Multiple sequence alignment - TraesCS3A01G318200

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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 TraesCS3A01G318200 chr3A 100.000 2240 0 0 1 2240 559525803 559528042 0.000000e+00 4137
1 TraesCS3A01G318200 chr3A 92.079 101 7 1 2018 2118 287684785 287684686 8.340000e-30 141
2 TraesCS3A01G318200 chr3B 92.352 1739 61 20 328 2022 556880038 556878328 0.000000e+00 2409
3 TraesCS3A01G318200 chr3B 86.765 272 35 1 1 271 417735566 417735295 3.620000e-78 302
4 TraesCS3A01G318200 chr3B 96.774 124 4 0 2117 2240 556878329 556878206 8.110000e-50 207
5 TraesCS3A01G318200 chr3D 93.486 1612 49 17 332 1889 427228862 427227253 0.000000e+00 2344
6 TraesCS3A01G318200 chr3D 94.355 124 7 0 2117 2240 427227148 427227025 8.170000e-45 191
7 TraesCS3A01G318200 chr4D 89.851 335 33 1 1 334 402544485 402544819 1.590000e-116 429
8 TraesCS3A01G318200 chr4D 93.137 102 5 2 2020 2121 310484236 310484137 4.980000e-32 148
9 TraesCS3A01G318200 chr4A 89.489 333 34 1 3 334 60033157 60033489 9.570000e-114 420
10 TraesCS3A01G318200 chr1D 86.726 339 42 3 1 337 465339148 465338811 7.550000e-100 374
11 TraesCS3A01G318200 chr7A 85.503 338 33 10 1 336 4617465 4617788 2.760000e-89 339
12 TraesCS3A01G318200 chr7A 80.556 252 31 8 1 251 90223063 90222829 6.360000e-41 178
13 TraesCS3A01G318200 chr6B 83.136 338 27 13 1 336 217162279 217161970 4.710000e-72 281
14 TraesCS3A01G318200 chr5D 85.252 278 28 7 60 325 449127245 449126969 7.880000e-70 274
15 TraesCS3A01G318200 chrUn 84.496 258 39 1 78 334 33996565 33996822 1.030000e-63 254
16 TraesCS3A01G318200 chr4B 93.023 172 11 1 1 171 498389600 498389771 1.330000e-62 250
17 TraesCS3A01G318200 chr1B 84.914 232 29 2 1 228 672423765 672423536 1.730000e-56 230
18 TraesCS3A01G318200 chr1B 93.684 95 4 2 2024 2118 600973426 600973518 8.340000e-30 141
19 TraesCS3A01G318200 chr5B 94.681 94 4 1 2025 2118 254944484 254944392 6.450000e-31 145
20 TraesCS3A01G318200 chr5B 93.684 95 5 1 2025 2119 428958906 428958999 8.340000e-30 141
21 TraesCS3A01G318200 chr5B 93.684 95 5 1 2025 2119 638485470 638485377 8.340000e-30 141
22 TraesCS3A01G318200 chr6A 92.000 100 7 1 2019 2118 11165054 11165152 3.000000e-29 139
23 TraesCS3A01G318200 chr6A 87.611 113 11 3 2025 2136 37459084 37459194 6.490000e-26 128
24 TraesCS3A01G318200 chr1A 93.548 93 5 1 2031 2123 238868751 238868660 1.080000e-28 137
25 TraesCS3A01G318200 chr5A 81.287 171 21 5 146 315 265273713 265273873 6.490000e-26 128


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 TraesCS3A01G318200 chr3A 559525803 559528042 2239 False 4137.0 4137 100.0000 1 2240 1 chr3A.!!$F1 2239
1 TraesCS3A01G318200 chr3B 556878206 556880038 1832 True 1308.0 2409 94.5630 328 2240 2 chr3B.!!$R2 1912
2 TraesCS3A01G318200 chr3D 427227025 427228862 1837 True 1267.5 2344 93.9205 332 2240 2 chr3D.!!$R1 1908

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
265 266 0.028902 GCAAACGTGTCCCACAAGAC 59.971 55.0 0.0 0.0 37.28 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1416 0.31716 ACGATCACAGCGGACAAGAA 59.683 50.0 0.0 0.0 0.0 2.52 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
28 29 7.451281 CATTGAGAATGTTGCTTGATTGATC 57.549 36.000 0.00 0.00 34.18 2.92
29 30 6.829229 TTGAGAATGTTGCTTGATTGATCT 57.171 33.333 0.00 0.00 0.00 2.75
30 31 7.926674 TTGAGAATGTTGCTTGATTGATCTA 57.073 32.000 0.00 0.00 0.00 1.98
31 32 8.515695 TTGAGAATGTTGCTTGATTGATCTAT 57.484 30.769 0.00 0.00 0.00 1.98
32 33 7.927048 TGAGAATGTTGCTTGATTGATCTATG 58.073 34.615 0.00 0.00 0.00 2.23
33 34 7.555195 TGAGAATGTTGCTTGATTGATCTATGT 59.445 33.333 0.00 0.00 0.00 2.29
34 35 7.928103 AGAATGTTGCTTGATTGATCTATGTC 58.072 34.615 0.00 0.00 0.00 3.06
35 36 5.723492 TGTTGCTTGATTGATCTATGTCG 57.277 39.130 0.00 0.00 0.00 4.35
36 37 5.178061 TGTTGCTTGATTGATCTATGTCGT 58.822 37.500 0.00 0.00 0.00 4.34
37 38 5.643348 TGTTGCTTGATTGATCTATGTCGTT 59.357 36.000 0.00 0.00 0.00 3.85
38 39 6.149308 TGTTGCTTGATTGATCTATGTCGTTT 59.851 34.615 0.00 0.00 0.00 3.60
39 40 6.110543 TGCTTGATTGATCTATGTCGTTTG 57.889 37.500 0.00 0.00 0.00 2.93
40 41 5.874261 TGCTTGATTGATCTATGTCGTTTGA 59.126 36.000 0.00 0.00 0.00 2.69
41 42 6.036408 TGCTTGATTGATCTATGTCGTTTGAG 59.964 38.462 0.00 0.00 0.00 3.02
42 43 5.973651 TGATTGATCTATGTCGTTTGAGC 57.026 39.130 0.00 0.00 0.00 4.26
43 44 5.418676 TGATTGATCTATGTCGTTTGAGCA 58.581 37.500 0.00 0.00 0.00 4.26
44 45 6.051074 TGATTGATCTATGTCGTTTGAGCAT 58.949 36.000 0.00 0.00 0.00 3.79
45 46 5.973651 TTGATCTATGTCGTTTGAGCATC 57.026 39.130 0.00 0.00 0.00 3.91
46 47 5.268118 TGATCTATGTCGTTTGAGCATCT 57.732 39.130 0.00 0.00 34.92 2.90
47 48 5.664457 TGATCTATGTCGTTTGAGCATCTT 58.336 37.500 0.00 0.00 34.92 2.40
48 49 6.108687 TGATCTATGTCGTTTGAGCATCTTT 58.891 36.000 0.00 0.00 34.92 2.52
49 50 6.595326 TGATCTATGTCGTTTGAGCATCTTTT 59.405 34.615 0.00 0.00 34.92 2.27
50 51 6.169419 TCTATGTCGTTTGAGCATCTTTTG 57.831 37.500 0.00 0.00 34.92 2.44
65 66 5.836009 CATCTTTTGCTTGTTTTATCGCAC 58.164 37.500 0.00 0.00 31.24 5.34
