genome.fa.s13.2.7.7.80.10.50.1000.162.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   

This is table  162  of  199  ( 23770 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)
47901686--47901739	27	1.9	29	85	7	76	40	1	11	46	1.50
47901737--47901804	31	2.2	31	86	5	93	27	7	23	41	1.81
47903711--47903881	86	2.0	85	88	4	254	21	28	25	24	1.99
47909587--47909618	16	2.0	16	93	0	55	15	12	6	65	1.44
47911295--47911333	12	3.2	12	85	7	53	53	0	0	46	1.00
47911296--47911330	17	2.1	17	94	0	61	51	0	0	48	1.00
47911482--47911532	25	2.0	26	88	3	77	41	7	9	41	1.67
47913868--47914140	138	2.0	136	82	7	338	32	26	20	20	1.97
47916559--47916590	12	2.7	12	95	0	55	71	0	9	18	1.12
47917051--47917083	16	2.1	16	88	11	50	21	3	0	75	0.93
47918022--47918071	6	7.8	6	80	8	55	78	2	18	2	0.95
47918030--47918071	13	3.2	13	82	3	57	78	2	19	0	0.86
47918830--47918863	18	1.9	18	88	5	52	50	0	5	44	1.26
47918842--47918874	16	1.9	18	88	11	52	54	0	0	45	0.99
47918887--47918930	23	1.9	23	86	9	63	70	4	6	18	1.27
47918900--47918934	17	2.0	18	88	5	54	71	5	8	14	1.29
47918905--47918943	18	2.2	18	86	9	53	74	7	10	7	1.22
47919378--47919411	17	1.9	18	88	5	52	41	0	23	35	1.55
47919858--47919927	21	3.4	21	70	7	54	21	17	24	37	1.94
47923142--47923187	7	6.6	7	82	7	58	69	0	0	30	0.89
47923211--47923272	7	9.0	7	91	3	99	43	0	43	12	1.43
47923425--47923591	64	2.6	64	89	0	253	25	19	7	47	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47932036--47932062	10	2.7	10	100	0	54	66	0	0	33	0.92
47932237--47932273	19	1.9	19	88	0	56	45	10	24	18	1.81
47942592--47942632	16	2.4	18	80	8	50	51	2	0	46	1.14
47945436--47945468	17	1.9	17	88	11	50	33	0	0	66	0.92
47945429--47945474	23	1.9	23	86	8	65	32	0	2	65	1.05
47948391--47948427	19	1.9	19	88	0	56	27	2	10	59	1.44
47948787--47948855	35	2.0	35	82	5	86	30	8	2	57	1.43
47948836--47948864	9	3.3	9	95	4	51	27	0	0	72	0.85
47950854--47950902	19	2.8	17	79	14	55	42	0	30	26	1.55
47951262--47951298	9	4.1	9	89	0	56	29	8	13	48	1.71
47951350--47951380	9	3.4	9	90	0	53	38	22	12	25	1.90
47956055--47956096	22	1.9	22	90	0	66	40	14	19	26	1.89
47956386--47956783	45	9.0	44	74	12	268	28	26	23	22	1.99
47956372--47956783	89	4.6	89	90	1	603	28	25	23	22	1.99
47958519--47958555	19	1.9	19	88	0	56	27	2	10	59	1.44
47960382--47960428	20	2.4	19	75	10	51	38	2	0	59	1.09
47960985--47961158	96	1.8	96	83	5	235	37	19	9	33	1.84
47961223--47961280	19	3.0	19	70	12	55	58	1	1	37	1.18
47961307--47961371	18	3.4	19	80	6	78	61	1	3	33	1.21
47961338--47961384	21	2.2	22	82	17	64	61	6	2	29	1.32
47961306--47961384	19	4.1	20	79	14	67	59	3	3	32	1.33
47961965--47962018	21	2.7	19	83	10	81	27	0	3	68	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47961975--47962021	21	2.2	21	96	0	85	29	0	2	68	1.02
47969200--47969225	3	8.7	3	100	0	52	69	0	0	30	0.89
47975188--47975234	2	23.0	2	95	4	85	48	0	2	48	1.13
47975282--47975394	56	2.0	56	93	3	192	33	7	23	35	1.82
47979050--47979181	63	2.1	63	84	2	167	26	19	8	45	1.79
47980304--47980457	30	5.2	28	77	9	146	38	19	3	38	1.68
47980816--47980858	10	4.0	11	82	14	54	76	0	23	0	0.78
47980832--47980874	7	6.3	7	89	10	63	83	0	16	0	0.64
47980826--47980873	20	2.4	19	89	6	69	81	0	18	0	0.70
47980820--47980874	26	2.1	27	89	3	85	80	0	20	0	0.72
47980820--47980883	26	2.3	29	84	10	80	79	0	20	0	0.73
47980820--47980883	6	10.3	6	85	9	67	79	0	20	0	0.73
47981148--47981245	10	9.1	11	78	14	107	80	0	18	1	0.77
47981162--47981242	21	4.0	19	80	12	90	81	0	17	1	0.76
47981147--47981243	22	4.5	21	77	13	83	81	0	17	1	0.75
47981565--47982330	18	42.5	18	70	16	303	29	12	10	46	1.75
