Multiple sequence alignment - TraesCS4B01G104900

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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 TraesCS4B01G104900 chr4B 100.000 6409 0 0 1 6409 112350316 112356724 0.000000e+00 11836
1 TraesCS4B01G104900 chr4D 95.612 5902 158 34 555 6409 80140423 80146270 0.000000e+00 9371
2 TraesCS4B01G104900 chr4D 92.308 78 4 1 169 244 80138125 80138202 6.790000e-20 110
3 TraesCS4B01G104900 chr4D 92.754 69 5 0 111 179 80138023 80138091 4.090000e-17 100
4 TraesCS4B01G104900 chr4A 94.800 5942 197 35 534 6409 505795327 505789432 0.000000e+00 9158
5 TraesCS4B01G104900 chr2A 85.886 2409 227 46 2146 4506 779205905 779203562 0.000000e+00 2460
6 TraesCS4B01G104900 chr2B 86.284 1203 131 12 2146 3325 777334778 777335969 0.000000e+00 1277
7 TraesCS4B01G104900 chr2B 83.946 816 84 24 3296 4093 777335979 777336765 0.000000e+00 737
8 TraesCS4B01G104900 chr2B 90.534 412 36 2 4097 4506 777336943 777337353 5.650000e-150 542
9 TraesCS4B01G104900 chr6D 92.027 301 22 2 233 533 14267962 14268260 7.680000e-114 422
10 TraesCS4B01G104900 chr6D 91.000 300 23 4 239 536 61311233 61311530 1.000000e-107 401
11 TraesCS4B01G104900 chr1D 92.517 294 20 2 241 533 142341428 142341720 2.760000e-113 420
12 TraesCS4B01G104900 chr1D 92.177 294 21 2 241 534 114353392 114353101 1.290000e-111 414
13 TraesCS4B01G104900 chr1D 91.753 291 24 0 241 531 41220152 41220442 7.740000e-109 405
14 TraesCS4B01G104900 chr1D 91.246 297 23 3 239 534 268331435 268331141 1.000000e-107 401
15 TraesCS4B01G104900 chr3D 90.970 299 25 2 239 536 115992599 115992896 1.000000e-107 401
16 TraesCS4B01G104900 chr2D 91.000 300 23 4 239 536 596846996 596846699 1.000000e-107 401
17 TraesCS4B01G104900 chr7D 90.164 305 27 3 230 533 549158183 549157881 1.670000e-105 394
18 TraesCS4B01G104900 chr5A 83.333 192 20 4 1382 1573 563769678 563769857 3.970000e-37 167
19 TraesCS4B01G104900 chr5A 88.350 103 11 1 1611 1713 563769863 563769964 8.730000e-24 122


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 TraesCS4B01G104900 chr4B 112350316 112356724 6408 False 11836.000000 11836 100.000000 1 6409 1 chr4B.!!$F1 6408
1 TraesCS4B01G104900 chr4D 80138023 80146270 8247 False 3193.666667 9371 93.558000 111 6409 3 chr4D.!!$F1 6298
2 TraesCS4B01G104900 chr4A 505789432 505795327 5895 True 9158.000000 9158 94.800000 534 6409 1 chr4A.!!$R1 5875
3 TraesCS4B01G104900 chr2A 779203562 779205905 2343 True 2460.000000 2460 85.886000 2146 4506 1 chr2A.!!$R1 2360
4 TraesCS4B01G104900 chr2B 777334778 777337353 2575 False 852.000000 1277 86.921333 2146 4506 3 chr2B.!!$F1 2360

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
345 392 0.103390 GAGAGAGAAGGTAAGCGGGC 59.897 60.000 0.00 0.00 0.00 6.13 F
347 394 0.103390 GAGAGAAGGTAAGCGGGCTC 59.897 60.000 0.00 0.00 0.00 4.70 F
356 403 0.108804 TAAGCGGGCTCTTCGTGAAG 60.109 55.000 3.17 3.17 39.71 3.02 F
2225 4236 0.101219 GTTCCATCAGCCGATTTGCC 59.899 55.000 0.00 0.00 0.00 4.52 F
2569 4592 0.108585 AGAAGAAGGGCGCTTTGTCA 59.891 50.000 17.99 0.00 0.00 3.58 F
2841 4864 2.027745 AGATGATGCACGGAACTCAAGT 60.028 45.455 0.00 0.00 0.00 3.16 F
4468 6750 0.389426 GCCCAACTGCTGCTCAATTG 60.389 55.000 0.00 0.00 32.12 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 3933 0.749454 GCAGCAGAATCCGGTTCCAT 60.749 55.000 0.00 0.00 37.56 3.41 R
2047 4057 4.454678 TCATCTCTGTTGACAGCAAAACT 58.545 39.130 6.27 0.00 43.46 2.66 R
2311 4329 5.444663 AGAAGAAAAGGTCAACAAGCATC 57.555 39.130 0.00 0.00 0.00 3.91 R
3743 5836 0.685097 ACCTGTGCACTGTATTCCGT 59.315 50.000 19.41 6.81 0.00 4.69 R
3894 5998 3.979948 TGCAAGTTTGATGTCACCATTG 58.020 40.909 0.00 0.00 0.00 2.82 R
4821 7103 3.070018 CTGGCACCACTAAGTTTCTCAG 58.930 50.000 0.00 0.00 0.00 3.35 R
6002 8295 0.984230 AGAGGGACATCGCCTTCAAA 59.016 50.000 0.00 0.00 36.56 2.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 9.906660 GTTTTTAGGTGATTACAACATGAATCA 57.093 29.630 0.00 1.17 39.24 2.57
46 47 8.900781 CATGAATCATGTTTCAGGAAATCTAGT 58.099 33.333 21.05 1.82 39.18 2.57
47 48 8.868522 TGAATCATGTTTCAGGAAATCTAGTT 57.131 30.769 13.94 0.00 32.07 2.24
48 49 9.300681 TGAATCATGTTTCAGGAAATCTAGTTT 57.699 29.630 13.94 0.00 32.07 2.66
51 52 9.918630 ATCATGTTTCAGGAAATCTAGTTTTTG 57.081 29.630 0.45 0.00 32.36 2.44
52 53 9.130661 TCATGTTTCAGGAAATCTAGTTTTTGA 57.869 29.630 0.45 0.00 32.36 2.69
53 54 9.748708 CATGTTTCAGGAAATCTAGTTTTTGAA 57.251 29.630 8.40 8.40 34.60 2.69
54 55 9.750125 ATGTTTCAGGAAATCTAGTTTTTGAAC 57.250 29.630 10.75 8.33 35.39 3.18
55 56 8.744652 TGTTTCAGGAAATCTAGTTTTTGAACA 58.255 29.630 10.75 9.89 35.39 3.18
56 57 9.581099 GTTTCAGGAAATCTAGTTTTTGAACAA 57.419 29.630 10.75 0.00 35.39 2.83
59 60 9.965824 TCAGGAAATCTAGTTTTTGAACAATTC 57.034 29.630 0.45 0.00 0.00 2.17
60 61 8.905702 CAGGAAATCTAGTTTTTGAACAATTCG 58.094 33.333 0.45 0.00 0.00 3.34
61 62 8.630037 AGGAAATCTAGTTTTTGAACAATTCGT 58.370 29.630 0.45 0.00 0.00 3.85
62 63 8.690840 GGAAATCTAGTTTTTGAACAATTCGTG 58.309 33.333 0.45 0.00 0.00 4.35
63 64 7.623268 AATCTAGTTTTTGAACAATTCGTGC 57.377 32.000 0.00 0.00 0.00 5.34
64 65 6.125327 TCTAGTTTTTGAACAATTCGTGCA 57.875 33.333 0.00 0.00 0.00 4.57
65 66 6.734137 TCTAGTTTTTGAACAATTCGTGCAT 58.266 32.000 0.00 0.00 31.23 3.96
