genome.fa.s1.2.7.7.80.10.50.1000.100.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  100  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)
29599487--29599571	30	2.8	30	92	0	152	41	5	7	45	1.55
29615336--29615368	9	3.7	9	91	0	57	39	12	18	30	1.87
29615336--29615370	18	1.9	18	100	0	70	40	11	17	31	1.85
29615421--29615449	9	3.2	9	100	0	58	48	10	10	31	1.71
29616353--29616379	14	1.9	14	100	0	54	25	0	14	59	1.36
29627376--29627438	29	2.1	29	83	13	76	61	0	0	38	0.96
29627368--29627441	30	2.5	30	79	16	82	63	0	0	36	0.95
29628687--29628721	16	2.2	16	94	0	61	25	11	25	37	1.90
29628741--29628777	19	1.9	19	88	0	56	40	5	16	37	1.71
29630591--29630626	11	3.2	11	92	4	54	38	0	0	61	0.96
29635610--29635683	27	2.7	27	72	15	64	66	1	2	29	1.14
29635612--29635665	26	2.0	27	82	10	67	64	0	1	33	1.04
29635668--29635783	10	11.8	10	70	14	62	61	1	2	34	1.20
29635632--29635798	57	2.9	57	76	8	167	61	1	4	32	1.25
29635953--29636048	9	10.6	9	68	14	54	33	1	2	63	1.13
29635953--29636013	28	2.2	29	88	5	90	34	0	1	63	1.04
29635975--29636013	20	2.0	21	90	10	64	35	0	0	64	0.94
29635976--29636018	20	2.2	20	84	12	54	39	2	0	58	1.11
29636459--29636510	19	2.8	17	75	16	50	48	0	7	44	1.31
29644549--29644592	14	3.0	15	84	12	56	77	0	4	18	0.94
29644549--29644590	16	2.8	15	82	10	50	78	0	4	16	0.91
29647575--29647632	30	1.9	31	86	10	84	39	6	22	31	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29647801--29648094	51	5.8	51	78	7	276	23	17	27	30	1.97
29647797--29648094	101	2.9	102	80	5	304	23	17	28	30	1.97
29647799--29648084	152	1.9	152	92	0	482	23	17	27	31	1.97
29653125--29653156	10	3.3	10	95	4	57	53	0	28	18	1.45
29655422--29655463	16	2.4	18	81	18	54	40	23	7	28	1.81
29656042--29656200	79	2.0	79	96	0	291	18	32	8	40	1.81
29660757--29660836	38	2.1	38	90	0	124	43	17	7	31	1.77
29661295--29661342	9	5.6	9	76	18	57	33	0	2	64	1.05
29661311--29661344	15	2.2	15	89	5	50	38	0	2	58	1.13
29661302--29661358	25	2.4	24	88	5	80	36	1	1	59	1.18
29661364--29661402	20	2.1	18	90	9	60	28	2	5	64	1.28
29667407--29667435	3	9.7	3	100	0	58	68	0	0	31	0.89
29669149--29669179	2	15.5	2	100	0	62	51	0	0	48	1.00
29669179--29669219	2	20.5	2	100	0	82	51	0	48	0	1.00
29692278--29692313	18	1.9	19	88	5	56	55	11	0	33	1.35
29711499--29711547	21	2.3	21	82	6	55	30	18	24	26	1.98
29714200--29714241	21	2.0	21	100	0	84	23	19	38	19	1.93
29719411--29719686	27	10.2	27	82	0	302	43	18	19	18	1.88
29720017--29720119	28	3.6	29	83	8	131	26	23	22	28	1.99
29720018--29720105	30	3.0	30	90	5	126	27	23	22	26	2.00
29726711--29726886	50	3.5	50	85	1	183	22	30	21	26	1.98
29726762--29726894	50	2.7	50	93	0	221	20	31	22	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29729754--29730042	27	10.7	27	84	0	362	42	19	19	18	1.89
29730388--29730477	30	3.0	30	88	4	130	23	25	23	27	2.00
29732222--29732270	24	2.0	24	84	7	64	48	0	4	46	1.20
29741469--29741533	6	10.8	6	100	0	130	32	0	0	67	0.91
29741969--29742029	22	2.7	22	87	2	77	49	1	1	47	1.21
29742005--29742044	16	2.5	16	91	0	62	47	2	7	42	1.45
29742033--29742175	68	2.1	67	93	2	252	41	4	9	44	1.57
29742117--29742144	9	3.1	9	100	0	56	32	0	10	57	1.33
29750504--29750580	10	7.2	10	72	17	57	79	0	12	7	0.94
29750504--29750580	17	4.3	17	74	11	64	79	0	12	7	0.94
29750515--29750580	27	2.5	26	82	5	78	80	0	13	6	0.89
29754024--29754077	27	2.0	27	85	0	72	40	7	12	38	1.72
29754647--29754741	36	2.6	35	77	9	93	22	22	25	30	1.99
29765969--29766018	15	3.3	15	85	0	64	46	4	20	30	1.69
29767258--29767349	31	3.0	31	73	9	80	39	14	6	40	1.71
29774636--29774660	12	2.1	12	100	0	50	16	16	24	44	1.86
