Multiple sequence alignment - TraesCS5B01G066400

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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 TraesCS5B01G066400 chr5B 100.000 4379 0 0 1 4379 74632584 74636962 0.000000e+00 8087.0
1 TraesCS5B01G066400 chr5B 88.053 226 24 3 1 224 375721474 375721698 9.340000e-67 265.0
2 TraesCS5B01G066400 chr5B 92.045 88 5 2 4263 4348 22532645 22532732 5.950000e-24 122.0
3 TraesCS5B01G066400 chr5D 96.158 4060 119 22 224 4262 68692891 68696934 0.000000e+00 6599.0
4 TraesCS5B01G066400 chr5A 93.686 4023 166 38 224 4187 59595805 59599798 0.000000e+00 5941.0
5 TraesCS5B01G066400 chr3D 87.013 231 24 5 1 227 496064023 496063795 5.620000e-64 255.0
6 TraesCS5B01G066400 chr3D 76.549 226 45 7 3 226 216447826 216447607 2.770000e-22 117.0
7 TraesCS5B01G066400 chr2D 86.726 226 28 2 1 224 602659344 602659569 2.610000e-62 250.0
8 TraesCS5B01G066400 chr2A 81.463 205 29 8 8 208 765276072 765276271 4.530000e-35 159.0
9 TraesCS5B01G066400 chr4A 83.436 163 23 4 1039 1199 556537589 556537749 9.810000e-32 148.0
10 TraesCS5B01G066400 chr4A 90.217 92 7 2 4263 4352 549880564 549880473 7.690000e-23 119.0
11 TraesCS5B01G066400 chr3B 90.625 96 5 4 4263 4355 452283202 452283108 1.650000e-24 124.0
12 TraesCS5B01G066400 chrUn 76.991 226 40 6 1 224 401892187 401892402 7.690000e-23 119.0
13 TraesCS5B01G066400 chr6B 89.474 95 6 4 4262 4353 551188306 551188213 2.770000e-22 117.0
14 TraesCS5B01G066400 chr6B 89.474 95 6 4 4262 4353 551443324 551443231 2.770000e-22 117.0
15 TraesCS5B01G066400 chr6B 89.474 95 6 4 4262 4353 551542714 551542621 2.770000e-22 117.0
16 TraesCS5B01G066400 chr6B 89.474 95 6 4 4262 4353 551589803 551589710 2.770000e-22 117.0
17 TraesCS5B01G066400 chr6B 89.474 95 6 4 4262 4353 551665787 551665694 2.770000e-22 117.0
18 TraesCS5B01G066400 chr6A 89.474 95 7 3 4262 4354 169203396 169203303 2.770000e-22 117.0
19 TraesCS5B01G066400 chr4D 79.104 134 23 4 94 224 341688185 341688316 2.170000e-13 87.9
20 TraesCS5B01G066400 chr2B 75.956 183 34 5 42 224 107386016 107386188 7.800000e-13 86.1


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 TraesCS5B01G066400 chr5B 74632584 74636962 4378 False 8087 8087 100.000 1 4379 1 chr5B.!!$F2 4378
1 TraesCS5B01G066400 chr5D 68692891 68696934 4043 False 6599 6599 96.158 224 4262 1 chr5D.!!$F1 4038
2 TraesCS5B01G066400 chr5A 59595805 59599798 3993 False 5941 5941 93.686 224 4187 1 chr5A.!!$F1 3963

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
164 165 0.099791 CGTTGGGACGCTTTTTGTGT 59.900 50.000 0.00 0.00 43.03 3.72 F
175 176 0.237235 TTTTTGTGTCCGCGCTGATC 59.763 50.000 5.56 2.95 0.00 2.92 F
452 454 0.818296 CGATTCCACCCTCGAACTCT 59.182 55.000 0.00 0.00 37.05 3.24 F
1357 1369 1.228184 CTCCATCCCCATCTGCTGC 60.228 63.158 0.00 0.00 0.00 5.25 F
1553 1568 1.747355 CAGCAGAATTTACAGGCCCAG 59.253 52.381 0.00 0.00 0.00 4.45 F
2829 2859 1.329913 GCCGCCCCTTTTGATCCATT 61.330 55.000 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 1347 0.689623 GCAGATGGGGATGGAGTAGG 59.310 60.000 0.00 0.00 0.00 3.18 R
1337 1349 1.427809 CAGCAGATGGGGATGGAGTA 58.572 55.000 0.00 0.00 0.00 2.59 R
1838 1853 2.579873 AGAATCACAGCAGCACAGTTT 58.420 42.857 0.00 0.00 0.00 2.66 R
2821 2851 0.465460 GGCCTGGCGTTAATGGATCA 60.465 55.000 13.40 0.00 0.00 2.92 R
3214 3249 1.067495 GCTTTACACAGAGCTCCTCGT 60.067 52.381 10.93 7.42 35.36 4.18 R
4055 4112 0.315568 ATGCTACGAGATCTTCCCGC 59.684 55.000 0.00 0.00 0.00 6.13 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
30 31 4.348495 AGGCCCGGGGAAGGAGAA 62.348 66.667 25.28 0.00 0.00 2.87
31 32 3.798511 GGCCCGGGGAAGGAGAAG 61.799 72.222 25.28 0.00 0.00 2.85
32 33 3.798511 GCCCGGGGAAGGAGAAGG 61.799 72.222 25.28 0.00 0.00 3.46
33 34 3.798511 CCCGGGGAAGGAGAAGGC 61.799 72.222 14.71 0.00 0.00 4.35
34 35 4.162690 CCGGGGAAGGAGAAGGCG 62.163 72.222 0.00 0.00 0.00 5.52
35 36 3.075005 CGGGGAAGGAGAAGGCGA 61.075 66.667 0.00 0.00 0.00 5.54
36 37 2.904131 GGGGAAGGAGAAGGCGAG 59.096 66.667 0.00 0.00 0.00 5.03
37 38 1.990614 GGGGAAGGAGAAGGCGAGT 60.991 63.158 0.00 0.00 0.00 4.18
38 39 1.219393 GGGAAGGAGAAGGCGAGTG 59.781 63.158 0.00 0.00 0.00 3.51
39 40 1.545706 GGGAAGGAGAAGGCGAGTGT 61.546 60.000 0.00 0.00 0.00 3.55
40 41 0.390472 GGAAGGAGAAGGCGAGTGTG 60.390 60.000 0.00 0.00 0.00 3.82
41 42 1.004440 AAGGAGAAGGCGAGTGTGC 60.004 57.895 0.00 0.00 0.00 4.57
42 43 2.771763 AAGGAGAAGGCGAGTGTGCG 62.772 60.000 0.00 0.00 35.06 5.34
