Multiple sequence alignment - TraesCS3D01G190400

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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 TraesCS3D01G190400 chr3D 100.000 2757 0 0 1 2757 178659513 178656757 0.000000e+00 5092.0
1 TraesCS3D01G190400 chr3B 92.350 2183 97 20 2 2123 257104113 257101940 0.000000e+00 3042.0
2 TraesCS3D01G190400 chr3B 83.034 613 23 31 2156 2757 257101944 257101402 5.340000e-132 481.0
3 TraesCS3D01G190400 chr3A 91.760 2148 99 48 124 2218 221279807 221277685 0.000000e+00 2915.0
4 TraesCS3D01G190400 chr3A 95.509 334 15 0 2424 2757 221277565 221277232 4.040000e-148 534.0
5 TraesCS3D01G190400 chr3A 93.706 143 6 2 1 140 221218232 221218374 7.740000e-51 211.0
6 TraesCS3D01G190400 chr3A 94.286 140 5 2 4 140 221294072 221293933 7.740000e-51 211.0
7 TraesCS3D01G190400 chr3A 92.308 52 0 1 2262 2309 221277662 221277611 1.370000e-08 71.3


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 TraesCS3D01G190400 chr3D 178656757 178659513 2756 True 5092.000000 5092 100.000000 1 2757 1 chr3D.!!$R1 2756
1 TraesCS3D01G190400 chr3B 257101402 257104113 2711 True 1761.500000 3042 87.692000 2 2757 2 chr3B.!!$R1 2755
2 TraesCS3D01G190400 chr3A 221277232 221279807 2575 True 1173.433333 2915 93.192333 124 2757 3 chr3A.!!$R2 2633

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
551 557 0.824759 CCTGAGTTCGACCCCTTAGG 59.175 60.0 0.0 0.0 43.78 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2372 2457 0.038166 ACTGAATGTGCCCGGTGAAT 59.962 50.0 0.0 0.0 0.0 2.57 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
77 78 7.928908 TTGCAATCTTTGTAATCAAACACTC 57.071 32.000 0.00 0.00 38.44 3.51
119 123 5.823045 AGAAAGAGGATTATGGCTTTTACCG 59.177 40.000 0.00 0.00 31.30 4.02
149 153 2.171027 GGGGATCCCAAACACGTATACA 59.829 50.000 32.07 0.00 44.65 2.29
176 180 2.892425 CCTCCATTGCGCCTCGAC 60.892 66.667 4.18 0.00 0.00 4.20
227 231 7.337938 TCTTAATGTCAGATTTAGCACCATGA 58.662 34.615 0.00 0.00 0.00 3.07
235 239 7.332926 GTCAGATTTAGCACCATGACATATAGG 59.667 40.741 0.00 0.00 37.56 2.57
300 305 9.588096 CCAAAATAATAGGGAGCCTAATAAACT 57.412 33.333 0.00 0.00 39.77 2.66
305 310 4.779993 AGGGAGCCTAATAAACTTGGAG 57.220 45.455 0.00 0.00 28.47 3.86
319 324 9.682465 AATAAACTTGGAGGGAAAGAGTATAAC 57.318 33.333 0.00 0.00 0.00 1.89
384 390 9.357652 CTGTCTAAACATTGGATTTGTATTTGG 57.642 33.333 0.00 0.00 34.13 3.28
421 427 7.282901 CCACCACATAATTTCTGTGACATATGA 59.717 37.037 10.38 0.00 45.44 2.15
483 489 5.344884 GGAGACTAACATGAGAGTAAGTGC 58.655 45.833 0.00 0.00 0.00 4.40
496 502 2.774234 AGTAAGTGCATGGGCTCATAGT 59.226 45.455 0.00 0.00 41.91 2.12
