genome.fa.s9.2.7.7.80.10.50.1000.151.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  151  of  226  ( 27023 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)
49478853--49478898	23	2.0	22	87	4	65	10	43	23	21	1.84
49479837--49479866	3	10.0	3	92	0	51	30	0	3	66	1.07
49481484--49481547	22	2.8	24	75	17	73	54	1	4	39	1.31
49483458--49483520	30	2.1	30	87	0	90	38	17	25	19	1.93
49483516--49483546	16	1.9	16	93	0	53	25	19	32	22	1.97
49487727--49487777	21	2.4	21	100	0	102	41	3	13	41	1.63
49488670--49488706	19	2.0	19	85	15	51	32	16	5	45	1.70
49490586--49490646	29	2.1	28	84	3	77	21	0	24	54	1.45
49494836--49494872	19	2.0	19	85	15	51	32	16	5	45	1.70
49496752--49496812	29	2.1	28	84	3	77	21	0	24	54	1.45
49500083--49500127	21	2.1	21	91	4	72	37	4	15	42	1.67
49501026--49501062	19	2.0	19	85	15	51	32	16	5	45	1.70
49518705--49518741	19	2.0	19	85	15	51	32	16	5	45	1.70
49525902--49525965	22	2.8	23	73	17	62	54	3	4	37	1.37
49532032--49532079	22	2.2	22	100	0	96	33	4	8	54	1.50
49539360--49539557	19	10.4	18	64	21	66	62	5	1	30	1.27
49539493--49539556	30	2.1	30	91	0	101	65	9	0	25	1.22
49539359--49539555	9	20.8	9	69	20	84	62	5	1	30	1.27
49542178--49542235	28	2.1	28	83	6	73	55	5	8	31	1.52
49543126--49543153	7	4.0	7	100	0	56	14	0	0	85	0.59
49543202--49543323	18	6.8	17	75	18	79	32	2	4	59	1.32
49543258--49543315	25	2.2	25	85	11	73	34	0	3	62	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49543273--49543328	25	2.3	23	77	17	58	35	0	3	60	1.14
49544387--49544518	40	3.3	39	74	6	122	35	19	23	21	1.96
49544404--49544538	40	3.4	41	74	6	127	39	20	20	19	1.93
49544580--49544733	41	3.8	41	82	1	184	22	20	24	32	1.98
49544575--49544733	82	1.9	82	85	2	221	22	22	24	31	1.98
49545020--49545053	15	2.2	16	94	5	61	20	0	32	47	1.51
49545140--49545221	7	11.9	7	71	14	55	19	2	43	34	1.64
49545893--49545931	19	2.1	18	85	4	51	76	2	5	15	1.06
49549800--49549847	5	9.4	5	80	13	53	20	22	14	41	1.89
49550545--49550664	9	14.2	9	75	13	112	46	18	2	32	1.62
49550545--49550664	25	4.8	25	82	4	152	46	18	2	32	1.62
49550518--49550664	50	2.9	50	81	6	163	48	17	2	30	1.61
49550549--49550664	16	7.0	16	74	13	78	46	18	2	32	1.62
49550549--49550664	34	3.5	33	74	15	89	46	18	2	32	1.62
49554409--49554436	14	2.0	14	100	0	56	42	28	21	7	1.79
49556232--49556376	65	2.2	66	85	6	188	40	17	28	13	1.87
49556384--49556445	21	3.0	21	78	0	70	37	16	38	8	1.78
49556394--49556458	21	3.1	21	81	0	85	35	15	43	6	1.72
49556803--49557064	43	6.0	43	78	3	292	22	17	30	29	1.96
49556762--49557064	87	3.5	86	85	3	331	22	16	30	30	1.96
49556803--49557222	43	9.7	43	74	5	276	23	20	28	26	1.99
49557308--49557350	22	2.0	22	95	0	77	41	27	20	9	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49561651--49561682	16	1.9	17	93	6	57	53	18	9	18	1.71
49561915--49561956	21	2.0	21	86	9	59	47	4	45	2	1.36
49567119--49567210	41	2.2	41	83	7	107	26	29	20	23	1.99
49567889--49567960	37	1.9	38	86	8	103	50	6	26	16	1.71
49579676--49579920	41	6.0	41	75	1	186	24	33	19	22	1.97
49579675--49579915	82	2.9	82	75	1	250	24	33	19	22	1.97
49579677--49579919	123	2.0	123	79	1	263	24	33	18	22	1.97
49579678--49579942	82	3.2	81	75	2	242	25	32	19	23	1.98
49582348--49582479	61	2.2	58	85	6	167	50	3	2	43	1.29
49582438--49582476	17	2.3	18	86	13	64	51	0	0	48	1.00
49599610--49599641	15	2.1	15	94	0	55	6	9	12	71	1.29
49599592--49599646	20	2.8	20	88	0	74	7	12	12	67	1.42
49599827--49599882	15	3.9	14	75	17	53	33	37	10	17	1.85
49600959--49601035	3	25.7	3	97	0	145	32	1	0	66	1.00
49601188--49601217	15	1.9	15	93	6	51	36	0	0	63	0.95
49601426--49601455	2	15.0	2	100	0	60	50	0	0	50	1.00
