATTTTGTCCGGAAG 59.307 43.478 5.23 0.00 41.49 3.46
152 153 3.688235 ACGGGAATTATTTTGTCCGGAA 58.312 40.909 5.23 0.00 41.49 4.30
153 154 3.353370 ACGGGAATTATTTTGTCCGGA 57.647 42.857 0.00 0.00 41.49 5.14
154 155 3.002965 GCTACGGGAATTATTTTGTCCGG 59.997 47.826 0.00 0.00 41.49 5.14
155 156 3.302870 CGCTACGGGAATTATTTTGTCCG 60.303 47.826 0.00 0.00 42.69 4.79
156 157 3.872771 TCGCTACGGGAATTATTTTGTCC 59.127 43.478 0.00 0.00 0.00 4.02
157 158 4.807304 TCTCGCTACGGGAATTATTTTGTC 59.193 41.667 0.00 0.00 31.57 3.18
158 159 4.761975 TCTCGCTACGGGAATTATTTTGT 58.238 39.130 0.00 0.00 31.57 2.83
159 160 5.728351 TTCTCGCTACGGGAATTATTTTG 57.272 39.130 0.00 0.00 41.63 2.44
168 169 1.076559 TCCCATTCTCGCTACGGGA 60.077 57.895 0.00 0.00 43.77 5.14
169 170 0.393077 AATCCCATTCTCGCTACGGG 59.607 55.000 0.00 0.00 38.34 5.28
170 171 2.135933 GAAATCCCATTCTCGCTACGG 58.864 52.381 0.00 0.00 0.00 4.02
171 172 2.135933 GGAAATCCCATTCTCGCTACG 58.864 52.381 0.00 0.00 34.14 3.51
172 173 3.194005 TGGAAATCCCATTCTCGCTAC 57.806 47.619 0.00 0.00 40.82 3.58
182 183 2.869101 TGATCGTTGTGGAAATCCCA 57.131 45.000 0.00 0.00 44.25 4.37
183 184 5.449999 GGTTTATGATCGTTGTGGAAATCCC 60.450 44.000 0.00 0.00 34.29 3.85
184 185 5.449999 GGGTTTATGATCGTTGTGGAAATCC 60.450 44.000 0.00 0.00 0.00 3.01
185 186 5.357032 AGGGTTTATGATCGTTGTGGAAATC 59.643 40.000 0.00 0.00 0.00 2.17
186 187 5.261216 AGGGTTTATGATCGTTGTGGAAAT 58.739 37.500 0.00 0.00 0.00 2.17
187 188 4.658063 AGGGTTTATGATCGTTGTGGAAA 58.342 39.130 0.00 0.00 0.00 3.13
188 189 4.295141 AGGGTTTATGATCGTTGTGGAA 57.705 40.909 0.00 0.00 0.00 3.53
189 190 3.992943 AGGGTTTATGATCGTTGTGGA 57.007 42.857 0.00 0.00 0.00 4.02
190 191 4.006989 TGAAGGGTTTATGATCGTTGTGG 58.993 43.478 0.00 0.00 0.00 4.17
191 192 5.818136 ATGAAGGGTTTATGATCGTTGTG 57.182 39.130 0.00 0.00 0.00 3.33
192 193 8.647796 TCTATATGAAGGGTTTATGATCGTTGT 58.352 33.333 0.00 0.00 0.00 3.32
193 194 9.489084 TTCTATATGAAGGGTTTATGATCGTTG 57.511 33.333 0.00 0.00 0.00 4.10
195 196 9.877178 GATTCTATATGAAGGGTTTATGATCGT 57.123 33.333 0.00 0.00 38.18 3.73
250 251 9.184523 ACCAAGATCGATTATTGGATTACAAAA 57.815 29.630 33.18 0.00 45.19 2.44
251 252 8.746052 ACCAAGATCGATTATTGGATTACAAA 57.254 30.769 33.18 0.00 45.19 2.83
252 253 8.746052 AACCAAGATCGATTATTGGATTACAA 57.254 30.769 33.18 0.00 45.19 2.41
253 254 9.489084 CTAACCAAGATCGATTATTGGATTACA 57.511 33.333 33.18 18.98 45.19 2.41
254 255 8.936864 CCTAACCAAGATCGATTATTGGATTAC 58.063 37.037 33.18 7.59 45.19 1.89
255 256 8.876181 TCCTAACCAAGATCGATTATTGGATTA 58.124 33.333 33.18 26.17 45.19 1.75
