genome.fa.s8.2.7.7.80.10.50.1000.55.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   

This is table  55  of  190  ( 22705 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)
15560213--15560280	29	2.3	29	87	5	93	47	11	7	33	1.68
15569148--15569172	7	3.6	7	100	0	50	40	0	0	60	0.97
15569600--15569629	3	10.0	3	100	0	60	33	33	0	33	1.58
15576605--15576635	9	3.4	9	90	0	53	25	12	22	38	1.90
15576688--15576724	9	4.1	9	92	0	65	45	13	10	29	1.77
15579086--15579137	24	2.2	24	82	6	61	40	9	36	13	1.77
15579094--15579148	24	2.3	24	84	6	76	43	7	34	14	1.73
15579719--15580271	279	2.0	280	81	1	660	28	22	18	31	1.97
15580601--15580651	26	2.0	26	96	0	93	19	13	23	43	1.87
15583351--15583525	95	1.8	95	85	0	242	29	26	20	23	1.98
15583614--15583885	102	2.6	102	84	2	348	29	18	17	33	1.94
15589743--15589775	2	16.5	2	100	0	66	51	0	0	48	1.00
15597344--15597391	15	3.1	15	81	3	51	72	2	0	25	0.95
15604121--15604172	24	2.1	25	82	3	61	40	19	26	13	1.88
15604514--15604555	21	2.0	21	85	0	57	38	23	0	38	1.55
15604525--15604555	10	2.9	11	90	9	55	35	29	0	35	1.58
15604988--15605052	32	2.1	32	97	2	123	30	9	12	47	1.72
15610773--15610813	3	13.7	3	100	0	82	31	0	0	68	0.90
15617087--15617142	25	2.2	26	93	3	96	25	28	23	23	1.99
15618749--15618888	46	3.0	46	94	0	244	28	26	8	36	1.86
15627001--15627046	24	1.9	24	95	0	83	23	6	15	54	1.64
15627008--15627063	24	2.4	24	84	3	69	25	7	19	48	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15634439--15634511	37	2.0	37	94	2	130	19	6	8	65	1.42
15648307--15648379	37	2.0	37	89	2	112	20	10	6	61	1.51
15653152--15653188	5	7.4	5	100	0	74	40	40	18	0	1.51
15653988--15654012	6	4.2	6	100	0	50	48	0	0	52	1.00
15660833--15661256	125	3.4	125	86	2	636	29	18	22	29	1.97
15666826--15666869	12	3.8	12	76	11	56	45	0	27	27	1.54
15670343--15670479	26	5.3	26	75	3	132	25	13	26	35	1.92
15672472--15672524	19	2.8	19	75	11	56	69	1	0	28	0.99
15672472--15672532	24	2.6	24	78	17	65	68	1	0	29	0.99
15678164--15678356	50	3.8	50	84	0	251	25	23	30	20	1.99
15680449--15680658	26	8.1	26	84	0	240	27	11	27	34	1.91
15687136--15687202	27	2.5	27	87	0	98	22	19	26	31	1.98
15687210--15687261	27	2.0	26	85	7	70	40	15	25	19	1.90
15688757--15689100	51	6.8	51	77	8	278	29	25	15	28	1.96
15688759--15689100	102	3.4	102	82	4	392	30	26	15	28	1.96
15688757--15689099	153	2.3	148	77	6	341	30	25	15	28	1.96
15689386--15689449	30	2.1	30	82	5	76	32	21	4	40	1.74
15696306--15696642	51	6.7	49	75	8	243	28	26	15	29	1.96
15696301--15696642	102	3.4	102	81	4	365	28	26	15	28	1.96
15703739--15703824	39	2.2	39	79	6	95	25	25	26	22	2.00
15707963--15708010	25	1.9	25	86	0	69	31	14	10	43	1.79
15714251--15714295	23	2.0	24	86	8	67	51	0	22	26	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15714658--15714751	37	2.5	35	79	14	91	43	1	22	32	1.60
15715465--15715509	2	22.5	2	100	0	90	48	0	0	51	1.00
15720971--15721028	30	1.9	30	82	6	73	29	25	5	39	1.77
15722744--15722928	95	1.9	95	94	0	325	30	9	22	37	1.86
15723999--15724051	26	2.0	26	100	0	106	54	15	11	18	1.70
15724213--15724237	5	5.0	5	100	0	50	40	0	0	60	0.97
15730283--15730393	43	2.6	43	79	13	138	22	22	27	27	1.99
15731493--15731532	22	2.0	20	85	14	55	25	2	17	55	1.55
15731914--15731942	2	14.5	2	100	0	58	51	0	0	48	1.00
15737228--15737286	23	2.5	23	76	15	57	18	25	18	37	1.94
15737276--15737327	25	2.1	25	89	7	79	21	21	21	36	1.95
15737224--15737378	73	2.1	73	83	4	197	19	23	21	34	1.96
15738405--15738485	42	1.9	42	85	9	112	23	27	29	19	1.98
15740176--15740227	9	5.8	9	77	8	52	28	7	3	59	1.43
15740173--15740215	15	2.9	15	82	0	50	32	6	0	60	1.23
