Multiple sequence alignment - TraesCS2B01G240000

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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 TraesCS2B01G240000 chr2B 100.000 2905 0 0 1 2905 244537608 244534704 0.000000e+00 5365
1 TraesCS2B01G240000 chr2B 96.364 165 6 0 1 165 720588146 720587982 3.690000e-69 272
2 TraesCS2B01G240000 chr2A 94.949 1881 66 16 168 2029 202044295 202042425 0.000000e+00 2920
3 TraesCS2B01G240000 chr2A 90.909 704 34 9 2209 2905 202042361 202041681 0.000000e+00 918
4 TraesCS2B01G240000 chr2A 95.455 66 3 0 2054 2119 202042426 202042361 3.960000e-19 106
5 TraesCS2B01G240000 chr2D 92.544 1435 59 19 275 1696 188434345 188432946 0.000000e+00 2013
6 TraesCS2B01G240000 chr2D 92.010 388 15 10 1728 2110 188432948 188432572 5.510000e-147 531
7 TraesCS2B01G240000 chr2D 95.152 330 12 3 2579 2905 188432084 188431756 4.290000e-143 518
8 TraesCS2B01G240000 chr2D 90.426 376 26 6 2209 2581 188432576 188432208 1.210000e-133 486
9 TraesCS2B01G240000 chr6A 95.210 167 6 2 1 166 574196742 574196907 2.220000e-66 263
10 TraesCS2B01G240000 chr6A 94.898 98 1 1 2115 2212 19884184 19884277 1.800000e-32 150
11 TraesCS2B01G240000 chr6B 94.937 158 8 0 5 162 87499576 87499733 6.220000e-62 248
12 TraesCS2B01G240000 chr6B 90.741 108 6 3 2118 2225 230468756 230468859 1.090000e-29 141
13 TraesCS2B01G240000 chr6B 93.684 95 4 1 2118 2212 230468848 230468756 1.090000e-29 141
14 TraesCS2B01G240000 chr6B 93.684 95 3 1 2118 2212 705793451 705793542 3.900000e-29 139
15 TraesCS2B01G240000 chr4A 93.750 160 10 0 3 162 53408761 53408920 1.040000e-59 241
16 TraesCS2B01G240000 chr4D 90.123 162 13 3 1 162 96153757 96153915 1.060000e-49 207
17 TraesCS2B01G240000 chr7B 95.876 97 3 1 2116 2212 524615369 524615464 3.880000e-34 156
18 TraesCS2B01G240000 chr7B 81.564 179 16 8 1 162 41653068 41652890 6.530000e-27 132
19 TraesCS2B01G240000 chr3D 92.929 99 4 3 2118 2215 8759963 8760059 1.090000e-29 141
20 TraesCS2B01G240000 chr5D 90.000 110 7 3 2118 2225 309186625 309186732 3.900000e-29 139
21 TraesCS2B01G240000 chr5D 93.684 95 2 2 2118 2212 443933799 443933889 3.900000e-29 139
22 TraesCS2B01G240000 chr3B 91.667 96 6 2 2118 2212 678884040 678884134 6.530000e-27 132


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 TraesCS2B01G240000 chr2B 244534704 244537608 2904 True 5365.000000 5365 100.000 1 2905 1 chr2B.!!$R1 2904
1 TraesCS2B01G240000 chr2A 202041681 202044295 2614 True 1314.666667 2920 93.771 168 2905 3 chr2A.!!$R1 2737
2 TraesCS2B01G240000 chr2D 188431756 188434345 2589 True 887.000000 2013 92.533 275 2905 4 chr2D.!!$R1 2630

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
379 385 0.03213 TCTATCGATGCAAGTCCGCC 59.968 55.0 8.54 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2220 2275 0.251077 CTTCTGGCTGTTGGGCTCTT 60.251 55.0 0.0 0.0 41.48 2.85 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
58 59 5.886960 ATTGTGTTGATAGTCTTTCCTGC 57.113 39.130 0.00 0.00 0.00 4.85
59 60 4.350368 TGTGTTGATAGTCTTTCCTGCA 57.650 40.909 0.00 0.00 0.00 4.41
60 61 4.910195 TGTGTTGATAGTCTTTCCTGCAT 58.090 39.130 0.00 0.00 0.00 3.96
61 62 4.696877 TGTGTTGATAGTCTTTCCTGCATG 59.303 41.667 0.00 0.00 0.00 4.06
62 63 3.691118 TGTTGATAGTCTTTCCTGCATGC 59.309 43.478 11.82 11.82 0.00 4.06
63 64 3.632643 TGATAGTCTTTCCTGCATGCA 57.367 42.857 21.29 21.29 0.00 3.96
64 65 4.160642 TGATAGTCTTTCCTGCATGCAT 57.839 40.909 22.97 6.08 0.00 3.96
65 66 5.294734 TGATAGTCTTTCCTGCATGCATA 57.705 39.130 22.97 9.99 0.00 3.14
66 67 5.059161 TGATAGTCTTTCCTGCATGCATAC 58.941 41.667 22.97 12.23 0.00 2.39
67 68 3.641434 AGTCTTTCCTGCATGCATACT 57.359 42.857 22.97 14.18 0.00 2.12
68 69 3.539604 AGTCTTTCCTGCATGCATACTC 58.460 45.455 22.97 8.33 0.00 2.59
69 70 3.199508 AGTCTTTCCTGCATGCATACTCT 59.800 43.478 22.97 10.42 0.00 3.24
70 71 3.944015 GTCTTTCCTGCATGCATACTCTT 59.056 43.478 22.97 0.00 0.00 2.85
71 72 3.943381 TCTTTCCTGCATGCATACTCTTG 59.057 43.478 22.97 7.39 0.00 3.02
72 73 2.336945 TCCTGCATGCATACTCTTGG 57.663 50.000 22.97 16.89 0.00 3.61
73 74 0.666913 CCTGCATGCATACTCTTGGC 59.333 55.000 22.97 0.00 0.00 4.52
74 75 0.666913 CTGCATGCATACTCTTGGCC 59.333 55.000 22.97 0.00 0.00 5.36
75 76 0.034283 TGCATGCATACTCTTGGCCA 60.034 50.000 18.46 0.00 0.00 5.36
76 77 1.105457 GCATGCATACTCTTGGCCAA 58.895 50.000 19.25 19.25 0.00 4.52
77 78 1.202336 GCATGCATACTCTTGGCCAAC 60.202 52.381 16.05 3.24 0.00 3.77
78 79 2.372264 CATGCATACTCTTGGCCAACT 58.628 47.619 16.05 2.17 0.00 3.16
79 80 3.544684 CATGCATACTCTTGGCCAACTA 58.455 45.455 16.05 4.70 0.00 2.24
80 81 3.931907 TGCATACTCTTGGCCAACTAT 57.068 42.857 16.05 6.90 0.00 2.12
81 82 4.235079 TGCATACTCTTGGCCAACTATT 57.765 40.909 16.05 2.56 0.00 1.73
