genome.fa.s6.2.7.7.80.10.50.1000.142.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  142  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)
41870755--41870820	24	2.7	23	81	9	78	34	0	4	60	1.17
41871553--41871582	11	2.7	11	89	0	51	0	13	0	86	0.57
41876111--41876135	3	8.3	3	100	0	50	64	0	36	0	0.94
41877278--41877355	35	2.2	36	81	6	88	62	3	8	24	1.41
41877509--41877555	24	2.0	24	87	4	69	61	6	6	25	1.44
41878810--41878848	18	2.2	18	85	0	51	33	0	10	56	1.33
41883435--41883468	11	2.8	13	91	8	54	44	11	8	35	1.72
41886682--41886719	11	3.4	11	88	3	58	39	5	0	55	1.23
41890074--41890212	46	3.0	46	88	4	208	34	9	25	30	1.88
41890527--41890579	2	26.5	2	100	0	106	49	0	0	50	1.00
41892155--41892221	31	2.2	31	91	0	107	40	20	11	26	1.88
41900854--41900893	19	2.0	19	85	9	53	65	5	0	30	1.14
41911009--41911045	2	18.5	2	94	0	65	45	0	2	51	1.15
41914816--41915660	153	5.5	153	86	4	1148	31	10	7	50	1.64
41914816--41915660	308	2.7	305	88	5	1247	31	10	7	50	1.64
41915909--41915946	18	2.1	19	85	5	51	15	0	7	76	1.01
41916763--41916799	9	4.1	9	92	0	65	45	13	10	29	1.77
41924762--41924800	2	19.5	2	89	0	60	48	2	2	46	1.29
41925818--41925857	20	2.0	20	90	0	62	0	50	0	50	1.00
41928344--41928392	23	2.1	23	81	7	55	57	0	2	40	1.10
41928717--41928756	14	2.7	16	77	18	50	60	7	0	32	1.25
41942013--41942056	12	3.8	12	81	3	54	52	0	2	45	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41951276--41951302	12	2.2	12	100	0	54	22	22	0	55	1.44
41955616--41955688	30	2.4	30	83	0	92	41	19	12	27	1.87
41959513--41959552	8	5.1	8	90	6	64	85	0	2	12	0.71
41959513--41959552	15	2.6	15	92	4	62	85	0	2	12	0.71
41962713--41962747	3	11.7	3	100	0	70	65	0	0	34	0.93
41965746--41965871	19	6.5	19	90	3	207	38	10	15	36	1.81
41965747--41965866	59	2.0	59	95	0	213	38	10	14	37	1.79
41974854--41974899	11	4.0	11	86	10	58	86	8	2	2	0.72
41976201--41976806	133	4.6	133	92	1	884	26	18	24	29	1.98
41976594--41976798	44	4.7	44	67	4	117	27	18	24	29	1.98
41977885--41978079	44	4.4	44	68	14	132	29	16	22	31	1.96
41977837--41978079	132	1.8	132	89	3	382	30	16	21	31	1.96
41978082--41978111	10	3.0	10	100	0	60	30	0	20	50	1.49
41978906--41978941	8	4.5	8	89	0	54	69	0	30	0	0.89
41978851--41978941	16	5.4	16	68	15	58	71	6	21	0	1.09
41981538--41981731	97	2.0	98	91	3	320	30	9	24	35	1.88
41991701--41991728	3	9.3	3	100	0	56	32	0	0	67	0.91
42007204--42008204	44	21.9	44	74	9	643	34	16	19	29	1.94
42007204--42008204	89	10.9	89	77	8	739	34	16	19	29	1.94
42007937--42008229	139	2.1	139	84	5	369	33	19	19	27	1.96
42008837--42008864	6	4.7	6	100	0	56	85	0	0	14	0.59
42009673--42009729	27	2.1	27	100	0	114	78	10	10	0	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42013028--42013060	16	2.1	15	94	5	57	27	6	0	66	1.15
42020971--42021018	24	2.0	24	100	0	96	41	20	8	29	1.81
42022307--42022430	62	2.0	62	100	0	248	22	4	27	45	1.73
42024168--42024199	2	16.0	2	100	0	64	50	0	0	50	1.00
42025285--42025418	21	6.5	21	86	1	164	16	26	17	39	1.91
42025681--42025707	8	3.4	8	100	0	54	37	0	14	48	1.45
42027574--42027620	22	2.1	22	96	0	85	17	23	17	42	1.88
42032809--42032875	20	3.3	20	72	4	55	53	8	19	17	1.70
42033721--42033812	44	2.1	44	100	0	184	34	14	13	38	1.84
42033746--42033816	23	3.2	23	62	13	58	29	15	14	40	1.86
42036527--42036581	3	18.3	3	100	0	110	32	0	0	67	0.91
42038060--42038115	28	2.0	28	96	0	103	41	14	16	28	1.87
42040261--42040307	22	2.3	20	82	13	60	65	0	2	31	1.04
42040263--42040309	21	2.2	22	88	3	69	70	0	2	27	0.99
42043469--42043558	41	2.2	41	84	4	110	23	13	14	48	1.79
