Multiple sequence alignment - TraesCS6A01G420300

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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 TraesCS6A01G420300 chr6A 100.000 2445 0 0 1 2445 617140248 617137804 0.000000e+00 4516.0
1 TraesCS6A01G420300 chr6A 96.176 2118 76 3 314 2429 575146400 575148514 0.000000e+00 3458.0
2 TraesCS6A01G420300 chr6A 100.000 33 0 0 107 139 612263385 612263353 7.300000e-06 62.1
3 TraesCS6A01G420300 chr5A 96.812 2133 67 1 313 2445 15993714 15995845 0.000000e+00 3561.0
4 TraesCS6A01G420300 chr5A 88.889 81 6 2 1 80 549392663 549392585 2.000000e-16 97.1
5 TraesCS6A01G420300 chr5A 89.189 74 7 1 1 74 670419155 670419227 9.310000e-15 91.6
6 TraesCS6A01G420300 chr7B 96.674 2135 65 5 314 2445 479506007 479508138 0.000000e+00 3544.0
7 TraesCS6A01G420300 chr7B 95.349 43 1 1 104 146 690975806 690975765 1.570000e-07 67.6
8 TraesCS6A01G420300 chr1B 96.487 2135 72 3 311 2445 8716874 8719005 0.000000e+00 3524.0
9 TraesCS6A01G420300 chr1B 92.754 69 5 0 1 69 523305464 523305396 1.550000e-17 100.0
10 TraesCS6A01G420300 chr2A 96.249 2133 73 3 314 2445 736071229 736073355 0.000000e+00 3489.0
11 TraesCS6A01G420300 chr2A 90.541 74 6 1 1 74 57446351 57446423 2.000000e-16 97.1
12 TraesCS6A01G420300 chr3D 96.156 2133 79 3 314 2445 599619664 599621794 0.000000e+00 3482.0
13 TraesCS6A01G420300 chr3D 93.023 43 2 1 97 138 214799453 214799411 7.300000e-06 62.1
14 TraesCS6A01G420300 chr4A 96.013 2132 83 2 314 2445 605418967 605416838 0.000000e+00 3465.0
15 TraesCS6A01G420300 chr4A 97.143 35 1 0 104 138 543606368 543606402 2.630000e-05 60.2
16 TraesCS6A01G420300 chr7A 96.013 2132 79 4 314 2445 733001808 733003933 0.000000e+00 3461.0
17 TraesCS6A01G420300 chr3B 95.833 2136 83 5 314 2445 49362319 49360186 0.000000e+00 3446.0
18 TraesCS6A01G420300 chr3B 95.652 46 0 2 104 149 760050301 760050344 3.370000e-09 73.1
19 TraesCS6A01G420300 chr6D 96.371 248 8 1 68 314 472541617 472541864 8.140000e-110 407.0
20 TraesCS6A01G420300 chr6D 90.541 74 6 1 1 74 266439657 266439729 2.000000e-16 97.1
21 TraesCS6A01G420300 chr6D 100.000 33 0 0 107 139 466324133 466324101 7.300000e-06 62.1
22 TraesCS6A01G420300 chr5D 91.892 74 6 0 1 74 354032043 354032116 1.200000e-18 104.0
23 TraesCS6A01G420300 chr3A 92.857 70 4 1 5 74 666239793 666239861 1.550000e-17 100.0
24 TraesCS6A01G420300 chr4B 89.189 74 7 1 1 74 603514434 603514506 9.310000e-15 91.6
25 TraesCS6A01G420300 chr1D 89.333 75 5 2 1 74 7423466 7423538 9.310000e-15 91.6
26 TraesCS6A01G420300 chr7D 100.000 32 0 0 107 138 539239197 539239166 2.630000e-05 60.2
27 TraesCS6A01G420300 chr1A 97.143 35 1 0 104 138 496651982 496652016 2.630000e-05 60.2


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 TraesCS6A01G420300 chr6A 617137804 617140248 2444 True 4516 4516 100.000 1 2445 1 chr6A.!!$R2 2444
1 TraesCS6A01G420300 chr6A 575146400 575148514 2114 False 3458 3458 96.176 314 2429 1 chr6A.!!$F1 2115
2 TraesCS6A01G420300 chr5A 15993714 15995845 2131 False 3561 3561 96.812 313 2445 1 chr5A.!!$F1 2132
3 TraesCS6A01G420300 chr7B 479506007 479508138 2131 False 3544 3544 96.674 314 2445 1 chr7B.!!$F1 2131
4 TraesCS6A01G420300 chr1B 8716874 8719005 2131 False 3524 3524 96.487 311 2445 1 chr1B.!!$F1 2134
5 TraesCS6A01G420300 chr2A 736071229 736073355 2126 False 3489 3489 96.249 314 2445 1 chr2A.!!$F2 2131
6 TraesCS6A01G420300 chr3D 599619664 599621794 2130 False 3482 3482 96.156 314 2445 1 chr3D.!!$F1 2131
7 TraesCS6A01G420300 chr4A 605416838 605418967 2129 True 3465 3465 96.013 314 2445 1 chr4A.!!$R1 2131
8 TraesCS6A01G420300 chr7A 733001808 733003933 2125 False 3461 3461 96.013 314 2445 1 chr7A.!!$F1 2131
9 TraesCS6A01G420300 chr3B 49360186 49362319 2133 True 3446 3446 95.833 314 2445 1 chr3B.!!$R1 2131

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
254 255 0.038526 GCTTCCGTTCTCGAAGACCA 60.039 55.0 1.84 0.0 39.71 4.02 F
291 292 0.249911 CATGCTCGGGGGCTACTAAC 60.250 60.0 0.00 0.0 0.00 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1282 0.318191 ATCATCGACGACATCCGCAG 60.318 55.0 0.0 0.0 43.32 5.18 R
2045 2060 0.739462 GCATCGACAATGACCCGACA 60.739 55.0 0.0 0.0 37.59 4.35 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
61 62 7.406799 AAAATGCTTTTCTTTCATTACACGG 57.593 32.000 0.00 0.00 30.98 4.94
62 63 5.705609 ATGCTTTTCTTTCATTACACGGT 57.294 34.783 0.00 0.00 0.00 4.83
63 64 6.811253 ATGCTTTTCTTTCATTACACGGTA 57.189 33.333 0.00 0.00 0.00 4.02
