Multiple sequence alignment - TraesCS5A01G094800

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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 TraesCS5A01G094800 chr5A 100.000 1423 0 0 890 2312 131803325 131801903 0.000000e+00 2628.0
1 TraesCS5A01G094800 chr5A 93.939 561 30 4 1753 2312 580214191 580214748 0.000000e+00 845.0
2 TraesCS5A01G094800 chr5A 100.000 425 0 0 1 425 131804214 131803790 0.000000e+00 785.0
3 TraesCS5A01G094800 chr5D 96.520 862 30 0 892 1753 120897369 120896508 0.000000e+00 1426.0
4 TraesCS5A01G094800 chr5D 97.222 72 2 0 335 406 120897745 120897674 3.120000e-24 122.0
5 TraesCS5A01G094800 chr5B 97.119 833 19 2 892 1723 134050654 134049826 0.000000e+00 1400.0
6 TraesCS5A01G094800 chr5B 98.611 72 1 0 335 406 134050903 134050832 6.700000e-26 128.0
7 TraesCS5A01G094800 chr7D 95.626 503 14 3 1811 2312 582056490 582055995 0.000000e+00 800.0
8 TraesCS5A01G094800 chr6D 85.113 309 35 9 2 304 93442168 93441865 2.890000e-79 305.0
9 TraesCS5A01G094800 chr6D 81.457 302 46 8 1 298 5904465 5904760 2.970000e-59 239.0
10 TraesCS5A01G094800 chr7A 83.553 304 39 8 1 298 112438839 112438541 8.140000e-70 274.0
11 TraesCS5A01G094800 chr4A 79.934 304 48 8 1 300 646583060 646582766 6.470000e-51 211.0
12 TraesCS5A01G094800 chr4A 91.743 109 8 1 1759 1866 514346249 514346141 1.430000e-32 150.0
13 TraesCS5A01G094800 chr6B 84.409 186 24 5 116 300 26786044 26786225 6.560000e-41 178.0
14 TraesCS5A01G094800 chr2B 100.000 43 0 0 1576 1618 133948215 133948257 1.900000e-11 80.5


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 TraesCS5A01G094800 chr5A 131801903 131804214 2311 True 1706.5 2628 100.000 1 2312 2 chr5A.!!$R1 2311
1 TraesCS5A01G094800 chr5A 580214191 580214748 557 False 845.0 845 93.939 1753 2312 1 chr5A.!!$F1 559
2 TraesCS5A01G094800 chr5D 120896508 120897745 1237 True 774.0 1426 96.871 335 1753 2 chr5D.!!$R1 1418
3 TraesCS5A01G094800 chr5B 134049826 134050903 1077 True 764.0 1400 97.865 335 1723 2 chr5B.!!$R1 1388

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
160 161 0.027586 GACCGCGCGCTTCATAATTT 59.972 50.0 30.48 1.61 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 1898 0.163146 GTGTTTTCTACCGAGCGCAC 59.837 55.0 11.47 0.96 0.0 5.34 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 4.735132 AAACTGCTCCGCGCGCTA 62.735 61.111 30.48 16.24 43.27 4.26
19 20 4.735132 AACTGCTCCGCGCGCTAA 62.735 61.111 30.48 15.83 43.27 3.09
20 21 4.735132 ACTGCTCCGCGCGCTAAA 62.735 61.111 30.48 13.09 43.27 1.85
21 22 3.487202 CTGCTCCGCGCGCTAAAA 61.487 61.111 30.48 10.40 43.27 1.52
22 23 3.022401 CTGCTCCGCGCGCTAAAAA 62.022 57.895 30.48 10.95 43.27 1.94
23 24 2.573428 GCTCCGCGCGCTAAAAAC 60.573 61.111 30.48 9.74 0.00 2.43
24 25 3.023591 GCTCCGCGCGCTAAAAACT 62.024 57.895 30.48 0.00 0.00 2.66
25 26 1.225745 CTCCGCGCGCTAAAAACTG 60.226 57.895 30.48 10.63 0.00 3.16
26 27 1.897398 CTCCGCGCGCTAAAAACTGT 61.897 55.000 30.48 0.00 0.00 3.55
27 28 1.082366 CCGCGCGCTAAAAACTGTT 60.082 52.632 30.48 0.00 0.00 3.16
28 29 0.659123 CCGCGCGCTAAAAACTGTTT 60.659 50.000 30.48 0.00 0.00 2.83
29 30 1.117234 CGCGCGCTAAAAACTGTTTT 58.883 45.000 30.48 12.50 40.15 2.43
30 31 1.515221 CGCGCGCTAAAAACTGTTTTT 59.485 42.857 30.48 28.02 44.43 1.94
49 50 4.815040 TTTTATTTTTGACGCGGAGACA 57.185 36.364 12.47 1.90 0.00 3.41
50 51 3.799137 TTATTTTTGACGCGGAGACAC 57.201 42.857 12.47 0.00 0.00 3.67
51 52 1.878953 ATTTTTGACGCGGAGACACT 58.121 45.000 12.47 0.00 0.00 3.55
52 53 1.658994 TTTTTGACGCGGAGACACTT 58.341 45.000 12.47 0.00 0.00 3.16
53 54 1.658994 TTTTGACGCGGAGACACTTT 58.341 45.000 12.47 0.00 0.00 2.66
54 55 2.512485 TTTGACGCGGAGACACTTTA 57.488 45.000 12.47 0.00 0.00 1.85
55 56 2.060326 TTGACGCGGAGACACTTTAG 57.940 50.000 12.47 0.00 0.00 1.85
56 57 0.388134 TGACGCGGAGACACTTTAGC 60.388 55.000 12.47 0.00 0.00 3.09
57 58 0.388134 GACGCGGAGACACTTTAGCA 60.388 55.000 12.47 0.00 0.00 3.49
58 59 0.388649 ACGCGGAGACACTTTAGCAG 60.389 55.000 12.47 0.00 0.00 4.24
59 60 0.109272 CGCGGAGACACTTTAGCAGA 60.109 55.000 0.00 0.00 0.00 4.26
60 61 1.469940 CGCGGAGACACTTTAGCAGAT 60.470 52.381 0.00 0.00 0.00 2.90
61 62 1.929836 GCGGAGACACTTTAGCAGATG 59.070 52.381 0.00 0.00 0.00 2.90
62 63 1.929836 CGGAGACACTTTAGCAGATGC 59.070 52.381 0.00 0.00 42.49 3.91
63 64 2.284190 GGAGACACTTTAGCAGATGCC 58.716 52.381 0.14 0.00 43.38 4.40
64 65 2.355108 GGAGACACTTTAGCAGATGCCA 60.355 50.000 0.14 0.00 43.38 4.92
