genome.fa.s6.2.7.7.80.10.50.1000.163.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  163  of  168  ( 20060 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)
48986749--48986774	11	2.4	11	100	0	52	53	0	7	38	1.30
49009342--49009387	23	2.0	23	95	0	83	36	30	23	8	1.85
49011379--49011617	50	4.6	50	83	5	255	21	28	22	27	1.99
49011378--49011624	100	2.4	105	83	6	306	21	28	22	27	1.99
49011965--49012022	30	1.9	31	82	6	75	29	22	5	43	1.75
49014483--49014516	6	5.7	6	96	0	50	70	0	5	23	1.09
49014520--49014549	2	15.0	2	100	0	60	50	0	0	50	1.00
49021896--49021950	15	3.4	15	79	18	65	41	7	20	30	1.79
49033307--49033338	2	16.0	2	93	0	55	46	0	0	53	1.00
49034038--49034073	2	18.0	2	100	0	72	50	0	0	50	1.00
49034490--49034542	23	2.2	24	86	3	81	32	0	3	64	1.12
49045999--49046052	24	2.2	25	78	15	60	33	1	0	64	1.04
49050319--49050353	6	5.8	6	100	0	70	85	0	14	0	0.59
49055470--49055538	19	3.6	19	81	16	81	39	0	5	55	1.24
49055430--49055538	19	5.5	19	73	17	71	39	0	5	55	1.23
49062898--49063062	21	7.9	21	75	6	120	17	20	18	44	1.87
49062933--49063068	42	3.2	42	85	3	175	16	19	19	44	1.86
49062896--49063032	63	2.2	61	81	6	166	16	18	18	45	1.86
49082189--49082293	52	2.0	52	100	0	210	37	13	13	36	1.84
49087457--49087483	2	13.5	2	100	0	54	51	0	0	48	1.00
49088046--49088087	18	2.3	18	88	8	59	23	11	2	61	1.42
49090119--49090145	2	13.5	2	100	0	54	0	0	48	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49090976--49091006	14	2.2	14	94	0	53	48	9	0	41	1.36
49094391--49094436	25	1.9	24	86	8	67	60	6	0	32	1.22
49097974--49098065	44	2.0	47	87	6	136	39	19	25	16	1.92
49097974--49098073	22	4.3	23	81	12	107	40	19	24	17	1.91
49099083--49099125	23	2.0	22	86	9	61	44	6	4	44	1.52
49109286--49109329	20	2.1	21	87	8	63	47	0	0	52	1.00
49114107--49114136	3	10.0	3	100	0	60	33	0	0	66	0.92
49122602--49122648	18	2.4	21	79	10	55	4	23	0	72	1.02
49123746--49123777	15	2.1	16	94	5	57	65	9	0	25	1.22
49126270--49126314	16	2.9	16	81	15	58	55	0	0	44	0.99
49128431--49128484	14	3.8	13	79	13	54	51	1	1	44	1.22
49128424--49128482	30	2.0	30	90	6	93	52	1	1	44	1.21
49131230--49131255	3	8.7	3	100	0	52	0	30	0	69	0.89
49133051--49133083	16	1.9	18	88	11	52	45	6	3	45	1.43
49138843--49138885	17	2.5	18	81	11	54	46	2	0	51	1.13
49139844--49139916	35	2.0	36	82	12	87	61	5	5	27	1.40
49140711--49140740	2	15.5	2	93	6	53	50	0	0	50	1.00
49152777--49152831	2	27.5	2	92	7	94	49	0	1	49	1.11
49156341--49156371	2	16.0	2	93	6	55	51	0	0	48	1.00
49158176--49158207	4	7.8	4	93	6	55	75	0	25	0	0.81
49167385--49167438	27	1.9	28	85	7	74	33	1	1	62	1.16
49167496--49167557	27	2.3	27	82	0	79	22	27	30	19	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49168572--49168653	33	2.5	33	80	9	87	24	10	45	19	1.82
49171530--49171648	60	2.0	60	94	0	211	53	12	0	33	1.39
49171803--49171848	20	2.3	20	81	3	58	0	30	0	69	0.89
49172000--49172072	27	2.7	27	89	0	110	15	31	27	26	1.95
49172160--49172205	22	2.1	22	84	11	60	56	2	0	41	1.11
49172135--49172204	25	2.8	25	72	20	67	58	1	1	38	1.16
49172930--49172976	19	2.6	17	83	12	51	70	14	2	12	1.26
49175697--49175740	23	1.9	23	85	0	61	70	6	2	20	1.21
49182706--49182882	69	2.6	69	92	0	300	37	20	12	29	1.90
49183839--49183879	3	13.7	3	100	0	82	68	0	0	31	0.90
49185299--49185530	84	2.8	84	93	0	392	29	12	15	42	1.84
49187719--49187768	26	1.9	26	87	0	73	16	12	8	64	1.49
49192024--49192078	25	2.2	24	87	3	83	14	25	21	38	1.92
49195638--49195704	22	3.0	22	82	0	80	41	17	23	16	1.89
49197109--49197147	14	2.8	14	84	0	51	35	12	23	28	1.91
