Multiple sequence alignment - TraesCS3A01G356900

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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 TraesCS3A01G356900 chr3A 100.000 2635 0 0 1 2635 604792038 604794672 0.000000e+00 4867.0
1 TraesCS3A01G356900 chr3A 92.593 81 3 2 250 327 523838452 523838372 2.140000e-21 113.0
2 TraesCS3A01G356900 chr5A 93.997 2332 103 13 317 2635 310018216 310020523 0.000000e+00 3496.0
3 TraesCS3A01G356900 chr5A 92.060 2330 144 13 318 2632 40241311 40239008 0.000000e+00 3240.0
4 TraesCS3A01G356900 chr5A 91.134 2346 131 23 318 2629 562122947 562120645 0.000000e+00 3109.0
5 TraesCS3A01G356900 chr5D 92.572 2329 133 15 318 2633 437728280 437725979 0.000000e+00 3306.0
6 TraesCS3A01G356900 chr5D 92.527 2315 140 13 325 2633 51585545 51583258 0.000000e+00 3286.0
7 TraesCS3A01G356900 chr1D 91.954 2324 150 13 325 2635 152626277 152628576 0.000000e+00 3221.0
8 TraesCS3A01G356900 chr1D 87.382 531 32 13 2106 2635 152482806 152483302 6.320000e-161 577.0
9 TraesCS3A01G356900 chr6A 91.577 2315 144 20 325 2635 577152222 577154489 0.000000e+00 3147.0
10 TraesCS3A01G356900 chr6A 91.693 2227 129 13 323 2546 553572475 553570302 0.000000e+00 3037.0
11 TraesCS3A01G356900 chr6A 95.092 326 15 1 1 325 592413352 592413027 1.810000e-141 512.0
12 TraesCS3A01G356900 chr6A 91.954 87 5 1 242 326 26674102 26674016 1.280000e-23 121.0
13 TraesCS3A01G356900 chr7A 90.170 2350 145 29 318 2629 49821416 49823717 0.000000e+00 2981.0
14 TraesCS3A01G356900 chr3B 90.256 2340 142 31 318 2635 823895703 823893428 0.000000e+00 2979.0
15 TraesCS3A01G356900 chr1A 90.933 2239 150 9 320 2546 16225037 16227234 0.000000e+00 2961.0
16 TraesCS3A01G356900 chr4A 92.426 2020 126 15 626 2635 314497557 314495555 0.000000e+00 2857.0
17 TraesCS3A01G356900 chr4A 92.661 327 21 2 1 326 549765184 549765508 3.970000e-128 468.0
18 TraesCS3A01G356900 chr4A 92.500 80 3 2 250 326 55017690 55017611 7.710000e-21 111.0
19 TraesCS3A01G356900 chr2B 90.442 1925 116 28 714 2635 32110230 32112089 0.000000e+00 2473.0
20 TraesCS3A01G356900 chr2B 89.810 1629 96 28 1013 2635 559330218 559328654 0.000000e+00 2025.0
21 TraesCS3A01G356900 chr2B 89.005 1628 86 28 1013 2635 152882418 152880879 0.000000e+00 1929.0
22 TraesCS3A01G356900 chr2B 91.358 81 4 2 249 326 311260675 311260595 9.970000e-20 108.0
23 TraesCS3A01G356900 chr2A 93.884 327 19 1 1 326 288447352 288447026 2.360000e-135 492.0
24 TraesCS3A01G356900 chr2A 91.985 262 18 3 1 262 619440742 619440484 5.360000e-97 364.0
25 TraesCS3A01G356900 chr4B 84.864 403 43 10 2234 2629 534345772 534345381 8.840000e-105 390.0
26 TraesCS3A01G356900 chrUn 93.902 82 4 1 246 326 30997838 30997757 3.560000e-24 122.0
27 TraesCS3A01G356900 chr6B 86.585 82 4 6 243 319 33366748 33366827 1.680000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G356900 chr3A 604792038 604794672 2634 False 4867 4867 100.000 1 2635 1 chr3A.!!$F1 2634
1 TraesCS3A01G356900 chr5A 310018216 310020523 2307 False 3496 3496 93.997 317 2635 1 chr5A.!!$F1 2318
2 TraesCS3A01G356900 chr5A 40239008 40241311 2303 True 3240 3240 92.060 318 2632 1 chr5A.!!$R1 2314
3 TraesCS3A01G356900 chr5A 562120645 562122947 2302 True 3109 3109 91.134 318 2629 1 chr5A.!!$R2 2311
4 TraesCS3A01G356900 chr5D 437725979 437728280 2301 True 3306 3306 92.572 318 2633 1 chr5D.!!$R2 2315
5 TraesCS3A01G356900 chr5D 51583258 51585545 2287 True 3286 3286 92.527 325 2633 1 chr5D.!!$R1 2308
6 TraesCS3A01G356900 chr1D 152626277 152628576 2299 False 3221 3221 91.954 325 2635 1 chr1D.!!$F2 2310
7 TraesCS3A01G356900 chr6A 577152222 577154489 2267 False 3147 3147 91.577 325 2635 1 chr6A.!!$F1 2310
8 TraesCS3A01G356900 chr6A 553570302 553572475 2173 True 3037 3037 91.693 323 2546 1 chr6A.!!$R2 2223
9 TraesCS3A01G356900 chr7A 49821416 49823717 2301 False 2981 2981 90.170 318 2629 1 chr7A.!!$F1 2311
10 TraesCS3A01G356900 chr3B 823893428 823895703 2275 True 2979 2979 90.256 318 2635 1 chr3B.!!$R1 2317
