Multiple sequence alignment - TraesCS1B01G404500

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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 TraesCS1B01G404500 chr1B 100.000 2213 0 0 1 2213 633707708 633709920 0.000000e+00 4087.0
1 TraesCS1B01G404500 chr2D 98.144 1886 30 5 330 2213 638424848 638426730 0.000000e+00 3284.0
2 TraesCS1B01G404500 chr2D 93.805 113 6 1 1 113 261959494 261959605 3.780000e-38 169.0
3 TraesCS1B01G404500 chr2D 91.453 117 6 1 185 297 261959634 261959750 8.180000e-35 158.0
4 TraesCS1B01G404500 chr2D 91.045 67 3 2 1 66 632807874 632807810 1.090000e-13 87.9
5 TraesCS1B01G404500 chr5D 97.774 1887 38 4 330 2213 503292214 503294099 0.000000e+00 3249.0
6 TraesCS1B01G404500 chr5D 97.031 1886 36 6 330 2213 6176573 6174706 0.000000e+00 3155.0
7 TraesCS1B01G404500 chr5D 98.261 1553 23 3 330 1879 512410528 512412079 0.000000e+00 2715.0
8 TraesCS1B01G404500 chr5D 98.261 1553 22 4 330 1879 512417465 512419015 0.000000e+00 2713.0
9 TraesCS1B01G404500 chr5D 93.648 488 28 3 1726 2213 12935856 12936340 0.000000e+00 726.0
10 TraesCS1B01G404500 chr5D 85.401 137 3 7 1 137 446475277 446475158 2.310000e-25 126.0
11 TraesCS1B01G404500 chr1D 97.720 1886 38 5 330 2213 254435377 254437259 0.000000e+00 3240.0
12 TraesCS1B01G404500 chr1D 96.235 1886 59 7 330 2213 51871594 51869719 0.000000e+00 3079.0
13 TraesCS1B01G404500 chr4B 96.930 1889 51 6 330 2213 308679425 308677539 0.000000e+00 3160.0
14 TraesCS1B01G404500 chr4D 94.597 1888 86 11 330 2213 207067882 207066007 0.000000e+00 2907.0
15 TraesCS1B01G404500 chr6D 87.774 319 16 10 1 299 381370298 381370613 3.500000e-93 351.0
16 TraesCS1B01G404500 chr5A 85.152 330 17 6 1 301 466718109 466718435 2.130000e-80 309.0
17 TraesCS1B01G404500 chr7A 86.861 274 12 4 1 252 450326955 450327226 3.600000e-73 285.0
18 TraesCS1B01G404500 chr7A 94.000 50 3 0 252 301 450373958 450374007 2.360000e-10 76.8
19 TraesCS1B01G404500 chr3D 96.350 137 5 0 1 137 141482952 141482816 2.210000e-55 226.0
20 TraesCS1B01G404500 chr3D 93.431 137 6 1 1 137 32169356 32169223 1.340000e-47 200.0
21 TraesCS1B01G404500 chr3D 92.701 137 9 1 1 137 380303321 380303186 1.730000e-46 196.0
22 TraesCS1B01G404500 chr3A 89.706 136 5 4 2 137 209137585 209137711 4.890000e-37 165.0
23 TraesCS1B01G404500 chr3A 95.455 44 2 0 258 301 209137733 209137776 1.100000e-08 71.3
24 TraesCS1B01G404500 chr3A 87.037 54 3 3 281 330 209137776 209137829 8.530000e-05 58.4


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 TraesCS1B01G404500 chr1B 633707708 633709920 2212 False 4087 4087 100.000 1 2213 1 chr1B.!!$F1 2212
1 TraesCS1B01G404500 chr2D 638424848 638426730 1882 False 3284 3284 98.144 330 2213 1 chr2D.!!$F1 1883
2 TraesCS1B01G404500 chr5D 503292214 503294099 1885 False 3249 3249 97.774 330 2213 1 chr5D.!!$F2 1883
3 TraesCS1B01G404500 chr5D 6174706 6176573 1867 True 3155 3155 97.031 330 2213 1 chr5D.!!$R1 1883
4 TraesCS1B01G404500 chr5D 512410528 512412079 1551 False 2715 2715 98.261 330 1879 1 chr5D.!!$F3 1549
5 TraesCS1B01G404500 chr5D 512417465 512419015 1550 False 2713 2713 98.261 330 1879 1 chr5D.!!$F4 1549
6 TraesCS1B01G404500 chr1D 254435377 254437259 1882 False 3240 3240 97.720 330 2213 1 chr1D.!!$F1 1883
7 TraesCS1B01G404500 chr1D 51869719 51871594 1875 True 3079 3079 96.235 330 2213 1 chr1D.!!$R1 1883
8 TraesCS1B01G404500 chr4B 308677539 308679425 1886 True 3160 3160 96.930 330 2213 1 chr4B.!!$R1 1883
9 TraesCS1B01G404500 chr4D 207066007 207067882 1875 True 2907 2907 94.597 330 2213 1 chr4D.!!$R1 1883

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 0.036294 AGCCTTTGCCTCGTTCCTAC 60.036 55.0 0.0 0.0 38.69 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 1831 1.477295 CGAAAGGGACAGTCTACCTCC 59.523 57.143 0.0 0.0 32.29 4.3 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
26 27 9.507329 GAGGGATTTTATGACTTAATATGCAGA 57.493 33.333 0.00 0.00 0.00 4.26
27 28 9.866655 AGGGATTTTATGACTTAATATGCAGAA 57.133 29.630 0.00 0.00 0.00 3.02
37 38 9.716531 TGACTTAATATGCAGAAATAGATGGAG 57.283 33.333 0.00 0.00 0.00 3.86
38 39 9.935241 GACTTAATATGCAGAAATAGATGGAGA 57.065 33.333 0.00 0.00 0.00 3.71
46 47 8.862325 TGCAGAAATAGATGGAGAAGTAAAAA 57.138 30.769 0.00 0.00 0.00 1.94
71 72 6.764308 AAAACATAGCTATCATGTTGCAGT 57.236 33.333 12.87 0.00 43.94 4.40
72 73 7.864108 AAAACATAGCTATCATGTTGCAGTA 57.136 32.000 12.87 0.00 43.94 2.74
73 74 6.851222 AACATAGCTATCATGTTGCAGTAC 57.149 37.500 11.64 0.00 43.27 2.73
74 75 5.917462 ACATAGCTATCATGTTGCAGTACA 58.083 37.500 2.34 0.00 32.72 2.90
75 76 5.987953 ACATAGCTATCATGTTGCAGTACAG 59.012 40.000 2.34 0.00 32.72 2.74
76 77 3.801698 AGCTATCATGTTGCAGTACAGG 58.198 45.455 0.00 0.00 0.00 4.00
77 78 3.198635 AGCTATCATGTTGCAGTACAGGT 59.801 43.478 3.37 0.00 32.07 4.00
