Multiple sequence alignment - TraesCS3A01G186900

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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 TraesCS3A01G186900 chr3A 100.000 2764 0 0 1 2764 221932515 221929752 0 5105
1 TraesCS3A01G186900 chr3B 91.893 2245 84 32 581 2764 257245373 257243166 0 3048
2 TraesCS3A01G186900 chr3B 98.458 389 6 0 1 389 35471996 35472384 0 686
3 TraesCS3A01G186900 chr3D 92.801 1667 58 16 451 2096 179169112 179167487 0 2357
4 TraesCS3A01G186900 chr3D 94.910 668 24 5 2098 2764 179167444 179166786 0 1037
5 TraesCS3A01G186900 chr5B 98.718 390 5 0 1 390 2635378 2635767 0 693
6 TraesCS3A01G186900 chrUn 98.458 389 6 0 1 389 302476525 302476913 0 686
7 TraesCS3A01G186900 chr6B 98.458 389 6 0 1 389 226664330 226664718 0 686
8 TraesCS3A01G186900 chr6A 98.458 389 6 0 1 389 52175425 52175813 0 686
9 TraesCS3A01G186900 chr5A 97.975 395 8 0 1 395 344330874 344330480 0 686
10 TraesCS3A01G186900 chr4A 98.458 389 6 0 1 389 574726750 574727138 0 686
11 TraesCS3A01G186900 chr2B 98.458 389 6 0 1 389 781191720 781191332 0 686
12 TraesCS3A01G186900 chr2A 97.975 395 8 0 1 395 593481562 593481168 0 686


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 TraesCS3A01G186900 chr3A 221929752 221932515 2763 True 5105 5105 100.0000 1 2764 1 chr3A.!!$R1 2763
1 TraesCS3A01G186900 chr3B 257243166 257245373 2207 True 3048 3048 91.8930 581 2764 1 chr3B.!!$R1 2183
2 TraesCS3A01G186900 chr3D 179166786 179169112 2326 True 1697 2357 93.8555 451 2764 2 chr3D.!!$R1 2313

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
267 268 0.028505 GCGATCGTAACCTAGCGTGA 59.971 55.0 17.81 0.0 0.0 4.35 F
403 404 0.109723 TAACACTGGGCTGGGTTGAC 59.890 55.0 8.48 0.0 0.0 3.18 F
417 418 0.310854 GTTGACGCCTGGGTTTTCTG 59.689 55.0 0.00 0.0 0.0 3.02 F
1351 1387 0.036732 TGTGTCCTGCAACCTGATCC 59.963 55.0 0.00 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 1362 0.463654 TCAGGTTGCAGGACACACAC 60.464 55.000 0.0 0.0 0.00 3.82 R
1330 1363 0.473755 ATCAGGTTGCAGGACACACA 59.526 50.000 0.0 0.0 0.00 3.72 R
1442 1478 2.281208 CCGTCGGCAAACCTGGAA 60.281 61.111 0.0 0.0 0.00 3.53 R
2598 2682 1.427592 GATGGCAGCTTGCGAGAGAC 61.428 60.000 4.7 0.0 46.21 3.36 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
31 32 2.504244 GGCGACGTGGAGAAGACG 60.504 66.667 0.11 0.00 42.62 4.18
32 33 2.504244 GCGACGTGGAGAAGACGG 60.504 66.667 0.11 0.00 41.21 4.79
33 34 2.974489 GCGACGTGGAGAAGACGGA 61.974 63.158 0.11 0.00 41.21 4.69
34 35 1.134901 CGACGTGGAGAAGACGGAG 59.865 63.158 0.00 0.00 41.21 4.63
35 36 1.153997 GACGTGGAGAAGACGGAGC 60.154 63.158 0.00 0.00 41.21 4.70
36 37 2.182030 CGTGGAGAAGACGGAGCC 59.818 66.667 0.00 0.00 33.08 4.70
37 38 2.182030 GTGGAGAAGACGGAGCCG 59.818 66.667 7.48 7.48 46.03 5.52
38 39 2.035155 TGGAGAAGACGGAGCCGA 59.965 61.111 16.83 0.00 42.83 5.54
39 40 1.379977 TGGAGAAGACGGAGCCGAT 60.380 57.895 16.83 0.54 42.83 4.18
40 41 1.066587 GGAGAAGACGGAGCCGATG 59.933 63.158 16.83 0.00 42.83 3.84
41 42 1.590259 GAGAAGACGGAGCCGATGC 60.590 63.158 16.83 2.40 42.83 3.91
51 52 2.514824 GCCGATGCTCCTTGTCCC 60.515 66.667 0.00 0.00 33.53 4.46
52 53 2.202932 CCGATGCTCCTTGTCCCG 60.203 66.667 0.00 0.00 0.00 5.14
53 54 2.721167 CCGATGCTCCTTGTCCCGA 61.721 63.158 0.00 0.00 0.00 5.14
54 55 1.443407 CGATGCTCCTTGTCCCGAT 59.557 57.895 0.00 0.00 0.00 4.18
55 56 0.598680 CGATGCTCCTTGTCCCGATC 60.599 60.000 0.00 0.00 0.00 3.69
56 57 0.598680 GATGCTCCTTGTCCCGATCG 60.599 60.000 8.51 8.51 0.00 3.69
57 58 2.032860 ATGCTCCTTGTCCCGATCGG 62.033 60.000 27.65 27.65 0.00 4.18
58 59 2.423898 GCTCCTTGTCCCGATCGGA 61.424 63.158 35.42 18.23 38.83 4.55
59 60 1.736586 CTCCTTGTCCCGATCGGAG 59.263 63.158 35.42 22.97 43.19 4.63
60 61 2.107141 CCTTGTCCCGATCGGAGC 59.893 66.667 35.42 25.06 43.19 4.70
61 62 2.107141 CTTGTCCCGATCGGAGCC 59.893 66.667 35.42 21.03 43.19 4.70
62 63 3.774959 CTTGTCCCGATCGGAGCCG 62.775 68.421 35.42 18.37 43.19 5.52
65 66 4.826404 TCCCGATCGGAGCCGGAA 62.826 66.667 35.42 8.40 43.80 4.30
66 67 4.587189 CCCGATCGGAGCCGGAAC 62.587 72.222 35.42 0.00 43.80 3.62
67 68 4.925576 CCGATCGGAGCCGGAACG 62.926 72.222 30.62 6.00 46.16 3.95
85 86 4.933064 GAGACGGCATCGAGCGGG 62.933 72.222 15.12 7.01 46.82 6.13
87 88 4.933064 GACGGCATCGAGCGGGAG 62.933 72.222 15.12 4.89 46.82 4.30
91 92 2.892425 GCATCGAGCGGGAGGTTG 60.892 66.667 0.00 0.00 43.00 3.77
94 95 3.760035 TCGAGCGGGAGGTTGAGC 61.760 66.667 0.00 0.00 45.22 4.26
95 96 4.069232 CGAGCGGGAGGTTGAGCA 62.069 66.667 0.00 0.00 44.43 4.26
96 97 2.125350 GAGCGGGAGGTTGAGCAG 60.125 66.667 0.00 0.00 43.00 4.24
97 98 2.604686 AGCGGGAGGTTGAGCAGA 60.605 61.111 0.00 0.00 37.18 4.26
98 99 2.125350 GCGGGAGGTTGAGCAGAG 60.125 66.667 0.00 0.00 0.00 3.35
99 100 2.125350 CGGGAGGTTGAGCAGAGC 60.125 66.667 0.00 0.00 0.00 4.09
100 101 2.270527 GGGAGGTTGAGCAGAGCC 59.729 66.667 0.00 0.00 0.00 4.70
101 102 2.125350 GGAGGTTGAGCAGAGCCG 60.125 66.667 0.00 0.00 0.00 5.52
102 103 2.817396 GAGGTTGAGCAGAGCCGC 60.817 66.667 0.00 0.00 0.00 6.53
103 104 3.596066 GAGGTTGAGCAGAGCCGCA 62.596 63.158 0.00 0.00 0.00 5.69
104 105 2.669569 GGTTGAGCAGAGCCGCAA 60.670 61.111 0.00 0.00 0.00 4.85
105 106 2.684843 GGTTGAGCAGAGCCGCAAG 61.685 63.158 0.00 0.00 0.00 4.01
106 107 1.669115 GTTGAGCAGAGCCGCAAGA 60.669 57.895 0.00 0.00 43.02 3.02
