genome.fa.s1.2.7.7.80.10.50.1000.60.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  60  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)
17633443--17633491	9	5.4	9	80	9	55	75	4	16	4	1.11
17633442--17633491	18	2.7	19	81	9	68	74	4	16	6	1.17
17634003--17634057	3	18.3	3	100	0	110	32	0	0	67	0.91
17634453--17634530	23	3.5	23	85	3	97	23	21	17	37	1.94
17640897--17640962	34	1.9	34	87	6	98	46	21	12	19	1.82
17642647--17642671	12	2.1	12	100	0	50	80	0	0	20	0.72
17644399--17644442	22	2.0	22	82	8	54	45	25	9	20	1.80
17645681--17645719	20	2.0	20	90	10	62	46	0	0	53	1.00
17646592--17646618	14	1.9	14	100	0	54	7	22	22	48	1.75
17646576--17646694	59	2.0	59	98	0	229	14	16	17	51	1.77
17646651--17646677	14	1.9	14	100	0	54	7	22	22	48	1.75
17646861--17646890	12	2.5	12	94	0	51	23	6	13	56	1.60
17646814--17646982	59	2.9	59	96	0	311	21	10	10	57	1.62
17650419--17650467	18	2.6	19	78	18	57	22	2	2	73	1.04
17650418--17650467	22	2.3	22	83	10	66	22	2	2	74	1.03
17657320--17657360	14	2.7	15	85	7	57	21	2	2	73	1.07
17678129--17678161	10	3.0	11	86	13	50	27	0	0	72	0.85
17678225--17678286	27	2.3	27	97	0	115	29	22	33	14	1.94
17678389--17678447	23	2.6	23	86	5	84	67	0	1	30	1.00
17679059--17679096	19	2.0	19	89	0	58	36	5	7	50	1.54
17679316--17679392	27	2.9	28	90	3	115	19	38	24	16	1.92
17682367--17682406	20	2.0	20	90	0	62	30	10	10	50	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17682353--17682418	34	1.9	34	87	6	98	33	7	12	46	1.69
17683925--17683957	14	2.4	14	94	0	57	24	0	6	69	1.10
17688046--17688119	21	3.6	21	72	15	66	37	2	1	58	1.21
17688045--17688107	21	3.0	22	75	15	69	38	1	1	58	1.17
17688400--17688459	20	3.0	20	72	13	61	40	5	1	53	1.33
17688487--17688541	16	3.2	18	80	12	62	38	5	0	56	1.23
17689076--17689142	24	2.8	24	88	0	98	23	10	22	43	1.84
17689075--17689161	24	3.8	23	81	4	79	24	11	20	43	1.85
17692009--17692073	19	3.4	18	74	17	69	47	7	6	38	1.57
17692006--17692082	38	2.0	38	100	0	154	50	7	7	33	1.60
17692019--17692079	19	3.2	19	73	17	72	50	6	8	34	1.58
17693073--17693323	23	10.7	23	82	5	279	40	19	13	27	1.88
17693073--17693325	48	5.4	48	79	7	277	40	19	13	27	1.88
17693085--17693323	71	3.4	71	88	0	327	41	19	12	26	1.87
17694304--17694434	43	3.0	42	72	20	108	31	29	18	21	1.97
17696490--17696518	15	2.0	15	93	6	51	44	0	27	27	1.54
17696531--17696621	44	2.1	44	100	0	182	21	13	21	42	1.87
17698427--17698460	16	2.1	16	94	0	59	35	17	2	44	1.64
17702919--17702963	21	2.0	22	87	8	65	62	6	17	13	1.52
17706321--17706379	32	1.9	30	86	6	82	25	3	8	62	1.39
17709173--17709204	15	2.1	16	94	5	57	71	6	3	18	1.20
17711593--17711650	28	2.1	28	96	0	107	17	6	12	63	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17717869--17717904	16	2.2	16	95	0	63	27	0	33	38	1.57
17719250--17719428	25	7.2	25	81	11	208	37	7	5	49	1.54
17719276--17719403	48	2.7	48	100	0	256	36	7	5	50	1.55
17719250--17719428	73	2.4	72	83	9	202	37	7	5	49	1.54
17720393--17720433	2	20.5	2	100	0	82	51	0	0	48	1.00
17729433--17729458	12	2.2	12	100	0	52	42	7	11	38	1.70
17736382--17736582	103	2.0	103	85	2	278	33	19	16	30	1.94
17739276--17739318	21	2.0	21	82	8	52	30	11	2	55	1.48
17753098--17753229	24	5.5	24	95	0	239	39	23	20	16	1.92
17754313--17754350	12	3.3	12	82	10	53	2	26	7	63	1.35
17754315--17754367	21	2.5	22	87	9	74	3	24	5	66	1.31
17754375--17754420	5	9.2	5	84	15	60	60	0	0	39	0.97
17754375--17754419	19	2.6	17	89	10	65	60	0	0	40	0.97
17754374--17754420	24	2.0	23	91	4	76	59	0	0	40	0.97
17754383--17754429	24	2.0	24	83	8	60	61	2	0	36	1.08
17760972--17761022	18	2.7	20	76	17	54	33	13	25	27	1.94
