genome.fa.s4.2.7.7.80.10.50.1000.77.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  77  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)
28868172--28868200	12	2.3	13	94	5	51	89	0	10	0	0.48
28878495--28878529	16	2.2	16	89	0	52	37	0	62	0	0.95
28878489--28878536	7	6.9	7	95	0	60	37	0	60	2	1.09
28879584--28879667	2	44.0	2	76	17	72	0	42	1	54	1.08
28879574--28879679	52	2.0	52	91	7	171	0	39	1	57	1.10
28884491--28884532	13	3.2	13	77	12	50	54	0	0	45	0.99
28885452--28885581	27	4.8	27	86	3	136	27	21	31	19	1.97
28885531--28885595	27	2.4	27	78	0	76	27	23	33	15	1.95
28885606--28885681	27	2.8	27	69	0	62	26	26	30	17	1.97
28885491--28885730	115	2.1	115	83	4	297	25	22	30	20	1.98
28885544--28885759	115	1.9	115	84	0	288	25	22	31	20	1.98
28885531--28885784	115	2.2	115	77	5	278	25	22	32	19	1.98
28885740--28885956	27	8.1	26	73	9	150	27	24	32	16	1.96
28885559--28885823	115	2.3	113	76	7	255	25	23	32	18	1.97
28885854--28885980	54	2.4	53	83	2	146	32	25	28	13	1.94
28892785--28892833	17	2.9	18	85	11	68	42	0	0	57	0.99
28918473--28918512	9	4.6	8	87	12	53	45	0	0	55	0.99
28918473--28918512	17	2.3	18	87	12	57	45	0	0	55	0.99
28918620--28918657	15	2.3	17	86	13	53	57	2	0	39	1.12
28925502--28925686	99	1.9	99	84	8	252	34	9	30	25	1.87
28936677--28936705	15	2.0	15	93	6	51	51	6	0	41	1.28
28937439--28937480	22	2.0	21	90	4	66	45	2	0	52	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
28941431--28941463	10	3.3	10	100	0	66	90	0	9	0	0.44
28941517--28941671	16	10.2	16	64	24	59	52	1	3	43	1.25
28941627--28941693	25	2.7	24	84	13	82	58	2	1	37	1.23
28941897--28941941	22	2.0	22	91	0	72	31	4	4	60	1.37
28942110--28942163	26	2.1	26	96	0	99	38	1	33	25	1.67
28946766--28946790	12	2.1	12	100	0	50	68	0	0	32	0.90
28946990--28947021	11	3.0	11	95	4	57	28	9	18	43	1.81
28946990--28947021	10	3.1	10	91	8	55	28	9	18	43	1.81
28968802--28968840	20	2.0	19	85	5	51	2	7	15	74	1.15
28983250--28983277	10	2.8	10	100	0	56	60	10	10	17	1.57
28988703--28988750	2	24.0	2	95	0	87	52	0	0	47	1.00
28991354--28991396	20	2.2	20	86	0	59	39	6	13	39	1.72
28996378--28996402	2	12.5	2	100	0	50	52	0	48	0	1.00
29002116--29002151	2	18.5	2	91	5	56	44	0	0	55	0.99
29006929--29006958	4	7.2	4	96	3	51	23	0	0	76	0.78
29007041--29007083	9	4.7	9	82	2	50	13	2	2	81	0.89
29018069--29018302	78	3.0	78	91	1	371	35	10	21	32	1.87
29018768--29018852	40	2.1	40	95	0	152	17	32	10	38	1.84
29018842--29018898	24	2.4	24	97	2	107	14	28	14	43	1.83
29021534--29021560	2	13.5	2	100	0	54	51	0	48	0	1.00
29033911--29033943	2	16.5	2	100	0	66	51	0	0	48	1.00
29036434--29036473	21	1.9	21	85	10	55	47	2	0	50	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29036904--29036946	2	21.5	2	100	0	86	48	0	0	51	1.00
29067358--29067430	37	1.9	38	83	2	94	42	13	12	31	1.81
29074666--29074769	2	54.0	2	83	7	126	50	0	0	48	1.07
29075231--29075301	27	2.6	27	81	0	88	16	18	29	35	1.93
29075326--29075400	30	2.5	30	95	0	132	17	12	32	38	1.86
29075254--29075559	132	2.3	132	89	0	477	14	16	31	37	1.89
29075462--29075880	30	14.4	30	72	18	241	17	16	31	34	1.92
29075450--29075942	114	4.3	114	70	20	396	16	16	32	35	1.91
29075593--29075643	21	2.4	21	96	0	93	17	13	31	37	1.89
29075576--29075673	51	1.9	51	95	0	178	18	15	30	35	1.92
29075330--29075864	165	3.4	158	85	10	675	15	15	31	36	1.90
29075587--29075953	183	2.0	177	91	3	590	15	15	32	35	1.90
29075669--29075944	87	3.0	94	76	16	288	15	15	32	35	1.90
29075783--29075940	27	5.6	27	72	11	129	17	15	31	35	1.92
29075912--29076067	45	3.6	44	76	6	151	10	17	34	37	1.85
