Multiple sequence alignment - TraesCS5B01G436200

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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 TraesCS5B01G436200 chr5B 100.000 2731 0 0 1 2731 610105394 610102664 0.000000e+00 5044
1 TraesCS5B01G436200 chr5B 95.012 2025 66 14 722 2731 517548853 517550857 0.000000e+00 3147
2 TraesCS5B01G436200 chr6B 95.891 2020 68 4 724 2731 672722226 672720210 0.000000e+00 3256
3 TraesCS5B01G436200 chr6B 95.842 2020 68 5 724 2731 672700398 672698383 0.000000e+00 3251
4 TraesCS5B01G436200 chr6B 95.391 2018 60 14 726 2731 17983514 17981518 0.000000e+00 3181
5 TraesCS5B01G436200 chr6B 92.169 945 35 11 1819 2731 704786744 704785807 0.000000e+00 1299
6 TraesCS5B01G436200 chr6B 94.917 787 27 2 1957 2731 40666279 40665494 0.000000e+00 1219
7 TraesCS5B01G436200 chr2B 95.682 2038 54 6 726 2731 800268249 800270284 0.000000e+00 3245
8 TraesCS5B01G436200 chr2B 94.494 2034 66 21 723 2731 4108413 4106401 0.000000e+00 3094
9 TraesCS5B01G436200 chr2B 94.453 2019 76 6 726 2731 155561584 155559589 0.000000e+00 3075
10 TraesCS5B01G436200 chr2B 94.297 2034 70 21 723 2731 4373261 4371249 0.000000e+00 3072
11 TraesCS5B01G436200 chr2B 94.251 2035 70 22 723 2731 4279863 4277850 0.000000e+00 3066
12 TraesCS5B01G436200 chr2B 95.575 791 21 3 1953 2731 43364791 43364003 0.000000e+00 1254
13 TraesCS5B01G436200 chr7B 95.441 2018 71 9 726 2731 646618097 646620105 0.000000e+00 3197
14 TraesCS5B01G436200 chr7B 95.394 2019 58 6 725 2731 677060107 677062102 0.000000e+00 3181
15 TraesCS5B01G436200 chr7B 91.658 947 42 12 1819 2731 732848915 732849858 0.000000e+00 1277
16 TraesCS5B01G436200 chr7B 91.447 947 44 12 1819 2731 732798657 732799600 0.000000e+00 1266
17 TraesCS5B01G436200 chr3B 95.094 2018 61 16 726 2731 789620988 789618997 0.000000e+00 3144
18 TraesCS5B01G436200 chr3B 94.483 2030 64 17 725 2731 803032234 803034238 0.000000e+00 3085
19 TraesCS5B01G436200 chr5A 82.073 714 92 20 1 698 617079987 617079294 6.560000e-161 577
20 TraesCS5B01G436200 chr5D 83.333 630 67 24 1 624 493937521 493938118 5.140000e-152 547
21 TraesCS5B01G436200 chr1B 80.808 396 70 3 9 398 658623649 658624044 3.420000e-79 305
22 TraesCS5B01G436200 chr4D 79.638 221 36 6 169 383 488705575 488705792 1.690000e-32 150


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 TraesCS5B01G436200 chr5B 610102664 610105394 2730 True 5044 5044 100.000 1 2731 1 chr5B.!!$R1 2730
1 TraesCS5B01G436200 chr5B 517548853 517550857 2004 False 3147 3147 95.012 722 2731 1 chr5B.!!$F1 2009
2 TraesCS5B01G436200 chr6B 672720210 672722226 2016 True 3256 3256 95.891 724 2731 1 chr6B.!!$R4 2007
3 TraesCS5B01G436200 chr6B 672698383 672700398 2015 True 3251 3251 95.842 724 2731 1 chr6B.!!$R3 2007
4 TraesCS5B01G436200 chr6B 17981518 17983514 1996 True 3181 3181 95.391 726 2731 1 chr6B.!!$R1 2005
5 TraesCS5B01G436200 chr6B 704785807 704786744 937 True 1299 1299 92.169 1819 2731 1 chr6B.!!$R5 912
6 TraesCS5B01G436200 chr6B 40665494 40666279 785 True 1219 1219 94.917 1957 2731 1 chr6B.!!$R2 774
7 TraesCS5B01G436200 chr2B 800268249 800270284 2035 False 3245 3245 95.682 726 2731 1 chr2B.!!$F1 2005
8 TraesCS5B01G436200 chr2B 4106401 4108413 2012 True 3094 3094 94.494 723 2731 1 chr2B.!!$R1 2008
9 TraesCS5B01G436200 chr2B 155559589 155561584 1995 True 3075 3075 94.453 726 2731 1 chr2B.!!$R5 2005
10 TraesCS5B01G436200 chr2B 4371249 4373261 2012 True 3072 3072 94.297 723 2731 1 chr2B.!!$R3 2008
11 TraesCS5B01G436200 chr2B 4277850 4279863 2013 True 3066 3066 94.251 723 2731 1 chr2B.!!$R2 2008
12 TraesCS5B01G436200 chr2B 43364003 43364791 788 True 1254 1254 95.575 1953 2731 1 chr2B.!!$R4 778
13 TraesCS5B01G436200 chr7B 646618097 646620105 2008 False 3197 3197 95.441 726 2731 1 chr7B.!!$F1 2005
14 TraesCS5B01G436200 chr7B 677060107 677062102 1995 False 3181 3181 95.394 725 2731 1 chr7B.!!$F2 2006
15 TraesCS5B01G436200 chr7B 732848915 732849858 943 False 1277 1277 91.658 1819 2731 1 chr7B.!!$F4 912
16 TraesCS5B01G436200 chr7B 732798657 732799600 943 False 1266 1266 91.447 1819 2731 1 chr7B.!!$F3 912
17 TraesCS5B01G436200 chr3B 789618997 789620988 1991 True 3144 3144 95.094 726 2731 1 chr3B.!!$R1 2005
18 TraesCS5B01G436200 chr3B 803032234 803034238 2004 False 3085 3085 94.483 725 2731 1 chr3B.!!$F1 2006
19 TraesCS5B01G436200 chr5A 617079294 617079987 693 True 577 577 82.073 1 698 1 chr5A.!!$R1 697
20 TraesCS5B01G436200 chr5D 493937521 493938118 597 False 547 547 83.333 1 624 1 chr5D.!!$F1 623

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
689 690 0.037605 GTACACCACCAACTCCGGAG 60.038 60.0 30.11 30.11 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2545 3084 1.430992 AGAACCCGAAGAAGAACCCA 58.569 50.0 0.0 0.0 0.0 4.51 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
22 23 4.826556 GGATAGAAGACCTCATATGCACC 58.173 47.826 0.00 0.00 0.00 5.01
23 24 4.284490 GGATAGAAGACCTCATATGCACCA 59.716 45.833 0.00 0.00 0.00 4.17
24 25 5.221722 GGATAGAAGACCTCATATGCACCAA 60.222 44.000 0.00 0.00 0.00 3.67
25 26 4.574674 AGAAGACCTCATATGCACCAAA 57.425 40.909 0.00 0.00 0.00 3.28