58 59 3.773630 CGCACGTCCGTCGCATTT 61.774 61.111 12.29 0.00 44.19 2.32
59 60 2.554272 GCACGTCCGTCGCATTTT 59.446 55.556 8.61 0.00 44.19 1.82
60 61 1.509162 GCACGTCCGTCGCATTTTC 60.509 57.895 8.61 0.00 44.19 2.29
61 62 1.225368 CACGTCCGTCGCATTTTCG 60.225 57.895 0.00 0.00 44.19 3.46
62 63 2.275812 CGTCCGTCGCATTTTCGC 60.276 61.111 0.00 0.00 0.00 4.70
70 71 2.869702 GCATTTTCGCGCCGACAC 60.870 61.111 0.00 0.00 34.89 3.67
71 72 2.553770 CATTTTCGCGCCGACACA 59.446 55.556 0.00 0.00 34.89 3.72
72 73 1.082431 CATTTTCGCGCCGACACAA 60.082 52.632 0.00 0.00 34.89 3.33
73 74 0.658829 CATTTTCGCGCCGACACAAA 60.659 50.000 0.00 1.17 34.89 2.83
74 75 0.239879 ATTTTCGCGCCGACACAAAT 59.760 45.000 0.00 3.50 34.89 2.32
75 76 0.384974 TTTTCGCGCCGACACAAATC 60.385 50.000 0.00 0.00 34.89 2.17
76 77 2.177654 TTTCGCGCCGACACAAATCC 62.178 55.000 0.00 0.00 34.89 3.01
77 78 4.499023 CGCGCCGACACAAATCCG 62.499 66.667 0.00 0.00 0.00 4.18
78 79 3.115892 GCGCCGACACAAATCCGA 61.116 61.111 0.00 0.00 0.00 4.55
79 80 2.776072 CGCCGACACAAATCCGAC 59.224 61.111 0.00 0.00 0.00 4.79
80 81 1.736645 CGCCGACACAAATCCGACT 60.737 57.895 0.00 0.00 0.00 4.18
81 82 0.457166 CGCCGACACAAATCCGACTA 60.457 55.000 0.00 0.00 0.00 2.59
82 83 1.717194 GCCGACACAAATCCGACTAA 58.283 50.000 0.00 0.00 0.00 2.24
83 84 1.659098 GCCGACACAAATCCGACTAAG 59.341 52.381 0.00 0.00 0.00 2.18
84 85 2.673043 GCCGACACAAATCCGACTAAGA 60.673 50.000 0.00 0.00 0.00 2.10
85 86 3.581755 CCGACACAAATCCGACTAAGAA 58.418 45.455 0.00 0.00 0.00 2.52
86 87 3.991773 CCGACACAAATCCGACTAAGAAA 59.008 43.478 0.00 0.00 0.00 2.52
87 88 4.630069 CCGACACAAATCCGACTAAGAAAT 59.370 41.667 0.00 0.00 0.00 2.17
88 89 5.808540 CCGACACAAATCCGACTAAGAAATA 59.191 40.000 0.00 0.00 0.00 1.40
89 90 6.019801 CCGACACAAATCCGACTAAGAAATAG 60.020 42.308 0.00 0.00 37.66 1.73
90 91 6.019801 CGACACAAATCCGACTAAGAAATAGG 60.020 42.308 0.00 0.00 35.81 2.57
91 92 6.708285 ACACAAATCCGACTAAGAAATAGGT 58.292 36.000 0.00 0.00 35.81 3.08
92 93 7.166167 ACACAAATCCGACTAAGAAATAGGTT 58.834 34.615 0.00 0.00 35.81 3.50
93 94 7.119262 ACACAAATCCGACTAAGAAATAGGTTG 59.881 37.037 0.00 0.00 35.81 3.77
94 95 6.093633 ACAAATCCGACTAAGAAATAGGTTGC 59.906 38.462 0.00 0.00 35.81 4.17
95 96 3.777478 TCCGACTAAGAAATAGGTTGCG 58.223 45.455 0.00 0.00 35.81 4.85
96 97 3.444742 TCCGACTAAGAAATAGGTTGCGA 59.555 43.478 0.00 0.00 35.81 5.10
97 98 4.082081 TCCGACTAAGAAATAGGTTGCGAA 60.082 41.667 0.00 0.00 35.81 4.70
98 99 4.809426 CCGACTAAGAAATAGGTTGCGAAT 59.191 41.667 0.00 0.00 35.81 3.34
99 100 5.276868 CCGACTAAGAAATAGGTTGCGAATG 60.277 44.000 0.00 0.00 35.81 2.67
100 101 5.518847 CGACTAAGAAATAGGTTGCGAATGA 59.481 40.000 0.00 0.00 35.81 2.57
101 102 6.291849 CGACTAAGAAATAGGTTGCGAATGAG 60.292 42.308 0.00 0.00 35.81 2.90
102 103 6.407202 ACTAAGAAATAGGTTGCGAATGAGT 58.593 36.000 0.00 0.00 35.81 3.41
103 104 5.803020 AAGAAATAGGTTGCGAATGAGTC 57.197 39.130 0.00 0.00 0.00 3.36
104 105 8.575720 ACTAAGAAATAGGTTGCGAATGAGTCG 61.576 40.741 0.00 0.00 43.34 4.18
112 113 4.508128 GAATGAGTCGCCCGCGGA 62.508 66.667 30.73 2.89 40.25 5.54
113 114 4.814294 AATGAGTCGCCCGCGGAC 62.814 66.667 30.73 16.23 40.25 4.79
137 138 2.549282 CGGAGCACGTTCGTTTGG 59.451 61.111 0.00 0.00 37.93 3.28
138 139 2.943653 GGAGCACGTTCGTTTGGG 59.056 61.111 0.00 0.00 0.00 4.12
139 140 1.890510 GGAGCACGTTCGTTTGGGT 60.891 57.895 0.00 0.00 0.00 4.51
140 141 1.568025 GAGCACGTTCGTTTGGGTC 59.432 57.895 0.00 0.00 0.00 4.46
141 142 2.154427 GAGCACGTTCGTTTGGGTCG 62.154 60.000 0.00 0.00 0.00 4.79
142 143 2.932905 CACGTTCGTTTGGGTCGG 59.067 61.111 0.00 0.00 0.00 4.79
143 144 2.968697 ACGTTCGTTTGGGTCGGC 60.969 61.111 0.00 0.00 0.00 5.54
144 145 4.067016 CGTTCGTTTGGGTCGGCG 62.067 66.667 0.00 0.00 0.00 6.46
145 146 4.379143 GTTCGTTTGGGTCGGCGC 62.379 66.667 0.00 0.00 0.00 6.53
149 150 4.676586 GTTTGGGTCGGCGCGTTG 62.677 66.667 8.43 0.00 0.00 4.10
163 164 2.866688 CGTTGGGACGCTTTTTGTG 58.133 52.632 0.00 0.00 43.03 3.33
164 165 0.099791 CGTTGGGACGCTTTTTGTGT 59.900 50.000 0.00 0.00 43.03 3.72
170 171 3.091022 CGCTTTTTGTGTCCGCGC 61.091 61.111 0.00 0.00 37.29 6.86
171 172 2.331451 GCTTTTTGTGTCCGCGCT 59.669 55.556 5.56 0.00 0.00 5.92
172 173 2.010817 GCTTTTTGTGTCCGCGCTG 61.011 57.895 5.56 0.00 0.00 5.18
173 174 1.646540 CTTTTTGTGTCCGCGCTGA 59.353 52.632 5.56 0.00 0.00 4.26
174 175 0.238289 CTTTTTGTGTCCGCGCTGAT 59.762 50.000 5.56 0.00 0.00 2.90
175 176 0.237235 TTTTTGTGTCCGCGCTGATC 59.763 50.000 5.56 2.95 0.00 2.92
