Multiple sequence alignment - TraesCS6D01G393800

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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 TraesCS6D01G393800 chr6D 100.000 3164 0 0 1 3164 467548351 467545188 0.000000e+00 5843.0
1 TraesCS6D01G393800 chr6D 88.783 1364 127 10 1045 2394 467319838 467318487 0.000000e+00 1648.0
2 TraesCS6D01G393800 chr6D 95.734 586 16 3 2544 3120 467539558 467538973 0.000000e+00 935.0
3 TraesCS6D01G393800 chr6D 91.643 359 24 1 2544 2896 467318169 467317811 2.840000e-135 492.0
4 TraesCS6D01G393800 chr6D 93.103 174 12 0 2282 2455 467539945 467539772 4.050000e-64 255.0
5 TraesCS6D01G393800 chr6D 88.177 203 16 5 1 201 189238256 189238452 5.280000e-58 235.0
6 TraesCS6D01G393800 chr6D 82.171 129 7 11 2411 2525 467318378 467318252 2.600000e-16 97.1
7 TraesCS6D01G393800 chr6D 94.828 58 0 2 2466 2520 467539737 467539680 1.560000e-13 87.9
8 TraesCS6D01G393800 chr6B 93.432 1279 72 7 1045 2311 712804344 712803066 0.000000e+00 1886.0
9 TraesCS6D01G393800 chr6B 86.812 1380 161 12 1045 2413 63417890 63416521 0.000000e+00 1520.0
10 TraesCS6D01G393800 chr6B 85.870 1288 157 15 1045 2311 712675947 712674664 0.000000e+00 1347.0
11 TraesCS6D01G393800 chr6B 96.154 676 15 6 377 1051 712805042 712804377 0.000000e+00 1094.0
12 TraesCS6D01G393800 chr6B 96.725 397 9 2 377 772 712907876 712907483 0.000000e+00 658.0
13 TraesCS6D01G393800 chr6B 90.556 360 26 4 2544 2896 712674138 712673780 1.330000e-128 470.0
14 TraesCS6D01G393800 chr6B 88.451 355 31 4 2551 2896 712801989 712801636 1.360000e-113 420.0
15 TraesCS6D01G393800 chr6A 89.239 1301 117 13 1045 2331 613773061 613771770 0.000000e+00 1605.0
16 TraesCS6D01G393800 chr6A 87.722 1238 120 14 1109 2328 613794014 613792791 0.000000e+00 1415.0
17 TraesCS6D01G393800 chr6A 89.802 353 27 2 2544 2896 613771172 613770829 8.050000e-121 444.0
18 TraesCS6D01G393800 chr6A 88.525 122 10 4 205 324 169948038 169948157 9.150000e-31 145.0
19 TraesCS6D01G393800 chr6A 94.545 55 0 1 2411 2465 613771437 613771386 7.270000e-12 82.4
20 TraesCS6D01G393800 chr4A 84.641 1198 144 20 1136 2326 705440063 705438899 0.000000e+00 1157.0
21 TraesCS6D01G393800 chr4A 87.430 358 36 3 2547 2895 595780868 595780511 1.370000e-108 403.0
22 TraesCS6D01G393800 chr4D 89.227 362 31 2 2541 2895 7779073 7779433 2.240000e-121 446.0
23 TraesCS6D01G393800 chr4D 83.770 191 21 8 39 226 277199181 277199364 4.200000e-39 172.0
24 TraesCS6D01G393800 chrUn 95.154 227 11 0 2892 3118 722714 722940 3.000000e-95 359.0
25 TraesCS6D01G393800 chrUn 95.154 227 11 0 2892 3118 229404253 229404027 3.000000e-95 359.0
26 TraesCS6D01G393800 chrUn 88.525 122 10 4 205 324 201317206 201317325 9.150000e-31 145.0
27 TraesCS6D01G393800 chr5D 91.919 198 13 2 1 196 24448835 24448639 1.120000e-69 274.0
28 TraesCS6D01G393800 chr7D 90.732 205 16 2 1 203 102337371 102337574 1.450000e-68 270.0
29 TraesCS6D01G393800 chr7D 88.525 122 10 4 205 324 101484565 101484684 9.150000e-31 145.0
30 TraesCS6D01G393800 chr4B 91.500 200 12 4 1 196 269632286 269632088 1.450000e-68 270.0
31 TraesCS6D01G393800 chr1D 91.304 184 14 2 18 201 89941203 89941022 1.880000e-62 250.0
32 TraesCS6D01G393800 chr1D 85.714 189 19 4 15 201 217255205 217255023 3.220000e-45 193.0
33 TraesCS6D01G393800 chr1D 88.525 122 10 4 205 324 4610833 4610952 9.150000e-31 145.0
34 TraesCS6D01G393800 chr3B 86.283 226 29 1 2892 3117 682072506 682072729 8.770000e-61 244.0
35 TraesCS6D01G393800 chr1A 97.500 120 3 0 205 324 405516771 405516652 4.140000e-49 206.0
36 TraesCS6D01G393800 chr1A 87.705 122 11 4 205 324 376710806 376710925 4.260000e-29 139.0
37 TraesCS6D01G393800 chr3D 84.314 204 22 7 1 201 255226114 255226310 1.160000e-44 191.0
38 TraesCS6D01G393800 chr3D 88.667 150 15 2 53 201 612762686 612762834 6.970000e-42 182.0
39 TraesCS6D01G393800 chr7A 88.525 122 10 4 205 324 690528841 690528960 9.150000e-31 145.0
40 TraesCS6D01G393800 chr3A 88.525 122 10 4 205 324 486122471 486122352 9.150000e-31 145.0
41 TraesCS6D01G393800 chr1B 87.705 122 11 4 205 324 491725780 491725661 4.260000e-29 139.0


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 TraesCS6D01G393800 chr6D 467545188 467548351 3163 True 5843.000000 5843 100.000000 1 3164 1 chr6D.!!$R1 3163
1 TraesCS6D01G393800 chr6D 467317811 467319838 2027 True 745.700000 1648 87.532333 1045 2896 3 chr6D.!!$R2 1851
2 TraesCS6D01G393800 chr6D 467538973 467539945 972 True 425.966667 935 94.555000 2282 3120 3 chr6D.!!$R3 838
3 TraesCS6D01G393800 chr6B 63416521 63417890 1369 True 1520.000000 1520 86.812000 1045 2413 1 chr6B.!!$R1 1368
4 TraesCS6D01G393800 chr6B 712801636 712805042 3406 True 1133.333333 1886 92.679000 377 2896 3 chr6B.!!$R4 2519
5 TraesCS6D01G393800 chr6B 712673780 712675947 2167 True 908.500000 1347 88.213000 1045 2896 2 chr6B.!!$R3 1851
6 TraesCS6D01G393800 chr6A 613792791 613794014 1223 True 1415.000000 1415 87.722000 1109 2328 1 chr6A.!!$R1 1219
7 TraesCS6D01G393800 chr6A 613770829 613773061 2232 True 710.466667 1605 91.195333 1045 2896 3 chr6A.!!$R2 1851
8 TraesCS6D01G393800 chr4A 705438899 705440063 1164 True 1157.000000 1157 84.641000 1136 2326 1 chr4A.!!$R2 1190

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
371 372 0.239879 ACGGCGCACATAAAAAGGTG 59.76 50.0 10.83 0.0 38.05 4.0 F