78 79 3.941483 GCTATCATGTTGCAGTACAGGTT 59.059 43.478 3.37 0.00 32.07 3.50
79 80 4.396166 GCTATCATGTTGCAGTACAGGTTT 59.604 41.667 3.37 0.00 32.07 3.27
80 81 4.771590 ATCATGTTGCAGTACAGGTTTG 57.228 40.909 3.37 0.00 32.07 2.93
81 82 3.814625 TCATGTTGCAGTACAGGTTTGA 58.185 40.909 3.37 0.00 32.07 2.69
82 83 3.814842 TCATGTTGCAGTACAGGTTTGAG 59.185 43.478 3.37 0.00 32.07 3.02
83 84 1.946768 TGTTGCAGTACAGGTTTGAGC 59.053 47.619 0.00 0.00 0.00 4.26
84 85 2.222027 GTTGCAGTACAGGTTTGAGCT 58.778 47.619 0.00 0.00 0.00 4.09
91 92 2.251600 CAGGTTTGAGCTGTCAGCC 58.748 57.895 21.32 13.02 43.77 4.85
92 93 0.535780 CAGGTTTGAGCTGTCAGCCA 60.536 55.000 21.32 15.41 43.77 4.75
93 94 0.183492 AGGTTTGAGCTGTCAGCCAA 59.817 50.000 21.32 19.90 43.77 4.52
94 95 0.595095 GGTTTGAGCTGTCAGCCAAG 59.405 55.000 21.32 0.00 43.77 3.61
95 96 1.597742 GTTTGAGCTGTCAGCCAAGA 58.402 50.000 21.32 11.98 43.77 3.02
96 97 1.949525 GTTTGAGCTGTCAGCCAAGAA 59.050 47.619 21.32 8.58 43.77 2.52
97 98 1.597742 TTGAGCTGTCAGCCAAGAAC 58.402 50.000 21.32 6.94 43.77 3.01
98 99 0.601046 TGAGCTGTCAGCCAAGAACG 60.601 55.000 21.32 0.00 43.77 3.95
99 100 1.294659 GAGCTGTCAGCCAAGAACGG 61.295 60.000 21.32 0.00 43.77 4.44
100 101 1.598130 GCTGTCAGCCAAGAACGGT 60.598 57.895 14.27 0.00 34.48 4.83
101 102 1.166531 GCTGTCAGCCAAGAACGGTT 61.167 55.000 14.27 0.00 34.48 4.44
102 103 0.588252 CTGTCAGCCAAGAACGGTTG 59.412 55.000 0.00 0.00 38.54 3.77
103 104 0.179234 TGTCAGCCAAGAACGGTTGA 59.821 50.000 0.00 0.00 43.21 3.18
104 105 1.202758 TGTCAGCCAAGAACGGTTGAT 60.203 47.619 0.00 0.00 46.36 2.57
105 106 1.464997 GTCAGCCAAGAACGGTTGATC 59.535 52.381 0.00 0.00 46.36 2.92
106 107 1.347707 TCAGCCAAGAACGGTTGATCT 59.652 47.619 0.00 0.00 40.89 2.75
107 108 2.154462 CAGCCAAGAACGGTTGATCTT 58.846 47.619 0.00 0.00 39.48 2.40
108 109 6.375151 GTCAGCCAAGAACGGTTGATCTTG 62.375 50.000 12.12 12.12 46.36 3.02
112 113 4.327854 CAAGAACGGTTGATCTTGTAGC 57.672 45.455 11.23 0.00 45.11 3.58
113 114 3.963428 AGAACGGTTGATCTTGTAGCT 57.037 42.857 0.00 0.00 0.00 3.32
114 115 5.168569 CAAGAACGGTTGATCTTGTAGCTA 58.831 41.667 11.23 0.00 45.11 3.32
115 116 5.599999 AGAACGGTTGATCTTGTAGCTAT 57.400 39.130 0.00 0.00 0.00 2.97
116 117 5.593010 AGAACGGTTGATCTTGTAGCTATC 58.407 41.667 0.00 0.00 0.00 2.08
117 118 4.323553 ACGGTTGATCTTGTAGCTATCC 57.676 45.455 0.00 0.00 0.00 2.59
118 119 3.961408 ACGGTTGATCTTGTAGCTATCCT 59.039 43.478 0.00 0.00 0.00 3.24
119 120 4.406003 ACGGTTGATCTTGTAGCTATCCTT 59.594 41.667 0.00 0.00 0.00 3.36
120 121 4.747108 CGGTTGATCTTGTAGCTATCCTTG 59.253 45.833 0.00 0.00 0.00 3.61
121 122 5.675538 GGTTGATCTTGTAGCTATCCTTGT 58.324 41.667 0.00 0.00 0.00 3.16
122 123 6.461092 CGGTTGATCTTGTAGCTATCCTTGTA 60.461 42.308 0.00 0.00 0.00 2.41
123 124 6.926272 GGTTGATCTTGTAGCTATCCTTGTAG 59.074 42.308 0.00 0.00 0.00 2.74
124 125 6.090483 TGATCTTGTAGCTATCCTTGTAGC 57.910 41.667 0.00 0.00 45.83 3.58
132 133 3.658709 GCTATCCTTGTAGCATGTCTCC 58.341 50.000 0.00 0.00 45.03 3.71
133 134 3.070159 GCTATCCTTGTAGCATGTCTCCA 59.930 47.826 0.00 0.00 45.03 3.86
134 135 4.262808 GCTATCCTTGTAGCATGTCTCCAT 60.263 45.833 0.00 0.00 45.03 3.41
135 136 5.047021 GCTATCCTTGTAGCATGTCTCCATA 60.047 44.000 0.00 0.00 45.03 2.74
136 137 4.672587 TCCTTGTAGCATGTCTCCATAC 57.327 45.455 0.00 0.00 0.00 2.39
137 138 3.068165 TCCTTGTAGCATGTCTCCATACG 59.932 47.826 0.00 0.00 0.00 3.06
138 139 3.384668 CTTGTAGCATGTCTCCATACGG 58.615 50.000 0.00 0.00 0.00 4.02
139 140 1.068588 TGTAGCATGTCTCCATACGGC 59.931 52.381 0.00 0.00 0.00 5.68
140 141 1.068588 GTAGCATGTCTCCATACGGCA 59.931 52.381 0.00 0.00 0.00 5.69
141 142 0.105593 AGCATGTCTCCATACGGCAG 59.894 55.000 0.00 0.00 0.00 4.85
142 143 1.502163 GCATGTCTCCATACGGCAGC 61.502 60.000 0.00 0.00 0.00 5.25
143 144 0.105593 CATGTCTCCATACGGCAGCT 59.894 55.000 0.00 0.00 0.00 4.24
144 145 0.105593 ATGTCTCCATACGGCAGCTG 59.894 55.000 10.11 10.11 0.00 4.24
145 146 1.884926 GTCTCCATACGGCAGCTGC 60.885 63.158 30.88 30.88 41.14 5.25
146 147 2.060383 TCTCCATACGGCAGCTGCT 61.060 57.895 35.82 21.35 41.70 4.24
153 154 2.357881 CGGCAGCTGCTGTCAAGA 60.358 61.111 34.82 0.00 42.29 3.02
154 155 1.744368 CGGCAGCTGCTGTCAAGAT 60.744 57.895 34.82 0.00 42.29 2.40
155 156 1.303799 CGGCAGCTGCTGTCAAGATT 61.304 55.000 34.82 0.00 42.29 2.40
156 157 1.742761 GGCAGCTGCTGTCAAGATTA 58.257 50.000 35.82 0.00 41.70 1.75
157 158 2.086869 GGCAGCTGCTGTCAAGATTAA 58.913 47.619 35.82 0.00 41.70 1.40
158 159 2.159462 GGCAGCTGCTGTCAAGATTAAC 60.159 50.000 35.82 12.52 41.70 2.01
159 160 2.475187 GCAGCTGCTGTCAAGATTAACG 60.475 50.000 31.33 1.07 38.21 3.18
160 161 2.094894 CAGCTGCTGTCAAGATTAACGG 59.905 50.000 21.21 0.00 0.00 4.44
161 162 2.028112 AGCTGCTGTCAAGATTAACGGA 60.028 45.455 0.00 0.00 0.00 4.69
162 163 2.349886 GCTGCTGTCAAGATTAACGGAG 59.650 50.000 0.00 0.00 0.00 4.63