107 108 1.375140 TTGAGCAGAGCCGCAAGAG 60.375 57.895 0.00 0.00 43.02 2.85
108 109 1.820010 TTGAGCAGAGCCGCAAGAGA 61.820 55.000 0.00 0.00 43.02 3.10
109 110 1.519013 GAGCAGAGCCGCAAGAGAG 60.519 63.158 0.00 0.00 43.02 3.20
110 111 2.511145 GCAGAGCCGCAAGAGAGG 60.511 66.667 0.00 0.00 43.02 3.69
117 118 4.521062 CGCAAGAGAGGCCGGGAG 62.521 72.222 2.18 0.00 43.02 4.30
141 142 4.988598 CGCAGCAGTGGAACCGGT 62.989 66.667 0.00 0.00 37.80 5.28
142 143 3.357079 GCAGCAGTGGAACCGGTG 61.357 66.667 8.52 0.00 37.80 4.94
143 144 2.669569 CAGCAGTGGAACCGGTGG 60.670 66.667 8.52 0.00 37.80 4.61
144 145 3.168528 AGCAGTGGAACCGGTGGT 61.169 61.111 8.52 0.00 37.80 4.16
145 146 2.978010 GCAGTGGAACCGGTGGTG 60.978 66.667 8.52 2.41 37.80 4.17
146 147 2.281484 CAGTGGAACCGGTGGTGG 60.281 66.667 8.52 0.00 37.80 4.61
147 148 4.265056 AGTGGAACCGGTGGTGGC 62.265 66.667 8.52 0.00 37.80 5.01
230 231 4.825252 GGCGACGGTGCGGGTATT 62.825 66.667 0.00 0.00 35.06 1.89
231 232 2.104729 GCGACGGTGCGGGTATTA 59.895 61.111 0.00 0.00 0.00 0.98
232 233 1.519013 GCGACGGTGCGGGTATTAA 60.519 57.895 0.00 0.00 0.00 1.40
233 234 1.485032 GCGACGGTGCGGGTATTAAG 61.485 60.000 0.00 0.00 0.00 1.85
234 235 0.872881 CGACGGTGCGGGTATTAAGG 60.873 60.000 0.00 0.00 0.00 2.69
235 236 0.176449 GACGGTGCGGGTATTAAGGT 59.824 55.000 0.00 0.00 0.00 3.50
236 237 0.614812 ACGGTGCGGGTATTAAGGTT 59.385 50.000 0.00 0.00 0.00 3.50
237 238 1.003464 ACGGTGCGGGTATTAAGGTTT 59.997 47.619 0.00 0.00 0.00 3.27
238 239 2.235898 ACGGTGCGGGTATTAAGGTTTA 59.764 45.455 0.00 0.00 0.00 2.01
239 240 2.867975 CGGTGCGGGTATTAAGGTTTAG 59.132 50.000 0.00 0.00 0.00 1.85
240 241 3.430651 CGGTGCGGGTATTAAGGTTTAGA 60.431 47.826 0.00 0.00 0.00 2.10
241 242 4.516323 GGTGCGGGTATTAAGGTTTAGAA 58.484 43.478 0.00 0.00 0.00 2.10
242 243 4.573607 GGTGCGGGTATTAAGGTTTAGAAG 59.426 45.833 0.00 0.00 0.00 2.85
243 244 4.034858 GTGCGGGTATTAAGGTTTAGAAGC 59.965 45.833 0.00 0.00 0.00 3.86
244 245 3.246936 GCGGGTATTAAGGTTTAGAAGCG 59.753 47.826 0.00 0.00 0.00 4.68
245 246 3.805971 CGGGTATTAAGGTTTAGAAGCGG 59.194 47.826 0.00 0.00 0.00 5.52
246 247 4.441913 CGGGTATTAAGGTTTAGAAGCGGA 60.442 45.833 0.00 0.00 0.00 5.54
247 248 5.430886 GGGTATTAAGGTTTAGAAGCGGAA 58.569 41.667 0.00 0.00 0.00 4.30
248 249 5.526479 GGGTATTAAGGTTTAGAAGCGGAAG 59.474 44.000 0.00 0.00 0.00 3.46
262 263 2.033793 CGGAAGCGATCGTAACCTAG 57.966 55.000 17.81 2.69 0.00 3.02
263 264 1.768510 GGAAGCGATCGTAACCTAGC 58.231 55.000 17.81 0.00 0.00 3.42
264 265 1.396644 GAAGCGATCGTAACCTAGCG 58.603 55.000 17.81 0.00 0.00 4.26
265 266 0.737219 AAGCGATCGTAACCTAGCGT 59.263 50.000 17.81 0.00 0.00 5.07
266 267 0.029035 AGCGATCGTAACCTAGCGTG 59.971 55.000 17.81 0.00 0.00 5.34
267 268 0.028505 GCGATCGTAACCTAGCGTGA 59.971 55.000 17.81 0.00 0.00 4.35
268 269 1.334779 GCGATCGTAACCTAGCGTGAT 60.335 52.381 17.81 0.00 0.00 3.06
269 270 2.096069 GCGATCGTAACCTAGCGTGATA 60.096 50.000 17.81 0.00 0.00 2.15
270 271 3.477122 CGATCGTAACCTAGCGTGATAC 58.523 50.000 7.03 0.00 0.00 2.24
271 272 3.666374 CGATCGTAACCTAGCGTGATACC 60.666 52.174 7.03 0.00 0.00 2.73
272 273 2.642427 TCGTAACCTAGCGTGATACCA 58.358 47.619 0.00 0.00 0.00 3.25
273 274 3.216800 TCGTAACCTAGCGTGATACCAT 58.783 45.455 0.00 0.00 0.00 3.55
274 275 3.004002 TCGTAACCTAGCGTGATACCATG 59.996 47.826 0.00 0.00 0.00 3.66
275 276 3.243301 CGTAACCTAGCGTGATACCATGT 60.243 47.826 0.00 0.00 0.00 3.21
276 277 4.023792 CGTAACCTAGCGTGATACCATGTA 60.024 45.833 0.00 0.00 0.00 2.29
277 278 5.506151 CGTAACCTAGCGTGATACCATGTAA 60.506 44.000 0.00 0.00 0.00 2.41
278 279 4.585955 ACCTAGCGTGATACCATGTAAG 57.414 45.455 0.00 0.00 0.00 2.34
279 280 4.212716 ACCTAGCGTGATACCATGTAAGA 58.787 43.478 0.00 0.00 0.00 2.10
280 281 4.037684 ACCTAGCGTGATACCATGTAAGAC 59.962 45.833 0.00 0.00 0.00 3.01
281 282 4.037565 CCTAGCGTGATACCATGTAAGACA 59.962 45.833 0.00 0.00 0.00 3.41
282 283 4.465632 AGCGTGATACCATGTAAGACAA 57.534 40.909 0.00 0.00 0.00 3.18
283 284 5.023533 AGCGTGATACCATGTAAGACAAT 57.976 39.130 0.00 0.00 0.00 2.71
284 285 6.156748 AGCGTGATACCATGTAAGACAATA 57.843 37.500 0.00 0.00 0.00 1.90
285 286 6.578944 AGCGTGATACCATGTAAGACAATAA 58.421 36.000 0.00 0.00 0.00 1.40
286 287 6.701841 AGCGTGATACCATGTAAGACAATAAG 59.298 38.462 0.00 0.00 0.00 1.73
287 288 6.479001 GCGTGATACCATGTAAGACAATAAGT 59.521 38.462 0.00 0.00 0.00 2.24
288 289 7.011109 GCGTGATACCATGTAAGACAATAAGTT 59.989 37.037 0.00 0.00 0.00 2.66
289 290 8.879759 CGTGATACCATGTAAGACAATAAGTTT 58.120 33.333 0.00 0.00 0.00 2.66
293 294 7.227049 ACCATGTAAGACAATAAGTTTTGGG 57.773 36.000 0.00 0.00 0.00 4.12
294 295 7.007723 ACCATGTAAGACAATAAGTTTTGGGA 58.992 34.615 0.00 0.00 0.00 4.37
295 296 7.507616 ACCATGTAAGACAATAAGTTTTGGGAA 59.492 33.333 0.00 0.00 0.00 3.97
296 297 7.812669 CCATGTAAGACAATAAGTTTTGGGAAC 59.187 37.037 0.00 0.00 0.00 3.62
309 310 4.081050 GGAACCAGCACAACCCTC 57.919 61.111 0.00 0.00 0.00 4.30
310 311 1.456287 GGAACCAGCACAACCCTCT 59.544 57.895 0.00 0.00 0.00 3.69
311 312 0.690762 GGAACCAGCACAACCCTCTA 59.309 55.000 0.00 0.00 0.00 2.43
312 313 1.339151 GGAACCAGCACAACCCTCTAG 60.339 57.143 0.00 0.00 0.00 2.43
313 314 0.693049 AACCAGCACAACCCTCTAGG 59.307 55.000 0.00 0.00 43.78 3.02
325 326 2.407340 CCTCTAGGGGTGGCTTATCT 57.593 55.000 0.00 0.00 0.00 1.98
