Multiple sequence alignment - TraesCS5A01G465500

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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 TraesCS5A01G465500 chr5A 100.000 2462 0 0 1 2462 644309463 644311924 0.000000e+00 4547.0
1 TraesCS5A01G465500 chr5A 87.617 1066 84 25 803 1846 619344064 619345103 0.000000e+00 1194.0
2 TraesCS5A01G465500 chr5A 83.863 1165 119 46 735 1846 625715147 625716295 0.000000e+00 1046.0
3 TraesCS5A01G465500 chr5B 91.479 1291 80 21 565 1846 649498138 649499407 0.000000e+00 1748.0
4 TraesCS5A01G465500 chr5B 88.207 1043 76 18 803 1839 611677573 611678574 0.000000e+00 1201.0
5 TraesCS5A01G465500 chr5B 87.234 987 94 15 721 1700 629926556 629925595 0.000000e+00 1096.0
6 TraesCS5A01G465500 chr5B 84.292 1165 123 34 699 1846 628724642 628723521 0.000000e+00 1083.0
7 TraesCS5A01G465500 chr5B 83.613 1190 123 46 699 1858 629953435 629952288 0.000000e+00 1051.0
8 TraesCS5A01G465500 chr5B 92.608 744 24 3 693 1435 649694140 649694853 0.000000e+00 1040.0
9 TraesCS5A01G465500 chr5B 83.725 1149 111 42 735 1846 633171156 633172265 0.000000e+00 1016.0
10 TraesCS5A01G465500 chr5B 86.536 713 63 19 1143 1846 625131203 625130515 0.000000e+00 754.0
11 TraesCS5A01G465500 chr5B 87.430 533 28 13 1932 2462 649695410 649695905 5.900000e-161 577.0
12 TraesCS5A01G465500 chr5B 89.822 393 16 5 1932 2324 649499507 649499875 1.320000e-132 483.0
13 TraesCS5A01G465500 chr5B 85.138 471 47 8 1394 1846 649694845 649695310 6.200000e-126 460.0
14 TraesCS5A01G465500 chr5B 79.812 426 53 19 1393 1808 639670610 639670208 1.860000e-71 279.0
15 TraesCS5A01G465500 chr5D 90.747 1286 80 24 367 1634 517212835 517214099 0.000000e+00 1679.0
16 TraesCS5A01G465500 chr5D 88.341 1055 89 21 805 1846 495199783 495200816 0.000000e+00 1236.0
17 TraesCS5A01G465500 chr5D 85.636 1093 110 24 699 1772 501450299 501449235 0.000000e+00 1105.0
18 TraesCS5A01G465500 chr5D 91.288 792 52 14 805 1589 495142356 495143137 0.000000e+00 1064.0
19 TraesCS5A01G465500 chr5D 90.807 533 23 10 1932 2462 517214297 517214805 0.000000e+00 689.0
20 TraesCS5A01G465500 chr5D 87.419 461 40 9 459 905 517305348 517305804 4.690000e-142 514.0
21 TraesCS5A01G465500 chr5D 86.825 463 41 13 459 905 517302960 517303418 1.310000e-137 499.0
22 TraesCS5A01G465500 chr5D 86.609 463 44 12 459 905 517303993 517304453 1.700000e-136 496.0
23 TraesCS5A01G465500 chr5D 81.200 250 25 9 1597 1846 296965697 296965924 5.410000e-42 182.0
24 TraesCS5A01G465500 chr7B 89.557 316 31 2 1 316 127624527 127624840 1.370000e-107 399.0
25 TraesCS5A01G465500 chr3D 88.889 315 32 2 1 313 20754847 20755160 3.840000e-103 385.0
26 TraesCS5A01G465500 chr3D 88.199 322 30 5 1 319 58405848 58405532 6.430000e-101 377.0
27 TraesCS5A01G465500 chr3D 88.816 304 33 1 10 313 459206296 459206598 2.990000e-99 372.0
28 TraesCS5A01G465500 chr7D 88.498 313 34 2 1 313 572265305 572265615 6.430000e-101 377.0
29 TraesCS5A01G465500 chr7D 88.179 313 35 2 2 313 22847464 22847775 2.990000e-99 372.0
30 TraesCS5A01G465500 chr7D 87.736 318 35 3 1 315 574071773 574072089 3.870000e-98 368.0
31 TraesCS5A01G465500 chr2D 87.195 328 33 5 1 319 499718950 499718623 5.000000e-97 364.0
32 TraesCS5A01G465500 chr2D 87.697 317 33 4 1 315 531479249 531478937 5.000000e-97 364.0
33 TraesCS5A01G465500 chr4D 81.982 111 17 2 1915 2025 347233271 347233164 9.380000e-15 91.6


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 TraesCS5A01G465500 chr5A 644309463 644311924 2461 False 4547.000000 4547 100.0000 1 2462 1 chr5A.!!$F3 2461
1 TraesCS5A01G465500 chr5A 619344064 619345103 1039 False 1194.000000 1194 87.6170 803 1846 1 chr5A.!!$F1 1043
2 TraesCS5A01G465500 chr5A 625715147 625716295 1148 False 1046.000000 1046 83.8630 735 1846 1 chr5A.!!$F2 1111
3 TraesCS5A01G465500 chr5B 611677573 611678574 1001 False 1201.000000 1201 88.2070 803 1839 1 chr5B.!!$F1 1036
4 TraesCS5A01G465500 chr5B 649498138 649499875 1737 False 1115.500000 1748 90.6505 565 2324 2 chr5B.!!$F3 1759
5 TraesCS5A01G465500 chr5B 629925595 629926556 961 True 1096.000000 1096 87.2340 721 1700 1 chr5B.!!$R3 979
6 TraesCS5A01G465500 chr5B 628723521 628724642 1121 True 1083.000000 1083 84.2920 699 1846 1 chr5B.!!$R2 1147
7 TraesCS5A01G465500 chr5B 629952288 629953435 1147 True 1051.000000 1051 83.6130 699 1858 1 chr5B.!!$R4 1159
8 TraesCS5A01G465500 chr5B 633171156 633172265 1109 False 1016.000000 1016 83.7250 735 1846 1 chr5B.!!$F2 1111
9 TraesCS5A01G465500 chr5B 625130515 625131203 688 True 754.000000 754 86.5360 1143 1846 1 chr5B.!!$R1 703
10 TraesCS5A01G465500 chr5B 649694140 649695905 1765 False 692.333333 1040 88.3920 693 2462 3 chr5B.!!$F4 1769
11 TraesCS5A01G465500 chr5D 495199783 495200816 1033 False 1236.000000 1236 88.3410 805 1846 1 chr5D.!!$F3 1041
