genome.fa.s6.2.7.7.80.10.50.1000.133.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  133  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)
38860385--38860484	49	2.0	49	100	0	200	42	18	8	32	1.79
38863743--38863803	25	2.4	25	97	0	113	37	3	0	59	1.14
38865048--38865094	9	5.2	9	77	10	51	0	21	10	68	1.20
38865048--38865094	18	2.6	18	77	12	60	0	21	10	68	1.20
38867980--38868127	33	4.4	34	69	25	98	35	29	16	18	1.93
38867865--38868233	103	3.6	103	93	1	614	33	29	18	18	1.95
38870234--38870258	12	2.1	12	100	0	50	40	16	0	44	1.47
38871594--38871669	39	1.9	39	82	10	93	46	0	0	53	1.00
38871667--38871737	16	4.2	16	68	19	54	49	1	0	49	1.09
38871662--38871746	26	3.3	26	72	6	82	48	3	0	48	1.18
38875473--38875567	42	2.3	42	84	0	127	40	15	24	20	1.91
38883752--38883791	21	1.9	21	90	10	64	30	30	0	40	1.57
38884933--38885005	36	2.0	36	84	10	96	32	4	8	54	1.49
38886044--38886080	2	18.5	2	94	0	65	51	0	0	48	1.00
38887543--38887571	5	5.8	5	100	0	58	41	0	0	58	0.98
38888324--38888387	30	2.1	30	94	0	110	32	0	21	45	1.52
38888392--38888423	15	2.1	16	94	5	57	46	0	9	43	1.35
38888592--38888641	22	2.3	22	82	0	64	12	30	18	40	1.86
38890238--38890309	25	2.9	25	95	0	135	16	16	25	41	1.89
38890308--38890375	22	3.1	22	93	0	109	17	26	14	41	1.88
38894223--38894261	5	8.0	5	94	5	71	41	0	0	58	0.98
38895228--38895306	25	3.2	25	87	0	113	15	20	22	41	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38895294--38895352	22	2.7	22	86	0	91	13	27	18	40	1.88
38901783--38901874	46	2.0	45	82	2	112	43	18	10	27	1.83
38902384--38902488	42	2.5	42	74	10	106	14	31	24	29	1.94
38903200--38903252	20	2.6	21	82	17	67	75	0	13	11	1.05
38903887--38903935	14	3.3	15	77	8	55	81	14	0	4	0.83
38905221--38905370	63	2.4	63	84	5	178	25	9	1	64	1.32
38915154--38915187	18	1.9	18	88	5	52	11	11	5	70	1.32
38929106--38929141	18	2.0	18	88	0	54	66	16	0	16	1.25
38930716--38931609	43	20.8	43	79	4	937	31	24	15	27	1.96
38930690--38931619	129	7.2	129	94	0	1617	31	24	15	28	1.96
38935642--38935713	24	3.0	24	87	2	108	40	8	30	20	1.82
38935834--38935895	21	3.0	21	70	0	70	16	29	17	37	1.92
38935763--38935918	42	3.7	42	77	0	134	17	26	16	39	1.90
38944247--38944271	4	6.2	4	100	0	50	24	0	0	76	0.80
38945570--38945606	18	2.0	19	89	5	58	29	2	5	62	1.31
38958355--38958398	19	2.5	17	81	7	52	61	4	9	25	1.45
38962147--38962289	21	6.9	21	75	7	103	20	16	16	46	1.84
38962147--38962194	20	2.3	20	85	3	60	22	16	16	43	1.87
38962146--38962295	42	3.6	43	78	2	137	19	15	17	48	1.82
38962242--38962301	21	2.8	20	80	9	66	16	11	18	53	1.72
38962242--38962310	21	3.3	20	74	8	57	17	13	18	50	1.77
38967341--38967394	27	2.0	27	92	0	90	46	9	7	37	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38968307--38968383	9	8.4	9	83	8	93	22	10	25	41	1.85
38968544--38968568	12	2.1	12	100	0	50	16	24	36	24	1.94
38976130--38976164	18	1.9	18	88	11	54	37	8	20	34	1.83
38979162--38979194	17	1.9	17	100	0	66	78	9	0	12	0.95
38985250--38985283	11	3.1	11	91	0	59	17	32	2	47	1.63
38985246--38985299	22	2.5	22	83	16	69	20	29	3	46	1.68
38985263--38985358	49	1.9	50	85	8	133	26	23	3	46	1.67
38985387--38985423	13	2.8	14	84	12	51	40	43	0	16	1.48
38985387--38985419	7	5.0	7	96	3	52	39	45	0	15	1.46
38985408--38985506	22	4.6	22	88	7	150	45	31	0	23	1.53
38985408--38985504	44	2.2	44	94	5	171	45	31	0	22	1.53
38985414--38985524	22	4.8	22	82	9	116	46	29	0	23	1.52
38985524--38985565	21	2.0	22	85	4	59	50	35	0	14	1.43
38985604--38985681	40	2.0	40	86	0	111	25	30	25	17	1.97
38988201--38988335	40	3.4	40	76	8	125	37	19	23	20	1.95
