genome.fa.s3.2.7.7.80.10.50.1000.142.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  142  of  150  ( 17918 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)
42837543--42837581	20	2.0	19	95	5	69	41	15	5	38	1.69
42838911--42839518	239	2.6	230	83	3	732	45	16	7	30	1.74
42840225--42840291	34	1.9	35	87	3	100	44	11	8	34	1.73
42844907--42845016	51	2.2	51	83	3	132	40	6	14	38	1.72
42848706--42848748	21	2.0	23	86	9	63	23	2	6	67	1.27
42852151--42852198	11	4.4	11	81	0	51	64	8	8	18	1.46
42852204--42852251	20	2.4	20	82	0	60	62	18	12	6	1.50
42855762--42855797	6	5.8	6	96	3	63	19	0	0	80	0.71
42858200--42858333	60	2.2	60	83	7	157	26	13	11	48	1.76
42858724--42858850	31	4.2	30	69	6	94	48	15	12	23	1.80
42864147--42864230	42	2.0	42	100	0	168	38	16	16	28	1.91
42865572--42865973	175	2.3	174	91	2	628	24	19	23	31	1.98
42871849--42871940	45	2.0	45	93	0	157	36	18	20	23	1.94
42877205--42877229	8	3.1	8	100	0	50	52	36	0	12	1.39
42884357--42884381	13	1.9	13	100	0	50	24	16	36	24	1.94
42884635--42884715	28	2.9	28	76	10	67	24	7	32	35	1.83
42886860--42886906	2	23.5	2	100	0	94	48	0	0	51	1.00
42887951--42887985	2	17.5	2	100	0	70	51	0	0	48	1.00
42894365--42894404	20	1.9	21	85	10	55	12	12	7	67	1.41
42898710--42898747	14	2.8	13	88	7	58	44	5	13	36	1.66
42898786--42898818	10	3.0	11	86	13	50	36	9	18	36	1.82
42915874--42915922	2	24.5	2	91	0	80	46	0	0	53	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42920358--42920416	28	2.2	27	87	6	84	40	20	16	22	1.91
42921868--42921924	19	2.9	19	84	7	71	42	1	3	52	1.28
42940290--42940532	2	121.0	2	81	4	256	42	0	53	3	1.18
42941815--42941852	18	2.2	18	85	4	51	44	2	2	50	1.30
42942048--42942095	21	2.5	20	80	10	55	47	0	2	50	1.12
42942340--42942374	18	2.0	18	88	5	54	31	0	11	57	1.34
42952023--42952081	29	2.0	29	86	3	82	55	11	3	28	1.52
42958561--42958627	3	22.3	3	100	0	134	0	67	0	32	0.91
42960181--42960220	14	2.9	14	84	0	53	32	7	17	42	1.77
42960204--42960243	20	2.0	20	90	0	62	27	10	12	50	1.72
42960189--42960255	34	1.9	35	90	3	109	31	8	13	46	1.74
42960183--42960259	14	5.0	15	71	20	52	32	9	15	42	1.78
42966459--42966526	21	3.4	21	76	11	63	51	0	0	48	1.00
42966471--42966535	21	3.2	21	79	10	73	49	0	0	50	1.00
42977229--42977348	41	2.9	39	81	9	132	29	18	23	29	1.98
42979706--42979862	86	1.8	85	84	9	212	24	17	24	33	1.97
42979699--42979862	43	3.8	42	77	9	172	24	17	25	32	1.97
42979708--42979885	86	2.1	86	79	8	184	24	17	24	33	1.96
42982374--42982467	11	8.5	10	71	25	57	53	1	2	43	1.19
42982371--42982466	22	4.3	21	72	16	77	53	1	2	43	1.19
42982357--42982467	56	2.0	57	89	7	174	52	0	1	45	1.17
42987223--42987266	6	7.3	6	100	0	88	52	0	15	31	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42994565--42994624	30	2.0	30	96	0	111	45	10	13	31	1.76
42996405--42996454	3	16.7	3	95	0	91	68	2	0	30	1.01
43007858--43007891	6	5.8	6	96	3	61	52	11	0	35	1.38
43007858--43007897	18	2.2	18	86	8	55	57	10	0	32	1.32
43007887--43007939	25	2.2	25	79	3	63	69	3	1	24	1.15
43007905--43007944	21	1.9	21	84	0	53	70	7	2	20	1.24
43008166--43008231	14	4.9	14	74	18	52	71	1	4	22	1.13
43008191--43008248	25	2.3	25	96	0	107	70	3	6	18	1.24
43011051--43011085	16	2.2	16	89	0	52	8	28	5	57	1.52
43013855--43013879	6	4.2	6	100	0	50	32	52	16	0	1.44
43023016--43023066	22	2.3	22	83	6	59	15	29	17	37	1.91
43024080--43024135	17	3.4	16	78	11	60	41	1	1	55	1.21
43024095--43024136	15	2.6	17	77	14	52	45	0	2	52	1.13
43024081--43024136	27	2.0	29	86	6	80	42	1	1	53	1.21
43029991--43030032	20	2.1	20	86	0	57	47	0	7	45	1.30
