genome.fa.s13.2.7.7.80.10.50.1000.17.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  17  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)
5228090--5228227	44	3.1	44	63	8	109	26	21	23	28	1.99
5227829--5228342	264	1.9	264	83	0	652	27	21	18	31	1.97
5228274--5228501	89	2.6	89	88	0	339	25	23	23	27	2.00
5229448--5229513	5	13.4	5	78	15	59	1	15	0	83	0.72
5229450--5229512	6	10.5	6	80	17	69	1	12	0	85	0.66
5229448--5229512	29	2.2	30	86	8	89	1	13	0	84	0.69
5232172--5232218	23	2.0	23	91	0	76	31	4	12	51	1.59
5234921--5234945	10	2.5	10	100	0	50	52	0	28	20	1.47
5237561--5237609	9	5.4	9	90	0	80	26	12	22	38	1.89
5237560--5237609	18	2.8	18	100	0	100	28	12	22	38	1.89
5237662--5237698	9	4.1	9	92	0	65	45	13	10	29	1.77
5244062--5244112	26	1.9	27	84	4	68	19	13	13	52	1.73
5244306--5244352	18	2.7	18	80	9	53	23	2	2	72	1.06
5246984--5247115	45	3.0	45	85	2	151	23	15	26	34	1.95
5249828--5249870	19	2.2	20	80	12	54	34	18	0	46	1.50
5250052--5250196	42	3.5	41	66	16	109	35	22	20	21	1.96
5250043--5250197	83	1.9	83	95	0	283	36	21	21	20	1.96
5250135--5250196	21	3.0	21	75	0	70	35	25	19	19	1.95
5250363--5250419	29	2.0	29	96	0	105	38	21	0	40	1.53
5252504--5252550	24	2.0	24	91	0	76	23	12	8	55	1.64
5257805--5257867	27	2.4	27	89	2	101	41	12	0	46	1.42
5257860--5257893	17	2.0	17	88	0	50	79	8	2	8	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5257924--5258026	27	3.8	26	75	7	98	25	21	33	20	1.97
5258244--5258290	3	15.7	3	95	0	85	31	0	2	65	1.04
5259139--5259181	18	2.4	18	80	0	50	25	6	48	18	1.73
5264795--5264861	28	2.3	31	80	19	81	0	29	0	70	0.88
5264825--5264974	18	8.2	17	72	16	79	0	28	0	71	0.86
5264797--5264959	37	4.6	34	75	18	127	0	30	0	69	0.88
5264855--5264974	4	30.0	4	75	20	83	0	28	0	71	0.86
5264794--5264966	78	2.3	74	91	6	276	0	29	0	70	0.87
5264863--5264940	33	2.4	33	82	16	92	0	29	0	70	0.87
5264794--5264970	30	5.9	30	69	18	93	0	29	0	70	0.87
5265013--5265064	27	1.9	27	88	0	77	17	30	25	26	1.97
5265123--5265185	28	2.4	27	92	7	103	47	0	11	41	1.39
5265332--5265379	24	2.0	24	100	0	96	45	8	4	41	1.53
5276869--5276902	17	2.0	17	88	0	50	55	14	5	23	1.61
5281966--5282033	25	2.7	25	72	4	66	26	20	30	22	1.98
5282140--5282223	25	3.4	25	81	0	96	34	21	27	16	1.95
5282487--5282609	61	2.0	61	100	0	246	27	22	8	41	1.82
5288217--5288271	25	2.2	25	81	12	60	49	3	3	43	1.37
5288276--5288310	17	2.0	18	94	5	63	51	5	0	42	1.25
5292149--5292196	21	2.3	21	85	0	60	39	12	20	27	1.89
5297386--5297446	27	2.3	27	80	5	70	49	6	0	44	1.28
5304353--5304386	16	2.1	16	94	0	59	70	2	11	14	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5306187--5306282	40	2.4	39	86	8	124	32	6	19	41	1.77
5306197--5306275	21	3.8	20	70	20	56	31	5	20	43	1.73
5306581--5306625	6	7.3	6	80	5	54	22	20	13	44	1.85
5306497--5306601	45	2.3	45	80	3	131	22	16	16	44	1.86
5314878--5314911	14	2.4	14	85	0	50	67	0	0	32	0.91
5314880--5314961	27	2.9	27	68	25	62	60	1	3	34	1.22
5317173--5317264	22	4.0	22	79	12	87	42	18	22	16	1.89
5317219--5317277	25	2.4	25	94	0	100	38	18	25	16	1.92
5317411--5317476	2	34.0	2	82	17	86	48	3	0	48	1.17
5322711--5322742	15	2.1	15	94	0	55	15	6	9	68	1.36
5335190--5335257	28	2.4	28	80	2	82	48	10	16	25	1.77
5335349--5335399	26	2.0	26	88	7	77	39	3	9	47	1.55
5335548--5335600	22	2.3	22	78	12	54	39	1	5	52	1.36
5338734--5338773	20	2.1	19	85	4	53	20	2	12	65	1.38
5339586--5339630	21	2.0	23	87	8	67	40	15	2	42	1.59
5343683--5343730	11	4.4	11	75	0	51	20	6	8	64	1.43
