genome.fa.s4.2.7.7.80.10.50.1000.12.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: chr4
Parameters: 2 7 7 80 10 50 1000
Length:  31929104

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   

This is table  12  of  82  ( 9773 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)
3811284--3811494	111	1.9	110	83	4	273	45	6	8	40	1.59
3817757--3817785	3	9.7	3	100	0	58	68	0	0	31	0.89
3821918--3821981	32	2.0	32	87	0	92	39	18	7	34	1.80
3823038--3823156	60	2.0	60	85	3	159	26	8	16	48	1.74
3823583--3823633	3	17.0	3	91	0	84	64	1	0	33	1.05
3824371--3824413	20	2.2	20	83	8	52	39	4	9	46	1.57
3830697--3830730	17	1.9	17	88	5	50	11	32	20	35	1.89
3839294--3839363	35	2.0	34	83	2	86	34	20	10	35	1.86
3850215--3850333	39	3.0	39	83	1	148	25	9	26	38	1.86
3851583--3852002	111	3.7	111	88	3	581	18	11	24	44	1.83
3851583--3852055	118	4.1	114	83	7	559	19	12	25	43	1.85
3856199--3856613	159	2.6	159	92	0	688	26	10	26	36	1.88
3856605--3856902	103	2.9	103	91	0	499	26	10	25	37	1.88
3856801--3856873	22	3.0	26	66	15	73	26	12	21	39	1.89
3858874--3858931	26	2.3	23	76	18	62	56	8	13	20	1.63
3858881--3858931	26	2.0	26	92	0	84	56	9	13	19	1.65
3860471--3860629	69	2.3	69	83	6	198	19	27	19	33	1.96
3860555--3860615	24	2.5	24	81	0	59	18	26	21	34	1.96
3862488--3862551	23	2.9	21	75	11	56	42	21	10	25	1.85
3863597--3863660	26	2.4	28	82	7	80	35	3	0	60	1.12
3865503--3865546	17	2.6	17	81	0	52	36	4	2	56	1.32
3867823--3867875	12	4.4	12	77	13	56	28	0	1	69	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3867823--3867875	18	2.9	18	76	18	65	28	0	1	69	0.99
3868097--3868123	13	2.1	13	100	0	54	37	7	7	48	1.59
3868428--3868457	10	3.0	10	95	0	51	30	3	0	66	1.07
3869210--3869471	34	7.6	34	78	11	150	22	41	16	19	1.89
3869211--3869471	70	3.8	70	75	13	227	22	41	16	19	1.90
3869236--3869471	104	2.3	105	81	9	295	22	41	15	20	1.89
3869747--3869780	17	2.1	17	88	5	52	8	17	0	73	1.08
3874998--3875045	22	2.3	22	86	10	66	45	18	0	35	1.50
3878042--3878085	2	22.0	2	100	0	88	50	0	50	0	1.00
3878957--3879003	22	2.1	22	100	0	94	53	27	14	4	1.60
3890198--3890249	28	1.9	27	84	7	70	28	21	19	30	1.97
3890295--3890340	20	2.3	20	96	0	83	45	21	4	28	1.71
3890663--3890786	42	3.0	42	86	0	185	21	33	22	22	1.98
3894708--3894770	7	8.7	7	81	11	74	0	34	0	65	0.93
3894708--3894773	29	2.3	29	86	5	98	0	36	0	63	0.95
3901405--3901653	35	7.2	35	80	5	229	43	12	7	36	1.70
3901406--3901653	106	2.4	104	81	5	304	43	12	7	36	1.70
3901394--3901660	141	1.9	138	86	3	383	43	12	7	37	1.70
3918497--3918526	2	15.0	2	100	0	60	50	0	0	50	1.00
3920375--3920431	17	3.2	18	83	11	64	29	0	1	68	1.00
3920391--3920438	25	1.9	25	83	8	62	27	0	2	70	0.98
3920386--3920431	19	2.6	18	89	6	67	28	0	0	71	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3924367--3924392	12	2.2	12	100	0	52	30	0	7	61	1.24
3931774--3931864	21	4.3	20	73	14	67	40	1	2	56	1.19
3933464--3933622	80	2.0	78	93	2	273	38	8	1	50	1.45
3939802--3939838	17	2.2	17	100	0	74	43	10	5	40	1.63
3942796--3942865	37	1.9	36	91	2	113	30	7	32	30	1.84
3959248--3959380	43	3.1	42	80	10	119	40	3	3	53	1.32
3960996--3961127	28	4.6	28	82	7	167	36	28	11	24	1.90
3960999--3961127	58	2.3	56	82	6	161	36	28	10	24	1.89
3961182--3961264	42	2.0	42	90	4	132	43	15	9	31	1.79
3961183--3961250	21	3.2	21	64	22	52	42	16	8	32	1.79
3967120--3967162	20	2.2	19	84	12	52	67	11	0	20	1.22
3968888--3968981	4	23.2	4	72	10	66	44	4	3	47	1.38
3968934--3968983	25	2.0	25	92	4	82	48	6	0	46	1.27
3973417--3973462	22	2.0	23	87	4	67	36	45	17	0	1.49
