Multiple sequence alignment - TraesCS7A01G090600

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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 TraesCS7A01G090600 chr7A 100.000 2386 0 0 1 2386 55162365 55159980 0.000000e+00 4407.0
1 TraesCS7A01G090600 chr7D 88.649 696 54 13 1704 2386 52947629 52948312 0.000000e+00 824.0
2 TraesCS7A01G090600 chr7D 85.283 795 59 40 301 1068 52945349 52946112 0.000000e+00 767.0
3 TraesCS7A01G090600 chr7D 90.559 572 46 6 1103 1672 52946194 52946759 0.000000e+00 750.0
4 TraesCS7A01G090600 chr4A 86.245 727 45 36 367 1068 667691838 667691142 0.000000e+00 737.0
5 TraesCS7A01G090600 chr4A 92.194 474 30 5 1076 1547 667691102 667690634 0.000000e+00 664.0
6 TraesCS7A01G090600 chr4A 88.186 237 17 7 2154 2386 667689177 667688948 3.020000e-69 272.0
7 TraesCS7A01G090600 chr6A 97.778 45 1 0 1623 1667 2218247 2218203 7.070000e-11 78.7
8 TraesCS7A01G090600 chr3A 95.652 46 2 0 1622 1667 53027995 53028040 9.150000e-10 75.0
9 TraesCS7A01G090600 chr3A 85.915 71 6 3 1597 1667 750297116 750297182 3.290000e-09 73.1
10 TraesCS7A01G090600 chr7B 85.915 71 7 2 1597 1667 414314563 414314496 3.290000e-09 73.1
11 TraesCS7A01G090600 chr5B 85.915 71 7 2 1597 1667 148556977 148557044 3.290000e-09 73.1
12 TraesCS7A01G090600 chr4B 90.741 54 4 1 1624 1677 598457039 598456987 1.180000e-08 71.3
13 TraesCS7A01G090600 chr1A 85.714 70 6 3 1598 1667 584082921 584082856 1.180000e-08 71.3
14 TraesCS7A01G090600 chr3D 86.364 66 6 3 1605 1667 71371543 71371478 4.260000e-08 69.4


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 TraesCS7A01G090600 chr7A 55159980 55162365 2385 True 4407.000000 4407 100.000000 1 2386 1 chr7A.!!$R1 2385
1 TraesCS7A01G090600 chr7D 52945349 52948312 2963 False 780.333333 824 88.163667 301 2386 3 chr7D.!!$F1 2085
2 TraesCS7A01G090600 chr4A 667688948 667691838 2890 True 557.666667 737 88.875000 367 2386 3 chr4A.!!$R1 2019

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
193 194 0.036952 CCGGACACACTCATCTGCTT 60.037 55.0 0.00 0.0 0.0 3.91 F
261 262 0.037232 AAGCACTCCCTCTGTAACGC 60.037 55.0 0.00 0.0 0.0 4.84 F
358 359 0.106918 TGAGAAAACAACCGGTGGCT 60.107 50.0 8.52 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1070 1118 0.302890 GCGTGCGAAAGGATCATCAG 59.697 55.000 0.0 0.0 0.00 2.90 R
1273 1369 0.539438 TGGCAAGGAACACATCACCC 60.539 55.000 0.0 0.0 0.00 4.61 R
1900 2850 1.153005 GATCCTGGCTTCTGGGCTG 60.153 63.158 0.0 0.0 41.48 4.85 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
41 42 9.615295 TTTTAATTATTGTAAGTGGACTTTCGC 57.385 29.630 0.00 0.00 37.40 4.70
42 43 5.813080 ATTATTGTAAGTGGACTTTCGCC 57.187 39.130 0.00 0.00 37.40 5.54
43 44 1.504359 TTGTAAGTGGACTTTCGCCG 58.496 50.000 0.00 0.00 37.40 6.46
44 45 0.320073 TGTAAGTGGACTTTCGCCGG 60.320 55.000 0.00 0.00 37.40 6.13
45 46 0.320160 GTAAGTGGACTTTCGCCGGT 60.320 55.000 1.90 0.00 37.40 5.28
46 47 0.320073 TAAGTGGACTTTCGCCGGTG 60.320 55.000 9.28 9.28 37.40 4.94
47 48 2.280592 GTGGACTTTCGCCGGTGT 60.281 61.111 16.01 0.00 0.00 4.16
48 49 1.890510 GTGGACTTTCGCCGGTGTT 60.891 57.895 16.01 0.00 0.00 3.32
49 50 1.153127 TGGACTTTCGCCGGTGTTT 60.153 52.632 16.01 0.00 0.00 2.83
50 51 0.106335 TGGACTTTCGCCGGTGTTTA 59.894 50.000 16.01 0.00 0.00 2.01
51 52 0.794473 GGACTTTCGCCGGTGTTTAG 59.206 55.000 16.01 12.75 0.00 1.85
52 53 1.505425 GACTTTCGCCGGTGTTTAGT 58.495 50.000 16.01 15.77 0.00 2.24
53 54 1.869132 GACTTTCGCCGGTGTTTAGTT 59.131 47.619 16.01 2.52 0.00 2.24
54 55 3.059166 GACTTTCGCCGGTGTTTAGTTA 58.941 45.455 16.01 0.00 0.00 2.24
55 56 3.667360 ACTTTCGCCGGTGTTTAGTTAT 58.333 40.909 16.01 0.00 0.00 1.89
56 57 4.067192 ACTTTCGCCGGTGTTTAGTTATT 58.933 39.130 16.01 0.00 0.00 1.40
57 58 4.083696 ACTTTCGCCGGTGTTTAGTTATTG 60.084 41.667 16.01 0.00 0.00 1.90
58 59 3.042871 TCGCCGGTGTTTAGTTATTGT 57.957 42.857 16.01 0.00 0.00 2.71
59 60 4.185467 TCGCCGGTGTTTAGTTATTGTA 57.815 40.909 16.01 0.00 0.00 2.41
60 61 4.564041 TCGCCGGTGTTTAGTTATTGTAA 58.436 39.130 16.01 0.00 0.00 2.41
61 62 4.993584 TCGCCGGTGTTTAGTTATTGTAAA 59.006 37.500 16.01 0.00 0.00 2.01
62 63 5.120519 TCGCCGGTGTTTAGTTATTGTAAAG 59.879 40.000 16.01 0.00 0.00 1.85
63 64 5.106987 CGCCGGTGTTTAGTTATTGTAAAGT 60.107 40.000 6.91 0.00 0.00 2.66
64 65 6.309436 GCCGGTGTTTAGTTATTGTAAAGTC 58.691 40.000 1.90 0.00 0.00 3.01
65 66 6.148315 GCCGGTGTTTAGTTATTGTAAAGTCT 59.852 38.462 1.90 0.00 0.00 3.24
66 67 7.308169 GCCGGTGTTTAGTTATTGTAAAGTCTT 60.308 37.037 1.90 0.00 0.00 3.01
67 68 9.206870 CCGGTGTTTAGTTATTGTAAAGTCTTA 57.793 33.333 0.00 0.00 0.00 2.10
113 114 9.834628 TCTTTCTATTATTTTTGTGGCTAAACG 57.165 29.630 0.00 0.00 0.00 3.60
114 115 8.973835 TTTCTATTATTTTTGTGGCTAAACGG 57.026 30.769 0.00 0.00 0.00 4.44
115 116 7.090953 TCTATTATTTTTGTGGCTAAACGGG 57.909 36.000 0.00 0.00 0.00 5.28
116 117 5.731957 ATTATTTTTGTGGCTAAACGGGT 57.268 34.783 0.00 0.00 0.00 5.28
117 118 2.873133 TTTTTGTGGCTAAACGGGTG 57.127 45.000 0.00 0.00 0.00 4.61
118 119 2.054232 TTTTGTGGCTAAACGGGTGA 57.946 45.000 0.00 0.00 0.00 4.02
