genome.fa.s3.2.7.7.80.10.50.1000.132.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  132  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)
39691109--39691148	18	2.2	18	90	0	62	42	7	30	20	1.79
39692982--39693026	11	3.9	12	78	18	51	46	0	28	24	1.53
39703802--39703851	18	2.9	17	80	11	50	62	8	2	28	1.35
39705831--39705893	30	2.1	30	93	0	108	25	3	14	57	1.52
39706015--39706045	11	2.8	11	100	0	62	64	0	0	35	0.94
39712164--39712223	31	1.9	32	83	10	79	43	10	10	36	1.72
39712223--39712286	31	2.2	29	86	8	85	51	15	1	31	1.53
39722864--39722914	27	1.9	27	88	4	77	27	9	9	52	1.65
39727776--39727816	6	6.8	6	88	0	55	63	0	19	17	1.31
39727964--39728035	26	2.8	25	82	12	85	44	8	13	33	1.74
39729522--39729606	13	6.4	13	76	15	66	16	2	3	77	1.01
39729527--39729599	19	3.7	18	78	14	65	16	1	4	78	0.98
39729546--39729598	6	8.5	6	76	15	54	15	0	3	81	0.83
39730217--39730271	21	2.6	21	88	0	74	12	34	32	20	1.90
39733109--39733144	14	2.6	14	90	0	54	55	19	2	22	1.56
39743030--39743183	21	7.3	21	69	7	98	46	17	20	15	1.84
39743030--39743184	42	3.7	42	79	6	163	47	17	20	15	1.83
39744676--39744790	21	5.5	21	82	4	133	19	20	13	46	1.83
39744677--39744807	21	6.3	21	80	1	104	17	19	16	47	1.83
39747749--39747780	12	2.6	13	85	14	50	56	6	0	37	1.25
39750278--39750344	2	32.5	2	94	5	116	47	2	0	49	1.16
39750479--39750666	2	93.0	2	87	4	243	45	5	1	47	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39753241--39753867	216	2.9	217	91	1	1003	28	17	20	34	1.95
39765539--39766134	87	6.8	88	73	8	457	29	21	22	26	1.99
39765539--39766140	44	13.8	45	71	11	344	29	21	22	26	1.99
39765539--39766203	348	1.9	348	87	4	984	30	22	21	26	1.99
39765539--39766135	174	3.4	174	95	0	1052	29	21	22	26	1.99
39768475--39769087	109	5.7	108	83	5	758	28	17	20	33	1.95
39768475--39769101	216	2.9	217	91	1	967	28	17	20	33	1.95
39769876--39769921	24	1.9	24	90	0	74	17	19	6	56	1.62
39781152--39781193	21	2.0	22	95	4	77	38	0	0	61	0.96
39781153--39781195	11	3.9	11	84	9	61	37	0	0	62	0.95
39787721--39787754	11	3.0	12	87	12	54	67	0	0	32	0.91
39788149--39788181	17	2.0	17	88	5	50	42	0	12	45	1.41
39788169--39788218	9	5.7	9	88	2	75	46	0	2	52	1.12
39788169--39788224	13	4.3	13	84	6	60	46	0	1	51	1.11
39788598--39788705	52	2.1	52	100	0	216	27	17	12	41	1.86
39788975--39789132	20	7.8	21	67	17	77	63	0	1	34	1.05
39788993--39789024	12	2.6	13	80	19	50	59	0	0	40	0.97
39789017--39789089	29	2.5	29	95	4	130	67	0	1	31	1.00
39789028--39789078	9	5.4	9	79	6	57	74	0	0	25	0.82
39788969--39789153	80	2.3	81	84	11	236	61	0	1	36	1.06
39788969--39789100	11	12.9	11	70	18	81	61	0	0	37	1.02
39788975--39789153	10	17.5	11	65	25	58	63	0	1	35	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39789712--39789744	7	5.0	7	92	7	52	15	24	0	60	1.35
39789751--39789840	45	2.0	46	82	6	112	32	18	7	41	1.79
39791600--39791631	2	16.0	2	100	0	64	50	0	0	50	1.00
39798167--39798214	3	16.0	3	82	0	60	33	4	2	60	1.27
39801697--39801844	69	2.1	69	93	0	251	35	12	22	29	1.92
39810145--39810169	12	2.1	12	100	0	50	24	32	8	36	1.84
39810790--39811134	132	2.6	131	89	1	528	30	20	23	25	1.98
39813205--39813248	20	2.2	20	83	0	52	52	2	22	22	1.58
39813831--39813867	9	4.1	9	92	0	65	29	10	13	45	1.77
39813921--39813951	9	3.4	9	90	0	53	38	22	12	25	1.90
39814572--39814622	3	17.0	3	83	0	66	33	3	1	60	1.26
39814572--39814622	15	3.4	15	86	10	77	33	3	1	60	1.26
39817646--39817700	26	2.1	26	86	0	74	43	1	1	52	1.22
39821830--39821890	19	3.3	18	86	8	86	72	1	0	26	0.94
39822094--39822138	19	2.3	20	85	11	58	24	4	4	66	1.29
39822090--39822138	21	2.4	21	80	13	57	24	6	4	65	1.33