176 177 1.573829 TTTTGTGTCCGCGCTGATCC 61.574 55.000 5.56 0.00 0.00 3.36
177 178 2.723586 TTTGTGTCCGCGCTGATCCA 62.724 55.000 5.56 2.40 0.00 3.41
178 179 2.434185 GTGTCCGCGCTGATCCAA 60.434 61.111 5.56 0.00 0.00 3.53
179 180 2.032634 GTGTCCGCGCTGATCCAAA 61.033 57.895 5.56 0.00 0.00 3.28
180 181 2.032634 TGTCCGCGCTGATCCAAAC 61.033 57.895 5.56 0.00 0.00 2.93
181 182 2.813474 TCCGCGCTGATCCAAACG 60.813 61.111 5.56 0.00 0.00 3.60
182 183 3.864686 CCGCGCTGATCCAAACGG 61.865 66.667 5.56 0.00 0.00 4.44
183 184 2.813474 CGCGCTGATCCAAACGGA 60.813 61.111 5.56 0.00 36.85 4.69
184 185 2.785258 GCGCTGATCCAAACGGAC 59.215 61.111 0.00 0.00 34.62 4.79
185 186 3.081133 CGCTGATCCAAACGGACG 58.919 61.111 0.00 0.00 34.62 4.79
186 187 2.452813 CGCTGATCCAAACGGACGG 61.453 63.158 0.00 0.00 34.62 4.79
187 188 1.375523 GCTGATCCAAACGGACGGT 60.376 57.895 0.00 0.00 34.62 4.83
188 189 1.635663 GCTGATCCAAACGGACGGTG 61.636 60.000 0.00 0.00 34.62 4.94
189 190 1.004320 TGATCCAAACGGACGGTGG 60.004 57.895 9.58 9.58 34.62 4.61
190 191 2.359478 ATCCAAACGGACGGTGGC 60.359 61.111 10.67 0.00 34.62 5.01
191 192 4.973055 TCCAAACGGACGGTGGCG 62.973 66.667 10.67 0.00 32.10 5.69
193 194 4.973055 CAAACGGACGGTGGCGGA 62.973 66.667 0.00 0.00 0.00 5.54
194 195 4.974989 AAACGGACGGTGGCGGAC 62.975 66.667 0.00 0.00 0.00 4.79
198 199 4.668118 GGACGGTGGCGGACGAAA 62.668 66.667 0.00 0.00 0.00 3.46
199 200 2.433664 GACGGTGGCGGACGAAAT 60.434 61.111 0.00 0.00 0.00 2.17
200 201 1.153784 GACGGTGGCGGACGAAATA 60.154 57.895 0.00 0.00 0.00 1.40
201 202 1.143969 GACGGTGGCGGACGAAATAG 61.144 60.000 0.00 0.00 0.00 1.73
202 203 1.881252 CGGTGGCGGACGAAATAGG 60.881 63.158 0.00 0.00 0.00 2.57
203 204 2.178235 GGTGGCGGACGAAATAGGC 61.178 63.158 0.00 0.00 0.00 3.93
204 205 2.178235 GTGGCGGACGAAATAGGCC 61.178 63.158 0.00 0.00 44.00 5.19
208 209 2.590859 GGACGAAATAGGCCGCCC 60.591 66.667 5.55 0.00 0.00 6.13
209 210 2.590859 GACGAAATAGGCCGCCCC 60.591 66.667 5.55 0.00 0.00 5.80
210 211 3.394635 GACGAAATAGGCCGCCCCA 62.395 63.158 5.55 0.00 35.39 4.96
211 212 2.113139 CGAAATAGGCCGCCCCAT 59.887 61.111 5.55 0.00 35.39 4.00
212 213 1.528309 CGAAATAGGCCGCCCCATT 60.528 57.895 5.55 3.27 35.39 3.16
213 214 1.795170 CGAAATAGGCCGCCCCATTG 61.795 60.000 5.55 0.00 35.39 2.82
214 215 1.457455 AAATAGGCCGCCCCATTGG 60.457 57.895 5.55 0.00 35.39 3.16
215 216 1.943730 AAATAGGCCGCCCCATTGGA 61.944 55.000 5.55 0.00 35.39 3.53
216 217 2.357593 AATAGGCCGCCCCATTGGAG 62.358 60.000 5.55 0.00 35.39 3.86
218 219 4.759205 GGCCGCCCCATTGGAGTT 62.759 66.667 3.62 0.00 35.39 3.01
219 220 3.451894 GCCGCCCCATTGGAGTTG 61.452 66.667 3.62 0.00 35.39 3.16
220 221 3.451894 CCGCCCCATTGGAGTTGC 61.452 66.667 3.62 0.53 35.39 4.17
221 222 2.361610 CGCCCCATTGGAGTTGCT 60.362 61.111 3.62 0.00 35.39 3.91
222 223 2.409870 CGCCCCATTGGAGTTGCTC 61.410 63.158 3.62 0.00 35.39 4.26
229 230 4.142093 CCCCATTGGAGTTGCTCTTATTTG 60.142 45.833 3.62 0.00 35.39 2.32
452 454 0.818296 CGATTCCACCCTCGAACTCT 59.182 55.000 0.00 0.00 37.05 3.24
999 1007 1.724082 GCTCTGCAAGAACGAGAAGAC 59.276 52.381 4.21 0.00 46.34 3.01
1012 1024 8.879342 AGAACGAGAAGACAGGATTATATTTG 57.121 34.615 0.00 0.00 0.00 2.32
1055 1067 1.997311 CATGGAGGAGGTGGAGGCA 60.997 63.158 0.00 0.00 0.00 4.75
1335 1347 1.448540 CTCATGTCCGGGAGTGCAC 60.449 63.158 9.40 9.40 0.00 4.57
1337 1349 2.607750 ATGTCCGGGAGTGCACCT 60.608 61.111 14.63 0.04 0.00 4.00
1357 1369 1.228184 CTCCATCCCCATCTGCTGC 60.228 63.158 0.00 0.00 0.00 5.25
1385 1397 4.974721 CAACTGCGGCCCCAGGTT 62.975 66.667 21.32 10.26 37.16 3.50
1553 1568 1.747355 CAGCAGAATTTACAGGCCCAG 59.253 52.381 0.00 0.00 0.00 4.45
1838 1853 6.707440 TGTCATTGCTCAAAAAGAAGGTAA 57.293 33.333 0.00 0.00 0.00 2.85
1843 1858 7.706179 TCATTGCTCAAAAAGAAGGTAAAACTG 59.294 33.333 0.00 0.00 0.00 3.16
1877 1892 8.414003 GTGATTCTTTTATAAGGGTTGGGAATC 58.586 37.037 0.00 0.00 37.84 2.52
1896 1911 3.354948 TCATGGTCTTGACCTGATTGG 57.645 47.619 19.11 4.59 42.93 3.16
1924 1939 6.627395 TTTCTTTTCTGCAGGAAATTACGA 57.373 33.333 20.49 11.38 42.63 3.43
2239 2257 3.317711 TGTGTTGCTTTACCTGTGGAATG 59.682 43.478 0.00 0.00 0.00 2.67
2588 2618 3.366781 GCTGCTGTTCCTCTTTCCAAATC 60.367 47.826 0.00 0.00 0.00 2.17
2611 2641 5.833667 TCTTTCTTGTCTCCACAGAAGACTA 59.166 40.000 5.03 0.00 32.71 2.59
2613 2643 5.455056 TCTTGTCTCCACAGAAGACTAAC 57.545 43.478 5.03 0.00 32.71 2.34
2614 2644 5.141182 TCTTGTCTCCACAGAAGACTAACT 58.859 41.667 5.03 0.00 32.71 2.24
2829 2859 1.329913 GCCGCCCCTTTTGATCCATT 61.330 55.000 0.00 0.00 0.00 3.16
