Multiple sequence alignment - TraesCS2D01G293600

Loading Multiple Alignment...

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 TraesCS2D01G293600 chr2D 100.000 2723 0 0 1 2723 376131130 376133852 0.000000e+00 5029.0
1 TraesCS2D01G293600 chr2B 93.496 2168 74 29 488 2617 447491569 447489431 0.000000e+00 3160.0
2 TraesCS2D01G293600 chr2B 83.465 381 44 8 1 364 447492200 447491822 1.210000e-88 337.0
3 TraesCS2D01G293600 chr2B 95.455 110 4 1 2615 2723 447489397 447489288 1.000000e-39 174.0
4 TraesCS2D01G293600 chr2B 73.009 226 40 10 7 211 774064746 774064971 2.930000e-05 60.2
5 TraesCS2D01G293600 chr2A 93.055 1699 65 24 582 2247 508514229 508515907 0.000000e+00 2435.0
6 TraesCS2D01G293600 chr2A 93.678 174 9 2 2291 2463 508515909 508516081 2.690000e-65 259.0
7 TraesCS2D01G293600 chr2A 94.375 160 5 1 2458 2617 508516322 508516477 2.710000e-60 243.0
8 TraesCS2D01G293600 chr2A 92.453 106 8 0 2615 2720 508516511 508516616 4.700000e-33 152.0
9 TraesCS2D01G293600 chr2A 84.211 76 11 1 20 94 30022773 30022848 3.760000e-09 73.1
10 TraesCS2D01G293600 chr3A 75.591 254 49 10 469 712 70845674 70845424 2.220000e-21 113.0
11 TraesCS2D01G293600 chr3A 74.803 254 51 10 469 712 70844729 70844479 4.800000e-18 102.0
12 TraesCS2D01G293600 chr3A 94.595 37 2 0 175 211 720844069 720844105 1.050000e-04 58.4
13 TraesCS2D01G293600 chr5B 77.512 209 30 8 20 211 549189505 549189297 2.870000e-20 110.0
14 TraesCS2D01G293600 chr5B 75.576 217 30 12 13 211 708335514 708335725 4.830000e-13 86.1
15 TraesCS2D01G293600 chr7A 79.730 148 18 8 68 207 21888417 21888560 2.230000e-16 97.1
16 TraesCS2D01G293600 chr7A 85.714 77 8 3 20 94 129302692 129302617 8.080000e-11 78.7
17 TraesCS2D01G293600 chr5A 76.077 209 33 8 20 211 568525657 568525865 2.890000e-15 93.5
18 TraesCS2D01G293600 chr7D 76.536 179 31 6 3 170 604464588 604464766 1.340000e-13 87.9
19 TraesCS2D01G293600 chr6D 78.295 129 14 7 95 211 224751769 224751643 1.350000e-08 71.3
20 TraesCS2D01G293600 chr3D 92.105 38 3 0 265 302 11773529 11773566 1.000000e-03 54.7
21 TraesCS2D01G293600 chr3D 92.308 39 2 1 177 215 67352468 67352505 1.000000e-03 54.7


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 TraesCS2D01G293600 chr2D 376131130 376133852 2722 False 5029.000000 5029 100.000000 1 2723 1 chr2D.!!$F1 2722
1 TraesCS2D01G293600 chr2B 447489288 447492200 2912 True 1223.666667 3160 90.805333 1 2723 3 chr2B.!!$R1 2722
