genome.fa.s13.2.7.7.80.10.50.1000.10.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   

This is table  10  of  199  ( 23770 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)
3244825--3244885	3	20.3	3	100	0	122	67	0	0	32	0.91
3245729--3245766	6	6.2	6	82	17	51	81	2	2	13	0.90
3245729--3245766	19	2.1	18	85	14	51	81	2	2	13	0.90
3246507--3246535	5	5.8	5	100	0	58	41	0	0	58	0.98
3246875--3246938	29	2.2	29	83	5	76	43	3	1	51	1.26
3247099--3247138	16	2.4	17	83	4	55	47	2	0	50	1.14
3249654--3249855	21	9.7	21	87	4	232	21	60	6	11	1.53
3249654--3249855	63	3.2	62	86	8	259	21	60	6	11	1.53
3249656--3249881	21	10.5	21	83	9	217	21	61	6	11	1.51
3249823--3249909	27	3.2	27	83	3	86	24	62	5	8	1.45
3249877--3249928	21	2.5	21	83	0	59	26	53	7	11	1.63
3253320--3253415	21	4.6	20	76	7	84	19	62	5	12	1.48
3253320--3253415	42	2.3	41	83	3	120	19	62	5	12	1.48
3256347--3256387	21	2.0	21	85	0	55	46	19	17	17	1.85
3257708--3257950	50	4.8	50	91	0	378	20	30	22	25	1.98
3259162--3259248	42	2.1	41	87	6	122	48	19	17	14	1.81
3261782--3261827	13	3.4	14	79	11	51	23	8	10	56	1.61
3267008--3267069	29	2.2	27	80	5	79	24	12	9	53	1.69
3267149--3267183	18	1.9	18	88	0	52	51	14	2	31	1.57
3270371--3270443	26	2.8	26	85	2	94	17	24	23	34	1.96
3271223--3271570	88	4.0	88	85	1	423	27	26	25	20	1.99
3271704--3271795	44	2.1	45	85	2	123	31	19	23	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3272160--3272186	13	2.1	13	100	0	54	37	18	22	22	1.95
3272729--3272784	27	2.1	27	96	0	103	17	16	26	39	1.91
3275346--3275375	2	15.0	2	100	0	60	50	0	0	50	1.00
3286422--3286471	14	3.7	13	78	19	57	56	2	6	36	1.36
3289879--3289935	23	2.4	23	80	11	71	57	1	1	38	1.19
3294354--3294760	218	1.9	212	87	7	597	29	16	23	30	1.96
3304077--3304107	2	15.5	2	100	0	62	48	0	0	51	1.00
3308109--3308200	37	2.5	37	85	0	130	31	9	20	38	1.85
3313547--3313592	19	2.4	19	85	3	56	60	4	4	30	1.35
3314119--3314163	18	2.3	20	85	14	60	42	0	0	57	0.98
3317617--3317656	20	2.0	20	95	0	71	70	2	0	27	1.01
3325015--3325045	16	1.9	16	93	0	53	41	22	0	35	1.54
3325815--3325998	42	4.3	42	79	4	190	38	21	17	23	1.93
3325833--3326020	42	4.4	42	81	3	189	39	21	17	21	1.92
3326415--3326484	35	2.0	35	100	0	140	45	20	8	25	1.79
3329627--3329945	84	3.8	84	96	0	584	36	26	16	20	1.94
3329579--3329986	41	9.7	41	81	7	428	34	26	17	21	1.96
3331235--3331276	21	2.0	20	86	4	57	54	0	2	42	1.13
3334891--3334949	25	2.4	25	85	0	73	20	22	18	38	1.93
3335023--3335091	27	2.7	26	74	12	70	15	24	21	37	1.93
3336977--3337045	33	2.1	32	94	2	120	53	2	15	27	1.56
3340433--3340556	36	3.4	37	76	8	130	41	5	21	30	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3348102--3348205	33	3.2	33	63	15	88	50	11	10	27	1.72
3348081--3348209	66	2.0	66	100	0	258	53	10	8	27	1.64
3355256--3355312	4	14.2	4	88	0	87	43	26	3	26	1.70
3357380--3357409	2	15.0	2	100	0	60	50	0	0	50	1.00
3357727--3357769	17	2.5	17	92	0	77	0	23	2	74	0.93
3357727--3357775	17	2.9	17	82	11	64	0	24	4	71	1.03
3359811--3359837	3	9.0	3	100	0	54	33	33	0	33	1.58
3363005--3363055	27	1.9	27	88	4	77	64	1	5	27	1.27
3363729--3364081	126	2.8	126	83	3	478	30	15	20	33	1.93
3367111--3367443	116	2.9	116	96	0	605	42	8	9	39	1.68
3367449--3367724	23	11.7	23	77	14	260	27	1	25	46	1.60
3367440--3367561	29	4.5	29	76	15	134	26	1	27	44	1.64
3367452--3367629	50	3.6	50	80	15	235	26	0	26	46	1.57
3367531--3367724	68	2.9	68	94	0	334	28	1	22	46	1.61
3367479--3367724	91	2.7	89	86	8	307	28	1	24	46	1.60