2842 2872 2.640581 ATCCATTAACGCCAGGCCCC 62.641 60.000 5.63 0.00 0.00 5.80
3098 3132 7.119407 ACACATCAAATCAAACTGAGAGATGAG 59.881 37.037 16.24 12.76 36.85 2.90
3211 3246 4.179133 AGGGAGATTTGAAGAAAGGAGGA 58.821 43.478 0.00 0.00 0.00 3.71
3214 3249 5.280727 GGGAGATTTGAAGAAAGGAGGAGAA 60.281 44.000 0.00 0.00 0.00 2.87
3216 3251 5.241662 AGATTTGAAGAAAGGAGGAGAACG 58.758 41.667 0.00 0.00 0.00 3.95
3362 3397 5.650543 TGTTTTCTCTTTTGGCAGAAGAAC 58.349 37.500 19.51 15.10 33.10 3.01
3363 3398 5.184864 TGTTTTCTCTTTTGGCAGAAGAACA 59.815 36.000 19.51 17.14 33.10 3.18
3364 3399 6.127366 TGTTTTCTCTTTTGGCAGAAGAACAT 60.127 34.615 19.51 0.00 33.10 2.71
3365 3400 7.068103 TGTTTTCTCTTTTGGCAGAAGAACATA 59.932 33.333 19.51 5.16 33.10 2.29
3457 3497 3.689649 GGTGTAATAGGAAGTTGCTGTGG 59.310 47.826 7.22 0.00 0.00 4.17
3499 3539 2.507484 TCAGTGTGAAGCTTTCCATGG 58.493 47.619 4.97 4.97 0.00 3.66
3548 3588 1.212935 GTGCTATCATGGGTGGGTTCT 59.787 52.381 0.00 0.00 0.00 3.01
3582 3622 5.960811 TCTCTCTCTGGTCTGGACAATAATT 59.039 40.000 3.10 0.00 0.00 1.40
3646 3691 5.545063 TCTTCCCCAAGAAAATTGTTTCC 57.455 39.130 0.00 0.00 43.65 3.13
3649 3694 3.319689 TCCCCAAGAAAATTGTTTCCGTC 59.680 43.478 0.00 0.00 43.65 4.79
3664 3709 7.441890 TGTTTCCGTCATAAAAATCTAAGCA 57.558 32.000 0.00 0.00 0.00 3.91
3667 3712 7.441890 TTCCGTCATAAAAATCTAAGCACAA 57.558 32.000 0.00 0.00 0.00 3.33
3707 3761 8.837788 TCAAGATGAACTATGCCATACAATAG 57.162 34.615 0.00 0.00 0.00 1.73
3711 3765 7.875041 AGATGAACTATGCCATACAATAGTGTC 59.125 37.037 0.00 0.00 39.30 3.67
3731 3785 3.557595 GTCTTATCAGTGCTCCCAAATCG 59.442 47.826 0.00 0.00 0.00 3.34
3750 3804 3.571571 TCGTAACGAGAGGTTGACAATG 58.428 45.455 0.00 0.00 39.75 2.82
3861 3917 1.134098 CGTGTGGGGCAAAGGATCTAT 60.134 52.381 0.00 0.00 0.00 1.98
4055 4112 1.639298 CTCCCTCTTTTTGCGCGAGG 61.639 60.000 18.26 18.26 43.11 4.63
4129 4201 2.620115 AGCATCGGATTAGGCAAACATG 59.380 45.455 0.00 0.00 0.00 3.21
4187 4260 5.320277 AGAAGATTTAGCTTCAAGCAAGGT 58.680 37.500 13.10 0.00 45.56 3.50
4239 4312 6.394025 ACTGCCTCCGTTTGTTTTTATAAA 57.606 33.333 0.00 0.00 0.00 1.40
4241 4314 6.698329 ACTGCCTCCGTTTGTTTTTATAAAAC 59.302 34.615 10.18 7.83 0.00 2.43
4262 4335 2.223340 CGTTTCAGACAGCTTGCTTTGT 60.223 45.455 0.00 0.00 0.00 2.83
4263 4336 3.002246 CGTTTCAGACAGCTTGCTTTGTA 59.998 43.478 0.00 0.00 0.00 2.41
4264 4337 4.282873 GTTTCAGACAGCTTGCTTTGTAC 58.717 43.478 0.00 0.00 0.00 2.90
4265 4338 2.494059 TCAGACAGCTTGCTTTGTACC 58.506 47.619 0.00 0.00 0.00 3.34
4266 4339 1.537202 CAGACAGCTTGCTTTGTACCC 59.463 52.381 0.00 0.00 0.00 3.69
4267 4340 0.881796 GACAGCTTGCTTTGTACCCC 59.118 55.000 0.00 0.00 0.00 4.95
4268 4341 0.478507 ACAGCTTGCTTTGTACCCCT 59.521 50.000 0.00 0.00 0.00 4.79
4269 4342 1.168714 CAGCTTGCTTTGTACCCCTC 58.831 55.000 0.00 0.00 0.00 4.30
4270 4343 0.038310 AGCTTGCTTTGTACCCCTCC 59.962 55.000 0.00 0.00 0.00 4.30
4271 4344 1.305930 GCTTGCTTTGTACCCCTCCG 61.306 60.000 0.00 0.00 0.00 4.63
4272 4345 0.036306 CTTGCTTTGTACCCCTCCGT 59.964 55.000 0.00 0.00 0.00 4.69
4273 4346 0.475044 TTGCTTTGTACCCCTCCGTT 59.525 50.000 0.00 0.00 0.00 4.44
4274 4347 0.475044 TGCTTTGTACCCCTCCGTTT 59.525 50.000 0.00 0.00 0.00 3.60
4275 4348 1.162698 GCTTTGTACCCCTCCGTTTC 58.837 55.000 0.00 0.00 0.00 2.78
4276 4349 1.543871 GCTTTGTACCCCTCCGTTTCA 60.544 52.381 0.00 0.00 0.00 2.69
4277 4350 2.878526 GCTTTGTACCCCTCCGTTTCAT 60.879 50.000 0.00 0.00 0.00 2.57
4278 4351 3.620472 GCTTTGTACCCCTCCGTTTCATA 60.620 47.826 0.00 0.00 0.00 2.15
4279 4352 4.581868 CTTTGTACCCCTCCGTTTCATAA 58.418 43.478 0.00 0.00 0.00 1.90
4280 4353 4.847990 TTGTACCCCTCCGTTTCATAAT 57.152 40.909 0.00 0.00 0.00 1.28
4281 4354 4.145365 TGTACCCCTCCGTTTCATAATG 57.855 45.455 0.00 0.00 0.00 1.90
4282 4355 3.520317 TGTACCCCTCCGTTTCATAATGT 59.480 43.478 0.00 0.00 0.00 2.71
4283 4356 4.715792 TGTACCCCTCCGTTTCATAATGTA 59.284 41.667 0.00 0.00 0.00 2.29
4284 4357 4.847990 ACCCCTCCGTTTCATAATGTAA 57.152 40.909 0.00 0.00 0.00 2.41
4285 4358 4.777463 ACCCCTCCGTTTCATAATGTAAG 58.223 43.478 0.00 0.00 0.00 2.34
4286 4359 4.472108 ACCCCTCCGTTTCATAATGTAAGA 59.528 41.667 0.00 0.00 0.00 2.10
4287 4360 4.814771 CCCCTCCGTTTCATAATGTAAGAC 59.185 45.833 0.00 0.00 0.00 3.01
4288 4361 4.506654 CCCTCCGTTTCATAATGTAAGACG 59.493 45.833 0.00 0.00 0.00 4.18
4289 4362 5.107133 CCTCCGTTTCATAATGTAAGACGT 58.893 41.667 0.00 0.00 0.00 4.34
4290 4363 5.579511 CCTCCGTTTCATAATGTAAGACGTT 59.420 40.000 0.00 0.00 0.00 3.99
