Multiple sequence alignment - TraesCS6A01G261400

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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 TraesCS6A01G261400 chr6A 100.000 2513 0 0 1 2513 484849550 484847038 0.000000e+00 4641
1 TraesCS6A01G261400 chr6B 92.374 1849 88 24 1 1821 519815179 519813356 0.000000e+00 2584
2 TraesCS6A01G261400 chr6B 94.141 495 23 4 2022 2513 519813270 519812779 0.000000e+00 749
3 TraesCS6A01G261400 chr6B 93.491 169 11 0 1220 1388 156279655 156279487 4.150000e-63 252
4 TraesCS6A01G261400 chr6D 91.281 1663 83 22 302 1932 344301117 344299485 0.000000e+00 2211
5 TraesCS6A01G261400 chr6D 95.968 496 14 5 2022 2513 344299481 344298988 0.000000e+00 800
6 TraesCS6A01G261400 chr6D 90.881 318 15 9 1 315 344301881 344301575 5.000000e-112 414
7 TraesCS6A01G261400 chrUn 86.486 481 46 11 1063 1525 79140674 79141153 6.200000e-141 510
8 TraesCS6A01G261400 chr5A 94.118 136 7 1 1220 1355 654117321 654117455 3.280000e-49 206
9 TraesCS6A01G261400 chr2D 84.000 200 32 0 1270 1469 563958852 563959051 2.550000e-45 193
10 TraesCS6A01G261400 chr1B 79.421 311 34 15 1063 1372 144928179 144928460 2.550000e-45 193
11 TraesCS6A01G261400 chr2B 83.500 200 33 0 1270 1469 674722796 674722995 1.190000e-43 187
12 TraesCS6A01G261400 chr2A 84.021 194 29 2 1277 1469 704005201 704005393 4.270000e-43 185


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 TraesCS6A01G261400 chr6A 484847038 484849550 2512 True 4641.000000 4641 100.0000 1 2513 1 chr6A.!!$R1 2512
1 TraesCS6A01G261400 chr6B 519812779 519815179 2400 True 1666.500000 2584 93.2575 1 2513 2 chr6B.!!$R2 2512
2 TraesCS6A01G261400 chr6D 344298988 344301881 2893 True 1141.666667 2211 92.7100 1 2513 3 chr6D.!!$R1 2512

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
666 1169 0.393077 AGCACTACGGTGGCCATATC 59.607 55.0 9.72 0.46 43.18 1.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 2397 0.107831 CCGGGAGACACAACCAGAAA 59.892 55.0 0.0 0.0 0.0 2.52 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
41 42 1.120530 AGTCAATAGTACGCAGGGGG 58.879 55.000 0.00 0.00 0.00 5.40
224 226 9.150348 CAAGGTTTTAACATTGTTTTTCTCTGT 57.850 29.630 7.45 0.00 43.46 3.41
245 247 9.653067 CTCTGTCTATAATGTAAAGTACGACTG 57.347 37.037 0.00 0.00 0.00 3.51
246 248 9.387257 TCTGTCTATAATGTAAAGTACGACTGA 57.613 33.333 0.00 0.00 0.00 3.41
276 278 5.320549 ACTAATACGTCCGTCAATTGACT 57.679 39.130 30.45 17.26 42.66 3.41
289 291 5.057149 GTCAATTGACTGTAGAAGTGGTGT 58.943 41.667 27.66 0.00 40.07 4.16
349 835 1.259840 GGCTTGGTTGGGTGATGCAT 61.260 55.000 0.00 0.00 0.00 3.96
475 969 8.673626 AATACTTCATAATTTGTTCAAGTGCG 57.326 30.769 0.00 0.00 0.00 5.34
480 974 6.085573 TCATAATTTGTTCAAGTGCGTGATG 58.914 36.000 0.00 0.00 0.00 3.07
556 1059 3.519913 GACCCTGACATCCTAGTTTCCTT 59.480 47.826 0.00 0.00 0.00 3.36