39822331--39822379	21	2.6	18	77	20	55	22	4	2	71	1.13
39822366--39822408	23	1.9	23	90	4	70	37	0	0	62	0.95
39822383--39822442	16	4.0	15	75	14	52	35	1	0	63	1.05
39822386--39822425	16	2.4	16	87	4	53	35	2	0	62	1.09
39822395--39822427	16	2.1	16	94	0	57	27	3	0	69	1.03
39823926--39823971	24	1.9	24	95	0	83	36	2	8	52	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39833553--39833585	15	2.1	16	88	5	50	48	15	0	36	1.45
39836344--39836411	25	2.7	25	84	11	86	22	25	20	32	1.98
39836345--39836425	25	3.2	26	76	13	80	19	27	18	34	1.95
39836344--39836457	50	2.3	49	80	7	124	21	26	18	34	1.96
39845884--39845938	28	2.0	26	82	6	65	41	3	1	52	1.29
39848123--39848164	22	1.9	22	85	0	57	14	14	14	57	1.66
39848131--39848181	22	2.3	22	82	0	57	21	9	9	58	1.58
39850019--39850102	42	2.0	42	95	0	150	33	16	16	33	1.92
39851430--39851495	24	2.7	25	72	9	64	43	3	4	48	1.38
39851838--39851890	27	2.0	27	100	0	106	41	15	9	33	1.79
39852378--39852493	20	5.6	20	72	16	67	62	3	0	33	1.18
39852385--39852436	20	2.6	20	90	6	79	61	5	0	32	1.20
39852413--39852467	25	2.3	23	75	9	56	60	1	1	36	1.18
39853694--39853925	116	2.0	116	100	0	464	36	17	14	31	1.90
39857489--39857670	11	17.9	11	71	19	94	61	0	2	36	1.08
39857489--39857680	40	4.8	40	84	9	232	61	0	2	35	1.07
39857554--39857582	12	2.4	12	100	0	58	79	0	0	20	0.74
39857535--39857601	17	3.6	17	76	18	71	65	0	0	34	0.93
39858400--39858434	19	1.9	18	88	11	54	45	28	8	17	1.77
39859171--39859204	11	3.0	11	95	4	59	35	0	0	64	0.94
39860895--39860928	2	17.0	2	100	0	68	50	0	0	50	1.00
39868734--39868771	17	2.2	18	86	13	53	21	5	2	71	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39869605--39869645	6	7.0	6	88	5	66	65	0	2	31	1.05
39869608--39869641	17	2.0	17	94	0	59	67	0	2	29	1.05
39873668--39873699	15	2.1	15	94	0	55	65	6	0	28	1.16
39879827--39879917	44	2.1	44	95	0	164	46	10	13	29	1.77
39879896--39879944	25	2.0	25	83	0	62	51	8	22	18	1.72
39886381--39886417	9	4.1	9	92	0	65	45	13	10	29	1.77
39887443--39887473	5	6.2	5	92	0	53	22	19	16	41	1.89
39922443--39922485	20	2.2	20	87	4	61	46	13	13	25	1.81
39927101--39927162	30	2.1	30	100	0	124	32	12	22	32	1.92
39927859--39927901	13	3.5	13	75	18	56	34	2	16	46	1.60
39927859--39927903	23	2.0	23	100	0	90	35	2	17	44	1.62
39928475--39928515	19	2.2	19	100	0	82	19	14	31	34	1.92
39930463--39930494	15	2.1	15	100	0	64	37	12	21	28	1.90
39936296--39936550	124	2.1	123	90	1	393	29	16	21	32	1.95
39938165--39938496	51	6.4	51	86	3	475	32	1	21	44	1.60
39938165--39938475	28	11.8	28	79	13	356	33	0	20	45	1.58
39940884--39940941	30	1.9	30	96	0	107	32	0	36	31	1.58
39940912--39940977	22	3.0	22	91	6	107	36	1	28	33	1.67
39946153--39946194	20	2.1	20	100	0	84	35	19	21	23	1.96
39957173--39957215	23	1.9	22	90	4	68	25	18	27	27	1.98
39958125--39958166	11	3.8	11	87	0	57	7	2	50	40	1.43
39960483--39960605	54	2.3	54	83	5	142	26	27	21	24	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39962377--39962410	17	1.9	17	88	5	50	47	14	5	32	1.69
39986575--39986631	3	18.3	3	75	13	53	57	5	0	36	1.21
39986578--39986629	27	2.0	26	88	3	77	57	5	0	36	1.23
39989919--39989992	24	3.1	24	94	0	130	8	37	28	25	1.84
39989931--39990048	60	2.0	60	83	6	150	9	37	27	25	1.87
39998701--39998743	7	6.1	7	97	0	68	13	0	9	76	1.01
40003430--40003475	24	1.9	24	95	0	83	23	26	6	43	1.78
40003435--40003486	24	2.2	24	82	0	59	26	26	3	42	1.73
40008142--40008357	51	4.4	51	85	8	304	31	12	24	31	1.93
40008198--40008353	44	3.4	44	87	6	195	30	13	25	30	1.94

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