genome.fa.s6.2.7.7.80.10.50.1000.144.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  144  of  168  ( 20060 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)
42364177--42364210	14	2.6	13	90	9	52	14	5	5	73	1.21
42364572--42364600	7	4.3	7	91	8	51	58	0	0	41	0.98
42364572--42364600	13	2.1	14	93	6	51	58	0	0	41	0.98
42377104--42377329	116	1.9	116	100	0	452	29	17	26	26	1.97
42379078--42379347	99	2.8	95	82	11	321	30	18	15	36	1.91
42379146--42379416	99	2.6	102	82	6	343	30	17	15	35	1.91
42379407--42379442	18	2.0	18	88	0	54	0	16	0	83	0.65
42383121--42383163	15	2.9	15	82	3	52	44	4	11	39	1.62
42385778--42385950	43	4.1	43	77	8	183	21	19	27	31	1.97
42391029--42391074	16	2.9	16	81	9	58	30	19	15	34	1.93
42392914--42392944	9	3.4	9	90	0	53	25	12	22	38	1.90
42392998--42393034	9	4.1	9	89	0	56	48	13	8	29	1.71
42393248--42393307	30	2.0	31	86	3	86	18	38	1	41	1.60
42394619--42394698	3	26.7	3	97	0	151	67	1	0	31	0.99
42407284--42407337	16	3.4	16	89	0	81	33	1	35	29	1.69
42407316--42407406	45	2.0	44	87	2	128	31	5	28	34	1.80
42407570--42407604	18	2.0	17	88	5	52	54	0	0	45	0.99
42407550--42407836	119	2.4	120	90	2	470	49	4	1	44	1.34
42407585--42407784	61	3.3	60	67	18	146	48	6	2	43	1.41
42418957--42418983	3	9.0	3	100	0	54	66	0	33	0	0.92
42419120--42419157	3	12.7	3	100	0	76	68	0	31	0	0.90
42429207--42429237	13	2.3	14	94	5	55	61	0	0	38	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42434592--42434651	29	2.1	29	100	0	120	28	6	21	43	1.78
42437521--42437590	36	1.9	36	97	0	131	21	25	12	40	1.89
42439158--42439214	30	1.9	30	82	13	73	47	3	0	49	1.18
42439389--42439439	13	3.9	13	81	0	66	35	23	7	33	1.84
42447867--42447906	21	1.9	21	94	0	71	32	0	25	42	1.55
42447873--42447915	21	2.0	21	82	8	52	39	2	20	37	1.66
42448332--42448362	2	15.5	2	93	0	53	48	3	0	48	1.17
42451360--42451524	82	2.0	82	85	3	224	49	9	8	32	1.66
42451714--42451773	29	2.1	29	81	6	68	45	3	5	46	1.41
42453969--42454031	30	2.1	30	82	5	74	33	4	3	58	1.35
42454927--42454968	20	2.2	19	83	12	50	19	9	2	69	1.28
42466876--42466937	27	2.3	27	80	5	72	38	1	3	56	1.25
42467091--42467144	20	2.7	20	77	11	56	66	1	3	27	1.19
42467613--42467664	18	2.8	18	78	13	61	38	1	0	59	1.08
42467616--42467680	19	3.5	18	76	17	62	35	1	1	61	1.15
42472133--42472204	30	2.4	31	90	4	112	26	25	18	30	1.98
42474795--42474903	51	2.2	50	93	1	182	29	23	13	33	1.93
42474857--42474940	36	2.3	37	89	2	125	33	26	14	26	1.94
42474806--42474990	87	2.1	87	92	0	307	31	24	14	29	1.94
42474893--42475002	51	2.2	50	95	1	193	31	25	12	30	1.93
42480465--42480491	6	4.5	6	100	0	54	18	51	14	14	1.76
42486764--42486803	20	2.0	20	85	5	53	35	0	5	60	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42486946--42486994	24	2.1	24	81	11	57	59	8	6	26	1.50
42492927--42492997	34	2.1	34	97	0	133	29	9	21	39	1.85
42495329--42495377	23	2.0	25	88	11	75	44	2	0	53	1.12
42495440--42495483	9	5.1	9	86	10	65	34	0	11	54	1.36
42495437--42495474	16	2.4	16	90	0	58	36	0	10	52	1.36
42495470--42495615	68	2.1	69	94	2	267	37	5	9	47	1.60
42495594--42495625	14	2.3	14	100	0	64	25	0	0	75	0.81
42496181--42496249	36	1.9	36	90	0	111	40	7	23	28	1.81
42496810--42496837	14	2.0	14	100	0	56	35	7	14	42	1.73
42496881--42496918	20	1.9	20	94	0	67	15	15	10	57	1.64
42498344--42498455	33	3.4	32	75	6	91	24	25	17	33	1.97
42502901--42502925	4	6.2	4	100	0	50	24	28	0	48	1.52
42506359--42506397	19	2.1	19	85	9	53	15	0	7	76	0.99
42512754--42512946	88	2.2	87	82	5	228	34	20	9	35	1.86
42513022--42513119	29	3.5	29	73	12	71	64	3	3	29	1.24