29776649--29776721	25	2.8	26	82	10	87	38	10	2	47	1.53
29788967--29789468	44	11.6	44	74	11	375	30	20	23	26	1.99
29789108--29789546	80	5.2	80	73	14	409	28	19	25	27	1.99
29789013--29789598	170	3.5	170	95	0	989	29	20	23	26	1.99
29788967--29789468	214	2.3	211	81	7	543	30	20	23	26	1.99
29791268--29791300	3	11.0	3	93	0	57	33	3	0	63	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29791357--29791407	25	2.0	25	92	0	84	39	9	1	49	1.47
29791359--29791415	25	2.5	23	81	15	73	36	10	1	50	1.47
29792920--29792981	28	2.1	30	85	8	83	66	4	3	25	1.27
29795223--29795255	17	1.9	17	93	0	57	24	0	3	72	0.98
29796659--29797000	116	2.9	116	87	0	486	28	15	21	33	1.94
29797092--29797143	23	2.2	24	80	10	63	13	42	1	42	1.55
29802359--29802559	43	4.7	42	79	5	206	26	15	26	31	1.96
29802359--29802551	86	2.2	86	84	5	248	27	15	26	31	1.95
29804269--29804298	11	2.7	11	89	0	51	63	0	0	36	0.95
29804269--29804306	12	3.3	12	85	10	53	63	0	0	36	0.95
29805086--29805126	2	20.5	2	94	0	73	51	2	0	46	1.14
29805187--29805227	18	2.4	17	84	8	55	51	19	0	29	1.47
29805552--29805577	13	2.0	13	100	0	52	0	30	7	61	1.24
29808118--29808170	27	2.0	27	96	0	97	37	0	13	49	1.42
29808392--29808422	16	1.9	16	93	0	53	58	9	9	22	1.59
29808462--29808490	6	4.8	6	100	0	58	31	0	17	51	1.45
29810086--29810133	18	2.8	18	74	22	50	43	0	0	56	0.99
29810103--29810154	15	3.6	15	80	12	56	44	0	1	53	1.11
29810136--29810333	66	3.2	66	67	21	199	41	3	7	47	1.48
29810171--29810358	61	3.1	60	66	17	172	42	2	6	47	1.44
29810223--29810274	15	3.6	15	80	12	56	44	0	1	53	1.11
29810064--29810390	120	2.7	120	98	0	627	42	2	5	48	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29810352--29810393	15	2.7	16	82	14	52	45	0	2	52	1.13
29810343--29810384	15	2.9	15	82	10	52	47	0	0	52	1.00
29810330--29810642	157	2.0	157	96	0	581	46	5	3	45	1.41
29810496--29810530	18	2.0	17	88	5	52	45	0	0	54	0.99
29810769--29810801	16	2.1	16	100	0	66	39	36	0	24	1.56
29811548--29811657	48	2.3	48	89	6	186	43	7	8	40	1.62
29812224--29812266	18	2.4	18	88	0	59	44	9	27	18	1.80
29814104--29814156	11	4.7	12	84	11	67	47	0	30	22	1.52
29814106--29814158	22	2.5	22	93	3	90	49	0	30	20	1.50
29817251--29817295	16	2.7	17	82	6	56	40	0	0	60	0.97
29817579--29817658	8	9.1	8	75	20	63	38	2	0	58	1.11
29817577--29817659	18	4.6	18	73	20	75	39	2	0	57	1.12
29817595--29817632	11	3.5	11	83	16	53	39	2	0	57	1.12
29817579--29817649	38	1.9	37	91	2	108	39	2	0	57	1.13
29818706--29818932	113	2.0	113	100	0	454	42	3	19	34	1.68
29819045--29819081	18	2.1	18	90	10	58	24	5	29	40	1.77
29820493--29820524	2	16.0	2	100	0	64	50	0	0	50	1.00
29822908--29822951	20	2.2	20	88	8	63	68	0	27	4	1.09
29825156--29825199	22	2.0	22	100	0	88	31	27	9	31	1.88
29827682--29827732	19	2.6	19	84	9	59	74	0	5	19	1.02
29827690--29827744	19	2.9	18	82	15	58	70	1	5	21	1.16
29827760--29827808	17	2.9	17	79	11	55	63	4	0	32	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29827729--29827813	8	10.0	8	75	22	59	61	4	1	32	1.24
29827751--29827813	26	2.3	27	81	13	67	58	4	1	34	1.29
29828296--29828488	10	19.6	10	67	17	50	30	2	4	62	1.27
29828370--29828488	20	6.2	18	75	16	62	30	1	3	64	1.19
29828428--29828487	8	6.8	8	80	19	66	26	3	1	68	1.15
29828410--29828481	28	2.5	29	80	13	78	30	2	1	65	1.15
29834135--29834160	5	5.2	5	100	0	52	19	0	38	42	1.51
29848740--29848794	20	2.8	20	91	0	83	23	30	0	45	1.53
29848841--29848881	21	2.0	21	90	0	64	43	17	9	29	1.80
29856162--29856277	27	4.4	25	75	18	78	43	19	16	19	1.87

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