genome.fa.s1.2.7.7.80.10.50.1000.8.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  8  of  187  ( 22383 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)
2879723--2879761	14	2.7	14	80	4	51	25	2	2	69	1.14
2879872--2879903	2	16.0	2	93	0	55	53	0	0	46	1.00
2882043--2882079	16	2.3	16	100	0	74	59	24	10	5	1.52
2882043--2882085	16	2.6	16	92	3	59	60	23	9	6	1.51
2887955--2888131	46	3.8	46	91	0	300	37	9	23	29	1.86
2890693--2890740	23	2.1	23	88	7	71	31	0	12	56	1.37
2891043--2891082	19	2.1	19	86	9	55	40	7	0	52	1.30
2893422--2893488	24	2.6	25	81	9	82	46	16	5	31	1.71
2894474--2894502	2	14.5	2	100	0	58	51	0	0	48	1.00
2902776--2902807	14	2.1	16	88	11	50	31	0	6	62	1.20
2921733--2921924	93	2.1	93	87	5	273	34	22	11	31	1.90
2923387--2923421	17	2.1	17	89	10	54	28	0	0	71	0.86
2934471--2934549	17	4.7	17	74	14	67	50	5	1	43	1.32
2934455--2934554	50	2.1	47	81	10	121	51	4	4	41	1.39
2936971--2936996	5	5.2	5	100	0	52	42	19	19	19	1.90
2937443--2937489	17	2.8	17	79	20	62	55	6	2	36	1.37
2938022--2938056	9	3.9	9	92	0	61	31	11	14	42	1.81
2938112--2938142	9	3.4	9	90	0	53	38	22	12	25	1.90
2941422--2941469	11	4.5	11	72	27	50	50	0	2	47	1.12
2943170--2943236	27	2.5	27	82	4	82	41	8	4	44	1.56
2943294--2943360	27	2.5	27	92	4	109	26	29	28	14	1.96
2943405--2943538	4	34.0	4	76	14	86	69	0	28	2	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2943438--2943583	41	3.7	40	77	15	158	66	0	32	1	1.00
2943405--2943569	19	9.1	17	72	20	90	69	0	29	1	0.99
2943414--2943536	65	1.9	64	80	11	144	69	0	29	1	0.98
2943418--2943552	12	10.0	15	69	24	56	68	0	30	1	0.99
2943438--2943567	39	3.2	40	83	10	167	68	0	30	1	0.99
2943533--2943595	27	2.3	27	83	10	74	68	0	31	0	0.90
2943451--2943583	39	3.4	39	81	8	162	65	0	33	0	0.98
2943410--2943600	80	2.5	75	78	20	195	69	0	29	1	0.96
2944236--2944381	75	1.9	77	83	8	192	54	8	4	33	1.49
2947272--2947348	34	2.2	35	81	11	95	54	10	0	35	1.35
2947499--2947554	3	18.7	3	100	0	112	67	32	0	0	0.91
2947553--2947580	3	9.3	3	100	0	56	67	0	0	32	0.91
2947704--2947732	10	2.7	11	89	10	51	0	27	0	72	0.85
2947817--2947917	27	3.7	27	89	5	134	15	28	29	25	1.96
2947974--2948025	27	1.9	27	96	0	95	53	0	7	38	1.30
2947973--2948031	27	2.2	26	88	8	91	50	0	8	40	1.33
2953926--2953977	16	3.3	15	78	7	59	50	0	32	17	1.47
2953936--2953985	16	3.2	16	82	2	66	52	0	32	16	1.44
2954398--2954473	35	2.2	35	90	2	118	18	6	17	57	1.60
2959689--2959718	15	1.9	16	93	6	53	0	33	3	63	1.11
2962171--2962206	18	1.9	18	88	5	54	58	2	0	38	1.13
2962897--2962924	14	2.0	14	100	0	56	28	0	7	64	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2962917--2962979	19	3.4	17	82	10	63	34	0	3	61	1.12
2962919--2962980	18	3.3	19	82	11	74	32	0	3	64	1.09
2966885--2966933	25	1.9	25	83	4	62	40	0	4	55	1.19
2966929--2967003	7	11.0	7	78	12	68	45	1	12	41	1.49
2970536--2970575	19	2.1	19	85	4	53	60	2	2	35	1.24
2973669--2973870	100	2.0	100	99	0	395	27	20	14	37	1.92
2974358--2974409	21	2.5	21	77	0	59	34	34	5	25	1.80
2981686--2981716	15	2.1	15	100	0	62	51	0	0	48	1.00
2981961--2982021	26	2.3	26	88	0	86	70	4	0	24	1.07
2981991--2982031	19	2.0	21	90	9	68	68	0	0	31	0.90
2981971--2982023	26	2.0	26	96	0	97	71	0	0	28	0.86
2992766--2992817	2	26.0	2	100	0	104	0	50	0	50	1.00
2995354--2995384	3	10.7	3	93	6	55	29	0	0	70	0.87
2998031--2998086	22	2.6	22	75	10	62	58	0	1	39	1.08
2998031--2998085	15	3.7	15	78	7	51	60	0	1	38	1.08