558 1061 3.519510 CCCTGACATCCTAGTTTCCTTGA 59.480 47.826 0.00 0.00 0.00 3.02
561 1064 4.168101 TGACATCCTAGTTTCCTTGAGGT 58.832 43.478 0.00 0.00 36.34 3.85
659 1162 2.457366 AAAAGAGAGCACTACGGTGG 57.543 50.000 0.00 0.00 43.18 4.61
666 1169 0.393077 AGCACTACGGTGGCCATATC 59.607 55.000 9.72 0.46 43.18 1.63
756 1259 1.301423 TCCAACTTCCAAACGAACCG 58.699 50.000 0.00 0.00 0.00 4.44
886 1398 0.678048 GCCTCCCATCACACACTTCC 60.678 60.000 0.00 0.00 0.00 3.46
920 1433 2.021106 CGAGCTACGACGACGACC 59.979 66.667 15.32 1.57 45.77 4.79
934 1470 1.299468 CGACCATCGACTAGCCAGC 60.299 63.158 0.00 0.00 43.74 4.85
935 1471 1.068250 GACCATCGACTAGCCAGCC 59.932 63.158 0.00 0.00 0.00 4.85
936 1472 1.676678 GACCATCGACTAGCCAGCCA 61.677 60.000 0.00 0.00 0.00 4.75
937 1473 1.068753 CCATCGACTAGCCAGCCAG 59.931 63.158 0.00 0.00 0.00 4.85
938 1474 1.593750 CATCGACTAGCCAGCCAGC 60.594 63.158 0.00 0.00 0.00 4.85
940 1476 2.025767 ATCGACTAGCCAGCCAGCTG 62.026 60.000 12.78 12.78 44.67 4.24
941 1477 2.513435 GACTAGCCAGCCAGCTGC 60.513 66.667 14.26 9.65 44.67 5.25
990 1526 3.146913 AGCTCAGCTCTCTCCCGC 61.147 66.667 0.00 0.00 30.62 6.13
1527 2063 1.226435 CTGACGTCGCTGTAGCTCC 60.226 63.158 11.62 0.00 39.32 4.70
1606 2146 0.179084 TAGCCGGTGCATAAGCTCAC 60.179 55.000 1.90 0.00 42.74 3.51
1610 2150 2.472909 GGTGCATAAGCTCACCGGC 61.473 63.158 0.00 0.00 42.67 6.13
1666 2206 2.229784 CCTGCTGGGTGTTGATTCTTTC 59.770 50.000 0.71 0.00 0.00 2.62
1795 2335 7.148755 GGAAGTTGCTATAAAAACATGCACTTG 60.149 37.037 0.00 0.00 33.13 3.16
1812 2352 0.968405 TTGGCTTGAACTGGGAATGC 59.032 50.000 0.00 0.00 0.00 3.56
1821 2391 1.923356 ACTGGGAATGCGAATTTGGT 58.077 45.000 0.00 0.00 0.00 3.67
1822 2392 2.247358 ACTGGGAATGCGAATTTGGTT 58.753 42.857 0.00 0.00 0.00 3.67
1823 2393 2.029110 ACTGGGAATGCGAATTTGGTTG 60.029 45.455 0.00 0.00 0.00 3.77
1826 2396 3.057174 TGGGAATGCGAATTTGGTTGTAC 60.057 43.478 0.00 0.00 0.00 2.90
1827 2397 3.192633 GGGAATGCGAATTTGGTTGTACT 59.807 43.478 0.00 0.00 0.00 2.73
1828 2398 4.321675 GGGAATGCGAATTTGGTTGTACTT 60.322 41.667 0.00 0.00 0.00 2.24
1829 2399 5.227152 GGAATGCGAATTTGGTTGTACTTT 58.773 37.500 0.00 0.00 0.00 2.66
1830 2400 5.344933 GGAATGCGAATTTGGTTGTACTTTC 59.655 40.000 0.00 0.00 0.00 2.62
1831 2401 5.705609 ATGCGAATTTGGTTGTACTTTCT 57.294 34.783 0.00 0.00 0.00 2.52
1832 2402 4.854399 TGCGAATTTGGTTGTACTTTCTG 58.146 39.130 0.00 0.00 0.00 3.02
1833 2403 4.226761 GCGAATTTGGTTGTACTTTCTGG 58.773 43.478 0.00 0.00 0.00 3.86
1834 2404 4.261447 GCGAATTTGGTTGTACTTTCTGGT 60.261 41.667 0.00 0.00 0.00 4.00
1835 2405 5.735070 GCGAATTTGGTTGTACTTTCTGGTT 60.735 40.000 0.00 0.00 0.00 3.67
1836 2406 5.685511 CGAATTTGGTTGTACTTTCTGGTTG 59.314 40.000 0.00 0.00 0.00 3.77
1837 2407 6.538945 AATTTGGTTGTACTTTCTGGTTGT 57.461 33.333 0.00 0.00 0.00 3.32
