genome.fa.s6.2.7.7.80.10.50.1000.113.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   

This is table  113  of  168  ( 20060 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33073253--33073311	29	2.0	29	81	12	68	25	5	3	66	1.28
33073668--33073724	22	2.6	22	91	0	96	35	19	33	12	1.89
33076043--33076094	24	2.2	24	89	0	77	38	1	9	50	1.46
33085046--33085148	51	2.0	51	92	3	172	38	2	26	32	1.71
33089044--33089241	99	2.0	99	100	0	396	24	17	27	31	1.97
33090213--33090298	32	2.6	32	90	7	129	60	0	2	37	1.10
33090200--33090284	11	7.6	11	75	16	68	62	0	2	35	1.08
33098707--33098811	21	5.1	20	74	14	70	46	17	20	16	1.84
33098712--33098811	42	2.4	42	77	3	103	47	17	19	17	1.84
33098724--33098825	42	2.4	42	81	3	107	43	15	22	18	1.88
33099433--33099466	17	2.0	17	88	0	50	61	5	2	29	1.34
33105676--33105708	15	2.1	16	88	5	50	27	3	0	69	1.03
33106030--33106379	125	2.8	125	86	3	519	29	16	22	32	1.95
33109295--33109512	116	1.9	116	97	0	409	42	9	8	39	1.68
33109514--33110113	50	12.0	50	69	18	301	27	2	25	44	1.67
33109599--33109674	29	2.6	29	87	4	109	23	1	27	47	1.60
33109566--33109639	35	2.1	36	84	2	96	27	2	31	39	1.70
33109519--33109726	111	1.8	113	89	3	330	25	2	27	44	1.68
33109759--33110002	23	10.4	23	76	15	232	27	2	24	45	1.66
33109757--33109849	49	2.0	46	86	12	129	30	2	24	43	1.66
33109683--33109944	72	3.5	72	80	11	239	29	3	24	43	1.70
33109826--33110002	90	1.9	92	89	5	277	27	2	24	45	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33110519--33110553	18	1.9	18	94	0	61	34	8	31	25	1.86
33111225--33111307	41	2.0	41	100	0	166	36	9	14	39	1.79
33112984--33113035	24	2.2	24	85	0	68	34	5	7	51	1.54
33117612--33117659	18	2.8	18	81	6	55	58	0	2	39	1.10
33119798--33119831	17	2.0	17	88	0	50	0	11	2	85	0.71
33120981--33121253	87	3.1	87	85	2	343	25	19	17	37	1.93
33133270--33133297	3	9.3	3	100	0	56	67	0	0	32	0.91
33135846--33135885	21	1.9	21	89	0	62	22	10	2	65	1.35
33136557--33136848	154	1.9	154	87	2	435	31	25	18	24	1.98
33137480--33137538	31	2.0	30	83	12	77	49	13	10	27	1.74
33140041--33140072	7	4.6	7	96	0	55	40	9	31	18	1.83
33139997--33140320	58	6.1	58	75	19	328	33	14	23	29	1.94
33140048--33140321	51	5.4	51	88	0	388	33	14	23	29	1.94
33140016--33140320	102	2.9	102	86	3	387	32	15	22	29	1.94
33142849--33143024	43	4.0	43	76	7	174	36	15	18	28	1.92
33142895--33143153	90	2.9	88	82	5	306	33	16	21	27	1.95
33142849--33143840	44	21.9	44	72	9	535	33	16	20	29	1.94
33143269--33143433	86	1.9	88	84	2	226	29	16	23	30	1.96
33143394--33143692	89	3.3	88	78	3	238	32	16	19	30	1.94
33142849--33143840	139	7.3	138	73	9	483	33	16	20	29	1.94
33143618--33143870	139	1.8	139	80	5	305	35	16	18	30	1.93
33144113--33144160	25	2.0	23	88	11	71	50	29	4	16	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33145460--33145507	13	3.8	13	81	13	64	27	6	0	66	1.15
33145467--33145517	21	2.4	21	81	12	68	25	3	1	68	1.17
33145460--33145507	25	1.9	25	87	8	71	27	6	0	66	1.15
33149881--33150182	162	1.9	159	86	3	435	23	9	18	47	1.78
33152443--33152483	20	2.1	20	86	4	57	70	2	2	24	1.11
33153695--33153736	22	2.0	21	90	4	66	26	9	7	57	1.56
33156871--33156950	27	3.0	27	88	0	124	35	40	11	13	1.81
33156955--33157070	24	4.8	24	89	0	124	25	46	13	14	1.81
33156955--33157085	48	2.7	48	84	0	145	27	45	14	12	1.82
33157015--33157085	24	3.0	24	97	0	133	35	42	12	9	1.76
33159868--33159910	16	2.7	16	77	0	50	20	13	20	44	1.86
33162863--33162930	22	3.3	21	78	10	68	48	0	0	51	1.00
33162885--33162937	18	2.9	17	78	15	61	41	0	0	58	0.98
33162919--33162960	13	2.9	14	80	13	50	54	0	0	45	0.99
33162923--33162959	16	2.3	16	86	13	58	59	0	0	40	0.97
