genome.fa.s4.2.7.7.80.10.50.1000.131.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  131  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)
41702832--41702913	5	16.0	5	75	16	53	37	3	1	57	1.24
41702830--41702904	28	2.7	28	93	0	123	37	4	2	56	1.32
41702834--41702907	23	3.0	23	82	9	67	37	4	1	56	1.27
41703239--41703280	19	2.2	20	86	4	59	66	4	0	28	1.12
41707683--41707782	42	2.4	42	94	0	173	20	28	15	37	1.92
41709503--41709566	24	2.7	24	77	0	65	48	1	31	18	1.58
41714334--41714440	46	2.4	45	87	4	153	21	18	17	42	1.90
41714420--41714468	6	7.8	6	86	2	62	18	18	14	48	1.80
41722623--41722683	27	2.3	27	94	0	113	55	22	4	16	1.60
41726160--41726466	83	3.6	85	76	9	272	42	11	14	31	1.81
41726604--41726692	6	14.8	6	89	5	119	66	0	0	33	0.92
41736270--41736306	2	18.5	2	100	0	74	48	0	0	51	1.00
41736692--41736754	13	4.8	13	82	0	72	36	7	20	34	1.82
41740669--41740933	4	66.2	4	100	0	530	50	24	0	24	1.50
41745128--41745206	38	2.1	38	100	0	158	48	5	10	36	1.59
41750147--41750195	10	4.5	11	85	12	57	55	2	4	38	1.31
41751552--41751614	27	2.3	27	89	5	92	28	26	19	25	1.98
41755102--41755155	25	2.1	26	86	10	76	31	3	1	62	1.23
41759508--41759532	13	1.9	13	100	0	50	16	12	8	64	1.49
41759969--41759993	9	2.8	9	100	0	50	32	0	0	68	0.90
41762445--41762473	3	9.7	3	100	0	58	34	0	0	65	0.93
41772407--41772572	81	2.1	81	98	1	325	47	15	2	34	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41772529--41772750	111	2.0	111	87	5	324	53	13	2	30	1.53
41778263--41778307	17	2.6	17	82	10	56	11	8	4	75	1.17
41789627--41789655	13	2.2	13	100	0	58	41	0	13	44	1.44
41789706--41790126	138	3.1	138	89	2	641	43	6	8	40	1.61
41799088--41799150	20	2.8	22	79	18	60	38	0	3	58	1.14
41811303--41811399	44	2.2	44	83	1	113	29	20	26	22	1.99
41811457--41811562	46	2.3	46	88	0	167	33	21	16	28	1.95
41818297--41818349	26	2.0	27	81	3	63	26	16	24	32	1.97
41824466--41824839	187	2.0	187	85	1	498	26	15	23	34	1.94
41828850--41828889	20	2.0	20	90	9	64	22	0	20	57	1.41
41842101--41842157	20	2.9	20	87	7	73	38	24	28	8	1.85
41846844--41846874	13	2.4	13	94	0	53	16	6	22	54	1.64
41847881--41847934	17	3.1	17	78	13	56	22	7	1	68	1.24
41847987--41848042	27	2.1	27	100	0	112	39	0	32	28	1.57
41853133--41853166	17	2.0	17	88	11	52	8	5	8	76	1.15
41855152--41855199	24	2.0	25	91	4	80	75	6	10	8	1.20
41861630--41861661	11	2.9	11	100	0	64	25	0	9	65	1.22
41867168--41867198	14	2.2	14	94	0	53	51	9	12	25	1.70
41868129--41868278	49	3.1	49	93	0	246	27	23	6	42	1.79
41869355--41869436	43	1.9	43	87	0	119	26	21	0	51	1.48
41870625--41870657	16	1.9	18	88	11	52	21	12	0	66	1.23
41870913--41870943	15	2.1	15	100	0	62	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41873046--41873166	49	2.5	49	81	6	129	17	24	22	35	1.95
41873029--41873169	25	5.7	24	72	15	92	17	26	21	34	1.96
41874195--41874257	27	2.3	27	78	8	74	33	20	22	23	1.97
41874386--41874450	22	3.0	21	75	4	67	44	20	20	15	1.86
41874442--41874612	32	5.4	31	79	6	164	38	19	20	21	1.94
41874442--41874612	64	2.7	64	82	0	209	38	19	20	21	1.94
41874656--41874715	27	2.2	27	88	11	88	31	21	25	21	1.98
41874794--41874858	24	2.7	24	92	2	112	56	29	1	12	1.45
41874928--41875641	27	26.6	27	89	1	1076	23	20	20	35	1.96
41874928--41875641	161	4.4	162	92	0	1094	23	20	20	35	1.96
41878246--41878321	37	2.1	37	92	0	125	22	19	22	35	1.96
41879309--41879336	14	2.0	14	100	0	56	71	0	0	28	0.86
41886532--41887021	44	10.8	47	71	18	174	31	17	20	30	1.96
41886592--41887382	44	17.6	43	71	11	338	32	17	20	29	1.95
41886733--41887243	221	2.3	221	90	1	792	31	17	20	30	1.95
41886595--41887389	133	5.9	133	81	5	688	32	17	20	29	1.95
