genome.fa.s4.2.7.7.80.10.50.1000.149.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  149  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)
47271634--47271685	11	4.4	12	75	20	56	46	0	1	51	1.12
47271791--47271846	3	18.7	3	100	0	112	33	0	0	66	0.92
47272099--47272154	3	18.7	3	100	0	112	33	0	0	66	0.92
47272179--47272217	17	2.2	18	90	4	62	76	5	12	5	1.11
47278538--47278595	30	1.9	30	89	0	89	41	3	24	31	1.71
47278808--47278838	13	2.4	13	94	0	53	32	0	12	54	1.38
47278933--47279175	50	4.8	50	93	0	405	25	23	31	20	1.98
47281406--47281483	24	3.2	23	77	16	68	15	24	20	39	1.91
47285038--47285373	131	2.6	131	87	1	496	23	23	22	30	1.99
47285334--47285586	43	5.9	43	88	0	364	23	22	20	33	1.97
47306841--47306877	17	2.2	17	95	0	65	51	5	13	29	1.63
47313943--47313993	27	1.9	27	88	11	79	27	3	15	52	1.60
47317093--47317145	2	26.5	2	100	0	106	49	0	50	0	1.00
47322511--47322570	30	2.0	30	86	3	84	40	0	40	20	1.52
47322784--47322820	9	4.1	9	89	0	56	29	8	13	48	1.71
47323726--47323764	16	2.5	16	83	4	53	33	7	12	46	1.71
47324449--47324497	23	2.1	23	84	0	62	28	18	24	28	1.98
47326648--47326695	20	2.4	20	89	6	71	27	14	16	41	1.87
47326648--47326701	20	2.8	18	84	13	56	24	16	14	44	1.85
47333423--47333483	25	2.4	25	78	10	61	57	1	1	39	1.18
47336025--47336064	18	2.2	18	86	0	53	10	17	10	62	1.53
47343262--47343328	24	2.7	24	81	11	64	62	0	2	34	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47343335--47343466	9	14.4	9	69	13	65	64	0	5	29	1.21
47343335--47343406	17	4.1	17	73	8	63	63	0	6	29	1.20
47343341--47343499	9	16.8	10	66	23	53	64	1	4	29	1.20
47343394--47343438	19	2.4	19	85	10	58	60	0	2	37	1.09
47343392--47343440	16	2.8	17	81	9	55	61	0	2	36	1.08
47343397--47343446	19	2.8	17	80	16	57	60	0	2	38	1.09
47343452--47343499	20	2.3	21	79	13	64	72	2	2	22	1.05
47344966--47345013	25	1.9	25	82	0	60	54	6	0	39	1.26
47349096--47349173	41	1.9	41	89	0	120	17	28	17	35	1.94
47349095--47349193	41	2.4	41	82	0	117	23	27	16	33	1.95
47349095--47349205	41	2.7	39	77	9	114	20	27	16	35	1.94
47350430--47350472	10	4.2	10	82	11	52	30	2	2	65	1.18
47350754--47350784	12	2.6	12	94	0	53	32	9	0	58	1.31
47368779--47368822	18	2.4	18	82	17	56	36	2	2	59	1.23
47373090--47373267	90	2.0	91	83	7	229	42	12	11	32	1.80
47377498--47377526	2	14.5	2	100	0	58	48	0	0	51	1.00
47378340--47378436	41	2.3	41	82	1	113	37	5	5	52	1.46
47378340--47378424	42	2.0	42	84	2	109	37	5	4	51	1.47
47380240--47380275	18	2.0	18	88	0	54	25	16	5	52	1.65
47387264--47387306	6	7.2	6	100	0	86	34	48	0	16	1.46
47387763--47387826	23	2.9	22	80	13	60	60	0	4	34	1.17
47394722--47394777	22	2.7	20	81	15	60	69	8	19	1	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47398189--47398243	28	2.0	26	86	6	74	61	9	10	18	1.54
47399058--47399112	26	2.1	27	83	10	69	65	1	5	27	1.25
47399148--47399178	14	2.3	14	94	5	55	77	0	22	0	0.77
47406647--47406681	13	2.6	14	91	8	56	77	0	22	0	0.78
47412780--47412855	23	3.3	23	96	0	143	31	26	21	21	1.98
47412942--47412970	8	3.6	8	100	0	58	34	27	13	24	1.93
47413075--47413113	18	2.2	17	86	13	53	46	20	0	33	1.51
47415781--47415827	23	2.0	23	84	8	60	38	8	0	53	1.32
47424707--47424760	20	2.6	21	82	5	65	25	5	33	35	1.80
47427189--47427238	20	2.5	20	90	0	82	48	16	6	30	1.70
47427417--47427494	29	2.7	29	100	0	156	43	24	11	20	1.85
47428138--47428181	23	1.9	23	90	0	70	31	4	4	59	1.38
47428578--47428619	22	1.9	22	85	0	57	47	2	4	45	1.36
47429931--47430003	32	2.2	33	83	7	87	52	0	6	41	1.28
47429916--47429999	37	2.3	36	76	13	93	50	0	5	44	1.26
47429925--47430004	33	2.4	32	81	8	90	50	0	6	43	1.27
