Multiple sequence alignment - TraesCS6A01G287500

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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 TraesCS6A01G287500 chr6A 100.000 2421 0 0 1 2421 519951248 519948828 0.000000e+00 4471.0
1 TraesCS6A01G287500 chr6A 80.395 607 58 30 699 1288 519596570 519596008 2.900000e-109 405.0
2 TraesCS6A01G287500 chr6D 93.805 2276 102 27 15 2272 378168622 378166368 0.000000e+00 3386.0
3 TraesCS6A01G287500 chr6D 80.464 604 55 32 701 1288 377975731 377975175 1.040000e-108 403.0
4 TraesCS6A01G287500 chr6B 90.261 2300 175 28 1 2272 564569939 564567661 0.000000e+00 2961.0
5 TraesCS6A01G287500 chr6B 80.682 528 55 27 775 1288 564509340 564508846 1.370000e-97 366.0
6 TraesCS6A01G287500 chr6B 88.889 45 5 0 1545 1589 398367045 398367089 3.360000e-04 56.5
7 TraesCS6A01G287500 chr5A 97.561 41 1 0 1552 1592 8060445 8060405 1.200000e-08 71.3
8 TraesCS6A01G287500 chr5A 89.130 46 5 0 1544 1589 634484243 634484288 9.350000e-05 58.4
9 TraesCS6A01G287500 chr3A 93.478 46 3 0 1615 1660 6246190 6246145 4.320000e-08 69.4
10 TraesCS6A01G287500 chr1A 89.130 46 5 0 1544 1589 17787252 17787297 9.350000e-05 58.4
11 TraesCS6A01G287500 chr4D 100.000 28 0 0 1561 1588 252218873 252218900 4.000000e-03 52.8


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 TraesCS6A01G287500 chr6A 519948828 519951248 2420 True 4471 4471 100.000 1 2421 1 chr6A.!!$R2 2420
1 TraesCS6A01G287500 chr6A 519596008 519596570 562 True 405 405 80.395 699 1288 1 chr6A.!!$R1 589
2 TraesCS6A01G287500 chr6D 378166368 378168622 2254 True 3386 3386 93.805 15 2272 1 chr6D.!!$R2 2257
3 TraesCS6A01G287500 chr6D 377975175 377975731 556 True 403 403 80.464 701 1288 1 chr6D.!!$R1 587
4 TraesCS6A01G287500 chr6B 564567661 564569939 2278 True 2961 2961 90.261 1 2272 1 chr6B.!!$R2 2271

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
965 977 1.378531 AGTTCACAACGCACACACAT 58.621 45.0 0.0 0.0 36.23 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 2396 0.034186 TCTGGTTGCTATTGGGCTGG 60.034 55.0 0.0 0.0 0.0 4.85 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
69 72 2.888414 TCTATAACATCCGATGCACCGA 59.112 45.455 0.00 0.00 0.00 4.69
87 90 3.069016 ACCGATAGCATCACAATTACGGA 59.931 43.478 0.00 0.00 40.78 4.69
104 107 2.158957 ACGGATGCAACGGATACATTCT 60.159 45.455 16.85 0.00 35.23 2.40
126 129 4.452733 GGGACGAGGCTCCCGTTG 62.453 72.222 9.32 0.00 40.86 4.10
406 409 2.897436 GGTACGGTGTAATCCCTTCAC 58.103 52.381 0.00 0.00 0.00 3.18