11 TraesCS3A01G356900 chr1A 16225037 16227234 2197 False 2961 2961 90.933 320 2546 1 chr1A.!!$F1 2226
12 TraesCS3A01G356900 chr4A 314495555 314497557 2002 True 2857 2857 92.426 626 2635 1 chr4A.!!$R2 2009
13 TraesCS3A01G356900 chr2B 32110230 32112089 1859 False 2473 2473 90.442 714 2635 1 chr2B.!!$F1 1921
14 TraesCS3A01G356900 chr2B 559328654 559330218 1564 True 2025 2025 89.810 1013 2635 1 chr2B.!!$R3 1622
15 TraesCS3A01G356900 chr2B 152880879 152882418 1539 True 1929 1929 89.005 1013 2635 1 chr2B.!!$R1 1622

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
30 31 0.246635 CGGAGAAGGGTCACGTGATT 59.753 55.0 23.12 12.32 0.00 2.57 F
48 49 0.755079 TTCGATCTGCATCCTCCTGG 59.245 55.0 0.00 0.00 0.00 4.45 F
237 238 0.949105 CCGCGCTAGAAACCTGTGTT 60.949 55.0 5.56 0.00 35.82 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1348 1397 1.166129 TCTCTGTGTCGGCAGTAGTC 58.834 55.000 0.0 0.0 37.70 2.59 R
1529 1582 1.611519 CACCAACATTAACCCACGGT 58.388 50.000 0.0 0.0 37.65 4.83 R
2168 2232 3.118149 ACAAAAACTTCGGTAGTCAGGGT 60.118 43.478 0.0 0.0 35.54 4.34 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
26 27 2.995574 CCCGGAGAAGGGTCACGT 60.996 66.667 0.73 0.00 46.38 4.49
27 28 2.261671 CCGGAGAAGGGTCACGTG 59.738 66.667 9.94 9.94 0.00 4.49
28 29 2.273179 CCGGAGAAGGGTCACGTGA 61.273 63.158 15.76 15.76 0.00 4.35
29 30 1.605058 CCGGAGAAGGGTCACGTGAT 61.605 60.000 23.12 5.10 0.00 3.06
30 31 0.246635 CGGAGAAGGGTCACGTGATT 59.753 55.000 23.12 12.32 0.00 2.57
31 32 1.736032 CGGAGAAGGGTCACGTGATTC 60.736 57.143 23.12 20.31 0.00 2.52
32 33 1.630148 GAGAAGGGTCACGTGATTCG 58.370 55.000 23.12 0.00 46.00 3.34
33 34 1.201647 GAGAAGGGTCACGTGATTCGA 59.798 52.381 23.12 0.00 42.86 3.71
34 35 1.825474 AGAAGGGTCACGTGATTCGAT 59.175 47.619 23.12 11.04 42.86 3.59
35 36 2.159226 AGAAGGGTCACGTGATTCGATC 60.159 50.000 23.12 17.85 42.86 3.69
36 37 1.475403 AGGGTCACGTGATTCGATCT 58.525 50.000 23.12 9.99 42.86 2.75
37 38 1.135139 AGGGTCACGTGATTCGATCTG 59.865 52.381 23.12 0.00 42.86 2.90
38 39 0.924090 GGTCACGTGATTCGATCTGC 59.076 55.000 23.12 4.95 42.86 4.26
39 40 1.629013 GTCACGTGATTCGATCTGCA 58.371 50.000 23.12 0.00 42.86 4.41
40 41 2.196749 GTCACGTGATTCGATCTGCAT 58.803 47.619 23.12 0.00 42.86 3.96
41 42 2.217393 GTCACGTGATTCGATCTGCATC 59.783 50.000 23.12 0.00 42.86 3.91
42 43 1.524355 CACGTGATTCGATCTGCATCC 59.476 52.381 10.90 0.00 42.86 3.51
43 44 1.410517 ACGTGATTCGATCTGCATCCT 59.589 47.619 0.00 0.00 42.86 3.24
44 45 2.057316 CGTGATTCGATCTGCATCCTC 58.943 52.381 0.00 0.00 42.86 3.71
45 46 2.411904 GTGATTCGATCTGCATCCTCC 58.588 52.381 0.00 0.00 0.00 4.30
46 47 2.036992 GTGATTCGATCTGCATCCTCCT 59.963 50.000 0.00 0.00 0.00 3.69
47 48 2.036862 TGATTCGATCTGCATCCTCCTG 59.963 50.000 0.00 0.00 0.00 3.86
48 49 0.755079 TTCGATCTGCATCCTCCTGG 59.245 55.000 0.00 0.00 0.00 4.45
49 50 1.117749 TCGATCTGCATCCTCCTGGG 61.118 60.000 0.00 0.00 0.00 4.45
50 51 1.072852 GATCTGCATCCTCCTGGGC 59.927 63.158 0.00 0.00 34.39 5.36
51 52 2.408880 GATCTGCATCCTCCTGGGCC 62.409 65.000 0.00 0.00 34.39 5.80
52 53 4.559063 CTGCATCCTCCTGGGCCG 62.559 72.222 0.00 0.00 34.39 6.13
89 90 4.803908 GCAAGAAGGCGGGGAGGG 62.804 72.222 0.00 0.00 0.00 4.30
90 91 4.115199 CAAGAAGGCGGGGAGGGG 62.115 72.222 0.00 0.00 0.00 4.79
91 92 4.348495 AAGAAGGCGGGGAGGGGA 62.348 66.667 0.00 0.00 0.00 4.81
92 93 4.806339 AGAAGGCGGGGAGGGGAG 62.806 72.222 0.00 0.00 0.00 4.30
132 133 3.020627 GCGCTGCCATGCTAGAAG 58.979 61.111 0.00 0.00 0.00 2.85
133 134 2.541120 GCGCTGCCATGCTAGAAGG 61.541 63.158 0.00 0.00 0.00 3.46
137 138 2.592861 GCCATGCTAGAAGGCGGG 60.593 66.667 0.00 0.00 38.86 6.13
138 139 2.111878 CCATGCTAGAAGGCGGGG 59.888 66.667 0.00 0.00 34.52 5.73
139 140 2.746375 CCATGCTAGAAGGCGGGGT 61.746 63.158 0.00 0.00 34.52 4.95
140 141 1.524621 CATGCTAGAAGGCGGGGTG 60.525 63.158 0.00 0.00 34.52 4.61
141 142 2.746375 ATGCTAGAAGGCGGGGTGG 61.746 63.158 0.00 0.00 34.52 4.61
142 143 4.176752 GCTAGAAGGCGGGGTGGG 62.177 72.222 0.00 0.00 0.00 4.61