66 67 4.926244 TCTTTTGCTTGTTTTATCGCACA 58.074 34.783 0.00 0.00 31.24 4.57
67 68 5.527951 TCTTTTGCTTGTTTTATCGCACAT 58.472 33.333 0.00 0.00 31.24 3.21
68 69 5.982516 TCTTTTGCTTGTTTTATCGCACATT 59.017 32.000 0.00 0.00 31.24 2.71
69 70 5.820926 TTTGCTTGTTTTATCGCACATTC 57.179 34.783 0.00 0.00 31.24 2.67
70 71 4.495911 TGCTTGTTTTATCGCACATTCA 57.504 36.364 0.00 0.00 0.00 2.57
71 72 5.058149 TGCTTGTTTTATCGCACATTCAT 57.942 34.783 0.00 0.00 0.00 2.57
72 73 4.858140 TGCTTGTTTTATCGCACATTCATG 59.142 37.500 0.00 0.00 0.00 3.07
73 74 5.094812 GCTTGTTTTATCGCACATTCATGA 58.905 37.500 0.00 0.00 0.00 3.07
74 75 5.572511 GCTTGTTTTATCGCACATTCATGAA 59.427 36.000 11.26 11.26 0.00 2.57
75 76 6.254157 GCTTGTTTTATCGCACATTCATGAAT 59.746 34.615 15.36 15.36 0.00 2.57
76 77 7.514125 GCTTGTTTTATCGCACATTCATGAATC 60.514 37.037 18.16 6.75 0.00 2.52
77 78 7.087409 TGTTTTATCGCACATTCATGAATCT 57.913 32.000 18.16 3.99 0.00 2.40
78 79 8.207521 TGTTTTATCGCACATTCATGAATCTA 57.792 30.769 18.16 0.45 0.00 1.98
79 80 8.672815 TGTTTTATCGCACATTCATGAATCTAA 58.327 29.630 18.16 6.90 0.00 2.10
80 81 9.502145 GTTTTATCGCACATTCATGAATCTAAA 57.498 29.630 18.16 11.49 0.00 1.85
81 82 9.502145 TTTTATCGCACATTCATGAATCTAAAC 57.498 29.630 18.16 5.81 0.00 2.01
82 83 6.932356 ATCGCACATTCATGAATCTAAACT 57.068 33.333 18.16 0.13 0.00 2.66
83 84 6.741992 TCGCACATTCATGAATCTAAACTT 57.258 33.333 18.16 0.00 0.00 2.66
84 85 6.545508 TCGCACATTCATGAATCTAAACTTG 58.454 36.000 18.16 8.73 0.00 3.16
85 86 6.371271 TCGCACATTCATGAATCTAAACTTGA 59.629 34.615 18.16 5.94 0.00 3.02
86 87 7.066163 TCGCACATTCATGAATCTAAACTTGAT 59.934 33.333 18.16 0.00 0.00 2.57
87 88 8.337532 CGCACATTCATGAATCTAAACTTGATA 58.662 33.333 18.16 0.00 0.00 2.15
88 89 9.443283 GCACATTCATGAATCTAAACTTGATAC 57.557 33.333 18.16 0.00 0.00 2.24
89 90 9.941664 CACATTCATGAATCTAAACTTGATACC 57.058 33.333 18.16 0.00 0.00 2.73
90 91 9.911788 ACATTCATGAATCTAAACTTGATACCT 57.088 29.630 18.16 0.00 0.00 3.08
92 93 8.648557 TTCATGAATCTAAACTTGATACCTCG 57.351 34.615 3.38 0.00 0.00 4.63
93 94 7.782049 TCATGAATCTAAACTTGATACCTCGT 58.218 34.615 0.00 0.00 0.00 4.18
94 95 8.258007 TCATGAATCTAAACTTGATACCTCGTT 58.742 33.333 0.00 0.00 0.00 3.85
95 96 8.883731 CATGAATCTAAACTTGATACCTCGTTT 58.116 33.333 0.00 0.00 34.37 3.60
96 97 8.251750 TGAATCTAAACTTGATACCTCGTTTG 57.748 34.615 0.00 0.00 32.46 2.93
97 98 7.876068 TGAATCTAAACTTGATACCTCGTTTGT 59.124 33.333 0.00 0.00 32.46 2.83
98 99 8.617290 AATCTAAACTTGATACCTCGTTTGTT 57.383 30.769 0.00 0.00 32.46 2.83
99 100 7.416154 TCTAAACTTGATACCTCGTTTGTTG 57.584 36.000 0.00 0.00 32.46 3.33
100 101 4.483476 AACTTGATACCTCGTTTGTTGC 57.517 40.909 0.00 0.00 0.00 4.17
101 102 2.478894 ACTTGATACCTCGTTTGTTGCG 59.521 45.455 0.00 0.00 0.00 4.85
102 103 0.793861 TGATACCTCGTTTGTTGCGC 59.206 50.000 0.00 0.00 0.00 6.09
103 104 0.793861 GATACCTCGTTTGTTGCGCA 59.206 50.000 5.66 5.66 0.00 6.09
104 105 1.396996 GATACCTCGTTTGTTGCGCAT 59.603 47.619 12.75 0.00 0.00 4.73
105 106 2.081725 TACCTCGTTTGTTGCGCATA 57.918 45.000 12.75 0.00 0.00 3.14
106 107 1.231221 ACCTCGTTTGTTGCGCATAA 58.769 45.000 12.75 7.29 0.00 1.90
107 108 1.810151 ACCTCGTTTGTTGCGCATAAT 59.190 42.857 12.75 0.00 0.00 1.28
108 109 2.176369 CCTCGTTTGTTGCGCATAATG 58.824 47.619 12.75 11.80 0.00 1.90
109 110 2.414029 CCTCGTTTGTTGCGCATAATGT 60.414 45.455 12.75 0.00 0.00 2.71
110 111 3.233578 CTCGTTTGTTGCGCATAATGTT 58.766 40.909 12.75 0.00 0.00 2.71
111 112 3.633235 TCGTTTGTTGCGCATAATGTTT 58.367 36.364 12.75 0.00 0.00 2.83
112 113 4.045104 TCGTTTGTTGCGCATAATGTTTT 58.955 34.783 12.75 0.00 0.00 2.43
113 114 5.212934 TCGTTTGTTGCGCATAATGTTTTA 58.787 33.333 12.75 0.00 0.00 1.52
114 115 5.859114 TCGTTTGTTGCGCATAATGTTTTAT 59.141 32.000 12.75 0.00 0.00 1.40
115 116 5.945261 CGTTTGTTGCGCATAATGTTTTATG 59.055 36.000 12.75 2.14 45.02 1.90
116 117 6.399459 CGTTTGTTGCGCATAATGTTTTATGT 60.399 34.615 12.75 0.00 44.37 2.29
195 196 9.922305 GTCATGATAAACTTGATAAGTGTAAGC 57.078 33.333 0.00 0.00 41.91 3.09
196 197 9.890629 TCATGATAAACTTGATAAGTGTAAGCT 57.109 29.630 0.00 0.00 41.91 3.74
214 215 9.450807 GTGTAAGCTTATTATTGTATTTGCAGG 57.549 33.333 9.88 0.00 0.00 4.85
215 216 9.402320 TGTAAGCTTATTATTGTATTTGCAGGA 57.598 29.630 9.88 0.00 0.00 3.86
216 217 9.665264 GTAAGCTTATTATTGTATTTGCAGGAC 57.335 33.333 9.88 0.00 0.00 3.85
217 218 6.959361 AGCTTATTATTGTATTTGCAGGACG 58.041 36.000 0.00 0.00 0.00 4.79
218 219 6.017109 AGCTTATTATTGTATTTGCAGGACGG 60.017 38.462 0.00 0.00 0.00 4.79
219 220 4.568152 ATTATTGTATTTGCAGGACGGC 57.432 40.909 0.00 0.00 0.00 5.68
220 221 0.732571 ATTGTATTTGCAGGACGGCG 59.267 50.000 4.80 4.80 36.28 6.46
221 222 0.320858 TTGTATTTGCAGGACGGCGA 60.321 50.000 16.62 0.00 36.28 5.54
222 223 0.739462 TGTATTTGCAGGACGGCGAG 60.739 55.000 16.62 0.95 36.28 5.03
223 224 1.813753 TATTTGCAGGACGGCGAGC 60.814 57.895 16.62 12.59 36.28 5.03
245 246 2.432628 CGGCGCGGAATAGATCCC 60.433 66.667 9.72 0.00 46.39 3.85
246 247 2.432628 GGCGCGGAATAGATCCCG 60.433 66.667 8.83 3.98 46.39 5.14
