Multiple sequence alignment - TraesCS2A01G446300

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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 TraesCS2A01G446300 chr2A 100.000 3428 0 0 1 3428 695468720 695472147 0.000000e+00 6331
1 TraesCS2A01G446300 chr2A 87.835 559 60 8 328 882 676380076 676379522 0.000000e+00 649
2 TraesCS2A01G446300 chr2B 92.969 2546 114 26 927 3428 663044930 663047454 0.000000e+00 3650
3 TraesCS2A01G446300 chr2B 91.737 1670 116 9 946 2601 54049020 54050681 0.000000e+00 2300
4 TraesCS2A01G446300 chr2B 92.525 1311 91 5 1297 2601 54034089 54035398 0.000000e+00 1871
5 TraesCS2A01G446300 chr2B 92.381 105 6 2 1 104 662906756 662906859 7.660000e-32 148
6 TraesCS2A01G446300 chr2D 91.141 2630 126 40 878 3420 556049356 556051965 0.000000e+00 3467
7 TraesCS2A01G446300 chr2D 93.119 218 3 5 1 218 556020355 556020560 3.320000e-80 309
8 TraesCS2A01G446300 chr2D 89.498 219 14 5 2725 2936 32609484 32609700 5.640000e-68 268
9 TraesCS2A01G446300 chr2D 97.115 104 3 0 1 104 555959798 555959901 3.520000e-40 176
10 TraesCS2A01G446300 chrUn 92.216 1092 75 5 946 2034 272459305 272458221 0.000000e+00 1537
11 TraesCS2A01G446300 chr6B 88.309 556 63 2 330 884 88941934 88942488 0.000000e+00 665
12 TraesCS2A01G446300 chr4B 88.193 559 58 8 328 882 124568461 124569015 0.000000e+00 660
13 TraesCS2A01G446300 chr6A 87.879 561 60 8 328 884 779616 779060 0.000000e+00 652
14 TraesCS2A01G446300 chr6A 87.835 559 58 10 328 882 445577441 445576889 0.000000e+00 647
15 TraesCS2A01G446300 chr7A 87.792 557 64 4 328 882 726103864 726104418 0.000000e+00 649
16 TraesCS2A01G446300 chr5A 87.701 561 61 8 328 884 138203248 138203804 0.000000e+00 647
17 TraesCS2A01G446300 chr5A 87.193 570 64 9 328 894 456428761 456429324 1.040000e-179 640
18 TraesCS2A01G446300 chr1D 87.612 557 65 4 328 882 453226451 453225897 0.000000e+00 643


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 TraesCS2A01G446300 chr2A 695468720 695472147 3427 False 6331 6331 100.000 1 3428 1 chr2A.!!$F1 3427
1 TraesCS2A01G446300 chr2A 676379522 676380076 554 True 649 649 87.835 328 882 1 chr2A.!!$R1 554
2 TraesCS2A01G446300 chr2B 663044930 663047454 2524 False 3650 3650 92.969 927 3428 1 chr2B.!!$F4 2501
3 TraesCS2A01G446300 chr2B 54049020 54050681 1661 False 2300 2300 91.737 946 2601 1 chr2B.!!$F2 1655
4 TraesCS2A01G446300 chr2B 54034089 54035398 1309 False 1871 1871 92.525 1297 2601 1 chr2B.!!$F1 1304
5 TraesCS2A01G446300 chr2D 556049356 556051965 2609 False 3467 3467 91.141 878 3420 1 chr2D.!!$F4 2542
6 TraesCS2A01G446300 chrUn 272458221 272459305 1084 True 1537 1537 92.216 946 2034 1 chrUn.!!$R1 1088
7 TraesCS2A01G446300 chr6B 88941934 88942488 554 False 665 665 88.309 330 884 1 chr6B.!!$F1 554
8 TraesCS2A01G446300 chr4B 124568461 124569015 554 False 660 660 88.193 328 882 1 chr4B.!!$F1 554
9 TraesCS2A01G446300 chr6A 779060 779616 556 True 652 652 87.879 328 884 1 chr6A.!!$R1 556
10 TraesCS2A01G446300 chr6A 445576889 445577441 552 True 647 647 87.835 328 882 1 chr6A.!!$R2 554
11 TraesCS2A01G446300 chr7A 726103864 726104418 554 False 649 649 87.792 328 882 1 chr7A.!!$F1 554
12 TraesCS2A01G446300 chr5A 138203248 138203804 556 False 647 647 87.701 328 884 1 chr5A.!!$F1 556
13 TraesCS2A01G446300 chr5A 456428761 456429324 563 False 640 640 87.193 328 894 1 chr5A.!!$F2 566
14 TraesCS2A01G446300 chr1D 453225897 453226451 554 True 643 643 87.612 328 882 1 chr1D.!!$R1 554

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
85 86 0.038343 GAGCGCTCTCCATCTCCATC 60.038 60.000 29.88 0.00 33.19 3.51 F
319 320 0.241481 GGACGGATCGGATAGTGCTC 59.759 60.000 7.35 0.00 0.00 4.26 F
901 902 0.249447 CACAGAATAGCATCGGCCGA 60.249 55.000 33.12 33.12 42.56 5.54 F
1696 1713 1.684049 AACTCCCTCCTCCTCGCTG 60.684 63.158 0.00 0.00 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1630 0.734942 CGGACGCGTGTAGATTTGGT 60.735 55.0 20.7 0.0 0.00 3.67 R
1818 1837 0.827925 ATCCTCGCGCCTTCTCCATA 60.828 55.0 0.0 0.0 0.00 2.74 R
1947 1966 2.756760 CCCACAAATCTCCATGTCCTTG 59.243 50.0 0.0 0.0 0.00 3.61 R
3263 3378 1.178534 GGCCTGCTGCTGTGGTTTTA 61.179 55.0 0.0 0.0 40.92 1.52 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
42 43 4.959596 GAGCATCCTCGCCGCCTC 62.960 72.222 0.00 0.00 0.00 4.70
63 64 4.847585 CGAGAGGTCGTCGTCGCG 62.848 72.222 12.78 12.78 42.61 5.87
64 65 4.517703 GAGAGGTCGTCGTCGCGG 62.518 72.222 6.13 0.00 36.96 6.46
78 79 4.521062 GCGGTGAGCGCTCTCCAT 62.521 66.667 41.50 11.76 41.88 3.41
79 80 2.279120 CGGTGAGCGCTCTCCATC 60.279 66.667 41.50 24.02 41.88 3.51
80 81 2.780094 CGGTGAGCGCTCTCCATCT 61.780 63.158 41.50 10.23 41.88 2.90
81 82 1.067250 GGTGAGCGCTCTCCATCTC 59.933 63.158 39.97 20.96 41.53 2.75
82 83 1.067250 GTGAGCGCTCTCCATCTCC 59.933 63.158 35.27 9.49 38.58 3.71
83 84 1.380380 TGAGCGCTCTCCATCTCCA 60.380 57.895 35.27 12.21 38.58 3.86
