Multiple sequence alignment - TraesCS7D01G236100

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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 TraesCS7D01G236100 chr7D 100.000 3224 0 0 1 3224 199345470 199348693 0.000000e+00 5954.0
1 TraesCS7D01G236100 chr7D 92.661 218 15 1 3 220 468774499 468774715 2.410000e-81 313.0
2 TraesCS7D01G236100 chr7D 100.000 39 0 0 2924 2962 199347746 199347784 4.460000e-09 73.1
3 TraesCS7D01G236100 chr7D 100.000 39 0 0 2277 2315 199348393 199348431 4.460000e-09 73.1
4 TraesCS7D01G236100 chr7B 94.290 1979 63 18 583 2532 163478541 163480498 0.000000e+00 2983.0
5 TraesCS7D01G236100 chr7B 91.781 365 9 6 2530 2892 163480612 163480957 3.740000e-134 488.0
6 TraesCS7D01G236100 chr7B 89.041 292 29 1 221 509 163477986 163478277 3.060000e-95 359.0
7 TraesCS7D01G236100 chr7B 88.077 260 6 3 2970 3224 163480960 163481199 5.260000e-73 285.0
8 TraesCS7D01G236100 chr7B 97.619 42 1 0 2924 2965 163480242 163480283 4.460000e-09 73.1
9 TraesCS7D01G236100 chr7A 96.648 1462 33 8 848 2297 209146619 209148076 0.000000e+00 2414.0
10 TraesCS7D01G236100 chr7A 97.196 642 15 2 2256 2895 209148076 209148716 0.000000e+00 1083.0
11 TraesCS7D01G236100 chr7A 84.117 617 72 12 221 835 209145795 209146387 1.000000e-159 573.0
12 TraesCS7D01G236100 chr7A 95.294 255 12 0 2970 3224 209148717 209148971 3.870000e-109 405.0
13 TraesCS7D01G236100 chr7A 97.619 42 1 0 2924 2965 209148097 209148138 4.460000e-09 73.1
14 TraesCS7D01G236100 chr1D 94.064 219 12 1 4 222 371892343 371892560 6.670000e-87 331.0
15 TraesCS7D01G236100 chr5D 93.119 218 15 0 3 220 219714337 219714554 1.440000e-83 320.0
16 TraesCS7D01G236100 chr5D 92.661 218 15 1 5 222 210226532 210226748 2.410000e-81 313.0
17 TraesCS7D01G236100 chr5D 91.818 220 18 0 3 222 197862952 197863171 1.120000e-79 307.0
18 TraesCS7D01G236100 chr6D 92.166 217 16 1 6 222 183826549 183826334 4.040000e-79 305.0
19 TraesCS7D01G236100 chr6D 91.364 220 18 1 3 222 314631759 314631977 1.880000e-77 300.0
20 TraesCS7D01G236100 chr6D 91.244 217 18 1 6 222 176886303 176886088 8.750000e-76 294.0
21 TraesCS7D01G236100 chr2D 91.403 221 17 2 4 222 296858208 296858428 5.230000e-78 302.0


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 TraesCS7D01G236100 chr7D 199345470 199348693 3223 False 2033.40 5954 100.0000 1 3224 3 chr7D.!!$F2 3223
1 TraesCS7D01G236100 chr7B 163477986 163481199 3213 False 837.62 2983 92.1616 221 3224 5 chr7B.!!$F1 3003
2 TraesCS7D01G236100 chr7A 209145795 209148971 3176 False 909.62 2414 94.1748 221 3224 5 chr7A.!!$F1 3003

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
539 544 0.106015 AACTGCCAACCAAAGCCTCT 60.106 50.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2488 2979 0.840617 TACCTGCCACACAAACCAGA 59.159 50.0 0.0 0.0 0.0 3.86 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
18 19 1.067582 GACGGCCTCCACTAATCCG 59.932 63.158 0.00 0.00 45.04 4.18
19 20 2.365095 GACGGCCTCCACTAATCCGG 62.365 65.000 0.00 0.00 43.93 5.14
20 21 2.131709 CGGCCTCCACTAATCCGGA 61.132 63.158 6.61 6.61 36.73 5.14
33 34 4.379243 CCGGAGGCGCTCAACACT 62.379 66.667 7.64 0.00 46.14 3.55
34 35 2.811317 CGGAGGCGCTCAACACTC 60.811 66.667 7.64 3.67 31.08 3.51
35 36 2.659610 GGAGGCGCTCAACACTCT 59.340 61.111 7.64 0.00 31.08 3.24
36 37 1.739562 GGAGGCGCTCAACACTCTG 60.740 63.158 7.64 0.00 31.08 3.35
37 38 1.739562 GAGGCGCTCAACACTCTGG 60.740 63.158 7.64 0.00 0.00 3.86
38 39 2.159819 GAGGCGCTCAACACTCTGGA 62.160 60.000 7.64 0.00 0.00 3.86
39 40 1.739562 GGCGCTCAACACTCTGGAG 60.740 63.158 7.64 0.00 0.00 3.86
40 41 1.739562 GCGCTCAACACTCTGGAGG 60.740 63.158 0.00 0.00 0.00 4.30
41 42 1.967535 CGCTCAACACTCTGGAGGA 59.032 57.895 2.58 0.00 0.00 3.71
42 43 0.318441 CGCTCAACACTCTGGAGGAA 59.682 55.000 2.58 0.00 0.00 3.36
43 44 1.671261 CGCTCAACACTCTGGAGGAAG 60.671 57.143 2.58 0.00 0.00 3.46
44 45 1.943507 GCTCAACACTCTGGAGGAAGC 60.944 57.143 2.58 0.77 0.00 3.86
45 46 1.345741 CTCAACACTCTGGAGGAAGCA 59.654 52.381 2.58 0.00 0.00 3.91
46 47 1.070758 TCAACACTCTGGAGGAAGCAC 59.929 52.381 2.58 0.00 0.00 4.40
47 48 1.071385 CAACACTCTGGAGGAAGCACT 59.929 52.381 2.58 0.00 0.00 4.40
48 49 0.683973 ACACTCTGGAGGAAGCACTG 59.316 55.000 2.58 0.00 0.00 3.66
49 50 0.673022 CACTCTGGAGGAAGCACTGC 60.673 60.000 2.58 0.00 0.00 4.40
50 51 1.123861 ACTCTGGAGGAAGCACTGCA 61.124 55.000 3.30 0.00 37.28 4.41
52 53 2.033141 TGGAGGAAGCACTGCAGC 59.967 61.111 15.27 0.57 33.68 5.25
53 54 3.123620 GGAGGAAGCACTGCAGCG 61.124 66.667 15.27 5.22 40.15 5.18
54 55 2.358003 GAGGAAGCACTGCAGCGT 60.358 61.111 15.27 0.00 40.15 5.07
55 56 2.667536 AGGAAGCACTGCAGCGTG 60.668 61.111 15.27 7.78 40.15 5.34
61 62 2.974148 CACTGCAGCGTGCTTCCA 60.974 61.111 15.27 0.00 45.31 3.53
62 63 2.033141 ACTGCAGCGTGCTTCCAT 59.967 55.556 15.27 0.00 45.31 3.41
63 64 2.037136 ACTGCAGCGTGCTTCCATC 61.037 57.895 15.27 0.00 45.31 3.51
64 65 3.092192 CTGCAGCGTGCTTCCATCG 62.092 63.158 0.00 0.00 45.31 3.84
65 66 3.121030 GCAGCGTGCTTCCATCGT 61.121 61.111 0.00 0.00 40.96 3.73
66 67 2.780643 CAGCGTGCTTCCATCGTG 59.219 61.111 0.00 0.00 0.00 4.35
67 68 2.434884 AGCGTGCTTCCATCGTGG 60.435 61.111 0.00 0.00 39.43 4.94
68 69 4.166011 GCGTGCTTCCATCGTGGC 62.166 66.667 0.00 0.00 37.47 5.01
69 70 3.853330 CGTGCTTCCATCGTGGCG 61.853 66.667 0.00 0.00 37.47 5.69
70 71 3.499737 GTGCTTCCATCGTGGCGG 61.500 66.667 0.00 0.00 37.47 6.13
