genome.fa.s4.2.7.7.80.10.50.1000.31.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  31  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)
9007934--9008621	31	22.6	31	72	18	402	40	2	12	45	1.54
9008004--9008090	9	10.6	9	83	14	109	32	0	22	44	1.53
9008004--9008090	16	5.3	16	78	13	97	32	0	22	44	1.53
9008025--9008085	7	7.9	7	79	13	50	31	0	24	44	1.54
9008004--9008090	32	2.7	34	85	8	119	32	0	22	44	1.53
9008004--9008090	41	2.1	41	89	8	133	32	0	22	44	1.53
9008201--9008265	9	6.8	9	75	19	51	38	0	10	50	1.37
9008203--9008284	22	3.5	23	81	15	87	40	0	9	50	1.36
9008370--9008449	9	9.6	9	74	17	57	35	2	17	45	1.62
9008398--9008471	32	2.4	31	84	6	87	40	2	12	44	1.56
9008483--9008562	38	2.1	39	95	2	144	42	0	10	47	1.37
9008420--9008609	94	2.0	94	97	0	362	44	1	10	43	1.48
9008495--9008553	17	3.2	17	70	25	57	42	0	6	50	1.28
9008555--9008647	25	3.5	25	72	21	89	46	2	12	38	1.54
9008521--9008653	56	2.4	56	97	0	248	43	1	12	42	1.52
9012609--9012887	41	6.8	40	82	5	281	34	27	23	14	1.94
9012609--9012887	82	3.4	82	85	3	339	34	27	23	14	1.94
9012625--9012887	123	2.1	122	82	8	311	35	28	22	13	1.92
9019954--9020051	28	3.5	28	81	0	115	30	15	24	29	1.95
9020644--9020915	23	11.6	23	70	9	120	25	15	16	41	1.88
9020629--9020917	70	4.1	70	83	5	368	26	14	16	42	1.87
9027734--9027935	23	8.6	23	73	10	167	25	15	15	42	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9027722--9027936	70	3.1	68	86	7	272	26	15	15	43	1.86
9035559--9035627	36	1.9	36	96	0	129	37	17	24	20	1.93
9046788--9047010	108	2.1	108	86	5	308	52	8	9	30	1.62
9050346--9050390	23	2.0	23	82	8	56	46	17	11	24	1.81
9064120--9064235	32	3.6	32	86	0	169	37	18	12	32	1.87
9070200--9070528	163	2.0	161	95	1	586	34	15	18	31	1.92
9077103--9077141	18	2.2	17	86	13	53	46	20	0	33	1.51
9081715--9084363	888	3.0	881	84	3	3192	27	22	14	36	1.93
9088251--9088279	2	14.5	2	100	0	58	0	48	0	51	1.00
9088337--9088362	6	4.3	6	100	0	52	69	0	0	30	0.89
9090629--9090688	32	1.9	31	86	10	86	45	3	20	31	1.67
9090769--9090814	22	2.1	22	87	0	65	10	8	15	65	1.47
9090784--9090839	22	2.5	22	85	0	67	19	3	8	67	1.32
9090813--9090855	14	3.1	14	82	0	50	23	0	6	69	1.12
9094140--9094184	22	2.0	22	82	4	54	62	2	0	35	1.08
9094456--9094519	26	2.5	26	76	0	65	34	17	9	39	1.82
9096091--9096130	14	2.9	14	84	0	53	32	7	17	42	1.77
9096099--9096165	35	1.9	35	87	3	100	31	10	13	44	1.77
9096114--9096153	20	2.0	20	85	0	53	27	12	12	47	1.77
9097510--9097579	27	2.6	27	80	8	79	50	21	2	25	1.63
9105958--9106004	21	2.3	20	82	13	60	34	0	8	57	1.29
9106012--9106315	59	5.1	60	73	10	298	44	0	3	50	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9105969--9106328	120	3.0	120	95	0	641	43	0	4	51	1.27
9106274--9106308	18	2.0	17	88	5	52	45	0	0	54	0.99
9106472--9106561	45	2.0	44	85	6	119	36	27	4	31	1.77
9106541--9106573	16	2.1	16	100	0	66	21	36	6	36	1.78
9113526--9113565	18	2.2	18	86	0	53	42	2	0	55	1.13
9119810--9119863	29	1.9	28	88	7	83	25	14	24	35	1.94
9119808--9119876	27	2.4	28	78	7	77	30	15	18	34	1.93
9121122--9121171	18	2.6	20	81	15	61	42	8	20	30	1.80
9121609--9121633	12	2.1	12	100	0	50	16	24	0	60	1.36
9122794--9122847	2	27.0	2	100	0	108	50	0	0	50	1.00
9141155--9141187	16	2.0	17	88	5	50	21	21	12	45	1.84
9142211--9142294	40	2.1	40	84	0	105	15	19	35	29	1.92
9142370--9142423	24	2.2	25	83	3	65	25	14	35	24	1.94
9144772--9144870	23	4.3	23	89	0	144	21	21	26	31	1.98
9146700--9146797	36	2.7	36	82	3	126	41	10	19	28	1.84