64 65 6.621316 TGCTTTTCTTTCATTACACGGTAA 57.379 33.333 0.00 0.00 0.00 2.85
65 66 7.209471 TGCTTTTCTTTCATTACACGGTAAT 57.791 32.000 4.14 4.14 0.00 1.89
66 67 7.302524 TGCTTTTCTTTCATTACACGGTAATC 58.697 34.615 6.38 0.00 0.00 1.75
67 68 7.041030 TGCTTTTCTTTCATTACACGGTAATCA 60.041 33.333 6.38 0.00 0.00 2.57
68 69 7.806014 GCTTTTCTTTCATTACACGGTAATCAA 59.194 33.333 6.38 0.00 0.00 2.57
69 70 9.672086 CTTTTCTTTCATTACACGGTAATCAAA 57.328 29.630 6.38 6.16 0.00 2.69
71 72 9.453325 TTTCTTTCATTACACGGTAATCAAAAC 57.547 29.630 6.38 0.00 0.00 2.43
72 73 7.586747 TCTTTCATTACACGGTAATCAAAACC 58.413 34.615 6.38 0.00 0.00 3.27
73 74 6.879276 TTCATTACACGGTAATCAAAACCA 57.121 33.333 6.38 0.00 36.78 3.67
74 75 7.455641 TTCATTACACGGTAATCAAAACCAT 57.544 32.000 6.38 0.00 36.78 3.55
75 76 6.847400 TCATTACACGGTAATCAAAACCATG 58.153 36.000 6.38 0.00 36.30 3.66
76 77 6.655425 TCATTACACGGTAATCAAAACCATGA 59.345 34.615 0.00 0.00 33.91 3.07
77 78 6.489127 TTACACGGTAATCAAAACCATGAG 57.511 37.500 0.00 0.00 33.91 2.90
78 79 4.647611 ACACGGTAATCAAAACCATGAGA 58.352 39.130 0.00 0.00 33.91 3.27
79 80 5.067273 ACACGGTAATCAAAACCATGAGAA 58.933 37.500 0.00 0.00 33.91 2.87
80 81 5.533154 ACACGGTAATCAAAACCATGAGAAA 59.467 36.000 0.00 0.00 33.91 2.52
81 82 6.039941 ACACGGTAATCAAAACCATGAGAAAA 59.960 34.615 0.00 0.00 33.91 2.29
82 83 6.920758 CACGGTAATCAAAACCATGAGAAAAA 59.079 34.615 0.00 0.00 31.90 1.94
83 84 7.598493 CACGGTAATCAAAACCATGAGAAAAAT 59.402 33.333 0.00 0.00 31.90 1.82
84 85 8.798402 ACGGTAATCAAAACCATGAGAAAAATA 58.202 29.630 0.00 0.00 36.78 1.40
85 86 9.801873 CGGTAATCAAAACCATGAGAAAAATAT 57.198 29.630 0.00 0.00 36.78 1.28
94 95 9.768662 AAACCATGAGAAAAATATATGATTGGC 57.231 29.630 0.00 0.00 0.00 4.52
95 96 8.481492 ACCATGAGAAAAATATATGATTGGCA 57.519 30.769 0.00 0.00 0.00 4.92
96 97 9.096823 ACCATGAGAAAAATATATGATTGGCAT 57.903 29.630 0.00 0.00 41.08 4.40
97 98 9.938280 CCATGAGAAAAATATATGATTGGCATT 57.062 29.630 0.00 0.00 38.44 3.56
118 119 6.939627 CATTACACAAAATGCAATAGCCATG 58.060 36.000 0.00 0.00 41.13 3.66
119 120 4.540359 ACACAAAATGCAATAGCCATGT 57.460 36.364 0.00 0.00 41.13 3.21
120 121 4.247258 ACACAAAATGCAATAGCCATGTG 58.753 39.130 0.00 2.58 40.98 3.21
121 122 3.062909 CACAAAATGCAATAGCCATGTGC 59.937 43.478 0.00 0.00 41.13 4.57
122 123 2.607631 AAATGCAATAGCCATGTGCC 57.392 45.000 0.00 0.00 42.71 5.01
123 124 0.754472 AATGCAATAGCCATGTGCCC 59.246 50.000 0.00 0.00 42.71 5.36
124 125 0.105862 ATGCAATAGCCATGTGCCCT 60.106 50.000 0.00 0.00 42.71 5.19
125 126 0.324552 TGCAATAGCCATGTGCCCTT 60.325 50.000 3.10 0.00 42.71 3.95
126 127 0.103572 GCAATAGCCATGTGCCCTTG 59.896 55.000 2.95 7.79 42.71 3.61
127 128 0.103572 CAATAGCCATGTGCCCTTGC 59.896 55.000 2.95 0.00 42.71 4.01
136 137 3.169378 TGCCCTTGCAGGTCATCA 58.831 55.556 0.00 0.00 44.23 3.07
137 138 1.459812 TGCCCTTGCAGGTCATCAA 59.540 52.632 0.00 0.00 44.23 2.57
138 139 0.895100 TGCCCTTGCAGGTCATCAAC 60.895 55.000 0.00 0.00 44.23 3.18
139 140 0.895100 GCCCTTGCAGGTCATCAACA 60.895 55.000 0.00 0.00 37.47 3.33
140 141 1.171308 CCCTTGCAGGTCATCAACAG 58.829 55.000 0.00 0.00 31.93 3.16
141 142 1.271543 CCCTTGCAGGTCATCAACAGA 60.272 52.381 0.00 0.00 31.93 3.41
142 143 1.808945 CCTTGCAGGTCATCAACAGAC 59.191 52.381 0.00 0.00 35.29 3.51
143 144 2.497138 CTTGCAGGTCATCAACAGACA 58.503 47.619 0.00 0.00 37.74 3.41
144 145 2.865119 TGCAGGTCATCAACAGACAT 57.135 45.000 0.00 0.00 37.74 3.06
145 146 2.429478 TGCAGGTCATCAACAGACATG 58.571 47.619 3.87 3.87 46.99 3.21
147 148 1.395954 CAGGTCATCAACAGACATGCG 59.604 52.381 0.00 0.00 40.29 4.73
148 149 1.276138 AGGTCATCAACAGACATGCGA 59.724 47.619 0.00 0.00 37.74 5.10
149 150 1.662629 GGTCATCAACAGACATGCGAG 59.337 52.381 0.00 0.00 37.74 5.03
150 151 1.662629 GTCATCAACAGACATGCGAGG 59.337 52.381 0.00 0.00 36.06 4.63
151 152 1.550072 TCATCAACAGACATGCGAGGA 59.450 47.619 0.00 0.00 0.00 3.71
152 153 1.931841 CATCAACAGACATGCGAGGAG 59.068 52.381 0.00 0.00 0.00 3.69
163 164 2.507992 CGAGGAGCGCTCACAAGG 60.508 66.667 36.27 17.53 0.00 3.61
164 165 2.125350 GAGGAGCGCTCACAAGGG 60.125 66.667 36.27 0.00 38.45 3.95
165 166 3.672295 GAGGAGCGCTCACAAGGGG 62.672 68.421 36.27 0.00 36.03 4.79
167 168 4.704833 GAGCGCTCACAAGGGGCA 62.705 66.667 31.91 0.00 43.57 5.36
168 169 4.711949 AGCGCTCACAAGGGGCAG 62.712 66.667 2.64 0.00 43.57 4.85
170 171 4.335647 CGCTCACAAGGGGCAGGT 62.336 66.667 0.00 0.00 0.00 4.00
171 172 2.360475 GCTCACAAGGGGCAGGTC 60.360 66.667 0.00 0.00 0.00 3.85
172 173 2.900106 GCTCACAAGGGGCAGGTCT 61.900 63.158 0.00 0.00 0.00 3.85
