genome.fa.s1.2.7.7.80.10.50.1000.178.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  178  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)
53255202--53255263	21	2.9	21	73	4	61	40	0	6	53	1.27
53262902--53262930	2	15.0	2	92	7	51	51	0	0	48	1.00
53268194--53268244	25	2.0	25	84	0	66	13	13	23	49	1.78
53271465--53271499	18	1.9	18	88	0	52	28	2	5	62	1.32
53281720--53281754	17	2.0	18	88	5	54	57	5	0	37	1.23
53294697--53294724	13	2.2	13	100	0	56	71	0	14	14	1.15
53295736--53295822	26	3.4	26	80	4	106	17	25	22	34	1.96
53298945--53298978	17	1.9	17	88	5	50	44	2	5	47	1.42
53299040--53299072	11	3.1	11	86	4	50	69	18	0	12	1.18
53299693--53299722	14	2.1	14	93	0	51	83	0	16	0	0.65
53311730--53311786	21	2.8	20	87	10	80	50	1	0	47	1.11
53316416--53316459	22	2.0	22	82	8	54	27	0	2	70	0.99
53316426--53316464	17	2.3	16	86	8	51	23	0	0	76	0.78
53318172--53318296	43	2.9	42	77	8	126	20	20	23	35	1.96
53318192--53318310	43	2.8	42	77	7	114	20	19	23	36	1.95
53318295--53318376	36	2.3	36	97	2	157	13	19	19	47	1.82
53328169--53328687	132	3.9	133	84	4	579	32	15	15	36	1.90
53328169--53328835	264	2.6	253	81	5	751	32	15	15	36	1.89
53328571--53328803	116	2.0	116	84	1	306	31	15	15	37	1.89
53335261--53335314	22	2.6	21	82	8	65	25	27	20	25	1.99
53336840--53336891	26	2.0	26	92	0	86	50	17	0	32	1.47
53338018--53338258	46	5.2	46	91	0	401	40	17	14	26	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53338905--53339053	41	3.7	40	81	5	156	34	26	14	23	1.94
53343080--53343138	24	2.4	24	80	11	66	42	10	1	45	1.48
53343092--53343141	26	1.9	26	87	0	73	42	12	2	44	1.53
53343235--53343306	2	37.5	2	75	8	60	48	6	0	44	1.29
53343204--53343280	22	3.3	23	83	9	84	37	5	1	55	1.30
53345143--53345214	22	3.3	22	94	0	117	25	27	16	30	1.97
53348656--53348943	97	3.0	97	93	2	481	27	16	8	47	1.75
53350033--53350137	44	2.4	44	80	6	115	32	20	20	27	1.97
53350063--53350167	44	2.4	44	81	0	111	29	19	25	25	1.98
53350195--53350460	139	1.9	139	88	0	397	30	18	21	29	1.97
53350410--53350569	45	3.6	46	75	5	150	28	20	21	28	1.98
53352195--53352257	3	20.7	3	87	9	92	31	3	1	63	1.19
53352319--53352352	18	2.0	17	88	11	52	29	5	0	64	1.17
53352328--53352390	26	2.4	26	81	0	72	38	11	3	47	1.55
53352453--53352503	18	3.0	17	76	18	52	29	3	1	64	1.22
53356847--53356916	29	2.3	30	85	4	88	24	14	12	48	1.78
53357135--53357190	3	18.7	3	100	0	112	67	0	0	32	0.91
53364943--53364993	27	1.9	26	84	11	68	54	11	9	23	1.66
53367422--53367446	10	2.5	10	100	0	50	28	8	0	64	1.22
53367932--53368070	51	2.7	50	83	3	179	32	29	16	21	1.95
53369864--53370008	48	3.0	48	85	0	146	24	29	18	26	1.98
53369916--53370014	48	2.1	48	94	0	171	24	26	21	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53370142--53370244	51	2.0	51	100	0	206	28	15	13	42	1.85
53375462--53375608	57	2.5	60	75	15	160	31	21	24	23	1.98
53375730--53375859	67	1.9	67	98	0	251	20	19	33	26	1.96
53396850--53396900	25	2.0	25	84	3	66	43	0	11	45	1.40
53403742--53403906	80	2.1	80	98	0	321	38	6	24	31	1.80
53407154--53407197	20	2.3	18	81	11	52	59	2	0	38	1.10
53421105--53421150	24	2.0	22	87	8	65	56	0	10	32	1.34
53421696--53421815	60	2.0	60	98	0	231	33	20	15	30	1.93
53429502--53429546	22	2.0	22	83	8	56	28	4	6	60	1.42
53430270--53430318	2	24.5	2	95	0	89	48	0	2	48	1.12
53430931--53431007	14	5.0	15	71	20	52	42	14	9	33	1.77
53430947--53430986	20	2.0	20	90	0	62	50	12	10	27	1.72
53430935--53431001	34	1.9	35	90	3	109	46	13	8	31	1.74
53432018--53432056	17	2.3	18	82	13	55	51	7	0	41	1.31
53438392--53438471	29	2.8	29	86	3	108	43	17	8	30	1.79