514 520 4.557554 CCATTCATGGTGGCGCTA 57.442 55.556 7.64 0.00 43.05 4.26
548 554 1.533469 CGACCTGAGTTCGACCCCTT 61.533 60.000 0.00 0.00 0.00 3.95
549 555 1.553706 GACCTGAGTTCGACCCCTTA 58.446 55.000 0.00 0.00 0.00 2.69
550 556 1.477295 GACCTGAGTTCGACCCCTTAG 59.523 57.143 0.00 0.00 0.00 2.18
551 557 0.824759 CCTGAGTTCGACCCCTTAGG 59.175 60.000 0.00 0.00 43.78 2.69
574 592 3.570125 TCGTGTGTCTCACATTCTCTCTT 59.430 43.478 5.88 0.00 46.32 2.85
575 593 4.760204 TCGTGTGTCTCACATTCTCTCTTA 59.240 41.667 5.88 0.00 46.32 2.10
586 604 1.919240 TCTCTCTTAGCGGTTGGTCA 58.081 50.000 0.00 0.00 0.00 4.02
910 930 2.024414 CCGTCTCAATTCCCCAATTCC 58.976 52.381 0.00 0.00 28.97 3.01
1489 1524 1.351350 TCACTCCTTCCTCTCTCGTCA 59.649 52.381 0.00 0.00 0.00 4.35
1503 1538 1.735018 CTCGTCACGTCAGATCTGTCT 59.265 52.381 21.92 4.62 34.14 3.41
1578 1613 2.431942 CCGAACAACGACTCCCCG 60.432 66.667 0.00 0.00 45.77 5.73
1632 1667 3.593942 TCAAGAAGGTAAACTCCCCTCA 58.406 45.455 0.00 0.00 0.00 3.86
1648 1683 0.101399 CTCATCCTCTGAACGTCCCG 59.899 60.000 0.00 0.00 32.14 5.14
1651 1686 1.605058 ATCCTCTGAACGTCCCGTGG 61.605 60.000 0.00 0.00 39.99 4.94
1656 1691 0.736325 CTGAACGTCCCGTGGTGATC 60.736 60.000 0.00 0.00 39.99 2.92
1657 1692 1.447314 GAACGTCCCGTGGTGATCC 60.447 63.158 0.00 0.00 39.99 3.36
1658 1693 3.291101 AACGTCCCGTGGTGATCCG 62.291 63.158 0.00 0.00 39.99 4.18
1710 1747 2.029290 GCTCCGTTCTCCTTCTTGTGTA 60.029 50.000 0.00 0.00 0.00 2.90
1711 1748 3.368531 GCTCCGTTCTCCTTCTTGTGTAT 60.369 47.826 0.00 0.00 0.00 2.29
1755 1792 3.188786 GCTCTACAAGCCGGCGTG 61.189 66.667 36.05 36.05 45.92 5.34
1780 1817 1.474143 GGAAGAAGAAGGCGGGATCTG 60.474 57.143 0.00 0.00 0.00 2.90
1794 1831 4.812476 TCTGTCGGATTGGCGGCG 62.812 66.667 0.51 0.51 0.00 6.46
1849 1905 7.985184 GTGTTGGATAGATACTTGGACATGTAA 59.015 37.037 0.00 0.00 0.00 2.41
1850 1906 8.713971 TGTTGGATAGATACTTGGACATGTAAT 58.286 33.333 0.00 0.00 0.00 1.89
2081 2149 8.068892 TGGGTTTCATACAAACTGTTTAAACT 57.931 30.769 18.72 0.64 31.56 2.66
2083 2151 7.436970 GGGTTTCATACAAACTGTTTAAACTGG 59.563 37.037 23.86 16.47 31.56 4.00
2128 2198 8.238481 ACAACAAAACATGTAAAAACAGTCAG 57.762 30.769 0.00 0.00 42.99 3.51
2133 2203 7.624360 AAACATGTAAAAACAGTCAGAGTGA 57.376 32.000 12.54 0.00 0.00 3.41
2135 2205 7.194607 ACATGTAAAAACAGTCAGAGTGATG 57.805 36.000 12.54 5.88 0.00 3.07
2136 2206 6.205464 ACATGTAAAAACAGTCAGAGTGATGG 59.795 38.462 12.54 0.00 0.00 3.51
2137 2207 5.063204 TGTAAAAACAGTCAGAGTGATGGG 58.937 41.667 12.54 0.00 0.00 4.00
2149 2219 0.462047 GTGATGGGAGTTAGGCCGTG 60.462 60.000 0.00 0.00 0.00 4.94
