Multiple sequence alignment - TraesCS5A01G186300

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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 TraesCS5A01G186300 chr5A 100.000 7392 0 0 1 7392 387398467 387405858 0.000000e+00 13651.0
1 TraesCS5A01G186300 chr5A 85.915 71 8 2 721 789 492035549 492035479 2.860000e-09 75.0
2 TraesCS5A01G186300 chr5B 93.086 6870 307 66 612 7392 335941980 335948770 0.000000e+00 9901.0
3 TraesCS5A01G186300 chr5B 93.069 101 5 2 1 99 335941841 335941941 5.980000e-31 147.0
4 TraesCS5A01G186300 chr5D 94.331 6033 201 55 808 6781 294418483 294424433 0.000000e+00 9116.0
5 TraesCS5A01G186300 chr5D 97.553 613 12 1 6780 7392 294424471 294425080 0.000000e+00 1046.0
6 TraesCS5A01G186300 chr5D 93.252 163 10 1 116 277 25040153 25039991 9.590000e-59 239.0
7 TraesCS5A01G186300 chr5D 93.671 158 9 1 121 277 368995355 368995512 1.240000e-57 235.0
8 TraesCS5A01G186300 chr5D 94.194 155 4 2 335 488 503215048 503214898 1.600000e-56 231.0
9 TraesCS5A01G186300 chr5D 94.194 155 4 2 335 488 560881642 560881492 1.600000e-56 231.0
10 TraesCS5A01G186300 chr5D 92.742 124 5 2 487 607 381175380 381175258 7.620000e-40 176.0
11 TraesCS5A01G186300 chr5D 92.222 90 5 2 12 99 294417774 294417863 7.790000e-25 126.0
12 TraesCS5A01G186300 chr5D 98.551 69 0 1 280 347 503322023 503322091 3.620000e-23 121.0
13 TraesCS5A01G186300 chr4A 93.210 162 9 2 122 282 252530993 252530833 3.450000e-58 237.0
14 TraesCS5A01G186300 chr4A 92.742 124 5 2 487 607 73809762 73809884 7.620000e-40 176.0
15 TraesCS5A01G186300 chr4A 92.742 124 5 2 487 607 73810794 73810916 7.620000e-40 176.0
16 TraesCS5A01G186300 chr4A 92.742 124 5 2 487 607 73811305 73811427 7.620000e-40 176.0
17 TraesCS5A01G186300 chr4A 98.551 69 0 1 280 347 309402097 309402029 3.620000e-23 121.0
18 TraesCS5A01G186300 chr1D 93.671 158 8 2 122 277 370849409 370849252 1.240000e-57 235.0
19 TraesCS5A01G186300 chr1D 90.751 173 11 5 109 277 77381499 77381670 7.460000e-55 226.0
20 TraesCS5A01G186300 chr1D 98.551 69 0 1 280 347 254467936 254468004 3.620000e-23 121.0
21 TraesCS5A01G186300 chr1D 98.551 69 0 1 280 347 459901360 459901428 3.620000e-23 121.0
22 TraesCS5A01G186300 chr1D 85.526 76 10 1 756 830 351913562 351913487 2.210000e-10 78.7
23 TraesCS5A01G186300 chrUn 94.194 155 4 2 335 488 93415171 93415321 1.600000e-56 231.0
24 TraesCS5A01G186300 chrUn 94.194 155 4 2 335 488 403668471 403668621 1.600000e-56 231.0
25 TraesCS5A01G186300 chrUn 93.548 155 5 2 335 488 93412803 93412953 7.460000e-55 226.0
26 TraesCS5A01G186300 chrUn 92.742 124 5 2 487 607 216517769 216517647 7.620000e-40 176.0
27 TraesCS5A01G186300 chrUn 92.742 124 5 2 487 607 346595660 346595538 7.620000e-40 176.0
28 TraesCS5A01G186300 chrUn 98.551 69 0 1 280 347 298935437 298935369 3.620000e-23 121.0
29 TraesCS5A01G186300 chrUn 98.551 69 0 1 280 347 359775102 359775170 3.620000e-23 121.0
30 TraesCS5A01G186300 chr7D 94.194 155 4 2 335 488 231600426 231600576 1.600000e-56 231.0
31 TraesCS5A01G186300 chr6A 94.194 155 4 2 335 488 271186603 271186453 1.600000e-56 231.0
32 TraesCS5A01G186300 chr4D 92.593 162 10 2 122 282 316114623 316114783 1.600000e-56 231.0
33 TraesCS5A01G186300 chr4D 92.073 164 9 3 122 282 90935534 90935372 2.070000e-55 228.0
34 TraesCS5A01G186300 chr4D 92.742 124 5 2 487 607 30387164 30387042 7.620000e-40 176.0
35 TraesCS5A01G186300 chr4D 98.551 69 0 1 280 347 19909205 19909273 3.620000e-23 121.0
36 TraesCS5A01G186300 chr3B 92.593 162 10 2 122 282 503553367 503553207 1.600000e-56 231.0
37 TraesCS5A01G186300 chr2D 94.194 155 4 2 335 488 635585723 635585873 1.600000e-56 231.0
38 TraesCS5A01G186300 chr1A 94.194 155 4 2 335 488 584780274 584780124 1.600000e-56 231.0
39 TraesCS5A01G186300 chr1A 92.742 124 5 2 487 607 554513082 554513204 7.620000e-40 176.0
40 TraesCS5A01G186300 chr1A 98.551 69 0 1 280 347 554490557 554490625 3.620000e-23 121.0
41 TraesCS5A01G186300 chr1A 87.838 74 7 2 756 827 523115992 523115919 1.320000e-12 86.1
42 TraesCS5A01G186300 chr7B 92.453 159 10 2 120 277 100414196 100414039 7.460000e-55 226.0
43 TraesCS5A01G186300 chr7B 98.551 69 0 1 280 347 662746542 662746474 3.620000e-23 121.0
44 TraesCS5A01G186300 chr6D 92.742 124 5 2 487 607 345105006 345104884 7.620000e-40 176.0
45 TraesCS5A01G186300 chr2A 87.179 78 8 2 756 831 663634195 663634118 3.670000e-13 87.9
46 TraesCS5A01G186300 chr2A 97.222 36 1 0 756 791 759542731 759542696 2.230000e-05 62.1
47 TraesCS5A01G186300 chr1B 85.393 89 8 5 747 832 372146107 372146193 3.670000e-13 87.9
48 TraesCS5A01G186300 chr1B 83.908 87 12 2 746 830 502091324 502091238 1.710000e-11 82.4
49 TraesCS5A01G186300 chr7A 85.965 57 6 2 735 789 130594517 130594461 8.010000e-05 60.2


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 TraesCS5A01G186300 chr5A 387398467 387405858 7391 False 13651.000000 13651 100.0000 1 7392 1 chr5A.!!$F1 7391
1 TraesCS5A01G186300 chr5B 335941841 335948770 6929 False 5024.000000 9901 93.0775 1 7392 2 chr5B.!!$F1 7391
2 TraesCS5A01G186300 chr5D 294417774 294425080 7306 False 3429.333333 9116 94.7020 12 7392 3 chr5D.!!$F3 7380
3 TraesCS5A01G186300 chrUn 93412803 93415321 2518 False 228.500000 231 93.8710 335 488 2 chrUn.!!$F3 153

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