84 85 0.758310 TGAGCGCTCTCCATCTCCAT 60.758 55.000 35.27 0.00 38.58 3.41
85 86 0.038343 GAGCGCTCTCCATCTCCATC 60.038 60.000 29.88 0.00 33.19 3.51
86 87 1.005156 GCGCTCTCCATCTCCATCC 60.005 63.158 0.00 0.00 0.00 3.51
87 88 1.752358 GCGCTCTCCATCTCCATCCA 61.752 60.000 0.00 0.00 0.00 3.41
88 89 0.317799 CGCTCTCCATCTCCATCCAG 59.682 60.000 0.00 0.00 0.00 3.86
89 90 0.686224 GCTCTCCATCTCCATCCAGG 59.314 60.000 0.00 0.00 39.47 4.45
90 91 1.350071 CTCTCCATCTCCATCCAGGG 58.650 60.000 0.00 0.00 38.24 4.45
91 92 0.765903 TCTCCATCTCCATCCAGGGC 60.766 60.000 0.00 0.00 38.24 5.19
92 93 0.767446 CTCCATCTCCATCCAGGGCT 60.767 60.000 0.00 0.00 38.24 5.19
93 94 0.765903 TCCATCTCCATCCAGGGCTC 60.766 60.000 0.00 0.00 38.24 4.70
94 95 0.767446 CCATCTCCATCCAGGGCTCT 60.767 60.000 0.00 0.00 38.24 4.09
95 96 0.397187 CATCTCCATCCAGGGCTCTG 59.603 60.000 6.61 6.61 40.59 3.35
96 97 1.417288 ATCTCCATCCAGGGCTCTGC 61.417 60.000 8.54 0.00 39.61 4.26
97 98 2.041762 TCCATCCAGGGCTCTGCT 59.958 61.111 8.54 0.00 39.61 4.24
98 99 2.192443 CCATCCAGGGCTCTGCTG 59.808 66.667 8.54 7.77 39.61 4.41
99 100 2.516460 CATCCAGGGCTCTGCTGC 60.516 66.667 8.54 0.00 39.61 5.25
100 101 4.172512 ATCCAGGGCTCTGCTGCG 62.173 66.667 8.54 0.00 39.61 5.18
134 135 3.448340 GGTACGCGTACGGGGGAA 61.448 66.667 35.36 16.74 46.04 3.97
135 136 2.571231 GTACGCGTACGGGGGAAA 59.429 61.111 31.27 14.44 46.04 3.13
136 137 1.141665 GTACGCGTACGGGGGAAAT 59.858 57.895 31.27 15.91 46.04 2.17
137 138 0.460109 GTACGCGTACGGGGGAAATT 60.460 55.000 31.27 15.24 46.04 1.82
138 139 0.248843 TACGCGTACGGGGGAAATTT 59.751 50.000 31.94 14.57 46.04 1.82
139 140 0.248843 ACGCGTACGGGGGAAATTTA 59.751 50.000 31.94 0.00 46.04 1.40
140 141 0.932399 CGCGTACGGGGGAAATTTAG 59.068 55.000 23.33 0.00 34.97 1.85
141 142 1.471327 CGCGTACGGGGGAAATTTAGA 60.471 52.381 23.33 0.00 34.97 2.10
142 143 2.207590 GCGTACGGGGGAAATTTAGAG 58.792 52.381 18.39 0.00 0.00 2.43
143 144 2.159057 GCGTACGGGGGAAATTTAGAGA 60.159 50.000 18.39 0.00 0.00 3.10
144 145 3.451526 CGTACGGGGGAAATTTAGAGAC 58.548 50.000 7.57 0.00 0.00 3.36
145 146 3.131755 CGTACGGGGGAAATTTAGAGACT 59.868 47.826 7.57 0.00 0.00 3.24
146 147 4.382362 CGTACGGGGGAAATTTAGAGACTT 60.382 45.833 7.57 0.00 0.00 3.01
147 148 4.652679 ACGGGGGAAATTTAGAGACTTT 57.347 40.909 0.00 0.00 0.00 2.66
148 149 4.586884 ACGGGGGAAATTTAGAGACTTTC 58.413 43.478 0.00 0.00 0.00 2.62
149 150 4.288887 ACGGGGGAAATTTAGAGACTTTCT 59.711 41.667 0.00 0.00 40.06 2.52
150 151 5.222068 ACGGGGGAAATTTAGAGACTTTCTT 60.222 40.000 0.00 0.00 37.36 2.52
151 152 5.710567 CGGGGGAAATTTAGAGACTTTCTTT 59.289 40.000 0.00 0.00 37.36 2.52
152 153 6.208797 CGGGGGAAATTTAGAGACTTTCTTTT 59.791 38.462 0.00 0.00 37.36 2.27
153 154 7.255836 CGGGGGAAATTTAGAGACTTTCTTTTT 60.256 37.037 0.00 0.00 37.36 1.94
154 155 7.872993 GGGGGAAATTTAGAGACTTTCTTTTTG 59.127 37.037 0.00 0.00 37.36 2.44
155 156 8.421784 GGGGAAATTTAGAGACTTTCTTTTTGT 58.578 33.333 0.00 0.00 37.36 2.83
156 157 9.817809 GGGAAATTTAGAGACTTTCTTTTTGTT 57.182 29.630 0.00 0.00 37.36 2.83
188 189 5.849357 TTGATTGACAGCATGAATTTTGC 57.151 34.783 0.00 6.28 39.69 3.68
189 190 3.921630 TGATTGACAGCATGAATTTTGCG 59.078 39.130 0.00 6.63 44.82 4.85
190 191 3.367992 TTGACAGCATGAATTTTGCGT 57.632 38.095 0.00 9.02 44.82 5.24
191 192 2.932498 TGACAGCATGAATTTTGCGTC 58.068 42.857 19.73 19.73 44.82 5.19
192 193 2.553602 TGACAGCATGAATTTTGCGTCT 59.446 40.909 23.01 9.18 44.82 4.18
193 194 3.750652 TGACAGCATGAATTTTGCGTCTA 59.249 39.130 23.01 14.97 44.82 2.59
194 195 4.083581 ACAGCATGAATTTTGCGTCTAC 57.916 40.909 0.00 0.00 44.82 2.59
195 196 3.501828 ACAGCATGAATTTTGCGTCTACA 59.498 39.130 0.00 0.00 44.82 2.74
196 197 4.023279 ACAGCATGAATTTTGCGTCTACAA 60.023 37.500 0.00 0.00 44.82 2.41
197 198 4.916831 CAGCATGAATTTTGCGTCTACAAA 59.083 37.500 0.00 0.00 44.82 2.83
198 199 5.401972 CAGCATGAATTTTGCGTCTACAAAA 59.598 36.000 0.00 5.04 45.63 2.44
199 200 6.399249 CAGCATGAATTTTGCGTCTACAAAAG 60.399 38.462 0.00 0.00 45.14 2.27
200 201 8.674100 CAGCATGAATTTTGCGTCTACAAAAGT 61.674 37.037 0.00 5.63 46.84 2.66
204 205 2.748461 TTGCGTCTACAAAAGTGTGC 57.252 45.000 0.00 0.00 38.82 4.57
205 206 1.948104 TGCGTCTACAAAAGTGTGCT 58.052 45.000 0.00 0.00 38.82 4.40
206 207 2.285083 TGCGTCTACAAAAGTGTGCTT 58.715 42.857 0.00 0.00 38.82 3.91
207 208 2.286833 TGCGTCTACAAAAGTGTGCTTC 59.713 45.455 0.00 0.00 38.82 3.86
208 209 2.544267 GCGTCTACAAAAGTGTGCTTCT 59.456 45.455 0.00 0.00 38.82 2.85
209 210 3.604772 GCGTCTACAAAAGTGTGCTTCTG 60.605 47.826 0.00 0.00 38.82 3.02
210 211 3.802139 CGTCTACAAAAGTGTGCTTCTGA 59.198 43.478 0.00 0.00 38.82 3.27
211 212 4.449068 CGTCTACAAAAGTGTGCTTCTGAT 59.551 41.667 0.00 0.00 38.82 2.90
212 213 5.050091 CGTCTACAAAAGTGTGCTTCTGATT 60.050 40.000 0.00 0.00 38.82 2.57
213 214 6.145534 CGTCTACAAAAGTGTGCTTCTGATTA 59.854 38.462 0.00 0.00 38.82 1.75
