genome.fa.s4.2.7.7.80.10.50.1000.176.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  176  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)
55087211--55087241	8	3.9	8	95	0	53	3	22	25	48	1.66
55087600--55087649	21	2.4	21	100	0	100	32	18	50	0	1.47
55087958--55088054	44	2.2	44	92	3	160	31	21	25	20	1.98
55087970--55088061	44	2.1	44	95	0	166	35	21	26	16	1.94
55087998--55088179	86	2.1	86	82	1	220	29	20	28	20	1.98
55088042--55088179	43	3.2	43	91	0	222	28	20	29	21	1.98
55094138--55094170	16	2.1	16	94	0	57	27	6	0	66	1.15
55116960--55117011	21	2.5	21	96	0	95	9	23	11	55	1.64
55116940--55117022	21	3.8	21	83	4	85	13	24	10	51	1.72
55117432--55117480	16	3.2	16	71	11	57	46	6	22	24	1.74
55117432--55117492	30	2.0	30	96	0	113	45	6	24	22	1.76
55117697--55117735	18	2.2	17	86	13	53	33	0	20	46	1.51
55117953--55118074	23	5.3	23	87	0	190	22	21	26	30	1.99
55117953--55118074	46	2.7	46	94	0	217	22	21	26	30	1.99
55121766--55121796	11	2.8	11	100	0	62	45	16	0	38	1.47
55122907--55122956	12	3.9	13	77	12	59	60	2	0	38	1.09
55126867--55126891	2	12.5	2	100	0	50	52	0	0	48	1.00
55139751--55139785	17	2.1	17	100	0	70	48	0	22	28	1.51
55140577--55140621	16	2.7	16	82	6	54	2	15	2	80	0.92
55140582--55140621	16	2.4	16	84	15	55	0	17	2	80	0.83
55142346--55142377	9	3.6	9	95	0	55	46	12	12	28	1.78
55142426--55142486	30	2.0	31	90	3	97	19	44	0	36	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55142579--55142619	19	2.1	20	82	13	50	26	36	0	36	1.57
55142742--55142774	18	1.9	17	88	11	50	27	30	0	42	1.56
55154586--55154627	21	2.0	21	85	0	57	11	2	40	45	1.54
55154810--55155222	125	3.3	125	92	0	666	32	18	19	28	1.96
55155434--55155464	9	3.4	9	100	0	62	22	12	22	41	1.88
55155760--55155819	30	2.0	31	83	3	77	20	38	0	41	1.52
55159046--55159166	49	2.5	49	97	0	224	44	8	3	43	1.50
55165555--55165599	21	2.1	21	95	0	81	28	26	13	31	1.94
55176597--55176693	42	2.3	42	89	3	142	37	10	26	25	1.88
55180400--55180424	2	12.5	2	100	0	50	52	0	0	48	1.00
55198240--55198296	23	2.6	21	89	10	96	22	29	0	47	1.52
55200981--55201102	23	5.3	23	88	0	190	29	27	22	21	1.99
55200981--55201100	46	2.6	46	95	0	213	29	27	22	20	1.99
55202090--55202150	30	2.0	30	83	0	77	34	44	14	6	1.72
55202211--55202253	18	2.4	18	84	7	52	18	25	11	44	1.84
55203229--55203516	126	2.3	126	91	0	459	28	20	19	31	1.97
55203591--55203747	53	3.1	53	63	20	136	37	19	2	40	1.65
55203598--55203747	48	3.1	46	64	14	113	37	18	2	42	1.64
55203590--55203895	98	3.2	95	82	3	344	39	18	1	40	1.62
55205019--55205096	18	4.4	16	77	19	68	65	2	2	29	1.19
55210899--55210953	22	2.6	21	88	11	85	7	23	12	56	1.61
55217715--55217754	18	2.2	18	95	0	71	7	37	2	52	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55219865--55219923	30	2.0	30	96	0	109	18	20	15	45	1.85
55221100--55221192	44	2.1	44	84	9	118	35	26	3	34	1.73
55221790--55221839	11	4.5	11	85	7	66	24	28	0	48	1.52
55221790--55221839	23	2.3	22	83	10	66	24	28	0	48	1.52
55223938--55223985	21	2.3	22	79	17	57	29	41	20	8	1.81
55224118--55224286	49	3.5	49	95	1	304	44	2	8	44	1.48
55227472--55227756	123	2.3	124	90	0	455	30	21	18	30	1.97
55227942--55227975	15	2.3	15	89	0	50	52	35	0	11	1.38
55229303--55229862	193	2.9	193	81	7	591	29	15	17	38	1.90
55234203--55234232	12	2.5	12	94	0	51	30	16	30	23	1.96
55239926--55239960	2	17.5	2	100	0	70	51	0	0	48	1.00
55244301--55244329	2	14.5	2	100	0	58	48	0	0	51	1.00
55245108--55245159	22	2.4	22	80	0	59	65	1	1	30	1.14
55248463--55248503	21	2.0	21	85	9	57	51	9	4	34	1.56
55262455--55262483	2	14.5	2	100	0	58	51	0	0	48	1.00