340 356 0.319125 GAAAAACGGGCGCCATGAAA 60.319 50.000 30.85 0.00 0.00 2.69 F
1175 1364 0.033504 GTCTTGTGCACCCGAGAGAA 59.966 55.000 15.69 0.00 0.00 2.87 F
1605 1794 0.109964 CATGTTTGGCCGGTAACACG 60.110 55.000 17.02 8.11 37.11 4.49 F
2739 2957 1.052124 AAAGTCAGGGTCACCGTCCA 61.052 55.000 0.00 0.00 43.47 4.02 F
2747 2965 1.653151 GGTCACCGTCCAGCTATTTC 58.347 55.000 0.00 0.00 0.00 2.17 F
3699 3925 1.741770 CCTTTCAGGCGAGGAACCG 60.742 63.158 0.00 0.00 34.91 4.44 F
4733 5709 1.337118 GACTCCTCTATCTGGCCAGG 58.663 60.000 32.23 16.55 0.00 4.45 F
5485 6491 1.265454 CCTCCCCAGGTACACTCCAC 61.265 65.000 0.00 0.00 34.60 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 2101 0.532862 CCATCGGCTACCACATCCAC 60.533 60.000 0.00 0.00 0.00 4.02 R
2733 2951 1.396996 CCAAACGAAATAGCTGGACGG 59.603 52.381 0.00 0.00 0.00 4.79 R
2747 2965 2.427232 TAGGTCACGAGTTCCAAACG 57.573 50.000 0.00 0.00 36.23 3.60 R
3907 4133 1.825090 CAAGGAATGCTAGCCACACA 58.175 50.000 13.29 0.00 0.00 3.72 R
3990 4216 3.118629 AGCTGGAATTAGATGCGTCTGAA 60.119 43.478 18.98 9.11 35.87 3.02 R
4918 5894 1.262417 TACAGAGTCACGGCAATCCA 58.738 50.000 0.00 0.00 0.00 3.41 R
5907 6914 0.685131 TGGGCATTTGATCAGGGCAG 60.685 55.000 15.91 0.74 0.00 4.85 R
6604 7640 1.308998 ACAGAGGCCAAGTGTTTTCG 58.691 50.000 5.01 0.00 0.00 3.46 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
78 79 1.180029 GCACCCTCTGACATTGCATT 58.820 50.000 0.00 0.00 33.24 3.56
79 80 1.133790 GCACCCTCTGACATTGCATTC 59.866 52.381 0.00 0.00 33.24 2.67
83 84 4.021719 CACCCTCTGACATTGCATTCTTTT 60.022 41.667 0.00 0.00 0.00 2.27
84 85 5.183713 CACCCTCTGACATTGCATTCTTTTA 59.816 40.000 0.00 0.00 0.00 1.52
85 86 5.954150 ACCCTCTGACATTGCATTCTTTTAT 59.046 36.000 0.00 0.00 0.00 1.40
86 87 6.438425 ACCCTCTGACATTGCATTCTTTTATT 59.562 34.615 0.00 0.00 0.00 1.40
87 88 6.755141 CCCTCTGACATTGCATTCTTTTATTG 59.245 38.462 0.00 0.00 0.00 1.90
88 89 6.755141 CCTCTGACATTGCATTCTTTTATTGG 59.245 38.462 0.00 0.00 0.00 3.16
89 90 7.230849 TCTGACATTGCATTCTTTTATTGGT 57.769 32.000 0.00 0.00 0.00 3.67
90 91 7.669427 TCTGACATTGCATTCTTTTATTGGTT 58.331 30.769 0.00 0.00 0.00 3.67
94 110 9.597999 GACATTGCATTCTTTTATTGGTTTTTC 57.402 29.630 0.00 0.00 0.00 2.29
149 165 6.628185 ACTCTCTCCGTTCGTAAATATTTGT 58.372 36.000 11.05 0.00 0.00 2.83
150 166 6.750963 ACTCTCTCCGTTCGTAAATATTTGTC 59.249 38.462 11.05 3.49 0.00 3.18
152 168 7.318141 TCTCTCCGTTCGTAAATATTTGTCTT 58.682 34.615 11.05 0.00 0.00 3.01
153 169 7.816031 TCTCTCCGTTCGTAAATATTTGTCTTT 59.184 33.333 11.05 0.00 0.00 2.52
155 171 8.776470 TCTCCGTTCGTAAATATTTGTCTTTTT 58.224 29.630 11.05 0.00 0.00 1.94
227 243 6.000219 ACAGTGTAGATTCACTCATTTTGCT 59.000 36.000 0.00 0.00 45.37 3.91
228 244 6.488006 ACAGTGTAGATTCACTCATTTTGCTT 59.512 34.615 0.00 0.00 45.37 3.91
229 245 7.020010 CAGTGTAGATTCACTCATTTTGCTTC 58.980 38.462 0.00 0.00 45.37 3.86
230 246 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
231 247 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
232 248 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
233 249 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
235 251 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
236 252 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
237 253 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
239 255 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
240 256 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
241 257 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
242 258 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
243 259 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
244 260 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
245 261 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
246 262 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
247 263 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
248 264 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
249 265 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
250 266 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
251 267 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
253 269 6.926826 TCGTATGTAGTCACTTGTTGAAATGT 59.073 34.615 0.00 0.00 35.39 2.71
254 270 7.115805 TCGTATGTAGTCACTTGTTGAAATGTC 59.884 37.037 0.00 0.00 35.39 3.06
255 271 7.116376 CGTATGTAGTCACTTGTTGAAATGTCT 59.884 37.037 0.00 0.00 35.39 3.41
256 272 9.419297 GTATGTAGTCACTTGTTGAAATGTCTA 57.581 33.333 0.00 0.00 35.39 2.59
257 273 8.902540 ATGTAGTCACTTGTTGAAATGTCTAA 57.097 30.769 0.00 0.00 35.39 2.10
258 274 8.725405 TGTAGTCACTTGTTGAAATGTCTAAA 57.275 30.769 0.00 0.00 35.39 1.85
259 275 9.168451 TGTAGTCACTTGTTGAAATGTCTAAAA 57.832 29.630 0.00 0.00 35.39 1.52
260 276 9.997482 GTAGTCACTTGTTGAAATGTCTAAAAA 57.003 29.630 0.00 0.00 35.39 1.94
262 278 8.956426 AGTCACTTGTTGAAATGTCTAAAAAGA 58.044 29.630 5.49 0.00 35.39 2.52
263 279 9.010366 GTCACTTGTTGAAATGTCTAAAAAGAC 57.990 33.333 0.00 0.00 35.39 3.01
295 311 4.962155 GGAATAGGTCCAATGTGAGTAGG 58.038 47.826 0.00 0.00 46.97 3.18
296 312 4.654262 GGAATAGGTCCAATGTGAGTAGGA 59.346 45.833 0.00 0.00 46.97 2.94
297 313 5.308237 GGAATAGGTCCAATGTGAGTAGGAT 59.692 44.000 0.00 0.00 46.97 3.24
298 314 6.426646 AATAGGTCCAATGTGAGTAGGATC 57.573 41.667 0.00 0.00 31.91 3.36
