genome.fa.s8.2.7.7.80.10.50.1000.23.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  23  of  190  ( 22705 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)
6546489--6546725	36	6.0	36	77	18	240	37	13	20	28	1.90
6546453--6546860	82	4.9	82	86	6	552	35	13	21	28	1.92
6546526--6546860	128	2.6	125	76	17	373	35	14	21	28	1.93
6558574--6558626	18	2.9	18	82	2	70	52	1	0	45	1.11
6564133--6564447	41	7.7	41	76	8	225	22	19	27	30	1.98
6564127--6564447	82	3.9	81	80	6	308	21	19	28	30	1.98
6564917--6564961	21	2.1	21	83	0	54	22	2	42	33	1.66
6565078--6565114	15	2.5	15	90	0	56	24	0	37	37	1.56
6565083--6565114	7	4.2	8	84	15	50	21	0	40	37	1.54
6565208--6565247	21	1.9	21	85	10	55	27	0	30	42	1.56
6565093--6565455	171	2.1	171	98	0	701	28	2	27	41	1.68
6565336--6565389	25	2.2	25	83	6	65	29	0	33	37	1.58
6565379--6565418	21	1.9	21	85	10	55	27	0	30	42	1.56
6565857--6566167	84	3.7	83	86	3	297	29	16	22	31	1.96
6565904--6566167	84	3.2	83	89	2	386	30	17	21	30	1.96
6567594--6567640	21	2.2	21	92	0	76	31	17	46	4	1.67
6567952--6568079	43	3.0	43	80	2	141	27	20	22	29	1.98
6569842--6570158	146	2.2	142	84	9	405	43	10	4	41	1.58
6569866--6570160	144	2.0	144	85	10	408	43	10	4	42	1.58
6575484--6575524	9	4.4	9	87	6	55	65	0	0	34	0.93
6584559--6584600	21	2.0	21	100	0	84	42	19	14	23	1.87
6584933--6584999	21	3.2	21	86	0	89	2	46	19	31	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6590140--6590211	36	2.0	36	100	0	144	30	19	25	25	1.98
6590661--6590947	25	11.2	25	92	2	439	34	0	19	45	1.51
6590663--6590947	102	2.8	101	93	3	473	35	0	20	44	1.51
6594047--6594099	22	2.4	22	81	12	56	39	1	3	54	1.29
6595248--6595296	8	6.2	8	78	4	55	38	44	2	14	1.56
6595246--6595295	23	2.2	23	85	7	66	36	46	2	16	1.58
6595259--6595301	15	2.8	16	82	6	54	34	44	2	18	1.63
6595590--6595912	114	2.8	114	76	9	275	25	24	24	26	2.00
6595688--6595910	113	2.0	114	80	8	258	23	25	24	26	2.00
6595871--6596051	72	2.5	71	82	9	226	21	23	24	29	1.99
6598997--6599048	25	2.0	26	85	3	70	71	3	0	25	1.03
6598997--6599086	37	2.4	37	78	9	101	71	2	1	25	1.05
6599648--6599679	3	10.7	3	100	0	64	65	0	0	34	0.93
6600669--6600702	17	2.0	17	88	0	50	50	0	11	38	1.39
6601312--6601356	2	22.5	2	100	0	90	48	0	0	51	1.00
6603948--6603976	3	9.7	3	100	0	58	34	0	65	0	0.93
6605977--6606193	105	2.1	101	86	5	292	29	16	26	27	1.97
6606114--6606191	33	2.4	33	78	8	95	30	16	25	26	1.97
6618592--6618653	28	2.2	27	83	11	72	58	6	1	33	1.34
6619161--6619218	22	2.6	22	84	7	73	43	17	3	36	1.66
6619174--6619243	21	3.4	19	84	11	68	41	15	7	35	1.75
6619515--6619615	43	2.4	43	85	6	143	22	13	32	30	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6626682--6626706	12	2.1	12	100	0	50	32	8	16	44	1.76
6627915--6627962	24	2.1	22	88	7	69	62	8	2	27	1.35
6627919--6627973	25	2.3	23	84	6	65	61	9	1	27	1.36
6627918--6627973	23	2.3	24	81	12	69	60	8	1	28	1.37
6628502--6628543	21	2.0	21	90	0	66	57	4	0	38	1.20
6628460--6628550	47	1.9	48	84	6	123	62	3	0	34	1.11
6628612--6628673	29	2.1	30	84	3	81	61	0	1	37	1.06
6628634--6628672	19	2.1	19	95	0	69	69	0	0	30	0.89
6628638--6628708	19	4.2	18	75	15	62	66	2	0	30	1.06
6637449--6637576	64	2.0	64	98	0	247	28	14	13	43	1.82
6648797--6648857	16	3.5	17	78	17	63	34	0	1	63	1.04
6648797--6648857	17	3.6	16	80	10	68	34	0	1	63	1.04
6650886--6650978	44	2.1	44	87	0	132	44	6	23	25	1.77
6668915--6668983	31	2.3	29	83	13	95	63	0	1	34	1.03
6668905--6668983	31	2.5	32	82	12	92	62	1	2	34	1.17
