genome.fa.s1.2.7.7.80.10.50.1000.103.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  103  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)
30380066--30380135	35	2.0	34	97	2	131	42	20	8	28	1.81
30386571--30386620	18	2.8	17	76	8	55	42	14	4	40	1.64
30393965--30394001	9	4.1	9	92	0	65	29	10	13	45	1.77
30394054--30394083	9	3.4	9	90	9	53	40	23	13	23	1.90
30395440--30395467	14	2.0	14	100	0	56	0	21	0	78	0.75
30400095--30400123	12	2.4	12	100	0	58	86	0	6	6	0.72
30405988--30406038	21	2.4	22	83	6	61	7	21	1	68	1.25
30408364--30408410	25	1.9	24	86	4	67	51	10	19	19	1.75
30420049--30420078	3	10.0	3	92	0	51	0	3	66	30	1.07
30425449--30425508	3	19.3	3	74	19	52	26	3	3	66	1.23
30425830--30425879	24	2.2	22	85	7	64	20	6	4	70	1.25
30425968--30426006	20	2.0	20	85	10	53	25	10	2	61	1.41
30426050--30426356	110	2.8	110	91	3	471	29	17	18	34	1.94
30429723--30429752	9	3.4	9	90	9	53	30	0	0	70	0.88
30429724--30429753	8	3.6	8	91	8	51	33	0	0	66	0.92
30429838--30429899	29	2.0	31	81	9	74	37	3	1	58	1.24
30429865--30429951	19	4.3	20	68	20	65	27	3	2	66	1.20
30430133--30430172	20	2.0	21	85	14	57	25	5	7	62	1.42
30434392--30434446	24	2.3	24	87	9	85	40	0	0	60	0.97
30434408--30434463	24	2.3	24	84	6	69	39	1	1	57	1.20
30434540--30434574	10	3.4	10	88	4	52	60	0	0	40	0.97
30443723--30443769	5	9.4	5	81	9	60	61	0	2	36	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30444098--30444145	25	2.0	24	91	4	78	72	2	25	0	0.95
30449672--30449742	33	2.2	33	81	0	79	33	21	23	21	1.97
30450129--30450182	26	2.1	26	82	0	63	40	25	16	16	1.89
30450337--30450395	26	2.2	26	84	3	73	23	18	18	38	1.93
30476235--30476280	13	3.5	13	87	3	65	34	23	4	36	1.75
30489411--30489457	23	2.0	23	100	0	94	34	29	14	21	1.93
30490567--30490603	19	1.9	19	94	0	65	35	0	0	64	0.94
30490568--30490610	20	2.2	19	87	4	59	34	0	2	62	1.08
30491367--30491559	50	3.7	50	82	8	219	23	29	21	25	1.99
30492516--30492555	20	2.0	20	100	0	80	45	20	20	15	1.86
30495612--30495888	40	6.9	40	81	0	311	32	17	28	21	1.96
30511916--30512222	40	7.8	40	80	2	316	32	18	28	20	1.96
30511937--30512220	119	2.4	120	82	3	324	30	18	29	21	1.97
30516827--30516866	21	1.9	21	90	10	64	70	2	5	22	1.19
30519010--30519085	35	2.2	35	82	15	97	30	9	19	40	1.83
30525690--30525958	23	11.8	23	71	10	117	21	4	32	41	1.73
30525693--30525939	115	2.2	113	91	3	395	21	4	31	42	1.73
30533179--30533219	21	2.0	21	95	0	73	12	34	26	26	1.92
30533180--30533226	21	2.2	21	88	0	67	17	38	23	21	1.93
30536958--30537122	71	2.3	71	88	1	240	35	30	9	24	1.88
30540304--30540403	42	2.4	42	94	0	173	24	28	12	36	1.91
30542939--30542980	22	1.9	22	95	0	75	21	9	11	57	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30544285--30544468	38	4.8	38	80	0	188	16	19	29	35	1.93
30546290--30546323	17	2.0	17	100	0	68	29	23	5	41	1.78
30546576--30546783	106	2.0	106	92	0	344	32	9	20	37	1.84
30557534--30557682	23	6.5	23	69	8	115	18	4	34	43	1.68
30572811--30572950	69	2.0	69	92	0	235	20	30	5	44	1.72
30577382--30577414	6	5.5	6	92	0	57	57	0	27	15	1.38
30586965--30587296	27	12.3	27	76	9	209	38	20	18	22	1.94
30586965--30587320	54	6.6	55	75	9	245	37	19	19	22	1.94
30587300--30587353	26	2.1	26	82	6	65	24	14	24	37	1.93
30587350--30587399	24	2.1	24	92	0	82	20	8	22	50	1.74
30587545--30587693	32	4.7	32	78	4	151	24	22	16	36	1.94
30587545--30587669	64	2.0	64	85	0	169	24	23	16	36	1.94
30600608--30600659	23	2.2	23	86	3	68	17	17	19	46	1.85
30603075--30603141	26	2.6	26	82	0	89	41	13	14	29	1.85
30614391--30614595	111	1.9	110	96	1	383	47	13	10	28	1.76
30629206--30629350	49	2.9	50	81	2	166	26	21	29	22	1.99