66 67 5.888412 AGTTTTTGAACAATTCGTGCATC 57.112 34.783 0.00 0.00 31.23 3.91
67 68 4.744631 AGTTTTTGAACAATTCGTGCATCC 59.255 37.500 0.00 0.00 31.23 3.51
68 69 3.998099 TTTGAACAATTCGTGCATCCA 57.002 38.095 0.00 0.00 31.23 3.41
69 70 3.998099 TTGAACAATTCGTGCATCCAA 57.002 38.095 0.00 0.00 31.23 3.53
70 71 3.998099 TGAACAATTCGTGCATCCAAA 57.002 38.095 0.00 0.00 0.00 3.28
71 72 3.637432 TGAACAATTCGTGCATCCAAAC 58.363 40.909 0.00 0.00 0.00 2.93
72 73 3.067320 TGAACAATTCGTGCATCCAAACA 59.933 39.130 0.00 0.00 0.00 2.83
73 74 3.724508 ACAATTCGTGCATCCAAACAA 57.275 38.095 0.00 0.00 0.00 2.83
74 75 3.380142 ACAATTCGTGCATCCAAACAAC 58.620 40.909 0.00 0.00 0.00 3.32
75 76 2.723124 ATTCGTGCATCCAAACAACC 57.277 45.000 0.00 0.00 0.00 3.77
76 77 0.671251 TTCGTGCATCCAAACAACCC 59.329 50.000 0.00 0.00 0.00 4.11
77 78 1.175983 TCGTGCATCCAAACAACCCC 61.176 55.000 0.00 0.00 0.00 4.95
78 79 1.459455 CGTGCATCCAAACAACCCCA 61.459 55.000 0.00 0.00 0.00 4.96
79 80 0.755686 GTGCATCCAAACAACCCCAA 59.244 50.000 0.00 0.00 0.00 4.12
80 81 1.139853 GTGCATCCAAACAACCCCAAA 59.860 47.619 0.00 0.00 0.00 3.28
81 82 1.415659 TGCATCCAAACAACCCCAAAG 59.584 47.619 0.00 0.00 0.00 2.77
82 83 1.270785 GCATCCAAACAACCCCAAAGG 60.271 52.381 0.00 0.00 43.78 3.11
83 84 2.324541 CATCCAAACAACCCCAAAGGA 58.675 47.619 0.00 0.00 39.89 3.36
84 85 2.552093 TCCAAACAACCCCAAAGGAA 57.448 45.000 0.00 0.00 39.89 3.36
85 86 2.112190 TCCAAACAACCCCAAAGGAAC 58.888 47.619 0.00 0.00 39.89 3.62
86 87 1.834263 CCAAACAACCCCAAAGGAACA 59.166 47.619 0.00 0.00 39.89 3.18
87 88 2.237392 CCAAACAACCCCAAAGGAACAA 59.763 45.455 0.00 0.00 39.89 2.83
88 89 3.118075 CCAAACAACCCCAAAGGAACAAT 60.118 43.478 0.00 0.00 39.89 2.71
89 90 4.101741 CCAAACAACCCCAAAGGAACAATA 59.898 41.667 0.00 0.00 39.89 1.90
90 91 5.296748 CAAACAACCCCAAAGGAACAATAG 58.703 41.667 0.00 0.00 39.89 1.73
91 92 4.463050 ACAACCCCAAAGGAACAATAGA 57.537 40.909 0.00 0.00 39.89 1.98
92 93 4.810345 ACAACCCCAAAGGAACAATAGAA 58.190 39.130 0.00 0.00 39.89 2.10
93 94 4.587262 ACAACCCCAAAGGAACAATAGAAC 59.413 41.667 0.00 0.00 39.89 3.01
94 95 4.463050 ACCCCAAAGGAACAATAGAACA 57.537 40.909 0.00 0.00 39.89 3.18
95 96 4.810345 ACCCCAAAGGAACAATAGAACAA 58.190 39.130 0.00 0.00 39.89 2.83
96 97 5.212745 ACCCCAAAGGAACAATAGAACAAA 58.787 37.500 0.00 0.00 39.89 2.83
97 98 5.304357 ACCCCAAAGGAACAATAGAACAAAG 59.696 40.000 0.00 0.00 39.89 2.77
98 99 5.304357 CCCCAAAGGAACAATAGAACAAAGT 59.696 40.000 0.00 0.00 38.24 2.66
99 100 6.183360 CCCCAAAGGAACAATAGAACAAAGTT 60.183 38.462 0.00 0.00 38.24 2.66
100 101 7.272244 CCCAAAGGAACAATAGAACAAAGTTT 58.728 34.615 0.00 0.00 33.47 2.66
101 102 7.768582 CCCAAAGGAACAATAGAACAAAGTTTT 59.231 33.333 0.00 0.00 33.47 2.43
102 103 8.603181 CCAAAGGAACAATAGAACAAAGTTTTG 58.397 33.333 3.17 3.17 43.62 2.44
103 104 9.364989 CAAAGGAACAATAGAACAAAGTTTTGA 57.635 29.630 11.29 0.00 40.55 2.69
106 107 9.750125 AGGAACAATAGAACAAAGTTTTGATTC 57.250 29.630 11.29 10.34 40.55 2.52
107 108 9.750125 GGAACAATAGAACAAAGTTTTGATTCT 57.250 29.630 11.29 15.47 40.55 2.40
144 145 7.696992 TGATTTAAACCGGCTTTTAGAGATT 57.303 32.000 0.00 0.00 0.00 2.40
146 147 5.789710 TTAAACCGGCTTTTAGAGATTCG 57.210 39.130 0.00 0.00 0.00 3.34
150 151 2.608090 CCGGCTTTTAGAGATTCGGTTC 59.392 50.000 0.00 0.00 33.40 3.62
179 180 1.850377 TTGAAGGCAACGCATGTTTG 58.150 45.000 0.00 0.00 46.39 2.93
180 181 0.597118 TGAAGGCAACGCATGTTTGC 60.597 50.000 20.07 20.07 45.78 3.68
214 261 0.181350 AGGCATGACGAGAAATCCCC 59.819 55.000 0.00 0.00 0.00 4.81
244 291 1.254026 CCCTCTCGTGTCACCACTAA 58.746 55.000 0.00 0.00 39.55 2.24
245 292 1.202582 CCCTCTCGTGTCACCACTAAG 59.797 57.143 0.00 0.00 39.55 2.18
246 293 2.160205 CCTCTCGTGTCACCACTAAGA 58.840 52.381 0.00 0.00 39.55 2.10
247 294 2.162608 CCTCTCGTGTCACCACTAAGAG 59.837 54.545 0.00 11.86 42.70 2.85
248 295 1.540267 TCTCGTGTCACCACTAAGAGC 59.460 52.381 0.00 0.00 39.55 4.09
249 296 1.269723 CTCGTGTCACCACTAAGAGCA 59.730 52.381 0.00 0.00 39.55 4.26
251 298 2.061773 CGTGTCACCACTAAGAGCAAG 58.938 52.381 0.00 0.00 39.55 4.01
252 299 2.545952 CGTGTCACCACTAAGAGCAAGT 60.546 50.000 0.00 0.00 39.55 3.16
255 302 3.639561 TGTCACCACTAAGAGCAAGTACA 59.360 43.478 0.00 0.00 0.00 2.90
257 304 5.221641 TGTCACCACTAAGAGCAAGTACAAT 60.222 40.000 0.00 0.00 0.00 2.71
258 305 6.014925 TGTCACCACTAAGAGCAAGTACAATA 60.015 38.462 0.00 0.00 0.00 1.90
260 307 6.436218 TCACCACTAAGAGCAAGTACAATAGA 59.564 38.462 0.00 0.00 0.00 1.98
261 308 6.754209 CACCACTAAGAGCAAGTACAATAGAG 59.246 42.308 0.00 0.00 0.00 2.43
262 309 5.751028 CCACTAAGAGCAAGTACAATAGAGC 59.249 44.000 0.00 0.00 0.00 4.09
263 310 6.406400 CCACTAAGAGCAAGTACAATAGAGCT 60.406 42.308 0.00 0.00 34.61 4.09
264 311 6.475076 CACTAAGAGCAAGTACAATAGAGCTG 59.525 42.308 0.00 0.00 31.61 4.24
265 312 5.667539 AAGAGCAAGTACAATAGAGCTGA 57.332 39.130 0.00 0.00 31.61 4.26
266 313 5.004922 AGAGCAAGTACAATAGAGCTGAC 57.995 43.478 0.00 0.00 31.61 3.51
267 314 4.709397 AGAGCAAGTACAATAGAGCTGACT 59.291 41.667 0.00 0.00 31.61 3.41
268 315 5.004922 AGCAAGTACAATAGAGCTGACTC 57.995 43.478 0.00 0.00 43.82 3.36
269 316 4.464244 AGCAAGTACAATAGAGCTGACTCA 59.536 41.667 0.00 0.00 46.09 3.41
270 317 4.803088 GCAAGTACAATAGAGCTGACTCAG 59.197 45.833 1.21 1.21 46.09 3.35