42516112--42516145	17	1.9	18	94	5	61	50	0	2	47	1.16
42516761--42516800	21	1.9	21	85	10	55	50	0	5	45	1.23
42517135--42517168	17	2.0	17	88	0	50	58	0	0	41	0.98
42527168--42527207	21	2.0	20	85	5	53	45	2	0	52	1.14
42528387--42528467	32	2.6	32	82	2	101	51	18	2	27	1.58
42533302--42533334	16	2.1	16	88	5	50	57	3	0	39	1.14
42533832--42533870	20	2.1	19	85	9	53	56	7	0	35	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42535828--42535896	32	2.1	33	91	2	113	55	7	1	36	1.37
42543559--42543592	15	2.3	15	89	0	50	52	0	47	0	1.00
42553286--42553482	105	1.9	101	87	4	286	27	23	15	32	1.95
42553358--42553482	33	3.7	33	75	6	108	28	24	15	32	1.95
42555268--42555315	20	2.5	20	79	3	53	52	4	2	41	1.32
42555748--42555780	11	2.9	12	86	13	52	33	0	0	66	0.92
42555902--42555964	30	2.1	30	90	0	99	60	14	1	23	1.43
42555940--42555985	18	2.5	19	82	13	60	65	8	0	26	1.21
42556471--42556510	16	2.4	18	84	16	59	40	0	0	60	0.97
42556481--42556580	32	3.3	31	79	8	91	38	3	0	59	1.13
42556493--42556554	11	5.6	11	75	12	65	40	4	0	54	1.22
42559284--42559347	33	1.9	33	84	6	85	46	4	4	43	1.45
42567092--42567118	2	13.5	2	100	0	54	48	0	0	51	1.00
42567447--42567484	16	2.4	17	86	8	53	57	2	0	39	1.12
42568512--42568626	51	2.3	51	96	0	212	27	30	0	41	1.56
42568635--42568678	10	4.4	10	83	11	63	50	0	0	50	1.00
42568641--42568684	20	2.2	20	96	4	81	40	0	0	59	0.98
42570701--42570799	23	4.3	23	92	0	153	20	20	27	32	1.97
42571028--42571060	15	2.1	16	88	5	50	45	0	12	42	1.41
42573528--42573596	25	2.7	25	81	2	93	44	2	13	39	1.58
42573592--42574036	18	25.1	18	78	15	482	48	21	0	29	1.52
42573689--42574036	47	7.7	46	74	20	265	47	22	0	29	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42573852--42573952	29	3.3	29	75	17	105	47	23	0	28	1.52
42573599--42574036	106	4.5	98	72	23	249	48	21	0	29	1.52
42574033--42574104	21	3.2	21	67	17	54	38	16	5	38	1.72
42574027--42574131	47	2.2	47	93	0	183	38	14	6	40	1.72
42574051--42574130	26	3.3	26	69	16	80	38	13	7	40	1.73
42574078--42574906	55	14.0	56	73	19	432	37	8	6	46	1.62
42574170--42574204	18	1.9	18	94	0	61	37	8	2	51	1.47
42574253--42574366	38	3.3	38	63	23	104	33	8	6	51	1.58
42574235--42574841	66	10.3	56	74	18	404	37	8	7	47	1.61
42574291--42574317	10	2.7	10	100	0	54	40	7	0	51	1.30
42574170--42574617	66	7.1	66	80	12	519	37	7	7	48	1.59
42574357--42574383	10	2.7	10	100	0	54	40	7	0	51	1.30
42574479--42574513	18	1.9	18	94	0	61	37	8	2	51	1.47
42574497--42574617	38	3.4	38	66	21	109	40	7	4	47	1.53
42574535--42574561	10	2.7	10	100	0	54	40	7	0	51	1.30
42574621--42574694	21	3.3	21	65	17	58	41	12	4	41	1.61
42574642--42574719	26	3.2	26	66	17	76	38	8	7	44	1.65
42574301--42574672	178	2.1	178	91	1	595	37	7	7	46	1.62
42574112--42574675	309	1.8	307	86	4	830	37	7	7	46	1.60
42574619--42574719	47	2.1	47	98	0	193	40	10	5	42	1.64
42574101--42574909	224	3.4	224	81	12	929	37	8	7	46	1.62
42574703--42574737	18	1.9	18	94	0	61	37	8	2	51	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42574721--42574841	38	3.4	38	66	25	111	34	8	4	52	1.53
42574759--42574785	10	2.7	10	100	0	54	40	7	0	51	1.30
42574703--42574914	66	3.2	66	90	4	324	37	8	5	48	1.57
42574825--42574851	10	2.7	10	100	0	54	40	7	0	51	1.30
42574890--42574914	10	2.5	10	100	0	50	44	8	0	48	1.32
42574258--42574940	234	2.9	229	77	14	654	37	8	7	46	1.62
42581709--42581736	9	3.1	9	100	0	56	32	10	10	46	1.73
42583343--42583390	25	1.9	25	83	8	62	39	12	0	47	1.41
42584523--42584635	60	1.9	60	81	3	138	20	18	16	44	1.87
42585078--42585126	25	2.0	25	91	0	80	46	8	20	24	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