214 215 7.148573 CGTCTACAAAAGTGTGCTTCTGATTAT 60.149 37.037 0.00 0.00 38.82 1.28
215 216 8.171840 GTCTACAAAAGTGTGCTTCTGATTATC 58.828 37.037 0.00 0.00 38.82 1.75
216 217 8.097038 TCTACAAAAGTGTGCTTCTGATTATCT 58.903 33.333 0.00 0.00 38.82 1.98
217 218 7.516198 ACAAAAGTGTGCTTCTGATTATCTT 57.484 32.000 0.00 0.00 36.31 2.40
218 219 7.588512 ACAAAAGTGTGCTTCTGATTATCTTC 58.411 34.615 0.00 0.00 36.31 2.87
219 220 7.229306 ACAAAAGTGTGCTTCTGATTATCTTCA 59.771 33.333 0.00 0.00 36.31 3.02
220 221 7.750229 AAAGTGTGCTTCTGATTATCTTCAA 57.250 32.000 0.00 0.00 33.01 2.69
221 222 6.734104 AGTGTGCTTCTGATTATCTTCAAC 57.266 37.500 0.00 0.00 0.00 3.18
222 223 6.233434 AGTGTGCTTCTGATTATCTTCAACA 58.767 36.000 0.00 0.00 0.00 3.33
223 224 6.370994 AGTGTGCTTCTGATTATCTTCAACAG 59.629 38.462 0.00 0.00 0.00 3.16
224 225 5.645067 TGTGCTTCTGATTATCTTCAACAGG 59.355 40.000 0.00 0.00 0.00 4.00
225 226 5.877012 GTGCTTCTGATTATCTTCAACAGGA 59.123 40.000 0.00 0.00 0.00 3.86
226 227 6.036953 GTGCTTCTGATTATCTTCAACAGGAG 59.963 42.308 0.00 0.00 37.29 3.69
227 228 6.112058 GCTTCTGATTATCTTCAACAGGAGT 58.888 40.000 0.00 0.00 36.79 3.85
228 229 6.597280 GCTTCTGATTATCTTCAACAGGAGTT 59.403 38.462 0.00 0.00 36.79 3.01
229 230 7.120432 GCTTCTGATTATCTTCAACAGGAGTTT 59.880 37.037 0.00 0.00 36.79 2.66
230 231 7.912056 TCTGATTATCTTCAACAGGAGTTTG 57.088 36.000 0.00 0.00 35.28 2.93
231 232 6.881065 TCTGATTATCTTCAACAGGAGTTTGG 59.119 38.462 0.00 0.00 35.28 3.28
232 233 6.778821 TGATTATCTTCAACAGGAGTTTGGA 58.221 36.000 0.00 0.00 35.28 3.53
233 234 6.881065 TGATTATCTTCAACAGGAGTTTGGAG 59.119 38.462 0.00 0.00 35.28 3.86
234 235 4.982241 ATCTTCAACAGGAGTTTGGAGA 57.018 40.909 0.00 0.00 35.28 3.71
235 236 4.073293 TCTTCAACAGGAGTTTGGAGAC 57.927 45.455 0.00 0.00 35.28 3.36
236 237 3.711704 TCTTCAACAGGAGTTTGGAGACT 59.288 43.478 0.00 0.00 35.28 3.24
237 238 3.753294 TCAACAGGAGTTTGGAGACTC 57.247 47.619 0.00 0.00 44.20 3.36
253 254 7.807977 TGGAGACTCCATCAATTAATTAAGC 57.192 36.000 20.74 0.00 42.67 3.09
254 255 7.345691 TGGAGACTCCATCAATTAATTAAGCA 58.654 34.615 20.74 0.00 42.67 3.91
255 256 7.500227 TGGAGACTCCATCAATTAATTAAGCAG 59.500 37.037 20.74 0.00 42.67 4.24
256 257 7.716998 GGAGACTCCATCAATTAATTAAGCAGA 59.283 37.037 17.10 2.33 36.28 4.26
257 258 9.282569 GAGACTCCATCAATTAATTAAGCAGAT 57.717 33.333 0.00 4.43 0.00 2.90
258 259 9.064706 AGACTCCATCAATTAATTAAGCAGATG 57.935 33.333 19.93 19.93 33.15 2.90
259 260 8.985315 ACTCCATCAATTAATTAAGCAGATGA 57.015 30.769 24.40 15.19 34.79 2.92
260 261 8.844244 ACTCCATCAATTAATTAAGCAGATGAC 58.156 33.333 24.40 0.00 34.79 3.06
261 262 8.750515 TCCATCAATTAATTAAGCAGATGACA 57.249 30.769 24.40 14.94 34.79 3.58
262 263 9.187996 TCCATCAATTAATTAAGCAGATGACAA 57.812 29.630 24.40 14.28 34.79 3.18
263 264 9.806203 CCATCAATTAATTAAGCAGATGACAAA 57.194 29.630 24.40 0.00 34.79 2.83
276 277 8.854614 AGCAGATGACAAATATTTAGATACCC 57.145 34.615 0.00 0.00 0.00 3.69
277 278 8.439971 AGCAGATGACAAATATTTAGATACCCA 58.560 33.333 0.00 0.00 0.00 4.51
278 279 9.066892 GCAGATGACAAATATTTAGATACCCAA 57.933 33.333 0.00 0.00 0.00 4.12
282 283 9.693739 ATGACAAATATTTAGATACCCAACACA 57.306 29.630 0.00 0.00 0.00 3.72
283 284 9.173021 TGACAAATATTTAGATACCCAACACAG 57.827 33.333 0.00 0.00 0.00 3.66
284 285 9.391006 GACAAATATTTAGATACCCAACACAGA 57.609 33.333 0.00 0.00 0.00 3.41
285 286 9.747898 ACAAATATTTAGATACCCAACACAGAA 57.252 29.630 0.00 0.00 0.00 3.02
290 291 8.980481 ATTTAGATACCCAACACAGAATTAGG 57.020 34.615 0.00 0.00 0.00 2.69
291 292 5.373812 AGATACCCAACACAGAATTAGGG 57.626 43.478 0.00 0.00 42.07 3.53
292 293 5.036916 AGATACCCAACACAGAATTAGGGA 58.963 41.667 0.00 0.00 39.60 4.20
293 294 5.672194 AGATACCCAACACAGAATTAGGGAT 59.328 40.000 0.00 0.00 39.60 3.85
294 295 3.968265 ACCCAACACAGAATTAGGGATG 58.032 45.455 0.00 0.00 39.60 3.51
295 296 3.290710 CCCAACACAGAATTAGGGATGG 58.709 50.000 0.00 2.86 38.60 3.51
296 297 3.053693 CCCAACACAGAATTAGGGATGGA 60.054 47.826 9.65 0.00 38.60 3.41
297 298 4.569653 CCCAACACAGAATTAGGGATGGAA 60.570 45.833 9.65 0.00 38.60 3.53
298 299 5.016173 CCAACACAGAATTAGGGATGGAAA 58.984 41.667 3.59 0.00 0.00 3.13
299 300 5.105756 CCAACACAGAATTAGGGATGGAAAC 60.106 44.000 3.59 0.00 0.00 2.78
300 301 4.261801 ACACAGAATTAGGGATGGAAACG 58.738 43.478 0.00 0.00 0.00 3.60
301 302 3.627577 CACAGAATTAGGGATGGAAACGG 59.372 47.826 0.00 0.00 0.00 4.44
302 303 3.521937 ACAGAATTAGGGATGGAAACGGA 59.478 43.478 0.00 0.00 0.00 4.69
303 304 3.877508 CAGAATTAGGGATGGAAACGGAC 59.122 47.826 0.00 0.00 0.00 4.79
304 305 2.614829 ATTAGGGATGGAAACGGACG 57.385 50.000 0.00 0.00 0.00 4.79
305 306 0.538118 TTAGGGATGGAAACGGACGG 59.462 55.000 0.00 0.00 0.00 4.79
306 307 0.324552 TAGGGATGGAAACGGACGGA 60.325 55.000 0.00 0.00 0.00 4.69
307 308 0.981277 AGGGATGGAAACGGACGGAT 60.981 55.000 0.00 0.00 0.00 4.18
308 309 0.532196 GGGATGGAAACGGACGGATC 60.532 60.000 0.00 0.00 0.00 3.36
309 310 0.874607 GGATGGAAACGGACGGATCG 60.875 60.000 0.00 0.00 0.00 3.69