71 72 3.700970 TGCTTCCATCGTGGCGGA 61.701 61.111 0.00 0.00 37.47 5.54
72 73 2.892425 GCTTCCATCGTGGCGGAG 60.892 66.667 0.00 0.44 37.47 4.63
86 87 4.101448 GGAGCACCGCACCCTGAT 62.101 66.667 0.00 0.00 33.27 2.90
87 88 2.821366 GAGCACCGCACCCTGATG 60.821 66.667 0.00 0.00 0.00 3.07
88 89 4.415150 AGCACCGCACCCTGATGG 62.415 66.667 0.00 0.00 41.37 3.51
98 99 3.170362 CCTGATGGGTGTGGTGGT 58.830 61.111 0.00 0.00 0.00 4.16
99 100 1.303561 CCTGATGGGTGTGGTGGTG 60.304 63.158 0.00 0.00 0.00 4.17
100 101 1.303561 CTGATGGGTGTGGTGGTGG 60.304 63.158 0.00 0.00 0.00 4.61
101 102 1.772156 TGATGGGTGTGGTGGTGGA 60.772 57.895 0.00 0.00 0.00 4.02
102 103 1.002134 GATGGGTGTGGTGGTGGAG 60.002 63.158 0.00 0.00 0.00 3.86
103 104 1.463214 ATGGGTGTGGTGGTGGAGA 60.463 57.895 0.00 0.00 0.00 3.71
104 105 1.065410 ATGGGTGTGGTGGTGGAGAA 61.065 55.000 0.00 0.00 0.00 2.87
105 106 1.073199 GGGTGTGGTGGTGGAGAAG 59.927 63.158 0.00 0.00 0.00 2.85
106 107 1.073199 GGTGTGGTGGTGGAGAAGG 59.927 63.158 0.00 0.00 0.00 3.46
107 108 1.705997 GGTGTGGTGGTGGAGAAGGT 61.706 60.000 0.00 0.00 0.00 3.50
108 109 0.182775 GTGTGGTGGTGGAGAAGGTT 59.817 55.000 0.00 0.00 0.00 3.50
109 110 0.472471 TGTGGTGGTGGAGAAGGTTC 59.528 55.000 0.00 0.00 0.00 3.62
110 111 0.472471 GTGGTGGTGGAGAAGGTTCA 59.528 55.000 0.00 0.00 0.00 3.18
111 112 0.764890 TGGTGGTGGAGAAGGTTCAG 59.235 55.000 0.00 0.00 0.00 3.02
112 113 0.765510 GGTGGTGGAGAAGGTTCAGT 59.234 55.000 0.00 0.00 0.00 3.41
113 114 1.270893 GGTGGTGGAGAAGGTTCAGTC 60.271 57.143 0.00 0.00 0.00 3.51
114 115 1.694696 GTGGTGGAGAAGGTTCAGTCT 59.305 52.381 0.00 0.00 0.00 3.24
115 116 1.694150 TGGTGGAGAAGGTTCAGTCTG 59.306 52.381 0.00 0.00 0.00 3.51
116 117 1.609320 GGTGGAGAAGGTTCAGTCTGC 60.609 57.143 0.00 0.00 33.19 4.26
117 118 1.346068 GTGGAGAAGGTTCAGTCTGCT 59.654 52.381 0.00 0.00 33.69 4.24
118 119 2.563179 GTGGAGAAGGTTCAGTCTGCTA 59.437 50.000 0.00 0.00 33.69 3.49
119 120 3.006967 GTGGAGAAGGTTCAGTCTGCTAA 59.993 47.826 0.00 0.00 33.69 3.09
120 121 3.646162 TGGAGAAGGTTCAGTCTGCTAAA 59.354 43.478 0.00 0.00 33.69 1.85
121 122 4.102524 TGGAGAAGGTTCAGTCTGCTAAAA 59.897 41.667 0.00 0.00 33.69 1.52
122 123 4.693095 GGAGAAGGTTCAGTCTGCTAAAAG 59.307 45.833 0.00 0.00 30.19 2.27
123 124 4.068599 AGAAGGTTCAGTCTGCTAAAAGC 58.931 43.478 0.00 0.00 42.82 3.51
124 125 2.417719 AGGTTCAGTCTGCTAAAAGCG 58.582 47.619 0.00 0.00 46.26 4.68
133 134 1.144969 TGCTAAAAGCGGACTGAACG 58.855 50.000 0.00 0.00 46.26 3.95
134 135 1.269883 TGCTAAAAGCGGACTGAACGA 60.270 47.619 0.00 0.00 46.26 3.85
135 136 1.796459 GCTAAAAGCGGACTGAACGAA 59.204 47.619 0.00 0.00 0.00 3.85
136 137 2.159827 GCTAAAAGCGGACTGAACGAAG 60.160 50.000 0.00 0.00 0.00 3.79
137 138 0.586802 AAAAGCGGACTGAACGAAGC 59.413 50.000 0.00 0.00 0.00 3.86
138 139 1.228657 AAAGCGGACTGAACGAAGCC 61.229 55.000 0.00 0.00 0.00 4.35
139 140 2.048127 GCGGACTGAACGAAGCCT 60.048 61.111 0.00 0.00 0.00 4.58
140 141 1.668151 GCGGACTGAACGAAGCCTT 60.668 57.895 0.00 0.00 0.00 4.35
141 142 1.627550 GCGGACTGAACGAAGCCTTC 61.628 60.000 0.00 0.00 0.00 3.46
142 143 0.319555 CGGACTGAACGAAGCCTTCA 60.320 55.000 5.14 0.00 0.00 3.02
143 144 1.149148 GGACTGAACGAAGCCTTCAC 58.851 55.000 5.14 0.00 0.00 3.18
144 145 1.270358 GGACTGAACGAAGCCTTCACT 60.270 52.381 5.14 0.00 0.00 3.41
145 146 2.029290 GGACTGAACGAAGCCTTCACTA 60.029 50.000 5.14 0.00 0.00 2.74
146 147 3.554337 GGACTGAACGAAGCCTTCACTAA 60.554 47.826 5.14 0.00 0.00 2.24
147 148 3.391049 ACTGAACGAAGCCTTCACTAAC 58.609 45.455 5.14 0.00 0.00 2.34
148 149 2.737252 CTGAACGAAGCCTTCACTAACC 59.263 50.000 5.14 0.00 0.00 2.85
149 150 2.367567 TGAACGAAGCCTTCACTAACCT 59.632 45.455 5.14 0.00 0.00 3.50
150 151 3.575256 TGAACGAAGCCTTCACTAACCTA 59.425 43.478 5.14 0.00 0.00 3.08
151 152 3.589495 ACGAAGCCTTCACTAACCTAC 57.411 47.619 5.14 0.00 0.00 3.18
152 153 3.163467 ACGAAGCCTTCACTAACCTACT 58.837 45.455 5.14 0.00 0.00 2.57
153 154 3.056749 ACGAAGCCTTCACTAACCTACTG 60.057 47.826 5.14 0.00 0.00 2.74
154 155 3.192844 CGAAGCCTTCACTAACCTACTGA 59.807 47.826 5.14 0.00 0.00 3.41
155 156 4.496360 GAAGCCTTCACTAACCTACTGAC 58.504 47.826 0.00 0.00 0.00 3.51
156 157 3.507411 AGCCTTCACTAACCTACTGACA 58.493 45.455 0.00 0.00 0.00 3.58
157 158 3.511934 AGCCTTCACTAACCTACTGACAG 59.488 47.826 0.00 0.00 0.00 3.51
158 159 3.368531 GCCTTCACTAACCTACTGACAGG 60.369 52.174 7.51 0.00 41.87 4.00
159 160 3.368531 CCTTCACTAACCTACTGACAGGC 60.369 52.174 7.51 0.00 39.53 4.85
160 161 3.170991 TCACTAACCTACTGACAGGCT 57.829 47.619 7.51 0.00 39.53 4.58
161 162 3.507411 TCACTAACCTACTGACAGGCTT 58.493 45.455 7.51 0.00 39.53 4.35
162 163 3.901844 TCACTAACCTACTGACAGGCTTT 59.098 43.478 7.51 0.00 39.53 3.51
163 164 3.997021 CACTAACCTACTGACAGGCTTTG 59.003 47.826 7.51 0.00 39.53 2.77
164 165 3.901844 ACTAACCTACTGACAGGCTTTGA 59.098 43.478 7.51 0.00 39.53 2.69
165 166 3.409026 AACCTACTGACAGGCTTTGAG 57.591 47.619 7.51 0.00 39.53 3.02
166 167 1.625818 ACCTACTGACAGGCTTTGAGG 59.374 52.381 7.51 5.94 39.53 3.86
167 168 1.625818 CCTACTGACAGGCTTTGAGGT 59.374 52.381 7.51 0.00 0.00 3.85
168 169 2.832129 CCTACTGACAGGCTTTGAGGTA 59.168 50.000 7.51 0.00 0.00 3.08
169 170 3.452627 CCTACTGACAGGCTTTGAGGTAT 59.547 47.826 7.51 0.00 0.00 2.73
170 171 3.340814 ACTGACAGGCTTTGAGGTATG 57.659 47.619 7.51 0.00 0.00 2.39
171 172 2.012673 CTGACAGGCTTTGAGGTATGC 58.987 52.381 0.00 0.00 0.00 3.14