15740176--15740237	27	2.3	27	83	5	72	32	6	4	56	1.46
15740595--15740650	2	28.5	2	85	3	78	46	0	3	50	1.19
15743274--15743320	22	2.1	22	88	7	69	36	4	21	38	1.73
15749884--15749917	16	2.1	16	88	0	50	20	14	20	44	1.87
15756037--15756061	6	4.2	6	100	0	50	36	32	16	16	1.90
15759817--15759919	45	2.3	45	79	3	118	27	17	28	27	1.98
15767745--15767795	21	2.4	21	93	0	84	1	45	17	35	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15767680--15767839	87	1.8	87	87	0	230	12	30	16	40	1.86
15773295--15773977	9	78.2	9	78	10	652	33	1	18	47	1.56
15773967--15774071	52	2.0	53	85	9	144	35	0	14	49	1.50
15773973--15774041	12	5.4	12	72	16	50	36	0	11	52	1.38
15774147--15774206	9	6.9	9	77	7	61	31	0	18	50	1.47
15773892--15774407	256	2.0	257	89	5	792	38	1	13	46	1.53
15774360--15774395	15	2.4	15	90	0	54	61	0	2	36	1.11
15774352--15774385	17	1.9	18	88	5	52	55	0	5	38	1.24
15774465--15774534	21	3.1	22	85	10	88	52	0	1	45	1.09
15774492--15774548	20	3.1	18	85	10	62	54	0	1	43	1.10
15776120--15776144	13	1.9	13	100	0	50	24	12	24	40	1.88
15777026--15777068	7	6.1	7	84	10	52	37	34	0	27	1.57
15777027--15777068	15	2.9	15	82	10	61	35	35	0	28	1.58
15777339--15777425	38	2.2	40	80	8	99	50	24	0	25	1.49
15777510--15777577	34	2.0	34	97	0	127	20	13	20	45	1.84
15777565--15777805	115	2.1	112	79	9	245	27	22	17	31	1.97
15799742--15799801	25	2.4	25	88	0	84	20	40	30	10	1.85
15803533--15803601	32	2.2	32	97	0	129	39	27	8	24	1.85
15803587--15803618	14	2.3	14	100	0	64	40	37	0	21	1.54
15807483--15807749	10	28.4	9	65	21	77	34	3	2	59	1.29
15807467--15807525	20	2.9	20	80	10	66	30	3	3	62	1.28
15807624--15807669	18	2.6	18	80	13	58	36	0	2	60	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15807607--15807673	27	2.4	27	87	7	91	32	1	4	61	1.25
15807600--15807669	35	2.0	35	83	8	88	35	1	2	60	1.21
15808804--15808844	2	20.5	2	100	0	82	51	0	0	48	1.00
15809469--15809508	14	2.9	14	84	0	53	32	7	17	42	1.77
15809492--15809531	20	2.0	20	90	0	62	27	10	12	50	1.72
15809477--15809543	34	1.9	35	90	3	109	31	8	13	46	1.74
15809958--15809985	13	2.2	13	100	0	56	32	0	14	53	1.41
15811389--15811416	12	2.3	12	100	0	56	46	17	7	28	1.75
15819118--15819186	16	4.2	16	96	3	129	24	0	37	37	1.56
15819118--15819186	33	2.1	32	97	2	129	24	0	37	37	1.56
15819422--15819456	18	2.0	17	88	5	52	54	0	0	45	0.99
15819309--15819625	157	2.0	157	95	0	562	44	3	5	47	1.42
15819596--15819646	18	2.5	20	78	18	61	45	3	1	49	1.32
15819562--15819856	120	2.4	121	88	5	427	49	4	5	41	1.45
15819853--15820082	92	2.5	92	82	9	238	46	3	4	44	1.43
15819888--15820082	92	2.1	93	86	5	279	46	4	5	44	1.44
15823994--15824084	46	2.0	46	86	2	130	35	2	15	47	1.58
15824394--15824439	23	2.0	23	95	0	83	41	17	19	21	1.90
15828821--15828909	40	2.2	40	95	0	160	38	5	33	22	1.78
15841947--15842038	25	3.6	25	79	2	85	26	21	28	23	1.99
15843497--15843647	54	2.8	54	79	4	144	23	23	34	19	1.96
15861759--15862003	27	9.1	27	78	8	241	41	20	17	20	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
15861761--15861990	54	4.3	54	81	3	275	43	20	17	19	1.89
15861761--15862001	81	3.0	81	85	3	308	41	20	17	19	1.90
15864134--15864201	33	2.1	33	97	0	127	51	17	8	22	1.72
15874032--15874091	26	2.3	27	80	13	72	53	18	1	26	1.54
15884927--15884973	24	2.0	24	82	0	58	42	17	2	38	1.61
15885450--15885635	41	4.5	41	84	2	214	28	21	20	29	1.98
15885497--15885651	82	1.9	82	83	2	204	30	18	21	29	1.96
15885497--15885635	41	3.4	41	91	0	215	29	18	20	30	1.97
15885748--15885878	61	2.1	61	81	2	156	40	16	8	35	1.78
15885878--15886037	65	2.5	62	78	12	175	43	15	8	33	1.76

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190