308 324 4.946478 GTGAGTAGGATCACTTAGCCAT 57.054 45.455 0.00 0.00 45.03 4.40
309 325 4.626042 GTGAGTAGGATCACTTAGCCATG 58.374 47.826 0.00 0.00 45.03 3.66
310 326 3.070159 TGAGTAGGATCACTTAGCCATGC 59.930 47.826 0.00 0.00 35.45 4.06
311 327 3.312890 AGTAGGATCACTTAGCCATGCT 58.687 45.455 0.00 0.00 43.41 3.79
312 328 3.713764 AGTAGGATCACTTAGCCATGCTT 59.286 43.478 0.00 0.00 40.44 3.91
314 330 2.507058 AGGATCACTTAGCCATGCTTCA 59.493 45.455 0.00 0.00 40.44 3.02
315 331 3.137913 AGGATCACTTAGCCATGCTTCAT 59.862 43.478 0.00 0.00 40.44 2.57
316 332 4.349048 AGGATCACTTAGCCATGCTTCATA 59.651 41.667 0.00 0.00 40.44 2.15
319 335 6.208204 GGATCACTTAGCCATGCTTCATAATT 59.792 38.462 0.00 0.00 40.44 1.40
320 336 6.381481 TCACTTAGCCATGCTTCATAATTG 57.619 37.500 0.00 0.00 40.44 2.32
321 337 5.300034 TCACTTAGCCATGCTTCATAATTGG 59.700 40.000 0.00 0.00 40.44 3.16
322 338 5.300034 CACTTAGCCATGCTTCATAATTGGA 59.700 40.000 0.00 0.00 40.44 3.53
323 339 5.893255 ACTTAGCCATGCTTCATAATTGGAA 59.107 36.000 0.00 0.00 40.44 3.53
324 340 6.380846 ACTTAGCCATGCTTCATAATTGGAAA 59.619 34.615 0.00 0.00 40.44 3.13
325 341 5.680594 AGCCATGCTTCATAATTGGAAAA 57.319 34.783 0.00 0.00 33.89 2.29
326 342 6.052405 AGCCATGCTTCATAATTGGAAAAA 57.948 33.333 0.00 0.00 33.89 1.94
327 343 5.876460 AGCCATGCTTCATAATTGGAAAAAC 59.124 36.000 0.00 0.00 33.89 2.43
328 344 5.220453 GCCATGCTTCATAATTGGAAAAACG 60.220 40.000 0.00 0.00 0.00 3.60
330 346 4.815269 TGCTTCATAATTGGAAAAACGGG 58.185 39.130 0.00 0.00 0.00 5.28
331 347 3.616821 GCTTCATAATTGGAAAAACGGGC 59.383 43.478 0.00 0.00 0.00 6.13
332 348 3.495670 TCATAATTGGAAAAACGGGCG 57.504 42.857 0.00 0.00 0.00 6.13
333 349 1.923864 CATAATTGGAAAAACGGGCGC 59.076 47.619 0.00 0.00 0.00 6.53
337 353 2.126110 GGAAAAACGGGCGCCATG 60.126 61.111 30.85 22.57 0.00 3.66
338 354 2.631580 GGAAAAACGGGCGCCATGA 61.632 57.895 30.85 0.00 0.00 3.07
339 355 1.287503 GAAAAACGGGCGCCATGAA 59.712 52.632 30.85 0.00 0.00 2.57
340 356 0.319125 GAAAAACGGGCGCCATGAAA 60.319 50.000 30.85 0.00 0.00 2.69
341 357 0.319469 AAAAACGGGCGCCATGAAAG 60.319 50.000 30.85 13.79 0.00 2.62
342 358 1.460273 AAAACGGGCGCCATGAAAGT 61.460 50.000 30.85 14.46 0.00 2.66
447 463 1.053424 ATAATAAAGAGCCGCCCGGA 58.947 50.000 11.48 0.00 37.50 5.14
516 534 8.084590 GAATCCCGATTCGACATTAAAAGTAT 57.915 34.615 7.83 0.00 37.97 2.12
518 536 9.720769 AATCCCGATTCGACATTAAAAGTATAT 57.279 29.630 7.83 0.00 0.00 0.86
521 539 8.984764 CCCGATTCGACATTAAAAGTATATTGA 58.015 33.333 7.83 0.00 0.00 2.57
591 609 9.787532 TTGATTCAATTCATAAATCGACTTTCC 57.212 29.630 0.00 0.00 33.13 3.13
593 611 7.938140 TTCAATTCATAAATCGACTTTCCCT 57.062 32.000 0.00 0.00 0.00 4.20
594 612 7.553881 TCAATTCATAAATCGACTTTCCCTC 57.446 36.000 0.00 0.00 0.00 4.30
595 613 6.542370 TCAATTCATAAATCGACTTTCCCTCC 59.458 38.462 0.00 0.00 0.00 4.30
596 614 5.693769 TTCATAAATCGACTTTCCCTCCT 57.306 39.130 0.00 0.00 0.00 3.69
597 615 6.801718 TTCATAAATCGACTTTCCCTCCTA 57.198 37.500 0.00 0.00 0.00 2.94
598 616 6.996180 TCATAAATCGACTTTCCCTCCTAT 57.004 37.500 0.00 0.00 0.00 2.57
599 617 6.759272 TCATAAATCGACTTTCCCTCCTATG 58.241 40.000 0.00 0.00 0.00 2.23
600 618 3.477210 AATCGACTTTCCCTCCTATGC 57.523 47.619 0.00 0.00 0.00 3.14
601 619 2.160721 TCGACTTTCCCTCCTATGCT 57.839 50.000 0.00 0.00 0.00 3.79
602 620 2.032620 TCGACTTTCCCTCCTATGCTC 58.967 52.381 0.00 0.00 0.00 4.26
603 621 2.035632 CGACTTTCCCTCCTATGCTCT 58.964 52.381 0.00 0.00 0.00 4.09
604 622 2.223923 CGACTTTCCCTCCTATGCTCTG 60.224 54.545 0.00 0.00 0.00 3.35
605 623 3.034635 GACTTTCCCTCCTATGCTCTGA 58.965 50.000 0.00 0.00 0.00 3.27
607 625 2.094100 TTCCCTCCTATGCTCTGAGG 57.906 55.000 6.83 0.00 44.34 3.86
609 627 3.858886 CCTCCTATGCTCTGAGGGA 57.141 57.895 6.83 3.67 41.64 4.20
696 715 1.573108 ACTTGTCCATGATCCCGTCT 58.427 50.000 0.00 0.00 0.00 4.18
697 716 1.482593 ACTTGTCCATGATCCCGTCTC 59.517 52.381 0.00 0.00 0.00 3.36
742 763 7.187244 TCTCTCGGTTAGTAAATACTCATCG 57.813 40.000 1.90 1.90 37.73 3.84
743 764 6.988580 TCTCTCGGTTAGTAAATACTCATCGA 59.011 38.462 9.14 9.14 37.73 3.59
745 766 7.637229 TCTCGGTTAGTAAATACTCATCGAAG 58.363 38.462 10.34 6.25 37.73 3.79
827 1013 3.918294 AATAATTTCGGACGGAGGGAA 57.082 42.857 0.00 0.00 0.00 3.97
837 1023 3.725490 GGACGGAGGGAATATTGTACAC 58.275 50.000 0.00 0.00 0.00 2.90
838 1024 3.387050 GGACGGAGGGAATATTGTACACT 59.613 47.826 0.00 0.00 0.00 3.55
842 1028 4.130118 GGAGGGAATATTGTACACTGCTG 58.870 47.826 0.00 0.00 0.00 4.41
858 1044 3.194542 ACTGCTGTACTCTCTGAATCCAC 59.805 47.826 0.00 0.00 0.00 4.02
876 1062 4.000325 TCCACGTTTCCTACATGTGAATG 59.000 43.478 9.11 6.23 32.39 2.67
880 1066 5.049749 CACGTTTCCTACATGTGAATGTCAA 60.050 40.000 9.11 0.00 36.08 3.18
881 1067 5.179368 ACGTTTCCTACATGTGAATGTCAAG 59.821 40.000 9.11 0.00 36.08 3.02
886 1072 8.862325 TTCCTACATGTGAATGTCAAGTAAAT 57.138 30.769 9.11 0.00 36.08 1.40
887 1073 9.952030 TTCCTACATGTGAATGTCAAGTAAATA 57.048 29.630 9.11 0.00 36.08 1.40
900 1086 5.010933 TCAAGTAAATATTTCAACGGGCCA 58.989 37.500 4.39 0.00 0.00 5.36
901 1087 5.477291 TCAAGTAAATATTTCAACGGGCCAA 59.523 36.000 4.39 0.00 0.00 4.52
912 1098 3.256136 TCAACGGGCCAATTCGTAATTTT 59.744 39.130 4.39 0.00 38.78 1.82
918 1104 1.923864 CCAATTCGTAATTTTGCCGCC 59.076 47.619 0.00 0.00 0.00 6.13
920 1106 0.806241 ATTCGTAATTTTGCCGCCGT 59.194 45.000 0.00 0.00 0.00 5.68