12 TraesCS5A01G465500 chr5D 517212835 517214805 1970 False 1184.000000 1679 90.7770 367 2462 2 chr5D.!!$F4 2095
13 TraesCS5A01G465500 chr5D 501449235 501450299 1064 True 1105.000000 1105 85.6360 699 1772 1 chr5D.!!$R1 1073
14 TraesCS5A01G465500 chr5D 495142356 495143137 781 False 1064.000000 1064 91.2880 805 1589 1 chr5D.!!$F2 784
15 TraesCS5A01G465500 chr5D 517302960 517305804 2844 False 503.000000 514 86.9510 459 905 3 chr5D.!!$F5 446

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
296 297 0.107081 AACGGACGAAATGGGTCACA 59.893 50.0 0.0 0.0 36.12 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 3600 0.398696 TGGGCGACAACCAACTATGT 59.601 50.0 0.0 0.0 34.44 2.29 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
17 18 4.504916 CAGCTGGGAGAGTCGCCG 62.505 72.222 5.57 0.00 0.00 6.46
20 21 3.068691 CTGGGAGAGTCGCCGGAA 61.069 66.667 5.05 0.00 0.00 4.30
21 22 2.602267 TGGGAGAGTCGCCGGAAA 60.602 61.111 5.05 0.00 0.00 3.13
22 23 2.167398 CTGGGAGAGTCGCCGGAAAA 62.167 60.000 5.05 0.00 0.00 2.29
23 24 1.004200 GGGAGAGTCGCCGGAAAAA 60.004 57.895 5.05 0.00 0.00 1.94
37 38 2.981350 AAAAATGGACGGCGGCGT 60.981 55.556 38.13 38.13 0.00 5.68
38 39 2.973316 AAAAATGGACGGCGGCGTC 61.973 57.895 44.98 44.98 38.09 5.19
71 72 3.365265 GGGCGAGGGTTGCTGTTG 61.365 66.667 0.00 0.00 0.00 3.33
72 73 3.365265 GGCGAGGGTTGCTGTTGG 61.365 66.667 0.00 0.00 0.00 3.77
73 74 2.281484 GCGAGGGTTGCTGTTGGA 60.281 61.111 0.00 0.00 0.00 3.53
74 75 1.675641 GCGAGGGTTGCTGTTGGAT 60.676 57.895 0.00 0.00 0.00 3.41
75 76 1.926511 GCGAGGGTTGCTGTTGGATG 61.927 60.000 0.00 0.00 0.00 3.51
76 77 1.308069 CGAGGGTTGCTGTTGGATGG 61.308 60.000 0.00 0.00 0.00 3.51
77 78 0.967380 GAGGGTTGCTGTTGGATGGG 60.967 60.000 0.00 0.00 0.00 4.00
78 79 1.984026 GGGTTGCTGTTGGATGGGG 60.984 63.158 0.00 0.00 0.00 4.96
79 80 1.984026 GGTTGCTGTTGGATGGGGG 60.984 63.158 0.00 0.00 0.00 5.40
80 81 1.076549 GTTGCTGTTGGATGGGGGA 59.923 57.895 0.00 0.00 0.00 4.81
81 82 0.541764 GTTGCTGTTGGATGGGGGAA 60.542 55.000 0.00 0.00 0.00 3.97
82 83 0.251742 TTGCTGTTGGATGGGGGAAG 60.252 55.000 0.00 0.00 0.00 3.46
83 84 1.380380 GCTGTTGGATGGGGGAAGG 60.380 63.158 0.00 0.00 0.00 3.46
84 85 1.380380 CTGTTGGATGGGGGAAGGC 60.380 63.158 0.00 0.00 0.00 4.35
85 86 2.042944 GTTGGATGGGGGAAGGCC 60.043 66.667 0.00 0.00 0.00 5.19
86 87 2.536633 TTGGATGGGGGAAGGCCA 60.537 61.111 5.01 0.00 35.15 5.36
87 88 2.173299 TTGGATGGGGGAAGGCCAA 61.173 57.895 5.01 0.00 36.35 4.52
88 89 1.526528 TTGGATGGGGGAAGGCCAAT 61.527 55.000 5.01 0.00 33.96 3.16
89 90 1.458209 GGATGGGGGAAGGCCAATG 60.458 63.158 5.01 0.00 35.15 2.82
90 91 1.311059 GATGGGGGAAGGCCAATGT 59.689 57.895 5.01 0.00 35.15 2.71
91 92 1.002017 ATGGGGGAAGGCCAATGTG 59.998 57.895 5.01 0.00 35.15 3.21
92 93 1.814292 ATGGGGGAAGGCCAATGTGT 61.814 55.000 5.01 0.00 35.15 3.72
93 94 1.682344 GGGGGAAGGCCAATGTGTC 60.682 63.158 5.01 0.00 35.15 3.67
94 95 1.076549 GGGGAAGGCCAATGTGTCA 59.923 57.895 5.01 0.00 35.15 3.58
95 96 1.250840 GGGGAAGGCCAATGTGTCAC 61.251 60.000 5.01 0.00 35.15 3.67
96 97 1.250840 GGGAAGGCCAATGTGTCACC 61.251 60.000 5.01 0.00 35.15 4.02
97 98 1.586154 GGAAGGCCAATGTGTCACCG 61.586 60.000 5.01 0.00 0.00 4.94
98 99 0.605319 GAAGGCCAATGTGTCACCGA 60.605 55.000 5.01 0.00 0.00 4.69
99 100 0.889186 AAGGCCAATGTGTCACCGAC 60.889 55.000 5.01 0.00 0.00 4.79
100 101 2.332654 GGCCAATGTGTCACCGACC 61.333 63.158 0.00 0.00 0.00 4.79
101 102 1.599518 GCCAATGTGTCACCGACCA 60.600 57.895 0.00 0.00 0.00 4.02
102 103 1.577328 GCCAATGTGTCACCGACCAG 61.577 60.000 0.00 0.00 0.00 4.00
103 104 1.577328 CCAATGTGTCACCGACCAGC 61.577 60.000 0.00 0.00 0.00 4.85
104 105 1.667830 AATGTGTCACCGACCAGCG 60.668 57.895 0.00 0.00 40.47 5.18
167 168 3.937062 CGCCGACGCAAATAGGGC 61.937 66.667 0.00 0.00 40.36 5.19
168 169 2.513897 GCCGACGCAAATAGGGCT 60.514 61.111 0.00 0.00 40.59 5.19
169 170 1.227438 GCCGACGCAAATAGGGCTA 60.227 57.895 0.00 0.00 40.59 3.93
170 171 0.812412 GCCGACGCAAATAGGGCTAA 60.812 55.000 0.00 0.00 40.59 3.09
171 172 1.658994 CCGACGCAAATAGGGCTAAA 58.341 50.000 0.00 0.00 0.00 1.85
172 173 2.011222 CCGACGCAAATAGGGCTAAAA 58.989 47.619 0.00 0.00 0.00 1.52
173 174 2.420722 CCGACGCAAATAGGGCTAAAAA 59.579 45.455 0.00 0.00 0.00 1.94
187 188 3.067985 AAAAAGGGGCCGGCAATG 58.932 55.556 30.85 0.00 0.00 2.82
188 189 2.592032 AAAAAGGGGCCGGCAATGG 61.592 57.895 30.85 0.00 0.00 3.16
205 206 4.668118 GGTCACCCGCGGACGAAA 62.668 66.667 30.73 3.87 43.93 3.46
206 207 2.662527 GTCACCCGCGGACGAAAA 60.663 61.111 30.73 2.20 43.93 2.29
207 208 2.356553 TCACCCGCGGACGAAAAG 60.357 61.111 30.73 10.69 43.93 2.27
208 209 4.084888 CACCCGCGGACGAAAAGC 62.085 66.667 30.73 0.00 43.93 3.51
213 214 4.130281 GCGGACGAAAAGCGGACG 62.130 66.667 0.00 0.00 46.49 4.79