173 174 1.002868 CTCACAAGGGGCAGGTCTG 60.003 63.158 0.00 0.00 0.00 3.51
184 185 3.776616 CAGGTCTGCAGGAATCCTC 57.223 57.895 15.13 0.00 0.00 3.71
185 186 0.179089 CAGGTCTGCAGGAATCCTCG 60.179 60.000 15.13 8.08 0.00 4.63
186 187 0.324738 AGGTCTGCAGGAATCCTCGA 60.325 55.000 15.13 0.00 0.00 4.04
187 188 0.103937 GGTCTGCAGGAATCCTCGAG 59.896 60.000 15.13 5.13 0.00 4.04
188 189 0.103937 GTCTGCAGGAATCCTCGAGG 59.896 60.000 26.32 26.32 0.00 4.63
189 190 0.324738 TCTGCAGGAATCCTCGAGGT 60.325 55.000 30.17 13.22 36.34 3.85
190 191 0.103937 CTGCAGGAATCCTCGAGGTC 59.896 60.000 30.17 20.94 36.34 3.85
191 192 0.614697 TGCAGGAATCCTCGAGGTCA 60.615 55.000 30.17 13.58 36.34 4.02
192 193 0.179097 GCAGGAATCCTCGAGGTCAC 60.179 60.000 30.17 20.34 36.34 3.67
193 194 0.101399 CAGGAATCCTCGAGGTCACG 59.899 60.000 30.17 12.44 36.34 4.35
194 195 1.227002 GGAATCCTCGAGGTCACGC 60.227 63.158 30.17 15.78 36.34 5.34
195 196 1.668101 GGAATCCTCGAGGTCACGCT 61.668 60.000 30.17 9.99 36.34 5.07
196 197 0.248702 GAATCCTCGAGGTCACGCTC 60.249 60.000 30.17 14.53 36.34 5.03
197 198 1.668101 AATCCTCGAGGTCACGCTCC 61.668 60.000 30.17 0.00 36.34 4.70
198 199 2.559922 ATCCTCGAGGTCACGCTCCT 62.560 60.000 30.17 3.35 38.09 3.69
199 200 1.451567 CCTCGAGGTCACGCTCCTA 60.452 63.158 24.04 0.00 35.20 2.94
200 201 1.440938 CCTCGAGGTCACGCTCCTAG 61.441 65.000 24.04 0.00 35.20 3.02
201 202 0.462225 CTCGAGGTCACGCTCCTAGA 60.462 60.000 3.91 4.54 35.88 2.43
202 203 0.462225 TCGAGGTCACGCTCCTAGAG 60.462 60.000 0.00 0.00 33.16 2.43
203 204 0.462225 CGAGGTCACGCTCCTAGAGA 60.462 60.000 0.00 0.00 35.20 3.10
204 205 1.018910 GAGGTCACGCTCCTAGAGAC 58.981 60.000 0.00 0.00 35.20 3.36
205 206 0.328592 AGGTCACGCTCCTAGAGACA 59.671 55.000 0.00 0.00 33.04 3.41
206 207 1.174783 GGTCACGCTCCTAGAGACAA 58.825 55.000 0.00 0.00 0.00 3.18
207 208 1.544691 GGTCACGCTCCTAGAGACAAA 59.455 52.381 0.00 0.00 0.00 2.83
208 209 2.416162 GGTCACGCTCCTAGAGACAAAG 60.416 54.545 0.00 0.00 0.00 2.77
209 210 1.202582 TCACGCTCCTAGAGACAAAGC 59.797 52.381 0.00 0.00 0.00 3.51
210 211 0.533032 ACGCTCCTAGAGACAAAGCC 59.467 55.000 0.00 0.00 0.00 4.35
211 212 0.532573 CGCTCCTAGAGACAAAGCCA 59.467 55.000 0.00 0.00 0.00 4.75
212 213 1.470632 CGCTCCTAGAGACAAAGCCAG 60.471 57.143 0.00 0.00 0.00 4.85
213 214 1.134551 GCTCCTAGAGACAAAGCCAGG 60.135 57.143 0.00 0.00 0.00 4.45
214 215 0.905357 TCCTAGAGACAAAGCCAGGC 59.095 55.000 1.84 1.84 0.00 4.85
215 216 0.615331 CCTAGAGACAAAGCCAGGCA 59.385 55.000 15.80 0.00 0.00 4.75
216 217 1.003580 CCTAGAGACAAAGCCAGGCAA 59.996 52.381 15.80 0.00 0.00 4.52
217 218 2.079925 CTAGAGACAAAGCCAGGCAAC 58.920 52.381 15.80 0.00 0.00 4.17
218 219 0.538287 AGAGACAAAGCCAGGCAACC 60.538 55.000 15.80 0.00 37.17 3.77
219 220 1.527433 GAGACAAAGCCAGGCAACCC 61.527 60.000 15.80 0.00 37.17 4.11
220 221 2.912025 ACAAAGCCAGGCAACCCG 60.912 61.111 15.80 0.00 35.76 5.28
221 222 4.362476 CAAAGCCAGGCAACCCGC 62.362 66.667 15.80 0.00 41.28 6.13
222 223 4.912395 AAAGCCAGGCAACCCGCA 62.912 61.111 15.80 0.00 45.17 5.69
223 224 4.684134 AAGCCAGGCAACCCGCAT 62.684 61.111 15.80 0.00 45.17 4.73
228 229 2.756400 AGGCAACCCGCATGAAGA 59.244 55.556 0.00 0.00 45.17 2.87
229 230 1.304282 AGGCAACCCGCATGAAGAT 59.696 52.632 0.00 0.00 45.17 2.40
230 231 0.546122 AGGCAACCCGCATGAAGATA 59.454 50.000 0.00 0.00 45.17 1.98
231 232 1.064758 AGGCAACCCGCATGAAGATAA 60.065 47.619 0.00 0.00 45.17 1.75
232 233 1.334869 GGCAACCCGCATGAAGATAAG 59.665 52.381 0.00 0.00 45.17 1.73
233 234 1.334869 GCAACCCGCATGAAGATAAGG 59.665 52.381 0.00 0.00 41.79 2.69
234 235 2.917933 CAACCCGCATGAAGATAAGGA 58.082 47.619 0.00 0.00 0.00 3.36
235 236 2.874701 CAACCCGCATGAAGATAAGGAG 59.125 50.000 0.00 0.00 0.00 3.69
236 237 1.202698 ACCCGCATGAAGATAAGGAGC 60.203 52.381 0.00 0.00 0.00 4.70
237 238 1.071385 CCCGCATGAAGATAAGGAGCT 59.929 52.381 0.00 0.00 0.00 4.09
238 239 2.486191 CCCGCATGAAGATAAGGAGCTT 60.486 50.000 0.00 0.00 32.77 3.74
239 240 2.805099 CCGCATGAAGATAAGGAGCTTC 59.195 50.000 0.00 0.00 46.33 3.86
240 241 2.805099 CGCATGAAGATAAGGAGCTTCC 59.195 50.000 0.00 0.00 45.70 3.46
241 242 2.805099 GCATGAAGATAAGGAGCTTCCG 59.195 50.000 0.00 0.00 45.70 4.30
242 243 3.742640 GCATGAAGATAAGGAGCTTCCGT 60.743 47.826 0.00 0.00 45.70 4.69
243 244 4.446371 CATGAAGATAAGGAGCTTCCGTT 58.554 43.478 0.00 0.00 45.70 4.44
244 245 4.124851 TGAAGATAAGGAGCTTCCGTTC 57.875 45.455 0.00 0.00 45.70 3.95
245 246 3.769844 TGAAGATAAGGAGCTTCCGTTCT 59.230 43.478 0.00 0.00 45.70 3.01
246 247 4.142138 TGAAGATAAGGAGCTTCCGTTCTC 60.142 45.833 0.00 0.00 45.70 2.87