1838 2408 4.974368 TTGGTTGTACTTTCTGGTTGTG 57.026 40.909 0.00 0.00 0.00 3.33
1839 2409 3.958018 TGGTTGTACTTTCTGGTTGTGT 58.042 40.909 0.00 0.00 0.00 3.72
1840 2410 3.942748 TGGTTGTACTTTCTGGTTGTGTC 59.057 43.478 0.00 0.00 0.00 3.67
1841 2411 4.196971 GGTTGTACTTTCTGGTTGTGTCT 58.803 43.478 0.00 0.00 0.00 3.41
1842 2412 4.272748 GGTTGTACTTTCTGGTTGTGTCTC 59.727 45.833 0.00 0.00 0.00 3.36
1843 2413 4.067972 TGTACTTTCTGGTTGTGTCTCC 57.932 45.455 0.00 0.00 0.00 3.71
1844 2414 2.640316 ACTTTCTGGTTGTGTCTCCC 57.360 50.000 0.00 0.00 0.00 4.30
1845 2415 1.202651 ACTTTCTGGTTGTGTCTCCCG 60.203 52.381 0.00 0.00 0.00 5.14
1846 2416 0.107831 TTTCTGGTTGTGTCTCCCGG 59.892 55.000 0.00 0.00 0.00 5.73
1847 2417 1.052124 TTCTGGTTGTGTCTCCCGGT 61.052 55.000 0.00 0.00 0.00 5.28
1848 2418 1.052124 TCTGGTTGTGTCTCCCGGTT 61.052 55.000 0.00 0.00 0.00 4.44
1849 2419 0.884704 CTGGTTGTGTCTCCCGGTTG 60.885 60.000 0.00 0.00 0.00 3.77
1850 2420 1.599797 GGTTGTGTCTCCCGGTTGG 60.600 63.158 0.00 0.00 0.00 3.77
1851 2421 1.448497 GTTGTGTCTCCCGGTTGGA 59.552 57.895 0.00 0.00 42.41 3.53
1852 2422 0.179040 GTTGTGTCTCCCGGTTGGAA 60.179 55.000 0.00 0.00 44.57 3.53
1853 2423 0.179040 TTGTGTCTCCCGGTTGGAAC 60.179 55.000 0.00 0.00 44.57 3.62
1854 2424 1.052124 TGTGTCTCCCGGTTGGAACT 61.052 55.000 0.00 0.00 44.57 3.01
1855 2425 0.971386 GTGTCTCCCGGTTGGAACTA 59.029 55.000 0.00 0.00 44.57 2.24
1856 2426 1.067071 GTGTCTCCCGGTTGGAACTAG 60.067 57.143 0.00 0.00 44.57 2.57
1861 2431 0.916809 CCCGGTTGGAACTAGGGAAT 59.083 55.000 14.50 0.00 44.07 3.01
1887 2458 7.259882 TGGCATAAGAATTTGCTAAAGACATG 58.740 34.615 0.22 0.00 38.88 3.21
1899 2470 7.520119 TGCTAAAGACATGTATACTGAAACG 57.480 36.000 0.00 0.00 0.00 3.60
1900 2471 6.533723 TGCTAAAGACATGTATACTGAAACGG 59.466 38.462 0.00 0.00 0.00 4.44
1901 2472 6.534079 GCTAAAGACATGTATACTGAAACGGT 59.466 38.462 0.00 0.00 0.00 4.83
1904 2475 3.777478 ACATGTATACTGAAACGGTCCG 58.223 45.455 10.48 10.48 0.00 4.79
1905 2476 3.194116 ACATGTATACTGAAACGGTCCGT 59.806 43.478 12.23 12.23 43.97 4.69
1926 2499 5.005107 CCGTAGTATAACTTTGGCGAAACTC 59.995 44.000 0.00 0.00 0.00 3.01
1932 2505 1.156736 CTTTGGCGAAACTCGTGGAT 58.843 50.000 0.00 0.00 42.81 3.41
1934 2507 0.034198 TTGGCGAAACTCGTGGATGA 59.966 50.000 0.00 0.00 42.81 2.92
1935 2508 0.389817 TGGCGAAACTCGTGGATGAG 60.390 55.000 0.00 0.00 42.81 2.90
1936 2509 1.696832 GGCGAAACTCGTGGATGAGC 61.697 60.000 0.00 0.00 42.81 4.26
1937 2510 1.991430 CGAAACTCGTGGATGAGCG 59.009 57.895 0.00 0.00 39.68 5.03
1938 2511 0.732880 CGAAACTCGTGGATGAGCGT 60.733 55.000 0.00 0.00 39.68 5.07
1939 2512 0.716108 GAAACTCGTGGATGAGCGTG 59.284 55.000 0.00 0.00 39.68 5.34
1940 2513 1.291877 AAACTCGTGGATGAGCGTGC 61.292 55.000 0.00 0.00 39.68 5.34
1941 2514 2.125952 CTCGTGGATGAGCGTGCA 60.126 61.111 0.00 0.00 0.00 4.57