9147012--9147075	29	2.2	29	85	0	83	28	12	31	28	1.93
9155966--9156103	67	2.1	67	98	0	267	32	9	23	34	1.87
9157533--9157630	17	5.4	17	64	13	52	32	4	14	48	1.62
9157528--9157639	37	3.0	37	94	0	197	33	5	15	45	1.68
9157549--9157639	17	4.9	19	65	14	64	34	5	15	45	1.69
9159852--9159876	13	1.9	13	100	0	50	24	16	16	44	1.86
9164080--9164147	2	34.0	2	100	0	136	0	50	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9180674--9180707	17	2.1	16	88	5	50	50	0	0	50	1.00
9181111--9181148	10	3.5	11	85	7	51	44	0	0	55	0.99
9185336--9185451	51	2.2	52	87	1	162	50	3	3	43	1.36
9185389--9185519	68	1.9	72	85	6	189	49	3	3	43	1.36
9185446--9185537	38	2.4	37	82	13	107	50	3	2	44	1.30
9185391--9185538	68	2.1	72	80	7	162	50	4	2	42	1.35
9188802--9188842	18	2.2	19	91	4	66	26	19	21	31	1.97
9193907--9193938	2	16.0	2	100	0	64	50	0	0	50	1.00
9196095--9196123	14	2.1	14	100	0	58	41	0	6	51	1.28
9199227--9199257	3	10.7	3	93	6	55	67	0	0	32	0.91
9203296--9203335	21	1.9	21	89	0	62	35	2	25	37	1.69
9213605--9213641	18	2.1	18	89	0	56	56	13	2	27	1.50
9216054--9216126	16	4.5	17	68	19	57	39	4	1	54	1.28
9219680--9219722	21	2.1	21	87	12	63	39	0	6	53	1.28
9221219--9221253	15	2.4	15	90	4	54	48	0	8	42	1.33
9223573--9223746	40	4.4	40	78	5	174	32	21	18	27	1.97
9224624--9224686	18	3.4	17	78	20	63	0	22	4	73	1.02
9224700--9224746	24	2.1	21	85	14	60	38	4	0	57	1.18
9224715--9224801	41	2.1	41	79	14	99	45	1	1	51	1.16
9230569--9230623	28	2.0	28	88	0	83	25	41	7	25	1.81
9233618--9233714	21	4.7	21	91	5	162	37	13	9	40	1.77
9233918--9234002	44	1.9	44	88	4	127	28	25	17	28	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9234000--9234954	132	7.3	132	93	1	1578	24	24	19	31	1.98
9234317--9234628	44	7.1	44	63	15	144	25	24	17	31	1.97
9234007--9234954	263	3.6	263	94	0	1623	24	24	19	31	1.98
9240120--9240200	40	2.0	40	90	0	126	17	33	8	40	1.80
9243899--9243962	19	3.3	19	93	4	101	37	14	9	39	1.78
9243897--9243961	21	3.2	21	89	8	107	38	12	9	40	1.75
9244943--9245068	40	3.4	38	74	26	135	36	3	0	60	1.13
9244941--9245036	30	3.2	31	94	4	162	37	4	0	58	1.18
9244983--9245081	30	3.3	30	85	7	112	37	2	0	60	1.08
9244931--9245057	60	2.1	59	82	7	157	36	3	0	60	1.13
9244971--9245077	40	2.6	39	89	7	160	36	1	0	61	1.07
9244972--9245093	11	11.9	11	69	19	77	39	1	0	59	1.08
9245001--9245093	40	2.3	40	88	5	134	40	1	0	58	1.05
9245012--9245093	30	2.7	30	88	7	114	39	1	0	59	1.05
9245589--9245640	27	2.0	27	88	7	81	42	3	0	53	1.19
9245708--9245784	27	2.9	27	90	0	109	27	25	31	15	1.96
9246071--9246115	3	15.0	3	100	0	90	33	0	0	66	0.92
9246594--9246623	14	2.1	14	100	0	60	56	0	6	36	1.26
9249055--9249092	18	2.1	18	90	0	58	15	44	5	34	1.69
9249058--9249099	18	2.3	18	83	0	57	21	47	2	28	1.63
9249831--9249870	3	13.3	3	100	0	80	67	0	0	32	0.91
9250158--9250234	27	2.9	27	94	0	127	14	31	28	25	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9250266--9250304	8	4.9	8	87	0	51	2	2	7	87	0.73
9261078--9261105	2	14.0	2	100	0	56	50	0	0	50	1.00
9269793--9269861	33	2.1	33	100	0	138	43	17	17	21	1.88
9278386--9278454	9	7.7	9	86	0	84	47	23	4	24	1.69
9278387--9278489	27	3.8	27	79	7	111	42	23	6	27	1.79
9278396--9278489	9	10.4	9	82	0	89	41	23	7	27	1.81
9278396--9278489	18	5.2	19	85	5	108	41	23	7	27	1.81
9278994--9279033	20	2.0	21	90	5	64	0	20	0	80	0.72
9278991--9279033	12	3.6	12	84	9	61	0	20	0	79	0.74
9286101--9286128	10	2.8	10	100	0	56	42	10	14	32	1.80

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