119 120 1.600023 TTTGTGGCTAAACGGGTGAG 58.400 50.000 0.00 0.00 0.00 3.51
120 121 0.887387 TTGTGGCTAAACGGGTGAGC 60.887 55.000 0.00 0.00 35.39 4.26
121 122 1.302192 GTGGCTAAACGGGTGAGCA 60.302 57.895 4.45 0.00 37.98 4.26
122 123 1.302192 TGGCTAAACGGGTGAGCAC 60.302 57.895 4.45 0.00 37.98 4.40
132 133 4.539152 GTGAGCACGCACCAAATG 57.461 55.556 0.00 0.00 32.68 2.32
141 142 4.798288 CACCAAATGCATCAGCCG 57.202 55.556 0.00 0.00 41.13 5.52
142 143 1.517694 CACCAAATGCATCAGCCGC 60.518 57.895 0.00 0.00 41.13 6.53
143 144 2.278336 CCAAATGCATCAGCCGCG 60.278 61.111 0.00 0.00 41.13 6.46
144 145 2.486504 CAAATGCATCAGCCGCGT 59.513 55.556 4.92 0.00 41.13 6.01
145 146 1.153978 CAAATGCATCAGCCGCGTT 60.154 52.632 4.92 0.00 40.26 4.84
146 147 1.153978 AAATGCATCAGCCGCGTTG 60.154 52.632 4.92 3.06 38.57 4.10
147 148 2.546645 AAATGCATCAGCCGCGTTGG 62.547 55.000 4.92 0.00 38.57 3.77
168 169 3.309582 CACCTATGCTCCCACGGT 58.690 61.111 0.00 0.00 0.00 4.83
169 170 1.144057 CACCTATGCTCCCACGGTC 59.856 63.158 0.00 0.00 0.00 4.79
170 171 1.305802 ACCTATGCTCCCACGGTCA 60.306 57.895 0.00 0.00 0.00 4.02
171 172 0.907704 ACCTATGCTCCCACGGTCAA 60.908 55.000 0.00 0.00 0.00 3.18
172 173 0.251916 CCTATGCTCCCACGGTCAAA 59.748 55.000 0.00 0.00 0.00 2.69
173 174 1.339631 CCTATGCTCCCACGGTCAAAA 60.340 52.381 0.00 0.00 0.00 2.44
174 175 1.737793 CTATGCTCCCACGGTCAAAAC 59.262 52.381 0.00 0.00 0.00 2.43
175 176 0.893727 ATGCTCCCACGGTCAAAACC 60.894 55.000 0.00 0.00 42.66 3.27
184 185 3.089788 GGTCAAAACCGGACACACT 57.910 52.632 9.46 0.00 37.00 3.55
185 186 0.942252 GGTCAAAACCGGACACACTC 59.058 55.000 9.46 0.00 37.00 3.51
186 187 1.658994 GTCAAAACCGGACACACTCA 58.341 50.000 9.46 0.00 35.36 3.41
187 188 2.218603 GTCAAAACCGGACACACTCAT 58.781 47.619 9.46 0.00 35.36 2.90
188 189 2.223377 GTCAAAACCGGACACACTCATC 59.777 50.000 9.46 0.00 35.36 2.92
189 190 2.104111 TCAAAACCGGACACACTCATCT 59.896 45.455 9.46 0.00 0.00 2.90
190 191 2.169832 AAACCGGACACACTCATCTG 57.830 50.000 9.46 0.00 0.00 2.90
191 192 0.320771 AACCGGACACACTCATCTGC 60.321 55.000 9.46 0.00 0.00 4.26
192 193 1.188219 ACCGGACACACTCATCTGCT 61.188 55.000 9.46 0.00 0.00 4.24
193 194 0.036952 CCGGACACACTCATCTGCTT 60.037 55.000 0.00 0.00 0.00 3.91
194 195 1.354040 CGGACACACTCATCTGCTTC 58.646 55.000 0.00 0.00 0.00 3.86
195 196 1.731720 GGACACACTCATCTGCTTCC 58.268 55.000 0.00 0.00 0.00 3.46
196 197 1.002430 GGACACACTCATCTGCTTCCA 59.998 52.381 0.00 0.00 0.00 3.53
197 198 2.550855 GGACACACTCATCTGCTTCCAA 60.551 50.000 0.00 0.00 0.00 3.53
198 199 3.141398 GACACACTCATCTGCTTCCAAA 58.859 45.455 0.00 0.00 0.00 3.28
199 200 3.554934 ACACACTCATCTGCTTCCAAAA 58.445 40.909 0.00 0.00 0.00 2.44
200 201 3.316308 ACACACTCATCTGCTTCCAAAAC 59.684 43.478 0.00 0.00 0.00 2.43
201 202 3.316029 CACACTCATCTGCTTCCAAAACA 59.684 43.478 0.00 0.00 0.00 2.83
202 203 3.567164 ACACTCATCTGCTTCCAAAACAG 59.433 43.478 0.00 0.00 0.00 3.16
203 204 3.817084 CACTCATCTGCTTCCAAAACAGA 59.183 43.478 0.00 0.00 44.06 3.41
204 205 3.817647 ACTCATCTGCTTCCAAAACAGAC 59.182 43.478 0.00 0.00 42.83 3.51
205 206 3.817084 CTCATCTGCTTCCAAAACAGACA 59.183 43.478 0.00 0.00 42.83 3.41
206 207 4.206375 TCATCTGCTTCCAAAACAGACAA 58.794 39.130 0.00 0.00 42.83 3.18
207 208 4.644234 TCATCTGCTTCCAAAACAGACAAA 59.356 37.500 0.00 0.00 42.83 2.83
208 209 5.126869 TCATCTGCTTCCAAAACAGACAAAA 59.873 36.000 0.00 0.00 42.83 2.44
209 210 5.398603 TCTGCTTCCAAAACAGACAAAAA 57.601 34.783 0.00 0.00 35.58 1.94
228 229 4.522722 AAAAAGACAAAAACCACGTCCA 57.477 36.364 0.00 0.00 0.00 4.02
229 230 4.729227 AAAAGACAAAAACCACGTCCAT 57.271 36.364 0.00 0.00 0.00 3.41
230 231 4.729227 AAAGACAAAAACCACGTCCATT 57.271 36.364 0.00 0.00 0.00 3.16
231 232 3.982576 AGACAAAAACCACGTCCATTC 57.017 42.857 0.00 0.00 0.00 2.67
232 233 2.289547 AGACAAAAACCACGTCCATTCG 59.710 45.455 0.00 0.00 0.00 3.34
233 234 1.335496 ACAAAAACCACGTCCATTCGG 59.665 47.619 0.00 0.00 34.94 4.30
234 235 0.312729 AAAAACCACGTCCATTCGGC 59.687 50.000 0.00 0.00 34.94 5.54
235 236 0.536460 AAAACCACGTCCATTCGGCT 60.536 50.000 0.00 0.00 34.94 5.52
236 237 1.234615 AAACCACGTCCATTCGGCTG 61.235 55.000 0.00 0.00 34.94 4.85
237 238 2.819595 CCACGTCCATTCGGCTGG 60.820 66.667 0.00 0.00 37.66 4.85
238 239 2.819595 CACGTCCATTCGGCTGGG 60.820 66.667 0.00 0.00 36.89 4.45
239 240 4.778143 ACGTCCATTCGGCTGGGC 62.778 66.667 0.00 2.04 37.56 5.36
249 250 2.124529 GGCTGGGCCTAAGCACTC 60.125 66.667 25.75 10.40 45.43 3.51
250 251 2.124529 GCTGGGCCTAAGCACTCC 60.125 66.667 21.57 0.00 45.43 3.85
251 252 2.592308 CTGGGCCTAAGCACTCCC 59.408 66.667 4.53 0.00 45.43 4.30
252 253 1.997874 CTGGGCCTAAGCACTCCCT 60.998 63.158 4.53 0.00 45.43 4.20
253 254 1.977293 CTGGGCCTAAGCACTCCCTC 61.977 65.000 4.53 0.00 45.43 4.30
254 255 1.690985 GGGCCTAAGCACTCCCTCT 60.691 63.158 0.84 0.00 40.27 3.69
255 256 1.524482 GGCCTAAGCACTCCCTCTG 59.476 63.158 0.00 0.00 42.56 3.35
256 257 1.268283 GGCCTAAGCACTCCCTCTGT 61.268 60.000 0.00 0.00 42.56 3.41
257 258 1.486211 GCCTAAGCACTCCCTCTGTA 58.514 55.000 0.00 0.00 39.53 2.74