3973881--3973929	20	2.4	21	86	3	73	0	24	44	30	1.54
3973894--3973936	20	2.2	20	86	0	59	2	23	41	32	1.67
3975425--3975485	2	30.5	2	96	0	113	50	1	0	47	1.10
3976250--3976313	18	3.6	18	74	17	62	28	10	15	45	1.80
3976470--3976515	16	2.9	16	72	15	51	15	2	13	69	1.28
3979093--3979303	68	3.0	70	88	4	329	32	11	16	39	1.85
3981571--3981605	12	2.8	13	86	8	54	22	0	2	74	0.95
3981597--3981640	10	4.5	10	78	16	56	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3986903--3987034	66	2.0	66	89	2	203	25	15	21	37	1.92
4004471--4004747	137	2.0	139	95	4	508	37	10	3	48	1.53
4005026--4005105	32	2.4	34	79	8	103	57	0	11	31	1.34
4005026--4005105	33	2.4	33	85	4	108	57	0	11	31	1.34
4011123--4011168	19	2.4	20	82	10	60	54	0	2	43	1.12
4011570--4011615	20	2.3	20	88	7	67	32	4	17	45	1.68
4011660--4011712	28	1.9	27	88	3	79	30	18	22	28	1.98
4011660--4011718	28	2.1	28	84	6	75	30	20	23	25	1.98
4012853--4012877	13	1.9	13	100	0	50	44	0	8	48	1.32
4017163--4017365	28	7.0	28	82	6	217	40	10	12	36	1.77
4017163--4017365	57	3.5	56	83	7	235	40	10	12	36	1.77
4017166--4017365	59	3.4	58	85	4	251	40	10	12	37	1.77
4019206--4019238	6	5.5	6	100	0	66	63	0	0	36	0.95
4027429--4027483	28	2.0	29	86	13	80	29	20	23	27	1.99
4028123--4028350	88	2.6	87	85	2	305	42	8	12	36	1.74
4028123--4028345	29	7.6	28	80	8	232	41	8	12	37	1.75
4032290--4032440	38	4.1	38	84	5	191	27	33	9	30	1.88
4032290--4032440	73	2.0	76	83	6	193	27	33	9	30	1.88
4038121--4038188	28	2.4	28	95	0	118	23	22	20	33	1.97
4038140--4038199	28	2.1	28	84	0	75	33	18	16	31	1.93
4043464--4043586	42	2.9	42	88	1	165	26	16	34	23	1.95
4043610--4043634	2	12.5	2	100	0	50	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4048551--4048582	16	2.1	16	94	5	57	34	0	0	65	0.93
4048834--4048925	27	3.6	26	73	18	77	42	1	1	55	1.14
4048975--4049061	28	3.1	27	76	12	70	40	0	3	56	1.16
4049205--4049246	15	2.7	15	88	3	57	47	0	0	52	1.00
4059209--4059277	30	2.3	31	92	2	113	31	11	23	33	1.90
4059249--4059394	36	4.0	36	86	4	170	29	20	14	35	1.92
4067851--4067973	43	2.9	43	81	7	151	28	16	34	21	1.95
4071638--4071681	22	2.0	22	95	0	79	15	13	6	63	1.49
4076316--4076360	21	2.0	23	83	8	58	57	8	0	33	1.30
4076312--4076365	23	2.3	25	75	18	62	53	11	0	35	1.36
4090300--4090342	17	2.6	17	85	3	52	27	20	37	13	1.91
4093922--4093979	30	1.9	31	89	3	91	29	12	12	46	1.77
4094036--4094112	33	2.3	33	84	0	100	32	16	19	31	1.94
4094505--4094551	21	2.3	21	82	7	62	38	4	12	44	1.62
4096648--4096692	2	22.5	2	100	0	90	48	0	0	51	1.00
4096723--4096762	2	20.0	2	100	0	80	50	0	0	50	1.00
4096803--4096967	42	3.9	42	82	3	190	26	32	21	20	1.97
4098199--4098240	22	2.0	22	86	13	61	47	33	9	9	1.68
4098220--4098310	36	2.6	35	82	6	114	37	30	12	19	1.88
4098161--4098358	92	2.2	92	88	0	299	37	31	10	20	1.86
4098504--4098533	12	2.4	13	94	5	53	0	30	0	70	0.88
4101518--4101557	19	2.0	20	95	4	73	42	27	0	30	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4106379--4106418	19	2.0	20	90	4	64	42	25	0	32	1.55
4121728--4121908	62	2.9	62	94	0	317	31	13	44	9	1.77
4123673--4123717	22	2.0	23	86	4	65	71	0	8	20	1.12
4123685--4123820	30	4.7	29	76	12	95	69	0	5	23	1.15
4123686--4123789	27	3.8	27	77	11	88	70	0	6	22	1.17
4123690--4123777	13	6.5	13	73	18	63	69	1	7	21	1.21
4123763--4123809	17	2.9	16	81	9	60	74	0	0	25	0.82
4123757--4123819	14	4.8	13	81	11	67	73	0	1	25	0.93
4127097--4127129	16	2.1	16	94	0	57	45	3	0	51	1.16
4128716--4129009	96	3.1	96	88	3	416	22	25	4	48	1.69

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