326 327 2.252714 CCTCTAGGGGTGGCTTATCTC 58.747 57.143 0.00 0.00 0.00 2.75
327 328 2.426414 CCTCTAGGGGTGGCTTATCTCA 60.426 54.545 0.00 0.00 0.00 3.27
328 329 3.515562 CTCTAGGGGTGGCTTATCTCAT 58.484 50.000 0.00 0.00 0.00 2.90
329 330 3.906846 CTCTAGGGGTGGCTTATCTCATT 59.093 47.826 0.00 0.00 0.00 2.57
330 331 5.087323 CTCTAGGGGTGGCTTATCTCATTA 58.913 45.833 0.00 0.00 0.00 1.90
331 332 5.665701 TCTAGGGGTGGCTTATCTCATTAT 58.334 41.667 0.00 0.00 0.00 1.28
332 333 6.811574 TCTAGGGGTGGCTTATCTCATTATA 58.188 40.000 0.00 0.00 0.00 0.98
333 334 7.430844 TCTAGGGGTGGCTTATCTCATTATAT 58.569 38.462 0.00 0.00 0.00 0.86
334 335 8.574853 TCTAGGGGTGGCTTATCTCATTATATA 58.425 37.037 0.00 0.00 0.00 0.86
335 336 9.386122 CTAGGGGTGGCTTATCTCATTATATAT 57.614 37.037 0.00 0.00 0.00 0.86
337 338 9.744125 AGGGGTGGCTTATCTCATTATATATAA 57.256 33.333 7.62 7.62 0.00 0.98
359 360 8.774890 ATAATGGTTGTGTTACAATACGTACA 57.225 30.769 0.00 0.00 40.59 2.90
360 361 7.675962 AATGGTTGTGTTACAATACGTACAT 57.324 32.000 0.00 0.00 40.59 2.29
361 362 8.774890 AATGGTTGTGTTACAATACGTACATA 57.225 30.769 0.00 0.00 40.59 2.29
362 363 7.815398 TGGTTGTGTTACAATACGTACATAG 57.185 36.000 0.00 0.00 40.59 2.23
363 364 7.377398 TGGTTGTGTTACAATACGTACATAGT 58.623 34.615 0.00 0.00 40.59 2.12
364 365 7.871973 TGGTTGTGTTACAATACGTACATAGTT 59.128 33.333 0.00 0.00 40.59 2.24
365 366 9.352784 GGTTGTGTTACAATACGTACATAGTTA 57.647 33.333 0.00 0.00 40.59 2.24
367 368 9.905171 TTGTGTTACAATACGTACATAGTTACA 57.095 29.630 0.00 2.19 32.34 2.41
368 369 9.905171 TGTGTTACAATACGTACATAGTTACAA 57.095 29.630 0.00 0.00 0.00 2.41
393 394 9.886132 AAAAGTTATACATAGTCTAACACTGGG 57.114 33.333 7.77 0.00 36.43 4.45
394 395 7.052142 AGTTATACATAGTCTAACACTGGGC 57.948 40.000 7.77 0.00 36.43 5.36
395 396 6.839657 AGTTATACATAGTCTAACACTGGGCT 59.160 38.462 7.77 0.00 36.43 5.19
396 397 3.895232 ACATAGTCTAACACTGGGCTG 57.105 47.619 0.00 0.00 36.43 4.85
397 398 2.501723 ACATAGTCTAACACTGGGCTGG 59.498 50.000 0.00 0.00 36.43 4.85
398 399 1.568504 TAGTCTAACACTGGGCTGGG 58.431 55.000 0.00 0.00 36.43 4.45
399 400 0.473886 AGTCTAACACTGGGCTGGGT 60.474 55.000 0.00 0.00 32.26 4.51
400 401 0.400594 GTCTAACACTGGGCTGGGTT 59.599 55.000 4.39 4.39 0.00 4.11
401 402 0.400213 TCTAACACTGGGCTGGGTTG 59.600 55.000 8.48 1.15 0.00 3.77
402 403 0.400213 CTAACACTGGGCTGGGTTGA 59.600 55.000 8.48 0.00 0.00 3.18
403 404 0.109723 TAACACTGGGCTGGGTTGAC 59.890 55.000 8.48 0.00 0.00 3.18
404 405 2.669569 CACTGGGCTGGGTTGACG 60.670 66.667 0.00 0.00 0.00 4.35
405 406 4.643387 ACTGGGCTGGGTTGACGC 62.643 66.667 0.00 0.00 0.00 5.19
411 412 3.953775 CTGGGTTGACGCCTGGGT 61.954 66.667 0.00 0.00 0.00 4.51
412 413 3.491598 CTGGGTTGACGCCTGGGTT 62.492 63.158 0.00 0.00 0.00 4.11
413 414 2.203437 GGGTTGACGCCTGGGTTT 60.203 61.111 0.00 0.00 0.00 3.27
414 415 1.830847 GGGTTGACGCCTGGGTTTT 60.831 57.895 0.00 0.00 0.00 2.43
415 416 1.658114 GGTTGACGCCTGGGTTTTC 59.342 57.895 0.00 0.00 0.00 2.29
416 417 0.822121 GGTTGACGCCTGGGTTTTCT 60.822 55.000 0.00 0.00 0.00 2.52
417 418 0.310854 GTTGACGCCTGGGTTTTCTG 59.689 55.000 0.00 0.00 0.00 3.02
418 419 1.452145 TTGACGCCTGGGTTTTCTGC 61.452 55.000 0.00 0.00 0.00 4.26
419 420 1.600916 GACGCCTGGGTTTTCTGCT 60.601 57.895 0.00 0.00 0.00 4.24
420 421 0.321298 GACGCCTGGGTTTTCTGCTA 60.321 55.000 0.00 0.00 0.00 3.49
421 422 0.328258 ACGCCTGGGTTTTCTGCTAT 59.672 50.000 0.00 0.00 0.00 2.97
422 423 0.734889 CGCCTGGGTTTTCTGCTATG 59.265 55.000 0.00 0.00 0.00 2.23
423 424 1.106285 GCCTGGGTTTTCTGCTATGG 58.894 55.000 0.00 0.00 0.00 2.74
424 425 1.767759 CCTGGGTTTTCTGCTATGGG 58.232 55.000 0.00 0.00 0.00 4.00
425 426 1.106285 CTGGGTTTTCTGCTATGGGC 58.894 55.000 0.00 0.00 42.22 5.36
426 427 0.704076 TGGGTTTTCTGCTATGGGCT 59.296 50.000 0.00 0.00 42.39 5.19
427 428 1.077005 TGGGTTTTCTGCTATGGGCTT 59.923 47.619 0.00 0.00 42.39 4.35
428 429 2.179427 GGGTTTTCTGCTATGGGCTTT 58.821 47.619 0.00 0.00 42.39 3.51
429 430 2.094026 GGGTTTTCTGCTATGGGCTTTG 60.094 50.000 0.00 0.00 42.39 2.77
430 431 2.562738 GGTTTTCTGCTATGGGCTTTGT 59.437 45.455 0.00 0.00 42.39 2.83
431 432 3.006859 GGTTTTCTGCTATGGGCTTTGTT 59.993 43.478 0.00 0.00 42.39 2.83
432 433 4.219725 GGTTTTCTGCTATGGGCTTTGTTA 59.780 41.667 0.00 0.00 42.39 2.41
433 434 5.402398 GTTTTCTGCTATGGGCTTTGTTAG 58.598 41.667 0.00 0.00 42.39 2.34
434 435 3.281727 TCTGCTATGGGCTTTGTTAGG 57.718 47.619 0.00 0.00 42.39 2.69
440 441 3.449227 GGCTTTGTTAGGCCCGGC 61.449 66.667 0.00 0.00 43.40 6.13
492 493 2.799371 CTCGTGGCGTAGGAGTCC 59.201 66.667 0.00 0.00 36.72 3.85
493 494 1.749638 CTCGTGGCGTAGGAGTCCT 60.750 63.158 17.78 17.78 36.72 3.85
494 495 0.463295 CTCGTGGCGTAGGAGTCCTA 60.463 60.000 15.33 15.33 36.72 2.94
500 501 3.429925 GTAGGAGTCCTACGCCGG 58.570 66.667 29.21 0.00 45.49 6.13
523 524 2.903284 GCGTCTACGGGAAACACAA 58.097 52.632 4.49 0.00 40.23 3.33
557 558 2.180017 CGTAGACACGTTCCCCGG 59.820 66.667 0.00 0.00 43.31 5.73
606 607 2.603652 CCAACCGAACCGTTTGAACATC 60.604 50.000 0.00 0.00 0.00 3.06
621 622 1.584724 ACATCCTCCCCGTCTTCAAT 58.415 50.000 0.00 0.00 0.00 2.57
624 630 1.651737 TCCTCCCCGTCTTCAATTCA 58.348 50.000 0.00 0.00 0.00 2.57
668 674 2.706890 TCCAAGGTAATCAGCGGAAAC 58.293 47.619 0.00 0.00 0.00 2.78
680 686 3.527434 CGGAAACTAAACCGCCTCT 57.473 52.632 0.00 0.00 42.55 3.69
