genome.fa.s6.2.7.7.80.10.50.1000.135.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  135  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)
39502326--39502516	61	3.2	61	66	20	157	43	2	5	48	1.38
39502377--39502411	18	2.0	17	88	5	52	45	0	0	54	0.99
39502265--39502553	120	2.4	120	88	2	429	44	2	4	48	1.35
39502767--39502802	16	2.2	16	95	0	63	38	33	0	27	1.57
39506104--39506182	32	2.4	33	79	10	81	29	1	13	55	1.46
39512204--39512249	14	3.4	14	84	3	58	56	10	2	30	1.46
39525399--39525453	26	2.1	26	86	6	76	43	9	21	25	1.82
39536251--39536333	43	1.9	43	100	0	166	38	7	15	38	1.75
39536257--39536327	24	3.2	24	65	19	71	33	7	16	42	1.76
39543887--39543938	24	2.2	24	85	0	68	38	3	7	50	1.50
39544504--39544600	7	13.6	7	85	4	122	44	37	0	18	1.50
39544504--39544597	22	4.4	22	82	9	122	45	35	0	19	1.50
39548381--39548432	24	2.2	24	85	0	68	38	3	7	50	1.50
39552349--39552387	20	2.0	20	84	0	51	61	2	5	30	1.31
39553803--39553836	2	17.0	2	100	0	68	50	0	0	50	1.00
39563136--39563187	25	2.1	25	100	0	104	61	7	11	19	1.53
39563619--39563742	43	2.9	43	78	4	124	29	29	19	21	1.98
39564650--39564674	5	5.0	5	100	0	50	60	0	0	40	0.97
39568031--39568122	40	2.3	40	92	0	148	32	17	29	20	1.96
39569130--39569165	2	18.0	2	100	0	72	50	0	0	50	1.00
39569702--39569728	2	13.5	2	100	0	54	51	0	0	48	1.00
39572748--39572791	17	2.6	17	96	0	79	45	15	0	38	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39572797--39572838	13	3.2	13	86	0	57	40	9	2	47	1.49
39576802--39576964	42	3.9	41	87	6	238	29	23	20	25	1.99
39577232--39577261	15	2.0	15	100	0	60	26	26	6	40	1.81
39584014--39584058	19	2.3	20	85	11	58	40	2	0	57	1.11
39602913--39602941	9	3.2	9	100	0	58	0	10	31	58	1.31
39606384--39606413	10	3.0	10	100	0	60	50	10	30	10	1.69
39608045--39608079	18	2.0	17	88	5	52	45	0	0	54	0.99
39608315--39608352	16	2.4	16	100	0	76	36	39	0	23	1.55
39614091--39614124	17	2.0	17	88	0	50	50	0	2	47	1.16
39614730--39614774	19	2.4	19	88	7	65	40	0	2	57	1.11
39614756--39614824	25	2.8	24	76	12	68	36	1	2	59	1.21
39614780--39614817	17	2.3	16	83	16	51	28	2	2	65	1.19
39614821--39614859	21	1.9	21	84	5	53	28	2	2	66	1.18
39622004--39622057	4	13.5	4	100	0	108	50	24	0	25	1.50
39637775--39638320	50	10.9	50	71	2	423	24	25	20	29	1.99
39637749--39638333	100	5.8	100	91	1	949	25	24	20	29	1.99
39639554--39639582	7	4.1	7	100	0	58	0	13	0	86	0.58
39643893--39643951	25	2.5	24	81	10	61	61	10	5	23	1.48
39643969--39644006	18	2.1	19	90	5	60	63	0	5	31	1.17
39643966--39644009	3	14.7	3	81	9	54	63	0	4	31	1.14
39650202--39650239	16	2.3	17	86	4	51	39	0	0	60	0.97
39652169--39652208	13	2.9	14	81	11	55	35	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39653179--39653205	7	3.9	7	100	0	54	59	0	0	40	0.98
39657845--39657898	24	2.2	25	90	6	85	46	12	9	31	1.74
39661859--39661904	14	3.3	14	93	0	83	41	0	2	56	1.11
39663016--39663110	21	4.5	21	90	4	138	14	24	27	33	1.94
39663003--39663110	42	2.5	41	85	7	144	16	24	25	33	1.96
39667209--39667249	7	5.9	7	100	0	82	58	0	0	41	0.98
39671216--39671242	12	2.2	12	100	0	54	44	7	14	33	1.73
39675575--39675608	13	2.6	14	86	13	54	32	17	5	44	1.73
39681413--39681441	14	2.1	14	100	0	58	41	6	0	51	1.28
39687381--39687421	20	2.0	21	85	4	57	24	9	19	46	1.80
39703122--39703167	2	23.0	2	100	0	92	50	0	0	50	1.00
39706935--39707006	27	2.7	27	88	0	90	16	23	16	43	1.88
39720036--39720083	14	3.1	16	74	20	57	47	0	0	52	1.00
39720035--39720096	30	2.0	31	87	12	92	53	0	0	46	1.00
39720102--39720171	21	3.5	19	77	12	70	40	4	4	51	1.41
39726359--39726402	23	1.9	23	90	9	72	36	0	4	59	1.18
39726387--39726446	31	2.0	31	87	6	88	53	0	3	43	1.17
