Multiple sequence alignment - TraesCS5A01G139000

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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 TraesCS5A01G139000 chr5A 100.000 4524 0 0 1 4524 311279667 311284190 0.000000e+00 8355
1 TraesCS5A01G139000 chr5D 96.953 4004 84 21 536 4522 241664676 241668658 0.000000e+00 6684
2 TraesCS5A01G139000 chr5B 96.132 3283 79 18 395 3666 262057970 262054725 0.000000e+00 5315
3 TraesCS5A01G139000 chr5B 95.309 469 15 3 4058 4524 262052787 262052324 0.000000e+00 737
4 TraesCS5A01G139000 chr5B 97.264 402 11 0 3658 4059 262053512 262053111 0.000000e+00 682
5 TraesCS5A01G139000 chr5B 87.397 365 38 8 1 360 540340824 540341185 3.260000e-111 412
6 TraesCS5A01G139000 chr5B 88.338 343 36 4 1 341 536570067 536569727 4.210000e-110 409
7 TraesCS5A01G139000 chr5B 87.755 343 38 4 1 341 608364209 608364549 9.120000e-107 398
8 TraesCS5A01G139000 chr2D 90.351 342 27 4 3 342 516853480 516853817 1.150000e-120 444
9 TraesCS5A01G139000 chr2D 82.955 352 48 9 1 345 143601439 143601093 1.580000e-79 307
10 TraesCS5A01G139000 chr2D 84.795 171 21 4 1 168 36130029 36130197 2.800000e-37 167
11 TraesCS5A01G139000 chr7B 86.236 356 35 8 1 345 123674845 123675197 1.540000e-99 374
12 TraesCS5A01G139000 chr3B 84.795 342 39 8 1 342 710431572 710431900 9.380000e-87 331
13 TraesCS5A01G139000 chr4D 84.751 341 24 12 3 341 124182233 124182547 2.630000e-82 316
14 TraesCS5A01G139000 chr1D 82.955 352 47 11 1 344 464849686 464850032 5.690000e-79 305


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 TraesCS5A01G139000 chr5A 311279667 311284190 4523 False 8355.000000 8355 100.000 1 4524 1 chr5A.!!$F1 4523
1 TraesCS5A01G139000 chr5D 241664676 241668658 3982 False 6684.000000 6684 96.953 536 4522 1 chr5D.!!$F1 3986
2 TraesCS5A01G139000 chr5B 262052324 262057970 5646 True 2244.666667 5315 96.235 395 4524 3 chr5B.!!$R2 4129

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
77 78 0.032678 AGCTGCGTGATAAGGATCCG 59.967 55.0 5.98 0.00 0.0 4.18 F
293 294 0.178924 ATGATGCATAAAGGGCCCCC 60.179 55.0 21.43 0.00 0.0 5.40 F
1219 1231 0.179240 CGTGAACTGCAGCGCTTTAG 60.179 55.0 15.27 12.02 0.0 1.85 F
1220 1232 0.868406 GTGAACTGCAGCGCTTTAGT 59.132 50.0 15.27 12.78 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1660 0.734889 CATAGAAGGGCTTTGCGGTG 59.265 55.000 0.00 0.00 0.00 4.94 R
1702 1726 1.302832 GCTGTCCAGGGACCAAGTG 60.303 63.158 15.53 2.86 43.97 3.16 R
2557 2581 0.976073 GGTACTGCTGGCTCCCTGTA 60.976 60.000 0.00 0.00 0.00 2.74 R
3876 5121 7.513371 TTCCTCTAGCTTATCTTAGTACTGC 57.487 40.000 5.39 0.00 0.00 4.40 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
67 68 9.542462 AATTATAAAGTAATTCTAGCTGCGTGA 57.458 29.630 0.00 0.00 0.00 4.35
68 69 9.712305 ATTATAAAGTAATTCTAGCTGCGTGAT 57.288 29.630 0.00 0.00 0.00 3.06
71 72 7.470289 AAAGTAATTCTAGCTGCGTGATAAG 57.530 36.000 0.00 0.00 0.00 1.73
72 73 5.533482 AGTAATTCTAGCTGCGTGATAAGG 58.467 41.667 0.00 0.00 0.00 2.69
73 74 4.672587 AATTCTAGCTGCGTGATAAGGA 57.327 40.909 0.00 0.00 0.00 3.36
74 75 4.881019 ATTCTAGCTGCGTGATAAGGAT 57.119 40.909 0.00 0.00 0.00 3.24
75 76 3.924918 TCTAGCTGCGTGATAAGGATC 57.075 47.619 0.00 0.00 0.00 3.36
76 77 2.558795 TCTAGCTGCGTGATAAGGATCC 59.441 50.000 2.48 2.48 0.00 3.36
77 78 0.032678 AGCTGCGTGATAAGGATCCG 59.967 55.000 5.98 0.00 0.00 4.18
78 79 0.249489 GCTGCGTGATAAGGATCCGT 60.249 55.000 5.98 5.61 31.95 4.69
79 80 1.806623 GCTGCGTGATAAGGATCCGTT 60.807 52.381 5.22 3.63 31.95 4.44
80 81 2.128035 CTGCGTGATAAGGATCCGTTC 58.872 52.381 5.22 5.13 31.95 3.95
81 82 1.478916 TGCGTGATAAGGATCCGTTCA 59.521 47.619 5.22 7.82 31.95 3.18
82 83 2.093921 TGCGTGATAAGGATCCGTTCAA 60.094 45.455 5.22 0.00 31.95 2.69
83 84 2.933906 GCGTGATAAGGATCCGTTCAAA 59.066 45.455 5.22 0.00 31.95 2.69
84 85 3.560068 GCGTGATAAGGATCCGTTCAAAT 59.440 43.478 5.22 0.00 31.95 2.32
85 86 4.748102 GCGTGATAAGGATCCGTTCAAATA 59.252 41.667 5.22 0.00 31.95 1.40
86 87 5.408604 GCGTGATAAGGATCCGTTCAAATAT 59.591 40.000 5.22 0.00 31.95 1.28
87 88 6.073222 GCGTGATAAGGATCCGTTCAAATATT 60.073 38.462 5.22 0.00 31.95 1.28
