genome.fa.s1.2.7.7.80.10.50.1000.20.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  20  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)
6752097--6752137	11	3.7	11	84	12	57	0	21	0	78	0.76
6757368--6757400	11	2.9	12	86	13	52	33	0	0	66	0.92
6762451--6762515	31	2.1	31	83	8	80	43	15	7	33	1.75
6765721--6765763	22	2.0	22	86	8	63	48	6	0	44	1.29
6768751--6768822	28	2.4	29	82	15	94	44	0	0	55	0.99
6769067--6769104	7	5.4	7	84	12	51	39	15	18	26	1.91
6771072--6771157	27	3.2	27	98	0	163	29	20	34	15	1.93
6771263--6771323	24	2.6	23	87	12	88	70	0	1	27	0.97
6771471--6771508	19	2.0	19	89	0	58	50	7	5	36	1.54
6771607--6771678	27	2.7	27	93	0	117	52	12	0	34	1.39
6771717--6771888	27	7.1	24	72	24	148	32	1	13	52	1.48
6771720--6771834	49	2.3	49	93	0	203	32	0	13	53	1.47
6771934--6771971	19	2.0	19	89	0	58	36	5	7	50	1.54
6772187--6772290	27	3.9	27	93	2	165	19	39	25	16	1.91
6773616--6773837	103	2.2	99	84	6	286	43	14	16	25	1.86
6781560--6781593	16	2.1	16	94	0	59	50	0	0	50	1.00
6781776--6781827	19	2.8	19	94	5	90	50	11	0	38	1.39
6781835--6781906	8	8.4	8	73	14	63	34	1	16	47	1.56
6782046--6782097	19	2.8	19	94	5	90	50	11	0	38	1.39
6781593--6782356	270	2.9	270	96	1	1413	39	4	9	46	1.57
6782151--6782176	8	3.2	8	100	0	52	38	0	11	50	1.39
6782316--6782356	19	2.2	19	95	0	73	51	17	0	31	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6788824--6788876	25	2.1	25	100	0	106	50	11	0	37	1.38
6789541--6789592	27	1.9	27	92	0	86	11	48	21	19	1.80
6790353--6790380	6	4.7	6	100	0	56	71	0	28	0	0.86
6790895--6790929	3	11.7	3	87	0	52	37	31	31	0	1.58
6790929--6790962	9	4.0	8	85	14	50	73	0	26	0	0.83
6795024--6795074	26	2.0	26	84	0	66	33	3	1	60	1.26
6796046--6796073	2	14.0	2	100	0	56	50	0	0	50	1.00
6797494--6797546	23	2.3	24	87	9	83	32	15	20	32	1.93
6814961--6814998	13	2.9	13	84	0	58	34	21	7	36	1.82
6815540--6815729	94	2.0	94	97	0	362	47	9	5	37	1.59
6815808--6815849	7	6.0	7	86	10	59	42	0	0	57	0.99
6816343--6816402	20	2.9	21	80	9	70	50	0	1	48	1.11
6828870--6828899	2	15.5	2	93	6	53	50	0	0	50	1.00
6840609--6840655	21	2.2	21	77	7	51	23	10	29	36	1.89
6840758--6840831	17	4.2	17	80	11	78	59	0	4	36	1.16
6840836--6840881	18	2.4	18	82	7	56	30	0	4	65	1.12
6841542--6841583	17	2.4	17	88	4	57	16	4	9	69	1.33
6843783--6843834	26	2.0	26	100	0	104	7	23	15	53	1.67
6846145--6846186	21	1.9	23	85	9	61	33	0	26	40	1.56
6853302--6853346	22	2.0	22	100	0	90	33	22	17	26	1.96
6856502--6856540	19	2.1	19	100	0	78	48	20	10	20	1.78
6862777--6862802	7	3.7	7	100	0	52	84	0	0	15	0.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6871116--6871192	16	4.5	17	73	15	61	18	16	29	35	1.93
6871095--6871192	50	1.9	52	82	12	123	21	17	25	35	1.95
6871933--6871978	22	2.0	24	87	8	69	50	6	0	43	1.28
6872921--6872998	28	2.7	29	78	7	88	42	5	16	35	1.71
6876449--6876483	2	17.5	2	100	0	70	51	48	0	0	1.00
6881570--6881624	10	5.4	10	79	12	58	60	0	3	36	1.15
6881568--6881624	21	2.8	20	72	15	62	61	0	3	35	1.13
6881572--6881655	30	2.7	31	85	5	100	57	0	4	38	1.20
6882950--6882988	19	2.1	19	100	0	78	30	15	30	23	1.95
6886821--6886860	20	2.0	20	90	0	62	27	10	12	50	1.72
6886806--6886872	34	1.9	35	90	3	109	31	8	13	46	1.74
6886800--6886876	14	5.0	15	71	20	52	33	9	14	42	1.77
6888516--6888599	27	3.1	25	73	26	73	65	1	7	26	1.25
6888515--6888599	28	3.1	27	75	12	84	65	1	7	25	1.25
6899930--6899975	21	2.1	23	92	8	78	36	0	0	63	0.95
