genome.fa.s4.2.7.7.80.10.50.1000.22.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  22  of  198  ( 23681 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)
6539221--6539285	30	2.2	30	82	0	76	35	21	21	21	1.96
6546506--6546645	40	3.5	40	81	6	169	30	25	17	26	1.98
6546829--6546866	2	19.0	2	100	0	76	50	0	0	50	1.00
6547650--6547678	12	2.3	13	94	5	51	55	0	0	44	0.99
6548574--6548688	46	2.5	46	91	0	194	37	13	13	34	1.85
6550924--6550948	12	2.1	12	100	0	50	32	16	16	36	1.90
6551698--6551750	25	2.1	25	82	10	63	24	1	3	69	1.15
6551710--6551757	17	2.8	18	78	9	55	33	2	2	62	1.18
6566311--6566416	43	2.4	43	82	6	124	48	0	3	47	1.26
6573487--6573579	5	19.8	5	76	13	65	81	0	11	6	0.86
6573488--6573579	14	6.6	14	74	9	89	81	0	11	6	0.86
6573493--6573582	23	3.9	23	80	11	112	80	0	12	7	0.91
6574466--6574576	44	2.5	44	85	1	132	29	18	20	30	1.97
6574462--6575767	45	28.8	45	68	14	259	32	17	20	29	1.95
6574787--6576554	44	39.7	43	68	14	245	31	17	20	29	1.96
6574457--6575042	180	3.3	180	88	0	841	32	17	20	30	1.95
6575245--6575915	45	14.9	44	69	14	273	31	17	21	30	1.96
6575474--6575915	181	2.5	180	90	2	683	29	17	22	30	1.96
6575821--6576026	111	1.9	111	93	0	358	27	18	23	30	1.98
6575941--6576593	44	14.7	44	72	9	396	30	18	21	30	1.97
6575640--6576205	290	1.9	290	93	1	972	29	18	22	30	1.97
6575934--6576377	179	2.5	180	89	1	667	30	18	21	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6575514--6576377	471	1.8	469	93	0	1413	29	17	21	30	1.97
6579057--6579120	32	2.0	32	100	0	128	28	25	15	31	1.96
6588010--6588039	9	3.2	9	90	9	51	23	0	0	76	0.78
6588003--6588039	19	1.9	19	94	0	65	29	0	0	70	0.88
6588066--6588134	21	3.2	20	72	13	57	63	10	1	24	1.34
6588930--6588988	24	2.4	25	91	2	93	38	0	1	59	1.08
6588919--6588971	12	4.5	12	76	2	54	39	1	0	58	1.09
6589650--6589687	17	2.2	17	90	0	58	31	26	15	26	1.96
6594170--6594341	41	4.2	40	80	6	161	29	12	23	34	1.91
6594170--6594341	82	2.1	80	82	7	204	29	12	23	34	1.91
6597108--6597165	26	2.2	26	90	6	91	18	22	24	34	1.96
6600165--6600208	21	2.1	21	86	0	61	63	0	2	34	1.07
6600830--6600886	2	28.5	2	100	0	114	0	49	0	50	1.00
6616667--6616716	8	5.7	9	77	11	50	76	0	4	20	0.95
6616674--6616724	5	10.0	5	76	19	52	76	0	1	21	0.88
6616675--6616716	17	2.4	17	84	4	57	78	0	2	19	0.86
6616667--6616724	20	2.7	21	82	12	66	75	0	3	20	0.94
6616675--6616726	12	4.5	11	77	17	52	76	0	1	21	0.87
6624636--6624751	35	3.3	35	86	3	153	14	12	31	42	1.82
6632250--6632360	28	4.0	28	97	0	213	26	0	30	43	1.55
6632313--6632427	28	4.0	28	79	12	106	34	1	25	38	1.66
6632368--6632423	27	2.1	27	100	0	112	39	0	25	35	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6632368--6632439	27	2.6	27	91	2	99	40	0	22	37	1.54
6632878--6633026	35	4.2	35	78	5	140	18	10	28	42	1.84
6632923--6633070	35	4.2	36	80	4	140	18	9	33	39	1.83
6633932--6633961	12	2.5	12	94	0	51	23	40	30	6	1.80
6646031--6646066	16	2.2	16	90	0	54	58	5	2	33	1.36
6647753--6647808	25	2.2	25	96	0	103	32	8	5	53	1.55
6651238--6651270	2	16.5	2	100	0	66	51	0	48	0	1.00
6658457--6658490	11	3.1	11	100	0	68	38	35	0	26	1.57
6659770--6659815	3	15.3	3	100	0	92	34	0	0	65	0.93
6660044--6660069	8	3.2	8	100	0	52	26	11	0	61	1.30
6670896--6670937	18	2.4	17	92	4	66	33	0	7	59	1.25
6671298--6671342	3	15.0	3	100	0	90	33	0	0	66	0.92
6671437--6671474	20	1.9	19	89	5	58	15	5	7	71	1.28
6673389--6673413	2	12.5	2	100	0	50	0	52	0	48	1.00
6680435--6680477	19	2.3	19	84	8	52	39	0	4	55	1.20