247 248 2.359531 AGATAAGGAGCTTCCGTTCTCG 59.640 50.000 0.00 0.00 42.75 4.04
248 249 1.830279 TAAGGAGCTTCCGTTCTCGA 58.170 50.000 0.00 0.00 42.75 4.04
249 250 0.966920 AAGGAGCTTCCGTTCTCGAA 59.033 50.000 0.00 0.00 42.75 3.71
250 251 0.528470 AGGAGCTTCCGTTCTCGAAG 59.472 55.000 0.00 0.00 42.75 3.79
251 252 0.526662 GGAGCTTCCGTTCTCGAAGA 59.473 55.000 1.84 0.00 39.71 2.87
252 253 1.619983 GAGCTTCCGTTCTCGAAGAC 58.380 55.000 1.84 0.00 39.71 3.01
253 254 0.244178 AGCTTCCGTTCTCGAAGACC 59.756 55.000 1.84 0.00 39.71 3.85
254 255 0.038526 GCTTCCGTTCTCGAAGACCA 60.039 55.000 1.84 0.00 39.71 4.02
255 256 1.604693 GCTTCCGTTCTCGAAGACCAA 60.605 52.381 1.84 0.00 39.71 3.67
256 257 2.059541 CTTCCGTTCTCGAAGACCAAC 58.940 52.381 0.00 0.00 39.71 3.77
257 258 1.325355 TCCGTTCTCGAAGACCAACT 58.675 50.000 0.00 0.00 39.71 3.16
258 259 2.507484 TCCGTTCTCGAAGACCAACTA 58.493 47.619 0.00 0.00 39.71 2.24
259 260 2.227388 TCCGTTCTCGAAGACCAACTAC 59.773 50.000 0.00 0.00 39.71 2.73
260 261 2.228343 CCGTTCTCGAAGACCAACTACT 59.772 50.000 0.00 0.00 39.71 2.57
261 262 3.490399 CGTTCTCGAAGACCAACTACTC 58.510 50.000 0.00 0.00 39.71 2.59
262 263 3.670091 CGTTCTCGAAGACCAACTACTCC 60.670 52.174 0.00 0.00 39.71 3.85
263 264 3.150458 TCTCGAAGACCAACTACTCCA 57.850 47.619 0.00 0.00 0.00 3.86
264 265 3.493334 TCTCGAAGACCAACTACTCCAA 58.507 45.455 0.00 0.00 0.00 3.53
265 266 3.255149 TCTCGAAGACCAACTACTCCAAC 59.745 47.826 0.00 0.00 0.00 3.77
266 267 3.228453 TCGAAGACCAACTACTCCAACT 58.772 45.455 0.00 0.00 0.00 3.16
267 268 3.255149 TCGAAGACCAACTACTCCAACTC 59.745 47.826 0.00 0.00 0.00 3.01
268 269 3.614390 CGAAGACCAACTACTCCAACTCC 60.614 52.174 0.00 0.00 0.00 3.85
269 270 2.972348 AGACCAACTACTCCAACTCCA 58.028 47.619 0.00 0.00 0.00 3.86
270 271 3.314693 AGACCAACTACTCCAACTCCAA 58.685 45.455 0.00 0.00 0.00 3.53
271 272 3.714798 AGACCAACTACTCCAACTCCAAA 59.285 43.478 0.00 0.00 0.00 3.28
272 273 3.813724 GACCAACTACTCCAACTCCAAAC 59.186 47.826 0.00 0.00 0.00 2.93
273 274 3.201266 ACCAACTACTCCAACTCCAAACA 59.799 43.478 0.00 0.00 0.00 2.83
274 275 4.141251 ACCAACTACTCCAACTCCAAACAT 60.141 41.667 0.00 0.00 0.00 2.71
275 276 4.216257 CCAACTACTCCAACTCCAAACATG 59.784 45.833 0.00 0.00 0.00 3.21
276 277 3.412386 ACTACTCCAACTCCAAACATGC 58.588 45.455 0.00 0.00 0.00 4.06
277 278 2.664402 ACTCCAACTCCAAACATGCT 57.336 45.000 0.00 0.00 0.00 3.79
278 279 2.508526 ACTCCAACTCCAAACATGCTC 58.491 47.619 0.00 0.00 0.00 4.26
279 280 1.466167 CTCCAACTCCAAACATGCTCG 59.534 52.381 0.00 0.00 0.00 5.03
280 281 0.523072 CCAACTCCAAACATGCTCGG 59.477 55.000 0.00 0.00 0.00 4.63
281 282 0.523072 CAACTCCAAACATGCTCGGG 59.477 55.000 0.00 0.00 0.00 5.14
282 283 0.609131 AACTCCAAACATGCTCGGGG 60.609 55.000 0.00 0.00 0.00 5.73
283 284 1.750399 CTCCAAACATGCTCGGGGG 60.750 63.158 0.00 0.00 0.00 5.40
284 285 3.451894 CCAAACATGCTCGGGGGC 61.452 66.667 0.00 0.00 0.00 5.80
285 286 2.361610 CAAACATGCTCGGGGGCT 60.362 61.111 0.00 0.00 0.00 5.19
286 287 1.077787 CAAACATGCTCGGGGGCTA 60.078 57.895 0.00 0.00 0.00 3.93
287 288 1.077716 AAACATGCTCGGGGGCTAC 60.078 57.895 0.00 0.00 0.00 3.58
288 289 1.562672 AAACATGCTCGGGGGCTACT 61.563 55.000 0.00 0.00 0.00 2.57
289 290 0.689745 AACATGCTCGGGGGCTACTA 60.690 55.000 0.00 0.00 0.00 1.82
290 291 0.689745 ACATGCTCGGGGGCTACTAA 60.690 55.000 0.00 0.00 0.00 2.24
291 292 0.249911 CATGCTCGGGGGCTACTAAC 60.250 60.000 0.00 0.00 0.00 2.34
292 293 1.745320 ATGCTCGGGGGCTACTAACG 61.745 60.000 0.00 0.00 0.00 3.18
293 294 2.421399 GCTCGGGGGCTACTAACGT 61.421 63.158 0.00 0.00 0.00 3.99
294 295 1.953231 GCTCGGGGGCTACTAACGTT 61.953 60.000 5.88 5.88 0.00 3.99
295 296 0.533951 CTCGGGGGCTACTAACGTTT 59.466 55.000 5.91 0.00 0.00 3.60
296 297 0.975887 TCGGGGGCTACTAACGTTTT 59.024 50.000 5.91 0.00 0.00 2.43
297 298 2.166254 CTCGGGGGCTACTAACGTTTTA 59.834 50.000 5.91 0.00 0.00 1.52
298 299 2.564947 TCGGGGGCTACTAACGTTTTAA 59.435 45.455 5.91 0.00 0.00 1.52
299 300 3.197549 TCGGGGGCTACTAACGTTTTAAT 59.802 43.478 5.91 0.00 0.00 1.40
300 301 4.404073 TCGGGGGCTACTAACGTTTTAATA 59.596 41.667 5.91 0.00 0.00 0.98
301 302 4.507756 CGGGGGCTACTAACGTTTTAATAC 59.492 45.833 5.91 0.00 0.00 1.89
302 303 5.427378 GGGGGCTACTAACGTTTTAATACA 58.573 41.667 5.91 0.00 0.00 2.29
303 304 6.057533 GGGGGCTACTAACGTTTTAATACAT 58.942 40.000 5.91 0.00 0.00 2.29
304 305 6.543465 GGGGGCTACTAACGTTTTAATACATT 59.457 38.462 5.91 0.00 0.00 2.71
305 306 7.412063 GGGGCTACTAACGTTTTAATACATTG 58.588 38.462 5.91 0.00 0.00 2.82