252 253 0.859232 CGGAATAGATCCCGCAAACG 59.141 55.000 0.00 0.00 46.39 3.60
253 254 1.805120 CGGAATAGATCCCGCAAACGT 60.805 52.381 0.00 0.00 46.39 3.99
254 255 1.597663 GGAATAGATCCCGCAAACGTG 59.402 52.381 0.00 0.00 43.00 4.49
255 256 2.277084 GAATAGATCCCGCAAACGTGT 58.723 47.619 0.00 0.00 37.70 4.49
256 257 1.935933 ATAGATCCCGCAAACGTGTC 58.064 50.000 0.00 0.00 37.70 3.67
257 258 0.108520 TAGATCCCGCAAACGTGTCC 60.109 55.000 0.00 0.00 37.70 4.02
258 259 2.359478 ATCCCGCAAACGTGTCCC 60.359 61.111 0.00 0.00 37.70 4.46
259 260 3.185299 ATCCCGCAAACGTGTCCCA 62.185 57.895 0.00 0.00 37.70 4.37
260 261 3.656045 CCCGCAAACGTGTCCCAC 61.656 66.667 0.00 0.00 37.70 4.61
261 262 2.897846 CCGCAAACGTGTCCCACA 60.898 61.111 0.00 0.00 37.70 4.17
262 263 2.473760 CCGCAAACGTGTCCCACAA 61.474 57.895 0.00 0.00 37.70 3.33
263 264 1.010125 CGCAAACGTGTCCCACAAG 60.010 57.895 0.00 0.00 33.40 3.16
264 265 1.433053 CGCAAACGTGTCCCACAAGA 61.433 55.000 0.00 0.00 33.40 3.02
265 266 0.028902 GCAAACGTGTCCCACAAGAC 59.971 55.000 0.00 0.00 37.28 3.01
266 267 1.374560 CAAACGTGTCCCACAAGACA 58.625 50.000 0.00 0.00 44.38 3.41
272 273 2.064434 TGTCCCACAAGACATTTGCA 57.936 45.000 0.00 0.00 41.78 4.08
273 274 1.955778 TGTCCCACAAGACATTTGCAG 59.044 47.619 0.00 0.00 41.78 4.41
274 275 1.270550 GTCCCACAAGACATTTGCAGG 59.729 52.381 0.00 0.00 36.73 4.85
275 276 1.144708 TCCCACAAGACATTTGCAGGA 59.855 47.619 0.00 0.00 0.00 3.86
276 277 1.270550 CCCACAAGACATTTGCAGGAC 59.729 52.381 0.00 0.00 0.00 3.85
277 278 1.955778 CCACAAGACATTTGCAGGACA 59.044 47.619 0.00 0.00 0.00 4.02
278 279 2.030540 CCACAAGACATTTGCAGGACAG 60.031 50.000 0.00 0.00 0.00 3.51
279 280 2.880268 CACAAGACATTTGCAGGACAGA 59.120 45.455 0.00 0.00 0.00 3.41
280 281 3.504906 CACAAGACATTTGCAGGACAGAT 59.495 43.478 0.00 0.00 0.00 2.90
281 282 4.022589 CACAAGACATTTGCAGGACAGATT 60.023 41.667 0.00 0.00 0.00 2.40
282 283 4.586001 ACAAGACATTTGCAGGACAGATTT 59.414 37.500 0.00 0.00 0.00 2.17
283 284 5.769662 ACAAGACATTTGCAGGACAGATTTA 59.230 36.000 0.00 0.00 0.00 1.40
284 285 5.886960 AGACATTTGCAGGACAGATTTAC 57.113 39.130 0.00 0.00 0.00 2.01
285 286 4.393062 AGACATTTGCAGGACAGATTTACG 59.607 41.667 0.00 0.00 0.00 3.18
286 287 3.440173 ACATTTGCAGGACAGATTTACGG 59.560 43.478 0.00 0.00 0.00 4.02
287 288 3.410631 TTTGCAGGACAGATTTACGGA 57.589 42.857 0.00 0.00 0.00 4.69
288 289 3.410631 TTGCAGGACAGATTTACGGAA 57.589 42.857 0.00 0.00 0.00 4.30
289 290 3.410631 TGCAGGACAGATTTACGGAAA 57.589 42.857 0.00 0.00 0.00 3.13
290 291 3.071479 TGCAGGACAGATTTACGGAAAC 58.929 45.455 0.00 0.00 0.00 2.78
291 292 3.071479 GCAGGACAGATTTACGGAAACA 58.929 45.455 0.00 0.00 0.00 2.83
292 293 3.125316 GCAGGACAGATTTACGGAAACAG 59.875 47.826 0.00 0.00 0.00 3.16
293 294 4.315803 CAGGACAGATTTACGGAAACAGT 58.684 43.478 0.00 0.00 0.00 3.55
294 295 4.755123 CAGGACAGATTTACGGAAACAGTT 59.245 41.667 0.00 0.00 0.00 3.16
295 296 4.995487 AGGACAGATTTACGGAAACAGTTC 59.005 41.667 0.00 0.00 0.00 3.01
304 305 1.145803 GGAAACAGTTCCGTCGAAGG 58.854 55.000 11.59 11.59 44.01 3.46
305 306 1.539712 GGAAACAGTTCCGTCGAAGGT 60.540 52.381 17.24 0.00 44.01 3.50
306 307 1.791204 GAAACAGTTCCGTCGAAGGTC 59.209 52.381 17.24 11.42 0.00 3.85
307 308 1.038280 AACAGTTCCGTCGAAGGTCT 58.962 50.000 17.24 13.34 0.00 3.85
308 309 0.597072 ACAGTTCCGTCGAAGGTCTC 59.403 55.000 17.24 8.79 0.00 3.36
313 314 4.099170 CGTCGAAGGTCTCGCCGT 62.099 66.667 0.00 0.00 43.53 5.68
314 315 3.996744 CGTCGAAGGTCTCGCCGTC 62.997 68.421 0.00 0.00 43.53 4.79
316 317 4.493747 CGAAGGTCTCGCCGTCCC 62.494 72.222 0.00 0.00 41.82 4.46
317 318 3.379445 GAAGGTCTCGCCGTCCCA 61.379 66.667 0.00 0.00 43.70 4.37
318 319 2.683933 AAGGTCTCGCCGTCCCAT 60.684 61.111 0.00 0.00 43.70 4.00
319 320 1.380785 AAGGTCTCGCCGTCCCATA 60.381 57.895 0.00 0.00 43.70 2.74
320 321 0.974010 AAGGTCTCGCCGTCCCATAA 60.974 55.000 0.00 0.00 43.70 1.90
321 322 0.974010 AGGTCTCGCCGTCCCATAAA 60.974 55.000 0.00 0.00 43.70 1.40
322 323 0.106149 GGTCTCGCCGTCCCATAAAT 59.894 55.000 0.00 0.00 0.00 1.40
323 324 1.342174 GGTCTCGCCGTCCCATAAATA 59.658 52.381 0.00 0.00 0.00 1.40
324 325 2.224113 GGTCTCGCCGTCCCATAAATAA 60.224 50.000 0.00 0.00 0.00 1.40
325 326 3.460103 GTCTCGCCGTCCCATAAATAAA 58.540 45.455 0.00 0.00 0.00 1.40
326 327 4.062991 GTCTCGCCGTCCCATAAATAAAT 58.937 43.478 0.00 0.00 0.00 1.40
330 331 6.095720 TCTCGCCGTCCCATAAATAAATTTTT 59.904 34.615 0.00 0.00 0.00 1.94
365 367 1.135373 AGAACACGCTGATACGGAGTG 60.135 52.381 11.58 11.58 45.73 3.51
404 407 2.482316 CGGTAGATGCCAAACGTATGGA 60.482 50.000 0.00 0.00 43.54 3.41
512 515 2.104170 GACGAGAGGATGGAAAGGTCT 58.896 52.381 0.00 0.00 0.00 3.85
519 527 4.534103 AGAGGATGGAAAGGTCTATATGCC 59.466 45.833 0.00 0.00 0.00 4.40
591 629 0.179045 CCATCAATCACCGTCCCCTC 60.179 60.000 0.00 0.00 0.00 4.30
604 642 2.844839 CCCTCCCGGAGTGGATCC 60.845 72.222 13.62 4.20 45.64 3.36
725 778 4.394712 CGCTCCACAGTCCACCCC 62.395 72.222 0.00 0.00 0.00 4.95
726 779 4.035102 GCTCCACAGTCCACCCCC 62.035 72.222 0.00 0.00 0.00 5.40