511 518 8.948631 TTAAAAATACTTCTCTCTCATCGCAT 57.051 30.769 0.00 0.00 0.00 4.73
535 542 6.053005 TGGTAATCAAGACCAATATCGTTCC 58.947 40.000 0.00 0.00 44.08 3.62
696 706 6.079336 TGTATATTTATTCGTGGAGGGAGGA 58.921 40.000 0.00 0.00 0.00 3.71
706 716 1.599576 GAGGGAGGAAGCAGGTGAC 59.400 63.158 0.00 0.00 0.00 3.67
965 977 1.378531 AGTTCACAACGCACACACAT 58.621 45.000 0.00 0.00 36.23 3.21
1119 1145 1.754226 TCTGGTTTTGGTTTCAGGTGC 59.246 47.619 0.00 0.00 0.00 5.01
1128 1154 0.884704 GTTTCAGGTGCTGCGAAGGA 60.885 55.000 0.00 0.00 0.00 3.36
1519 1545 3.658757 TTGCTTGAAGAAAAATCCCGG 57.341 42.857 0.00 0.00 0.00 5.73
1542 1568 9.667107 CCGGTGTATCCAATAAGACAATAATAT 57.333 33.333 0.00 0.00 35.57 1.28
1555 1584 7.458409 AGACAATAATATATACACCGTCCGT 57.542 36.000 0.00 0.00 0.00 4.69
1556 1585 7.889469 AGACAATAATATATACACCGTCCGTT 58.111 34.615 0.00 0.00 0.00 4.44
1557 1586 8.362639 AGACAATAATATATACACCGTCCGTTT 58.637 33.333 0.00 0.00 0.00 3.60
1683 1721 8.415950 AGGGAGTACTAATGACATATTCAGAG 57.584 38.462 0.00 0.00 37.77 3.35
1690 1729 7.432869 ACTAATGACATATTCAGAGCTGTCTC 58.567 38.462 0.00 0.00 37.77 3.36
1692 1731 5.512753 TGACATATTCAGAGCTGTCTCTC 57.487 43.478 0.00 0.00 46.32 3.20
1693 1732 5.199723 TGACATATTCAGAGCTGTCTCTCT 58.800 41.667 0.00 0.00 46.32 3.10
1694 1733 6.360618 TGACATATTCAGAGCTGTCTCTCTA 58.639 40.000 0.00 0.00 46.32 2.43
1707 1746 6.070881 AGCTGTCTCTCTATGTGAATGTCTTT 60.071 38.462 0.00 0.00 0.00 2.52
1804 1844 1.892209 ATTTGGGAGGTCACGTTCAC 58.108 50.000 0.00 0.00 0.00 3.18
2157 2207 6.586463 CGAGTGCTTTTCTGTTAGTTCTATGA 59.414 38.462 0.00 0.00 0.00 2.15
2301 2352 8.762481 TCATAGTAGACTAAATTCTAGCACCA 57.238 34.615 0.00 0.00 31.39 4.17
2302 2353 9.197306 TCATAGTAGACTAAATTCTAGCACCAA 57.803 33.333 0.00 0.00 31.39 3.67
2303 2354 9.250624 CATAGTAGACTAAATTCTAGCACCAAC 57.749 37.037 0.00 0.00 31.39 3.77
2304 2355 7.241042 AGTAGACTAAATTCTAGCACCAACA 57.759 36.000 0.00 0.00 0.00 3.33
2305 2356 7.852263 AGTAGACTAAATTCTAGCACCAACAT 58.148 34.615 0.00 0.00 0.00 2.71
2306 2357 8.978472 AGTAGACTAAATTCTAGCACCAACATA 58.022 33.333 0.00 0.00 0.00 2.29
2307 2358 9.032420 GTAGACTAAATTCTAGCACCAACATAC 57.968 37.037 0.00 0.00 0.00 2.39
2308 2359 7.852263 AGACTAAATTCTAGCACCAACATACT 58.148 34.615 0.00 0.00 0.00 2.12
2309 2360 7.982354 AGACTAAATTCTAGCACCAACATACTC 59.018 37.037 0.00 0.00 0.00 2.59
2310 2361 7.852263 ACTAAATTCTAGCACCAACATACTCT 58.148 34.615 0.00 0.00 0.00 3.24
2311 2362 7.982354 ACTAAATTCTAGCACCAACATACTCTC 59.018 37.037 0.00 0.00 0.00 3.20