258 259 1.831736 GCCTAAGCACTCCCTCTGTAA 59.168 52.381 0.00 0.00 39.53 2.41
259 260 2.418884 GCCTAAGCACTCCCTCTGTAAC 60.419 54.545 0.00 0.00 39.53 2.50
260 261 2.159226 CCTAAGCACTCCCTCTGTAACG 60.159 54.545 0.00 0.00 0.00 3.18
261 262 0.037232 AAGCACTCCCTCTGTAACGC 60.037 55.000 0.00 0.00 0.00 4.84
262 263 1.185618 AGCACTCCCTCTGTAACGCA 61.186 55.000 0.00 0.00 0.00 5.24
263 264 0.320421 GCACTCCCTCTGTAACGCAA 60.320 55.000 0.00 0.00 0.00 4.85
264 265 1.876416 GCACTCCCTCTGTAACGCAAA 60.876 52.381 0.00 0.00 0.00 3.68
265 266 1.798813 CACTCCCTCTGTAACGCAAAC 59.201 52.381 0.00 0.00 0.00 2.93
334 335 3.469863 AAGAACACCCGCTTGCCGA 62.470 57.895 0.00 0.00 40.02 5.54
353 354 1.602377 GACCAGTGAGAAAACAACCGG 59.398 52.381 0.00 0.00 0.00 5.28
358 359 0.106918 TGAGAAAACAACCGGTGGCT 60.107 50.000 8.52 0.00 0.00 4.75
360 361 1.407618 GAGAAAACAACCGGTGGCTTT 59.592 47.619 8.52 9.51 0.00 3.51
361 362 2.619646 GAGAAAACAACCGGTGGCTTTA 59.380 45.455 8.52 0.00 0.00 1.85
362 363 2.359848 AGAAAACAACCGGTGGCTTTAC 59.640 45.455 8.52 3.61 0.00 2.01
363 364 1.034356 AAACAACCGGTGGCTTTACC 58.966 50.000 8.52 0.00 37.37 2.85
376 385 0.937304 CTTTACCATCCGGATGCACG 59.063 55.000 34.77 24.50 37.49 5.34
385 394 1.442520 CGGATGCACGCAAACTTGG 60.443 57.895 0.00 0.00 0.00 3.61
386 395 1.851021 CGGATGCACGCAAACTTGGA 61.851 55.000 0.00 0.00 0.00 3.53
387 396 0.313672 GGATGCACGCAAACTTGGAA 59.686 50.000 0.00 0.00 0.00 3.53
388 397 1.666888 GGATGCACGCAAACTTGGAAG 60.667 52.381 0.00 0.00 0.00 3.46
407 417 1.767759 GCATGGGCTGGTTATTCAGT 58.232 50.000 0.00 0.00 37.12 3.41
417 427 4.636206 GCTGGTTATTCAGTCCCTAACTTG 59.364 45.833 0.00 0.00 35.45 3.16
422 436 6.713450 GGTTATTCAGTCCCTAACTTGAAACA 59.287 38.462 0.00 0.00 35.45 2.83
425 439 5.560722 TCAGTCCCTAACTTGAAACATGA 57.439 39.130 0.00 0.00 35.45 3.07
426 440 6.126863 TCAGTCCCTAACTTGAAACATGAT 57.873 37.500 0.00 0.00 35.45 2.45
446 460 0.758734 TGTGGTAGCTGAGTTGCACT 59.241 50.000 0.00 0.00 34.99 4.40
447 461 1.140852 TGTGGTAGCTGAGTTGCACTT 59.859 47.619 0.00 0.00 34.99 3.16
448 462 1.532868 GTGGTAGCTGAGTTGCACTTG 59.467 52.381 0.00 0.00 34.99 3.16
449 463 0.519077 GGTAGCTGAGTTGCACTTGC 59.481 55.000 0.00 0.00 42.50 4.01
461 475 1.237285 GCACTTGCACGAAGGGATGT 61.237 55.000 0.00 0.00 37.23 3.06
483 497 1.666553 GTTGCCACGACGACCATGA 60.667 57.895 0.00 0.00 0.00 3.07
493 507 2.664151 CGACGACCATGAGATGATCGAG 60.664 54.545 7.33 0.00 36.64 4.04
494 508 1.000827 ACGACCATGAGATGATCGAGC 60.001 52.381 7.33 0.00 36.64 5.03
583 603 1.750778 CTGCACCCACAAGTCAAAACT 59.249 47.619 0.00 0.00 37.32 2.66
586 606 2.427095 GCACCCACAAGTCAAAACTTCT 59.573 45.455 0.00 0.00 43.99 2.85
623 644 0.878416 AACACACACACCACACACAC 59.122 50.000 0.00 0.00 0.00 3.82
624 645 0.250510 ACACACACACCACACACACA 60.251 50.000 0.00 0.00 0.00 3.72
625 646 0.167908 CACACACACCACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
626 647 0.250510 ACACACACCACACACACACA 60.251 50.000 0.00 0.00 0.00 3.72
627 648 0.167908 CACACACCACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
685 706 5.888161 CCTAGCTTTCTCTCTCTCTTTCTCT 59.112 44.000 0.00 0.00 0.00 3.10
686 707 5.904362 AGCTTTCTCTCTCTCTTTCTCTC 57.096 43.478 0.00 0.00 0.00 3.20
703 724 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
708 729 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
721 742 5.596361 TCTCTCTCTCTCTCTCTCTCTCTTC 59.404 48.000 0.00 0.00 0.00 2.87
726 747 6.881065 TCTCTCTCTCTCTCTCTCTTCTTTTG 59.119 42.308 0.00 0.00 0.00 2.44
727 755 6.778821 TCTCTCTCTCTCTCTCTTCTTTTGA 58.221 40.000 0.00 0.00 0.00 2.69
785 813 2.731572 CGACCCTTCTACCAACCTAGA 58.268 52.381 0.00 0.00 0.00 2.43
792 820 6.137559 CCCTTCTACCAACCTAGATAGTCTT 58.862 44.000 0.00 0.00 0.00 3.01
793 821 6.612049 CCCTTCTACCAACCTAGATAGTCTTT 59.388 42.308 0.00 0.00 0.00 2.52
806 836 6.611613 AGATAGTCTTTTGTCATGGACTCA 57.388 37.500 3.68 0.00 39.39 3.41
809 839 3.072184 AGTCTTTTGTCATGGACTCAGCT 59.928 43.478 0.00 0.00 34.44 4.24
842 872 2.126189 GTGTAGGGCCGTGACGTC 60.126 66.667 9.11 9.11 0.00 4.34
882 912 0.825840 GCCGCCTATAAAATGCCCCA 60.826 55.000 0.00 0.00 0.00 4.96
901 931 4.082408 CCCCATATGCATATCAAGTTGCTG 60.082 45.833 16.46 3.89 39.60 4.41
966 998 0.859788 CGTCGTTGTTTGTGGTGCAC 60.860 55.000 8.80 8.80 34.56 4.57
988 1020 0.525761 ACTGTTGCGTGCACAGTTTT 59.474 45.000 18.64 0.00 41.36 2.43
993 1025 2.397777 TGCGTGCACAGTTTTGTATG 57.602 45.000 18.64 0.00 35.25 2.39
998 1030 3.479006 GTGCACAGTTTTGTATGTAGCG 58.521 45.455 13.17 0.00 35.25 4.26
1068 1116 4.321378 GGGGTTAACAAAGGTACGTACGTA 60.321 45.833 23.60 23.60 0.00 3.57
1069 1117 5.224135 GGGTTAACAAAGGTACGTACGTAA 58.776 41.667 28.34 9.87 31.86 3.18
1070 1118 5.118050 GGGTTAACAAAGGTACGTACGTAAC 59.882 44.000 31.26 31.26 38.50 2.50
1072 1120 6.129194 GGTTAACAAAGGTACGTACGTAACTG 60.129 42.308 38.57 30.51 46.74 3.16
1073 1121 4.829064 ACAAAGGTACGTACGTAACTGA 57.171 40.909 38.57 14.93 46.74 3.41
1074 1122 5.376854 ACAAAGGTACGTACGTAACTGAT 57.623 39.130 38.57 28.91 46.74 2.90