256 257 7.745717 TCCTAACCAAGATCGATTATTGGATT 58.254 34.615 33.18 26.36 45.19 3.01
257 258 7.316393 TCCTAACCAAGATCGATTATTGGAT 57.684 36.000 33.18 27.36 45.19 3.41
258 259 6.740944 TCCTAACCAAGATCGATTATTGGA 57.259 37.500 33.18 19.67 45.19 3.53
260 261 8.783833 ATCATCCTAACCAAGATCGATTATTG 57.216 34.615 14.26 14.26 0.00 1.90
263 264 9.706691 GTTAATCATCCTAACCAAGATCGATTA 57.293 33.333 0.00 0.00 30.28 1.75
264 265 7.661847 GGTTAATCATCCTAACCAAGATCGATT 59.338 37.037 0.00 0.00 45.21 3.34
265 266 7.162082 GGTTAATCATCCTAACCAAGATCGAT 58.838 38.462 0.00 0.00 45.21 3.59
266 267 6.522054 GGTTAATCATCCTAACCAAGATCGA 58.478 40.000 6.84 0.00 45.21 3.59
267 268 5.405571 CGGTTAATCATCCTAACCAAGATCG 59.594 44.000 11.27 0.00 45.88 3.69
268 269 6.522054 TCGGTTAATCATCCTAACCAAGATC 58.478 40.000 11.27 0.00 45.88 2.75
269 270 6.099845 ACTCGGTTAATCATCCTAACCAAGAT 59.900 38.462 11.27 0.00 45.88 2.40
270 271 5.424252 ACTCGGTTAATCATCCTAACCAAGA 59.576 40.000 11.27 2.28 45.88 3.02
271 272 5.671493 ACTCGGTTAATCATCCTAACCAAG 58.329 41.667 11.27 5.60 45.88 3.61
272 273 5.687166 ACTCGGTTAATCATCCTAACCAA 57.313 39.130 11.27 0.00 45.88 3.67
273 274 5.687166 AACTCGGTTAATCATCCTAACCA 57.313 39.130 11.27 0.28 45.88 3.67
274 275 6.872547 GGATAACTCGGTTAATCATCCTAACC 59.127 42.308 2.29 2.29 43.30 2.85
275 276 7.439381 TGGATAACTCGGTTAATCATCCTAAC 58.561 38.462 13.09 0.00 31.56 2.34
276 277 7.606135 TGGATAACTCGGTTAATCATCCTAA 57.394 36.000 13.09 0.00 31.56 2.69
277 278 7.606135 TTGGATAACTCGGTTAATCATCCTA 57.394 36.000 13.09 6.90 31.56 2.94
278 279 6.494666 TTGGATAACTCGGTTAATCATCCT 57.505 37.500 13.09 0.00 31.56 3.24
279 280 7.562454 TTTTGGATAACTCGGTTAATCATCC 57.438 36.000 8.31 8.31 31.56 3.51
308 309 9.306280 CGTTTAATTATTCGAATGTATCAGCAG 57.694 33.333 20.87 2.04 0.00 4.24
309 310 8.822855 ACGTTTAATTATTCGAATGTATCAGCA 58.177 29.630 20.87 0.00 0.00 4.41
310 311 9.646336 AACGTTTAATTATTCGAATGTATCAGC 57.354 29.630 20.87 5.59 0.00 4.26
316 317 9.666626 TTGTGAAACGTTTAATTATTCGAATGT 57.333 25.926 20.87 6.48 42.39 2.71
318 319 9.887406 ACTTGTGAAACGTTTAATTATTCGAAT 57.113 25.926 14.65 16.15 42.39 3.34
321 322 9.801714 ACTACTTGTGAAACGTTTAATTATTCG 57.198 29.630 14.65 3.16 42.39 3.34
365 366 9.010029 CCTGTGGAAATAGTTGTTAGTTGTAAT 57.990 33.333 0.00 0.00 0.00 1.89
366 367 7.994334 ACCTGTGGAAATAGTTGTTAGTTGTAA 59.006 33.333 0.00 0.00 0.00 2.41
367 368 7.511268 ACCTGTGGAAATAGTTGTTAGTTGTA 58.489 34.615 0.00 0.00 0.00 2.41
368 369 6.362248 ACCTGTGGAAATAGTTGTTAGTTGT 58.638 36.000 0.00 0.00 0.00 3.32
369 370 6.877611 ACCTGTGGAAATAGTTGTTAGTTG 57.122 37.500 0.00 0.00 0.00 3.16
