Multiple sequence alignment - TraesCS6D01G253200

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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 TraesCS6D01G253200 chr6D 100.000 2414 0 0 1 2414 357454087 357451674 0.000000e+00 4458
1 TraesCS6D01G253200 chr6D 94.130 1891 86 8 433 2306 273130997 273132879 0.000000e+00 2854
2 TraesCS6D01G253200 chr6D 92.033 615 37 7 1 609 91438695 91439303 0.000000e+00 854
3 TraesCS6D01G253200 chr2D 93.926 2338 101 11 1 2306 260388095 260385767 0.000000e+00 3493
4 TraesCS6D01G253200 chr2D 92.488 2343 132 12 1 2306 471597567 471595232 0.000000e+00 3312
5 TraesCS6D01G253200 chr5D 93.291 2340 112 12 1 2306 249656403 249654075 0.000000e+00 3410
6 TraesCS6D01G253200 chr5D 92.056 642 44 6 1 635 311825236 311825877 0.000000e+00 896
7 TraesCS6D01G253200 chr3D 93.003 2358 107 24 1 2306 541034915 541032564 0.000000e+00 3387
8 TraesCS6D01G253200 chr3D 92.778 2340 129 15 1 2306 397849370 397851703 0.000000e+00 3349
9 TraesCS6D01G253200 chr3D 92.569 2355 122 16 1 2306 415199886 415197536 0.000000e+00 3330
10 TraesCS6D01G253200 chr3D 92.200 641 41 6 1 635 67331663 67332300 0.000000e+00 898
11 TraesCS6D01G253200 chr3D 92.007 613 42 6 1 608 77500047 77499437 0.000000e+00 854
12 TraesCS6D01G253200 chr3D 88.235 476 21 14 1866 2306 437447931 437447456 9.820000e-149 536
13 TraesCS6D01G253200 chr3D 99.074 108 1 0 2307 2414 279217857 279217964 6.810000e-46 195
14 TraesCS6D01G253200 chr4D 93.574 2272 104 11 65 2302 65499330 65497067 0.000000e+00 3349
15 TraesCS6D01G253200 chr4D 90.645 620 41 13 1 613 364999033 364999642 0.000000e+00 808
16 TraesCS6D01G253200 chr4D 92.014 288 19 3 2017 2302 509563746 509563461 3.740000e-108 401
17 TraesCS6D01G253200 chr2A 92.605 2326 138 17 1 2306 652910300 652912611 0.000000e+00 3312
18 TraesCS6D01G253200 chr5B 88.710 2365 163 56 1 2302 64374155 64371832 0.000000e+00 2793
19 TraesCS6D01G253200 chr5B 91.181 635 49 5 1 630 590791137 590791769 0.000000e+00 856
20 TraesCS6D01G253200 chr4B 91.137 2031 133 24 1 2022 426578978 426576986 0.000000e+00 2710
21 TraesCS6D01G253200 chr1A 92.694 1834 108 9 494 2302 252021470 252023302 0.000000e+00 2621
22 TraesCS6D01G253200 chr1A 99.074 108 1 0 2307 2414 290392280 290392173 6.810000e-46 195
23 TraesCS6D01G253200 chr1A 99.074 108 1 0 2307 2414 462238979 462239086 6.810000e-46 195
24 TraesCS6D01G253200 chr1A 99.074 108 1 0 2307 2414 504191107 504191000 6.810000e-46 195
25 TraesCS6D01G253200 chr7B 87.357 2365 160 59 1 2302 549364208 549361920 0.000000e+00 2582