1942 2515 1.520120 CTCGTGGATGAGCGTGCAT 60.520 57.895 0.00 0.00 0.00 3.96
1943 2516 1.759293 CTCGTGGATGAGCGTGCATG 61.759 60.000 0.09 0.09 0.00 4.06
1944 2517 2.102438 CGTGGATGAGCGTGCATGT 61.102 57.895 7.93 0.00 0.00 3.21
1945 2518 1.426621 GTGGATGAGCGTGCATGTG 59.573 57.895 7.93 0.00 0.00 3.21
1946 2519 2.400962 TGGATGAGCGTGCATGTGC 61.401 57.895 7.93 4.03 42.50 4.57
1956 2529 4.324471 GCATGTGCATCACTGGGA 57.676 55.556 0.00 0.00 41.59 4.37
1957 2530 2.104267 GCATGTGCATCACTGGGAG 58.896 57.895 0.00 0.00 41.59 4.30
1958 2531 0.679002 GCATGTGCATCACTGGGAGT 60.679 55.000 0.00 0.00 41.59 3.85
1959 2532 2.879163 GCATGTGCATCACTGGGAGTG 61.879 57.143 0.00 0.00 43.28 3.51
1960 2533 0.694771 ATGTGCATCACTGGGAGTGT 59.305 50.000 3.75 0.00 46.03 3.55
1961 2534 0.035317 TGTGCATCACTGGGAGTGTC 59.965 55.000 3.75 0.00 46.03 3.67
1962 2535 0.674895 GTGCATCACTGGGAGTGTCC 60.675 60.000 3.75 0.00 46.03 4.02
1963 2536 0.837691 TGCATCACTGGGAGTGTCCT 60.838 55.000 3.75 0.00 46.03 3.85
1964 2537 1.195115 GCATCACTGGGAGTGTCCTA 58.805 55.000 3.75 0.00 46.03 2.94
1971 2544 2.427506 CTGGGAGTGTCCTAGTTTTGC 58.572 52.381 0.00 0.00 39.95 3.68
1972 2545 1.771854 TGGGAGTGTCCTAGTTTTGCA 59.228 47.619 0.00 0.00 36.57 4.08
1973 2546 2.375174 TGGGAGTGTCCTAGTTTTGCAT 59.625 45.455 0.00 0.00 36.57 3.96
1974 2547 3.010420 GGGAGTGTCCTAGTTTTGCATC 58.990 50.000 0.00 0.00 36.57 3.91
1975 2548 3.010420 GGAGTGTCCTAGTTTTGCATCC 58.990 50.000 0.00 0.00 32.53 3.51
1976 2549 3.559171 GGAGTGTCCTAGTTTTGCATCCA 60.559 47.826 0.00 0.00 32.53 3.41
1977 2550 3.679389 AGTGTCCTAGTTTTGCATCCAG 58.321 45.455 0.00 0.00 0.00 3.86
1978 2551 3.327757 AGTGTCCTAGTTTTGCATCCAGA 59.672 43.478 0.00 0.00 0.00 3.86
1979 2552 4.018960 AGTGTCCTAGTTTTGCATCCAGAT 60.019 41.667 0.00 0.00 0.00 2.90
1980 2553 4.702131 GTGTCCTAGTTTTGCATCCAGATT 59.298 41.667 0.00 0.00 0.00 2.40
1981 2554 5.183904 GTGTCCTAGTTTTGCATCCAGATTT 59.816 40.000 0.00 0.00 0.00 2.17
1982 2555 5.183713 TGTCCTAGTTTTGCATCCAGATTTG 59.816 40.000 0.00 0.00 0.00 2.32
1983 2556 5.183904 GTCCTAGTTTTGCATCCAGATTTGT 59.816 40.000 0.00 0.00 0.00 2.83
1984 2557 6.374333 GTCCTAGTTTTGCATCCAGATTTGTA 59.626 38.462 0.00 0.00 0.00 2.41
1985 2558 6.374333 TCCTAGTTTTGCATCCAGATTTGTAC 59.626 38.462 0.00 0.00 0.00 2.90
1986 2559 6.375455 CCTAGTTTTGCATCCAGATTTGTACT 59.625 38.462 0.00 0.00 0.00 2.73
1987 2560 7.552687 CCTAGTTTTGCATCCAGATTTGTACTA 59.447 37.037 0.00 0.00 0.00 1.82
1988 2561 7.145932 AGTTTTGCATCCAGATTTGTACTAC 57.854 36.000 0.00 0.00 0.00 2.73
1989 2562 6.714810 AGTTTTGCATCCAGATTTGTACTACA 59.285 34.615 0.00 0.00 0.00 2.74
1990 2563 6.494893 TTTGCATCCAGATTTGTACTACAC 57.505 37.500 0.00 0.00 0.00 2.90
1991 2564 5.420725 TGCATCCAGATTTGTACTACACT 57.579 39.130 0.00 0.00 0.00 3.55
