genome.fa.s13.2.7.7.80.10.50.1000.170.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   199   

This is table  170  of  199  ( 23770 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)
49693034--49693066	13	2.3	15	90	10	52	39	18	18	24	1.92
49700664--49700709	21	2.0	24	84	12	62	39	4	8	47	1.54
49708194--49708243	25	2.0	25	92	0	82	36	22	24	18	1.95
49708423--49708456	14	2.4	14	90	5	50	50	8	0	41	1.34
49710651--49710689	19	2.0	20	85	5	53	58	7	10	23	1.56
49711201--49711243	18	2.5	17	79	20	54	34	2	0	62	1.08
49711293--49711331	12	2.9	13	85	14	53	28	0	5	66	1.12
49712977--49713003	4	6.8	4	100	0	54	74	0	0	25	0.83
49726981--49727046	31	2.1	33	82	5	82	15	28	0	56	1.40
49729505--49729558	17	3.1	17	70	19	56	46	14	12	25	1.81
49729488--49729558	36	2.0	36	97	0	133	46	12	12	28	1.78
49729490--49729550	17	3.5	17	72	16	61	47	11	13	27	1.77
49734767--49734820	17	3.1	17	70	19	56	46	14	12	25	1.81
49734750--49734820	36	2.0	36	97	0	133	46	12	12	28	1.78
49734752--49734812	17	3.5	17	72	16	61	47	11	13	27	1.77
49736698--49736731	16	2.2	15	89	5	50	29	8	0	61	1.26
49736756--49736852	49	2.0	49	93	0	167	24	7	6	61	1.45
49741103--49741132	2	15.0	2	100	0	60	50	0	0	50	1.00
49742733--49742772	20	2.0	20	90	0	62	27	10	12	50	1.72
49742718--49742784	34	1.9	35	90	3	109	31	8	13	46	1.74
49742712--49742788	14	5.0	15	71	20	52	33	9	14	42	1.77
49742877--49742923	18	2.5	19	75	10	51	42	2	0	55	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49744970--49745022	8	6.6	8	85	6	54	50	1	0	47	1.12
49748622--49748671	24	2.1	24	85	7	66	28	0	6	66	1.15
49748654--49748711	24	2.4	24	79	0	62	31	3	10	55	1.50
49748643--49748712	3	23.3	3	72	5	52	30	2	8	58	1.42
49753769--49753826	25	2.3	26	93	3	100	41	12	13	32	1.82
49768309--49768343	16	2.2	16	89	0	52	45	17	17	20	1.85
49769497--49769541	20	2.2	21	84	11	58	53	2	15	28	1.54
49771806--49771893	46	1.9	46	95	0	158	22	6	19	51	1.70
49773770--49773799	15	2.0	15	100	0	60	73	0	0	26	0.84
49781616--49781647	12	2.6	13	85	14	50	68	0	0	31	0.90
49783695--49784067	53	6.8	54	70	17	150	46	11	12	29	1.77
49783744--49783861	21	6.1	20	72	19	90	49	9	11	29	1.71
49784089--49784135	24	2.0	24	87	8	69	38	6	8	46	1.60
49783695--49784229	18	29.1	18	71	16	316	46	11	11	29	1.76
49784221--49784265	24	1.9	24	82	13	58	37	2	13	46	1.55
49784473--49784517	20	2.2	20	84	7	65	44	8	13	33	1.75
49784456--49784521	19	3.5	18	78	15	62	42	9	16	31	1.80
49784681--49784708	5	5.6	5	100	0	56	64	0	0	35	0.94
49784874--49784938	22	3.0	20	80	12	76	0	21	0	78	0.75
49784874--49784928	24	2.3	23	82	14	67	0	20	0	80	0.72
49784868--49784936	26	2.6	25	80	15	77	1	18	0	79	0.80
49784860--49784934	34	2.3	34	86	6	102	2	17	0	80	0.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49785208--49785234	3	9.0	3	100	0	54	0	33	0	66	0.92
49785562--49785730	30	5.7	30	77	5	137	39	4	21	34	1.74
49785575--49785713	59	2.3	59	86	4	181	41	3	18	35	1.68
49785666--49785745	30	2.6	29	86	9	97	48	5	16	30	1.67
49785920--49786345	74	5.6	74	91	3	663	34	21	16	27	1.95
49785920--49786362	150	2.9	150	92	4	692	35	20	16	27	1.94
49787211--49787256	23	2.0	23	83	8	58	6	4	6	82	0.94
49795970--49796094	53	2.4	53	82	2	153	47	11	10	31	1.73
49796055--49796130	19	3.8	20	76	11	66	47	7	9	35	1.65
49796114--49796210	37	2.7	36	76	12	99	45	12	12	29	1.78
49795970--49796515	35	15.1	36	70	13	140	45	10	11	32	1.75
49796271--49796316	17	2.6	18	89	3	67	45	6	15	32	1.71
49795961--49796479	18	28.6	18	68	16	250	44	10	11	32	1.76
49796362--49796526	18	9.4	17	72	12	95	44	9	12	33	1.75
49796415--49796528	35	3.2	36	81	7	117	43	7	11	36	1.70
