genome.fa.s4.2.7.7.80.10.50.1000.166.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  166  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)
52137264--52137298	18	1.9	18	94	0	61	14	22	42	20	1.88
52138119--52138144	13	2.0	13	100	0	52	38	7	15	38	1.76
52139776--52139821	4	12.2	4	86	4	53	73	0	2	23	0.94
52139803--52139846	12	3.7	11	82	14	52	65	0	4	29	1.12
52147232--52147264	13	2.4	14	85	10	50	15	15	15	54	1.71
52148099--52148147	17	2.8	18	85	11	66	63	4	0	32	1.13
52148100--52148150	18	2.8	18	88	8	68	64	3	0	31	1.11
52150678--52150760	41	2.0	41	100	0	166	32	12	19	36	1.88
52151863--52151917	19	2.7	21	91	5	87	40	10	12	36	1.79
52153483--52153507	7	3.6	7	100	0	50	72	0	16	12	1.13
52157745--52157787	21	2.0	22	90	4	70	44	34	4	16	1.68
52166065--52166258	101	1.9	99	89	4	293	32	5	12	48	1.64
52176247--52176647	109	3.7	109	89	2	560	35	18	16	29	1.93
52177363--52177455	41	2.3	39	76	18	93	47	1	10	40	1.45
52177571--52177613	3	14.0	3	85	4	59	62	2	2	32	1.20
52178662--52178736	20	3.8	20	70	20	59	54	0	9	36	1.33
52183198--52183237	19	2.3	17	87	12	55	25	0	0	75	0.81
52184395--52184442	13	3.6	14	80	11	55	14	12	16	56	1.68
52193273--52193307	18	2.1	16	89	10	52	22	8	0	68	1.16
52204065--52204109	16	2.7	17	86	6	65	46	8	0	44	1.34
52204139--52204193	27	2.0	27	96	0	101	43	9	5	41	1.59
52206675--52206759	31	2.8	30	78	5	100	40	14	10	35	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52217049--52217695	132	4.9	132	94	0	1109	28	19	23	28	1.98
52217396--52217590	44	4.4	45	68	15	111	31	16	24	28	1.96
52219113--52219192	2	41.0	2	73	9	58	41	5	2	51	1.37
52219486--52219515	4	7.2	4	92	7	51	23	3	0	73	0.98
52219828--52220024	98	2.0	98	93	0	340	29	10	23	37	1.88
52222360--52222399	2	20.0	2	100	0	80	50	0	0	50	1.00
52223420--52223452	13	2.5	13	90	0	57	66	0	18	15	1.25
52223840--52223864	13	1.9	13	100	0	50	12	24	8	56	1.62
52226018--52226057	2	21.0	2	85	10	57	45	0	0	55	0.99
52227823--52228084	132	2.0	131	94	0	461	28	19	25	27	1.99
52227899--52228083	44	4.2	44	63	10	117	27	20	24	28	1.99
52228102--52228201	45	2.2	45	83	11	118	27	19	30	24	1.98
52228176--52228287	44	2.5	44	82	5	138	30	22	19	27	1.98
52228178--52228415	128	1.9	128	85	3	336	29	22	21	27	1.99
52230310--52230423	60	1.9	61	82	8	144	32	11	1	54	1.46
52232294--52232319	13	2.0	13	100	0	52	30	7	15	46	1.74
52232350--52232391	19	2.2	19	83	8	50	28	21	9	40	1.84
52233823--52233866	22	2.0	22	100	0	88	36	27	13	22	1.92
52234287--52234328	21	2.0	21	90	0	66	11	11	7	69	1.37
52235227--52235271	22	2.1	21	84	12	56	66	0	20	13	1.24
52236540--52237204	89	7.5	89	92	0	1010	32	16	22	27	1.96
52237200--52237498	132	2.3	132	95	0	537	29	19	23	27	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52237198--52237499	44	6.9	44	65	13	174	29	19	23	26	1.98
52237511--52237616	45	2.4	45	84	10	130	28	16	32	22	1.96
52237590--52237834	44	5.7	44	73	12	161	29	21	22	26	1.99
52237589--52237840	128	2.0	129	83	5	323	29	21	22	26	1.99
52239792--52239852	28	2.3	26	80	5	68	32	9	1	55	1.42
52239906--52239963	21	2.8	21	78	0	71	43	5	3	48	1.42
52252932--52252986	3	18.3	3	100	0	110	34	0	0	65	0.93
52253050--52253081	6	5.3	6	96	0	55	18	0	0	81	0.70
52253284--52253334	21	2.4	21	73	17	52	56	1	3	37	1.29
52254704--52254737	14	2.2	16	90	10	54	64	0	0	35	0.94
52257066--52257132	22	3.1	21	78	20	75	44	14	20	19	1.86
52258266--52258342	37	2.1	37	100	0	154	24	22	2	50	1.61
52259025--52259112	43	2.0	43	97	0	167	30	14	14	39	1.87
52262731--52262773	23	1.9	23	86	13	63	37	0	32	30	1.58
52270474--52270526	21	2.5	22	78	9	56	7	22	0	69	1.13
52276977--52277019	14	3.3	14	81	12	56	46	11	6	34	1.67