922 1108 1.208103 CGTAATTTTGCCGCCGTGT 59.792 52.632 0.00 0.00 0.00 4.49
1102 1291 2.586792 CTCCGCCTCCTTTCCCAG 59.413 66.667 0.00 0.00 0.00 4.45
1103 1292 3.689002 CTCCGCCTCCTTTCCCAGC 62.689 68.421 0.00 0.00 0.00 4.85
1110 1299 2.746277 CCTTTCCCAGCCCGAACG 60.746 66.667 0.00 0.00 0.00 3.95
1175 1364 0.033504 GTCTTGTGCACCCGAGAGAA 59.966 55.000 15.69 0.00 0.00 2.87
1246 1435 1.446618 GCAATCCCAAGCCGCAAAG 60.447 57.895 0.00 0.00 0.00 2.77
1251 1440 1.603455 CCCAAGCCGCAAAGAAGGA 60.603 57.895 0.00 0.00 0.00 3.36
1256 1445 1.692411 AGCCGCAAAGAAGGAGTTTT 58.308 45.000 0.00 0.00 0.00 2.43
1605 1794 0.109964 CATGTTTGGCCGGTAACACG 60.110 55.000 17.02 8.11 37.11 4.49
1614 1803 1.749153 CCGGTAACACGCAAAACAAG 58.251 50.000 0.00 0.00 0.00 3.16
1655 1844 2.614983 TCTTTAACCAGCGCGTCTTTTT 59.385 40.909 8.43 3.61 0.00 1.94
1685 1876 5.467063 GCTTCTACTGTAGTTTGCTTTCAGT 59.533 40.000 14.11 0.00 39.75 3.41
1686 1877 6.017852 GCTTCTACTGTAGTTTGCTTTCAGTT 60.018 38.462 14.11 0.00 38.54 3.16
1687 1878 7.170998 GCTTCTACTGTAGTTTGCTTTCAGTTA 59.829 37.037 14.11 0.00 38.54 2.24
1688 1879 7.941795 TCTACTGTAGTTTGCTTTCAGTTAC 57.058 36.000 14.11 0.00 38.54 2.50
1689 1880 7.723324 TCTACTGTAGTTTGCTTTCAGTTACT 58.277 34.615 14.11 0.00 38.54 2.24
1690 1881 6.604735 ACTGTAGTTTGCTTTCAGTTACTG 57.395 37.500 5.94 5.94 36.25 2.74
1732 1923 1.328279 ACTGCTGCACCTTTTTACCC 58.672 50.000 0.00 0.00 0.00 3.69
1738 1929 1.232621 GCACCTTTTTACCCGCTCGT 61.233 55.000 0.00 0.00 0.00 4.18
1835 2026 7.413438 GCTCAAACTCCAAACTATGTACATCTG 60.413 40.741 12.68 9.28 0.00 2.90
1879 2071 8.602328 CAGTATATCTGCACTCTCTTCTTTTTG 58.398 37.037 0.00 0.00 37.36 2.44
1909 2101 4.690280 GTGGTGCTAATTTGGTGGATTTTG 59.310 41.667 0.00 0.00 0.00 2.44
2050 2242 5.295431 TGTTGACATTGATCATCGGTTTC 57.705 39.130 0.00 0.00 0.00 2.78
2093 2285 4.504514 CCATATCCAAGTGTGAGGATCCAG 60.505 50.000 15.82 0.00 43.39 3.86
2101 2293 2.235898 GTGTGAGGATCCAGCTCTTTCT 59.764 50.000 15.82 0.00 0.00 2.52
2180 2372 4.400251 CCCTAAGCATTCATTTCTCAAGCA 59.600 41.667 0.00 0.00 0.00 3.91
2249 2441 7.106890 AGTTTGCCTCTTTTCTAGGTATCTTC 58.893 38.462 0.00 0.00 36.43 2.87
2255 2447 7.281324 GCCTCTTTTCTAGGTATCTTCCTTTTC 59.719 40.741 0.00 0.00 38.86 2.29
2267 2459 8.483758 GGTATCTTCCTTTTCAAGTATGAGGTA 58.516 37.037 0.00 0.00 36.78 3.08
2326 2518 2.859165 TTCGAGGGATCTTGCTTGTT 57.141 45.000 0.00 0.00 0.00 2.83
2363 2555 6.419484 AAAGTTAGGCTGGCAAATTAGTTT 57.581 33.333 3.38 0.00 0.00 2.66
2420 2612 8.907685 GCAATTAACGCTATTCTGTTTTGTTTA 58.092 29.630 0.00 0.00 0.00 2.01
2506 2698 2.716217 GCCTTTGTCTGGCTCACTTAT 58.284 47.619 0.00 0.00 46.38 1.73
2507 2699 3.873910 GCCTTTGTCTGGCTCACTTATA 58.126 45.455 0.00 0.00 46.38 0.98
2509 2701 4.624125 GCCTTTGTCTGGCTCACTTATACT 60.624 45.833 0.00 0.00 46.38 2.12
2511 2703 6.640518 CCTTTGTCTGGCTCACTTATACTTA 58.359 40.000 0.00 0.00 0.00 2.24
2512 2704 7.103641 CCTTTGTCTGGCTCACTTATACTTAA 58.896 38.462 0.00 0.00 0.00 1.85
2513 2705 7.770897 CCTTTGTCTGGCTCACTTATACTTAAT 59.229 37.037 0.00 0.00 0.00 1.40
2558 2750 6.739112 ACTTGTTTCCATGAAAAGAAGTAGC 58.261 36.000 16.72 0.00 45.51 3.58
2692 2910 5.120519 TCCATTAAACGATACGACCAACAAC 59.879 40.000 0.00 0.00 0.00 3.32
2733 2951 1.230324 GAGCACAAAGTCAGGGTCAC 58.770 55.000 0.00 0.00 0.00 3.67
2739 2957 1.052124 AAAGTCAGGGTCACCGTCCA 61.052 55.000 0.00 0.00 43.47 4.02
2747 2965 1.653151 GGTCACCGTCCAGCTATTTC 58.347 55.000 0.00 0.00 0.00 2.17
2769 2987 3.725490 GTTTGGAACTCGTGACCTAACT 58.275 45.455 16.95 0.00 36.82 2.24
2960 3179 4.214119 ACTCAGAATTGTTGGTTGACATCG 59.786 41.667 0.00 0.00 0.00 3.84
2970 3189 5.172934 GTTGGTTGACATCGTTATACTCCA 58.827 41.667 0.00 0.00 0.00 3.86
3080 3306 4.981674 ACAAATACAATGTTTGTTCAGCGG 59.018 37.500 0.00 0.00 44.84 5.52
3345 3571 1.895131 CCCCTAAACTGCTGCATTTGT 59.105 47.619 1.31 0.00 0.00 2.83
3636 3862 4.757149 AGAATGCTAGAAAACGAAGTGCTT 59.243 37.500 0.00 0.00 45.00 3.91
3699 3925 1.741770 CCTTTCAGGCGAGGAACCG 60.742 63.158 0.00 0.00 34.91 4.44
3744 3970 3.503363 GGTGCCGCAGCTGATGTC 61.503 66.667 20.43 0.00 40.80 3.06
3907 4133 5.053978 AGGAGTTTGGTCTTCTCACATTT 57.946 39.130 0.00 0.00 0.00 2.32
3958 4184 8.960591 CAGATAACAAAGGTGAGGATTGTAATT 58.039 33.333 0.00 0.00 36.33 1.40
3959 4185 8.960591 AGATAACAAAGGTGAGGATTGTAATTG 58.039 33.333 0.00 0.00 36.33 2.32
4026 4252 4.640771 TTCCAGCTTCTTACCAAGTCAT 57.359 40.909 0.00 0.00 0.00 3.06
4348 5324 9.410556 ACATACAAATGCTGTCACTTTATTTTC 57.589 29.630 0.00 0.00 39.64 2.29
4556 5532 6.470278 TCCATGCTGATTTATGTAGATCCTG 58.530 40.000 0.00 0.00 0.00 3.86
4606 5582 9.460019 TGTGTTCCAAATATCAATCTTATCACA 57.540 29.630 0.00 0.00 0.00 3.58
4685 5661 8.443953 AACTTAGAGATTCAAAGCCATACATC 57.556 34.615 0.00 0.00 0.00 3.06
4733 5709 1.337118 GACTCCTCTATCTGGCCAGG 58.663 60.000 32.23 16.55 0.00 4.45
4741 5717 2.061061 CTATCTGGCCAGGGATCCTTT 58.939 52.381 32.23 9.70 0.00 3.11
4793 5769 3.192212 AGAAATGCTGCTGCTTTTAGGAC 59.808 43.478 23.28 14.07 43.53 3.85
4918 5894 1.751924 GGCGTGACTACCTCTCTTCAT 59.248 52.381 0.00 0.00 0.00 2.57
4923 5899 4.098654 CGTGACTACCTCTCTTCATGGATT 59.901 45.833 0.00 0.00 0.00 3.01
4976 5952 2.753931 CTTGGGCCGCTTTGAGCAAC 62.754 60.000 0.00 0.00 42.58 4.17
4988 5964 5.615544 CGCTTTGAGCAACATATATACAGGC 60.616 44.000 0.50 0.00 42.58 4.85
