genome.fa.s8.2.7.7.80.10.50.1000.69.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  69  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)
20065977--20066013	18	2.1	18	94	0	65	48	18	10	21	1.78
20066268--20066326	17	3.4	17	71	17	57	35	3	3	57	1.32
20066351--20066399	19	2.5	19	76	3	53	44	2	12	40	1.53
20067817--20067877	3	20.3	3	100	0	122	67	0	32	0	0.91
20068902--20068939	18	2.1	18	90	0	58	39	13	26	21	1.89
20072897--20072937	17	2.3	18	87	4	57	51	14	14	19	1.77
20085016--20085317	102	3.0	102	93	0	487	33	27	18	20	1.96
20085161--20085315	33	4.6	33	71	21	133	38	26	17	18	1.92
20086890--20086932	17	2.4	18	84	7	61	58	9	11	20	1.61
20089539--20089587	21	2.4	20	83	6	62	22	26	8	42	1.81
20089760--20089817	21	2.9	21	89	5	84	44	18	24	12	1.84
20089967--20090045	39	2.0	39	92	0	131	50	20	1	27	1.56
20091690--20091766	30	2.6	30	95	0	136	35	14	20	29	1.92
20094855--20094888	14	2.4	15	85	14	54	26	5	23	44	1.76
20095268--20095328	3	20.3	3	93	0	104	68	29	0	1	0.99
20097381--20097447	34	1.9	35	84	3	91	64	7	1	26	1.29
20099859--20099940	13	5.6	14	72	21	69	20	2	12	64	1.38
20099862--20099943	30	2.7	30	92	0	137	21	2	13	62	1.43
20101925--20102047	45	2.7	45	84	0	165	26	13	26	33	1.94
20105541--20105578	3	12.7	3	100	0	76	68	0	0	31	0.90
20106067--20106106	18	2.2	18	86	8	55	15	30	0	55	1.41
20106876--20106935	2	29.0	2	90	6	93	48	5	0	46	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20108131--20108155	13	1.9	13	100	0	50	16	0	0	84	0.63
20108553--20108601	20	2.5	19	77	6	53	16	12	6	65	1.45
20109367--20109401	17	2.1	17	100	0	70	22	17	5	54	1.64
20110181--20110205	13	1.9	13	100	0	50	40	28	8	24	1.83
20113116--20113155	21	1.9	21	84	0	53	35	10	22	32	1.87
20115297--20115373	14	5.0	15	71	20	52	42	14	9	33	1.77
20115313--20115352	20	2.0	20	90	0	62	50	12	10	27	1.72
20115301--20115367	34	1.9	35	90	3	109	46	13	8	31	1.74
20117341--20117451	49	2.2	50	83	13	131	17	16	37	28	1.91
20119182--20119435	40	6.4	40	84	6	295	32	16	20	30	1.94
20119182--20119436	119	2.1	119	89	2	379	32	16	20	30	1.94
20120129--20120319	47	4.0	47	89	2	285	43	16	12	27	1.84
20120188--20120311	25	5.2	25	77	18	156	44	16	12	26	1.83
20120180--20120303	22	5.4	22	77	17	135	44	16	13	25	1.84
20121254--20121352	28	3.6	27	78	9	110	29	28	11	31	1.91
20126345--20126436	32	2.8	35	74	14	88	61	2	1	34	1.15
20126345--20126432	18	5.3	16	74	17	65	62	1	1	35	1.10
20126651--20126698	3	16.0	3	100	0	96	66	0	0	33	0.92
20127237--20127294	25	2.4	25	81	13	70	48	1	1	48	1.22
20141283--20141336	23	2.3	23	87	0	81	38	18	20	22	1.93
20146084--20146108	5	5.0	5	100	0	50	40	20	0	40	1.52
20156547--20156593	23	2.0	23	95	0	85	34	21	0	44	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20156810--20156840	9	3.4	9	90	0	53	25	12	22	38	1.90
20156893--20156929	9	4.1	9	92	0	65	45	13	10	29	1.77
20157682--20157708	5	5.4	5	100	0	54	18	18	18	44	1.87
20157822--20157855	18	1.9	17	88	5	50	47	2	0	50	1.16
20160044--20160098	25	2.2	25	86	0	74	30	23	16	29	1.96
20161788--20161826	20	2.0	20	94	0	69	10	20	23	46	1.81
20161795--20161881	20	4.3	20	78	5	77	12	24	20	42	1.87
20161795--20161881	40	2.2	40	80	0	102	12	24	20	42	1.87
20162036--20162090	24	2.3	24	93	0	92	41	9	14	34	1.77
20163891--20163925	17	2.1	17	100	0	70	45	22	0	31	1.53
20165698--20165742	21	2.1	21	87	4	63	13	15	4	66	1.39
20166223--20166292	19	3.7	18	79	5	77	58	0	5	35	1.22
20168969--20168999	9	3.4	9	90	0	53	25	12	22	38	1.90
20169053--20169089	9	4.1	9	92	0	65	45	13	10	29	1.77
20169415--20169451	20	1.9	19	89	10	58	24	32	0	43	1.55