52277087--52277156	23	3.0	23	79	4	95	42	24	14	18	1.87
52277656--52277689	13	2.7	13	86	4	52	61	8	5	23	1.47
52279387--52279438	14	3.7	14	84	0	68	46	32	0	21	1.52
52279565--52279634	22	3.2	21	76	11	61	37	31	1	30	1.66
52279645--52279693	14	3.4	14	86	5	71	40	36	0	22	1.54
52280043--52280163	42	2.9	41	90	2	170	29	29	19	20	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52286763--52286796	18	2.0	18	88	11	54	29	0	5	64	1.17
52294760--52294789	14	2.1	14	100	0	60	13	33	20	33	1.91
52301889--52301926	19	2.1	18	85	9	51	0	13	23	63	1.30
52303742--52303874	41	3.2	41	92	0	212	29	24	21	24	1.99
52305514--52305565	28	1.9	26	92	7	86	46	7	0	46	1.31
52305901--52306310	44	9.5	43	69	12	162	27	25	18	28	1.98
52305895--52306374	173	2.8	173	88	1	694	27	25	18	28	1.98
52324366--52324427	32	2.0	31	93	3	106	38	6	22	32	1.80
52339881--52339906	13	2.0	13	100	0	52	30	7	15	46	1.74
52342717--52342827	28	4.0	28	87	0	150	47	19	21	10	1.80
52342721--52342827	56	1.9	56	90	0	169	46	20	21	11	1.81
52343571--52343686	58	2.0	59	86	1	162	46	6	18	27	1.75
52348851--52348891	21	2.0	21	95	0	73	19	12	14	53	1.72
52353003--52353159	43	3.7	41	80	10	183	22	19	28	29	1.98
52353004--52353159	84	1.9	84	85	8	219	22	18	28	30	1.97
52354061--52354102	2	21.5	2	95	4	77	50	0	0	50	1.00
52367650--52367760	50	2.2	50	98	0	213	20	33	21	24	1.97
52367855--52367884	13	2.3	13	94	0	51	50	13	3	33	1.58
52369171--52369538	124	3.0	124	89	0	547	32	22	14	30	1.94
52369900--52369924	13	1.9	13	100	0	50	64	0	0	36	0.94
52369892--52369936	22	2.0	22	83	8	56	57	0	0	42	0.98
52376731--52376804	10	7.3	10	74	18	64	67	0	1	31	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52376672--52376785	11	10.9	11	73	16	66	58	0	3	37	1.15
52376740--52376835	41	2.3	41	90	1	147	62	0	4	33	1.14
52376678--52376817	62	2.3	62	79	10	153	62	0	4	33	1.15
52376672--52376826	52	3.0	52	80	13	176	59	0	4	36	1.18
52376766--52376838	19	3.7	19	73	10	74	58	0	4	36	1.17
52378975--52379033	22	2.7	21	75	10	55	44	15	5	35	1.68
52388074--52388332	50	5.2	50	71	1	223	26	25	19	28	1.99
52388074--52388387	100	3.1	100	92	0	504	25	25	20	29	1.99
52388108--52388382	50	5.5	51	71	3	218	25	25	20	28	1.99
52400815--52400891	7	11.6	7	69	22	51	70	0	2	27	1.01
52400838--52400884	18	2.7	18	77	12	53	72	0	2	25	0.96
52400815--52400891	19	4.2	18	79	17	88	70	0	2	27	1.01
52405204--52405235	3	10.7	3	100	0	64	68	0	0	31	0.90
52414519--52414636	57	2.1	57	96	0	218	33	12	19	33	1.90
52424125--52424182	29	2.0	30	82	3	73	34	6	10	48	1.64
52424683--52424738	22	2.5	23	76	21	57	17	0	25	57	1.41
52424667--52424714	23	2.0	24	84	8	62	16	2	22	58	1.49
52455736--52455777	12	3.5	12	80	0	57	14	19	14	52	1.75
52457399--52457424	12	2.2	12	100	0	52	23	46	0	30	1.53
52461648--52461703	28	2.0	28	85	0	76	12	35	16	35	1.86
52468032--52469058	132	7.8	132	92	0	1651	25	24	19	29	1.98
52468082--52469057	44	22.2	44	64	9	299	25	24	19	29	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52495673--52495750	40	1.9	42	84	5	106	21	25	26	25	2.00
52496263--52496516	97	2.6	97	93	1	420	40	17	1	40	1.61
52500870--52500910	21	1.9	21	85	5	55	41	12	14	31	1.83
52501047--52501099	21	2.5	21	79	11	63	47	15	11	26	1.79
52508293--52508374	42	2.0	42	88	4	123	41	10	2	45	1.53
52508483--52508536	17	3.3	17	75	19	69	46	9	5	38	1.59
52508481--52508550	32	2.2	32	89	2	115	45	8	5	40	1.58
52508481--52508529	15	3.1	15	76	21	55	46	8	6	38	1.58
52509231--52509282	24	2.2	24	89	0	77	38	3	5	51	1.44
52512463--52513048	196	3.0	195	92	1	958	31	17	21	29	1.96

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