Multiple sequence alignment - TraesCS5D01G190000

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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 TraesCS5D01G190000 chr5D 100.000 4712 0 0 1 4712 292276176 292271465 0.000000e+00 8702.0
1 TraesCS5D01G190000 chr5B 94.983 3887 118 26 282 4114 333029918 333026055 0.000000e+00 6026.0
2 TraesCS5D01G190000 chr5B 93.298 567 16 4 4147 4712 333026056 333025511 0.000000e+00 817.0
3 TraesCS5D01G190000 chr5A 93.801 3791 149 40 282 4003 384954758 384950985 0.000000e+00 5620.0
4 TraesCS5D01G190000 chr5A 91.991 462 27 4 4170 4626 384950741 384950285 1.430000e-179 640.0
5 TraesCS5D01G190000 chr5A 94.662 281 13 2 3 282 631741795 631741516 7.240000e-118 435.0
6 TraesCS5D01G190000 chr5A 92.832 279 18 2 4 281 617258379 617258102 2.040000e-108 403.0
7 TraesCS5D01G190000 chr5A 92.157 102 6 1 4611 4712 384950266 384950167 4.920000e-30 143.0
8 TraesCS5D01G190000 chr2B 95.307 277 11 2 3 278 765218671 765218946 5.600000e-119 438.0
9 TraesCS5D01G190000 chr3D 94.118 289 14 3 1 287 400997441 400997154 2.010000e-118 436.0
10 TraesCS5D01G190000 chr4B 94.286 280 14 2 3 281 650952995 650952717 1.210000e-115 427.0
11 TraesCS5D01G190000 chr7A 92.958 284 17 2 1 282 664109941 664109659 1.220000e-110 411.0
12 TraesCS5D01G190000 chr7A 92.000 50 4 0 3251 3300 55426299 55426250 2.350000e-08 71.3
13 TraesCS5D01G190000 chr6D 92.933 283 17 2 1 281 436885550 436885269 4.390000e-110 409.0
14 TraesCS5D01G190000 chr2A 92.832 279 16 4 4 281 656365621 656365346 7.340000e-108 401.0
15 TraesCS5D01G190000 chr2A 92.226 283 19 3 1 282 740045530 740045250 9.500000e-107 398.0
16 TraesCS5D01G190000 chr4A 92.000 50 4 0 3251 3300 668108327 668108278 2.350000e-08 71.3
17 TraesCS5D01G190000 chr7D 87.500 56 7 0 3245 3300 52697283 52697338 1.090000e-06 65.8


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 TraesCS5D01G190000 chr5D 292271465 292276176 4711 True 8702.000000 8702 100.000000 1 4712 1 chr5D.!!$R1 4711
1 TraesCS5D01G190000 chr5B 333025511 333029918 4407 True 3421.500000 6026 94.140500 282 4712 2 chr5B.!!$R1 4430
2 TraesCS5D01G190000 chr5A 384950167 384954758 4591 True 2134.333333 5620 92.649667 282 4712 3 chr5A.!!$R3 4430

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
25 26 0.047176 AGAGAGAGAGGAGGGGAGGA 59.953 60.0 0.0 0.0 0.00 3.71 F
128 129 0.107410 GCCGGTCCCACATGTCATAA 60.107 55.0 1.9 0.0 0.00 1.90 F
2006 2048 0.111061 AAGCACTGGGTTGCATGAGA 59.889 50.0 0.0 0.0 45.62 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2048 0.251787 GCAAACACCCCAGGGATTCT 60.252 55.000 7.25 0.0 38.96 2.40 R
2023 2065 2.203422 CCAACCAACCGGGAAGCA 60.203 61.111 6.32 0.0 41.15 3.91 R
3957 4037 0.106217 CACCTTGTTTCCCCACCAGT 60.106 55.000 0.00 0.0 0.00 4.00 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
19 20 1.566211 TGCCAAAGAGAGAGAGGAGG 58.434 55.000 0.00 0.00 0.00 4.30
20 21 0.829990 GCCAAAGAGAGAGAGGAGGG 59.170 60.000 0.00 0.00 0.00 4.30
21 22 1.494960 CCAAAGAGAGAGAGGAGGGG 58.505 60.000 0.00 0.00 0.00 4.79
22 23 1.007721 CCAAAGAGAGAGAGGAGGGGA 59.992 57.143 0.00 0.00 0.00 4.81
23 24 2.387757 CAAAGAGAGAGAGGAGGGGAG 58.612 57.143 0.00 0.00 0.00 4.30
24 25 0.933700 AAGAGAGAGAGGAGGGGAGG 59.066 60.000 0.00 0.00 0.00 4.30
25 26 0.047176 AGAGAGAGAGGAGGGGAGGA 59.953 60.000 0.00 0.00 0.00 3.71
26 27 0.930726 GAGAGAGAGGAGGGGAGGAA 59.069 60.000 0.00 0.00 0.00 3.36
27 28 0.933700 AGAGAGAGGAGGGGAGGAAG 59.066 60.000 0.00 0.00 0.00 3.46
28 29 0.930726 GAGAGAGGAGGGGAGGAAGA 59.069 60.000 0.00 0.00 0.00 2.87
29 30 1.289530 GAGAGAGGAGGGGAGGAAGAA 59.710 57.143 0.00 0.00 0.00 2.52
30 31 1.290732 AGAGAGGAGGGGAGGAAGAAG 59.709 57.143 0.00 0.00 0.00 2.85
31 32 1.289530 GAGAGGAGGGGAGGAAGAAGA 59.710 57.143 0.00 0.00 0.00 2.87
32 33 1.725182 AGAGGAGGGGAGGAAGAAGAA 59.275 52.381 0.00 0.00 0.00 2.52
33 34 2.115427 GAGGAGGGGAGGAAGAAGAAG 58.885 57.143 0.00 0.00 0.00 2.85
34 35 1.208706 GGAGGGGAGGAAGAAGAAGG 58.791 60.000 0.00 0.00 0.00 3.46
35 36 1.556002 GGAGGGGAGGAAGAAGAAGGT 60.556 57.143 0.00 0.00 0.00 3.50
36 37 2.270858 GAGGGGAGGAAGAAGAAGGTT 58.729 52.381 0.00 0.00 0.00 3.50
37 38 1.988846 AGGGGAGGAAGAAGAAGGTTG 59.011 52.381 0.00 0.00 0.00 3.77
38 39 1.985895 GGGGAGGAAGAAGAAGGTTGA 59.014 52.381 0.00 0.00 0.00 3.18
39 40 2.578480 GGGGAGGAAGAAGAAGGTTGAT 59.422 50.000 0.00 0.00 0.00 2.57
40 41 3.615155 GGGAGGAAGAAGAAGGTTGATG 58.385 50.000 0.00 0.00 0.00 3.07
41 42 3.264450 GGGAGGAAGAAGAAGGTTGATGA 59.736 47.826 0.00 0.00 0.00 2.92
42 43 4.080072 GGGAGGAAGAAGAAGGTTGATGAT 60.080 45.833 0.00 0.00 0.00 2.45
43 44 4.880696 GGAGGAAGAAGAAGGTTGATGATG 59.119 45.833 0.00 0.00 0.00 3.07
44 45 5.338708 GGAGGAAGAAGAAGGTTGATGATGA 60.339 44.000 0.00 0.00 0.00 2.92
45 46 5.495640 AGGAAGAAGAAGGTTGATGATGAC 58.504 41.667 0.00 0.00 0.00 3.06
46 47 4.331168 GGAAGAAGAAGGTTGATGATGACG 59.669 45.833 0.00 0.00 0.00 4.35
47 48 4.543590 AGAAGAAGGTTGATGATGACGT 57.456 40.909 0.00 0.00 0.00 4.34
48 49 4.248859 AGAAGAAGGTTGATGATGACGTG 58.751 43.478 0.00 0.00 0.00 4.49