172 173 1.009829 GACAGGCTTTGAGGTATGCG 58.990 55.000 0.00 0.00 0.00 4.73
173 174 0.613260 ACAGGCTTTGAGGTATGCGA 59.387 50.000 0.00 0.00 0.00 5.10
174 175 1.009829 CAGGCTTTGAGGTATGCGAC 58.990 55.000 0.00 0.00 0.00 5.19
175 176 0.613260 AGGCTTTGAGGTATGCGACA 59.387 50.000 0.00 0.00 0.00 4.35
176 177 1.210478 AGGCTTTGAGGTATGCGACAT 59.790 47.619 0.00 0.00 0.00 3.06
177 178 2.434336 AGGCTTTGAGGTATGCGACATA 59.566 45.455 0.00 0.00 0.00 2.29
178 179 3.118408 AGGCTTTGAGGTATGCGACATAA 60.118 43.478 0.00 0.00 0.00 1.90
179 180 3.815401 GGCTTTGAGGTATGCGACATAAT 59.185 43.478 0.00 0.00 0.00 1.28
180 181 4.319766 GGCTTTGAGGTATGCGACATAATG 60.320 45.833 0.00 0.00 0.00 1.90
181 182 4.273480 GCTTTGAGGTATGCGACATAATGT 59.727 41.667 0.00 0.00 0.00 2.71
182 183 5.220854 GCTTTGAGGTATGCGACATAATGTT 60.221 40.000 0.00 0.00 0.00 2.71
183 184 5.984233 TTGAGGTATGCGACATAATGTTC 57.016 39.130 0.00 0.00 0.00 3.18
184 185 5.276461 TGAGGTATGCGACATAATGTTCT 57.724 39.130 0.00 0.00 0.00 3.01
185 186 6.399639 TGAGGTATGCGACATAATGTTCTA 57.600 37.500 0.00 0.00 0.00 2.10
186 187 6.811954 TGAGGTATGCGACATAATGTTCTAA 58.188 36.000 0.00 0.00 0.00 2.10
187 188 7.269316 TGAGGTATGCGACATAATGTTCTAAA 58.731 34.615 0.00 0.00 0.00 1.85
188 189 7.223971 TGAGGTATGCGACATAATGTTCTAAAC 59.776 37.037 0.00 0.00 0.00 2.01
189 190 7.045416 AGGTATGCGACATAATGTTCTAAACA 58.955 34.615 0.00 0.00 46.94 2.83
190 191 7.011109 AGGTATGCGACATAATGTTCTAAACAC 59.989 37.037 0.00 0.00 45.50 3.32
191 192 6.985188 ATGCGACATAATGTTCTAAACACT 57.015 33.333 0.00 0.00 45.50 3.55
192 193 6.795098 TGCGACATAATGTTCTAAACACTT 57.205 33.333 0.00 0.00 45.50 3.16
193 194 7.197071 TGCGACATAATGTTCTAAACACTTT 57.803 32.000 0.00 0.00 45.50 2.66
194 195 7.644490 TGCGACATAATGTTCTAAACACTTTT 58.356 30.769 0.00 0.00 45.50 2.27
195 196 8.775527 TGCGACATAATGTTCTAAACACTTTTA 58.224 29.630 0.00 0.00 45.50 1.52
196 197 9.769093 GCGACATAATGTTCTAAACACTTTTAT 57.231 29.630 0.00 0.00 45.50 1.40
228 229 5.820423 GGAATATACCTGTGTACAATGTGCA 59.180 40.000 0.00 0.00 0.00 4.57
274 275 2.411701 CCGGCGACATCGAAGCTA 59.588 61.111 9.30 0.00 43.02 3.32
367 369 3.117851 ACTCGGAGGACATCTACTCATGA 60.118 47.826 10.23 0.00 35.45 3.07
446 451 1.466856 ATAGGCTCGTACAACGGTGA 58.533 50.000 7.88 0.00 42.81 4.02
488 493 2.552802 GTCTTCCAGAGACGACGGA 58.447 57.895 0.00 0.00 44.90 4.69
529 534 5.593010 AGAAGATAGATACGAACTGCCAAC 58.407 41.667 0.00 0.00 0.00 3.77
536 541 1.007387 CGAACTGCCAACCAAAGCC 60.007 57.895 0.00 0.00 0.00 4.35
537 542 1.455383 CGAACTGCCAACCAAAGCCT 61.455 55.000 0.00 0.00 0.00 4.58
539 544 0.106015 AACTGCCAACCAAAGCCTCT 60.106 50.000 0.00 0.00 0.00 3.69
543 548 1.304464 CCAACCAAAGCCTCTCCCC 60.304 63.158 0.00 0.00 0.00 4.81
544 549 1.304464 CAACCAAAGCCTCTCCCCC 60.304 63.158 0.00 0.00 0.00 5.40
545 550 1.466186 AACCAAAGCCTCTCCCCCT 60.466 57.895 0.00 0.00 0.00 4.79
546 551 0.178843 AACCAAAGCCTCTCCCCCTA 60.179 55.000 0.00 0.00 0.00 3.53
548 553 0.914417 CCAAAGCCTCTCCCCCTACA 60.914 60.000 0.00 0.00 0.00 2.74
550 555 1.354368 CAAAGCCTCTCCCCCTACAAA 59.646 52.381 0.00 0.00 0.00 2.83
552 557 0.992695 AGCCTCTCCCCCTACAAAAC 59.007 55.000 0.00 0.00 0.00 2.43
554 559 1.285078 GCCTCTCCCCCTACAAAACAT 59.715 52.381 0.00 0.00 0.00 2.71
555 560 2.508300 GCCTCTCCCCCTACAAAACATA 59.492 50.000 0.00 0.00 0.00 2.29
556 561 3.053917 GCCTCTCCCCCTACAAAACATAA 60.054 47.826 0.00 0.00 0.00 1.90
557 562 4.781934 CCTCTCCCCCTACAAAACATAAG 58.218 47.826 0.00 0.00 0.00 1.73
558 563 4.473559 CCTCTCCCCCTACAAAACATAAGA 59.526 45.833 0.00 0.00 0.00 2.10
559 564 5.045140 CCTCTCCCCCTACAAAACATAAGAA 60.045 44.000 0.00 0.00 0.00 2.52
560 565 5.812286 TCTCCCCCTACAAAACATAAGAAC 58.188 41.667 0.00 0.00 0.00 3.01
561 566 5.311121 TCTCCCCCTACAAAACATAAGAACA 59.689 40.000 0.00 0.00 0.00 3.18
562 567 5.954757 TCCCCCTACAAAACATAAGAACAA 58.045 37.500 0.00 0.00 0.00 2.83
563 568 6.557568 TCCCCCTACAAAACATAAGAACAAT 58.442 36.000 0.00 0.00 0.00 2.71
564 569 6.661805 TCCCCCTACAAAACATAAGAACAATC 59.338 38.462 0.00 0.00 0.00 2.67
565 570 6.435904 CCCCCTACAAAACATAAGAACAATCA 59.564 38.462 0.00 0.00 0.00 2.57
566 571 7.124147 CCCCCTACAAAACATAAGAACAATCAT 59.876 37.037 0.00 0.00 0.00 2.45
567 572 7.975616 CCCCTACAAAACATAAGAACAATCATG 59.024 37.037 0.00 0.00 0.00 3.07
568 573 7.975616 CCCTACAAAACATAAGAACAATCATGG 59.024 37.037 0.00 0.00 0.00 3.66
569 574 7.489113 CCTACAAAACATAAGAACAATCATGGC 59.511 37.037 0.00 0.00 0.00 4.40
570 575 6.757237 ACAAAACATAAGAACAATCATGGCA 58.243 32.000 0.00 0.00 0.00 4.92
571 576 7.388437 ACAAAACATAAGAACAATCATGGCAT 58.612 30.769 0.00 0.00 0.00 4.40
572 577 7.332430 ACAAAACATAAGAACAATCATGGCATG 59.668 33.333 21.42 21.42 0.00 4.06
596 791 3.120792 GCATCATGGTCAAATCACATGC 58.879 45.455 0.00 0.00 41.22 4.06
598 793 4.749976 CATCATGGTCAAATCACATGCAA 58.250 39.130 0.00 0.00 41.22 4.08
612 807 1.040339 ATGCAACAACAACCCACCGT 61.040 50.000 0.00 0.00 0.00 4.83
622 817 1.477685 AACCCACCGTCCGACAATCT 61.478 55.000 0.00 0.00 0.00 2.40
672 867 4.607293 AGAGAATCACTAAGCACACACA 57.393 40.909 0.00 0.00 37.82 3.72
746 942 6.705825 ACTTTCGATTTTAAGGCTGCAAAAAT 59.294 30.769 15.08 15.08 35.95 1.82
793 989 3.073356 TCAAACGGACTTGGAAATAGGGT 59.927 43.478 0.00 0.00 0.00 4.34
797 993 3.181437 ACGGACTTGGAAATAGGGTTTGT 60.181 43.478 0.00 0.00 0.00 2.83
798 994 4.041938 ACGGACTTGGAAATAGGGTTTGTA 59.958 41.667 0.00 0.00 0.00 2.41