1992 2565 5.178061 TGCATCCAGATTTGTACTACACTG 58.822 41.667 0.00 0.00 0.00 3.66
1993 2566 5.178797 GCATCCAGATTTGTACTACACTGT 58.821 41.667 0.00 0.00 0.00 3.55
1994 2567 6.071051 TGCATCCAGATTTGTACTACACTGTA 60.071 38.462 0.00 0.00 0.00 2.74
1995 2568 6.816640 GCATCCAGATTTGTACTACACTGTAA 59.183 38.462 0.00 0.00 0.00 2.41
1996 2569 7.333423 GCATCCAGATTTGTACTACACTGTAAA 59.667 37.037 0.00 0.00 0.00 2.01
1997 2570 9.214957 CATCCAGATTTGTACTACACTGTAAAA 57.785 33.333 0.00 0.00 0.00 1.52
1998 2571 9.787435 ATCCAGATTTGTACTACACTGTAAAAA 57.213 29.630 0.00 0.00 35.07 1.94
1999 2572 9.268268 TCCAGATTTGTACTACACTGTAAAAAG 57.732 33.333 0.00 0.00 34.36 2.27
2000 2573 8.504005 CCAGATTTGTACTACACTGTAAAAAGG 58.496 37.037 0.00 0.00 34.36 3.11
2001 2574 9.052759 CAGATTTGTACTACACTGTAAAAAGGT 57.947 33.333 0.00 0.00 34.36 3.50
2002 2575 9.052759 AGATTTGTACTACACTGTAAAAAGGTG 57.947 33.333 0.00 0.00 34.36 4.00
2003 2576 8.741603 ATTTGTACTACACTGTAAAAAGGTGT 57.258 30.769 0.00 0.00 44.75 4.16
2004 2577 8.564509 TTTGTACTACACTGTAAAAAGGTGTT 57.435 30.769 3.37 0.00 42.92 3.32
2005 2578 8.564509 TTGTACTACACTGTAAAAAGGTGTTT 57.435 30.769 3.37 0.00 42.92 2.83
2006 2579 8.564509 TGTACTACACTGTAAAAAGGTGTTTT 57.435 30.769 3.37 0.00 42.92 2.43
2007 2580 8.667463 TGTACTACACTGTAAAAAGGTGTTTTC 58.333 33.333 3.37 0.00 42.92 2.29
2008 2581 7.933215 ACTACACTGTAAAAAGGTGTTTTCT 57.067 32.000 3.37 0.00 42.92 2.52
2010 2583 9.452287 ACTACACTGTAAAAAGGTGTTTTCTAA 57.548 29.630 3.37 0.00 42.92 2.10
2269 2848 8.547069 CAATAAACATTCAAACCGTTTCACAAT 58.453 29.630 0.00 0.00 34.78 2.71
2333 2912 2.318578 CAAAGTGCCAACATAGCAACG 58.681 47.619 0.00 0.00 43.02 4.10
2429 3008 3.687698 TCCTAGCAGATTTTACGCAAACC 59.312 43.478 0.00 0.00 0.00 3.27
2452 3031 0.950836 TGGTGTTGAGGCGAACAATG 59.049 50.000 6.69 0.00 37.58 2.82
2458 3037 3.496884 TGTTGAGGCGAACAATGTACTTC 59.503 43.478 3.05 0.00 32.84 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 180 3.745799 TGACTTATCCGAGCAACCAAAA 58.254 40.909 0.00 0.00 0.00 2.44
218 220 9.610705 AGTCGTACTTTACATTATAGACAGAGA 57.389 33.333 0.00 0.00 0.00 3.10
219 221 9.653067 CAGTCGTACTTTACATTATAGACAGAG 57.347 37.037 0.00 0.00 0.00 3.35
220 222 9.387257 TCAGTCGTACTTTACATTATAGACAGA 57.613 33.333 0.00 0.00 0.00 3.41
227 229 9.229784 CGTTGTATCAGTCGTACTTTACATTAT 57.770 33.333 0.00 0.00 29.59 1.28
230 232 6.744537 GTCGTTGTATCAGTCGTACTTTACAT 59.255 38.462 0.00 0.00 29.59 2.29
232 234 6.310197 AGTCGTTGTATCAGTCGTACTTTAC 58.690 40.000 0.00 0.00 0.00 2.01
245 247 4.837567 ACGGACGTATTAGTCGTTGTATC 58.162 43.478 0.00 0.00 41.64 2.24
246 248 4.332543 TGACGGACGTATTAGTCGTTGTAT 59.667 41.667 0.00 0.00 41.64 2.29
250 252 3.829886 TTGACGGACGTATTAGTCGTT 57.170 42.857 0.00 0.00 41.64 3.85
276 278 8.536175 TCAATTATGTCATACACCACTTCTACA 58.464 33.333 0.00 0.00 0.00 2.74
