Multiple sequence alignment - TraesCS5D01G183500

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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 TraesCS5D01G183500 chr5D 100.000 2886 0 0 1 2886 285246655 285249540 0.000000e+00 5330.0
1 TraesCS5D01G183500 chr5D 93.617 47 3 0 2214 2260 335051197 335051151 1.430000e-08 71.3
2 TraesCS5D01G183500 chr5D 100.000 30 0 0 789 818 113391895 113391866 4.020000e-04 56.5
3 TraesCS5D01G183500 chr5B 93.792 2078 97 18 316 2378 322858242 322860302 0.000000e+00 3094.0
4 TraesCS5D01G183500 chr5B 91.783 572 37 8 2321 2886 322860305 322860872 0.000000e+00 787.0
5 TraesCS5D01G183500 chr5B 93.085 188 7 1 1 188 322857971 322858152 1.320000e-68 270.0
6 TraesCS5D01G183500 chr5A 93.512 1680 76 25 343 2004 377119164 377120828 0.000000e+00 2468.0
7 TraesCS5D01G183500 chr5A 93.437 838 35 12 1995 2829 377120849 377121669 0.000000e+00 1225.0
8 TraesCS5D01G183500 chr5A 84.433 591 56 25 1 577 377118786 377119354 1.510000e-152 549.0
9 TraesCS5D01G183500 chr5A 93.617 47 3 0 2214 2260 436331771 436331725 1.430000e-08 71.3
10 TraesCS5D01G183500 chr3D 96.552 58 0 2 778 834 252334793 252334849 8.510000e-16 95.3
11 TraesCS5D01G183500 chr3D 93.617 47 3 0 2214 2260 47491036 47491082 1.430000e-08 71.3
12 TraesCS5D01G183500 chr3D 90.385 52 4 1 2214 2264 547615599 547615650 1.860000e-07 67.6
13 TraesCS5D01G183500 chr3B 96.491 57 2 0 778 834 313808026 313808082 8.510000e-16 95.3
14 TraesCS5D01G183500 chr3A 100.000 51 0 0 784 834 332220139 332220089 8.510000e-16 95.3
15 TraesCS5D01G183500 chr6D 98.039 51 1 0 784 834 52724695 52724645 3.960000e-14 89.8
16 TraesCS5D01G183500 chr6D 85.938 64 6 2 2205 2266 450139687 450139749 6.670000e-07 65.8
17 TraesCS5D01G183500 chr6B 98.039 51 1 0 784 834 119849607 119849557 3.960000e-14 89.8
18 TraesCS5D01G183500 chr6A 98.039 51 1 0 784 834 63610635 63610585 3.960000e-14 89.8
19 TraesCS5D01G183500 chr2D 95.652 46 2 0 2214 2259 548040439 548040394 1.110000e-09 75.0
20 TraesCS5D01G183500 chr2A 93.478 46 3 0 2214 2259 657520779 657520734 5.160000e-08 69.4


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 TraesCS5D01G183500 chr5D 285246655 285249540 2885 False 5330.000000 5330 100.000000 1 2886 1 chr5D.!!$F1 2885
1 TraesCS5D01G183500 chr5B 322857971 322860872 2901 False 1383.666667 3094 92.886667 1 2886 3 chr5B.!!$F1 2885
2 TraesCS5D01G183500 chr5A 377118786 377121669 2883 False 1414.000000 2468 90.460667 1 2829 3 chr5A.!!$F1 2828

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