82 83 4.599041 TGCATACTCTTGGCCAACTATTT 58.401 39.130 16.05 0.00 0.00 1.40
83 84 5.016173 TGCATACTCTTGGCCAACTATTTT 58.984 37.500 16.05 0.00 0.00 1.82
84 85 5.480073 TGCATACTCTTGGCCAACTATTTTT 59.520 36.000 16.05 0.00 0.00 1.94
85 86 6.036470 GCATACTCTTGGCCAACTATTTTTC 58.964 40.000 16.05 0.00 0.00 2.29
86 87 6.127619 GCATACTCTTGGCCAACTATTTTTCT 60.128 38.462 16.05 0.00 0.00 2.52
87 88 7.577616 GCATACTCTTGGCCAACTATTTTTCTT 60.578 37.037 16.05 0.00 0.00 2.52
88 89 6.089249 ACTCTTGGCCAACTATTTTTCTTG 57.911 37.500 16.05 0.00 0.00 3.02
89 90 5.833131 ACTCTTGGCCAACTATTTTTCTTGA 59.167 36.000 16.05 4.73 0.00 3.02
90 91 6.494835 ACTCTTGGCCAACTATTTTTCTTGAT 59.505 34.615 16.05 0.00 0.00 2.57
91 92 7.015584 ACTCTTGGCCAACTATTTTTCTTGATT 59.984 33.333 16.05 0.00 0.00 2.57
92 93 8.415950 TCTTGGCCAACTATTTTTCTTGATTA 57.584 30.769 16.05 0.00 0.00 1.75
93 94 9.034800 TCTTGGCCAACTATTTTTCTTGATTAT 57.965 29.630 16.05 0.00 0.00 1.28
133 134 6.895607 TTTTTCTTTAAAAGTTCGCCCTTG 57.104 33.333 0.00 0.00 36.02 3.61
134 135 4.577834 TTCTTTAAAAGTTCGCCCTTGG 57.422 40.909 0.00 0.00 0.00 3.61
135 136 3.558033 TCTTTAAAAGTTCGCCCTTGGT 58.442 40.909 0.00 0.00 0.00 3.67
136 137 4.716794 TCTTTAAAAGTTCGCCCTTGGTA 58.283 39.130 0.00 0.00 0.00 3.25
137 138 5.131784 TCTTTAAAAGTTCGCCCTTGGTAA 58.868 37.500 0.00 0.00 0.00 2.85
138 139 4.834357 TTAAAAGTTCGCCCTTGGTAAC 57.166 40.909 0.00 0.00 0.00 2.50
139 140 2.651382 AAAGTTCGCCCTTGGTAACT 57.349 45.000 0.00 0.00 34.31 2.24
140 141 2.651382 AAGTTCGCCCTTGGTAACTT 57.349 45.000 8.85 8.85 36.74 2.66
141 142 2.180432 AGTTCGCCCTTGGTAACTTC 57.820 50.000 0.00 0.00 30.75 3.01
142 143 1.418637 AGTTCGCCCTTGGTAACTTCA 59.581 47.619 0.00 0.00 30.75 3.02
143 144 2.158726 AGTTCGCCCTTGGTAACTTCAA 60.159 45.455 0.00 0.00 30.75 2.69
144 145 2.619646 GTTCGCCCTTGGTAACTTCAAA 59.380 45.455 0.00 0.00 37.61 2.69
145 146 3.149005 TCGCCCTTGGTAACTTCAAAT 57.851 42.857 0.00 0.00 37.61 2.32
146 147 3.078837 TCGCCCTTGGTAACTTCAAATC 58.921 45.455 0.00 0.00 37.61 2.17
147 148 2.163613 CGCCCTTGGTAACTTCAAATCC 59.836 50.000 0.00 0.00 37.61 3.01
148 149 2.496070 GCCCTTGGTAACTTCAAATCCC 59.504 50.000 0.00 0.00 37.61 3.85
149 150 2.752903 CCCTTGGTAACTTCAAATCCCG 59.247 50.000 0.00 0.00 37.61 5.14
150 151 2.752903 CCTTGGTAACTTCAAATCCCGG 59.247 50.000 0.00 0.00 37.61 5.73
151 152 3.560453 CCTTGGTAACTTCAAATCCCGGA 60.560 47.826 0.73 0.00 37.61 5.14
152 153 4.270008 CTTGGTAACTTCAAATCCCGGAT 58.730 43.478 0.73 0.00 37.61 4.18
153 154 3.881220 TGGTAACTTCAAATCCCGGATC 58.119 45.455 0.73 0.00 37.61 3.36
154 155 3.211865 GGTAACTTCAAATCCCGGATCC 58.788 50.000 0.73 0.00 0.00 3.36
155 156 2.038387 AACTTCAAATCCCGGATCCG 57.962 50.000 27.65 27.65 39.44 4.18
156 157 0.463833 ACTTCAAATCCCGGATCCGC 60.464 55.000 29.12 0.00 38.24 5.54
157 158 1.153046 TTCAAATCCCGGATCCGCC 60.153 57.895 29.12 0.00 38.24 6.13
158 159 1.916206 TTCAAATCCCGGATCCGCCA 61.916 55.000 29.12 16.87 38.24 5.69
159 160 2.186826 CAAATCCCGGATCCGCCAC 61.187 63.158 29.12 0.00 38.24 5.01
160 161 2.375345 AAATCCCGGATCCGCCACT 61.375 57.895 29.12 9.84 38.24 4.00
161 162 2.608970 AAATCCCGGATCCGCCACTG 62.609 60.000 29.12 14.30 38.24 3.66
163 164 4.530857 CCCGGATCCGCCACTGTC 62.531 72.222 29.12 0.00 38.24 3.51
164 165 3.770040 CCGGATCCGCCACTGTCA 61.770 66.667 29.12 0.00 38.24 3.58
165 166 2.509336 CGGATCCGCCACTGTCAC 60.509 66.667 23.37 0.00 35.94 3.67
166 167 2.125106 GGATCCGCCACTGTCACC 60.125 66.667 0.00 0.00 36.34 4.02
175 176 4.065281 ACTGTCACCGCGCCCTAC 62.065 66.667 0.00 0.00 0.00 3.18
191 192 2.354805 CCCTACTAGGCCACAACTTCAC 60.355 54.545 5.01 0.00 32.73 3.18
195 196 0.034337 TAGGCCACAACTTCACGACC 59.966 55.000 5.01 0.00 0.00 4.79
200 201 0.937304 CACAACTTCACGACCACCTG 59.063 55.000 0.00 0.00 0.00 4.00
206 207 0.762418 TTCACGACCACCTGGACAAT 59.238 50.000 0.00 0.00 38.94 2.71
213 214 1.073923 ACCACCTGGACAATTGAGGTC 59.926 52.381 13.59 0.00 38.07 3.85
214 215 1.073763 CCACCTGGACAATTGAGGTCA 59.926 52.381 13.59 3.82 38.07 4.02
216 217 1.352352 ACCTGGACAATTGAGGTCAGG 59.648 52.381 24.66 24.66 34.94 3.86
233 234 3.006752 GTCAGGGTTGAATCCATTGCAAA 59.993 43.478 1.71 0.00 34.49 3.68
252 253 4.262617 CAAACCCTAAGACCCTAAGCTTC 58.737 47.826 0.00 0.00 0.00 3.86
254 255 2.046025 ACCCTAAGACCCTAAGCTTCCT 59.954 50.000 0.00 0.00 0.00 3.36
264 265 3.906846 CCCTAAGCTTCCTCATAGGATGT 59.093 47.826 11.56 0.00 45.34 3.06
265 266 4.020662 CCCTAAGCTTCCTCATAGGATGTC 60.021 50.000 11.56 3.98 45.34 3.06
270 271 0.179001 TCCTCATAGGATGTCGGCGA 60.179 55.000 4.99 4.99 40.06 5.54
271 272 0.039074 CCTCATAGGATGTCGGCGAC 60.039 60.000 31.68 31.68 37.67 5.19
272 273 0.668535 CTCATAGGATGTCGGCGACA 59.331 55.000 40.35 40.35 46.90 4.35
