genome.fa.s6.2.7.7.80.10.50.1000.103.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  103  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)
30381753--30381840	33	2.8	31	79	17	85	48	2	0	48	1.13
30382119--30382150	2	16.0	2	100	0	64	50	0	0	50	1.00
30386457--30386515	24	2.5	24	81	8	68	38	16	18	25	1.92
30386921--30387147	89	2.6	89	90	1	348	28	25	23	22	1.99
30386889--30387141	89	2.9	89	88	1	321	27	26	24	22	1.99
30387467--30387712	44	5.6	44	74	9	162	30	19	22	28	1.98
30387788--30387939	44	3.5	44	79	8	141	27	17	23	30	1.97
30387338--30387941	312	1.9	312	89	2	937	30	18	21	29	1.97
30388225--30388387	44	3.7	45	79	3	170	27	20	25	26	1.99
30388030--30388527	228	2.2	225	84	2	624	29	19	22	28	1.98
30389997--30390042	2	23.0	2	100	0	92	50	0	0	50	1.00
30389997--30390086	8	10.4	9	79	19	63	44	6	0	48	1.29
30399035--30399067	16	2.1	16	88	11	50	45	3	3	48	1.33
30409020--30409068	25	2.0	25	84	8	64	32	2	18	46	1.60
30410156--30410255	42	2.4	42	93	0	164	38	15	27	20	1.92
30414595--30414628	3	11.7	3	93	6	61	32	0	0	67	0.91
30423804--30423855	21	2.5	21	76	17	54	34	3	1	59	1.27
30430061--30430534	62	7.4	64	78	8	419	48	10	14	25	1.76
30430121--30430572	134	3.4	131	78	8	404	49	10	14	25	1.75
30430306--30430572	72	3.9	70	76	14	216	48	9	14	27	1.75
30432163--30432450	91	3.2	91	80	1	344	32	26	15	25	1.95
30454219--30454267	18	2.7	19	78	9	57	42	14	0	42	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30461372--30461413	21	2.0	22	90	4	68	38	26	4	30	1.77
30463532--30463639	42	2.5	42	90	1	171	29	26	14	28	1.95
30493577--30493755	89	2.0	89	98	0	349	41	17	22	18	1.90
30495265--30495312	17	2.8	18	78	15	57	27	4	10	58	1.49
30496093--30496134	20	2.1	20	86	0	57	47	0	7	45	1.30
30503057--30504258	609	2.0	609	96	0	2219	34	20	14	30	1.93
30508659--30508775	62	1.9	59	87	5	171	50	4	2	42	1.35
30508754--30508860	20	5.8	18	70	22	62	52	2	2	42	1.30
30510802--30510867	3	22.0	3	87	6	98	33	3	1	62	1.20
30514702--30514759	4	14.8	4	74	16	50	74	5	1	18	1.10
30515086--30515131	23	2.1	22	88	8	67	56	6	6	30	1.50
30516660--30516699	2	20.0	2	100	0	80	50	0	0	50	1.00
30523415--30523474	26	2.3	26	85	0	84	31	21	8	38	1.83
30527011--30527078	32	2.1	32	86	5	91	58	8	14	17	1.61
30527022--30527096	32	2.4	32	84	2	89	50	8	18	22	1.73
30531693--30531719	2	13.5	2	100	0	54	48	0	0	51	1.00
30541162--30541195	14	2.4	14	95	0	59	35	17	8	38	1.81
30542094--30542155	19	3.0	21	76	19	60	53	1	1	43	1.20
30542094--30542167	22	3.5	21	71	15	64	54	1	2	41	1.23
30546786--30546820	17	2.0	18	88	5	54	11	5	14	68	1.37
30550871--30551026	74	2.1	74	80	2	170	38	12	14	34	1.84
30550947--30551129	74	2.5	70	73	15	165	40	8	13	37	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30553505--30555408	951	2.0	940	85	2	2575	24	16	22	36	1.94
30558187--30558236	20	2.5	20	86	0	64	24	26	2	48	1.62
30561562--30561596	18	1.9	18	88	0	52	0	8	14	77	0.99
30585734--30585791	19	3.0	20	73	14	59	37	1	6	53	1.38
30585808--30585845	20	1.9	20	84	10	51	26	5	7	60	1.46
30586012--30586055	22	2.0	22	95	0	79	25	18	4	52	1.64
30592013--30592052	19	2.1	19	100	0	80	62	15	5	17	1.49
30594360--30594470	43	2.6	43	82	7	134	30	14	23	31	1.94
30597432--30597473	22	1.9	22	85	9	59	66	7	0	26	1.17
30603018--30603058	13	3.1	14	79	10	50	51	17	14	17	1.77
30607837--30607887	20	2.5	20	93	0	93	56	3	7	31	1.46
30608245--30608296	21	2.4	22	77	6	61	46	0	1	51	1.12
30609721--30609753	8	4.1	8	96	0	57	39	0	0	60	0.97
30611970--30612041	22	3.3	22	94	0	117	30	16	27	25	1.97
30621848--30621951	49	2.1	49	92	0	172	31	7	10	50	1.65
