genome.fa.s4.2.7.7.80.10.50.1000.36.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  36  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)
10762390--10762420	15	2.0	16	93	6	55	25	22	19	32	1.97
10775638--10775673	2	18.0	2	94	0	63	47	0	2	50	1.15
10791764--10791806	19	2.3	20	80	11	56	16	4	13	65	1.43
10791904--10791949	17	2.5	18	80	19	51	26	0	6	67	1.15
10799408--10799454	23	2.0	23	100	0	94	34	8	8	48	1.64
10801755--10801805	23	2.2	23	89	0	75	29	9	19	41	1.84
10803950--10804104	26	6.0	26	76	0	130	20	16	26	36	1.93
10808082--10808170	34	2.6	34	96	0	160	43	14	7	33	1.74
10831151--10831208	22	2.6	22	81	7	64	41	17	5	36	1.72
10831683--10832058	131	2.9	132	87	0	538	26	26	19	27	1.99
10832094--10832394	89	3.4	89	88	0	424	25	22	23	27	1.99
10832476--10832592	44	2.7	44	78	4	119	29	22	21	27	1.99
10832696--10832816	42	2.8	44	82	5	149	28	24	19	28	1.98
10832696--10832859	42	3.9	42	77	8	145	29	23	17	28	1.97
10832475--10832958	225	2.2	225	83	3	582	28	21	18	31	1.97
10832969--10833467	44	11.2	45	78	7	391	28	22	18	31	1.97
10832969--10833465	222	2.2	223	87	3	741	28	22	18	31	1.97
10832994--10833464	178	2.6	177	82	4	491	28	22	18	30	1.97
10839815--10839847	15	2.1	16	88	5	50	63	0	6	30	1.18
10840674--10840731	22	2.6	22	81	7	64	41	17	5	36	1.72
10841715--10841970	20	12.8	20	70	5	113	36	20	28	14	1.91
10841762--10841964	40	5.1	40	80	2	192	36	20	29	13	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10841762--10841970	80	2.6	80	80	3	224	36	20	29	13	1.91
10853045--10853203	71	2.2	71	88	0	228	28	21	16	33	1.95
10861339--10861449	56	1.9	59	87	7	165	43	3	7	45	1.48
10863213--10863252	21	1.9	21	89	0	62	62	10	12	15	1.54
10888477--10888501	8	3.1	8	100	0	50	12	0	12	76	1.04
10892863--10892899	11	3.5	11	85	7	58	16	29	10	43	1.82
10904770--10904813	21	2.1	22	87	8	65	54	18	6	20	1.66
10905844--10906240	100	4.0	100	81	3	458	37	17	20	23	1.94
10905860--10906251	200	2.0	200	85	2	536	37	18	20	23	1.94
10907066--10907210	55	2.6	55	98	0	281	42	8	21	27	1.83
10913926--10914249	51	6.4	51	93	1	544	31	24	13	31	1.93
10913926--10914249	101	3.2	101	94	0	558	31	24	13	31	1.93
10914323--10914355	17	1.9	17	88	11	50	45	21	0	33	1.52
10917170--10917201	9	3.6	9	91	0	55	43	12	12	31	1.80
10922658--10922708	5	10.2	5	100	0	102	39	0	0	60	0.97
10924070--10924108	17	2.3	17	95	0	69	46	0	5	48	1.24
10924264--10926341	711	2.9	709	84	3	2668	32	14	20	32	1.93
10934368--10934447	25	3.2	25	82	3	90	25	12	23	38	1.90
10937141--10937221	40	2.0	40	100	0	162	22	16	22	39	1.92
10947062--10947217	44	3.5	44	85	3	224	30	25	14	30	1.94
10957751--10957819	3	23.0	3	100	0	138	66	0	0	33	0.92
10972964--10972993	16	1.9	16	93	6	53	30	0	20	50	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11000046--11000150	41	2.6	41	89	0	156	32	27	22	17	1.96
11001561--11001593	17	1.9	17	93	0	57	21	27	24	27	1.99
11003427--11003477	21	2.4	21	93	0	84	21	27	11	39	1.88
11007499--11007646	41	3.6	42	78	8	153	33	26	22	18	1.97
11007588--11007619	16	2.0	16	93	0	55	28	25	28	18	1.98
11017117--11017581	40	11.7	40	81	0	504	33	17	29	19	1.95
11017147--11017208	20	3.1	20	65	9	54	35	17	33	12	1.88
11017249--11017300	20	2.6	20	70	11	52	26	21	32	19	1.97
11017127--11017569	199	2.2	200	85	1	586	33	18	29	18	1.95
11021953--11021993	21	1.9	22	90	5	66	41	12	12	34	1.80
11022744--11022787	22	1.9	24	86	9	65	43	2	13	40	1.57
11022983--11023023	21	1.9	22	85	5	57	41	17	9	31	1.82
11023624--11023690	33	2.0	33	86	11	93	40	4	22	32	1.74
11023717--11023791	37	2.0	37	97	0	141	32	8	25	34	1.85
11023809--11023854	22	2.0	23	84	12	60	39	4	15	41	1.67
