genome.fa.s5.2.7.7.80.10.50.1000.11.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   

This is table  11  of  208  ( 24913 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)
3330199--3330237	17	2.3	17	86	0	51	46	7	0	46	1.31
3330212--3330260	25	1.9	26	83	4	64	48	4	0	46	1.20
3330361--3330407	24	2.0	24	91	0	76	31	10	12	44	1.77
3330603--3330655	26	2.0	26	100	0	106	39	7	11	41	1.69
3334501--3334540	21	2.0	21	90	5	64	55	0	0	45	0.99
3337709--3337776	20	3.5	19	77	16	68	61	4	2	30	1.30
3344836--3344905	26	2.7	26	84	2	88	22	11	8	57	1.61
3344836--3344905	25	2.8	25	84	2	86	22	11	8	57	1.61
3354459--3354515	28	2.0	28	86	0	78	47	1	1	49	1.22
3377113--3377244	9	14.2	9	69	21	51	62	2	3	31	1.25
3377153--3377203	19	2.7	19	77	11	52	66	0	1	31	1.03
3377308--3377366	29	2.0	30	83	3	75	28	6	15	49	1.70
3377589--3377622	9	3.4	10	88	12	52	55	0	0	44	0.99
3377589--3377631	19	2.3	19	88	8	61	55	2	0	41	1.12
3378108--3378163	22	2.7	20	76	13	58	32	0	3	64	1.11
3378269--3378329	28	2.2	30	77	17	76	22	1	4	70	1.15
3378188--3378341	9	17.0	9	72	13	68	28	2	3	65	1.21
3378189--3378341	19	8.4	19	69	15	76	28	2	3	66	1.21
3381808--3381851	22	2.0	22	82	8	54	50	6	4	38	1.50
3383303--3383403	47	2.4	38	75	25	121	50	2	2	43	1.32
3383316--3383405	47	1.9	47	100	0	180	45	4	3	46	1.39
3385351--3385376	11	2.4	11	100	0	52	15	0	19	65	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3386547--3386616	23	3.0	23	93	0	122	35	11	8	44	1.71
3398420--3398455	18	2.1	17	89	5	54	5	52	41	0	1.24
3408545--3408588	21	2.1	21	91	0	70	50	27	11	11	1.72
3409010--3409143	66	2.0	66	95	0	241	37	10	29	23	1.88
3412040--3412076	14	2.6	14	100	0	74	16	51	13	18	1.76
3412938--3413003	20	3.3	20	70	16	55	28	3	3	65	1.23
3416026--3416069	22	2.0	22	82	4	54	45	0	0	54	0.99
3448089--3448154	34	1.9	34	90	0	105	53	10	10	25	1.68
3450028--3450107	29	2.8	27	83	11	88	35	6	3	55	1.43
3455124--3455168	23	2.0	23	86	8	65	62	2	4	31	1.27
3459605--3459658	25	2.3	25	87	9	78	48	14	12	24	1.79
3459613--3459664	25	2.1	25	92	3	88	38	17	19	25	1.93
3463005--3463039	18	1.9	18	94	0	61	31	14	25	28	1.95
3464160--3464211	25	2.1	25	92	3	88	38	17	19	25	1.93
3467752--3467851	48	2.1	48	90	0	155	44	24	5	27	1.74
3473705--3473729	5	5.0	5	100	0	50	40	0	0	60	0.97
3476780--3476848	24	2.8	24	80	8	68	47	10	15	26	1.77
3476783--3476897	25	4.6	25	75	13	74	49	8	15	26	1.73
3476804--3476904	12	7.9	12	69	14	60	50	9	13	25	1.73
3476893--3476930	19	2.0	19	85	10	51	63	7	13	15	1.51
3478944--3478992	22	2.3	21	89	3	71	65	0	2	32	1.04
3478944--3478992	21	2.3	22	85	3	64	65	0	2	32	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3478908--3478958	15	3.2	16	73	13	52	62	0	0	37	0.95
3478923--3479035	49	2.2	49	81	4	145	61	0	1	37	1.07
3483208--3483255	24	2.0	25	91	4	80	39	14	12	33	1.84
3511581--3511947	103	3.6	103	90	2	544	18	20	29	31	1.96
3511761--3511812	27	1.9	27	100	0	104	13	23	32	30	1.93
3512167--3512210	22	2.0	22	82	8	54	50	2	22	25	1.61
3517182--3517211	15	2.0	15	100	0	60	40	13	0	46	1.43
3517183--3517217	15	2.3	15	90	0	52	37	20	0	42	1.52
3517804--3517845	20	2.1	20	86	0	57	66	0	4	28	1.12
3518855--3518899	22	2.0	23	82	4	56	60	4	6	28	1.42
3523108--3523155	24	2.0	25	91	4	80	39	14	12	33	1.84
3526959--3526991	17	1.9	17	93	0	57	6	42	0	51	1.26
3528286--3528397	10	11.2	10	78	14	108	52	0	1	45	1.11
3528279--3528368	43	2.1	40	82	15	101	52	0	1	46	1.07
3528287--3528438	53	2.9	50	79	15	164	53	0	2	43	1.14