920 922 0.250124 TCGGCCGTCAACAACAGAAT 60.25 50.0 27.15 0.0 0.00 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2180 0.106918 TCTTGCCGTCCTTGTTGGTT 60.107 50.0 0.00 0.00 37.07 3.67 R
2538 3688 1.101049 CCAATCCGCCGGCTTACAAT 61.101 55.0 26.68 7.46 0.00 2.71 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 4.737346 AGGGTAGGAGCCATGAGG 57.263 61.111 0.00 0.00 38.48 3.86
18 19 1.074167 AGGGTAGGAGCCATGAGGG 60.074 63.158 0.00 0.00 38.48 4.30
19 20 2.150051 GGGTAGGAGCCATGAGGGG 61.150 68.421 0.00 0.00 35.40 4.79
20 21 2.150051 GGTAGGAGCCATGAGGGGG 61.150 68.421 0.00 0.00 37.04 5.40
45 46 4.726351 GCGGCTCGGATCGGGATC 62.726 72.222 0.00 0.00 37.11 3.36
46 47 4.406173 CGGCTCGGATCGGGATCG 62.406 72.222 0.00 0.00 38.69 3.69
47 48 4.057428 GGCTCGGATCGGGATCGG 62.057 72.222 9.27 9.27 38.69 4.18
48 49 4.057428 GCTCGGATCGGGATCGGG 62.057 72.222 13.97 6.31 38.69 5.14
49 50 3.374402 CTCGGATCGGGATCGGGG 61.374 72.222 13.97 8.60 38.69 5.73
50 51 4.988716 TCGGATCGGGATCGGGGG 62.989 72.222 13.97 0.63 38.69 5.40
51 52 4.988716 CGGATCGGGATCGGGGGA 62.989 72.222 8.01 0.00 38.69 4.81
52 53 2.997897 GGATCGGGATCGGGGGAG 60.998 72.222 2.80 0.00 38.69 4.30
53 54 2.997897 GATCGGGATCGGGGGAGG 60.998 72.222 0.00 0.00 36.95 4.30
54 55 3.518484 ATCGGGATCGGGGGAGGA 61.518 66.667 0.00 0.00 36.95 3.71
55 56 2.807036 GATCGGGATCGGGGGAGGAT 62.807 65.000 0.00 0.00 36.95 3.24
56 57 2.807036 ATCGGGATCGGGGGAGGATC 62.807 65.000 0.00 0.00 39.63 3.36
57 58 2.204319 GGGATCGGGGGAGGATCA 59.796 66.667 0.00 0.00 41.62 2.92
58 59 1.915769 GGGATCGGGGGAGGATCAG 60.916 68.421 0.00 0.00 41.62 2.90
59 60 1.915769 GGATCGGGGGAGGATCAGG 60.916 68.421 0.00 0.00 41.62 3.86
60 61 1.152226 GATCGGGGGAGGATCAGGT 60.152 63.158 0.00 0.00 40.01 4.00
61 62 1.460305 ATCGGGGGAGGATCAGGTG 60.460 63.158 0.00 0.00 36.25 4.00
62 63 2.972589 ATCGGGGGAGGATCAGGTGG 62.973 65.000 0.00 0.00 36.25 4.61
63 64 2.372688 GGGGGAGGATCAGGTGGA 59.627 66.667 0.00 0.00 36.25 4.02
64 65 1.073397 GGGGGAGGATCAGGTGGAT 60.073 63.158 0.00 0.00 39.53 3.41
73 74 0.833287 ATCAGGTGGATCTTGTCGGG 59.167 55.000 0.00 0.00 0.00 5.14
74 75 1.221840 CAGGTGGATCTTGTCGGGG 59.778 63.158 0.00 0.00 0.00 5.73
75 76 2.124695 GGTGGATCTTGTCGGGGC 60.125 66.667 0.00 0.00 0.00 5.80
76 77 2.511600 GTGGATCTTGTCGGGGCG 60.512 66.667 0.00 0.00 0.00 6.13
77 78 3.781307 TGGATCTTGTCGGGGCGG 61.781 66.667 0.00 0.00 0.00 6.13
92 93 4.109675 CGGCCTTGGGATCCCGTT 62.110 66.667 26.03 0.00 39.42 4.44
93 94 2.440247 GGCCTTGGGATCCCGTTG 60.440 66.667 26.03 16.54 39.42 4.10
94 95 2.440247 GCCTTGGGATCCCGTTGG 60.440 66.667 26.03 25.01 39.42 3.77
95 96 3.087065 CCTTGGGATCCCGTTGGT 58.913 61.111 26.03 0.00 39.42 3.67
96 97 1.077716 CCTTGGGATCCCGTTGGTC 60.078 63.158 26.03 0.23 39.42 4.02
97 98 1.449601 CTTGGGATCCCGTTGGTCG 60.450 63.158 26.03 4.96 39.42 4.79
118 119 4.379243 CGGCGGCAGTTCAGGAGT 62.379 66.667 10.53 0.00 0.00 3.85
119 120 2.032681 GGCGGCAGTTCAGGAGTT 59.967 61.111 3.07 0.00 0.00 3.01
120 121 2.035442 GGCGGCAGTTCAGGAGTTC 61.035 63.158 3.07 0.00 0.00 3.01
121 122 2.383527 GCGGCAGTTCAGGAGTTCG 61.384 63.158 0.00 0.00 0.00 3.95
122 123 1.738099 CGGCAGTTCAGGAGTTCGG 60.738 63.158 0.00 0.00 0.00 4.30
123 124 1.376037 GGCAGTTCAGGAGTTCGGG 60.376 63.158 0.00 0.00 0.00 5.14
124 125 1.671742 GCAGTTCAGGAGTTCGGGA 59.328 57.895 0.00 0.00 0.00 5.14
125 126 0.390472 GCAGTTCAGGAGTTCGGGAG 60.390 60.000 0.00 0.00 0.00 4.30
126 127 0.247736 CAGTTCAGGAGTTCGGGAGG 59.752 60.000 0.00 0.00 0.00 4.30
127 128 0.905337 AGTTCAGGAGTTCGGGAGGG 60.905 60.000 0.00 0.00 0.00 4.30
128 129 2.291043 TTCAGGAGTTCGGGAGGGC 61.291 63.158 0.00 0.00 0.00 5.19
129 130 3.787001 CAGGAGTTCGGGAGGGCC 61.787 72.222 0.00 0.00 0.00 5.80
157 158 3.713902 CCTTATAGGGGCTGCTGTG 57.286 57.895 0.00 0.00 0.00 3.66
158 159 1.131638 CCTTATAGGGGCTGCTGTGA 58.868 55.000 0.00 0.00 0.00 3.58
159 160 1.701847 CCTTATAGGGGCTGCTGTGAT 59.298 52.381 0.00 0.00 0.00 3.06
160 161 2.289945 CCTTATAGGGGCTGCTGTGATC 60.290 54.545 0.00 0.00 0.00 2.92
161 162 1.352083 TATAGGGGCTGCTGTGATCC 58.648 55.000 0.00 0.00 0.00 3.36
162 163 0.695462 ATAGGGGCTGCTGTGATCCA 60.695 55.000 0.00 0.00 0.00 3.41
163 164 0.913934 TAGGGGCTGCTGTGATCCAA 60.914 55.000 0.00 0.00 0.00 3.53
164 165 1.304381 GGGGCTGCTGTGATCCAAA 60.304 57.895 0.00 0.00 0.00 3.28
165 166 0.685458 GGGGCTGCTGTGATCCAAAT 60.685 55.000 0.00 0.00 0.00 2.32
166 167 1.410083 GGGGCTGCTGTGATCCAAATA 60.410 52.381 0.00 0.00 0.00 1.40
167 168 2.378038 GGGCTGCTGTGATCCAAATAA 58.622 47.619 0.00 0.00 0.00 1.40
168 169 2.760092 GGGCTGCTGTGATCCAAATAAA 59.240 45.455 0.00 0.00 0.00 1.40
169 170 3.385755 GGGCTGCTGTGATCCAAATAAAT 59.614 43.478 0.00 0.00 0.00 1.40
170 171 4.584325 GGGCTGCTGTGATCCAAATAAATA 59.416 41.667 0.00 0.00 0.00 1.40
171 172 5.244626 GGGCTGCTGTGATCCAAATAAATAT 59.755 40.000 0.00 0.00 0.00 1.28
172 173 6.239402 GGGCTGCTGTGATCCAAATAAATATT 60.239 38.462 0.00 0.00 0.00 1.28
173 174 6.865205 GGCTGCTGTGATCCAAATAAATATTC 59.135 38.462 0.00 0.00 0.00 1.75
174 175 7.255730 GGCTGCTGTGATCCAAATAAATATTCT 60.256 37.037 0.00 0.00 0.00 2.40
175 176 8.786898 GCTGCTGTGATCCAAATAAATATTCTA 58.213 33.333 0.00 0.00 0.00 2.10
196 197 3.567478 ATCCTGGGATTAGAACAGTGC 57.433 47.619 0.00 0.00 0.00 4.40
197 198 2.551270 TCCTGGGATTAGAACAGTGCT 58.449 47.619 0.00 0.00 0.00 4.40
198 199 2.237143 TCCTGGGATTAGAACAGTGCTG 59.763 50.000 0.00 0.00 0.00 4.41
199 200 7.049902 AATCCTGGGATTAGAACAGTGCTGT 62.050 44.000 12.62 0.00 43.10 4.40