5045 6028 7.698836 AAAAACATACATTGTCACTTTGAGC 57.301 32.000 0.00 0.00 37.68 4.26
5046 6029 6.389830 AAACATACATTGTCACTTTGAGCA 57.610 33.333 0.00 0.00 37.68 4.26
5047 6030 6.389830 AACATACATTGTCACTTTGAGCAA 57.610 33.333 0.00 0.00 37.68 3.91
5048 6031 5.762045 ACATACATTGTCACTTTGAGCAAC 58.238 37.500 0.00 0.00 30.89 4.17
5050 6033 4.924305 ACATTGTCACTTTGAGCAACAT 57.076 36.364 0.00 0.00 0.00 2.71
5051 6034 7.174772 ACATACATTGTCACTTTGAGCAACATA 59.825 33.333 0.00 0.00 30.89 2.29
5145 6146 5.128663 GCACCACCTATATGGACCAATTTTT 59.871 40.000 0.00 0.00 43.02 1.94
5149 6150 7.559897 ACCACCTATATGGACCAATTTTTACTG 59.440 37.037 0.00 0.00 43.02 2.74
5154 6155 4.946478 TGGACCAATTTTTACTGTTGGG 57.054 40.909 8.10 0.00 45.17 4.12
5155 6156 4.290942 TGGACCAATTTTTACTGTTGGGT 58.709 39.130 8.10 0.00 45.17 4.51
5156 6157 4.717280 TGGACCAATTTTTACTGTTGGGTT 59.283 37.500 8.10 0.00 45.17 4.11
5402 6408 2.433318 GTCACTGCAGGGCTCGTC 60.433 66.667 19.93 0.00 0.00 4.20
5485 6491 1.265454 CCTCCCCAGGTACACTCCAC 61.265 65.000 0.00 0.00 34.60 4.02
5593 6599 3.350612 GCTACCGCCACGTTTGCA 61.351 61.111 7.52 0.00 0.00 4.08
5617 6623 5.929058 TGATGTTCTCTGCTTCTATGTCT 57.071 39.130 0.00 0.00 0.00 3.41
5784 6791 1.467374 GCGTTCGTTGCTGCCATTATT 60.467 47.619 0.00 0.00 0.00 1.40
5883 6890 4.005650 TCTTCATCAGCGCAATTTCTCTT 58.994 39.130 11.47 0.00 0.00 2.85
5906 6913 5.301555 TGGTACATTTTCGAACATCTGACA 58.698 37.500 0.00 0.00 0.00 3.58
5907 6914 5.178623 TGGTACATTTTCGAACATCTGACAC 59.821 40.000 0.00 0.00 0.00 3.67
5923 6930 1.133790 GACACTGCCCTGATCAAATGC 59.866 52.381 0.00 0.12 0.00 3.56
5951 6958 7.741216 CACTGTTTTTGAACTTTGAACAATGTG 59.259 33.333 6.80 0.00 30.72 3.21
5952 6959 7.440856 ACTGTTTTTGAACTTTGAACAATGTGT 59.559 29.630 6.80 0.00 30.72 3.72
5953 6960 8.818141 TGTTTTTGAACTTTGAACAATGTGTA 57.182 26.923 6.80 0.00 0.00 2.90
5954 6961 9.261180 TGTTTTTGAACTTTGAACAATGTGTAA 57.739 25.926 6.80 3.90 0.00 2.41
5955 6962 9.523730 GTTTTTGAACTTTGAACAATGTGTAAC 57.476 29.630 6.80 4.82 37.35 2.50
5998 7010 1.075450 AGGTGGGGTCGGTATCTCC 60.075 63.158 0.00 0.00 0.00 3.71
6135 7147 7.396055 AGGAACCGGAATTAAATTGAAGATTCA 59.604 33.333 9.46 0.00 34.92 2.57
6159 7171 4.927267 TCATAGGTGGTTCAGGTTTCAT 57.073 40.909 0.00 0.00 0.00 2.57
6161 7173 5.741011 TCATAGGTGGTTCAGGTTTCATAC 58.259 41.667 0.00 0.00 0.00 2.39
6176 7188 7.582667 GGTTTCATACCTTTAGCCATGTAAT 57.417 36.000 0.00 0.00 44.10 1.89
6195 7207 6.512297 TGTAATCAGAATGTAATCTAGCGCA 58.488 36.000 11.47 0.00 37.40 6.09
6369 7384 5.509832 TCTTATGCCCTGCAGAATATCAT 57.490 39.130 17.39 12.34 43.65 2.45
6371 7386 3.801307 ATGCCCTGCAGAATATCATCA 57.199 42.857 17.39 1.22 43.65 3.07
6499 7535 4.200092 GTTTCTGGATGTCCTACCCATTC 58.800 47.826 0.09 0.00 36.82 2.67
6513 7549 6.667414 TCCTACCCATTCAACAAAAATAGCAT 59.333 34.615 0.00 0.00 0.00 3.79
6604 7640 0.029834 CGCCAATAATCAGTGCTGCC 59.970 55.000 0.00 0.00 0.00 4.85
6654 7690 8.099364 TCTCTTAATTTGAACCAACATCAGAC 57.901 34.615 0.00 0.00 0.00 3.51
6754 7796 3.310774 CGCTTACATCCTTCCAGAACATG 59.689 47.826 0.00 0.00 0.00 3.21
6859 7940 6.647895 ACATTCCTCAATTTGCATTCTCAAAC 59.352 34.615 0.00 0.00 38.58 2.93
6977 8058 7.492524 ACATTCTCCTTTTTCCTTTCTGAAAC 58.507 34.615 0.00 0.00 34.13 2.78
7063 8144 9.595823 TTCTAACCCATAACGAAGATTTCTAAG 57.404 33.333 0.00 0.00 0.00 2.18
7065 8146 9.595823 CTAACCCATAACGAAGATTTCTAAGAA 57.404 33.333 0.00 0.00 0.00 2.52
7279 8361 4.537015 GCGTTGTTTTTAGCATCTGAAGT 58.463 39.130 0.00 0.00 0.00 3.01
7369 8451 5.452777 GTTGGCTCACTCAAAACATACTTC 58.547 41.667 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.268845 CGCAAGTTGGTGGTGGTTTAC 60.269 52.381 4.75 0.00 0.00 2.01
86 87 9.765795 TGAAAAAGAAACACTAAAGAAAAACCA 57.234 25.926 0.00 0.00 0.00 3.67
125 141 6.628185 ACAAATATTTACGAACGGAGAGAGT 58.372 36.000 0.00 0.00 0.00 3.24
126 142 6.973474 AGACAAATATTTACGAACGGAGAGAG 59.027 38.462 0.00 0.00 0.00 3.20
127 143 6.860080 AGACAAATATTTACGAACGGAGAGA 58.140 36.000 0.00 0.00 0.00 3.10
128 144 7.521509 AAGACAAATATTTACGAACGGAGAG 57.478 36.000 0.00 0.00 0.00 3.20
129 145 7.894376 AAAGACAAATATTTACGAACGGAGA 57.106 32.000 0.00 0.00 0.00 3.71
207 223 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
209 225 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
210 226 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
211 227 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
212 228 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
214 230 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
216 232 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
217 233 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
218 234 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
220 236 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
221 237 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
222 238 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
223 239 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
225 241 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
227 243 7.439955 ACATTTCAACAAGTGACTACATACGAA 59.560 33.333 0.00 0.00 35.39 3.85
228 244 6.926826 ACATTTCAACAAGTGACTACATACGA 59.073 34.615 0.00 0.00 35.39 3.43
229 245 7.116376 AGACATTTCAACAAGTGACTACATACG 59.884 37.037 0.00 0.00 35.39 3.06
230 246 8.311650 AGACATTTCAACAAGTGACTACATAC 57.688 34.615 0.00 0.00 35.39 2.39
