Multiple sequence alignment - TraesCS3B01G202400

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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 TraesCS3B01G202400 chr3B 100.000 6029 0 0 1 6029 236362311 236356283 0.000000e+00 11134.0
1 TraesCS3B01G202400 chr3B 93.913 115 7 0 4769 4883 2509403 2509517 2.230000e-39 174.0
2 TraesCS3B01G202400 chr3B 93.617 47 2 1 808 853 69816239 69816285 1.080000e-07 69.4
3 TraesCS3B01G202400 chr3A 94.646 4128 107 32 362 4398 185182501 185178397 0.000000e+00 6294.0
4 TraesCS3B01G202400 chr3A 96.391 1635 51 5 4400 6029 185178294 185176663 0.000000e+00 2686.0
5 TraesCS3B01G202400 chr3A 95.652 230 8 2 11 240 185182725 185182498 9.550000e-98 368.0
6 TraesCS3B01G202400 chr3A 92.233 103 8 0 4769 4871 514471 514573 4.870000e-31 147.0
7 TraesCS3B01G202400 chr3A 89.011 91 9 1 362 452 714473216 714473127 1.780000e-20 111.0
8 TraesCS3B01G202400 chr3D 95.643 2272 49 13 2176 4398 159622908 159620638 0.000000e+00 3602.0
9 TraesCS3B01G202400 chr3D 96.999 1633 43 4 4400 6029 159620535 159618906 0.000000e+00 2739.0
10 TraesCS3B01G202400 chr3D 96.265 1553 47 3 635 2180 159624621 159623073 0.000000e+00 2536.0
11 TraesCS3B01G202400 chr3D 95.319 235 6 3 362 593 159624943 159624711 9.550000e-98 368.0
12 TraesCS3B01G202400 chr3D 93.478 230 11 3 11 240 159625165 159624940 7.480000e-89 339.0
13 TraesCS3B01G202400 chrUn 84.906 265 20 6 4769 5027 43316606 43316856 3.610000e-62 250.0
14 TraesCS3B01G202400 chrUn 90.323 62 4 2 5754 5814 84439889 84439829 5.010000e-11 80.5
15 TraesCS3B01G202400 chr2A 99.254 134 1 0 239 372 630094622 630094755 6.040000e-60 243.0
16 TraesCS3B01G202400 chr2A 97.143 35 1 0 5762 5796 638310525 638310491 6.530000e-05 60.2
17 TraesCS3B01G202400 chr6D 98.496 133 2 0 236 368 435990508 435990640 1.010000e-57 235.0
18 TraesCS3B01G202400 chr4D 97.080 137 4 0 236 372 106682381 106682245 1.310000e-56 231.0
19 TraesCS3B01G202400 chr4B 96.454 141 4 1 232 372 180671295 180671156 1.310000e-56 231.0
20 TraesCS3B01G202400 chr2D 97.080 137 4 0 236 372 62390419 62390555 1.310000e-56 231.0
21 TraesCS3B01G202400 chr2D 97.744 133 3 0 236 368 468789170 468789302 4.700000e-56 230.0
22 TraesCS3B01G202400 chr2D 97.436 39 1 0 5762 5800 36689398 36689360 3.900000e-07 67.6
23 TraesCS3B01G202400 chr2B 95.205 146 5 2 226 369 536806021 536806166 4.700000e-56 230.0
24 TraesCS3B01G202400 chr1B 96.403 139 5 0 234 372 623732116 623731978 4.700000e-56 230.0
25 TraesCS3B01G202400 chr5D 96.403 139 4 1 230 368 211375757 211375620 1.690000e-55 228.0
26 TraesCS3B01G202400 chr7B 92.308 52 2 2 5750 5800 718469089 718469039 8.380000e-09 73.1
27 TraesCS3B01G202400 chr7B 93.478 46 3 0 5754 5799 159137630 159137585 1.080000e-07 69.4
28 TraesCS3B01G202400 chr7B 97.368 38 1 0 5768 5805 540052558 540052521 1.400000e-06 65.8
29 TraesCS3B01G202400 chr7D 91.489 47 4 0 5754 5800 195308323 195308277 1.400000e-06 65.8


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 TraesCS3B01G202400 chr3B 236356283 236362311 6028 True 11134.0 11134 100.0000 1 6029 1 chr3B.!!$R1 6028
1 TraesCS3B01G202400 chr3A 185176663 185182725 6062 True 3116.0 6294 95.5630 11 6029 3 chr3A.!!$R2 6018
2 TraesCS3B01G202400 chr3D 159618906 159625165 6259 True 1916.8 3602 95.5408 11 6029 5 chr3D.!!$R1 6018

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
255 257 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.0 0.0 0.0 0.00 3.28 F
768 826 0.251165 CGAAGTCAACCCCACCCAAT 60.251 55.0 0.0 0.0 0.00 3.16 F
2387 2638 0.362179 CGACACTGACGTTGTATGCG 59.638 55.0 0.0 0.0 0.00 4.73 F
3794 4076 0.613777 ACACTGTACCCTAGCCTTGC 59.386 55.0 0.0 0.0 0.00 4.01 F
4902 5304 0.911525 ATGCTGCTACTGGTCCACCT 60.912 55.0 0.0 0.0 36.82 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 1961 0.104855 TCTTCCTCGATTCCCATGCG 59.895 55.000 0.0 0.0 0.00 4.73 R