65 66 2.675348 GAGACACTTTAGCAGATGCCAC 59.325 50.000 0.14 0.00 43.38 5.01
66 67 2.038952 AGACACTTTAGCAGATGCCACA 59.961 45.455 0.14 0.00 43.38 4.17
67 68 2.813754 GACACTTTAGCAGATGCCACAA 59.186 45.455 0.14 0.00 43.38 3.33
68 69 3.221771 ACACTTTAGCAGATGCCACAAA 58.778 40.909 0.14 0.00 43.38 2.83
69 70 3.636300 ACACTTTAGCAGATGCCACAAAA 59.364 39.130 0.14 0.00 43.38 2.44
70 71 4.281688 ACACTTTAGCAGATGCCACAAAAT 59.718 37.500 0.14 0.00 43.38 1.82
71 72 5.476599 ACACTTTAGCAGATGCCACAAAATA 59.523 36.000 0.14 0.00 43.38 1.40
72 73 6.015519 ACACTTTAGCAGATGCCACAAAATAA 60.016 34.615 0.14 0.00 43.38 1.40
73 74 7.037438 CACTTTAGCAGATGCCACAAAATAAT 58.963 34.615 0.14 0.00 43.38 1.28
74 75 7.009815 CACTTTAGCAGATGCCACAAAATAATG 59.990 37.037 0.14 0.00 43.38 1.90
75 76 3.788937 AGCAGATGCCACAAAATAATGC 58.211 40.909 0.14 0.00 43.38 3.56
76 77 3.196039 AGCAGATGCCACAAAATAATGCA 59.804 39.130 0.14 0.00 43.38 3.96
77 78 3.307782 GCAGATGCCACAAAATAATGCAC 59.692 43.478 0.00 0.00 34.33 4.57
78 79 4.496360 CAGATGCCACAAAATAATGCACA 58.504 39.130 0.00 0.00 34.33 4.57
79 80 5.113383 CAGATGCCACAAAATAATGCACAT 58.887 37.500 0.00 0.00 34.33 3.21
80 81 5.006261 CAGATGCCACAAAATAATGCACATG 59.994 40.000 0.00 0.00 34.33 3.21
81 82 3.001414 TGCCACAAAATAATGCACATGC 58.999 40.909 0.00 0.00 42.50 4.06
100 101 2.331451 AAAAACTGCTCCGCACGC 59.669 55.556 0.00 0.00 33.79 5.34
101 102 3.521308 AAAAACTGCTCCGCACGCG 62.521 57.895 3.53 3.53 33.79 6.01
107 108 3.784412 GCTCCGCACGCGCTAAAA 61.784 61.111 5.73 0.00 38.24 1.52
108 109 2.395690 CTCCGCACGCGCTAAAAG 59.604 61.111 5.73 0.00 38.24 2.27
109 110 3.083600 CTCCGCACGCGCTAAAAGG 62.084 63.158 5.73 1.13 38.24 3.11
110 111 4.811761 CCGCACGCGCTAAAAGGC 62.812 66.667 5.73 0.00 38.24 4.35
127 128 3.553765 CGCTATCGCACGCTGCAA 61.554 61.111 0.00 0.00 45.36 4.08
128 129 2.784596 GCTATCGCACGCTGCAAA 59.215 55.556 0.00 0.00 45.36 3.68
129 130 1.353103 GCTATCGCACGCTGCAAAT 59.647 52.632 0.00 5.76 45.36 2.32
130 131 0.927083 GCTATCGCACGCTGCAAATG 60.927 55.000 0.00 0.00 45.36 2.32
131 132 0.374758 CTATCGCACGCTGCAAATGT 59.625 50.000 0.00 0.00 45.36 2.71
132 133 0.801872 TATCGCACGCTGCAAATGTT 59.198 45.000 0.00 0.00 45.36 2.71
133 134 0.730155 ATCGCACGCTGCAAATGTTG 60.730 50.000 0.00 0.00 45.36 3.33
134 135 2.366584 CGCACGCTGCAAATGTTGG 61.367 57.895 0.00 0.00 45.36 3.77
135 136 1.007502 GCACGCTGCAAATGTTGGA 60.008 52.632 0.00 0.00 44.26 3.53
136 137 1.277495 GCACGCTGCAAATGTTGGAC 61.277 55.000 0.00 0.00 44.26 4.02
137 138 0.998226 CACGCTGCAAATGTTGGACG 60.998 55.000 0.00 0.00 34.05 4.79
138 139 2.082366 CGCTGCAAATGTTGGACGC 61.082 57.895 0.00 0.00 0.00 5.19
139 140 1.734117 GCTGCAAATGTTGGACGCC 60.734 57.895 0.00 0.00 0.00 5.68
140 141 1.442520 CTGCAAATGTTGGACGCCG 60.443 57.895 0.00 0.00 0.00 6.46
141 142 2.126502 GCAAATGTTGGACGCCGG 60.127 61.111 0.00 0.00 0.00 6.13
142 143 2.622011 GCAAATGTTGGACGCCGGA 61.622 57.895 5.05 0.00 0.00 5.14
143 144 1.209127 CAAATGTTGGACGCCGGAC 59.791 57.895 5.05 0.00 0.00 4.79
144 145 1.969589 AAATGTTGGACGCCGGACC 60.970 57.895 5.05 5.62 0.00 4.46
145 146 4.752879 ATGTTGGACGCCGGACCG 62.753 66.667 5.05 6.99 0.00 4.79
157 158 2.888534 GGACCGCGCGCTTCATAA 60.889 61.111 30.48 0.00 0.00 1.90
158 159 2.244651 GGACCGCGCGCTTCATAAT 61.245 57.895 30.48 5.88 0.00 1.28
159 160 1.641677 GACCGCGCGCTTCATAATT 59.358 52.632 30.48 3.33 0.00 1.40
160 161 0.027586 GACCGCGCGCTTCATAATTT 59.972 50.000 30.48 1.61 0.00 1.82
161 162 0.248054 ACCGCGCGCTTCATAATTTG 60.248 50.000 30.48 8.64 0.00 2.32
162 163 1.531522 CCGCGCGCTTCATAATTTGC 61.532 55.000 30.48 0.00 0.00 3.68
163 164 0.861034 CGCGCGCTTCATAATTTGCA 60.861 50.000 30.48 0.00 0.00 4.08
164 165 0.567509 GCGCGCTTCATAATTTGCAC 59.432 50.000 26.67 0.00 0.00 4.57
165 166 1.795162 GCGCGCTTCATAATTTGCACT 60.795 47.619 26.67 0.00 0.00 4.40
166 167 1.841944 CGCGCTTCATAATTTGCACTG 59.158 47.619 5.56 0.00 0.00 3.66
167 168 2.728846 CGCGCTTCATAATTTGCACTGT 60.729 45.455 5.56 0.00 0.00 3.55
168 169 2.595536 GCGCTTCATAATTTGCACTGTG 59.404 45.455 0.00 2.76 0.00 3.66
169 170 3.825308 CGCTTCATAATTTGCACTGTGT 58.175 40.909 9.86 0.00 0.00 3.72
170 171 3.605056 CGCTTCATAATTTGCACTGTGTG 59.395 43.478 9.86 0.00 36.51 3.82
171 172 4.549458 GCTTCATAATTTGCACTGTGTGT 58.451 39.130 9.86 0.00 35.75 3.72
172 173 4.984161 GCTTCATAATTTGCACTGTGTGTT 59.016 37.500 9.86 2.61 35.75 3.32