6670099--6670163	27	2.4	27	89	0	94	30	21	35	12	1.90
6670290--6670339	14	3.6	13	84	10	55	62	0	36	2	1.07
6670302--6670345	3	15.3	3	81	9	56	63	0	34	2	1.07
6670290--6670350	20	3.6	17	72	24	56	63	0	34	1	1.04
6670304--6670349	14	3.4	13	88	8	58	65	0	32	2	1.05
6670498--6670584	22	4.2	21	82	11	99	31	0	11	57	1.34
6670522--6670578	19	2.9	19	86	2	78	33	0	14	52	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6670722--6670963	27	9.8	25	78	17	258	31	0	13	54	1.44
6670712--6670963	49	5.2	49	89	1	382	31	0	13	54	1.44
6670718--6670963	97	2.5	98	95	1	449	31	0	13	54	1.44
6670885--6670942	22	2.9	19	71	14	53	34	1	12	51	1.49
6670885--6670963	19	4.6	19	69	23	66	34	1	12	51	1.48
6674237--6674303	22	3.1	21	89	6	91	1	32	1	64	1.12
6674390--6674442	27	2.0	27	100	0	106	22	41	20	15	1.89
6684875--6684911	19	1.9	19	88	0	56	29	8	29	32	1.86
6687438--6687468	16	1.9	16	93	0	53	29	0	25	45	1.54
6687983--6688058	35	2.1	35	85	7	100	14	13	35	36	1.85
6697259--6697406	80	1.9	80	90	5	237	44	10	2	43	1.49
6697923--6697988	31	2.1	31	100	0	132	30	12	9	48	1.71
6700127--6700157	5	6.2	5	100	0	62	41	19	19	19	1.90
6701182--6701218	9	4.1	9	92	0	65	29	10	13	45	1.77
6711589--6711645	18	3.2	18	67	5	53	33	26	15	24	1.95
6714101--6714269	84	2.0	84	95	0	302	43	3	20	33	1.69
6715195--6715260	29	2.3	29	83	0	87	36	16	25	21	1.94
6714955--6715279	163	2.0	165	85	2	440	42	17	18	20	1.89
6722904--6722968	17	3.9	17	74	11	62	24	1	3	70	1.10
6722907--6722968	33	1.9	32	83	6	81	22	1	3	72	1.08
6725484--6725524	21	2.0	21	95	0	73	21	17	31	29	1.96
6726180--6726333	81	1.9	82	94	1	274	28	6	16	48	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6729617--6729652	18	2.0	18	100	0	72	22	5	0	72	1.05
6730875--6730934	3	20.0	3	77	13	61	30	3	1	65	1.19
6731864--6731907	18	2.4	18	81	11	54	22	0	0	77	0.77
6732898--6732925	8	3.5	8	100	0	56	35	0	0	64	0.94
6733186--6733226	13	3.2	13	86	3	57	70	0	29	0	0.87
6733603--6733638	18	2.0	18	89	10	56	38	2	19	38	1.66
6733701--6733808	37	2.9	35	78	15	92	37	6	19	37	1.78
6733974--6734093	51	2.3	51	85	7	179	18	20	20	40	1.92
6740886--6741033	42	3.5	42	77	6	140	18	18	17	44	1.87
6742980--6743079	45	2.2	45	82	5	121	26	20	14	40	1.90
6743663--6743710	2	24.5	2	95	4	89	47	0	0	52	1.00
6748333--6748374	21	2.0	21	100	0	84	23	19	14	42	1.87
6749090--6749154	28	2.3	29	81	10	89	38	32	9	20	1.84
6752653--6752681	13	2.3	13	94	5	51	37	6	0	55	1.27
6752993--6753035	2	21.5	2	100	0	86	51	0	0	48	1.00
6756210--6756252	15	2.8	15	82	3	50	44	27	0	27	1.55
6759039--6759084	21	2.1	21	88	4	65	26	13	2	58	1.46
6759159--6759202	11	3.9	11	90	3	70	45	0	31	22	1.53
6759159--6759202	22	2.0	23	95	4	81	45	0	31	22	1.53
6761209--6761245	14	2.6	15	87	12	60	43	5	10	40	1.63
6761797--6761857	18	3.3	18	75	18	54	50	0	1	47	1.10
6761803--6761891	42	2.0	46	81	12	107	55	1	1	42	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6771831--6771968	44	3.1	44	70	17	147	47	4	1	47	1.31
6771768--6772052	91	3.1	91	93	1	457	45	3	2	47	1.35
6771997--6772102	10	10.7	10	67	19	53	48	1	0	50	1.12
6772085--6772374	120	2.4	121	91	1	467	44	3	4	48	1.39
6772155--6772345	61	3.2	61	68	11	158	42	3	6	47	1.46
6771950--6772374	226	1.8	236	80	9	525	45	3	3	47	1.38
6772050--6772374	59	5.5	59	69	15	206	44	3	3	48	1.36
6772326--6772360	18	2.0	17	88	5	52	45	0	0	54	0.99
6772322--6772371	15	3.2	16	79	17	52	52	0	0	48	1.00
6772517--6772613	45	2.2	45	85	5	126	34	28	5	31	1.79

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