273 274 1.067060 CTCATAGGATGTCGGCGACAA 59.933 52.381 41.49 27.82 45.96 3.18
338 339 0.107654 GGAAGTCGGGTGAGGAATGG 60.108 60.000 0.00 0.00 0.00 3.16
379 385 0.032130 TCTATCGATGCAAGTCCGCC 59.968 55.000 8.54 0.00 0.00 6.13
417 423 4.608948 AGGGCGAGAAACATAGATTAGG 57.391 45.455 0.00 0.00 0.00 2.69
425 431 2.682952 ACATAGATTAGGTCGACGCG 57.317 50.000 9.92 3.53 0.00 6.01
437 443 2.093783 GGTCGACGCGAATCTGAAAAAT 59.906 45.455 15.93 0.00 37.72 1.82
446 452 4.032900 GCGAATCTGAAAAATAGACTGCGA 59.967 41.667 0.00 0.00 0.00 5.10
750 759 1.008875 CACCGTCGACACATGTCTGG 61.009 60.000 17.16 8.30 42.66 3.86
918 927 5.707298 CGTCCTCCTCATATATTTTTGCCAT 59.293 40.000 0.00 0.00 0.00 4.40
968 977 4.714308 AGAGGGATAAGAGAGAAACACAGG 59.286 45.833 0.00 0.00 0.00 4.00
1280 1289 2.294791 AGCTGCTCGTACATCATCTACC 59.705 50.000 0.00 0.00 0.00 3.18
1286 1295 6.235664 TGCTCGTACATCATCTACCATACTA 58.764 40.000 0.00 0.00 0.00 1.82
1288 1297 7.148239 TGCTCGTACATCATCTACCATACTATG 60.148 40.741 0.00 0.00 0.00 2.23
1308 1317 8.795842 ACTATGCTCGCTTTAGTAGACTATAT 57.204 34.615 4.16 0.00 0.00 0.86
1309 1318 9.887629 ACTATGCTCGCTTTAGTAGACTATATA 57.112 33.333 4.16 0.00 0.00 0.86
1365 1388 3.660111 GGTGTGTGTTCAGCCGGC 61.660 66.667 21.89 21.89 0.00 6.13
1560 1583 1.939113 CCTCAGGGCCTCCTACCTA 59.061 63.158 0.95 0.00 42.67 3.08
1566 1589 0.251698 GGGCCTCCTACCTACGCTAT 60.252 60.000 0.84 0.00 0.00 2.97
1746 1772 6.506500 AATTCTTACTGCATCAAACCTGAG 57.493 37.500 0.00 0.00 34.23 3.35
1793 1822 0.034059 AACAGGTGTGAGCTTCTCCG 59.966 55.000 0.00 0.00 0.00 4.63
1913 1942 2.902486 CAAGCTAGGCTAGATGGATCCA 59.098 50.000 25.37 18.88 38.25 3.41
2029 2084 9.757227 GCACTTAAGTATGATTCTATCTTGAGT 57.243 33.333 8.04 0.00 0.00 3.41
2037 2092 9.809096 GTATGATTCTATCTTGAGTCTTTCACA 57.191 33.333 0.00 0.00 34.94 3.58
2038 2093 8.945481 ATGATTCTATCTTGAGTCTTTCACAG 57.055 34.615 0.00 0.00 34.94 3.66
2039 2094 8.127150 TGATTCTATCTTGAGTCTTTCACAGA 57.873 34.615 0.00 0.00 34.94 3.41
2040 2095 8.756927 TGATTCTATCTTGAGTCTTTCACAGAT 58.243 33.333 0.00 0.00 37.40 2.90
2041 2096 8.945481 ATTCTATCTTGAGTCTTTCACAGATG 57.055 34.615 0.00 0.00 35.90 2.90
2042 2097 7.709149 TCTATCTTGAGTCTTTCACAGATGA 57.291 36.000 0.00 0.00 35.90 2.92
2043 2098 8.127150 TCTATCTTGAGTCTTTCACAGATGAA 57.873 34.615 0.00 0.00 43.28 2.57
2110 2165 2.013400 TGCGCACAAATCCGATGTAAT 58.987 42.857 5.66 0.00 0.00 1.89
2113 2168 4.274705 TGCGCACAAATCCGATGTAATAAT 59.725 37.500 5.66 0.00 0.00 1.28
2114 2169 5.467063 TGCGCACAAATCCGATGTAATAATA 59.533 36.000 5.66 0.00 0.00 0.98
2126 2181 8.755977 TCCGATGTAATAATAAATACTCCCTCC 58.244 37.037 0.00 0.00 0.00 4.30
2127 2182 7.705325 CCGATGTAATAATAAATACTCCCTCCG 59.295 40.741 0.00 0.00 0.00 4.63
2128 2183 8.248945 CGATGTAATAATAAATACTCCCTCCGT 58.751 37.037 0.00 0.00 0.00 4.69
2129 2184 9.939802 GATGTAATAATAAATACTCCCTCCGTT 57.060 33.333 0.00 0.00 0.00 4.44
2130 2185 9.939802 ATGTAATAATAAATACTCCCTCCGTTC 57.060 33.333 0.00 0.00 0.00 3.95
2131 2186 8.370182 TGTAATAATAAATACTCCCTCCGTTCC 58.630 37.037 0.00 0.00 0.00 3.62
2132 2187 7.383156 AATAATAAATACTCCCTCCGTTCCA 57.617 36.000 0.00 0.00 0.00 3.53
2133 2188 5.703730 AATAAATACTCCCTCCGTTCCAA 57.296 39.130 0.00 0.00 0.00 3.53
2134 2189 5.703730 ATAAATACTCCCTCCGTTCCAAA 57.296 39.130 0.00 0.00 0.00 3.28
2135 2190 4.586306 AAATACTCCCTCCGTTCCAAAT 57.414 40.909 0.00 0.00 0.00 2.32
2136 2191 4.586306 AATACTCCCTCCGTTCCAAATT 57.414 40.909 0.00 0.00 0.00 1.82
2137 2192 5.703730 AATACTCCCTCCGTTCCAAATTA 57.296 39.130 0.00 0.00 0.00 1.40
2138 2193 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2139 2194 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2140 2195 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2141 2196 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2142 2197 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2143 2198 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2144 2199 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2145 2200 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
2146 2201 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
2147 2202 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
2148 2203 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
2149 2204 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
2150 2205 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
2151 2206 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
2152 2207 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
2153 2208 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
2154 2209 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
2155 2210 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
2156 2211 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