173 174 5.463061 GCTTCATAATTTGCACTGTGTGTTT 59.537 36.000 9.86 1.82 35.75 2.83
174 175 6.018832 GCTTCATAATTTGCACTGTGTGTTTT 60.019 34.615 9.86 2.16 35.75 2.43
175 176 7.465781 GCTTCATAATTTGCACTGTGTGTTTTT 60.466 33.333 9.86 0.84 35.75 1.94
190 191 2.202756 TTTTTGGGCGCGCGTTTT 60.203 50.000 32.35 0.00 0.00 2.43
191 192 1.810030 TTTTTGGGCGCGCGTTTTT 60.810 47.368 32.35 0.00 0.00 1.94
214 215 9.894783 TTTTTGGCATATGAAAAATCAATGTTG 57.105 25.926 6.97 0.00 0.00 3.33
215 216 8.618702 TTTGGCATATGAAAAATCAATGTTGT 57.381 26.923 6.97 0.00 0.00 3.32
216 217 7.830940 TGGCATATGAAAAATCAATGTTGTC 57.169 32.000 6.97 0.00 0.00 3.18
217 218 6.817641 TGGCATATGAAAAATCAATGTTGTCC 59.182 34.615 6.97 0.00 0.00 4.02
218 219 6.817641 GGCATATGAAAAATCAATGTTGTCCA 59.182 34.615 6.97 0.00 0.00 4.02
219 220 7.201548 GGCATATGAAAAATCAATGTTGTCCAC 60.202 37.037 6.97 0.00 0.00 4.02
220 221 7.463119 GCATATGAAAAATCAATGTTGTCCACG 60.463 37.037 6.97 0.00 0.00 4.94
221 222 5.506686 TGAAAAATCAATGTTGTCCACGA 57.493 34.783 0.00 0.00 0.00 4.35
222 223 5.277825 TGAAAAATCAATGTTGTCCACGAC 58.722 37.500 0.00 0.00 0.00 4.34
223 224 3.536158 AAATCAATGTTGTCCACGACG 57.464 42.857 0.00 0.00 34.95 5.12
224 225 0.796312 ATCAATGTTGTCCACGACGC 59.204 50.000 0.00 0.00 34.95 5.19
225 226 1.154672 CAATGTTGTCCACGACGCG 60.155 57.895 3.53 3.53 34.95 6.01
226 227 2.950172 AATGTTGTCCACGACGCGC 61.950 57.895 5.73 0.00 34.95 6.86
227 228 3.858868 ATGTTGTCCACGACGCGCT 62.859 57.895 5.73 0.00 34.95 5.92
228 229 2.429571 GTTGTCCACGACGCGCTA 60.430 61.111 5.73 0.00 34.95 4.26
229 230 2.017783 GTTGTCCACGACGCGCTAA 61.018 57.895 5.73 0.00 34.95 3.09
230 231 1.300003 TTGTCCACGACGCGCTAAA 60.300 52.632 5.73 0.00 34.95 1.85
231 232 0.875040 TTGTCCACGACGCGCTAAAA 60.875 50.000 5.73 0.00 34.95 1.52
232 233 1.279527 TGTCCACGACGCGCTAAAAG 61.280 55.000 5.73 0.00 34.95 2.27
233 234 1.007038 TCCACGACGCGCTAAAAGT 60.007 52.632 5.73 0.00 0.00 2.66
234 235 1.129809 CCACGACGCGCTAAAAGTG 59.870 57.895 5.73 7.60 0.00 3.16
244 245 3.658351 CGCTAAAAGTGCTATGGTGAC 57.342 47.619 0.00 0.00 0.00 3.67
245 246 2.029244 CGCTAAAAGTGCTATGGTGACG 59.971 50.000 0.00 0.00 0.00 4.35
246 247 2.223044 GCTAAAAGTGCTATGGTGACGC 60.223 50.000 0.00 0.00 0.00 5.19
247 248 2.185004 AAAAGTGCTATGGTGACGCT 57.815 45.000 0.00 0.00 0.00 5.07
248 249 1.442769 AAAGTGCTATGGTGACGCTG 58.557 50.000 0.00 0.00 0.00 5.18
249 250 0.321671 AAGTGCTATGGTGACGCTGT 59.678 50.000 0.00 0.00 0.00 4.40
250 251 1.182667 AGTGCTATGGTGACGCTGTA 58.817 50.000 0.00 0.00 0.00 2.74
251 252 1.548719 AGTGCTATGGTGACGCTGTAA 59.451 47.619 0.00 0.00 0.00 2.41
252 253 2.028476 AGTGCTATGGTGACGCTGTAAA 60.028 45.455 0.00 0.00 0.00 2.01
253 254 2.739913 GTGCTATGGTGACGCTGTAAAA 59.260 45.455 0.00 0.00 0.00 1.52
254 255 3.374058 GTGCTATGGTGACGCTGTAAAAT 59.626 43.478 0.00 0.00 0.00 1.82
255 256 4.569162 GTGCTATGGTGACGCTGTAAAATA 59.431 41.667 0.00 0.00 0.00 1.40
256 257 5.236478 GTGCTATGGTGACGCTGTAAAATAT 59.764 40.000 0.00 0.00 0.00 1.28
257 258 5.820423 TGCTATGGTGACGCTGTAAAATATT 59.180 36.000 0.00 0.00 0.00 1.28
258 259 6.317642 TGCTATGGTGACGCTGTAAAATATTT 59.682 34.615 0.00 0.00 0.00 1.40
259 260 7.148154 TGCTATGGTGACGCTGTAAAATATTTT 60.148 33.333 17.18 17.18 0.00 1.82
260 261 8.339714 GCTATGGTGACGCTGTAAAATATTTTA 58.660 33.333 15.19 15.19 0.00 1.52
261 262 9.864034 CTATGGTGACGCTGTAAAATATTTTAG 57.136 33.333 18.76 12.27 33.66 1.85
262 263 6.548171 TGGTGACGCTGTAAAATATTTTAGC 58.452 36.000 18.76 19.08 33.66 3.09
267 268 4.603146 CGCTGTAAAATATTTTAGCGCTCG 59.397 41.667 30.24 20.13 43.63 5.03
268 269 5.555631 CGCTGTAAAATATTTTAGCGCTCGA 60.556 40.000 30.24 0.00 43.63 4.04
269 270 6.363473 GCTGTAAAATATTTTAGCGCTCGAT 58.637 36.000 16.34 9.37 33.66 3.59
270 271 7.507304 GCTGTAAAATATTTTAGCGCTCGATA 58.493 34.615 16.34 11.48 33.66 2.92
271 272 8.169268 GCTGTAAAATATTTTAGCGCTCGATAT 58.831 33.333 16.34 13.35 33.66 1.63
277 278 7.781763 ATATTTTAGCGCTCGATATTTTTGC 57.218 32.000 16.34 0.00 0.00 3.68
279 280 1.006832 AGCGCTCGATATTTTTGCGT 58.993 45.000 2.64 0.00 46.94 5.24
280 281 1.004927 AGCGCTCGATATTTTTGCGTC 60.005 47.619 2.64 6.95 46.94 5.19
281 282 1.004927 GCGCTCGATATTTTTGCGTCT 60.005 47.619 13.37 0.00 46.94 4.18
282 283 2.217847 GCGCTCGATATTTTTGCGTCTA 59.782 45.455 13.37 0.00 46.94 2.59
283 284 3.120991 GCGCTCGATATTTTTGCGTCTAT 60.121 43.478 13.37 0.00 46.94 1.98
284 285 4.377758 CGCTCGATATTTTTGCGTCTATG 58.622 43.478 4.96 0.00 41.45 2.23