2445 2697 1.247567 AACTTCCATTTGGCGGACAG 58.752 50.000 0.0 0.0 34.44 3.51 R
4003 4285 1.243902 TTCGGAGACATTTGGTTGGC 58.756 50.000 0.0 0.0 34.32 4.52 R
4962 5364 1.463056 TGAAACTCGCCATAAGCAACG 59.537 47.619 0.0 0.0 44.04 4.10 R
6003 6410 4.157840 ACTCAAAAGGAAATATTGCGGACC 59.842 41.667 0.0 0.0 0.00 4.46 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
22 23 3.376540 CCTTCTGCTCTAGTTCGCATAC 58.623 50.000 4.98 0.00 35.32 2.39
123 124 7.559590 AGTGTGGATTATATCTGCTGTTTTC 57.440 36.000 0.00 0.00 0.00 2.29
144 145 0.947244 CAAACAGAGGCACGAGCTTT 59.053 50.000 4.48 0.00 41.70 3.51
153 154 1.402511 GCACGAGCTTTGCTTCTTTG 58.597 50.000 12.76 0.00 39.88 2.77
161 162 2.608016 GCTTTGCTTCTTTGTAGGTGGC 60.608 50.000 0.00 0.00 0.00 5.01
240 242 6.896021 TCTTATGGAGGCATGTAGTAGTAC 57.104 41.667 0.37 0.37 0.00 2.73
241 243 6.611785 TCTTATGGAGGCATGTAGTAGTACT 58.388 40.000 8.14 8.14 0.00 2.73
242 244 6.715718 TCTTATGGAGGCATGTAGTAGTACTC 59.284 42.308 5.96 0.00 0.00 2.59
243 245 3.563223 TGGAGGCATGTAGTAGTACTCC 58.437 50.000 5.96 1.30 42.50 3.85
244 246 2.892215 GGAGGCATGTAGTAGTACTCCC 59.108 54.545 5.96 0.00 37.62 4.30
245 247 3.436761 GGAGGCATGTAGTAGTACTCCCT 60.437 52.174 5.96 10.59 37.62 4.20
246 248 3.822167 GAGGCATGTAGTAGTACTCCCTC 59.178 52.174 5.96 17.92 34.37 4.30
247 249 2.892215 GGCATGTAGTAGTACTCCCTCC 59.108 54.545 5.96 0.00 0.00 4.30
248 250 2.553172 GCATGTAGTAGTACTCCCTCCG 59.447 54.545 5.96 0.00 0.00 4.63
249 251 3.818180 CATGTAGTAGTACTCCCTCCGT 58.182 50.000 5.96 0.00 0.00 4.69
250 252 3.550437 TGTAGTAGTACTCCCTCCGTC 57.450 52.381 5.96 0.00 0.00 4.79
251 253 2.171448 TGTAGTAGTACTCCCTCCGTCC 59.829 54.545 5.96 0.00 0.00 4.79
252 254 0.550432 AGTAGTACTCCCTCCGTCCC 59.450 60.000 0.00 0.00 0.00 4.46
253 255 0.257039 GTAGTACTCCCTCCGTCCCA 59.743 60.000 0.00 0.00 0.00 4.37
254 256 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
255 257 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
256 258 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
257 259 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
258 260 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
259 261 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
260 262 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
261 263 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
262 264 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
263 265 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
264 266 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
265 267 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
266 268 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
267 269 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
268 270 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
269 271 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
270 272 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
271 273 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
272 274 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
273 275 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
274 276 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
275 277 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
276 278 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
284 286 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
285 287 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
287 289 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
288 290 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
295 297 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
296 298 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
297 299 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
298 300 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
299 301 7.919091 GTCTAAATACGGATGTATCAAGTCACA 59.081 37.037 0.00 0.00 40.42 3.58
