genome.fa.s6.2.7.7.80.10.50.1000.10.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  10  of  168  ( 20060 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)
2861205--2861306	43	2.4	43	84	0	132	45	14	7	32	1.74
2866613--2866657	18	2.7	16	80	12	54	11	15	0	73	1.10
2866622--2866681	12	4.8	12	75	6	57	15	11	0	73	1.10
2866622--2866680	18	3.2	18	77	13	50	15	10	0	74	1.06
2868481--2868535	20	2.8	20	74	15	62	47	0	1	50	1.11
2868491--2868590	35	2.9	33	78	11	103	48	0	5	47	1.24
2868482--2868578	24	4.1	23	72	23	62	47	0	4	48	1.21
2870767--2870820	22	2.5	21	84	3	72	16	16	18	48	1.82
2881417--2881447	12	2.6	12	94	0	53	0	25	3	70	1.02
2881474--2881517	18	2.5	18	85	10	56	38	9	0	52	1.33
2881953--2882022	12	5.8	11	70	17	50	55	2	4	37	1.34
2885489--2885572	35	2.4	36	84	8	109	38	1	13	47	1.50
2885484--2885601	35	3.3	34	75	17	98	37	0	15	46	1.52
2885559--2885723	28	5.7	28	66	19	79	31	3	20	45	1.66
2886145--2886179	18	1.9	18	88	0	52	40	14	5	40	1.69
2886693--2886735	22	2.0	22	95	0	77	25	11	30	32	1.91
2888278--2888393	61	1.9	58	86	11	164	43	5	5	46	1.48
2888212--2888352	68	2.1	67	79	10	144	43	3	4	48	1.39
2891037--2891084	24	2.0	24	100	0	96	37	4	12	45	1.61
2891789--2891857	27	2.6	27	88	9	97	13	21	36	28	1.91
2893921--2894004	42	2.0	42	95	0	150	50	13	1	35	1.49
2896376--2896420	22	2.0	23	87	8	67	13	17	6	62	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2900132--2900158	6	4.5	6	100	0	54	33	37	0	29	1.58
2901136--2901346	107	2.0	107	89	0	323	28	19	18	32	1.96
2904249--2904290	16	2.5	17	82	14	52	30	2	0	66	1.04
2908061--2908140	32	2.5	33	82	10	103	18	20	20	41	1.91
2910309--2910350	22	1.9	22	90	0	66	23	2	11	61	1.42
2913881--2914272	116	3.4	114	74	9	345	31	17	17	32	1.94
2919398--2919473	38	2.0	39	94	2	136	35	10	14	39	1.81
2926572--2926611	18	2.2	19	86	4	55	65	2	2	30	1.19
2940604--2940653	25	1.9	25	84	15	66	78	6	8	8	1.11
2941244--2941386	43	3.4	42	83	9	164	22	20	29	27	1.99
2941267--2941578	43	7.3	43	80	5	238	26	28	21	22	1.99
2941374--2941620	86	2.9	86	84	0	287	29	30	17	22	1.97
2941310--2941620	43	7.2	43	80	2	223	28	29	19	22	1.98
2941374--2941620	129	1.9	129	82	1	307	29	30	17	22	1.97
2941928--2941999	21	3.4	21	78	0	81	9	43	13	33	1.77
2941984--2942032	21	2.3	21	78	0	53	6	38	20	34	1.77
2941996--2942040	21	2.1	21	87	0	63	4	37	17	40	1.70
2942011--2942176	66	2.5	66	87	3	219	13	28	19	39	1.89
2947577--2947797	9	26.3	9	66	18	120	32	2	19	46	1.62
2947637--2947797	25	6.4	25	77	5	148	34	1	18	45	1.60
2947599--2947797	16	11.9	17	68	18	82	33	2	18	46	1.60
2947635--2947797	75	2.2	74	93	4	274	34	1	17	46	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2947937--2947994	26	2.3	25	82	8	64	27	1	18	51	1.56
2948186--2948274	18	4.8	18	79	14	101	41	0	12	46	1.41
2948190--2948423	39	6.0	37	75	13	177	41	2	11	44	1.52
2948188--2948292	31	3.5	31	71	21	100	42	0	13	43	1.43
2948315--2948406	13	6.9	13	71	18	73	42	3	8	45	1.51
2948300--2948423	40	3.1	39	85	5	151	40	3	10	45	1.54
2948441--2948473	10	3.1	11	86	8	50	36	21	9	33	1.85
2951845--2951975	7	18.0	7	71	16	70	32	45	0	21	1.58
2951846--2951954	14	7.4	15	80	7	107	31	46	0	21	1.57
2951846--2951947	29	3.4	30	82	5	127	31	46	0	21	1.58
2951846--2951972	29	4.3	29	80	5	121	31	46	0	21	1.57
2952651--2952693	18	2.3	19	92	4	70	16	2	2	79	0.95
2952651--2952693	19	2.3	18	88	4	59	16	2	2	79	0.95
2952823--2952863	18	2.2	19	86	4	57	51	17	0	31	1.46
2953995--2954190	41	4.8	41	83	6	216	32	26	20	20	1.97