26 TraesCS6D01G253200 chr7A 91.930 1772 97 14 549 2301 481818091 481816347 0.000000e+00 2438
27 TraesCS6D01G253200 chr3B 90.297 639 56 6 1 635 463197479 463196843 0.000000e+00 832
28 TraesCS6D01G253200 chr3B 99.074 108 1 0 2307 2414 513478254 513478147 6.810000e-46 195
29 TraesCS6D01G253200 chr3A 89.375 640 61 6 1 635 477701983 477701346 0.000000e+00 798
30 TraesCS6D01G253200 chr3A 100.000 108 0 0 2307 2414 153988854 153988747 1.460000e-47 200
31 TraesCS6D01G253200 chr7D 88.889 459 26 7 1867 2306 337552612 337553064 2.110000e-150 542
32 TraesCS6D01G253200 chr7D 99.074 108 1 0 2307 2414 523239780 523239673 6.810000e-46 195
33 TraesCS6D01G253200 chr1D 92.643 367 27 0 1940 2306 216333785 216333419 1.640000e-146 529
34 TraesCS6D01G253200 chr6A 99.074 108 1 0 2307 2414 18693882 18693989 6.810000e-46 195
35 TraesCS6D01G253200 chr6A 99.074 108 1 0 2307 2414 478361827 478361934 6.810000e-46 195


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 TraesCS6D01G253200 chr6D 357451674 357454087 2413 True 4458 4458 100.000 1 2414 1 chr6D.!!$R1 2413
1 TraesCS6D01G253200 chr6D 273130997 273132879 1882 False 2854 2854 94.130 433 2306 1 chr6D.!!$F2 1873
2 TraesCS6D01G253200 chr6D 91438695 91439303 608 False 854 854 92.033 1 609 1 chr6D.!!$F1 608
3 TraesCS6D01G253200 chr2D 260385767 260388095 2328 True 3493 3493 93.926 1 2306 1 chr2D.!!$R1 2305
4 TraesCS6D01G253200 chr2D 471595232 471597567 2335 True 3312 3312 92.488 1 2306 1 chr2D.!!$R2 2305
5 TraesCS6D01G253200 chr5D 249654075 249656403 2328 True 3410 3410 93.291 1 2306 1 chr5D.!!$R1 2305
6 TraesCS6D01G253200 chr5D 311825236 311825877 641 False 896 896 92.056 1 635 1 chr5D.!!$F1 634
7 TraesCS6D01G253200 chr3D 541032564 541034915 2351 True 3387 3387 93.003 1 2306 1 chr3D.!!$R4 2305
8 TraesCS6D01G253200 chr3D 397849370 397851703 2333 False 3349 3349 92.778 1 2306 1 chr3D.!!$F3 2305
9 TraesCS6D01G253200 chr3D 415197536 415199886 2350 True 3330 3330 92.569 1 2306 1 chr3D.!!$R2 2305
10 TraesCS6D01G253200 chr3D 67331663 67332300 637 False 898 898 92.200 1 635 1 chr3D.!!$F1 634
11 TraesCS6D01G253200 chr3D 77499437 77500047 610 True 854 854 92.007 1 608 1 chr3D.!!$R1 607
12 TraesCS6D01G253200 chr4D 65497067 65499330 2263 True 3349 3349 93.574 65 2302 1 chr4D.!!$R1 2237
13 TraesCS6D01G253200 chr4D 364999033 364999642 609 False 808 808 90.645 1 613 1 chr4D.!!$F1 612
14 TraesCS6D01G253200 chr2A 652910300 652912611 2311 False 3312 3312 92.605 1 2306 1 chr2A.!!$F1 2305
15 TraesCS6D01G253200 chr5B 64371832 64374155 2323 True 2793 2793 88.710 1 2302 1 chr5B.!!$R1 2301