5345317--5345374	18	3.2	18	82	7	64	44	0	1	53	1.10
5348871--5348915	22	2.0	22	95	0	81	44	8	28	17	1.79
5351220--5351247	9	3.1	9	100	0	56	46	10	10	32	1.73
5352397--5352443	23	2.0	23	100	0	94	27	17	17	38	1.91
5352564--5352623	21	2.9	21	97	0	111	10	15	23	51	1.72
5352704--5352970	43	6.3	42	84	5	324	26	29	19	24	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5352704--5352970	85	3.1	84	86	1	363	26	29	19	24	1.98
5352704--5352968	128	2.1	128	84	2	354	26	29	19	24	1.98
5353185--5353210	9	2.9	9	100	0	52	30	11	11	46	1.76
5356516--5356562	25	1.9	25	86	4	69	36	8	4	51	1.52
5357410--5357464	21	2.5	22	76	2	67	38	36	0	25	1.56
5357528--5357564	7	5.3	7	100	0	74	27	59	0	13	1.35
5357519--5357564	21	2.2	21	92	0	74	30	56	0	13	1.37
5357643--5357689	14	3.4	14	81	0	58	31	42	0	25	1.55
5357344--5357682	110	2.9	114	78	10	350	42	29	0	27	1.62
5358102--5358257	41	3.8	41	89	0	240	30	24	20	25	1.99
5358291--5358425	40	3.4	40	82	3	148	20	22	22	34	1.96
5359941--5359973	3	11.0	3	93	0	57	69	0	0	30	0.88
5361515--5362620	44	25.2	44	64	14	334	26	23	18	30	1.98
5361462--5362618	132	8.8	132	93	0	1911	26	23	18	30	1.98
5361534--5362449	88	10.4	89	66	12	368	27	23	18	30	1.98
5361462--5362618	527	2.2	528	93	0	1974	26	23	18	30	1.98
5362635--5362878	89	2.7	87	83	4	308	29	23	15	31	1.95
5362597--5362878	44	6.4	44	73	5	219	29	24	14	31	1.95
5364057--5364087	14	2.3	13	94	5	53	12	16	0	70	1.16
5364057--5364104	16	3.2	16	85	8	57	12	18	2	66	1.33
5364997--5365036	18	2.2	18	86	0	53	60	10	17	12	1.59
5366615--5366656	18	2.3	18	84	8	59	42	2	0	54	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5366807--5366858	26	2.0	27	85	10	74	19	5	11	63	1.47
5366981--5367286	109	2.8	108	87	7	444	30	16	18	33	1.93
5369296--5369334	19	2.0	20	85	5	53	46	7	20	25	1.77
5372493--5372531	14	2.7	15	80	11	55	30	17	10	41	1.83
5372924--5372971	15	3.3	14	85	8	60	14	0	20	64	1.28
5372924--5372972	14	3.3	15	88	5	64	14	0	20	65	1.27
5373682--5373741	29	2.0	31	87	6	88	30	11	13	45	1.79
5377644--5377673	14	2.1	14	93	0	51	3	13	0	83	0.77
5377795--5377854	28	2.1	28	87	6	86	0	28	0	71	0.86
5378238--5378355	28	4.1	28	81	4	119	47	3	15	33	1.62
5378257--5378355	29	3.4	28	84	8	119	47	3	15	34	1.61
5378358--5378398	14	2.7	15	88	7	57	24	4	4	65	1.32
5389642--5389708	34	1.9	35	87	3	100	44	14	8	31	1.76
5391415--5391458	15	2.7	17	89	6	65	29	36	20	13	1.91
5391417--5391473	17	3.5	17	85	4	64	38	35	17	8	1.81
5395654--5395883	114	2.0	114	96	0	424	39	18	20	21	1.93
5406294--5407363	516	2.1	506	88	4	1551	38	18	14	28	1.90
5407364--5407440	38	2.0	38	100	0	154	41	14	15	28	1.86
5407293--5407510	108	2.0	108	90	3	341	41	14	16	28	1.87
5407402--5407538	70	2.0	70	95	0	247	40	13	17	28	1.88
5410117--5410164	21	2.3	21	92	0	78	29	37	10	22	1.88
5416476--5416536	32	1.9	31	83	9	79	44	6	8	40	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5419870--5419896	2	13.5	2	100	0	54	51	0	0	48	1.00
5423372--5423417	3	15.3	3	81	0	56	30	34	0	34	1.58
5429709--5429861	43	3.6	43	87	0	209	30	17	26	26	1.97
5431968--5432016	25	2.0	25	100	0	98	40	30	8	20	1.81
5434001--5434053	23	2.3	23	78	12	56	64	5	0	30	1.17
5435201--5435227	13	2.1	13	100	0	54	51	0	14	33	1.43
5436617--5436706	47	1.9	47	100	0	180	26	8	15	48	1.74
5442742--5442817	26	2.9	27	80	7	68	35	21	21	22	1.96
5444308--5444374	34	1.9	35	87	3	100	31	8	14	44	1.76
5445106--5445130	11	2.3	11	100	0	50	52	0	20	28	1.47

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