genome.fa.s1.2.7.7.80.10.50.1000.57.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  57  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)
16796941--16797005	10	7.0	9	79	11	53	78	0	20	1	0.83
16796946--16797005	16	3.9	16	75	18	56	78	0	20	1	0.84
16796940--16796996	11	4.8	12	74	23	57	77	0	22	0	0.77
16796940--16797005	9	6.8	10	78	13	59	77	0	21	1	0.85
16797267--16797305	18	2.2	17	95	4	69	87	0	12	0	0.55
16797626--16797664	20	2.0	20	100	0	78	38	10	10	41	1.73
16797769--16797836	35	1.9	35	84	0	91	32	16	5	45	1.71
16797847--16797980	71	1.9	72	90	1	216	29	15	9	44	1.79
16797809--16798111	36	8.4	35	75	10	236	28	16	11	44	1.82
16797809--16798095	107	2.7	106	79	14	279	28	16	11	43	1.82
16801638--16801667	2	15.0	2	100	0	60	50	0	0	50	1.00
16801932--16802114	84	2.2	86	80	9	216	37	3	14	44	1.63
16802360--16802628	41	6.6	41	93	2	434	23	18	24	33	1.96
16802360--16802628	122	2.2	123	91	2	434	23	18	24	33	1.96
16802365--16802669	163	1.9	164	84	2	416	23	17	25	33	1.96
16803094--16803250	71	2.2	70	84	4	208	31	10	15	42	1.81
16804306--16804335	16	1.9	16	93	6	53	43	0	16	40	1.48
16804859--16804996	60	2.3	60	88	0	204	34	30	21	13	1.92
16811671--16811739	35	2.0	35	94	0	120	26	14	15	43	1.85
16817733--16817788	26	2.2	24	81	9	67	19	5	1	73	1.12
16817748--16817826	10	8.2	10	82	13	71	21	2	2	73	1.07
16817761--16817874	4	26.5	4	80	8	86	21	3	3	71	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16817748--16817874	20	6.6	19	71	21	88	21	3	3	71	1.16
16817761--16817874	52	2.2	53	81	10	137	21	3	3	71	1.15
16817999--16818322	108	3.0	109	88	2	438	30	16	19	33	1.94
16821454--16821497	22	2.0	22	100	0	88	22	36	0	40	1.54
16823199--16823657	105	4.4	104	80	3	445	29	23	14	32	1.94
16826326--16826375	20	2.6	18	85	14	73	62	0	0	38	0.96
16827721--16827770	24	2.1	24	92	0	82	60	14	14	12	1.60
16830719--16830744	5	5.2	5	100	0	52	38	0	0	61	0.96
16833588--16834471	441	2.0	440	96	0	1633	33	22	15	29	1.94
16839035--16839255	76	2.9	74	88	5	309	23	18	25	32	1.97
16839125--16839258	33	3.8	34	75	17	137	20	20	26	31	1.98
16839030--16839256	75	3.0	75	88	3	314	24	17	25	32	1.97
16839305--16839360	2	28.0	2	100	0	112	50	0	0	50	1.00
16841402--16841477	11	6.8	11	72	21	52	39	2	3	53	1.33
16842538--16842590	20	2.7	20	90	0	79	54	13	13	18	1.70
16842676--16842713	20	1.9	20	94	0	67	55	18	2	23	1.55
16849779--16849846	28	2.3	30	92	5	113	26	0	2	70	1.01
16849780--16849846	16	4.6	16	78	17	83	26	0	2	70	1.02
16849778--16849857	28	2.9	27	81	9	90	26	1	2	70	1.08
16849798--16849848	11	4.0	12	75	20	50	27	0	1	70	0.98
16851468--16851544	30	2.6	28	80	13	75	32	11	11	44	1.77
16851927--16851964	20	2.0	20	85	10	53	31	2	7	57	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16852543--16852584	17	2.6	16	85	7	59	57	0	0	42	0.99
16853860--16854024	64	2.6	64	80	6	183	21	27	21	30	1.98
16855424--16855448	9	2.8	9	100	0	50	68	0	0	32	0.90
16858755--16858814	25	2.3	26	80	2	68	40	10	0	50	1.36
16859194--16859326	70	1.9	70	89	1	205	29	20	17	33	1.95
16861174--16861221	24	2.0	24	91	0	78	52	10	4	33	1.55
16865905--16866011	26	4.1	26	85	0	133	36	21	21	20	1.95
16866176--16866316	27	5.2	27	80	8	162	20	19	20	39	1.93
16872572--16872604	2	16.5	2	100	0	66	51	0	0	48	1.00
16872831--16872860	15	2.0	15	100	0	60	33	20	6	40	1.78
16874584--16874613	15	1.9	16	93	6	53	53	13	0	33	1.40
16875100--16875153	21	2.6	20	74	14	56	51	7	3	37	1.48
16877581--16877614	17	1.9	18	88	5	52	64	2	2	29	1.22
16880561--16880593	2	16.5	2	100	0	66	48	0	0	51	1.00
16889031--16889148	34	3.5	33	80	5	130	33	30	14	22	1.93