1124 1219 2.163412 GCATGGAATTAACAAGCGGTGA 59.837 45.455 0.00 0.00 0.00 4.02
1171 1266 1.672363 TGCTCTGTGTGTTTTCTGCAG 59.328 47.619 7.63 7.63 0.00 4.41
1192 1288 2.024414 GGGTTCCAACTGATGTATGCC 58.976 52.381 0.00 0.00 0.00 4.40
1226 1322 4.230314 CATATATGCCTCGGATCCTACG 57.770 50.000 10.75 0.00 0.00 3.51
1249 1345 3.441222 TGCAGCAGGTCTTTGAATATGTG 59.559 43.478 0.00 0.00 0.00 3.21
1255 1351 9.710900 CAGCAGGTCTTTGAATATGTGTATATA 57.289 33.333 0.00 0.00 0.00 0.86
1292 1388 0.539438 GGGTGATGTGTTCCTTGCCA 60.539 55.000 0.00 0.00 0.00 4.92
1315 1411 3.181451 TGATCTTTGTCAGGTGAGCAGTT 60.181 43.478 0.00 0.00 0.00 3.16
1335 1431 1.945354 CTTCGCTGTTCCGGCCTCTA 61.945 60.000 0.00 0.00 31.00 2.43
1412 1508 3.059884 TGTGAGCGAAGATGAACTTGTC 58.940 45.455 0.00 0.00 39.13 3.18
1450 1546 4.422840 CATGACAACTGCACAAACTGAAA 58.577 39.130 0.00 0.00 0.00 2.69
1455 1551 6.696583 TGACAACTGCACAAACTGAAATAATG 59.303 34.615 0.00 0.00 0.00 1.90
1457 1553 7.041107 ACAACTGCACAAACTGAAATAATGTT 58.959 30.769 0.00 0.00 0.00 2.71
1526 1623 8.989653 AAAAACAAAGGTTCAAAATCGTCTAA 57.010 26.923 0.00 0.00 35.82 2.10
1551 1648 6.542821 TCCTTAGCTCAAAATTCTCTGGAAA 58.457 36.000 0.00 0.00 34.90 3.13
1553 1650 7.040409 TCCTTAGCTCAAAATTCTCTGGAAAAC 60.040 37.037 0.00 0.00 34.90 2.43
1555 1652 5.836347 AGCTCAAAATTCTCTGGAAAACAC 58.164 37.500 0.00 0.00 34.90 3.32
1556 1653 5.360714 AGCTCAAAATTCTCTGGAAAACACA 59.639 36.000 0.00 0.00 34.90 3.72
1557 1654 6.042143 GCTCAAAATTCTCTGGAAAACACAA 58.958 36.000 0.00 0.00 34.90 3.33
1558 1655 6.019559 GCTCAAAATTCTCTGGAAAACACAAC 60.020 38.462 0.00 0.00 34.90 3.32
1559 1656 7.169158 TCAAAATTCTCTGGAAAACACAACT 57.831 32.000 0.00 0.00 34.90 3.16
1566 1663 5.827797 TCTCTGGAAAACACAACTAAAGCAT 59.172 36.000 0.00 0.00 0.00 3.79
1567 1664 5.830912 TCTGGAAAACACAACTAAAGCATG 58.169 37.500 0.00 0.00 0.00 4.06
1568 1665 4.942852 TGGAAAACACAACTAAAGCATGG 58.057 39.130 0.00 0.00 0.00 3.66
1573 1670 2.884639 ACACAACTAAAGCATGGACACC 59.115 45.455 0.00 0.00 0.00 4.16
1576 1673 3.569701 ACAACTAAAGCATGGACACCTTG 59.430 43.478 0.00 0.00 0.00 3.61
1600 1697 9.656040 TTGTTATGATGCTTTGCAAATATCTTT 57.344 25.926 24.84 18.40 43.62 2.52
1608 1705 7.978982 TGCTTTGCAAATATCTTTCTAGAGAC 58.021 34.615 13.23 0.00 34.76 3.36
1623 1720 8.819643 TTTCTAGAGACTTTTCAGCTAAGAAC 57.180 34.615 1.70 0.00 0.00 3.01
1682 1779 6.913873 TCACTAAACTTTACAACTCCACAC 57.086 37.500 0.00 0.00 0.00 3.82
1683 1780 5.521010 TCACTAAACTTTACAACTCCACACG 59.479 40.000 0.00 0.00 0.00 4.49
1684 1781 5.292589 CACTAAACTTTACAACTCCACACGT 59.707 40.000 0.00 0.00 0.00 4.49
1690 2146 5.355910 ACTTTACAACTCCACACGTTTGAAT 59.644 36.000 2.58 0.00 0.00 2.57
1745 2692 4.522405 CCATTTTTCATACAGGTCCACACA 59.478 41.667 0.00 0.00 0.00 3.72
1747 2694 5.703978 TTTTTCATACAGGTCCACACATG 57.296 39.130 0.00 0.00 40.31 3.21
1749 2696 4.365514 TTCATACAGGTCCACACATGTT 57.634 40.909 0.00 0.00 45.23 2.71
1750 2697 3.937814 TCATACAGGTCCACACATGTTC 58.062 45.455 0.00 0.00 45.23 3.18
1751 2698 3.326297 TCATACAGGTCCACACATGTTCA 59.674 43.478 0.00 0.00 45.23 3.18
1859 2809 8.600449 TGTGTTGACAAAATTTCAGAACTTTT 57.400 26.923 5.59 5.59 0.00 2.27
1860 2810 9.698309 TGTGTTGACAAAATTTCAGAACTTTTA 57.302 25.926 10.09 0.00 0.00 1.52
1891 2841 9.105206 CTTCAATTTGCGGTTTTCAAATTTATG 57.895 29.630 10.01 2.88 46.15 1.90
1907 2857 6.475596 AATTTATGAAAATCTCCAGCCCAG 57.524 37.500 0.00 0.00 34.12 4.45
1914 2864 1.633915 ATCTCCAGCCCAGAAGCCAG 61.634 60.000 0.00 0.00 0.00 4.85
1974 2924 7.903995 ACCATTTTTGTTGGTTATGCATAAG 57.096 32.000 19.41 5.78 45.19 1.73
2000 2950 7.707035 GTGGTACCACATGAAAAATGTTTTACA 59.293 33.333 35.21 0.00 45.53 2.41
2038 2990 6.863275 TGTAATCGTTCACTCACATAGTCAT 58.137 36.000 0.00 0.00 35.76 3.06
2040 2992 7.913821 TGTAATCGTTCACTCACATAGTCATAC 59.086 37.037 0.00 0.00 35.76 2.39
2041 2993 6.701145 ATCGTTCACTCACATAGTCATACT 57.299 37.500 0.00 0.00 35.76 2.12
2043 2995 6.920817 TCGTTCACTCACATAGTCATACTTT 58.079 36.000 0.00 0.00 35.76 2.66
2046 3002 9.135843 CGTTCACTCACATAGTCATACTTTTTA 57.864 33.333 0.00 0.00 35.76 1.52
2111 3068 6.252995 AGAACACATAAATTTGGAAGGCCTA 58.747 36.000 5.16 0.00 34.31 3.93
2126 3083 6.776603 TGGAAGGCCTAGACTATTACTTAGAC 59.223 42.308 5.16 0.00 34.31 2.59
2186 3214 5.839063 CCTCCCTACATATACACCTTTCTGA 59.161 44.000 0.00 0.00 0.00 3.27
2190 3221 6.761714 CCCTACATATACACCTTTCTGAACAC 59.238 42.308 0.00 0.00 0.00 3.32
2192 3223 7.987458 CCTACATATACACCTTTCTGAACACAT 59.013 37.037 0.00 0.00 0.00 3.21
2251 3282 4.881273 CCATGCATGCACCTAGTTAAAGTA 59.119 41.667 25.37 0.00 0.00 2.24
2296 3329 8.409371 TGCAATTAAATTAATATCCAGCAACGA 58.591 29.630 0.00 0.00 0.00 3.85
2304 3337 9.778741 AATTAATATCCAGCAACGATTCTAAGA 57.221 29.630 0.00 0.00 0.00 2.10
2305 3338 9.778741 ATTAATATCCAGCAACGATTCTAAGAA 57.221 29.630 0.00 0.00 0.00 2.52
2306 3339 9.607988 TTAATATCCAGCAACGATTCTAAGAAA 57.392 29.630 0.00 0.00 0.00 2.52
2307 3340 8.506168 AATATCCAGCAACGATTCTAAGAAAA 57.494 30.769 0.00 0.00 0.00 2.29
2308 3341 5.862924 TCCAGCAACGATTCTAAGAAAAG 57.137 39.130 0.00 0.00 0.00 2.27