49 50 3.685139 AGAAGGTTGATGATGACGTGT 57.315 42.857 0.00 0.00 0.00 4.49
50 51 3.329386 AGAAGGTTGATGATGACGTGTG 58.671 45.455 0.00 0.00 0.00 3.82
51 52 2.099141 AGGTTGATGATGACGTGTGG 57.901 50.000 0.00 0.00 0.00 4.17
52 53 1.086696 GGTTGATGATGACGTGTGGG 58.913 55.000 0.00 0.00 0.00 4.61
53 54 1.610624 GGTTGATGATGACGTGTGGGT 60.611 52.381 0.00 0.00 0.00 4.51
54 55 1.732259 GTTGATGATGACGTGTGGGTC 59.268 52.381 0.00 0.00 37.45 4.46
55 56 0.249120 TGATGATGACGTGTGGGTCC 59.751 55.000 0.00 0.00 36.07 4.46
56 57 0.462047 GATGATGACGTGTGGGTCCC 60.462 60.000 0.00 0.00 36.07 4.46
57 58 1.198094 ATGATGACGTGTGGGTCCCA 61.198 55.000 6.47 6.47 36.07 4.37
69 70 2.043992 TGGGTCCCACCTATCATAACG 58.956 52.381 6.47 0.00 38.64 3.18
70 71 1.346722 GGGTCCCACCTATCATAACGG 59.653 57.143 1.78 0.00 38.64 4.44
71 72 2.044758 GGTCCCACCTATCATAACGGT 58.955 52.381 0.00 0.00 34.73 4.83
72 73 2.436911 GGTCCCACCTATCATAACGGTT 59.563 50.000 0.00 0.00 34.73 4.44
73 74 3.642848 GGTCCCACCTATCATAACGGTTA 59.357 47.826 2.62 2.62 34.73 2.85
74 75 4.101430 GGTCCCACCTATCATAACGGTTAA 59.899 45.833 4.47 0.00 34.73 2.01
75 76 5.052481 GTCCCACCTATCATAACGGTTAAC 58.948 45.833 4.47 0.00 0.00 2.01
76 77 4.964262 TCCCACCTATCATAACGGTTAACT 59.036 41.667 4.47 0.00 0.00 2.24
77 78 5.426185 TCCCACCTATCATAACGGTTAACTT 59.574 40.000 4.47 0.00 0.00 2.66
78 79 5.526111 CCCACCTATCATAACGGTTAACTTG 59.474 44.000 4.47 0.00 0.00 3.16
79 80 6.342906 CCACCTATCATAACGGTTAACTTGA 58.657 40.000 4.47 5.03 0.00 3.02
80 81 6.257193 CCACCTATCATAACGGTTAACTTGAC 59.743 42.308 4.47 0.00 0.00 3.18
81 82 6.814644 CACCTATCATAACGGTTAACTTGACA 59.185 38.462 4.47 0.00 0.00 3.58
82 83 7.010183 CACCTATCATAACGGTTAACTTGACAG 59.990 40.741 4.47 3.40 0.00 3.51
83 84 7.039882 CCTATCATAACGGTTAACTTGACAGT 58.960 38.462 4.47 0.00 33.11 3.55
84 85 6.963049 ATCATAACGGTTAACTTGACAGTC 57.037 37.500 4.47 0.00 30.45 3.51
85 86 5.845103 TCATAACGGTTAACTTGACAGTCA 58.155 37.500 4.47 0.00 30.45 3.41
86 87 6.282167 TCATAACGGTTAACTTGACAGTCAA 58.718 36.000 15.39 15.39 34.79 3.18
87 88 6.762187 TCATAACGGTTAACTTGACAGTCAAA 59.238 34.615 16.85 0.00 35.73 2.69
88 89 5.883503 AACGGTTAACTTGACAGTCAAAA 57.116 34.783 16.85 6.16 35.73 2.44
89 90 6.445357 AACGGTTAACTTGACAGTCAAAAT 57.555 33.333 16.85 10.81 35.73 1.82
90 91 7.556733 AACGGTTAACTTGACAGTCAAAATA 57.443 32.000 16.85 9.89 35.73 1.40
91 92 7.556733 ACGGTTAACTTGACAGTCAAAATAA 57.443 32.000 16.85 14.58 35.73 1.40
92 93 7.987649 ACGGTTAACTTGACAGTCAAAATAAA 58.012 30.769 16.85 6.67 35.73 1.40
93 94 7.911727 ACGGTTAACTTGACAGTCAAAATAAAC 59.088 33.333 16.85 17.55 35.73 2.01
94 95 7.911205 CGGTTAACTTGACAGTCAAAATAAACA 59.089 33.333 23.09 3.05 35.73 2.83
95 96 9.233232 GGTTAACTTGACAGTCAAAATAAACAG 57.767 33.333 20.75 10.39 35.73 3.16
96 97 9.997482 GTTAACTTGACAGTCAAAATAAACAGA 57.003 29.630 16.85 0.00 35.73 3.41
98 99 7.865706 ACTTGACAGTCAAAATAAACAGAGT 57.134 32.000 16.85 4.60 35.73 3.24
99 100 8.281212 ACTTGACAGTCAAAATAAACAGAGTT 57.719 30.769 16.85 0.00 35.73 3.01
100 101 8.184192 ACTTGACAGTCAAAATAAACAGAGTTG 58.816 33.333 16.85 3.13 35.73 3.16
101 102 7.857734 TGACAGTCAAAATAAACAGAGTTGA 57.142 32.000 0.00 0.00 0.00 3.18
102 103 7.693952 TGACAGTCAAAATAAACAGAGTTGAC 58.306 34.615 0.00 6.71 45.37 3.18
107 108 7.831562 GTCAAAATAAACAGAGTTGACTTTGC 58.168 34.615 7.42 0.00 42.96 3.68
108 109 7.702348 GTCAAAATAAACAGAGTTGACTTTGCT 59.298 33.333 7.42 0.00 42.96 3.91
109 110 7.701924 TCAAAATAAACAGAGTTGACTTTGCTG 59.298 33.333 1.95 0.00 31.90 4.41
110 111 3.427161 AAACAGAGTTGACTTTGCTGC 57.573 42.857 1.95 0.00 31.90 5.25
111 112 1.312815 ACAGAGTTGACTTTGCTGCC 58.687 50.000 0.00 0.00 31.90 4.85
112 113 0.236711 CAGAGTTGACTTTGCTGCCG 59.763 55.000 0.00 0.00 0.00 5.69
113 114 0.886490 AGAGTTGACTTTGCTGCCGG 60.886 55.000 0.00 0.00 0.00 6.13
114 115 1.152963 AGTTGACTTTGCTGCCGGT 60.153 52.632 1.90 0.00 0.00 5.28
115 116 1.166531 AGTTGACTTTGCTGCCGGTC 61.167 55.000 1.90 3.62 0.00 4.79
116 117 1.896660 TTGACTTTGCTGCCGGTCC 60.897 57.895 1.90 0.00 0.00 4.46
117 118 3.056328 GACTTTGCTGCCGGTCCC 61.056 66.667 1.90 0.00 0.00 4.46
118 119 3.842925 GACTTTGCTGCCGGTCCCA 62.843 63.158 1.90 0.00 0.00 4.37
119 120 3.365265 CTTTGCTGCCGGTCCCAC 61.365 66.667 1.90 0.00 0.00 4.61
120 121 4.196778 TTTGCTGCCGGTCCCACA 62.197 61.111 1.90 0.00 0.00 4.17
121 122 3.505790 TTTGCTGCCGGTCCCACAT 62.506 57.895 1.90 0.00 0.00 3.21
122 123 4.720902 TGCTGCCGGTCCCACATG 62.721 66.667 1.90 0.00 0.00 3.21
123 124 4.722700 GCTGCCGGTCCCACATGT 62.723 66.667 1.90 0.00 0.00 3.21
124 125 2.436646 CTGCCGGTCCCACATGTC 60.437 66.667 1.90 0.00 0.00 3.06
125 126 3.245346 TGCCGGTCCCACATGTCA 61.245 61.111 1.90 0.00 0.00 3.58
126 127 2.272146 GCCGGTCCCACATGTCAT 59.728 61.111 1.90 0.00 0.00 3.06
127 128 1.268283 TGCCGGTCCCACATGTCATA 61.268 55.000 1.90 0.00 0.00 2.15
128 129 0.107410 GCCGGTCCCACATGTCATAA 60.107 55.000 1.90 0.00 0.00 1.90
129 130 1.680555 GCCGGTCCCACATGTCATAAA 60.681 52.381 1.90 0.00 0.00 1.40