889 960 4.028490 TTTCTCCACCGCCGGCAT 62.028 61.111 28.98 11.47 0.00 4.40
963 1034 3.403558 GGGTGGACAGAGCCCTCC 61.404 72.222 0.00 0.00 39.31 4.30
1341 1416 2.908940 GGCTTATGCATGGCGCCT 60.909 61.111 29.70 9.54 41.33 5.52
1371 1451 2.191802 CTGTGATCGTCAGCTCATGTC 58.808 52.381 5.09 0.00 0.00 3.06
1383 1463 5.235186 GTCAGCTCATGTCAATGTACATACC 59.765 44.000 9.21 0.70 38.01 2.73
1546 1626 8.377034 AGAAATCAATCAAAATTGGGTTCATGA 58.623 29.630 0.00 0.00 42.19 3.07
1736 1816 0.603707 CGCCTTCTTGAACTCTGCCA 60.604 55.000 0.00 0.00 0.00 4.92
1747 1827 0.469705 ACTCTGCCAAATGGTTGCCA 60.470 50.000 0.71 0.00 38.19 4.92
1804 1884 2.190981 GCGTCCACCTTTATGTACTCG 58.809 52.381 0.00 0.00 0.00 4.18
1807 1887 3.432782 GTCCACCTTTATGTACTCGTCG 58.567 50.000 0.00 0.00 0.00 5.12
1893 1973 4.357325 AGGTCATATATCTTGCGGATCCT 58.643 43.478 10.75 0.00 35.98 3.24
1897 1977 4.777366 TCATATATCTTGCGGATCCTGGAA 59.223 41.667 10.75 9.94 35.98 3.53
1913 1993 1.717032 GGAAACAGCCCTTTTTCCCT 58.283 50.000 12.73 0.00 43.47 4.20
1915 1995 2.037251 GGAAACAGCCCTTTTTCCCTTC 59.963 50.000 12.73 0.00 43.47 3.46
1917 1997 0.539669 ACAGCCCTTTTTCCCTTCGG 60.540 55.000 0.00 0.00 0.00 4.30
1927 2008 2.561478 TTCCCTTCGGAAAAGAGTGG 57.439 50.000 0.00 0.00 45.54 4.00
1938 2019 4.142469 CGGAAAAGAGTGGTGTGTTTTCTT 60.142 41.667 6.28 0.00 38.88 2.52
1976 2057 1.266178 ATTGCACTAGTTTTGGCCCC 58.734 50.000 0.00 0.00 0.00 5.80
1991 2072 3.381983 CCCCTTTTCCGGCTTGCC 61.382 66.667 0.00 0.75 0.00 4.52
2000 2081 0.827368 TCCGGCTTGCCTTTTGTTTT 59.173 45.000 10.12 0.00 0.00 2.43
2001 2082 2.032620 TCCGGCTTGCCTTTTGTTTTA 58.967 42.857 10.12 0.00 0.00 1.52
2002 2083 2.630580 TCCGGCTTGCCTTTTGTTTTAT 59.369 40.909 10.12 0.00 0.00 1.40
2003 2084 3.070302 TCCGGCTTGCCTTTTGTTTTATT 59.930 39.130 10.12 0.00 0.00 1.40
2009 2090 6.072783 GGCTTGCCTTTTGTTTTATTATGCAA 60.073 34.615 4.11 0.00 35.22 4.08
2026 2107 5.859205 ATGCAATTTTCTCTCATAACCCC 57.141 39.130 0.00 0.00 0.00 4.95
2027 2108 4.671831 TGCAATTTTCTCTCATAACCCCA 58.328 39.130 0.00 0.00 0.00 4.96
2028 2109 4.462483 TGCAATTTTCTCTCATAACCCCAC 59.538 41.667 0.00 0.00 0.00 4.61
2029 2110 4.706962 GCAATTTTCTCTCATAACCCCACT 59.293 41.667 0.00 0.00 0.00 4.00
2030 2111 5.393461 GCAATTTTCTCTCATAACCCCACTG 60.393 44.000 0.00 0.00 0.00 3.66
2031 2112 4.993705 TTTTCTCTCATAACCCCACTGT 57.006 40.909 0.00 0.00 0.00 3.55
2032 2113 4.553330 TTTCTCTCATAACCCCACTGTC 57.447 45.455 0.00 0.00 0.00 3.51
2033 2114 3.474798 TCTCTCATAACCCCACTGTCT 57.525 47.619 0.00 0.00 0.00 3.41
2034 2115 3.366396 TCTCTCATAACCCCACTGTCTC 58.634 50.000 0.00 0.00 0.00 3.36
2035 2116 3.099905 CTCTCATAACCCCACTGTCTCA 58.900 50.000 0.00 0.00 0.00 3.27
2036 2117 3.515502 CTCTCATAACCCCACTGTCTCAA 59.484 47.826 0.00 0.00 0.00 3.02
2037 2118 3.907474 TCTCATAACCCCACTGTCTCAAA 59.093 43.478 0.00 0.00 0.00 2.69
2038 2119 4.349636 TCTCATAACCCCACTGTCTCAAAA 59.650 41.667 0.00 0.00 0.00 2.44
2039 2120 5.014123 TCTCATAACCCCACTGTCTCAAAAT 59.986 40.000 0.00 0.00 0.00 1.82
2040 2121 6.214615 TCTCATAACCCCACTGTCTCAAAATA 59.785 38.462 0.00 0.00 0.00 1.40
2041 2122 6.785076 TCATAACCCCACTGTCTCAAAATAA 58.215 36.000 0.00 0.00 0.00 1.40
2042 2123 6.884295 TCATAACCCCACTGTCTCAAAATAAG 59.116 38.462 0.00 0.00 0.00 1.73
2043 2124 4.724279 ACCCCACTGTCTCAAAATAAGT 57.276 40.909 0.00 0.00 0.00 2.24
2044 2125 4.398319 ACCCCACTGTCTCAAAATAAGTG 58.602 43.478 0.00 0.00 38.36 3.16
2045 2126 4.104102 ACCCCACTGTCTCAAAATAAGTGA 59.896 41.667 2.80 0.00 40.54 3.41
2046 2127 4.455877 CCCCACTGTCTCAAAATAAGTGAC 59.544 45.833 2.80 0.00 40.54 3.67
2047 2128 5.308825 CCCACTGTCTCAAAATAAGTGACT 58.691 41.667 2.80 0.00 40.54 3.41
2048 2129 5.409826 CCCACTGTCTCAAAATAAGTGACTC 59.590 44.000 2.80 0.00 40.54 3.36
2049 2130 5.991606 CCACTGTCTCAAAATAAGTGACTCA 59.008 40.000 2.80 0.00 40.54 3.41
2050 2131 6.483307 CCACTGTCTCAAAATAAGTGACTCAA 59.517 38.462 2.80 0.00 40.54 3.02
2051 2132 7.173907 CCACTGTCTCAAAATAAGTGACTCAAT 59.826 37.037 2.80 0.00 40.54 2.57
2052 2133 8.562892 CACTGTCTCAAAATAAGTGACTCAATT 58.437 33.333 0.00 0.00 40.54 2.32
2053 2134 9.125026 ACTGTCTCAAAATAAGTGACTCAATTT 57.875 29.630 0.00 0.00 32.38 1.82
2054 2135 9.956720 CTGTCTCAAAATAAGTGACTCAATTTT 57.043 29.630 10.89 10.89 33.07 1.82
2055 2136 9.734620 TGTCTCAAAATAAGTGACTCAATTTTG 57.265 29.630 25.10 25.10 44.73 2.44
2056 2137 9.736023 GTCTCAAAATAAGTGACTCAATTTTGT 57.264 29.630 27.30 8.05 44.18 2.83
2067 2148 9.174166 AGTGACTCAATTTTGTACTAACTTTGT 57.826 29.630 0.00 0.00 0.00 2.83
2103 2184 9.965824 AATACAAAGTTGAGTCACTTATTTTGG 57.034 29.630 12.94 0.78 35.87 3.28
2104 2185 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
2105 2186 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
2106 2187 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
2107 2188 5.941788 AGTTGAGTCACTTATTTTGGGACT 58.058 37.500 0.00 0.00 41.22 3.85
2108 2189 5.765182 AGTTGAGTCACTTATTTTGGGACTG 59.235 40.000 3.22 0.00 38.82 3.51
2109 2190 4.651778 TGAGTCACTTATTTTGGGACTGG 58.348 43.478 3.22 0.00 38.82 4.00
2110 2191 4.349636 TGAGTCACTTATTTTGGGACTGGA 59.650 41.667 3.22 0.00 38.82 3.86
