genome.fa.s1.2.7.7.80.10.50.1000.184.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  184  of  187  ( 22383 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)
55084128--55084190	28	2.2	30	85	8	94	38	0	1	60	1.07
55084281--55084316	16	2.3	15	90	4	54	25	0	5	69	1.10
55084281--55084330	15	3.3	15	85	2	55	24	0	6	70	1.10
55085889--55086091	84	2.4	84	97	0	379	32	23	20	23	1.98
55086001--55086280	124	2.3	124	88	3	420	31	23	15	28	1.95
55086867--55086912	20	2.2	22	84	7	60	41	2	2	54	1.25
55106416--55106462	18	2.6	18	82	0	58	12	36	4	46	1.62
55108861--55108892	15	2.1	15	94	0	55	15	6	9	68	1.36
55118245--55118318	37	2.0	37	91	0	121	21	18	12	47	1.81
55120477--55120508	13	2.5	13	94	0	55	15	28	12	43	1.83
55121450--55121526	21	3.6	21	77	6	73	36	24	22	16	1.94
55121443--55121545	23	4.7	22	80	5	95	35	25	20	18	1.95
55122508--55122537	14	2.1	14	100	0	60	20	6	0	73	1.05
55124237--55124307	36	2.0	36	88	0	106	38	21	2	38	1.68
55131475--55131544	35	2.0	36	88	2	106	37	22	10	30	1.87
55134666--55134890	78	3.0	76	81	12	279	29	19	12	38	1.88
55134751--55134889	68	2.0	68	88	0	206	30	17	12	39	1.86
55138890--55138921	2	17.0	2	87	12	50	53	0	46	0	1.00
55142911--55142951	3	13.7	3	100	0	82	31	0	0	68	0.90
55170645--55170708	2	32.5	2	73	9	51	43	7	0	48	1.32
55170643--55170696	29	1.9	29	85	7	76	42	5	0	51	1.25
55170627--55170762	39	3.5	40	73	14	113	38	5	0	55	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55170608--55170755	39	3.9	38	72	11	106	39	7	0	52	1.35
55170652--55170708	12	4.8	12	79	10	64	42	8	0	49	1.34
55170652--55170786	39	3.5	39	81	8	123	38	7	0	54	1.29
55171955--55172539	120	4.9	120	97	0	1091	48	5	2	42	1.42
55172058--55172104	16	3.0	16	78	12	53	51	2	0	46	1.13
55172201--55172237	16	2.2	17	86	13	51	54	0	2	43	1.14
55172314--55172353	14	2.9	15	82	14	50	52	0	0	47	1.00
55172321--55172357	16	2.2	17	86	13	51	59	0	0	40	0.97
55172441--55172477	16	2.2	17	86	13	51	54	0	2	43	1.14
55205057--55205089	16	2.1	15	94	5	57	57	0	0	42	0.98
55207381--55207550	74	2.3	72	78	10	191	38	19	22	20	1.94
55207521--55207578	26	2.2	26	87	0	89	37	22	20	18	1.94
55207533--55207593	26	2.3	26	88	5	88	34	24	24	16	1.95
55207651--55207697	25	1.9	25	86	4	69	42	19	19	19	1.89
55207958--55208006	18	2.7	18	77	3	53	40	44	2	12	1.53
55208119--55208183	9	7.2	9	76	13	71	29	10	20	40	1.86
55208119--55208183	27	2.4	27	82	10	87	29	10	20	40	1.86
55216618--55216663	15	3.1	15	84	12	60	21	8	0	69	1.15
55216624--55216668	15	3.2	14	85	14	58	20	6	0	73	1.05
55224490--55224557	29	2.4	29	74	16	70	30	4	8	55	1.50
55227131--55227193	20	3.3	18	81	14	72	39	4	9	46	1.58
55229722--55229833	41	2.7	41	87	5	172	20	27	24	27	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55230357--55230401	2	22.5	2	100	0	90	51	0	0	48	1.00
55231432--55231503	36	2.0	35	89	2	108	33	8	27	30	1.86
55231801--55231896	48	2.0	48	87	0	138	20	14	20	43	1.87
55236622--55236693	36	2.0	35	89	2	108	33	8	27	30	1.86
55236991--55237086	48	2.0	48	91	0	156	19	15	21	42	1.88
55240336--55240433	28	3.5	28	76	6	99	48	18	15	17	1.81
55247589--55247657	15	4.7	14	74	10	50	43	1	2	52	1.25
55253969--55254024	22	2.6	21	77	8	58	25	17	33	23	1.96
55255668--55255906	116	2.1	116	99	0	469	21	25	2	51	1.59
55256050--55256090	20	2.0	20	95	0	73	36	36	17	9	1.82
55261318--55261393	31	2.4	32	80	10	86	35	14	6	43	1.71
55266345--55266414	29	2.3	29	85	4	86	22	14	15	47	1.82
55266961--55267037	29	2.6	29	83	4	91	48	14	12	24	1.79
55266986--55267059	29	2.5	29	86	8	96	48	14	13	22	1.79
55268235--55268259	7	3.6	7	100	0	50	28	0	0	72	0.86