163 164 3.849911 CTGCTGTCAAGATTAACGGAGA 58.150 45.455 0.00 0.00 0.00 3.71
164 165 3.585862 TGCTGTCAAGATTAACGGAGAC 58.414 45.455 0.00 0.00 0.00 3.36
178 179 0.924090 GGAGACGACGATGTTGATGC 59.076 55.000 0.00 0.00 0.00 3.91
179 180 0.924090 GAGACGACGATGTTGATGCC 59.076 55.000 0.00 0.00 0.00 4.40
180 181 0.802222 AGACGACGATGTTGATGCCG 60.802 55.000 0.00 0.00 0.00 5.69
181 182 1.076533 GACGACGATGTTGATGCCGT 61.077 55.000 0.00 0.00 38.01 5.68
182 183 1.076533 ACGACGATGTTGATGCCGTC 61.077 55.000 0.00 0.00 45.34 4.79
183 184 0.802222 CGACGATGTTGATGCCGTCT 60.802 55.000 0.00 0.00 46.24 4.18
184 185 0.647410 GACGATGTTGATGCCGTCTG 59.353 55.000 0.00 0.00 45.35 3.51
185 186 0.037326 ACGATGTTGATGCCGTCTGT 60.037 50.000 0.00 0.00 0.00 3.41
186 187 0.371301 CGATGTTGATGCCGTCTGTG 59.629 55.000 0.00 0.00 0.00 3.66
187 188 0.097674 GATGTTGATGCCGTCTGTGC 59.902 55.000 0.00 0.00 0.00 4.57
188 189 1.638388 ATGTTGATGCCGTCTGTGCG 61.638 55.000 0.00 0.00 0.00 5.34
189 190 2.030412 TTGATGCCGTCTGTGCGT 59.970 55.556 0.00 0.00 0.00 5.24
190 191 2.316867 TTGATGCCGTCTGTGCGTG 61.317 57.895 0.00 0.00 0.00 5.34
191 192 2.738521 GATGCCGTCTGTGCGTGT 60.739 61.111 0.00 0.00 0.00 4.49
192 193 3.015293 GATGCCGTCTGTGCGTGTG 62.015 63.158 0.00 0.00 0.00 3.82
195 196 2.587753 CCGTCTGTGCGTGTGGTT 60.588 61.111 0.00 0.00 0.00 3.67
196 197 2.625906 CGTCTGTGCGTGTGGTTG 59.374 61.111 0.00 0.00 0.00 3.77
197 198 1.880796 CGTCTGTGCGTGTGGTTGA 60.881 57.895 0.00 0.00 0.00 3.18
198 199 1.821241 CGTCTGTGCGTGTGGTTGAG 61.821 60.000 0.00 0.00 0.00 3.02
199 200 1.887242 TCTGTGCGTGTGGTTGAGC 60.887 57.895 0.00 0.00 0.00 4.26
200 201 2.896801 CTGTGCGTGTGGTTGAGCC 61.897 63.158 0.00 0.00 37.90 4.70
201 202 2.591715 GTGCGTGTGGTTGAGCCT 60.592 61.111 0.00 0.00 38.35 4.58
202 203 2.186826 GTGCGTGTGGTTGAGCCTT 61.187 57.895 0.00 0.00 38.35 4.35
203 204 1.453015 TGCGTGTGGTTGAGCCTTT 60.453 52.632 0.00 0.00 38.35 3.11
204 205 1.008538 GCGTGTGGTTGAGCCTTTG 60.009 57.895 0.00 0.00 38.35 2.77
205 206 1.008538 CGTGTGGTTGAGCCTTTGC 60.009 57.895 0.00 0.00 38.35 3.68
206 207 1.363807 GTGTGGTTGAGCCTTTGCC 59.636 57.895 0.00 0.00 38.69 4.52
207 208 1.109323 GTGTGGTTGAGCCTTTGCCT 61.109 55.000 0.00 0.00 38.69 4.75
208 209 0.823356 TGTGGTTGAGCCTTTGCCTC 60.823 55.000 0.00 0.00 38.69 4.70
209 210 1.600636 TGGTTGAGCCTTTGCCTCG 60.601 57.895 0.00 0.00 38.69 4.63
210 211 1.600916 GGTTGAGCCTTTGCCTCGT 60.601 57.895 0.00 0.00 38.69 4.18
211 212 1.172812 GGTTGAGCCTTTGCCTCGTT 61.173 55.000 0.00 0.00 38.69 3.85
212 213 0.238553 GTTGAGCCTTTGCCTCGTTC 59.761 55.000 0.00 0.00 38.69 3.95
213 214 0.889186 TTGAGCCTTTGCCTCGTTCC 60.889 55.000 0.00 0.00 38.69 3.62
214 215 1.003233 GAGCCTTTGCCTCGTTCCT 60.003 57.895 0.00 0.00 38.69 3.36
215 216 0.249398 GAGCCTTTGCCTCGTTCCTA 59.751 55.000 0.00 0.00 38.69 2.94
216 217 0.036294 AGCCTTTGCCTCGTTCCTAC 60.036 55.000 0.00 0.00 38.69 3.18
217 218 1.025113 GCCTTTGCCTCGTTCCTACC 61.025 60.000 0.00 0.00 0.00 3.18
218 219 0.323629 CCTTTGCCTCGTTCCTACCA 59.676 55.000 0.00 0.00 0.00 3.25
219 220 1.065418 CCTTTGCCTCGTTCCTACCAT 60.065 52.381 0.00 0.00 0.00 3.55
220 221 2.169769 CCTTTGCCTCGTTCCTACCATA 59.830 50.000 0.00 0.00 0.00 2.74
221 222 3.370103 CCTTTGCCTCGTTCCTACCATAA 60.370 47.826 0.00 0.00 0.00 1.90
222 223 4.451900 CTTTGCCTCGTTCCTACCATAAT 58.548 43.478 0.00 0.00 0.00 1.28
223 224 4.497291 TTGCCTCGTTCCTACCATAATT 57.503 40.909 0.00 0.00 0.00 1.40
224 225 4.497291 TGCCTCGTTCCTACCATAATTT 57.503 40.909 0.00 0.00 0.00 1.82
225 226 4.850680 TGCCTCGTTCCTACCATAATTTT 58.149 39.130 0.00 0.00 0.00 1.82
226 227 5.258051 TGCCTCGTTCCTACCATAATTTTT 58.742 37.500 0.00 0.00 0.00 1.94
227 228 5.355910 TGCCTCGTTCCTACCATAATTTTTC 59.644 40.000 0.00 0.00 0.00 2.29
228 229 5.589050 GCCTCGTTCCTACCATAATTTTTCT 59.411 40.000 0.00 0.00 0.00 2.52
229 230 6.458342 GCCTCGTTCCTACCATAATTTTTCTG 60.458 42.308 0.00 0.00 0.00 3.02
230 231 6.038271 CCTCGTTCCTACCATAATTTTTCTGG 59.962 42.308 0.00 0.00 36.09 3.86
231 232 5.355910 TCGTTCCTACCATAATTTTTCTGGC 59.644 40.000 0.00 0.00 33.12 4.85
232 233 5.449999 CGTTCCTACCATAATTTTTCTGGCC 60.450 44.000 0.00 0.00 33.12 5.36
233 234 4.204012 TCCTACCATAATTTTTCTGGCCG 58.796 43.478 0.00 0.00 33.12 6.13
234 235 2.959507 ACCATAATTTTTCTGGCCGC 57.040 45.000 0.00 0.00 33.12 6.53
235 236 2.456577 ACCATAATTTTTCTGGCCGCT 58.543 42.857 0.00 0.00 33.12 5.52
236 237 2.427095 ACCATAATTTTTCTGGCCGCTC 59.573 45.455 0.00 0.00 33.12 5.03
237 238 2.223805 CCATAATTTTTCTGGCCGCTCC 60.224 50.000 0.00 0.00 0.00 4.70
238 239 1.470051 TAATTTTTCTGGCCGCTCCC 58.530 50.000 0.00 0.00 0.00 4.30
239 240 0.251787 AATTTTTCTGGCCGCTCCCT 60.252 50.000 0.00 0.00 0.00 4.20
240 241 0.251787 ATTTTTCTGGCCGCTCCCTT 60.252 50.000 0.00 0.00 0.00 3.95