310 311 0.874607 GATGGAAACGGACGGATCGG 60.875 60.000 0.00 0.00 0.00 4.18
311 312 1.324740 ATGGAAACGGACGGATCGGA 61.325 55.000 7.35 0.00 0.00 4.55
312 313 1.324740 TGGAAACGGACGGATCGGAT 61.325 55.000 7.35 0.00 0.00 4.18
313 314 0.670162 GGAAACGGACGGATCGGATA 59.330 55.000 7.35 0.00 0.00 2.59
314 315 1.335689 GGAAACGGACGGATCGGATAG 60.336 57.143 7.35 0.37 0.00 2.08
315 316 1.336125 GAAACGGACGGATCGGATAGT 59.664 52.381 7.35 0.00 0.00 2.12
316 317 0.666913 AACGGACGGATCGGATAGTG 59.333 55.000 7.35 0.00 0.00 2.74
317 318 1.081376 CGGACGGATCGGATAGTGC 60.081 63.158 7.35 5.65 0.00 4.40
318 319 1.516365 CGGACGGATCGGATAGTGCT 61.516 60.000 7.35 0.00 0.00 4.40
319 320 0.241481 GGACGGATCGGATAGTGCTC 59.759 60.000 7.35 0.00 0.00 4.26
320 321 1.240256 GACGGATCGGATAGTGCTCT 58.760 55.000 7.35 0.00 0.00 4.09
321 322 1.609555 GACGGATCGGATAGTGCTCTT 59.390 52.381 7.35 0.00 0.00 2.85
322 323 2.812591 GACGGATCGGATAGTGCTCTTA 59.187 50.000 7.35 0.00 0.00 2.10
323 324 3.422796 ACGGATCGGATAGTGCTCTTAT 58.577 45.455 7.35 0.00 0.00 1.73
324 325 3.440872 ACGGATCGGATAGTGCTCTTATC 59.559 47.826 7.35 0.00 0.00 1.75
325 326 3.440522 CGGATCGGATAGTGCTCTTATCA 59.559 47.826 0.00 0.00 0.00 2.15
326 327 4.673061 CGGATCGGATAGTGCTCTTATCAC 60.673 50.000 0.00 0.00 34.80 3.06
336 337 6.942532 AGTGCTCTTATCACTTTCAAAACA 57.057 33.333 0.00 0.00 41.61 2.83
375 376 6.656632 ACGGATGTTATCAGATACAGATGT 57.343 37.500 0.00 0.00 0.00 3.06
378 379 6.294731 CGGATGTTATCAGATACAGATGTGGA 60.295 42.308 0.00 0.00 0.00 4.02
380 381 8.753133 GGATGTTATCAGATACAGATGTGGATA 58.247 37.037 0.00 0.00 0.00 2.59
393 394 7.577303 ACAGATGTGGATAGGATGTTATTTGT 58.423 34.615 0.00 0.00 0.00 2.83
436 437 8.833231 ATGTTTATTCGATTCAGAACGGATAT 57.167 30.769 6.85 0.00 31.47 1.63
507 508 7.269084 GTGACATGAAATAATCAACTTGTGACG 59.731 37.037 0.00 0.00 42.54 4.35
659 660 6.709846 TGTTGGGGCTAGAATTTTGAAAATTG 59.290 34.615 19.47 7.56 0.00 2.32
790 791 9.722184 TGCAGATAATTTCCATTTTCATTTTGA 57.278 25.926 0.00 0.00 0.00 2.69
901 902 0.249447 CACAGAATAGCATCGGCCGA 60.249 55.000 33.12 33.12 42.56 5.54
1613 1630 2.125326 CCGCCCTCGAGATGTACCA 61.125 63.158 15.71 0.00 38.10 3.25
1696 1713 1.684049 AACTCCCTCCTCCTCGCTG 60.684 63.158 0.00 0.00 0.00 5.18
1947 1966 1.202746 GGGATGGCAGAGGAGATGTTC 60.203 57.143 0.00 0.00 0.00 3.18
2052 2079 1.300971 ATGCTGCGATGCTTGTTCGT 61.301 50.000 0.00 0.00 38.81 3.85
2145 2172 0.682855 AGAGGAGAGTTGAGGAGGCG 60.683 60.000 0.00 0.00 0.00 5.52
2149 2176 1.757699 GGAGAGTTGAGGAGGCGTTAT 59.242 52.381 0.00 0.00 0.00 1.89
2298 2325 0.034477 GGAAGGGATTCAAAGCCGGA 60.034 55.000 5.05 0.00 34.61 5.14
2415 2442 0.842030 AGGATGGCAGTGACCTGGAA 60.842 55.000 0.00 0.00 39.22 3.53
2510 2537 7.528996 TGTCTCATCCAATTTTGTTCATCTT 57.471 32.000 0.00 0.00 0.00 2.40
2531 2558 9.809096 CATCTTCAGTCTTTACACTGTACATAT 57.191 33.333 0.00 0.00 43.80 1.78
2549 2589 9.890629 TGTACATATTAGAGCACAAAAATCTCT 57.109 29.630 0.00 0.00 40.08 3.10
2562 2602 7.748241 GCACAAAAATCTCTGAGTTGTATCTTC 59.252 37.037 10.03 0.00 31.44 2.87
2610 2657 8.041323 GTCTTCCACCTCTATCTGTGAATTTTA 58.959 37.037 0.00 0.00 34.37 1.52
2639 2686 2.189594 TCATGACTTCTGGCTGGTTG 57.810 50.000 0.00 0.00 0.00 3.77
2668 2715 7.726033 AACTACTTTAGTGATCATCTCCTGT 57.274 36.000 0.00 0.00 39.39 4.00
2716 2772 7.744087 TTACAGCTTACATCAATCTTTGTGT 57.256 32.000 0.00 0.00 0.00 3.72
2717 2773 6.246420 ACAGCTTACATCAATCTTTGTGTC 57.754 37.500 0.00 0.00 0.00 3.67
2718 2774 5.764686 ACAGCTTACATCAATCTTTGTGTCA 59.235 36.000 0.00 0.00 0.00 3.58
2719 2775 6.432162 ACAGCTTACATCAATCTTTGTGTCAT 59.568 34.615 0.00 0.00 0.00 3.06
2720 2776 6.745907 CAGCTTACATCAATCTTTGTGTCATG 59.254 38.462 0.00 0.00 0.00 3.07
2721 2777 5.514204 GCTTACATCAATCTTTGTGTCATGC 59.486 40.000 0.00 0.00 0.00 4.06
2722 2778 6.572167 TTACATCAATCTTTGTGTCATGCA 57.428 33.333 0.00 0.00 0.00 3.96
2755 2811 7.764141 TGCCATTGATATATAGTTGTTGCAT 57.236 32.000 0.00 0.00 0.00 3.96
2757 2813 9.465199 TGCCATTGATATATAGTTGTTGCATAT 57.535 29.630 0.00 0.00 0.00 1.78
2758 2814 9.726232 GCCATTGATATATAGTTGTTGCATATG 57.274 33.333 0.00 0.00 0.00 1.78
2766 2822 8.995027 ATATAGTTGTTGCATATGAAAAGGGA 57.005 30.769 6.97 0.00 0.00 4.20
2767 2823 5.391312 AGTTGTTGCATATGAAAAGGGAC 57.609 39.130 6.97 0.00 0.00 4.46
2810 2872 2.802787 AGATCTGCGGTACATGTAGC 57.197 50.000 22.36 22.36 0.00 3.58
2877 2944 3.376234 CCACATGGACTGCAACTATGAAG 59.624 47.826 18.54 12.16 38.30 3.02
2879 2946 5.178061 CACATGGACTGCAACTATGAAGTA 58.822 41.667 18.54 0.00 45.99 2.24
2880 2947 5.063944 CACATGGACTGCAACTATGAAGTAC 59.936 44.000 18.54 0.00 45.99 2.73
2969 3057 6.964934 CCGACTGTAGCCAAAAATAACAATAC 59.035 38.462 0.00 0.00 0.00 1.89
2971 3059 8.234546 CGACTGTAGCCAAAAATAACAATACTT 58.765 33.333 0.00 0.00 0.00 2.24
2994 3082 1.621317 TCTTATGTCACAGTTCCGCCA 59.379 47.619 0.00 0.00 0.00 5.69