2242 2323 6.328672 TCAAGAAGGGAAAATGGATTTTTGGA 59.671 34.615 0.00 0.00 39.86 3.53
2243 2324 6.762077 AGAAGGGAAAATGGATTTTTGGAA 57.238 33.333 0.00 0.00 39.86 3.53
2244 2325 7.333779 AGAAGGGAAAATGGATTTTTGGAAT 57.666 32.000 0.00 0.00 39.86 3.01
2248 2329 8.218423 AGGGAAAATGGATTTTTGGAATAGTT 57.782 30.769 0.00 0.00 39.86 2.24
2309 2394 2.109128 TCTATTCAAACCAGGGGTGCAA 59.891 45.455 0.00 0.00 35.34 4.08
2310 2395 1.799933 ATTCAAACCAGGGGTGCAAA 58.200 45.000 0.00 0.00 35.34 3.68
2311 2396 1.118838 TTCAAACCAGGGGTGCAAAG 58.881 50.000 0.00 0.00 35.34 2.77
2312 2397 0.758685 TCAAACCAGGGGTGCAAAGG 60.759 55.000 0.00 0.00 35.34 3.11
2313 2398 0.758685 CAAACCAGGGGTGCAAAGGA 60.759 55.000 0.00 0.00 35.34 3.36
2316 2401 1.383799 CCAGGGGTGCAAAGGATGA 59.616 57.895 0.00 0.00 0.00 2.92
2349 2434 4.145756 GCTGAAAACATAAACACGAAACGG 59.854 41.667 0.00 0.00 0.00 4.44
2352 2437 6.320171 TGAAAACATAAACACGAAACGGAAA 58.680 32.000 0.00 0.00 0.00 3.13
2355 2440 5.427036 ACATAAACACGAAACGGAAACAT 57.573 34.783 0.00 0.00 0.00 2.71
2356 2441 6.542574 ACATAAACACGAAACGGAAACATA 57.457 33.333 0.00 0.00 0.00 2.29
2357 2442 6.957150 ACATAAACACGAAACGGAAACATAA 58.043 32.000 0.00 0.00 0.00 1.90
2358 2443 7.416022 ACATAAACACGAAACGGAAACATAAA 58.584 30.769 0.00 0.00 0.00 1.40
2359 2444 7.376601 ACATAAACACGAAACGGAAACATAAAC 59.623 33.333 0.00 0.00 0.00 2.01
2363 2448 5.209240 CACGAAACGGAAACATAAACACAT 58.791 37.500 0.00 0.00 0.00 3.21
2364 2449 5.338559 CACGAAACGGAAACATAAACACATC 59.661 40.000 0.00 0.00 0.00 3.06
2367 2452 2.780993 CGGAAACATAAACACATCCGC 58.219 47.619 0.00 0.00 42.64 5.54
2369 2454 3.727673 CGGAAACATAAACACATCCGCTG 60.728 47.826 0.00 0.00 42.64 5.18
2370 2455 3.438781 GGAAACATAAACACATCCGCTGA 59.561 43.478 0.00 0.00 0.00 4.26
2371 2456 4.083003 GGAAACATAAACACATCCGCTGAA 60.083 41.667 0.00 0.00 0.00 3.02
2372 2457 5.446143 AAACATAAACACATCCGCTGAAA 57.554 34.783 0.00 0.00 0.00 2.69
2373 2458 5.643379 AACATAAACACATCCGCTGAAAT 57.357 34.783 0.00 0.00 0.00 2.17
2374 2459 5.643379 ACATAAACACATCCGCTGAAATT 57.357 34.783 0.00 0.00 0.00 1.82
2375 2460 5.640732 ACATAAACACATCCGCTGAAATTC 58.359 37.500 0.00 0.00 0.00 2.17
2376 2461 5.182950 ACATAAACACATCCGCTGAAATTCA 59.817 36.000 0.00 0.00 0.00 2.57
2377 2462 3.559238 AACACATCCGCTGAAATTCAC 57.441 42.857 0.00 0.00 0.00 3.18
2378 2463 1.812571 ACACATCCGCTGAAATTCACC 59.187 47.619 0.00 0.00 0.00 4.02
2379 2464 1.086696 ACATCCGCTGAAATTCACCG 58.913 50.000 3.88 3.88 0.00 4.94
2380 2465 0.378257 CATCCGCTGAAATTCACCGG 59.622 55.000 20.35 20.35 44.65 5.28
2381 2466 0.748005 ATCCGCTGAAATTCACCGGG 60.748 55.000 24.29 11.54 43.75 5.73