300 302 8.638873 TCTAAATACGGATGTATCAAGTCACAT 58.361 33.333 0.00 0.00 40.42 3.21
301 303 9.261180 CTAAATACGGATGTATCAAGTCACATT 57.739 33.333 0.00 0.00 40.42 2.71
302 304 8.506168 AAATACGGATGTATCAAGTCACATTT 57.494 30.769 0.00 0.00 40.42 2.32
303 305 8.506168 AATACGGATGTATCAAGTCACATTTT 57.494 30.769 0.00 0.00 40.42 1.82
304 306 9.607988 AATACGGATGTATCAAGTCACATTTTA 57.392 29.630 0.00 0.00 40.42 1.52
305 307 7.539712 ACGGATGTATCAAGTCACATTTTAG 57.460 36.000 0.00 0.00 35.55 1.85
306 308 7.103641 ACGGATGTATCAAGTCACATTTTAGT 58.896 34.615 0.00 0.00 35.55 2.24
307 309 8.255206 ACGGATGTATCAAGTCACATTTTAGTA 58.745 33.333 0.00 0.00 35.55 1.82
308 310 9.261180 CGGATGTATCAAGTCACATTTTAGTAT 57.739 33.333 0.00 0.00 35.55 2.12
320 322 8.975439 GTCACATTTTAGTATTAGGTACATCCG 58.025 37.037 0.00 0.00 41.99 4.18
321 323 8.698210 TCACATTTTAGTATTAGGTACATCCGT 58.302 33.333 0.00 0.00 41.99 4.69
322 324 9.970395 CACATTTTAGTATTAGGTACATCCGTA 57.030 33.333 0.00 0.00 41.99 4.02
330 332 8.600668 AGTATTAGGTACATCCGTATCTAGACA 58.399 37.037 0.00 0.00 41.33 3.41
331 333 9.224267 GTATTAGGTACATCCGTATCTAGACAA 57.776 37.037 0.00 0.00 41.33 3.18
332 334 8.701908 ATTAGGTACATCCGTATCTAGACAAA 57.298 34.615 0.00 0.00 41.33 2.83
333 335 8.701908 TTAGGTACATCCGTATCTAGACAAAT 57.298 34.615 0.00 0.00 41.33 2.32
334 336 7.216973 AGGTACATCCGTATCTAGACAAATC 57.783 40.000 0.00 0.00 37.29 2.17
335 337 7.005296 AGGTACATCCGTATCTAGACAAATCT 58.995 38.462 0.00 0.00 37.29 2.40
336 338 8.162085 AGGTACATCCGTATCTAGACAAATCTA 58.838 37.037 0.00 0.00 37.29 1.98
337 339 8.790718 GGTACATCCGTATCTAGACAAATCTAA 58.209 37.037 0.00 0.00 36.98 2.10
338 340 9.828852 GTACATCCGTATCTAGACAAATCTAAG 57.171 37.037 0.00 0.00 36.98 2.18
339 341 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
340 342 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
341 343 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
342 344 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
343 345 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
344 346 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
352 354 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
353 355 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
354 356 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
355 357 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
356 358 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
357 359 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
358 360 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
359 361 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
360 362 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
361 363 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
362 364 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
363 365 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
364 366 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
411 413 4.385405 ACAGAGGAGTGCAGCGCC 62.385 66.667 2.29 0.00 37.31 6.53
440 442 6.488769 TCTTTTGAGGTTGTACTTGAGGTA 57.511 37.500 0.00 0.00 0.00 3.08
513 515 2.965831 AGCTCCTACTTGTCACAACTGA 59.034 45.455 0.00 0.00 0.00 3.41
618 653 6.019237 GCTAGTTTATAGACGGTAGCAAAACC 60.019 42.308 8.82 0.00 34.34 3.27
665 718 7.390440 GCTAGAAATGCATGTGTATGGGTAATA 59.610 37.037 0.00 0.00 34.79 0.98
740 798 5.667539 TCCAATCAAACAACAAAAGGTGA 57.332 34.783 0.00 0.00 0.00 4.02
750 808 5.768317 ACAACAAAAGGTGATTATCCAACG 58.232 37.500 0.00 0.00 0.00 4.10
768 826 0.251165 CGAAGTCAACCCCACCCAAT 60.251 55.000 0.00 0.00 0.00 3.16
787 863 4.202202 CCAATCAAACAACAAAGGTGGCTA 60.202 41.667 0.00 0.00 0.00 3.93
788 864 5.511202 CCAATCAAACAACAAAGGTGGCTAT 60.511 40.000 0.00 0.00 0.00 2.97
789 865 4.846779 TCAAACAACAAAGGTGGCTATC 57.153 40.909 0.00 0.00 0.00 2.08
790 866 3.572255 TCAAACAACAAAGGTGGCTATCC 59.428 43.478 0.00 0.00 0.00 2.59
791 867 3.525800 AACAACAAAGGTGGCTATCCT 57.474 42.857 0.00 0.00 36.81 3.24