3057 3146 5.126707 GGAAGATCCTTGAGACAATGCAAAT 59.873 40.000 0.00 0.00 32.53 2.32
3062 3151 7.778853 AGATCCTTGAGACAATGCAAATTATCT 59.221 33.333 0.00 0.00 0.00 1.98
3109 3205 3.199508 ACCTCTCATGATCAGGACTTTGG 59.800 47.826 22.23 8.49 0.00 3.28
3118 3232 1.490490 TCAGGACTTTGGCAGAACTGT 59.510 47.619 3.77 0.00 33.90 3.55
3140 3254 2.191128 ATTGACAAGGGTGAGAGTGC 57.809 50.000 0.00 0.00 0.00 4.40
3154 3268 6.294342 GGGTGAGAGTGCGTGTTATATACATA 60.294 42.308 0.00 0.00 39.39 2.29
3159 3273 6.204301 AGAGTGCGTGTTATATACATACGTCT 59.796 38.462 0.00 10.58 39.39 4.18
3225 3340 1.734047 GCAAGACAGTAGTGAGAGGCG 60.734 57.143 4.09 0.00 0.00 5.52
3253 3368 0.034896 ATCACCGTGGTCAGTGTTCC 59.965 55.000 0.00 0.00 35.45 3.62
3263 3378 1.067212 GTCAGTGTTCCGTCAGTCAGT 59.933 52.381 0.00 0.00 0.00 3.41
3272 3387 2.431419 TCCGTCAGTCAGTAAAACCACA 59.569 45.455 0.00 0.00 0.00 4.17
3319 3434 4.202010 GCTTTGGTGTGATGTGTGTAAAGT 60.202 41.667 0.00 0.00 0.00 2.66
3322 3437 5.994887 TGGTGTGATGTGTGTAAAGTTAC 57.005 39.130 0.00 0.00 0.00 2.50
3324 3460 5.061179 GGTGTGATGTGTGTAAAGTTACCT 58.939 41.667 0.00 0.00 32.72 3.08
3363 3499 7.381139 CCTTGCTTTAAAACGAATTTGCTTCTA 59.619 33.333 0.00 0.00 32.27 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.040763 GATGCTCCGCGAGATGGC 61.041 66.667 8.23 4.79 0.00 4.40
15 16 2.356793 GGATGCTCCGCGAGATGG 60.357 66.667 8.23 0.00 0.00 3.51
16 17 1.372748 GAGGATGCTCCGCGAGATG 60.373 63.158 8.23 0.00 42.75 2.90
17 18 3.046870 GAGGATGCTCCGCGAGAT 58.953 61.111 8.23 0.00 42.75 2.75
25 26 4.959596 GAGGCGGCGAGGATGCTC 62.960 72.222 12.98 3.74 34.52 4.26
40 41 3.878519 GACGACCTCTCGCCGGAG 61.879 72.222 5.05 0.00 44.33 4.63
44 45 4.517703 CGACGACGACCTCTCGCC 62.518 72.222 0.00 0.00 44.33 5.54
46 47 4.847585 CGCGACGACGACCTCTCG 62.848 72.222 12.29 0.41 46.06 4.04
47 48 4.517703 CCGCGACGACGACCTCTC 62.518 72.222 8.23 0.00 42.66 3.20
62 63 2.279120 GATGGAGAGCGCTCACCG 60.279 66.667 37.42 0.00 42.27 4.94
63 64 1.067250 GAGATGGAGAGCGCTCACC 59.933 63.158 37.61 37.61 43.14 4.02
64 65 1.067250 GGAGATGGAGAGCGCTCAC 59.933 63.158 36.87 30.70 43.14 3.51
65 66 0.758310 ATGGAGATGGAGAGCGCTCA 60.758 55.000 36.87 19.72 43.14 4.26
66 67 0.038343 GATGGAGATGGAGAGCGCTC 60.038 60.000 30.01 30.01 40.54 5.03
67 68 1.470996 GGATGGAGATGGAGAGCGCT 61.471 60.000 11.27 11.27 0.00 5.92
68 69 1.005156 GGATGGAGATGGAGAGCGC 60.005 63.158 0.00 0.00 0.00 5.92
69 70 0.317799 CTGGATGGAGATGGAGAGCG 59.682 60.000 0.00 0.00 0.00 5.03
70 71 0.686224 CCTGGATGGAGATGGAGAGC 59.314 60.000 0.00 0.00 38.35 4.09
71 72 1.350071 CCCTGGATGGAGATGGAGAG 58.650 60.000 0.00 0.00 38.35 3.20
72 73 0.765903 GCCCTGGATGGAGATGGAGA 60.766 60.000 0.00 0.00 38.35 3.71
73 74 0.767446 AGCCCTGGATGGAGATGGAG 60.767 60.000 0.00 0.00 38.35 3.86
74 75 0.765903 GAGCCCTGGATGGAGATGGA 60.766 60.000 0.00 0.00 38.35 3.41
75 76 0.767446 AGAGCCCTGGATGGAGATGG 60.767 60.000 0.00 0.00 38.35 3.51
76 77 0.397187 CAGAGCCCTGGATGGAGATG 59.603 60.000 0.00 0.00 38.35 2.90
77 78 1.417288 GCAGAGCCCTGGATGGAGAT 61.417 60.000 0.00 0.00 40.72 2.75
78 79 2.068821 GCAGAGCCCTGGATGGAGA 61.069 63.158 0.00 0.00 40.72 3.71
79 80 2.071262 AGCAGAGCCCTGGATGGAG 61.071 63.158 0.00 0.00 40.72 3.86
80 81 2.041762 AGCAGAGCCCTGGATGGA 59.958 61.111 0.00 0.00 40.72 3.41
81 82 2.192443 CAGCAGAGCCCTGGATGG 59.808 66.667 0.00 0.00 40.72 3.51
82 83 2.516460 GCAGCAGAGCCCTGGATG 60.516 66.667 0.00 0.00 40.72 3.51
83 84 4.172512 CGCAGCAGAGCCCTGGAT 62.173 66.667 0.00 0.00 40.72 3.41
117 118 2.296814 ATTTCCCCCGTACGCGTACC 62.297 60.000 36.14 21.95 36.15 3.34
118 119 0.460109 AATTTCCCCCGTACGCGTAC 60.460 55.000 33.94 33.94 36.15 3.67
119 120 0.248843 AAATTTCCCCCGTACGCGTA 59.751 50.000 16.41 16.41 36.15 4.42
120 121 0.248843 TAAATTTCCCCCGTACGCGT 59.751 50.000 19.17 19.17 36.15 6.01
121 122 0.932399 CTAAATTTCCCCCGTACGCG 59.068 55.000 10.49 3.53 37.95 6.01
122 123 2.159057 TCTCTAAATTTCCCCCGTACGC 60.159 50.000 10.49 0.00 0.00 4.42
123 124 3.131755 AGTCTCTAAATTTCCCCCGTACG 59.868 47.826 8.69 8.69 0.00 3.67
124 125 4.750021 AGTCTCTAAATTTCCCCCGTAC 57.250 45.455 0.00 0.00 0.00 3.67
125 126 5.486419 AGAAAGTCTCTAAATTTCCCCCGTA 59.514 40.000 0.00 0.00 34.23 4.02
126 127 4.288887 AGAAAGTCTCTAAATTTCCCCCGT 59.711 41.667 0.00 0.00 34.23 5.28
127 128 4.844884 AGAAAGTCTCTAAATTTCCCCCG 58.155 43.478 0.00 0.00 34.23 5.73
128 129 7.540474 AAAAGAAAGTCTCTAAATTTCCCCC 57.460 36.000 0.00 0.00 34.23 5.40
129 130 8.421784 ACAAAAAGAAAGTCTCTAAATTTCCCC 58.578 33.333 0.00 0.00 34.23 4.81
130 131 9.817809 AACAAAAAGAAAGTCTCTAAATTTCCC 57.182 29.630 0.00 0.00 34.23 3.97
162 163 7.806014 GCAAAATTCATGCTGTCAATCAAAATT 59.194 29.630 8.50 0.00 40.64 1.82
163 164 7.302524 GCAAAATTCATGCTGTCAATCAAAAT 58.697 30.769 8.50 0.00 40.64 1.82
164 165 6.564312 CGCAAAATTCATGCTGTCAATCAAAA 60.564 34.615 12.65 0.00 41.64 2.44
165 166 5.107414 CGCAAAATTCATGCTGTCAATCAAA 60.107 36.000 12.65 0.00 41.64 2.69
