Multiple sequence alignment - TraesCS5B01G313700

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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 TraesCS5B01G313700 chr5B 100.000 3885 0 0 1 3885 496262515 496266399 0.000000e+00 7175.0
1 TraesCS5B01G313700 chr5B 84.848 165 18 4 5 162 154041696 154041860 4.020000e-35 159.0
2 TraesCS5B01G313700 chr5B 100.000 36 0 0 2277 2312 496264747 496264782 2.510000e-07 67.6
3 TraesCS5B01G313700 chr5B 100.000 36 0 0 2233 2268 496264791 496264826 2.510000e-07 67.6
4 TraesCS5B01G313700 chr5D 92.327 3219 129 47 277 3434 412307156 412310317 0.000000e+00 4468.0
5 TraesCS5B01G313700 chr5D 94.118 391 16 3 3498 3885 412310522 412310908 4.320000e-164 588.0
6 TraesCS5B01G313700 chr5D 100.000 36 0 0 2277 2312 412309095 412309130 2.510000e-07 67.6
7 TraesCS5B01G313700 chr5D 100.000 36 0 0 2233 2268 412309139 412309174 2.510000e-07 67.6
8 TraesCS5B01G313700 chr5A 92.165 2425 106 35 796 3169 524047710 524050101 0.000000e+00 3349.0
9 TraesCS5B01G313700 chr5A 91.517 389 21 2 3498 3885 524050466 524050843 3.440000e-145 525.0
10 TraesCS5B01G313700 chr5A 88.828 367 21 7 389 735 524047341 524047707 2.140000e-117 433.0
11 TraesCS5B01G313700 chr5A 92.271 207 12 3 3228 3434 524050099 524050301 1.370000e-74 291.0
12 TraesCS5B01G313700 chr5A 100.000 36 0 0 2277 2312 524049177 524049212 2.510000e-07 67.6
13 TraesCS5B01G313700 chr5A 100.000 36 0 0 2233 2268 524049221 524049256 2.510000e-07 67.6
14 TraesCS5B01G313700 chr6D 90.643 171 10 3 8 172 354198493 354198323 5.050000e-54 222.0
15 TraesCS5B01G313700 chr1D 90.789 152 8 3 8 153 165744524 165744675 8.510000e-47 198.0
16 TraesCS5B01G313700 chr1D 92.063 126 10 0 1 126 161731677 161731802 1.110000e-40 178.0
17 TraesCS5B01G313700 chr1D 81.481 189 25 8 1 179 187363155 187363343 3.130000e-31 147.0
18 TraesCS5B01G313700 chr4B 86.577 149 14 1 11 153 330404593 330404741 4.020000e-35 159.0
19 TraesCS5B01G313700 chr2D 84.024 169 19 7 11 172 268643817 268643650 5.200000e-34 156.0
20 TraesCS5B01G313700 chr2D 82.486 177 25 3 2 172 274702882 274703058 2.420000e-32 150.0
21 TraesCS5B01G313700 chr7A 82.955 176 23 6 1 169 294661222 294661397 6.720000e-33 152.0
22 TraesCS5B01G313700 chr7A 87.273 55 6 1 3296 3350 706574595 706574648 1.170000e-05 62.1
23 TraesCS5B01G313700 chr7D 80.137 146 24 4 3286 3430 613910872 613911013 1.910000e-18 104.0
24 TraesCS5B01G313700 chr7D 85.714 56 7 1 3296 3351 614389707 614389761 1.510000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G313700 chr5B 496262515 496266399 3884 False 2436.733333 7175 100.000000 1 3885 3 chr5B.!!$F2 3884
1 TraesCS5B01G313700 chr5D 412307156 412310908 3752 False 1297.800000 4468 96.611250 277 3885 4 chr5D.!!$F1 3608
2 TraesCS5B01G313700 chr5A 524047341 524050843 3502 False 788.866667 3349 94.130167 389 3885 6 chr5A.!!$F1 3496

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
124 125 0.033504 GTGAGTGCGAGAACCCTCAA 59.966 55.000 0.00 0.00 39.39 3.02 F
150 151 0.242017 CCTTTTCCTTGCGCTTCTGG 59.758 55.000 9.73 5.56 0.00 3.86 F
160 161 0.312102 GCGCTTCTGGTTGCTCTTTT 59.688 50.000 0.00 0.00 0.00 2.27 F
680 701 0.315706 GAGCGCATAAAGCAAGCTCG 60.316 55.000 11.47 0.00 43.47 5.03 F
1991 2030 1.687123 AGCACTTCCCGCTATTCGTAT 59.313 47.619 0.00 0.00 38.15 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 1747 0.318762 GTCGAGCCAGAACTCCTGTT 59.681 55.000 0.00 0.00 41.33 3.16 R
1718 1748 0.827925 TGTCGAGCCAGAACTCCTGT 60.828 55.000 0.00 0.00 41.33 4.00 R
2157 2229 0.749454 CAGGGGCCACTGCAGATAAC 60.749 60.000 25.05 7.69 40.13 1.89 R
2179 2251 1.132262 CATGTTCCAACGGCCATACAC 59.868 52.381 2.24 0.00 0.00 2.90 R
3675 3954 0.249615 CACGCATGATCTCATCCGGT 60.250 55.000 8.26 0.00 41.51 5.28 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
17 18 3.797353 TCCATCGGCCTTCCCAGC 61.797 66.667 0.00 0.00 0.00 4.85
24 25 3.278157 GCCTTCCCAGCCTTTTCG 58.722 61.111 0.00 0.00 0.00 3.46
25 26 2.343426 GCCTTCCCAGCCTTTTCGG 61.343 63.158 0.00 0.00 0.00 4.30
68 69 3.660111 GCACGCGGCAACTTCCTT 61.660 61.111 12.47 0.00 43.97 3.36
69 70 2.252260 CACGCGGCAACTTCCTTG 59.748 61.111 12.47 0.00 0.00 3.61
76 77 2.676471 CAACTTCCTTGCCGGGGG 60.676 66.667 2.18 0.00 0.00 5.40
87 88 4.778143 CCGGGGGCTTCGGTCTTG 62.778 72.222 10.09 0.00 42.33 3.02
88 89 4.778143 CGGGGGCTTCGGTCTTGG 62.778 72.222 0.00 0.00 0.00 3.61
91 92 4.035102 GGGCTTCGGTCTTGGCCT 62.035 66.667 3.32 0.00 43.62 5.19
92 93 2.034221 GGCTTCGGTCTTGGCCTT 59.966 61.111 3.32 0.00 41.20 4.35
93 94 2.041115 GGCTTCGGTCTTGGCCTTC 61.041 63.158 3.32 0.00 41.20 3.46
94 95 1.003233 GCTTCGGTCTTGGCCTTCT 60.003 57.895 3.32 0.00 0.00 2.85
95 96 0.606673 GCTTCGGTCTTGGCCTTCTT 60.607 55.000 3.32 0.00 0.00 2.52
96 97 1.160137 CTTCGGTCTTGGCCTTCTTG 58.840 55.000 3.32 0.00 0.00 3.02
97 98 0.889186 TTCGGTCTTGGCCTTCTTGC 60.889 55.000 3.32 0.00 0.00 4.01
