Multiple sequence alignment - TraesCS5D01G038900

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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 TraesCS5D01G038900 chr5D 100.000 2498 0 0 1 2498 40022658 40025155 0.000000e+00 4614.0
1 TraesCS5D01G038900 chr5D 87.395 119 15 0 1171 1289 489188629 489188747 1.200000e-28 137.0
2 TraesCS5D01G038900 chr5B 92.103 2254 106 30 275 2498 33757696 33755485 0.000000e+00 3110.0
3 TraesCS5D01G038900 chr5B 87.395 119 15 0 1171 1289 602844123 602844241 1.200000e-28 137.0
4 TraesCS5D01G038900 chr5B 92.308 52 3 1 2062 2113 33755956 33755906 3.450000e-09 73.1
5 TraesCS5D01G038900 chr5A 89.986 1428 79 22 275 1693 27937463 27938835 0.000000e+00 1786.0
6 TraesCS5D01G038900 chr5A 81.538 390 48 13 2126 2498 27939118 27939500 1.450000e-77 300.0
7 TraesCS5D01G038900 chr5A 87.395 119 15 0 1171 1289 610231211 610231329 1.200000e-28 137.0
8 TraesCS5D01G038900 chr2D 91.958 286 21 2 2 285 414214797 414215082 1.390000e-107 399.0
9 TraesCS5D01G038900 chr2D 90.592 287 25 2 1 285 414187654 414187940 1.810000e-101 379.0
10 TraesCS5D01G038900 chr4D 92.364 275 17 3 1 273 371785707 371785979 3.010000e-104 388.0
11 TraesCS5D01G038900 chr1D 91.259 286 23 2 2 285 259265899 259266184 3.010000e-104 388.0
12 TraesCS5D01G038900 chr6D 91.228 285 23 2 2 284 157916975 157916691 1.080000e-103 387.0
13 TraesCS5D01G038900 chr7D 90.877 285 24 2 3 285 239521093 239521377 5.040000e-102 381.0
14 TraesCS5D01G038900 chr3D 90.877 285 25 1 2 285 417526157 417525873 5.040000e-102 381.0
15 TraesCS5D01G038900 chr3D 83.929 112 13 3 1181 1288 2537470 2537360 4.400000e-18 102.0
16 TraesCS5D01G038900 chr7B 90.493 284 26 1 3 285 162920663 162920380 8.440000e-100 374.0
17 TraesCS5D01G038900 chr3A 90.210 286 26 2 2 285 621415273 621414988 3.030000e-99 372.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G038900 chr5D 40022658 40025155 2497 False 4614.00 4614 100.0000 1 2498 1 chr5D.!!$F1 2497
1 TraesCS5D01G038900 chr5B 33755485 33757696 2211 True 1591.55 3110 92.2055 275 2498 2 chr5B.!!$R1 2223
2 TraesCS5D01G038900 chr5A 27937463 27939500 2037 False 1043.00 1786 85.7620 275 2498 2 chr5A.!!$F2 2223

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
216 217 0.03759 TCGTCCCTTGTTCCCCATTG 59.962 55.0 0.0 0.0 0.0 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2144 0.097674 GCTCGCAACCATGTCATGAC 59.902 55.0 19.27 19.27 0.0 3.06 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
39 40 3.849563 AAGGGTTTTGGTTTTTAGGGC 57.150 42.857 0.00 0.00 0.00 5.19
40 41 3.054779 AGGGTTTTGGTTTTTAGGGCT 57.945 42.857 0.00 0.00 0.00 5.19
41 42 4.201894 AGGGTTTTGGTTTTTAGGGCTA 57.798 40.909 0.00 0.00 0.00 3.93
42 43 4.157246 AGGGTTTTGGTTTTTAGGGCTAG 58.843 43.478 0.00 0.00 0.00 3.42
43 44 4.140876 AGGGTTTTGGTTTTTAGGGCTAGA 60.141 41.667 0.00 0.00 0.00 2.43
44 45 4.219944 GGGTTTTGGTTTTTAGGGCTAGAG 59.780 45.833 0.00 0.00 0.00 2.43
45 46 4.321750 GGTTTTGGTTTTTAGGGCTAGAGC 60.322 45.833 0.00 0.00 41.14 4.09
46 47 3.799432 TTGGTTTTTAGGGCTAGAGCA 57.201 42.857 3.54 0.00 44.36 4.26
47 48 3.799432 TGGTTTTTAGGGCTAGAGCAA 57.201 42.857 3.54 0.00 44.36 3.91
48 49 3.418047 TGGTTTTTAGGGCTAGAGCAAC 58.582 45.455 3.54 0.00 44.36 4.17
49 50 3.181438 TGGTTTTTAGGGCTAGAGCAACA 60.181 43.478 3.54 0.00 44.36 3.33
50 51 4.017126 GGTTTTTAGGGCTAGAGCAACAT 58.983 43.478 3.54 0.00 44.36 2.71
51 52 4.096532 GGTTTTTAGGGCTAGAGCAACATC 59.903 45.833 3.54 0.00 44.36 3.06
52 53 3.560636 TTTAGGGCTAGAGCAACATCC 57.439 47.619 3.54 0.00 44.36 3.51
53 54 2.174685 TAGGGCTAGAGCAACATCCA 57.825 50.000 3.54 0.00 44.36 3.41
54 55 1.516110 AGGGCTAGAGCAACATCCAT 58.484 50.000 3.54 0.00 44.36 3.41
55 56 1.419387 AGGGCTAGAGCAACATCCATC 59.581 52.381 3.54 0.00 44.36 3.51
56 57 1.506493 GGCTAGAGCAACATCCATCG 58.494 55.000 3.54 0.00 44.36 3.84
57 58 0.864455 GCTAGAGCAACATCCATCGC 59.136 55.000 0.00 0.00 41.59 4.58
58 59 1.506493 CTAGAGCAACATCCATCGCC 58.494 55.000 0.00 0.00 0.00 5.54
59 60 0.106708 TAGAGCAACATCCATCGCCC 59.893 55.000 0.00 0.00 0.00 6.13
60 61 2.124151 AGCAACATCCATCGCCCC 60.124 61.111 0.00 0.00 0.00 5.80
61 62 3.585990 GCAACATCCATCGCCCCG 61.586 66.667 0.00 0.00 0.00 5.73
62 63 2.124736 CAACATCCATCGCCCCGT 60.125 61.111 0.00 0.00 0.00 5.28
63 64 2.180204 CAACATCCATCGCCCCGTC 61.180 63.158 0.00 0.00 0.00 4.79
64 65 2.665089 AACATCCATCGCCCCGTCA 61.665 57.895 0.00 0.00 0.00 4.35
65 66 2.189257 CATCCATCGCCCCGTCAA 59.811 61.111 0.00 0.00 0.00 3.18
66 67 2.180204 CATCCATCGCCCCGTCAAC 61.180 63.158 0.00 0.00 0.00 3.18
67 68 3.400599 ATCCATCGCCCCGTCAACC 62.401 63.158 0.00 0.00 0.00 3.77
68 69 4.096003 CCATCGCCCCGTCAACCT 62.096 66.667 0.00 0.00 0.00 3.50
69 70 2.727392 CCATCGCCCCGTCAACCTA 61.727 63.158 0.00 0.00 0.00 3.08
70 71 1.227263 CATCGCCCCGTCAACCTAG 60.227 63.158 0.00 0.00 0.00 3.02
71 72 2.432300 ATCGCCCCGTCAACCTAGG 61.432 63.158 7.41 7.41 0.00 3.02
72 73 4.157120 CGCCCCGTCAACCTAGGG 62.157 72.222 14.81 0.00 44.67 3.53
73 74 3.007323 GCCCCGTCAACCTAGGGT 61.007 66.667 14.81 2.44 43.58 4.34
75 76 2.072366 CCCCGTCAACCTAGGGTTT 58.928 57.895 14.81 0.00 44.33 3.27
76 77 1.278537 CCCCGTCAACCTAGGGTTTA 58.721 55.000 14.81 0.00 44.33 2.01
77 78 1.208776 CCCCGTCAACCTAGGGTTTAG 59.791 57.143 14.81 0.00 44.33 1.85
78 79 1.406477 CCCGTCAACCTAGGGTTTAGC 60.406 57.143 14.81 0.00 44.33 3.09