2312 3345 7.117812 TCCAGCAACGATTCTAAGAAAAGTAAG 59.882 37.037 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.615295 GCGAAAGTCCACTTACAATAATTAAAA 57.385 29.630 0.00 0.00 34.61 1.52
16 17 8.238631 GGCGAAAGTCCACTTACAATAATTAAA 58.761 33.333 0.00 0.00 34.61 1.52
17 18 7.413219 CGGCGAAAGTCCACTTACAATAATTAA 60.413 37.037 0.00 0.00 34.61 1.40
18 19 6.036300 CGGCGAAAGTCCACTTACAATAATTA 59.964 38.462 0.00 0.00 34.61 1.40
19 20 5.163794 CGGCGAAAGTCCACTTACAATAATT 60.164 40.000 0.00 0.00 34.61 1.40
20 21 4.331717 CGGCGAAAGTCCACTTACAATAAT 59.668 41.667 0.00 0.00 34.61 1.28
21 22 3.680937 CGGCGAAAGTCCACTTACAATAA 59.319 43.478 0.00 0.00 34.61 1.40
22 23 3.255725 CGGCGAAAGTCCACTTACAATA 58.744 45.455 0.00 0.00 34.61 1.90
23 24 2.073816 CGGCGAAAGTCCACTTACAAT 58.926 47.619 0.00 0.00 34.61 2.71
24 25 1.504359 CGGCGAAAGTCCACTTACAA 58.496 50.000 0.00 0.00 34.61 2.41
25 26 0.320073 CCGGCGAAAGTCCACTTACA 60.320 55.000 9.30 0.00 34.61 2.41
26 27 0.320160 ACCGGCGAAAGTCCACTTAC 60.320 55.000 9.30 0.00 34.61 2.34
27 28 0.320073 CACCGGCGAAAGTCCACTTA 60.320 55.000 9.30 0.00 34.61 2.24
28 29 1.597027 CACCGGCGAAAGTCCACTT 60.597 57.895 9.30 0.00 37.91 3.16
29 30 2.030562 CACCGGCGAAAGTCCACT 59.969 61.111 9.30 0.00 0.00 4.00
30 31 1.441732 AAACACCGGCGAAAGTCCAC 61.442 55.000 9.30 0.00 0.00 4.02
31 32 0.106335 TAAACACCGGCGAAAGTCCA 59.894 50.000 9.30 0.00 0.00 4.02
32 33 0.794473 CTAAACACCGGCGAAAGTCC 59.206 55.000 9.30 0.00 0.00 3.85
33 34 1.505425 ACTAAACACCGGCGAAAGTC 58.495 50.000 9.30 0.00 0.00 3.01
34 35 1.957668 AACTAAACACCGGCGAAAGT 58.042 45.000 9.30 0.00 0.00 2.66
35 36 4.083696 ACAATAACTAAACACCGGCGAAAG 60.084 41.667 9.30 0.00 0.00 2.62
36 37 3.814283 ACAATAACTAAACACCGGCGAAA 59.186 39.130 9.30 0.00 0.00 3.46
37 38 3.401182 ACAATAACTAAACACCGGCGAA 58.599 40.909 9.30 0.00 0.00 4.70
38 39 3.042871 ACAATAACTAAACACCGGCGA 57.957 42.857 9.30 0.00 0.00 5.54
39 40 4.925061 TTACAATAACTAAACACCGGCG 57.075 40.909 0.00 0.00 0.00 6.46
40 41 6.148315 AGACTTTACAATAACTAAACACCGGC 59.852 38.462 0.00 0.00 0.00 6.13
41 42 7.662604 AGACTTTACAATAACTAAACACCGG 57.337 36.000 0.00 0.00 0.00 5.28
87 88 9.834628 CGTTTAGCCACAAAAATAATAGAAAGA 57.165 29.630 0.00 0.00 0.00 2.52
88 89 9.072294 CCGTTTAGCCACAAAAATAATAGAAAG 57.928 33.333 0.00 0.00 0.00 2.62
89 90 8.030106 CCCGTTTAGCCACAAAAATAATAGAAA 58.970 33.333 0.00 0.00 0.00 2.52
90 91 7.177041 ACCCGTTTAGCCACAAAAATAATAGAA 59.823 33.333 0.00 0.00 0.00 2.10
91 92 6.660094 ACCCGTTTAGCCACAAAAATAATAGA 59.340 34.615 0.00 0.00 0.00 1.98
92 93 6.750039 CACCCGTTTAGCCACAAAAATAATAG 59.250 38.462 0.00 0.00 0.00 1.73
93 94 6.433404 TCACCCGTTTAGCCACAAAAATAATA 59.567 34.615 0.00 0.00 0.00 0.98
94 95 5.244178 TCACCCGTTTAGCCACAAAAATAAT 59.756 36.000 0.00 0.00 0.00 1.28
95 96 4.583489 TCACCCGTTTAGCCACAAAAATAA 59.417 37.500 0.00 0.00 0.00 1.40
96 97 4.142790 TCACCCGTTTAGCCACAAAAATA 58.857 39.130 0.00 0.00 0.00 1.40
97 98 2.959707 TCACCCGTTTAGCCACAAAAAT 59.040 40.909 0.00 0.00 0.00 1.82
98 99 2.359531 CTCACCCGTTTAGCCACAAAAA 59.640 45.455 0.00 0.00 0.00 1.94
99 100 1.950909 CTCACCCGTTTAGCCACAAAA 59.049 47.619 0.00 0.00 0.00 2.44
100 101 1.600023 CTCACCCGTTTAGCCACAAA 58.400 50.000 0.00 0.00 0.00 2.83
101 102 0.887387 GCTCACCCGTTTAGCCACAA 60.887 55.000 0.00 0.00 0.00 3.33
102 103 1.302192 GCTCACCCGTTTAGCCACA 60.302 57.895 0.00 0.00 0.00 4.17
103 104 1.302192 TGCTCACCCGTTTAGCCAC 60.302 57.895 0.00 0.00 35.33 5.01
104 105 1.302192 GTGCTCACCCGTTTAGCCA 60.302 57.895 0.00 0.00 35.33 4.75
105 106 2.388232 CGTGCTCACCCGTTTAGCC 61.388 63.158 0.00 0.00 35.33 3.93
106 107 3.023591 GCGTGCTCACCCGTTTAGC 62.024 63.158 0.00 0.00 36.77 3.09
107 108 1.666553 TGCGTGCTCACCCGTTTAG 60.667 57.895 0.00 0.00 0.00 1.85
108 109 1.957186 GTGCGTGCTCACCCGTTTA 60.957 57.895 0.00 0.00 0.00 2.01
109 110 3.276846 GTGCGTGCTCACCCGTTT 61.277 61.111 0.00 0.00 0.00 3.60
115 116 1.730547 GCATTTGGTGCGTGCTCAC 60.731 57.895 0.00 0.00 45.23 3.51
116 117 2.644418 GCATTTGGTGCGTGCTCA 59.356 55.556 0.00 0.00 45.23 4.26
124 125 1.517694 GCGGCTGATGCATTTGGTG 60.518 57.895 0.00 0.00 41.91 4.17
125 126 2.887360 GCGGCTGATGCATTTGGT 59.113 55.556 0.00 0.00 41.91 3.67
126 127 2.278336 CGCGGCTGATGCATTTGG 60.278 61.111 0.00 0.00 41.91 3.28
127 128 1.153978 AACGCGGCTGATGCATTTG 60.154 52.632 12.47 0.00 41.91 2.32
128 129 1.153978 CAACGCGGCTGATGCATTT 60.154 52.632 12.47 0.00 41.91 2.32
129 130 2.486504 CAACGCGGCTGATGCATT 59.513 55.556 12.47 0.00 41.91 3.56
130 131 3.511595 CCAACGCGGCTGATGCAT 61.512 61.111 12.47 0.00 41.91 3.96
142 143 3.876198 GCATAGGTGCGCCCAACG 61.876 66.667 14.07 0.00 42.28 4.10
151 152 1.144057 GACCGTGGGAGCATAGGTG 59.856 63.158 0.00 0.00 35.00 4.00
152 153 0.907704 TTGACCGTGGGAGCATAGGT 60.908 55.000 0.00 0.00 38.00 3.08
153 154 0.251916 TTTGACCGTGGGAGCATAGG 59.748 55.000 0.00 0.00 0.00 2.57
154 155 1.737793 GTTTTGACCGTGGGAGCATAG 59.262 52.381 0.00 0.00 0.00 2.23
155 156 1.612199 GGTTTTGACCGTGGGAGCATA 60.612 52.381 0.00 0.00 0.00 3.14