130 131 2.014128 CCGGTCCCACATGTCATAAAC 58.986 52.381 0.00 0.00 0.00 2.01
131 132 2.616765 CCGGTCCCACATGTCATAAACA 60.617 50.000 0.00 0.00 43.51 2.83
132 133 2.677836 CGGTCCCACATGTCATAAACAG 59.322 50.000 0.00 0.00 42.37 3.16
133 134 3.016736 GGTCCCACATGTCATAAACAGG 58.983 50.000 0.00 0.00 45.14 4.00
168 169 5.376854 AAAAAGTCATCAACTCAATCGGG 57.623 39.130 0.00 0.00 37.17 5.14
169 170 3.703001 AAGTCATCAACTCAATCGGGT 57.297 42.857 0.00 0.00 37.17 5.28
170 171 4.819105 AAGTCATCAACTCAATCGGGTA 57.181 40.909 0.00 0.00 37.17 3.69
171 172 4.392921 AGTCATCAACTCAATCGGGTAG 57.607 45.455 0.00 0.00 30.02 3.18
172 173 3.769844 AGTCATCAACTCAATCGGGTAGT 59.230 43.478 0.00 0.00 30.02 2.73
173 174 4.223032 AGTCATCAACTCAATCGGGTAGTT 59.777 41.667 0.00 0.00 30.02 2.24
174 175 4.935808 GTCATCAACTCAATCGGGTAGTTT 59.064 41.667 0.00 0.00 31.21 2.66
175 176 5.411669 GTCATCAACTCAATCGGGTAGTTTT 59.588 40.000 0.00 0.00 31.21 2.43
176 177 6.001460 TCATCAACTCAATCGGGTAGTTTTT 58.999 36.000 0.00 0.00 31.21 1.94
198 199 8.722342 TTTTTGTCACGAAATTAGCACTAATC 57.278 30.769 3.47 0.00 34.90 1.75
199 200 7.667043 TTTGTCACGAAATTAGCACTAATCT 57.333 32.000 3.47 0.00 34.90 2.40
200 201 6.647212 TGTCACGAAATTAGCACTAATCTG 57.353 37.500 3.47 0.57 34.90 2.90
201 202 6.394809 TGTCACGAAATTAGCACTAATCTGA 58.605 36.000 3.47 1.26 34.90 3.27
202 203 6.871492 TGTCACGAAATTAGCACTAATCTGAA 59.129 34.615 3.47 0.00 34.90 3.02
203 204 7.063426 TGTCACGAAATTAGCACTAATCTGAAG 59.937 37.037 3.47 0.00 34.90 3.02
204 205 7.063544 GTCACGAAATTAGCACTAATCTGAAGT 59.936 37.037 3.47 0.00 34.90 3.01
205 206 7.602644 TCACGAAATTAGCACTAATCTGAAGTT 59.397 33.333 3.47 0.00 34.90 2.66
206 207 8.230486 CACGAAATTAGCACTAATCTGAAGTTT 58.770 33.333 3.47 0.00 34.90 2.66
207 208 8.784043 ACGAAATTAGCACTAATCTGAAGTTTT 58.216 29.630 3.47 0.00 34.90 2.43
208 209 9.612620 CGAAATTAGCACTAATCTGAAGTTTTT 57.387 29.630 3.47 0.00 34.90 1.94
210 211 9.696917 AAATTAGCACTAATCTGAAGTTTTTGG 57.303 29.630 3.47 0.00 34.90 3.28
211 212 7.817418 TTAGCACTAATCTGAAGTTTTTGGT 57.183 32.000 0.00 0.00 0.00 3.67
212 213 6.319141 AGCACTAATCTGAAGTTTTTGGTC 57.681 37.500 0.00 0.00 0.00 4.02
213 214 5.827797 AGCACTAATCTGAAGTTTTTGGTCA 59.172 36.000 0.00 0.00 0.00 4.02
214 215 6.016777 AGCACTAATCTGAAGTTTTTGGTCAG 60.017 38.462 0.00 0.00 40.15 3.51
215 216 6.238759 GCACTAATCTGAAGTTTTTGGTCAGT 60.239 38.462 0.00 0.00 39.82 3.41
216 217 7.682021 GCACTAATCTGAAGTTTTTGGTCAGTT 60.682 37.037 0.00 0.00 39.82 3.16
217 218 8.190784 CACTAATCTGAAGTTTTTGGTCAGTTT 58.809 33.333 0.00 0.00 39.82 2.66
218 219 8.749354 ACTAATCTGAAGTTTTTGGTCAGTTTT 58.251 29.630 0.00 0.00 39.82 2.43
219 220 9.586435 CTAATCTGAAGTTTTTGGTCAGTTTTT 57.414 29.630 0.00 0.00 39.82 1.94
221 222 9.936759 AATCTGAAGTTTTTGGTCAGTTTTTAA 57.063 25.926 0.00 0.00 39.82 1.52
222 223 9.936759 ATCTGAAGTTTTTGGTCAGTTTTTAAA 57.063 25.926 0.00 0.00 39.82 1.52
223 224 9.765795 TCTGAAGTTTTTGGTCAGTTTTTAAAA 57.234 25.926 0.00 0.00 39.82 1.52
228 229 8.726068 AGTTTTTGGTCAGTTTTTAAAATGTGG 58.274 29.630 0.55 0.00 35.64 4.17
229 230 8.508062 GTTTTTGGTCAGTTTTTAAAATGTGGT 58.492 29.630 0.55 0.00 35.64 4.16
230 231 9.720769 TTTTTGGTCAGTTTTTAAAATGTGGTA 57.279 25.926 0.55 0.00 35.64 3.25
231 232 8.934507 TTTGGTCAGTTTTTAAAATGTGGTAG 57.065 30.769 0.55 0.00 35.64 3.18
232 233 7.648039 TGGTCAGTTTTTAAAATGTGGTAGT 57.352 32.000 0.55 0.00 35.64 2.73
233 234 8.068892 TGGTCAGTTTTTAAAATGTGGTAGTT 57.931 30.769 0.55 0.00 35.64 2.24
234 235 8.192110 TGGTCAGTTTTTAAAATGTGGTAGTTC 58.808 33.333 0.55 0.00 35.64 3.01
235 236 8.410912 GGTCAGTTTTTAAAATGTGGTAGTTCT 58.589 33.333 0.55 0.00 35.64 3.01
236 237 9.233232 GTCAGTTTTTAAAATGTGGTAGTTCTG 57.767 33.333 0.55 0.00 35.64 3.02
237 238 8.962679 TCAGTTTTTAAAATGTGGTAGTTCTGT 58.037 29.630 0.55 0.00 35.64 3.41
238 239 9.019764 CAGTTTTTAAAATGTGGTAGTTCTGTG 57.980 33.333 0.55 0.00 0.00 3.66
239 240 8.194769 AGTTTTTAAAATGTGGTAGTTCTGTGG 58.805 33.333 0.55 0.00 0.00 4.17
240 241 7.883391 TTTTAAAATGTGGTAGTTCTGTGGA 57.117 32.000 0.00 0.00 0.00 4.02
241 242 7.883391 TTTAAAATGTGGTAGTTCTGTGGAA 57.117 32.000 0.00 0.00 0.00 3.53
266 267 6.980051 GGATACGTGAAATCTGGTAGTTTT 57.020 37.500 0.00 0.00 0.00 2.43
267 268 7.373778 GGATACGTGAAATCTGGTAGTTTTT 57.626 36.000 0.00 0.00 0.00 1.94
296 297 2.032680 ATTCGAATGTACCCAACCCG 57.967 50.000 10.50 0.00 0.00 5.28
307 308 1.738099 CCAACCCGACTCGAAGCAG 60.738 63.158 0.00 0.00 0.00 4.24
314 315 1.699656 CGACTCGAAGCAGCCATTGG 61.700 60.000 0.00 0.00 0.00 3.16
388 390 6.926272 AGCTTAGCTCTAGTTATCAAAATCGG 59.074 38.462 0.00 0.00 30.62 4.18
403 405 1.382522 ATCGGTTGCGCTGATCAAAT 58.617 45.000 9.73 0.00 38.82 2.32
436 438 2.094258 CACGATGACCCAGTCAAAATCG 59.906 50.000 14.37 14.37 45.96 3.34
474 478 5.841957 ATTAGACACCTCAATTGATTGCC 57.158 39.130 8.96 2.15 37.68 4.52
594 599 2.776312 CATGCACTCCATCTTCATGC 57.224 50.000 0.00 0.00 36.81 4.06
599 604 4.271661 TGCACTCCATCTTCATGCATAAA 58.728 39.130 0.00 0.00 41.18 1.40
604 609 7.485810 CACTCCATCTTCATGCATAAATTTCA 58.514 34.615 0.00 0.00 0.00 2.69