38988369--38988606	41	5.8	41	91	3	338	19	21	25	32	1.97
38988703--38988753	26	2.0	26	84	0	66	58	5	11	23	1.55
38990159--38990286	38	3.4	38	93	0	229	22	19	11	46	1.82
38991645--38991711	9	7.9	9	75	24	58	43	17	0	38	1.50
38991680--38991711	16	2.0	16	100	0	64	43	25	0	31	1.55
38993469--38993636	66	2.5	66	88	3	232	41	18	27	13	1.87
38993607--38993723	21	5.6	21	80	5	69	35	17	41	5	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38993627--38993719	42	2.2	42	84	0	114	34	16	44	5	1.70
38994071--38994227	43	3.7	42	77	6	154	21	19	30	28	1.98
38994972--38995046	30	2.5	30	86	0	105	33	13	17	36	1.88
38999938--38999989	24	2.2	24	89	0	77	36	3	9	50	1.54
39004351--39004402	24	2.2	24	92	0	86	36	1	9	51	1.46
39004664--39004797	67	2.0	67	100	0	268	31	11	13	43	1.80
39004682--39004786	33	3.2	33	62	22	83	32	12	11	43	1.78
39013170--39013204	2	17.5	2	93	0	61	2	48	0	48	1.16
39017899--39017926	14	2.0	14	100	0	56	28	14	21	35	1.92
39019903--39019948	20	2.1	23	84	11	62	54	2	2	41	1.25
39020387--39020426	19	2.1	19	85	4	53	30	2	0	67	1.04
39025499--39025543	20	2.2	21	92	4	74	60	2	2	35	1.22
39025499--39025562	19	3.3	19	80	8	67	57	1	4	35	1.29
39025582--39025637	29	2.0	29	89	3	87	71	3	1	23	1.11
39035888--39035958	35	2.0	35	97	0	133	33	12	5	47	1.65
39039079--39039115	2	18.5	2	94	0	65	51	45	0	2	1.15
39039078--39039121	10	4.4	10	91	0	61	50	40	0	9	1.34
39039113--39039145	16	2.1	16	94	0	57	51	15	0	33	1.43
39046168--39046410	43	5.7	43	90	1	310	25	20	19	34	1.96
39046168--39046410	85	2.9	85	86	2	319	25	20	19	34	1.96
39070626--39070712	42	2.1	42	85	8	115	16	22	18	42	1.89
39072851--39072945	27	3.6	27	75	12	90	60	6	5	28	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39072863--39073015	53	3.0	51	74	17	138	56	5	9	28	1.52
39072921--39072966	22	2.1	22	88	4	67	63	2	4	30	1.26
39072925--39072972	22	2.2	22	81	7	53	62	2	6	29	1.31
39077620--39077718	23	4.3	23	93	0	162	31	27	21	20	1.98
39084257--39084318	21	3.0	21	75	0	79	14	24	19	41	1.88
39084213--39084318	42	2.5	42	87	6	144	15	24	17	42	1.88
39084484--39084543	24	2.5	24	94	2	102	38	3	0	58	1.15
39084484--39084567	24	3.5	24	84	9	75	41	2	0	55	1.12
39090721--39090778	29	2.0	29	80	12	66	37	13	10	37	1.79
39100721--39100753	11	3.1	11	86	4	50	36	0	0	63	0.95
39100875--39100937	30	2.1	30	93	0	108	57	14	3	25	1.52
39100971--39100997	14	1.9	14	100	0	54	51	14	11	22	1.73
39106099--39106131	3	11.0	3	93	0	57	66	3	0	30	1.06
39107592--39107704	44	2.6	44	85	2	138	30	25	15	27	1.96
39107879--39108106	125	1.8	125	93	0	393	24	17	22	35	1.95
39108184--39108711	50	10.7	50	79	4	495	24	20	22	31	1.98
39108008--39108718	100	7.2	99	86	3	756	23	20	23	32	1.98
39109050--39109138	44	2.0	44	95	0	160	37	23	12	26	1.90
39109874--39109976	43	2.4	44	80	11	115	30	23	14	32	1.94
39110053--39110091	15	2.7	15	92	4	62	0	12	0	87	0.55
39110054--39110096	20	2.2	19	87	4	59	0	11	2	86	0.67
39110053--39110088	8	4.6	8	86	6	56	0	13	0	86	0.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39111256--39111304	6	8.0	6	86	13	73	0	18	0	81	0.69
39111316--39111371	9	6.3	9	87	4	87	10	0	10	78	0.96
39111316--39111370	17	3.2	17	87	5	83	10	0	10	78	0.98
39111316--39111370	8	6.4	8	85	10	65	10	0	10	78	0.98
39115248--39115307	3	20.0	3	100	0	120	66	0	0	33	0.92
39118507--39118561	25	2.2	24	81	6	65	58	0	5	36	1.21
39118520--39118568	25	2.0	25	84	8	64	57	0	2	40	1.10
39122632--39122669	10	3.9	10	86	3	51	60	0	2	36	1.11
39124329--39124401	22	3.3	22	84	9	87	10	0	41	47	1.39
39134115--39134165	23	2.2	23	92	0	84	23	5	9	60	1.50

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