genome.fa.s4.2.7.7.80.10.50.1000.2.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  2  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)
119202--119246	16	2.6	18	82	17	67	64	0	0	35	0.94
119211--119359	15	9.8	15	67	13	65	67	0	3	28	1.12
119203--119249	22	2.1	22	84	7	60	63	0	0	36	0.94
119580--119645	23	2.8	23	72	4	60	39	1	0	59	1.07
125834--125882	24	2.0	25	92	4	82	36	16	4	42	1.67
129720--129770	19	2.7	20	81	9	70	31	11	9	47	1.73
134340--134370	2	15.5	2	100	0	62	51	0	0	48	1.00
138496--138525	14	2.1	14	100	0	60	46	13	0	40	1.43
140808--140833	2	13.0	2	100	0	52	50	0	50	0	1.00
144946--144982	3	12.3	3	94	0	65	67	2	0	29	1.04
151196--151240	23	2.0	23	95	0	81	37	11	11	40	1.76
155562--155657	27	3.5	27	82	5	95	41	12	13	32	1.82
159384--159490	41	2.6	41	98	1	205	30	1	25	42	1.66
163148--163233	39	2.1	41	85	6	113	18	18	19	43	1.89
168228--168268	21	2.0	21	85	0	55	34	29	21	14	1.93
168275--168340	28	2.4	28	89	2	98	39	12	16	31	1.85
168275--168360	27	3.1	28	86	3	113	38	11	18	31	1.87
172569--172694	47	2.7	46	82	1	153	51	10	10	27	1.68
174198--174241	20	2.2	20	88	8	63	47	11	0	40	1.39
174364--174420	27	2.2	25	81	9	62	50	10	0	38	1.37
176409--176438	6	5.0	6	95	0	51	80	3	0	16	0.85
176769--176805	16	2.3	17	86	9	51	45	10	2	40	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
176867--176927	16	3.6	16	72	14	59	78	1	0	19	0.83
176867--176925	20	2.9	19	80	14	66	77	1	0	20	0.85
176865--176931	26	2.6	26	84	11	93	77	1	0	20	0.85
181795--181889	29	3.3	28	80	4	100	37	8	11	42	1.72
181785--181871	28	3.1	28	83	3	111	42	9	12	35	1.75
188030--188075	16	2.7	17	86	6	58	63	0	28	8	1.24
188544--188594	19	2.7	20	79	17	63	43	0	5	50	1.26
194041--194141	27	3.7	26	74	12	96	39	16	13	29	1.88
194041--194149	55	2.0	54	80	1	119	41	15	13	29	1.86
194971--195138	29	6.0	29	74	12	111	32	14	14	38	1.86
195008--195112	26	4.0	26	77	14	90	28	15	15	40	1.87
195696--195725	15	2.0	15	100	0	60	33	33	13	20	1.91
197691--197855	60	2.7	61	82	6	192	26	30	15	27	1.96
198461--198499	3	13.0	3	100	0	78	33	0	0	66	0.92
198586--198713	66	2.0	65	84	4	168	5	40	3	50	1.44
198695--198808	48	2.4	48	86	4	151	4	40	6	49	1.48
198801--198853	18	3.0	18	75	20	58	3	28	0	67	1.07
203293--203504	61	3.5	62	85	4	263	25	34	14	25	1.94
204028--204072	3	15.7	3	81	9	58	28	0	0	71	0.87
204281--204346	30	2.1	32	83	5	82	0	39	1	59	1.07
204286--204346	8	7.3	9	71	22	53	0	37	1	60	1.07
204303--204346	16	2.8	16	100	0	88	0	36	0	63	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
204286--204344	26	2.4	26	80	8	70	0	37	1	61	1.07
204312--204448	48	2.7	50	79	10	145	3	40	4	51	1.39
204228--204394	80	2.1	79	84	4	212	2	41	4	51	1.36
204418--204451	17	2.1	16	88	5	50	0	29	0	70	0.87
209822--209880	28	2.1	29	84	9	77	30	5	11	52	1.59
213924--213964	22	1.9	22	90	5	66	51	2	4	41	1.36
218007--218069	18	3.6	17	79	12	67	22	0	1	76	0.88
217999--218069	33	2.2	33	84	5	90	23	0	1	74	0.90
218014--218066	14	3.8	14	80	14	65	20	0	1	77	0.87
218014--218067	28	2.0	27	85	10	74	20	0	1	77	0.86
218014--218070	22	2.4	23	82	11	71	21	0	1	77	0.86
218023--218078	27	2.0	28	86	3	78	19	1	3	75	1.05
233933--233979	2	23.5	2	100	0	94	51	0	0	48	1.00
236575--236797	103	2.2	100	89	3	338	21	7	21	49	1.74
270752--270870	30	4.0	30	85	4	150	14	7	49	28	1.70