104 105 2.437895 GGCCTTCTTGCCGGTACC 60.438 66.667 1.90 0.16 42.54 3.34
105 106 2.818274 GCCTTCTTGCCGGTACCG 60.818 66.667 27.68 27.68 39.44 4.02
106 107 2.660802 CCTTCTTGCCGGTACCGT 59.339 61.111 31.24 0.00 37.81 4.83
107 108 1.740296 CCTTCTTGCCGGTACCGTG 60.740 63.158 31.24 22.95 37.81 4.94
108 109 1.290955 CTTCTTGCCGGTACCGTGA 59.709 57.895 31.24 19.97 37.81 4.35
109 110 0.736325 CTTCTTGCCGGTACCGTGAG 60.736 60.000 31.24 23.61 37.81 3.51
110 111 1.466025 TTCTTGCCGGTACCGTGAGT 61.466 55.000 31.24 0.00 37.81 3.41
111 112 1.736645 CTTGCCGGTACCGTGAGTG 60.737 63.158 31.24 17.35 37.81 3.51
112 113 3.869473 TTGCCGGTACCGTGAGTGC 62.869 63.158 31.24 25.76 37.81 4.40
114 115 3.740397 CCGGTACCGTGAGTGCGA 61.740 66.667 31.24 0.00 37.81 5.10
115 116 2.202440 CGGTACCGTGAGTGCGAG 60.202 66.667 26.39 0.00 34.35 5.03
116 117 2.683859 CGGTACCGTGAGTGCGAGA 61.684 63.158 26.39 0.00 34.35 4.04
117 118 1.582968 GGTACCGTGAGTGCGAGAA 59.417 57.895 0.00 0.00 30.59 2.87
118 119 0.731855 GGTACCGTGAGTGCGAGAAC 60.732 60.000 0.00 0.00 30.59 3.01
119 120 0.731855 GTACCGTGAGTGCGAGAACC 60.732 60.000 0.00 0.00 0.00 3.62
120 121 1.870055 TACCGTGAGTGCGAGAACCC 61.870 60.000 0.00 0.00 0.00 4.11
121 122 2.651361 CGTGAGTGCGAGAACCCT 59.349 61.111 0.00 0.00 0.00 4.34
122 123 1.444553 CGTGAGTGCGAGAACCCTC 60.445 63.158 0.00 0.00 36.08 4.30
123 124 1.666011 GTGAGTGCGAGAACCCTCA 59.334 57.895 0.00 0.00 39.39 3.86
124 125 0.033504 GTGAGTGCGAGAACCCTCAA 59.966 55.000 0.00 0.00 39.39 3.02
125 126 0.033504 TGAGTGCGAGAACCCTCAAC 59.966 55.000 0.00 0.00 39.39 3.18
126 127 1.006102 AGTGCGAGAACCCTCAACG 60.006 57.895 0.00 0.00 39.39 4.10
127 128 2.027625 GTGCGAGAACCCTCAACGG 61.028 63.158 0.00 0.00 39.39 4.44
128 129 3.119096 GCGAGAACCCTCAACGGC 61.119 66.667 0.00 0.00 39.39 5.68
129 130 2.657237 CGAGAACCCTCAACGGCT 59.343 61.111 0.00 0.00 39.39 5.52
130 131 1.738099 CGAGAACCCTCAACGGCTG 60.738 63.158 0.00 0.00 39.39 4.85
131 132 2.032681 AGAACCCTCAACGGCTGC 59.967 61.111 0.00 0.00 0.00 5.25
132 133 3.056328 GAACCCTCAACGGCTGCC 61.056 66.667 9.11 9.11 0.00 4.85
133 134 3.553095 GAACCCTCAACGGCTGCCT 62.553 63.158 17.92 0.55 0.00 4.75
134 135 3.133365 AACCCTCAACGGCTGCCTT 62.133 57.895 17.92 4.00 0.00 4.35
135 136 2.282462 CCCTCAACGGCTGCCTTT 60.282 61.111 17.92 11.27 0.00 3.11
136 137 1.903404 CCCTCAACGGCTGCCTTTT 60.903 57.895 17.92 6.85 0.00 2.27
137 138 1.581447 CCTCAACGGCTGCCTTTTC 59.419 57.895 17.92 0.00 0.00 2.29
138 139 1.581447 CTCAACGGCTGCCTTTTCC 59.419 57.895 17.92 0.00 0.00 3.13
139 140 0.890996 CTCAACGGCTGCCTTTTCCT 60.891 55.000 17.92 0.00 0.00 3.36
140 141 0.467290 TCAACGGCTGCCTTTTCCTT 60.467 50.000 17.92 0.00 0.00 3.36
141 142 0.318955 CAACGGCTGCCTTTTCCTTG 60.319 55.000 17.92 0.40 0.00 3.61
142 143 2.087462 AACGGCTGCCTTTTCCTTGC 62.087 55.000 17.92 0.00 0.00 4.01
143 144 2.259511 GGCTGCCTTTTCCTTGCG 59.740 61.111 12.43 0.00 0.00 4.85
144 145 2.431430 GCTGCCTTTTCCTTGCGC 60.431 61.111 0.00 0.00 0.00 6.09
145 146 2.924105 GCTGCCTTTTCCTTGCGCT 61.924 57.895 9.73 0.00 0.00 5.92
146 147 1.662044 CTGCCTTTTCCTTGCGCTT 59.338 52.632 9.73 0.00 0.00 4.68
147 148 0.387750 CTGCCTTTTCCTTGCGCTTC 60.388 55.000 9.73 0.00 0.00 3.86
148 149 0.823356 TGCCTTTTCCTTGCGCTTCT 60.823 50.000 9.73 0.00 0.00 2.85
149 150 0.387750 GCCTTTTCCTTGCGCTTCTG 60.388 55.000 9.73 0.00 0.00 3.02
150 151 0.242017 CCTTTTCCTTGCGCTTCTGG 59.758 55.000 9.73 5.56 0.00 3.86
151 152 0.954452 CTTTTCCTTGCGCTTCTGGT 59.046 50.000 9.73 0.00 0.00 4.00
152 153 1.338020 CTTTTCCTTGCGCTTCTGGTT 59.662 47.619 9.73 0.00 0.00 3.67
153 154 0.667993 TTTCCTTGCGCTTCTGGTTG 59.332 50.000 9.73 0.00 0.00 3.77
154 155 1.795170 TTCCTTGCGCTTCTGGTTGC 61.795 55.000 9.73 0.00 0.00 4.17
155 156 2.263741 CCTTGCGCTTCTGGTTGCT 61.264 57.895 9.73 0.00 0.00 3.91
156 157 1.208614 CTTGCGCTTCTGGTTGCTC 59.791 57.895 9.73 0.00 0.00 4.26
157 158 1.227943 TTGCGCTTCTGGTTGCTCT 60.228 52.632 9.73 0.00 0.00 4.09
158 159 0.819259 TTGCGCTTCTGGTTGCTCTT 60.819 50.000 9.73 0.00 0.00 2.85
159 160 0.819259 TGCGCTTCTGGTTGCTCTTT 60.819 50.000 9.73 0.00 0.00 2.52
160 161 0.312102 GCGCTTCTGGTTGCTCTTTT 59.688 50.000 0.00 0.00 0.00 2.27
161 162 1.269257 GCGCTTCTGGTTGCTCTTTTT 60.269 47.619 0.00 0.00 0.00 1.94
162 163 2.031157 GCGCTTCTGGTTGCTCTTTTTA 60.031 45.455 0.00 0.00 0.00 1.52
163 164 3.366374 GCGCTTCTGGTTGCTCTTTTTAT 60.366 43.478 0.00 0.00 0.00 1.40
164 165 4.798574 CGCTTCTGGTTGCTCTTTTTATT 58.201 39.130 0.00 0.00 0.00 1.40
165 166 4.853743 CGCTTCTGGTTGCTCTTTTTATTC 59.146 41.667 0.00 0.00 0.00 1.75
166 167 5.335191 CGCTTCTGGTTGCTCTTTTTATTCT 60.335 40.000 0.00 0.00 0.00 2.40
167 168 6.450545 GCTTCTGGTTGCTCTTTTTATTCTT 58.549 36.000 0.00 0.00 0.00 2.52
168 169 6.584184 GCTTCTGGTTGCTCTTTTTATTCTTC 59.416 38.462 0.00 0.00 0.00 2.87
169 170 6.575162 TCTGGTTGCTCTTTTTATTCTTCC 57.425 37.500 0.00 0.00 0.00 3.46
170 171 6.306987 TCTGGTTGCTCTTTTTATTCTTCCT 58.693 36.000 0.00 0.00 0.00 3.36