3528296--3528382	43	2.0	44	93	6	151	55	0	2	42	1.12
3528367--3528445	41	1.9	41	87	5	115	50	0	3	45	1.19
3534145--3534209	30	2.2	30	88	0	94	35	7	23	33	1.83
3534541--3534687	33	4.3	33	71	24	101	17	21	27	34	1.95
3534541--3534764	103	2.2	104	88	7	332	17	21	28	32	1.96
3541552--3541604	23	2.4	21	75	12	52	16	5	16	60	1.54
3542704--3542871	86	2.0	86	96	0	309	18	11	29	40	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3545907--3546012	49	2.1	49	87	5	151	17	14	20	47	1.83
3548005--3548048	23	1.9	23	100	0	88	34	2	27	36	1.70
3555403--3555446	6	7.0	6	85	10	61	65	0	0	34	0.93
3558318--3558472	56	2.7	57	79	2	186	31	11	19	37	1.88
3562500--3562526	14	1.9	14	100	0	54	74	0	0	25	0.83
3565151--3565201	25	2.0	25	100	0	102	33	11	31	23	1.91
3569160--3569296	56	2.4	59	78	10	151	31	12	18	37	1.88
3574276--3574300	2	12.5	2	100	0	50	52	0	0	48	1.00
3576838--3576885	6	7.7	6	84	11	53	43	16	18	20	1.88
3576864--3576970	45	2.4	45	85	3	153	42	19	17	20	1.90
3577419--3577482	21	3.1	21	72	17	62	37	20	9	32	1.85
3578256--3578306	9	5.8	9	84	9	61	3	13	3	78	1.03
3578256--3578320	9	7.2	8	78	18	58	7	12	3	76	1.10
3578256--3578319	26	2.4	27	82	12	71	7	12	3	76	1.11
3578256--3578316	18	3.4	18	84	11	72	8	13	3	75	1.15
3578733--3578832	3	33.7	3	80	9	107	60	2	2	36	1.20
3582152--3582182	14	2.2	14	100	0	62	48	22	12	16	1.80
3589176--3589222	23	2.0	23	100	0	94	34	8	0	57	1.29
3591752--3591781	15	2.0	15	100	0	60	26	0	33	40	1.57
3600984--3601069	30	2.9	29	78	20	90	43	13	2	40	1.57
3607589--3607646	15	3.9	15	76	0	53	27	20	1	50	1.58
3617085--3617262	57	3.1	57	77	4	180	28	13	17	39	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3617598--3617711	57	2.0	57	84	1	149	32	10	16	40	1.83
3617929--3618023	49	1.9	49	85	4	129	40	11	9	38	1.74
3622114--3622308	57	3.6	55	71	17	165	31	11	19	37	1.88
3624688--3624734	19	2.4	20	85	3	60	34	2	8	55	1.42
3624717--3624810	49	1.9	48	82	2	116	36	5	6	52	1.50
3624717--3624808	24	3.8	23	71	7	69	35	5	6	52	1.51
3631335--3631380	23	2.1	21	84	8	56	58	4	6	30	1.43
3633256--3633409	56	2.7	55	74	9	148	31	12	17	38	1.88
3635595--3635790	57	3.6	56	77	7	208	30	12	19	37	1.89
3635968--3635999	12	2.7	12	100	0	64	40	15	15	28	1.88
3644032--3644406	18	20.2	19	67	17	112	44	9	12	33	1.75
3644303--3644433	36	3.8	34	83	8	149	49	9	12	27	1.73
3644366--3644418	16	3.2	16	76	10	61	47	7	15	30	1.73
3644391--3644431	16	2.5	16	84	4	55	53	14	12	19	1.72
3644424--3644463	19	2.0	21	85	9	57	40	10	5	45	1.60
3644580--3644617	20	1.9	20	88	0	58	42	7	13	36	1.73
3645059--3645099	14	2.9	14	85	0	55	0	31	0	68	0.90
3645633--3645803	58	2.9	58	76	15	147	38	5	23	32	1.77
3645667--3645803	30	4.7	29	78	12	138	38	4	21	35	1.74
3645722--3645818	30	3.3	30	87	5	101	41	3	22	32	1.70
3646014--3646299	75	3.8	74	86	6	337	34	22	15	27	1.95
3647349--3647414	18	3.8	16	81	15	69	3	4	7	84	0.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3647366--3647409	20	2.1	21	91	4	72	4	0	9	86	0.70
3647373--3647414	6	7.2	6	84	10	52	4	0	9	85	0.72
3647348--3647424	35	2.2	36	81	6	86	3	7	6	81	0.96
3653212--3653270	18	3.3	18	83	9	75	35	10	13	40	1.78
3653212--3653269	17	3.3	18	79	15	68	36	10	13	39	1.79
3653194--3653268	36	2.1	38	85	9	104	41	10	12	36	1.77
3653230--3653289	20	3.1	20	76	4	61	36	6	13	43	1.70
3653310--3653346	17	2.1	18	90	5	58	54	16	10	18	1.71
3653343--3653381	18	2.2	18	95	0	69	35	5	5	53	1.45
3653381--3653480	19	5.1	19	64	21	53	46	10	14	30	1.77

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