Multiple sequence alignment - TraesCS3D01G535900

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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 TraesCS3D01G535900 chr3D 100.000 2198 0 0 1 2198 609930056 609927859 0.000000e+00 4060.0
1 TraesCS3D01G535900 chr3D 86.270 488 40 17 872 1345 609922918 609922444 2.520000e-139 505.0
2 TraesCS3D01G535900 chr3D 92.647 68 3 2 260 326 263330481 263330415 1.800000e-16 97.1
3 TraesCS3D01G535900 chr3B 93.495 1399 73 10 208 1599 821090318 821088931 0.000000e+00 2063.0
4 TraesCS3D01G535900 chr3B 85.216 487 47 15 872 1345 821077108 821076634 5.490000e-131 477.0
5 TraesCS3D01G535900 chr3B 96.392 194 7 0 1597 1790 821088655 821088462 9.790000e-84 320.0
6 TraesCS3D01G535900 chr3B 86.496 274 17 7 5 260 821077858 821077587 1.280000e-72 283.0
7 TraesCS3D01G535900 chr3B 89.956 229 3 3 1970 2198 821087697 821087489 5.980000e-71 278.0
8 TraesCS3D01G535900 chr3B 92.308 195 8 2 1780 1974 821088217 821088030 1.000000e-68 270.0
9 TraesCS3D01G535900 chr3B 84.559 272 21 12 5 257 787973795 787973526 1.300000e-62 250.0
10 TraesCS3D01G535900 chr3B 93.168 161 10 1 100 260 821090374 821090215 3.650000e-58 235.0
11 TraesCS3D01G535900 chr3B 97.391 115 3 0 208 322 821077689 821077575 1.720000e-46 196.0
12 TraesCS3D01G535900 chr3B 93.043 115 5 3 210 322 787973624 787973511 4.850000e-37 165.0
13 TraesCS3D01G535900 chr3B 89.516 124 10 1 327 450 821077270 821077150 1.050000e-33 154.0
14 TraesCS3D01G535900 chr3A 93.592 1186 62 6 222 1402 743759020 743757844 0.000000e+00 1757.0
15 TraesCS3D01G535900 chr3A 86.094 489 40 18 872 1345 743674421 743673946 3.260000e-138 501.0
16 TraesCS3D01G535900 chr3A 85.833 240 12 5 38 260 743759164 743758930 3.650000e-58 235.0
17 TraesCS3D01G535900 chr7A 93.110 537 34 2 208 743 707133517 707134051 0.000000e+00 784.0
18 TraesCS3D01G535900 chr7A 91.975 162 10 3 100 260 707133461 707133620 7.900000e-55 224.0
19 TraesCS3D01G535900 chr5D 81.212 495 67 12 327 803 437352721 437352235 2.060000e-100 375.0
20 TraesCS3D01G535900 chr5D 80.780 359 41 11 327 660 437353907 437353552 2.800000e-64 255.0
21 TraesCS3D01G535900 chr5A 81.250 480 67 11 327 791 552546491 552546020 1.240000e-97 366.0
22 TraesCS3D01G535900 chr5A 83.230 322 37 7 327 634 552548644 552548326 1.660000e-71 279.0
23 TraesCS3D01G535900 chr4A 91.139 237 15 4 964 1200 414423480 414423250 1.270000e-82 316.0
24 TraesCS3D01G535900 chr4D 90.295 237 17 4 964 1200 216533944 216534174 2.740000e-79 305.0
25 TraesCS3D01G535900 chr4B 90.295 237 17 4 964 1200 245682943 245682713 2.740000e-79 305.0