143 144 3.480133 CTAGAAGGCGGGGTGGGG 61.480 72.222 0.00 0.00 0.00 4.96
144 145 3.995809 CTAGAAGGCGGGGTGGGGA 62.996 68.421 0.00 0.00 0.00 4.81
145 146 3.995809 TAGAAGGCGGGGTGGGGAG 62.996 68.421 0.00 0.00 0.00 4.30
159 160 3.866582 GGAGGGGGCCATCGTCTG 61.867 72.222 4.39 0.00 0.00 3.51
160 161 4.554036 GAGGGGGCCATCGTCTGC 62.554 72.222 4.39 0.00 0.00 4.26
186 187 4.530857 CCGCGCTAGAAGGTGGGG 62.531 72.222 5.56 0.00 41.89 4.96
187 188 3.771160 CGCGCTAGAAGGTGGGGT 61.771 66.667 5.56 0.00 0.00 4.95
188 189 2.125106 GCGCTAGAAGGTGGGGTG 60.125 66.667 0.00 0.00 0.00 4.61
189 190 2.584608 CGCTAGAAGGTGGGGTGG 59.415 66.667 0.00 0.00 0.00 4.61
190 191 2.998949 GCTAGAAGGTGGGGTGGG 59.001 66.667 0.00 0.00 0.00 4.61
191 192 2.680370 GCTAGAAGGTGGGGTGGGG 61.680 68.421 0.00 0.00 0.00 4.96
192 193 1.082206 CTAGAAGGTGGGGTGGGGA 59.918 63.158 0.00 0.00 0.00 4.81
193 194 0.983378 CTAGAAGGTGGGGTGGGGAG 60.983 65.000 0.00 0.00 0.00 4.30
194 195 2.486410 TAGAAGGTGGGGTGGGGAGG 62.486 65.000 0.00 0.00 0.00 4.30
203 204 2.612746 GTGGGGAGGGGGTTGCTA 60.613 66.667 0.00 0.00 0.00 3.49
204 205 2.006991 GTGGGGAGGGGGTTGCTAT 61.007 63.158 0.00 0.00 0.00 2.97
205 206 1.696314 TGGGGAGGGGGTTGCTATC 60.696 63.158 0.00 0.00 0.00 2.08
206 207 2.461739 GGGGAGGGGGTTGCTATCC 61.462 68.421 0.00 0.00 0.00 2.59
207 208 1.386057 GGGAGGGGGTTGCTATCCT 60.386 63.158 0.00 0.00 0.00 3.24
208 209 1.419720 GGGAGGGGGTTGCTATCCTC 61.420 65.000 0.00 0.00 43.65 3.71
209 210 1.749033 GAGGGGGTTGCTATCCTCG 59.251 63.158 0.00 0.00 36.78 4.63
210 211 1.759459 GAGGGGGTTGCTATCCTCGG 61.759 65.000 0.00 0.00 36.78 4.63
211 212 2.819284 GGGGGTTGCTATCCTCGGG 61.819 68.421 0.00 0.00 0.00 5.14
212 213 2.819284 GGGGTTGCTATCCTCGGGG 61.819 68.421 0.00 0.00 0.00 5.73
213 214 2.070650 GGGTTGCTATCCTCGGGGT 61.071 63.158 0.00 0.00 0.00 4.95
214 215 1.146263 GGTTGCTATCCTCGGGGTG 59.854 63.158 0.00 0.00 0.00 4.61
215 216 1.523938 GTTGCTATCCTCGGGGTGC 60.524 63.158 0.00 5.43 0.00 5.01
216 217 1.689233 TTGCTATCCTCGGGGTGCT 60.689 57.895 0.00 0.00 0.00 4.40
217 218 1.971505 TTGCTATCCTCGGGGTGCTG 61.972 60.000 0.00 0.00 0.00 4.41
218 219 2.423446 CTATCCTCGGGGTGCTGC 59.577 66.667 0.00 0.00 0.00 5.25
219 220 3.161450 TATCCTCGGGGTGCTGCC 61.161 66.667 0.00 0.00 0.00 4.85
229 230 3.118454 GTGCTGCCGCGCTAGAAA 61.118 61.111 5.56 0.00 43.21 2.52
230 231 3.118454 TGCTGCCGCGCTAGAAAC 61.118 61.111 5.56 0.00 39.65 2.78
231 232 3.865830 GCTGCCGCGCTAGAAACC 61.866 66.667 5.56 0.00 0.00 3.27
232 233 2.125512 CTGCCGCGCTAGAAACCT 60.126 61.111 5.56 0.00 0.00 3.50
233 234 2.434185 TGCCGCGCTAGAAACCTG 60.434 61.111 5.56 0.00 0.00 4.00
234 235 2.434359 GCCGCGCTAGAAACCTGT 60.434 61.111 5.56 0.00 0.00 4.00
235 236 2.740714 GCCGCGCTAGAAACCTGTG 61.741 63.158 5.56 0.00 0.00 3.66
236 237 1.374252 CCGCGCTAGAAACCTGTGT 60.374 57.895 5.56 0.00 0.00 3.72
237 238 0.949105 CCGCGCTAGAAACCTGTGTT 60.949 55.000 5.56 0.00 35.82 3.32
238 239 1.670674 CCGCGCTAGAAACCTGTGTTA 60.671 52.381 5.56 0.00 33.30 2.41
239 240 2.063266 CGCGCTAGAAACCTGTGTTAA 58.937 47.619 5.56 0.00 33.30 2.01
240 241 2.092211 CGCGCTAGAAACCTGTGTTAAG 59.908 50.000 5.56 0.00 33.30 1.85
241 242 3.064931 GCGCTAGAAACCTGTGTTAAGT 58.935 45.455 0.00 0.00 33.30 2.24
242 243 3.120649 GCGCTAGAAACCTGTGTTAAGTG 60.121 47.826 0.00 0.00 33.30 3.16
243 244 3.432252 CGCTAGAAACCTGTGTTAAGTGG 59.568 47.826 0.00 0.00 33.30 4.00
244 245 3.751698 GCTAGAAACCTGTGTTAAGTGGG 59.248 47.826 0.00 0.00 33.30 4.61
245 246 3.223674 AGAAACCTGTGTTAAGTGGGG 57.776 47.619 0.00 0.00 33.30 4.96
246 247 2.158519 AGAAACCTGTGTTAAGTGGGGG 60.159 50.000 0.00 0.00 33.30 5.40
265 266 3.487372 GGGGGTGTTATGAGAATAAGGC 58.513 50.000 0.00 0.00 0.00 4.35
266 267 3.138468 GGGGGTGTTATGAGAATAAGGCT 59.862 47.826 0.00 0.00 0.00 4.58
267 268 4.386424 GGGGGTGTTATGAGAATAAGGCTT 60.386 45.833 4.58 4.58 0.00 4.35
268 269 5.201243 GGGGTGTTATGAGAATAAGGCTTT 58.799 41.667 4.45 0.00 0.00 3.51
269 270 5.067805 GGGGTGTTATGAGAATAAGGCTTTG 59.932 44.000 4.45 0.00 0.00 2.77
270 271 5.652452 GGGTGTTATGAGAATAAGGCTTTGT 59.348 40.000 4.45 0.00 0.00 2.83