29082263--29082298	18	2.0	18	88	0	54	88	5	2	2	0.67
29082921--29083334	51	8.1	51	97	0	765	12	18	47	22	1.81
29085967--29086474	201	2.5	201	90	0	793	13	24	29	32	1.93
29089427--29089477	26	2.0	26	84	7	68	66	0	5	27	1.14
29091403--29091604	100	2.0	100	94	0	350	31	18	10	38	1.86
29097421--29097467	20	2.5	19	83	12	62	2	21	6	70	1.20
29103444--29103470	14	1.9	14	100	0	54	29	14	7	48	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29111829--29111875	2	24.0	2	86	4	69	44	0	4	51	1.21
29113489--29113582	49	1.9	48	97	0	170	41	2	4	51	1.33
29126488--29126537	24	2.1	24	88	3	75	48	10	6	36	1.61
29126581--29126648	29	2.3	29	84	0	82	42	7	11	38	1.69
29158680--29158736	29	2.0	29	100	0	114	29	24	10	35	1.89
29159532--29159562	2	15.5	2	93	0	53	48	3	0	48	1.17
29176559--29176622	32	2.0	32	93	6	112	25	45	10	18	1.82
29180000--29180061	23	2.7	23	89	2	88	40	6	8	45	1.59
29183504--29183549	23	2.0	23	95	0	83	39	13	10	36	1.79
29197513--29197552	15	2.6	15	84	15	55	0	37	5	57	1.21
29200266--29200304	13	3.2	13	85	10	55	48	0	0	51	1.00
29200274--29200339	20	3.2	20	74	18	64	42	0	3	54	1.15
29200265--29200348	23	3.9	23	73	19	72	44	0	2	53	1.13
29200444--29200480	14	2.6	14	91	4	56	40	0	2	56	1.13
29203497--29203531	4	8.8	4	93	0	61	54	22	0	22	1.45
29203529--29203562	17	2.0	17	88	0	50	52	0	0	47	1.00
29205696--29205750	27	2.0	27	89	0	83	23	16	27	32	1.96
29207812--29207846	3	12.0	3	93	6	63	0	0	31	68	0.90
29212941--29213082	45	3.2	45	95	0	257	38	26	19	16	1.92
29213585--29213642	14	4.0	14	75	20	57	53	0	1	44	1.10
29213803--29213860	28	2.1	28	87	6	82	48	31	6	13	1.69
29214679--29214704	2	13.0	2	100	0	52	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29219020--29219060	21	2.0	21	95	0	73	19	19	17	43	1.88
29229980--29230062	21	4.0	21	72	12	64	25	7	22	44	1.78
29230022--29230070	21	2.3	22	78	3	55	26	6	22	44	1.76
29231023--29231066	20	2.0	21	83	12	54	29	15	13	40	1.86
29235713--29235739	6	4.5	6	100	0	54	37	0	48	14	1.45
29245693--29245724	3	10.7	3	100	0	64	65	0	34	0	0.93
29247394--29247423	6	5.0	6	100	0	60	50	16	33	0	1.46
29258390--29258416	3	9.0	3	100	0	54	33	0	0	66	0.92
29263827--29263852	2	13.0	2	100	0	52	50	0	50	0	1.00
29263978--29264010	2	16.5	2	93	0	57	51	0	48	0	1.00
29264449--29264484	2	18.0	2	100	0	72	50	0	50	0	1.00
29270812--29270836	12	2.1	12	100	0	50	28	24	0	48	1.52
29278400--29278430	2	15.5	2	100	0	62	48	0	0	51	1.00
29281163--29281239	38	2.0	38	100	0	154	29	2	12	54	1.52
29303479--29303544	2	32.5	2	81	14	73	43	1	48	4	1.32
29306153--29306182	3	10.0	3	92	0	51	0	30	0	70	0.88
29306734--29306773	21	1.9	21	90	10	64	30	20	20	30	1.97
29319828--29319875	25	2.0	25	87	4	71	45	4	8	41	1.53
29321543--29321587	22	2.0	23	91	4	74	44	6	8	40	1.62
29322913--29322946	2	17.0	2	100	0	68	50	0	0	50	1.00
29323721--29323765	15	2.7	17	80	13	58	48	2	0	48	1.13
29323741--29323806	18	3.7	17	76	8	51	48	1	1	48	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29327971--29328002	3	10.7	3	100	0	64	65	0	34	0	0.93
29347058--29347095	16	2.3	17	86	4	51	71	7	7	13	1.31
29347111--29347165	26	2.1	26	100	0	110	38	12	10	38	1.79
29349303--29349332	15	1.9	16	93	6	53	63	6	0	30	1.20
29349469--29349507	20	2.0	20	84	0	51	71	0	7	20	1.10
29350633--29350673	21	2.0	21	85	9	57	46	2	0	51	1.14
29350629--29350698	23	3.0	23	83	10	81	48	5	0	45	1.26
29350635--29351270	210	3.0	212	82	7	836	41	7	4	46	1.52
29353937--29353972	10	3.9	10	82	17	51	72	0	0	27	0.85
29353941--29353982	17	2.5	17	84	0	57	73	0	2	23	0.94

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