genome.fa.s9.2.7.7.80.10.50.1000.7.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  7  of  226  ( 27023 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)
2809518--2809570	13	4.1	13	76	9	54	41	20	3	33	1.70
2809518--2809567	26	1.9	26	84	8	66	40	20	4	36	1.71
2817611--2817697	43	2.0	43	100	0	174	48	12	4	34	1.62
2817800--2817847	17	2.8	17	81	15	55	60	12	0	27	1.32
2820974--2820998	4	6.2	4	100	0	50	48	0	0	52	1.00
2834790--2834822	14	2.4	14	89	0	57	6	18	0	75	1.00
2836729--2836753	3	8.3	3	100	0	50	32	0	0	68	0.90
2853522--2853583	31	2.0	32	87	3	90	32	11	20	35	1.88
2853424--2853642	90	2.4	91	77	4	228	39	11	17	31	1.86
2857212--2857243	14	2.3	14	94	0	55	15	15	15	53	1.74
2861745--2861776	14	2.3	14	94	0	55	15	15	15	53	1.74
2864090--2864121	15	2.1	15	94	0	55	12	6	43	37	1.68
2864095--2864128	15	2.3	15	94	0	59	8	2	50	38	1.49
2864151--2864191	21	2.0	21	90	0	64	17	4	56	21	1.60
2868705--2868774	22	3.5	20	70	12	63	32	0	4	62	1.14
2869154--2869203	26	1.9	26	91	0	82	52	2	2	44	1.24
2869350--2869398	20	2.3	21	75	6	55	36	0	2	61	1.08
2893449--2893561	55	2.1	55	100	0	226	52	11	19	16	1.74
2902981--2903054	18	3.9	18	71	13	60	40	2	1	55	1.22
2902981--2903050	13	5.5	13	77	13	65	40	2	1	55	1.23
2903220--2903259	14	2.9	14	82	14	55	37	5	12	45	1.64
2903228--2903293	34	1.9	34	90	6	107	34	7	10	46	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2904232--2904376	73	2.0	72	91	4	238	24	20	16	38	1.92
2904233--2904377	37	4.0	37	91	3	233	24	20	16	37	1.93
2904341--2904702	46	7.6	46	77	15	333	27	22	14	36	1.92
2904358--2904702	98	3.6	97	80	11	447	28	22	14	35	1.93
2918604--2918643	20	2.0	20	90	0	62	27	10	12	50	1.72
2918589--2918655	34	1.9	35	90	3	109	31	8	13	46	1.74
2918583--2918659	14	5.0	15	71	20	52	33	9	14	42	1.77
2920647--2921073	215	2.0	210	94	2	737	30	14	17	37	1.90
2924454--2924485	2	16.0	2	100	0	64	0	50	0	50	1.00
2928627--2928662	2	18.0	2	100	0	72	50	0	0	50	1.00
2930416--2930454	20	1.9	21	94	5	71	33	0	0	66	0.92
2930417--2930461	20	2.2	21	88	4	65	33	0	2	64	1.06
2931651--2931681	2	15.5	2	93	0	53	54	0	45	0	0.99
2948975--2949000	2	13.0	2	100	0	52	50	50	0	0	1.00
2959651--2959715	28	2.3	27	84	12	78	32	1	1	64	1.12
2960999--2961033	15	2.3	15	85	0	52	42	0	0	57	0.99
2961043--2961082	19	2.1	19	95	0	71	40	15	2	42	1.60
2962758--2962827	31	2.3	31	85	2	97	45	2	5	45	1.41
2967843--2967877	18	1.9	18	88	0	52	62	5	0	31	1.18
2991235--2991303	33	2.1	34	97	2	131	36	14	13	36	1.85
3006561--3006608	15	2.9	17	72	12	55	47	6	6	39	1.54
3011391--3011588	67	3.0	67	97	0	369	28	33	17	20	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3018209--3018238	2	15.5	2	93	6	53	46	0	0	53	1.00
3019950--3020002	20	2.7	21	80	8	51	47	1	0	50	1.12
3037401--3037434	15	2.1	16	89	10	52	58	0	0	41	0.98
3047410--3047443	17	1.9	18	88	5	52	61	8	11	17	1.54
3058205--3058287	21	4.0	21	83	0	112	15	22	15	45	1.84
3060090--3060220	61	2.1	61	80	5	149	35	7	17	39	1.78
3060331--3060473	41	3.5	41	90	0	232	31	19	18	30	1.96
3060331--3060516	82	2.3	82	84	3	241	30	20	19	29	1.97
3063714--3063757	23	1.9	22	82	17	54	36	25	0	38	1.56
3063803--3063890	45	2.0	45	86	0	122	34	20	17	28	1.95
3063892--3064087	51	3.9	50	84	4	268	30	28	17	23	1.97
3063899--3064083	101	1.8	101	92	3	318	30	27	17	23	1.97
3067275--3067330	23	2.4	23	87	0	76	26	7	21	44	1.78
3089149--3089198	25	2.0	25	84	7	66	60	0	0	40	0.97
3091857--3091902	20	2.4	19	82	13	58	32	2	0	65	1.05
3096226--3096370	47	3.1	47	73	16	158	43	2	4	50	1.33