79 80 1.553704 CCGTCAACCTAGGGTTTAGCT 59.446 52.381 14.81 0.00 44.33 3.32
80 81 2.418334 CCGTCAACCTAGGGTTTAGCTC 60.418 54.545 14.81 0.00 44.33 4.09
81 82 2.734492 CGTCAACCTAGGGTTTAGCTCG 60.734 54.545 14.81 0.95 44.33 5.03
82 83 1.206371 TCAACCTAGGGTTTAGCTCGC 59.794 52.381 14.81 0.00 44.33 5.03
83 84 0.540454 AACCTAGGGTTTAGCTCGCC 59.460 55.000 14.81 0.00 44.33 5.54
84 85 0.325390 ACCTAGGGTTTAGCTCGCCT 60.325 55.000 14.81 0.00 27.29 5.52
85 86 0.105039 CCTAGGGTTTAGCTCGCCTG 59.895 60.000 0.00 0.00 0.00 4.85
86 87 1.112113 CTAGGGTTTAGCTCGCCTGA 58.888 55.000 0.00 0.00 0.00 3.86
87 88 1.689273 CTAGGGTTTAGCTCGCCTGAT 59.311 52.381 0.00 0.00 0.00 2.90
88 89 0.466124 AGGGTTTAGCTCGCCTGATC 59.534 55.000 0.00 0.00 0.00 2.92
89 90 0.466124 GGGTTTAGCTCGCCTGATCT 59.534 55.000 0.00 0.00 0.00 2.75
90 91 1.539280 GGGTTTAGCTCGCCTGATCTC 60.539 57.143 0.00 0.00 0.00 2.75
91 92 1.482278 GTTTAGCTCGCCTGATCTCG 58.518 55.000 0.00 0.00 0.00 4.04
92 93 0.385751 TTTAGCTCGCCTGATCTCGG 59.614 55.000 0.00 0.00 0.00 4.63
93 94 1.456196 TTAGCTCGCCTGATCTCGGG 61.456 60.000 0.00 0.33 45.30 5.14
94 95 4.292178 GCTCGCCTGATCTCGGGG 62.292 72.222 7.17 10.92 42.72 5.73
95 96 2.835431 CTCGCCTGATCTCGGGGT 60.835 66.667 14.91 0.00 42.72 4.95
96 97 1.528542 CTCGCCTGATCTCGGGGTA 60.529 63.158 14.91 5.29 42.72 3.69
97 98 1.519751 CTCGCCTGATCTCGGGGTAG 61.520 65.000 14.91 9.48 42.72 3.18
98 99 1.528542 CGCCTGATCTCGGGGTAGA 60.529 63.158 7.17 0.00 42.72 2.59
99 100 0.896019 CGCCTGATCTCGGGGTAGAT 60.896 60.000 7.17 0.00 42.72 1.98
104 105 2.188062 GATCTCGGGGTAGATCGACT 57.812 55.000 5.91 0.00 41.75 4.18
105 106 2.078392 GATCTCGGGGTAGATCGACTC 58.922 57.143 5.91 1.15 41.75 3.36
106 107 1.129917 TCTCGGGGTAGATCGACTCT 58.870 55.000 5.77 0.00 38.06 3.24
107 108 1.202663 TCTCGGGGTAGATCGACTCTG 60.203 57.143 8.30 8.30 35.28 3.35
108 109 0.545171 TCGGGGTAGATCGACTCTGT 59.455 55.000 13.65 0.00 35.28 3.41
109 110 1.764723 TCGGGGTAGATCGACTCTGTA 59.235 52.381 13.65 0.00 35.28 2.74
110 111 2.171237 TCGGGGTAGATCGACTCTGTAA 59.829 50.000 13.65 0.00 35.28 2.41
111 112 2.290093 CGGGGTAGATCGACTCTGTAAC 59.710 54.545 6.51 0.00 35.28 2.50
112 113 2.622470 GGGGTAGATCGACTCTGTAACC 59.378 54.545 5.77 7.01 35.28 2.85
113 114 3.285484 GGGTAGATCGACTCTGTAACCA 58.715 50.000 5.91 0.00 33.42 3.67
114 115 3.890147 GGGTAGATCGACTCTGTAACCAT 59.110 47.826 5.91 0.00 33.42 3.55
115 116 5.068636 GGGTAGATCGACTCTGTAACCATA 58.931 45.833 5.91 0.00 33.42 2.74
116 117 5.711036 GGGTAGATCGACTCTGTAACCATAT 59.289 44.000 5.91 0.00 33.42 1.78
117 118 6.127952 GGGTAGATCGACTCTGTAACCATATC 60.128 46.154 5.91 0.00 33.42 1.63
118 119 6.430308 GGTAGATCGACTCTGTAACCATATCA 59.570 42.308 5.91 0.00 32.44 2.15
119 120 7.121463 GGTAGATCGACTCTGTAACCATATCAT 59.879 40.741 5.91 0.00 32.44 2.45
120 121 9.163899 GTAGATCGACTCTGTAACCATATCATA 57.836 37.037 0.00 0.00 35.28 2.15
121 122 8.815565 AGATCGACTCTGTAACCATATCATAT 57.184 34.615 0.00 0.00 31.12 1.78
122 123 9.907229 AGATCGACTCTGTAACCATATCATATA 57.093 33.333 0.00 0.00 31.12 0.86
123 124 9.938670 GATCGACTCTGTAACCATATCATATAC 57.061 37.037 0.00 0.00 0.00 1.47
124 125 8.857694 TCGACTCTGTAACCATATCATATACA 57.142 34.615 0.00 0.00 0.00 2.29
125 126 9.462606 TCGACTCTGTAACCATATCATATACAT 57.537 33.333 0.00 0.00 0.00 2.29
126 127 9.723447 CGACTCTGTAACCATATCATATACATC 57.277 37.037 0.00 0.00 0.00 3.06
145 146 5.883661 ACATCAAAATAATCAAGCAGGACG 58.116 37.500 0.00 0.00 0.00 4.79
146 147 5.415701 ACATCAAAATAATCAAGCAGGACGT 59.584 36.000 0.00 0.00 0.00 4.34
147 148 6.597672 ACATCAAAATAATCAAGCAGGACGTA 59.402 34.615 0.00 0.00 0.00 3.57
148 149 6.662414 TCAAAATAATCAAGCAGGACGTAG 57.338 37.500 0.00 0.00 0.00 3.51
149 150 5.584649 TCAAAATAATCAAGCAGGACGTAGG 59.415 40.000 0.00 0.00 0.00 3.18
150 151 3.753294 ATAATCAAGCAGGACGTAGGG 57.247 47.619 0.00 0.00 0.00 3.53
151 152 1.276622 AATCAAGCAGGACGTAGGGT 58.723 50.000 0.00 0.00 0.00 4.34
152 153 1.276622 ATCAAGCAGGACGTAGGGTT 58.723 50.000 0.00 0.00 0.00 4.11
153 154 1.053424 TCAAGCAGGACGTAGGGTTT 58.947 50.000 0.00 0.00 0.00 3.27
154 155 1.418637 TCAAGCAGGACGTAGGGTTTT 59.581 47.619 0.00 0.00 0.00 2.43
155 156 2.633967 TCAAGCAGGACGTAGGGTTTTA 59.366 45.455 0.00 0.00 0.00 1.52
156 157 2.740447 CAAGCAGGACGTAGGGTTTTAC 59.260 50.000 0.00 0.00 0.00 2.01
157 158 1.277273 AGCAGGACGTAGGGTTTTACC 59.723 52.381 0.00 0.00 37.60 2.85
158 159 1.277273 GCAGGACGTAGGGTTTTACCT 59.723 52.381 0.00 0.00 44.75 3.08
159 160 2.676176 GCAGGACGTAGGGTTTTACCTC 60.676 54.545 0.00 0.00 42.09 3.85
160 161 2.830321 CAGGACGTAGGGTTTTACCTCT 59.170 50.000 0.00 0.00 42.09 3.69
161 162 3.260128 CAGGACGTAGGGTTTTACCTCTT 59.740 47.826 0.00 0.00 42.09 2.85
162 163 3.513119 AGGACGTAGGGTTTTACCTCTTC 59.487 47.826 0.00 0.00 42.09 2.87
163 164 3.505836 GACGTAGGGTTTTACCTCTTCG 58.494 50.000 0.00 9.82 42.09 3.79
164 165 3.157087 ACGTAGGGTTTTACCTCTTCGA 58.843 45.455 14.92 0.00 42.09 3.71
165 166 3.192212 ACGTAGGGTTTTACCTCTTCGAG 59.808 47.826 14.92 0.00 42.09 4.04
166 167 3.441572 CGTAGGGTTTTACCTCTTCGAGA 59.558 47.826 0.00 0.00 42.09 4.04
167 168 4.438472 CGTAGGGTTTTACCTCTTCGAGAG 60.438 50.000 5.27 5.27 42.09 3.20
174 175 2.440430 CTCTTCGAGAGGGCCCGA 60.440 66.667 18.44 6.98 38.67 5.14
175 176 2.036731 TCTTCGAGAGGGCCCGAA 59.963 61.111 18.44 15.13 41.71 4.30
