Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

Liu, Zhandong; Venkatesh, Santosh S; Maley, Carlo C

doi:10.1186/1471-2164-9-509

BMC Genomics

Table 2 Ultra-frequent n-mers in the human genome

From: Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

5-mer	Freq	6-mer	Freq	7-mer	Freq	8-mer	Freq
AAAAA	38,658,471	AAAAAA	19,638,479	AAAAAAA	12,559,969	AAAAAAAA	9,155,123
ATTTT	23,349,997	AAAAAT	9,299,025	AAATAAA	3,521,836	ATATATAT	1,863,212
TATTT	19,344,297	TATTTT	8,283,181	AAAAAAT	3,335,157	TGTGTGTG	1,701,426
AGAAA	18,271,461	AAATAA	7,271,302	AAAGAAA	3,255,464	TTTTAAAA	1,574,448
AAATT	16,119,174	AGAAAA	7,027,241	TTTTAAA	3,218,950	AAAATAAA	1,562,386
TTATT	15,608,707	TTTATT	7,015,408	TTATTTT	3,132,222	AAAGAAAA	1,467,003
TTTTC	15,579,017	TTTTAA	6,910,624	ATATATA	3,034,879	AAAAGAAA	1,444,255
CAAAA	15,364,161	TTTCTT	6,890,187	TTAAAAA	2,961,520	AAAAATTA	1,392,585
TTCTT	15,093,160	TTTAAA	6,820,966	TTTTCTT	2,913,461	TAAAAATA	1,363,753
TCTTT	15,053,533	AAAATT	6,559,595	TTTTATT	2,814,631	CCAGCCTG	1,308,899
CTTTT	14,643,705	TTCTTT	6,476,513	TAAAAAT	2,811,575	CAGCCTGG	1,266,975
CATTT	13,897,384	ATAAAA	6,284,494	AAAAATT	2,773,210	CTTTTTTT	1,238,232
AAACA	13,686,083	TTTTTG	5,979,892	TTCTTTT	2,693,599	AAAAAGAA	1,228,463
TTTGT	13,634,981	ATTTTA	5,829,423	AGAAAAA	2,614,232	CAAAAAAA	1,223,343
TAAAT	13,334,177	AAATAT	5,784,598	AAAATTA	2,572,747	AAAACAAA	1,216,247
ATATA	13,333,472	AAAAGA	5,708,574	ACAAAAA	2,554,220	TTTTTCTT	1,175,794
TGAAA	13,099,712	TTTTGT	5,622,008	TTTGTTT	2,514,354	ATTTATTT	1,171,982
ATATT	13,067,844	TATATA	5,551,066	TGTGTGT	2,500,827	TTTTGTTT	1,155,387
AAAAC	12,161,846	TGTTTT	5,550,449	TTTTTTA	2,460,695	TTAAAAAA	1,145,762
AGAGA	12,078,839	CTTTTT	5,515,339	TTTTTTG	2,436,880	AAAAAATA	1,143,587
9-mer	Freq	10-mer	Freq			11-mer	Freq
AAAAAAAAA	7,276,886	AAAAAAAAAA	5,952,617			AAAAAAAAAAA	4,945,619
TGTGTGTGT	1,424,846	TGTGTGTGTG	1,168,929			TGTGTGTGTGT	1,067,659
ATATATATA	1,253,711	ATATATATAT	967,302			CTGTAATCCCA	804,201
CCAGGCTGG	1,043,029	TGTAATCCCA	857,278			ATATATATATA	785,762
CTGGGATTA	921,482	GCTGGGATTA	840,776			TGTAATCCCAG	782,505
CCTGTAATC	917,990	GGATTACAGG	835,847			CCTGTAATCCC	762,833
GGATTACAG	916,302	CTGTAATCCC	826,256			GTAATCCCAGC	744,961
GAGGCTGAG	911,055	GGAGGCTGAG	810,203			CCTCAGCCTCC	729,303
GCTGGGATT	899,822	CTGGGATTAC	802,982			GAGGCTGAGGC	602,716
TGTAATCCC	897,744	CCTCAGCCTC	795,109			GCCTGTAATCC	579,838
GGAGGCTGA	891,406	AGGCTGAGGC	644,447			AAAATACAAAA	564,984
GTAATCCCA	887,639	CCAGCCTGGG	644,416			CCTCCCAAAGT	561,106
AGGCTGAGG	881,036	GCCTGTAATC	629,425			GGGAGGCTGAG	556,004
TTGGGAGGC	847,581	AAAAAAAAAG	626,192			AGGCTGAGGCA	555,758