231 247 9.990360 TTAGACATTTCAACAAGTGACTACATA 57.010 29.630 0.00 0.00 35.39 2.29
232 248 8.902540 TTAGACATTTCAACAAGTGACTACAT 57.097 30.769 0.00 0.00 35.39 2.29
233 249 8.725405 TTTAGACATTTCAACAAGTGACTACA 57.275 30.769 0.00 0.00 35.39 2.74
236 252 8.956426 TCTTTTTAGACATTTCAACAAGTGACT 58.044 29.630 0.00 0.00 35.39 3.41
237 253 9.010366 GTCTTTTTAGACATTTCAACAAGTGAC 57.990 33.333 0.00 0.00 38.59 3.67
239 255 8.909708 TGTCTTTTTAGACATTTCAACAAGTG 57.090 30.769 3.99 0.00 43.09 3.16
240 256 9.921637 TTTGTCTTTTTAGACATTTCAACAAGT 57.078 25.926 8.65 0.00 46.61 3.16
262 278 9.936329 ACATTGGACCTATTCCTAAATATTTGT 57.064 29.630 11.05 0.00 46.10 2.83
265 281 9.799106 CTCACATTGGACCTATTCCTAAATATT 57.201 33.333 0.00 0.00 46.10 1.28
266 282 8.949421 ACTCACATTGGACCTATTCCTAAATAT 58.051 33.333 0.00 0.00 46.10 1.28
268 284 7.213178 ACTCACATTGGACCTATTCCTAAAT 57.787 36.000 0.00 0.00 46.10 1.40
269 285 6.636454 ACTCACATTGGACCTATTCCTAAA 57.364 37.500 0.00 0.00 46.10 1.85
271 287 5.839063 CCTACTCACATTGGACCTATTCCTA 59.161 44.000 0.00 0.00 46.10 2.94
272 288 4.656112 CCTACTCACATTGGACCTATTCCT 59.344 45.833 0.00 0.00 46.10 3.36
273 289 4.654262 TCCTACTCACATTGGACCTATTCC 59.346 45.833 0.00 0.00 46.13 3.01
274 290 5.871396 TCCTACTCACATTGGACCTATTC 57.129 43.478 0.00 0.00 0.00 1.75
275 291 5.905331 TGATCCTACTCACATTGGACCTATT 59.095 40.000 0.00 0.00 0.00 1.73
276 292 5.305644 GTGATCCTACTCACATTGGACCTAT 59.694 44.000 0.00 0.00 44.03 2.57
278 294 3.452627 GTGATCCTACTCACATTGGACCT 59.547 47.826 0.00 0.00 44.03 3.85
279 295 3.452627 AGTGATCCTACTCACATTGGACC 59.547 47.826 6.95 0.00 46.45 4.46
281 297 5.163405 GCTAAGTGATCCTACTCACATTGGA 60.163 44.000 6.95 0.00 46.45 3.53
282 298 5.053145 GCTAAGTGATCCTACTCACATTGG 58.947 45.833 6.95 2.60 46.45 3.16
283 299 5.053145 GGCTAAGTGATCCTACTCACATTG 58.947 45.833 6.95 0.00 46.45 2.82
286 302 3.708451 TGGCTAAGTGATCCTACTCACA 58.292 45.455 6.95 0.00 46.45 3.58
287 303 4.626042 CATGGCTAAGTGATCCTACTCAC 58.374 47.826 0.00 0.00 44.78 3.51
288 304 3.070159 GCATGGCTAAGTGATCCTACTCA 59.930 47.826 0.00 0.00 0.00 3.41
289 305 3.323403 AGCATGGCTAAGTGATCCTACTC 59.677 47.826 0.00 0.00 36.99 2.59
290 306 3.312890 AGCATGGCTAAGTGATCCTACT 58.687 45.455 0.00 0.00 36.99 2.57
291 307 3.760580 AGCATGGCTAAGTGATCCTAC 57.239 47.619 0.00 0.00 36.99 3.18
292 308 3.711190 TGAAGCATGGCTAAGTGATCCTA 59.289 43.478 0.00 0.00 38.25 2.94
293 309 2.507058 TGAAGCATGGCTAAGTGATCCT 59.493 45.455 0.00 0.00 38.25 3.24
294 310 2.923121 TGAAGCATGGCTAAGTGATCC 58.077 47.619 0.00 0.00 38.25 3.36
295 311 6.814506 ATTATGAAGCATGGCTAAGTGATC 57.185 37.500 0.00 0.00 38.25 2.92
296 312 6.015688 CCAATTATGAAGCATGGCTAAGTGAT 60.016 38.462 0.00 0.00 38.25 3.06
297 313 5.300034 CCAATTATGAAGCATGGCTAAGTGA 59.700 40.000 0.00 0.00 38.25 3.41
298 314 5.300034 TCCAATTATGAAGCATGGCTAAGTG 59.700 40.000 0.00 0.00 38.25 3.16
300 316 6.395426 TTCCAATTATGAAGCATGGCTAAG 57.605 37.500 0.00 0.00 38.25 2.18
301 317 6.788598 TTTCCAATTATGAAGCATGGCTAA 57.211 33.333 0.00 0.00 38.25 3.09
305 321 5.291614 CCGTTTTTCCAATTATGAAGCATGG 59.708 40.000 0.00 0.00 0.00 3.66
306 322 5.291614 CCCGTTTTTCCAATTATGAAGCATG 59.708 40.000 0.00 0.00 0.00 4.06
307 323 5.418676 CCCGTTTTTCCAATTATGAAGCAT 58.581 37.500 0.00 0.00 0.00 3.79
308 324 4.815269 CCCGTTTTTCCAATTATGAAGCA 58.185 39.130 0.00 0.00 0.00 3.91
309 325 3.616821 GCCCGTTTTTCCAATTATGAAGC 59.383 43.478 0.00 0.00 0.00 3.86
310 326 3.857093 CGCCCGTTTTTCCAATTATGAAG 59.143 43.478 0.00 0.00 0.00 3.02
311 327 3.839293 CGCCCGTTTTTCCAATTATGAA 58.161 40.909 0.00 0.00 0.00 2.57
312 328 2.416162 GCGCCCGTTTTTCCAATTATGA 60.416 45.455 0.00 0.00 0.00 2.15
314 330 1.134936 GGCGCCCGTTTTTCCAATTAT 60.135 47.619 18.11 0.00 0.00 1.28
315 331 0.244178 GGCGCCCGTTTTTCCAATTA 59.756 50.000 18.11 0.00 0.00 1.40
316 332 1.005512 GGCGCCCGTTTTTCCAATT 60.006 52.632 18.11 0.00 0.00 2.32
319 335 2.598985 ATGGCGCCCGTTTTTCCA 60.599 55.556 26.77 0.73 0.00 3.53
320 336 2.126110 CATGGCGCCCGTTTTTCC 60.126 61.111 26.77 0.00 0.00 3.13
321 337 0.319125 TTTCATGGCGCCCGTTTTTC 60.319 50.000 26.77 0.00 0.00 2.29
322 338 0.319469 CTTTCATGGCGCCCGTTTTT 60.319 50.000 26.77 0.00 0.00 1.94
323 339 1.288752 CTTTCATGGCGCCCGTTTT 59.711 52.632 26.77 0.00 0.00 2.43
324 340 0.606944 TACTTTCATGGCGCCCGTTT 60.607 50.000 26.77 2.73 0.00 3.60
325 341 0.606944 TTACTTTCATGGCGCCCGTT 60.607 50.000 26.77 5.78 0.00 4.44
326 342 0.393808 ATTACTTTCATGGCGCCCGT 60.394 50.000 26.77 10.28 0.00 5.28
327 343 0.029300 CATTACTTTCATGGCGCCCG 59.971 55.000 26.77 15.98 0.00 6.13
328 344 1.102978 ACATTACTTTCATGGCGCCC 58.897 50.000 26.77 6.44 0.00 6.13
330 346 3.698029 ATCACATTACTTTCATGGCGC 57.302 42.857 0.00 0.00 0.00 6.53
331 347 5.682862 GCTTTATCACATTACTTTCATGGCG 59.317 40.000 0.00 0.00 0.00 5.69
332 348 6.563422 TGCTTTATCACATTACTTTCATGGC 58.437 36.000 0.00 0.00 0.00 4.40
333 349 8.407832 TGATGCTTTATCACATTACTTTCATGG 58.592 33.333 0.00 0.00 40.82 3.66
488 506 3.543680 AATGTCGAATCGGGATTCACT 57.456 42.857 18.52 6.33 45.60 3.41
491 509 6.359480 ACTTTTAATGTCGAATCGGGATTC 57.641 37.500 10.65 10.65 42.76 2.52
493 511 9.720769 AATATACTTTTAATGTCGAATCGGGAT 57.279 29.630 1.76 0.00 0.00 3.85
565 583 9.787532 GGAAAGTCGATTTATGAATTGAATCAA 57.212 29.630 0.00 0.00 37.40 2.57