176 177 2.184579 CTTCGAGAGGGCCCGAAC 59.815 66.667 18.44 12.45 39.49 3.95
177 178 3.372554 CTTCGAGAGGGCCCGAACC 62.373 68.421 18.44 7.31 39.49 3.62
178 179 3.899545 TTCGAGAGGGCCCGAACCT 62.900 63.158 18.44 12.55 39.49 3.50
179 180 4.148825 CGAGAGGGCCCGAACCTG 62.149 72.222 18.44 1.23 38.79 4.00
180 181 3.787001 GAGAGGGCCCGAACCTGG 61.787 72.222 18.44 0.00 38.79 4.45
188 189 2.936928 CCCGAACCTGGGTAAACAC 58.063 57.895 0.00 0.00 44.76 3.32
189 190 0.607217 CCCGAACCTGGGTAAACACC 60.607 60.000 0.00 0.00 44.76 4.16
190 191 0.952010 CCGAACCTGGGTAAACACCG 60.952 60.000 0.00 0.00 0.00 4.94
191 192 0.249996 CGAACCTGGGTAAACACCGT 60.250 55.000 0.00 0.00 0.00 4.83
192 193 1.232119 GAACCTGGGTAAACACCGTG 58.768 55.000 0.00 0.00 0.00 4.94
193 194 0.547553 AACCTGGGTAAACACCGTGT 59.452 50.000 0.00 0.00 0.00 4.49
194 195 0.547553 ACCTGGGTAAACACCGTGTT 59.452 50.000 11.24 11.24 43.41 3.32
195 196 1.232119 CCTGGGTAAACACCGTGTTC 58.768 55.000 17.11 6.01 40.14 3.18
196 197 1.202722 CCTGGGTAAACACCGTGTTCT 60.203 52.381 17.11 10.05 40.14 3.01
197 198 2.567985 CTGGGTAAACACCGTGTTCTT 58.432 47.619 17.11 5.66 40.14 2.52
198 199 2.546789 CTGGGTAAACACCGTGTTCTTC 59.453 50.000 17.11 10.22 40.14 2.87
199 200 1.528161 GGGTAAACACCGTGTTCTTCG 59.472 52.381 17.11 0.00 40.14 3.79
200 201 2.204237 GGTAAACACCGTGTTCTTCGT 58.796 47.619 17.11 4.23 40.14 3.85
201 202 2.219445 GGTAAACACCGTGTTCTTCGTC 59.781 50.000 17.11 5.05 40.14 4.20
202 203 1.292992 AAACACCGTGTTCTTCGTCC 58.707 50.000 17.11 0.00 40.14 4.79
203 204 0.531311 AACACCGTGTTCTTCGTCCC 60.531 55.000 11.24 0.00 35.27 4.46
204 205 1.366366 CACCGTGTTCTTCGTCCCT 59.634 57.895 0.00 0.00 0.00 4.20
205 206 0.249741 CACCGTGTTCTTCGTCCCTT 60.250 55.000 0.00 0.00 0.00 3.95
206 207 0.249741 ACCGTGTTCTTCGTCCCTTG 60.250 55.000 0.00 0.00 0.00 3.61
207 208 0.249741 CCGTGTTCTTCGTCCCTTGT 60.250 55.000 0.00 0.00 0.00 3.16
208 209 1.578583 CGTGTTCTTCGTCCCTTGTT 58.421 50.000 0.00 0.00 0.00 2.83
209 210 1.525619 CGTGTTCTTCGTCCCTTGTTC 59.474 52.381 0.00 0.00 0.00 3.18
210 211 1.871676 GTGTTCTTCGTCCCTTGTTCC 59.128 52.381 0.00 0.00 0.00 3.62
211 212 1.202722 TGTTCTTCGTCCCTTGTTCCC 60.203 52.381 0.00 0.00 0.00 3.97
212 213 0.399075 TTCTTCGTCCCTTGTTCCCC 59.601 55.000 0.00 0.00 0.00 4.81
213 214 0.765135 TCTTCGTCCCTTGTTCCCCA 60.765 55.000 0.00 0.00 0.00 4.96
214 215 0.328258 CTTCGTCCCTTGTTCCCCAT 59.672 55.000 0.00 0.00 0.00 4.00
215 216 0.774908 TTCGTCCCTTGTTCCCCATT 59.225 50.000 0.00 0.00 0.00 3.16
216 217 0.037590 TCGTCCCTTGTTCCCCATTG 59.962 55.000 0.00 0.00 0.00 2.82
217 218 0.037590 CGTCCCTTGTTCCCCATTGA 59.962 55.000 0.00 0.00 0.00 2.57
218 219 1.340991 CGTCCCTTGTTCCCCATTGAT 60.341 52.381 0.00 0.00 0.00 2.57
219 220 2.379005 GTCCCTTGTTCCCCATTGATC 58.621 52.381 0.00 0.00 0.00 2.92
220 221 1.287739 TCCCTTGTTCCCCATTGATCC 59.712 52.381 0.00 0.00 0.00 3.36
221 222 1.288932 CCCTTGTTCCCCATTGATCCT 59.711 52.381 0.00 0.00 0.00 3.24
222 223 2.513738 CCCTTGTTCCCCATTGATCCTA 59.486 50.000 0.00 0.00 0.00 2.94
223 224 3.435601 CCCTTGTTCCCCATTGATCCTAG 60.436 52.174 0.00 0.00 0.00 3.02
224 225 3.459598 CCTTGTTCCCCATTGATCCTAGA 59.540 47.826 0.00 0.00 0.00 2.43
225 226 4.105377 CCTTGTTCCCCATTGATCCTAGAT 59.895 45.833 0.00 0.00 0.00 1.98
226 227 4.982241 TGTTCCCCATTGATCCTAGATC 57.018 45.455 0.00 0.00 0.00 2.75
227 228 4.570926 TGTTCCCCATTGATCCTAGATCT 58.429 43.478 0.00 0.00 0.00 2.75
228 229 5.726560 TGTTCCCCATTGATCCTAGATCTA 58.273 41.667 1.69 1.69 0.00 1.98
229 230 5.544176 TGTTCCCCATTGATCCTAGATCTAC 59.456 44.000 0.00 0.00 0.00 2.59
230 231 5.354184 TCCCCATTGATCCTAGATCTACA 57.646 43.478 0.00 0.00 0.00 2.74
231 232 5.336945 TCCCCATTGATCCTAGATCTACAG 58.663 45.833 0.00 0.00 0.00 2.74
232 233 4.081198 CCCCATTGATCCTAGATCTACAGC 60.081 50.000 0.00 0.00 0.00 4.40
233 234 4.776837 CCCATTGATCCTAGATCTACAGCT 59.223 45.833 0.00 0.00 0.00 4.24
234 235 5.105392 CCCATTGATCCTAGATCTACAGCTC 60.105 48.000 0.00 0.00 0.00 4.09
235 236 5.392919 CCATTGATCCTAGATCTACAGCTCG 60.393 48.000 0.00 0.00 0.00 5.03
236 237 3.680490 TGATCCTAGATCTACAGCTCGG 58.320 50.000 0.00 0.00 0.00 4.63
237 238 2.570415 TCCTAGATCTACAGCTCGGG 57.430 55.000 0.00 0.00 0.00 5.14
238 239 2.055579 TCCTAGATCTACAGCTCGGGA 58.944 52.381 0.00 0.00 0.00 5.14
239 240 2.156098 CCTAGATCTACAGCTCGGGAC 58.844 57.143 0.00 0.00 0.00 4.46
240 241 2.156098 CTAGATCTACAGCTCGGGACC 58.844 57.143 0.00 0.00 0.00 4.46
241 242 0.468400 AGATCTACAGCTCGGGACCC 60.468 60.000 0.00 0.00 0.00 4.46
242 243 1.457831 ATCTACAGCTCGGGACCCC 60.458 63.158 4.46 0.00 0.00 4.95
243 244 1.950748 ATCTACAGCTCGGGACCCCT 61.951 60.000 4.46 0.00 0.00 4.79
244 245 1.229359 CTACAGCTCGGGACCCCTA 59.771 63.158 4.46 0.00 0.00 3.53
245 246 0.178958 CTACAGCTCGGGACCCCTAT 60.179 60.000 4.46 0.00 0.00 2.57
246 247 0.178970 TACAGCTCGGGACCCCTATC 60.179 60.000 4.46 0.00 0.00 2.08
247 248 2.201771 AGCTCGGGACCCCTATCC 59.798 66.667 4.46 0.00 38.13 2.59
248 249 3.303928 GCTCGGGACCCCTATCCG 61.304 72.222 4.46 0.00 44.59 4.18
250 251 2.519441 TCGGGACCCCTATCCGAG 59.481 66.667 4.46 0.00 46.48 4.63
251 252 2.080536 TCGGGACCCCTATCCGAGA 61.081 63.158 4.46 0.00 46.48 4.04
252 253 1.076906 CGGGACCCCTATCCGAGAT 59.923 63.158 4.46 0.00 45.96 2.75
253 254 0.966370 CGGGACCCCTATCCGAGATC 60.966 65.000 4.46 0.00 45.96 2.75