88 89 7.117236 GCGTGATAAGGATCCGTTCAAATATTA 59.883 37.037 5.22 0.00 31.95 0.98
89 90 9.151471 CGTGATAAGGATCCGTTCAAATATTAT 57.849 33.333 5.22 1.16 0.00 1.28
96 97 9.801873 AGGATCCGTTCAAATATTATTTTTGTG 57.198 29.630 5.98 1.50 35.90 3.33
97 98 9.581099 GGATCCGTTCAAATATTATTTTTGTGT 57.419 29.630 0.00 0.00 35.90 3.72
99 100 9.921637 ATCCGTTCAAATATTATTTTTGTGTGT 57.078 25.926 7.72 0.00 35.90 3.72
100 101 9.186323 TCCGTTCAAATATTATTTTTGTGTGTG 57.814 29.630 7.72 0.00 35.90 3.82
101 102 8.431593 CCGTTCAAATATTATTTTTGTGTGTGG 58.568 33.333 7.72 2.52 35.90 4.17
102 103 7.949428 CGTTCAAATATTATTTTTGTGTGTGGC 59.051 33.333 7.72 0.00 35.90 5.01
103 104 8.768955 GTTCAAATATTATTTTTGTGTGTGGCA 58.231 29.630 7.72 0.00 35.90 4.92
129 130 9.302345 ACACTATATATGAAATATACACTGCGC 57.698 33.333 0.00 0.00 43.99 6.09
130 131 8.472236 CACTATATATGAAATATACACTGCGCG 58.528 37.037 0.00 0.00 43.99 6.86
131 132 2.949714 ATGAAATATACACTGCGCGC 57.050 45.000 27.26 27.26 0.00 6.86
132 133 1.646189 TGAAATATACACTGCGCGCA 58.354 45.000 34.12 34.12 0.00 6.09
133 134 2.003301 TGAAATATACACTGCGCGCAA 58.997 42.857 35.50 21.15 0.00 4.85
134 135 2.222931 TGAAATATACACTGCGCGCAAC 60.223 45.455 35.50 14.90 0.00 4.17
135 136 1.651987 AATATACACTGCGCGCAACT 58.348 45.000 35.50 20.17 0.00 3.16
136 137 1.651987 ATATACACTGCGCGCAACTT 58.348 45.000 35.50 22.59 0.00 2.66
137 138 0.996462 TATACACTGCGCGCAACTTC 59.004 50.000 35.50 3.27 0.00 3.01
138 139 1.635663 ATACACTGCGCGCAACTTCC 61.636 55.000 35.50 2.41 0.00 3.46
139 140 2.709125 TACACTGCGCGCAACTTCCT 62.709 55.000 35.50 15.84 0.00 3.36
140 141 2.591715 ACTGCGCGCAACTTCCTT 60.592 55.556 35.50 10.13 0.00 3.36
141 142 2.127118 CTGCGCGCAACTTCCTTG 60.127 61.111 35.50 16.91 0.00 3.61
142 143 3.599792 CTGCGCGCAACTTCCTTGG 62.600 63.158 35.50 16.11 0.00 3.61
144 145 3.659092 CGCGCAACTTCCTTGGCA 61.659 61.111 8.75 0.00 0.00 4.92
145 146 2.727544 GCGCAACTTCCTTGGCAA 59.272 55.556 0.30 0.00 0.00 4.52
146 147 1.067250 GCGCAACTTCCTTGGCAAA 59.933 52.632 0.30 0.00 0.00 3.68
147 148 0.529555 GCGCAACTTCCTTGGCAAAA 60.530 50.000 0.30 0.00 0.00 2.44
148 149 1.873486 GCGCAACTTCCTTGGCAAAAT 60.873 47.619 0.30 0.00 0.00 1.82
149 150 2.482864 CGCAACTTCCTTGGCAAAATT 58.517 42.857 0.00 0.00 0.00 1.82
150 151 2.871633 CGCAACTTCCTTGGCAAAATTT 59.128 40.909 0.00 0.00 0.00 1.82
151 152 4.054671 CGCAACTTCCTTGGCAAAATTTA 58.945 39.130 0.00 0.00 0.00 1.40
152 153 4.509600 CGCAACTTCCTTGGCAAAATTTAA 59.490 37.500 0.00 0.00 0.00 1.52
153 154 5.007136 CGCAACTTCCTTGGCAAAATTTAAA 59.993 36.000 0.00 0.00 0.00 1.52
154 155 6.429624 GCAACTTCCTTGGCAAAATTTAAAG 58.570 36.000 0.00 1.97 0.00 1.85
155 156 6.259829 GCAACTTCCTTGGCAAAATTTAAAGA 59.740 34.615 0.00 0.00 0.00 2.52
156 157 7.201688 GCAACTTCCTTGGCAAAATTTAAAGAA 60.202 33.333 0.00 0.00 0.00 2.52
157 158 8.672815 CAACTTCCTTGGCAAAATTTAAAGAAA 58.327 29.630 0.00 0.00 0.00 2.52
158 159 8.437360 ACTTCCTTGGCAAAATTTAAAGAAAG 57.563 30.769 0.00 0.00 0.00 2.62
159 160 8.264347 ACTTCCTTGGCAAAATTTAAAGAAAGA 58.736 29.630 0.00 0.00 0.00 2.52
160 161 9.276590 CTTCCTTGGCAAAATTTAAAGAAAGAT 57.723 29.630 0.00 0.00 0.00 2.40
162 163 9.927668 TCCTTGGCAAAATTTAAAGAAAGATAG 57.072 29.630 0.00 0.00 0.00 2.08
163 164 9.927668 CCTTGGCAAAATTTAAAGAAAGATAGA 57.072 29.630 0.00 0.00 0.00 1.98
204 205 9.815936 ATTCGGTTAAATTACAAAACTAAGTCG 57.184 29.630 0.00 0.00 0.00 4.18
205 206 8.586570 TCGGTTAAATTACAAAACTAAGTCGA 57.413 30.769 0.00 0.00 0.00 4.20
206 207 8.487176 TCGGTTAAATTACAAAACTAAGTCGAC 58.513 33.333 7.70 7.70 0.00 4.20
207 208 8.274939 CGGTTAAATTACAAAACTAAGTCGACA 58.725 33.333 19.50 0.00 0.00 4.35
210 211 9.601971 TTAAATTACAAAACTAAGTCGACATGC 57.398 29.630 19.50 0.00 0.00 4.06
211 212 5.600908 TTACAAAACTAAGTCGACATGCC 57.399 39.130 19.50 0.00 0.00 4.40
212 213 2.478894 ACAAAACTAAGTCGACATGCCG 59.521 45.455 19.50 0.00 0.00 5.69
213 214 2.450609 AAACTAAGTCGACATGCCGT 57.549 45.000 19.50 4.32 0.00 5.68
214 215 2.450609 AACTAAGTCGACATGCCGTT 57.549 45.000 19.50 10.16 0.00 4.44
215 216 2.450609 ACTAAGTCGACATGCCGTTT 57.549 45.000 19.50 3.68 0.00 3.60
216 217 2.762745 ACTAAGTCGACATGCCGTTTT 58.237 42.857 19.50 2.90 0.00 2.43