CTTTTTTTT	794,742	TTTGTATTTT	619,817			CACTTTGGGAG	554,429
TTTTATTTT	780,751	TTTGGGAGGC	619,461			CTTTGGGAGGC	553,151
CAAAAAAAA	758,731	AAATACAAAA	611,794			AGTAGCTGGGA	546,426
AAAAAAAAT	741,719	CAAAAAAAAA	602,719			AAAAATACAAA	542,436
AAATACAAA	740,229	ACTTTGGGAG	600,711			CAGGCTGGAGT	536,630
CCCAGGCTG	740,090	TCAGCCTCCC	600,206			TCCCAAAGTGC	534,617
12-mer	Freq	13-mer	Freq			14-mer	Freq
AAAAAAAAAAAA	4,144,156	AAAAAAAAAAAAA	3,468,084			AAAAAAAAAAAAAA	2,889,704
TGTGTGTGTGTG	928,266	TGTGTGTGTGTGT	867,556			GTGTGTGTGTGTGT	775,928
TGGGATTACAGG	744,980	CTGTAATCCCAGC	687,709			CCTGTAATCCCAGC	639,010
CTGGGATTACAG	737,944	CTGGGATTACAGG	684,576			ATATATATATATAT	503,574
GCTGGGATTACA	727,608	ATATATATATATA	571,291			CTGGGATTACAGGC	478,945
ATATATATATAT	664,692	GCCTGTAATCCCA	520,611			AGCACTTTGGGAGG	459,948
GGAGGCTGAGGC	562,149	GCCTCCCAAAGTG	493,408			GCACTTTGGGAGGC	448,768
GCCTGTAATCCC	532,230	GGAGGCTGAGGCA	489,998			AAGTGCTGGGATTA	448,388
GCCTCCCAAAGT	527,552	CTCCCAAAGTGCT	486,025			AAAGTGCTGGGATT	445,915
TGCCTCAGCCTC	523,666	GCACTTTGGGAGG	474,289			CTCCCAAAGTGCTG	443,681
CCTCCCAAAGTG	522,504	CAGCACTTTGGGA	471,479			GGAGGCTGAGGCAG	437,319
TCCCAAAGTGCT	517,353	AGTGCTGGGATTA	468,425			CAAAGTGCTGGGAT	436,625
AAAAATACAAAA	513,200	TGCACTCCAGCCT	466,972			CAGGCTGGAGTGCA	436,504
GGGAGGCTGAGG	507,919	GAGGCTGAGGCAG	465,893			CCAGCACTTTGGGA	434,713
GCACTTTGGGAG	501,469	AAGTGCTGGGATT	464,827			TGCTGGGATTACAG	428,229
CCAGGCTGGAGT	499,800	ATCCCAGCACTTT	460,277			CCAGGCTGGAGTGC	425,904
AGGCTGAGGCAG	492,943	GCACTCCAGCCTG	454,751			CCTGCCTCAGCCTC	423,801
AGGCTGGAGTGC	486,794	TGTAATCCCAGCA	453,696			TCCCAGCACTTTGG	423,684
AGTGCTGGGATT	486,236	CCAGGCTGGAGTG	453,312			TGTAATCCCAGCAC	417,426
CAGGCTGGAGTG	484,927	TCCCAGCACTTTG	448,301			AGTGCTGGGATTAC	416,557
15-mer	Freq	16-mer	Freq			17-mer	Freq
AAAAAAAAAAAAAAA	2,397,399	AAAAAAAAAAAAAAAA	1,981,757			AAAAAAAAAAAAAAAAA	1,634,441
TGTGTGTGTGTGTGT	729,915	TGTGTGTGTGTGTGTG	662,157			TGTGTGTGTGTGTGTGT	624,344
GCCTGTAATCCCAGC	448,640	TAATCCCAGCACTTTG	408,698			TAATCCCAGCACTTTGG	386,886
ATATATATATATATA	446,009	ATATATATATATATAT	402,936			ATCCCAGCACTTTGGGA	385,642
AGCACTTTGGGAGGC	435,271	CCAAAGTGCTGGGATT	400,385			AATCCCAGCACTTTGGG	381,085
TAATCCCAGCACTTT	430,431	GCCTCCCAAAGTGCTG	398,210			AAAGTGCTGGGATTACA	375,216
CAAAGTGCTGGGATT	423,190	TCCCAGCACTTTGGGA	395,536			CTCCCAAAGTGCTGGGA	373,151
CCTCCCAAAGTGCTG	420,378	CCCAAAGTGCTGGGAT	392,938			AAGTGCTGGGATTACAG	369,056
ATCCCAGCACTTTGG	412,897	TGTAATCCCAGCACTT	390,400			GCCTCCCAAAGTGCTGG	368,350
CCAGCACTTTGGGAG	409,630	CCTCCCAAAGTGCTGG	388,489			CAAAGTGCTGGGATTAC	364,621
CCAGGCTGGAGTGCA	409,063	CTGTAATCCCAGCACT	385,038			CCCAGCACTTTGGGAGG	363,569
