genome.fa.s8.2.7.7.80.10.50.1000.12.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: 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  12  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)
3633951--3633976	13	2.0	13	100	0	52	53	30	0	15	1.42
3646660--3646720	31	2.0	31	90	0	95	32	16	8	42	1.78
3648182--3648212	2	15.5	2	100	0	62	51	0	0	48	1.00
3648453--3648482	5	6.0	5	100	0	60	40	0	0	60	0.97
3649237--3649552	156	2.0	156	98	0	605	32	19	18	29	1.96
3652790--3652815	2	13.0	2	100	0	52	50	0	0	50	1.00
3663257--3663304	10	4.9	10	76	5	53	54	0	0	45	0.99
3663247--3663304	19	3.0	20	82	7	66	51	0	1	46	1.11
3663522--3663579	31	1.9	31	89	3	91	25	6	1	65	1.27
3663563--3663637	19	3.8	20	71	15	75	28	4	4	64	1.30
3663522--3663606	30	2.8	30	82	8	84	28	5	2	63	1.30
3663637--3663688	26	1.9	28	84	7	72	38	0	3	57	1.17
3663745--3663935	89	2.1	89	87	2	267	35	9	20	34	1.85
3664586--3664644	29	2.0	29	100	0	118	37	20	3	38	1.69
3664687--3664731	2	22.5	2	100	0	90	51	0	0	48	1.00
3665499--3665559	30	2.0	31	93	3	106	37	0	42	19	1.52
3665688--3665718	9	3.4	9	90	0	53	38	22	12	25	1.90
3668180--3668346	83	2.0	83	98	0	325	28	15	11	44	1.82
3675491--3675545	28	2.0	29	85	7	78	23	7	5	63	1.41
3676781--3676946	20	8.5	19	70	20	76	63	4	1	29	1.25
3676804--3676946	10	14.4	10	64	20	59	65	4	1	29	1.20
3676841--3676881	21	2.0	20	85	4	55	60	4	0	34	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3677375--3677429	9	6.1	9	74	16	51	32	1	1	63	1.15
3677421--3677467	22	2.2	22	88	3	69	38	2	4	55	1.31
3677371--3677482	49	2.3	48	80	8	113	37	1	2	58	1.23
3677486--3677520	18	1.9	18	94	0	61	25	2	2	68	1.17
3679082--3679150	30	2.3	30	85	5	86	27	34	18	18	1.95
3685283--3685434	30	5.1	30	80	6	148	30	22	3	42	1.72
3685303--3685434	59	2.2	59	83	5	167	31	21	3	43	1.70
3685736--3685776	21	2.1	19	86	13	57	78	7	14	0	0.96
3685918--3685972	3	18.3	3	96	0	101	65	0	32	1	1.03
3686258--3686319	6	10.5	6	73	26	53	80	1	16	1	0.87
3686254--3686319	21	3.1	21	78	8	73	80	1	16	1	0.87
3686243--3686319	27	2.8	28	82	11	79	79	1	18	1	0.88
3686242--3686319	15	5.0	15	75	14	61	78	1	19	1	0.90
3686470--3686527	28	2.1	28	90	6	91	39	3	0	56	1.16
3686782--3686879	37	2.8	34	82	15	119	35	11	9	43	1.72
3686785--3686879	34	2.7	33	83	15	111	36	10	9	43	1.72
3686787--3686882	19	5.4	18	67	18	67	39	10	9	40	1.72
3692084--3692205	43	2.8	43	81	7	158	26	29	18	25	1.98
3701958--3702016	30	2.0	30	93	0	100	47	15	15	22	1.82
3705566--3705650	25	3.4	25	85	3	82	29	21	25	23	1.99
3705555--3705650	50	1.9	50	81	8	115	30	19	26	23	1.98
3705581--3705785	25	8.4	24	71	5	99	36	20	24	18	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3705613--3705722	47	2.3	47	82	3	130	34	20	26	18	1.96
3705643--3705746	47	2.2	47	83	13	124	35	21	25	18	1.95
3712663--3712703	19	2.2	19	91	4	66	58	4	0	36	1.20
3713890--3713975	40	2.2	40	82	0	109	37	4	6	51	1.50
3716967--3717028	3	20.7	3	93	0	106	29	0	3	67	1.06
3718180--3718237	23	2.2	28	77	22	72	48	6	1	43	1.40
3718186--3718240	23	2.2	26	90	9	89	47	5	1	45	1.36
3728343--3728444	9	10.8	9	74	15	55	67	0	1	29	1.08
3728395--3728461	29	2.4	27	82	7	73	67	2	0	29	1.06
3728395--3728444	20	2.7	19	88	11	77	70	0	0	30	0.88
3728478--3728556	31	2.7	30	71	7	72	62	2	2	32	1.22
3729106--3729268	9	17.6	9	70	13	82	26	3	4	65	1.26
3729198--3729279	30	2.9	28	80	7	78	21	2	2	73	1.07
3733019--3733102	41	2.0	41	100	0	168	33	16	9	40	1.81
3737714--3737746	13	2.5	13	95	0	57	27	42	18	12	1.85