2382 2467 2.485122 CGCTGAAATTCACCGGGC 59.515 61.111 6.32 0.00 0.00 6.13
2383 2468 2.331893 CGCTGAAATTCACCGGGCA 61.332 57.895 6.32 0.00 0.00 5.36
2384 2469 1.212751 GCTGAAATTCACCGGGCAC 59.787 57.895 6.32 0.00 0.00 5.01
2385 2470 1.523154 GCTGAAATTCACCGGGCACA 61.523 55.000 6.32 0.00 0.00 4.57
2389 2474 1.543802 GAAATTCACCGGGCACATTCA 59.456 47.619 6.32 0.00 0.00 2.57
2391 2476 0.038166 ATTCACCGGGCACATTCAGT 59.962 50.000 6.32 0.00 0.00 3.41
2402 2487 3.545633 GCACATTCAGTCAAAAGTCGAC 58.454 45.455 7.70 7.70 0.00 4.20
2404 2489 3.058914 CACATTCAGTCAAAAGTCGACCC 60.059 47.826 13.01 0.00 33.70 4.46
2416 2501 1.068474 GTCGACCCGTTTCAGTCATG 58.932 55.000 3.51 0.00 33.08 3.07
2418 2503 1.067846 TCGACCCGTTTCAGTCATGAG 60.068 52.381 0.00 0.00 36.61 2.90
2419 2504 1.079503 GACCCGTTTCAGTCATGAGC 58.920 55.000 0.00 0.00 36.61 4.26
2420 2505 0.687354 ACCCGTTTCAGTCATGAGCT 59.313 50.000 0.00 0.00 36.61 4.09
2421 2506 1.338200 ACCCGTTTCAGTCATGAGCTC 60.338 52.381 6.82 6.82 36.61 4.09
2422 2507 1.363744 CCGTTTCAGTCATGAGCTCC 58.636 55.000 12.15 0.00 36.61 4.70
2423 2508 1.338105 CCGTTTCAGTCATGAGCTCCA 60.338 52.381 12.15 0.00 36.61 3.86
2424 2509 2.625737 CGTTTCAGTCATGAGCTCCAT 58.374 47.619 12.15 1.88 36.61 3.41
2425 2510 3.430790 CCGTTTCAGTCATGAGCTCCATA 60.431 47.826 12.15 0.00 36.61 2.74
2426 2511 4.183865 CGTTTCAGTCATGAGCTCCATAA 58.816 43.478 12.15 0.00 36.61 1.90
2427 2512 4.813161 CGTTTCAGTCATGAGCTCCATAAT 59.187 41.667 12.15 0.00 36.61 1.28
2428 2513 5.985530 CGTTTCAGTCATGAGCTCCATAATA 59.014 40.000 12.15 0.00 36.61 0.98
2429 2514 6.648310 CGTTTCAGTCATGAGCTCCATAATAT 59.352 38.462 12.15 0.00 36.61 1.28
2430 2515 7.172190 CGTTTCAGTCATGAGCTCCATAATATT 59.828 37.037 12.15 0.00 36.61 1.28
2431 2516 9.494271 GTTTCAGTCATGAGCTCCATAATATTA 57.506 33.333 12.15 0.00 36.61 0.98
2525 2628 2.398588 CTCCTCCAGGGTACAATGCTA 58.601 52.381 0.00 0.00 36.25 3.49
2526 2629 2.366916 CTCCTCCAGGGTACAATGCTAG 59.633 54.545 0.00 0.00 36.25 3.42
2527 2630 1.417890 CCTCCAGGGTACAATGCTAGG 59.582 57.143 0.00 0.00 0.00 3.02
2528 2631 0.837272 TCCAGGGTACAATGCTAGGC 59.163 55.000 0.00 0.00 0.00 3.93
2529 2632 0.532862 CCAGGGTACAATGCTAGGCG 60.533 60.000 0.00 0.00 0.00 5.52
2530 2633 0.532862 CAGGGTACAATGCTAGGCGG 60.533 60.000 0.00 0.00 0.00 6.13
2531 2634 1.227853 GGGTACAATGCTAGGCGGG 60.228 63.158 0.00 0.00 0.00 6.13
2532 2635 1.892391 GGTACAATGCTAGGCGGGC 60.892 63.158 0.00 0.00 0.00 6.13
2533 2636 2.108157 TACAATGCTAGGCGGGCG 59.892 61.111 0.00 0.00 0.00 6.13
2534 2637 3.454587 TACAATGCTAGGCGGGCGG 62.455 63.158 0.00 0.00 0.00 6.13