26 27 5.121380 AGAAGACCTCATATGCACCAAAT 57.879 39.130 0.00 0.00 0.00 2.32
27 28 5.128919 AGAAGACCTCATATGCACCAAATC 58.871 41.667 0.00 0.00 0.00 2.17
28 29 4.508551 AGACCTCATATGCACCAAATCA 57.491 40.909 0.00 0.00 0.00 2.57
29 30 4.858850 AGACCTCATATGCACCAAATCAA 58.141 39.130 0.00 0.00 0.00 2.57
30 31 5.263599 AGACCTCATATGCACCAAATCAAA 58.736 37.500 0.00 0.00 0.00 2.69
31 32 5.895534 AGACCTCATATGCACCAAATCAAAT 59.104 36.000 0.00 0.00 0.00 2.32
32 33 6.040166 AGACCTCATATGCACCAAATCAAATC 59.960 38.462 0.00 0.00 0.00 2.17
33 34 5.657745 ACCTCATATGCACCAAATCAAATCA 59.342 36.000 0.00 0.00 0.00 2.57
34 35 6.154877 ACCTCATATGCACCAAATCAAATCAA 59.845 34.615 0.00 0.00 0.00 2.57
35 36 6.700081 CCTCATATGCACCAAATCAAATCAAG 59.300 38.462 0.00 0.00 0.00 3.02
36 37 7.172868 TCATATGCACCAAATCAAATCAAGT 57.827 32.000 0.00 0.00 0.00 3.16
37 38 8.291191 TCATATGCACCAAATCAAATCAAGTA 57.709 30.769 0.00 0.00 0.00 2.24
38 39 8.747471 TCATATGCACCAAATCAAATCAAGTAA 58.253 29.630 0.00 0.00 0.00 2.24
39 40 9.368674 CATATGCACCAAATCAAATCAAGTAAA 57.631 29.630 0.00 0.00 0.00 2.01
51 52 9.851686 ATCAAATCAAGTAAATATAGACCAGCA 57.148 29.630 0.00 0.00 0.00 4.41
52 53 9.679661 TCAAATCAAGTAAATATAGACCAGCAA 57.320 29.630 0.00 0.00 0.00 3.91
53 54 9.941664 CAAATCAAGTAAATATAGACCAGCAAG 57.058 33.333 0.00 0.00 0.00 4.01
54 55 9.686683 AAATCAAGTAAATATAGACCAGCAAGT 57.313 29.630 0.00 0.00 0.00 3.16
55 56 8.894768 ATCAAGTAAATATAGACCAGCAAGTC 57.105 34.615 0.00 0.00 37.01 3.01
56 57 7.847096 TCAAGTAAATATAGACCAGCAAGTCA 58.153 34.615 8.62 0.00 39.34 3.41
57 58 7.764443 TCAAGTAAATATAGACCAGCAAGTCAC 59.236 37.037 8.62 0.00 39.34 3.67
58 59 7.182817 AGTAAATATAGACCAGCAAGTCACA 57.817 36.000 8.62 0.00 39.34 3.58
59 60 7.796054 AGTAAATATAGACCAGCAAGTCACAT 58.204 34.615 8.62 4.36 39.34 3.21
60 61 8.924303 AGTAAATATAGACCAGCAAGTCACATA 58.076 33.333 8.62 6.09 39.34 2.29
61 62 9.542462 GTAAATATAGACCAGCAAGTCACATAA 57.458 33.333 8.62 0.00 39.34 1.90
63 64 8.613060 AATATAGACCAGCAAGTCACATAATG 57.387 34.615 8.62 0.00 39.34 1.90
64 65 3.614092 AGACCAGCAAGTCACATAATGG 58.386 45.455 8.62 0.00 39.34 3.16
65 66 3.264193 AGACCAGCAAGTCACATAATGGA 59.736 43.478 8.62 0.00 39.34 3.41
66 67 4.009675 GACCAGCAAGTCACATAATGGAA 58.990 43.478 1.56 0.00 36.73 3.53
67 68 4.603131 ACCAGCAAGTCACATAATGGAAT 58.397 39.130 0.00 0.00 0.00 3.01
68 69 4.641989 ACCAGCAAGTCACATAATGGAATC 59.358 41.667 0.00 0.00 0.00 2.52
69 70 4.641541 CCAGCAAGTCACATAATGGAATCA 59.358 41.667 0.00 0.00 0.00 2.57
70 71 5.301045 CCAGCAAGTCACATAATGGAATCAT 59.699 40.000 0.00 0.00 34.56 2.45
71 72 6.487668 CCAGCAAGTCACATAATGGAATCATA 59.512 38.462 0.00 0.00 32.44 2.15
72 73 7.176165 CCAGCAAGTCACATAATGGAATCATAT 59.824 37.037 0.00 0.00 32.44 1.78
73 74 8.021396 CAGCAAGTCACATAATGGAATCATATG 58.979 37.037 0.00 0.00 32.44 1.78
74 75 6.805271 GCAAGTCACATAATGGAATCATATGC 59.195 38.462 0.00 0.00 32.44 3.14
75 76 7.522562 GCAAGTCACATAATGGAATCATATGCA 60.523 37.037 0.00 0.00 32.44 3.96
76 77 8.354426 CAAGTCACATAATGGAATCATATGCAA 58.646 33.333 0.00 0.00 32.44 4.08
77 78 7.879070 AGTCACATAATGGAATCATATGCAAC 58.121 34.615 0.00 0.00 32.44 4.17
78 79 7.040201 AGTCACATAATGGAATCATATGCAACC 60.040 37.037 0.00 1.71 32.44 3.77
79 80 6.072563 TCACATAATGGAATCATATGCAACCG 60.073 38.462 0.00 0.00 32.44 4.44
80 81 5.769662 ACATAATGGAATCATATGCAACCGT 59.230 36.000 0.00 0.00 32.44 4.83
81 82 6.939730 ACATAATGGAATCATATGCAACCGTA 59.060 34.615 0.00 0.00 32.44 4.02
82 83 5.947228 AATGGAATCATATGCAACCGTAG 57.053 39.130 0.00 0.00 32.44 3.51
83 84 4.681074 TGGAATCATATGCAACCGTAGA 57.319 40.909 0.00 0.00 0.00 2.59
84 85 5.029807 TGGAATCATATGCAACCGTAGAA 57.970 39.130 0.00 0.00 0.00 2.10
85 86 5.620206 TGGAATCATATGCAACCGTAGAAT 58.380 37.500 0.00 0.00 0.00 2.40
86 87 5.700832 TGGAATCATATGCAACCGTAGAATC 59.299 40.000 0.00 0.00 0.00 2.52
87 88 5.163953 GGAATCATATGCAACCGTAGAATCG 60.164 44.000 0.00 0.00 0.00 3.34
88 89 4.577834 TCATATGCAACCGTAGAATCGA 57.422 40.909 0.00 0.00 0.00 3.59
89 90 4.295870 TCATATGCAACCGTAGAATCGAC 58.704 43.478 0.00 0.00 0.00 4.20
90 91 2.665649 ATGCAACCGTAGAATCGACA 57.334 45.000 0.00 0.00 0.00 4.35
91 92 2.442212 TGCAACCGTAGAATCGACAA 57.558 45.000 0.00 0.00 0.00 3.18
92 93 2.063266 TGCAACCGTAGAATCGACAAC 58.937 47.619 0.00 0.00 0.00 3.32
93 94 2.063266 GCAACCGTAGAATCGACAACA 58.937 47.619 0.00 0.00 0.00 3.33
94 95 2.671396 GCAACCGTAGAATCGACAACAT 59.329 45.455 0.00 0.00 0.00 2.71
95 96 3.124636 GCAACCGTAGAATCGACAACATT 59.875 43.478 0.00 0.00 0.00 2.71
96 97 4.378046 GCAACCGTAGAATCGACAACATTT 60.378 41.667 0.00 0.00 0.00 2.32
97 98 5.685841 CAACCGTAGAATCGACAACATTTT 58.314 37.500 0.00 0.00 0.00 1.82
98 99 6.619018 GCAACCGTAGAATCGACAACATTTTA 60.619 38.462 0.00 0.00 0.00 1.52
99 100 7.461107 CAACCGTAGAATCGACAACATTTTAT 58.539 34.615 0.00 0.00 0.00 1.40
100 101 7.000575 ACCGTAGAATCGACAACATTTTATG 57.999 36.000 0.00 0.00 0.00 1.90
162 163 7.885297 AGAAATACAAAGCATACACATGTTGT 58.115 30.769 0.00 0.54 42.84 3.32
163 164 8.023128 AGAAATACAAAGCATACACATGTTGTC 58.977 33.333 0.00 0.00 39.91 3.18
164 165 6.816134 ATACAAAGCATACACATGTTGTCA 57.184 33.333 0.00 0.00 39.91 3.58
