genome.fa.s6.2.7.7.80.10.50.1000.14.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: Chr1
Parameters: 2 7 7 80 10 50 1000
Length:  35726063

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   

This is table  14  of  109  ( 13028 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)
4853108--4853141	16	2.1	16	94	0	59	50	5	2	41	1.42
4854798--4854961	80	2.0	81	98	1	321	40	4	9	45	1.59
4855517--4855553	17	2.4	16	86	13	51	43	2	5	48	1.40
4861681--4861863	43	4.3	42	75	4	125	37	19	21	21	1.95
4861681--4861918	42	5.6	42	76	4	165	38	19	20	21	1.94
4861681--4861918	86	2.8	87	72	6	218	38	19	20	21	1.94
4864631--4864663	17	1.9	17	93	0	57	51	0	3	45	1.16
4864850--4864891	14	3.1	14	79	6	59	30	0	7	61	1.22
4864837--4864890	27	2.0	26	92	3	90	25	1	7	64	1.30
4871437--4871464	3	9.3	3	100	0	56	0	35	32	32	1.58
4883031--4883072	11	3.4	12	84	15	59	4	7	4	83	0.91
4885280--4885610	178	1.9	179	92	0	556	40	11	15	32	1.83
4886829--4886867	14	2.8	13	81	11	51	41	0	0	58	0.98
4889521--4889568	19	2.5	20	82	3	62	35	0	2	62	1.07
4899393--4899426	18	2.0	18	88	11	54	35	0	0	64	0.94
4908691--4908747	27	2.1	27	86	0	78	15	3	15	64	1.42
4913501--4913550	11	4.6	11	75	20	52	72	16	6	6	1.25
4915323--4915358	2	18.0	2	100	0	72	50	0	0	50	1.00
4915758--4915830	36	2.0	36	100	0	146	41	10	10	36	1.76
4924080--4924147	29	2.3	29	92	5	111	11	10	47	30	1.74
4927656--4927730	29	2.6	28	75	8	69	21	28	24	26	1.99
4929706--4929895	50	3.8	50	91	0	308	21	31	23	24	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4929865--4930067	29	7.0	29	100	0	406	24	27	24	24	2.00
4934015--4934084	34	2.1	34	83	5	88	30	12	14	42	1.83
4945228--4945283	17	3.4	17	78	14	55	67	0	3	28	1.07
4949878--4949927	24	2.1	24	96	0	91	22	4	46	28	1.70
4955670--4955709	10	3.8	11	87	9	57	12	7	2	77	1.07
4955664--4955710	5	9.4	5	77	9	51	14	6	2	76	1.08
4955664--4955709	21	2.3	20	88	7	67	13	6	2	78	1.04
4956301--4956329	15	1.9	15	100	0	58	31	0	0	68	0.89
4961330--4961375	7	6.7	7	76	14	51	69	0	15	15	1.19
4961340--4961374	13	2.7	13	86	0	52	71	0	14	14	1.15
4962686--4963976	44	29.3	43	85	5	1381	32	13	22	31	1.92
4964908--4964944	12	3.2	12	88	3	58	10	8	0	81	0.89
4964908--4964960	12	4.7	11	86	6	54	11	7	1	79	1.01
4968340--4968386	20	2.5	19	86	6	60	23	6	23	46	1.75
4969603--4969690	39	2.2	42	88	10	130	54	6	1	37	1.35
4969991--4970029	21	1.9	20	84	5	51	43	12	17	25	1.85
4970284--4970324	19	2.2	19	86	4	57	39	0	0	60	0.96
4970318--4970356	18	2.1	17	86	13	51	51	0	5	43	1.24
4970327--4970369	18	2.4	18	84	7	61	46	0	2	51	1.13
4970368--4970401	12	2.9	11	91	8	50	23	0	8	67	1.18
4978756--4978801	21	2.2	21	85	11	60	26	41	21	10	1.86
4986213--4986246	17	2.0	17	94	0	59	44	11	38	5	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4986467--4986511	6	7.3	6	95	5	81	66	0	0	33	0.92
4991673--4991708	6	6.0	6	90	0	54	0	16	33	50	1.46
4995135--4995200	21	3.1	20	74	10	60	10	15	1	72	1.18
4996297--4996339	19	2.2	20	91	4	70	60	0	0	39	0.97
4996280--4996365	27	3.0	29	75	19	81	65	1	1	32	1.08
4999644--4999675	14	2.3	14	100	0	64	46	6	12	34	1.67
4999734--4999768	12	2.8	12	91	4	52	34	5	11	48	1.63
5002165--5002189	8	3.1	8	100	0	50	52	24	12	12	1.72
5003212--5003284	36	2.0	36	94	0	128	43	2	19	34	1.65
5003215--5003300	36	2.6	32	83	10	95	39	3	20	36	1.70
5006133--5006161	14	2.0	15	93	6	51	10	13	0	75	1.04
5009182--5009460	144	2.0	137	88	9	417	46	17	4	31	1.67
5009340--5009371	12	2.7	12	95	0	55	43	21	0	34	1.53
5011998--5012055	23	2.5	23	85	0	80	51	25	6	15	1.68
