Multiple sequence alignment - TraesCS7B01G311800

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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 TraesCS7B01G311800 chr7B 100.000 2514 0 0 1 2514 557245222 557247735 0.000000e+00 4643
1 TraesCS7B01G311800 chr7B 96.671 2313 77 0 1 2313 112898387 112900699 0.000000e+00 3845
2 TraesCS7B01G311800 chr7B 89.320 206 21 1 2310 2514 662841064 662841269 8.920000e-65 257
3 TraesCS7B01G311800 chr7B 87.805 205 22 2 2310 2514 662810466 662810667 1.160000e-58 237
4 TraesCS7B01G311800 chr7B 88.108 185 17 4 2311 2493 30838450 30838269 5.450000e-52 215
5 TraesCS7B01G311800 chr4B 96.596 2321 77 2 1 2321 554204779 554207097 0.000000e+00 3847
6 TraesCS7B01G311800 chr4B 96.384 2323 82 2 1 2321 95357242 95354920 0.000000e+00 3823
7 TraesCS7B01G311800 chr4B 96.165 2321 85 4 1 2321 646936510 646938826 0.000000e+00 3790
8 TraesCS7B01G311800 chr2B 96.512 2322 76 3 1 2321 87791490 87793807 0.000000e+00 3834
9 TraesCS7B01G311800 chr2B 90.863 197 17 1 2309 2504 735612853 735613049 1.920000e-66 263
10 TraesCS7B01G311800 chr2B 86.765 204 25 2 2303 2504 740984470 740984673 2.520000e-55 226
11 TraesCS7B01G311800 chr3B 96.368 2313 83 1 1 2313 48679970 48682281 0.000000e+00 3805
12 TraesCS7B01G311800 chr1B 96.079 2321 89 2 1 2321 661028329 661030647 0.000000e+00 3781
13 TraesCS7B01G311800 chr1B 95.984 2316 90 2 1 2313 83652243 83654558 0.000000e+00 3759
14 TraesCS7B01G311800 chr5B 95.878 2329 89 6 1 2328 541962817 541965139 0.000000e+00 3762
15 TraesCS7B01G311800 chr5B 91.748 206 15 2 2311 2514 664213957 664214162 4.090000e-73 285
16 TraesCS7B01G311800 chr5B 89.320 206 20 2 2311 2514 677242044 677242249 8.920000e-65 257
17 TraesCS7B01G311800 chr5B 87.778 180 20 2 2308 2487 76124960 76125137 2.530000e-50 209
18 TraesCS7B01G311800 chr7D 91.005 189 16 1 2317 2505 63101295 63101108 1.150000e-63 254


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 TraesCS7B01G311800 chr7B 557245222 557247735 2513 False 4643 4643 100.000 1 2514 1 chr7B.!!$F2 2513
1 TraesCS7B01G311800 chr7B 112898387 112900699 2312 False 3845 3845 96.671 1 2313 1 chr7B.!!$F1 2312
2 TraesCS7B01G311800 chr4B 554204779 554207097 2318 False 3847 3847 96.596 1 2321 1 chr4B.!!$F1 2320
3 TraesCS7B01G311800 chr4B 95354920 95357242 2322 True 3823 3823 96.384 1 2321 1 chr4B.!!$R1 2320
4 TraesCS7B01G311800 chr4B 646936510 646938826 2316 False 3790 3790 96.165 1 2321 1 chr4B.!!$F2 2320
5 TraesCS7B01G311800 chr2B 87791490 87793807 2317 False 3834 3834 96.512 1 2321 1 chr2B.!!$F1 2320
6 TraesCS7B01G311800 chr3B 48679970 48682281 2311 False 3805 3805 96.368 1 2313 1 chr3B.!!$F1 2312