281 328 2.430546 CTGACTCAGCGGGCTATAAG 57.569 55.000 0.00 0.00 0.00 1.73
282 329 1.957177 CTGACTCAGCGGGCTATAAGA 59.043 52.381 0.00 0.00 0.00 2.10
283 330 2.362397 CTGACTCAGCGGGCTATAAGAA 59.638 50.000 0.00 0.00 0.00 2.52
284 331 2.764010 TGACTCAGCGGGCTATAAGAAA 59.236 45.455 0.00 0.00 0.00 2.52
286 333 4.587262 TGACTCAGCGGGCTATAAGAAATA 59.413 41.667 0.00 0.00 0.00 1.40
287 334 5.069914 TGACTCAGCGGGCTATAAGAAATAA 59.930 40.000 0.00 0.00 0.00 1.40
288 335 5.925509 ACTCAGCGGGCTATAAGAAATAAA 58.074 37.500 0.00 0.00 0.00 1.40
290 337 5.925509 TCAGCGGGCTATAAGAAATAAACT 58.074 37.500 0.00 0.00 0.00 2.66
291 338 7.058023 TCAGCGGGCTATAAGAAATAAACTA 57.942 36.000 0.00 0.00 0.00 2.24
294 341 8.086522 CAGCGGGCTATAAGAAATAAACTAGTA 58.913 37.037 0.00 0.00 0.00 1.82
295 342 8.813951 AGCGGGCTATAAGAAATAAACTAGTAT 58.186 33.333 0.00 0.00 0.00 2.12
337 384 6.508030 AAAAGAGAAAAGGAGAGAGAAGGT 57.492 37.500 0.00 0.00 0.00 3.50
338 385 7.619512 AAAAGAGAAAAGGAGAGAGAAGGTA 57.380 36.000 0.00 0.00 0.00 3.08
339 386 7.619512 AAAGAGAAAAGGAGAGAGAAGGTAA 57.380 36.000 0.00 0.00 0.00 2.85
342 389 3.878160 AAAGGAGAGAGAAGGTAAGCG 57.122 47.619 0.00 0.00 0.00 4.68
343 390 1.770294 AGGAGAGAGAAGGTAAGCGG 58.230 55.000 0.00 0.00 0.00 5.52
344 391 0.747852 GGAGAGAGAAGGTAAGCGGG 59.252 60.000 0.00 0.00 0.00 6.13
345 392 0.103390 GAGAGAGAAGGTAAGCGGGC 59.897 60.000 0.00 0.00 0.00 6.13
346 393 0.324830 AGAGAGAAGGTAAGCGGGCT 60.325 55.000 0.00 0.00 0.00 5.19
347 394 0.103390 GAGAGAAGGTAAGCGGGCTC 59.897 60.000 0.00 0.00 0.00 4.70
348 395 0.324830 AGAGAAGGTAAGCGGGCTCT 60.325 55.000 0.00 0.00 0.00 4.09
349 396 0.537653 GAGAAGGTAAGCGGGCTCTT 59.462 55.000 0.00 0.00 0.00 2.85
350 397 0.537653 AGAAGGTAAGCGGGCTCTTC 59.462 55.000 10.83 10.83 35.41 2.87
351 398 0.806492 GAAGGTAAGCGGGCTCTTCG 60.806 60.000 0.00 0.00 0.00 3.79
352 399 1.542187 AAGGTAAGCGGGCTCTTCGT 61.542 55.000 0.00 0.00 0.00 3.85
353 400 1.810030 GGTAAGCGGGCTCTTCGTG 60.810 63.158 0.00 0.00 0.00 4.35
356 403 0.108804 TAAGCGGGCTCTTCGTGAAG 60.109 55.000 3.17 3.17 39.71 3.02
357 404 1.816863 AAGCGGGCTCTTCGTGAAGA 61.817 55.000 11.54 11.54 44.47 2.87
358 405 1.374252 GCGGGCTCTTCGTGAAGAA 60.374 57.895 12.94 0.00 45.75 2.52
363 410 0.793250 GCTCTTCGTGAAGAACCAGC 59.207 55.000 12.94 9.21 45.75 4.85
365 412 2.333014 CTCTTCGTGAAGAACCAGCTC 58.667 52.381 12.94 0.00 45.75 4.09
366 413 1.964223 TCTTCGTGAAGAACCAGCTCT 59.036 47.619 9.78 0.00 43.79 4.09
367 414 3.154710 TCTTCGTGAAGAACCAGCTCTA 58.845 45.455 9.78 0.00 43.79 2.43
369 416 1.202582 TCGTGAAGAACCAGCTCTAGC 59.797 52.381 0.00 0.00 42.49 3.42
370 417 1.067565 CGTGAAGAACCAGCTCTAGCA 60.068 52.381 4.54 0.00 45.16 3.49
371 418 2.417924 CGTGAAGAACCAGCTCTAGCAT 60.418 50.000 4.54 0.00 45.16 3.79
372 419 3.181486 CGTGAAGAACCAGCTCTAGCATA 60.181 47.826 4.54 0.00 45.16 3.14
374 421 4.749099 GTGAAGAACCAGCTCTAGCATATG 59.251 45.833 4.54 0.00 45.16 1.78
375 422 3.399440 AGAACCAGCTCTAGCATATGC 57.601 47.619 20.36 20.36 45.16 3.14
387 434 2.557920 GCATATGCTCCTAGGCACTT 57.442 50.000 20.64 0.00 45.36 3.16
388 435 2.856222 GCATATGCTCCTAGGCACTTT 58.144 47.619 20.64 0.00 45.36 2.66
390 437 3.813443 CATATGCTCCTAGGCACTTTGT 58.187 45.455 2.96 0.00 45.36 2.83
391 438 2.119801 ATGCTCCTAGGCACTTTGTG 57.880 50.000 2.96 0.00 45.36 3.33
392 439 1.055849 TGCTCCTAGGCACTTTGTGA 58.944 50.000 2.96 0.00 41.75 3.58
393 440 1.002430 TGCTCCTAGGCACTTTGTGAG 59.998 52.381 2.96 0.00 41.75 3.51
396 443 3.620966 GCTCCTAGGCACTTTGTGAGAAT 60.621 47.826 2.96 0.00 41.75 2.40
397 444 3.937706 CTCCTAGGCACTTTGTGAGAATG 59.062 47.826 2.96 0.00 41.75 2.67
398 445 3.582647 TCCTAGGCACTTTGTGAGAATGA 59.417 43.478 2.96 0.00 41.75 2.57
399 446 4.041567 TCCTAGGCACTTTGTGAGAATGAA 59.958 41.667 2.96 0.00 41.75 2.57
400 447 4.761739 CCTAGGCACTTTGTGAGAATGAAA 59.238 41.667 0.00 0.00 41.75 2.69
401 448 5.416952 CCTAGGCACTTTGTGAGAATGAAAT 59.583 40.000 0.00 0.00 41.75 2.17
402 449 6.599244 CCTAGGCACTTTGTGAGAATGAAATA 59.401 38.462 0.00 0.00 41.75 1.40
403 450 7.284034 CCTAGGCACTTTGTGAGAATGAAATAT 59.716 37.037 0.00 0.00 41.75 1.28
404 451 6.860080 AGGCACTTTGTGAGAATGAAATATG 58.140 36.000 1.52 0.00 35.23 1.78
405 452 6.038356 GGCACTTTGTGAGAATGAAATATGG 58.962 40.000 1.52 0.00 35.23 2.74
407 454 6.038356 CACTTTGTGAGAATGAAATATGGGC 58.962 40.000 0.00 0.00 35.23 5.36
408 455 5.127682 ACTTTGTGAGAATGAAATATGGGCC 59.872 40.000 0.00 0.00 0.00 5.80
409 456 4.248174 TGTGAGAATGAAATATGGGCCA 57.752 40.909 9.61 9.61 0.00 5.36
410 457 3.953612 TGTGAGAATGAAATATGGGCCAC 59.046 43.478 9.28 0.00 0.00 5.01
411 458 3.953612 GTGAGAATGAAATATGGGCCACA 59.046 43.478 9.28 0.00 0.00 4.17
412 459 4.586001 GTGAGAATGAAATATGGGCCACAT 59.414 41.667 9.28 0.00 43.68 3.21
413 460 5.769662 GTGAGAATGAAATATGGGCCACATA 59.230 40.000 9.28 10.73 45.60 2.29
414 461 6.265196 GTGAGAATGAAATATGGGCCACATAA 59.735 38.462 9.28 0.00 44.75 1.90
416 463 8.169393 TGAGAATGAAATATGGGCCACATAATA 58.831 33.333 9.28 0.00 44.75 0.98
444 491 3.498774 AGTGCACTCTTTTGATCCACT 57.501 42.857 15.25 0.00 0.00 4.00
445 492 4.623932 AGTGCACTCTTTTGATCCACTA 57.376 40.909 15.25 0.00 0.00 2.74
446 493 5.171339 AGTGCACTCTTTTGATCCACTAT 57.829 39.130 15.25 0.00 0.00 2.12