156 157 0.893727 GGTTTTGACCGTGGGAGCAT 60.894 55.000 0.00 0.00 0.00 3.79
157 158 1.527380 GGTTTTGACCGTGGGAGCA 60.527 57.895 0.00 0.00 0.00 4.26
158 159 3.351450 GGTTTTGACCGTGGGAGC 58.649 61.111 0.00 0.00 0.00 4.70
166 167 0.942252 GAGTGTGTCCGGTTTTGACC 59.058 55.000 0.00 0.00 31.60 4.02
167 168 1.658994 TGAGTGTGTCCGGTTTTGAC 58.341 50.000 0.00 0.00 0.00 3.18
168 169 2.104111 AGATGAGTGTGTCCGGTTTTGA 59.896 45.455 0.00 0.00 0.00 2.69
169 170 2.224079 CAGATGAGTGTGTCCGGTTTTG 59.776 50.000 0.00 0.00 0.00 2.44
170 171 2.494059 CAGATGAGTGTGTCCGGTTTT 58.506 47.619 0.00 0.00 0.00 2.43
171 172 1.878102 GCAGATGAGTGTGTCCGGTTT 60.878 52.381 0.00 0.00 0.00 3.27
172 173 0.320771 GCAGATGAGTGTGTCCGGTT 60.321 55.000 0.00 0.00 0.00 4.44
173 174 1.188219 AGCAGATGAGTGTGTCCGGT 61.188 55.000 0.00 0.00 0.00 5.28
174 175 0.036952 AAGCAGATGAGTGTGTCCGG 60.037 55.000 0.00 0.00 0.00 5.14
175 176 1.354040 GAAGCAGATGAGTGTGTCCG 58.646 55.000 0.00 0.00 0.00 4.79
176 177 1.002430 TGGAAGCAGATGAGTGTGTCC 59.998 52.381 0.00 0.00 0.00 4.02
177 178 2.462456 TGGAAGCAGATGAGTGTGTC 57.538 50.000 0.00 0.00 0.00 3.67
178 179 2.936919 TTGGAAGCAGATGAGTGTGT 57.063 45.000 0.00 0.00 0.00 3.72
179 180 3.316029 TGTTTTGGAAGCAGATGAGTGTG 59.684 43.478 0.00 0.00 0.00 3.82
180 181 3.554934 TGTTTTGGAAGCAGATGAGTGT 58.445 40.909 0.00 0.00 0.00 3.55
181 182 3.817084 TCTGTTTTGGAAGCAGATGAGTG 59.183 43.478 3.55 0.00 34.72 3.51
182 183 3.817647 GTCTGTTTTGGAAGCAGATGAGT 59.182 43.478 9.81 0.00 40.72 3.41
183 184 3.817084 TGTCTGTTTTGGAAGCAGATGAG 59.183 43.478 9.81 0.00 40.72 2.90
184 185 3.819368 TGTCTGTTTTGGAAGCAGATGA 58.181 40.909 9.81 0.00 40.72 2.92
185 186 4.572985 TTGTCTGTTTTGGAAGCAGATG 57.427 40.909 9.81 0.00 40.72 2.90
186 187 5.596836 TTTTGTCTGTTTTGGAAGCAGAT 57.403 34.783 9.81 0.00 40.72 2.90
187 188 5.398603 TTTTTGTCTGTTTTGGAAGCAGA 57.601 34.783 3.55 3.55 36.97 4.26
207 208 4.522722 TGGACGTGGTTTTTGTCTTTTT 57.477 36.364 0.00 0.00 33.21 1.94
208 209 4.729227 ATGGACGTGGTTTTTGTCTTTT 57.271 36.364 0.00 0.00 33.21 2.27
209 210 4.678622 GAATGGACGTGGTTTTTGTCTTT 58.321 39.130 0.00 0.00 33.21 2.52
210 211 3.242936 CGAATGGACGTGGTTTTTGTCTT 60.243 43.478 0.00 0.00 33.21 3.01
211 212 2.289547 CGAATGGACGTGGTTTTTGTCT 59.710 45.455 0.00 0.00 33.21 3.41
212 213 2.603652 CCGAATGGACGTGGTTTTTGTC 60.604 50.000 0.00 0.00 37.49 3.18
213 214 1.335496 CCGAATGGACGTGGTTTTTGT 59.665 47.619 0.00 0.00 37.49 2.83
214 215 1.928595 GCCGAATGGACGTGGTTTTTG 60.929 52.381 0.00 0.00 37.49 2.44
215 216 0.312729 GCCGAATGGACGTGGTTTTT 59.687 50.000 0.00 0.00 37.49 1.94
216 217 0.536460 AGCCGAATGGACGTGGTTTT 60.536 50.000 0.00 0.00 37.49 2.43
217 218 1.072505 AGCCGAATGGACGTGGTTT 59.927 52.632 0.00 0.00 37.49 3.27
218 219 1.671054 CAGCCGAATGGACGTGGTT 60.671 57.895 0.00 0.00 37.49 3.67
219 220 2.047274 CAGCCGAATGGACGTGGT 60.047 61.111 0.00 0.00 37.49 4.16
220 221 2.819595 CCAGCCGAATGGACGTGG 60.820 66.667 0.00 0.00 43.57 4.94
221 222 2.819595 CCCAGCCGAATGGACGTG 60.820 66.667 0.00 0.00 43.57 4.49
222 223 4.778143 GCCCAGCCGAATGGACGT 62.778 66.667 7.38 0.00 43.57 4.34
233 234 2.124529 GGAGTGCTTAGGCCCAGC 60.125 66.667 16.30 16.30 37.74 4.85
234 235 1.977293 GAGGGAGTGCTTAGGCCCAG 61.977 65.000 0.00 0.00 43.20 4.45
235 236 1.995626 GAGGGAGTGCTTAGGCCCA 60.996 63.158 0.00 0.00 43.20 5.36
236 237 1.690985 AGAGGGAGTGCTTAGGCCC 60.691 63.158 0.00 0.00 41.00 5.80
237 238 1.268283 ACAGAGGGAGTGCTTAGGCC 61.268 60.000 0.00 0.00 37.74 5.19
238 239 1.486211 TACAGAGGGAGTGCTTAGGC 58.514 55.000 0.00 0.00 39.26 3.93
239 240 2.159226 CGTTACAGAGGGAGTGCTTAGG 60.159 54.545 0.00 0.00 0.00 2.69
240 241 2.735762 GCGTTACAGAGGGAGTGCTTAG 60.736 54.545 0.00 0.00 0.00 2.18
241 242 1.203994 GCGTTACAGAGGGAGTGCTTA 59.796 52.381 0.00 0.00 0.00 3.09
242 243 0.037232 GCGTTACAGAGGGAGTGCTT 60.037 55.000 0.00 0.00 0.00 3.91
243 244 1.185618 TGCGTTACAGAGGGAGTGCT 61.186 55.000 0.00 0.00 0.00 4.40
244 245 0.320421 TTGCGTTACAGAGGGAGTGC 60.320 55.000 0.00 0.00 0.00 4.40
245 246 1.798813 GTTTGCGTTACAGAGGGAGTG 59.201 52.381 0.00 0.00 0.00 3.51
246 247 1.604693 CGTTTGCGTTACAGAGGGAGT 60.605 52.381 0.00 0.00 0.00 3.85
247 248 1.068474 CGTTTGCGTTACAGAGGGAG 58.932 55.000 0.00 0.00 0.00 4.30
248 249 3.204505 CGTTTGCGTTACAGAGGGA 57.795 52.632 0.00 0.00 0.00 4.20
280 281 8.974408 CGCTGCTAATTGTGTACTATATACAAA 58.026 33.333 0.00 0.00 41.88 2.83
281 282 8.354426 TCGCTGCTAATTGTGTACTATATACAA 58.646 33.333 0.00 1.37 42.58 2.41
282 283 7.806487 GTCGCTGCTAATTGTGTACTATATACA 59.194 37.037 0.00 0.00 0.00 2.29
283 284 7.007188 CGTCGCTGCTAATTGTGTACTATATAC 59.993 40.741 0.00 0.00 0.00 1.47
284 285 7.019418 CGTCGCTGCTAATTGTGTACTATATA 58.981 38.462 0.00 0.00 0.00 0.86
285 286 5.856986 CGTCGCTGCTAATTGTGTACTATAT 59.143 40.000 0.00 0.00 0.00 0.86
286 287 5.209977 CGTCGCTGCTAATTGTGTACTATA 58.790 41.667 0.00 0.00 0.00 1.31
287 288 4.042398 CGTCGCTGCTAATTGTGTACTAT 58.958 43.478 0.00 0.00 0.00 2.12
288 289 3.119743 ACGTCGCTGCTAATTGTGTACTA 60.120 43.478 0.00 0.00 0.00 1.82