26 TraesCS3D01G535900 chr5B 78.492 451 52 17 327 759 531551575 531551152 1.010000e-63 254.0
27 TraesCS3D01G535900 chr7D 83.643 269 23 6 10 259 560402563 560402829 1.310000e-57 233.0
28 TraesCS3D01G535900 chr6D 83.333 270 24 15 10 260 279707209 279706942 1.700000e-56 230.0
29 TraesCS3D01G535900 chr2A 93.846 65 3 1 259 322 139645643 139645707 1.800000e-16 97.1
30 TraesCS3D01G535900 chr1A 93.750 64 3 1 260 322 8937084 8937021 6.460000e-16 95.3


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 TraesCS3D01G535900 chr3D 609927859 609930056 2197 True 4060.0 4060 100.00000 1 2198 1 chr3D.!!$R3 2197
1 TraesCS3D01G535900 chr3B 821087489 821090374 2885 True 633.2 2063 93.06380 100 2198 5 chr3B.!!$R3 2098
2 TraesCS3D01G535900 chr3B 821076634 821077858 1224 True 277.5 477 89.65475 5 1345 4 chr3B.!!$R2 1340
3 TraesCS3D01G535900 chr3A 743757844 743759164 1320 True 996.0 1757 89.71250 38 1402 2 chr3A.!!$R2 1364
4 TraesCS3D01G535900 chr7A 707133461 707134051 590 False 504.0 784 92.54250 100 743 2 chr7A.!!$F1 643
5 TraesCS3D01G535900 chr5D 437352235 437353907 1672 True 315.0 375 80.99600 327 803 2 chr5D.!!$R1 476
6 TraesCS3D01G535900 chr5A 552546020 552548644 2624 True 322.5 366 82.24000 327 791 2 chr5A.!!$R1 464

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
820 2754 0.03254 CAGTGTTTCTGCTTTGGGCC 59.967 55.0 0.0 0.0 40.92 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 4012 0.397675 ACATCCATGCTCGAGGAGGA 60.398 55.0 20.64 20.91 37.9 3.71 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
30 31 0.674895 GGACATTTGCGTGCTCTCCT 60.675 55.000 0.00 0.00 0.00 3.69
47 48 4.026052 TCTCCTGTATGATCTCAAGTGCA 58.974 43.478 0.00 0.00 0.00 4.57
113 132 2.408050 AGAACAGTGCATCAGTTCGTC 58.592 47.619 17.47 2.33 43.94 4.20
132 151 1.347707 TCGTTTCTGATGGTGCTCCTT 59.652 47.619 6.34 0.00 34.23 3.36
262 282 4.361451 CAACTCTGCAGTGTTTCTGTTT 57.639 40.909 27.01 6.34 45.23 2.83
263 283 4.346129 CAACTCTGCAGTGTTTCTGTTTC 58.654 43.478 27.01 0.00 45.23 2.78
265 285 3.624861 ACTCTGCAGTGTTTCTGTTTCTG 59.375 43.478 15.49 0.00 45.23 3.02
266 286 3.872696 TCTGCAGTGTTTCTGTTTCTGA 58.127 40.909 14.67 0.00 45.23 3.27
267 287 4.260985 TCTGCAGTGTTTCTGTTTCTGAA 58.739 39.130 14.67 0.00 45.23 3.02
269 289 5.357878 TCTGCAGTGTTTCTGTTTCTGAATT 59.642 36.000 14.67 0.00 45.23 2.17
270 290 5.964758 TGCAGTGTTTCTGTTTCTGAATTT 58.035 33.333 0.00 0.00 45.23 1.82
272 292 7.542890 TGCAGTGTTTCTGTTTCTGAATTTAA 58.457 30.769 0.00 0.00 45.23 1.52
273 293 7.487829 TGCAGTGTTTCTGTTTCTGAATTTAAC 59.512 33.333 0.00 0.00 45.23 2.01
274 294 7.702348 GCAGTGTTTCTGTTTCTGAATTTAACT 59.298 33.333 0.00 0.00 45.23 2.24