646 671 6.808008 TCAGGATGAAACAGTCTTCATTTC 57.192 37.500 10.47 0.00 45.97 2.17
775 804 1.202222 GCCTGCATTTCCATTGACTCG 60.202 52.381 0.00 0.00 0.00 4.18
779 808 1.462616 CATTTCCATTGACTCGGGCA 58.537 50.000 0.00 0.00 0.00 5.36
780 809 1.133025 CATTTCCATTGACTCGGGCAC 59.867 52.381 0.00 0.00 0.00 5.01
781 810 0.953471 TTTCCATTGACTCGGGCACG 60.953 55.000 0.00 0.00 42.74 5.34
782 811 2.047274 CCATTGACTCGGGCACGT 60.047 61.111 8.89 0.00 41.85 4.49
783 812 2.390599 CCATTGACTCGGGCACGTG 61.391 63.158 12.28 12.28 41.85 4.49
903 939 3.506067 CCAATTTACTCACTTCACCACCC 59.494 47.826 0.00 0.00 0.00 4.61
984 1020 3.931247 ACACCGGCACCGCAGTAA 61.931 61.111 0.00 0.00 38.24 2.24
990 1026 3.431725 GCACCGCAGTAAGCCACC 61.432 66.667 0.00 0.00 41.38 4.61
1429 1471 2.492090 CGGAGCCTCAACCTCTCG 59.508 66.667 0.00 0.00 0.00 4.04
1759 1801 1.002868 CCAGGAGCAGTTGAGGGTG 60.003 63.158 0.00 0.00 0.00 4.61
1827 1869 2.100418 GGTATTCTGGTACGTCCCTCAC 59.900 54.545 0.00 0.00 34.77 3.51
1858 1900 3.069729 ACCTGTCAAGTAACGAGCTTCTT 59.930 43.478 0.00 0.00 0.00 2.52
1867 1909 2.586648 ACGAGCTTCTTGGGGAATTT 57.413 45.000 0.00 0.00 33.01 1.82
1933 1975 2.631160 TCAACCAGTTGTCCACGAAT 57.369 45.000 10.17 0.00 41.16 3.34
1948 1990 1.062002 ACGAATAATTTGCTGGCGTCG 59.938 47.619 0.00 0.00 0.00 5.12
2006 2048 0.111061 AAGCACTGGGTTGCATGAGA 59.889 50.000 0.00 0.00 45.62 3.27
2023 2065 1.636003 GAGAGAATCCCTGGGGTGTTT 59.364 52.381 14.00 1.84 33.66 2.83
2178 2220 2.622942 TGTCACTGGTCAAGAAATTGGC 59.377 45.455 0.00 0.00 0.00 4.52
2311 2353 1.086696 CTGTAAACCCGGACAGCATG 58.913 55.000 0.73 0.00 46.00 4.06
2380 2422 0.961753 TGCTCACGCTCTTCTTCTCA 59.038 50.000 0.00 0.00 36.97 3.27
2459 2501 4.006989 TGACACATTTCCCGTTGATAAGG 58.993 43.478 0.00 0.00 0.00 2.69
2794 2836 2.710377 CTGGGACGGATCAAACATTCA 58.290 47.619 0.00 0.00 36.31 2.57
2947 2989 1.907739 CACCGACACATGGGAGGAT 59.092 57.895 18.42 3.27 0.00 3.24
3008 3050 2.046023 CTGCGGCATGGAGGTTCA 60.046 61.111 1.75 0.00 31.26 3.18
3010 3052 2.825836 GCGGCATGGAGGTTCAGG 60.826 66.667 0.00 0.00 0.00 3.86
3016 3058 1.171308 CATGGAGGTTCAGGCACAAG 58.829 55.000 0.00 0.00 0.00 3.16
3019 3061 1.425066 TGGAGGTTCAGGCACAAGATT 59.575 47.619 0.00 0.00 0.00 2.40
3023 3065 1.547372 GGTTCAGGCACAAGATTGCAT 59.453 47.619 0.00 0.00 44.94 3.96
3271 3313 1.463444 GACGTTTACAGCTTCGGCATT 59.537 47.619 0.00 0.00 44.74 3.56
3511 3553 1.028330 CCATGCAGCAGATCGTTGGT 61.028 55.000 0.00 0.00 0.00 3.67
3556 3598 4.111916 GAGTAGCAGATGAGAACTGAAGC 58.888 47.826 0.00 0.00 37.54 3.86
3594 3637 2.185004 ATTTTAGGCGTGTGAGCAGT 57.815 45.000 0.00 0.00 39.27 4.40
3728 3775 5.758296 CACACTTGCTCCTTTACTAACAGAA 59.242 40.000 0.00 0.00 0.00 3.02
3769 3817 4.207891 AGTAATCACAGCGGAAATGACT 57.792 40.909 0.00 0.00 0.00 3.41
3778 3827 1.392589 CGGAAATGACTCATTGGGGG 58.607 55.000 4.99 0.00 34.04 5.40
3779 3828 1.114627 GGAAATGACTCATTGGGGGC 58.885 55.000 4.99 0.00 34.04 5.80
3780 3829 0.740737 GAAATGACTCATTGGGGGCG 59.259 55.000 4.99 0.00 34.04 6.13
3781 3830 0.331278 AAATGACTCATTGGGGGCGA 59.669 50.000 4.99 0.00 34.04 5.54
3782 3831 0.552848 AATGACTCATTGGGGGCGAT 59.447 50.000 3.32 0.00 32.39 4.58
3783 3832 0.179009 ATGACTCATTGGGGGCGATG 60.179 55.000 0.00 0.00 0.00 3.84
3784 3833 2.124151 ACTCATTGGGGGCGATGC 60.124 61.111 0.00 0.00 0.00 3.91
3839 3894 2.104111 AGGAAAGTGTGTCGTGGATTGA 59.896 45.455 0.00 0.00 0.00 2.57
3845 3900 0.950555 GTGTCGTGGATTGAGCAGCA 60.951 55.000 0.00 0.00 0.00 4.41
3847 3902 1.375908 TCGTGGATTGAGCAGCACC 60.376 57.895 0.00 0.00 0.00 5.01
3864 3919 0.250124 ACCGCCTCATTTTGTGTCGA 60.250 50.000 0.00 0.00 0.00 4.20
3865 3920 0.165944 CCGCCTCATTTTGTGTCGAC 59.834 55.000 9.11 9.11 0.00 4.20
3866 3921 0.179250 CGCCTCATTTTGTGTCGACG 60.179 55.000 11.62 0.00 0.00 5.12
3869 3924 1.726791 CCTCATTTTGTGTCGACGGAG 59.273 52.381 11.62 8.37 0.00 4.63
3870 3925 2.609491 CCTCATTTTGTGTCGACGGAGA 60.609 50.000 11.62 1.20 0.00 3.71
3871 3926 2.400399 TCATTTTGTGTCGACGGAGAC 58.600 47.619 11.62 3.83 41.30 3.36
3920 4000 2.124570 CTTGGTGGCTGGGATCGG 60.125 66.667 0.00 0.00 0.00 4.18
3921 4001 4.424711 TTGGTGGCTGGGATCGGC 62.425 66.667 0.00 0.00 44.31 5.54
3923 4003 4.195334 GGTGGCTGGGATCGGCAT 62.195 66.667 0.00 0.00 46.76 4.40
3924 4004 2.592861 GTGGCTGGGATCGGCATC 60.593 66.667 0.00 0.00 46.76 3.91
3925 4005 4.240103 TGGCTGGGATCGGCATCG 62.240 66.667 6.35 0.00 46.76 3.84
3957 4037 2.805897 CCAAAGGTGGTTGCTGTCA 58.194 52.632 0.00 0.00 40.42 3.58
4123 4250 2.717580 GGGGGCAAAGTTCTAAAACG 57.282 50.000 0.00 0.00 40.48 3.60
4338 4500 6.748333 AGTGTCATTTTTCATGTCGATGAT 57.252 33.333 0.00 0.00 38.43 2.45
4349 4511 3.224884 TGTCGATGATGCGTGAACTTA 57.775 42.857 0.00 0.00 0.00 2.24
4374 4536 1.275505 TGCGCAATTGTGTTGTGTTG 58.724 45.000 19.60 0.00 32.87 3.33
4379 4541 3.122613 CGCAATTGTGTTGTGTTGTGTTT 59.877 39.130 10.93 0.00 0.00 2.83
4380 4542 4.376819 CGCAATTGTGTTGTGTTGTGTTTT 60.377 37.500 10.93 0.00 0.00 2.43
4381 4543 4.845060 GCAATTGTGTTGTGTTGTGTTTTG 59.155 37.500 7.40 0.00 0.00 2.44