166 167 4.386350 CGCAAAATTCATGCTGTCAATCAA 59.614 37.500 12.65 0.00 41.64 2.57
167 168 3.921630 CGCAAAATTCATGCTGTCAATCA 59.078 39.130 12.65 0.00 41.64 2.57
168 169 3.922240 ACGCAAAATTCATGCTGTCAATC 59.078 39.130 12.65 0.00 41.64 2.67
169 170 3.916761 ACGCAAAATTCATGCTGTCAAT 58.083 36.364 12.65 0.00 41.64 2.57
170 171 3.004629 AGACGCAAAATTCATGCTGTCAA 59.995 39.130 24.76 0.00 43.32 3.18
171 172 2.553602 AGACGCAAAATTCATGCTGTCA 59.446 40.909 24.76 0.00 43.32 3.58
172 173 3.207474 AGACGCAAAATTCATGCTGTC 57.793 42.857 20.41 20.41 42.30 3.51
173 174 3.501828 TGTAGACGCAAAATTCATGCTGT 59.498 39.130 12.65 11.67 41.64 4.40
174 175 4.082274 TGTAGACGCAAAATTCATGCTG 57.918 40.909 12.65 9.31 41.64 4.41
175 176 4.764679 TTGTAGACGCAAAATTCATGCT 57.235 36.364 12.65 2.58 41.64 3.79
176 177 5.402270 ACTTTTGTAGACGCAAAATTCATGC 59.598 36.000 10.03 6.19 44.25 4.06
177 178 6.417635 ACACTTTTGTAGACGCAAAATTCATG 59.582 34.615 10.03 0.00 44.25 3.07
178 179 6.417635 CACACTTTTGTAGACGCAAAATTCAT 59.582 34.615 10.03 0.00 44.25 2.57
179 180 5.741510 CACACTTTTGTAGACGCAAAATTCA 59.258 36.000 10.03 0.00 44.25 2.57
180 181 5.331532 GCACACTTTTGTAGACGCAAAATTC 60.332 40.000 10.03 0.00 44.25 2.17
181 182 4.502645 GCACACTTTTGTAGACGCAAAATT 59.497 37.500 10.03 4.31 44.25 1.82
182 183 4.041723 GCACACTTTTGTAGACGCAAAAT 58.958 39.130 10.03 1.88 44.25 1.82
183 184 3.127895 AGCACACTTTTGTAGACGCAAAA 59.872 39.130 9.47 9.47 43.46 2.44
184 185 2.680841 AGCACACTTTTGTAGACGCAAA 59.319 40.909 0.00 0.00 36.67 3.68
185 186 2.285083 AGCACACTTTTGTAGACGCAA 58.715 42.857 0.00 0.00 33.30 4.85
186 187 1.948104 AGCACACTTTTGTAGACGCA 58.052 45.000 0.00 0.00 33.30 5.24
187 188 2.544267 AGAAGCACACTTTTGTAGACGC 59.456 45.455 0.00 0.00 35.82 5.19
188 189 3.802139 TCAGAAGCACACTTTTGTAGACG 59.198 43.478 0.00 0.00 38.73 4.18
189 190 5.931441 ATCAGAAGCACACTTTTGTAGAC 57.069 39.130 0.00 0.00 38.73 2.59
190 191 8.097038 AGATAATCAGAAGCACACTTTTGTAGA 58.903 33.333 0.00 0.00 38.73 2.59
191 192 8.261492 AGATAATCAGAAGCACACTTTTGTAG 57.739 34.615 0.00 0.00 38.73 2.74
192 193 8.621532 AAGATAATCAGAAGCACACTTTTGTA 57.378 30.769 0.00 0.00 38.73 2.41
193 194 7.229306 TGAAGATAATCAGAAGCACACTTTTGT 59.771 33.333 0.00 0.00 38.73 2.83
194 195 7.587629 TGAAGATAATCAGAAGCACACTTTTG 58.412 34.615 0.00 0.00 38.93 2.44
195 196 7.750229 TGAAGATAATCAGAAGCACACTTTT 57.250 32.000 0.00 0.00 35.82 2.27
196 197 7.229306 TGTTGAAGATAATCAGAAGCACACTTT 59.771 33.333 0.00 0.00 35.82 2.66
197 198 6.712095 TGTTGAAGATAATCAGAAGCACACTT 59.288 34.615 0.00 0.00 39.43 3.16
198 199 6.233434 TGTTGAAGATAATCAGAAGCACACT 58.767 36.000 0.00 0.00 0.00 3.55
199 200 6.402983 CCTGTTGAAGATAATCAGAAGCACAC 60.403 42.308 0.00 0.00 0.00 3.82
200 201 5.645067 CCTGTTGAAGATAATCAGAAGCACA 59.355 40.000 0.00 0.00 0.00 4.57
201 202 5.877012 TCCTGTTGAAGATAATCAGAAGCAC 59.123 40.000 0.00 0.00 0.00 4.40
202 203 6.053632 TCCTGTTGAAGATAATCAGAAGCA 57.946 37.500 0.00 0.00 0.00 3.91
203 204 6.112058 ACTCCTGTTGAAGATAATCAGAAGC 58.888 40.000 0.00 0.00 0.00 3.86
204 205 8.449397 CAAACTCCTGTTGAAGATAATCAGAAG 58.551 37.037 0.00 0.00 36.39 2.85
205 206 7.391554 CCAAACTCCTGTTGAAGATAATCAGAA 59.608 37.037 0.00 0.00 36.39 3.02
206 207 6.881065 CCAAACTCCTGTTGAAGATAATCAGA 59.119 38.462 0.00 0.00 36.39 3.27
207 208 6.881065 TCCAAACTCCTGTTGAAGATAATCAG 59.119 38.462 0.00 0.00 36.39 2.90
208 209 6.778821 TCCAAACTCCTGTTGAAGATAATCA 58.221 36.000 0.00 0.00 36.39 2.57
209 210 7.065204 GTCTCCAAACTCCTGTTGAAGATAATC 59.935 40.741 0.00 0.00 36.39 1.75
210 211 6.881602 GTCTCCAAACTCCTGTTGAAGATAAT 59.118 38.462 0.00 0.00 36.39 1.28
211 212 6.043243 AGTCTCCAAACTCCTGTTGAAGATAA 59.957 38.462 0.00 0.00 36.39 1.75
212 213 5.544176 AGTCTCCAAACTCCTGTTGAAGATA 59.456 40.000 0.00 0.00 36.39 1.98
213 214 4.349342 AGTCTCCAAACTCCTGTTGAAGAT 59.651 41.667 0.00 0.00 36.39 2.40
214 215 3.711704 AGTCTCCAAACTCCTGTTGAAGA 59.288 43.478 0.00 0.00 36.39 2.87
215 216 4.061596 GAGTCTCCAAACTCCTGTTGAAG 58.938 47.826 0.00 0.00 39.85 3.02
216 217 4.073293 GAGTCTCCAAACTCCTGTTGAA 57.927 45.455 0.00 0.00 39.85 2.69
217 218 3.753294 GAGTCTCCAAACTCCTGTTGA 57.247 47.619 0.00 0.00 39.85 3.18
230 231 7.716998 TCTGCTTAATTAATTGATGGAGTCTCC 59.283 37.037 12.40 12.40 36.96 3.71
231 232 8.668510 TCTGCTTAATTAATTGATGGAGTCTC 57.331 34.615 11.05 0.00 0.00 3.36
232 233 9.064706 CATCTGCTTAATTAATTGATGGAGTCT 57.935 33.333 11.05 2.29 0.00 3.24
233 234 9.060347 TCATCTGCTTAATTAATTGATGGAGTC 57.940 33.333 21.62 0.00 33.03 3.36
234 235 8.844244 GTCATCTGCTTAATTAATTGATGGAGT 58.156 33.333 21.62 6.63 33.03 3.85
235 236 8.843262 TGTCATCTGCTTAATTAATTGATGGAG 58.157 33.333 21.62 14.24 33.03 3.86
236 237 8.750515 TGTCATCTGCTTAATTAATTGATGGA 57.249 30.769 21.62 9.08 33.03 3.41
237 238 9.806203 TTTGTCATCTGCTTAATTAATTGATGG 57.194 29.630 21.62 6.46 33.03 3.51
250 251 9.289782 GGGTATCTAAATATTTGTCATCTGCTT 57.710 33.333 11.05 0.00 0.00 3.91