49601569--49601599	2	15.5	2	100	0	62	51	0	0	48	1.00
49603634--49603661	8	3.5	8	100	0	56	25	0	0	75	0.81
49604000--49604038	21	1.9	20	94	5	69	38	0	0	61	0.96
49606896--49606941	20	2.3	20	88	3	67	34	13	8	43	1.74
49606953--49606995	20	2.2	20	91	4	70	44	4	6	44	1.52
49607059--49607106	20	2.4	20	80	13	55	35	6	8	50	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49607076--49607148	20	3.6	21	78	10	64	36	10	8	43	1.70
49607296--49607407	20	5.7	20	70	15	63	34	8	14	41	1.77
49607362--49607404	19	2.2	20	83	4	52	41	4	16	37	1.69
49607435--49607577	20	7.1	20	72	7	92	38	11	9	40	1.74
49607435--49607578	40	3.6	39	82	5	135	38	11	9	40	1.74
49607642--49607692	20	2.5	20	80	0	57	33	11	15	39	1.84
49610275--49610338	32	2.0	32	100	0	128	34	12	15	37	1.85
49616261--49616318	22	2.6	23	78	10	66	37	5	3	53	1.40
49618664--49618703	18	2.3	18	86	4	55	60	2	27	10	1.42
49621062--49621103	20	2.0	21	86	4	59	59	0	4	35	1.19
49621095--49621178	27	3.0	27	89	8	116	46	0	0	53	1.00
49621111--49621198	39	2.2	39	84	9	108	44	1	0	54	1.07
49621105--49621192	27	3.1	28	81	12	85	44	1	0	54	1.07
49621239--49621280	19	2.2	19	83	8	50	66	2	0	30	1.04
49621257--49621390	9	16.3	9	65	22	55	47	2	1	48	1.23
49621248--49621285	19	2.0	19	89	0	58	63	0	2	34	1.09
49621293--49621397	17	5.9	17	78	18	99	44	0	0	53	1.13
49621300--49621391	9	10.3	9	71	19	61	43	1	1	54	1.14
49621449--49621485	17	2.2	17	90	0	56	54	0	5	40	1.24
49621421--49621494	36	2.0	39	86	7	109	52	0	6	40	1.28
49633015--49633190	88	2.0	88	92	0	289	25	23	27	23	2.00
49632906--49633302	202	2.0	203	90	0	625	23	23	28	24	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49633103--49633393	116	2.5	114	88	1	384	23	23	27	25	2.00
49634558--49634955	147	2.7	146	76	5	351	27	14	22	35	1.93
49634608--49634955	146	2.4	145	77	6	344	27	14	21	36	1.92
49636943--49637107	13	12.5	13	72	10	120	40	10	3	46	1.56
49636967--49637116	53	2.8	53	95	2	266	40	10	3	45	1.55
49637483--49637840	9	41.3	9	73	14	290	45	20	1	32	1.59
49637463--49637629	43	3.9	43	81	10	207	48	20	0	30	1.54
49637483--49637848	88	4.2	87	83	9	392	45	20	1	32	1.58
49637434--49637836	25	15.8	25	71	17	109	46	20	1	31	1.61
49640159--49640206	21	2.3	21	85	7	62	37	18	41	2	1.63
49640191--49640218	12	2.3	12	100	0	56	39	17	42	0	1.50
49640412--49640506	31	3.1	31	72	3	77	42	12	8	36	1.73
49641156--49641211	21	2.7	21	82	0	67	28	7	33	30	1.84
49649813--49650058	57	4.4	57	83	4	306	29	25	31	13	1.94
49649783--49650054	27	10.0	27	78	11	243	29	25	30	14	1.95
49649837--49650054	84	2.6	83	82	8	296	29	25	31	14	1.94
49650770--49650810	20	2.1	19	86	9	55	29	2	7	60	1.36
49650768--49650836	21	3.5	19	80	9	68	27	2	5	63	1.31
49651538--49651585	22	2.2	22	96	0	87	29	29	0	41	1.56
49655102--49655453	126	2.8	125	90	1	537	33	21	15	29	1.94
49656383--49656413	16	1.9	16	93	0	53	16	3	6	74	1.16
49656628--49656653	9	2.9	9	100	0	52	57	0	0	42	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49657921--49657977	24	2.4	24	77	8	62	26	10	7	56	1.59
49659208--49659323	23	5.0	23	89	0	178	30	24	21	24	1.99
49659209--49659321	46	2.5	46	97	0	208	30	24	22	23	1.99
49659550--49659587	18	2.2	17	86	13	51	47	18	0	34	1.49
49660788--49660847	22	2.6	23	76	12	61	40	5	0	55	1.22
49664320--49664358	15	2.6	16	84	12	55	35	0	0	64	0.94
49664513--49664551	16	2.4	16	86	0	60	61	2	0	35	1.10
49665002--49665044	20	2.1	21	91	4	70	48	9	6	34	1.62
49667751--49667784	16	2.1	16	88	0	50	32	0	2	64	1.08
49673535--49673581	24	2.0	24	100	0	94	38	8	0	53	1.32

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   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226