370 371 7.057894 TGAACCTGTGGAAATAGTTGTTAGTT 58.942 34.615 0.00 0.00 0.00 2.24
371 372 6.597562 TGAACCTGTGGAAATAGTTGTTAGT 58.402 36.000 0.00 0.00 0.00 2.24
372 373 6.934645 TCTGAACCTGTGGAAATAGTTGTTAG 59.065 38.462 0.00 0.00 0.00 2.34
373 374 6.833041 TCTGAACCTGTGGAAATAGTTGTTA 58.167 36.000 0.00 0.00 0.00 2.41
374 375 5.690865 TCTGAACCTGTGGAAATAGTTGTT 58.309 37.500 0.00 0.00 0.00 2.83
375 376 5.304686 TCTGAACCTGTGGAAATAGTTGT 57.695 39.130 0.00 0.00 0.00 3.32
376 377 6.002062 GTTCTGAACCTGTGGAAATAGTTG 57.998 41.667 9.38 0.00 0.00 3.16
390 391 8.143835 CCATTATGGATTAAATGGTTCTGAACC 58.856 37.037 28.50 28.50 46.02 3.62
400 401 5.804944 TGCCCACCATTATGGATTAAATG 57.195 39.130 19.23 4.29 43.02 2.32
401 402 6.821616 TTTGCCCACCATTATGGATTAAAT 57.178 33.333 19.23 0.00 43.02 1.40
402 403 6.590068 CATTTGCCCACCATTATGGATTAAA 58.410 36.000 19.23 11.18 43.02 1.52
403 404 5.454471 GCATTTGCCCACCATTATGGATTAA 60.454 40.000 19.23 3.07 43.02 1.40
404 405 4.040217 GCATTTGCCCACCATTATGGATTA 59.960 41.667 19.23 0.00 43.02 1.75
405 406 3.181452 GCATTTGCCCACCATTATGGATT 60.181 43.478 19.23 0.00 43.02 3.01
406 407 2.369532 GCATTTGCCCACCATTATGGAT 59.630 45.455 19.23 0.00 43.02 3.41
407 408 1.761784 GCATTTGCCCACCATTATGGA 59.238 47.619 19.23 0.00 43.02 3.41
408 409 1.485480 TGCATTTGCCCACCATTATGG 59.515 47.619 10.08 10.08 41.49 2.74
409 410 2.983907 TGCATTTGCCCACCATTATG 57.016 45.000 0.00 0.00 41.18 1.90
410 411 5.627182 TTTATGCATTTGCCCACCATTAT 57.373 34.783 3.54 0.00 41.18 1.28
411 412 5.627182 ATTTATGCATTTGCCCACCATTA 57.373 34.783 3.54 0.00 41.18 1.90
412 413 3.996921 TTTATGCATTTGCCCACCATT 57.003 38.095 3.54 0.00 41.18 3.16
413 414 5.829062 ATATTTATGCATTTGCCCACCAT 57.171 34.783 3.54 0.00 41.18 3.55
414 415 6.931790 ATATATTTATGCATTTGCCCACCA 57.068 33.333 3.54 0.00 41.18 4.17
415 416 6.818142 GGAATATATTTATGCATTTGCCCACC 59.182 38.462 3.54 0.00 41.18 4.61
416 417 7.546667 CAGGAATATATTTATGCATTTGCCCAC 59.453 37.037 3.54 0.00 41.18 4.61
417 418 7.454066 TCAGGAATATATTTATGCATTTGCCCA 59.546 33.333 3.54 0.00 41.18 5.36
418 419 7.839907 TCAGGAATATATTTATGCATTTGCCC 58.160 34.615 3.54 0.00 41.18 5.36
419 420 9.709495 TTTCAGGAATATATTTATGCATTTGCC 57.291 29.630 3.54 0.00 41.18 4.52
430 431 8.560903 ACCCACTTCTCTTTCAGGAATATATTT 58.439 33.333 0.00 0.00 0.00 1.40
431 432 8.107196 ACCCACTTCTCTTTCAGGAATATATT 57.893 34.615 0.00 0.00 0.00 1.28
432 433 7.698163 ACCCACTTCTCTTTCAGGAATATAT 57.302 36.000 0.00 0.00 0.00 0.86
433 434 8.065627 TCTACCCACTTCTCTTTCAGGAATATA 58.934 37.037 0.00 0.00 0.00 0.86
434 435 6.903534 TCTACCCACTTCTCTTTCAGGAATAT 59.096 38.462 0.00 0.00 0.00 1.28