447 494 5.564550 AGTGCACTCTTTTGATCCACTATT 58.435 37.500 15.25 0.00 0.00 1.73
448 495 6.711277 AGTGCACTCTTTTGATCCACTATTA 58.289 36.000 15.25 0.00 0.00 0.98
449 496 7.341805 AGTGCACTCTTTTGATCCACTATTAT 58.658 34.615 15.25 0.00 0.00 1.28
450 497 8.486210 AGTGCACTCTTTTGATCCACTATTATA 58.514 33.333 15.25 0.00 0.00 0.98
452 499 7.438160 TGCACTCTTTTGATCCACTATTATACG 59.562 37.037 0.00 0.00 0.00 3.06
456 503 9.314321 CTCTTTTGATCCACTATTATACGTGTT 57.686 33.333 0.00 0.00 0.00 3.32
457 504 9.093970 TCTTTTGATCCACTATTATACGTGTTG 57.906 33.333 0.00 0.00 0.00 3.33
458 505 7.780008 TTTGATCCACTATTATACGTGTTGG 57.220 36.000 0.00 0.00 0.00 3.77
459 506 5.294356 TGATCCACTATTATACGTGTTGGC 58.706 41.667 0.00 0.00 0.00 4.52
461 508 6.265876 TGATCCACTATTATACGTGTTGGCTA 59.734 38.462 0.00 0.00 0.00 3.93
462 509 6.659745 TCCACTATTATACGTGTTGGCTAT 57.340 37.500 0.00 0.00 0.00 2.97
463 510 7.764141 TCCACTATTATACGTGTTGGCTATA 57.236 36.000 0.00 0.00 0.00 1.31
464 511 8.180706 TCCACTATTATACGTGTTGGCTATAA 57.819 34.615 0.00 0.00 0.00 0.98
465 512 8.640651 TCCACTATTATACGTGTTGGCTATAAA 58.359 33.333 0.00 0.00 0.00 1.40
466 513 9.263538 CCACTATTATACGTGTTGGCTATAAAA 57.736 33.333 0.00 0.00 0.00 1.52
471 518 8.951787 TTATACGTGTTGGCTATAAAATGAGT 57.048 30.769 0.00 0.00 0.00 3.41
472 519 5.545658 ACGTGTTGGCTATAAAATGAGTG 57.454 39.130 0.00 0.00 0.00 3.51
473 520 5.242434 ACGTGTTGGCTATAAAATGAGTGA 58.758 37.500 0.00 0.00 0.00 3.41
474 521 5.880332 ACGTGTTGGCTATAAAATGAGTGAT 59.120 36.000 0.00 0.00 0.00 3.06
475 522 7.045416 ACGTGTTGGCTATAAAATGAGTGATA 58.955 34.615 0.00 0.00 0.00 2.15
476 523 7.551262 ACGTGTTGGCTATAAAATGAGTGATAA 59.449 33.333 0.00 0.00 0.00 1.75
477 524 8.394877 CGTGTTGGCTATAAAATGAGTGATAAA 58.605 33.333 0.00 0.00 0.00 1.40
491 538 7.457024 TGAGTGATAAATGATATGGCATTGG 57.543 36.000 4.78 0.00 38.42 3.16
493 540 6.014647 AGTGATAAATGATATGGCATTGGCT 58.985 36.000 4.78 0.03 38.42 4.75
494 541 6.495872 AGTGATAAATGATATGGCATTGGCTT 59.504 34.615 4.78 7.77 38.42 4.35
495 542 7.670979 AGTGATAAATGATATGGCATTGGCTTA 59.329 33.333 4.78 9.79 38.42 3.09
496 543 8.472413 GTGATAAATGATATGGCATTGGCTTAT 58.528 33.333 15.67 15.67 38.42 1.73
497 544 9.697990 TGATAAATGATATGGCATTGGCTTATA 57.302 29.630 15.70 5.84 38.42 0.98
523 570 5.701290 CCAACAGCTGGCTATACTATTAACC 59.299 44.000 19.93 0.00 38.76 2.85
524 571 6.288294 CAACAGCTGGCTATACTATTAACCA 58.712 40.000 19.93 0.00 0.00 3.67
525 572 6.688073 ACAGCTGGCTATACTATTAACCAT 57.312 37.500 19.93 0.00 0.00 3.55
528 575 5.249393 AGCTGGCTATACTATTAACCATGCT 59.751 40.000 0.00 0.00 31.38 3.79
529 576 5.582665 GCTGGCTATACTATTAACCATGCTC 59.417 44.000 0.00 0.00 0.00 4.26
530 577 6.575254 GCTGGCTATACTATTAACCATGCTCT 60.575 42.308 0.00 0.00 0.00 4.09
531 578 7.363880 GCTGGCTATACTATTAACCATGCTCTA 60.364 40.741 0.00 0.00 0.00 2.43
620 2577 0.586802 GCGAGTGACCAAGGAAACAC 59.413 55.000 0.00 0.00 0.00 3.32
679 2636 3.356639 TTCTAGCAGCGCGTCCCTG 62.357 63.158 8.43 8.01 0.00 4.45
712 2669 2.019408 CACGTCACGCGACATCCAA 61.019 57.895 15.93 0.00 42.74 3.53
909 2871 1.040646 TGAGCTCGAGACAACCAACT 58.959 50.000 18.75 0.00 0.00 3.16
1050 3025 2.174876 CTCCCTGTCTCCCACCCTCT 62.175 65.000 0.00 0.00 0.00 3.69
1058 3033 4.101448 CCCACCCTCTTGCTCCCG 62.101 72.222 0.00 0.00 0.00 5.14
1538 3520 3.960755 CCATACTGATCACCACCAGAGTA 59.039 47.826 0.00 0.00 34.65 2.59
1539 3521 4.202161 CCATACTGATCACCACCAGAGTAC 60.202 50.000 0.00 0.00 34.65 2.73
1555 3537 5.417894 CCAGAGTACACATACTAGTTGGTCA 59.582 44.000 0.00 0.00 41.98 4.02
1663 3648 6.251801 CGTGTTGAATTCGGTGTAAAGTTTTT 59.748 34.615 0.04 0.00 0.00 1.94
1673 3658 4.636648 GGTGTAAAGTTTTTGTTTTGGGGG 59.363 41.667 0.00 0.00 0.00 5.40
1696 3681 1.942657 CTAGGCGTGGCGTACTAGTTA 59.057 52.381 0.00 0.00 34.52 2.24
1752 3737 7.420184 TTGTTGAATATATATGCCGTCAGTG 57.580 36.000 0.00 0.00 0.00 3.66
1825 3824 4.479786 TTAGGTTTTTGTGGCTGCTTTT 57.520 36.364 0.00 0.00 0.00 2.27
1832 3831 0.603707 TGTGGCTGCTTTTCTCGGAG 60.604 55.000 0.00 0.00 0.00 4.63
1833 3832 1.672356 TGGCTGCTTTTCTCGGAGC 60.672 57.895 0.00 0.00 43.97 4.70
1834 3833 1.376553 GGCTGCTTTTCTCGGAGCT 60.377 57.895 0.00 0.00 44.12 4.09
1835 3834 1.642952 GGCTGCTTTTCTCGGAGCTG 61.643 60.000 0.00 0.00 44.12 4.24
1836 3835 1.792941 CTGCTTTTCTCGGAGCTGC 59.207 57.895 0.00 0.00 39.60 5.25
1837 3836 0.952497 CTGCTTTTCTCGGAGCTGCA 60.952 55.000 5.91 6.95 39.60 4.41
1838 3837 0.952497 TGCTTTTCTCGGAGCTGCAG 60.952 55.000 10.11 10.11 39.60 4.41
1839 3838 1.792941 CTTTTCTCGGAGCTGCAGC 59.207 57.895 31.53 31.53 42.49 5.25
1990 4000 7.501559 TGGATCTCCTTGAATCTTTGATTCATC 59.498 37.037 19.47 13.86 37.79 2.92
1993 4003 7.859540 TCTCCTTGAATCTTTGATTCATCTCT 58.140 34.615 19.47 0.00 37.79 3.10
2047 4057 4.204012 CTGGGCTTTATTCGATGGGTTTA 58.796 43.478 0.00 0.00 0.00 2.01
2129 4139 1.600023 TGGATCTCCGTTTGCGTTTT 58.400 45.000 0.00 0.00 39.43 2.43
2164 4174 6.668323 AGTGATGTCTTTACGGTGATTTTTG 58.332 36.000 0.00 0.00 0.00 2.44
2177 4188 5.799936 CGGTGATTTTTGGTTGCTGTTATAG 59.200 40.000 0.00 0.00 0.00 1.31
2225 4236 0.101219 GTTCCATCAGCCGATTTGCC 59.899 55.000 0.00 0.00 0.00 4.52
2279 4293 1.079543 CTCGAACTCTGTGGCCCAG 60.080 63.158 13.43 13.43 42.97 4.45
2382 4401 6.165700 ACATTCCTTCAATCCCAATTATGC 57.834 37.500 0.00 0.00 0.00 3.14
