genome.fa.s8.2.7.7.80.10.50.1000.11.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  11  of  190  ( 22705 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)
3317818--3317845	14	2.0	14	100	0	56	35	28	14	21	1.92
3319103--3319139	19	1.9	19	94	0	65	35	0	0	64	0.94
3319104--3319146	19	2.2	19	87	4	59	32	0	4	62	1.15
3319296--3319321	13	2.0	13	100	0	52	30	15	23	30	1.95
3330571--3330612	22	1.9	22	90	0	66	16	7	4	71	1.26
3330707--3330767	21	3.0	20	79	11	72	36	0	1	62	1.05
3330706--3330767	20	3.0	21	73	19	60	35	0	1	62	1.05
3330686--3330749	34	1.9	33	84	9	85	35	0	0	64	0.94
3330710--3330775	21	3.2	21	83	10	57	42	0	1	56	1.08
3330828--3330889	31	2.0	32	87	6	92	33	0	1	64	1.03
3330965--3331019	22	2.7	20	82	5	65	60	0	5	34	1.20
3334402--3334429	7	4.0	7	100	0	56	42	0	0	57	0.99
3334658--3334704	24	2.0	24	83	8	60	51	0	0	48	1.00
3334649--3334749	21	5.0	22	79	14	94	48	0	0	51	1.00
3334645--3334769	42	3.0	41	76	18	109	50	0	0	49	1.00
3334681--3334774	20	4.5	22	81	12	108	52	0	0	47	1.00
3336571--3336605	2	17.5	2	100	0	70	51	0	0	48	1.00
3337057--3337137	27	3.0	28	71	12	71	58	8	2	30	1.42
3340341--3340421	29	2.8	29	98	0	153	24	8	13	53	1.68
3341591--3341630	13	3.1	13	79	13	55	35	25	7	32	1.84
3341901--3341952	16	3.2	16	94	0	86	28	0	36	34	1.58
3342387--3342424	16	2.4	17	82	13	53	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3342387--3342434	15	3.3	15	82	11	55	54	0	0	45	0.99
3345660--3345697	20	1.9	20	94	0	67	39	15	31	13	1.86
3363517--3363551	18	2.1	16	89	10	52	45	0	0	54	0.99
3378785--3378857	34	2.1	34	100	0	146	36	16	10	35	1.84
3382691--3382729	3	13.0	3	100	0	78	66	0	0	33	0.92
3386155--3386431	124	2.2	126	93	2	470	33	20	15	31	1.93
3392543--3392594	24	2.2	24	85	0	68	38	3	7	50	1.50
3397162--3397234	33	2.2	34	80	7	87	58	12	4	24	1.51
3400726--3400811	22	3.9	22	90	0	118	27	15	27	29	1.96
3404910--3404940	13	2.4	13	88	0	53	0	12	0	87	0.55
3418430--3418472	21	2.0	21	82	8	52	60	16	16	6	1.56
3429328--3429373	17	2.6	18	77	19	51	41	4	2	52	1.33
3431023--3431178	75	2.1	75	92	0	258	35	26	17	20	1.94
3431465--3431530	16	4.1	16	96	0	123	27	0	34	37	1.57
3431746--3431787	15	2.7	16	82	14	52	52	2	0	45	1.13
3431755--3431801	15	3.3	15	79	11	53	53	0	0	46	1.00
3439676--3439752	30	2.5	32	81	8	88	62	1	0	36	1.04
3441071--3441107	9	4.1	9	85	0	56	48	13	8	29	1.71
3441329--3441388	30	2.0	31	83	3	77	20	38	0	41	1.52
3447818--3447852	13	2.8	12	83	8	52	28	0	2	68	1.04
3447868--3447892	9	2.8	9	100	0	50	68	0	0	32	0.90
3447981--3448016	19	2.0	17	89	10	54	66	11	2	19	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3451656--3451726	24	3.0	24	82	0	88	15	8	54	21	1.67
3454146--3454293	76	2.0	75	86	5	212	36	8	11	43	1.72
3456817--3456856	19	2.2	17	86	8	53	75	0	7	17	1.03
3457653--3458417	44	17.8	44	73	10	374	28	22	19	30	1.97
3457653--3458417	90	8.9	88	72	10	242	28	22	19	30	1.97
3457752--3458378	170	3.7	170	93	0	1053	28	22	19	30	1.98
3466454--3466490	17	2.1	18	90	5	58	45	0	24	29	1.53
3470925--3470962	20	1.9	20	100	0	76	76	5	13	5	1.13
3472386--3472446	21	3.0	20	82	4	68	36	27	8	27	1.85
3475442--3475490	19	2.4	21	83	10	57	73	6	2	18	1.14
3481625--3481663	16	2.4	16	86	0	60	53	5	15	25	1.62
3481748--3481850	51	2.0	51	98	0	197	29	12	20	37	1.89
3482984--3483070	25	3.6	25	70	14	65	41	2	3	52	1.31
3482997--3483115	62	1.9	63	87	5	179	43	2	5	48	1.38
3484134--3484395	43	6.1	43	76	5	219	30	25	16	26	1.97
3493043--3493085	23	1.9	22	86	13	61	46	2	2	48	1.27