20169424--20169499	20	4.0	20	73	16	56	25	28	0	46	1.53
20169577--20169657	17	4.6	17	72	20	69	38	3	2	55	1.31
20170104--20170129	5	5.2	5	100	0	52	19	19	19	42	1.90
20172946--20173002	19	2.8	19	81	10	51	19	5	1	73	1.11
20172968--20173017	9	5.1	9	79	15	55	12	6	2	80	0.98
20172969--20173023	21	2.8	19	83	5	65	16	5	1	76	1.06
20176056--20176083	14	2.0	14	100	0	56	50	0	14	35	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20185333--20185368	15	2.5	14	86	8	54	55	11	2	30	1.49
20196507--20196541	6	5.8	6	100	0	70	17	34	31	17	1.93
20205855--20205879	13	1.9	13	100	0	50	12	40	8	40	1.72
20210103--20210186	33	2.6	32	78	12	91	46	16	9	27	1.78
20210180--20210219	20	2.0	20	100	0	80	50	15	5	30	1.65
20210480--20210517	14	2.7	14	91	0	58	36	2	18	42	1.64
20210501--20210540	20	2.0	20	100	0	80	30	10	15	45	1.78
20210486--20210550	34	1.9	33	87	9	96	33	6	15	44	1.71
20210638--20210676	20	2.0	20	94	0	69	48	2	0	48	1.15
20211928--20211988	32	1.9	32	96	0	113	50	18	3	27	1.62
20211928--20212001	32	2.5	30	87	10	100	51	18	2	27	1.60
20211929--20212015	27	3.0	27	83	11	77	51	18	2	27	1.58
20215819--20216037	51	4.3	51	94	1	368	33	15	22	27	1.95
20218127--20218244	59	2.0	59	90	3	184	40	7	15	36	1.76
20220231--20220267	17	2.2	17	95	0	65	51	10	0	37	1.37
20220982--20221045	30	2.1	30	100	0	128	39	12	17	31	1.87
20230237--20230306	33	2.1	33	100	0	140	34	14	8	42	1.76
20233640--20233724	20	4.2	20	73	11	66	35	21	34	9	1.85
20233640--20233724	40	2.1	40	80	8	93	35	21	34	9	1.85
20233640--20233790	61	2.5	60	82	1	185	36	19	31	11	1.89
20240716--20240832	59	1.9	59	84	5	153	44	0	4	50	1.27
20240767--20240804	12	3.2	12	82	17	53	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20242692--20242734	21	2.0	22	90	4	70	67	6	0	25	1.15
20244324--20244358	18	2.0	17	88	5	52	25	0	17	57	1.40
20246791--20246826	16	2.2	16	100	0	72	25	0	36	38	1.56
20246949--20247265	157	2.0	157	96	0	580	44	3	5	47	1.42
20247199--20247240	15	2.7	16	82	14	52	52	2	0	45	1.13
20247208--20247249	15	2.9	15	82	10	52	52	0	0	47	1.00
20247197--20247493	120	2.5	121	93	4	505	49	4	2	43	1.37
20247318--20247369	15	3.6	15	80	12	56	53	1	0	44	1.11
20247534--20247581	26	1.9	25	84	16	64	52	2	0	45	1.12
20247509--20247717	92	2.3	91	85	6	262	46	3	3	45	1.39
20252847--20252873	7	3.9	7	100	0	54	44	0	44	11	1.39
20256141--20256193	22	2.4	22	78	9	63	16	24	20	37	1.93
20267301--20267345	17	2.6	18	80	16	51	42	0	6	51	1.28
20277716--20277813	23	4.3	23	93	2	171	31	27	20	20	1.97
20277716--20277813	45	2.2	46	92	3	171	31	27	20	20	1.97
20285323--20285369	20	2.3	20	96	0	85	61	14	12	10	1.56
20287957--20288157	58	3.4	59	92	2	341	50	14	23	11	1.75
20289114--20289166	26	2.0	26	92	0	88	18	20	33	26	1.96
20289140--20289420	43	6.6	41	77	12	264	22	15	27	34	1.94
20289140--20289420	85	3.3	85	91	0	436	22	15	27	34	1.94
20291488--20291532	6	6.8	6	81	18	54	20	2	0	77	0.87
20291498--20291549	22	2.4	21	78	9	59	23	3	1	71	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20292385--20292409	13	1.9	13	100	0	50	0	16	0	84	0.63
20311084--20311116	13	2.4	14	85	10	50	75	0	3	21	0.93
20311078--20311130	22	2.6	21	82	11	65	73	0	5	20	1.03
20320882--20321285	114	3.5	114	81	5	492	34	16	21	28	1.95
20320811--20321300	228	2.1	227	85	3	653	33	16	21	29	1.95
20322165--20322191	12	2.2	12	100	0	54	59	0	0	40	0.98
20323543--20323571	14	2.0	15	93	6	51	6	6	17	68	1.34
20323499--20323577	39	2.0	38	85	9	106	15	11	21	51	1.74
20324229--20324316	44	2.0	44	97	0	167	43	10	13	32	1.78
20324832--20324916	25	3.3	24	69	15	71	40	15	3	41	1.64

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