819 1015 2.593346 AAGATACAAGCTCTCAGCCG 57.407 50.000 0.00 0.00 43.77 5.52
871 1293 6.601741 TCAAACAAAATGCAAAACATCCTC 57.398 33.333 0.00 0.00 38.34 3.71
872 1294 5.526846 TCAAACAAAATGCAAAACATCCTCC 59.473 36.000 0.00 0.00 38.34 4.30
873 1295 4.961438 ACAAAATGCAAAACATCCTCCT 57.039 36.364 0.00 0.00 38.34 3.69
952 1374 0.835543 CCCAAGCAAACCCCATTCCA 60.836 55.000 0.00 0.00 0.00 3.53
1453 1887 4.326826 AGATTTGGAGAATTTCGTCTGCA 58.673 39.130 0.00 0.00 43.38 4.41
1549 1983 1.063341 TCAGAGAGCCTAGTCCTGCAT 60.063 52.381 0.00 0.00 0.00 3.96
1675 2109 4.200283 GCGAGGGGTCAGAGAGCG 62.200 72.222 0.00 0.00 0.00 5.03
1748 2182 2.107041 TTGGCGATCAACGGGTCACT 62.107 55.000 0.00 0.00 42.83 3.41
1798 2232 2.149383 TCTGTCTTGGCAGGGCAGT 61.149 57.895 27.30 0.00 37.12 4.40
1836 2270 4.273318 AGAGGCAGAATGGATTGGTTTAC 58.727 43.478 0.00 0.00 35.86 2.01
2003 2452 5.862134 TTGCACTGGAGTGTAAAGGTAAACA 60.862 40.000 7.73 0.00 45.20 2.83
2138 2587 3.594134 AGTCAAGTAAGCAGACAGATGC 58.406 45.455 0.00 0.00 46.88 3.91
2315 2805 2.834549 AGTAACTGTATCCTGTGCTGCT 59.165 45.455 0.00 0.00 0.00 4.24
2325 2815 3.365472 TCCTGTGCTGCTCTCTACATTA 58.635 45.455 0.00 0.00 0.00 1.90
2488 2979 7.680730 AGGAATTCATACTGTTCAGTAGTTGT 58.319 34.615 16.08 0.00 0.00 3.32
2502 2993 1.102978 AGTTGTCTGGTTTGTGTGGC 58.897 50.000 0.00 0.00 0.00 5.01
2812 3421 4.331717 GCAAGCCCATCTGAAAATGATTTG 59.668 41.667 0.00 0.00 0.00 2.32
2819 3428 5.935789 CCATCTGAAAATGATTTGCCACTTT 59.064 36.000 0.00 0.00 0.00 2.66
2845 3454 7.145985 GTGTAACTGATGAGTAGAGTGTTTCA 58.854 38.462 0.00 0.00 0.00 2.69
2892 3501 5.682943 TGCTTTTGTTGTATGTACCTGTC 57.317 39.130 0.00 0.00 0.00 3.51
2893 3502 5.126779 TGCTTTTGTTGTATGTACCTGTCA 58.873 37.500 0.00 0.00 0.00 3.58
2894 3503 5.767665 TGCTTTTGTTGTATGTACCTGTCAT 59.232 36.000 0.00 0.00 0.00 3.06
2895 3504 6.072728 TGCTTTTGTTGTATGTACCTGTCATC 60.073 38.462 0.00 0.00 0.00 2.92
2896 3505 6.072728 GCTTTTGTTGTATGTACCTGTCATCA 60.073 38.462 0.00 0.00 0.00 3.07
2897 3506 7.521423 GCTTTTGTTGTATGTACCTGTCATCAA 60.521 37.037 0.00 0.00 0.00 2.57
2898 3507 7.994425 TTTGTTGTATGTACCTGTCATCAAT 57.006 32.000 0.00 0.00 0.00 2.57
2899 3508 6.983474 TGTTGTATGTACCTGTCATCAATG 57.017 37.500 0.00 0.00 0.00 2.82
2900 3509 6.472016 TGTTGTATGTACCTGTCATCAATGT 58.528 36.000 0.00 0.00 0.00 2.71
2901 3510 6.939730 TGTTGTATGTACCTGTCATCAATGTT 59.060 34.615 0.00 0.00 0.00 2.71
2902 3511 7.119116 TGTTGTATGTACCTGTCATCAATGTTC 59.881 37.037 0.00 0.00 0.00 3.18
2903 3512 6.112734 TGTATGTACCTGTCATCAATGTTCC 58.887 40.000 0.00 0.00 0.00 3.62
2904 3513 4.632327 TGTACCTGTCATCAATGTTCCA 57.368 40.909 0.00 0.00 0.00 3.53
2905 3514 5.178096 TGTACCTGTCATCAATGTTCCAT 57.822 39.130 0.00 0.00 0.00 3.41
2906 3515 5.185454 TGTACCTGTCATCAATGTTCCATC 58.815 41.667 0.00 0.00 0.00 3.51
2907 3516 4.581309 ACCTGTCATCAATGTTCCATCT 57.419 40.909 0.00 0.00 0.00 2.90
2908 3517 5.698741 ACCTGTCATCAATGTTCCATCTA 57.301 39.130 0.00 0.00 0.00 1.98
2909 3518 6.065976 ACCTGTCATCAATGTTCCATCTAA 57.934 37.500 0.00 0.00 0.00 2.10
2910 3519 5.882557 ACCTGTCATCAATGTTCCATCTAAC 59.117 40.000 0.00 0.00 0.00 2.34
2911 3520 5.882000 CCTGTCATCAATGTTCCATCTAACA 59.118 40.000 0.00 0.00 43.16 2.41
2912 3521 6.037940 CCTGTCATCAATGTTCCATCTAACAG 59.962 42.308 0.00 0.00 42.33 3.16
2913 3522 5.355071 TGTCATCAATGTTCCATCTAACAGC 59.645 40.000 0.00 0.00 42.33 4.40
2914 3523 4.571984 TCATCAATGTTCCATCTAACAGCG 59.428 41.667 0.00 0.00 42.33 5.18
2915 3524 3.270027 TCAATGTTCCATCTAACAGCGG 58.730 45.455 0.00 0.00 42.33 5.52
2916 3525 3.055458 TCAATGTTCCATCTAACAGCGGA 60.055 43.478 0.00 0.00 42.33 5.54
2917 3526 3.845781 ATGTTCCATCTAACAGCGGAT 57.154 42.857 0.00 0.00 42.33 4.18
2918 3527 3.179443 TGTTCCATCTAACAGCGGATC 57.821 47.619 0.00 0.00 34.50 3.36
2919 3528 2.158957 TGTTCCATCTAACAGCGGATCC 60.159 50.000 0.00 0.00 34.50 3.36
2920 3529 1.048601 TCCATCTAACAGCGGATCCC 58.951 55.000 6.06 0.00 0.00 3.85
2921 3530 0.758734 CCATCTAACAGCGGATCCCA 59.241 55.000 6.06 0.00 0.00 4.37
2922 3531 1.140852 CCATCTAACAGCGGATCCCAA 59.859 52.381 6.06 0.00 0.00 4.12
2923 3532 2.421388 CCATCTAACAGCGGATCCCAAA 60.421 50.000 6.06 0.00 0.00 3.28
2924 3533 2.691409 TCTAACAGCGGATCCCAAAG 57.309 50.000 6.06 0.00 0.00 2.77
2925 3534 1.906574 TCTAACAGCGGATCCCAAAGT 59.093 47.619 6.06 0.00 0.00 2.66
2926 3535 2.304761 TCTAACAGCGGATCCCAAAGTT 59.695 45.455 6.06 8.74 0.00 2.66
2927 3536 2.871096 AACAGCGGATCCCAAAGTTA 57.129 45.000 6.06 0.00 0.00 2.24
2928 3537 3.366052 AACAGCGGATCCCAAAGTTAT 57.634 42.857 6.06 0.00 0.00 1.89
2929 3538 4.497291 AACAGCGGATCCCAAAGTTATA 57.503 40.909 6.06 0.00 0.00 0.98
2930 3539 4.706842 ACAGCGGATCCCAAAGTTATAT 57.293 40.909 6.06 0.00 0.00 0.86
2931 3540 5.818678 ACAGCGGATCCCAAAGTTATATA 57.181 39.130 6.06 0.00 0.00 0.86
2932 3541 6.374417 ACAGCGGATCCCAAAGTTATATAT 57.626 37.500 6.06 0.00 0.00 0.86
2933 3542 6.779860 ACAGCGGATCCCAAAGTTATATATT 58.220 36.000 6.06 0.00 0.00 1.28
2934 3543 7.231467 ACAGCGGATCCCAAAGTTATATATTT 58.769 34.615 6.06 0.00 0.00 1.40
2935 3544 7.724061 ACAGCGGATCCCAAAGTTATATATTTT 59.276 33.333 6.06 0.00 0.00 1.82
2936 3545 8.237267 CAGCGGATCCCAAAGTTATATATTTTC 58.763 37.037 6.06 0.00 0.00 2.29
2937 3546 8.164070 AGCGGATCCCAAAGTTATATATTTTCT 58.836 33.333 6.06 0.00 0.00 2.52
2938 3547 8.793592 GCGGATCCCAAAGTTATATATTTTCTT 58.206 33.333 6.06 0.00 0.00 2.52
2957 3566 7.962964 TTTCTTTCAGTAACTGTATCCTGTG 57.037 36.000 0.00 0.00 32.61 3.66