792 868 3.525800 ACAACAAAGGTGGCTATCCTT 57.474 42.857 4.02 4.02 45.84 3.36
793 869 4.650972 ACAACAAAGGTGGCTATCCTTA 57.349 40.909 8.92 0.00 43.50 2.69
794 870 4.993028 ACAACAAAGGTGGCTATCCTTAA 58.007 39.130 8.92 0.00 43.50 1.85
795 871 4.765339 ACAACAAAGGTGGCTATCCTTAAC 59.235 41.667 8.92 0.00 43.50 2.01
796 872 3.964411 ACAAAGGTGGCTATCCTTAACC 58.036 45.455 8.92 0.00 43.50 2.85
797 873 3.332485 ACAAAGGTGGCTATCCTTAACCA 59.668 43.478 8.92 0.00 43.50 3.67
798 874 3.933861 AAGGTGGCTATCCTTAACCAG 57.066 47.619 7.25 0.00 42.63 4.00
799 875 2.127708 AGGTGGCTATCCTTAACCAGG 58.872 52.381 0.00 0.00 45.64 4.45
800 876 1.844497 GGTGGCTATCCTTAACCAGGT 59.156 52.381 0.00 0.00 44.37 4.00
801 877 2.421529 GGTGGCTATCCTTAACCAGGTG 60.422 54.545 0.00 0.00 44.37 4.00
802 878 1.843851 TGGCTATCCTTAACCAGGTGG 59.156 52.381 0.00 0.00 44.37 4.61
803 879 1.477014 GGCTATCCTTAACCAGGTGGC 60.477 57.143 0.00 0.00 44.37 5.01
804 880 1.211949 GCTATCCTTAACCAGGTGGCA 59.788 52.381 0.00 0.00 44.37 4.92
810 886 0.849094 TTAACCAGGTGGCAGGGGAT 60.849 55.000 0.00 0.00 39.32 3.85
946 1022 9.916397 CAGATTCGCTAAATAACGTATTTTCTT 57.084 29.630 0.00 0.00 39.06 2.52
1038 1114 8.001292 TCAAGTCCTGAGATAGATGATGAACTA 58.999 37.037 0.00 0.00 0.00 2.24
1165 1241 2.371179 TCAGATGATGAAGATGAGCCCC 59.629 50.000 0.00 0.00 34.02 5.80
1215 1291 3.391955 TCACTAGTAGAGAGGCTAGGGTC 59.608 52.174 3.59 0.00 39.18 4.46
1370 1446 9.674824 GGCATTTATTCTGATTACTTGATTGAG 57.325 33.333 0.00 0.00 0.00 3.02
1538 1614 5.625150 AGTCTTGCTTTATCCTTTGTGACT 58.375 37.500 0.00 0.00 0.00 3.41
1612 1688 9.638239 AACAGCATTAAAACGTGATCATTATTT 57.362 25.926 0.00 3.41 0.00 1.40
1640 1716 8.547967 TTTAGTGAAATGTAGTTCCATGACTC 57.452 34.615 0.00 0.00 0.00 3.36
1671 1750 6.129179 TGGAATTGGTATCTCCTCCATTTTC 58.871 40.000 0.00 0.00 34.45 2.29
1824 1904 1.197492 TCGTGCATCAACAGCATTCAC 59.803 47.619 0.00 0.00 44.79 3.18
1916 1996 5.606505 GAGGAAGAATAGAAGGGCTACTTG 58.393 45.833 0.00 0.00 40.21 3.16
1922 2002 6.198639 AGAATAGAAGGGCTACTTGAAGAGA 58.801 40.000 0.00 0.00 40.21 3.10
2013 2093 3.520290 TGTACGGAAGCTAACATCCTG 57.480 47.619 0.83 0.00 31.18 3.86
2029 2109 7.574021 AACATCCTGATATAAGAATGCCCTA 57.426 36.000 0.00 0.00 0.00 3.53
2068 2148 7.671398 AGGTTTATGGATAGCAATGGGATAAAG 59.329 37.037 0.00 0.00 0.00 1.85
2116 2196 3.599343 TCAGTTGATTCCCTTCATCACG 58.401 45.455 0.00 0.00 30.09 4.35
2117 2197 3.007940 TCAGTTGATTCCCTTCATCACGT 59.992 43.478 0.00 0.00 30.09 4.49
2361 2612 5.532032 TGCAAATGATCAACCATATCGACAT 59.468 36.000 0.00 0.00 0.00 3.06
2387 2638 0.362179 CGACACTGACGTTGTATGCG 59.638 55.000 0.00 0.00 0.00 4.73
2445 2697 9.813080 CTCTTGCAAAACTATTACTGTTTACTC 57.187 33.333 0.00 0.00 36.72 2.59
2526 2779 7.393515 ACAGAAGTGTTAAAGACTTGTCCTTTT 59.606 33.333 5.98 0.00 33.71 2.27
3079 3333 6.655078 ATGAGCCAGACATTTAAACAACTT 57.345 33.333 0.00 0.00 0.00 2.66
3091 3345 8.655970 ACATTTAAACAACTTGAGCAAAAGAAC 58.344 29.630 5.50 0.00 0.00 3.01
3330 3584 2.617021 GCCGTTATTCCTCCTTTCACCA 60.617 50.000 0.00 0.00 0.00 4.17
3387 3641 9.732130 ATCTGGAACTAAAATCTATATCTTGCC 57.268 33.333 0.00 0.00 0.00 4.52
3389 3643 9.566432 CTGGAACTAAAATCTATATCTTGCCTT 57.434 33.333 0.00 0.00 0.00 4.35
3417 3671 4.943705 TCCTTTTGCTGAAGCTTATACCAG 59.056 41.667 0.00 3.48 42.66 4.00
3463 3717 4.800471 GTCCAATCAAAATCTCCATTTCGC 59.200 41.667 0.00 0.00 30.37 4.70
3519 3773 3.490348 GTGGGAATAGCCAATATGCTGT 58.510 45.455 0.00 0.00 42.77 4.40
3725 3979 5.566395 CGCGAGGTAAATTTCTTTTTGGTAC 59.434 40.000 0.00 0.00 0.00 3.34
3794 4076 0.613777 ACACTGTACCCTAGCCTTGC 59.386 55.000 0.00 0.00 0.00 4.01
3964 4246 9.796120 TGTTGTTTTACATTTCTTGGTCTAAAG 57.204 29.630 0.00 0.00 0.00 1.85
4027 4309 5.296748 CCAACCAAATGTCTCCGAATTTTT 58.703 37.500 0.00 0.00 0.00 1.94
4176 4466 5.335191 GGATGAGCAGTTGGTTTCAGTAAAG 60.335 44.000 0.00 0.00 0.00 1.85