55268354--55268399	22	2.0	24	87	8	69	45	0	21	32	1.52
55268918--55268961	21	2.1	21	87	8	63	36	0	15	47	1.46
55269510--55269560	24	2.1	24	92	0	84	19	25	17	37	1.94
55269524--55269577	24	2.2	25	83	9	67	16	22	24	37	1.94
55270589--55270635	24	2.0	24	84	16	62	31	0	17	51	1.46
55270606--55270657	21	2.5	21	73	14	54	36	0	15	48	1.45
55270791--55270924	39	3.5	38	74	11	121	27	16	22	33	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55271068--55271107	20	2.0	20	95	0	71	40	7	20	32	1.80
55272574--55272619	21	2.2	21	84	7	58	47	21	4	26	1.69
55277458--55277529	32	2.2	32	85	4	92	38	8	11	41	1.71
55278553--55278656	52	2.0	52	90	3	165	25	26	25	22	2.00
55281819--55281844	11	2.4	11	100	0	52	38	7	0	53	1.30
55281841--55281903	9	6.4	10	76	20	53	30	1	0	68	0.99
55281830--55281893	30	2.1	29	83	11	76	34	3	0	62	1.11
55281830--55281936	41	3.1	35	75	23	100	29	3	0	65	1.16
55281807--55281915	40	2.7	42	83	7	145	34	4	0	60	1.17
55288919--55288958	6	6.7	6	82	0	53	2	32	17	47	1.61
55289677--55289713	13	2.9	13	92	4	58	40	43	0	16	1.48
55289695--55289810	38	3.0	38	93	2	196	50	26	2	19	1.60
55289944--55290004	17	3.4	17	68	12	50	32	3	13	50	1.57
55289939--55290013	37	2.0	37	97	0	141	34	5	14	45	1.68
55290012--55290052	9	4.6	9	90	0	64	24	9	21	43	1.83
55297125--55297150	4	6.5	4	100	0	52	0	23	0	76	0.78
55299345--55299394	15	3.2	15	76	20	57	50	14	0	36	1.43
55299372--55299418	24	2.0	24	84	16	62	51	17	0	31	1.46
55312754--55312800	20	2.3	21	82	17	64	36	0	8	55	1.31
55312754--55312805	19	2.7	20	85	14	65	32	0	7	59	1.26
55320287--55320375	36	2.5	36	74	18	87	46	2	2	49	1.26
55321645--55321754	56	1.9	56	83	5	141	40	17	22	20	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55321756--55321974	111	1.9	112	86	4	307	30	15	20	33	1.94
55322544--55322715	53	3.2	52	85	6	238	51	1	22	25	1.55
55324567--55324635	28	2.6	27	78	15	72	68	0	7	24	1.15
55324723--55324784	3	19.3	3	78	18	63	59	4	0	35	1.19
55324724--55324783	29	2.0	29	84	15	79	61	5	0	33	1.17
55327063--55327087	13	1.9	13	100	0	50	24	0	0	76	0.80
55327115--55327152	18	2.1	19	85	5	51	15	7	0	76	1.01
55327663--55327812	56	2.7	55	85	4	183	18	24	17	39	1.92
55332506--55332550	22	2.0	23	83	12	58	44	2	2	51	1.26
55338082--55338165	41	2.0	41	97	0	159	26	9	8	55	1.60
55358505--55358557	19	3.0	17	73	10	52	35	9	20	33	1.85
55358529--55358573	23	2.0	23	86	4	65	40	2	17	40	1.62
55363640--55363692	19	3.0	17	76	10	61	37	7	18	35	1.80
55363664--55363721	22	2.7	21	86	7	80	34	3	18	43	1.68
55368232--55368273	21	2.0	21	100	0	84	38	28	9	23	1.86
55368895--55368940	22	2.1	22	84	8	58	34	2	4	58	1.30
55368995--55369093	40	2.6	36	81	10	110	49	7	4	39	1.49
55371590--55371631	2	21.0	2	100	0	84	50	0	50	0	1.00
55373025--55373100	37	2.1	37	94	0	134	28	15	27	27	1.96
55375026--55375067	16	2.8	16	89	7	61	54	0	4	40	1.21
55377565--55377589	12	2.1	12	100	0	50	76	0	16	8	1.02
55379810--55379853	2	22.0	2	100	0	88	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55382131--55382156	3	8.7	3	100	0	52	0	34	0	65	0.93
55391590--55391628	21	1.9	20	85	15	53	61	0	7	30	1.24
55391580--55391626	24	1.9	25	95	4	87	57	0	8	34	1.29
55391793--55391858	25	2.6	25	95	0	114	28	21	39	10	1.86
55391994--55392135	40	3.5	40	83	3	178	16	21	19	42	1.88
55391996--55392188	40	4.8	41	81	1	140	17	22	20	39	1.92
55394903--55394952	12	4.2	12	73	21	52	38	0	0	62	0.96
55394901--55394958	23	2.6	24	75	22	63	39	0	0	60	0.97
55394903--55394956	16	3.1	17	79	15	58	37	0	0	62	0.95
55405546--55405583	20	2.0	20	89	5	60	2	0	23	73	0.95

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