165 166 5.512753 ACAAAGCATACACATGTTGTCAA 57.487 34.783 0.00 0.00 39.91 3.18
166 167 5.280945 ACAAAGCATACACATGTTGTCAAC 58.719 37.500 8.86 8.86 39.91 3.18
167 168 5.163571 ACAAAGCATACACATGTTGTCAACA 60.164 36.000 20.28 20.28 46.94 3.33
179 180 5.994887 TGTTGTCAACATGTTACTGTACC 57.005 39.130 14.48 0.00 36.25 3.34
180 181 4.817464 TGTTGTCAACATGTTACTGTACCC 59.183 41.667 14.48 0.00 36.25 3.69
181 182 4.691326 TGTCAACATGTTACTGTACCCA 57.309 40.909 11.53 0.00 0.00 4.51
182 183 5.037383 TGTCAACATGTTACTGTACCCAA 57.963 39.130 11.53 0.00 0.00 4.12
183 184 4.817464 TGTCAACATGTTACTGTACCCAAC 59.183 41.667 11.53 0.00 0.00 3.77
184 185 5.061179 GTCAACATGTTACTGTACCCAACT 58.939 41.667 11.53 0.00 0.00 3.16
185 186 5.529800 GTCAACATGTTACTGTACCCAACTT 59.470 40.000 11.53 0.00 0.00 2.66
186 187 5.529430 TCAACATGTTACTGTACCCAACTTG 59.471 40.000 11.53 12.03 34.95 3.16
187 188 3.818773 ACATGTTACTGTACCCAACTTGC 59.181 43.478 0.00 0.00 33.15 4.01
188 189 3.562343 TGTTACTGTACCCAACTTGCA 57.438 42.857 0.00 0.00 0.00 4.08
189 190 3.887352 TGTTACTGTACCCAACTTGCAA 58.113 40.909 0.00 0.00 0.00 4.08
190 191 4.465886 TGTTACTGTACCCAACTTGCAAT 58.534 39.130 0.00 0.00 0.00 3.56
191 192 4.890581 TGTTACTGTACCCAACTTGCAATT 59.109 37.500 0.00 0.00 0.00 2.32
192 193 5.009210 TGTTACTGTACCCAACTTGCAATTC 59.991 40.000 0.00 0.00 0.00 2.17
193 194 3.561143 ACTGTACCCAACTTGCAATTCA 58.439 40.909 0.00 0.00 0.00 2.57
194 195 4.151883 ACTGTACCCAACTTGCAATTCAT 58.848 39.130 0.00 0.00 0.00 2.57
195 196 5.321102 ACTGTACCCAACTTGCAATTCATA 58.679 37.500 0.00 0.00 0.00 2.15
196 197 5.951747 ACTGTACCCAACTTGCAATTCATAT 59.048 36.000 0.00 0.00 0.00 1.78
197 198 6.437162 ACTGTACCCAACTTGCAATTCATATT 59.563 34.615 0.00 0.00 0.00 1.28
198 199 7.039082 ACTGTACCCAACTTGCAATTCATATTT 60.039 33.333 0.00 0.00 0.00 1.40
199 200 7.095910 TGTACCCAACTTGCAATTCATATTTG 58.904 34.615 0.00 0.00 0.00 2.32
201 202 4.333372 CCCAACTTGCAATTCATATTTGCC 59.667 41.667 0.00 0.00 46.97 4.52
202 203 4.333372 CCAACTTGCAATTCATATTTGCCC 59.667 41.667 0.00 0.00 46.97 5.36
203 204 4.822685 ACTTGCAATTCATATTTGCCCA 57.177 36.364 0.00 0.00 46.97 5.36
204 205 4.761975 ACTTGCAATTCATATTTGCCCAG 58.238 39.130 0.00 6.71 46.97 4.45
205 206 3.182341 TGCAATTCATATTTGCCCAGC 57.818 42.857 7.88 0.00 46.97 4.85
206 207 2.158928 TGCAATTCATATTTGCCCAGCC 60.159 45.455 7.88 0.00 46.97 4.85
207 208 2.807837 GCAATTCATATTTGCCCAGCCC 60.808 50.000 0.00 0.00 42.84 5.19
208 209 2.701951 CAATTCATATTTGCCCAGCCCT 59.298 45.455 0.00 0.00 0.00 5.19
209 210 3.896888 CAATTCATATTTGCCCAGCCCTA 59.103 43.478 0.00 0.00 0.00 3.53
210 211 3.901570 TTCATATTTGCCCAGCCCTAT 57.098 42.857 0.00 0.00 0.00 2.57
211 212 3.901570 TCATATTTGCCCAGCCCTATT 57.098 42.857 0.00 0.00 0.00 1.73
212 213 4.197559 TCATATTTGCCCAGCCCTATTT 57.802 40.909 0.00 0.00 0.00 1.40
213 214 4.555689 TCATATTTGCCCAGCCCTATTTT 58.444 39.130 0.00 0.00 0.00 1.82
214 215 4.968080 TCATATTTGCCCAGCCCTATTTTT 59.032 37.500 0.00 0.00 0.00 1.94
241 242 9.613428 TTATGAATATGGCTGCCTAATATACAC 57.387 33.333 21.03 10.63 0.00 2.90
242 243 7.257790 TGAATATGGCTGCCTAATATACACT 57.742 36.000 21.03 0.86 0.00 3.55
243 244 8.374184 TGAATATGGCTGCCTAATATACACTA 57.626 34.615 21.03 0.00 0.00 2.74
244 245 8.478066 TGAATATGGCTGCCTAATATACACTAG 58.522 37.037 21.03 0.00 0.00 2.57
245 246 8.609617 AATATGGCTGCCTAATATACACTAGA 57.390 34.615 21.03 0.00 0.00 2.43
246 247 6.935240 ATGGCTGCCTAATATACACTAGAA 57.065 37.500 21.03 0.00 0.00 2.10
247 248 6.740944 TGGCTGCCTAATATACACTAGAAA 57.259 37.500 21.03 0.00 0.00 2.52
248 249 6.522054 TGGCTGCCTAATATACACTAGAAAC 58.478 40.000 21.03 0.00 0.00 2.78
249 250 5.932883 GGCTGCCTAATATACACTAGAAACC 59.067 44.000 12.43 0.00 0.00 3.27
250 251 6.463897 GGCTGCCTAATATACACTAGAAACCA 60.464 42.308 12.43 0.00 0.00 3.67
251 252 6.424207 GCTGCCTAATATACACTAGAAACCAC 59.576 42.308 0.00 0.00 0.00 4.16
252 253 7.670605 TGCCTAATATACACTAGAAACCACT 57.329 36.000 0.00 0.00 0.00 4.00
253 254 8.771521 TGCCTAATATACACTAGAAACCACTA 57.228 34.615 0.00 0.00 0.00 2.74
254 255 8.636213 TGCCTAATATACACTAGAAACCACTAC 58.364 37.037 0.00 0.00 0.00 2.73
255 256 8.858094 GCCTAATATACACTAGAAACCACTACT 58.142 37.037 0.00 0.00 0.00 2.57
273 274 9.871238 ACCACTACTAAGATATTTGTTAGTGTG 57.129 33.333 13.64 16.09 40.87 3.82
274 275 9.871238 CCACTACTAAGATATTTGTTAGTGTGT 57.129 33.333 20.09 14.48 40.87 3.72
502 503 8.447833 ACTGTATGACAACAATTGTTATAACCG 58.552 33.333 22.87 12.25 45.52 4.44
503 504 8.325421 TGTATGACAACAATTGTTATAACCGT 57.675 30.769 22.87 15.26 45.52 4.83
504 505 8.784994 TGTATGACAACAATTGTTATAACCGTT 58.215 29.630 22.87 8.21 45.52 4.44
505 506 9.057365 GTATGACAACAATTGTTATAACCGTTG 57.943 33.333 22.87 22.53 45.52 4.10
506 507 7.028926 TGACAACAATTGTTATAACCGTTGT 57.971 32.000 26.23 26.23 45.52 3.32
507 508 7.481642 TGACAACAATTGTTATAACCGTTGTT 58.518 30.769 26.45 26.45 45.52 2.83
508 509 7.974501 TGACAACAATTGTTATAACCGTTGTTT 59.025 29.630 28.03 22.48 45.52 2.83
509 510 9.448294 GACAACAATTGTTATAACCGTTGTTTA 57.552 29.630 28.03 5.26 45.52 2.01
510 511 9.235537 ACAACAATTGTTATAACCGTTGTTTAC 57.764 29.630 28.03 2.53 41.84 2.01
511 512 9.234384 CAACAATTGTTATAACCGTTGTTTACA 57.766 29.630 28.03 4.69 40.38 2.41