568 586 8.525290 AGGGAAAGTCGATTTATGAATTGAAT 57.475 30.769 1.85 0.00 37.40 2.57
570 588 6.542370 GGAGGGAAAGTCGATTTATGAATTGA 59.458 38.462 0.00 0.00 34.07 2.57
571 589 6.543831 AGGAGGGAAAGTCGATTTATGAATTG 59.456 38.462 0.00 0.00 0.00 2.32
572 590 6.663734 AGGAGGGAAAGTCGATTTATGAATT 58.336 36.000 0.00 0.00 0.00 2.17
573 591 6.253946 AGGAGGGAAAGTCGATTTATGAAT 57.746 37.500 0.00 0.00 0.00 2.57
574 592 5.693769 AGGAGGGAAAGTCGATTTATGAA 57.306 39.130 0.00 0.00 0.00 2.57
575 593 6.741521 GCATAGGAGGGAAAGTCGATTTATGA 60.742 42.308 0.00 0.00 0.00 2.15
576 594 5.409826 GCATAGGAGGGAAAGTCGATTTATG 59.590 44.000 0.00 0.00 0.00 1.90
578 596 4.654262 AGCATAGGAGGGAAAGTCGATTTA 59.346 41.667 0.00 0.00 0.00 1.40
581 599 2.630580 GAGCATAGGAGGGAAAGTCGAT 59.369 50.000 0.00 0.00 0.00 3.59
582 600 2.032620 GAGCATAGGAGGGAAAGTCGA 58.967 52.381 0.00 0.00 0.00 4.20
584 602 3.034635 TCAGAGCATAGGAGGGAAAGTC 58.965 50.000 0.00 0.00 0.00 3.01
586 604 2.368221 CCTCAGAGCATAGGAGGGAAAG 59.632 54.545 0.00 0.00 43.59 2.62
587 605 2.402564 CCTCAGAGCATAGGAGGGAAA 58.597 52.381 0.00 0.00 43.59 3.13
588 606 2.094100 CCTCAGAGCATAGGAGGGAA 57.906 55.000 0.00 0.00 43.59 3.97
589 607 3.858886 CCTCAGAGCATAGGAGGGA 57.141 57.895 0.00 0.00 43.59 4.20
591 609 1.631405 CTCCCTCAGAGCATAGGAGG 58.369 60.000 11.08 0.00 46.24 4.30
601 619 5.642165 ACACTAAGAAACTACTCCCTCAGA 58.358 41.667 0.00 0.00 0.00 3.27
602 620 5.986501 ACACTAAGAAACTACTCCCTCAG 57.013 43.478 0.00 0.00 0.00 3.35
603 621 6.325545 TGAAACACTAAGAAACTACTCCCTCA 59.674 38.462 0.00 0.00 0.00 3.86
604 622 6.645827 GTGAAACACTAAGAAACTACTCCCTC 59.354 42.308 0.00 0.00 36.32 4.30
605 623 6.099269 TGTGAAACACTAAGAAACTACTCCCT 59.901 38.462 0.00 0.00 45.67 4.20
631 649 3.304458 GGTAAACAAAGGAGAACTTGGCG 60.304 47.826 0.00 0.00 39.96 5.69
680 699 1.114627 CTGAGACGGGATCATGGACA 58.885 55.000 0.00 0.00 0.00 4.02
685 704 2.894126 GGTATGACTGAGACGGGATCAT 59.106 50.000 0.00 0.00 34.48 2.45
799 965 6.642131 CCTCCGTCCGAAATTATTTATCGTAA 59.358 38.462 0.00 0.00 34.90 3.18
816 1002 3.387050 AGTGTACAATATTCCCTCCGTCC 59.613 47.826 0.00 0.00 0.00 4.79
820 1006 4.130118 CAGCAGTGTACAATATTCCCTCC 58.870 47.826 0.00 0.00 0.00 4.30
837 1023 3.733380 CGTGGATTCAGAGAGTACAGCAG 60.733 52.174 0.00 0.00 0.00 4.24
838 1024 2.164422 CGTGGATTCAGAGAGTACAGCA 59.836 50.000 0.00 0.00 0.00 4.41
842 1028 4.082136 AGGAAACGTGGATTCAGAGAGTAC 60.082 45.833 0.00 0.00 0.00 2.73
848 1034 4.503910 CATGTAGGAAACGTGGATTCAGA 58.496 43.478 0.00 0.00 40.80 3.27
858 1044 5.179368 ACTTGACATTCACATGTAGGAAACG 59.821 40.000 0.00 0.00 44.22 3.60
876 1062 5.106078 TGGCCCGTTGAAATATTTACTTGAC 60.106 40.000 0.00 0.00 0.00 3.18
880 1066 6.538945 AATTGGCCCGTTGAAATATTTACT 57.461 33.333 0.00 0.00 0.00 2.24
881 1067 5.457473 CGAATTGGCCCGTTGAAATATTTAC 59.543 40.000 0.00 0.00 0.00 2.01
886 1072 2.438411 ACGAATTGGCCCGTTGAAATA 58.562 42.857 0.00 0.00 35.21 1.40
887 1073 1.253100 ACGAATTGGCCCGTTGAAAT 58.747 45.000 0.00 0.00 35.21 2.17
889 1075 1.893544 TTACGAATTGGCCCGTTGAA 58.106 45.000 10.07 0.00 39.86 2.69
900 1086 1.200484 ACGGCGGCAAAATTACGAATT 59.800 42.857 13.24 0.00 0.00 2.17
901 1087 0.806241 ACGGCGGCAAAATTACGAAT 59.194 45.000 13.24 0.00 0.00 3.34
918 1104 4.873827 AGTTTGCAATATACCCACTACACG 59.126 41.667 0.00 0.00 0.00 4.49
920 1106 4.638421 GCAGTTTGCAATATACCCACTACA 59.362 41.667 0.00 0.00 44.26 2.74
1137 1326 1.006102 AGACGTGCGGGAAAGACAG 60.006 57.895 0.00 0.00 0.00 3.51
1175 1364 3.662078 TCTCTGGATGATTCCTGATGGT 58.338 45.455 2.58 0.00 45.66 3.55
1246 1435 9.794685 GAGAAATCATGGAATTAAAACTCCTTC 57.205 33.333 0.00 0.45 32.51 3.46
1251 1440 7.398332 AGCCTGAGAAATCATGGAATTAAAACT 59.602 33.333 0.00 0.00 0.00 2.66
1256 1445 6.005066 TGAGCCTGAGAAATCATGGAATTA 57.995 37.500 0.00 0.00 0.00 1.40
1344 1533 2.032981 CAACTTCCTGCACCGCTTT 58.967 52.632 0.00 0.00 0.00 3.51
1655 1844 7.463961 AGCAAACTACAGTAGAAGCTAGTAA 57.536 36.000 14.94 0.00 32.35 2.24
1687 1878 9.851686 TTCATCTCATGGCTAATAAAATACAGT 57.148 29.630 0.00 0.00 0.00 3.55
1689 1880 9.851686 AGTTCATCTCATGGCTAATAAAATACA 57.148 29.630 0.00 0.00 0.00 2.29
1732 1923 1.265635 TGAATTCCCACAAAACGAGCG 59.734 47.619 2.27 0.00 0.00 5.03
1738 1929 4.141824 GGGTCAAACTGAATTCCCACAAAA 60.142 41.667 2.27 0.00 32.21 2.44
1863 2054 7.020010 CACACATATCAAAAAGAAGAGAGTGC 58.980 38.462 0.00 0.00 0.00 4.40
1864 2055 7.173907 ACCACACATATCAAAAAGAAGAGAGTG 59.826 37.037 0.00 0.00 0.00 3.51
1865 2056 7.173907 CACCACACATATCAAAAAGAAGAGAGT 59.826 37.037 0.00 0.00 0.00 3.24
1866 2057 7.524912 CACCACACATATCAAAAAGAAGAGAG 58.475 38.462 0.00 0.00 0.00 3.20
1867 2058 6.072508 GCACCACACATATCAAAAAGAAGAGA 60.073 38.462 0.00 0.00 0.00 3.10
1879 2071 5.450412 CCACCAAATTAGCACCACACATATC 60.450 44.000 0.00 0.00 0.00 1.63
1909 2101 0.532862 CCATCGGCTACCACATCCAC 60.533 60.000 0.00 0.00 0.00 4.02
2050 2242 2.160417 GGCAGTTGAAGACTTTGGATCG 59.840 50.000 0.00 0.00 36.10 3.69
2093 2285 6.753180 AGAAGAAAATCCCAAAAGAAAGAGC 58.247 36.000 0.00 0.00 0.00 4.09
2101 2293 5.453198 GGCACAGAAGAAGAAAATCCCAAAA 60.453 40.000 0.00 0.00 0.00 2.44
2160 2352 6.519679 ACATGCTTGAGAAATGAATGCTTA 57.480 33.333 6.60 0.00 0.00 3.09
2180 2372 1.555075 ACAGGACCGCATACTGAACAT 59.445 47.619 4.19 0.00 36.17 2.71
2196 2388 5.449588 GCACACATGAAGGAATCATTACAGG 60.450 44.000 0.00 0.00 46.85 4.00