270853--271304	48	9.4	48	94	0	661	15	9	50	24	1.74
271172--271251	27	3.2	27	59	20	64	17	7	50	25	1.72
271267--271368	27	3.8	27	70	14	75	14	13	49	22	1.79
273373--273417	16	3.0	14	79	17	54	80	4	15	0	0.87
273373--273418	20	2.2	20	85	11	58	78	4	17	0	0.91
275715--275744	2	15.0	2	100	0	60	50	0	0	50	1.00
289914--289978	7	9.1	7	81	3	76	30	13	26	29	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
299580--299626	2	23.5	2	100	0	94	48	0	0	51	1.00
326109--326145	16	2.2	16	90	4	56	64	2	5	27	1.28
329307--329342	16	2.2	17	90	5	56	50	0	5	44	1.25
329569--329742	84	2.1	84	94	0	303	40	5	8	44	1.59
330360--330400	21	2.0	21	90	9	66	75	0	0	24	0.80
330362--330401	16	2.5	15	80	11	53	75	0	0	25	0.81
331531--331618	28	3.2	27	77	6	70	68	4	4	22	1.27
335345--335390	23	2.0	23	95	0	83	39	6	13	41	1.70
338676--338721	23	2.0	23	95	0	83	41	6	13	39	1.70
343244--343727	86	5.6	85	79	3	396	41	13	9	36	1.77
343244--343734	171	2.9	169	81	3	527	40	13	9	36	1.76
343303--343733	86	5.0	86	79	4	431	41	13	9	35	1.77
343733--343814	2	43.0	2	89	9	127	51	0	0	47	1.00
349773--349798	2	13.0	2	100	0	52	50	0	0	50	1.00
353070--353114	14	3.5	12	82	8	54	48	4	0	46	1.22
353576--353619	18	2.4	19	92	3	72	27	2	0	70	0.99
353589--353625	17	2.2	17	85	4	58	37	0	0	62	0.96
353819--353857	19	2.1	19	100	0	78	25	5	10	58	1.51
354142--354173	13	2.4	14	90	10	50	65	0	0	34	0.93
354149--354272	33	3.9	32	72	21	116	55	0	0	43	1.05
354192--354260	26	2.5	28	88	9	106	55	0	1	43	1.08
354176--354275	29	3.2	29	67	19	85	54	0	1	45	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
354455--354513	24	2.5	24	77	2	66	66	0	0	33	0.92
362264--362319	24	2.3	23	82	11	60	51	3	0	44	1.18
362970--363027	1	58.0	1	100	0	116	100	0	0	0	0.00
363781--363819	20	2.0	20	89	0	60	30	7	5	56	1.49
365643--365667	13	1.9	13	100	0	50	48	8	0	44	1.32
373361--373429	20	3.5	20	69	13	63	52	0	0	47	1.00
373393--373448	24	2.3	23	82	11	60	51	3	0	44	1.18
392686--392936	129	1.9	130	92	2	425	33	20	13	32	1.91
440175--440271	35	2.8	36	79	7	110	45	16	12	25	1.82
442385--442419	2	17.5	2	87	0	52	0	54	0	45	0.99
447842--447956	57	2.0	57	83	3	142	32	19	17	31	1.95
448030--448204	63	2.9	60	79	9	192	37	18	24	20	1.94
448442--448542	45	2.2	45	82	3	114	29	25	20	23	1.99
449301--449354	28	1.9	28	92	0	90	64	14	1	18	1.37
449673--449707	18	1.9	18	94	0	61	54	2	0	42	1.15
504014--504063	2	25.0	2	95	0	91	50	2	0	48	1.12
504078--504125	2	24.0	2	100	0	96	50	0	0	50	1.00
505258--505295	10	3.9	10	83	16	53	68	0	0	31	0.90
505220--505282	29	2.3	27	77	17	67	55	1	0	42	1.09
505261--505310	18	2.9	17	85	5	64	72	0	2	26	0.96
505264--505310	17	2.7	18	86	6	69	74	0	2	23	0.93
511896--511971	30	2.6	29	79	8	91	57	1	0	40	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
517648--517675	4	7.0	4	100	0	56	75	0	0	25	0.81
521212--521259	22	2.2	23	77	7	55	45	0	10	43	1.38
521068--521708	211	3.0	213	86	5	936	45	4	7	41	1.55
521996--522044	17	2.9	17	73	11	55	57	0	0	42	0.99
530394--530446	27	2.0	27	96	0	97	39	7	30	22	1.82
534474--534513	21	1.9	21	89	0	62	42	2	0	55	1.13
535565--535589	12	2.1	12	100	0	50	32	0	0	68	0.90
535640--535679	18	2.2	18	86	0	53	37	5	17	40	1.72
545456--545491	2	18.0	2	94	0	63	52	0	0	47	1.00
546050--546128	30	2.6	30	91	0	122	59	17	13	8	1.59

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