214 215 4.130281 CGGACGAAAAGCGGACGC 62.130 66.667 8.91 8.91 46.49 5.19
226 227 4.712873 GGACGCGCGTTCGTTTGG 62.713 66.667 38.03 3.89 43.42 3.28
227 228 4.712873 GACGCGCGTTCGTTTGGG 62.713 66.667 38.03 3.01 43.42 4.12
229 230 4.712873 CGCGCGTTCGTTTGGGTC 62.713 66.667 24.19 0.00 38.14 4.46
230 231 4.712873 GCGCGTTCGTTTGGGTCG 62.713 66.667 8.43 0.00 38.14 4.79
231 232 4.067016 CGCGTTCGTTTGGGTCGG 62.067 66.667 0.00 0.00 0.00 4.79
232 233 4.379143 GCGTTCGTTTGGGTCGGC 62.379 66.667 0.00 0.00 0.00 5.54
233 234 4.067016 CGTTCGTTTGGGTCGGCG 62.067 66.667 0.00 0.00 0.00 6.46
234 235 4.379143 GTTCGTTTGGGTCGGCGC 62.379 66.667 0.00 0.00 0.00 6.53
238 239 4.676586 GTTTGGGTCGGCGCGTTG 62.677 66.667 8.43 0.00 0.00 4.10
248 249 4.279043 GCGCGTTGGGCCAACTTT 62.279 61.111 38.24 0.00 41.62 2.66
249 250 2.415426 CGCGTTGGGCCAACTTTT 59.585 55.556 38.24 0.00 41.62 2.27
250 251 1.227118 CGCGTTGGGCCAACTTTTT 60.227 52.632 38.24 0.00 41.62 1.94
264 265 2.127042 TTTTTGTGCGCGCCGATC 60.127 55.556 30.77 16.46 0.00 3.69
265 266 3.602924 TTTTTGTGCGCGCCGATCC 62.603 57.895 30.77 11.61 0.00 3.36
269 270 3.876198 GTGCGCGCCGATCCAAAT 61.876 61.111 30.77 0.00 0.00 2.32
270 271 2.202946 TGCGCGCCGATCCAAATA 60.203 55.556 30.77 1.61 0.00 1.40
271 272 2.243957 TGCGCGCCGATCCAAATAG 61.244 57.895 30.77 0.00 0.00 1.73
272 273 1.954146 GCGCGCCGATCCAAATAGA 60.954 57.895 23.24 0.00 0.00 1.98
273 274 1.853319 CGCGCCGATCCAAATAGAC 59.147 57.895 0.00 0.00 0.00 2.59
274 275 1.853319 GCGCCGATCCAAATAGACG 59.147 57.895 0.00 0.00 0.00 4.18
275 276 1.853319 CGCCGATCCAAATAGACGC 59.147 57.895 0.00 0.00 0.00 5.19
276 277 1.557443 CGCCGATCCAAATAGACGCC 61.557 60.000 0.00 0.00 0.00 5.68
277 278 0.531974 GCCGATCCAAATAGACGCCA 60.532 55.000 0.00 0.00 0.00 5.69
278 279 1.948104 CCGATCCAAATAGACGCCAA 58.052 50.000 0.00 0.00 0.00 4.52
279 280 1.597663 CCGATCCAAATAGACGCCAAC 59.402 52.381 0.00 0.00 0.00 3.77
281 282 1.597663 GATCCAAATAGACGCCAACGG 59.402 52.381 0.00 0.00 46.04 4.44
282 283 0.609151 TCCAAATAGACGCCAACGGA 59.391 50.000 0.00 0.00 46.04 4.69
283 284 0.725117 CCAAATAGACGCCAACGGAC 59.275 55.000 0.00 0.00 46.04 4.79
284 285 0.368907 CAAATAGACGCCAACGGACG 59.631 55.000 0.00 0.00 46.04 4.79
285 286 0.244450 AAATAGACGCCAACGGACGA 59.756 50.000 0.00 0.00 46.04 4.20
286 287 0.244450 AATAGACGCCAACGGACGAA 59.756 50.000 0.00 0.00 46.04 3.85
287 288 0.244450 ATAGACGCCAACGGACGAAA 59.756 50.000 0.00 0.00 46.04 3.46
288 289 0.244450 TAGACGCCAACGGACGAAAT 59.756 50.000 0.00 0.00 46.04 2.17
289 290 1.131826 GACGCCAACGGACGAAATG 59.868 57.895 0.00 0.00 46.04 2.32
290 291 2.235536 GACGCCAACGGACGAAATGG 62.236 60.000 0.00 5.27 46.04 3.16
291 292 2.874751 GCCAACGGACGAAATGGG 59.125 61.111 14.13 0.00 33.45 4.00
292 293 1.969589 GCCAACGGACGAAATGGGT 60.970 57.895 14.13 0.00 33.45 4.51
293 294 1.918868 GCCAACGGACGAAATGGGTC 61.919 60.000 14.13 0.00 33.45 4.46
294 295 0.604243 CCAACGGACGAAATGGGTCA 60.604 55.000 0.00 0.00 36.12 4.02
295 296 0.515564 CAACGGACGAAATGGGTCAC 59.484 55.000 0.00 0.00 36.12 3.67
296 297 0.107081 AACGGACGAAATGGGTCACA 59.893 50.000 0.00 0.00 36.12 3.58
297 298 0.601841 ACGGACGAAATGGGTCACAC 60.602 55.000 0.00 0.00 36.12 3.82
298 299 1.296056 CGGACGAAATGGGTCACACC 61.296 60.000 0.00 0.00 36.12 4.16
299 300 1.296056 GGACGAAATGGGTCACACCG 61.296 60.000 0.00 0.00 39.83 4.94
300 301 0.601841 GACGAAATGGGTCACACCGT 60.602 55.000 0.00 0.00 39.83 4.83
301 302 0.179040 ACGAAATGGGTCACACCGTT 60.179 50.000 0.00 0.00 39.83 4.44
302 303 0.237235 CGAAATGGGTCACACCGTTG 59.763 55.000 0.00 0.00 39.83 4.10
303 304 0.596082 GAAATGGGTCACACCGTTGG 59.404 55.000 0.00 0.00 39.83 3.77
304 305 0.183971 AAATGGGTCACACCGTTGGA 59.816 50.000 0.00 0.00 39.83 3.53
305 306 0.250727 AATGGGTCACACCGTTGGAG 60.251 55.000 0.00 0.00 39.83 3.86
306 307 1.415672 ATGGGTCACACCGTTGGAGT 61.416 55.000 0.00 0.00 39.83 3.85
307 308 1.147600 GGGTCACACCGTTGGAGTT 59.852 57.895 0.00 0.00 39.83 3.01
308 309 1.164041 GGGTCACACCGTTGGAGTTG 61.164 60.000 0.00 0.00 39.83 3.16
309 310 1.647084 GTCACACCGTTGGAGTTGC 59.353 57.895 0.00 0.00 0.00 4.17
310 311 0.814010 GTCACACCGTTGGAGTTGCT 60.814 55.000 0.00 0.00 0.00 3.91
311 312 0.531974 TCACACCGTTGGAGTTGCTC 60.532 55.000 0.00 0.00 0.00 4.26
312 313 0.532862 CACACCGTTGGAGTTGCTCT 60.533 55.000 0.00 0.00 0.00 4.09
313 314 1.045407 ACACCGTTGGAGTTGCTCTA 58.955 50.000 0.00 0.00 0.00 2.43
314 315 1.414919 ACACCGTTGGAGTTGCTCTAA 59.585 47.619 0.00 0.00 0.00 2.10
315 316 2.038557 ACACCGTTGGAGTTGCTCTAAT 59.961 45.455 0.00 0.00 33.81 1.73
316 317 3.259876 ACACCGTTGGAGTTGCTCTAATA 59.740 43.478 0.00 0.00 33.81 0.98
317 318 4.081087 ACACCGTTGGAGTTGCTCTAATAT 60.081 41.667 0.00 0.00 33.81 1.28
318 319 4.876107 CACCGTTGGAGTTGCTCTAATATT 59.124 41.667 0.00 0.00 33.81 1.28