4199 4491 8.926092 AAGAAAAGTAGAGTTAAAATGAGCCT 57.074 30.769 0.00 0.00 0.00 4.58
4213 4511 0.955919 GAGCCTTGTTTGAGGTCCCG 60.956 60.000 0.00 0.00 39.11 5.14
4251 4549 2.260844 TCTTGGAAGGACTGCACTTG 57.739 50.000 0.00 0.00 0.00 3.16
4374 4675 3.383185 CCAAAGGGCAAGACAACTTACAA 59.617 43.478 0.00 0.00 34.70 2.41
4375 4676 4.359706 CAAAGGGCAAGACAACTTACAAC 58.640 43.478 0.00 0.00 34.70 3.32
4398 4699 8.612619 CAACACTTGCGAGGACTAATAATTTAT 58.387 33.333 5.79 0.00 0.00 1.40
4511 4913 8.352201 GCTGGTGCAAAGTAATATGATATTTGA 58.648 33.333 2.64 0.00 39.41 2.69
4623 5025 4.095782 TCAAGTTTCAACCTTGCAGTACAC 59.904 41.667 0.00 0.00 0.00 2.90
4628 5030 3.616219 TCAACCTTGCAGTACACTTGTT 58.384 40.909 0.00 0.00 0.00 2.83
4690 5092 5.763204 ACTTGACTGTGGTGTTTACTAATGG 59.237 40.000 0.00 0.00 0.00 3.16
4702 5104 9.626045 GGTGTTTACTAATGGAATTCTTCTTTG 57.374 33.333 5.23 1.20 37.87 2.77
4902 5304 0.911525 ATGCTGCTACTGGTCCACCT 60.912 55.000 0.00 0.00 36.82 4.00
4962 5364 0.674895 ATTCTGCTCCAAGGCGTCAC 60.675 55.000 0.00 0.00 34.52 3.67
4964 5366 3.865929 CTGCTCCAAGGCGTCACGT 62.866 63.158 0.00 0.00 34.52 4.49
5113 5518 7.715265 AATGTATTTAGACATAGCCTTCACG 57.285 36.000 0.00 0.00 39.16 4.35
5148 5553 0.887387 GCACAAAGGTAAGGCGGTGA 60.887 55.000 0.00 0.00 0.00 4.02
5170 5575 5.486063 TGATCCAGGTAAGTTAGGTAAAGCA 59.514 40.000 0.00 0.00 0.00 3.91
5175 5580 6.817140 CCAGGTAAGTTAGGTAAAGCAGTTAG 59.183 42.308 0.00 0.00 0.00 2.34
5188 5593 0.179161 CAGTTAGAGGGTCGCGACTG 60.179 60.000 35.50 20.79 0.00 3.51
5221 5626 1.617357 AGACACGGACTTGGTAACCTC 59.383 52.381 0.00 0.00 0.00 3.85
5449 5854 4.641396 CAGTCTCCAGTACCATCACAAAA 58.359 43.478 0.00 0.00 0.00 2.44
5459 5864 3.152341 ACCATCACAAAAGAAGCAGGAG 58.848 45.455 0.00 0.00 0.00 3.69
5698 6103 8.649841 CATTGCAGTTTATTGTATCCTTGTTTG 58.350 33.333 0.00 0.00 0.00 2.93
5778 6185 6.215121 CAGTATCATTTGAACTGCCAAAACA 58.785 36.000 0.00 0.00 39.20 2.83
5811 6218 5.669164 AGGAACAGAGGATGTAACTCTTC 57.331 43.478 0.00 0.00 42.41 2.87
5920 6327 6.182507 TCACTACCACTTTGTAGGATTTGT 57.817 37.500 3.54 0.00 42.04 2.83
5934 6341 5.472301 AGGATTTGTATTGGAGGGTTGAT 57.528 39.130 0.00 0.00 0.00 2.57
5938 6345 6.324770 GGATTTGTATTGGAGGGTTGATGAAT 59.675 38.462 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.108615 TGCGAACTAGAGCAGAAGGC 60.109 55.000 0.00 0.00 45.30 4.35
16 17 3.013276 TCCAGCTATTCTTCGTATGCG 57.987 47.619 0.00 0.00 39.92 4.73
22 23 7.151308 ACTAGATCAAATCCAGCTATTCTTCG 58.849 38.462 0.00 0.00 0.00 3.79
123 124 2.328099 GCTCGTGCCTCTGTTTGGG 61.328 63.158 0.00 0.00 0.00 4.12
144 145 0.476338 TGGCCACCTACAAAGAAGCA 59.524 50.000 0.00 0.00 0.00 3.91
153 154 3.572255 TGAAAAGTCATTTGGCCACCTAC 59.428 43.478 3.88 1.09 0.00 3.18
161 162 8.870160 TTGTTTACATCTGAAAAGTCATTTGG 57.130 30.769 0.00 0.00 31.85 3.28
240 242 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
241 243 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
242 244 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
243 245 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
244 246 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
245 247 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
246 248 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
247 249 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
248 250 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
249 251 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
250 252 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
258 260 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
259 261 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
261 263 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
262 264 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
269 271 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
270 272 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