2535 2638 4.856801 CAATGCTAGGCGGGCGGT 62.857 66.667 0.00 0.00 0.00 5.68
2536 2639 3.158648 AATGCTAGGCGGGCGGTA 61.159 61.111 0.00 0.00 0.00 4.02
2537 2640 3.456105 AATGCTAGGCGGGCGGTAC 62.456 63.158 0.00 0.00 0.00 3.34
2539 2642 4.151582 GCTAGGCGGGCGGTACAA 62.152 66.667 0.00 0.00 0.00 2.41
2540 2643 2.106332 CTAGGCGGGCGGTACAAG 59.894 66.667 0.00 0.00 0.00 3.16
2541 2644 4.151582 TAGGCGGGCGGTACAAGC 62.152 66.667 4.22 4.22 0.00 4.01
2596 2699 0.602106 ACGACTGAACCGAGAGACGA 60.602 55.000 0.00 0.00 45.77 4.20
2745 2848 0.940991 CAAGCGCTTGGAAACTTGGC 60.941 55.000 36.86 0.00 36.67 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 9.729023 TTGTTGTATGAGTGTTTGATTACAAAG 57.271 29.630 0.00 0.00 44.97 2.77
61 62 9.509855 GTTGTTGTATGAGTGTTTGATTACAAA 57.490 29.630 0.00 0.00 42.66 2.83
68 69 4.025229 GCGAGTTGTTGTATGAGTGTTTGA 60.025 41.667 0.00 0.00 0.00 2.69
77 78 2.863739 TCTCTCGCGAGTTGTTGTATG 58.136 47.619 33.33 13.98 38.45 2.39
83 87 1.068194 CCTCTTTCTCTCGCGAGTTGT 60.068 52.381 33.33 0.00 38.45 3.32
96 100 5.505819 GCGGTAAAAGCCATAATCCTCTTTC 60.506 44.000 0.00 0.00 0.00 2.62
149 153 1.679944 CGCAATGGAGGACACAAGGAT 60.680 52.381 0.00 0.00 0.00 3.24
176 180 4.052159 AGTATGAACGGAGCTTGATCTG 57.948 45.455 0.00 0.00 0.00 2.90
300 305 7.510675 AATCAGTTATACTCTTTCCCTCCAA 57.489 36.000 0.00 0.00 0.00 3.53
305 310 7.769044 TGTAGCAAATCAGTTATACTCTTTCCC 59.231 37.037 0.00 0.00 0.00 3.97
360 366 9.921637 TTCCAAATACAAATCCAATGTTTAGAC 57.078 29.630 0.00 0.00 32.27 2.59
365 371 8.814931 TCATCTTCCAAATACAAATCCAATGTT 58.185 29.630 0.00 0.00 32.27 2.71
366 372 8.365060 TCATCTTCCAAATACAAATCCAATGT 57.635 30.769 0.00 0.00 34.81 2.71
367 373 9.826574 AATCATCTTCCAAATACAAATCCAATG 57.173 29.630 0.00 0.00 0.00 2.82
369 375 9.874205 GAAATCATCTTCCAAATACAAATCCAA 57.126 29.630 0.00 0.00 0.00 3.53
370 376 8.477256 GGAAATCATCTTCCAAATACAAATCCA 58.523 33.333 0.00 0.00 43.84 3.41
371 377 8.877808 GGAAATCATCTTCCAAATACAAATCC 57.122 34.615 0.00 0.00 43.84 3.01
384 390 8.689972 AGAAATTATGTGGTGGAAATCATCTTC 58.310 33.333 0.00 0.00 0.00 2.87
387 393 7.703621 CACAGAAATTATGTGGTGGAAATCATC 59.296 37.037 12.47 0.00 43.47 2.92
441 447 7.121382 AGTCTCCCATGTATTCAATGTCAAAT 58.879 34.615 0.00 0.00 0.00 2.32
449 455 7.125659 TCTCATGTTAGTCTCCCATGTATTCAA 59.874 37.037 10.05 0.00 37.73 2.69
458 464 5.419155 CACTTACTCTCATGTTAGTCTCCCA 59.581 44.000 6.07 0.00 28.87 4.37
483 489 3.497103 TGAATGGACTATGAGCCCATG 57.503 47.619 0.00 0.00 40.31 3.66
500 506 0.034574 AACCATAGCGCCACCATGAA 60.035 50.000 2.29 0.00 0.00 2.57
512 518 2.237751 CGGCTCGGCGAAACCATAG 61.238 63.158 23.46 7.45 39.03 2.23
