genome.fa.s3.2.7.7.80.10.50.1000.19.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  19  of  150  ( 17918 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)
5107438--5107468	2	15.5	2	100	0	62	51	0	0	48	1.00
5110671--5110713	22	2.0	22	86	9	61	41	0	2	55	1.12
5111196--5111225	13	2.4	13	94	5	53	0	26	0	73	0.84
5114063--5114103	22	1.9	21	85	5	55	46	0	0	53	1.00
5114066--5114179	33	3.6	31	87	5	149	40	1	2	55	1.24
5116220--5116262	22	2.0	22	90	0	68	9	13	27	48	1.73
5116334--5116482	43	3.5	43	93	3	239	31	24	20	22	1.98
5116921--5116964	22	2.0	21	82	4	52	54	0	22	22	1.45
5117097--5117139	22	2.0	22	90	0	68	9	13	27	48	1.73
5117213--5117522	43	7.3	42	85	4	358	31	22	20	25	1.98
5117942--5117981	12	3.3	12	89	0	53	5	37	15	42	1.68
5117966--5118034	21	3.3	21	81	0	84	4	42	17	36	1.69
5123485--5123583	16	5.9	17	76	13	73	28	3	21	47	1.65
5123485--5123592	9	12.6	9	75	16	86	28	2	21	47	1.65
5123659--5123720	12	5.5	11	87	11	74	29	1	16	53	1.52
5123666--5123720	12	4.8	12	88	4	78	29	1	16	52	1.54
5123659--5123727	24	3.0	24	87	8	92	27	1	17	53	1.52
5123679--5123733	24	2.5	22	85	8	67	27	1	21	49	1.60
5123858--5123920	19	3.3	19	73	8	65	53	1	0	44	1.10
5123864--5123920	17	3.1	17	76	16	60	56	1	0	42	1.10
5123860--5123923	21	3.3	20	74	22	66	56	1	0	42	1.09
5123921--5124001	9	9.0	9	67	15	51	38	1	18	41	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5123958--5124006	18	2.9	17	85	8	64	42	2	18	36	1.62
5125701--5125791	45	2.0	45	89	0	137	35	8	31	24	1.86
5127033--5127079	7	6.6	7	80	4	58	40	42	0	17	1.49
5127495--5127904	114	3.6	114	81	4	470	29	22	18	30	1.97
5127453--5127849	115	3.5	114	82	4	503	29	21	18	29	1.97
5127436--5127862	229	1.9	229	90	2	678	30	22	18	29	1.97
5130134--5130186	13	4.1	12	76	13	52	32	7	24	35	1.84
5130134--5130186	26	2.0	26	88	0	79	32	7	24	35	1.84
5139133--5139311	50	3.5	50	79	4	160	25	20	29	24	1.99
5139575--5139613	12	3.2	12	85	7	53	53	7	23	15	1.67
5141967--5142125	64	2.5	64	86	0	219	23	30	22	24	1.99
5151871--5151895	11	2.3	11	100	0	50	16	28	8	48	1.74
5160257--5160294	20	1.9	20	89	10	60	42	13	5	39	1.66
5163850--5163902	24	2.2	24	89	0	79	52	7	3	35	1.48
5165868--5165907	11	3.7	11	83	6	55	72	0	27	0	0.85
5165933--5165971	19	2.0	21	85	10	55	23	0	10	66	1.22
5166041--5166090	3	16.7	3	100	0	100	0	0	32	68	0.90
5169450--5169894	160	2.8	156	73	15	458	31	12	6	49	1.67
5169794--5169991	98	2.0	99	85	7	271	28	14	6	51	1.65
5171156--5171237	3	27.0	3	77	11	78	28	2	1	68	1.10
5171156--5171237	32	2.5	33	84	7	98	28	2	1	68	1.10
5171565--5171618	22	2.4	22	84	9	56	35	5	3	55	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5173268--5173311	14	3.4	14	76	23	60	0	29	0	70	0.88
5173268--5173372	4	26.5	4	70	24	55	0	30	0	68	0.96
5173269--5173378	57	1.9	58	83	12	147	1	31	0	66	1.02
5173252--5173373	24	5.5	24	72	22	97	0	31	0	66	1.03
5173279--5173373	10	9.0	10	72	25	63	1	30	0	68	0.97
5173326--5173372	14	3.4	14	80	16	53	0	27	0	72	0.85
5180304--5180360	29	2.0	29	100	0	114	36	24	14	24	1.92
5180597--5180657	22	2.7	22	87	2	77	49	1	1	47	1.21
5180633--5180672	16	2.5	16	91	0	62	47	2	7	42	1.45
5180907--5180977	31	2.2	33	82	10	83	22	30	16	29	1.96
5181986--5182124	44	3.2	44	64	13	106	23	25	24	25	2.00
5181982--5182695	263	2.7	260	89	1	1088	26	23	24	25	2.00
5181982--5182699	88	8.2	88	90	1	1068	26	24	24	25	2.00
5183208--5183246	21	1.9	21	89	5	62	51	30	2	15	1.57
5184254--5184320	3	22.3	3	77	11	66	28	2	1	67	1.14
5184613--5184687	32	2.5	30	81	18	93	36	5	2	56	1.36