11030704--11030843	27	5.2	27	84	2	158	44	18	21	15	1.87
11031018--11031094	26	3.0	26	80	0	91	16	24	19	38	1.92
11031205--11031294	27	3.2	28	83	9	112	24	22	23	30	1.99
11031205--11031283	30	2.8	27	85	9	104	22	22	24	30	1.99
11038341--11038520	51	3.6	50	78	8	168	25	17	27	30	1.97
11038441--11038522	26	3.2	26	68	22	82	24	13	28	34	1.93
11038524--11038622	46	2.2	43	81	12	110	24	20	24	31	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11038746--11038777	16	2.0	16	93	0	55	59	0	15	25	1.36
11041817--11041871	26	2.1	26	100	0	110	29	7	21	41	1.80
11044545--11044772	51	4.5	51	75	9	189	24	17	28	30	1.97
11044689--11044769	26	3.2	26	65	28	73	22	14	29	33	1.94
11044771--11044869	46	2.2	43	81	12	110	23	18	24	34	1.96
11044993--11045024	16	2.0	16	93	0	55	59	0	15	25	1.36
11049124--11049158	16	2.1	17	89	5	54	37	0	51	11	1.38
11055417--11055560	27	5.3	27	80	9	93	36	20	20	23	1.95
11055435--11055705	27	10.4	27	76	11	201	33	19	22	23	1.97
11055585--11055681	45	2.2	45	86	0	131	32	19	23	23	1.97
11055751--11055809	24	2.4	25	88	5	86	22	5	25	47	1.71
11055924--11055973	26	1.9	26	91	0	82	16	20	26	38	1.92
11055980--11056150	32	5.3	32	75	8	125	18	20	22	38	1.94
11055977--11056194	64	3.4	64	78	6	226	18	21	23	36	1.95
11056007--11056176	32	5.3	32	78	0	133	17	22	23	36	1.95
11056206--11056270	22	3.0	21	75	4	58	16	20	18	44	1.87
11056264--11056316	26	2.0	26	85	0	70	20	28	18	32	1.97
11062061--11062250	51	3.7	51	83	3	206	26	16	26	30	1.97
11066197--11066252	21	2.6	21	82	5	67	33	0	50	16	1.45
11066211--11066252	7	6.0	7	94	0	66	30	0	52	16	1.44
11067613--11067647	18	1.9	18	88	0	52	48	11	11	28	1.74
11072808--11072840	12	2.8	12	95	0	57	42	24	24	9	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11091589--11091661	34	2.1	34	82	2	83	34	8	16	41	1.78
11091778--11091900	43	2.8	43	82	1	147	22	16	28	32	1.96
11091871--11092032	43	3.8	43	77	4	150	27	16	23	33	1.95
11096707--11096731	13	1.9	13	100	0	50	24	0	8	68	1.16
11097115--11097158	23	2.0	22	82	13	54	45	9	15	29	1.77
11105821--11105877	28	2.0	28	86	0	78	33	19	22	24	1.97
11106125--11106232	32	3.4	32	78	0	126	35	22	21	21	1.96
11106107--11106258	64	2.4	64	87	2	216	36	21	19	23	1.95
11106104--11106258	32	4.8	32	75	3	125	36	21	19	22	1.95
11106435--11106494	24	2.5	24	83	0	75	48	21	5	25	1.70
11106565--11106705	27	5.2	28	75	13	125	19	18	19	42	1.89
11106562--11106705	54	2.7	53	82	6	175	19	18	20	41	1.90
11109850--11109952	32	3.2	32	62	24	79	33	6	20	38	1.79
11109838--11109988	66	2.3	66	94	1	257	33	8	17	39	1.81
11112434--11112500	35	1.9	35	90	0	107	19	26	14	38	1.91
11120713--11120742	16	1.9	16	93	6	53	46	6	13	33	1.69
11126521--11126551	15	2.1	15	100	0	62	38	6	32	22	1.80
11126631--11126657	9	3.0	9	100	0	54	11	0	0	88	0.50
11130864--11130894	15	2.1	15	100	0	62	38	6	32	22	1.80
11132640--11132671	3	10.7	3	93	0	55	65	0	3	31	1.08
11134204--11134758	114	4.9	113	78	10	537	23	23	25	27	2.00
11134206--11134758	228	2.4	226	81	8	633	24	23	25	27	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11135045--11135106	7	8.4	7	82	10	79	14	1	38	45	1.55
11135048--11135085	8	5.0	8	87	6	53	18	0	42	39	1.50
11135045--11135106	15	4.2	14	86	10	79	14	1	38	45	1.55
11135043--11135106	22	2.9	22	88	2	92	15	1	39	43	1.56
11145633--11145725	42	2.2	42	82	7	107	27	29	20	22	1.98
11145863--11145906	21	2.1	21	91	0	70	40	29	18	11	1.85
11148952--11148982	16	1.9	16	100	0	62	38	12	0	48	1.42
11151023--11151134	57	2.0	57	89	0	170	48	18	15	17	1.82
11153609--11153641	10	3.2	10	95	4	57	81	0	0	18	0.68
11153620--11153663	17	2.8	16	79	6	54	77	2	2	18	0.98

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