53439929--53440009	19	4.1	19	78	13	74	44	2	3	49	1.33
53442298--53442332	15	2.4	15	90	4	54	48	2	5	42	1.41
53446287--53446352	17	4.1	15	75	17	53	18	4	0	77	0.94
53446296--53446369	7	10.7	7	75	17	57	21	5	0	72	1.04
53446286--53446356	20	3.4	21	81	14	85	21	4	0	74	0.98
53446289--53446370	12	6.6	12	73	22	55	20	6	0	73	1.05
53447834--53447873	15	2.7	15	96	0	71	50	0	12	37	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53470570--53470716	75	2.0	75	79	5	163	10	8	51	29	1.66
53470631--53470929	96	3.1	91	80	13	332	13	9	49	27	1.72
53470700--53470930	48	4.8	48	94	0	390	13	9	48	28	1.72
53470780--53470869	27	3.6	27	66	22	77	15	10	48	25	1.76
53470892--53470971	33	2.4	33	85	0	106	12	5	50	32	1.62
53473115--53473165	25	2.0	25	88	0	75	35	17	5	41	1.74
53473549--53473638	23	4.0	23	82	7	114	36	23	21	18	1.95
53474250--53474288	3	13.0	3	100	0	78	66	0	0	33	0.92
53474875--53474921	23	2.0	23	91	0	76	42	6	4	46	1.48
53474896--53474925	15	2.0	15	93	0	51	36	6	3	53	1.44
53477518--53477637	34	3.5	34	94	0	204	38	8	14	39	1.76
53489199--53489227	13	2.2	13	100	0	58	62	0	37	0	0.96
53489204--53489319	20	5.8	19	71	13	65	67	0	30	2	1.04
53489219--53489276	10	5.7	10	79	2	62	72	0	25	1	0.94
53489213--53489295	30	2.7	30	92	1	130	68	0	28	2	1.02
53489238--53489293	15	3.7	15	76	9	69	66	0	30	3	1.09
53489284--53489397	43	2.7	43	72	5	97	62	1	34	1	1.16
53489624--53489657	16	2.2	16	94	5	61	73	5	5	14	1.21
53489624--53489665	16	2.6	16	88	7	50	76	4	4	14	1.12
53489654--53490077	160	2.7	160	90	2	649	54	7	10	27	1.61
53492185--53492282	40	2.4	40	98	1	187	41	11	5	41	1.63
53495272--53495317	3	15.3	3	100	0	92	67	0	0	32	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53495296--53495394	40	2.6	39	80	12	114	54	6	5	34	1.47
53499854--53499930	28	2.8	28	81	0	100	27	0	22	50	1.49
53500272--53500368	49	2.0	49	89	4	151	24	24	6	44	1.77
53501644--53501729	43	2.0	43	88	0	127	20	24	2	52	1.58
53502932--53502982	3	17.0	3	92	8	86	31	1	0	66	1.03
53502915--53502982	9	7.9	8	87	9	66	27	2	1	67	1.13
53509648--53509682	14	2.5	15	90	9	56	34	0	0	65	0.93
53527715--53527909	103	1.9	104	89	5	306	20	21	27	30	1.98
53535345--53535426	27	2.8	28	87	10	103	14	23	30	31	1.94
53535268--53535468	103	2.0	102	93	3	341	19	18	27	33	1.96
53535407--53535511	42	2.5	43	98	1	203	25	15	25	33	1.95
53535304--53535614	145	2.1	146	92	0	507	21	19	27	31	1.97
53535451--53535645	103	1.9	104	89	1	302	20	21	27	30	1.98
53539393--53539746	103	3.4	103	85	2	460	33	28	18	19	1.95
53541010--53541040	13	2.4	13	94	0	53	16	3	0	80	0.83
53545659--53545744	41	2.1	41	95	0	154	30	12	4	52	1.60
53555671--53555722	2	25.5	2	96	3	95	50	1	0	48	1.12
53556444--53556496	21	2.5	21	90	0	88	30	7	32	30	1.85
53561868--53561896	6	4.8	6	100	0	58	17	65	17	0	1.27
53563526--53563593	33	2.1	32	91	2	109	33	25	13	27	1.93
53565074--53565115	2	21.0	2	100	0	84	50	0	0	50	1.00
53574781--53574829	24	2.0	25	84	11	66	48	4	0	46	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53582992--53583019	6	4.7	6	100	0	56	14	35	0	50	1.43
53587589--53587618	2	15.0	2	92	0	51	53	0	0	46	1.00
53591615--53591662	19	2.5	19	83	6	53	62	8	0	29	1.24
53604923--53604949	11	2.5	11	100	0	54	25	0	14	59	1.36
53607562--53607587	12	2.2	12	100	0	52	26	34	0	38	1.57
53615467--53615496	2	15.0	2	100	0	60	50	0	0	50	1.00
53617837--53617876	17	2.3	18	91	4	64	20	15	2	62	1.43
53617817--53617874	15	3.7	15	77	8	53	24	17	3	55	1.57
53640854--53640887	13	2.6	13	95	0	59	32	0	5	61	1.20
53646480--53646513	13	2.6	13	95	0	59	32	0	5	61	1.20

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