2958 3567 5.479306 TCTTTCAGTAACTGTATCCTGTGC 58.521 41.667 0.00 0.00 32.61 4.57
2959 3568 5.246203 TCTTTCAGTAACTGTATCCTGTGCT 59.754 40.000 0.00 0.00 32.61 4.40
2960 3569 4.456280 TCAGTAACTGTATCCTGTGCTG 57.544 45.455 0.00 0.00 32.61 4.41
2961 3570 2.932614 CAGTAACTGTATCCTGTGCTGC 59.067 50.000 0.00 0.00 0.00 5.25
2962 3571 2.093447 AGTAACTGTATCCTGTGCTGCC 60.093 50.000 0.00 0.00 0.00 4.85
2963 3572 0.035056 AACTGTATCCTGTGCTGCCC 60.035 55.000 0.00 0.00 0.00 5.36
2964 3573 0.911525 ACTGTATCCTGTGCTGCCCT 60.912 55.000 0.00 0.00 0.00 5.19
2965 3574 0.254178 CTGTATCCTGTGCTGCCCTT 59.746 55.000 0.00 0.00 0.00 3.95
2966 3575 0.253044 TGTATCCTGTGCTGCCCTTC 59.747 55.000 0.00 0.00 0.00 3.46
2967 3576 0.811616 GTATCCTGTGCTGCCCTTCG 60.812 60.000 0.00 0.00 0.00 3.79
2968 3577 0.975556 TATCCTGTGCTGCCCTTCGA 60.976 55.000 0.00 0.00 0.00 3.71
3002 3611 4.015872 GGTCATTTACCTCAGGTGTTGA 57.984 45.455 6.61 3.75 45.75 3.18
3024 3633 8.739972 GTTGAGGATTTTAGTGTGTTCCATTAT 58.260 33.333 0.00 0.00 0.00 1.28
3220 3834 4.021102 AGGAGTTCATGTTGTGTTAGGG 57.979 45.455 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.067582 CGGATTAGTGGAGGCCGTC 59.932 63.158 0.00 0.00 37.35 4.79
1 2 2.432300 CCGGATTAGTGGAGGCCGT 61.432 63.158 0.00 0.00 40.33 5.68
2 3 2.088674 CTCCGGATTAGTGGAGGCCG 62.089 65.000 3.57 0.00 46.55 6.13
3 4 1.749033 CTCCGGATTAGTGGAGGCC 59.251 63.158 3.57 0.00 46.55 5.19
7 8 2.792947 GCGCCTCCGGATTAGTGGA 61.793 63.158 3.57 0.00 34.32 4.02
8 9 2.280186 GCGCCTCCGGATTAGTGG 60.280 66.667 3.57 2.80 34.32 4.00
9 10 1.300233 GAGCGCCTCCGGATTAGTG 60.300 63.158 3.57 4.93 34.32 2.74
10 11 1.327690 TTGAGCGCCTCCGGATTAGT 61.328 55.000 3.57 0.00 34.32 2.24
11 12 0.876342 GTTGAGCGCCTCCGGATTAG 60.876 60.000 3.57 0.00 34.32 1.73
12 13 1.143183 GTTGAGCGCCTCCGGATTA 59.857 57.895 3.57 0.00 34.32 1.75
13 14 2.125106 GTTGAGCGCCTCCGGATT 60.125 61.111 3.57 0.00 34.32 3.01
14 15 3.390521 TGTTGAGCGCCTCCGGAT 61.391 61.111 3.57 0.00 34.32 4.18
15 16 4.373116 GTGTTGAGCGCCTCCGGA 62.373 66.667 2.93 2.93 34.32 5.14
16 17 4.379243 AGTGTTGAGCGCCTCCGG 62.379 66.667 2.29 0.00 34.32 5.14
17 18 2.811317 GAGTGTTGAGCGCCTCCG 60.811 66.667 2.29 0.00 37.57 4.63
18 19 1.739562 CAGAGTGTTGAGCGCCTCC 60.740 63.158 2.29 0.00 0.00 4.30
19 20 1.739562 CCAGAGTGTTGAGCGCCTC 60.740 63.158 2.29 1.72 0.00 4.70
20 21 2.164865 CTCCAGAGTGTTGAGCGCCT 62.165 60.000 2.29 0.00 0.00 5.52
21 22 1.739562 CTCCAGAGTGTTGAGCGCC 60.740 63.158 2.29 0.00 0.00 6.53
22 23 1.739562 CCTCCAGAGTGTTGAGCGC 60.740 63.158 0.00 0.00 0.00 5.92
23 24 0.318441 TTCCTCCAGAGTGTTGAGCG 59.682 55.000 0.00 0.00 0.00 5.03
24 25 1.943507 GCTTCCTCCAGAGTGTTGAGC 60.944 57.143 0.00 0.00 0.00 4.26
25 26 1.345741 TGCTTCCTCCAGAGTGTTGAG 59.654 52.381 0.00 0.00 0.00 3.02
26 27 1.070758 GTGCTTCCTCCAGAGTGTTGA 59.929 52.381 0.00 0.00 0.00 3.18
27 28 1.071385 AGTGCTTCCTCCAGAGTGTTG 59.929 52.381 0.00 0.00 0.00 3.33
28 29 1.071385 CAGTGCTTCCTCCAGAGTGTT 59.929 52.381 0.00 0.00 0.00 3.32
29 30 0.683973 CAGTGCTTCCTCCAGAGTGT 59.316 55.000 0.00 0.00 0.00 3.55
30 31 0.673022 GCAGTGCTTCCTCCAGAGTG 60.673 60.000 8.18 0.00 0.00 3.51
31 32 1.123861 TGCAGTGCTTCCTCCAGAGT 61.124 55.000 17.60 0.00 0.00 3.24
32 33 0.391395 CTGCAGTGCTTCCTCCAGAG 60.391 60.000 17.60 0.00 0.00 3.35
33 34 1.675801 CTGCAGTGCTTCCTCCAGA 59.324 57.895 17.60 0.00 0.00 3.86
34 35 2.039405 GCTGCAGTGCTTCCTCCAG 61.039 63.158 17.60 4.26 0.00 3.86
35 36 2.033141 GCTGCAGTGCTTCCTCCA 59.967 61.111 17.60 0.00 0.00 3.86
36 37 3.123620 CGCTGCAGTGCTTCCTCC 61.124 66.667 15.44 0.00 0.00 4.30
37 38 2.358003 ACGCTGCAGTGCTTCCTC 60.358 61.111 26.78 0.07 0.00 3.71
38 39 2.667536 CACGCTGCAGTGCTTCCT 60.668 61.111 26.78 4.19 35.17 3.36
48 49 3.121030 ACGATGGAAGCACGCTGC 61.121 61.111 0.00 2.28 45.46 5.25
49 50 2.743752 CCACGATGGAAGCACGCTG 61.744 63.158 0.00 0.00 40.96 5.18
50 51 2.434884 CCACGATGGAAGCACGCT 60.435 61.111 0.00 0.00 40.96 5.07
51 52 4.166011 GCCACGATGGAAGCACGC 62.166 66.667 8.04 0.00 40.96 5.34
52 53 3.853330 CGCCACGATGGAAGCACG 61.853 66.667 8.04 0.00 40.96 5.34
53 54 3.499737 CCGCCACGATGGAAGCAC 61.500 66.667 8.04 0.00 40.96 4.40
54 55 3.664025 CTCCGCCACGATGGAAGCA 62.664 63.158 8.04 0.00 40.96 3.91
55 56 2.892425 CTCCGCCACGATGGAAGC 60.892 66.667 8.04 0.00 40.96 3.86
56 57 2.892425 GCTCCGCCACGATGGAAG 60.892 66.667 8.04 3.67 40.96 3.46
57 58 3.700970 TGCTCCGCCACGATGGAA 61.701 61.111 8.04 0.00 40.96 3.53
58 59 4.451150 GTGCTCCGCCACGATGGA 62.451 66.667 8.04 0.00 40.96 3.41
69 70 4.101448 ATCAGGGTGCGGTGCTCC 62.101 66.667 1.37 1.37 40.94 4.70
70 71 2.821366 CATCAGGGTGCGGTGCTC 60.821 66.667 0.00 0.00 0.00 4.26
71 72 4.415150 CCATCAGGGTGCGGTGCT 62.415 66.667 0.00 0.00 0.00 4.40
81 82 1.303561 CACCACCACACCCATCAGG 60.304 63.158 0.00 0.00 43.78 3.86
82 83 1.303561 CCACCACCACACCCATCAG 60.304 63.158 0.00 0.00 0.00 2.90
83 84 1.772156 TCCACCACCACACCCATCA 60.772 57.895 0.00 0.00 0.00 3.07
84 85 1.002134 CTCCACCACCACACCCATC 60.002 63.158 0.00 0.00 0.00 3.51
85 86 1.065410 TTCTCCACCACCACACCCAT 61.065 55.000 0.00 0.00 0.00 4.00
86 87 1.694525 TTCTCCACCACCACACCCA 60.695 57.895 0.00 0.00 0.00 4.51
87 88 1.073199 CTTCTCCACCACCACACCC 59.927 63.158 0.00 0.00 0.00 4.61
88 89 1.073199 CCTTCTCCACCACCACACC 59.927 63.158 0.00 0.00 0.00 4.16
89 90 0.182775 AACCTTCTCCACCACCACAC 59.817 55.000 0.00 0.00 0.00 3.82