2111 2192 4.911390 AGTCACTTATTTTGGGACTGGAG 58.089 43.478 0.00 0.00 37.43 3.86
2112 2193 4.010349 GTCACTTATTTTGGGACTGGAGG 58.990 47.826 0.00 0.00 0.00 4.30
2113 2194 3.010138 TCACTTATTTTGGGACTGGAGGG 59.990 47.826 0.00 0.00 0.00 4.30
2114 2195 3.010138 CACTTATTTTGGGACTGGAGGGA 59.990 47.826 0.00 0.00 0.00 4.20
2115 2196 3.267031 ACTTATTTTGGGACTGGAGGGAG 59.733 47.826 0.00 0.00 0.00 4.30
2116 2197 1.760405 ATTTTGGGACTGGAGGGAGT 58.240 50.000 0.00 0.00 0.00 3.85
2117 2198 2.426431 TTTTGGGACTGGAGGGAGTA 57.574 50.000 0.00 0.00 0.00 2.59
2160 2241 2.875933 CCGAACAAAAGCACTTACCTCA 59.124 45.455 0.00 0.00 0.00 3.86
2166 2247 4.141711 ACAAAAGCACTTACCTCAGACTCA 60.142 41.667 0.00 0.00 0.00 3.41
2214 2295 4.682050 GCTTCAATCTCTCCCCAGTAGAAC 60.682 50.000 0.00 0.00 0.00 3.01
2235 2316 2.576191 CCCAGATTCCTCCCACAAGTTA 59.424 50.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.258441 AGATCAATCAAGCAACATTCTCAATG 58.742 34.615 0.00 0.00 44.48 2.82
5 6 7.406031 AGATCAATCAAGCAACATTCTCAAT 57.594 32.000 0.00 0.00 0.00 2.57
6 7 6.829229 AGATCAATCAAGCAACATTCTCAA 57.171 33.333 0.00 0.00 0.00 3.02
7 8 7.555195 ACATAGATCAATCAAGCAACATTCTCA 59.445 33.333 0.00 0.00 0.00 3.27
8 9 7.928103 ACATAGATCAATCAAGCAACATTCTC 58.072 34.615 0.00 0.00 0.00 2.87
9 10 7.254692 CGACATAGATCAATCAAGCAACATTCT 60.255 37.037 0.00 0.00 0.00 2.40
10 11 6.849811 CGACATAGATCAATCAAGCAACATTC 59.150 38.462 0.00 0.00 0.00 2.67
11 12 6.317140 ACGACATAGATCAATCAAGCAACATT 59.683 34.615 0.00 0.00 0.00 2.71
12 13 5.819379 ACGACATAGATCAATCAAGCAACAT 59.181 36.000 0.00 0.00 0.00 2.71
13 14 5.178061 ACGACATAGATCAATCAAGCAACA 58.822 37.500 0.00 0.00 0.00 3.33
14 15 5.725110 ACGACATAGATCAATCAAGCAAC 57.275 39.130 0.00 0.00 0.00 4.17
15 16 6.371271 TCAAACGACATAGATCAATCAAGCAA 59.629 34.615 0.00 0.00 0.00 3.91
16 17 5.874261 TCAAACGACATAGATCAATCAAGCA 59.126 36.000 0.00 0.00 0.00 3.91
17 18 6.349973 TCAAACGACATAGATCAATCAAGC 57.650 37.500 0.00 0.00 0.00 4.01
18 19 6.036408 TGCTCAAACGACATAGATCAATCAAG 59.964 38.462 0.00 0.00 0.00 3.02
19 20 5.874261 TGCTCAAACGACATAGATCAATCAA 59.126 36.000 0.00 0.00 0.00 2.57
20 21 5.418676 TGCTCAAACGACATAGATCAATCA 58.581 37.500 0.00 0.00 0.00 2.57
21 22 5.973651 TGCTCAAACGACATAGATCAATC 57.026 39.130 0.00 0.00 0.00 2.67
22 23 6.286758 AGATGCTCAAACGACATAGATCAAT 58.713 36.000 0.00 0.00 0.00 2.57
23 24 5.664457 AGATGCTCAAACGACATAGATCAA 58.336 37.500 0.00 0.00 0.00 2.57
24 25 5.268118 AGATGCTCAAACGACATAGATCA 57.732 39.130 0.00 0.00 0.00 2.92
25 26 6.595772 AAAGATGCTCAAACGACATAGATC 57.404 37.500 0.00 0.00 0.00 2.75
26 27 6.779117 CAAAAGATGCTCAAACGACATAGAT 58.221 36.000 0.00 0.00 0.00 1.98
27 28 6.169419 CAAAAGATGCTCAAACGACATAGA 57.831 37.500 0.00 0.00 0.00 1.98
42 43 5.401972 TGTGCGATAAAACAAGCAAAAGATG 59.598 36.000 0.00 0.00 41.56 2.90
43 44 5.527951 TGTGCGATAAAACAAGCAAAAGAT 58.472 33.333 0.00 0.00 41.56 2.40
44 45 4.926244 TGTGCGATAAAACAAGCAAAAGA 58.074 34.783 0.00 0.00 41.56 2.52
45 46 5.827568 ATGTGCGATAAAACAAGCAAAAG 57.172 34.783 0.00 0.00 41.56 2.27
46 47 5.750547 TGAATGTGCGATAAAACAAGCAAAA 59.249 32.000 0.00 0.00 41.56 2.44
47 48 5.284864 TGAATGTGCGATAAAACAAGCAAA 58.715 33.333 0.00 0.00 41.56 3.68
48 49 4.864633 TGAATGTGCGATAAAACAAGCAA 58.135 34.783 0.00 0.00 41.56 3.91
49 50 4.495911 TGAATGTGCGATAAAACAAGCA 57.504 36.364 0.00 0.00 37.26 3.91
50 51 5.094812 TCATGAATGTGCGATAAAACAAGC 58.905 37.500 0.00 0.00 0.00 4.01
51 52 7.699391 AGATTCATGAATGTGCGATAAAACAAG 59.301 33.333 25.37 0.00 0.00 3.16
52 53 7.537715 AGATTCATGAATGTGCGATAAAACAA 58.462 30.769 25.37 0.00 0.00 2.83
53 54 7.087409 AGATTCATGAATGTGCGATAAAACA 57.913 32.000 25.37 0.00 0.00 2.83
54 55 9.502145 TTTAGATTCATGAATGTGCGATAAAAC 57.498 29.630 25.37 6.47 0.00 2.43
55 56 9.502145 GTTTAGATTCATGAATGTGCGATAAAA 57.498 29.630 25.37 13.77 0.00 1.52
56 57 8.892723 AGTTTAGATTCATGAATGTGCGATAAA 58.107 29.630 25.37 14.42 0.00 1.40
57 58 8.437360 AGTTTAGATTCATGAATGTGCGATAA 57.563 30.769 25.37 9.35 0.00 1.75
58 59 8.337532 CAAGTTTAGATTCATGAATGTGCGATA 58.662 33.333 25.37 3.32 0.00 2.92
59 60 6.932356 AGTTTAGATTCATGAATGTGCGAT 57.068 33.333 25.37 7.39 0.00 4.58
60 61 6.371271 TCAAGTTTAGATTCATGAATGTGCGA 59.629 34.615 25.37 9.38 0.00 5.10
61 62 6.545508 TCAAGTTTAGATTCATGAATGTGCG 58.454 36.000 25.37 8.14 0.00 5.34
62 63 9.443283 GTATCAAGTTTAGATTCATGAATGTGC 57.557 33.333 25.37 14.89 0.00 4.57
63 64 9.941664 GGTATCAAGTTTAGATTCATGAATGTG 57.058 33.333 25.37 8.60 0.00 3.21
64 65 9.911788 AGGTATCAAGTTTAGATTCATGAATGT 57.088 29.630 25.37 22.77 0.00 2.71
66 67 9.265901 CGAGGTATCAAGTTTAGATTCATGAAT 57.734 33.333 20.85 20.85 0.00 2.57
67 68 8.258007 ACGAGGTATCAAGTTTAGATTCATGAA 58.742 33.333 11.26 11.26 0.00 2.57
68 69 7.782049 ACGAGGTATCAAGTTTAGATTCATGA 58.218 34.615 0.00 0.00 0.00 3.07
69 70 8.425577 AACGAGGTATCAAGTTTAGATTCATG 57.574 34.615 0.00 0.00 0.00 3.07
70 71 8.883731 CAAACGAGGTATCAAGTTTAGATTCAT 58.116 33.333 0.00 0.00 35.36 2.57
71 72 7.876068 ACAAACGAGGTATCAAGTTTAGATTCA 59.124 33.333 0.00 0.00 35.36 2.57