306 307 7.412063 GGGCTACTAACGTTTTAATACATTGG 58.588 38.462 5.91 0.00 0.00 3.16
307 308 7.412063 GGCTACTAACGTTTTAATACATTGGG 58.588 38.462 5.91 0.00 0.00 4.12
308 309 7.412063 GCTACTAACGTTTTAATACATTGGGG 58.588 38.462 5.91 0.00 0.00 4.96
309 310 7.066163 GCTACTAACGTTTTAATACATTGGGGT 59.934 37.037 5.91 0.00 0.00 4.95
310 311 7.764141 ACTAACGTTTTAATACATTGGGGTT 57.236 32.000 5.91 0.00 0.00 4.11
311 312 8.860780 ACTAACGTTTTAATACATTGGGGTTA 57.139 30.769 5.91 0.00 0.00 2.85
335 336 3.756963 CACTAGTAGAAAAGGGGGCAAAC 59.243 47.826 3.59 0.00 0.00 2.93
351 352 2.406002 AAACGTTCAGGCCGGGTCAT 62.406 55.000 2.18 0.00 0.00 3.06
402 403 2.691732 CCATGGGGGCATTGGACT 59.308 61.111 2.85 0.00 0.00 3.85
501 502 2.357881 GGACGAACCGGGACCAAC 60.358 66.667 6.32 0.00 0.00 3.77
607 610 1.378762 CCAACCGGGACCAATGAGT 59.621 57.895 6.32 0.00 40.01 3.41
696 703 1.133809 AGGGCTTGGTGGTGCTCTAA 61.134 55.000 0.00 0.00 38.38 2.10
1166 1175 1.957877 GTGAACCGGAAATTCCAACCA 59.042 47.619 9.46 1.43 35.91 3.67
1182 1191 3.558321 CCAACCAACCCTATTGTCGAGAA 60.558 47.826 0.00 0.00 0.00 2.87
1192 1201 8.040716 ACCCTATTGTCGAGAAGTTAAATTTG 57.959 34.615 0.22 0.00 0.00 2.32
1269 1282 5.241064 AGAAGATGATATTGGAGTTGCATGC 59.759 40.000 11.82 11.82 0.00 4.06
1330 1343 5.039333 GCAATGCGCTTGAAGATTAGAAAT 58.961 37.500 19.38 0.00 36.97 2.17
1332 1345 6.141369 GCAATGCGCTTGAAGATTAGAAATAC 59.859 38.462 19.38 0.00 36.97 1.89
1722 1735 2.555325 CTGAGGCAAACAAGCAGAATGA 59.445 45.455 0.00 0.00 39.69 2.57
1777 1790 7.417116 GGGAATACGATGTCTTACTCTAACCAA 60.417 40.741 0.00 0.00 0.00 3.67
1908 1922 1.680338 GATGACAACTATGTGCCCCC 58.320 55.000 0.00 0.00 40.74 5.40
2020 2035 4.383989 GCTGAAGATCAAGAGGAACCAGAT 60.384 45.833 0.00 0.00 0.00 2.90
2045 2060 2.028294 GTGCCCGATGATGATGATCTCT 60.028 50.000 0.00 0.00 0.00 3.10
2108 2123 3.971245 AGGAGAAGCTGAAGTTCGATT 57.029 42.857 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 6.512297 ACCGTGTAATGAAAGAAAAGCATTT 58.488 32.000 0.00 0.00 42.41 2.32
39 40 6.084326 ACCGTGTAATGAAAGAAAAGCATT 57.916 33.333 0.00 0.00 36.35 3.56
40 41 5.705609 ACCGTGTAATGAAAGAAAAGCAT 57.294 34.783 0.00 0.00 0.00 3.79
41 42 6.621316 TTACCGTGTAATGAAAGAAAAGCA 57.379 33.333 0.00 0.00 0.00 3.91
42 43 7.302524 TGATTACCGTGTAATGAAAGAAAAGC 58.697 34.615 12.23 0.00 0.00 3.51
43 44 9.672086 TTTGATTACCGTGTAATGAAAGAAAAG 57.328 29.630 12.23 0.00 0.00 2.27
45 46 9.453325 GTTTTGATTACCGTGTAATGAAAGAAA 57.547 29.630 15.27 5.33 0.00 2.52
46 47 8.077386 GGTTTTGATTACCGTGTAATGAAAGAA 58.923 33.333 15.27 5.79 0.00 2.52
47 48 7.228906 TGGTTTTGATTACCGTGTAATGAAAGA 59.771 33.333 15.27 8.75 38.55 2.52
48 49 7.364200 TGGTTTTGATTACCGTGTAATGAAAG 58.636 34.615 15.27 0.00 38.55 2.62
49 50 7.273320 TGGTTTTGATTACCGTGTAATGAAA 57.727 32.000 12.23 12.80 38.55 2.69
50 51 6.879276 TGGTTTTGATTACCGTGTAATGAA 57.121 33.333 12.23 8.58 38.55 2.57
51 52 6.847400 CATGGTTTTGATTACCGTGTAATGA 58.153 36.000 12.23 3.71 44.21 2.57
58 59 6.642707 TTTTCTCATGGTTTTGATTACCGT 57.357 33.333 0.00 0.00 38.55 4.83
59 60 9.801873 ATATTTTTCTCATGGTTTTGATTACCG 57.198 29.630 0.00 0.00 38.55 4.02
68 69 9.768662 GCCAATCATATATTTTTCTCATGGTTT 57.231 29.630 0.00 0.00 0.00 3.27
69 70 8.926374 TGCCAATCATATATTTTTCTCATGGTT 58.074 29.630 0.00 0.00 0.00 3.67
70 71 8.481492 TGCCAATCATATATTTTTCTCATGGT 57.519 30.769 0.00 0.00 0.00 3.55
71 72 9.938280 AATGCCAATCATATATTTTTCTCATGG 57.062 29.630 0.00 0.00 34.33 3.66
94 95 6.535865 ACATGGCTATTGCATTTTGTGTAATG 59.464 34.615 0.66 0.00 42.18 1.90
95 96 6.535865 CACATGGCTATTGCATTTTGTGTAAT 59.464 34.615 0.66 0.00 44.06 1.89
96 97 5.868258 CACATGGCTATTGCATTTTGTGTAA 59.132 36.000 0.66 0.00 41.91 2.41
97 98 5.409211 CACATGGCTATTGCATTTTGTGTA 58.591 37.500 0.66 0.00 41.91 2.90
98 99 4.247258 CACATGGCTATTGCATTTTGTGT 58.753 39.130 0.66 0.00 41.91 3.72
99 100 3.062909 GCACATGGCTATTGCATTTTGTG 59.937 43.478 14.03 14.03 41.91 3.33
100 101 3.264104 GCACATGGCTATTGCATTTTGT 58.736 40.909 0.66 0.00 41.91 2.83
101 102 2.610374 GGCACATGGCTATTGCATTTTG 59.390 45.455 15.26 0.00 44.01 2.44
102 103 2.420408 GGGCACATGGCTATTGCATTTT 60.420 45.455 15.26 0.00 44.01 1.82
103 104 1.139455 GGGCACATGGCTATTGCATTT 59.861 47.619 15.26 0.00 44.01 2.32
104 105 0.754472 GGGCACATGGCTATTGCATT 59.246 50.000 15.26 0.00 44.01 3.56
105 106 0.105862 AGGGCACATGGCTATTGCAT 60.106 50.000 15.26 4.80 44.01 3.96
106 107 0.324552 AAGGGCACATGGCTATTGCA 60.325 50.000 15.26 0.00 44.01 4.08
107 108 0.103572 CAAGGGCACATGGCTATTGC 59.896 55.000 5.33 8.13 44.01 3.56
108 109 0.103572 GCAAGGGCACATGGCTATTG 59.896 55.000 14.95 14.95 44.01 1.90
