genome.fa.s6.2.7.7.80.10.50.1000.136.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  136  of  168  ( 20060 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)
39797223--39797335	33	3.6	32	77	17	121	0	31	0	68	0.90
39799227--39799287	10	6.8	9	75	12	54	39	1	0	59	1.08
39799227--39799350	27	4.3	27	74	21	99	40	2	0	57	1.12
39799234--39799385	11	14.8	11	70	24	95	40	2	0	56	1.13
39799234--39799373	52	2.8	50	82	9	160	39	2	0	57	1.13
39799307--39799339	16	2.0	17	94	5	59	39	0	0	60	0.97
39800056--39800085	14	2.1	14	93	0	51	30	0	0	70	0.88
39802161--39802190	14	2.1	14	93	0	51	53	3	3	40	1.34
39805482--39805515	14	2.7	12	90	9	50	79	0	14	5	0.91
39805561--39805602	17	2.4	17	85	14	59	71	0	0	28	0.86
39805561--39805602	12	3.6	12	78	15	52	71	0	0	28	0.86
39807458--39807607	70	2.1	70	85	4	196	32	19	16	32	1.93
39809581--39809606	5	5.2	5	100	0	52	0	61	19	19	1.35
39820365--39820389	2	12.5	2	100	0	50	52	0	0	48	1.00
39823994--39824037	22	2.0	22	86	0	61	11	18	25	45	1.82
39824087--39824208	39	3.0	41	87	6	185	21	21	21	36	1.96
39824084--39824214	42	3.2	42	86	6	196	19	21	22	36	1.95
39824530--39824574	21	2.1	21	91	0	72	2	46	17	33	1.61
39828124--39828169	7	6.6	7	79	0	56	28	47	2	21	1.62
39828243--39828333	7	13.3	7	81	9	89	34	45	0	20	1.52
39828243--39828364	21	5.8	21	72	18	60	36	41	0	21	1.59
39828356--39828389	15	2.3	15	90	5	52	35	29	0	35	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39828623--39829172	114	4.8	114	87	2	768	28	25	22	23	1.99
39832674--39832737	28	2.4	24	76	20	65	64	1	3	31	1.19
39832669--39832799	39	3.3	39	77	15	135	64	0	2	32	1.12
39835741--39835842	2	51.0	2	100	0	204	0	50	0	50	1.00
39838943--39838977	15	2.4	15	90	4	54	48	0	8	42	1.33
39842504--39843135	314	2.0	313	97	0	1201	30	18	13	36	1.90
39849878--39849938	20	3.0	20	77	18	56	37	4	1	55	1.31
39849896--39849939	21	2.1	21	91	8	72	43	4	0	52	1.22
39850151--39850186	2	18.0	2	94	0	63	50	2	0	47	1.15
39853233--39853257	12	2.1	12	100	0	50	40	0	8	52	1.31
39853688--39853721	3	11.3	3	93	0	50	38	32	0	29	1.58
39853721--39853770	3	16.7	3	95	0	91	30	0	2	68	1.01
39856894--39856940	24	2.0	24	87	8	69	46	8	6	38	1.60
39861319--39861370	24	2.2	24	82	6	61	50	9	5	34	1.59
39864022--39864091	33	2.1	34	86	5	97	45	11	5	37	1.64
39868673--39868831	67	2.4	67	92	2	257	29	8	19	42	1.81
39870339--39870373	2	17.5	2	100	0	70	48	0	0	51	1.00
39878896--39878986	34	2.7	33	88	8	130	39	0	15	45	1.46
39879048--39879443	126	3.1	126	82	3	494	37	16	15	30	1.90
39885019--39885075	25	2.3	24	77	11	62	52	3	0	43	1.18
39885029--39885210	89	2.0	90	95	1	330	54	4	3	37	1.39
39885574--39885616	18	2.4	18	88	0	59	44	9	25	20	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39891382--39891435	18	2.9	18	83	2	63	40	44	1	12	1.54
39891456--39891509	6	8.7	6	86	8	63	68	9	0	22	1.17
39891456--39891517	18	3.3	19	84	6	72	66	9	1	22	1.30
39892256--39892503	57	4.4	57	84	3	297	31	10	15	42	1.81
39892256--39892540	56	5.1	56	81	5	240	30	11	15	42	1.82
39899752--39899790	18	2.2	17	86	13	53	33	0	20	46	1.51
39900016--39900160	23	6.3	23	93	0	236	18	20	27	33	1.96
39900290--39900361	36	1.9	38	83	10	96	44	1	22	31	1.61
39901310--39901369	2	30.0	2	100	0	120	50	0	0	50	1.00
39902190--39902339	77	2.0	76	89	2	230	32	18	11	38	1.86
39902393--39902422	11	2.7	11	94	0	51	73	0	3	23	0.98
39912975--39913029	26	2.3	23	77	17	65	27	9	20	43	1.81
39912983--39913033	26	2.0	26	96	0	93	23	7	21	47	1.77
39919085--39919119	6	5.5	6	87	12	52	65	0	20	14	1.26
39919034--39919162	64	2.0	64	85	8	174	47	5	20	27	1.72