7 TraesCS7B01G311800 chr1B 661028329 661030647 2318 False 3781 3781 96.079 1 2321 1 chr1B.!!$F2 2320
8 TraesCS7B01G311800 chr1B 83652243 83654558 2315 False 3759 3759 95.984 1 2313 1 chr1B.!!$F1 2312
9 TraesCS7B01G311800 chr5B 541962817 541965139 2322 False 3762 3762 95.878 1 2328 1 chr5B.!!$F2 2327

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
129 130 0.546988 GGTAGTTCACCCACCTCCCT 60.547 60.0 0.0 0.0 42.07 4.2 F
1044 1051 1.830279 CACCACATGACCAGCAAGAT 58.170 50.0 0.0 0.0 0.00 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1132 1139 0.533491 TCGGCATGCGTAGTAAGGTT 59.467 50.0 12.44 0.0 0.00 3.5 R
2445 2453 0.746063 TGTACGTGTCGGTTCAACCT 59.254 50.0 4.68 0.0 35.66 3.5 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
73 74 6.459024 GCAGATACGATATCTGAGGATACCAC 60.459 46.154 25.88 10.71 46.25 4.16
129 130 0.546988 GGTAGTTCACCCACCTCCCT 60.547 60.000 0.00 0.00 42.07 4.20
207 208 1.950909 TCGTCAAGCGGTTTGGAAATT 59.049 42.857 0.00 0.00 41.72 1.82
320 322 7.383572 CCATTCATCTTCTTCGTACTTCCTATG 59.616 40.741 0.00 0.00 0.00 2.23
435 438 4.952957 TGGACAGAACCAAAGTCATTCAAA 59.047 37.500 0.00 0.00 36.96 2.69
908 913 2.201830 TCAACTACCCCCACCCATAAG 58.798 52.381 0.00 0.00 0.00 1.73
922 928 5.184864 CCACCCATAAGCAAAACATTCTACA 59.815 40.000 0.00 0.00 0.00 2.74
965 972 5.412904 CCCTCTCTTGTTCTTTATGTGAACC 59.587 44.000 0.00 0.00 42.04 3.62
994 1001 9.468532 GCTTCTCATTTCTTCACTTTTAAATGT 57.531 29.630 1.06 1.06 39.32 2.71
1044 1051 1.830279 CACCACATGACCAGCAAGAT 58.170 50.000 0.00 0.00 0.00 2.40
1119 1126 4.346730 AGGTGCTTGATTCAATCCATTCA 58.653 39.130 0.00 0.00 0.00 2.57
1132 1139 3.076079 TCCATTCAGAAGCTGATGCAA 57.924 42.857 0.00 0.00 40.39 4.08
1619 1627 2.279502 ATCACGCGGCGATACACACT 62.280 55.000 30.94 0.00 0.00 3.55
1646 1654 2.884012 CACACCTTACATTCTGTTGCCA 59.116 45.455 0.00 0.00 0.00 4.92
1686 1694 9.057089 ACTATCTCTTTTGTTCTCGTCAAAAAT 57.943 29.630 0.00 0.00 41.87 1.82
1752 1760 1.491668 TGTAGTGGTGGTGTGTGAGT 58.508 50.000 0.00 0.00 0.00 3.41
1864 1872 4.724074 ATGGTTTCATCGTTTGCATCAT 57.276 36.364 0.00 0.00 0.00 2.45
1872 1880 1.876799 TCGTTTGCATCATCCGTTTGT 59.123 42.857 0.00 0.00 0.00 2.83
1959 1967 5.660629 ACGTCATTGTCGTTGTTCATTTA 57.339 34.783 3.09 0.00 38.38 1.40
1986 1994 6.312426 ACGTCTTGCTTCTTCTATTTCATCAG 59.688 38.462 0.00 0.00 0.00 2.90
2031 2039 4.603131 AGGTTTGATCATGTAGCCACAAT 58.397 39.130 0.00 0.00 38.42 2.71
2094 2102 7.225784 TGTTTCCTATACATTGCACACAATT 57.774 32.000 0.00 0.00 44.21 2.32
2115 2123 5.717078 TTCACTATGTGTCTCTAAACCGT 57.283 39.130 0.00 0.00 34.79 4.83
2167 2175 6.179756 TGCAGAGTCATTACAAATACCATGT 58.820 36.000 0.00 0.00 34.81 3.21
2261 2269 6.071051 TGGCAGATACAGTACAACTAACATGA 60.071 38.462 0.00 0.00 0.00 3.07