2998046--2998092	21	2.2	22	84	3	60	68	0	2	29	1.02
2998046--2998093	23	2.2	22	77	7	53	68	0	2	29	1.01
3003357--3003383	13	2.1	13	100	0	54	77	7	0	14	0.97
3006791--3006832	22	2.0	20	86	9	57	47	0	7	45	1.30
3010451--3010479	2	14.5	2	100	0	58	51	0	0	48	1.00
3012084--3012117	16	2.1	16	88	0	50	35	2	35	26	1.72
3017497--3017532	18	2.0	18	100	0	72	38	11	16	33	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3022466--3022510	2	22.0	2	95	4	81	48	0	48	2	1.13
3031316--3031374	30	2.0	29	86	3	82	59	5	0	35	1.20
3031358--3031408	25	2.1	24	92	3	84	64	0	0	35	0.94
3031600--3031652	20	2.7	20	85	8	72	28	0	5	66	1.15
3031599--3031645	19	2.3	22	82	14	64	23	0	6	70	1.10
3039976--3040054	31	2.5	32	76	13	76	50	3	5	40	1.42
3040340--3040402	31	2.0	31	90	6	101	47	3	7	41	1.48
3044324--3044389	30	2.2	31	83	8	82	43	10	7	37	1.68
3044798--3044911	58	2.0	58	92	0	192	33	14	17	34	1.91
3051589--3051630	21	2.0	20	82	13	50	40	7	0	52	1.29
3055364--3055393	15	2.1	15	93	6	53	43	6	0	50	1.28
3073267--3073419	22	7.0	22	90	0	225	26	26	14	32	1.94
3078795--3078821	9	3.0	9	100	0	54	44	0	0	55	0.99
3081576--3081643	31	2.2	32	78	7	77	41	0	5	52	1.25
3083236--3083292	3	19.0	3	92	0	96	63	0	1	35	1.05
3090284--3090336	26	2.0	27	81	7	63	37	1	1	58	1.20
3097057--3097132	21	3.6	21	92	0	125	23	9	36	30	1.86
3097050--3097104	21	2.3	27	64	35	68	20	10	40	29	1.86
3097244--3097299	18	3.1	18	72	23	55	55	3	1	39	1.28
3101155--3101199	20	2.2	21	88	11	67	42	2	0	55	1.12
3108930--3108969	21	2.0	19	85	9	53	57	7	2	32	1.40
3112190--3112223	4	8.5	4	93	0	50	44	26	5	23	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3114124--3114151	12	2.3	12	100	0	56	42	28	17	10	1.83
3114265--3114292	12	2.3	12	100	0	56	42	28	17	10	1.83
3114048--3114326	141	2.0	141	99	0	549	30	20	13	35	1.91
3119427--3119458	12	2.4	14	90	10	50	71	0	3	25	1.00
3123456--3123531	26	2.8	26	84	11	100	51	43	0	5	1.24
3123458--3123543	6	14.5	6	73	21	58	51	44	0	4	1.22
3123456--3123534	29	2.9	26	87	9	106	51	43	0	5	1.23
3123488--3123549	11	5.5	11	75	19	56	50	43	0	6	1.28
3124948--3125018	28	2.7	26	82	10	90	28	7	2	61	1.36
3124911--3125028	28	4.1	27	72	16	87	29	9	2	58	1.43
3125076--3125160	26	3.3	26	78	6	84	28	8	4	58	1.47
3128478--3128521	22	2.0	22	100	0	88	18	36	18	27	1.94
3144013--3144085	29	2.5	30	82	6	87	41	15	15	28	1.87
3150801--3150844	17	2.6	17	82	10	56	54	20	4	20	1.62
3152997--3153024	2	14.0	2	100	0	56	50	0	0	50	1.00
3162250--3162290	18	2.2	18	87	12	57	24	2	7	65	1.30
3166238--3166263	5	5.2	5	100	0	52	61	0	38	0	0.96
3170821--3170918	49	2.0	50	88	8	146	40	5	1	53	1.30
3170834--3170939	49	2.2	48	81	8	124	40	7	1	50	1.42
3175882--3175921	21	1.9	21	84	0	53	27	22	5	45	1.73
3177197--3177249	20	2.7	20	80	14	56	37	0	0	62	0.96
3177783--3177824	2	21.0	2	100	0	84	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3183563--3183614	3	17.3	3	100	0	104	67	0	0	32	0.91
3185560--3185634	33	2.3	33	81	4	89	38	17	16	28	1.91
3188323--3188529	46	4.6	46	94	1	332	33	14	23	28	1.94
3188323--3188529	91	2.3	91	91	3	330	33	14	23	28	1.94
3191830--3191991	81	2.0	81	100	0	324	30	14	23	30	1.95
3194079--3194111	2	16.5	2	100	0	66	51	0	0	48	1.00
3194192--3194238	19	2.5	19	82	10	60	53	0	6	40	1.27
3204081--3204125	23	1.9	24	82	13	58	35	8	28	26	1.87
3205359--3205401	2	21.5	2	100	0	86	51	0	0	48	1.00
3205962--3205986	4	6.2	4	100	0	50	0	0	24	76	0.80

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