109 110 2.508361 GCAAGGGCACATGGCTATT 58.492 52.632 5.33 0.00 44.01 1.73
110 111 4.265206 GCAAGGGCACATGGCTAT 57.735 55.556 5.33 0.00 44.01 2.97
123 124 2.497138 TGTCTGTTGATGACCTGCAAG 58.503 47.619 0.00 0.00 33.83 4.01
124 125 2.636647 TGTCTGTTGATGACCTGCAA 57.363 45.000 0.00 0.00 33.83 4.08
125 126 2.429478 CATGTCTGTTGATGACCTGCA 58.571 47.619 0.00 0.00 33.83 4.41
126 127 1.131883 GCATGTCTGTTGATGACCTGC 59.868 52.381 7.98 7.98 44.19 4.85
127 128 1.395954 CGCATGTCTGTTGATGACCTG 59.604 52.381 0.00 0.00 34.64 4.00
128 129 1.276138 TCGCATGTCTGTTGATGACCT 59.724 47.619 0.00 0.00 33.83 3.85
129 130 1.662629 CTCGCATGTCTGTTGATGACC 59.337 52.381 0.00 0.00 33.83 4.02
130 131 1.662629 CCTCGCATGTCTGTTGATGAC 59.337 52.381 0.00 0.00 35.21 3.06
131 132 1.550072 TCCTCGCATGTCTGTTGATGA 59.450 47.619 0.00 0.00 0.00 2.92
132 133 1.931841 CTCCTCGCATGTCTGTTGATG 59.068 52.381 0.00 0.00 0.00 3.07
133 134 1.741732 GCTCCTCGCATGTCTGTTGAT 60.742 52.381 0.00 0.00 38.92 2.57
134 135 0.390340 GCTCCTCGCATGTCTGTTGA 60.390 55.000 0.00 0.00 38.92 3.18
135 136 1.690283 CGCTCCTCGCATGTCTGTTG 61.690 60.000 0.00 0.00 39.08 3.33
136 137 1.446792 CGCTCCTCGCATGTCTGTT 60.447 57.895 0.00 0.00 39.08 3.16
137 138 2.182791 CGCTCCTCGCATGTCTGT 59.817 61.111 0.00 0.00 39.08 3.41
146 147 2.507992 CCTTGTGAGCGCTCCTCG 60.508 66.667 33.23 18.44 43.82 4.63
147 148 2.125350 CCCTTGTGAGCGCTCCTC 60.125 66.667 33.23 25.03 41.15 3.71
148 149 3.710722 CCCCTTGTGAGCGCTCCT 61.711 66.667 33.23 0.00 0.00 3.69
150 151 4.704833 TGCCCCTTGTGAGCGCTC 62.705 66.667 30.42 30.42 0.00 5.03
151 152 4.711949 CTGCCCCTTGTGAGCGCT 62.712 66.667 11.27 11.27 0.00 5.92
153 154 4.335647 ACCTGCCCCTTGTGAGCG 62.336 66.667 0.00 0.00 0.00 5.03
154 155 2.360475 GACCTGCCCCTTGTGAGC 60.360 66.667 0.00 0.00 0.00 4.26
155 156 1.002868 CAGACCTGCCCCTTGTGAG 60.003 63.158 0.00 0.00 0.00 3.51
156 157 3.160585 CAGACCTGCCCCTTGTGA 58.839 61.111 0.00 0.00 0.00 3.58
166 167 0.179089 CGAGGATTCCTGCAGACCTG 60.179 60.000 17.39 0.00 31.76 4.00
167 168 0.324738 TCGAGGATTCCTGCAGACCT 60.325 55.000 17.39 17.15 31.76 3.85
168 169 0.103937 CTCGAGGATTCCTGCAGACC 59.896 60.000 17.39 12.66 31.76 3.85
169 170 0.103937 CCTCGAGGATTCCTGCAGAC 59.896 60.000 28.21 3.47 37.39 3.51
170 171 0.324738 ACCTCGAGGATTCCTGCAGA 60.325 55.000 37.69 6.00 38.94 4.26
171 172 0.103937 GACCTCGAGGATTCCTGCAG 59.896 60.000 37.69 6.78 38.94 4.41
172 173 0.614697 TGACCTCGAGGATTCCTGCA 60.615 55.000 37.69 18.39 38.94 4.41
173 174 0.179097 GTGACCTCGAGGATTCCTGC 60.179 60.000 37.69 16.24 38.94 4.85
174 175 0.101399 CGTGACCTCGAGGATTCCTG 59.899 60.000 37.69 17.09 38.94 3.86
175 176 1.668101 GCGTGACCTCGAGGATTCCT 61.668 60.000 37.69 15.45 38.94 3.36
176 177 1.227002 GCGTGACCTCGAGGATTCC 60.227 63.158 37.69 21.48 38.94 3.01
177 178 0.248702 GAGCGTGACCTCGAGGATTC 60.249 60.000 37.69 24.89 38.94 2.52
178 179 1.668101 GGAGCGTGACCTCGAGGATT 61.668 60.000 37.69 17.15 38.94 3.01
179 180 2.122167 GGAGCGTGACCTCGAGGAT 61.122 63.158 37.69 21.39 38.94 3.24
180 181 1.907222 TAGGAGCGTGACCTCGAGGA 61.907 60.000 37.69 14.23 38.76 3.71
181 182 1.440938 CTAGGAGCGTGACCTCGAGG 61.441 65.000 30.11 30.11 38.76 4.63
182 183 0.462225 TCTAGGAGCGTGACCTCGAG 60.462 60.000 5.13 5.13 38.76 4.04
183 184 0.462225 CTCTAGGAGCGTGACCTCGA 60.462 60.000 0.00 0.00 38.76 4.04
184 185 0.462225 TCTCTAGGAGCGTGACCTCG 60.462 60.000 0.00 0.00 38.76 4.63
185 186 1.018910 GTCTCTAGGAGCGTGACCTC 58.981 60.000 0.00 0.00 38.76 3.85
186 187 0.328592 TGTCTCTAGGAGCGTGACCT 59.671 55.000 0.00 0.00 41.05 3.85
187 188 1.174783 TTGTCTCTAGGAGCGTGACC 58.825 55.000 0.00 0.00 0.00 4.02
188 189 2.869897 CTTTGTCTCTAGGAGCGTGAC 58.130 52.381 0.00 0.00 0.00 3.67
189 190 1.202582 GCTTTGTCTCTAGGAGCGTGA 59.797 52.381 0.00 0.00 0.00 4.35
190 191 1.634702 GCTTTGTCTCTAGGAGCGTG 58.365 55.000 0.00 0.00 0.00 5.34
191 192 0.533032 GGCTTTGTCTCTAGGAGCGT 59.467 55.000 0.00 0.00 34.27 5.07
192 193 0.532573 TGGCTTTGTCTCTAGGAGCG 59.467 55.000 0.00 0.00 34.27 5.03
193 194 1.134551 CCTGGCTTTGTCTCTAGGAGC 60.135 57.143 0.00 0.00 0.00 4.70
194 195 1.134551 GCCTGGCTTTGTCTCTAGGAG 60.135 57.143 12.43 0.00 0.00 3.69
195 196 0.905357 GCCTGGCTTTGTCTCTAGGA 59.095 55.000 12.43 0.00 0.00 2.94
196 197 0.615331 TGCCTGGCTTTGTCTCTAGG 59.385 55.000 21.03 0.00 0.00 3.02
197 198 2.079925 GTTGCCTGGCTTTGTCTCTAG 58.920 52.381 21.03 0.00 0.00 2.43
198 199 1.271379 GGTTGCCTGGCTTTGTCTCTA 60.271 52.381 21.03 0.00 0.00 2.43