241 242 0.469144 TTTTTCTGGCCGCTCCCTTT 60.469 50.000 0.00 0.00 0.00 3.11
242 243 0.469144 TTTTCTGGCCGCTCCCTTTT 60.469 50.000 0.00 0.00 0.00 2.27
243 244 0.469144 TTTCTGGCCGCTCCCTTTTT 60.469 50.000 0.00 0.00 0.00 1.94
244 245 0.402504 TTCTGGCCGCTCCCTTTTTA 59.597 50.000 0.00 0.00 0.00 1.52
245 246 0.623723 TCTGGCCGCTCCCTTTTTAT 59.376 50.000 0.00 0.00 0.00 1.40
246 247 1.025041 CTGGCCGCTCCCTTTTTATC 58.975 55.000 0.00 0.00 0.00 1.75
247 248 0.623723 TGGCCGCTCCCTTTTTATCT 59.376 50.000 0.00 0.00 0.00 1.98
248 249 1.005450 TGGCCGCTCCCTTTTTATCTT 59.995 47.619 0.00 0.00 0.00 2.40
249 250 2.100197 GGCCGCTCCCTTTTTATCTTT 58.900 47.619 0.00 0.00 0.00 2.52
250 251 3.284617 GGCCGCTCCCTTTTTATCTTTA 58.715 45.455 0.00 0.00 0.00 1.85
251 252 3.697542 GGCCGCTCCCTTTTTATCTTTAA 59.302 43.478 0.00 0.00 0.00 1.52
252 253 4.341235 GGCCGCTCCCTTTTTATCTTTAAT 59.659 41.667 0.00 0.00 0.00 1.40
253 254 5.533528 GGCCGCTCCCTTTTTATCTTTAATA 59.466 40.000 0.00 0.00 0.00 0.98
254 255 6.040054 GGCCGCTCCCTTTTTATCTTTAATAA 59.960 38.462 0.00 0.00 0.00 1.40
255 256 6.916387 GCCGCTCCCTTTTTATCTTTAATAAC 59.084 38.462 0.00 0.00 0.00 1.89
256 257 7.201794 GCCGCTCCCTTTTTATCTTTAATAACT 60.202 37.037 0.00 0.00 0.00 2.24
257 258 8.129211 CCGCTCCCTTTTTATCTTTAATAACTG 58.871 37.037 0.00 0.00 0.00 3.16
258 259 8.889717 CGCTCCCTTTTTATCTTTAATAACTGA 58.110 33.333 0.00 0.00 0.00 3.41
261 262 9.169592 TCCCTTTTTATCTTTAATAACTGACCG 57.830 33.333 0.00 0.00 0.00 4.79
262 263 8.953313 CCCTTTTTATCTTTAATAACTGACCGT 58.047 33.333 0.00 0.00 0.00 4.83
263 264 9.983804 CCTTTTTATCTTTAATAACTGACCGTC 57.016 33.333 0.00 0.00 0.00 4.79
269 270 7.884816 TCTTTAATAACTGACCGTCTCTTTG 57.115 36.000 0.00 0.00 0.00 2.77
270 271 6.367969 TCTTTAATAACTGACCGTCTCTTTGC 59.632 38.462 0.00 0.00 0.00 3.68
271 272 2.060326 TAACTGACCGTCTCTTTGCG 57.940 50.000 0.00 0.00 0.00 4.85
276 277 3.578456 CCGTCTCTTTGCGGCAAT 58.422 55.556 17.19 0.00 41.53 3.56
277 278 1.135315 CCGTCTCTTTGCGGCAATG 59.865 57.895 17.19 18.38 41.53 2.82
278 279 1.512734 CGTCTCTTTGCGGCAATGC 60.513 57.895 17.19 0.00 0.00 3.56
279 280 1.580942 GTCTCTTTGCGGCAATGCA 59.419 52.632 17.19 6.16 44.61 3.96
280 281 0.171903 GTCTCTTTGCGGCAATGCAT 59.828 50.000 17.19 0.00 45.78 3.96
281 282 0.171679 TCTCTTTGCGGCAATGCATG 59.828 50.000 17.19 11.67 45.78 4.06
282 283 0.108992 CTCTTTGCGGCAATGCATGT 60.109 50.000 17.19 0.00 45.78 3.21
283 284 0.388778 TCTTTGCGGCAATGCATGTG 60.389 50.000 17.19 2.08 45.78 3.21
284 285 1.962092 CTTTGCGGCAATGCATGTGC 61.962 55.000 17.19 19.37 45.78 4.57
295 296 3.495124 GCATGTGCATGTTTTCCGT 57.505 47.368 12.96 0.00 40.80 4.69
296 297 2.627863 GCATGTGCATGTTTTCCGTA 57.372 45.000 12.96 0.00 40.80 4.02
297 298 2.940147 GCATGTGCATGTTTTCCGTAA 58.060 42.857 12.96 0.00 40.80 3.18
298 299 2.661195 GCATGTGCATGTTTTCCGTAAC 59.339 45.455 12.96 0.00 40.80 2.50
299 300 2.672188 TGTGCATGTTTTCCGTAACG 57.328 45.000 0.00 0.00 0.00 3.18
300 301 1.941294 TGTGCATGTTTTCCGTAACGT 59.059 42.857 0.00 0.00 0.00 3.99
301 302 2.032722 TGTGCATGTTTTCCGTAACGTC 60.033 45.455 0.00 0.00 0.00 4.34
302 303 2.222445 GTGCATGTTTTCCGTAACGTCT 59.778 45.455 0.00 0.00 0.00 4.18
303 304 2.477375 TGCATGTTTTCCGTAACGTCTC 59.523 45.455 0.00 0.00 0.00 3.36
304 305 2.477375 GCATGTTTTCCGTAACGTCTCA 59.523 45.455 0.00 0.00 0.00 3.27
305 306 3.423123 GCATGTTTTCCGTAACGTCTCAG 60.423 47.826 0.00 0.00 0.00 3.35
306 307 2.746269 TGTTTTCCGTAACGTCTCAGG 58.254 47.619 0.00 0.00 0.00 3.86
307 308 2.361757 TGTTTTCCGTAACGTCTCAGGA 59.638 45.455 0.00 0.00 0.00 3.86
308 309 3.006110 TGTTTTCCGTAACGTCTCAGGAT 59.994 43.478 0.00 0.00 0.00 3.24
309 310 4.218200 TGTTTTCCGTAACGTCTCAGGATA 59.782 41.667 0.00 0.00 0.00 2.59
310 311 5.105635 TGTTTTCCGTAACGTCTCAGGATAT 60.106 40.000 0.00 0.00 0.00 1.63
311 312 5.587388 TTTCCGTAACGTCTCAGGATATT 57.413 39.130 0.00 0.00 0.00 1.28
312 313 4.825546 TCCGTAACGTCTCAGGATATTC 57.174 45.455 0.00 0.00 0.00 1.75
313 314 3.567164 TCCGTAACGTCTCAGGATATTCC 59.433 47.826 0.00 0.00 36.58 3.01
315 316 4.037684 CCGTAACGTCTCAGGATATTCCTT 59.962 45.833 0.00 0.00 46.91 3.36
316 317 5.213675 CGTAACGTCTCAGGATATTCCTTC 58.786 45.833 0.00 0.00 46.91 3.46
317 318 5.220989 CGTAACGTCTCAGGATATTCCTTCA 60.221 44.000 0.00 0.00 46.91 3.02
318 319 5.878406 AACGTCTCAGGATATTCCTTCAT 57.122 39.130 0.00 0.00 46.91 2.57
319 320 5.461032 ACGTCTCAGGATATTCCTTCATC 57.539 43.478 0.00 0.00 46.91 2.92
320 321 4.895889 ACGTCTCAGGATATTCCTTCATCA 59.104 41.667 0.00 0.00 46.91 3.07
321 322 5.221342 ACGTCTCAGGATATTCCTTCATCAC 60.221 44.000 0.00 0.00 46.91 3.06
322 323 5.221322 CGTCTCAGGATATTCCTTCATCACA 60.221 44.000 0.00 0.00 46.91 3.58
323 324 6.222389 GTCTCAGGATATTCCTTCATCACAG 58.778 44.000 0.00 0.00 46.91 3.66
324 325 4.965814 TCAGGATATTCCTTCATCACAGC 58.034 43.478 0.00 0.00 46.91 4.40