285 286 4.085055 CGCTCGATATTTTTGCGTCTATGT 60.085 41.667 4.96 0.00 41.45 2.29
286 287 5.556382 CGCTCGATATTTTTGCGTCTATGTT 60.556 40.000 4.96 0.00 41.45 2.71
287 288 5.617187 GCTCGATATTTTTGCGTCTATGTTG 59.383 40.000 0.00 0.00 0.00 3.33
288 289 6.043327 TCGATATTTTTGCGTCTATGTTGG 57.957 37.500 0.00 0.00 0.00 3.77
289 290 5.813157 TCGATATTTTTGCGTCTATGTTGGA 59.187 36.000 0.00 0.00 0.00 3.53
290 291 6.019075 TCGATATTTTTGCGTCTATGTTGGAG 60.019 38.462 0.00 0.00 0.00 3.86
291 292 6.019075 CGATATTTTTGCGTCTATGTTGGAGA 60.019 38.462 0.00 0.00 0.00 3.71
292 293 7.307396 CGATATTTTTGCGTCTATGTTGGAGAT 60.307 37.037 0.00 0.00 0.00 2.75
293 294 4.944962 TTTTGCGTCTATGTTGGAGATG 57.055 40.909 0.00 0.00 33.76 2.90
297 298 3.724508 CGTCTATGTTGGAGATGCTCT 57.275 47.619 0.00 0.00 0.00 4.09
298 299 4.837896 CGTCTATGTTGGAGATGCTCTA 57.162 45.455 0.00 0.00 0.00 2.43
299 300 5.188327 CGTCTATGTTGGAGATGCTCTAA 57.812 43.478 0.00 0.00 0.00 2.10
300 301 5.592054 CGTCTATGTTGGAGATGCTCTAAA 58.408 41.667 0.00 0.00 33.06 1.85
301 302 5.689514 CGTCTATGTTGGAGATGCTCTAAAG 59.310 44.000 0.00 0.00 33.06 1.85
302 303 6.460261 CGTCTATGTTGGAGATGCTCTAAAGA 60.460 42.308 0.00 0.00 33.06 2.52
303 304 6.922957 GTCTATGTTGGAGATGCTCTAAAGAG 59.077 42.308 2.47 2.47 44.75 2.85
304 305 5.946942 ATGTTGGAGATGCTCTAAAGAGA 57.053 39.130 11.20 0.00 44.74 3.10
319 320 8.125728 CTCTAAAGAGAGCAATGCTACTTTAC 57.874 38.462 26.94 10.74 42.86 2.01
320 321 7.841956 TCTAAAGAGAGCAATGCTACTTTACT 58.158 34.615 26.94 14.44 41.51 2.24
321 322 8.314751 TCTAAAGAGAGCAATGCTACTTTACTT 58.685 33.333 26.94 16.41 41.51 2.24
322 323 6.976636 AAGAGAGCAATGCTACTTTACTTC 57.023 37.500 8.12 0.00 39.88 3.01
323 324 5.105752 AGAGAGCAATGCTACTTTACTTCG 58.894 41.667 8.12 0.00 39.88 3.79
324 325 5.073311 AGAGCAATGCTACTTTACTTCGA 57.927 39.130 8.12 0.00 39.88 3.71
325 326 5.479306 AGAGCAATGCTACTTTACTTCGAA 58.521 37.500 8.12 0.00 39.88 3.71
326 327 5.348997 AGAGCAATGCTACTTTACTTCGAAC 59.651 40.000 8.12 0.00 39.88 3.95
327 328 5.238583 AGCAATGCTACTTTACTTCGAACT 58.761 37.500 5.69 0.00 36.99 3.01
328 329 6.395629 AGCAATGCTACTTTACTTCGAACTA 58.604 36.000 5.69 0.00 36.99 2.24
329 330 6.310711 AGCAATGCTACTTTACTTCGAACTAC 59.689 38.462 5.69 0.00 36.99 2.73
330 331 6.455246 GCAATGCTACTTTACTTCGAACTACC 60.455 42.308 0.00 0.00 0.00 3.18
331 332 5.064441 TGCTACTTTACTTCGAACTACCC 57.936 43.478 0.00 0.00 0.00 3.69
332 333 4.768968 TGCTACTTTACTTCGAACTACCCT 59.231 41.667 0.00 0.00 0.00 4.34
333 334 5.100943 GCTACTTTACTTCGAACTACCCTG 58.899 45.833 0.00 0.00 0.00 4.45
419 448 6.098124 TCACATCAAAAACTGACCCTCAATTT 59.902 34.615 0.00 0.00 36.69 1.82
420 449 6.762661 CACATCAAAAACTGACCCTCAATTTT 59.237 34.615 0.00 0.00 37.39 1.82
421 450 6.762661 ACATCAAAAACTGACCCTCAATTTTG 59.237 34.615 12.44 12.44 35.13 2.44
422 451 5.115480 TCAAAAACTGACCCTCAATTTTGC 58.885 37.500 13.21 0.00 35.13 3.68
423 452 4.751767 AAAACTGACCCTCAATTTTGCA 57.248 36.364 0.00 0.00 34.94 4.08
424 453 3.733443 AACTGACCCTCAATTTTGCAC 57.267 42.857 0.00 0.00 0.00 4.57
952 981 4.712337 AGCATACTAGCTAACACCAAGTCT 59.288 41.667 0.00 0.00 44.50 3.24
962 991 6.608002 AGCTAACACCAAGTCTATTACTAGCT 59.392 38.462 0.00 0.00 37.50 3.32
1007 1036 4.899239 CCTGCCGGCGATGGAGAC 62.899 72.222 23.90 0.00 0.00 3.36
1323 1352 2.047844 CTCTGACCACGGGTGCAG 60.048 66.667 0.00 7.84 35.25 4.41
1385 1414 1.889105 CAAGCATGTATCCGCCGCT 60.889 57.895 0.00 0.00 33.45 5.52
1549 1579 4.868171 TGGAATAACGCATACAAGTGTCTC 59.132 41.667 0.00 0.00 0.00 3.36
1673 1703 2.615240 CCATGTTCCATTCCACGAGTGA 60.615 50.000 4.59 0.00 0.00 3.41
1699 1729 4.270008 GCAAAGATGGCCTTTTAGGAGTA 58.730 43.478 3.32 0.00 42.13 2.59
1703 1733 7.231519 GCAAAGATGGCCTTTTAGGAGTATAAT 59.768 37.037 3.32 0.00 42.13 1.28
1734 1764 5.881443 TGAAGGTAGAAACACGGAAAAGAAA 59.119 36.000 0.00 0.00 0.00 2.52
1750 1780 3.685139 AGAAATGCCTTTGACGAGAGA 57.315 42.857 0.00 0.00 0.00 3.10
1753 1783 4.220821 AGAAATGCCTTTGACGAGAGAGTA 59.779 41.667 0.00 0.00 0.00 2.59
1754 1784 4.744795 AATGCCTTTGACGAGAGAGTAT 57.255 40.909 0.00 0.00 0.00 2.12
1755 1785 5.854010 AATGCCTTTGACGAGAGAGTATA 57.146 39.130 0.00 0.00 0.00 1.47
1756 1786 5.854010 ATGCCTTTGACGAGAGAGTATAA 57.146 39.130 0.00 0.00 0.00 0.98
1757 1787 4.995124 TGCCTTTGACGAGAGAGTATAAC 58.005 43.478 0.00 0.00 0.00 1.89
1794 1824 4.038763 TCCATATCCGCGACAAGTAATTCT 59.961 41.667 8.23 0.00 0.00 2.40
1803 1833 4.034510 GCGACAAGTAATTCTGAATGGAGG 59.965 45.833 3.22 0.00 0.00 4.30