2271 2279 4.256920 ACAACTAACATGACAGATCCAGC 58.743 43.478 0.00 0.00 0.00 4.85
2313 2321 4.153117 GCAGTACAACTAGCATGGCATATC 59.847 45.833 0.00 0.00 0.00 1.63
2316 2324 7.326454 CAGTACAACTAGCATGGCATATCTAT 58.674 38.462 0.00 0.00 0.00 1.98
2351 2359 7.907214 ATACAGAAGACAAATAAGACACCAC 57.093 36.000 0.00 0.00 0.00 4.16
2352 2360 4.750098 ACAGAAGACAAATAAGACACCACG 59.250 41.667 0.00 0.00 0.00 4.94
2353 2361 4.750098 CAGAAGACAAATAAGACACCACGT 59.250 41.667 0.00 0.00 0.00 4.49
2354 2362 5.236478 CAGAAGACAAATAAGACACCACGTT 59.764 40.000 0.00 0.00 0.00 3.99
2355 2363 5.465724 AGAAGACAAATAAGACACCACGTTC 59.534 40.000 0.00 0.00 0.00 3.95
2356 2364 4.957296 AGACAAATAAGACACCACGTTCT 58.043 39.130 0.00 0.00 0.00 3.01
2357 2365 5.365619 AGACAAATAAGACACCACGTTCTT 58.634 37.500 5.61 5.61 0.00 2.52
2358 2366 5.465724 AGACAAATAAGACACCACGTTCTTC 59.534 40.000 3.56 0.00 0.00 2.87
2359 2367 4.514066 ACAAATAAGACACCACGTTCTTCC 59.486 41.667 3.56 0.00 0.00 3.46
2360 2368 4.345859 AATAAGACACCACGTTCTTCCA 57.654 40.909 3.56 0.00 0.00 3.53
2361 2369 1.949465 AAGACACCACGTTCTTCCAC 58.051 50.000 0.00 0.00 0.00 4.02
2362 2370 0.828022 AGACACCACGTTCTTCCACA 59.172 50.000 0.00 0.00 0.00 4.17
2363 2371 1.416401 AGACACCACGTTCTTCCACAT 59.584 47.619 0.00 0.00 0.00 3.21
2364 2372 2.631062 AGACACCACGTTCTTCCACATA 59.369 45.455 0.00 0.00 0.00 2.29
2365 2373 3.070446 AGACACCACGTTCTTCCACATAA 59.930 43.478 0.00 0.00 0.00 1.90
2366 2374 3.399330 ACACCACGTTCTTCCACATAAG 58.601 45.455 0.00 0.00 0.00 1.73
2367 2375 2.159627 CACCACGTTCTTCCACATAAGC 59.840 50.000 0.00 0.00 0.00 3.09
2368 2376 2.038557 ACCACGTTCTTCCACATAAGCT 59.961 45.455 0.00 0.00 0.00 3.74
2369 2377 3.259876 ACCACGTTCTTCCACATAAGCTA 59.740 43.478 0.00 0.00 0.00 3.32
2370 2378 4.250464 CCACGTTCTTCCACATAAGCTAA 58.750 43.478 0.00 0.00 0.00 3.09
2371 2379 4.693566 CCACGTTCTTCCACATAAGCTAAA 59.306 41.667 0.00 0.00 0.00 1.85
2372 2380 5.180492 CCACGTTCTTCCACATAAGCTAAAA 59.820 40.000 0.00 0.00 0.00 1.52
2373 2381 6.077838 CACGTTCTTCCACATAAGCTAAAAC 58.922 40.000 0.00 0.00 0.00 2.43
2374 2382 5.761234 ACGTTCTTCCACATAAGCTAAAACA 59.239 36.000 0.00 0.00 0.00 2.83
2375 2383 6.261381 ACGTTCTTCCACATAAGCTAAAACAA 59.739 34.615 0.00 0.00 0.00 2.83
2376 2384 7.040686 ACGTTCTTCCACATAAGCTAAAACAAT 60.041 33.333 0.00 0.00 0.00 2.71
2377 2385 8.447833 CGTTCTTCCACATAAGCTAAAACAATA 58.552 33.333 0.00 0.00 0.00 1.90
2384 2392 9.811655 CCACATAAGCTAAAACAATATACATCG 57.188 33.333 0.00 0.00 0.00 3.84
2405 2413 8.706035 ACATCGTTGATTAGTAATATTTACGGC 58.294 33.333 0.00 0.00 0.00 5.68
2406 2414 8.922676 CATCGTTGATTAGTAATATTTACGGCT 58.077 33.333 13.75 4.92 0.00 5.52