325 326 4.409901 TCAGGATATTCCTTCATCACAGCA 59.590 41.667 0.00 0.00 46.91 4.41
326 327 5.104402 TCAGGATATTCCTTCATCACAGCAA 60.104 40.000 0.00 0.00 46.91 3.91
327 328 5.008415 CAGGATATTCCTTCATCACAGCAAC 59.992 44.000 0.00 0.00 46.91 4.17
328 329 4.024556 GGATATTCCTTCATCACAGCAACG 60.025 45.833 0.00 0.00 32.53 4.10
1026 1041 8.736097 TGGTAGCTTGGAGGATTAGAAATATA 57.264 34.615 0.00 0.00 0.00 0.86
1499 1520 4.785669 ATATATACCGTAGCGAGCGTAC 57.214 45.455 0.00 0.00 0.00 3.67
1700 1722 2.517959 CTTCCTTTGCATCCCACTCAA 58.482 47.619 0.00 0.00 0.00 3.02
1741 1764 2.352960 GGCAGAAATAGAACTCGCCAAG 59.647 50.000 0.00 0.00 37.98 3.61
1782 1805 5.106830 GGTATTAACTGAGACAAACAACGGG 60.107 44.000 0.00 0.00 0.00 5.28
1807 1831 5.364778 CAAACTGTTTTTAAAGGGAAGGGG 58.635 41.667 2.41 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.507329 TCTGCATATTAAGTCATAAAATCCCTC 57.493 33.333 0.00 0.00 0.00 4.30
1 2 9.866655 TTCTGCATATTAAGTCATAAAATCCCT 57.133 29.630 0.00 0.00 0.00 4.20
11 12 9.716531 CTCCATCTATTTCTGCATATTAAGTCA 57.283 33.333 0.00 0.00 0.00 3.41
12 13 9.935241 TCTCCATCTATTTCTGCATATTAAGTC 57.065 33.333 0.00 0.00 0.00 3.01
20 21 9.466497 TTTTTACTTCTCCATCTATTTCTGCAT 57.534 29.630 0.00 0.00 0.00 3.96
21 22 8.862325 TTTTTACTTCTCCATCTATTTCTGCA 57.138 30.769 0.00 0.00 0.00 4.41
47 48 7.161773 ACTGCAACATGATAGCTATGTTTTT 57.838 32.000 11.94 0.00 44.04 1.94
48 49 6.764308 ACTGCAACATGATAGCTATGTTTT 57.236 33.333 11.94 0.00 44.04 2.43
49 50 6.823182 TGTACTGCAACATGATAGCTATGTTT 59.177 34.615 11.94 0.00 44.04 2.83
50 51 6.348498 TGTACTGCAACATGATAGCTATGTT 58.652 36.000 11.94 9.29 46.54 2.71
51 52 5.917462 TGTACTGCAACATGATAGCTATGT 58.083 37.500 11.94 2.39 40.30 2.29
52 53 5.407691 CCTGTACTGCAACATGATAGCTATG 59.592 44.000 11.94 1.64 0.00 2.23
53 54 5.070981 ACCTGTACTGCAACATGATAGCTAT 59.929 40.000 5.76 5.76 0.00 2.97
54 55 4.405680 ACCTGTACTGCAACATGATAGCTA 59.594 41.667 0.00 0.00 0.00 3.32
55 56 3.198635 ACCTGTACTGCAACATGATAGCT 59.801 43.478 0.00 0.00 0.00 3.32
56 57 3.535561 ACCTGTACTGCAACATGATAGC 58.464 45.455 0.00 0.27 0.00 2.97
57 58 5.643348 TCAAACCTGTACTGCAACATGATAG 59.357 40.000 0.00 0.00 0.00 2.08
58 59 5.555966 TCAAACCTGTACTGCAACATGATA 58.444 37.500 0.00 0.00 0.00 2.15
59 60 4.397420 TCAAACCTGTACTGCAACATGAT 58.603 39.130 0.00 0.00 0.00 2.45
60 61 3.814625 TCAAACCTGTACTGCAACATGA 58.185 40.909 0.00 0.00 0.00 3.07
61 62 3.610114 GCTCAAACCTGTACTGCAACATG 60.610 47.826 0.00 0.00 0.00 3.21
62 63 2.554032 GCTCAAACCTGTACTGCAACAT 59.446 45.455 0.00 0.00 0.00 2.71
63 64 1.946768 GCTCAAACCTGTACTGCAACA 59.053 47.619 0.00 0.00 0.00 3.33
64 65 2.031682 CAGCTCAAACCTGTACTGCAAC 60.032 50.000 0.00 0.00 0.00 4.17
65 66 2.221169 CAGCTCAAACCTGTACTGCAA 58.779 47.619 0.00 0.00 0.00 4.08
66 67 1.140852 ACAGCTCAAACCTGTACTGCA 59.859 47.619 0.00 0.00 41.47 4.41
67 68 1.801178 GACAGCTCAAACCTGTACTGC 59.199 52.381 0.00 0.00 43.17 4.40
68 69 3.062763 CTGACAGCTCAAACCTGTACTG 58.937 50.000 0.00 0.00 43.17 2.74
69 70 2.548920 GCTGACAGCTCAAACCTGTACT 60.549 50.000 20.41 0.00 43.17 2.73
70 71 1.801178 GCTGACAGCTCAAACCTGTAC 59.199 52.381 20.41 0.00 43.17 2.90
71 72 1.270839 GGCTGACAGCTCAAACCTGTA 60.271 52.381 25.92 0.00 43.17 2.74
72 73 0.536006 GGCTGACAGCTCAAACCTGT 60.536 55.000 25.92 0.00 45.61 4.00
73 74 0.535780 TGGCTGACAGCTCAAACCTG 60.536 55.000 25.92 0.00 41.99 4.00
74 75 0.183492 TTGGCTGACAGCTCAAACCT 59.817 50.000 25.92 0.00 41.99 3.50
75 76 0.595095 CTTGGCTGACAGCTCAAACC 59.405 55.000 25.92 9.56 41.99 3.27
76 77 1.597742 TCTTGGCTGACAGCTCAAAC 58.402 50.000 25.92 10.28 41.99 2.93
77 78 1.949525 GTTCTTGGCTGACAGCTCAAA 59.050 47.619 25.92 16.49 41.99 2.69
78 79 1.597742 GTTCTTGGCTGACAGCTCAA 58.402 50.000 25.92 23.66 41.99 3.02
79 80 0.601046 CGTTCTTGGCTGACAGCTCA 60.601 55.000 25.92 18.79 41.99 4.26
80 81 1.294659 CCGTTCTTGGCTGACAGCTC 61.295 60.000 25.92 16.53 41.99 4.09
81 82 1.302033 CCGTTCTTGGCTGACAGCT 60.302 57.895 25.92 0.00 41.99 4.24
82 83 1.166531 AACCGTTCTTGGCTGACAGC 61.167 55.000 19.55 19.55 41.46 4.40
83 84 0.588252 CAACCGTTCTTGGCTGACAG 59.412 55.000 0.00 0.00 0.00 3.51
84 85 0.179234 TCAACCGTTCTTGGCTGACA 59.821 50.000 0.00 0.00 29.35 3.58
85 86 1.464997 GATCAACCGTTCTTGGCTGAC 59.535 52.381 0.00 0.00 36.96 3.51
86 87 1.347707 AGATCAACCGTTCTTGGCTGA 59.652 47.619 0.00 0.00 38.41 4.26
87 88 1.813513 AGATCAACCGTTCTTGGCTG 58.186 50.000 0.00 0.00 0.00 4.85
88 89 2.154462 CAAGATCAACCGTTCTTGGCT 58.846 47.619 0.00 0.00 41.94 4.75
89 90 1.880027 ACAAGATCAACCGTTCTTGGC 59.120 47.619 14.94 0.00 46.51 4.52
90 91 3.125316 GCTACAAGATCAACCGTTCTTGG 59.875 47.826 14.94 2.37 46.51 3.61
92 93 4.273148 AGCTACAAGATCAACCGTTCTT 57.727 40.909 0.00 0.00 32.48 2.52
93 94 3.963428 AGCTACAAGATCAACCGTTCT 57.037 42.857 0.00 0.00 0.00 3.01
94 95 4.745620 GGATAGCTACAAGATCAACCGTTC 59.254 45.833 0.00 0.00 0.00 3.95