33163338--33163372	16	2.2	16	94	0	61	71	0	2	25	1.00
33163512--33163547	14	2.6	14	95	0	63	33	22	0	44	1.53
33172565--33172618	19	2.8	19	94	0	99	37	11	14	37	1.82
33172565--33172649	19	4.1	21	86	4	88	41	8	12	37	1.74
33172867--33172911	23	2.0	23	81	0	54	22	0	15	62	1.33
33175595--33175625	12	2.6	12	100	0	62	45	0	25	29	1.54
33177172--33177206	18	2.0	17	88	5	52	45	0	0	54	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33177452--33177508	16	3.6	16	90	0	78	33	31	0	35	1.58
33189519--33189600	22	3.7	22	86	0	119	29	25	14	30	1.95
33191612--33191726	23	5.0	23	93	0	176	45	4	28	21	1.71
33192167--33192215	18	2.6	18	83	6	53	38	18	18	24	1.93
33192970--33193049	27	3.0	27	100	0	160	21	11	7	60	1.55
33193155--33193187	8	4.1	8	96	0	57	57	0	0	42	0.98
33193393--33193428	17	2.1	17	100	0	72	36	5	5	52	1.48
33195638--33195696	24	2.5	24	94	0	100	42	0	27	30	1.56
33195746--33195843	17	5.4	17	64	13	52	33	4	12	50	1.59
33195737--33195845	37	3.0	37	91	1	175	33	5	12	47	1.65
33195850--33196013	9	17.6	9	83	7	202	21	7	33	36	1.83
33195853--33196014	29	5.8	28	88	5	204	20	8	33	37	1.82
33200160--33200254	23	4.1	23	88	0	136	45	4	28	22	1.71
33204807--33204832	12	2.2	12	100	0	52	7	15	30	46	1.74
33204848--33204933	39	2.2	41	85	6	115	34	19	23	22	1.96
33204965--33205246	41	6.9	41	90	0	420	25	21	23	30	1.99
33205723--33205896	82	2.1	82	83	1	222	25	2	25	46	1.64
33205747--33205908	82	2.0	82	88	2	245	25	2	27	44	1.67
33206966--33207052	41	2.1	41	97	0	165	27	16	18	37	1.92
33210655--33210820	43	3.9	43	93	2	264	23	18	27	30	1.98
33223757--33223805	3	16.7	3	95	4	91	32	0	0	67	0.91
33248141--33248193	25	2.2	24	89	3	79	22	24	16	35	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33248158--33248222	25	2.6	25	82	0	67	23	21	21	33	1.97
33251312--33251346	16	2.2	16	100	0	70	37	20	5	37	1.76
33251822--33251878	22	2.6	23	83	8	73	43	19	22	14	1.86
33252851--33252893	5	8.6	5	100	0	86	60	0	0	39	0.97
33252851--33252936	10	8.0	10	74	14	55	51	2	1	45	1.21
33258881--33258922	15	2.8	15	78	10	50	33	2	0	64	1.07
33269208--33269270	28	2.2	30	88	5	94	25	20	7	46	1.78
33269217--33269294	28	2.7	28	82	9	77	29	23	5	42	1.75
33269252--33269330	30	2.7	29	76	18	81	37	20	1	40	1.60
33269581--33269619	21	1.9	20	84	5	51	71	10	12	5	1.28
33269889--33269964	11	7.0	11	77	15	70	77	0	22	0	0.77
33269886--33269970	23	3.6	22	79	16	82	77	0	22	0	0.77
33269882--33269945	33	1.9	34	87	9	96	73	0	26	0	0.84
33269890--33269970	24	3.4	24	77	17	80	77	0	22	0	0.76
33269895--33269964	33	2.2	32	84	7	88	78	0	21	0	0.75
33269898--33269969	10	6.9	10	77	17	51	79	0	20	0	0.74
33269986--33270011	13	2.0	13	100	0	52	23	61	15	0	1.33
33270864--33271268	18	22.3	18	70	16	212	32	13	9	44	1.76
33271013--33271268	53	4.8	53	79	10	233	28	14	10	46	1.78
33273546--33273586	17	2.5	17	88	7	59	39	2	14	43	1.59
33273820--33274029	41	5.1	41	94	0	366	28	20	28	22	1.99
33274226--33274310	37	2.5	35	81	11	106	28	10	27	34	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33294138--33294185	2	24.5	2	95	4	89	50	0	0	50	1.00
33294206--33294243	2	19.5	2	83	5	51	47	0	2	50	1.15
33295137--33295184	18	2.5	19	87	12	64	10	16	8	64	1.48
33296128--33296659	89	6.0	89	92	0	803	26	21	19	31	1.97
33308570--33308594	9	2.8	9	100	0	50	92	0	8	0	0.40
33308637--33308680	2	22.0	2	100	0	88	50	0	0	50	1.00
33308703--33308733	15	2.1	15	93	0	53	38	6	22	32	1.80
33309593--33309638	18	2.4	19	86	13	60	8	17	8	65	1.45
33311597--33311645	12	4.3	12	72	15	50	38	2	0	59	1.09
33320776--33320804	11	2.5	12	94	5	51	68	3	0	27	1.05

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168