1804 1834 5.419542 CGACAAGTAATTCTGAATGGAGGA 58.580 41.667 3.22 0.00 0.00 3.71
1809 1839 8.552296 ACAAGTAATTCTGAATGGAGGAAGTAT 58.448 33.333 3.22 0.00 0.00 2.12
1851 1881 1.578915 GATAACAAAATGTGCGCTGCG 59.421 47.619 19.17 19.17 0.00 5.18
1854 1884 0.521291 ACAAAATGTGCGCTGCGTAT 59.479 45.000 24.04 12.67 0.00 3.06
1857 1887 0.744414 AAATGTGCGCTGCGTATCCT 60.744 50.000 24.04 5.13 0.00 3.24
1858 1888 0.104120 AATGTGCGCTGCGTATCCTA 59.896 50.000 24.04 7.75 0.00 2.94
1922 1952 1.227823 CAGGTGGCGTGGAAGTTGA 60.228 57.895 0.00 0.00 0.00 3.18
1948 1978 4.412207 GTTGCACGGGAGATTAAACATTC 58.588 43.478 0.00 0.00 0.00 2.67
1984 2014 8.886719 TCTCTTGATTAATACTGTTCATTGCAG 58.113 33.333 0.00 0.00 39.67 4.41
2055 2085 0.658368 TGCGTGCGTGTGTTTGTATT 59.342 45.000 0.00 0.00 0.00 1.89
2056 2086 1.865340 TGCGTGCGTGTGTTTGTATTA 59.135 42.857 0.00 0.00 0.00 0.98
2057 2087 2.096664 TGCGTGCGTGTGTTTGTATTAG 60.097 45.455 0.00 0.00 0.00 1.73
2059 2089 2.732500 CGTGCGTGTGTTTGTATTAGGA 59.267 45.455 0.00 0.00 0.00 2.94
2060 2090 3.422603 CGTGCGTGTGTTTGTATTAGGAC 60.423 47.826 0.00 0.00 0.00 3.85
2062 2092 4.024725 GTGCGTGTGTTTGTATTAGGACAA 60.025 41.667 0.00 0.00 37.54 3.18
2063 2093 4.575236 TGCGTGTGTTTGTATTAGGACAAA 59.425 37.500 0.00 0.00 44.89 2.83
2073 2103 8.736751 TTTGTATTAGGACAAAAGAAATTCGC 57.263 30.769 0.00 0.00 44.30 4.70
2074 2104 7.681939 TGTATTAGGACAAAAGAAATTCGCT 57.318 32.000 0.00 0.00 0.00 4.93
2168 2198 0.250513 ATCCTCACTCGCCCAAGAAC 59.749 55.000 0.00 0.00 0.00 3.01
2174 2204 2.093658 TCACTCGCCCAAGAACTTATCC 60.094 50.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.225745 CAGTTTTTAGCGCGCGGAG 60.226 57.895 33.06 3.70 0.00 4.63
8 9 1.500512 AACAGTTTTTAGCGCGCGGA 61.501 50.000 33.06 15.73 0.00 5.54
9 10 0.659123 AAACAGTTTTTAGCGCGCGG 60.659 50.000 33.06 13.78 0.00 6.46
10 11 1.117234 AAAACAGTTTTTAGCGCGCG 58.883 45.000 28.44 28.44 32.90 6.86
27 28 4.971220 GTGTCTCCGCGTCAAAAATAAAAA 59.029 37.500 4.92 0.00 0.00 1.94
28 29 4.273969 AGTGTCTCCGCGTCAAAAATAAAA 59.726 37.500 4.92 0.00 0.00 1.52
29 30 3.810941 AGTGTCTCCGCGTCAAAAATAAA 59.189 39.130 4.92 0.00 0.00 1.40
30 31 3.395639 AGTGTCTCCGCGTCAAAAATAA 58.604 40.909 4.92 0.00 0.00 1.40
31 32 3.034721 AGTGTCTCCGCGTCAAAAATA 57.965 42.857 4.92 0.00 0.00 1.40
32 33 1.878953 AGTGTCTCCGCGTCAAAAAT 58.121 45.000 4.92 0.00 0.00 1.82
33 34 1.658994 AAGTGTCTCCGCGTCAAAAA 58.341 45.000 4.92 0.00 0.00 1.94
34 35 1.658994 AAAGTGTCTCCGCGTCAAAA 58.341 45.000 4.92 0.00 0.00 2.44
35 36 2.400399 CTAAAGTGTCTCCGCGTCAAA 58.600 47.619 4.92 0.00 0.00 2.69
36 37 1.933500 GCTAAAGTGTCTCCGCGTCAA 60.934 52.381 4.92 0.00 0.00 3.18
37 38 0.388134 GCTAAAGTGTCTCCGCGTCA 60.388 55.000 4.92 0.00 0.00 4.35
38 39 0.388134 TGCTAAAGTGTCTCCGCGTC 60.388 55.000 4.92 0.00 0.00 5.19
39 40 0.388649 CTGCTAAAGTGTCTCCGCGT 60.389 55.000 4.92 0.00 0.00 6.01
40 41 0.109272 TCTGCTAAAGTGTCTCCGCG 60.109 55.000 0.00 0.00 0.00 6.46
41 42 1.929836 CATCTGCTAAAGTGTCTCCGC 59.070 52.381 0.00 0.00 0.00 5.54
42 43 1.929836 GCATCTGCTAAAGTGTCTCCG 59.070 52.381 0.00 0.00 38.21 4.63
43 44 2.284190 GGCATCTGCTAAAGTGTCTCC 58.716 52.381 1.70 0.00 41.70 3.71
44 45 2.675348 GTGGCATCTGCTAAAGTGTCTC 59.325 50.000 1.70 0.00 41.70 3.36
45 46 2.038952 TGTGGCATCTGCTAAAGTGTCT 59.961 45.455 1.70 0.00 41.70 3.41
46 47 2.426522 TGTGGCATCTGCTAAAGTGTC 58.573 47.619 1.70 0.00 41.70 3.67
47 48 2.566833 TGTGGCATCTGCTAAAGTGT 57.433 45.000 1.70 0.00 41.70 3.55
48 49 3.921119 TTTGTGGCATCTGCTAAAGTG 57.079 42.857 1.70 0.00 41.70 3.16
49 50 6.588719 TTATTTTGTGGCATCTGCTAAAGT 57.411 33.333 1.70 2.38 41.70 2.66
50 51 6.019318 GCATTATTTTGTGGCATCTGCTAAAG 60.019 38.462 1.70 0.00 41.70 1.85
51 52 5.811613 GCATTATTTTGTGGCATCTGCTAAA 59.188 36.000 1.70 0.00 41.70 1.85
52 53 5.105432 TGCATTATTTTGTGGCATCTGCTAA 60.105 36.000 1.70 0.00 41.70 3.09
53 54 4.401837 TGCATTATTTTGTGGCATCTGCTA 59.598 37.500 1.70 0.00 41.70 3.49
54 55 3.196039 TGCATTATTTTGTGGCATCTGCT 59.804 39.130 1.70 0.00 41.70 4.24
55 56 3.307782 GTGCATTATTTTGTGGCATCTGC 59.692 43.478 0.00 0.00 36.79 4.26
56 57 4.496360 TGTGCATTATTTTGTGGCATCTG 58.504 39.130 0.00 0.00 36.79 2.90
57 58 4.804868 TGTGCATTATTTTGTGGCATCT 57.195 36.364 0.00 0.00 36.79 2.90
58 59 4.260456 GCATGTGCATTATTTTGTGGCATC 60.260 41.667 0.00 0.00 41.59 3.91
59 60 3.623960 GCATGTGCATTATTTTGTGGCAT 59.376 39.130 0.00 0.00 41.59 4.40