49197696--49197720	9	2.8	9	100	0	50	88	0	0	12	0.53
49198093--49198128	18	1.9	18	88	5	54	58	2	0	38	1.13
49205842--49205909	30	2.3	31	87	7	104	29	1	0	69	0.98
49210507--49210531	6	4.2	6	100	0	50	84	0	0	16	0.63
49212572--49212650	39	2.0	39	95	0	140	30	11	26	31	1.91
49215839--49216019	43	4.3	43	83	6	228	29	29	17	23	1.97
49215839--49216034	84	2.3	82	80	13	245	31	28	15	23	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49221899--49221938	19	2.0	20	85	4	55	32	0	0	67	0.91
49221952--49221982	2	15.5	2	100	0	62	51	0	0	48	1.00
49230737--49230774	15	2.6	15	83	4	51	44	15	7	31	1.75
49230913--49230950	16	2.3	17	86	4	51	55	31	5	7	1.51
49241419--49241488	28	2.6	26	76	12	70	37	1	2	58	1.22
49241452--49241488	16	2.3	16	90	0	56	40	2	0	56	1.13
49241419--49241498	27	2.9	27	75	19	67	37	1	2	58	1.19
49244410--49244453	22	2.0	22	90	0	70	15	27	4	52	1.63
49248148--49248251	49	2.1	49	90	0	163	30	8	11	49	1.69
49249895--49250085	61	3.2	59	70	14	174	42	1	5	50	1.33
49249946--49249980	18	2.0	17	94	5	61	40	0	2	57	1.14
49249861--49250120	120	2.2	120	92	0	421	42	0	5	51	1.29
49250225--49250320	45	2.2	44	85	9	124	35	28	5	31	1.79
49250306--49250338	16	2.1	16	94	0	57	24	30	6	39	1.79
49264415--49264445	2	15.5	2	93	0	53	48	3	0	48	1.17
49267195--49267259	26	2.4	28	84	5	80	47	29	3	20	1.65
49273309--49273359	21	2.4	21	83	9	59	43	5	0	50	1.26
49275817--49275934	30	3.9	30	96	0	209	19	33	26	21	1.97
49276867--49276928	24	2.5	25	74	7	65	37	24	20	17	1.94
49277503--49277553	21	2.4	21	83	6	59	39	17	0	43	1.49
49282399--49282423	2	12.5	2	100	0	50	48	0	0	52	1.00
49293057--49293099	23	1.9	23	95	4	79	53	6	9	30	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49295906--49295960	24	2.2	24	75	15	58	40	7	1	50	1.40
49297298--49297324	7	3.9	7	100	0	54	59	0	0	40	0.98
49306955--49307018	19	3.2	19	78	17	67	53	1	0	45	1.10
49307891--49308030	61	2.3	60	81	10	155	50	3	0	45	1.24
49312026--49312190	82	2.0	82	100	0	330	47	15	10	26	1.79
49313824--49313871	4	12.0	4	91	8	80	25	0	25	50	1.50
49315298--49315351	26	2.0	28	85	7	76	42	5	3	48	1.44
49315480--49315528	14	3.5	14	75	10	55	63	0	2	34	1.06
49323327--49323360	3	11.3	3	93	0	59	70	0	29	0	0.87
49324294--49324332	3	13.0	3	83	0	51	28	35	5	30	1.79
49339196--49339248	4	13.2	4	100	0	106	24	0	24	50	1.49
49342409--49342477	29	2.3	31	85	7	88	31	2	10	55	1.48
49345049--49345093	24	1.9	24	82	13	58	35	8	4	51	1.54
49346064--49346101	3	12.7	3	83	10	51	34	0	2	63	1.09
49346126--49346161	9	4.1	9	85	7	56	77	8	13	0	0.98
49347828--49347983	57	2.7	57	94	1	267	30	23	12	33	1.92
49349665--49349703	16	2.4	16	87	8	53	48	2	25	23	1.63
49349976--49350085	23	5.1	21	85	7	141	20	21	21	36	1.95
49364254--49364281	6	4.7	6	100	0	56	46	0	0	53	1.00
49364780--49364823	22	2.0	23	90	4	72	34	0	15	50	1.45
49367730--49367793	25	2.4	27	74	10	69	50	1	3	45	1.27
49372539--49372901	91	4.0	91	92	2	561	46	2	4	46	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49372602--49372851	44	5.6	44	67	13	141	46	3	4	46	1.39
49372843--49372877	18	1.9	18	100	0	70	37	0	0	62	0.95
49372812--49373156	120	2.9	121	91	2	543	44	2	4	48	1.36
49373062--49373091	15	1.9	16	93	6	53	40	3	6	50	1.45
49373084--49373119	18	2.1	17	90	10	56	36	2	0	61	1.11
49373048--49373243	106	1.9	105	92	1	329	43	2	4	49	1.34
49373209--49373287	27	3.4	22	68	21	63	45	1	2	50	1.23
49373465--49373509	16	2.8	16	100	0	90	24	26	4	44	1.72
49381517--49381546	6	5.0	6	91	0	51	50	0	3	46	1.18
49386530--49387023	51	9.7	51	79	3	466	30	14	25	29	1.95

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