200 201 3.265791 CTGGGATTAGAACAGTGCTGTC 58.734 50.000 5.22 0.35 44.13 3.51
201 202 2.637382 TGGGATTAGAACAGTGCTGTCA 59.363 45.455 5.22 0.00 44.13 3.58
202 203 3.264193 TGGGATTAGAACAGTGCTGTCAT 59.736 43.478 5.22 0.53 44.13 3.06
203 204 3.624861 GGGATTAGAACAGTGCTGTCATG 59.375 47.826 5.22 0.00 44.13 3.07
204 205 4.256920 GGATTAGAACAGTGCTGTCATGT 58.743 43.478 5.22 0.00 44.13 3.21
205 206 4.093998 GGATTAGAACAGTGCTGTCATGTG 59.906 45.833 5.22 0.00 44.13 3.21
206 207 1.233019 AGAACAGTGCTGTCATGTGC 58.767 50.000 5.22 0.00 44.13 4.57
207 208 0.946528 GAACAGTGCTGTCATGTGCA 59.053 50.000 5.22 6.68 44.13 4.57
208 209 1.334556 GAACAGTGCTGTCATGTGCAA 59.665 47.619 5.22 0.00 44.13 4.08
209 210 0.664761 ACAGTGCTGTCATGTGCAAC 59.335 50.000 11.05 7.18 40.24 4.17
211 212 3.522725 ACAGTGCTGTCATGTGCAACAA 61.523 45.455 11.05 0.00 46.81 2.83
212 213 4.803223 ACAGTGCTGTCATGTGCAACAAT 61.803 43.478 11.05 2.59 46.81 2.71
213 214 6.565224 ACAGTGCTGTCATGTGCAACAATC 62.565 45.833 11.05 1.75 46.81 2.67
222 223 2.712057 GTGCAACAATCTTGTGGAGG 57.288 50.000 1.55 0.00 41.31 4.30
223 224 1.956477 GTGCAACAATCTTGTGGAGGT 59.044 47.619 1.55 0.00 41.31 3.85
224 225 3.146066 GTGCAACAATCTTGTGGAGGTA 58.854 45.455 1.55 0.00 41.31 3.08
225 226 3.189287 GTGCAACAATCTTGTGGAGGTAG 59.811 47.826 1.55 0.00 41.31 3.18
226 227 2.162408 GCAACAATCTTGTGGAGGTAGC 59.838 50.000 1.55 0.00 41.31 3.58
227 228 3.411446 CAACAATCTTGTGGAGGTAGCA 58.589 45.455 0.00 0.00 41.31 3.49
228 229 3.788227 ACAATCTTGTGGAGGTAGCAA 57.212 42.857 0.00 0.00 40.49 3.91
229 230 4.307032 ACAATCTTGTGGAGGTAGCAAT 57.693 40.909 0.00 0.00 40.49 3.56
230 231 4.265073 ACAATCTTGTGGAGGTAGCAATC 58.735 43.478 0.00 0.00 40.49 2.67
231 232 4.263462 ACAATCTTGTGGAGGTAGCAATCA 60.263 41.667 0.00 0.00 40.49 2.57
232 233 4.785346 ATCTTGTGGAGGTAGCAATCAT 57.215 40.909 0.00 0.00 0.00 2.45
233 234 5.894298 ATCTTGTGGAGGTAGCAATCATA 57.106 39.130 0.00 0.00 0.00 2.15
234 235 5.282055 TCTTGTGGAGGTAGCAATCATAG 57.718 43.478 0.00 0.00 0.00 2.23
235 236 3.475566 TGTGGAGGTAGCAATCATAGC 57.524 47.619 0.00 0.00 0.00 2.97
236 237 2.104792 TGTGGAGGTAGCAATCATAGCC 59.895 50.000 0.00 0.00 0.00 3.93
237 238 2.104792 GTGGAGGTAGCAATCATAGCCA 59.895 50.000 0.00 0.00 0.00 4.75
238 239 2.104792 TGGAGGTAGCAATCATAGCCAC 59.895 50.000 0.00 0.00 0.00 5.01
239 240 2.104792 GGAGGTAGCAATCATAGCCACA 59.895 50.000 0.00 0.00 0.00 4.17
240 241 3.244700 GGAGGTAGCAATCATAGCCACAT 60.245 47.826 0.00 0.00 0.00 3.21
241 242 3.748083 AGGTAGCAATCATAGCCACATG 58.252 45.455 0.00 0.00 0.00 3.21
242 243 3.137176 AGGTAGCAATCATAGCCACATGT 59.863 43.478 0.00 0.00 0.00 3.21
243 244 3.885297 GGTAGCAATCATAGCCACATGTT 59.115 43.478 0.00 0.00 0.00 2.71
244 245 4.261322 GGTAGCAATCATAGCCACATGTTG 60.261 45.833 0.00 0.00 0.00 3.33
245 246 3.623703 AGCAATCATAGCCACATGTTGA 58.376 40.909 0.14 0.00 0.00 3.18
246 247 3.630769 AGCAATCATAGCCACATGTTGAG 59.369 43.478 0.14 0.00 0.00 3.02
247 248 3.794475 GCAATCATAGCCACATGTTGAGC 60.794 47.826 0.14 2.61 0.00 4.26
248 249 3.572632 ATCATAGCCACATGTTGAGCT 57.427 42.857 16.56 16.56 36.22 4.09
249 250 3.354948 TCATAGCCACATGTTGAGCTT 57.645 42.857 17.32 5.89 34.62 3.74
250 251 3.011818 TCATAGCCACATGTTGAGCTTG 58.988 45.455 17.32 14.70 34.62 4.01
251 252 1.825090 TAGCCACATGTTGAGCTTGG 58.175 50.000 17.32 6.07 34.62 3.61
252 253 0.896940 AGCCACATGTTGAGCTTGGG 60.897 55.000 8.61 0.19 30.12 4.12
253 254 0.895100 GCCACATGTTGAGCTTGGGA 60.895 55.000 0.14 0.00 0.00 4.37
254 255 1.843368 CCACATGTTGAGCTTGGGAT 58.157 50.000 0.00 0.00 0.00 3.85
255 256 1.747355 CCACATGTTGAGCTTGGGATC 59.253 52.381 0.00 0.00 0.00 3.36
256 257 2.619849 CCACATGTTGAGCTTGGGATCT 60.620 50.000 0.00 0.00 0.00 2.75
257 258 2.422479 CACATGTTGAGCTTGGGATCTG 59.578 50.000 0.00 0.00 0.00 2.90
258 259 2.022195 CATGTTGAGCTTGGGATCTGG 58.978 52.381 0.00 0.00 0.00 3.86
259 260 1.067295 TGTTGAGCTTGGGATCTGGT 58.933 50.000 0.00 0.00 0.00 4.00
260 261 1.003580 TGTTGAGCTTGGGATCTGGTC 59.996 52.381 0.00 0.00 0.00 4.02
272 273 2.826128 GGATCTGGTCCAAAACTTTCCC 59.174 50.000 1.02 0.00 46.96 3.97
273 274 2.375014 TCTGGTCCAAAACTTTCCCC 57.625 50.000 0.00 0.00 0.00 4.81
274 275 1.856920 TCTGGTCCAAAACTTTCCCCT 59.143 47.619 0.00 0.00 0.00 4.79
275 276 1.963515 CTGGTCCAAAACTTTCCCCTG 59.036 52.381 0.00 0.00 0.00 4.45
276 277 1.289530 TGGTCCAAAACTTTCCCCTGT 59.710 47.619 0.00 0.00 0.00 4.00
277 278 2.292587 TGGTCCAAAACTTTCCCCTGTT 60.293 45.455 0.00 0.00 0.00 3.16
278 279 3.052793 TGGTCCAAAACTTTCCCCTGTTA 60.053 43.478 0.00 0.00 0.00 2.41
279 280 3.572682 GGTCCAAAACTTTCCCCTGTTAG 59.427 47.826 0.00 0.00 0.00 2.34
280 281 3.005472 GTCCAAAACTTTCCCCTGTTAGC 59.995 47.826 0.00 0.00 0.00 3.09
281 282 2.962421 CCAAAACTTTCCCCTGTTAGCA 59.038 45.455 0.00 0.00 0.00 3.49
282 283 3.578282 CCAAAACTTTCCCCTGTTAGCAT 59.422 43.478 0.00 0.00 0.00 3.79
283 284 4.040339 CCAAAACTTTCCCCTGTTAGCATT 59.960 41.667 0.00 0.00 0.00 3.56
284 285 5.454613 CCAAAACTTTCCCCTGTTAGCATTT 60.455 40.000 0.00 0.00 0.00 2.32
285 286 5.468540 AAACTTTCCCCTGTTAGCATTTC 57.531 39.130 0.00 0.00 0.00 2.17
286 287 4.388577 ACTTTCCCCTGTTAGCATTTCT 57.611 40.909 0.00 0.00 0.00 2.52
287 288 4.740902 ACTTTCCCCTGTTAGCATTTCTT 58.259 39.130 0.00 0.00 0.00 2.52
288 289 4.524328 ACTTTCCCCTGTTAGCATTTCTTG 59.476 41.667 0.00 0.00 0.00 3.02
336 337 8.534954 TTTCCTCTTATAGCCATATATACGCT 57.465 34.615 10.23 10.23 36.63 5.07
337 338 9.636789 TTTCCTCTTATAGCCATATATACGCTA 57.363 33.333 13.20 13.20 39.31 4.26