2449 4472 5.015515 TGATGCCAAGTGATTGGTTCATAA 58.984 37.500 8.69 0.00 43.90 1.90
2514 4537 8.939201 ATAGGATATCAGATGCAAATAGAACG 57.061 34.615 4.83 0.00 0.00 3.95
2569 4592 0.108585 AGAAGAAGGGCGCTTTGTCA 59.891 50.000 17.99 0.00 0.00 3.58
2586 4609 7.483307 GCTTTGTCATAAATAATCTGGCTTCA 58.517 34.615 0.00 0.00 0.00 3.02
2841 4864 2.027745 AGATGATGCACGGAACTCAAGT 60.028 45.455 0.00 0.00 0.00 3.16
3049 5084 9.939802 ACCTTTCCTTTGTACAGTATACTTAAG 57.060 33.333 1.56 0.00 0.00 1.85
3683 5776 5.127682 GCTTCAAGAATATGGTCCATTTGGT 59.872 40.000 10.33 0.00 36.34 3.67
3894 5998 7.010339 AGGAGCAAATATACTTGTAGATCCC 57.990 40.000 0.00 0.00 0.00 3.85
4468 6750 0.389426 GCCCAACTGCTGCTCAATTG 60.389 55.000 0.00 0.00 32.12 2.32
4611 6893 6.035435 CAGTCTATGACTATGCACTGTCAAAC 59.965 42.308 22.08 19.22 44.81 2.93
4638 6920 5.427157 TGGGCTATATTATGAAATCCGCCTA 59.573 40.000 0.00 0.00 34.61 3.93
4658 6940 5.163784 GCCTATGCTTGTGCTATGTATGATG 60.164 44.000 0.00 0.00 40.48 3.07
4694 6976 7.828223 GGCTGGATGACATTATCTCTCATATTT 59.172 37.037 0.00 0.00 0.00 1.40
4740 7022 6.488683 TGGTGTCCTTTAATTTCTAACCACTG 59.511 38.462 0.00 0.00 30.48 3.66
4873 7155 3.793797 TCCTTCGATATCAACTCGCAA 57.206 42.857 3.12 0.00 36.11 4.85
5080 7363 1.133513 AGTTGTTTGCCATCACCTCCA 60.134 47.619 0.00 0.00 0.00 3.86
5129 7412 5.680619 CCAACTACAGCCCTATCAACAATA 58.319 41.667 0.00 0.00 0.00 1.90
5143 7426 5.685520 TCAACAATATGCTGTACCCTACA 57.314 39.130 0.00 0.00 37.13 2.74
5176 7459 1.194781 ATCTCACAGACCCGTGGCTT 61.195 55.000 0.00 0.00 37.50 4.35
5239 7522 7.912250 CCAAGAAGATTGTAGAAATTCCAATCG 59.088 37.037 14.68 5.33 45.69 3.34
5242 7525 9.838339 AGAAGATTGTAGAAATTCCAATCGTAT 57.162 29.630 14.68 9.31 45.69 3.06
5387 7679 4.154195 CCTCGTCCTTTGTACAAATTCAGG 59.846 45.833 20.83 17.77 0.00 3.86
5624 7917 3.687125 TCTGTATGTCACCGTCTTCTCT 58.313 45.455 0.00 0.00 0.00 3.10
5627 7920 2.638556 ATGTCACCGTCTTCTCTTCG 57.361 50.000 0.00 0.00 0.00 3.79
5729 8022 2.084546 GTCCCAGTGTCAGTATTTGCC 58.915 52.381 0.00 0.00 0.00 4.52
5754 8047 2.373169 TCCCAGACAAAGCTGAAGACAT 59.627 45.455 0.00 0.00 38.14 3.06
6140 8433 1.298859 GGTCCGTGAACATGTCCAGC 61.299 60.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.906660 TGATTCATGTTGTAATCACCTAAAAAC 57.093 29.630 3.99 0.00 37.23 2.43
20 21 8.900781 ACTAGATTTCCTGAAACATGATTCATG 58.099 33.333 22.22 22.22 46.18 3.07
21 22 9.471702 AACTAGATTTCCTGAAACATGATTCAT 57.528 29.630 17.56 3.90 38.55 2.57
22 23 8.868522 AACTAGATTTCCTGAAACATGATTCA 57.131 30.769 16.49 16.49 37.70 2.57
25 26 9.918630 CAAAAACTAGATTTCCTGAAACATGAT 57.081 29.630 0.00 0.00 32.51 2.45
26 27 9.130661 TCAAAAACTAGATTTCCTGAAACATGA 57.869 29.630 0.00 0.00 32.51 3.07
27 28 9.748708 TTCAAAAACTAGATTTCCTGAAACATG 57.251 29.630 9.09 0.00 32.84 3.21
28 29 9.750125 GTTCAAAAACTAGATTTCCTGAAACAT 57.250 29.630 11.83 0.00 35.44 2.71
29 30 8.744652 TGTTCAAAAACTAGATTTCCTGAAACA 58.255 29.630 11.83 10.19 35.44 2.83
30 31 9.581099 TTGTTCAAAAACTAGATTTCCTGAAAC 57.419 29.630 11.83 8.55 35.44 2.78
33 34 9.965824 GAATTGTTCAAAAACTAGATTTCCTGA 57.034 29.630 0.00 0.00 36.30 3.86
34 35 8.905702 CGAATTGTTCAAAAACTAGATTTCCTG 58.094 33.333 0.00 0.00 36.30 3.86
35 36 8.630037 ACGAATTGTTCAAAAACTAGATTTCCT 58.370 29.630 0.00 0.00 36.30 3.36
36 37 8.690840 CACGAATTGTTCAAAAACTAGATTTCC 58.309 33.333 0.00 0.00 36.30 3.13
37 38 8.207906 GCACGAATTGTTCAAAAACTAGATTTC 58.792 33.333 0.00 0.00 36.30 2.17
38 39 7.704472 TGCACGAATTGTTCAAAAACTAGATTT 59.296 29.630 0.00 0.00 36.30 2.17
39 40 7.199766 TGCACGAATTGTTCAAAAACTAGATT 58.800 30.769 0.00 0.00 36.30 2.40
40 41 6.734137 TGCACGAATTGTTCAAAAACTAGAT 58.266 32.000 0.00 0.00 36.30 1.98
41 42 6.125327 TGCACGAATTGTTCAAAAACTAGA 57.875 33.333 0.00 0.00 36.30 2.43
42 43 6.088085 GGATGCACGAATTGTTCAAAAACTAG 59.912 38.462 0.00 0.00 36.30 2.57
43 44 5.918011 GGATGCACGAATTGTTCAAAAACTA 59.082 36.000 0.00 0.00 36.30 2.24
44 45 4.744631 GGATGCACGAATTGTTCAAAAACT 59.255 37.500 0.00 0.00 36.30 2.66
45 46 4.505922 TGGATGCACGAATTGTTCAAAAAC 59.494 37.500 0.00 0.00 35.85 2.43
46 47 4.686972 TGGATGCACGAATTGTTCAAAAA 58.313 34.783 0.00 0.00 0.00 1.94
47 48 4.313277 TGGATGCACGAATTGTTCAAAA 57.687 36.364 0.00 0.00 0.00 2.44
48 49 3.998099 TGGATGCACGAATTGTTCAAA 57.002 38.095 0.00 0.00 0.00 2.69
49 50 3.998099 TTGGATGCACGAATTGTTCAA 57.002 38.095 0.00 0.00 0.00 2.69
50 51 3.067320 TGTTTGGATGCACGAATTGTTCA 59.933 39.130 0.00 0.00 0.00 3.18
51 52 3.637432 TGTTTGGATGCACGAATTGTTC 58.363 40.909 0.00 0.00 0.00 3.18
52 53 3.724508 TGTTTGGATGCACGAATTGTT 57.275 38.095 0.00 0.00 0.00 2.83
53 54 3.380142 GTTGTTTGGATGCACGAATTGT 58.620 40.909 0.00 0.00 0.00 2.71
54 55 2.730928 GGTTGTTTGGATGCACGAATTG 59.269 45.455 0.00 0.00 0.00 2.32
55 56 2.288763 GGGTTGTTTGGATGCACGAATT 60.289 45.455 0.00 0.00 0.00 2.17
56 57 1.272212 GGGTTGTTTGGATGCACGAAT 59.728 47.619 0.00 0.00 0.00 3.34
57 58 0.671251 GGGTTGTTTGGATGCACGAA 59.329 50.000 0.00 0.00 0.00 3.85
58 59 1.175983 GGGGTTGTTTGGATGCACGA 61.176 55.000 0.00 0.00 0.00 4.35
59 60 1.288752 GGGGTTGTTTGGATGCACG 59.711 57.895 0.00 0.00 0.00 5.34
60 61 0.755686 TTGGGGTTGTTTGGATGCAC 59.244 50.000 0.00 0.00 0.00 4.57
61 62 1.415659 CTTTGGGGTTGTTTGGATGCA 59.584 47.619 0.00 0.00 0.00 3.96
62 63 1.270785 CCTTTGGGGTTGTTTGGATGC 60.271 52.381 0.00 0.00 0.00 3.91
