genome.fa.s4.2.7.7.80.10.50.1000.109.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   188   189   190   191   192   
          193   194   195   196   197   198   

This is table  109  of  198  ( 23681 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)
34911152--34911180	13	2.2	13	100	0	58	41	20	10	27	1.85
34919679--34919717	12	3.5	11	90	10	62	61	0	0	38	0.96
34921431--34921477	24	2.0	24	83	4	60	55	2	2	40	1.24
34926191--34926217	13	2.1	13	100	0	54	0	14	0	85	0.61
34929252--34929312	24	2.5	24	81	7	70	31	34	11	22	1.90
34929361--34929484	32	3.9	32	84	0	167	20	12	28	37	1.90
34929495--34929568	23	3.2	23	80	0	85	33	18	20	27	1.96
34934758--34934887	43	3.0	43	73	12	131	23	18	25	32	1.97
34940395--34940554	43	3.8	41	76	8	117	31	24	14	29	1.94
34940442--34940550	42	2.6	43	79	5	114	33	24	14	27	1.95
34945552--34945680	54	2.4	53	78	7	134	27	23	26	22	1.99
34958705--34958756	21	2.5	21	96	0	95	61	0	0	38	0.96
34958696--34958756	21	3.0	20	90	4	79	57	0	0	42	0.98
34965297--34965341	20	2.3	20	85	11	58	24	6	2	66	1.27
34969524--34969552	12	2.4	12	100	0	58	44	24	13	17	1.85
34972267--34972304	2	19.0	2	94	0	67	2	0	47	50	1.15
34988289--34988335	10	4.6	10	77	12	51	61	2	2	34	1.20
34988293--34988335	22	2.0	21	86	4	59	58	2	2	37	1.24
34988671--34988732	27	2.3	26	83	2	70	20	19	27	32	1.97
34990203--34990229	12	2.2	12	100	0	54	51	0	0	48	1.00
34990944--34990986	11	3.8	11	80	17	52	65	2	2	30	1.18
34993869--34993992	29	4.2	28	72	15	106	30	20	23	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35004666--35004715	19	2.5	20	83	3	75	10	28	22	40	1.86
35007955--35008036	36	2.2	39	78	10	89	15	18	9	56	1.66
35010887--35010966	37	2.2	35	84	4	97	70	2	7	20	1.24
35017813--35018092	27	10.4	26	84	4	328	43	20	16	18	1.88
35017812--35018107	54	5.5	53	85	6	366	42	20	16	19	1.89
35033352--35033427	6	12.3	6	86	10	64	72	0	2	25	0.98
35033367--35033429	3	21.3	3	84	9	85	69	0	1	28	0.97
35047248--35047287	21	1.9	21	85	10	55	52	2	0	45	1.14
35060627--35060773	50	2.9	50	82	4	163	27	22	30	19	1.98
35067354--35067700	50	6.8	50	80	3	311	28	21	27	23	1.99
35067358--35067700	150	2.3	150	80	6	352	28	21	26	23	1.99
35070395--35070425	16	1.9	16	93	0	53	22	0	9	67	1.19
35081237--35081291	7	7.4	7	79	18	58	1	18	10	69	1.27
35083086--35083140	3	18.3	3	100	0	110	32	0	0	67	0.91
35086683--35086741	25	2.3	27	82	8	70	47	1	3	47	1.29
35086744--35086787	21	2.2	20	91	4	70	77	4	11	6	1.11
35086764--35086794	15	2.0	16	93	6	55	70	9	12	6	1.31
35102218--35102267	24	2.0	24	81	11	57	38	2	0	60	1.09
35102223--35102261	17	2.4	16	80	12	53	35	0	0	64	0.94
35102402--35102441	20	1.9	20	85	10	53	30	2	0	67	1.04
35105135--35105281	39	3.7	40	88	8	194	32	3	0	63	1.16
35105174--35105205	16	2.0	16	93	0	55	28	0	0	71	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35105172--35105232	9	6.4	9	72	23	54	26	1	0	72	0.94
35105238--35105299	32	1.9	32	83	0	79	32	1	3	62	1.20
35111760--35111818	19	2.9	19	77	22	66	30	1	6	61	1.32
35119515--35119569	21	2.6	21	85	0	74	32	36	7	23	1.82
35127296--35127356	3	20.0	3	89	3	86	34	4	0	60	1.18
35132834--35132877	23	1.9	23	90	0	70	43	4	9	43	1.56
35134265--35134313	23	2.1	23	88	0	71	24	20	16	38	1.92
35142576--35142642	34	1.9	35	87	3	100	37	22	22	17	1.94
35145631--35145684	20	2.7	20	88	0	72	46	1	29	22	1.62
35147218--35147293	38	2.0	38	97	0	143	31	26	17	25	1.97
35151850--35151983	68	2.0	68	96	0	250	29	11	18	40	1.85
35154020--35154061	10	4.2	10	76	11	50	30	0	2	66	1.04
35155957--35155989	7	4.7	7	96	0	57	48	0	21	30	1.50
35155938--35155989	14	3.7	14	84	5	52	50	1	15	32	1.55
35155950--35155989	21	1.9	21	84	0	53	50	0	17	32	1.47