512 513 9.798994 AACAATTGTTATAACCGTTGTTTACAA 57.201 25.926 26.45 10.50 39.90 2.41
513 514 9.798994 ACAATTGTTATAACCGTTGTTTACAAA 57.201 25.926 20.96 5.05 37.63 2.83
515 516 9.798994 AATTGTTATAACCGTTGTTTACAAACA 57.201 25.926 13.01 3.44 46.35 2.83
520 521 4.722361 ACCGTTGTTTACAAACATGGTT 57.278 36.364 18.98 0.00 46.77 3.67
521 522 5.831702 ACCGTTGTTTACAAACATGGTTA 57.168 34.783 18.98 0.92 46.77 2.85
522 523 6.394025 ACCGTTGTTTACAAACATGGTTAT 57.606 33.333 18.98 0.00 46.77 1.89
523 524 6.210078 ACCGTTGTTTACAAACATGGTTATG 58.790 36.000 18.98 7.27 46.77 1.90
524 525 7.226056 ACCGTTGTTTACAAACATGGTTATGC 61.226 38.462 18.98 0.00 46.77 3.14
526 527 4.799678 TGTTTACAAACATGGTTATGCGG 58.200 39.130 0.00 0.00 43.45 5.69
527 528 4.278669 TGTTTACAAACATGGTTATGCGGT 59.721 37.500 0.00 0.00 43.45 5.68
528 529 5.221263 TGTTTACAAACATGGTTATGCGGTT 60.221 36.000 0.00 0.00 43.45 4.44
529 530 6.016527 TGTTTACAAACATGGTTATGCGGTTA 60.017 34.615 0.00 0.00 43.45 2.85
530 531 6.570672 TTACAAACATGGTTATGCGGTTAA 57.429 33.333 0.00 0.00 37.85 2.01
531 532 5.054390 ACAAACATGGTTATGCGGTTAAG 57.946 39.130 0.00 0.00 37.85 1.85
532 533 4.521256 ACAAACATGGTTATGCGGTTAAGT 59.479 37.500 0.00 0.00 37.85 2.24
533 534 5.706369 ACAAACATGGTTATGCGGTTAAGTA 59.294 36.000 0.00 0.00 37.85 2.24
534 535 5.806366 AACATGGTTATGCGGTTAAGTAC 57.194 39.130 0.00 0.00 37.85 2.73
535 536 4.834534 ACATGGTTATGCGGTTAAGTACA 58.165 39.130 0.00 0.00 37.85 2.90
536 537 5.247084 ACATGGTTATGCGGTTAAGTACAA 58.753 37.500 0.00 0.00 37.85 2.41
537 538 5.883673 ACATGGTTATGCGGTTAAGTACAAT 59.116 36.000 0.00 0.00 37.85 2.71
538 539 5.804692 TGGTTATGCGGTTAAGTACAATG 57.195 39.130 0.00 0.00 0.00 2.82
539 540 4.636648 TGGTTATGCGGTTAAGTACAATGG 59.363 41.667 0.00 0.00 0.00 3.16
540 541 4.496840 GGTTATGCGGTTAAGTACAATGGC 60.497 45.833 0.00 0.00 0.00 4.40
541 542 2.483014 TGCGGTTAAGTACAATGGCT 57.517 45.000 0.00 0.00 0.00 4.75
542 543 3.613494 TGCGGTTAAGTACAATGGCTA 57.387 42.857 0.00 0.00 0.00 3.93
543 544 3.940319 TGCGGTTAAGTACAATGGCTAA 58.060 40.909 0.00 0.00 0.00 3.09
544 545 3.936453 TGCGGTTAAGTACAATGGCTAAG 59.064 43.478 0.00 0.00 0.00 2.18
545 546 3.937079 GCGGTTAAGTACAATGGCTAAGT 59.063 43.478 0.00 0.00 0.00 2.24
546 547 5.111293 GCGGTTAAGTACAATGGCTAAGTA 58.889 41.667 0.00 0.00 0.00 2.24
547 548 5.581874 GCGGTTAAGTACAATGGCTAAGTAA 59.418 40.000 0.00 0.00 0.00 2.24
548 549 6.259387 GCGGTTAAGTACAATGGCTAAGTAAT 59.741 38.462 0.00 0.00 0.00 1.89
549 550 7.439056 GCGGTTAAGTACAATGGCTAAGTAATA 59.561 37.037 0.00 0.00 0.00 0.98
550 551 9.316730 CGGTTAAGTACAATGGCTAAGTAATAA 57.683 33.333 0.00 0.00 0.00 1.40
640 641 7.603963 AATTGTTTTATATTTTTGGACCGGC 57.396 32.000 0.00 0.00 0.00 6.13
641 642 5.986501 TGTTTTATATTTTTGGACCGGCT 57.013 34.783 0.00 0.00 0.00 5.52
642 643 5.956642 TGTTTTATATTTTTGGACCGGCTC 58.043 37.500 0.00 0.00 0.00 4.70
643 644 5.712917 TGTTTTATATTTTTGGACCGGCTCT 59.287 36.000 0.00 0.00 0.00 4.09
644 645 5.828299 TTTATATTTTTGGACCGGCTCTG 57.172 39.130 0.00 0.00 0.00 3.35
645 646 1.459450 TATTTTTGGACCGGCTCTGC 58.541 50.000 0.00 0.00 0.00 4.26
646 647 1.250840 ATTTTTGGACCGGCTCTGCC 61.251 55.000 0.00 0.00 46.75 4.85
661 662 3.393089 TCTGCCAAGAGAGACAAGTTC 57.607 47.619 0.00 0.00 0.00 3.01
662 663 2.064762 CTGCCAAGAGAGACAAGTTCG 58.935 52.381 0.00 0.00 0.00 3.95
663 664 1.270305 TGCCAAGAGAGACAAGTTCGG 60.270 52.381 0.00 0.00 0.00 4.30
664 665 1.941668 GCCAAGAGAGACAAGTTCGGG 60.942 57.143 0.00 0.00 0.00 5.14
665 666 1.344763 CCAAGAGAGACAAGTTCGGGT 59.655 52.381 0.00 0.00 0.00 5.28
666 667 2.610727 CCAAGAGAGACAAGTTCGGGTC 60.611 54.545 0.00 0.00 0.00 4.46
667 668 2.296073 AGAGAGACAAGTTCGGGTCT 57.704 50.000 0.00 0.00 46.51 3.85
668 669 3.436577 AGAGAGACAAGTTCGGGTCTA 57.563 47.619 0.00 0.00 44.03 2.59
669 670 3.083293 AGAGAGACAAGTTCGGGTCTAC 58.917 50.000 0.00 0.00 44.03 2.59
670 671 1.811359 AGAGACAAGTTCGGGTCTACG 59.189 52.381 0.00 0.00 44.03 3.51
671 672 1.538950 GAGACAAGTTCGGGTCTACGT 59.461 52.381 0.00 0.00 44.03 3.57
672 673 2.744202 GAGACAAGTTCGGGTCTACGTA 59.256 50.000 0.00 0.00 44.03 3.57
673 674 2.485814 AGACAAGTTCGGGTCTACGTAC 59.514 50.000 0.00 0.00 42.30 3.67
674 675 2.226437 GACAAGTTCGGGTCTACGTACA 59.774 50.000 0.00 0.00 36.74 2.90
675 676 2.030805 ACAAGTTCGGGTCTACGTACAC 60.031 50.000 0.00 0.00 36.74 2.90
676 677 1.168714 AGTTCGGGTCTACGTACACC 58.831 55.000 11.27 11.27 36.74 4.16
677 678 0.881118 GTTCGGGTCTACGTACACCA 59.119 55.000 19.92 0.00 34.81 4.17
678 679 0.881118 TTCGGGTCTACGTACACCAC 59.119 55.000 19.92 9.61 33.91 4.16
679 680 0.960364 TCGGGTCTACGTACACCACC 60.960 60.000 19.92 10.18 33.91 4.61
680 681 1.243342 CGGGTCTACGTACACCACCA 61.243 60.000 19.92 0.00 33.91 4.17
681 682 0.968405 GGGTCTACGTACACCACCAA 59.032 55.000 19.92 0.00 33.91 3.67
682 683 1.337167 GGGTCTACGTACACCACCAAC 60.337 57.143 19.92 0.60 33.91 3.77
683 684 1.615392 GGTCTACGTACACCACCAACT 59.385 52.381 14.44 0.00 32.33 3.16
684 685 2.352127 GGTCTACGTACACCACCAACTC 60.352 54.545 14.44 0.00 32.33 3.01
685 686 1.888512 TCTACGTACACCACCAACTCC 59.111 52.381 0.00 0.00 0.00 3.85
686 687 0.597568 TACGTACACCACCAACTCCG 59.402 55.000 0.00 0.00 0.00 4.63
