genome.fa.s1.2.7.7.80.10.50.1000.99.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  99  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)
29364730--29364798	19	3.7	18	78	16	70	33	0	2	63	1.09
29364701--29364800	9	10.8	9	77	16	80	33	0	3	64	1.09
29364791--29364837	22	2.1	23	84	4	60	31	4	6	57	1.43
29368620--29368760	71	2.0	71	87	2	203	30	18	17	34	1.94
29369074--29369118	22	2.0	22	87	8	65	44	11	6	37	1.66
29375268--29375355	22	4.0	23	68	10	67	25	19	35	20	1.96
29375396--29375686	26	11.3	26	68	10	123	34	15	22	27	1.94
29375389--29375685	52	5.8	52	75	3	258	34	14	22	27	1.94
29375611--29375707	26	3.7	25	78	8	77	34	12	25	27	1.92
29378809--29378868	31	2.0	30	90	3	93	53	5	31	10	1.56
29381666--29381705	19	2.1	19	86	9	55	0	25	0	75	0.81
29381674--29381711	20	1.9	20	84	10	51	0	31	0	68	0.90
29382110--29382206	30	3.2	30	91	0	158	25	28	30	14	1.95
29391710--29391734	13	1.9	13	100	0	50	32	24	8	36	1.84
29393625--29393735	46	2.4	47	80	15	117	53	1	6	38	1.37
29393992--29394046	3	18.3	3	92	0	92	67	0	1	30	1.01
29394978--29395016	8	4.8	8	87	6	60	0	17	7	74	1.05
29395050--29395091	20	2.1	20	90	0	66	16	21	42	19	1.89
29395858--29396613	46	16.5	46	90	0	1084	29	25	16	28	1.97
29396824--29396859	16	2.3	16	95	4	65	33	5	22	38	1.77
29397533--29397731	97	2.0	99	84	3	260	47	9	16	26	1.77
29397999--29398066	17	4.1	15	80	17	73	1	14	0	83	0.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29397999--29398066	24	2.8	24	82	10	86	1	14	0	83	0.71
29398001--29398066	34	2.0	33	87	3	96	1	15	0	83	0.72
29402680--29402737	3	19.3	3	96	0	107	65	0	1	32	1.03
29403660--29403696	17	2.2	16	90	4	56	0	21	5	72	1.04
29405736--29405776	8	5.4	8	88	8	59	65	0	0	34	0.93
29405735--29405777	15	3.0	14	84	15	61	65	0	0	34	0.93
29407478--29407549	31	2.4	31	90	2	110	41	19	15	23	1.89
29417051--29417086	19	1.9	19	88	5	56	30	19	8	41	1.81
29417275--29417333	16	3.2	17	77	22	66	52	0	0	47	1.00
29417280--29417323	22	2.0	22	86	8	63	54	0	0	45	0.99
29417350--29417383	15	2.1	16	89	10	52	58	0	0	41	0.98
29420517--29420565	22	2.2	22	88	0	71	42	14	24	18	1.87
29420530--29420572	22	2.0	22	95	0	77	44	16	23	16	1.86
29420896--29420920	12	2.1	12	100	0	50	28	16	8	48	1.74
29425903--29425936	13	2.6	13	90	9	52	70	0	5	23	1.09
29425882--29425938	16	3.8	16	77	15	59	66	1	7	24	1.26
29426001--29426127	3	41.7	3	69	14	73	67	2	5	24	1.24
29425997--29426127	15	8.6	15	73	14	90	67	2	5	24	1.23
29429235--29429260	13	2.0	13	100	0	52	23	7	30	38	1.83
29429779--29429831	11	4.6	11	76	15	54	60	5	5	28	1.42
29433013--29433065	23	2.2	24	83	6	63	71	1	0	26	0.96
29435544--29435583	16	2.5	17	76	15	50	22	5	10	62	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29435769--29435810	22	1.9	23	85	9	61	14	38	42	4	1.66
29436376--29436412	18	2.1	18	100	0	74	48	16	0	35	1.46
29443042--29443103	31	2.0	31	100	0	124	45	6	19	29	1.75
29448467--29448630	84	1.9	86	81	7	201	29	20	20	29	1.98
29448250--29448599	44	8.1	42	71	12	185	29	20	22	28	1.98
29454685--29454738	25	2.2	25	83	6	65	70	11	7	11	1.34
29464342--29464412	36	2.0	36	97	0	133	38	19	19	22	1.94
29465970--29466007	20	1.9	20	88	0	58	34	2	2	60	1.24
29465971--29466014	20	2.2	20	83	0	52	34	4	2	59	1.30
29471910--29471994	44	1.9	45	92	2	145	32	8	7	51	1.59
29479476--29479601	60	2.1	60	100	0	252	15	38	0	46	1.46
29483180--29483214	5	7.0	5	86	0	52	74	2	20	2	1.08
29483180--29483218	20	2.0	20	100	0	78	69	5	20	5	1.28
29489294--29489345	5	10.2	5	82	12	52	34	15	26	23	1.94
29489294--29489345	26	2.0	26	81	7	61	34	15	26	23	1.94