171 172 6.431234 TCTGGTTGCTCTTTTTATTCTTCCTC 59.569 38.462 0.00 0.00 0.00 3.71
172 173 5.181245 TGGTTGCTCTTTTTATTCTTCCTCG 59.819 40.000 0.00 0.00 0.00 4.63
173 174 5.392057 GGTTGCTCTTTTTATTCTTCCTCGG 60.392 44.000 0.00 0.00 0.00 4.63
174 175 3.689649 TGCTCTTTTTATTCTTCCTCGGC 59.310 43.478 0.00 0.00 0.00 5.54
175 176 3.065510 GCTCTTTTTATTCTTCCTCGGCC 59.934 47.826 0.00 0.00 0.00 6.13
176 177 3.267483 TCTTTTTATTCTTCCTCGGCCG 58.733 45.455 22.12 22.12 0.00 6.13
177 178 2.032680 TTTTATTCTTCCTCGGCCGG 57.967 50.000 27.83 16.14 0.00 6.13
178 179 0.463116 TTTATTCTTCCTCGGCCGGC 60.463 55.000 27.83 21.18 0.00 6.13
179 180 2.319890 TTATTCTTCCTCGGCCGGCC 62.320 60.000 36.69 36.69 0.00 6.13
197 198 3.470645 GCCCGAGCCTTATTCTCTAAA 57.529 47.619 0.00 0.00 0.00 1.85
198 199 3.805207 GCCCGAGCCTTATTCTCTAAAA 58.195 45.455 0.00 0.00 0.00 1.52
199 200 4.196971 GCCCGAGCCTTATTCTCTAAAAA 58.803 43.478 0.00 0.00 0.00 1.94
229 230 5.559148 AAAAGTAAATTGTCCAATGGCCA 57.441 34.783 8.56 8.56 0.00 5.36
230 231 5.559148 AAAGTAAATTGTCCAATGGCCAA 57.441 34.783 10.96 0.00 0.00 4.52
231 232 5.760484 AAGTAAATTGTCCAATGGCCAAT 57.240 34.783 10.96 2.27 0.00 3.16
232 233 5.760484 AGTAAATTGTCCAATGGCCAATT 57.240 34.783 14.74 14.74 39.72 2.32
233 234 6.125589 AGTAAATTGTCCAATGGCCAATTT 57.874 33.333 29.09 29.09 45.60 1.82
234 235 6.172630 AGTAAATTGTCCAATGGCCAATTTC 58.827 36.000 29.75 21.97 43.78 2.17
235 236 4.914177 AATTGTCCAATGGCCAATTTCT 57.086 36.364 14.74 0.00 35.79 2.52
236 237 3.959535 TTGTCCAATGGCCAATTTCTC 57.040 42.857 10.96 0.00 0.00 2.87
237 238 2.178580 TGTCCAATGGCCAATTTCTCC 58.821 47.619 10.96 0.00 0.00 3.71
238 239 2.225343 TGTCCAATGGCCAATTTCTCCT 60.225 45.455 10.96 0.00 0.00 3.69
239 240 2.833943 GTCCAATGGCCAATTTCTCCTT 59.166 45.455 10.96 0.00 0.00 3.36
240 241 2.833338 TCCAATGGCCAATTTCTCCTTG 59.167 45.455 10.96 7.04 0.00 3.61
241 242 2.624636 CAATGGCCAATTTCTCCTTGC 58.375 47.619 10.96 0.00 0.00 4.01
242 243 1.941377 ATGGCCAATTTCTCCTTGCA 58.059 45.000 10.96 0.00 0.00 4.08
243 244 1.714541 TGGCCAATTTCTCCTTGCAA 58.285 45.000 0.61 0.00 0.00 4.08
244 245 2.045524 TGGCCAATTTCTCCTTGCAAA 58.954 42.857 0.61 0.00 0.00 3.68
245 246 2.437281 TGGCCAATTTCTCCTTGCAAAA 59.563 40.909 0.61 0.00 0.00 2.44
246 247 3.069289 GGCCAATTTCTCCTTGCAAAAG 58.931 45.455 0.00 1.05 0.00 2.27
247 248 3.069289 GCCAATTTCTCCTTGCAAAAGG 58.931 45.455 0.00 0.00 41.35 3.11
248 249 3.244181 GCCAATTTCTCCTTGCAAAAGGA 60.244 43.478 6.95 6.95 46.20 3.36
285 286 7.259882 TCGTTAGACAAAGAACAAAGTAGACA 58.740 34.615 0.00 0.00 0.00 3.41
312 313 3.908382 GCTTTGCTCGACAGTAACAATTG 59.092 43.478 3.24 3.24 0.00 2.32
361 362 2.050350 CGGCCAGTAGGAGACGGAA 61.050 63.158 2.24 0.00 36.89 4.30
473 488 3.991051 CACCACCGAGCACCGAGT 61.991 66.667 0.00 0.00 41.76 4.18
500 515 1.826385 AAGGGGAGAAATCTTGTGCG 58.174 50.000 0.00 0.00 0.00 5.34
586 607 1.142870 TCCACAACTTCCACTCCCTTG 59.857 52.381 0.00 0.00 0.00 3.61
680 701 0.315706 GAGCGCATAAAGCAAGCTCG 60.316 55.000 11.47 0.00 43.47 5.03
955 976 2.564947 CTCACCCTCTACTGTTGAGCTT 59.435 50.000 12.82 0.42 0.00 3.74
1203 1228 4.493747 AACTACGCGCGCCTCCTC 62.494 66.667 32.58 0.00 0.00 3.71
1275 1300 4.103311 GCTATCCCAAAGAAGGAGGTGTAT 59.897 45.833 0.00 0.00 36.67 2.29
1428 1457 7.856145 TTTATGACAAAACCTTGTGCAAATT 57.144 28.000 0.00 0.00 45.98 1.82
1460 1489 5.406649 TGCAAATTAATAAAACTGCGGGAG 58.593 37.500 0.00 0.00 31.91 4.30
1471 1500 3.202829 ACTGCGGGAGTTTGAGTTTTA 57.797 42.857 0.00 0.00 0.00 1.52
1490 1519 9.984190 GAGTTTTATTTTGGGGTATTGTTTGTA 57.016 29.630 0.00 0.00 0.00 2.41
1518 1547 7.961326 ATAAAGGTGCAGGAATATGAGTTTT 57.039 32.000 0.00 0.00 0.00 2.43
1541 1570 3.603965 TGGGGGTGAAGTTTGTGTTAT 57.396 42.857 0.00 0.00 0.00 1.89
1618 1647 3.125146 TCAAACGCCGATTTGAAGATGAG 59.875 43.478 10.81 0.00 43.81 2.90
1635 1664 8.292448 TGAAGATGAGCTTGTTTGATTAGTTTC 58.708 33.333 0.00 0.00 36.83 2.78
1638 1667 8.854117 AGATGAGCTTGTTTGATTAGTTTCTTT 58.146 29.630 0.00 0.00 0.00 2.52
1679 1709 8.110860 ACTGTTGCTAATTTGTTATTGCTAGT 57.889 30.769 0.00 0.00 0.00 2.57
1680 1710 8.576442 ACTGTTGCTAATTTGTTATTGCTAGTT 58.424 29.630 0.00 0.00 0.00 2.24
1681 1711 9.410556 CTGTTGCTAATTTGTTATTGCTAGTTT 57.589 29.630 0.00 0.00 0.00 2.66
1682 1712 9.190858 TGTTGCTAATTTGTTATTGCTAGTTTG 57.809 29.630 0.00 0.00 0.00 2.93
1683 1713 7.810766 TGCTAATTTGTTATTGCTAGTTTGC 57.189 32.000 0.00 0.00 0.00 3.68
1684 1714 7.601856 TGCTAATTTGTTATTGCTAGTTTGCT 58.398 30.769 0.00 0.00 0.00 3.91
1685 1715 8.735315 TGCTAATTTGTTATTGCTAGTTTGCTA 58.265 29.630 0.00 0.00 0.00 3.49
1717 1747 4.819105 AATTCAGTATCTGGTCCGTTGA 57.181 40.909 0.00 0.00 31.51 3.18
1718 1748 4.819105 ATTCAGTATCTGGTCCGTTGAA 57.181 40.909 0.00 0.00 31.51 2.69
1879 1910 6.354130 ACCAAATACGACAGCTTATAATGGT 58.646 36.000 0.00 7.33 30.44 3.55
1913 1944 6.749923 AGAAACTTTATGCCATGACTTCTC 57.250 37.500 0.00 0.00 0.00 2.87