72 73 8.252964 ACAAACGAGGTATCAAGTTTAGATTC 57.747 34.615 0.00 0.00 35.36 2.52
73 74 8.504005 CAACAAACGAGGTATCAAGTTTAGATT 58.496 33.333 0.00 0.00 35.36 2.40
74 75 7.360946 GCAACAAACGAGGTATCAAGTTTAGAT 60.361 37.037 0.00 0.00 35.36 1.98
75 76 6.073440 GCAACAAACGAGGTATCAAGTTTAGA 60.073 38.462 0.00 0.00 35.36 2.10
76 77 6.077838 GCAACAAACGAGGTATCAAGTTTAG 58.922 40.000 0.00 0.00 35.36 1.85
77 78 5.333492 CGCAACAAACGAGGTATCAAGTTTA 60.333 40.000 0.00 0.00 35.36 2.01
78 79 4.553938 CGCAACAAACGAGGTATCAAGTTT 60.554 41.667 0.00 0.00 37.29 2.66
79 80 3.059188 CGCAACAAACGAGGTATCAAGTT 60.059 43.478 0.00 0.00 0.00 2.66
80 81 2.478894 CGCAACAAACGAGGTATCAAGT 59.521 45.455 0.00 0.00 0.00 3.16
81 82 2.724839 GCGCAACAAACGAGGTATCAAG 60.725 50.000 0.30 0.00 0.00 3.02
82 83 1.195900 GCGCAACAAACGAGGTATCAA 59.804 47.619 0.30 0.00 0.00 2.57
83 84 0.793861 GCGCAACAAACGAGGTATCA 59.206 50.000 0.30 0.00 0.00 2.15
84 85 0.793861 TGCGCAACAAACGAGGTATC 59.206 50.000 8.16 0.00 0.00 2.24
85 86 1.448985 ATGCGCAACAAACGAGGTAT 58.551 45.000 17.11 0.00 0.00 2.73
86 87 2.081725 TATGCGCAACAAACGAGGTA 57.918 45.000 17.11 0.00 0.00 3.08
87 88 1.231221 TTATGCGCAACAAACGAGGT 58.769 45.000 17.11 0.00 0.00 3.85
88 89 2.176369 CATTATGCGCAACAAACGAGG 58.824 47.619 17.11 0.00 0.00 4.63
89 90 2.850321 ACATTATGCGCAACAAACGAG 58.150 42.857 17.11 6.10 0.00 4.18
90 91 2.979401 ACATTATGCGCAACAAACGA 57.021 40.000 17.11 0.00 0.00 3.85
91 92 4.367716 AAAACATTATGCGCAACAAACG 57.632 36.364 17.11 9.93 0.00 3.60
92 93 6.731505 CACATAAAACATTATGCGCAACAAAC 59.268 34.615 17.11 0.00 38.20 2.93
93 94 6.642540 TCACATAAAACATTATGCGCAACAAA 59.357 30.769 17.11 10.16 38.20 2.83
94 95 6.152379 TCACATAAAACATTATGCGCAACAA 58.848 32.000 17.11 12.70 38.20 2.83
95 96 5.703876 TCACATAAAACATTATGCGCAACA 58.296 33.333 17.11 3.70 38.20 3.33
96 97 6.471841 TCATCACATAAAACATTATGCGCAAC 59.528 34.615 17.11 0.00 38.20 4.17
97 98 6.558909 TCATCACATAAAACATTATGCGCAA 58.441 32.000 17.11 0.00 38.20 4.85
98 99 6.129053 TCATCACATAAAACATTATGCGCA 57.871 33.333 14.96 14.96 38.20 6.09
99 100 7.448588 TTTCATCACATAAAACATTATGCGC 57.551 32.000 0.00 0.00 38.20 6.09
155 156 9.404848 AGTTTATCATGACAAGTTCATCATCAT 57.595 29.630 0.00 0.00 43.68 2.45
156 157 8.797350 AGTTTATCATGACAAGTTCATCATCA 57.203 30.769 0.00 0.00 43.68 3.07
157 158 9.499585 CAAGTTTATCATGACAAGTTCATCATC 57.500 33.333 0.00 0.00 43.68 2.92
158 159 9.234827 TCAAGTTTATCATGACAAGTTCATCAT 57.765 29.630 0.00 0.00 43.68 2.45
159 160 8.620116 TCAAGTTTATCATGACAAGTTCATCA 57.380 30.769 0.00 0.00 43.68 3.07
165 166 9.507329 ACACTTATCAAGTTTATCATGACAAGT 57.493 29.630 0.00 0.00 40.55 3.16
169 170 9.922305 GCTTACACTTATCAAGTTTATCATGAC 57.078 33.333 0.00 0.00 40.46 3.06
170 171 9.890629 AGCTTACACTTATCAAGTTTATCATGA 57.109 29.630 0.00 0.00 40.46 3.07
188 189 9.450807 CCTGCAAATACAATAATAAGCTTACAC 57.549 33.333 8.70 0.00 0.00 2.90
189 190 9.402320 TCCTGCAAATACAATAATAAGCTTACA 57.598 29.630 8.70 0.00 0.00 2.41
190 191 9.665264 GTCCTGCAAATACAATAATAAGCTTAC 57.335 33.333 8.70 0.00 0.00 2.34
191 192 8.556194 CGTCCTGCAAATACAATAATAAGCTTA 58.444 33.333 8.99 8.99 0.00 3.09
192 193 7.417612 CGTCCTGCAAATACAATAATAAGCTT 58.582 34.615 3.48 3.48 0.00 3.74
193 194 6.017109 CCGTCCTGCAAATACAATAATAAGCT 60.017 38.462 0.00 0.00 0.00 3.74
194 195 6.142817 CCGTCCTGCAAATACAATAATAAGC 58.857 40.000 0.00 0.00 0.00 3.09
195 196 6.142817 GCCGTCCTGCAAATACAATAATAAG 58.857 40.000 0.00 0.00 0.00 1.73
196 197 5.277586 CGCCGTCCTGCAAATACAATAATAA 60.278 40.000 0.00 0.00 0.00 1.40
197 198 4.212425 CGCCGTCCTGCAAATACAATAATA 59.788 41.667 0.00 0.00 0.00 0.98
198 199 3.003275 CGCCGTCCTGCAAATACAATAAT 59.997 43.478 0.00 0.00 0.00 1.28
199 200 2.353269 CGCCGTCCTGCAAATACAATAA 59.647 45.455 0.00 0.00 0.00 1.40
200 201 1.937223 CGCCGTCCTGCAAATACAATA 59.063 47.619 0.00 0.00 0.00 1.90
201 202 0.732571 CGCCGTCCTGCAAATACAAT 59.267 50.000 0.00 0.00 0.00 2.71
202 203 0.320858 TCGCCGTCCTGCAAATACAA 60.321 50.000 0.00 0.00 0.00 2.41
203 204 0.739462 CTCGCCGTCCTGCAAATACA 60.739 55.000 0.00 0.00 0.00 2.29
204 205 2.006772 CTCGCCGTCCTGCAAATAC 58.993 57.895 0.00 0.00 0.00 1.89
205 206 1.813753 GCTCGCCGTCCTGCAAATA 60.814 57.895 0.00 0.00 0.00 1.40
206 207 3.127533 GCTCGCCGTCCTGCAAAT 61.128 61.111 0.00 0.00 0.00 2.32
228 229 2.432628 GGGATCTATTCCGCGCCG 60.433 66.667 0.00 0.00 46.52 6.46
229 230 2.432628 CGGGATCTATTCCGCGCC 60.433 66.667 0.00 0.00 46.52 6.53
233 234 0.859232 CGTTTGCGGGATCTATTCCG 59.141 55.000 5.25 5.25 46.52 4.30
234 235 1.597663 CACGTTTGCGGGATCTATTCC 59.402 52.381 0.00 0.00 45.97 3.01
235 236 2.277084 ACACGTTTGCGGGATCTATTC 58.723 47.619 0.00 0.00 45.97 1.75
236 237 2.277084 GACACGTTTGCGGGATCTATT 58.723 47.619 0.00 0.00 45.97 1.73
237 238 1.472728 GGACACGTTTGCGGGATCTAT 60.473 52.381 0.00 0.00 45.97 1.98
238 239 0.108520 GGACACGTTTGCGGGATCTA 60.109 55.000 0.00 0.00 45.97 1.98
239 240 1.375523 GGACACGTTTGCGGGATCT 60.376 57.895 0.00 0.00 45.97 2.75
240 241 2.396157 GGGACACGTTTGCGGGATC 61.396 63.158 0.00 0.00 45.97 3.36
