genome.fa.s8.2.7.7.80.10.50.1000.42.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  42  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)
11711978--11712049	10	6.6	11	72	20	53	31	0	2	65	1.07
11711997--11712042	16	2.8	17	77	9	51	28	0	4	67	1.10
11711961--11712090	9	14.3	9	72	13	79	33	1	4	60	1.27
11712020--11712066	19	2.5	19	86	3	60	34	0	4	61	1.15
11716506--11716536	9	3.4	9	90	0	53	25	12	22	38	1.90
11716590--11716644	9	6.1	9	89	0	83	45	12	10	30	1.77
11716590--11716644	18	3.1	18	94	0	92	45	12	10	30	1.77
11716854--11716913	30	2.0	31	83	3	77	21	36	0	41	1.54
11722275--11722343	27	2.5	26	86	4	84	17	36	28	17	1.93
11722406--11722514	5	22.4	5	71	13	59	65	0	33	0	0.99
11722396--11722506	24	4.8	24	77	14	110	67	0	31	0	0.97
11722438--11722535	48	2.0	48	86	3	135	67	0	32	0	0.91
11722444--11722496	14	3.6	14	76	16	54	71	0	28	0	0.86
11722404--11722565	68	2.4	67	83	9	188	67	0	32	0	0.96
11722421--11722526	24	4.4	24	72	13	92	66	0	33	0	0.92
11722412--11722556	49	2.8	50	79	8	132	66	0	33	0	0.97
11723651--11723680	16	1.9	15	93	6	51	70	0	3	26	1.03
11722930--11723788	286	3.0	285	93	1	1501	50	6	11	31	1.63
11723499--11723917	159	2.6	153	75	16	440	49	7	12	31	1.67
11727080--11727195	40	2.8	40	74	19	112	51	9	5	33	1.56
11727484--11727549	27	2.4	27	92	0	105	15	30	33	21	1.94
11728599--11728631	2	16.5	2	100	0	66	51	0	48	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11732640--11732667	4	7.0	4	100	0	56	25	0	0	75	0.81
11763076--11763149	36	2.1	36	89	5	114	39	14	13	32	1.86
11768485--11768526	3	14.0	3	100	0	84	33	33	0	33	1.58
11775475--11775511	18	2.0	19	89	5	58	37	0	40	21	1.54
11779063--11780004	325	2.9	323	94	1	1613	35	19	5	40	1.74
11784585--11784629	17	2.6	17	79	13	56	20	6	0	73	1.05
11785643--11785686	20	2.4	18	82	14	54	50	2	4	43	1.35
11785602--11785732	68	1.9	68	87	3	192	52	4	2	40	1.34
11786851--11786910	16	3.8	16	84	4	68	46	15	23	15	1.82
11787374--11787399	12	2.2	12	100	0	52	23	19	15	42	1.89
11794774--11794951	51	3.5	49	82	5	205	24	17	26	30	1.97
11794875--11794955	26	3.2	26	65	28	73	22	13	29	34	1.92
11794957--11795055	46	2.2	43	81	12	110	24	19	24	32	1.97
11795179--11795210	16	2.0	16	93	0	55	59	0	15	25	1.36
11797108--11797150	8	5.2	8	78	15	52	13	2	46	37	1.57
11799918--11800088	50	3.4	50	80	4	166	25	12	26	35	1.92
11799963--11800121	25	6.4	25	70	13	103	26	14	27	32	1.95
11799946--11800030	25	3.5	24	72	22	61	22	15	29	32	1.94
11808162--11808487	149	2.2	149	83	6	389	41	4	11	41	1.63
11812133--11812189	28	2.0	28	96	0	105	33	17	8	40	1.81
11820294--11820342	4	12.2	4	77	0	53	20	26	4	48	1.67
11825165--11825193	14	2.0	15	93	6	51	3	13	0	82	0.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11825604--11826250	148	4.3	150	87	7	811	42	5	9	42	1.60
11825646--11826250	300	2.0	299	87	6	877	42	5	9	42	1.60
11826666--11826704	13	2.9	13	85	7	51	20	2	15	61	1.45
11828604--11828781	35	4.9	35	68	16	110	45	9	6	38	1.62
11828619--11828669	16	2.8	19	67	27	56	50	11	0	37	1.39
11828645--11828831	59	3.3	58	71	15	192	42	8	9	39	1.67
11828608--11828932	112	3.0	110	87	9	515	43	8	8	39	1.67
11828867--11829085	58	3.8	58	76	11	263	41	8	9	40	1.68
11828757--11829085	170	2.0	164	90	5	522	42	8	9	39	1.68
11829122--11829181	22	2.7	22	87	7	77	46	1	1	50	1.21
11829107--11829139	16	2.1	16	94	0	57	51	3	0	45	1.16
11831047--11831079	17	2.0	17	88	5	50	48	0	0	51	1.00
11831367--11831409	20	2.2	20	84	12	54	16	23	18	41	1.89
11831472--11831510	19	2.1	19	85	9	53	30	2	5	61	1.31
11832265--11832308	5	8.6	5	82	12	54	43	0	0	56	0.99
11833247--11833371	47	2.7	46	85	6	164	16	27	19	36	1.93