771 781 1.581147 CGAGCGGAATTCAAAGCGC 60.581 57.895 16.06 16.06 34.34 5.92
778 788 1.606606 GAATTCAAAGCGCGGTCAAG 58.393 50.000 12.91 4.61 0.00 3.02
796 806 0.554792 AGCCTCCATCATCAAAGGGG 59.445 55.000 0.00 0.00 0.00 4.79
847 857 2.902423 AAAACCACACGCCTGGAGCA 62.902 55.000 5.97 0.00 44.04 4.26
1037 1070 1.201429 GGTTCCTCCTCCAAGCCTGA 61.201 60.000 0.00 0.00 0.00 3.86
1084 1117 1.368345 CCTTGCATTCGTCGCCATCA 61.368 55.000 0.00 0.00 0.00 3.07
1086 1119 1.643868 TTGCATTCGTCGCCATCACC 61.644 55.000 0.00 0.00 0.00 4.02
1255 1288 5.165961 TCTCATCGTTTCTTCCATTTCCT 57.834 39.130 0.00 0.00 0.00 3.36
1256 1289 4.937620 TCTCATCGTTTCTTCCATTTCCTG 59.062 41.667 0.00 0.00 0.00 3.86
1257 1290 3.440173 TCATCGTTTCTTCCATTTCCTGC 59.560 43.478 0.00 0.00 0.00 4.85
1258 1291 2.159382 TCGTTTCTTCCATTTCCTGCC 58.841 47.619 0.00 0.00 0.00 4.85
1259 1292 1.885887 CGTTTCTTCCATTTCCTGCCA 59.114 47.619 0.00 0.00 0.00 4.92
1260 1293 2.351738 CGTTTCTTCCATTTCCTGCCAC 60.352 50.000 0.00 0.00 0.00 5.01
1261 1294 2.627699 GTTTCTTCCATTTCCTGCCACA 59.372 45.455 0.00 0.00 0.00 4.17
1262 1295 1.909700 TCTTCCATTTCCTGCCACAC 58.090 50.000 0.00 0.00 0.00 3.82
1263 1296 1.144708 TCTTCCATTTCCTGCCACACA 59.855 47.619 0.00 0.00 0.00 3.72
1264 1297 1.962807 CTTCCATTTCCTGCCACACAA 59.037 47.619 0.00 0.00 0.00 3.33
1265 1298 2.307496 TCCATTTCCTGCCACACAAT 57.693 45.000 0.00 0.00 0.00 2.71
1266 1299 2.607499 TCCATTTCCTGCCACACAATT 58.393 42.857 0.00 0.00 0.00 2.32
1267 1300 3.772387 TCCATTTCCTGCCACACAATTA 58.228 40.909 0.00 0.00 0.00 1.40
1268 1301 3.509575 TCCATTTCCTGCCACACAATTAC 59.490 43.478 0.00 0.00 0.00 1.89
1269 1302 3.368323 CCATTTCCTGCCACACAATTACC 60.368 47.826 0.00 0.00 0.00 2.85
1291 1324 1.817911 TACCATGTCACCAACGGCGA 61.818 55.000 16.62 0.00 0.00 5.54
1315 1348 4.025563 GCGTACTTGTGTTGTGTGTGATTA 60.026 41.667 0.00 0.00 0.00 1.75
1316 1349 5.428770 CGTACTTGTGTTGTGTGTGATTAC 58.571 41.667 0.00 0.00 0.00 1.89
1330 1363 2.244695 TGATTACTCACAGGGTCGTGT 58.755 47.619 0.00 0.00 38.12 4.49
1351 1387 0.036732 TGTGTCCTGCAACCTGATCC 59.963 55.000 0.00 0.00 0.00 3.36
1353 1389 0.325933 TGTCCTGCAACCTGATCCTG 59.674 55.000 0.00 0.00 0.00 3.86
1451 1487 1.858505 GGACCCCCTTTCCAGGTTT 59.141 57.895 0.00 0.00 38.79 3.27
1780 1816 5.473931 TCAGTGATCAGTTTGCTCTTCTAC 58.526 41.667 0.00 0.00 0.00 2.59
1852 1888 4.080129 AGAGTTCATCCGGTGGTACTAGTA 60.080 45.833 0.00 0.00 0.00 1.82
1941 1981 4.655762 TTCTTCGATCCCTATGACTGTG 57.344 45.455 0.00 0.00 0.00 3.66
1951 1991 5.741011 TCCCTATGACTGTGTTTGGATTAC 58.259 41.667 0.00 0.00 0.00 1.89
1985 2026 7.187824 AGTAGTATTCCTTGAATCTTCTGCA 57.812 36.000 0.00 0.00 33.95 4.41
1990 2031 4.090761 TCCTTGAATCTTCTGCAAGTGT 57.909 40.909 0.00 0.00 37.82 3.55
2035 2077 7.972832 ACTTTTCGAGTTTACATCAATGGTA 57.027 32.000 0.00 0.00 33.92 3.25
2036 2078 7.803724 ACTTTTCGAGTTTACATCAATGGTAC 58.196 34.615 0.00 0.00 33.92 3.34
2080 2122 6.643770 TCGGTGAACATAACTGAAAAGACTAC 59.356 38.462 0.00 0.00 29.97 2.73
2100 2183 9.871238 AGACTACAAATTGATACGAGTTAATGT 57.129 29.630 0.00 0.00 0.00 2.71
2136 2219 1.003355 ATGTGAGAACGGCACCAGG 60.003 57.895 0.00 0.00 35.43 4.45
2266 2349 2.100584 GAGTGTCTACCATGGCTCAGAG 59.899 54.545 13.04 1.66 0.00 3.35
2358 2441 0.249489 GCCGTGAGAGTGTTCACTGT 60.249 55.000 10.29 6.25 44.13 3.55
2492 2576 8.415553 CAGATTTGAAGATAAATACCATGGCAA 58.584 33.333 13.04 0.00 30.78 4.52
2503 2587 2.733956 ACCATGGCAATTTGGTACGAT 58.266 42.857 13.04 0.00 44.36 3.73
2598 2682 5.071519 AGGGATTGTGATTCAGTAGGATCAG 59.928 44.000 0.00 0.00 0.00 2.90
2643 2727 4.233632 TGCATGGTATGAATGAACCTGA 57.766 40.909 0.00 0.00 36.67 3.86
2652 2736 3.942829 TGAATGAACCTGATCAGTGACC 58.057 45.455 21.11 8.08 31.76 4.02
2678 2762 7.092716 GCTAGAAAATGCAGATTTGGAGAAAA 58.907 34.615 5.10 0.00 31.83 2.29
2689 2773 3.412237 TTGGAGAAAACGGGACTTAGG 57.588 47.619 0.00 0.00 0.00 2.69
2690 2774 1.626825 TGGAGAAAACGGGACTTAGGG 59.373 52.381 0.00 0.00 0.00 3.53
2691 2775 1.627329 GGAGAAAACGGGACTTAGGGT 59.373 52.381 0.00 0.00 0.00 4.34
2693 2777 3.261643 GGAGAAAACGGGACTTAGGGTAA 59.738 47.826 0.00 0.00 0.00 2.85
2694 2778 4.263025 GGAGAAAACGGGACTTAGGGTAAA 60.263 45.833 0.00 0.00 0.00 2.01
2695 2779 5.494724 GAGAAAACGGGACTTAGGGTAAAT 58.505 41.667 0.00 0.00 0.00 1.40
2696 2780 6.352137 GGAGAAAACGGGACTTAGGGTAAATA 60.352 42.308 0.00 0.00 0.00 1.40
2697 2781 6.409704 AGAAAACGGGACTTAGGGTAAATAC 58.590 40.000 0.00 0.00 0.00 1.89
2739 2823 6.071391 GGCCTATCTGTTTCCAAAATTCTTGA 60.071 38.462 0.00 0.00 0.00 3.02
2740 2824 7.364144 GGCCTATCTGTTTCCAAAATTCTTGAT 60.364 37.037 0.00 0.00 0.00 2.57
2741 2825 7.490402 GCCTATCTGTTTCCAAAATTCTTGATG 59.510 37.037 3.00 0.00 0.00 3.07
2752 2836 6.352394 CCAAAATTCTTGATGATGGGGAACAT 60.352 38.462 0.00 0.00 44.18 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.744719 TCTTCTCCACGTCGCCGG 61.745 66.667 0.00 0.00 38.78 6.13
13 14 2.504244 GTCTTCTCCACGTCGCCG 60.504 66.667 0.00 0.00 40.83 6.46
14 15 2.504244 CGTCTTCTCCACGTCGCC 60.504 66.667 0.00 0.00 32.41 5.54
15 16 2.504244 CCGTCTTCTCCACGTCGC 60.504 66.667 0.00 0.00 35.39 5.19
16 17 1.134901 CTCCGTCTTCTCCACGTCG 59.865 63.158 0.00 0.00 35.39 5.12
17 18 1.153997 GCTCCGTCTTCTCCACGTC 60.154 63.158 0.00 0.00 35.39 4.34
18 19 2.637383 GGCTCCGTCTTCTCCACGT 61.637 63.158 0.00 0.00 35.39 4.49