338 339 8.618702 TCCTCTTATAGCCATATATACGCTAC 57.381 38.462 13.12 0.00 37.89 3.58
339 340 7.387122 TCCTCTTATAGCCATATATACGCTACG 59.613 40.741 13.12 7.39 37.89 3.51
340 341 7.361031 CCTCTTATAGCCATATATACGCTACGG 60.361 44.444 13.12 8.29 37.89 4.02
341 342 2.865343 AGCCATATATACGCTACGGC 57.135 50.000 4.67 2.88 38.36 5.68
351 352 3.961729 GCTACGGCGGTTTTGACT 58.038 55.556 13.24 0.00 0.00 3.41
352 353 3.126729 GCTACGGCGGTTTTGACTA 57.873 52.632 13.24 0.00 0.00 2.59
353 354 0.717784 GCTACGGCGGTTTTGACTAC 59.282 55.000 13.24 0.00 0.00 2.73
354 355 0.986992 CTACGGCGGTTTTGACTACG 59.013 55.000 13.24 0.00 0.00 3.51
355 356 0.388391 TACGGCGGTTTTGACTACGG 60.388 55.000 13.24 0.00 0.00 4.02
356 357 2.865308 GGCGGTTTTGACTACGGC 59.135 61.111 0.00 0.00 44.25 5.68
357 358 2.472934 GCGGTTTTGACTACGGCG 59.527 61.111 4.80 4.80 33.22 6.46
358 359 2.472934 CGGTTTTGACTACGGCGC 59.527 61.111 6.90 0.00 0.00 6.53
359 360 2.311701 CGGTTTTGACTACGGCGCA 61.312 57.895 10.83 0.00 0.00 6.09
360 361 1.205820 GGTTTTGACTACGGCGCAC 59.794 57.895 10.83 0.00 0.00 5.34
361 362 1.500512 GGTTTTGACTACGGCGCACA 61.501 55.000 10.83 0.00 0.00 4.57
362 363 0.515564 GTTTTGACTACGGCGCACAT 59.484 50.000 10.83 0.00 0.00 3.21
363 364 1.727880 GTTTTGACTACGGCGCACATA 59.272 47.619 10.83 0.00 0.00 2.29
364 365 2.081725 TTTGACTACGGCGCACATAA 57.918 45.000 10.83 0.00 0.00 1.90
365 366 2.081725 TTGACTACGGCGCACATAAA 57.918 45.000 10.83 0.00 0.00 1.40
366 367 2.081725 TGACTACGGCGCACATAAAA 57.918 45.000 10.83 0.00 0.00 1.52
367 368 2.414806 TGACTACGGCGCACATAAAAA 58.585 42.857 10.83 0.00 0.00 1.94
368 369 2.413796 TGACTACGGCGCACATAAAAAG 59.586 45.455 10.83 0.00 0.00 2.27
369 370 1.735571 ACTACGGCGCACATAAAAAGG 59.264 47.619 10.83 0.00 0.00 3.11
370 371 1.735571 CTACGGCGCACATAAAAAGGT 59.264 47.619 10.83 0.00 0.00 3.50
371 372 0.239879 ACGGCGCACATAAAAAGGTG 59.760 50.000 10.83 0.00 38.05 4.00
372 373 0.455972 CGGCGCACATAAAAAGGTGG 60.456 55.000 10.83 0.00 35.58 4.61
373 374 0.601057 GGCGCACATAAAAAGGTGGT 59.399 50.000 10.83 0.00 35.58 4.16
374 375 1.000394 GGCGCACATAAAAAGGTGGTT 60.000 47.619 10.83 0.00 35.58 3.67
375 376 2.547007 GGCGCACATAAAAAGGTGGTTT 60.547 45.455 10.83 0.00 35.58 3.27
376 377 2.474735 GCGCACATAAAAAGGTGGTTTG 59.525 45.455 0.30 0.00 35.58 2.93
377 378 3.797184 GCGCACATAAAAAGGTGGTTTGA 60.797 43.478 0.30 0.00 35.58 2.69
378 379 3.980775 CGCACATAAAAAGGTGGTTTGAG 59.019 43.478 0.00 0.00 35.58 3.02
379 380 3.740832 GCACATAAAAAGGTGGTTTGAGC 59.259 43.478 0.00 0.00 35.58 4.26
380 381 4.306600 CACATAAAAAGGTGGTTTGAGCC 58.693 43.478 0.00 0.00 0.00 4.70
381 382 3.964031 ACATAAAAAGGTGGTTTGAGCCA 59.036 39.130 0.00 0.00 35.93 4.75
424 425 5.621329 CGACAAGTCAGGAAAAACCAAACTT 60.621 40.000 0.72 0.00 42.37 2.66
450 451 5.182001 GTGACATCTCATGCAACTAAAACCT 59.818 40.000 0.00 0.00 0.00 3.50
452 453 5.316167 ACATCTCATGCAACTAAAACCTGA 58.684 37.500 0.00 0.00 0.00 3.86
569 570 6.900189 TGCATGCAATATTTGAAACCAAAAG 58.100 32.000 20.30 0.00 37.12 2.27
708 709 4.402616 TGGTTTTCTGATCCCTTGGAAT 57.597 40.909 0.00 0.00 34.34 3.01
713 714 6.070596 GGTTTTCTGATCCCTTGGAATCAAAT 60.071 38.462 0.00 0.00 34.34 2.32
747 748 5.965922 AGTTTTCTTGTTTGAAAGGGTCAG 58.034 37.500 0.00 0.00 37.61 3.51
769 771 4.035208 AGCGCAACCTCCTTAATATTTTCG 59.965 41.667 11.47 0.00 0.00 3.46
808 810 1.403780 CCCTGGTACGGCGCTATATTC 60.404 57.143 6.90 0.00 0.00 1.75
849 851 4.985538 TCCCCAAGCATTATCCAGAATAC 58.014 43.478 0.00 0.00 0.00 1.89
860 862 3.383698 TCCAGAATACTCCGACTCCTT 57.616 47.619 0.00 0.00 0.00 3.36
861 863 3.288964 TCCAGAATACTCCGACTCCTTC 58.711 50.000 0.00 0.00 0.00 3.46
862 864 3.053544 TCCAGAATACTCCGACTCCTTCT 60.054 47.826 0.00 0.00 0.00 2.85
863 865 3.702045 CCAGAATACTCCGACTCCTTCTT 59.298 47.826 0.00 0.00 0.00 2.52
870 872 1.014564 CCGACTCCTTCTTGAACCGC 61.015 60.000 0.00 0.00 0.00 5.68
878 880 1.216941 TTCTTGAACCGCGTTCGTCC 61.217 55.000 4.92 0.00 44.55 4.79
879 881 2.662527 TTGAACCGCGTTCGTCCC 60.663 61.111 4.92 0.00 44.55 4.46
880 882 3.154584 TTGAACCGCGTTCGTCCCT 62.155 57.895 4.92 0.00 44.55 4.20
891 893 2.670509 CGTTCGTCCCTCCTCTACAAAC 60.671 54.545 0.00 0.00 0.00 2.93
903 905 1.272490 TCTACAAACACCCTCTGCTCG 59.728 52.381 0.00 0.00 0.00 5.03
920 922 0.250124 TCGGCCGTCAACAACAGAAT 60.250 50.000 27.15 0.00 0.00 2.40
1023 1025 1.349259 CGTTCTTTGGCTACGACCCG 61.349 60.000 0.00 0.00 37.47 5.28
1275 1319 2.636412 CGACTCCAACTCTCCGCCA 61.636 63.158 0.00 0.00 0.00 5.69
1725 1781 1.374125 CGAGACAACCGACATGGCA 60.374 57.895 0.00 0.00 43.94 4.92
1743 1799 0.745486 CAGCGATGGAGGTTGATGCA 60.745 55.000 0.00 0.00 0.00 3.96
1843 1899 1.078143 GGTGAGTGGGAGATGGTGC 60.078 63.158 0.00 0.00 0.00 5.01
1844 1900 1.557269 GGTGAGTGGGAGATGGTGCT 61.557 60.000 0.00 0.00 0.00 4.40
2055 2120 4.314440 GCTGAGCGGGTGGACACA 62.314 66.667 4.69 0.00 0.00 3.72
2115 2180 0.889186 GCAGGCGGAGGAACAAGAAA 60.889 55.000 0.00 0.00 0.00 2.52
2269 2364 5.900339 TGATCGTGTGAACAAACTTAGAC 57.100 39.130 0.00 0.00 0.00 2.59
2341 2437 7.147976 AGCTTTCAAAATTGGAACACATCTAC 58.852 34.615 0.00 0.00 39.29 2.59
2344 2440 5.309638 TCAAAATTGGAACACATCTACGGA 58.690 37.500 0.00 0.00 39.29 4.69
2538 3688 4.344104 GGGGAAGAATGTCAAAATGAGGA 58.656 43.478 0.00 0.00 0.00 3.71
2540 3690 5.423290 GGGGAAGAATGTCAAAATGAGGATT 59.577 40.000 0.00 0.00 0.00 3.01
2542 3692 6.071165 GGGAAGAATGTCAAAATGAGGATTGT 60.071 38.462 0.00 0.00 0.00 2.71