254 255 0.410270 GGGACCCCTATCCGAGATCT 59.590 60.000 0.00 0.00 39.97 2.75
255 256 1.551452 GGACCCCTATCCGAGATCTG 58.449 60.000 0.00 0.00 0.00 2.90
256 257 0.892063 GACCCCTATCCGAGATCTGC 59.108 60.000 0.00 0.00 0.00 4.26
257 258 0.543174 ACCCCTATCCGAGATCTGCC 60.543 60.000 0.00 0.00 0.00 4.85
258 259 1.599606 CCCCTATCCGAGATCTGCCG 61.600 65.000 0.00 0.00 0.00 5.69
259 260 1.599606 CCCTATCCGAGATCTGCCGG 61.600 65.000 15.06 15.06 46.57 6.13
260 261 0.896019 CCTATCCGAGATCTGCCGGT 60.896 60.000 19.18 11.18 45.48 5.28
261 262 0.962489 CTATCCGAGATCTGCCGGTT 59.038 55.000 19.18 14.62 45.48 4.44
262 263 1.341531 CTATCCGAGATCTGCCGGTTT 59.658 52.381 19.18 12.24 45.48 3.27
263 264 0.541863 ATCCGAGATCTGCCGGTTTT 59.458 50.000 19.18 6.39 45.48 2.43
264 265 0.391130 TCCGAGATCTGCCGGTTTTG 60.391 55.000 19.18 0.00 45.48 2.44
265 266 0.391130 CCGAGATCTGCCGGTTTTGA 60.391 55.000 13.39 0.00 40.78 2.69
266 267 0.721718 CGAGATCTGCCGGTTTTGAC 59.278 55.000 0.00 0.00 0.00 3.18
267 268 1.808411 GAGATCTGCCGGTTTTGACA 58.192 50.000 0.00 0.00 0.00 3.58
268 269 1.464997 GAGATCTGCCGGTTTTGACAC 59.535 52.381 0.00 0.00 0.00 3.67
269 270 0.521735 GATCTGCCGGTTTTGACACC 59.478 55.000 1.90 0.00 0.00 4.16
299 300 3.185299 TTTCCACGCCGTGACCCAT 62.185 57.895 20.57 0.00 35.23 4.00
307 308 1.602237 CCGTGACCCATGCCTACTT 59.398 57.895 0.00 0.00 0.00 2.24
334 335 1.157257 CGCAACACTAGCACACACCA 61.157 55.000 0.00 0.00 0.00 4.17
335 336 1.238439 GCAACACTAGCACACACCAT 58.762 50.000 0.00 0.00 0.00 3.55
336 337 2.422597 GCAACACTAGCACACACCATA 58.577 47.619 0.00 0.00 0.00 2.74
360 361 3.812019 CGGACACGACCCTCTCCG 61.812 72.222 0.00 0.00 44.60 4.63
398 399 1.499007 AGTTTTCAAAGCCCTCCCTGA 59.501 47.619 0.00 0.00 0.00 3.86
437 438 1.372087 GCCTCGCCACTTCCTTCATG 61.372 60.000 0.00 0.00 0.00 3.07
449 450 2.507484 TCCTTCATGAGTGGCACAAAG 58.493 47.619 21.41 13.57 44.16 2.77
455 456 4.713553 TCATGAGTGGCACAAAGTAAAGA 58.286 39.130 21.41 3.67 44.16 2.52
461 462 1.235724 GCACAAAGTAAAGAGGGCGT 58.764 50.000 0.00 0.00 0.00 5.68
490 496 0.827925 TGGCTCTAGGGTATCTGCCG 60.828 60.000 0.00 0.00 42.87 5.69
508 515 3.996124 CGAGGGCCGATGCTAGGG 61.996 72.222 0.00 0.00 41.76 3.53
534 541 5.883503 ACCAAAACGTTTTGTTCTGTCTA 57.116 34.783 37.80 0.00 44.52 2.59
539 546 4.128554 ACGTTTTGTTCTGTCTATTGCG 57.871 40.909 0.00 0.00 0.00 4.85
555 562 6.092259 GTCTATTGCGTTCCTTGTAGTCAATT 59.908 38.462 0.00 0.00 32.82 2.32
699 714 8.119226 GTGATCTCTGTAGCAATTATGTTGTTC 58.881 37.037 0.00 0.00 0.00 3.18
700 715 7.823799 TGATCTCTGTAGCAATTATGTTGTTCA 59.176 33.333 0.00 0.00 0.00 3.18
701 716 7.601073 TCTCTGTAGCAATTATGTTGTTCAG 57.399 36.000 0.00 0.00 0.00 3.02
702 717 7.161404 TCTCTGTAGCAATTATGTTGTTCAGT 58.839 34.615 0.00 0.00 0.00 3.41
703 718 7.661437 TCTCTGTAGCAATTATGTTGTTCAGTT 59.339 33.333 0.00 0.00 0.00 3.16
704 719 7.806690 TCTGTAGCAATTATGTTGTTCAGTTC 58.193 34.615 0.00 0.00 0.00 3.01
705 720 6.908825 TGTAGCAATTATGTTGTTCAGTTCC 58.091 36.000 0.00 0.00 0.00 3.62
706 721 6.714810 TGTAGCAATTATGTTGTTCAGTTCCT 59.285 34.615 0.00 0.00 0.00 3.36
707 722 6.655078 AGCAATTATGTTGTTCAGTTCCTT 57.345 33.333 0.00 0.00 0.00 3.36
708 723 6.449698 AGCAATTATGTTGTTCAGTTCCTTG 58.550 36.000 0.00 0.00 0.00 3.61
709 724 5.119125 GCAATTATGTTGTTCAGTTCCTTGC 59.881 40.000 0.00 0.00 0.00 4.01
710 725 4.846779 TTATGTTGTTCAGTTCCTTGCC 57.153 40.909 0.00 0.00 0.00 4.52
895 910 2.149383 ACCCAAGCAGAGCTCACCA 61.149 57.895 17.77 0.00 38.25 4.17
989 1004 5.003160 TCAAAAGCATTCGATCTCCTTTGA 58.997 37.500 7.86 7.86 0.00 2.69
1021 1036 3.636231 CGGCTCCACCACCTTCCA 61.636 66.667 0.00 0.00 39.03 3.53
1029 1044 1.614317 CCACCACCTTCCACCTTCATC 60.614 57.143 0.00 0.00 0.00 2.92
1148 1169 2.992689 TGGCAATGGCAGTGGCAG 60.993 61.111 35.29 13.15 45.61 4.85
1152 1173 4.085876 AATGGCAGTGGCAGTGAC 57.914 55.556 25.96 23.79 42.43 3.67
1153 1174 1.151221 AATGGCAGTGGCAGTGACA 59.849 52.632 31.63 31.63 41.53 3.58
1154 1175 0.467844 AATGGCAGTGGCAGTGACAA 60.468 50.000 32.93 17.48 40.50 3.18
1155 1176 1.174712 ATGGCAGTGGCAGTGACAAC 61.175 55.000 32.93 15.58 40.50 3.32
1245 1266 3.948719 GGGGGACACCAGAACGCA 61.949 66.667 0.00 0.00 42.91 5.24
1331 1352 3.592814 CGCTGATGCCATGCCCAG 61.593 66.667 0.00 0.00 35.36 4.45
1332 1353 2.441532 GCTGATGCCATGCCCAGT 60.442 61.111 0.00 0.00 33.21 4.00
1599 1620 7.908453 TCTTTCTCTTCTCCCTTTTTAGTAGG 58.092 38.462 0.00 0.00 0.00 3.18
1600 1621 7.513091 TCTTTCTCTTCTCCCTTTTTAGTAGGT 59.487 37.037 0.00 0.00 0.00 3.08
1601 1622 6.607004 TCTCTTCTCCCTTTTTAGTAGGTG 57.393 41.667 0.00 0.00 0.00 4.00
1602 1623 6.082707 TCTCTTCTCCCTTTTTAGTAGGTGT 58.917 40.000 0.00 0.00 0.00 4.16
1628 1649 4.694037 GTGGGTACTTGGTTAATGAGTGTC 59.306 45.833 0.00 0.00 0.00 3.67
1700 1721 3.982576 AGTTGTTCGATTGTTTGGGAC 57.017 42.857 0.00 0.00 0.00 4.46
1726 1747 9.020813 CAAGAATCAGAAATATTGCACATTCTG 57.979 33.333 15.73 17.48 46.36 3.02
1757 1778 7.928307 AACATCTACACATAATCTTGCTGTT 57.072 32.000 0.00 0.00 0.00 3.16
1852 1873 6.601613 TGTTTTGAGCTTCTCCAAAGTTCTAA 59.398 34.615 0.00 0.34 28.21 2.10
1921 1959 6.971602 TGTCACCGCAAGTAATTAATTGAAA 58.028 32.000 25.42 0.67 33.49 2.69
1958 1996 9.657419 AAATGTTTCTTTTTCTGAACAATCACT 57.343 25.926 0.00 0.00 0.00 3.41
1980 2018 0.548510 GGAGAAAGGATCCCCACCTG 59.451 60.000 8.55 0.00 37.85 4.00
2027 2065 4.455533 TGGATGACAGAGTTACATGTTTGC 59.544 41.667 2.30 0.00 0.00 3.68