4382 4544 5.559799 GCAATTGTGTTGTGTTGTGTTTTGT 60.560 36.000 7.40 0.00 0.00 2.83
4383 4545 6.425504 CAATTGTGTTGTGTTGTGTTTTGTT 58.574 32.000 0.00 0.00 0.00 2.83
4384 4546 5.395325 TTGTGTTGTGTTGTGTTTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
4385 4547 4.682787 TGTGTTGTGTTGTGTTTTGTTGA 58.317 34.783 0.00 0.00 0.00 3.18
4386 4548 5.109210 TGTGTTGTGTTGTGTTTTGTTGAA 58.891 33.333 0.00 0.00 0.00 2.69
4387 4549 5.233050 TGTGTTGTGTTGTGTTTTGTTGAAG 59.767 36.000 0.00 0.00 0.00 3.02
4388 4550 5.460419 GTGTTGTGTTGTGTTTTGTTGAAGA 59.540 36.000 0.00 0.00 0.00 2.87
4389 4551 5.460419 TGTTGTGTTGTGTTTTGTTGAAGAC 59.540 36.000 0.00 0.00 0.00 3.01
4645 4844 7.431376 CACATCTACACCGTAGTTATTAGTGTG 59.569 40.741 4.45 0.00 41.51 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.566211 CCTCCTCTCTCTCTTTGGCA 58.434 55.000 0.00 0.00 0.00 4.92
1 2 0.829990 CCCTCCTCTCTCTCTTTGGC 59.170 60.000 0.00 0.00 0.00 4.52
2 3 1.007721 TCCCCTCCTCTCTCTCTTTGG 59.992 57.143 0.00 0.00 0.00 3.28
3 4 2.387757 CTCCCCTCCTCTCTCTCTTTG 58.612 57.143 0.00 0.00 0.00 2.77
4 5 1.290732 CCTCCCCTCCTCTCTCTCTTT 59.709 57.143 0.00 0.00 0.00 2.52
5 6 0.933700 CCTCCCCTCCTCTCTCTCTT 59.066 60.000 0.00 0.00 0.00 2.85
6 7 0.047176 TCCTCCCCTCCTCTCTCTCT 59.953 60.000 0.00 0.00 0.00 3.10
7 8 0.930726 TTCCTCCCCTCCTCTCTCTC 59.069 60.000 0.00 0.00 0.00 3.20
8 9 0.933700 CTTCCTCCCCTCCTCTCTCT 59.066 60.000 0.00 0.00 0.00 3.10
9 10 0.930726 TCTTCCTCCCCTCCTCTCTC 59.069 60.000 0.00 0.00 0.00 3.20
10 11 1.290732 CTTCTTCCTCCCCTCCTCTCT 59.709 57.143 0.00 0.00 0.00 3.10
11 12 1.289530 TCTTCTTCCTCCCCTCCTCTC 59.710 57.143 0.00 0.00 0.00 3.20
12 13 1.398799 TCTTCTTCCTCCCCTCCTCT 58.601 55.000 0.00 0.00 0.00 3.69
13 14 2.115427 CTTCTTCTTCCTCCCCTCCTC 58.885 57.143 0.00 0.00 0.00 3.71
14 15 1.274126 CCTTCTTCTTCCTCCCCTCCT 60.274 57.143 0.00 0.00 0.00 3.69
15 16 1.208706 CCTTCTTCTTCCTCCCCTCC 58.791 60.000 0.00 0.00 0.00 4.30
16 17 1.959710 ACCTTCTTCTTCCTCCCCTC 58.040 55.000 0.00 0.00 0.00 4.30
17 18 1.988846 CAACCTTCTTCTTCCTCCCCT 59.011 52.381 0.00 0.00 0.00 4.79
18 19 1.985895 TCAACCTTCTTCTTCCTCCCC 59.014 52.381 0.00 0.00 0.00 4.81
19 20 3.264450 TCATCAACCTTCTTCTTCCTCCC 59.736 47.826 0.00 0.00 0.00 4.30
20 21 4.559862 TCATCAACCTTCTTCTTCCTCC 57.440 45.455 0.00 0.00 0.00 4.30
21 22 5.584251 GTCATCATCAACCTTCTTCTTCCTC 59.416 44.000 0.00 0.00 0.00 3.71
22 23 5.495640 GTCATCATCAACCTTCTTCTTCCT 58.504 41.667 0.00 0.00 0.00 3.36
23 24 4.331168 CGTCATCATCAACCTTCTTCTTCC 59.669 45.833 0.00 0.00 0.00 3.46
24 25 4.932200 ACGTCATCATCAACCTTCTTCTTC 59.068 41.667 0.00 0.00 0.00 2.87
25 26 4.692625 CACGTCATCATCAACCTTCTTCTT 59.307 41.667 0.00 0.00 0.00 2.52
26 27 4.248859 CACGTCATCATCAACCTTCTTCT 58.751 43.478 0.00 0.00 0.00 2.85
27 28 3.997021 ACACGTCATCATCAACCTTCTTC 59.003 43.478 0.00 0.00 0.00 2.87
28 29 3.748048 CACACGTCATCATCAACCTTCTT 59.252 43.478 0.00 0.00 0.00 2.52
29 30 3.329386 CACACGTCATCATCAACCTTCT 58.671 45.455 0.00 0.00 0.00 2.85
30 31 2.416547 CCACACGTCATCATCAACCTTC 59.583 50.000 0.00 0.00 0.00 3.46
31 32 2.426522 CCACACGTCATCATCAACCTT 58.573 47.619 0.00 0.00 0.00 3.50
32 33 1.339055 CCCACACGTCATCATCAACCT 60.339 52.381 0.00 0.00 0.00 3.50
33 34 1.086696 CCCACACGTCATCATCAACC 58.913 55.000 0.00 0.00 0.00 3.77
34 35 1.732259 GACCCACACGTCATCATCAAC 59.268 52.381 0.00 0.00 32.74 3.18
35 36 1.338674 GGACCCACACGTCATCATCAA 60.339 52.381 0.00 0.00 34.24 2.57
36 37 0.249120 GGACCCACACGTCATCATCA 59.751 55.000 0.00 0.00 34.24 3.07
37 38 0.462047 GGGACCCACACGTCATCATC 60.462 60.000 5.33 0.00 34.24 2.92
38 39 1.198094 TGGGACCCACACGTCATCAT 61.198 55.000 9.95 0.00 34.24 2.45
39 40 1.839296 TGGGACCCACACGTCATCA 60.839 57.895 9.95 0.00 34.24 3.07
40 41 3.065306 TGGGACCCACACGTCATC 58.935 61.111 9.95 0.00 34.24 2.92
49 50 2.043992 CGTTATGATAGGTGGGACCCA 58.956 52.381 9.95 9.95 39.75 4.51
50 51 1.346722 CCGTTATGATAGGTGGGACCC 59.653 57.143 2.45 2.45 39.75 4.46
51 52 2.044758 ACCGTTATGATAGGTGGGACC 58.955 52.381 0.00 0.00 36.81 4.46
52 53 3.832615 AACCGTTATGATAGGTGGGAC 57.167 47.619 0.00 0.00 38.44 4.46
53 54 4.964262 AGTTAACCGTTATGATAGGTGGGA 59.036 41.667 0.88 0.00 38.44 4.37
54 55 5.286267 AGTTAACCGTTATGATAGGTGGG 57.714 43.478 0.88 0.00 38.44 4.61
55 56 6.257193 GTCAAGTTAACCGTTATGATAGGTGG 59.743 42.308 0.88 0.00 38.44 4.61
56 57 6.814644 TGTCAAGTTAACCGTTATGATAGGTG 59.185 38.462 0.88 0.00 38.44 4.00
57 58 6.938507 TGTCAAGTTAACCGTTATGATAGGT 58.061 36.000 0.88 0.00 40.50 3.08
58 59 7.039882 ACTGTCAAGTTAACCGTTATGATAGG 58.960 38.462 15.74 5.87 30.14 2.57
59 60 7.758076 TGACTGTCAAGTTAACCGTTATGATAG 59.242 37.037 8.27 12.22 36.52 2.08
60 61 7.604549 TGACTGTCAAGTTAACCGTTATGATA 58.395 34.615 8.27 0.00 36.52 2.15
61 62 6.460781 TGACTGTCAAGTTAACCGTTATGAT 58.539 36.000 8.27 0.00 36.52 2.45
62 63 5.845103 TGACTGTCAAGTTAACCGTTATGA 58.155 37.500 8.27 0.00 36.52 2.15
63 64 6.533819 TTGACTGTCAAGTTAACCGTTATG 57.466 37.500 18.69 0.00 36.52 1.90
64 65 7.556733 TTTTGACTGTCAAGTTAACCGTTAT 57.443 32.000 21.13 0.00 37.70 1.89