2255 2447 7.772166 TCAATCAGTACAGTACCTCATACTTG 58.228 38.462 7.13 3.12 41.71 3.16
2267 2459 5.122869 GCACACATGAATCAATCAGTACAGT 59.877 40.000 0.00 0.00 42.53 3.55
2326 2518 3.882888 CCTAACTTTCCAACAGCAACAGA 59.117 43.478 0.00 0.00 0.00 3.41
2420 2612 6.214819 ACCATCACAAGTTACCTACCTAACAT 59.785 38.462 0.00 0.00 0.00 2.71
2513 2705 9.953565 ACAAGTAAACATAGACTTAGCCATTAA 57.046 29.630 0.00 0.00 34.13 1.40
2517 2709 7.389607 GGAAACAAGTAAACATAGACTTAGCCA 59.610 37.037 0.00 0.00 34.13 4.75
2518 2710 7.389607 TGGAAACAAGTAAACATAGACTTAGCC 59.610 37.037 0.00 0.00 37.44 3.93
2558 2750 5.730550 TGTATAGCCTTCACACCTTTGTAG 58.269 41.667 0.00 0.00 33.30 2.74
2692 2910 2.619177 AGTTCGGTAGATGGAGACGATG 59.381 50.000 0.00 0.00 33.26 3.84
2733 2951 1.396996 CCAAACGAAATAGCTGGACGG 59.603 52.381 0.00 0.00 0.00 4.79
2739 2957 3.432252 CACGAGTTCCAAACGAAATAGCT 59.568 43.478 0.00 0.00 36.23 3.32
2747 2965 2.427232 TAGGTCACGAGTTCCAAACG 57.573 50.000 0.00 0.00 36.23 3.60
2789 3007 5.293569 GCATTGTTATAAGGTTGTAGACGCT 59.706 40.000 0.00 0.00 0.00 5.07
2929 3148 4.785376 ACCAACAATTCTGAGTAGAGGGAT 59.215 41.667 0.00 0.00 33.70 3.85
2940 3159 4.488126 ACGATGTCAACCAACAATTCTG 57.512 40.909 0.00 0.00 31.81 3.02
2970 3189 9.965902 ACCAGAGATTTCTATGAATTGTACTTT 57.034 29.630 3.83 0.00 37.37 2.66
3527 3753 2.620251 AAGGGGCAAACAAAAGAAGC 57.380 45.000 0.00 0.00 0.00 3.86
3636 3862 8.812513 ATATTTTGATTTGGTGACAGATGAGA 57.187 30.769 0.00 0.00 44.54 3.27
3699 3925 3.024547 TGTAGAGAGTGGTGCATACTCC 58.975 50.000 22.81 16.62 44.35 3.85
3744 3970 2.159338 CGCTTCATCTGAATGGGGTTTG 60.159 50.000 0.00 0.00 33.01 2.93
3791 4017 5.482878 AGATCTCCAACAAATGCAAGGAATT 59.517 36.000 0.00 0.00 0.00 2.17
3907 4133 1.825090 CAAGGAATGCTAGCCACACA 58.175 50.000 13.29 0.00 0.00 3.72
3990 4216 3.118629 AGCTGGAATTAGATGCGTCTGAA 60.119 43.478 18.98 9.11 35.87 3.02
4733 5709 4.956075 TCCAAAGAATAGGCAAAAGGATCC 59.044 41.667 2.48 2.48 0.00 3.36
4741 5717 5.187576 CCCAGATTTTCCAAAGAATAGGCAA 59.812 40.000 0.00 0.00 0.00 4.52
4793 5769 3.399330 ACACGTGGACTATGGTTTTCAG 58.601 45.455 21.57 0.00 0.00 3.02
4902 5878 4.141846 GCAATCCATGAAGAGAGGTAGTCA 60.142 45.833 0.00 0.00 0.00 3.41
4918 5894 1.262417 TACAGAGTCACGGCAATCCA 58.738 50.000 0.00 0.00 0.00 3.41
4923 5899 1.961394 AGAGTTTACAGAGTCACGGCA 59.039 47.619 0.00 0.00 0.00 5.69
4976 5952 3.309296 AGGATCCCCGCCTGTATATATG 58.691 50.000 8.55 0.00 37.58 1.78
5145 6146 3.868619 AGCCAAGTAAACCCAACAGTA 57.131 42.857 0.00 0.00 0.00 2.74
5149 6150 6.015772 TCAGAAATTAGCCAAGTAAACCCAAC 60.016 38.462 0.00 0.00 0.00 3.77
5156 6157 9.679661 TCATAATGTCAGAAATTAGCCAAGTAA 57.320 29.630 0.00 0.00 0.00 2.24
5402 6408 2.100631 CAAACCTAGCAGACCGCCG 61.101 63.158 0.00 0.00 44.04 6.46
5593 6599 6.762187 CAGACATAGAAGCAGAGAACATCATT 59.238 38.462 0.00 0.00 0.00 2.57
5617 6623 4.338012 TCAAGAGGTAGTATTCCACGACA 58.662 43.478 0.00 0.00 34.68 4.35
5784 6791 0.909133 TCCTGACTACATGCTGCCCA 60.909 55.000 0.00 0.00 0.00 5.36
5883 6890 5.178623 GTGTCAGATGTTCGAAAATGTACCA 59.821 40.000 5.31 0.00 0.00 3.25
5906 6913 0.685458 GGGCATTTGATCAGGGCAGT 60.685 55.000 15.91 0.00 0.00 4.40
5907 6914 0.685131 TGGGCATTTGATCAGGGCAG 60.685 55.000 15.91 0.74 0.00 4.85
5923 6930 5.233988 TGTTCAAAGTTCAAAAACAGTGGG 58.766 37.500 0.00 0.00 37.88 4.61
5957 6964 5.766222 TGAAGATTGAAAAGAAGCAGCTTC 58.234 37.500 25.46 25.46 40.45 3.86
5998 7010 4.157105 TGCTCCATCTTGTGAATCATGTTG 59.843 41.667 0.00 0.00 0.00 3.33
6077 7089 0.878416 TGCACATGAACGTTAAGCCC 59.122 50.000 0.00 0.00 0.00 5.19
6135 7147 5.640147 TGAAACCTGAACCACCTATGAATT 58.360 37.500 0.00 0.00 0.00 2.17
6159 7171 7.573710 ACATTCTGATTACATGGCTAAAGGTA 58.426 34.615 0.00 0.00 0.00 3.08
6161 7173 6.949352 ACATTCTGATTACATGGCTAAAGG 57.051 37.500 0.00 0.00 0.00 3.11
6176 7188 4.385358 TGTGCGCTAGATTACATTCTGA 57.615 40.909 9.73 0.00 0.00 3.27
6195 7207 1.880027 GCGGTGACCTCTGATTTTTGT 59.120 47.619 0.00 0.00 0.00 2.83
6290 7304 2.499693 TGAGATAGGCACGGTGAATTGA 59.500 45.455 13.29 0.00 0.00 2.57
6369 7384 6.430616 TCTGACAACAAAATGCACATCTATGA 59.569 34.615 0.00 0.00 0.00 2.15
6371 7386 6.822667 TCTGACAACAAAATGCACATCTAT 57.177 33.333 0.00 0.00 0.00 1.98
6499 7535 8.578308 TCTGAAGAAACATGCTATTTTTGTTG 57.422 30.769 0.00 0.00 34.04 3.33
6604 7640 1.308998 ACAGAGGCCAAGTGTTTTCG 58.691 50.000 5.01 0.00 0.00 3.46
6654 7690 6.166279 AGTACTGAGTGTTACATGTTCATGG 58.834 40.000 2.30 0.00 0.00 3.66
6693 7734 2.044946 GGAGTGCTTCCCCGCAAT 60.045 61.111 0.00 0.00 42.32 3.56
6702 7743 5.446860 TGCTACTATAGTACTGGAGTGCTT 58.553 41.667 17.41 0.00 41.24 3.91
6704 7745 5.336055 CCATGCTACTATAGTACTGGAGTGC 60.336 48.000 18.45 17.22 0.00 4.40
6754 7796 4.701765 ACAAGATATCTGGTGATGCTGAC 58.298 43.478 12.20 0.00 34.32 3.51
6859 7940 3.142162 TGCCCATGCATTGCCTCG 61.142 61.111 13.83 0.00 44.23 4.63
6960 8041 6.143919 GGCAATACGTTTCAGAAAGGAAAAAG 59.856 38.462 20.03 8.36 38.41 2.27
6977 8058 9.203421 TGATATAAGTTGAAGTATGGCAATACG 57.797 33.333 5.57 0.00 43.03 3.06
7063 8144 4.382160 GTGCTACTGTAAACACGAGTCTTC 59.618 45.833 0.00 0.00 0.00 2.87
7065 8146 3.305199 GGTGCTACTGTAAACACGAGTCT 60.305 47.826 12.04 0.00 33.81 3.24
7137 8219 7.144661 AGCATACAATGTTCTCTTCTATCTCG 58.855 38.462 0.00 0.00 0.00 4.04
7369 8451 3.002656 CAGGTGCTAAATATGAACTGCCG 59.997 47.826 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.