3493837--3493879	19	2.3	18	80	7	50	53	2	2	41	1.26
3493870--3493910	22	1.9	22	85	5	57	58	4	0	36	1.20
3494344--3494383	20	2.2	17	86	13	53	55	2	7	35	1.42
3494423--3494470	21	2.4	20	79	6	53	50	0	10	39	1.37
3494501--3494538	20	1.9	20	88	0	58	71	0	2	26	1.00
3494501--3494544	20	2.2	20	83	0	52	75	0	2	22	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3510217--3510268	24	2.2	23	93	3	86	42	1	0	55	1.10
3510219--3510281	24	2.7	25	76	13	73	47	3	0	49	1.17
3510940--3510981	19	2.2	20	76	16	54	52	0	4	42	1.22
3512531--3512578	15	3.2	15	71	11	53	52	6	4	37	1.46
3514027--3514063	19	1.9	19	88	0	56	32	2	0	64	1.07
3516661--3516707	2	24.0	2	95	4	87	48	0	0	51	1.00
3535043--3535093	26	2.0	26	100	0	102	21	7	23	47	1.77
3535453--3535662	106	2.0	106	100	0	420	30	19	18	31	1.95
3537090--3537121	16	2.0	16	100	0	64	18	18	25	37	1.94
3544435--3544460	13	2.0	13	100	0	52	46	0	23	30	1.53
3544725--3545157	50	8.7	50	82	4	489	27	21	28	21	1.99
3544725--3545205	150	3.2	148	83	4	628	28	21	28	22	1.99
3546684--3546734	23	2.2	23	89	0	75	43	21	7	27	1.80
3548322--3548687	103	3.6	102	90	2	538	17	21	29	31	1.96
3551865--3551932	2	34.0	2	100	0	136	50	0	0	50	1.00
3554398--3554433	9	3.9	9	88	3	54	30	22	25	22	1.99
3555503--3555568	29	2.2	30	89	2	98	27	13	24	34	1.93
3556205--3556233	7	4.1	7	100	0	58	86	0	0	13	0.58
3568374--3568409	18	2.0	18	88	0	54	16	5	19	58	1.58
3570342--3570374	17	2.0	17	88	5	50	48	0	3	48	1.17
3570349--3570396	21	2.3	21	81	0	51	43	2	2	52	1.24
3570343--3570402	13	4.8	13	77	6	61	45	1	3	50	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3570343--3570401	25	2.4	25	82	0	73	44	1	3	50	1.28
3575912--3575959	25	2.0	25	88	8	73	35	16	18	29	1.93
3576010--3576082	16	4.6	16	75	0	74	42	2	27	27	1.69
3577433--3577485	26	2.0	26	100	0	106	52	3	11	32	1.55
3577426--3577480	26	2.3	22	75	21	65	52	3	9	34	1.50
3587576--3587607	14	2.3	14	94	0	55	34	28	15	21	1.94
3587523--3587658	65	2.1	65	83	2	166	31	28	16	23	1.96
3587595--3587776	51	3.6	50	79	6	197	28	29	17	25	1.97
3589787--3589821	4	8.8	4	93	0	61	45	0	2	51	1.16
3603673--3603698	13	2.0	13	100	0	52	61	7	7	23	1.49
3604316--3604355	12	3.1	13	89	7	55	77	2	2	17	0.99
3604321--3604355	6	5.7	6	86	6	52	80	2	0	17	0.84
3605177--3606079	44	20.3	44	73	6	611	27	24	18	29	1.98
3605153--3605902	89	8.5	89	83	4	924	27	24	18	29	1.98
3606205--3606299	45	2.2	44	84	3	120	29	22	17	30	1.97
3607535--3607656	51	2.4	51	81	5	142	12	28	15	43	1.83
3610358--3610397	19	2.0	20	85	4	55	47	10	20	22	1.79
3612159--3612184	13	2.0	13	100	0	52	61	7	7	23	1.49
3612159--3612192	12	2.8	12	90	4	50	55	8	8	26	1.59
3612624--3612683	18	3.3	19	81	9	63	66	0	6	26	1.16
3612642--3612683	9	4.7	9	82	11	50	71	0	2	26	0.98
3613393--3613430	12	2.9	13	88	7	51	78	2	2	15	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3615904--3616075	11	16.9	11	68	20	81	62	0	1	36	1.03
3615963--3616013	9	5.4	9	77	9	57	74	0	0	25	0.82
3615952--3616024	29	2.5	29	97	0	137	67	0	1	31	1.00
3615963--3616083	40	3.1	39	85	9	165	66	0	1	31	1.01
3615904--3616083	80	2.2	79	86	9	240	63	0	1	35	1.02
3623735--3623797	27	2.3	27	86	5	83	30	20	17	31	1.96
3623745--3623801	27	2.1	27	93	0	96	26	21	15	36	1.93
3629517--3629641	64	2.0	64	88	3	189	49	3	10	36	1.53
3629879--3629917	18	2.3	16	86	8	51	30	0	0	69	0.89
3629880--3629930	26	1.9	27	92	4	86	29	0	1	68	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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190