16 TraesCS6D01G253200 chr5B 590791137 590791769 632 False 856 856 91.181 1 630 1 chr5B.!!$F1 629
17 TraesCS6D01G253200 chr4B 426576986 426578978 1992 True 2710 2710 91.137 1 2022 1 chr4B.!!$R1 2021
18 TraesCS6D01G253200 chr1A 252021470 252023302 1832 False 2621 2621 92.694 494 2302 1 chr1A.!!$F1 1808
19 TraesCS6D01G253200 chr7B 549361920 549364208 2288 True 2582 2582 87.357 1 2302 1 chr7B.!!$R1 2301
20 TraesCS6D01G253200 chr7A 481816347 481818091 1744 True 2438 2438 91.930 549 2301 1 chr7A.!!$R1 1752
21 TraesCS6D01G253200 chr3B 463196843 463197479 636 True 832 832 90.297 1 635 1 chr3B.!!$R1 634
22 TraesCS6D01G253200 chr3A 477701346 477701983 637 True 798 798 89.375 1 635 1 chr3A.!!$R2 634

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
958 1061 0.179051 CTCTGCCATCTGCCCTTCTC 60.179 60.0 0.0 0.0 40.16 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1888 0.465705 GCATGCACTAGCTAGGTGGA 59.534 55.0 24.35 19.44 42.74 4.02 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
140 155 9.444600 TGACCATAGACCAAGTTTAGTATTTTC 57.555 33.333 0.00 0.00 0.00 2.29
238 265 0.887836 AAAGCCTTCGAAACCCCGTC 60.888 55.000 0.00 0.00 0.00 4.79
373 401 1.285078 GAAGGAATTAGGTGGGCTGGT 59.715 52.381 0.00 0.00 0.00 4.00
619 689 5.842619 TTGCATCGTTTGAAATCAATTGG 57.157 34.783 5.42 0.00 35.55 3.16
625 695 5.295950 TCGTTTGAAATCAATTGGCATTGT 58.704 33.333 5.42 0.00 40.78 2.71
809 912 4.047059 ACGCGTGTACACTCCCGG 62.047 66.667 23.01 8.78 0.00 5.73
958 1061 0.179051 CTCTGCCATCTGCCCTTCTC 60.179 60.000 0.00 0.00 40.16 2.87
989 1092 4.100373 ACCACTTCTCCTTCTTCTAGCAT 58.900 43.478 0.00 0.00 0.00 3.79
1195 1298 1.001974 CTCCAAGGATGTTCCGTGTCA 59.998 52.381 8.35 0.00 43.22 3.58
1399 1502 0.322187 GTACCCCATCAACAACGCCT 60.322 55.000 0.00 0.00 0.00 5.52
1400 1503 0.402504 TACCCCATCAACAACGCCTT 59.597 50.000 0.00 0.00 0.00 4.35
1404 1507 0.958091 CCATCAACAACGCCTTGGAA 59.042 50.000 0.51 0.00 0.00 3.53
1679 1806 8.349245 TCTACATGTATGTTGGTTGTTTTCTTG 58.651 33.333 5.91 0.00 41.97 3.02
1761 1888 8.574251 TTCTTACACAAGCCACAAATATGTAT 57.426 30.769 0.00 0.00 37.82 2.29
1858 1985 2.297033 TGGATCAAAAAGGCTGCAACTC 59.703 45.455 0.50 0.00 0.00 3.01
1863 1990 0.242017 AAAAGGCTGCAACTCATCGC 59.758 50.000 0.50 0.00 0.00 4.58
1906 2036 4.054671 GAGGAGACAAATATGCGAGAAGG 58.945 47.826 0.00 0.00 0.00 3.46
2077 2298 3.303135 AGGCTTCTGTCGTGGCGA 61.303 61.111 0.00 0.00 0.00 5.54
2172 2412 4.396790 TCAAAGTTAACGGTCAAAGCACTT 59.603 37.500 0.00 0.00 0.00 3.16