65 66 6.981762 TTTTGACTGTCAAGTTAACCGTTA 57.018 33.333 21.13 2.16 37.70 3.18
66 67 5.883503 TTTTGACTGTCAAGTTAACCGTT 57.116 34.783 21.13 0.00 37.70 4.44
67 68 7.556733 TTATTTTGACTGTCAAGTTAACCGT 57.443 32.000 21.13 3.96 37.70 4.83
68 69 7.911205 TGTTTATTTTGACTGTCAAGTTAACCG 59.089 33.333 21.13 0.00 37.70 4.44
69 70 9.233232 CTGTTTATTTTGACTGTCAAGTTAACC 57.767 33.333 21.13 15.42 37.70 2.85
70 71 9.997482 TCTGTTTATTTTGACTGTCAAGTTAAC 57.003 29.630 21.13 20.78 37.70 2.01
72 73 9.391006 ACTCTGTTTATTTTGACTGTCAAGTTA 57.609 29.630 21.13 14.48 37.70 2.24
73 74 8.281212 ACTCTGTTTATTTTGACTGTCAAGTT 57.719 30.769 21.13 15.35 37.70 2.66
74 75 7.865706 ACTCTGTTTATTTTGACTGTCAAGT 57.134 32.000 21.13 16.51 37.70 3.16
75 76 8.397906 TCAACTCTGTTTATTTTGACTGTCAAG 58.602 33.333 21.13 9.03 37.70 3.02
76 77 8.181573 GTCAACTCTGTTTATTTTGACTGTCAA 58.818 33.333 18.69 18.69 41.78 3.18
77 78 7.693952 GTCAACTCTGTTTATTTTGACTGTCA 58.306 34.615 6.36 6.36 41.78 3.58
82 83 7.702348 AGCAAAGTCAACTCTGTTTATTTTGAC 59.298 33.333 13.08 4.90 44.18 3.18
83 84 7.701924 CAGCAAAGTCAACTCTGTTTATTTTGA 59.298 33.333 13.08 0.00 0.00 2.69
84 85 7.515684 GCAGCAAAGTCAACTCTGTTTATTTTG 60.516 37.037 7.67 7.67 0.00 2.44
85 86 6.476706 GCAGCAAAGTCAACTCTGTTTATTTT 59.523 34.615 0.00 0.00 0.00 1.82
86 87 5.979517 GCAGCAAAGTCAACTCTGTTTATTT 59.020 36.000 0.00 0.00 0.00 1.40
87 88 5.507985 GGCAGCAAAGTCAACTCTGTTTATT 60.508 40.000 0.00 0.00 0.00 1.40
88 89 4.022849 GGCAGCAAAGTCAACTCTGTTTAT 60.023 41.667 0.00 0.00 0.00 1.40
89 90 3.315191 GGCAGCAAAGTCAACTCTGTTTA 59.685 43.478 0.00 0.00 0.00 2.01
90 91 2.099756 GGCAGCAAAGTCAACTCTGTTT 59.900 45.455 0.00 0.00 0.00 2.83
91 92 1.678101 GGCAGCAAAGTCAACTCTGTT 59.322 47.619 0.00 0.00 0.00 3.16
92 93 1.312815 GGCAGCAAAGTCAACTCTGT 58.687 50.000 0.00 0.00 0.00 3.41
93 94 0.236711 CGGCAGCAAAGTCAACTCTG 59.763 55.000 0.00 0.00 0.00 3.35
94 95 0.886490 CCGGCAGCAAAGTCAACTCT 60.886 55.000 0.00 0.00 0.00 3.24
95 96 1.166531 ACCGGCAGCAAAGTCAACTC 61.167 55.000 0.00 0.00 0.00 3.01
96 97 1.152963 ACCGGCAGCAAAGTCAACT 60.153 52.632 0.00 0.00 0.00 3.16
97 98 1.282875 GACCGGCAGCAAAGTCAAC 59.717 57.895 0.00 0.00 0.00 3.18
98 99 1.896660 GGACCGGCAGCAAAGTCAA 60.897 57.895 0.00 0.00 0.00 3.18
99 100 2.281484 GGACCGGCAGCAAAGTCA 60.281 61.111 0.00 0.00 0.00 3.41
100 101 3.056328 GGGACCGGCAGCAAAGTC 61.056 66.667 0.00 0.00 0.00 3.01
101 102 3.884774 TGGGACCGGCAGCAAAGT 61.885 61.111 0.00 0.00 0.00 2.66
102 103 3.365265 GTGGGACCGGCAGCAAAG 61.365 66.667 0.00 0.00 0.00 2.77
103 104 3.505790 ATGTGGGACCGGCAGCAAA 62.506 57.895 0.00 0.00 0.00 3.68
104 105 3.965258 ATGTGGGACCGGCAGCAA 61.965 61.111 0.00 0.00 0.00 3.91
105 106 4.720902 CATGTGGGACCGGCAGCA 62.721 66.667 0.00 0.00 0.00 4.41
106 107 4.722700 ACATGTGGGACCGGCAGC 62.723 66.667 0.00 0.00 0.00 5.25
107 108 2.436646 GACATGTGGGACCGGCAG 60.437 66.667 1.15 0.00 0.00 4.85
108 109 1.268283 TATGACATGTGGGACCGGCA 61.268 55.000 1.15 0.00 0.00 5.69
109 110 0.107410 TTATGACATGTGGGACCGGC 60.107 55.000 1.15 0.00 0.00 6.13
110 111 2.014128 GTTTATGACATGTGGGACCGG 58.986 52.381 1.15 0.00 0.00 5.28
111 112 2.677836 CTGTTTATGACATGTGGGACCG 59.322 50.000 1.15 0.00 37.69 4.79
112 113 3.016736 CCTGTTTATGACATGTGGGACC 58.983 50.000 1.15 0.00 37.69 4.46
113 114 3.686016 ACCTGTTTATGACATGTGGGAC 58.314 45.455 1.15 0.00 36.03 4.46
114 115 4.380843 AACCTGTTTATGACATGTGGGA 57.619 40.909 1.15 0.00 37.22 4.37
115 116 6.582677 TTAAACCTGTTTATGACATGTGGG 57.417 37.500 1.15 0.00 37.22 4.61
116 117 9.139174 GATTTTAAACCTGTTTATGACATGTGG 57.861 33.333 1.15 0.00 37.22 4.17
117 118 9.689976 TGATTTTAAACCTGTTTATGACATGTG 57.310 29.630 1.15 0.00 37.22 3.21
146 147 4.827284 ACCCGATTGAGTTGATGACTTTTT 59.173 37.500 0.00 0.00 39.19 1.94
147 148 4.398319 ACCCGATTGAGTTGATGACTTTT 58.602 39.130 0.00 0.00 39.19 2.27
148 149 4.021102 ACCCGATTGAGTTGATGACTTT 57.979 40.909 0.00 0.00 39.19 2.66
149 150 3.703001 ACCCGATTGAGTTGATGACTT 57.297 42.857 0.00 0.00 39.19 3.01
150 151 3.769844 ACTACCCGATTGAGTTGATGACT 59.230 43.478 0.00 0.00 42.70 3.41
151 152 4.124851 ACTACCCGATTGAGTTGATGAC 57.875 45.455 0.00 0.00 0.00 3.06
152 153 4.819105 AACTACCCGATTGAGTTGATGA 57.181 40.909 0.00 0.00 32.25 2.92
153 154 5.880054 AAAACTACCCGATTGAGTTGATG 57.120 39.130 0.00 0.00 33.75 3.07
173 174 8.564574 AGATTAGTGCTAATTTCGTGACAAAAA 58.435 29.630 5.99 0.00 36.02 1.94
174 175 8.015087 CAGATTAGTGCTAATTTCGTGACAAAA 58.985 33.333 5.99 0.00 36.02 2.44
175 176 7.386573 TCAGATTAGTGCTAATTTCGTGACAAA 59.613 33.333 5.99 0.00 36.02 2.83
176 177 6.871492 TCAGATTAGTGCTAATTTCGTGACAA 59.129 34.615 5.99 0.00 36.02 3.18
177 178 6.394809 TCAGATTAGTGCTAATTTCGTGACA 58.605 36.000 5.99 0.00 36.02 3.58
178 179 6.887376 TCAGATTAGTGCTAATTTCGTGAC 57.113 37.500 5.99 0.00 36.02 3.67
179 180 7.097192 ACTTCAGATTAGTGCTAATTTCGTGA 58.903 34.615 5.99 5.13 36.02 4.35
180 181 7.295952 ACTTCAGATTAGTGCTAATTTCGTG 57.704 36.000 5.99 3.32 36.02 4.35
181 182 7.907214 AACTTCAGATTAGTGCTAATTTCGT 57.093 32.000 5.99 0.00 36.02 3.85