2157 2212 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
2158 2213 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
2159 2214 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
2160 2215 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
2161 2216 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
2162 2217 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
2163 2218 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
2164 2219 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
2165 2220 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
2185 2240 7.569677 TTGAACTTTTTGAACTAAAACCACG 57.430 32.000 0.00 0.00 37.96 4.94
2186 2241 6.910995 TGAACTTTTTGAACTAAAACCACGA 58.089 32.000 0.00 0.00 37.96 4.35
2187 2242 6.802834 TGAACTTTTTGAACTAAAACCACGAC 59.197 34.615 0.00 0.00 37.96 4.34
2188 2243 5.326292 ACTTTTTGAACTAAAACCACGACG 58.674 37.500 0.00 0.00 37.96 5.12
2189 2244 5.122082 ACTTTTTGAACTAAAACCACGACGA 59.878 36.000 0.00 0.00 37.96 4.20
2190 2245 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
2191 2246 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
2192 2247 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
2193 2248 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
2194 2249 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
2195 2250 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
2196 2251 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
2197 2252 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
2198 2253 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
2199 2254 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
2200 2255 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
2201 2256 3.731089 ACCACGACGAGTAATTTGGAAA 58.269 40.909 0.00 0.00 0.00 3.13
2202 2257 3.744426 ACCACGACGAGTAATTTGGAAAG 59.256 43.478 0.00 0.00 0.00 2.62
2203 2258 3.124636 CCACGACGAGTAATTTGGAAAGG 59.875 47.826 0.00 0.00 0.00 3.11
2204 2259 3.991773 CACGACGAGTAATTTGGAAAGGA 59.008 43.478 0.00 0.00 0.00 3.36
2205 2260 4.091509 CACGACGAGTAATTTGGAAAGGAG 59.908 45.833 0.00 0.00 0.00 3.69
2206 2261 3.617263 CGACGAGTAATTTGGAAAGGAGG 59.383 47.826 0.00 0.00 0.00 4.30
2207 2262 3.939592 GACGAGTAATTTGGAAAGGAGGG 59.060 47.826 0.00 0.00 0.00 4.30
2208 2263 3.585732 ACGAGTAATTTGGAAAGGAGGGA 59.414 43.478 0.00 0.00 0.00 4.20
2209 2264 4.192317 CGAGTAATTTGGAAAGGAGGGAG 58.808 47.826 0.00 0.00 0.00 4.30
2210 2265 4.323562 CGAGTAATTTGGAAAGGAGGGAGT 60.324 45.833 0.00 0.00 0.00 3.85
2211 2266 5.105064 CGAGTAATTTGGAAAGGAGGGAGTA 60.105 44.000 0.00 0.00 0.00 2.59
2212 2267 6.575649 CGAGTAATTTGGAAAGGAGGGAGTAA 60.576 42.308 0.00 0.00 0.00 2.24
2213 2268 6.482524 AGTAATTTGGAAAGGAGGGAGTAAC 58.517 40.000 0.00 0.00 0.00 2.50
2214 2269 5.600669 AATTTGGAAAGGAGGGAGTAACT 57.399 39.130 0.00 0.00 0.00 2.24
2215 2270 5.600669 ATTTGGAAAGGAGGGAGTAACTT 57.399 39.130 0.00 0.00 0.00 2.66
2216 2271 6.713731 ATTTGGAAAGGAGGGAGTAACTTA 57.286 37.500 0.00 0.00 0.00 2.24
2217 2272 5.757099 TTGGAAAGGAGGGAGTAACTTAG 57.243 43.478 0.00 0.00 0.00 2.18
2218 2273 4.759953 TGGAAAGGAGGGAGTAACTTAGT 58.240 43.478 0.00 0.00 0.00 2.24
2219 2274 5.160386 TGGAAAGGAGGGAGTAACTTAGTT 58.840 41.667 2.32 2.32 0.00 2.24
2220 2275 6.325352 TGGAAAGGAGGGAGTAACTTAGTTA 58.675 40.000 0.03 0.03 0.00 2.24
2236 2291 1.168714 GTTAAGAGCCCAACAGCCAG 58.831 55.000 0.00 0.00 0.00 4.85
2237 2292 1.064003 TTAAGAGCCCAACAGCCAGA 58.936 50.000 0.00 0.00 0.00 3.86
2249 2306 4.213482 CCAACAGCCAGAAGTACAGTTTAC 59.787 45.833 0.00 0.00 0.00 2.01
2257 2314 4.995487 CAGAAGTACAGTTTACTCCAACCC 59.005 45.833 0.00 0.00 0.00 4.11
2261 2318 5.948842 AGTACAGTTTACTCCAACCCAATT 58.051 37.500 0.00 0.00 0.00 2.32
2281 2338 9.538508 CCCAATTATTCATCCAAATCTTCTTTC 57.461 33.333 0.00 0.00 0.00 2.62
2432 2490 3.006323 CAGCCTAGTCATCTGGGACATAC 59.994 52.174 1.92 0.00 43.79 2.39
2479 2537 4.455877 ACAGCAAAGACCAGCTAAACATAC 59.544 41.667 0.00 0.00 39.50 2.39
2480 2538 4.010349 AGCAAAGACCAGCTAAACATACC 58.990 43.478 0.00 0.00 39.78 2.73
2488 2546 1.014352 GCTAAACATACCACCAGGCG 58.986 55.000 0.00 0.00 39.06 5.52
2595 2779 8.484641 TTTGAGATGTAACAGAAATCAGCTAG 57.515 34.615 0.00 0.00 0.00 3.42
2598 2782 6.047870 AGATGTAACAGAAATCAGCTAGCAG 58.952 40.000 18.83 9.54 0.00 4.24
2622 2806 2.869192 GCTACAACTCCAGCTGATAAGC 59.131 50.000 17.39 9.99 34.86 3.09
2638 2822 1.739067 AAGCGTTTATCCTGTCAGGC 58.261 50.000 14.64 0.32 34.61 4.85
2642 2826 2.802816 GCGTTTATCCTGTCAGGCATAG 59.197 50.000 14.64 4.53 34.61 2.23
2676 2860 5.416952 ACATTTCAGTTGAATGGGCTAGAAG 59.583 40.000 0.00 0.00 33.54 2.85
2677 2861 4.908601 TTCAGTTGAATGGGCTAGAAGA 57.091 40.909 0.00 0.00 0.00 2.87