2578 3813 0.180406 AGTTGTTCGACAGCTTGGGT 59.820 50.000 0.00 0.00 36.18 4.51
2694 3930 1.107114 CCTGCTCCGAGTGACACTAT 58.893 55.000 8.41 0.00 0.00 2.12
2903 4172 7.707035 TGTAACGAAGCAAACACCATTTAAATT 59.293 29.630 0.00 0.00 0.00 1.82
2904 4173 7.546778 AACGAAGCAAACACCATTTAAATTT 57.453 28.000 0.00 0.00 0.00 1.82
2907 4176 9.099454 ACGAAGCAAACACCATTTAAATTTAAA 57.901 25.926 22.20 22.20 37.08 1.52
3001 4270 6.773200 TGTTGTGAATATGTTCCCTACAACAA 59.227 34.615 24.55 14.37 45.57 2.83
3120 4389 2.175811 GAACGATGCCAACCACGC 59.824 61.111 0.00 0.00 0.00 5.34
3121 4390 2.593148 AACGATGCCAACCACGCA 60.593 55.556 0.00 0.00 41.28 5.24
3122 4391 2.780149 GAACGATGCCAACCACGCAC 62.780 60.000 0.00 0.00 39.49 5.34
3123 4392 3.049674 CGATGCCAACCACGCACT 61.050 61.111 0.00 0.00 39.49 4.40
3124 4393 1.739929 CGATGCCAACCACGCACTA 60.740 57.895 0.00 0.00 39.49 2.74
3125 4394 1.794222 GATGCCAACCACGCACTAC 59.206 57.895 0.00 0.00 39.49 2.73
3135 4404 3.777925 CGCACTACGCCACAGCAC 61.778 66.667 0.00 0.00 39.83 4.40
3136 4405 3.777925 GCACTACGCCACAGCACG 61.778 66.667 0.00 0.00 39.83 5.34
3137 4406 3.112075 CACTACGCCACAGCACGG 61.112 66.667 0.00 0.00 39.83 4.94
3138 4407 3.299977 ACTACGCCACAGCACGGA 61.300 61.111 0.00 0.00 39.83 4.69
3139 4408 2.184322 CTACGCCACAGCACGGAT 59.816 61.111 0.00 0.00 39.83 4.18
3140 4409 2.125713 TACGCCACAGCACGGATG 60.126 61.111 0.00 0.00 39.83 3.51
3151 4420 2.161831 CACGGATGCAACGACATGT 58.838 52.632 19.17 0.00 34.93 3.21
3152 4421 1.355005 CACGGATGCAACGACATGTA 58.645 50.000 19.17 0.00 34.93 2.29
3153 4422 1.933181 CACGGATGCAACGACATGTAT 59.067 47.619 19.17 0.00 34.93 2.29
3154 4423 2.351418 CACGGATGCAACGACATGTATT 59.649 45.455 19.17 0.00 34.93 1.89
3155 4424 2.607635 ACGGATGCAACGACATGTATTC 59.392 45.455 19.17 0.00 34.93 1.75
3156 4425 2.866156 CGGATGCAACGACATGTATTCT 59.134 45.455 8.30 0.00 0.00 2.40
3157 4426 3.302675 CGGATGCAACGACATGTATTCTG 60.303 47.826 8.30 0.00 0.00 3.02
3158 4427 3.546815 GGATGCAACGACATGTATTCTGC 60.547 47.826 0.00 6.54 32.43 4.26
3159 4428 1.737236 TGCAACGACATGTATTCTGCC 59.263 47.619 15.23 0.00 31.07 4.85
3160 4429 1.267532 GCAACGACATGTATTCTGCCG 60.268 52.381 0.00 0.00 0.00 5.69
3161 4430 1.327460 CAACGACATGTATTCTGCCGG 59.673 52.381 0.00 0.00 0.00 6.13
3162 4431 0.179084 ACGACATGTATTCTGCCGGG 60.179 55.000 2.18 0.00 0.00 5.73
3163 4432 0.104120 CGACATGTATTCTGCCGGGA 59.896 55.000 2.18 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.074167 CCCTCATGGCTCCTACCCT 60.074 63.158 0.00 0.00 0.00 4.34
1 2 2.150051 CCCCTCATGGCTCCTACCC 61.150 68.421 0.00 0.00 0.00 3.69
3 4 3.568578 CCCCCTCATGGCTCCTAC 58.431 66.667 0.00 0.00 0.00 3.18
28 29 4.726351 GATCCCGATCCGAGCCGC 62.726 72.222 0.00 0.00 31.76 6.53
29 30 4.406173 CGATCCCGATCCGAGCCG 62.406 72.222 0.00 0.00 38.22 5.52
30 31 4.057428 CCGATCCCGATCCGAGCC 62.057 72.222 0.00 0.00 38.22 4.70
31 32 4.057428 CCCGATCCCGATCCGAGC 62.057 72.222 0.00 0.00 38.22 5.03
32 33 3.374402 CCCCGATCCCGATCCGAG 61.374 72.222 0.00 0.00 38.22 4.63
33 34 4.988716 CCCCCGATCCCGATCCGA 62.989 72.222 0.00 0.00 38.22 4.55
34 35 4.988716 TCCCCCGATCCCGATCCG 62.989 72.222 0.00 0.00 38.22 4.18
35 36 2.997897 CTCCCCCGATCCCGATCC 60.998 72.222 0.00 0.00 38.22 3.36
36 37 2.807036 ATCCTCCCCCGATCCCGATC 62.807 65.000 0.00 0.00 38.22 3.69
37 38 2.807036 GATCCTCCCCCGATCCCGAT 62.807 65.000 0.00 0.00 38.22 4.18
38 39 3.518484 ATCCTCCCCCGATCCCGA 61.518 66.667 0.00 0.00 38.22 5.14
39 40 2.997897 GATCCTCCCCCGATCCCG 60.998 72.222 0.00 0.00 31.69 5.14
40 41 1.915769 CTGATCCTCCCCCGATCCC 60.916 68.421 0.00 0.00 36.15 3.85
41 42 1.915769 CCTGATCCTCCCCCGATCC 60.916 68.421 0.00 0.00 36.15 3.36
42 43 1.152226 ACCTGATCCTCCCCCGATC 60.152 63.158 0.00 0.00 37.29 3.69
43 44 1.460305 CACCTGATCCTCCCCCGAT 60.460 63.158 0.00 0.00 0.00 4.18
44 45 2.041922 CACCTGATCCTCCCCCGA 60.042 66.667 0.00 0.00 0.00 5.14
45 46 2.972589 ATCCACCTGATCCTCCCCCG 62.973 65.000 0.00 0.00 0.00 5.73
46 47 1.073397 ATCCACCTGATCCTCCCCC 60.073 63.158 0.00 0.00 0.00 5.40
47 48 2.457759 GATCCACCTGATCCTCCCC 58.542 63.158 0.00 0.00 43.53 4.81
54 55 0.833287 CCCGACAAGATCCACCTGAT 59.167 55.000 0.00 0.00 36.01 2.90
55 56 1.264749 CCCCGACAAGATCCACCTGA 61.265 60.000 0.00 0.00 0.00 3.86
56 57 1.221840 CCCCGACAAGATCCACCTG 59.778 63.158 0.00 0.00 0.00 4.00
57 58 2.670148 GCCCCGACAAGATCCACCT 61.670 63.158 0.00 0.00 0.00 4.00
58 59 2.124695 GCCCCGACAAGATCCACC 60.125 66.667 0.00 0.00 0.00 4.61
59 60 2.511600 CGCCCCGACAAGATCCAC 60.512 66.667 0.00 0.00 0.00 4.02
60 61 3.781307 CCGCCCCGACAAGATCCA 61.781 66.667 0.00 0.00 0.00 3.41
75 76 4.109675 AACGGGATCCCAAGGCCG 62.110 66.667 30.42 17.07 33.28 6.13
76 77 2.440247 CAACGGGATCCCAAGGCC 60.440 66.667 30.42 0.00 35.37 5.19
77 78 2.440247 CCAACGGGATCCCAAGGC 60.440 66.667 30.42 3.02 35.59 4.35
78 79 1.077716 GACCAACGGGATCCCAAGG 60.078 63.158 30.42 27.08 38.05 3.61
79 80 1.449601 CGACCAACGGGATCCCAAG 60.450 63.158 30.42 17.39 38.46 3.61
80 81 2.666207 CGACCAACGGGATCCCAA 59.334 61.111 30.42 0.00 38.46 4.12
101 102 3.883744 AACTCCTGAACTGCCGCCG 62.884 63.158 0.00 0.00 0.00 6.46
102 103 2.032681 AACTCCTGAACTGCCGCC 59.967 61.111 0.00 0.00 0.00 6.13
103 104 2.383527 CGAACTCCTGAACTGCCGC 61.384 63.158 0.00 0.00 0.00 6.53
104 105 1.738099 CCGAACTCCTGAACTGCCG 60.738 63.158 0.00 0.00 0.00 5.69
105 106 1.376037 CCCGAACTCCTGAACTGCC 60.376 63.158 0.00 0.00 0.00 4.85
106 107 0.390472 CTCCCGAACTCCTGAACTGC 60.390 60.000 0.00 0.00 0.00 4.40