49796699--49796761	20	3.2	20	84	6	76	41	9	14	34	1.78
49796700--49796765	19	3.5	19	82	11	66	43	9	15	31	1.77
49797093--49797163	25	2.9	26	78	17	73	4	16	0	78	0.90
49797103--49797167	26	2.5	25	80	14	78	3	16	0	80	0.85
49797091--49797169	34	2.3	36	85	12	105	3	17	0	78	0.90
49797117--49797163	24	1.9	24	91	4	76	2	21	0	76	0.89
49797095--49797171	36	2.2	37	86	9	108	3	15	0	80	0.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49797197--49797257	24	2.6	22	75	17	61	0	19	45	34	1.51
49797323--49797349	14	1.9	14	100	0	54	0	0	11	88	0.50
49797463--49797514	3	17.0	3	84	11	70	0	32	1	65	1.04
49797454--49797513	18	3.1	18	72	23	50	0	28	1	70	0.97
49797858--49798003	30	4.9	30	84	5	172	39	3	23	32	1.72
49797867--49798003	58	2.3	60	84	3	197	40	3	23	32	1.72
49800498--49800569	4	17.8	4	75	16	51	72	1	6	19	1.15
49814022--49814176	57	2.7	57	97	0	292	15	34	23	25	1.94
49815625--49815669	14	3.0	15	77	9	56	60	2	2	35	1.22
49815627--49815694	29	2.3	30	87	2	93	60	2	7	29	1.39
49817378--49817438	18	3.3	19	79	6	54	70	1	4	22	1.15
49817398--49817608	9	22.6	9	65	18	60	57	4	3	34	1.36
49817488--49817532	21	2.2	21	88	4	65	53	8	2	35	1.45
49824435--49824461	6	4.5	6	100	0	54	33	0	0	66	0.92
49828947--49828984	14	2.7	14	95	0	67	36	7	21	34	1.82
49833193--49833233	20	2.0	21	85	4	57	53	0	0	46	1.00
49839697--49839744	22	2.2	22	100	0	96	25	33	0	41	1.55
49839719--49839831	51	2.2	51	90	3	174	29	29	1	39	1.67
49839833--49839895	30	2.1	30	96	0	117	33	0	0	66	0.92
49840976--49841000	7	3.6	7	100	0	50	28	0	12	60	1.32
49842217--49842398	25	7.6	25	62	20	75	38	1	13	46	1.54
49842215--49842414	71	2.8	71	96	0	375	37	2	14	46	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49842420--49842690	29	9.2	29	90	5	427	45	28	0	25	1.54
49842428--49842684	64	4.2	63	88	9	383	45	29	0	24	1.54
49842420--49842684	93	2.9	93	89	7	438	46	29	0	24	1.53
49842686--49842849	55	3.0	55	94	2	285	38	12	4	44	1.62
49842833--49842857	10	2.5	10	100	0	50	44	8	0	48	1.32
49845968--49846322	125	2.8	126	90	2	570	32	21	15	30	1.94
49856992--49857020	2	14.5	2	100	0	58	51	0	0	48	1.00
49857283--49857356	24	3.1	24	100	0	148	33	25	12	28	1.92
49857622--49857719	25	4.0	24	77	12	99	32	22	22	22	1.98
49863095--49863584	248	2.0	250	93	2	844	32	10	20	36	1.87
49863979--49864040	31	2.0	31	96	0	115	33	9	22	33	1.87
49871144--49871183	9	4.4	9	81	12	55	65	0	2	32	1.06
49871445--49871480	18	2.1	17	89	5	54	27	16	11	44	1.82
49871649--49871726	21	3.9	20	80	9	88	35	1	2	60	1.19
49871728--49871771	21	2.2	19	84	8	52	43	0	2	54	1.12
49871755--49871818	18	3.6	17	74	19	60	43	3	0	53	1.16
49871752--49871818	8	7.6	9	74	24	54	43	2	0	53	1.16
49871728--49871818	26	3.2	28	77	14	82	42	2	1	53	1.20
49871964--49872001	19	2.0	19	89	0	58	57	0	0	42	0.98
49889095--49889274	43	4.2	43	87	1	261	20	18	34	27	1.95
49889107--49889296	87	2.2	86	83	6	249	23	19	31	25	1.98
49892052--49892121	28	2.5	28	93	4	115	38	10	1	50	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49892170--49892247	27	2.9	26	87	11	104	28	26	29	15	1.96
49892629--49892684	3	18.7	3	100	0	112	33	0	0	66	0.92
49892629--49892794	12	13.6	12	71	13	79	35	0	6	57	1.30
49897233--49897310	27	2.9	27	88	3	104	15	29	26	28	1.96
49897356--49897425	27	2.5	28	90	6	108	47	1	10	41	1.46
49898045--49898070	5	5.2	5	100	0	52	38	19	0	42	1.51
49904604--49904659	28	2.0	29	92	3	96	25	16	19	39	1.91
49908207--49908237	15	2.1	15	93	0	53	29	0	0	70	0.87
49914994--49915290	50	5.8	50	80	3	274	28	20	27	23	1.99
49914994--49915241	100	2.4	103	83	5	306	27	20	28	23	1.99

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   199