11833249--11833372	22	5.3	24	75	13	109	16	26	19	37	1.93
11835414--11835456	19	2.2	20	87	4	61	53	6	0	39	1.28
11836388--11836428	22	2.0	20	85	9	55	43	0	2	53	1.13
11838368--11838462	50	1.9	50	93	0	163	29	13	32	24	1.93
11845736--11845775	21	1.9	21	84	0	53	42	10	15	32	1.79
11852162--11852212	11	4.8	11	75	18	54	39	31	0	29	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11852151--11852212	20	2.9	22	79	13	67	38	30	0	30	1.58
11856078--11856111	15	2.3	15	100	0	68	26	55	11	5	1.58
11858309--11858376	30	2.3	30	82	5	75	44	5	2	47	1.42
11858537--11858600	26	2.5	26	81	0	83	35	20	6	37	1.78
11858537--11858602	13	5.1	13	75	0	69	36	21	6	36	1.78
11859945--11859993	24	2.0	24	96	0	89	40	10	12	36	1.77
11860621--11860692	36	2.0	36	97	0	135	45	5	6	41	1.54
11865982--11866054	24	3.0	24	97	0	137	52	8	12	27	1.67
11873896--11873940	23	2.0	23	84	16	60	44	2	0	53	1.13
11878683--11878720	5	7.8	5	91	5	60	81	0	15	2	0.80
11891280--11891322	9	4.7	9	82	5	50	81	4	13	0	0.84
11891939--11892039	42	2.4	42	90	3	150	29	13	29	26	1.94
11891952--11892020	21	3.3	21	66	18	54	30	13	33	23	1.92
11893349--11893773	50	8.5	50	68	5	248	28	23	25	22	1.99
11893338--11893804	100	4.7	100	88	0	655	29	22	25	22	1.99
11893338--11893833	50	9.9	50	67	3	170	28	22	25	23	1.99
11898131--11898228	27	3.7	27	79	6	110	28	24	11	35	1.90
11900534--11900597	29	2.2	29	83	8	78	70	0	1	28	0.97
11900644--11900694	26	2.0	26	96	3	95	47	17	0	35	1.48
11900878--11900965	29	3.1	28	75	18	83	32	6	1	59	1.31
11900840--11900961	19	6.5	19	68	18	76	29	8	1	60	1.35
11900876--11901003	57	2.3	55	82	8	150	31	6	1	60	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11900926--11900997	38	1.9	37	82	2	90	34	5	0	59	1.21
11900968--11901044	30	2.6	30	80	12	95	36	1	1	61	1.13
11900907--11901035	9	13.7	9	66	15	64	33	3	0	62	1.19
11904644--11904701	30	2.0	28	83	12	73	43	0	37	18	1.51
11905108--11905172	3	21.7	3	96	0	112	30	0	3	66	1.07
11905306--11905388	16	5.2	16	69	22	68	54	10	0	34	1.36
11905309--11905396	31	2.8	31	93	5	142	54	11	1	32	1.43
11905330--11905384	15	3.6	15	68	22	51	54	12	0	32	1.38
11913146--11913291	9	16.0	9	78	5	150	32	2	16	48	1.58
11913146--11913267	27	4.6	27	89	2	183	31	0	16	51	1.45
11913260--11913500	116	2.1	116	96	1	439	38	6	12	42	1.68
11913356--11913405	21	2.4	21	89	0	73	38	12	16	34	1.85
11913562--11913680	62	1.9	62	81	3	141	47	10	5	36	1.59
11913624--11913661	16	2.4	16	91	4	60	52	5	0	42	1.24
11913658--11913707	13	3.5	13	80	19	64	48	8	8	36	1.62
11913656--11913701	17	3.0	16	81	18	62	52	8	6	32	1.58
11915495--11915547	23	2.3	24	75	12	58	60	18	3	16	1.51
11917688--11918242	114	4.9	114	87	2	785	25	26	23	25	2.00
11918311--11918336	12	2.2	12	100	0	52	46	30	15	7	1.74
11921817--11921857	20	2.0	20	85	4	55	36	39	4	19	1.73
11922206--11922635	133	3.2	130	78	9	429	30	20	15	32	1.94
11932371--11932419	25	2.0	24	84	8	62	42	0	2	55	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11933276--11933316	8	5.2	8	91	5	66	53	0	0	46	1.00
11946942--11947279	51	6.7	51	84	4	391	28	26	15	29	1.96
11946936--11947279	102	3.4	102	89	1	494	29	25	15	29	1.96
11948684--11948716	16	2.1	17	88	11	52	54	0	0	45	0.99
11949111--11949144	17	2.0	17	94	0	59	38	0	0	61	0.96
11950753--11950791	17	2.3	17	86	8	53	20	2	2	74	1.06
11952344--11952429	30	3.0	29	85	12	117	43	6	24	25	1.79
11952343--11952430	25	3.1	30	85	12	123	42	6	26	25	1.80
11956980--11957065	30	3.0	29	85	12	117	43	6	24	25	1.79
11956978--11957066	25	3.1	30	85	12	125	41	6	25	25	1.80

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