30637224--30637253	7	4.3	7	91	0	51	50	13	36	0	1.42
30644833--30644877	10	4.3	10	81	10	54	31	0	13	55	1.38
30646677--30646725	20	2.5	20	81	15	66	57	6	24	12	1.58
30649415--30649766	55	6.4	55	78	10	301	31	10	18	40	1.84
30649431--30649704	82	3.3	82	84	5	331	31	9	19	39	1.83
30649437--30649736	27	10.9	27	78	11	247	31	9	20	39	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30649751--30649787	18	2.0	19	89	5	58	37	13	13	35	1.84
30649696--30649842	73	2.0	73	85	2	197	30	10	18	40	1.84
30649669--30649866	100	2.0	100	82	5	240	30	10	18	40	1.83
30649769--30649872	27	3.8	27	77	6	102	28	9	21	40	1.84
30653852--30653890	17	2.5	16	84	16	55	15	46	0	38	1.46
30653855--30653896	19	2.2	19	86	0	57	14	47	0	38	1.44
30662033--30662061	11	2.6	11	100	0	58	27	0	0	72	0.85
30662771--30662805	15	2.4	15	90	4	54	48	0	8	42	1.33
30675527--30675599	30	2.4	30	83	2	83	24	17	6	50	1.70
30677288--30677564	50	5.5	50	87	6	362	23	31	20	24	1.98
30681348--30681382	16	2.1	17	89	5	54	11	48	0	40	1.39
30683978--30684171	50	3.9	50	79	0	192	29	20	27	22	1.98
30684383--30684416	14	2.7	12	90	9	50	61	0	14	23	1.33
30690825--30691071	50	4.8	50	79	5	210	29	20	26	23	1.99
30705275--30705305	15	2.1	15	100	0	62	35	0	12	51	1.40
30709880--30709921	5	8.2	5	89	5	66	61	2	0	35	1.09
30711088--30711141	26	2.1	26	100	0	108	33	7	0	59	1.25
30713461--30713509	19	2.7	17	84	9	62	24	46	20	8	1.77
30714064--30714097	15	2.3	15	94	0	59	61	8	11	17	1.54
30714466--30714512	21	2.3	20	89	7	69	68	8	0	23	1.17
30720717--30720754	20	1.9	20	89	10	60	60	5	0	34	1.19
30727433--30727470	17	2.2	17	90	9	60	36	0	47	15	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30727436--30727477	15	2.7	15	83	16	59	35	0	50	14	1.43
30755647--30755697	26	2.0	26	84	0	66	19	27	31	21	1.97
30755671--30756078	85	4.8	85	89	2	597	23	16	26	33	1.95
30755674--30756076	43	9.5	41	70	16	247	23	16	26	33	1.95
30763287--30763319	12	2.8	12	86	4	50	81	0	15	3	0.80
30765920--30765980	29	2.1	29	90	0	95	18	31	29	21	1.96
30770251--30770288	10	3.5	11	86	13	53	63	2	0	34	1.09
30777945--30777972	14	2.0	14	100	0	56	57	7	14	21	1.61
30778555--30778581	9	3.0	9	100	0	54	44	22	11	22	1.84
30781205--30781253	21	2.3	21	75	6	55	26	40	22	10	1.86
30788283--30788324	15	2.8	15	92	0	66	54	2	2	40	1.26
30792332--30792360	3	9.7	3	100	0	58	0	34	0	65	0.93
30803917--30804056	53	2.6	53	88	2	199	43	20	17	19	1.88
30803917--30804056	27	5.2	27	87	1	192	43	20	17	19	1.88
30803917--30804084	53	3.1	53	80	6	171	42	19	17	20	1.89
30804216--30804295	26	3.1	26	89	3	135	20	21	22	36	1.95
30804406--30804468	28	2.3	27	86	5	90	20	23	25	30	1.99
30804487--30804522	14	2.6	14	100	0	72	16	16	22	44	1.86
30816383--30816433	23	2.3	23	86	3	68	33	7	21	37	1.82
30823277--30823316	21	1.9	21	85	10	55	37	2	5	55	1.35
30827407--30827445	20	2.0	19	85	14	53	46	10	12	30	1.75
30839033--30839075	10	4.3	10	81	0	59	53	39	4	2	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30841438--30841559	23	5.3	23	83	3	156	22	21	24	31	1.98
30841438--30841559	46	2.7	46	90	2	192	22	21	24	31	1.98
30846323--30846404	30	2.7	30	85	7	112	32	19	6	41	1.76
30846997--30847052	13	4.5	13	78	14	55	75	0	25	0	0.81
30846981--30847052	24	2.7	27	74	22	64	70	0	29	0	0.87
30847147--30847208	7	8.3	7	78	18	63	82	0	14	3	0.80
30847141--30847208	22	3.0	21	78	19	75	80	0	16	2	0.82
30847154--30847208	15	3.7	14	88	11	83	83	0	12	3	0.77
30847148--30847209	31	2.0	31	90	6	99	80	0	14	4	0.87
30847571--30847609	15	2.5	15	79	4	51	74	0	25	0	0.82

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