2407 2415 8.289440 TCGTTGATTAGTAATATTTACGGCTG 57.711 34.615 13.75 0.00 0.00 4.85
2408 2416 8.136800 TCGTTGATTAGTAATATTTACGGCTGA 58.863 33.333 0.00 0.00 0.00 4.26
2409 2417 8.425491 CGTTGATTAGTAATATTTACGGCTGAG 58.575 37.037 0.00 0.00 0.00 3.35
2410 2418 9.472361 GTTGATTAGTAATATTTACGGCTGAGA 57.528 33.333 0.00 0.00 0.00 3.27
2425 2433 7.639162 ACGGCTGAGATTTAAAGATATTACG 57.361 36.000 0.00 0.00 0.00 3.18
2426 2434 7.208080 ACGGCTGAGATTTAAAGATATTACGT 58.792 34.615 0.00 0.00 0.00 3.57
2427 2435 7.709613 ACGGCTGAGATTTAAAGATATTACGTT 59.290 33.333 0.00 0.00 0.00 3.99
2428 2436 9.188588 CGGCTGAGATTTAAAGATATTACGTTA 57.811 33.333 0.00 0.00 0.00 3.18
2430 2438 9.990888 GCTGAGATTTAAAGATATTACGTTACG 57.009 33.333 2.19 2.19 0.00 3.18
2431 2439 9.990888 CTGAGATTTAAAGATATTACGTTACGC 57.009 33.333 4.09 0.00 0.00 4.42
2432 2440 8.971321 TGAGATTTAAAGATATTACGTTACGCC 58.029 33.333 4.09 0.00 0.00 5.68
2433 2441 8.302965 AGATTTAAAGATATTACGTTACGCCC 57.697 34.615 4.09 0.00 0.00 6.13
2434 2442 7.927629 AGATTTAAAGATATTACGTTACGCCCA 59.072 33.333 4.09 0.00 0.00 5.36
2435 2443 7.840342 TTTAAAGATATTACGTTACGCCCAA 57.160 32.000 4.09 0.00 0.00 4.12
2436 2444 7.840342 TTAAAGATATTACGTTACGCCCAAA 57.160 32.000 4.09 0.00 0.00 3.28
2437 2445 6.740411 AAAGATATTACGTTACGCCCAAAA 57.260 33.333 4.09 0.00 0.00 2.44
2438 2446 5.978934 AGATATTACGTTACGCCCAAAAG 57.021 39.130 4.09 0.00 0.00 2.27
2439 2447 5.422145 AGATATTACGTTACGCCCAAAAGT 58.578 37.500 4.09 0.00 0.00 2.66
2440 2448 5.876460 AGATATTACGTTACGCCCAAAAGTT 59.124 36.000 4.09 0.00 0.00 2.66
2441 2449 7.041107 AGATATTACGTTACGCCCAAAAGTTA 58.959 34.615 4.09 0.00 0.00 2.24
2442 2450 7.712205 AGATATTACGTTACGCCCAAAAGTTAT 59.288 33.333 4.09 0.00 0.00 1.89
2443 2451 8.885494 ATATTACGTTACGCCCAAAAGTTATA 57.115 30.769 4.09 0.00 0.00 0.98
2444 2452 7.790823 ATTACGTTACGCCCAAAAGTTATAT 57.209 32.000 4.09 0.00 0.00 0.86
2445 2453 8.885494 ATTACGTTACGCCCAAAAGTTATATA 57.115 30.769 4.09 0.00 0.00 0.86
2446 2454 6.833342 ACGTTACGCCCAAAAGTTATATAG 57.167 37.500 4.09 0.00 0.00 1.31
2447 2455 5.754890 ACGTTACGCCCAAAAGTTATATAGG 59.245 40.000 4.09 0.00 0.00 2.57
2448 2456 5.754890 CGTTACGCCCAAAAGTTATATAGGT 59.245 40.000 0.00 0.00 0.00 3.08
2449 2457 6.258507 CGTTACGCCCAAAAGTTATATAGGTT 59.741 38.462 0.00 0.00 0.00 3.50
2450 2458 7.412063 GTTACGCCCAAAAGTTATATAGGTTG 58.588 38.462 0.00 0.00 0.00 3.77
2451 2459 5.747342 ACGCCCAAAAGTTATATAGGTTGA 58.253 37.500 0.00 0.00 0.00 3.18
2452 2460 6.181908 ACGCCCAAAAGTTATATAGGTTGAA 58.818 36.000 0.00 0.00 0.00 2.69
2453 2461 6.094464 ACGCCCAAAAGTTATATAGGTTGAAC 59.906 38.462 0.00 0.00 0.00 3.18
2454 2462 6.459161 CGCCCAAAAGTTATATAGGTTGAACC 60.459 42.308 6.16 6.16 38.99 3.62