251 252 8.439971 TGGGTATCTAAATATTTGTCATCTGCT 58.560 33.333 11.05 0.00 0.00 4.24
252 253 8.621532 TGGGTATCTAAATATTTGTCATCTGC 57.378 34.615 11.05 0.00 0.00 4.26
256 257 9.693739 TGTGTTGGGTATCTAAATATTTGTCAT 57.306 29.630 11.05 2.88 0.00 3.06
257 258 9.173021 CTGTGTTGGGTATCTAAATATTTGTCA 57.827 33.333 11.05 0.00 0.00 3.58
258 259 9.391006 TCTGTGTTGGGTATCTAAATATTTGTC 57.609 33.333 11.05 0.00 0.00 3.18
259 260 9.747898 TTCTGTGTTGGGTATCTAAATATTTGT 57.252 29.630 11.05 0.08 0.00 2.83
265 266 7.998964 CCCTAATTCTGTGTTGGGTATCTAAAT 59.001 37.037 0.00 0.00 0.00 1.40
266 267 7.183112 TCCCTAATTCTGTGTTGGGTATCTAAA 59.817 37.037 0.00 0.00 36.23 1.85
267 268 6.674861 TCCCTAATTCTGTGTTGGGTATCTAA 59.325 38.462 0.00 0.00 36.23 2.10
268 269 6.206787 TCCCTAATTCTGTGTTGGGTATCTA 58.793 40.000 0.00 0.00 36.23 1.98
269 270 5.036916 TCCCTAATTCTGTGTTGGGTATCT 58.963 41.667 0.00 0.00 36.23 1.98
270 271 5.367945 TCCCTAATTCTGTGTTGGGTATC 57.632 43.478 0.00 0.00 36.23 2.24
271 272 5.399038 CCATCCCTAATTCTGTGTTGGGTAT 60.399 44.000 0.00 0.00 36.23 2.73
272 273 4.080015 CCATCCCTAATTCTGTGTTGGGTA 60.080 45.833 0.00 0.00 36.23 3.69
273 274 3.309121 CCATCCCTAATTCTGTGTTGGGT 60.309 47.826 0.00 0.00 36.23 4.51
274 275 3.053693 TCCATCCCTAATTCTGTGTTGGG 60.054 47.826 0.00 0.00 36.14 4.12
275 276 4.235079 TCCATCCCTAATTCTGTGTTGG 57.765 45.455 0.00 0.00 0.00 3.77
276 277 5.391950 CGTTTCCATCCCTAATTCTGTGTTG 60.392 44.000 0.00 0.00 0.00 3.33
277 278 4.700213 CGTTTCCATCCCTAATTCTGTGTT 59.300 41.667 0.00 0.00 0.00 3.32
278 279 4.261801 CGTTTCCATCCCTAATTCTGTGT 58.738 43.478 0.00 0.00 0.00 3.72
279 280 3.627577 CCGTTTCCATCCCTAATTCTGTG 59.372 47.826 0.00 0.00 0.00 3.66
280 281 3.521937 TCCGTTTCCATCCCTAATTCTGT 59.478 43.478 0.00 0.00 0.00 3.41
281 282 3.877508 GTCCGTTTCCATCCCTAATTCTG 59.122 47.826 0.00 0.00 0.00 3.02
282 283 3.431766 CGTCCGTTTCCATCCCTAATTCT 60.432 47.826 0.00 0.00 0.00 2.40
283 284 2.870411 CGTCCGTTTCCATCCCTAATTC 59.130 50.000 0.00 0.00 0.00 2.17
284 285 2.420967 CCGTCCGTTTCCATCCCTAATT 60.421 50.000 0.00 0.00 0.00 1.40
285 286 1.140252 CCGTCCGTTTCCATCCCTAAT 59.860 52.381 0.00 0.00 0.00 1.73
286 287 0.538118 CCGTCCGTTTCCATCCCTAA 59.462 55.000 0.00 0.00 0.00 2.69
287 288 0.324552 TCCGTCCGTTTCCATCCCTA 60.325 55.000 0.00 0.00 0.00 3.53
288 289 0.981277 ATCCGTCCGTTTCCATCCCT 60.981 55.000 0.00 0.00 0.00 4.20
289 290 0.532196 GATCCGTCCGTTTCCATCCC 60.532 60.000 0.00 0.00 0.00 3.85
290 291 0.874607 CGATCCGTCCGTTTCCATCC 60.875 60.000 0.00 0.00 0.00 3.51
291 292 0.874607 CCGATCCGTCCGTTTCCATC 60.875 60.000 0.00 0.00 0.00 3.51
292 293 1.143183 CCGATCCGTCCGTTTCCAT 59.857 57.895 0.00 0.00 0.00 3.41
293 294 1.324740 ATCCGATCCGTCCGTTTCCA 61.325 55.000 0.00 0.00 0.00 3.53
294 295 0.670162 TATCCGATCCGTCCGTTTCC 59.330 55.000 0.00 0.00 0.00 3.13
295 296 1.336125 ACTATCCGATCCGTCCGTTTC 59.664 52.381 0.00 0.00 0.00 2.78
296 297 1.066605 CACTATCCGATCCGTCCGTTT 59.933 52.381 0.00 0.00 0.00 3.60
297 298 0.666913 CACTATCCGATCCGTCCGTT 59.333 55.000 0.00 0.00 0.00 4.44
298 299 1.793134 GCACTATCCGATCCGTCCGT 61.793 60.000 0.00 0.00 0.00 4.69
299 300 1.081376 GCACTATCCGATCCGTCCG 60.081 63.158 0.00 0.00 0.00 4.79
300 301 0.241481 GAGCACTATCCGATCCGTCC 59.759 60.000 0.00 0.00 0.00 4.79
301 302 1.240256 AGAGCACTATCCGATCCGTC 58.760 55.000 0.00 0.00 0.00 4.79
302 303 1.693627 AAGAGCACTATCCGATCCGT 58.306 50.000 0.00 0.00 0.00 4.69
303 304 3.440522 TGATAAGAGCACTATCCGATCCG 59.559 47.826 0.00 0.00 0.00 4.18
304 305 4.461081 AGTGATAAGAGCACTATCCGATCC 59.539 45.833 0.00 0.00 44.27 3.36
305 306 5.637006 AGTGATAAGAGCACTATCCGATC 57.363 43.478 0.00 0.00 44.27 3.69
306 307 6.040955 TGAAAGTGATAAGAGCACTATCCGAT 59.959 38.462 0.00 0.00 45.27 4.18
307 308 5.359860 TGAAAGTGATAAGAGCACTATCCGA 59.640 40.000 0.00 0.00 45.27 4.55
308 309 5.592054 TGAAAGTGATAAGAGCACTATCCG 58.408 41.667 0.00 0.00 45.27 4.18
309 310 7.849804 TTTGAAAGTGATAAGAGCACTATCC 57.150 36.000 0.00 0.00 45.27 2.59
310 311 8.721478 TGTTTTGAAAGTGATAAGAGCACTATC 58.279 33.333 0.00 0.00 45.27 2.08
311 312 8.621532 TGTTTTGAAAGTGATAAGAGCACTAT 57.378 30.769 0.00 0.00 45.27 2.12
312 313 8.445275 TTGTTTTGAAAGTGATAAGAGCACTA 57.555 30.769 0.00 0.00 45.27 2.74
314 315 7.985634 TTTGTTTTGAAAGTGATAAGAGCAC 57.014 32.000 0.00 0.00 36.53 4.40
315 316 9.677567 GTATTTGTTTTGAAAGTGATAAGAGCA 57.322 29.630 0.00 0.00 0.00 4.26
316 317 8.840867 CGTATTTGTTTTGAAAGTGATAAGAGC 58.159 33.333 0.00 0.00 0.00 4.09
322 323 9.325150 CGTATTCGTATTTGTTTTGAAAGTGAT 57.675 29.630 0.00 0.00 0.00 3.06
323 324 8.549548 TCGTATTCGTATTTGTTTTGAAAGTGA 58.450 29.630 0.00 0.00 38.33 3.41
324 325 8.702408 TCGTATTCGTATTTGTTTTGAAAGTG 57.298 30.769 0.00 0.00 38.33 3.16
325 326 9.887406 ATTCGTATTCGTATTTGTTTTGAAAGT 57.113 25.926 0.00 0.00 38.33 2.66
336 337 7.935338 AACATCCGTATTCGTATTCGTATTT 57.065 32.000 0.91 0.00 38.33 1.40