2178 2418 1.296056 CGGTCAAAGCACTTACCCGG 61.296 60.000 0.00 0.00 0.00 5.73
2236 2476 1.074889 GCAAGGGAGTGGGGAAAACTA 59.925 52.381 0.00 0.00 0.00 2.24
2306 2546 2.430694 GGGCACAGATGTAAAAATCCCC 59.569 50.000 0.00 0.00 0.00 4.81
2307 2547 3.365472 GGCACAGATGTAAAAATCCCCT 58.635 45.455 0.00 0.00 0.00 4.79
2308 2548 3.381590 GGCACAGATGTAAAAATCCCCTC 59.618 47.826 0.00 0.00 0.00 4.30
2309 2549 4.016444 GCACAGATGTAAAAATCCCCTCA 58.984 43.478 0.00 0.00 0.00 3.86
2310 2550 4.646492 GCACAGATGTAAAAATCCCCTCAT 59.354 41.667 0.00 0.00 0.00 2.90
2311 2551 5.450965 GCACAGATGTAAAAATCCCCTCATG 60.451 44.000 0.00 0.00 0.00 3.07
2312 2552 5.887598 CACAGATGTAAAAATCCCCTCATGA 59.112 40.000 0.00 0.00 0.00 3.07
2313 2553 6.548622 CACAGATGTAAAAATCCCCTCATGAT 59.451 38.462 0.00 0.00 0.00 2.45
2314 2554 7.720957 CACAGATGTAAAAATCCCCTCATGATA 59.279 37.037 0.00 0.00 0.00 2.15
2315 2555 8.281531 ACAGATGTAAAAATCCCCTCATGATAA 58.718 33.333 0.00 0.00 0.00 1.75
2316 2556 8.571336 CAGATGTAAAAATCCCCTCATGATAAC 58.429 37.037 0.00 0.00 0.00 1.89
2317 2557 7.725844 AGATGTAAAAATCCCCTCATGATAACC 59.274 37.037 0.00 0.00 0.00 2.85
2318 2558 6.980577 TGTAAAAATCCCCTCATGATAACCT 58.019 36.000 0.00 0.00 0.00 3.50
2319 2559 7.418378 TGTAAAAATCCCCTCATGATAACCTT 58.582 34.615 0.00 0.00 0.00 3.50
2320 2560 6.796785 AAAAATCCCCTCATGATAACCTTG 57.203 37.500 0.00 0.00 0.00 3.61
2321 2561 5.732331 AAATCCCCTCATGATAACCTTGA 57.268 39.130 0.00 0.00 0.00 3.02
2322 2562 5.732331 AATCCCCTCATGATAACCTTGAA 57.268 39.130 0.00 0.00 0.00 2.69
2323 2563 4.778213 TCCCCTCATGATAACCTTGAAG 57.222 45.455 0.00 0.00 0.00 3.02
2324 2564 4.370776 TCCCCTCATGATAACCTTGAAGA 58.629 43.478 0.00 0.00 0.00 2.87
2325 2565 4.977739 TCCCCTCATGATAACCTTGAAGAT 59.022 41.667 0.00 0.00 0.00 2.40
2326 2566 6.150332 TCCCCTCATGATAACCTTGAAGATA 58.850 40.000 0.00 0.00 0.00 1.98
2327 2567 6.794493 TCCCCTCATGATAACCTTGAAGATAT 59.206 38.462 0.00 0.00 0.00 1.63
2328 2568 7.038017 TCCCCTCATGATAACCTTGAAGATATC 60.038 40.741 0.00 2.69 0.00 1.63
2329 2569 7.037730 CCCCTCATGATAACCTTGAAGATATCT 60.038 40.741 0.00 0.00 0.00 1.98
2330 2570 8.381636 CCCTCATGATAACCTTGAAGATATCTT 58.618 37.037 17.96 17.96 39.23 2.40
2342 2582 4.762289 AAGATATCTTCACGAAGCCCTT 57.238 40.909 12.37 0.90 38.28 3.95
2343 2583 4.065321 AGATATCTTCACGAAGCCCTTG 57.935 45.455 0.00 0.00 38.28 3.61
2344 2584 2.691409 TATCTTCACGAAGCCCTTGG 57.309 50.000 1.75 0.00 38.28 3.61
2345 2585 0.984230 ATCTTCACGAAGCCCTTGGA 59.016 50.000 1.75 0.00 38.28 3.53
2346 2586 0.984230 TCTTCACGAAGCCCTTGGAT 59.016 50.000 1.75 0.00 38.28 3.41