319 320 6.046593 CACCGTTGGAGTTGCTCTAATATTA 58.953 40.000 0.00 0.00 33.81 0.98
320 321 6.018994 CACCGTTGGAGTTGCTCTAATATTAC 60.019 42.308 0.00 0.00 33.81 1.89
321 322 5.465724 CCGTTGGAGTTGCTCTAATATTACC 59.534 44.000 0.00 0.00 33.81 2.85
322 323 5.465724 CGTTGGAGTTGCTCTAATATTACCC 59.534 44.000 0.00 0.00 33.81 3.69
323 324 6.592870 GTTGGAGTTGCTCTAATATTACCCT 58.407 40.000 0.00 0.00 33.81 4.34
324 325 6.420913 TGGAGTTGCTCTAATATTACCCTC 57.579 41.667 0.00 0.00 0.00 4.30
325 326 5.903010 TGGAGTTGCTCTAATATTACCCTCA 59.097 40.000 0.00 0.00 0.00 3.86
326 327 6.558775 TGGAGTTGCTCTAATATTACCCTCAT 59.441 38.462 0.00 0.00 0.00 2.90
327 328 6.876257 GGAGTTGCTCTAATATTACCCTCATG 59.124 42.308 0.00 0.00 0.00 3.07
328 329 7.380423 AGTTGCTCTAATATTACCCTCATGT 57.620 36.000 0.00 0.00 0.00 3.21
329 330 8.492415 AGTTGCTCTAATATTACCCTCATGTA 57.508 34.615 0.00 0.00 0.00 2.29
330 331 8.934697 AGTTGCTCTAATATTACCCTCATGTAA 58.065 33.333 0.00 0.00 35.33 2.41
331 332 9.555727 GTTGCTCTAATATTACCCTCATGTAAA 57.444 33.333 0.00 0.00 34.59 2.01
344 345 8.950007 ACCCTCATGTAAAATAAAAAGAGGAA 57.050 30.769 0.00 0.00 43.07 3.36
345 346 9.374711 ACCCTCATGTAAAATAAAAAGAGGAAA 57.625 29.630 0.00 0.00 43.07 3.13
363 364 7.909267 AGAGGAAATTTCTTTTTCTTTTTGCG 58.091 30.769 17.42 0.00 32.99 4.85
364 365 7.011389 AGAGGAAATTTCTTTTTCTTTTTGCGG 59.989 33.333 17.42 0.00 32.99 5.69
365 366 6.038161 AGGAAATTTCTTTTTCTTTTTGCGGG 59.962 34.615 17.42 0.00 36.17 6.13
366 367 6.037720 GGAAATTTCTTTTTCTTTTTGCGGGA 59.962 34.615 17.42 0.00 36.17 5.14
367 368 6.993786 AATTTCTTTTTCTTTTTGCGGGAA 57.006 29.167 0.00 0.00 0.00 3.97
368 369 6.993786 ATTTCTTTTTCTTTTTGCGGGAAA 57.006 29.167 0.00 0.00 0.00 3.13
369 370 6.803154 TTTCTTTTTCTTTTTGCGGGAAAA 57.197 29.167 3.11 3.11 37.23 2.29
370 371 6.803154 TTCTTTTTCTTTTTGCGGGAAAAA 57.197 29.167 17.34 17.34 42.65 1.94
523 525 1.427368 TGTGGTTCATTACTTGGCCCT 59.573 47.619 0.00 0.00 0.00 5.19
559 562 3.823304 AGATTCCTGTTGAAGAACCTTGC 59.177 43.478 0.00 0.00 36.14 4.01
573 576 3.473113 ACCTTGCATCCAAATAACCCT 57.527 42.857 0.00 0.00 0.00 4.34
590 594 2.209273 CCCTTTTTGTTTTTGAGCCGG 58.791 47.619 0.00 0.00 0.00 6.13
712 739 2.881111 ACTAGAAAGGAAGGGGTTGC 57.119 50.000 0.00 0.00 0.00 4.17
822 850 1.815003 CATCGCAGCCGTCCATTCA 60.815 57.895 0.00 0.00 35.54 2.57
927 2038 0.179040 AACCCGTCGTCCAACACAAT 60.179 50.000 0.00 0.00 0.00 2.71
996 2156 1.997874 CCAACCCCTGCCTCTAGCT 60.998 63.158 0.00 0.00 44.23 3.32
1425 2629 1.261238 CGGAGAAGGAGCCCAAGTCT 61.261 60.000 0.00 0.00 0.00 3.24
1463 2760 1.354705 GTCCCCCAAGAAGGCTTAGTT 59.645 52.381 0.00 0.00 35.39 2.24
1526 2836 6.202762 TGTTTGGATAATGATGTCGATGTAGC 59.797 38.462 0.00 0.00 0.00 3.58
1589 2905 6.472016 TGTCTGACCTGCAGTAAATTCATTA 58.528 36.000 13.81 0.00 45.14 1.90
1757 3480 2.298411 CTGAAGAAGCTGAGGAGAGC 57.702 55.000 0.00 0.00 39.46 4.09
1762 3485 3.030873 AGAAGCTGAGGAGAGCATACT 57.969 47.619 0.00 0.00 41.83 2.12
1842 3588 2.081462 AGTACTACCAAATGCCAACGC 58.919 47.619 0.00 0.00 0.00 4.84
1846 3592 1.812571 CTACCAAATGCCAACGCTTCT 59.187 47.619 0.00 0.00 35.36 2.85
1847 3593 0.314935 ACCAAATGCCAACGCTTCTG 59.685 50.000 0.00 0.00 35.36 3.02
1848 3594 0.314935 CCAAATGCCAACGCTTCTGT 59.685 50.000 0.00 0.00 35.36 3.41
1849 3595 1.539388 CCAAATGCCAACGCTTCTGTA 59.461 47.619 0.00 0.00 35.36 2.74
1850 3596 2.414559 CCAAATGCCAACGCTTCTGTAG 60.415 50.000 0.00 0.00 35.36 2.74
1851 3597 2.472695 AATGCCAACGCTTCTGTAGA 57.527 45.000 0.00 0.00 35.36 2.59
1853 3599 0.679505 TGCCAACGCTTCTGTAGAGT 59.320 50.000 0.00 0.00 38.67 3.24
1854 3600 1.890489 TGCCAACGCTTCTGTAGAGTA 59.110 47.619 0.00 0.00 35.70 2.59
1855 3601 2.260481 GCCAACGCTTCTGTAGAGTAC 58.740 52.381 0.00 0.00 35.70 2.73
1856 3602 2.352421 GCCAACGCTTCTGTAGAGTACA 60.352 50.000 0.00 0.00 35.70 2.90
1859 3652 5.274718 CCAACGCTTCTGTAGAGTACATAG 58.725 45.833 0.00 0.00 35.70 2.23
1886 3679 0.916086 TCGCCCAACCCAATATCACT 59.084 50.000 0.00 0.00 0.00 3.41
1894 3687 6.690460 GCCCAACCCAATATCACTACATTCTA 60.690 42.308 0.00 0.00 0.00 2.10
1895 3688 6.936900 CCCAACCCAATATCACTACATTCTAG 59.063 42.308 0.00 0.00 0.00 2.43
1896 3689 7.202093 CCCAACCCAATATCACTACATTCTAGA 60.202 40.741 0.00 0.00 0.00 2.43
1897 3690 8.210946 CCAACCCAATATCACTACATTCTAGAA 58.789 37.037 7.82 7.82 0.00 2.10
1898 3691 9.046296 CAACCCAATATCACTACATTCTAGAAC 57.954 37.037 7.48 0.00 0.00 3.01
1899 3692 8.319057 ACCCAATATCACTACATTCTAGAACA 57.681 34.615 7.48 0.00 0.00 3.18
1900 3693 8.938883 ACCCAATATCACTACATTCTAGAACAT 58.061 33.333 7.48 1.26 0.00 2.71
1901 3694 9.212641 CCCAATATCACTACATTCTAGAACATG 57.787 37.037 7.48 5.92 0.00 3.21
1902 3695 9.987272 CCAATATCACTACATTCTAGAACATGA 57.013 33.333 7.48 7.72 0.00 3.07
1922 3715 8.833231 ACATGATAGTACTACATTATGTTGCC 57.167 34.615 4.31 0.00 0.00 4.52