346 347 7.174426 TCTGTATCTGATAACATCCGTATTCGT 59.826 37.037 0.00 0.00 35.01 3.85
598 599 6.934083 CCAACATAAAAGCCAAATAAGTGGTT 59.066 34.615 0.00 0.00 41.12 3.67
631 632 6.432403 TTCAAAATTCTAGCCCCAACATTT 57.568 33.333 0.00 0.00 0.00 2.32
659 660 4.553330 TCCGAATAAGATTATGGGAGGC 57.447 45.455 0.00 0.00 0.00 4.70
753 754 7.771183 TGGAAATTATCTGCACCTGAATTTAC 58.229 34.615 6.62 6.62 32.99 2.01
763 764 9.763465 CAAAATGAAAATGGAAATTATCTGCAC 57.237 29.630 0.00 0.00 0.00 4.57
862 863 2.263545 GTAGGGGTGGAAAGTGGTAGT 58.736 52.381 0.00 0.00 0.00 2.73
901 902 3.365472 GGGATTTTGTTGGTAGCCAGAT 58.635 45.455 0.00 0.00 33.81 2.90
958 975 4.514401 TCAGAGTCAGAAGTGCTATCGTA 58.486 43.478 0.00 0.00 0.00 3.43
1613 1630 0.734942 CGGACGCGTGTAGATTTGGT 60.735 55.000 20.70 0.00 0.00 3.67
1696 1713 1.078426 ACTTGCCATGGCGGTAGAC 60.078 57.895 30.87 4.18 45.51 2.59
1818 1837 0.827925 ATCCTCGCGCCTTCTCCATA 60.828 55.000 0.00 0.00 0.00 2.74
1947 1966 2.756760 CCCACAAATCTCCATGTCCTTG 59.243 50.000 0.00 0.00 0.00 3.61
2145 2172 6.767902 TCATCTCTGCCCTCAAAATACATAAC 59.232 38.462 0.00 0.00 0.00 1.89
2149 2176 4.842531 TCATCTCTGCCCTCAAAATACA 57.157 40.909 0.00 0.00 0.00 2.29
2298 2325 4.202441 CAAAAGCATGGTATACCTCAGCT 58.798 43.478 22.41 22.38 38.82 4.24
2403 2430 2.989909 TGCATACATTCCAGGTCACTG 58.010 47.619 0.00 0.00 44.51 3.66
2531 2558 6.767902 ACAACTCAGAGATTTTTGTGCTCTAA 59.232 34.615 3.79 0.00 36.91 2.10
2562 2602 6.496565 AGACCCTCAGACTCCATATATTTCTG 59.503 42.308 0.00 0.00 35.93 3.02
2610 2657 4.702131 GCCAGAAGTCATGAACCTAACAAT 59.298 41.667 0.00 0.00 0.00 2.71
2639 2686 9.303537 GGAGATGATCACTAAAGTAGTTAACAC 57.696 37.037 8.61 4.37 36.76 3.32
2689 2736 9.121517 CACAAAGATTGATGTAAGCTGTAAAAG 57.878 33.333 0.00 0.00 34.71 2.27
2690 2737 8.629158 ACACAAAGATTGATGTAAGCTGTAAAA 58.371 29.630 0.00 0.00 34.71 1.52
2721 2777 4.783764 ATATCAATGGCATGCATGAGTG 57.216 40.909 30.64 18.79 0.00 3.51
2722 2778 7.344134 ACTATATATCAATGGCATGCATGAGT 58.656 34.615 30.64 15.76 0.00 3.41
2723 2779 7.803279 ACTATATATCAATGGCATGCATGAG 57.197 36.000 30.64 15.12 0.00 2.90
2755 2811 8.756927 TGCAAAAATCATATGTCCCTTTTCATA 58.243 29.630 1.90 0.00 0.00 2.15
2757 2813 7.002250 TGCAAAAATCATATGTCCCTTTTCA 57.998 32.000 1.90 0.00 0.00 2.69
2758 2814 6.536224 CCTGCAAAAATCATATGTCCCTTTTC 59.464 38.462 1.90 0.00 0.00 2.29
2760 2816 5.484998 ACCTGCAAAAATCATATGTCCCTTT 59.515 36.000 1.90 0.00 0.00 3.11
2761 2817 5.025453 ACCTGCAAAAATCATATGTCCCTT 58.975 37.500 1.90 0.00 0.00 3.95
2762 2818 4.613437 ACCTGCAAAAATCATATGTCCCT 58.387 39.130 1.90 0.00 0.00 4.20
2763 2819 5.343307 AACCTGCAAAAATCATATGTCCC 57.657 39.130 1.90 0.00 0.00 4.46
2764 2820 6.165577 ACAAACCTGCAAAAATCATATGTCC 58.834 36.000 1.90 0.00 0.00 4.02
2765 2821 7.656707 AACAAACCTGCAAAAATCATATGTC 57.343 32.000 1.90 0.00 0.00 3.06
2766 2822 9.206870 CTTAACAAACCTGCAAAAATCATATGT 57.793 29.630 1.90 0.00 0.00 2.29
2767 2823 9.421806 TCTTAACAAACCTGCAAAAATCATATG 57.578 29.630 0.00 0.00 0.00 1.78
2810 2872 2.827921 AGCTGGCCAATTAACTCTTTGG 59.172 45.455 7.01 1.80 44.29 3.28
2877 2944 9.849607 CTACATACATCGAACATGAAATTGTAC 57.150 33.333 0.00 0.00 0.00 2.90
2879 2946 8.390354 CACTACATACATCGAACATGAAATTGT 58.610 33.333 0.00 0.00 0.00 2.71
2880 2947 8.390354 ACACTACATACATCGAACATGAAATTG 58.610 33.333 0.00 0.00 0.00 2.32
2969 3057 5.006746 GGCGGAACTGTGACATAAGAATAAG 59.993 44.000 0.00 0.00 0.00 1.73
2971 3059 4.081365 TGGCGGAACTGTGACATAAGAATA 60.081 41.667 0.00 0.00 0.00 1.75
2994 3082 3.341823 CAGCACTTGCCAACTCTCTTAT 58.658 45.455 0.00 0.00 43.38 1.73
3042 3131 7.177216 AGGAACAGATAATTTGCATTGTCTCAA 59.823 33.333 0.00 0.00 38.46 3.02
3057 3146 2.168313 TGATGCGCTCAGGAACAGATAA 59.832 45.455 9.73 0.00 0.00 1.75
3062 3151 1.375908 GGTGATGCGCTCAGGAACA 60.376 57.895 9.73 0.00 33.51 3.18
3109 3205 5.065218 CACCCTTGTCAATATACAGTTCTGC 59.935 44.000 0.00 0.00 0.00 4.26
3118 3232 4.441495 CGCACTCTCACCCTTGTCAATATA 60.441 45.833 0.00 0.00 0.00 0.86
3140 3254 7.590322 AGCTTTCAGACGTATGTATATAACACG 59.410 37.037 10.41 9.33 42.09 4.49
3154 3268 1.267806 CAATTGCCAGCTTTCAGACGT 59.732 47.619 0.00 0.00 0.00 4.34
3159 3273 2.485903 CTTTGCAATTGCCAGCTTTCA 58.514 42.857 26.94 3.21 41.18 2.69
3198 3312 4.584743 TCTCACTACTGTCTTGCTTCTTCA 59.415 41.667 0.00 0.00 0.00 3.02
3225 3340 2.277084 GACCACGGTGATGAACATACC 58.723 52.381 10.28 0.00 0.00 2.73
3253 3368 2.221055 GCTGTGGTTTTACTGACTGACG 59.779 50.000 0.00 0.00 0.00 4.35
3263 3378 1.178534 GGCCTGCTGCTGTGGTTTTA 61.179 55.000 0.00 0.00 40.92 1.52
3272 3387 2.669849 CTTCTCTGGCCTGCTGCT 59.330 61.111 3.32 0.00 40.92 4.24
3319 3434 4.394729 CAAGGTAAAGAGTGCCAAGGTAA 58.605 43.478 0.00 0.00 33.55 2.85
3322 3437 1.541588 GCAAGGTAAAGAGTGCCAAGG 59.458 52.381 0.00 0.00 33.55 3.61
3324 3460 2.656947 AGCAAGGTAAAGAGTGCCAA 57.343 45.000 0.00 0.00 37.73 4.52


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

AutoCloner maintained by Alex Coulton.