genome.fa.s1.2.7.7.80.10.50.1000.111.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  111  of  187  ( 22383 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)
33150698--33150749	19	2.8	19	77	8	54	38	0	1	59	1.08
33150784--33150910	61	2.1	61	86	0	173	41	14	12	31	1.83
33152465--33152626	62	2.6	61	76	11	143	43	11	4	40	1.62
33152927--33153046	61	2.0	60	83	1	150	30	13	10	45	1.77
33153460--33153584	62	2.0	62	84	3	162	48	12	14	25	1.78
33153561--33153608	24	2.0	24	91	0	78	41	10	18	29	1.84
33153499--33153672	88	2.0	87	97	2	332	45	12	16	25	1.82
33159042--33159087	24	1.9	24	91	8	76	36	0	2	60	1.09
33159184--33159211	9	3.1	9	100	0	56	57	10	0	32	1.33
33159154--33159363	68	3.1	68	97	1	388	45	9	4	40	1.57
33159252--33159279	9	3.1	9	100	0	56	57	10	0	32	1.33
33159352--33159393	16	2.6	16	88	0	57	45	4	2	47	1.36
33159352--33159419	22	3.4	20	71	23	54	45	2	1	50	1.26
33159367--33159427	22	2.7	23	87	7	90	49	0	1	49	1.10
33164379--33164440	24	2.6	24	86	0	88	32	30	8	29	1.86
33166204--33166265	26	2.4	26	91	0	97	43	14	9	32	1.78
33171847--33171888	20	2.2	20	87	12	61	57	4	21	16	1.58
33172337--33172366	16	1.9	16	93	6	53	30	0	20	50	1.49
33175208--33175238	15	2.1	15	93	0	53	29	9	25	35	1.88
33201485--33201547	21	3.2	20	74	24	55	42	19	1	36	1.61
33205909--33206015	25	4.3	25	81	11	114	32	20	21	25	1.97
33222077--33222152	25	3.0	25	90	0	125	31	17	21	30	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33222078--33222201	50	2.5	50	83	10	139	31	19	19	29	1.96
33226124--33226219	50	1.9	49	87	6	140	25	22	32	19	1.98
33226132--33226246	50	2.3	50	80	4	126	26	24	27	20	1.99
33226520--33226568	20	2.5	20	81	15	66	57	6	24	12	1.58
33237613--33237654	21	1.9	23	90	9	70	30	11	14	42	1.81
33238099--33238193	47	2.0	47	100	0	190	37	10	16	34	1.84
33247595--33247662	20	3.2	22	77	10	70	13	32	22	32	1.92
33257503--33257549	20	2.3	20	85	10	60	29	19	12	38	1.89
33258248--33258272	13	1.9	13	100	0	50	40	0	12	48	1.40
33258408--33258441	18	1.9	17	88	5	50	61	0	8	29	1.26
33259673--33259715	3	14.3	3	100	0	86	32	0	0	67	0.91
33259843--33259902	23	2.6	22	73	17	59	40	3	1	55	1.27
33259909--33259952	21	2.1	21	82	0	52	29	6	0	63	1.20
33264489--33264532	18	2.4	19	85	11	56	34	0	9	56	1.31
33265029--33265081	20	2.6	20	79	8	54	56	7	1	33	1.38
33273319--33273377	8	7.1	8	77	7	55	13	6	1	77	1.03
33273321--33273389	32	2.1	33	86	2	95	14	7	1	76	1.06
33280100--33280171	26	2.8	25	85	6	99	36	5	23	34	1.78
33280704--33280775	37	1.9	37	97	0	135	40	6	23	29	1.81
33289125--33289188	26	2.5	26	86	0	83	37	6	20	35	1.78
33293398--33293432	18	1.9	18	88	0	52	25	25	0	48	1.51
33296071--33296106	18	2.0	18	94	0	63	50	11	13	25	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33297621--33297667	21	2.2	21	88	0	67	36	29	2	31	1.70
33297621--33297658	7	5.4	7	96	0	67	39	31	0	28	1.57
33298567--33298601	16	2.1	18	89	10	56	65	0	0	34	0.93
33307083--33307120	19	2.0	19	85	10	51	68	0	2	28	1.03
33308656--33308703	10	4.9	10	76	2	53	66	2	6	25	1.26
33308726--33308761	15	2.5	14	86	8	54	44	8	0	47	1.33
33309325--33309372	16	2.9	18	82	14	59	22	2	0	75	0.91
33310112--33310142	3	10.3	3	100	0	62	64	35	0	0	0.94
33310497--33310556	22	2.8	21	84	5	66	16	10	48	25	1.77
33314217--33314252	15	2.5	14	86	8	54	44	8	0	47	1.33
33316506--33316590	9	9.4	9	81	0	107	25	9	21	43	1.82
33316506--33316590	27	3.1	27	86	0	125	25	9	21	43	1.82
33321280--33321312	13	2.5	13	95	0	57	42	0	0	57	0.98
33321278--33321335	26	2.2	25	79	8	62	50	0	1	48	1.11
33324834--33324865	15	2.1	15	100	0	64	43	6	12	37	1.68
33325381--33325413	16	2.1	16	94	0	57	45	0	15	39	1.46