271 273 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
272 274 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
273 275 7.919091 TGTGACTTGATACATCCGTATTTAGAC 59.081 37.037 0.00 0.00 38.48 2.59
274 276 8.002984 TGTGACTTGATACATCCGTATTTAGA 57.997 34.615 0.00 0.00 38.48 2.10
275 277 8.818141 ATGTGACTTGATACATCCGTATTTAG 57.182 34.615 0.00 0.00 38.48 1.85
276 278 9.607988 AAATGTGACTTGATACATCCGTATTTA 57.392 29.630 0.00 0.00 38.48 1.40
277 279 8.506168 AAATGTGACTTGATACATCCGTATTT 57.494 30.769 0.00 0.00 38.48 1.40
278 280 8.506168 AAAATGTGACTTGATACATCCGTATT 57.494 30.769 0.00 0.00 38.48 1.89
279 281 9.261180 CTAAAATGTGACTTGATACATCCGTAT 57.739 33.333 0.00 0.00 41.16 3.06
280 282 8.255206 ACTAAAATGTGACTTGATACATCCGTA 58.745 33.333 0.00 0.00 36.56 4.02
281 283 7.103641 ACTAAAATGTGACTTGATACATCCGT 58.896 34.615 0.00 0.00 36.56 4.69
282 284 7.539712 ACTAAAATGTGACTTGATACATCCG 57.460 36.000 0.00 0.00 36.56 4.18
294 296 8.975439 CGGATGTACCTAATACTAAAATGTGAC 58.025 37.037 0.00 0.00 34.56 3.67
295 297 8.698210 ACGGATGTACCTAATACTAAAATGTGA 58.302 33.333 0.00 0.00 34.56 3.58
296 298 8.882415 ACGGATGTACCTAATACTAAAATGTG 57.118 34.615 0.00 0.00 34.56 3.21
304 306 8.600668 TGTCTAGATACGGATGTACCTAATACT 58.399 37.037 0.00 0.00 34.56 2.12
305 307 8.783833 TGTCTAGATACGGATGTACCTAATAC 57.216 38.462 0.00 0.00 36.31 1.89
306 308 9.797642 TTTGTCTAGATACGGATGTACCTAATA 57.202 33.333 0.00 0.00 36.31 0.98
307 309 8.701908 TTTGTCTAGATACGGATGTACCTAAT 57.298 34.615 0.00 0.00 36.31 1.73
308 310 8.701908 ATTTGTCTAGATACGGATGTACCTAA 57.298 34.615 0.00 0.00 36.31 2.69
309 311 8.162085 AGATTTGTCTAGATACGGATGTACCTA 58.838 37.037 0.00 0.00 36.31 3.08
310 312 7.005296 AGATTTGTCTAGATACGGATGTACCT 58.995 38.462 0.00 0.00 36.31 3.08
311 313 7.216973 AGATTTGTCTAGATACGGATGTACC 57.783 40.000 0.00 0.00 32.26 3.34
312 314 9.828852 CTTAGATTTGTCTAGATACGGATGTAC 57.171 37.037 0.00 0.00 32.26 2.90
313 315 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
314 316 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
315 317 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
316 318 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
317 319 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
318 320 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
326 328 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
327 329 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
328 330 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
329 331 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
330 332 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
331 333 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
332 334 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
333 335 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
334 336 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
335 337 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
336 338 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
337 339 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
338 340 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
339 341 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
340 342 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
341 343 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
342 344 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
343 345 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
344 346 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
345 347 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
346 348 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
347 349 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
348 350 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
349 351 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
350 352 2.378378 ATTACTACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