289 290 2.259618 CGTCGCTGCTAATTGTGTACT 58.740 47.619 0.00 0.00 0.00 2.73
290 291 1.990563 ACGTCGCTGCTAATTGTGTAC 59.009 47.619 0.00 0.00 0.00 2.90
291 292 2.256174 GACGTCGCTGCTAATTGTGTA 58.744 47.619 0.00 0.00 0.00 2.90
292 293 1.068474 GACGTCGCTGCTAATTGTGT 58.932 50.000 0.00 0.00 0.00 3.72
293 294 0.023732 CGACGTCGCTGCTAATTGTG 59.976 55.000 26.59 0.00 0.00 3.33
294 295 2.359792 CGACGTCGCTGCTAATTGT 58.640 52.632 26.59 0.00 0.00 2.71
305 306 2.427905 TGTTCTTCCGCGACGTCG 60.428 61.111 32.57 32.57 43.27 5.12
316 317 2.978010 CGGCAAGCGGGTGTTCTT 60.978 61.111 0.00 0.00 0.00 2.52
326 327 0.884704 TTTCTCACTGGTCGGCAAGC 60.885 55.000 0.00 0.00 0.00 4.01
334 335 1.064979 ACCGGTTGTTTTCTCACTGGT 60.065 47.619 0.00 0.00 0.00 4.00
337 338 1.675552 CCACCGGTTGTTTTCTCACT 58.324 50.000 2.97 0.00 0.00 3.41
339 340 0.106918 AGCCACCGGTTGTTTTCTCA 60.107 50.000 2.97 0.00 0.00 3.27
358 359 1.092921 GCGTGCATCCGGATGGTAAA 61.093 55.000 38.49 12.39 39.16 2.01
360 361 2.108157 GCGTGCATCCGGATGGTA 59.892 61.111 38.49 20.35 39.16 3.25
361 362 3.620419 TTGCGTGCATCCGGATGGT 62.620 57.895 38.49 8.56 39.16 3.55
362 363 2.405805 TTTGCGTGCATCCGGATGG 61.406 57.895 38.49 25.86 39.16 3.51
363 364 1.226379 GTTTGCGTGCATCCGGATG 60.226 57.895 35.50 35.50 41.60 3.51
364 365 0.960364 AAGTTTGCGTGCATCCGGAT 60.960 50.000 12.38 12.38 0.00 4.18
365 366 1.599518 AAGTTTGCGTGCATCCGGA 60.600 52.632 6.61 6.61 0.00 5.14
376 385 0.671472 GCCCATGCTTCCAAGTTTGC 60.671 55.000 0.00 0.00 33.53 3.68
388 397 1.678101 GACTGAATAACCAGCCCATGC 59.322 52.381 0.00 0.00 37.68 4.06
400 410 7.685481 TCATGTTTCAAGTTAGGGACTGAATA 58.315 34.615 0.00 0.00 41.52 1.75
407 417 5.476599 CCACAATCATGTTTCAAGTTAGGGA 59.523 40.000 0.00 0.00 37.82 4.20
417 427 4.697352 ACTCAGCTACCACAATCATGTTTC 59.303 41.667 0.00 0.00 37.82 2.78
422 436 3.012518 GCAACTCAGCTACCACAATCAT 58.987 45.455 0.00 0.00 0.00 2.45
425 439 2.154462 GTGCAACTCAGCTACCACAAT 58.846 47.619 0.00 0.00 34.99 2.71
426 440 1.593196 GTGCAACTCAGCTACCACAA 58.407 50.000 0.00 0.00 34.99 3.33
446 460 1.851021 CGCAACATCCCTTCGTGCAA 61.851 55.000 0.00 0.00 0.00 4.08
447 461 2.324330 CGCAACATCCCTTCGTGCA 61.324 57.895 0.00 0.00 0.00 4.57
448 462 1.852067 AACGCAACATCCCTTCGTGC 61.852 55.000 0.00 0.00 33.38 5.34
449 463 0.110238 CAACGCAACATCCCTTCGTG 60.110 55.000 0.00 0.00 33.38 4.35
450 464 1.852067 GCAACGCAACATCCCTTCGT 61.852 55.000 0.00 0.00 34.63 3.85
451 465 1.154225 GCAACGCAACATCCCTTCG 60.154 57.895 0.00 0.00 0.00 3.79
483 497 0.882484 TCTCTCGCGCTCGATCATCT 60.882 55.000 5.56 0.00 44.56 2.90
493 507 2.811317 CACCAACCTCTCTCGCGC 60.811 66.667 0.00 0.00 0.00 6.86
494 508 2.811317 GCACCAACCTCTCTCGCG 60.811 66.667 0.00 0.00 0.00 5.87
583 603 1.484227 CGTTGTCGCGTTGGTGAGAA 61.484 55.000 5.77 0.00 34.02 2.87
604 625 0.878416 GTGTGTGTGGTGTGTGTGTT 59.122 50.000 0.00 0.00 0.00 3.32
607 628 0.250510 TGTGTGTGTGTGGTGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
641 662 1.691434 GGTAGCTAGCAGATGGAGCTT 59.309 52.381 18.83 0.00 44.08 3.74
666 687 7.108847 AGAGAGAGAGAAAGAGAGAGAGAAAG 58.891 42.308 0.00 0.00 0.00 2.62
667 688 7.020827 AGAGAGAGAGAAAGAGAGAGAGAAA 57.979 40.000 0.00 0.00 0.00 2.52
668 689 6.441924 AGAGAGAGAGAGAAAGAGAGAGAGAA 59.558 42.308 0.00 0.00 0.00 2.87
669 690 5.960811 AGAGAGAGAGAGAAAGAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
670 691 6.098124 AGAGAGAGAGAGAGAAAGAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
671 692 5.960811 AGAGAGAGAGAGAGAAAGAGAGAGA 59.039 44.000 0.00 0.00 0.00 3.10
672 693 6.098124 AGAGAGAGAGAGAGAGAAAGAGAGAG 59.902 46.154 0.00 0.00 0.00 3.20
676 697 6.098124 AGAGAGAGAGAGAGAGAGAGAAAGAG 59.902 46.154 0.00 0.00 0.00 2.85
678 699 6.098124 AGAGAGAGAGAGAGAGAGAGAGAAAG 59.902 46.154 0.00 0.00 0.00 2.62
685 706 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
686 707 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
703 724 6.778821 TCAAAAGAAGAGAGAGAGAGAGAGA 58.221 40.000 0.00 0.00 0.00 3.10
708 729 5.480073 TCCCTTCAAAAGAAGAGAGAGAGAG 59.520 44.000 6.79 0.00 34.26 3.20
721 742 1.882623 AGCTCGCTTTCCCTTCAAAAG 59.117 47.619 0.00 0.00 36.91 2.27
726 747 0.176910 AGCTAGCTCGCTTTCCCTTC 59.823 55.000 12.68 0.00 36.74 3.46
727 755 1.137282 GTAGCTAGCTCGCTTTCCCTT 59.863 52.381 23.26 0.00 41.30 3.95
785 813 5.046014 AGCTGAGTCCATGACAAAAGACTAT 60.046 40.000 0.00 0.00 39.62 2.12
792 820 1.338105 CCGAGCTGAGTCCATGACAAA 60.338 52.381 0.00 0.00 34.60 2.83
793 821 0.247460 CCGAGCTGAGTCCATGACAA 59.753 55.000 0.00 0.00 34.60 3.18
842 872 0.108233 GAGTCAGAAGGCAGAGGCAG 60.108 60.000 0.00 0.00 43.71 4.85
846 876 0.108233 GGCAGAGTCAGAAGGCAGAG 60.108 60.000 0.00 0.00 0.00 3.35
901 931 2.223112 GCTATGTGCTATGTGTGTGTGC 60.223 50.000 0.00 0.00 38.95 4.57
966 998 1.297819 CTGTGCACGCAACAGTGTG 60.298 57.895 13.13 4.90 44.49 3.82
988 1020 3.129113 ACGACCAACATACGCTACATACA 59.871 43.478 0.00 0.00 0.00 2.29
993 1025 1.186030 CGACGACCAACATACGCTAC 58.814 55.000 0.00 0.00 0.00 3.58
1025 1069 3.238497 CGTGAGTCCCCACCACCA 61.238 66.667 0.00 0.00 33.67 4.17