2035 2073 5.063944 CAGAGTTACATGTTTGCGCTAGAAT 59.936 40.000 9.73 0.00 0.00 2.40
2082 2120 2.605837 TGGTTGTGCTAGAACGTGAA 57.394 45.000 0.00 0.00 0.00 3.18
2096 2144 1.135083 ACGTGAAGAGAGGTATTGCCG 60.135 52.381 0.00 0.00 43.70 5.69
2109 2157 1.838112 ATTGCCGTCATGACATGGTT 58.162 45.000 24.93 4.37 0.00 3.67
2110 2158 0.880441 TTGCCGTCATGACATGGTTG 59.120 50.000 24.93 7.83 0.00 3.77
2114 2162 0.371301 CGTCATGACATGGTTGCGAG 59.629 55.000 24.93 1.35 0.00 5.03
2179 2227 9.857656 AGAAATCAGCAATAATCTTCCTAATGA 57.142 29.630 0.00 0.00 0.00 2.57
2207 2255 1.869767 CTGAAGAGTGAGTGTTGTGCC 59.130 52.381 0.00 0.00 0.00 5.01
2212 2260 0.107410 AGTGAGTGTTGTGCCGGAAA 60.107 50.000 5.05 0.00 0.00 3.13
2380 2441 7.138692 CTAGCTAAGCATTTGTGTTTTCTCT 57.861 36.000 0.00 0.00 0.00 3.10
2385 2446 7.486232 GCTAAGCATTTGTGTTTTCTCTATTCC 59.514 37.037 0.00 0.00 0.00 3.01
2389 2450 6.808704 GCATTTGTGTTTTCTCTATTCCTTCC 59.191 38.462 0.00 0.00 0.00 3.46
2438 2499 9.539825 ACTGCACATAATTGTCAAAACATTTTA 57.460 25.926 0.00 0.00 34.73 1.52
2441 2502 9.592720 GCACATAATTGTCAAAACATTTTAACC 57.407 29.630 0.00 0.00 34.73 2.85
2485 2549 6.760770 CCAATTGCTCAAGAACCTTTTTAACA 59.239 34.615 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.880490 GCCCTAAAAACCAAAACCCTTTG 59.120 43.478 0.00 0.00 41.45 2.77
18 19 3.783642 AGCCCTAAAAACCAAAACCCTTT 59.216 39.130 0.00 0.00 0.00 3.11
19 20 3.389866 AGCCCTAAAAACCAAAACCCTT 58.610 40.909 0.00 0.00 0.00 3.95
20 21 3.054779 AGCCCTAAAAACCAAAACCCT 57.945 42.857 0.00 0.00 0.00 4.34
21 22 4.154176 TCTAGCCCTAAAAACCAAAACCC 58.846 43.478 0.00 0.00 0.00 4.11
22 23 4.321750 GCTCTAGCCCTAAAAACCAAAACC 60.322 45.833 0.00 0.00 34.31 3.27
23 24 4.279922 TGCTCTAGCCCTAAAAACCAAAAC 59.720 41.667 0.00 0.00 41.18 2.43
24 25 4.475345 TGCTCTAGCCCTAAAAACCAAAA 58.525 39.130 0.00 0.00 41.18 2.44
25 26 4.107127 TGCTCTAGCCCTAAAAACCAAA 57.893 40.909 0.00 0.00 41.18 3.28
26 27 3.799432 TGCTCTAGCCCTAAAAACCAA 57.201 42.857 0.00 0.00 41.18 3.67
27 28 3.181438 TGTTGCTCTAGCCCTAAAAACCA 60.181 43.478 0.00 0.00 41.18 3.67
28 29 3.418047 TGTTGCTCTAGCCCTAAAAACC 58.582 45.455 0.00 0.00 41.18 3.27
29 30 4.096532 GGATGTTGCTCTAGCCCTAAAAAC 59.903 45.833 0.00 0.00 41.18 2.43
30 31 4.263727 TGGATGTTGCTCTAGCCCTAAAAA 60.264 41.667 0.00 0.00 41.18 1.94
31 32 3.265737 TGGATGTTGCTCTAGCCCTAAAA 59.734 43.478 0.00 0.00 41.18 1.52
32 33 2.843730 TGGATGTTGCTCTAGCCCTAAA 59.156 45.455 0.00 0.00 41.18 1.85
33 34 2.477245 TGGATGTTGCTCTAGCCCTAA 58.523 47.619 0.00 0.00 41.18 2.69
34 35 2.174685 TGGATGTTGCTCTAGCCCTA 57.825 50.000 0.00 0.00 41.18 3.53
35 36 1.419387 GATGGATGTTGCTCTAGCCCT 59.581 52.381 0.00 0.00 41.18 5.19
36 37 1.875576 CGATGGATGTTGCTCTAGCCC 60.876 57.143 0.00 0.00 41.18 5.19
37 38 1.506493 CGATGGATGTTGCTCTAGCC 58.494 55.000 0.00 0.00 41.18 3.93
38 39 0.864455 GCGATGGATGTTGCTCTAGC 59.136 55.000 0.00 0.00 42.50 3.42
39 40 1.506493 GGCGATGGATGTTGCTCTAG 58.494 55.000 0.00 0.00 0.00 2.43
40 41 0.106708 GGGCGATGGATGTTGCTCTA 59.893 55.000 0.00 0.00 0.00 2.43
41 42 1.153086 GGGCGATGGATGTTGCTCT 60.153 57.895 0.00 0.00 0.00 4.09
42 43 2.189499 GGGGCGATGGATGTTGCTC 61.189 63.158 0.00 0.00 0.00 4.26
43 44 2.124151 GGGGCGATGGATGTTGCT 60.124 61.111 0.00 0.00 0.00 3.91
44 45 3.585990 CGGGGCGATGGATGTTGC 61.586 66.667 0.00 0.00 0.00 4.17
45 46 2.124736 ACGGGGCGATGGATGTTG 60.125 61.111 0.00 0.00 0.00 3.33
46 47 2.189521 GACGGGGCGATGGATGTT 59.810 61.111 0.00 0.00 0.00 2.71
47 48 2.665089 TTGACGGGGCGATGGATGT 61.665 57.895 0.00 0.00 0.00 3.06
48 49 2.180204 GTTGACGGGGCGATGGATG 61.180 63.158 0.00 0.00 0.00 3.51
49 50 2.189521 GTTGACGGGGCGATGGAT 59.810 61.111 0.00 0.00 0.00 3.41
50 51 4.090588 GGTTGACGGGGCGATGGA 62.091 66.667 0.00 0.00 0.00 3.41
51 52 2.644555 CTAGGTTGACGGGGCGATGG 62.645 65.000 0.00 0.00 0.00 3.51
52 53 1.227263 CTAGGTTGACGGGGCGATG 60.227 63.158 0.00 0.00 0.00 3.84
53 54 2.432300 CCTAGGTTGACGGGGCGAT 61.432 63.158 0.00 0.00 0.00 4.58
54 55 3.072468 CCTAGGTTGACGGGGCGA 61.072 66.667 0.00 0.00 0.00 5.54
55 56 4.157120 CCCTAGGTTGACGGGGCG 62.157 72.222 8.29 0.00 34.22 6.13
56 57 2.133359 AAACCCTAGGTTGACGGGGC 62.133 60.000 8.29 0.00 46.20 5.80
57 58 1.208776 CTAAACCCTAGGTTGACGGGG 59.791 57.143 8.29 0.00 46.20 5.73
58 59 1.406477 GCTAAACCCTAGGTTGACGGG 60.406 57.143 8.29 0.00 46.20 5.28
59 60 1.553704 AGCTAAACCCTAGGTTGACGG 59.446 52.381 8.29 0.00 46.20 4.79
60 61 2.734492 CGAGCTAAACCCTAGGTTGACG 60.734 54.545 8.29 0.00 46.20 4.35
61 62 2.889852 CGAGCTAAACCCTAGGTTGAC 58.110 52.381 8.29 0.00 46.20 3.18
62 63 1.206371 GCGAGCTAAACCCTAGGTTGA 59.794 52.381 8.29 0.00 46.20 3.18
63 64 1.653151 GCGAGCTAAACCCTAGGTTG 58.347 55.000 8.29 0.00 46.20 3.77
65 66 0.325390 AGGCGAGCTAAACCCTAGGT 60.325 55.000 8.29 0.00 37.65 3.08
66 67 0.105039 CAGGCGAGCTAAACCCTAGG 59.895 60.000 0.06 0.06 0.00 3.02
67 68 1.112113 TCAGGCGAGCTAAACCCTAG 58.888 55.000 0.00 0.00 0.00 3.02
68 69 1.687123 GATCAGGCGAGCTAAACCCTA 59.313 52.381 0.00 0.00 0.00 3.53
69 70 0.466124 GATCAGGCGAGCTAAACCCT 59.534 55.000 0.00 0.00 0.00 4.34
70 71 0.466124 AGATCAGGCGAGCTAAACCC 59.534 55.000 0.00 0.00 35.69 4.11
71 72 1.859383 GAGATCAGGCGAGCTAAACC 58.141 55.000 0.00 0.00 38.23 3.27
72 73 1.482278 CGAGATCAGGCGAGCTAAAC 58.518 55.000 0.00 0.00 38.23 2.01