3368237--3368271	18	1.9	18	94	0	61	34	8	31	25	1.86
3368924--3368948	7	3.6	7	100	0	50	60	12	0	28	1.32
3370092--3370207	51	2.3	51	93	0	205	44	0	27	27	1.54
3370179--3370230	22	2.4	22	100	0	104	40	0	32	26	1.57
3370179--3370236	22	2.6	23	94	5	93	37	0	32	29	1.58
3370722--3370759	19	2.0	20	89	5	60	50	5	0	44	1.24
3373372--3373403	12	2.6	13	90	9	50	28	21	0	50	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3380176--3380225	25	2.0	25	96	0	91	54	0	10	36	1.34
3391120--3391324	44	4.3	49	78	15	207	33	14	23	28	1.94
3391174--3391320	44	3.3	44	91	0	231	31	14	25	29	1.95
3395340--3395386	22	2.1	22	100	0	94	23	17	34	25	1.96
3397177--3397334	43	3.7	42	79	7	142	29	25	18	26	1.98
3397177--3397291	43	2.7	43	85	4	144	28	25	19	26	1.98
3398419--3398443	13	1.9	13	100	0	50	40	24	4	32	1.73
3399713--3399761	25	1.9	26	87	4	73	32	0	4	63	1.13
3402780--3403049	126	2.2	124	82	6	323	28	16	17	37	1.92
3403104--3403183	33	2.4	30	77	20	88	48	8	0	42	1.34
3403119--3403182	34	1.9	34	87	3	94	46	10	0	42	1.39
3405979--3406008	13	2.3	13	94	0	51	33	3	13	50	1.58
3406103--3406337	50	4.7	50	91	0	353	25	22	30	20	1.98
3415274--3415922	78	8.3	77	81	8	704	27	17	19	36	1.94
3415282--3415884	153	3.9	153	86	3	773	27	17	20	34	1.95
3416029--3416069	10	4.2	10	81	12	50	78	0	21	0	0.76
3416024--3416069	19	2.4	19	82	14	58	76	0	23	0	0.79
3416026--3416070	20	2.1	22	88	12	67	77	0	22	0	0.76
3416145--3416199	21	2.5	20	83	13	65	80	7	9	3	1.02
3416381--3416482	10	10.5	10	72	13	70	81	0	18	0	0.69
3416382--3416483	9	11.8	9	74	21	76	80	0	19	0	0.71
3416401--3416480	28	3.0	28	83	5	85	80	0	20	0	0.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3416381--3416484	17	6.0	17	74	17	90	79	0	20	0	0.73
3416383--3416481	8	11.9	8	75	16	94	80	0	19	0	0.71
3416975--3417026	16	3.3	15	79	17	52	36	15	13	34	1.87
3416974--3417274	18	16.9	16	72	17	77	33	12	10	43	1.77
3416964--3417027	32	2.0	33	87	3	94	34	14	14	37	1.86
3417024--3417248	18	12.4	18	75	12	133	34	10	9	45	1.71
3417062--3417263	36	5.6	34	74	12	165	34	10	10	44	1.74
3417023--3417232	73	2.9	74	79	11	186	35	10	9	45	1.70
3417250--3417319	36	1.9	37	88	8	108	27	12	11	48	1.75
3417260--3417333	36	2.1	36	82	5	87	28	13	8	50	1.70
3419019--3419057	18	2.1	19	86	13	55	25	12	23	38	1.90
3419909--3419954	18	2.6	18	82	3	58	78	0	13	8	0.97
3424449--3424492	23	1.9	23	90	0	70	63	4	0	31	1.14
3426538--3426576	18	2.2	17	86	13	53	33	0	20	46	1.51
3426802--3426900	23	4.3	23	92	0	153	21	21	26	31	1.98
3435363--3435618	124	2.1	124	88	3	381	29	15	22	32	1.95
3438889--3439039	28	5.0	32	79	18	150	31	0	21	47	1.56
3438909--3439081	28	6.4	28	87	6	239	32	0	19	47	1.54
3441208--3441261	22	2.5	22	78	3	65	64	5	0	29	1.16
3441358--3441408	26	2.0	26	92	7	86	54	1	0	43	1.11
3441449--3441558	22	5.0	22	82	8	134	37	0	28	33	1.64
3443242--3443267	5	5.2	5	100	0	52	38	19	19	23	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3443216--3443267	26	2.0	26	81	7	61	34	15	26	23	1.94
3443780--3443831	16	3.0	16	83	13	59	44	0	32	23	1.54
3444115--3444154	21	2.0	20	85	5	53	47	0	30	22	1.52
3445082--3445125	22	2.1	22	87	8	65	68	4	2	25	1.20
3445158--3445233	34	2.2	34	84	9	93	39	0	5	55	1.23
3445931--3445969	19	2.0	20	95	5	71	43	5	35	15	1.69
3446778--3446839	24	2.7	22	80	9	79	32	3	3	61	1.28
3446807--3446898	46	2.0	46	80	6	105	35	9	2	52	1.47
3448337--3448383	3	15.3	3	78	12	51	61	0	4	34	1.15
3448337--3448383	14	3.5	14	80	13	55	61	0	4	34	1.15

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