genome.fa.s6.2.7.7.80.10.50.1000.146.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  146  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)
42955733--42955772	21	1.9	21	90	10	64	45	12	0	42	1.42
42955742--42955783	21	2.0	21	85	0	57	40	19	2	38	1.64
42957350--42957430	31	2.6	31	76	18	80	38	1	2	58	1.20
42957419--42957514	50	1.9	50	83	8	124	34	2	2	61	1.19
42957450--42957507	22	2.7	22	80	19	61	37	0	1	60	1.07
42957448--42957507	21	2.8	20	79	20	68	38	0	1	60	1.07
42957649--42957742	31	2.9	32	77	3	91	47	8	21	22	1.77
42966388--42966436	17	3.0	16	77	11	55	69	2	0	28	1.00
42966729--42966758	15	2.1	14	93	6	51	43	0	0	56	0.99
42966797--42966827	15	2.1	15	93	0	53	41	0	0	58	0.98
42974163--42974401	80	3.0	80	78	12	217	38	11	7	42	1.69
42975070--42975115	25	1.9	23	86	8	65	30	0	2	67	1.03
42979824--42979862	19	2.1	19	90	9	62	38	0	0	61	0.96
42979826--42979874	22	2.3	21	86	10	64	38	0	0	61	0.96
42979932--42980056	27	4.6	27	83	0	142	24	22	28	24	1.99
42984475--42984607	60	2.2	60	87	1	185	57	12	0	28	1.41
42984687--42984724	16	2.4	16	82	13	51	0	26	0	73	0.83
42984688--42984724	19	1.9	19	94	0	65	0	24	0	75	0.80
42984866--42984922	27	2.1	27	93	0	96	19	26	26	28	1.99
42991571--42991618	26	1.9	24	84	16	62	54	8	8	29	1.60
42997315--42997372	20	2.9	21	73	21	61	46	5	5	43	1.48
43000670--43000701	3	10.7	3	100	0	64	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43001608--43001663	22	2.5	22	100	0	112	32	17	14	35	1.90
43005113--43005137	2	12.5	2	100	0	50	52	0	0	48	1.00
43009667--43009703	3	12.3	3	94	0	65	29	0	2	67	1.04
43010690--43010787	31	3.2	31	64	30	82	30	7	25	36	1.83
43010667--43010792	62	2.0	62	100	0	252	32	7	23	35	1.84
43021587--43021656	20	3.7	19	72	16	65	64	0	27	8	1.22
43022522--43022623	53	2.0	51	84	5	134	45	7	22	24	1.79
43023042--43023086	18	2.4	19	88	7	65	35	0	0	64	0.94
43023042--43023086	19	2.4	18	85	14	56	35	0	0	64	0.94
43042478--43042544	28	2.4	27	82	7	80	65	2	7	23	1.32
43046413--43046478	18	3.7	18	78	8	71	33	0	1	65	1.02
43046409--43046445	11	3.8	10	82	17	51	27	0	0	72	0.84
43046433--43046472	17	2.3	18	91	4	64	32	0	2	65	1.06
43047531--43047579	26	2.0	24	88	8	71	53	2	0	44	1.12
43047837--43047867	15	2.1	15	100	0	62	32	0	6	61	1.21
43079245--43079487	50	4.8	50	89	0	369	25	23	30	19	1.98
43087154--43087263	25	4.5	24	85	7	125	41	20	21	16	1.90
43087181--43087263	25	3.3	25	93	3	132	38	22	22	15	1.92
43088288--43088313	11	2.4	11	100	0	52	0	42	7	50	1.31
43088369--43088408	5	7.6	5	83	10	53	60	0	0	40	0.97
43088369--43088409	16	2.6	16	92	0	73	60	0	0	39	0.96
43088374--43088403	8	3.8	8	90	0	51	60	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43093151--43093356	52	4.1	52	86	9	300	34	15	22	27	1.94
43093217--43093373	46	3.3	46	85	10	224	36	14	22	27	1.92
43093165--43093373	98	2.1	98	95	0	373	35	14	22	27	1.93
43093263--43093373	52	2.1	53	91	1	179	36	13	22	27	1.92
43093337--43093445	37	3.0	37	90	2	177	36	17	22	23	1.94
43094375--43094471	49	2.0	50	89	2	151	23	15	27	32	1.95
43100580--43100616	19	1.9	19	100	0	74	48	0	5	45	1.25
43119016--43119077	29	2.1	29	84	0	79	24	12	6	56	1.60
43119549--43119575	3	9.0	3	100	0	54	33	0	0	66	0.92
43127614--43127695	29	2.7	30	86	3	112	39	3	4	52	1.41
43127670--43127707	19	2.0	19	89	0	58	36	5	5	52	1.47
43133621--43133692	36	2.0	36	97	0	135	20	22	15	41	1.89
43143236--43143274	6	6.5	6	100	0	78	15	33	0	51	1.44
43144378--43144435	25	2.3	26	75	21	61	44	0	3	51	1.18
43153884--43153912	4	7.5	4	92	7	51	72	0	27	0	0.85
43167907--43167953	19	2.5	19	77	19	53	51	2	2	44	1.25