55263479--55263579	17	5.6	17	70	13	76	49	16	3	29	1.64
55263496--55263562	20	3.5	20	70	12	68	44	17	5	31	1.73
55263473--55263584	37	3.0	37	97	0	206	46	16	5	32	1.69
55269546--55269618	36	2.0	36	94	0	128	38	15	20	26	1.92
55269667--55269776	36	3.1	36	95	0	202	37	10	20	31	1.87
55273376--55273406	2	15.5	2	100	0	62	51	48	0	0	1.00
55275548--55275578	15	2.1	15	93	0	53	64	9	6	19	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55276790--55276835	21	2.0	24	84	12	62	52	2	0	45	1.13
55280186--55280220	13	2.7	13	95	0	61	17	22	25	34	1.96
55282612--55282738	43	3.0	42	79	17	152	29	28	18	22	1.98
55297878--55297948	10	6.8	10	70	13	54	56	4	2	36	1.34
55311825--55311859	18	1.9	19	88	11	56	71	2	0	25	1.00
55318111--55318167	2	28.5	2	89	0	87	49	3	0	47	1.18
55322813--55322862	3	16.7	3	100	0	100	68	0	32	0	0.90
55323321--55323732	44	9.1	45	69	12	155	32	18	20	28	1.96
55323292--55323671	138	2.8	138	84	2	467	29	18	22	30	1.97
55323324--55323714	138	2.8	137	84	3	430	30	18	21	29	1.97
55325344--55325379	3	12.0	3	100	0	72	33	0	0	66	0.92
55325452--55325477	9	2.9	9	100	0	52	42	11	0	46	1.40
55329246--55329293	2	24.0	2	100	0	96	50	0	0	50	1.00
55329348--55329385	12	3.2	12	82	10	51	55	0	10	34	1.34
55329339--55329385	24	2.0	24	87	8	69	57	0	10	31	1.33
55343082--55343114	17	1.9	17	93	0	57	51	12	0	36	1.39
55344640--55344682	17	2.5	16	82	14	50	6	27	2	62	1.33
55344653--55344693	17	2.4	18	80	12	50	4	31	4	58	1.40
55345327--55345363	3	12.3	3	100	0	74	67	0	0	32	0.91
55346300--55346349	26	1.9	26	91	0	82	52	12	8	28	1.66
55351419--55351498	3	26.7	3	89	0	115	60	3	0	36	1.15
55352403--55352440	14	2.4	17	87	12	55	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55352420--55352463	12	3.7	11	80	14	52	45	2	0	52	1.13
55352415--55352477	24	2.7	23	78	9	65	50	1	0	47	1.10
55352432--55352480	20	2.5	20	76	6	55	53	2	0	44	1.12
55352908--55352981	36	2.1	36	92	0	121	33	12	5	48	1.63
55359705--55359754	15	3.2	16	73	21	52	22	22	0	56	1.43
55362883--55362934	10	4.9	10	80	13	59	38	0	3	57	1.17
55362883--55362934	22	2.4	21	83	3	68	38	0	3	57	1.17
55362883--55362928	10	4.3	11	84	13	60	32	0	4	63	1.14
55363294--55363373	38	2.1	38	100	0	160	27	16	12	43	1.83
55366762--55366788	14	1.9	14	100	0	54	40	7	7	44	1.60
55367945--55367986	2	21.0	2	95	0	75	47	0	0	52	1.00
55375195--55375226	15	2.1	15	100	0	64	34	18	6	40	1.76
55378112--55378309	99	2.0	101	90	4	312	40	14	12	32	1.83
55383249--55383324	23	3.3	23	83	0	107	23	19	25	31	1.98
55384352--55384384	2	16.5	2	100	0	66	48	0	0	51	1.00
55388268--55388305	13	2.9	13	92	0	67	28	7	23	39	1.83
55392046--55392081	14	2.6	14	90	0	54	27	25	8	38	1.84
55393719--55394182	232	2.0	232	97	0	885	33	14	16	34	1.90
55397369--55397413	11	4.4	11	78	13	51	31	6	0	62	1.21
55401332--55401371	20	2.0	20	90	0	62	32	27	12	27	1.93
55408773--55408799	9	3.0	9	100	0	54	88	0	0	11	0.50
55409642--55409827	100	1.9	100	88	0	282	28	22	25	23	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55409642--55409853	50	4.2	50	72	3	167	30	21	24	23	1.99
55409642--55409853	100	2.1	100	84	1	273	30	21	24	23	1.99
55411486--55411530	11	4.4	11	78	13	51	31	6	0	62	1.21
55411835--55411877	2	21.5	2	85	0	59	46	2	2	48	1.27
55413344--55413520	93	1.9	93	83	0	228	23	25	21	29	1.99
55425654--55425806	42	3.6	42	93	3	272	56	4	31	7	1.46
55425654--55425806	21	7.3	21	94	2	247	56	4	31	7	1.46
55426617--55426670	25	2.2	25	96	0	99	27	12	20	38	1.89
55429703--55429731	2	14.5	2	100	0	58	51	0	0	48	1.00
55442518--55442628	46	2.4	46	95	1	197	29	21	17	31	1.96

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