289 291 7.595130 CGAGATTCCGAGTTCAATTATGTCATA 59.405 37.037 0.00 0.00 0.00 2.15
349 835 1.149288 AGGAGGATAACCATCGGCCTA 59.851 52.381 0.00 0.00 35.05 3.93
457 951 5.220080 GCATCACGCACTTGAACAAATTATG 60.220 40.000 0.00 0.00 41.79 1.90
471 965 5.409643 AAATTAGACATAGCATCACGCAC 57.590 39.130 0.00 0.00 46.13 5.34
474 968 6.219473 AGAGGAAATTAGACATAGCATCACG 58.781 40.000 0.00 0.00 0.00 4.35
475 969 8.144478 TGTAGAGGAAATTAGACATAGCATCAC 58.856 37.037 0.00 0.00 0.00 3.06
480 974 7.671302 TCCATGTAGAGGAAATTAGACATAGC 58.329 38.462 0.00 0.00 30.71 2.97
556 1059 2.550855 GGTCAACATGAGCAAGACCTCA 60.551 50.000 0.00 0.00 43.79 3.86
558 1061 2.191128 GGTCAACATGAGCAAGACCT 57.809 50.000 0.00 0.00 43.79 3.85
561 1064 5.016831 TCTACTAGGTCAACATGAGCAAGA 58.983 41.667 11.61 6.21 46.52 3.02
659 1162 2.024918 CCACACGGCTTGATATGGC 58.975 57.895 0.00 0.00 0.00 4.40
684 1187 2.921754 GGTTCCAATACTTCGTCACTCG 59.078 50.000 0.00 0.00 41.41 4.18
719 1222 3.754965 TGGAACTTGAAAGTGGATCCTG 58.245 45.455 14.23 0.00 39.66 3.86
756 1259 1.219393 GTAGGCAGGTCAGTGGAGC 59.781 63.158 0.00 0.00 41.86 4.70
836 1348 3.452474 CTGGCTTATATAGAGATGGCGC 58.548 50.000 0.00 0.00 0.00 6.53
838 1350 3.131223 TCGCTGGCTTATATAGAGATGGC 59.869 47.826 0.00 0.00 0.00 4.40
886 1398 3.787001 GGGGGAGGAAGCGTGGAG 61.787 72.222 0.00 0.00 0.00 3.86
920 1433 1.593750 GCTGGCTGGCTAGTCGATG 60.594 63.158 7.70 0.00 0.00 3.84
1046 1582 1.803519 GAGTTGAGCGAGTCCTGCG 60.804 63.158 0.00 0.00 37.44 5.18
1554 2090 2.039418 ACACTTTTCCCTTGGCCTTTC 58.961 47.619 3.32 0.00 0.00 2.62
1606 2146 4.338379 AGGTAAATAAGAAGCTAGCCGG 57.662 45.455 12.13 0.00 0.00 6.13
1610 2150 9.103861 CCAAGAGAAAGGTAAATAAGAAGCTAG 57.896 37.037 0.00 0.00 0.00 3.42
1666 2206 2.145397 TCCAGAGTAGCCACACCTAG 57.855 55.000 0.00 0.00 0.00 3.02
1795 2335 0.960364 TCGCATTCCCAGTTCAAGCC 60.960 55.000 0.00 0.00 0.00 4.35
1812 2352 5.432885 ACCAGAAAGTACAACCAAATTCG 57.567 39.130 0.00 0.00 0.00 3.34
1821 2391 4.448210 GGAGACACAACCAGAAAGTACAA 58.552 43.478 0.00 0.00 0.00 2.41
1822 2392 3.181458 GGGAGACACAACCAGAAAGTACA 60.181 47.826 0.00 0.00 0.00 2.90
1823 2393 3.400255 GGGAGACACAACCAGAAAGTAC 58.600 50.000 0.00 0.00 0.00 2.73
1826 2396 1.512926 CGGGAGACACAACCAGAAAG 58.487 55.000 0.00 0.00 0.00 2.62
1827 2397 0.107831 CCGGGAGACACAACCAGAAA 59.892 55.000 0.00 0.00 0.00 2.52
1828 2398 1.052124 ACCGGGAGACACAACCAGAA 61.052 55.000 6.32 0.00 0.00 3.02
1829 2399 1.052124 AACCGGGAGACACAACCAGA 61.052 55.000 6.32 0.00 0.00 3.86
1830 2400 0.884704 CAACCGGGAGACACAACCAG 60.885 60.000 6.32 0.00 0.00 4.00
1831 2401 1.147376 CAACCGGGAGACACAACCA 59.853 57.895 6.32 0.00 0.00 3.67
1832 2402 1.599797 CCAACCGGGAGACACAACC 60.600 63.158 6.32 0.00 40.01 3.77
1833 2403 1.448497 TCCAACCGGGAGACACAAC 59.552 57.895 6.32 0.00 42.15 3.32
1834 2404 3.973458 TCCAACCGGGAGACACAA 58.027 55.556 6.32 0.00 42.15 3.33