63 64 2.324541 TCCTTTGGGGTTGTTTGGATG 58.675 47.619 0.00 0.00 36.25 3.51
64 65 2.703536 GTTCCTTTGGGGTTGTTTGGAT 59.296 45.455 0.00 0.00 36.25 3.41
65 66 2.112190 GTTCCTTTGGGGTTGTTTGGA 58.888 47.619 0.00 0.00 36.25 3.53
66 67 1.834263 TGTTCCTTTGGGGTTGTTTGG 59.166 47.619 0.00 0.00 36.25 3.28
67 68 3.618690 TTGTTCCTTTGGGGTTGTTTG 57.381 42.857 0.00 0.00 36.25 2.93
68 69 5.212745 TCTATTGTTCCTTTGGGGTTGTTT 58.787 37.500 0.00 0.00 36.25 2.83
69 70 4.810345 TCTATTGTTCCTTTGGGGTTGTT 58.190 39.130 0.00 0.00 36.25 2.83
70 71 4.463050 TCTATTGTTCCTTTGGGGTTGT 57.537 40.909 0.00 0.00 36.25 3.32
71 72 4.586841 TGTTCTATTGTTCCTTTGGGGTTG 59.413 41.667 0.00 0.00 36.25 3.77
72 73 4.810345 TGTTCTATTGTTCCTTTGGGGTT 58.190 39.130 0.00 0.00 36.25 4.11
73 74 4.463050 TGTTCTATTGTTCCTTTGGGGT 57.537 40.909 0.00 0.00 36.25 4.95
74 75 5.304357 ACTTTGTTCTATTGTTCCTTTGGGG 59.696 40.000 0.00 0.00 0.00 4.96
75 76 6.405278 ACTTTGTTCTATTGTTCCTTTGGG 57.595 37.500 0.00 0.00 0.00 4.12
76 77 8.603181 CAAAACTTTGTTCTATTGTTCCTTTGG 58.397 33.333 0.00 0.00 33.59 3.28
77 78 9.364989 TCAAAACTTTGTTCTATTGTTCCTTTG 57.635 29.630 2.30 0.00 39.18 2.77
80 81 9.750125 GAATCAAAACTTTGTTCTATTGTTCCT 57.250 29.630 2.30 0.00 39.18 3.36
81 82 9.750125 AGAATCAAAACTTTGTTCTATTGTTCC 57.250 29.630 13.56 0.00 37.08 3.62
120 121 7.413657 CGAATCTCTAAAAGCCGGTTTAAATCA 60.414 37.037 3.14 0.00 0.00 2.57
121 122 6.905609 CGAATCTCTAAAAGCCGGTTTAAATC 59.094 38.462 3.14 0.00 0.00 2.17
146 147 3.057019 GCCTTCAAATTTGTTCGGAACC 58.943 45.455 17.47 1.39 0.00 3.62
150 151 2.470999 CGTTGCCTTCAAATTTGTTCGG 59.529 45.455 17.47 15.73 33.37 4.30
244 291 4.709397 AGTCAGCTCTATTGTACTTGCTCT 59.291 41.667 0.00 0.00 0.00 4.09
245 292 5.004922 AGTCAGCTCTATTGTACTTGCTC 57.995 43.478 0.00 0.00 0.00 4.26
246 293 4.464244 TGAGTCAGCTCTATTGTACTTGCT 59.536 41.667 0.00 0.00 42.13 3.91
247 294 4.748892 TGAGTCAGCTCTATTGTACTTGC 58.251 43.478 0.00 0.00 42.13 4.01
262 309 1.957177 TCTTATAGCCCGCTGAGTCAG 59.043 52.381 16.21 16.21 34.12 3.51
263 310 2.067365 TCTTATAGCCCGCTGAGTCA 57.933 50.000 0.00 0.00 0.00 3.41
264 311 3.454371 TTTCTTATAGCCCGCTGAGTC 57.546 47.619 0.00 0.00 0.00 3.36
265 312 5.546621 TTATTTCTTATAGCCCGCTGAGT 57.453 39.130 0.00 0.00 0.00 3.41
266 313 5.992217 AGTTTATTTCTTATAGCCCGCTGAG 59.008 40.000 0.00 0.00 0.00 3.35
267 314 5.925509 AGTTTATTTCTTATAGCCCGCTGA 58.074 37.500 0.00 0.00 0.00 4.26
268 315 6.929606 ACTAGTTTATTTCTTATAGCCCGCTG 59.070 38.462 0.00 0.00 0.00 5.18
269 316 7.063934 ACTAGTTTATTTCTTATAGCCCGCT 57.936 36.000 0.00 0.00 0.00 5.52
270 317 8.999220 ATACTAGTTTATTTCTTATAGCCCGC 57.001 34.615 0.00 0.00 0.00 6.13
313 360 6.905736 ACCTTCTCTCTCCTTTTCTCTTTTT 58.094 36.000 0.00 0.00 0.00 1.94
314 361 6.508030 ACCTTCTCTCTCCTTTTCTCTTTT 57.492 37.500 0.00 0.00 0.00 2.27
315 362 7.619512 TTACCTTCTCTCTCCTTTTCTCTTT 57.380 36.000 0.00 0.00 0.00 2.52
317 364 5.186992 GCTTACCTTCTCTCTCCTTTTCTCT 59.813 44.000 0.00 0.00 0.00 3.10
320 367 4.177783 CGCTTACCTTCTCTCTCCTTTTC 58.822 47.826 0.00 0.00 0.00 2.29
321 368 3.055747 CCGCTTACCTTCTCTCTCCTTTT 60.056 47.826 0.00 0.00 0.00 2.27
323 370 2.104170 CCGCTTACCTTCTCTCTCCTT 58.896 52.381 0.00 0.00 0.00 3.36
324 371 1.686741 CCCGCTTACCTTCTCTCTCCT 60.687 57.143 0.00 0.00 0.00 3.69
326 373 0.103390 GCCCGCTTACCTTCTCTCTC 59.897 60.000 0.00 0.00 0.00 3.20
327 374 0.324830 AGCCCGCTTACCTTCTCTCT 60.325 55.000 0.00 0.00 0.00 3.10
329 376 0.324830 AGAGCCCGCTTACCTTCTCT 60.325 55.000 0.00 0.00 0.00 3.10
330 377 0.537653 AAGAGCCCGCTTACCTTCTC 59.462 55.000 0.00 0.00 0.00 2.87
331 378 0.537653 GAAGAGCCCGCTTACCTTCT 59.462 55.000 8.59 0.00 32.72 2.85
332 379 0.806492 CGAAGAGCCCGCTTACCTTC 60.806 60.000 6.57 6.57 0.00 3.46
334 381 1.982938 ACGAAGAGCCCGCTTACCT 60.983 57.895 0.00 0.00 0.00 3.08
336 383 0.389426 TTCACGAAGAGCCCGCTTAC 60.389 55.000 0.00 0.00 0.00 2.34
337 384 0.108804 CTTCACGAAGAGCCCGCTTA 60.109 55.000 0.20 0.00 40.79 3.09
338 385 1.374758 CTTCACGAAGAGCCCGCTT 60.375 57.895 0.20 0.00 40.79 4.68
339 386 1.816863 TTCTTCACGAAGAGCCCGCT 61.817 55.000 9.32 0.00 46.80 5.52
344 391 0.793250 GCTGGTTCTTCACGAAGAGC 59.207 55.000 13.46 13.46 46.80 4.09
345 392 2.029470 AGAGCTGGTTCTTCACGAAGAG 60.029 50.000 9.32 0.42 46.80 2.85
346 393 1.964223 AGAGCTGGTTCTTCACGAAGA 59.036 47.619 5.38 5.38 44.94 2.87
347 394 2.447244 AGAGCTGGTTCTTCACGAAG 57.553 50.000 0.00 0.08 39.71 3.79
348 395 2.352814 GCTAGAGCTGGTTCTTCACGAA 60.353 50.000 0.00 0.00 38.21 3.85
349 396 1.202582 GCTAGAGCTGGTTCTTCACGA 59.797 52.381 0.00 0.00 38.21 4.35
350 397 1.067565 TGCTAGAGCTGGTTCTTCACG 60.068 52.381 2.72 0.00 42.66 4.35
351 398 2.751166 TGCTAGAGCTGGTTCTTCAC 57.249 50.000 2.72 0.00 42.66 3.18
352 399 4.741837 GCATATGCTAGAGCTGGTTCTTCA 60.742 45.833 20.64 0.00 42.66 3.02
353 400 3.745458 GCATATGCTAGAGCTGGTTCTTC 59.255 47.826 20.64 0.00 42.66 2.87
369 416 3.562973 CACAAAGTGCCTAGGAGCATATG 59.437 47.826 14.75 6.17 46.24 1.78
370 417 3.455910 TCACAAAGTGCCTAGGAGCATAT 59.544 43.478 14.75 0.00 46.24 1.78
371 418 2.837591 TCACAAAGTGCCTAGGAGCATA 59.162 45.455 14.75 0.00 46.24 3.14
372 419 1.630369 TCACAAAGTGCCTAGGAGCAT 59.370 47.619 14.75 0.00 46.24 3.79
374 421 1.276421 TCTCACAAAGTGCCTAGGAGC 59.724 52.381 14.75 3.68 32.98 4.70