2 TraesCS2D01G293600 chr2A 508514229 508516616 2387 False 772.250000 2435 93.390250 582 2720 4 chr2A.!!$F2 2138

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
839 1038 0.106918 GTGAAACCCACCAGTCACCA 60.107 55.0 0.0 0.0 39.86 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2347 2565 0.459899 TCTCACGACATAAGCGGCAT 59.54 50.0 1.45 0.0 0.0 4.4 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
25 26 8.770438 TGTACAAAAATTTGAGCTTTCAAACT 57.230 26.923 12.54 0.00 41.63 2.66
92 94 5.561919 GCTTGTAATGATCTCGAGTCGATCT 60.562 44.000 16.94 6.18 38.43 2.75
94 96 5.301555 TGTAATGATCTCGAGTCGATCTCT 58.698 41.667 16.94 5.86 40.75 3.10
96 98 5.356882 AATGATCTCGAGTCGATCTCTTC 57.643 43.478 16.94 9.11 40.75 2.87
109 111 7.942990 AGTCGATCTCTTCCGAACTAAATAAT 58.057 34.615 0.00 0.00 36.50 1.28
169 172 7.173218 ACAAGATAGACCACAACACAACATAAG 59.827 37.037 0.00 0.00 0.00 1.73
171 174 3.820557 AGACCACAACACAACATAAGCT 58.179 40.909 0.00 0.00 0.00 3.74
172 175 4.207165 AGACCACAACACAACATAAGCTT 58.793 39.130 3.48 3.48 0.00 3.74
173 176 5.373222 AGACCACAACACAACATAAGCTTA 58.627 37.500 8.99 8.99 0.00 3.09
175 178 6.320164 AGACCACAACACAACATAAGCTTAAA 59.680 34.615 10.85 0.00 0.00 1.52
182 193 9.248291 CAACACAACATAAGCTTAAATTTGACT 57.752 29.630 22.33 10.33 0.00 3.41
194 205 9.950496 AGCTTAAATTTGACTTATTCTCTCTCA 57.050 29.630 0.00 0.00 0.00 3.27
206 217 8.956426 ACTTATTCTCTCTCAACTGAAGACTAG 58.044 37.037 0.00 0.00 0.00 2.57
209 220 7.675962 TTCTCTCTCAACTGAAGACTAGTAC 57.324 40.000 0.00 0.00 0.00 2.73
217 228 4.255301 ACTGAAGACTAGTACTCACTCCG 58.745 47.826 0.00 0.00 36.14 4.63
221 232 4.556592 AGACTAGTACTCACTCCGTCTT 57.443 45.455 0.00 0.00 40.21 3.01
222 233 4.255301 AGACTAGTACTCACTCCGTCTTG 58.745 47.826 0.00 0.00 40.21 3.02
227 238 6.883217 ACTAGTACTCACTCCGTCTTGAATTA 59.117 38.462 0.00 0.00 36.14 1.40
228 239 6.777213 AGTACTCACTCCGTCTTGAATTAT 57.223 37.500 0.00 0.00 0.00 1.28
229 240 7.876936 AGTACTCACTCCGTCTTGAATTATA 57.123 36.000 0.00 0.00 0.00 0.98
233 244 7.036220 ACTCACTCCGTCTTGAATTATACTTG 58.964 38.462 0.00 0.00 0.00 3.16
235 246 7.383687 TCACTCCGTCTTGAATTATACTTGTT 58.616 34.615 0.00 0.00 0.00 2.83
255 266 9.804758 ACTTGTTTTAGATTTCTCTAGATACGG 57.195 33.333 0.00 0.00 35.43 4.02
279 290 6.208402 GGATAGTGTCTAGCAAGAGATCATGA 59.792 42.308 0.00 0.00 30.45 3.07
317 335 2.514205 AAAAAGGTGTGCATGCACTC 57.486 45.000 41.43 37.68 46.30 3.51
325 343 3.243367 GGTGTGCATGCACTCAAACTTTA 60.243 43.478 41.43 22.02 46.30 1.85
