genome.fa.s4.2.7.7.80.10.50.1000.47.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  47  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)
14044329--14044354	2	13.0	2	100	0	52	50	0	0	50	1.00
14044991--14045042	24	2.2	24	85	0	68	50	9	5	34	1.59
14049405--14049456	24	2.2	24	92	0	86	48	9	7	34	1.65
14052120--14052234	57	2.0	58	89	1	178	46	8	18	26	1.77
14074477--14074576	47	2.1	47	86	0	137	32	21	21	26	1.98
14080091--14080147	3	19.0	3	100	0	114	66	0	0	33	0.92
14080375--14080509	40	3.4	39	79	6	139	35	24	18	21	1.95
14080544--14080863	41	7.8	41	84	4	364	18	19	28	33	1.96
14081220--14081352	15	9.4	14	69	12	65	19	0	33	46	1.50
14081220--14081352	7	18.7	7	70	11	65	19	0	33	46	1.50
14082029--14082060	13	2.3	15	89	10	50	43	0	0	56	0.99
14082250--14082300	13	3.6	14	78	7	59	60	0	1	37	1.08
14082250--14082282	16	2.1	16	88	11	50	57	0	3	39	1.14
14087609--14087655	25	1.9	24	86	4	67	10	12	10	65	1.46
14087971--14088011	21	2.0	21	90	0	64	31	36	4	26	1.78
14089051--14089192	43	3.3	43	82	0	167	21	18	29	30	1.97
14089053--14089213	86	1.9	86	81	1	196	26	18	27	27	1.98
14089357--14089399	18	2.4	18	84	7	52	30	13	0	55	1.39
14089367--14089399	9	3.8	9	92	4	50	24	15	0	60	1.35
14098586--14098630	23	2.0	23	81	0	54	44	22	13	20	1.85
14103501--14103534	9	3.8	9	88	0	50	70	2	0	26	1.01
14103501--14103535	18	1.9	18	94	0	61	68	2	0	28	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
14103820--14103867	2	24.0	2	100	0	96	50	0	0	50	1.00
14103941--14103984	3	14.7	3	100	0	88	34	0	0	65	0.93
14105075--14105124	25	2.0	27	81	18	63	60	0	2	38	1.09
14117794--14117840	2	23.5	2	95	0	85	46	0	0	53	1.00
14129943--14129979	2	18.5	2	94	0	65	45	0	2	51	1.15
14131048--14131078	2	15.5	2	100	0	62	48	0	0	51	1.00
14131144--14131340	107	1.8	109	83	6	267	40	5	9	44	1.61
14131739--14131811	30	2.5	28	80	10	76	56	6	5	31	1.49
14140682--14140750	34	2.0	34	100	0	138	59	2	14	23	1.49
14147725--14147825	47	2.1	49	81	3	116	46	0	4	48	1.23
14150522--14150578	29	2.1	27	83	9	71	40	14	17	28	1.88
14157106--14157141	10	3.6	10	88	0	54	30	0	2	66	1.06
14157724--14157757	12	2.9	12	86	4	52	58	2	0	38	1.13
14167418--14167468	20	2.7	18	79	11	57	17	17	11	52	1.73
14172526--14172828	138	2.2	138	89	2	459	31	16	21	31	1.95
14172800--14172938	45	3.1	45	83	1	154	30	15	23	30	1.96
14172856--14172958	45	2.3	45	86	0	143	33	10	25	30	1.90
14172663--14173131	226	2.1	227	86	2	665	31	15	21	31	1.94
14173192--14173368	96	1.8	96	81	2	221	31	16	22	29	1.96
14174739--14174777	4	9.8	4	88	0	60	23	2	2	71	1.10
14185815--14186717	44	19.9	43	73	13	539	32	18	20	28	1.97
14185862--14186350	89	5.4	91	77	11	298	32	19	20	28	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
14185873--14186717	182	4.7	179	77	7	687	32	19	20	28	1.97
14186413--14186543	51	2.7	50	79	8	137	35	15	16	32	1.90
14187070--14187118	25	2.0	25	83	0	62	44	30	10	14	1.78
14188334--14188368	4	8.8	4	87	0	52	22	2	2	71	1.13
14189395--14189510	44	2.6	44	84	0	151	26	19	21	31	1.97
14189398--14189529	44	3.0	43	76	4	113	29	18	21	29	1.97
14192162--14192196	16	2.2	16	100	0	70	31	28	11	28	1.92
14193124--14193184	14	4.4	14	74	0	59	57	6	18	18	1.61
14193124--14193184	28	2.2	28	88	5	88	57	6	18	18	1.61
14194824--14194861	20	1.9	20	88	0	58	50	5	2	42	1.39
14196111--14196263	41	3.7	41	89	2	200	32	30	18	18	1.95
14197427--14197458	16	1.9	17	93	6	57	37	21	0	40	1.54
14199881--14200017	34	4.1	34	76	9	145	30	13	13	41	1.84
14200154--14202391	320	7.0	321	88	0	3428	31	15	19	33	1.93
14200154--14202391	640	3.5	640	96	0	4091	31	15	19	33	1.93
14215636--14215775	34	4.1	34	86	0	190	32	18	18	30	1.95