29489996--29490055	30	2.0	31	86	3	86	40	0	40	20	1.52
29490932--29490974	20	2.2	20	87	4	61	0	25	0	74	0.82
29493967--29493993	6	4.5	6	100	0	54	0	14	29	55	1.40
29494023--29494072	23	2.2	23	85	7	66	46	2	0	52	1.12
29496581--29496776	97	2.0	98	93	1	340	37	25	9	27	1.87
29499123--29499192	21	3.5	19	78	9	61	37	10	8	44	1.69
29503853--29503889	7	5.3	7	96	0	65	59	10	0	29	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29504206--29504252	23	2.0	23	100	0	94	34	8	4	53	1.51
29509051--29509088	14	2.7	14	91	0	58	36	7	18	36	1.80
29509072--29509111	20	2.0	20	100	0	80	30	10	15	45	1.78
29509057--29509121	34	1.9	33	87	9	96	33	9	15	41	1.79
29509283--29509333	26	2.2	24	78	21	56	60	5	0	33	1.21
29511800--29511826	2	13.5	2	100	0	54	51	0	0	48	1.00
29512228--29512261	6	5.7	6	96	0	50	38	0	61	0	0.96
29512230--29512264	17	2.1	17	88	0	52	40	0	60	0	0.97
29515632--29515664	11	2.8	12	86	13	50	51	0	21	27	1.48
29517297--29517368	26	2.8	26	81	8	83	44	11	13	30	1.79
29522193--29522227	15	2.3	15	85	0	52	68	0	11	20	1.20
29528190--29528301	56	2.0	56	98	0	215	28	31	21	18	1.97
29530094--29530213	31	4.0	30	82	5	127	40	15	10	34	1.82
29530155--29530235	31	2.6	31	96	0	144	43	13	11	32	1.79
29530697--29530754	17	3.6	17	77	15	61	37	3	1	56	1.26
29530767--29530882	61	1.9	58	87	5	169	42	5	1	50	1.34
29533417--29533561	50	2.9	50	83	0	182	26	21	29	22	1.99
29540616--29540658	22	2.0	22	85	0	59	30	4	25	39	1.76
29543304--29543374	22	3.2	22	80	7	90	35	25	1	38	1.65
29543345--29543403	30	2.0	30	96	0	109	32	35	0	32	1.58
29543375--29543416	22	1.9	22	85	0	57	33	30	0	35	1.58
29545279--29545313	18	1.9	18	88	0	52	31	34	5	28	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29545812--29546091	28	10.3	28	79	15	302	44	21	0	33	1.57
29545791--29546087	51	5.6	51	74	19	190	44	21	1	33	1.59
29545791--29545844	23	2.3	23	87	0	81	42	16	3	37	1.66
29545825--29545896	34	2.1	34	94	0	126	44	25	0	30	1.54
29545859--29546091	51	4.5	51	83	5	322	44	22	0	32	1.56
29547765--29548030	124	2.1	124	88	1	399	31	22	16	29	1.96
29548625--29548674	19	2.6	20	78	18	61	52	2	0	46	1.12
29549558--29549592	19	1.9	18	88	11	54	25	5	0	68	1.11
29550764--29550855	46	2.0	46	91	4	152	26	4	29	40	1.75
29550762--29550872	46	2.6	42	78	15	138	27	3	30	37	1.74
29551085--29551124	20	2.0	21	85	5	55	60	5	0	35	1.19
29551092--29551171	28	2.8	28	81	11	92	56	1	0	42	1.07
29554926--29554993	29	2.4	27	79	15	75	55	7	2	33	1.42
29555533--29555558	7	3.7	7	100	0	52	0	11	0	88	0.52
29568435--29568467	17	1.9	17	93	0	57	39	0	15	45	1.46
29568688--29568856	41	4.1	41	92	0	284	28	20	27	23	1.98
29568688--29568850	82	2.0	82	100	0	326	28	19	28	23	1.98
29569049--29569166	37	3.5	37	82	13	130	27	10	27	33	1.89
29574770--29574799	12	2.5	12	94	0	51	36	10	3	50	1.53
29574833--29574948	58	1.9	59	82	6	144	41	4	4	50	1.42
29574878--29574912	11	3.3	11	84	8	54	48	0	0	51	1.00
29574881--29574915	10	3.4	10	84	7	52	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29576395--29576429	17	2.1	17	88	0	52	40	2	14	42	1.60
29577745--29577793	25	1.9	26	88	12	75	24	2	6	67	1.24
29577741--29577795	19	2.9	19	72	22	53	25	1	7	65	1.28
29579388--29579446	7	7.7	7	83	12	64	16	0	1	81	0.78
29579390--29579446	8	7.2	8	81	13	57	15	0	1	82	0.75
29579390--29579439	25	2.1	24	88	7	75	14	0	2	84	0.72
29579388--29579442	13	4.3	12	84	15	67	16	0	1	81	0.77
29587198--29587227	13	2.3	13	94	0	51	43	0	3	53	1.17
29589748--29589957	45	4.7	45	79	7	192	40	14	20	24	1.90
29591331--29591450	56	2.2	56	83	4	145	32	7	13	46	1.71

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