90 91 0.472471 GAACCTTCTCCACCACCACA 59.528 55.000 0.00 0.00 0.00 4.17
91 92 0.472471 TGAACCTTCTCCACCACCAC 59.528 55.000 0.00 0.00 0.00 4.16
92 93 0.764890 CTGAACCTTCTCCACCACCA 59.235 55.000 0.00 0.00 0.00 4.17
93 94 0.765510 ACTGAACCTTCTCCACCACC 59.234 55.000 0.00 0.00 0.00 4.61
94 95 1.694696 AGACTGAACCTTCTCCACCAC 59.305 52.381 0.00 0.00 0.00 4.16
95 96 1.694150 CAGACTGAACCTTCTCCACCA 59.306 52.381 0.00 0.00 0.00 4.17
96 97 1.609320 GCAGACTGAACCTTCTCCACC 60.609 57.143 6.65 0.00 0.00 4.61
97 98 1.346068 AGCAGACTGAACCTTCTCCAC 59.654 52.381 6.65 0.00 0.00 4.02
98 99 1.722034 AGCAGACTGAACCTTCTCCA 58.278 50.000 6.65 0.00 0.00 3.86
99 100 3.963428 TTAGCAGACTGAACCTTCTCC 57.037 47.619 6.65 0.00 0.00 3.71
100 101 4.153296 GCTTTTAGCAGACTGAACCTTCTC 59.847 45.833 6.65 0.00 41.89 2.87
101 102 4.068599 GCTTTTAGCAGACTGAACCTTCT 58.931 43.478 6.65 0.00 41.89 2.85
102 103 3.120511 CGCTTTTAGCAGACTGAACCTTC 60.121 47.826 6.65 0.00 42.58 3.46
103 104 2.808543 CGCTTTTAGCAGACTGAACCTT 59.191 45.455 6.65 0.00 42.58 3.50
104 105 2.417719 CGCTTTTAGCAGACTGAACCT 58.582 47.619 6.65 0.00 42.58 3.50
105 106 1.464997 CCGCTTTTAGCAGACTGAACC 59.535 52.381 6.65 0.00 42.58 3.62
106 107 2.157863 GTCCGCTTTTAGCAGACTGAAC 59.842 50.000 6.65 0.00 43.43 3.18
107 108 2.413837 GTCCGCTTTTAGCAGACTGAA 58.586 47.619 6.65 0.00 43.43 3.02
108 109 2.080286 GTCCGCTTTTAGCAGACTGA 57.920 50.000 6.65 0.00 43.43 3.41
111 112 2.080286 TCAGTCCGCTTTTAGCAGAC 57.920 50.000 6.89 6.89 46.26 3.51
112 113 2.413837 GTTCAGTCCGCTTTTAGCAGA 58.586 47.619 0.00 0.00 42.58 4.26
113 114 1.126846 CGTTCAGTCCGCTTTTAGCAG 59.873 52.381 0.00 0.00 42.58 4.24
114 115 1.144969 CGTTCAGTCCGCTTTTAGCA 58.855 50.000 0.00 0.00 42.58 3.49
115 116 1.425412 TCGTTCAGTCCGCTTTTAGC 58.575 50.000 0.00 0.00 38.02 3.09
116 117 2.159827 GCTTCGTTCAGTCCGCTTTTAG 60.160 50.000 0.00 0.00 0.00 1.85
117 118 1.796459 GCTTCGTTCAGTCCGCTTTTA 59.204 47.619 0.00 0.00 0.00 1.52
118 119 0.586802 GCTTCGTTCAGTCCGCTTTT 59.413 50.000 0.00 0.00 0.00 2.27
119 120 1.228657 GGCTTCGTTCAGTCCGCTTT 61.229 55.000 0.00 0.00 0.00 3.51
120 121 1.668151 GGCTTCGTTCAGTCCGCTT 60.668 57.895 0.00 0.00 0.00 4.68
121 122 2.048127 GGCTTCGTTCAGTCCGCT 60.048 61.111 0.00 0.00 0.00 5.52
122 123 1.627550 GAAGGCTTCGTTCAGTCCGC 61.628 60.000 12.12 0.00 0.00 5.54
123 124 0.319555 TGAAGGCTTCGTTCAGTCCG 60.320 55.000 21.42 0.00 34.10 4.79
124 125 1.149148 GTGAAGGCTTCGTTCAGTCC 58.851 55.000 21.42 0.00 38.60 3.85
125 126 2.156343 AGTGAAGGCTTCGTTCAGTC 57.844 50.000 21.42 6.60 37.34 3.51
126 127 3.391049 GTTAGTGAAGGCTTCGTTCAGT 58.609 45.455 21.42 10.65 42.20 3.41
127 128 2.737252 GGTTAGTGAAGGCTTCGTTCAG 59.263 50.000 21.42 0.00 38.60 3.02
128 129 2.367567 AGGTTAGTGAAGGCTTCGTTCA 59.632 45.455 21.42 2.42 36.18 3.18
129 130 3.041508 AGGTTAGTGAAGGCTTCGTTC 57.958 47.619 21.42 14.13 0.00 3.95
130 131 3.577415 AGTAGGTTAGTGAAGGCTTCGTT 59.423 43.478 21.42 14.34 0.00 3.85
131 132 3.056749 CAGTAGGTTAGTGAAGGCTTCGT 60.057 47.826 21.42 13.93 0.00 3.85
132 133 3.192844 TCAGTAGGTTAGTGAAGGCTTCG 59.807 47.826 21.42 3.68 35.31 3.79
133 134 4.021368 TGTCAGTAGGTTAGTGAAGGCTTC 60.021 45.833 20.27 20.27 39.64 3.86
134 135 3.901844 TGTCAGTAGGTTAGTGAAGGCTT 59.098 43.478 0.00 0.00 39.64 4.35
135 136 3.507411 TGTCAGTAGGTTAGTGAAGGCT 58.493 45.455 0.00 0.00 39.64 4.58
136 137 3.368531 CCTGTCAGTAGGTTAGTGAAGGC 60.369 52.174 0.00 0.00 39.64 4.35
137 138 3.368531 GCCTGTCAGTAGGTTAGTGAAGG 60.369 52.174 0.00 12.69 39.64 3.46
138 139 3.511934 AGCCTGTCAGTAGGTTAGTGAAG 59.488 47.826 0.00 0.00 39.64 3.02
139 140 3.507411 AGCCTGTCAGTAGGTTAGTGAA 58.493 45.455 0.00 0.00 39.64 3.18
140 141 3.170991 AGCCTGTCAGTAGGTTAGTGA 57.829 47.619 0.00 0.00 40.11 3.41
141 142 3.963428 AAGCCTGTCAGTAGGTTAGTG 57.037 47.619 0.00 0.00 40.11 2.74
142 143 3.901844 TCAAAGCCTGTCAGTAGGTTAGT 59.098 43.478 0.00 0.00 40.11 2.24
143 144 4.499183 CTCAAAGCCTGTCAGTAGGTTAG 58.501 47.826 0.00 0.00 40.11 2.34
144 145 3.260884 CCTCAAAGCCTGTCAGTAGGTTA 59.739 47.826 0.00 0.00 40.11 2.85
145 146 2.039084 CCTCAAAGCCTGTCAGTAGGTT 59.961 50.000 0.00 0.00 40.11 3.50
146 147 1.625818 CCTCAAAGCCTGTCAGTAGGT 59.374 52.381 0.00 0.00 40.11 3.08
147 148 1.625818 ACCTCAAAGCCTGTCAGTAGG 59.374 52.381 0.00 0.00 40.95 3.18
148 149 4.437239 CATACCTCAAAGCCTGTCAGTAG 58.563 47.826 0.00 0.00 0.00 2.57
149 150 3.369471 GCATACCTCAAAGCCTGTCAGTA 60.369 47.826 0.00 0.00 0.00 2.74
150 151 2.616510 GCATACCTCAAAGCCTGTCAGT 60.617 50.000 0.00 0.00 0.00 3.41
151 152 2.012673 GCATACCTCAAAGCCTGTCAG 58.987 52.381 0.00 0.00 0.00 3.51
152 153 1.675714 CGCATACCTCAAAGCCTGTCA 60.676 52.381 0.00 0.00 0.00 3.58
153 154 1.009829 CGCATACCTCAAAGCCTGTC 58.990 55.000 0.00 0.00 0.00 3.51
154 155 0.613260 TCGCATACCTCAAAGCCTGT 59.387 50.000 0.00 0.00 0.00 4.00
155 156 1.009829 GTCGCATACCTCAAAGCCTG 58.990 55.000 0.00 0.00 0.00 4.85
156 157 0.613260 TGTCGCATACCTCAAAGCCT 59.387 50.000 0.00 0.00 0.00 4.58
157 158 1.668419 ATGTCGCATACCTCAAAGCC 58.332 50.000 0.00 0.00 0.00 4.35
158 159 4.273480 ACATTATGTCGCATACCTCAAAGC 59.727 41.667 0.00 0.00 0.00 3.51
159 160 5.991328 ACATTATGTCGCATACCTCAAAG 57.009 39.130 0.00 0.00 0.00 2.77
160 161 6.112734 AGAACATTATGTCGCATACCTCAAA 58.887 36.000 0.00 0.00 0.00 2.69
161 162 5.670485 AGAACATTATGTCGCATACCTCAA 58.330 37.500 0.00 0.00 0.00 3.02
162 163 5.276461 AGAACATTATGTCGCATACCTCA 57.724 39.130 0.00 0.00 0.00 3.86