514 520 4.077184 TCGGCTCGGCGAAACCAT 62.077 61.111 23.46 0.00 39.03 3.55
910 930 1.140134 TTGAGAGGGTTTGGAGGGGG 61.140 60.000 0.00 0.00 0.00 5.40
926 946 1.229529 GGGAGGGTGGAGAGGTTGA 60.230 63.158 0.00 0.00 0.00 3.18
1466 1494 2.288666 CGAGAGAGGAAGGAGTGAGAG 58.711 57.143 0.00 0.00 0.00 3.20
1489 1524 4.328536 ACAAGTAGAGACAGATCTGACGT 58.671 43.478 29.27 16.98 34.34 4.34
1503 1538 4.161565 AGACCACACAAGACAACAAGTAGA 59.838 41.667 0.00 0.00 0.00 2.59
1578 1613 4.030452 GCCGCCTGTGTGTTGAGC 62.030 66.667 0.00 0.00 0.00 4.26
1648 1683 1.066143 ACAGGTTGATCGGATCACCAC 60.066 52.381 26.73 20.59 39.39 4.16
1651 1686 3.252974 AGAACAGGTTGATCGGATCAC 57.747 47.619 19.79 14.20 39.39 3.06
1656 1691 2.185004 ACCAAGAACAGGTTGATCGG 57.815 50.000 0.00 0.00 35.33 4.18
1710 1747 2.575279 ACCATCTTCCTGAACTCTGCAT 59.425 45.455 0.00 0.00 0.00 3.96
1711 1748 1.980765 ACCATCTTCCTGAACTCTGCA 59.019 47.619 0.00 0.00 0.00 4.41
1755 1792 1.406205 CCCGCCTTCTTCTTCCTCTTC 60.406 57.143 0.00 0.00 0.00 2.87
1849 1905 1.474077 GCAATCGAAGCTCCAACCAAT 59.526 47.619 6.02 0.00 0.00 3.16
1850 1906 0.881118 GCAATCGAAGCTCCAACCAA 59.119 50.000 6.02 0.00 0.00 3.67
1962 2024 8.579850 AGCATCCAACAGTTGAAAAATCTATA 57.420 30.769 15.36 0.00 0.00 1.31
1972 2034 2.618241 GTCACAAGCATCCAACAGTTGA 59.382 45.455 15.36 1.51 0.00 3.18
1985 2052 4.388773 TCGAATCAGTTACATGTCACAAGC 59.611 41.667 12.50 0.00 0.00 4.01
2017 2084 2.685388 TCGAACATGCCAGACAAAAACA 59.315 40.909 0.00 0.00 0.00 2.83
2018 2085 3.347958 TCGAACATGCCAGACAAAAAC 57.652 42.857 0.00 0.00 0.00 2.43
2059 2126 8.192110 TCCCAGTTTAAACAGTTTGTATGAAAC 58.808 33.333 20.06 10.31 31.77 2.78
2066 2133 4.020543 TGCTCCCAGTTTAAACAGTTTGT 58.979 39.130 20.06 0.00 0.00 2.83
2083 2151 2.934553 GTTGTCGTATAAGGGTTGCTCC 59.065 50.000 0.00 0.00 0.00 4.70
2128 2198 0.105039 CGGCCTAACTCCCATCACTC 59.895 60.000 0.00 0.00 0.00 3.51
2133 2203 1.972660 GAGCACGGCCTAACTCCCAT 61.973 60.000 0.00 0.00 0.00 4.00
2135 2205 2.187163 GAGCACGGCCTAACTCCC 59.813 66.667 0.00 0.00 0.00 4.30
2136 2206 2.187163 GGAGCACGGCCTAACTCC 59.813 66.667 16.29 16.29 41.81 3.85
2137 2207 2.180159 TTGGGAGCACGGCCTAACTC 62.180 60.000 0.00 4.06 0.00 3.01
2149 2219 1.609208 TTGCAGAGAGTTTTGGGAGC 58.391 50.000 0.00 0.00 0.00 4.70
2242 2323 4.388577 ACCAGAAGCAAGGGAAACTATT 57.611 40.909 0.00 0.00 0.00 1.73
2243 2324 5.717119 ATACCAGAAGCAAGGGAAACTAT 57.283 39.130 0.00 0.00 0.00 2.12
2244 2325 6.630203 TTATACCAGAAGCAAGGGAAACTA 57.370 37.500 0.00 0.00 0.00 2.24
2248 2329 6.311735 ACTTTTTATACCAGAAGCAAGGGAA 58.688 36.000 0.00 0.00 0.00 3.97