47433362--47433439	41	1.9	41	97	0	147	32	25	20	21	1.98
47435639--47435690	21	2.5	21	80	0	59	38	15	40	5	1.71
47435574--47435864	87	3.3	87	88	0	420	42	16	27	13	1.85
47435727--47435772	21	2.2	21	84	0	56	43	17	34	4	1.69
47436213--47436387	43	4.1	43	79	5	176	33	17	26	22	1.96
47437914--47437938	12	2.1	12	100	0	50	52	8	0	40	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47445181--47445225	23	2.0	23	82	8	56	33	26	0	40	1.57
47445370--47445413	3	14.7	3	100	0	88	65	0	0	34	0.93
47446871--47446934	30	2.1	31	82	2	76	45	7	0	46	1.32
47447037--47447077	3	13.7	3	89	0	64	65	0	2	31	1.05
47453377--47453438	22	2.8	22	79	15	74	33	22	0	43	1.54
47453380--47453434	27	2.2	25	84	15	71	32	23	0	43	1.54
47453590--47453636	3	15.7	3	100	0	94	65	0	0	34	0.93
47454498--47454561	30	2.1	31	82	2	76	45	7	0	46	1.32
47454664--47454701	3	12.7	3	94	0	67	63	0	2	34	1.09
47462341--47462368	14	2.0	14	100	0	56	50	0	14	35	1.43
47462578--47462622	16	2.8	16	77	12	56	57	0	2	40	1.11
47462691--47462745	22	2.5	22	76	8	58	58	3	9	29	1.46
47472778--47472802	13	1.9	13	100	0	50	40	28	8	24	1.83
47475078--47475133	22	2.4	24	85	5	71	16	23	51	8	1.72
47484238--47484580	171	2.0	173	93	1	582	40	14	10	34	1.80
47490002--47490026	6	4.2	6	100	0	50	84	0	16	0	0.63
47492315--47492344	11	2.7	11	89	0	51	66	6	6	20	1.38
47499056--47499090	2	17.5	2	100	0	70	51	0	0	48	1.00
47504635--47504780	40	3.7	40	83	3	177	21	26	16	34	1.95
47505401--47505568	80	2.1	80	88	0	255	23	22	27	25	2.00
47506079--47506137	29	2.1	29	81	9	68	55	3	3	37	1.33
47507541--47507609	28	2.5	28	83	9	88	62	5	8	23	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47507909--47507950	19	2.2	19	91	0	66	4	26	19	50	1.67
47507927--47507975	25	2.0	25	91	0	80	2	22	24	51	1.59
47507952--47507988	19	1.9	19	94	0	65	0	24	18	56	1.41
47508808--47508936	67	1.9	66	90	6	206	48	10	14	25	1.76
47510715--47510762	18	2.7	18	93	0	78	33	12	14	39	1.84
47511187--47511359	72	2.4	72	81	5	224	26	6	13	54	1.62
47521949--47522016	23	3.0	23	81	12	68	36	26	19	17	1.94
47521981--47522116	23	5.9	23	77	3	130	44	26	16	11	1.82
47521981--47522116	69	2.0	69	85	2	184	44	26	16	11	1.82
47521995--47522136	46	3.1	46	83	4	153	44	27	17	10	1.82
47521979--47522136	23	6.9	23	77	2	111	44	27	17	10	1.82
47525187--47525230	23	1.9	22	82	17	54	36	25	0	38	1.56
47525370--47525559	51	3.8	49	79	4	182	32	27	15	24	1.95
47525372--47525556	101	1.8	101	84	5	257	32	26	16	24	1.96
47531657--47531769	46	2.5	46	82	7	149	19	21	14	45	1.85
47531743--47531905	45	3.6	44	77	7	125	22	18	17	41	1.90
47531820--47531914	46	2.1	46	86	4	129	21	14	15	48	1.81
47533331--47533491	61	2.7	60	79	13	170	42	1	3	52	1.27
47536662--47536709	16	2.9	15	77	22	51	41	2	0	56	1.11
47546898--47546948	13	3.9	13	81	0	66	33	9	17	39	1.83
47546896--47546948	26	2.0	26	89	7	81	32	9	18	39	1.83
47550767--47550819	26	2.0	26	100	0	106	11	7	7	73	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47558174--47558580	50	8.2	50	70	4	268	32	20	20	27	1.97
47558124--47558554	99	4.3	100	87	1	607	31	20	21	26	1.98
47558124--47558554	199	2.2	199	88	2	616	31	20	21	26	1.98
47558587--47558911	44	7.5	43	73	12	204	29	19	22	28	1.98
47560570--47560646	25	3.0	24	78	17	84	32	0	3	63	1.12
47562368--47562429	30	2.1	29	85	5	81	17	45	0	37	1.49
47562511--47562570	30	2.0	31	86	3	86	20	40	0	40	1.52
47563825--47563852	8	3.5	8	100	0	56	50	0	0	50	1.00
47568028--47568071	22	2.0	23	86	4	63	43	9	0	47	1.35
47573358--47573512	63	2.5	63	84	6	181	32	33	7	26	1.85

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