2683 2867 3.955471 TGAATGGGCTAGAAGAACTTGG 58.045 45.455 0.00 0.00 0.00 3.61
2712 2896 4.273148 ACACCTCAATCCTGACACTTAC 57.727 45.455 0.00 0.00 0.00 2.34
2713 2897 3.646162 ACACCTCAATCCTGACACTTACA 59.354 43.478 0.00 0.00 0.00 2.41
2765 2949 6.198029 CGAAATTAACAAGTCATTGCAACACA 59.802 34.615 0.00 0.00 40.27 3.72
2841 3028 3.551846 TGTTCTGAGAAAAAGGGGTCAC 58.448 45.455 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 8.462016 GCAGGAAAGACTATCAACACAATAAAT 58.538 33.333 0.00 0.00 0.00 1.40
33 34 7.446931 TGCAGGAAAGACTATCAACACAATAAA 59.553 33.333 0.00 0.00 0.00 1.40
34 35 6.939730 TGCAGGAAAGACTATCAACACAATAA 59.060 34.615 0.00 0.00 0.00 1.40
35 36 6.472016 TGCAGGAAAGACTATCAACACAATA 58.528 36.000 0.00 0.00 0.00 1.90
36 37 5.316167 TGCAGGAAAGACTATCAACACAAT 58.684 37.500 0.00 0.00 0.00 2.71
37 38 4.713553 TGCAGGAAAGACTATCAACACAA 58.286 39.130 0.00 0.00 0.00 3.33
38 39 4.350368 TGCAGGAAAGACTATCAACACA 57.650 40.909 0.00 0.00 0.00 3.72
39 40 4.437930 GCATGCAGGAAAGACTATCAACAC 60.438 45.833 14.21 0.00 0.00 3.32
40 41 3.691118 GCATGCAGGAAAGACTATCAACA 59.309 43.478 14.21 0.00 0.00 3.33
41 42 3.691118 TGCATGCAGGAAAGACTATCAAC 59.309 43.478 18.46 0.00 0.00 3.18
42 43 3.954200 TGCATGCAGGAAAGACTATCAA 58.046 40.909 18.46 0.00 0.00 2.57
43 44 3.632643 TGCATGCAGGAAAGACTATCA 57.367 42.857 18.46 0.00 0.00 2.15
44 45 5.303971 AGTATGCATGCAGGAAAGACTATC 58.696 41.667 26.69 5.98 0.00 2.08
45 46 5.071519 AGAGTATGCATGCAGGAAAGACTAT 59.928 40.000 26.69 14.82 0.00 2.12
46 47 4.406972 AGAGTATGCATGCAGGAAAGACTA 59.593 41.667 26.69 7.91 0.00 2.59
47 48 3.199508 AGAGTATGCATGCAGGAAAGACT 59.800 43.478 26.69 19.26 0.00 3.24
48 49 3.539604 AGAGTATGCATGCAGGAAAGAC 58.460 45.455 26.69 15.26 0.00 3.01
49 50 3.920231 AGAGTATGCATGCAGGAAAGA 57.080 42.857 26.69 0.00 0.00 2.52
50 51 3.066342 CCAAGAGTATGCATGCAGGAAAG 59.934 47.826 26.69 11.73 0.00 2.62
51 52 3.018856 CCAAGAGTATGCATGCAGGAAA 58.981 45.455 26.69 8.58 0.00 3.13
52 53 2.646930 CCAAGAGTATGCATGCAGGAA 58.353 47.619 26.69 11.23 0.00 3.36
53 54 1.748244 GCCAAGAGTATGCATGCAGGA 60.748 52.381 26.69 13.76 0.00 3.86
54 55 0.666913 GCCAAGAGTATGCATGCAGG 59.333 55.000 26.69 19.67 0.00 4.85
55 56 0.666913 GGCCAAGAGTATGCATGCAG 59.333 55.000 26.69 10.66 0.00 4.41
56 57 0.034283 TGGCCAAGAGTATGCATGCA 60.034 50.000 25.04 25.04 0.00 3.96
57 58 1.105457 TTGGCCAAGAGTATGCATGC 58.895 50.000 16.05 11.82 0.00 4.06
58 59 2.372264 AGTTGGCCAAGAGTATGCATG 58.628 47.619 21.21 0.00 0.00 4.06
59 60 2.814805 AGTTGGCCAAGAGTATGCAT 57.185 45.000 21.21 3.79 0.00 3.96
60 61 3.931907 ATAGTTGGCCAAGAGTATGCA 57.068 42.857 21.21 0.00 0.00 3.96
61 62 5.582689 AAAATAGTTGGCCAAGAGTATGC 57.417 39.130 21.21 4.99 0.00 3.14
62 63 7.396540 AGAAAAATAGTTGGCCAAGAGTATG 57.603 36.000 21.21 0.00 0.00 2.39
63 64 7.669722 TCAAGAAAAATAGTTGGCCAAGAGTAT 59.330 33.333 21.21 13.36 0.00 2.12
64 65 7.001674 TCAAGAAAAATAGTTGGCCAAGAGTA 58.998 34.615 21.21 11.49 0.00 2.59
65 66 5.833131 TCAAGAAAAATAGTTGGCCAAGAGT 59.167 36.000 21.21 9.39 0.00 3.24
66 67 6.331369 TCAAGAAAAATAGTTGGCCAAGAG 57.669 37.500 21.21 0.00 0.00 2.85
67 68 6.916360 ATCAAGAAAAATAGTTGGCCAAGA 57.084 33.333 21.21 10.82 0.00 3.02
110 111 5.813157 CCAAGGGCGAACTTTTAAAGAAAAA 59.187 36.000 12.02 0.00 34.16 1.94
111 112 5.105269 ACCAAGGGCGAACTTTTAAAGAAAA 60.105 36.000 12.02 0.00 33.48 2.29
112 113 4.403113 ACCAAGGGCGAACTTTTAAAGAAA 59.597 37.500 12.02 0.00 0.00 2.52
113 114 3.955551 ACCAAGGGCGAACTTTTAAAGAA 59.044 39.130 12.02 0.00 0.00 2.52
114 115 3.558033 ACCAAGGGCGAACTTTTAAAGA 58.442 40.909 12.02 0.00 0.00 2.52
115 116 5.009310 AGTTACCAAGGGCGAACTTTTAAAG 59.991 40.000 2.81 2.81 30.95 1.85
116 117 4.888823 AGTTACCAAGGGCGAACTTTTAAA 59.111 37.500 0.00 0.00 30.95 1.52
117 118 4.463070 AGTTACCAAGGGCGAACTTTTAA 58.537 39.130 0.00 0.00 30.95 1.52
118 119 4.089408 AGTTACCAAGGGCGAACTTTTA 57.911 40.909 0.00 0.00 30.95 1.52
119 120 2.940158 AGTTACCAAGGGCGAACTTTT 58.060 42.857 0.00 0.00 30.95 2.27
120 121 2.651382 AGTTACCAAGGGCGAACTTT 57.349 45.000 0.00 0.00 30.95 2.66
121 122 2.158726 TGAAGTTACCAAGGGCGAACTT 60.159 45.455 12.95 12.95 41.66 2.66
122 123 1.418637 TGAAGTTACCAAGGGCGAACT 59.581 47.619 0.00 0.00 34.83 3.01
123 124 1.886886 TGAAGTTACCAAGGGCGAAC 58.113 50.000 0.00 0.00 0.00 3.95
124 125 2.642154 TTGAAGTTACCAAGGGCGAA 57.358 45.000 0.00 0.00 0.00 4.70
125 126 2.642154 TTTGAAGTTACCAAGGGCGA 57.358 45.000 0.00 0.00 0.00 5.54
126 127 2.163613 GGATTTGAAGTTACCAAGGGCG 59.836 50.000 0.00 0.00 0.00 6.13
127 128 2.496070 GGGATTTGAAGTTACCAAGGGC 59.504 50.000 0.00 0.00 0.00 5.19
128 129 2.752903 CGGGATTTGAAGTTACCAAGGG 59.247 50.000 0.00 0.00 0.00 3.95
129 130 2.752903 CCGGGATTTGAAGTTACCAAGG 59.247 50.000 0.00 0.00 0.00 3.61