1923 3716 8.651389 ACATGATAGTACTACATTATGTTGCCT 58.349 33.333 4.31 4.25 0.00 4.75
1924 3717 8.929746 CATGATAGTACTACATTATGTTGCCTG 58.070 37.037 4.31 0.00 0.00 4.85
1925 3718 8.245195 TGATAGTACTACATTATGTTGCCTGA 57.755 34.615 4.31 0.00 0.00 3.86
1926 3719 8.870116 TGATAGTACTACATTATGTTGCCTGAT 58.130 33.333 4.31 0.00 0.00 2.90
1927 3720 9.144747 GATAGTACTACATTATGTTGCCTGATG 57.855 37.037 4.31 0.00 0.00 3.07
1928 3721 6.291377 AGTACTACATTATGTTGCCTGATGG 58.709 40.000 2.23 0.00 0.00 3.51
1950 3743 3.810373 CGGAATAAGTTCAGTTGCACAC 58.190 45.455 0.00 0.00 36.01 3.82
1951 3744 3.498397 CGGAATAAGTTCAGTTGCACACT 59.502 43.478 0.00 0.00 36.01 3.55
2046 3844 8.519492 TGCATTGCTTGTTTTTCTATCTAAAC 57.481 30.769 10.49 0.00 35.38 2.01
2084 3882 9.502091 TCTTGATGTATATGTATTGGCTAAACC 57.498 33.333 0.00 0.00 39.84 3.27
2113 3911 9.855021 ACCACACTAATTATAAAAATCAGCAAC 57.145 29.630 0.00 0.00 0.00 4.17
2129 3927 5.976458 TCAGCAACTGATACACACATGATA 58.024 37.500 0.00 0.00 35.39 2.15
2141 3939 6.441093 ACACACATGATAGTTGCCAAATAG 57.559 37.500 0.00 0.00 0.00 1.73
2143 3941 6.830324 ACACACATGATAGTTGCCAAATAGAT 59.170 34.615 0.00 0.00 0.00 1.98
2144 3942 7.992608 ACACACATGATAGTTGCCAAATAGATA 59.007 33.333 0.00 0.00 0.00 1.98
2146 3944 7.173907 ACACATGATAGTTGCCAAATAGATAGC 59.826 37.037 0.00 0.00 0.00 2.97
2148 3946 7.605691 ACATGATAGTTGCCAAATAGATAGCTC 59.394 37.037 0.00 0.00 0.00 4.09
2149 3947 7.066307 TGATAGTTGCCAAATAGATAGCTCA 57.934 36.000 0.00 0.00 0.00 4.26
2150 3948 7.508687 TGATAGTTGCCAAATAGATAGCTCAA 58.491 34.615 0.00 0.00 0.00 3.02
2153 3951 6.183347 AGTTGCCAAATAGATAGCTCAAACT 58.817 36.000 0.00 0.00 0.00 2.66
2154 3952 6.660949 AGTTGCCAAATAGATAGCTCAAACTT 59.339 34.615 0.00 0.00 0.00 2.66
2155 3953 6.683974 TGCCAAATAGATAGCTCAAACTTC 57.316 37.500 0.00 0.00 0.00 3.01
2157 3955 6.317140 TGCCAAATAGATAGCTCAAACTTCAG 59.683 38.462 0.00 0.00 0.00 3.02
2158 3956 6.317391 GCCAAATAGATAGCTCAAACTTCAGT 59.683 38.462 0.00 0.00 0.00 3.41
2160 3958 9.039870 CCAAATAGATAGCTCAAACTTCAGTAG 57.960 37.037 0.00 0.00 0.00 2.57
2161 3959 9.593134 CAAATAGATAGCTCAAACTTCAGTAGT 57.407 33.333 0.00 0.00 39.32 2.73
2239 4037 5.807011 CAGTGGATAATTAAGCAAGTTTGGC 59.193 40.000 0.00 0.00 0.00 4.52
2259 4057 2.159338 GCTGATGTCGCAAATGGTCATT 60.159 45.455 0.00 0.00 0.00 2.57
2327 4125 5.140454 ACCAATTTATGCCTGATAAGGGTC 58.860 41.667 0.00 0.00 28.57 4.46
2329 4127 5.598005 CCAATTTATGCCTGATAAGGGTCAA 59.402 40.000 0.00 0.00 0.00 3.18
2332 4130 6.713762 TTTATGCCTGATAAGGGTCAAATG 57.286 37.500 0.00 0.00 0.00 2.32
2335 4133 3.205056 TGCCTGATAAGGGTCAAATGGAT 59.795 43.478 0.00 0.00 0.00 3.41
2375 4174 5.380043 AGATGGCAAATTCGGTGATCTTAT 58.620 37.500 0.00 0.00 0.00 1.73
2421 4221 4.898861 ACAAGGACCAATAACCACAACAAT 59.101 37.500 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.504916 CGGCGACTCTCCCAGCTG 62.505 72.222 6.78 6.78 0.00 4.24
3 4 2.167398 TTTTCCGGCGACTCTCCCAG 62.167 60.000 9.30 0.00 0.00 4.45
4 5 1.760479 TTTTTCCGGCGACTCTCCCA 61.760 55.000 9.30 0.00 0.00 4.37
5 6 1.004200 TTTTTCCGGCGACTCTCCC 60.004 57.895 9.30 0.00 0.00 4.30
6 7 4.687464 TTTTTCCGGCGACTCTCC 57.313 55.556 9.30 0.00 0.00 3.71
20 21 2.981350 ACGCCGCCGTCCATTTTT 60.981 55.556 0.00 0.00 46.39 1.94
54 55 3.365265 CAACAGCAACCCTCGCCC 61.365 66.667 0.00 0.00 0.00 6.13
55 56 3.365265 CCAACAGCAACCCTCGCC 61.365 66.667 0.00 0.00 0.00 5.54
56 57 1.675641 ATCCAACAGCAACCCTCGC 60.676 57.895 0.00 0.00 0.00 5.03
57 58 1.308069 CCATCCAACAGCAACCCTCG 61.308 60.000 0.00 0.00 0.00 4.63
58 59 0.967380 CCCATCCAACAGCAACCCTC 60.967 60.000 0.00 0.00 0.00 4.30
59 60 1.077265 CCCATCCAACAGCAACCCT 59.923 57.895 0.00 0.00 0.00 4.34
60 61 1.984026 CCCCATCCAACAGCAACCC 60.984 63.158 0.00 0.00 0.00 4.11
61 62 1.984026 CCCCCATCCAACAGCAACC 60.984 63.158 0.00 0.00 0.00 3.77
62 63 0.541764 TTCCCCCATCCAACAGCAAC 60.542 55.000 0.00 0.00 0.00 4.17
63 64 0.251742 CTTCCCCCATCCAACAGCAA 60.252 55.000 0.00 0.00 0.00 3.91
64 65 1.383799 CTTCCCCCATCCAACAGCA 59.616 57.895 0.00 0.00 0.00 4.41
65 66 1.380380 CCTTCCCCCATCCAACAGC 60.380 63.158 0.00 0.00 0.00 4.40
66 67 1.380380 GCCTTCCCCCATCCAACAG 60.380 63.158 0.00 0.00 0.00 3.16
67 68 2.770130 GCCTTCCCCCATCCAACA 59.230 61.111 0.00 0.00 0.00 3.33
68 69 2.042944 GGCCTTCCCCCATCCAAC 60.043 66.667 0.00 0.00 0.00 3.77
69 70 1.526528 ATTGGCCTTCCCCCATCCAA 61.527 55.000 3.32 0.00 40.59 3.53
70 71 1.940742 ATTGGCCTTCCCCCATCCA 60.941 57.895 3.32 0.00 31.26 3.41
71 72 1.458209 CATTGGCCTTCCCCCATCC 60.458 63.158 3.32 0.00 31.26 3.51
72 73 1.044790 CACATTGGCCTTCCCCCATC 61.045 60.000 3.32 0.00 31.26 3.51
73 74 1.002017 CACATTGGCCTTCCCCCAT 59.998 57.895 3.32 0.00 31.26 4.00
74 75 2.439553 GACACATTGGCCTTCCCCCA 62.440 60.000 3.32 0.00 0.00 4.96
