genome.fa.s1.2.7.7.80.10.50.1000.157.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  157  of  187  ( 22383 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)
46419530--46419576	9	5.6	9	82	12	55	76	0	0	23	0.78
46419758--46419823	20	3.4	19	72	8	53	18	16	10	54	1.70
46419778--46419834	19	2.9	19	71	5	60	19	21	7	52	1.69
46419757--46419834	39	2.0	39	94	0	138	19	19	8	52	1.71
46420420--46420579	44	3.6	44	90	1	250	29	26	16	26	1.97
46420644--46420810	89	1.9	89	96	0	307	28	19	17	33	1.95
46420531--46420942	221	1.9	221	88	3	632	29	20	18	31	1.97
46420637--46420933	44	6.7	45	66	8	135	27	21	18	32	1.96
46420723--46421386	132	5.0	132	94	0	1085	29	23	18	29	1.97
46421698--46421734	9	4.1	9	92	0	65	45	13	10	29	1.77
46422649--46422674	5	5.2	5	100	0	52	23	19	19	38	1.93
46422764--46422789	5	5.2	5	100	0	52	19	19	19	42	1.90
46431557--46431613	3	19.0	3	100	0	114	66	0	0	33	0.92
46431792--46431857	20	3.4	18	72	8	51	21	16	9	53	1.71
46431787--46431868	39	2.1	39	93	0	137	20	19	8	51	1.73
46440610--46440689	18	4.4	18	69	16	58	35	1	2	61	1.18
46446847--46446872	9	2.9	9	100	0	52	23	19	23	34	1.96
46449458--46449504	20	2.3	21	82	17	64	36	0	8	55	1.31
46449458--46449509	19	2.7	20	85	14	65	32	0	7	59	1.26
46450223--46450251	6	4.8	6	100	0	58	82	0	0	17	0.66
46451401--46451445	19	2.4	19	81	3	56	26	0	2	71	0.98
46452226--46452321	47	2.0	47	97	0	183	34	14	12	38	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46452368--46452433	25	2.7	23	76	17	69	59	1	0	39	1.07
46452439--46452465	2	13.5	2	100	0	54	51	0	0	48	1.00
46452947--46452988	2	21.0	2	100	0	84	0	50	0	50	1.00
46455399--46455438	21	1.9	21	89	0	62	20	10	37	32	1.85
46455405--46455449	21	2.1	21	91	0	72	15	4	46	33	1.66
46456046--46456086	12	3.2	12	89	10	55	70	2	2	24	1.11
46456146--46456175	4	7.5	4	92	0	51	70	3	0	26	1.03
46456256--46456297	19	2.2	19	83	8	50	66	0	11	21	1.23
46456313--46456359	4	11.8	4	81	0	58	68	0	4	27	1.08
46463244--46463398	24	6.2	25	71	10	104	34	20	23	21	1.96
46463328--46463424	49	2.0	50	82	10	119	38	19	23	18	1.93
46465353--46465396	23	1.9	22	82	17	54	36	25	0	38	1.56
46465442--46465534	45	2.1	45	91	0	150	32	21	19	26	1.97
46465539--46465676	51	2.7	50	80	9	163	31	26	18	24	1.97
46465537--46465706	51	3.3	50	76	9	155	30	27	16	25	1.97
46469087--46469174	21	4.1	21	71	7	61	37	23	21	17	1.94
46469142--46469196	23	2.4	23	87	0	74	34	23	20	21	1.97
46470227--46470259	6	5.5	6	86	13	50	0	18	0	81	0.68
46470226--46470259	17	1.9	18	94	5	61	0	20	0	79	0.73
46476530--46476708	25	7.1	26	71	16	81	32	18	26	22	1.97
46476590--46476706	24	4.7	24	71	12	85	31	18	28	21	1.97
46476608--46476704	25	3.8	27	71	15	89	31	16	27	23	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46477077--46477124	12	4.3	12	75	17	50	60	0	2	37	1.09
46477076--46477115	21	1.9	21	94	0	71	62	0	2	35	1.09
46477108--46477207	17	5.7	17	76	11	94	62	0	0	38	0.96
46477153--46477178	11	2.4	11	100	0	52	61	0	0	38	0.96
46477087--46477202	54	2.1	55	93	1	198	63	0	0	35	1.00
46477154--46477208	9	6.1	9	79	12	51	60	0	0	40	0.97
46485615--46485660	20	2.3	21	85	11	69	23	43	0	32	1.54
46487308--46487343	19	1.9	19	88	5	56	77	0	5	16	0.94
46487599--46487640	21	2.0	21	90	0	66	30	14	9	45	1.77
46489904--46489939	2	18.0	2	100	0	72	50	0	0	50	1.00
46497995--46498049	27	2.0	27	100	0	110	40	14	20	25	1.90
46501785--46501874	20	4.4	20	74	4	74	42	17	25	14	1.87
46506638--46506668	15	2.1	15	100	0	62	29	0	0	70	0.87
46506646--46506698	15	3.7	15	71	19	51	26	1	0	71	0.96
46507767--46507800	16	2.0	18	88	11	54	23	0	20	55	1.43
46511968--46512001	18	1.9	18	88	5	52	32	14	11	41	1.82