60 61 3.001414 GCATGTGCATTATTTTGTGGCA 58.999 40.909 0.00 0.00 41.59 4.92
61 62 3.661758 GCATGTGCATTATTTTGTGGC 57.338 42.857 0.00 0.00 41.59 5.01
117 118 1.007502 TCCAACATTTGCAGCGTGC 60.008 52.632 3.44 3.44 45.29 5.34
118 119 0.998226 CGTCCAACATTTGCAGCGTG 60.998 55.000 0.00 0.00 0.00 5.34
119 120 1.282570 CGTCCAACATTTGCAGCGT 59.717 52.632 0.00 0.00 0.00 5.07
120 121 2.082366 GCGTCCAACATTTGCAGCG 61.082 57.895 0.00 0.00 0.00 5.18
121 122 1.734117 GGCGTCCAACATTTGCAGC 60.734 57.895 0.00 0.00 0.00 5.25
122 123 1.442520 CGGCGTCCAACATTTGCAG 60.443 57.895 0.00 0.00 0.00 4.41
123 124 2.642129 CGGCGTCCAACATTTGCA 59.358 55.556 0.00 0.00 0.00 4.08
124 125 2.126502 CCGGCGTCCAACATTTGC 60.127 61.111 6.01 0.00 0.00 3.68
125 126 1.209127 GTCCGGCGTCCAACATTTG 59.791 57.895 6.01 0.00 0.00 2.32
126 127 1.969589 GGTCCGGCGTCCAACATTT 60.970 57.895 6.01 0.00 0.00 2.32
127 128 2.359478 GGTCCGGCGTCCAACATT 60.359 61.111 6.01 0.00 0.00 2.71
128 129 4.752879 CGGTCCGGCGTCCAACAT 62.753 66.667 6.01 0.00 0.00 2.71
140 141 1.772063 AATTATGAAGCGCGCGGTCC 61.772 55.000 36.00 25.38 0.00 4.46
141 142 0.027586 AAATTATGAAGCGCGCGGTC 59.972 50.000 36.00 26.30 0.00 4.79
142 143 0.248054 CAAATTATGAAGCGCGCGGT 60.248 50.000 30.98 30.98 0.00 5.68
143 144 1.531522 GCAAATTATGAAGCGCGCGG 61.532 55.000 33.06 13.66 0.00 6.46
144 145 0.861034 TGCAAATTATGAAGCGCGCG 60.861 50.000 28.44 28.44 0.00 6.86
145 146 0.567509 GTGCAAATTATGAAGCGCGC 59.432 50.000 26.66 26.66 0.00 6.86
146 147 1.841944 CAGTGCAAATTATGAAGCGCG 59.158 47.619 0.00 0.00 41.96 6.86
147 148 2.595536 CACAGTGCAAATTATGAAGCGC 59.404 45.455 0.00 0.00 37.74 5.92
148 149 3.605056 CACACAGTGCAAATTATGAAGCG 59.395 43.478 0.00 0.00 0.00 4.68
149 150 4.549458 ACACACAGTGCAAATTATGAAGC 58.451 39.130 0.00 0.00 36.98 3.86
150 151 7.467557 AAAACACACAGTGCAAATTATGAAG 57.532 32.000 0.00 0.00 36.98 3.02
151 152 7.840342 AAAAACACACAGTGCAAATTATGAA 57.160 28.000 0.00 0.00 36.98 2.57
173 174 1.810030 AAAAACGCGCGCCCAAAAA 60.810 47.368 32.58 0.00 0.00 1.94
174 175 2.202756 AAAAACGCGCGCCCAAAA 60.203 50.000 32.58 0.00 0.00 2.44
188 189 9.894783 CAACATTGATTTTTCATATGCCAAAAA 57.105 25.926 14.11 14.11 36.25 1.94
189 190 9.064706 ACAACATTGATTTTTCATATGCCAAAA 57.935 25.926 12.42 12.42 0.00 2.44
190 191 8.618702 ACAACATTGATTTTTCATATGCCAAA 57.381 26.923 0.00 0.00 0.00 3.28
191 192 7.333921 GGACAACATTGATTTTTCATATGCCAA 59.666 33.333 0.00 0.00 0.00 4.52
192 193 6.817641 GGACAACATTGATTTTTCATATGCCA 59.182 34.615 0.00 0.00 0.00 4.92
193 194 6.817641 TGGACAACATTGATTTTTCATATGCC 59.182 34.615 0.00 0.00 0.00 4.40
194 195 7.463119 CGTGGACAACATTGATTTTTCATATGC 60.463 37.037 0.00 0.00 0.00 3.14
195 196 7.754475 TCGTGGACAACATTGATTTTTCATATG 59.246 33.333 0.00 0.00 0.00 1.78
196 197 7.754924 GTCGTGGACAACATTGATTTTTCATAT 59.245 33.333 0.00 0.00 32.09 1.78
197 198 7.081349 GTCGTGGACAACATTGATTTTTCATA 58.919 34.615 0.00 0.00 32.09 2.15
198 199 5.920273 GTCGTGGACAACATTGATTTTTCAT 59.080 36.000 0.00 0.00 32.09 2.57
199 200 5.277825 GTCGTGGACAACATTGATTTTTCA 58.722 37.500 0.00 0.00 32.09 2.69
200 201 4.378616 CGTCGTGGACAACATTGATTTTTC 59.621 41.667 0.00 0.00 32.09 2.29
201 202 4.286910 CGTCGTGGACAACATTGATTTTT 58.713 39.130 0.00 0.00 32.09 1.94
202 203 3.851838 GCGTCGTGGACAACATTGATTTT 60.852 43.478 0.00 0.00 32.09 1.82
203 204 2.350388 GCGTCGTGGACAACATTGATTT 60.350 45.455 0.00 0.00 32.09 2.17
204 205 1.196808 GCGTCGTGGACAACATTGATT 59.803 47.619 0.00 0.00 32.09 2.57
205 206 0.796312 GCGTCGTGGACAACATTGAT 59.204 50.000 0.00 0.00 32.09 2.57
206 207 1.553195 CGCGTCGTGGACAACATTGA 61.553 55.000 0.00 0.00 32.09 2.57
207 208 1.154672 CGCGTCGTGGACAACATTG 60.155 57.895 0.00 0.00 32.09 2.82
208 209 2.950172 GCGCGTCGTGGACAACATT 61.950 57.895 8.43 0.00 32.09 2.71
209 210 2.480853 TAGCGCGTCGTGGACAACAT 62.481 55.000 8.43 0.00 32.09 2.71
210 211 2.680693 TTAGCGCGTCGTGGACAACA 62.681 55.000 8.43 0.00 32.09 3.33
211 212 1.550659 TTTAGCGCGTCGTGGACAAC 61.551 55.000 8.43 0.00 32.09 3.32
212 213 0.875040 TTTTAGCGCGTCGTGGACAA 60.875 50.000 8.43 0.00 32.09 3.18
213 214 1.279527 CTTTTAGCGCGTCGTGGACA 61.280 55.000 8.43 0.00 32.09 4.02
214 215 1.280206 ACTTTTAGCGCGTCGTGGAC 61.280 55.000 8.43 0.00 0.00 4.02
215 216 1.007038 ACTTTTAGCGCGTCGTGGA 60.007 52.632 8.43 0.00 0.00 4.02
216 217 1.129809 CACTTTTAGCGCGTCGTGG 59.870 57.895 8.43 0.00 0.00 4.94
217 218 1.507096 GCACTTTTAGCGCGTCGTG 60.507 57.895 8.43 7.83 0.00 4.35