2347 2587 1.089920 CTTCACGAAGCCCTTGGATG 58.910 55.000 0.00 0.00 0.00 3.51
2348 2588 0.690192 TTCACGAAGCCCTTGGATGA 59.310 50.000 0.00 0.00 0.00 2.92
2349 2589 0.690192 TCACGAAGCCCTTGGATGAA 59.310 50.000 0.00 0.00 0.00 2.57
2350 2590 1.089920 CACGAAGCCCTTGGATGAAG 58.910 55.000 0.00 0.00 0.00 3.02
2351 2591 0.678048 ACGAAGCCCTTGGATGAAGC 60.678 55.000 0.00 0.00 0.00 3.86
2352 2592 0.677731 CGAAGCCCTTGGATGAAGCA 60.678 55.000 0.00 0.00 0.00 3.91
2353 2593 1.549203 GAAGCCCTTGGATGAAGCAA 58.451 50.000 0.00 0.00 0.00 3.91
2354 2594 1.475682 GAAGCCCTTGGATGAAGCAAG 59.524 52.381 0.00 0.00 0.00 4.01
2355 2595 0.700564 AGCCCTTGGATGAAGCAAGA 59.299 50.000 0.00 0.00 0.00 3.02
2356 2596 1.287146 AGCCCTTGGATGAAGCAAGAT 59.713 47.619 0.00 0.00 0.00 2.40
2357 2597 2.105766 GCCCTTGGATGAAGCAAGATT 58.894 47.619 0.00 0.00 0.00 2.40
2358 2598 2.498885 GCCCTTGGATGAAGCAAGATTT 59.501 45.455 0.00 0.00 0.00 2.17
2359 2599 3.429960 GCCCTTGGATGAAGCAAGATTTC 60.430 47.826 0.00 0.00 0.00 2.17
2360 2600 3.181493 CCCTTGGATGAAGCAAGATTTCG 60.181 47.826 0.00 0.00 0.00 3.46
2361 2601 3.432782 CTTGGATGAAGCAAGATTTCGC 58.567 45.455 0.00 0.00 0.00 4.70
2362 2602 1.398041 TGGATGAAGCAAGATTTCGCG 59.602 47.619 0.00 0.00 0.00 5.87
2363 2603 1.665679 GGATGAAGCAAGATTTCGCGA 59.334 47.619 3.71 3.71 0.00 5.87
2364 2604 2.286067 GGATGAAGCAAGATTTCGCGAG 60.286 50.000 9.59 0.00 0.00 5.03
2365 2605 1.795768 TGAAGCAAGATTTCGCGAGT 58.204 45.000 9.59 1.58 0.00 4.18
2366 2606 2.143122 TGAAGCAAGATTTCGCGAGTT 58.857 42.857 9.59 0.00 0.00 3.01
2367 2607 3.322369 TGAAGCAAGATTTCGCGAGTTA 58.678 40.909 9.59 0.00 0.00 2.24
2368 2608 3.743911 TGAAGCAAGATTTCGCGAGTTAA 59.256 39.130 9.59 0.49 0.00 2.01
2369 2609 3.999229 AGCAAGATTTCGCGAGTTAAG 57.001 42.857 9.59 0.28 0.00 1.85
2370 2610 2.673368 AGCAAGATTTCGCGAGTTAAGG 59.327 45.455 9.59 0.41 0.00 2.69
2371 2611 2.788065 GCAAGATTTCGCGAGTTAAGGC 60.788 50.000 9.59 7.50 0.00 4.35
2372 2612 2.380084 AGATTTCGCGAGTTAAGGCA 57.620 45.000 9.59 0.00 0.00 4.75
2373 2613 2.906354 AGATTTCGCGAGTTAAGGCAT 58.094 42.857 9.59 0.00 0.00 4.40
2374 2614 2.609459 AGATTTCGCGAGTTAAGGCATG 59.391 45.455 9.59 0.00 0.00 4.06
2375 2615 2.087501 TTTCGCGAGTTAAGGCATGA 57.912 45.000 9.59 0.00 0.00 3.07
2376 2616 1.640428 TTCGCGAGTTAAGGCATGAG 58.360 50.000 9.59 0.00 0.00 2.90
2377 2617 0.806102 TCGCGAGTTAAGGCATGAGC 60.806 55.000 3.71 0.00 41.10 4.26
2378 2618 0.807667 CGCGAGTTAAGGCATGAGCT 60.808 55.000 0.00 0.00 41.70 4.09
2379 2619 1.536072 CGCGAGTTAAGGCATGAGCTA 60.536 52.381 0.00 0.00 41.70 3.32
2380 2620 2.550978 GCGAGTTAAGGCATGAGCTAA 58.449 47.619 0.00 0.00 41.70 3.09