271 272 6.152831 GGGTGTTATGAGAATAAGGCTTTGTT 59.847 38.462 4.45 0.60 0.00 2.83
272 273 7.338449 GGGTGTTATGAGAATAAGGCTTTGTTA 59.662 37.037 4.45 0.00 0.00 2.41
273 274 8.903820 GGTGTTATGAGAATAAGGCTTTGTTAT 58.096 33.333 4.45 0.00 0.00 1.89
274 275 9.722056 GTGTTATGAGAATAAGGCTTTGTTATG 57.278 33.333 4.45 0.00 0.00 1.90
275 276 9.679661 TGTTATGAGAATAAGGCTTTGTTATGA 57.320 29.630 4.45 0.00 0.00 2.15
279 280 9.638176 ATGAGAATAAGGCTTTGTTATGAGAAT 57.362 29.630 4.45 0.00 0.00 2.40
284 285 9.700831 AATAAGGCTTTGTTATGAGAATAAGGT 57.299 29.630 4.45 0.00 0.00 3.50
285 286 7.631717 AAGGCTTTGTTATGAGAATAAGGTC 57.368 36.000 0.00 0.00 0.00 3.85
286 287 6.963322 AGGCTTTGTTATGAGAATAAGGTCT 58.037 36.000 0.00 0.00 0.00 3.85
287 288 7.406104 AGGCTTTGTTATGAGAATAAGGTCTT 58.594 34.615 0.00 0.00 0.00 3.01
288 289 8.548877 AGGCTTTGTTATGAGAATAAGGTCTTA 58.451 33.333 0.00 0.00 0.00 2.10
289 290 9.174166 GGCTTTGTTATGAGAATAAGGTCTTAA 57.826 33.333 0.00 0.00 0.00 1.85
292 293 9.681062 TTTGTTATGAGAATAAGGTCTTAAGGG 57.319 33.333 1.85 0.00 0.00 3.95
293 294 7.802117 TGTTATGAGAATAAGGTCTTAAGGGG 58.198 38.462 1.85 0.00 0.00 4.79
294 295 7.404980 TGTTATGAGAATAAGGTCTTAAGGGGT 59.595 37.037 1.85 0.00 0.00 4.95
295 296 5.693769 TGAGAATAAGGTCTTAAGGGGTG 57.306 43.478 1.85 0.00 0.00 4.61
296 297 5.098663 TGAGAATAAGGTCTTAAGGGGTGT 58.901 41.667 1.85 0.00 0.00 4.16
297 298 5.550403 TGAGAATAAGGTCTTAAGGGGTGTT 59.450 40.000 1.85 0.00 0.00 3.32
298 299 6.731919 TGAGAATAAGGTCTTAAGGGGTGTTA 59.268 38.462 1.85 0.00 0.00 2.41
299 300 7.404980 TGAGAATAAGGTCTTAAGGGGTGTTAT 59.595 37.037 1.85 0.00 0.00 1.89
300 301 7.574607 AGAATAAGGTCTTAAGGGGTGTTATG 58.425 38.462 1.85 0.00 0.00 1.90
301 302 7.404980 AGAATAAGGTCTTAAGGGGTGTTATGA 59.595 37.037 1.85 0.00 0.00 2.15
302 303 5.437191 AAGGTCTTAAGGGGTGTTATGAG 57.563 43.478 1.85 0.00 0.00 2.90
303 304 4.695606 AGGTCTTAAGGGGTGTTATGAGA 58.304 43.478 1.85 0.00 0.00 3.27
304 305 5.098663 AGGTCTTAAGGGGTGTTATGAGAA 58.901 41.667 1.85 0.00 0.00 2.87
305 306 5.731678 AGGTCTTAAGGGGTGTTATGAGAAT 59.268 40.000 1.85 0.00 0.00 2.40
306 307 6.906901 AGGTCTTAAGGGGTGTTATGAGAATA 59.093 38.462 1.85 0.00 0.00 1.75
307 308 7.071321 AGGTCTTAAGGGGTGTTATGAGAATAG 59.929 40.741 1.85 0.00 0.00 1.73
308 309 7.070821 GGTCTTAAGGGGTGTTATGAGAATAGA 59.929 40.741 1.85 0.00 0.00 1.98
309 310 7.927092 GTCTTAAGGGGTGTTATGAGAATAGAC 59.073 40.741 1.85 0.00 0.00 2.59
310 311 5.632034 AAGGGGTGTTATGAGAATAGACC 57.368 43.478 0.00 0.00 0.00 3.85
311 312 3.974642 AGGGGTGTTATGAGAATAGACCC 59.025 47.826 0.00 0.00 40.85 4.46
312 313 3.714798 GGGGTGTTATGAGAATAGACCCA 59.285 47.826 0.00 0.00 42.99 4.51
313 314 4.444449 GGGGTGTTATGAGAATAGACCCAC 60.444 50.000 0.00 0.00 42.99 4.61
314 315 4.444449 GGGTGTTATGAGAATAGACCCACC 60.444 50.000 0.00 0.00 41.17 4.61
315 316 4.444449 GGTGTTATGAGAATAGACCCACCC 60.444 50.000 0.00 0.00 35.03 4.61
452 465 3.555377 CCAATGGAGTTGAATTGCAGCAA 60.555 43.478 11.07 11.07 40.37 3.91
494 507 7.759489 TCAATTCTTGGGCAATATATGGTAC 57.241 36.000 0.00 0.00 0.00 3.34
508 522 9.784531 CAATATATGGTACTTTCCACTCTTCAT 57.215 33.333 0.00 0.00 40.51 2.57
601 615 2.895680 GCACCTCGCAGGATCTCA 59.104 61.111 8.91 0.00 37.67 3.27
739 779 8.687292 ACATATATGCATGAAACTGAGATTGT 57.313 30.769 10.16 0.00 0.00 2.71
774 814 6.976934 ACACAAGATACACCCTTTGAATTT 57.023 33.333 0.00 0.00 0.00 1.82
810 851 8.784043 GTTCAGTTTTGTATATTCTTCACCAGT 58.216 33.333 0.00 0.00 0.00 4.00
839 880 5.914898 TCATGCTTGTAACTAGTGCTCTA 57.085 39.130 0.00 0.00 0.00 2.43
895 936 3.845781 TCCCAACCTTCTATCATGCTC 57.154 47.619 0.00 0.00 0.00 4.26
1070 1111 2.511218 ACATGTCCTGGAGTGCCATTAT 59.489 45.455 0.00 0.00 44.91 1.28
1161 1210 4.836125 TTCGTCCGTCTGTAGTTAACTT 57.164 40.909 14.49 0.00 0.00 2.66
1181 1230 2.897271 AGTTGTGCCCCATTGATGTA 57.103 45.000 0.00 0.00 0.00 2.29
1287 1336 7.952671 TCTTAAGAGACACTTCTAGCTTTTCA 58.047 34.615 0.00 0.00 39.72 2.69
1338 1387 6.374333 ACATGGGTTTTACTACTGCTAACATG 59.626 38.462 0.00 0.00 37.44 3.21