217 218 3.135994 ACTAAGTCGACATGCCGTTTTT 58.864 40.909 19.50 2.14 0.00 1.94
242 243 9.496873 TTTCACTCCATCGATAAAAAGTTAAGA 57.503 29.630 0.00 0.00 0.00 2.10
243 244 8.703604 TCACTCCATCGATAAAAAGTTAAGAG 57.296 34.615 0.00 0.00 0.00 2.85
244 245 8.311836 TCACTCCATCGATAAAAAGTTAAGAGT 58.688 33.333 0.00 0.00 0.00 3.24
245 246 9.582431 CACTCCATCGATAAAAAGTTAAGAGTA 57.418 33.333 0.00 0.00 0.00 2.59
248 249 9.374838 TCCATCGATAAAAAGTTAAGAGTAACC 57.625 33.333 0.00 0.00 40.55 2.85
249 250 8.610035 CCATCGATAAAAAGTTAAGAGTAACCC 58.390 37.037 0.00 0.00 40.55 4.11
250 251 8.610035 CATCGATAAAAAGTTAAGAGTAACCCC 58.390 37.037 0.00 0.00 40.55 4.95
251 252 7.910584 TCGATAAAAAGTTAAGAGTAACCCCT 58.089 34.615 0.00 0.00 40.55 4.79
252 253 8.377799 TCGATAAAAAGTTAAGAGTAACCCCTT 58.622 33.333 0.00 0.00 40.55 3.95
253 254 9.006839 CGATAAAAAGTTAAGAGTAACCCCTTT 57.993 33.333 0.00 0.00 40.55 3.11
290 291 3.900446 GCATGATGCATAAAGGGCC 57.100 52.632 13.36 0.00 44.26 5.80
291 292 0.319405 GCATGATGCATAAAGGGCCC 59.681 55.000 16.46 16.46 44.26 5.80
292 293 0.971386 CATGATGCATAAAGGGCCCC 59.029 55.000 21.43 1.37 0.00 5.80
293 294 0.178924 ATGATGCATAAAGGGCCCCC 60.179 55.000 21.43 0.00 0.00 5.40
294 295 1.903404 GATGCATAAAGGGCCCCCG 60.903 63.158 21.43 3.30 41.95 5.73
295 296 3.451056 ATGCATAAAGGGCCCCCGG 62.451 63.158 21.43 5.02 41.95 5.73
296 297 4.137615 GCATAAAGGGCCCCCGGT 62.138 66.667 21.43 3.35 41.95 5.28
297 298 2.687266 CATAAAGGGCCCCCGGTT 59.313 61.111 21.43 10.62 41.95 4.44
298 299 1.001120 CATAAAGGGCCCCCGGTTT 59.999 57.895 21.43 15.31 41.95 3.27
299 300 0.616395 CATAAAGGGCCCCCGGTTTT 60.616 55.000 21.43 14.89 41.95 2.43
300 301 0.616395 ATAAAGGGCCCCCGGTTTTG 60.616 55.000 21.43 0.00 41.95 2.44
301 302 2.021318 TAAAGGGCCCCCGGTTTTGT 62.021 55.000 21.43 0.00 41.95 2.83
302 303 2.900269 AAAGGGCCCCCGGTTTTGTT 62.900 55.000 21.43 0.00 41.95 2.83
303 304 2.845317 GGGCCCCCGGTTTTGTTT 60.845 61.111 12.23 0.00 0.00 2.83
304 305 2.445119 GGGCCCCCGGTTTTGTTTT 61.445 57.895 12.23 0.00 0.00 2.43
305 306 1.527854 GGCCCCCGGTTTTGTTTTT 59.472 52.632 0.00 0.00 0.00 1.94
330 331 3.708013 GGGCTCCCGAAATCTTAGG 57.292 57.895 0.00 0.00 0.00 2.69
331 332 1.129058 GGGCTCCCGAAATCTTAGGA 58.871 55.000 0.00 0.00 0.00 2.94
332 333 1.202663 GGGCTCCCGAAATCTTAGGAC 60.203 57.143 0.00 0.00 0.00 3.85
333 334 1.202663 GGCTCCCGAAATCTTAGGACC 60.203 57.143 0.00 0.00 0.00 4.46
334 335 1.538419 GCTCCCGAAATCTTAGGACCG 60.538 57.143 0.00 0.00 0.00 4.79
335 336 1.068741 CTCCCGAAATCTTAGGACCGG 59.931 57.143 0.00 0.00 34.41 5.28
336 337 0.532196 CCCGAAATCTTAGGACCGGC 60.532 60.000 0.00 0.00 33.79 6.13
337 338 0.532196 CCGAAATCTTAGGACCGGCC 60.532 60.000 0.00 3.58 0.00 6.13
338 339 0.532196 CGAAATCTTAGGACCGGCCC 60.532 60.000 0.00 0.00 37.37 5.80
339 340 0.837940 GAAATCTTAGGACCGGCCCT 59.162 55.000 15.88 15.88 40.29 5.19
340 341 0.546598 AAATCTTAGGACCGGCCCTG 59.453 55.000 21.23 3.27 37.10 4.45
341 342 1.984288 AATCTTAGGACCGGCCCTGC 61.984 60.000 21.23 0.00 37.10 4.85
342 343 4.530857 CTTAGGACCGGCCCTGCG 62.531 72.222 21.23 6.15 37.10 5.18
352 353 4.166011 GCCCTGCGCGTTGATGAC 62.166 66.667 8.43 0.00 0.00 3.06
353 354 2.434884 CCCTGCGCGTTGATGACT 60.435 61.111 8.43 0.00 0.00 3.41
354 355 2.456119 CCCTGCGCGTTGATGACTC 61.456 63.158 8.43 0.00 0.00 3.36
355 356 2.691522 CTGCGCGTTGATGACTCG 59.308 61.111 8.43 0.00 39.38 4.18
356 357 2.049526 TGCGCGTTGATGACTCGT 60.050 55.556 8.43 0.00 38.66 4.18
357 358 1.617755 CTGCGCGTTGATGACTCGTT 61.618 55.000 8.43 0.00 38.66 3.85
358 359 1.057361 GCGCGTTGATGACTCGTTC 59.943 57.895 8.43 0.00 38.66 3.95
359 360 1.344942 GCGCGTTGATGACTCGTTCT 61.345 55.000 8.43 0.00 38.66 3.01
360 361 1.891178 CGCGTTGATGACTCGTTCTA 58.109 50.000 0.00 0.00 32.08 2.10
361 362 2.247637 CGCGTTGATGACTCGTTCTAA 58.752 47.619 0.00 0.00 32.08 2.10
362 363 2.026507 CGCGTTGATGACTCGTTCTAAC 59.973 50.000 0.00 0.00 32.08 2.34
363 364 2.984471 GCGTTGATGACTCGTTCTAACA 59.016 45.455 0.00 0.00 0.00 2.41
364 365 3.612860 GCGTTGATGACTCGTTCTAACAT 59.387 43.478 0.00 0.00 0.00 2.71
365 366 4.259451 GCGTTGATGACTCGTTCTAACATC 60.259 45.833 0.00 0.00 38.13 3.06