351 353 3.571828 GGTAATTACTACTCCCTCCGTCC 59.428 52.174 15.05 0.00 0.00 4.79
352 354 4.037327 GTGGTAATTACTACTCCCTCCGTC 59.963 50.000 21.18 0.00 35.17 4.79
353 355 3.956848 GTGGTAATTACTACTCCCTCCGT 59.043 47.826 21.18 0.00 35.17 4.69
354 356 4.213513 AGTGGTAATTACTACTCCCTCCG 58.786 47.826 24.36 0.00 43.31 4.63
355 357 6.556974 AAAGTGGTAATTACTACTCCCTCC 57.443 41.667 28.36 5.69 45.56 4.30
356 358 8.756927 AGTTAAAGTGGTAATTACTACTCCCTC 58.243 37.037 28.36 19.95 45.56 4.30
357 359 8.676397 AGTTAAAGTGGTAATTACTACTCCCT 57.324 34.615 28.36 19.51 45.56 4.20
364 366 9.734984 ATGCTGTTAGTTAAAGTGGTAATTACT 57.265 29.630 15.05 0.00 0.00 2.24
411 413 0.947244 ACAACCTCAAAAGAGCAGCG 59.053 50.000 0.00 0.00 0.00 5.18
440 442 2.954318 GCTCATGGATAGCACACCAAAT 59.046 45.455 0.21 0.00 39.83 2.32
513 515 9.672673 ACAAATAGCTCAATTACACTTATCAGT 57.327 29.630 0.00 0.00 0.00 3.41
611 646 2.614057 CCATATCCTCACTCGGTTTTGC 59.386 50.000 0.00 0.00 0.00 3.68
618 653 4.219507 AGCTCAATACCATATCCTCACTCG 59.780 45.833 0.00 0.00 0.00 4.18
665 718 6.897966 TCACCTCTTTACTATGAGAAGGTGAT 59.102 38.462 15.37 0.00 40.78 3.06
740 798 3.009695 TGGGGTTGACTTCGTTGGATAAT 59.990 43.478 0.00 0.00 0.00 1.28
750 808 1.203001 TGATTGGGTGGGGTTGACTTC 60.203 52.381 0.00 0.00 0.00 3.01
768 826 3.572255 GGATAGCCACCTTTGTTGTTTGA 59.428 43.478 0.00 0.00 0.00 2.69
790 866 1.000896 CCCCTGCCACCTGGTTAAG 60.001 63.158 0.00 0.00 37.57 1.85
791 867 0.849094 ATCCCCTGCCACCTGGTTAA 60.849 55.000 0.00 0.00 37.57 2.01
792 868 0.045008 TATCCCCTGCCACCTGGTTA 59.955 55.000 0.00 0.00 37.57 2.85
793 869 0.627469 ATATCCCCTGCCACCTGGTT 60.627 55.000 0.00 0.00 37.57 3.67
794 870 1.006092 ATATCCCCTGCCACCTGGT 59.994 57.895 0.00 0.00 37.57 4.00
795 871 1.763770 GATATCCCCTGCCACCTGG 59.236 63.158 0.00 0.00 38.53 4.45
796 872 0.769776 AGGATATCCCCTGCCACCTG 60.770 60.000 18.56 0.00 34.68 4.00
797 873 0.474660 GAGGATATCCCCTGCCACCT 60.475 60.000 18.56 0.00 36.49 4.00
798 874 0.768221 TGAGGATATCCCCTGCCACC 60.768 60.000 18.56 0.00 36.49 4.61
799 875 0.689623 CTGAGGATATCCCCTGCCAC 59.310 60.000 18.56 2.66 36.49 5.01
800 876 1.130054 GCTGAGGATATCCCCTGCCA 61.130 60.000 20.36 9.96 36.49 4.92
801 877 1.682257 GCTGAGGATATCCCCTGCC 59.318 63.158 20.36 6.41 36.49 4.85
802 878 1.130054 TGGCTGAGGATATCCCCTGC 61.130 60.000 22.15 22.15 36.49 4.85
803 879 1.072965 GTTGGCTGAGGATATCCCCTG 59.927 57.143 18.56 11.80 36.49 4.45
804 880 1.439543 GTTGGCTGAGGATATCCCCT 58.560 55.000 18.56 0.00 39.77 4.79
810 886 1.635817 GGCTGGGTTGGCTGAGGATA 61.636 60.000 0.00 0.00 0.00 2.59
946 1022 2.821437 TCACCACCAAAACAGGGAAAA 58.179 42.857 0.00 0.00 0.00 2.29
1005 1081 6.281190 TCTATCTCAGGACTTGATTCCCTA 57.719 41.667 0.00 0.00 36.12 3.53
1038 1114 6.441604 AGGCTTTCCCATAAACTTCATTGAAT 59.558 34.615 0.00 0.00 35.39 2.57
1165 1241 0.533755 GGGACAGCATTGGGATCTCG 60.534 60.000 0.00 0.00 0.00 4.04
1215 1291 1.475930 GCCTTAGCTTTAGCCTCCCAG 60.476 57.143 0.00 0.00 43.38 4.45
1370 1446 9.712305 AGTGCAGTAGTCCATTATGTATTTATC 57.288 33.333 0.00 0.00 0.00 1.75
1538 1614 6.412362 TTTTTCTAAAATTAGGTGCTGCCA 57.588 33.333 0.00 0.00 40.61 4.92
1577 1653 7.167302 TCACGTTTTAATGCTGTTTGATTGAAG 59.833 33.333 0.00 0.00 0.00 3.02
1755 1835 5.245075 CAGGACCAAATTAGCTGGGTTAAAA 59.755 40.000 0.00 0.00 38.36 1.52
1799 1879 1.197492 TGCTGTTGATGCACGATTGAC 59.803 47.619 0.00 0.00 35.31 3.18
1824 1904 1.233950 TGGCGCCAGTGTACACAATG 61.234 55.000 29.03 17.09 41.16 2.82
1877 1957 2.874694 CTCGATTCCCATGCGTGCG 61.875 63.158 0.00 0.00 0.00 5.34
1881 1961 0.104855 TCTTCCTCGATTCCCATGCG 59.895 55.000 0.00 0.00 0.00 4.73
1916 1996 6.154706 TGGGTTCTATTCCTAACTGTCTCTTC 59.845 42.308 0.00 0.00 0.00 2.87
1922 2002 6.023603 TCTTCTGGGTTCTATTCCTAACTGT 58.976 40.000 0.00 0.00 0.00 3.55
2013 2093 7.208064 TGGGGTTATAGGGCATTCTTATATC 57.792 40.000 0.00 0.00 0.00 1.63