14227776--14227872	43	2.3	43	87	0	131	31	30	13	23	1.93
14231687--14231733	14	3.4	14	81	0	58	34	38	0	27	1.57
14231673--14231736	14	4.5	14	80	2	56	37	32	0	29	1.58
14236543--14236711	43	4.0	43	72	11	141	33	28	15	21	1.95
14237696--14237871	91	1.9	90	85	3	237	43	21	6	27	1.78
14238203--14238244	14	3.0	14	76	13	50	59	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
14239138--14239250	43	2.6	42	75	15	115	24	19	28	27	1.99
14240241--14240428	47	4.0	47	86	2	155	22	17	17	42	1.89
14240251--14240428	70	2.5	70	89	0	257	23	17	16	42	1.88
14240250--14240635	117	3.3	117	78	5	413	26	14	17	41	1.88
14240321--14240453	47	2.8	47	95	0	239	23	18	16	42	1.89
14240321--14240635	47	6.7	47	78	3	235	26	14	17	40	1.89
14240415--14240677	70	3.7	70	88	2	384	27	12	18	41	1.86
14240391--14240707	140	2.2	140	85	3	395	27	12	17	41	1.86
14240251--14240661	23	17.6	23	72	8	231	25	14	17	42	1.87
14244497--14244544	15	3.1	15	77	11	51	64	2	10	22	1.35
14244527--14244583	22	2.7	20	76	12	60	64	1	8	24	1.31
14244530--14244718	21	8.3	21	72	19	107	63	0	11	24	1.31
14244554--14244869	47	6.6	46	74	16	175	61	0	13	24	1.34
14244570--14244772	49	4.2	48	88	5	275	61	0	14	24	1.33
14244593--14244772	97	1.9	95	90	4	290	60	0	14	25	1.35
14244593--14244847	74	3.5	76	79	12	259	60	0	14	25	1.37
14244537--14244875	171	2.0	164	88	5	491	61	0	13	23	1.36
14244829--14244865	18	2.0	20	89	10	60	67	0	0	32	0.91
14244537--14244875	49	7.1	48	69	20	151	61	0	13	23	1.36
14244862--14244929	5	12.6	5	80	9	64	60	2	19	17	1.49
14244862--14244929	11	6.3	10	79	14	64	60	2	19	17	1.49
14244862--14244929	22	3.1	21	82	2	82	60	2	19	17	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
14245441--14245529	18	4.7	18	77	13	90	61	3	8	25	1.41
14245533--14245570	11	3.5	11	80	20	53	55	0	21	23	1.44
14245523--14245573	5	9.6	5	79	12	57	56	0	19	23	1.42
14245522--14245570	16	3.0	16	87	3	62	53	0	20	26	1.46
14250372--14250614	89	2.7	89	77	4	229	57	12	4	25	1.54
14254536--14254591	18	2.9	18	80	17	60	64	1	1	32	1.14
14254773--14254816	23	2.0	22	82	13	54	47	0	0	52	1.00
14263159--14263205	21	2.2	22	88	3	69	23	38	17	21	1.93
14267805--14267923	50	2.4	49	82	8	143	35	11	15	36	1.85
14270017--14270237	40	5.6	40	81	4	261	42	28	15	12	1.84
14277541--14277581	19	2.2	19	86	0	55	75	17	4	2	1.08
14278216--14278256	13	3.2	12	90	10	64	87	0	12	0	0.53
14278215--14278256	21	2.0	21	90	4	66	85	0	14	0	0.59
14278282--14278314	16	2.1	16	88	11	50	0	12	30	57	1.35
14289492--14289604	56	2.0	56	98	0	217	28	18	18	34	1.95
14295085--14295125	21	1.9	22	85	5	57	60	2	0	36	1.10
14298740--14298799	30	2.0	30	83	3	75	41	0	38	20	1.52
14299013--14299049	9	4.1	9	92	0	65	29	10	13	45	1.77
14299107--14299162	9	6.1	9	79	4	67	33	19	14	32	1.92
14299092--14299151	28	2.1	28	96	0	111	31	18	16	33	1.93
14299391--14299464	16	4.4	16	76	17	62	28	0	4	67	1.09
14300717--14300781	20	3.5	20	74	20	77	44	0	27	27	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
14301052--14301088	18	2.1	18	94	0	65	40	18	10	29	1.85
14311513--14311557	21	2.3	20	81	11	58	46	6	11	35	1.66
14312339--14312379	19	2.2	19	90	0	64	34	7	12	46	1.69
14315270--14315506	85	2.8	85	85	0	323	34	23	17	24	1.96
14315275--14315506	42	5.5	41	72	15	154	34	23	16	24	1.95
14320092--14320594	251	2.0	250	97	0	943	30	7	21	40	1.82
14322663--14322689	12	2.2	12	100	0	54	7	22	40	29	1.81
14323640--14323696	20	2.8	20	89	0	78	22	29	0	47	1.52
14328774--14328812	20	2.0	20	94	0	69	48	0	2	48	1.15
14328777--14328822	20	2.3	20	80	0	56	52	0	6	41	1.27

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