182 183 9.612620 AAAAACTTCAGATTAGTGCTAATTTCG 57.387 29.630 5.99 0.00 36.02 3.46
184 185 9.696917 CCAAAAACTTCAGATTAGTGCTAATTT 57.303 29.630 5.99 0.00 36.02 1.82
185 186 8.860088 ACCAAAAACTTCAGATTAGTGCTAATT 58.140 29.630 5.99 0.00 36.02 1.40
186 187 8.409358 ACCAAAAACTTCAGATTAGTGCTAAT 57.591 30.769 4.30 4.30 38.38 1.73
187 188 7.500892 TGACCAAAAACTTCAGATTAGTGCTAA 59.499 33.333 0.00 0.00 0.00 3.09
188 189 6.995686 TGACCAAAAACTTCAGATTAGTGCTA 59.004 34.615 0.00 0.00 0.00 3.49
189 190 5.827797 TGACCAAAAACTTCAGATTAGTGCT 59.172 36.000 0.00 0.00 0.00 4.40
190 191 6.072112 TGACCAAAAACTTCAGATTAGTGC 57.928 37.500 0.00 0.00 0.00 4.40
191 192 7.264373 ACTGACCAAAAACTTCAGATTAGTG 57.736 36.000 4.88 0.00 33.15 2.74
192 193 7.881775 AACTGACCAAAAACTTCAGATTAGT 57.118 32.000 4.88 0.00 33.15 2.24
193 194 9.586435 AAAAACTGACCAAAAACTTCAGATTAG 57.414 29.630 4.88 0.00 33.15 1.73
195 196 9.936759 TTAAAAACTGACCAAAAACTTCAGATT 57.063 25.926 4.88 0.00 33.15 2.40
196 197 9.936759 TTTAAAAACTGACCAAAAACTTCAGAT 57.063 25.926 4.88 0.00 33.15 2.90
197 198 9.765795 TTTTAAAAACTGACCAAAAACTTCAGA 57.234 25.926 0.00 0.00 33.15 3.27
202 203 8.726068 CCACATTTTAAAAACTGACCAAAAACT 58.274 29.630 4.44 0.00 0.00 2.66
203 204 8.508062 ACCACATTTTAAAAACTGACCAAAAAC 58.492 29.630 4.44 0.00 0.00 2.43
204 205 8.622948 ACCACATTTTAAAAACTGACCAAAAA 57.377 26.923 4.44 0.00 0.00 1.94
205 206 9.372369 CTACCACATTTTAAAAACTGACCAAAA 57.628 29.630 4.44 0.00 0.00 2.44
206 207 8.532819 ACTACCACATTTTAAAAACTGACCAAA 58.467 29.630 4.44 0.00 0.00 3.28
207 208 8.068892 ACTACCACATTTTAAAAACTGACCAA 57.931 30.769 4.44 0.00 0.00 3.67
208 209 7.648039 ACTACCACATTTTAAAAACTGACCA 57.352 32.000 4.44 0.00 0.00 4.02
209 210 8.410912 AGAACTACCACATTTTAAAAACTGACC 58.589 33.333 4.44 0.00 0.00 4.02
210 211 9.233232 CAGAACTACCACATTTTAAAAACTGAC 57.767 33.333 4.44 0.00 0.00 3.51
211 212 8.962679 ACAGAACTACCACATTTTAAAAACTGA 58.037 29.630 4.44 0.00 0.00 3.41
212 213 9.019764 CACAGAACTACCACATTTTAAAAACTG 57.980 33.333 4.44 2.42 0.00 3.16
213 214 8.194769 CCACAGAACTACCACATTTTAAAAACT 58.805 33.333 4.44 0.00 0.00 2.66
214 215 8.192110 TCCACAGAACTACCACATTTTAAAAAC 58.808 33.333 4.44 0.00 0.00 2.43
215 216 8.294954 TCCACAGAACTACCACATTTTAAAAA 57.705 30.769 4.44 0.00 0.00 1.94
216 217 7.883391 TCCACAGAACTACCACATTTTAAAA 57.117 32.000 2.51 2.51 0.00 1.52
217 218 7.883391 TTCCACAGAACTACCACATTTTAAA 57.117 32.000 0.00 0.00 0.00 1.52
242 243 4.303086 ACTACCAGATTTCACGTATCCG 57.697 45.455 0.00 0.00 40.83 4.18
243 244 6.980051 AAAACTACCAGATTTCACGTATCC 57.020 37.500 0.00 0.00 0.00 2.59
265 266 8.577296 TGGGTACATTCGAATAATTGACAAAAA 58.423 29.630 10.97 0.00 0.00 1.94
266 267 8.112016 TGGGTACATTCGAATAATTGACAAAA 57.888 30.769 10.97 0.00 0.00 2.44
267 268 7.689446 TGGGTACATTCGAATAATTGACAAA 57.311 32.000 10.97 0.00 0.00 2.83
268 269 7.362229 GGTTGGGTACATTCGAATAATTGACAA 60.362 37.037 10.97 9.32 0.00 3.18
269 270 6.094325 GGTTGGGTACATTCGAATAATTGACA 59.906 38.462 10.97 3.64 0.00 3.58
270 271 6.459161 GGGTTGGGTACATTCGAATAATTGAC 60.459 42.308 10.97 4.66 0.00 3.18
271 272 5.591067 GGGTTGGGTACATTCGAATAATTGA 59.409 40.000 10.97 0.00 0.00 2.57
272 273 5.504994 CGGGTTGGGTACATTCGAATAATTG 60.505 44.000 10.97 2.32 0.00 2.32
273 274 4.577283 CGGGTTGGGTACATTCGAATAATT 59.423 41.667 10.97 0.85 0.00 1.40
274 275 4.131596 CGGGTTGGGTACATTCGAATAAT 58.868 43.478 10.97 4.83 0.00 1.28
275 276 3.197333 TCGGGTTGGGTACATTCGAATAA 59.803 43.478 10.97 0.00 0.00 1.40
276 277 2.765135 TCGGGTTGGGTACATTCGAATA 59.235 45.455 10.97 0.00 0.00 1.75
277 278 1.555992 TCGGGTTGGGTACATTCGAAT 59.444 47.619 4.39 4.39 0.00 3.34
278 279 0.975135 TCGGGTTGGGTACATTCGAA 59.025 50.000 0.00 0.00 0.00 3.71
279 280 0.247185 GTCGGGTTGGGTACATTCGA 59.753 55.000 0.00 0.00 0.00 3.71
280 281 0.248289 AGTCGGGTTGGGTACATTCG 59.752 55.000 0.00 0.00 0.00 3.34
296 297 1.986575 GCCAATGGCTGCTTCGAGTC 61.987 60.000 18.47 0.00 46.69 3.36
314 315 4.337060 GCGTGGTTCCCCGTTTGC 62.337 66.667 0.00 0.00 0.00 3.68
342 344 1.412710 CCCTAGAAATGGTGCTCGCTA 59.587 52.381 0.00 0.00 0.00 4.26
388 390 0.986992 GTGCATTTGATCAGCGCAAC 59.013 50.000 11.47 7.99 38.56 4.17
436 438 8.893727 AGGTGTCTAATTGTGTATTTTATCTGC 58.106 33.333 0.00 0.00 0.00 4.26
455 459 3.087031 CAGGCAATCAATTGAGGTGTCT 58.913 45.455 18.59 18.59 40.14 3.41
474 478 2.886081 CTCCGTGAGTTTGGATCTCAG 58.114 52.381 0.00 0.00 41.66 3.35
599 604 9.699410 TGATTTGGTCAGGAAATAGTATGAAAT 57.301 29.630 0.00 0.00 31.80 2.17
642 667 5.242069 TCATTGTTGTGTTGTCACGAAAT 57.758 34.783 0.00 0.00 46.49 2.17
646 671 7.621832 ATTTAATCATTGTTGTGTTGTCACG 57.378 32.000 0.00 0.00 46.49 4.35
775 804 3.649277 ATCAGACTCGCACGTGCCC 62.649 63.158 33.23 19.59 37.91 5.36
779 808 3.181486 ACATATTCATCAGACTCGCACGT 60.181 43.478 0.00 0.00 0.00 4.49
780 809 3.181178 CACATATTCATCAGACTCGCACG 59.819 47.826 0.00 0.00 0.00 5.34
781 810 4.115516 ACACATATTCATCAGACTCGCAC 58.884 43.478 0.00 0.00 0.00 5.34
782 811 4.098501 AGACACATATTCATCAGACTCGCA 59.901 41.667 0.00 0.00 0.00 5.10