263 274 0.036732 TGCTGCCTAAACCCTGTCTG 59.963 55.0 0.0 0.0 0.00 3.51 F
264 275 0.036875 GCTGCCTAAACCCTGTCTGT 59.963 55.0 0.0 0.0 0.00 3.41 F
742 804 0.179018 GTTGCTGGTCCTGTTGGAGT 60.179 55.0 0.0 0.0 44.16 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1813 1.069427 GCAGCAGATGATCTCGCCT 59.931 57.895 11.45 0.00 0.00 5.52 R
1847 1919 1.602888 CTATGGGCTGGCTCCATGC 60.603 63.158 18.81 0.00 44.08 4.06 R
2612 2783 1.076332 GGCACGACAGTGTCCATTAC 58.924 55.000 17.57 3.14 46.65 1.89 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
168 172 2.158173 AGCTTCAATTCCCTTTTCCCCA 60.158 45.455 0.00 0.00 0.00 4.96
200 204 1.636003 CCCTTGCTAGGTTTCCTTCCT 59.364 52.381 13.38 0.00 40.19 3.36
201 205 2.041755 CCCTTGCTAGGTTTCCTTCCTT 59.958 50.000 13.38 0.00 40.19 3.36
202 206 3.348119 CCTTGCTAGGTTTCCTTCCTTC 58.652 50.000 5.98 0.00 36.74 3.46
204 208 1.278127 TGCTAGGTTTCCTTCCTTCCG 59.722 52.381 0.00 0.00 36.60 4.30
205 209 2.012554 GCTAGGTTTCCTTCCTTCCGC 61.013 57.143 0.00 0.00 36.60 5.54
208 212 1.677966 GTTTCCTTCCTTCCGCCCC 60.678 63.158 0.00 0.00 0.00 5.80
209 213 2.157452 TTTCCTTCCTTCCGCCCCA 61.157 57.895 0.00 0.00 0.00 4.96
211 215 4.803908 CCTTCCTTCCGCCCCAGC 62.804 72.222 0.00 0.00 0.00 4.85
212 216 3.721706 CTTCCTTCCGCCCCAGCT 61.722 66.667 0.00 0.00 36.60 4.24
213 217 3.689002 CTTCCTTCCGCCCCAGCTC 62.689 68.421 0.00 0.00 36.60 4.09
221 225 4.643387 GCCCCAGCTCCGTTGTGT 62.643 66.667 0.00 0.00 35.50 3.72
222 226 2.113139 CCCCAGCTCCGTTGTGTT 59.887 61.111 0.00 0.00 0.00 3.32
223 227 2.260869 CCCCAGCTCCGTTGTGTTG 61.261 63.158 0.00 0.00 0.00 3.33
225 229 1.893808 CCAGCTCCGTTGTGTTGCT 60.894 57.895 0.00 0.00 0.00 3.91
227 231 1.893808 AGCTCCGTTGTGTTGCTGG 60.894 57.895 0.00 0.00 32.32 4.85
231 241 2.353839 CGTTGTGTTGCTGGCAGC 60.354 61.111 31.91 31.91 42.82 5.25
232 242 2.837883 CGTTGTGTTGCTGGCAGCT 61.838 57.895 36.50 0.00 42.97 4.24
235 245 2.018727 TTGTGTTGCTGGCAGCTTGG 62.019 55.000 36.50 3.39 42.97 3.61
236 246 2.913578 TGTTGCTGGCAGCTTGGG 60.914 61.111 36.50 2.57 42.97 4.12
259 270 3.595819 GCTGCTGCCTAAACCCTG 58.404 61.111 3.85 0.00 0.00 4.45
260 271 1.303643 GCTGCTGCCTAAACCCTGT 60.304 57.895 3.85 0.00 0.00 4.00
261 272 1.308783 GCTGCTGCCTAAACCCTGTC 61.309 60.000 3.85 0.00 0.00 3.51
262 273 0.326264 CTGCTGCCTAAACCCTGTCT 59.674 55.000 0.00 0.00 0.00 3.41
263 274 0.036732 TGCTGCCTAAACCCTGTCTG 59.963 55.000 0.00 0.00 0.00 3.51
264 275 0.036875 GCTGCCTAAACCCTGTCTGT 59.963 55.000 0.00 0.00 0.00 3.41
265 276 1.946283 GCTGCCTAAACCCTGTCTGTC 60.946 57.143 0.00 0.00 0.00 3.51