375 422 3.685139 TTCTCACAAAGTGCCTAGGAG 57.315 47.619 14.75 0.00 32.98 3.69
378 425 5.947228 TTTCATTCTCACAAAGTGCCTAG 57.053 39.130 0.00 0.00 32.98 3.02
379 426 7.067372 CCATATTTCATTCTCACAAAGTGCCTA 59.933 37.037 0.00 0.00 32.98 3.93
380 427 6.127535 CCATATTTCATTCTCACAAAGTGCCT 60.128 38.462 0.00 0.00 32.98 4.75
381 428 6.038356 CCATATTTCATTCTCACAAAGTGCC 58.962 40.000 0.00 0.00 32.98 5.01
382 429 6.038356 CCCATATTTCATTCTCACAAAGTGC 58.962 40.000 0.00 0.00 32.98 4.40
383 430 6.038356 GCCCATATTTCATTCTCACAAAGTG 58.962 40.000 0.00 0.00 34.45 3.16
384 431 5.127682 GGCCCATATTTCATTCTCACAAAGT 59.872 40.000 0.00 0.00 0.00 2.66
386 433 5.022122 TGGCCCATATTTCATTCTCACAAA 58.978 37.500 0.00 0.00 0.00 2.83
387 434 4.402155 GTGGCCCATATTTCATTCTCACAA 59.598 41.667 0.00 0.00 0.00 3.33
388 435 3.953612 GTGGCCCATATTTCATTCTCACA 59.046 43.478 0.00 0.00 0.00 3.58
390 437 4.248174 TGTGGCCCATATTTCATTCTCA 57.752 40.909 0.00 0.00 0.00 3.27
391 438 6.899393 TTATGTGGCCCATATTTCATTCTC 57.101 37.500 12.88 0.00 35.96 2.87
392 439 8.954834 TTATTATGTGGCCCATATTTCATTCT 57.045 30.769 12.88 0.00 35.96 2.40
393 440 9.995003 TTTTATTATGTGGCCCATATTTCATTC 57.005 29.630 12.88 0.00 35.96 2.67
420 467 6.006449 AGTGGATCAAAAGAGTGCACTATTT 58.994 36.000 28.97 28.97 41.75 1.40
421 468 5.564550 AGTGGATCAAAAGAGTGCACTATT 58.435 37.500 21.73 21.16 41.75 1.73
422 469 5.171339 AGTGGATCAAAAGAGTGCACTAT 57.829 39.130 21.73 15.20 41.75 2.12
423 470 4.623932 AGTGGATCAAAAGAGTGCACTA 57.376 40.909 21.73 2.67 41.75 2.74
424 471 3.498774 AGTGGATCAAAAGAGTGCACT 57.501 42.857 21.88 21.88 39.30 4.40
426 473 7.438160 CGTATAATAGTGGATCAAAAGAGTGCA 59.562 37.037 0.00 0.00 0.00 4.57
429 476 8.475639 ACACGTATAATAGTGGATCAAAAGAGT 58.524 33.333 0.00 0.00 42.25 3.24
431 478 9.093970 CAACACGTATAATAGTGGATCAAAAGA 57.906 33.333 0.00 0.00 42.25 2.52
432 479 8.335356 CCAACACGTATAATAGTGGATCAAAAG 58.665 37.037 0.00 0.00 42.25 2.27
433 480 7.201661 GCCAACACGTATAATAGTGGATCAAAA 60.202 37.037 0.00 0.00 42.25 2.44
434 481 6.259167 GCCAACACGTATAATAGTGGATCAAA 59.741 38.462 0.00 0.00 42.25 2.69
435 482 5.756347 GCCAACACGTATAATAGTGGATCAA 59.244 40.000 0.00 0.00 42.25 2.57
436 483 5.069914 AGCCAACACGTATAATAGTGGATCA 59.930 40.000 0.00 0.00 42.25 2.92
437 484 5.539048 AGCCAACACGTATAATAGTGGATC 58.461 41.667 0.00 0.00 42.25 3.36
438 485 5.546621 AGCCAACACGTATAATAGTGGAT 57.453 39.130 0.00 0.00 42.25 3.41
445 492 9.555727 ACTCATTTTATAGCCAACACGTATAAT 57.444 29.630 0.00 0.00 0.00 1.28
446 493 8.822855 CACTCATTTTATAGCCAACACGTATAA 58.177 33.333 0.00 0.00 0.00 0.98
447 494 8.198778 TCACTCATTTTATAGCCAACACGTATA 58.801 33.333 0.00 0.00 0.00 1.47
448 495 7.045416 TCACTCATTTTATAGCCAACACGTAT 58.955 34.615 0.00 0.00 0.00 3.06
449 496 6.399743 TCACTCATTTTATAGCCAACACGTA 58.600 36.000 0.00 0.00 0.00 3.57
450 497 5.242434 TCACTCATTTTATAGCCAACACGT 58.758 37.500 0.00 0.00 0.00 4.49
464 511 9.923143 CAATGCCATATCATTTATCACTCATTT 57.077 29.630 0.00 0.00 34.68 2.32
465 512 8.528643 CCAATGCCATATCATTTATCACTCATT 58.471 33.333 0.00 0.00 34.68 2.57
466 513 7.363530 GCCAATGCCATATCATTTATCACTCAT 60.364 37.037 0.00 0.00 34.68 2.90
467 514 6.071784 GCCAATGCCATATCATTTATCACTCA 60.072 38.462 0.00 0.00 34.68 3.41
468 515 6.152323 AGCCAATGCCATATCATTTATCACTC 59.848 38.462 0.00 0.00 38.69 3.51
469 516 6.014647 AGCCAATGCCATATCATTTATCACT 58.985 36.000 0.00 0.00 38.69 3.41
471 518 6.921486 AAGCCAATGCCATATCATTTATCA 57.079 33.333 0.00 0.00 38.69 2.15
473 520 8.636213 GCTATAAGCCAATGCCATATCATTTAT 58.364 33.333 0.00 0.00 38.69 1.40
474 521 7.999679 GCTATAAGCCAATGCCATATCATTTA 58.000 34.615 0.00 0.00 38.69 1.40
475 522 6.870769 GCTATAAGCCAATGCCATATCATTT 58.129 36.000 0.00 0.00 38.69 2.32
476 523 6.461110 GCTATAAGCCAATGCCATATCATT 57.539 37.500 0.00 0.00 38.69 2.57
500 547 6.288294 TGGTTAATAGTATAGCCAGCTGTTG 58.712 40.000 13.81 0.00 32.02 3.33
501 548 6.494666 TGGTTAATAGTATAGCCAGCTGTT 57.505 37.500 13.81 2.90 32.02 3.16
502 549 6.467677 CATGGTTAATAGTATAGCCAGCTGT 58.532 40.000 13.81 0.00 39.18 4.40
505 552 5.491982 AGCATGGTTAATAGTATAGCCAGC 58.508 41.667 0.00 8.73 39.18 4.85
507 554 6.935240 AGAGCATGGTTAATAGTATAGCCA 57.065 37.500 0.00 3.65 39.96 4.75
514 561 9.712305 GTGATGTATTAGAGCATGGTTAATAGT 57.288 33.333 0.00 2.77 0.00 2.12
516 563 8.655901 TGGTGATGTATTAGAGCATGGTTAATA 58.344 33.333 0.00 7.07 0.00 0.98
517 564 7.517320 TGGTGATGTATTAGAGCATGGTTAAT 58.483 34.615 0.00 7.97 0.00 1.40
518 565 6.894682 TGGTGATGTATTAGAGCATGGTTAA 58.105 36.000 0.00 0.68 0.00 2.01
520 567 5.104360 ACTGGTGATGTATTAGAGCATGGTT 60.104 40.000 0.00 0.00 0.00 3.67
521 568 4.410228 ACTGGTGATGTATTAGAGCATGGT 59.590 41.667 0.00 0.00 0.00 3.55
523 570 4.212847 GCACTGGTGATGTATTAGAGCATG 59.787 45.833 4.79 0.00 0.00 4.06
524 571 4.102210 AGCACTGGTGATGTATTAGAGCAT 59.898 41.667 4.79 0.00 0.00 3.79
525 572 3.452264 AGCACTGGTGATGTATTAGAGCA 59.548 43.478 4.79 0.00 0.00 4.26
528 575 5.658634 AGAAGAGCACTGGTGATGTATTAGA 59.341 40.000 4.79 0.00 0.00 2.10
529 576 5.911752 AGAAGAGCACTGGTGATGTATTAG 58.088 41.667 4.79 0.00 0.00 1.73
530 577 5.939764 AGAAGAGCACTGGTGATGTATTA 57.060 39.130 4.79 0.00 0.00 0.98
531 578 4.833478 AGAAGAGCACTGGTGATGTATT 57.167 40.909 4.79 0.00 0.00 1.89