328 346 4.222114 GTGCATGCACTCAAACTTTAGTC 58.778 43.478 37.48 11.16 43.12 2.59
337 355 7.497579 TGCACTCAAACTTTAGTCAGAATAACA 59.502 33.333 0.00 0.00 0.00 2.41
369 387 6.627087 AATACTCTCTCTGTTCCATTCCAA 57.373 37.500 0.00 0.00 0.00 3.53
370 388 4.982241 ACTCTCTCTGTTCCATTCCAAA 57.018 40.909 0.00 0.00 0.00 3.28
372 390 5.885465 ACTCTCTCTGTTCCATTCCAAATT 58.115 37.500 0.00 0.00 0.00 1.82
374 392 7.108847 ACTCTCTCTGTTCCATTCCAAATTAG 58.891 38.462 0.00 0.00 0.00 1.73
375 393 5.882557 TCTCTCTGTTCCATTCCAAATTAGC 59.117 40.000 0.00 0.00 0.00 3.09
377 395 5.649395 TCTCTGTTCCATTCCAAATTAGCTG 59.351 40.000 0.00 0.00 0.00 4.24
378 396 5.569355 TCTGTTCCATTCCAAATTAGCTGA 58.431 37.500 0.00 0.00 0.00 4.26
379 397 5.415701 TCTGTTCCATTCCAAATTAGCTGAC 59.584 40.000 0.00 0.00 0.00 3.51
381 399 5.415701 TGTTCCATTCCAAATTAGCTGACTC 59.584 40.000 0.00 0.00 0.00 3.36
395 447 7.881775 TTAGCTGACTCTGTTAGATACATCA 57.118 36.000 0.00 0.00 35.85 3.07
400 452 8.356657 GCTGACTCTGTTAGATACATCAGTATT 58.643 37.037 0.00 0.00 40.83 1.89
434 545 9.751542 ATATAAGACAACTAATTTGAGACCGAG 57.248 33.333 0.00 0.00 38.73 4.63
441 552 9.530633 ACAACTAATTTGAGACCGAGATAATAC 57.469 33.333 0.00 0.00 38.73 1.89
445 556 9.914131 CTAATTTGAGACCGAGATAATACATGA 57.086 33.333 0.00 0.00 0.00 3.07
447 558 5.707242 TGAGACCGAGATAATACATGACC 57.293 43.478 0.00 0.00 0.00 4.02
457 568 7.116376 CGAGATAATACATGACCAACCACATAC 59.884 40.741 0.00 0.00 0.00 2.39
458 569 8.034313 AGATAATACATGACCAACCACATACT 57.966 34.615 0.00 0.00 0.00 2.12
460 571 9.772973 GATAATACATGACCAACCACATACTAA 57.227 33.333 0.00 0.00 0.00 2.24
465 576 6.152661 ACATGACCAACCACATACTAAATTGG 59.847 38.462 0.00 0.00 41.92 3.16
467 578 6.307776 TGACCAACCACATACTAAATTGGAA 58.692 36.000 7.77 0.00 39.15 3.53
468 579 6.207810 TGACCAACCACATACTAAATTGGAAC 59.792 38.462 7.77 2.78 39.15 3.62
488 599 6.205853 TGGAACTAAATTTTCTCTGCGCTTAA 59.794 34.615 9.73 0.00 0.00 1.85
520 667 9.897744 CTTCATGTTTGAAAGTAGCTAAAATGA 57.102 29.630 0.00 0.00 41.22 2.57
637 787 4.397420 TCAAGCTAAAATGAGTGAGCCAA 58.603 39.130 0.00 0.00 35.45 4.52
639 789 6.179756 TCAAGCTAAAATGAGTGAGCCAATA 58.820 36.000 0.00 0.00 35.45 1.90
641 791 6.874288 AGCTAAAATGAGTGAGCCAATATC 57.126 37.500 0.00 0.00 35.45 1.63
665 815 4.327024 GCTTAAAATCAGCTCGTTTCTCG 58.673 43.478 0.00 0.00 41.41 4.04
714 910 7.862648 ACTCTAATTTCTTTTTGAGTCGAACC 58.137 34.615 0.00 0.00 29.57 3.62
731 928 2.584835 ACCTTTGTTGCAGCCTATCA 57.415 45.000 0.00 0.00 0.00 2.15
732 929 2.875296 ACCTTTGTTGCAGCCTATCAA 58.125 42.857 0.00 0.00 0.00 2.57