47981678--47982312	17	35.8	17	67	17	203	29	12	10	48	1.74
47981636--47982367	35	20.5	34	69	16	258	29	12	10	47	1.74
47993131--47993216	34	2.5	34	88	5	120	83	12	3	0	0.76
47993131--47993216	26	3.4	25	79	7	86	83	12	3	0	0.76
47993131--47993195	6	11.3	6	87	9	100	84	15	0	0	0.62
47994083--47994209	59	2.1	60	97	2	238	30	16	23	29	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47994144--47994832	153	4.5	153	92	3	1111	26	15	20	37	1.93
47994144--47994803	76	8.7	77	94	1	1111	27	15	21	36	1.93
47994996--47995121	29	4.2	28	81	9	144	37	19	3	40	1.67
47994996--47995121	59	2.1	59	86	4	173	37	19	3	40	1.67
47995483--47995537	3	19.0	3	84	3	69	74	0	25	0	0.82
47995481--47995556	34	2.2	34	81	11	93	75	0	25	0	0.81
47995493--47995557	22	3.0	22	76	14	55	78	0	21	0	0.75
47995484--47995546	6	10.3	6	91	3	72	76	0	23	0	0.79
47995821--47995899	7	10.4	7	72	20	61	78	1	20	0	0.82
47995821--47995897	12	6.2	12	79	11	93	77	1	20	0	0.83
47996289--47996411	18	6.9	18	76	14	67	32	10	8	47	1.69
47996224--47996918	36	19.4	36	70	15	154	30	12	10	46	1.75
47996332--47996567	53	4.5	52	78	9	162	28	10	9	50	1.68
47996287--47996978	17	39.0	18	71	13	429	30	11	10	47	1.74
47996867--47996977	36	3.1	34	78	14	98	28	10	11	48	1.73
47998356--47998390	2	17.5	2	100	0	70	51	0	0	48	1.00
48007247--48007289	3	14.0	3	80	4	50	30	4	2	62	1.28
48007457--48007493	17	2.2	17	90	4	58	40	8	0	51	1.32
48007466--48007516	24	2.2	24	82	6	61	41	5	1	50	1.37
48014877--48015059	60	3.0	60	69	20	182	50	6	1	42	1.34
48019574--48019634	21	2.9	22	85	7	72	49	3	6	40	1.45
48019584--48019634	21	2.4	21	93	0	84	50	3	7	37	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48019557--48019610	27	1.9	29	85	7	76	38	1	12	46	1.53
48022121--48022210	27	3.3	26	86	11	128	20	17	23	38	1.93
48024038--48024208	86	2.0	86	88	2	254	22	26	25	25	2.00
48027269--48027332	21	3.1	21	80	4	78	54	4	26	14	1.59
48028135--48028296	24	7.0	22	70	13	85	32	6	4	56	1.45
48028164--48028285	47	2.7	46	75	13	108	34	7	2	55	1.41
48028102--48028352	70	3.7	67	74	15	176	33	7	4	54	1.49
48028326--48028374	23	2.2	23	85	10	66	32	2	2	63	1.17
48030863--48030896	3	11.3	3	87	0	50	61	2	2	32	1.26
48031906--48031939	16	2.1	16	89	10	52	82	0	2	14	0.79
48032438--48032620	44	4.1	44	69	6	118	30	25	15	27	1.96
48032702--48033326	132	4.8	132	88	2	888	24	24	20	29	1.99
48033327--48033629	45	6.8	45	89	0	464	29	25	17	27	1.97
48033327--48033651	134	2.4	133	88	1	339	29	24	16	29	1.96
48034924--48034963	13	3.3	13	76	20	50	5	10	0	85	0.75
48039308--48039338	13	2.3	14	94	5	55	0	12	9	77	0.99
48040208--48040257	13	3.8	13	86	7	57	36	0	4	60	1.16
48040243--48040302	25	2.3	26	80	2	68	40	10	0	50	1.36
48041623--48041657	13	2.7	13	86	0	52	17	11	40	31	1.85
48044222--48044296	19	3.8	19	92	3	123	36	10	16	37	1.83
48049623--48049834	44	4.8	44	81	4	241	28	17	25	28	1.98
48049627--48049831	87	2.3	88	86	1	286	27	18	25	28	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48049932--48050412	216	2.2	216	89	2	736	29	19	24	26	1.98
48051037--48051111	19	3.8	19	93	6	132	37	10	16	36	1.83
48051322--48051380	23	2.6	23	100	0	118	15	3	18	62	1.45
48053331--48053445	40	2.9	38	80	6	131	33	21	21	23	1.98
48053503--48053817	41	7.7	41	86	3	379	20	22	27	29	1.99
48053502--48053817	123	2.6	122	85	4	422	20	22	27	29	1.99
48054224--48054257	14	2.3	15	85	5	52	35	0	29	35	1.58
48054343--48054611	89	3.1	86	83	11	343	26	1	27	43	1.65
48054409--48054581	82	2.1	82	90	4	269	27	2	26	43	1.69
48054993--48055026	16	2.1	16	88	5	50	70	2	2	23	1.15

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