275 295 9.573133 CAGTGTTTCTGTTTCTGAATTTAACTT 57.427 29.630 0.00 0.00 39.17 2.66
276 296 9.573133 AGTGTTTCTGTTTCTGAATTTAACTTG 57.427 29.630 0.00 0.00 0.00 3.16
277 297 8.321005 GTGTTTCTGTTTCTGAATTTAACTTGC 58.679 33.333 0.00 0.00 0.00 4.01
278 298 8.031864 TGTTTCTGTTTCTGAATTTAACTTGCA 58.968 29.630 0.00 0.00 0.00 4.08
279 299 9.034544 GTTTCTGTTTCTGAATTTAACTTGCAT 57.965 29.630 0.00 0.00 0.00 3.96
281 301 8.169977 TCTGTTTCTGAATTTAACTTGCATCT 57.830 30.769 0.00 0.00 0.00 2.90
282 302 9.283768 TCTGTTTCTGAATTTAACTTGCATCTA 57.716 29.630 0.00 0.00 0.00 1.98
287 307 9.897744 TTCTGAATTTAACTTGCATCTAAACAG 57.102 29.630 0.00 0.00 0.00 3.16
289 309 9.552114 CTGAATTTAACTTGCATCTAAACAGAG 57.448 33.333 0.00 0.00 0.00 3.35
290 310 8.514594 TGAATTTAACTTGCATCTAAACAGAGG 58.485 33.333 0.00 0.00 0.00 3.69
291 311 5.880054 TTAACTTGCATCTAAACAGAGGC 57.120 39.130 4.44 4.44 44.72 4.70
324 644 7.149973 CAGTGTTCCTGAATCACATTTCAATT 58.850 34.615 12.06 0.00 44.49 2.32
325 645 8.298854 CAGTGTTCCTGAATCACATTTCAATTA 58.701 33.333 12.06 0.00 44.49 1.40
420 2326 4.082571 CCCTTGAATGTTTAAGCTCAGTGG 60.083 45.833 0.00 0.00 0.00 4.00
465 2371 3.927142 CAGGTTCCTGATCTTCAACGTAC 59.073 47.826 13.02 0.00 36.24 3.67
479 2385 2.040606 GTACCCCTGGCCCTCTCA 59.959 66.667 0.00 0.00 0.00 3.27
480 2386 2.066999 GTACCCCTGGCCCTCTCAG 61.067 68.421 0.00 0.00 0.00 3.35
517 2423 2.702478 CCTTGATCAGATGCAGGTCCTA 59.298 50.000 2.64 0.00 0.00 2.94
581 2487 0.719465 GTTGTGGTAACGATGGAGCG 59.281 55.000 0.00 0.00 42.51 5.03
691 2623 2.127708 AGGAAACAAGTCACTCCCTGT 58.872 47.619 0.00 0.00 0.00 4.00
709 2641 4.935808 CCCTGTGAGTGTTAATAACTGTCC 59.064 45.833 4.67 0.00 0.00 4.02
723 2655 2.325761 ACTGTCCTTCGTTCGAATTCG 58.674 47.619 21.78 21.78 41.45 3.34
766 2700 4.806342 TCTGTTCTTTTACAGCGGTTTC 57.194 40.909 0.00 0.00 44.10 2.78
820 2754 0.032540 CAGTGTTTCTGCTTTGGGCC 59.967 55.000 0.00 0.00 40.92 5.80
829 2763 1.074951 GCTTTGGGCCCACAGTAGT 59.925 57.895 33.35 0.00 34.27 2.73
1164 3108 1.599047 CGACATCCTCACCCTGCTT 59.401 57.895 0.00 0.00 0.00 3.91
1216 3164 4.275936 GCTAAGCACTTTCTTTTCACCTGA 59.724 41.667 0.00 0.00 0.00 3.86
1229 3177 2.248248 TCACCTGACTGTCTTCGGAAT 58.752 47.619 9.51 0.00 0.00 3.01
1231 3179 2.738846 CACCTGACTGTCTTCGGAATTG 59.261 50.000 9.51 0.00 0.00 2.32
1235 3183 2.037121 TGACTGTCTTCGGAATTGCTCA 59.963 45.455 9.51 0.00 0.00 4.26
1275 3223 3.368116 GCCTTCTTACTCTACCGCTTTCA 60.368 47.826 0.00 0.00 0.00 2.69
1283 3231 4.642429 ACTCTACCGCTTTCATCTTTTGT 58.358 39.130 0.00 0.00 0.00 2.83
1324 3273 3.740115 TGAGTTTCCTTCTGTTGCCTAC 58.260 45.455 0.00 0.00 0.00 3.18
1353 3302 3.361644 GTGCACTTGATGTTATTGTTGCG 59.638 43.478 10.32 0.00 0.00 4.85