163 164 7.223971 TGTTTAGAACATTATGTCGCATACCTC 59.776 37.037 0.00 0.00 36.25 3.85
164 165 7.011109 GTGTTTAGAACATTATGTCGCATACCT 59.989 37.037 0.00 0.00 44.35 3.08
165 166 7.011109 AGTGTTTAGAACATTATGTCGCATACC 59.989 37.037 0.00 0.00 44.35 2.73
166 167 7.906160 AGTGTTTAGAACATTATGTCGCATAC 58.094 34.615 0.00 0.00 44.35 2.39
167 168 8.487313 AAGTGTTTAGAACATTATGTCGCATA 57.513 30.769 0.00 0.00 44.35 3.14
168 169 6.985188 AGTGTTTAGAACATTATGTCGCAT 57.015 33.333 0.00 0.00 44.35 4.73
169 170 6.795098 AAGTGTTTAGAACATTATGTCGCA 57.205 33.333 0.00 0.00 44.35 5.10
170 171 9.769093 ATAAAAGTGTTTAGAACATTATGTCGC 57.231 29.630 0.00 0.00 44.35 5.19
199 200 9.381038 ACATTGTACACAGGTATATTCCTCTAT 57.619 33.333 0.00 0.00 35.37 1.98
200 201 8.638873 CACATTGTACACAGGTATATTCCTCTA 58.361 37.037 0.00 0.00 35.37 2.43
201 202 7.500992 CACATTGTACACAGGTATATTCCTCT 58.499 38.462 0.00 0.00 35.37 3.69
202 203 6.202954 GCACATTGTACACAGGTATATTCCTC 59.797 42.308 0.00 0.00 35.37 3.71
203 204 6.055588 GCACATTGTACACAGGTATATTCCT 58.944 40.000 0.00 0.00 38.51 3.36
204 205 5.820423 TGCACATTGTACACAGGTATATTCC 59.180 40.000 0.00 0.00 0.00 3.01
205 206 6.538742 ACTGCACATTGTACACAGGTATATTC 59.461 38.462 13.24 0.00 32.60 1.75
206 207 6.414732 ACTGCACATTGTACACAGGTATATT 58.585 36.000 13.24 0.00 32.60 1.28
207 208 5.989477 ACTGCACATTGTACACAGGTATAT 58.011 37.500 13.24 0.00 32.60 0.86
208 209 5.414789 ACTGCACATTGTACACAGGTATA 57.585 39.130 13.24 0.00 32.60 1.47
209 210 4.253685 GACTGCACATTGTACACAGGTAT 58.746 43.478 13.24 0.00 32.60 2.73
210 211 3.659786 GACTGCACATTGTACACAGGTA 58.340 45.455 13.24 0.00 32.60 3.08
211 212 2.494059 GACTGCACATTGTACACAGGT 58.506 47.619 13.24 2.16 32.60 4.00
212 213 1.460743 CGACTGCACATTGTACACAGG 59.539 52.381 13.24 1.59 32.60 4.00
213 214 2.096762 CACGACTGCACATTGTACACAG 60.097 50.000 8.46 8.46 0.00 3.66
214 215 1.864082 CACGACTGCACATTGTACACA 59.136 47.619 0.00 0.00 0.00 3.72
215 216 1.398451 GCACGACTGCACATTGTACAC 60.398 52.381 0.00 0.00 43.62 2.90
216 217 0.865111 GCACGACTGCACATTGTACA 59.135 50.000 0.00 0.00 43.62 2.90
217 218 1.148310 AGCACGACTGCACATTGTAC 58.852 50.000 0.52 0.00 46.97 2.90
218 219 1.877637 AAGCACGACTGCACATTGTA 58.122 45.000 0.52 0.00 46.97 2.41
219 220 1.024271 AAAGCACGACTGCACATTGT 58.976 45.000 0.52 0.00 46.97 2.71
228 229 0.946221 CTCCTCGCAAAAGCACGACT 60.946 55.000 0.00 0.00 34.08 4.18
256 257 3.768185 TAGCTTCGATGTCGCCGGC 62.768 63.158 19.07 19.07 39.60 6.13
262 263 0.382515 ACCTCGCTAGCTTCGATGTC 59.617 55.000 13.93 0.00 35.25 3.06
274 275 3.391382 GTAGCCACCCACCTCGCT 61.391 66.667 0.00 0.00 35.34 4.93
311 313 3.058016 ACCATCTTTGTCGTTCAGCAATG 60.058 43.478 0.00 0.00 0.00 2.82
367 369 1.989706 AGGTTATTTGCCACAACCGT 58.010 45.000 0.00 0.00 45.22 4.83
446 451 3.751175 CCCACAAAATCTACACACATCGT 59.249 43.478 0.00 0.00 0.00 3.73
455 460 4.906618 TGGAAGACTCCCACAAAATCTAC 58.093 43.478 0.00 0.00 41.64 2.59
458 463 4.006319 CTCTGGAAGACTCCCACAAAATC 58.994 47.826 0.00 0.00 38.67 2.17
482 487 2.562635 TCCTCTCTCTGTATTCCGTCG 58.437 52.381 0.00 0.00 0.00 5.12
488 493 9.354673 CTATCTTCTTCTTCCTCTCTCTGTATT 57.645 37.037 0.00 0.00 0.00 1.89
529 534 0.914417 TGTAGGGGGAGAGGCTTTGG 60.914 60.000 0.00 0.00 0.00 3.28
536 541 5.693769 TCTTATGTTTTGTAGGGGGAGAG 57.306 43.478 0.00 0.00 0.00 3.20
537 542 5.311121 TGTTCTTATGTTTTGTAGGGGGAGA 59.689 40.000 0.00 0.00 0.00 3.71
539 544 5.586155 TGTTCTTATGTTTTGTAGGGGGA 57.414 39.130 0.00 0.00 0.00 4.81
543 548 7.489113 GCCATGATTGTTCTTATGTTTTGTAGG 59.511 37.037 0.00 0.00 0.00 3.18
544 549 8.028354 TGCCATGATTGTTCTTATGTTTTGTAG 58.972 33.333 0.00 0.00 0.00 2.74
545 550 7.890515 TGCCATGATTGTTCTTATGTTTTGTA 58.109 30.769 0.00 0.00 0.00 2.41
546 551 6.757237 TGCCATGATTGTTCTTATGTTTTGT 58.243 32.000 0.00 0.00 0.00 2.83
548 553 7.613585 TCATGCCATGATTGTTCTTATGTTTT 58.386 30.769 2.53 0.00 33.59 2.43
550 555 6.778834 TCATGCCATGATTGTTCTTATGTT 57.221 33.333 2.53 0.00 33.59 2.71
571 576 4.017808 TGTGATTTGACCATGATGCATCA 58.982 39.130 30.47 30.47 41.70 3.07
572 577 4.642445 TGTGATTTGACCATGATGCATC 57.358 40.909 20.14 20.14 0.00 3.91
596 791 1.731093 GGACGGTGGGTTGTTGTTG 59.269 57.895 0.00 0.00 0.00 3.33
598 793 2.203098 CGGACGGTGGGTTGTTGT 60.203 61.111 0.00 0.00 0.00 3.32
612 807 4.925054 CGGTTAACTTTGTAGATTGTCGGA 59.075 41.667 5.42 0.00 0.00 4.55
622 817 3.285484 TGGTTTGCCGGTTAACTTTGTA 58.715 40.909 16.77 0.00 37.67 2.41
726 921 7.992180 AGATATTTTTGCAGCCTTAAAATCG 57.008 32.000 8.85 0.00 34.39 3.34
755 951 4.438148 CGTTTGATTTCTGTGGGGTTTTT 58.562 39.130 0.00 0.00 0.00 1.94
793 989 6.986817 GGCTGAGAGCTTGTATCTTATACAAA 59.013 38.462 12.23 0.00 41.99 2.83
797 993 4.827835 ACGGCTGAGAGCTTGTATCTTATA 59.172 41.667 0.00 0.00 41.99 0.98
798 994 3.639094 ACGGCTGAGAGCTTGTATCTTAT 59.361 43.478 0.00 0.00 41.99 1.73
835 1031 8.394877 TGCATTTTGTTTGAATATACTCCGTAG 58.605 33.333 0.00 0.00 0.00 3.51
836 1032 8.270080 TGCATTTTGTTTGAATATACTCCGTA 57.730 30.769 0.00 0.00 0.00 4.02
837 1033 7.151999 TGCATTTTGTTTGAATATACTCCGT 57.848 32.000 0.00 0.00 0.00 4.69
838 1034 8.459521 TTTGCATTTTGTTTGAATATACTCCG 57.540 30.769 0.00 0.00 0.00 4.63
871 1293 5.325239 ACCCAACTAGATTTTGGAAAGAGG 58.675 41.667 11.28 0.00 45.69 3.69
872 1294 6.071896 GGAACCCAACTAGATTTTGGAAAGAG 60.072 42.308 11.28 0.00 45.69 2.85
873 1295 5.773176 GGAACCCAACTAGATTTTGGAAAGA 59.227 40.000 11.28 0.00 45.69 2.52