19 20 2.182030 GGCTCCGTCTTCTCCACG 59.818 66.667 0.00 0.00 36.99 4.94
20 21 1.668101 ATCGGCTCCGTCTTCTCCAC 61.668 60.000 8.28 0.00 40.74 4.02
21 22 1.379977 ATCGGCTCCGTCTTCTCCA 60.380 57.895 8.28 0.00 40.74 3.86
22 23 1.066587 CATCGGCTCCGTCTTCTCC 59.933 63.158 8.28 0.00 40.74 3.71
23 24 1.590259 GCATCGGCTCCGTCTTCTC 60.590 63.158 8.28 0.00 40.74 2.87
24 25 2.496817 GCATCGGCTCCGTCTTCT 59.503 61.111 8.28 0.00 40.74 2.85
34 35 2.514824 GGGACAAGGAGCATCGGC 60.515 66.667 0.00 0.00 41.61 5.54
35 36 2.032860 ATCGGGACAAGGAGCATCGG 62.033 60.000 0.00 0.00 34.37 4.18
36 37 0.598680 GATCGGGACAAGGAGCATCG 60.599 60.000 0.00 0.00 34.37 3.84
37 38 0.598680 CGATCGGGACAAGGAGCATC 60.599 60.000 7.38 0.00 0.00 3.91
38 39 1.443407 CGATCGGGACAAGGAGCAT 59.557 57.895 7.38 0.00 0.00 3.79
39 40 2.721167 CCGATCGGGACAAGGAGCA 61.721 63.158 26.95 0.00 38.47 4.26
40 41 2.107141 CCGATCGGGACAAGGAGC 59.893 66.667 26.95 0.00 38.47 4.70
41 42 1.736586 CTCCGATCGGGACAAGGAG 59.263 63.158 32.79 17.47 40.94 3.69
42 43 2.423898 GCTCCGATCGGGACAAGGA 61.424 63.158 32.79 11.72 40.94 3.36
43 44 2.107141 GCTCCGATCGGGACAAGG 59.893 66.667 32.79 16.51 40.94 3.61
44 45 2.107141 GGCTCCGATCGGGACAAG 59.893 66.667 32.79 23.08 40.94 3.16
45 46 3.833645 CGGCTCCGATCGGGACAA 61.834 66.667 32.79 13.65 40.94 3.18
48 49 4.826404 TTCCGGCTCCGATCGGGA 62.826 66.667 32.79 19.13 45.69 5.14
49 50 4.587189 GTTCCGGCTCCGATCGGG 62.587 72.222 32.79 23.49 45.69 5.14
50 51 4.925576 CGTTCCGGCTCCGATCGG 62.926 72.222 28.62 28.62 46.89 4.18
51 52 4.925576 CCGTTCCGGCTCCGATCG 62.926 72.222 8.51 8.51 41.17 3.69
61 62 2.582498 GATGCCGTCTCCGTTCCG 60.582 66.667 0.00 0.00 0.00 4.30
62 63 2.582498 CGATGCCGTCTCCGTTCC 60.582 66.667 0.00 0.00 0.00 3.62
63 64 1.586564 CTCGATGCCGTCTCCGTTC 60.587 63.158 0.00 0.00 37.05 3.95
64 65 2.490217 CTCGATGCCGTCTCCGTT 59.510 61.111 0.00 0.00 37.05 4.44
65 66 4.194720 GCTCGATGCCGTCTCCGT 62.195 66.667 0.00 0.00 37.05 4.69
67 68 4.933064 CCGCTCGATGCCGTCTCC 62.933 72.222 0.00 0.00 38.78 3.71
68 69 4.933064 CCCGCTCGATGCCGTCTC 62.933 72.222 0.00 0.00 38.78 3.36
70 71 4.933064 CTCCCGCTCGATGCCGTC 62.933 72.222 0.00 0.00 38.78 4.79
73 74 4.162690 AACCTCCCGCTCGATGCC 62.163 66.667 0.00 0.00 38.78 4.40
74 75 2.892425 CAACCTCCCGCTCGATGC 60.892 66.667 0.00 0.00 38.57 3.91
75 76 1.227089 CTCAACCTCCCGCTCGATG 60.227 63.158 0.00 0.00 0.00 3.84
76 77 3.082579 GCTCAACCTCCCGCTCGAT 62.083 63.158 0.00 0.00 0.00 3.59
77 78 3.760035 GCTCAACCTCCCGCTCGA 61.760 66.667 0.00 0.00 0.00 4.04
78 79 3.997064 CTGCTCAACCTCCCGCTCG 62.997 68.421 0.00 0.00 0.00 5.03
79 80 2.125350 CTGCTCAACCTCCCGCTC 60.125 66.667 0.00 0.00 0.00 5.03
80 81 2.604686 TCTGCTCAACCTCCCGCT 60.605 61.111 0.00 0.00 0.00 5.52
81 82 2.125350 CTCTGCTCAACCTCCCGC 60.125 66.667 0.00 0.00 0.00 6.13
82 83 2.125350 GCTCTGCTCAACCTCCCG 60.125 66.667 0.00 0.00 0.00 5.14
83 84 2.270527 GGCTCTGCTCAACCTCCC 59.729 66.667 0.00 0.00 0.00 4.30
84 85 2.125350 CGGCTCTGCTCAACCTCC 60.125 66.667 0.00 0.00 0.00 4.30
85 86 2.817396 GCGGCTCTGCTCAACCTC 60.817 66.667 0.00 0.00 0.00 3.85
86 87 3.182590 TTGCGGCTCTGCTCAACCT 62.183 57.895 0.00 0.00 35.36 3.50
87 88 2.669569 TTGCGGCTCTGCTCAACC 60.670 61.111 0.00 0.00 35.36 3.77
88 89 1.633852 CTCTTGCGGCTCTGCTCAAC 61.634 60.000 0.00 0.00 35.36 3.18
89 90 1.375140 CTCTTGCGGCTCTGCTCAA 60.375 57.895 0.00 0.00 35.36 3.02
90 91 2.223200 CTCTCTTGCGGCTCTGCTCA 62.223 60.000 0.00 0.00 35.36 4.26
91 92 1.519013 CTCTCTTGCGGCTCTGCTC 60.519 63.158 0.00 0.00 35.36 4.26
92 93 2.578128 CTCTCTTGCGGCTCTGCT 59.422 61.111 0.00 0.00 35.36 4.24
93 94 2.511145 CCTCTCTTGCGGCTCTGC 60.511 66.667 0.00 0.00 0.00 4.26
94 95 2.511145 GCCTCTCTTGCGGCTCTG 60.511 66.667 0.00 0.00 40.68 3.35
95 96 3.780173 GGCCTCTCTTGCGGCTCT 61.780 66.667 0.00 0.00 43.22 4.09
100 101 4.521062 CTCCCGGCCTCTCTTGCG 62.521 72.222 0.00 0.00 0.00 4.85
101 102 4.168291 CCTCCCGGCCTCTCTTGC 62.168 72.222 0.00 0.00 0.00 4.01
102 103 1.965754 CTTCCTCCCGGCCTCTCTTG 61.966 65.000 0.00 0.00 0.00 3.02
103 104 1.687493 CTTCCTCCCGGCCTCTCTT 60.687 63.158 0.00 0.00 0.00 2.85
104 105 2.042435 CTTCCTCCCGGCCTCTCT 60.042 66.667 0.00 0.00 0.00 3.10
105 106 3.855853 GCTTCCTCCCGGCCTCTC 61.856 72.222 0.00 0.00 0.00 3.20
115 116 4.400961 ACTGCTGCGGGCTTCCTC 62.401 66.667 13.87 0.00 42.39 3.71
116 117 4.711949 CACTGCTGCGGGCTTCCT 62.712 66.667 13.87 0.00 42.39 3.36
118 119 4.704833 TCCACTGCTGCGGGCTTC 62.705 66.667 13.87 0.00 42.39 3.86
119 120 4.269523 TTCCACTGCTGCGGGCTT 62.270 61.111 13.87 0.00 42.39 4.35
124 125 4.988598 ACCGGTTCCACTGCTGCG 62.989 66.667 0.00 0.00 0.00 5.18
125 126 3.357079 CACCGGTTCCACTGCTGC 61.357 66.667 2.97 0.00 0.00 5.25
126 127 2.669569 CCACCGGTTCCACTGCTG 60.670 66.667 2.97 0.00 0.00 4.41
127 128 3.168528 ACCACCGGTTCCACTGCT 61.169 61.111 2.97 0.00 27.29 4.24
128 129 2.978010 CACCACCGGTTCCACTGC 60.978 66.667 2.97 0.00 31.02 4.40
129 130 2.281484 CCACCACCGGTTCCACTG 60.281 66.667 2.97 0.00 31.02 3.66
130 131 4.265056 GCCACCACCGGTTCCACT 62.265 66.667 2.97 0.00 31.02 4.00
213 214 2.904470 TTAATACCCGCACCGTCGCC 62.904 60.000 0.00 0.00 0.00 5.54
214 215 1.485032 CTTAATACCCGCACCGTCGC 61.485 60.000 0.00 0.00 0.00 5.19
215 216 0.872881 CCTTAATACCCGCACCGTCG 60.873 60.000 0.00 0.00 0.00 5.12
216 217 0.176449 ACCTTAATACCCGCACCGTC 59.824 55.000 0.00 0.00 0.00 4.79