266 277 0.690762 TGCCTAAACCCTGTCTGTCC 59.309 55.000 0.00 0.00 0.00 4.02
267 278 0.690762 GCCTAAACCCTGTCTGTCCA 59.309 55.000 0.00 0.00 0.00 4.02
268 279 1.073284 GCCTAAACCCTGTCTGTCCAA 59.927 52.381 0.00 0.00 0.00 3.53
269 280 2.876079 GCCTAAACCCTGTCTGTCCAAG 60.876 54.545 0.00 0.00 0.00 3.61
270 281 2.290323 CCTAAACCCTGTCTGTCCAAGG 60.290 54.545 0.00 0.00 0.00 3.61
271 282 1.222567 AAACCCTGTCTGTCCAAGGT 58.777 50.000 0.00 0.00 0.00 3.50
272 283 0.474184 AACCCTGTCTGTCCAAGGTG 59.526 55.000 0.00 0.00 0.00 4.00
273 284 1.376466 CCCTGTCTGTCCAAGGTGG 59.624 63.158 0.00 0.00 39.43 4.61
274 285 1.127567 CCCTGTCTGTCCAAGGTGGA 61.128 60.000 0.00 0.00 45.98 4.02
301 312 4.828925 GCTCGCCACCTCAGCCTC 62.829 72.222 0.00 0.00 0.00 4.70
302 313 4.154347 CTCGCCACCTCAGCCTCC 62.154 72.222 0.00 0.00 0.00 4.30
304 315 4.020617 CGCCACCTCAGCCTCCAA 62.021 66.667 0.00 0.00 0.00 3.53
306 317 2.352805 CCACCTCAGCCTCCAACC 59.647 66.667 0.00 0.00 0.00 3.77
307 318 2.227036 CCACCTCAGCCTCCAACCT 61.227 63.158 0.00 0.00 0.00 3.50
308 319 1.298014 CACCTCAGCCTCCAACCTC 59.702 63.158 0.00 0.00 0.00 3.85
309 320 1.920835 ACCTCAGCCTCCAACCTCC 60.921 63.158 0.00 0.00 0.00 4.30
310 321 1.920325 CCTCAGCCTCCAACCTCCA 60.920 63.158 0.00 0.00 0.00 3.86
311 322 1.601171 CTCAGCCTCCAACCTCCAG 59.399 63.158 0.00 0.00 0.00 3.86
312 323 2.045536 CAGCCTCCAACCTCCAGC 60.046 66.667 0.00 0.00 0.00 4.85
313 324 3.334054 AGCCTCCAACCTCCAGCC 61.334 66.667 0.00 0.00 0.00 4.85
314 325 3.334054 GCCTCCAACCTCCAGCCT 61.334 66.667 0.00 0.00 0.00 4.58
330 341 3.056322 CCAGCCTTTCTTCCCAAATCTTG 60.056 47.826 0.00 0.00 0.00 3.02
331 342 3.828451 CAGCCTTTCTTCCCAAATCTTGA 59.172 43.478 0.00 0.00 0.00 3.02
332 343 4.465305 CAGCCTTTCTTCCCAAATCTTGAT 59.535 41.667 0.00 0.00 0.00 2.57
333 344 4.708909 AGCCTTTCTTCCCAAATCTTGATC 59.291 41.667 0.00 0.00 0.00 2.92
341 353 7.689299 TCTTCCCAAATCTTGATCTTGACTTA 58.311 34.615 0.00 0.00 0.00 2.24
437 494 0.254299 ATCCATTTCCCAGGGGAGGT 60.254 55.000 5.33 0.00 46.06 3.85
456 513 3.966665 AGGTTCTGCCAAAAATTCCTTCA 59.033 39.130 0.00 0.00 40.61 3.02
551 608 1.130373 GCCGAAATTTGATCTGCGACA 59.870 47.619 0.00 0.00 0.00 4.35
622 681 2.035832 GCCACATAGCACCAAAACTTGT 59.964 45.455 0.00 0.00 0.00 3.16
677 736 7.781056 TCATTTGCAAGGTAAAGAAAAGAGTT 58.219 30.769 0.00 0.00 0.00 3.01
700 759 7.933577 AGTTTGTTGTGTTCTTGATGATAGAGA 59.066 33.333 0.00 0.00 0.00 3.10
742 804 0.179018 GTTGCTGGTCCTGTTGGAGT 60.179 55.000 0.00 0.00 44.16 3.85
1053 1119 3.999285 ACCCGGAGCTCCAGGTCT 61.999 66.667 31.69 13.30 43.14 3.85