107 108 0.247736 CCTCCCGAACTCCTGAACTG 59.752 60.000 0.00 0.00 0.00 3.16
108 109 0.905337 CCCTCCCGAACTCCTGAACT 60.905 60.000 0.00 0.00 0.00 3.01
109 110 1.597461 CCCTCCCGAACTCCTGAAC 59.403 63.158 0.00 0.00 0.00 3.18
110 111 2.291043 GCCCTCCCGAACTCCTGAA 61.291 63.158 0.00 0.00 0.00 3.02
111 112 2.683933 GCCCTCCCGAACTCCTGA 60.684 66.667 0.00 0.00 0.00 3.86
112 113 3.787001 GGCCCTCCCGAACTCCTG 61.787 72.222 0.00 0.00 0.00 3.86
128 129 0.478507 CCTATAAGGGCCCAACAGGG 59.521 60.000 27.56 16.39 46.03 4.45
139 140 1.131638 TCACAGCAGCCCCTATAAGG 58.868 55.000 0.00 0.00 34.30 2.69
140 141 2.289945 GGATCACAGCAGCCCCTATAAG 60.290 54.545 0.00 0.00 0.00 1.73
141 142 1.699634 GGATCACAGCAGCCCCTATAA 59.300 52.381 0.00 0.00 0.00 0.98
142 143 1.352083 GGATCACAGCAGCCCCTATA 58.648 55.000 0.00 0.00 0.00 1.31
143 144 0.695462 TGGATCACAGCAGCCCCTAT 60.695 55.000 0.00 0.00 0.00 2.57
144 145 0.913934 TTGGATCACAGCAGCCCCTA 60.914 55.000 0.00 0.00 0.00 3.53
145 146 1.792757 TTTGGATCACAGCAGCCCCT 61.793 55.000 0.00 0.00 0.00 4.79
146 147 0.685458 ATTTGGATCACAGCAGCCCC 60.685 55.000 0.00 0.00 0.00 5.80
147 148 2.057137 TATTTGGATCACAGCAGCCC 57.943 50.000 0.00 0.00 0.00 5.19
148 149 4.660789 ATTTATTTGGATCACAGCAGCC 57.339 40.909 0.00 0.00 0.00 4.85
149 150 7.655490 AGAATATTTATTTGGATCACAGCAGC 58.345 34.615 0.00 0.00 0.00 5.25
173 174 9.475170 ACAGCACTGTTCTAATCCCAGGATTAG 62.475 44.444 29.21 29.21 46.31 1.73
174 175 4.721776 AGCACTGTTCTAATCCCAGGATTA 59.278 41.667 16.43 16.43 43.66 1.75
175 176 3.525199 AGCACTGTTCTAATCCCAGGATT 59.475 43.478 15.93 15.93 45.58 3.01
176 177 3.118112 CAGCACTGTTCTAATCCCAGGAT 60.118 47.826 0.00 0.00 36.23 3.24
177 178 2.237143 CAGCACTGTTCTAATCCCAGGA 59.763 50.000 0.00 0.00 0.00 3.86
178 179 2.026822 ACAGCACTGTTCTAATCCCAGG 60.027 50.000 0.00 0.00 41.83 4.45
179 180 3.265791 GACAGCACTGTTCTAATCCCAG 58.734 50.000 4.52 0.00 45.05 4.45
180 181 2.637382 TGACAGCACTGTTCTAATCCCA 59.363 45.455 4.52 0.00 45.05 4.37
181 182 3.334583 TGACAGCACTGTTCTAATCCC 57.665 47.619 4.52 0.00 45.05 3.85
182 183 4.093998 CACATGACAGCACTGTTCTAATCC 59.906 45.833 4.52 0.00 45.05 3.01
183 184 4.436584 GCACATGACAGCACTGTTCTAATC 60.437 45.833 4.52 0.00 45.05 1.75
184 185 3.438087 GCACATGACAGCACTGTTCTAAT 59.562 43.478 4.52 0.00 45.05 1.73
185 186 2.807967 GCACATGACAGCACTGTTCTAA 59.192 45.455 4.52 0.00 45.05 2.10
186 187 2.224257 TGCACATGACAGCACTGTTCTA 60.224 45.455 4.52 0.00 45.05 2.10
187 188 1.233019 GCACATGACAGCACTGTTCT 58.767 50.000 4.52 0.00 45.05 3.01
188 189 0.946528 TGCACATGACAGCACTGTTC 59.053 50.000 4.52 0.00 45.05 3.18
189 190 1.066002 GTTGCACATGACAGCACTGTT 59.934 47.619 4.52 0.00 45.05 3.16
191 192 0.664224 TGTTGCACATGACAGCACTG 59.336 50.000 0.00 0.00 41.05 3.66
192 193 1.391577 TTGTTGCACATGACAGCACT 58.608 45.000 0.00 0.00 41.05 4.40
193 194 2.030540 AGATTGTTGCACATGACAGCAC 60.031 45.455 0.00 3.05 41.05 4.40
194 195 2.232399 AGATTGTTGCACATGACAGCA 58.768 42.857 0.00 3.73 39.32 4.41
195 196 2.984471 CAAGATTGTTGCACATGACAGC 59.016 45.455 0.00 0.68 0.00 4.40
196 197 3.978855 CACAAGATTGTTGCACATGACAG 59.021 43.478 0.00 0.00 39.91 3.51
197 198 3.243468 CCACAAGATTGTTGCACATGACA 60.243 43.478 0.00 0.00 39.91 3.58
198 199 3.004629 TCCACAAGATTGTTGCACATGAC 59.995 43.478 0.00 0.00 39.91 3.06
199 200 3.220940 TCCACAAGATTGTTGCACATGA 58.779 40.909 0.00 0.00 39.91 3.07
200 201 3.571571 CTCCACAAGATTGTTGCACATG 58.428 45.455 0.00 0.00 39.91 3.21
201 202 2.559668 CCTCCACAAGATTGTTGCACAT 59.440 45.455 0.00 0.00 39.91 3.21
202 203 1.955778 CCTCCACAAGATTGTTGCACA 59.044 47.619 0.00 0.00 39.91 4.57
203 204 1.956477 ACCTCCACAAGATTGTTGCAC 59.044 47.619 0.00 0.00 39.91 4.57
204 205 2.363306 ACCTCCACAAGATTGTTGCA 57.637 45.000 0.00 0.00 39.91 4.08
205 206 2.162408 GCTACCTCCACAAGATTGTTGC 59.838 50.000 0.00 0.00 39.91 4.17
206 207 3.411446 TGCTACCTCCACAAGATTGTTG 58.589 45.455 0.00 0.00 39.91 3.33
207 208 3.788227 TGCTACCTCCACAAGATTGTT 57.212 42.857 0.00 0.00 39.91 2.83
208 209 3.788227 TTGCTACCTCCACAAGATTGT 57.212 42.857 0.00 0.00 43.36 2.71
209 210 4.264253 TGATTGCTACCTCCACAAGATTG 58.736 43.478 0.00 0.00 0.00 2.67
210 211 4.574674 TGATTGCTACCTCCACAAGATT 57.425 40.909 0.00 0.00 0.00 2.40
211 212 4.785346 ATGATTGCTACCTCCACAAGAT 57.215 40.909 0.00 0.00 0.00 2.40
212 213 4.443457 GCTATGATTGCTACCTCCACAAGA 60.443 45.833 0.00 0.00 0.00 3.02
213 214 3.812053 GCTATGATTGCTACCTCCACAAG 59.188 47.826 0.00 0.00 0.00 3.16
214 215 3.433598 GGCTATGATTGCTACCTCCACAA 60.434 47.826 0.00 0.00 0.00 3.33
215 216 2.104792 GGCTATGATTGCTACCTCCACA 59.895 50.000 0.00 0.00 0.00 4.17
216 217 2.104792 TGGCTATGATTGCTACCTCCAC 59.895 50.000 0.00 0.00 0.00 4.02
217 218 2.104792 GTGGCTATGATTGCTACCTCCA 59.895 50.000 4.19 0.00 36.18 3.86
218 219 2.104792 TGTGGCTATGATTGCTACCTCC 59.895 50.000 12.06 0.00 40.46 4.30
219 220 3.475566 TGTGGCTATGATTGCTACCTC 57.524 47.619 12.06 0.00 40.46 3.85
220 221 3.137176 ACATGTGGCTATGATTGCTACCT 59.863 43.478 12.06 0.62 40.46 3.08
221 222 3.480470 ACATGTGGCTATGATTGCTACC 58.520 45.455 12.06 0.00 40.46 3.18
222 223 4.576053 TCAACATGTGGCTATGATTGCTAC 59.424 41.667 8.26 8.26 41.34 3.58
223 224 4.779696 TCAACATGTGGCTATGATTGCTA 58.220 39.130 0.00 0.00 0.00 3.49
224 225 3.623703 TCAACATGTGGCTATGATTGCT 58.376 40.909 0.00 0.00 0.00 3.91
225 226 3.794475 GCTCAACATGTGGCTATGATTGC 60.794 47.826 0.00 0.00 0.00 3.56