75 76 1.682344 GACACATTGGCCTTCCCCC 60.682 63.158 3.32 0.00 0.00 5.40
76 77 1.076549 TGACACATTGGCCTTCCCC 59.923 57.895 3.32 0.00 0.00 4.81
77 78 1.250840 GGTGACACATTGGCCTTCCC 61.251 60.000 3.32 0.00 0.00 3.97
78 79 1.586154 CGGTGACACATTGGCCTTCC 61.586 60.000 3.32 0.00 0.00 3.46
79 80 0.605319 TCGGTGACACATTGGCCTTC 60.605 55.000 3.32 0.00 0.00 3.46
80 81 0.889186 GTCGGTGACACATTGGCCTT 60.889 55.000 3.32 0.00 32.09 4.35
81 82 1.302511 GTCGGTGACACATTGGCCT 60.303 57.895 3.32 0.00 32.09 5.19
82 83 2.332654 GGTCGGTGACACATTGGCC 61.333 63.158 8.08 0.00 33.68 5.36
83 84 1.577328 CTGGTCGGTGACACATTGGC 61.577 60.000 8.08 0.00 33.68 4.52
84 85 1.577328 GCTGGTCGGTGACACATTGG 61.577 60.000 8.08 0.00 33.68 3.16
85 86 1.868997 GCTGGTCGGTGACACATTG 59.131 57.895 8.08 0.00 33.68 2.82
86 87 1.667830 CGCTGGTCGGTGACACATT 60.668 57.895 8.08 0.00 33.68 2.71
87 88 2.048222 CGCTGGTCGGTGACACAT 60.048 61.111 8.08 0.00 33.68 3.21
150 151 2.964438 TAGCCCTATTTGCGTCGGCG 62.964 60.000 4.29 4.29 44.56 6.46
151 152 0.812412 TTAGCCCTATTTGCGTCGGC 60.812 55.000 0.00 0.00 40.03 5.54
152 153 1.658994 TTTAGCCCTATTTGCGTCGG 58.341 50.000 0.00 0.00 0.00 4.79
153 154 3.750639 TTTTTAGCCCTATTTGCGTCG 57.249 42.857 0.00 0.00 0.00 5.12
170 171 2.592032 CCATTGCCGGCCCCTTTTT 61.592 57.895 26.77 0.00 0.00 1.94
171 172 3.002583 CCATTGCCGGCCCCTTTT 61.003 61.111 26.77 0.00 0.00 2.27
189 190 2.662527 TTTTCGTCCGCGGGTGAC 60.663 61.111 27.83 15.79 38.89 3.67
190 191 2.356553 CTTTTCGTCCGCGGGTGA 60.357 61.111 27.83 20.55 38.89 4.02
191 192 4.084888 GCTTTTCGTCCGCGGGTG 62.085 66.667 27.83 18.36 38.89 4.61
195 196 4.130281 GTCCGCTTTTCGTCCGCG 62.130 66.667 0.00 0.00 45.86 6.46
196 197 4.130281 CGTCCGCTTTTCGTCCGC 62.130 66.667 0.00 0.00 36.19 5.54
197 198 4.130281 GCGTCCGCTTTTCGTCCG 62.130 66.667 4.10 0.00 38.26 4.79
198 199 4.130281 CGCGTCCGCTTTTCGTCC 62.130 66.667 10.21 0.00 39.32 4.79
209 210 4.712873 CCAAACGAACGCGCGTCC 62.713 66.667 37.77 25.37 44.86 4.79
210 211 4.712873 CCCAAACGAACGCGCGTC 62.713 66.667 37.77 26.32 44.86 5.19
212 213 4.712873 GACCCAAACGAACGCGCG 62.713 66.667 30.96 30.96 42.48 6.86
213 214 4.712873 CGACCCAAACGAACGCGC 62.713 66.667 5.73 0.00 42.48 6.86
214 215 4.067016 CCGACCCAAACGAACGCG 62.067 66.667 3.53 3.53 44.79 6.01
215 216 4.379143 GCCGACCCAAACGAACGC 62.379 66.667 0.00 0.00 0.00 4.84
216 217 4.067016 CGCCGACCCAAACGAACG 62.067 66.667 0.00 0.00 0.00 3.95
217 218 4.379143 GCGCCGACCCAAACGAAC 62.379 66.667 0.00 0.00 0.00 3.95
221 222 4.676586 CAACGCGCCGACCCAAAC 62.677 66.667 5.73 0.00 0.00 2.93
247 248 2.127042 GATCGGCGCGCACAAAAA 60.127 55.556 34.42 11.07 0.00 1.94
248 249 4.096558 GGATCGGCGCGCACAAAA 62.097 61.111 34.42 13.00 0.00 2.44
252 253 2.430080 CTATTTGGATCGGCGCGCAC 62.430 60.000 34.42 20.89 0.00 5.34
253 254 2.202946 TATTTGGATCGGCGCGCA 60.203 55.556 34.42 14.59 0.00 6.09
254 255 1.954146 TCTATTTGGATCGGCGCGC 60.954 57.895 25.94 25.94 0.00 6.86
255 256 1.853319 GTCTATTTGGATCGGCGCG 59.147 57.895 0.00 0.00 0.00 6.86
256 257 1.853319 CGTCTATTTGGATCGGCGC 59.147 57.895 0.00 0.00 0.00 6.53
257 258 1.557443 GGCGTCTATTTGGATCGGCG 61.557 60.000 0.00 0.00 37.34 6.46
258 259 0.531974 TGGCGTCTATTTGGATCGGC 60.532 55.000 0.00 0.00 44.83 5.54
259 260 1.597663 GTTGGCGTCTATTTGGATCGG 59.402 52.381 0.00 0.00 0.00 4.18
260 261 1.257936 CGTTGGCGTCTATTTGGATCG 59.742 52.381 0.00 0.00 0.00 3.69
261 262 1.597663 CCGTTGGCGTCTATTTGGATC 59.402 52.381 0.00 0.00 36.15 3.36
262 263 1.208535 TCCGTTGGCGTCTATTTGGAT 59.791 47.619 0.00 0.00 36.15 3.41
263 264 0.609151 TCCGTTGGCGTCTATTTGGA 59.391 50.000 0.00 0.00 36.15 3.53
264 265 0.725117 GTCCGTTGGCGTCTATTTGG 59.275 55.000 0.00 0.00 36.15 3.28
265 266 0.368907 CGTCCGTTGGCGTCTATTTG 59.631 55.000 0.00 0.00 36.15 2.32
266 267 0.244450 TCGTCCGTTGGCGTCTATTT 59.756 50.000 0.00 0.00 36.15 1.40
267 268 0.244450 TTCGTCCGTTGGCGTCTATT 59.756 50.000 0.00 0.00 36.15 1.73
268 269 0.244450 TTTCGTCCGTTGGCGTCTAT 59.756 50.000 0.00 0.00 36.15 1.98
269 270 0.244450 ATTTCGTCCGTTGGCGTCTA 59.756 50.000 0.00 0.00 36.15 2.59
270 271 1.005394 ATTTCGTCCGTTGGCGTCT 60.005 52.632 0.00 0.00 36.15 4.18
271 272 1.131826 CATTTCGTCCGTTGGCGTC 59.868 57.895 0.00 0.00 36.15 5.19
272 273 2.322081 CCATTTCGTCCGTTGGCGT 61.322 57.895 0.00 0.00 36.15 5.68
273 274 2.478746 CCATTTCGTCCGTTGGCG 59.521 61.111 0.00 0.00 37.95 5.69
274 275 1.918868 GACCCATTTCGTCCGTTGGC 61.919 60.000 0.00 0.00 0.00 4.52
275 276 0.604243 TGACCCATTTCGTCCGTTGG 60.604 55.000 0.00 0.00 0.00 3.77
276 277 0.515564 GTGACCCATTTCGTCCGTTG 59.484 55.000 0.00 0.00 0.00 4.10
277 278 0.107081 TGTGACCCATTTCGTCCGTT 59.893 50.000 0.00 0.00 0.00 4.44
278 279 0.601841 GTGTGACCCATTTCGTCCGT 60.602 55.000 0.00 0.00 0.00 4.69
279 280 1.296056 GGTGTGACCCATTTCGTCCG 61.296 60.000 0.00 0.00 30.04 4.79