2381 2621 2.936498 GCGAGTTAAGGCATGAGCTAAA 59.064 45.455 0.00 0.00 41.70 1.85
2382 2622 3.561725 GCGAGTTAAGGCATGAGCTAAAT 59.438 43.478 0.00 0.00 41.70 1.40
2383 2623 4.750098 GCGAGTTAAGGCATGAGCTAAATA 59.250 41.667 0.00 0.00 41.70 1.40
2384 2624 5.409826 GCGAGTTAAGGCATGAGCTAAATAT 59.590 40.000 0.00 0.00 41.70 1.28
2385 2625 6.401581 GCGAGTTAAGGCATGAGCTAAATATC 60.402 42.308 0.00 0.00 41.70 1.63
2386 2626 6.646653 CGAGTTAAGGCATGAGCTAAATATCA 59.353 38.462 0.00 0.00 41.70 2.15
2387 2627 7.332926 CGAGTTAAGGCATGAGCTAAATATCAT 59.667 37.037 0.00 0.00 41.70 2.45
2388 2628 8.930846 AGTTAAGGCATGAGCTAAATATCATT 57.069 30.769 0.00 0.00 41.70 2.57
2389 2629 8.790718 AGTTAAGGCATGAGCTAAATATCATTG 58.209 33.333 0.00 0.00 41.70 2.82
2390 2630 8.786898 GTTAAGGCATGAGCTAAATATCATTGA 58.213 33.333 0.00 0.00 41.70 2.57
2391 2631 9.524496 TTAAGGCATGAGCTAAATATCATTGAT 57.476 29.630 4.28 4.28 41.70 2.57
2392 2632 8.418597 AAGGCATGAGCTAAATATCATTGATT 57.581 30.769 4.14 0.00 41.70 2.57
2393 2633 8.053026 AGGCATGAGCTAAATATCATTGATTC 57.947 34.615 4.14 0.00 41.70 2.52
2394 2634 6.965500 GGCATGAGCTAAATATCATTGATTCG 59.035 38.462 4.14 0.00 41.70 3.34
2395 2635 7.148356 GGCATGAGCTAAATATCATTGATTCGA 60.148 37.037 4.14 0.00 41.70 3.71
2396 2636 7.903946 GCATGAGCTAAATATCATTGATTCGAG 59.096 37.037 4.14 0.00 33.91 4.04
2397 2637 7.356641 TGAGCTAAATATCATTGATTCGAGC 57.643 36.000 4.14 8.93 0.00 5.03
2398 2638 6.930722 TGAGCTAAATATCATTGATTCGAGCA 59.069 34.615 17.49 0.00 31.92 4.26
2399 2639 7.442062 TGAGCTAAATATCATTGATTCGAGCAA 59.558 33.333 17.49 5.43 31.92 3.91
2400 2640 8.332996 AGCTAAATATCATTGATTCGAGCAAT 57.667 30.769 17.49 9.10 36.45 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 155 7.329226 TCGTTTTATAAGACAAACTAACGAGGG 59.671 37.037 11.45 0.00 38.66 4.30
238 265 0.955919 GAGGGGTTTTGAGCTGGTCG 60.956 60.000 0.00 0.00 0.00 4.79
285 312 1.734477 CGACTGACGTTGGGAGCTG 60.734 63.158 0.00 0.00 37.22 4.24
573 641 1.151777 ACAGAGCCAACACGTTCACG 61.152 55.000 0.00 0.00 46.33 4.35
619 689 7.656707 AATTTGGTCATTTTCTACACAATGC 57.343 32.000 0.00 0.00 31.47 3.56
625 695 9.771534 CCCTTAAAAATTTGGTCATTTTCTACA 57.228 29.630 0.00 0.00 35.67 2.74
742 845 3.923017 AAAAGAAGCTAATTGCACGCT 57.077 38.095 0.00 0.00 45.94 5.07
809 912 0.179124 TTTCAAACCAACCGCAGCAC 60.179 50.000 0.00 0.00 0.00 4.40
819 922 5.422331 TGTGAAGTAACCCATTTTCAAACCA 59.578 36.000 0.00 0.00 31.98 3.67
989 1092 2.103094 GTGTACTGCATGGCTGAGGATA 59.897 50.000 0.00 0.00 0.00 2.59
1195 1298 1.271926 CCCGTTTTGGATGACCTCCTT 60.272 52.381 0.00 0.00 45.21 3.36