17764927--17764953	7	3.9	7	100	0	54	29	55	0	14	1.40
17769441--17769518	39	2.0	39	89	0	120	33	8	7	50	1.63
17772310--17772388	42	2.0	39	85	11	108	40	8	8	41	1.67
17772319--17772403	42	2.0	42	86	6	120	42	5	8	43	1.58
17772484--17772559	38	2.0	38	97	0	143	48	5	7	38	1.55
17773948--17773986	15	2.4	17	83	12	55	30	5	0	64	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17774935--17774973	17	2.1	19	86	13	55	41	0	2	56	1.13
17775919--17775973	29	2.0	27	86	13	76	47	5	0	47	1.25
17778949--17779039	44	2.1	44	89	4	139	31	7	9	50	1.64
17781961--17781998	16	2.3	17	83	16	53	18	0	26	55	1.43
17791624--17791681	30	1.9	30	85	0	80	39	5	24	31	1.77
17791894--17791924	13	2.4	13	94	0	53	32	0	12	54	1.38
17793815--17793860	22	2.1	22	95	0	83	36	13	23	26	1.91
17797203--17797233	13	2.4	13	94	0	53	54	12	0	32	1.38
17798323--17798571	50	4.8	50	87	3	327	21	28	22	26	1.99
17798666--17798697	13	2.5	13	94	0	55	56	12	0	31	1.37
17798909--17798966	30	1.9	30	89	0	89	31	24	3	41	1.71
17803823--17803861	19	2.1	19	85	0	51	15	0	41	43	1.46
17810905--17811430	44	11.7	44	75	10	350	29	19	18	32	1.96
17810971--17811430	132	3.4	131	79	8	401	29	19	17	33	1.95
17811096--17811392	89	3.4	87	84	5	341	29	19	17	33	1.95
17819196--17819248	19	2.8	20	85	5	74	43	7	22	26	1.80
17825151--17825237	6	14.5	6	100	0	174	50	16	0	33	1.45
17825436--17825745	6	51.7	6	97	0	539	50	2	16	31	1.57
17833562--17833601	19	2.1	19	86	9	55	60	7	0	32	1.25
17834048--17834148	17	5.6	17	69	17	53	42	4	2	49	1.39
17834787--17835037	49	5.2	48	77	6	211	20	27	18	32	1.96
17834769--17834971	48	4.2	48	77	8	160	20	29	19	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17834839--17835015	96	1.8	96	79	6	205	22	27	17	32	1.96
17838035--17838073	12	3.2	12	85	0	51	20	23	5	51	1.67
17838283--17838464	50	3.5	50	82	6	188	25	25	20	28	1.99
17845067--17845361	46	6.3	46	90	4	374	34	13	21	29	1.92
17845001--17845350	98	3.6	98	90	4	559	34	14	21	29	1.93
17845067--17845361	92	3.1	92	90	5	464	34	13	21	29	1.92
17845001--17845361	144	2.5	138	87	5	506	34	13	22	29	1.93
17845001--17845361	190	1.9	190	93	0	623	34	13	22	29	1.93
17845327--17845433	37	2.9	37	91	2	173	37	14	21	26	1.92
17846737--17846778	21	2.0	21	86	9	59	30	0	9	59	1.29
17850389--17850457	28	2.5	28	92	2	113	39	10	1	49	1.46
17850459--17850493	13	2.8	12	87	8	52	85	11	2	0	0.69
17850522--17850599	27	2.9	28	80	7	97	26	21	42	8	1.83
17850654--17850745	14	6.4	14	74	9	71	69	0	29	1	0.95
17850679--17850745	18	3.6	18	78	7	80	67	0	31	1	1.00
17850663--17850752	10	9.4	10	72	18	75	67	0	31	1	0.98
17850654--17850714	24	2.5	24	84	7	79	72	0	27	0	0.85
17850679--17850807	38	3.4	38	80	14	151	67	0	31	0	1.02
17850669--17850752	28	3.0	27	76	10	80	66	0	32	1	0.99
17851473--17851524	19	2.7	19	87	0	68	25	0	7	67	1.17
17851560--17851628	27	2.5	28	90	6	106	40	8	0	50	1.33
17852217--17852245	14	2.1	14	100	0	58	37	6	0	55	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17852658--17852736	27	2.9	27	82	0	113	10	44	20	25	1.82
17861475--17861523	20	2.6	19	83	6	55	22	6	4	67	1.30
17861545--17861587	18	2.5	17	81	7	50	39	0	6	53	1.28
17861550--17861605	19	2.8	20	81	10	62	41	0	7	51	1.29
17861559--17861605	21	2.4	18	86	10	58	44	0	4	51	1.21
17867205--17867258	26	2.0	27	92	3	92	37	14	9	38	1.79
17867633--17867677	20	2.2	21	84	11	58	20	6	0	73	1.05
17870200--17870356	77	2.0	78	97	1	298	42	12	11	33	1.78
17879541--17879996	245	1.9	245	98	0	887	33	12	14	39	1.83
17881493--17881570	34	2.3	34	95	2	138	48	12	12	25	1.77

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