1348 1397 6.810911 ACTACTGCTAACATGGAGAGTATTG 58.189 40.000 0.00 0.00 0.00 1.90
1399 1451 2.703416 TGCTACCTGATGAGTGCTTTG 58.297 47.619 0.00 0.00 0.00 2.77
1461 1514 5.618056 TTGAACTCTGCATGAGATGAAAC 57.382 39.130 16.81 5.35 45.39 2.78
1500 1553 7.708752 TGTTTTTCTGAACTTGTTTTCACTGTT 59.291 29.630 0.00 0.00 32.02 3.16
1501 1554 7.636259 TTTTCTGAACTTGTTTTCACTGTTG 57.364 32.000 0.00 0.00 32.02 3.33
1769 1826 2.030457 GTGATGTTAGTATGCGTGTGCC 59.970 50.000 0.00 0.00 41.78 5.01
1805 1862 7.611467 TGTTAGATCTTGCCAGTTGAATGTATT 59.389 33.333 0.00 0.00 0.00 1.89
1979 2043 5.066505 AGCATGGTACTAGCTAAATTTGTGC 59.933 40.000 0.00 5.47 37.39 4.57
2121 2185 1.198759 TTGGTCCCAGCCCTGACTAC 61.199 60.000 0.00 0.00 0.00 2.73
2168 2232 3.843619 TGTTCATCTGACTATGGTCCCAA 59.156 43.478 6.77 0.00 41.47 4.12
2219 2294 8.593945 ATTGAAGTTTCTTAGAAATATGGGCA 57.406 30.769 10.77 2.06 0.00 5.36
2233 2308 2.659610 GGCAAGTCCAGCGAGTCT 59.340 61.111 0.00 0.00 34.01 3.24
2280 2372 7.834068 CTTGTGAAGCAGTACTGTATTACAT 57.166 36.000 23.44 0.00 0.00 2.29
2282 2374 7.595311 TGTGAAGCAGTACTGTATTACATTG 57.405 36.000 23.44 0.00 0.00 2.82
2283 2375 7.158697 TGTGAAGCAGTACTGTATTACATTGT 58.841 34.615 23.44 0.00 0.00 2.71
2284 2376 8.308207 TGTGAAGCAGTACTGTATTACATTGTA 58.692 33.333 23.44 0.00 0.00 2.41
2285 2377 8.808529 GTGAAGCAGTACTGTATTACATTGTAG 58.191 37.037 23.44 0.00 0.00 2.74
2286 2378 8.745590 TGAAGCAGTACTGTATTACATTGTAGA 58.254 33.333 23.44 0.00 0.00 2.59
2287 2379 9.239002 GAAGCAGTACTGTATTACATTGTAGAG 57.761 37.037 23.44 0.00 0.00 2.43
2288 2380 7.203910 AGCAGTACTGTATTACATTGTAGAGC 58.796 38.462 23.44 3.42 0.00 4.09
2289 2381 7.068839 AGCAGTACTGTATTACATTGTAGAGCT 59.931 37.037 23.44 5.72 0.00 4.09
2290 2382 7.707035 GCAGTACTGTATTACATTGTAGAGCTT 59.293 37.037 23.44 0.00 0.00 3.74
2291 2383 9.025020 CAGTACTGTATTACATTGTAGAGCTTG 57.975 37.037 15.06 0.00 0.00 4.01
2365 2475 3.988517 GGCACGGATAGAGCTTGTATTAC 59.011 47.826 0.00 0.00 36.65 1.89
2400 2512 8.732531 GTTGCCCTTGTTTAAGTATTATGTGTA 58.267 33.333 0.00 0.00 31.80 2.90
2515 2627 4.196971 ACCTGTTACCAGAACTTGACAAC 58.803 43.478 0.00 0.00 41.50 3.32
2526 2640 1.499007 ACTTGACAACTGGGACCCATT 59.501 47.619 15.39 5.38 30.82 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.605058 ATCACGTGACCCTTCTCCGG 61.605 60.000 22.71 0.00 0.00 5.14
11 12 0.246635 AATCACGTGACCCTTCTCCG 59.753 55.000 22.71 0.00 0.00 4.63
12 13 1.736032 CGAATCACGTGACCCTTCTCC 60.736 57.143 22.71 3.13 37.22 3.71
13 14 1.201647 TCGAATCACGTGACCCTTCTC 59.798 52.381 22.71 9.56 43.13 2.87
14 15 1.254026 TCGAATCACGTGACCCTTCT 58.746 50.000 22.71 0.00 43.13 2.85
15 16 2.159226 AGATCGAATCACGTGACCCTTC 60.159 50.000 22.71 19.10 43.13 3.46
16 17 1.825474 AGATCGAATCACGTGACCCTT 59.175 47.619 22.71 11.86 43.13 3.95
17 18 1.135139 CAGATCGAATCACGTGACCCT 59.865 52.381 22.71 8.48 43.13 4.34
18 19 1.560923 CAGATCGAATCACGTGACCC 58.439 55.000 22.71 14.31 43.13 4.46
19 20 0.924090 GCAGATCGAATCACGTGACC 59.076 55.000 22.71 14.69 43.13 4.02
20 21 1.629013 TGCAGATCGAATCACGTGAC 58.371 50.000 22.71 8.36 43.13 3.67
21 22 2.463876 GATGCAGATCGAATCACGTGA 58.536 47.619 22.48 22.48 43.13 4.35
22 23 1.524355 GGATGCAGATCGAATCACGTG 59.476 52.381 9.94 9.94 43.13 4.49
23 24 1.410517 AGGATGCAGATCGAATCACGT 59.589 47.619 0.00 0.00 43.13 4.49
24 25 2.057316 GAGGATGCAGATCGAATCACG 58.943 52.381 0.00 0.00 44.09 4.35
25 26 2.036992 AGGAGGATGCAGATCGAATCAC 59.963 50.000 0.00 2.57 0.00 3.06
26 27 2.036862 CAGGAGGATGCAGATCGAATCA 59.963 50.000 0.00 0.00 0.00 2.57
27 28 2.612471 CCAGGAGGATGCAGATCGAATC 60.612 54.545 0.00 0.00 36.89 2.52
28 29 1.347050 CCAGGAGGATGCAGATCGAAT 59.653 52.381 0.00 0.00 36.89 3.34
29 30 0.755079 CCAGGAGGATGCAGATCGAA 59.245 55.000 0.00 0.00 36.89 3.71
30 31 1.117749 CCCAGGAGGATGCAGATCGA 61.118 60.000 0.00 0.00 38.24 3.59
31 32 1.370437 CCCAGGAGGATGCAGATCG 59.630 63.158 0.00 0.00 38.24 3.69
32 33 1.072852 GCCCAGGAGGATGCAGATC 59.927 63.158 0.00 0.00 38.24 2.75
33 34 2.459086 GGCCCAGGAGGATGCAGAT 61.459 63.158 0.00 0.00 38.24 2.90