217 218 0.614812 AACCTTAATACCCGCACCGT 59.385 50.000 0.00 0.00 0.00 4.83
218 219 1.741528 AAACCTTAATACCCGCACCG 58.258 50.000 0.00 0.00 0.00 4.94
219 220 4.141233 TCTAAACCTTAATACCCGCACC 57.859 45.455 0.00 0.00 0.00 5.01
220 221 4.034858 GCTTCTAAACCTTAATACCCGCAC 59.965 45.833 0.00 0.00 0.00 5.34
221 222 4.193865 GCTTCTAAACCTTAATACCCGCA 58.806 43.478 0.00 0.00 0.00 5.69
222 223 3.246936 CGCTTCTAAACCTTAATACCCGC 59.753 47.826 0.00 0.00 0.00 6.13
223 224 3.805971 CCGCTTCTAAACCTTAATACCCG 59.194 47.826 0.00 0.00 0.00 5.28
224 225 5.027293 TCCGCTTCTAAACCTTAATACCC 57.973 43.478 0.00 0.00 0.00 3.69
225 226 5.007430 GCTTCCGCTTCTAAACCTTAATACC 59.993 44.000 0.00 0.00 0.00 2.73
226 227 5.276726 CGCTTCCGCTTCTAAACCTTAATAC 60.277 44.000 0.00 0.00 0.00 1.89
227 228 4.807304 CGCTTCCGCTTCTAAACCTTAATA 59.193 41.667 0.00 0.00 0.00 0.98
228 229 3.621715 CGCTTCCGCTTCTAAACCTTAAT 59.378 43.478 0.00 0.00 0.00 1.40
229 230 2.997986 CGCTTCCGCTTCTAAACCTTAA 59.002 45.455 0.00 0.00 0.00 1.85
230 231 2.231964 TCGCTTCCGCTTCTAAACCTTA 59.768 45.455 0.00 0.00 0.00 2.69
231 232 1.001633 TCGCTTCCGCTTCTAAACCTT 59.998 47.619 0.00 0.00 0.00 3.50
232 233 0.606604 TCGCTTCCGCTTCTAAACCT 59.393 50.000 0.00 0.00 0.00 3.50
233 234 1.593469 GATCGCTTCCGCTTCTAAACC 59.407 52.381 0.00 0.00 0.00 3.27
234 235 1.255600 CGATCGCTTCCGCTTCTAAAC 59.744 52.381 0.26 0.00 0.00 2.01
235 236 1.135199 ACGATCGCTTCCGCTTCTAAA 60.135 47.619 16.60 0.00 0.00 1.85
236 237 0.454600 ACGATCGCTTCCGCTTCTAA 59.545 50.000 16.60 0.00 0.00 2.10
237 238 1.302366 TACGATCGCTTCCGCTTCTA 58.698 50.000 16.60 0.00 0.00 2.10
238 239 0.454600 TTACGATCGCTTCCGCTTCT 59.545 50.000 16.60 0.00 0.00 2.85
239 240 0.571197 GTTACGATCGCTTCCGCTTC 59.429 55.000 16.60 0.00 0.00 3.86
240 241 0.804933 GGTTACGATCGCTTCCGCTT 60.805 55.000 16.60 0.00 0.00 4.68
241 242 1.226888 GGTTACGATCGCTTCCGCT 60.227 57.895 16.60 0.00 0.00 5.52
242 243 0.029834 TAGGTTACGATCGCTTCCGC 59.970 55.000 16.60 0.00 0.00 5.54
243 244 1.925068 GCTAGGTTACGATCGCTTCCG 60.925 57.143 16.60 4.59 0.00 4.30
244 245 1.768510 GCTAGGTTACGATCGCTTCC 58.231 55.000 16.60 14.35 0.00 3.46
245 246 1.268437 ACGCTAGGTTACGATCGCTTC 60.268 52.381 16.60 5.25 0.00 3.86
246 247 0.737219 ACGCTAGGTTACGATCGCTT 59.263 50.000 16.60 0.00 0.00 4.68
247 248 0.029035 CACGCTAGGTTACGATCGCT 59.971 55.000 16.60 6.62 0.00 4.93
248 249 0.028505 TCACGCTAGGTTACGATCGC 59.971 55.000 16.60 0.00 0.00 4.58
249 250 2.682952 ATCACGCTAGGTTACGATCG 57.317 50.000 14.88 14.88 0.00 3.69
250 251 3.251729 TGGTATCACGCTAGGTTACGATC 59.748 47.826 0.00 0.00 0.00 3.69
251 252 3.216800 TGGTATCACGCTAGGTTACGAT 58.783 45.455 0.00 0.00 0.00 3.73
252 253 2.642427 TGGTATCACGCTAGGTTACGA 58.358 47.619 0.00 0.00 0.00 3.43
253 254 3.243301 ACATGGTATCACGCTAGGTTACG 60.243 47.826 0.00 0.00 0.00 3.18
254 255 4.317671 ACATGGTATCACGCTAGGTTAC 57.682 45.455 0.00 0.00 0.00 2.50
255 256 5.829391 TCTTACATGGTATCACGCTAGGTTA 59.171 40.000 0.00 0.00 0.00 2.85
256 257 4.647853 TCTTACATGGTATCACGCTAGGTT 59.352 41.667 0.00 0.00 0.00 3.50
257 258 4.037684 GTCTTACATGGTATCACGCTAGGT 59.962 45.833 0.00 0.00 0.00 3.08
258 259 4.037565 TGTCTTACATGGTATCACGCTAGG 59.962 45.833 0.00 0.00 0.00 3.02
259 260 5.183014 TGTCTTACATGGTATCACGCTAG 57.817 43.478 0.00 0.00 0.00 3.42
260 261 5.585820 TTGTCTTACATGGTATCACGCTA 57.414 39.130 0.00 0.00 0.00 4.26
261 262 4.465632 TTGTCTTACATGGTATCACGCT 57.534 40.909 0.00 0.00 0.00 5.07
262 263 6.479001 ACTTATTGTCTTACATGGTATCACGC 59.521 38.462 0.00 0.00 0.00 5.34
263 264 8.420374 AACTTATTGTCTTACATGGTATCACG 57.580 34.615 0.00 0.00 0.00 4.35
267 268 8.966868 CCCAAAACTTATTGTCTTACATGGTAT 58.033 33.333 0.00 0.00 0.00 2.73
268 269 8.164733 TCCCAAAACTTATTGTCTTACATGGTA 58.835 33.333 0.00 0.00 0.00 3.25
269 270 7.007723 TCCCAAAACTTATTGTCTTACATGGT 58.992 34.615 0.00 0.00 0.00 3.55
270 271 7.461182 TCCCAAAACTTATTGTCTTACATGG 57.539 36.000 0.00 0.00 0.00 3.66
271 272 7.812669 GGTTCCCAAAACTTATTGTCTTACATG 59.187 37.037 0.00 0.00 0.00 3.21
272 273 7.507616 TGGTTCCCAAAACTTATTGTCTTACAT 59.492 33.333 0.00 0.00 0.00 2.29
273 274 6.834451 TGGTTCCCAAAACTTATTGTCTTACA 59.166 34.615 0.00 0.00 0.00 2.41
274 275 7.279750 TGGTTCCCAAAACTTATTGTCTTAC 57.720 36.000 0.00 0.00 0.00 2.34
275 276 6.015772 GCTGGTTCCCAAAACTTATTGTCTTA 60.016 38.462 0.00 0.00 30.80 2.10
276 277 5.221441 GCTGGTTCCCAAAACTTATTGTCTT 60.221 40.000 0.00 0.00 30.80 3.01
277 278 4.280929 GCTGGTTCCCAAAACTTATTGTCT 59.719 41.667 0.00 0.00 30.80 3.41
278 279 4.038642 TGCTGGTTCCCAAAACTTATTGTC 59.961 41.667 0.00 0.00 30.80 3.18
279 280 3.964031 TGCTGGTTCCCAAAACTTATTGT 59.036 39.130 0.00 0.00 30.80 2.71
280 281 4.202202 TGTGCTGGTTCCCAAAACTTATTG 60.202 41.667 0.00 0.00 30.80 1.90
281 282 3.964031 TGTGCTGGTTCCCAAAACTTATT 59.036 39.130 0.00 0.00 30.80 1.40
282 283 3.571590 TGTGCTGGTTCCCAAAACTTAT 58.428 40.909 0.00 0.00 30.80 1.73
283 284 3.019799 TGTGCTGGTTCCCAAAACTTA 57.980 42.857 0.00 0.00 30.80 2.24
284 285 1.859302 TGTGCTGGTTCCCAAAACTT 58.141 45.000 0.00 0.00 30.80 2.66
285 286 1.480545 GTTGTGCTGGTTCCCAAAACT 59.519 47.619 0.00 0.00 30.80 2.66
286 287 1.472552 GGTTGTGCTGGTTCCCAAAAC 60.473 52.381 0.00 0.00 30.80 2.43
287 288 0.827368 GGTTGTGCTGGTTCCCAAAA 59.173 50.000 0.00 0.00 30.80 2.44