280 281 1.296056 CGGTGTGACCCATTTCGTCC 61.296 60.000 0.00 0.00 33.75 4.79
281 282 0.601841 ACGGTGTGACCCATTTCGTC 60.602 55.000 0.00 0.00 33.75 4.20
282 283 0.179040 AACGGTGTGACCCATTTCGT 60.179 50.000 0.00 0.00 33.75 3.85
283 284 0.237235 CAACGGTGTGACCCATTTCG 59.763 55.000 0.00 0.00 33.75 3.46
284 285 0.596082 CCAACGGTGTGACCCATTTC 59.404 55.000 0.00 0.00 33.75 2.17
285 286 0.183971 TCCAACGGTGTGACCCATTT 59.816 50.000 0.00 0.00 33.75 2.32
286 287 0.250727 CTCCAACGGTGTGACCCATT 60.251 55.000 0.00 0.00 33.75 3.16
287 288 1.374947 CTCCAACGGTGTGACCCAT 59.625 57.895 0.00 0.00 33.75 4.00
288 289 1.628238 AACTCCAACGGTGTGACCCA 61.628 55.000 0.00 0.00 33.75 4.51
289 290 1.147600 AACTCCAACGGTGTGACCC 59.852 57.895 0.00 0.00 33.75 4.46
290 291 1.782028 GCAACTCCAACGGTGTGACC 61.782 60.000 0.00 0.00 34.05 4.02
291 292 0.814010 AGCAACTCCAACGGTGTGAC 60.814 55.000 0.00 0.00 29.35 3.67
292 293 0.531974 GAGCAACTCCAACGGTGTGA 60.532 55.000 0.00 0.00 29.35 3.58
293 294 0.532862 AGAGCAACTCCAACGGTGTG 60.533 55.000 0.00 0.00 29.35 3.82
294 295 1.045407 TAGAGCAACTCCAACGGTGT 58.955 50.000 0.00 0.00 0.00 4.16
295 296 2.163818 TTAGAGCAACTCCAACGGTG 57.836 50.000 0.00 0.00 0.00 4.94
296 297 4.755266 ATATTAGAGCAACTCCAACGGT 57.245 40.909 0.00 0.00 0.00 4.83
297 298 5.465724 GGTAATATTAGAGCAACTCCAACGG 59.534 44.000 0.00 0.00 0.00 4.44
298 299 5.465724 GGGTAATATTAGAGCAACTCCAACG 59.534 44.000 0.00 0.00 0.00 4.10
299 300 6.592870 AGGGTAATATTAGAGCAACTCCAAC 58.407 40.000 0.00 0.00 0.00 3.77
300 301 6.385759 TGAGGGTAATATTAGAGCAACTCCAA 59.614 38.462 0.00 0.00 0.00 3.53
301 302 5.903010 TGAGGGTAATATTAGAGCAACTCCA 59.097 40.000 0.00 0.00 0.00 3.86
302 303 6.420913 TGAGGGTAATATTAGAGCAACTCC 57.579 41.667 0.00 0.00 0.00 3.85
303 304 7.445945 ACATGAGGGTAATATTAGAGCAACTC 58.554 38.462 0.00 0.00 0.00 3.01
304 305 7.380423 ACATGAGGGTAATATTAGAGCAACT 57.620 36.000 0.00 0.00 0.00 3.16
305 306 9.555727 TTTACATGAGGGTAATATTAGAGCAAC 57.444 33.333 0.00 0.00 33.56 4.17
319 320 8.950007 TTCCTCTTTTTATTTTACATGAGGGT 57.050 30.769 0.00 0.00 39.96 4.34
337 338 8.390354 CGCAAAAAGAAAAAGAAATTTCCTCTT 58.610 29.630 14.61 13.57 39.59 2.85
338 339 7.011389 CCGCAAAAAGAAAAAGAAATTTCCTCT 59.989 33.333 14.61 8.80 39.59 3.69
339 340 7.125755 CCGCAAAAAGAAAAAGAAATTTCCTC 58.874 34.615 14.61 6.79 39.59 3.71
340 341 6.038161 CCCGCAAAAAGAAAAAGAAATTTCCT 59.962 34.615 14.61 0.00 39.59 3.36
341 342 6.037720 TCCCGCAAAAAGAAAAAGAAATTTCC 59.962 34.615 14.61 0.00 39.59 3.13
342 343 7.010697 TCCCGCAAAAAGAAAAAGAAATTTC 57.989 32.000 10.33 10.33 39.16 2.17
343 344 6.993786 TCCCGCAAAAAGAAAAAGAAATTT 57.006 29.167 0.00 0.00 0.00 1.82
344 345 6.993786 TTCCCGCAAAAAGAAAAAGAAATT 57.006 29.167 0.00 0.00 0.00 1.82
345 346 6.993786 TTTCCCGCAAAAAGAAAAAGAAAT 57.006 29.167 0.00 0.00 0.00 2.17
346 347 6.803154 TTTTCCCGCAAAAAGAAAAAGAAA 57.197 29.167 0.00 0.00 36.75 2.52
347 348 6.803154 TTTTTCCCGCAAAAAGAAAAAGAA 57.197 29.167 5.93 0.00 41.87 2.52
500 502 3.306019 GGGCCAAGTAATGAACCACAAAG 60.306 47.826 4.39 0.00 0.00 2.77
532 534 8.413229 CAAGGTTCTTCAACAGGAATCTTTAAA 58.587 33.333 0.00 0.00 39.83 1.52
533 535 7.470009 GCAAGGTTCTTCAACAGGAATCTTTAA 60.470 37.037 0.00 0.00 39.83 1.52
536 538 4.279420 GCAAGGTTCTTCAACAGGAATCTT 59.721 41.667 0.00 0.00 41.72 2.40
543 546 2.886523 TGGATGCAAGGTTCTTCAACAG 59.113 45.455 0.00 0.00 33.70 3.16
545 548 4.320608 TTTGGATGCAAGGTTCTTCAAC 57.679 40.909 0.00 0.00 0.00 3.18
559 562 8.897752 TCAAAAACAAAAAGGGTTATTTGGATG 58.102 29.630 3.63 0.00 40.09 3.51
573 576 6.037281 GGTTTATTCCGGCTCAAAAACAAAAA 59.963 34.615 0.00 0.00 0.00 1.94
590 594 5.014202 TGGCTTACCAAGGAAGGTTTATTC 58.986 41.667 0.00 0.00 45.37 1.75
644 651 7.908827 ACAAATAAAAAGGGAACGTTTGTTT 57.091 28.000 0.46 0.00 46.19 2.83
677 697 9.765295 TCCTTTCTAGTAGGAATAGTACAAGTT 57.235 33.333 12.16 0.00 38.83 2.66
678 698 9.765295 TTCCTTTCTAGTAGGAATAGTACAAGT 57.235 33.333 18.89 0.00 44.72 3.16
688 708 4.431158 ACCCCTTCCTTTCTAGTAGGAA 57.569 45.455 20.49 20.49 46.77 3.36
689 709 4.101856 CAACCCCTTCCTTTCTAGTAGGA 58.898 47.826 10.95 10.95 40.01 2.94
690 710 3.370633 GCAACCCCTTCCTTTCTAGTAGG 60.371 52.174 7.18 7.18 0.00 3.18
694 714 1.278127 TCGCAACCCCTTCCTTTCTAG 59.722 52.381 0.00 0.00 0.00 2.43
712 739 0.857935 GCAGAAATCGGATCAGCTCG 59.142 55.000 0.00 0.00 0.00 5.03
822 850 2.660802 GACGGTTGGATCGGTGGT 59.339 61.111 0.00 0.00 0.00 4.16
927 2038 1.125093 TTTGAGAAGGCGGGAGTGGA 61.125 55.000 0.00 0.00 0.00 4.02
1365 2535 1.984026 GGGGTTGATGTTGGGCAGG 60.984 63.158 0.00 0.00 0.00 4.85
1425 2629 3.567579 CTTGGCGGCCTTCTTGGGA 62.568 63.158 21.46 0.00 36.00 4.37
1463 2760 7.904558 ATCAGGAATCACTAGACAGTAATCA 57.095 36.000 0.00 0.00 32.21 2.57
1526 2836 6.732531 TTTCTCAGCAGAACAGAACATATG 57.267 37.500 0.00 0.00 38.44 1.78