1189 1255 0.390472 CCTCTCCTCGCAGGTTTGTC 60.390 60.000 2.68 0.00 36.53 3.18
1203 1269 2.375146 GTTTGTCACACCCTTCCAAGT 58.625 47.619 0.00 0.00 0.00 3.16
1323 1391 1.061799 CGCGCTCAAGCATGTGAAAC 61.062 55.000 5.56 0.00 42.21 2.78
1331 1399 5.695816 GCTCAAGCATGTGAAACCAAAAATA 59.304 36.000 0.00 0.00 41.59 1.40
1348 1416 5.975693 AAAATAGATGAAAACGAAGGCCA 57.024 34.783 5.01 0.00 0.00 5.36
1349 1417 4.965119 AATAGATGAAAACGAAGGCCAC 57.035 40.909 5.01 0.00 0.00 5.01
1351 1419 1.073923 AGATGAAAACGAAGGCCACCT 59.926 47.619 5.01 0.00 33.87 4.00
1352 1420 2.304761 AGATGAAAACGAAGGCCACCTA 59.695 45.455 5.01 0.00 31.13 3.08
1434 1503 5.820947 CCTACCTAACACTTTGAACAACACT 59.179 40.000 0.00 0.00 0.00 3.55
1445 1514 9.086336 CACTTTGAACAACACTACAAATTCATT 57.914 29.630 0.00 0.00 33.01 2.57
1458 1527 9.404848 ACTACAAATTCATTCATCATCATGAGT 57.595 29.630 0.09 0.00 40.28 3.41
1465 1534 7.868906 TCATTCATCATCATGAGTTGCTTAA 57.131 32.000 0.09 0.00 40.28 1.85
1482 1553 9.297037 AGTTGCTTAATTTATAACAGGTTGAGT 57.703 29.630 0.00 0.00 0.00 3.41
1501 1572 8.780249 GGTTGAGTTTTTATCAAACTAGTAGCA 58.220 33.333 0.00 0.00 40.49 3.49
1506 1577 8.818057 AGTTTTTATCAAACTAGTAGCATAGCG 58.182 33.333 0.00 0.00 38.58 4.26
1507 1578 8.601476 GTTTTTATCAAACTAGTAGCATAGCGT 58.399 33.333 0.00 0.00 0.00 5.07
1546 1617 7.973944 ACATGAAAGAAAACCTAACAAGAACAC 59.026 33.333 0.00 0.00 0.00 3.32
1550 1621 5.667466 AGAAAACCTAACAAGAACACGAGA 58.333 37.500 0.00 0.00 0.00 4.04
1660 1732 2.282391 GTGCTGGGCATGACCACA 60.282 61.111 19.12 17.30 41.91 4.17
1780 1852 3.254166 GCATGAACTCAATCACCAACACT 59.746 43.478 0.00 0.00 30.82 3.55
1782 1854 3.884895 TGAACTCAATCACCAACACTGT 58.115 40.909 0.00 0.00 0.00 3.55
1786 1858 4.464008 ACTCAATCACCAACACTGTGAAT 58.536 39.130 15.86 0.00 45.15 2.57
1790 1862 1.492599 TCACCAACACTGTGAATCCCA 59.507 47.619 15.86 0.00 39.66 4.37
1829 1901 3.463505 CAAGCAGTGCCTACGACG 58.536 61.111 12.58 0.00 0.00 5.12
1927 2002 2.546899 TGTTGTCATAGCTGGTAGGGT 58.453 47.619 0.00 0.00 0.00 4.34
1995 2070 2.440796 CCATTGATGCGTGCCCCT 60.441 61.111 0.00 0.00 0.00 4.79
2005 2110 1.893919 GCGTGCCCCTCTCTCTCTTT 61.894 60.000 0.00 0.00 0.00 2.52
2016 2121 8.211629 GCCCCTCTCTCTCTTTATTGTTTATTA 58.788 37.037 0.00 0.00 0.00 0.98
2070 2175 1.202940 GGTAGGAGGGGAATTGATGGC 60.203 57.143 0.00 0.00 0.00 4.40
2086 2193 3.258872 TGATGGCCCATTTTGTCAAAGAG 59.741 43.478 0.00 0.00 0.00 2.85
2087 2194 2.956132 TGGCCCATTTTGTCAAAGAGA 58.044 42.857 0.00 0.00 0.00 3.10
2088 2195 2.892852 TGGCCCATTTTGTCAAAGAGAG 59.107 45.455 0.00 0.00 0.00 3.20