1991 2030 1.687123 AGCACTTCCCGCTATTCGTAT 59.313 47.619 0.00 0.00 38.15 3.06
1992 2031 1.792949 GCACTTCCCGCTATTCGTATG 59.207 52.381 0.00 0.00 36.19 2.39
1993 2032 2.802057 GCACTTCCCGCTATTCGTATGT 60.802 50.000 0.00 0.00 36.19 2.29
1994 2033 3.454375 CACTTCCCGCTATTCGTATGTT 58.546 45.455 0.00 0.00 36.19 2.71
1996 2035 5.045215 CACTTCCCGCTATTCGTATGTTTA 58.955 41.667 0.00 0.00 36.19 2.01
1997 2036 5.175126 CACTTCCCGCTATTCGTATGTTTAG 59.825 44.000 0.00 0.00 36.19 1.85
1999 2038 2.735134 CCCGCTATTCGTATGTTTAGCC 59.265 50.000 10.99 0.00 34.86 3.93
2000 2039 3.386486 CCGCTATTCGTATGTTTAGCCA 58.614 45.455 10.99 0.00 34.86 4.75
2001 2040 3.183775 CCGCTATTCGTATGTTTAGCCAC 59.816 47.826 10.99 0.00 34.86 5.01
2016 2077 3.228188 AGCCACTTGAACTCCAAATGA 57.772 42.857 0.00 0.00 34.14 2.57
2179 2251 2.207501 ATCTGCAGTGGCCCCTGAAG 62.208 60.000 20.52 18.65 39.19 3.02
2186 2258 0.394352 GTGGCCCCTGAAGTGTATGG 60.394 60.000 0.00 0.00 0.00 2.74
2188 2260 1.453928 GCCCCTGAAGTGTATGGCC 60.454 63.158 0.00 0.00 32.74 5.36
2322 2394 1.465387 TGTTTGCTTTACCGGCATACG 59.535 47.619 0.00 0.00 41.88 3.06
2335 2407 3.009301 GGCATACGACTACGCATAAGT 57.991 47.619 0.00 0.00 43.96 2.24
2336 2408 2.724690 GGCATACGACTACGCATAAGTG 59.275 50.000 0.00 0.00 43.96 3.16
2337 2409 3.369385 GCATACGACTACGCATAAGTGT 58.631 45.455 0.00 0.00 43.96 3.55
2338 2410 3.179795 GCATACGACTACGCATAAGTGTG 59.820 47.826 0.00 0.00 43.96 3.82
2340 2412 5.504392 CATACGACTACGCATAAGTGTGTA 58.496 41.667 0.00 2.36 46.66 2.90
2343 2415 5.404946 ACGACTACGCATAAGTGTGTATTT 58.595 37.500 2.71 0.00 46.80 1.40
2344 2416 5.865552 ACGACTACGCATAAGTGTGTATTTT 59.134 36.000 2.71 0.00 46.80 1.82
2346 2418 7.703621 ACGACTACGCATAAGTGTGTATTTTAT 59.296 33.333 2.71 0.00 46.80 1.40
2347 2419 7.996551 CGACTACGCATAAGTGTGTATTTTATG 59.003 37.037 2.71 0.00 46.80 1.90
2348 2420 8.712285 ACTACGCATAAGTGTGTATTTTATGT 57.288 30.769 2.71 0.00 46.80 2.29
2349 2421 8.600625 ACTACGCATAAGTGTGTATTTTATGTG 58.399 33.333 12.75 12.75 46.80 3.21
2350 2422 7.372451 ACGCATAAGTGTGTATTTTATGTGT 57.628 32.000 13.73 13.73 46.66 3.72
2402 2492 5.435686 TGGTTATAGAGCCACAATGTTCT 57.564 39.130 0.00 0.00 0.00 3.01
2479 2569 2.194271 CGTTCGGTTGCTTATCTCTCC 58.806 52.381 0.00 0.00 0.00 3.71
2560 2650 3.243401 ACAGCCTGTTTTTCCGAATTCAC 60.243 43.478 6.22 0.00 0.00 3.18
2563 2653 3.611766 GCCTGTTTTTCCGAATTCACCTC 60.612 47.826 6.22 0.00 0.00 3.85
2662 2752 1.982660 TCCAGCTATCGACTTCGGAT 58.017 50.000 0.00 0.00 40.29 4.18
2754 2844 0.728466 GTCGTGAAGGACTCGAACGG 60.728 60.000 3.97 0.00 44.07 4.44
2768 2858 1.472552 CGAACGGGCCACTGAATATCA 60.473 52.381 4.39 0.00 0.00 2.15
2885 2975 3.630311 GGGACCTGGGAGTTATGAGTAGT 60.630 52.174 0.00 0.00 0.00 2.73
2955 3045 2.191354 TACTTCCTCCGTCGTGTGCG 62.191 60.000 0.00 0.00 39.92 5.34
3017 3107 3.591527 TGTAATTGGAGGGGTGAGTGATT 59.408 43.478 0.00 0.00 0.00 2.57
3075 3165 3.674753 GCATGTCACACCTTGTAAATTGC 59.325 43.478 0.00 0.00 0.00 3.56
3154 3256 5.857268 CAAACCTTGGTTGGATCAAATTCT 58.143 37.500 5.74 0.00 0.00 2.40
3159 3261 3.609853 TGGTTGGATCAAATTCTCCTCG 58.390 45.455 0.00 0.00 32.47 4.63
3161 3263 3.873952 GGTTGGATCAAATTCTCCTCGAG 59.126 47.826 5.13 5.13 32.47 4.04
3211 3318 0.901580 CTCCCTTGTGGCCTGCAAAT 60.902 55.000 3.32 0.00 0.00 2.32
3383 3494 0.255890 GCCACCATGTATGTCCCACT 59.744 55.000 0.00 0.00 0.00 4.00
3434 3545 4.820897 GTCAACTCACCATGACACTATGA 58.179 43.478 0.00 0.00 44.19 2.15
3435 3546 5.423015 GTCAACTCACCATGACACTATGAT 58.577 41.667 0.00 0.00 44.19 2.45
3450 3729 3.822735 ACTATGATTGCATCCAATTCCCG 59.177 43.478 0.00 0.00 41.60 5.14
3452 3731 0.746063 GATTGCATCCAATTCCCGCA 59.254 50.000 0.00 0.00 41.60 5.69
3453 3732 0.748450 ATTGCATCCAATTCCCGCAG 59.252 50.000 0.00 0.00 38.49 5.18
3467 3746 2.668212 GCAGCAACGCACAGGGTA 60.668 61.111 0.00 0.00 0.00 3.69
3469 3748 1.586154 GCAGCAACGCACAGGGTATT 61.586 55.000 0.00 0.00 0.00 1.89
3470 3749 0.881118 CAGCAACGCACAGGGTATTT 59.119 50.000 0.00 0.00 0.00 1.40
3471 3750 1.269448 CAGCAACGCACAGGGTATTTT 59.731 47.619 0.00 0.00 0.00 1.82
3472 3751 1.539827 AGCAACGCACAGGGTATTTTC 59.460 47.619 0.00 0.00 0.00 2.29
3473 3752 1.539827 GCAACGCACAGGGTATTTTCT 59.460 47.619 0.00 0.00 0.00 2.52
3474 3753 2.414161 GCAACGCACAGGGTATTTTCTC 60.414 50.000 0.00 0.00 0.00 2.87
3475 3754 3.074412 CAACGCACAGGGTATTTTCTCT 58.926 45.455 0.00 0.00 0.00 3.10
3476 3755 4.250464 CAACGCACAGGGTATTTTCTCTA 58.750 43.478 0.00 0.00 0.00 2.43
3477 3756 4.124851 ACGCACAGGGTATTTTCTCTAG 57.875 45.455 0.00 0.00 0.00 2.43
3478 3757 3.514309 ACGCACAGGGTATTTTCTCTAGT 59.486 43.478 0.00 0.00 0.00 2.57
3479 3758 4.020485 ACGCACAGGGTATTTTCTCTAGTT 60.020 41.667 0.00 0.00 0.00 2.24
3480 3759 4.935808 CGCACAGGGTATTTTCTCTAGTTT 59.064 41.667 0.00 0.00 0.00 2.66
3481 3760 5.411669 CGCACAGGGTATTTTCTCTAGTTTT 59.588 40.000 0.00 0.00 0.00 2.43
3482 3761 6.402226 CGCACAGGGTATTTTCTCTAGTTTTC 60.402 42.308 0.00 0.00 0.00 2.29