580 2536 3.570638 CTGCCGGCAGAGCGATTG 61.571 66.667 46.72 21.90 46.30 2.67
602 2558 0.859232 CGTGTTTCCTTGGTCACTCG 59.141 55.000 0.00 6.18 0.00 4.18
609 2565 2.548480 GGAAGAGTTCGTGTTTCCTTGG 59.452 50.000 0.00 0.00 36.88 3.61
620 2577 2.097038 CGGCTGCAGGAAGAGTTCG 61.097 63.158 17.12 0.00 0.00 3.95
704 2661 2.040544 CGGTGGTGGCTTGGATGTC 61.041 63.158 0.00 0.00 0.00 3.06
1034 3009 1.986413 CAAGAGGGTGGGAGACAGG 59.014 63.158 0.00 0.00 0.00 4.00
1058 3033 0.503117 GAAATGGCTATCGTCGTCGC 59.497 55.000 0.00 0.00 36.96 5.19
1250 3232 2.553765 CTTCTCCCCGTCTCTCCCGA 62.554 65.000 0.00 0.00 0.00 5.14
1257 3239 1.305381 CCTGTCCTTCTCCCCGTCT 60.305 63.158 0.00 0.00 0.00 4.18
1538 3520 5.331069 ACTACCTGACCAACTAGTATGTGT 58.669 41.667 0.00 0.00 0.00 3.72
1539 3521 5.916661 ACTACCTGACCAACTAGTATGTG 57.083 43.478 0.00 0.00 0.00 3.21
1555 3537 5.491982 CCAAACTCAGCAGATTAACTACCT 58.508 41.667 0.00 0.00 0.00 3.08
1663 3648 2.034999 CCTAGCGCCCCCAAAACA 59.965 61.111 2.29 0.00 0.00 2.83
1685 3670 3.852536 CAGCAGAACAGTAACTAGTACGC 59.147 47.826 0.00 0.00 37.81 4.42
1752 3737 0.831711 AACACCACCTCCAATTGCCC 60.832 55.000 0.00 0.00 0.00 5.36
1832 3831 2.228343 AGAGAAACATCAAAGCTGCAGC 59.772 45.455 31.53 31.53 42.49 5.25
1833 3832 3.366070 CCAGAGAAACATCAAAGCTGCAG 60.366 47.826 10.11 10.11 0.00 4.41
1834 3833 2.555325 CCAGAGAAACATCAAAGCTGCA 59.445 45.455 1.02 0.00 0.00 4.41
1835 3834 2.555757 ACCAGAGAAACATCAAAGCTGC 59.444 45.455 0.00 0.00 0.00 5.25
1836 3835 4.843220 AACCAGAGAAACATCAAAGCTG 57.157 40.909 0.00 0.00 0.00 4.24
1837 3836 5.221322 GGAAAACCAGAGAAACATCAAAGCT 60.221 40.000 0.00 0.00 0.00 3.74
1838 3837 4.984785 GGAAAACCAGAGAAACATCAAAGC 59.015 41.667 0.00 0.00 0.00 3.51
1839 3838 6.396829 AGGAAAACCAGAGAAACATCAAAG 57.603 37.500 0.00 0.00 0.00 2.77
1840 3839 5.301805 GGAGGAAAACCAGAGAAACATCAAA 59.698 40.000 0.00 0.00 0.00 2.69
1841 3840 4.827284 GGAGGAAAACCAGAGAAACATCAA 59.173 41.667 0.00 0.00 0.00 2.57
1842 3841 4.398319 GGAGGAAAACCAGAGAAACATCA 58.602 43.478 0.00 0.00 0.00 3.07
1923 3933 0.749454 GCAGCAGAATCCGGTTCCAT 60.749 55.000 0.00 0.00 37.56 3.41
2034 4044 4.522789 ACAGCAAAACTAAACCCATCGAAT 59.477 37.500 0.00 0.00 0.00 3.34
2047 4057 4.454678 TCATCTCTGTTGACAGCAAAACT 58.545 39.130 6.27 0.00 43.46 2.66
2129 4139 7.255569 CGTAAAGACATCACTAATCCAGTACA 58.744 38.462 0.00 0.00 34.98 2.90
2177 4188 7.376601 CCTTGAAAAATTAATGCAAACAACAGC 59.623 33.333 0.00 0.00 0.00 4.40
2188 4199 7.603404 TGATGGAACTGCCTTGAAAAATTAATG 59.397 33.333 0.00 0.00 37.63 1.90
2225 4236 9.297586 CACAATAACAAATTCCAGATGAGATTG 57.702 33.333 0.00 0.00 0.00 2.67
2311 4329 5.444663 AGAAGAAAAGGTCAACAAGCATC 57.555 39.130 0.00 0.00 0.00 3.91
2382 4401 9.232082 GCATTCTAGAGCTATCATATCTTAACG 57.768 37.037 0.00 0.00 0.00 3.18
2449 4472 3.376859 TCAAGTCAGTTGAAACGCACATT 59.623 39.130 0.00 0.00 42.49 2.71
2514 4537 2.546494 CCGAGAATCAATGGCCGGC 61.546 63.158 21.18 21.18 33.17 6.13
2586 4609 5.411781 GGTTCACACGATCTGTTATTCTCT 58.588 41.667 0.00 0.00 0.00 3.10
2841 4864 0.472471 GAGGAAGTGGGTGTGGTGAA 59.528 55.000 0.00 0.00 0.00 3.18
2913 4948 2.177016 ACTGCCTAACAACTTCCCCTTT 59.823 45.455 0.00 0.00 0.00 3.11
3049 5084 5.122239 TCACTGCATTACATTTAGAGTGCAC 59.878 40.000 9.40 9.40 37.63 4.57
3743 5836 0.685097 ACCTGTGCACTGTATTCCGT 59.315 50.000 19.41 6.81 0.00 4.69
3894 5998 3.979948 TGCAAGTTTGATGTCACCATTG 58.020 40.909 0.00 0.00 0.00 2.82
4468 6750 5.586643 GTCTTTCACCCAAGGATGTTCTATC 59.413 44.000 0.00 0.00 0.00 2.08
4611 6893 5.065218 GCGGATTTCATAATATAGCCCACTG 59.935 44.000 0.00 0.00 0.00 3.66
4617 6899 6.892691 GCATAGGCGGATTTCATAATATAGC 58.107 40.000 0.00 0.00 0.00 2.97
4638 6920 4.758674 GGTCATCATACATAGCACAAGCAT 59.241 41.667 0.00 0.00 45.49 3.79
4740 7022 7.327032 GCTTGTCTTTACCTGAAATTTGATCAC 59.673 37.037 0.00 0.00 0.00 3.06
4821 7103 3.070018 CTGGCACCACTAAGTTTCTCAG 58.930 50.000 0.00 0.00 0.00 3.35
4950 7233 6.096001 GCTGGACAAATCAGATTACCAGATTT 59.904 38.462 29.01 9.37 43.91 2.17
5129 7412 1.520666 GCCGTGTAGGGTACAGCAT 59.479 57.895 0.00 0.00 39.77 3.79
5143 7426 0.613260 TGAGATAGTTGCTTGGCCGT 59.387 50.000 0.00 0.00 0.00 5.68
5176 7459 0.183971 TTTTCTGGCGAGGGGTTTCA 59.816 50.000 0.00 0.00 0.00 2.69
5330 7618 1.223077 AGGGGAGATACATACAGGGCA 59.777 52.381 0.00 0.00 0.00 5.36
5509 7801 1.757118 CACCCGGCTTCTGAAGATAGA 59.243 52.381 21.06 0.00 0.00 1.98
5524 7817 4.766375 ACACCTTATCTGTAAATCACCCG 58.234 43.478 0.00 0.00 0.00 5.28
5525 7818 5.163652 GCAACACCTTATCTGTAAATCACCC 60.164 44.000 0.00 0.00 0.00 4.61
5624 7917 3.172106 TGGGGCCTTGGTGTCGAA 61.172 61.111 0.84 0.00 0.00 3.71
5627 7920 2.142292 ATCTGTGGGGCCTTGGTGTC 62.142 60.000 0.84 0.00 0.00 3.67
5706 7999 4.564821 GGCAAATACTGACACTGGGACTAA 60.565 45.833 0.00 0.00 30.79 2.24
5794 8087 3.270000 TCGACGGCGATGAACTCA 58.730 55.556 10.67 0.00 42.51 3.41
6002 8295 0.984230 AGAGGGACATCGCCTTCAAA 59.016 50.000 0.00 0.00 36.56 2.69
6056 8349 1.075601 AGAAGGTGGAGGCCATGAAA 58.924 50.000 5.01 0.00 35.28 2.69
6140 8433 2.608752 GGCAAAGACATGGCAAGAAGTG 60.609 50.000 0.00 0.00 44.66 3.16
6248 8541 4.473520 GCCTGCGCCAGCTTCCTA 62.474 66.667 4.18 0.00 45.42 2.94


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

AutoCloner maintained by Alex Coulton.