42054174--42054236	32	2.0	32	83	0	81	42	6	7	42	1.59
42054380--42054422	16	2.7	16	82	10	52	41	2	0	55	1.12
42054679--42054734	20	2.6	21	78	21	62	41	0	0	58	0.98
42054683--42054748	24	2.7	26	72	15	68	42	0	0	57	0.98
42055042--42055107	13	5.3	12	76	20	57	72	0	27	0	0.85
42055049--42055102	22	2.4	23	81	12	67	72	0	27	0	0.85
42055271--42055389	60	2.0	60	94	0	211	33	0	12	53	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42055942--42055981	21	1.9	21	85	10	55	50	0	0	50	1.00
42062084--42062108	13	1.9	13	100	0	50	8	0	24	68	1.16
42063226--42063319	19	4.8	19	90	5	152	37	10	15	36	1.83
42063226--42063326	40	2.7	38	88	8	152	37	9	16	35	1.82
42063258--42063342	21	4.0	22	79	14	81	37	7	16	38	1.76
42063308--42063352	23	2.0	23	86	4	65	33	4	15	46	1.66
42064492--42064533	19	2.2	20	86	4	59	33	7	9	50	1.62
42065421--42065453	12	2.8	12	90	4	50	36	3	9	51	1.49
42065312--42065521	114	1.8	114	97	0	402	40	4	13	41	1.65
42065859--42066008	41	3.7	41	90	1	230	28	18	28	25	1.98
42072176--42072233	30	1.9	30	86	6	82	39	5	24	31	1.77
42072446--42072476	13	2.4	13	94	0	53	32	0	12	54	1.38
42072571--42072863	50	5.8	50	93	0	487	25	22	31	20	1.98
42075848--42075901	22	2.3	23	78	15	58	50	3	0	46	1.19
42079654--42079698	22	2.0	24	83	16	60	60	8	11	20	1.57
42081259--42081301	19	2.3	19	92	8	70	58	0	0	41	0.98
42081986--42082036	21	2.3	21	83	6	57	39	5	1	52	1.37
42082026--42082064	18	2.1	19	95	4	71	51	0	0	48	1.00
42092027--42092096	35	2.0	34	88	2	104	47	0	11	41	1.40
42092857--42093058	44	4.5	44	74	14	128	24	20	24	30	1.99
42093143--42093877	50	14.7	50	73	2	591	24	22	22	31	1.98
42093193--42093883	100	6.9	100	88	0	997	24	21	22	32	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42093192--42093883	299	2.3	299	89	2	1030	24	21	22	32	1.98
42095142--42095226	6	14.8	6	74	18	74	0	21	0	78	0.74
42095141--42095212	11	6.5	11	77	17	69	0	20	0	79	0.74
42095139--42095226	25	3.6	25	77	11	92	0	22	0	77	0.77
42095150--42095201	20	2.6	20	79	11	61	0	21	0	78	0.74
42095168--42095230	10	6.5	10	76	22	55	0	22	0	77	0.76
42095154--42095226	33	2.1	35	78	9	71	0	21	0	78	0.76
42095147--42095225	36	2.0	40	88	11	121	0	20	0	79	0.73
42099464--42099505	18	2.3	18	87	0	57	42	0	9	47	1.36
42099465--42099505	12	3.4	12	86	0	55	41	0	9	48	1.36
42099892--42099945	3	18.0	3	100	0	108	66	0	0	33	0.92
42100592--42100633	2	21.0	2	100	0	84	50	0	0	50	1.00
42102086--42102129	9	4.9	9	91	0	70	34	20	34	11	1.88
42102906--42102953	25	1.9	25	100	0	96	39	4	8	47	1.53
42103024--42103057	16	2.1	16	94	0	59	50	5	2	41	1.42
42106747--42106772	3	8.7	3	100	0	52	34	34	0	30	1.58
42109938--42110062	62	2.0	63	88	1	189	33	9	15	41	1.79
42116081--42116150	21	3.4	21	72	18	67	37	1	8	52	1.41
42116167--42116212	18	2.6	18	86	3	58	43	0	2	54	1.12
42116406--42116451	18	2.6	18	86	3	58	43	0	2	54	1.12
42116115--42116550	119	3.7	119	94	0	766	41	1	5	51	1.33
42122498--42122721	120	1.9	120	96	2	414	43	1	4	51	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42122860--42122947	44	2.0	44	84	10	117	37	28	4	29	1.77
42127894--42127927	16	2.1	16	88	0	50	35	14	0	50	1.44
42129023--42129056	7	4.9	7	96	0	59	47	26	0	26	1.53
42130811--42130852	21	1.9	21	85	9	57	47	2	9	40	1.49
42141408--42141432	13	1.9	13	100	0	50	72	0	0	28	0.86
42145942--42146106	83	2.0	84	93	1	287	35	10	12	42	1.76
42149927--42149959	15	2.1	17	88	11	52	60	12	6	21	1.53
42150515--42150562	21	2.2	23	85	14	66	70	2	4	22	1.15
42154562--42154603	15	2.8	15	85	0	66	69	0	0	30	0.89
42161051--42161089	3	13.0	3	100	0	78	0	33	0	66	0.92

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