2312 2363 5.939764 ATTCTAGCACCAACATACTCTCA 57.060 39.130 0.00 0.00 0.00 3.27
2313 2364 5.738619 TTCTAGCACCAACATACTCTCAA 57.261 39.130 0.00 0.00 0.00 3.02
2314 2365 5.738619 TCTAGCACCAACATACTCTCAAA 57.261 39.130 0.00 0.00 0.00 2.69
2315 2366 6.299805 TCTAGCACCAACATACTCTCAAAT 57.700 37.500 0.00 0.00 0.00 2.32
2316 2367 6.108687 TCTAGCACCAACATACTCTCAAATG 58.891 40.000 0.00 0.00 0.00 2.32
2317 2368 4.655963 AGCACCAACATACTCTCAAATGT 58.344 39.130 0.00 0.00 37.94 2.71
2318 2369 5.804639 AGCACCAACATACTCTCAAATGTA 58.195 37.500 0.00 0.00 35.30 2.29
2319 2370 5.877012 AGCACCAACATACTCTCAAATGTAG 59.123 40.000 0.00 0.00 35.30 2.74
2320 2371 5.874810 GCACCAACATACTCTCAAATGTAGA 59.125 40.000 0.00 0.00 35.30 2.59
2321 2372 6.540189 GCACCAACATACTCTCAAATGTAGAT 59.460 38.462 0.00 0.00 35.30 1.98
2322 2373 7.466455 GCACCAACATACTCTCAAATGTAGATG 60.466 40.741 0.00 0.00 35.30 2.90
2323 2374 6.540189 ACCAACATACTCTCAAATGTAGATGC 59.460 38.462 0.00 0.00 35.30 3.91
2324 2375 6.765036 CCAACATACTCTCAAATGTAGATGCT 59.235 38.462 0.00 0.00 35.30 3.79
2325 2376 7.928167 CCAACATACTCTCAAATGTAGATGCTA 59.072 37.037 0.00 0.00 35.30 3.49
2326 2377 8.976471 CAACATACTCTCAAATGTAGATGCTAG 58.024 37.037 0.00 0.00 35.30 3.42
2327 2378 8.470657 ACATACTCTCAAATGTAGATGCTAGA 57.529 34.615 0.00 0.00 34.61 2.43
2328 2379 8.918116 ACATACTCTCAAATGTAGATGCTAGAA 58.082 33.333 0.00 0.00 34.61 2.10
2329 2380 9.926158 CATACTCTCAAATGTAGATGCTAGAAT 57.074 33.333 0.00 0.00 0.00 2.40
2342 2393 9.601971 GTAGATGCTAGAATTTAGTCTACTTCG 57.398 37.037 0.00 0.00 35.75 3.79
2343 2394 7.653647 AGATGCTAGAATTTAGTCTACTTCGG 58.346 38.462 0.00 0.00 0.00 4.30
2344 2395 6.145338 TGCTAGAATTTAGTCTACTTCGGG 57.855 41.667 0.00 0.00 0.00 5.14
2345 2396 4.983538 GCTAGAATTTAGTCTACTTCGGGC 59.016 45.833 0.00 0.00 0.00 6.13
2346 2397 4.403585 AGAATTTAGTCTACTTCGGGCC 57.596 45.455 0.00 0.00 0.00 5.80
2347 2398 3.773119 AGAATTTAGTCTACTTCGGGCCA 59.227 43.478 4.39 0.00 0.00 5.36
2348 2399 3.821421 ATTTAGTCTACTTCGGGCCAG 57.179 47.619 4.39 0.00 0.00 4.85
2349 2400 0.822164 TTAGTCTACTTCGGGCCAGC 59.178 55.000 4.39 0.00 0.00 4.85
2350 2401 1.041447 TAGTCTACTTCGGGCCAGCC 61.041 60.000 4.39 0.00 0.00 4.85
2360 2411 3.210302 GGCCAGCCCAATAGCAAC 58.790 61.111 0.00 0.00 34.23 4.17
2361 2412 2.426406 GGCCAGCCCAATAGCAACC 61.426 63.158 0.00 0.00 34.23 3.77
2362 2413 1.682005 GCCAGCCCAATAGCAACCA 60.682 57.895 0.00 0.00 34.23 3.67
2363 2414 1.669999 GCCAGCCCAATAGCAACCAG 61.670 60.000 0.00 0.00 34.23 4.00
2364 2415 0.034186 CCAGCCCAATAGCAACCAGA 60.034 55.000 0.00 0.00 34.23 3.86