4291 4364 6.091713 CCTCCGTTTCATAATGTAAGACGTTT 59.908 38.462 0.00 0.00 0.00 3.60
4292 4365 7.360607 CCTCCGTTTCATAATGTAAGACGTTTT 60.361 37.037 0.00 0.00 0.00 2.43
4293 4366 7.863666 TCCGTTTCATAATGTAAGACGTTTTT 58.136 30.769 0.00 0.00 0.00 1.94
4338 4411 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
4339 4412 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
4340 4413 3.317149 CGTCTTACATTATGGGACGGAGA 59.683 47.826 20.50 4.50 43.69 3.71
4341 4414 4.202080 CGTCTTACATTATGGGACGGAGAA 60.202 45.833 20.50 0.00 43.69 2.87
4342 4415 5.290386 GTCTTACATTATGGGACGGAGAAG 58.710 45.833 0.00 0.00 0.00 2.85
4343 4416 4.960469 TCTTACATTATGGGACGGAGAAGT 59.040 41.667 0.00 0.00 0.00 3.01
4344 4417 6.040166 GTCTTACATTATGGGACGGAGAAGTA 59.960 42.308 0.00 0.00 0.00 2.24
4345 4418 4.667519 ACATTATGGGACGGAGAAGTAC 57.332 45.455 0.00 0.00 0.00 2.73
4346 4419 4.287552 ACATTATGGGACGGAGAAGTACT 58.712 43.478 0.00 0.00 0.00 2.73
4347 4420 5.452255 ACATTATGGGACGGAGAAGTACTA 58.548 41.667 0.00 0.00 0.00 1.82
4348 4421 6.075984 ACATTATGGGACGGAGAAGTACTAT 58.924 40.000 0.00 0.00 30.91 2.12
4349 4422 6.553852 ACATTATGGGACGGAGAAGTACTATT 59.446 38.462 0.00 0.00 28.73 1.73
4350 4423 7.070821 ACATTATGGGACGGAGAAGTACTATTT 59.929 37.037 0.00 0.00 28.73 1.40
4351 4424 5.952347 ATGGGACGGAGAAGTACTATTTT 57.048 39.130 0.00 0.00 0.00 1.82
4352 4425 8.537728 TTATGGGACGGAGAAGTACTATTTTA 57.462 34.615 0.00 0.00 28.73 1.52
4353 4426 6.855763 TGGGACGGAGAAGTACTATTTTAA 57.144 37.500 0.00 0.00 0.00 1.52
4354 4427 7.243604 TGGGACGGAGAAGTACTATTTTAAA 57.756 36.000 0.00 0.00 0.00 1.52
4355 4428 7.099120 TGGGACGGAGAAGTACTATTTTAAAC 58.901 38.462 0.00 0.00 0.00 2.01
4356 4429 7.099120 GGGACGGAGAAGTACTATTTTAAACA 58.901 38.462 0.00 0.00 0.00 2.83
4357 4430 7.277319 GGGACGGAGAAGTACTATTTTAAACAG 59.723 40.741 0.00 0.00 0.00 3.16
4358 4431 7.816513 GGACGGAGAAGTACTATTTTAAACAGT 59.183 37.037 0.00 0.00 0.00 3.55
4359 4432 8.530269 ACGGAGAAGTACTATTTTAAACAGTG 57.470 34.615 0.00 0.00 0.00 3.66
4360 4433 8.146412 ACGGAGAAGTACTATTTTAAACAGTGT 58.854 33.333 0.00 0.00 0.00 3.55
4361 4434 8.985805 CGGAGAAGTACTATTTTAAACAGTGTT 58.014 33.333 1.64 1.64 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.348495 TTCTCCTTCCCCGGGCCT 62.348 66.667 17.73 0.00 0.00 5.19
14 15 3.798511 CTTCTCCTTCCCCGGGCC 61.799 72.222 17.73 0.00 0.00 5.80
15 16 3.798511 CCTTCTCCTTCCCCGGGC 61.799 72.222 17.73 0.00 0.00 6.13
16 17 3.798511 GCCTTCTCCTTCCCCGGG 61.799 72.222 15.80 15.80 0.00 5.73
17 18 4.162690 CGCCTTCTCCTTCCCCGG 62.163 72.222 0.00 0.00 0.00 5.73
18 19 3.075005 TCGCCTTCTCCTTCCCCG 61.075 66.667 0.00 0.00 0.00 5.73
19 20 1.990614 ACTCGCCTTCTCCTTCCCC 60.991 63.158 0.00 0.00 0.00 4.81
20 21 1.219393 CACTCGCCTTCTCCTTCCC 59.781 63.158 0.00 0.00 0.00 3.97
21 22 0.390472 CACACTCGCCTTCTCCTTCC 60.390 60.000 0.00 0.00 0.00 3.46
22 23 1.016653 GCACACTCGCCTTCTCCTTC 61.017 60.000 0.00 0.00 0.00 3.46
23 24 1.004440 GCACACTCGCCTTCTCCTT 60.004 57.895 0.00 0.00 0.00 3.36
24 25 2.659610 GCACACTCGCCTTCTCCT 59.340 61.111 0.00 0.00 0.00 3.69
25 26 2.811317 CGCACACTCGCCTTCTCC 60.811 66.667 0.00 0.00 0.00 3.71
41 42 3.289816 AAAATGCGACGGACGTGCG 62.290 57.895 28.33 28.33 44.60 5.34
42 43 1.509162 GAAAATGCGACGGACGTGC 60.509 57.895 0.53 7.17 44.60 5.34
43 44 1.225368 CGAAAATGCGACGGACGTG 60.225 57.895 0.53 0.00 44.60 4.49
44 45 3.007070 GCGAAAATGCGACGGACGT 62.007 57.895 0.00 0.00 44.60 4.34
45 46 2.275812 GCGAAAATGCGACGGACG 60.276 61.111 0.00 0.00 45.66 4.79
53 54 2.869702 GTGTCGGCGCGAAAATGC 60.870 61.111 12.10 0.00 37.72 3.56
54 55 0.658829 TTTGTGTCGGCGCGAAAATG 60.659 50.000 12.10 0.00 37.72 2.32
55 56 0.239879 ATTTGTGTCGGCGCGAAAAT 59.760 45.000 12.10 0.01 37.72 1.82
56 57 0.384974 GATTTGTGTCGGCGCGAAAA 60.385 50.000 12.10 0.00 37.72 2.29
57 58 1.205568 GATTTGTGTCGGCGCGAAA 59.794 52.632 12.10 4.13 37.72 3.46
58 59 2.673114 GGATTTGTGTCGGCGCGAA 61.673 57.895 12.10 5.58 37.72 4.70
59 60 3.115892 GGATTTGTGTCGGCGCGA 61.116 61.111 12.10 0.00 0.00 5.87
60 61 4.499023 CGGATTTGTGTCGGCGCG 62.499 66.667 0.00 0.00 0.00 6.86
61 62 3.115892 TCGGATTTGTGTCGGCGC 61.116 61.111 0.00 0.00 0.00 6.53
62 63 0.457166 TAGTCGGATTTGTGTCGGCG 60.457 55.000 0.00 0.00 33.41 6.46
63 64 1.659098 CTTAGTCGGATTTGTGTCGGC 59.341 52.381 0.00 0.00 0.00 5.54
64 65 3.226346 TCTTAGTCGGATTTGTGTCGG 57.774 47.619 0.00 0.00 0.00 4.79
65 66 5.779806 ATTTCTTAGTCGGATTTGTGTCG 57.220 39.130 0.00 0.00 0.00 4.35
66 67 6.817140 ACCTATTTCTTAGTCGGATTTGTGTC 59.183 38.462 0.00 0.00 0.00 3.67