2455 2463 6.459161 GCCCAAAAGTTATATAGGTTGAACCG 60.459 42.308 8.98 0.00 44.90 4.44
2456 2464 6.824704 CCCAAAAGTTATATAGGTTGAACCGA 59.175 38.462 8.98 3.77 44.90 4.69
2457 2465 7.201670 CCCAAAAGTTATATAGGTTGAACCGAC 60.202 40.741 8.98 2.82 44.90 4.79
2458 2466 7.334921 CCAAAAGTTATATAGGTTGAACCGACA 59.665 37.037 8.98 0.00 44.90 4.35
2459 2467 7.838771 AAAGTTATATAGGTTGAACCGACAC 57.161 36.000 8.98 1.82 44.90 3.67
2460 2468 5.585390 AGTTATATAGGTTGAACCGACACG 58.415 41.667 8.98 0.00 44.90 4.49
2461 2469 5.126061 AGTTATATAGGTTGAACCGACACGT 59.874 40.000 8.98 0.00 44.90 4.49
2462 2470 6.318648 AGTTATATAGGTTGAACCGACACGTA 59.681 38.462 8.98 0.00 44.90 3.57
2463 2471 2.704725 TAGGTTGAACCGACACGTAC 57.295 50.000 8.98 0.00 44.90 3.67
2464 2472 0.746063 AGGTTGAACCGACACGTACA 59.254 50.000 8.98 0.00 44.90 2.90
2465 2473 1.136695 AGGTTGAACCGACACGTACAA 59.863 47.619 8.98 0.00 44.90 2.41
2466 2474 1.258720 GGTTGAACCGACACGTACAAC 59.741 52.381 0.00 0.00 37.47 3.32
2467 2475 8.951639 TATAGGTTGAACCGACACGTACAACG 62.952 46.154 8.98 0.00 45.41 4.10
2482 2490 6.932901 CGTACAACGTGTAGGAATAAGAAA 57.067 37.500 10.39 0.00 40.14 2.52
2483 2491 7.515957 CGTACAACGTGTAGGAATAAGAAAT 57.484 36.000 10.39 0.00 40.14 2.17
2484 2492 7.956558 CGTACAACGTGTAGGAATAAGAAATT 58.043 34.615 10.39 0.00 40.14 1.82
2485 2493 8.437742 CGTACAACGTGTAGGAATAAGAAATTT 58.562 33.333 10.39 0.00 40.14 1.82
2486 2494 9.537848 GTACAACGTGTAGGAATAAGAAATTTG 57.462 33.333 0.00 0.00 32.84 2.32
2487 2495 8.161699 ACAACGTGTAGGAATAAGAAATTTGT 57.838 30.769 0.00 0.00 0.00 2.83
2488 2496 9.275398 ACAACGTGTAGGAATAAGAAATTTGTA 57.725 29.630 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 2.110967 CGGGCTCGTAGTCTTCCGA 61.111 63.158 0.00 0.00 39.83 4.55
207 208 2.282674 CTTGCTGCTGGCCCTCAA 60.283 61.111 0.00 0.00 40.92 3.02
320 322 0.441145 AAAACGTAAGCGGATCGTGC 59.559 50.000 0.00 0.55 43.45 5.34
435 438 4.157958 GACGTACGTCGCTCCGCT 62.158 66.667 30.48 0.18 44.19 5.52
488 491 5.472148 ACTACATTCGTCGACATTTTACCA 58.528 37.500 17.16 0.00 0.00 3.25
624 627 5.591099 GTGTTGAGCAAAATTCTTCCTCAA 58.409 37.500 0.00 0.00 39.44 3.02
947 954 4.520492 AGCAGGGTTCACATAAAGAACAAG 59.480 41.667 8.15 0.00 45.45 3.16
965 972 5.702349 AAAGTGAAGAAATGAGAAGCAGG 57.298 39.130 0.00 0.00 0.00 4.85
1065 1072 4.103153 TGGTTCTTCAGGTCAAGACAGATT 59.897 41.667 2.29 0.00 31.88 2.40
1119 1126 4.026356 AGTAAGGTTTGCATCAGCTTCT 57.974 40.909 12.72 8.47 42.74 2.85
1132 1139 0.533491 TCGGCATGCGTAGTAAGGTT 59.467 50.000 12.44 0.00 0.00 3.50
1418 1426 2.884639 ACTTTGCAAAGTATTCCAGCGT 59.115 40.909 37.07 14.28 46.75 5.07
1512 1520 6.618287 TGTTGAAATCTTCATTCGTGAACT 57.382 33.333 0.00 0.00 39.84 3.01