2365 2416 1.386533 CAGCCCAATAGCAACCAGAG 58.613 55.000 0.00 0.00 34.23 3.35
2366 2417 0.257039 AGCCCAATAGCAACCAGAGG 59.743 55.000 0.00 0.00 34.23 3.69
2367 2418 0.753111 GCCCAATAGCAACCAGAGGG 60.753 60.000 0.00 0.00 41.29 4.30
2368 2419 0.918983 CCCAATAGCAACCAGAGGGA 59.081 55.000 0.00 0.00 36.96 4.20
2369 2420 1.408822 CCCAATAGCAACCAGAGGGAC 60.409 57.143 0.00 0.00 36.96 4.46
2370 2421 1.281867 CCAATAGCAACCAGAGGGACA 59.718 52.381 0.00 0.00 38.05 4.02
2371 2422 2.092212 CCAATAGCAACCAGAGGGACAT 60.092 50.000 0.00 0.00 38.05 3.06
2372 2423 3.624777 CAATAGCAACCAGAGGGACATT 58.375 45.455 0.00 0.00 38.05 2.71
2373 2424 4.019174 CAATAGCAACCAGAGGGACATTT 58.981 43.478 0.00 0.00 38.05 2.32
2374 2425 2.683211 AGCAACCAGAGGGACATTTT 57.317 45.000 0.00 0.00 38.05 1.82
2375 2426 3.806949 AGCAACCAGAGGGACATTTTA 57.193 42.857 0.00 0.00 38.05 1.52
2376 2427 3.690460 AGCAACCAGAGGGACATTTTAG 58.310 45.455 0.00 0.00 38.05 1.85
2377 2428 3.074538 AGCAACCAGAGGGACATTTTAGT 59.925 43.478 0.00 0.00 38.05 2.24
2378 2429 3.440522 GCAACCAGAGGGACATTTTAGTC 59.559 47.826 0.00 0.00 38.05 2.59
2379 2430 4.807643 GCAACCAGAGGGACATTTTAGTCT 60.808 45.833 0.00 0.00 38.57 3.24
2380 2431 5.570844 GCAACCAGAGGGACATTTTAGTCTA 60.571 44.000 0.00 0.00 38.57 2.59
2381 2432 6.653989 CAACCAGAGGGACATTTTAGTCTAT 58.346 40.000 0.00 0.00 38.57 1.98
2382 2433 6.240549 ACCAGAGGGACATTTTAGTCTATG 57.759 41.667 0.00 0.00 38.57 2.23
2383 2434 5.726793 ACCAGAGGGACATTTTAGTCTATGT 59.273 40.000 0.00 0.00 38.57 2.29
2384 2435 6.215636 ACCAGAGGGACATTTTAGTCTATGTT 59.784 38.462 0.00 0.00 38.57 2.71
2385 2436 6.540189 CCAGAGGGACATTTTAGTCTATGTTG 59.460 42.308 0.00 0.00 38.57 3.33
2386 2437 6.540189 CAGAGGGACATTTTAGTCTATGTTGG 59.460 42.308 0.00 0.00 38.57 3.77
2387 2438 6.443849 AGAGGGACATTTTAGTCTATGTTGGA 59.556 38.462 0.00 0.00 38.57 3.53
2388 2439 7.027874 AGGGACATTTTAGTCTATGTTGGAA 57.972 36.000 0.00 0.00 38.57 3.53
2389 2440 7.643123 AGGGACATTTTAGTCTATGTTGGAAT 58.357 34.615 0.00 0.00 38.57 3.01
2390 2441 8.778059 AGGGACATTTTAGTCTATGTTGGAATA 58.222 33.333 0.00 0.00 38.57 1.75
2391 2442 9.574516 GGGACATTTTAGTCTATGTTGGAATAT 57.425 33.333 0.00 0.00 38.57 1.28
2400 2451 7.619050 AGTCTATGTTGGAATATAGATGCTGG 58.381 38.462 8.54 0.00 39.98 4.85
2401 2452 7.455953 AGTCTATGTTGGAATATAGATGCTGGA 59.544 37.037 8.54 0.00 39.98 3.86
2402 2453 8.097038 GTCTATGTTGGAATATAGATGCTGGAA 58.903 37.037 8.54 0.00 39.98 3.53
2403 2454 8.829746 TCTATGTTGGAATATAGATGCTGGAAT 58.170 33.333 2.63 0.00 35.18 3.01