67 68 6.708285 ACCTATTTCTTAGTCGGATTTGTGT 58.292 36.000 0.00 0.00 0.00 3.72
68 69 7.464358 CAACCTATTTCTTAGTCGGATTTGTG 58.536 38.462 0.00 0.00 0.00 3.33
69 70 6.093633 GCAACCTATTTCTTAGTCGGATTTGT 59.906 38.462 0.00 0.00 0.00 2.83
70 71 6.487103 GCAACCTATTTCTTAGTCGGATTTG 58.513 40.000 0.00 0.00 0.00 2.32
71 72 5.293569 CGCAACCTATTTCTTAGTCGGATTT 59.706 40.000 0.00 0.00 0.00 2.17
72 73 4.809426 CGCAACCTATTTCTTAGTCGGATT 59.191 41.667 0.00 0.00 0.00 3.01
73 74 4.098960 TCGCAACCTATTTCTTAGTCGGAT 59.901 41.667 0.00 0.00 0.00 4.18
74 75 3.444742 TCGCAACCTATTTCTTAGTCGGA 59.555 43.478 0.00 0.00 0.00 4.55
75 76 3.777478 TCGCAACCTATTTCTTAGTCGG 58.223 45.455 0.00 0.00 0.00 4.79
76 77 5.518847 TCATTCGCAACCTATTTCTTAGTCG 59.481 40.000 0.00 0.00 0.00 4.18
77 78 6.535508 ACTCATTCGCAACCTATTTCTTAGTC 59.464 38.462 0.00 0.00 0.00 2.59
78 79 6.407202 ACTCATTCGCAACCTATTTCTTAGT 58.593 36.000 0.00 0.00 0.00 2.24
79 80 6.291849 CGACTCATTCGCAACCTATTTCTTAG 60.292 42.308 0.00 0.00 41.87 2.18
80 81 5.518847 CGACTCATTCGCAACCTATTTCTTA 59.481 40.000 0.00 0.00 41.87 2.10
81 82 4.330074 CGACTCATTCGCAACCTATTTCTT 59.670 41.667 0.00 0.00 41.87 2.52
82 83 3.865745 CGACTCATTCGCAACCTATTTCT 59.134 43.478 0.00 0.00 41.87 2.52
83 84 4.183539 CGACTCATTCGCAACCTATTTC 57.816 45.455 0.00 0.00 41.87 2.17
95 96 4.508128 TCCGCGGGCGACTCATTC 62.508 66.667 27.83 0.00 42.83 2.67
96 97 4.814294 GTCCGCGGGCGACTCATT 62.814 66.667 27.83 0.00 42.83 2.57
107 108 3.838795 CTCCGCTTTTCGTCCGCG 61.839 66.667 0.00 0.00 45.86 6.46
108 109 4.148645 GCTCCGCTTTTCGTCCGC 62.149 66.667 0.00 0.00 36.19 5.54
109 110 2.736995 TGCTCCGCTTTTCGTCCG 60.737 61.111 0.00 0.00 36.19 4.79
110 111 2.861006 GTGCTCCGCTTTTCGTCC 59.139 61.111 0.00 0.00 36.19 4.79
111 112 1.828331 AACGTGCTCCGCTTTTCGTC 61.828 55.000 0.00 0.00 41.42 4.20
112 113 1.828331 GAACGTGCTCCGCTTTTCGT 61.828 55.000 0.00 0.00 41.42 3.85
113 114 1.154654 GAACGTGCTCCGCTTTTCG 60.155 57.895 0.00 0.00 41.42 3.46
114 115 1.154654 CGAACGTGCTCCGCTTTTC 60.155 57.895 0.00 0.00 41.42 2.29
115 116 1.433837 AACGAACGTGCTCCGCTTTT 61.434 50.000 0.00 0.00 41.42 2.27
116 117 1.433837 AAACGAACGTGCTCCGCTTT 61.434 50.000 0.00 0.00 41.42 3.51
117 118 1.885850 AAACGAACGTGCTCCGCTT 60.886 52.632 0.00 0.00 41.42 4.68
118 119 2.279918 AAACGAACGTGCTCCGCT 60.280 55.556 0.00 0.00 41.42 5.52
119 120 2.127758 CAAACGAACGTGCTCCGC 60.128 61.111 0.00 0.00 41.42 5.54
120 121 2.549282 CCAAACGAACGTGCTCCG 59.451 61.111 0.00 0.00 44.03 4.63
121 122 1.838568 GACCCAAACGAACGTGCTCC 61.839 60.000 0.00 0.00 0.00 4.70
122 123 1.568025 GACCCAAACGAACGTGCTC 59.432 57.895 0.00 0.00 0.00 4.26
123 124 2.241880 CGACCCAAACGAACGTGCT 61.242 57.895 0.00 0.00 0.00 4.40
124 125 2.247267 CGACCCAAACGAACGTGC 59.753 61.111 0.00 0.00 0.00 5.34
125 126 2.932905 CCGACCCAAACGAACGTG 59.067 61.111 0.00 0.00 0.00 4.49
126 127 2.968697 GCCGACCCAAACGAACGT 60.969 61.111 0.00 0.00 0.00 3.99
127 128 4.067016 CGCCGACCCAAACGAACG 62.067 66.667 0.00 0.00 0.00 3.95
128 129 4.379143 GCGCCGACCCAAACGAAC 62.379 66.667 0.00 0.00 0.00 3.95
132 133 4.676586 CAACGCGCCGACCCAAAC 62.677 66.667 5.73 0.00 0.00 2.93
146 147 1.535226 GGACACAAAAAGCGTCCCAAC 60.535 52.381 0.00 0.00 42.47 3.77
147 148 0.741915 GGACACAAAAAGCGTCCCAA 59.258 50.000 0.00 0.00 42.47 4.12
148 149 1.440938 CGGACACAAAAAGCGTCCCA 61.441 55.000 0.00 0.00 44.88 4.37
149 150 1.281656 CGGACACAAAAAGCGTCCC 59.718 57.895 0.00 0.00 44.88 4.46
150 151 1.370051 GCGGACACAAAAAGCGTCC 60.370 57.895 0.00 0.00 44.37 4.79
151 152 1.721133 CGCGGACACAAAAAGCGTC 60.721 57.895 0.00 0.00 44.96 5.19
152 153 2.326550 CGCGGACACAAAAAGCGT 59.673 55.556 0.00 0.00 44.96 5.07
154 155 2.010817 CAGCGCGGACACAAAAAGC 61.011 57.895 8.83 0.00 0.00 3.51
155 156 0.238289 ATCAGCGCGGACACAAAAAG 59.762 50.000 13.72 0.00 0.00 2.27
156 157 0.237235 GATCAGCGCGGACACAAAAA 59.763 50.000 13.72 0.00 0.00 1.94
157 158 1.573829 GGATCAGCGCGGACACAAAA 61.574 55.000 13.72 0.00 0.00 2.44
158 159 2.032634 GGATCAGCGCGGACACAAA 61.033 57.895 13.72 0.00 0.00 2.83
159 160 2.434185 GGATCAGCGCGGACACAA 60.434 61.111 13.72 0.00 0.00 3.33
160 161 2.723586 TTTGGATCAGCGCGGACACA 62.724 55.000 13.72 12.08 0.00 3.72
161 162 2.032634 TTTGGATCAGCGCGGACAC 61.033 57.895 13.72 9.37 0.00 3.67
162 163 2.032634 GTTTGGATCAGCGCGGACA 61.033 57.895 13.72 4.36 0.00 4.02
163 164 2.785258 GTTTGGATCAGCGCGGAC 59.215 61.111 13.72 6.98 0.00 4.79
164 165 2.813474 CGTTTGGATCAGCGCGGA 60.813 61.111 13.82 13.82 0.00 5.54