366 367 4.028429 CGTTGATGACTCGTTCTAACATCG 60.028 45.833 0.00 0.00 39.77 3.84
367 368 4.696899 TGATGACTCGTTCTAACATCGT 57.303 40.909 0.00 0.00 39.77 3.73
368 369 5.055642 TGATGACTCGTTCTAACATCGTT 57.944 39.130 0.00 0.00 39.77 3.85
369 370 5.093457 TGATGACTCGTTCTAACATCGTTC 58.907 41.667 0.00 0.00 39.77 3.95
370 371 3.485633 TGACTCGTTCTAACATCGTTCG 58.514 45.455 0.00 0.00 0.00 3.95
371 372 2.844804 GACTCGTTCTAACATCGTTCGG 59.155 50.000 0.00 0.00 0.00 4.30
372 373 2.227388 ACTCGTTCTAACATCGTTCGGT 59.773 45.455 0.00 0.00 0.00 4.69
373 374 2.587956 TCGTTCTAACATCGTTCGGTG 58.412 47.619 3.85 3.85 0.00 4.94
374 375 1.652124 CGTTCTAACATCGTTCGGTGG 59.348 52.381 10.17 0.00 0.00 4.61
375 376 2.680577 GTTCTAACATCGTTCGGTGGT 58.319 47.619 10.17 5.84 0.00 4.16
376 377 2.642139 TCTAACATCGTTCGGTGGTC 57.358 50.000 10.17 0.00 0.00 4.02
377 378 2.165167 TCTAACATCGTTCGGTGGTCT 58.835 47.619 10.17 0.00 0.00 3.85
378 379 2.559668 TCTAACATCGTTCGGTGGTCTT 59.440 45.455 10.17 0.00 0.00 3.01
379 380 3.758023 TCTAACATCGTTCGGTGGTCTTA 59.242 43.478 10.17 0.00 0.00 2.10
380 381 3.389925 AACATCGTTCGGTGGTCTTAA 57.610 42.857 10.17 0.00 0.00 1.85
381 382 3.389925 ACATCGTTCGGTGGTCTTAAA 57.610 42.857 10.17 0.00 0.00 1.52
382 383 3.731089 ACATCGTTCGGTGGTCTTAAAA 58.269 40.909 10.17 0.00 0.00 1.52
383 384 4.320870 ACATCGTTCGGTGGTCTTAAAAT 58.679 39.130 10.17 0.00 0.00 1.82
384 385 4.390909 ACATCGTTCGGTGGTCTTAAAATC 59.609 41.667 10.17 0.00 0.00 2.17
385 386 4.261578 TCGTTCGGTGGTCTTAAAATCT 57.738 40.909 0.00 0.00 0.00 2.40
386 387 4.634199 TCGTTCGGTGGTCTTAAAATCTT 58.366 39.130 0.00 0.00 0.00 2.40
387 388 4.449743 TCGTTCGGTGGTCTTAAAATCTTG 59.550 41.667 0.00 0.00 0.00 3.02
388 389 4.449743 CGTTCGGTGGTCTTAAAATCTTGA 59.550 41.667 0.00 0.00 0.00 3.02
389 390 5.121768 CGTTCGGTGGTCTTAAAATCTTGAT 59.878 40.000 0.00 0.00 0.00 2.57
390 391 6.311935 CGTTCGGTGGTCTTAAAATCTTGATA 59.688 38.462 0.00 0.00 0.00 2.15
391 392 7.011109 CGTTCGGTGGTCTTAAAATCTTGATAT 59.989 37.037 0.00 0.00 0.00 1.63
392 393 9.321562 GTTCGGTGGTCTTAAAATCTTGATATA 57.678 33.333 0.00 0.00 0.00 0.86
426 427 6.638096 TGTTTGAGATTCTCTGCATTTTGA 57.362 33.333 14.54 0.00 0.00 2.69
484 486 2.807967 CAAGAGTTTTCAGATCACGGCA 59.192 45.455 0.00 0.00 0.00 5.69
493 495 1.662629 CAGATCACGGCACAGATGAAC 59.337 52.381 0.00 0.00 0.00 3.18
503 505 1.983605 CACAGATGAACGACGGTGTAC 59.016 52.381 0.00 0.00 0.00 2.90
514 516 4.054455 GGTGTACGTGCGTGCGTG 62.054 66.667 14.68 0.00 45.33 5.34
515 517 4.696172 GTGTACGTGCGTGCGTGC 62.696 66.667 14.68 13.74 45.33 5.34
533 535 2.359107 CTGCCCATCAGCACACGT 60.359 61.111 0.00 0.00 38.00 4.49
559 561 6.843676 CAAAATGTATTTTGCTCACGAGAG 57.156 37.500 14.85 5.40 46.66 3.20
584 586 1.264288 GGTGTTTCTCCAACTCTTGCG 59.736 52.381 0.00 0.00 36.21 4.85
600 602 2.036006 GCGTGGCGGGTGTAATCAA 61.036 57.895 0.00 0.00 0.00 2.57
658 660 3.315191 TGCTGAAAAGAAGAAAACCCTCG 59.685 43.478 0.00 0.00 0.00 4.63
721 723 6.726230 TGAGACCTCGATTATCTTTTACTCG 58.274 40.000 0.00 0.00 0.00 4.18
836 838 3.441922 GGAACTGAGCAAAAGGAGGAATC 59.558 47.826 0.00 0.00 0.00 2.52
865 867 3.853330 CCGCGCACACTTGATCCG 61.853 66.667 8.75 0.00 0.00 4.18
869 871 2.456119 CGCACACTTGATCCGCCTC 61.456 63.158 0.00 0.00 0.00 4.70
885 887 1.780503 CCTCCCCAATCAAATCACCC 58.219 55.000 0.00 0.00 0.00 4.61
1149 1161 1.001641 GCCTTCAGGTGAGCATGGT 60.002 57.895 0.00 0.00 37.57 3.55
1170 1182 1.517257 CAGCGTCAGTCCGTGATCC 60.517 63.158 0.00 0.00 37.56 3.36
1171 1183 2.579787 GCGTCAGTCCGTGATCCG 60.580 66.667 0.00 0.00 37.56 4.18
1216 1228 3.349006 CCGTGAACTGCAGCGCTT 61.349 61.111 15.27 0.00 0.00 4.68
1218 1230 1.565156 CCGTGAACTGCAGCGCTTTA 61.565 55.000 15.27 0.00 0.00 1.85
1219 1231 0.179240 CGTGAACTGCAGCGCTTTAG 60.179 55.000 15.27 12.02 0.00 1.85
1220 1232 0.868406 GTGAACTGCAGCGCTTTAGT 59.132 50.000 15.27 12.78 0.00 2.24
1221 1233 1.136224 GTGAACTGCAGCGCTTTAGTC 60.136 52.381 20.08 14.65 0.00 2.59
1286 1310 1.539827 GGTTCACCCCAAACTCAATCG 59.460 52.381 0.00 0.00 0.00 3.34
1301 1325 4.081752 ACTCAATCGCTTGACATCTTCTCT 60.082 41.667 0.00 0.00 36.46 3.10
1327 1351 7.120285 TCTGACTGAAGAATTCCATGATGTTTC 59.880 37.037 0.65 0.00 46.93 2.78