34 35 3.092511 GGCCCAGGAGGATGCAGA 61.093 66.667 0.00 0.00 38.24 4.26
35 36 4.559063 CGGCCCAGGAGGATGCAG 62.559 72.222 0.00 0.00 38.24 4.41
72 73 4.803908 CCCTCCCCGCCTTCTTGC 62.804 72.222 0.00 0.00 0.00 4.01
73 74 4.115199 CCCCTCCCCGCCTTCTTG 62.115 72.222 0.00 0.00 0.00 3.02
74 75 4.348495 TCCCCTCCCCGCCTTCTT 62.348 66.667 0.00 0.00 0.00 2.52
75 76 4.806339 CTCCCCTCCCCGCCTTCT 62.806 72.222 0.00 0.00 0.00 2.85
115 116 2.541120 CCTTCTAGCATGGCAGCGC 61.541 63.158 0.00 0.00 40.15 5.92
116 117 2.541120 GCCTTCTAGCATGGCAGCG 61.541 63.158 13.22 0.00 43.61 5.18
117 118 2.541120 CGCCTTCTAGCATGGCAGC 61.541 63.158 16.65 0.00 44.25 5.25
118 119 1.890979 CCGCCTTCTAGCATGGCAG 60.891 63.158 16.65 10.89 44.25 4.85
119 120 2.190313 CCGCCTTCTAGCATGGCA 59.810 61.111 16.65 0.00 44.25 4.92
120 121 2.592861 CCCGCCTTCTAGCATGGC 60.593 66.667 9.48 9.48 41.20 4.40
121 122 2.111878 CCCCGCCTTCTAGCATGG 59.888 66.667 0.00 0.00 0.00 3.66
122 123 1.524621 CACCCCGCCTTCTAGCATG 60.525 63.158 0.00 0.00 0.00 4.06
123 124 2.746375 CCACCCCGCCTTCTAGCAT 61.746 63.158 0.00 0.00 0.00 3.79
124 125 3.399181 CCACCCCGCCTTCTAGCA 61.399 66.667 0.00 0.00 0.00 3.49
125 126 4.176752 CCCACCCCGCCTTCTAGC 62.177 72.222 0.00 0.00 0.00 3.42
126 127 3.480133 CCCCACCCCGCCTTCTAG 61.480 72.222 0.00 0.00 0.00 2.43
127 128 3.995809 CTCCCCACCCCGCCTTCTA 62.996 68.421 0.00 0.00 0.00 2.10
142 143 3.866582 CAGACGATGGCCCCCTCC 61.867 72.222 0.00 0.00 0.00 4.30
143 144 4.554036 GCAGACGATGGCCCCCTC 62.554 72.222 0.00 0.00 0.00 4.30
169 170 4.530857 CCCCACCTTCTAGCGCGG 62.531 72.222 8.83 0.00 0.00 6.46
170 171 3.771160 ACCCCACCTTCTAGCGCG 61.771 66.667 0.00 0.00 0.00 6.86
171 172 2.125106 CACCCCACCTTCTAGCGC 60.125 66.667 0.00 0.00 0.00 5.92
172 173 2.584608 CCACCCCACCTTCTAGCG 59.415 66.667 0.00 0.00 0.00 4.26
173 174 2.680370 CCCCACCCCACCTTCTAGC 61.680 68.421 0.00 0.00 0.00 3.42
174 175 0.983378 CTCCCCACCCCACCTTCTAG 60.983 65.000 0.00 0.00 0.00 2.43
175 176 1.082206 CTCCCCACCCCACCTTCTA 59.918 63.158 0.00 0.00 0.00 2.10
176 177 2.204151 CTCCCCACCCCACCTTCT 60.204 66.667 0.00 0.00 0.00 2.85
177 178 3.339093 CCTCCCCACCCCACCTTC 61.339 72.222 0.00 0.00 0.00 3.46
186 187 1.996070 GATAGCAACCCCCTCCCCAC 61.996 65.000 0.00 0.00 0.00 4.61
187 188 1.696314 GATAGCAACCCCCTCCCCA 60.696 63.158 0.00 0.00 0.00 4.96
188 189 2.461739 GGATAGCAACCCCCTCCCC 61.462 68.421 0.00 0.00 0.00 4.81
189 190 1.386057 AGGATAGCAACCCCCTCCC 60.386 63.158 0.00 0.00 0.00 4.30
190 191 1.759459 CGAGGATAGCAACCCCCTCC 61.759 65.000 0.00 0.00 41.54 4.30
191 192 1.749033 CGAGGATAGCAACCCCCTC 59.251 63.158 0.00 0.00 41.25 4.30
192 193 1.766461 CCGAGGATAGCAACCCCCT 60.766 63.158 0.00 0.00 0.00 4.79
193 194 2.819284 CCCGAGGATAGCAACCCCC 61.819 68.421 0.00 0.00 0.00 5.40
194 195 2.819284 CCCCGAGGATAGCAACCCC 61.819 68.421 0.00 0.00 33.47 4.95
195 196 2.070650 ACCCCGAGGATAGCAACCC 61.071 63.158 0.00 0.00 36.73 4.11
196 197 1.146263 CACCCCGAGGATAGCAACC 59.854 63.158 0.00 0.00 36.73 3.77
197 198 1.523938 GCACCCCGAGGATAGCAAC 60.524 63.158 0.00 0.00 36.73 4.17
198 199 1.689233 AGCACCCCGAGGATAGCAA 60.689 57.895 0.00 0.00 36.73 3.91
199 200 2.041922 AGCACCCCGAGGATAGCA 60.042 61.111 0.00 0.00 36.73 3.49
200 201 2.423446 CAGCACCCCGAGGATAGC 59.577 66.667 0.00 0.00 36.73 2.97
201 202 2.423446 GCAGCACCCCGAGGATAG 59.577 66.667 0.00 0.00 36.73 2.08
202 203 3.161450 GGCAGCACCCCGAGGATA 61.161 66.667 0.00 0.00 36.73 2.59
212 213 3.118454 TTTCTAGCGCGGCAGCAC 61.118 61.111 8.83 0.00 45.49 4.40
213 214 3.118454 GTTTCTAGCGCGGCAGCA 61.118 61.111 8.83 0.00 45.49 4.41
214 215 3.865830 GGTTTCTAGCGCGGCAGC 61.866 66.667 8.83 0.00 40.74 5.25
215 216 2.125512 AGGTTTCTAGCGCGGCAG 60.126 61.111 8.83 0.33 0.00 4.85
216 217 2.434185 CAGGTTTCTAGCGCGGCA 60.434 61.111 8.83 0.00 0.00 5.69
217 218 2.434359 ACAGGTTTCTAGCGCGGC 60.434 61.111 8.83 0.00 0.00 6.53
218 219 0.949105 AACACAGGTTTCTAGCGCGG 60.949 55.000 8.83 0.00 31.83 6.46
219 220 1.705256 TAACACAGGTTTCTAGCGCG 58.295 50.000 0.00 0.00 38.45 6.86