43168231--43168264	17	1.9	18	94	5	61	64	2	5	26	1.30
43170465--43170528	31	2.1	31	84	0	83	43	10	10	34	1.75
43191900--43191941	20	2.0	21	86	4	59	21	0	4	73	1.01
43191909--43191948	20	2.0	20	85	0	53	22	0	2	75	0.93
43203888--43203912	1	25.0	1	100	0	50	0	0	0	100	0.00
43206246--43206281	18	2.0	18	94	0	63	63	0	0	36	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43208872--43208897	5	5.2	5	100	0	52	0	38	0	61	0.96
43211998--43212035	14	2.7	14	91	0	67	55	15	7	21	1.66
43211973--43212069	50	1.9	50	97	0	185	46	16	11	25	1.80
43212012--43212088	36	2.1	36	95	0	136	42	16	12	27	1.85
43214543--43214579	18	2.0	20	84	10	51	56	5	24	13	1.58
43220018--43220061	23	1.9	23	95	0	79	38	0	18	43	1.50
43220782--43220812	10	3.1	10	90	0	53	9	9	19	61	1.54
43221341--43221370	3	10.0	3	100	0	60	33	0	33	33	1.58
43223490--43223534	13	3.2	15	72	15	51	28	4	4	62	1.34
43229734--43229758	13	1.9	13	100	0	50	12	8	0	80	0.92
43230973--43231030	26	2.2	26	84	6	71	34	10	0	55	1.34
43230948--43231019	21	3.4	21	76	14	85	34	6	1	56	1.35
43236965--43237302	139	2.4	140	82	4	371	32	19	20	27	1.97
43237971--43237995	13	1.9	13	100	0	50	12	8	0	80	0.92
43239339--43239389	2	25.5	2	84	7	68	45	3	0	50	1.20
43240595--43240738	9	15.4	9	66	21	66	65	0	2	31	1.12
43240595--43240722	28	4.6	29	79	12	126	64	0	2	32	1.12
43240621--43240747	10	13.2	10	65	14	52	63	0	3	32	1.15
43240687--43240771	39	2.2	40	81	10	95	62	2	5	29	1.31
43241068--43241131	10	6.8	9	74	13	58	32	3	0	64	1.10
43241055--43241124	29	2.4	30	81	13	83	31	4	0	64	1.13
43241068--43241131	19	3.4	18	75	14	58	32	3	0	64	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43241081--43241139	19	3.2	17	81	13	73	33	1	0	64	1.04
43241002--43241138	9	14.4	9	70	15	73	31	3	0	64	1.10
43241964--43242082	6	19.8	6	84	3	123	6	47	15	31	1.71
43245710--43245781	27	2.6	29	79	14	80	56	2	4	36	1.33
43260448--43260472	3	8.3	3	100	0	50	68	0	32	0	0.90
43269017--43269042	2	13.0	2	100	0	52	50	0	50	0	1.00
43279817--43279917	49	2.1	49	96	0	184	23	15	15	44	1.85
43281513--43281568	27	2.1	27	100	0	112	25	14	19	41	1.89
43287063--43287095	15	2.2	15	94	0	57	60	0	3	36	1.12
43299559--43299600	18	2.4	18	84	11	52	38	4	7	50	1.51
43300381--43300445	32	2.1	32	94	2	114	30	9	10	49	1.69
43300745--43300803	3	19.7	3	100	0	118	32	0	0	67	0.91
43301069--43301099	12	2.6	12	94	0	53	70	19	9	0	1.14
43302770--43302810	3	13.7	3	100	0	82	34	0	0	65	0.93
43306359--43306405	24	2.0	24	87	8	69	44	0	0	55	0.99
43311072--43311100	15	1.9	15	100	0	58	48	6	10	34	1.64
43311206--43311235	15	2.0	15	93	0	51	76	0	6	16	0.99
43317488--43317569	27	3.1	27	77	5	96	59	1	3	35	1.23
43317484--43317616	9	14.4	9	70	14	69	61	3	3	32	1.26
43317634--43317674	20	2.1	20	86	4	57	60	12	2	24	1.43
43317951--43318079	10	14.0	9	68	22	56	34	2	0	62	1.13
43317843--43317994	69	2.2	70	76	11	163	30	3	3	61	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43317941--43318048	29	3.8	29	76	11	100	32	2	0	63	1.15
43317997--43318080	28	3.1	26	78	8	78	35	2	1	60	1.17
43318008--43318068	17	3.5	17	73	22	54	31	3	1	63	1.20
43318961--43319148	42	4.6	41	87	4	236	34	3	0	62	1.11
43319006--43319084	39	2.2	33	80	14	86	30	3	0	65	1.10
43319056--43319148	11	8.9	11	67	22	58	40	2	0	56	1.11
43321138--43321172	11	3.1	12	92	8	56	80	5	5	8	1.03
43329711--43329745	16	2.2	16	89	0	52	37	5	20	37	1.76
43337875--43337940	29	2.2	29	78	2	69	39	6	10	43	1.64
43339614--43339678	24	2.9	23	77	13	64	10	18	0	70	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