130 131 3.681593 TCCGGGATTTGAAGTTACCAAG 58.318 45.455 0.00 0.00 0.00 3.61
131 132 3.791953 TCCGGGATTTGAAGTTACCAA 57.208 42.857 0.00 0.00 0.00 3.67
132 133 3.371166 GGATCCGGGATTTGAAGTTACCA 60.371 47.826 11.57 0.00 0.00 3.25
133 134 3.211865 GGATCCGGGATTTGAAGTTACC 58.788 50.000 11.57 0.32 0.00 2.85
134 135 2.870411 CGGATCCGGGATTTGAAGTTAC 59.130 50.000 26.95 0.00 35.56 2.50
135 136 2.743838 GCGGATCCGGGATTTGAAGTTA 60.744 50.000 33.98 0.00 40.19 2.24
136 137 2.017113 GCGGATCCGGGATTTGAAGTT 61.017 52.381 33.98 0.00 40.19 2.66
137 138 0.463833 GCGGATCCGGGATTTGAAGT 60.464 55.000 33.98 0.00 40.19 3.01
138 139 1.166531 GGCGGATCCGGGATTTGAAG 61.167 60.000 33.98 3.88 40.19 3.02
139 140 1.153046 GGCGGATCCGGGATTTGAA 60.153 57.895 33.98 0.00 40.19 2.69
140 141 2.371259 TGGCGGATCCGGGATTTGA 61.371 57.895 33.98 0.00 40.19 2.69
141 142 2.186826 GTGGCGGATCCGGGATTTG 61.187 63.158 33.98 7.95 40.19 2.32
142 143 2.192175 GTGGCGGATCCGGGATTT 59.808 61.111 33.98 0.00 40.19 2.17
143 144 2.768344 AGTGGCGGATCCGGGATT 60.768 61.111 33.98 0.00 40.19 3.01
144 145 3.550431 CAGTGGCGGATCCGGGAT 61.550 66.667 33.98 9.85 40.19 3.85
146 147 4.530857 GACAGTGGCGGATCCGGG 62.531 72.222 33.98 9.39 40.19 5.73
147 148 3.770040 TGACAGTGGCGGATCCGG 61.770 66.667 33.98 19.76 40.19 5.14
148 149 2.509336 GTGACAGTGGCGGATCCG 60.509 66.667 30.03 30.03 43.09 4.18
149 150 2.125106 GGTGACAGTGGCGGATCC 60.125 66.667 0.00 0.00 0.00 3.36
150 151 2.509336 CGGTGACAGTGGCGGATC 60.509 66.667 0.00 0.00 0.00 3.36
151 152 4.760047 GCGGTGACAGTGGCGGAT 62.760 66.667 0.00 0.00 0.00 4.18
157 158 4.063967 TAGGGCGCGGTGACAGTG 62.064 66.667 8.83 0.00 0.00 3.66
158 159 4.065281 GTAGGGCGCGGTGACAGT 62.065 66.667 8.83 0.00 0.00 3.55
159 160 2.337749 CTAGTAGGGCGCGGTGACAG 62.338 65.000 8.83 0.00 0.00 3.51
160 161 2.361483 TAGTAGGGCGCGGTGACA 60.361 61.111 8.83 0.00 0.00 3.58
161 162 2.412112 CTAGTAGGGCGCGGTGAC 59.588 66.667 8.83 0.00 0.00 3.67
162 163 2.831742 CCTAGTAGGGCGCGGTGA 60.832 66.667 8.83 0.00 0.00 4.02
163 164 4.587189 GCCTAGTAGGGCGCGGTG 62.587 72.222 18.13 0.00 42.82 4.94
175 176 1.429463 GTCGTGAAGTTGTGGCCTAG 58.571 55.000 3.32 0.00 0.00 3.02
183 184 0.105964 TCCAGGTGGTCGTGAAGTTG 59.894 55.000 0.00 0.00 36.34 3.16
191 192 1.442769 CTCAATTGTCCAGGTGGTCG 58.557 55.000 5.13 0.00 36.34 4.79
195 196 2.430465 CTGACCTCAATTGTCCAGGTG 58.570 52.381 19.17 5.24 40.85 4.00
200 201 2.162681 CAACCCTGACCTCAATTGTCC 58.837 52.381 5.13 0.00 31.60 4.02
206 207 2.061848 TGGATTCAACCCTGACCTCAA 58.938 47.619 0.00 0.00 0.00 3.02
213 214 3.328505 GTTTGCAATGGATTCAACCCTG 58.671 45.455 0.00 0.00 0.00 4.45
214 215 2.302733 GGTTTGCAATGGATTCAACCCT 59.697 45.455 0.00 0.00 0.00 4.34
216 217 2.302733 AGGGTTTGCAATGGATTCAACC 59.697 45.455 0.00 1.55 0.00 3.77
233 234 2.046025 AGGAAGCTTAGGGTCTTAGGGT 59.954 50.000 0.00 0.00 0.00 4.34
252 253 0.039074 GTCGCCGACATCCTATGAGG 60.039 60.000 13.23 0.00 35.72 3.86
254 255 1.107945 TTGTCGCCGACATCCTATGA 58.892 50.000 21.92 0.43 42.40 2.15
338 339 4.710423 TCACAATGTGAGCTAGAGAGAC 57.290 45.455 12.63 0.00 37.67 3.36
379 385 0.937304 CCTATTTCACCGGCGATGTG 59.063 55.000 9.30 9.48 35.01 3.21
389 395 5.357257 TCTATGTTTCTCGCCCTATTTCAC 58.643 41.667 0.00 0.00 0.00 3.18
417 423 2.848562 TTTTTCAGATTCGCGTCGAC 57.151 45.000 5.77 5.18 34.89 4.20
425 431 6.533367 AGAGTCGCAGTCTATTTTTCAGATTC 59.467 38.462 0.00 0.00 0.00 2.52
437 443 2.885266 ACAACTCAAGAGTCGCAGTCTA 59.115 45.455 2.78 0.00 41.58 2.59
446 452 3.350219 ACCACAACACAACTCAAGAGT 57.650 42.857 0.00 0.00 44.94 3.24
750 759 3.455469 GCCCTGGCCAATGAGTGC 61.455 66.667 7.01 0.00 34.56 4.40
968 977 3.261580 GCTTCTCTCTTCTCTTCTTGCC 58.738 50.000 0.00 0.00 0.00 4.52
1140 1149 2.685017 ACTCCGCTGGCCATGAGA 60.685 61.111 25.52 14.13 0.00 3.27
1280 1289 6.904498 AGTCTACTAAAGCGAGCATAGTATG 58.096 40.000 15.89 5.73 33.11 2.39
1560 1583 0.456221 CGGTCTTGAGGTCATAGCGT 59.544 55.000 6.37 0.00 32.28 5.07
1566 1589 1.819288 GAGATGACGGTCTTGAGGTCA 59.181 52.381 9.88 6.83 44.00 4.02
1793 1822 2.615869 TGGTCAAGCTGCAAACAAAAC 58.384 42.857 1.02 0.00 0.00 2.43
1913 1942 0.680921 AAGCAGCACGGCCATTATGT 60.681 50.000 2.24 0.00 0.00 2.29
1927 1956 4.525912 AACATAAAAGGCCTGAAAGCAG 57.474 40.909 5.69 0.00 41.93 4.24
2032 2087 5.065235 TCTGCTTGTGATTTCATCTGTGAA 58.935 37.500 0.00 0.00 42.41 3.18
2033 2088 4.644498 TCTGCTTGTGATTTCATCTGTGA 58.356 39.130 0.00 0.00 0.00 3.58
2034 2089 5.562506 ATCTGCTTGTGATTTCATCTGTG 57.437 39.130 0.00 0.00 0.00 3.66
2035 2090 5.708697 TGAATCTGCTTGTGATTTCATCTGT 59.291 36.000 0.00 0.00 34.67 3.41
2036 2091 6.127980 ACTGAATCTGCTTGTGATTTCATCTG 60.128 38.462 0.00 0.00 34.67 2.90
2037 2092 5.944599 ACTGAATCTGCTTGTGATTTCATCT 59.055 36.000 0.00 0.00 34.67 2.90