1510 1534 1.600916 GGCCACCAACACAGAGACC 60.601 63.158 0.00 0.00 0.00 3.85
1621 1645 1.946475 GCGTGTACCAGGAGGAGTCC 61.946 65.000 0.00 0.00 44.33 3.85
1889 1913 1.708993 TTCTCAGCCACTGGTTGCCT 61.709 55.000 7.04 0.00 33.87 4.75
2464 2488 2.094894 CCGAACTGCTAATGAGTTGCTG 59.905 50.000 0.00 0.00 33.71 4.41
2485 2509 5.636543 GCTGAAGCAAATAAAACAGCATTCT 59.363 36.000 0.00 0.00 46.30 2.40
2557 2581 4.400961 GAGGCTCGCTTGGCTGGT 62.401 66.667 0.00 0.00 43.09 4.00
3617 3641 5.630415 ATGCACTGGGCTATTCTTAAGTA 57.370 39.130 2.50 0.00 45.15 2.24
3876 5121 6.405286 GCATCTATGACTATGTAGCCACTAGG 60.405 46.154 0.00 0.00 38.23 3.02
4065 5635 4.781934 AGTGCCCAGTATCATAAGGTTTC 58.218 43.478 0.00 0.00 0.00 2.78
4143 5713 4.283337 TCAGCATCATCAATTCAATGGGT 58.717 39.130 0.00 0.00 0.00 4.51
4226 5796 3.068024 TCTGGTTCTTGTTGTTTGATGCC 59.932 43.478 0.00 0.00 0.00 4.40
4388 5958 5.841957 GTCAACTAAATTGGCATGATCCT 57.158 39.130 0.00 0.00 42.89 3.24
4402 5972 4.614535 GCATGATCCTGTTTCACACACTTC 60.615 45.833 0.00 0.00 0.00 3.01
4431 6001 4.697828 TCACAGTTTCATGCCGCTAATTTA 59.302 37.500 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 9.542462 TCACGCAGCTAGAATTACTTTATAATT 57.458 29.630 0.00 0.00 0.00 1.40
42 43 9.712305 ATCACGCAGCTAGAATTACTTTATAAT 57.288 29.630 0.00 0.00 0.00 1.28
45 46 9.197694 CTTATCACGCAGCTAGAATTACTTTAT 57.802 33.333 0.00 0.00 0.00 1.40
46 47 7.652105 CCTTATCACGCAGCTAGAATTACTTTA 59.348 37.037 0.00 0.00 0.00 1.85
47 48 6.480320 CCTTATCACGCAGCTAGAATTACTTT 59.520 38.462 0.00 0.00 0.00 2.66
48 49 5.986135 CCTTATCACGCAGCTAGAATTACTT 59.014 40.000 0.00 0.00 0.00 2.24
49 50 5.302059 TCCTTATCACGCAGCTAGAATTACT 59.698 40.000 0.00 0.00 0.00 2.24
50 51 5.529791 TCCTTATCACGCAGCTAGAATTAC 58.470 41.667 0.00 0.00 0.00 1.89
51 52 5.784578 TCCTTATCACGCAGCTAGAATTA 57.215 39.130 0.00 0.00 0.00 1.40
52 53 4.672587 TCCTTATCACGCAGCTAGAATT 57.327 40.909 0.00 0.00 0.00 2.17
53 54 4.322349 GGATCCTTATCACGCAGCTAGAAT 60.322 45.833 3.84 0.00 33.41 2.40
54 55 3.005897 GGATCCTTATCACGCAGCTAGAA 59.994 47.826 3.84 0.00 33.41 2.10
55 56 2.558795 GGATCCTTATCACGCAGCTAGA 59.441 50.000 3.84 0.00 33.41 2.43
56 57 2.669670 CGGATCCTTATCACGCAGCTAG 60.670 54.545 10.75 0.00 33.41 3.42
57 58 1.269723 CGGATCCTTATCACGCAGCTA 59.730 52.381 10.75 0.00 33.41 3.32
58 59 0.032678 CGGATCCTTATCACGCAGCT 59.967 55.000 10.75 0.00 33.41 4.24
59 60 0.249489 ACGGATCCTTATCACGCAGC 60.249 55.000 10.75 0.00 33.41 5.25
60 61 2.128035 GAACGGATCCTTATCACGCAG 58.872 52.381 10.75 0.00 33.41 5.18
61 62 1.478916 TGAACGGATCCTTATCACGCA 59.521 47.619 10.75 0.00 33.41 5.24
62 63 2.218953 TGAACGGATCCTTATCACGC 57.781 50.000 10.75 0.00 33.41 5.34
63 64 7.421530 AATATTTGAACGGATCCTTATCACG 57.578 36.000 10.75 0.00 33.41 4.35
70 71 9.801873 CACAAAAATAATATTTGAACGGATCCT 57.198 29.630 10.75 0.00 39.56 3.24
71 72 9.581099 ACACAAAAATAATATTTGAACGGATCC 57.419 29.630 0.00 0.00 39.56 3.36
73 74 9.921637 ACACACAAAAATAATATTTGAACGGAT 57.078 25.926 0.00 0.00 39.56 4.18
74 75 9.186323 CACACACAAAAATAATATTTGAACGGA 57.814 29.630 0.00 0.00 39.56 4.69
75 76 8.431593 CCACACACAAAAATAATATTTGAACGG 58.568 33.333 0.00 0.00 39.56 4.44
76 77 7.949428 GCCACACACAAAAATAATATTTGAACG 59.051 33.333 0.00 0.00 39.56 3.95
77 78 8.768955 TGCCACACACAAAAATAATATTTGAAC 58.231 29.630 0.00 0.00 39.56 3.18
78 79 8.893219 TGCCACACACAAAAATAATATTTGAA 57.107 26.923 0.00 0.00 39.56 2.69
103 104 9.302345 GCGCAGTGTATATTTCATATATAGTGT 57.698 33.333 0.30 0.00 39.99 3.55
104 105 8.472236 CGCGCAGTGTATATTTCATATATAGTG 58.528 37.037 8.75 9.43 40.41 2.74
105 106 7.167635 GCGCGCAGTGTATATTTCATATATAGT 59.832 37.037 29.10 0.00 41.96 2.12
106 107 7.167468 TGCGCGCAGTGTATATTTCATATATAG 59.833 37.037 33.09 0.00 41.96 1.31
107 108 6.975772 TGCGCGCAGTGTATATTTCATATATA 59.024 34.615 33.09 0.00 41.96 0.86
108 109 5.810074 TGCGCGCAGTGTATATTTCATATAT 59.190 36.000 33.09 0.00 41.96 0.86
109 110 5.164954 TGCGCGCAGTGTATATTTCATATA 58.835 37.500 33.09 0.00 41.96 0.86
110 111 3.993736 TGCGCGCAGTGTATATTTCATAT 59.006 39.130 33.09 0.00 41.96 1.78
111 112 3.385577 TGCGCGCAGTGTATATTTCATA 58.614 40.909 33.09 0.00 41.96 2.15