2089 2196 3.157087 GGCCCATTTTGTCAAAGAGAGA 58.843 45.455 0.00 0.00 0.00 3.10
2151 2258 6.263392 GGTGATGTCTAGCTAGTAAGATGTGA 59.737 42.308 20.10 0.00 0.00 3.58
2268 2375 8.536340 AGGACGAAGGGAGTATATAATTATCC 57.464 38.462 0.00 0.00 0.00 2.59
2302 2409 1.400846 TCTCTTATCGCACGTGTCTCC 59.599 52.381 18.38 0.00 0.00 3.71
2408 2576 5.731957 TTGCAGTGGTGTAGATGTAAGTA 57.268 39.130 0.00 0.00 0.00 2.24
2422 2590 5.939883 AGATGTAAGTACAGAAGCATGCAAA 59.060 36.000 21.98 0.00 39.92 3.68
2432 2601 4.324402 CAGAAGCATGCAAAATTTACGGAC 59.676 41.667 21.98 0.00 0.00 4.79
2439 2608 6.510960 GCATGCAAAATTTACGGACAAAAGTT 60.511 34.615 14.21 0.00 0.00 2.66
2460 2629 7.592885 AGTTGAATATTGCTCTATTGCCATT 57.407 32.000 0.00 0.00 0.00 3.16
2596 2767 2.289547 ACCAACGTGTGTAAATGTGAGC 59.710 45.455 0.00 0.00 0.00 4.26
2612 2783 0.931005 GAGCGCTAGGATTTGAACCG 59.069 55.000 11.50 0.00 0.00 4.44
2620 2791 4.272748 GCTAGGATTTGAACCGTAATGGAC 59.727 45.833 0.00 0.00 42.00 4.02
2641 2812 0.583438 CTGTCGTGCCTCAACAACTG 59.417 55.000 0.00 0.00 0.00 3.16
2694 2865 4.142534 CCTCTGCATTGTTCAATGTACAGG 60.143 45.833 21.38 19.30 32.87 4.00
2716 2887 2.735762 GCCTCAACTTACTACAGAGCCG 60.736 54.545 0.00 0.00 0.00 5.52
2810 2981 1.073923 AGCACAAACCCACCTAAGGAG 59.926 52.381 0.00 0.00 0.00 3.69
2818 2989 2.247635 ACCCACCTAAGGAGAGAGCATA 59.752 50.000 0.00 0.00 0.00 3.14
2847 3018 4.437682 TTATAATCTGCAAGGGGGTCAG 57.562 45.455 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 172 2.911926 GCAAGGGAGCTGGGGAAGT 61.912 63.158 0.00 0.00 0.00 3.01
204 208 4.643387 ACACAACGGAGCTGGGGC 62.643 66.667 0.00 0.00 26.78 5.80
205 209 2.113139 AACACAACGGAGCTGGGG 59.887 61.111 0.00 0.00 26.78 4.96
208 212 1.280746 CAGCAACACAACGGAGCTG 59.719 57.895 0.00 0.00 45.44 4.24
209 213 1.893808 CCAGCAACACAACGGAGCT 60.894 57.895 0.00 0.00 35.63 4.09
211 215 2.121564 CTGCCAGCAACACAACGGAG 62.122 60.000 0.00 0.00 0.00 4.63
212 216 2.124529 TGCCAGCAACACAACGGA 60.125 55.556 0.00 0.00 0.00 4.69
213 217 2.332514 CTGCCAGCAACACAACGG 59.667 61.111 0.00 0.00 0.00 4.44
214 218 2.340453 AAGCTGCCAGCAACACAACG 62.340 55.000 20.53 0.00 45.56 4.10
215 219 0.872881 CAAGCTGCCAGCAACACAAC 60.873 55.000 20.53 0.00 45.56 3.32
216 220 1.438399 CAAGCTGCCAGCAACACAA 59.562 52.632 20.53 0.00 45.56 3.33
217 221 2.491897 CCAAGCTGCCAGCAACACA 61.492 57.895 20.53 0.00 45.56 3.72
219 223 2.913578 CCCAAGCTGCCAGCAACA 60.914 61.111 20.53 0.00 45.56 3.33
220 224 2.914097 ACCCAAGCTGCCAGCAAC 60.914 61.111 20.53 0.00 45.56 4.17
221 225 2.598394 GACCCAAGCTGCCAGCAA 60.598 61.111 20.53 0.00 45.56 3.91