241 242 2.359478 GGGACACGTTTGCGGGAT 60.359 61.111 0.00 0.00 45.97 3.85
242 243 3.862991 TGGGACACGTTTGCGGGA 61.863 61.111 0.00 0.00 45.97 5.14
254 255 1.270550 CCTGCAAATGTCTTGTGGGAC 59.729 52.381 0.00 0.00 36.81 4.46
255 256 1.144708 TCCTGCAAATGTCTTGTGGGA 59.855 47.619 0.00 0.00 0.00 4.37
256 257 1.270550 GTCCTGCAAATGTCTTGTGGG 59.729 52.381 0.00 0.00 0.00 4.61
257 258 1.955778 TGTCCTGCAAATGTCTTGTGG 59.044 47.619 0.00 0.00 0.00 4.17
258 259 2.880268 TCTGTCCTGCAAATGTCTTGTG 59.120 45.455 0.00 0.00 0.00 3.33
259 260 3.213206 TCTGTCCTGCAAATGTCTTGT 57.787 42.857 0.00 0.00 0.00 3.16
260 261 4.778534 AATCTGTCCTGCAAATGTCTTG 57.221 40.909 0.00 0.00 0.00 3.02
261 262 5.106555 CGTAAATCTGTCCTGCAAATGTCTT 60.107 40.000 0.00 0.00 0.00 3.01
262 263 4.393062 CGTAAATCTGTCCTGCAAATGTCT 59.607 41.667 0.00 0.00 0.00 3.41
263 264 4.437390 CCGTAAATCTGTCCTGCAAATGTC 60.437 45.833 0.00 0.00 0.00 3.06
264 265 3.440173 CCGTAAATCTGTCCTGCAAATGT 59.560 43.478 0.00 0.00 0.00 2.71
265 266 3.689161 TCCGTAAATCTGTCCTGCAAATG 59.311 43.478 0.00 0.00 0.00 2.32
266 267 3.950397 TCCGTAAATCTGTCCTGCAAAT 58.050 40.909 0.00 0.00 0.00 2.32
267 268 3.410631 TCCGTAAATCTGTCCTGCAAA 57.589 42.857 0.00 0.00 0.00 3.68
268 269 3.410631 TTCCGTAAATCTGTCCTGCAA 57.589 42.857 0.00 0.00 0.00 4.08
269 270 3.071479 GTTTCCGTAAATCTGTCCTGCA 58.929 45.455 0.00 0.00 0.00 4.41
270 271 3.071479 TGTTTCCGTAAATCTGTCCTGC 58.929 45.455 0.00 0.00 0.00 4.85
271 272 4.315803 ACTGTTTCCGTAAATCTGTCCTG 58.684 43.478 0.00 0.00 0.00 3.86
272 273 4.618920 ACTGTTTCCGTAAATCTGTCCT 57.381 40.909 0.00 0.00 0.00 3.85
273 274 4.153655 GGAACTGTTTCCGTAAATCTGTCC 59.846 45.833 0.00 0.00 42.20 4.02
274 275 5.278964 GGAACTGTTTCCGTAAATCTGTC 57.721 43.478 0.00 0.00 42.20 3.51
286 287 1.791204 GACCTTCGACGGAACTGTTTC 59.209 52.381 15.91 0.00 0.00 2.78
287 288 1.411612 AGACCTTCGACGGAACTGTTT 59.588 47.619 15.91 0.00 0.00 2.83
288 289 1.000496 GAGACCTTCGACGGAACTGTT 60.000 52.381 15.91 0.00 0.00 3.16
289 290 0.597072 GAGACCTTCGACGGAACTGT 59.403 55.000 15.91 0.00 0.00 3.55
290 291 3.403276 GAGACCTTCGACGGAACTG 57.597 57.895 15.91 0.00 0.00 3.16
300 301 1.389609 TATGGGACGGCGAGACCTTC 61.390 60.000 16.62 0.00 35.94 3.46
301 302 0.974010 TTATGGGACGGCGAGACCTT 60.974 55.000 16.62 12.77 35.00 3.50
302 303 0.974010 TTTATGGGACGGCGAGACCT 60.974 55.000 16.62 5.35 35.00 3.85
303 304 0.106149 ATTTATGGGACGGCGAGACC 59.894 55.000 16.62 13.18 0.00 3.85
304 305 2.806608 TATTTATGGGACGGCGAGAC 57.193 50.000 16.62 4.28 0.00 3.36
305 306 3.823281 TTTATTTATGGGACGGCGAGA 57.177 42.857 16.62 0.00 0.00 4.04
306 307 5.432885 AAATTTATTTATGGGACGGCGAG 57.567 39.130 16.62 0.00 0.00 5.03
307 308 5.838531 AAAATTTATTTATGGGACGGCGA 57.161 34.783 16.62 0.00 0.00 5.54
308 309 5.172411 CGAAAAATTTATTTATGGGACGGCG 59.828 40.000 4.80 4.80 0.00 6.46
309 310 5.460748 CCGAAAAATTTATTTATGGGACGGC 59.539 40.000 0.00 0.00 0.00 5.68
310 311 6.797454 TCCGAAAAATTTATTTATGGGACGG 58.203 36.000 0.00 0.00 36.27 4.79
311 312 7.477494 ACTCCGAAAAATTTATTTATGGGACG 58.523 34.615 0.00 0.00 0.00 4.79
324 325 9.292195 TGTTCTATCCTTTTACTCCGAAAAATT 57.708 29.630 0.00 0.00 0.00 1.82
325 326 8.727910 GTGTTCTATCCTTTTACTCCGAAAAAT 58.272 33.333 0.00 0.00 0.00 1.82
326 327 7.095523 CGTGTTCTATCCTTTTACTCCGAAAAA 60.096 37.037 0.00 0.00 0.00 1.94
330 331 4.676196 GCGTGTTCTATCCTTTTACTCCGA 60.676 45.833 0.00 0.00 0.00 4.55
365 367 1.400990 CGCGCTACGTGTCTGTTACC 61.401 60.000 5.56 0.00 36.87 2.85
404 407 1.104577 ACGCCAACGGATTGTTTGGT 61.105 50.000 2.50 0.00 46.04 3.67
519 527 1.515521 GGTCAGGACAAAAGCCGGTG 61.516 60.000 1.90 0.00 0.00 4.94
591 629 2.635787 TAGTCGGGATCCACTCCGGG 62.636 65.000 15.23 0.00 46.01 5.73
604 642 3.119137 TGTGTGATGGAATGTCTAGTCGG 60.119 47.826 0.00 0.00 0.00 4.79
871 942 2.862674 TATGCCGGCGGTGGAGAAAC 62.863 60.000 28.82 8.47 0.00 2.78
889 960 2.290450 GGTTCTGGTGTTTTCCGGGATA 60.290 50.000 0.00 0.00 34.81 2.59
1311 1386 2.871133 CATAAGCCGAGAACACGTACA 58.129 47.619 0.00 0.00 0.00 2.90
1341 1416 0.317160 ACGATCACAGCGGACAAGAA 59.683 50.000 0.00 0.00 0.00 2.52
1371 1451 7.099764 ACTTCTTCTGACAGGTATGTACATTG 58.900 38.462 14.77 9.04 40.68 2.82
1383 1463 5.101628 GTCTGCATCTACTTCTTCTGACAG 58.898 45.833 0.00 0.00 0.00 3.51
1491 1571 1.333115 CACACGATTGCACAATGCTG 58.667 50.000 0.00 0.00 45.31 4.41
1546 1626 4.408276 AGTACATAGTCTGTCACCACACT 58.592 43.478 0.00 0.00 39.39 3.55
1714 1794 2.079925 GCAGAGTTCAAGAAGGCGATT 58.920 47.619 0.00 0.00 0.00 3.34
1736 1816 1.963515 GGTCTTCAGTGGCAACCATTT 59.036 47.619 0.00 0.00 35.28 2.32
1747 1827 0.679505 TAAGCGTGCAGGTCTTCAGT 59.320 50.000 15.84 0.67 0.00 3.41
1897 1977 1.328279 CGAAGGGAAAAAGGGCTGTT 58.672 50.000 0.00 0.00 0.00 3.16
1912 1992 2.561569 ACACACCACTCTTTTCCGAAG 58.438 47.619 0.00 0.00 0.00 3.79
1913 1993 2.702592 ACACACCACTCTTTTCCGAA 57.297 45.000 0.00 0.00 0.00 4.30
1915 1995 3.377172 AGAAAACACACCACTCTTTTCCG 59.623 43.478 0.00 0.00 34.49 4.30
1917 1997 5.949735 TCAAGAAAACACACCACTCTTTTC 58.050 37.500 0.00 0.00 34.27 2.29