435 436 6.154706 GTCTACCCACTTCTCTTTCAGGAATA 59.845 42.308 0.00 0.00 0.00 1.75
436 437 5.046231 GTCTACCCACTTCTCTTTCAGGAAT 60.046 44.000 0.00 0.00 0.00 3.01
437 438 4.283722 GTCTACCCACTTCTCTTTCAGGAA 59.716 45.833 0.00 0.00 0.00 3.36
438 439 3.833070 GTCTACCCACTTCTCTTTCAGGA 59.167 47.826 0.00 0.00 0.00 3.86
439 440 3.578716 TGTCTACCCACTTCTCTTTCAGG 59.421 47.826 0.00 0.00 0.00 3.86
440 441 4.873746 TGTCTACCCACTTCTCTTTCAG 57.126 45.455 0.00 0.00 0.00 3.02
441 442 5.365619 GTTTGTCTACCCACTTCTCTTTCA 58.634 41.667 0.00 0.00 0.00 2.69
442 443 4.448060 CGTTTGTCTACCCACTTCTCTTTC 59.552 45.833 0.00 0.00 0.00 2.62
443 444 4.141779 ACGTTTGTCTACCCACTTCTCTTT 60.142 41.667 0.00 0.00 0.00 2.52
444 445 3.387050 ACGTTTGTCTACCCACTTCTCTT 59.613 43.478 0.00 0.00 0.00 2.85
445 446 2.963782 ACGTTTGTCTACCCACTTCTCT 59.036 45.455 0.00 0.00 0.00 3.10
446 447 3.382048 ACGTTTGTCTACCCACTTCTC 57.618 47.619 0.00 0.00 0.00 2.87
447 448 4.942761 TTACGTTTGTCTACCCACTTCT 57.057 40.909 0.00 0.00 0.00 2.85
448 449 7.656707 TTTATTACGTTTGTCTACCCACTTC 57.343 36.000 0.00 0.00 0.00 3.01
449 450 8.449251 TTTTTATTACGTTTGTCTACCCACTT 57.551 30.769 0.00 0.00 0.00 3.16
567 568 3.358111 TGAAAGCCATATTTCGACCCA 57.642 42.857 0.00 0.00 41.21 4.51
651 652 2.103771 GCCTCTGCCATTCTATGAGTCA 59.896 50.000 0.00 0.00 0.00 3.41
752 753 9.964354 TGATTCTCCTTCTATTGATTCTTTTCA 57.036 29.630 0.00 0.00 0.00 2.69
778 779 6.866770 TGTTTGTTTCGAGAAAGATATCGTCT 59.133 34.615 10.68 10.68 40.97 4.18
1113 3856 8.877864 TCAGAAGAAGAATTAGGCCAAAAATA 57.122 30.769 5.01 0.00 0.00 1.40
1158 3901 9.588096 AAATAGAACCAAGGTCTATCTTTTTGT 57.412 29.630 2.75 0.00 0.00 2.83
1336 4079 7.522399 ACATTCAATGTACTCTACGGATAGAGC 60.522 40.741 0.00 0.00 45.54 4.09
1476 4219 8.701895 CCAGACAATAGGTAGGAACATAAACTA 58.298 37.037 0.00 0.00 0.00 2.24
1522 4265 7.618019 ATTTCATAGTAGCCTCATTAGACCA 57.382 36.000 0.00 0.00 0.00 4.02
1871 4614 8.791675 TGATGGATATAAGCGCAATTGAAATTA 58.208 29.630 11.47 4.51 0.00 1.40
1927 4670 3.564352 GGAGTCCATTGATGAAAAGGGGT 60.564 47.826 3.60 0.00 31.82 4.95
1953 4696 4.039973 ACGAACCAAACTCCTTCATAGACA 59.960 41.667 0.00 0.00 0.00 3.41
1968 4711 3.207778 AGGAATTTGTCGAACGAACCAA 58.792 40.909 0.00 0.00 0.00 3.67
2048 4791 2.808202 CGGAGTGGGGATAGCATTTCTG 60.808 54.545 0.00 0.00 0.00 3.02
2290 5033 4.156190 CGGATGCTCCTATTACACTCGTAT 59.844 45.833 1.51 0.00 33.30 3.06
2324 5067 7.395617 CATGAGATGATCATCTTAGGGTGATT 58.604 38.462 33.30 14.01 46.01 2.57


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

AutoCloner maintained by Alex Coulton.