288 289 1.045911 GGGTTGTGCTGGTTCCCAAA 61.046 55.000 0.00 0.00 38.15 3.28
289 290 1.456705 GGGTTGTGCTGGTTCCCAA 60.457 57.895 0.00 0.00 38.15 4.12
290 291 2.197324 GGGTTGTGCTGGTTCCCA 59.803 61.111 0.00 0.00 38.15 4.37
291 292 1.603739 GAGGGTTGTGCTGGTTCCC 60.604 63.158 0.00 0.00 38.50 3.97
292 293 0.690762 TAGAGGGTTGTGCTGGTTCC 59.309 55.000 0.00 0.00 0.00 3.62
293 294 1.339151 CCTAGAGGGTTGTGCTGGTTC 60.339 57.143 0.00 0.00 0.00 3.62
294 295 0.693049 CCTAGAGGGTTGTGCTGGTT 59.307 55.000 0.00 0.00 0.00 3.67
295 296 2.377136 CCTAGAGGGTTGTGCTGGT 58.623 57.895 0.00 0.00 0.00 4.00
306 307 2.252714 GAGATAAGCCACCCCTAGAGG 58.747 57.143 0.00 0.00 0.00 3.69
307 308 2.964209 TGAGATAAGCCACCCCTAGAG 58.036 52.381 0.00 0.00 0.00 2.43
308 309 3.637821 ATGAGATAAGCCACCCCTAGA 57.362 47.619 0.00 0.00 0.00 2.43
309 310 7.682787 ATATAATGAGATAAGCCACCCCTAG 57.317 40.000 0.00 0.00 0.00 3.02
311 312 9.744125 TTATATATAATGAGATAAGCCACCCCT 57.256 33.333 0.81 0.00 0.00 4.79
333 334 9.866798 TGTACGTATTGTAACACAACCATTATA 57.133 29.630 0.00 0.00 41.40 0.98
334 335 8.774890 TGTACGTATTGTAACACAACCATTAT 57.225 30.769 0.00 0.00 41.40 1.28
335 336 8.774890 ATGTACGTATTGTAACACAACCATTA 57.225 30.769 0.00 0.00 41.40 1.90
336 337 7.675962 ATGTACGTATTGTAACACAACCATT 57.324 32.000 0.00 0.00 41.40 3.16
337 338 8.036575 ACTATGTACGTATTGTAACACAACCAT 58.963 33.333 0.00 0.00 41.40 3.55
338 339 7.377398 ACTATGTACGTATTGTAACACAACCA 58.623 34.615 0.00 0.00 41.40 3.67
339 340 7.816945 ACTATGTACGTATTGTAACACAACC 57.183 36.000 0.00 0.00 41.40 3.77
341 342 9.905171 TGTAACTATGTACGTATTGTAACACAA 57.095 29.630 0.00 0.00 42.95 3.33
342 343 9.905171 TTGTAACTATGTACGTATTGTAACACA 57.095 29.630 0.00 0.00 34.07 3.72
367 368 9.886132 CCCAGTGTTAGACTATGTATAACTTTT 57.114 33.333 13.79 1.20 39.84 2.27
368 369 7.985752 GCCCAGTGTTAGACTATGTATAACTTT 59.014 37.037 13.79 3.04 39.84 2.66
369 370 7.344871 AGCCCAGTGTTAGACTATGTATAACTT 59.655 37.037 13.79 3.30 39.84 2.66
370 371 6.839657 AGCCCAGTGTTAGACTATGTATAACT 59.160 38.462 13.79 0.00 39.84 2.24
371 372 6.924060 CAGCCCAGTGTTAGACTATGTATAAC 59.076 42.308 7.91 7.91 39.66 1.89
372 373 6.041637 CCAGCCCAGTGTTAGACTATGTATAA 59.958 42.308 0.00 0.00 31.73 0.98
373 374 5.538813 CCAGCCCAGTGTTAGACTATGTATA 59.461 44.000 0.00 0.00 31.73 1.47
374 375 4.345257 CCAGCCCAGTGTTAGACTATGTAT 59.655 45.833 0.00 0.00 31.73 2.29
375 376 3.704566 CCAGCCCAGTGTTAGACTATGTA 59.295 47.826 0.00 0.00 31.73 2.29
376 377 2.501723 CCAGCCCAGTGTTAGACTATGT 59.498 50.000 0.00 0.00 31.73 2.29
377 378 2.158900 CCCAGCCCAGTGTTAGACTATG 60.159 54.545 0.00 0.00 31.73 2.23
378 379 2.119495 CCCAGCCCAGTGTTAGACTAT 58.881 52.381 0.00 0.00 31.73 2.12
379 380 1.203262 ACCCAGCCCAGTGTTAGACTA 60.203 52.381 0.00 0.00 31.73 2.59
380 381 0.473886 ACCCAGCCCAGTGTTAGACT 60.474 55.000 0.00 0.00 34.02 3.24
381 382 0.400594 AACCCAGCCCAGTGTTAGAC 59.599 55.000 0.00 0.00 0.00 2.59
382 383 0.400213 CAACCCAGCCCAGTGTTAGA 59.600 55.000 0.00 0.00 0.00 2.10
383 384 0.400213 TCAACCCAGCCCAGTGTTAG 59.600 55.000 0.00 0.00 0.00 2.34
384 385 0.109723 GTCAACCCAGCCCAGTGTTA 59.890 55.000 0.00 0.00 0.00 2.41
385 386 1.152756 GTCAACCCAGCCCAGTGTT 60.153 57.895 0.00 0.00 0.00 3.32
386 387 2.515901 GTCAACCCAGCCCAGTGT 59.484 61.111 0.00 0.00 0.00 3.55
387 388 2.669569 CGTCAACCCAGCCCAGTG 60.670 66.667 0.00 0.00 0.00 3.66
388 389 4.643387 GCGTCAACCCAGCCCAGT 62.643 66.667 0.00 0.00 0.00 4.00
394 395 2.976494 AAACCCAGGCGTCAACCCAG 62.976 60.000 0.00 0.00 0.00 4.45
395 396 2.575455 AAAACCCAGGCGTCAACCCA 62.575 55.000 0.00 0.00 0.00 4.51
396 397 1.802337 GAAAACCCAGGCGTCAACCC 61.802 60.000 0.00 0.00 0.00 4.11
397 398 0.822121 AGAAAACCCAGGCGTCAACC 60.822 55.000 0.00 0.00 0.00 3.77
398 399 0.310854 CAGAAAACCCAGGCGTCAAC 59.689 55.000 0.00 0.00 0.00 3.18
399 400 1.452145 GCAGAAAACCCAGGCGTCAA 61.452 55.000 0.00 0.00 0.00 3.18
400 401 1.896660 GCAGAAAACCCAGGCGTCA 60.897 57.895 0.00 0.00 0.00 4.35
401 402 0.321298 TAGCAGAAAACCCAGGCGTC 60.321 55.000 0.00 0.00 0.00 5.19
402 403 0.328258 ATAGCAGAAAACCCAGGCGT 59.672 50.000 0.00 0.00 0.00 5.68
403 404 0.734889 CATAGCAGAAAACCCAGGCG 59.265 55.000 0.00 0.00 0.00 5.52
404 405 1.106285 CCATAGCAGAAAACCCAGGC 58.894 55.000 0.00 0.00 0.00 4.85
405 406 1.767759 CCCATAGCAGAAAACCCAGG 58.232 55.000 0.00 0.00 0.00 4.45
406 407 1.106285 GCCCATAGCAGAAAACCCAG 58.894 55.000 0.00 0.00 42.97 4.45
407 408 3.281332 GCCCATAGCAGAAAACCCA 57.719 52.632 0.00 0.00 42.97 4.51
417 418 1.032794 GGCCTAACAAAGCCCATAGC 58.967 55.000 0.00 0.00 43.76 2.97
424 425 3.449227 GGCCGGGCCTAACAAAGC 61.449 66.667 30.86 0.00 46.69 3.51
439 440 1.302033 CATATGTCAGGCTCCGGGC 60.302 63.158 0.00 3.56 40.90 6.13
440 441 1.372683 CCATATGTCAGGCTCCGGG 59.627 63.158 0.00 0.00 0.00 5.73
448 449 3.582647 TGGTATACCTGGCCATATGTCAG 59.417 47.826 22.41 13.37 36.82 3.51
449 450 3.326588 GTGGTATACCTGGCCATATGTCA 59.673 47.826 22.41 2.83 36.82 3.58
515 516 8.991810 CGTTTTTCCGTATGTATATTGTGTTTC 58.008 33.333 0.00 0.00 0.00 2.78
517 518 8.031848 ACGTTTTTCCGTATGTATATTGTGTT 57.968 30.769 0.00 0.00 39.73 3.32
523 524 7.376866 CGTGTCTACGTTTTTCCGTATGTATAT 59.623 37.037 0.00 0.00 44.99 0.86
557 558 2.403252 TGAATCTTTTCTCCTCGGGC 57.597 50.000 0.00 0.00 32.78 6.13
606 607 2.489938 TTGAATTGAAGACGGGGAGG 57.510 50.000 0.00 0.00 0.00 4.30