35155971--35156025	21	2.7	20	83	8	65	47	0	16	36	1.47
35156806--35156864	22	2.7	22	97	0	109	25	27	13	33	1.93
35165258--35166024	45	17.7	46	69	19	238	26	23	20	28	1.99
35165398--35165507	43	2.5	45	82	5	136	28	20	22	28	1.99
35165210--35166024	44	18.8	45	70	13	320	26	23	20	28	1.99
35165473--35166022	89	6.3	89	68	16	296	26	23	21	28	1.99
35165224--35166024	216	3.7	216	92	1	1311	26	23	21	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35180207--35180289	10	7.9	10	70	12	51	60	6	4	28	1.41
35180653--35180696	10	4.3	10	80	5	52	34	2	0	63	1.07
35180781--35180819	19	2.0	21	90	10	64	51	0	5	43	1.24
35183134--35183193	11	5.4	11	73	9	50	45	0	1	53	1.10
35193590--35193632	9	4.9	9	78	16	54	72	2	0	25	0.97
35193590--35193620	16	1.9	16	93	0	53	70	0	0	29	0.87
35194620--35194645	12	2.2	12	100	0	52	38	7	7	46	1.61
35197980--35198017	18	2.1	18	90	0	58	50	2	0	47	1.15
35205800--35205956	76	2.1	76	100	0	314	37	22	7	31	1.83
35211343--35211367	12	2.1	12	100	0	50	24	36	24	16	1.94
35211526--35211593	9	7.4	9	85	9	84	41	26	10	22	1.85
35211733--35211762	13	2.3	13	100	0	60	16	0	43	40	1.48
35229415--35229506	45	2.0	45	85	0	121	38	20	16	25	1.93
35233797--35233856	31	2.0	30	90	3	93	33	11	10	45	1.74
35239466--35239530	26	2.3	29	82	7	73	40	6	0	53	1.26
35240907--35240967	3	20.3	3	100	0	122	67	0	0	32	0.91
35248378--35248415	18	2.1	18	90	9	60	26	0	0	73	0.83
35250009--35250052	21	2.2	20	83	4	52	43	2	2	52	1.26
35250073--35250114	8	5.2	8	94	0	75	50	0	0	50	1.00
35250055--35250114	24	2.5	24	83	2	77	43	0	3	53	1.17
35250802--35250844	20	2.2	19	87	4	59	13	13	0	72	1.13
35252889--35252950	3	20.0	3	90	6	97	66	1	1	30	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35254286--35254319	16	2.1	16	88	0	50	5	23	5	64	1.38
35254551--35254579	14	2.0	15	93	6	51	20	0	27	51	1.47
35255867--35255942	35	2.2	35	90	0	116	53	11	2	31	1.51
35257093--35257129	19	2.0	19	94	5	67	40	0	5	54	1.24
35257094--35257136	19	2.4	18	85	11	61	44	0	6	48	1.29
35260351--35260376	7	3.7	7	100	0	52	88	0	0	11	0.52
35261458--35261539	32	2.6	32	82	0	101	51	19	2	26	1.59
35265012--35265112	4	25.2	4	100	0	202	50	24	0	24	1.49
35266078--35266111	17	1.9	18	88	5	52	47	8	2	41	1.50
35283513--35283601	28	3.2	28	77	1	81	26	24	23	24	2.00
35283706--35283785	26	3.1	26	80	7	99	38	25	21	15	1.92
35283979--35284098	27	4.5	26	78	6	78	18	15	24	42	1.88
35283994--35284241	27	9.2	27	80	8	238	22	13	17	46	1.82
35283994--35284241	81	3.1	78	82	10	268	22	13	17	46	1.82
35292673--35292772	28	3.6	28	81	4	123	33	23	21	23	1.98
35293102--35293563	27	17.2	27	82	5	445	21	14	18	45	1.85
35305196--35305229	10	3.1	11	87	12	52	88	8	2	0	0.62
35307401--35307455	23	2.5	21	77	19	58	16	1	29	52	1.54
35312305--35312341	18	2.1	18	94	0	65	18	18	51	10	1.75
35313171--35313208	18	2.2	18	85	4	51	31	0	15	52	1.43
35314762--35314856	29	3.3	29	86	1	111	42	20	12	25	1.87
35314777--35314926	29	5.2	28	76	10	126	37	22	14	26	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35317864--35317903	21	2.0	20	85	5	53	55	7	22	15	1.65
35319904--35320137	112	2.1	114	86	2	339	38	12	21	26	1.90
35327172--35327207	18	2.0	18	94	0	63	11	13	2	72	1.23
35330390--35330469	30	2.7	30	84	0	106	47	11	21	20	1.80
35349180--35349219	14	2.9	14	84	0	53	32	7	17	42	1.77
35349203--35349242	20	2.0	20	90	0	62	27	10	12	50	1.72
35349188--35349254	34	1.9	35	90	3	109	31	8	13	46	1.74
35349182--35349258	14	5.0	15	71	20	52	32	9	15	42	1.78
35349235--35349320	33	2.6	32	75	12	93	26	9	17	46	1.78
35349341--35349379	20	2.0	20	94	0	69	48	2	0	48	1.15

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   188   189   190   191   192   
          193   194   195   196   197   198