5184630--5184684	27	1.9	28	85	10	76	38	5	0	56	1.23
5184641--5184702	26	2.3	26	81	8	63	38	3	4	53	1.39
5185197--5185402	112	1.8	112	94	0	367	33	15	18	33	1.92
5186182--5186269	21	4.1	21	72	15	74	0	30	3	65	1.09
5186225--5186282	10	5.7	10	72	25	50	0	31	1	67	1.01
5186225--5186276	23	2.2	24	93	3	88	0	30	1	67	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5187381--5187466	40	2.3	36	80	13	93	32	5	9	52	1.57
5190932--5190961	16	1.9	15	93	6	51	26	3	0	70	1.03
5190967--5191012	23	1.9	25	86	8	69	26	4	6	63	1.38
5190887--5191763	160	5.6	157	70	16	648	30	11	6	51	1.63
5190750--5191764	325	3.2	323	92	3	1652	31	11	6	50	1.63
5191665--5191861	98	2.0	97	83	8	249	28	13	5	51	1.63
5191526--5192020	256	1.9	255	90	2	789	31	11	6	50	1.65
5193795--5193851	16	3.7	15	79	6	51	26	5	0	68	1.11
5196026--5196067	19	2.2	19	83	8	50	28	21	9	40	1.84
5197955--5197995	20	2.0	20	90	9	66	14	14	4	65	1.42
5198915--5198956	7	6.0	7	81	18	52	71	0	14	14	1.15
5198915--5198956	21	2.0	21	90	9	68	71	0	14	14	1.15
5200256--5200967	44	16.1	44	80	6	676	30	13	23	32	1.93
5200245--5200967	88	8.2	88	88	3	904	30	13	23	32	1.93
5200986--5201113	45	2.9	45	77	12	122	30	20	23	25	1.98
5201047--5201202	44	3.6	45	69	20	132	30	21	19	28	1.98
5202904--5202930	2	13.5	2	100	0	54	48	0	0	51	1.00
5203291--5203336	20	2.3	20	85	3	58	34	6	13	45	1.69
5205125--5205294	8	22.0	8	68	24	57	0	30	0	69	0.93
5205142--5205293	4	37.8	4	74	22	76	0	27	0	71	0.90
5205142--5205294	10	14.8	10	71	18	93	0	28	0	71	0.91
5205151--5205294	14	10.0	13	72	20	85	0	28	0	70	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5205142--5205285	34	4.1	34	79	11	134	0	27	0	72	0.90
5205146--5205294	44	3.7	38	76	20	144	0	28	0	71	0.91
5209972--5210013	19	2.2	19	83	8	50	23	21	11	42	1.86
5212627--5212766	47	3.0	47	89	1	210	45	17	25	12	1.84
5212628--5212766	46	3.0	46	87	1	197	45	17	24	12	1.83
5214034--5214532	133	3.8	133	80	1	561	29	17	24	29	1.97
5214034--5214445	177	2.3	177	83	1	511	29	16	24	29	1.97
5214034--5214401	89	4.1	89	87	0	495	28	16	24	29	1.97
5219523--5219550	12	2.3	12	100	0	56	32	25	25	17	1.97
5220649--5220833	60	3.2	59	87	5	254	35	16	15	31	1.91
5223111--5223459	114	3.1	113	87	8	501	31	18	15	33	1.93
5223227--5223502	114	2.6	101	82	12	320	33	18	15	32	1.92
5227872--5227938	35	1.9	35	93	0	116	26	8	31	32	1.87
5231422--5231520	51	2.0	48	94	5	171	33	2	17	47	1.59
5235269--5235363	38	2.5	40	78	16	94	60	2	0	37	1.09
5237457--5237482	2	13.0	2	100	0	52	50	0	0	50	1.00
5244915--5244978	28	2.5	26	82	14	71	17	15	3	64	1.42
5248500--5248609	1	110.0	1	66	0	58	83	0	12	3	0.77
5248500--5248616	5	25.0	5	79	15	92	82	0	14	3	0.81
5248509--5248615	13	8.1	13	77	13	94	82	0	14	3	0.81
5248500--5248616	28	4.2	28	77	15	125	82	0	14	3	0.81
5249774--5250318	87	6.4	87	79	8	582	29	21	23	26	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5249771--5250359	44	13.8	40	69	16	271	28	21	23	26	1.99
5249939--5250421	127	3.8	127	94	0	840	28	21	22	27	1.99
5249767--5250318	214	2.6	216	78	7	669	29	21	23	26	1.99
5251430--5251469	21	1.9	21	85	10	55	25	7	0	67	1.16
5259230--5259494	43	6.3	43	76	5	211	29	26	17	26	1.98
5259230--5259476	42	5.9	43	77	3	227	27	26	18	27	1.98
5259275--5259494	85	2.6	84	81	5	228	30	26	17	25	1.97
5264529--5264608	40	2.0	40	100	0	160	37	22	10	30	1.87
5264796--5264825	15	2.0	15	93	0	51	26	36	0	36	1.57
5265326--5265366	20	2.0	20	100	0	82	24	24	9	41	1.85

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