3483 3762 6.655425 GCACAGGGTATTTTCTCTAGTTTTCT 59.345 38.462 0.00 0.00 0.00 2.52
3484 3763 7.175119 GCACAGGGTATTTTCTCTAGTTTTCTT 59.825 37.037 0.00 0.00 0.00 2.52
3485 3764 9.720769 CACAGGGTATTTTCTCTAGTTTTCTTA 57.279 33.333 0.00 0.00 0.00 2.10
3495 3774 9.614792 TTTCTCTAGTTTTCTTAAAGCTTCACT 57.385 29.630 0.00 0.00 33.77 3.41
3516 3795 7.810658 TCACTAAAAGCAAAGAGATCATGAAC 58.189 34.615 0.00 0.00 0.00 3.18
3529 3808 6.921857 AGAGATCATGAACAGCAAAACAAAAG 59.078 34.615 0.00 0.00 0.00 2.27
3533 3812 2.665537 TGAACAGCAAAACAAAAGCACG 59.334 40.909 0.00 0.00 0.00 5.34
3561 3840 2.837532 ATTGTTTGTTGGGGACATGC 57.162 45.000 0.00 0.00 42.32 4.06
3568 3847 0.614415 GTTGGGGACATGCCATTCCA 60.614 55.000 8.20 4.20 42.32 3.53
3581 3860 0.964860 CATTCCATTGGGGCGTGTGA 60.965 55.000 2.09 0.00 36.21 3.58
3675 3954 0.321919 GCTGACACTGAGGATGCCAA 60.322 55.000 0.00 0.00 0.00 4.52
3762 4044 7.286775 ACCACATCCACACTTTACAACTTTATT 59.713 33.333 0.00 0.00 0.00 1.40
3767 4049 8.514330 TCCACACTTTACAACTTTATTCAACT 57.486 30.769 0.00 0.00 0.00 3.16
3774 4056 9.893305 CTTTACAACTTTATTCAACTAACCAGG 57.107 33.333 0.00 0.00 0.00 4.45
3782 4064 7.880160 TTATTCAACTAACCAGGGAATGATG 57.120 36.000 0.00 0.00 34.06 3.07
3786 4068 6.493166 TCAACTAACCAGGGAATGATGATTT 58.507 36.000 0.00 0.00 0.00 2.17
3834 4116 7.869429 ACTTTTTAAAAGATGAGATGCCAACAG 59.131 33.333 22.31 0.00 0.00 3.16
3840 4122 1.896220 TGAGATGCCAACAGGAACAC 58.104 50.000 0.00 0.00 0.00 3.32
3851 4133 2.260822 ACAGGAACACCTATCAGCACT 58.739 47.619 0.00 0.00 32.14 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.797353 GCTGGGAAGGCCGATGGA 61.797 66.667 0.00 0.00 33.83 3.41
1 2 4.883354 GGCTGGGAAGGCCGATGG 62.883 72.222 0.00 0.00 40.19 3.51
7 8 2.343426 CCGAAAAGGCTGGGAAGGC 61.343 63.158 0.00 0.00 0.00 4.35
8 9 4.002797 CCGAAAAGGCTGGGAAGG 57.997 61.111 0.00 0.00 0.00 3.46
51 52 3.660111 AAGGAAGTTGCCGCGTGC 61.660 61.111 4.92 9.16 41.77 5.34
52 53 2.252260 CAAGGAAGTTGCCGCGTG 59.748 61.111 4.92 0.00 0.00 5.34
59 60 2.676471 CCCCCGGCAAGGAAGTTG 60.676 66.667 0.00 0.00 45.00 3.16
71 72 4.778143 CCAAGACCGAAGCCCCCG 62.778 72.222 0.00 0.00 0.00 5.73
75 76 2.034221 AAGGCCAAGACCGAAGCC 59.966 61.111 5.01 0.00 46.13 4.35
76 77 0.606673 AAGAAGGCCAAGACCGAAGC 60.607 55.000 5.01 0.00 33.69 3.86
77 78 1.160137 CAAGAAGGCCAAGACCGAAG 58.840 55.000 5.01 0.00 33.69 3.79
78 79 0.889186 GCAAGAAGGCCAAGACCGAA 60.889 55.000 5.01 0.00 33.69 4.30
79 80 1.302511 GCAAGAAGGCCAAGACCGA 60.303 57.895 5.01 0.00 33.69 4.69
80 81 3.267974 GCAAGAAGGCCAAGACCG 58.732 61.111 5.01 0.00 33.69 4.79
88 89 2.818274 CGGTACCGGCAAGAAGGC 60.818 66.667 27.00 0.00 39.93 4.35
89 90 1.740296 CACGGTACCGGCAAGAAGG 60.740 63.158 35.86 12.16 44.69 3.46
90 91 0.736325 CTCACGGTACCGGCAAGAAG 60.736 60.000 35.86 19.20 44.69 2.85
91 92 1.290955 CTCACGGTACCGGCAAGAA 59.709 57.895 35.86 14.38 44.69 2.52
92 93 1.904865 ACTCACGGTACCGGCAAGA 60.905 57.895 35.86 24.89 44.69 3.02
93 94 1.736645 CACTCACGGTACCGGCAAG 60.737 63.158 35.86 28.67 44.69 4.01
94 95 2.340809 CACTCACGGTACCGGCAA 59.659 61.111 35.86 20.13 44.69 4.52
95 96 4.367023 GCACTCACGGTACCGGCA 62.367 66.667 35.86 21.38 44.69 5.69
97 98 3.678717 CTCGCACTCACGGTACCGG 62.679 68.421 35.86 24.55 44.69 5.28
98 99 2.191354 TTCTCGCACTCACGGTACCG 62.191 60.000 32.22 32.22 46.03 4.02
99 100 0.731855 GTTCTCGCACTCACGGTACC 60.732 60.000 0.16 0.16 0.00 3.34
100 101 0.731855 GGTTCTCGCACTCACGGTAC 60.732 60.000 0.00 0.00 0.00 3.34
101 102 1.582968 GGTTCTCGCACTCACGGTA 59.417 57.895 0.00 0.00 0.00 4.02
102 103 2.338984 GGTTCTCGCACTCACGGT 59.661 61.111 0.00 0.00 0.00 4.83
103 104 2.432628 GGGTTCTCGCACTCACGG 60.433 66.667 0.00 0.00 0.00 4.94
104 105 1.444553 GAGGGTTCTCGCACTCACG 60.445 63.158 0.00 0.00 0.00 4.35
105 106 0.033504 TTGAGGGTTCTCGCACTCAC 59.966 55.000 0.00 0.00 42.79 3.51
106 107 0.033504 GTTGAGGGTTCTCGCACTCA 59.966 55.000 0.00 0.00 42.79 3.41
107 108 1.009389 CGTTGAGGGTTCTCGCACTC 61.009 60.000 0.00 0.00 42.79 3.51
108 109 1.006102 CGTTGAGGGTTCTCGCACT 60.006 57.895 0.00 0.00 42.79 4.40
109 110 2.027625 CCGTTGAGGGTTCTCGCAC 61.028 63.158 0.00 0.00 42.79 5.34
110 111 2.342279 CCGTTGAGGGTTCTCGCA 59.658 61.111 0.00 0.00 42.79 5.10
111 112 3.119096 GCCGTTGAGGGTTCTCGC 61.119 66.667 0.00 0.00 42.79 5.03
118 119 1.866853 GAAAAGGCAGCCGTTGAGGG 61.867 60.000 13.94 0.00 41.48 4.30
119 120 1.581447 GAAAAGGCAGCCGTTGAGG 59.419 57.895 13.94 0.00 44.97 3.86
120 121 0.890996 AGGAAAAGGCAGCCGTTGAG 60.891 55.000 13.94 0.00 0.00 3.02
121 122 0.467290 AAGGAAAAGGCAGCCGTTGA 60.467 50.000 13.94 0.00 0.00 3.18
122 123 0.318955 CAAGGAAAAGGCAGCCGTTG 60.319 55.000 13.94 4.58 0.00 4.10
123 124 2.041153 CAAGGAAAAGGCAGCCGTT 58.959 52.632 6.82 6.82 0.00 4.44
124 125 2.564721 GCAAGGAAAAGGCAGCCGT 61.565 57.895 5.55 0.00 0.00 5.68
125 126 2.259511 GCAAGGAAAAGGCAGCCG 59.740 61.111 5.55 0.00 0.00 5.52
126 127 2.259511 CGCAAGGAAAAGGCAGCC 59.740 61.111 1.84 1.84 0.00 4.85
