genome.fa.s4.2.7.7.80.10.50.1000.174.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  174  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)
54500995--54501061	11	6.4	11	75	18	54	61	0	2	35	1.12
54500986--54501077	40	2.3	40	92	3	152	65	0	2	32	1.05
54500986--54501089	40	2.6	39	85	13	147	63	0	1	34	1.06
54501650--54501681	16	2.0	16	93	0	55	71	0	0	28	0.86
54501913--54501976	26	2.3	29	86	7	89	62	1	0	35	1.05
54501915--54501976	28	2.3	25	84	13	79	62	1	0	35	1.05
54509405--54509439	2	17.5	2	100	0	70	51	48	0	0	1.00
54514988--54515039	23	2.3	22	78	15	52	46	11	28	13	1.78
54543980--54544005	4	6.5	4	100	0	52	23	0	0	76	0.78
54545844--54545892	14	3.1	17	77	22	52	42	2	2	53	1.24
54545967--54545997	12	2.6	12	94	0	53	70	3	25	0	1.02
54546688--54546764	40	1.9	40	82	10	95	42	3	20	32	1.70
54547389--54547552	80	2.0	80	95	0	292	25	25	21	28	1.99
54555331--54555359	13	2.2	13	100	0	58	31	6	6	55	1.53
54566533--54566623	43	2.1	43	88	6	132	29	3	1	65	1.15
54566607--54566647	18	2.2	18	95	4	73	19	0	0	80	0.71
54566533--54566643	42	2.6	42	84	5	136	29	2	0	66	1.11
54566565--54566680	59	1.9	61	92	5	200	31	1	0	67	1.01
54567708--54567759	16	3.2	16	100	0	104	25	0	36	38	1.56
54572437--54572507	29	2.4	30	82	13	85	33	5	1	59	1.30
54575813--54575916	51	2.0	51	90	0	163	31	19	23	25	1.98
54582245--54582270	11	2.4	11	100	0	52	76	0	0	23	0.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54582511--54582560	21	2.4	21	96	0	91	34	36	8	22	1.83
54582618--54582678	23	2.7	23	97	0	113	36	37	8	18	1.80
54582948--54582989	16	2.5	17	88	7	68	66	0	0	33	0.92
54584658--54584718	22	2.7	23	80	17	74	59	1	0	39	1.08
54584658--54584715	21	2.6	22	84	13	66	60	1	0	37	1.07
54597795--54597864	29	2.3	29	85	4	86	44	15	7	32	1.74
54598118--54598162	22	2.0	22	86	0	63	55	8	8	26	1.60
54599969--54600020	24	2.2	24	85	0	68	38	3	7	50	1.50
54600608--54600858	42	5.8	42	90	4	342	35	21	20	23	1.96
54601534--54601583	21	2.4	21	79	0	64	2	46	18	34	1.60
54602388--54602419	15	2.2	14	94	5	55	34	12	6	46	1.67
54604998--54605312	114	2.8	114	95	0	558	25	25	16	33	1.96
54605232--54605387	75	2.1	75	93	2	269	22	23	16	37	1.94
54605307--54605749	114	3.9	114	94	0	760	26	26	15	32	1.95
54605118--54605501	189	2.0	189	95	1	698	25	24	15	34	1.95
54605003--54605615	303	2.0	304	93	0	1059	25	25	15	33	1.95
54604998--54605786	417	1.9	418	90	1	1278	26	25	15	33	1.95
54610995--54611030	17	2.2	17	95	5	65	61	5	0	33	1.19
54610990--54611029	17	2.6	15	82	17	55	55	5	0	40	1.22
54617963--54618000	19	1.9	19	85	15	51	36	18	5	39	1.73
54629626--54629681	24	2.3	25	81	9	71	42	35	12	8	1.74
54636837--54636906	21	3.3	20	76	4	68	21	22	15	40	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54636843--54637030	42	4.5	42	90	1	216	16	24	17	41	1.89
54636875--54637033	21	7.6	21	68	8	92	15	25	18	41	1.89
54636850--54637030	84	2.2	84	86	0	254	16	23	18	41	1.89
54644780--54644886	25	4.3	24	75	14	101	35	18	27	18	1.95
54644791--54644888	49	2.0	49	86	4	135	35	18	27	18	1.94
54644792--54644894	25	4.2	25	79	7	120	35	16	29	18	1.93
54644792--54644907	25	4.7	25	77	10	112	36	16	28	18	1.93
54645230--54645273	21	2.1	21	82	0	52	45	20	0	34	1.51
54647939--54647990	23	2.3	23	86	0	77	38	25	9	26	1.86
54668491--54668520	9	3.3	9	90	0	51	46	23	0	30	1.52
54670242--54670274	16	2.1	16	94	0	57	3	15	6	75	1.11
54672259--54672292	6	5.8	6	93	6	61	85	0	0	14	0.60
54672259--54672292	17	1.9	18	94	5	61	85	0	0	14	0.60
54681178--54681215	20	2.0	20	85	15	53	34	0	7	57	1.28
54683297--54683441	46	3.1	46	62	16	118	38	18	4	37	1.72