2309 2394 4.811969 TCAGCATGCAAAATTCATCCTT 57.188 36.364 21.98 0.00 34.76 3.36
2310 2395 4.811969 TTCAGCATGCAAAATTCATCCT 57.188 36.364 21.98 0.00 34.76 3.24
2311 2396 5.179742 TGTTTTCAGCATGCAAAATTCATCC 59.820 36.000 21.98 6.43 31.99 3.51
2312 2397 6.230849 TGTTTTCAGCATGCAAAATTCATC 57.769 33.333 21.98 7.07 31.99 2.92
2313 2398 6.811253 ATGTTTTCAGCATGCAAAATTCAT 57.189 29.167 21.98 19.91 31.99 2.57
2316 2401 7.856894 GTGTTTATGTTTTCAGCATGCAAAATT 59.143 29.630 21.98 12.19 31.99 1.82
2349 2434 4.678509 TCAGCGGATGTGTTTATGTTTC 57.321 40.909 0.00 0.00 0.00 2.78
2352 2437 5.182950 TGAATTTCAGCGGATGTGTTTATGT 59.817 36.000 0.00 0.00 0.00 2.29
2355 2440 4.083003 GGTGAATTTCAGCGGATGTGTTTA 60.083 41.667 12.39 0.00 35.04 2.01
2356 2441 3.305335 GGTGAATTTCAGCGGATGTGTTT 60.305 43.478 12.39 0.00 35.04 2.83
2357 2442 2.228822 GGTGAATTTCAGCGGATGTGTT 59.771 45.455 12.39 0.00 35.04 3.32
2358 2443 1.812571 GGTGAATTTCAGCGGATGTGT 59.187 47.619 12.39 0.00 35.04 3.72
2359 2444 2.549633 GGTGAATTTCAGCGGATGTG 57.450 50.000 12.39 0.00 35.04 3.21
2366 2451 1.212751 GTGCCCGGTGAATTTCAGC 59.787 57.895 16.72 16.72 41.16 4.26
2367 2452 1.176527 ATGTGCCCGGTGAATTTCAG 58.823 50.000 0.00 0.00 0.00 3.02
2369 2454 1.543802 TGAATGTGCCCGGTGAATTTC 59.456 47.619 0.00 0.00 0.00 2.17
2370 2455 1.545582 CTGAATGTGCCCGGTGAATTT 59.454 47.619 0.00 0.00 0.00 1.82
2371 2456 1.176527 CTGAATGTGCCCGGTGAATT 58.823 50.000 0.00 0.00 0.00 2.17
2372 2457 0.038166 ACTGAATGTGCCCGGTGAAT 59.962 50.000 0.00 0.00 0.00 2.57
2373 2458 0.605319 GACTGAATGTGCCCGGTGAA 60.605 55.000 0.00 0.00 0.00 3.18
2374 2459 1.003839 GACTGAATGTGCCCGGTGA 60.004 57.895 0.00 0.00 0.00 4.02
2375 2460 0.888736 TTGACTGAATGTGCCCGGTG 60.889 55.000 0.00 0.00 0.00 4.94
2376 2461 0.179004 TTTGACTGAATGTGCCCGGT 60.179 50.000 0.00 0.00 0.00 5.28
2377 2462 0.958091 TTTTGACTGAATGTGCCCGG 59.042 50.000 0.00 0.00 0.00 5.73
2378 2463 1.608590 ACTTTTGACTGAATGTGCCCG 59.391 47.619 0.00 0.00 0.00 6.13
2379 2464 2.350772 CGACTTTTGACTGAATGTGCCC 60.351 50.000 0.00 0.00 0.00 5.36
2380 2465 2.548057 TCGACTTTTGACTGAATGTGCC 59.452 45.455 0.00 0.00 0.00 5.01
2381 2466 3.545633 GTCGACTTTTGACTGAATGTGC 58.454 45.455 8.70 0.00 33.54 4.57
2382 2467 3.058914 GGGTCGACTTTTGACTGAATGTG 60.059 47.826 16.46 0.00 36.58 3.21
2383 2468 3.139077 GGGTCGACTTTTGACTGAATGT 58.861 45.455 16.46 0.00 36.58 2.71
2384 2469 2.157668 CGGGTCGACTTTTGACTGAATG 59.842 50.000 16.46 0.00 36.58 2.67
2385 2470 2.224209 ACGGGTCGACTTTTGACTGAAT 60.224 45.455 16.46 0.00 36.58 2.57
2389 2474 2.207590 GAAACGGGTCGACTTTTGACT 58.792 47.619 16.46 0.00 36.58 3.41