127 128 2.426122 AAGCGCAAGGAAAAGGCAGC 62.426 55.000 11.47 0.00 38.28 5.25
128 129 0.387750 GAAGCGCAAGGAAAAGGCAG 60.388 55.000 11.47 0.00 38.28 4.85
129 130 0.823356 AGAAGCGCAAGGAAAAGGCA 60.823 50.000 11.47 0.00 38.28 4.75
130 131 0.387750 CAGAAGCGCAAGGAAAAGGC 60.388 55.000 11.47 0.00 38.28 4.35
131 132 0.242017 CCAGAAGCGCAAGGAAAAGG 59.758 55.000 11.47 0.00 38.28 3.11
132 133 0.954452 ACCAGAAGCGCAAGGAAAAG 59.046 50.000 11.47 0.00 38.28 2.27
133 134 1.066908 CAACCAGAAGCGCAAGGAAAA 59.933 47.619 11.47 0.00 38.28 2.29
134 135 0.667993 CAACCAGAAGCGCAAGGAAA 59.332 50.000 11.47 0.00 38.28 3.13
135 136 1.795170 GCAACCAGAAGCGCAAGGAA 61.795 55.000 11.47 0.00 38.28 3.36
136 137 2.260869 GCAACCAGAAGCGCAAGGA 61.261 57.895 11.47 0.00 38.28 3.36
137 138 2.192608 GAGCAACCAGAAGCGCAAGG 62.193 60.000 11.47 8.12 35.48 3.61
138 139 1.208614 GAGCAACCAGAAGCGCAAG 59.791 57.895 11.47 0.00 35.48 4.01
139 140 0.819259 AAGAGCAACCAGAAGCGCAA 60.819 50.000 11.47 0.00 35.48 4.85
140 141 0.819259 AAAGAGCAACCAGAAGCGCA 60.819 50.000 11.47 0.00 35.48 6.09
141 142 0.312102 AAAAGAGCAACCAGAAGCGC 59.688 50.000 0.00 0.00 35.48 5.92
142 143 2.781945 AAAAAGAGCAACCAGAAGCG 57.218 45.000 0.00 0.00 35.48 4.68
143 144 6.018589 AGAATAAAAAGAGCAACCAGAAGC 57.981 37.500 0.00 0.00 0.00 3.86
144 145 7.040132 AGGAAGAATAAAAAGAGCAACCAGAAG 60.040 37.037 0.00 0.00 0.00 2.85
145 146 6.777580 AGGAAGAATAAAAAGAGCAACCAGAA 59.222 34.615 0.00 0.00 0.00 3.02
146 147 6.306987 AGGAAGAATAAAAAGAGCAACCAGA 58.693 36.000 0.00 0.00 0.00 3.86
147 148 6.581171 AGGAAGAATAAAAAGAGCAACCAG 57.419 37.500 0.00 0.00 0.00 4.00
148 149 5.181245 CGAGGAAGAATAAAAAGAGCAACCA 59.819 40.000 0.00 0.00 0.00 3.67
149 150 5.392057 CCGAGGAAGAATAAAAAGAGCAACC 60.392 44.000 0.00 0.00 0.00 3.77
150 151 5.631992 CCGAGGAAGAATAAAAAGAGCAAC 58.368 41.667 0.00 0.00 0.00 4.17
151 152 4.156008 GCCGAGGAAGAATAAAAAGAGCAA 59.844 41.667 0.00 0.00 0.00 3.91
152 153 3.689649 GCCGAGGAAGAATAAAAAGAGCA 59.310 43.478 0.00 0.00 0.00 4.26
153 154 3.065510 GGCCGAGGAAGAATAAAAAGAGC 59.934 47.826 0.00 0.00 0.00 4.09
154 155 3.309954 CGGCCGAGGAAGAATAAAAAGAG 59.690 47.826 24.07 0.00 0.00 2.85
155 156 3.267483 CGGCCGAGGAAGAATAAAAAGA 58.733 45.455 24.07 0.00 0.00 2.52
156 157 2.354821 CCGGCCGAGGAAGAATAAAAAG 59.645 50.000 30.73 0.00 0.00 2.27
157 158 2.361789 CCGGCCGAGGAAGAATAAAAA 58.638 47.619 30.73 0.00 0.00 1.94
158 159 2.015081 GCCGGCCGAGGAAGAATAAAA 61.015 52.381 30.73 0.00 0.00 1.52
159 160 0.463116 GCCGGCCGAGGAAGAATAAA 60.463 55.000 30.73 0.00 0.00 1.40
160 161 1.145377 GCCGGCCGAGGAAGAATAA 59.855 57.895 30.73 0.00 0.00 1.40
161 162 2.803817 GGCCGGCCGAGGAAGAATA 61.804 63.158 33.60 0.00 0.00 1.75
162 163 4.176752 GGCCGGCCGAGGAAGAAT 62.177 66.667 33.60 0.00 0.00 2.40
177 178 3.470645 TTTAGAGAATAAGGCTCGGGC 57.529 47.619 0.00 0.00 37.46 6.13
206 207 5.934781 TGGCCATTGGACAATTTACTTTTT 58.065 33.333 9.38 0.00 38.06 1.94
207 208 5.559148 TGGCCATTGGACAATTTACTTTT 57.441 34.783 9.38 0.00 38.06 2.27
217 218 2.178580 GGAGAAATTGGCCATTGGACA 58.821 47.619 7.30 7.30 40.08 4.02
218 219 2.460669 AGGAGAAATTGGCCATTGGAC 58.539 47.619 6.09 3.54 0.00 4.02
219 220 2.833338 CAAGGAGAAATTGGCCATTGGA 59.167 45.455 6.09 0.00 0.00 3.53
220 221 2.678769 GCAAGGAGAAATTGGCCATTGG 60.679 50.000 6.09 0.00 0.00 3.16
221 222 2.027929 TGCAAGGAGAAATTGGCCATTG 60.028 45.455 6.09 6.68 0.00 2.82
222 223 2.259012 TGCAAGGAGAAATTGGCCATT 58.741 42.857 6.09 0.00 0.00 3.16
223 224 1.941377 TGCAAGGAGAAATTGGCCAT 58.059 45.000 6.09 0.00 0.00 4.40
224 225 1.714541 TTGCAAGGAGAAATTGGCCA 58.285 45.000 0.00 0.00 0.00 5.36
225 226 2.837532 TTTGCAAGGAGAAATTGGCC 57.162 45.000 0.00 0.00 0.00 5.36
252 253 7.007313 TGTTCTTTGTCTAACGATCGTTTTT 57.993 32.000 35.66 17.04 39.31 1.94
253 254 6.592798 TGTTCTTTGTCTAACGATCGTTTT 57.407 33.333 35.66 17.80 39.31 2.43
254 255 6.592798 TTGTTCTTTGTCTAACGATCGTTT 57.407 33.333 35.66 20.59 39.31 3.60
255 256 6.257193 ACTTTGTTCTTTGTCTAACGATCGTT 59.743 34.615 33.45 33.45 41.65 3.85
256 257 5.751990 ACTTTGTTCTTTGTCTAACGATCGT 59.248 36.000 16.60 16.60 0.00 3.73
257 258 6.211664 ACTTTGTTCTTTGTCTAACGATCG 57.788 37.500 14.88 14.88 0.00 3.69
258 259 8.426251 GTCTACTTTGTTCTTTGTCTAACGATC 58.574 37.037 0.00 0.00 0.00 3.69
259 260 7.924412 TGTCTACTTTGTTCTTTGTCTAACGAT 59.076 33.333 0.00 0.00 0.00 3.73
260 261 7.259882 TGTCTACTTTGTTCTTTGTCTAACGA 58.740 34.615 0.00 0.00 0.00 3.85
261 262 7.459394 TGTCTACTTTGTTCTTTGTCTAACG 57.541 36.000 0.00 0.00 0.00 3.18
265 266 7.702348 GCAAAATGTCTACTTTGTTCTTTGTCT 59.298 33.333 0.00 0.00 35.42 3.41
266 267 7.702348 AGCAAAATGTCTACTTTGTTCTTTGTC 59.298 33.333 0.00 0.00 35.42 3.18
267 268 7.547227 AGCAAAATGTCTACTTTGTTCTTTGT 58.453 30.769 0.00 0.00 35.42 2.83
268 269 7.992180 AGCAAAATGTCTACTTTGTTCTTTG 57.008 32.000 0.00 0.00 35.42 2.77
269 270 8.872845 CAAAGCAAAATGTCTACTTTGTTCTTT 58.127 29.630 0.00 0.00 41.30 2.52