112 113 2.209273 TGCGCGCAGTGTATATTTCAT 58.791 42.857 33.09 0.00 41.96 2.57
113 114 1.646189 TGCGCGCAGTGTATATTTCA 58.354 45.000 33.09 1.22 41.96 2.69
114 115 2.030457 AGTTGCGCGCAGTGTATATTTC 59.970 45.455 34.25 14.08 41.96 2.17
115 116 2.006888 AGTTGCGCGCAGTGTATATTT 58.993 42.857 34.25 8.05 41.96 1.40
116 117 1.651987 AGTTGCGCGCAGTGTATATT 58.348 45.000 34.25 12.40 41.96 1.28
117 118 1.593006 GAAGTTGCGCGCAGTGTATAT 59.407 47.619 34.25 16.67 41.96 0.86
118 119 0.996462 GAAGTTGCGCGCAGTGTATA 59.004 50.000 34.25 16.09 41.96 1.47
119 120 1.635663 GGAAGTTGCGCGCAGTGTAT 61.636 55.000 34.25 19.23 41.96 2.29
120 121 2.314647 GGAAGTTGCGCGCAGTGTA 61.315 57.895 34.25 17.38 41.96 2.90
121 122 3.649986 GGAAGTTGCGCGCAGTGT 61.650 61.111 34.25 22.19 41.96 3.55
122 123 2.896801 AAGGAAGTTGCGCGCAGTG 61.897 57.895 34.25 0.00 43.41 3.66
123 124 2.591715 AAGGAAGTTGCGCGCAGT 60.592 55.556 34.25 22.64 0.00 4.40
124 125 2.127118 CAAGGAAGTTGCGCGCAG 60.127 61.111 34.25 16.24 0.00 5.18
125 126 3.659092 CCAAGGAAGTTGCGCGCA 61.659 61.111 33.09 33.09 34.45 6.09
127 128 2.676016 TTTGCCAAGGAAGTTGCGCG 62.676 55.000 0.00 0.00 35.96 6.86
128 129 0.529555 TTTTGCCAAGGAAGTTGCGC 60.530 50.000 0.00 0.00 34.45 6.09
129 130 2.153366 ATTTTGCCAAGGAAGTTGCG 57.847 45.000 0.00 0.00 34.45 4.85
130 131 6.259829 TCTTTAAATTTTGCCAAGGAAGTTGC 59.740 34.615 0.00 0.00 34.45 4.17
131 132 7.784633 TCTTTAAATTTTGCCAAGGAAGTTG 57.215 32.000 0.00 0.00 35.71 3.16
132 133 8.800370 TTTCTTTAAATTTTGCCAAGGAAGTT 57.200 26.923 0.00 0.00 0.00 2.66
133 134 8.264347 TCTTTCTTTAAATTTTGCCAAGGAAGT 58.736 29.630 14.07 0.00 33.43 3.01
134 135 8.661352 TCTTTCTTTAAATTTTGCCAAGGAAG 57.339 30.769 0.00 5.17 33.08 3.46
136 137 9.927668 CTATCTTTCTTTAAATTTTGCCAAGGA 57.072 29.630 0.00 0.00 0.00 3.36
137 138 9.927668 TCTATCTTTCTTTAAATTTTGCCAAGG 57.072 29.630 0.00 0.00 0.00 3.61
178 179 9.815936 CGACTTAGTTTTGTAATTTAACCGAAT 57.184 29.630 0.00 0.00 0.00 3.34
179 180 9.039870 TCGACTTAGTTTTGTAATTTAACCGAA 57.960 29.630 0.00 0.00 0.00 4.30
180 181 8.487176 GTCGACTTAGTTTTGTAATTTAACCGA 58.513 33.333 8.70 0.00 0.00 4.69
181 182 8.274939 TGTCGACTTAGTTTTGTAATTTAACCG 58.725 33.333 17.92 0.00 0.00 4.44
184 185 9.601971 GCATGTCGACTTAGTTTTGTAATTTAA 57.398 29.630 17.92 0.00 0.00 1.52
185 186 8.231837 GGCATGTCGACTTAGTTTTGTAATTTA 58.768 33.333 17.92 0.00 0.00 1.40
186 187 7.081976 GGCATGTCGACTTAGTTTTGTAATTT 58.918 34.615 17.92 0.00 0.00 1.82
187 188 6.608610 GGCATGTCGACTTAGTTTTGTAATT 58.391 36.000 17.92 0.00 0.00 1.40
188 189 5.163893 CGGCATGTCGACTTAGTTTTGTAAT 60.164 40.000 16.21 0.00 0.00 1.89
189 190 4.150980 CGGCATGTCGACTTAGTTTTGTAA 59.849 41.667 16.21 0.00 0.00 2.41
190 191 3.676172 CGGCATGTCGACTTAGTTTTGTA 59.324 43.478 16.21 0.00 0.00 2.41
191 192 2.478894 CGGCATGTCGACTTAGTTTTGT 59.521 45.455 16.21 0.00 0.00 2.83
192 193 2.478894 ACGGCATGTCGACTTAGTTTTG 59.521 45.455 28.94 4.41 0.00 2.44
193 194 2.762745 ACGGCATGTCGACTTAGTTTT 58.237 42.857 28.94 0.00 0.00 2.43
194 195 2.450609 ACGGCATGTCGACTTAGTTT 57.549 45.000 28.94 0.00 0.00 2.66
195 196 2.450609 AACGGCATGTCGACTTAGTT 57.549 45.000 28.94 5.87 0.00 2.24
196 197 2.450609 AAACGGCATGTCGACTTAGT 57.549 45.000 28.94 0.00 0.00 2.24
197 198 3.806316 AAAAACGGCATGTCGACTTAG 57.194 42.857 28.94 7.57 0.00 2.18
216 217 9.496873 TCTTAACTTTTTATCGATGGAGTGAAA 57.503 29.630 8.54 0.00 0.00 2.69
217 218 9.151471 CTCTTAACTTTTTATCGATGGAGTGAA 57.849 33.333 8.54 5.27 0.00 3.18
218 219 8.311836 ACTCTTAACTTTTTATCGATGGAGTGA 58.688 33.333 8.54 0.00 0.00 3.41
219 220 8.480643 ACTCTTAACTTTTTATCGATGGAGTG 57.519 34.615 8.54 0.00 0.00 3.51
222 223 9.374838 GGTTACTCTTAACTTTTTATCGATGGA 57.625 33.333 8.54 0.00 38.17 3.41
223 224 8.610035 GGGTTACTCTTAACTTTTTATCGATGG 58.390 37.037 8.54 0.00 38.17 3.51
224 225 8.610035 GGGGTTACTCTTAACTTTTTATCGATG 58.390 37.037 8.54 0.00 38.17 3.84
225 226 8.546322 AGGGGTTACTCTTAACTTTTTATCGAT 58.454 33.333 2.16 2.16 38.17 3.59
226 227 7.910584 AGGGGTTACTCTTAACTTTTTATCGA 58.089 34.615 0.00 0.00 38.17 3.59
227 228 8.557592 AAGGGGTTACTCTTAACTTTTTATCG 57.442 34.615 0.00 0.00 38.17 2.92
