genome.fa.s4.2.7.7.80.10.50.1000.167.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  167  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)
52513573--52513624	24	2.2	24	85	0	68	38	3	7	50	1.50
52517456--52517526	26	2.6	27	80	8	81	50	0	7	42	1.29
52518547--52518590	14	2.9	16	80	13	56	75	2	18	4	1.09
52518891--52518937	24	2.0	24	84	12	62	10	8	31	48	1.68
52519393--52519441	9	5.4	9	87	0	71	42	18	8	30	1.79
52521579--52521606	13	2.2	13	100	0	56	71	0	0	28	0.86
52524711--52525009	29	10.3	29	76	12	151	39	24	15	21	1.91
52524711--52524893	58	3.2	57	79	8	192	42	22	14	21	1.88
52524844--52525010	87	1.9	86	81	6	203	38	27	14	19	1.91
52525451--52525600	39	3.8	39	90	0	228	13	22	33	31	1.92
52528906--52528939	7	4.7	7	96	3	59	44	0	14	41	1.45
52530441--52530544	40	2.6	40	77	11	97	34	18	32	14	1.91
52530441--52530685	80	3.1	81	80	6	234	34	16	31	17	1.92
52530479--52530685	40	5.2	40	80	5	224	34	15	30	18	1.92
52530596--52530655	20	3.0	21	69	14	63	40	13	30	16	1.87
52530520--52530665	20	7.3	20	61	6	55	35	15	30	18	1.92
52530481--52530685	79	2.6	79	82	5	243	34	16	31	18	1.92
52538596--52538631	2	18.0	2	94	0	63	52	0	0	47	1.00
52541964--52541995	17	1.9	16	93	6	55	28	28	18	25	1.98
52546352--52546389	19	2.0	19	89	0	58	39	18	5	36	1.73
52556561--52556705	52	2.8	52	98	0	281	31	11	16	40	1.83
52558767--52558864	29	3.3	29	91	4	153	16	29	14	39	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52558853--52559041	29	6.4	29	79	10	161	24	25	12	36	1.91
52558853--52559041	58	3.2	58	77	5	209	24	25	12	36	1.91
52578670--52578756	42	2.1	42	84	4	113	43	21	6	27	1.78
52579796--52579884	44	2.0	44	100	0	178	22	17	17	41	1.90
52588622--52588818	27	7.3	28	75	7	137	43	18	16	20	1.88
52588658--52588798	53	2.6	53	83	4	158	44	19	16	19	1.87
52588643--52588818	80	2.2	81	82	9	200	44	18	17	20	1.87
52588859--52588954	24	4.0	24	81	9	108	23	9	25	41	1.84
52588861--52588965	47	2.2	47	81	8	115	23	9	24	41	1.84
52588896--52588963	24	2.8	24	84	0	91	20	8	26	44	1.81
52589040--52589096	27	2.1	27	84	12	73	19	24	24	31	1.98
52591758--52591882	43	2.9	43	77	7	119	35	27	16	20	1.94
52598401--52598564	30	5.5	30	75	4	107	21	26	14	36	1.93
52600926--52600983	20	2.7	23	76	17	70	15	27	29	27	1.96
52604033--52604086	21	2.6	21	82	5	56	16	22	33	27	1.95
52606676--52606731	27	2.1	27	86	0	76	35	23	17	23	1.95
52619551--52619636	42	2.0	42	100	0	172	24	9	23	43	1.83
52626797--52626834	15	2.5	15	84	12	51	47	7	0	44	1.32
52635463--52635514	21	2.5	21	76	17	54	19	36	25	19	1.95
52635527--52635582	20	2.8	20	83	2	67	19	33	23	23	1.97
52638574--52638820	27	9.1	27	82	6	243	42	19	16	22	1.89
52638574--52638833	54	4.8	54	84	2	308	42	20	15	21	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52638574--52638820	81	3.0	81	80	3	282	42	19	16	22	1.89
52638757--52638850	27	3.5	26	85	8	109	40	21	20	18	1.92
52638574--52638850	81	3.4	81	80	4	272	42	19	15	21	1.88
52638744--52638876	27	5.0	26	80	6	76	40	22	19	17	1.91
52639152--52639367	32	6.8	32	75	7	170	20	19	22	37	1.94
52639152--52639367	64	3.4	63	82	8	260	20	19	22	37	1.94
52641586--52642042	233	2.0	233	96	0	842	24	25	25	24	2.00
52645200--52645455	81	3.2	81	82	2	307	41	19	14	25	1.88
52645200--52645467	27	9.9	27	84	0	275	40	20	13	25	1.89
52648821--52648870	11	4.5	11	82	5	55	64	2	0	34	1.05
52653821--52653940	35	3.4	36	80	4	102	27	12	15	45	1.82
52653851--52653940	35	2.6	35	85	0	117	26	12	15	45	1.81
52655241--52655431	96	2.0	96	98	0	373	31	21	17	28	1.97
52657921--52658039	60	2.0	58	95	3	211	25	9	19	46	1.79
52671433--52671493	25	2.5	24	80	17	63	40	21	18	19	1.91