5016771--5016809	2	20.0	2	94	5	71	48	0	0	51	1.00
5017978--5018010	2	17.0	2	93	6	59	51	0	0	48	1.00
5025023--5025059	2	19.0	2	94	5	67	48	0	0	51	1.00
5026750--5027788	521	2.0	517	95	0	1862	28	24	15	31	1.96
5027312--5028669	677	2.0	679	96	0	2497	27	24	17	31	1.97
5028927--5029014	43	2.0	43	97	0	167	39	15	12	31	1.85
5036183--5036226	15	2.8	16	79	6	54	68	6	0	25	1.14
5036374--5036414	21	1.9	22	85	5	57	26	0	4	68	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5041570--5041749	45	4.0	45	86	4	231	35	27	15	22	1.93
5046943--5046982	7	5.7	7	93	0	71	17	0	37	45	1.49
5046937--5046989	21	2.5	22	93	6	99	18	0	33	47	1.49
5055463--5055682	72	3.1	72	98	0	422	45	14	13	26	1.82
5058083--5058108	8	3.2	8	100	0	52	11	0	0	88	0.52
5058366--5058450	29	2.9	28	75	13	82	56	0	3	40	1.16
5058517--5058566	10	5.4	9	75	20	50	26	2	4	68	1.18
5058685--5058837	29	5.5	28	74	12	122	32	1	1	64	1.16
5058685--5058823	10	14.6	10	71	16	82	32	2	2	63	1.18
5058772--5058837	26	2.6	25	83	11	80	31	0	1	66	1.01
5058685--5058837	9	16.4	9	68	18	75	32	1	1	64	1.16
5058685--5058837	19	8.2	19	71	15	97	32	1	1	64	1.16
5058806--5058837	16	2.0	16	100	0	64	31	0	0	68	0.90
5067787--5067819	16	2.1	16	88	5	50	3	12	12	72	1.23
5069373--5069463	25	3.6	25	74	5	76	32	20	23	23	1.98
5069505--5069645	25	5.6	25	67	15	78	37	22	20	19	1.94
5069586--5069660	26	2.9	26	86	4	98	38	22	20	18	1.93
5071025--5071049	12	2.1	12	100	0	50	24	36	24	16	1.94
5071209--5071271	9	6.9	9	81	3	81	39	30	7	22	1.82
5071416--5071444	13	2.2	13	100	0	58	17	0	41	41	1.49
5072159--5072204	23	2.0	23	100	0	92	30	17	30	21	1.96
5077550--5077585	15	2.4	15	95	0	63	47	0	19	33	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5080350--5080382	10	3.0	11	86	13	50	27	0	0	72	0.85
5083898--5083942	22	2.0	23	91	4	74	53	6	0	40	1.27
5083985--5084188	88	2.3	88	82	9	256	39	17	7	35	1.78
5084045--5084208	88	1.9	88	86	7	235	35	19	10	34	1.86
5084295--5084340	22	2.1	22	84	4	58	71	0	4	23	1.03
5084563--5084762	91	2.2	91	84	6	253	33	7	21	38	1.81
5085423--5085454	10	2.8	12	81	18	50	28	0	0	71	0.86
5088325--5088361	19	2.0	19	89	5	58	35	0	8	56	1.29
5088330--5088373	19	2.2	21	84	11	58	34	0	9	56	1.31
5089262--5089308	19	2.5	20	82	10	62	42	14	6	36	1.72
5091551--5091783	94	2.5	91	79	4	245	38	18	11	30	1.87
5092395--5092579	89	2.1	89	83	8	234	41	10	7	40	1.67
5099689--5099842	84	1.9	81	84	9	204	34	5	2	57	1.35
5099778--5099833	19	2.9	19	84	7	78	26	3	1	67	1.16
5099741--5099833	37	2.5	38	80	5	100	33	3	2	61	1.24
5099914--5100117	87	2.3	87	78	5	223	33	9	18	39	1.82
5100510--5100545	18	2.1	18	90	10	58	61	0	0	38	0.96
5100758--5100806	20	2.5	20	83	6	64	18	8	2	71	1.21
5103896--5103933	19	2.0	19	100	0	76	36	21	15	26	1.93
5107781--5108062	141	2.0	141	83	2	361	35	13	20	30	1.91
5109929--5109972	17	2.5	18	85	7	63	45	4	20	29	1.71
5113548--5113747	49	4.1	50	79	10	225	17	26	20	36	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5113555--5113766	25	8.6	25	76	10	172	18	25	20	34	1.96
5113605--5113766	73	2.2	74	80	7	170	18	25	21	34	1.96
5113677--5113778	50	2.1	49	85	5	134	22	23	19	34	1.97
5114985--5115084	39	2.6	39	88	0	155	25	12	29	34	1.91
5119251--5119280	14	2.1	14	100	0	60	30	6	6	56	1.51
5123355--5123399	23	2.0	23	95	0	81	37	8	26	26	1.86
5123995--5124019	8	3.1	8	100	0	50	76	0	0	24	0.80
5128537--5129860	662	2.0	662	100	0	2648	35	16	20	27	1.94
5130124--5130206	9	9.2	9	69	21	50	42	0	1	56	1.07
5130157--5130206	17	3.0	16	80	8	55	44	0	0	56	0.99

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