272 273 0.319405 GGGCCCTTTATGCATCATGC 59.681 55.000 17.04 1.35 45.29 4.06
273 274 0.971386 GGGGCCCTTTATGCATCATG 59.029 55.000 24.38 0.00 0.00 3.07
274 275 0.178924 GGGGGCCCTTTATGCATCAT 60.179 55.000 24.38 0.00 0.00 2.45
275 276 1.232792 GGGGGCCCTTTATGCATCA 59.767 57.895 24.38 0.00 0.00 3.07
276 277 1.903404 CGGGGGCCCTTTATGCATC 60.903 63.158 24.38 0.03 0.00 3.91
277 278 2.198426 CGGGGGCCCTTTATGCAT 59.802 61.111 24.38 3.79 0.00 3.96
278 279 4.136199 CCGGGGGCCCTTTATGCA 62.136 66.667 24.38 0.00 0.00 3.96
279 280 3.672338 AACCGGGGGCCCTTTATGC 62.672 63.158 24.38 2.70 0.00 3.14
280 281 0.616395 AAAACCGGGGGCCCTTTATG 60.616 55.000 24.38 8.75 0.00 1.90
281 282 0.616395 CAAAACCGGGGGCCCTTTAT 60.616 55.000 24.38 3.88 0.00 1.40
282 283 1.228925 CAAAACCGGGGGCCCTTTA 60.229 57.895 24.38 0.00 0.00 1.85
283 284 2.525629 CAAAACCGGGGGCCCTTT 60.526 61.111 24.38 12.78 0.00 3.11
284 285 2.900269 AAACAAAACCGGGGGCCCTT 62.900 55.000 24.38 6.04 0.00 3.95
285 286 2.900269 AAAACAAAACCGGGGGCCCT 62.900 55.000 24.38 0.00 0.00 5.19
286 287 1.985460 AAAAACAAAACCGGGGGCCC 61.985 55.000 15.76 15.76 0.00 5.80
287 288 1.527854 AAAAACAAAACCGGGGGCC 59.472 52.632 6.32 0.00 0.00 5.80
312 313 1.129058 TCCTAAGATTTCGGGAGCCC 58.871 55.000 0.00 0.00 0.00 5.19
313 314 1.202663 GGTCCTAAGATTTCGGGAGCC 60.203 57.143 0.00 0.00 39.56 4.70
314 315 1.538419 CGGTCCTAAGATTTCGGGAGC 60.538 57.143 0.00 0.00 41.32 4.70
315 316 1.068741 CCGGTCCTAAGATTTCGGGAG 59.931 57.143 0.00 0.00 32.71 4.30
316 317 1.117150 CCGGTCCTAAGATTTCGGGA 58.883 55.000 0.00 0.00 32.71 5.14
317 318 0.532196 GCCGGTCCTAAGATTTCGGG 60.532 60.000 1.90 0.00 35.13 5.14
318 319 0.532196 GGCCGGTCCTAAGATTTCGG 60.532 60.000 1.90 0.00 36.58 4.30
319 320 0.532196 GGGCCGGTCCTAAGATTTCG 60.532 60.000 20.78 0.00 34.39 3.46
320 321 0.837940 AGGGCCGGTCCTAAGATTTC 59.162 55.000 30.70 0.00 34.92 2.17
321 322 0.546598 CAGGGCCGGTCCTAAGATTT 59.453 55.000 31.20 0.00 34.92 2.17
322 323 1.984288 GCAGGGCCGGTCCTAAGATT 61.984 60.000 31.20 0.25 34.92 2.40
323 324 2.444256 GCAGGGCCGGTCCTAAGAT 61.444 63.158 31.20 1.25 34.92 2.40
324 325 3.081409 GCAGGGCCGGTCCTAAGA 61.081 66.667 31.20 0.00 34.92 2.10
325 326 4.530857 CGCAGGGCCGGTCCTAAG 62.531 72.222 31.20 21.12 34.92 2.18
337 338 2.792290 CGAGTCATCAACGCGCAGG 61.792 63.158 5.73 0.00 44.07 4.85
338 339 2.691522 CGAGTCATCAACGCGCAG 59.308 61.111 5.73 2.42 44.07 5.18
342 343 2.984471 TGTTAGAACGAGTCATCAACGC 59.016 45.455 0.00 0.00 0.00 4.84
343 344 4.028429 CGATGTTAGAACGAGTCATCAACG 60.028 45.833 0.00 0.00 35.91 4.10
344 345 4.857588 ACGATGTTAGAACGAGTCATCAAC 59.142 41.667 0.00 0.00 35.91 3.18
345 346 5.055642 ACGATGTTAGAACGAGTCATCAA 57.944 39.130 0.00 0.00 35.91 2.57
346 347 4.696899 ACGATGTTAGAACGAGTCATCA 57.303 40.909 0.00 0.00 35.91 3.07
347 348 4.202558 CGAACGATGTTAGAACGAGTCATC 59.797 45.833 0.00 0.00 33.75 2.92
348 349 4.096311 CGAACGATGTTAGAACGAGTCAT 58.904 43.478 0.00 0.00 0.00 3.06
349 350 3.485633 CGAACGATGTTAGAACGAGTCA 58.514 45.455 0.00 0.00 0.00 3.41
350 351 2.844804 CCGAACGATGTTAGAACGAGTC 59.155 50.000 0.00 0.00 0.00 3.36
351 352 2.227388 ACCGAACGATGTTAGAACGAGT 59.773 45.455 0.00 0.00 0.00 4.18
352 353 2.592897 CACCGAACGATGTTAGAACGAG 59.407 50.000 0.00 0.00 0.00 4.18
353 354 2.587956 CACCGAACGATGTTAGAACGA 58.412 47.619 0.00 0.00 0.00 3.85
354 355 1.652124 CCACCGAACGATGTTAGAACG 59.348 52.381 0.00 0.00 0.00 3.95
355 356 2.665052 GACCACCGAACGATGTTAGAAC 59.335 50.000 0.00 0.00 0.00 3.01
356 357 2.559668 AGACCACCGAACGATGTTAGAA 59.440 45.455 0.00 0.00 0.00 2.10
357 358 2.165167 AGACCACCGAACGATGTTAGA 58.835 47.619 0.00 0.00 0.00 2.10
358 359 2.649331 AGACCACCGAACGATGTTAG 57.351 50.000 0.00 0.00 0.00 2.34
359 360 4.517952 TTAAGACCACCGAACGATGTTA 57.482 40.909 0.00 0.00 0.00 2.41
360 361 3.389925 TTAAGACCACCGAACGATGTT 57.610 42.857 0.00 0.00 0.00 2.71
361 362 3.389925 TTTAAGACCACCGAACGATGT 57.610 42.857 0.00 0.00 0.00 3.06
362 363 4.630069 AGATTTTAAGACCACCGAACGATG 59.370 41.667 0.00 0.00 0.00 3.84
363 364 4.828829 AGATTTTAAGACCACCGAACGAT 58.171 39.130 0.00 0.00 0.00 3.73
364 365 4.261578 AGATTTTAAGACCACCGAACGA 57.738 40.909 0.00 0.00 0.00 3.85