783 812 4.443725 CAGACACATATTCATCAGACTCGC 59.556 45.833 0.00 0.00 0.00 5.03
903 939 2.892334 CGCGGCCATAAATCGTGGG 61.892 63.158 2.24 0.00 37.22 4.61
990 1026 0.657368 GTGTTTCTCTTGGCGCGTTG 60.657 55.000 8.43 0.00 0.00 4.10
1613 1655 1.118356 AGATCCATGGAGACGAGGCC 61.118 60.000 21.33 0.00 0.00 5.19
1759 1801 2.608090 GCGGTTGTTGCTAAGGTCTATC 59.392 50.000 0.00 0.00 0.00 2.08
1827 1869 0.879765 ACTTGACAGGTCGAGGTACG 59.120 55.000 18.41 0.00 43.75 3.67
1858 1900 2.777146 GGGAGGCCAAATTCCCCA 59.223 61.111 15.65 0.00 46.15 4.96
1933 1975 1.400142 CCAATCGACGCCAGCAAATTA 59.600 47.619 0.00 0.00 0.00 1.40
1948 1990 6.376581 ACTCCAATGAAGAAATCTCACCAATC 59.623 38.462 0.00 0.00 0.00 2.67
2006 2048 0.251787 GCAAACACCCCAGGGATTCT 60.252 55.000 7.25 0.00 38.96 2.40
2023 2065 2.203422 CCAACCAACCGGGAAGCA 60.203 61.111 6.32 0.00 41.15 3.91
2178 2220 4.568359 AGAAGTTGAATCGATCCATTGACG 59.432 41.667 0.00 0.00 0.00 4.35
2459 2501 3.665173 GTCTTTGAATGACGATGGCTC 57.335 47.619 0.00 0.00 0.00 4.70
2755 2797 2.948648 CGCTCAAGCTCTCTCGCG 60.949 66.667 0.00 0.00 39.32 5.87
2794 2836 1.687563 CGGTCAAAGGAACCAGGTTT 58.312 50.000 6.21 0.00 0.00 3.27
2906 2948 1.506493 CAGTCTTCAGTGGTCTGCAC 58.494 55.000 0.00 0.00 41.10 4.57
2947 2989 3.674906 GCCACGCCACCATTGTTA 58.325 55.556 0.00 0.00 0.00 2.41
2968 3010 0.176680 CCTCTGGGGTGATGTTCTCG 59.823 60.000 0.00 0.00 0.00 4.04
3008 3050 1.753073 GCCTAATGCAATCTTGTGCCT 59.247 47.619 0.00 0.00 44.26 4.75
3010 3052 1.831343 CGCCTAATGCAATCTTGTGC 58.169 50.000 0.00 0.00 45.15 4.57
3016 3058 4.622364 GCAGCGCCTAATGCAATC 57.378 55.556 13.81 0.00 42.11 2.67
3023 3065 4.343323 TGCCCTTGCAGCGCCTAA 62.343 61.111 2.29 0.00 44.23 2.69
3511 3553 7.565398 ACTCTAGGCTCAATGTCCTTTAATAGA 59.435 37.037 0.00 0.03 34.02 1.98
3573 3616 3.435327 CACTGCTCACACGCCTAAAATAA 59.565 43.478 0.00 0.00 0.00 1.40
3594 3637 3.323979 GGAAACAACTAGGACCTCACTCA 59.676 47.826 0.00 0.00 0.00 3.41
3743 3790 5.580691 TCATTTCCGCTGTGATTACTTGTAG 59.419 40.000 0.00 0.00 0.00 2.74
3744 3791 5.350365 GTCATTTCCGCTGTGATTACTTGTA 59.650 40.000 0.00 0.00 0.00 2.41
3787 3836 2.981914 TACAGGACACGTGGGGTCGT 62.982 60.000 21.57 12.21 45.10 4.34
3788 3837 2.209064 CTACAGGACACGTGGGGTCG 62.209 65.000 21.57 6.60 36.12 4.79
3789 3838 1.590147 CTACAGGACACGTGGGGTC 59.410 63.158 21.57 8.36 34.52 4.46
3790 3839 1.911766 CCTACAGGACACGTGGGGT 60.912 63.158 21.57 13.82 37.39 4.95
3791 3840 1.189524 TTCCTACAGGACACGTGGGG 61.190 60.000 21.57 8.41 45.39 4.96
3817 3866 2.457366 ATCCACGACACACTTTCCTC 57.543 50.000 0.00 0.00 0.00 3.71
3839 3894 1.604593 AAAATGAGGCGGTGCTGCT 60.605 52.632 0.00 0.00 34.52 4.24
3845 3900 0.250124 TCGACACAAAATGAGGCGGT 60.250 50.000 3.32 0.00 0.00 5.68
3847 3902 0.179250 CGTCGACACAAAATGAGGCG 60.179 55.000 17.16 0.00 33.20 5.52
3869 3924 1.656652 CATCCATGAAGACCACCGTC 58.343 55.000 0.00 0.00 39.50 4.79
3870 3925 0.253044 CCATCCATGAAGACCACCGT 59.747 55.000 0.00 0.00 0.00 4.83
3871 3926 0.253044 ACCATCCATGAAGACCACCG 59.747 55.000 0.00 0.00 0.00 4.94
3874 3929 1.066215 CGACACCATCCATGAAGACCA 60.066 52.381 0.00 0.00 0.00 4.02
3875 3930 1.656652 CGACACCATCCATGAAGACC 58.343 55.000 0.00 0.00 0.00 3.85
3879 3934 1.449423 CGGCGACACCATCCATGAA 60.449 57.895 0.00 0.00 39.03 2.57
3953 4033 0.626382 TTGTTTCCCCACCAGTGACA 59.374 50.000 0.00 0.00 0.00 3.58
3957 4037 0.106217 CACCTTGTTTCCCCACCAGT 60.106 55.000 0.00 0.00 0.00 4.00
3987 4070 5.915628 TGGAGCTGGGATAGGAGAAATATA 58.084 41.667 0.00 0.00 0.00 0.86
4108 4235 5.212194 TGCTTCATCGTTTTAGAACTTTGC 58.788 37.500 0.00 0.00 33.51 3.68
4123 4250 5.363101 TCTGGATAAGTGTGATGCTTCATC 58.637 41.667 5.49 3.09 40.88 2.92
4309 4471 6.018588 TCGACATGAAAAATGACACTAACGTT 60.019 34.615 5.88 5.88 0.00 3.99
4338 4500 1.463056 CGCAAAGGATAAGTTCACGCA 59.537 47.619 0.00 0.00 0.00 5.24
4349 4511 2.224018 ACAACACAATTGCGCAAAGGAT 60.224 40.909 28.81 7.68 0.00 3.24
4374 4536 4.016113 AGCTTCGTCTTCAACAAAACAC 57.984 40.909 0.00 0.00 0.00 3.32
4379 4541 1.946768 CCCAAGCTTCGTCTTCAACAA 59.053 47.619 0.00 0.00 0.00 2.83
4380 4542 1.134220 ACCCAAGCTTCGTCTTCAACA 60.134 47.619 0.00 0.00 0.00 3.33
4381 4543 1.594331 ACCCAAGCTTCGTCTTCAAC 58.406 50.000 0.00 0.00 0.00 3.18
4382 4544 3.181458 ACTTACCCAAGCTTCGTCTTCAA 60.181 43.478 0.00 0.00 34.94 2.69
4383 4545 2.367567 ACTTACCCAAGCTTCGTCTTCA 59.632 45.455 0.00 0.00 34.94 3.02
4384 4546 3.041508 ACTTACCCAAGCTTCGTCTTC 57.958 47.619 0.00 0.00 34.94 2.87
4385 4547 3.487120 AACTTACCCAAGCTTCGTCTT 57.513 42.857 0.00 0.00 34.94 3.01
4386 4548 3.181458 TGAAACTTACCCAAGCTTCGTCT 60.181 43.478 0.00 0.00 38.95 4.18
4387 4549 3.135994 TGAAACTTACCCAAGCTTCGTC 58.864 45.455 0.00 0.00 38.95 4.20
4388 4550 3.202829 TGAAACTTACCCAAGCTTCGT 57.797 42.857 0.00 0.00 38.95 3.85
4389 4551 3.127030 GGATGAAACTTACCCAAGCTTCG 59.873 47.826 0.00 0.00 38.95 3.79
4462 4624 9.754382 ATTTTGATAATCATCCCAAAAGATTCG 57.246 29.630 0.00 0.00 40.41 3.34
4645 4844 1.610673 TCAGTCCTCCTCCAGTGCC 60.611 63.158 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.