43035066--43035107	20	2.1	20	86	0	57	47	0	7	45	1.30
43037787--43037817	14	2.1	15	94	5	55	22	12	3	61	1.46
43039116--43039174	31	1.9	31	85	0	82	42	11	11	33	1.78
43040271--43040295	2	12.5	2	100	0	50	52	0	48	0	1.00
43043358--43043391	13	2.6	13	90	0	50	44	0	0	55	0.99
43043462--43043496	16	2.1	17	89	5	54	31	5	2	60	1.35
43061783--43061852	33	2.2	33	86	2	97	41	12	11	34	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43071220--43071248	7	4.1	7	100	0	58	27	17	13	41	1.87
43082436--43082499	13	4.9	13	84	0	92	29	9	25	35	1.87
43095441--43095520	32	2.5	32	83	0	97	51	10	2	36	1.49
43097747--43097871	42	3.0	42	83	3	126	44	16	14	24	1.85
43099206--43099234	6	4.8	6	100	0	58	34	17	13	34	1.89
43109210--43109253	13	3.4	13	87	6	63	20	0	2	77	0.88
43115182--43115221	20	2.0	19	85	9	53	70	2	0	27	1.01
43115715--43115754	21	2.0	20	90	9	64	30	0	0	70	0.88
43117890--43117966	14	5.0	15	71	20	52	42	15	9	32	1.78
43117906--43117945	20	2.0	20	90	0	62	50	12	10	27	1.72
43117894--43117960	34	1.9	35	90	3	109	46	13	8	31	1.74
43117929--43117968	14	2.9	14	84	0	53	42	17	7	32	1.77
43120681--43120716	2	18.0	2	100	0	72	50	0	0	50	1.00
43135401--43135431	16	1.9	16	93	0	53	51	0	0	48	1.00
43136272--43136301	11	2.6	11	94	5	51	36	3	0	60	1.14
43138521--43138681	33	4.8	32	70	8	97	29	22	14	32	1.94
43138501--43138684	101	1.8	101	89	0	287	29	22	14	33	1.94
43147414--43147462	17	2.8	17	78	6	53	51	4	2	42	1.32
43148538--43148578	2	20.5	2	100	0	82	48	0	0	51	1.00
43150611--43150843	103	2.3	102	82	3	290	29	22	16	31	1.96
43154319--43154352	17	2.0	17	94	0	59	79	0	5	14	0.91
43170798--43170848	24	2.0	26	85	7	70	35	1	1	60	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43171483--43171507	6	4.2	6	100	0	50	20	48	0	32	1.50
43183398--43183427	15	2.0	15	93	0	51	10	20	3	66	1.35
43195246--43195305	30	2.0	30	83	3	75	41	0	38	20	1.52
43195520--43195556	9	4.1	9	92	0	65	29	10	13	45	1.77
43195611--43195641	9	3.4	9	90	0	53	38	22	12	25	1.90
43195940--43195973	8	4.2	8	100	0	68	38	14	0	47	1.45
43196276--43196303	2	14.0	2	100	0	56	50	0	0	50	1.00
43197173--43197250	40	1.9	42	84	10	108	58	1	1	38	1.14
43202909--43202942	16	2.1	17	88	5	52	58	0	0	41	0.98
43203218--43203274	19	2.9	19	84	2	69	33	0	15	50	1.44
43203194--43203453	41	6.1	40	72	19	170	31	0	13	55	1.44
43203328--43203424	49	2.0	49	89	0	149	32	1	13	52	1.47
43203409--43203565	49	3.2	50	88	1	246	30	0	13	55	1.43
43203498--43203555	22	2.9	19	80	14	71	34	0	12	53	1.38
43203194--43203549	22	15.9	22	76	16	272	31	0	12	54	1.42
43203764--43203842	27	2.9	27	96	0	140	24	39	20	16	1.92
43204859--43204900	16	2.6	16	88	0	57	42	2	33	21	1.66
43204871--43204907	16	2.3	16	95	0	65	40	0	32	27	1.57
43205121--43205162	15	2.7	16	82	14	52	52	2	0	45	1.13
43205130--43205171	15	2.9	15	82	10	52	52	0	0	47	1.00
43205473--43205510	16	2.3	17	86	4	51	55	5	2	36	1.37
43208668--43208707	6	6.8	6	94	5	64	70	15	2	12	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43208772--43208799	14	2.0	14	100	0	56	64	0	28	7	1.20
43208775--43208819	19	2.5	18	82	17	58	66	0	26	6	1.16
43213440--43213502	27	2.3	27	89	5	92	22	33	15	28	1.95
43214738--43214784	24	2.0	24	95	0	85	21	12	23	42	1.87
43218812--43218847	6	5.8	6	96	3	63	80	0	2	16	0.83
43221637--43221672	3	12.0	3	100	0	72	0	33	0	66	0.92
43226104--43226160	23	2.5	23	77	2	62	36	7	7	49	1.57
43230584--43230626	19	2.3	18	80	7	50	25	2	4	67	1.22
43230598--43230635	19	2.0	19	89	0	58	26	0	5	68	1.11
43250347--43250371	12	2.1	12	100	0	50	20	16	32	32	1.94

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