1516 1524 4.319115 CGCTTGTTGAAATCTTCATTCGTG 59.681 41.667 0.00 0.00 39.84 4.35
1619 1627 1.346395 AGAATGTAAGGTGTGCGTCCA 59.654 47.619 0.00 0.00 0.00 4.02
1646 1654 9.892130 CAAAAGAGATAGTACCTTACATTCCTT 57.108 33.333 0.00 0.00 0.00 3.36
1686 1694 7.010091 CAGTCATAACATAGCACACGAACATAA 59.990 37.037 0.00 0.00 0.00 1.90
1864 1872 2.722071 GCATTCGAAACAACAAACGGA 58.278 42.857 0.00 0.00 0.00 4.69
1872 1880 1.209998 TCGTGACGCATTCGAAACAA 58.790 45.000 0.00 0.00 39.41 2.83
1959 1967 5.784177 TGAAATAGAAGAAGCAAGACGTCT 58.216 37.500 13.58 13.58 38.93 4.18
1986 1994 1.933853 CATGCTAGCCGGTGAAGTTAC 59.066 52.381 13.29 0.00 0.00 2.50
2031 2039 1.068610 GTGCATAAACCGCAGCAAAGA 60.069 47.619 0.00 0.00 40.78 2.52
2094 2102 4.521639 ACACGGTTTAGAGACACATAGTGA 59.478 41.667 3.88 0.00 36.96 3.41
2115 2123 7.119116 GGCATATATTTCCATGACAATACGACA 59.881 37.037 0.00 0.00 30.05 4.35
2167 2175 7.012327 GCCATGTTAGCTGTACTGAAAATATGA 59.988 37.037 17.33 0.00 0.00 2.15
2261 2269 2.936919 TTCAGTTGTGCTGGATCTGT 57.063 45.000 0.00 0.00 45.08 3.41
2271 2279 2.029739 TGCATCTGCCATTTCAGTTGTG 60.030 45.455 0.00 0.00 41.18 3.33
2325 2333 9.431887 GTGGTGTCTTATTTGTCTTCTGTATTA 57.568 33.333 0.00 0.00 0.00 0.98
2327 2335 6.590292 CGTGGTGTCTTATTTGTCTTCTGTAT 59.410 38.462 0.00 0.00 0.00 2.29
2328 2336 5.924254 CGTGGTGTCTTATTTGTCTTCTGTA 59.076 40.000 0.00 0.00 0.00 2.74
2329 2337 4.750098 CGTGGTGTCTTATTTGTCTTCTGT 59.250 41.667 0.00 0.00 0.00 3.41
2330 2338 4.750098 ACGTGGTGTCTTATTTGTCTTCTG 59.250 41.667 0.00 0.00 0.00 3.02
2331 2339 4.957296 ACGTGGTGTCTTATTTGTCTTCT 58.043 39.130 0.00 0.00 0.00 2.85
2332 2340 5.465724 AGAACGTGGTGTCTTATTTGTCTTC 59.534 40.000 0.00 0.00 0.00 2.87
2333 2341 5.365619 AGAACGTGGTGTCTTATTTGTCTT 58.634 37.500 0.00 0.00 0.00 3.01
2334 2342 4.957296 AGAACGTGGTGTCTTATTTGTCT 58.043 39.130 0.00 0.00 0.00 3.41
2335 2343 5.333875 GGAAGAACGTGGTGTCTTATTTGTC 60.334 44.000 0.33 0.00 0.00 3.18
2336 2344 4.514066 GGAAGAACGTGGTGTCTTATTTGT 59.486 41.667 0.33 0.00 0.00 2.83
2337 2345 4.513692 TGGAAGAACGTGGTGTCTTATTTG 59.486 41.667 0.33 0.00 0.00 2.32
2338 2346 4.514066 GTGGAAGAACGTGGTGTCTTATTT 59.486 41.667 0.33 0.00 0.00 1.40
2339 2347 4.062991 GTGGAAGAACGTGGTGTCTTATT 58.937 43.478 0.33 0.00 0.00 1.40
2340 2348 3.070446 TGTGGAAGAACGTGGTGTCTTAT 59.930 43.478 0.33 0.00 0.00 1.73
2341 2349 2.431419 TGTGGAAGAACGTGGTGTCTTA 59.569 45.455 0.33 0.00 0.00 2.10
2342 2350 1.208535 TGTGGAAGAACGTGGTGTCTT 59.791 47.619 0.00 0.00 0.00 3.01
2343 2351 0.828022 TGTGGAAGAACGTGGTGTCT 59.172 50.000 0.00 0.00 0.00 3.41
2344 2352 1.878953 ATGTGGAAGAACGTGGTGTC 58.121 50.000 0.00 0.00 0.00 3.67
2345 2353 3.399330 CTTATGTGGAAGAACGTGGTGT 58.601 45.455 0.00 0.00 0.00 4.16