73 74 0.385751 CCGAGATCAGGCGAGCTAAA 59.614 55.000 0.00 0.00 38.23 1.85
74 75 1.456196 CCCGAGATCAGGCGAGCTAA 61.456 60.000 0.00 0.00 38.23 3.09
75 76 1.899054 CCCGAGATCAGGCGAGCTA 60.899 63.158 0.00 0.00 38.23 3.32
76 77 3.222855 CCCGAGATCAGGCGAGCT 61.223 66.667 0.00 0.00 41.70 4.09
77 78 4.292178 CCCCGAGATCAGGCGAGC 62.292 72.222 0.00 0.00 0.00 5.03
78 79 1.519751 CTACCCCGAGATCAGGCGAG 61.520 65.000 0.00 0.00 0.00 5.03
79 80 1.528542 CTACCCCGAGATCAGGCGA 60.529 63.158 0.00 0.00 0.00 5.54
80 81 0.896019 ATCTACCCCGAGATCAGGCG 60.896 60.000 0.00 0.00 29.85 5.52
81 82 3.059287 ATCTACCCCGAGATCAGGC 57.941 57.895 0.00 0.00 29.85 4.85
85 86 2.078392 GAGTCGATCTACCCCGAGATC 58.922 57.143 3.75 3.75 45.73 2.75
86 87 1.700739 AGAGTCGATCTACCCCGAGAT 59.299 52.381 0.00 0.00 38.94 2.75
87 88 1.129917 AGAGTCGATCTACCCCGAGA 58.870 55.000 0.00 0.00 36.10 4.04
88 89 1.231221 CAGAGTCGATCTACCCCGAG 58.769 60.000 0.00 0.00 36.10 4.63
89 90 0.545171 ACAGAGTCGATCTACCCCGA 59.455 55.000 0.00 0.00 36.10 5.14
90 91 2.251409 TACAGAGTCGATCTACCCCG 57.749 55.000 0.00 0.00 36.10 5.73
91 92 2.622470 GGTTACAGAGTCGATCTACCCC 59.378 54.545 0.00 0.00 36.10 4.95
92 93 3.285484 TGGTTACAGAGTCGATCTACCC 58.715 50.000 0.00 0.00 34.45 3.69
93 94 6.430308 TGATATGGTTACAGAGTCGATCTACC 59.570 42.308 0.00 0.00 36.10 3.18
94 95 7.436430 TGATATGGTTACAGAGTCGATCTAC 57.564 40.000 0.00 0.00 36.10 2.59
95 96 9.907229 ATATGATATGGTTACAGAGTCGATCTA 57.093 33.333 0.00 0.00 36.10 1.98
96 97 8.815565 ATATGATATGGTTACAGAGTCGATCT 57.184 34.615 0.00 0.00 39.56 2.75
97 98 9.938670 GTATATGATATGGTTACAGAGTCGATC 57.061 37.037 0.00 0.00 0.00 3.69
98 99 9.462606 TGTATATGATATGGTTACAGAGTCGAT 57.537 33.333 0.00 0.00 0.00 3.59
99 100 8.857694 TGTATATGATATGGTTACAGAGTCGA 57.142 34.615 0.00 0.00 0.00 4.20
100 101 9.723447 GATGTATATGATATGGTTACAGAGTCG 57.277 37.037 0.00 0.00 0.00 4.18
119 120 8.773645 CGTCCTGCTTGATTATTTTGATGTATA 58.226 33.333 0.00 0.00 0.00 1.47
120 121 7.283127 ACGTCCTGCTTGATTATTTTGATGTAT 59.717 33.333 0.00 0.00 0.00 2.29
121 122 6.597672 ACGTCCTGCTTGATTATTTTGATGTA 59.402 34.615 0.00 0.00 0.00 2.29
122 123 5.415701 ACGTCCTGCTTGATTATTTTGATGT 59.584 36.000 0.00 0.00 0.00 3.06
123 124 5.883661 ACGTCCTGCTTGATTATTTTGATG 58.116 37.500 0.00 0.00 0.00 3.07
124 125 6.260936 CCTACGTCCTGCTTGATTATTTTGAT 59.739 38.462 0.00 0.00 0.00 2.57
125 126 5.584649 CCTACGTCCTGCTTGATTATTTTGA 59.415 40.000 0.00 0.00 0.00 2.69
126 127 5.220854 CCCTACGTCCTGCTTGATTATTTTG 60.221 44.000 0.00 0.00 0.00 2.44
127 128 4.881850 CCCTACGTCCTGCTTGATTATTTT 59.118 41.667 0.00 0.00 0.00 1.82
128 129 4.080526 ACCCTACGTCCTGCTTGATTATTT 60.081 41.667 0.00 0.00 0.00 1.40
129 130 3.454812 ACCCTACGTCCTGCTTGATTATT 59.545 43.478 0.00 0.00 0.00 1.40
130 131 3.039011 ACCCTACGTCCTGCTTGATTAT 58.961 45.455 0.00 0.00 0.00 1.28
131 132 2.463752 ACCCTACGTCCTGCTTGATTA 58.536 47.619 0.00 0.00 0.00 1.75
132 133 1.276622 ACCCTACGTCCTGCTTGATT 58.723 50.000 0.00 0.00 0.00 2.57
133 134 1.276622 AACCCTACGTCCTGCTTGAT 58.723 50.000 0.00 0.00 0.00 2.57
134 135 1.053424 AAACCCTACGTCCTGCTTGA 58.947 50.000 0.00 0.00 0.00 3.02
135 136 1.892209 AAAACCCTACGTCCTGCTTG 58.108 50.000 0.00 0.00 0.00 4.01
136 137 2.289882 GGTAAAACCCTACGTCCTGCTT 60.290 50.000 0.00 0.00 30.04 3.91
137 138 1.277273 GGTAAAACCCTACGTCCTGCT 59.723 52.381 0.00 0.00 30.04 4.24
138 139 1.277273 AGGTAAAACCCTACGTCCTGC 59.723 52.381 0.00 0.00 39.75 4.85
139 140 2.830321 AGAGGTAAAACCCTACGTCCTG 59.170 50.000 0.00 0.00 39.75 3.86
140 141 3.181393 AGAGGTAAAACCCTACGTCCT 57.819 47.619 0.00 0.00 39.75 3.85
141 142 3.674410 CGAAGAGGTAAAACCCTACGTCC 60.674 52.174 0.00 0.00 39.75 4.79
142 143 3.191371 TCGAAGAGGTAAAACCCTACGTC 59.809 47.826 0.00 0.00 39.75 4.34
143 144 3.157087 TCGAAGAGGTAAAACCCTACGT 58.843 45.455 0.00 0.00 39.75 3.57
144 145 3.855689 TCGAAGAGGTAAAACCCTACG 57.144 47.619 0.00 0.00 39.75 3.51
158 159 2.036731 TTCGGGCCCTCTCGAAGA 59.963 61.111 22.43 4.41 39.94 2.87
159 160 2.184579 GTTCGGGCCCTCTCGAAG 59.815 66.667 22.43 1.43 44.43 3.79
160 161 3.387947 GGTTCGGGCCCTCTCGAA 61.388 66.667 22.43 15.45 42.12 3.71
161 162 4.377760 AGGTTCGGGCCCTCTCGA 62.378 66.667 22.43 9.26 0.00 4.04
162 163 4.148825 CAGGTTCGGGCCCTCTCG 62.149 72.222 22.43 6.49 0.00 4.04
163 164 3.787001 CCAGGTTCGGGCCCTCTC 61.787 72.222 22.43 9.34 0.00 3.20
171 172 0.952010 CGGTGTTTACCCAGGTTCGG 60.952 60.000 0.00 0.00 44.53 4.30
172 173 0.249996 ACGGTGTTTACCCAGGTTCG 60.250 55.000 0.00 0.00 44.53 3.95
173 174 1.232119 CACGGTGTTTACCCAGGTTC 58.768 55.000 0.00 0.00 44.53 3.62
174 175 0.547553 ACACGGTGTTTACCCAGGTT 59.452 50.000 8.21 0.00 44.53 3.50
175 176 0.547553 AACACGGTGTTTACCCAGGT 59.452 50.000 20.23 0.00 44.53 4.00
176 177 1.202722 AGAACACGGTGTTTACCCAGG 60.203 52.381 25.73 0.00 41.28 4.45
177 178 2.249844 AGAACACGGTGTTTACCCAG 57.750 50.000 25.73 0.00 41.28 4.45
178 179 2.563702 GAAGAACACGGTGTTTACCCA 58.436 47.619 25.73 0.00 41.28 4.51
179 180 1.528161 CGAAGAACACGGTGTTTACCC 59.472 52.381 25.73 13.94 41.28 3.69
180 181 2.204237 ACGAAGAACACGGTGTTTACC 58.796 47.619 25.73 14.27 41.28 2.85
181 182 2.219445 GGACGAAGAACACGGTGTTTAC 59.781 50.000 25.73 14.94 41.28 2.01
182 183 2.472816 GGACGAAGAACACGGTGTTTA 58.527 47.619 25.73 0.00 41.28 2.01
183 184 1.292992 GGACGAAGAACACGGTGTTT 58.707 50.000 25.73 12.54 41.28 2.83