218 219 0.387622 TAGCACTTTTAGCGCGTCGT 60.388 50.000 8.43 0.00 37.01 4.34
219 220 0.921347 ATAGCACTTTTAGCGCGTCG 59.079 50.000 8.43 0.00 37.01 5.12
220 221 1.004927 CCATAGCACTTTTAGCGCGTC 60.005 52.381 8.43 0.00 37.01 5.19
221 222 1.006832 CCATAGCACTTTTAGCGCGT 58.993 50.000 8.43 0.00 37.01 6.01
222 223 1.006832 ACCATAGCACTTTTAGCGCG 58.993 50.000 0.00 0.00 37.01 6.86
223 224 2.006888 TCACCATAGCACTTTTAGCGC 58.993 47.619 0.00 0.00 37.01 5.92
224 225 2.029244 CGTCACCATAGCACTTTTAGCG 59.971 50.000 0.00 0.00 37.01 4.26
225 226 2.223044 GCGTCACCATAGCACTTTTAGC 60.223 50.000 0.00 0.00 0.00 3.09
226 227 3.062639 CAGCGTCACCATAGCACTTTTAG 59.937 47.826 0.00 0.00 0.00 1.85
227 228 3.000041 CAGCGTCACCATAGCACTTTTA 59.000 45.455 0.00 0.00 0.00 1.52
228 229 1.806542 CAGCGTCACCATAGCACTTTT 59.193 47.619 0.00 0.00 0.00 2.27
229 230 1.270839 ACAGCGTCACCATAGCACTTT 60.271 47.619 0.00 0.00 0.00 2.66
230 231 0.321671 ACAGCGTCACCATAGCACTT 59.678 50.000 0.00 0.00 0.00 3.16
231 232 1.182667 TACAGCGTCACCATAGCACT 58.817 50.000 0.00 0.00 0.00 4.40
232 233 2.004583 TTACAGCGTCACCATAGCAC 57.995 50.000 0.00 0.00 0.00 4.40
233 234 2.753055 TTTACAGCGTCACCATAGCA 57.247 45.000 0.00 0.00 0.00 3.49
234 235 5.924475 ATATTTTACAGCGTCACCATAGC 57.076 39.130 0.00 0.00 0.00 2.97
235 236 9.864034 CTAAAATATTTTACAGCGTCACCATAG 57.136 33.333 15.19 0.96 0.00 2.23
236 237 8.339714 GCTAAAATATTTTACAGCGTCACCATA 58.660 33.333 15.19 0.00 0.00 2.74
237 238 7.193595 GCTAAAATATTTTACAGCGTCACCAT 58.806 34.615 15.19 0.00 0.00 3.55
238 239 6.548171 GCTAAAATATTTTACAGCGTCACCA 58.452 36.000 15.19 0.00 0.00 4.17
239 240 5.675444 CGCTAAAATATTTTACAGCGTCACC 59.325 40.000 31.49 9.94 44.16 4.02
240 241 6.697193 CGCTAAAATATTTTACAGCGTCAC 57.303 37.500 31.49 10.43 44.16 3.67
245 246 5.734311 TCGAGCGCTAAAATATTTTACAGC 58.266 37.500 22.68 22.68 33.66 4.40
251 252 8.690840 GCAAAAATATCGAGCGCTAAAATATTT 58.309 29.630 24.36 24.36 35.23 1.40
252 253 7.059488 CGCAAAAATATCGAGCGCTAAAATATT 59.941 33.333 11.50 16.44 41.95 1.28
253 254 6.519761 CGCAAAAATATCGAGCGCTAAAATAT 59.480 34.615 11.50 11.21 41.95 1.28
254 255 5.843878 CGCAAAAATATCGAGCGCTAAAATA 59.156 36.000 11.50 9.17 41.95 1.40
255 256 4.670621 CGCAAAAATATCGAGCGCTAAAAT 59.329 37.500 11.50 6.91 41.95 1.82
256 257 4.025750 CGCAAAAATATCGAGCGCTAAAA 58.974 39.130 11.50 0.00 41.95 1.52
257 258 3.603379 CGCAAAAATATCGAGCGCTAAA 58.397 40.909 11.50 0.47 41.95 1.85
258 259 3.233164 CGCAAAAATATCGAGCGCTAA 57.767 42.857 11.50 0.95 41.95 3.09
259 260 2.922504 CGCAAAAATATCGAGCGCTA 57.077 45.000 11.50 0.00 41.95 4.26
260 261 3.806257 CGCAAAAATATCGAGCGCT 57.194 47.368 11.27 11.27 41.95 5.92
263 264 5.330271 ACATAGACGCAAAAATATCGAGC 57.670 39.130 0.00 0.00 0.00 5.03
264 265 6.019075 TCCAACATAGACGCAAAAATATCGAG 60.019 38.462 0.00 0.00 0.00 4.04
265 266 5.813157 TCCAACATAGACGCAAAAATATCGA 59.187 36.000 0.00 0.00 0.00 3.59
266 267 6.019075 TCTCCAACATAGACGCAAAAATATCG 60.019 38.462 0.00 0.00 0.00 2.92
267 268 7.246674 TCTCCAACATAGACGCAAAAATATC 57.753 36.000 0.00 0.00 0.00 1.63
268 269 7.642669 CATCTCCAACATAGACGCAAAAATAT 58.357 34.615 0.00 0.00 0.00 1.28
269 270 6.458206 GCATCTCCAACATAGACGCAAAAATA 60.458 38.462 0.00 0.00 32.62 1.40
270 271 5.677091 GCATCTCCAACATAGACGCAAAAAT 60.677 40.000 0.00 0.00 32.62 1.82
271 272 4.379394 GCATCTCCAACATAGACGCAAAAA 60.379 41.667 0.00 0.00 32.62 1.94
272 273 3.126858 GCATCTCCAACATAGACGCAAAA 59.873 43.478 0.00 0.00 32.62 2.44
273 274 2.677836 GCATCTCCAACATAGACGCAAA 59.322 45.455 0.00 0.00 32.62 3.68
274 275 2.093500 AGCATCTCCAACATAGACGCAA 60.093 45.455 0.00 0.00 34.72 4.85
275 276 1.482182 AGCATCTCCAACATAGACGCA 59.518 47.619 0.00 0.00 34.72 5.24
276 277 2.131183 GAGCATCTCCAACATAGACGC 58.869 52.381 0.00 0.00 32.51 5.19
295 296 7.841956 AGTAAAGTAGCATTGCTCTCTTTAGA 58.158 34.615 28.84 18.73 41.11 2.10
296 297 8.485976 AAGTAAAGTAGCATTGCTCTCTTTAG 57.514 34.615 28.84 0.00 41.11 1.85
297 298 7.275779 CGAAGTAAAGTAGCATTGCTCTCTTTA 59.724 37.037 26.76 26.76 40.42 1.85
298 299 6.091441 CGAAGTAAAGTAGCATTGCTCTCTTT 59.909 38.462 28.06 28.06 41.60 2.52
299 300 5.578727 CGAAGTAAAGTAGCATTGCTCTCTT 59.421 40.000 15.81 16.91 40.44 2.85
300 301 5.105716 TCGAAGTAAAGTAGCATTGCTCTCT 60.106 40.000 15.81 11.97 40.44 3.10
301 302 5.103000 TCGAAGTAAAGTAGCATTGCTCTC 58.897 41.667 15.81 9.83 40.44 3.20
302 303 5.073311 TCGAAGTAAAGTAGCATTGCTCT 57.927 39.130 15.81 9.41 40.44 4.09
