genome.fa.s9.2.7.7.80.10.50.1000.176.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  176  of  226  ( 27023 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)
56300539--56300631	47	2.0	48	84	2	125	32	27	16	23	1.96
56303218--56303332	46	2.5	46	94	0	194	30	26	20	22	1.98
56303218--56303331	23	5.0	23	85	2	158	30	26	21	21	1.98
56306969--56306994	3	8.7	3	100	0	52	0	34	0	65	0.93
56308808--56308833	3	8.7	3	100	0	52	34	0	30	34	1.58
56311996--56312037	6	7.0	6	94	0	57	50	42	0	7	1.30
56311997--56312037	12	3.4	12	89	0	64	51	41	0	7	1.30
56314243--56314274	13	2.5	13	100	0	64	46	18	6	28	1.73
56315906--56315943	20	1.9	20	89	10	60	47	13	2	36	1.56
56316838--56316900	27	2.3	27	81	13	76	36	4	1	57	1.30
56317105--56317150	18	2.5	19	82	6	60	43	2	2	52	1.25
56317237--56317550	163	1.9	160	86	6	438	45	3	6	44	1.45
56317656--56317688	12	2.6	13	85	9	50	54	0	0	45	0.99
56324801--56324849	18	2.7	17	84	6	62	40	18	0	40	1.50
56328580--56328822	50	4.8	50	88	0	324	21	30	21	26	1.98
56345563--56345636	37	2.0	37	97	0	139	40	22	2	33	1.69
56354642--56354676	13	2.8	12	87	8	52	5	34	0	60	1.21
56354627--56354676	25	2.0	26	84	4	66	8	32	0	60	1.26
56360124--56360820	70	10.0	70	80	3	643	29	26	18	26	1.98
56360116--56360791	210	3.2	209	82	2	730	29	25	18	26	1.98
56362630--56362702	37	1.9	38	88	2	112	31	20	4	43	1.70
56362690--56362733	23	1.9	22	82	17	54	38	22	0	38	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56362907--56363046	50	2.8	51	82	6	185	31	27	15	25	1.95
56367117--56367646	39	13.6	39	91	0	810	44	19	4	32	1.70
56371319--56371409	39	2.3	39	81	3	112	43	15	4	36	1.67
56375745--56375950	104	2.0	105	94	0	360	27	23	17	31	1.97
56378624--56378883	127	2.1	122	89	4	387	38	16	8	37	1.78
56384021--56384067	18	2.6	19	76	10	53	40	6	0	53	1.27
56384296--56384367	27	2.8	25	81	10	92	34	0	1	63	1.03
56384296--56384369	26	2.8	26	85	4	96	35	0	1	63	1.03
56385326--56385351	3	8.7	3	100	0	52	34	34	0	30	1.58
56388109--56388227	28	4.3	28	86	5	154	26	24	13	35	1.93
56390660--56390749	25	3.6	24	75	11	83	32	22	18	26	1.97
56392731--56392831	42	2.4	42	76	3	105	33	19	16	29	1.94
56398775--56398813	20	2.0	20	85	10	53	35	0	17	46	1.49
56409721--56409816	41	2.3	41	85	0	120	22	20	25	31	1.98
56413383--56413456	28	2.7	28	82	2	87	48	10	13	27	1.75
56414047--56414077	16	2.0	16	93	6	55	45	19	16	19	1.86
56440124--56440188	34	1.9	34	81	12	80	30	18	21	29	1.97
56443527--56443780	88	2.8	89	79	8	280	28	14	10	47	1.76
56444212--56444316	37	2.7	38	77	5	104	38	20	21	20	1.94
56444902--56445098	14	13.9	14	70	12	89	21	1	28	48	1.59
56444902--56445027	7	17.7	7	70	9	67	19	1	29	50	1.57
56445063--56445106	13	3.1	14	83	9	54	18	0	34	47	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56445065--56445106	20	2.0	20	90	4	66	16	0	33	50	1.46
56452447--56452508	27	2.3	27	97	0	115	29	22	33	14	1.94
56452611--56452654	21	2.2	19	92	8	70	70	0	2	27	0.99
56452816--56452853	19	2.0	19	89	0	58	50	7	5	36	1.54
56466107--56466226	22	5.2	22	74	9	89	54	6	16	22	1.65
56466107--56466336	24	10.4	22	67	16	93	52	8	16	22	1.70
56466138--56466382	129	1.9	134	79	7	288	52	9	16	20	1.72
56469254--56469315	30	2.1	29	82	11	72	50	3	0	46	1.17
56472798--56472894	48	2.0	48	100	0	194	40	30	12	16	1.85
56474796--56474850	27	2.0	27	100	0	110	40	10	3	45	1.57
56478998--56479394	126	3.2	126	85	5	484	29	16	15	38	1.90
56479453--56479558	34	3.2	33	85	5	140	42	14	0	43	1.45
56479455--56479581	68	1.9	68	86	0	182	42	14	0	42	1.50
56479465--56479581	34	3.4	34	81	9	139	40	15	0	43	1.52
56480769--56480809	20	2.0	20	95	0	73	63	4	7	24	1.40
56483496--56484031	268	2.0	265	85	4	729	34	13	19	32	1.91