270 271 7.010460 GCAAAGCAAAATGTCTACTTTGTTCTT 59.990 33.333 13.45 0.00 45.61 2.52
271 272 6.476706 GCAAAGCAAAATGTCTACTTTGTTCT 59.523 34.615 13.45 0.00 45.61 3.01
272 273 6.476706 AGCAAAGCAAAATGTCTACTTTGTTC 59.523 34.615 13.45 1.08 45.61 3.18
273 274 6.340522 AGCAAAGCAAAATGTCTACTTTGTT 58.659 32.000 13.45 6.51 45.61 2.83
274 275 5.906073 AGCAAAGCAAAATGTCTACTTTGT 58.094 33.333 13.45 1.15 45.61 2.83
275 276 5.116074 CGAGCAAAGCAAAATGTCTACTTTG 59.884 40.000 8.93 8.93 46.25 2.77
285 286 4.036262 TGTTACTGTCGAGCAAAGCAAAAT 59.964 37.500 0.00 0.00 0.00 1.82
312 313 2.005451 CTGACTGCTATTGTGTGCCTC 58.995 52.381 0.00 0.00 0.00 4.70
361 362 2.355108 CGATGATTCACCCAGTTCACCT 60.355 50.000 0.00 0.00 0.00 4.00
416 421 1.954146 GTTTCGTGCTCGTCTGCCA 60.954 57.895 8.17 0.00 38.33 4.92
424 429 2.668280 GCGAGGTGGTTTCGTGCTC 61.668 63.158 0.00 0.00 40.08 4.26
462 467 2.725203 TTTTCCCCACTCGGTGCTCG 62.725 60.000 0.00 0.00 40.90 5.03
473 488 2.727454 AGATTTCTCCCCTTTTTCCCCA 59.273 45.455 0.00 0.00 0.00 4.96
518 539 1.136110 AGTTGGTTTTGTTCTTGCCCG 59.864 47.619 0.00 0.00 0.00 6.13
556 577 0.878961 AAGTTGTGGAAGACGACCGC 60.879 55.000 0.00 0.00 39.59 5.68
680 701 0.391793 CGAAGAAGGTTCTGGCTCCC 60.392 60.000 0.00 0.00 37.65 4.30
784 805 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
785 806 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
883 904 2.510238 CTTGGAGAAGAGCGGCGG 60.510 66.667 9.78 0.00 0.00 6.13
975 996 3.487417 TCGCTCGACCGAGAAGAG 58.513 61.111 21.91 10.05 44.53 2.85
1254 1279 4.141482 GCATACACCTCCTTCTTTGGGATA 60.141 45.833 0.00 0.00 31.89 2.59
1260 1285 1.739067 GCGCATACACCTCCTTCTTT 58.261 50.000 0.30 0.00 0.00 2.52
1460 1489 8.896320 ACAATACCCCAAAATAAAACTCAAAC 57.104 30.769 0.00 0.00 0.00 2.93
1490 1519 9.646522 AACTCATATTCCTGCACCTTTATTAAT 57.353 29.630 0.00 0.00 0.00 1.40
1518 1547 2.541466 ACACAAACTTCACCCCCAAAA 58.459 42.857 0.00 0.00 0.00 2.44
1522 1551 6.041182 ACTTTAATAACACAAACTTCACCCCC 59.959 38.462 0.00 0.00 0.00 5.40
1541 1570 9.877178 TTTAAAACTCAAATTCCTGCACTTTAA 57.123 25.926 0.00 0.00 0.00 1.52
1588 1617 5.764131 TCAAATCGGCGTTTGAAACTAATT 58.236 33.333 24.63 6.32 43.12 1.40
1680 1710 5.112220 CTGAATTTCAGTTGCAGTAGCAA 57.888 39.130 16.71 0.00 45.78 3.91
1681 1711 4.754372 CTGAATTTCAGTTGCAGTAGCA 57.246 40.909 16.71 0.00 43.19 3.49
1717 1747 0.318762 GTCGAGCCAGAACTCCTGTT 59.681 55.000 0.00 0.00 41.33 3.16
1718 1748 0.827925 TGTCGAGCCAGAACTCCTGT 60.828 55.000 0.00 0.00 41.33 4.00
1879 1910 9.866655 ATGGCATAAAGTTTCTATTAATGAGGA 57.133 29.630 0.00 0.00 0.00 3.71
1922 1953 5.814705 GGAGTTCAGATACTCATCCACAAAG 59.185 44.000 12.19 0.00 45.07 2.77
1991 2030 3.569194 TGGAGTTCAAGTGGCTAAACA 57.431 42.857 0.00 0.00 0.00 2.83
1992 2031 4.911514 TTTGGAGTTCAAGTGGCTAAAC 57.088 40.909 0.00 0.00 36.62 2.01
1993 2032 5.136828 TCATTTGGAGTTCAAGTGGCTAAA 58.863 37.500 6.80 0.00 41.58 1.85
1994 2033 4.724399 TCATTTGGAGTTCAAGTGGCTAA 58.276 39.130 6.80 0.00 41.58 3.09
1996 2035 3.228188 TCATTTGGAGTTCAAGTGGCT 57.772 42.857 6.80 0.00 41.58 4.75
1997 2036 3.841643 CATCATTTGGAGTTCAAGTGGC 58.158 45.455 6.80 0.00 41.58 5.01
1999 2038 4.508461 TGCATCATTTGGAGTTCAAGTG 57.492 40.909 0.15 0.15 42.31 3.16
2000 2039 5.069516 AGTTTGCATCATTTGGAGTTCAAGT 59.930 36.000 0.00 0.00 36.62 3.16
2001 2040 5.535333 AGTTTGCATCATTTGGAGTTCAAG 58.465 37.500 0.00 0.00 36.62 3.02
2016 2077 3.758554 GGGAGTGTTGATGTAGTTTGCAT 59.241 43.478 0.00 0.00 0.00 3.96
2157 2229 0.749454 CAGGGGCCACTGCAGATAAC 60.749 60.000 25.05 7.69 40.13 1.89
2179 2251 1.132262 CATGTTCCAACGGCCATACAC 59.868 52.381 2.24 0.00 0.00 2.90
2186 2258 1.742831 TGCTTATCATGTTCCAACGGC 59.257 47.619 0.00 0.00 0.00 5.68
2188 2260 4.870426 ACTACTGCTTATCATGTTCCAACG 59.130 41.667 0.00 0.00 0.00 4.10
2314 2386 1.976728 CTTATGCGTAGTCGTATGCCG 59.023 52.381 1.95 0.00 41.87 5.69
2322 2394 8.814235 ACATAAAATACACACTTATGCGTAGTC 58.186 33.333 0.00 0.00 36.79 2.59
2325 2397 8.481974 ACACATAAAATACACACTTATGCGTA 57.518 30.769 0.00 0.00 36.79 4.42
2328 2400 9.405587 ACAAACACATAAAATACACACTTATGC 57.594 29.630 0.00 0.00 36.79 3.14
2332 2404 9.944663 CTGTACAAACACATAAAATACACACTT 57.055 29.630 0.00 0.00 0.00 3.16
2334 2406 9.724839 AACTGTACAAACACATAAAATACACAC 57.275 29.630 0.00 0.00 0.00 3.82
2335 2407 9.723447 CAACTGTACAAACACATAAAATACACA 57.277 29.630 0.00 0.00 0.00 3.72
2336 2408 9.724839 ACAACTGTACAAACACATAAAATACAC 57.275 29.630 0.00 0.00 0.00 2.90
2337 2409 9.723447 CACAACTGTACAAACACATAAAATACA 57.277 29.630 0.00 0.00 0.00 2.29
2338 2410 8.687301 GCACAACTGTACAAACACATAAAATAC 58.313 33.333 0.00 0.00 0.00 1.89
2339 2411 8.625651 AGCACAACTGTACAAACACATAAAATA 58.374 29.630 0.00 0.00 0.00 1.40
2340 2412 7.488322 AGCACAACTGTACAAACACATAAAAT 58.512 30.769 0.00 0.00 0.00 1.82
2343 2415 6.443934 AAGCACAACTGTACAAACACATAA 57.556 33.333 0.00 0.00 0.00 1.90