1411 3360 1.896220 TGATTTGAGTGCTGGTGGTC 58.104 50.000 0.00 0.00 0.00 4.02
1423 3372 3.519107 TGCTGGTGGTCTAAATCTGATCA 59.481 43.478 0.00 0.00 0.00 2.92
1424 3373 3.873952 GCTGGTGGTCTAAATCTGATCAC 59.126 47.826 0.00 0.00 42.87 3.06
1451 3401 9.719355 TTCTACTTGTTAAATCATCTGTGCTTA 57.281 29.630 0.00 0.00 0.00 3.09
1474 3424 9.149225 CTTATAAGCACTCATATGAGATTCCAC 57.851 37.037 34.16 17.52 44.74 4.02
1475 3425 5.627182 AAGCACTCATATGAGATTCCACT 57.373 39.130 34.16 19.09 44.74 4.00
1476 3426 6.737720 AAGCACTCATATGAGATTCCACTA 57.262 37.500 34.16 0.00 44.74 2.74
1534 3484 6.594159 ACATGACACTTAATTCCTCTTTACGG 59.406 38.462 0.00 0.00 0.00 4.02
1536 3486 4.901868 ACACTTAATTCCTCTTTACGGCA 58.098 39.130 0.00 0.00 0.00 5.69
1583 3533 1.080025 GCGGTGAGGTCTTAGCGTT 60.080 57.895 14.01 0.00 41.20 4.84
1618 3846 2.232696 ACCAACAACAACCACAACTTCC 59.767 45.455 0.00 0.00 0.00 3.46
1637 3865 3.885724 CCACCTCAACAAGTGGTTTTT 57.114 42.857 0.94 0.00 46.99 1.94
1683 3911 4.864247 GGTTTTGTATGTGTCCATGAATGC 59.136 41.667 0.00 0.00 32.29 3.56
1733 3961 3.751479 AAGGGTTGTTGCAAGAATTCC 57.249 42.857 12.62 15.87 0.00 3.01
1765 3993 1.009829 CAACTGCCGCTACCATTCTC 58.990 55.000 0.00 0.00 0.00 2.87
1767 3995 1.320344 ACTGCCGCTACCATTCTCGA 61.320 55.000 0.00 0.00 0.00 4.04
1784 4012 4.660168 TCTCGAGAAGGTAGTTGGTACTT 58.340 43.478 14.01 0.00 35.78 2.24
1796 4279 0.039180 TGGTACTTCCTCCTCGAGCA 59.961 55.000 6.99 0.00 37.07 4.26
1810 4293 1.134699 TCGAGCATGGATGTTGACTCC 60.135 52.381 0.00 0.00 0.00 3.85
1840 4323 1.527370 GACTAGTGGCATGGGGTCC 59.473 63.158 0.00 0.00 0.00 4.46
1870 4353 0.395724 ATGGGAAAGTTGGATCGGGC 60.396 55.000 0.00 0.00 0.00 6.13
1871 4354 2.112815 GGGAAAGTTGGATCGGGCG 61.113 63.158 0.00 0.00 0.00 6.13
1873 4356 1.366854 GGAAAGTTGGATCGGGCGTC 61.367 60.000 0.00 0.00 0.00 5.19
1876 4359 1.910580 AAGTTGGATCGGGCGTCCAT 61.911 55.000 6.96 0.00 44.75 3.41
1877 4360 1.451387 GTTGGATCGGGCGTCCATT 60.451 57.895 6.96 0.00 44.75 3.16
1878 4361 1.153249 TTGGATCGGGCGTCCATTC 60.153 57.895 6.96 0.98 44.75 2.67
1879 4362 2.280865 GGATCGGGCGTCCATTCC 60.281 66.667 6.96 7.81 35.76 3.01
1880 4363 2.661866 GATCGGGCGTCCATTCCG 60.662 66.667 6.96 0.00 44.59 4.30
1906 4389 3.460995 CCTCCTCGGGTCTATGGC 58.539 66.667 0.00 0.00 0.00 4.40
1910 4393 2.728817 CTCGGGTCTATGGCGGTC 59.271 66.667 0.00 0.00 0.00 4.79
1963 4446 3.549794 CCCTCCTCCTAAGCTTGATTTG 58.450 50.000 9.86 0.00 0.00 2.32
2017 4837 9.683069 AAGTATCATTTGAACAGTTCATTGAAC 57.317 29.630 23.28 19.64 42.25 3.18
2018 4838 8.849168 AGTATCATTTGAACAGTTCATTGAACA 58.151 29.630 26.73 15.69 44.11 3.18