687 688 1.373748 CGTACACCACCAACTCCGG 60.374 63.158 0.00 0.00 0.00 5.14
688 689 1.808531 CGTACACCACCAACTCCGGA 61.809 60.000 2.93 2.93 0.00 5.14
689 690 0.037605 GTACACCACCAACTCCGGAG 60.038 60.000 30.11 30.11 0.00 4.63
703 704 3.695606 GGAGGCGAGCAGTGGTGA 61.696 66.667 0.00 0.00 0.00 4.02
704 705 2.433318 GAGGCGAGCAGTGGTGAC 60.433 66.667 0.00 0.00 0.00 3.67
705 706 3.226429 GAGGCGAGCAGTGGTGACA 62.226 63.158 0.00 0.00 38.70 3.58
706 707 2.740055 GGCGAGCAGTGGTGACAG 60.740 66.667 0.00 0.00 44.46 3.51
708 709 2.024319 GCGAGCAGTGGTGACAGTC 61.024 63.158 0.00 0.00 43.90 3.51
709 710 1.363807 CGAGCAGTGGTGACAGTCA 59.636 57.895 0.00 0.00 43.90 3.41
710 711 0.941463 CGAGCAGTGGTGACAGTCAC 60.941 60.000 23.60 23.60 43.90 3.67
711 712 0.390860 GAGCAGTGGTGACAGTCACT 59.609 55.000 28.81 11.58 46.19 3.41
714 715 1.447643 AGTGGTGACAGTCACTGGC 59.552 57.895 28.81 19.49 46.19 4.85
718 719 2.421314 TGACAGTCACTGGCACCG 59.579 61.111 10.15 0.00 42.40 4.94
719 720 2.357517 GACAGTCACTGGCACCGG 60.358 66.667 5.49 0.00 39.71 5.28
720 721 3.883744 GACAGTCACTGGCACCGGG 62.884 68.421 5.49 0.00 39.71 5.73
721 722 4.704833 CAGTCACTGGCACCGGGG 62.705 72.222 6.32 0.84 0.00 5.73
883 884 0.905809 TCGTAAGCTGTTGGGGGCTA 60.906 55.000 0.00 0.00 37.87 3.93
978 979 4.753662 CGGGACCCACCTCCTCGA 62.754 72.222 12.15 0.00 38.98 4.04
1000 1001 0.108804 CTAGAAAAGACGAGCGCCCA 60.109 55.000 2.29 0.00 0.00 5.36
1049 1050 2.077803 TCCCCTTTCCCCAATCTTTCA 58.922 47.619 0.00 0.00 0.00 2.69
1057 1058 2.308866 TCCCCAATCTTTCACTTCTCCC 59.691 50.000 0.00 0.00 0.00 4.30
1147 1148 0.469705 AACAAGGTGCCCTGAATGCA 60.470 50.000 0.00 0.00 32.13 3.96
1250 1251 0.545071 AAACCAATGGCAGGAAGGGG 60.545 55.000 0.00 0.00 0.00 4.79
1417 1418 9.288576 GGAGTGGATTGATGAATATGTTGATAA 57.711 33.333 0.00 0.00 0.00 1.75
1746 1748 4.829492 GTCATTAGAATGGGCATTTAGGCT 59.171 41.667 2.52 0.00 43.56 4.58
1860 1862 4.729227 TTCCCCTGTTTTTGTTCTTCAC 57.271 40.909 0.00 0.00 0.00 3.18
2196 2269 0.255890 GTTTGCATGGGGCTCCTAGA 59.744 55.000 3.07 0.00 45.15 2.43
2217 2293 4.165950 AGATGCATGTCTATGGTTTGGGTA 59.834 41.667 2.46 0.00 34.79 3.69
2637 3183 2.738846 CCTTCACTCCTCGTTGTTGATG 59.261 50.000 0.00 0.00 0.00 3.07
2638 3184 2.455674 TCACTCCTCGTTGTTGATGG 57.544 50.000 0.00 0.00 0.00 3.51
2651 3197 2.766651 GATGGGGGTACGGGAGCA 60.767 66.667 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.858850 TGATTTGGTGCATATGAGGTCTT 58.141 39.130 6.97 0.00 0.00 3.01
10 11 6.151663 TGATTTGATTTGGTGCATATGAGG 57.848 37.500 6.97 0.00 0.00 3.86
11 12 7.262772 ACTTGATTTGATTTGGTGCATATGAG 58.737 34.615 6.97 0.00 0.00 2.90
12 13 7.172868 ACTTGATTTGATTTGGTGCATATGA 57.827 32.000 6.97 0.00 0.00 2.15
13 14 8.929827 TTACTTGATTTGATTTGGTGCATATG 57.070 30.769 0.00 0.00 0.00 1.78
25 26 9.851686 TGCTGGTCTATATTTACTTGATTTGAT 57.148 29.630 0.00 0.00 0.00 2.57
26 27 9.679661 TTGCTGGTCTATATTTACTTGATTTGA 57.320 29.630 0.00 0.00 0.00 2.69
27 28 9.941664 CTTGCTGGTCTATATTTACTTGATTTG 57.058 33.333 0.00 0.00 0.00 2.32
28 29 9.686683 ACTTGCTGGTCTATATTTACTTGATTT 57.313 29.630 0.00 0.00 0.00 2.17
29 30 9.331282 GACTTGCTGGTCTATATTTACTTGATT 57.669 33.333 3.10 0.00 33.81 2.57
30 31 8.486210 TGACTTGCTGGTCTATATTTACTTGAT 58.514 33.333 10.07 0.00 37.16 2.57
31 32 7.764443 GTGACTTGCTGGTCTATATTTACTTGA 59.236 37.037 10.07 0.00 37.16 3.02
32 33 7.549134 TGTGACTTGCTGGTCTATATTTACTTG 59.451 37.037 10.07 0.00 37.16 3.16
33 34 7.620880 TGTGACTTGCTGGTCTATATTTACTT 58.379 34.615 10.07 0.00 37.16 2.24
34 35 7.182817 TGTGACTTGCTGGTCTATATTTACT 57.817 36.000 10.07 0.00 37.16 2.24
35 36 9.542462 TTATGTGACTTGCTGGTCTATATTTAC 57.458 33.333 10.07 1.19 37.16 2.01
37 38 9.060347 CATTATGTGACTTGCTGGTCTATATTT 57.940 33.333 10.07 1.26 37.16 1.40
38 39 7.663081 CCATTATGTGACTTGCTGGTCTATATT 59.337 37.037 10.07 4.76 37.16 1.28
39 40 7.016563 TCCATTATGTGACTTGCTGGTCTATAT 59.983 37.037 10.07 5.64 37.16 0.86
40 41 6.326323 TCCATTATGTGACTTGCTGGTCTATA 59.674 38.462 10.07 6.95 37.16 1.31
41 42 5.130975 TCCATTATGTGACTTGCTGGTCTAT 59.869 40.000 10.07 7.66 37.16 1.98
42 43 4.469586 TCCATTATGTGACTTGCTGGTCTA 59.530 41.667 10.07 2.08 37.16 2.59
43 44 3.264193 TCCATTATGTGACTTGCTGGTCT 59.736 43.478 10.07 0.00 37.16 3.85
44 45 3.609853 TCCATTATGTGACTTGCTGGTC 58.390 45.455 3.33 3.33 36.81 4.02
45 46 3.719268 TCCATTATGTGACTTGCTGGT 57.281 42.857 0.00 0.00 0.00 4.00
46 47 4.641541 TGATTCCATTATGTGACTTGCTGG 59.358 41.667 0.00 0.00 0.00 4.85
47 48 5.823209 TGATTCCATTATGTGACTTGCTG 57.177 39.130 0.00 0.00 0.00 4.41
48 49 7.309012 GCATATGATTCCATTATGTGACTTGCT 60.309 37.037 6.97 0.00 34.31 3.91
49 50 6.805271 GCATATGATTCCATTATGTGACTTGC 59.195 38.462 6.97 0.00 34.31 4.01
50 51 7.878036 TGCATATGATTCCATTATGTGACTTG 58.122 34.615 6.97 0.00 34.31 3.16
51 52 8.355169 GTTGCATATGATTCCATTATGTGACTT 58.645 33.333 6.97 0.00 34.31 3.01
52 53 7.040201 GGTTGCATATGATTCCATTATGTGACT 60.040 37.037 6.97 0.00 34.31 3.41
53 54 7.086376 GGTTGCATATGATTCCATTATGTGAC 58.914 38.462 6.97 0.00 34.31 3.67
54 55 6.072563 CGGTTGCATATGATTCCATTATGTGA 60.073 38.462 6.97 0.00 34.31 3.58
55 56 6.088173 CGGTTGCATATGATTCCATTATGTG 58.912 40.000 6.97 0.00 34.31 3.21