2344 2416 6.317642 AGAAAGCACAACTGTACAAACACATA 59.682 34.615 0.00 0.00 0.00 2.29
2346 2418 4.457603 AGAAAGCACAACTGTACAAACACA 59.542 37.500 0.00 0.00 0.00 3.72
2347 2419 4.981794 AGAAAGCACAACTGTACAAACAC 58.018 39.130 0.00 0.00 0.00 3.32
2348 2420 4.697828 TGAGAAAGCACAACTGTACAAACA 59.302 37.500 0.00 0.00 0.00 2.83
2349 2421 5.229921 TGAGAAAGCACAACTGTACAAAC 57.770 39.130 0.00 0.00 0.00 2.93
2350 2422 5.636837 GTTGAGAAAGCACAACTGTACAAA 58.363 37.500 0.00 0.00 40.84 2.83
2402 2492 7.336931 GGACTTCTCTTATCTGCCAAATGTTTA 59.663 37.037 0.00 0.00 0.00 2.01
2560 2650 2.034066 TTGAAAGGCCTGCCGAGG 59.966 61.111 5.69 0.00 43.19 4.63
2563 2653 4.107051 CGCTTGAAAGGCCTGCCG 62.107 66.667 5.69 0.00 41.95 5.69
2754 2844 3.193267 TGCAAACTTGATATTCAGTGGCC 59.807 43.478 0.00 0.00 0.00 5.36
2768 2858 6.006449 AGTCTATCTGAACCATTGCAAACTT 58.994 36.000 1.71 0.00 0.00 2.66
2956 3046 2.058829 AAAACACCGACAGCCGCAAG 62.059 55.000 0.00 0.00 36.84 4.01
2980 3070 7.201732 CCTCCAATTACATTCACATTACAGGAC 60.202 40.741 0.00 0.00 0.00 3.85
2992 3082 3.947834 CACTCACCCCTCCAATTACATTC 59.052 47.826 0.00 0.00 0.00 2.67
3017 3107 9.681062 CTATACAGGGACAAGAGGAAATAAAAA 57.319 33.333 0.00 0.00 0.00 1.94
3038 3128 4.450419 GTGACATGCTTGATGCTCCTATAC 59.550 45.833 6.60 0.00 43.37 1.47
3075 3165 6.499172 ACATGTATATCTGTCACTGAACTCG 58.501 40.000 0.00 0.00 0.00 4.18
3144 3246 5.017294 AGGAACTCGAGGAGAATTTGATC 57.983 43.478 18.41 0.00 33.32 2.92
3154 3256 9.346005 AGTTAAAAATAAAAAGGAACTCGAGGA 57.654 29.630 18.41 0.00 38.49 3.71
3189 3296 2.270986 GCAGGCCACAAGGGAGTTG 61.271 63.158 5.01 0.00 42.48 3.16
3194 3301 0.819582 CTATTTGCAGGCCACAAGGG 59.180 55.000 5.01 0.00 40.85 3.95
3211 3318 6.295916 GGACCAGAAACCTCAAGATTTCTCTA 60.296 42.308 0.00 0.00 42.03 2.43
3298 3405 9.998106 TTAGTGGAGATAAACTATTTAGGCATC 57.002 33.333 0.00 0.00 0.00 3.91
3299 3406 9.780186 GTTAGTGGAGATAAACTATTTAGGCAT 57.220 33.333 0.00 0.00 0.00 4.40
3300 3407 8.989131 AGTTAGTGGAGATAAACTATTTAGGCA 58.011 33.333 0.00 0.00 30.62 4.75
3301 3408 9.478768 GAGTTAGTGGAGATAAACTATTTAGGC 57.521 37.037 0.00 0.00 32.51 3.93
3332 3440 8.970691 AGTTTGACATAATTGCATGTTAAGAC 57.029 30.769 0.00 0.00 39.25 3.01
3405 3516 6.499234 TGTCATGGTGAGTTGACATAATTG 57.501 37.500 1.84 0.00 45.35 2.32
3434 3545 0.748450 CTGCGGGAATTGGATGCAAT 59.252 50.000 6.63 6.63 34.78 3.56
3435 3546 1.947597 GCTGCGGGAATTGGATGCAA 61.948 55.000 0.79 0.79 34.78 4.08
3450 3729 1.586154 AATACCCTGTGCGTTGCTGC 61.586 55.000 0.00 0.00 0.00 5.25
3452 3731 1.539827 GAAAATACCCTGTGCGTTGCT 59.460 47.619 0.00 0.00 0.00 3.91
3453 3732 1.539827 AGAAAATACCCTGTGCGTTGC 59.460 47.619 0.00 0.00 0.00 4.17
3469 3748 9.614792 AGTGAAGCTTTAAGAAAACTAGAGAAA 57.385 29.630 0.00 0.00 0.00 2.52
3475 3754 9.946165 GCTTTTAGTGAAGCTTTAAGAAAACTA 57.054 29.630 0.00 0.00 46.55 2.24
3476 3755 8.858003 GCTTTTAGTGAAGCTTTAAGAAAACT 57.142 30.769 0.00 0.00 46.55 2.66
3489 3768 8.037382 TCATGATCTCTTTGCTTTTAGTGAAG 57.963 34.615 0.00 0.00 0.00 3.02
3490 3769 7.984422 TCATGATCTCTTTGCTTTTAGTGAA 57.016 32.000 0.00 0.00 0.00 3.18
3491 3770 7.445096 TGTTCATGATCTCTTTGCTTTTAGTGA 59.555 33.333 0.00 0.00 0.00 3.41
3492 3771 7.587629 TGTTCATGATCTCTTTGCTTTTAGTG 58.412 34.615 0.00 0.00 0.00 2.74
3493 3772 7.574592 GCTGTTCATGATCTCTTTGCTTTTAGT 60.575 37.037 0.00 0.00 0.00 2.24
3494 3773 6.746364 GCTGTTCATGATCTCTTTGCTTTTAG 59.254 38.462 0.00 0.00 0.00 1.85
3495 3774 6.207221 TGCTGTTCATGATCTCTTTGCTTTTA 59.793 34.615 0.00 0.00 0.00 1.52
3496 3775 5.010314 TGCTGTTCATGATCTCTTTGCTTTT 59.990 36.000 0.00 0.00 0.00 2.27
3508 3787 5.006941 GTGCTTTTGTTTTGCTGTTCATGAT 59.993 36.000 0.00 0.00 0.00 2.45
3509 3788 4.329528 GTGCTTTTGTTTTGCTGTTCATGA 59.670 37.500 0.00 0.00 0.00 3.07
3511 3790 3.306703 CGTGCTTTTGTTTTGCTGTTCAT 59.693 39.130 0.00 0.00 0.00 2.57
3516 3795 0.929615 CCCGTGCTTTTGTTTTGCTG 59.070 50.000 0.00 0.00 0.00 4.41
3529 3808 1.864082 CAAACAATTTTCCACCCGTGC 59.136 47.619 0.00 0.00 0.00 5.34
3533 3812 3.210227 CCCAACAAACAATTTTCCACCC 58.790 45.455 0.00 0.00 0.00 4.61
3561 3840 1.682005 ACACGCCCCAATGGAATGG 60.682 57.895 0.00 0.00 40.35 3.16
3568 3847 1.682005 CCCATTCACACGCCCCAAT 60.682 57.895 0.00 0.00 0.00 3.16
3581 3860 2.228841 GAGCACACCCCATCCCCATT 62.229 60.000 0.00 0.00 0.00 3.16
3675 3954 0.249615 CACGCATGATCTCATCCGGT 60.250 55.000 8.26 0.00 41.51 5.28
3762 4044 5.715439 ATCATCATTCCCTGGTTAGTTGA 57.285 39.130 0.00 0.00 0.00 3.18
3767 4049 7.233632 CCTGATAAATCATCATTCCCTGGTTA 58.766 38.462 0.00 0.00 42.82 2.85
3774 4056 8.355913 GTTCTTTCCCTGATAAATCATCATTCC 58.644 37.037 0.00 0.00 42.82 3.01
3786 4068 8.990163 AAGTTTAAGTTGTTCTTTCCCTGATA 57.010 30.769 0.00 0.00 37.56 2.15
3834 4116 1.555075 TCCAGTGCTGATAGGTGTTCC 59.445 52.381 0.02 0.00 0.00 3.62
3840 4122 4.502259 GGTGTAGATTCCAGTGCTGATAGG 60.502 50.000 0.02 0.00 0.00 2.57
3851 4133 2.039418 CTCCATCCGGTGTAGATTCCA 58.961 52.381 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.