33326104--33326164	20	3.3	20	69	21	69	60	0	31	8	1.26
33339037--33339195	63	2.5	63	79	8	164	26	27	20	25	1.99
33342520--33342557	20	2.0	20	85	15	53	57	0	7	34	1.28
33342520--33342557	19	1.9	19	85	15	51	57	0	7	34	1.28
33343771--33343893	20	6.2	20	72	13	103	13	30	18	37	1.90
33353246--33353281	19	1.9	18	88	5	54	22	27	25	25	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33355960--33356030	26	2.7	27	84	4	83	42	4	18	35	1.70
33360258--33360457	95	2.1	93	81	9	228	21	23	18	37	1.94
33362809--33362856	16	3.2	16	76	23	52	39	0	8	52	1.32
33367895--33367932	16	2.3	16	90	4	58	42	2	0	55	1.14
33369915--33369972	23	2.5	22	75	10	62	48	1	8	41	1.44
33373827--33373865	17	2.3	17	100	0	78	25	35	20	17	1.95
33376823--33376851	13	2.1	14	93	6	51	62	10	6	20	1.50
33377310--33377428	28	4.3	28	89	3	170	42	11	21	24	1.86
33387815--33387986	26	6.5	26	80	5	166	28	22	9	39	1.86
33387855--33387991	54	2.6	54	82	4	163	27	18	9	43	1.81
33390713--33390782	33	2.1	35	79	15	85	41	1	4	52	1.30
33393264--33393306	17	2.6	16	78	10	50	20	6	18	53	1.67
33395346--33395375	15	2.0	15	100	0	60	40	13	20	26	1.89
33395659--33395687	13	2.1	14	93	6	51	34	6	6	51	1.55
33427647--33427673	5	5.4	5	100	0	54	59	0	0	40	0.98
33429241--33429273	14	2.4	14	100	0	66	45	18	0	36	1.49
33436874--33437049	25	7.4	25	69	13	111	43	20	18	18	1.89
33436874--33437059	47	4.0	47	84	4	250	44	19	17	18	1.88
33436898--33437024	22	5.5	21	68	18	67	44	18	18	18	1.88
33437033--33437080	22	2.1	23	88	3	71	54	20	14	10	1.70
33436843--33437070	94	2.4	94	81	5	280	45	20	17	16	1.86
33442000--33442061	29	2.2	29	88	8	92	54	0	25	19	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33443805--33443859	27	2.1	26	86	3	74	40	1	0	58	1.09
33444131--33444202	22	3.3	22	94	0	117	30	16	27	25	1.97
33444814--33444851	13	2.7	14	92	8	60	84	13	0	2	0.73
33444814--33444857	14	3.1	14	81	12	54	84	11	2	2	0.81
33444814--33444851	7	5.4	7	90	9	60	84	13	0	2	0.73
33446582--33446620	17	2.3	17	86	0	51	43	7	5	43	1.55
33457277--33457647	94	3.9	94	81	4	381	34	18	20	26	1.96
33457282--33457647	188	1.9	189	80	6	429	33	18	21	27	1.96
33463676--33464182	274	1.8	275	85	6	724	30	13	21	35	1.92
33472086--33472218	71	1.9	71	81	6	162	27	15	10	46	1.78
33472440--33472567	56	2.3	55	85	6	159	29	14	7	48	1.70
33472428--33472611	57	3.2	56	81	6	194	30	13	7	48	1.69
33478319--33478361	21	2.2	20	87	8	61	23	23	32	20	1.98
33478325--33478374	21	2.4	21	89	0	73	18	20	34	28	1.95
33479207--33479240	5	6.8	5	100	0	68	82	0	0	17	0.67
33481836--33481876	15	2.5	17	80	11	50	43	2	2	51	1.28
33500113--33500149	19	2.0	19	89	5	58	40	16	2	40	1.62
33504810--33504856	21	2.2	21	96	0	85	23	36	17	23	1.95
33515816--33515858	21	2.1	20	86	4	59	55	0	0	44	0.99
33515825--33515858	11	3.2	11	87	8	52	52	0	0	47	1.00
33516269--33516327	9	6.4	9	75	11	57	35	1	1	61	1.16
33519278--33519316	15	2.5	16	87	8	62	5	38	0	56	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33519622--33519664	15	2.8	16	75	7	52	37	23	6	32	1.82
33533366--33533405	14	2.8	14	92	3	62	40	0	10	50	1.36
33550477--33550564	28	3.2	27	80	13	83	28	21	20	29	1.98
33550496--33550564	28	2.5	28	86	9	88	28	23	18	28	1.98
33550526--33550698	57	3.1	57	81	5	192	28	22	16	31	1.96
33550829--33550987	53	3.0	53	82	1	185	28	22	12	37	1.90
33551900--33551942	22	2.0	22	100	0	86	23	25	13	37	1.92
33552895--33552929	2	17.5	2	100	0	70	48	0	0	51	1.00
33554066--33554092	4	6.8	4	100	0	54	0	22	0	77	0.76
33555979--33556020	11	3.6	11	81	12	57	40	0	2	57	1.12

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