56 57 5.769662 ACGGTTGCATATGATTCCATTATGT 59.230 36.000 6.97 0.00 34.31 2.29
57 58 6.258230 ACGGTTGCATATGATTCCATTATG 57.742 37.500 6.97 0.00 34.31 1.90
58 59 7.394016 TCTACGGTTGCATATGATTCCATTAT 58.606 34.615 6.97 0.00 34.31 1.28
59 60 6.764379 TCTACGGTTGCATATGATTCCATTA 58.236 36.000 6.97 0.00 34.31 1.90
60 61 5.620206 TCTACGGTTGCATATGATTCCATT 58.380 37.500 6.97 0.00 34.31 3.16
61 62 5.227569 TCTACGGTTGCATATGATTCCAT 57.772 39.130 6.97 0.00 36.81 3.41
62 63 4.681074 TCTACGGTTGCATATGATTCCA 57.319 40.909 6.97 0.00 0.00 3.53
63 64 5.163953 CGATTCTACGGTTGCATATGATTCC 60.164 44.000 6.97 3.83 0.00 3.01
64 65 5.633601 TCGATTCTACGGTTGCATATGATTC 59.366 40.000 6.97 0.00 0.00 2.52
65 66 5.405571 GTCGATTCTACGGTTGCATATGATT 59.594 40.000 6.97 0.00 0.00 2.57
66 67 4.923871 GTCGATTCTACGGTTGCATATGAT 59.076 41.667 6.97 0.00 0.00 2.45
67 68 4.202070 TGTCGATTCTACGGTTGCATATGA 60.202 41.667 6.97 0.00 0.00 2.15
68 69 4.048504 TGTCGATTCTACGGTTGCATATG 58.951 43.478 0.00 0.00 0.00 1.78
69 70 4.316205 TGTCGATTCTACGGTTGCATAT 57.684 40.909 0.00 0.00 0.00 1.78
70 71 3.786516 TGTCGATTCTACGGTTGCATA 57.213 42.857 0.00 0.00 0.00 3.14
71 72 2.665649 TGTCGATTCTACGGTTGCAT 57.334 45.000 0.00 0.00 0.00 3.96
72 73 2.063266 GTTGTCGATTCTACGGTTGCA 58.937 47.619 0.00 0.00 0.00 4.08
73 74 2.063266 TGTTGTCGATTCTACGGTTGC 58.937 47.619 0.00 0.00 0.00 4.17
74 75 4.921470 AATGTTGTCGATTCTACGGTTG 57.079 40.909 0.00 0.00 0.00 3.77
75 76 5.934935 AAAATGTTGTCGATTCTACGGTT 57.065 34.783 0.00 0.00 0.00 4.44
76 77 6.592607 ACATAAAATGTTGTCGATTCTACGGT 59.407 34.615 0.00 0.00 41.63 4.83
77 78 7.000575 ACATAAAATGTTGTCGATTCTACGG 57.999 36.000 0.00 0.00 41.63 4.02
136 137 9.008965 ACAACATGTGTATGCTTTGTATTTCTA 57.991 29.630 0.00 0.00 39.29 2.10
137 138 7.885297 ACAACATGTGTATGCTTTGTATTTCT 58.115 30.769 0.00 0.00 39.29 2.52
138 139 7.807433 TGACAACATGTGTATGCTTTGTATTTC 59.193 33.333 0.00 0.00 41.96 2.17
139 140 7.656412 TGACAACATGTGTATGCTTTGTATTT 58.344 30.769 0.00 0.00 41.96 1.40
140 141 7.213216 TGACAACATGTGTATGCTTTGTATT 57.787 32.000 0.00 0.00 41.96 1.89
141 142 6.816134 TGACAACATGTGTATGCTTTGTAT 57.184 33.333 0.00 0.00 41.96 2.29
142 143 6.038714 TGTTGACAACATGTGTATGCTTTGTA 59.961 34.615 17.02 0.00 41.96 2.41
143 144 5.163571 TGTTGACAACATGTGTATGCTTTGT 60.164 36.000 17.02 0.00 41.96 2.83
144 145 5.280164 TGTTGACAACATGTGTATGCTTTG 58.720 37.500 17.02 0.00 41.96 2.77
145 146 5.512753 TGTTGACAACATGTGTATGCTTT 57.487 34.783 17.02 0.00 41.96 3.51
157 158 4.817464 GGGTACAGTAACATGTTGACAACA 59.183 41.667 22.61 22.61 46.94 3.33
158 159 4.817464 TGGGTACAGTAACATGTTGACAAC 59.183 41.667 21.42 11.54 34.56 3.32
159 160 5.037383 TGGGTACAGTAACATGTTGACAA 57.963 39.130 21.42 0.00 34.56 3.18
160 161 4.691326 TGGGTACAGTAACATGTTGACA 57.309 40.909 21.42 0.00 34.56 3.58
161 162 5.061179 AGTTGGGTACAGTAACATGTTGAC 58.939 41.667 21.42 14.12 34.56 3.18
162 163 5.298989 AGTTGGGTACAGTAACATGTTGA 57.701 39.130 21.42 2.67 34.56 3.18
163 164 5.757886 CAAGTTGGGTACAGTAACATGTTG 58.242 41.667 21.42 7.93 34.56 3.33
164 165 4.277423 GCAAGTTGGGTACAGTAACATGTT 59.723 41.667 16.68 16.68 34.56 2.71
165 166 3.818773 GCAAGTTGGGTACAGTAACATGT 59.181 43.478 4.75 0.00 37.19 3.21
166 167 3.818210 TGCAAGTTGGGTACAGTAACATG 59.182 43.478 4.75 0.00 0.00 3.21
167 168 4.093472 TGCAAGTTGGGTACAGTAACAT 57.907 40.909 4.75 0.00 0.00 2.71
168 169 3.562343 TGCAAGTTGGGTACAGTAACA 57.438 42.857 4.75 0.00 0.00 2.41
169 170 5.009210 TGAATTGCAAGTTGGGTACAGTAAC 59.991 40.000 4.94 0.00 0.00 2.50
170 171 5.133941 TGAATTGCAAGTTGGGTACAGTAA 58.866 37.500 4.94 0.00 0.00 2.24
171 172 4.720046 TGAATTGCAAGTTGGGTACAGTA 58.280 39.130 4.94 0.00 0.00 2.74
172 173 3.561143 TGAATTGCAAGTTGGGTACAGT 58.439 40.909 4.94 0.00 0.00 3.55
173 174 4.789012 ATGAATTGCAAGTTGGGTACAG 57.211 40.909 4.94 0.00 0.00 2.74
174 175 6.849085 AATATGAATTGCAAGTTGGGTACA 57.151 33.333 4.94 0.00 0.00 2.90
175 176 7.524294 CAAATATGAATTGCAAGTTGGGTAC 57.476 36.000 4.94 0.00 0.00 3.34
187 188 2.701951 AGGGCTGGGCAAATATGAATTG 59.298 45.455 0.00 0.00 0.00 2.32
188 189 3.050523 AGGGCTGGGCAAATATGAATT 57.949 42.857 0.00 0.00 0.00 2.17
189 190 2.781403 AGGGCTGGGCAAATATGAAT 57.219 45.000 0.00 0.00 0.00 2.57
190 191 3.901570 ATAGGGCTGGGCAAATATGAA 57.098 42.857 0.00 0.00 0.00 2.57
191 192 3.901570 AATAGGGCTGGGCAAATATGA 57.098 42.857 0.00 0.00 0.00 2.15
192 193 4.961438 AAAATAGGGCTGGGCAAATATG 57.039 40.909 0.00 0.00 0.00 1.78
215 216 9.613428 GTGTATATTAGGCAGCCATATTCATAA 57.387 33.333 15.80 1.51 0.00 1.90
216 217 8.992349 AGTGTATATTAGGCAGCCATATTCATA 58.008 33.333 15.80 0.40 0.00 2.15
217 218 7.865820 AGTGTATATTAGGCAGCCATATTCAT 58.134 34.615 15.80 1.40 0.00 2.57
218 219 7.257790 AGTGTATATTAGGCAGCCATATTCA 57.742 36.000 15.80 10.19 0.00 2.57
219 220 8.696374 TCTAGTGTATATTAGGCAGCCATATTC 58.304 37.037 15.80 7.71 0.00 1.75
220 221 8.609617 TCTAGTGTATATTAGGCAGCCATATT 57.390 34.615 15.80 0.00 0.00 1.28
221 222 8.609617 TTCTAGTGTATATTAGGCAGCCATAT 57.390 34.615 15.80 11.59 0.00 1.78
222 223 8.311836 GTTTCTAGTGTATATTAGGCAGCCATA 58.688 37.037 15.80 3.83 0.00 2.74
223 224 6.935240 TTCTAGTGTATATTAGGCAGCCAT 57.065 37.500 15.80 1.16 0.00 4.40