733 930 3.434309 ACCTTTGTTGCAGCCTATCAAT 58.566 40.909 0.00 0.00 0.00 2.57
734 931 3.445096 ACCTTTGTTGCAGCCTATCAATC 59.555 43.478 0.00 0.00 0.00 2.67
735 932 3.444742 CCTTTGTTGCAGCCTATCAATCA 59.555 43.478 0.00 0.00 0.00 2.57
736 933 4.418392 CTTTGTTGCAGCCTATCAATCAC 58.582 43.478 0.00 0.00 0.00 3.06
737 934 2.009051 TGTTGCAGCCTATCAATCACG 58.991 47.619 0.00 0.00 0.00 4.35
738 935 2.009774 GTTGCAGCCTATCAATCACGT 58.990 47.619 0.00 0.00 0.00 4.49
739 936 1.939974 TGCAGCCTATCAATCACGTC 58.060 50.000 0.00 0.00 0.00 4.34
740 937 1.482182 TGCAGCCTATCAATCACGTCT 59.518 47.619 0.00 0.00 0.00 4.18
741 938 2.131183 GCAGCCTATCAATCACGTCTC 58.869 52.381 0.00 0.00 0.00 3.36
833 1032 4.262420 CCCATAAAAAGTGAAACCCACCAG 60.262 45.833 0.00 0.00 46.87 4.00
834 1033 4.343814 CCATAAAAAGTGAAACCCACCAGT 59.656 41.667 0.00 0.00 46.87 4.00
835 1034 5.508994 CCATAAAAAGTGAAACCCACCAGTC 60.509 44.000 0.00 0.00 46.87 3.51
836 1035 2.818751 AAAGTGAAACCCACCAGTCA 57.181 45.000 0.00 0.00 46.87 3.41
837 1036 2.052782 AAGTGAAACCCACCAGTCAC 57.947 50.000 0.00 0.00 46.87 3.67
838 1037 0.182775 AGTGAAACCCACCAGTCACC 59.817 55.000 0.00 0.00 46.87 4.02
839 1038 0.106918 GTGAAACCCACCAGTCACCA 60.107 55.000 0.00 0.00 39.86 4.17
1140 1355 1.936547 GACTTCATGTTCTCATCCGCC 59.063 52.381 0.00 0.00 31.15 6.13
1141 1356 1.303309 CTTCATGTTCTCATCCGCCC 58.697 55.000 0.00 0.00 31.15 6.13
1142 1357 0.107214 TTCATGTTCTCATCCGCCCC 60.107 55.000 0.00 0.00 31.15 5.80
1143 1358 1.224315 CATGTTCTCATCCGCCCCA 59.776 57.895 0.00 0.00 31.15 4.96
1144 1359 0.816825 CATGTTCTCATCCGCCCCAG 60.817 60.000 0.00 0.00 31.15 4.45
1145 1360 1.274703 ATGTTCTCATCCGCCCCAGT 61.275 55.000 0.00 0.00 0.00 4.00
1146 1361 1.153349 GTTCTCATCCGCCCCAGTC 60.153 63.158 0.00 0.00 0.00 3.51
1147 1362 2.721167 TTCTCATCCGCCCCAGTCG 61.721 63.158 0.00 0.00 0.00 4.18
1148 1363 4.899239 CTCATCCGCCCCAGTCGC 62.899 72.222 0.00 0.00 0.00 5.19
1698 1913 3.103911 GTACGCGACGCTGTGCTT 61.104 61.111 15.93 0.00 0.00 3.91
1746 1961 1.676678 GGCGAGGTGATGTGGCTCTA 61.677 60.000 0.00 0.00 0.00 2.43
1787 2002 9.982651 TTAGAGTCATAGATTGGTTACATTAGC 57.017 33.333 0.00 0.00 0.00 3.09
2125 2343 6.412362 TGCATTTTGTTGTGGTAAGGTTAT 57.588 33.333 0.00 0.00 0.00 1.89
2191 2409 6.852853 CGTAATTGATATGCTGTTCAACCATC 59.147 38.462 0.00 0.00 34.87 3.51
2256 2474 4.021981 CAGTATGATCCCACGCAGAATCTA 60.022 45.833 0.00 0.00 39.69 1.98
2271 2489 7.183580 GCAGAATCTACTTATGCTTTCGAAT 57.816 36.000 0.00 0.00 46.27 3.34