1841 2411 0.178897 TTCCCTAGTTCCAACCGGGA 60.179 55.000 6.32 11.34 46.61 5.14
1842 2412 0.916809 ATTCCCTAGTTCCAACCGGG 59.083 55.000 6.32 7.73 39.95 5.73
1843 2413 2.365582 CAATTCCCTAGTTCCAACCGG 58.634 52.381 0.00 0.00 0.00 5.28
1844 2414 2.365582 CCAATTCCCTAGTTCCAACCG 58.634 52.381 0.00 0.00 0.00 4.44
1845 2415 2.100197 GCCAATTCCCTAGTTCCAACC 58.900 52.381 0.00 0.00 0.00 3.77
1846 2416 2.802719 TGCCAATTCCCTAGTTCCAAC 58.197 47.619 0.00 0.00 0.00 3.77
1847 2417 3.756082 ATGCCAATTCCCTAGTTCCAA 57.244 42.857 0.00 0.00 0.00 3.53
1848 2418 4.476846 TCTTATGCCAATTCCCTAGTTCCA 59.523 41.667 0.00 0.00 0.00 3.53
1849 2419 5.048846 TCTTATGCCAATTCCCTAGTTCC 57.951 43.478 0.00 0.00 0.00 3.62
1850 2420 7.588497 AATTCTTATGCCAATTCCCTAGTTC 57.412 36.000 0.00 0.00 0.00 3.01
1851 2421 7.633553 GCAAATTCTTATGCCAATTCCCTAGTT 60.634 37.037 0.00 0.00 36.56 2.24
1852 2422 6.183360 GCAAATTCTTATGCCAATTCCCTAGT 60.183 38.462 0.00 0.00 36.56 2.57
1853 2423 6.041296 AGCAAATTCTTATGCCAATTCCCTAG 59.959 38.462 0.00 0.00 43.57 3.02
1854 2424 5.898972 AGCAAATTCTTATGCCAATTCCCTA 59.101 36.000 0.00 0.00 43.57 3.53
1855 2425 4.718276 AGCAAATTCTTATGCCAATTCCCT 59.282 37.500 0.00 0.00 43.57 4.20
1856 2426 5.027293 AGCAAATTCTTATGCCAATTCCC 57.973 39.130 0.00 0.00 43.57 3.97
1861 2431 7.225784 TGTCTTTAGCAAATTCTTATGCCAA 57.774 32.000 0.00 0.00 43.57 4.52
1887 2458 4.622701 ACTACGGACCGTTTCAGTATAC 57.377 45.455 27.06 0.00 41.54 1.47
1898 2469 3.118542 GCCAAAGTTATACTACGGACCG 58.881 50.000 13.61 13.61 0.00 4.79
1899 2470 3.118542 CGCCAAAGTTATACTACGGACC 58.881 50.000 0.00 0.00 0.00 4.46
1900 2471 4.032703 TCGCCAAAGTTATACTACGGAC 57.967 45.455 0.00 0.00 0.00 4.79
1901 2472 4.717233 TTCGCCAAAGTTATACTACGGA 57.283 40.909 0.00 0.00 0.00 4.69
1904 2475 5.574443 ACGAGTTTCGCCAAAGTTATACTAC 59.426 40.000 0.00 0.00 45.12 2.73
1905 2476 5.574055 CACGAGTTTCGCCAAAGTTATACTA 59.426 40.000 0.00 0.00 45.12 1.82
1926 2499 2.102438 ACATGCACGCTCATCCACG 61.102 57.895 0.00 0.00 0.00 4.94
1939 2512 0.679002 ACTCCCAGTGATGCACATGC 60.679 55.000 0.00 0.00 36.74 4.06
1940 2513 3.564262 ACTCCCAGTGATGCACATG 57.436 52.632 0.00 0.00 36.74 3.21
1950 2523 2.224548 GCAAAACTAGGACACTCCCAGT 60.225 50.000 0.00 0.00 37.19 4.00
1951 2524 2.224523 TGCAAAACTAGGACACTCCCAG 60.225 50.000 0.00 0.00 37.19 4.45
1952 2525 1.771854 TGCAAAACTAGGACACTCCCA 59.228 47.619 0.00 0.00 37.19 4.37
1953 2526 2.561478 TGCAAAACTAGGACACTCCC 57.439 50.000 0.00 0.00 37.19 4.30
1954 2527 3.010420 GGATGCAAAACTAGGACACTCC 58.990 50.000 0.00 0.00 36.58 3.85
1955 2528 3.674997 TGGATGCAAAACTAGGACACTC 58.325 45.455 0.00 0.00 0.00 3.51
1956 2529 3.327757 TCTGGATGCAAAACTAGGACACT 59.672 43.478 0.00 0.00 0.00 3.55
1957 2530 3.674997 TCTGGATGCAAAACTAGGACAC 58.325 45.455 0.00 0.00 0.00 3.67