224 225 6.463897 GGTTTCTAGTGTATATTAGGCAGCCA 60.464 42.308 15.80 0.00 0.00 4.75
225 226 5.932883 GGTTTCTAGTGTATATTAGGCAGCC 59.067 44.000 1.84 1.84 0.00 4.85
226 227 6.424207 GTGGTTTCTAGTGTATATTAGGCAGC 59.576 42.308 0.00 0.00 0.00 5.25
227 228 7.727181 AGTGGTTTCTAGTGTATATTAGGCAG 58.273 38.462 0.00 0.00 0.00 4.85
228 229 7.670605 AGTGGTTTCTAGTGTATATTAGGCA 57.329 36.000 0.00 0.00 0.00 4.75
229 230 8.858094 AGTAGTGGTTTCTAGTGTATATTAGGC 58.142 37.037 0.00 0.00 0.00 3.93
247 248 9.871238 CACACTAACAAATATCTTAGTAGTGGT 57.129 33.333 11.40 2.95 37.35 4.16
248 249 9.871238 ACACACTAACAAATATCTTAGTAGTGG 57.129 33.333 18.97 4.65 36.94 4.00
476 477 8.447833 CGGTTATAACAATTGTTGTCATACAGT 58.552 33.333 29.72 5.77 44.59 3.55
477 478 8.447833 ACGGTTATAACAATTGTTGTCATACAG 58.552 33.333 29.72 22.12 44.59 2.74
478 479 8.325421 ACGGTTATAACAATTGTTGTCATACA 57.675 30.769 29.72 11.55 44.59 2.29
479 480 9.057365 CAACGGTTATAACAATTGTTGTCATAC 57.943 33.333 29.72 20.65 44.59 2.39
480 481 8.784994 ACAACGGTTATAACAATTGTTGTCATA 58.215 29.630 29.72 18.15 43.31 2.15
481 482 7.653647 ACAACGGTTATAACAATTGTTGTCAT 58.346 30.769 29.72 19.08 43.31 3.06
482 483 7.028926 ACAACGGTTATAACAATTGTTGTCA 57.971 32.000 29.72 14.88 43.31 3.58
483 484 7.917720 AACAACGGTTATAACAATTGTTGTC 57.082 32.000 29.81 14.41 45.27 3.18
485 486 9.234384 TGTAAACAACGGTTATAACAATTGTTG 57.766 29.630 30.43 27.60 42.56 3.33
486 487 9.798994 TTGTAAACAACGGTTATAACAATTGTT 57.201 25.926 27.39 27.39 43.91 2.83
487 488 9.798994 TTTGTAAACAACGGTTATAACAATTGT 57.201 25.926 21.90 21.90 39.01 2.71
489 490 9.798994 TGTTTGTAAACAACGGTTATAACAATT 57.201 25.926 17.16 7.71 45.17 2.32
505 506 4.800784 ACCGCATAACCATGTTTGTAAAC 58.199 39.130 0.65 0.65 39.33 2.01
506 507 5.455056 AACCGCATAACCATGTTTGTAAA 57.545 34.783 0.00 0.00 34.40 2.01
507 508 6.207025 ACTTAACCGCATAACCATGTTTGTAA 59.793 34.615 0.00 0.00 34.40 2.41
508 509 5.706369 ACTTAACCGCATAACCATGTTTGTA 59.294 36.000 0.00 0.00 34.40 2.41
509 510 4.521256 ACTTAACCGCATAACCATGTTTGT 59.479 37.500 0.00 0.00 34.40 2.83
510 511 5.054390 ACTTAACCGCATAACCATGTTTG 57.946 39.130 0.00 0.00 34.40 2.93
511 512 5.706369 TGTACTTAACCGCATAACCATGTTT 59.294 36.000 0.00 0.00 34.40 2.83
512 513 5.247084 TGTACTTAACCGCATAACCATGTT 58.753 37.500 0.00 0.00 34.40 2.71
513 514 4.834534 TGTACTTAACCGCATAACCATGT 58.165 39.130 0.00 0.00 34.40 3.21
514 515 5.804692 TTGTACTTAACCGCATAACCATG 57.195 39.130 0.00 0.00 35.07 3.66
515 516 5.298276 CCATTGTACTTAACCGCATAACCAT 59.702 40.000 0.00 0.00 0.00 3.55
516 517 4.636648 CCATTGTACTTAACCGCATAACCA 59.363 41.667 0.00 0.00 0.00 3.67
517 518 4.496840 GCCATTGTACTTAACCGCATAACC 60.497 45.833 0.00 0.00 0.00 2.85
518 519 4.334481 AGCCATTGTACTTAACCGCATAAC 59.666 41.667 0.00 0.00 0.00 1.89
519 520 4.519213 AGCCATTGTACTTAACCGCATAA 58.481 39.130 0.00 0.00 0.00 1.90
520 521 4.145365 AGCCATTGTACTTAACCGCATA 57.855 40.909 0.00 0.00 0.00 3.14
521 522 2.999331 AGCCATTGTACTTAACCGCAT 58.001 42.857 0.00 0.00 0.00 4.73
522 523 2.483014 AGCCATTGTACTTAACCGCA 57.517 45.000 0.00 0.00 0.00 5.69
523 524 3.937079 ACTTAGCCATTGTACTTAACCGC 59.063 43.478 0.00 0.00 0.00 5.68
524 525 7.781548 ATTACTTAGCCATTGTACTTAACCG 57.218 36.000 0.00 0.00 0.00 4.44
614 615 8.508062 GCCGGTCCAAAAATATAAAACAATTTT 58.492 29.630 1.90 0.00 36.98 1.82
615 616 7.880713 AGCCGGTCCAAAAATATAAAACAATTT 59.119 29.630 1.90 0.00 0.00 1.82
616 617 7.390823 AGCCGGTCCAAAAATATAAAACAATT 58.609 30.769 1.90 0.00 0.00 2.32
617 618 6.941857 AGCCGGTCCAAAAATATAAAACAAT 58.058 32.000 1.90 0.00 0.00 2.71
618 619 6.209788 AGAGCCGGTCCAAAAATATAAAACAA 59.790 34.615 1.90 0.00 0.00 2.83
619 620 5.712917 AGAGCCGGTCCAAAAATATAAAACA 59.287 36.000 1.90 0.00 0.00 2.83
620 621 6.033966 CAGAGCCGGTCCAAAAATATAAAAC 58.966 40.000 1.90 0.00 0.00 2.43
621 622 5.393678 GCAGAGCCGGTCCAAAAATATAAAA 60.394 40.000 1.90 0.00 0.00 1.52
622 623 4.097286 GCAGAGCCGGTCCAAAAATATAAA 59.903 41.667 1.90 0.00 0.00 1.40
623 624 3.630312 GCAGAGCCGGTCCAAAAATATAA 59.370 43.478 1.90 0.00 0.00 0.98
624 625 3.211045 GCAGAGCCGGTCCAAAAATATA 58.789 45.455 1.90 0.00 0.00 0.86
625 626 2.024414 GCAGAGCCGGTCCAAAAATAT 58.976 47.619 1.90 0.00 0.00 1.28
626 627 1.459450 GCAGAGCCGGTCCAAAAATA 58.541 50.000 1.90 0.00 0.00 1.40
627 628 1.250840 GGCAGAGCCGGTCCAAAAAT 61.251 55.000 1.90 0.00 39.62 1.82
628 629 1.901464 GGCAGAGCCGGTCCAAAAA 60.901 57.895 1.90 0.00 39.62 1.94
629 630 2.282180 GGCAGAGCCGGTCCAAAA 60.282 61.111 1.90 0.00 39.62 2.44
639 640 1.001860 ACTTGTCTCTCTTGGCAGAGC 59.998 52.381 8.52 0.00 45.80 4.09
641 642 2.288457 CGAACTTGTCTCTCTTGGCAGA 60.288 50.000 0.00 0.00 0.00 4.26
642 643 2.064762 CGAACTTGTCTCTCTTGGCAG 58.935 52.381 0.00 0.00 0.00 4.85
643 644 1.270305 CCGAACTTGTCTCTCTTGGCA 60.270 52.381 0.00 0.00 0.00 4.92
644 645 1.433534 CCGAACTTGTCTCTCTTGGC 58.566 55.000 0.00 0.00 0.00 4.52
645 646 1.344763 ACCCGAACTTGTCTCTCTTGG 59.655 52.381 0.00 0.00 0.00 3.61
646 647 2.297597 AGACCCGAACTTGTCTCTCTTG 59.702 50.000 0.00 0.00 37.24 3.02
647 648 2.599677 AGACCCGAACTTGTCTCTCTT 58.400 47.619 0.00 0.00 37.24 2.85
648 649 2.296073 AGACCCGAACTTGTCTCTCT 57.704 50.000 0.00 0.00 37.24 3.10