220 221 3.064931 ACTTAACACAGGTTTCTAGCGC 58.935 45.455 0.00 0.00 38.45 5.92
221 222 3.432252 CCACTTAACACAGGTTTCTAGCG 59.568 47.826 0.00 0.00 38.45 4.26
222 223 3.751698 CCCACTTAACACAGGTTTCTAGC 59.248 47.826 0.00 0.00 38.45 3.42
223 224 4.324267 CCCCACTTAACACAGGTTTCTAG 58.676 47.826 0.00 0.00 38.45 2.43
224 225 3.073356 CCCCCACTTAACACAGGTTTCTA 59.927 47.826 0.00 0.00 38.45 2.10
225 226 2.158519 CCCCCACTTAACACAGGTTTCT 60.159 50.000 0.00 0.00 38.45 2.52
226 227 2.235891 CCCCCACTTAACACAGGTTTC 58.764 52.381 0.00 0.00 38.45 2.78
227 228 2.375014 CCCCCACTTAACACAGGTTT 57.625 50.000 0.00 0.00 38.45 3.27
244 245 3.138468 AGCCTTATTCTCATAACACCCCC 59.862 47.826 0.00 0.00 0.00 5.40
245 246 4.439253 AGCCTTATTCTCATAACACCCC 57.561 45.455 0.00 0.00 0.00 4.95
246 247 5.652452 ACAAAGCCTTATTCTCATAACACCC 59.348 40.000 0.00 0.00 0.00 4.61
247 248 6.759497 ACAAAGCCTTATTCTCATAACACC 57.241 37.500 0.00 0.00 0.00 4.16
248 249 9.722056 CATAACAAAGCCTTATTCTCATAACAC 57.278 33.333 0.00 0.00 0.00 3.32
249 250 9.679661 TCATAACAAAGCCTTATTCTCATAACA 57.320 29.630 0.00 0.00 0.00 2.41
253 254 9.638176 ATTCTCATAACAAAGCCTTATTCTCAT 57.362 29.630 0.00 0.00 0.00 2.90
258 259 9.700831 ACCTTATTCTCATAACAAAGCCTTATT 57.299 29.630 0.00 0.00 0.00 1.40
259 260 9.343539 GACCTTATTCTCATAACAAAGCCTTAT 57.656 33.333 0.00 0.00 0.00 1.73
260 261 8.548877 AGACCTTATTCTCATAACAAAGCCTTA 58.451 33.333 0.00 0.00 0.00 2.69
261 262 7.406104 AGACCTTATTCTCATAACAAAGCCTT 58.594 34.615 0.00 0.00 0.00 4.35
262 263 6.963322 AGACCTTATTCTCATAACAAAGCCT 58.037 36.000 0.00 0.00 0.00 4.58
263 264 7.631717 AAGACCTTATTCTCATAACAAAGCC 57.368 36.000 0.00 0.00 0.00 4.35
266 267 9.681062 CCCTTAAGACCTTATTCTCATAACAAA 57.319 33.333 3.36 0.00 0.00 2.83
267 268 8.272173 CCCCTTAAGACCTTATTCTCATAACAA 58.728 37.037 3.36 0.00 0.00 2.83
268 269 7.404980 ACCCCTTAAGACCTTATTCTCATAACA 59.595 37.037 3.36 0.00 0.00 2.41
269 270 7.715686 CACCCCTTAAGACCTTATTCTCATAAC 59.284 40.741 3.36 0.00 0.00 1.89
270 271 7.404980 ACACCCCTTAAGACCTTATTCTCATAA 59.595 37.037 3.36 0.00 0.00 1.90
271 272 6.906901 ACACCCCTTAAGACCTTATTCTCATA 59.093 38.462 3.36 0.00 0.00 2.15
272 273 5.731678 ACACCCCTTAAGACCTTATTCTCAT 59.268 40.000 3.36 0.00 0.00 2.90
273 274 5.098663 ACACCCCTTAAGACCTTATTCTCA 58.901 41.667 3.36 0.00 0.00 3.27
274 275 5.695424 ACACCCCTTAAGACCTTATTCTC 57.305 43.478 3.36 0.00 0.00 2.87
275 276 7.404980 TCATAACACCCCTTAAGACCTTATTCT 59.595 37.037 3.36 0.00 0.00 2.40
276 277 7.571025 TCATAACACCCCTTAAGACCTTATTC 58.429 38.462 3.36 0.00 0.00 1.75
277 278 7.404980 TCTCATAACACCCCTTAAGACCTTATT 59.595 37.037 3.36 0.00 0.00 1.40
278 279 6.906901 TCTCATAACACCCCTTAAGACCTTAT 59.093 38.462 3.36 0.00 0.00 1.73
279 280 6.266080 TCTCATAACACCCCTTAAGACCTTA 58.734 40.000 3.36 0.00 0.00 2.69
280 281 5.098663 TCTCATAACACCCCTTAAGACCTT 58.901 41.667 3.36 0.00 0.00 3.50
281 282 4.695606 TCTCATAACACCCCTTAAGACCT 58.304 43.478 3.36 0.00 0.00 3.85
282 283 5.431179 TTCTCATAACACCCCTTAAGACC 57.569 43.478 3.36 0.00 0.00 3.85
283 284 7.927092 GTCTATTCTCATAACACCCCTTAAGAC 59.073 40.741 3.36 0.00 0.00 3.01
284 285 7.070821 GGTCTATTCTCATAACACCCCTTAAGA 59.929 40.741 3.36 0.00 0.00 2.10
285 286 7.217906 GGTCTATTCTCATAACACCCCTTAAG 58.782 42.308 0.00 0.00 0.00 1.85
286 287 6.100714 GGGTCTATTCTCATAACACCCCTTAA 59.899 42.308 0.00 0.00 34.43 1.85
287 288 5.605488 GGGTCTATTCTCATAACACCCCTTA 59.395 44.000 0.00 0.00 34.43 2.69
288 289 4.412528 GGGTCTATTCTCATAACACCCCTT 59.587 45.833 0.00 0.00 34.43 3.95
289 290 3.974642 GGGTCTATTCTCATAACACCCCT 59.025 47.826 0.00 0.00 34.43 4.79
290 291 3.714798 TGGGTCTATTCTCATAACACCCC 59.285 47.826 1.78 0.00 37.30 4.95
291 292 4.444449 GGTGGGTCTATTCTCATAACACCC 60.444 50.000 0.00 0.00 39.82 4.61
292 293 4.444449 GGGTGGGTCTATTCTCATAACACC 60.444 50.000 0.00 0.00 43.73 4.16
293 294 4.409247 AGGGTGGGTCTATTCTCATAACAC 59.591 45.833 0.00 0.00 0.00 3.32
294 295 4.631234 AGGGTGGGTCTATTCTCATAACA 58.369 43.478 0.00 0.00 0.00 2.41