1927 2008 4.729595 AGTTCCGTTTCAAGAAAACACAC 58.270 39.130 0.00 0.00 46.33 3.82
1938 2019 5.639506 TGCAATTTTCAAAAGTTCCGTTTCA 59.360 32.000 0.00 0.00 0.00 2.69
1976 2057 0.392706 AAAAGGCAAGCCGGAAAAGG 59.607 50.000 5.05 0.00 41.95 3.11
2000 2081 9.077885 GGGGTTATGAGAGAAAATTGCATAATA 57.922 33.333 0.00 0.00 34.93 0.98
2001 2082 7.564660 TGGGGTTATGAGAGAAAATTGCATAAT 59.435 33.333 0.00 0.00 34.93 1.28
2002 2083 6.894654 TGGGGTTATGAGAGAAAATTGCATAA 59.105 34.615 0.00 0.00 0.00 1.90
2003 2084 6.321181 GTGGGGTTATGAGAGAAAATTGCATA 59.679 38.462 0.00 0.00 0.00 3.14
2009 2090 5.251700 AGACAGTGGGGTTATGAGAGAAAAT 59.748 40.000 0.00 0.00 0.00 1.82
2022 2103 4.104102 TCACTTATTTTGAGACAGTGGGGT 59.896 41.667 0.00 0.00 36.34 4.95
2023 2104 4.455877 GTCACTTATTTTGAGACAGTGGGG 59.544 45.833 0.00 0.00 36.34 4.96
2024 2105 5.308825 AGTCACTTATTTTGAGACAGTGGG 58.691 41.667 0.00 0.00 36.34 4.61
2025 2106 5.991606 TGAGTCACTTATTTTGAGACAGTGG 59.008 40.000 0.00 0.00 36.34 4.00
2026 2107 7.482654 TTGAGTCACTTATTTTGAGACAGTG 57.517 36.000 0.00 0.00 36.91 3.66
2027 2108 8.682936 AATTGAGTCACTTATTTTGAGACAGT 57.317 30.769 0.00 0.00 0.00 3.55
2028 2109 9.956720 AAAATTGAGTCACTTATTTTGAGACAG 57.043 29.630 11.47 0.00 31.14 3.51
2029 2110 9.734620 CAAAATTGAGTCACTTATTTTGAGACA 57.265 29.630 24.58 0.00 44.64 3.41
2030 2111 9.736023 ACAAAATTGAGTCACTTATTTTGAGAC 57.264 29.630 30.39 8.03 44.64 3.36
2041 2122 9.174166 ACAAAGTTAGTACAAAATTGAGTCACT 57.826 29.630 0.00 0.00 0.00 3.41
2077 2158 9.965824 CCAAAATAAGTGACTCAACTTTGTATT 57.034 29.630 0.00 0.00 40.77 1.89
2078 2159 8.576442 CCCAAAATAAGTGACTCAACTTTGTAT 58.424 33.333 0.00 0.00 40.77 2.29
2079 2160 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
2080 2161 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
2081 2162 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
2082 2163 6.833933 AGTCCCAAAATAAGTGACTCAACTTT 59.166 34.615 0.00 0.00 40.77 2.66
2083 2164 6.263168 CAGTCCCAAAATAAGTGACTCAACTT 59.737 38.462 0.00 0.00 42.89 2.66
2084 2165 5.765182 CAGTCCCAAAATAAGTGACTCAACT 59.235 40.000 0.00 0.00 34.21 3.16
2085 2166 5.048713 CCAGTCCCAAAATAAGTGACTCAAC 60.049 44.000 0.00 0.00 34.21 3.18
2086 2167 5.070001 CCAGTCCCAAAATAAGTGACTCAA 58.930 41.667 0.00 0.00 34.21 3.02
2087 2168 4.349636 TCCAGTCCCAAAATAAGTGACTCA 59.650 41.667 0.00 0.00 34.21 3.41
2088 2169 4.906618 TCCAGTCCCAAAATAAGTGACTC 58.093 43.478 0.00 0.00 34.21 3.36
2089 2170 4.263506 CCTCCAGTCCCAAAATAAGTGACT 60.264 45.833 0.00 0.00 36.77 3.41
2090 2171 4.010349 CCTCCAGTCCCAAAATAAGTGAC 58.990 47.826 0.00 0.00 0.00 3.67
2091 2172 3.010138 CCCTCCAGTCCCAAAATAAGTGA 59.990 47.826 0.00 0.00 0.00 3.41
2092 2173 3.010138 TCCCTCCAGTCCCAAAATAAGTG 59.990 47.826 0.00 0.00 0.00 3.16
2093 2174 3.265489 TCCCTCCAGTCCCAAAATAAGT 58.735 45.455 0.00 0.00 0.00 2.24
2094 2175 3.267031 ACTCCCTCCAGTCCCAAAATAAG 59.733 47.826 0.00 0.00 0.00 1.73
2095 2176 3.265489 ACTCCCTCCAGTCCCAAAATAA 58.735 45.455 0.00 0.00 0.00 1.40
2096 2177 2.929301 ACTCCCTCCAGTCCCAAAATA 58.071 47.619 0.00 0.00 0.00 1.40
2097 2178 1.760405 ACTCCCTCCAGTCCCAAAAT 58.240 50.000 0.00 0.00 0.00 1.82
2098 2179 2.426431 TACTCCCTCCAGTCCCAAAA 57.574 50.000 0.00 0.00 0.00 2.44
2099 2180 2.661176 ATACTCCCTCCAGTCCCAAA 57.339 50.000 0.00 0.00 0.00 3.28
2100 2181 3.208922 TGATATACTCCCTCCAGTCCCAA 59.791 47.826 0.00 0.00 0.00 4.12
2101 2182 2.795360 TGATATACTCCCTCCAGTCCCA 59.205 50.000 0.00 0.00 0.00 4.37
2102 2183 3.166679 GTGATATACTCCCTCCAGTCCC 58.833 54.545 0.00 0.00 0.00 4.46
2103 2184 3.829601 CTGTGATATACTCCCTCCAGTCC 59.170 52.174 0.00 0.00 0.00 3.85
2104 2185 3.257127 GCTGTGATATACTCCCTCCAGTC 59.743 52.174 0.00 0.00 0.00 3.51
2105 2186 3.235200 GCTGTGATATACTCCCTCCAGT 58.765 50.000 0.00 0.00 0.00 4.00
2106 2187 2.230025 CGCTGTGATATACTCCCTCCAG 59.770 54.545 0.00 0.00 0.00 3.86
2107 2188 2.239400 CGCTGTGATATACTCCCTCCA 58.761 52.381 0.00 0.00 0.00 3.86
2108 2189 2.029828 CACGCTGTGATATACTCCCTCC 60.030 54.545 3.04 0.00 35.23 4.30
2109 2190 2.623889 ACACGCTGTGATATACTCCCTC 59.376 50.000 14.18 0.00 36.96 4.30
2110 2191 2.667470 ACACGCTGTGATATACTCCCT 58.333 47.619 14.18 0.00 36.96 4.20
2111 2192 4.785511 ATACACGCTGTGATATACTCCC 57.214 45.455 14.18 0.00 36.96 4.30
2112 2193 5.529791 ACAATACACGCTGTGATATACTCC 58.470 41.667 14.18 0.00 36.96 3.85
2113 2194 6.562270 GCAACAATACACGCTGTGATATACTC 60.562 42.308 14.18 0.00 36.96 2.59
2114 2195 5.234329 GCAACAATACACGCTGTGATATACT 59.766 40.000 14.18 0.00 36.96 2.12
2115 2196 5.432157 GCAACAATACACGCTGTGATATAC 58.568 41.667 14.18 0.00 36.96 1.47
2116 2197 4.509970 GGCAACAATACACGCTGTGATATA 59.490 41.667 14.18 0.00 36.96 0.86
2117 2198 3.312421 GGCAACAATACACGCTGTGATAT 59.688 43.478 14.18 6.76 36.96 1.63
2160 2241 5.544176 TCTCAAGTTTGATAGGGTTGAGTCT 59.456 40.000 9.54 0.00 43.04 3.24
2166 2247 5.561679 GGAACTCTCAAGTTTGATAGGGTT 58.438 41.667 10.71 5.87 45.80 4.11
2214 2295 0.995024 ACTTGTGGGAGGAATCTGGG 59.005 55.000 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.