95 96 4.406003 AGGATAGCTACAAGATCAACCGTT 59.594 41.667 0.00 0.00 0.00 4.44
96 97 3.961408 AGGATAGCTACAAGATCAACCGT 59.039 43.478 0.00 0.00 0.00 4.83
97 98 4.592485 AGGATAGCTACAAGATCAACCG 57.408 45.455 0.00 0.00 0.00 4.44
98 99 5.675538 ACAAGGATAGCTACAAGATCAACC 58.324 41.667 0.00 0.00 0.00 3.77
99 100 6.422400 GCTACAAGGATAGCTACAAGATCAAC 59.578 42.308 0.00 0.00 43.62 3.18
100 101 6.098266 TGCTACAAGGATAGCTACAAGATCAA 59.902 38.462 0.00 0.00 46.54 2.57
101 102 5.598417 TGCTACAAGGATAGCTACAAGATCA 59.402 40.000 0.00 0.00 46.54 2.92
102 103 6.090483 TGCTACAAGGATAGCTACAAGATC 57.910 41.667 0.00 0.00 46.54 2.75
103 104 6.042552 ACATGCTACAAGGATAGCTACAAGAT 59.957 38.462 0.00 0.00 46.54 2.40
104 105 5.363868 ACATGCTACAAGGATAGCTACAAGA 59.636 40.000 0.00 0.00 46.54 3.02
105 106 5.605534 ACATGCTACAAGGATAGCTACAAG 58.394 41.667 0.00 0.00 46.54 3.16
106 107 5.363868 AGACATGCTACAAGGATAGCTACAA 59.636 40.000 0.00 0.00 46.54 2.41
107 108 4.895889 AGACATGCTACAAGGATAGCTACA 59.104 41.667 0.00 0.00 46.54 2.74
108 109 5.461032 AGACATGCTACAAGGATAGCTAC 57.539 43.478 0.00 0.00 46.54 3.58
109 110 4.524714 GGAGACATGCTACAAGGATAGCTA 59.475 45.833 0.00 0.00 46.54 3.32
110 111 3.323403 GGAGACATGCTACAAGGATAGCT 59.677 47.826 6.37 0.00 46.54 3.32
111 112 3.070159 TGGAGACATGCTACAAGGATAGC 59.930 47.826 0.00 0.00 41.31 2.97
112 113 4.944619 TGGAGACATGCTACAAGGATAG 57.055 45.455 0.00 0.00 33.41 2.08
125 126 3.836871 GCAGCTGCCGTATGGAGACAT 62.837 57.143 28.76 0.00 44.58 3.06
126 127 2.578163 GCAGCTGCCGTATGGAGACA 62.578 60.000 28.76 0.00 39.26 3.41
127 128 1.884926 GCAGCTGCCGTATGGAGAC 60.885 63.158 28.76 0.00 37.49 3.36
128 129 2.060383 AGCAGCTGCCGTATGGAGA 61.060 57.895 34.39 0.00 43.38 3.71
129 130 1.886313 CAGCAGCTGCCGTATGGAG 60.886 63.158 34.39 10.84 43.38 3.86
130 131 2.187685 CAGCAGCTGCCGTATGGA 59.812 61.111 34.39 0.00 43.38 3.41
131 132 2.124983 ACAGCAGCTGCCGTATGG 60.125 61.111 34.39 18.69 43.38 2.74
132 133 1.020861 TTGACAGCAGCTGCCGTATG 61.021 55.000 34.39 26.78 43.38 2.39
133 134 0.742281 CTTGACAGCAGCTGCCGTAT 60.742 55.000 34.39 17.73 43.38 3.06
134 135 1.374631 CTTGACAGCAGCTGCCGTA 60.375 57.895 34.39 15.78 43.38 4.02
135 136 2.460662 ATCTTGACAGCAGCTGCCGT 62.461 55.000 34.39 30.79 43.38 5.68
136 137 1.303799 AATCTTGACAGCAGCTGCCG 61.304 55.000 34.39 27.45 43.38 5.69
137 138 1.742761 TAATCTTGACAGCAGCTGCC 58.257 50.000 34.39 20.05 43.38 4.85
138 139 2.475187 CGTTAATCTTGACAGCAGCTGC 60.475 50.000 31.53 31.53 42.49 5.25
139 140 2.094894 CCGTTAATCTTGACAGCAGCTG 59.905 50.000 21.54 21.54 37.52 4.24
140 141 2.028112 TCCGTTAATCTTGACAGCAGCT 60.028 45.455 0.00 0.00 0.00 4.24
141 142 2.346803 TCCGTTAATCTTGACAGCAGC 58.653 47.619 0.00 0.00 0.00 5.25
142 143 3.614616 GTCTCCGTTAATCTTGACAGCAG 59.385 47.826 0.00 0.00 0.00 4.24
143 144 3.585862 GTCTCCGTTAATCTTGACAGCA 58.414 45.455 0.00 0.00 0.00 4.41
144 145 2.599082 CGTCTCCGTTAATCTTGACAGC 59.401 50.000 0.00 0.00 0.00 4.40
145 146 3.852536 GTCGTCTCCGTTAATCTTGACAG 59.147 47.826 0.00 0.00 35.01 3.51
146 147 3.668757 CGTCGTCTCCGTTAATCTTGACA 60.669 47.826 0.00 0.00 35.01 3.58
147 148 2.844804 CGTCGTCTCCGTTAATCTTGAC 59.155 50.000 0.00 0.00 35.01 3.18
148 149 2.743664 TCGTCGTCTCCGTTAATCTTGA 59.256 45.455 0.00 0.00 35.01 3.02
149 150 3.127081 TCGTCGTCTCCGTTAATCTTG 57.873 47.619 0.00 0.00 35.01 3.02
150 151 3.128242 ACATCGTCGTCTCCGTTAATCTT 59.872 43.478 0.00 0.00 35.01 2.40
151 152 2.681848 ACATCGTCGTCTCCGTTAATCT 59.318 45.455 0.00 0.00 35.01 2.40
152 153 3.062323 ACATCGTCGTCTCCGTTAATC 57.938 47.619 0.00 0.00 35.01 1.75
153 154 3.119743 TCAACATCGTCGTCTCCGTTAAT 60.120 43.478 0.00 0.00 35.01 1.40
154 155 2.226200 TCAACATCGTCGTCTCCGTTAA 59.774 45.455 0.00 0.00 35.01 2.01
155 156 1.805943 TCAACATCGTCGTCTCCGTTA 59.194 47.619 0.00 0.00 35.01 3.18
156 157 0.594602 TCAACATCGTCGTCTCCGTT 59.405 50.000 0.00 0.00 35.01 4.44
157 158 0.809385 ATCAACATCGTCGTCTCCGT 59.191 50.000 0.00 0.00 35.01 4.69
158 159 1.191944 CATCAACATCGTCGTCTCCG 58.808 55.000 0.00 0.00 0.00 4.63
159 160 0.924090 GCATCAACATCGTCGTCTCC 59.076 55.000 0.00 0.00 0.00 3.71
160 161 0.924090 GGCATCAACATCGTCGTCTC 59.076 55.000 0.00 0.00 0.00 3.36
161 162 0.802222 CGGCATCAACATCGTCGTCT 60.802 55.000 0.00 0.00 0.00 4.18
162 163 1.076533 ACGGCATCAACATCGTCGTC 61.077 55.000 0.00 0.00 0.00 4.20
163 164 1.076533 GACGGCATCAACATCGTCGT 61.077 55.000 0.00 0.00 41.60 4.34
164 165 1.631072 GACGGCATCAACATCGTCG 59.369 57.895 0.00 0.00 41.60 5.12
166 167 0.037326 ACAGACGGCATCAACATCGT 60.037 50.000 0.00 0.00 38.62 3.73
167 168 0.371301 CACAGACGGCATCAACATCG 59.629 55.000 0.00 0.00 0.00 3.84
168 169 0.097674 GCACAGACGGCATCAACATC 59.902 55.000 0.00 0.00 0.00 3.06
169 170 1.638388 CGCACAGACGGCATCAACAT 61.638 55.000 0.00 0.00 0.00 2.71