2404 2455 9.458727 CTATGTTGGAATATAGATGCTGGAATT 57.541 33.333 0.00 0.00 33.46 2.17
2405 2456 7.750229 TGTTGGAATATAGATGCTGGAATTC 57.250 36.000 0.00 0.00 0.00 2.17
2406 2457 7.289310 TGTTGGAATATAGATGCTGGAATTCA 58.711 34.615 7.93 0.00 0.00 2.57
2407 2458 7.446319 TGTTGGAATATAGATGCTGGAATTCAG 59.554 37.037 7.93 4.33 46.03 3.02
2419 2470 4.130118 CTGGAATTCAGCACCTACATACC 58.870 47.826 7.93 0.00 36.60 2.73
2420 2471 3.118038 TGGAATTCAGCACCTACATACCC 60.118 47.826 7.93 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 56 1.873903 GCTATCGGTGCATCGGATGTT 60.874 52.381 21.08 2.34 37.33 2.71
54 57 0.319900 GCTATCGGTGCATCGGATGT 60.320 55.000 21.08 6.13 37.33 3.06
87 90 3.179443 ACGAGAATGTATCCGTTGCAT 57.821 42.857 0.00 0.00 33.14 3.96
126 129 3.112580 GTCTCGCTTCTCTATCAACTGC 58.887 50.000 0.00 0.00 0.00 4.40
248 251 2.585247 GCCGATGAGGGTGCGTAC 60.585 66.667 0.00 0.00 41.48 3.67
406 409 4.565564 GCCTAATATACACTTATTCGCGGG 59.434 45.833 6.13 0.00 0.00 6.13
486 491 8.820933 CATGCGATGAGAGAGAAGTATTTTTAA 58.179 33.333 0.00 0.00 0.00 1.52
487 492 7.439356 CCATGCGATGAGAGAGAAGTATTTTTA 59.561 37.037 0.00 0.00 0.00 1.52
508 515 5.470098 ACGATATTGGTCTTGATTACCATGC 59.530 40.000 0.00 0.00 46.16 4.06
511 518 6.053005 GGAACGATATTGGTCTTGATTACCA 58.947 40.000 7.95 0.00 45.26 3.25
529 536 2.179427 AGGAGATCATGTGTGGAACGA 58.821 47.619 0.00 0.00 42.39 3.85
531 538 7.337942 AGAAATTAAGGAGATCATGTGTGGAAC 59.662 37.037 0.00 0.00 37.35 3.62
535 542 8.722480 TGTAGAAATTAAGGAGATCATGTGTG 57.278 34.615 0.00 0.00 0.00 3.82
591 599 4.081420 TGCAAACCACTATCTCTCCTCTTC 60.081 45.833 0.00 0.00 0.00 2.87
676 686 4.202326 GCTTCCTCCCTCCACGAATAAATA 60.202 45.833 0.00 0.00 0.00 1.40
696 706 0.463654 TGTTCGCTTGTCACCTGCTT 60.464 50.000 0.00 0.00 0.00 3.91
706 716 0.662619 TGTGCTCCTTTGTTCGCTTG 59.337 50.000 0.00 0.00 0.00 4.01
935 947 3.002246 GCGTTGTGAACTTGTGATGAGAA 59.998 43.478 0.00 0.00 0.00 2.87
965 977 7.774134 TGTCACTTACTTACACACTTACTCAA 58.226 34.615 0.00 0.00 0.00 3.02
1043 1060 0.966920 ACTATGCGTAATCGAGGGGG 59.033 55.000 0.00 0.00 39.71 5.40
1048 1065 8.830580 ACTACTAGTAAAACTATGCGTAATCGA 58.169 33.333 3.76 0.00 32.64 3.59
1049 1066 9.443283 AACTACTAGTAAAACTATGCGTAATCG 57.557 33.333 3.76 0.00 33.43 3.34
1542 1568 6.397272 AGTAATTTGAAACGGACGGTGTATA 58.603 36.000 0.00 0.00 0.00 1.47
1548 1577 4.212636 AGACAAGTAATTTGAAACGGACGG 59.787 41.667 0.00 0.00 39.21 4.79
1640 1678 3.526019 TCCCTCCCTTCGTTCCAAATTAT 59.474 43.478 0.00 0.00 0.00 1.28
1649 1687 3.463048 TTAGTACTCCCTCCCTTCGTT 57.537 47.619 0.00 0.00 0.00 3.85