3096211--3096426	91	2.4	91	88	0	324	45	3	4	46	1.40
3096424--3096964	121	4.5	121	97	1	1000	43	2	4	48	1.38
3096424--3096964	241	2.2	241	96	1	998	43	2	4	48	1.38
3096916--3096950	18	2.0	17	88	5	52	45	0	0	54	0.99
3097096--3097204	45	2.6	40	77	8	103	32	26	4	36	1.77
3098086--3098112	5	5.4	5	100	0	54	22	0	22	55	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3108764--3108819	24	2.3	24	96	0	103	66	0	0	33	0.92
3110872--3110897	12	2.2	12	100	0	52	57	0	15	26	1.38
3123363--3123398	2	18.0	2	94	0	63	52	0	47	0	1.00
3125729--3125772	23	2.0	23	86	4	63	45	9	4	40	1.56
3128137--3128169	15	2.3	15	90	10	52	9	6	9	75	1.18
3140504--3140650	75	2.0	75	93	0	249	25	16	17	40	1.90
3148825--3148872	22	2.2	21	85	3	60	35	2	0	62	1.07
3148841--3148881	21	2.1	19	90	9	64	29	0	0	70	0.87
3156223--3156468	46	5.6	46	85	9	336	32	16	23	27	1.96
3156361--3156432	37	1.9	37	100	0	144	30	15	26	27	1.96
3156315--3156468	83	1.9	81	94	2	272	31	15	24	27	1.96
3157077--3157144	26	2.5	27	77	15	70	33	8	5	51	1.57
3161870--3161920	24	2.2	24	77	22	56	33	0	5	60	1.21
3170308--3170340	17	1.9	17	100	0	66	18	18	6	57	1.60
3190858--3190903	21	2.2	21	84	7	58	50	0	0	50	1.00
3191138--3191174	2	19.0	2	88	5	58	48	2	0	48	1.15
3192893--3192931	18	2.2	18	86	9	53	43	17	0	38	1.50
3207659--3207704	20	2.3	20	85	7	58	28	4	17	50	1.65
3209286--3209319	14	2.5	14	90	4	52	58	11	0	29	1.33
3211729--3211781	11	4.7	12	81	6	58	47	1	28	22	1.62
3211734--3211783	22	2.3	22	87	12	77	52	2	28	18	1.56
3218025--3218070	24	2.0	24	82	4	58	45	2	4	47	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3218471--3218496	6	4.3	6	100	0	52	19	30	19	30	1.96
3223788--3223857	29	2.4	31	83	9	92	62	0	2	34	1.10
3223851--3223884	17	2.0	17	100	0	68	64	0	0	35	0.94
3223852--3223890	17	2.2	17	90	4	60	69	0	0	30	0.89
3232084--3232358	125	2.2	124	89	1	415	32	23	15	28	1.95
3233476--3233667	10	20.0	9	72	17	88	63	1	3	31	1.21
3233476--3233667	19	10.0	18	69	19	88	63	1	3	31	1.21
3234420--3234450	3	10.3	3	100	0	62	32	0	0	67	0.91
3252602--3252647	24	1.9	24	86	0	65	39	6	6	47	1.55
3262264--3262293	15	1.9	16	93	6	53	33	0	0	66	0.92
3263136--3263193	30	1.9	30	82	0	71	37	13	0	48	1.43
3269589--3269655	33	2.0	34	94	2	118	28	20	4	46	1.70
3281139--3281191	24	2.2	24	100	0	106	18	11	22	47	1.81
3281251--3281315	24	2.8	24	88	2	96	24	10	21	43	1.84
3283525--3284715	594	2.0	594	90	1	1870	31	14	19	34	1.91
3287403--3287476	33	2.2	33	82	0	85	24	20	17	37	1.93
3292139--3292168	15	2.0	15	100	0	60	53	6	33	6	1.53
3301040--3301095	9	6.1	9	72	12	51	42	3	1	51	1.29
3301040--3301106	7	7.9	8	76	23	50	47	2	1	47	1.26
3306562--3306594	12	2.8	12	86	4	50	54	0	0	45	0.99
3312630--3312760	64	2.0	65	92	4	221	39	16	16	27	1.90
3314363--3314399	18	2.1	17	90	5	56	24	5	0	70	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3316039--3316083	19	2.4	19	88	7	65	42	0	13	44	1.43
3316164--3316319	46	3.5	46	95	2	273	33	16	23	27	1.95
3317507--3317545	16	2.4	16	100	0	78	12	25	41	20	1.88
3318325--3318370	5	9.4	5	97	2	85	41	0	0	58	0.98
3319276--3319411	40	3.5	40	71	9	118	25	16	23	33	1.96
3325488--3325680	49	3.9	49	95	0	323	23	15	30	31	1.95
3333644--3333836	49	3.9	49	95	0	323	23	15	30	31	1.95
3339991--3340028	20	1.9	20	88	0	58	42	7	5	44	1.56
3346041--3346096	2	28.0	2	85	0	76	50	3	3	42	1.37
3355703--3355780	38	2.1	38	100	0	156	56	7	17	17	1.64

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   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226