6680441--6680475	18	1.9	19	88	11	56	42	0	2	54	1.15
6680526--6680551	13	2.0	13	100	0	52	46	15	0	38	1.46
6690396--6690425	12	2.4	12	94	5	51	20	0	23	56	1.42
6695022--6695050	8	3.6	8	100	0	58	65	10	10	13	1.47
6696146--6696186	21	2.0	21	90	0	64	19	0	39	41	1.52
6702461--6702490	13	2.3	13	94	0	51	60	3	0	36	1.14
6702744--6702771	8	3.5	8	100	0	56	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6704667--6704737	35	2.0	35	100	0	142	28	8	32	30	1.87
6718647--6718692	9	5.1	9	83	0	56	15	39	10	34	1.82
6720951--6721011	13	4.6	13	78	11	70	57	3	1	37	1.25
6720951--6721018	13	5.2	12	76	16	64	57	2	2	36	1.29
6720833--6721200	182	2.0	182	97	0	700	47	7	7	38	1.60
6721133--6721203	13	5.4	13	80	9	72	54	2	4	38	1.34
6721133--6721203	27	2.7	26	82	8	90	54	2	4	38	1.34
6721575--6721686	58	1.9	59	87	1	163	50	15	18	15	1.77
6721674--6721711	11	3.4	11	85	7	58	57	7	10	23	1.58
6721901--6721943	16	2.7	15	85	10	50	44	2	44	9	1.49
6721914--6721945	16	2.1	15	94	5	55	43	0	50	6	1.27
6723795--6723847	27	2.0	27	92	0	88	7	16	28	47	1.74
6726945--6727036	3	29.7	3	80	8	96	27	4	2	66	1.22
6727000--6727048	21	2.3	20	76	10	53	26	12	0	61	1.31
6728233--6728257	6	4.2	6	100	0	50	0	20	16	64	1.30
6735629--6735669	2	20.5	2	100	0	82	0	51	0	48	1.00
6739433--6739478	4	11.5	4	78	17	51	71	0	6	21	1.08
6739690--6739731	19	2.1	21	91	8	70	71	2	4	21	1.16
6740484--6740512	14	2.0	15	93	6	51	0	0	24	75	0.80
6746035--6746073	16	2.4	16	82	0	51	51	2	10	35	1.50
6746345--6746381	3	12.3	3	88	0	56	62	0	2	35	1.10
6747773--6748013	132	1.8	132	96	0	446	26	22	19	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6750069--6750964	88	10.2	88	93	0	1506	25	24	22	26	2.00
6752179--6752253	9	8.6	9	81	12	86	13	13	0	73	1.10
6752179--6752252	16	4.3	17	82	14	89	13	13	0	72	1.11
6752179--6752226	8	6.0	8	90	9	80	12	12	0	75	1.06
6753101--6753125	7	3.6	7	100	0	50	12	0	12	76	1.04
6753101--6753147	6	7.8	6	86	11	53	6	0	12	80	0.88
6756549--6756587	16	2.4	16	82	0	51	51	2	10	35	1.50
6760025--6760061	19	1.9	19	94	0	65	78	2	2	16	0.98
6760956--6760996	20	2.0	20	85	0	55	58	2	4	34	1.32
6764691--6764757	33	2.0	33	100	0	134	49	2	20	26	1.64
6765155--6765216	26	2.4	26	97	0	115	46	0	1	51	1.10
6765391--6765445	25	2.2	24	81	15	60	45	1	0	52	1.11
6765660--6765705	16	2.9	16	93	0	74	32	34	0	32	1.58
6765662--6765713	16	3.2	16	86	5	70	34	34	0	30	1.58
6766041--6766091	17	3.0	17	94	0	84	52	0	9	37	1.34
6769216--6769240	10	2.5	10	100	0	50	32	40	0	28	1.57
6773374--6773509	67	2.0	67	98	0	263	37	21	12	28	1.90
6776074--6776102	14	2.0	15	93	6	51	6	10	6	75	1.17
6788340--6788365	5	5.2	5	100	0	52	80	19	0	0	0.71
6788914--6788947	18	1.9	17	88	5	50	61	5	20	11	1.50
6789286--6790102	153	5.4	151	86	8	1075	52	7	10	29	1.63
6789286--6790102	305	2.7	304	88	4	1177	52	7	10	29	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6792054--6792275	113	2.0	109	92	3	363	37	13	18	30	1.89
6793731--6793790	20	3.1	19	75	2	57	15	0	35	50	1.44
6798166--6798211	23	2.0	23	84	12	60	19	0	17	63	1.32
6798792--6798821	9	3.3	9	95	0	51	90	3	0	6	0.56
6805357--6805441	25	3.4	25	69	6	73	31	16	28	23	1.96
6805327--6805447	50	2.4	50	90	0	179	33	17	28	21	1.96
6805568--6805691	64	1.9	64	88	0	185	34	21	21	21	1.97
6812135--6812197	25	2.5	24	80	17	67	39	17	23	19	1.92
6812140--6812211	24	3.0	25	76	13	62	38	18	23	19	1.93
6814224--6814288	32	2.0	32	100	0	130	23	24	9	43	1.83

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