2038 2093 6.128090 TGACTGAATCTGCTTGTGATTTCATC 60.128 38.462 0.00 0.00 34.67 2.92
2039 2094 5.708697 TGACTGAATCTGCTTGTGATTTCAT 59.291 36.000 0.00 0.00 34.67 2.57
2040 2095 5.065235 TGACTGAATCTGCTTGTGATTTCA 58.935 37.500 0.00 0.00 34.67 2.69
2041 2096 5.618056 TGACTGAATCTGCTTGTGATTTC 57.382 39.130 0.00 0.00 34.67 2.17
2042 2097 7.555195 TCATATGACTGAATCTGCTTGTGATTT 59.445 33.333 0.00 0.00 34.67 2.17
2043 2098 7.052248 TCATATGACTGAATCTGCTTGTGATT 58.948 34.615 0.00 0.00 36.91 2.57
2044 2099 6.589135 TCATATGACTGAATCTGCTTGTGAT 58.411 36.000 0.00 0.00 0.00 3.06
2045 2100 5.981174 TCATATGACTGAATCTGCTTGTGA 58.019 37.500 0.00 0.00 0.00 3.58
2046 2101 6.537660 TCTTCATATGACTGAATCTGCTTGTG 59.462 38.462 4.48 0.00 34.76 3.33
2047 2102 6.647229 TCTTCATATGACTGAATCTGCTTGT 58.353 36.000 4.48 0.00 34.76 3.16
2048 2103 6.762187 ACTCTTCATATGACTGAATCTGCTTG 59.238 38.462 4.48 0.00 34.76 4.01
2049 2104 6.887013 ACTCTTCATATGACTGAATCTGCTT 58.113 36.000 4.48 0.00 34.76 3.91
2050 2105 6.482898 ACTCTTCATATGACTGAATCTGCT 57.517 37.500 4.48 0.00 34.76 4.24
2051 2106 8.547069 GTTTACTCTTCATATGACTGAATCTGC 58.453 37.037 4.48 0.00 34.76 4.26
2052 2107 9.591792 TGTTTACTCTTCATATGACTGAATCTG 57.408 33.333 4.48 0.00 34.76 2.90
2110 2165 6.811634 TTGGAACGGAGGGAGTATTTATTA 57.188 37.500 0.00 0.00 0.00 0.98
2113 2168 5.703730 ATTTGGAACGGAGGGAGTATTTA 57.296 39.130 0.00 0.00 0.00 1.40
2114 2169 4.586306 ATTTGGAACGGAGGGAGTATTT 57.414 40.909 0.00 0.00 0.00 1.40
2119 2174 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2121 2176 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2122 2177 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2125 2180 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
2126 2181 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
2127 2182 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
2128 2183 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
2129 2184 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
2130 2185 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
2131 2186 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
2132 2187 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
2133 2188 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
2134 2189 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
2135 2190 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
2136 2191 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
2137 2192 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
2138 2193 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
2139 2194 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
2140 2195 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
2141 2196 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
2159 2214 8.652463 CGTGGTTTTAGTTCAAAAAGTTCAAAT 58.348 29.630 0.00 0.00 37.85 2.32
2160 2215 7.866393 TCGTGGTTTTAGTTCAAAAAGTTCAAA 59.134 29.630 0.00 0.00 37.85 2.69
2161 2216 7.326547 GTCGTGGTTTTAGTTCAAAAAGTTCAA 59.673 33.333 0.00 0.00 37.85 2.69
2162 2217 6.802834 GTCGTGGTTTTAGTTCAAAAAGTTCA 59.197 34.615 0.00 0.00 37.85 3.18
2163 2218 6.022017 CGTCGTGGTTTTAGTTCAAAAAGTTC 60.022 38.462 0.00 0.00 37.85 3.01
2164 2219 5.796437 CGTCGTGGTTTTAGTTCAAAAAGTT 59.204 36.000 0.00 0.00 37.85 2.66
2165 2220 5.122082 TCGTCGTGGTTTTAGTTCAAAAAGT 59.878 36.000 0.00 0.00 37.85 2.66
2166 2221 5.561993 TCGTCGTGGTTTTAGTTCAAAAAG 58.438 37.500 0.00 0.00 37.85 2.27
2167 2222 5.122082 ACTCGTCGTGGTTTTAGTTCAAAAA 59.878 36.000 0.00 0.00 37.85 1.94
2168 2223 4.630940 ACTCGTCGTGGTTTTAGTTCAAAA 59.369 37.500 0.00 0.00 33.66 2.44
2169 2224 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
2170 2225 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
2171 2226 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
2172 2227 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
2173 2228 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
2174 2229 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
2175 2230 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
2176 2231 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
2177 2232 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
2178 2233 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
2179 2234 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
2180 2235 3.389925 TTCCAAATTACTCGTCGTGGT 57.610 42.857 0.00 0.00 0.00 4.16
2181 2236 3.124636 CCTTTCCAAATTACTCGTCGTGG 59.875 47.826 0.00 0.00 0.00 4.94
2182 2237 3.991773 TCCTTTCCAAATTACTCGTCGTG 59.008 43.478 0.00 0.00 0.00 4.35
2183 2238 4.243270 CTCCTTTCCAAATTACTCGTCGT 58.757 43.478 0.00 0.00 0.00 4.34
2184 2239 3.617263 CCTCCTTTCCAAATTACTCGTCG 59.383 47.826 0.00 0.00 0.00 5.12