170 171 2.316867 CGCACAGACGGCATCAACA 61.317 57.895 0.00 0.00 0.00 3.33
171 172 2.317609 ACGCACAGACGGCATCAAC 61.318 57.895 0.00 0.00 37.37 3.18
172 173 2.030412 ACGCACAGACGGCATCAA 59.970 55.556 0.00 0.00 37.37 2.57
173 174 2.738139 CACGCACAGACGGCATCA 60.738 61.111 0.00 0.00 37.37 3.07
174 175 2.738521 ACACGCACAGACGGCATC 60.739 61.111 0.00 0.00 37.37 3.91
175 176 3.043713 CACACGCACAGACGGCAT 61.044 61.111 0.00 0.00 37.37 4.40
178 179 2.587753 AACCACACGCACAGACGG 60.588 61.111 0.00 0.00 37.37 4.79
179 180 1.821241 CTCAACCACACGCACAGACG 61.821 60.000 0.00 0.00 39.50 4.18
180 181 1.934463 CTCAACCACACGCACAGAC 59.066 57.895 0.00 0.00 0.00 3.51
181 182 1.887242 GCTCAACCACACGCACAGA 60.887 57.895 0.00 0.00 0.00 3.41
182 183 2.633657 GCTCAACCACACGCACAG 59.366 61.111 0.00 0.00 0.00 3.66
183 184 2.884997 AAGGCTCAACCACACGCACA 62.885 55.000 0.00 0.00 43.14 4.57
184 185 1.724582 AAAGGCTCAACCACACGCAC 61.725 55.000 0.00 0.00 43.14 5.34
185 186 1.453015 AAAGGCTCAACCACACGCA 60.453 52.632 0.00 0.00 43.14 5.24
186 187 1.008538 CAAAGGCTCAACCACACGC 60.009 57.895 0.00 0.00 43.14 5.34
187 188 1.008538 GCAAAGGCTCAACCACACG 60.009 57.895 0.00 0.00 43.14 4.49
188 189 1.109323 AGGCAAAGGCTCAACCACAC 61.109 55.000 0.00 0.00 43.14 3.82
189 190 1.229927 AGGCAAAGGCTCAACCACA 59.770 52.632 0.00 0.00 43.14 4.17
190 191 4.181051 AGGCAAAGGCTCAACCAC 57.819 55.556 0.00 0.00 43.14 4.16
197 198 0.036294 GTAGGAACGAGGCAAAGGCT 60.036 55.000 0.00 0.00 42.48 4.58
198 199 1.025113 GGTAGGAACGAGGCAAAGGC 61.025 60.000 0.00 0.00 40.13 4.35
199 200 0.323629 TGGTAGGAACGAGGCAAAGG 59.676 55.000 0.00 0.00 0.00 3.11
200 201 2.403252 ATGGTAGGAACGAGGCAAAG 57.597 50.000 0.00 0.00 0.00 2.77
201 202 3.985019 TTATGGTAGGAACGAGGCAAA 57.015 42.857 0.00 0.00 0.00 3.68
202 203 4.497291 AATTATGGTAGGAACGAGGCAA 57.503 40.909 0.00 0.00 0.00 4.52
203 204 4.497291 AAATTATGGTAGGAACGAGGCA 57.503 40.909 0.00 0.00 0.00 4.75
204 205 5.589050 AGAAAAATTATGGTAGGAACGAGGC 59.411 40.000 0.00 0.00 0.00 4.70
205 206 6.038271 CCAGAAAAATTATGGTAGGAACGAGG 59.962 42.308 0.00 0.00 0.00 4.63
206 207 6.458342 GCCAGAAAAATTATGGTAGGAACGAG 60.458 42.308 5.73 0.00 36.43 4.18
207 208 5.355910 GCCAGAAAAATTATGGTAGGAACGA 59.644 40.000 5.73 0.00 36.43 3.85
208 209 5.449999 GGCCAGAAAAATTATGGTAGGAACG 60.450 44.000 0.00 0.00 36.43 3.95
209 210 5.449999 CGGCCAGAAAAATTATGGTAGGAAC 60.450 44.000 2.24 0.00 36.43 3.62
210 211 4.642885 CGGCCAGAAAAATTATGGTAGGAA 59.357 41.667 2.24 0.00 36.43 3.36
211 212 4.204012 CGGCCAGAAAAATTATGGTAGGA 58.796 43.478 2.24 0.00 36.43 2.94
212 213 3.243401 GCGGCCAGAAAAATTATGGTAGG 60.243 47.826 2.24 0.00 36.43 3.18
213 214 3.632145 AGCGGCCAGAAAAATTATGGTAG 59.368 43.478 2.24 2.07 36.43 3.18
214 215 3.626930 AGCGGCCAGAAAAATTATGGTA 58.373 40.909 2.24 0.00 36.43 3.25
215 216 2.427095 GAGCGGCCAGAAAAATTATGGT 59.573 45.455 2.24 0.00 36.43 3.55
216 217 2.223805 GGAGCGGCCAGAAAAATTATGG 60.224 50.000 2.24 0.00 36.34 2.74
217 218 2.223805 GGGAGCGGCCAGAAAAATTATG 60.224 50.000 2.24 0.00 38.95 1.90
218 219 2.031870 GGGAGCGGCCAGAAAAATTAT 58.968 47.619 2.24 0.00 38.95 1.28
219 220 1.005450 AGGGAGCGGCCAGAAAAATTA 59.995 47.619 2.24 0.00 38.95 1.40
220 221 0.251787 AGGGAGCGGCCAGAAAAATT 60.252 50.000 2.24 0.00 38.95 1.82
221 222 0.251787 AAGGGAGCGGCCAGAAAAAT 60.252 50.000 2.24 0.00 38.95 1.82
222 223 0.469144 AAAGGGAGCGGCCAGAAAAA 60.469 50.000 2.24 0.00 38.95 1.94
223 224 0.469144 AAAAGGGAGCGGCCAGAAAA 60.469 50.000 2.24 0.00 38.95 2.29
224 225 0.469144 AAAAAGGGAGCGGCCAGAAA 60.469 50.000 2.24 0.00 38.95 2.52
225 226 0.402504 TAAAAAGGGAGCGGCCAGAA 59.597 50.000 2.24 0.00 38.95 3.02
226 227 0.623723 ATAAAAAGGGAGCGGCCAGA 59.376 50.000 2.24 0.00 38.95 3.86
227 228 1.025041 GATAAAAAGGGAGCGGCCAG 58.975 55.000 2.24 0.00 38.95 4.85
228 229 0.623723 AGATAAAAAGGGAGCGGCCA 59.376 50.000 2.24 0.00 38.95 5.36
229 230 1.763968 AAGATAAAAAGGGAGCGGCC 58.236 50.000 0.00 0.00 0.00 6.13
230 231 4.976224 TTAAAGATAAAAAGGGAGCGGC 57.024 40.909 0.00 0.00 0.00 6.53
231 232 8.129211 CAGTTATTAAAGATAAAAAGGGAGCGG 58.871 37.037 0.00 0.00 0.00 5.52
232 233 8.889717 TCAGTTATTAAAGATAAAAAGGGAGCG 58.110 33.333 0.00 0.00 0.00 5.03
235 236 9.169592 CGGTCAGTTATTAAAGATAAAAAGGGA 57.830 33.333 0.00 0.00 0.00 4.20
236 237 8.953313 ACGGTCAGTTATTAAAGATAAAAAGGG 58.047 33.333 0.00 0.00 0.00 3.95
237 238 9.983804 GACGGTCAGTTATTAAAGATAAAAAGG 57.016 33.333 2.62 0.00 0.00 3.11
243 244 9.582431 CAAAGAGACGGTCAGTTATTAAAGATA 57.418 33.333 11.27 0.00 0.00 1.98
244 245 7.064728 GCAAAGAGACGGTCAGTTATTAAAGAT 59.935 37.037 11.27 0.00 0.00 2.40
245 246 6.367969 GCAAAGAGACGGTCAGTTATTAAAGA 59.632 38.462 11.27 0.00 0.00 2.52
246 247 6.534934 GCAAAGAGACGGTCAGTTATTAAAG 58.465 40.000 11.27 0.00 0.00 1.85
247 248 5.119588 CGCAAAGAGACGGTCAGTTATTAAA 59.880 40.000 11.27 0.00 0.00 1.52