1683 1721 5.261209 AGACATTCACATAGAGAGACAGC 57.739 43.478 0.00 0.00 0.00 4.40
1690 1729 7.730084 TCCTATCCAAAGACATTCACATAGAG 58.270 38.462 0.00 0.00 0.00 2.43
1692 1731 7.989741 AGTTCCTATCCAAAGACATTCACATAG 59.010 37.037 0.00 0.00 0.00 2.23
1693 1732 7.861629 AGTTCCTATCCAAAGACATTCACATA 58.138 34.615 0.00 0.00 0.00 2.29
1694 1733 6.725364 AGTTCCTATCCAAAGACATTCACAT 58.275 36.000 0.00 0.00 0.00 3.21
1707 1746 5.338632 TGTCCTGTTTCTAGTTCCTATCCA 58.661 41.667 0.00 0.00 0.00 3.41
1804 1844 8.684973 TTGAACTTCAAATTTTGCATTTTTGG 57.315 26.923 13.38 4.85 32.71 3.28
1838 1878 7.759489 TTGTTTCTCTATACCTTGCAAATGT 57.241 32.000 0.00 3.43 0.00 2.71
1880 1920 2.535012 TAGTGATGCACCGTTTGTCA 57.465 45.000 0.00 0.00 34.49 3.58
2015 2061 7.215789 TGCAATGAAAACTTCAAACATACCAT 58.784 30.769 0.00 0.00 43.95 3.55
2275 2326 9.197306 TGGTGCTAGAATTTAGTCTACTATGAA 57.803 33.333 0.00 0.00 0.00 2.57
2276 2327 8.762481 TGGTGCTAGAATTTAGTCTACTATGA 57.238 34.615 0.00 0.00 0.00 2.15
2277 2328 9.250624 GTTGGTGCTAGAATTTAGTCTACTATG 57.749 37.037 0.00 0.00 0.00 2.23
2278 2329 8.978472 TGTTGGTGCTAGAATTTAGTCTACTAT 58.022 33.333 0.00 0.00 0.00 2.12
2279 2330 8.357290 TGTTGGTGCTAGAATTTAGTCTACTA 57.643 34.615 0.00 0.00 0.00 1.82
2280 2331 7.241042 TGTTGGTGCTAGAATTTAGTCTACT 57.759 36.000 0.00 0.00 0.00 2.57
2281 2332 9.032420 GTATGTTGGTGCTAGAATTTAGTCTAC 57.968 37.037 0.00 0.00 0.00 2.59
2282 2333 8.978472 AGTATGTTGGTGCTAGAATTTAGTCTA 58.022 33.333 0.00 0.00 0.00 2.59
2283 2334 7.852263 AGTATGTTGGTGCTAGAATTTAGTCT 58.148 34.615 0.00 0.00 0.00 3.24
2284 2335 7.982354 AGAGTATGTTGGTGCTAGAATTTAGTC 59.018 37.037 0.00 0.00 0.00 2.59
2285 2336 7.852263 AGAGTATGTTGGTGCTAGAATTTAGT 58.148 34.615 0.00 0.00 0.00 2.24
2286 2337 7.981789 TGAGAGTATGTTGGTGCTAGAATTTAG 59.018 37.037 0.00 0.00 0.00 1.85
2287 2338 7.847096 TGAGAGTATGTTGGTGCTAGAATTTA 58.153 34.615 0.00 0.00 0.00 1.40
2288 2339 6.711277 TGAGAGTATGTTGGTGCTAGAATTT 58.289 36.000 0.00 0.00 0.00 1.82
2289 2340 6.299805 TGAGAGTATGTTGGTGCTAGAATT 57.700 37.500 0.00 0.00 0.00 2.17
2290 2341 5.939764 TGAGAGTATGTTGGTGCTAGAAT 57.060 39.130 0.00 0.00 0.00 2.40
2291 2342 5.738619 TTGAGAGTATGTTGGTGCTAGAA 57.261 39.130 0.00 0.00 0.00 2.10
2292 2343 5.738619 TTTGAGAGTATGTTGGTGCTAGA 57.261 39.130 0.00 0.00 0.00 2.43
2293 2344 5.877012 ACATTTGAGAGTATGTTGGTGCTAG 59.123 40.000 0.00 0.00 31.14 3.42
2294 2345 5.804639 ACATTTGAGAGTATGTTGGTGCTA 58.195 37.500 0.00 0.00 31.14 3.49
2295 2346 4.655963 ACATTTGAGAGTATGTTGGTGCT 58.344 39.130 0.00 0.00 31.14 4.40