1399 1502 0.250901 GCCCTTCACTGCTCTTCCAA 60.251 55.000 0.00 0.00 0.00 3.53
1400 1503 1.376466 GCCCTTCACTGCTCTTCCA 59.624 57.895 0.00 0.00 0.00 3.53
1404 1507 4.400961 GGCGCCCTTCACTGCTCT 62.401 66.667 18.11 0.00 0.00 4.09
1679 1806 2.371910 ACTAACAAAGCGAGCTCTCC 57.628 50.000 12.85 2.47 0.00 3.71
1761 1888 0.465705 GCATGCACTAGCTAGGTGGA 59.534 55.000 24.35 19.44 42.74 4.02
2088 2310 1.830477 GGCCATCCCTTGCATTAAACA 59.170 47.619 0.00 0.00 0.00 2.83
2152 2392 4.274214 GGTAAGTGCTTTGACCGTTAACTT 59.726 41.667 3.71 0.00 0.00 2.66
2236 2476 2.293399 CCCACGCTCTTAACTTTTGCTT 59.707 45.455 0.00 0.00 0.00 3.91
2321 2561 4.446371 CAAGGGCTTCGTGAAGATATCTT 58.554 43.478 17.96 17.96 40.79 2.40
2322 2562 3.181461 CCAAGGGCTTCGTGAAGATATCT 60.181 47.826 13.60 0.00 40.79 1.98
2323 2563 3.134458 CCAAGGGCTTCGTGAAGATATC 58.866 50.000 13.60 0.00 40.79 1.63
2324 2564 2.771943 TCCAAGGGCTTCGTGAAGATAT 59.228 45.455 13.60 0.00 40.79 1.63
2325 2565 2.184533 TCCAAGGGCTTCGTGAAGATA 58.815 47.619 13.60 0.00 40.79 1.98
2326 2566 0.984230 TCCAAGGGCTTCGTGAAGAT 59.016 50.000 13.60 0.00 40.79 2.40
2327 2567 0.984230 ATCCAAGGGCTTCGTGAAGA 59.016 50.000 13.60 0.00 40.79 2.87
2328 2568 1.089920 CATCCAAGGGCTTCGTGAAG 58.910 55.000 5.24 5.24 41.24 3.02
2329 2569 0.690192 TCATCCAAGGGCTTCGTGAA 59.310 50.000 0.00 0.00 0.00 3.18
2330 2570 0.690192 TTCATCCAAGGGCTTCGTGA 59.310 50.000 0.00 0.00 0.00 4.35
2331 2571 1.089920 CTTCATCCAAGGGCTTCGTG 58.910 55.000 0.00 0.00 0.00 4.35
2332 2572 0.678048 GCTTCATCCAAGGGCTTCGT 60.678 55.000 0.00 0.00 31.94 3.85
2333 2573 0.677731 TGCTTCATCCAAGGGCTTCG 60.678 55.000 0.00 0.00 31.94 3.79
2334 2574 1.475682 CTTGCTTCATCCAAGGGCTTC 59.524 52.381 0.00 0.00 36.82 3.86
2335 2575 1.076024 TCTTGCTTCATCCAAGGGCTT 59.924 47.619 0.00 0.00 40.00 4.35
2336 2576 0.700564 TCTTGCTTCATCCAAGGGCT 59.299 50.000 0.00 0.00 40.00 5.19
2337 2577 1.772836 ATCTTGCTTCATCCAAGGGC 58.227 50.000 0.00 0.00 40.00 5.19
2338 2578 3.181493 CGAAATCTTGCTTCATCCAAGGG 60.181 47.826 0.00 0.00 40.00 3.95
2339 2579 3.733077 GCGAAATCTTGCTTCATCCAAGG 60.733 47.826 0.00 0.00 40.00 3.61
2340 2580 3.432782 GCGAAATCTTGCTTCATCCAAG 58.567 45.455 0.00 0.00 40.72 3.61
2341 2581 2.159531 CGCGAAATCTTGCTTCATCCAA 60.160 45.455 0.00 0.00 0.00 3.53
2342 2582 1.398041 CGCGAAATCTTGCTTCATCCA 59.602 47.619 0.00 0.00 0.00 3.41
2343 2583 1.665679 TCGCGAAATCTTGCTTCATCC 59.334 47.619 6.20 0.00 0.00 3.51
2344 2584 2.349886 ACTCGCGAAATCTTGCTTCATC 59.650 45.455 11.33 0.00 0.00 2.92