165 166 3.864686 CCGTTTGGATCAGCGCGG 61.865 66.667 8.83 0.00 37.49 6.46
166 167 2.813474 TCCGTTTGGATCAGCGCG 60.813 61.111 0.00 0.00 40.17 6.86
174 175 4.973055 CGCCACCGTCCGTTTGGA 62.973 66.667 8.35 0.00 43.88 3.53
176 177 4.973055 TCCGCCACCGTCCGTTTG 62.973 66.667 0.00 0.00 0.00 2.93
177 178 4.974989 GTCCGCCACCGTCCGTTT 62.975 66.667 0.00 0.00 0.00 3.60
181 182 2.561549 TATTTCGTCCGCCACCGTCC 62.562 60.000 0.00 0.00 0.00 4.79
182 183 1.143969 CTATTTCGTCCGCCACCGTC 61.144 60.000 0.00 0.00 0.00 4.79
183 184 1.153706 CTATTTCGTCCGCCACCGT 60.154 57.895 0.00 0.00 0.00 4.83
184 185 1.881252 CCTATTTCGTCCGCCACCG 60.881 63.158 0.00 0.00 0.00 4.94
185 186 2.178235 GCCTATTTCGTCCGCCACC 61.178 63.158 0.00 0.00 0.00 4.61
186 187 2.178235 GGCCTATTTCGTCCGCCAC 61.178 63.158 0.00 0.00 39.50 5.01
187 188 2.188469 GGCCTATTTCGTCCGCCA 59.812 61.111 0.00 0.00 39.50 5.69
188 189 2.965462 CGGCCTATTTCGTCCGCC 60.965 66.667 0.00 0.00 35.20 6.13
190 191 2.965462 GGCGGCCTATTTCGTCCG 60.965 66.667 12.87 0.00 44.29 4.79
191 192 2.590859 GGGCGGCCTATTTCGTCC 60.591 66.667 22.87 0.00 43.99 4.79
192 193 2.590859 GGGGCGGCCTATTTCGTC 60.591 66.667 28.80 4.21 0.00 4.20
193 194 2.279037 AATGGGGCGGCCTATTTCGT 62.279 55.000 30.35 11.93 0.00 3.85
194 195 1.528309 AATGGGGCGGCCTATTTCG 60.528 57.895 30.35 0.00 0.00 3.46
195 196 1.463553 CCAATGGGGCGGCCTATTTC 61.464 60.000 32.81 15.10 0.00 2.17
196 197 1.457455 CCAATGGGGCGGCCTATTT 60.457 57.895 32.81 18.62 0.00 1.40
197 198 2.198426 CCAATGGGGCGGCCTATT 59.802 61.111 30.35 30.35 0.00 1.73
198 199 2.776526 TCCAATGGGGCGGCCTAT 60.777 61.111 28.80 25.32 36.21 2.57
199 200 3.488569 CTCCAATGGGGCGGCCTA 61.489 66.667 28.80 23.99 36.21 3.93
201 202 4.759205 AACTCCAATGGGGCGGCC 62.759 66.667 22.00 22.00 36.21 6.13
202 203 3.451894 CAACTCCAATGGGGCGGC 61.452 66.667 0.00 0.00 36.21 6.53
203 204 3.451894 GCAACTCCAATGGGGCGG 61.452 66.667 0.00 0.00 36.21 6.13
204 205 2.361610 AGCAACTCCAATGGGGCG 60.362 61.111 0.00 0.00 36.21 6.13
205 206 0.613012 AAGAGCAACTCCAATGGGGC 60.613 55.000 0.00 0.00 36.21 5.80
206 207 2.806945 TAAGAGCAACTCCAATGGGG 57.193 50.000 0.00 0.00 38.37 4.96
207 208 4.463891 ACAAATAAGAGCAACTCCAATGGG 59.536 41.667 0.00 0.00 0.00 4.00
208 209 5.649782 ACAAATAAGAGCAACTCCAATGG 57.350 39.130 0.00 0.00 0.00 3.16
209 210 6.095377 GGAACAAATAAGAGCAACTCCAATG 58.905 40.000 0.00 0.00 0.00 2.82
210 211 5.774690 TGGAACAAATAAGAGCAACTCCAAT 59.225 36.000 0.00 0.00 31.92 3.16
211 212 5.136828 TGGAACAAATAAGAGCAACTCCAA 58.863 37.500 0.00 0.00 31.92 3.53
212 213 4.724399 TGGAACAAATAAGAGCAACTCCA 58.276 39.130 0.00 0.00 31.92 3.86
355 357 2.841988 GTTGCTTTGGGTGGGGCA 60.842 61.111 0.00 0.00 0.00 5.36
672 680 3.373565 GGGAAAGCACCGGCCAAG 61.374 66.667 0.00 0.00 42.56 3.61
828 836 3.496507 CGCAAAACACCAAATTTTAGGGG 59.503 43.478 0.00 0.00 0.00 4.79
832 840 4.669318 TCGTCGCAAAACACCAAATTTTA 58.331 34.783 0.00 0.00 0.00 1.52
901 909 7.181845 ACCTGAGAGAGAAGGAAGATACAAATT 59.818 37.037 0.00 0.00 37.01 1.82
916 924 1.005332 CCCTCACTGACCTGAGAGAGA 59.995 57.143 0.00 0.00 40.28 3.10
917 925 1.473258 CCCTCACTGACCTGAGAGAG 58.527 60.000 0.00 0.00 40.28 3.20
1012 1024 5.667156 GCGCAAGAAAAATCAATTGAGAAGC 60.667 40.000 14.54 7.99 43.02 3.86
1335 1347 0.689623 GCAGATGGGGATGGAGTAGG 59.310 60.000 0.00 0.00 0.00 3.18
1337 1349 1.427809 CAGCAGATGGGGATGGAGTA 58.572 55.000 0.00 0.00 0.00 2.59
1553 1568 3.188048 CACTGTTGCTCCTCTTGAACATC 59.812 47.826 0.00 0.00 0.00 3.06
1838 1853 2.579873 AGAATCACAGCAGCACAGTTT 58.420 42.857 0.00 0.00 0.00 2.66
1843 1858 6.261118 CCTTATAAAAGAATCACAGCAGCAC 58.739 40.000 0.00 0.00 34.37 4.40
1924 1939 5.589050 GGGCACTTTAATCGACCTCTTAATT 59.411 40.000 0.00 0.00 0.00 1.40
2058 2073 9.899661 ACATATTTTAAGCAGATAGTTGGTGTA 57.100 29.630 0.00 0.00 0.00 2.90
2060 2075 8.131100 CCACATATTTTAAGCAGATAGTTGGTG 58.869 37.037 0.00 0.00 0.00 4.17
2102 2118 5.722021 AGTGTTATTTTGACCAATGTCCC 57.278 39.130 0.00 0.00 41.01 4.46
2588 2618 4.954875 AGTCTTCTGTGGAGACAAGAAAG 58.045 43.478 8.51 0.00 46.06 2.62
2611 2641 0.738389 CAAGTGAACGGCCACAAGTT 59.262 50.000 2.24 0.00 39.42 2.66
2613 2643 1.021202 TTCAAGTGAACGGCCACAAG 58.979 50.000 2.24 0.00 39.42 3.16
2614 2644 0.736053 GTTCAAGTGAACGGCCACAA 59.264 50.000 2.24 0.00 43.97 3.33
2639 2669 3.244561 GCTGCATTTATAGTAGCCCCTGA 60.245 47.826 0.00 0.00 38.55 3.86
2821 2851 0.465460 GGCCTGGCGTTAATGGATCA 60.465 55.000 13.40 0.00 0.00 2.92