184 185 0.531311 GGGACGAAGAACACGGTGTT 60.531 55.000 25.33 25.33 44.37 3.32
185 186 1.068585 GGGACGAAGAACACGGTGT 59.931 57.895 8.21 8.21 34.93 4.16
186 187 0.249741 AAGGGACGAAGAACACGGTG 60.250 55.000 6.58 6.58 34.93 4.94
187 188 0.249741 CAAGGGACGAAGAACACGGT 60.250 55.000 0.00 0.00 34.93 4.83
188 189 0.249741 ACAAGGGACGAAGAACACGG 60.250 55.000 0.00 0.00 34.93 4.94
189 190 1.525619 GAACAAGGGACGAAGAACACG 59.474 52.381 0.00 0.00 0.00 4.49
190 191 1.871676 GGAACAAGGGACGAAGAACAC 59.128 52.381 0.00 0.00 0.00 3.32
191 192 1.202722 GGGAACAAGGGACGAAGAACA 60.203 52.381 0.00 0.00 0.00 3.18
192 193 1.520494 GGGAACAAGGGACGAAGAAC 58.480 55.000 0.00 0.00 0.00 3.01
193 194 0.399075 GGGGAACAAGGGACGAAGAA 59.601 55.000 0.00 0.00 0.00 2.52
194 195 0.765135 TGGGGAACAAGGGACGAAGA 60.765 55.000 0.00 0.00 0.00 2.87
195 196 0.328258 ATGGGGAACAAGGGACGAAG 59.672 55.000 0.00 0.00 0.00 3.79
196 197 0.774908 AATGGGGAACAAGGGACGAA 59.225 50.000 0.00 0.00 0.00 3.85
197 198 0.037590 CAATGGGGAACAAGGGACGA 59.962 55.000 0.00 0.00 0.00 4.20
198 199 0.037590 TCAATGGGGAACAAGGGACG 59.962 55.000 0.00 0.00 0.00 4.79
199 200 2.379005 GATCAATGGGGAACAAGGGAC 58.621 52.381 0.00 0.00 0.00 4.46
200 201 1.287739 GGATCAATGGGGAACAAGGGA 59.712 52.381 0.00 0.00 0.00 4.20
201 202 1.288932 AGGATCAATGGGGAACAAGGG 59.711 52.381 0.00 0.00 0.00 3.95
202 203 2.834638 AGGATCAATGGGGAACAAGG 57.165 50.000 0.00 0.00 0.00 3.61
203 204 4.778213 TCTAGGATCAATGGGGAACAAG 57.222 45.455 0.00 0.00 0.00 3.16
204 205 4.977739 AGATCTAGGATCAATGGGGAACAA 59.022 41.667 9.71 0.00 0.00 2.83
205 206 4.570926 AGATCTAGGATCAATGGGGAACA 58.429 43.478 9.71 0.00 0.00 3.18
206 207 5.544176 TGTAGATCTAGGATCAATGGGGAAC 59.456 44.000 1.64 0.00 0.00 3.62
207 208 5.726560 TGTAGATCTAGGATCAATGGGGAA 58.273 41.667 1.64 0.00 0.00 3.97
208 209 5.336945 CTGTAGATCTAGGATCAATGGGGA 58.663 45.833 1.64 0.00 0.00 4.81
209 210 4.081198 GCTGTAGATCTAGGATCAATGGGG 60.081 50.000 1.64 0.00 0.00 4.96
210 211 4.776837 AGCTGTAGATCTAGGATCAATGGG 59.223 45.833 1.64 0.00 0.00 4.00
211 212 5.392919 CGAGCTGTAGATCTAGGATCAATGG 60.393 48.000 16.20 2.49 0.00 3.16
212 213 5.392919 CCGAGCTGTAGATCTAGGATCAATG 60.393 48.000 16.20 5.26 0.00 2.82
213 214 4.704540 CCGAGCTGTAGATCTAGGATCAAT 59.295 45.833 16.20 0.73 0.00 2.57
214 215 4.075682 CCGAGCTGTAGATCTAGGATCAA 58.924 47.826 16.20 0.00 0.00 2.57
215 216 3.560239 CCCGAGCTGTAGATCTAGGATCA 60.560 52.174 16.20 6.28 0.00 2.92
216 217 3.013921 CCCGAGCTGTAGATCTAGGATC 58.986 54.545 1.64 6.75 0.00 3.36
217 218 2.645297 TCCCGAGCTGTAGATCTAGGAT 59.355 50.000 1.64 0.00 29.49 3.24
218 219 2.055579 TCCCGAGCTGTAGATCTAGGA 58.944 52.381 1.64 1.56 31.18 2.94
219 220 2.156098 GTCCCGAGCTGTAGATCTAGG 58.844 57.143 1.64 0.00 0.00 3.02
220 221 2.156098 GGTCCCGAGCTGTAGATCTAG 58.844 57.143 1.64 0.00 0.00 2.43
221 222 1.202903 GGGTCCCGAGCTGTAGATCTA 60.203 57.143 0.00 0.00 0.00 1.98
222 223 0.468400 GGGTCCCGAGCTGTAGATCT 60.468 60.000 0.00 0.00 0.00 2.75
223 224 1.465200 GGGGTCCCGAGCTGTAGATC 61.465 65.000 0.48 0.00 0.00 2.75
224 225 1.457831 GGGGTCCCGAGCTGTAGAT 60.458 63.158 0.48 0.00 0.00 1.98
225 226 1.284111 TAGGGGTCCCGAGCTGTAGA 61.284 60.000 0.48 0.00 41.95 2.59
226 227 0.178958 ATAGGGGTCCCGAGCTGTAG 60.179 60.000 0.48 0.00 41.95 2.74
227 228 0.178970 GATAGGGGTCCCGAGCTGTA 60.179 60.000 0.48 0.00 41.95 2.74
228 229 1.457831 GATAGGGGTCCCGAGCTGT 60.458 63.158 0.48 0.00 41.95 4.40
229 230 2.210711 GGATAGGGGTCCCGAGCTG 61.211 68.421 0.48 0.00 41.95 4.24
230 231 2.201771 GGATAGGGGTCCCGAGCT 59.798 66.667 0.48 0.00 41.95 4.09
231 232 3.303928 CGGATAGGGGTCCCGAGC 61.304 72.222 0.48 0.00 45.58 5.03
232 233 2.519441 TCGGATAGGGGTCCCGAG 59.481 66.667 0.48 0.00 46.17 4.63
234 235 0.966370 GATCTCGGATAGGGGTCCCG 60.966 65.000 0.48 0.00 44.22 5.14
235 236 0.410270 AGATCTCGGATAGGGGTCCC 59.590 60.000 0.00 0.00 34.67 4.46
236 237 1.551452 CAGATCTCGGATAGGGGTCC 58.449 60.000 0.00 0.00 34.82 4.46
237 238 0.892063 GCAGATCTCGGATAGGGGTC 59.108 60.000 0.00 0.00 0.00 4.46
238 239 0.543174 GGCAGATCTCGGATAGGGGT 60.543 60.000 0.00 0.00 0.00 4.95
239 240 1.599606 CGGCAGATCTCGGATAGGGG 61.600 65.000 0.00 0.00 0.00 4.79
240 241 1.886585 CGGCAGATCTCGGATAGGG 59.113 63.158 0.00 0.00 0.00 3.53
247 248 0.721718 GTCAAAACCGGCAGATCTCG 59.278 55.000 0.00 0.00 0.00 4.04
248 249 1.464997 GTGTCAAAACCGGCAGATCTC 59.535 52.381 0.00 0.00 0.00 2.75
249 250 1.523758 GTGTCAAAACCGGCAGATCT 58.476 50.000 0.00 0.00 0.00 2.75
250 251 0.521735 GGTGTCAAAACCGGCAGATC 59.478 55.000 0.00 0.00 0.00 2.75
251 252 2.641197 GGTGTCAAAACCGGCAGAT 58.359 52.632 0.00 0.00 0.00 2.90
252 253 4.150994 GGTGTCAAAACCGGCAGA 57.849 55.556 0.00 0.00 0.00 4.26
258 259 1.170290 CCCCTGTCGGTGTCAAAACC 61.170 60.000 0.00 0.00 36.82 3.27
259 260 1.170290 CCCCCTGTCGGTGTCAAAAC 61.170 60.000 0.00 0.00 0.00 2.43
260 261 1.149627 CCCCCTGTCGGTGTCAAAA 59.850 57.895 0.00 0.00 0.00 2.44
261 262 2.833227 CCCCCTGTCGGTGTCAAA 59.167 61.111 0.00 0.00 0.00 2.69
281 282 3.185299 ATGGGTCACGGCGTGGAAA 62.185 57.895 36.30 21.19 33.87 3.13
299 300 1.362717 GCGCGGATAGAAGTAGGCA 59.637 57.895 8.83 0.00 0.00 4.75
307 308 0.248907 GCTAGTGTTGCGCGGATAGA 60.249 55.000 8.83 0.00 0.00 1.98
334 335 1.065273 GTCGTGTCCGATGGCGTAT 59.935 57.895 0.00 0.00 46.30 3.06
335 336 2.486504 GTCGTGTCCGATGGCGTA 59.513 61.111 0.00 0.00 46.30 4.42