199 200 0.538287 GGTTGCCTGGCTTTGTCTCT 60.538 55.000 21.03 0.00 0.00 3.10
200 201 1.527433 GGGTTGCCTGGCTTTGTCTC 61.527 60.000 21.03 2.00 0.00 3.36
201 202 1.531602 GGGTTGCCTGGCTTTGTCT 60.532 57.895 21.03 0.00 0.00 3.41
202 203 2.919494 CGGGTTGCCTGGCTTTGTC 61.919 63.158 21.03 5.02 0.00 3.18
203 204 2.912025 CGGGTTGCCTGGCTTTGT 60.912 61.111 21.03 0.00 0.00 2.83
204 205 4.362476 GCGGGTTGCCTGGCTTTG 62.362 66.667 21.03 6.43 37.76 2.77
205 206 4.912395 TGCGGGTTGCCTGGCTTT 62.912 61.111 21.03 0.00 45.60 3.51
206 207 4.684134 ATGCGGGTTGCCTGGCTT 62.684 61.111 21.03 0.00 45.60 4.35
209 210 2.676121 TTCATGCGGGTTGCCTGG 60.676 61.111 0.00 0.00 45.60 4.45
210 211 1.033746 ATCTTCATGCGGGTTGCCTG 61.034 55.000 0.00 0.00 45.60 4.85
211 212 0.546122 TATCTTCATGCGGGTTGCCT 59.454 50.000 0.00 0.00 45.60 4.75
212 213 1.334869 CTTATCTTCATGCGGGTTGCC 59.665 52.381 0.00 0.00 45.60 4.52
213 214 1.334869 CCTTATCTTCATGCGGGTTGC 59.665 52.381 0.00 0.00 46.70 4.17
214 215 2.874701 CTCCTTATCTTCATGCGGGTTG 59.125 50.000 0.00 0.00 0.00 3.77
215 216 2.746472 GCTCCTTATCTTCATGCGGGTT 60.746 50.000 0.00 0.00 0.00 4.11
216 217 1.202698 GCTCCTTATCTTCATGCGGGT 60.203 52.381 0.00 0.00 0.00 5.28
217 218 1.071385 AGCTCCTTATCTTCATGCGGG 59.929 52.381 0.00 0.00 0.00 6.13
218 219 2.540265 AGCTCCTTATCTTCATGCGG 57.460 50.000 0.00 0.00 0.00 5.69
219 220 2.805099 GGAAGCTCCTTATCTTCATGCG 59.195 50.000 0.00 0.00 40.20 4.73
220 221 2.805099 CGGAAGCTCCTTATCTTCATGC 59.195 50.000 0.00 0.00 40.20 4.06
221 222 4.065321 ACGGAAGCTCCTTATCTTCATG 57.935 45.455 0.00 0.00 40.20 3.07
222 223 4.407296 AGAACGGAAGCTCCTTATCTTCAT 59.593 41.667 0.00 0.00 40.20 2.57
223 224 3.769844 AGAACGGAAGCTCCTTATCTTCA 59.230 43.478 0.00 0.00 40.20 3.02
224 225 4.364860 GAGAACGGAAGCTCCTTATCTTC 58.635 47.826 0.00 0.00 38.30 2.87
225 226 3.181485 CGAGAACGGAAGCTCCTTATCTT 60.181 47.826 0.00 0.00 33.30 2.40
226 227 2.359531 CGAGAACGGAAGCTCCTTATCT 59.640 50.000 0.00 0.00 33.30 1.98
227 228 2.358267 TCGAGAACGGAAGCTCCTTATC 59.642 50.000 0.00 0.00 40.21 1.75
228 229 2.376109 TCGAGAACGGAAGCTCCTTAT 58.624 47.619 0.00 0.00 40.21 1.73
229 230 1.830279 TCGAGAACGGAAGCTCCTTA 58.170 50.000 0.00 0.00 40.21 2.69
230 231 0.966920 TTCGAGAACGGAAGCTCCTT 59.033 50.000 0.00 0.00 40.21 3.36
231 232 0.528470 CTTCGAGAACGGAAGCTCCT 59.472 55.000 0.00 0.00 40.21 3.69
232 233 0.526662 TCTTCGAGAACGGAAGCTCC 59.473 55.000 0.00 0.00 40.21 4.70
233 234 1.619983 GTCTTCGAGAACGGAAGCTC 58.380 55.000 0.00 0.00 40.21 4.09
234 235 0.244178 GGTCTTCGAGAACGGAAGCT 59.756 55.000 0.00 0.00 40.21 3.74
235 236 0.038526 TGGTCTTCGAGAACGGAAGC 60.039 55.000 0.00 0.00 33.73 3.86
236 237 2.059541 GTTGGTCTTCGAGAACGGAAG 58.940 52.381 0.00 0.00 33.73 3.46
237 238 1.684983 AGTTGGTCTTCGAGAACGGAA 59.315 47.619 0.00 0.00 33.73 4.30
238 239 1.325355 AGTTGGTCTTCGAGAACGGA 58.675 50.000 0.00 0.00 33.73 4.69
239 240 2.228343 AGTAGTTGGTCTTCGAGAACGG 59.772 50.000 0.00 0.00 33.73 4.44
240 241 3.490399 GAGTAGTTGGTCTTCGAGAACG 58.510 50.000 0.00 0.00 33.73 3.95
241 242 3.255149 TGGAGTAGTTGGTCTTCGAGAAC 59.745 47.826 0.00 0.00 31.00 3.01
242 243 3.493334 TGGAGTAGTTGGTCTTCGAGAA 58.507 45.455 0.00 0.00 0.00 2.87
243 244 3.150458 TGGAGTAGTTGGTCTTCGAGA 57.850 47.619 0.00 0.00 0.00 4.04
244 245 3.256136 AGTTGGAGTAGTTGGTCTTCGAG 59.744 47.826 0.00 0.00 0.00 4.04
245 246 3.228453 AGTTGGAGTAGTTGGTCTTCGA 58.772 45.455 0.00 0.00 0.00 3.71
246 247 3.576648 GAGTTGGAGTAGTTGGTCTTCG 58.423 50.000 0.00 0.00 0.00 3.79
247 248 3.323979 TGGAGTTGGAGTAGTTGGTCTTC 59.676 47.826 0.00 0.00 0.00 2.87
248 249 3.314693 TGGAGTTGGAGTAGTTGGTCTT 58.685 45.455 0.00 0.00 0.00 3.01
249 250 2.972348 TGGAGTTGGAGTAGTTGGTCT 58.028 47.619 0.00 0.00 0.00 3.85
250 251 3.764237 TTGGAGTTGGAGTAGTTGGTC 57.236 47.619 0.00 0.00 0.00 4.02
251 252 3.201266 TGTTTGGAGTTGGAGTAGTTGGT 59.799 43.478 0.00 0.00 0.00 3.67
252 253 3.815809 TGTTTGGAGTTGGAGTAGTTGG 58.184 45.455 0.00 0.00 0.00 3.77
253 254 4.320494 GCATGTTTGGAGTTGGAGTAGTTG 60.320 45.833 0.00 0.00 0.00 3.16
254 255 3.821033 GCATGTTTGGAGTTGGAGTAGTT 59.179 43.478 0.00 0.00 0.00 2.24
255 256 3.073062 AGCATGTTTGGAGTTGGAGTAGT 59.927 43.478 0.00 0.00 0.00 2.73
256 257 3.679389 AGCATGTTTGGAGTTGGAGTAG 58.321 45.455 0.00 0.00 0.00 2.57
257 258 3.674997 GAGCATGTTTGGAGTTGGAGTA 58.325 45.455 0.00 0.00 0.00 2.59
258 259 2.508526 GAGCATGTTTGGAGTTGGAGT 58.491 47.619 0.00 0.00 0.00 3.85
259 260 1.466167 CGAGCATGTTTGGAGTTGGAG 59.534 52.381 0.00 0.00 0.00 3.86
260 261 1.522668 CGAGCATGTTTGGAGTTGGA 58.477 50.000 0.00 0.00 0.00 3.53