2290 2508 8.777865 TTCGAATTTCAGAGTTCATTATGTCT 57.222 30.769 0.00 0.00 0.00 3.41
2291 2509 9.869757 TTCGAATTTCAGAGTTCATTATGTCTA 57.130 29.630 0.00 0.00 0.00 2.59
2364 2582 1.006086 CAATGCCGCTTATGTCGTGA 58.994 50.000 0.00 0.00 0.00 4.35
2429 2647 8.697292 GTTCTCCAGTCATAAGGTATTCTAGTT 58.303 37.037 0.00 0.00 0.00 2.24
2599 3064 6.710597 TTAGGTGTAGTATTCTAGTGGCAG 57.289 41.667 0.00 0.00 0.00 4.85
2657 3159 6.752351 TCTTTCTGTGTCGATACTTATGCTTC 59.248 38.462 13.73 0.00 0.00 3.86
2664 3166 3.066203 TCGATACTTATGCTTCGCTGTGA 59.934 43.478 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.942376 TCGCTCAGTTTGAAAGCTCAAA 59.058 40.909 0.00 0.00 46.88 2.69
37 38 6.456988 CGAGTCACTTTTTACAGCTGAACTTT 60.457 38.462 23.35 0.00 0.00 2.66
38 39 5.006746 CGAGTCACTTTTTACAGCTGAACTT 59.993 40.000 23.35 0.00 0.00 2.66
39 40 4.508124 CGAGTCACTTTTTACAGCTGAACT 59.492 41.667 23.35 8.65 0.00 3.01
43 44 4.795970 AACGAGTCACTTTTTACAGCTG 57.204 40.909 13.48 13.48 0.00 4.24
141 143 6.350103 TGTTGTGTTGTGGTCTATCTTGTTA 58.650 36.000 0.00 0.00 0.00 2.41
144 147 5.947228 ATGTTGTGTTGTGGTCTATCTTG 57.053 39.130 0.00 0.00 0.00 3.02
154 157 9.029243 TCAAATTTAAGCTTATGTTGTGTTGTG 57.971 29.630 7.08 0.74 0.00 3.33
173 176 9.784531 TCAGTTGAGAGAGAATAAGTCAAATTT 57.215 29.630 0.00 0.00 0.00 1.82
175 178 9.434420 CTTCAGTTGAGAGAGAATAAGTCAAAT 57.566 33.333 0.00 0.00 0.00 2.32
182 193 8.871629 ACTAGTCTTCAGTTGAGAGAGAATAA 57.128 34.615 0.00 0.00 0.00 1.40
184 195 8.107095 AGTACTAGTCTTCAGTTGAGAGAGAAT 58.893 37.037 0.00 0.00 0.00 2.40
194 205 4.696402 CGGAGTGAGTACTAGTCTTCAGTT 59.304 45.833 14.62 6.02 37.25 3.16
196 207 4.255301 ACGGAGTGAGTACTAGTCTTCAG 58.745 47.826 0.00 0.00 42.51 3.02
229 240 9.804758 CCGTATCTAGAGAAATCTAAAACAAGT 57.195 33.333 0.00 0.00 0.00 3.16
251 262 5.032327 TCTCTTGCTAGACACTATCCGTA 57.968 43.478 0.00 0.00 0.00 4.02
253 264 4.517075 TGATCTCTTGCTAGACACTATCCG 59.483 45.833 0.00 0.00 0.00 4.18
255 266 7.213216 TCATGATCTCTTGCTAGACACTATC 57.787 40.000 0.00 0.00 0.00 2.08
309 327 5.929697 TCTGACTAAAGTTTGAGTGCATG 57.070 39.130 0.00 0.00 0.00 4.06
310 328 8.507249 GTTATTCTGACTAAAGTTTGAGTGCAT 58.493 33.333 0.00 0.00 0.00 3.96
314 332 8.429641 TCCTGTTATTCTGACTAAAGTTTGAGT 58.570 33.333 0.00 0.00 0.00 3.41
337 355 9.661954 TGGAACAGAGAGAGTATTAAATATCCT 57.338 33.333 0.00 0.00 0.00 3.24
364 382 7.004555 TCTAACAGAGTCAGCTAATTTGGAA 57.995 36.000 0.00 0.00 0.00 3.53
365 383 6.605471 TCTAACAGAGTCAGCTAATTTGGA 57.395 37.500 0.00 0.00 0.00 3.53