30623435--30623468	17	2.0	17	100	0	68	41	0	0	58	0.98
30623449--30623629	41	4.5	41	63	18	110	41	1	4	51	1.33
30623554--30623588	18	2.0	17	94	5	61	40	2	0	57	1.14
30623340--30623726	120	3.2	119	94	2	670	43	2	4	50	1.34
30623942--30623979	16	2.4	16	86	0	58	23	34	5	36	1.78
30624921--30624966	20	2.2	20	84	7	56	28	28	34	8	1.87
30627811--30627949	40	3.5	40	82	6	176	38	23	20	17	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30627982--30628303	41	7.9	41	87	0	437	21	21	28	28	1.98
30628400--30628450	26	2.0	26	84	0	66	58	5	11	23	1.55
30628634--30628667	14	2.4	14	95	0	59	20	0	35	44	1.52
30628884--30628918	7	5.0	7	89	10	54	14	0	42	42	1.45
30628827--30628988	69	2.4	67	86	7	220	28	0	27	44	1.55
30628956--30629000	14	3.2	14	83	0	54	22	2	42	33	1.66
30628956--30629000	21	2.1	21	84	8	56	22	2	42	33	1.66
30630522--30630584	32	2.0	32	93	0	108	28	12	23	34	1.92
30633335--30633519	43	4.3	43	84	1	219	22	17	28	31	1.97
30638714--30638761	25	1.9	25	86	0	69	33	16	2	47	1.58
30642427--30642474	7	6.9	7	81	9	62	31	0	2	66	1.03
30642442--30642481	14	2.8	14	88	3	62	35	0	0	65	0.93
30642474--30642519	20	2.2	21	84	3	67	41	4	6	47	1.49
30642874--30643075	42	4.8	42	91	1	325	34	22	20	21	1.97
30642874--30643075	83	2.4	84	89	0	325	34	22	20	21	1.97
30642874--30643117	125	1.9	125	84	0	317	34	21	20	22	1.96
30648974--30649058	9	9.9	9	77	8	70	29	3	23	43	1.70
30648983--30649062	34	2.4	34	89	0	124	28	5	22	43	1.74
30650741--30650800	9	6.3	9	80	17	50	1	5	6	86	0.75
30650738--30650800	16	3.9	16	83	10	67	1	6	6	85	0.79
30650741--30650799	14	4.5	13	77	10	57	1	5	6	86	0.76
30650759--30650792	7	4.9	7	96	0	59	2	0	8	88	0.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30657230--30658226	132	7.6	132	91	1	1561	30	23	18	27	1.98
30657512--30658220	44	16.1	45	64	17	181	31	23	18	26	1.97
30657377--30658021	88	7.3	90	63	13	214	31	23	17	27	1.97
30658943--30659077	67	2.0	67	97	0	252	32	18	14	34	1.92
30660113--30660195	6	14.3	6	77	15	59	0	14	3	81	0.81
30660113--30660194	18	4.8	17	78	13	80	0	14	3	81	0.82
30660113--30660196	17	4.8	17	76	8	80	0	14	4	80	0.86
30665034--30665085	25	2.0	26	85	3	70	59	1	5	32	1.32
30665233--30665274	14	3.1	14	81	18	54	76	7	0	16	1.00
30670844--30670891	26	1.9	24	84	16	62	47	2	6	43	1.40
30673406--30673485	33	2.4	34	80	12	87	57	3	1	37	1.25
30673426--30673483	22	2.6	22	71	15	57	60	3	1	34	1.24
30677099--30677296	35	5.4	35	66	16	105	34	21	21	21	1.97
30677046--30677368	75	4.3	74	80	4	369	34	22	21	21	1.96
30677209--30677344	40	3.5	39	70	13	129	39	22	19	19	1.92
30677046--30677371	150	2.2	151	82	2	406	35	22	21	21	1.96
30677629--30677654	2	13.0	2	100	0	52	50	0	0	50	1.00
30679728--30679837	42	2.6	42	81	5	116	19	32	22	25	1.97
30683520--30683562	22	2.0	22	86	4	61	41	0	2	55	1.12
30687929--30688720	418	1.9	421	86	2	1128	31	14	18	35	1.91
30691608--30691721	41	2.7	41	83	5	131	31	17	26	24	1.97
30693396--30693593	57	3.5	57	86	0	263	52	17	4	25	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30705206--30705257	26	2.0	26	96	0	95	40	23	5	30	1.78
30708933--30709062	63	2.0	64	98	1	253	36	14	15	33	1.88
30710247--30710281	17	2.1	17	88	0	52	51	8	2	37	1.47
30710287--30710314	6	4.7	6	100	0	56	50	0	0	50	1.00
30712578--30712625	19	2.4	20	93	6	80	64	6	0	29	1.18
30715730--30715792	33	1.9	33	83	0	81	31	1	3	63	1.19
30716686--30716744	29	2.0	29	96	0	109	20	16	6	55	1.63
30718512--30718557	24	2.0	23	83	12	58	4	6	30	58	1.43
30737129--30737159	5	6.0	5	96	3	53	80	0	19	0	0.71
30737977--30738132	84	1.9	84	81	12	196	23	18	28	28	1.98

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