39726950--39727000	23	2.3	22	83	10	59	49	0	3	47	1.20
39737790--39737825	19	1.9	19	88	5	56	36	0	2	61	1.11
39742879--39742932	18	2.9	20	76	15	62	18	5	7	68	1.33
39743570--39743617	25	1.9	25	87	8	71	12	6	4	77	1.11
39744229--39744296	26	2.6	27	81	6	77	42	5	4	47	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39744556--39744580	2	12.5	2	100	0	50	48	0	0	52	1.00
39748162--39748533	46	8.6	46	85	12	493	29	22	14	34	1.94
39748343--39748497	36	4.0	36	81	15	193	29	20	14	36	1.91
39748297--39748533	82	2.9	82	96	0	429	29	21	13	35	1.91
39748162--39748533	128	2.9	133	82	14	449	29	22	14	34	1.94
39752776--39752821	13	3.5	13	80	13	58	63	0	19	17	1.32
39754098--39755039	44	21.3	44	77	6	855	30	13	22	33	1.93
39754098--39755039	133	7.1	132	86	3	1034	30	13	22	33	1.93
39754099--39755039	177	5.3	175	80	5	889	30	13	22	33	1.93
39754897--39755065	89	1.9	89	85	0	230	29	14	23	32	1.94
39755925--39755969	17	2.6	18	82	3	56	15	4	2	77	1.02
39756140--39756207	26	2.6	27	81	6	77	42	5	4	47	1.48
39756467--39756503	2	18.5	2	100	0	74	48	0	0	51	1.00
39757984--39758642	335	2.0	321	89	4	1003	31	18	11	38	1.87
39759178--39759228	20	2.5	20	75	9	50	54	19	19	5	1.64
39759664--39759690	13	2.1	13	100	0	54	44	25	7	22	1.79
39760496--39760642	37	4.0	37	93	1	244	25	21	15	37	1.93
39760648--39760693	7	6.7	7	80	12	51	21	28	4	45	1.71
39760655--39760786	59	2.3	59	92	5	216	25	25	12	37	1.90
39760665--39760992	46	6.2	52	73	19	302	28	22	14	34	1.93
39760670--39761006	108	3.3	102	89	8	504	28	22	14	34	1.94
39760824--39761006	98	1.9	96	97	2	348	29	22	14	33	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39763586--39763638	18	2.9	18	80	2	61	41	45	1	11	1.51
39763653--39763728	21	3.8	20	81	10	57	61	9	2	26	1.39
39763680--39763716	12	3.0	12	92	4	56	59	16	2	21	1.49
39763748--39763823	9	8.4	9	81	5	73	28	7	21	42	1.81
39763748--39763823	27	2.8	27	81	0	89	28	7	21	42	1.81
39766328--39766358	13	2.4	13	94	0	53	25	12	12	48	1.77
39767891--39767927	9	4.1	9	92	0	65	45	13	10	29	1.77
39770879--39770917	19	2.0	21	85	10	55	15	10	5	69	1.34
39771131--39771202	3	23.7	3	74	13	58	27	5	2	63	1.30
39774391--39774419	14	2.1	14	100	0	58	34	31	6	27	1.83
39776822--39777578	44	17.2	45	74	12	592	28	15	25	29	1.96
39776822--39777578	132	5.7	132	90	1	1155	28	15	25	29	1.96
39777699--39777904	44	4.7	44	80	5	238	25	19	26	28	1.99
39778081--39778384	88	3.5	88	93	0	518	26	28	24	20	1.99
39778398--39778603	44	4.7	44	78	8	222	26	17	27	28	1.98
39779012--39779069	23	2.5	23	100	0	116	31	5	20	43	1.74
39779241--39779279	19	2.0	21	85	10	55	15	10	5	69	1.34
39779492--39779563	3	23.7	3	74	13	58	27	5	2	63	1.30
39783175--39783224	3	16.7	3	100	0	100	34	0	32	34	1.58
39786286--39786362	27	2.9	27	90	3	120	16	24	38	19	1.92
39786573--39786610	19	2.0	19	89	0	58	50	7	5	36	1.54
39786871--39786945	27	2.8	27	91	2	116	36	0	10	53	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39787041--39787078	19	2.0	19	89	0	58	36	5	7	50	1.54
39787616--39787650	10	3.2	11	92	8	54	65	0	0	34	0.93
39793811--39793837	11	2.5	11	100	0	54	40	14	7	37	1.74
39796281--39796318	13	2.9	13	81	11	51	28	0	0	71	0.87
39796284--39796319	16	2.1	16	90	10	54	27	0	0	72	0.85
39796047--39796820	158	4.9	150	71	15	598	29	10	9	50	1.67
39796047--39796820	318	2.4	318	94	0	1334	29	10	9	50	1.67
39797148--39797334	5	38.8	5	69	14	56	0	30	0	68	0.93
39797180--39797335	10	15.3	10	73	24	75	0	31	0	68	0.90
39797151--39797335	43	4.3	43	75	18	129	0	30	0	68	0.94

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   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168