649 650 2.159544 CGTAGACCCGAACTTGTCTCTC 60.160 54.545 0.00 0.00 40.84 3.20
650 651 1.811359 CGTAGACCCGAACTTGTCTCT 59.189 52.381 0.00 0.00 40.84 3.10
651 652 1.538950 ACGTAGACCCGAACTTGTCTC 59.461 52.381 0.00 0.00 40.84 3.36
652 653 1.613836 ACGTAGACCCGAACTTGTCT 58.386 50.000 0.00 0.00 43.85 3.41
653 654 2.226437 TGTACGTAGACCCGAACTTGTC 59.774 50.000 0.00 0.00 0.00 3.18
654 655 2.030805 GTGTACGTAGACCCGAACTTGT 60.031 50.000 11.64 0.00 0.00 3.16
655 656 2.589014 GTGTACGTAGACCCGAACTTG 58.411 52.381 11.64 0.00 0.00 3.16
656 657 1.541588 GGTGTACGTAGACCCGAACTT 59.458 52.381 27.23 0.00 33.79 2.66
657 658 1.168714 GGTGTACGTAGACCCGAACT 58.831 55.000 27.23 0.00 33.79 3.01
658 659 0.881118 TGGTGTACGTAGACCCGAAC 59.119 55.000 32.22 12.94 38.76 3.95
659 660 0.881118 GTGGTGTACGTAGACCCGAA 59.119 55.000 32.22 16.17 38.76 4.30
660 661 0.960364 GGTGGTGTACGTAGACCCGA 60.960 60.000 32.22 16.84 38.76 5.14
661 662 1.243342 TGGTGGTGTACGTAGACCCG 61.243 60.000 32.22 0.00 38.76 5.28
662 663 0.968405 TTGGTGGTGTACGTAGACCC 59.032 55.000 32.22 24.02 38.76 4.46
663 664 1.615392 AGTTGGTGGTGTACGTAGACC 59.385 52.381 29.85 29.85 39.87 3.85
664 665 2.352127 GGAGTTGGTGGTGTACGTAGAC 60.352 54.545 14.16 14.16 0.00 2.59
665 666 1.888512 GGAGTTGGTGGTGTACGTAGA 59.111 52.381 0.00 0.00 0.00 2.59
666 667 1.401931 CGGAGTTGGTGGTGTACGTAG 60.402 57.143 0.00 0.00 0.00 3.51
667 668 0.597568 CGGAGTTGGTGGTGTACGTA 59.402 55.000 0.00 0.00 0.00 3.57
668 669 1.364901 CGGAGTTGGTGGTGTACGT 59.635 57.895 0.00 0.00 0.00 3.57
669 670 1.373748 CCGGAGTTGGTGGTGTACG 60.374 63.158 0.00 0.00 0.00 3.67
670 671 0.037605 CTCCGGAGTTGGTGGTGTAC 60.038 60.000 24.04 0.00 0.00 2.90
671 672 1.189524 CCTCCGGAGTTGGTGGTGTA 61.190 60.000 29.25 0.00 37.78 2.90
672 673 2.516888 CCTCCGGAGTTGGTGGTGT 61.517 63.158 29.25 0.00 37.78 4.16
673 674 2.347490 CCTCCGGAGTTGGTGGTG 59.653 66.667 29.25 8.19 37.78 4.17
674 675 3.637273 GCCTCCGGAGTTGGTGGT 61.637 66.667 29.25 0.00 43.24 4.16
675 676 4.760047 CGCCTCCGGAGTTGGTGG 62.760 72.222 29.25 15.48 43.98 4.61
676 677 3.649277 CTCGCCTCCGGAGTTGGTG 62.649 68.421 29.25 21.34 34.56 4.17
677 678 3.382832 CTCGCCTCCGGAGTTGGT 61.383 66.667 29.25 0.00 34.56 3.67
678 679 4.821589 GCTCGCCTCCGGAGTTGG 62.822 72.222 29.25 17.01 34.56 3.77
679 680 3.997064 CTGCTCGCCTCCGGAGTTG 62.997 68.421 29.25 20.54 34.56 3.16
680 681 3.764466 CTGCTCGCCTCCGGAGTT 61.764 66.667 29.25 0.00 34.56 3.01
682 683 4.504916 CACTGCTCGCCTCCGGAG 62.505 72.222 25.36 25.36 34.56 4.63
686 687 3.695606 TCACCACTGCTCGCCTCC 61.696 66.667 0.00 0.00 0.00 4.30
687 688 2.433318 GTCACCACTGCTCGCCTC 60.433 66.667 0.00 0.00 0.00 4.70
688 689 3.231889 CTGTCACCACTGCTCGCCT 62.232 63.158 0.00 0.00 0.00 5.52
689 690 2.740055 CTGTCACCACTGCTCGCC 60.740 66.667 0.00 0.00 0.00 5.54
690 691 2.024319 GACTGTCACCACTGCTCGC 61.024 63.158 2.24 0.00 0.00 5.03
691 692 0.941463 GTGACTGTCACCACTGCTCG 60.941 60.000 26.50 0.00 41.37 5.03
692 693 2.906047 GTGACTGTCACCACTGCTC 58.094 57.895 26.50 2.58 41.37 4.26
701 702 2.421314 CGGTGCCAGTGACTGTCA 59.579 61.111 12.15 6.36 0.00 3.58
702 703 2.357517 CCGGTGCCAGTGACTGTC 60.358 66.667 12.15 0.00 0.00 3.51
703 704 3.941188 CCCGGTGCCAGTGACTGT 61.941 66.667 12.15 0.00 0.00 3.55
704 705 4.704833 CCCCGGTGCCAGTGACTG 62.705 72.222 5.42 5.42 0.00 3.51
705 706 4.954118 TCCCCGGTGCCAGTGACT 62.954 66.667 0.00 0.00 0.00 3.41
706 707 3.948719 TTCCCCGGTGCCAGTGAC 61.949 66.667 0.00 0.00 0.00 3.67
707 708 3.948719 GTTCCCCGGTGCCAGTGA 61.949 66.667 0.00 0.00 0.00 3.41
717 718 2.203153 CTATTGGCCCGTTCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
718 719 2.518587 GCTATTGGCCCGTTCCCC 60.519 66.667 0.00 0.00 34.27 4.81
719 720 1.526225 GAGCTATTGGCCCGTTCCC 60.526 63.158 0.00 0.00 43.05 3.97
720 721 0.179018 ATGAGCTATTGGCCCGTTCC 60.179 55.000 0.00 0.00 43.05 3.62
721 722 0.947244 CATGAGCTATTGGCCCGTTC 59.053 55.000 0.00 0.00 43.05 3.95
883 884 0.902531 CGTGGATAAGTGGTGGGTCT 59.097 55.000 0.00 0.00 0.00 3.85
978 979 1.351153 GCGCTCGTCTTTTCTAGCTT 58.649 50.000 0.00 0.00 32.73 3.74
1049 1050 2.416432 GCTAGGTCGCGGGAGAAGT 61.416 63.158 6.13 0.00 0.00 3.01
1147 1148 0.834687 TTAAGAGGGTCTGGGCGTGT 60.835 55.000 0.00 0.00 0.00 4.49
1250 1251 3.618690 ACTGAGATCTAACCTTGCCAC 57.381 47.619 0.00 0.00 0.00 5.01
1391 1392 7.756395 ATCAACATATTCATCAATCCACTCC 57.244 36.000 0.00 0.00 0.00 3.85
1417 1418 4.851639 ACATAGCCCTCAAACTGAATCT 57.148 40.909 0.00 0.00 0.00 2.40
1746 1748 3.184382 TCACATCCTCTACCCTGACAA 57.816 47.619 0.00 0.00 0.00 3.18
1860 1862 6.485313 TGAATTTGGGTGTGTACTCTGTTAAG 59.515 38.462 0.00 0.00 0.00 1.85
2196 2269 3.386932 ACCCAAACCATAGACATGCAT 57.613 42.857 0.00 0.00 0.00 3.96
2402 2510 2.710096 ATCGTGGAACTATGGGTTGG 57.290 50.000 0.00 0.00 38.41 3.77
2545 3084 1.430992 AGAACCCGAAGAAGAACCCA 58.569 50.000 0.00 0.00 0.00 4.51
2637 3183 3.087906 ACATGCTCCCGTACCCCC 61.088 66.667 0.00 0.00 0.00 5.40
2638 3184 2.189521 CACATGCTCCCGTACCCC 59.810 66.667 0.00 0.00 0.00 4.95
2651 3197 2.030363 CCAACAACGGTGTTATGCACAT 60.030 45.455 20.26 0.00 46.47 3.21


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

AutoCloner maintained by Alex Coulton.