2345 2585 2.350522 ACTCGCGAAATCTTGCTTCAT 58.649 42.857 11.33 0.00 0.00 2.57
2346 2586 1.795768 ACTCGCGAAATCTTGCTTCA 58.204 45.000 11.33 0.00 0.00 3.02
2347 2587 2.882742 AACTCGCGAAATCTTGCTTC 57.117 45.000 11.33 0.00 0.00 3.86
2348 2588 3.125316 CCTTAACTCGCGAAATCTTGCTT 59.875 43.478 11.33 0.00 0.00 3.91
2349 2589 2.673368 CCTTAACTCGCGAAATCTTGCT 59.327 45.455 11.33 0.00 0.00 3.91
2350 2590 2.788065 GCCTTAACTCGCGAAATCTTGC 60.788 50.000 11.33 5.88 0.00 4.01
2351 2591 2.415168 TGCCTTAACTCGCGAAATCTTG 59.585 45.455 11.33 0.00 0.00 3.02
2352 2592 2.695359 TGCCTTAACTCGCGAAATCTT 58.305 42.857 11.33 1.67 0.00 2.40
2353 2593 2.380084 TGCCTTAACTCGCGAAATCT 57.620 45.000 11.33 0.00 0.00 2.40
2354 2594 2.607635 TCATGCCTTAACTCGCGAAATC 59.392 45.455 11.33 0.00 0.00 2.17
2355 2595 2.609459 CTCATGCCTTAACTCGCGAAAT 59.391 45.455 11.33 4.16 0.00 2.17
2356 2596 1.999735 CTCATGCCTTAACTCGCGAAA 59.000 47.619 11.33 0.00 0.00 3.46
2357 2597 1.640428 CTCATGCCTTAACTCGCGAA 58.360 50.000 11.33 0.00 0.00 4.70
2358 2598 0.806102 GCTCATGCCTTAACTCGCGA 60.806 55.000 9.26 9.26 0.00 5.87
2359 2599 0.807667 AGCTCATGCCTTAACTCGCG 60.808 55.000 0.00 0.00 40.80 5.87
2360 2600 2.225068 TAGCTCATGCCTTAACTCGC 57.775 50.000 0.00 0.00 40.80 5.03
2361 2601 6.646653 TGATATTTAGCTCATGCCTTAACTCG 59.353 38.462 0.00 0.00 40.80 4.18
2362 2602 7.969536 TGATATTTAGCTCATGCCTTAACTC 57.030 36.000 0.00 0.00 40.80 3.01
2363 2603 8.790718 CAATGATATTTAGCTCATGCCTTAACT 58.209 33.333 0.00 0.00 40.80 2.24
2364 2604 8.786898 TCAATGATATTTAGCTCATGCCTTAAC 58.213 33.333 0.00 0.00 40.80 2.01
2365 2605 8.922931 TCAATGATATTTAGCTCATGCCTTAA 57.077 30.769 0.00 0.00 40.80 1.85
2366 2606 9.524496 AATCAATGATATTTAGCTCATGCCTTA 57.476 29.630 0.00 0.00 40.80 2.69
2367 2607 8.418597 AATCAATGATATTTAGCTCATGCCTT 57.581 30.769 0.00 0.00 40.80 4.35
2368 2608 7.148289 CGAATCAATGATATTTAGCTCATGCCT 60.148 37.037 0.00 0.00 40.80 4.75
2369 2609 6.965500 CGAATCAATGATATTTAGCTCATGCC 59.035 38.462 0.00 0.00 40.80 4.40
2370 2610 7.745972 TCGAATCAATGATATTTAGCTCATGC 58.254 34.615 0.00 0.00 40.05 4.06
2371 2611 7.903946 GCTCGAATCAATGATATTTAGCTCATG 59.096 37.037 0.00 0.00 32.56 3.07
2372 2612 7.605309 TGCTCGAATCAATGATATTTAGCTCAT 59.395 33.333 15.69 0.00 33.59 2.90
2373 2613 6.930722 TGCTCGAATCAATGATATTTAGCTCA 59.069 34.615 15.69 0.00 31.78 4.26
2374 2614 7.356641 TGCTCGAATCAATGATATTTAGCTC 57.643 36.000 15.69 1.65 31.78 4.09
2375 2615 7.734924 TTGCTCGAATCAATGATATTTAGCT 57.265 32.000 15.69 0.00 31.78 3.32


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

AutoCloner maintained by Alex Coulton.