295 296 6.936968 ATAGGGTGGGTCTATTCTCATAAC 57.063 41.667 0.00 0.00 0.00 1.89
303 304 9.603189 GCAGTATATATATAGGGTGGGTCTATT 57.397 37.037 2.53 0.00 0.00 1.73
304 305 8.971894 AGCAGTATATATATAGGGTGGGTCTAT 58.028 37.037 2.53 0.00 0.00 1.98
305 306 8.359404 AGCAGTATATATATAGGGTGGGTCTA 57.641 38.462 2.53 0.00 0.00 2.59
306 307 7.240390 AGCAGTATATATATAGGGTGGGTCT 57.760 40.000 2.53 0.00 0.00 3.85
307 308 9.026121 CATAGCAGTATATATATAGGGTGGGTC 57.974 40.741 2.53 0.00 0.00 4.46
308 309 7.455008 GCATAGCAGTATATATATAGGGTGGGT 59.545 40.741 2.53 0.89 0.00 4.51
309 310 7.676043 AGCATAGCAGTATATATATAGGGTGGG 59.324 40.741 2.53 3.50 0.00 4.61
310 311 8.657387 AGCATAGCAGTATATATATAGGGTGG 57.343 38.462 2.53 3.77 0.00 4.61
361 374 9.539825 CACTGATTGATGAAGCTACTAATTAGT 57.460 33.333 21.35 21.35 40.24 2.24
364 377 6.261826 GCCACTGATTGATGAAGCTACTAATT 59.738 38.462 0.00 0.00 0.00 1.40
452 465 1.251251 GAACCCAGCTTTGACATGCT 58.749 50.000 0.00 0.00 40.54 3.79
494 507 2.205022 TGGGCATGAAGAGTGGAAAG 57.795 50.000 0.00 0.00 0.00 2.62
508 522 2.092484 TGCAGCATACTAATCTTGGGCA 60.092 45.455 0.00 0.00 0.00 5.36
593 607 1.562672 CGGGGTTTGGGTGAGATCCT 61.563 60.000 0.00 0.00 0.00 3.24
601 615 1.789576 AAGATGAGCGGGGTTTGGGT 61.790 55.000 0.00 0.00 0.00 4.51
739 779 7.282224 GGGTGTATCTTGTGTAAATGATGCTAA 59.718 37.037 0.00 0.00 0.00 3.09
793 833 9.421399 TGATAGAAGACTGGTGAAGAATATACA 57.579 33.333 0.00 0.00 0.00 2.29
810 851 6.980978 GCACTAGTTACAAGCATGATAGAAGA 59.019 38.462 0.00 0.00 0.00 2.87
839 880 8.345565 GTGAAAATCTTGTCTTACAACATGAGT 58.654 33.333 0.00 0.00 36.93 3.41
895 936 4.214437 GTCGTGCAAAGAAGAATCTTGTG 58.786 43.478 0.00 0.00 45.19 3.33
998 1039 1.678728 CCAAGGTGATGGCGTACATGT 60.679 52.381 2.69 2.69 40.72 3.21
1161 1210 2.897271 ACATCAATGGGGCACAACTA 57.103 45.000 0.00 0.00 0.00 2.24
1318 1367 6.403878 TCTCCATGTTAGCAGTAGTAAAACC 58.596 40.000 0.00 0.00 0.00 3.27
1338 1387 2.950309 TCGGCAGTAGTCAATACTCTCC 59.050 50.000 0.00 0.00 43.13 3.71
1348 1397 1.166129 TCTCTGTGTCGGCAGTAGTC 58.834 55.000 0.00 0.00 37.70 2.59
1399 1451 8.178964 TGCATACGAAGGTGAAATATTACAAAC 58.821 33.333 0.00 0.00 0.00 2.93
1500 1553 9.045223 CAAGTACAAGCAAGTATATATCAAGCA 57.955 33.333 0.00 0.00 0.00 3.91
1501 1554 9.261180 TCAAGTACAAGCAAGTATATATCAAGC 57.739 33.333 0.00 0.00 0.00 4.01
1529 1582 1.611519 CACCAACATTAACCCACGGT 58.388 50.000 0.00 0.00 37.65 4.83
1531 1584 1.611519 ACCACCAACATTAACCCACG 58.388 50.000 0.00 0.00 0.00 4.94
1769 1826 5.985530 TGGCAAGATCTAACAATACTCATCG 59.014 40.000 0.00 0.00 0.00 3.84
1805 1862 8.255206 ACAAAATACCATTCTACTATCACGACA 58.745 33.333 0.00 0.00 0.00 4.35
1999 2063 8.690203 TTATGAACAGACCATTCAAGAAAAGA 57.310 30.769 0.00 0.00 39.43 2.52
2168 2232 3.118149 ACAAAAACTTCGGTAGTCAGGGT 60.118 43.478 0.00 0.00 35.54 4.34
2219 2294 3.622630 ACATACTAGACTCGCTGGACTT 58.377 45.455 0.00 0.00 0.00 3.01
2233 2308 5.187772 AGCTCCTGTCATGAACAACATACTA 59.812 40.000 0.00 0.00 37.45 1.82
2280 2372 7.046292 TCTACAAGTGTAACAAGCTCTACAA 57.954 36.000 5.18 0.00 41.43 2.41
2282 2374 5.573669 GCTCTACAAGTGTAACAAGCTCTAC 59.426 44.000 10.59 0.00 41.43 2.59
2283 2375 5.477291 AGCTCTACAAGTGTAACAAGCTCTA 59.523 40.000 13.09 0.00 41.43 2.43
2284 2376 4.282195 AGCTCTACAAGTGTAACAAGCTCT 59.718 41.667 13.09 0.00 41.43 4.09
2285 2377 4.561105 AGCTCTACAAGTGTAACAAGCTC 58.439 43.478 13.09 0.00 41.43 4.09
2286 2378 4.608948 AGCTCTACAAGTGTAACAAGCT 57.391 40.909 13.09 13.09 41.43 3.74
2287 2379 4.511826 ACAAGCTCTACAAGTGTAACAAGC 59.488 41.667 10.14 10.14 41.43 4.01
2288 2380 7.709269 TTACAAGCTCTACAAGTGTAACAAG 57.291 36.000 1.66 0.00 41.43 3.16
2289 2381 7.767198 ACTTTACAAGCTCTACAAGTGTAACAA 59.233 33.333 4.75 0.00 41.43 2.83
2290 2382 7.270047 ACTTTACAAGCTCTACAAGTGTAACA 58.730 34.615 4.75 0.00 41.43 2.41
2291 2383 7.710766 ACTTTACAAGCTCTACAAGTGTAAC 57.289 36.000 4.75 0.00 0.00 2.50
2515 2627 2.356125 CCACTAGTCAAATGGGTCCCAG 60.356 54.545 17.70 2.71 36.75 4.45
2526 2640 9.589461 TTTTTATTAAATGGGTCCACTAGTCAA 57.411 29.630 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.