222 226 3.137385 AAGACCCAAGCTGCCAGCA 62.137 57.895 20.53 0.36 45.56 4.41
223 227 2.282745 AAGACCCAAGCTGCCAGC 60.283 61.111 9.13 9.13 42.84 4.85
225 229 2.115910 CCAAGACCCAAGCTGCCA 59.884 61.111 0.00 0.00 0.00 4.92
227 231 2.282745 AGCCAAGACCCAAGCTGC 60.283 61.111 0.00 0.00 33.41 5.25
231 241 2.633509 GCAGCAGCCAAGACCCAAG 61.634 63.158 0.00 0.00 33.58 3.61
232 242 2.598394 GCAGCAGCCAAGACCCAA 60.598 61.111 0.00 0.00 33.58 4.12
254 264 4.750289 ACCTTGGACAGACAGGGT 57.250 55.556 0.00 0.00 44.93 4.34
264 275 0.621082 TTGTGTGTGTCCACCTTGGA 59.379 50.000 0.00 0.00 45.98 3.53
265 276 1.024271 CTTGTGTGTGTCCACCTTGG 58.976 55.000 0.00 0.00 41.09 3.61
266 277 0.381801 GCTTGTGTGTGTCCACCTTG 59.618 55.000 0.00 0.00 41.09 3.61
267 278 0.255890 AGCTTGTGTGTGTCCACCTT 59.744 50.000 0.00 0.00 41.09 3.50
268 279 0.179045 GAGCTTGTGTGTGTCCACCT 60.179 55.000 0.00 0.00 41.09 4.00
269 280 1.498865 CGAGCTTGTGTGTGTCCACC 61.499 60.000 0.00 0.00 41.09 4.61
270 281 1.934463 CGAGCTTGTGTGTGTCCAC 59.066 57.895 0.00 0.00 42.19 4.02
271 282 1.887242 GCGAGCTTGTGTGTGTCCA 60.887 57.895 2.14 0.00 0.00 4.02
272 283 2.607892 GGCGAGCTTGTGTGTGTCC 61.608 63.158 2.14 0.00 0.00 4.02
273 284 1.887242 TGGCGAGCTTGTGTGTGTC 60.887 57.895 2.14 0.00 0.00 3.67
274 285 2.180204 GTGGCGAGCTTGTGTGTGT 61.180 57.895 2.14 0.00 0.00 3.72
275 286 2.633657 GTGGCGAGCTTGTGTGTG 59.366 61.111 2.14 0.00 0.00 3.82
276 287 2.591715 GGTGGCGAGCTTGTGTGT 60.592 61.111 2.14 0.00 0.00 3.72
277 288 2.281070 AGGTGGCGAGCTTGTGTG 60.281 61.111 2.14 0.00 0.00 3.82
278 289 2.031163 GAGGTGGCGAGCTTGTGT 59.969 61.111 0.82 0.00 0.00 3.72
281 292 3.123620 GCTGAGGTGGCGAGCTTG 61.124 66.667 0.82 0.00 0.00 4.01
300 311 1.073923 GAAGAAAGGCTGGAGGTTGGA 59.926 52.381 0.00 0.00 0.00 3.53
301 312 1.539157 GAAGAAAGGCTGGAGGTTGG 58.461 55.000 0.00 0.00 0.00 3.77
302 313 1.539157 GGAAGAAAGGCTGGAGGTTG 58.461 55.000 0.00 0.00 0.00 3.77
303 314 0.405973 GGGAAGAAAGGCTGGAGGTT 59.594 55.000 0.00 0.00 0.00 3.50
304 315 0.772124 TGGGAAGAAAGGCTGGAGGT 60.772 55.000 0.00 0.00 0.00 3.85
306 317 2.292828 TTTGGGAAGAAAGGCTGGAG 57.707 50.000 0.00 0.00 0.00 3.86
307 318 2.379907 AGATTTGGGAAGAAAGGCTGGA 59.620 45.455 0.00 0.00 0.00 3.86
308 319 2.812658 AGATTTGGGAAGAAAGGCTGG 58.187 47.619 0.00 0.00 0.00 4.85
309 320 3.828451 TCAAGATTTGGGAAGAAAGGCTG 59.172 43.478 0.00 0.00 0.00 4.85
310 321 4.118168 TCAAGATTTGGGAAGAAAGGCT 57.882 40.909 0.00 0.00 0.00 4.58
311 322 4.708909 AGATCAAGATTTGGGAAGAAAGGC 59.291 41.667 0.00 0.00 0.00 4.35