336 337 4.430765 GGTCGTGTCCGATGGCGT 62.431 66.667 0.00 0.00 46.30 5.68
377 378 2.091333 TCAGGGAGGGCTTTGAAAACTT 60.091 45.455 0.00 0.00 0.00 2.66
426 427 1.421268 TGTGCCACTCATGAAGGAAGT 59.579 47.619 16.06 0.00 0.00 3.01
437 438 2.814336 CCCTCTTTACTTTGTGCCACTC 59.186 50.000 0.00 0.00 0.00 3.51
449 450 1.221021 CCCTCCACGCCCTCTTTAC 59.779 63.158 0.00 0.00 0.00 2.01
461 462 1.306997 CTAGAGCCAACCCCCTCCA 60.307 63.158 0.00 0.00 0.00 3.86
470 474 1.424638 GGCAGATACCCTAGAGCCAA 58.575 55.000 0.00 0.00 41.63 4.52
490 496 4.671569 CCTAGCATCGGCCCTCGC 62.672 72.222 0.00 0.00 42.56 5.03
534 541 8.559536 CATATAATTGACTACAAGGAACGCAAT 58.440 33.333 0.00 0.00 39.46 3.56
580 587 5.128827 GGAATATGGCCATCCTTATCTACGA 59.871 44.000 24.80 0.00 33.12 3.43
581 588 5.104941 TGGAATATGGCCATCCTTATCTACG 60.105 44.000 24.80 0.00 33.12 3.51
596 603 6.686630 TGTTGTTGTAGCTTTTGGAATATGG 58.313 36.000 0.00 0.00 0.00 2.74
699 714 0.111253 AGGAACTGGGCAAGGAACTG 59.889 55.000 0.00 0.00 35.75 3.16
700 715 0.853530 AAGGAACTGGGCAAGGAACT 59.146 50.000 0.00 0.00 40.86 3.01
701 716 1.248486 GAAGGAACTGGGCAAGGAAC 58.752 55.000 0.00 0.00 40.86 3.62
702 717 0.850100 TGAAGGAACTGGGCAAGGAA 59.150 50.000 0.00 0.00 40.86 3.36
703 718 0.401738 CTGAAGGAACTGGGCAAGGA 59.598 55.000 0.00 0.00 40.86 3.36
704 719 0.610232 CCTGAAGGAACTGGGCAAGG 60.610 60.000 0.00 0.00 40.86 3.61
705 720 0.610232 CCCTGAAGGAACTGGGCAAG 60.610 60.000 0.00 0.00 40.86 4.01
706 721 1.460255 CCCTGAAGGAACTGGGCAA 59.540 57.895 0.00 0.00 40.86 4.52
707 722 3.170362 CCCTGAAGGAACTGGGCA 58.830 61.111 0.00 0.00 40.86 5.36
710 725 0.326264 CCTCACCCTGAAGGAACTGG 59.674 60.000 0.00 0.00 40.86 4.00
895 910 2.291670 ACTACTAGGTAGCTGCTGGTGT 60.292 50.000 13.43 6.63 39.51 4.16
989 1004 2.224402 GGAGCCGCCATTCTTTAGAGAT 60.224 50.000 0.00 0.00 36.34 2.75
1018 1033 0.956902 TCGTCGTCGATGAAGGTGGA 60.957 55.000 18.55 5.39 41.35 4.02
1029 1044 1.259770 TCCATATCTTCGTCGTCGTCG 59.740 52.381 5.50 5.50 38.33 5.12
1233 1254 0.107897 TCTTGTGTGCGTTCTGGTGT 60.108 50.000 0.00 0.00 0.00 4.16
1245 1266 3.306364 CGATGTTCCTCTCCTTCTTGTGT 60.306 47.826 0.00 0.00 0.00 3.72
1330 1351 2.494870 GGTACATCGTCTGGTGGTTACT 59.505 50.000 0.00 0.00 0.00 2.24
1331 1352 2.417787 GGGTACATCGTCTGGTGGTTAC 60.418 54.545 0.00 0.00 0.00 2.50
1332 1353 1.826720 GGGTACATCGTCTGGTGGTTA 59.173 52.381 0.00 0.00 0.00 2.85
1554 1575 7.931948 AGAAAGAGAGGAAAACATCGACTAAAA 59.068 33.333 0.00 0.00 0.00 1.52
1599 1620 0.184211 AACCAAGTACCCACCCACAC 59.816 55.000 0.00 0.00 0.00 3.82
1600 1621 1.817087 TAACCAAGTACCCACCCACA 58.183 50.000 0.00 0.00 0.00 4.17
1601 1622 2.955342 TTAACCAAGTACCCACCCAC 57.045 50.000 0.00 0.00 0.00 4.61
1602 1623 2.987437 TCATTAACCAAGTACCCACCCA 59.013 45.455 0.00 0.00 0.00 4.51
1628 1649 1.086696 CGGTACAATCAGCACAAGGG 58.913 55.000 0.00 0.00 0.00 3.95
1700 1721 9.020813 CAGAATGTGCAATATTTCTGATTCTTG 57.979 33.333 17.63 2.88 30.34 3.02
1764 1785 7.310299 CCAGCTGACCAGATTATGTATAGATGT 60.310 40.741 17.39 0.00 0.00 3.06
1885 1922 6.167685 ACTTGCGGTGACATTACACTAATTA 58.832 36.000 0.00 0.00 40.22 1.40
1887 1924 4.575885 ACTTGCGGTGACATTACACTAAT 58.424 39.130 0.00 0.00 40.22 1.73
1888 1925 3.997762 ACTTGCGGTGACATTACACTAA 58.002 40.909 0.00 0.00 40.22 2.24
1921 1959 9.639601 AGAAAAAGAAACATTTCGAAGACTTTT 57.360 25.926 0.00 8.54 41.92 2.27
1925 1963 8.524267 GTTCAGAAAAAGAAACATTTCGAAGAC 58.476 33.333 0.00 0.00 41.92 3.01
1941 1979 6.837312 TCTCCCTAGTGATTGTTCAGAAAAA 58.163 36.000 0.00 0.00 30.85 1.94
1946 1984 5.046304 TCCTTTCTCCCTAGTGATTGTTCAG 60.046 44.000 0.00 0.00 30.85 3.02
1980 2018 6.441093 TGATCACCTTTGAGTAATGCATTC 57.559 37.500 16.86 7.93 34.35 2.67
2035 2073 1.823295 GGCAATACCTCTCCTCGCA 59.177 57.895 0.00 0.00 34.51 5.10
2038 2076 1.112113 TGACGGCAATACCTCTCCTC 58.888 55.000 0.00 0.00 35.61 3.71
2040 2078 1.541233 CCATGACGGCAATACCTCTCC 60.541 57.143 0.00 0.00 35.61 3.71
2082 2120 2.101582 GTCATGACGGCAATACCTCTCT 59.898 50.000 10.69 0.00 35.61 3.10
2096 2144 0.097674 GCTCGCAACCATGTCATGAC 59.902 55.000 19.27 19.27 0.00 3.06
2109 2157 4.072131 AGAATCCTTGTAAAAAGCTCGCA 58.928 39.130 0.00 0.00 0.00 5.10
2110 2158 4.686839 AGAATCCTTGTAAAAAGCTCGC 57.313 40.909 0.00 0.00 0.00 5.03
2138 2186 7.118723 TGCTGATTTCTACCTTTGGACATATT 58.881 34.615 0.00 0.00 0.00 1.28
2179 2227 4.093011 ACACTCACTCTTCAGCCTCTTAT 58.907 43.478 0.00 0.00 0.00 1.73
2181 2229 2.324541 ACACTCACTCTTCAGCCTCTT 58.675 47.619 0.00 0.00 0.00 2.85
2207 2255 4.575885 TCTAGGAATGTTCAGGTTTTCCG 58.424 43.478 0.00 0.00 46.35 4.30
2212 2260 4.540099 TGGGATTCTAGGAATGTTCAGGTT 59.460 41.667 0.00 0.00 0.00 3.50
2377 2438 5.411977 CAGCTATGCATTGGAAGGAATAGAG 59.588 44.000 3.54 0.00 0.00 2.43
2380 2441 5.308976 TCAGCTATGCATTGGAAGGAATA 57.691 39.130 3.54 0.00 0.00 1.75
2385 2446 7.249147 GCTATTAATCAGCTATGCATTGGAAG 58.751 38.462 3.54 0.00 36.07 3.46
2438 2499 7.309770 TGGCTTAATTTGGAGTTAATTGGTT 57.690 32.000 0.00 0.00 0.00 3.67
2439 2500 6.926630 TGGCTTAATTTGGAGTTAATTGGT 57.073 33.333 0.00 0.00 0.00 3.67
2440 2501 8.667463 CAATTGGCTTAATTTGGAGTTAATTGG 58.333 33.333 0.00 0.00 36.87 3.16
2441 2502 8.177013 GCAATTGGCTTAATTTGGAGTTAATTG 58.823 33.333 7.72 0.00 36.87 2.32


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

AutoCloner maintained by Alex Coulton.