2029 2109 4.480537 TCCATAAACCTGTGATGGGGTTAT 59.519 41.667 10.15 0.00 44.69 1.89
2068 2148 6.647481 GGAAGACTTAAGAAAACAGAGACCTC 59.353 42.308 10.09 0.00 0.00 3.85
2116 2196 5.054477 TGCAACAACTTGGAAGTAGAGTAC 58.946 41.667 0.00 0.00 38.57 2.73
2117 2197 5.284861 TGCAACAACTTGGAAGTAGAGTA 57.715 39.130 0.00 0.00 38.57 2.59
2286 2537 5.582953 TCAAATGGAAGAATGAGGAATGGT 58.417 37.500 0.00 0.00 0.00 3.55
2287 2538 6.097839 ACATCAAATGGAAGAATGAGGAATGG 59.902 38.462 0.00 0.00 33.60 3.16
2334 2585 5.007921 TCGATATGGTTGATCATTTGCACTG 59.992 40.000 0.00 0.00 0.00 3.66
2361 2612 3.904571 ACAACGTCAGTGTCGCTATTAA 58.095 40.909 9.72 0.00 0.00 1.40
2445 2697 1.247567 AACTTCCATTTGGCGGACAG 58.752 50.000 0.00 0.00 34.44 3.51
2501 2754 6.927294 AAGGACAAGTCTTTAACACTTCTG 57.073 37.500 0.00 0.00 31.40 3.02
3079 3333 2.101249 CCAAAGGCAGTTCTTTTGCTCA 59.899 45.455 0.00 0.00 41.27 4.26
3091 3345 1.762370 ACAAAAAGGGACCAAAGGCAG 59.238 47.619 0.00 0.00 0.00 4.85
3251 3505 8.746052 TCAAAGAAGTCTAAAATCTTTCACCA 57.254 30.769 0.00 0.00 40.44 4.17
3387 3641 4.941657 AGCTTCAGCAAAAGGAAGAAAAG 58.058 39.130 0.75 0.00 42.39 2.27
3389 3643 6.655078 ATAAGCTTCAGCAAAAGGAAGAAA 57.345 33.333 0.00 0.00 42.39 2.52
3463 3717 3.181439 GGGGTTCATCAAGATAAGAGGGG 60.181 52.174 0.00 0.00 0.00 4.79
3725 3979 8.261492 ACAGAGAAATTTCAAGCAGTATACTG 57.739 34.615 25.68 25.68 46.40 2.74
3923 4205 9.921637 TGTAAAACAACACTTTGAAGAAGAAAT 57.078 25.926 0.00 0.00 36.48 2.17
3964 4246 5.246307 ACATGAAGTTACTAAAGACCAGCC 58.754 41.667 0.00 0.00 0.00 4.85
4003 4285 1.243902 TTCGGAGACATTTGGTTGGC 58.756 50.000 0.00 0.00 34.32 4.52
4027 4309 1.378531 GCATTGCGATACCAGAACCA 58.621 50.000 0.00 0.00 0.00 3.67
4176 4466 8.568794 ACAAGGCTCATTTTAACTCTACTTTTC 58.431 33.333 0.00 0.00 0.00 2.29
4199 4491 5.046159 ACAAGTATATCGGGACCTCAAACAA 60.046 40.000 0.00 0.00 0.00 2.83
4213 4511 5.471456 CCAAGATGCTGGGAACAAGTATATC 59.529 44.000 0.00 0.00 42.06 1.63
4251 4549 2.936919 TGGTGGATATGCACCATCTC 57.063 50.000 36.95 17.06 45.54 2.75
4374 4675 7.769044 ACATAAATTATTAGTCCTCGCAAGTGT 59.231 33.333 0.00 0.00 39.48 3.55
4375 4676 8.142994 ACATAAATTATTAGTCCTCGCAAGTG 57.857 34.615 0.00 0.00 39.48 3.16
4585 4987 9.516314 GTTGAAACTTGAATAGGCATAATTACC 57.484 33.333 0.00 0.00 0.00 2.85
4623 5025 9.940166 ATAAAAGGTAAAACACTACGAAACAAG 57.060 29.630 0.00 0.00 0.00 3.16
4628 5030 9.107177 TCAACATAAAAGGTAAAACACTACGAA 57.893 29.630 0.00 0.00 0.00 3.85
4702 5104 9.522804 CCTCATTTCTCTAAGTGACTGTATTAC 57.477 37.037 0.00 0.00 29.30 1.89
4930 5332 6.656632 TGGAGCAGAATAGTTATCAGTAGG 57.343 41.667 0.00 0.00 0.00 3.18
4962 5364 1.463056 TGAAACTCGCCATAAGCAACG 59.537 47.619 0.00 0.00 44.04 4.10
4964 5366 1.468520 GCTGAAACTCGCCATAAGCAA 59.531 47.619 0.00 0.00 44.04 3.91
5113 5518 4.893424 TTGTGCCAGTTTCTTGAACTAC 57.107 40.909 0.00 0.00 46.75 2.73
5148 5553 5.487845 ACTGCTTTACCTAACTTACCTGGAT 59.512 40.000 0.00 0.00 0.00 3.41
5170 5575 1.935327 GCAGTCGCGACCCTCTAACT 61.935 60.000 34.08 11.69 0.00 2.24
5188 5593 2.988493 TCCGTGTCTATTGTTGTAACGC 59.012 45.455 0.00 0.00 0.00 4.84
5221 5626 5.368989 GGTCAACACCTCCTAATAAGATGG 58.631 45.833 0.00 0.00 40.00 3.51
5299 5704 2.373169 ACTCAGATTCCTCACAAAGGCA 59.627 45.455 0.00 0.00 45.78 4.75
5459 5864 8.627428 GTGATGTCTTAATTTCGTTTTAACAGC 58.373 33.333 0.00 0.00 0.00 4.40
5698 6103 8.102800 TGCATATGACCATTGATGAGAATAAC 57.897 34.615 6.97 0.00 0.00 1.89
5712 6117 4.504864 GGGTACTAGCATTGCATATGACCA 60.505 45.833 11.91 0.00 0.00 4.02
5778 6185 8.095452 ACATCCTCTGTTCCTAAATGTAAGAT 57.905 34.615 0.00 0.00 32.90 2.40
5811 6218 6.710744 ACCCACTTTATACTTTCTCACAACTG 59.289 38.462 0.00 0.00 0.00 3.16
5920 6327 8.203485 GCAATTAAATTCATCAACCCTCCAATA 58.797 33.333 0.00 0.00 0.00 1.90
5971 6378 7.213178 ACTTAATTTCTCCTGGATACCATGT 57.787 36.000 0.00 0.00 30.82 3.21
6003 6410 4.157840 ACTCAAAAGGAAATATTGCGGACC 59.842 41.667 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.