2391 2476 2.206750 CTGAAACGGGTCGACTTTTGA 58.793 47.619 16.46 6.22 0.00 2.69
2402 2487 1.363744 GAGCTCATGACTGAAACGGG 58.636 55.000 9.40 0.00 0.00 5.28
2404 2489 2.084610 TGGAGCTCATGACTGAAACG 57.915 50.000 17.19 0.00 0.00 3.60
2416 2501 6.256757 GCCGATGACTTAATATTATGGAGCTC 59.743 42.308 4.71 4.71 0.00 4.09
2418 2503 5.294552 GGCCGATGACTTAATATTATGGAGC 59.705 44.000 11.77 5.97 0.00 4.70
2419 2504 6.644347 AGGCCGATGACTTAATATTATGGAG 58.356 40.000 11.77 2.99 0.00 3.86
2420 2505 6.620877 AGGCCGATGACTTAATATTATGGA 57.379 37.500 11.77 0.77 0.00 3.41
2421 2506 7.607991 AGAAAGGCCGATGACTTAATATTATGG 59.392 37.037 11.77 4.49 0.00 2.74
2422 2507 8.446273 CAGAAAGGCCGATGACTTAATATTATG 58.554 37.037 0.00 6.78 0.00 1.90
2423 2508 8.375506 TCAGAAAGGCCGATGACTTAATATTAT 58.624 33.333 0.00 0.00 0.00 1.28
2424 2509 7.732025 TCAGAAAGGCCGATGACTTAATATTA 58.268 34.615 0.00 0.00 0.00 0.98
2425 2510 6.591935 TCAGAAAGGCCGATGACTTAATATT 58.408 36.000 0.00 0.00 0.00 1.28
2426 2511 6.174720 TCAGAAAGGCCGATGACTTAATAT 57.825 37.500 0.00 0.00 0.00 1.28
2427 2512 5.607939 TCAGAAAGGCCGATGACTTAATA 57.392 39.130 0.00 0.00 0.00 0.98
2428 2513 4.487714 TCAGAAAGGCCGATGACTTAAT 57.512 40.909 0.00 0.00 0.00 1.40
2429 2514 3.973206 TCAGAAAGGCCGATGACTTAA 57.027 42.857 0.00 0.00 0.00 1.85
2430 2515 3.450817 TCATCAGAAAGGCCGATGACTTA 59.549 43.478 14.20 0.00 40.37 2.24
2431 2516 2.237143 TCATCAGAAAGGCCGATGACTT 59.763 45.455 14.20 0.00 40.37 3.01
2529 2632 3.127533 CTGCAGCTTGTACCGCCC 61.128 66.667 0.00 0.00 0.00 6.13
2530 2633 2.358737 ACTGCAGCTTGTACCGCC 60.359 61.111 15.27 0.00 0.00 6.13
2531 2634 2.680913 CCACTGCAGCTTGTACCGC 61.681 63.158 15.27 0.00 0.00 5.68
2532 2635 1.301716 ACCACTGCAGCTTGTACCG 60.302 57.895 15.27 0.00 0.00 4.02
2533 2636 1.237285 CCACCACTGCAGCTTGTACC 61.237 60.000 15.27 0.00 0.00 3.34
2534 2637 0.535102 ACCACCACTGCAGCTTGTAC 60.535 55.000 15.27 0.00 0.00 2.90
2535 2638 0.250295 GACCACCACTGCAGCTTGTA 60.250 55.000 15.27 0.00 0.00 2.41
2536 2639 1.526917 GACCACCACTGCAGCTTGT 60.527 57.895 15.27 5.51 0.00 3.16
2537 2640 1.512996 CTGACCACCACTGCAGCTTG 61.513 60.000 15.27 8.25 0.00 4.01
2538 2641 1.228063 CTGACCACCACTGCAGCTT 60.228 57.895 15.27 0.00 0.00 3.74
2539 2642 2.429058 CTGACCACCACTGCAGCT 59.571 61.111 15.27 0.00 0.00 4.24
2540 2643 3.360340 GCTGACCACCACTGCAGC 61.360 66.667 15.27 0.00 45.64 5.25
2541 2644 1.526686 TTGCTGACCACCACTGCAG 60.527 57.895 13.48 13.48 41.52 4.41
2542 2645 1.823470 GTTGCTGACCACCACTGCA 60.823 57.895 0.00 0.00 39.60 4.41
2596 2699 6.434340 ACCGCTTTAATTCAGATTCCTCTTTT 59.566 34.615 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.