3748852--3748894	3	14.3	3	100	0	86	32	0	0	67	0.91
3760838--3760877	16	2.5	16	91	0	62	47	2	7	42	1.45
3760810--3760862	22	2.4	22	87	0	70	52	1	1	43	1.23
3760880--3760999	59	2.1	59	90	1	197	41	5	9	44	1.58
3761065--3761110	24	1.9	24	91	8	76	60	2	0	36	1.09
3761578--3761617	20	1.9	22	90	10	66	60	0	0	40	0.97
3761572--3761623	22	2.7	19	76	21	54	61	0	0	38	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3773255--3773323	16	4.2	16	96	3	129	24	0	37	37	1.56
3773255--3773323	33	2.1	32	97	2	129	24	0	37	37	1.56
3773304--3773394	45	2.0	45	85	2	121	27	6	28	37	1.82
3773558--3773592	18	2.0	17	88	5	52	54	0	0	45	0.99
3773536--3773801	120	2.2	119	93	1	442	49	4	1	43	1.35
3773676--3773712	16	2.2	17	86	13	51	54	0	2	43	1.14
3777596--3777643	20	2.2	21	82	10	62	62	4	6	27	1.38
3779472--3779588	62	1.9	62	100	0	234	30	28	11	29	1.92
3779791--3779826	2	18.0	2	88	0	54	50	0	44	5	1.25
3779791--3779826	16	2.2	16	100	0	72	50	0	44	5	1.25
3782525--3782561	2	18.5	2	100	0	74	48	0	0	51	1.00
3785238--3785293	25	2.2	25	87	6	78	28	5	19	46	1.72
3788421--3788459	17	2.3	17	86	8	53	30	0	20	48	1.50
3788598--3788705	21	5.3	20	82	2	94	16	21	17	44	1.87
3788656--3788702	19	2.5	19	96	0	85	17	25	17	40	1.90
3791980--3792031	21	2.5	20	84	6	68	38	5	28	26	1.79
3794231--3794294	21	3.0	22	75	9	78	35	25	20	18	1.95
3797080--3797115	18	2.1	18	89	5	56	33	25	0	41	1.55
3797867--3797904	14	2.4	17	87	12	55	52	0	0	47	1.00
3797884--3797935	12	4.8	11	73	21	56	46	1	0	51	1.12
3801188--3801373	90	2.1	89	93	2	320	24	1	17	57	1.46
3801369--3801590	114	2.0	113	90	2	347	27	1	13	58	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3801505--3801685	92	2.0	87	88	5	263	26	0	15	57	1.43
3802206--3802258	21	2.5	21	87	0	70	30	33	9	26	1.88
3806571--3806721	54	2.9	54	71	16	143	57	9	1	31	1.40
3806571--3806730	51	3.1	51	72	13	137	58	10	1	30	1.40
3807015--3807063	24	2.0	25	92	4	82	67	0	0	32	0.91
3814702--3814742	20	2.2	20	86	8	59	58	2	2	36	1.24
3814711--3814768	29	2.0	28	83	6	71	62	3	3	31	1.29
3817619--3817824	69	3.1	63	79	13	168	33	15	5	44	1.70
3817717--3817893	69	2.6	68	87	4	241	36	15	4	43	1.68
3819424--3819459	18	1.9	18	88	5	54	55	25	0	19	1.43
3821020--3821168	69	2.2	69	85	2	192	36	18	5	38	1.74
3821165--3821208	21	2.0	22	91	4	72	45	9	0	45	1.35
3837115--3837158	18	2.4	18	81	7	54	59	0	2	38	1.10
3837160--3837234	21	3.8	20	77	21	68	58	1	2	37	1.20
3837115--3837343	10	23.4	9	69	17	104	58	3	2	35	1.27
3837932--3838013	19	4.2	19	71	17	51	32	2	4	59	1.31
3838039--3838118	31	2.6	31	75	9	83	42	1	2	53	1.22
3844480--3844576	33	2.8	35	72	20	89	50	1	3	45	1.24
3848009--3848500	243	2.0	243	94	0	867	33	18	23	24	1.97
3851138--3851495	177	2.0	177	98	0	689	31	24	19	24	1.98
3864163--3864231	28	2.5	28	83	4	86	33	26	14	26	1.94
3864163--3864245	28	3.0	28	81	0	76	33	22	15	27	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3865640--3865664	12	2.1	12	100	0	50	84	0	0	16	0.63
3870478--3870511	12	2.9	11	91	8	50	0	14	17	67	1.23
3876448--3876486	20	1.9	20	89	5	60	20	17	23	38	1.93
3876575--3876622	21	2.2	22	77	3	53	54	0	0	45	0.99
3876636--3876685	17	2.7	18	82	14	50	64	2	4	30	1.23
3876798--3876863	30	2.2	30	82	12	75	28	4	1	65	1.21
3877237--3877285	22	2.3	22	83	13	59	24	6	4	65	1.33
3880936--3880965	13	2.3	13	100	0	60	46	10	6	36	1.64
3885041--3885073	15	2.1	16	88	5	50	15	12	27	45	1.81
3886041--3886077	19	1.9	19	88	0	56	2	27	18	51	1.60

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