6899935--6899986	21	2.4	21	81	12	61	38	0	1	59	1.08
6902715--6902872	48	3.3	48	90	0	244	44	17	14	23	1.85
6903437--6903532	42	2.3	42	87	1	129	32	22	16	28	1.96
6903449--6903534	42	2.0	43	90	2	138	32	25	17	24	1.97
6907799--6907847	9	5.4	9	87	0	71	28	10	18	42	1.83
6907799--6907847	18	2.7	18	93	0	80	28	10	18	42	1.83
6908101--6908218	58	2.0	58	98	0	227	40	17	11	29	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6914070--6914354	146	2.0	146	99	0	561	46	12	18	21	1.83
6914919--6914958	13	3.1	13	85	0	62	35	27	7	30	1.84
6915329--6915377	11	4.0	11	78	21	53	42	0	0	57	0.99
6915316--6915372	26	2.2	25	90	3	87	40	0	1	57	1.09
6915336--6915371	15	2.4	15	85	0	54	44	0	0	55	0.99
6915357--6915405	20	2.5	20	80	6	55	38	2	2	57	1.22
6915682--6915708	7	3.9	7	100	0	54	29	25	0	44	1.54
6921726--6921783	18	3.1	19	78	16	66	58	3	0	37	1.15
6921726--6921784	19	3.2	19	69	11	50	57	3	0	38	1.15
6922189--6922215	2	13.5	2	100	0	54	48	0	0	51	1.00
6923004--6923060	25	2.3	24	76	8	60	47	0	1	50	1.11
6923748--6923802	27	2.0	27	100	0	110	32	14	18	34	1.91
6923947--6923977	16	1.9	16	93	0	53	74	0	19	6	1.03
6925113--6925146	13	2.6	13	90	0	50	20	38	5	35	1.77
6928113--6928297	46	4.0	46	82	2	219	31	25	15	26	1.96
6942995--6943027	2	16.5	2	100	0	66	51	0	0	48	1.00
6945467--6945527	2	31.0	2	96	3	115	49	0	0	50	1.00
6947711--6947743	14	2.4	14	85	14	50	60	0	3	36	1.12
6950114--6950160	3	15.7	3	100	0	94	34	0	0	65	0.93
6952182--6952223	18	2.4	17	81	18	50	16	16	0	66	1.25
6960345--6960409	34	2.0	34	87	6	98	49	3	7	40	1.47
6960664--6960724	30	2.0	31	87	3	88	32	16	4	45	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6963683--6963773	44	2.1	44	82	0	110	45	12	13	29	1.79
6964012--6964208	102	1.9	102	97	0	376	25	24	16	33	1.96
6964785--6964845	31	2.0	31	90	0	95	44	9	11	34	1.74
6966204--6966232	3	9.7	3	100	0	58	0	34	31	34	1.58
6975652--6975691	14	2.9	14	84	0	53	35	7	15	42	1.75
6975675--6975714	20	2.0	20	90	0	62	30	10	10	50	1.69
6975660--6975726	34	1.9	35	87	3	100	32	8	11	46	1.72
6975813--6975840	14	2.0	14	100	0	56	42	0	0	57	0.99
6979898--6979949	25	2.1	25	92	7	88	38	9	26	25	1.86
6982004--6982043	21	1.9	21	84	0	53	32	2	20	45	1.64
6984337--6984367	9	3.4	9	90	0	53	25	12	22	38	1.90
6984420--6984456	9	4.1	9	89	0	56	45	10	10	32	1.74
6984660--6984774	29	4.0	29	81	4	124	33	18	6	41	1.75
6985124--6985178	3	17.3	3	85	10	74	69	0	29	1	0.99
6985124--6985178	10	5.8	9	87	8	74	69	0	29	1	0.99
6985170--6985214	8	5.8	8	82	12	58	80	0	20	0	0.72
6985123--6985211	35	2.6	35	79	13	96	73	0	25	1	0.91
6985123--6985214	6	14.5	6	80	13	69	73	0	25	1	0.89
6985148--6985214	7	9.1	7	80	6	53	76	0	22	1	0.87
6985169--6985214	13	3.6	13	80	14	60	80	0	19	0	0.71
6985318--6985368	13	3.6	14	84	12	61	80	9	7	1	0.98
6985378--6985430	26	2.0	26	85	0	70	30	47	18	3	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6985510--6985558	11	4.5	11	75	14	57	81	0	18	0	0.69
6985512--6985553	13	3.2	13	83	13	50	83	0	16	0	0.65
6985510--6985558	19	2.6	19	81	15	66	81	0	18	0	0.69
6985705--6985748	17	2.7	16	82	10	54	36	2	0	61	1.09
6985911--6985952	21	2.0	20	90	4	66	35	14	9	40	1.78
6985911--6985952	20	2.1	19	86	8	57	35	14	9	40	1.78
6986058--6986187	35	3.7	35	78	4	145	33	13	9	44	1.75
6986058--6986185	17	7.2	17	73	9	87	32	13	9	45	1.75
6986058--6986186	18	7.3	18	72	10	95	32	13	9	44	1.75
6986129--6986240	55	2.0	57	81	10	133	34	11	9	43	1.74

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