2019 4839 9.462174 GTATCATTTGAACAGTTCATTGAACAA 57.538 29.630 26.73 14.10 44.11 2.83
2020 4840 7.990541 TCATTTGAACAGTTCATTGAACAAG 57.009 32.000 26.73 20.95 44.11 3.16
2021 4841 6.979817 TCATTTGAACAGTTCATTGAACAAGG 59.020 34.615 26.73 18.69 44.11 3.61
2022 4842 6.522625 TTTGAACAGTTCATTGAACAAGGA 57.477 33.333 26.73 7.90 44.11 3.36
2038 4858 7.632861 TGAACAAGGATCATTGAAGAAGGATA 58.367 34.615 25.68 0.27 32.76 2.59
2039 4859 8.277197 TGAACAAGGATCATTGAAGAAGGATAT 58.723 33.333 25.68 0.00 32.76 1.63
2080 4900 6.559921 TGGAGGATCATTGAAGAAGGATATCA 59.440 38.462 4.83 0.00 32.76 2.15
2081 4901 7.239143 TGGAGGATCATTGAAGAAGGATATCAT 59.761 37.037 4.83 0.00 32.76 2.45
2082 4902 8.108364 GGAGGATCATTGAAGAAGGATATCATT 58.892 37.037 1.48 1.48 32.76 2.57
2083 4903 9.165035 GAGGATCATTGAAGAAGGATATCATTC 57.835 37.037 19.89 19.89 32.76 2.67
2151 4971 2.016318 CAACTCAATGCATCCGCCTTA 58.984 47.619 0.00 0.00 37.32 2.69
2177 4997 1.304381 TCCATGCTTCCTTGCCACC 60.304 57.895 0.00 0.00 0.00 4.61
2180 5000 3.210012 ATGCTTCCTTGCCACCCGT 62.210 57.895 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.415168 ACGCAAATGTCCGTGAATGTAG 59.585 45.455 0.00 0.00 36.18 2.74
20 21 2.620585 TGAGATCATACAGGAGAGCACG 59.379 50.000 0.00 0.00 0.00 5.34
30 31 5.101648 TCCATTGCACTTGAGATCATACA 57.898 39.130 0.00 0.00 0.00 2.29
47 48 2.233922 ACAGCTAGCGTACACTTCCATT 59.766 45.455 9.55 0.00 0.00 3.16
113 132 1.734465 GAAGGAGCACCATCAGAAACG 59.266 52.381 2.07 0.00 38.94 3.60
257 277 9.897744 TTAGATGCAAGTTAAATTCAGAAACAG 57.102 29.630 0.00 0.00 0.00 3.16
262 282 9.283768 TCTGTTTAGATGCAAGTTAAATTCAGA 57.716 29.630 0.00 4.26 0.00 3.27
263 283 9.552114 CTCTGTTTAGATGCAAGTTAAATTCAG 57.448 33.333 0.00 2.08 31.21 3.02
265 285 7.486232 GCCTCTGTTTAGATGCAAGTTAAATTC 59.514 37.037 0.00 0.00 42.17 2.17
266 286 7.039784 TGCCTCTGTTTAGATGCAAGTTAAATT 60.040 33.333 5.06 0.00 46.86 1.82
267 287 6.434028 TGCCTCTGTTTAGATGCAAGTTAAAT 59.566 34.615 5.06 0.00 46.86 1.40
269 289 5.312895 TGCCTCTGTTTAGATGCAAGTTAA 58.687 37.500 5.06 0.00 46.86 2.01
270 290 4.905429 TGCCTCTGTTTAGATGCAAGTTA 58.095 39.130 5.06 0.00 46.86 2.24
272 292 3.423539 TGCCTCTGTTTAGATGCAAGT 57.576 42.857 5.06 0.00 46.86 3.16
276 296 3.604582 AGAGTTGCCTCTGTTTAGATGC 58.395 45.455 0.00 0.00 46.45 3.91
300 320 6.906157 ATTGAAATGTGATTCAGGAACACT 57.094 33.333 12.52 0.00 40.21 3.55
301 321 9.643693 AATAATTGAAATGTGATTCAGGAACAC 57.356 29.630 0.00 0.00 40.21 3.32
324 644 1.075542 CTGGACGCGCACAAGAAATA 58.924 50.000 5.73 0.00 0.00 1.40
325 645 1.868997 CTGGACGCGCACAAGAAAT 59.131 52.632 5.73 0.00 0.00 2.17
479 2385 1.022903 AGGAGAAGATCAGGGACCCT 58.977 55.000 7.44 7.44 0.00 4.34