2185 2240 3.939592 CCCTCCTTTCCAAATTACTCGTC 59.060 47.826 0.00 0.00 0.00 4.20
2186 2241 3.585732 TCCCTCCTTTCCAAATTACTCGT 59.414 43.478 0.00 0.00 0.00 4.18
2187 2242 4.192317 CTCCCTCCTTTCCAAATTACTCG 58.808 47.826 0.00 0.00 0.00 4.18
2188 2243 5.180810 ACTCCCTCCTTTCCAAATTACTC 57.819 43.478 0.00 0.00 0.00 2.59
2189 2244 6.274908 AGTTACTCCCTCCTTTCCAAATTACT 59.725 38.462 0.00 0.00 0.00 2.24
2190 2245 6.482524 AGTTACTCCCTCCTTTCCAAATTAC 58.517 40.000 0.00 0.00 0.00 1.89
2191 2246 6.713731 AGTTACTCCCTCCTTTCCAAATTA 57.286 37.500 0.00 0.00 0.00 1.40
2192 2247 5.600669 AGTTACTCCCTCCTTTCCAAATT 57.399 39.130 0.00 0.00 0.00 1.82
2193 2248 5.600669 AAGTTACTCCCTCCTTTCCAAAT 57.399 39.130 0.00 0.00 0.00 2.32
2194 2249 5.609708 ACTAAGTTACTCCCTCCTTTCCAAA 59.390 40.000 0.00 0.00 0.00 3.28
2195 2250 5.160386 ACTAAGTTACTCCCTCCTTTCCAA 58.840 41.667 0.00 0.00 0.00 3.53
2196 2251 4.759953 ACTAAGTTACTCCCTCCTTTCCA 58.240 43.478 0.00 0.00 0.00 3.53
2197 2252 5.758790 AACTAAGTTACTCCCTCCTTTCC 57.241 43.478 0.00 0.00 0.00 3.13
2198 2253 8.131847 TCTTAACTAAGTTACTCCCTCCTTTC 57.868 38.462 0.00 0.00 34.93 2.62
2199 2254 7.310547 GCTCTTAACTAAGTTACTCCCTCCTTT 60.311 40.741 0.00 0.00 34.93 3.11
2200 2255 6.154877 GCTCTTAACTAAGTTACTCCCTCCTT 59.845 42.308 0.00 0.00 34.93 3.36
2201 2256 5.657745 GCTCTTAACTAAGTTACTCCCTCCT 59.342 44.000 0.00 0.00 34.93 3.69
2202 2257 5.163426 GGCTCTTAACTAAGTTACTCCCTCC 60.163 48.000 0.00 0.00 34.93 4.30
2203 2258 5.163426 GGGCTCTTAACTAAGTTACTCCCTC 60.163 48.000 0.00 0.00 34.93 4.30
2204 2259 4.715792 GGGCTCTTAACTAAGTTACTCCCT 59.284 45.833 0.00 0.00 34.93 4.20
2205 2260 4.468868 TGGGCTCTTAACTAAGTTACTCCC 59.531 45.833 0.00 0.00 34.93 4.30
2206 2261 5.672421 TGGGCTCTTAACTAAGTTACTCC 57.328 43.478 0.00 0.00 34.93 3.85
2207 2262 6.461640 TGTTGGGCTCTTAACTAAGTTACTC 58.538 40.000 0.00 0.00 34.93 2.59
2208 2263 6.429521 TGTTGGGCTCTTAACTAAGTTACT 57.570 37.500 0.00 0.00 34.93 2.24
2209 2264 5.121925 GCTGTTGGGCTCTTAACTAAGTTAC 59.878 44.000 0.00 0.00 34.93 2.50
2210 2265 5.243207 GCTGTTGGGCTCTTAACTAAGTTA 58.757 41.667 0.00 0.00 34.93 2.24
2211 2266 4.072839 GCTGTTGGGCTCTTAACTAAGTT 58.927 43.478 0.00 0.00 34.93 2.66
2212 2267 3.559384 GGCTGTTGGGCTCTTAACTAAGT 60.559 47.826 0.00 0.00 37.53 2.24
2213 2268 3.010420 GGCTGTTGGGCTCTTAACTAAG 58.990 50.000 0.00 0.00 37.53 2.18
2214 2269 2.373836 TGGCTGTTGGGCTCTTAACTAA 59.626 45.455 0.00 0.00 41.48 2.24
2215 2270 1.982226 TGGCTGTTGGGCTCTTAACTA 59.018 47.619 0.00 0.00 41.48 2.24
2216 2271 0.771127 TGGCTGTTGGGCTCTTAACT 59.229 50.000 0.00 0.00 41.48 2.24
2217 2272 1.168714 CTGGCTGTTGGGCTCTTAAC 58.831 55.000 0.00 0.00 41.48 2.01
2218 2273 1.064003 TCTGGCTGTTGGGCTCTTAA 58.936 50.000 0.00 0.00 41.48 1.85
2219 2274 1.003580 CTTCTGGCTGTTGGGCTCTTA 59.996 52.381 0.00 0.00 41.48 2.10
2220 2275 0.251077 CTTCTGGCTGTTGGGCTCTT 60.251 55.000 0.00 0.00 41.48 2.85
2236 2291 4.964593 TGGGTTGGAGTAAACTGTACTTC 58.035 43.478 0.00 0.00 0.00 3.01
2237 2292 5.376756 TTGGGTTGGAGTAAACTGTACTT 57.623 39.130 0.00 0.00 0.00 2.24
2249 2306 6.543430 TTTGGATGAATAATTGGGTTGGAG 57.457 37.500 0.00 0.00 0.00 3.86
2257 2314 8.749499 GCGAAAGAAGATTTGGATGAATAATTG 58.251 33.333 0.00 0.00 0.00 2.32
2261 2318 7.630242 AAGCGAAAGAAGATTTGGATGAATA 57.370 32.000 0.00 0.00 0.00 1.75
2298 2355 4.473477 AGCACTGACTGGGAACTAATAC 57.527 45.455 0.00 0.00 0.00 1.89
2304 2361 2.841442 ACTTAGCACTGACTGGGAAC 57.159 50.000 0.00 0.00 0.00 3.62
2432 2490 2.009774 CGTTGATCTAGCAGTTTGGGG 58.990 52.381 0.00 0.00 0.00 4.96
2479 2537 2.676342 GTTTTAGATGTACGCCTGGTGG 59.324 50.000 12.58 0.00 0.00 4.61
2480 2538 2.676342 GGTTTTAGATGTACGCCTGGTG 59.324 50.000 5.54 5.54 0.00 4.17
2488 2546 5.484715 TGGTAGCTGTGGTTTTAGATGTAC 58.515 41.667 0.00 0.00 0.00 2.90
2595 2779 1.012841 GCTGGAGTTGTAGCATCTGC 58.987 55.000 0.00 0.00 39.67 4.26
2598 2782 2.680312 TCAGCTGGAGTTGTAGCATC 57.320 50.000 15.13 0.00 42.29 3.91
2622 2806 4.322080 TCTATGCCTGACAGGATAAACG 57.678 45.455 26.25 7.54 37.67 3.60
2642 2826 9.013490 CCATTCAACTGAAATGTCGAAATAATC 57.987 33.333 0.00 0.00 37.61 1.75
2676 2860 3.181454 TGAGGTGTTCTCTTCCCAAGTTC 60.181 47.826 0.00 0.00 42.86 3.01
2677 2861 2.777692 TGAGGTGTTCTCTTCCCAAGTT 59.222 45.455 0.00 0.00 42.86 2.66
2683 2867 3.261897 TCAGGATTGAGGTGTTCTCTTCC 59.738 47.826 0.00 0.00 42.86 3.46
2712 2896 7.254084 GGAAGTTTTGTACAAGCACTGAATTTG 60.254 37.037 18.42 0.00 0.00 2.32
2713 2897 6.756542 GGAAGTTTTGTACAAGCACTGAATTT 59.243 34.615 18.42 8.85 0.00 1.82
2765 2949 0.259065 TCTACCCGGAGCACATCTCT 59.741 55.000 0.73 0.00 41.60 3.10
2841 3028 4.133078 GGGGAGAATATCTTGCAAGTCAG 58.867 47.826 25.19 0.99 0.00 3.51


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

AutoCloner maintained by Alex Coulton.