2842 2872 2.159572 CCGTATCTTCAAACAAAGGCCG 60.160 50.000 0.00 0.00 0.00 6.13
3098 3132 2.425143 TGCATGTTCTTCCCTCCATC 57.575 50.000 0.00 0.00 0.00 3.51
3163 3198 3.809905 ACTCTTTCAAACACACTCCCTC 58.190 45.455 0.00 0.00 0.00 4.30
3211 3246 2.201921 TACACAGAGCTCCTCGTTCT 57.798 50.000 10.93 0.00 35.36 3.01
3214 3249 1.067495 GCTTTACACAGAGCTCCTCGT 60.067 52.381 10.93 7.42 35.36 4.18
3362 3397 5.536161 CCACCACCTTTAATCCTGGAATATG 59.464 44.000 0.00 0.00 0.00 1.78
3363 3398 5.195756 ACCACCACCTTTAATCCTGGAATAT 59.804 40.000 0.00 0.00 0.00 1.28
3364 3399 4.542525 ACCACCACCTTTAATCCTGGAATA 59.457 41.667 0.00 0.00 0.00 1.75
3365 3400 3.336694 ACCACCACCTTTAATCCTGGAAT 59.663 43.478 0.00 0.00 0.00 3.01
3457 3497 5.008019 TGAAGTTGAAGCATGACTGAGAAAC 59.992 40.000 0.00 0.00 0.00 2.78
3499 3539 5.470368 TCATGTCAAAGTCACTACTGCTAC 58.530 41.667 0.00 0.00 35.62 3.58
3616 3656 5.592587 TTTTCTTGGGGAAGAACTGGATA 57.407 39.130 0.00 0.00 38.41 2.59
3617 3657 4.469469 TTTTCTTGGGGAAGAACTGGAT 57.531 40.909 0.00 0.00 38.41 3.41
3664 3709 6.409524 TCTTGAATTTTCCTGAGCAATTGT 57.590 33.333 7.40 0.00 0.00 2.71
3667 3712 6.845758 TCATCTTGAATTTTCCTGAGCAAT 57.154 33.333 0.00 0.00 0.00 3.56
3707 3761 3.334583 TTGGGAGCACTGATAAGACAC 57.665 47.619 0.00 0.00 0.00 3.67
3711 3765 3.535561 ACGATTTGGGAGCACTGATAAG 58.464 45.455 0.00 0.00 0.00 1.73
3731 3785 3.921677 TCCATTGTCAACCTCTCGTTAC 58.078 45.455 0.00 0.00 31.77 2.50
3750 3804 1.137404 GCATCATGTGGCGTGTTCC 59.863 57.895 0.00 0.00 0.00 3.62
3861 3917 1.973281 GGCTAGGTGCTGCTTTGCA 60.973 57.895 0.00 0.00 42.39 4.08
4055 4112 0.315568 ATGCTACGAGATCTTCCCGC 59.684 55.000 0.00 0.00 0.00 6.13
4058 4115 6.425504 CAAATGAAATGCTACGAGATCTTCC 58.574 40.000 0.00 0.00 0.00 3.46
4129 4201 1.796459 CCACACACAAAGTAGCGTACC 59.204 52.381 0.00 0.00 0.00 3.34
4187 4260 4.397103 CCTTGCTTGCAAGTCAGAATATGA 59.603 41.667 26.55 8.24 34.79 2.15
4219 4292 6.131137 CGTTTTATAAAAACAAACGGAGGC 57.869 37.500 12.14 0.00 45.72 4.70
4239 4312 1.668419 AGCAAGCTGTCTGAAACGTT 58.332 45.000 0.00 0.00 0.00 3.99
4241 4314 2.223340 ACAAAGCAAGCTGTCTGAAACG 60.223 45.455 0.00 0.00 0.00 3.60
4262 4335 5.662208 TCTTACATTATGAAACGGAGGGGTA 59.338 40.000 0.00 0.00 0.00 3.69
4263 4336 4.472108 TCTTACATTATGAAACGGAGGGGT 59.528 41.667 0.00 0.00 0.00 4.95
4264 4337 4.814771 GTCTTACATTATGAAACGGAGGGG 59.185 45.833 0.00 0.00 0.00 4.79
4265 4338 4.506654 CGTCTTACATTATGAAACGGAGGG 59.493 45.833 0.00 0.00 0.00 4.30
4266 4339 5.107133 ACGTCTTACATTATGAAACGGAGG 58.893 41.667 0.00 0.00 0.00 4.30
4267 4340 6.642683 AACGTCTTACATTATGAAACGGAG 57.357 37.500 0.00 0.00 0.00 4.63
4268 4341 7.424227 AAAACGTCTTACATTATGAAACGGA 57.576 32.000 0.00 0.00 0.00 4.69
4313 4386 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
4314 4387 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
4315 4388 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
4316 4389 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
4317 4390 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
4319 4392 4.931661 TCTCCGTCCCATAATGTAAGAC 57.068 45.455 0.00 0.00 0.00 3.01
4320 4393 4.960469 ACTTCTCCGTCCCATAATGTAAGA 59.040 41.667 0.00 0.00 0.00 2.10
4321 4394 5.277857 ACTTCTCCGTCCCATAATGTAAG 57.722 43.478 0.00 0.00 0.00 2.34
4322 4395 5.895534 AGTACTTCTCCGTCCCATAATGTAA 59.104 40.000 0.00 0.00 0.00 2.41
4323 4396 5.452255 AGTACTTCTCCGTCCCATAATGTA 58.548 41.667 0.00 0.00 0.00 2.29
4324 4397 4.287552 AGTACTTCTCCGTCCCATAATGT 58.712 43.478 0.00 0.00 0.00 2.71
4325 4398 4.939052 AGTACTTCTCCGTCCCATAATG 57.061 45.455 0.00 0.00 0.00 1.90
4326 4399 7.613551 AAATAGTACTTCTCCGTCCCATAAT 57.386 36.000 0.00 0.00 0.00 1.28
4327 4400 7.427989 AAAATAGTACTTCTCCGTCCCATAA 57.572 36.000 0.00 0.00 0.00 1.90
4328 4401 8.537728 TTAAAATAGTACTTCTCCGTCCCATA 57.462 34.615 0.00 0.00 0.00 2.74
4329 4402 5.952347 AAAATAGTACTTCTCCGTCCCAT 57.048 39.130 0.00 0.00 0.00 4.00
4330 4403 6.855763 TTAAAATAGTACTTCTCCGTCCCA 57.144 37.500 0.00 0.00 0.00 4.37
4331 4404 7.099120 TGTTTAAAATAGTACTTCTCCGTCCC 58.901 38.462 0.00 0.00 0.00 4.46
4332 4405 7.816513 ACTGTTTAAAATAGTACTTCTCCGTCC 59.183 37.037 0.00 0.00 30.51 4.79
4333 4406 8.645487 CACTGTTTAAAATAGTACTTCTCCGTC 58.355 37.037 0.00 0.00 31.17 4.79
4334 4407 8.146412 ACACTGTTTAAAATAGTACTTCTCCGT 58.854 33.333 0.00 0.00 31.17 4.69
4335 4408 8.530269 ACACTGTTTAAAATAGTACTTCTCCG 57.470 34.615 0.00 0.00 31.17 4.63


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

AutoCloner maintained by Alex Coulton.