480 2386 1.488393 CAAGGAGAAGATCAGGGACCC 59.512 57.143 0.59 0.59 0.00 4.46
517 2423 1.967066 CAGGAGTTCAGTCTGACCACT 59.033 52.381 0.78 4.37 0.00 4.00
581 2487 0.250338 AGGCAGTTCAAGAACCGTCC 60.250 55.000 9.20 8.10 42.06 4.79
691 2623 6.092955 ACGAAGGACAGTTATTAACACTCA 57.907 37.500 9.15 0.00 0.00 3.41
709 2641 3.215244 CAAACACCGAATTCGAACGAAG 58.785 45.455 28.76 13.16 43.02 3.79
723 2655 6.316390 CAGATAAATCTACTGGTCCAAACACC 59.684 42.308 0.00 0.00 34.85 4.16
766 2700 7.175641 ACAGAAACCAGAGAAATTATTGGTCTG 59.824 37.037 8.88 8.88 42.86 3.51
820 2754 6.173339 ACTATTTGGAACATGACTACTGTGG 58.827 40.000 0.00 0.00 39.30 4.17
853 2787 5.869344 TCATACATACAAGAGAGCACACAAC 59.131 40.000 0.00 0.00 0.00 3.32
1164 3108 3.071206 GCCTCCCGCTCAGACTCA 61.071 66.667 0.00 0.00 0.00 3.41
1216 3164 2.839486 TGAGCAATTCCGAAGACAGT 57.161 45.000 0.00 0.00 0.00 3.55
1229 3177 3.508402 ACAGCACATCATTTCATGAGCAA 59.492 39.130 0.00 0.00 43.53 3.91
1231 3179 3.777465 ACAGCACATCATTTCATGAGC 57.223 42.857 0.00 0.00 43.53 4.26
1235 3183 2.829720 AGGCAACAGCACATCATTTCAT 59.170 40.909 0.00 0.00 41.41 2.57
1275 3223 5.441718 TCTCCATAGCCAAGACAAAAGAT 57.558 39.130 0.00 0.00 0.00 2.40
1283 3231 5.604231 ACTCATTACATCTCCATAGCCAAGA 59.396 40.000 0.00 0.00 0.00 3.02
1324 3273 8.746922 ACAATAACATCAAGTGCACTTTAATG 57.253 30.769 31.56 31.56 33.11 1.90
1423 3372 7.880195 AGCACAGATGATTTAACAAGTAGAAGT 59.120 33.333 0.00 0.00 0.00 3.01
1424 3373 8.261492 AGCACAGATGATTTAACAAGTAGAAG 57.739 34.615 0.00 0.00 0.00 2.85
1451 3401 7.313740 AGTGGAATCTCATATGAGTGCTTAT 57.686 36.000 27.80 13.85 42.60 1.73
1455 3405 6.338214 TCTAGTGGAATCTCATATGAGTGC 57.662 41.667 27.80 17.51 42.60 4.40
1456 3406 7.950512 AGTTCTAGTGGAATCTCATATGAGTG 58.049 38.462 27.80 8.91 42.60 3.51
1472 3422 9.823647 ACCAAATCACTAATCATAGTTCTAGTG 57.176 33.333 2.38 2.38 40.44 2.74
1473 3423 9.823647 CACCAAATCACTAATCATAGTTCTAGT 57.176 33.333 0.00 0.00 40.44 2.57
1474 3424 9.823647 ACACCAAATCACTAATCATAGTTCTAG 57.176 33.333 0.00 0.00 40.44 2.43
1475 3425 9.599866 CACACCAAATCACTAATCATAGTTCTA 57.400 33.333 0.00 0.00 40.44 2.10
1476 3426 7.066284 GCACACCAAATCACTAATCATAGTTCT 59.934 37.037 0.00 0.00 40.44 3.01
1534 3484 4.096081 CAGGTCCAAGATCAAAGAATCTGC 59.904 45.833 0.00 0.00 36.14 4.26
1536 3486 5.768980 TCAGGTCCAAGATCAAAGAATCT 57.231 39.130 0.00 0.00 37.61 2.40
1583 3533 8.301002 GGTTGTTGTTGGTATTATAAAGAGCAA 58.699 33.333 9.92 9.92 0.00 3.91
1618 3846 3.194542 TCCAAAAACCACTTGTTGAGGTG 59.805 43.478 0.00 0.00 39.58 4.00
1637 3865 1.588674 GGTGACAATCGTGTTGTCCA 58.411 50.000 23.54 14.25 46.01 4.02
1683 3911 5.125900 TCAACAGGCATGGATCATTTAAGTG 59.874 40.000 2.31 0.00 0.00 3.16