312 323 6.435277 TCAAGATCAAGATTTGGGAAGAAAGG 59.565 38.462 0.00 0.00 0.00 3.11
313 324 7.176340 AGTCAAGATCAAGATTTGGGAAGAAAG 59.824 37.037 0.00 0.00 0.00 2.62
314 325 7.006509 AGTCAAGATCAAGATTTGGGAAGAAA 58.993 34.615 0.00 0.00 0.00 2.52
330 341 3.069443 CAGAGCCTCCCTAAGTCAAGATC 59.931 52.174 0.00 0.00 0.00 2.75
331 342 3.037549 CAGAGCCTCCCTAAGTCAAGAT 58.962 50.000 0.00 0.00 0.00 2.40
332 343 2.461695 CAGAGCCTCCCTAAGTCAAGA 58.538 52.381 0.00 0.00 0.00 3.02
333 344 1.134551 GCAGAGCCTCCCTAAGTCAAG 60.135 57.143 0.00 0.00 0.00 3.02
407 419 2.381275 GGGAAATGGATGATGGGAGGAT 59.619 50.000 0.00 0.00 0.00 3.24
411 423 1.500303 CCTGGGAAATGGATGATGGGA 59.500 52.381 0.00 0.00 0.00 4.37
413 425 1.481802 CCCCTGGGAAATGGATGATGG 60.482 57.143 16.20 0.00 37.50 3.51
437 494 3.243704 CGGTGAAGGAATTTTTGGCAGAA 60.244 43.478 0.00 0.00 0.00 3.02
456 513 1.143684 CCCTGGAAATGGATGATCGGT 59.856 52.381 0.00 0.00 0.00 4.69
551 608 2.450886 ACCTCCCCTTGGAAATGAAACT 59.549 45.455 0.00 0.00 41.17 2.66
607 666 7.067615 TGTTTTCAGATACAAGTTTTGGTGCTA 59.932 33.333 0.00 0.00 34.12 3.49
677 736 6.366061 CGTCTCTATCATCAAGAACACAACAA 59.634 38.462 0.00 0.00 0.00 2.83
700 759 0.809385 ATCTACACGTGCTACTGCGT 59.191 50.000 17.22 0.00 43.34 5.24
742 804 3.181399 ACCATAAATCCGGAGAGGGGATA 60.181 47.826 11.34 0.00 43.43 2.59
865 927 9.961265 TTGATTATGTTACTAGTATGAACTCCG 57.039 33.333 2.79 0.00 37.15 4.63
981 1047 2.910688 TGGTCACCTCTCAACAACTC 57.089 50.000 0.00 0.00 0.00 3.01
1134 1200 2.202878 TTGCGCACCCTAGATCGC 60.203 61.111 11.12 9.71 46.78 4.58
1189 1255 2.496899 AGCATACTTGGAAGGGTGTG 57.503 50.000 0.00 0.00 0.00 3.82
1309 1377 7.048629 TCTATTTTTGGTTTCACATGCTTGA 57.951 32.000 6.60 0.00 0.00 3.02
1323 1391 5.576774 GGCCTTCGTTTTCATCTATTTTTGG 59.423 40.000 0.00 0.00 0.00 3.28
1331 1399 1.073923 AGGTGGCCTTCGTTTTCATCT 59.926 47.619 3.32 0.00 0.00 2.90
1348 1416 7.665559 TGTTTTGTCTGAGCAGATATTTTAGGT 59.334 33.333 3.19 0.00 39.97 3.08
1349 1417 8.044060 TGTTTTGTCTGAGCAGATATTTTAGG 57.956 34.615 3.19 0.00 39.97 2.69
1352 1420 9.236006 ACTATGTTTTGTCTGAGCAGATATTTT 57.764 29.630 3.19 0.00 39.97 1.82
1482 1553 8.712285 ACGCTATGCTACTAGTTTGATAAAAA 57.288 30.769 0.00 0.00 0.00 1.94
1486 1557 8.235226 GTGATACGCTATGCTACTAGTTTGATA 58.765 37.037 0.00 0.00 0.00 2.15
1497 1568 5.966742 AGAAGATGTGATACGCTATGCTA 57.033 39.130 0.00 0.00 0.00 3.49
1501 1572 7.454260 TCATGTAGAAGATGTGATACGCTAT 57.546 36.000 0.00 0.00 0.00 2.97
1502 1573 6.877611 TCATGTAGAAGATGTGATACGCTA 57.122 37.500 0.00 0.00 0.00 4.26