366 384 7.981789 TGTATCTAACAGAGTCAGCTAATTTGG 59.018 37.037 0.00 0.00 33.01 3.28
367 385 8.932945 TGTATCTAACAGAGTCAGCTAATTTG 57.067 34.615 0.00 0.00 33.01 2.32
369 387 8.918116 TGATGTATCTAACAGAGTCAGCTAATT 58.082 33.333 0.00 0.00 42.70 1.40
370 388 8.470657 TGATGTATCTAACAGAGTCAGCTAAT 57.529 34.615 0.00 0.00 42.70 1.73
372 390 7.057264 ACTGATGTATCTAACAGAGTCAGCTA 58.943 38.462 0.00 0.00 42.62 3.32
374 392 6.142818 ACTGATGTATCTAACAGAGTCAGC 57.857 41.667 0.00 2.97 42.62 4.26
379 397 9.632807 GGCTAAATACTGATGTATCTAACAGAG 57.367 37.037 0.00 0.00 42.70 3.35
381 399 9.764363 TTGGCTAAATACTGATGTATCTAACAG 57.236 33.333 0.00 0.00 42.70 3.16
410 462 7.837863 TCTCGGTCTCAAATTAGTTGTCTTAT 58.162 34.615 0.00 0.00 38.47 1.73
413 465 5.723672 TCTCGGTCTCAAATTAGTTGTCT 57.276 39.130 0.00 0.00 38.47 3.41
414 466 8.649973 ATTATCTCGGTCTCAAATTAGTTGTC 57.350 34.615 0.00 0.00 38.47 3.18
415 467 9.530633 GTATTATCTCGGTCTCAAATTAGTTGT 57.469 33.333 0.00 0.00 38.47 3.32
428 539 4.989168 GGTTGGTCATGTATTATCTCGGTC 59.011 45.833 0.00 0.00 0.00 4.79
430 541 4.750098 GTGGTTGGTCATGTATTATCTCGG 59.250 45.833 0.00 0.00 0.00 4.63
434 545 9.772973 TTAGTATGTGGTTGGTCATGTATTATC 57.227 33.333 0.00 0.00 0.00 1.75
441 552 6.376864 TCCAATTTAGTATGTGGTTGGTCATG 59.623 38.462 0.00 0.00 37.82 3.07
445 556 6.311735 AGTTCCAATTTAGTATGTGGTTGGT 58.688 36.000 0.00 0.00 37.82 3.67
457 568 9.065871 CGCAGAGAAAATTTAGTTCCAATTTAG 57.934 33.333 0.00 0.00 33.56 1.85
458 569 7.540745 GCGCAGAGAAAATTTAGTTCCAATTTA 59.459 33.333 0.30 0.00 33.56 1.40
460 571 5.863935 GCGCAGAGAAAATTTAGTTCCAATT 59.136 36.000 0.30 0.00 0.00 2.32
462 573 4.518970 AGCGCAGAGAAAATTTAGTTCCAA 59.481 37.500 11.47 0.00 0.00 3.53
465 576 8.675040 AATTAAGCGCAGAGAAAATTTAGTTC 57.325 30.769 11.47 0.00 0.00 3.01
617 766 6.017605 CGATATTGGCTCACTCATTTTAGCTT 60.018 38.462 0.00 0.00 35.30 3.74
637 787 4.632153 ACGAGCTGATTTTAAGCCGATAT 58.368 39.130 0.00 0.00 41.82 1.63
639 789 2.906354 ACGAGCTGATTTTAAGCCGAT 58.094 42.857 0.00 0.00 41.82 4.18
641 791 3.125316 AGAAACGAGCTGATTTTAAGCCG 59.875 43.478 0.00 0.00 41.82 5.52
699 849 4.265320 GCAACAAAGGTTCGACTCAAAAAG 59.735 41.667 0.00 0.00 34.21 2.27
714 910 4.418392 GTGATTGATAGGCTGCAACAAAG 58.582 43.478 0.50 0.00 0.00 2.77
731 928 4.814294 GGGGCGCGAGACGTGATT 62.814 66.667 12.10 0.00 43.44 2.57
734 931 2.137425 TATATGGGGCGCGAGACGTG 62.137 60.000 12.10 0.00 43.44 4.49
735 932 1.457823 TTATATGGGGCGCGAGACGT 61.458 55.000 12.10 1.81 43.44 4.34