56488032--56488076	7	6.3	7	79	5	54	15	0	37	46	1.46
56488028--56488076	22	2.2	22	88	0	71	14	0	40	44	1.45
56488229--56488303	37	2.0	39	87	10	111	62	1	4	32	1.22
56488515--56488554	6	6.7	6	94	0	71	20	0	45	35	1.51
56492649--56492889	50	4.8	50	90	0	365	25	22	31	20	1.98
56493290--56493351	17	3.6	17	100	0	124	54	6	14	24	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56498784--56498883	51	2.0	51	92	4	166	46	2	28	24	1.64
56498800--56498892	11	8.7	11	70	18	63	45	2	29	23	1.65
56501949--56501982	6	5.7	6	100	0	68	52	0	0	47	1.00
56505397--56505541	47	3.1	47	72	16	158	44	2	3	49	1.30
56505382--56505597	91	2.4	91	93	0	369	46	2	3	46	1.35
56505474--56505665	101	2.0	92	78	15	194	47	3	2	46	1.32
56505413--56505556	47	3.1	47	69	20	140	45	2	2	50	1.28
56505990--56506028	16	2.4	16	91	0	60	20	30	5	43	1.73
56506148--56506209	32	1.9	32	93	0	106	56	14	0	29	1.39
56507352--56507394	22	2.0	22	86	9	61	41	0	13	44	1.44
56508365--56508403	20	1.9	21	84	5	53	35	2	0	61	1.10
56511896--56512067	45	3.8	45	83	4	177	41	14	22	22	1.89
56511986--56512112	45	2.8	44	80	4	121	41	13	21	23	1.88
56522273--56522319	20	2.2	22	85	11	62	51	12	2	34	1.52
56529774--56529914	25	6.0	24	70	16	107	43	19	12	24	1.85
56529798--56529920	47	2.6	47	96	1	221	44	18	10	26	1.82
56530851--56530949	28	3.6	27	81	11	112	28	28	12	31	1.92
56535170--56535209	20	2.0	20	85	9	55	42	22	27	7	1.80
56542456--56542664	45	4.6	45	88	0	274	47	10	19	23	1.79
56544842--56544884	24	1.9	23	86	13	63	32	11	18	37	1.87
56554968--56554997	15	1.9	16	93	6	53	56	0	0	43	0.99
56563778--56563835	29	2.0	29	93	0	98	53	15	8	22	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56565359--56565409	26	2.0	24	85	7	66	31	0	1	66	1.03
56567006--56567037	14	2.1	16	88	11	50	53	3	0	43	1.16
56572985--56573011	10	2.7	10	100	0	54	18	7	0	74	1.05
56585218--56587045	132	13.9	132	90	1	2806	31	21	23	23	1.98
56586018--56586994	44	22.2	44	64	9	130	31	21	23	23	1.99
56593545--56593590	24	2.0	24	86	4	67	41	8	8	41	1.67
56596997--56597087	30	3.0	30	78	0	110	25	12	21	40	1.88
56601983--56602023	15	2.8	15	88	3	57	75	4	7	12	1.16
56602736--56602810	26	2.9	26	82	13	84	41	37	5	16	1.71
56606579--56606609	16	1.9	16	100	0	62	58	6	0	35	1.24
56609130--56609414	125	2.3	125	90	0	444	34	18	21	25	1.96
56612598--56612694	34	2.7	35	85	7	117	47	6	3	43	1.44
56612825--56612871	21	2.2	21	85	7	60	6	21	40	31	1.78
56613113--56613155	18	2.4	18	88	0	59	44	9	30	16	1.79
56613781--56613805	7	3.6	7	100	0	50	60	12	0	28	1.32
56615015--56615095	11	7.4	11	86	9	112	45	0	34	19	1.51
56615684--56615789	54	2.0	54	85	5	144	34	7	11	46	1.68
56620380--56620446	6	11.0	6	81	15	66	76	4	4	14	1.11
56622035--56622111	5	14.0	5	77	14	64	72	1	6	19	1.13
56622056--56622119	21	3.2	20	76	20	71	75	0	6	18	1.01
56622035--56622119	11	7.5	11	75	15	68	72	1	7	18	1.13
56622026--56622129	26	3.9	26	73	14	79	72	1	6	19	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56624068--56624265	50	3.8	50	83	4	234	22	27	21	28	1.99
56626830--56626935	40	2.7	40	80	4	133	16	27	17	37	1.92
56631666--56631714	7	7.3	7	81	4	57	16	0	36	46	1.47
56633171--56633241	25	2.8	24	70	16	63	19	5	26	47	1.71
56633771--56634054	143	2.0	143	89	0	433	28	10	21	39	1.86
56634642--56638348	705	5.4	697	79	8	3436	36	12	13	37	1.82
56642010--56642164	39	4.0	39	81	3	177	17	29	18	34	1.94
56642014--56642116	20	5.2	20	61	17	54	14	32	19	33	1.92
56642007--56642184	78	2.3	78	86	1	232	17	29	17	34	1.93
56642002--56642189	39	4.8	39	78	1	171	17	28	18	35	1.94

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   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226