1453 1887 1.452651 CTGTGGGGCAGCAATCGAT 60.453 57.895 0.00 0.00 38.52 3.59
1686 2120 3.147595 TCTGGCAGGTCCCGATCG 61.148 66.667 15.73 8.51 0.00 3.69
1691 2125 3.775654 CCTCGTCTGGCAGGTCCC 61.776 72.222 15.73 0.00 0.00 4.46
1748 2182 1.071542 TGCCAGAACGTGAAATCCTCA 59.928 47.619 0.00 0.00 0.00 3.86
1811 2245 2.029623 CCAATCCATTCTGCCTCTTGG 58.970 52.381 0.00 0.00 0.00 3.61
1836 2270 3.906720 TCCTCATTAACCTTCCTTCCG 57.093 47.619 0.00 0.00 0.00 4.30
2003 2452 1.208844 TCTCGGACTCTCCTGAGGGT 61.209 60.000 0.00 0.00 46.67 4.34
2138 2587 3.243201 GGTCTTGTTTCCAGTGCTTTCAG 60.243 47.826 0.00 0.00 0.00 3.02
2288 2778 5.246203 AGCACAGGATACAGTTACTGAAAGA 59.754 40.000 20.07 1.66 36.47 2.52
2315 2805 9.653287 CCTACAACTGAAACAATAATGTAGAGA 57.347 33.333 10.65 0.00 40.56 3.10
2325 2815 5.590530 TGTTTGCCTACAACTGAAACAAT 57.409 34.783 0.00 0.00 34.46 2.71
2488 2979 0.840617 TACCTGCCACACAAACCAGA 59.159 50.000 0.00 0.00 0.00 3.86
2684 3291 2.149578 CCAGAGACACAAAGGAGCTTG 58.850 52.381 0.00 0.00 0.00 4.01
2812 3421 3.815401 ACTCATCAGTTACACAAAGTGGC 59.185 43.478 1.93 0.00 38.79 5.01
2819 3428 6.650427 AACACTCTACTCATCAGTTACACA 57.350 37.500 0.00 0.00 33.62 3.72
2845 3454 3.685550 GCCACTATTCCCATGCAGTAACT 60.686 47.826 0.00 0.00 0.00 2.24
2899 3508 2.484889 GGATCCGCTGTTAGATGGAAC 58.515 52.381 0.00 0.00 33.48 3.62
2900 3509 1.416401 GGGATCCGCTGTTAGATGGAA 59.584 52.381 5.45 0.00 33.48 3.53
2901 3510 1.048601 GGGATCCGCTGTTAGATGGA 58.951 55.000 5.45 0.00 34.45 3.41
2902 3511 0.758734 TGGGATCCGCTGTTAGATGG 59.241 55.000 5.45 0.00 0.00 3.51
2903 3512 2.620251 TTGGGATCCGCTGTTAGATG 57.380 50.000 5.45 0.00 0.00 2.90
2904 3513 2.505819 ACTTTGGGATCCGCTGTTAGAT 59.494 45.455 5.45 0.00 0.00 1.98
2905 3514 1.906574 ACTTTGGGATCCGCTGTTAGA 59.093 47.619 5.45 0.00 0.00 2.10
2906 3515 2.403252 ACTTTGGGATCCGCTGTTAG 57.597 50.000 5.45 0.00 0.00 2.34
2907 3516 2.871096 AACTTTGGGATCCGCTGTTA 57.129 45.000 5.45 0.00 0.00 2.41
2908 3517 2.871096 TAACTTTGGGATCCGCTGTT 57.129 45.000 5.45 10.38 0.00 3.16
2909 3518 4.706842 ATATAACTTTGGGATCCGCTGT 57.293 40.909 5.45 0.00 0.00 4.40
2910 3519 7.687941 AAATATATAACTTTGGGATCCGCTG 57.312 36.000 5.45 0.00 0.00 5.18
2911 3520 8.164070 AGAAAATATATAACTTTGGGATCCGCT 58.836 33.333 5.45 0.00 0.00 5.52
2912 3521 8.336801 AGAAAATATATAACTTTGGGATCCGC 57.663 34.615 5.45 0.00 0.00 5.54
2931 3540 9.003658 CACAGGATACAGTTACTGAAAGAAAAT 57.996 33.333 20.07 0.00 36.47 1.82
2932 3541 7.041372 GCACAGGATACAGTTACTGAAAGAAAA 60.041 37.037 20.07 0.00 36.47 2.29
2933 3542 6.426937 GCACAGGATACAGTTACTGAAAGAAA 59.573 38.462 20.07 0.00 36.47 2.52
2934 3543 5.932303 GCACAGGATACAGTTACTGAAAGAA 59.068 40.000 20.07 0.00 36.47 2.52
2935 3544 5.246203 AGCACAGGATACAGTTACTGAAAGA 59.754 40.000 20.07 1.66 36.47 2.52
2936 3545 5.349817 CAGCACAGGATACAGTTACTGAAAG 59.650 44.000 20.07 5.14 38.98 2.62
2937 3546 5.237815 CAGCACAGGATACAGTTACTGAAA 58.762 41.667 20.07 6.99 38.98 2.69
2938 3547 4.820897 CAGCACAGGATACAGTTACTGAA 58.179 43.478 20.07 0.00 38.98 3.02
2939 3548 3.368427 GCAGCACAGGATACAGTTACTGA 60.368 47.826 20.07 3.21 38.98 3.41
2940 3549 2.932614 GCAGCACAGGATACAGTTACTG 59.067 50.000 11.21 11.21 39.40 2.74
2941 3550 2.093447 GGCAGCACAGGATACAGTTACT 60.093 50.000 0.00 0.00 41.41 2.24
2942 3551 2.280628 GGCAGCACAGGATACAGTTAC 58.719 52.381 0.00 0.00 41.41 2.50
2943 3552 1.209504 GGGCAGCACAGGATACAGTTA 59.790 52.381 0.00 0.00 41.41 2.24
2944 3553 0.035056 GGGCAGCACAGGATACAGTT 60.035 55.000 0.00 0.00 41.41 3.16
2945 3554 0.911525 AGGGCAGCACAGGATACAGT 60.912 55.000 0.00 0.00 41.41 3.55
2946 3555 0.254178 AAGGGCAGCACAGGATACAG 59.746 55.000 0.00 0.00 41.41 2.74
2947 3556 0.253044 GAAGGGCAGCACAGGATACA 59.747 55.000 0.00 0.00 41.41 2.29
2948 3557 0.811616 CGAAGGGCAGCACAGGATAC 60.812 60.000 0.00 0.00 0.00 2.24
2949 3558 0.975556 TCGAAGGGCAGCACAGGATA 60.976 55.000 0.00 0.00 0.00 2.59
2950 3559 1.630126 ATCGAAGGGCAGCACAGGAT 61.630 55.000 0.00 0.00 0.00 3.24
2951 3560 2.244117 GATCGAAGGGCAGCACAGGA 62.244 60.000 0.00 0.00 0.00 3.86
2952 3561 1.817099 GATCGAAGGGCAGCACAGG 60.817 63.158 0.00 0.00 0.00 4.00
2953 3562 1.817099 GGATCGAAGGGCAGCACAG 60.817 63.158 0.00 0.00 0.00 3.66
2954 3563 2.268920 GGATCGAAGGGCAGCACA 59.731 61.111 0.00 0.00 0.00 4.57
2955 3564 2.514824 GGGATCGAAGGGCAGCAC 60.515 66.667 0.00 0.00 0.00 4.40
2956 3565 1.925285 AATGGGATCGAAGGGCAGCA 61.925 55.000 0.00 0.00 0.00 4.41
2957 3566 0.753111 AAATGGGATCGAAGGGCAGC 60.753 55.000 0.00 0.00 0.00 5.25
2958 3567 1.406539 CAAAATGGGATCGAAGGGCAG 59.593 52.381 0.00 0.00 0.00 4.85
2959 3568 1.272425 ACAAAATGGGATCGAAGGGCA 60.272 47.619 0.00 0.00 0.00 5.36
2960 3569 1.474330 ACAAAATGGGATCGAAGGGC 58.526 50.000 0.00 0.00 0.00 5.19
2961 3570 2.166254 CCAACAAAATGGGATCGAAGGG 59.834 50.000 0.00 0.00 36.79 3.95
2962 3571 2.825532 ACCAACAAAATGGGATCGAAGG 59.174 45.455 0.00 0.00 45.18 3.46
2963 3572 3.505680 TGACCAACAAAATGGGATCGAAG 59.494 43.478 0.00 0.00 45.18 3.79
2964 3573 3.491342 TGACCAACAAAATGGGATCGAA 58.509 40.909 0.00 0.00 45.18 3.71
2965 3574 3.147553 TGACCAACAAAATGGGATCGA 57.852 42.857 0.00 0.00 45.18 3.59
2966 3575 4.454728 AATGACCAACAAAATGGGATCG 57.545 40.909 0.00 0.00 45.18 3.69
3024 3633 1.663643 GCATTCGAACTACCGATGCAA 59.336 47.619 11.65 0.00 39.94 4.08


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

AutoCloner maintained by Alex Coulton.