226 227 3.630769 AGCTCAACATGTGGCTATGATTG 59.369 43.478 16.24 1.47 33.54 2.67
227 228 3.894759 AGCTCAACATGTGGCTATGATT 58.105 40.909 16.24 0.00 33.54 2.57
228 229 3.572632 AGCTCAACATGTGGCTATGAT 57.427 42.857 16.24 0.00 33.54 2.45
229 230 3.011818 CAAGCTCAACATGTGGCTATGA 58.988 45.455 17.52 8.82 34.00 2.15
230 231 2.098607 CCAAGCTCAACATGTGGCTATG 59.901 50.000 17.52 16.21 34.00 2.23
231 232 2.372264 CCAAGCTCAACATGTGGCTAT 58.628 47.619 17.52 8.61 34.00 2.97
232 233 1.614051 CCCAAGCTCAACATGTGGCTA 60.614 52.381 17.52 0.00 34.00 3.93
233 234 0.896940 CCCAAGCTCAACATGTGGCT 60.897 55.000 13.25 13.25 35.88 4.75
234 235 0.895100 TCCCAAGCTCAACATGTGGC 60.895 55.000 0.00 4.80 0.00 5.01
235 236 1.747355 GATCCCAAGCTCAACATGTGG 59.253 52.381 0.00 0.00 0.00 4.17
236 237 2.422479 CAGATCCCAAGCTCAACATGTG 59.578 50.000 0.00 0.00 0.00 3.21
237 238 2.619849 CCAGATCCCAAGCTCAACATGT 60.620 50.000 0.00 0.00 0.00 3.21
238 239 2.022195 CCAGATCCCAAGCTCAACATG 58.978 52.381 0.00 0.00 0.00 3.21
239 240 1.637553 ACCAGATCCCAAGCTCAACAT 59.362 47.619 0.00 0.00 0.00 2.71
240 241 1.003580 GACCAGATCCCAAGCTCAACA 59.996 52.381 0.00 0.00 0.00 3.33
241 242 1.680249 GGACCAGATCCCAAGCTCAAC 60.680 57.143 0.00 0.00 42.46 3.18
242 243 0.620556 GGACCAGATCCCAAGCTCAA 59.379 55.000 0.00 0.00 42.46 3.02
243 244 2.300996 GGACCAGATCCCAAGCTCA 58.699 57.895 0.00 0.00 42.46 4.26
252 253 2.826128 GGGGAAAGTTTTGGACCAGATC 59.174 50.000 0.00 0.00 0.00 2.75
253 254 2.450886 AGGGGAAAGTTTTGGACCAGAT 59.549 45.455 0.00 0.00 0.00 2.90
254 255 1.856920 AGGGGAAAGTTTTGGACCAGA 59.143 47.619 0.00 0.00 0.00 3.86
255 256 1.963515 CAGGGGAAAGTTTTGGACCAG 59.036 52.381 0.00 0.00 0.00 4.00
256 257 1.289530 ACAGGGGAAAGTTTTGGACCA 59.710 47.619 0.00 0.00 0.00 4.02
257 258 2.082140 ACAGGGGAAAGTTTTGGACC 57.918 50.000 0.00 0.00 0.00 4.46
258 259 3.005472 GCTAACAGGGGAAAGTTTTGGAC 59.995 47.826 0.00 0.00 0.00 4.02
259 260 3.227614 GCTAACAGGGGAAAGTTTTGGA 58.772 45.455 0.00 0.00 0.00 3.53
260 261 2.962421 TGCTAACAGGGGAAAGTTTTGG 59.038 45.455 0.00 0.00 0.00 3.28
261 262 4.871933 ATGCTAACAGGGGAAAGTTTTG 57.128 40.909 0.00 0.00 0.00 2.44
262 263 5.602561 AGAAATGCTAACAGGGGAAAGTTTT 59.397 36.000 0.00 0.00 0.00 2.43
263 264 5.147767 AGAAATGCTAACAGGGGAAAGTTT 58.852 37.500 0.00 0.00 0.00 2.66
264 265 4.740902 AGAAATGCTAACAGGGGAAAGTT 58.259 39.130 0.00 0.00 0.00 2.66
265 266 4.388577 AGAAATGCTAACAGGGGAAAGT 57.611 40.909 0.00 0.00 0.00 2.66
266 267 5.064441 CAAGAAATGCTAACAGGGGAAAG 57.936 43.478 0.00 0.00 0.00 2.62
310 311 9.148879 AGCGTATATATGGCTATAAGAGGAAAT 57.851 33.333 10.39 0.00 34.75 2.17
311 312 8.534954 AGCGTATATATGGCTATAAGAGGAAA 57.465 34.615 10.39 0.00 34.75 3.13
312 313 9.064706 GTAGCGTATATATGGCTATAAGAGGAA 57.935 37.037 17.90 0.00 40.94 3.36
313 314 7.387122 CGTAGCGTATATATGGCTATAAGAGGA 59.613 40.741 17.90 0.00 40.94 3.71
314 315 7.361031 CCGTAGCGTATATATGGCTATAAGAGG 60.361 44.444 17.90 13.69 40.94 3.69
315 316 7.519843 CCGTAGCGTATATATGGCTATAAGAG 58.480 42.308 17.90 10.48 40.94 2.85
316 317 7.430992 CCGTAGCGTATATATGGCTATAAGA 57.569 40.000 17.90 1.58 40.94 2.10
334 335 0.717784 GTAGTCAAAACCGCCGTAGC 59.282 55.000 0.00 0.00 0.00 3.58
335 336 0.986992 CGTAGTCAAAACCGCCGTAG 59.013 55.000 0.00 0.00 0.00 3.51
336 337 0.388391 CCGTAGTCAAAACCGCCGTA 60.388 55.000 0.00 0.00 0.00 4.02
337 338 1.665599 CCGTAGTCAAAACCGCCGT 60.666 57.895 0.00 0.00 0.00 5.68
338 339 3.018840 GCCGTAGTCAAAACCGCCG 62.019 63.158 0.00 0.00 0.00 6.46
339 340 2.865308 GCCGTAGTCAAAACCGCC 59.135 61.111 0.00 0.00 0.00 6.13
340 341 2.472934 CGCCGTAGTCAAAACCGC 59.527 61.111 0.00 0.00 0.00 5.68
341 342 2.311701 TGCGCCGTAGTCAAAACCG 61.312 57.895 4.18 0.00 0.00 4.44
342 343 1.205820 GTGCGCCGTAGTCAAAACC 59.794 57.895 4.18 0.00 0.00 3.27
343 344 0.515564 ATGTGCGCCGTAGTCAAAAC 59.484 50.000 4.18 0.00 0.00 2.43
344 345 2.081725 TATGTGCGCCGTAGTCAAAA 57.918 45.000 4.18 0.00 0.00 2.44
345 346 2.081725 TTATGTGCGCCGTAGTCAAA 57.918 45.000 4.18 0.00 0.00 2.69
346 347 2.081725 TTTATGTGCGCCGTAGTCAA 57.918 45.000 4.18 0.00 0.00 3.18
347 348 2.081725 TTTTATGTGCGCCGTAGTCA 57.918 45.000 4.18 0.00 0.00 3.41
348 349 2.222953 CCTTTTTATGTGCGCCGTAGTC 60.223 50.000 4.18 0.00 0.00 2.59
349 350 1.735571 CCTTTTTATGTGCGCCGTAGT 59.264 47.619 4.18 0.00 0.00 2.73
350 351 1.735571 ACCTTTTTATGTGCGCCGTAG 59.264 47.619 4.18 0.00 0.00 3.51
351 352 1.465387 CACCTTTTTATGTGCGCCGTA 59.535 47.619 4.18 0.00 0.00 4.02
352 353 0.239879 CACCTTTTTATGTGCGCCGT 59.760 50.000 4.18 0.00 0.00 5.68
353 354 0.455972 CCACCTTTTTATGTGCGCCG 60.456 55.000 4.18 0.00 0.00 6.46
354 355 0.601057 ACCACCTTTTTATGTGCGCC 59.399 50.000 4.18 0.00 0.00 6.53
355 356 2.432206 AACCACCTTTTTATGTGCGC 57.568 45.000 0.00 0.00 0.00 6.09
356 357 3.971150 TCAAACCACCTTTTTATGTGCG 58.029 40.909 0.00 0.00 0.00 5.34
357 358 3.740832 GCTCAAACCACCTTTTTATGTGC 59.259 43.478 0.00 0.00 0.00 4.57
358 359 4.202202 TGGCTCAAACCACCTTTTTATGTG 60.202 41.667 0.00 0.00 33.75 3.21
359 360 3.964031 TGGCTCAAACCACCTTTTTATGT 59.036 39.130 0.00 0.00 33.75 2.29
360 361 4.599047 TGGCTCAAACCACCTTTTTATG 57.401 40.909 0.00 0.00 33.75 1.90
370 371 2.103432 TCTACTTTCGTGGCTCAAACCA 59.897 45.455 0.00 0.00 37.38 3.67
371 372 2.762745 TCTACTTTCGTGGCTCAAACC 58.237 47.619 0.00 0.00 0.00 3.27
372 373 3.125316 CCATCTACTTTCGTGGCTCAAAC 59.875 47.826 0.00 0.00 0.00 2.93
373 374 3.334691 CCATCTACTTTCGTGGCTCAAA 58.665 45.455 0.00 0.00 0.00 2.69