1958 2531 4.574674 ATCTGGATGCAAAACTAGGACA 57.425 40.909 0.00 0.00 0.00 4.02
1959 2532 5.183904 ACAAATCTGGATGCAAAACTAGGAC 59.816 40.000 0.00 0.00 0.00 3.85
1960 2533 5.324409 ACAAATCTGGATGCAAAACTAGGA 58.676 37.500 0.00 0.00 0.00 2.94
1961 2534 5.649782 ACAAATCTGGATGCAAAACTAGG 57.350 39.130 0.00 0.00 0.00 3.02
1962 2535 7.383102 AGTACAAATCTGGATGCAAAACTAG 57.617 36.000 0.00 0.00 0.00 2.57
1963 2536 7.880713 TGTAGTACAAATCTGGATGCAAAACTA 59.119 33.333 0.00 0.00 0.00 2.24
1964 2537 6.714810 TGTAGTACAAATCTGGATGCAAAACT 59.285 34.615 0.00 0.00 0.00 2.66
1965 2538 6.801862 GTGTAGTACAAATCTGGATGCAAAAC 59.198 38.462 4.11 0.00 0.00 2.43
1966 2539 6.714810 AGTGTAGTACAAATCTGGATGCAAAA 59.285 34.615 4.11 0.00 0.00 2.44
1967 2540 6.149308 CAGTGTAGTACAAATCTGGATGCAAA 59.851 38.462 4.11 0.00 0.00 3.68
1968 2541 5.643348 CAGTGTAGTACAAATCTGGATGCAA 59.357 40.000 4.11 0.00 0.00 4.08
1969 2542 5.178061 CAGTGTAGTACAAATCTGGATGCA 58.822 41.667 4.11 0.00 0.00 3.96
1970 2543 5.178797 ACAGTGTAGTACAAATCTGGATGC 58.821 41.667 18.48 0.00 27.76 3.91
1971 2544 8.771920 TTTACAGTGTAGTACAAATCTGGATG 57.228 34.615 18.48 6.47 27.76 3.51
1972 2545 9.787435 TTTTTACAGTGTAGTACAAATCTGGAT 57.213 29.630 18.48 6.22 27.76 3.41
1973 2546 9.268268 CTTTTTACAGTGTAGTACAAATCTGGA 57.732 33.333 18.48 10.87 27.76 3.86
1974 2547 8.504005 CCTTTTTACAGTGTAGTACAAATCTGG 58.496 37.037 18.48 5.43 27.76 3.86
1975 2548 9.052759 ACCTTTTTACAGTGTAGTACAAATCTG 57.947 33.333 14.65 14.65 0.00 2.90
1976 2549 9.052759 CACCTTTTTACAGTGTAGTACAAATCT 57.947 33.333 4.11 0.00 0.00 2.40
1977 2550 8.833493 ACACCTTTTTACAGTGTAGTACAAATC 58.167 33.333 4.11 0.00 42.71 2.17
1978 2551 8.741603 ACACCTTTTTACAGTGTAGTACAAAT 57.258 30.769 4.11 0.00 42.71 2.32
1979 2552 8.564509 AACACCTTTTTACAGTGTAGTACAAA 57.435 30.769 4.11 0.00 43.69 2.83
1980 2553 8.564509 AAACACCTTTTTACAGTGTAGTACAA 57.435 30.769 4.11 0.00 43.69 2.41
1981 2554 8.564509 AAAACACCTTTTTACAGTGTAGTACA 57.435 30.769 2.68 0.00 43.69 2.90
1982 2555 8.886719 AGAAAACACCTTTTTACAGTGTAGTAC 58.113 33.333 2.68 0.00 43.69 2.73
1984 2557 7.933215 AGAAAACACCTTTTTACAGTGTAGT 57.067 32.000 2.68 0.00 43.69 2.73
2110 2683 1.092348 ACACGAGTACTGCGCTATGA 58.908 50.000 9.73 0.00 0.00 2.15
2191 2770 6.428083 GGAGAAACCCCCATCTTTTAAAAA 57.572 37.500 1.66 0.00 0.00 1.94
2212 2791 4.380843 TTGATAAAAGTTGAGGCTGGGA 57.619 40.909 0.00 0.00 0.00 4.37
2269 2848 1.835494 ACTCTAGTTGTAGCCGAGCA 58.165 50.000 0.00 0.00 0.00 4.26
2333 2912 4.094887 GTGGATGATGTGTTATGTGTGACC 59.905 45.833 0.00 0.00 0.00 4.02
2429 3008 0.307760 GTTCGCCTCAACACCAACTG 59.692 55.000 0.00 0.00 0.00 3.16
2452 3031 3.865745 CCACGGATGATCAACAGAAGTAC 59.134 47.826 9.96 0.00 0.00 2.73
2458 3037 1.600957 GATGCCACGGATGATCAACAG 59.399 52.381 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.