1765 3993 3.762823 AGGAAGTACCAACTACCTTCTCG 59.237 47.826 0.00 0.00 42.04 4.04
1767 3995 4.095211 GGAGGAAGTACCAACTACCTTCT 58.905 47.826 0.00 0.00 42.04 2.85
1784 4012 0.397675 ACATCCATGCTCGAGGAGGA 60.398 55.000 20.64 20.91 37.90 3.71
1796 4279 1.990424 TGGCGGAGTCAACATCCAT 59.010 52.632 0.00 0.00 42.02 3.41
1870 4353 2.202298 GCAAACGCGGAATGGACG 60.202 61.111 12.47 0.00 0.00 4.79
1871 4354 2.178273 GGCAAACGCGGAATGGAC 59.822 61.111 12.47 0.00 0.00 4.02
1873 4356 4.128388 GGGGCAAACGCGGAATGG 62.128 66.667 12.47 0.00 0.00 3.16
1906 4389 2.107141 GGCGAGGGAATCAGACCG 59.893 66.667 0.00 0.00 0.00 4.79
1910 4393 0.467384 ATGTGAGGCGAGGGAATCAG 59.533 55.000 0.00 0.00 0.00 2.90
1963 4446 4.094442 CGAACCCAATTAGCTAAGTTGGTC 59.906 45.833 24.72 20.20 40.57 4.02
2009 4829 7.094075 CCTTCTTCAATGATCCTTGTTCAATGA 60.094 37.037 10.09 0.00 32.59 2.57
2010 4830 7.033791 CCTTCTTCAATGATCCTTGTTCAATG 58.966 38.462 10.09 0.00 0.00 2.82
2011 4831 6.950041 TCCTTCTTCAATGATCCTTGTTCAAT 59.050 34.615 10.09 0.00 0.00 2.57
2012 4832 6.306199 TCCTTCTTCAATGATCCTTGTTCAA 58.694 36.000 10.09 0.00 0.00 2.69
2013 4833 5.879763 TCCTTCTTCAATGATCCTTGTTCA 58.120 37.500 10.09 0.00 0.00 3.18
2014 4834 8.688747 ATATCCTTCTTCAATGATCCTTGTTC 57.311 34.615 10.09 0.00 0.00 3.18
2015 4835 8.277197 TGATATCCTTCTTCAATGATCCTTGTT 58.723 33.333 10.09 0.00 0.00 2.83
2016 4836 7.809238 TGATATCCTTCTTCAATGATCCTTGT 58.191 34.615 10.09 0.00 0.00 3.16
2017 4837 8.865420 ATGATATCCTTCTTCAATGATCCTTG 57.135 34.615 4.48 4.48 0.00 3.61
2018 4838 9.298250 CAATGATATCCTTCTTCAATGATCCTT 57.702 33.333 0.00 0.00 0.00 3.36
2019 4839 8.666821 TCAATGATATCCTTCTTCAATGATCCT 58.333 33.333 0.00 0.00 27.35 3.24
2020 4840 8.859236 TCAATGATATCCTTCTTCAATGATCC 57.141 34.615 0.00 0.00 27.35 3.36
2022 4842 9.636789 TGTTCAATGATATCCTTCTTCAATGAT 57.363 29.630 0.00 0.00 31.40 2.45
2038 4858 5.139727 TCCTCCAAAGTTGTGTTCAATGAT 58.860 37.500 0.00 0.00 35.92 2.45
2039 4859 4.531854 TCCTCCAAAGTTGTGTTCAATGA 58.468 39.130 0.00 0.00 35.92 2.57
2080 4900 7.834881 AGTTTCTTGGATCATATGCATGAAT 57.165 32.000 10.16 0.00 44.27 2.57
2081 4901 7.123098 ACAAGTTTCTTGGATCATATGCATGAA 59.877 33.333 10.16 0.00 44.27 2.57
2082 4902 6.604396 ACAAGTTTCTTGGATCATATGCATGA 59.396 34.615 10.16 0.00 45.15 3.07
2083 4903 6.802608 ACAAGTTTCTTGGATCATATGCATG 58.197 36.000 10.16 0.00 0.00 4.06
2151 4971 3.383825 GCAAGGAAGCATGGAGAATGAAT 59.616 43.478 0.00 0.00 38.72 2.57
2177 4997 1.808411 TCTTTTGCAAGAGCCTACGG 58.192 50.000 12.02 0.00 41.13 4.02


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

AutoCloner maintained by Alex Coulton.