261 262 0.523072 CCGAGCATGTTTGGAGTTGG 59.477 55.000 10.27 0.00 0.00 3.77
262 263 0.523072 CCCGAGCATGTTTGGAGTTG 59.477 55.000 17.08 0.00 0.00 3.16
263 264 0.609131 CCCCGAGCATGTTTGGAGTT 60.609 55.000 17.08 0.00 0.00 3.01
264 265 1.002134 CCCCGAGCATGTTTGGAGT 60.002 57.895 17.08 0.00 0.00 3.85
265 266 1.750399 CCCCCGAGCATGTTTGGAG 60.750 63.158 17.08 3.77 0.00 3.86
266 267 2.354729 CCCCCGAGCATGTTTGGA 59.645 61.111 17.08 0.00 0.00 3.53
267 268 2.550699 TAGCCCCCGAGCATGTTTGG 62.551 60.000 8.86 8.86 34.23 3.28
268 269 1.077787 TAGCCCCCGAGCATGTTTG 60.078 57.895 0.00 0.00 34.23 2.93
269 270 1.077716 GTAGCCCCCGAGCATGTTT 60.078 57.895 0.00 0.00 34.23 2.83
270 271 0.689745 TAGTAGCCCCCGAGCATGTT 60.690 55.000 0.00 0.00 34.23 2.71
271 272 0.689745 TTAGTAGCCCCCGAGCATGT 60.690 55.000 0.00 0.00 34.23 3.21
272 273 0.249911 GTTAGTAGCCCCCGAGCATG 60.250 60.000 0.00 0.00 34.23 4.06
273 274 1.745320 CGTTAGTAGCCCCCGAGCAT 61.745 60.000 0.00 0.00 34.23 3.79
274 275 2.420568 CGTTAGTAGCCCCCGAGCA 61.421 63.158 0.00 0.00 34.23 4.26
275 276 1.953231 AACGTTAGTAGCCCCCGAGC 61.953 60.000 0.00 0.00 0.00 5.03
276 277 0.533951 AAACGTTAGTAGCCCCCGAG 59.466 55.000 0.00 0.00 0.00 4.63
277 278 0.975887 AAAACGTTAGTAGCCCCCGA 59.024 50.000 0.00 0.00 0.00 5.14
278 279 2.671130 TAAAACGTTAGTAGCCCCCG 57.329 50.000 0.00 0.00 0.00 5.73
279 280 5.427378 TGTATTAAAACGTTAGTAGCCCCC 58.573 41.667 0.00 0.00 0.00 5.40
280 281 7.412063 CAATGTATTAAAACGTTAGTAGCCCC 58.588 38.462 0.00 0.00 0.00 5.80
281 282 7.412063 CCAATGTATTAAAACGTTAGTAGCCC 58.588 38.462 0.00 0.00 0.00 5.19
282 283 7.412063 CCCAATGTATTAAAACGTTAGTAGCC 58.588 38.462 0.00 0.00 0.00 3.93
283 284 7.066163 ACCCCAATGTATTAAAACGTTAGTAGC 59.934 37.037 0.00 0.00 0.00 3.58
284 285 8.496707 ACCCCAATGTATTAAAACGTTAGTAG 57.503 34.615 0.00 0.00 0.00 2.57
285 286 8.860780 AACCCCAATGTATTAAAACGTTAGTA 57.139 30.769 0.00 0.00 0.00 1.82
286 287 7.764141 AACCCCAATGTATTAAAACGTTAGT 57.236 32.000 0.00 0.00 0.00 2.24
287 288 8.183536 GGTAACCCCAATGTATTAAAACGTTAG 58.816 37.037 0.00 0.00 0.00 2.34
288 289 7.667219 TGGTAACCCCAATGTATTAAAACGTTA 59.333 33.333 0.00 0.00 41.50 3.18
289 290 6.492772 TGGTAACCCCAATGTATTAAAACGTT 59.507 34.615 0.00 0.00 41.50 3.99
290 291 6.008960 TGGTAACCCCAATGTATTAAAACGT 58.991 36.000 0.00 0.00 41.50 3.99
291 292 6.512342 TGGTAACCCCAATGTATTAAAACG 57.488 37.500 0.00 0.00 41.50 3.60
304 305 4.533311 CCTTTTCTACTAGTGGTAACCCCA 59.467 45.833 5.39 0.00 42.51 4.96
305 306 4.080695 CCCTTTTCTACTAGTGGTAACCCC 60.081 50.000 5.39 0.00 0.00 4.95
306 307 4.080695 CCCCTTTTCTACTAGTGGTAACCC 60.081 50.000 5.39 0.00 0.00 4.11
307 308 4.080695 CCCCCTTTTCTACTAGTGGTAACC 60.081 50.000 5.39 0.00 0.00 2.85
308 309 4.624843 GCCCCCTTTTCTACTAGTGGTAAC 60.625 50.000 5.39 0.00 0.00 2.50
309 310 3.520721 GCCCCCTTTTCTACTAGTGGTAA 59.479 47.826 5.39 0.00 0.00 2.85
310 311 3.109928 GCCCCCTTTTCTACTAGTGGTA 58.890 50.000 5.39 0.00 0.00 3.25
311 312 1.914108 GCCCCCTTTTCTACTAGTGGT 59.086 52.381 5.39 0.00 0.00 4.16
335 336 2.511600 GATGACCCGGCCTGAACG 60.512 66.667 0.00 0.00 0.00 3.95
351 352 1.200519 CTGAACCGGGACTAATGGGA 58.799 55.000 6.32 0.00 0.00 4.37
463 464 2.570284 CCAACCGGGACCAAAAGGC 61.570 63.158 6.32 0.00 40.01 4.35
607 610 3.036091 GCGAGGGGGTATATATAGGCAA 58.964 50.000 0.00 0.00 0.00 4.52
674 681 2.360475 GCACCACCAAGCCCTCTC 60.360 66.667 0.00 0.00 0.00 3.20
696 703 1.644509 TGTGTGCATAGGAGGTGAGT 58.355 50.000 0.00 0.00 0.00 3.41
1166 1175 8.512138 CAAATTTAACTTCTCGACAATAGGGTT 58.488 33.333 0.00 0.00 0.00 4.11
1182 1191 9.936759 TGTTTTCTTCTTCAACCAAATTTAACT 57.063 25.926 0.00 0.00 0.00 2.24
1269 1282 0.318191 ATCATCGACGACATCCGCAG 60.318 55.000 0.00 0.00 43.32 5.18
1332 1345 8.517878 CCTTGGTATGAATGGCATATTTTCTAG 58.482 37.037 0.00 0.00 41.29 2.43
1722 1735 9.669887 ATTTAATGCATGGACAACACATAAAAT 57.330 25.926 0.00 0.00 0.00 1.82
1777 1790 2.965147 CAGGTGGGTGTGAAGGATTTTT 59.035 45.455 0.00 0.00 0.00 1.94
1908 1922 1.655484 TGCAGCATCACCGTATTCAG 58.345 50.000 0.00 0.00 0.00 3.02
1980 1994 2.639286 CAGCTTCACCCGTTGCAC 59.361 61.111 0.00 0.00 0.00 4.57
2020 2035 1.417145 TCATCATCATCGGGCACATCA 59.583 47.619 0.00 0.00 0.00 3.07
2045 2060 0.739462 GCATCGACAATGACCCGACA 60.739 55.000 0.00 0.00 37.59 4.35
2242 2257 7.781324 TGGAAGCTTCTTCTCCAATATTTTT 57.219 32.000 25.05 0.00 0.00 1.94
2252 2267 5.064071 CGTTATCCTTTGGAAGCTTCTTCTC 59.936 44.000 25.05 9.74 34.34 2.87


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

AutoCloner maintained by Alex Coulton.