303 304 5.348997 AGTTCGAAGTAAAGTAGCATTGCTC 59.651 40.000 15.81 7.18 40.44 4.26
304 305 5.238583 AGTTCGAAGTAAAGTAGCATTGCT 58.761 37.500 16.63 16.63 43.41 3.91
305 306 5.532025 AGTTCGAAGTAAAGTAGCATTGC 57.468 39.130 2.97 0.00 0.00 3.56
306 307 6.035758 GGGTAGTTCGAAGTAAAGTAGCATTG 59.964 42.308 14.17 0.00 33.64 2.82
307 308 6.070938 AGGGTAGTTCGAAGTAAAGTAGCATT 60.071 38.462 14.17 0.00 33.64 3.56
308 309 5.421374 AGGGTAGTTCGAAGTAAAGTAGCAT 59.579 40.000 14.17 0.00 33.64 3.79
309 310 4.768968 AGGGTAGTTCGAAGTAAAGTAGCA 59.231 41.667 14.17 0.00 33.64 3.49
310 311 5.100943 CAGGGTAGTTCGAAGTAAAGTAGC 58.899 45.833 14.17 4.02 32.04 3.58
311 312 6.404513 CCTCAGGGTAGTTCGAAGTAAAGTAG 60.405 46.154 14.17 8.44 0.00 2.57
312 313 5.416952 CCTCAGGGTAGTTCGAAGTAAAGTA 59.583 44.000 14.17 0.00 0.00 2.24
313 314 4.220163 CCTCAGGGTAGTTCGAAGTAAAGT 59.780 45.833 14.17 0.00 0.00 2.66
314 315 4.220163 ACCTCAGGGTAGTTCGAAGTAAAG 59.780 45.833 14.17 7.26 45.32 1.85
315 316 4.154942 ACCTCAGGGTAGTTCGAAGTAAA 58.845 43.478 14.17 0.00 45.32 2.01
316 317 3.771216 ACCTCAGGGTAGTTCGAAGTAA 58.229 45.455 14.17 0.00 45.32 2.24
317 318 3.446442 ACCTCAGGGTAGTTCGAAGTA 57.554 47.619 8.66 8.66 45.32 2.24
318 319 2.305858 ACCTCAGGGTAGTTCGAAGT 57.694 50.000 10.90 10.90 45.32 3.01
889 918 1.774254 TGGTCCTGTGATTTGTGGTCT 59.226 47.619 0.00 0.00 0.00 3.85
890 919 1.880027 GTGGTCCTGTGATTTGTGGTC 59.120 52.381 0.00 0.00 0.00 4.02
952 981 8.687292 TGTCTTCTTTCGGATAGCTAGTAATA 57.313 34.615 0.00 0.00 0.00 0.98
962 991 3.924686 GCGTTCTTGTCTTCTTTCGGATA 59.075 43.478 0.00 0.00 0.00 2.59
1202 1231 0.179111 CTTGCCGCCGATGAAGACTA 60.179 55.000 0.00 0.00 0.00 2.59
1315 1344 1.028330 ATGAACTGATGCTGCACCCG 61.028 55.000 3.57 0.00 0.00 5.28
1323 1352 1.760192 AAGCTGGGATGAACTGATGC 58.240 50.000 0.00 0.00 0.00 3.91
1385 1414 7.923878 GCAAAATTTTCCCTACTTGTGTTAAGA 59.076 33.333 0.00 0.00 0.00 2.10
1549 1579 9.507280 ACGTAATAAATTGCATTTCTCATTCAG 57.493 29.630 0.00 0.00 33.82 3.02
1699 1729 7.974501 CGTGTTTCTACCTTCACTGAGTATTAT 59.025 37.037 0.00 0.00 0.00 1.28
1703 1733 4.022589 CCGTGTTTCTACCTTCACTGAGTA 60.023 45.833 0.00 0.00 0.00 2.59
1723 1753 3.550030 CGTCAAAGGCATTTCTTTTCCGT 60.550 43.478 0.00 0.00 35.04 4.69
1734 1764 5.127194 TGTTATACTCTCTCGTCAAAGGCAT 59.873 40.000 0.00 0.00 0.00 4.40
1753 1783 9.427821 GGATATGGAGGTATCTAGATGTGTTAT 57.572 37.037 15.79 5.66 32.78 1.89
1754 1784 7.556635 CGGATATGGAGGTATCTAGATGTGTTA 59.443 40.741 15.79 0.00 32.78 2.41
1755 1785 6.378564 CGGATATGGAGGTATCTAGATGTGTT 59.621 42.308 15.79 0.00 32.78 3.32
1756 1786 5.888724 CGGATATGGAGGTATCTAGATGTGT 59.111 44.000 15.79 0.00 32.78 3.72
1757 1787 5.221145 GCGGATATGGAGGTATCTAGATGTG 60.221 48.000 15.79 0.00 32.78 3.21
1794 1824 8.000709 AGCAATGAATAATACTTCCTCCATTCA 58.999 33.333 0.00 0.00 36.96 2.57
1866 1896 1.076332 GTTTTCTACCGAGCGCACAT 58.924 50.000 11.47 0.00 0.00 3.21
1868 1898 0.163146 GTGTTTTCTACCGAGCGCAC 59.837 55.000 11.47 0.96 0.00 5.34
1948 1978 9.197694 CAGTATTAATCAAGAGAGTAATTCGGG 57.802 37.037 3.92 0.00 40.91 5.14
1984 2014 8.878333 GCGCACATTTTGTTTTCTTAAATAAAC 58.122 29.630 0.30 5.55 35.11 2.01
2055 2085 5.305585 ACTGAGCGAATTTCTTTTGTCCTA 58.694 37.500 0.00 0.00 0.00 2.94
2056 2086 4.137543 ACTGAGCGAATTTCTTTTGTCCT 58.862 39.130 0.00 0.00 0.00 3.85
2057 2087 4.489679 ACTGAGCGAATTTCTTTTGTCC 57.510 40.909 0.00 0.00 0.00 4.02
2059 2089 6.861065 TTCTACTGAGCGAATTTCTTTTGT 57.139 33.333 0.00 0.00 0.00 2.83
2060 2090 7.643764 TGTTTTCTACTGAGCGAATTTCTTTTG 59.356 33.333 0.00 0.00 0.00 2.44
2062 2092 7.259290 TGTTTTCTACTGAGCGAATTTCTTT 57.741 32.000 0.00 0.00 0.00 2.52
2063 2093 6.566753 GCTGTTTTCTACTGAGCGAATTTCTT 60.567 38.462 0.00 0.00 0.00 2.52
2064 2094 5.106908 GCTGTTTTCTACTGAGCGAATTTCT 60.107 40.000 0.00 0.00 0.00 2.52
2065 2095 5.082723 GCTGTTTTCTACTGAGCGAATTTC 58.917 41.667 0.00 0.00 0.00 2.17
2066 2096 4.515191 TGCTGTTTTCTACTGAGCGAATTT 59.485 37.500 0.00 0.00 30.44 1.82
2067 2097 4.065088 TGCTGTTTTCTACTGAGCGAATT 58.935 39.130 0.00 0.00 30.44 2.17
2068 2098 3.664107 TGCTGTTTTCTACTGAGCGAAT 58.336 40.909 0.00 0.00 30.44 3.34
2070 2100 2.812358 TGCTGTTTTCTACTGAGCGA 57.188 45.000 0.00 0.00 30.44 4.93
2072 2102 4.061596 AGACTTGCTGTTTTCTACTGAGC 58.938 43.478 0.00 0.00 0.00 4.26
2073 2103 5.588568 CAGACTTGCTGTTTTCTACTGAG 57.411 43.478 0.00 0.00 39.85 3.35


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

AutoCloner maintained by Alex Coulton.