2346 2354 2.159627 GCTTATGTGGAAGAACGTGGTG 59.840 50.000 0.00 0.00 0.00 4.17
2347 2355 2.038557 AGCTTATGTGGAAGAACGTGGT 59.961 45.455 0.00 0.00 0.00 4.16
2348 2356 2.699954 AGCTTATGTGGAAGAACGTGG 58.300 47.619 0.00 0.00 0.00 4.94
2349 2357 5.856126 TTTAGCTTATGTGGAAGAACGTG 57.144 39.130 0.00 0.00 0.00 4.49
2350 2358 5.761234 TGTTTTAGCTTATGTGGAAGAACGT 59.239 36.000 0.00 0.00 0.00 3.99
2351 2359 6.236017 TGTTTTAGCTTATGTGGAAGAACG 57.764 37.500 0.00 0.00 0.00 3.95
2358 2366 9.811655 CGATGTATATTGTTTTAGCTTATGTGG 57.188 33.333 0.00 0.00 0.00 4.17
2379 2387 8.706035 GCCGTAAATATTACTAATCAACGATGT 58.294 33.333 0.00 0.00 0.00 3.06
2380 2388 8.922676 AGCCGTAAATATTACTAATCAACGATG 58.077 33.333 0.00 0.00 0.00 3.84
2381 2389 8.922676 CAGCCGTAAATATTACTAATCAACGAT 58.077 33.333 0.00 0.00 0.00 3.73
2382 2390 8.136800 TCAGCCGTAAATATTACTAATCAACGA 58.863 33.333 0.00 0.00 0.00 3.85
2383 2391 8.289440 TCAGCCGTAAATATTACTAATCAACG 57.711 34.615 0.00 0.00 0.00 4.10
2384 2392 9.472361 TCTCAGCCGTAAATATTACTAATCAAC 57.528 33.333 0.00 0.00 0.00 3.18
2399 2407 9.188588 CGTAATATCTTTAAATCTCAGCCGTAA 57.811 33.333 0.00 0.00 0.00 3.18
2400 2408 8.355169 ACGTAATATCTTTAAATCTCAGCCGTA 58.645 33.333 0.00 0.00 0.00 4.02
2401 2409 7.208080 ACGTAATATCTTTAAATCTCAGCCGT 58.792 34.615 0.00 0.00 0.00 5.68
2402 2410 7.639162 ACGTAATATCTTTAAATCTCAGCCG 57.361 36.000 0.00 0.00 0.00 5.52
2404 2412 9.990888 CGTAACGTAATATCTTTAAATCTCAGC 57.009 33.333 0.00 0.00 0.00 4.26
2405 2413 9.990888 GCGTAACGTAATATCTTTAAATCTCAG 57.009 33.333 0.00 0.00 0.00 3.35
2406 2414 8.971321 GGCGTAACGTAATATCTTTAAATCTCA 58.029 33.333 0.00 0.00 0.00 3.27
2407 2415 8.430828 GGGCGTAACGTAATATCTTTAAATCTC 58.569 37.037 0.00 0.00 0.00 2.75
2408 2416 7.927629 TGGGCGTAACGTAATATCTTTAAATCT 59.072 33.333 0.00 0.00 0.00 2.40
2409 2417 8.075593 TGGGCGTAACGTAATATCTTTAAATC 57.924 34.615 0.00 0.00 0.00 2.17
2410 2418 8.436046 TTGGGCGTAACGTAATATCTTTAAAT 57.564 30.769 0.00 0.00 0.00 1.40
2411 2419 7.840342 TTGGGCGTAACGTAATATCTTTAAA 57.160 32.000 0.00 0.00 0.00 1.52
2412 2420 7.840342 TTTGGGCGTAACGTAATATCTTTAA 57.160 32.000 0.00 0.00 0.00 1.52
2413 2421 7.548780 ACTTTTGGGCGTAACGTAATATCTTTA 59.451 33.333 0.00 0.00 0.00 1.85
2414 2422 6.372381 ACTTTTGGGCGTAACGTAATATCTTT 59.628 34.615 0.00 0.00 0.00 2.52
2415 2423 5.876460 ACTTTTGGGCGTAACGTAATATCTT 59.124 36.000 0.00 0.00 0.00 2.40
2416 2424 5.422145 ACTTTTGGGCGTAACGTAATATCT 58.578 37.500 0.00 0.00 0.00 1.98
2417 2425 5.723492 ACTTTTGGGCGTAACGTAATATC 57.277 39.130 0.00 0.00 0.00 1.63
2418 2426 7.790823 ATAACTTTTGGGCGTAACGTAATAT 57.209 32.000 0.00 0.00 0.00 1.28
2419 2427 8.885494 ATATAACTTTTGGGCGTAACGTAATA 57.115 30.769 0.00 0.00 0.00 0.98