41890142--41890201	30	2.0	31	83	3	77	20	38	0	41	1.52
41892316--41892547	29	8.0	29	80	1	250	39	15	23	21	1.91
41892281--41892547	87	3.0	88	85	2	331	39	14	23	22	1.91
41892318--41892548	88	2.6	87	86	3	295	39	14	24	21	1.91
41897032--41897092	28	2.2	27	80	13	70	54	6	1	37	1.37
41902736--41902778	18	2.4	18	96	0	77	51	0	2	46	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41905890--41905923	3	11.3	3	100	0	68	67	0	0	32	0.91
41916153--41916212	18	3.3	18	70	25	63	25	8	28	38	1.84
41916129--41916234	36	2.9	36	87	5	160	28	10	27	33	1.90
41926362--41926675	50	6.3	50	72	0	250	24	25	21	28	1.99
41926378--41926673	100	3.0	100	94	1	513	24	25	21	28	1.99
41934733--41934772	20	2.0	20	90	0	62	32	12	22	32	1.91
41938248--41938293	14	3.2	15	81	9	60	60	8	0	30	1.26
41968216--41968255	13	3.1	13	85	0	62	40	20	7	32	1.80
41969076--41969126	20	2.5	20	83	3	57	50	0	5	43	1.26
41970858--41970951	20	4.7	20	72	7	75	10	31	21	36	1.88
41980760--41980800	22	2.0	22	85	9	59	9	9	41	39	1.71
41982667--41982719	14	3.9	13	75	7	52	18	9	1	69	1.25
41988368--41988405	18	2.1	18	95	0	67	28	0	36	34	1.58
41992808--41992995	51	3.7	51	81	7	231	28	15	25	29	1.96
41997045--41997071	13	2.1	13	100	0	54	33	7	29	29	1.85
42003731--42003769	2	19.5	2	100	0	78	51	0	0	48	1.00
42004042--42004091	19	2.7	18	85	11	66	68	4	4	24	1.24
42005247--42005277	5	6.2	5	100	0	62	19	0	0	80	0.71
42014640--42014726	45	1.9	45	90	0	138	31	22	18	27	1.97
42014728--42014923	51	3.9	50	79	4	214	31	28	16	23	1.96
42014735--42014919	101	1.8	101	88	3	282	31	28	16	23	1.96
42016815--42016845	15	2.1	15	93	0	53	29	0	6	64	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42033031--42033055	4	6.2	4	100	0	50	72	0	0	28	0.86
42033680--42033727	25	2.1	23	85	14	64	20	10	0	68	1.18
42034327--42034399	38	2.0	37	94	5	130	31	19	9	39	1.84
42040584--42040647	13	4.9	13	77	7	76	35	25	6	32	1.81
42044934--42044975	4	10.2	4	87	5	57	78	2	0	19	0.86
42046599--42046639	17	2.4	17	91	4	64	34	9	2	53	1.47
42047124--42047189	31	2.2	31	91	2	107	46	7	10	34	1.67
42047216--42047312	28	3.4	28	90	7	142	48	14	3	34	1.59
42047214--42047291	14	5.5	13	69	19	57	48	12	5	33	1.63
42047183--42047312	28	4.5	28	81	11	138	49	13	4	33	1.62
42047183--42047312	61	2.2	58	84	11	160	49	13	4	33	1.62
42050959--42051004	23	1.9	24	82	8	58	34	19	2	43	1.63
42051945--42052127	46	4.0	45	90	4	276	28	27	9	34	1.88
42053352--42053399	17	2.9	17	87	3	71	50	20	2	27	1.60
42059131--42059223	29	3.2	29	78	0	78	19	21	35	23	1.96
42059287--42059348	29	2.1	29	81	0	70	22	22	30	24	1.99
42066129--42066602	87	5.4	87	89	0	714	24	23	22	29	1.99
42067840--42067874	7	5.0	7	89	10	54	14	14	0	71	1.15
42067848--42067874	13	2.1	13	100	0	54	14	14	0	70	1.17
42068320--42068354	12	2.8	13	91	8	56	11	0	14	74	1.08
42068264--42068341	32	2.5	31	83	8	88	8	10	12	67	1.41
42068748--42069038	150	1.9	150	98	0	564	26	21	15	36	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42074415--42074461	20	2.4	20	82	10	53	2	12	19	65	1.35
42075310--42075431	37	3.3	36	78	8	122	40	25	14	18	1.89
42076574--42076627	26	2.1	26	100	0	108	33	11	0	55	1.35
42077885--42077941	28	1.9	28	82	10	69	45	15	5	33	1.69
42089196--42089281	24	3.6	24	80	0	109	36	18	10	34	1.85
42089440--42089491	20	2.6	20	81	0	68	50	19	23	7	1.73
42093100--42093223	38	3.3	38	87	0	176	27	21	20	29	1.98
42095416--42095531	56	2.1	57	85	4	155	30	18	6	45	1.73
42100275--42100310	17	2.1	17	100	0	72	27	19	16	36	1.93
42108801--42108890	35	2.6	36	84	8	114	40	12	22	25	1.88

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