1503 1574 5.774498 TCATGTAGAAGATGTGATACGCT 57.226 39.130 0.00 0.00 0.00 5.07
1504 1575 6.697455 TCTTTCATGTAGAAGATGTGATACGC 59.303 38.462 0.00 0.00 37.57 4.42
1505 1576 8.634475 TTCTTTCATGTAGAAGATGTGATACG 57.366 34.615 8.35 0.00 37.57 3.06
1741 1813 1.069427 GCAGCAGATGATCTCGCCT 59.931 57.895 11.45 0.00 0.00 5.52
1847 1919 1.602888 CTATGGGCTGGCTCCATGC 60.603 63.158 18.81 0.00 44.08 4.06
1927 2002 4.100653 CAGAACCTGATGCCTTCATAGAGA 59.899 45.833 0.00 0.00 32.44 3.10
2005 2110 8.744652 CAACCCAACCTCACATAATAAACAATA 58.255 33.333 0.00 0.00 0.00 1.90
2016 2121 3.181423 ACCATTACAACCCAACCTCACAT 60.181 43.478 0.00 0.00 0.00 3.21
2070 2175 5.555017 TCTCTCTCTCTTTGACAAAATGGG 58.445 41.667 1.62 0.00 0.00 4.00
2086 2193 2.054799 TCCCTAGCCTCTCTCTCTCTC 58.945 57.143 0.00 0.00 0.00 3.20
2087 2194 2.206322 TCCCTAGCCTCTCTCTCTCT 57.794 55.000 0.00 0.00 0.00 3.10
2088 2195 3.525800 AATCCCTAGCCTCTCTCTCTC 57.474 52.381 0.00 0.00 0.00 3.20
2089 2196 3.991628 AAATCCCTAGCCTCTCTCTCT 57.008 47.619 0.00 0.00 0.00 3.10
2193 2300 4.614475 AGTCAGGGAGTACATGAAGATGA 58.386 43.478 0.00 0.00 33.36 2.92
2243 2350 7.564292 GGGATAATTATATACTCCCTTCGTCCT 59.436 40.741 12.19 0.00 42.00 3.85
2268 2375 1.710816 AAGAGAAGGATCTAGGCGGG 58.289 55.000 0.00 0.00 35.54 6.13
2302 2409 3.703001 TGAGCCTAACCAAGAGGAAAG 57.297 47.619 0.00 0.00 35.99 2.62
2408 2576 4.022416 TCCGTAAATTTTGCATGCTTCTGT 60.022 37.500 20.33 2.50 0.00 3.41
2422 2590 8.921670 GCAATATTCAACTTTTGTCCGTAAATT 58.078 29.630 0.00 0.00 0.00 1.82
2432 2601 7.760794 TGGCAATAGAGCAATATTCAACTTTTG 59.239 33.333 0.00 0.00 35.83 2.44
2439 2608 5.563280 CGCAATGGCAATAGAGCAATATTCA 60.563 40.000 0.00 0.00 41.24 2.57
2460 2629 1.891919 GTCACCTTGCCTTGTCGCA 60.892 57.895 0.00 0.00 36.85 5.10
2596 2767 3.247648 CCATTACGGTTCAAATCCTAGCG 59.752 47.826 0.00 0.00 38.60 4.26
2612 2783 1.076332 GGCACGACAGTGTCCATTAC 58.924 55.000 17.57 3.14 46.65 1.89
2694 2865 2.418884 GGCTCTGTAGTAAGTTGAGGCC 60.419 54.545 0.00 0.00 42.18 5.19
2716 2887 3.005155 GGGCTATCATGAGGATTTTGCAC 59.995 47.826 0.09 0.00 37.44 4.57
2751 2922 2.425829 GGACTTTGTTTTCCCTCCCCTT 60.426 50.000 0.00 0.00 0.00 3.95
2810 2981 9.086336 GCAGATTATAATCTCTTGTATGCTCTC 57.914 37.037 22.54 0.00 43.65 3.20
2818 2989 6.302269 CCCCTTGCAGATTATAATCTCTTGT 58.698 40.000 22.54 2.02 43.65 3.16
2835 3006 0.686789 AAAATTGCTGACCCCCTTGC 59.313 50.000 0.00 0.00 0.00 4.01
2847 3018 7.629130 TGATGTTTTTGTAAGCAGAAAATTGC 58.371 30.769 0.00 0.00 44.41 3.56


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

AutoCloner maintained by Alex Coulton.