1589 2905 8.571461 AAATCATGAACACACAGATAACAGAT 57.429 30.769 0.00 0.00 0.00 2.90
1602 2924 3.645884 AGCACTGCAAAATCATGAACAC 58.354 40.909 0.00 0.00 0.00 3.32
1670 3379 5.625311 GGTGAATTTGTCAGATTCAAACGAC 59.375 40.000 17.74 7.46 43.06 4.34
1757 3480 7.822334 TGACAGGTAAAATACAGGTTGAGTATG 59.178 37.037 0.00 0.00 32.78 2.39
1762 3485 4.992319 CGTGACAGGTAAAATACAGGTTGA 59.008 41.667 0.00 0.00 0.00 3.18
1842 3588 7.603651 ACAACCAACTATGTACTCTACAGAAG 58.396 38.462 0.00 0.00 42.77 2.85
1846 3592 5.620654 GCGACAACCAACTATGTACTCTACA 60.621 44.000 0.00 0.00 43.80 2.74
1847 3593 4.797349 GCGACAACCAACTATGTACTCTAC 59.203 45.833 0.00 0.00 0.00 2.59
1848 3594 4.142315 GGCGACAACCAACTATGTACTCTA 60.142 45.833 0.00 0.00 0.00 2.43
1849 3595 3.368116 GGCGACAACCAACTATGTACTCT 60.368 47.826 0.00 0.00 0.00 3.24
1850 3596 2.928116 GGCGACAACCAACTATGTACTC 59.072 50.000 0.00 0.00 0.00 2.59
1851 3597 2.354403 GGGCGACAACCAACTATGTACT 60.354 50.000 0.00 0.00 0.00 2.73
1853 3599 1.624312 TGGGCGACAACCAACTATGTA 59.376 47.619 0.00 0.00 34.44 2.29
1854 3600 0.398696 TGGGCGACAACCAACTATGT 59.601 50.000 0.00 0.00 34.44 2.29
1855 3601 1.529226 TTGGGCGACAACCAACTATG 58.471 50.000 0.00 0.00 42.75 2.23
1896 3689 9.273016 GGCAACATAATGTAGTACTATCATGTT 57.727 33.333 18.70 18.70 36.17 2.71
1897 3690 8.651389 AGGCAACATAATGTAGTACTATCATGT 58.349 33.333 5.75 10.02 41.41 3.21
1898 3691 8.929746 CAGGCAACATAATGTAGTACTATCATG 58.070 37.037 5.75 9.46 41.41 3.07
1899 3692 8.870116 TCAGGCAACATAATGTAGTACTATCAT 58.130 33.333 5.75 8.69 41.41 2.45
1900 3693 8.245195 TCAGGCAACATAATGTAGTACTATCA 57.755 34.615 5.75 6.74 41.41 2.15
1901 3694 9.144747 CATCAGGCAACATAATGTAGTACTATC 57.855 37.037 5.75 1.02 41.41 2.08
1902 3695 8.097038 CCATCAGGCAACATAATGTAGTACTAT 58.903 37.037 5.75 0.00 41.41 2.12
1903 3696 7.441836 CCATCAGGCAACATAATGTAGTACTA 58.558 38.462 0.00 0.00 41.41 1.82
1904 3697 6.291377 CCATCAGGCAACATAATGTAGTACT 58.709 40.000 0.00 0.00 41.41 2.73
1905 3698 6.545504 CCATCAGGCAACATAATGTAGTAC 57.454 41.667 0.00 0.00 41.41 2.73
1918 3711 6.921308 TGAACTTATTCCGCCATCAGGCAA 62.921 45.833 7.34 0.00 46.54 4.52
1919 3712 5.513768 TGAACTTATTCCGCCATCAGGCA 62.514 47.826 7.34 0.00 46.54 4.75
1920 3713 3.004849 TGAACTTATTCCGCCATCAGGC 61.005 50.000 0.00 0.00 43.51 4.85
1921 3714 2.874701 CTGAACTTATTCCGCCATCAGG 59.125 50.000 0.00 0.00 33.49 3.86
1922 3715 3.535561 ACTGAACTTATTCCGCCATCAG 58.464 45.455 0.00 0.00 38.91 2.90
1923 3716 3.627395 ACTGAACTTATTCCGCCATCA 57.373 42.857 0.00 0.00 33.49 3.07
1924 3717 3.487544 GCAACTGAACTTATTCCGCCATC 60.488 47.826 0.00 0.00 33.49 3.51
1925 3718 2.423538 GCAACTGAACTTATTCCGCCAT 59.576 45.455 0.00 0.00 33.49 4.40
1926 3719 1.810151 GCAACTGAACTTATTCCGCCA 59.190 47.619 0.00 0.00 33.49 5.69
1927 3720 1.810151 TGCAACTGAACTTATTCCGCC 59.190 47.619 0.00 0.00 33.49 6.13
1928 3721 2.225491 TGTGCAACTGAACTTATTCCGC 59.775 45.455 0.00 0.00 38.04 5.54
1929 3722 3.498397 AGTGTGCAACTGAACTTATTCCG 59.502 43.478 0.00 0.00 37.88 4.30
1930 3723 5.239525 AGAAGTGTGCAACTGAACTTATTCC 59.760 40.000 0.00 0.00 39.81 3.01
1934 3727 4.765273 TCAGAAGTGTGCAACTGAACTTA 58.235 39.130 0.00 0.00 39.81 2.24
1950 3743 6.199719 GGTTTTCTCTGCATTTGTTTCAGAAG 59.800 38.462 0.00 0.00 36.54 2.85
1951 3744 6.042143 GGTTTTCTCTGCATTTGTTTCAGAA 58.958 36.000 0.00 0.00 36.54 3.02
2084 3882 9.221775 GCTGATTTTTATAATTAGTGTGGTTCG 57.778 33.333 0.00 0.00 0.00 3.95
2113 3911 5.118286 TGGCAACTATCATGTGTGTATCAG 58.882 41.667 0.00 0.00 37.61 2.90
2129 3927 6.183347 AGTTTGAGCTATCTATTTGGCAACT 58.817 36.000 0.00 0.00 37.61 3.16
2153 3951 8.777578 TCTAGCCCTGAATATAAACTACTGAA 57.222 34.615 0.00 0.00 0.00 3.02
2154 3952 8.958060 ATCTAGCCCTGAATATAAACTACTGA 57.042 34.615 0.00 0.00 0.00 3.41
2158 3956 9.702253 CCTCTATCTAGCCCTGAATATAAACTA 57.298 37.037 0.00 0.00 0.00 2.24
2160 3958 8.596781 TCCTCTATCTAGCCCTGAATATAAAC 57.403 38.462 0.00 0.00 0.00 2.01
2161 3959 8.402683 ACTCCTCTATCTAGCCCTGAATATAAA 58.597 37.037 0.00 0.00 0.00 1.40
2162 3960 7.945278 ACTCCTCTATCTAGCCCTGAATATAA 58.055 38.462 0.00 0.00 0.00 0.98
2163 3961 7.532459 ACTCCTCTATCTAGCCCTGAATATA 57.468 40.000 0.00 0.00 0.00 0.86
2239 4037 3.431856 CAATGACCATTTGCGACATCAG 58.568 45.455 0.00 0.00 0.00 2.90
2259 4057 2.554344 GGGACACTAAAACAGGGATGCA 60.554 50.000 0.00 0.00 0.00 3.96
2316 4114 5.052693 TGGATCCATTTGACCCTTATCAG 57.947 43.478 11.44 0.00 0.00 2.90
2332 4130 7.225341 GCCATCTTAATTGTTCAAAATGGATCC 59.775 37.037 4.20 4.20 35.50 3.36
2335 4133 7.002250 TGCCATCTTAATTGTTCAAAATGGA 57.998 32.000 0.00 3.22 35.50 3.41
2343 4142 6.034898 CACCGAATTTGCCATCTTAATTGTTC 59.965 38.462 0.00 0.00 0.00 3.18
2375 4174 8.313944 TGTATAGGACCTTGTTTCTAGCATAA 57.686 34.615 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.