621 622 1.132436 CGCGCGCTCTTGATTTGAA 59.868 52.632 30.48 0.00 0.00 2.69
624 630 4.505217 CGCGCGCGCTCTTGATTT 62.505 61.111 45.97 0.00 39.32 2.17
650 656 5.391629 GGTTTAGTTTCCGCTGATTACCTTG 60.392 44.000 0.00 0.00 0.00 3.61
668 674 2.289444 TGAAGGTGAAGAGGCGGTTTAG 60.289 50.000 0.00 0.00 0.00 1.85
680 686 0.991920 GGGGAGGATGTGAAGGTGAA 59.008 55.000 0.00 0.00 0.00 3.18
771 781 0.178767 TGATGATGGAGGCTTGACCG 59.821 55.000 0.00 0.00 46.52 4.79
778 788 0.552848 TCCCCTTTGATGATGGAGGC 59.447 55.000 0.00 0.00 0.00 4.70
796 806 1.993948 AAGGGAGGCCGGGTAACTC 60.994 63.158 2.18 1.49 0.00 3.01
975 1008 1.011019 CTCGACGACCTCGGATTCG 60.011 63.158 0.00 7.41 43.16 3.34
1240 1273 2.627699 TGTGGCAGGAAATGGAAGAAAC 59.372 45.455 0.00 0.00 0.00 2.78
1255 1288 2.108425 TGGTAAGGGTAATTGTGTGGCA 59.892 45.455 0.00 0.00 0.00 4.92
1256 1289 2.797786 TGGTAAGGGTAATTGTGTGGC 58.202 47.619 0.00 0.00 0.00 5.01
1257 1290 4.340617 ACATGGTAAGGGTAATTGTGTGG 58.659 43.478 0.00 0.00 0.00 4.17
1258 1291 5.007034 TGACATGGTAAGGGTAATTGTGTG 58.993 41.667 0.00 0.00 0.00 3.82
1259 1292 5.007682 GTGACATGGTAAGGGTAATTGTGT 58.992 41.667 0.00 0.00 0.00 3.72
1260 1293 4.398044 GGTGACATGGTAAGGGTAATTGTG 59.602 45.833 0.00 0.00 0.00 3.33
1261 1294 4.043561 TGGTGACATGGTAAGGGTAATTGT 59.956 41.667 0.00 0.00 33.40 2.71
1262 1295 4.594970 TGGTGACATGGTAAGGGTAATTG 58.405 43.478 0.00 0.00 33.40 2.32
1263 1296 4.938575 TGGTGACATGGTAAGGGTAATT 57.061 40.909 0.00 0.00 33.40 1.40
1264 1297 4.595986 GTTGGTGACATGGTAAGGGTAAT 58.404 43.478 0.00 0.00 42.32 1.89
1265 1298 3.557475 CGTTGGTGACATGGTAAGGGTAA 60.557 47.826 0.00 0.00 42.32 2.85
1266 1299 2.027929 CGTTGGTGACATGGTAAGGGTA 60.028 50.000 0.00 0.00 42.32 3.69
1267 1300 1.271163 CGTTGGTGACATGGTAAGGGT 60.271 52.381 0.00 0.00 42.32 4.34
1268 1301 1.448985 CGTTGGTGACATGGTAAGGG 58.551 55.000 0.00 0.00 42.32 3.95
1269 1302 1.448985 CCGTTGGTGACATGGTAAGG 58.551 55.000 0.00 0.00 42.32 2.69
1291 1324 1.663643 CACACACAACACAAGTACGCT 59.336 47.619 0.00 0.00 0.00 5.07
1315 1348 1.327690 ACACACACGACCCTGTGAGT 61.328 55.000 10.50 6.09 43.77 3.41
1316 1349 0.875908 CACACACACGACCCTGTGAG 60.876 60.000 10.50 5.49 43.77 3.51
1322 1355 1.594293 CAGGACACACACACGACCC 60.594 63.158 0.00 0.00 0.00 4.46
1324 1357 1.087202 TTGCAGGACACACACACGAC 61.087 55.000 0.00 0.00 0.00 4.34
1327 1360 0.748005 AGGTTGCAGGACACACACAC 60.748 55.000 0.00 0.00 0.00 3.82
1328 1361 0.747644 CAGGTTGCAGGACACACACA 60.748 55.000 0.00 0.00 0.00 3.72
1329 1362 0.463654 TCAGGTTGCAGGACACACAC 60.464 55.000 0.00 0.00 0.00 3.82
1330 1363 0.473755 ATCAGGTTGCAGGACACACA 59.526 50.000 0.00 0.00 0.00 3.72
1351 1387 6.382869 ACTTGAAGTCTGGAATCAAAACAG 57.617 37.500 0.00 0.00 33.08 3.16
1353 1389 6.202188 TCGTACTTGAAGTCTGGAATCAAAAC 59.798 38.462 0.00 0.00 33.08 2.43
1442 1478 2.281208 CCGTCGGCAAACCTGGAA 60.281 61.111 0.00 0.00 0.00 3.53
1962 2003 7.550906 ACTTGCAGAAGATTCAAGGAATACTAC 59.449 37.037 6.23 0.00 40.93 2.73
1981 2022 3.620374 GGATCACAGTATCACACTTGCAG 59.380 47.826 0.00 0.00 34.26 4.41
1985 2026 3.368427 CCACGGATCACAGTATCACACTT 60.368 47.826 0.00 0.00 34.26 3.16
1990 2031 4.464951 AGTTTACCACGGATCACAGTATCA 59.535 41.667 0.00 0.00 0.00 2.15
2035 2077 5.125097 ACCGAAGAACTTGTACGAGATATGT 59.875 40.000 17.37 2.10 0.00 2.29
2036 2078 5.455849 CACCGAAGAACTTGTACGAGATATG 59.544 44.000 17.37 1.74 0.00 1.78
2085 2127 6.399743 TGGCACTTTACATTAACTCGTATCA 58.600 36.000 0.00 0.00 0.00 2.15
2096 2138 7.760794 CACATGTTTGATATGGCACTTTACATT 59.239 33.333 0.00 0.00 0.00 2.71
2100 2183 6.883756 TCTCACATGTTTGATATGGCACTTTA 59.116 34.615 0.00 0.00 0.00 1.85
2104 2187 5.335127 GTTCTCACATGTTTGATATGGCAC 58.665 41.667 0.00 0.00 0.00 5.01
2136 2219 9.252962 CAAGCATTTATGAAATGGGACTAAATC 57.747 33.333 12.53 0.00 46.47 2.17
2266 2349 4.359706 CTGCAAGTTACTGGACCAAAAAC 58.640 43.478 9.60 9.60 0.00 2.43
2466 2549 7.944061 TGCCATGGTATTTATCTTCAAATCTG 58.056 34.615 14.67 0.00 30.84 2.90
2492 2576 6.167685 TGCAGTACTTAACATCGTACCAAAT 58.832 36.000 0.00 0.00 37.33 2.32
2503 2587 4.286297 AGATTGCCTGCAGTACTTAACA 57.714 40.909 13.81 0.00 0.00 2.41
2598 2682 1.427592 GATGGCAGCTTGCGAGAGAC 61.428 60.000 4.70 0.00 46.21 3.36
2643 2727 2.939103 GCATTTTCTAGCGGTCACTGAT 59.061 45.455 0.00 0.00 0.00 2.90
2652 2736 4.333649 TCTCCAAATCTGCATTTTCTAGCG 59.666 41.667 0.00 0.00 28.97 4.26
2678 2762 4.613437 TCTGTATTTACCCTAAGTCCCGT 58.387 43.478 0.00 0.00 0.00 5.28
2689 2773 7.545615 CCATTGCCTTTCTTTTCTGTATTTACC 59.454 37.037 0.00 0.00 0.00 2.85
2690 2774 7.063426 GCCATTGCCTTTCTTTTCTGTATTTAC 59.937 37.037 0.00 0.00 0.00 2.01
2691 2775 7.096551 GCCATTGCCTTTCTTTTCTGTATTTA 58.903 34.615 0.00 0.00 0.00 1.40
2693 2777 5.482006 GCCATTGCCTTTCTTTTCTGTATT 58.518 37.500 0.00 0.00 0.00 1.89
2694 2778 5.077134 GCCATTGCCTTTCTTTTCTGTAT 57.923 39.130 0.00 0.00 0.00 2.29
2695 2779 4.519540 GCCATTGCCTTTCTTTTCTGTA 57.480 40.909 0.00 0.00 0.00 2.74
2696 2780 3.391506 GCCATTGCCTTTCTTTTCTGT 57.608 42.857 0.00 0.00 0.00 3.41
2739 2823 3.693526 ACATTCCATGTTCCCCATCAT 57.306 42.857 0.00 0.00 41.63 2.45
2740 2824 3.268072 TGTACATTCCATGTTCCCCATCA 59.732 43.478 0.00 0.00 41.63 3.07
2741 2825 3.885297 CTGTACATTCCATGTTCCCCATC 59.115 47.826 0.00 0.00 41.63 3.51


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

AutoCloner maintained by Alex Coulton.