39919111--39919197	44	2.0	44	88	0	129	40	8	19	32	1.81
39921182--39921267	25	3.4	25	77	6	84	22	26	18	32	1.97
39924948--39925041	21	4.4	21	88	6	127	54	1	3	41	1.23
39924968--39925045	23	3.5	23	96	3	142	53	0	3	42	1.19
39927522--39927551	15	2.0	15	93	0	51	3	6	16	73	1.18
39931536--39931578	18	2.4	18	80	7	52	60	0	0	39	0.97
39932007--39932034	11	2.5	11	100	0	56	7	39	10	42	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39935528--39935562	18	2.0	17	88	5	52	45	0	0	54	0.99
39935684--39935718	18	2.0	17	88	5	52	45	0	0	54	0.99
39935516--39935831	156	2.0	157	95	0	562	47	4	3	44	1.41
39935864--39935987	45	2.9	43	76	15	116	35	30	5	28	1.80
39943324--39943382	27	2.2	27	93	0	100	33	16	11	37	1.86
39950807--39950838	2	15.5	2	93	6	55	50	46	0	3	1.17
39952759--39952912	40	3.8	39	77	9	143	35	20	22	20	1.96
39952951--39953228	41	6.8	41	83	1	342	20	24	24	30	1.98
39952976--39953233	124	2.1	123	86	2	347	19	26	24	29	1.98
39953197--39953262	34	1.9	35	84	6	91	28	24	19	27	1.99
39955298--39955648	43	8.2	42	86	3	441	18	19	32	28	1.96
39955298--39955648	86	4.1	86	87	0	497	18	19	32	28	1.96
39955298--39955648	129	2.7	129	88	0	515	18	19	32	28	1.96
39955700--39955742	22	2.0	22	90	0	68	44	27	18	9	1.80
39957353--39957471	61	2.0	61	87	0	175	42	13	12	31	1.82
39961032--39961106	3	28.0	3	73	26	71	61	0	0	38	0.96
39961024--39961107	5	15.8	5	89	10	123	59	0	0	40	0.97
39961023--39961107	43	2.0	43	93	6	145	58	0	0	41	0.98
39971122--39971179	25	2.3	25	87	0	80	41	6	12	39	1.69
39971699--39971748	21	2.2	24	80	20	63	38	2	4	56	1.30
39974647--39974782	31	4.5	31	71	22	117	27	17	12	42	1.85
39974678--39974790	60	1.9	60	90	0	181	24	15	12	46	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39975689--39975748	23	2.8	23	73	16	58	55	0	3	41	1.16
39981983--39982028	20	2.3	20	78	17	51	43	2	6	47	1.41
39989215--39989291	38	2.0	38	85	5	102	61	6	1	31	1.30
39992780--39992836	29	2.0	28	82	6	69	43	1	12	42	1.52
39993127--39993166	2	20.0	2	100	0	80	50	0	0	50	1.00
39999220--39999254	14	2.5	14	95	0	61	34	20	5	40	1.76
39999857--39999890	12	2.8	12	90	0	50	23	35	35	5	1.79
40000445--40000536	48	1.9	48	90	0	148	50	9	7	32	1.64
40000470--40000720	62	4.1	62	91	2	416	49	6	6	38	1.54
40000470--40000720	122	2.0	123	93	1	423	49	6	6	38	1.54
40005126--40005274	40	3.6	40	87	8	185	35	3	0	61	1.13
40022612--40022656	20	2.2	20	96	0	81	42	4	20	33	1.72
40036448--40036487	20	2.1	20	86	9	57	45	2	2	50	1.28
40040125--40040205	23	3.4	24	73	18	64	44	2	3	49	1.33
40040133--40040171	15	2.6	15	79	0	51	38	2	5	53	1.37
40040940--40041006	19	3.2	21	76	20	70	41	1	2	53	1.25
40042572--40042613	18	2.3	18	95	0	75	19	38	26	16	1.92
40053011--40053104	46	2.0	46	95	0	170	19	29	18	32	1.95
40054600--40054797	105	1.9	101	83	6	254	31	17	24	26	1.97
40054738--40054814	33	2.3	32	80	6	82	31	18	24	25	1.97
40054633--40054831	105	1.9	105	82	6	251	33	18	23	25	1.97
40063715--40063767	26	2.0	26	81	0	61	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40064149--40064173	2	12.5	2	100	0	50	48	0	0	52	1.00
40068525--40068603	3	26.3	3	100	0	158	67	0	0	32	0.91
40073219--40073257	19	2.1	19	100	0	78	30	30	5	33	1.79
40074711--40074753	3	14.0	3	95	4	77	65	0	34	0	0.93
40074712--40074758	6	7.4	7	95	2	50	61	0	38	0	0.96
40075803--40075858	26	2.2	26	100	0	112	35	23	12	28	1.91
40078561--40078605	17	2.7	16	80	10	54	11	8	0	80	0.92
40078553--40078605	24	2.2	24	83	12	74	15	7	0	77	0.98
40079601--40079625	13	1.9	13	100	0	50	76	0	24	0	0.80
40082183--40082331	37	4.0	37	95	0	262	26	20	14	38	1.91

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