16893019--16893078	29	2.1	29	93	0	102	31	16	20	31	1.95
16898548--16898597	24	2.0	25	84	3	66	64	6	6	24	1.39
16899675--16900037	113	3.2	111	77	8	403	33	16	21	28	1.95
16899825--16900226	186	2.1	188	91	2	650	32	16	22	28	1.96
16900033--16900269	114	2.1	114	80	7	259	32	16	23	27	1.96
16909641--16909678	12	3.2	12	96	0	67	42	15	39	2	1.61
16910103--16910297	85	2.3	84	82	9	220	28	22	18	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16910103--16910310	42	4.9	42	84	6	219	26	22	19	31	1.98
16910145--16910322	84	2.1	86	86	5	245	24	22	20	32	1.98
16912432--16912460	12	2.3	13	94	5	51	58	17	0	24	1.38
16916855--16916901	18	2.6	18	79	0	58	34	4	2	59	1.29
16918812--16918858	24	1.9	24	86	4	67	36	0	36	27	1.57
16919131--16919332	27	7.8	27	73	14	151	43	18	16	20	1.88
16919131--16919272	74	1.9	74	82	0	176	43	21	16	18	1.88
16936668--16936718	26	2.0	26	84	0	66	39	17	21	21	1.93
16938796--16938943	57	2.5	60	82	9	178	24	25	19	30	1.98
16941110--16941135	12	2.2	12	100	0	52	7	7	7	76	1.15
16941619--16941663	22	2.1	21	88	8	65	35	24	20	20	1.96
16941627--16941683	22	2.6	22	86	2	71	36	26	19	17	1.94
16941692--16941800	56	1.9	56	94	0	191	42	22	16	18	1.89
16943271--16943327	22	2.6	22	91	0	87	35	15	26	22	1.94
16950192--16950233	22	2.0	22	95	4	77	76	7	0	16	1.00
16950192--16950233	21	2.0	22	90	4	68	76	7	0	16	1.00
16950642--16950678	11	3.4	11	100	0	74	32	0	0	67	0.91
16950731--16950791	31	2.0	31	90	6	97	16	21	29	32	1.95
16959253--16959316	31	2.1	31	82	5	76	29	12	14	43	1.81
16960641--16960734	22	4.3	22	86	2	127	36	27	0	36	1.57
16960771--16960820	26	2.0	26	88	11	77	42	0	2	56	1.11
16960909--16960962	26	2.1	25	83	10	65	37	0	5	57	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16963102--16963181	23	3.5	23	89	0	115	47	20	2	30	1.63
16963174--16963517	30	11.7	30	85	7	440	46	25	1	27	1.60
16963112--16963518	117	3.5	115	89	7	555	45	25	1	27	1.62
16963113--16963517	147	2.8	145	88	7	560	45	25	1	27	1.62
16963370--16963417	24	2.0	23	88	4	69	47	27	0	25	1.52
16969011--16969048	20	1.9	20	94	0	67	26	36	5	31	1.79
16971263--16971301	15	2.7	15	88	7	55	61	10	0	28	1.28
16973027--16973079	21	2.5	23	76	17	60	37	0	11	50	1.38
16973241--16973289	25	2.0	25	87	0	71	20	30	16	32	1.94
16973378--16973574	25	7.8	24	71	16	80	16	25	23	34	1.95
16977136--16977207	31	2.3	31	81	9	85	55	6	1	36	1.35
16977115--16977199	31	2.6	34	83	9	97	54	4	1	40	1.29
16977138--16977199	31	1.9	33	90	6	101	56	6	1	35	1.35
16978439--16978696	86	3.0	86	98	0	498	40	14	6	37	1.73
16980947--16980975	10	2.9	10	100	0	58	31	10	27	31	1.90
16983851--16983888	18	2.1	18	95	0	67	23	26	10	39	1.87
16984307--16984354	25	1.9	25	87	8	71	33	0	4	62	1.14
16984398--16984445	25	1.9	25	87	8	71	33	2	4	60	1.27
16987632--16987666	16	2.2	16	94	0	61	25	14	0	60	1.35
16987524--16987792	143	1.9	141	86	4	380	28	17	15	38	1.90
16987865--16987991	34	3.8	34	75	9	111	45	17	0	37	1.49
16987865--16987991	68	1.9	65	79	10	141	45	17	0	37	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
16990441--16990491	2	25.5	2	95	0	93	52	0	47	0	1.00
16994372--16994406	14	2.6	13	91	8	61	51	37	0	11	1.38
16998065--16998091	2	13.5	2	100	0	54	51	0	0	48	1.00
16999846--16999936	45	2.0	44	82	2	110	28	6	29	35	1.83
17000101--17000135	18	2.0	17	88	5	52	54	0	0	45	0.99
17000318--17000375	16	3.9	15	80	8	57	51	1	0	46	1.11
17001632--17001715	23	3.7	23	88	0	132	44	28	7	20	1.78
17001701--17001746	22	2.1	21	84	4	56	58	19	4	17	1.55
17002491--17002518	10	2.8	10	100	0	56	10	17	7	64	1.47
17023531--17023573	22	2.0	21	86	8	61	65	9	0	25	1.22

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