46512552--46512613	13	4.8	13	80	7	81	37	24	6	32	1.81
46515091--46515212	64	1.9	64	84	3	165	41	13	8	36	1.74
46518286--46518314	13	2.1	14	93	6	51	82	0	3	13	0.79
46526082--46526128	24	2.0	24	83	8	60	38	0	23	38	1.55
46530845--46530894	15	3.1	16	74	20	50	54	0	0	46	1.00
46532635--46532685	27	1.9	26	88	11	77	47	3	5	43	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46536298--46536347	24	2.1	24	85	7	66	30	0	8	62	1.24
46537378--46537406	13	2.1	14	93	6	51	0	17	0	82	0.66
46555093--46555159	30	2.3	30	82	7	84	34	13	8	43	1.75
46555965--46556015	22	2.3	23	82	6	68	17	9	11	60	1.57
46555973--46556021	22	2.2	22	82	7	55	18	10	10	61	1.55
46559380--46559437	7	8.3	7	84	0	80	41	41	1	15	1.57
46559383--46559446	14	4.6	14	86	0	56	42	40	3	14	1.61
46567780--46567823	14	3.1	14	80	6	52	13	11	4	70	1.31
46577794--46578008	113	1.9	113	83	7	285	28	10	20	40	1.85
46581113--46581137	9	2.8	9	100	0	50	68	8	0	24	1.16
46581989--46582036	21	2.4	19	80	16	53	60	2	0	37	1.09
46583762--46583829	34	2.0	34	100	0	136	44	11	8	35	1.72
46585255--46585496	50	4.7	50	75	6	175	24	27	21	26	1.99
46585920--46585994	35	2.1	35	100	0	150	22	14	10	52	1.73
46592827--46592886	5	12.0	5	100	0	120	40	0	0	60	0.97
46593882--46594072	40	4.7	40	84	3	132	33	20	23	21	1.97
46593923--46594088	81	2.0	81	83	2	208	32	20	22	24	1.98
46593923--46594088	40	4.1	40	84	2	188	32	20	22	24	1.98
46594132--46594260	40	3.2	40	80	5	143	33	21	20	24	1.97
46594166--46594260	41	2.3	40	87	5	129	32	21	23	23	1.98
46594190--46594268	41	1.9	41	89	0	122	31	21	22	24	1.98
46593987--46594427	198	2.3	186	81	6	506	30	17	22	29	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46594597--46594638	21	2.0	21	85	0	57	19	0	26	54	1.44
46594614--46594657	14	3.1	14	86	0	61	20	0	25	54	1.45
46594848--46594994	7	20.9	7	67	15	63	23	1	29	46	1.61
46594836--46594998	14	11.6	14	71	3	85	21	1	30	46	1.59
46594836--46594998	21	7.7	21	72	6	105	21	1	30	46	1.59
46599871--46600141	43	6.3	43	81	5	305	25	16	24	32	1.96
46601504--46601541	20	2.0	20	89	5	60	36	0	5	57	1.21
46606498--46606527	12	2.5	12	88	0	51	23	16	26	33	1.96
46610885--46610927	22	2.0	22	81	9	52	51	0	2	46	1.13
46617791--46617830	18	2.2	18	91	8	64	65	12	0	22	1.26
46617914--46617972	30	2.0	30	89	0	91	55	10	5	28	1.54
46629749--46629806	19	3.1	18	83	16	66	58	5	0	36	1.20
46629749--46629859	21	5.5	19	71	23	77	59	4	0	36	1.18
46629743--46629863	64	1.9	62	81	9	147	58	4	0	36	1.20
46636750--46636821	28	2.6	28	84	8	85	44	0	4	51	1.20
46636862--46637154	120	2.4	120	93	3	493	42	2	4	50	1.36
46636987--46637038	15	3.6	15	80	12	56	44	0	1	53	1.11
46637103--46637137	18	2.0	17	88	5	52	45	0	0	54	0.99
46637091--46637407	157	2.0	157	96	0	589	48	4	3	43	1.39
46643378--46643421	23	1.9	22	82	17	54	38	22	0	38	1.55
46643505--46643589	46	1.9	45	83	7	111	38	24	12	23	1.90
46643598--46643777	51	3.5	51	82	5	213	30	26	17	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46643585--46643777	101	1.9	101	84	3	253	30	26	17	25	1.97
46649437--46649674	106	2.2	106	95	0	431	32	15	19	32	1.93
46663763--46664235	88	5.4	88	85	2	621	29	20	27	22	1.98
46663763--46664235	132	3.6	132	84	2	648	29	20	27	22	1.98
46663763--46664311	219	2.5	219	85	3	703	29	20	26	22	1.99
46663763--46664273	44	11.6	44	83	5	561	29	20	27	22	1.98
46666579--46666816	106	2.2	106	95	0	431	31	14	20	32	1.93
46670474--46670534	32	1.9	32	89	0	95	24	14	9	50	1.73
46673634--46673700	21	3.2	21	71	0	62	32	1	1	64	1.12
46675715--46675747	13	2.5	13	95	0	57	42	12	9	36	1.74

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