52679772--52679887	57	2.0	57	86	3	162	25	21	36	17	1.95
52685782--52685842	30	2.0	30	90	0	95	24	6	29	39	1.80
52687982--52688024	15	2.9	15	82	0	59	53	2	16	27	1.55
52687980--52688030	15	3.4	15	77	0	57	52	1	15	29	1.54
52688222--52688261	5	8.2	5	91	5	64	65	0	0	35	0.93
52688217--52688261	15	3.1	14	90	6	63	64	0	0	35	0.94
52688996--52689102	38	2.8	38	92	2	171	34	2	20	42	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52689072--52689132	30	2.0	30	87	0	86	36	1	16	45	1.57
52689872--52689922	27	2.0	27	92	7	88	50	0	5	43	1.26
52697984--52698034	27	2.0	27	92	7	88	50	0	5	43	1.26
52698925--52699004	42	1.9	42	86	0	115	23	20	23	32	1.98
52700734--52700758	2	12.5	2	100	0	50	52	0	0	48	1.00
52701256--52701293	15	2.5	15	86	0	58	50	5	0	44	1.24
52701390--52701442	26	2.0	27	82	10	65	37	5	1	54	1.35
52701524--52701571	16	2.7	18	81	15	55	29	2	2	66	1.14
52701962--52702006	23	2.0	23	82	8	56	28	11	6	53	1.61
52702166--52702220	29	1.9	29	85	10	78	58	1	12	27	1.45
52704306--52704391	45	1.9	45	92	0	145	25	16	30	27	1.97
52707932--52707963	2	16.0	2	100	0	64	50	0	0	50	1.00
52716053--52716138	32	2.8	30	78	8	84	6	10	6	75	1.18
52726413--52726452	7	5.7	7	100	0	80	27	42	0	30	1.56
52730066--52730379	95	3.3	95	88	6	467	40	1	19	38	1.60
52730066--52730379	96	3.3	95	88	7	460	40	1	19	38	1.60
52735668--52735707	21	1.9	21	90	10	64	25	10	10	55	1.64
52735790--52735848	31	1.9	31	82	0	73	40	13	8	37	1.75
52738618--52738664	24	2.0	24	95	4	87	48	17	0	34	1.47
52738619--52738672	24	2.3	23	90	3	81	50	14	0	35	1.44
52745316--52745419	41	2.5	42	80	7	113	32	25	17	24	1.96
52750562--52750600	20	2.0	20	94	0	69	56	2	2	38	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52750616--52750663	3	16.0	3	95	0	87	64	0	2	33	1.05
52750662--52750688	3	9.0	3	100	0	54	33	0	33	33	1.58
52756179--52756206	2	14.0	2	100	0	56	50	0	0	50	1.00
52757688--52757729	22	1.9	22	95	0	75	21	21	11	45	1.84
52759393--52759423	9	3.4	9	90	0	53	29	9	19	41	1.83
52761935--52762036	20	5.3	19	71	18	68	36	3	0	59	1.16
52761932--52761980	20	2.5	20	90	6	75	32	0	0	67	0.91
52762171--52762235	29	2.2	29	91	0	103	30	21	23	24	1.99
52762890--52762933	17	2.6	17	96	0	79	36	13	18	31	1.90
52770651--52770732	28	2.9	29	82	8	91	35	2	9	52	1.48
52776887--52777027	75	1.9	75	92	0	237	34	21	19	24	1.96
52779958--52780018	26	2.5	26	79	12	67	59	0	0	40	0.98
52779959--52780022	25	2.6	26	74	16	73	59	0	0	40	0.97
52779988--52780048	18	3.4	18	71	8	61	49	0	3	47	1.18
52781020--52781050	16	1.9	16	93	0	53	41	3	0	54	1.16
52784280--52784584	56	5.8	52	87	7	381	22	28	22	25	1.99
52784279--52784584	100	2.9	102	86	8	395	23	28	22	25	1.99
52791378--52791733	50	6.9	50	81	7	390	23	29	20	26	1.99
52791378--52791728	106	3.4	105	90	4	507	23	29	20	26	1.99
52791378--52791725	156	2.2	155	84	8	447	23	29	20	26	1.99
52804841--52804886	23	2.0	23	88	12	69	52	10	15	21	1.73
52804802--52804947	12	11.2	13	70	18	63	54	8	13	24	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52805581--52805790	68	3.1	67	91	6	336	45	8	5	40	1.56
52805679--52805706	9	3.1	9	100	0	56	57	10	0	32	1.33
52805779--52805820	16	2.6	16	92	0	66	42	7	2	47	1.43
52805794--52805855	23	2.8	23	80	4	65	46	1	1	50	1.20
52811210--52811262	11	5.0	10	78	14	54	20	26	1	50	1.58
52811210--52811262	22	2.5	22	82	11	65	20	26	1	50	1.58
52814424--52814714	126	2.3	126	90	0	456	26	23	18	31	1.97
52815170--52815210	6	6.8	6	94	0	73	34	46	0	19	1.50
52816197--52816229	16	2.1	16	88	11	50	27	3	0	69	1.03
52822803--52822828	13	2.0	13	100	0	52	15	0	0	84	0.62

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