2954230--2954364	39	3.5	39	80	5	148	18	20	22	37	1.94
2955756--2955787	7	4.6	7	100	0	64	59	0	0	40	0.97
2960870--2960912	21	2.0	22	86	13	63	44	0	13	41	1.44
2960870--2960913	20	2.1	21	84	12	56	45	0	13	40	1.44
2960944--2960988	2	22.5	2	100	0	90	48	0	0	51	1.00
2961042--2961119	41	1.9	41	84	5	104	21	17	26	33	1.96
2964298--2964329	7	4.6	7	96	0	55	65	3	0	31	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2966661--2966717	23	2.5	23	85	5	71	50	26	14	8	1.71
2966661--2966731	23	3.1	23	83	0	70	49	25	16	8	1.74
2966728--2966790	25	2.5	25	77	10	65	42	12	20	23	1.86
2981717--2981850	57	2.3	56	82	7	144	50	3	0	44	1.25
2982075--2982120	23	2.0	23	95	0	83	52	10	0	36	1.37
2993915--2994111	50	3.9	50	79	12	204	27	20	27	23	1.99
2996697--2996749	21	2.5	22	78	12	56	45	5	13	35	1.67
2996916--2996944	13	2.2	13	100	0	58	17	13	24	44	1.85
2997710--2997739	16	1.9	15	93	6	51	36	3	6	53	1.44
2997675--2997786	56	2.0	56	98	0	215	34	5	10	49	1.61
2998328--2998552	103	2.2	102	91	4	355	54	3	1	40	1.26
2998454--2998536	44	1.9	44	85	4	116	61	1	0	37	1.04
2998520--2998582	30	2.1	30	100	0	126	50	6	0	42	1.27
2998417--2998679	133	2.0	133	93	3	449	54	3	0	41	1.24
2998520--2998598	30	2.6	30	90	4	97	54	6	0	39	1.26
2998588--2998674	40	2.2	37	77	20	95	56	2	1	40	1.19
3008603--3008643	20	2.1	20	86	4	57	51	4	2	41	1.36
3011316--3011369	18	2.9	18	86	2	72	11	1	46	40	1.50
3014650--3014722	19	3.8	19	94	0	128	35	9	16	38	1.81
3014664--3014745	19	4.0	22	88	6	86	36	7	17	39	1.77
3023000--3023029	15	1.9	16	93	6	53	43	0	10	46	1.37
3029033--3029104	34	2.1	34	82	5	83	44	16	12	26	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3031434--3032086	330	2.0	326	93	3	1123	41	8	22	26	1.83
3034831--3034866	16	2.2	16	95	0	63	50	8	2	38	1.47
3035038--3035082	3	15.0	3	100	0	90	66	0	0	33	0.92
3037177--3037217	19	2.2	19	87	12	59	56	0	4	39	1.21
3046677--3047195	147	3.5	147	97	0	966	23	22	21	32	1.98
3047438--3047476	14	3.0	12	85	14	51	33	0	2	64	1.08
3047439--3047468	14	2.1	14	100	0	60	36	0	0	63	0.95
3052279--3052320	19	2.2	19	86	0	57	50	0	2	47	1.14
3055449--3055594	45	3.0	45	65	16	112	41	4	32	21	1.72
3055438--3055620	99	1.8	99	86	6	264	41	4	32	21	1.73
3058859--3058899	2	20.5	2	84	0	55	48	4	0	46	1.23
3059508--3059561	19	2.9	17	76	13	54	62	1	7	27	1.32
3061974--3062137	43	3.8	43	80	7	156	20	20	26	32	1.97
3061993--3062157	86	1.9	86	82	4	208	21	21	24	32	1.98
3062125--3062331	89	2.4	89	83	11	250	29	30	19	20	1.97
3062125--3062330	43	4.7	42	84	10	238	29	30	19	20	1.97
3068833--3068868	18	2.0	18	94	0	63	33	0	13	52	1.41
3069013--3069223	16	13.1	16	70	24	92	37	1	16	44	1.58
3069012--3069066	25	2.2	25	84	12	69	32	0	23	43	1.54
3069012--3069293	9	31.6	9	71	17	112	38	2	14	44	1.58
3069029--3069288	81	3.2	81	100	0	520	38	2	14	44	1.58
3069126--3069587	65	6.9	64	82	11	516	41	2	10	45	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3069207--3069587	130	2.9	129	91	2	602	41	2	9	45	1.51
3069207--3069587	195	2.0	195	88	3	579	41	2	9	45	1.51
3069548--3069632	25	3.7	25	69	26	87	42	1	8	48	1.40
3069538--3069621	43	2.0	43	92	0	141	41	1	9	47	1.44
3073082--3073406	115	2.9	112	84	6	431	31	24	20	23	1.98
3076281--3076318	18	2.2	17	90	9	60	42	0	5	52	1.24
3082829--3082874	22	2.1	22	100	0	92	45	13	13	28	1.80
3082639--3083040	212	1.9	212	98	0	786	28	18	15	37	1.92
3083821--3083850	13	2.2	14	94	5	53	70	0	6	23	1.11
3086035--3086072	2	19.0	2	94	0	67	52	0	0	47	1.00

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