54683288--54683479	93	2.1	93	98	0	375	42	15	6	35	1.72
54685000--54685067	36	1.9	36	84	3	93	30	25	7	36	1.83
54685880--54685906	2	13.5	2	100	0	54	51	0	0	48	1.00
54688026--54688087	30	2.1	30	90	6	99	29	3	9	58	1.46
54688212--54688244	11	2.9	12	86	13	52	66	0	0	33	0.92
54693992--54694062	20	3.6	19	81	7	81	59	5	0	35	1.21
54693986--54694110	9	12.6	9	68	17	52	60	4	1	33	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54694268--54694312	22	2.0	22	86	0	63	33	4	4	57	1.38
54695591--54695637	13	3.5	13	81	16	51	42	2	2	53	1.25
54703839--54703863	2	12.5	2	100	0	50	52	0	0	48	1.00
54714864--54714894	6	5.3	6	96	3	55	51	0	0	48	1.00
54719373--54719410	19	2.0	19	90	10	60	57	7	0	34	1.28
54719400--54719442	19	2.3	18	84	4	50	58	2	2	37	1.24
54725081--54725179	46	2.2	46	96	0	180	44	3	8	44	1.49
54725140--54725197	19	3.1	19	76	14	66	50	1	8	39	1.43
54725196--54725726	29	17.0	29	73	19	340	29	3	24	42	1.71
54725196--54725726	57	8.5	58	77	18	514	29	3	24	42	1.71
54725319--54725467	38	4.3	38	76	16	137	30	2	22	43	1.67
54725332--54725363	15	2.1	15	94	0	55	37	3	12	46	1.57
54725218--54725728	129	4.0	127	72	22	422	29	3	23	43	1.71
54725433--54725464	15	2.1	15	100	0	64	37	6	12	43	1.68
54725404--54725593	44	4.0	44	73	19	186	31	3	20	44	1.68
54725247--54725726	173	2.9	164	68	23	192	29	3	23	43	1.71
54725533--54725564	15	2.1	15	94	0	55	37	3	12	46	1.57
54725761--54725826	25	2.6	25	100	0	132	39	12	0	48	1.40
54726310--54726344	18	1.9	18	94	0	61	34	8	31	25	1.86
54728211--54728245	10	3.2	11	88	12	54	45	0	37	17	1.48
54730710--54730851	61	2.3	61	97	0	266	28	22	26	23	1.99
54732638--54732672	18	2.0	17	88	5	52	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)
54732756--54732792	16	2.2	17	86	13	51	54	0	2	43	1.14
54732624--54732816	57	3.3	57	69	18	169	48	4	2	45	1.35
54732797--54732942	47	3.2	46	71	20	151	46	3	2	47	1.33
54732732--54733015	91	3.0	96	84	10	356	46	2	3	47	1.33
54732834--54732976	44	3.2	43	71	20	139	48	2	2	46	1.25
54732856--54733000	47	3.2	45	71	20	138	48	3	2	44	1.33
54734868--54734919	21	2.5	21	96	0	95	36	5	30	26	1.80
54741283--54741334	24	2.2	24	89	0	77	55	9	1	32	1.43
54750501--54750547	7	7.1	7	83	9	55	10	51	0	38	1.37
54751352--54751408	28	2.0	29	82	3	71	50	3	17	28	1.62
54751480--54751554	37	2.0	37	97	0	141	28	4	18	49	1.65
54751919--54752035	43	2.7	42	83	11	148	23	18	28	29	1.98
54752872--54753070	46	4.3	46	97	0	371	26	19	16	38	1.92
54753171--54753295	24	5.3	23	69	5	88	27	20	14	38	1.91
54753171--54753295	47	2.6	47	89	2	178	27	20	14	38	1.91
54760462--54760509	19	2.3	21	75	17	55	56	2	0	41	1.11
54760458--54760501	19	2.3	19	84	0	61	59	2	0	38	1.10
54761196--54761339	73	2.0	73	86	2	200	32	15	13	38	1.87
54762042--54762118	31	2.5	31	91	4	120	20	16	9	53	1.70
54772904--54772940	16	2.3	16	86	13	58	56	2	0	40	1.13
54781091--54781137	23	2.0	23	100	0	94	42	8	10	38	1.70
54792133--54792176	3	14.7	3	100	0	88	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54805476--54805521	20	2.3	20	85	3	58	56	6	4	32	1.45
54807365--54807406	2	21.0	2	100	0	84	50	0	0	50	1.00
54808994--54809052	29	2.0	30	83	9	77	47	15	8	28	1.74
54810840--54810883	23	1.9	23	90	0	70	31	2	4	61	1.28
54813394--54813442	16	3.0	16	77	14	55	22	0	4	73	1.00
54824958--54825024	29	2.3	29	81	2	80	28	16	16	38	1.90
54828728--54828779	23	2.3	23	86	0	68	30	3	23	42	1.72
54828692--54828979	28	10.4	28	87	6	392	30	1	22	45	1.61
54828692--54828979	113	2.6	113	89	4	419	30	1	22	45	1.61
54831189--54831222	15	2.3	15	90	5	52	67	5	0	26	1.13

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