374 375 2.972625 CCATCTACTTTCGTGGCTCAA 58.027 47.619 0.00 0.00 0.00 3.02
375 376 2.672961 CCATCTACTTTCGTGGCTCA 57.327 50.000 0.00 0.00 0.00 4.26
379 380 1.942657 CCATGCCATCTACTTTCGTGG 59.057 52.381 0.00 0.00 34.84 4.94
380 381 1.331756 GCCATGCCATCTACTTTCGTG 59.668 52.381 0.00 0.00 0.00 4.35
381 382 1.668419 GCCATGCCATCTACTTTCGT 58.332 50.000 0.00 0.00 0.00 3.85
382 383 0.583438 CGCCATGCCATCTACTTTCG 59.417 55.000 0.00 0.00 0.00 3.46
383 384 1.599542 GTCGCCATGCCATCTACTTTC 59.400 52.381 0.00 0.00 0.00 2.62
424 425 2.865119 AGTTGCATGAGATGTCACCA 57.135 45.000 0.00 0.00 34.75 4.17
425 426 5.393962 GTTTTAGTTGCATGAGATGTCACC 58.606 41.667 0.00 0.00 34.75 4.02
426 427 5.182001 AGGTTTTAGTTGCATGAGATGTCAC 59.818 40.000 0.00 0.00 34.75 3.67
569 570 7.175990 CCTCTAGACTCTAGTATTTCCCACATC 59.824 44.444 12.06 0.00 0.00 3.06
708 709 4.569162 AGAAAACTCGAACGTGTCATTTGA 59.431 37.500 0.00 0.00 0.00 2.69
713 714 3.255725 ACAAGAAAACTCGAACGTGTCA 58.744 40.909 0.00 0.00 0.00 3.58
747 748 4.279659 CGAAAATATTAAGGAGGTTGCGC 58.720 43.478 0.00 0.00 0.00 6.09
769 771 0.106894 GCCGGCCCATATATAGGAGC 59.893 60.000 18.11 0.00 0.00 4.70
849 851 1.402984 CGGTTCAAGAAGGAGTCGGAG 60.403 57.143 0.00 0.00 0.00 4.63
860 862 1.662446 GGACGAACGCGGTTCAAGA 60.662 57.895 12.47 0.00 42.05 3.02
861 863 2.664436 GGGACGAACGCGGTTCAAG 61.664 63.158 12.47 0.00 42.05 3.02
862 864 2.662527 GGGACGAACGCGGTTCAA 60.663 61.111 12.47 0.00 42.05 2.69
863 865 3.562779 GAGGGACGAACGCGGTTCA 62.563 63.158 12.47 0.00 42.05 3.18
870 872 1.171308 TTGTAGAGGAGGGACGAACG 58.829 55.000 0.00 0.00 0.00 3.95
878 880 2.234908 CAGAGGGTGTTTGTAGAGGAGG 59.765 54.545 0.00 0.00 0.00 4.30
879 881 2.354203 GCAGAGGGTGTTTGTAGAGGAG 60.354 54.545 0.00 0.00 0.00 3.69
880 882 1.623811 GCAGAGGGTGTTTGTAGAGGA 59.376 52.381 0.00 0.00 0.00 3.71
903 905 0.521735 GGATTCTGTTGTTGACGGCC 59.478 55.000 0.00 0.00 34.46 6.13
920 922 0.391793 TGCGCACGATTATGTTGGGA 60.392 50.000 5.66 0.00 0.00 4.37
1023 1025 0.950116 AGCCATAGCCGTAGTCGTAC 59.050 55.000 0.00 0.00 41.25 3.67
1275 1319 4.400961 GGCTTCCTCGGCACAGCT 62.401 66.667 0.00 0.00 32.52 4.24
1451 1495 4.812476 CGAGGCCGATCCGTGCAA 62.812 66.667 0.00 0.00 40.77 4.08
1618 1668 3.328931 TCTTCCTCTGCATCCTGAACTTT 59.671 43.478 0.00 0.00 0.00 2.66
1725 1781 0.463295 CTGCATCAACCTCCATCGCT 60.463 55.000 0.00 0.00 0.00 4.93
1908 1967 0.820891 CCTGTGCCTGTTCTTGCTGT 60.821 55.000 0.00 0.00 0.00 4.40
2068 2133 3.702048 CTCCTCAACCCGCCGGAA 61.702 66.667 5.05 0.00 0.00 4.30
2115 2180 0.106918 TCTTGCCGTCCTTGTTGGTT 60.107 50.000 0.00 0.00 37.07 3.67
2234 2323 6.558771 TCACACGATCAACAGAATTGAAAT 57.441 33.333 0.00 0.00 31.55 2.17
2244 2333 4.955925 AAGTTTGTTCACACGATCAACA 57.044 36.364 0.00 0.00 31.97 3.33
2251 2343 6.398621 CGACATAGTCTAAGTTTGTTCACACG 60.399 42.308 0.00 0.00 0.00 4.49
2269 2364 7.967854 TGAAACTAATGAAATTTGCCGACATAG 59.032 33.333 0.00 0.00 37.87 2.23
2505 3624 4.375313 ACATTCTTCCCCCTCTGTTAGAT 58.625 43.478 0.00 0.00 0.00 1.98
2507 3626 3.519510 TGACATTCTTCCCCCTCTGTTAG 59.480 47.826 0.00 0.00 0.00 2.34
2509 3628 2.348472 TGACATTCTTCCCCCTCTGTT 58.652 47.619 0.00 0.00 0.00 3.16
2510 3629 2.044793 TGACATTCTTCCCCCTCTGT 57.955 50.000 0.00 0.00 0.00 3.41
2511 3630 3.439857 TTTGACATTCTTCCCCCTCTG 57.560 47.619 0.00 0.00 0.00 3.35
2538 3688 1.101049 CCAATCCGCCGGCTTACAAT 61.101 55.000 26.68 7.46 0.00 2.71
2540 3690 1.615165 TACCAATCCGCCGGCTTACA 61.615 55.000 26.68 5.30 0.00 2.41
2542 3692 1.332144 ACTACCAATCCGCCGGCTTA 61.332 55.000 26.68 12.95 0.00 3.09
2578 3813 1.226974 GCTCGCGGTGATCAAGCTA 60.227 57.895 18.48 9.72 0.00 3.32
2694 3930 5.386958 ACTGTCGACTACTTTGCAGATAA 57.613 39.130 17.92 0.00 0.00 1.75
2903 4172 5.476599 ACACCATACATGCAGCTTTCTTTAA 59.523 36.000 0.00 0.00 0.00 1.52
2904 4173 5.009631 ACACCATACATGCAGCTTTCTTTA 58.990 37.500 0.00 0.00 0.00 1.85
2907 4176 2.751259 CACACCATACATGCAGCTTTCT 59.249 45.455 0.00 0.00 0.00 2.52
3071 4340 0.925267 CTGCACAACACGAAGCAACG 60.925 55.000 0.00 1.28 36.44 4.10
3100 4369 1.964373 GTGGTTGGCATCGTTCGGT 60.964 57.895 0.00 0.00 0.00 4.69
3120 4389 2.835701 ATCCGTGCTGTGGCGTAGTG 62.836 60.000 0.00 0.00 42.25 2.74
3121 4390 2.646175 ATCCGTGCTGTGGCGTAGT 61.646 57.895 0.00 0.00 42.25 2.73
3122 4391 2.167219 CATCCGTGCTGTGGCGTAG 61.167 63.158 0.00 0.00 42.25 3.51
3123 4392 2.125713 CATCCGTGCTGTGGCGTA 60.126 61.111 0.00 0.00 42.25 4.42
3133 4402 1.355005 TACATGTCGTTGCATCCGTG 58.645 50.000 0.00 1.24 0.00 4.94
3134 4403 2.309528 ATACATGTCGTTGCATCCGT 57.690 45.000 0.00 0.00 0.00 4.69
3135 4404 2.866156 AGAATACATGTCGTTGCATCCG 59.134 45.455 0.00 0.00 0.00 4.18
3136 4405 3.546815 GCAGAATACATGTCGTTGCATCC 60.547 47.826 0.00 0.00 0.00 3.51
3137 4406 3.546815 GGCAGAATACATGTCGTTGCATC 60.547 47.826 19.52 6.17 0.00 3.91
3138 4407 2.355756 GGCAGAATACATGTCGTTGCAT 59.644 45.455 19.52 0.00 0.00 3.96
3139 4408 1.737236 GGCAGAATACATGTCGTTGCA 59.263 47.619 19.52 0.00 0.00 4.08
3140 4409 1.267532 CGGCAGAATACATGTCGTTGC 60.268 52.381 0.00 8.73 40.74 4.17
3141 4410 1.327460 CCGGCAGAATACATGTCGTTG 59.673 52.381 0.00 0.00 43.99 4.10
3142 4411 1.651987 CCGGCAGAATACATGTCGTT 58.348 50.000 0.00 0.00 43.99 3.85
3143 4412 0.179084 CCCGGCAGAATACATGTCGT 60.179 55.000 0.00 0.00 43.99 4.34
3144 4413 0.104120 TCCCGGCAGAATACATGTCG 59.896 55.000 0.00 0.00 45.03 4.35


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

AutoCloner maintained by Alex Coulton.