2296 2347 5.874810 TCTACATTTGAGAGTATGTTGGTGC 59.125 40.000 0.00 0.00 36.46 5.01
2297 2348 7.466455 GCATCTACATTTGAGAGTATGTTGGTG 60.466 40.741 0.00 0.00 39.77 4.17
2298 2349 6.540189 GCATCTACATTTGAGAGTATGTTGGT 59.460 38.462 0.00 0.00 36.46 3.67
2299 2350 6.765036 AGCATCTACATTTGAGAGTATGTTGG 59.235 38.462 0.00 0.00 36.46 3.77
2300 2351 7.783090 AGCATCTACATTTGAGAGTATGTTG 57.217 36.000 0.00 0.00 36.46 3.33
2301 2352 8.918116 TCTAGCATCTACATTTGAGAGTATGTT 58.082 33.333 0.00 0.00 36.46 2.71
2302 2353 8.470657 TCTAGCATCTACATTTGAGAGTATGT 57.529 34.615 0.00 0.00 38.46 2.29
2303 2354 9.926158 ATTCTAGCATCTACATTTGAGAGTATG 57.074 33.333 0.00 0.00 0.00 2.39
2316 2367 9.601971 CGAAGTAGACTAAATTCTAGCATCTAC 57.398 37.037 0.00 0.00 38.10 2.59
2317 2368 8.784994 CCGAAGTAGACTAAATTCTAGCATCTA 58.215 37.037 6.97 0.00 0.00 1.98
2318 2369 7.255660 CCCGAAGTAGACTAAATTCTAGCATCT 60.256 40.741 6.97 0.00 0.00 2.90
2319 2370 6.864165 CCCGAAGTAGACTAAATTCTAGCATC 59.136 42.308 6.97 0.00 0.00 3.91
2320 2371 6.739008 GCCCGAAGTAGACTAAATTCTAGCAT 60.739 42.308 11.22 0.00 0.00 3.79
2321 2372 5.451520 GCCCGAAGTAGACTAAATTCTAGCA 60.452 44.000 11.22 0.00 0.00 3.49
2322 2373 4.983538 GCCCGAAGTAGACTAAATTCTAGC 59.016 45.833 6.97 5.96 0.00 3.42
2323 2374 5.068723 TGGCCCGAAGTAGACTAAATTCTAG 59.931 44.000 0.00 0.00 0.00 2.43
2324 2375 4.957954 TGGCCCGAAGTAGACTAAATTCTA 59.042 41.667 0.00 0.00 0.00 2.10
2325 2376 3.773119 TGGCCCGAAGTAGACTAAATTCT 59.227 43.478 0.00 0.00 0.00 2.40
2326 2377 4.120589 CTGGCCCGAAGTAGACTAAATTC 58.879 47.826 0.00 0.00 0.00 2.17
2327 2378 3.681874 GCTGGCCCGAAGTAGACTAAATT 60.682 47.826 0.00 0.00 0.00 1.82
2328 2379 2.158943 GCTGGCCCGAAGTAGACTAAAT 60.159 50.000 0.00 0.00 0.00 1.40
2329 2380 1.206371 GCTGGCCCGAAGTAGACTAAA 59.794 52.381 0.00 0.00 0.00 1.85
2330 2381 0.822164 GCTGGCCCGAAGTAGACTAA 59.178 55.000 0.00 0.00 0.00 2.24
2331 2382 1.041447 GGCTGGCCCGAAGTAGACTA 61.041 60.000 0.00 0.00 0.00 2.59
2332 2383 2.359967 GGCTGGCCCGAAGTAGACT 61.360 63.158 0.00 0.00 0.00 3.24
2333 2384 2.187163 GGCTGGCCCGAAGTAGAC 59.813 66.667 0.00 0.00 0.00 2.59
2343 2394 2.426406 GGTTGCTATTGGGCTGGCC 61.426 63.158 14.23 14.23 0.00 5.36
2344 2395 1.669999 CTGGTTGCTATTGGGCTGGC 61.670 60.000 0.00 0.00 0.00 4.85
2345 2396 0.034186 TCTGGTTGCTATTGGGCTGG 60.034 55.000 0.00 0.00 0.00 4.85
2346 2397 1.386533 CTCTGGTTGCTATTGGGCTG 58.613 55.000 0.00 0.00 0.00 4.85
2347 2398 0.257039 CCTCTGGTTGCTATTGGGCT 59.743 55.000 0.00 0.00 0.00 5.19