TGTAATCCCAGCACT	407,346	AAAGTGCTGGGATTAC	383,514			ATATATATATATATATA	363,206
CCCAGCACTTTGGGA	406,238	CCCAGCACTTTGGGAG	383,068			AGTGCTGGGATTACAGG	358,629
TCCCAGCACTTTGGG	403,080	GTGCTGGGATTACAGG	367,247			TCTACTAAAAATACAAA	340,685
AAGTGCTGGGATTAC	399,124	TGCACTCCAGCCTGGG	361,996			CTACTAAAAATACAAAA	340,602
CCTGCCTCAGCCTCC	398,260	TACTAAAAATACAAAA	360,995			CTCCTGCCTCAGCCTCC	328,239
TGCTGGGATTACAGG	398,070	GAGGCTGAGGCAGGAG	349,118			TTGTATTTTTAGTAGAG	325,500
GTGCTGGGATTACAG	394,430	CTACTAAAAATACAAA	348,511			TTCTCCTGCCTCAGCCT	324,096
GCACTCCAGCCTGGG	376,640	TCCTGCCTCAGCCTCC	346,669			TCTCTACTAAAAATACA	319,930
TTTTGTATTTTTAGT	374,747	TTGTATTTTTAGTAGA	346,193			GGCTGAGGCAGGAGAAT	318,655
18-mer	Freq	19-mer	Freq			20-mer	Freq
AAAAAAAAAAAAAAAAAA	1,345,821	AAAAAAAAAAAAAAAAAAA	1,104,496			AAAAAAAAAAAAAAAAAAAA	901,140
GTGTGTGTGTGTGTGTGT	569,504	TGTGTGTGTGTGTGTGTGT	536,547			TGTGTGTGTGTGTGTGTGTG	489,597
TCCCAAAGTGCTGGGATT	374,035	TAATCCCAGCACTTTGGGA	361,679			CTCCCAAAGTGCTGGGATTA	341,542
TAATCCCAGCACTTTGGG	368,428	AATCCCAGCACTTTGGGAG	353,065			AATCCCAGCACTTTGGGAGG	335,334
ATCCCAGCACTTTGGGAG	363,933	ATCCCAGCACTTTGGGAGG	345,608			GCCTCCCAAAGTGCTGGGAT	328,159
TGTAATCCCAGCACTTTG	356,809	TGTAATCCCAGCACTTTGG	338,285			GTAATCCCAGCACTTTGGGA	323,542
CTGTAATCCCAGCACTTT	354,805	CAAAGTGCTGGGATTACAG	337,559			CCCAAAGTGCTGGGATTACA	322,532
TCCCAGCACTTTGGGAGG	354,247	GCCTCCCAAAGTGCTGGGA	336,291			CTGTAATCCCAGCACTTTGG	320,216
GTAATCCCAGCACTTTGG	345,648	CCTGTAATCCCAGCACTTT	330,885			CAAAGTGCTGGGATTACAGG	315,005
CCCAGCACTTTGGGAGGC	345,007	CCCAAAGTGCTGGGATTAC	329,491			TTTTGTATTTTTAGTAGAGA	300,256
CCTGTAATCCCAGCACTT	343,923	CTCTACTAAAAATACAAAA	313,148			ATTCTCCTGCCTCAGCCTCC	280,115
TTTTGTATTTTTAGTAGA	333,004	TCTCTACTAAAAATACAAA	307,152			ATATATATATATATATATAT	279,576
ATATATATATATATATAT	332,710	ATATATATATATATATATA	302,986			TTTTTGTATTTTTAGTAGAG	272,798
TTTGTATTTTTAGTAGAG	320,328	GAGGCTGAGGCAGGAGAAT	296,297			CCACTGCACTCCAGCCTGGG	239,735
TCTCTACTAAAAATACAA	312,108	GGAGGCTGAGGCAGGAGAA	291,488			GCCTGTAATCCCAGCACTTT	238,538
AGGCTGAGGCAGGAGAAT	311,358	TTTTTGTATTTTTAGTAGA	290,073			GGCCTCCCAAAGTGCTGGGA	224,951
GAGGCTGAGGCAGGAGAA	308,372	CCAGGCTGGAGTGCAGTGG	273,189			GTCTCTACTAAAAATACAAA	195,075
TCTCCTGCCTCAGCCTCC	298,682	CACTGCACTCCAGCCTGGG	256,220			TTCTCCTGCCTCAGCCTCCC	191,155
TTTTTGTATTTTTAGTAG	296,585	GCCTGTAATCCCAGCACTT	247,562			GCCACTGCACTCCAGCCTGG	183,392
CCAGGCTGGAGTGCAGTG	292,150	GGCCTCCCAAAGTGCTGGG	230,427			TTTTTTTTTTTTTTTTGAGA	167,522

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ISSN: 1471-2164

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