736 933 1.007336 GTTATATGGGGCGCGAGACG 61.007 60.000 12.10 0.00 43.44 4.18
737 934 0.669625 GGTTATATGGGGCGCGAGAC 60.670 60.000 12.10 0.00 39.70 3.36
738 935 1.669440 GGTTATATGGGGCGCGAGA 59.331 57.895 12.10 0.00 0.00 4.04
739 936 1.736645 CGGTTATATGGGGCGCGAG 60.737 63.158 12.10 0.00 0.00 5.03
740 937 2.149803 CTCGGTTATATGGGGCGCGA 62.150 60.000 12.10 0.00 0.00 5.87
741 938 1.736645 CTCGGTTATATGGGGCGCG 60.737 63.158 0.00 0.00 0.00 6.86
833 1032 1.939980 AGGTAAGGAGGTCTGGTGAC 58.060 55.000 0.00 0.00 42.22 3.67
834 1033 2.111972 AGAAGGTAAGGAGGTCTGGTGA 59.888 50.000 0.00 0.00 0.00 4.02
835 1034 2.498078 GAGAAGGTAAGGAGGTCTGGTG 59.502 54.545 0.00 0.00 0.00 4.17
836 1035 2.560158 GGAGAAGGTAAGGAGGTCTGGT 60.560 54.545 0.00 0.00 0.00 4.00
837 1036 2.112190 GGAGAAGGTAAGGAGGTCTGG 58.888 57.143 0.00 0.00 0.00 3.86
838 1037 2.112190 GGGAGAAGGTAAGGAGGTCTG 58.888 57.143 0.00 0.00 0.00 3.51
839 1038 1.008571 GGGGAGAAGGTAAGGAGGTCT 59.991 57.143 0.00 0.00 0.00 3.85
1496 1711 0.962356 CTTGTCCATTGCCGGCTTCT 60.962 55.000 29.70 9.24 0.00 2.85
1746 1961 7.896383 ATGACTCTAAGCTGAATAGAAGTCT 57.104 36.000 16.18 0.00 33.51 3.24
1787 2002 7.477144 TCTACAACGCCACAAGAATTATATG 57.523 36.000 0.00 0.00 0.00 1.78
2191 2409 6.097554 TGAAATTCTCTAGGAAGTAGGCAGAG 59.902 42.308 0.00 0.00 37.36 3.35
2256 2474 7.173218 TGAACTCTGAAATTCGAAAGCATAAGT 59.827 33.333 0.00 5.09 0.00 2.24
2290 2508 6.756299 TTGATACATTGCTTGCAGTTCATA 57.244 33.333 0.00 0.00 0.00 2.15
2291 2509 5.648178 TTGATACATTGCTTGCAGTTCAT 57.352 34.783 0.00 0.00 0.00 2.57
2292 2510 5.009911 AGTTTGATACATTGCTTGCAGTTCA 59.990 36.000 0.00 0.00 0.00 3.18
2347 2565 0.459899 TCTCACGACATAAGCGGCAT 59.540 50.000 1.45 0.00 0.00 4.40
2364 2582 2.031870 GGCACCAACCAAAGTTCTTCT 58.968 47.619 0.00 0.00 32.45 2.85
2429 2647 8.548877 AGAAAAGCTCACCTAATAAGACCATAA 58.451 33.333 0.00 0.00 0.00 1.90
2493 2958 8.815912 ACCAATCCAAACTAGCAAATCTTTTAT 58.184 29.630 0.00 0.00 0.00 1.40
2494 2959 8.087750 CACCAATCCAAACTAGCAAATCTTTTA 58.912 33.333 0.00 0.00 0.00 1.52
2495 2960 6.930722 CACCAATCCAAACTAGCAAATCTTTT 59.069 34.615 0.00 0.00 0.00 2.27
2504 2969 1.202348 GTGCCACCAATCCAAACTAGC 59.798 52.381 0.00 0.00 0.00 3.42
2599 3064 4.090761 TGAATGGATAAGACCAGATGGC 57.909 45.455 0.00 0.00 43.49 4.40
2664 3166 5.611374 ACTACAGTTTTCAGCAGTGTATGT 58.389 37.500 0.00 0.00 31.15 2.29


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

AutoCloner maintained by Alex Coulton.