2420 2428 7.790823 ATATAACTTTTGGGCGTAACGTAAT 57.209 32.000 0.00 0.00 0.00 1.89
2421 2429 7.437862 CCTATATAACTTTTGGGCGTAACGTAA 59.562 37.037 0.00 0.00 0.00 3.18
2422 2430 6.922957 CCTATATAACTTTTGGGCGTAACGTA 59.077 38.462 0.00 0.00 0.00 3.57
2423 2431 5.754890 CCTATATAACTTTTGGGCGTAACGT 59.245 40.000 0.00 0.00 0.00 3.99
2424 2432 5.754890 ACCTATATAACTTTTGGGCGTAACG 59.245 40.000 0.00 0.00 0.00 3.18
2425 2433 7.280652 TCAACCTATATAACTTTTGGGCGTAAC 59.719 37.037 0.00 0.00 0.00 2.50
2426 2434 7.337167 TCAACCTATATAACTTTTGGGCGTAA 58.663 34.615 0.00 0.00 0.00 3.18
2427 2435 6.887013 TCAACCTATATAACTTTTGGGCGTA 58.113 36.000 0.00 0.00 0.00 4.42
2428 2436 5.747342 TCAACCTATATAACTTTTGGGCGT 58.253 37.500 0.00 0.00 0.00 5.68
2429 2437 6.459161 GGTTCAACCTATATAACTTTTGGGCG 60.459 42.308 0.00 0.00 34.73 6.13
2430 2438 6.459161 CGGTTCAACCTATATAACTTTTGGGC 60.459 42.308 4.68 0.00 35.66 5.36
2431 2439 6.824704 TCGGTTCAACCTATATAACTTTTGGG 59.175 38.462 4.68 0.00 35.66 4.12
2432 2440 7.334921 TGTCGGTTCAACCTATATAACTTTTGG 59.665 37.037 4.68 0.00 35.66 3.28
2433 2441 8.173130 GTGTCGGTTCAACCTATATAACTTTTG 58.827 37.037 4.68 0.00 35.66 2.44
2434 2442 7.063780 CGTGTCGGTTCAACCTATATAACTTTT 59.936 37.037 4.68 0.00 35.66 2.27
2435 2443 6.532657 CGTGTCGGTTCAACCTATATAACTTT 59.467 38.462 4.68 0.00 35.66 2.66
2436 2444 6.038356 CGTGTCGGTTCAACCTATATAACTT 58.962 40.000 4.68 0.00 35.66 2.66
2437 2445 5.126061 ACGTGTCGGTTCAACCTATATAACT 59.874 40.000 4.68 0.00 35.66 2.24
2438 2446 5.343249 ACGTGTCGGTTCAACCTATATAAC 58.657 41.667 4.68 0.00 35.66 1.89
2439 2447 5.581126 ACGTGTCGGTTCAACCTATATAA 57.419 39.130 4.68 0.00 35.66 0.98
2440 2448 5.588246 TGTACGTGTCGGTTCAACCTATATA 59.412 40.000 4.68 0.00 35.66 0.86
2441 2449 4.398988 TGTACGTGTCGGTTCAACCTATAT 59.601 41.667 4.68 0.00 35.66 0.86
2442 2450 3.755905 TGTACGTGTCGGTTCAACCTATA 59.244 43.478 4.68 0.00 35.66 1.31
2443 2451 2.557924 TGTACGTGTCGGTTCAACCTAT 59.442 45.455 4.68 0.00 35.66 2.57
2444 2452 1.952990 TGTACGTGTCGGTTCAACCTA 59.047 47.619 4.68 0.00 35.66 3.08
2445 2453 0.746063 TGTACGTGTCGGTTCAACCT 59.254 50.000 4.68 0.00 35.66 3.50
2446 2454 1.258720 GTTGTACGTGTCGGTTCAACC 59.741 52.381 0.00 0.00 33.66 3.77
2447 2455 1.071959 CGTTGTACGTGTCGGTTCAAC 60.072 52.381 0.00 5.47 36.74 3.18
2448 2456 1.198767 CGTTGTACGTGTCGGTTCAA 58.801 50.000 0.00 0.00 36.74 2.69
2449 2457 2.870690 CGTTGTACGTGTCGGTTCA 58.129 52.632 0.00 0.00 36.74 3.18
2460 2468 9.537848 CAAATTTCTTATTCCTACACGTTGTAC 57.462 33.333 0.00 0.00 0.00 2.90
2461 2469 9.275398 ACAAATTTCTTATTCCTACACGTTGTA 57.725 29.630 0.00 0.00 0.00 2.41
2462 2470 8.161699 ACAAATTTCTTATTCCTACACGTTGT 57.838 30.769 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.