248 249 4.624024 CGCAAAGAGACGGTCAGTTATTAA 59.376 41.667 11.27 0.00 0.00 1.40
249 250 4.171005 CGCAAAGAGACGGTCAGTTATTA 58.829 43.478 11.27 0.00 0.00 0.98
250 251 2.993899 CGCAAAGAGACGGTCAGTTATT 59.006 45.455 11.27 0.00 0.00 1.40
251 252 2.607187 CGCAAAGAGACGGTCAGTTAT 58.393 47.619 11.27 0.00 0.00 1.89
252 253 1.336517 CCGCAAAGAGACGGTCAGTTA 60.337 52.381 11.27 0.00 44.46 2.24
253 254 0.600255 CCGCAAAGAGACGGTCAGTT 60.600 55.000 11.27 0.00 44.46 3.16
254 255 1.006102 CCGCAAAGAGACGGTCAGT 60.006 57.895 11.27 0.00 44.46 3.41
255 256 3.862124 CCGCAAAGAGACGGTCAG 58.138 61.111 11.27 0.00 44.46 3.51
260 261 1.512734 GCATTGCCGCAAAGAGACG 60.513 57.895 10.42 0.00 0.00 4.18
261 262 0.171903 ATGCATTGCCGCAAAGAGAC 59.828 50.000 10.42 0.00 46.87 3.36
262 263 0.171679 CATGCATTGCCGCAAAGAGA 59.828 50.000 10.42 0.00 46.87 3.10
263 264 0.108992 ACATGCATTGCCGCAAAGAG 60.109 50.000 10.42 4.65 46.87 2.85
264 265 0.388778 CACATGCATTGCCGCAAAGA 60.389 50.000 10.42 0.00 46.87 2.52
265 266 1.962092 GCACATGCATTGCCGCAAAG 61.962 55.000 10.42 6.96 46.87 2.77
266 267 2.028179 GCACATGCATTGCCGCAAA 61.028 52.632 10.42 0.00 46.87 3.68
267 268 2.432800 GCACATGCATTGCCGCAA 60.433 55.556 17.74 8.55 46.87 4.85
277 278 2.627863 TACGGAAAACATGCACATGC 57.372 45.000 10.50 0.00 42.39 4.06
278 279 2.908009 CGTTACGGAAAACATGCACATG 59.092 45.455 9.06 9.06 44.15 3.21
279 280 2.550606 ACGTTACGGAAAACATGCACAT 59.449 40.909 10.20 0.00 0.00 3.21
280 281 1.941294 ACGTTACGGAAAACATGCACA 59.059 42.857 10.20 0.00 0.00 4.57
281 282 2.222445 AGACGTTACGGAAAACATGCAC 59.778 45.455 10.20 0.00 0.00 4.57
282 283 2.477375 GAGACGTTACGGAAAACATGCA 59.523 45.455 10.20 0.00 0.00 3.96
283 284 2.477375 TGAGACGTTACGGAAAACATGC 59.523 45.455 10.20 0.00 0.00 4.06
284 285 3.122948 CCTGAGACGTTACGGAAAACATG 59.877 47.826 10.20 0.00 0.00 3.21
285 286 3.006110 TCCTGAGACGTTACGGAAAACAT 59.994 43.478 10.20 0.00 0.00 2.71
286 287 2.361757 TCCTGAGACGTTACGGAAAACA 59.638 45.455 10.20 1.42 0.00 2.83
287 288 3.017265 TCCTGAGACGTTACGGAAAAC 57.983 47.619 10.20 0.00 0.00 2.43
288 289 3.947910 ATCCTGAGACGTTACGGAAAA 57.052 42.857 10.20 0.00 0.00 2.29
289 290 5.450965 GGAATATCCTGAGACGTTACGGAAA 60.451 44.000 10.20 0.00 32.53 3.13
290 291 4.037208 GGAATATCCTGAGACGTTACGGAA 59.963 45.833 10.20 0.00 32.53 4.30
291 292 3.567164 GGAATATCCTGAGACGTTACGGA 59.433 47.826 10.20 0.00 32.53 4.69
292 293 3.898529 GGAATATCCTGAGACGTTACGG 58.101 50.000 10.20 0.00 32.53 4.02
305 306 4.024556 CGTTGCTGTGATGAAGGAATATCC 60.025 45.833 0.00 0.00 36.58 2.59
306 307 4.572389 ACGTTGCTGTGATGAAGGAATATC 59.428 41.667 0.00 0.00 0.00 1.63
307 308 4.517285 ACGTTGCTGTGATGAAGGAATAT 58.483 39.130 0.00 0.00 0.00 1.28
308 309 3.937814 ACGTTGCTGTGATGAAGGAATA 58.062 40.909 0.00 0.00 0.00 1.75
309 310 2.783135 ACGTTGCTGTGATGAAGGAAT 58.217 42.857 0.00 0.00 0.00 3.01
310 311 2.254546 ACGTTGCTGTGATGAAGGAA 57.745 45.000 0.00 0.00 0.00 3.36
311 312 1.872952 CAACGTTGCTGTGATGAAGGA 59.127 47.619 16.51 0.00 0.00 3.36
312 313 1.603802 ACAACGTTGCTGTGATGAAGG 59.396 47.619 27.61 0.00 0.00 3.46
313 314 2.602933 CCACAACGTTGCTGTGATGAAG 60.603 50.000 27.61 3.24 45.80 3.02
314 315 1.333308 CCACAACGTTGCTGTGATGAA 59.667 47.619 27.61 0.00 45.80 2.57
315 316 0.943673 CCACAACGTTGCTGTGATGA 59.056 50.000 27.61 0.00 45.80 2.92
316 317 0.040157 CCCACAACGTTGCTGTGATG 60.040 55.000 27.61 16.50 45.80 3.07
317 318 1.795170 GCCCACAACGTTGCTGTGAT 61.795 55.000 27.61 4.49 45.80 3.06
318 319 2.477176 GCCCACAACGTTGCTGTGA 61.477 57.895 27.61 0.00 45.80 3.58
319 320 2.026014 GCCCACAACGTTGCTGTG 59.974 61.111 27.61 18.87 43.15 3.66
320 321 3.216292 GGCCCACAACGTTGCTGT 61.216 61.111 27.61 6.90 0.00 4.40
321 322 2.086251 AATGGCCCACAACGTTGCTG 62.086 55.000 27.61 22.03 0.00 4.41
322 323 1.398958 AAATGGCCCACAACGTTGCT 61.399 50.000 27.61 12.42 0.00 3.91
323 324 0.315568 TAAATGGCCCACAACGTTGC 59.684 50.000 27.61 13.81 0.00 4.17
324 325 2.605030 CATAAATGGCCCACAACGTTG 58.395 47.619 26.20 26.20 0.00 4.10
325 326 1.548269 CCATAAATGGCCCACAACGTT 59.452 47.619 0.00 0.00 41.75 3.99
326 327 1.181786 CCATAAATGGCCCACAACGT 58.818 50.000 0.00 0.00 41.75 3.99
570 577 4.168101 TCCCTCTCTCTCCTTTTGCTTAA 58.832 43.478 0.00 0.00 0.00 1.85
807 820 2.772077 TTTCACAAGCGGGTATAGCA 57.228 45.000 4.02 0.00 37.01 3.49
1026 1041 6.840780 ACAGCTAATTGGAAAGCAATAGTT 57.159 33.333 1.03 0.00 41.32 2.24
1430 1451 2.291670 ACCTTCTATGTCTGGGTCGACT 60.292 50.000 16.46 0.00 35.00 4.18
1499 1520 7.068593 TGGCAAGGAGATATTTTACCATTGAAG 59.931 37.037 0.00 0.00 0.00 3.02
1782 1805 4.814234 CCTTCCCTTTAAAAACAGTTTGCC 59.186 41.667 0.00 0.00 0.00 4.52
1807 1831 1.477295 CGAAAGGGACAGTCTACCTCC 59.523 57.143 0.00 0.00 32.29 4.30


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

AutoCloner maintained by Alex Coulton.