2348 2399 0.753111 CCCTCTGGTTGCTATTGGGC 60.753 60.000 0.00 0.00 0.00 5.36
2349 2400 0.918983 TCCCTCTGGTTGCTATTGGG 59.081 55.000 0.00 0.00 34.76 4.12
2350 2401 1.281867 TGTCCCTCTGGTTGCTATTGG 59.718 52.381 0.00 0.00 0.00 3.16
2351 2402 2.787473 TGTCCCTCTGGTTGCTATTG 57.213 50.000 0.00 0.00 0.00 1.90
2352 2403 4.322057 AAATGTCCCTCTGGTTGCTATT 57.678 40.909 0.00 0.00 0.00 1.73
2353 2404 4.322057 AAAATGTCCCTCTGGTTGCTAT 57.678 40.909 0.00 0.00 0.00 2.97
2354 2405 3.806949 AAAATGTCCCTCTGGTTGCTA 57.193 42.857 0.00 0.00 0.00 3.49
2355 2406 2.683211 AAAATGTCCCTCTGGTTGCT 57.317 45.000 0.00 0.00 0.00 3.91
2356 2407 3.421844 ACTAAAATGTCCCTCTGGTTGC 58.578 45.455 0.00 0.00 0.00 4.17
2357 2408 4.911390 AGACTAAAATGTCCCTCTGGTTG 58.089 43.478 0.00 0.00 37.66 3.77
2358 2409 6.215636 ACATAGACTAAAATGTCCCTCTGGTT 59.784 38.462 0.00 0.00 37.66 3.67
2359 2410 5.726793 ACATAGACTAAAATGTCCCTCTGGT 59.273 40.000 0.00 0.00 37.66 4.00
2360 2411 6.240549 ACATAGACTAAAATGTCCCTCTGG 57.759 41.667 0.00 0.00 37.66 3.86
2361 2412 6.540189 CCAACATAGACTAAAATGTCCCTCTG 59.460 42.308 0.00 0.00 35.30 3.35
2362 2413 6.443849 TCCAACATAGACTAAAATGTCCCTCT 59.556 38.462 0.00 0.00 35.30 3.69
2363 2414 6.650120 TCCAACATAGACTAAAATGTCCCTC 58.350 40.000 0.00 0.00 35.30 4.30
2364 2415 6.636454 TCCAACATAGACTAAAATGTCCCT 57.364 37.500 0.00 0.00 35.30 4.20
2365 2416 7.881775 ATTCCAACATAGACTAAAATGTCCC 57.118 36.000 0.00 0.00 35.30 4.46
2374 2425 8.753133 CCAGCATCTATATTCCAACATAGACTA 58.247 37.037 0.00 0.00 36.76 2.59
2375 2426 7.455953 TCCAGCATCTATATTCCAACATAGACT 59.544 37.037 0.00 0.00 36.76 3.24
2376 2427 7.615403 TCCAGCATCTATATTCCAACATAGAC 58.385 38.462 0.00 0.00 36.76 2.59
2377 2428 7.797121 TCCAGCATCTATATTCCAACATAGA 57.203 36.000 0.00 0.00 37.96 1.98
2378 2429 9.458727 AATTCCAGCATCTATATTCCAACATAG 57.541 33.333 0.00 0.00 0.00 2.23
2379 2430 9.453572 GAATTCCAGCATCTATATTCCAACATA 57.546 33.333 0.00 0.00 0.00 2.29
2380 2431 7.946219 TGAATTCCAGCATCTATATTCCAACAT 59.054 33.333 2.27 0.00 0.00 2.71
2381 2432 7.289310 TGAATTCCAGCATCTATATTCCAACA 58.711 34.615 2.27 0.00 0.00 3.33
2382 2433 7.750229 TGAATTCCAGCATCTATATTCCAAC 57.250 36.000 2.27 0.00 0.00 3.77
2383 2434 7.991084 CTGAATTCCAGCATCTATATTCCAA 57.009 36.000 2.27 0.00 35.89 3.53
2397 2448 4.130118 GGTATGTAGGTGCTGAATTCCAG 58.870 47.826 2.27 1.99 45.67 3.86
2398 2449 3.118038 GGGTATGTAGGTGCTGAATTCCA 60.118 47.826 2.27 0.00 0.00 3.53
2399 2450 3.477530 GGGTATGTAGGTGCTGAATTCC 58.522 50.000 2.27 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.