1026 1070 4.016706 CCGTGAGTCCCCACCACC 62.017 72.222 0.00 0.00 33.67 4.61
1068 1116 2.002586 CGTGCGAAAGGATCATCAGTT 58.997 47.619 0.00 0.00 0.00 3.16
1069 1117 1.645034 CGTGCGAAAGGATCATCAGT 58.355 50.000 0.00 0.00 0.00 3.41
1070 1118 0.302890 GCGTGCGAAAGGATCATCAG 59.697 55.000 0.00 0.00 0.00 2.90
1072 1120 0.302890 CTGCGTGCGAAAGGATCATC 59.697 55.000 0.00 0.00 0.00 2.92
1073 1121 1.709147 GCTGCGTGCGAAAGGATCAT 61.709 55.000 0.00 0.00 0.00 2.45
1074 1122 2.390599 GCTGCGTGCGAAAGGATCA 61.391 57.895 0.00 0.00 0.00 2.92
1143 1238 6.315642 CAGAAAACACACAGAGCAGATCATAT 59.684 38.462 0.00 0.00 0.00 1.78
1144 1239 5.640783 CAGAAAACACACAGAGCAGATCATA 59.359 40.000 0.00 0.00 0.00 2.15
1153 1248 1.605710 CCCTGCAGAAAACACACAGAG 59.394 52.381 17.39 0.00 0.00 3.35
1171 1266 2.024414 GCATACATCAGTTGGAACCCC 58.976 52.381 0.00 0.00 0.00 4.95
1226 1322 3.441572 ACATATTCAAAGACCTGCTGCAC 59.558 43.478 0.00 0.00 0.00 4.57
1255 1351 8.825774 ACATCACCCACATACATACATATACAT 58.174 33.333 0.00 0.00 0.00 2.29
1261 1357 5.372343 ACACATCACCCACATACATACAT 57.628 39.130 0.00 0.00 0.00 2.29
1263 1359 4.574828 GGAACACATCACCCACATACATAC 59.425 45.833 0.00 0.00 0.00 2.39
1265 1361 3.266772 AGGAACACATCACCCACATACAT 59.733 43.478 0.00 0.00 0.00 2.29
1267 1363 3.350219 AGGAACACATCACCCACATAC 57.650 47.619 0.00 0.00 0.00 2.39
1271 1367 0.598065 GCAAGGAACACATCACCCAC 59.402 55.000 0.00 0.00 0.00 4.61
1273 1369 0.539438 TGGCAAGGAACACATCACCC 60.539 55.000 0.00 0.00 0.00 4.61
1292 1388 3.008813 ACTGCTCACCTGACAAAGATCAT 59.991 43.478 0.00 0.00 0.00 2.45
1315 1411 3.296709 GAGGCCGGAACAGCGAAGA 62.297 63.158 5.05 0.00 0.00 2.87
1398 1494 5.876612 ATGCTTCAGACAAGTTCATCTTC 57.123 39.130 0.00 0.00 33.63 2.87
1483 1579 2.570415 TTTGTCAACCCGCCTCATTA 57.430 45.000 0.00 0.00 0.00 1.90
1526 1623 6.319048 TCCAGAGAATTTTGAGCTAAGGAT 57.681 37.500 0.00 0.00 0.00 3.24
1551 1648 3.317993 GGTGTCCATGCTTTAGTTGTGTT 59.682 43.478 0.00 0.00 0.00 3.32
1553 1650 3.149196 AGGTGTCCATGCTTTAGTTGTG 58.851 45.455 0.00 0.00 0.00 3.33
1555 1652 3.569701 ACAAGGTGTCCATGCTTTAGTTG 59.430 43.478 0.00 0.00 0.00 3.16
1556 1653 3.832527 ACAAGGTGTCCATGCTTTAGTT 58.167 40.909 0.00 0.00 0.00 2.24
1557 1654 3.508845 ACAAGGTGTCCATGCTTTAGT 57.491 42.857 0.00 0.00 0.00 2.24
1558 1655 5.647658 TCATAACAAGGTGTCCATGCTTTAG 59.352 40.000 0.00 0.00 0.00 1.85
1559 1656 5.565509 TCATAACAAGGTGTCCATGCTTTA 58.434 37.500 0.00 0.00 0.00 1.85
1566 1663 3.719268 AGCATCATAACAAGGTGTCCA 57.281 42.857 0.00 0.00 0.00 4.02
1567 1664 4.737054 CAAAGCATCATAACAAGGTGTCC 58.263 43.478 0.00 0.00 0.00 4.02
1568 1665 4.168760 GCAAAGCATCATAACAAGGTGTC 58.831 43.478 0.00 0.00 0.00 3.67
1573 1670 8.867112 AGATATTTGCAAAGCATCATAACAAG 57.133 30.769 26.24 0.00 38.76 3.16
1576 1673 9.525409 AGAAAGATATTTGCAAAGCATCATAAC 57.475 29.630 26.24 17.97 38.76 1.89
1600 1697 7.768807 AGTTCTTAGCTGAAAAGTCTCTAGA 57.231 36.000 0.00 0.00 0.00 2.43
1608 1705 6.043854 AGGGAGTAGTTCTTAGCTGAAAAG 57.956 41.667 0.00 0.00 0.00 2.27
1657 1754 7.383029 CGTGTGGAGTTGTAAAGTTTAGTGATA 59.617 37.037 0.00 0.00 0.00 2.15
1672 1769 3.362295 CACATTCAAACGTGTGGAGTTG 58.638 45.455 5.75 0.00 41.46 3.16
1673 1770 3.691049 CACATTCAAACGTGTGGAGTT 57.309 42.857 5.75 0.00 41.46 3.01
1728 2675 4.202409 TGAACATGTGTGGACCTGTATGAA 60.202 41.667 0.00 0.00 31.38 2.57
1730 2677 3.673902 TGAACATGTGTGGACCTGTATG 58.326 45.455 0.00 0.00 31.38 2.39
1762 2709 7.564793 AGGCATATTTTCATCTGTGTACTACA 58.435 34.615 0.00 0.00 37.78 2.74
1773 2720 8.597662 AATTTGCATGTAGGCATATTTTCATC 57.402 30.769 2.23 0.00 44.48 2.92
1827 2777 9.891828 TCTGAAATTTTGTCAACACATATGTAC 57.108 29.630 8.32 3.74 38.45 2.90
1859 2809 6.565234 TGAAAACCGCAAATTGAAGTTTCTA 58.435 32.000 12.12 4.72 30.66 2.10
1860 2810 5.415221 TGAAAACCGCAAATTGAAGTTTCT 58.585 33.333 12.12 5.53 30.66 2.52
1891 2841 1.747924 GCTTCTGGGCTGGAGATTTTC 59.252 52.381 0.00 0.00 0.00 2.29
1900 2850 1.153005 GATCCTGGCTTCTGGGCTG 60.153 63.158 0.00 0.00 41.48 4.85
1907 2857 2.169352 TCTAAGTGCAGATCCTGGCTTC 59.831 50.000 0.00 0.00 31.21 3.86
1914 2864 4.634184 TTAGTCGTCTAAGTGCAGATCC 57.366 45.455 0.00 0.00 33.00 3.36
1951 2901 7.148440 CCACTTATGCATAACCAACAAAAATGG 60.148 37.037 15.21 0.75 43.84 3.16
1963 2913 5.820423 TCATGTGGTACCACTTATGCATAAC 59.180 40.000 37.91 14.07 46.30 1.89
1974 2924 7.707035 TGTAAAACATTTTTCATGTGGTACCAC 59.293 33.333 33.97 33.97 46.33 4.16
2083 3039 8.040727 GGCCTTCCAAATTTATGTGTTCTAATT 58.959 33.333 0.00 0.00 0.00 1.40
2084 3040 7.400052 AGGCCTTCCAAATTTATGTGTTCTAAT 59.600 33.333 0.00 0.00 33.74 1.73
2095 3052 8.999895 AGTAATAGTCTAGGCCTTCCAAATTTA 58.000 33.333 12.58 0.00 33.74 1.40
2098 3055 7.453141 AAGTAATAGTCTAGGCCTTCCAAAT 57.547 36.000 12.58 0.00 33.74 2.32
2126 3083 7.827701 TGTTTGGAGTAGTAGAACTATCTGTG 58.172 38.462 0.00 0.00 37.10 3.66
2219 3250 2.431782 GGTGCATGCATGGTTAAGGATT 59.568 45.455 25.64 0.00 0.00 3.01
2319 3352 8.731605 CCTCTCTTCGATATGCACTATACTTTA 58.268 37.037 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.