365 366 4.449743 TCAAGATTTTAAGACCACCGAACG 59.550 41.667 0.00 0.00 0.00 3.95
366 367 5.934935 TCAAGATTTTAAGACCACCGAAC 57.065 39.130 0.00 0.00 0.00 3.95
463 464 2.807967 TGCCGTGATCTGAAAACTCTTG 59.192 45.455 0.00 0.00 0.00 3.02
467 469 2.146342 CTGTGCCGTGATCTGAAAACT 58.854 47.619 0.00 0.00 0.00 2.66
472 474 1.185315 TCATCTGTGCCGTGATCTGA 58.815 50.000 0.00 0.00 0.00 3.27
475 477 0.647410 CGTTCATCTGTGCCGTGATC 59.353 55.000 0.00 0.00 0.00 2.92
484 486 1.400629 CGTACACCGTCGTTCATCTGT 60.401 52.381 0.00 0.00 0.00 3.41
512 514 3.446570 GTGCTGATGGGCAGGCAC 61.447 66.667 0.00 0.00 45.03 5.01
513 515 3.969119 TGTGCTGATGGGCAGGCA 61.969 61.111 0.00 0.00 45.03 4.75
514 516 3.446570 GTGTGCTGATGGGCAGGC 61.447 66.667 0.00 0.00 45.03 4.85
515 517 3.129502 CGTGTGCTGATGGGCAGG 61.130 66.667 0.00 0.00 45.03 4.85
555 557 0.906066 GGAGAAACACCCTCCCTCTC 59.094 60.000 0.00 0.00 43.37 3.20
584 586 0.170339 GCTTTGATTACACCCGCCAC 59.830 55.000 0.00 0.00 0.00 5.01
658 660 2.441532 ATGGTGGCTCCTGCATGC 60.442 61.111 11.82 11.82 41.91 4.06
721 723 4.127907 GGTGGCTGGCTAATAAGTAAGTC 58.872 47.826 2.00 0.00 0.00 3.01
763 765 2.888414 CCGGAGCTGGTAAAAGGAAAAA 59.112 45.455 0.00 0.00 0.00 1.94
796 798 4.200283 CCAGCGGCGAGGTCTCTC 62.200 72.222 12.98 0.00 36.69 3.20
865 867 1.114627 GGTGATTTGATTGGGGAGGC 58.885 55.000 0.00 0.00 0.00 4.70
869 871 1.288932 AGAGGGGTGATTTGATTGGGG 59.711 52.381 0.00 0.00 0.00 4.96
897 899 1.042559 GGGGCAGACAGAGAGAGAGG 61.043 65.000 0.00 0.00 0.00 3.69
926 928 4.179599 GGGGGAGGAGAGAGGGGG 62.180 77.778 0.00 0.00 0.00 5.40
1110 1122 3.849951 GATCCTTGGCGAGGCGGA 61.850 66.667 16.55 0.00 45.87 5.54
1113 1125 1.958205 CATCGATCCTTGGCGAGGC 60.958 63.158 16.55 1.99 45.87 4.70
1149 1161 4.662961 CACGGACTGACGCTGGCA 62.663 66.667 0.00 0.00 37.37 4.92
1170 1182 4.758251 TGGTGGCGATGACAGGCG 62.758 66.667 0.00 0.00 36.92 5.52
1171 1183 2.821366 CTGGTGGCGATGACAGGC 60.821 66.667 0.00 0.00 0.00 4.85
1194 1206 1.571460 GCTGCAGTTCACGGACTTG 59.429 57.895 16.64 0.00 0.00 3.16
1216 1228 3.709653 ACAGGAAGGAACACACTGACTAA 59.290 43.478 0.00 0.00 33.57 2.24
1218 1230 2.119495 ACAGGAAGGAACACACTGACT 58.881 47.619 0.00 0.00 33.57 3.41
1219 1231 2.622064 ACAGGAAGGAACACACTGAC 57.378 50.000 0.00 0.00 33.57 3.51
1220 1232 4.974645 ATAACAGGAAGGAACACACTGA 57.025 40.909 0.00 0.00 33.57 3.41
1221 1233 6.263168 AGAAAATAACAGGAAGGAACACACTG 59.737 38.462 0.00 0.00 35.40 3.66
1266 1278 1.539827 CGATTGAGTTTGGGGTGAACC 59.460 52.381 0.00 0.00 39.11 3.62
1286 1310 4.082300 TCAGTCAGAGAGAAGATGTCAAGC 60.082 45.833 0.00 0.00 0.00 4.01
1301 1325 6.058553 ACATCATGGAATTCTTCAGTCAGA 57.941 37.500 5.23 0.00 0.00 3.27
1327 1351 2.031012 TGCTCCACAGAACCTGCG 59.969 61.111 0.00 0.00 34.37 5.18
1464 1488 4.738998 TGGCCACGGGAGCATTGG 62.739 66.667 0.00 0.00 0.00 3.16
1510 1534 1.374252 CCAGTCTTCGGGGTTGTCG 60.374 63.158 0.00 0.00 0.00 4.35
1543 1567 2.445316 CTGATGTAGTTGAGCGACTCG 58.555 52.381 0.00 0.00 32.35 4.18
1636 1660 0.734889 CATAGAAGGGCTTTGCGGTG 59.265 55.000 0.00 0.00 0.00 4.94
1702 1726 1.302832 GCTGTCCAGGGACCAAGTG 60.303 63.158 15.53 2.86 43.97 3.16
1858 1882 3.359194 CTGAGAAGATCGGCCACAG 57.641 57.895 2.24 0.00 0.00 3.66
1889 1913 3.503363 GCATCAGAAACACCACTTGATGA 59.497 43.478 14.84 0.00 35.14 2.92
2464 2488 7.814587 ACCTTAGAATGCTGTTTTATTTGCTTC 59.185 33.333 0.00 0.00 0.00 3.86
2485 2509 2.424234 GCTGCCATCCCCATTTACCTTA 60.424 50.000 0.00 0.00 0.00 2.69
2557 2581 0.976073 GGTACTGCTGGCTCCCTGTA 60.976 60.000 0.00 0.00 0.00 2.74
3876 5121 7.513371 TTCCTCTAGCTTATCTTAGTACTGC 57.487 40.000 5.39 0.00 0.00 4.40
3983 5228 8.612486 TTGGTTACTACTAATTAGGATGGTCA 57.388 34.615 16.73 4.42 31.13 4.02
4035 5280 7.667219 CCTTATGATACTGGGCACTTGATTAAT 59.333 37.037 0.00 0.00 0.00 1.40
4065 5635 7.872993 TCATACACTCAAGGAAGTCAAAAGTAG 59.127 37.037 0.00 0.00 0.00 2.57
4110 5680 1.522668 TGATGCTGAACCCAAACTCG 58.477 50.000 0.00 0.00 0.00 4.18
4226 5796 6.990341 TGTCTGATCAGATTACAACAATGG 57.010 37.500 27.51 0.00 39.97 3.16
4402 5972 1.133025 GGCATGAAACTGTGAATCCCG 59.867 52.381 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.